From df9cf17027b8d24d3559a12da1dae411077cde4b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 6 Nov 2023 15:23:52 -0500
Subject: [PATCH 0001/1492] Start Remote class

---
 src/Remote.cpp | 20 ++++++++++++++++++++
 src/Remote.h   | 18 ++++++++++++++++++
 2 files changed, 38 insertions(+)
 create mode 100644 src/Remote.cpp
 create mode 100644 src/Remote.h

diff --git a/src/Remote.cpp b/src/Remote.cpp
new file mode 100644
index 0000000000..16585188d9
--- /dev/null
+++ b/src/Remote.cpp
@@ -0,0 +1,20 @@
+#include "Remote.h"
+#include "CpptrajStdio.h"
+
+using namespace Cpptraj;
+
+/** CONSTRUCTOR */
+Remote::Remote() {}
+
+/** CONSTRUCTOR - base url */
+Remote::Remote(std::string const& baseUrl) :
+  url_(baseUrl)
+{}
+
+/** Download file from base URL */
+int Remote::DownloadFile(std::string const& fname, std::string const& outputFname)
+const
+{
+  return 0;
+}
+  
diff --git a/src/Remote.h b/src/Remote.h
new file mode 100644
index 0000000000..a1cca47d4d
--- /dev/null
+++ b/src/Remote.h
@@ -0,0 +1,18 @@
+#ifndef INC_REMOTE_H
+#define INC_REMOTE_H
+#include <string>
+namespace Cpptraj {
+/// Class for downloading remote files.
+class Remote {
+  public:
+    /// CONSTRUCTOR
+    Remote();
+    /// CONSTRUCTOR - Take remote base URL
+    Remote(std::string const&);
+    /// Download file assuming URL is remote directory
+    int DownloadFile(std::string const&, std::string const&) const;
+  private:
+    std::string url_; ///< Remote base URL
+};
+}
+#endif

From 0f876da874e617440a6c3e3c155c8b74d39c1922 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 6 Nov 2023 15:46:31 -0500
Subject: [PATCH 0002/1492] Start download function

---
 src/Remote.cpp | 52 +++++++++++++++++++++++++++++++++++++++++++++++---
 src/Remote.h   |  4 ++++
 2 files changed, 53 insertions(+), 3 deletions(-)

diff --git a/src/Remote.cpp b/src/Remote.cpp
index 16585188d9..c7962a6276 100644
--- a/src/Remote.cpp
+++ b/src/Remote.cpp
@@ -1,20 +1,66 @@
 #include "Remote.h"
 #include "CpptrajStdio.h"
+#include "FileName.h"
+#include <cstdlib> // system
 
 using namespace Cpptraj;
 
+/** The remote download command. */
+std::string Remote::cmd_ = "";
+
 /** CONSTRUCTOR */
-Remote::Remote() {}
+Remote::Remote() {
+  setRemoteDownloadCommand();
+}
 
 /** CONSTRUCTOR - base url */
 Remote::Remote(std::string const& baseUrl) :
   url_(baseUrl)
-{}
+{
+  setRemoteDownloadCommand();
+}
+
+/** Set the remote download command. */
+int Remote::setRemoteDownloadCommand() {
+  if (!cmd_.empty()) return 0;
+  // First try curl
+  int err = system("curl --version");
+  if (err == 0) {
+    mprintf("\tcurl found.\n");
+    cmd_.assign("curl -L -o");
+  } else {
+    err = system("wget --version");
+    if (err == 0) {
+      mprintf("\twget found.\n");
+      cmd_.assign("wget -O");
+    } else {
+      mprinterr("Error: No working remote command found.\n");
+      return 1;
+    }
+  }
+  return 0;
+}
 
 /** Download file from base URL */
-int Remote::DownloadFile(std::string const& fname, std::string const& outputFname)
+int Remote::DownloadFile(std::string const& fname, std::string const& outputFnameIn)
 const
 {
+  if (cmd_.empty()) {
+    mprinterr("Error: No remote download command set.\n");
+    return 1;
+  }
+  if (fname.empty()) {
+    mprinterr("Error: No file name to download specified.\n");
+    return 1;
+  }
+  FileName fileName(fname);
+  // Set output file name if necessary
+  FileName outputFname;
+  if (outputFnameIn.empty())
+    outputFname = fileName;
+  else
+    outputFname.SetFileName( outputFnameIn );
+
   return 0;
 }
   
diff --git a/src/Remote.h b/src/Remote.h
index a1cca47d4d..875de8ab56 100644
--- a/src/Remote.h
+++ b/src/Remote.h
@@ -12,7 +12,11 @@ class Remote {
     /// Download file assuming URL is remote directory
     int DownloadFile(std::string const&, std::string const&) const;
   private:
+    /// Set remote download command
+    int setRemoteDownloadCommand();
+
     std::string url_; ///< Remote base URL
+    static std::string cmd_; ///< Command to call to download remote files
 };
 }
 #endif

From ef372705a79fcbeb5cc9bb3c884e5848e0446230 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 6 Nov 2023 15:55:52 -0500
Subject: [PATCH 0003/1492] Set up the actual command to call

---
 src/Remote.cpp | 14 ++++++++++++--
 src/Remote.h   |  1 +
 2 files changed, 13 insertions(+), 2 deletions(-)

diff --git a/src/Remote.cpp b/src/Remote.cpp
index c7962a6276..3a9dd12349 100644
--- a/src/Remote.cpp
+++ b/src/Remote.cpp
@@ -8,6 +8,8 @@ using namespace Cpptraj;
 /** The remote download command. */
 std::string Remote::cmd_ = "";
 
+std::string Remote::oflag_ = "";
+
 /** CONSTRUCTOR */
 Remote::Remote() {
   setRemoteDownloadCommand();
@@ -27,12 +29,14 @@ int Remote::setRemoteDownloadCommand() {
   int err = system("curl --version");
   if (err == 0) {
     mprintf("\tcurl found.\n");
-    cmd_.assign("curl -L -o");
+    cmd_.assign("curl -L ");
+    oflag_.assign("-o ");
   } else {
     err = system("wget --version");
     if (err == 0) {
       mprintf("\twget found.\n");
-      cmd_.assign("wget -O");
+      cmd_.assign("wget ");
+      oflag_.assign("-O ");
     } else {
       mprinterr("Error: No working remote command found.\n");
       return 1;
@@ -61,6 +65,12 @@ const
   else
     outputFname.SetFileName( outputFnameIn );
 
+  std::string remoteUrl = url_ + "/" + fileName.Full();
+  mprintf("\t %s => %s\n", remoteUrl.c_str(), outputFname.full());
+
+  std::string remoteCmd = cmd_ + remoteUrl + " " + oflag_ + outputFname.Full();
+  mprintf("DEBUG: %s\n", remoteCmd.c_str());
+
   return 0;
 }
   
diff --git a/src/Remote.h b/src/Remote.h
index 875de8ab56..b5508308c1 100644
--- a/src/Remote.h
+++ b/src/Remote.h
@@ -17,6 +17,7 @@ class Remote {
 
     std::string url_; ///< Remote base URL
     static std::string cmd_; ///< Command to call to download remote files
+    static std::string oflag_; ///< Command output file flag
 };
 }
 #endif

From 35175b27b8dc3cfbe1c3fa83d6ae28e343f4d610 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 6 Nov 2023 15:57:27 -0500
Subject: [PATCH 0004/1492] Actually call the download command

---
 src/Remote.cpp | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/src/Remote.cpp b/src/Remote.cpp
index 3a9dd12349..08c3ad5fc4 100644
--- a/src/Remote.cpp
+++ b/src/Remote.cpp
@@ -70,6 +70,11 @@ const
 
   std::string remoteCmd = cmd_ + remoteUrl + " " + oflag_ + outputFname.Full();
   mprintf("DEBUG: %s\n", remoteCmd.c_str());
+  int err = system(remoteCmd.c_str());
+  if (err != 0) {
+    mprinterr("Error: Could not download %s => %s\n", remoteUrl.c_str(), outputFname.full());
+    return 1;
+  }
 
   return 0;
 }

From 663a8b2aea1db4515337068fb954773eb7e4a4ad Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 7 Nov 2023 08:55:07 -0500
Subject: [PATCH 0005/1492] When nothing specified use base

---
 src/Remote.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Remote.cpp b/src/Remote.cpp
index 08c3ad5fc4..ba2527cb4e 100644
--- a/src/Remote.cpp
+++ b/src/Remote.cpp
@@ -61,7 +61,7 @@ const
   // Set output file name if necessary
   FileName outputFname;
   if (outputFnameIn.empty())
-    outputFname = fileName;
+    outputFname = fileName.Base();
   else
     outputFname.SetFileName( outputFnameIn );
 

From 6981d5d4fb16a3f1773bb8b43c5c756b0fde2816 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 7 Nov 2023 09:03:49 -0500
Subject: [PATCH 0006/1492] Have option to overwrite files or not

---
 src/Remote.cpp | 27 ++++++++++++++++++++++-----
 src/Remote.h   |  7 +++++--
 2 files changed, 27 insertions(+), 7 deletions(-)

diff --git a/src/Remote.cpp b/src/Remote.cpp
index ba2527cb4e..3bb871a358 100644
--- a/src/Remote.cpp
+++ b/src/Remote.cpp
@@ -11,17 +11,25 @@ std::string Remote::cmd_ = "";
 std::string Remote::oflag_ = "";
 
 /** CONSTRUCTOR */
-Remote::Remote() {
+Remote::Remote() :
+  overwrite_(false)
+{
   setRemoteDownloadCommand();
 }
 
 /** CONSTRUCTOR - base url */
 Remote::Remote(std::string const& baseUrl) :
+  overwrite_(false),
   url_(baseUrl)
 {
   setRemoteDownloadCommand();
 }
 
+/** Set whether to overwrite existing files or not. */
+void Remote::SetOverwrite(bool b) {
+  overwrite_ = b;
+}
+
 /** Set the remote download command. */
 int Remote::setRemoteDownloadCommand() {
   if (!cmd_.empty()) return 0;
@@ -58,16 +66,26 @@ const
     return 1;
   }
   FileName fileName(fname);
-  // Set output file name if necessary
+  // Set output file name
   FileName outputFname;
   if (outputFnameIn.empty())
     outputFname = fileName.Base();
   else
     outputFname.SetFileName( outputFnameIn );
-
+  bool fileExists = File::Exists( outputFname );
+  if (overwrite_) {
+    if (fileExists)
+      mprintf("Warning: Overwriting existing file '%s'\n", outputFname.full());
+  } else {
+    if (fileExists) {
+      mprintf("Warning: Not overwriting existing file '%s'\n", outputFname.full());
+      return 0;
+    }
+  }
+  // Set remote URL
   std::string remoteUrl = url_ + "/" + fileName.Full();
   mprintf("\t %s => %s\n", remoteUrl.c_str(), outputFname.full());
-
+  // Download File
   std::string remoteCmd = cmd_ + remoteUrl + " " + oflag_ + outputFname.Full();
   mprintf("DEBUG: %s\n", remoteCmd.c_str());
   int err = system(remoteCmd.c_str());
@@ -78,4 +96,3 @@ const
 
   return 0;
 }
-  
diff --git a/src/Remote.h b/src/Remote.h
index b5508308c1..0ef6919e6d 100644
--- a/src/Remote.h
+++ b/src/Remote.h
@@ -9,14 +9,17 @@ class Remote {
     Remote();
     /// CONSTRUCTOR - Take remote base URL
     Remote(std::string const&);
+    /// Set whether to overwrite files or not.
+    void SetOverwrite(bool);
     /// Download file assuming URL is remote directory
     int DownloadFile(std::string const&, std::string const&) const;
   private:
     /// Set remote download command
     int setRemoteDownloadCommand();
 
-    std::string url_; ///< Remote base URL
-    static std::string cmd_; ///< Command to call to download remote files
+    bool overwrite_;           ///< If true overwrite any existing files
+    std::string url_;          ///< Remote base URL
+    static std::string cmd_;   ///< Command to call to download remote files
     static std::string oflag_; ///< Command output file flag
 };
 }

From 992e25a7f4dfbdac72575c3c04cbcf30327a45b2 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 7 Nov 2023 09:52:38 -0500
Subject: [PATCH 0007/1492] Add debug level

---
 src/Remote.cpp | 12 ++++++++++--
 src/Remote.h   |  3 +++
 2 files changed, 13 insertions(+), 2 deletions(-)

diff --git a/src/Remote.cpp b/src/Remote.cpp
index 3bb871a358..88c8b6b5e9 100644
--- a/src/Remote.cpp
+++ b/src/Remote.cpp
@@ -8,11 +8,13 @@ using namespace Cpptraj;
 /** The remote download command. */
 std::string Remote::cmd_ = "";
 
+/** Flag for setting output file for remote command. */
 std::string Remote::oflag_ = "";
 
 /** CONSTRUCTOR */
 Remote::Remote() :
-  overwrite_(false)
+  overwrite_(false),
+  debug_(0)
 {
   setRemoteDownloadCommand();
 }
@@ -20,6 +22,7 @@ Remote::Remote() :
 /** CONSTRUCTOR - base url */
 Remote::Remote(std::string const& baseUrl) :
   overwrite_(false),
+  debug_(0),
   url_(baseUrl)
 {
   setRemoteDownloadCommand();
@@ -30,6 +33,11 @@ void Remote::SetOverwrite(bool b) {
   overwrite_ = b;
 }
 
+/** Set debug level */
+void Remote::SetDebug(int d) {
+  debug_ = d;
+}
+
 /** Set the remote download command. */
 int Remote::setRemoteDownloadCommand() {
   if (!cmd_.empty()) return 0;
@@ -87,7 +95,7 @@ const
   mprintf("\t %s => %s\n", remoteUrl.c_str(), outputFname.full());
   // Download File
   std::string remoteCmd = cmd_ + remoteUrl + " " + oflag_ + outputFname.Full();
-  mprintf("DEBUG: %s\n", remoteCmd.c_str());
+  if (debug_ > 0) mprintf("DEBUG: %s\n", remoteCmd.c_str());
   int err = system(remoteCmd.c_str());
   if (err != 0) {
     mprinterr("Error: Could not download %s => %s\n", remoteUrl.c_str(), outputFname.full());
diff --git a/src/Remote.h b/src/Remote.h
index 0ef6919e6d..b47723b87a 100644
--- a/src/Remote.h
+++ b/src/Remote.h
@@ -11,6 +11,8 @@ class Remote {
     Remote(std::string const&);
     /// Set whether to overwrite files or not.
     void SetOverwrite(bool);
+    /// Set debug level
+    void SetDebug(int);
     /// Download file assuming URL is remote directory
     int DownloadFile(std::string const&, std::string const&) const;
   private:
@@ -18,6 +20,7 @@ class Remote {
     int setRemoteDownloadCommand();
 
     bool overwrite_;           ///< If true overwrite any existing files
+    int debug_;
     std::string url_;          ///< Remote base URL
     static std::string cmd_;   ///< Command to call to download remote files
     static std::string oflag_; ///< Command output file flag

From da9e8d694972589b72f7162da9d40e54cfc116be Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 7 Nov 2023 09:55:06 -0500
Subject: [PATCH 0008/1492] Add Remote.cpp, update depends

---
 src/cpptrajdepend | 1 +
 src/cpptrajfiles  | 1 +
 2 files changed, 2 insertions(+)

diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index e379d7ca83..cd68bbf84c 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -426,6 +426,7 @@ Range.o : Range.cpp ArgList.h CpptrajStdio.h Range.h StringRoutines.h
 ReadLine.o : ReadLine.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdInput.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReadLine.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 ReferenceAction.o : ReferenceAction.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h Dimension.h FileIO.h FileName.h Frame.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TypeNameHolder.h Unit.h Vec3.h
 RemdReservoirNC.o : RemdReservoirNC.cpp Atom.h AtomMask.h Box.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h RemdReservoirNC.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Unit.h Vec3.h
+Remote.o : Remote.cpp CpptrajStdio.h FileName.h Remote.h
 Residue.o : Residue.cpp NameType.h Residue.h
 SDFfile.o : SDFfile.cpp Atom.h CpptrajFile.h FileIO.h FileName.h NameType.h Parallel.h SDFfile.h StringRoutines.h SymbolExporting.h
 SimplexMin.o : SimplexMin.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Random.h Range.h SimplexMin.h TextFormat.h
diff --git a/src/cpptrajfiles b/src/cpptrajfiles
index 2d534859fb..a8d821136f 100644
--- a/src/cpptrajfiles
+++ b/src/cpptrajfiles
@@ -387,6 +387,7 @@ COMMON_SOURCES= \
         ExternalFxn.cpp \
         Random.cpp \
         Range.cpp \
+        Remote.cpp \
         RNG.cpp \
         RNG_Marsaglia.cpp \
         RNG_MersenneTwister.cpp \

From cc8aa44e6ecb2092a742dc706c6182a409ee85c2 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 7 Nov 2023 10:26:35 -0500
Subject: [PATCH 0009/1492] Create a list of unrecognized residues to find
 parameters for.

---
 src/Exec_PrepareForLeap.cpp | 28 +++++++++++++++++++++++++++-
 1 file changed, 27 insertions(+), 1 deletion(-)

diff --git a/src/Exec_PrepareForLeap.cpp b/src/Exec_PrepareForLeap.cpp
index 8afe438afc..f608c319e7 100644
--- a/src/Exec_PrepareForLeap.cpp
+++ b/src/Exec_PrepareForLeap.cpp
@@ -1028,6 +1028,33 @@ Exec::RetType Exec_PrepareForLeap::Execute(CpptrajState& State, ArgList& argIn)
     mprintf("\tNot preparing sugars.\n");
   }
 
+  // Determine unknown residues we may want to find parameters for
+  NameType solvName(solventResName_);
+  SetType residuesToFindParamsFor;
+  for (ResStatArray::iterator it = resStat.begin(); it != resStat.end(); ++it)
+  {
+    NameType const& residueName = topIn.Res(it-resStat.begin()).Name();
+    // Skip water if not removing water
+    if (!remove_water && residueName == solvName) continue;
+    // If status is unknown, see if this is a common residue name
+    if ( *it == ResStatArray::UNKNOWN ) {
+      SetType::const_iterator pname = pdb_res_names_.find( residueName );
+      if (pname == pdb_res_names_.end()) {
+        mprintf("\t%s is an unrecognized name and may not have parameters.\n",
+                topIn.TruncResNameOnumId(it-resStat.begin()).c_str());
+        residuesToFindParamsFor.insert( residueName );
+      } else
+        *it = ResStatArray::VALIDATED;
+    }
+  }
+  if (!residuesToFindParamsFor.empty()) {
+    mprintf("\tResidues to find parameters for:");
+    for (SetType::const_iterator it = residuesToFindParamsFor.begin();
+                                 it != residuesToFindParamsFor.end(); ++it)
+      mprintf(" %s", it->Truncated().c_str());
+    mprintf("\n");
+  }
+
   // Create LEaP input for bonds that need to be made in LEaP
   for (std::vector<BondType>::const_iterator bnd = LeapBonds.begin();
                                              bnd != LeapBonds.end(); ++bnd)
@@ -1035,7 +1062,6 @@ Exec::RetType Exec_PrepareForLeap::Execute(CpptrajState& State, ArgList& argIn)
 
   // Count any solvent molecules
   if (!remove_water) {
-    NameType solvName(solventResName_);
     unsigned int nsolvent = 0;
     for (Topology::res_iterator res = topIn.ResStart(); res != topIn.ResEnd(); ++res) {
       if ( res->Name() == solvName) {

From 94974fe05458f880bde82720aa57265283f4b0c5 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 7 Nov 2023 10:42:42 -0500
Subject: [PATCH 0010/1492] Add version not specifying output file

---
 src/Remote.cpp | 5 +++++
 src/Remote.h   | 4 +++-
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/src/Remote.cpp b/src/Remote.cpp
index 88c8b6b5e9..1d6b640afd 100644
--- a/src/Remote.cpp
+++ b/src/Remote.cpp
@@ -104,3 +104,8 @@ const
 
   return 0;
 }
+
+/** Download file from base URL */
+int Remote::DownloadFile(std::string const& fname) const {
+  return DownloadFile(fname, "");
+}
diff --git a/src/Remote.h b/src/Remote.h
index b47723b87a..497b425f85 100644
--- a/src/Remote.h
+++ b/src/Remote.h
@@ -13,8 +13,10 @@ class Remote {
     void SetOverwrite(bool);
     /// Set debug level
     void SetDebug(int);
-    /// Download file assuming URL is remote directory
+    /// Download file to output file assuming URL is remote directory
     int DownloadFile(std::string const&, std::string const&) const;
+    /// Download file assuming URL is remote directory
+    int DownloadFile(std::string const&) const;
   private:
     /// Set remote download command
     int setRemoteDownloadCommand();

From ad3fac0f29a21f333749a775ec2f19222bdbaf78 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 7 Nov 2023 11:05:55 -0500
Subject: [PATCH 0011/1492] Initial attempt at downloading files. Works ok, but
 not yet capturing when parameters not found.

---
 src/Exec_PrepareForLeap.cpp | 46 +++++++++++++++++++++++++++++++++++++
 src/Exec_PrepareForLeap.h   | 10 ++++----
 src/cpptrajdepend           |  2 +-
 3 files changed, 53 insertions(+), 5 deletions(-)

diff --git a/src/Exec_PrepareForLeap.cpp b/src/Exec_PrepareForLeap.cpp
index f608c319e7..fa679bd831 100644
--- a/src/Exec_PrepareForLeap.cpp
+++ b/src/Exec_PrepareForLeap.cpp
@@ -4,6 +4,7 @@
 #include "DataSet_Coords_CRD.h"
 #include "LeapInterface.h"
 #include "ParmFile.h"
+#include "Remote.h"
 #include "StringRoutines.h"
 #include "Structure/Disulfide.h"
 #include "Structure/HisProt.h"
@@ -12,6 +13,7 @@
 #include "Structure/Sugar.h"
 #include "Trajout_Single.h"
 #include <stack> // FindTerByBonds
+#include <cctype> // tolower
 
 using namespace Cpptraj::Structure;
 
@@ -634,6 +636,43 @@ void Exec_PrepareForLeap::LeapFxnGroupWarning(Topology const& topIn, int rnum) {
   }
 }
 
+/** Try to download missing parameters. */
+int Exec_PrepareForLeap::DownloadParameters(ResStatArray& resStat, SetType const& resNames)
+const
+{
+  Cpptraj::Remote remote( parameterURL_ );
+  remote.SetDebug(1); // FIXME
+  for (SetType::const_iterator it = resNames.begin(); it != resNames.end(); ++it)
+  {
+    std::string rname = it->Truncated();
+    mprintf("\t\tSearching for parameters for residue '%s'\n", rname.c_str());
+    // Assume parameters are in a subdirectory starting with lowercase version
+    // of the first letter of the residue.
+    char lcase = tolower( rname[0] );
+    std::string rfbase = std::string(1, lcase) + "/" + rname;
+    mprintf("DEBUG: Base name: %s\n", rfbase.c_str());
+    int err = 0;
+    err += remote.DownloadFile( rfbase + ".mol2" );
+    if (err == 0) {
+      err += remote.DownloadFile( rfbase + ".frcmod" );
+      if (err != 0)
+        mprintf("Warning: Could not download %s.frcmod\n", rfbase.c_str());
+    } else {
+      mprintf("Warning: Could not download %s.mol2\n", rfbase.c_str());
+    }
+    if (err != 0)
+      mprintf("Warning: Could not download parameter files for '%s'\n", rname.c_str());
+    else {
+      // Sanity check - make sure the files are there.
+      if (!File::Exists(rname + ".mol2") || !File::Exists(rname + ".frcmod")) {
+        mprinterr("Error: Problem downloading parameter files for '%s'\n", rname.c_str());
+        return 1;
+      }
+    }
+  } // END loop over residue names to get parameters for
+  return 0;
+}
+
 // Exec_PrepareForLeap::Help()
 void Exec_PrepareForLeap::Help() const
 {
@@ -1053,6 +1092,13 @@ Exec::RetType Exec_PrepareForLeap::Execute(CpptrajState& State, ArgList& argIn)
                                  it != residuesToFindParamsFor.end(); ++it)
       mprintf(" %s", it->Truncated().c_str());
     mprintf("\n");
+    // Set default parameter URL if not yet set.
+    if (parameterURL_.empty())
+      parameterURL_.assign("https://raw.githubusercontent.com/phenix-project/geostd/master");
+    if (DownloadParameters(resStat, residuesToFindParamsFor)) {
+      mprinterr("Error: Download parameters failed.\n");
+      return CpptrajState::ERR;
+    }
   }
 
   // Create LEaP input for bonds that need to be made in LEaP
diff --git a/src/Exec_PrepareForLeap.h b/src/Exec_PrepareForLeap.h
index 57e27c6ff8..985d02a778 100644
--- a/src/Exec_PrepareForLeap.h
+++ b/src/Exec_PrepareForLeap.h
@@ -4,6 +4,7 @@
 namespace Cpptraj {
 namespace Structure {
 class SugarBuilder;
+class ResStatArray;
 }
 }
 /// Do common tasks to prepare a structure to be loaded into tleap 
@@ -15,6 +16,7 @@ class Exec_PrepareForLeap : public Exec {
     RetType Execute(CpptrajState&, ArgList&);
   private:
     typedef std::vector<int> Iarray;
+    typedef std::set<NameType> SetType;
 
     /// Set PDB residue names recognized by Amber FFs
     void SetPdbResNames();
@@ -30,27 +32,27 @@ class Exec_PrepareForLeap : public Exec {
     /// Try to determine where TER cards should be placed based on bonds
     int FindTerByBonds(Topology&, CharMask const&) const;
 
-
-    
     /// Remove specified atoms
     int ModifyCoords(Topology&, Frame&, bool, std::string const&, std::string const&,
                      std::string const&, Iarray const&) const;
     /// Remove hydrogen atoms
     int RemoveHydrogens(Topology&, Frame&) const;
 
-    
     /// Run leap to generate topology, perform any modifications
     int RunLeap(std::string const&, std::string const&) const;
     /// Print a warning for residues that will need modification after leap
     static void LeapFxnGroupWarning(Topology const&, int);
 
+    /// Download missing parameters
+    int DownloadParameters(Cpptraj::Structure::ResStatArray&, SetType const&) const;
+
     // -----------------------
-    typedef std::set<NameType> SetType;
     SetType pdb_res_names_; ///< PDB residue names recognized by Amber FFs
 
     std::string leapunitname_;
     bool errorsAreFatal_;   ///< If false, try to skip errors.
     int debug_;             ///< Debug level
     std::string solventResName_; ///< Solvent residue name
+    std::string parameterURL_;   ///< URL to download parameters from
 };
 #endif
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index cd68bbf84c..d2c7d7b566 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -318,7 +318,7 @@ Exec_ParmWrite.o : Exec_ParmWrite.cpp Action.h ActionList.h ActionState.h Analys
 Exec_ParseTiming.o : Exec_ParseTiming.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParseTiming.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_PermuteDihedrals.o : Exec_PermuteDihedrals.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h DistRoutines.h EnsembleIn.h EnsembleOutList.h ExclusionArray.h Exec.h Exec_PermuteDihedrals.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Precision.o : Exec_Precision.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Precision.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_PrepareForLeap.o : Exec_PrepareForLeap.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_PrepareForLeap.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h LeapInterface.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/Disulfide.h Structure/HisProt.h Structure/ResStatArray.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Exec_PrepareForLeap.o : Exec_PrepareForLeap.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_PrepareForLeap.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h LeapInterface.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h Remote.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/Disulfide.h Structure/HisProt.h Structure/ResStatArray.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Exec_PrintData.o : Exec_PrintData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_PrintData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Random.o : Exec_Random.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Random.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_ReadData.o : Exec_ReadData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ReadData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h

From c579ffb4030a9d7f26ed258581be1a102c8e59cc Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 7 Nov 2023 11:20:57 -0500
Subject: [PATCH 0012/1492] Make less verbose

---
 src/Remote.cpp | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/Remote.cpp b/src/Remote.cpp
index 1d6b640afd..52cc4bd4ce 100644
--- a/src/Remote.cpp
+++ b/src/Remote.cpp
@@ -45,13 +45,13 @@ int Remote::setRemoteDownloadCommand() {
   int err = system("curl --version");
   if (err == 0) {
     mprintf("\tcurl found.\n");
-    cmd_.assign("curl -L ");
+    cmd_.assign("curl -s --show-error -f -L ");
     oflag_.assign("-o ");
   } else {
     err = system("wget --version");
     if (err == 0) {
       mprintf("\twget found.\n");
-      cmd_.assign("wget ");
+      cmd_.assign("wget --quiet ");
       oflag_.assign("-O ");
     } else {
       mprinterr("Error: No working remote command found.\n");
@@ -99,6 +99,7 @@ const
   int err = system(remoteCmd.c_str());
   if (err != 0) {
     mprinterr("Error: Could not download %s => %s\n", remoteUrl.c_str(), outputFname.full());
+    // FIXME: wget will leave behind empty files here
     return 1;
   }
 

From 81e400202c8a5ec65f21f608629e1b44d3fe3c93 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 7 Nov 2023 11:28:02 -0500
Subject: [PATCH 0013/1492] Add necessary leap input

---
 src/Exec_PrepareForLeap.cpp | 19 +++++++++++++------
 src/Exec_PrepareForLeap.h   |  2 +-
 2 files changed, 14 insertions(+), 7 deletions(-)

diff --git a/src/Exec_PrepareForLeap.cpp b/src/Exec_PrepareForLeap.cpp
index fa679bd831..f131483655 100644
--- a/src/Exec_PrepareForLeap.cpp
+++ b/src/Exec_PrepareForLeap.cpp
@@ -637,7 +637,8 @@ void Exec_PrepareForLeap::LeapFxnGroupWarning(Topology const& topIn, int rnum) {
 }
 
 /** Try to download missing parameters. */
-int Exec_PrepareForLeap::DownloadParameters(ResStatArray& resStat, SetType const& resNames)
+int Exec_PrepareForLeap::DownloadParameters(ResStatArray& resStat, SetType const& resNames,
+                                            CpptrajFile* leapInput)
 const
 {
   Cpptraj::Remote remote( parameterURL_ );
@@ -668,6 +669,11 @@ const
         mprinterr("Error: Problem downloading parameter files for '%s'\n", rname.c_str());
         return 1;
       }
+      // Add leap input
+      if (leapInput != 0) {
+        leapInput->Printf("%s = loadmol2 %s.mol2\n", rname.c_str(), rname.c_str());
+        leapInput->Printf("parm%s = loadamberparams %s.frcmod\n", rname.c_str(), rname.c_str());
+      }
     }
   } // END loop over residue names to get parameters for
   return 0;
@@ -1032,10 +1038,6 @@ Exec::RetType Exec_PrepareForLeap::Execute(CpptrajState& State, ArgList& argIn)
   if (outfile == 0) return CpptrajState::ERR;
   mprintf("\tLEaP input containing 'loadpdb' and bond commands for disulfides,\n"
           "\t  sugars, etc will be written to '%s'\n", outfile->Filename().full());
-  // Add the loadpdb command if we are writing a PDB file.
-  // TODO add 'addPdbResMap { { 1 "NH2" "NHE" } }' to recognize NHE?
-  if (!pdbout.empty())
-    outfile->Printf("%s = loadpdb %s\n", leapunitname_.c_str(), pdbout.c_str());
 
   // Array that will hold bonds that need to be made in LEaP
   std::vector<BondType> LeapBonds;
@@ -1095,12 +1097,17 @@ Exec::RetType Exec_PrepareForLeap::Execute(CpptrajState& State, ArgList& argIn)
     // Set default parameter URL if not yet set.
     if (parameterURL_.empty())
       parameterURL_.assign("https://raw.githubusercontent.com/phenix-project/geostd/master");
-    if (DownloadParameters(resStat, residuesToFindParamsFor)) {
+    if (DownloadParameters(resStat, residuesToFindParamsFor, outfile)) {
       mprinterr("Error: Download parameters failed.\n");
       return CpptrajState::ERR;
     }
   }
 
+  // Add the loadpdb command if we are writing a PDB file.
+  // TODO add 'addPdbResMap { { 1 "NH2" "NHE" } }' to recognize NHE?
+  if (!pdbout.empty())
+    outfile->Printf("%s = loadpdb %s\n", leapunitname_.c_str(), pdbout.c_str());
+
   // Create LEaP input for bonds that need to be made in LEaP
   for (std::vector<BondType>::const_iterator bnd = LeapBonds.begin();
                                              bnd != LeapBonds.end(); ++bnd)
diff --git a/src/Exec_PrepareForLeap.h b/src/Exec_PrepareForLeap.h
index 985d02a778..052672a7dd 100644
--- a/src/Exec_PrepareForLeap.h
+++ b/src/Exec_PrepareForLeap.h
@@ -44,7 +44,7 @@ class Exec_PrepareForLeap : public Exec {
     static void LeapFxnGroupWarning(Topology const&, int);
 
     /// Download missing parameters
-    int DownloadParameters(Cpptraj::Structure::ResStatArray&, SetType const&) const;
+    int DownloadParameters(Cpptraj::Structure::ResStatArray&, SetType const&, CpptrajFile*) const;
 
     // -----------------------
     SetType pdb_res_names_; ///< PDB residue names recognized by Amber FFs

From 90af0e5b973d527e1a3b09e2f3de35fde4d61f59 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 7 Nov 2023 16:07:49 -0500
Subject: [PATCH 0014/1492] Start ResNameIndices class

---
 src/Structure/ResNameIndices.h | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)
 create mode 100644 src/Structure/ResNameIndices.h

diff --git a/src/Structure/ResNameIndices.h b/src/Structure/ResNameIndices.h
new file mode 100644
index 0000000000..6390049470
--- /dev/null
+++ b/src/Structure/ResNameIndices.h
@@ -0,0 +1,33 @@
+#ifndef INC_STRUCTURE_RESNAMEINDICES_H
+#define INC_STRUCTURE_RESNAMEINDICES_H
+#include <vector>
+#include "../NameType.h"
+namespace Cpptraj {
+namespace Structure {
+class ResNameIndices {
+    typedef std::vector<int> Iarray;
+  public:
+    ResNameIndices() {}
+    /// CONSTRUCTOR - Residue name and index
+    ResNameIndices(NameType const& n, int r) : resname_(n), resnums_(1, r) {}
+    /// Add residue index
+    void AddResnum(int r) { resnums_.push_back( r ); }
+    /// Sort only by resname
+    bool operator<(ResNameIndices const& rhs) const {
+      return (resname_ < rhs.resname_);
+    }
+    /// \return Residue name
+    NameType const& Resname() const { return resname_; }
+    /// Iterator over residue numbers
+    typedef Iarray::const_iterator const_iterator;
+    /// \return Beginning of residue numbers
+    const_iterator begin() const { return resnums_.begin(); }
+    /// \return Ending of residue numbers
+    const_iterator end() const { return resnums_.end(); }
+  private:
+    NameType resname_; ///< Residue name
+    Iarray resnums_;   ///< Residue indices with this name
+};
+}
+}
+#endif

From 3a7454121039d7a41647615dd1f2c210a40ae205 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 8 Nov 2023 08:31:39 -0500
Subject: [PATCH 0015/1492] Different constructor

---
 src/Structure/ResNameIndices.h | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/Structure/ResNameIndices.h b/src/Structure/ResNameIndices.h
index 6390049470..e11e26109a 100644
--- a/src/Structure/ResNameIndices.h
+++ b/src/Structure/ResNameIndices.h
@@ -9,7 +9,9 @@ class ResNameIndices {
   public:
     ResNameIndices() {}
     /// CONSTRUCTOR - Residue name and index
-    ResNameIndices(NameType const& n, int r) : resname_(n), resnums_(1, r) {}
+    //ResNameIndices(NameType const& n, int r) : resname_(n), resnums_(1, r) {}
+    /// CONSTRUCTOR - Residue name
+    ResNameIndices(NameType const& n) : resname_(n) {}
     /// Add residue index
     void AddResnum(int r) { resnums_.push_back( r ); }
     /// Sort only by resname

From 3c69f650f87820e044c0b334decc7dff1dd606ea Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 8 Nov 2023 08:31:51 -0500
Subject: [PATCH 0016/1492] Using a map instead

---
 src/Structure/ResNameIndices.h | 35 ----------------------------------
 1 file changed, 35 deletions(-)
 delete mode 100644 src/Structure/ResNameIndices.h

diff --git a/src/Structure/ResNameIndices.h b/src/Structure/ResNameIndices.h
deleted file mode 100644
index e11e26109a..0000000000
--- a/src/Structure/ResNameIndices.h
+++ /dev/null
@@ -1,35 +0,0 @@
-#ifndef INC_STRUCTURE_RESNAMEINDICES_H
-#define INC_STRUCTURE_RESNAMEINDICES_H
-#include <vector>
-#include "../NameType.h"
-namespace Cpptraj {
-namespace Structure {
-class ResNameIndices {
-    typedef std::vector<int> Iarray;
-  public:
-    ResNameIndices() {}
-    /// CONSTRUCTOR - Residue name and index
-    //ResNameIndices(NameType const& n, int r) : resname_(n), resnums_(1, r) {}
-    /// CONSTRUCTOR - Residue name
-    ResNameIndices(NameType const& n) : resname_(n) {}
-    /// Add residue index
-    void AddResnum(int r) { resnums_.push_back( r ); }
-    /// Sort only by resname
-    bool operator<(ResNameIndices const& rhs) const {
-      return (resname_ < rhs.resname_);
-    }
-    /// \return Residue name
-    NameType const& Resname() const { return resname_; }
-    /// Iterator over residue numbers
-    typedef Iarray::const_iterator const_iterator;
-    /// \return Beginning of residue numbers
-    const_iterator begin() const { return resnums_.begin(); }
-    /// \return Ending of residue numbers
-    const_iterator end() const { return resnums_.end(); }
-  private:
-    NameType resname_; ///< Residue name
-    Iarray resnums_;   ///< Residue indices with this name
-};
-}
-}
-#endif

From 7dcb392d0ce2df50a3edf8abd4c1c03115394014 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 8 Nov 2023 08:35:33 -0500
Subject: [PATCH 0017/1492] Clean up any downloaded parameters

---
 test/Test_PrepareForLeap/RunTest.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/Test_PrepareForLeap/RunTest.sh b/test/Test_PrepareForLeap/RunTest.sh
index 681b41cca2..deea079740 100755
--- a/test/Test_PrepareForLeap/RunTest.sh
+++ b/test/Test_PrepareForLeap/RunTest.sh
@@ -4,7 +4,7 @@
 
 CleanFiles cpptraj.in 1qos.cpptraj.pdb leap.1qos.in \
            leap.4zzw.in 4zzw.cpptraj.pdb 1qos.cpptraj.pdb.2 \
-           leap.1qos.in.2
+           leap.1qos.in.2 *.mol2 *.frcmod 
 
 INPUT='-i cpptraj.in'
 

From 452ff08f7db43e2343653298068fc523f28edc83 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 8 Nov 2023 08:36:01 -0500
Subject: [PATCH 0018/1492] Save residue numbers of residues to get parameters
 for

---
 src/Exec_PrepareForLeap.cpp | 27 ++++++++++++++++++---------
 src/Exec_PrepareForLeap.h   |  5 ++++-
 2 files changed, 22 insertions(+), 10 deletions(-)

diff --git a/src/Exec_PrepareForLeap.cpp b/src/Exec_PrepareForLeap.cpp
index f131483655..17a8305856 100644
--- a/src/Exec_PrepareForLeap.cpp
+++ b/src/Exec_PrepareForLeap.cpp
@@ -637,16 +637,19 @@ void Exec_PrepareForLeap::LeapFxnGroupWarning(Topology const& topIn, int rnum) {
 }
 
 /** Try to download missing parameters. */
-int Exec_PrepareForLeap::DownloadParameters(ResStatArray& resStat, SetType const& resNames,
+int Exec_PrepareForLeap::DownloadParameters(ResStatArray& resStat, RmapType const& resNames,
                                             CpptrajFile* leapInput)
 const
 {
   Cpptraj::Remote remote( parameterURL_ );
   remote.SetDebug(1); // FIXME
-  for (SetType::const_iterator it = resNames.begin(); it != resNames.end(); ++it)
+  for (RmapType::const_iterator it = resNames.begin(); it != resNames.end(); ++it)
   {
-    std::string rname = it->Truncated();
-    mprintf("\t\tSearching for parameters for residue '%s'\n", rname.c_str());
+    std::string rname = it->first.Truncated();
+    mprintf("\t\tSearching for parameters for residue '%s'", rname.c_str());
+    for (Iarray::const_iterator rn = it->second.begin(); rn != it->second.end(); ++rn)
+      mprintf(" %i", *rn + 1);
+    mprintf("\n");
     // Assume parameters are in a subdirectory starting with lowercase version
     // of the first letter of the residue.
     char lcase = tolower( rname[0] );
@@ -1071,7 +1074,7 @@ Exec::RetType Exec_PrepareForLeap::Execute(CpptrajState& State, ArgList& argIn)
 
   // Determine unknown residues we may want to find parameters for
   NameType solvName(solventResName_);
-  SetType residuesToFindParamsFor;
+  RmapType residuesToFindParamsFor;
   for (ResStatArray::iterator it = resStat.begin(); it != resStat.end(); ++it)
   {
     NameType const& residueName = topIn.Res(it-resStat.begin()).Name();
@@ -1083,16 +1086,22 @@ Exec::RetType Exec_PrepareForLeap::Execute(CpptrajState& State, ArgList& argIn)
       if (pname == pdb_res_names_.end()) {
         mprintf("\t%s is an unrecognized name and may not have parameters.\n",
                 topIn.TruncResNameOnumId(it-resStat.begin()).c_str());
-        residuesToFindParamsFor.insert( residueName );
+        RmapType::iterator ret = residuesToFindParamsFor.lower_bound( residueName );
+        if (ret == residuesToFindParamsFor.end() || ret->first != residueName)
+        {
+          // New residue to get params for
+          ret = residuesToFindParamsFor.insert(ret, RpairType(residueName, Iarray()));
+        }
+        ret->second.push_back( it - resStat.begin() );
       } else
         *it = ResStatArray::VALIDATED;
     }
   }
   if (!residuesToFindParamsFor.empty()) {
     mprintf("\tResidues to find parameters for:");
-    for (SetType::const_iterator it = residuesToFindParamsFor.begin();
-                                 it != residuesToFindParamsFor.end(); ++it)
-      mprintf(" %s", it->Truncated().c_str());
+    for (RmapType::const_iterator it = residuesToFindParamsFor.begin();
+                                  it != residuesToFindParamsFor.end(); ++it)
+      mprintf(" %s", it->first.Truncated().c_str());
     mprintf("\n");
     // Set default parameter URL if not yet set.
     if (parameterURL_.empty())
diff --git a/src/Exec_PrepareForLeap.h b/src/Exec_PrepareForLeap.h
index 052672a7dd..1a5d464ce8 100644
--- a/src/Exec_PrepareForLeap.h
+++ b/src/Exec_PrepareForLeap.h
@@ -5,6 +5,7 @@ namespace Cpptraj {
 namespace Structure {
 class SugarBuilder;
 class ResStatArray;
+class ResNameIndices;
 }
 }
 /// Do common tasks to prepare a structure to be loaded into tleap 
@@ -17,6 +18,8 @@ class Exec_PrepareForLeap : public Exec {
   private:
     typedef std::vector<int> Iarray;
     typedef std::set<NameType> SetType;
+    typedef std::pair<NameType,Iarray> RpairType;
+    typedef std::map<NameType,Iarray> RmapType;
 
     /// Set PDB residue names recognized by Amber FFs
     void SetPdbResNames();
@@ -44,7 +47,7 @@ class Exec_PrepareForLeap : public Exec {
     static void LeapFxnGroupWarning(Topology const&, int);
 
     /// Download missing parameters
-    int DownloadParameters(Cpptraj::Structure::ResStatArray&, SetType const&, CpptrajFile*) const;
+    int DownloadParameters(Cpptraj::Structure::ResStatArray&, RmapType const&, CpptrajFile*) const;
 
     // -----------------------
     SetType pdb_res_names_; ///< PDB residue names recognized by Amber FFs

From 21e582fcea2b8da7902a1f39c47f6920a9a5c454 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 8 Nov 2023 08:43:38 -0500
Subject: [PATCH 0019/1492] Detect residue connectivity for unknown residues

---
 src/Exec_PrepareForLeap.cpp | 19 +++++++++++++++++--
 src/Exec_PrepareForLeap.h   |  3 ++-
 2 files changed, 19 insertions(+), 3 deletions(-)

diff --git a/src/Exec_PrepareForLeap.cpp b/src/Exec_PrepareForLeap.cpp
index 17a8305856..821cbc6096 100644
--- a/src/Exec_PrepareForLeap.cpp
+++ b/src/Exec_PrepareForLeap.cpp
@@ -638,7 +638,7 @@ void Exec_PrepareForLeap::LeapFxnGroupWarning(Topology const& topIn, int rnum) {
 
 /** Try to download missing parameters. */
 int Exec_PrepareForLeap::DownloadParameters(ResStatArray& resStat, RmapType const& resNames,
-                                            CpptrajFile* leapInput)
+                                            Topology const& topIn, CpptrajFile* leapInput)
 const
 {
   Cpptraj::Remote remote( parameterURL_ );
@@ -677,6 +677,21 @@ const
         leapInput->Printf("%s = loadmol2 %s.mol2\n", rname.c_str(), rname.c_str());
         leapInput->Printf("parm%s = loadamberparams %s.frcmod\n", rname.c_str(), rname.c_str());
       }
+      // Downloaded mol2 files do not have connectivity, so we need to add bonds.
+      for (Iarray::const_iterator rn = it->second.begin(); rn != it->second.end(); ++rn)
+      {
+        Residue const& currentRes = topIn.Res( *rn );
+        // Check each atom for bonds to another residue
+        for (int at = currentRes.FirstAtom(); at != currentRes.LastAtom(); ++at) {
+          for (Atom::bond_iterator bat = topIn[at].bondbegin(); bat != topIn[at].bondend(); ++bat) {
+            if ( topIn[*bat].ResNum() != *rn ) {
+              mprintf("\t\t\tRes %s is bonded to res %s\n",
+                      topIn.TruncResAtomName(at).c_str(),
+                      topIn.TruncResAtomName(*bat).c_str());
+            }
+          } // END loop over bonded atoms
+        } // END loop over atoms in residue
+      } // END loop over residue numbers
     }
   } // END loop over residue names to get parameters for
   return 0;
@@ -1106,7 +1121,7 @@ Exec::RetType Exec_PrepareForLeap::Execute(CpptrajState& State, ArgList& argIn)
     // Set default parameter URL if not yet set.
     if (parameterURL_.empty())
       parameterURL_.assign("https://raw.githubusercontent.com/phenix-project/geostd/master");
-    if (DownloadParameters(resStat, residuesToFindParamsFor, outfile)) {
+    if (DownloadParameters(resStat, residuesToFindParamsFor, topIn, outfile)) {
       mprinterr("Error: Download parameters failed.\n");
       return CpptrajState::ERR;
     }
diff --git a/src/Exec_PrepareForLeap.h b/src/Exec_PrepareForLeap.h
index 1a5d464ce8..ce1df12bdc 100644
--- a/src/Exec_PrepareForLeap.h
+++ b/src/Exec_PrepareForLeap.h
@@ -47,7 +47,8 @@ class Exec_PrepareForLeap : public Exec {
     static void LeapFxnGroupWarning(Topology const&, int);
 
     /// Download missing parameters
-    int DownloadParameters(Cpptraj::Structure::ResStatArray&, RmapType const&, CpptrajFile*) const;
+    int DownloadParameters(Cpptraj::Structure::ResStatArray&, RmapType const&,
+                           Topology const&, CpptrajFile*) const;
 
     // -----------------------
     SetType pdb_res_names_; ///< PDB residue names recognized by Amber FFs

From de91632226149708cb54c683e6832dcf936e2571 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 8 Nov 2023 09:23:29 -0500
Subject: [PATCH 0020/1492] Add == operator

---
 src/ParameterTypes.h | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/src/ParameterTypes.h b/src/ParameterTypes.h
index 69b64b3bde..7564a61069 100644
--- a/src/ParameterTypes.h
+++ b/src/ParameterTypes.h
@@ -64,6 +64,11 @@ class BondType {
         return (a2_ < rhs.a2_);
       } else return (a1_ < rhs.a1_);
     }
+    bool operator==(const BondType& rhs) const {
+      if ( (a1_ == rhs.a1_ && a2_ == rhs.a2_) ||
+           (a2_ == rhs.a1_ && a1_ == rhs.a2_) ) return true;
+      return false;
+    }
   private:
     int a1_;
     int a2_;

From b15831b4f2d35ba6c91db29e9c93a27fa26f154f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 8 Nov 2023 09:23:50 -0500
Subject: [PATCH 0021/1492] Add detected bonds from unknown residues to other
 residues. Remove any duplicates.

---
 src/Exec_PrepareForLeap.cpp | 12 ++++++++++--
 src/Exec_PrepareForLeap.h   |  3 ++-
 2 files changed, 12 insertions(+), 3 deletions(-)

diff --git a/src/Exec_PrepareForLeap.cpp b/src/Exec_PrepareForLeap.cpp
index 821cbc6096..1efd2a83a5 100644
--- a/src/Exec_PrepareForLeap.cpp
+++ b/src/Exec_PrepareForLeap.cpp
@@ -14,6 +14,7 @@
 #include "Trajout_Single.h"
 #include <stack> // FindTerByBonds
 #include <cctype> // tolower
+#include <algorithm> // unique
 
 using namespace Cpptraj::Structure;
 
@@ -638,7 +639,8 @@ void Exec_PrepareForLeap::LeapFxnGroupWarning(Topology const& topIn, int rnum) {
 
 /** Try to download missing parameters. */
 int Exec_PrepareForLeap::DownloadParameters(ResStatArray& resStat, RmapType const& resNames,
-                                            Topology const& topIn, CpptrajFile* leapInput)
+                                            Topology const& topIn, CpptrajFile* leapInput,
+                                            std::vector<BondType>& LeapBonds)
 const
 {
   Cpptraj::Remote remote( parameterURL_ );
@@ -688,6 +690,7 @@ const
               mprintf("\t\t\tRes %s is bonded to res %s\n",
                       topIn.TruncResAtomName(at).c_str(),
                       topIn.TruncResAtomName(*bat).c_str());
+              LeapBonds.push_back( BondType(at, *bat, -1) );
             }
           } // END loop over bonded atoms
         } // END loop over atoms in residue
@@ -1121,7 +1124,7 @@ Exec::RetType Exec_PrepareForLeap::Execute(CpptrajState& State, ArgList& argIn)
     // Set default parameter URL if not yet set.
     if (parameterURL_.empty())
       parameterURL_.assign("https://raw.githubusercontent.com/phenix-project/geostd/master");
-    if (DownloadParameters(resStat, residuesToFindParamsFor, topIn, outfile)) {
+    if (DownloadParameters(resStat, residuesToFindParamsFor, topIn, outfile, LeapBonds)) {
       mprinterr("Error: Download parameters failed.\n");
       return CpptrajState::ERR;
     }
@@ -1132,6 +1135,11 @@ Exec::RetType Exec_PrepareForLeap::Execute(CpptrajState& State, ArgList& argIn)
   if (!pdbout.empty())
     outfile->Printf("%s = loadpdb %s\n", leapunitname_.c_str(), pdbout.c_str());
 
+  // Remove any duplicate bonds
+  std::sort( LeapBonds.begin(), LeapBonds.end() );
+  std::vector<BondType>::const_iterator it = std::unique( LeapBonds.begin(), LeapBonds.end() );
+  LeapBonds.resize( it - LeapBonds.begin() );
+
   // Create LEaP input for bonds that need to be made in LEaP
   for (std::vector<BondType>::const_iterator bnd = LeapBonds.begin();
                                              bnd != LeapBonds.end(); ++bnd)
diff --git a/src/Exec_PrepareForLeap.h b/src/Exec_PrepareForLeap.h
index ce1df12bdc..f9b64d3ca3 100644
--- a/src/Exec_PrepareForLeap.h
+++ b/src/Exec_PrepareForLeap.h
@@ -1,6 +1,7 @@
 #ifndef INC_EXEC_PREPAREFORLEAP_H
 #define INC_EXEC_PREPAREFORLEAP_H
 #include "Exec.h"
+class BondType;
 namespace Cpptraj {
 namespace Structure {
 class SugarBuilder;
@@ -48,7 +49,7 @@ class Exec_PrepareForLeap : public Exec {
 
     /// Download missing parameters
     int DownloadParameters(Cpptraj::Structure::ResStatArray&, RmapType const&,
-                           Topology const&, CpptrajFile*) const;
+                           Topology const&, CpptrajFile*, std::vector<BondType>&) const;
 
     // -----------------------
     SetType pdb_res_names_; ///< PDB residue names recognized by Amber FFs

From 240f48f8ab798429602a16f66f09259ad95cdd7d Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 8 Nov 2023 09:31:47 -0500
Subject: [PATCH 0022/1492] Output is the same but bonds are now sorted

---
 test/Test_PrepareForLeap/leap.1qos.in.save | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/Test_PrepareForLeap/leap.1qos.in.save b/test/Test_PrepareForLeap/leap.1qos.in.save
index 32c3565874..fe1929faba 100644
--- a/test/Test_PrepareForLeap/leap.1qos.in.save
+++ b/test/Test_PrepareForLeap/leap.1qos.in.save
@@ -1,7 +1,7 @@
 m = loadpdb 1qos.cpptraj.pdb
 bond m.182.SG m.419.SG
 bond m.475.C1 m.476.O1
-bond m.478.C1 m.479.O1
-bond m.483.C1 m.110.OG
 bond m.475.O4 m.477.C1
+bond m.478.C1 m.479.O1
 bond m.478.O4 m.480.C1
+bond m.483.C1 m.110.OG

From 7254fcda20232d423d3da0f57ea20a797d1b40ab Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 8 Nov 2023 10:31:30 -0500
Subject: [PATCH 0023/1492] If we could find parameters for residues, mark them
 as validated.

---
 src/Exec_PrepareForLeap.cpp | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/Exec_PrepareForLeap.cpp b/src/Exec_PrepareForLeap.cpp
index 1efd2a83a5..59b7a538f6 100644
--- a/src/Exec_PrepareForLeap.cpp
+++ b/src/Exec_PrepareForLeap.cpp
@@ -682,6 +682,8 @@ const
       // Downloaded mol2 files do not have connectivity, so we need to add bonds.
       for (Iarray::const_iterator rn = it->second.begin(); rn != it->second.end(); ++rn)
       {
+        // Assume we are all good with parameters for these residues now.
+        resStat[*rn] = ResStatArray::VALIDATED;
         Residue const& currentRes = topIn.Res( *rn );
         // Check each atom for bonds to another residue
         for (int at = currentRes.FirstAtom(); at != currentRes.LastAtom(); ++at) {

From 0a130525a8cc581c7e6fee5df46e40a27c72e9e3 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 9 Nov 2023 09:22:27 -0500
Subject: [PATCH 0024/1492] Add dlparams/nodlparams keywords. Do not check for
 unknown residues twice.

---
 src/Exec_PrepareForLeap.cpp  | 27 ++++++++++++++++++++-------
 src/Exec_PrepareForLeap.h    |  9 +++++----
 src/Structure/ResStatArray.h |  6 ++++++
 3 files changed, 31 insertions(+), 11 deletions(-)

diff --git a/src/Exec_PrepareForLeap.cpp b/src/Exec_PrepareForLeap.cpp
index 59b7a538f6..82020e049b 100644
--- a/src/Exec_PrepareForLeap.cpp
+++ b/src/Exec_PrepareForLeap.cpp
@@ -21,6 +21,7 @@ using namespace Cpptraj::Structure;
 /** CONSTRUCTOR */
 Exec_PrepareForLeap::Exec_PrepareForLeap() : Exec(COORDS),
   errorsAreFatal_(true),
+  downloadParams_(true),
   debug_(0)
 {
   SetHidden(false);
@@ -708,7 +709,7 @@ void Exec_PrepareForLeap::Help() const
   mprintf("\tcrdset <coords set> [frame <#>] name <out coords set>\n"
           "\t[pdbout <pdbfile> [terbymol]]\n"
           "\t[leapunitname <unit>] [out <leap input file> [runleap <ff file>]]\n"
-          "\t[skiperrors]\n"
+          "\t[skiperrors] [{dlparams|nodlparams}]\n"
           "\t[nowat [watermask <watermask>] [noh]\n"
           "\t[keepaltloc {<alt loc ID>|highestocc}]\n"
           "\t[stripmask <stripmask>] [solventresname <solventresname>]\n"
@@ -733,6 +734,8 @@ void Exec_PrepareForLeap::Help() const
           "  have any inter-residue bonds removed, and the appropriate LEaP\n"
           "  input to add the bonds back once the structure has been loaded\n"
           "  into LEaP will be written to <leap input file>.\n"
+          "  The command will attempt to download parameters for unknown\n"
+          "  residues unless 'nodlparams' is specified.\n"
          );
 }
 
@@ -745,6 +748,12 @@ Exec::RetType Exec_PrepareForLeap::Execute(CpptrajState& State, ArgList& argIn)
           "#           J. Comp. Chem. (2022), V. 43, I. 13, pp 930-935.\n" );
   debug_ = State.Debug();
   errorsAreFatal_ = !argIn.hasKey("skiperrors");
+  if (argIn.hasKey("dlparams"))
+    downloadParams_ = true;
+  else if (argIn.hasKey("nodlparams"))
+    downloadParams_ = false;
+  else
+    downloadParams_ = true;
   // Get input coords
   std::string crdset = argIn.GetStringKey("crdset");
   if (crdset.empty()) {
@@ -847,6 +856,10 @@ Exec::RetType Exec_PrepareForLeap::Execute(CpptrajState& State, ArgList& argIn)
     for (SetType::const_iterator it = pdb_res_names_.begin(); it != pdb_res_names_.end(); ++it)
       mprintf("\t  %s\n", *(*it));
   }
+  if (downloadParams_)
+    mprintf("\tWill attempt to download parameters for unknown residues.\n");
+  else
+    mprintf("\tWill not attempt to download paramters for unknown residues.\n");
 
   // Load PDB to glycam residue name map
   SugarBuilder sugarBuilder(debug_);
@@ -1117,7 +1130,7 @@ Exec::RetType Exec_PrepareForLeap::Execute(CpptrajState& State, ArgList& argIn)
         *it = ResStatArray::VALIDATED;
     }
   }
-  if (!residuesToFindParamsFor.empty()) {
+  if (downloadParams_ && !residuesToFindParamsFor.empty()) {
     mprintf("\tResidues to find parameters for:");
     for (RmapType::const_iterator it = residuesToFindParamsFor.begin();
                                   it != residuesToFindParamsFor.end(); ++it)
@@ -1166,7 +1179,7 @@ Exec::RetType Exec_PrepareForLeap::Execute(CpptrajState& State, ArgList& argIn)
   int fatal_errors = 0;
   static const char* msg1 = "Potential problem : ";
   static const char* msg2 = "Fatal problem     : ";
-  for (ResStatArray::iterator it = resStat.begin(); it != resStat.end(); ++it)
+  for (ResStatArray::const_iterator it = resStat.begin(); it != resStat.end(); ++it)
   {
     LeapFxnGroupWarning(topIn, it-resStat.begin());
     //if ( *it == VALIDATED )
@@ -1175,12 +1188,12 @@ Exec::RetType Exec_PrepareForLeap::Execute(CpptrajState& State, ArgList& argIn)
     //  mprintf("\t\t%s UNKNOWN\n", topIn.TruncResNameOnumId(it-resStat_.begin()).c_str());
     // ----- Warnings --------
     if ( *it == ResStatArray::UNKNOWN ) {
-      SetType::const_iterator pname = pdb_res_names_.find( topIn.Res(it-resStat.begin()).Name() );
-      if (pname == pdb_res_names_.end())
+      //SetType::const_iterator pname = pdb_res_names_.find( topIn.Res(it-resStat.begin()).Name() );
+      //if (pname == pdb_res_names_.end())
         mprintf("\t%s%s is an unrecognized name and may not have parameters.\n",
                 msg1, topIn.TruncResNameOnumId(it-resStat.begin()).c_str());
-      else
-        *it = ResStatArray::VALIDATED;
+      //else
+      //  *it = ResStatArray::VALIDATED;
     } else if ( *it == ResStatArray::SUGAR_NAME_MISMATCH ) {
         mprintf("\t%s%s sugar anomer type and/or configuration is not consistent with name.\n",
                 msg1, topIn.TruncResNameOnumId(it-resStat.begin()).c_str());
diff --git a/src/Exec_PrepareForLeap.h b/src/Exec_PrepareForLeap.h
index f9b64d3ca3..eb163c31f8 100644
--- a/src/Exec_PrepareForLeap.h
+++ b/src/Exec_PrepareForLeap.h
@@ -52,11 +52,12 @@ class Exec_PrepareForLeap : public Exec {
                            Topology const&, CpptrajFile*, std::vector<BondType>&) const;
 
     // -----------------------
-    SetType pdb_res_names_; ///< PDB residue names recognized by Amber FFs
+    SetType pdb_res_names_;      ///< PDB residue names recognized by Amber FFs
 
-    std::string leapunitname_;
-    bool errorsAreFatal_;   ///< If false, try to skip errors.
-    int debug_;             ///< Debug level
+    std::string leapunitname_;   ///< Unit name to use when loading molecule
+    bool errorsAreFatal_;        ///< If false, try to skip errors.
+    bool downloadParams_;        ///< If true, try to download parameters for missing residues
+    int debug_;                  ///< Debug level
     std::string solventResName_; ///< Solvent residue name
     std::string parameterURL_;   ///< URL to download parameters from
 };
diff --git a/src/Structure/ResStatArray.h b/src/Structure/ResStatArray.h
index 04d443718f..02a522e924 100644
--- a/src/Structure/ResStatArray.h
+++ b/src/Structure/ResStatArray.h
@@ -27,6 +27,12 @@ class ResStatArray {
     iterator begin() { return resStat_.begin(); }
     /// \return iterator to end
     iterator end()   { return resStat_.end(); }
+
+    typedef std::vector<Type>::const_iterator const_iterator;
+    /// \return const iterator to beginning
+    const_iterator begin() const { return resStat_.begin(); }
+    /// \return iterator to end
+    const_iterator end()   const { return resStat_.end(); }
   private:
     typedef std::vector<Type> Rarray;
     Rarray resStat_; ///< Status of each residue in a topology

From 45bb375e845d0fb47ca90abb3b5ebb252be26eb6 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 9 Nov 2023 09:23:58 -0500
Subject: [PATCH 0025/1492] Add LJ 1-4 pairs to ParameterSet

---
 src/ParameterSet.cpp |  8 ++++++++
 src/ParameterSet.h   | 40 ++++++++++++++++++++--------------------
 2 files changed, 28 insertions(+), 20 deletions(-)

diff --git a/src/ParameterSet.cpp b/src/ParameterSet.cpp
index 7d85cfb647..ccfc35bde6 100644
--- a/src/ParameterSet.cpp
+++ b/src/ParameterSet.cpp
@@ -27,6 +27,12 @@ void ParameterSet::Debug(const char* fnameIn) const {
     for (ParmHolder<NonbondType>::const_iterator nb = nbParm_.begin(); nb != nbParm_.end(); ++nb)
       Out.Printf("\t%6s %6s : %12.4E %12.4E\n", (*nb->first[0]), (*nb->first[1]), nb->second.A(), nb->second.B());
   }
+  if (!nb14Parm_.empty()) {
+    Out.Printf("LJ 1-4 parameters:\n");
+    Out.Printf("\t%6s %6s : %12s %12s\n", "Type1", "Type2", "A", "B");
+    for (ParmHolder<NonbondType>::const_iterator nb = nb14Parm_.begin(); nb != nb14Parm_.end(); ++nb)
+      Out.Printf("\t%6s %6s : %12.4E %12.4E\n", (*nb->first[0]), (*nb->first[1]), nb->second.A(), nb->second.B());
+  }
   if (!bondParm_.empty()) {
     Out.Printf("Bond parameters:\n");
     Out.Printf("\t%6s %6s : %12s %12s\n", "Type1", "Type2", "Rk", "Req");
@@ -85,6 +91,8 @@ int ParameterSet::UpdateParamSet(ParameterSet const& set1, UpdateCount& uc, int
   uc.nAtomTypeUpdated_ = UpdateParameters< ParmHolder<AtomType> >(set0.AT(), set1.AT(), "atom type");
   // LJ Pairs
   uc.nLJparamsUpdated_ = UpdateParameters< ParmHolder<NonbondType> >(set0.NB(), set1.NB(), "LJ A-B");
+  // LJ 1-4 Pairs
+  uc.nLJ14paramsUpdated_ = UpdateParameters< ParmHolder<NonbondType> >(set0.NB14(), set1.NB14(), "LJ A-B 1-4");
 
   if (debugIn > 0) set0.Debug("newp.dat");
   return 0;
diff --git a/src/ParameterSet.h b/src/ParameterSet.h
index e5b1844220..eb5b787ebd 100644
--- a/src/ParameterSet.h
+++ b/src/ParameterSet.h
@@ -10,24 +10,24 @@ class ParameterSet {
 
     ParmHolder<AtomType>& AT()         { return atomTypes_; }
     ParmHolder<NonbondType>& NB()      { return nbParm_;    }
-    ParmHolder<BondParmType>& BP()     { return bondParm_; }
+    ParmHolder<NonbondType>& NB14()    { return nb14Parm_;  }
+    ParmHolder<BondParmType>& BP()     { return bondParm_;  }
     ParmHolder<AngleParmType>& AP()    { return angleParm_; }
-    ParmHolder<BondParmType>& UB()     { return ubParm_; }
-    //ParmHolder<DihedralParmType>& DP() { return dihParm_; }
-    ParmHolder<DihedralParmType>& IP() { return impParm_; }
-    DihedralParmHolder& DP()           { return dihParm_; }
+    ParmHolder<BondParmType>& UB()     { return ubParm_;    }
+    ParmHolder<DihedralParmType>& IP() { return impParm_;   }
+    DihedralParmHolder& DP()           { return dihParm_;   }
 
     void SetHasLJparams(bool b) { hasLJparams_ = b; }
     bool HasLJparams() const { return hasLJparams_; }
 
     ParmHolder<AtomType> const& AT()         const { return atomTypes_; }
     ParmHolder<NonbondType> const& NB()      const { return nbParm_;    }
-    ParmHolder<BondParmType> const& BP()     const { return bondParm_; }
+    ParmHolder<NonbondType> const& NB14()    const { return nb14Parm_;  }
+    ParmHolder<BondParmType> const& BP()     const { return bondParm_;  }
     ParmHolder<AngleParmType> const& AP()    const { return angleParm_; }
-    ParmHolder<BondParmType> const& UB()     const { return ubParm_; }
-    //ParmHolder<DihedralParmType> const& DP() const { return dihParm_; }
-    ParmHolder<DihedralParmType> const& IP() const { return impParm_; }
-    DihedralParmHolder const& DP()           const { return dihParm_; }
+    ParmHolder<BondParmType> const& UB()     const { return ubParm_;    }
+    ParmHolder<DihedralParmType> const& IP() const { return impParm_;   }
+    DihedralParmHolder const& DP()           const { return dihParm_;   }
 
     void Debug(const char*) const;
     void Debug() const { return Debug(""); }
@@ -38,7 +38,7 @@ class ParameterSet {
         UpdateCount() : nBondsUpdated_(0), nAnglesUpdated_(0),
                         nDihedralsUpdated_(0), nImpropersUpdated_(0),
                         nUreyBradleyUpdated_(0), nAtomTypeUpdated_(0),
-                        nLJparamsUpdated_(0) {}
+                        nLJparamsUpdated_(0), nLJ14paramsUpdated_(0) {}
         unsigned int nBondsUpdated_;
         unsigned int nAnglesUpdated_;
         unsigned int nDihedralsUpdated_;
@@ -46,21 +46,21 @@ class ParameterSet {
         unsigned int nUreyBradleyUpdated_;
         unsigned int nAtomTypeUpdated_;
         unsigned int nLJparamsUpdated_;
+        unsigned int nLJ14paramsUpdated_;
     };
     /// Update this set with parameters from given set
     int UpdateParamSet(ParameterSet const&, UpdateCount&, int);
     /// \return Size in memory in bytes
     size_t DataSize() const;
   private:
-    //AtomTypeArray atomTypes_;
-    ParmHolder<AtomType> atomTypes_;
-    ParmHolder<NonbondType> nbParm_;
-    ParmHolder<BondParmType> bondParm_;
-    ParmHolder<AngleParmType> angleParm_;
-    ParmHolder<BondParmType> ubParm_;
-    //ParmHolder<DihedralParmType> dihParm_;
-    ParmHolder<DihedralParmType> impParm_;
-    DihedralParmHolder dihParm_;
+    ParmHolder<AtomType> atomTypes_;       ///< Atom types
+    ParmHolder<NonbondType> nbParm_;       ///< Lennard-Jones 6-12 A-B parameters
+    ParmHolder<NonbondType> nb14Parm_;     ///< LJ 6-12 A-B parameters for 1-4 interactions
+    ParmHolder<BondParmType> bondParm_;    ///< Hooke's law bond potential parameters
+    ParmHolder<AngleParmType> angleParm_;  ///< Hooke's law angle potential parameters
+    ParmHolder<BondParmType> ubParm_;      ///< Urey-Bradley parameters
+    ParmHolder<DihedralParmType> impParm_; ///< Improper dihedral parameters
+    DihedralParmHolder dihParm_;           ///< Cosine-series dihedral parameters
     bool hasLJparams_;
 };
 #endif

From 4c7f7d8d73d3f1826f554f8d94b5981a196f76d8 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 9 Nov 2023 09:38:04 -0500
Subject: [PATCH 0026/1492] Add nodlparams keyword

---
 test/Test_PrepareForLeap/RunTest.sh | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/test/Test_PrepareForLeap/RunTest.sh b/test/Test_PrepareForLeap/RunTest.sh
index deea079740..a2855ece19 100755
--- a/test/Test_PrepareForLeap/RunTest.sh
+++ b/test/Test_PrepareForLeap/RunTest.sh
@@ -20,7 +20,7 @@ cat > cpptraj.in <<EOF
 parm 1qos.pdb
 loadcrd 1qos.pdb name MyCrd
 
-prepareforleap \
+prepareforleap nodlparams \
   crdset MyCrd \
   name Final \
   out leap.1qos.in \
@@ -35,7 +35,7 @@ DoTest 1qos.cpptraj.pdb.save 1qos.cpptraj.pdb
 cat > cpptraj.in <<EOF
 parm 1qos.cpptraj.pdb.save
 loadcrd 1qos.cpptraj.pdb.save name MyCrd
-prepareforleap \
+prepareforleap nodlparams \
   hasglycam \
   crdset MyCrd \
   name Final \
@@ -52,7 +52,7 @@ cat > cpptraj.in <<EOF
 parm 4zzw.pdb
 loadcrd 4zzw.pdb name MyCrd
 
-prepareforleap \
+prepareforleap nodlparams \
   crdset MyCrd \
   name Final \
   out leap.4zzw.in \

From bee61f6df01a13e854632e4ab07a830516106c8a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 9 Nov 2023 09:38:42 -0500
Subject: [PATCH 0027/1492] Bonds are now order by atom #

---
 test/Test_PrepareForLeap/leap.4zzw.in.save | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/Test_PrepareForLeap/leap.4zzw.in.save b/test/Test_PrepareForLeap/leap.4zzw.in.save
index 08d4bc42f4..f6fabc9c1a 100644
--- a/test/Test_PrepareForLeap/leap.4zzw.in.save
+++ b/test/Test_PrepareForLeap/leap.4zzw.in.save
@@ -8,9 +8,9 @@ bond m.176.SG m.206.SG
 bond m.235.SG m.240.SG
 bond m.258.SG m.331.SG
 bond m.436.C1 m.203.ND2
+bond m.436.O4 m.437.C1
 bond m.438.C1 m.439.O1
+bond m.438.O4 m.440.C1
 bond m.441.C1 m.57.ND2
 bond m.442.C1 m.429.ND2
 bond m.443.C1 m.196.OG
-bond m.436.O4 m.437.C1
-bond m.438.O4 m.440.C1

From 0e75c306588e4fcc15f875d74e84037531d15398 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 9 Nov 2023 09:44:30 -0500
Subject: [PATCH 0028/1492] Start download params test

---
 test/Test_PrepareForLeap/RunTest.sh | 25 ++++++++++++++++++++++++-
 1 file changed, 24 insertions(+), 1 deletion(-)

diff --git a/test/Test_PrepareForLeap/RunTest.sh b/test/Test_PrepareForLeap/RunTest.sh
index a2855ece19..a1f3660312 100755
--- a/test/Test_PrepareForLeap/RunTest.sh
+++ b/test/Test_PrepareForLeap/RunTest.sh
@@ -4,7 +4,9 @@
 
 CleanFiles cpptraj.in 1qos.cpptraj.pdb leap.1qos.in \
            leap.4zzw.in 4zzw.cpptraj.pdb 1qos.cpptraj.pdb.2 \
-           leap.1qos.in.2 *.mol2 *.frcmod 
+           leap.1qos.in.2 PEG.mol2 PEG.frcmod GOL.mol2 GOL.frcmod \
+           PCA.mol2 PCA.frcmod MG.mol2 MG.frcmod \
+           dlparams.leap.4zzw.in dlparams.4zzw.cpptraj.pdb 
 
 INPUT='-i cpptraj.in'
 
@@ -64,4 +66,25 @@ RunCpptraj "Prepare PDB 4zzw for LEaP"
 DoTest leap.4zzw.in.save leap.4zzw.in
 DoTest 4zzw.cpptraj.pdb.save 4zzw.cpptraj.pdb
 
+# Test remote connectivity.
+PINGCMD=`which ping`
+if [ ! -z "$PINGCMD" ] ; then
+  $PINGCMD -c 1 raw.githubusercontent.com
+  if [ $? -eq 0 ] ; then
+    cat > cpptraj.in <<EOF
+parm 4zzw.pdb
+loadcrd 4zzw.pdb name MyCrd
+
+prepareforleap dlparams \
+  crdset MyCrd \
+  name Final \
+  out dlparams.leap.4zzw.in \
+  leapunitname m \
+  pdbout dlparams.4zzw.cpptraj.pdb \
+  nowat noh keepaltloc highestocc
+EOF
+    RunCpptraj "Prepare PDB 4zzw for LEaP, download missing parameters"
+  fi
+fi
+
 EndTest

From 09f6771d0bd72aaefa8abfbd1da13c02e9f8ede9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 9 Nov 2023 09:48:48 -0500
Subject: [PATCH 0029/1492] Ensure test will be skipped if no connectivity

---
 test/Test_PrepareForLeap/RunTest.sh | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/test/Test_PrepareForLeap/RunTest.sh b/test/Test_PrepareForLeap/RunTest.sh
index a1f3660312..ebd616fd53 100755
--- a/test/Test_PrepareForLeap/RunTest.sh
+++ b/test/Test_PrepareForLeap/RunTest.sh
@@ -67,10 +67,14 @@ DoTest leap.4zzw.in.save leap.4zzw.in
 DoTest 4zzw.cpptraj.pdb.save 4zzw.cpptraj.pdb
 
 # Test remote connectivity.
+UNITNAME="Prepare PDB 4zzw for LEaP, download missing parameters"
 PINGCMD=`which ping`
 if [ ! -z "$PINGCMD" ] ; then
   $PINGCMD -c 1 raw.githubusercontent.com
-  if [ $? -eq 0 ] ; then
+  if [ $? -ne 0 ] ; then
+    echo "Warning: Could not ping raw.githubusercontent.com, no internet connectivity."
+    SkipCheck "$UNITNAME"
+  else
     cat > cpptraj.in <<EOF
 parm 4zzw.pdb
 loadcrd 4zzw.pdb name MyCrd
@@ -83,8 +87,11 @@ prepareforleap dlparams \
   pdbout dlparams.4zzw.cpptraj.pdb \
   nowat noh keepaltloc highestocc
 EOF
-    RunCpptraj "Prepare PDB 4zzw for LEaP, download missing parameters"
+    RunCpptraj "$UNITNAME"
   fi
+else
+  echo "Warning: No 'ping' found, cannot check for internet connectivity."
+  SkipCheck "$UNITNAME"
 fi
 
 EndTest

From 82325b2997792b865445cfef32dcf683aecfeeb8 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 9 Nov 2023 09:50:39 -0500
Subject: [PATCH 0030/1492] Add test save

---
 test/Test_PrepareForLeap/RunTest.sh           |  1 +
 .../dlparams.leap.4zzw.in.save                | 23 +++++++++++++++++++
 2 files changed, 24 insertions(+)
 create mode 100644 test/Test_PrepareForLeap/dlparams.leap.4zzw.in.save

diff --git a/test/Test_PrepareForLeap/RunTest.sh b/test/Test_PrepareForLeap/RunTest.sh
index ebd616fd53..ca73c1fada 100755
--- a/test/Test_PrepareForLeap/RunTest.sh
+++ b/test/Test_PrepareForLeap/RunTest.sh
@@ -88,6 +88,7 @@ prepareforleap dlparams \
   nowat noh keepaltloc highestocc
 EOF
     RunCpptraj "$UNITNAME"
+    DoTest dlparams.leap.4zzw.in.save dlparams.leap.4zzw.in
   fi
 else
   echo "Warning: No 'ping' found, cannot check for internet connectivity."
diff --git a/test/Test_PrepareForLeap/dlparams.leap.4zzw.in.save b/test/Test_PrepareForLeap/dlparams.leap.4zzw.in.save
new file mode 100644
index 0000000000..52bca364c1
--- /dev/null
+++ b/test/Test_PrepareForLeap/dlparams.leap.4zzw.in.save
@@ -0,0 +1,23 @@
+GOL = loadmol2 GOL.mol2
+parmGOL = loadamberparams GOL.frcmod
+PCA = loadmol2 PCA.mol2
+parmPCA = loadamberparams PCA.frcmod
+PEG = loadmol2 PEG.mol2
+parmPEG = loadamberparams PEG.frcmod
+m = loadpdb dlparams.4zzw.cpptraj.pdb
+bond m.1.C m.2.N
+bond m.19.SG m.25.SG
+bond m.50.SG m.71.SG
+bond m.61.SG m.67.SG
+bond m.138.SG m.399.SG
+bond m.172.SG m.207.SG
+bond m.176.SG m.206.SG
+bond m.235.SG m.240.SG
+bond m.258.SG m.331.SG
+bond m.436.C1 m.203.ND2
+bond m.436.O4 m.437.C1
+bond m.438.C1 m.439.O1
+bond m.438.O4 m.440.C1
+bond m.441.C1 m.57.ND2
+bond m.442.C1 m.429.ND2
+bond m.443.C1 m.196.OG

From 2198d64d7e9ea79737369b1f93a5c54053fd2c0a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 9 Nov 2023 20:55:35 -0500
Subject: [PATCH 0031/1492] Start Amber force field param file class

---
 src/DataIO_AmberFF.cpp | 67 ++++++++++++++++++++++++++++++++++++++++++
 src/DataIO_AmberFF.h   | 17 +++++++++++
 2 files changed, 84 insertions(+)
 create mode 100644 src/DataIO_AmberFF.cpp
 create mode 100644 src/DataIO_AmberFF.h

diff --git a/src/DataIO_AmberFF.cpp b/src/DataIO_AmberFF.cpp
new file mode 100644
index 0000000000..a872b0ec01
--- /dev/null
+++ b/src/DataIO_AmberFF.cpp
@@ -0,0 +1,67 @@
+#include "DataIO_AmberFF.h"
+#include "CpptrajStdio.h"
+#include "BufferedLine.h"
+
+/// CONSTRUCTOR
+DataIO_AmberFF::DataIO_AmberFF()
+{
+
+}
+
+// DataIO_AmberFF::ID_DataFormat()
+bool DataIO_AmberFF::ID_DataFormat(CpptrajFile& infile)
+{
+  //if (infile.OpenFile()) return false;
+  //std::string line = infile.GetLine(); // Title
+  //infile.CloseFile();
+  //bool isLib = (line == "!!index array str");
+  return false;
+}
+
+// DataIO_AmberFF::ReadHelp()
+void DataIO_AmberFF::ReadHelp()
+{
+
+}
+
+// DataIO_AmberFF::processReadArgs()
+int DataIO_AmberFF::processReadArgs(ArgList& argIn)
+{
+
+  return 0;
+}
+
+// DataIO_AmberFF::ReadData()
+int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::string const& dsname)
+{
+  BufferedLine infile;
+  if (infile.OpenFileRead( fname )) {
+    mprinterr("Error: Could not open file '%s' as Amber FF.\n", fname.full());
+    return 1;
+  }
+  std::string title = infile.GetLine();
+  mprintf("\tTitle: %s\n", title.c_str());
+
+  infile.CloseFile();
+  return 0;
+}
+
+// DataIO_AmberFF::WriteHelp()
+void DataIO_AmberFF::WriteHelp()
+{
+
+}
+
+// DataIO_AmberFF::processWriteArgs()
+int DataIO_AmberFF::processWriteArgs(ArgList& argIn)
+{
+
+  return 0;
+}
+
+// DataIO_AmberFF::WriteData()
+int DataIO_AmberFF::WriteData(FileName const& fname, DataSetList const& dsl)
+{
+
+  return 1;
+}
diff --git a/src/DataIO_AmberFF.h b/src/DataIO_AmberFF.h
new file mode 100644
index 0000000000..323d198403
--- /dev/null
+++ b/src/DataIO_AmberFF.h
@@ -0,0 +1,17 @@
+#ifndef INC_DATAIO_AMBERFF_H
+#define INC_DATAIO_AMBERFF_H
+#include "DataIO.h"
+/// <Enter description of DataIO_AmberFF here>
+class DataIO_AmberFF : public DataIO {
+  public:
+    DataIO_AmberFF();
+    static void ReadHelp();
+    static void WriteHelp();
+    static BaseIOtype* Alloc() { return (BaseIOtype*)new DataIO_AmberFF(); }
+    int processReadArgs(ArgList&);
+    int ReadData(FileName const&, DataSetList&, std::string const&);
+    int processWriteArgs(ArgList&);
+    int WriteData(FileName const&, DataSetList const&);
+    bool ID_DataFormat(CpptrajFile&);
+};
+#endif

From f347d6710dbbf88ab1eebd39aa2a122587361846 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 9 Nov 2023 20:59:39 -0500
Subject: [PATCH 0032/1492] Enable amber ff format for testing

---
 src/DataFile.cpp  | 3 +++
 src/DataFile.h    | 2 +-
 src/cpptrajdepend | 3 ++-
 src/cpptrajfiles  | 1 +
 4 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/src/DataFile.cpp b/src/DataFile.cpp
index b215286b34..c393ddb4e3 100644
--- a/src/DataFile.cpp
+++ b/src/DataFile.cpp
@@ -34,6 +34,7 @@
 #include "DataIO_Numpy.h"
 #include "DataIO_AmberPrep.h"
 #include "DataIO_AmberLib.h"
+#include "DataIO_AmberFF.h"
 
 // CONSTRUCTOR
 DataFile::DataFile() :
@@ -89,6 +90,7 @@ const FileTypes::AllocToken DataFile::DF_AllocArray[] = {
   { "Numpy array",        0,                             0,            DataIO_Numpy::Alloc},
   { "Amber Prep File",    DataIO_AmberPrep::ReadHelp,    0,            DataIO_AmberPrep::Alloc},
   { "Amber OFF File",     0,                             0,            DataIO_AmberLib::Alloc},
+  { "Amber Force Field",  0,                             0,            DataIO_AmberFF::Alloc},
   { "Unknown Data file",  0,                       0,                        0                    }
 };
 
@@ -118,6 +120,7 @@ const FileTypes::KeyToken DataFile::DF_KeyArray[] = {
   { AMBERPREP,    "prepin",       ".prepin" },
   { AMBERLIB,     "off",          ".off" },
   { AMBERLIB,     "off",          ".lib" },
+  { AMBERFF,      "amberff",      ".parm" },
   { UNKNOWN_DATA, 0,        0        }
 };
 
diff --git a/src/DataFile.h b/src/DataFile.h
index f5f6b0b92a..6cce13ed11 100644
--- a/src/DataFile.h
+++ b/src/DataFile.h
@@ -18,7 +18,7 @@ class DataFile {
       DATAFILE=0, XMGRACE, GNUPLOT, XPLOR, OPENDX, REMLOG, MDOUT, EVECS,
       VECTRAJ, XVG, CCP4, CHARMMREPD, CHARMMFASTREP,
       CHARMMOUT, CPOUT, CHARMMRTFPRM, CMATRIX_BINARY, CMATRIX_NETCDF, PEAKS,
-      NETCDFDATA, AMBERENE, NUMPY, AMBERPREP, AMBERLIB,
+      NETCDFDATA, AMBERENE, NUMPY, AMBERPREP, AMBERLIB, AMBERFF,
       UNKNOWN_DATA 
     };
     DataFile();
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index d2c7d7b566..af6ad3ff40 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -199,11 +199,12 @@ CpptrajFile.o : CpptrajFile.cpp CpptrajFile.h CpptrajStdio.h FileIO.h FileIO_Bzi
 CpptrajState.o : CpptrajState.cpp Action.h ActionList.h ActionState.h Action_CreateCrd.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_Topology.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleNavigator.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 CpptrajStdio.o : CpptrajStdio.cpp Parallel.h
 CurveFit.o : CurveFit.cpp CurveFit.h
-DataFile.o : DataFile.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Cluster/Cframes.h Cluster/Cmatrix_NC.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataFile.h DataIO.h DataIO_AmberEne.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_CCP4.h DataIO_CharmmFastRep.h DataIO_CharmmOutput.h DataIO_CharmmRepLog.h DataIO_CharmmRtfPrm.h DataIO_Cmatrix_Binary.h DataIO_Cmatrix_NC.h DataIO_Cpout.h DataIO_Evecs.h DataIO_Gnuplot.h DataIO_Grace.h DataIO_Mdout.h DataIO_NetCDF.h DataIO_Numpy.h DataIO_OpenDx.h DataIO_Peaks.h DataIO_RemLog.h DataIO_Std.h DataIO_VecTraj.h DataIO_XVG.h DataIO_Xplor.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TypeNameHolder.h Unit.h Vec3.h
+DataFile.o : DataFile.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Cluster/Cframes.h Cluster/Cmatrix_NC.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataFile.h DataIO.h DataIO_AmberEne.h DataIO_AmberFF.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_CCP4.h DataIO_CharmmFastRep.h DataIO_CharmmOutput.h DataIO_CharmmRepLog.h DataIO_CharmmRtfPrm.h DataIO_Cmatrix_Binary.h DataIO_Cmatrix_NC.h DataIO_Cpout.h DataIO_Evecs.h DataIO_Gnuplot.h DataIO_Grace.h DataIO_Mdout.h DataIO_NetCDF.h DataIO_Numpy.h DataIO_OpenDx.h DataIO_Peaks.h DataIO_RemLog.h DataIO_Std.h DataIO_VecTraj.h DataIO_XVG.h DataIO_Xplor.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TypeNameHolder.h Unit.h Vec3.h
 DataFileList.o : DataFileList.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataFilter.o : DataFilter.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_integer.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO.o : DataIO.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_AmberEne.o : DataIO_AmberEne.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberEne.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_AmberFF.o : DataIO_AmberFF.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberFF.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_AmberLib.o : DataIO_AmberLib.cpp ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberLib.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_AmberPrep.o : DataIO_AmberPrep.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberPrep.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_CCP4.o : DataIO_CCP4.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ByteRoutines.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CCP4.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
diff --git a/src/cpptrajfiles b/src/cpptrajfiles
index a8d821136f..dd53d39862 100644
--- a/src/cpptrajfiles
+++ b/src/cpptrajfiles
@@ -175,6 +175,7 @@ COMMON_SOURCES= \
         DataFilter.cpp \
         DataIO.cpp \
         DataIO_AmberEne.cpp \
+        DataIO_AmberFF.cpp \
         DataIO_AmberLib.cpp \
         DataIO_AmberPrep.cpp \
         DataIO_CCP4.cpp \

From 22c764056b99d836e13061ce8c05a1b5ffd3e198 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 9 Nov 2023 21:01:02 -0500
Subject: [PATCH 0033/1492] Allocate data set

---
 src/DataIO_AmberFF.cpp | 16 ++++++++++++++++
 src/cpptrajdepend      |  2 +-
 2 files changed, 17 insertions(+), 1 deletion(-)

diff --git a/src/DataIO_AmberFF.cpp b/src/DataIO_AmberFF.cpp
index a872b0ec01..94443e63ae 100644
--- a/src/DataIO_AmberFF.cpp
+++ b/src/DataIO_AmberFF.cpp
@@ -1,6 +1,7 @@
 #include "DataIO_AmberFF.h"
 #include "CpptrajStdio.h"
 #include "BufferedLine.h"
+#include "DataSet_Parameters.h"
 
 /// CONSTRUCTOR
 DataIO_AmberFF::DataIO_AmberFF()
@@ -34,6 +35,21 @@ int DataIO_AmberFF::processReadArgs(ArgList& argIn)
 // DataIO_AmberFF::ReadData()
 int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::string const& dsname)
 {
+  // Allocate data set
+  MetaData md( dsname );
+  DataSet* ds = dsl.CheckForSet( md );
+  if (ds != 0) {
+    if (ds->Type() != DataSet::PARAMETERS) {
+      mprinterr("Error: Set '%s' does not have parameters, cannot append.\n", ds->legend());
+      return 1;
+    }
+    mprintf("\tAdding to existing set %s\n", ds->legend());
+  } else {
+    ds = dsl.AddSet( DataSet::PARAMETERS, md );
+    if (ds == 0) return 1;
+  }
+  DataSet_Parameters& prm = static_cast<DataSet_Parameters&>( *ds ); 
+
   BufferedLine infile;
   if (infile.OpenFileRead( fname )) {
     mprinterr("Error: Could not open file '%s' as Amber FF.\n", fname.full());
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index af6ad3ff40..46acb9fc99 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -204,7 +204,7 @@ DataFileList.o : DataFileList.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h A
 DataFilter.o : DataFilter.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_integer.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO.o : DataIO.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_AmberEne.o : DataIO_AmberEne.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberEne.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_AmberFF.o : DataIO_AmberFF.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberFF.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_AmberFF.o : DataIO_AmberFF.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberFF.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_AmberLib.o : DataIO_AmberLib.cpp ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberLib.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_AmberPrep.o : DataIO_AmberPrep.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberPrep.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_CCP4.o : DataIO_CCP4.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ByteRoutines.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CCP4.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h

From 982057996c1b1081257ec700611c465d02732d69 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 9 Nov 2023 21:09:43 -0500
Subject: [PATCH 0034/1492] Start reading sections

---
 src/DataIO_AmberFF.cpp | 24 +++++++++++++++++++++++-
 1 file changed, 23 insertions(+), 1 deletion(-)

diff --git a/src/DataIO_AmberFF.cpp b/src/DataIO_AmberFF.cpp
index 94443e63ae..7f96441f3f 100644
--- a/src/DataIO_AmberFF.cpp
+++ b/src/DataIO_AmberFF.cpp
@@ -50,13 +50,35 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
   }
   DataSet_Parameters& prm = static_cast<DataSet_Parameters&>( *ds ); 
 
+  // Read title
   BufferedLine infile;
   if (infile.OpenFileRead( fname )) {
     mprinterr("Error: Could not open file '%s' as Amber FF.\n", fname.full());
     return 1;
   }
-  std::string title = infile.GetLine();
+  const char* ptr = infile.Line();
+  if (ptr == 0) {
+    mprinterr("Error: Could not read anything from Amber FF file %s\n", fname.full());
+    return 1;
+  }
+  std::string title(ptr);
   mprintf("\tTitle: %s\n", title.c_str());
+  // Read file
+  enum SectionType { ATYPE = 0, UNKNOWN };
+  SectionType section = ATYPE;
+  while (ptr != 0) {
+    if (*ptr == '\0') {
+      // Section Change
+      if (section != UNKNOWN) {
+        section = (SectionType)((int)section + 1);
+      }
+    } else if (section == ATYPE) {
+      // Input for atom symbols and masses
+      // Format (A2,2X,F10.2x,f10.2)
+      mprintf("DEBUG: Atype: %s\n", ptr);
+    }
+    ptr = infile.Line();
+  }
 
   infile.CloseFile();
   return 0;

From 3d9d05f0c96f5920d6d92d20aea8c69fa2c875c3 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 10 Nov 2023 15:14:14 -0500
Subject: [PATCH 0035/1492] Add atomic polarizability

---
 src/AtomType.h | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/src/AtomType.h b/src/AtomType.h
index b74de65677..75cec029e3 100644
--- a/src/AtomType.h
+++ b/src/AtomType.h
@@ -4,11 +4,14 @@
 /// Hold parameters for a unique atom type
 class AtomType {
   public:
-    AtomType() : mass_(0.0), oidx_(-1) {}
-    AtomType(double r, double d, int o) : lj_(r, d), mass_(0.0), oidx_(o) {} // TODO deprecate
-    /// Mass only
+    /// CONSTRUCTOR
+    AtomType() : mass_(0.0), polarizability_(0.0), oidx_(-1) {}
+    AtomType(double r, double d, int o) : lj_(r, d), mass_(0.0), polarizability_(0.0), oidx_(o) {} // TODO deprecate
+    /// CONSTRUCTOR - Mass, polarizability
+    AtomType(double m, double p) : mass_(0.0), polarizability_(p), oidx_(-1) {}
+    /// CONSTRUCTOR - Mass only
     AtomType(double m) : mass_(m), oidx_(-1) {}
-    /// Radius, well depth, mass
+    /// CONSTRUCTOR - Radius, well depth, mass
     AtomType(double r, double d, double m) : lj_(r, d), mass_(m), oidx_(-1) {}
     /// \return default LJ parameters
     LJparmType const& LJ() const { return lj_; }
@@ -27,6 +30,7 @@ class AtomType {
   private:
     LJparmType lj_; ///< Default Lennard-Jones parameters (always valid for self).
     double mass_;   ///< Mass in amu
+    double polarizability_; ///< Atomic polarizability in Ang^3
     int oidx_; ///< Original atom type index. TODO deprecate
 };
 #endif

From 564a65e7517293cf34a59bef12af411db416397d Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 10 Nov 2023 15:34:32 -0500
Subject: [PATCH 0036/1492] Read in atom types

---
 src/DataIO_AmberFF.cpp | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/src/DataIO_AmberFF.cpp b/src/DataIO_AmberFF.cpp
index 7f96441f3f..8a41cb301a 100644
--- a/src/DataIO_AmberFF.cpp
+++ b/src/DataIO_AmberFF.cpp
@@ -2,6 +2,7 @@
 #include "CpptrajStdio.h"
 #include "BufferedLine.h"
 #include "DataSet_Parameters.h"
+#include <cstdio> // sscanf
 
 /// CONSTRUCTOR
 DataIO_AmberFF::DataIO_AmberFF()
@@ -66,6 +67,7 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
   // Read file
   enum SectionType { ATYPE = 0, UNKNOWN };
   SectionType section = ATYPE;
+  ptr = infile.Line();
   while (ptr != 0) {
     if (*ptr == '\0') {
       // Section Change
@@ -76,6 +78,26 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
       // Input for atom symbols and masses
       // Format (A2,2X,F10.2x,f10.2)
       mprintf("DEBUG: Atype: %s\n", ptr);
+      char kndsym[16];
+      double amass;
+      double atpol;
+      int nscan = sscanf(ptr, "%s %lf %lf", kndsym, &amass, &atpol);
+      ParameterHolders::RetType ret;
+      if (nscan == 3) {
+        ret = prm.AT().AddParm( TypeNameHolder(kndsym),
+                                AtomType(amass, atpol),
+                                true );
+      } else if (nscan == 2) {
+        // Only mass
+        ret = prm.AT().AddParm( TypeNameHolder(kndsym),
+                                AtomType(amass),
+                                true );
+      } else {
+        mprinterr("Error: Expected atom type, mass, polarizability, got only %i\n", nscan);
+        return 1;
+      }
+      if (ret == ParameterHolders::UPDATED)
+        mprintf("Warning: Redefining atom type %s\n", kndsym);
     }
     ptr = infile.Line();
   }

From 30a3483842f816f12f6046a36ca7b3dbfb55251e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 10 Nov 2023 16:23:39 -0500
Subject: [PATCH 0037/1492] Report atomic polarizability

---
 src/AtomType.h         | 4 +++-
 src/DataIO_AmberFF.cpp | 1 +
 src/ParameterSet.cpp   | 4 ++--
 3 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/src/AtomType.h b/src/AtomType.h
index 75cec029e3..13ba56aaa4 100644
--- a/src/AtomType.h
+++ b/src/AtomType.h
@@ -8,7 +8,7 @@ class AtomType {
     AtomType() : mass_(0.0), polarizability_(0.0), oidx_(-1) {}
     AtomType(double r, double d, int o) : lj_(r, d), mass_(0.0), polarizability_(0.0), oidx_(o) {} // TODO deprecate
     /// CONSTRUCTOR - Mass, polarizability
-    AtomType(double m, double p) : mass_(0.0), polarizability_(p), oidx_(-1) {}
+    AtomType(double m, double p) : mass_(m), polarizability_(p), oidx_(-1) {}
     /// CONSTRUCTOR - Mass only
     AtomType(double m) : mass_(m), oidx_(-1) {}
     /// CONSTRUCTOR - Radius, well depth, mass
@@ -17,6 +17,8 @@ class AtomType {
     LJparmType const& LJ() const { return lj_; }
     /// \return Atom mass in amu
     double Mass()          const { return mass_;   }
+    /// \return Atomic polarizability in Ang^3
+    double Polarizability() const { return polarizability_; }
     /// \return Original atom type index. Useful when checking for off-diagonal NB parameters.
     int OriginalIdx()      const { return oidx_; }
     /// \return true if LJ params are less than incoming
diff --git a/src/DataIO_AmberFF.cpp b/src/DataIO_AmberFF.cpp
index 8a41cb301a..1959ae79d1 100644
--- a/src/DataIO_AmberFF.cpp
+++ b/src/DataIO_AmberFF.cpp
@@ -102,6 +102,7 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
     ptr = infile.Line();
   }
 
+  prm.Debug(); // TODO debug level
   infile.CloseFile();
   return 0;
 }
diff --git a/src/ParameterSet.cpp b/src/ParameterSet.cpp
index ccfc35bde6..854a6c914e 100644
--- a/src/ParameterSet.cpp
+++ b/src/ParameterSet.cpp
@@ -17,9 +17,9 @@ void ParameterSet::Debug(const char* fnameIn) const {
   CpptrajFile Out;
   Out.OpenWrite( fnameIn );
   Out.Printf("Atom Types:\n");
-  Out.Printf("\t%6s %8s %12s %12s %12s\n", "Name", "TypeIdx", "Radius", "Depth", "Mass");
+  Out.Printf("\t%6s %8s %12s %12s %12s %12s\n", "Name", "TypeIdx", "Radius", "Depth", "Mass", "Polar.");
   for (ParmHolder<AtomType>::const_iterator at = atomTypes_.begin(); at != atomTypes_.end(); ++at) {
-    Out.Printf("\t%6s %8li %12.4f %12.4f %12.4f\n", *(at->first[0]), at - atomTypes_.begin(), at->second.LJ().Radius(), at->second.LJ().Depth(), at->second.Mass());
+    Out.Printf("\t%6s %8li %12.4f %12.4f %12.4f %12.4f\n", *(at->first[0]), at - atomTypes_.begin(), at->second.LJ().Radius(), at->second.LJ().Depth(), at->second.Mass(), at->second.Polarizability());
   }
   if (!nbParm_.empty()) {
     Out.Printf("LJ parameters:\n");

From c2cea85ab69e0ce1198c4ebc98afaa587dbf97f3 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 10 Nov 2023 16:33:18 -0500
Subject: [PATCH 0038/1492] Start reading hydrophilic atom types

---
 src/DataIO_AmberFF.cpp | 19 ++++++++++++++++++-
 1 file changed, 18 insertions(+), 1 deletion(-)

diff --git a/src/DataIO_AmberFF.cpp b/src/DataIO_AmberFF.cpp
index 1959ae79d1..09139a5d74 100644
--- a/src/DataIO_AmberFF.cpp
+++ b/src/DataIO_AmberFF.cpp
@@ -65,7 +65,7 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
   std::string title(ptr);
   mprintf("\tTitle: %s\n", title.c_str());
   // Read file
-  enum SectionType { ATYPE = 0, UNKNOWN };
+  enum SectionType { ATYPE = 0, HYDROPHILIC, UNKNOWN };
   SectionType section = ATYPE;
   ptr = infile.Line();
   while (ptr != 0) {
@@ -74,6 +74,23 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
       if (section != UNKNOWN) {
         section = (SectionType)((int)section + 1);
       }
+      // Special case; hydrophilic atom types. One line.
+      // FORMAT(20(A2,2X))
+      if (section == HYDROPHILIC) {
+        ptr = infile.Line();
+        mprintf("DEBUG: Hydrophilic: %s\n", ptr);
+        char htype[5];
+        htype[4] = '\0';
+        std::string hline(ptr);
+        for (unsigned int idx = 0; idx < hline.size(); idx+=4) {
+          htype[0] = hline[idx  ];
+          htype[1] = hline[idx+1];
+          htype[2] = hline[idx+2];
+          htype[3] = hline[idx+3];
+          mprintf("DEBUG:\t%s\n", htype);
+        }
+        section = (SectionType)((int)section + 1);
+      }
     } else if (section == ATYPE) {
       // Input for atom symbols and masses
       // Format (A2,2X,F10.2x,f10.2)

From debec8292bc199c43c1eb79880c500227971f50e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 10 Nov 2023 16:50:42 -0500
Subject: [PATCH 0039/1492] Add read and saving of hydrophilic atom types.

---
 src/DataIO_AmberFF.cpp |  3 ++-
 src/ParameterSet.cpp   | 20 ++++++++++++++++++++
 src/ParameterSet.h     |  5 +++++
 3 files changed, 27 insertions(+), 1 deletion(-)

diff --git a/src/DataIO_AmberFF.cpp b/src/DataIO_AmberFF.cpp
index 09139a5d74..ab3db72e71 100644
--- a/src/DataIO_AmberFF.cpp
+++ b/src/DataIO_AmberFF.cpp
@@ -87,7 +87,8 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
           htype[1] = hline[idx+1];
           htype[2] = hline[idx+2];
           htype[3] = hline[idx+3];
-          mprintf("DEBUG:\t%s\n", htype);
+          //mprintf("DEBUG:\t%s\n", htype);
+          prm.AddHydrophilicAtomType( NameType(htype) );
         }
         section = (SectionType)((int)section + 1);
       }
diff --git a/src/ParameterSet.cpp b/src/ParameterSet.cpp
index 854a6c914e..635b9e2b4f 100644
--- a/src/ParameterSet.cpp
+++ b/src/ParameterSet.cpp
@@ -65,6 +65,12 @@ void ParameterSet::Debug(const char* fnameIn) const {
     for (ParmHolder<DihedralParmType>::const_iterator bp = impParm_.begin(); bp != impParm_.end(); ++bp)
       Out.Printf("\t%6s %6s %6s %6s : %12.4f %12.4f %12.4f\n", *(bp->first[0]), *(bp->first[1]), *(bp->first[2]), *(bp->first[3]), bp->second.Pk(), bp->second.Pn(), bp->second.Phase());
   }
+  if (!hydrophilicAtomTypes_.empty()) {
+    Out.Printf("Hydrophilic atom types:");
+    for (NsetType::const_iterator it = hydrophilicAtomTypes_.begin(); it != hydrophilicAtomTypes_.end(); ++it)
+      Out.Printf(" %s", it->Truncated().c_str());
+    Out.Printf("\n");
+  }
 }
 
 /** Update/add to parameters in this topology with those from given set. */
@@ -97,3 +103,17 @@ int ParameterSet::UpdateParamSet(ParameterSet const& set1, UpdateCount& uc, int
   if (debugIn > 0) set0.Debug("newp.dat");
   return 0;
 }
+
+/** Add hydrophilic atom type. */
+int ParameterSet::AddHydrophilicAtomType(NameType const& atype) {
+  for (NsetType::const_iterator it = hydrophilicAtomTypes_.begin(); it != hydrophilicAtomTypes_.end(); ++it)
+  {
+    if (atype == *it) {
+      mprintf("Warning: %s already defined as hydrophilic atom type.\n", atype.Truncated().c_str());
+      return 0;
+    }
+  }
+  // TODO check against existing types?
+  hydrophilicAtomTypes_.push_back( atype );
+  return 0;
+}
diff --git a/src/ParameterSet.h b/src/ParameterSet.h
index eb5b787ebd..fbfadc82ec 100644
--- a/src/ParameterSet.h
+++ b/src/ParameterSet.h
@@ -50,9 +50,13 @@ class ParameterSet {
     };
     /// Update this set with parameters from given set
     int UpdateParamSet(ParameterSet const&, UpdateCount&, int);
+    /// Add hydrophilic atom type
+    int AddHydrophilicAtomType(NameType const&);
     /// \return Size in memory in bytes
     size_t DataSize() const;
   private:
+    typedef std::vector<NameType> NsetType;
+
     ParmHolder<AtomType> atomTypes_;       ///< Atom types
     ParmHolder<NonbondType> nbParm_;       ///< Lennard-Jones 6-12 A-B parameters
     ParmHolder<NonbondType> nb14Parm_;     ///< LJ 6-12 A-B parameters for 1-4 interactions
@@ -61,6 +65,7 @@ class ParameterSet {
     ParmHolder<BondParmType> ubParm_;      ///< Urey-Bradley parameters
     ParmHolder<DihedralParmType> impParm_; ///< Improper dihedral parameters
     DihedralParmHolder dihParm_;           ///< Cosine-series dihedral parameters
+    NsetType hydrophilicAtomTypes_;        ///< Hold names of hydrophilic atom types
     bool hasLJparams_;
 };
 #endif

From 429048b3a0e3ab663510147b6d9239410d27e9dc Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 10 Nov 2023 19:40:57 -0500
Subject: [PATCH 0040/1492] Use whitespace delimiting; more future-proof

---
 src/DataIO_AmberFF.cpp | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/src/DataIO_AmberFF.cpp b/src/DataIO_AmberFF.cpp
index ab3db72e71..62dfcd9cd7 100644
--- a/src/DataIO_AmberFF.cpp
+++ b/src/DataIO_AmberFF.cpp
@@ -79,6 +79,11 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
       if (section == HYDROPHILIC) {
         ptr = infile.Line();
         mprintf("DEBUG: Hydrophilic: %s\n", ptr);
+        // Take advantage of the fact that we expect whitespace-delimiters
+        ArgList hsymbols( ptr, " " );
+        for (int iarg = 0; iarg != hsymbols.Nargs(); ++iarg)
+          prm.AddHydrophilicAtomType( NameType( hsymbols[iarg] ) );
+        /*
         char htype[5];
         htype[4] = '\0';
         std::string hline(ptr);
@@ -89,7 +94,7 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
           htype[3] = hline[idx+3];
           //mprintf("DEBUG:\t%s\n", htype);
           prm.AddHydrophilicAtomType( NameType(htype) );
-        }
+        }*/
         section = (SectionType)((int)section + 1);
       }
     } else if (section == ATYPE) {

From fdc7852c4207374bb3fffbf652194565a838c61b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 10 Nov 2023 20:18:46 -0500
Subject: [PATCH 0041/1492] Start bond section

---
 src/DataIO_AmberFF.cpp | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/DataIO_AmberFF.cpp b/src/DataIO_AmberFF.cpp
index 62dfcd9cd7..e4235ac83e 100644
--- a/src/DataIO_AmberFF.cpp
+++ b/src/DataIO_AmberFF.cpp
@@ -65,7 +65,7 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
   std::string title(ptr);
   mprintf("\tTitle: %s\n", title.c_str());
   // Read file
-  enum SectionType { ATYPE = 0, HYDROPHILIC, UNKNOWN };
+  enum SectionType { ATYPE = 0, HYDROPHILIC, BOND, UNKNOWN };
   SectionType section = ATYPE;
   ptr = infile.Line();
   while (ptr != 0) {
@@ -121,6 +121,8 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
       }
       if (ret == ParameterHolders::UPDATED)
         mprintf("Warning: Redefining atom type %s\n", kndsym);
+    } else if (section == BOND) {
+      mprintf("DEBUG: Bond: %s\n", ptr);
     }
     ptr = infile.Line();
   }

From 552234b0bd00e48e17ba3068d93e47a454a8d78d Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 10 Nov 2023 20:27:45 -0500
Subject: [PATCH 0042/1492] Start bond param scan

---
 src/DataIO_AmberFF.cpp | 20 ++++++++++++++++++--
 1 file changed, 18 insertions(+), 2 deletions(-)

diff --git a/src/DataIO_AmberFF.cpp b/src/DataIO_AmberFF.cpp
index e4235ac83e..b8fb15ae59 100644
--- a/src/DataIO_AmberFF.cpp
+++ b/src/DataIO_AmberFF.cpp
@@ -36,6 +36,7 @@ int DataIO_AmberFF::processReadArgs(ArgList& argIn)
 // DataIO_AmberFF::ReadData()
 int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::string const& dsname)
 {
+  static const int MAXSYMLEN = 16;
   // Allocate data set
   MetaData md( dsname );
   DataSet* ds = dsl.CheckForSet( md );
@@ -101,7 +102,7 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
       // Input for atom symbols and masses
       // Format (A2,2X,F10.2x,f10.2)
       mprintf("DEBUG: Atype: %s\n", ptr);
-      char kndsym[16];
+      char kndsym[MAXSYMLEN];
       double amass;
       double atpol;
       int nscan = sscanf(ptr, "%s %lf %lf", kndsym, &amass, &atpol);
@@ -116,13 +117,28 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
                                 AtomType(amass),
                                 true );
       } else {
-        mprinterr("Error: Expected atom type, mass, polarizability, got only %i\n", nscan);
+        mprinterr("Error: Expected atom type, mass, polarizability, got only %i columns.\n", nscan);
         return 1;
       }
       if (ret == ParameterHolders::UPDATED)
         mprintf("Warning: Redefining atom type %s\n", kndsym);
     } else if (section == BOND) {
+      // Bond parameters
+      // IBT , JBT , RK , REQ
+      // FORMAT(A2,1X,A2,2F10.2)
       mprintf("DEBUG: Bond: %s\n", ptr);
+      char ibt[MAXSYMLEN];
+      char jbt[MAXSYMLEN];
+      double RK, REQ;
+      int nscan = sscanf(ptr, "%s %s %lf %lf", ibt, jbt, &RK, &REQ);
+      if (nscan != 4) {
+        mprinterr("Error: Expected atom type 1, atom type 2, RK, REQ, got only %i columns,\n", nscan);
+        return 1;
+      }
+      TypeNameHolder types(2);
+      types.AddName( ibt );
+      types.AddName( jbt );
+      prm.BP().AddParm(types, BondParmType(RK, REQ), false);
     }
     ptr = infile.Line();
   }

From a21be7f17047758b5afdb534e120ceb962eab877 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 11 Nov 2023 09:03:52 -0500
Subject: [PATCH 0043/1492] New way to read in symbols

---
 src/DataIO_AmberFF.cpp | 34 +++++++++++++++++++++++++++++++++-
 src/DataIO_AmberFF.h   |  2 ++
 2 files changed, 35 insertions(+), 1 deletion(-)

diff --git a/src/DataIO_AmberFF.cpp b/src/DataIO_AmberFF.cpp
index b8fb15ae59..13fba0b226 100644
--- a/src/DataIO_AmberFF.cpp
+++ b/src/DataIO_AmberFF.cpp
@@ -33,6 +33,29 @@ int DataIO_AmberFF::processReadArgs(ArgList& argIn)
   return 0;
 }
 
+/** Read symbols delimited by - and space. */
+int DataIO_AmberFF::read_symbols(const char* ptrIn, std::vector<std::string>& symbols, int nsymbols)
+{
+  int isymbol = 0;
+  int idx = 0;
+  bool char_has_been_read = false;
+  const char* ptr = ptrIn;
+  for (; *ptr != '\0'; ++ptr)
+  {
+    if (*ptr == '-') {
+      isymbol++;
+      idx = 0;
+      char_has_been_read = false;
+    } else if (*ptr == ' ' && isymbol + 1 == nsymbols && char_has_been_read) {
+      break;
+    } else {
+      symbols[isymbol][idx++] = *ptr;
+      if (*ptr != ' ') char_has_been_read = true;
+    }
+  }
+  return (ptr - ptrIn);
+}
+
 // DataIO_AmberFF::ReadData()
 int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::string const& dsname)
 {
@@ -127,6 +150,15 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
       // IBT , JBT , RK , REQ
       // FORMAT(A2,1X,A2,2F10.2)
       mprintf("DEBUG: Bond: %s\n", ptr);
+      std::vector<std::string> symbols(2);
+      symbols[0].assign(MAXSYMLEN, ' ');
+      symbols[1].assign(MAXSYMLEN, ' ');
+      //char symbols[2][MAXSYMLEN];
+      //symbols[0][MAXSYMLEN-1] = '\0';
+      //symbols[1][MAXSYMLEN-1] = '\0';
+      read_symbols(ptr, symbols, 2);
+      mprintf("DEBUG: %s %s\n", symbols[0].c_str(), symbols[1].c_str());
+/*
       char ibt[MAXSYMLEN];
       char jbt[MAXSYMLEN];
       double RK, REQ;
@@ -138,7 +170,7 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
       TypeNameHolder types(2);
       types.AddName( ibt );
       types.AddName( jbt );
-      prm.BP().AddParm(types, BondParmType(RK, REQ), false);
+      prm.BP().AddParm(types, BondParmType(RK, REQ), false);*/
     }
     ptr = infile.Line();
   }
diff --git a/src/DataIO_AmberFF.h b/src/DataIO_AmberFF.h
index 323d198403..ab89e8fb09 100644
--- a/src/DataIO_AmberFF.h
+++ b/src/DataIO_AmberFF.h
@@ -13,5 +13,7 @@ class DataIO_AmberFF : public DataIO {
     int processWriteArgs(ArgList&);
     int WriteData(FileName const&, DataSetList const&);
     bool ID_DataFormat(CpptrajFile&);
+  private:
+    static int read_symbols(const char*, std::vector<std::string>&, int);
 };
 #endif

From d96364ca7bd4c5da79e2e5c2dafd4139978db475 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 11 Nov 2023 15:37:24 -0500
Subject: [PATCH 0044/1492] Trap errors, do not presize the strings

---
 src/DataIO_AmberFF.cpp | 24 +++++++++++++-----------
 1 file changed, 13 insertions(+), 11 deletions(-)

diff --git a/src/DataIO_AmberFF.cpp b/src/DataIO_AmberFF.cpp
index 13fba0b226..b23a0b5f96 100644
--- a/src/DataIO_AmberFF.cpp
+++ b/src/DataIO_AmberFF.cpp
@@ -37,23 +37,20 @@ int DataIO_AmberFF::processReadArgs(ArgList& argIn)
 int DataIO_AmberFF::read_symbols(const char* ptrIn, std::vector<std::string>& symbols, int nsymbols)
 {
   int isymbol = 0;
-  int idx = 0;
   bool char_has_been_read = false;
-  const char* ptr = ptrIn;
-  for (; *ptr != '\0'; ++ptr)
+  for (const char* ptr = ptrIn; *ptr != '\0'; ++ptr)
   {
     if (*ptr == '-') {
       isymbol++;
-      idx = 0;
       char_has_been_read = false;
     } else if (*ptr == ' ' && isymbol + 1 == nsymbols && char_has_been_read) {
-      break;
+      return (ptr - ptrIn);
     } else {
-      symbols[isymbol][idx++] = *ptr;
+      symbols[isymbol] += *ptr;
       if (*ptr != ' ') char_has_been_read = true;
     }
   }
-  return (ptr - ptrIn);
+  return -1;
 }
 
 // DataIO_AmberFF::ReadData()
@@ -151,13 +148,18 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
       // FORMAT(A2,1X,A2,2F10.2)
       mprintf("DEBUG: Bond: %s\n", ptr);
       std::vector<std::string> symbols(2);
-      symbols[0].assign(MAXSYMLEN, ' ');
-      symbols[1].assign(MAXSYMLEN, ' ');
+      //symbols[0].assign(MAXSYMLEN, ' ');
+      //symbols[1].assign(MAXSYMLEN, ' ');
       //char symbols[2][MAXSYMLEN];
       //symbols[0][MAXSYMLEN-1] = '\0';
       //symbols[1][MAXSYMLEN-1] = '\0';
-      read_symbols(ptr, symbols, 2);
-      mprintf("DEBUG: %s %s\n", symbols[0].c_str(), symbols[1].c_str());
+      int pos = read_symbols(ptr, symbols, 2);
+      if (pos < 0) {
+        mprinterr("Error: Could not read symbols for bond from %s\n", ptr);
+        return 1;
+      }
+      mprintf("DEBUG: %s %s '%s'\n", symbols[0].c_str(), symbols[1].c_str(), ptr+pos);
+      
 /*
       char ibt[MAXSYMLEN];
       char jbt[MAXSYMLEN];

From 2c064255cb2127983984bc1e1dceffcaea17ed38 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 11 Nov 2023 15:49:22 -0500
Subject: [PATCH 0045/1492] Finish bond parm read

---
 src/DataIO_AmberFF.cpp | 15 +++++++++++----
 1 file changed, 11 insertions(+), 4 deletions(-)

diff --git a/src/DataIO_AmberFF.cpp b/src/DataIO_AmberFF.cpp
index b23a0b5f96..ad91ab626c 100644
--- a/src/DataIO_AmberFF.cpp
+++ b/src/DataIO_AmberFF.cpp
@@ -159,20 +159,27 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
         return 1;
       }
       mprintf("DEBUG: %s %s '%s'\n", symbols[0].c_str(), symbols[1].c_str(), ptr+pos);
-      
+      double RK, REQ;
+      int nscan = sscanf(ptr+pos, "%lf %lf", &RK, &REQ);
+      if (nscan != 2) {
+        mprinterr("Error: Expected RK, REQ, got only %i elements\n", nscan);
+        return 1;
+      }
+      TypeNameHolder types(2);
+      types.AddName( symbols[0] );
+      types.AddName( symbols[1] );
+      prm.BP().AddParm(types, BondParmType(RK, REQ), false);
 /*
       char ibt[MAXSYMLEN];
       char jbt[MAXSYMLEN];
-      double RK, REQ;
       int nscan = sscanf(ptr, "%s %s %lf %lf", ibt, jbt, &RK, &REQ);
       if (nscan != 4) {
         mprinterr("Error: Expected atom type 1, atom type 2, RK, REQ, got only %i columns,\n", nscan);
         return 1;
       }
-      TypeNameHolder types(2);
       types.AddName( ibt );
       types.AddName( jbt );
-      prm.BP().AddParm(types, BondParmType(RK, REQ), false);*/
+*/
     }
     ptr = infile.Line();
   }

From 3e0e27ee623c72c2f5440ee14058026d582e6238 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 11 Nov 2023 19:23:25 -0500
Subject: [PATCH 0046/1492] Read angle parameters

---
 src/DataIO_AmberFF.cpp | 49 +++++++++++++++++++-----------------------
 1 file changed, 22 insertions(+), 27 deletions(-)

diff --git a/src/DataIO_AmberFF.cpp b/src/DataIO_AmberFF.cpp
index ad91ab626c..f3a6658d3f 100644
--- a/src/DataIO_AmberFF.cpp
+++ b/src/DataIO_AmberFF.cpp
@@ -86,7 +86,7 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
   std::string title(ptr);
   mprintf("\tTitle: %s\n", title.c_str());
   // Read file
-  enum SectionType { ATYPE = 0, HYDROPHILIC, BOND, UNKNOWN };
+  enum SectionType { ATYPE = 0, HYDROPHILIC, BOND, ANGLE, UNKNOWN };
   SectionType section = ATYPE;
   ptr = infile.Line();
   while (ptr != 0) {
@@ -104,18 +104,6 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
         ArgList hsymbols( ptr, " " );
         for (int iarg = 0; iarg != hsymbols.Nargs(); ++iarg)
           prm.AddHydrophilicAtomType( NameType( hsymbols[iarg] ) );
-        /*
-        char htype[5];
-        htype[4] = '\0';
-        std::string hline(ptr);
-        for (unsigned int idx = 0; idx < hline.size(); idx+=4) {
-          htype[0] = hline[idx  ];
-          htype[1] = hline[idx+1];
-          htype[2] = hline[idx+2];
-          htype[3] = hline[idx+3];
-          //mprintf("DEBUG:\t%s\n", htype);
-          prm.AddHydrophilicAtomType( NameType(htype) );
-        }*/
         section = (SectionType)((int)section + 1);
       }
     } else if (section == ATYPE) {
@@ -148,11 +136,6 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
       // FORMAT(A2,1X,A2,2F10.2)
       mprintf("DEBUG: Bond: %s\n", ptr);
       std::vector<std::string> symbols(2);
-      //symbols[0].assign(MAXSYMLEN, ' ');
-      //symbols[1].assign(MAXSYMLEN, ' ');
-      //char symbols[2][MAXSYMLEN];
-      //symbols[0][MAXSYMLEN-1] = '\0';
-      //symbols[1][MAXSYMLEN-1] = '\0';
       int pos = read_symbols(ptr, symbols, 2);
       if (pos < 0) {
         mprinterr("Error: Could not read symbols for bond from %s\n", ptr);
@@ -169,17 +152,29 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
       types.AddName( symbols[0] );
       types.AddName( symbols[1] );
       prm.BP().AddParm(types, BondParmType(RK, REQ), false);
-/*
-      char ibt[MAXSYMLEN];
-      char jbt[MAXSYMLEN];
-      int nscan = sscanf(ptr, "%s %s %lf %lf", ibt, jbt, &RK, &REQ);
-      if (nscan != 4) {
-        mprinterr("Error: Expected atom type 1, atom type 2, RK, REQ, got only %i columns,\n", nscan);
+    } else if (section == ANGLE) {
+      // Angle parameters
+      //ITT , JTT , KTT , TK , TEQ
+      //FORMAT(A2,1X,A2,1X,A2,2F10.2)
+      mprintf("DEBUG: Angle: %s\n", ptr);
+      std::vector<std::string> symbols(3);
+      int pos = read_symbols(ptr, symbols, 3);
+      if (pos < 0) {
+        mprinterr("Error: Could not read symbols for angle from %s\n", ptr);
+        return 1;
+      }
+      mprintf("DEBUG: %s %s %s '%s'\n", symbols[0].c_str(), symbols[1].c_str(), symbols[2].c_str(), ptr+pos);
+      double TK, TEQ;
+      int nscan = sscanf(ptr+pos, "%lf %lf", &TK, &TEQ);
+      if (nscan != 2) {
+        mprinterr("Error: Expected TK, TEQ, got only %i elements\n", nscan);
         return 1;
       }
-      types.AddName( ibt );
-      types.AddName( jbt );
-*/
+      TypeNameHolder types(3);
+      types.AddName( symbols[0] );
+      types.AddName( symbols[1] );
+      types.AddName( symbols[2] );
+      prm.AP().AddParm(types, AngleParmType(TK, TEQ), false);
     }
     ptr = infile.Line();
   }

From 988a38f6e927ed60b122d32bb2d500728fd08b91 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 11 Nov 2023 19:35:39 -0500
Subject: [PATCH 0047/1492] Add dihedral parm read

---
 src/DataIO_AmberFF.cpp | 39 ++++++++++++++++++++++++++++++++++++---
 1 file changed, 36 insertions(+), 3 deletions(-)

diff --git a/src/DataIO_AmberFF.cpp b/src/DataIO_AmberFF.cpp
index f3a6658d3f..c9200e0624 100644
--- a/src/DataIO_AmberFF.cpp
+++ b/src/DataIO_AmberFF.cpp
@@ -86,7 +86,7 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
   std::string title(ptr);
   mprintf("\tTitle: %s\n", title.c_str());
   // Read file
-  enum SectionType { ATYPE = 0, HYDROPHILIC, BOND, ANGLE, UNKNOWN };
+  enum SectionType { ATYPE = 0, HYDROPHILIC, BOND, ANGLE, DIHEDRAL, UNKNOWN };
   SectionType section = ATYPE;
   ptr = infile.Line();
   while (ptr != 0) {
@@ -154,8 +154,8 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
       prm.BP().AddParm(types, BondParmType(RK, REQ), false);
     } else if (section == ANGLE) {
       // Angle parameters
-      //ITT , JTT , KTT , TK , TEQ
-      //FORMAT(A2,1X,A2,1X,A2,2F10.2)
+      // ITT , JTT , KTT , TK , TEQ
+      // FORMAT(A2,1X,A2,1X,A2,2F10.2)
       mprintf("DEBUG: Angle: %s\n", ptr);
       std::vector<std::string> symbols(3);
       int pos = read_symbols(ptr, symbols, 3);
@@ -175,6 +175,39 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
       types.AddName( symbols[1] );
       types.AddName( symbols[2] );
       prm.AP().AddParm(types, AngleParmType(TK, TEQ), false);
+    } else if (section == DIHEDRAL) {
+      // Dihedral parameters
+      // IPT , JPT , KPT , LPT , IDIVF , PK , PHASE , PN
+      // FORMAT(A2,1X,A2,1X,A2,1X,A2,I4,3F15.2)
+      // If IPT .eq. 'X ' .and. LPT .eq. 'X ' then any dihedrals in the
+      // system involving the atoms "JPT" and and "KPT" are assigned 
+      // the same parameters.  This is called the general dihedral type
+      // and is of the form "X "-"JPT"-"KPT"-"X ".
+      // IDIVF is the factor by which the torsional barrier is divided.
+      // Consult Weiner, et al., JACS 106:765 (1984) p. 769 for
+      // details. Basically, the actual torsional potential is
+      //   (PK/IDIVF) * (1 + cos(PN*phi - PHASE))
+      mprintf("DEBUG: Dihedral: %s\n", ptr);
+      std::vector<std::string> symbols(4);
+      int pos = read_symbols(ptr, symbols, 4);
+      if (pos < 0) {
+        mprinterr("Error: Could not read symbols for dihedral from %s\n", ptr);
+        return 1;
+      }
+      mprintf("DEBUG: %s %s %s %s '%s'\n", symbols[0].c_str(), symbols[1].c_str(), symbols[2].c_str(), symbols[3].c_str(), ptr+pos);
+      int IDIVF;
+      double PK, PHASE, PN;
+      int nscan = sscanf(ptr+pos, "%i %lf %lf %lf", &IDIVF, &PK, &PHASE, &PN);
+      if (nscan != 4) {
+        mprinterr("Error: Expected IDIVF, PK, PHASE, PN, got only %i elements\n", nscan);
+        return 1;
+      }
+      TypeNameHolder types(4);
+      types.AddName( symbols[0] );
+      types.AddName( symbols[1] );
+      types.AddName( symbols[2] );
+      types.AddName( symbols[3] );
+      prm.DP().AddParm(types, DihedralParmType(PK / (double)IDIVF, PN, PHASE), false);
     }
     ptr = infile.Line();
   }

From adbf534f850379b873460678331951862be1d44c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 11 Nov 2023 20:23:47 -0500
Subject: [PATCH 0048/1492] Add improper param read. Ensure whitespace chars
 are skipped when looking for section changes.

---
 src/DataIO_AmberFF.cpp | 30 +++++++++++++++++++++++++++++-
 1 file changed, 29 insertions(+), 1 deletion(-)

diff --git a/src/DataIO_AmberFF.cpp b/src/DataIO_AmberFF.cpp
index c9200e0624..b52309fba3 100644
--- a/src/DataIO_AmberFF.cpp
+++ b/src/DataIO_AmberFF.cpp
@@ -86,13 +86,17 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
   std::string title(ptr);
   mprintf("\tTitle: %s\n", title.c_str());
   // Read file
-  enum SectionType { ATYPE = 0, HYDROPHILIC, BOND, ANGLE, DIHEDRAL, UNKNOWN };
+  enum SectionType { ATYPE = 0, HYDROPHILIC, BOND, ANGLE, DIHEDRAL, IMPROPER, UNKNOWN };
   SectionType section = ATYPE;
   ptr = infile.Line();
   while (ptr != 0) {
+    // Advance to first non-space char
+    while (*ptr == ' ' && *ptr != '\0') ++ptr;
+    mprintf("DEBUG: First char: %c (%i)\n", *ptr, (int)*ptr);
     if (*ptr == '\0') {
       // Section Change
       if (section != UNKNOWN) {
+        mprintf("SECTION %i change to %i\n", (int)section, (int)section + 1);
         section = (SectionType)((int)section + 1);
       }
       // Special case; hydrophilic atom types. One line.
@@ -208,6 +212,30 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
       types.AddName( symbols[2] );
       types.AddName( symbols[3] );
       prm.DP().AddParm(types, DihedralParmType(PK / (double)IDIVF, PN, PHASE), false);
+    } else if (section == IMPROPER) {
+      // Improper parameters
+      // IPT , JPT , KPT , LPT , IDIVF , PK , PHASE , PN
+      // FORMAT(A2,1X,A2,1X,A2,1X,A2,I4,3F15.2)
+      mprintf("DEBUG: Improper: %s\n", ptr);
+      std::vector<std::string> symbols(4);
+      int pos = read_symbols(ptr, symbols, 4);
+      if (pos < 0) {
+        mprinterr("Error: Could not read symbols for improper from %s\n", ptr);
+        return 1;
+      }
+      mprintf("DEBUG: %s %s %s %s '%s'\n", symbols[0].c_str(), symbols[1].c_str(), symbols[2].c_str(), symbols[3].c_str(), ptr+pos);
+      double PK, PHASE, PN;
+      int nscan = sscanf(ptr+pos, "%lf %lf %lf", &PK, &PHASE, &PN);
+      if (nscan != 3) {
+        mprinterr("Error: Expected PK, PHASE, PN, got only %i elements\n", nscan);
+        return 1;
+      }
+      TypeNameHolder types(4);
+      types.AddName( symbols[0] );
+      types.AddName( symbols[1] );
+      types.AddName( symbols[2] );
+      types.AddName( symbols[3] );
+      prm.IP().AddParm(types, DihedralParmType(PK, PN, PHASE), false);
     }
     ptr = infile.Line();
   }

From 8c85b7e4efda0cf8326809096c05226a7b9bee6e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 12 Nov 2023 14:43:13 -0500
Subject: [PATCH 0049/1492] Start LJ 10-12 read. Add lookahead after
 hydrophilic section to deal with older parm files.

---
 src/DataIO_AmberFF.cpp | 28 ++++++++++++++++++++++++++--
 1 file changed, 26 insertions(+), 2 deletions(-)

diff --git a/src/DataIO_AmberFF.cpp b/src/DataIO_AmberFF.cpp
index b52309fba3..877dca7ef8 100644
--- a/src/DataIO_AmberFF.cpp
+++ b/src/DataIO_AmberFF.cpp
@@ -86,7 +86,8 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
   std::string title(ptr);
   mprintf("\tTitle: %s\n", title.c_str());
   // Read file
-  enum SectionType { ATYPE = 0, HYDROPHILIC, BOND, ANGLE, DIHEDRAL, IMPROPER, UNKNOWN };
+  enum SectionType { ATYPE = 0, HYDROPHILIC, BOND, ANGLE, DIHEDRAL, IMPROPER, 
+                     LJ1012, UNKNOWN };
   SectionType section = ATYPE;
   ptr = infile.Line();
   while (ptr != 0) {
@@ -109,6 +110,11 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
         for (int iarg = 0; iarg != hsymbols.Nargs(); ++iarg)
           prm.AddHydrophilicAtomType( NameType( hsymbols[iarg] ) );
         section = (SectionType)((int)section + 1);
+        // Look ahead. Older parm files have the hydrophilic section delimited
+        // with a newline.
+        ptr = infile.Line();
+        while (*ptr == ' ' && *ptr != '\0') ++ptr;
+        if (*ptr != '\0') continue;
       }
     } else if (section == ATYPE) {
       // Input for atom symbols and masses
@@ -236,7 +242,25 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
       types.AddName( symbols[2] );
       types.AddName( symbols[3] );
       prm.IP().AddParm(types, DihedralParmType(PK, PN, PHASE), false);
-    }
+    } else if (section == LJ1012) {
+      // Lennard-Jones 10-12 hydrogen bonding term
+      // KT1 , KT2 , A , B , ASOLN , BSOLN , HCUT , IC
+      // FORMAT(2X,A2,2X,A2,2x,5F10.2,I2)
+      // NOTE: The ASOLN, BSOLN, HCUT, and IC columns are no longer used
+      //       and so are not read.
+      char KT1[MAXSYMLEN], KT2[MAXSYMLEN];
+      double A, B;
+      //double ASOLN, BSOLN, HCUT;
+      //int IC;
+      mprintf("DEBUG: LJ 10-12: %s\n", ptr);
+      //int nscan = sscanf(ptr, "%s %s %lf %lf %lf %lf %lf %i\n",
+      int nscan = sscanf(ptr, "%s %s %lf %lf", KT1, KT2, &A, &B);
+      if (nscan < 4) {
+        mprinterr("Error: Expected at least KT1, KT2, A, B, got only %i elements\n", nscan);
+        return 1;
+      }
+    } 
+      
     ptr = infile.Line();
   }
 

From 2a537ce31ea26e1e53f069a3bf38c5d04f0b2902 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 12 Nov 2023 15:06:15 -0500
Subject: [PATCH 0050/1492] Scan HBcut. Add LJ 10-12 to ParameterSet

---
 src/DataIO_AmberFF.cpp | 15 ++++++++-------
 src/ParameterSet.cpp   | 10 +++++++++-
 src/ParameterSet.h     |  7 ++++++-
 3 files changed, 23 insertions(+), 9 deletions(-)

diff --git a/src/DataIO_AmberFF.cpp b/src/DataIO_AmberFF.cpp
index 877dca7ef8..395ac5ce35 100644
--- a/src/DataIO_AmberFF.cpp
+++ b/src/DataIO_AmberFF.cpp
@@ -243,20 +243,21 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
       types.AddName( symbols[3] );
       prm.IP().AddParm(types, DihedralParmType(PK, PN, PHASE), false);
     } else if (section == LJ1012) {
-      // Lennard-Jones 10-12 hydrogen bonding term
+      // Lennard-Jones 10-12 hydrogen bonding term.
+      // According to the docs, the format should be:
       // KT1 , KT2 , A , B , ASOLN , BSOLN , HCUT , IC
       // FORMAT(2X,A2,2X,A2,2x,5F10.2,I2)
-      // NOTE: The ASOLN, BSOLN, HCUT, and IC columns are no longer used
-      //       and so are not read.
+      // In practive (in e.g. parm91.dat), the actual format appears to be:
+      // KT1, KT2, A, B, HCUT
       char KT1[MAXSYMLEN], KT2[MAXSYMLEN];
-      double A, B;
+      double A, B, HCUT;
       //double ASOLN, BSOLN, HCUT;
       //int IC;
       mprintf("DEBUG: LJ 10-12: %s\n", ptr);
       //int nscan = sscanf(ptr, "%s %s %lf %lf %lf %lf %lf %i\n",
-      int nscan = sscanf(ptr, "%s %s %lf %lf", KT1, KT2, &A, &B);
-      if (nscan < 4) {
-        mprinterr("Error: Expected at least KT1, KT2, A, B, got only %i elements\n", nscan);
+      int nscan = sscanf(ptr, "%s %s %lf %lf %lf", KT1, KT2, &A, &B, &HCUT);
+      if (nscan < 5) {
+        mprinterr("Error: Expected at least KT1, KT2, A, B, HCUT, got only %i elements\n", nscan);
         return 1;
       }
     } 
diff --git a/src/ParameterSet.cpp b/src/ParameterSet.cpp
index 635b9e2b4f..9134bc2ec0 100644
--- a/src/ParameterSet.cpp
+++ b/src/ParameterSet.cpp
@@ -10,7 +10,9 @@ size_t ParameterSet::DataSize() const {
           angleParm_.DataSize() +
           ubParm_.DataSize() +
           dihParm_.DataSize() +
-          impParm_.DataSize());
+          impParm_.DataSize() +
+          HBparm_.DataSize() +
+          (hydrophilicAtomTypes_.size() * NameType::DataSize()));
 }
 
 void ParameterSet::Debug(const char* fnameIn) const {
@@ -33,6 +35,12 @@ void ParameterSet::Debug(const char* fnameIn) const {
     for (ParmHolder<NonbondType>::const_iterator nb = nb14Parm_.begin(); nb != nb14Parm_.end(); ++nb)
       Out.Printf("\t%6s %6s : %12.4E %12.4E\n", (*nb->first[0]), (*nb->first[1]), nb->second.A(), nb->second.B());
   }
+  if (!HBparm_.empty()) {
+    Out.Printf("HB LJ 10-12 parameters:\n");
+    Out.Printf("\t%6s %6s : %12s %12s %12s\n", "Type1", "Type2", "Asol", "Bsol", "HBcut");
+    for (ParmHolder<HB_ParmType>::const_iterator hb = HBparm_.begin(); hb != HBparm_.end(); ++hb)
+      Out.Printf("\t%6s %6s : %12.4f %124.f %12.4f\n", *(hb->first[0]), *(hb->first[1]), hb->second.Asol(), hb->second.Bsol(), hb->second.HBcut());
+  }
   if (!bondParm_.empty()) {
     Out.Printf("Bond parameters:\n");
     Out.Printf("\t%6s %6s : %12s %12s\n", "Type1", "Type2", "Rk", "Req");
diff --git a/src/ParameterSet.h b/src/ParameterSet.h
index fbfadc82ec..42964ca3eb 100644
--- a/src/ParameterSet.h
+++ b/src/ParameterSet.h
@@ -16,6 +16,7 @@ class ParameterSet {
     ParmHolder<BondParmType>& UB()     { return ubParm_;    }
     ParmHolder<DihedralParmType>& IP() { return impParm_;   }
     DihedralParmHolder& DP()           { return dihParm_;   }
+    ParmHolder<HB_ParmType>& HB()      { return HBparm_;    }
 
     void SetHasLJparams(bool b) { hasLJparams_ = b; }
     bool HasLJparams() const { return hasLJparams_; }
@@ -28,6 +29,7 @@ class ParameterSet {
     ParmHolder<BondParmType> const& UB()     const { return ubParm_;    }
     ParmHolder<DihedralParmType> const& IP() const { return impParm_;   }
     DihedralParmHolder const& DP()           const { return dihParm_;   }
+    ParmHolder<HB_ParmType> const& HB()      const { return HBparm_;    }
 
     void Debug(const char*) const;
     void Debug() const { return Debug(""); }
@@ -38,7 +40,8 @@ class ParameterSet {
         UpdateCount() : nBondsUpdated_(0), nAnglesUpdated_(0),
                         nDihedralsUpdated_(0), nImpropersUpdated_(0),
                         nUreyBradleyUpdated_(0), nAtomTypeUpdated_(0),
-                        nLJparamsUpdated_(0), nLJ14paramsUpdated_(0) {}
+                        nLJparamsUpdated_(0), nLJ14paramsUpdated_(0),
+                        nHBparamsUpdated_(0) {}
         unsigned int nBondsUpdated_;
         unsigned int nAnglesUpdated_;
         unsigned int nDihedralsUpdated_;
@@ -47,6 +50,7 @@ class ParameterSet {
         unsigned int nAtomTypeUpdated_;
         unsigned int nLJparamsUpdated_;
         unsigned int nLJ14paramsUpdated_;
+        unsigned int nHBparamsUpdated_;
     };
     /// Update this set with parameters from given set
     int UpdateParamSet(ParameterSet const&, UpdateCount&, int);
@@ -65,6 +69,7 @@ class ParameterSet {
     ParmHolder<BondParmType> ubParm_;      ///< Urey-Bradley parameters
     ParmHolder<DihedralParmType> impParm_; ///< Improper dihedral parameters
     DihedralParmHolder dihParm_;           ///< Cosine-series dihedral parameters
+    ParmHolder<HB_ParmType> HBparm_;       ///< LJ 10-12 A-B parameters for hydrogen bonds
     NsetType hydrophilicAtomTypes_;        ///< Hold names of hydrophilic atom types
     bool hasLJparams_;
 };

From 5f1eb35933dd99ae2f9daf8f12aad5f1616ad8c5 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 12 Nov 2023 15:19:50 -0500
Subject: [PATCH 0051/1492] Finish reading HB 10-12 params

---
 src/DataIO_AmberFF.cpp |  4 ++++
 src/ParameterSet.cpp   |  2 +-
 src/ParameterTypes.h   | 29 +++++++++++++++++++++++++++++
 3 files changed, 34 insertions(+), 1 deletion(-)

diff --git a/src/DataIO_AmberFF.cpp b/src/DataIO_AmberFF.cpp
index 395ac5ce35..1d21880cff 100644
--- a/src/DataIO_AmberFF.cpp
+++ b/src/DataIO_AmberFF.cpp
@@ -260,6 +260,10 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
         mprinterr("Error: Expected at least KT1, KT2, A, B, HCUT, got only %i elements\n", nscan);
         return 1;
       }
+      TypeNameHolder types(2);
+      types.AddName( KT1 );
+      types.AddName( KT2 );
+      prm.HB().AddParm(types, HB_ParmType(A, B, HCUT), false);
     } 
       
     ptr = infile.Line();
diff --git a/src/ParameterSet.cpp b/src/ParameterSet.cpp
index 9134bc2ec0..b35819b07c 100644
--- a/src/ParameterSet.cpp
+++ b/src/ParameterSet.cpp
@@ -39,7 +39,7 @@ void ParameterSet::Debug(const char* fnameIn) const {
     Out.Printf("HB LJ 10-12 parameters:\n");
     Out.Printf("\t%6s %6s : %12s %12s %12s\n", "Type1", "Type2", "Asol", "Bsol", "HBcut");
     for (ParmHolder<HB_ParmType>::const_iterator hb = HBparm_.begin(); hb != HBparm_.end(); ++hb)
-      Out.Printf("\t%6s %6s : %12.4f %124.f %12.4f\n", *(hb->first[0]), *(hb->first[1]), hb->second.Asol(), hb->second.Bsol(), hb->second.HBcut());
+      Out.Printf("\t%6s %6s : %12.4f %12.4f %12.4f\n", *(hb->first[0]), *(hb->first[1]), hb->second.Asol(), hb->second.Bsol(), hb->second.HBcut());
   }
   if (!bondParm_.empty()) {
     Out.Printf("Bond parameters:\n");
diff --git a/src/ParameterTypes.h b/src/ParameterTypes.h
index 7564a61069..4908d653eb 100644
--- a/src/ParameterTypes.h
+++ b/src/ParameterTypes.h
@@ -258,6 +258,12 @@ typedef std::vector<DihedralType> DihedralArray;
 // ----- NON-BONDED PARAMETERS -------------------------------------------------
 /// Hold LJ 10-12 hbond params
 class HB_ParmType {
+    /** Tolerance for comparison. A little larger than SMALL because A
+      * and B tend to be large.
+      */
+    // NOTE: Probably should check __cpluscplus here instead of using a
+    //       define, but this is guaranteed to be portable.
+#     define tol_ 0.00000001
   public:
     HB_ParmType() : asol_(0), bsol_(0), hbcut_(0) {}
     HB_ParmType(double a, double b, double c) :
@@ -268,10 +274,33 @@ class HB_ParmType {
     void SetAsol(double a)  { asol_ = a;  }
     void SetBsol(double b)  { bsol_ = b;  }
     void SetHBcut(double h) { hbcut_ = h; }
+    /// \return True if A, B, and HBcut match
+    bool operator==(HB_ParmType const& rhs) const {
+      return ( (fabs(asol_ - rhs.asol_) < tol_) &&
+               (fabs(bsol_ - rhs.bsol_) < tol_) &&
+               (fabs(hbcut_ - rhs.hbcut_) < tol_) );
+    }
+    /// \return True if A, B, or HBcut do not match
+    bool operator!=(HB_ParmType const& rhs) const {
+      return ( (fabs(asol_ - rhs.asol_) > tol_) ||
+               (fabs(bsol_ - rhs.bsol_) > tol_) ||
+               (fabs(hbcut_ - rhs.hbcut_) > tol_) );
+    }
+    /// \return True if A less than zero, or B if A is equal. TODO add hbcut?
+    bool operator<(HB_ParmType const& rhs) const {
+      if (*this != rhs) {
+        if ( (fabs(asol_ - rhs.asol_) < tol_) )
+          return (bsol_ < rhs.bsol_);
+        else
+          return (asol_ < rhs.asol_);
+      } else
+        return false;
+    }
   private:
     double asol_;
     double bsol_;
     double hbcut_;
+#   undef tol_
 };
 typedef std::vector<HB_ParmType> HB_ParmArray;
 /// Hold Lennard-Jones 6-12 interaction A and B parameters

From 81c82ec3adbc88a36eb5d305ad740e0fc3f2118d Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 12 Nov 2023 19:02:49 -0500
Subject: [PATCH 0052/1492] Start nonbonded equivalent and nonbonded reads

---
 src/DataIO_AmberFF.cpp | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/src/DataIO_AmberFF.cpp b/src/DataIO_AmberFF.cpp
index 1d21880cff..79d4aaa4e3 100644
--- a/src/DataIO_AmberFF.cpp
+++ b/src/DataIO_AmberFF.cpp
@@ -87,7 +87,7 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
   mprintf("\tTitle: %s\n", title.c_str());
   // Read file
   enum SectionType { ATYPE = 0, HYDROPHILIC, BOND, ANGLE, DIHEDRAL, IMPROPER, 
-                     LJ1012, UNKNOWN };
+                     LJ1012, NB_EQUIV, NONBOND, UNKNOWN };
   SectionType section = ATYPE;
   ptr = infile.Line();
   while (ptr != 0) {
@@ -115,6 +115,14 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
         ptr = infile.Line();
         while (*ptr == ' ' && *ptr != '\0') ++ptr;
         if (*ptr != '\0') continue;
+      } else if (section == NONBOND) {
+        // Special case: first read the line:
+        // LABEL , KINDNB
+        // FORMAT(A4,6X,A2)
+        ptr = infile.Line();
+        char nb_label[MAXSYMLEN], nb_kind[MAXSYMLEN];
+        sscanf(ptr, "%s %s", nb_label, nb_kind);
+        mprintf("DEBUG: NB label= %s  NB kind = %s\n", nb_label, nb_kind);
       }
     } else if (section == ATYPE) {
       // Input for atom symbols and masses
@@ -264,7 +272,11 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
       types.AddName( KT1 );
       types.AddName( KT2 );
       prm.HB().AddParm(types, HB_ParmType(A, B, HCUT), false);
-    } 
+    } else if (section == NB_EQUIV) {
+      mprintf("DEBUG: Nonbond equiv: %s\n", ptr);
+    } else if (section == NONBOND) {
+      mprintf("DEBUG: Nonbond: %s\n", ptr);
+    }
       
     ptr = infile.Line();
   }

From c1c197a82e49b421171006d975159550b81b92ab Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 12 Nov 2023 19:07:39 -0500
Subject: [PATCH 0053/1492] Check that nonbond parameters are type RE

---
 src/DataIO_AmberFF.cpp | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/src/DataIO_AmberFF.cpp b/src/DataIO_AmberFF.cpp
index 79d4aaa4e3..bcb05f29f1 100644
--- a/src/DataIO_AmberFF.cpp
+++ b/src/DataIO_AmberFF.cpp
@@ -100,9 +100,10 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
         mprintf("SECTION %i change to %i\n", (int)section, (int)section + 1);
         section = (SectionType)((int)section + 1);
       }
-      // Special case; hydrophilic atom types. One line.
-      // FORMAT(20(A2,2X))
+      // Special cases
       if (section == HYDROPHILIC) {
+        // Special case: hydrophilic atom types. One line.
+        // FORMAT(20(A2,2X))
         ptr = infile.Line();
         mprintf("DEBUG: Hydrophilic: %s\n", ptr);
         // Take advantage of the fact that we expect whitespace-delimiters
@@ -116,13 +117,17 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
         while (*ptr == ' ' && *ptr != '\0') ++ptr;
         if (*ptr != '\0') continue;
       } else if (section == NONBOND) {
-        // Special case: first read the line:
+        // Special case: first read the line.
         // LABEL , KINDNB
         // FORMAT(A4,6X,A2)
         ptr = infile.Line();
         char nb_label[MAXSYMLEN], nb_kind[MAXSYMLEN];
         sscanf(ptr, "%s %s", nb_label, nb_kind);
         mprintf("DEBUG: NB label= %s  NB kind = %s\n", nb_label, nb_kind);
+        if (nb_kind[0] != 'R' || nb_kind[1] != 'E') {
+          mprinterr("Error: Nonbond parameters are not of type 'RE' (Rmin, Epsilon).\n");
+          return 1;
+        }
       }
     } else if (section == ATYPE) {
       // Input for atom symbols and masses

From c85d1f7e1c2e7e1060412eb3fb18b76eacffa91c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 12 Nov 2023 19:24:01 -0500
Subject: [PATCH 0054/1492] Start reading nonbond params

---
 src/DataIO_AmberFF.cpp | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/src/DataIO_AmberFF.cpp b/src/DataIO_AmberFF.cpp
index bcb05f29f1..d22b70c6c2 100644
--- a/src/DataIO_AmberFF.cpp
+++ b/src/DataIO_AmberFF.cpp
@@ -280,7 +280,25 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
     } else if (section == NB_EQUIV) {
       mprintf("DEBUG: Nonbond equiv: %s\n", ptr);
     } else if (section == NONBOND) {
+      // ***** ONLY IF KINDNB .EQ. 'RE' *****
+      // LTYNB , R , EDEP
       mprintf("DEBUG: Nonbond: %s\n", ptr);
+      char LTYNB[MAXSYMLEN];
+      double R, EDEP;
+      double R14, E14;
+      int nscan = sscanf(ptr, "%s %lf %lf %lf %lf", LTYNB, &R, &EDEP, &R14, &E14);
+      
+      if (nscan == 3 || nscan == 5) {
+        // symbol, rmin, epsilon
+        ParmHolder<AtomType>::iterator it = prm.AT().GetParam( TypeNameHolder(LTYNB) );
+        if (it == prm.AT().end()) {
+          mprintf("Warning: Nonbond parameters defined for previously undefined type '%s'."
+                          " Skipping.\n", LTYNB);
+        } else {
+          it->second.SetLJ().SetRadius( R );
+          it->second.SetLJ().SetDepth( EDEP );
+        }
+      }
     }
       
     ptr = infile.Line();

From 5672f3caf298c20d7a301b9ec8832a5a45998193 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 12 Nov 2023 20:40:02 -0500
Subject: [PATCH 0055/1492] Start handling multiple NB sets in same parm

---
 src/DataIO_AmberFF.cpp | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/src/DataIO_AmberFF.cpp b/src/DataIO_AmberFF.cpp
index d22b70c6c2..c1ab590e0d 100644
--- a/src/DataIO_AmberFF.cpp
+++ b/src/DataIO_AmberFF.cpp
@@ -53,6 +53,15 @@ int DataIO_AmberFF::read_symbols(const char* ptrIn, std::vector<std::string>& sy
   return -1;
 }
 
+/// Hold a set of nonbonded parameters
+class NonbondSet {
+  public:
+    NonbondSet(std::string const& n) : name_(n) {}
+
+    std::string name_;          ///< Name of set parameters
+    ParmHolder<LJparmType> LJ_; ///< Hold LJ 6-12 parameters
+};
+
 // DataIO_AmberFF::ReadData()
 int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::string const& dsname)
 {
@@ -72,6 +81,9 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
   }
   DataSet_Parameters& prm = static_cast<DataSet_Parameters&>( *ds ); 
 
+  typedef std::vector<NonbondSet> NbSetArrayType;
+  NbSetArrayType NBsets;
+
   // Read title
   BufferedLine infile;
   if (infile.OpenFileRead( fname )) {
@@ -128,6 +140,7 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
           mprinterr("Error: Nonbond parameters are not of type 'RE' (Rmin, Epsilon).\n");
           return 1;
         }
+        NBsets.push_back( NonbondSet( std::string(nb_label) ) );
       }
     } else if (section == ATYPE) {
       // Input for atom symbols and masses

From 8841d722a98c05001969b34b499f8f46f229f015 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 12 Nov 2023 20:55:31 -0500
Subject: [PATCH 0056/1492] Try to handle multiple nonbond sets

---
 src/DataIO_AmberFF.cpp | 25 ++++++++++++++++++++++---
 1 file changed, 22 insertions(+), 3 deletions(-)

diff --git a/src/DataIO_AmberFF.cpp b/src/DataIO_AmberFF.cpp
index c1ab590e0d..b843b49bb9 100644
--- a/src/DataIO_AmberFF.cpp
+++ b/src/DataIO_AmberFF.cpp
@@ -98,6 +98,7 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
   std::string title(ptr);
   mprintf("\tTitle: %s\n", title.c_str());
   // Read file
+  bool ljedit = false;
   enum SectionType { ATYPE = 0, HYDROPHILIC, BOND, ANGLE, DIHEDRAL, IMPROPER, 
                      LJ1012, NB_EQUIV, NONBOND, UNKNOWN };
   SectionType section = ATYPE;
@@ -109,8 +110,23 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
     if (*ptr == '\0') {
       // Section Change
       if (section != UNKNOWN) {
-        mprintf("SECTION %i change to %i\n", (int)section, (int)section + 1);
-        section = (SectionType)((int)section + 1);
+        if (section == NONBOND) {
+          // Do a lookahead to see if there are multiple NB sets.
+          // It will either be another set, END, or LJEDIT
+          ptr = infile.Line();
+          while (*ptr == ' ' && *ptr != '\0') ++ptr;
+          std::string nbline(ptr);
+          if (nbline == "END") {
+            mprintf("END\n");
+            section = UNKNOWN;
+          } else if (nbline == "LJEDIT") {
+            ljedit = true;
+            section = UNKNOWN;
+          } // Otherwise assume another nonbond section
+        } else {
+          mprintf("SECTION %i change to %i\n", (int)section, (int)section + 1);
+          section = (SectionType)((int)section + 1);
+        }
       }
       // Special cases
       if (section == HYDROPHILIC) {
@@ -132,7 +148,8 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
         // Special case: first read the line.
         // LABEL , KINDNB
         // FORMAT(A4,6X,A2)
-        ptr = infile.Line();
+        if (NBsets.empty())
+          ptr = infile.Line();
         char nb_label[MAXSYMLEN], nb_kind[MAXSYMLEN];
         sscanf(ptr, "%s %s", nb_label, nb_kind);
         mprintf("DEBUG: NB label= %s  NB kind = %s\n", nb_label, nb_kind);
@@ -312,6 +329,8 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
           it->second.SetLJ().SetDepth( EDEP );
         }
       }
+    } else if (ljedit) {
+      mprintf("DEBUG: LJedit: %s\n", ptr);
     }
       
     ptr = infile.Line();

From 8a375e6f07a773c49c1598ff37afd70855c72a5d Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 12 Nov 2023 21:01:38 -0500
Subject: [PATCH 0057/1492] Actually save the nonbonded param

---
 src/DataIO_AmberFF.cpp | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/DataIO_AmberFF.cpp b/src/DataIO_AmberFF.cpp
index b843b49bb9..715484c205 100644
--- a/src/DataIO_AmberFF.cpp
+++ b/src/DataIO_AmberFF.cpp
@@ -320,6 +320,7 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
       
       if (nscan == 3 || nscan == 5) {
         // symbol, rmin, epsilon
+        NBsets.back().LJ_.AddParm( TypeNameHolder(LTYNB), LJparmType(R, EDEP), false );
         ParmHolder<AtomType>::iterator it = prm.AT().GetParam( TypeNameHolder(LTYNB) );
         if (it == prm.AT().end()) {
           mprintf("Warning: Nonbond parameters defined for previously undefined type '%s'."

From dd3ef4bbf304a12ec08911943f06f2e92bab7617 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 13 Nov 2023 11:22:56 -0500
Subject: [PATCH 0058/1492] Add ability to choose from multiple nonbond parm
 sets

---
 src/DataFile.cpp       |  2 +-
 src/DataIO_AmberFF.cpp | 36 ++++++++++++++++++++++++++++++++++--
 src/DataIO_AmberFF.h   |  2 ++
 3 files changed, 37 insertions(+), 3 deletions(-)

diff --git a/src/DataFile.cpp b/src/DataFile.cpp
index c393ddb4e3..b2e6bbaa59 100644
--- a/src/DataFile.cpp
+++ b/src/DataFile.cpp
@@ -90,7 +90,7 @@ const FileTypes::AllocToken DataFile::DF_AllocArray[] = {
   { "Numpy array",        0,                             0,            DataIO_Numpy::Alloc},
   { "Amber Prep File",    DataIO_AmberPrep::ReadHelp,    0,            DataIO_AmberPrep::Alloc},
   { "Amber OFF File",     0,                             0,            DataIO_AmberLib::Alloc},
-  { "Amber Force Field",  0,                             0,            DataIO_AmberFF::Alloc},
+  { "Amber Force Field",  DataIO_AmberFF::ReadHelp,      0,            DataIO_AmberFF::Alloc},
   { "Unknown Data file",  0,                       0,                        0                    }
 };
 
diff --git a/src/DataIO_AmberFF.cpp b/src/DataIO_AmberFF.cpp
index 715484c205..e5f027bb44 100644
--- a/src/DataIO_AmberFF.cpp
+++ b/src/DataIO_AmberFF.cpp
@@ -23,13 +23,13 @@ bool DataIO_AmberFF::ID_DataFormat(CpptrajFile& infile)
 // DataIO_AmberFF::ReadHelp()
 void DataIO_AmberFF::ReadHelp()
 {
-
+  mprintf("\tnbset <nonbond set name> : Nonbonded set name to use when multiple nonbond parameter sets.\n");
 }
 
 // DataIO_AmberFF::processReadArgs()
 int DataIO_AmberFF::processReadArgs(ArgList& argIn)
 {
-
+  nbsetname_ = argIn.GetStringKey("nbset");
   return 0;
 }
 
@@ -335,6 +335,38 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
     }
       
     ptr = infile.Line();
+  } // END loop over file.
+  // Deal with nonbond and equivalence
+  if (!NBsets.empty()) {
+    int nbsetidx = 0;
+    if (NBsets.size() > 1 || !nbsetname_.empty()) {
+      // Choose from multiple nbsets
+      if (nbsetname_.empty()) {
+        mprinterr("Error: Parm set in file '%s' contains %zu nonbonded parameter sets\n"
+                  "Error:  but no set has been specified.\n", fname.full(), NBsets.size());
+        mprinterr("Error: Need to specify one of");
+        for (NbSetArrayType::const_iterator it = NBsets.begin(); it != NBsets.end(); ++it)
+          mprinterr(" %s", it->name_.c_str());
+        mprinterr("\n");
+      } else {
+        nbsetidx = -1;
+        for (NbSetArrayType::const_iterator it = NBsets.begin(); it != NBsets.end(); ++it) {
+          if (it->name_ == nbsetname_) {
+            nbsetidx = it - NBsets.begin();
+            break;
+          }
+        }
+        if (nbsetidx < 0) {
+          mprinterr("Error: Nonbonded set '%s' not found.\n", nbsetname_.c_str());
+          mprinterr("Error: Need to specify one of");
+          for (NbSetArrayType::const_iterator it = NBsets.begin(); it != NBsets.end(); ++it)
+            mprinterr(" %s", it->name_.c_str());
+          mprinterr("\n");
+          return 1;
+        }
+      }
+    }
+    mprintf("\tUsing nonbonded parm set: %s\n", NBsets[nbsetidx].name_.c_str());
   }
 
   prm.Debug(); // TODO debug level
diff --git a/src/DataIO_AmberFF.h b/src/DataIO_AmberFF.h
index ab89e8fb09..5d0af59568 100644
--- a/src/DataIO_AmberFF.h
+++ b/src/DataIO_AmberFF.h
@@ -15,5 +15,7 @@ class DataIO_AmberFF : public DataIO {
     bool ID_DataFormat(CpptrajFile&);
   private:
     static int read_symbols(const char*, std::vector<std::string>&, int);
+
+    std::string nbsetname_; ///< Nonbonded parameter set name to use
 };
 #endif

From e3f4b52fa4edae86bc33f5da1471b890062c17c7 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 13 Nov 2023 11:38:43 -0500
Subject: [PATCH 0059/1492] Add nb params from the chosen set

---
 src/DataIO_AmberFF.cpp | 18 +++++++++++++++---
 1 file changed, 15 insertions(+), 3 deletions(-)

diff --git a/src/DataIO_AmberFF.cpp b/src/DataIO_AmberFF.cpp
index e5f027bb44..a8f6b61a3b 100644
--- a/src/DataIO_AmberFF.cpp
+++ b/src/DataIO_AmberFF.cpp
@@ -321,14 +321,14 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
       if (nscan == 3 || nscan == 5) {
         // symbol, rmin, epsilon
         NBsets.back().LJ_.AddParm( TypeNameHolder(LTYNB), LJparmType(R, EDEP), false );
-        ParmHolder<AtomType>::iterator it = prm.AT().GetParam( TypeNameHolder(LTYNB) );
+        /*ParmHolder<AtomType>::iterator it = prm.AT().GetParam( TypeNameHolder(LTYNB) );
         if (it == prm.AT().end()) {
           mprintf("Warning: Nonbond parameters defined for previously undefined type '%s'."
                           " Skipping.\n", LTYNB);
         } else {
           it->second.SetLJ().SetRadius( R );
           it->second.SetLJ().SetDepth( EDEP );
-        }
+        }*/
       }
     } else if (ljedit) {
       mprintf("DEBUG: LJedit: %s\n", ptr);
@@ -367,7 +367,19 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
       }
     }
     mprintf("\tUsing nonbonded parm set: %s\n", NBsets[nbsetidx].name_.c_str());
-  }
+    for (ParmHolder<LJparmType>::const_iterator it = NBsets[nbsetidx].LJ_.begin();
+                                                it != NBsets[nbsetidx].LJ_.end(); ++it)
+    {
+      ParmHolder<AtomType>::iterator at = prm.AT().GetParam( it->first );
+      if (at == prm.AT().end()) {
+        mprintf("Warning: Nonbond parameters defined for previously undefined type '%s'."
+                        " Skipping.\n", *(it->first[0]));
+      } else {
+        at->second.SetLJ().SetRadius( it->second.Radius() );
+        at->second.SetLJ().SetDepth( it->second.Depth() );
+      }
+    }
+  } // END nonbond parameters
 
   prm.Debug(); // TODO debug level
   infile.CloseFile();

From 535162010e35f8652f1689e8ae68094d3f580867 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 13 Nov 2023 14:05:26 -0500
Subject: [PATCH 0060/1492] Do equivalent NB params

---
 src/DataIO_AmberFF.cpp | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

diff --git a/src/DataIO_AmberFF.cpp b/src/DataIO_AmberFF.cpp
index a8f6b61a3b..ad8aeab231 100644
--- a/src/DataIO_AmberFF.cpp
+++ b/src/DataIO_AmberFF.cpp
@@ -81,8 +81,13 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
   }
   DataSet_Parameters& prm = static_cast<DataSet_Parameters&>( *ds ); 
 
+  // For files with > 1 set of NB params
   typedef std::vector<NonbondSet> NbSetArrayType;
   NbSetArrayType NBsets;
+  // For holding equivalent NB type names
+  typedef std::vector<NameType> Narray;
+  typedef std::vector<Narray> XNarray;
+  XNarray EquivalentNames;
 
   // Read title
   BufferedLine infile;
@@ -308,7 +313,14 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
       types.AddName( KT2 );
       prm.HB().AddParm(types, HB_ParmType(A, B, HCUT), false);
     } else if (section == NB_EQUIV) {
+      // EQUIVALENCING ATOM SYMBOLS FOR THE NON-BONDED 6-12 POTENTIAL PARAMETERS
+      // IORG , IEQV(I) , I = 1 , 19
+      // FORMAT(20(A2,2X))
       mprintf("DEBUG: Nonbond equiv: %s\n", ptr);
+      EquivalentNames.push_back( Narray() );
+      ArgList equiv_line( ptr, " " );
+      for (int iarg = 0; iarg != equiv_line.Nargs(); iarg++)
+        EquivalentNames.back().push_back( equiv_line[iarg] );
     } else if (section == NONBOND) {
       // ***** ONLY IF KINDNB .EQ. 'RE' *****
       // LTYNB , R , EDEP
@@ -379,6 +391,29 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
         at->second.SetLJ().SetDepth( it->second.Depth() );
       }
     }
+    // Do equivalent atoms.
+    for (XNarray::const_iterator equivAts = EquivalentNames.begin();
+                                 equivAts != EquivalentNames.end(); ++equivAts)
+    {
+      // First name is the type to copy TODO check size?
+      Narray::const_iterator typeName = equivAts->begin();
+      ParmHolder<AtomType>::const_iterator at0 = prm.AT().GetParam( *typeName );
+      if (at0 == prm.AT().end()) {
+        mprinterr("Error: Equivalent atom type '%s' not found.\n", *(*typeName) );
+        return 1;
+      }
+      ++typeName;
+      for (; typeName != equivAts->end(); ++typeName) {
+        ParmHolder<AtomType>::iterator at1 = prm.AT().GetParam( *typeName );
+        if (at1 == prm.AT().end()) {
+          mprinterr("Error: Equivalent atom type '%s' (base '%s') not found.\n", *(*typeName), *(at0->first[0]));
+          return 1;
+        }
+        mprintf("DEBUG: Equiv '%s' => '%s'\n", *(at0->first[0]), *(*typeName));
+        at1->second.SetLJ().SetRadius( at0->second.LJ().Radius() );
+        at1->second.SetLJ().SetDepth( at0->second.LJ().Depth() );
+      }
+    } // END loop over EquivalentNames
   } // END nonbond parameters
 
   prm.Debug(); // TODO debug level

From 3378980f11bef3c406f4597256f4bc017bb0e4d3 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 13 Nov 2023 14:09:40 -0500
Subject: [PATCH 0061/1492] Update 10-12 pairs

---
 src/ParameterSet.cpp   | 2 ++
 src/UpdateParameters.h | 1 +
 2 files changed, 3 insertions(+)

diff --git a/src/ParameterSet.cpp b/src/ParameterSet.cpp
index b35819b07c..3833c8fad3 100644
--- a/src/ParameterSet.cpp
+++ b/src/ParameterSet.cpp
@@ -107,6 +107,8 @@ int ParameterSet::UpdateParamSet(ParameterSet const& set1, UpdateCount& uc, int
   uc.nLJparamsUpdated_ = UpdateParameters< ParmHolder<NonbondType> >(set0.NB(), set1.NB(), "LJ A-B");
   // LJ 1-4 Pairs
   uc.nLJ14paramsUpdated_ = UpdateParameters< ParmHolder<NonbondType> >(set0.NB14(), set1.NB14(), "LJ A-B 1-4");
+  // HB LJ 10-12 Pairs
+  uc.nHBparamsUpdated_ = UpdateParameters< ParmHolder<HB_ParmType> >(set0.HB(), set1.HB(), "LJ HB 10-12");
 
   if (debugIn > 0) set0.Debug("newp.dat");
   return 0;
diff --git a/src/UpdateParameters.h b/src/UpdateParameters.h
index 8d9240fc0f..9dcd79b04c 100644
--- a/src/UpdateParameters.h
+++ b/src/UpdateParameters.h
@@ -14,6 +14,7 @@ static inline void PrintParmType(DihedralParmArray const& dpa) {
 }
 static inline void PrintParmType(AtomType const& at) { mprintf(" %12.4f %12.4f %12.4f\n", at.LJ().Radius(), at.LJ().Depth(), at.Mass()); }
 static inline void PrintParmType(NonbondType const& nb) { mprintf(" %12.4E %12.4E\n", nb.A(), nb.B()); }
+static inline void PrintParmType(HB_ParmType const& hb) { mprintf(" %12.4E %12.4E %12.4E\n", hb.Asol(), hb.Bsol(), hb.HBcut()); }
 
 /** Add update parameters.
   * \param0 Parameters to add to/update.

From 4a043d6779eb49af02db5f7fcc1850c8849f6b7e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 13 Nov 2023 14:19:56 -0500
Subject: [PATCH 0062/1492] Save parameter set name and NB set name

---
 src/DataIO_AmberFF.cpp |  2 ++
 src/ParameterSet.cpp   | 14 ++++++++++++++
 src/ParameterSet.h     |  7 +++++++
 3 files changed, 23 insertions(+)

diff --git a/src/DataIO_AmberFF.cpp b/src/DataIO_AmberFF.cpp
index ad8aeab231..52bc494f8e 100644
--- a/src/DataIO_AmberFF.cpp
+++ b/src/DataIO_AmberFF.cpp
@@ -102,6 +102,7 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
   }
   std::string title(ptr);
   mprintf("\tTitle: %s\n", title.c_str());
+  prm.SetParamSetName( title );
   // Read file
   bool ljedit = false;
   enum SectionType { ATYPE = 0, HYDROPHILIC, BOND, ANGLE, DIHEDRAL, IMPROPER, 
@@ -379,6 +380,7 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
       }
     }
     mprintf("\tUsing nonbonded parm set: %s\n", NBsets[nbsetidx].name_.c_str());
+    prm.SetNbParamName( NBsets[nbsetidx].name_ );
     for (ParmHolder<LJparmType>::const_iterator it = NBsets[nbsetidx].LJ_.begin();
                                                 it != NBsets[nbsetidx].LJ_.end(); ++it)
     {
diff --git a/src/ParameterSet.cpp b/src/ParameterSet.cpp
index 3833c8fad3..4a1b4defaf 100644
--- a/src/ParameterSet.cpp
+++ b/src/ParameterSet.cpp
@@ -18,6 +18,10 @@ size_t ParameterSet::DataSize() const {
 void ParameterSet::Debug(const char* fnameIn) const {
   CpptrajFile Out;
   Out.OpenWrite( fnameIn );
+  if (!name_.empty())
+    Out.Printf("Parameter set: %s\n", name_.c_str());
+  if (!NBname_.empty())
+    Out.Printf("Nonbond parameters name: %s\n", NBname_.c_str());
   Out.Printf("Atom Types:\n");
   Out.Printf("\t%6s %8s %12s %12s %12s %12s\n", "Name", "TypeIdx", "Radius", "Depth", "Mass", "Polar.");
   for (ParmHolder<AtomType>::const_iterator at = atomTypes_.begin(); at != atomTypes_.end(); ++at) {
@@ -127,3 +131,13 @@ int ParameterSet::AddHydrophilicAtomType(NameType const& atype) {
   hydrophilicAtomTypes_.push_back( atype );
   return 0;
 }
+
+/** Set parameter set name. */
+void ParameterSet::SetParamSetName(std::string const& nameIn) {
+  name_ = nameIn;
+}
+
+/** Set nonbond parameter set name. */
+void ParameterSet::SetNbParamName(std::string const& nameIn) {
+  NBname_ = nameIn;
+}
diff --git a/src/ParameterSet.h b/src/ParameterSet.h
index 42964ca3eb..59f71ada8b 100644
--- a/src/ParameterSet.h
+++ b/src/ParameterSet.h
@@ -56,11 +56,18 @@ class ParameterSet {
     int UpdateParamSet(ParameterSet const&, UpdateCount&, int);
     /// Add hydrophilic atom type
     int AddHydrophilicAtomType(NameType const&);
+    /// Set parameter set name
+    void SetParamSetName(std::string const&);
+    /// Set nonbond parameter set name
+    void SetNbParamName(std::string const&);
     /// \return Size in memory in bytes
     size_t DataSize() const;
   private:
     typedef std::vector<NameType> NsetType;
 
+    std::string name_;                     ///< Parameter set name
+    std::string NBname_;                   ///< Nonbond set name
+
     ParmHolder<AtomType> atomTypes_;       ///< Atom types
     ParmHolder<NonbondType> nbParm_;       ///< Lennard-Jones 6-12 A-B parameters
     ParmHolder<NonbondType> nb14Parm_;     ///< LJ 6-12 A-B parameters for 1-4 interactions

From 2b32914765d69a0450182b314984d421403c0b91 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 13 Nov 2023 15:17:40 -0500
Subject: [PATCH 0063/1492] Fix up the LJEDIT section processing (not finished
 yet). Fix detection of 1-4 params when included with NONBOND.

---
 src/DataIO_AmberFF.cpp | 90 +++++++++++++++++++++++++++++-------------
 src/cpptrajdepend      |  2 +-
 2 files changed, 64 insertions(+), 28 deletions(-)

diff --git a/src/DataIO_AmberFF.cpp b/src/DataIO_AmberFF.cpp
index 52bc494f8e..aa54b7936f 100644
--- a/src/DataIO_AmberFF.cpp
+++ b/src/DataIO_AmberFF.cpp
@@ -2,6 +2,7 @@
 #include "CpptrajStdio.h"
 #include "BufferedLine.h"
 #include "DataSet_Parameters.h"
+#include "StringRoutines.h"
 #include <cstdio> // sscanf
 
 /// CONSTRUCTOR
@@ -104,9 +105,8 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
   mprintf("\tTitle: %s\n", title.c_str());
   prm.SetParamSetName( title );
   // Read file
-  bool ljedit = false;
   enum SectionType { ATYPE = 0, HYDROPHILIC, BOND, ANGLE, DIHEDRAL, IMPROPER, 
-                     LJ1012, NB_EQUIV, NONBOND, UNKNOWN };
+                     LJ1012, NB_EQUIV, NONBOND, LJEDIT, UNKNOWN };
   SectionType section = ATYPE;
   ptr = infile.Line();
   while (ptr != 0) {
@@ -126,8 +126,7 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
             mprintf("END\n");
             section = UNKNOWN;
           } else if (nbline == "LJEDIT") {
-            ljedit = true;
-            section = UNKNOWN;
+            section = LJEDIT;
           } // Otherwise assume another nonbond section
         } else {
           mprintf("SECTION %i change to %i\n", (int)section, (int)section + 1);
@@ -326,25 +325,62 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
       // ***** ONLY IF KINDNB .EQ. 'RE' *****
       // LTYNB , R , EDEP
       mprintf("DEBUG: Nonbond: %s\n", ptr);
-      char LTYNB[MAXSYMLEN];
-      double R, EDEP;
-      double R14, E14;
-      int nscan = sscanf(ptr, "%s %lf %lf %lf %lf", LTYNB, &R, &EDEP, &R14, &E14);
-      
-      if (nscan == 3 || nscan == 5) {
-        // symbol, rmin, epsilon
-        NBsets.back().LJ_.AddParm( TypeNameHolder(LTYNB), LJparmType(R, EDEP), false );
-        /*ParmHolder<AtomType>::iterator it = prm.AT().GetParam( TypeNameHolder(LTYNB) );
-        if (it == prm.AT().end()) {
-          mprintf("Warning: Nonbond parameters defined for previously undefined type '%s'."
-                          " Skipping.\n", LTYNB);
-        } else {
-          it->second.SetLJ().SetRadius( R );
-          it->second.SetLJ().SetDepth( EDEP );
-        }*/
+      //char LTYNB[MAXSYMLEN];
+      //double R, EDEP;
+      //double R14, E14;
+      // This section is a little tricky. Apparently CHARMM-style Amber FF
+      // files can have 14 LJ params here. Try to detect this.
+      ArgList nbargs( ptr, " " );
+      if (nbargs.Nargs() < 3) {
+        mprinterr("Error: Expected at least TYPE, R, DEPTH, got %i elements.\n", nbargs.Nargs());
+        return 1;
       }
-    } else if (ljedit) {
+      bool has_14 = false;
+      if (nbargs.Nargs() >= 5) {
+        if (validDouble( nbargs[3] ) && validDouble( nbargs[4] )) {
+          has_14 = true;
+        }
+      }
+      if (has_14) mprintf("DEBUG: NB HAS CHARMM.\n");
+      double R = convertToDouble( nbargs[1] );
+      double EDEP = convertToDouble( nbargs[2] );
+      NBsets.back().LJ_.AddParm( TypeNameHolder(nbargs[0]), LJparmType(R, EDEP), false );
+      //int nscan = sscanf(ptr, "%s %lf %lf %lf %lf", LTYNB, &R, &EDEP, &R14, &E14);
+
+      //if (nscan >= 5) {
+      //  // symbol, rmin, epsilon
+      //  NBsets.back().LJ_.AddParm( TypeNameHolder(LTYNB), LJparmType(R, EDEP), false );
+      //  /*ParmHolder<AtomType>::iterator it = prm.AT().GetParam( TypeNameHolder(LTYNB) );
+      //  if (it == prm.AT().end()) {
+      //    mprintf("Warning: Nonbond parameters defined for previously undefined type '%s'."
+      //                    " Skipping.\n", LTYNB);
+      //  } else {
+      //    it->second.SetLJ().SetRadius( R );
+      //    it->second.SetLJ().SetDepth( EDEP );
+      //  }*/
+      //}
+    } else if (section == LJEDIT) {
       mprintf("DEBUG: LJedit: %s\n", ptr);
+      // Lennard-Jones sigma and epsilon of the first atom type when it
+      // interacts with anything under the normal rules, then the sigma
+      // and epsilon of the second atom type when it interacts with the first.
+      char AT1[MAXSYMLEN], AT2[MAXSYMLEN];
+      double sig1, eps1, sig2, eps2;
+      int nscan = sscanf(ptr, "%s %s %lf %lf %lf %lf", AT1, AT2, &sig1, &eps1, &sig2, &eps2);
+      if (nscan != 6) {
+        mprinterr("Error: Expected AT1, AT2, SIG1, EPS1, SIG2, EPS2, got %i elements.\n", nscan);
+        return 1;
+      }
+      LJparmType LJ1(sig1, eps1);
+      LJparmType LJ2(sig2, eps2);
+      ParmHolder<AtomType>::iterator it = prm.AT().GetParam( TypeNameHolder(AT1) );
+      if (it == prm.AT().end()) {
+        mprinterr("Error: Off-diagonal nonbond parameters defined for previously undefined type '%s'.\n",
+                  AT1);
+        return 1;
+      }
+      it->second.SetLJ().SetRadius( LJ1.Radius() );
+      it->second.SetLJ().SetDepth( LJ1.Depth() );
     }
       
     ptr = infile.Line();
@@ -386,12 +422,12 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
     {
       ParmHolder<AtomType>::iterator at = prm.AT().GetParam( it->first );
       if (at == prm.AT().end()) {
-        mprintf("Warning: Nonbond parameters defined for previously undefined type '%s'."
-                        " Skipping.\n", *(it->first[0]));
-      } else {
-        at->second.SetLJ().SetRadius( it->second.Radius() );
-        at->second.SetLJ().SetDepth( it->second.Depth() );
-      }
+        mprinterr("Error: Nonbond parameters defined for previously undefined type '%s'.\n",
+                  *(it->first[0]));
+        return 1;
+      } 
+      at->second.SetLJ().SetRadius( it->second.Radius() );
+      at->second.SetLJ().SetDepth( it->second.Depth() );
     }
     // Do equivalent atoms.
     for (XNarray::const_iterator equivAts = EquivalentNames.begin();
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 46acb9fc99..59dfdcab32 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -204,7 +204,7 @@ DataFileList.o : DataFileList.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h A
 DataFilter.o : DataFilter.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_integer.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO.o : DataIO.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_AmberEne.o : DataIO_AmberEne.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberEne.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_AmberFF.o : DataIO_AmberFF.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberFF.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_AmberFF.o : DataIO_AmberFF.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberFF.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_AmberLib.o : DataIO_AmberLib.cpp ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberLib.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_AmberPrep.o : DataIO_AmberPrep.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberPrep.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_CCP4.o : DataIO_CCP4.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ByteRoutines.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CCP4.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h

From 16b331e552a936434ab552c664a2630f3effd203 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 13 Nov 2023 15:24:51 -0500
Subject: [PATCH 0064/1492] Set off-diagonal

---
 src/DataIO_AmberFF.cpp | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/src/DataIO_AmberFF.cpp b/src/DataIO_AmberFF.cpp
index aa54b7936f..292095f463 100644
--- a/src/DataIO_AmberFF.cpp
+++ b/src/DataIO_AmberFF.cpp
@@ -373,6 +373,7 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
       }
       LJparmType LJ1(sig1, eps1);
       LJparmType LJ2(sig2, eps2);
+      // Set type 1
       ParmHolder<AtomType>::iterator it = prm.AT().GetParam( TypeNameHolder(AT1) );
       if (it == prm.AT().end()) {
         mprinterr("Error: Off-diagonal nonbond parameters defined for previously undefined type '%s'.\n",
@@ -381,6 +382,12 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
       }
       it->second.SetLJ().SetRadius( LJ1.Radius() );
       it->second.SetLJ().SetDepth( LJ1.Depth() );
+      // Set off-diagonal for type1-type2
+      TypeNameHolder types(2);
+      types.AddName( AT1 );
+      types.AddName( AT2 );
+      // FIXME different combine rules?
+      prm.NB().AddParm(types, LJ1.Combine_LB(LJ2), false);
     }
       
     ptr = infile.Line();

From 225a13f5f95a5388e24b66657126aec2f32bfd2d Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 13 Nov 2023 15:43:36 -0500
Subject: [PATCH 0065/1492] Ensure off-diagonal mods are processed after the
 main NB params

---
 src/DataIO_AmberFF.cpp | 57 +++++++++++++++++++++++++++++-------------
 1 file changed, 40 insertions(+), 17 deletions(-)

diff --git a/src/DataIO_AmberFF.cpp b/src/DataIO_AmberFF.cpp
index 292095f463..b99d3df322 100644
--- a/src/DataIO_AmberFF.cpp
+++ b/src/DataIO_AmberFF.cpp
@@ -63,6 +63,21 @@ class NonbondSet {
     ParmHolder<LJparmType> LJ_; ///< Hold LJ 6-12 parameters
 };
 
+/// Hold an off-diagonal NB modification
+class OffdiagNB {
+  public:
+    OffdiagNB(NameType const& AT1, NameType const& AT2, double sig1, double eps1, double sig2, double eps2) :
+      types_(2), LJ1_(sig1, eps1), LJ2_(sig2, eps2)
+    {
+      types_.AddName(AT1);
+      types_.AddName(AT2);
+    }
+
+    TypeNameHolder types_;
+    LJparmType LJ1_;
+    LJparmType LJ2_;
+};
+
 // DataIO_AmberFF::ReadData()
 int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::string const& dsname)
 {
@@ -89,6 +104,9 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
   typedef std::vector<NameType> Narray;
   typedef std::vector<Narray> XNarray;
   XNarray EquivalentNames;
+  // For holding off-diagonal mods
+  typedef std::vector<OffdiagNB> Oarray;
+  Oarray Offdiag;
 
   // Read title
   BufferedLine infile;
@@ -371,27 +389,12 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
         mprinterr("Error: Expected AT1, AT2, SIG1, EPS1, SIG2, EPS2, got %i elements.\n", nscan);
         return 1;
       }
-      LJparmType LJ1(sig1, eps1);
-      LJparmType LJ2(sig2, eps2);
-      // Set type 1
-      ParmHolder<AtomType>::iterator it = prm.AT().GetParam( TypeNameHolder(AT1) );
-      if (it == prm.AT().end()) {
-        mprinterr("Error: Off-diagonal nonbond parameters defined for previously undefined type '%s'.\n",
-                  AT1);
-        return 1;
-      }
-      it->second.SetLJ().SetRadius( LJ1.Radius() );
-      it->second.SetLJ().SetDepth( LJ1.Depth() );
-      // Set off-diagonal for type1-type2
-      TypeNameHolder types(2);
-      types.AddName( AT1 );
-      types.AddName( AT2 );
-      // FIXME different combine rules?
-      prm.NB().AddParm(types, LJ1.Combine_LB(LJ2), false);
+      Offdiag.push_back( OffdiagNB(AT1, AT2, sig1, eps1, sig2, eps2) );
     }
       
     ptr = infile.Line();
   } // END loop over file.
+
   // Deal with nonbond and equivalence
   if (!NBsets.empty()) {
     int nbsetidx = 0;
@@ -461,6 +464,26 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
     } // END loop over EquivalentNames
   } // END nonbond parameters
 
+  // Do off diagonal NB mods
+  if (!Offdiag.empty()) {
+    for (Oarray::const_iterator od = Offdiag.begin(); od != Offdiag.end(); ++od)
+    {
+      mprintf("DEBUG: Off diag %s %s\n", *(od->types_[0]), *(od->types_[1]));
+      // Set type 1
+      ParmHolder<AtomType>::iterator it = prm.AT().GetParam( od->types_[0] );
+      if (it == prm.AT().end()) {
+        mprinterr("Error: Off-diagonal nonbond parameters defined for previously undefined type '%s'.\n",
+                  *(od->types_[0]));
+        return 1;
+      }
+      it->second.SetLJ().SetRadius( od->LJ1_.Radius() );
+      it->second.SetLJ().SetDepth( od->LJ1_.Depth() );
+      // Set off-diagonal for type1-type2
+      // FIXME different combine rules?
+      prm.NB().AddParm(od->types_, od->LJ1_.Combine_LB(od->LJ2_), false);
+    }
+  } // END off-diagonal NB mods
+
   prm.Debug(); // TODO debug level
   infile.CloseFile();
   return 0;

From d7a7ac3fb36b708b016fa7cb61c82a5afdef8e78 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 13 Nov 2023 15:49:02 -0500
Subject: [PATCH 0066/1492] Update info printout

---
 src/DataSet_Parameters.cpp | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/src/DataSet_Parameters.cpp b/src/DataSet_Parameters.cpp
index 45535f063b..200aa79ad1 100644
--- a/src/DataSet_Parameters.cpp
+++ b/src/DataSet_Parameters.cpp
@@ -18,13 +18,15 @@ size_t DataSet_Parameters::Size() const {
 void DataSet_Parameters::Info() const {
   if (Size() > 0) {
     mprintf(" (");
-    if (AT().size() > 0) mprintf(" types=%zu", AT().size());
-    if (NB().size() > 0) mprintf(" LJ pairs=%zu", NB().size());
-    if (BP().size() > 0) mprintf(" bnd=%zu", BP().size());
-    if (AP().size() > 0) mprintf(" ang=%zu", AP().size());
-    if (UB().size() > 0) mprintf(" UB=%zu", UB().size());
-    if (DP().size() > 0) mprintf(" dih=%zu", DP().size());
-    if (IP().size() > 0) mprintf(" imp=%zu", IP().size());
+    if (AT().size() > 0)   mprintf(" types=%zu", AT().size());
+    if (NB().size() > 0)   mprintf(" LJ pairs=%zu", NB().size());
+    if (NB14().size() > 0) mprintf(" LJ14 pairs=%zu", NB14().size());
+    if (HB().size() > 0)   mprintf(" HB pairs=%zu", HB().size());
+    if (BP().size() > 0)   mprintf(" bnd=%zu", BP().size());
+    if (AP().size() > 0)   mprintf(" ang=%zu", AP().size());
+    if (UB().size() > 0)   mprintf(" UB=%zu", UB().size());
+    if (DP().size() > 0)   mprintf(" dih=%zu", DP().size());
+    if (IP().size() > 0)   mprintf(" imp=%zu", IP().size());
     mprintf(" )");
   }
 }

From 60a5d8daf73181dae2ab7409851f74f97ef7a427 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 13 Nov 2023 20:05:42 -0500
Subject: [PATCH 0067/1492] Start write function

---
 src/DataIO_AmberFF.cpp | 30 +++++++++++++++++++++++++++++-
 src/DataIO_AmberFF.h   |  1 +
 2 files changed, 30 insertions(+), 1 deletion(-)

diff --git a/src/DataIO_AmberFF.cpp b/src/DataIO_AmberFF.cpp
index b99d3df322..3284881bb0 100644
--- a/src/DataIO_AmberFF.cpp
+++ b/src/DataIO_AmberFF.cpp
@@ -8,7 +8,8 @@
 /// CONSTRUCTOR
 DataIO_AmberFF::DataIO_AmberFF()
 {
-
+  SetValid( DataSet::PARAMETERS );
+  // TODO Topology too?
 }
 
 // DataIO_AmberFF::ID_DataFormat()
@@ -505,6 +506,33 @@ int DataIO_AmberFF::processWriteArgs(ArgList& argIn)
 // DataIO_AmberFF::WriteData()
 int DataIO_AmberFF::WriteData(FileName const& fname, DataSetList const& dsl)
 {
+  std::vector<DataSet_Parameters*> toWrite;
+  for (DataSetList::const_iterator it = dsl.begin(); it != dsl.end(); ++it)
+  {
+    if ( (*it)->Type() == DataSet::PARAMETERS )
+      toWrite.push_back( (DataSet_Parameters*)(*it) );
+  }
+  if (toWrite.empty()) {
+    mprinterr("Error: No parameter sets to write.\n");
+    return 1;
+  } else if (toWrite.size() == 1) {
+    return writeParameterSet( *(toWrite.front()) );
+  } else {
+    // Create a combined parameter set
+    ParameterSet prm;
+    for (std::vector<DataSet_Parameters*>::const_iterator it = toWrite.begin();
+                                                          it != toWrite.end(); ++it)
+    {
+      ParameterSet::UpdateCount UC;
+      prm.UpdateParamSet( *(*it), UC, debug_ );
+    }
+    return writeParameterSet( prm );
+  }
 
   return 1;
 }
+
+int DataIO_AmberFF::writeParameterSet(ParameterSet const& prm) const {
+
+  return 0;
+}
diff --git a/src/DataIO_AmberFF.h b/src/DataIO_AmberFF.h
index 5d0af59568..b5c6ea4386 100644
--- a/src/DataIO_AmberFF.h
+++ b/src/DataIO_AmberFF.h
@@ -15,6 +15,7 @@ class DataIO_AmberFF : public DataIO {
     bool ID_DataFormat(CpptrajFile&);
   private:
     static int read_symbols(const char*, std::vector<std::string>&, int);
+    int writeParameterSet(ParameterSet const&) const;
 
     std::string nbsetname_; ///< Nonbonded parameter set name to use
 };

From a41a2424c65ef960ce9b6a71f8d9ad8fcff4a7d0 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 13 Nov 2023 20:17:34 -0500
Subject: [PATCH 0068/1492] Start a write routine

---
 src/DataFile.cpp       |  1 +
 src/DataIO_AmberFF.cpp | 15 ++++++++++++---
 src/DataIO_AmberFF.h   |  2 +-
 src/ParameterSet.h     |  2 ++
 4 files changed, 16 insertions(+), 4 deletions(-)

diff --git a/src/DataFile.cpp b/src/DataFile.cpp
index b2e6bbaa59..2189eeba3e 100644
--- a/src/DataFile.cpp
+++ b/src/DataFile.cpp
@@ -142,6 +142,7 @@ const FileTypes::KeyToken DataFile::DF_WriteKeyArray[] = {
   { CHARMMRTFPRM, "charmmrtfprm", ".prm" },
   { PEAKS,        "peaks",  ".peaks" },
   { NETCDFDATA,   "netcdf", ".nc" },
+  { AMBERFF,      "amberff",".parm"},
   { UNKNOWN_DATA, 0,        0        }
 };
 
diff --git a/src/DataIO_AmberFF.cpp b/src/DataIO_AmberFF.cpp
index 3284881bb0..04f7f0ef46 100644
--- a/src/DataIO_AmberFF.cpp
+++ b/src/DataIO_AmberFF.cpp
@@ -516,7 +516,7 @@ int DataIO_AmberFF::WriteData(FileName const& fname, DataSetList const& dsl)
     mprinterr("Error: No parameter sets to write.\n");
     return 1;
   } else if (toWrite.size() == 1) {
-    return writeParameterSet( *(toWrite.front()) );
+    return writeParameterSet( fname, *(toWrite.front()) );
   } else {
     // Create a combined parameter set
     ParameterSet prm;
@@ -526,13 +526,22 @@ int DataIO_AmberFF::WriteData(FileName const& fname, DataSetList const& dsl)
       ParameterSet::UpdateCount UC;
       prm.UpdateParamSet( *(*it), UC, debug_ );
     }
-    return writeParameterSet( prm );
+    return writeParameterSet( fname, prm );
   }
 
   return 1;
 }
 
-int DataIO_AmberFF::writeParameterSet(ParameterSet const& prm) const {
+int DataIO_AmberFF::writeParameterSet(FileName const& fname, ParameterSet const& prm) const {
+  CpptrajFile outfile;
+  if (outfile.OpenWrite(fname)) return 1;
+
+  std::string title;
+  if (prm.ParamSetName().empty())
+    title.assign("Parameters written from CPPTRAJ");
+  else
+    title = prm.ParamSetName();
+  outfile.Printf("%s\n", title.c_str());
 
   return 0;
 }
diff --git a/src/DataIO_AmberFF.h b/src/DataIO_AmberFF.h
index b5c6ea4386..631b5baac2 100644
--- a/src/DataIO_AmberFF.h
+++ b/src/DataIO_AmberFF.h
@@ -15,7 +15,7 @@ class DataIO_AmberFF : public DataIO {
     bool ID_DataFormat(CpptrajFile&);
   private:
     static int read_symbols(const char*, std::vector<std::string>&, int);
-    int writeParameterSet(ParameterSet const&) const;
+    int writeParameterSet(FileName const&, ParameterSet const&) const;
 
     std::string nbsetname_; ///< Nonbonded parameter set name to use
 };
diff --git a/src/ParameterSet.h b/src/ParameterSet.h
index 59f71ada8b..3cfd233e2d 100644
--- a/src/ParameterSet.h
+++ b/src/ParameterSet.h
@@ -30,6 +30,8 @@ class ParameterSet {
     ParmHolder<DihedralParmType> const& IP() const { return impParm_;   }
     DihedralParmHolder const& DP()           const { return dihParm_;   }
     ParmHolder<HB_ParmType> const& HB()      const { return HBparm_;    }
+    std::string const& ParamSetName()        const { return name_;      }
+    std::string const& NbParamName()         const { return NBname_;    }
 
     void Debug(const char*) const;
     void Debug() const { return Debug(""); }

From ce1b3e1d27e09fd1c934f3f7859ddf7a9a462d63 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 16 Nov 2023 11:53:44 -0500
Subject: [PATCH 0069/1492] Print atom type symbols

---
 src/DataIO_AmberFF.cpp | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/src/DataIO_AmberFF.cpp b/src/DataIO_AmberFF.cpp
index 04f7f0ef46..2940550a90 100644
--- a/src/DataIO_AmberFF.cpp
+++ b/src/DataIO_AmberFF.cpp
@@ -535,13 +535,22 @@ int DataIO_AmberFF::WriteData(FileName const& fname, DataSetList const& dsl)
 int DataIO_AmberFF::writeParameterSet(FileName const& fname, ParameterSet const& prm) const {
   CpptrajFile outfile;
   if (outfile.OpenWrite(fname)) return 1;
-
+  // 1 - Title
   std::string title;
   if (prm.ParamSetName().empty())
     title.assign("Parameters written from CPPTRAJ");
   else
     title = prm.ParamSetName();
   outfile.Printf("%s\n", title.c_str());
+  // 2 - Atom symbols and masses
+  for (ParmHolder<AtomType>::const_iterator at = prm.AT().begin(); at != prm.AT().end(); ++at)
+  {
+    std::string asym = at->first[0].Truncated();
+    if (asym.size() > 2)
+      mprintf("Warning: Atom symbol %s is larger than 2 characters, which breaks Amber FF format.\n");
+
+    outfile.Printf("%-2s  %10.2f %10.2f\n", asym.c_str(), at->second.Mass(), at->second.Polarizability());
+  }
 
   return 0;
 }

From d46b6eb8001b023ba8fbeb538c342da403ac304b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 16 Nov 2023 13:24:27 -0500
Subject: [PATCH 0070/1492] Still trying to figure out if Amber FF files
 actually have a format or not

---
 src/DataIO_AmberFF.cpp | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/src/DataIO_AmberFF.cpp b/src/DataIO_AmberFF.cpp
index 2940550a90..1f8a2045d6 100644
--- a/src/DataIO_AmberFF.cpp
+++ b/src/DataIO_AmberFF.cpp
@@ -548,8 +548,16 @@ int DataIO_AmberFF::writeParameterSet(FileName const& fname, ParameterSet const&
     std::string asym = at->first[0].Truncated();
     if (asym.size() > 2)
       mprintf("Warning: Atom symbol %s is larger than 2 characters, which breaks Amber FF format.\n");
+    outfile.Printf("%-2s", asym.c_str());
+    if (at->second.Mass() < 10.0)
+      outfile.Printf(" %-10.3f", at->second.Mass());
+    else if (at->second.Mass() < 100.0)
+      outfile.Printf(" %-10.2f", at->second.Mass());
+    else
+      outfile.Printf(" %-10.1f", at->second.Mass());
+    outfile.Printf(" %10.3f\n", at->second.Polarizability());
 
-    outfile.Printf("%-2s  %10.2f %10.2f\n", asym.c_str(), at->second.Mass(), at->second.Polarizability());
+    //outfile.Printf("%-2s  %-10.2f %-10.2f\n", asym.c_str(), at->second.Mass(), at->second.Polarizability());
   }
 
   return 0;

From 86b5419cea1021a76f1c2eba473bd005df805b80 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 16 Nov 2023 17:38:47 -0500
Subject: [PATCH 0071/1492] Ensure vars are initialized

---
 src/DataIO_AmberFF.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/DataIO_AmberFF.cpp b/src/DataIO_AmberFF.cpp
index 1f8a2045d6..ac3152225f 100644
--- a/src/DataIO_AmberFF.cpp
+++ b/src/DataIO_AmberFF.cpp
@@ -188,8 +188,8 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
       // Format (A2,2X,F10.2x,f10.2)
       mprintf("DEBUG: Atype: %s\n", ptr);
       char kndsym[MAXSYMLEN];
-      double amass;
-      double atpol;
+      double amass = 0;
+      double atpol = 0;
       int nscan = sscanf(ptr, "%s %lf %lf", kndsym, &amass, &atpol);
       ParameterHolders::RetType ret;
       if (nscan == 3) {

From 0356f9ddde4697df5cc600a89e0c0f128d36f418 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 16 Nov 2023 17:41:52 -0500
Subject: [PATCH 0072/1492] Add check

---
 src/DataIO_AmberFF.cpp | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/src/DataIO_AmberFF.cpp b/src/DataIO_AmberFF.cpp
index ac3152225f..a7ffa145aa 100644
--- a/src/DataIO_AmberFF.cpp
+++ b/src/DataIO_AmberFF.cpp
@@ -175,7 +175,11 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
         if (NBsets.empty())
           ptr = infile.Line();
         char nb_label[MAXSYMLEN], nb_kind[MAXSYMLEN];
-        sscanf(ptr, "%s %s", nb_label, nb_kind);
+        int nscan = sscanf(ptr, "%s %s", nb_label, nb_kind);
+        if (nscan != 2) {
+          mprinterr("Error: Expected nonbond label, nonbond kind, got %i elements.\n", nscan);
+          return 1;
+        }
         mprintf("DEBUG: NB label= %s  NB kind = %s\n", nb_label, nb_kind);
         if (nb_kind[0] != 'R' || nb_kind[1] != 'E') {
           mprinterr("Error: Nonbond parameters are not of type 'RE' (Rmin, Epsilon).\n");

From 6ea220cf9901573cfc2f353ec7def83cbe9936b5 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 19 Nov 2023 16:53:53 -0500
Subject: [PATCH 0073/1492] Start makeing a separate Amber param file class

---
 src/AmberParamFile.cpp | 490 +++++++++++++++++++++++++++++++++++++++++
 src/AmberParamFile.h   |  18 ++
 2 files changed, 508 insertions(+)
 create mode 100644 src/AmberParamFile.cpp
 create mode 100644 src/AmberParamFile.h

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
new file mode 100644
index 0000000000..6a22bb91af
--- /dev/null
+++ b/src/AmberParamFile.cpp
@@ -0,0 +1,490 @@
+#include "AmberParamFile.h"
+#include "ArgList.h"
+#include "CpptrajStdio.h"
+#include "BufferedLine.h"
+#include "ParameterHolders.h"
+#include "StringRoutines.h"
+#include "ParameterSet.h"
+#include <cstdio> // sscanf
+
+/// CONSTRUCTOR
+AmberParamFile::AmberParamFile() {}
+
+/** Read symbols delimited by - and space. */
+int AmberParamFile::read_symbols(const char* ptrIn, std::vector<std::string>& symbols, int nsymbols)
+{
+  int isymbol = 0;
+  bool char_has_been_read = false;
+  for (const char* ptr = ptrIn; *ptr != '\0'; ++ptr)
+  {
+    if (*ptr == '-') {
+      isymbol++;
+      char_has_been_read = false;
+    } else if (*ptr == ' ' && isymbol + 1 == nsymbols && char_has_been_read) {
+      return (ptr - ptrIn);
+    } else {
+      symbols[isymbol] += *ptr;
+      if (*ptr != ' ') char_has_been_read = true;
+    }
+  }
+  return -1;
+}
+
+/// Hold a set of nonbonded parameters
+class NonbondSet {
+  public:
+    NonbondSet(std::string const& n) : name_(n) {}
+
+    std::string name_;          ///< Name of set parameters
+    ParmHolder<LJparmType> LJ_; ///< Hold LJ 6-12 parameters
+};
+
+/// Hold an off-diagonal NB modification
+class OffdiagNB {
+  public:
+    OffdiagNB(NameType const& AT1, NameType const& AT2, double sig1, double eps1, double sig2, double eps2) :
+      types_(2), LJ1_(sig1, eps1), LJ2_(sig2, eps2)
+    {
+      types_.AddName(AT1);
+      types_.AddName(AT2);
+    }
+
+    TypeNameHolder types_;
+    LJparmType LJ1_;
+    LJparmType LJ2_;
+};
+
+// DataIO_AmberFF::ReadData()
+int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
+                               std::string const& nbsetnameIn, int debugIn) const
+{
+  static const int MAXSYMLEN = 16;
+
+  // For files with > 1 set of NB params
+  typedef std::vector<NonbondSet> NbSetArrayType;
+  NbSetArrayType NBsets;
+  // For holding equivalent NB type names
+  typedef std::vector<NameType> Narray;
+  typedef std::vector<Narray> XNarray;
+  XNarray EquivalentNames;
+  // For holding off-diagonal mods
+  typedef std::vector<OffdiagNB> Oarray;
+  Oarray Offdiag;
+
+  // Read title
+  BufferedLine infile;
+  if (infile.OpenFileRead( fname )) {
+    mprinterr("Error: Could not open file '%s' as Amber FF.\n", fname.full());
+    return 1;
+  }
+  const char* ptr = infile.Line();
+  if (ptr == 0) {
+    mprinterr("Error: Could not read anything from Amber FF file %s\n", fname.full());
+    return 1;
+  }
+  std::string title(ptr);
+  mprintf("\tTitle: %s\n", title.c_str());
+  prm.SetParamSetName( title );
+  // Read file
+  enum SectionType { ATYPE = 0, HYDROPHILIC, BOND, ANGLE, DIHEDRAL, IMPROPER, 
+                     LJ1012, NB_EQUIV, NONBOND, LJEDIT, UNKNOWN };
+  SectionType section = ATYPE;
+  ptr = infile.Line();
+  while (ptr != 0) {
+    // Advance to first non-space char
+    while (*ptr == ' ' && *ptr != '\0') ++ptr;
+    mprintf("DEBUG: First char: %c (%i)\n", *ptr, (int)*ptr);
+    if (*ptr == '\0') {
+      // Section Change
+      if (section != UNKNOWN) {
+        if (section == NONBOND) {
+          // Do a lookahead to see if there are multiple NB sets.
+          // It will either be another set, END, or LJEDIT
+          ptr = infile.Line();
+          while (*ptr == ' ' && *ptr != '\0') ++ptr;
+          std::string nbline(ptr);
+          if (nbline == "END") {
+            mprintf("END\n");
+            section = UNKNOWN;
+          } else if (nbline == "LJEDIT") {
+            section = LJEDIT;
+          } // Otherwise assume another nonbond section
+        } else {
+          mprintf("SECTION %i change to %i\n", (int)section, (int)section + 1);
+          section = (SectionType)((int)section + 1);
+        }
+      }
+      // Special cases
+      if (section == HYDROPHILIC) {
+        // Special case: hydrophilic atom types. One line.
+        // FORMAT(20(A2,2X))
+        ptr = infile.Line();
+        mprintf("DEBUG: Hydrophilic: %s\n", ptr);
+        // Take advantage of the fact that we expect whitespace-delimiters
+        ArgList hsymbols( ptr, " " );
+        for (int iarg = 0; iarg != hsymbols.Nargs(); ++iarg)
+          prm.AddHydrophilicAtomType( NameType( hsymbols[iarg] ) );
+        section = (SectionType)((int)section + 1);
+        // Look ahead. Older parm files have the hydrophilic section delimited
+        // with a newline.
+        ptr = infile.Line();
+        while (*ptr == ' ' && *ptr != '\0') ++ptr;
+        if (*ptr != '\0') continue;
+      } else if (section == NONBOND) {
+        // Special case: first read the line.
+        // LABEL , KINDNB
+        // FORMAT(A4,6X,A2)
+        if (NBsets.empty())
+          ptr = infile.Line();
+        char nb_label[MAXSYMLEN], nb_kind[MAXSYMLEN];
+        int nscan = sscanf(ptr, "%s %s", nb_label, nb_kind);
+        if (nscan != 2) {
+          mprinterr("Error: Expected nonbond label, nonbond kind, got %i elements.\n", nscan);
+          return 1;
+        }
+        mprintf("DEBUG: NB label= %s  NB kind = %s\n", nb_label, nb_kind);
+        if (nb_kind[0] != 'R' || nb_kind[1] != 'E') {
+          mprinterr("Error: Nonbond parameters are not of type 'RE' (Rmin, Epsilon).\n");
+          return 1;
+        }
+        NBsets.push_back( NonbondSet( std::string(nb_label) ) );
+      }
+    } else if (section == ATYPE) {
+      // Input for atom symbols and masses
+      // Format (A2,2X,F10.2x,f10.2)
+      mprintf("DEBUG: Atype: %s\n", ptr);
+      char kndsym[MAXSYMLEN];
+      double amass = 0;
+      double atpol = 0;
+      int nscan = sscanf(ptr, "%s %lf %lf", kndsym, &amass, &atpol);
+      ParameterHolders::RetType ret;
+      if (nscan == 3) {
+        ret = prm.AT().AddParm( TypeNameHolder(kndsym),
+                                AtomType(amass, atpol),
+                                true );
+      } else if (nscan == 2) {
+        // Only mass
+        ret = prm.AT().AddParm( TypeNameHolder(kndsym),
+                                AtomType(amass),
+                                true );
+      } else {
+        mprinterr("Error: Expected atom type, mass, polarizability, got only %i columns.\n", nscan);
+        return 1;
+      }
+      if (ret == ParameterHolders::UPDATED)
+        mprintf("Warning: Redefining atom type %s\n", kndsym);
+    } else if (section == BOND) {
+      // Bond parameters
+      // IBT , JBT , RK , REQ
+      // FORMAT(A2,1X,A2,2F10.2)
+      mprintf("DEBUG: Bond: %s\n", ptr);
+      std::vector<std::string> symbols(2);
+      int pos = read_symbols(ptr, symbols, 2);
+      if (pos < 0) {
+        mprinterr("Error: Could not read symbols for bond from %s\n", ptr);
+        return 1;
+      }
+      mprintf("DEBUG: %s %s '%s'\n", symbols[0].c_str(), symbols[1].c_str(), ptr+pos);
+      double RK, REQ;
+      int nscan = sscanf(ptr+pos, "%lf %lf", &RK, &REQ);
+      if (nscan != 2) {
+        mprinterr("Error: Expected RK, REQ, got only %i elements\n", nscan);
+        return 1;
+      }
+      TypeNameHolder types(2);
+      types.AddName( symbols[0] );
+      types.AddName( symbols[1] );
+      prm.BP().AddParm(types, BondParmType(RK, REQ), false);
+    } else if (section == ANGLE) {
+      // Angle parameters
+      // ITT , JTT , KTT , TK , TEQ
+      // FORMAT(A2,1X,A2,1X,A2,2F10.2)
+      mprintf("DEBUG: Angle: %s\n", ptr);
+      std::vector<std::string> symbols(3);
+      int pos = read_symbols(ptr, symbols, 3);
+      if (pos < 0) {
+        mprinterr("Error: Could not read symbols for angle from %s\n", ptr);
+        return 1;
+      }
+      mprintf("DEBUG: %s %s %s '%s'\n", symbols[0].c_str(), symbols[1].c_str(), symbols[2].c_str(), ptr+pos);
+      double TK, TEQ;
+      int nscan = sscanf(ptr+pos, "%lf %lf", &TK, &TEQ);
+      if (nscan != 2) {
+        mprinterr("Error: Expected TK, TEQ, got only %i elements\n", nscan);
+        return 1;
+      }
+      TypeNameHolder types(3);
+      types.AddName( symbols[0] );
+      types.AddName( symbols[1] );
+      types.AddName( symbols[2] );
+      prm.AP().AddParm(types, AngleParmType(TK, TEQ), false);
+    } else if (section == DIHEDRAL) {
+      // Dihedral parameters
+      // IPT , JPT , KPT , LPT , IDIVF , PK , PHASE , PN
+      // FORMAT(A2,1X,A2,1X,A2,1X,A2,I4,3F15.2)
+      // If IPT .eq. 'X ' .and. LPT .eq. 'X ' then any dihedrals in the
+      // system involving the atoms "JPT" and and "KPT" are assigned 
+      // the same parameters.  This is called the general dihedral type
+      // and is of the form "X "-"JPT"-"KPT"-"X ".
+      // IDIVF is the factor by which the torsional barrier is divided.
+      // Consult Weiner, et al., JACS 106:765 (1984) p. 769 for
+      // details. Basically, the actual torsional potential is
+      //   (PK/IDIVF) * (1 + cos(PN*phi - PHASE))
+      mprintf("DEBUG: Dihedral: %s\n", ptr);
+      std::vector<std::string> symbols(4);
+      int pos = read_symbols(ptr, symbols, 4);
+      if (pos < 0) {
+        mprinterr("Error: Could not read symbols for dihedral from %s\n", ptr);
+        return 1;
+      }
+      mprintf("DEBUG: %s %s %s %s '%s'\n", symbols[0].c_str(), symbols[1].c_str(), symbols[2].c_str(), symbols[3].c_str(), ptr+pos);
+      int IDIVF;
+      double PK, PHASE, PN;
+      int nscan = sscanf(ptr+pos, "%i %lf %lf %lf", &IDIVF, &PK, &PHASE, &PN);
+      if (nscan != 4) {
+        mprinterr("Error: Expected IDIVF, PK, PHASE, PN, got only %i elements\n", nscan);
+        return 1;
+      }
+      TypeNameHolder types(4);
+      types.AddName( symbols[0] );
+      types.AddName( symbols[1] );
+      types.AddName( symbols[2] );
+      types.AddName( symbols[3] );
+      prm.DP().AddParm(types, DihedralParmType(PK / (double)IDIVF, PN, PHASE), false);
+    } else if (section == IMPROPER) {
+      // Improper parameters
+      // IPT , JPT , KPT , LPT , IDIVF , PK , PHASE , PN
+      // FORMAT(A2,1X,A2,1X,A2,1X,A2,I4,3F15.2)
+      mprintf("DEBUG: Improper: %s\n", ptr);
+      std::vector<std::string> symbols(4);
+      int pos = read_symbols(ptr, symbols, 4);
+      if (pos < 0) {
+        mprinterr("Error: Could not read symbols for improper from %s\n", ptr);
+        return 1;
+      }
+      mprintf("DEBUG: %s %s %s %s '%s'\n", symbols[0].c_str(), symbols[1].c_str(), symbols[2].c_str(), symbols[3].c_str(), ptr+pos);
+      double PK, PHASE, PN;
+      int nscan = sscanf(ptr+pos, "%lf %lf %lf", &PK, &PHASE, &PN);
+      if (nscan != 3) {
+        mprinterr("Error: Expected PK, PHASE, PN, got only %i elements\n", nscan);
+        return 1;
+      }
+      TypeNameHolder types(4);
+      types.AddName( symbols[0] );
+      types.AddName( symbols[1] );
+      types.AddName( symbols[2] );
+      types.AddName( symbols[3] );
+      prm.IP().AddParm(types, DihedralParmType(PK, PN, PHASE), false);
+    } else if (section == LJ1012) {
+      // Lennard-Jones 10-12 hydrogen bonding term.
+      // According to the docs, the format should be:
+      // KT1 , KT2 , A , B , ASOLN , BSOLN , HCUT , IC
+      // FORMAT(2X,A2,2X,A2,2x,5F10.2,I2)
+      // In practive (in e.g. parm91.dat), the actual format appears to be:
+      // KT1, KT2, A, B, HCUT
+      char KT1[MAXSYMLEN], KT2[MAXSYMLEN];
+      double A, B, HCUT;
+      //double ASOLN, BSOLN, HCUT;
+      //int IC;
+      mprintf("DEBUG: LJ 10-12: %s\n", ptr);
+      //int nscan = sscanf(ptr, "%s %s %lf %lf %lf %lf %lf %i\n",
+      int nscan = sscanf(ptr, "%s %s %lf %lf %lf", KT1, KT2, &A, &B, &HCUT);
+      if (nscan < 5) {
+        mprinterr("Error: Expected at least KT1, KT2, A, B, HCUT, got only %i elements\n", nscan);
+        return 1;
+      }
+      TypeNameHolder types(2);
+      types.AddName( KT1 );
+      types.AddName( KT2 );
+      prm.HB().AddParm(types, HB_ParmType(A, B, HCUT), false);
+    } else if (section == NB_EQUIV) {
+      // EQUIVALENCING ATOM SYMBOLS FOR THE NON-BONDED 6-12 POTENTIAL PARAMETERS
+      // IORG , IEQV(I) , I = 1 , 19
+      // FORMAT(20(A2,2X))
+      mprintf("DEBUG: Nonbond equiv: %s\n", ptr);
+      EquivalentNames.push_back( Narray() );
+      ArgList equiv_line( ptr, " " );
+      for (int iarg = 0; iarg != equiv_line.Nargs(); iarg++)
+        EquivalentNames.back().push_back( equiv_line[iarg] );
+    } else if (section == NONBOND) {
+      // ***** ONLY IF KINDNB .EQ. 'RE' *****
+      // LTYNB , R , EDEP
+      mprintf("DEBUG: Nonbond: %s\n", ptr);
+      //char LTYNB[MAXSYMLEN];
+      //double R, EDEP;
+      //double R14, E14;
+      // This section is a little tricky. Apparently CHARMM-style Amber FF
+      // files can have 14 LJ params here. Try to detect this.
+      ArgList nbargs( ptr, " " );
+      if (nbargs.Nargs() < 3) {
+        mprinterr("Error: Expected at least TYPE, R, DEPTH, got %i elements.\n", nbargs.Nargs());
+        return 1;
+      }
+      bool has_14 = false;
+      if (nbargs.Nargs() >= 5) {
+        if (validDouble( nbargs[3] ) && validDouble( nbargs[4] )) {
+          has_14 = true;
+        }
+      }
+      if (has_14) mprintf("DEBUG: NB HAS CHARMM.\n");
+      double R = convertToDouble( nbargs[1] );
+      double EDEP = convertToDouble( nbargs[2] );
+      NBsets.back().LJ_.AddParm( TypeNameHolder(nbargs[0]), LJparmType(R, EDEP), false );
+      //int nscan = sscanf(ptr, "%s %lf %lf %lf %lf", LTYNB, &R, &EDEP, &R14, &E14);
+
+      //if (nscan >= 5) {
+      //  // symbol, rmin, epsilon
+      //  NBsets.back().LJ_.AddParm( TypeNameHolder(LTYNB), LJparmType(R, EDEP), false );
+      //  /*ParmHolder<AtomType>::iterator it = prm.AT().GetParam( TypeNameHolder(LTYNB) );
+      //  if (it == prm.AT().end()) {
+      //    mprintf("Warning: Nonbond parameters defined for previously undefined type '%s'."
+      //                    " Skipping.\n", LTYNB);
+      //  } else {
+      //    it->second.SetLJ().SetRadius( R );
+      //    it->second.SetLJ().SetDepth( EDEP );
+      //  }*/
+      //}
+    } else if (section == LJEDIT) {
+      mprintf("DEBUG: LJedit: %s\n", ptr);
+      // Lennard-Jones sigma and epsilon of the first atom type when it
+      // interacts with anything under the normal rules, then the sigma
+      // and epsilon of the second atom type when it interacts with the first.
+      char AT1[MAXSYMLEN], AT2[MAXSYMLEN];
+      double sig1, eps1, sig2, eps2;
+      int nscan = sscanf(ptr, "%s %s %lf %lf %lf %lf", AT1, AT2, &sig1, &eps1, &sig2, &eps2);
+      if (nscan != 6) {
+        mprinterr("Error: Expected AT1, AT2, SIG1, EPS1, SIG2, EPS2, got %i elements.\n", nscan);
+        return 1;
+      }
+      Offdiag.push_back( OffdiagNB(AT1, AT2, sig1, eps1, sig2, eps2) );
+    }
+      
+    ptr = infile.Line();
+  } // END loop over file.
+
+  // Deal with nonbond and equivalence
+  if (!NBsets.empty()) {
+    int nbsetidx = 0;
+    if (NBsets.size() > 1 || !nbsetnameIn.empty()) {
+      // Choose from multiple nbsets
+      if (nbsetnameIn.empty()) {
+        mprinterr("Error: Parm set in file '%s' contains %zu nonbonded parameter sets\n"
+                  "Error:  but no set has been specified.\n", fname.full(), NBsets.size());
+        mprinterr("Error: Need to specify one of");
+        for (NbSetArrayType::const_iterator it = NBsets.begin(); it != NBsets.end(); ++it)
+          mprinterr(" %s", it->name_.c_str());
+        mprinterr("\n");
+      } else {
+        nbsetidx = -1;
+        for (NbSetArrayType::const_iterator it = NBsets.begin(); it != NBsets.end(); ++it) {
+          if (it->name_ == nbsetnameIn) {
+            nbsetidx = it - NBsets.begin();
+            break;
+          }
+        }
+        if (nbsetidx < 0) {
+          mprinterr("Error: Nonbonded set '%s' not found.\n", nbsetnameIn.c_str());
+          mprinterr("Error: Need to specify one of");
+          for (NbSetArrayType::const_iterator it = NBsets.begin(); it != NBsets.end(); ++it)
+            mprinterr(" %s", it->name_.c_str());
+          mprinterr("\n");
+          return 1;
+        }
+      }
+    }
+    mprintf("\tUsing nonbonded parm set: %s\n", NBsets[nbsetidx].name_.c_str());
+    prm.SetNbParamName( NBsets[nbsetidx].name_ );
+    for (ParmHolder<LJparmType>::const_iterator it = NBsets[nbsetidx].LJ_.begin();
+                                                it != NBsets[nbsetidx].LJ_.end(); ++it)
+    {
+      ParmHolder<AtomType>::iterator at = prm.AT().GetParam( it->first );
+      if (at == prm.AT().end()) {
+        mprinterr("Error: Nonbond parameters defined for previously undefined type '%s'.\n",
+                  *(it->first[0]));
+        return 1;
+      } 
+      at->second.SetLJ().SetRadius( it->second.Radius() );
+      at->second.SetLJ().SetDepth( it->second.Depth() );
+    }
+    // Do equivalent atoms.
+    for (XNarray::const_iterator equivAts = EquivalentNames.begin();
+                                 equivAts != EquivalentNames.end(); ++equivAts)
+    {
+      // First name is the type to copy TODO check size?
+      Narray::const_iterator typeName = equivAts->begin();
+      ParmHolder<AtomType>::const_iterator at0 = prm.AT().GetParam( *typeName );
+      if (at0 == prm.AT().end()) {
+        mprinterr("Error: Equivalent atom type '%s' not found.\n", *(*typeName) );
+        return 1;
+      }
+      ++typeName;
+      for (; typeName != equivAts->end(); ++typeName) {
+        ParmHolder<AtomType>::iterator at1 = prm.AT().GetParam( *typeName );
+        if (at1 == prm.AT().end()) {
+          mprinterr("Error: Equivalent atom type '%s' (base '%s') not found.\n", *(*typeName), *(at0->first[0]));
+          return 1;
+        }
+        mprintf("DEBUG: Equiv '%s' => '%s'\n", *(at0->first[0]), *(*typeName));
+        at1->second.SetLJ().SetRadius( at0->second.LJ().Radius() );
+        at1->second.SetLJ().SetDepth( at0->second.LJ().Depth() );
+      }
+    } // END loop over EquivalentNames
+  } // END nonbond parameters
+
+  // Do off diagonal NB mods
+  if (!Offdiag.empty()) {
+    for (Oarray::const_iterator od = Offdiag.begin(); od != Offdiag.end(); ++od)
+    {
+      mprintf("DEBUG: Off diag %s %s\n", *(od->types_[0]), *(od->types_[1]));
+      // Set type 1
+      ParmHolder<AtomType>::iterator it = prm.AT().GetParam( od->types_[0] );
+      if (it == prm.AT().end()) {
+        mprinterr("Error: Off-diagonal nonbond parameters defined for previously undefined type '%s'.\n",
+                  *(od->types_[0]));
+        return 1;
+      }
+      it->second.SetLJ().SetRadius( od->LJ1_.Radius() );
+      it->second.SetLJ().SetDepth( od->LJ1_.Depth() );
+      // Set off-diagonal for type1-type2
+      // FIXME different combine rules?
+      prm.NB().AddParm(od->types_, od->LJ1_.Combine_LB(od->LJ2_), false);
+    }
+  } // END off-diagonal NB mods
+
+  prm.Debug(); // TODO debug level
+  infile.CloseFile();
+  return 0;
+}
+
+// DataIO_AmberFF::WriteData()
+int AmberParamFile::WriteParams(ParameterSet& prm, FileName const& fname, int debugIn) const
+{
+  CpptrajFile outfile;
+  if (outfile.OpenWrite(fname)) return 1;
+  // 1 - Title
+  std::string title;
+  if (prm.ParamSetName().empty())
+    title.assign("Parameters written from CPPTRAJ");
+  else
+    title = prm.ParamSetName();
+  outfile.Printf("%s\n", title.c_str());
+  // 2 - Atom symbols and masses
+  for (ParmHolder<AtomType>::const_iterator at = prm.AT().begin(); at != prm.AT().end(); ++at)
+  {
+    std::string asym = at->first[0].Truncated();
+    if (asym.size() > 2)
+      mprintf("Warning: Atom symbol %s is larger than 2 characters, which breaks Amber FF format.\n");
+    outfile.Printf("%-2s", asym.c_str());
+    if (at->second.Mass() < 10.0)
+      outfile.Printf(" %-10.3f", at->second.Mass());
+    else if (at->second.Mass() < 100.0)
+      outfile.Printf(" %-10.2f", at->second.Mass());
+    else
+      outfile.Printf(" %-10.1f", at->second.Mass());
+    outfile.Printf(" %10.3f\n", at->second.Polarizability());
+
+    //outfile.Printf("%-2s  %-10.2f %-10.2f\n", asym.c_str(), at->second.Mass(), at->second.Polarizability());
+  }
+
+  return 0;
+}
diff --git a/src/AmberParamFile.h b/src/AmberParamFile.h
new file mode 100644
index 0000000000..a533e44adb
--- /dev/null
+++ b/src/AmberParamFile.h
@@ -0,0 +1,18 @@
+#ifndef INC_AMBERPARAMFILE_H
+#define INC_AMBERPARAMFILE_H
+#include <vector>
+#include <string>
+class ParameterSet;
+//class BufferedLine;
+class FileName;
+/// Used to read in Amber parameters from Amber FF/FRCMOD file.
+class AmberParamFile {
+  public:
+    AmberParamFile();
+    int ReadParams(ParameterSet&, FileName const&, std::string const&, int) const;
+    int WriteParams(ParameterSet&, FileName const&, int) const;
+  private:
+    static int read_symbols(const char*, std::vector<std::string>&, int);
+    //int ReadInput(std::string&, BufferedLine&) const;
+};
+#endif

From 9c6f5b5db4ac3ab057effdaae70ed9aefaea93d4 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 19 Nov 2023 16:55:35 -0500
Subject: [PATCH 0074/1492] Update dependencies

---
 src/cpptrajdepend | 1 +
 src/cpptrajfiles  | 1 +
 2 files changed, 2 insertions(+)

diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 59dfdcab32..855dcd91ec 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -91,6 +91,7 @@ Action_Volmap.o : Action_Volmap.cpp Action.h ActionState.h Action_Volmap.h ArgLi
 Action_Volume.o : Action_Volume.cpp Action.h ActionState.h Action_Volume.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Action_Watershell.o : Action_Watershell.cpp Action.h ActionState.h Action_Watershell.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h ImageRoutines.h ImageTypes.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h cuda_kernels/kernel_wrappers.cuh
 Action_XtalSymm.o : Action_XtalSymm.cpp Action.h ActionState.h Action_XtalSymm.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SpaceGroup.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+AmberParamFile.o : AmberParamFile.cpp AmberParamFile.h ArgList.h AtomType.h BufferedLine.h Constants.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h StringRoutines.h TypeNameHolder.h
 AnalysisList.o : AnalysisList.cpp ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Analysis_AmdBias.o : Analysis_AmdBias.cpp ActionState.h Analysis.h AnalysisState.h Analysis_AmdBias.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Analysis_AutoCorr.o : Analysis_AutoCorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_AutoCorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
diff --git a/src/cpptrajfiles b/src/cpptrajfiles
index dd53d39862..8c7fb6c8a2 100644
--- a/src/cpptrajfiles
+++ b/src/cpptrajfiles
@@ -94,6 +94,7 @@ COMMON_SOURCES= \
         Action_Volume.cpp \
         Action_Watershell.cpp \
         Action_XtalSymm.cpp \
+        AmberParamFile.cpp \
         AnalysisList.cpp \
         Analysis_AmdBias.cpp \
         Analysis_AutoCorr.cpp \

From e647d4183c0e1748f9ed4d65e5f6f425d3feca39 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 19 Nov 2023 19:24:35 -0500
Subject: [PATCH 0075/1492] Use AmberParamFile

---
 src/DataIO_AmberFF.cpp | 482 +----------------------------------------
 src/DataIO_AmberFF.h   |   2 -
 src/cpptrajdepend      |   2 +-
 3 files changed, 10 insertions(+), 476 deletions(-)

diff --git a/src/DataIO_AmberFF.cpp b/src/DataIO_AmberFF.cpp
index a7ffa145aa..07fc9487ef 100644
--- a/src/DataIO_AmberFF.cpp
+++ b/src/DataIO_AmberFF.cpp
@@ -1,9 +1,7 @@
 #include "DataIO_AmberFF.h"
 #include "CpptrajStdio.h"
-#include "BufferedLine.h"
+#include "AmberParamFile.h"
 #include "DataSet_Parameters.h"
-#include "StringRoutines.h"
-#include <cstdio> // sscanf
 
 /// CONSTRUCTOR
 DataIO_AmberFF::DataIO_AmberFF()
@@ -35,54 +33,9 @@ int DataIO_AmberFF::processReadArgs(ArgList& argIn)
   return 0;
 }
 
-/** Read symbols delimited by - and space. */
-int DataIO_AmberFF::read_symbols(const char* ptrIn, std::vector<std::string>& symbols, int nsymbols)
-{
-  int isymbol = 0;
-  bool char_has_been_read = false;
-  for (const char* ptr = ptrIn; *ptr != '\0'; ++ptr)
-  {
-    if (*ptr == '-') {
-      isymbol++;
-      char_has_been_read = false;
-    } else if (*ptr == ' ' && isymbol + 1 == nsymbols && char_has_been_read) {
-      return (ptr - ptrIn);
-    } else {
-      symbols[isymbol] += *ptr;
-      if (*ptr != ' ') char_has_been_read = true;
-    }
-  }
-  return -1;
-}
-
-/// Hold a set of nonbonded parameters
-class NonbondSet {
-  public:
-    NonbondSet(std::string const& n) : name_(n) {}
-
-    std::string name_;          ///< Name of set parameters
-    ParmHolder<LJparmType> LJ_; ///< Hold LJ 6-12 parameters
-};
-
-/// Hold an off-diagonal NB modification
-class OffdiagNB {
-  public:
-    OffdiagNB(NameType const& AT1, NameType const& AT2, double sig1, double eps1, double sig2, double eps2) :
-      types_(2), LJ1_(sig1, eps1), LJ2_(sig2, eps2)
-    {
-      types_.AddName(AT1);
-      types_.AddName(AT2);
-    }
-
-    TypeNameHolder types_;
-    LJparmType LJ1_;
-    LJparmType LJ2_;
-};
-
 // DataIO_AmberFF::ReadData()
 int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::string const& dsname)
 {
-  static const int MAXSYMLEN = 16;
   // Allocate data set
   MetaData md( dsname );
   DataSet* ds = dsl.CheckForSet( md );
@@ -98,400 +51,13 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
   }
   DataSet_Parameters& prm = static_cast<DataSet_Parameters&>( *ds ); 
 
-  // For files with > 1 set of NB params
-  typedef std::vector<NonbondSet> NbSetArrayType;
-  NbSetArrayType NBsets;
-  // For holding equivalent NB type names
-  typedef std::vector<NameType> Narray;
-  typedef std::vector<Narray> XNarray;
-  XNarray EquivalentNames;
-  // For holding off-diagonal mods
-  typedef std::vector<OffdiagNB> Oarray;
-  Oarray Offdiag;
-
-  // Read title
-  BufferedLine infile;
-  if (infile.OpenFileRead( fname )) {
-    mprinterr("Error: Could not open file '%s' as Amber FF.\n", fname.full());
-    return 1;
-  }
-  const char* ptr = infile.Line();
-  if (ptr == 0) {
-    mprinterr("Error: Could not read anything from Amber FF file %s\n", fname.full());
-    return 1;
+  AmberParamFile infile;
+  int err = infile.ReadParams(prm, fname, nbsetname_, debug_);
+  if (err != 0) {
+    mprinterr("Error: Could not read '%s'\n", fname.full());
   }
-  std::string title(ptr);
-  mprintf("\tTitle: %s\n", title.c_str());
-  prm.SetParamSetName( title );
-  // Read file
-  enum SectionType { ATYPE = 0, HYDROPHILIC, BOND, ANGLE, DIHEDRAL, IMPROPER, 
-                     LJ1012, NB_EQUIV, NONBOND, LJEDIT, UNKNOWN };
-  SectionType section = ATYPE;
-  ptr = infile.Line();
-  while (ptr != 0) {
-    // Advance to first non-space char
-    while (*ptr == ' ' && *ptr != '\0') ++ptr;
-    mprintf("DEBUG: First char: %c (%i)\n", *ptr, (int)*ptr);
-    if (*ptr == '\0') {
-      // Section Change
-      if (section != UNKNOWN) {
-        if (section == NONBOND) {
-          // Do a lookahead to see if there are multiple NB sets.
-          // It will either be another set, END, or LJEDIT
-          ptr = infile.Line();
-          while (*ptr == ' ' && *ptr != '\0') ++ptr;
-          std::string nbline(ptr);
-          if (nbline == "END") {
-            mprintf("END\n");
-            section = UNKNOWN;
-          } else if (nbline == "LJEDIT") {
-            section = LJEDIT;
-          } // Otherwise assume another nonbond section
-        } else {
-          mprintf("SECTION %i change to %i\n", (int)section, (int)section + 1);
-          section = (SectionType)((int)section + 1);
-        }
-      }
-      // Special cases
-      if (section == HYDROPHILIC) {
-        // Special case: hydrophilic atom types. One line.
-        // FORMAT(20(A2,2X))
-        ptr = infile.Line();
-        mprintf("DEBUG: Hydrophilic: %s\n", ptr);
-        // Take advantage of the fact that we expect whitespace-delimiters
-        ArgList hsymbols( ptr, " " );
-        for (int iarg = 0; iarg != hsymbols.Nargs(); ++iarg)
-          prm.AddHydrophilicAtomType( NameType( hsymbols[iarg] ) );
-        section = (SectionType)((int)section + 1);
-        // Look ahead. Older parm files have the hydrophilic section delimited
-        // with a newline.
-        ptr = infile.Line();
-        while (*ptr == ' ' && *ptr != '\0') ++ptr;
-        if (*ptr != '\0') continue;
-      } else if (section == NONBOND) {
-        // Special case: first read the line.
-        // LABEL , KINDNB
-        // FORMAT(A4,6X,A2)
-        if (NBsets.empty())
-          ptr = infile.Line();
-        char nb_label[MAXSYMLEN], nb_kind[MAXSYMLEN];
-        int nscan = sscanf(ptr, "%s %s", nb_label, nb_kind);
-        if (nscan != 2) {
-          mprinterr("Error: Expected nonbond label, nonbond kind, got %i elements.\n", nscan);
-          return 1;
-        }
-        mprintf("DEBUG: NB label= %s  NB kind = %s\n", nb_label, nb_kind);
-        if (nb_kind[0] != 'R' || nb_kind[1] != 'E') {
-          mprinterr("Error: Nonbond parameters are not of type 'RE' (Rmin, Epsilon).\n");
-          return 1;
-        }
-        NBsets.push_back( NonbondSet( std::string(nb_label) ) );
-      }
-    } else if (section == ATYPE) {
-      // Input for atom symbols and masses
-      // Format (A2,2X,F10.2x,f10.2)
-      mprintf("DEBUG: Atype: %s\n", ptr);
-      char kndsym[MAXSYMLEN];
-      double amass = 0;
-      double atpol = 0;
-      int nscan = sscanf(ptr, "%s %lf %lf", kndsym, &amass, &atpol);
-      ParameterHolders::RetType ret;
-      if (nscan == 3) {
-        ret = prm.AT().AddParm( TypeNameHolder(kndsym),
-                                AtomType(amass, atpol),
-                                true );
-      } else if (nscan == 2) {
-        // Only mass
-        ret = prm.AT().AddParm( TypeNameHolder(kndsym),
-                                AtomType(amass),
-                                true );
-      } else {
-        mprinterr("Error: Expected atom type, mass, polarizability, got only %i columns.\n", nscan);
-        return 1;
-      }
-      if (ret == ParameterHolders::UPDATED)
-        mprintf("Warning: Redefining atom type %s\n", kndsym);
-    } else if (section == BOND) {
-      // Bond parameters
-      // IBT , JBT , RK , REQ
-      // FORMAT(A2,1X,A2,2F10.2)
-      mprintf("DEBUG: Bond: %s\n", ptr);
-      std::vector<std::string> symbols(2);
-      int pos = read_symbols(ptr, symbols, 2);
-      if (pos < 0) {
-        mprinterr("Error: Could not read symbols for bond from %s\n", ptr);
-        return 1;
-      }
-      mprintf("DEBUG: %s %s '%s'\n", symbols[0].c_str(), symbols[1].c_str(), ptr+pos);
-      double RK, REQ;
-      int nscan = sscanf(ptr+pos, "%lf %lf", &RK, &REQ);
-      if (nscan != 2) {
-        mprinterr("Error: Expected RK, REQ, got only %i elements\n", nscan);
-        return 1;
-      }
-      TypeNameHolder types(2);
-      types.AddName( symbols[0] );
-      types.AddName( symbols[1] );
-      prm.BP().AddParm(types, BondParmType(RK, REQ), false);
-    } else if (section == ANGLE) {
-      // Angle parameters
-      // ITT , JTT , KTT , TK , TEQ
-      // FORMAT(A2,1X,A2,1X,A2,2F10.2)
-      mprintf("DEBUG: Angle: %s\n", ptr);
-      std::vector<std::string> symbols(3);
-      int pos = read_symbols(ptr, symbols, 3);
-      if (pos < 0) {
-        mprinterr("Error: Could not read symbols for angle from %s\n", ptr);
-        return 1;
-      }
-      mprintf("DEBUG: %s %s %s '%s'\n", symbols[0].c_str(), symbols[1].c_str(), symbols[2].c_str(), ptr+pos);
-      double TK, TEQ;
-      int nscan = sscanf(ptr+pos, "%lf %lf", &TK, &TEQ);
-      if (nscan != 2) {
-        mprinterr("Error: Expected TK, TEQ, got only %i elements\n", nscan);
-        return 1;
-      }
-      TypeNameHolder types(3);
-      types.AddName( symbols[0] );
-      types.AddName( symbols[1] );
-      types.AddName( symbols[2] );
-      prm.AP().AddParm(types, AngleParmType(TK, TEQ), false);
-    } else if (section == DIHEDRAL) {
-      // Dihedral parameters
-      // IPT , JPT , KPT , LPT , IDIVF , PK , PHASE , PN
-      // FORMAT(A2,1X,A2,1X,A2,1X,A2,I4,3F15.2)
-      // If IPT .eq. 'X ' .and. LPT .eq. 'X ' then any dihedrals in the
-      // system involving the atoms "JPT" and and "KPT" are assigned 
-      // the same parameters.  This is called the general dihedral type
-      // and is of the form "X "-"JPT"-"KPT"-"X ".
-      // IDIVF is the factor by which the torsional barrier is divided.
-      // Consult Weiner, et al., JACS 106:765 (1984) p. 769 for
-      // details. Basically, the actual torsional potential is
-      //   (PK/IDIVF) * (1 + cos(PN*phi - PHASE))
-      mprintf("DEBUG: Dihedral: %s\n", ptr);
-      std::vector<std::string> symbols(4);
-      int pos = read_symbols(ptr, symbols, 4);
-      if (pos < 0) {
-        mprinterr("Error: Could not read symbols for dihedral from %s\n", ptr);
-        return 1;
-      }
-      mprintf("DEBUG: %s %s %s %s '%s'\n", symbols[0].c_str(), symbols[1].c_str(), symbols[2].c_str(), symbols[3].c_str(), ptr+pos);
-      int IDIVF;
-      double PK, PHASE, PN;
-      int nscan = sscanf(ptr+pos, "%i %lf %lf %lf", &IDIVF, &PK, &PHASE, &PN);
-      if (nscan != 4) {
-        mprinterr("Error: Expected IDIVF, PK, PHASE, PN, got only %i elements\n", nscan);
-        return 1;
-      }
-      TypeNameHolder types(4);
-      types.AddName( symbols[0] );
-      types.AddName( symbols[1] );
-      types.AddName( symbols[2] );
-      types.AddName( symbols[3] );
-      prm.DP().AddParm(types, DihedralParmType(PK / (double)IDIVF, PN, PHASE), false);
-    } else if (section == IMPROPER) {
-      // Improper parameters
-      // IPT , JPT , KPT , LPT , IDIVF , PK , PHASE , PN
-      // FORMAT(A2,1X,A2,1X,A2,1X,A2,I4,3F15.2)
-      mprintf("DEBUG: Improper: %s\n", ptr);
-      std::vector<std::string> symbols(4);
-      int pos = read_symbols(ptr, symbols, 4);
-      if (pos < 0) {
-        mprinterr("Error: Could not read symbols for improper from %s\n", ptr);
-        return 1;
-      }
-      mprintf("DEBUG: %s %s %s %s '%s'\n", symbols[0].c_str(), symbols[1].c_str(), symbols[2].c_str(), symbols[3].c_str(), ptr+pos);
-      double PK, PHASE, PN;
-      int nscan = sscanf(ptr+pos, "%lf %lf %lf", &PK, &PHASE, &PN);
-      if (nscan != 3) {
-        mprinterr("Error: Expected PK, PHASE, PN, got only %i elements\n", nscan);
-        return 1;
-      }
-      TypeNameHolder types(4);
-      types.AddName( symbols[0] );
-      types.AddName( symbols[1] );
-      types.AddName( symbols[2] );
-      types.AddName( symbols[3] );
-      prm.IP().AddParm(types, DihedralParmType(PK, PN, PHASE), false);
-    } else if (section == LJ1012) {
-      // Lennard-Jones 10-12 hydrogen bonding term.
-      // According to the docs, the format should be:
-      // KT1 , KT2 , A , B , ASOLN , BSOLN , HCUT , IC
-      // FORMAT(2X,A2,2X,A2,2x,5F10.2,I2)
-      // In practive (in e.g. parm91.dat), the actual format appears to be:
-      // KT1, KT2, A, B, HCUT
-      char KT1[MAXSYMLEN], KT2[MAXSYMLEN];
-      double A, B, HCUT;
-      //double ASOLN, BSOLN, HCUT;
-      //int IC;
-      mprintf("DEBUG: LJ 10-12: %s\n", ptr);
-      //int nscan = sscanf(ptr, "%s %s %lf %lf %lf %lf %lf %i\n",
-      int nscan = sscanf(ptr, "%s %s %lf %lf %lf", KT1, KT2, &A, &B, &HCUT);
-      if (nscan < 5) {
-        mprinterr("Error: Expected at least KT1, KT2, A, B, HCUT, got only %i elements\n", nscan);
-        return 1;
-      }
-      TypeNameHolder types(2);
-      types.AddName( KT1 );
-      types.AddName( KT2 );
-      prm.HB().AddParm(types, HB_ParmType(A, B, HCUT), false);
-    } else if (section == NB_EQUIV) {
-      // EQUIVALENCING ATOM SYMBOLS FOR THE NON-BONDED 6-12 POTENTIAL PARAMETERS
-      // IORG , IEQV(I) , I = 1 , 19
-      // FORMAT(20(A2,2X))
-      mprintf("DEBUG: Nonbond equiv: %s\n", ptr);
-      EquivalentNames.push_back( Narray() );
-      ArgList equiv_line( ptr, " " );
-      for (int iarg = 0; iarg != equiv_line.Nargs(); iarg++)
-        EquivalentNames.back().push_back( equiv_line[iarg] );
-    } else if (section == NONBOND) {
-      // ***** ONLY IF KINDNB .EQ. 'RE' *****
-      // LTYNB , R , EDEP
-      mprintf("DEBUG: Nonbond: %s\n", ptr);
-      //char LTYNB[MAXSYMLEN];
-      //double R, EDEP;
-      //double R14, E14;
-      // This section is a little tricky. Apparently CHARMM-style Amber FF
-      // files can have 14 LJ params here. Try to detect this.
-      ArgList nbargs( ptr, " " );
-      if (nbargs.Nargs() < 3) {
-        mprinterr("Error: Expected at least TYPE, R, DEPTH, got %i elements.\n", nbargs.Nargs());
-        return 1;
-      }
-      bool has_14 = false;
-      if (nbargs.Nargs() >= 5) {
-        if (validDouble( nbargs[3] ) && validDouble( nbargs[4] )) {
-          has_14 = true;
-        }
-      }
-      if (has_14) mprintf("DEBUG: NB HAS CHARMM.\n");
-      double R = convertToDouble( nbargs[1] );
-      double EDEP = convertToDouble( nbargs[2] );
-      NBsets.back().LJ_.AddParm( TypeNameHolder(nbargs[0]), LJparmType(R, EDEP), false );
-      //int nscan = sscanf(ptr, "%s %lf %lf %lf %lf", LTYNB, &R, &EDEP, &R14, &E14);
-
-      //if (nscan >= 5) {
-      //  // symbol, rmin, epsilon
-      //  NBsets.back().LJ_.AddParm( TypeNameHolder(LTYNB), LJparmType(R, EDEP), false );
-      //  /*ParmHolder<AtomType>::iterator it = prm.AT().GetParam( TypeNameHolder(LTYNB) );
-      //  if (it == prm.AT().end()) {
-      //    mprintf("Warning: Nonbond parameters defined for previously undefined type '%s'."
-      //                    " Skipping.\n", LTYNB);
-      //  } else {
-      //    it->second.SetLJ().SetRadius( R );
-      //    it->second.SetLJ().SetDepth( EDEP );
-      //  }*/
-      //}
-    } else if (section == LJEDIT) {
-      mprintf("DEBUG: LJedit: %s\n", ptr);
-      // Lennard-Jones sigma and epsilon of the first atom type when it
-      // interacts with anything under the normal rules, then the sigma
-      // and epsilon of the second atom type when it interacts with the first.
-      char AT1[MAXSYMLEN], AT2[MAXSYMLEN];
-      double sig1, eps1, sig2, eps2;
-      int nscan = sscanf(ptr, "%s %s %lf %lf %lf %lf", AT1, AT2, &sig1, &eps1, &sig2, &eps2);
-      if (nscan != 6) {
-        mprinterr("Error: Expected AT1, AT2, SIG1, EPS1, SIG2, EPS2, got %i elements.\n", nscan);
-        return 1;
-      }
-      Offdiag.push_back( OffdiagNB(AT1, AT2, sig1, eps1, sig2, eps2) );
-    }
-      
-    ptr = infile.Line();
-  } // END loop over file.
-
-  // Deal with nonbond and equivalence
-  if (!NBsets.empty()) {
-    int nbsetidx = 0;
-    if (NBsets.size() > 1 || !nbsetname_.empty()) {
-      // Choose from multiple nbsets
-      if (nbsetname_.empty()) {
-        mprinterr("Error: Parm set in file '%s' contains %zu nonbonded parameter sets\n"
-                  "Error:  but no set has been specified.\n", fname.full(), NBsets.size());
-        mprinterr("Error: Need to specify one of");
-        for (NbSetArrayType::const_iterator it = NBsets.begin(); it != NBsets.end(); ++it)
-          mprinterr(" %s", it->name_.c_str());
-        mprinterr("\n");
-      } else {
-        nbsetidx = -1;
-        for (NbSetArrayType::const_iterator it = NBsets.begin(); it != NBsets.end(); ++it) {
-          if (it->name_ == nbsetname_) {
-            nbsetidx = it - NBsets.begin();
-            break;
-          }
-        }
-        if (nbsetidx < 0) {
-          mprinterr("Error: Nonbonded set '%s' not found.\n", nbsetname_.c_str());
-          mprinterr("Error: Need to specify one of");
-          for (NbSetArrayType::const_iterator it = NBsets.begin(); it != NBsets.end(); ++it)
-            mprinterr(" %s", it->name_.c_str());
-          mprinterr("\n");
-          return 1;
-        }
-      }
-    }
-    mprintf("\tUsing nonbonded parm set: %s\n", NBsets[nbsetidx].name_.c_str());
-    prm.SetNbParamName( NBsets[nbsetidx].name_ );
-    for (ParmHolder<LJparmType>::const_iterator it = NBsets[nbsetidx].LJ_.begin();
-                                                it != NBsets[nbsetidx].LJ_.end(); ++it)
-    {
-      ParmHolder<AtomType>::iterator at = prm.AT().GetParam( it->first );
-      if (at == prm.AT().end()) {
-        mprinterr("Error: Nonbond parameters defined for previously undefined type '%s'.\n",
-                  *(it->first[0]));
-        return 1;
-      } 
-      at->second.SetLJ().SetRadius( it->second.Radius() );
-      at->second.SetLJ().SetDepth( it->second.Depth() );
-    }
-    // Do equivalent atoms.
-    for (XNarray::const_iterator equivAts = EquivalentNames.begin();
-                                 equivAts != EquivalentNames.end(); ++equivAts)
-    {
-      // First name is the type to copy TODO check size?
-      Narray::const_iterator typeName = equivAts->begin();
-      ParmHolder<AtomType>::const_iterator at0 = prm.AT().GetParam( *typeName );
-      if (at0 == prm.AT().end()) {
-        mprinterr("Error: Equivalent atom type '%s' not found.\n", *(*typeName) );
-        return 1;
-      }
-      ++typeName;
-      for (; typeName != equivAts->end(); ++typeName) {
-        ParmHolder<AtomType>::iterator at1 = prm.AT().GetParam( *typeName );
-        if (at1 == prm.AT().end()) {
-          mprinterr("Error: Equivalent atom type '%s' (base '%s') not found.\n", *(*typeName), *(at0->first[0]));
-          return 1;
-        }
-        mprintf("DEBUG: Equiv '%s' => '%s'\n", *(at0->first[0]), *(*typeName));
-        at1->second.SetLJ().SetRadius( at0->second.LJ().Radius() );
-        at1->second.SetLJ().SetDepth( at0->second.LJ().Depth() );
-      }
-    } // END loop over EquivalentNames
-  } // END nonbond parameters
-
-  // Do off diagonal NB mods
-  if (!Offdiag.empty()) {
-    for (Oarray::const_iterator od = Offdiag.begin(); od != Offdiag.end(); ++od)
-    {
-      mprintf("DEBUG: Off diag %s %s\n", *(od->types_[0]), *(od->types_[1]));
-      // Set type 1
-      ParmHolder<AtomType>::iterator it = prm.AT().GetParam( od->types_[0] );
-      if (it == prm.AT().end()) {
-        mprinterr("Error: Off-diagonal nonbond parameters defined for previously undefined type '%s'.\n",
-                  *(od->types_[0]));
-        return 1;
-      }
-      it->second.SetLJ().SetRadius( od->LJ1_.Radius() );
-      it->second.SetLJ().SetDepth( od->LJ1_.Depth() );
-      // Set off-diagonal for type1-type2
-      // FIXME different combine rules?
-      prm.NB().AddParm(od->types_, od->LJ1_.Combine_LB(od->LJ2_), false);
-    }
-  } // END off-diagonal NB mods
 
-  prm.Debug(); // TODO debug level
-  infile.CloseFile();
-  return 0;
+  return err;
 }
 
 // DataIO_AmberFF::WriteHelp()
@@ -510,6 +76,7 @@ int DataIO_AmberFF::processWriteArgs(ArgList& argIn)
 // DataIO_AmberFF::WriteData()
 int DataIO_AmberFF::WriteData(FileName const& fname, DataSetList const& dsl)
 {
+  AmberParamFile outfile;
   std::vector<DataSet_Parameters*> toWrite;
   for (DataSetList::const_iterator it = dsl.begin(); it != dsl.end(); ++it)
   {
@@ -520,7 +87,7 @@ int DataIO_AmberFF::WriteData(FileName const& fname, DataSetList const& dsl)
     mprinterr("Error: No parameter sets to write.\n");
     return 1;
   } else if (toWrite.size() == 1) {
-    return writeParameterSet( fname, *(toWrite.front()) );
+    return outfile.WriteParams( *(toWrite.front()), fname, debug_ );
   } else {
     // Create a combined parameter set
     ParameterSet prm;
@@ -530,39 +97,8 @@ int DataIO_AmberFF::WriteData(FileName const& fname, DataSetList const& dsl)
       ParameterSet::UpdateCount UC;
       prm.UpdateParamSet( *(*it), UC, debug_ );
     }
-    return writeParameterSet( fname, prm );
+    return outfile.WriteParams( prm, fname, debug_ );
   }
 
   return 1;
 }
-
-int DataIO_AmberFF::writeParameterSet(FileName const& fname, ParameterSet const& prm) const {
-  CpptrajFile outfile;
-  if (outfile.OpenWrite(fname)) return 1;
-  // 1 - Title
-  std::string title;
-  if (prm.ParamSetName().empty())
-    title.assign("Parameters written from CPPTRAJ");
-  else
-    title = prm.ParamSetName();
-  outfile.Printf("%s\n", title.c_str());
-  // 2 - Atom symbols and masses
-  for (ParmHolder<AtomType>::const_iterator at = prm.AT().begin(); at != prm.AT().end(); ++at)
-  {
-    std::string asym = at->first[0].Truncated();
-    if (asym.size() > 2)
-      mprintf("Warning: Atom symbol %s is larger than 2 characters, which breaks Amber FF format.\n");
-    outfile.Printf("%-2s", asym.c_str());
-    if (at->second.Mass() < 10.0)
-      outfile.Printf(" %-10.3f", at->second.Mass());
-    else if (at->second.Mass() < 100.0)
-      outfile.Printf(" %-10.2f", at->second.Mass());
-    else
-      outfile.Printf(" %-10.1f", at->second.Mass());
-    outfile.Printf(" %10.3f\n", at->second.Polarizability());
-
-    //outfile.Printf("%-2s  %-10.2f %-10.2f\n", asym.c_str(), at->second.Mass(), at->second.Polarizability());
-  }
-
-  return 0;
-}
diff --git a/src/DataIO_AmberFF.h b/src/DataIO_AmberFF.h
index 631b5baac2..1f73866cea 100644
--- a/src/DataIO_AmberFF.h
+++ b/src/DataIO_AmberFF.h
@@ -14,8 +14,6 @@ class DataIO_AmberFF : public DataIO {
     int WriteData(FileName const&, DataSetList const&);
     bool ID_DataFormat(CpptrajFile&);
   private:
-    static int read_symbols(const char*, std::vector<std::string>&, int);
-    int writeParameterSet(FileName const&, ParameterSet const&) const;
 
     std::string nbsetname_; ///< Nonbonded parameter set name to use
 };
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 855dcd91ec..ae9c0202de 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -205,7 +205,7 @@ DataFileList.o : DataFileList.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h A
 DataFilter.o : DataFilter.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_integer.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO.o : DataIO.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_AmberEne.o : DataIO_AmberEne.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberEne.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_AmberFF.o : DataIO_AmberFF.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberFF.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_AmberFF.o : DataIO_AmberFF.cpp AmberParamFile.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberFF.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_AmberLib.o : DataIO_AmberLib.cpp ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberLib.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_AmberPrep.o : DataIO_AmberPrep.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberPrep.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_CCP4.o : DataIO_CCP4.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ByteRoutines.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CCP4.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h

From 0bab1611d50c9ca8cfb21da09d3ac3e93a536f6f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 20 Nov 2023 14:50:58 -0500
Subject: [PATCH 0076/1492] Start frcmod file IO

---
 src/AmberParamFile.cpp     | 23 +++++++++++-
 src/AmberParamFile.h       |  4 ++
 src/DataIO_AmberFrcmod.cpp | 77 ++++++++++++++++++++++++++++++++++++++
 src/DataIO_AmberFrcmod.h   | 17 +++++++++
 4 files changed, 120 insertions(+), 1 deletion(-)
 create mode 100644 src/DataIO_AmberFrcmod.cpp
 create mode 100644 src/DataIO_AmberFrcmod.h

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 6a22bb91af..599c1ec1c2 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -54,7 +54,28 @@ class OffdiagNB {
     LJparmType LJ2_;
 };
 
-// DataIO_AmberFF::ReadData()
+/** Read parametrers from Amber frcmod file. */
+int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int debugIn) const
+{
+ // Read title
+  BufferedLine infile;
+  if (infile.OpenFileRead( fname )) {
+    mprinterr("Error: Could not open file '%s' as Amber FF.\n", fname.full());
+    return 1;
+  }
+  const char* ptr = infile.Line();
+  if (ptr == 0) {
+    mprinterr("Error: Could not read anything from Amber FF file %s\n", fname.full());
+    return 1;
+  }
+  std::string title(ptr);
+  mprintf("\tTitle: %s\n", title.c_str());
+  //prm.SetParamSetName( title ); TODO append title
+
+  return 0;
+}
+
+/** Read parameters from Amber main FF parameter file. */
 int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
                                std::string const& nbsetnameIn, int debugIn) const
 {
diff --git a/src/AmberParamFile.h b/src/AmberParamFile.h
index a533e44adb..1405c426fc 100644
--- a/src/AmberParamFile.h
+++ b/src/AmberParamFile.h
@@ -9,7 +9,11 @@ class FileName;
 class AmberParamFile {
   public:
     AmberParamFile();
+    /// Read main Amber FF file
     int ReadParams(ParameterSet&, FileName const&, std::string const&, int) const;
+    /// Read Amber frcmod file
+    int ReadFrcmod(ParameterSet&, FileName const&, int) const;
+    /// Write main Amber FF file
     int WriteParams(ParameterSet&, FileName const&, int) const;
   private:
     static int read_symbols(const char*, std::vector<std::string>&, int);
diff --git a/src/DataIO_AmberFrcmod.cpp b/src/DataIO_AmberFrcmod.cpp
new file mode 100644
index 0000000000..b1d2db5f2c
--- /dev/null
+++ b/src/DataIO_AmberFrcmod.cpp
@@ -0,0 +1,77 @@
+#include "DataIO_AmberFrcmod.h"
+#include "CpptrajStdio.h"
+#include "DataSet_Parameters.h"
+#include "AmberParamFile.h"
+
+/// CONSTRUCTOR
+DataIO_AmberFrcmod::DataIO_AmberFrcmod()
+{
+
+}
+
+// DataIO_AmberFrcmod::ID_DataFormat()
+bool DataIO_AmberFrcmod::ID_DataFormat(CpptrajFile& infile)
+{
+
+  return false;
+}
+
+// DataIO_AmberFrcmod::ReadHelp()
+void DataIO_AmberFrcmod::ReadHelp()
+{
+
+}
+
+// DataIO_AmberFrcmod::processReadArgs()
+int DataIO_AmberFrcmod::processReadArgs(ArgList& argIn)
+{
+
+  return 0;
+}
+
+// DataIO_AmberFrcmod::ReadData()
+int DataIO_AmberFrcmod::ReadData(FileName const& fname, DataSetList& dsl, std::string const& dsname)
+{
+  // Allocate data set
+  MetaData md( dsname );
+  DataSet* ds = dsl.CheckForSet( md );
+  if (ds != 0) {
+    if (ds->Type() != DataSet::PARAMETERS) {
+      mprinterr("Error: Set '%s' does not have parameters, cannot append.\n", ds->legend());
+      return 1;
+    }
+    mprintf("\tAdding to existing set %s\n", ds->legend());
+  } else {
+    ds = dsl.AddSet( DataSet::PARAMETERS, md );
+    if (ds == 0) return 1;
+  }
+  DataSet_Parameters& prm = static_cast<DataSet_Parameters&>( *ds );
+
+  AmberParamFile infile;
+  if (infile.ReadFrcmod(prm, fname, debug_)) {
+    mprinterr("Error: Could not read Amber frcmod file '%s'\n", fname.full());
+    return 1;
+  }
+
+  return 0;
+}
+
+// DataIO_AmberFrcmod::WriteHelp()
+void DataIO_AmberFrcmod::WriteHelp()
+{
+
+}
+
+// DataIO_AmberFrcmod::processWriteArgs()
+int DataIO_AmberFrcmod::processWriteArgs(ArgList& argIn)
+{
+
+  return 0;
+}
+
+// DataIO_AmberFrcmod::WriteData()
+int DataIO_AmberFrcmod::WriteData(FileName const& fname, DataSetList const& dsl)
+{
+
+  return 1;
+}
diff --git a/src/DataIO_AmberFrcmod.h b/src/DataIO_AmberFrcmod.h
new file mode 100644
index 0000000000..bf792d4e48
--- /dev/null
+++ b/src/DataIO_AmberFrcmod.h
@@ -0,0 +1,17 @@
+#ifndef INC_DATAIO_AMBERFRCMOD_H
+#define INC_DATAIO_AMBERFRCMOD_H
+#include "DataIO.h"
+/// <Enter description of DataIO_AmberFrcmod here>
+class DataIO_AmberFrcmod : public DataIO {
+  public:
+    DataIO_AmberFrcmod();
+    static void ReadHelp();
+    static void WriteHelp();
+    static BaseIOtype* Alloc() { return (BaseIOtype*)new DataIO_AmberFrcmod(); }
+    int processReadArgs(ArgList&);
+    int ReadData(FileName const&, DataSetList&, std::string const&);
+    int processWriteArgs(ArgList&);
+    int WriteData(FileName const&, DataSetList const&);
+    bool ID_DataFormat(CpptrajFile&);
+};
+#endif

From 612a9aab710f5b4bfcee29a2bf3d27ce708e20be Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 20 Nov 2023 14:55:45 -0500
Subject: [PATCH 0077/1492] Enable for testing

---
 src/DataFile.cpp  | 3 +++
 src/DataFile.h    | 2 +-
 src/cpptrajdepend | 3 ++-
 src/cpptrajfiles  | 1 +
 4 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/src/DataFile.cpp b/src/DataFile.cpp
index 2189eeba3e..4403b0d6e9 100644
--- a/src/DataFile.cpp
+++ b/src/DataFile.cpp
@@ -35,6 +35,7 @@
 #include "DataIO_AmberPrep.h"
 #include "DataIO_AmberLib.h"
 #include "DataIO_AmberFF.h"
+#include "DataIO_AmberFrcmod.h"
 
 // CONSTRUCTOR
 DataFile::DataFile() :
@@ -91,6 +92,7 @@ const FileTypes::AllocToken DataFile::DF_AllocArray[] = {
   { "Amber Prep File",    DataIO_AmberPrep::ReadHelp,    0,            DataIO_AmberPrep::Alloc},
   { "Amber OFF File",     0,                             0,            DataIO_AmberLib::Alloc},
   { "Amber Force Field",  DataIO_AmberFF::ReadHelp,      0,            DataIO_AmberFF::Alloc},
+  { "Amber Frcmod File",  0,                             0,            DataIO_AmberFrcmod::Alloc},
   { "Unknown Data file",  0,                       0,                        0                    }
 };
 
@@ -121,6 +123,7 @@ const FileTypes::KeyToken DataFile::DF_KeyArray[] = {
   { AMBERLIB,     "off",          ".off" },
   { AMBERLIB,     "off",          ".lib" },
   { AMBERFF,      "amberff",      ".parm" },
+  { AMBERFRCMOD,  "frcmod",       ".frcmod" },
   { UNKNOWN_DATA, 0,        0        }
 };
 
diff --git a/src/DataFile.h b/src/DataFile.h
index 6cce13ed11..7cd62360b7 100644
--- a/src/DataFile.h
+++ b/src/DataFile.h
@@ -18,7 +18,7 @@ class DataFile {
       DATAFILE=0, XMGRACE, GNUPLOT, XPLOR, OPENDX, REMLOG, MDOUT, EVECS,
       VECTRAJ, XVG, CCP4, CHARMMREPD, CHARMMFASTREP,
       CHARMMOUT, CPOUT, CHARMMRTFPRM, CMATRIX_BINARY, CMATRIX_NETCDF, PEAKS,
-      NETCDFDATA, AMBERENE, NUMPY, AMBERPREP, AMBERLIB, AMBERFF,
+      NETCDFDATA, AMBERENE, NUMPY, AMBERPREP, AMBERLIB, AMBERFF, AMBERFRCMOD,
       UNKNOWN_DATA 
     };
     DataFile();
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index e813c5d642..347343a149 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -200,12 +200,13 @@ CpptrajFile.o : CpptrajFile.cpp CpptrajFile.h CpptrajStdio.h FileIO.h FileIO_Bzi
 CpptrajState.o : CpptrajState.cpp Action.h ActionList.h ActionState.h Action_CreateCrd.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_Topology.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleNavigator.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 CpptrajStdio.o : CpptrajStdio.cpp Parallel.h
 CurveFit.o : CurveFit.cpp CurveFit.h
-DataFile.o : DataFile.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Cluster/Cframes.h Cluster/Cmatrix_NC.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataFile.h DataIO.h DataIO_AmberEne.h DataIO_AmberFF.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_CCP4.h DataIO_CharmmFastRep.h DataIO_CharmmOutput.h DataIO_CharmmRepLog.h DataIO_CharmmRtfPrm.h DataIO_Cmatrix_Binary.h DataIO_Cmatrix_NC.h DataIO_Cpout.h DataIO_Evecs.h DataIO_Gnuplot.h DataIO_Grace.h DataIO_Mdout.h DataIO_NetCDF.h DataIO_Numpy.h DataIO_OpenDx.h DataIO_Peaks.h DataIO_RemLog.h DataIO_Std.h DataIO_VecTraj.h DataIO_XVG.h DataIO_Xplor.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TypeNameHolder.h Unit.h Vec3.h
+DataFile.o : DataFile.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Cluster/Cframes.h Cluster/Cmatrix_NC.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataFile.h DataIO.h DataIO_AmberEne.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_CCP4.h DataIO_CharmmFastRep.h DataIO_CharmmOutput.h DataIO_CharmmRepLog.h DataIO_CharmmRtfPrm.h DataIO_Cmatrix_Binary.h DataIO_Cmatrix_NC.h DataIO_Cpout.h DataIO_Evecs.h DataIO_Gnuplot.h DataIO_Grace.h DataIO_Mdout.h DataIO_NetCDF.h DataIO_Numpy.h DataIO_OpenDx.h DataIO_Peaks.h DataIO_RemLog.h DataIO_Std.h DataIO_VecTraj.h DataIO_XVG.h DataIO_Xplor.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TypeNameHolder.h Unit.h Vec3.h
 DataFileList.o : DataFileList.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataFilter.o : DataFilter.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_integer.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO.o : DataIO.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_AmberEne.o : DataIO_AmberEne.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberEne.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_AmberFF.o : DataIO_AmberFF.cpp AmberParamFile.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberFF.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_AmberFrcmod.o : DataIO_AmberFrcmod.cpp AmberParamFile.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberFrcmod.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_AmberLib.o : DataIO_AmberLib.cpp ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberLib.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_AmberPrep.o : DataIO_AmberPrep.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberPrep.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_CCP4.o : DataIO_CCP4.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ByteRoutines.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CCP4.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
diff --git a/src/cpptrajfiles b/src/cpptrajfiles
index 46eb2f8d29..a8a487d7b1 100644
--- a/src/cpptrajfiles
+++ b/src/cpptrajfiles
@@ -177,6 +177,7 @@ COMMON_SOURCES= \
         DataIO.cpp \
         DataIO_AmberEne.cpp \
         DataIO_AmberFF.cpp \
+        DataIO_AmberFrcmod.cpp \
         DataIO_AmberLib.cpp \
         DataIO_AmberPrep.cpp \
         DataIO_CCP4.cpp \

From 05caafa11956b6e6a73bdea9185d1d6d7d7f3773 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 20 Nov 2023 15:05:40 -0500
Subject: [PATCH 0078/1492] ID sections

---
 src/AmberParamFile.cpp | 24 ++++++++++++++++++++++--
 src/AmberParamFile.h   |  2 ++
 2 files changed, 24 insertions(+), 2 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 599c1ec1c2..084cd53af9 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -71,6 +71,28 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int deb
   std::string title(ptr);
   mprintf("\tTitle: %s\n", title.c_str());
   //prm.SetParamSetName( title ); TODO append title
+  // Read file
+  SectionType section = UNKNOWN;
+  ptr = infile.Line();
+  while (ptr != 0) {
+    // Is this a recognized section keyword?
+    if (*ptr != '\0') {
+      std::string line(ptr);
+      if      (line.compare(0, 4, "MASS") == 0) section = ATYPE;
+      else if (line.compare(0, 4, "BOND") == 0) section = BOND;
+      else if (line.compare(0, 4, "ANGL") == 0) section = ANGLE;
+      else if (line.compare(0, 4, "DIHE") == 0) section = DIHEDRAL;
+      else if (line.compare(0, 4, "IMPR") == 0) section = IMPROPER;
+      else if (line.compare(0, 4, "HBON") == 0) section = LJ1012;
+      else if (line.compare(0, 4, "NONB") == 0) {
+        section = NONBOND;
+        // TODO check RE
+      } else {
+        mprintf("DEBUG: Section %i: %s\n", (int)section, ptr);
+      }
+    }
+    ptr = infile.Line();
+  }
 
   return 0;
 }
@@ -107,8 +129,6 @@ int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
   mprintf("\tTitle: %s\n", title.c_str());
   prm.SetParamSetName( title );
   // Read file
-  enum SectionType { ATYPE = 0, HYDROPHILIC, BOND, ANGLE, DIHEDRAL, IMPROPER, 
-                     LJ1012, NB_EQUIV, NONBOND, LJEDIT, UNKNOWN };
   SectionType section = ATYPE;
   ptr = infile.Line();
   while (ptr != 0) {
diff --git a/src/AmberParamFile.h b/src/AmberParamFile.h
index 1405c426fc..c65da9756d 100644
--- a/src/AmberParamFile.h
+++ b/src/AmberParamFile.h
@@ -16,6 +16,8 @@ class AmberParamFile {
     /// Write main Amber FF file
     int WriteParams(ParameterSet&, FileName const&, int) const;
   private:
+    enum SectionType { ATYPE = 0, HYDROPHILIC, BOND, ANGLE, DIHEDRAL, IMPROPER, 
+                       LJ1012, NB_EQUIV, NONBOND, LJEDIT, UNKNOWN };
     static int read_symbols(const char*, std::vector<std::string>&, int);
     //int ReadInput(std::string&, BufferedLine&) const;
 };

From d365305d0db065b2e9f35a2294bf36661e13ddc3 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 20 Nov 2023 15:24:37 -0500
Subject: [PATCH 0079/1492] Start splitting off into separate read functions
 that can be used for both FF and frcmod

---
 src/AmberParamFile.cpp | 69 +++++++++++++++++++++++++++---------------
 src/AmberParamFile.h   |  4 +++
 2 files changed, 48 insertions(+), 25 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 084cd53af9..39d0de74f5 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -7,6 +7,8 @@
 #include "ParameterSet.h"
 #include <cstdio> // sscanf
 
+const int AmberParamFile::MAXSYMLEN = 16;
+
 /// CONSTRUCTOR
 AmberParamFile::AmberParamFile() {}
 
@@ -54,6 +56,35 @@ class OffdiagNB {
     LJparmType LJ2_;
 };
 
+/** Read input for atom symbols and masses. */
+int AmberParamFile::read_atype(ParameterSet& prm, const char* ptr)
+const
+{
+  // Format (A2,2X,F10.2x,f10.2)
+  mprintf("DEBUG: Atype: %s\n", ptr);
+  char kndsym[MAXSYMLEN];
+  double amass = 0;
+  double atpol = 0;
+  int nscan = sscanf(ptr, "%s %lf %lf", kndsym, &amass, &atpol);
+  ParameterHolders::RetType ret;
+  if (nscan == 3) {
+    ret = prm.AT().AddParm( TypeNameHolder(kndsym),
+                            AtomType(amass, atpol),
+                            true );
+  } else if (nscan == 2) {
+    // Only mass
+    ret = prm.AT().AddParm( TypeNameHolder(kndsym),
+                            AtomType(amass),
+                            true );
+  } else {
+    mprinterr("Error: Expected atom type, mass, polarizability, got only %i columns.\n", nscan);
+    return 1;
+  }
+  if (ret == ParameterHolders::UPDATED)
+    mprintf("Warning: Redefining atom type %s\n", kndsym);
+  return 0;
+}
+
 /** Read parametrers from Amber frcmod file. */
 int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int debugIn) const
 {
@@ -89,6 +120,13 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int deb
         // TODO check RE
       } else {
         mprintf("DEBUG: Section %i: %s\n", (int)section, ptr);
+        int err = 0;
+        if (section == ATYPE)
+          err = read_atype(prm, ptr);
+        if (err != 0) {
+          mprinterr("Error: Reading line: %s\n", ptr);
+          return 1;
+        }
       }
     }
     ptr = infile.Line();
@@ -101,7 +139,6 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int deb
 int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
                                std::string const& nbsetnameIn, int debugIn) const
 {
-  static const int MAXSYMLEN = 16;
 
   // For files with > 1 set of NB params
   typedef std::vector<NonbondSet> NbSetArrayType;
@@ -135,6 +172,7 @@ int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
     // Advance to first non-space char
     while (*ptr == ' ' && *ptr != '\0') ++ptr;
     mprintf("DEBUG: First char: %c (%i)\n", *ptr, (int)*ptr);
+    int read_err = 0;
     if (*ptr == '\0') {
       // Section Change
       if (section != UNKNOWN) {
@@ -191,29 +229,7 @@ int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
         NBsets.push_back( NonbondSet( std::string(nb_label) ) );
       }
     } else if (section == ATYPE) {
-      // Input for atom symbols and masses
-      // Format (A2,2X,F10.2x,f10.2)
-      mprintf("DEBUG: Atype: %s\n", ptr);
-      char kndsym[MAXSYMLEN];
-      double amass = 0;
-      double atpol = 0;
-      int nscan = sscanf(ptr, "%s %lf %lf", kndsym, &amass, &atpol);
-      ParameterHolders::RetType ret;
-      if (nscan == 3) {
-        ret = prm.AT().AddParm( TypeNameHolder(kndsym),
-                                AtomType(amass, atpol),
-                                true );
-      } else if (nscan == 2) {
-        // Only mass
-        ret = prm.AT().AddParm( TypeNameHolder(kndsym),
-                                AtomType(amass),
-                                true );
-      } else {
-        mprinterr("Error: Expected atom type, mass, polarizability, got only %i columns.\n", nscan);
-        return 1;
-      }
-      if (ret == ParameterHolders::UPDATED)
-        mprintf("Warning: Redefining atom type %s\n", kndsym);
+      read_err = read_atype(prm, ptr);
     } else if (section == BOND) {
       // Bond parameters
       // IBT , JBT , RK , REQ
@@ -399,7 +415,10 @@ int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
       }
       Offdiag.push_back( OffdiagNB(AT1, AT2, sig1, eps1, sig2, eps2) );
     }
-      
+    if (read_err != 0) {
+      mprinterr("Error: Reading line: %s\n", ptr);
+      return 1;
+    } 
     ptr = infile.Line();
   } // END loop over file.
 
diff --git a/src/AmberParamFile.h b/src/AmberParamFile.h
index c65da9756d..16fa0cd698 100644
--- a/src/AmberParamFile.h
+++ b/src/AmberParamFile.h
@@ -16,9 +16,13 @@ class AmberParamFile {
     /// Write main Amber FF file
     int WriteParams(ParameterSet&, FileName const&, int) const;
   private:
+    static const int MAXSYMLEN;
+
     enum SectionType { ATYPE = 0, HYDROPHILIC, BOND, ANGLE, DIHEDRAL, IMPROPER, 
                        LJ1012, NB_EQUIV, NONBOND, LJEDIT, UNKNOWN };
     static int read_symbols(const char*, std::vector<std::string>&, int);
+    /// Read atom type line
+    int read_atype(ParameterSet&, const char*) const;
     //int ReadInput(std::string&, BufferedLine&) const;
 };
 #endif

From 22f213d3bf5fd780343e1045645d2a14afb1466e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 20 Nov 2023 15:27:37 -0500
Subject: [PATCH 0080/1492] Hide some debug info

---
 src/AmberParamFile.cpp | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 39d0de74f5..71d7df34e1 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -119,7 +119,7 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int deb
         section = NONBOND;
         // TODO check RE
       } else {
-        mprintf("DEBUG: Section %i: %s\n", (int)section, ptr);
+        //mprintf("DEBUG: Section %i: %s\n", (int)section, ptr);
         int err = 0;
         if (section == ATYPE)
           err = read_atype(prm, ptr);
@@ -131,6 +131,8 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int deb
     }
     ptr = infile.Line();
   }
+  prm.Debug(); // TODO debug level
+  infile.CloseFile();
 
   return 0;
 }
@@ -171,7 +173,7 @@ int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
   while (ptr != 0) {
     // Advance to first non-space char
     while (*ptr == ' ' && *ptr != '\0') ++ptr;
-    mprintf("DEBUG: First char: %c (%i)\n", *ptr, (int)*ptr);
+    //mprintf("DEBUG: First char: %c (%i)\n", *ptr, (int)*ptr);
     int read_err = 0;
     if (*ptr == '\0') {
       // Section Change

From 6b5141439337ed1072387649b27635b5412fb3f3 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 20 Nov 2023 15:43:36 -0500
Subject: [PATCH 0081/1492] Functions for reading bonds and angles. Allow
 updates, report when they happen

---
 src/AmberParamFile.cpp | 113 +++++++++++++++++++++++++----------------
 src/AmberParamFile.h   |   4 ++
 2 files changed, 74 insertions(+), 43 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 71d7df34e1..0f75bfe035 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -85,6 +85,70 @@ const
   return 0;
 }
 
+/** Read input for bond. */
+int AmberParamFile::read_bond(ParameterSet& prm, const char* ptr)
+const
+{
+  // Bond parameters
+  // IBT , JBT , RK , REQ
+  // FORMAT(A2,1X,A2,2F10.2)
+  mprintf("DEBUG: Bond: %s\n", ptr);
+  std::vector<std::string> symbols(2);
+  int pos = read_symbols(ptr, symbols, 2);
+  if (pos < 0) {
+    mprinterr("Error: Could not read symbols for bond from %s\n", ptr);
+    return 1;
+  }
+  mprintf("DEBUG: %s %s '%s'\n", symbols[0].c_str(), symbols[1].c_str(), ptr+pos);
+  double RK, REQ;
+  int nscan = sscanf(ptr+pos, "%lf %lf", &RK, &REQ);
+  if (nscan != 2) {
+    mprinterr("Error: Expected RK, REQ, got only %i elements\n", nscan);
+    return 1;
+  }
+  TypeNameHolder types(2);
+  types.AddName( symbols[0] );
+  types.AddName( symbols[1] );
+  ParameterHolders::RetType ret = prm.BP().AddParm(types, BondParmType(RK, REQ), true);
+  if (ret == ParameterHolders::UPDATED)
+    mprintf("Warning: Redefining bond type %s - %s\n", *(types[0]), *(types[1]));
+
+  return 0;
+}
+
+/** Read input for angle. */
+int AmberParamFile::read_angle(ParameterSet& prm, const char* ptr)
+const
+{
+  // Angle parameters
+  // ITT , JTT , KTT , TK , TEQ
+  // FORMAT(A2,1X,A2,1X,A2,2F10.2)
+  mprintf("DEBUG: Angle: %s\n", ptr);
+  std::vector<std::string> symbols(3);
+  int pos = read_symbols(ptr, symbols, 3);
+  if (pos < 0) {
+    mprinterr("Error: Could not read symbols for angle from %s\n", ptr);
+    return 1;
+  }
+  mprintf("DEBUG: %s %s %s '%s'\n", symbols[0].c_str(), symbols[1].c_str(), symbols[2].c_str(), ptr+pos);
+  double TK, TEQ;
+  int nscan = sscanf(ptr+pos, "%lf %lf", &TK, &TEQ);
+  if (nscan != 2) {
+    mprinterr("Error: Expected TK, TEQ, got only %i elements\n", nscan);
+    return 1;
+  }
+  TypeNameHolder types(3);
+  types.AddName( symbols[0] );
+  types.AddName( symbols[1] );
+  types.AddName( symbols[2] );
+  ParameterHolders::RetType ret = prm.AP().AddParm(types, AngleParmType(TK, TEQ), true);
+  if (ret == ParameterHolders::UPDATED)
+    mprintf("Warning: Redefining angle type %s - %s - %s\n", *(types[0]), *(types[1]), *(types[2]));
+
+  return 0;
+}
+
+
 /** Read parametrers from Amber frcmod file. */
 int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int debugIn) const
 {
@@ -123,6 +187,10 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int deb
         int err = 0;
         if (section == ATYPE)
           err = read_atype(prm, ptr);
+        else if (section == BOND)
+          err = read_bond(prm, ptr);
+        else if (section == ANGLE)
+          err = read_angle(prm, ptr);
         if (err != 0) {
           mprinterr("Error: Reading line: %s\n", ptr);
           return 1;
@@ -233,50 +301,9 @@ int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
     } else if (section == ATYPE) {
       read_err = read_atype(prm, ptr);
     } else if (section == BOND) {
-      // Bond parameters
-      // IBT , JBT , RK , REQ
-      // FORMAT(A2,1X,A2,2F10.2)
-      mprintf("DEBUG: Bond: %s\n", ptr);
-      std::vector<std::string> symbols(2);
-      int pos = read_symbols(ptr, symbols, 2);
-      if (pos < 0) {
-        mprinterr("Error: Could not read symbols for bond from %s\n", ptr);
-        return 1;
-      }
-      mprintf("DEBUG: %s %s '%s'\n", symbols[0].c_str(), symbols[1].c_str(), ptr+pos);
-      double RK, REQ;
-      int nscan = sscanf(ptr+pos, "%lf %lf", &RK, &REQ);
-      if (nscan != 2) {
-        mprinterr("Error: Expected RK, REQ, got only %i elements\n", nscan);
-        return 1;
-      }
-      TypeNameHolder types(2);
-      types.AddName( symbols[0] );
-      types.AddName( symbols[1] );
-      prm.BP().AddParm(types, BondParmType(RK, REQ), false);
+      read_err = read_bond(prm, ptr);
     } else if (section == ANGLE) {
-      // Angle parameters
-      // ITT , JTT , KTT , TK , TEQ
-      // FORMAT(A2,1X,A2,1X,A2,2F10.2)
-      mprintf("DEBUG: Angle: %s\n", ptr);
-      std::vector<std::string> symbols(3);
-      int pos = read_symbols(ptr, symbols, 3);
-      if (pos < 0) {
-        mprinterr("Error: Could not read symbols for angle from %s\n", ptr);
-        return 1;
-      }
-      mprintf("DEBUG: %s %s %s '%s'\n", symbols[0].c_str(), symbols[1].c_str(), symbols[2].c_str(), ptr+pos);
-      double TK, TEQ;
-      int nscan = sscanf(ptr+pos, "%lf %lf", &TK, &TEQ);
-      if (nscan != 2) {
-        mprinterr("Error: Expected TK, TEQ, got only %i elements\n", nscan);
-        return 1;
-      }
-      TypeNameHolder types(3);
-      types.AddName( symbols[0] );
-      types.AddName( symbols[1] );
-      types.AddName( symbols[2] );
-      prm.AP().AddParm(types, AngleParmType(TK, TEQ), false);
+      read_err = read_angle(prm, ptr);
     } else if (section == DIHEDRAL) {
       // Dihedral parameters
       // IPT , JPT , KPT , LPT , IDIVF , PK , PHASE , PN
diff --git a/src/AmberParamFile.h b/src/AmberParamFile.h
index 16fa0cd698..7313dc2322 100644
--- a/src/AmberParamFile.h
+++ b/src/AmberParamFile.h
@@ -23,6 +23,10 @@ class AmberParamFile {
     static int read_symbols(const char*, std::vector<std::string>&, int);
     /// Read atom type line
     int read_atype(ParameterSet&, const char*) const;
+    /// Read bond line
+    int read_bond(ParameterSet&, const char*) const;
+    /// Read angle line
+    int read_angle(ParameterSet&, const char*) const;
     //int ReadInput(std::string&, BufferedLine&) const;
 };
 #endif

From 19c96481a0c75498ad53ac4c198846c84499ee26 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 20 Nov 2023 15:47:48 -0500
Subject: [PATCH 0082/1492] Function for dihedrals

---
 src/AmberParamFile.cpp | 77 ++++++++++++++++++++++++------------------
 src/AmberParamFile.h   |  2 ++
 2 files changed, 47 insertions(+), 32 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 0f75bfe035..9c3b52ee5f 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -148,6 +148,48 @@ const
   return 0;
 }
 
+/** Read input for dihedral. */
+int AmberParamFile::read_dihedral(ParameterSet& prm, const char* ptr)
+const
+{
+  // Dihedral parameters
+  // IPT , JPT , KPT , LPT , IDIVF , PK , PHASE , PN
+  // FORMAT(A2,1X,A2,1X,A2,1X,A2,I4,3F15.2)
+  // If IPT .eq. 'X ' .and. LPT .eq. 'X ' then any dihedrals in the
+  // system involving the atoms "JPT" and and "KPT" are assigned 
+  // the same parameters.  This is called the general dihedral type
+  // and is of the form "X "-"JPT"-"KPT"-"X ".
+  // IDIVF is the factor by which the torsional barrier is divided.
+  // Consult Weiner, et al., JACS 106:765 (1984) p. 769 for
+  // details. Basically, the actual torsional potential is
+  //   (PK/IDIVF) * (1 + cos(PN*phi - PHASE))
+  mprintf("DEBUG: Dihedral: %s\n", ptr);
+  std::vector<std::string> symbols(4);
+  int pos = read_symbols(ptr, symbols, 4);
+  if (pos < 0) {
+    mprinterr("Error: Could not read symbols for dihedral from %s\n", ptr);
+    return 1;
+  }
+  mprintf("DEBUG: %s %s %s %s '%s'\n", symbols[0].c_str(), symbols[1].c_str(), symbols[2].c_str(), symbols[3].c_str(), ptr+pos);
+  int IDIVF;
+  double PK, PHASE, PN;
+  int nscan = sscanf(ptr+pos, "%i %lf %lf %lf", &IDIVF, &PK, &PHASE, &PN);
+  if (nscan != 4) {
+    mprinterr("Error: Expected IDIVF, PK, PHASE, PN, got only %i elements\n", nscan);
+    return 1;
+  }
+  TypeNameHolder types(4);
+  types.AddName( symbols[0] );
+  types.AddName( symbols[1] );
+  types.AddName( symbols[2] );
+  types.AddName( symbols[3] );
+  ParameterHolders::RetType ret =
+    prm.DP().AddParm(types, DihedralParmType(PK / (double)IDIVF, PN, PHASE), true);
+  if (ret == ParameterHolders::UPDATED)
+    mprintf("Warning: Redefining angle type %s - %s - %s - %s\n",
+            *(types[0]), *(types[1]), *(types[2]), *(types[3]));
+  return 0;
+}
 
 /** Read parametrers from Amber frcmod file. */
 int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int debugIn) const
@@ -191,6 +233,8 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int deb
           err = read_bond(prm, ptr);
         else if (section == ANGLE)
           err = read_angle(prm, ptr);
+        else if (section == DIHEDRAL)
+          err = read_dihedral(prm, ptr);
         if (err != 0) {
           mprinterr("Error: Reading line: %s\n", ptr);
           return 1;
@@ -305,38 +349,7 @@ int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
     } else if (section == ANGLE) {
       read_err = read_angle(prm, ptr);
     } else if (section == DIHEDRAL) {
-      // Dihedral parameters
-      // IPT , JPT , KPT , LPT , IDIVF , PK , PHASE , PN
-      // FORMAT(A2,1X,A2,1X,A2,1X,A2,I4,3F15.2)
-      // If IPT .eq. 'X ' .and. LPT .eq. 'X ' then any dihedrals in the
-      // system involving the atoms "JPT" and and "KPT" are assigned 
-      // the same parameters.  This is called the general dihedral type
-      // and is of the form "X "-"JPT"-"KPT"-"X ".
-      // IDIVF is the factor by which the torsional barrier is divided.
-      // Consult Weiner, et al., JACS 106:765 (1984) p. 769 for
-      // details. Basically, the actual torsional potential is
-      //   (PK/IDIVF) * (1 + cos(PN*phi - PHASE))
-      mprintf("DEBUG: Dihedral: %s\n", ptr);
-      std::vector<std::string> symbols(4);
-      int pos = read_symbols(ptr, symbols, 4);
-      if (pos < 0) {
-        mprinterr("Error: Could not read symbols for dihedral from %s\n", ptr);
-        return 1;
-      }
-      mprintf("DEBUG: %s %s %s %s '%s'\n", symbols[0].c_str(), symbols[1].c_str(), symbols[2].c_str(), symbols[3].c_str(), ptr+pos);
-      int IDIVF;
-      double PK, PHASE, PN;
-      int nscan = sscanf(ptr+pos, "%i %lf %lf %lf", &IDIVF, &PK, &PHASE, &PN);
-      if (nscan != 4) {
-        mprinterr("Error: Expected IDIVF, PK, PHASE, PN, got only %i elements\n", nscan);
-        return 1;
-      }
-      TypeNameHolder types(4);
-      types.AddName( symbols[0] );
-      types.AddName( symbols[1] );
-      types.AddName( symbols[2] );
-      types.AddName( symbols[3] );
-      prm.DP().AddParm(types, DihedralParmType(PK / (double)IDIVF, PN, PHASE), false);
+      read_err = read_dihedral(prm, ptr);
     } else if (section == IMPROPER) {
       // Improper parameters
       // IPT , JPT , KPT , LPT , IDIVF , PK , PHASE , PN
diff --git a/src/AmberParamFile.h b/src/AmberParamFile.h
index 7313dc2322..31bc402f7e 100644
--- a/src/AmberParamFile.h
+++ b/src/AmberParamFile.h
@@ -27,6 +27,8 @@ class AmberParamFile {
     int read_bond(ParameterSet&, const char*) const;
     /// Read angle line
     int read_angle(ParameterSet&, const char*) const;
+    /// Read dihedral line
+    int read_dihedral(ParameterSet&, const char*) const;
     //int ReadInput(std::string&, BufferedLine&) const;
 };
 #endif

From 863ad0eb51f69e81ff29db90cb4236a23d2da262 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 20 Nov 2023 16:06:52 -0500
Subject: [PATCH 0083/1492] Add improper function

---
 src/AmberParamFile.cpp | 63 ++++++++++++++++++++++++++----------------
 src/AmberParamFile.h   |  2 ++
 2 files changed, 41 insertions(+), 24 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 9c3b52ee5f..28a02f125f 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -186,11 +186,46 @@ const
   ParameterHolders::RetType ret =
     prm.DP().AddParm(types, DihedralParmType(PK / (double)IDIVF, PN, PHASE), true);
   if (ret == ParameterHolders::UPDATED)
-    mprintf("Warning: Redefining angle type %s - %s - %s - %s\n",
+    mprintf("Warning: Redefining dihedral type %s - %s - %s - %s\n",
             *(types[0]), *(types[1]), *(types[2]), *(types[3]));
   return 0;
 }
 
+/** Read input for improper. */
+int AmberParamFile::read_improper(ParameterSet& prm, const char* ptr)
+const
+{
+  // Improper parameters
+  // IPT , JPT , KPT , LPT , IDIVF , PK , PHASE , PN
+  // FORMAT(A2,1X,A2,1X,A2,1X,A2,I4,3F15.2)
+  mprintf("DEBUG: Improper: %s\n", ptr);
+  std::vector<std::string> symbols(4);
+  int pos = read_symbols(ptr, symbols, 4);
+  if (pos < 0) {
+    mprinterr("Error: Could not read symbols for improper from %s\n", ptr);
+    return 1;
+  }
+  mprintf("DEBUG: %s %s %s %s '%s'\n", symbols[0].c_str(), symbols[1].c_str(), symbols[2].c_str(), symbols[3].c_str(), ptr+pos);
+  double PK, PHASE, PN;
+  int nscan = sscanf(ptr+pos, "%lf %lf %lf", &PK, &PHASE, &PN);
+  if (nscan != 3) {
+    mprinterr("Error: Expected PK, PHASE, PN, got only %i elements\n", nscan);
+    return 1;
+  }
+  TypeNameHolder types(4);
+  types.AddName( symbols[0] );
+  types.AddName( symbols[1] );
+  types.AddName( symbols[2] );
+  types.AddName( symbols[3] );
+  ParameterHolders::RetType ret =
+    prm.IP().AddParm(types, DihedralParmType(PK, PN, PHASE), false);
+  if (ret == ParameterHolders::UPDATED)
+    mprintf("Warning: Redefining improper type %s - %s - %s - %s\n",
+            *(types[0]), *(types[1]), *(types[2]), *(types[3]));
+
+  return 0;
+}
+
 /** Read parametrers from Amber frcmod file. */
 int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int debugIn) const
 {
@@ -235,6 +270,8 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int deb
           err = read_angle(prm, ptr);
         else if (section == DIHEDRAL)
           err = read_dihedral(prm, ptr);
+        else if (section == IMPROPER)
+          err = read_improper(prm, ptr);
         if (err != 0) {
           mprinterr("Error: Reading line: %s\n", ptr);
           return 1;
@@ -351,29 +388,7 @@ int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
     } else if (section == DIHEDRAL) {
       read_err = read_dihedral(prm, ptr);
     } else if (section == IMPROPER) {
-      // Improper parameters
-      // IPT , JPT , KPT , LPT , IDIVF , PK , PHASE , PN
-      // FORMAT(A2,1X,A2,1X,A2,1X,A2,I4,3F15.2)
-      mprintf("DEBUG: Improper: %s\n", ptr);
-      std::vector<std::string> symbols(4);
-      int pos = read_symbols(ptr, symbols, 4);
-      if (pos < 0) {
-        mprinterr("Error: Could not read symbols for improper from %s\n", ptr);
-        return 1;
-      }
-      mprintf("DEBUG: %s %s %s %s '%s'\n", symbols[0].c_str(), symbols[1].c_str(), symbols[2].c_str(), symbols[3].c_str(), ptr+pos);
-      double PK, PHASE, PN;
-      int nscan = sscanf(ptr+pos, "%lf %lf %lf", &PK, &PHASE, &PN);
-      if (nscan != 3) {
-        mprinterr("Error: Expected PK, PHASE, PN, got only %i elements\n", nscan);
-        return 1;
-      }
-      TypeNameHolder types(4);
-      types.AddName( symbols[0] );
-      types.AddName( symbols[1] );
-      types.AddName( symbols[2] );
-      types.AddName( symbols[3] );
-      prm.IP().AddParm(types, DihedralParmType(PK, PN, PHASE), false);
+      read_err = read_improper(prm, ptr);
     } else if (section == LJ1012) {
       // Lennard-Jones 10-12 hydrogen bonding term.
       // According to the docs, the format should be:
diff --git a/src/AmberParamFile.h b/src/AmberParamFile.h
index 31bc402f7e..a4e2292d3a 100644
--- a/src/AmberParamFile.h
+++ b/src/AmberParamFile.h
@@ -29,6 +29,8 @@ class AmberParamFile {
     int read_angle(ParameterSet&, const char*) const;
     /// Read dihedral line
     int read_dihedral(ParameterSet&, const char*) const;
+    /// Read improper line
+    int read_improper(ParameterSet&, const char*) const;
     //int ReadInput(std::string&, BufferedLine&) const;
 };
 #endif

From 2bf76a5e6b5da776ab27fa42b4ba4725c6dad58b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 20 Nov 2023 16:10:34 -0500
Subject: [PATCH 0084/1492] Add function for LJ 10-12 hbond

---
 src/AmberParamFile.cpp | 54 ++++++++++++++++++++++++++----------------
 src/AmberParamFile.h   |  2 ++
 2 files changed, 35 insertions(+), 21 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 28a02f125f..b35c99424b 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -226,6 +226,36 @@ const
   return 0;
 }
 
+/** Read input for LJ 10-12 hbond. */
+int AmberParamFile::read_lj1012(ParameterSet& prm, const char* ptr)
+const
+{
+  // Lennard-Jones 10-12 hydrogen bonding term.
+  // According to the docs, the format should be:
+  // KT1 , KT2 , A , B , ASOLN , BSOLN , HCUT , IC
+  // FORMAT(2X,A2,2X,A2,2x,5F10.2,I2)
+  // In practive (in e.g. parm91.dat), the actual format appears to be:
+  // KT1, KT2, A, B, HCUT
+  char KT1[MAXSYMLEN], KT2[MAXSYMLEN];
+  double A, B, HCUT;
+  //double ASOLN, BSOLN, HCUT;
+  //int IC;
+  mprintf("DEBUG: LJ 10-12: %s\n", ptr);
+  //int nscan = sscanf(ptr, "%s %s %lf %lf %lf %lf %lf %i\n",
+  int nscan = sscanf(ptr, "%s %s %lf %lf %lf", KT1, KT2, &A, &B, &HCUT);
+  if (nscan < 5) {
+    mprinterr("Error: Expected at least KT1, KT2, A, B, HCUT, got only %i elements\n", nscan);
+    return 1;
+  }
+  TypeNameHolder types(2);
+  types.AddName( KT1 );
+  types.AddName( KT2 );
+  ParameterHolders::RetType ret = prm.HB().AddParm(types, HB_ParmType(A, B, HCUT), false);
+  if (ret == ParameterHolders::UPDATED)
+    mprintf("Warning: Redefining LJ 10-12 hbond type %s %s\n", *(types[0]), *(types[1]));
+  return 0;
+}
+
 /** Read parametrers from Amber frcmod file. */
 int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int debugIn) const
 {
@@ -272,6 +302,8 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int deb
           err = read_dihedral(prm, ptr);
         else if (section == IMPROPER)
           err = read_improper(prm, ptr);
+        else if (section == LJ1012)
+          err = read_lj1012(prm, ptr);
         if (err != 0) {
           mprinterr("Error: Reading line: %s\n", ptr);
           return 1;
@@ -390,27 +422,7 @@ int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
     } else if (section == IMPROPER) {
       read_err = read_improper(prm, ptr);
     } else if (section == LJ1012) {
-      // Lennard-Jones 10-12 hydrogen bonding term.
-      // According to the docs, the format should be:
-      // KT1 , KT2 , A , B , ASOLN , BSOLN , HCUT , IC
-      // FORMAT(2X,A2,2X,A2,2x,5F10.2,I2)
-      // In practive (in e.g. parm91.dat), the actual format appears to be:
-      // KT1, KT2, A, B, HCUT
-      char KT1[MAXSYMLEN], KT2[MAXSYMLEN];
-      double A, B, HCUT;
-      //double ASOLN, BSOLN, HCUT;
-      //int IC;
-      mprintf("DEBUG: LJ 10-12: %s\n", ptr);
-      //int nscan = sscanf(ptr, "%s %s %lf %lf %lf %lf %lf %i\n",
-      int nscan = sscanf(ptr, "%s %s %lf %lf %lf", KT1, KT2, &A, &B, &HCUT);
-      if (nscan < 5) {
-        mprinterr("Error: Expected at least KT1, KT2, A, B, HCUT, got only %i elements\n", nscan);
-        return 1;
-      }
-      TypeNameHolder types(2);
-      types.AddName( KT1 );
-      types.AddName( KT2 );
-      prm.HB().AddParm(types, HB_ParmType(A, B, HCUT), false);
+      read_err = read_lj1012(prm, ptr);
     } else if (section == NB_EQUIV) {
       // EQUIVALENCING ATOM SYMBOLS FOR THE NON-BONDED 6-12 POTENTIAL PARAMETERS
       // IORG , IEQV(I) , I = 1 , 19
diff --git a/src/AmberParamFile.h b/src/AmberParamFile.h
index a4e2292d3a..a2b93498c1 100644
--- a/src/AmberParamFile.h
+++ b/src/AmberParamFile.h
@@ -31,6 +31,8 @@ class AmberParamFile {
     int read_dihedral(ParameterSet&, const char*) const;
     /// Read improper line
     int read_improper(ParameterSet&, const char*) const;
+    /// Read LJ 10-12 hbond line
+    int read_lj1012(ParameterSet&, const char*) const;
     //int ReadInput(std::string&, BufferedLine&) const;
 };
 #endif

From 1857f30789347d303fbe8c21ef52f79d50046447 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 20 Nov 2023 16:12:33 -0500
Subject: [PATCH 0085/1492] Allow parameters to be updated

---
 src/AmberParamFile.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index b35c99424b..133481738f 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -218,7 +218,7 @@ const
   types.AddName( symbols[2] );
   types.AddName( symbols[3] );
   ParameterHolders::RetType ret =
-    prm.IP().AddParm(types, DihedralParmType(PK, PN, PHASE), false);
+    prm.IP().AddParm(types, DihedralParmType(PK, PN, PHASE), true);
   if (ret == ParameterHolders::UPDATED)
     mprintf("Warning: Redefining improper type %s - %s - %s - %s\n",
             *(types[0]), *(types[1]), *(types[2]), *(types[3]));
@@ -250,7 +250,7 @@ const
   TypeNameHolder types(2);
   types.AddName( KT1 );
   types.AddName( KT2 );
-  ParameterHolders::RetType ret = prm.HB().AddParm(types, HB_ParmType(A, B, HCUT), false);
+  ParameterHolders::RetType ret = prm.HB().AddParm(types, HB_ParmType(A, B, HCUT), true);
   if (ret == ParameterHolders::UPDATED)
     mprintf("Warning: Redefining LJ 10-12 hbond type %s %s\n", *(types[0]), *(types[1]));
   return 0;

From 3e827c0d645121dccb0c9c2b7fcd69e03b29a3ee Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 20 Nov 2023 16:17:05 -0500
Subject: [PATCH 0086/1492] Start adding nonbond set read.

---
 src/AmberParamFile.cpp | 33 ++++++++++++++++++++++++++++++++-
 src/AmberParamFile.h   |  5 +++++
 2 files changed, 37 insertions(+), 1 deletion(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 133481738f..b83928dde2 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -33,7 +33,7 @@ int AmberParamFile::read_symbols(const char* ptrIn, std::vector<std::string>& sy
 }
 
 /// Hold a set of nonbonded parameters
-class NonbondSet {
+class AmberParamFile::NonbondSet {
   public:
     NonbondSet(std::string const& n) : name_(n) {}
 
@@ -256,6 +256,37 @@ const
   return 0;
 }
 
+/** Read radius/depth input for LJ 6-12 nonbond. */
+int AmberParamFile::read_nb_RE(NonbondSet& nbset, const char* ptr)
+const
+{
+  // ***** ONLY IF KINDNB .EQ. 'RE' *****
+  // LTYNB , R , EDEP
+  mprintf("DEBUG: Nonbond: %s\n", ptr);
+  //char LTYNB[MAXSYMLEN];
+  //double R, EDEP;
+  //double R14, E14;
+  // This section is a little tricky. Apparently CHARMM-style Amber FF
+  // files can have 14 LJ params here. Try to detect this.
+  ArgList nbargs( ptr, " " );
+  if (nbargs.Nargs() < 3) {
+    mprinterr("Error: Expected at least TYPE, R, DEPTH, got %i elements.\n", nbargs.Nargs());
+    return 1;
+  }
+  bool has_14 = false;
+  if (nbargs.Nargs() >= 5) {
+    if (validDouble( nbargs[3] ) && validDouble( nbargs[4] )) {
+      has_14 = true;
+    }
+  }
+  if (has_14) mprintf("DEBUG: NB HAS CHARMM.\n");
+  double R = convertToDouble( nbargs[1] );
+  double EDEP = convertToDouble( nbargs[2] );
+  nbset.LJ_.AddParm( TypeNameHolder(nbargs[0]), LJparmType(R, EDEP), false );
+  return 0;
+}
+
+
 /** Read parametrers from Amber frcmod file. */
 int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int debugIn) const
 {
diff --git a/src/AmberParamFile.h b/src/AmberParamFile.h
index a2b93498c1..b1b93d1246 100644
--- a/src/AmberParamFile.h
+++ b/src/AmberParamFile.h
@@ -20,6 +20,9 @@ class AmberParamFile {
 
     enum SectionType { ATYPE = 0, HYDROPHILIC, BOND, ANGLE, DIHEDRAL, IMPROPER, 
                        LJ1012, NB_EQUIV, NONBOND, LJEDIT, UNKNOWN };
+
+    class NonbondSet;
+
     static int read_symbols(const char*, std::vector<std::string>&, int);
     /// Read atom type line
     int read_atype(ParameterSet&, const char*) const;
@@ -33,6 +36,8 @@ class AmberParamFile {
     int read_improper(ParameterSet&, const char*) const;
     /// Read LJ 10-12 hbond line
     int read_lj1012(ParameterSet&, const char*) const;
+    /// Read LJ 6-12 R/depth line
+    int read_nb_RE(NonbondSet&, const char*) const;
     //int ReadInput(std::string&, BufferedLine&) const;
 };
 #endif

From 3c7a13148480b1b6355e2c02933d38a8ce09f721 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 20 Nov 2023 19:36:29 -0500
Subject: [PATCH 0087/1492] Nonbonds for frcmod

---
 src/AmberParamFile.cpp | 22 +++++++++++++++++++++-
 1 file changed, 21 insertions(+), 1 deletion(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index b83928dde2..57bb1f13c7 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -282,7 +282,10 @@ const
   if (has_14) mprintf("DEBUG: NB HAS CHARMM.\n");
   double R = convertToDouble( nbargs[1] );
   double EDEP = convertToDouble( nbargs[2] );
-  nbset.LJ_.AddParm( TypeNameHolder(nbargs[0]), LJparmType(R, EDEP), false );
+  TypeNameHolder types( nbargs[0] );
+  ParameterHolders::RetType ret = nbset.LJ_.AddParm( types, LJparmType(R, EDEP), true );
+  if (ret == ParameterHolders::UPDATED)
+    mprintf("Warning: Redefining LJ 6-12 type %s\n", *(types[0]));
   return 0;
 }
 
@@ -304,6 +307,7 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int deb
   std::string title(ptr);
   mprintf("\tTitle: %s\n", title.c_str());
   //prm.SetParamSetName( title ); TODO append title
+  NonbondSet nbset(title);
   // Read file
   SectionType section = UNKNOWN;
   ptr = infile.Line();
@@ -335,6 +339,8 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int deb
           err = read_improper(prm, ptr);
         else if (section == LJ1012)
           err = read_lj1012(prm, ptr);
+        else if (section == NONBOND)
+          err = read_nb_RE(nbset, ptr);
         if (err != 0) {
           mprinterr("Error: Reading line: %s\n", ptr);
           return 1;
@@ -343,6 +349,20 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int deb
     }
     ptr = infile.Line();
   }
+  // Nonbonds
+  for (ParmHolder<LJparmType>::const_iterator it = nbset.LJ_.begin();
+                                              it != nbset.LJ_.end(); ++it)
+  {
+    ParmHolder<AtomType>::iterator at = prm.AT().GetParam( it->first );
+    if (at == prm.AT().end()) {
+      mprinterr("Error: Nonbond parameters defined for previously undefined type '%s'.\n",
+                *(it->first[0]));
+      return 1;
+    } 
+    at->second.SetLJ().SetRadius( it->second.Radius() );
+    at->second.SetLJ().SetDepth( it->second.Depth() );
+  }
+
   prm.Debug(); // TODO debug level
   infile.CloseFile();
 

From 892c3eff0467ec2dcd1dc956b60f3ca0d033a275 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 20 Nov 2023 20:04:25 -0500
Subject: [PATCH 0088/1492] Nonbond parameter assignment fxn

---
 src/AmberParamFile.cpp | 44 +++++++++++++++++++-----------------------
 src/AmberParamFile.h   |  2 ++
 2 files changed, 22 insertions(+), 24 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 57bb1f13c7..5545af4e69 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -289,6 +289,23 @@ const
   return 0;
 }
 
+/** Assign nonbond parameters from a NonbondSet to ParameterSet */
+int AmberParamFile::assign_nb(ParameterSet& prm, NonbondSet const& nbset) const {
+  // Nonbonds
+  for (ParmHolder<LJparmType>::const_iterator it = nbset.LJ_.begin();
+                                              it != nbset.LJ_.end(); ++it)
+  {
+    ParmHolder<AtomType>::iterator at = prm.AT().GetParam( it->first );
+    if (at == prm.AT().end()) {
+      mprinterr("Error: Nonbond parameters defined for previously undefined type '%s'.\n",
+                *(it->first[0]));
+      return 1;
+    } 
+    at->second.SetLJ().SetRadius( it->second.Radius() );
+    at->second.SetLJ().SetDepth( it->second.Depth() );
+  }
+  return 0;
+}
 
 /** Read parametrers from Amber frcmod file. */
 int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int debugIn) const
@@ -350,18 +367,7 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int deb
     ptr = infile.Line();
   }
   // Nonbonds
-  for (ParmHolder<LJparmType>::const_iterator it = nbset.LJ_.begin();
-                                              it != nbset.LJ_.end(); ++it)
-  {
-    ParmHolder<AtomType>::iterator at = prm.AT().GetParam( it->first );
-    if (at == prm.AT().end()) {
-      mprinterr("Error: Nonbond parameters defined for previously undefined type '%s'.\n",
-                *(it->first[0]));
-      return 1;
-    } 
-    at->second.SetLJ().SetRadius( it->second.Radius() );
-    at->second.SetLJ().SetDepth( it->second.Depth() );
-  }
+  if (assign_nb(prm, nbset)) return 1;
 
   prm.Debug(); // TODO debug level
   infile.CloseFile();
@@ -574,18 +580,8 @@ int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
     }
     mprintf("\tUsing nonbonded parm set: %s\n", NBsets[nbsetidx].name_.c_str());
     prm.SetNbParamName( NBsets[nbsetidx].name_ );
-    for (ParmHolder<LJparmType>::const_iterator it = NBsets[nbsetidx].LJ_.begin();
-                                                it != NBsets[nbsetidx].LJ_.end(); ++it)
-    {
-      ParmHolder<AtomType>::iterator at = prm.AT().GetParam( it->first );
-      if (at == prm.AT().end()) {
-        mprinterr("Error: Nonbond parameters defined for previously undefined type '%s'.\n",
-                  *(it->first[0]));
-        return 1;
-      } 
-      at->second.SetLJ().SetRadius( it->second.Radius() );
-      at->second.SetLJ().SetDepth( it->second.Depth() );
-    }
+    if (assign_nb(prm, NBsets[nbsetidx])) return 1;
+    
     // Do equivalent atoms.
     for (XNarray::const_iterator equivAts = EquivalentNames.begin();
                                  equivAts != EquivalentNames.end(); ++equivAts)
diff --git a/src/AmberParamFile.h b/src/AmberParamFile.h
index b1b93d1246..e816c0473d 100644
--- a/src/AmberParamFile.h
+++ b/src/AmberParamFile.h
@@ -38,6 +38,8 @@ class AmberParamFile {
     int read_lj1012(ParameterSet&, const char*) const;
     /// Read LJ 6-12 R/depth line
     int read_nb_RE(NonbondSet&, const char*) const;
+    /// Assign parameters from NonbondSet to ParameterSet
+    int assign_nb(ParameterSet&, NonbondSet const&) const;
     //int ReadInput(std::string&, BufferedLine&) const;
 };
 #endif

From 5cc888a531aa95848f876255d6f42b5e1c618a8d Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 20 Nov 2023 20:13:19 -0500
Subject: [PATCH 0089/1492] Use read_nb_RE function

---
 src/AmberParamFile.cpp | 37 +------------------------------------
 1 file changed, 1 insertion(+), 36 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 5545af4e69..6eb786b1fc 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -491,42 +491,7 @@ int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
         EquivalentNames.back().push_back( equiv_line[iarg] );
     } else if (section == NONBOND) {
       // ***** ONLY IF KINDNB .EQ. 'RE' *****
-      // LTYNB , R , EDEP
-      mprintf("DEBUG: Nonbond: %s\n", ptr);
-      //char LTYNB[MAXSYMLEN];
-      //double R, EDEP;
-      //double R14, E14;
-      // This section is a little tricky. Apparently CHARMM-style Amber FF
-      // files can have 14 LJ params here. Try to detect this.
-      ArgList nbargs( ptr, " " );
-      if (nbargs.Nargs() < 3) {
-        mprinterr("Error: Expected at least TYPE, R, DEPTH, got %i elements.\n", nbargs.Nargs());
-        return 1;
-      }
-      bool has_14 = false;
-      if (nbargs.Nargs() >= 5) {
-        if (validDouble( nbargs[3] ) && validDouble( nbargs[4] )) {
-          has_14 = true;
-        }
-      }
-      if (has_14) mprintf("DEBUG: NB HAS CHARMM.\n");
-      double R = convertToDouble( nbargs[1] );
-      double EDEP = convertToDouble( nbargs[2] );
-      NBsets.back().LJ_.AddParm( TypeNameHolder(nbargs[0]), LJparmType(R, EDEP), false );
-      //int nscan = sscanf(ptr, "%s %lf %lf %lf %lf", LTYNB, &R, &EDEP, &R14, &E14);
-
-      //if (nscan >= 5) {
-      //  // symbol, rmin, epsilon
-      //  NBsets.back().LJ_.AddParm( TypeNameHolder(LTYNB), LJparmType(R, EDEP), false );
-      //  /*ParmHolder<AtomType>::iterator it = prm.AT().GetParam( TypeNameHolder(LTYNB) );
-      //  if (it == prm.AT().end()) {
-      //    mprintf("Warning: Nonbond parameters defined for previously undefined type '%s'."
-      //                    " Skipping.\n", LTYNB);
-      //  } else {
-      //    it->second.SetLJ().SetRadius( R );
-      //    it->second.SetLJ().SetDepth( EDEP );
-      //  }*/
-      //}
+      read_err = read_nb_RE(NBsets.back(), ptr);
     } else if (section == LJEDIT) {
       mprintf("DEBUG: LJedit: %s\n", ptr);
       // Lennard-Jones sigma and epsilon of the first atom type when it

From ffe52beb6e4ce22d214014a33dbac7457cee3f6f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 20 Nov 2023 20:20:51 -0500
Subject: [PATCH 0090/1492] Add function for reading off-diagonal LJ mods

---
 src/AmberParamFile.cpp | 27 +++++++++++++++++++++++++--
 src/AmberParamFile.h   |  4 ++++
 2 files changed, 29 insertions(+), 2 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 6eb786b1fc..5705328d04 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -42,7 +42,7 @@ class AmberParamFile::NonbondSet {
 };
 
 /// Hold an off-diagonal NB modification
-class OffdiagNB {
+class AmberParamFile::OffdiagNB {
   public:
     OffdiagNB(NameType const& AT1, NameType const& AT2, double sig1, double eps1, double sig2, double eps2) :
       types_(2), LJ1_(sig1, eps1), LJ2_(sig2, eps2)
@@ -289,6 +289,26 @@ const
   return 0;
 }
 
+/** Read LJ off-diagonal modifications */
+int AmberParamFile::read_ljedit(Oarray& Offdiag, const char* ptr)
+const
+{
+  mprintf("DEBUG: LJedit: %s\n", ptr);
+  // Lennard-Jones sigma and epsilon of the first atom type when it
+  // interacts with anything under the normal rules, then the sigma
+  // and epsilon of the second atom type when it interacts with the first.
+  char AT1[MAXSYMLEN], AT2[MAXSYMLEN];
+  double sig1, eps1, sig2, eps2;
+  int nscan = sscanf(ptr, "%s %s %lf %lf %lf %lf", AT1, AT2, &sig1, &eps1, &sig2, &eps2);
+  if (nscan != 6) {
+    mprinterr("Error: Expected AT1, AT2, SIG1, EPS1, SIG2, EPS2, got %i elements.\n", nscan);
+    return 1;
+  }
+  Offdiag.push_back( OffdiagNB(AT1, AT2, sig1, eps1, sig2, eps2) );
+  return 0;
+}
+
+
 /** Assign nonbond parameters from a NonbondSet to ParameterSet */
 int AmberParamFile::assign_nb(ParameterSet& prm, NonbondSet const& nbset) const {
   // Nonbonds
@@ -325,6 +345,7 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int deb
   mprintf("\tTitle: %s\n", title.c_str());
   //prm.SetParamSetName( title ); TODO append title
   NonbondSet nbset(title);
+  Oarray Offdiag;
   // Read file
   SectionType section = UNKNOWN;
   ptr = infile.Line();
@@ -338,6 +359,7 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int deb
       else if (line.compare(0, 4, "DIHE") == 0) section = DIHEDRAL;
       else if (line.compare(0, 4, "IMPR") == 0) section = IMPROPER;
       else if (line.compare(0, 4, "HBON") == 0) section = LJ1012;
+      else if (line.compare(0, 6, "LJEDIT") == 0) section = LJEDIT;
       else if (line.compare(0, 4, "NONB") == 0) {
         section = NONBOND;
         // TODO check RE
@@ -358,6 +380,8 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int deb
           err = read_lj1012(prm, ptr);
         else if (section == NONBOND)
           err = read_nb_RE(nbset, ptr);
+        else if (section == LJEDIT)
+          err = read_ljedit(Offdiag, ptr);
         if (err != 0) {
           mprinterr("Error: Reading line: %s\n", ptr);
           return 1;
@@ -388,7 +412,6 @@ int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
   typedef std::vector<Narray> XNarray;
   XNarray EquivalentNames;
   // For holding off-diagonal mods
-  typedef std::vector<OffdiagNB> Oarray;
   Oarray Offdiag;
 
   // Read title
diff --git a/src/AmberParamFile.h b/src/AmberParamFile.h
index e816c0473d..cb30b5ca6c 100644
--- a/src/AmberParamFile.h
+++ b/src/AmberParamFile.h
@@ -22,6 +22,8 @@ class AmberParamFile {
                        LJ1012, NB_EQUIV, NONBOND, LJEDIT, UNKNOWN };
 
     class NonbondSet;
+    class OffdiagNB;
+    typedef std::vector<OffdiagNB> Oarray;
 
     static int read_symbols(const char*, std::vector<std::string>&, int);
     /// Read atom type line
@@ -38,6 +40,8 @@ class AmberParamFile {
     int read_lj1012(ParameterSet&, const char*) const;
     /// Read LJ 6-12 R/depth line
     int read_nb_RE(NonbondSet&, const char*) const;
+    /// Read LJ 6-12 off-diagonal modifications
+    int read_ljedit(Oarray&, const char*) const;
     /// Assign parameters from NonbondSet to ParameterSet
     int assign_nb(ParameterSet&, NonbondSet const&) const;
     //int ReadInput(std::string&, BufferedLine&) const;

From 3d6363168c417e93f4369c224a4898f0e0e3e2d6 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 20 Nov 2023 20:27:59 -0500
Subject: [PATCH 0091/1492] Function for assigning off-diagonal NB params

---
 src/AmberParamFile.cpp | 26 ++++++++++++++++++++++++++
 src/AmberParamFile.h   |  2 ++
 2 files changed, 28 insertions(+)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 5705328d04..620420f9e8 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -327,6 +327,30 @@ int AmberParamFile::assign_nb(ParameterSet& prm, NonbondSet const& nbset) const
   return 0;
 }
 
+/** Assign off-diagonal nonbond parameters from an OffdiagNB array to ParameterSet */
+int AmberParamFile::assign_offdiag(ParameterSet& prm, Oarray const& Offdiag) const {
+  // Do off diagonal NB mods
+  if (!Offdiag.empty()) {
+    for (Oarray::const_iterator od = Offdiag.begin(); od != Offdiag.end(); ++od)
+    {
+      mprintf("DEBUG: Off diag %s %s\n", *(od->types_[0]), *(od->types_[1]));
+      // Set type 1
+      ParmHolder<AtomType>::iterator it = prm.AT().GetParam( od->types_[0] );
+      if (it == prm.AT().end()) {
+        mprinterr("Error: Off-diagonal nonbond parameters defined for previously undefined type '%s'.\n",
+                  *(od->types_[0]));
+        return 1;
+      }
+      it->second.SetLJ().SetRadius( od->LJ1_.Radius() );
+      it->second.SetLJ().SetDepth( od->LJ1_.Depth() );
+      // Set off-diagonal for type1-type2
+      // FIXME different combine rules?
+      prm.NB().AddParm(od->types_, od->LJ1_.Combine_LB(od->LJ2_), false);
+    }
+  } // END off-diagonal NB mods
+  return 0;
+}
+
 /** Read parametrers from Amber frcmod file. */
 int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int debugIn) const
 {
@@ -392,6 +416,8 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int deb
   }
   // Nonbonds
   if (assign_nb(prm, nbset)) return 1;
+  // Off-diagonal NB modifications
+  if (assign_offdiag(prm, Offdiag)) return 1;
 
   prm.Debug(); // TODO debug level
   infile.CloseFile();
diff --git a/src/AmberParamFile.h b/src/AmberParamFile.h
index cb30b5ca6c..8658cf8f73 100644
--- a/src/AmberParamFile.h
+++ b/src/AmberParamFile.h
@@ -44,6 +44,8 @@ class AmberParamFile {
     int read_ljedit(Oarray&, const char*) const;
     /// Assign parameters from NonbondSet to ParameterSet
     int assign_nb(ParameterSet&, NonbondSet const&) const;
+    /// Assign parameters from OffdiagNB array to ParameterSet
+    int assign_offdiag(ParameterSet&, Oarray const&) const;
     //int ReadInput(std::string&, BufferedLine&) const;
 };
 #endif

From b159c83773536d52595683b1c8f7971fbae7fb7c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 20 Nov 2023 20:28:54 -0500
Subject: [PATCH 0092/1492] Use assign_offdiag

---
 src/AmberParamFile.cpp | 19 +------------------
 1 file changed, 1 insertion(+), 18 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 620420f9e8..d075b79ee5 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -622,24 +622,7 @@ int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
   } // END nonbond parameters
 
   // Do off diagonal NB mods
-  if (!Offdiag.empty()) {
-    for (Oarray::const_iterator od = Offdiag.begin(); od != Offdiag.end(); ++od)
-    {
-      mprintf("DEBUG: Off diag %s %s\n", *(od->types_[0]), *(od->types_[1]));
-      // Set type 1
-      ParmHolder<AtomType>::iterator it = prm.AT().GetParam( od->types_[0] );
-      if (it == prm.AT().end()) {
-        mprinterr("Error: Off-diagonal nonbond parameters defined for previously undefined type '%s'.\n",
-                  *(od->types_[0]));
-        return 1;
-      }
-      it->second.SetLJ().SetRadius( od->LJ1_.Radius() );
-      it->second.SetLJ().SetDepth( od->LJ1_.Depth() );
-      // Set off-diagonal for type1-type2
-      // FIXME different combine rules?
-      prm.NB().AddParm(od->types_, od->LJ1_.Combine_LB(od->LJ2_), false);
-    }
-  } // END off-diagonal NB mods
+  if (assign_offdiag(prm, Offdiag)) return 1;
 
   prm.Debug(); // TODO debug level
   infile.CloseFile();

From 9381d0362da502f761ca725f87adccb25da69010 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 21 Nov 2023 08:54:54 -0500
Subject: [PATCH 0093/1492] Use read_ljedit. Hide some debug info. Ensure has
 LJ params flag is set.

---
 src/AmberParamFile.cpp | 58 ++++++++++++++++++++----------------------
 src/AmberParamFile.h   |  4 +++
 2 files changed, 32 insertions(+), 30 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index d075b79ee5..0a7f55426e 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -10,7 +10,14 @@
 const int AmberParamFile::MAXSYMLEN = 16;
 
 /// CONSTRUCTOR
-AmberParamFile::AmberParamFile() {}
+AmberParamFile::AmberParamFile() :
+  debug_(0)
+{}
+
+/** Set debug level */
+void AmberParamFile::SetDebug(int d) {
+  debug_ = d;
+}
 
 /** Read symbols delimited by - and space. */
 int AmberParamFile::read_symbols(const char* ptrIn, std::vector<std::string>& symbols, int nsymbols)
@@ -61,7 +68,7 @@ int AmberParamFile::read_atype(ParameterSet& prm, const char* ptr)
 const
 {
   // Format (A2,2X,F10.2x,f10.2)
-  mprintf("DEBUG: Atype: %s\n", ptr);
+  if (debug_ > 1) mprintf("DEBUG: Atype: %s\n", ptr);
   char kndsym[MAXSYMLEN];
   double amass = 0;
   double atpol = 0;
@@ -92,14 +99,14 @@ const
   // Bond parameters
   // IBT , JBT , RK , REQ
   // FORMAT(A2,1X,A2,2F10.2)
-  mprintf("DEBUG: Bond: %s\n", ptr);
+  if (debug_ > 1) mprintf("DEBUG: Bond: %s\n", ptr);
   std::vector<std::string> symbols(2);
   int pos = read_symbols(ptr, symbols, 2);
   if (pos < 0) {
     mprinterr("Error: Could not read symbols for bond from %s\n", ptr);
     return 1;
   }
-  mprintf("DEBUG: %s %s '%s'\n", symbols[0].c_str(), symbols[1].c_str(), ptr+pos);
+  //mprintf("DEBUG: %s %s '%s'\n", symbols[0].c_str(), symbols[1].c_str(), ptr+pos);
   double RK, REQ;
   int nscan = sscanf(ptr+pos, "%lf %lf", &RK, &REQ);
   if (nscan != 2) {
@@ -123,14 +130,14 @@ const
   // Angle parameters
   // ITT , JTT , KTT , TK , TEQ
   // FORMAT(A2,1X,A2,1X,A2,2F10.2)
-  mprintf("DEBUG: Angle: %s\n", ptr);
+  if (debug_ > 1) mprintf("DEBUG: Angle: %s\n", ptr);
   std::vector<std::string> symbols(3);
   int pos = read_symbols(ptr, symbols, 3);
   if (pos < 0) {
     mprinterr("Error: Could not read symbols for angle from %s\n", ptr);
     return 1;
   }
-  mprintf("DEBUG: %s %s %s '%s'\n", symbols[0].c_str(), symbols[1].c_str(), symbols[2].c_str(), ptr+pos);
+  //mprintf("DEBUG: %s %s %s '%s'\n", symbols[0].c_str(), symbols[1].c_str(), symbols[2].c_str(), ptr+pos);
   double TK, TEQ;
   int nscan = sscanf(ptr+pos, "%lf %lf", &TK, &TEQ);
   if (nscan != 2) {
@@ -163,14 +170,14 @@ const
   // Consult Weiner, et al., JACS 106:765 (1984) p. 769 for
   // details. Basically, the actual torsional potential is
   //   (PK/IDIVF) * (1 + cos(PN*phi - PHASE))
-  mprintf("DEBUG: Dihedral: %s\n", ptr);
+  if (debug_ > 1) mprintf("DEBUG: Dihedral: %s\n", ptr);
   std::vector<std::string> symbols(4);
   int pos = read_symbols(ptr, symbols, 4);
   if (pos < 0) {
     mprinterr("Error: Could not read symbols for dihedral from %s\n", ptr);
     return 1;
   }
-  mprintf("DEBUG: %s %s %s %s '%s'\n", symbols[0].c_str(), symbols[1].c_str(), symbols[2].c_str(), symbols[3].c_str(), ptr+pos);
+  //mprintf("DEBUG: %s %s %s %s '%s'\n", symbols[0].c_str(), symbols[1].c_str(), symbols[2].c_str(), symbols[3].c_str(), ptr+pos);
   int IDIVF;
   double PK, PHASE, PN;
   int nscan = sscanf(ptr+pos, "%i %lf %lf %lf", &IDIVF, &PK, &PHASE, &PN);
@@ -198,14 +205,14 @@ const
   // Improper parameters
   // IPT , JPT , KPT , LPT , IDIVF , PK , PHASE , PN
   // FORMAT(A2,1X,A2,1X,A2,1X,A2,I4,3F15.2)
-  mprintf("DEBUG: Improper: %s\n", ptr);
+  if (debug_ > 1) mprintf("DEBUG: Improper: %s\n", ptr);
   std::vector<std::string> symbols(4);
   int pos = read_symbols(ptr, symbols, 4);
   if (pos < 0) {
     mprinterr("Error: Could not read symbols for improper from %s\n", ptr);
     return 1;
   }
-  mprintf("DEBUG: %s %s %s %s '%s'\n", symbols[0].c_str(), symbols[1].c_str(), symbols[2].c_str(), symbols[3].c_str(), ptr+pos);
+  //mprintf("DEBUG: %s %s %s %s '%s'\n", symbols[0].c_str(), symbols[1].c_str(), symbols[2].c_str(), symbols[3].c_str(), ptr+pos);
   double PK, PHASE, PN;
   int nscan = sscanf(ptr+pos, "%lf %lf %lf", &PK, &PHASE, &PN);
   if (nscan != 3) {
@@ -240,7 +247,7 @@ const
   double A, B, HCUT;
   //double ASOLN, BSOLN, HCUT;
   //int IC;
-  mprintf("DEBUG: LJ 10-12: %s\n", ptr);
+  if (debug_ > 1) mprintf("DEBUG: LJ 10-12: %s\n", ptr);
   //int nscan = sscanf(ptr, "%s %s %lf %lf %lf %lf %lf %i\n",
   int nscan = sscanf(ptr, "%s %s %lf %lf %lf", KT1, KT2, &A, &B, &HCUT);
   if (nscan < 5) {
@@ -262,7 +269,7 @@ const
 {
   // ***** ONLY IF KINDNB .EQ. 'RE' *****
   // LTYNB , R , EDEP
-  mprintf("DEBUG: Nonbond: %s\n", ptr);
+  if (debug_ > 1) mprintf("DEBUG: Nonbond: %s\n", ptr);
   //char LTYNB[MAXSYMLEN];
   //double R, EDEP;
   //double R14, E14;
@@ -279,7 +286,7 @@ const
       has_14 = true;
     }
   }
-  if (has_14) mprintf("DEBUG: NB HAS CHARMM.\n");
+  if (has_14) mprintf("DEBUG: NB HAS 1-4 LJ PARAMS.\n"); // FIXME save these
   double R = convertToDouble( nbargs[1] );
   double EDEP = convertToDouble( nbargs[2] );
   TypeNameHolder types( nbargs[0] );
@@ -293,7 +300,7 @@ const
 int AmberParamFile::read_ljedit(Oarray& Offdiag, const char* ptr)
 const
 {
-  mprintf("DEBUG: LJedit: %s\n", ptr);
+  if (debug_ > 1) mprintf("DEBUG: LJedit: %s\n", ptr);
   // Lennard-Jones sigma and epsilon of the first atom type when it
   // interacts with anything under the normal rules, then the sigma
   // and epsilon of the second atom type when it interacts with the first.
@@ -333,7 +340,7 @@ int AmberParamFile::assign_offdiag(ParameterSet& prm, Oarray const& Offdiag) con
   if (!Offdiag.empty()) {
     for (Oarray::const_iterator od = Offdiag.begin(); od != Offdiag.end(); ++od)
     {
-      mprintf("DEBUG: Off diag %s %s\n", *(od->types_[0]), *(od->types_[1]));
+      if (debug_ > 1) mprintf("DEBUG: Off diag %s %s\n", *(od->types_[0]), *(od->types_[1]));
       // Set type 1
       ParmHolder<AtomType>::iterator it = prm.AT().GetParam( od->types_[0] );
       if (it == prm.AT().end()) {
@@ -386,6 +393,7 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int deb
       else if (line.compare(0, 6, "LJEDIT") == 0) section = LJEDIT;
       else if (line.compare(0, 4, "NONB") == 0) {
         section = NONBOND;
+        prm.SetHasLJparams( true );
         // TODO check RE
       } else {
         //mprintf("DEBUG: Section %i: %s\n", (int)section, ptr);
@@ -487,7 +495,7 @@ int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
         // Special case: hydrophilic atom types. One line.
         // FORMAT(20(A2,2X))
         ptr = infile.Line();
-        mprintf("DEBUG: Hydrophilic: %s\n", ptr);
+        if (debug_ > 1) mprintf("DEBUG: Hydrophilic: %s\n", ptr);
         // Take advantage of the fact that we expect whitespace-delimiters
         ArgList hsymbols( ptr, " " );
         for (int iarg = 0; iarg != hsymbols.Nargs(); ++iarg)
@@ -499,6 +507,7 @@ int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
         while (*ptr == ' ' && *ptr != '\0') ++ptr;
         if (*ptr != '\0') continue;
       } else if (section == NONBOND) {
+        prm.SetHasLJparams( true );
         // Special case: first read the line.
         // LABEL , KINDNB
         // FORMAT(A4,6X,A2)
@@ -533,7 +542,7 @@ int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
       // EQUIVALENCING ATOM SYMBOLS FOR THE NON-BONDED 6-12 POTENTIAL PARAMETERS
       // IORG , IEQV(I) , I = 1 , 19
       // FORMAT(20(A2,2X))
-      mprintf("DEBUG: Nonbond equiv: %s\n", ptr);
+      if (debug_ > 1) mprintf("DEBUG: Nonbond equiv: %s\n", ptr);
       EquivalentNames.push_back( Narray() );
       ArgList equiv_line( ptr, " " );
       for (int iarg = 0; iarg != equiv_line.Nargs(); iarg++)
@@ -542,18 +551,7 @@ int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
       // ***** ONLY IF KINDNB .EQ. 'RE' *****
       read_err = read_nb_RE(NBsets.back(), ptr);
     } else if (section == LJEDIT) {
-      mprintf("DEBUG: LJedit: %s\n", ptr);
-      // Lennard-Jones sigma and epsilon of the first atom type when it
-      // interacts with anything under the normal rules, then the sigma
-      // and epsilon of the second atom type when it interacts with the first.
-      char AT1[MAXSYMLEN], AT2[MAXSYMLEN];
-      double sig1, eps1, sig2, eps2;
-      int nscan = sscanf(ptr, "%s %s %lf %lf %lf %lf", AT1, AT2, &sig1, &eps1, &sig2, &eps2);
-      if (nscan != 6) {
-        mprinterr("Error: Expected AT1, AT2, SIG1, EPS1, SIG2, EPS2, got %i elements.\n", nscan);
-        return 1;
-      }
-      Offdiag.push_back( OffdiagNB(AT1, AT2, sig1, eps1, sig2, eps2) );
+      read_err = read_ljedit(Offdiag, ptr);
     }
     if (read_err != 0) {
       mprinterr("Error: Reading line: %s\n", ptr);
@@ -614,7 +612,7 @@ int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
           mprinterr("Error: Equivalent atom type '%s' (base '%s') not found.\n", *(*typeName), *(at0->first[0]));
           return 1;
         }
-        mprintf("DEBUG: Equiv '%s' => '%s'\n", *(at0->first[0]), *(*typeName));
+        if (debug_ > 1) mprintf("DEBUG: Equiv '%s' => '%s'\n", *(at0->first[0]), *(*typeName));
         at1->second.SetLJ().SetRadius( at0->second.LJ().Radius() );
         at1->second.SetLJ().SetDepth( at0->second.LJ().Depth() );
       }
diff --git a/src/AmberParamFile.h b/src/AmberParamFile.h
index 8658cf8f73..8a3cff620a 100644
--- a/src/AmberParamFile.h
+++ b/src/AmberParamFile.h
@@ -15,6 +15,8 @@ class AmberParamFile {
     int ReadFrcmod(ParameterSet&, FileName const&, int) const;
     /// Write main Amber FF file
     int WriteParams(ParameterSet&, FileName const&, int) const;
+    /// Set debug level
+    void SetDebug(int);
   private:
     static const int MAXSYMLEN;
 
@@ -47,5 +49,7 @@ class AmberParamFile {
     /// Assign parameters from OffdiagNB array to ParameterSet
     int assign_offdiag(ParameterSet&, Oarray const&) const;
     //int ReadInput(std::string&, BufferedLine&) const;
+
+    int debug_;
 };
 #endif

From ad24d2bf20d83986dba0c1772e15204e529a4799 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 21 Nov 2023 08:56:32 -0500
Subject: [PATCH 0094/1492] Set nonbonded flag for LJEDIT as well

---
 src/AmberParamFile.cpp | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 0a7f55426e..49f3239c3c 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -390,8 +390,10 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int deb
       else if (line.compare(0, 4, "DIHE") == 0) section = DIHEDRAL;
       else if (line.compare(0, 4, "IMPR") == 0) section = IMPROPER;
       else if (line.compare(0, 4, "HBON") == 0) section = LJ1012;
-      else if (line.compare(0, 6, "LJEDIT") == 0) section = LJEDIT;
-      else if (line.compare(0, 4, "NONB") == 0) {
+      else if (line.compare(0, 6, "LJEDIT") == 0) {
+        section = LJEDIT;
+        prm.SetHasLJparams( true );
+      } else if (line.compare(0, 4, "NONB") == 0) {
         section = NONBOND;
         prm.SetHasLJparams( true );
         // TODO check RE
@@ -484,6 +486,7 @@ int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
             section = UNKNOWN;
           } else if (nbline == "LJEDIT") {
             section = LJEDIT;
+            prm.SetHasLJparams( true );
           } // Otherwise assume another nonbond section
         } else {
           mprintf("SECTION %i change to %i\n", (int)section, (int)section + 1);

From 22103f65bb19794c211e70ea1f58b08d25756310 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 21 Nov 2023 09:18:49 -0500
Subject: [PATCH 0095/1492] Allow ParameterSet to store multiple titles for
 better tracking of what parameter sets are actually present

---
 src/AmberParamFile.cpp |  2 +-
 src/ParameterSet.cpp   | 17 +++++++++++++++--
 src/ParameterSet.h     |  5 +++--
 3 files changed, 19 insertions(+), 5 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 49f3239c3c..579d89c24d 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -374,7 +374,7 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int deb
   }
   std::string title(ptr);
   mprintf("\tTitle: %s\n", title.c_str());
-  //prm.SetParamSetName( title ); TODO append title
+  prm.SetParamSetName( title );
   NonbondSet nbset(title);
   Oarray Offdiag;
   // Read file
diff --git a/src/ParameterSet.cpp b/src/ParameterSet.cpp
index 4a1b4defaf..def78e59b9 100644
--- a/src/ParameterSet.cpp
+++ b/src/ParameterSet.cpp
@@ -19,7 +19,7 @@ void ParameterSet::Debug(const char* fnameIn) const {
   CpptrajFile Out;
   Out.OpenWrite( fnameIn );
   if (!name_.empty())
-    Out.Printf("Parameter set: %s\n", name_.c_str());
+    Out.Printf("Parameter set: %s\n", ParamSetName().c_str());
   if (!NBname_.empty())
     Out.Printf("Nonbond parameters name: %s\n", NBname_.c_str());
   Out.Printf("Atom Types:\n");
@@ -132,9 +132,22 @@ int ParameterSet::AddHydrophilicAtomType(NameType const& atype) {
   return 0;
 }
 
+/** \return Single string with total parameter set name */
+std::string ParameterSet::ParamSetName() const {
+  if (name_.size() == 1)
+    return name_.front();
+  else if (name_.size() > 1) {
+    std::string out = name_.front();
+    for (unsigned int idx = 1; idx < name_.size(); idx++)
+      out.append(" + " + name_[idx]);
+    return out;
+  }
+  return std::string();
+}
+
 /** Set parameter set name. */
 void ParameterSet::SetParamSetName(std::string const& nameIn) {
-  name_ = nameIn;
+  name_.push_back( nameIn );
 }
 
 /** Set nonbond parameter set name. */
diff --git a/src/ParameterSet.h b/src/ParameterSet.h
index 3cfd233e2d..d842f6a8dc 100644
--- a/src/ParameterSet.h
+++ b/src/ParameterSet.h
@@ -30,8 +30,8 @@ class ParameterSet {
     ParmHolder<DihedralParmType> const& IP() const { return impParm_;   }
     DihedralParmHolder const& DP()           const { return dihParm_;   }
     ParmHolder<HB_ParmType> const& HB()      const { return HBparm_;    }
-    std::string const& ParamSetName()        const { return name_;      }
     std::string const& NbParamName()         const { return NBname_;    }
+    std::string ParamSetName()               const;
 
     void Debug(const char*) const;
     void Debug() const { return Debug(""); }
@@ -66,8 +66,9 @@ class ParameterSet {
     size_t DataSize() const;
   private:
     typedef std::vector<NameType> NsetType;
+    typedef std::vector<std::string> Sarray;
 
-    std::string name_;                     ///< Parameter set name
+    Sarray name_;                          ///< Parameter set name(s)
     std::string NBname_;                   ///< Nonbond set name
 
     ParmHolder<AtomType> atomTypes_;       ///< Atom types

From f0eaab5a4d278eb59c8fe8e6a3f39dddfb00b9cc Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 21 Nov 2023 09:46:24 -0500
Subject: [PATCH 0096/1492] Use print function built into ParameterSet to write
 parameters as generic data

---
 src/DataIO_Std.cpp   | 30 ++++++++++++++++++++++++++++++
 src/DataIO_Std.h     |  1 +
 src/ParameterSet.cpp |  7 +++++++
 src/ParameterSet.h   |  6 +++++-
 src/cpptrajdepend    |  2 +-
 5 files changed, 44 insertions(+), 2 deletions(-)

diff --git a/src/DataIO_Std.cpp b/src/DataIO_Std.cpp
index 280707d5bd..466399d77e 100644
--- a/src/DataIO_Std.cpp
+++ b/src/DataIO_Std.cpp
@@ -21,6 +21,7 @@
 #include "DataSet_MatrixFlt.h"
 #include "DataSet_MatrixDbl.h"
 #include "DataSet_3D.h"
+#include "DataSet_Parameters.h"
 
 // CONSTRUCTOR
 DataIO_Std::DataIO_Std() :
@@ -44,6 +45,7 @@ DataIO_Std::DataIO_Std() :
   dims_[0] = 0;
   dims_[1] = 0;
   dims_[2] = 0;
+  SetValid( DataSet::PARAMETERS );
 }
 
 static void PrintColumnError(int idx) {
@@ -1173,11 +1175,39 @@ int DataIO_Std::WriteData(FileName const& fname, DataSetList const& SetList)
       err = WriteData2D(file, SetList);
     else if (SetList[0]->Ndim() == 3)
       err = WriteData3D(file, SetList);
+    else if (SetList[0]->Type() == DataSet::PARAMETERS)
+      err = WriteParameters(file, SetList);
+    else
+      mprintf("Warning: Could not determine how to write dat based on set '%s'\n",
+              SetList[0]->legend());
     file.CloseFile();
   }
   return err;
 }
 
+/** Write parameters to data file. */
+int DataIO_Std::WriteParameters(CpptrajFile& file, DataSetList const& Sets) const {
+  if (Sets.size() == 1) {
+    DataSet_Parameters const& prm = static_cast<DataSet_Parameters const&>( *(Sets[0]) );
+    prm.Print(file);
+  } else if (Sets.size() > 1) {
+    // Create a combined parameter set
+    ParameterSet prm;
+    for (DataSetList::const_iterator it = Sets.begin(); it != Sets.end(); ++it)
+    {
+      if ((*it)->Type() == DataSet::PARAMETERS) {
+        DataSet_Parameters const& param = static_cast<DataSet_Parameters const&>( *(*it) );
+        ParameterSet::UpdateCount UC;
+        prm.UpdateParamSet( param, UC, debug_ );
+      } else {
+        mprintf("Warning: Set '%s' is not a parameter set, skipping.\n", (*it)->legend());
+      }
+    }
+    prm.Print(file);
+  }
+  return 0;
+}
+
 // DataIO_Std::WriteCmatrix()
 int DataIO_Std::WriteCmatrix(CpptrajFile& file, DataSetList const& Sets) {
   for (DataSetList::const_iterator ds = Sets.begin(); ds != Sets.end(); ++ds)
diff --git a/src/DataIO_Std.h b/src/DataIO_Std.h
index 087be23cca..74292bfe06 100644
--- a/src/DataIO_Std.h
+++ b/src/DataIO_Std.h
@@ -38,6 +38,7 @@ class DataIO_Std : public DataIO {
     int WriteData3D(CpptrajFile&, DataSetList const&);
     int WriteSet2D(DataSet const&, CpptrajFile&);
     int WriteSet3D(DataSet const&, CpptrajFile&);
+    int WriteParameters(CpptrajFile&, DataSetList const&) const;
 
     modeType mode_;    ///< Read mode
     precType prec_;    ///< 3d reads, data set precision
diff --git a/src/ParameterSet.cpp b/src/ParameterSet.cpp
index def78e59b9..94b4bc1b36 100644
--- a/src/ParameterSet.cpp
+++ b/src/ParameterSet.cpp
@@ -15,9 +15,16 @@ size_t ParameterSet::DataSize() const {
           (hydrophilicAtomTypes_.size() * NameType::DataSize()));
 }
 
+/** Write parameters out to file with given name. */
 void ParameterSet::Debug(const char* fnameIn) const {
   CpptrajFile Out;
   Out.OpenWrite( fnameIn );
+  Print( Out );
+  Out.CloseFile();
+}
+
+/** Write parameters out to given file. */
+void ParameterSet::Print(CpptrajFile& Out) const {
   if (!name_.empty())
     Out.Printf("Parameter set: %s\n", ParamSetName().c_str());
   if (!NBname_.empty())
diff --git a/src/ParameterSet.h b/src/ParameterSet.h
index d842f6a8dc..d565f29868 100644
--- a/src/ParameterSet.h
+++ b/src/ParameterSet.h
@@ -3,6 +3,7 @@
 #include "ParameterTypes.h"
 #include "ParameterHolders.h"
 #include "AtomType.h"
+class CpptrajFile;
 /// Hold a set of parameters for atom types, bonds, angles, etc.
 class ParameterSet {
   public:
@@ -32,9 +33,12 @@ class ParameterSet {
     ParmHolder<HB_ParmType> const& HB()      const { return HBparm_;    }
     std::string const& NbParamName()         const { return NBname_;    }
     std::string ParamSetName()               const;
-
+    /// Write parameters to file with given name
     void Debug(const char*) const;
+    /// Write parameters to stdout
     void Debug() const { return Debug(""); }
+    /// Print parameters to given file
+    void Print(CpptrajFile&) const;
 
     /// Used to track what parameters were updated during UpdateParams
     class UpdateCount {
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 347343a149..8d28b6c184 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -226,7 +226,7 @@ DataIO_Numpy.o : DataIO_Numpy.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h A
 DataIO_OpenDx.o : DataIO_OpenDx.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_OpenDx.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridDbl.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Peaks.o : DataIO_Peaks.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Peaks.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector_Scalar.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_RemLog.o : DataIO_RemLog.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_RemLog.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_Std.o : DataIO_Std.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Cluster/Cframes.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Std.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_string.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_Std.o : DataIO_Std.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Cluster/Cframes.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Std.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_Parameters.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_string.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_VecTraj.o : DataIO_VecTraj.cpp ActionFrameCounter.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_VecTraj.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_XVG.o : DataIO_XVG.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_XVG.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Xplor.o : DataIO_Xplor.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Xplor.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h

From d860e66a4904ae31af4ab9adfe771aa426754f60 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 21 Nov 2023 09:50:43 -0500
Subject: [PATCH 0097/1492] Hide more debug info

---
 src/AmberParamFile.cpp | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 579d89c24d..20eda87552 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -429,7 +429,7 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int deb
   // Off-diagonal NB modifications
   if (assign_offdiag(prm, Offdiag)) return 1;
 
-  prm.Debug(); // TODO debug level
+  if (debug_ > 0) prm.Debug();
   infile.CloseFile();
 
   return 0;
@@ -489,7 +489,7 @@ int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
             prm.SetHasLJparams( true );
           } // Otherwise assume another nonbond section
         } else {
-          mprintf("SECTION %i change to %i\n", (int)section, (int)section + 1);
+          if (debug_ > 0) mprintf("SECTION %i change to %i\n", (int)section, (int)section + 1);
           section = (SectionType)((int)section + 1);
         }
       }
@@ -625,7 +625,7 @@ int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
   // Do off diagonal NB mods
   if (assign_offdiag(prm, Offdiag)) return 1;
 
-  prm.Debug(); // TODO debug level
+  if (debug_ > 0) prm.Debug();
   infile.CloseFile();
   return 0;
 }

From b9c7d85852e0eb124f6ae95e780b8797c92bf2dd Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 21 Nov 2023 10:40:46 -0500
Subject: [PATCH 0098/1492] When updating dihedral, report multiplicity

---
 src/AmberParamFile.cpp | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 20eda87552..18e7a343cf 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -192,9 +192,11 @@ const
   types.AddName( symbols[3] );
   ParameterHolders::RetType ret =
     prm.DP().AddParm(types, DihedralParmType(PK / (double)IDIVF, PN, PHASE), true);
-  if (ret == ParameterHolders::UPDATED)
-    mprintf("Warning: Redefining dihedral type %s - %s - %s - %s\n",
-            *(types[0]), *(types[1]), *(types[2]), *(types[3]));
+  if (ret == ParameterHolders::UPDATED) {
+    mprintf("Warning: Redefining dihedral type %s - %s - %s - %s (PN=%g)\n",
+            *(types[0]), *(types[1]), *(types[2]), *(types[3]), PN);
+    //mprintf("DEBUG: %s\n", ptr);
+  }
   return 0;
 }
 

From b59d31f50df9ae9058dda347631e326edf75b8e9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 21 Nov 2023 11:09:19 -0500
Subject: [PATCH 0099/1492] Start adding frcmod read test

---
 test/Test_ReadAmberFF/RunTest.sh    | 15 +++++++++++++++
 test/Test_ReadAmberFF/frcmod.tip3pf | 17 +++++++++++++++++
 2 files changed, 32 insertions(+)
 create mode 100755 test/Test_ReadAmberFF/RunTest.sh
 create mode 100644 test/Test_ReadAmberFF/frcmod.tip3pf

diff --git a/test/Test_ReadAmberFF/RunTest.sh b/test/Test_ReadAmberFF/RunTest.sh
new file mode 100755
index 0000000000..c403f6d4ff
--- /dev/null
+++ b/test/Test_ReadAmberFF/RunTest.sh
@@ -0,0 +1,15 @@
+#!/bin/bash
+
+. ../MasterTest.sh
+
+CleanFiles cpptraj.in tip3pf.parm.dat
+
+INPUT='-i cpptraj.in'
+
+cat > cpptraj.in <<EOF
+readdata frcmod.tip3pf as frcmod name PARM
+writedata tip3pf.parm.dat PARM
+EOF
+RunCpptraj "Test read Amber force modification file."
+
+EndTest
diff --git a/test/Test_ReadAmberFF/frcmod.tip3pf b/test/Test_ReadAmberFF/frcmod.tip3pf
new file mode 100644
index 0000000000..71695ee7c8
--- /dev/null
+++ b/test/Test_ReadAmberFF/frcmod.tip3pf
@@ -0,0 +1,17 @@
+This is TIP3P (model F) of Price and Brooks, JCP 121:10096, 2004 
+MASS
+OW    16.0
+HW     1.008   0.000
+ 
+BOND
+OW-HW  553.0    0.9572      TIP3P water
+HW-HW  553.0    1.5136      TIP3P water
+ 
+ANGLE
+
+DIHE
+
+NONBON
+  OW       1.7926    0.098 
+  HW          0.0000  0.0000
+

From 8470156995d75540070152e24b3990c43b92c021 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 21 Nov 2023 11:12:10 -0500
Subject: [PATCH 0100/1492] Ensure we skip leading whitespace

---
 src/AmberParamFile.cpp | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 18e7a343cf..1663fad019 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -383,6 +383,8 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int deb
   SectionType section = UNKNOWN;
   ptr = infile.Line();
   while (ptr != 0) {
+    // Advance to first non-space char
+    while (*ptr == ' ' && *ptr != '\0') ++ptr;
     // Is this a recognized section keyword?
     if (*ptr != '\0') {
       std::string line(ptr);

From 08aaf110eee6ccf1f061ee5cb8c55cb025c673c9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 21 Nov 2023 11:12:40 -0500
Subject: [PATCH 0101/1492] Add frcmod read test save

---
 test/Test_ReadAmberFF/RunTest.sh           | 1 +
 test/Test_ReadAmberFF/tip3pf.parm.dat.save | 9 +++++++++
 2 files changed, 10 insertions(+)
 create mode 100644 test/Test_ReadAmberFF/tip3pf.parm.dat.save

diff --git a/test/Test_ReadAmberFF/RunTest.sh b/test/Test_ReadAmberFF/RunTest.sh
index c403f6d4ff..951aaa5680 100755
--- a/test/Test_ReadAmberFF/RunTest.sh
+++ b/test/Test_ReadAmberFF/RunTest.sh
@@ -11,5 +11,6 @@ readdata frcmod.tip3pf as frcmod name PARM
 writedata tip3pf.parm.dat PARM
 EOF
 RunCpptraj "Test read Amber force modification file."
+DoTest tip3pf.parm.dat.save tip3pf.parm.dat
 
 EndTest
diff --git a/test/Test_ReadAmberFF/tip3pf.parm.dat.save b/test/Test_ReadAmberFF/tip3pf.parm.dat.save
new file mode 100644
index 0000000000..caf195f526
--- /dev/null
+++ b/test/Test_ReadAmberFF/tip3pf.parm.dat.save
@@ -0,0 +1,9 @@
+Parameter set: This is TIP3P (model F) of Price and Brooks, JCP 121:10096, 2004 
+Atom Types:
+	  Name  TypeIdx       Radius        Depth         Mass       Polar.
+	    OW        0       1.7926       0.0980      16.0000       0.0000
+	    HW        1       0.0000       0.0000       1.0080       0.0000
+Bond parameters:
+	 Type1  Type2 :           Rk          Req
+	    OW     HW :     553.0000       0.9572
+	    HW     HW :     553.0000       1.5136

From fc22746d6c82301a92a624db925241955ce55e20 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 21 Nov 2023 11:17:50 -0500
Subject: [PATCH 0102/1492] Add read amber FF file

---
 test/Test_ReadAmberFF/RunTest.sh           |   8 +-
 test/Test_ReadAmberFF/toyrna.parm.dat.save | 137 +++++++++++++++++++++
 2 files changed, 143 insertions(+), 2 deletions(-)
 create mode 100644 test/Test_ReadAmberFF/toyrna.parm.dat.save

diff --git a/test/Test_ReadAmberFF/RunTest.sh b/test/Test_ReadAmberFF/RunTest.sh
index 951aaa5680..b75a167ece 100755
--- a/test/Test_ReadAmberFF/RunTest.sh
+++ b/test/Test_ReadAmberFF/RunTest.sh
@@ -2,15 +2,19 @@
 
 . ../MasterTest.sh
 
-CleanFiles cpptraj.in tip3pf.parm.dat
+CleanFiles cpptraj.in tip3pf.parm.dat toyrna.parm.dat
 
 INPUT='-i cpptraj.in'
 
 cat > cpptraj.in <<EOF
 readdata frcmod.tip3pf as frcmod name PARM
 writedata tip3pf.parm.dat PARM
+
+readdata toyrna.dat as amberff name TOYRNA
+writedata toyrna.parm.dat TOYRNA
 EOF
-RunCpptraj "Test read Amber force modification file."
+RunCpptraj "Test read Amber FF and force modification files."
 DoTest tip3pf.parm.dat.save tip3pf.parm.dat
+DoTest toyrna.parm.dat.save toyrna.parm.dat
 
 EndTest
diff --git a/test/Test_ReadAmberFF/toyrna.parm.dat.save b/test/Test_ReadAmberFF/toyrna.parm.dat.save
new file mode 100644
index 0000000000..9e403254e2
--- /dev/null
+++ b/test/Test_ReadAmberFF/toyrna.parm.dat.save
@@ -0,0 +1,137 @@
+Parameter set: toyrna force field
+Nonbond parameters name: MOD4
+Atom Types:
+	  Name  TypeIdx       Radius        Depth         Mass       Polar.
+	    CB        0       2.0000       0.2000      56.0000       0.0000
+	    CS        1       2.0000       0.2000      43.0000       0.0000
+	    G9        2       1.8000       0.3000      25.0000       0.0000
+	    G7        3       1.8000       0.2000      25.0000       0.0000
+	    G6        4       1.8000       0.2000      25.0000       0.0000
+	    G1        5       1.8000       0.2000      25.0000       0.0000
+	    G2        6       1.8000       0.2000      25.0000       0.0000
+	    G3        7       1.8000       0.2000      25.0000       0.0000
+	    A9        8       1.8000       0.3000      26.8000       0.0000
+	    A7        9       1.8000       0.2000      26.8000       0.0000
+	    A6       10       1.8000       0.2000      26.8000       0.0000
+	    A1       11       1.8000       0.2000      26.8000       0.0000
+	    A3       12       1.8000       0.2000      26.8000       0.0000
+	    U1       13       1.8000       0.3000      27.7500       0.0000
+	    U3       14       1.8000       0.2000      27.7500       0.0000
+	    U4       15       1.8000       0.2000      27.7500       0.0000
+	    U2       16       1.8000       0.2000      27.7500       0.0000
+	    C1       17       1.8000       0.3000      27.5000       0.0000
+	    C3       18       1.8000       0.2000      27.5000       0.0000
+	    C4       19       1.8000       0.2000      27.5000       0.0000
+	    C2       20       1.8000       0.2000      27.5000       0.0000
+	     P       21       3.0000       0.2000      95.0000       0.0000
+HB LJ 10-12 parameters:
+	 Type1  Type2 :         Asol         Bsol        HBcut
+	    G6     C4 :       5.0000       3.0000       0.0000
+	    G1     C3 :       5.0000       3.0000       0.0000
+	    G2     C2 :       5.0000       3.0000       0.0000
+	    A6     U4 :       5.0000       3.0000       0.0000
+	    A1     U3 :       5.0000       3.0000       0.0000
+	    G7     C4 :       5.0000       6.0000       0.0000
+	    G3     C2 :       5.0000       5.2500       0.0000
+Bond parameters:
+	 Type1  Type2 :           Rk          Req
+	     P     CB :     150.0000       3.9000
+	    CB     CS :     100.0000       2.3500
+	    CS     G9 :     150.0000       1.4800
+	    CS     A9 :     150.0000       1.4800
+	    CS     U1 :     150.0000       1.4800
+	    CS     C1 :     150.0000       1.4800
+	    A9     A7 :     100.0000       2.2400
+	    A7     A6 :     100.0000       3.0800
+	    A6     A1 :     100.0000       2.3100
+	    A1     A3 :     100.0000       2.3900
+	    A3     A9 :     100.0000       2.4300
+	    G9     G7 :     100.0000       2.2500
+	    G7     G6 :     100.0000       3.0900
+	    G6     G1 :     100.0000       2.2700
+	    G1     G2 :     100.0000       2.2900
+	    G2     G3 :     100.0000       2.3100
+	    G3     G9 :     100.0000       2.4200
+	    U1     U4 :     100.0000       4.0400
+	    U4     U3 :     100.0000       2.2700
+	    U3     U2 :     100.0000       2.2800
+	    U2     U1 :     100.0000       2.2900
+	    C1     C4 :     100.0000       4.0400
+	    C4     C3 :     100.0000       2.3100
+	    C3     C2 :     100.0000       2.2600
+	    C2     C1 :     100.0000       2.2700
+Angle parameters:
+	 Type1  Type2  Type3 :           Tk          Teq
+	    CS     A9     A7 :      45.0000     160.9000
+	    A9     A7     A6 :      50.0000     118.9000
+	    A7     A6     A1 :      50.0000      85.4000
+	    A6     A1     A3 :      50.0000     123.9000
+	    A1     A3     A9 :      50.0000     112.1000
+	    A3     A9     A7 :      50.0000      99.7000
+	    CS     A9     A3 :      45.0000      99.1000
+	    CS     G9     G7 :      45.0000     161.2000
+	    G9     G7     G6 :      50.0000     117.7000
+	    G7     G6     G1 :      50.0000      85.2000
+	    G6     G1     G2 :      10.0000     175.1000
+	    G1     G2     G3 :      50.0000      62.2000
+	    G2     G3     G9 :      50.0000     169.6000
+	    G3     G9     G7 :      50.0000     100.3000
+	    CS     G9     G3 :      45.0000      97.9000
+	    CS     U1     U4 :       0.0000     180.0000
+	    U1     U4     U3 :      50.0000      29.5000
+	    U4     U3     U2 :       0.0000     180.0000
+	    U3     U2     U1 :      50.0000      61.8000
+	    U2     U1     U4 :      50.0000      87.3000
+	    CS     U1     U2 :      45.0000      90.8000
+	    CS     C1     C4 :       0.0000     180.0000
+	    C1     C4     C3 :      50.0000      30.0000
+	    C4     C3     C2 :       0.0000     180.0000
+	    C3     C2     C1 :      50.0000      62.3000
+	    C2     C1     C4 :      50.0000      87.7000
+	    CS     C1     C2 :      45.0000      89.2000
+	     P     CB      P :      22.0000      97.0000
+	    CB      P     CB :      30.0000     103.0000
+	     P     CB     CS :      30.0000     104.0000
+	    CB     CS     G9 :      30.0000     122.5000
+	    CB     CS     A9 :      30.0000     122.5000
+	    CB     CS     U1 :      30.0000     122.5000
+	    CB     CS     C1 :      30.0000     122.5000
+Dihedral parameters:
+	 Type1  Type2  Type3  Type4           Pk           Pn        Phase
+	     X     CB     CS      X :       7.5000       1.0000    -165.0000
+	     X      P     CB      X :       0.0000       2.0000     180.0000
+	     X     CS     G9      X :       0.0000       2.0000     180.0000
+	     X     CS     A9      X :       0.0000       2.0000     180.0000
+	     X     CS     U1      X :       0.0000       2.0000     180.0000
+	     X     CS     C1      X :       0.0000       2.0000     180.0000
+	     X     A9     A7      X :       0.0000       2.0000     180.0000
+	     X     A7     A6      X :       0.0000       2.0000     180.0000
+	     X     A6     A1      X :       0.0000       2.0000     180.0000
+	     X     A1     A3      X :       0.0000       2.0000     180.0000
+	     X     A3     A9      X :       0.0000       2.0000     180.0000
+	     X     G9     G7      X :       0.0000       2.0000     180.0000
+	     X     G7     G6      X :       0.0000       2.0000     180.0000
+	     X     G6     G1      X :       0.0000       2.0000     180.0000
+	     X     G1     G2      X :       0.0000       2.0000     180.0000
+	     X     G2     G3      X :       0.0000       2.0000     180.0000
+	     X     G3     G9      X :       0.0000       2.0000     180.0000
+	     X     U1     U4      X :       0.0000       2.0000     180.0000
+	     X     U4     U3      X :       0.0000       2.0000     180.0000
+	     X     U3     U2      X :       0.0000       2.0000     180.0000
+	     X     U2     U1      X :       0.0000       2.0000     180.0000
+	     X     C1     C4      X :       0.0000       2.0000     180.0000
+	     X     C4     C3      X :       0.0000       2.0000     180.0000
+	     X     C3     C2      X :       0.0000       2.0000     180.0000
+	     X     C2     C1      X :       0.0000       2.0000     180.0000
+	    CS     C1     C2     C3 :       2.0000       2.0000     180.0000
+	    C4     C1     C2     C3 :       2.0000       2.0000     180.0000
+	    CS     U1     U2     U3 :       2.0000       2.0000     180.0000
+	    U4     U1     U2     U3 :       2.0000       2.0000     180.0000
+	    CS     G9     G7     G6 :       2.0000       2.0000     180.0000
+	    G9     G7     G6     G1 :       2.0000       2.0000     180.0000
+	    CS     A9     A7     A6 :       2.0000       2.0000     180.0000
+	    A9     A7     A6     A1 :       2.0000       2.0000     180.0000
+	    CB     CS     C1     C2 :       2.0000       2.0000     180.0000
+	    CB     CS     U1     U2 :       2.0000       2.0000     180.0000
+	    CB     CS     G9     G3 :       2.0000       2.0000     180.0000
+	    CB     CS     A9     A3 :       2.0000       2.0000     180.0000

From e64d521f0dda8c6872abb446213b4a748b9d3a20 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 21 Nov 2023 11:20:52 -0500
Subject: [PATCH 0103/1492] Add combo test

---
 test/Test_ReadAmberFF/RunTest.sh              |  11 +-
 .../toyrna.tip3pf.parm.dat.save               | 141 ++++++++++++++++++
 2 files changed, 149 insertions(+), 3 deletions(-)
 create mode 100644 test/Test_ReadAmberFF/toyrna.tip3pf.parm.dat.save

diff --git a/test/Test_ReadAmberFF/RunTest.sh b/test/Test_ReadAmberFF/RunTest.sh
index b75a167ece..67bc7b4045 100755
--- a/test/Test_ReadAmberFF/RunTest.sh
+++ b/test/Test_ReadAmberFF/RunTest.sh
@@ -2,19 +2,24 @@
 
 . ../MasterTest.sh
 
-CleanFiles cpptraj.in tip3pf.parm.dat toyrna.parm.dat
+CleanFiles cpptraj.in tip3pf.parm.dat toyrna.parm.dat toyrna.tip3pf.parm.dat
 
 INPUT='-i cpptraj.in'
 
 cat > cpptraj.in <<EOF
-readdata frcmod.tip3pf as frcmod name PARM
-writedata tip3pf.parm.dat PARM
+readdata frcmod.tip3pf as frcmod name TIP3PF
+writedata tip3pf.parm.dat TIP3PF
 
 readdata toyrna.dat as amberff name TOYRNA
 writedata toyrna.parm.dat TOYRNA
+
+readdata toyrna.dat as amberff name PARM
+readdata frcmod.tip3pf as frcmod name PARM
+writedata toyrna.tip3pf.parm.dat PARM
 EOF
 RunCpptraj "Test read Amber FF and force modification files."
 DoTest tip3pf.parm.dat.save tip3pf.parm.dat
 DoTest toyrna.parm.dat.save toyrna.parm.dat
+DoTest toyrna.tip3pf.parm.dat.save toyrna.tip3pf.parm.dat
 
 EndTest
diff --git a/test/Test_ReadAmberFF/toyrna.tip3pf.parm.dat.save b/test/Test_ReadAmberFF/toyrna.tip3pf.parm.dat.save
new file mode 100644
index 0000000000..e62ee5b37a
--- /dev/null
+++ b/test/Test_ReadAmberFF/toyrna.tip3pf.parm.dat.save
@@ -0,0 +1,141 @@
+Parameter set: toyrna force field + This is TIP3P (model F) of Price and Brooks, JCP 121:10096, 2004 
+Nonbond parameters name: MOD4
+Atom Types:
+	  Name  TypeIdx       Radius        Depth         Mass       Polar.
+	    CB        0       2.0000       0.2000      56.0000       0.0000
+	    CS        1       2.0000       0.2000      43.0000       0.0000
+	    G9        2       1.8000       0.3000      25.0000       0.0000
+	    G7        3       1.8000       0.2000      25.0000       0.0000
+	    G6        4       1.8000       0.2000      25.0000       0.0000
+	    G1        5       1.8000       0.2000      25.0000       0.0000
+	    G2        6       1.8000       0.2000      25.0000       0.0000
+	    G3        7       1.8000       0.2000      25.0000       0.0000
+	    A9        8       1.8000       0.3000      26.8000       0.0000
+	    A7        9       1.8000       0.2000      26.8000       0.0000
+	    A6       10       1.8000       0.2000      26.8000       0.0000
+	    A1       11       1.8000       0.2000      26.8000       0.0000
+	    A3       12       1.8000       0.2000      26.8000       0.0000
+	    U1       13       1.8000       0.3000      27.7500       0.0000
+	    U3       14       1.8000       0.2000      27.7500       0.0000
+	    U4       15       1.8000       0.2000      27.7500       0.0000
+	    U2       16       1.8000       0.2000      27.7500       0.0000
+	    C1       17       1.8000       0.3000      27.5000       0.0000
+	    C3       18       1.8000       0.2000      27.5000       0.0000
+	    C4       19       1.8000       0.2000      27.5000       0.0000
+	    C2       20       1.8000       0.2000      27.5000       0.0000
+	     P       21       3.0000       0.2000      95.0000       0.0000
+	    OW       22       1.7926       0.0980      16.0000       0.0000
+	    HW       23       0.0000       0.0000       1.0080       0.0000
+HB LJ 10-12 parameters:
+	 Type1  Type2 :         Asol         Bsol        HBcut
+	    G6     C4 :       5.0000       3.0000       0.0000
+	    G1     C3 :       5.0000       3.0000       0.0000
+	    G2     C2 :       5.0000       3.0000       0.0000
+	    A6     U4 :       5.0000       3.0000       0.0000
+	    A1     U3 :       5.0000       3.0000       0.0000
+	    G7     C4 :       5.0000       6.0000       0.0000
+	    G3     C2 :       5.0000       5.2500       0.0000
+Bond parameters:
+	 Type1  Type2 :           Rk          Req
+	     P     CB :     150.0000       3.9000
+	    CB     CS :     100.0000       2.3500
+	    CS     G9 :     150.0000       1.4800
+	    CS     A9 :     150.0000       1.4800
+	    CS     U1 :     150.0000       1.4800
+	    CS     C1 :     150.0000       1.4800
+	    A9     A7 :     100.0000       2.2400
+	    A7     A6 :     100.0000       3.0800
+	    A6     A1 :     100.0000       2.3100
+	    A1     A3 :     100.0000       2.3900
+	    A3     A9 :     100.0000       2.4300
+	    G9     G7 :     100.0000       2.2500
+	    G7     G6 :     100.0000       3.0900
+	    G6     G1 :     100.0000       2.2700
+	    G1     G2 :     100.0000       2.2900
+	    G2     G3 :     100.0000       2.3100
+	    G3     G9 :     100.0000       2.4200
+	    U1     U4 :     100.0000       4.0400
+	    U4     U3 :     100.0000       2.2700
+	    U3     U2 :     100.0000       2.2800
+	    U2     U1 :     100.0000       2.2900
+	    C1     C4 :     100.0000       4.0400
+	    C4     C3 :     100.0000       2.3100
+	    C3     C2 :     100.0000       2.2600
+	    C2     C1 :     100.0000       2.2700
+	    OW     HW :     553.0000       0.9572
+	    HW     HW :     553.0000       1.5136
+Angle parameters:
+	 Type1  Type2  Type3 :           Tk          Teq
+	    CS     A9     A7 :      45.0000     160.9000
+	    A9     A7     A6 :      50.0000     118.9000
+	    A7     A6     A1 :      50.0000      85.4000
+	    A6     A1     A3 :      50.0000     123.9000
+	    A1     A3     A9 :      50.0000     112.1000
+	    A3     A9     A7 :      50.0000      99.7000
+	    CS     A9     A3 :      45.0000      99.1000
+	    CS     G9     G7 :      45.0000     161.2000
+	    G9     G7     G6 :      50.0000     117.7000
+	    G7     G6     G1 :      50.0000      85.2000
+	    G6     G1     G2 :      10.0000     175.1000
+	    G1     G2     G3 :      50.0000      62.2000
+	    G2     G3     G9 :      50.0000     169.6000
+	    G3     G9     G7 :      50.0000     100.3000
+	    CS     G9     G3 :      45.0000      97.9000
+	    CS     U1     U4 :       0.0000     180.0000
+	    U1     U4     U3 :      50.0000      29.5000
+	    U4     U3     U2 :       0.0000     180.0000
+	    U3     U2     U1 :      50.0000      61.8000
+	    U2     U1     U4 :      50.0000      87.3000
+	    CS     U1     U2 :      45.0000      90.8000
+	    CS     C1     C4 :       0.0000     180.0000
+	    C1     C4     C3 :      50.0000      30.0000
+	    C4     C3     C2 :       0.0000     180.0000
+	    C3     C2     C1 :      50.0000      62.3000
+	    C2     C1     C4 :      50.0000      87.7000
+	    CS     C1     C2 :      45.0000      89.2000
+	     P     CB      P :      22.0000      97.0000
+	    CB      P     CB :      30.0000     103.0000
+	     P     CB     CS :      30.0000     104.0000
+	    CB     CS     G9 :      30.0000     122.5000
+	    CB     CS     A9 :      30.0000     122.5000
+	    CB     CS     U1 :      30.0000     122.5000
+	    CB     CS     C1 :      30.0000     122.5000
+Dihedral parameters:
+	 Type1  Type2  Type3  Type4           Pk           Pn        Phase
+	     X     CB     CS      X :       7.5000       1.0000    -165.0000
+	     X      P     CB      X :       0.0000       2.0000     180.0000
+	     X     CS     G9      X :       0.0000       2.0000     180.0000
+	     X     CS     A9      X :       0.0000       2.0000     180.0000
+	     X     CS     U1      X :       0.0000       2.0000     180.0000
+	     X     CS     C1      X :       0.0000       2.0000     180.0000
+	     X     A9     A7      X :       0.0000       2.0000     180.0000
+	     X     A7     A6      X :       0.0000       2.0000     180.0000
+	     X     A6     A1      X :       0.0000       2.0000     180.0000
+	     X     A1     A3      X :       0.0000       2.0000     180.0000
+	     X     A3     A9      X :       0.0000       2.0000     180.0000
+	     X     G9     G7      X :       0.0000       2.0000     180.0000
+	     X     G7     G6      X :       0.0000       2.0000     180.0000
+	     X     G6     G1      X :       0.0000       2.0000     180.0000
+	     X     G1     G2      X :       0.0000       2.0000     180.0000
+	     X     G2     G3      X :       0.0000       2.0000     180.0000
+	     X     G3     G9      X :       0.0000       2.0000     180.0000
+	     X     U1     U4      X :       0.0000       2.0000     180.0000
+	     X     U4     U3      X :       0.0000       2.0000     180.0000
+	     X     U3     U2      X :       0.0000       2.0000     180.0000
+	     X     U2     U1      X :       0.0000       2.0000     180.0000
+	     X     C1     C4      X :       0.0000       2.0000     180.0000
+	     X     C4     C3      X :       0.0000       2.0000     180.0000
+	     X     C3     C2      X :       0.0000       2.0000     180.0000
+	     X     C2     C1      X :       0.0000       2.0000     180.0000
+	    CS     C1     C2     C3 :       2.0000       2.0000     180.0000
+	    C4     C1     C2     C3 :       2.0000       2.0000     180.0000
+	    CS     U1     U2     U3 :       2.0000       2.0000     180.0000
+	    U4     U1     U2     U3 :       2.0000       2.0000     180.0000
+	    CS     G9     G7     G6 :       2.0000       2.0000     180.0000
+	    G9     G7     G6     G1 :       2.0000       2.0000     180.0000
+	    CS     A9     A7     A6 :       2.0000       2.0000     180.0000
+	    A9     A7     A6     A1 :       2.0000       2.0000     180.0000
+	    CB     CS     C1     C2 :       2.0000       2.0000     180.0000
+	    CB     CS     U1     U2 :       2.0000       2.0000     180.0000
+	    CB     CS     G9     G3 :       2.0000       2.0000     180.0000
+	    CB     CS     A9     A3 :       2.0000       2.0000     180.0000

From 03573e38d00a700317252cb98a74bc434f22d29a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 28 Nov 2023 14:40:34 -0500
Subject: [PATCH 0104/1492] Start GenerateAngles

---
 src/Structure/CMakeLists.txt     |  1 +
 src/Structure/GenerateAngles.cpp | 29 +++++++++++++++++++++++++++++
 src/Structure/GenerateAngles.h   | 10 ++++++++++
 src/Structure/structuredepend    |  1 +
 src/Structure/structurefiles     |  1 +
 5 files changed, 42 insertions(+)
 create mode 100644 src/Structure/GenerateAngles.cpp
 create mode 100644 src/Structure/GenerateAngles.h

diff --git a/src/Structure/CMakeLists.txt b/src/Structure/CMakeLists.txt
index 88701e311c..c88fecfe3f 100644
--- a/src/Structure/CMakeLists.txt
+++ b/src/Structure/CMakeLists.txt
@@ -5,6 +5,7 @@ target_sources(cpptraj_common_obj PRIVATE
   ${CMAKE_CURRENT_LIST_DIR}/Disulfide.cpp
   ${CMAKE_CURRENT_LIST_DIR}/FunctionalGroup.cpp
   ${CMAKE_CURRENT_LIST_DIR}/FxnGroupBuilder.cpp
+  ${CMAKE_CURRENT_LIST_DIR}/GenerateAngles.cpp
   ${CMAKE_CURRENT_LIST_DIR}/HisProt.cpp
   ${CMAKE_CURRENT_LIST_DIR}/InternalCoords.cpp
   ${CMAKE_CURRENT_LIST_DIR}/Model.cpp
diff --git a/src/Structure/GenerateAngles.cpp b/src/Structure/GenerateAngles.cpp
new file mode 100644
index 0000000000..94c0dbcc20
--- /dev/null
+++ b/src/Structure/GenerateAngles.cpp
@@ -0,0 +1,29 @@
+#include "GenerateAngles.h"
+#include "../CpptrajStdio.h"
+#include "../ParameterTypes.h"
+#include "../Topology.h"
+#include <algorithm> // std::sort
+
+int Cpptraj::Structure::GenerateAngles(Topology& topIn) {
+  if (topIn.Nbonds() < 1) {
+    mprintf("Warning: No bonds in '%s', no angles to generate.\n", topIn.c_str());
+    return 0;
+  }
+  // Create a combined bonds array
+  BondArray allBonds;
+  allBonds.reserve(topIn.Nbonds());
+
+  for (BondArray::const_iterator it = topIn.Bonds().begin(); it != topIn.Bonds().end(); ++it)
+    allBonds.push_back( *it );
+  for (BondArray::const_iterator it = topIn.BondsH().begin(); it != topIn.BondsH().end(); ++it)
+    allBonds.push_back( *it );
+  std::sort( allBonds.begin(), allBonds.end() );
+
+  mprintf("DEBUG: Sorted bonds:\n");
+  for (BondArray::const_iterator it = allBonds.begin(); it != allBonds.end(); ++it)
+    mprintf("\t%s - %s\n",
+            topIn.AtomMaskName(it->A1()).c_str(),
+            topIn.AtomMaskName(it->A2()).c_str());
+
+  return 0;
+}
diff --git a/src/Structure/GenerateAngles.h b/src/Structure/GenerateAngles.h
new file mode 100644
index 0000000000..b3e1c141c2
--- /dev/null
+++ b/src/Structure/GenerateAngles.h
@@ -0,0 +1,10 @@
+#ifndef INC_STRUCTURE_GENERATEANGLES_H
+#define INC_STRUCTURE_GENERATEANGLES_H
+class Topology;
+namespace Cpptraj {
+namespace Structure {
+/// Generate angles from bonds in a Topology
+int GenerateAngles(Topology&);
+}
+}
+#endif
diff --git a/src/Structure/structuredepend b/src/Structure/structuredepend
index 786f57a3d6..bd21185aeb 100644
--- a/src/Structure/structuredepend
+++ b/src/Structure/structuredepend
@@ -3,6 +3,7 @@ Chirality.o : Chirality.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Co
 Disulfide.o : Disulfide.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Disulfide.h ResStatArray.h StructureRoutines.h
 FunctionalGroup.o : FunctionalGroup.cpp ../Atom.h ../AtomMap.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h FunctionalGroup.h
 FxnGroupBuilder.o : FxnGroupBuilder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h FunctionalGroup.h FxnGroupBuilder.h StructureRoutines.h Sugar.h SugarToken.h
+GenerateAngles.o : GenerateAngles.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h GenerateAngles.h
 HisProt.o : HisProt.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h HisProt.h StructureRoutines.h
 InternalCoords.o : InternalCoords.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h InternalCoords.h
 Model.o : Model.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h Model.h StructureEnum.h
diff --git a/src/Structure/structurefiles b/src/Structure/structurefiles
index 0a0a55cc57..a6449d535b 100644
--- a/src/Structure/structurefiles
+++ b/src/Structure/structurefiles
@@ -5,6 +5,7 @@ STRUCTURE_SOURCES= \
   Disulfide.cpp \
   FunctionalGroup.cpp \
   FxnGroupBuilder.cpp \
+  GenerateAngles.cpp \
   HisProt.cpp \
   InternalCoords.cpp \
   Model.cpp \

From c196851dbbdb53dde026cf8ae56c30926c6fecee Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 28 Nov 2023 14:41:31 -0500
Subject: [PATCH 0105/1492] Update depends

---
 src/cpptrajdepend | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 8d28b6c184..4759c572ca 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -444,6 +444,7 @@ Structure/Chirality.o : Structure/Chirality.cpp Atom.h AtomMask.h AtomType.h Box
 Structure/Disulfide.o : Structure/Disulfide.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Disulfide.h Structure/ResStatArray.h Structure/StructureRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/FunctionalGroup.o : Structure/FunctionalGroup.cpp Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/FxnGroupBuilder.o : Structure/FxnGroupBuilder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h Structure/FxnGroupBuilder.h Structure/StructureRoutines.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Structure/GenerateAngles.o : Structure/GenerateAngles.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/GenerateAngles.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/HisProt.o : Structure/HisProt.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/HisProt.h Structure/StructureRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/InternalCoords.o : Structure/InternalCoords.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/InternalCoords.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/Model.o : Structure/Model.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/Model.h Structure/StructureEnum.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h

From 7dcc62f33708661f77f733eca87e38b0c3cf790e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 28 Nov 2023 14:55:12 -0500
Subject: [PATCH 0106/1492] Enumerate angles, ignoring doubles

---
 src/Structure/GenerateAngles.cpp | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/src/Structure/GenerateAngles.cpp b/src/Structure/GenerateAngles.cpp
index 94c0dbcc20..7d0e0c6607 100644
--- a/src/Structure/GenerateAngles.cpp
+++ b/src/Structure/GenerateAngles.cpp
@@ -4,6 +4,21 @@
 #include "../Topology.h"
 #include <algorithm> // std::sort
 
+static inline void enumerateAngles(int at1, int at2, Topology const& topIn) {
+  Atom const& A2 = topIn[at2];
+  if (A2.Nbonds() > 1) {
+    for (Atom::bond_iterator bat = A2.bondbegin(); bat != A2.bondend(); ++bat)
+    {
+      if (*bat != at1 && at1 < *bat) {
+        mprintf("%s - %s - %s\n",
+                topIn.AtomMaskName(at1).c_str(),
+                topIn.AtomMaskName(at2).c_str(),
+                topIn.AtomMaskName(*bat).c_str());
+      }
+    }
+  }
+}
+
 int Cpptraj::Structure::GenerateAngles(Topology& topIn) {
   if (topIn.Nbonds() < 1) {
     mprintf("Warning: No bonds in '%s', no angles to generate.\n", topIn.c_str());
@@ -25,5 +40,15 @@ int Cpptraj::Structure::GenerateAngles(Topology& topIn) {
             topIn.AtomMaskName(it->A1()).c_str(),
             topIn.AtomMaskName(it->A2()).c_str());
 
+  // Angles
+  AngleArray angles;
+  AngleArray anglesH;
+  for (BondArray::const_iterator it = allBonds.begin(); it != allBonds.end(); ++it)
+  {
+    // Forward direction. A1-A2-X
+    enumerateAngles( it->A1(), it->A2(), topIn );
+    // Reverse direction. A2-A1-X
+    enumerateAngles( it->A2(), it->A1(), topIn );
+  }
   return 0;
 }

From b4aec9f01caea49262af4dbf9bf2a0dba7924a3f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 28 Nov 2023 15:23:17 -0500
Subject: [PATCH 0107/1492] Add dihedral enumeration

---
 src/Structure/GenerateAngles.cpp | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/src/Structure/GenerateAngles.cpp b/src/Structure/GenerateAngles.cpp
index 7d0e0c6607..246537ae25 100644
--- a/src/Structure/GenerateAngles.cpp
+++ b/src/Structure/GenerateAngles.cpp
@@ -19,6 +19,30 @@ static inline void enumerateAngles(int at1, int at2, Topology const& topIn) {
   }
 }
 
+static inline void enumerateDihedrals(int at1, int at2, Topology const& topIn) {
+  Atom const& A1 = topIn[at1];
+  Atom const& A2 = topIn[at2];
+  if (A1.Nbonds() > 1 && A2.Nbonds() > 1) {
+    for (Atom::bond_iterator bat1 = A1.bondbegin(); bat1 != A1.bondend(); ++bat1)
+    {
+      if (*bat1 != at2) {
+        for (Atom::bond_iterator bat2 = A2.bondbegin(); bat2 != A2.bondend(); ++bat2)
+        {
+          if (*bat2 != at1) {
+            mprintf("%s - %s - %s - %s\n",
+                    topIn.AtomMaskName(*bat1).c_str(),
+                    topIn.AtomMaskName(at1).c_str(),
+                    topIn.AtomMaskName(at2).c_str(),
+                    topIn.AtomMaskName(*bat2).c_str());
+          }
+        }
+      }
+    }
+  }
+}
+
+        
+
 int Cpptraj::Structure::GenerateAngles(Topology& topIn) {
   if (topIn.Nbonds() < 1) {
     mprintf("Warning: No bonds in '%s', no angles to generate.\n", topIn.c_str());
@@ -49,6 +73,8 @@ int Cpptraj::Structure::GenerateAngles(Topology& topIn) {
     enumerateAngles( it->A1(), it->A2(), topIn );
     // Reverse direction. A2-A1-X
     enumerateAngles( it->A2(), it->A1(), topIn );
+    // Dihedrals
+    enumerateDihedrals( it->A1(), it->A2(), topIn );
   }
   return 0;
 }

From 186cb89cd8ac92cc2f32736576c20ef600f19bd0 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 29 Nov 2023 15:01:07 -0500
Subject: [PATCH 0108/1492] Generate angles during sequence

---
 src/Exec_Sequence.cpp | 9 +++++++++
 src/cpptrajdepend     | 2 +-
 2 files changed, 10 insertions(+), 1 deletion(-)

diff --git a/src/Exec_Sequence.cpp b/src/Exec_Sequence.cpp
index 63a69b2bf1..89fe0f823d 100644
--- a/src/Exec_Sequence.cpp
+++ b/src/Exec_Sequence.cpp
@@ -2,6 +2,7 @@
 #include "CpptrajStdio.h"
 #include "AssociatedData_Connect.h"
 #include "Structure/Builder.h"
+#include "Structure/GenerateAngles.h"
 
 /** Generate and build the specified sequence. */
 int Exec_Sequence::generate_sequence(DataSet_Coords* OUT,
@@ -114,6 +115,14 @@ const
     }
   }
 
+  // Generate angles and dihedrals
+ if (combinedTop.Nbonds() > 0) {
+   if (Cpptraj::Structure::GenerateAngles(combinedTop)) {
+     mprinterr("Error: Angle generation failed.\n");
+     return 1;
+   }
+ }
+
   OUT->CoordsSetup(combinedTop, CombinedFrame.CoordsInfo());
   OUT->AddFrame( CombinedFrame );
 
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 4759c572ca..fe1b3bb225 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -330,7 +330,7 @@ Exec_ReadInput.o : Exec_ReadInput.cpp Action.h ActionList.h ActionState.h Analys
 Exec_RotateDihedral.o : Exec_RotateDihedral.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_RotateDihedral.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_RunAnalysis.o : Exec_RunAnalysis.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_RunAnalysis.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_ScaleDihedralK.o : Exec_ScaleDihedralK.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ScaleDihedralK.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Sequence.o : Exec_Sequence.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Sequence.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Sequence.o : Exec_Sequence.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Sequence.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/GenerateAngles.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_SequenceAlign.o : Exec_SequenceAlign.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SequenceAlign.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Set.o : Exec_Set.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_StringVar.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Set.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Show.o : Exec_Show.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_StringVar.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Show.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h

From 97e2969f00040163221f79015029553a6afc942e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 29 Nov 2023 16:08:30 -0500
Subject: [PATCH 0109/1492] Actually add dihedrals and angles

---
 src/Structure/GenerateAngles.cpp | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/src/Structure/GenerateAngles.cpp b/src/Structure/GenerateAngles.cpp
index 246537ae25..838fabfbeb 100644
--- a/src/Structure/GenerateAngles.cpp
+++ b/src/Structure/GenerateAngles.cpp
@@ -4,12 +4,13 @@
 #include "../Topology.h"
 #include <algorithm> // std::sort
 
-static inline void enumerateAngles(int at1, int at2, Topology const& topIn) {
+static inline void enumerateAngles(int at1, int at2, Topology& topIn) {
   Atom const& A2 = topIn[at2];
   if (A2.Nbonds() > 1) {
     for (Atom::bond_iterator bat = A2.bondbegin(); bat != A2.bondend(); ++bat)
     {
       if (*bat != at1 && at1 < *bat) {
+        topIn.AddAngle(at1, at2, *bat);
         mprintf("%s - %s - %s\n",
                 topIn.AtomMaskName(at1).c_str(),
                 topIn.AtomMaskName(at2).c_str(),
@@ -19,7 +20,7 @@ static inline void enumerateAngles(int at1, int at2, Topology const& topIn) {
   }
 }
 
-static inline void enumerateDihedrals(int at1, int at2, Topology const& topIn) {
+static inline void enumerateDihedrals(int at1, int at2, Topology& topIn) {
   Atom const& A1 = topIn[at1];
   Atom const& A2 = topIn[at2];
   if (A1.Nbonds() > 1 && A2.Nbonds() > 1) {
@@ -29,6 +30,7 @@ static inline void enumerateDihedrals(int at1, int at2, Topology const& topIn) {
         for (Atom::bond_iterator bat2 = A2.bondbegin(); bat2 != A2.bondend(); ++bat2)
         {
           if (*bat2 != at1) {
+            topIn.AddDihedral(*bat1, at1, at2, *bat2);
             mprintf("%s - %s - %s - %s\n",
                     topIn.AtomMaskName(*bat1).c_str(),
                     topIn.AtomMaskName(at1).c_str(),
@@ -48,6 +50,14 @@ int Cpptraj::Structure::GenerateAngles(Topology& topIn) {
     mprintf("Warning: No bonds in '%s', no angles to generate.\n", topIn.c_str());
     return 0;
   }
+  if (topIn.Nangles() > 0) {
+    mprintf("Warning: Topology '%s' already has angle information.\n", topIn.c_str());
+    return 0;
+  }
+  if (topIn.Ndihedrals() > 0) {
+    mprintf("Warning: Topology '%s' already has dihedral information.\n", topIn.c_str());
+    return 0;
+  }
   // Create a combined bonds array
   BondArray allBonds;
   allBonds.reserve(topIn.Nbonds());

From dd5b97ceae3bd5529f958fa04b4997aa0a411414 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 4 Dec 2023 15:31:55 -0500
Subject: [PATCH 0110/1492] Start the build command

---
 src/Command.cpp                  |  2 ++
 src/Exec_Build.cpp               | 45 ++++++++++++++++++++++++++++++++
 src/Exec_Build.h                 | 12 +++++++++
 src/Structure/GenerateAngles.cpp | 27 ++++++++++++-------
 src/cpptrajdepend                |  3 ++-
 src/cpptrajfiles                 |  1 +
 6 files changed, 79 insertions(+), 11 deletions(-)
 create mode 100644 src/Exec_Build.cpp
 create mode 100644 src/Exec_Build.h

diff --git a/src/Command.cpp b/src/Command.cpp
index e098f8c9bd..4b3e12aed2 100644
--- a/src/Command.cpp
+++ b/src/Command.cpp
@@ -58,6 +58,7 @@
 #include "Exec_ExtendedComparison.h"
 #include "Exec_Zmatrix.h"
 #include "Exec_Sequence.h"
+#include "Exec_Build.h"
 // ----- TRAJECTORY ------------------------------------------------------------
 #include "Exec_Traj.h"
 // ----- TOPOLOGY --------------------------------------------------------------
@@ -268,6 +269,7 @@ void Command::Init() {
   // SYSTEM
   Command::AddCmd( new Exec_System(), Cmd::EXE, 6, "gnuplot", "head", "less", "ls", "pwd", "xmgrace" );
   // COORDS
+  Command::AddCmd( new Exec_Build(),            Cmd::EXE, 1, "build" );
   Command::AddCmd( new Exec_CatCrd(),           Cmd::EXE, 1, "catcrd" );
   Command::AddCmd( new Exec_CombineCoords(),    Cmd::EXE, 1, "combinecrd" ); 
   Command::AddCmd( new Exec_CrdAction(),        Cmd::EXE, 1, "crdaction" );
diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
new file mode 100644
index 0000000000..cfb1ef171e
--- /dev/null
+++ b/src/Exec_Build.cpp
@@ -0,0 +1,45 @@
+#include "Exec_Build.h"
+#include "CpptrajStdio.h"
+#include "Structure/GenerateAngles.h"
+
+// Exec_Build::Help()
+void Exec_Build::Help() const
+{
+  mprintf("\tcrdset <COORDS set> [frame <#>]\n");
+}
+
+// Exec_Build::Execute()
+Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
+{
+  // Get input coords
+  std::string crdset = argIn.GetStringKey("crdset");
+  if (crdset.empty()) {
+    mprinterr("Error: Must specify input COORDS set with 'crdset'\n");
+    return CpptrajState::ERR;
+  }
+  DataSet* ds = State.DSL().FindSetOfGroup( crdset, DataSet::COORDINATES );
+  if (ds == 0) {
+    mprinterr("Error: No COORDS set found matching %s\n", crdset.c_str());
+    return CpptrajState::ERR;
+  }
+  DataSet_Coords& coords = static_cast<DataSet_Coords&>( *((DataSet_Coords*)ds) );
+  // Get frame from input coords
+  int tgtframe = argIn.getKeyInt("frame", 1) - 1;
+  mprintf("\tUsing frame %i from COORDS set %s\n", tgtframe+1, coords.legend());
+  if (tgtframe < 0 || tgtframe >= (int)coords.Size()) {
+    mprinterr("Error: Frame is out of range.\n");
+    return CpptrajState::ERR;
+  }
+  Frame frameIn = coords.AllocateFrame();
+  coords.GetFrame(tgtframe, frameIn);
+  // Get modifiable topology
+  Topology& topIn = *(coords.TopPtr());
+
+  // Generate angles
+  if (Cpptraj::Structure::GenerateAngles(topIn)) {
+    mprinterr("Error: Could not generate angles/dihedrals for '%s'\n", topIn.c_str());
+    return CpptrajState::ERR;
+  }
+
+  return CpptrajState::OK;
+}
diff --git a/src/Exec_Build.h b/src/Exec_Build.h
new file mode 100644
index 0000000000..9225f7e3bf
--- /dev/null
+++ b/src/Exec_Build.h
@@ -0,0 +1,12 @@
+#ifndef INC_EXEC_BUILD_H
+#define INC_EXEC_BUILD_H
+#include "Exec.h"
+/// Used to build a structure 
+class Exec_Build : public Exec {
+  public:
+    Exec_Build() : Exec(GENERAL) {}
+    void Help() const;
+    DispatchObject* Alloc() const { return (DispatchObject*)new Exec_Build(); }
+    RetType Execute(CpptrajState&, ArgList&);
+};
+#endif
diff --git a/src/Structure/GenerateAngles.cpp b/src/Structure/GenerateAngles.cpp
index 838fabfbeb..61fabb25bf 100644
--- a/src/Structure/GenerateAngles.cpp
+++ b/src/Structure/GenerateAngles.cpp
@@ -50,14 +50,17 @@ int Cpptraj::Structure::GenerateAngles(Topology& topIn) {
     mprintf("Warning: No bonds in '%s', no angles to generate.\n", topIn.c_str());
     return 0;
   }
-  if (topIn.Nangles() > 0) {
+  bool has_angles = topIn.Nangles() > 0;
+  if (has_angles) {
     mprintf("Warning: Topology '%s' already has angle information.\n", topIn.c_str());
-    return 0;
+    //return 0;
   }
-  if (topIn.Ndihedrals() > 0) {
+  bool has_dihedrals = topIn.Ndihedrals() > 0;
+  if (has_dihedrals) {
     mprintf("Warning: Topology '%s' already has dihedral information.\n", topIn.c_str());
-    return 0;
+    //return 0;
   }
+  if (has_angles && has_dihedrals) return 0;
   // Create a combined bonds array
   BondArray allBonds;
   allBonds.reserve(topIn.Nbonds());
@@ -79,12 +82,16 @@ int Cpptraj::Structure::GenerateAngles(Topology& topIn) {
   AngleArray anglesH;
   for (BondArray::const_iterator it = allBonds.begin(); it != allBonds.end(); ++it)
   {
-    // Forward direction. A1-A2-X
-    enumerateAngles( it->A1(), it->A2(), topIn );
-    // Reverse direction. A2-A1-X
-    enumerateAngles( it->A2(), it->A1(), topIn );
-    // Dihedrals
-    enumerateDihedrals( it->A1(), it->A2(), topIn );
+    if (!has_angles) {
+      // Forward direction. A1-A2-X
+      enumerateAngles( it->A1(), it->A2(), topIn );
+      // Reverse direction. A2-A1-X
+      enumerateAngles( it->A2(), it->A1(), topIn );
+    }
+    if (!has_dihedrals) {
+      // Dihedrals
+      enumerateDihedrals( it->A1(), it->A2(), topIn );
+    }
   }
   return 0;
 }
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index fe1b3bb225..e736d60b26 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -187,7 +187,7 @@ ClusterMap.o : ClusterMap.cpp AssociatedData.h ClusterMap.h Constants.h CpptrajF
 Cmd.o : Cmd.cpp Cmd.h DispatchObject.h
 CmdInput.o : CmdInput.cpp CmdInput.h StringRoutines.h
 CmdList.o : CmdList.cpp Cmd.h CmdList.h DispatchObject.h
-Command.o : Command.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h ActionTopWriter.h Action_Align.h Action_Angle.h Action_AreaPerMol.h Action_AtomMap.h Action_AtomicCorr.h Action_AtomicFluct.h Action_AutoImage.h Action_Average.h Action_AvgBox.h Action_Bounds.h Action_Box.h Action_Center.h Action_Channel.h Action_CheckChirality.h Action_CheckStructure.h Action_Closest.h Action_ClusterDihedral.h Action_Contacts.h Action_CreateCrd.h Action_CreateReservoir.h Action_DNAionTracker.h Action_DSSP.h Action_Density.h Action_Diffusion.h Action_Dihedral.h Action_DihedralRMS.h Action_Dipole.h Action_DistRmsd.h Action_Distance.h Action_Energy.h Action_Esander.h Action_FilterByData.h Action_FixAtomOrder.h Action_FixImagedBonds.h Action_GIST.h Action_Grid.h Action_GridFreeEnergy.h Action_HydrogenBond.h Action_Image.h Action_InfraredSpectrum.h Action_Jcoupling.h Action_Keep.h Action_LESsplit.h Action_LIE.h Action_LipidOrder.h Action_MakeStructure.h Action_Mask.h Action_Matrix.h Action_MinImage.h Action_Molsurf.h Action_MultiDihedral.h Action_MultiPucker.h Action_MultiVector.h Action_NAstruct.h Action_NMRrst.h Action_NativeContacts.h Action_OrderParameter.h Action_Outtraj.h Action_PairDist.h Action_Pairwise.h Action_Principal.h Action_Projection.h Action_Pucker.h Action_Radgyr.h Action_Radial.h Action_RandomizeIons.h Action_Remap.h Action_ReplicateCell.h Action_Rmsd.h Action_Rotate.h Action_RunningAvg.h Action_STFC_Diffusion.h Action_Scale.h Action_SetVelocity.h Action_Spam.h Action_Strip.h Action_Surf.h Action_SymmetricRmsd.h Action_Temperature.h Action_Time.h Action_ToroidalDiffusion.h Action_Translate.h Action_Unstrip.h Action_Unwrap.h Action_Vector.h Action_VelocityAutoCorr.h Action_Volmap.h Action_Volume.h Action_Watershell.h Action_XtalSymm.h Analysis.h AnalysisList.h AnalysisState.h Analysis_AmdBias.h Analysis_AutoCorr.h Analysis_Average.h Analysis_CalcDiffusion.h Analysis_Clustering.h Analysis_ConstantPHStats.h Analysis_Corr.h Analysis_CrankShaft.h Analysis_CrdFluct.h Analysis_CrossCorr.h Analysis_CurveFit.h Analysis_Divergence.h Analysis_EvalPlateau.h Analysis_FFT.h Analysis_HausdorffDistance.h Analysis_Hist.h Analysis_IRED.h Analysis_Integrate.h Analysis_KDE.h Analysis_Lifetime.h Analysis_LowestCurve.h Analysis_Matrix.h Analysis_MeltCurve.h Analysis_Modes.h Analysis_MultiHist.h Analysis_Multicurve.h Analysis_Overlap.h Analysis_PhiPsi.h Analysis_Regression.h Analysis_RemLog.h Analysis_Rms2d.h Analysis_RmsAvgCorr.h Analysis_Rotdif.h Analysis_RunningAvg.h Analysis_Slope.h Analysis_Spline.h Analysis_State.h Analysis_Statistics.h Analysis_TI.h Analysis_TICA.h Analysis_Timecorr.h Analysis_VectorMath.h Analysis_Wavelet.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h AxisType.h BaseIOtype.h Box.h BoxArgs.h BufferedLine.h CharMask.h Cluster/Algorithm.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Control.h Cluster/DrawGraph.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Sieve.h Cluster/Silhouette.h ClusterMap.h Cmd.h CmdInput.h CmdList.h Command.h CompactFrameArray.h ComplexArray.h Constants.h Constraints.h ControlBlock.h ControlBlock_For.h CoordinateInfo.h Corr.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_RemLog.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h Deprecated.h DiffusionResults.h DihedralSearch.h Dimension.h DispatchObject.h Energy.h Energy_Sander.h EnsembleIn.h EnsembleOutList.h Ewald.h EwaldOptions.h Ewald_ParticleMesh.h ExclusionArray.h Exec.h Exec_AddMissingRes.h Exec_Analyze.h Exec_Calc.h Exec_CatCrd.h Exec_Change.h Exec_ClusterMap.h Exec_CombineCoords.h Exec_Commands.h Exec_CompareClusters.h Exec_CompareEnergy.h Exec_CompareTop.h Exec_CrdAction.h Exec_CrdOut.h Exec_CrdTransform.h Exec_CreateSet.h Exec_DataFile.h Exec_DataFilter.h Exec_DataSetCmd.h Exec_Emin.h Exec_ExtendedComparison.h Exec_Flatten.h Exec_GenerateAmberRst.h Exec_Graft.h Exec_Help.h Exec_HmassRepartition.h Exec_LoadCrd.h Exec_LoadTraj.h Exec_ParallelAnalysis.h Exec_ParmBox.h Exec_ParmSolvent.h Exec_ParmStrip.h Exec_ParmWrite.h Exec_ParseTiming.h Exec_PermuteDihedrals.h Exec_Precision.h Exec_PrepareForLeap.h Exec_PrintData.h Exec_Random.h Exec_ReadData.h Exec_ReadEnsembleData.h Exec_ReadInput.h Exec_RotateDihedral.h Exec_RunAnalysis.h Exec_ScaleDihedralK.h Exec_Sequence.h Exec_SequenceAlign.h Exec_Set.h Exec_Show.h Exec_SortEnsembleData.h Exec_SplitCoords.h Exec_System.h Exec_Top.h Exec_Traj.h Exec_UpdateParameters.h Exec_ViewRst.h Exec_Zmatrix.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h GIST_PME.h Grid.h GridAction.h GridBin.h GridMover.h HistBin.h Hungarian.h ImageOption.h ImageTypes.h InputTrajCommon.h MapAtom.h MaskArray.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h OnlineVarT.h OutputTrajCommon.h PDBfile.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PubFFT.h Pucker.h Pucker_PuckerMask.h Pucker_PuckerSearch.h Pucker_PuckerToken.h RPNcalc.h Random.h Range.h ReferenceAction.h ReferenceFrame.h RemdReservoirNC.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h SplineFxnTable.h StructureCheck.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h cuda_kernels/GistCudaSetup.cuh helpme_standalone.h molsurf.h
+Command.o : Command.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h ActionTopWriter.h Action_Align.h Action_Angle.h Action_AreaPerMol.h Action_AtomMap.h Action_AtomicCorr.h Action_AtomicFluct.h Action_AutoImage.h Action_Average.h Action_AvgBox.h Action_Bounds.h Action_Box.h Action_Center.h Action_Channel.h Action_CheckChirality.h Action_CheckStructure.h Action_Closest.h Action_ClusterDihedral.h Action_Contacts.h Action_CreateCrd.h Action_CreateReservoir.h Action_DNAionTracker.h Action_DSSP.h Action_Density.h Action_Diffusion.h Action_Dihedral.h Action_DihedralRMS.h Action_Dipole.h Action_DistRmsd.h Action_Distance.h Action_Energy.h Action_Esander.h Action_FilterByData.h Action_FixAtomOrder.h Action_FixImagedBonds.h Action_GIST.h Action_Grid.h Action_GridFreeEnergy.h Action_HydrogenBond.h Action_Image.h Action_InfraredSpectrum.h Action_Jcoupling.h Action_Keep.h Action_LESsplit.h Action_LIE.h Action_LipidOrder.h Action_MakeStructure.h Action_Mask.h Action_Matrix.h Action_MinImage.h Action_Molsurf.h Action_MultiDihedral.h Action_MultiPucker.h Action_MultiVector.h Action_NAstruct.h Action_NMRrst.h Action_NativeContacts.h Action_OrderParameter.h Action_Outtraj.h Action_PairDist.h Action_Pairwise.h Action_Principal.h Action_Projection.h Action_Pucker.h Action_Radgyr.h Action_Radial.h Action_RandomizeIons.h Action_Remap.h Action_ReplicateCell.h Action_Rmsd.h Action_Rotate.h Action_RunningAvg.h Action_STFC_Diffusion.h Action_Scale.h Action_SetVelocity.h Action_Spam.h Action_Strip.h Action_Surf.h Action_SymmetricRmsd.h Action_Temperature.h Action_Time.h Action_ToroidalDiffusion.h Action_Translate.h Action_Unstrip.h Action_Unwrap.h Action_Vector.h Action_VelocityAutoCorr.h Action_Volmap.h Action_Volume.h Action_Watershell.h Action_XtalSymm.h Analysis.h AnalysisList.h AnalysisState.h Analysis_AmdBias.h Analysis_AutoCorr.h Analysis_Average.h Analysis_CalcDiffusion.h Analysis_Clustering.h Analysis_ConstantPHStats.h Analysis_Corr.h Analysis_CrankShaft.h Analysis_CrdFluct.h Analysis_CrossCorr.h Analysis_CurveFit.h Analysis_Divergence.h Analysis_EvalPlateau.h Analysis_FFT.h Analysis_HausdorffDistance.h Analysis_Hist.h Analysis_IRED.h Analysis_Integrate.h Analysis_KDE.h Analysis_Lifetime.h Analysis_LowestCurve.h Analysis_Matrix.h Analysis_MeltCurve.h Analysis_Modes.h Analysis_MultiHist.h Analysis_Multicurve.h Analysis_Overlap.h Analysis_PhiPsi.h Analysis_Regression.h Analysis_RemLog.h Analysis_Rms2d.h Analysis_RmsAvgCorr.h Analysis_Rotdif.h Analysis_RunningAvg.h Analysis_Slope.h Analysis_Spline.h Analysis_State.h Analysis_Statistics.h Analysis_TI.h Analysis_TICA.h Analysis_Timecorr.h Analysis_VectorMath.h Analysis_Wavelet.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h AxisType.h BaseIOtype.h Box.h BoxArgs.h BufferedLine.h CharMask.h Cluster/Algorithm.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Control.h Cluster/DrawGraph.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Sieve.h Cluster/Silhouette.h ClusterMap.h Cmd.h CmdInput.h CmdList.h Command.h CompactFrameArray.h ComplexArray.h Constants.h Constraints.h ControlBlock.h ControlBlock_For.h CoordinateInfo.h Corr.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_RemLog.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h Deprecated.h DiffusionResults.h DihedralSearch.h Dimension.h DispatchObject.h Energy.h Energy_Sander.h EnsembleIn.h EnsembleOutList.h Ewald.h EwaldOptions.h Ewald_ParticleMesh.h ExclusionArray.h Exec.h Exec_AddMissingRes.h Exec_Analyze.h Exec_Build.h Exec_Calc.h Exec_CatCrd.h Exec_Change.h Exec_ClusterMap.h Exec_CombineCoords.h Exec_Commands.h Exec_CompareClusters.h Exec_CompareEnergy.h Exec_CompareTop.h Exec_CrdAction.h Exec_CrdOut.h Exec_CrdTransform.h Exec_CreateSet.h Exec_DataFile.h Exec_DataFilter.h Exec_DataSetCmd.h Exec_Emin.h Exec_ExtendedComparison.h Exec_Flatten.h Exec_GenerateAmberRst.h Exec_Graft.h Exec_Help.h Exec_HmassRepartition.h Exec_LoadCrd.h Exec_LoadTraj.h Exec_ParallelAnalysis.h Exec_ParmBox.h Exec_ParmSolvent.h Exec_ParmStrip.h Exec_ParmWrite.h Exec_ParseTiming.h Exec_PermuteDihedrals.h Exec_Precision.h Exec_PrepareForLeap.h Exec_PrintData.h Exec_Random.h Exec_ReadData.h Exec_ReadEnsembleData.h Exec_ReadInput.h Exec_RotateDihedral.h Exec_RunAnalysis.h Exec_ScaleDihedralK.h Exec_Sequence.h Exec_SequenceAlign.h Exec_Set.h Exec_Show.h Exec_SortEnsembleData.h Exec_SplitCoords.h Exec_System.h Exec_Top.h Exec_Traj.h Exec_UpdateParameters.h Exec_ViewRst.h Exec_Zmatrix.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h GIST_PME.h Grid.h GridAction.h GridBin.h GridMover.h HistBin.h Hungarian.h ImageOption.h ImageTypes.h InputTrajCommon.h MapAtom.h MaskArray.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h OnlineVarT.h OutputTrajCommon.h PDBfile.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PubFFT.h Pucker.h Pucker_PuckerMask.h Pucker_PuckerSearch.h Pucker_PuckerToken.h RPNcalc.h Random.h Range.h ReferenceAction.h ReferenceFrame.h RemdReservoirNC.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h SplineFxnTable.h StructureCheck.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h cuda_kernels/GistCudaSetup.cuh helpme_standalone.h molsurf.h
 CompactFrameArray.o : CompactFrameArray.cpp Box.h CompactFrameArray.h CoordinateInfo.h CpptrajStdio.h Matrix_3x3.h Parallel.h ReplicaDimArray.h Vec3.h
 ComplexArray.o : ComplexArray.cpp ArrayIterator.h ComplexArray.h
 Constraints.o : Constraints.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
@@ -288,6 +288,7 @@ Ewald_Regular.o : Ewald_Regular.cpp Atom.h AtomMask.h Box.h Constants.h Coordina
 ExclusionArray.o : ExclusionArray.cpp Atom.h AtomMask.h CharMask.h CpptrajStdio.h ExclusionArray.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Unit.h
 Exec_AddMissingRes.o : Exec_AddMissingRes.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CharMask.h CompactFrameArray.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_AddMissingRes.h Exec_AddMissingRes_Pres.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Analyze.o : Exec_Analyze.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Analyze.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Build.o : Exec_Build.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/GenerateAngles.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Calc.o : Exec_Calc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Calc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_CatCrd.o : Exec_CatCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CatCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Change.o : Exec_Change.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Change.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
diff --git a/src/cpptrajfiles b/src/cpptrajfiles
index a8a487d7b1..7bcfb827aa 100644
--- a/src/cpptrajfiles
+++ b/src/cpptrajfiles
@@ -258,6 +258,7 @@ COMMON_SOURCES= \
         ExclusionArray.cpp \
         Exec_AddMissingRes.cpp \
         Exec_Analyze.cpp \
+        Exec_Build.cpp \
         Exec_Calc.cpp \
         Exec_CatCrd.cpp \
         Exec_Change.cpp \

From 0d2c6cca5f5abdd733867521b5b9fd18bd67aafb Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 5 Dec 2023 11:33:08 -0500
Subject: [PATCH 0111/1492] Get parameter set(s) to use

---
 src/Exec_Build.cpp | 53 ++++++++++++++++++++++++++++++++++++++++++++--
 src/cpptrajdepend  |  2 +-
 2 files changed, 52 insertions(+), 3 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index cfb1ef171e..0bdbd065cf 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -1,11 +1,12 @@
 #include "Exec_Build.h"
 #include "CpptrajStdio.h"
+#include "DataSet_Parameters.h"
 #include "Structure/GenerateAngles.h"
 
 // Exec_Build::Help()
 void Exec_Build::Help() const
 {
-  mprintf("\tcrdset <COORDS set> [frame <#>]\n");
+  mprintf("\tcrdset <COORDS set> [frame <#>] [parmset <param set> ...]\n");
 }
 
 // Exec_Build::Execute()
@@ -35,11 +36,59 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
   // Get modifiable topology
   Topology& topIn = *(coords.TopPtr());
 
-  // Generate angles
+  // Fill in atoms with templates
+
+  // Generate angles/dihedrals
   if (Cpptraj::Structure::GenerateAngles(topIn)) {
     mprinterr("Error: Could not generate angles/dihedrals for '%s'\n", topIn.c_str());
     return CpptrajState::ERR;
   }
 
+  // Get parameter sets.
+  typedef std::vector<DataSet_Parameters*> Parray;
+  Parray ParamSets;
+  std::string parmset = argIn.GetStringKey("parmset");
+  if (parmset.empty()) {
+    mprintf("\tNo parameter set(s) specified with 'parmset'; using any loaded sets.\n");
+    // See if there are any parameter sets.
+    DataSetList sets = State.DSL().GetSetsOfType( "*", DataSet::PARAMETERS );
+    for (DataSetList::const_iterator it = sets.begin(); it != sets.end(); ++it)
+      ParamSets.push_back( (DataSet_Parameters*)(*it) );
+  } else {
+    while (!parmset.empty()) {
+      DataSetList sets = State.DSL().GetSetsOfType( parmset, DataSet::PARAMETERS );
+      if (sets.empty()) {
+        mprintf("Warning: No parameter sets corresponding to '%s'\n", parmset.c_str());
+      } else {
+        for (DataSetList::const_iterator it = sets.begin(); it != sets.end(); ++it)
+          ParamSets.push_back( (DataSet_Parameters*)(*it) );
+      }
+      parmset = argIn.GetStringKey("parmset");
+    }
+  }
+  if (ParamSets.empty()) {
+    mprinterr("Error: No parameter sets.\n");
+    return CpptrajState::ERR;
+  }
+  mprintf("\tParameter sets:\n");
+  for (Parray::const_iterator it = ParamSets.begin(); it != ParamSets.end(); ++it)
+    mprintf("\t  %s\n", (*it)->legend());
+
+  // Combine parameters if needed
+  DataSet_Parameters* mainParmSet = 0;
+  bool free_parmset_mem = false;
+  if (ParamSets.size() == 1)
+    mainParmSet = ParamSets.front();
+  else {
+    free_parmset_mem = true;
+    mainParmSet = new DataSet_Parameters();
+    mprintf("\tCombining parameter sets.\n");
+    ParameterSet::UpdateCount UC;
+    for (Parray::const_iterator it = ParamSets.begin(); it != ParamSets.end(); ++it)
+      mainParmSet->UpdateParamSet( *(*it), UC, State.Debug() );
+  }
+
+  if (free_parmset_mem && mainParmSet != 0) delete mainParmSet;
+
   return CpptrajState::OK;
 }
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index e736d60b26..1b0de8cf2f 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -288,7 +288,7 @@ Ewald_Regular.o : Ewald_Regular.cpp Atom.h AtomMask.h Box.h Constants.h Coordina
 ExclusionArray.o : ExclusionArray.cpp Atom.h AtomMask.h CharMask.h CpptrajStdio.h ExclusionArray.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Unit.h
 Exec_AddMissingRes.o : Exec_AddMissingRes.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CharMask.h CompactFrameArray.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_AddMissingRes.h Exec_AddMissingRes_Pres.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Analyze.o : Exec_Analyze.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Analyze.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Build.o : Exec_Build.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/GenerateAngles.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Build.o : Exec_Build.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/GenerateAngles.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Calc.o : Exec_Calc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Calc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_CatCrd.o : Exec_CatCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CatCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Change.o : Exec_Change.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Change.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h

From db09b5f10bf7e3e35757657a15ce3a67e2c35b11 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 5 Dec 2023 11:37:49 -0500
Subject: [PATCH 0112/1492] Actually update the parameters. Not yet matching 
 leap for angles

---
 src/Exec_Build.cpp | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 0bdbd065cf..56684e8f84 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -88,7 +88,14 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
       mainParmSet->UpdateParamSet( *(*it), UC, State.Debug() );
   }
 
+  // Update parameters
+  Exec::RetType ret = CpptrajState::OK;
+  if ( topIn.UpdateParams( *mainParmSet  ) ) {
+    mprinterr("Error: Could not update parameters for '%s'.\n", topIn.c_str());
+    ret = CpptrajState::ERR;
+  }
+
   if (free_parmset_mem && mainParmSet != 0) delete mainParmSet;
 
-  return CpptrajState::OK;
+  return ret;
 }

From e9b84b2f73293a3980f240240ef9cf72d82ed7eb Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 5 Dec 2023 12:21:21 -0500
Subject: [PATCH 0113/1492] Angle equilibrium value should be internally in
 radians

---
 src/AmberParamFile.cpp | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 1663fad019..7cd39078ca 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -5,6 +5,7 @@
 #include "ParameterHolders.h"
 #include "StringRoutines.h"
 #include "ParameterSet.h"
+#include "Constants.h"
 #include <cstdio> // sscanf
 
 const int AmberParamFile::MAXSYMLEN = 16;
@@ -148,7 +149,7 @@ const
   types.AddName( symbols[0] );
   types.AddName( symbols[1] );
   types.AddName( symbols[2] );
-  ParameterHolders::RetType ret = prm.AP().AddParm(types, AngleParmType(TK, TEQ), true);
+  ParameterHolders::RetType ret = prm.AP().AddParm(types, AngleParmType(TK, TEQ*Constants::DEGRAD), true);
   if (ret == ParameterHolders::UPDATED)
     mprintf("Warning: Redefining angle type %s - %s - %s\n", *(types[0]), *(types[1]), *(types[2]));
 

From 18bcda9fda2deba839afc233a3c638f195b32551 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 5 Dec 2023 12:21:45 -0500
Subject: [PATCH 0114/1492] Add notes about angle param units

---
 src/ParameterTypes.h | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/ParameterTypes.h b/src/ParameterTypes.h
index 4908d653eb..6980b48209 100644
--- a/src/ParameterTypes.h
+++ b/src/ParameterTypes.h
@@ -101,8 +101,8 @@ class AngleParmType {
         return false;
     }
   private:
-    double tk_;
-    double teq_;
+    double tk_;  ///< Angle force constant in kcal/mol*rad^2
+    double teq_; ///< Angle equilibirum value in rad
 };
 typedef std::vector<AngleParmType> AngleParmArray;
 /// Hold angle atom indices and parameter index

From 0994987cb4265554a339bb53dda169765e4ae888 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 5 Dec 2023 12:27:07 -0500
Subject: [PATCH 0115/1492] When combining param sets, just make a copy of the
 first

---
 src/Exec_Build.cpp | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 56684e8f84..3922c89c79 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -81,10 +81,12 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
     mainParmSet = ParamSets.front();
   else {
     free_parmset_mem = true;
-    mainParmSet = new DataSet_Parameters();
     mprintf("\tCombining parameter sets.\n");
+    Parray::const_iterator it = ParamSets.begin();
+    mainParmSet = new DataSet_Parameters( *(*it) );
+    ++it;
     ParameterSet::UpdateCount UC;
-    for (Parray::const_iterator it = ParamSets.begin(); it != ParamSets.end(); ++it)
+    for (; it != ParamSets.end(); ++it)
       mainParmSet->UpdateParamSet( *(*it), UC, State.Debug() );
   }
 

From c79c80c3cf915b82db6fa7c3578f4e20c488c870 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 5 Dec 2023 12:44:19 -0500
Subject: [PATCH 0116/1492] Ensure mass/polarizability are updated

---
 src/Topology.cpp | 22 ++++++++++++++++++++++
 src/Topology.h   |  1 +
 2 files changed, 23 insertions(+)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index be832190aa..f683dba573 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2564,6 +2564,24 @@ void AssignParm(std::vector<Atom> const& atoms,
   }
 }*/
 
+/** Set parameters for atoms via given atom type parameter holder. */
+void Topology::AssignAtomTypeParm(ParmHolder<AtomType> const& newAtomTypeParams)
+{
+  for (unsigned int iat = 0; iat != atoms_.size(); iat++)
+  {
+    bool found;
+    TypeNameHolder atype( atoms_[iat].Type() );
+    AtomType at = newAtomTypeParams.FindParam( atype, found );
+    if (found) {
+      // Update mass
+      atoms_[iat].SetMass( at.Mass() );
+      // Update polarizability
+      atoms_[iat].SetPolar( at.Polarizability() );
+    } else
+      mprintf("Warning: Atom type parameter not found for %s\n", *atype[0]);
+  }
+}
+
 /** Set parameters for bonds in given bond array. */
 void Topology::AssignBondParm(ParmHolder<BondParmType> const& newBondParams,
                               ParmHolder<int>& currentIndices,
@@ -2960,6 +2978,10 @@ int Topology::UpdateParams(ParameterSet const& set1) {
   }
   // Atom types
   updateCount = UpdateParameters< ParmHolder<AtomType> >(set0.AT(), set1.AT(), "atom type");
+  if (updateCount > 0) {
+    mprintf("\tRegenerating atom type parameters.\n");
+    AssignAtomTypeParm( set0.AT() );
+  }
   updateCount += UpdateParameters< ParmHolder<NonbondType> >(set0.NB(), set1.NB(), "LJ A-B");
   if (updateCount > 0) {
     mprintf("\tRegenerating nonbond parameters.\n");
diff --git a/src/Topology.h b/src/Topology.h
index 805698a1f8..410c21e2ea 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -284,6 +284,7 @@ class Topology {
     inline void AddAngleArray(AngleArray const&, AngleParmArray const&, int);
     inline void AddDihArray(DihedralArray const&, DihedralParmArray const&, int);
 
+    void AssignAtomTypeParm(ParmHolder<AtomType> const&);
     void AssignBondParm(ParmHolder<BondParmType> const&, ParmHolder<int>&, BondArray&, BondParmArray&, const char*);
     void AssignAngleParm(ParmHolder<AngleParmType> const&, ParmHolder<int>&, AngleArray&);
     void AssignImproperParm(ParmHolder<DihedralParmType> const&, ParmHolder<int>&, DihedralArray&);

From 1d5823c3b98e1d4ee04232c0529cb7899ae0b09f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 5 Dec 2023 12:53:13 -0500
Subject: [PATCH 0117/1492] Using the update in ParameterSet

---
 src/Topology.cpp  | 39 +++++++++++++++++++++++----------------
 src/cpptrajdepend |  2 +-
 2 files changed, 24 insertions(+), 17 deletions(-)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index f683dba573..6f272ebe98 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -8,7 +8,6 @@
 #include "AtomType.h"
 #include "AtomMask.h"
 #include "CharMask.h"
-#include "UpdateParameters.h"
 
 const NonbondType Topology::LJ_EMPTY = NonbondType();
 
@@ -2944,49 +2943,57 @@ int Topology::UpdateParams(ParameterSet const& set1) {
     mprintf("DEBUG: Saving original parameters in originalp.dat, new parameters in newp.dat\n");
     set0.Debug("originalp.dat");
   }
+  // Update existing parameters with new parameters
+  ParameterSet::UpdateCount UC;
+  if (set0.UpdateParamSet( set1, UC, debug_ )) {
+    mprinterr("Error: Could not merge topology '%s' parameters with '%s' parameters.\n",
+              c_str(), set1.ParamSetName().c_str());
+    return 1;
+  }
 
-  unsigned int updateCount;
+//  unsigned int updateCount;
   // Bond parameters
-  updateCount = UpdateParameters< ParmHolder<BondParmType> >(set0.BP(), set1.BP(), "bond");
-  if (updateCount > 0) {
+//  updateCount = UpdateParameters< ParmHolder<BondParmType> >(set0.BP(), set1.BP(), "bond");
+  if (UC.nBondsUpdated_ > 0) {
     mprintf("\tRegenerating bond parameters.\n");
     AssignBondParams( set0.BP() );
   }
   // Angle parameters
-  updateCount = UpdateParameters< ParmHolder<AngleParmType> >(set0.AP(), set1.AP(), "angle");
-  if (updateCount > 0) {
+//  updateCount = UpdateParameters< ParmHolder<AngleParmType> >(set0.AP(), set1.AP(), "angle");
+  if (UC.nAnglesUpdated_ > 0) {
     mprintf("\tRegenerating angle parameters.\n");
     AssignAngleParams( set0.AP() );
   }
   // Dihedral parameters
-  updateCount = UpdateParameters< DihedralParmHolder >(set0.DP(), set1.DP(), "dihedral");
-  if (updateCount > 0) {
+//  updateCount = UpdateParameters< DihedralParmHolder >(set0.DP(), set1.DP(), "dihedral");
+  if (UC.nDihedralsUpdated_ > 0) {
     mprintf("\tRegenerating dihedral parameters.\n");
     AssignDihedralParams( set0.DP() );
   }
   // Urey-Bradley
-  updateCount = UpdateParameters< ParmHolder<BondParmType> >(set0.UB(), set1.UB(), "Urey-Bradley");
-  if (updateCount > 0) {
+//  updateCount = UpdateParameters< ParmHolder<BondParmType> >(set0.UB(), set1.UB(), "Urey-Bradley");
+  if (UC.nUreyBradleyUpdated_ > 0) {
     mprintf("\tRegenerating UB parameters.\n");
     AssignUBParams( set0.UB() );
   }
   // Improper parameters
-  updateCount = UpdateParameters< ParmHolder<DihedralParmType> >(set0.IP(), set1.IP(), "improper");
-  if (updateCount > 0) {
+//  updateCount = UpdateParameters< ParmHolder<DihedralParmType> >(set0.IP(), set1.IP(), "improper");
+  if (UC.nImpropersUpdated_ > 0) {
     mprintf("\tRegenerating improper parameters.\n");
     AssignImproperParams( set0.IP() );
   }
   // Atom types
-  updateCount = UpdateParameters< ParmHolder<AtomType> >(set0.AT(), set1.AT(), "atom type");
-  if (updateCount > 0) {
+//  updateCount = UpdateParameters< ParmHolder<AtomType> >(set0.AT(), set1.AT(), "atom type");
+  if (UC.nAtomTypeUpdated_ > 0) {
     mprintf("\tRegenerating atom type parameters.\n");
     AssignAtomTypeParm( set0.AT() );
   }
-  updateCount += UpdateParameters< ParmHolder<NonbondType> >(set0.NB(), set1.NB(), "LJ A-B");
-  if (updateCount > 0) {
+//  updateCount += UpdateParameters< ParmHolder<NonbondType> >(set0.NB(), set1.NB(), "LJ A-B");
+  if (UC.nAtomTypeUpdated_ > 0) {
     mprintf("\tRegenerating nonbond parameters.\n");
     AssignNonbondParams( set0.AT(), set0.NB() );
   }
+  // TODO LJ14 and HB
 
   if (debug_ > 0) set0.Debug("newp.dat");
   return 0;
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 1b0de8cf2f..e465ed3ccb 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -464,7 +464,7 @@ TextFormat.o : TextFormat.cpp StringRoutines.h TextFormat.h
 Timer.o : Timer.cpp CpptrajStdio.h Timer.h
 TinkerFile.o : TinkerFile.cpp ArgList.h Atom.h AtomMask.h Box.h BufferedLine.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TinkerFile.h Unit.h Vec3.h
 TopInfo.o : TopInfo.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h DistRoutines.h FileIO.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Mol.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h TopInfo.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Topology.o : Topology.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h UpdateParameters.h Vec3.h
+Topology.o : Topology.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 TorsionRoutines.o : TorsionRoutines.cpp Constants.h TorsionRoutines.h Vec3.h
 TrajFrameCounter.o : TrajFrameCounter.cpp ArgList.h CpptrajStdio.h TrajFrameCounter.h
 TrajIOarray.o : TrajIOarray.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryFile.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h

From 9163cfbf8d1c3dfb696b81c980514b74cfd695bd Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 5 Dec 2023 13:04:54 -0500
Subject: [PATCH 0118/1492] change var name to be more clear

---
 src/Topology.cpp | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index 6f272ebe98..c2581efcc8 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2807,8 +2807,8 @@ void Topology::AssignDihedralParams(DihedralParmHolder const& newDihedralParams)
 /** Replace current nonbond parameters with given nonbond parameters. */
 //TODO Accept array of atom type names?
 void Topology::AssignNonbondParams(ParmHolder<AtomType> const& newTypes, ParmHolder<NonbondType> const& newNB) {
-  // Generate array of existing types.
-  ParmHolder<AtomType> atomTypes;
+  // Generate array of only the types that are currently in Topology.
+  ParmHolder<AtomType> currentAtomTypes;
   for (std::vector<Atom>::const_iterator atm = atoms_.begin(); atm != atoms_.end(); ++atm)
   {
     if (atm->Type().len() > 0) {
@@ -2821,27 +2821,27 @@ void Topology::AssignNonbondParams(ParmHolder<AtomType> const& newTypes, ParmHol
         mprintf("Warning: No atom type information for type '%s'\n", *types[0]);
         newAT = AtomType(atm->Mass());
       }
-      atomTypes.AddParm( types, newAT, true );
+      currentAtomTypes.AddParm( types, newAT, true );
     }
   }
-  if (atomTypes.size() < 1) {
+  if (currentAtomTypes.size() < 1) {
     mprintf("Warning: No atom type information in %s - cannot assign nonbond parameters.\n",
             c_str());
     return;
   }
   // Regenerate nonbond params for existing types
   nonbond_.Clear();
-  nonbond_.SetupLJforNtypes( atomTypes.size() );
+  nonbond_.SetupLJforNtypes( currentAtomTypes.size() );
   int nidx1 = 0;
   NameIdxMapType nameIdxMap;
-  for (ParmHolder<AtomType>::const_iterator t1 = atomTypes.begin(); t1 != atomTypes.end(); ++t1, nidx1++)
+  for (ParmHolder<AtomType>::const_iterator t1 = currentAtomTypes.begin(); t1 != currentAtomTypes.end(); ++t1, nidx1++)
   {
     NameType const& name1 = t1->first[0];
     //mprintf("DEBUG: Type1= %s (%i)\n", *name1, nidx1);
     AtomType const& type1 = t1->second;
     nameIdxMap.insert( std::pair<NameType, int>(name1, nidx1) );
     int nidx2 = nidx1;
-    for (ParmHolder<AtomType>::const_iterator t2 = t1; t2 != atomTypes.end(); ++t2, nidx2++)
+    for (ParmHolder<AtomType>::const_iterator t2 = t1; t2 != currentAtomTypes.end(); ++t2, nidx2++)
     {
       NameType const& name2 = t2->first[0];
       //mprintf("DEBUG:\t\tType2= %s (%i)\n", *name2, nidx2);
@@ -2872,7 +2872,7 @@ void Topology::AssignNonbondParams(ParmHolder<AtomType> const& newTypes, ParmHol
               TruncResAtomNameNum( atm - atoms_.begin() ).c_str(),
               *(atm->Type()));
     } else {
-      if (it->second < 0 || it->second >= (int)atomTypes.size()) {
+      if (it->second < 0 || it->second >= (int)currentAtomTypes.size()) {
         mprinterr("Internal Error: Type index for %s (type %s) out of range: %i\n",
                   TruncResAtomNameNum( atm - atoms_.begin() ).c_str(),
                   *(atm->Type()), it->second);

From 0dd77c01df01ebc8465dc5e4a216a4f8aef8c69e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 5 Dec 2023 14:28:59 -0500
Subject: [PATCH 0119/1492] Start LJ 10-12 param update

---
 src/Parm_CharmmPsf.cpp |  2 +-
 src/Topology.cpp       | 33 +++++++++++++++++++++------------
 src/Topology.h         |  3 ++-
 3 files changed, 24 insertions(+), 14 deletions(-)

diff --git a/src/Parm_CharmmPsf.cpp b/src/Parm_CharmmPsf.cpp
index 8abc2cffe4..0f59b32efb 100644
--- a/src/Parm_CharmmPsf.cpp
+++ b/src/Parm_CharmmPsf.cpp
@@ -372,7 +372,7 @@ int Parm_CharmmPsf::ReadParm(FileName const& fname, Topology &parmOut) {
 
   // Add nonbonded parameters
   if (params_.HasLJparams()) {
-    parmOut.AssignNonbondParams( atomTypes, params_.NB() );
+    parmOut.AssignNonbondParams( atomTypes, params_.NB(), params_.HB() );
   }
 
   return 0;
diff --git a/src/Topology.cpp b/src/Topology.cpp
index c2581efcc8..1ff412c8e5 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2806,8 +2806,11 @@ void Topology::AssignDihedralParams(DihedralParmHolder const& newDihedralParams)
 
 /** Replace current nonbond parameters with given nonbond parameters. */
 //TODO Accept array of atom type names?
-void Topology::AssignNonbondParams(ParmHolder<AtomType> const& newTypes, ParmHolder<NonbondType> const& newNB) {
-  // Generate array of only the types that are currently in Topology.
+void Topology::AssignNonbondParams(ParmHolder<AtomType> const& newTypes,
+                                   ParmHolder<NonbondType> const& newNB,
+                                   ParmHolder<HB_ParmType> const& newHB)
+{
+  // Generate array of only the types that are currently in Topology. TODO should this be a permanent part of Topology?
   ParmHolder<AtomType> currentAtomTypes;
   for (std::vector<Atom>::const_iterator atm = atoms_.begin(); atm != atoms_.end(); ++atm)
   {
@@ -2849,17 +2852,23 @@ void Topology::AssignNonbondParams(ParmHolder<AtomType> const& newTypes, ParmHol
       TypeNameHolder types(2);
       types.AddName( name1 );
       types.AddName( name2 );
-      // See if this parameter exists in the given nonbond array.
-      NonbondType LJAB;
-      ParmHolder<NonbondType>::const_iterator it = newNB.GetParam( types );
-      if (it == newNB.end()) {
-        mprintf("NB parameter for %s %s not found. Generating.\n", *name1, *name2);
-        LJAB = type1.LJ().Combine_LB( type2.LJ() );
+      // Check LJ10-12
+      ParmHolder<HB_ParmType>::const_iterator hb = newHB.GetParam( types );
+      if (hb != newHB.end()) {
+        mprintf("DEBUG: LJ 10-12 parameter found for %s %s\n", *name1, *name2);
       } else {
-        mprintf("Using existing NB parameter for %s %s\n", *name1, *name2);
-        LJAB = it->second;
+        // See if this parameter exists in the given nonbond array.
+        NonbondType LJAB;
+        ParmHolder<NonbondType>::const_iterator it = newNB.GetParam( types );
+        if (it == newNB.end()) {
+          mprintf("NB parameter for %s %s not found. Generating.\n", *name1, *name2);
+          LJAB = type1.LJ().Combine_LB( type2.LJ() );
+        } else {
+          mprintf("Using existing NB parameter for %s %s\n", *name1, *name2);
+          LJAB = it->second;
+        }
+        nonbond_.AddLJterm(nidx1, nidx2, LJAB);
       }
-      nonbond_.AddLJterm(nidx1, nidx2, LJAB);
     }
   }
   // Reset the atom type indices.
@@ -2991,7 +3000,7 @@ int Topology::UpdateParams(ParameterSet const& set1) {
 //  updateCount += UpdateParameters< ParmHolder<NonbondType> >(set0.NB(), set1.NB(), "LJ A-B");
   if (UC.nAtomTypeUpdated_ > 0) {
     mprintf("\tRegenerating nonbond parameters.\n");
-    AssignNonbondParams( set0.AT(), set0.NB() );
+    AssignNonbondParams( set0.AT(), set0.NB(), set0.HB() );
   }
   // TODO LJ14 and HB
 
diff --git a/src/Topology.h b/src/Topology.h
index 410c21e2ea..830c36dca7 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -156,7 +156,8 @@ class Topology {
     double GetVDWdepth(int) const;
     /// \return Lennard-Jones 6-12 parameters for given pair of atoms
     inline NonbondType const& GetLJparam(int, int) const;
-    void AssignNonbondParams(ParmHolder<AtomType> const&, ParmHolder<NonbondType> const&);
+    void AssignNonbondParams(ParmHolder<AtomType> const&, ParmHolder<NonbondType> const&,
+                             ParmHolder<HB_ParmType> const&);
     /// \return True if any charge is non-zero
     bool HasChargeInfo() const;
     /// Redistribute charge on atoms in topology to match target total charge

From 56aedb30e23e09a0e6fa0e37366eb23fe9995002 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 5 Dec 2023 14:57:47 -0500
Subject: [PATCH 0120/1492] Set default SCEE and SCNB values, attempt to read
 if glycam

---
 src/AmberParamFile.cpp | 17 ++++++++++++++---
 1 file changed, 14 insertions(+), 3 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 7cd39078ca..f62d6bf329 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -181,18 +181,29 @@ const
   //mprintf("DEBUG: %s %s %s %s '%s'\n", symbols[0].c_str(), symbols[1].c_str(), symbols[2].c_str(), symbols[3].c_str(), ptr+pos);
   int IDIVF;
   double PK, PHASE, PN;
-  int nscan = sscanf(ptr+pos, "%i %lf %lf %lf", &IDIVF, &PK, &PHASE, &PN);
-  if (nscan != 4) {
+  char sSCEE[128];
+  char sSCNB[128];
+  int nscan = sscanf(ptr+pos, "%i %lf %lf %lf %s %s", &IDIVF, &PK, &PHASE, &PN, sSCEE, sSCNB);
+  if (nscan < 4) {
     mprinterr("Error: Expected IDIVF, PK, PHASE, PN, got only %i elements\n", nscan);
     return 1;
   }
+  double scee = 1.2; // AMBER DEFAULT
+  double scnb = 2.0; // AMBER DEFAULT
+  if (nscan == 6) {
+    // Check for SCEE/SCNB (GLYCAM)
+    if (sSCEE[0] == 'S' && sSCEE[1] == 'C' && sSCEE[2] == 'E' && sSCEE[3] == 'E')
+     sscanf( sSCEE, "SCEE=%lf", &scee);
+    if (sSCNB[0] == 'S' && sSCNB[1] == 'C' && sSCNB[2] == 'N' && sSCNB[3] == 'B')
+     sscanf( sSCNB, "SCNB=%lf", &scnb);
+  }
   TypeNameHolder types(4);
   types.AddName( symbols[0] );
   types.AddName( symbols[1] );
   types.AddName( symbols[2] );
   types.AddName( symbols[3] );
   ParameterHolders::RetType ret =
-    prm.DP().AddParm(types, DihedralParmType(PK / (double)IDIVF, PN, PHASE), true);
+    prm.DP().AddParm(types, DihedralParmType(PK / (double)IDIVF, PN, PHASE, scee, scnb), true);
   if (ret == ParameterHolders::UPDATED) {
     mprintf("Warning: Redefining dihedral type %s - %s - %s - %s (PN=%g)\n",
             *(types[0]), *(types[1]), *(types[2]), *(types[3]), PN);

From 457ba731a3322d3356ac9d33837d32d63b1762a1 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 5 Dec 2023 15:26:21 -0500
Subject: [PATCH 0121/1492] Dont set # of atom types explicitly; calculate it
 based on the actual number of atom types.

---
 src/Parm_Amber.cpp |  4 ++--
 src/Topology.cpp   | 27 +++++++++++++++++++++++----
 src/Topology.h     |  5 +----
 3 files changed, 26 insertions(+), 10 deletions(-)

diff --git a/src/Parm_Amber.cpp b/src/Parm_Amber.cpp
index d75ef15d83..d6f8b6bfd0 100644
--- a/src/Parm_Amber.cpp
+++ b/src/Parm_Amber.cpp
@@ -669,7 +669,7 @@ int Parm_Amber::ReadPointers(int Npointers, Topology& TopIn, FortranData const&
   TopIn.SetNonbond().SetupLJforNtypes( values_[NTYPES] );
   numLJparm_ = TopIn.Nonbond().NBarray().size();
   TopIn.SetNonbond().SetNHBterms( values_[NPHB] );
-  TopIn.SetNatyp( values_[NATYP] );
+  //TopIn.SetNatyp( values_[NATYP] );
   return 0;
 }
 
@@ -2088,7 +2088,7 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
 
   // SOLTY - Currently unused but must be written.
   if (BufferAlloc(F_SOLTY, TopOut.NatomTypes())) return 1;
-  for (int idx = 0; idx != TopOut.NatomTypes(); idx++)
+  for (unsigned int idx = 0; idx != TopOut.NatomTypes(); idx++)
     file_.DblToBuffer( 0.0 );
   file_.FlushBuffer();
 
diff --git a/src/Topology.cpp b/src/Topology.cpp
index 1ff412c8e5..03241605c1 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -17,8 +17,7 @@ Topology::Topology() :
   ipol_(0),
   NsolventMolecules_(0),
   pindex_(0),
-  n_extra_pts_(0),
-  n_atom_types_(0)
+  n_extra_pts_(0)
 { }
 
 // Topology::SetParmName()
@@ -48,6 +47,28 @@ unsigned int Topology::HeavyAtomCount() const {
   return hac;
 }
 
+/** \return Total number of unique atom types. */
+unsigned int Topology::NatomTypes() const {
+  ParmHolder<int> currentAtomTypes;
+  for (std::vector<Atom>::const_iterator atm = atoms_.begin(); atm != atoms_.end(); ++atm)
+  {
+    if (atm->Type().len() > 0) {
+      TypeNameHolder atype( atm->Type() );
+      // Find in currentAtomTypes.
+      bool found;
+      currentAtomTypes.FindParam( atype, found );
+      if (!found) {
+        currentAtomTypes.AddParm( atype, atm->TypeIndex(), false );
+      }
+    }
+  }
+  mprintf("DEBUG: Unique atom types in %s\n", c_str());
+  for (ParmHolder<int>::const_iterator it = currentAtomTypes.begin();
+                                       it != currentAtomTypes.end(); ++it)
+    mprintf("\t\t%s %i\n", *(it->first[0]), it->second);
+  return currentAtomTypes.size();
+}
+
 /** Reset all PDB-related info.
   * NOTE: This routine is used by AmbPDB.
   */
@@ -659,7 +680,6 @@ void Topology::Resize(Pointers const& pIn) {
   ipol_ = 0;
   NsolventMolecules_ = 0;
   n_extra_pts_ = 0;
-  n_atom_types_ = 0;
 
   atoms_.resize( pIn.natom_ );
   residues_.resize( pIn.nres_ );
@@ -1482,7 +1502,6 @@ Topology* Topology::ModifyByMap(std::vector<int> const& MapIn, bool setupFullPar
   newParm->fileName_ = fileName_;
   newParm->radius_set_ = radius_set_;
   newParm->debug_ = debug_;
-  newParm->n_atom_types_ = n_atom_types_;
 
   // Reverse Atom map
   std::vector<int> atomMap( atoms_.size(),-1 );
diff --git a/src/Topology.h b/src/Topology.h
index 830c36dca7..cd0bc88f5b 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -25,8 +25,6 @@ class Topology {
     void SetGBradiiSet(std::string const& s) { radius_set_ = s;              }
     void SetParmName(std::string const&, FileName const&);
     void SetDistMaskRef( Frame const& );
-    /// Set value of NATYP from Amber Topology. Only needed for Amber.
-    void SetNatyp(int n)                     { n_atom_types_ = n;            }
     // ----- Return internal variables -----------
     int Ipol()                     const { return ipol_;                  }
     int Pindex()                   const { return pindex_;                }
@@ -35,7 +33,7 @@ class Topology {
     int Nmol()                     const { return (int)molecules_.size(); }
     int Nsolvent()                 const { return NsolventMolecules_;     }
     int NextraPts()                const { return n_extra_pts_;           }
-    inline int NatomTypes()        const { return n_atom_types_;          }
+    unsigned int NatomTypes()      const;
     std::string const& ParmName()         const { return parmName_;       }
     FileName const& OriginalFilename()    const { return fileName_;       }
     std::string const& GBradiiSet()       const { return radius_set_;     }
@@ -336,7 +334,6 @@ class Topology {
     int NsolventMolecules_; ///< Number of molecules marked SOLVENT
     int pindex_;            ///< Internal index used to ID Topology 
     int n_extra_pts_;       ///< Number of extra points.
-    int n_atom_types_;      ///< Number of unique atom types.
 };
 // ----- INLINE FUNCTIONS ------------------------------------------------------
 NonbondType const& Topology::GetLJparam(int a1, int a2) const {

From 33aca47b062a1db718d21d6e03e27e6e9c6ea9e3 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 5 Dec 2023 15:33:21 -0500
Subject: [PATCH 0122/1492] Update for corrected SOLTY

---
 test/Test_CharmmParams/test3.parm7.save | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/test/Test_CharmmParams/test3.parm7.save b/test/Test_CharmmParams/test3.parm7.save
index 9746a76ce0..85bd66be2f 100644
--- a/test/Test_CharmmParams/test3.parm7.save
+++ b/test/Test_CharmmParams/test3.parm7.save
@@ -1,11 +1,11 @@
-%VERSION  VERSION_STAMP = V0001.000  DATE = 10/22/18 14:47:36                  
+%VERSION  VERSION_STAMP = V0001.000  DATE = 12/05/23 15:27:10                  
 %FLAG CTITLE                                                                    
 %FORMAT(a80)                                                                    
                                                                                 
 %FLAG POINTERS                                                                  
 %FORMAT(10I8)                                                                   
       23      12      11      11      26      12      42      19       0       0
-     114       1      11      12      19      13      22      36       1       0
+     114       1      11      12      19      13      22      36      12       0
        0       0       0       0       0       0       0       1      23       0
        0
 %FLAG FORCE_FIELD_TYPE                                                          
@@ -185,7 +185,9 @@ LYS
   0.00000000E+00
 %FLAG SOLTY                                                                     
 %FORMAT(5E16.8)                                                                 
-  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00
 %FLAG LENNARD_JONES_ACOEF                                                       
 %FORMAT(3E24.16)                                                                
   1.3165904011680079E+06  6.0933367984903236E+02  3.0882604789375229E-06

From cbb6950d47c574148528763b0a419689141e1389 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 5 Dec 2023 15:35:00 -0500
Subject: [PATCH 0123/1492] Update for fixed SOLTY

---
 test/Test_Charmm/strip.chamber.parm7.save | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/test/Test_Charmm/strip.chamber.parm7.save b/test/Test_Charmm/strip.chamber.parm7.save
index 433bd15132..86ca2d049d 100644
--- a/test/Test_Charmm/strip.chamber.parm7.save
+++ b/test/Test_Charmm/strip.chamber.parm7.save
@@ -1,11 +1,11 @@
-%VERSION  VERSION_STAMP = V0001.000  DATE = 01/19/18 10:10:48                  
+%VERSION  VERSION_STAMP = V0001.000  DATE = 12/05/23 15:27:09                  
 %FLAG CTITLE                                                                    
 %FORMAT(a80)                                                                    
                                                                                 
 %FLAG POINTERS                                                                  
 %FORMAT(10I8)                                                                   
       16       8       8       7      17       8      22       7       0       0
-      69       1       7       8       7       9      16      17       1       0
+      69       1       7       8       7       9      16      17       8       0
        0       0       0       0       0       0       0       0      16       0
        0
 %FLAG FORCE_FIELD_TYPE                                                          
@@ -140,7 +140,8 @@ ALA
   0.00000000E+00  0.00000000E+00  6.09119909E-01
 %FLAG SOLTY                                                                     
 %FORMAT(5E16.8)                                                                 
-  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00
 %FLAG LENNARD_JONES_ACOEF                                                       
 %FORMAT(3E24.16)                                                                
   1.9136238690375928E+06  9.3273170044881190E+04  2.5215628838626608E+03

From c79154f258d0052b72845d9c51823baca380ad86 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 6 Dec 2023 09:24:05 -0500
Subject: [PATCH 0124/1492] Remove unused constructor. Add Polarizability to
 constructor. Add function to set type index (will not deprecate after all).

---
 src/AtomType.h | 27 ++++++++++++++-------------
 1 file changed, 14 insertions(+), 13 deletions(-)

diff --git a/src/AtomType.h b/src/AtomType.h
index 13ba56aaa4..4b1d734853 100644
--- a/src/AtomType.h
+++ b/src/AtomType.h
@@ -6,33 +6,34 @@ class AtomType {
   public:
     /// CONSTRUCTOR
     AtomType() : mass_(0.0), polarizability_(0.0), oidx_(-1) {}
-    AtomType(double r, double d, int o) : lj_(r, d), mass_(0.0), polarizability_(0.0), oidx_(o) {} // TODO deprecate
-    /// CONSTRUCTOR - Mass, polarizability
-    AtomType(double m, double p) : mass_(m), polarizability_(p), oidx_(-1) {}
     /// CONSTRUCTOR - Mass only
     AtomType(double m) : mass_(m), oidx_(-1) {}
-    /// CONSTRUCTOR - Radius, well depth, mass
-    AtomType(double r, double d, double m) : lj_(r, d), mass_(m), oidx_(-1) {}
+    /// CONSTRUCTOR - Mass, polarizability
+    AtomType(double m, double p) : mass_(m), polarizability_(p), oidx_(-1) {}
+    /// CONSTRUCTOR - Radius, well depth, mass, polarizability
+    AtomType(double r, double d, double m, double p) : lj_(r, d), mass_(m), oidx_(-1) {}
+    /// Set type index
+    void SetTypeIdx(int i) { oidx_ = i; }
     /// \return default LJ parameters
-    LJparmType const& LJ() const { return lj_; }
+    LJparmType const& LJ()  const { return lj_; }
     /// \return Atom mass in amu
-    double Mass()          const { return mass_;   }
+    double Mass()           const { return mass_;   }
     /// \return Atomic polarizability in Ang^3
     double Polarizability() const { return polarizability_; }
     /// \return Original atom type index. Useful when checking for off-diagonal NB parameters.
-    int OriginalIdx()      const { return oidx_; }
+    int OriginalIdx()       const { return oidx_; }
     /// \return true if LJ params are less than incoming
     bool operator<(AtomType const& rhs) const { return lj_ < rhs.lj_; }
     /// \return true if LJ params are the same
     bool operator==(AtomType const& rhs) const { return lj_ == rhs.lj_; }
     /// Used to modify LJ params
     LJparmType& SetLJ() { return lj_; }
-    /// \return data size
-    static size_t DataSize() { return (3*sizeof(double)) + sizeof(int); }
+    /// \return data size  (2 double for LJparmType)
+    static size_t DataSize() { return (4*sizeof(double)) + sizeof(int); }
   private:
-    LJparmType lj_; ///< Default Lennard-Jones parameters (always valid for self).
-    double mass_;   ///< Mass in amu
+    LJparmType lj_;         ///< Default Lennard-Jones parameters (always valid for self).
+    double mass_;           ///< Mass in amu
     double polarizability_; ///< Atomic polarizability in Ang^3
-    int oidx_; ///< Original atom type index. TODO deprecate
+    int oidx_;              ///< Original atom type index, for indexing nonbond parameters.
 };
 #endif

From 0b0918ec2bcdb70b31c628831125d6970c87a15e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 6 Dec 2023 09:26:26 -0500
Subject: [PATCH 0125/1492] Use relative error to compare LJ types since A and
 B tend to be large and several orders of magnitude different from each other.

---
 src/ParameterTypes.h | 22 +++++++++++++++-------
 1 file changed, 15 insertions(+), 7 deletions(-)

diff --git a/src/ParameterTypes.h b/src/ParameterTypes.h
index 6980b48209..141b7d8673 100644
--- a/src/ParameterTypes.h
+++ b/src/ParameterTypes.h
@@ -19,6 +19,13 @@ static inline bool FNE(double v1, double v2) {
   return (delta > Constants::SMALL);
 }
 
+/// Calculate relative error of A1 from A0 TODO check A0?
+static inline double RELERR(double A0, double A1) {
+  double delta = A0 - A1;
+  if (delta < 0.0) delta = -delta;
+  return (delta / A0);
+}
+
 // ----- BOND/ANGLE/DIHEDRAL PARAMETERS ----------------------------------------
 /// Hold bond parameters
 class BondParmType {
@@ -305,8 +312,9 @@ class HB_ParmType {
 typedef std::vector<HB_ParmType> HB_ParmArray;
 /// Hold Lennard-Jones 6-12 interaction A and B parameters
 class NonbondType {
-    /** Tolerance for comparison. A little larger than SMALL because A
-      * and B tend to be large.
+    /** Tolerance for comparison. Using relative error here since A and
+      * B tend to be large (particularly A) and are different magnitudes
+      * from each other. Not using Constants::SMALL for the same reason.
       */
     // NOTE: Probably should check __cpluscplus here instead of using a
     //       define, but this is guaranteed to be portable.
@@ -333,18 +341,18 @@ class NonbondType {
     }
     /// \return True if A and B match
     bool operator==(NonbondType const& rhs) const {
-      return ( (fabs(A_ - rhs.A_) < tol_) &&
-               (fabs(B_ - rhs.B_) < tol_) );
+      return ( RELERR(A_, rhs.A_) < tol_ &&
+               RELERR(B_, rhs.B_) < tol_ );
     }
     /// \return True if A and B do not match
     bool operator!=(NonbondType const& rhs) const {
-      return ( (fabs(A_ - rhs.A_) > tol_) ||
-               (fabs(B_ - rhs.B_) > tol_) );
+      return ( RELERR(A_, rhs.A_) > tol_ ||
+               RELERR(B_, rhs.B_) > tol_ );
     }
     /// \return True if A less than zero, or B if A is equal.
     bool operator<(NonbondType const& rhs) const {
       if (*this != rhs) {
-        if ( (fabs(A_ - rhs.A_) < tol_) )
+        if ( RELERR(A_, rhs.A_) < tol_ )
           return (B_ < rhs.B_);
         else
           return (A_ < rhs.A_);

From cc6cff7832cd02855521431b57085c9d7c52e657 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 6 Dec 2023 09:29:13 -0500
Subject: [PATCH 0126/1492] Get rid of all dependence on map; no need since we
 can store type index in AtomType. Start a new strategy for combine; use
 UpdateParams to re-generate the proper parameters for the combined top.

---
 src/Topology.cpp | 292 ++++++++++++-----------------------------------
 src/Topology.h   |   3 +
 2 files changed, 74 insertions(+), 221 deletions(-)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index 03241605c1..fb72193fcd 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -1,5 +1,4 @@
 #include <algorithm> // find
-#include <map> // For atom types in append
 #include <stack> // For large system molecule search
 #include "Topology.h"
 #include "CpptrajStdio.h"
@@ -2105,43 +2104,6 @@ void Topology::AddDihArray(DihedralArray const& darray, DihedralParmArray const&
                                  dih->Type() ), dp[dih->Idx()] );
 }
 
-/// Map type indices to LJ parameters 
-class TypeArray {
-  public:
-    typedef std::map<int,AtomType> Tarray;
-    typedef Tarray::const_iterator const_iterator;
-    typedef std::pair<int,AtomType> Tpair;
-    TypeArray() {}
-    size_t size()    const { return types_.size();  }
-    const_iterator begin() const { return types_.begin(); }
-    const_iterator end()   const { return types_.end();   }
-    AtomType const& LastType() const { return lastType_->second; }
-    /// Add params for atom to array if not present
-    int AddAtomType(Atom const& atom, int anum, Topology const& top) {
-      if (atom.TypeIndex() < 0 || atom.Type().len() < 1) {
-        mprintf("Warning: Invalid atom type information in '%s'\n", top.c_str());
-        return 1;
-      }
-      //mprintf("DEBUG: %s %s %i %s\n", *(atom.Name()), *(atom.Type()), anum, top.c_str());
-      // See if index already present.
-      Tarray::iterator it = types_.find( atom.TypeIndex() );
-      if (it == types_.end()) {
-        AtomType type(top.GetVDWradius(anum), top.GetVDWdepth(anum), atom.TypeIndex());
-        //mprintf("\tAdding [%4zu] %4i %s %12.5g %12.5g (%s)\n", types_.size(), 
-        //         atom.TypeIndex(), *(atom.Type()),
-        //         type.Radius(), type.Depth(), top.c_str());
-        std::pair<Tarray::iterator, bool> ret = types_.insert( Tpair(atom.TypeIndex(), type) );
-        lastType_ = ret.first;
-      }
-      return 0;
-    }
-    /// Add to array
-    void AddType(int idx, AtomType const& typeIn) { types_.insert(Tpair(idx, typeIn)); }
-  private:
-    Tarray types_;
-    Tarray::iterator lastType_;
-};
-
 /** This template can be used when doing Append() on a generic std::vector array
   * of type T. The array will be appended to a given array of the same type.
   * If one is empty and the other is not, values will be filled in if necessary.
@@ -2174,45 +2136,11 @@ int Topology::AppendTop(Topology const& NewTop) {
   int atomOffset = (int)atoms_.size();
   //int resOffset = (int)residues_.size();
 
-  // NONBONDS
-  // Make sure that either both topologies have non-bond parameters or neither
-  // do. If the current topology is empty just check incoming topology.
-  bool doNonBond = true;
-  if (atoms_.empty()) {
-    doNonBond = NewTop.Nonbond().HasNonbond();
-  } else {
-    doNonBond = (Nonbond().HasNonbond() && NewTop.Nonbond().HasNonbond());
-    if (!doNonBond && (Nonbond().HasNonbond() != NewTop.Nonbond().HasNonbond())) {
-      if (Nonbond().HasNonbond())
-        mprintf("Warning: Topology '%s' does not have non-bond parameters.\n", NewTop.c_str());
-      else
-        mprintf("Warning: Topology '%s' does not have non-bond parameters.\n", c_str());
-    }
-  }
-  // Create an array of existing nonbond types so we can compare to incoming.
-  TypeArray ExistingTypes;
-  if (doNonBond) {
-    for (atom_iterator atom = atoms_.begin(); atom != atoms_.end(); ++atom) {
-      if (ExistingTypes.AddAtomType(*atom, atom-atoms_.begin(), *this)) {
-        doNonBond = false;
-        break;
-      }
-    }
-    // DEBUG
-    if (debug_ > 0) {
-      mprintf("DEBUG: %zu existing atom type indices:\n", ExistingTypes.size());
-      for (TypeArray::const_iterator ti = ExistingTypes.begin();
-                                     ti != ExistingTypes.end(); ++ti)
-        mprintf("\t%8i %12.5g %12.5g\n", ti->first, ti->second.LJ().Radius(), ti->second.LJ().Depth());
-    }
-  }
-  int NexistingAtomTypes = (int)ExistingTypes.size();
-  int currentTypeIdx = NexistingAtomTypes;
+  // Save old parameters
+  mprintf("DEBUG: Getting old parameters.\n");
+  ParameterSet oldParams = GetParameters();
 
-  // ATOMS
-  typedef std::map<int,int> TypeMap;
-  TypeMap type_newToExisting; ///< Track what existing atom type new types correspond to.
-  TypeArray NewTypes;
+  // Append NewTop atoms to this topology.
   for (atom_iterator atom = NewTop.begin(); atom != NewTop.end(); ++atom)
   {
     if (debug_ > 1)
@@ -2222,120 +2150,32 @@ int Topology::AppendTop(Topology const& NewTop) {
     Residue const& res = NewTop.Res( CurrentAtom.ResNum() );
     // Bonds need to be cleared and re-added.
     CurrentAtom.ClearBonds();
-    // NONBONDS
-    if (doNonBond) {
-      if (NewTypes.AddAtomType(*atom, atom-NewTop.begin(), NewTop)) {
-        doNonBond = false;
-      } else {
-        // Update type index
-        int newTypeIdx = -1;
-        // Check if this atom type has already been added to existing types.
-        TypeMap::iterator it = type_newToExisting.find( atom->TypeIndex() );
-        if (it == type_newToExisting.end()) {
-          // Type has not yet been mapped. See if it is an existing type.
-          for (TypeArray::const_iterator et = ExistingTypes.begin();
-                                         et != ExistingTypes.end(); ++et)
-            if (et->second == NewTypes.LastType()) {
-              newTypeIdx = et->first;
-              type_newToExisting.insert(std::pair<int,int>(atom->TypeIndex(), newTypeIdx));
-              if (debug_ > 1)
-                mprintf("\tType (%i) matches existing type (%i)\n",
-                        atom->TypeIndex(), newTypeIdx);
-              break;
-            }
-          if (newTypeIdx == -1) {
-            // Type not found among existing types. Need new type index.
-            if (debug_ > 1)
-              mprintf("\tNeed new type. Converting %i to %i\n",
-                      atom->TypeIndex(), currentTypeIdx);
-            newTypeIdx = currentTypeIdx;
-            type_newToExisting.insert(std::pair<int,int>(atom->TypeIndex(), newTypeIdx));
-            ExistingTypes.AddType(newTypeIdx, NewTypes.LastType());
-            currentTypeIdx++;
-          }
-        } else {
-          // Type has been mapped.
-          newTypeIdx = it->second;
-          if (debug_ > 1)
-            mprintf("\tType %i already present as %i.\n", atom->TypeIndex(),newTypeIdx);
-        }
-        // Update type index
-        CurrentAtom.SetTypeIndex( newTypeIdx );
-      }
-    }
-    //AddTopAtom( CurrentAtom, Residue(res.Name(), CurrentAtom.ResNum() + resOffset + 1,
     AddTopAtom( CurrentAtom, Residue(res.Name(), res.OriginalResNum(),
                                      res.Icode(), res.ChainId()) );
-  } // END loop over incoming atoms
-  // NONBONDS
-  if (!doNonBond) {
-    if (Nonbond().HasNonbond()) {
-      mprintf("Warning: Removing non-bond parameters\n");
-      nonbond_.Clear();
-    }
-  } else {
-    // DEBUG
-    if (debug_ > 0) {
-      mprintf("DEBUG: %zu new atom type indices:\n", NewTypes.size());
-      for (TypeArray::const_iterator ti = NewTypes.begin();
-                                     ti != NewTypes.end(); ++ti)
-        mprintf("\t%8i %12.5g %12.5g\n", ti->first, ti->second.LJ().Radius(), ti->second.LJ().Depth());
-      mprintf("DEBUG: New to existing mapping:\n");
-      for (TypeMap::const_iterator it = type_newToExisting.begin();
-                                   it != type_newToExisting.end(); ++it)
-        mprintf("\t%6i to %6i\n", it->first, it->second);
-      mprintf("DEBUG: Atom Types:\n");
-      for (TypeArray::const_iterator it = ExistingTypes.begin();
-                                     it != ExistingTypes.end(); ++it)
-      {
-        mprintf("\t%8i %12.5g %12.5g (%8i)", it->first, it->second.LJ().Radius(),
-                it->second.LJ().Depth(), it->second.OriginalIdx());
-        if (it->first >= NexistingAtomTypes)
-          mprintf(" (NEW)\n");
-        else
-          mprintf(" (EXISTING)\n");
-      }
-    }
-    // Set up new nonbond array.
-    NonbondParmType newNB;
-    newNB.SetupLJforNtypes( ExistingTypes.size() );
-    // Go through all interactions.
-    for (TypeArray::const_iterator t1 = ExistingTypes.begin();
-                                   t1 != ExistingTypes.end(); ++t1)
-    {
-      for (TypeArray::const_iterator t2 = ExistingTypes.begin();
-                                     t2 != ExistingTypes.end(); ++t2)
-      {
-        if (t1->first >= t2->first)
-        {
-          bool OneIsNew = (t1->first >= NexistingAtomTypes);
-          bool TwoIsNew = (t2->first >= NexistingAtomTypes);
-          NonbondType LJ = LJ_EMPTY;
-          if (OneIsNew && TwoIsNew) {
-            // Both types from new topology. Look there for LJ params using
-            // the original atom indices.
-            int nbidx = NewTop.Nonbond().GetLJindex( t1->second.OriginalIdx(),
-                                                     t2->second.OriginalIdx() );
-            if (nbidx >= 0)
-              LJ = NewTop.Nonbond().NBarray( nbidx );
-          } else if (!OneIsNew && !TwoIsNew) {
-            // Both types from existing topology. Look here for LJ params.
-            int nbidx = nonbond_.GetLJindex( t1->first, t2->first );
-            if (nbidx >= 0)
-              LJ = nonbond_.NBarray( nbidx );
-          } else {
-            // Mix new and existing.
-            LJ = t1->second.LJ().Combine_LB( t2->second.LJ() );
-          }
-          if (debug_ > 1)
-            mprintf("DEBUG: Adding LJ term for %i %i A=%g B=%g\n", t1->first, t2->first,
-                    LJ.A(), LJ.B()); 
-          newNB.AddLJterm(t1->first, t2->first, LJ);
-        }
-      }
-    }
-    nonbond_ = newNB;
   }
+  // Recreate bonds for the added atoms
+  for (BondArray::const_iterator bond = NewTop.Bonds().begin(); bond != NewTop.Bonds().end(); ++bond)
+    AddBond( bond->A1() + atomOffset, bond->A2() + atomOffset );
+  for (BondArray::const_iterator bond = NewTop.BondsH().begin(); bond != NewTop.BondsH().end(); ++bond)
+    AddBond( bond->A1() + atomOffset, bond->A2() + atomOffset );
+  // Recreate angles for the added atoms
+  for (AngleArray::const_iterator angle = NewTop.Angles().begin(); angle != NewTop.Angles().end(); ++angle)
+      AddAngle( angle->A1() + atomOffset, angle->A2() + atomOffset, angle->A3() + atomOffset );
+  for (AngleArray::const_iterator angle = NewTop.AnglesH().begin(); angle != NewTop.AnglesH().end(); ++angle)
+      AddAngle( angle->A1() + atomOffset, angle->A2() + atomOffset, angle->A3() + atomOffset );
+  // Recreate dihedrals for the added atoms
+  for (DihedralArray::const_iterator dih = NewTop.Dihedrals().begin(); dih != NewTop.Dihedrals().end(); ++dih)
+      AddDihedral( DihedralType( dih->A1() + atomOffset, dih->A2() + atomOffset,
+                                 dih->A3() + atomOffset, dih->A4() + atomOffset,
+                                 dih->Type() ), -1 );
+  for (DihedralArray::const_iterator dih = NewTop.DihedralsH().begin(); dih != NewTop.DihedralsH().end(); ++dih)
+      AddDihedral( DihedralType( dih->A1() + atomOffset, dih->A2() + atomOffset,
+                                 dih->A3() + atomOffset, dih->A4() + atomOffset,
+                                 dih->Type() ), -1 );
+  // Update parameters
+  mprintf("DEBUG: Updating with new parameters.\n");
+  updateParams( oldParams, NewTop.GetParameters() );
+
   // EXTRA ATOM INFO
   TopVecAppend<NameType> appendNameType;
   appendNameType.Append( tree_, NewTop.tree_, NewTop.Natom() );
@@ -2349,7 +2189,7 @@ int Topology::AppendTop(Topology const& NewTop) {
   appendFloat.Append( occupancy_, NewTop.occupancy_, NewTop.Natom() );
   appendFloat.Append( bfactor_, NewTop.bfactor_, NewTop.Natom() );
 
-  // BONDS
+ /* // BONDS
   AddBondArray(NewTop.Bonds(),  NewTop.BondParm(), atomOffset);
   AddBondArray(NewTop.BondsH(), NewTop.BondParm(), atomOffset);
   // ANGLES
@@ -2357,7 +2197,7 @@ int Topology::AppendTop(Topology const& NewTop) {
   AddAngleArray(NewTop.AnglesH(), NewTop.AngleParm(), atomOffset);
   // DIHEDRALS
   AddDihArray(NewTop.Dihedrals(),  NewTop.DihedralParm(), atomOffset);
-  AddDihArray(NewTop.DihedralsH(), NewTop.DihedralParm(), atomOffset);
+  AddDihArray(NewTop.DihedralsH(), NewTop.DihedralParm(), atomOffset);*/
 
   // TODO append missing stuff?
 
@@ -2441,36 +2281,37 @@ static inline void GetDihedralParams(DihedralParmHolder& DP, std::vector<Atom> c
   }
 }
 
-/** Used to map type names to type indices to access nonbond parameters. */
-typedef std::map<NameType, int> NameIdxMapType;
-
 /** \param atomTypes Output array of atom types.
-  * \param NB1 Current nonbond parameters.
-  * \param atoms Array of atoms.
-  * \param NB0 Output array of nonbond parameters.
+  * \param NB1 Output array of nonbond parameters.
+  * \param atoms Current array of atoms.
+  * \param NB0 Current nonbond parameters.
   */
 static inline void GetLJAtomTypes( ParmHolder<AtomType>& atomTypes, ParmHolder<NonbondType>& NB1, std::vector<Atom> const& atoms, NonbondParmType const& NB0, int debugIn)
 {
-  // TODO check for off-diagonal terms
   if (NB0.HasNonbond()) {
-    // Map type names to type indices to access nonbond parameters.
-    NameIdxMapType nameIdxMap;
+    // Nonbonded parameters are present.
     for (std::vector<Atom>::const_iterator atm = atoms.begin(); atm != atoms.end(); ++atm)
     {
       // TODO check for blank type name?
-      TypeNameHolder types(1);
-      types.AddName( atm->Type() );
+      TypeNameHolder atype( atm->Type() );
+      // Check for self parameters to back-calculate LJ depth/radius
       int idx = NB0.GetLJindex( atm->TypeIndex(), atm->TypeIndex() );
-      ParameterHolders::RetType ret;
+      AtomType thisType;
       if (idx > -1) {
         NonbondType const& LJ = NB0.NBarray( idx );
-        ret = atomTypes.AddParm( types, AtomType(LJ.Radius(), LJ.Depth(), atm->Mass()), true );
-      } else
-        ret = atomTypes.AddParm( types, AtomType(atm->Mass()), true );
-      if (ret == ParameterHolders::ADDED)
-        nameIdxMap.insert( std::pair<NameType, int>(atm->Type(), atm->TypeIndex()) );
+        thisType = AtomType(LJ.Radius(), LJ.Depth(), atm->Mass(), atm->Polar());
+      } else {
+        // TODO LJ 10-12
+        thisType = AtomType(atm->Mass(), atm->Polar());
+      }
+      thisType.SetTypeIdx( atm->TypeIndex() );
+      ParameterHolders::RetType ret = atomTypes.AddParm( atype, thisType, true );
+      if (ret == ParameterHolders::ADDED) {
+        mprintf("DEBUG: New atom type: %s R=%g D=%g M=%g P=%g\n", *(atype[0]), thisType.LJ().Radius(), thisType.LJ().Depth(), thisType.Mass(), thisType.Polarizability());
+      }
     }
-    // Do atom type pairs
+    // Do atom type pairs, check for off-diagonal elements.
+    // Explicitly store pairs instead of regenerating to avoid round-off issues.
     unsigned int nModifiedOffDiagonal = 0;
     for (ParmHolder<AtomType>::const_iterator i1 = atomTypes.begin(); i1 != atomTypes.end(); ++i1)
     {
@@ -2483,10 +2324,8 @@ static inline void GetLJAtomTypes( ParmHolder<AtomType>& atomTypes, ParmHolder<N
         AtomType const& type2 = i2->second;
         NonbondType lj0 = type1.LJ().Combine_LB( type2.LJ() );
         // Extract original A and B parameters.
-        NameIdxMapType::const_iterator t1 = nameIdxMap.find( name1 );
-        NameIdxMapType::const_iterator t2 = nameIdxMap.find( name2 );
-        int idx1 = t1->second;
-        int idx2 = t2->second;
+        int idx1 = type1.OriginalIdx();//t1->second;
+        int idx2 = type2.OriginalIdx();//t2->second;
         int idx = NB0.GetLJindex( idx1, idx2 );
         if (idx < 0) {
           mprinterr("Error: No off-diagonal LJ for  %s %s (%i %i)\n",
@@ -2497,13 +2336,16 @@ static inline void GetLJAtomTypes( ParmHolder<AtomType>& atomTypes, ParmHolder<N
         // Compare them
         if (lj0 != lj1) {
           nModifiedOffDiagonal++;
-          if (debugIn > 0) {
+          //if (debugIn > 0) {
             double deltaA = fabs(lj0.A() - lj1.A());
             double deltaB = fabs(lj0.B() - lj1.B());
             mprintf("DEBUG: Potential off-diagonal LJ: %s %s expect A=%g B=%g, actual A=%g B=%g\n",
                     *name1, *name2, lj0.A(), lj0.B(), lj1.A(), lj1.B());
             mprintf("DEBUG:\tdeltaA= %g    deltaB= %g\n", deltaA, deltaB);
-          }
+            double pe_a = (fabs(lj0.A() - lj1.A()) / lj0.A());
+            double pe_b = (fabs(lj0.B() - lj1.B()) / lj0.B());
+            mprintf("DEBUG:\tPEA= %g  PEB= %g\n", pe_a, pe_b);
+          //}
         }
         TypeNameHolder types(2);
         types.AddName( name1 );
@@ -2514,9 +2356,10 @@ static inline void GetLJAtomTypes( ParmHolder<AtomType>& atomTypes, ParmHolder<N
     if (nModifiedOffDiagonal > 0)
       mprintf("Warning: %u modified off-diagonal LJ terms present.\n", nModifiedOffDiagonal);
   } else {
+    // No nonbonded parameters. Just save mass/polarizability.
     for (std::vector<Atom>::const_iterator atm = atoms.begin(); atm != atoms.end(); ++atm)
       if (atm->Type().len() > 0)
-        atomTypes.AddParm( TypeNameHolder(atm->Type()), AtomType(atm->Mass()), true );
+        atomTypes.AddParm( TypeNameHolder(atm->Type()), AtomType(atm->Mass(), atm->Polar()), true );
   }
 }
 
@@ -2854,14 +2697,16 @@ void Topology::AssignNonbondParams(ParmHolder<AtomType> const& newTypes,
   // Regenerate nonbond params for existing types
   nonbond_.Clear();
   nonbond_.SetupLJforNtypes( currentAtomTypes.size() );
+  // Set type indices
   int nidx1 = 0;
-  NameIdxMapType nameIdxMap;
+  for (ParmHolder<AtomType>::iterator t1 = currentAtomTypes.begin(); t1 != currentAtomTypes.end(); ++t1, nidx1++)
+    t1->second.SetTypeIdx( nidx1 );
+  nidx1 = 0;
   for (ParmHolder<AtomType>::const_iterator t1 = currentAtomTypes.begin(); t1 != currentAtomTypes.end(); ++t1, nidx1++)
   {
     NameType const& name1 = t1->first[0];
     //mprintf("DEBUG: Type1= %s (%i)\n", *name1, nidx1);
     AtomType const& type1 = t1->second;
-    nameIdxMap.insert( std::pair<NameType, int>(name1, nidx1) );
     int nidx2 = nidx1;
     for (ParmHolder<AtomType>::const_iterator t2 = t1; t2 != currentAtomTypes.end(); ++t2, nidx2++)
     {
@@ -2894,18 +2739,18 @@ void Topology::AssignNonbondParams(ParmHolder<AtomType> const& newTypes,
   for (std::vector<Atom>::iterator atm = atoms_.begin(); atm != atoms_.end(); ++atm)
   {
     int tidx = -1;
-    NameIdxMapType::const_iterator it = nameIdxMap.find( atm->Type() );
-    if (it == nameIdxMap.end()) {
+    ParmHolder<AtomType>::const_iterator it = currentAtomTypes.GetParam( TypeNameHolder(atm->Type()) );
+    if (it == currentAtomTypes.end()) {
       mprintf("Warning: Atom type not found for %s (type %s)\n",
               TruncResAtomNameNum( atm - atoms_.begin() ).c_str(),
               *(atm->Type()));
     } else {
-      if (it->second < 0 || it->second >= (int)currentAtomTypes.size()) {
+      if (it->second.OriginalIdx() < 0 || it->second.OriginalIdx() >= (int)currentAtomTypes.size()) {
         mprinterr("Internal Error: Type index for %s (type %s) out of range: %i\n",
                   TruncResAtomNameNum( atm - atoms_.begin() ).c_str(),
-                  *(atm->Type()), it->second);
+                  *(atm->Type()), it->second.OriginalIdx());
       } else
-        tidx = it->second;
+        tidx = it->second.OriginalIdx();
     }
     atm->SetTypeIndex( tidx );
   }
@@ -2964,6 +2809,11 @@ int Topology::RedistributeCharge(double charge) {
 /** Update/add to parameters in this topology with those from given set. */
 int Topology::UpdateParams(ParameterSet const& set1) {
   ParameterSet set0 = GetParameters();
+  return updateParams(set0, set1);
+}
+
+/** Update/add to parameters in this topology by combining those from given sets. */
+int Topology::updateParams(ParameterSet& set0, ParameterSet const& set1) {
   // Check
   if (set0.AT().size() < 1)
     mprintf("Warning: No atom type information in '%s'\n", c_str());
diff --git a/src/Topology.h b/src/Topology.h
index cd0bc88f5b..28acbd863e 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -283,6 +283,9 @@ class Topology {
     inline void AddAngleArray(AngleArray const&, AngleParmArray const&, int);
     inline void AddDihArray(DihedralArray const&, DihedralParmArray const&, int);
 
+    /// Update parameters in this Topology with those from combined sets.
+    int updateParams(ParameterSet&, ParameterSet const&);
+
     void AssignAtomTypeParm(ParmHolder<AtomType> const&);
     void AssignBondParm(ParmHolder<BondParmType> const&, ParmHolder<int>&, BondArray&, BondParmArray&, const char*);
     void AssignAngleParm(ParmHolder<AngleParmType> const&, ParmHolder<int>&, AngleArray&);

From bf2c7a8e611a7d05173c298c08e89177aabb5bab Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 6 Dec 2023 10:52:10 -0500
Subject: [PATCH 0127/1492] Add 'extra' keyword to dihedral print command for
 printing SCEE/SCNB

---
 src/Exec_Top.cpp |  7 ++++---
 src/TopInfo.cpp  | 21 ++++++++++++++-------
 src/TopInfo.h    |  4 ++--
 3 files changed, 20 insertions(+), 12 deletions(-)

diff --git a/src/Exec_Top.cpp b/src/Exec_Top.cpp
index 253e7ede25..ae4ac0528d 100644
--- a/src/Exec_Top.cpp
+++ b/src/Exec_Top.cpp
@@ -100,7 +100,7 @@ Exec::RetType Exec_AngleInfo::Execute(CpptrajState& State, ArgList& argIn) {
 }
 // -----------------------------------------------------------------------------
 void Exec_DihedralInfo::Help() const {
-  mprintf("\t[%s] [<mask1>] [<mask2> <mask3> <mask4>]\n\t[out <file>]\n", DataSetList::TopIdxArgs);
+  mprintf("\t[%s] [<mask1>] [<mask2> <mask3> <mask4>]\n\t[out <file>] [extra]\n", DataSetList::TopIdxArgs);
   mprintf("  For specified topology (first by default) either print dihedral info for all\n"
           "  atoms in <mask1>, or print info for dihedrals with first atom in <mask1>,\n"
           "  second atom in <mask2>, third atom in <mask3>, and fourth atom in <mask4>.\n");
@@ -112,12 +112,13 @@ Exec::RetType Exec_DihedralInfo::Execute(CpptrajState& State, ArgList& argIn) {
               "Error:   selection please use 4 masks.\n");
     return CpptrajState::ERR;
   }
+  bool printExtraInfo = argIn.hasKey("extra");
   TopInfo info;
   if (CommonSetup(info, State, argIn, "Dihedral info")) return CpptrajState::ERR;
   std::string mask1 = argIn.GetMaskNext();
   std::string mask2 = argIn.GetMaskNext();
   std::string mask3 = argIn.GetMaskNext();
-  if (info.PrintDihedralInfo( mask1, mask2, mask3, argIn.GetMaskNext(), false ))
+  if (info.PrintDihedralInfo( mask1, mask2, mask3, argIn.GetMaskNext(), false, printExtraInfo ))
     return CpptrajState::ERR;
   return CpptrajState::OK;
 }
@@ -141,7 +142,7 @@ Exec::RetType Exec_ImproperInfo::Execute(CpptrajState& State, ArgList& argIn) {
   std::string mask1 = argIn.GetMaskNext();
   std::string mask2 = argIn.GetMaskNext();
   std::string mask3 = argIn.GetMaskNext();
-  if (info.PrintDihedralInfo( mask1, mask2, mask3, argIn.GetMaskNext(), true ))
+  if (info.PrintDihedralInfo( mask1, mask2, mask3, argIn.GetMaskNext(), true, false ))
     return CpptrajState::ERR;
   return CpptrajState::OK;
 }
diff --git a/src/TopInfo.cpp b/src/TopInfo.cpp
index 6c8256403c..69c0796484 100644
--- a/src/TopInfo.cpp
+++ b/src/TopInfo.cpp
@@ -589,7 +589,8 @@ int TopInfo::PrintAngleInfo(std::string const& mask1exp, std::string const& mask
 // TopInfo::PrintDihedrals()
 void TopInfo::PrintDihedrals(DihedralArray const& darray, DihedralParmArray const& dihedralparm,
                              CharMask const& mask1, CharMask const& mask2,
-                             CharMask const& mask3, CharMask const& mask4, int nw, int& nd) const
+                             CharMask const& mask3, CharMask const& mask4, int nw, int& nd,
+                             bool printExtraInfo) const
 {
   if (darray.empty()) return;
   for (DihedralArray::const_iterator dih = darray.begin();
@@ -618,9 +619,12 @@ void TopInfo::PrintDihedrals(DihedralArray const& darray, DihedralParmArray cons
       else if (dih->Type() == DihedralType::BOTH    ) type = 'B';
       outfile_->Printf("%c %*i", type, nw, nd);
       int didx = dih->Idx();
-      if ( didx > -1 )
+      if ( didx > -1 ) {
         outfile_->Printf(" %7.3f %5.2f %4.1f",dihedralparm[didx].Pk(),dihedralparm[didx].Phase(),
                  dihedralparm[didx].Pn());
+        if (printExtraInfo)
+          outfile_->Printf(" %4.1f %4.1f", dihedralparm[didx].SCEE(), dihedralparm[didx].SCNB());
+      }
       if ( !coords_.empty() )
         outfile_->Printf(" %7.2f", Torsion( coords_.XYZ(atom1),
                                             coords_.XYZ(atom2),
@@ -648,7 +652,7 @@ void TopInfo::PrintDihedrals(DihedralArray const& darray, DihedralParmArray cons
 // TopInfo::PrintDihedralInfo()
 int TopInfo::PrintDihedralInfo(std::string const& mask1exp, std::string const& mask2exp,
                                std::string const& mask3exp, std::string const& mask4exp,
-                               bool printImpropers) const
+                               bool printImpropers, bool printExtraInfo) const
 {
   CharMask mask1( mask1exp );
   if (SetupMask( mask1 )) return 1;
@@ -675,8 +679,11 @@ int TopInfo::PrintDihedralInfo(std::string const& mask1exp, std::string const& m
   }
   int nw = std::max(3, DigitWidth(n_torsions));
   outfile_->Printf("# %*s", nw, label);
-  if (hasParams)
+  if (hasParams) {
     outfile_->Printf(" %7s %5s %4s", "PK", "Phase", "PN");
+    if (printExtraInfo)
+      outfile_->Printf(" %4s %4s", "SCEE", "SCNB");
+  }
   if (!coords_.empty())
     outfile_->Printf(" %7s", "Value");
   outfile_->Printf(" %-*s %-*s %-*s %-*s %*s %*s %*s %*s %*s %*s %*s %*s\n",
@@ -688,10 +695,10 @@ int TopInfo::PrintDihedralInfo(std::string const& mask1exp, std::string const& m
                    max_type_len_, "T3", max_type_len_, "T4");
   int nd = 1;
   if (printImpropers) {
-    PrintDihedrals( parm_->Chamber().Impropers(), parm_->Chamber().ImproperParm(), mask1, mask2, mask3, mask4, nw, nd );
+    PrintDihedrals( parm_->Chamber().Impropers(), parm_->Chamber().ImproperParm(), mask1, mask2, mask3, mask4, nw, nd, printExtraInfo );
   } else {
-    PrintDihedrals( parm_->DihedralsH(), parm_->DihedralParm(), mask1, mask2, mask3, mask4, nw, nd );
-    PrintDihedrals( parm_->Dihedrals(),  parm_->DihedralParm(), mask1, mask2, mask3, mask4, nw, nd );
+    PrintDihedrals( parm_->DihedralsH(), parm_->DihedralParm(), mask1, mask2, mask3, mask4, nw, nd, printExtraInfo );
+    PrintDihedrals( parm_->Dihedrals(),  parm_->DihedralParm(), mask1, mask2, mask3, mask4, nw, nd, printExtraInfo );
   }
   return 0;
 }
diff --git a/src/TopInfo.h b/src/TopInfo.h
index bb62d983cb..bb7fa11da8 100644
--- a/src/TopInfo.h
+++ b/src/TopInfo.h
@@ -26,7 +26,7 @@ class TopInfo {
     int PrintBondInfo(std::string const&, std::string const&, bool) const;
     int PrintAngleInfo(std::string const&, std::string const&, std::string const&) const;
     int PrintDihedralInfo(std::string const&, std::string const&,
-                          std::string const&, std::string const&,bool) const;
+                          std::string const&, std::string const&,bool,bool) const;
     int PrintChargeInfo(std::string const&, double&) const;
     int PrintMassInfo(std::string const&, double&) const;
   private:
@@ -45,7 +45,7 @@ class TopInfo {
                      int, int&) const;
     void PrintDihedrals(DihedralArray const&, DihedralParmArray const&,
                         CharMask const&, CharMask const&,
-                        CharMask const&, CharMask const&, int, int&) const;
+                        CharMask const&, CharMask const&, int, int&,bool) const;
 
     CpptrajFile* outfile_;
     Topology const* parm_;

From d517d767671dd54c74a59bb599efe916e055651c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 6 Dec 2023 10:53:22 -0500
Subject: [PATCH 0128/1492] Replace == comparison of floating point numbers
 with FEQ()

---
 src/ParameterTypes.h | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/ParameterTypes.h b/src/ParameterTypes.h
index 141b7d8673..21a16bca43 100644
--- a/src/ParameterTypes.h
+++ b/src/ParameterTypes.h
@@ -166,10 +166,10 @@ class DihedralParmType {
                FEQ(scnb_, rhs.scnb_) );
     }
     bool operator<(DihedralParmType const& rhs) const {
-      if (pk_ == rhs.pk_) {
-        if (pn_ == rhs.pn_) {
-          if (phase_ == rhs.phase_) {
-            if (scee_ == rhs.scee_) {
+      if (FEQ(pk_, rhs.pk_)) {
+        if (FEQ(pn_, rhs.pn_)) {
+          if (FEQ(phase_, rhs.phase_)) {
+            if (FEQ(scee_, rhs.scee_)) {
               return (scnb_ < rhs.scnb_);
             } else return (scee_ < rhs.scee_);
           } else return (phase_ < rhs.phase_);

From ca8d1f8669b39ebd8435073a649db5c01243fe50 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 6 Dec 2023 14:11:57 -0500
Subject: [PATCH 0129/1492] Add != operator that depends only on atom indices

---
 src/ParameterTypes.h | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/src/ParameterTypes.h b/src/ParameterTypes.h
index 21a16bca43..9098f561a4 100644
--- a/src/ParameterTypes.h
+++ b/src/ParameterTypes.h
@@ -252,6 +252,13 @@ class DihedralType {
         } else return (a2_ < rhs.a2_);
       } else return (a1_ < rhs.a1_);
     }
+    /// \return true if any atom indices do not match
+    bool operator!=(DihedralType const& rhs) const {
+      return (a1_ != rhs.a1_ ||
+              a2_ != rhs.a2_ ||
+              a3_ != rhs.a3_ ||
+              a4_ != rhs.a4_);
+    }
   private:
     int a1_;
     int a2_;

From 80340763424718ad318f2a0cb0cddfc155082054 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 6 Dec 2023 14:12:31 -0500
Subject: [PATCH 0130/1492] Atom order swapping for dihedrals is Amber specific
 so put it in Parm_Amber

---
 src/Parm_Amber.cpp | 37 ++++++++++++++++++++++++++++---------
 1 file changed, 28 insertions(+), 9 deletions(-)

diff --git a/src/Parm_Amber.cpp b/src/Parm_Amber.cpp
index d6f8b6bfd0..771974345c 100644
--- a/src/Parm_Amber.cpp
+++ b/src/Parm_Amber.cpp
@@ -1611,20 +1611,38 @@ int Parm_Amber::WriteAngles(FlagType flag, AngleArray const& ANG) {
 
 /** Amber dihedral array. Indices must be x3, parameters index +1. End 
   * dihedrals have the third atom index negative, impropers have fourth.
+  * Because of this, atom index 0 cannot be in the third or fourth
+  * position. If this happens, reverse the ordering.
   */
 int Parm_Amber::WriteDihedrals(FlagType flag, DihedralArray const& DIH) {
   if (BufferAlloc(flag, DIH.size()*5)) return 1;
   for (DihedralArray::const_iterator it = DIH.begin(); it != DIH.end(); ++it) {
-    file_.IntToBuffer( it->A1()*3 );
-    file_.IntToBuffer( it->A2()*3 );
+    int dihIdxs[4];
+    if (it->Type() != DihedralType::NORMAL && (it->A3() == 0 || it->A4() == 0)) {
+      mprintf("Warning: Had to turn torsion around to avoid K,L == 0\n");
+      mprintf("Warning: Old order (i j k l): %i %i %i %i\n", it->A1(), it->A2(), it->A3(), it->A4());
+      dihIdxs[0] = it->A4()*3;
+      dihIdxs[1] = it->A3()*3;
+      dihIdxs[2] = it->A2()*3;
+      dihIdxs[3] = it->A1()*3;
+      mprintf("Warning: New order (i j k l): %i %i %i %i\n", it->A4(), it->A3(), it->A2(), it->A1());
+    } else {
+      dihIdxs[0] = it->A1()*3;
+      dihIdxs[1] = it->A2()*3;
+      dihIdxs[2] = it->A3()*3;
+      dihIdxs[3] = it->A4()*3;
+    }
+
+    file_.IntToBuffer( dihIdxs[0] );
+    file_.IntToBuffer( dihIdxs[1] );
     if ( it->Type() == DihedralType::BOTH || it->Type() == DihedralType::END)
-      file_.IntToBuffer( -(it->A3()*3) );
+      file_.IntToBuffer( -(dihIdxs[2]) );
     else
-      file_.IntToBuffer( it->A3()*3 );
+      file_.IntToBuffer( dihIdxs[2] );
     if ( it->Type() == DihedralType::BOTH || it->Type() == DihedralType::IMPROPER)
-      file_.IntToBuffer( -(it->A4()*3) );
+      file_.IntToBuffer( -(dihIdxs[3]) );
     else
-      file_.IntToBuffer( it->A4()*3 );
+      file_.IntToBuffer( dihIdxs[3] );
     file_.IntToBuffer( it->Idx()+1 );
   }
   file_.FlushBuffer();
@@ -1872,7 +1890,8 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
   file_.IntToBuffer( TopOut.BondParm().size() ); // NUMBND
   file_.IntToBuffer( TopOut.AngleParm().size() ); // NUMANG
   file_.IntToBuffer( TopOut.DihedralParm().size() ); // NPTRA
-  file_.IntToBuffer( TopOut.NatomTypes() ); // NATYP, only for SOLTY
+  unsigned int n_unique_atom_types = TopOut.NatomTypes();
+  file_.IntToBuffer( n_unique_atom_types ); // NATYP, only for SOLTY
   file_.IntToBuffer( TopOut.Nonbond().HBarray().size() ); // NPHB
   file_.IntToBuffer( 0 ); // IFPERT
   file_.IntToBuffer( 0 ); // NBPER
@@ -2087,8 +2106,8 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
   }
 
   // SOLTY - Currently unused but must be written.
-  if (BufferAlloc(F_SOLTY, TopOut.NatomTypes())) return 1;
-  for (unsigned int idx = 0; idx != TopOut.NatomTypes(); idx++)
+  if (BufferAlloc(F_SOLTY, n_unique_atom_types)) return 1;
+  for (unsigned int idx = 0; idx != n_unique_atom_types; idx++)
     file_.DblToBuffer( 0.0 );
   file_.FlushBuffer();
 

From 1ca054a915a2a99ec6fe1a6c8155dfcf1c0f056b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 6 Dec 2023 14:14:40 -0500
Subject: [PATCH 0131/1492] Fix assignment of dihedral parameters since in
 Amber impropers are lumped in with the regular dihedrals. Add some debug
 info.

---
 src/Topology.cpp | 176 +++++++++++++++++++++++++++++++----------------
 src/Topology.h   |   4 +-
 2 files changed, 118 insertions(+), 62 deletions(-)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index fb72193fcd..1f7a57a66c 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -1962,10 +1962,10 @@ DihedralArray Topology::StripDihedralArray(DihedralArray const& dihIn, std::vect
           if (newA4 != -1) {
             // Since in Amber improper/end dihedrals are stored as negative #s,
             // atom index 0 cannot be in 3rd or 4th position. Reverse.
-            if (olddih->Type() != DihedralType::NORMAL && (newA3 == 0 || newA4 == 0))
-              dihOut.push_back( DihedralType( newA4, newA3, newA2, newA1, 
-                                              olddih->Type(), olddih->Idx() ) );
-            else
+            //if (olddih->Type() != DihedralType::NORMAL && (newA3 == 0 || newA4 == 0))
+            //  dihOut.push_back( DihedralType( newA4, newA3, newA2, newA1, 
+            //                                  olddih->Type(), olddih->Idx() ) );
+            //else
               dihOut.push_back( DihedralType( newA1, newA2, newA3, newA4, 
                                               olddih->Type(), olddih->Idx() ) );
           }
@@ -2134,11 +2134,13 @@ template <class T> class TopVecAppend {
 // Topology::AppendTop()
 int Topology::AppendTop(Topology const& NewTop) {
   int atomOffset = (int)atoms_.size();
+  mprintf("DEBUG: Appending '%s' to '%s' (offset= %i)\n", NewTop.c_str(), c_str(), atomOffset);
   //int resOffset = (int)residues_.size();
 
   // Save old parameters
   mprintf("DEBUG: Getting old parameters.\n");
   ParameterSet oldParams = GetParameters();
+  oldParams.Debug(); // DEBUG
 
   // Append NewTop atoms to this topology.
   for (atom_iterator atom = NewTop.begin(); atom != NewTop.end(); ++atom)
@@ -2167,11 +2169,11 @@ int Topology::AppendTop(Topology const& NewTop) {
   for (DihedralArray::const_iterator dih = NewTop.Dihedrals().begin(); dih != NewTop.Dihedrals().end(); ++dih)
       AddDihedral( DihedralType( dih->A1() + atomOffset, dih->A2() + atomOffset,
                                  dih->A3() + atomOffset, dih->A4() + atomOffset,
-                                 dih->Type() ), -1 );
+                                 dih->Type() ) );
   for (DihedralArray::const_iterator dih = NewTop.DihedralsH().begin(); dih != NewTop.DihedralsH().end(); ++dih)
       AddDihedral( DihedralType( dih->A1() + atomOffset, dih->A2() + atomOffset,
                                  dih->A3() + atomOffset, dih->A4() + atomOffset,
-                                 dih->Type() ), -1 );
+                                 dih->Type() ) );
   // Update parameters
   mprintf("DEBUG: Updating with new parameters.\n");
   updateParams( oldParams, NewTop.GetParameters() );
@@ -2264,7 +2266,7 @@ static inline void GetImproperParams(ParmHolder<DihedralParmType>& IP, std::vect
 }
 
 // GetDihedralParams()
-static inline void GetDihedralParams(DihedralParmHolder& DP, std::vector<Atom> const& atoms, DihedralArray const& dih, DihedralParmArray const& dpa) {
+static inline void GetDihedralParams(DihedralParmHolder& DP, ParmHolder<DihedralParmType>& IP, std::vector<Atom> const& atoms, DihedralArray const& dih, DihedralParmArray const& dpa) {
   for (DihedralArray::const_iterator b = dih.begin(); b != dih.end(); ++b)
   {
     if (b->Idx() != -1) {
@@ -2274,9 +2276,27 @@ static inline void GetDihedralParams(DihedralParmHolder& DP, std::vector<Atom> c
       types.AddName( atoms[b->A3()].Type() );
       types.AddName( atoms[b->A4()].Type() );
       //mprintf("DEBUG: dihedral %li ( %i %i %i %i )\n", b - dih.begin() + 1, b->A1()+1, b->A2()+1, b->A3()+1, b->A4()+1);
-      ParameterHolders::RetType ret = DP.AddParm( types, dpa[b->Idx()], false );
-      if (ret == ParameterHolders::ERR)
+      //mprintf("DEBUG: dihedral %li %s %s %s %s idx=%i type=%i PK=%g PN=%g Phase=%g SCEE=%g SCNB=%g\n", b - dih.begin() + 1,
+      //        *(types[0]), *(types[1]), *(types[2]), *(types[3]), b->Idx(), (int)b->Type(),
+      //        dpa[b->Idx()].Pk(), dpa[b->Idx()].Pn(), dpa[b->Idx()].Phase(), dpa[b->Idx()].SCEE(), dpa[b->Idx()].SCNB());
+      ParameterHolders::RetType ret;
+      if (b->IsImproper()) {
+        ret = IP.AddParm( types, dpa[b->Idx()], false );
+      } else {
+        ret = DP.AddParm( types, dpa[b->Idx()], false );
+      }
+      if (ret == ParameterHolders::ERR) {
         paramOverwriteWarning("dihedral");
+        mprintf("Warning: Dihedral %s %s %s %s PK=%g PN=%g Phase=%g SCEE=%g SCNB=%g\n",
+                *(types[0]), *(types[1]), *(types[2]), *(types[3]),
+                dpa[b->Idx()].Pk(), dpa[b->Idx()].Pn(), dpa[b->Idx()].Phase(), dpa[b->Idx()].SCEE(), dpa[b->Idx()].SCNB());
+        //bool found;
+        //DihedralParmArray dpa = DP.FindParam(types, found);
+        //mprintf("Warning: Existing params:\n");
+        //for (DihedralParmArray::const_iterator d = dpa.begin(); d != dpa.end(); ++d)
+        //  mprintf("Warning:\t\tPK=%g PN=%g Phase=%g SCEE=%g SCNB=%g\n",
+        //          d->Pk(), d->Pn(), d->Phase(), d->SCEE(), d->SCNB());
+      }
     }
   }
 }
@@ -2289,6 +2309,7 @@ static inline void GetDihedralParams(DihedralParmHolder& DP, std::vector<Atom> c
 static inline void GetLJAtomTypes( ParmHolder<AtomType>& atomTypes, ParmHolder<NonbondType>& NB1, std::vector<Atom> const& atoms, NonbondParmType const& NB0, int debugIn)
 {
   if (NB0.HasNonbond()) {
+    mprintf("DEBUG: Topology has nonbond parameters.\n");
     // Nonbonded parameters are present.
     for (std::vector<Atom>::const_iterator atm = atoms.begin(); atm != atoms.end(); ++atm)
     {
@@ -2356,6 +2377,7 @@ static inline void GetLJAtomTypes( ParmHolder<AtomType>& atomTypes, ParmHolder<N
     if (nModifiedOffDiagonal > 0)
       mprintf("Warning: %u modified off-diagonal LJ terms present.\n", nModifiedOffDiagonal);
   } else {
+    mprintf("DEBUG: Topology does not have nonbond parameters.\n");
     // No nonbonded parameters. Just save mass/polarizability.
     for (std::vector<Atom>::const_iterator atm = atoms.begin(); atm != atoms.end(); ++atm)
       if (atm->Type().len() > 0)
@@ -2375,8 +2397,8 @@ ParameterSet Topology::GetParameters() const {
   GetAngleParams( Params.AP(), atoms_, angles_, angleparm_);
   GetAngleParams( Params.AP(), atoms_, anglesh_, angleparm_);
   // Dihedral parameters.
-  GetDihedralParams( Params.DP(), atoms_, dihedrals_, dihedralparm_);
-  GetDihedralParams( Params.DP(), atoms_, dihedralsh_, dihedralparm_);
+  GetDihedralParams( Params.DP(), Params.IP(), atoms_, dihedrals_, dihedralparm_);
+  GetDihedralParams( Params.DP(), Params.IP(), atoms_, dihedralsh_, dihedralparm_);
   // CHARMM parameters
   if (chamber_.HasChamber()) {
     // UB parameters
@@ -2578,24 +2600,27 @@ void Topology::AssignImproperParams(ParmHolder<DihedralParmType> const& newImpro
 
 /** Set parameters for dihedrals in given dihedral array. */
 void Topology::AssignDihedralParm(DihedralParmHolder const& newDihedralParams,
+                                  ParmHolder<DihedralParmType> const& newImproperParams,
                                   DihedralArray& dihedralsIn)
 {
   // Dihedrals can be a bit of a pain since there can be multiple
   // multiplicities for a single dihedral type. In case multiplicities
   // change, start with a fresh dihedral array containing only unique
   // dihedrals.
-  DihedralArray tmpdih = dihedralsIn;
-  std::sort( tmpdih.begin(), tmpdih.end() );
+  //DihedralArray tmpdih = dihedralsIn;
+  //std::sort( tmpdih.begin(), tmpdih.end() );
+  // Assume dihedrals with multiple terms are consecutive already
   DihedralArray dihedrals;
-  for (DihedralArray::iterator dih = tmpdih.begin(); dih != tmpdih.end(); ++dih) {
+  for (DihedralArray::const_iterator dih = dihedralsIn.begin(); dih != dihedralsIn.end(); ++dih) {
     if (dihedrals.empty())
       dihedrals.push_back( *dih );
     else {
-      DihedralType const& last = dihedrals.back();
-      if ( last.A1() != dih->A1() ||
-           last.A2() != dih->A2() ||
-           last.A3() != dih->A3() ||
-           last.A4() != dih->A4() )
+      if ( *dih != dihedrals.back() )
+      //DihedralType const& last = dihedrals.back();
+      //if ( last.A1() != dih->A1() ||
+      //     last.A2() != dih->A2() ||
+      //     last.A3() != dih->A3() ||
+      //     last.A4() != dih->A4() )
         dihedrals.push_back( *dih );
     }
   }
@@ -2604,7 +2629,9 @@ void Topology::AssignDihedralParm(DihedralParmHolder const& newDihedralParams,
             dihedralsIn.size(), dihedrals.size());
 
   ParmHolder< std::vector<int> > currentIndices;
+  ParmHolder< int > improperIndices;
   dihedralsIn.clear();
+  // Loop over all dihedrals
   for (DihedralArray::iterator dih = dihedrals.begin(); dih != dihedrals.end(); ++dih) {
     TypeNameHolder types(4);
     types.AddName( atoms_[dih->A1()].Type() );
@@ -2612,58 +2639,86 @@ void Topology::AssignDihedralParm(DihedralParmHolder const& newDihedralParams,
     types.AddName( atoms_[dih->A3()].Type() );
     types.AddName( atoms_[dih->A4()].Type() );
     bool found;
-    // See if parameter already present.
-    std::vector<int> idxs = currentIndices.FindParam( types, found );
-    if (!found) {
-      // Not yet present; search in newDihedralParams for parameter(s).
-      DihedralParmArray dpa = newDihedralParams.FindParam( types, found );
-      if (found) {
-        for (DihedralParmArray::const_iterator it = dpa.begin(); it != dpa.end(); ++it)
-        {
+    if (dih->IsImproper()) {
+      // ----- This is actually an improper dihedral. ----------------
+      int idx = improperIndices.FindParam( types, found );
+      if (!found) {
+        // Not yet present; search in newImproperParams for parameter
+        DihedralParmType ip = newImproperParams.FindParam( types, found );
+        if (found) {
           // Add parameter and save the index
-          int idx = (int)dihedralparm_.size();
-          idxs.push_back( idx );
-          dihedralparm_.push_back( *it );
-        }
-        currentIndices.AddParm( types, idxs, false );
+          idx = (int)dihedralparm_.size();
+          improperIndices.AddParm( types, idx, false );
+          dihedralparm_.push_back( ip );
+        } else
+          idx = -1;
+      }
+      if (idx == -1) {
+        mprintf("Warning: Improper parameters not found for dihedral %s-%s-%s-%s (%s-%s-%s-%s)\n",
+                TruncResAtomNameNum(dih->A1()).c_str(),
+                TruncResAtomNameNum(dih->A2()).c_str(),
+                TruncResAtomNameNum(dih->A3()).c_str(),
+                TruncResAtomNameNum(dih->A4()).c_str(),
+                *types[0], *types[1], *types[2], *types[3]);
+        
       }
-    }
-    if (idxs.empty()) {
-      mprintf("Warning: Dihedral parameters not found for dihedral %s-%s-%s-%s (%s-%s-%s-%s)\n",
-              TruncResAtomNameNum(dih->A1()).c_str(),
-              TruncResAtomNameNum(dih->A2()).c_str(),
-              TruncResAtomNameNum(dih->A3()).c_str(),
-              TruncResAtomNameNum(dih->A4()).c_str(),
-              *types[0], *types[1], *types[3], *types[4]);
       DihedralType mydih = *dih;
-      mydih.SetIdx( -1 );
+      mydih.SetIdx( idx );
       dihedralsIn.push_back( mydih );
     } else {
-      bool multi = idxs.size() > 1;
-      // Actually add the dihedrals
-      for (std::vector<int>::const_iterator dpidx = idxs.begin(); dpidx != idxs.end(); ++dpidx)
-      {
-        DihedralType mydih = *dih;
-        mydih.SetIdx( *dpidx );
-        if (multi) {
-          // If there are multiple parameters for the same dihedral, all but
-          // one of the 1-4 calcs need to be skipped.
-          if (dpidx+1 != idxs.end())
-            mydih.SetSkip14(true);
-          else
-            mydih.SetSkip14(false);
+      // -----Regular dihedral. See if parameter already present. ----
+      std::vector<int> idxs = currentIndices.FindParam( types, found );
+      if (!found) {
+        // Not yet present; search in newDihedralParams for parameter(s).
+        DihedralParmArray dpa = newDihedralParams.FindParam( types, found );
+        if (found) {
+          for (DihedralParmArray::const_iterator it = dpa.begin(); it != dpa.end(); ++it)
+          {
+            // Add parameter and save the index
+            int idx = (int)dihedralparm_.size();
+            idxs.push_back( idx );
+            dihedralparm_.push_back( *it );
+          }
+          currentIndices.AddParm( types, idxs, false );
         }
+      }
+      if (idxs.empty()) {
+        mprintf("Warning: Dihedral parameters not found for dihedral %s-%s-%s-%s (%s-%s-%s-%s)\n",
+                TruncResAtomNameNum(dih->A1()).c_str(),
+                TruncResAtomNameNum(dih->A2()).c_str(),
+                TruncResAtomNameNum(dih->A3()).c_str(),
+                TruncResAtomNameNum(dih->A4()).c_str(),
+                *types[0], *types[1], *types[2], *types[3]);
+        DihedralType mydih = *dih;
+        mydih.SetIdx( -1 );
         dihedralsIn.push_back( mydih );
+      } else {
+        bool multi = idxs.size() > 1;
+        // Actually add the dihedrals
+        for (std::vector<int>::const_iterator dpidx = idxs.begin(); dpidx != idxs.end(); ++dpidx)
+        {
+          DihedralType mydih = *dih;
+          mydih.SetIdx( *dpidx );
+          if (multi) {
+            // If there are multiple parameters for the same dihedral, all but
+            // one of the 1-4 calcs need to be skipped.
+            if (dpidx+1 != idxs.end())
+              mydih.SetSkip14(true);
+            else
+              mydih.SetSkip14(false);
+          }
+          dihedralsIn.push_back( mydih );
+        }
       }
     }
-  }
+  } // END loop over all dihedrals
 }
 
 /** Replace any current dihedral parameters with given dihedral parameters. */
-void Topology::AssignDihedralParams(DihedralParmHolder const& newDihedralParams) {
+void Topology::AssignDihedralParams(DihedralParmHolder const& newDihedralParams, ParmHolder<DihedralParmType> const& newImproperParams) {
   dihedralparm_.clear();
-  AssignDihedralParm( newDihedralParams, dihedrals_ );
-  AssignDihedralParm( newDihedralParams, dihedralsh_ );
+  AssignDihedralParm( newDihedralParams, newImproperParams, dihedrals_ );
+  AssignDihedralParm( newDihedralParams, newImproperParams, dihedralsh_ );
 }
 
 /** Replace current nonbond parameters with given nonbond parameters. */
@@ -2814,7 +2869,8 @@ int Topology::UpdateParams(ParameterSet const& set1) {
 
 /** Update/add to parameters in this topology by combining those from given sets. */
 int Topology::updateParams(ParameterSet& set0, ParameterSet const& set1) {
-  // Check
+  set1.Debug(); // DEBUG
+  // Check TODO is this necessary?
   if (set0.AT().size() < 1)
     mprintf("Warning: No atom type information in '%s'\n", c_str());
   if (debug_ > 0) {
@@ -2846,7 +2902,7 @@ int Topology::updateParams(ParameterSet& set0, ParameterSet const& set1) {
 //  updateCount = UpdateParameters< DihedralParmHolder >(set0.DP(), set1.DP(), "dihedral");
   if (UC.nDihedralsUpdated_ > 0) {
     mprintf("\tRegenerating dihedral parameters.\n");
-    AssignDihedralParams( set0.DP() );
+    AssignDihedralParams( set0.DP(), set0.IP() );
   }
   // Urey-Bradley
 //  updateCount = UpdateParameters< ParmHolder<BondParmType> >(set0.UB(), set1.UB(), "Urey-Bradley");
diff --git a/src/Topology.h b/src/Topology.h
index 28acbd863e..9f5917964c 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -138,7 +138,7 @@ class Topology {
     void AddDihedral(DihedralType const&, bool);
     void AddDihedral(DihedralType const&, DihedralParmType const&);
     void AssignImproperParams(ParmHolder<DihedralParmType> const&);
-    void AssignDihedralParams(DihedralParmHolder const&);
+    void AssignDihedralParams(DihedralParmHolder const&, ParmHolder<DihedralParmType> const&);
     // ----- CMAP-specific routines --------------
     bool                     HasCmap()      const { return !cmapGrid_.empty(); }
     CmapGridArray     const& CmapGrid()     const { return cmapGrid_;     }
@@ -290,7 +290,7 @@ class Topology {
     void AssignBondParm(ParmHolder<BondParmType> const&, ParmHolder<int>&, BondArray&, BondParmArray&, const char*);
     void AssignAngleParm(ParmHolder<AngleParmType> const&, ParmHolder<int>&, AngleArray&);
     void AssignImproperParm(ParmHolder<DihedralParmType> const&, ParmHolder<int>&, DihedralArray&);
-    void AssignDihedralParm(DihedralParmHolder const&, DihedralArray&);
+    void AssignDihedralParm(DihedralParmHolder const&, ParmHolder<DihedralParmType> const&, DihedralArray&);
 
     static const NonbondType LJ_EMPTY;
     std::vector<Atom> atoms_;

From 36eca562e0717ef71d85058eb4999351d1d1c2fb Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 6 Dec 2023 14:30:46 -0500
Subject: [PATCH 0132/1492] By convention calculate the first 1-4, skip the
 rest

---
 src/Topology.cpp | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index 1f7a57a66c..3ae22b843e 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2702,10 +2702,10 @@ void Topology::AssignDihedralParm(DihedralParmHolder const& newDihedralParams,
           if (multi) {
             // If there are multiple parameters for the same dihedral, all but
             // one of the 1-4 calcs need to be skipped.
-            if (dpidx+1 != idxs.end())
-              mydih.SetSkip14(true);
-            else
+            if (dpidx == idxs.begin())
               mydih.SetSkip14(false);
+            else
+              mydih.SetSkip14(true);
           }
           dihedralsIn.push_back( mydih );
         }

From 2816fc329adc9b6f3d7636d79b3ef9550e7097a8 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 6 Dec 2023 15:54:40 -0500
Subject: [PATCH 0133/1492] Ensure dihedral parameter array is packed when
 assigning parameters

---
 src/Topology.cpp | 81 ++++++++++++++++--------------------------------
 src/Topology.h   |  6 ++--
 2 files changed, 30 insertions(+), 57 deletions(-)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index 3ae22b843e..c32257e5c4 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -513,7 +513,7 @@ int Topology::CommonSetup(bool molsearch, bool renumberResidues)
   // TODO: Make bond parm assignment / molecule search optional?
   // Assign default lengths if necessary (for e.g. CheckStructure)
   if (bondparm_.empty())
-    AssignBondParameters();
+    generateBondParameters();
   if (molsearch) {
     // Determine molecule info from bonds
     if (DetermineMolecules())
@@ -747,8 +747,8 @@ void Topology::AddBondParam(BondType& bnd, BP_mapType& bpMap)
   bnd.SetIdx( bp_idx );
 }
 
-// Topology::AssignBondParameters()
-void Topology::AssignBondParameters() {
+/** Fill in bond parameters based on atomic element types. */
+void Topology::generateBondParameters() {
   mprintf("Warning: Determining bond length parameters from element types for '%s'.\n", c_str());
   bondparm_.clear();
   // Hold indices into bondparm for unique element pairs
@@ -939,25 +939,21 @@ void Topology::AddAngle(AngleType const& angIn, bool isH) {
 }
 
 // -----------------------------------------------
-// Topology::AddTorsionParm()
 /** Check if given dihedral parm exists in given dihedral parm array. Add if not.
   * \return Index in dihedral parm array.
   */
-int Topology::AddTorsionParm(DihedralParmArray& dparray, DihedralParmType const& DPin)
+int Topology::addTorsionParm(DihedralParmArray& dparray, DihedralParmType const& DPin)
 {
   // See if the DihedralParm exists.
   int pidx = -1;
   for (DihedralParmArray::const_iterator dp = dparray.begin();
                                          dp != dparray.end(); ++dp)
-    if ( fabs(DPin.Pk()    - dp->Pk()   ) < Constants::SMALL &&
-         fabs(DPin.Pn()    - dp->Pn()   ) < Constants::SMALL &&
-         fabs(DPin.Phase() - dp->Phase()) < Constants::SMALL &&
-         fabs(DPin.SCEE()  - dp->SCEE() ) < Constants::SMALL &&
-         fabs(DPin.SCNB()  - dp->SCNB() ) < Constants::SMALL )
-    {
+  {
+    if (DPin == *dp) {
       pidx = (int)(dp - dparray.begin());
       break;
     }
+  }
   if (pidx == -1) {
     pidx = (int)dparray.size();
     dparray.push_back( DPin );
@@ -997,7 +993,7 @@ DihedralType Topology::SetTorsionParmIndex(DihedralType const& dihIn,
 /** Add given dihedral with given dihedral parm to dihedral array. */
 void Topology::AddDihedral(DihedralType const& dih, DihedralParmType const& DPin)
 {
-  int pidx = AddTorsionParm(dihedralparm_, DPin);
+  int pidx = addTorsionParm(dihedralparm_, DPin);
   if (CheckTorsionRange(dih, "dihedral")) return;
   AddDihedral(dih, pidx);
 }
@@ -1028,7 +1024,7 @@ void Topology::AddDihedral(DihedralType const& dihIn, bool isH) {
 /** Add given Charmm improper with given improper parm to Charmm improper array. */
 void Topology::AddCharmmImproper(DihedralType const& imp, DihedralParmType const& IPin)
 {
-  int pidx = AddTorsionParm(chamber_.SetImproperParm(), IPin);
+  int pidx = addTorsionParm(chamber_.SetImproperParm(), IPin);
   if (CheckTorsionRange(imp, "CHARMM improper")) return;
   AddCharmmImproper(imp, pidx);
 }
@@ -2628,8 +2624,8 @@ void Topology::AssignDihedralParm(DihedralParmHolder const& newDihedralParams,
     mprintf("DEBUG: %zu incoming dihedrals, %zu unique dihedrals.\n",
             dihedralsIn.size(), dihedrals.size());
 
-  ParmHolder< std::vector<int> > currentIndices;
-  ParmHolder< int > improperIndices;
+  //ParmHolder< std::vector<int> > currentIndices;
+  //ParmHolder< int > improperIndices;
   dihedralsIn.clear();
   // Loop over all dihedrals
   for (DihedralArray::iterator dih = dihedrals.begin(); dih != dihedrals.end(); ++dih) {
@@ -2641,48 +2637,26 @@ void Topology::AssignDihedralParm(DihedralParmHolder const& newDihedralParams,
     bool found;
     if (dih->IsImproper()) {
       // ----- This is actually an improper dihedral. ----------------
-      int idx = improperIndices.FindParam( types, found );
+      DihedralParmType ip = newImproperParams.FindParam( types, found );
+      int idx;
       if (!found) {
-        // Not yet present; search in newImproperParams for parameter
-        DihedralParmType ip = newImproperParams.FindParam( types, found );
-        if (found) {
-          // Add parameter and save the index
-          idx = (int)dihedralparm_.size();
-          improperIndices.AddParm( types, idx, false );
-          dihedralparm_.push_back( ip );
-        } else
-          idx = -1;
-      }
-      if (idx == -1) {
+        idx = -1;
         mprintf("Warning: Improper parameters not found for dihedral %s-%s-%s-%s (%s-%s-%s-%s)\n",
                 TruncResAtomNameNum(dih->A1()).c_str(),
                 TruncResAtomNameNum(dih->A2()).c_str(),
                 TruncResAtomNameNum(dih->A3()).c_str(),
                 TruncResAtomNameNum(dih->A4()).c_str(),
                 *types[0], *types[1], *types[2], *types[3]);
-        
+      } else {
+        idx = addTorsionParm( dihedralparm_, ip );
       }
       DihedralType mydih = *dih;
       mydih.SetIdx( idx );
       dihedralsIn.push_back( mydih );
     } else {
       // -----Regular dihedral. See if parameter already present. ----
-      std::vector<int> idxs = currentIndices.FindParam( types, found );
+      DihedralParmArray dpa = newDihedralParams.FindParam( types, found );
       if (!found) {
-        // Not yet present; search in newDihedralParams for parameter(s).
-        DihedralParmArray dpa = newDihedralParams.FindParam( types, found );
-        if (found) {
-          for (DihedralParmArray::const_iterator it = dpa.begin(); it != dpa.end(); ++it)
-          {
-            // Add parameter and save the index
-            int idx = (int)dihedralparm_.size();
-            idxs.push_back( idx );
-            dihedralparm_.push_back( *it );
-          }
-          currentIndices.AddParm( types, idxs, false );
-        }
-      }
-      if (idxs.empty()) {
         mprintf("Warning: Dihedral parameters not found for dihedral %s-%s-%s-%s (%s-%s-%s-%s)\n",
                 TruncResAtomNameNum(dih->A1()).c_str(),
                 TruncResAtomNameNum(dih->A2()).c_str(),
@@ -2693,20 +2667,17 @@ void Topology::AssignDihedralParm(DihedralParmHolder const& newDihedralParams,
         mydih.SetIdx( -1 );
         dihedralsIn.push_back( mydih );
       } else {
-        bool multi = idxs.size() > 1;
         // Actually add the dihedrals
-        for (std::vector<int>::const_iterator dpidx = idxs.begin(); dpidx != idxs.end(); ++dpidx)
-        {
+        for (DihedralParmArray::const_iterator it = dpa.begin(); it != dpa.end(); ++it) {
           DihedralType mydih = *dih;
-          mydih.SetIdx( *dpidx );
-          if (multi) {
-            // If there are multiple parameters for the same dihedral, all but
-            // one of the 1-4 calcs need to be skipped.
-            if (dpidx == idxs.begin())
-              mydih.SetSkip14(false);
-            else
-              mydih.SetSkip14(true);
-          }
+          int idx = addTorsionParm( dihedralparm_, *it );
+          // If there are multiple parameters for the same dihedral, all but
+          // one of the 1-4 calcs need to be skipped.
+          if (it == dpa.begin())
+            mydih.SetSkip14(false);
+          else
+            mydih.SetSkip14(true);
+          mydih.SetIdx( idx );
           dihedralsIn.push_back( mydih );
         }
       }
diff --git a/src/Topology.h b/src/Topology.h
index 9f5917964c..525a4bc7ee 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -250,8 +250,10 @@ class Topology {
     // NOTE: Use set so that elements are always sorted.
     typedef std::vector< std::set<Atom::AtomicElementType> > BP_mapType;
     void AddBondParam(BondType&, BP_mapType&);
-    void AssignBondParameters();
-    static inline int AddTorsionParm(DihedralParmArray&, DihedralParmType const&);
+    /// Fill in bond parameters with estimations based on atomic element types
+    void generateBondParameters();
+    /// \return Index of existing/added dihedral parameter in given array
+    static inline int addTorsionParm(DihedralParmArray&, DihedralParmType const&);
     bool CheckTorsionRange(DihedralType const& dihIn, const char*) const;
     static inline DihedralType SetTorsionParmIndex(DihedralType const&,
                                                    DihedralParmArray const&,

From 62cb3cd1e41e1cfd345d8621fee146dc0dd71249 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 6 Dec 2023 19:51:00 -0500
Subject: [PATCH 0134/1492] Add addBondParm. Change name to genBondParam to
 better reflect what it does.

---
 src/Topology.cpp | 29 +++++++++++++++++++++++++----
 src/Topology.h   |  5 ++++-
 2 files changed, 29 insertions(+), 5 deletions(-)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index c32257e5c4..18205f3fe2 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -723,9 +723,30 @@ void Topology::SetAtomBondInfo(BondArray const& bonds) {
 }
 
 // -----------------------------------------------------------------------------
-// Topology::AddBondParam()
+/** Check if given bond parm exists in given bond parm array. Add if not.
+  * \return Index in bond parm array.
+  */
+int Topology::addBondParm(BondParmArray& bparray, BondParmType const& BPin)
+{
+  // See if the BondParm exists.
+  int pidx = -1;
+  for (BondParmArray::const_iterator bp = bparray.begin();
+                                     bp != bparray.end(); ++bp)
+  {
+    if (BPin == *bp) {
+      pidx = (int)(bp - bparray.begin());
+      break;
+    }
+  }
+  if (pidx == -1) {
+    pidx = (int)bparray.size();
+    bparray.push_back( BPin );
+  }
+  return pidx;
+}
+
 /** Create parameters for given bond based on element types. */
-void Topology::AddBondParam(BondType& bnd, BP_mapType& bpMap)
+void Topology::genBondParam(BondType& bnd, BP_mapType& bpMap)
 {
   unsigned int bp_idx;
   Atom::AtomicElementType a1Elt = atoms_[bnd.A1()].Element();
@@ -754,9 +775,9 @@ void Topology::generateBondParameters() {
   // Hold indices into bondparm for unique element pairs
   BP_mapType bpMap;
   for (BondArray::iterator bnd = bondsh_.begin(); bnd != bondsh_.end(); ++bnd)
-    AddBondParam( *bnd, bpMap ); 
+    genBondParam( *bnd, bpMap ); 
   for (BondArray::iterator bnd = bonds_.begin(); bnd != bonds_.end(); ++bnd)
-    AddBondParam( *bnd, bpMap );
+    genBondParam( *bnd, bpMap );
 } 
 
 // Topology::AddBond()
diff --git a/src/Topology.h b/src/Topology.h
index 525a4bc7ee..527961064b 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -249,11 +249,14 @@ class Topology {
     void SetAtomBondInfo(BondArray const&);
     // NOTE: Use set so that elements are always sorted.
     typedef std::vector< std::set<Atom::AtomicElementType> > BP_mapType;
-    void AddBondParam(BondType&, BP_mapType&);
+    /// Generate a bond parameter for the given bond based on atom elements
+    void genBondParam(BondType&, BP_mapType&);
     /// Fill in bond parameters with estimations based on atomic element types
     void generateBondParameters();
     /// \return Index of existing/added dihedral parameter in given array
     static inline int addTorsionParm(DihedralParmArray&, DihedralParmType const&);
+    /// \return Index of existing/added bond parameter in given array
+    static inline int addBondParm(BondParmArray&, BondParmType const&);
     bool CheckTorsionRange(DihedralType const& dihIn, const char*) const;
     static inline DihedralType SetTorsionParmIndex(DihedralType const&,
                                                    DihedralParmArray const&,

From 8867369f6a6a2576cc6f6a06862734ce7aaef635 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 7 Dec 2023 08:26:45 -0500
Subject: [PATCH 0135/1492] Use addBondParm routine

---
 src/Topology.cpp | 32 +++++++-------------------------
 1 file changed, 7 insertions(+), 25 deletions(-)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index 18205f3fe2..764af6bc36 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -783,18 +783,7 @@ void Topology::generateBondParameters() {
 // Topology::AddBond()
 void Topology::AddBond(int atom1, int atom2, BondParmType const& BPin) {
   // See if the BondParm exists.
-  int pidx = -1;
-  for (BondParmArray::const_iterator bp = bondparm_.begin(); bp != bondparm_.end(); ++bp)
-    if ( fabs(BPin.Rk()  - bp->Rk() ) < Constants::SMALL &&
-         fabs(BPin.Req() - bp->Req()) < Constants::SMALL )
-    {
-      pidx = (int)(bp - bondparm_.begin());
-      break;
-    }
-  if (pidx == -1) {
-    pidx = (int)bondparm_.size();
-    bondparm_.push_back( BPin );
-  }
+  int pidx = addBondParm( bondparm_, BPin );;
   AddBond( atom1, atom2, pidx );
 }
 
@@ -2492,24 +2481,17 @@ void Topology::AssignBondParm(ParmHolder<BondParmType> const& newBondParams,
     types.AddName( atoms_[bnd->A1()].Type() );
     types.AddName( atoms_[bnd->A2()].Type() );
     bool found;
-    // See if parameter already present.
-    int idx = currentIndices.FindParam( types, found );
+    // See if parameter is present.
+    int idx = -1;
+    BondParmType bp = newBondParams.FindParam( types, found );
     if (!found) {
-      // Search in new
-      BondParmType bp = newBondParams.FindParam( types, found );
-      if (found) {
-        // Add parameter
-        idx = (int)bpa.size();
-        bpa.push_back( bp );
-        currentIndices.AddParm( types, idx, false );
-      } else
-        idx = -1;
-    }
-    if (idx == -1)
       mprintf("Warning: parameter not found for %s %s-%s (%s-%s)\n", desc,
               TruncResAtomNameNum(bnd->A1()).c_str(),
               TruncResAtomNameNum(bnd->A2()).c_str(),
               *types[0], *types[1]);
+    } else {
+      idx = addBondParm( bondparm_, bp );
+    }
     bnd->SetIdx( idx );
   }
 }

From 0da9ef9f840b16ae0327da7e176d3037804be661 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 7 Dec 2023 10:59:07 -0500
Subject: [PATCH 0136/1492] Ensure angle/improper parameters are packed

---
 src/Topology.cpp | 200 +++++++++++++++++++++--------------------------
 src/Topology.h   |   8 +-
 2 files changed, 95 insertions(+), 113 deletions(-)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index 764af6bc36..2c8bcb3af9 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -898,21 +898,32 @@ void Topology::AddBond(BondType const& bndIn, bool isH) {
   atoms_[bndIn.A2()].AddBondToIdx( bndIn.A1() );
 }
 
-// Topology::AddAngle() 
-void Topology::AddAngle(int atom1, int atom2, int atom3, AngleParmType const& APin) {
+/** Check if given angle parm exists in given angle parm array. Add if not.
+  * \return Index in angle parm array.
+  */
+int Topology::addAngleParm(AngleParmArray& aparray, AngleParmType const& APin)
+{
   // See if the AngleParm exists.
   int pidx = -1;
-  for (AngleParmArray::const_iterator ap = angleparm_.begin(); ap != angleparm_.end(); ++ap)
-    if ( fabs(APin.Tk()  - ap->Tk() ) < Constants::SMALL &&
-         fabs(APin.Teq() - ap->Teq()) < Constants::SMALL )
-    {
-      pidx = (int)(ap - angleparm_.begin());
+  for (AngleParmArray::const_iterator ap = aparray.begin();
+                                      ap != aparray.end(); ++ap)
+  {
+    if (APin == *ap) {
+      pidx = (int)(ap - aparray.begin());
       break;
     }
+  }
   if (pidx == -1) {
-    pidx = (int)angleparm_.size();
-    angleparm_.push_back( APin );
+    pidx = (int)aparray.size();
+    aparray.push_back( APin );
   }
+  return pidx;
+}
+
+// Topology::AddAngle() 
+void Topology::AddAngle(int atom1, int atom2, int atom3, AngleParmType const& APin) {
+  // See if the AngleParm exists.
+  int pidx = addAngleParm( angleparm_, APin );
   AddAngle( atom1, atom2, atom3, pidx );
 }
 
@@ -2473,7 +2484,6 @@ void Topology::AssignAtomTypeParm(ParmHolder<AtomType> const& newAtomTypeParams)
 
 /** Set parameters for bonds in given bond array. */
 void Topology::AssignBondParm(ParmHolder<BondParmType> const& newBondParams,
-                              ParmHolder<int>& currentIndices,
                               BondArray& bonds, BondParmArray& bpa, const char* desc)
 {
   for (BondArray::iterator bnd = bonds.begin(); bnd != bonds.end(); ++bnd) {
@@ -2499,22 +2509,18 @@ void Topology::AssignBondParm(ParmHolder<BondParmType> const& newBondParams,
 /** Replace any current bond parameters with given bond parameters. */
 void Topology::AssignBondParams(ParmHolder<BondParmType> const& newBondParams) {
   bondparm_.clear();
-  ParmHolder<int> currentIndices;
-  //AssignParm<BondParmType, BondArray, BondParmArray>( atoms, newBondParams, currentIndices, bonds_, bondparm_ );
-  AssignBondParm( newBondParams, currentIndices, bonds_,  bondparm_, "bond" );
-  AssignBondParm( newBondParams, currentIndices, bondsh_, bondparm_, "bond" );
+  AssignBondParm( newBondParams, bonds_,  bondparm_, "bond" );
+  AssignBondParm( newBondParams, bondsh_, bondparm_, "bond" );
 }
 
 /** Replace any current Urey-Bradley parameters with given UB parameters. */
 void Topology::AssignUBParams(ParmHolder<BondParmType> const& newBondParams) {
   chamber_.SetUBparm().clear();
-  ParmHolder<int> currentIndices;
-  AssignBondParm( newBondParams, currentIndices, chamber_.SetUB(), chamber_.SetUBparm(), "UB term" );
+  AssignBondParm( newBondParams, chamber_.SetUB(), chamber_.SetUBparm(), "UB term" );
 }
 
 /** Set parameters for angles in given angle array. */
 void Topology::AssignAngleParm(ParmHolder<AngleParmType> const& newAngleParams,
-                              ParmHolder<int>& currentIndices,
                               AngleArray& angles)
 {
   for (AngleArray::iterator ang = angles.begin(); ang != angles.end(); ++ang) {
@@ -2523,25 +2529,18 @@ void Topology::AssignAngleParm(ParmHolder<AngleParmType> const& newAngleParams,
     types.AddName( atoms_[ang->A2()].Type() );
     types.AddName( atoms_[ang->A3()].Type() );
     bool found;
-    // See if parameter already present.
-    int idx = currentIndices.FindParam( types, found );
+    // See if parameter is present.
+    int idx = -1;
+    AngleParmType ap = newAngleParams.FindParam( types, found );
     if (!found) {
-      // Search in new
-      AngleParmType ap = newAngleParams.FindParam( types, found );
-      if (found) {
-        // Add parameter
-        idx = (int)angleparm_.size();
-        angleparm_.push_back( ap );
-        currentIndices.AddParm( types, idx, false );
-      } else
-        idx = -1;
-    }
-    if (idx == -1)
       mprintf("Warning: Angle parameter not found for angle %s-%s-%s (%s-%s-%s)\n",
               TruncResAtomNameNum(ang->A1()).c_str(),
               TruncResAtomNameNum(ang->A2()).c_str(),
               TruncResAtomNameNum(ang->A3()).c_str(),
               *types[0], *types[1], *types[3]);
+    } else {
+      idx = addAngleParm( angleparm_, ap );
+    }
     ang->SetIdx( idx );
   }
 }
@@ -2549,14 +2548,12 @@ void Topology::AssignAngleParm(ParmHolder<AngleParmType> const& newAngleParams,
 /** Replace any current angle parameters with given angle parameters. */
 void Topology::AssignAngleParams(ParmHolder<AngleParmType> const& newAngleParams) {
   angleparm_.clear();
-  ParmHolder<int> currentIndices;
-  AssignAngleParm( newAngleParams, currentIndices, angles_ );
-  AssignAngleParm( newAngleParams, currentIndices, anglesh_ );
+  AssignAngleParm( newAngleParams, angles_ );
+  AssignAngleParm( newAngleParams, anglesh_ );
 }
 
-/** Set parameters for dihedrals in given dihedral array. */
+/** Set parameters for improper dihedrals in given improper dihedral array. */
 void Topology::AssignImproperParm(ParmHolder<DihedralParmType> const& newImproperParams,
-                                  ParmHolder<int>& currentIndices,
                                   DihedralArray& impropers)
 {
   for (DihedralArray::iterator imp = impropers.begin(); imp != impropers.end(); ++imp) {
@@ -2566,26 +2563,19 @@ void Topology::AssignImproperParm(ParmHolder<DihedralParmType> const& newImprope
     types.AddName( atoms_[imp->A3()].Type() );
     types.AddName( atoms_[imp->A4()].Type() );
     bool found;
-    // See if parameter already present.
-    int idx = currentIndices.FindParam( types, found );
+    // See if parameter is present.
+    int idx = -1;
+    DihedralParmType ip = newImproperParams.FindParam( types, found );
     if (!found) {
-      // Search in new
-      DihedralParmType ip = newImproperParams.FindParam( types, found );
-      if (found) {
-        // Add parameter
-        idx = (int)chamber_.ImproperParm().size();
-        chamber_.SetImproperParm().push_back( ip );
-        currentIndices.AddParm( types, idx, false );
-      } else
-        idx = -1;
-    }
-    if (idx == -1)
       mprintf("Warning: Parameter not found for improper %s-%s-%s-%s (%s-%s-%s-%s)\n",
               TruncResAtomNameNum(imp->A1()).c_str(),
               TruncResAtomNameNum(imp->A2()).c_str(),
               TruncResAtomNameNum(imp->A3()).c_str(),
               TruncResAtomNameNum(imp->A4()).c_str(),
               *types[0], *types[1], *types[3], *types[4]);
+    } else {
+      idx = addTorsionParm( chamber_.SetImproperParm(), ip );
+    }
     imp->SetIdx( idx );
   }
 }
@@ -2593,8 +2583,7 @@ void Topology::AssignImproperParm(ParmHolder<DihedralParmType> const& newImprope
 /** Replace any current improper parameters with given improper parameters. */
 void Topology::AssignImproperParams(ParmHolder<DihedralParmType> const& newImproperParams) {
   chamber_.SetImproperParm().clear();
-  ParmHolder<int> currentIndices;
-  AssignImproperParm( newImproperParams, currentIndices, chamber_.SetImpropers() );
+  AssignImproperParm( newImproperParams, chamber_.SetImpropers() );
 }
 
 /** Set parameters for dihedrals in given dihedral array. */
@@ -2615,11 +2604,6 @@ void Topology::AssignDihedralParm(DihedralParmHolder const& newDihedralParams,
       dihedrals.push_back( *dih );
     else {
       if ( *dih != dihedrals.back() )
-      //DihedralType const& last = dihedrals.back();
-      //if ( last.A1() != dih->A1() ||
-      //     last.A2() != dih->A2() ||
-      //     last.A3() != dih->A3() ||
-      //     last.A4() != dih->A4() )
         dihedrals.push_back( *dih );
     }
   }
@@ -2627,8 +2611,6 @@ void Topology::AssignDihedralParm(DihedralParmHolder const& newDihedralParams,
     mprintf("DEBUG: %zu incoming dihedrals, %zu unique dihedrals.\n",
             dihedralsIn.size(), dihedrals.size());
 
-  //ParmHolder< std::vector<int> > currentIndices;
-  //ParmHolder< int > improperIndices;
   dihedralsIn.clear();
   // Loop over all dihedrals
   for (DihedralArray::iterator dih = dihedrals.begin(); dih != dihedrals.end(); ++dih) {
@@ -2641,10 +2623,9 @@ void Topology::AssignDihedralParm(DihedralParmHolder const& newDihedralParams,
     if (dih->IsImproper()) {
       // ----- This is actually an improper dihedral. ----------------
       DihedralParmType ip = newImproperParams.FindParam( types, found );
-      int idx;
+      int idx = -1;
       if (!found) {
-        idx = -1;
-        mprintf("Warning: Improper parameters not found for dihedral %s-%s-%s-%s (%s-%s-%s-%s)\n",
+        mprintf("Warning: Improper parameters not found for improper dihedral %s-%s-%s-%s (%s-%s-%s-%s)\n",
                 TruncResAtomNameNum(dih->A1()).c_str(),
                 TruncResAtomNameNum(dih->A2()).c_str(),
                 TruncResAtomNameNum(dih->A3()).c_str(),
@@ -2785,56 +2766,6 @@ void Topology::AssignNonbondParams(ParmHolder<AtomType> const& newTypes,
   }
 }
 
-/** \return True if any atom has a non-zero charge. */
-bool Topology::HasChargeInfo() const {
-  for (std::vector<Atom>::const_iterator at = atoms_.begin();
-                                         at != atoms_.end(); ++at)
-    if (at->Charge() > 0.0 || at->Charge() < 0.0)
-      return true;
-  return false;
-}
-
-/** Redistribute charge on atoms to match given total target charge. */
-int Topology::RedistributeCharge(double charge) {
-  //mprintf("DEBUG: Redistribute charge for %s, total charge = %g\n", topIn.c_str(), charge);
-  double pcharge = 0;
-  double ncharge = 0;
-  for (unsigned int iat = 0; iat != atoms_.size(); iat++) {
-    if (atoms_[iat].Charge() > 0)
-      pcharge += atoms_[iat].Charge();
-    else if (atoms_[iat].Charge() < 0)
-      ncharge += atoms_[iat].Charge();
-  }
-  //if (fabs(pcharge) < Constants::SMALL)
-  bool PchargeZero = false;
-  if (pcharge == 0) {
-    mprintf("\tTotal positive charge is 0.0\n");
-    PchargeZero = true;
-  }
-  bool NchargeZero = false;
-  //if (fabs(ncharge) < Constants::SMALL)
-  if (ncharge == 0) {
-    mprintf("\tTotal negative charge is 0.0\n");
-    NchargeZero = true;
-  }
-  if (!PchargeZero && !NchargeZero) {
-    //double total_charge = 0;
-    for (unsigned int iat = 0; iat != atoms_.size(); iat++) {
-      double delta = atoms_[iat].Charge() * (charge - pcharge - ncharge) / (pcharge - ncharge);
-      if (atoms_[iat].Charge() >= 0) {
-        atoms_[iat].SetCharge( atoms_[iat].Charge() + delta );
-      } else {
-        atoms_[iat].SetCharge( atoms_[iat].Charge() - delta );
-      }
-      //total_charge += topIn[iat].Charge();
-    }
-    //mprintf("DEBUG: Total charge after redistribute: %g\n", total_charge);
-  }
-  return 0;
-}
-
-// -----------------------------------------------------------------------------
-
 /** Update/add to parameters in this topology with those from given set. */
 int Topology::UpdateParams(ParameterSet const& set1) {
   ParameterSet set0 = GetParameters();
@@ -2906,3 +2837,52 @@ int Topology::updateParams(ParameterSet& set0, ParameterSet const& set1) {
   if (debug_ > 0) set0.Debug("newp.dat");
   return 0;
 }
+
+// -----------------------------------------------------------------------------
+/** \return True if any atom has a non-zero charge. */
+bool Topology::HasChargeInfo() const {
+  for (std::vector<Atom>::const_iterator at = atoms_.begin();
+                                         at != atoms_.end(); ++at)
+    if (at->Charge() > 0.0 || at->Charge() < 0.0)
+      return true;
+  return false;
+}
+
+/** Redistribute charge on atoms to match given total target charge. */
+int Topology::RedistributeCharge(double charge) {
+  //mprintf("DEBUG: Redistribute charge for %s, total charge = %g\n", topIn.c_str(), charge);
+  double pcharge = 0;
+  double ncharge = 0;
+  for (unsigned int iat = 0; iat != atoms_.size(); iat++) {
+    if (atoms_[iat].Charge() > 0)
+      pcharge += atoms_[iat].Charge();
+    else if (atoms_[iat].Charge() < 0)
+      ncharge += atoms_[iat].Charge();
+  }
+  //if (fabs(pcharge) < Constants::SMALL)
+  bool PchargeZero = false;
+  if (pcharge == 0) {
+    mprintf("\tTotal positive charge is 0.0\n");
+    PchargeZero = true;
+  }
+  bool NchargeZero = false;
+  //if (fabs(ncharge) < Constants::SMALL)
+  if (ncharge == 0) {
+    mprintf("\tTotal negative charge is 0.0\n");
+    NchargeZero = true;
+  }
+  if (!PchargeZero && !NchargeZero) {
+    //double total_charge = 0;
+    for (unsigned int iat = 0; iat != atoms_.size(); iat++) {
+      double delta = atoms_[iat].Charge() * (charge - pcharge - ncharge) / (pcharge - ncharge);
+      if (atoms_[iat].Charge() >= 0) {
+        atoms_[iat].SetCharge( atoms_[iat].Charge() + delta );
+      } else {
+        atoms_[iat].SetCharge( atoms_[iat].Charge() - delta );
+      }
+      //total_charge += topIn[iat].Charge();
+    }
+    //mprintf("DEBUG: Total charge after redistribute: %g\n", total_charge);
+  }
+  return 0;
+}
diff --git a/src/Topology.h b/src/Topology.h
index 527961064b..baa7c31418 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -257,6 +257,8 @@ class Topology {
     static inline int addTorsionParm(DihedralParmArray&, DihedralParmType const&);
     /// \return Index of existing/added bond parameter in given array
     static inline int addBondParm(BondParmArray&, BondParmType const&);
+    /// \return Index of existing/added angle parameter in given array
+    static inline int addAngleParm(AngleParmArray&, AngleParmType const&);
     bool CheckTorsionRange(DihedralType const& dihIn, const char*) const;
     static inline DihedralType SetTorsionParmIndex(DihedralType const&,
                                                    DihedralParmArray const&,
@@ -292,9 +294,9 @@ class Topology {
     int updateParams(ParameterSet&, ParameterSet const&);
 
     void AssignAtomTypeParm(ParmHolder<AtomType> const&);
-    void AssignBondParm(ParmHolder<BondParmType> const&, ParmHolder<int>&, BondArray&, BondParmArray&, const char*);
-    void AssignAngleParm(ParmHolder<AngleParmType> const&, ParmHolder<int>&, AngleArray&);
-    void AssignImproperParm(ParmHolder<DihedralParmType> const&, ParmHolder<int>&, DihedralArray&);
+    void AssignBondParm(ParmHolder<BondParmType> const&, BondArray&, BondParmArray&, const char*);
+    void AssignAngleParm(ParmHolder<AngleParmType> const&, AngleArray&);
+    void AssignImproperParm(ParmHolder<DihedralParmType> const&, DihedralArray&);
     void AssignDihedralParm(DihedralParmHolder const&, ParmHolder<DihedralParmType> const&, DihedralArray&);
 
     static const NonbondType LJ_EMPTY;

From 8be515320d92d4ffb581bcfd8c3c1c154d6017e6 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 7 Dec 2023 12:43:14 -0500
Subject: [PATCH 0137/1492] Use passed in bond parameter array so UB terms are
 also assigned. Make const.

---
 src/Topology.cpp | 39 ++-------------------------------------
 src/Topology.h   |  2 +-
 2 files changed, 3 insertions(+), 38 deletions(-)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index 2c8bcb3af9..fa9fb01292 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2428,42 +2428,6 @@ ParameterSet Topology::GetParameters() const {
 }
 
 // -----------------------------------------------------------------------------
-/** Set parameters in array V for objects in array U using parameters from array T. 
-  */
-/*
-template<typename T, typename U, typename V>
-void AssignParm(std::vector<Atom> const& atoms,
-                ParmHolder<T> const& newParams,  // BondParmType
-                ParmHolder<int>& currentIndices,
-                U& objects,                      // BondArray
-                V& currentParams)                // BondParmArray
-{
-  for (typename U::iterator obj = objects.begin(); obj != objects.end(); ++obj) {
-    TypeNameHolder types(obj->Nidx());
-    for (unsigned int idx = 0; idx != obj->Nidx(); idx++)
-      types.AddName( atoms[obj->Atom(idx)].Type() );
-    bool found;
-    // See if parameter already present.
-    int idx = currentIndices.FindParam( types, found );
-    if (!found) {
-      // Search in new
-      T param = newParams.FindParam( types, found );
-      if (found) {
-        // Add parameter
-        idx = (int)currentParams.size();
-        currentParams.push_back( param );
-      } else
-        idx = -1;
-    }
-    //if (idx == -1)
-    //  mprintf("Warning: Bond parameter not found for bond %s-%s (%s-%s)\n",
-    //          TruncResAtomNameNum(bnd->A1()).c_str(),
-    //          TruncResAtomNameNum(bnd->A2()).c_str(),
-    //          *types[0], *types[1]);
-    obj->SetIdx( idx );
-  }
-}*/
-
 /** Set parameters for atoms via given atom type parameter holder. */
 void Topology::AssignAtomTypeParm(ParmHolder<AtomType> const& newAtomTypeParams)
 {
@@ -2485,6 +2449,7 @@ void Topology::AssignAtomTypeParm(ParmHolder<AtomType> const& newAtomTypeParams)
 /** Set parameters for bonds in given bond array. */
 void Topology::AssignBondParm(ParmHolder<BondParmType> const& newBondParams,
                               BondArray& bonds, BondParmArray& bpa, const char* desc)
+const
 {
   for (BondArray::iterator bnd = bonds.begin(); bnd != bonds.end(); ++bnd) {
     TypeNameHolder types(2);
@@ -2500,7 +2465,7 @@ void Topology::AssignBondParm(ParmHolder<BondParmType> const& newBondParams,
               TruncResAtomNameNum(bnd->A2()).c_str(),
               *types[0], *types[1]);
     } else {
-      idx = addBondParm( bondparm_, bp );
+      idx = addBondParm( bpa, bp );
     }
     bnd->SetIdx( idx );
   }
diff --git a/src/Topology.h b/src/Topology.h
index baa7c31418..cd0afac3b7 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -294,7 +294,7 @@ class Topology {
     int updateParams(ParameterSet&, ParameterSet const&);
 
     void AssignAtomTypeParm(ParmHolder<AtomType> const&);
-    void AssignBondParm(ParmHolder<BondParmType> const&, BondArray&, BondParmArray&, const char*);
+    void AssignBondParm(ParmHolder<BondParmType> const&, BondArray&, BondParmArray&, const char*) const;
     void AssignAngleParm(ParmHolder<AngleParmType> const&, AngleArray&);
     void AssignImproperParm(ParmHolder<DihedralParmType> const&, DihedralArray&);
     void AssignDihedralParm(DihedralParmHolder const&, ParmHolder<DihedralParmType> const&, DihedralArray&);

From a3df3f26b3bf09d705b2c1137a4c9e495b4c9cf7 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 7 Dec 2023 12:58:43 -0500
Subject: [PATCH 0138/1492] Ensure LJ 1012 term is added

---
 src/Topology.cpp | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index fa9fb01292..1f906897b6 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2672,10 +2672,11 @@ void Topology::AssignNonbondParams(ParmHolder<AtomType> const& newTypes,
   // Regenerate nonbond params for existing types
   nonbond_.Clear();
   nonbond_.SetupLJforNtypes( currentAtomTypes.size() );
-  // Set type indices
+  // Set type indices in order.
   int nidx1 = 0;
   for (ParmHolder<AtomType>::iterator t1 = currentAtomTypes.begin(); t1 != currentAtomTypes.end(); ++t1, nidx1++)
     t1->second.SetTypeIdx( nidx1 );
+  // Loop over all atom type pairs
   nidx1 = 0;
   for (ParmHolder<AtomType>::const_iterator t1 = currentAtomTypes.begin(); t1 != currentAtomTypes.end(); ++t1, nidx1++)
   {
@@ -2691,10 +2692,11 @@ void Topology::AssignNonbondParams(ParmHolder<AtomType> const& newTypes,
       TypeNameHolder types(2);
       types.AddName( name1 );
       types.AddName( name2 );
-      // Check LJ10-12
+      // Check for LJ10-12 first
       ParmHolder<HB_ParmType>::const_iterator hb = newHB.GetParam( types );
       if (hb != newHB.end()) {
-        mprintf("DEBUG: LJ 10-12 parameter found for %s %s\n", *name1, *name2);
+        mprintf("LJ 10-12 parameter found for %s %s\n", *name1, *name2);
+        nonbond_.AddHBterm(nidx1, nidx2, hb->second);
       } else {
         // See if this parameter exists in the given nonbond array.
         NonbondType LJAB;
@@ -2797,7 +2799,7 @@ int Topology::updateParams(ParameterSet& set0, ParameterSet const& set1) {
     mprintf("\tRegenerating nonbond parameters.\n");
     AssignNonbondParams( set0.AT(), set0.NB(), set0.HB() );
   }
-  // TODO LJ14 and HB
+  // TODO LJ14
 
   if (debug_ > 0) set0.Debug("newp.dat");
   return 0;

From e544085d06b47840d66b5a8bd3994ac3aa197e88 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 7 Dec 2023 13:59:27 -0500
Subject: [PATCH 0139/1492] Have the < and == operators take mass and
 polarizability into account

---
 src/AtomType.h | 22 ++++++++++++++++++----
 1 file changed, 18 insertions(+), 4 deletions(-)

diff --git a/src/AtomType.h b/src/AtomType.h
index 4b1d734853..659e84fc8e 100644
--- a/src/AtomType.h
+++ b/src/AtomType.h
@@ -22,10 +22,24 @@ class AtomType {
     double Polarizability() const { return polarizability_; }
     /// \return Original atom type index. Useful when checking for off-diagonal NB parameters.
     int OriginalIdx()       const { return oidx_; }
-    /// \return true if LJ params are less than incoming
-    bool operator<(AtomType const& rhs) const { return lj_ < rhs.lj_; }
-    /// \return true if LJ params are the same
-    bool operator==(AtomType const& rhs) const { return lj_ == rhs.lj_; }
+    /// \return true if mass, polarizability, or LJ params are less than incoming
+    bool operator<(AtomType const& rhs) const {
+      if (FEQ(mass_, rhs.mass_)) {
+        if (FEQ(polarizability_, rhs.polarizability_)) {
+          return lj_ < rhs.lj_;
+        } else {
+          return polarizability_ < rhs.polarizability_;
+        }
+      } else {
+        return mass_ < rhs.mass_;
+      }
+    }
+    /// \return true if mass, polarizability, and LJ params are the same
+    bool operator==(AtomType const& rhs) const {
+      return (FEQ(mass_, rhs.mass_) &&
+              FEQ(polarizability_, rhs.polarizability_) &&
+              lj_ == rhs.lj_);
+    }
     /// Used to modify LJ params
     LJparmType& SetLJ() { return lj_; }
     /// \return data size  (2 double for LJparmType)

From 7b231274367deb9016f3dee3d5bfadf23174f327 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 7 Dec 2023 14:38:32 -0500
Subject: [PATCH 0140/1492] Pack the nonbond array by detecting equivalent
 types

---
 src/Topology.cpp | 40 +++++++++++++++++++++++++++-------------
 1 file changed, 27 insertions(+), 13 deletions(-)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index 1f906897b6..dc1ddb95d4 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -46,9 +46,10 @@ unsigned int Topology::HeavyAtomCount() const {
   return hac;
 }
 
-/** \return Total number of unique atom types. */
+/** \return Total number of unique nonbonded atom types. */
 unsigned int Topology::NatomTypes() const {
-  ParmHolder<int> currentAtomTypes;
+  return nonbond_.Ntypes();
+/*  ParmHolder<int> currentAtomTypes;
   for (std::vector<Atom>::const_iterator atm = atoms_.begin(); atm != atoms_.end(); ++atm)
   {
     if (atm->Type().len() > 0) {
@@ -65,7 +66,7 @@ unsigned int Topology::NatomTypes() const {
   for (ParmHolder<int>::const_iterator it = currentAtomTypes.begin();
                                        it != currentAtomTypes.end(); ++it)
     mprintf("\t\t%s %i\n", *(it->first[0]), it->second);
-  return currentAtomTypes.size();
+  return currentAtomTypes.size();*/
 }
 
 /** Reset all PDB-related info.
@@ -2671,20 +2672,33 @@ void Topology::AssignNonbondParams(ParmHolder<AtomType> const& newTypes,
   }
   // Regenerate nonbond params for existing types
   nonbond_.Clear();
-  nonbond_.SetupLJforNtypes( currentAtomTypes.size() );
   // Set type indices in order.
-  int nidx1 = 0;
-  for (ParmHolder<AtomType>::iterator t1 = currentAtomTypes.begin(); t1 != currentAtomTypes.end(); ++t1, nidx1++)
-    t1->second.SetTypeIdx( nidx1 );
+  for (ParmHolder<AtomType>::iterator t1 = currentAtomTypes.begin(); t1 != currentAtomTypes.end(); ++t1)
+    t1->second.SetTypeIdx( -1 );
+  int n_unique_lj_types = 0;
+  for (ParmHolder<AtomType>::iterator t1 = currentAtomTypes.begin(); t1 != currentAtomTypes.end(); ++t1)
+  {
+    if (t1->second.OriginalIdx() == -1) {
+      t1->second.SetTypeIdx( n_unique_lj_types );
+      // Look for equivalent nonbond types
+      for (ParmHolder<AtomType>::iterator t2 = t1 + 1; t2 != currentAtomTypes.end(); ++t2) {
+        if (t2->second.OriginalIdx() == -1 && t1->second.LJ() == t2->second.LJ()) {
+          mprintf("DEBUG: Type %s equivalent to type %s\n", *(t1->first[0]), *(t2->first[0]));
+          t2->second.SetTypeIdx( n_unique_lj_types );
+        }
+      }
+      n_unique_lj_types++;
+    }
+  }
+  mprintf("DEBUG: Setting up nonbond array for %i unique LJ types.\n", n_unique_lj_types);
+  nonbond_.SetupLJforNtypes( n_unique_lj_types );
   // Loop over all atom type pairs
-  nidx1 = 0;
-  for (ParmHolder<AtomType>::const_iterator t1 = currentAtomTypes.begin(); t1 != currentAtomTypes.end(); ++t1, nidx1++)
+  for (ParmHolder<AtomType>::const_iterator t1 = currentAtomTypes.begin(); t1 != currentAtomTypes.end(); ++t1)
   {
     NameType const& name1 = t1->first[0];
     //mprintf("DEBUG: Type1= %s (%i)\n", *name1, nidx1);
     AtomType const& type1 = t1->second;
-    int nidx2 = nidx1;
-    for (ParmHolder<AtomType>::const_iterator t2 = t1; t2 != currentAtomTypes.end(); ++t2, nidx2++)
+    for (ParmHolder<AtomType>::const_iterator t2 = t1; t2 != currentAtomTypes.end(); ++t2)
     {
       NameType const& name2 = t2->first[0];
       //mprintf("DEBUG:\t\tType2= %s (%i)\n", *name2, nidx2);
@@ -2696,7 +2710,7 @@ void Topology::AssignNonbondParams(ParmHolder<AtomType> const& newTypes,
       ParmHolder<HB_ParmType>::const_iterator hb = newHB.GetParam( types );
       if (hb != newHB.end()) {
         mprintf("LJ 10-12 parameter found for %s %s\n", *name1, *name2);
-        nonbond_.AddHBterm(nidx1, nidx2, hb->second);
+        nonbond_.AddHBterm(t1->second.OriginalIdx(), t2->second.OriginalIdx(), hb->second);
       } else {
         // See if this parameter exists in the given nonbond array.
         NonbondType LJAB;
@@ -2708,7 +2722,7 @@ void Topology::AssignNonbondParams(ParmHolder<AtomType> const& newTypes,
           mprintf("Using existing NB parameter for %s %s\n", *name1, *name2);
           LJAB = it->second;
         }
-        nonbond_.AddLJterm(nidx1, nidx2, LJAB);
+        nonbond_.AddLJterm(t1->second.OriginalIdx(), t2->second.OriginalIdx(), LJAB);
       }
     }
   }

From 1d5d5dc7fc133e996bc55276536f23bf7fe11936 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 7 Dec 2023 14:48:38 -0500
Subject: [PATCH 0141/1492] Need total number of unique atoms for solty array,
 not unique LJ types

---
 src/Parm_Amber.cpp | 2 +-
 src/Topology.cpp   | 9 ++++-----
 src/Topology.h     | 3 ++-
 3 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/Parm_Amber.cpp b/src/Parm_Amber.cpp
index 771974345c..9552a3e141 100644
--- a/src/Parm_Amber.cpp
+++ b/src/Parm_Amber.cpp
@@ -1890,7 +1890,7 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
   file_.IntToBuffer( TopOut.BondParm().size() ); // NUMBND
   file_.IntToBuffer( TopOut.AngleParm().size() ); // NUMANG
   file_.IntToBuffer( TopOut.DihedralParm().size() ); // NPTRA
-  unsigned int n_unique_atom_types = TopOut.NatomTypes();
+  unsigned int n_unique_atom_types = TopOut.NuniqueAtomTypes();
   file_.IntToBuffer( n_unique_atom_types ); // NATYP, only for SOLTY
   file_.IntToBuffer( TopOut.Nonbond().HBarray().size() ); // NPHB
   file_.IntToBuffer( 0 ); // IFPERT
diff --git a/src/Topology.cpp b/src/Topology.cpp
index dc1ddb95d4..8af9c36c43 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -46,10 +46,9 @@ unsigned int Topology::HeavyAtomCount() const {
   return hac;
 }
 
-/** \return Total number of unique nonbonded atom types. */
-unsigned int Topology::NatomTypes() const {
-  return nonbond_.Ntypes();
-/*  ParmHolder<int> currentAtomTypes;
+/** \return Total number of unique atom types. */
+unsigned int Topology::NuniqueAtomTypes() const {
+  ParmHolder<int> currentAtomTypes;
   for (std::vector<Atom>::const_iterator atm = atoms_.begin(); atm != atoms_.end(); ++atm)
   {
     if (atm->Type().len() > 0) {
@@ -66,7 +65,7 @@ unsigned int Topology::NatomTypes() const {
   for (ParmHolder<int>::const_iterator it = currentAtomTypes.begin();
                                        it != currentAtomTypes.end(); ++it)
     mprintf("\t\t%s %i\n", *(it->first[0]), it->second);
-  return currentAtomTypes.size();*/
+  return currentAtomTypes.size();
 }
 
 /** Reset all PDB-related info.
diff --git a/src/Topology.h b/src/Topology.h
index cd0afac3b7..7ef90fa9bd 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -33,7 +33,8 @@ class Topology {
     int Nmol()                     const { return (int)molecules_.size(); }
     int Nsolvent()                 const { return NsolventMolecules_;     }
     int NextraPts()                const { return n_extra_pts_;           }
-    unsigned int NatomTypes()      const;
+    /// \return number of unique atom types
+    unsigned int NuniqueAtomTypes() const;
     std::string const& ParmName()         const { return parmName_;       }
     FileName const& OriginalFilename()    const { return fileName_;       }
     std::string const& GBradiiSet()       const { return radius_set_;     }

From 0228fb6482a804b0388e5f6afe68452e0f4485d2 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 7 Dec 2023 16:16:39 -0500
Subject: [PATCH 0142/1492] Some attempts at bond sorting to match leap

---
 src/Exec_UpdateParameters.cpp |  3 +++
 src/Topology.cpp              | 46 +++++++++++++++++++++++++++++++++--
 src/Topology.h                |  1 +
 3 files changed, 48 insertions(+), 2 deletions(-)

diff --git a/src/Exec_UpdateParameters.cpp b/src/Exec_UpdateParameters.cpp
index d42b174e29..c07ede5e7d 100644
--- a/src/Exec_UpdateParameters.cpp
+++ b/src/Exec_UpdateParameters.cpp
@@ -44,6 +44,9 @@ Exec::RetType Exec_UpdateParameters::Execute(CpptrajState& State, ArgList& argIn
   mprintf("\tUpdating parameters in topology '%s' using those in set '%s'\n",
           top.c_str(), ds->legend());
 
+  // Sort topology bond arrays to be consistent with LEaP
+  top.SortBonds();
+
   if (ds->Type() == DataSet::PARAMETERS)
     top.UpdateParams(static_cast<DataSet_Parameters const&>( *ds ));
   else if (ds->Type() == DataSet::TOPOLOGY) {
diff --git a/src/Topology.cpp b/src/Topology.cpp
index 8af9c36c43..b94c1a36b8 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -1,9 +1,9 @@
-#include <algorithm> // find
+#include <algorithm> // find, copy, fill
 #include <stack> // For large system molecule search
 #include "Topology.h"
 #include "CpptrajStdio.h"
 #include "StringRoutines.h" // integerToString 
-#include "Constants.h" // RADDEG, SMALL
+#include "Constants.h" // SMALL
 #include "AtomType.h"
 #include "AtomMask.h"
 #include "CharMask.h"
@@ -898,6 +898,12 @@ void Topology::AddBond(BondType const& bndIn, bool isH) {
   atoms_[bndIn.A2()].AddBondToIdx( bndIn.A1() );
 }
 
+/** Sort bond arrays. May want to do this to e.g. match LEAP bond ordering. */
+void Topology::SortBonds() {
+  std::sort(bonds_.begin(), bonds_.end());
+  std::sort(bondsh_.begin(), bondsh_.end());
+}
+
 /** Check if given angle parm exists in given angle parm array. Add if not.
   * \return Index in angle parm array.
   */
@@ -2476,6 +2482,42 @@ void Topology::AssignBondParams(ParmHolder<BondParmType> const& newBondParams) {
   bondparm_.clear();
   AssignBondParm( newBondParams, bonds_,  bondparm_, "bond" );
   AssignBondParm( newBondParams, bondsh_, bondparm_, "bond" );
+/**  // Try to match leap bond ordering. Appears to be by index with priority
+  // given to heavy atoms.
+  BondArray tmpBonds;
+  tmpBonds.resize( bonds_.size() + bondsh_.size() );
+  std::copy( bonds_.begin(), bonds_.end(), tmpBonds.begin() );
+  std::copy( bondsh_.begin(), bondsh_.end(), tmpBonds.begin() + bonds_.size() );
+  std::sort( tmpBonds.begin(), tmpBonds.end() );**/
+/*
+  BondArray::iterator b1 = bonds_.begin();
+  BondArray::iterator b2 = bondsh_.begin();
+  while (b1 != bonds_.end() || b2 != bondsh_.end()) {
+    int iat = b1->A1();
+    tmpBonds.push_back( *b1 );
+    ++b1;
+    while (b1 != bonds_.end() && b1->A1() == iat) {
+      tmpBonds.push_back( *b1 );
+      ++b1;
+    }
+    while (b2 != bondsh_.end() && b2->A1() == iat) {
+      tmpBonds.push_back( *b2 );
+      ++b2;
+    }
+  }
+  if (tmpBonds.size() != bonds_.size() + bondsh_.size()) {
+    mprinterr("Internal Error: AssignBondParams: Size of temp. bonds array %zu != total # bonds %zu\n",
+              tmpBonds.size(), bonds_.size() + bondsh_.size());
+  }*/
+/**  AssignBondParm( newBondParams, tmpBonds, bondparm_, "bond" );
+  bonds_.clear();
+  bondsh_.clear();
+  for (BondArray::const_iterator it = tmpBonds.begin(); it != tmpBonds.end(); ++it)
+    if ( atoms_[it->A1()].Element() == Atom::HYDROGEN ||
+         atoms_[it->A2()].Element() == Atom::HYDROGEN)
+      bondsh_.push_back( *it );
+    else
+      bonds_.push_back( *it );**/
 }
 
 /** Replace any current Urey-Bradley parameters with given UB parameters. */
diff --git a/src/Topology.h b/src/Topology.h
index 7ef90fa9bd..10f3d3996c 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -115,6 +115,7 @@ class Topology {
     void AddBond(BondType const&, bool);
     void AddBond(int, int, BondParmType const&);
     int RemoveBond(int, int);
+    void SortBonds();
     void AssignBondParams(ParmHolder<BondParmType> const&);
     // ----- Angle-specific routines -------------
     size_t Nangles()                           const { return angles_.size()+anglesh_.size(); }

From 5bc700bcf886e7ecfd3c6910b21e3f11085cd791 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 11 Dec 2023 08:48:45 -0500
Subject: [PATCH 0143/1492] Add a verbosity option

---
 src/UpdateParameters.h | 19 ++++++++++++-------
 1 file changed, 12 insertions(+), 7 deletions(-)

diff --git a/src/UpdateParameters.h b/src/UpdateParameters.h
index 9dcd79b04c..ea7221eceb 100644
--- a/src/UpdateParameters.h
+++ b/src/UpdateParameters.h
@@ -20,8 +20,9 @@ static inline void PrintParmType(HB_ParmType const& hb) { mprintf(" %12.4E %12.4
   * \param0 Parameters to add to/update.
   * \param1 New parameters.
   * \param desc Description of parameters.
+  * \param verbose Verbosity: 0 - silent,  1 - updated only, 2 - updated & same, 3 - all
   */
-template <typename T> int UpdateParameters(T& param0, T const& param1, const char* desc)
+template <typename T> int UpdateParameters(T& param0, T const& param1, const char* desc, int verbose)
 {
   // DEBUG
 //  mprintf("DEBUG: Current %s Parameters:\n", desc);
@@ -33,16 +34,20 @@ template <typename T> int UpdateParameters(T& param0, T const& param1, const cha
   {
     ParameterHolders::RetType ret = param0.AddParm( newp->first, newp->second, true );
     if (ret != ParameterHolders::ERR) {
+      bool print = false;
       if (ret == ParameterHolders::ADDED) {
-        mprintf("\tAdded NEW %s parameter:", desc);
+        if (verbose > 2) { mprintf("\tAdded NEW %s parameter:", desc); print = true; }
         updateCount++;
       } else if (ret == ParameterHolders::UPDATED) {
-        mprintf("\tUpdated %s parameter:", desc);
+        if (verbose > 0) { mprintf("\tUpdated %s parameter:", desc); print = true; }
         updateCount++;
-      } else if (ret == ParameterHolders::SAME)
-        mprintf("\tParameter for %s already present:", desc);
-      mprintf(" %s", newp->first.TypeString().c_str());
-      PrintParmType( newp->second );
+      } else if (ret == ParameterHolders::SAME) {
+        if (verbose > 1) { mprintf("\tParameter for %s already present:", desc); print = true; }
+      }
+      if (print) {
+        mprintf(" %s", newp->first.TypeString().c_str());
+        PrintParmType( newp->second );
+      }
       //mprintf(" %s %s %12.4f %12.4f\n", 
       //        *(newp->first[0]), *(newp->first[1]), newp->second.Rk(), newp->second.Req());
     }

From dc7ef75e4fd47f179a80619511d4d536e870c789 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 11 Dec 2023 08:49:30 -0500
Subject: [PATCH 0144/1492] Use debug in place of verbosity for now

---
 src/DataIO_AmberFF.cpp      | 2 +-
 src/DataIO_CharmmRtfPrm.cpp | 4 ++--
 src/DataIO_Std.cpp          | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/DataIO_AmberFF.cpp b/src/DataIO_AmberFF.cpp
index 07fc9487ef..94378f3d30 100644
--- a/src/DataIO_AmberFF.cpp
+++ b/src/DataIO_AmberFF.cpp
@@ -95,7 +95,7 @@ int DataIO_AmberFF::WriteData(FileName const& fname, DataSetList const& dsl)
                                                           it != toWrite.end(); ++it)
     {
       ParameterSet::UpdateCount UC;
-      prm.UpdateParamSet( *(*it), UC, debug_ );
+      prm.UpdateParamSet( *(*it), UC, debug_, debug_ ); // FIXME verbose
     }
     return outfile.WriteParams( prm, fname, debug_ );
   }
diff --git a/src/DataIO_CharmmRtfPrm.cpp b/src/DataIO_CharmmRtfPrm.cpp
index 9fc751ac05..917b02bac8 100644
--- a/src/DataIO_CharmmRtfPrm.cpp
+++ b/src/DataIO_CharmmRtfPrm.cpp
@@ -79,14 +79,14 @@ int DataIO_CharmmRtfPrm::WriteData(FileName const& fname, DataSetList const& dsl
     {
       mprintf("\tUsing parameter set '%s'\n", (*it)->legend());
       DataSet_Parameters const& dsPrm = static_cast<DataSet_Parameters const&>( *(*it) );
-      pout.UpdateParamSet( dsPrm, ucount, debug_ );
+      pout.UpdateParamSet( dsPrm, ucount, debug_, debug_ ); // FIXME verbose
     }
     else if ( (*it)->Type() == DataSet::TOPOLOGY )
     {
       mprintf("\tUsing parameters from topology '%s'\n", (*it)->legend());
       // Convert topology to parameter set
       DataSet_Topology const& dsTop = static_cast<DataSet_Topology const&>( *(*it) );
-      pout.UpdateParamSet( dsTop.Top().GetParameters(), ucount, debug_ );
+      pout.UpdateParamSet( dsTop.Top().GetParameters(), ucount, debug_, debug_ ); // FIXME verbose
     } else {
       mprintf("Warning: '%s' is not a valid parameter/topology set, skipping.\n",
               (*it)->legend());
diff --git a/src/DataIO_Std.cpp b/src/DataIO_Std.cpp
index 466399d77e..8fecb410da 100644
--- a/src/DataIO_Std.cpp
+++ b/src/DataIO_Std.cpp
@@ -1198,7 +1198,7 @@ int DataIO_Std::WriteParameters(CpptrajFile& file, DataSetList const& Sets) cons
       if ((*it)->Type() == DataSet::PARAMETERS) {
         DataSet_Parameters const& param = static_cast<DataSet_Parameters const&>( *(*it) );
         ParameterSet::UpdateCount UC;
-        prm.UpdateParamSet( param, UC, debug_ );
+        prm.UpdateParamSet( param, UC, debug_, debug_ ); // FIXME verbose
       } else {
         mprintf("Warning: Set '%s' is not a parameter set, skipping.\n", (*it)->legend());
       }

From 62d269dd877db7bd2d4a174ef9d3e6ff951c2cd0 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 11 Dec 2023 08:50:22 -0500
Subject: [PATCH 0145/1492] Add summary function and verbosity argument

---
 src/ParameterSet.cpp | 39 ++++++++++++++++++++++++++++-----------
 src/ParameterSet.h   |  4 +++-
 2 files changed, 31 insertions(+), 12 deletions(-)

diff --git a/src/ParameterSet.cpp b/src/ParameterSet.cpp
index 94b4bc1b36..ff6dc6c5b7 100644
--- a/src/ParameterSet.cpp
+++ b/src/ParameterSet.cpp
@@ -23,6 +23,23 @@ void ParameterSet::Debug(const char* fnameIn) const {
   Out.CloseFile();
 }
 
+/** Write summary to stdout. */
+void ParameterSet::Summary() const {
+  mprintf("\tParameter set: %s\n", ParamSetName().c_str());
+  mprintf("\t  %zu atom types:", atomTypes_.size());
+  for (ParmHolder<AtomType>::const_iterator at = atomTypes_.begin(); at != atomTypes_.end(); ++at)
+    mprintf(" %s", *(at->first[0]));
+  mprintf("\n");
+  mprintf("\t  %zu LJ 6-12 parameters.\n", nbParm_.size());
+  mprintf("\t  %zu LJ 6-12 1-4 parameters.\n", nb14Parm_.size());
+  mprintf("\t  %zu LJ 10-12 parameters.\n", HBparm_.size());
+  mprintf("\t  %zu bond parameters.\n", bondParm_.size());
+  mprintf("\t  %zu angle parameters.\n", angleParm_.size());
+  mprintf("\t  %zu UB parameters.\n", ubParm_.size());
+  mprintf("\t  %zu dihedral parameters.\n", dihParm_.size());
+  mprintf("\t  %zu improper parameters.\n", impParm_.size());
+}
+
 /** Write parameters out to given file. */
 void ParameterSet::Print(CpptrajFile& Out) const {
   if (!name_.empty())
@@ -35,7 +52,7 @@ void ParameterSet::Print(CpptrajFile& Out) const {
     Out.Printf("\t%6s %8li %12.4f %12.4f %12.4f %12.4f\n", *(at->first[0]), at - atomTypes_.begin(), at->second.LJ().Radius(), at->second.LJ().Depth(), at->second.Mass(), at->second.Polarizability());
   }
   if (!nbParm_.empty()) {
-    Out.Printf("LJ parameters:\n");
+    Out.Printf("LJ 6-12 parameters:\n");
     Out.Printf("\t%6s %6s : %12s %12s\n", "Type1", "Type2", "A", "B");
     for (ParmHolder<NonbondType>::const_iterator nb = nbParm_.begin(); nb != nbParm_.end(); ++nb)
       Out.Printf("\t%6s %6s : %12.4E %12.4E\n", (*nb->first[0]), (*nb->first[1]), nb->second.A(), nb->second.B());
@@ -93,7 +110,7 @@ void ParameterSet::Print(CpptrajFile& Out) const {
 }
 
 /** Update/add to parameters in this topology with those from given set. */
-int ParameterSet::UpdateParamSet(ParameterSet const& set1, UpdateCount& uc, int debugIn) {
+int ParameterSet::UpdateParamSet(ParameterSet const& set1, UpdateCount& uc, int debugIn, int verbose) {
   ParameterSet& set0 = *this;
   // Check
   if (debugIn > 0) {
@@ -103,23 +120,23 @@ int ParameterSet::UpdateParamSet(ParameterSet const& set1, UpdateCount& uc, int
   }
 
   // Bond parameters
-  uc.nBondsUpdated_ = UpdateParameters< ParmHolder<BondParmType> >(set0.BP(), set1.BP(), "bond");
+  uc.nBondsUpdated_ = UpdateParameters< ParmHolder<BondParmType> >(set0.BP(), set1.BP(), "bond", verbose);
   // Angle parameters
-  uc.nAnglesUpdated_ = UpdateParameters< ParmHolder<AngleParmType> >(set0.AP(), set1.AP(), "angle");
+  uc.nAnglesUpdated_ = UpdateParameters< ParmHolder<AngleParmType> >(set0.AP(), set1.AP(), "angle", verbose);
   // Dihedral/improper parameters
-  uc.nDihedralsUpdated_ = UpdateParameters< DihedralParmHolder >(set0.DP(), set1.DP(), "dihedral");
+  uc.nDihedralsUpdated_ = UpdateParameters< DihedralParmHolder >(set0.DP(), set1.DP(), "dihedral", verbose);
   // Improper parameters
-  uc.nImpropersUpdated_ = UpdateParameters< ParmHolder<DihedralParmType> >(set0.IP(), set1.IP(), "improper");
+  uc.nImpropersUpdated_ = UpdateParameters< ParmHolder<DihedralParmType> >(set0.IP(), set1.IP(), "improper", verbose);
   // Urey-Bradley parameters
-  uc.nUreyBradleyUpdated_ = UpdateParameters< ParmHolder<BondParmType> >(set0.UB(), set1.UB(), "Urey-Bradley");
+  uc.nUreyBradleyUpdated_ = UpdateParameters< ParmHolder<BondParmType> >(set0.UB(), set1.UB(), "Urey-Bradley", verbose);
   // Atom types
-  uc.nAtomTypeUpdated_ = UpdateParameters< ParmHolder<AtomType> >(set0.AT(), set1.AT(), "atom type");
+  uc.nAtomTypeUpdated_ = UpdateParameters< ParmHolder<AtomType> >(set0.AT(), set1.AT(), "atom type", verbose);
   // LJ Pairs
-  uc.nLJparamsUpdated_ = UpdateParameters< ParmHolder<NonbondType> >(set0.NB(), set1.NB(), "LJ A-B");
+  uc.nLJparamsUpdated_ = UpdateParameters< ParmHolder<NonbondType> >(set0.NB(), set1.NB(), "LJ A-B", verbose);
   // LJ 1-4 Pairs
-  uc.nLJ14paramsUpdated_ = UpdateParameters< ParmHolder<NonbondType> >(set0.NB14(), set1.NB14(), "LJ A-B 1-4");
+  uc.nLJ14paramsUpdated_ = UpdateParameters< ParmHolder<NonbondType> >(set0.NB14(), set1.NB14(), "LJ A-B 1-4", verbose);
   // HB LJ 10-12 Pairs
-  uc.nHBparamsUpdated_ = UpdateParameters< ParmHolder<HB_ParmType> >(set0.HB(), set1.HB(), "LJ HB 10-12");
+  uc.nHBparamsUpdated_ = UpdateParameters< ParmHolder<HB_ParmType> >(set0.HB(), set1.HB(), "LJ HB 10-12", verbose);
 
   if (debugIn > 0) set0.Debug("newp.dat");
   return 0;
diff --git a/src/ParameterSet.h b/src/ParameterSet.h
index d565f29868..072e4c598f 100644
--- a/src/ParameterSet.h
+++ b/src/ParameterSet.h
@@ -39,6 +39,8 @@ class ParameterSet {
     void Debug() const { return Debug(""); }
     /// Print parameters to given file
     void Print(CpptrajFile&) const;
+    /// Print a summary to stdout
+    void Summary() const;
 
     /// Used to track what parameters were updated during UpdateParams
     class UpdateCount {
@@ -59,7 +61,7 @@ class ParameterSet {
         unsigned int nHBparamsUpdated_;
     };
     /// Update this set with parameters from given set
-    int UpdateParamSet(ParameterSet const&, UpdateCount&, int);
+    int UpdateParamSet(ParameterSet const&, UpdateCount&, int, int);
     /// Add hydrophilic atom type
     int AddHydrophilicAtomType(NameType const&);
     /// Set parameter set name

From 5e46c6a8e622a966242572e80933fd10bde61eaa Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 11 Dec 2023 08:50:58 -0500
Subject: [PATCH 0146/1492] Hide some debug info

---
 src/Topology.cpp | 19 +++++++++++--------
 1 file changed, 11 insertions(+), 8 deletions(-)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index b94c1a36b8..0693255632 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2163,7 +2163,7 @@ int Topology::AppendTop(Topology const& NewTop) {
   // Save old parameters
   mprintf("DEBUG: Getting old parameters.\n");
   ParameterSet oldParams = GetParameters();
-  oldParams.Debug(); // DEBUG
+  oldParams.Summary(); // DEBUG
 
   // Append NewTop atoms to this topology.
   for (atom_iterator atom = NewTop.begin(); atom != NewTop.end(); ++atom)
@@ -2350,8 +2350,10 @@ static inline void GetLJAtomTypes( ParmHolder<AtomType>& atomTypes, ParmHolder<N
       }
       thisType.SetTypeIdx( atm->TypeIndex() );
       ParameterHolders::RetType ret = atomTypes.AddParm( atype, thisType, true );
-      if (ret == ParameterHolders::ADDED) {
-        mprintf("DEBUG: New atom type: %s R=%g D=%g M=%g P=%g\n", *(atype[0]), thisType.LJ().Radius(), thisType.LJ().Depth(), thisType.Mass(), thisType.Polarizability());
+      if (debugIn > 0) {
+        if (ret == ParameterHolders::ADDED) {
+          mprintf("DEBUG: New atom type: %s R=%g D=%g M=%g P=%g\n", *(atype[0]), thisType.LJ().Radius(), thisType.LJ().Depth(), thisType.Mass(), thisType.Polarizability());
+        }
       }
     }
     // Do atom type pairs, check for off-diagonal elements.
@@ -2689,6 +2691,7 @@ void Topology::AssignNonbondParams(ParmHolder<AtomType> const& newTypes,
                                    ParmHolder<NonbondType> const& newNB,
                                    ParmHolder<HB_ParmType> const& newHB)
 {
+  static const int verbose = 0 ; // FIXME temporarily silence output
   // Generate array of only the types that are currently in Topology. TODO should this be a permanent part of Topology?
   ParmHolder<AtomType> currentAtomTypes;
   for (std::vector<Atom>::const_iterator atm = atoms_.begin(); atm != atoms_.end(); ++atm)
@@ -2750,17 +2753,17 @@ void Topology::AssignNonbondParams(ParmHolder<AtomType> const& newTypes,
       // Check for LJ10-12 first
       ParmHolder<HB_ParmType>::const_iterator hb = newHB.GetParam( types );
       if (hb != newHB.end()) {
-        mprintf("LJ 10-12 parameter found for %s %s\n", *name1, *name2);
+        if (verbose > 0) mprintf("LJ 10-12 parameter found for %s %s\n", *name1, *name2);
         nonbond_.AddHBterm(t1->second.OriginalIdx(), t2->second.OriginalIdx(), hb->second);
       } else {
         // See if this parameter exists in the given nonbond array.
         NonbondType LJAB;
         ParmHolder<NonbondType>::const_iterator it = newNB.GetParam( types );
         if (it == newNB.end()) {
-          mprintf("NB parameter for %s %s not found. Generating.\n", *name1, *name2);
+          if (verbose > 0) mprintf("NB parameter for %s %s not found. Generating.\n", *name1, *name2);
           LJAB = type1.LJ().Combine_LB( type2.LJ() );
         } else {
-          mprintf("Using existing NB parameter for %s %s\n", *name1, *name2);
+          if (verbose > 0) mprintf("Using existing NB parameter for %s %s\n", *name1, *name2);
           LJAB = it->second;
         }
         nonbond_.AddLJterm(t1->second.OriginalIdx(), t2->second.OriginalIdx(), LJAB);
@@ -2796,7 +2799,7 @@ int Topology::UpdateParams(ParameterSet const& set1) {
 
 /** Update/add to parameters in this topology by combining those from given sets. */
 int Topology::updateParams(ParameterSet& set0, ParameterSet const& set1) {
-  set1.Debug(); // DEBUG
+  set1.Summary(); // DEBUG
   // Check TODO is this necessary?
   if (set0.AT().size() < 1)
     mprintf("Warning: No atom type information in '%s'\n", c_str());
@@ -2806,7 +2809,7 @@ int Topology::updateParams(ParameterSet& set0, ParameterSet const& set1) {
   }
   // Update existing parameters with new parameters
   ParameterSet::UpdateCount UC;
-  if (set0.UpdateParamSet( set1, UC, debug_ )) {
+  if (set0.UpdateParamSet( set1, UC, debug_, debug_ )) { // FIXME verbose
     mprinterr("Error: Could not merge topology '%s' parameters with '%s' parameters.\n",
               c_str(), set1.ParamSetName().c_str());
     return 1;

From 4bc848e90c8939bdf2010665d23981c87e7a47e4 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 11 Dec 2023 08:51:09 -0500
Subject: [PATCH 0147/1492] Use debug in place of verbosity for now

---
 src/Exec_Build.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 3922c89c79..dee7222833 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -87,7 +87,7 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
     ++it;
     ParameterSet::UpdateCount UC;
     for (; it != ParamSets.end(); ++it)
-      mainParmSet->UpdateParamSet( *(*it), UC, State.Debug() );
+      mainParmSet->UpdateParamSet( *(*it), UC, State.Debug(), State.Debug() ); // FIXME verbose
   }
 
   // Update parameters

From 51c4190590a9d58ce2e125af5c51ffcab8ca5f3a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 11 Dec 2023 09:38:06 -0500
Subject: [PATCH 0148/1492] Add keyword 'noindices' to make comparing
 parameters easier (only dihedrals for now and hidden)

---
 src/Exec_Top.cpp |  2 ++
 src/TopInfo.cpp  | 14 ++++++++++----
 src/TopInfo.h    |  3 +++
 3 files changed, 15 insertions(+), 4 deletions(-)

diff --git a/src/Exec_Top.cpp b/src/Exec_Top.cpp
index ae4ac0528d..89f40e53e1 100644
--- a/src/Exec_Top.cpp
+++ b/src/Exec_Top.cpp
@@ -47,6 +47,8 @@ static int CommonSetup(TopInfo& info, CpptrajState& State, ArgList& argIn, const
   }
   if (argIn.hasKey("nointrares"))
     info.SetNoIntraRes(true);
+  if (argIn.hasKey("noindices"))
+    info.SetPrintParameterIndices(false);
   return err;
 }
 
diff --git a/src/TopInfo.cpp b/src/TopInfo.cpp
index 69c0796484..8a54ebaeb5 100644
--- a/src/TopInfo.cpp
+++ b/src/TopInfo.cpp
@@ -18,7 +18,8 @@ TopInfo::TopInfo() :
   amn_width_(0),
   max_aname_len_(0),
   toStdout_(false),
-  noIntraRes_(false)
+  noIntraRes_(false),
+  printIndices_(true)
 {}
 
 /// CONSTRUCTOR - To Stdout
@@ -30,7 +31,8 @@ TopInfo::TopInfo(Topology const* pIn) :
   max_type_len_(0),
   max_aname_len_(0),
   toStdout_(false),
-  noIntraRes_(false)
+  noIntraRes_(false),
+  printIndices_(true)
 {
   SetupTopInfo( 0, pIn, 0 );
 }
@@ -42,7 +44,8 @@ TopInfo::~TopInfo() {
 }
 
 // TopInfo::SetupTopInfo()
-int TopInfo::SetupTopInfo(CpptrajFile* fIn, Topology const* pIn, DataSet_Coords* cIn) {
+int TopInfo::SetupTopInfo(CpptrajFile* fIn, Topology const* pIn, DataSet_Coords* cIn)
+{
   if (cIn == 0 && pIn == 0) {
     mprinterr("Internal Error: TopInfo: Null topology\n");
     return 1;
@@ -617,7 +620,10 @@ void TopInfo::PrintDihedrals(DihedralArray const& darray, DihedralParmArray cons
       if      (dih->Type() == DihedralType::END     ) type = 'E';
       else if (dih->Type() == DihedralType::IMPROPER) type = 'I';
       else if (dih->Type() == DihedralType::BOTH    ) type = 'B';
-      outfile_->Printf("%c %*i", type, nw, nd);
+      if (printIndices_)
+        outfile_->Printf("%c %*i", type, nw, nd);
+      else
+        outfile_->Printf("%c %*c", type, nw, ' ');
       int didx = dih->Idx();
       if ( didx > -1 ) {
         outfile_->Printf(" %7.3f %5.2f %4.1f",dihedralparm[didx].Pk(),dihedralparm[didx].Phase(),
diff --git a/src/TopInfo.h b/src/TopInfo.h
index bb7fa11da8..a7f219edf5 100644
--- a/src/TopInfo.h
+++ b/src/TopInfo.h
@@ -17,6 +17,8 @@ class TopInfo {
     void SetNoIntraRes(bool b) { noIntraRes_ = b; }
     int SetupTopInfo(CpptrajFile*, Topology const*, DataSet_Coords*);
     int SetupTopInfo(Topology const* p, DataSet_Coords* c) { return SetupTopInfo(0, p, c); }
+    /// Toggle printing of parameter indices
+    void SetPrintParameterIndices(bool b) { printIndices_ = b; }
 
     int PrintAtomInfo(std::string const&) const;
     int PrintShortResInfo(std::string const&, int) const;
@@ -56,5 +58,6 @@ class TopInfo {
     int max_aname_len_; ///< Max width of atom name in topology
     bool toStdout_;
     bool noIntraRes_;   ///< If true, ignore intra-residue bonds/angles/dihedrals etc
+    bool printIndices_; ///< If true, print leading indices
 };
 #endif

From 9314248d566b33c56ae64d1dc66783750d56f1bb Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 11 Dec 2023 11:18:39 -0500
Subject: [PATCH 0149/1492] Fix detection of 1-4 interactions. Make sure we are
 looking for cases where A1 and A4 are already part of a bond or angle.

---
 src/Topology.cpp | 71 ++++++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 69 insertions(+), 2 deletions(-)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index 0693255632..0d58b42d01 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2621,13 +2621,22 @@ void Topology::AssignDihedralParm(DihedralParmHolder const& newDihedralParams,
             dihedralsIn.size(), dihedrals.size());
 
   dihedralsIn.clear();
+  // Keep track of 1-4 interactions
+  typedef std::pair<int,int> Ipair;
+  typedef std::set<Ipair> Imap;
+  Imap PairMap;
   // Loop over all dihedrals
   for (DihedralArray::iterator dih = dihedrals.begin(); dih != dihedrals.end(); ++dih) {
+
     TypeNameHolder types(4);
     types.AddName( atoms_[dih->A1()].Type() );
     types.AddName( atoms_[dih->A2()].Type() );
     types.AddName( atoms_[dih->A3()].Type() );
     types.AddName( atoms_[dih->A4()].Type() );
+//    mprintf("DEBUG: Assigning dihedral %4i %4i %4i %4i (%2s %2s %2s %2s) isImproper=%i skip14=%i\n",
+//            dih->A1()+1, dih->A2()+1, dih->A3()+1, dih->A4()+1,
+//            *types[0], *types[1], *types[2], *types[3],
+//            (int)dih->IsImproper(), (int)dih->Skip14());
     bool found;
     if (dih->IsImproper()) {
       // ----- This is actually an improper dihedral. ----------------
@@ -2645,6 +2654,9 @@ void Topology::AssignDihedralParm(DihedralParmHolder const& newDihedralParams,
       }
       DihedralType mydih = *dih;
       mydih.SetIdx( idx );
+      mydih.SetImproper( true );
+      // Always skip impropers FIXME is this always true? 
+      mydih.SetSkip14( true );
       dihedralsIn.push_back( mydih );
     } else {
       // -----Regular dihedral. See if parameter already present. ----
@@ -2660,18 +2672,73 @@ void Topology::AssignDihedralParm(DihedralParmHolder const& newDihedralParams,
         mydih.SetIdx( -1 );
         dihedralsIn.push_back( mydih );
       } else {
-        // Actually add the dihedrals
+        // Actually add parameters for this dihedral.
+        // Determine if this is actually a 1-4 interaction by making
+        // sure that A4 isnt part of a bond or angle with A1.
+        bool skip14 = false;
+        for (Atom::bond_iterator bat1 = atoms_[dih->A1()].bondbegin();
+                                 bat1 != atoms_[dih->A1()].bondend(); ++bat1)
+        {
+          if (*bat1 != dih->A2()) {
+            if (*bat1 == dih->A4()) {
+              skip14 = true;
+              break;
+            }
+            // Loop over angles, dih->A1() - bat1 - bat2
+            for (Atom::bond_iterator bat2 = atoms_[*bat1].bondbegin();
+                                     bat2 != atoms_[*bat1].bondend(); ++bat2)
+            {
+              //if (dih->A1() == 442 && dih->A4() == 444) { // DEBUG
+              //  mprintf("DEBUG: %4i %4i %4i %4i Checking angle %4i %4i %4i\n", dih->A1()+1, dih->A2()+1, dih->A3()+1, dih->A4()+1, dih->A1()+1, *bat1 + 1, *bat2 + 1);
+              //}
+              if (*bat2 != *bat1) {
+                if (*bat2 == dih->A4()) {
+                  skip14 = true;
+                  break;
+                }
+              }
+            } // END loop over bat1 bonded atoms
+            if (skip14) break;
+          }
+        } // END loop over dih->A1() bonded atoms
+        if (!skip14) {
+          // Determine if 1-4 interaction already calculated by previous dihedral.
+          // Make the lower end atom first. 
+          Ipair pair14;
+          if (dih->A1() < dih->A4()) {
+            pair14.first = dih->A1();
+            pair14.second = dih->A4();
+          } else {
+            pair14.first = dih->A4();
+            pair14.second = dih->A1();
+          }
+          Imap::const_iterator it = PairMap.find( pair14 );
+          if (it == PairMap.end()) {
+            skip14 = false;
+            PairMap.insert( pair14 );
+          } else {
+            skip14 = true;
+          }
+        }
+        // Loop over multiplicities
+        //if (dih->A1() == 442 && dih->A4() == 444) { // DEBUG
+        //  mprintf("DEBUG: Skip14= %i\n", (int)skip14);
+        //}
         for (DihedralParmArray::const_iterator it = dpa.begin(); it != dpa.end(); ++it) {
           DihedralType mydih = *dih;
           int idx = addTorsionParm( dihedralparm_, *it );
           // If there are multiple parameters for the same dihedral, all but
           // one of the 1-4 calcs need to be skipped.
           if (it == dpa.begin())
-            mydih.SetSkip14(false);
+            mydih.SetSkip14(skip14);
           else
             mydih.SetSkip14(true);
           mydih.SetIdx( idx );
           dihedralsIn.push_back( mydih );
+//          mprintf("DEBUG: Assigned %4i %4i %4i %4i (%2s %2s %2s %2s) isImproper=%i skip14=%i\n",
+//            mydih.A1()+1, mydih.A2()+1, mydih.A3()+1, mydih.A4()+1,
+//            *types[0], *types[1], *types[2], *types[3],
+//            (int)mydih.IsImproper(), (int)mydih.Skip14());
         }
       }
     }

From b8ba20cb0b5d84d4b9a0dfb8efe3192e1325078d Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 11 Dec 2023 13:44:26 -0500
Subject: [PATCH 0150/1492] Actually want to test the combined topology

---
 test/Test_CombineCrd/RunTest.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/Test_CombineCrd/RunTest.sh b/test/Test_CombineCrd/RunTest.sh
index e241b2b7e0..ed8b4e1fd4 100755
--- a/test/Test_CombineCrd/RunTest.sh
+++ b/test/Test_CombineCrd/RunTest.sh
@@ -71,7 +71,7 @@ crdaction TCS strip !:TCS
 combinecrd FabI NDP TCS parmname combinedParm crdname combinedCrd
 # Get recombined system energies. Should match exactly.
 crdaction combinedCrd energy out E2.dat noheader
-parmwrite out FabI.NDP.TCS.parm7
+parmwrite out FabI.NDP.TCS.parm7 crdset combinedCrd
 EOF
   RunCpptraj "Split coords and recombine test."
   DoTest E1.dat E2.dat

From ad7559c26217c8bb9c2cc4f5eda287a71a98e809 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 11 Dec 2023 13:47:40 -0500
Subject: [PATCH 0151/1492] Disable bond sort for now. Use improper dihedral
 detection.

---
 src/Topology.cpp | 26 +++++++++++++++++++++-----
 src/Topology.h   |  2 +-
 2 files changed, 22 insertions(+), 6 deletions(-)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index 0d58b42d01..e4dd1cb7ed 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -899,10 +899,10 @@ void Topology::AddBond(BondType const& bndIn, bool isH) {
 }
 
 /** Sort bond arrays. May want to do this to e.g. match LEAP bond ordering. */
-void Topology::SortBonds() {
+/*void Topology::SortBonds() {
   std::sort(bonds_.begin(), bonds_.end());
   std::sort(bondsh_.begin(), bondsh_.end());
-}
+}*/
 
 /** Check if given angle parm exists in given angle parm array. Add if not.
   * \return Index in angle parm array.
@@ -2595,7 +2595,10 @@ void Topology::AssignImproperParams(ParmHolder<DihedralParmType> const& newImpro
   AssignImproperParm( newImproperParams, chamber_.SetImpropers() );
 }
 
-/** Set parameters for dihedrals in given dihedral array. */
+/** Set parameters for dihedrals in given dihedral array.
+  * Bond and angle information must be set up prior to calling
+  * this function in order for improper and 1-4 detection to work.
+  */
 void Topology::AssignDihedralParm(DihedralParmHolder const& newDihedralParams,
                                   ParmHolder<DihedralParmType> const& newImproperParams,
                                   DihedralArray& dihedralsIn)
@@ -2637,8 +2640,20 @@ void Topology::AssignDihedralParm(DihedralParmHolder const& newDihedralParams,
 //            dih->A1()+1, dih->A2()+1, dih->A3()+1, dih->A4()+1,
 //            *types[0], *types[1], *types[2], *types[3],
 //            (int)dih->IsImproper(), (int)dih->Skip14());
+    // Determine improper
+    bool isImproper = (!atoms_[dih->A1()].IsBondedTo(dih->A2())) ||
+                      (!atoms_[dih->A2()].IsBondedTo(dih->A3())) ||
+                      (!atoms_[dih->A3()].IsBondedTo(dih->A4()));
+    if (isImproper != dih->IsImproper()) {
+      mprintf("Warning: dihedral %s-%s-%s-%s improper status %i does not match detected (%i)\n",
+              TruncResAtomNameNum(dih->A1()).c_str(),
+              TruncResAtomNameNum(dih->A2()).c_str(),
+              TruncResAtomNameNum(dih->A3()).c_str(),
+              TruncResAtomNameNum(dih->A4()).c_str(),
+              (int)dih->IsImproper(), (int)isImproper);
+    }
     bool found;
-    if (dih->IsImproper()) {
+    if (isImproper) {
       // ----- This is actually an improper dihedral. ----------------
       DihedralParmType ip = newImproperParams.FindParam( types, found );
       int idx = -1;
@@ -2655,7 +2670,7 @@ void Topology::AssignDihedralParm(DihedralParmHolder const& newDihedralParams,
       DihedralType mydih = *dih;
       mydih.SetIdx( idx );
       mydih.SetImproper( true );
-      // Always skip impropers FIXME is this always true? 
+      // Always skip 1-4 for impropers
       mydih.SetSkip14( true );
       dihedralsIn.push_back( mydih );
     } else {
@@ -2718,6 +2733,7 @@ void Topology::AssignDihedralParm(DihedralParmHolder const& newDihedralParams,
             PairMap.insert( pair14 );
           } else {
             skip14 = true;
+            //mprintf("DEBUG: Prior 1-4 calc detected.\n");
           }
         }
         // Loop over multiplicities
diff --git a/src/Topology.h b/src/Topology.h
index 10f3d3996c..466de2d36d 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -115,7 +115,7 @@ class Topology {
     void AddBond(BondType const&, bool);
     void AddBond(int, int, BondParmType const&);
     int RemoveBond(int, int);
-    void SortBonds();
+    //void SortBonds();
     void AssignBondParams(ParmHolder<BondParmType> const&);
     // ----- Angle-specific routines -------------
     size_t Nangles()                           const { return angles_.size()+anglesh_.size(); }

From fb513b8bf16844954a5801a5246b45b05b9b6691 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 11 Dec 2023 13:48:04 -0500
Subject: [PATCH 0152/1492] Not trying to sort bonds.

---
 src/Exec_UpdateParameters.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Exec_UpdateParameters.cpp b/src/Exec_UpdateParameters.cpp
index c07ede5e7d..329056f7f4 100644
--- a/src/Exec_UpdateParameters.cpp
+++ b/src/Exec_UpdateParameters.cpp
@@ -45,7 +45,7 @@ Exec::RetType Exec_UpdateParameters::Execute(CpptrajState& State, ArgList& argIn
           top.c_str(), ds->legend());
 
   // Sort topology bond arrays to be consistent with LEaP
-  top.SortBonds();
+  //top.SortBonds();
 
   if (ds->Type() == DataSet::PARAMETERS)
     top.UpdateParams(static_cast<DataSet_Parameters const&>( *ds ));

From c183cb8e42aac70c543c77b5e85f526b18bc4fc3 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 11 Dec 2023 14:38:20 -0500
Subject: [PATCH 0153/1492] Update for fixed SOLTY array

---
 test/Test_Strip/ligand.tz2.truncoct.parm7.save   | 10 +++-------
 test/Test_Strip/receptor.tz2.truncoct.parm7.save |  6 +++---
 test/Test_Strip/strip.pdb.chignolin.parm7.save   |  7 +++----
 3 files changed, 9 insertions(+), 14 deletions(-)

diff --git a/test/Test_Strip/ligand.tz2.truncoct.parm7.save b/test/Test_Strip/ligand.tz2.truncoct.parm7.save
index edd97a00fc..401565ec6c 100644
--- a/test/Test_Strip/ligand.tz2.truncoct.parm7.save
+++ b/test/Test_Strip/ligand.tz2.truncoct.parm7.save
@@ -1,11 +1,11 @@
-%VERSION  VERSION_STAMP = V0001.000  DATE = 02/04/15  10:39:23                  
+%VERSION  VERSION_STAMP = V0001.000  DATE = 12/11/23 13:48:31                  
 %FLAG TITLE                                                                     
 %FORMAT(20a4)                                                                   
                                                                                 
 %FLAG POINTERS                                                                  
 %FORMAT(10I8)                                                                   
        3       2       3       0       0       0       0       0       0       0
-       4       1       0       0       0       2       0       0      23       1
+       4       1       0       0       0       2       0       0       2       1
        0       0       0       0       0       0       0       2       3       0
        0
 %FLAG ATOM_NAME                                                                 
@@ -64,11 +64,7 @@ WAT
 
 %FLAG SOLTY                                                                     
 %FORMAT(5E16.8)                                                                 
-  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
-  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
-  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
-  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
-  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00
 %FLAG LENNARD_JONES_ACOEF                                                       
 %FORMAT(5E16.8)                                                                 
   5.81935564E+05  0.00000000E+00  0.00000000E+00
diff --git a/test/Test_Strip/receptor.tz2.truncoct.parm7.save b/test/Test_Strip/receptor.tz2.truncoct.parm7.save
index e2f17a97d8..e068c06d11 100644
--- a/test/Test_Strip/receptor.tz2.truncoct.parm7.save
+++ b/test/Test_Strip/receptor.tz2.truncoct.parm7.save
@@ -1,11 +1,11 @@
-%VERSION  VERSION_STAMP = V0001.000  DATE = 02/04/15  10:39:23                  
+%VERSION  VERSION_STAMP = V0001.000  DATE = 12/11/23 13:48:31                  
 %FLAG TITLE                                                                     
 %FORMAT(20a4)                                                                   
                                                                                 
 %FLAG POINTERS                                                                  
 %FORMAT(10I8)                                                                   
      220      12     104     123     233     169     481     372       0       0
-    1211      13     123     169     372      31      68      35      23       0
+    1211      13     123     169     372      31      68      35      21       0
        0       0       0       0       0       0       0       2      24       0
        0
 %FLAG ATOM_NAME                                                                 
@@ -310,7 +310,7 @@ SER TRP THR TRP GLU ASN GLY LYS TRP THR TRP LYS NHE
   0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
   0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
   0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
-  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00
 %FLAG LENNARD_JONES_ACOEF                                                       
 %FORMAT(5E16.8)                                                                 
   9.44293233E+05  2.12601181E+03  1.39982777E-01  9.95480466E+05  2.56678134E+03
diff --git a/test/Test_Strip/strip.pdb.chignolin.parm7.save b/test/Test_Strip/strip.pdb.chignolin.parm7.save
index 7baa301340..3e96e8af45 100644
--- a/test/Test_Strip/strip.pdb.chignolin.parm7.save
+++ b/test/Test_Strip/strip.pdb.chignolin.parm7.save
@@ -1,11 +1,11 @@
-%VERSION  VERSION_STAMP = V0001.000  DATE = 10/16/20 10:23:23                  
+%VERSION  VERSION_STAMP = V0001.000  DATE = 12/11/23 13:48:31                  
 %FLAG TITLE                                                                     
 %FORMAT(20a4)                                                                   
 default_name                                                                    
 %FLAG POINTERS                                                                  
 %FORMAT(10I8)                                                                   
       93       5       0      98       0     136       0     387       0       0
-     385      10      98     136     387      28      48      88      24       0
+     385      10      98     136     387      28      48      88      17       0
        0       0       0       0       0       0       0       0      14       0
        0
 %FLAG ATOM_NAME                                                                 
@@ -249,8 +249,7 @@ TYR TYR ASP PRO GLU THR GLY THR TRP TYR
   0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
   0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
   0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
-  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
-  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00
 %FLAG LENNARD_JONES_ACOEF                                                       
 %FORMAT(5E16.8)                                                                 
   9.44293233E+05  9.95480466E+05  1.04308023E+06  8.82619071E+05  9.24822270E+05

From c7536bc1d97f11c3388539a72e35affe71616ed2 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 12 Dec 2023 10:39:11 -0500
Subject: [PATCH 0154/1492] Go back to the previous way of appending, should be
 less computationally intensive

---
 src/Topology.cpp | 329 +++++++++++++++++++++++++----------------------
 1 file changed, 175 insertions(+), 154 deletions(-)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index e4dd1cb7ed..fee49a5508 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -7,6 +7,7 @@
 #include "AtomType.h"
 #include "AtomMask.h"
 #include "CharMask.h"
+#include "UpdateParameters.h"
 
 const NonbondType Topology::LJ_EMPTY = NonbondType();
 
@@ -2078,159 +2079,6 @@ void Topology::StripDihedralParmArray(DihedralArray& newDihedralArray, std::vect
   }
 }
 
-// Topology::AddBondArray()
-void Topology::AddBondArray(BondArray const& barray, BondParmArray const& bp, int atomOffset) {
-  if (bp.empty()) {
-    for (BondArray::const_iterator bond = barray.begin(); bond != barray.end(); ++bond)
-      AddBond( bond->A1() + atomOffset, bond->A2() + atomOffset );
-  } else {
-    bool missingParameters = false;
-    for (BondArray::const_iterator bond = barray.begin(); bond != barray.end(); ++bond) {
-      if (bond->Idx() > -1)
-        AddBond( bond->A1() + atomOffset, bond->A2() + atomOffset, bp[bond->Idx()] );
-      else {
-        missingParameters = true;
-        AddBond( bond->A1() + atomOffset, bond->A2() + atomOffset );
-      }
-    }
-    if (missingParameters)
-      mprintf("Warning: Some bonds were missing parameters.\n");
-  }
-}
-
-// Topology::AddAngleArray()
-void Topology::AddAngleArray(AngleArray const& aarray, AngleParmArray const& ap, int atomOffset) {
-  if (ap.empty())
-    for (AngleArray::const_iterator angle = aarray.begin(); angle != aarray.end(); ++angle)
-      AddAngle( angle->A1() + atomOffset,
-                angle->A2() + atomOffset,
-                angle->A3() + atomOffset );
-  else
-    for (AngleArray::const_iterator angle = aarray.begin(); angle != aarray.end(); ++angle)
-      AddAngle( angle->A1() + atomOffset,
-                angle->A2() + atomOffset,
-                angle->A3() + atomOffset, ap[angle->Idx()] );
-}
-
-// Topology::AddDihArray()
-void Topology::AddDihArray(DihedralArray const& darray, DihedralParmArray const& dp, int atomOffset)
-{
-  if (dp.empty())
-    for (DihedralArray::const_iterator dih = darray.begin(); dih != darray.end(); ++dih)
-      AddDihedral( DihedralType( dih->A1() + atomOffset, dih->A2() + atomOffset,
-                                 dih->A3() + atomOffset, dih->A4() + atomOffset,
-                                 dih->Type() ), -1 );
-  else
-    for (DihedralArray::const_iterator dih = darray.begin(); dih != darray.end(); ++dih)
-      AddDihedral( DihedralType( dih->A1() + atomOffset, dih->A2() + atomOffset,
-                                 dih->A3() + atomOffset, dih->A4() + atomOffset,
-                                 dih->Type() ), dp[dih->Idx()] );
-}
-
-/** This template can be used when doing Append() on a generic std::vector array
-  * of type T. The array will be appended to a given array of the same type.
-  * If one is empty and the other is not, values will be filled in if necessary.
-  */
-template <class T> class TopVecAppend {
-  public:
-    /// CONSTRUCTOR
-    TopVecAppend() {}
-    /// Append current array to given array of same type
-    void Append(std::vector<T>& arrayOut, std::vector<T> const& arrayToAdd, unsigned int expectedSize)
-    {
-      if (arrayToAdd.empty() && arrayOut.empty()) {
-        // Both arrays are empty. Nothing to do.
-        return;
-      } else if (arrayToAdd.empty()) {
-        // The current array is empty but the given array is not. Fill in 
-        // array to append with blank values.
-        for (unsigned int idx = 0; idx != expectedSize; idx++)
-          arrayOut.push_back( T() );
-      } else {
-        // Append current array to array to given array. TODO use std::copy?
-        for (typename std::vector<T>::const_iterator it = arrayToAdd.begin(); it != arrayToAdd.end(); ++it)
-          arrayOut.push_back( *it );
-      }
-    }
-};
-
-// Topology::AppendTop()
-int Topology::AppendTop(Topology const& NewTop) {
-  int atomOffset = (int)atoms_.size();
-  mprintf("DEBUG: Appending '%s' to '%s' (offset= %i)\n", NewTop.c_str(), c_str(), atomOffset);
-  //int resOffset = (int)residues_.size();
-
-  // Save old parameters
-  mprintf("DEBUG: Getting old parameters.\n");
-  ParameterSet oldParams = GetParameters();
-  oldParams.Summary(); // DEBUG
-
-  // Append NewTop atoms to this topology.
-  for (atom_iterator atom = NewTop.begin(); atom != NewTop.end(); ++atom)
-  {
-    if (debug_ > 1)
-      mprintf("DBG: %6li %s %s %4i\n", atom-NewTop.begin(), 
-              *(atom->Name()), *(atom->Type()), atom->TypeIndex());
-    Atom CurrentAtom = *atom;
-    Residue const& res = NewTop.Res( CurrentAtom.ResNum() );
-    // Bonds need to be cleared and re-added.
-    CurrentAtom.ClearBonds();
-    AddTopAtom( CurrentAtom, Residue(res.Name(), res.OriginalResNum(),
-                                     res.Icode(), res.ChainId()) );
-  }
-  // Recreate bonds for the added atoms
-  for (BondArray::const_iterator bond = NewTop.Bonds().begin(); bond != NewTop.Bonds().end(); ++bond)
-    AddBond( bond->A1() + atomOffset, bond->A2() + atomOffset );
-  for (BondArray::const_iterator bond = NewTop.BondsH().begin(); bond != NewTop.BondsH().end(); ++bond)
-    AddBond( bond->A1() + atomOffset, bond->A2() + atomOffset );
-  // Recreate angles for the added atoms
-  for (AngleArray::const_iterator angle = NewTop.Angles().begin(); angle != NewTop.Angles().end(); ++angle)
-      AddAngle( angle->A1() + atomOffset, angle->A2() + atomOffset, angle->A3() + atomOffset );
-  for (AngleArray::const_iterator angle = NewTop.AnglesH().begin(); angle != NewTop.AnglesH().end(); ++angle)
-      AddAngle( angle->A1() + atomOffset, angle->A2() + atomOffset, angle->A3() + atomOffset );
-  // Recreate dihedrals for the added atoms
-  for (DihedralArray::const_iterator dih = NewTop.Dihedrals().begin(); dih != NewTop.Dihedrals().end(); ++dih)
-      AddDihedral( DihedralType( dih->A1() + atomOffset, dih->A2() + atomOffset,
-                                 dih->A3() + atomOffset, dih->A4() + atomOffset,
-                                 dih->Type() ) );
-  for (DihedralArray::const_iterator dih = NewTop.DihedralsH().begin(); dih != NewTop.DihedralsH().end(); ++dih)
-      AddDihedral( DihedralType( dih->A1() + atomOffset, dih->A2() + atomOffset,
-                                 dih->A3() + atomOffset, dih->A4() + atomOffset,
-                                 dih->Type() ) );
-  // Update parameters
-  mprintf("DEBUG: Updating with new parameters.\n");
-  updateParams( oldParams, NewTop.GetParameters() );
-
-  // EXTRA ATOM INFO
-  TopVecAppend<NameType> appendNameType;
-  appendNameType.Append( tree_, NewTop.tree_, NewTop.Natom() );
-  TopVecAppend<int> appendInt;
-  appendInt.Append( ijoin_, NewTop.ijoin_, NewTop.Natom() );
-  appendInt.Append( irotat_, NewTop.irotat_, NewTop.Natom() );
-  appendInt.Append( pdbSerialNum_, NewTop.pdbSerialNum_, NewTop.Natom() );
-  TopVecAppend<char> appendChar;
-  appendChar.Append( atom_altloc_, NewTop.atom_altloc_, NewTop.Natom() );
-  TopVecAppend<float> appendFloat;
-  appendFloat.Append( occupancy_, NewTop.occupancy_, NewTop.Natom() );
-  appendFloat.Append( bfactor_, NewTop.bfactor_, NewTop.Natom() );
-
- /* // BONDS
-  AddBondArray(NewTop.Bonds(),  NewTop.BondParm(), atomOffset);
-  AddBondArray(NewTop.BondsH(), NewTop.BondParm(), atomOffset);
-  // ANGLES
-  AddAngleArray(NewTop.Angles(),  NewTop.AngleParm(), atomOffset);
-  AddAngleArray(NewTop.AnglesH(), NewTop.AngleParm(), atomOffset);
-  // DIHEDRALS
-  AddDihArray(NewTop.Dihedrals(),  NewTop.DihedralParm(), atomOffset);
-  AddDihArray(NewTop.DihedralsH(), NewTop.DihedralParm(), atomOffset);*/
-
-  // TODO append missing stuff?
-
-  // Re-set up this topology
-  // TODO: Could get expensive for multiple appends.
-  return CommonSetup();
-}
-
 // -----------------------------------------------------------------------------
 static void paramOverwriteWarning(const char* type) {
   mprintf("Warning: An existing %s parameter would have been overwritten. This\n"
@@ -2435,6 +2283,179 @@ ParameterSet Topology::GetParameters() const {
   return Params;
 }
 
+// -----------------------------------------------------------------------------
+// Topology::AddBondArray()
+void Topology::AddBondArray(BondArray const& barray, BondParmArray const& bp, int atomOffset) {
+  if (bp.empty()) {
+    for (BondArray::const_iterator bond = barray.begin(); bond != barray.end(); ++bond)
+      AddBond( bond->A1() + atomOffset, bond->A2() + atomOffset );
+  } else {
+    bool missingParameters = false;
+    for (BondArray::const_iterator bond = barray.begin(); bond != barray.end(); ++bond) {
+      if (bond->Idx() > -1)
+        AddBond( bond->A1() + atomOffset, bond->A2() + atomOffset, bp[bond->Idx()] );
+      else {
+        missingParameters = true;
+        AddBond( bond->A1() + atomOffset, bond->A2() + atomOffset );
+      }
+    }
+    if (missingParameters)
+      mprintf("Warning: Some bonds were missing parameters.\n");
+  }
+}
+
+// Topology::AddAngleArray()
+void Topology::AddAngleArray(AngleArray const& aarray, AngleParmArray const& ap, int atomOffset) {
+  if (ap.empty())
+    for (AngleArray::const_iterator angle = aarray.begin(); angle != aarray.end(); ++angle)
+      AddAngle( angle->A1() + atomOffset,
+                angle->A2() + atomOffset,
+                angle->A3() + atomOffset );
+  else
+    for (AngleArray::const_iterator angle = aarray.begin(); angle != aarray.end(); ++angle)
+      AddAngle( angle->A1() + atomOffset,
+                angle->A2() + atomOffset,
+                angle->A3() + atomOffset, ap[angle->Idx()] );
+}
+
+// Topology::AddDihArray()
+void Topology::AddDihArray(DihedralArray const& darray, DihedralParmArray const& dp, int atomOffset)
+{
+  if (dp.empty())
+    for (DihedralArray::const_iterator dih = darray.begin(); dih != darray.end(); ++dih)
+      AddDihedral( DihedralType( dih->A1() + atomOffset, dih->A2() + atomOffset,
+                                 dih->A3() + atomOffset, dih->A4() + atomOffset,
+                                 dih->Type() ), -1 );
+  else
+    for (DihedralArray::const_iterator dih = darray.begin(); dih != darray.end(); ++dih)
+      AddDihedral( DihedralType( dih->A1() + atomOffset, dih->A2() + atomOffset,
+                                 dih->A3() + atomOffset, dih->A4() + atomOffset,
+                                 dih->Type() ), dp[dih->Idx()] );
+}
+
+/** This template can be used when doing Append() on a generic std::vector array
+  * of type T. The array will be appended to a given array of the same type.
+  * If one is empty and the other is not, values will be filled in if necessary.
+  */
+template <class T> class TopVecAppend {
+  public:
+    /// CONSTRUCTOR
+    TopVecAppend() {}
+    /// Append current array to given array of same type
+    void Append(std::vector<T>& arrayOut, std::vector<T> const& arrayToAdd, unsigned int expectedSize)
+    {
+      if (arrayToAdd.empty() && arrayOut.empty()) {
+        // Both arrays are empty. Nothing to do.
+        return;
+      } else if (arrayToAdd.empty()) {
+        // The current array is empty but the given array is not. Fill in 
+        // array to append with blank values.
+        for (unsigned int idx = 0; idx != expectedSize; idx++)
+          arrayOut.push_back( T() );
+      } else {
+        // Append current array to array to given array. TODO use std::copy?
+        for (typename std::vector<T>::const_iterator it = arrayToAdd.begin(); it != arrayToAdd.end(); ++it)
+          arrayOut.push_back( *it );
+      }
+    }
+};
+
+// Topology::AppendTop()
+int Topology::AppendTop(Topology const& NewTop) {
+  int atomOffset = (int)atoms_.size();
+  mprintf("DEBUG: Appending '%s' to '%s' (offset= %i)\n", NewTop.c_str(), c_str(), atomOffset);
+  //int resOffset = (int)residues_.size();
+
+// NOTE: Lines commented out with //# can be used to test appending via the
+//       parameter update functionality. This is slower, but is a good test
+//       that the parameter update function is working correctly.
+//#  // Save old parameters
+//#  mprintf("DEBUG: Getting old parameters.\n");
+//#  ParameterSet oldParams = GetParameters();
+//#  oldParams.Summary(); // DEBUG
+  // Save nonbonded parameters from each topology TODO LJ 10-12
+  ParmHolder<AtomType> myAtomTypes, newAtomTypes;
+  ParmHolder<NonbondType> myNB, newNB;
+  //ParmHolder<HB_ParmType> myHB, newHB;
+  GetLJAtomTypes( myAtomTypes, myNB, atoms_, nonbond_, debug_ );
+  GetLJAtomTypes( newAtomTypes, newNB, NewTop.atoms_, NewTop.nonbond_, debug_ );
+  int nAtomTypeUpdated = UpdateParameters< ParmHolder<AtomType> >( myAtomTypes, newAtomTypes, "atom type", 1 ); // TODO verbose 
+  int nLJparamsUpdated = UpdateParameters< ParmHolder<NonbondType> >( myNB, newNB, "LJ A-B", 1 ); // TODO verbose
+  mprintf("\t%i atom types updated, %i LJ params updated.\n", nAtomTypeUpdated, nLJparamsUpdated);
+
+  // Append NewTop atoms to this topology.
+  for (atom_iterator atom = NewTop.begin(); atom != NewTop.end(); ++atom)
+  {
+    if (debug_ > 1)
+      mprintf("DBG: %6li %s %s %4i\n", atom-NewTop.begin(), 
+              *(atom->Name()), *(atom->Type()), atom->TypeIndex());
+    Atom CurrentAtom = *atom;
+    Residue const& res = NewTop.Res( CurrentAtom.ResNum() );
+    // Bonds need to be cleared and re-added.
+    CurrentAtom.ClearBonds();
+    AddTopAtom( CurrentAtom, Residue(res.Name(), res.OriginalResNum(),
+                                     res.Icode(), res.ChainId()) );
+  }
+//#  // Recreate bonds for the added atoms
+//#  for (BondArray::const_iterator bond = NewTop.Bonds().begin(); bond != NewTop.Bonds().end(); ++bond)
+//#    AddBond( bond->A1() + atomOffset, bond->A2() + atomOffset );
+//#  for (BondArray::const_iterator bond = NewTop.BondsH().begin(); bond != NewTop.BondsH().end(); ++bond)
+//#    AddBond( bond->A1() + atomOffset, bond->A2() + atomOffset );
+//#  // Recreate angles for the added atoms
+//#  for (AngleArray::const_iterator angle = NewTop.Angles().begin(); angle != NewTop.Angles().end(); ++angle)
+//#      AddAngle( angle->A1() + atomOffset, angle->A2() + atomOffset, angle->A3() + atomOffset );
+//#  for (AngleArray::const_iterator angle = NewTop.AnglesH().begin(); angle != NewTop.AnglesH().end(); ++angle)
+//#      AddAngle( angle->A1() + atomOffset, angle->A2() + atomOffset, angle->A3() + atomOffset );
+//#  // Recreate dihedrals for the added atoms
+//#  for (DihedralArray::const_iterator dih = NewTop.Dihedrals().begin(); dih != NewTop.Dihedrals().end(); ++dih)
+//#      AddDihedral( DihedralType( dih->A1() + atomOffset, dih->A2() + atomOffset,
+//#                                 dih->A3() + atomOffset, dih->A4() + atomOffset,
+//#                                 dih->Type() ) );
+//#  for (DihedralArray::const_iterator dih = NewTop.DihedralsH().begin(); dih != NewTop.DihedralsH().end(); ++dih)
+//#      AddDihedral( DihedralType( dih->A1() + atomOffset, dih->A2() + atomOffset,
+//#                                 dih->A3() + atomOffset, dih->A4() + atomOffset,
+//#                                 dih->Type() ) );
+//#  // Update parameters
+//#  mprintf("DEBUG: Updating with new parameters.\n");
+//#  updateParams( oldParams, NewTop.GetParameters() );
+
+  // EXTRA ATOM INFO
+  TopVecAppend<NameType> appendNameType;
+  appendNameType.Append( tree_, NewTop.tree_, NewTop.Natom() );
+  TopVecAppend<int> appendInt;
+  appendInt.Append( ijoin_, NewTop.ijoin_, NewTop.Natom() );
+  appendInt.Append( irotat_, NewTop.irotat_, NewTop.Natom() );
+  appendInt.Append( pdbSerialNum_, NewTop.pdbSerialNum_, NewTop.Natom() );
+  TopVecAppend<char> appendChar;
+  appendChar.Append( atom_altloc_, NewTop.atom_altloc_, NewTop.Natom() );
+  TopVecAppend<float> appendFloat;
+  appendFloat.Append( occupancy_, NewTop.occupancy_, NewTop.Natom() );
+  appendFloat.Append( bfactor_, NewTop.bfactor_, NewTop.Natom() );
+
+  // BONDS
+  AddBondArray(NewTop.Bonds(),  NewTop.BondParm(), atomOffset);
+  AddBondArray(NewTop.BondsH(), NewTop.BondParm(), atomOffset);
+  // ANGLES
+  AddAngleArray(NewTop.Angles(),  NewTop.AngleParm(), atomOffset);
+  AddAngleArray(NewTop.AnglesH(), NewTop.AngleParm(), atomOffset);
+  // DIHEDRALS
+  AddDihArray(NewTop.Dihedrals(),  NewTop.DihedralParm(), atomOffset);
+  AddDihArray(NewTop.DihedralsH(), NewTop.DihedralParm(), atomOffset);
+  // UREY-BRADLEY TODO
+  // IMPROPERS TODO
+  // CMAP TODO
+
+  // Need to regenerate nonbonded info TODO verbose TODO LJ 10-12
+  mprintf("\tRegenerating nonbond parameters.\n");
+  AssignNonbondParams( myAtomTypes, myNB, ParmHolder<HB_ParmType>() ); //FIXME LJ 10-12
+
+  // TODO append missing stuff?
+
+  // Re-set up this topology
+  // TODO: Could get expensive for multiple appends.
+  return CommonSetup();
+}
+
 // -----------------------------------------------------------------------------
 /** Set parameters for atoms via given atom type parameter holder. */
 void Topology::AssignAtomTypeParm(ParmHolder<AtomType> const& newAtomTypeParams)
@@ -2810,7 +2831,7 @@ void Topology::AssignNonbondParams(ParmHolder<AtomType> const& newTypes,
       // Look for equivalent nonbond types
       for (ParmHolder<AtomType>::iterator t2 = t1 + 1; t2 != currentAtomTypes.end(); ++t2) {
         if (t2->second.OriginalIdx() == -1 && t1->second.LJ() == t2->second.LJ()) {
-          mprintf("DEBUG: Type %s equivalent to type %s\n", *(t1->first[0]), *(t2->first[0]));
+          mprintf("DEBUG: Type %s equivalent to type %s\n", *(t2->first[0]), *(t1->first[0]));
           t2->second.SetTypeIdx( n_unique_lj_types );
         }
       }

From 7be6340d19c3c004d36c61fc8a14da029bfc5e94 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 12 Dec 2023 12:15:49 -0500
Subject: [PATCH 0155/1492] Do not pack arrays by default

---
 src/Topology.cpp | 285 ++++++++++++++++++++++++++++-------------------
 1 file changed, 169 insertions(+), 116 deletions(-)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index fee49a5508..101c8adc1f 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2480,21 +2480,29 @@ void Topology::AssignBondParm(ParmHolder<BondParmType> const& newBondParams,
                               BondArray& bonds, BondParmArray& bpa, const char* desc)
 const
 {
+  ParmHolder<int> currentTypes;
   for (BondArray::iterator bnd = bonds.begin(); bnd != bonds.end(); ++bnd) {
     TypeNameHolder types(2);
     types.AddName( atoms_[bnd->A1()].Type() );
     types.AddName( atoms_[bnd->A2()].Type() );
     bool found;
     // See if parameter is present.
-    int idx = -1;
-    BondParmType bp = newBondParams.FindParam( types, found );
+    int idx = currentTypes.FindParam(types, found);
     if (!found) {
-      mprintf("Warning: parameter not found for %s %s-%s (%s-%s)\n", desc,
-              TruncResAtomNameNum(bnd->A1()).c_str(),
-              TruncResAtomNameNum(bnd->A2()).c_str(),
-              *types[0], *types[1]);
-    } else {
-      idx = addBondParm( bpa, bp );
+      idx = -1;
+      // Not yet present in current types.
+      BondParmType bp = newBondParams.FindParam( types, found );
+      if (!found) {
+        mprintf("Warning: parameter not found for %s %s-%s (%s-%s)\n", desc,
+                TruncResAtomNameNum(bnd->A1()).c_str(),
+                TruncResAtomNameNum(bnd->A2()).c_str(),
+                *types[0], *types[1]);
+      } else {
+        //idx = addBondParm( bpa, bp ); TODO handle array packing
+        idx = (int)bpa.size();
+        bpa.push_back( bp );
+        currentTypes.AddParm(types, idx, false);
+      }
     }
     bnd->SetIdx( idx );
   }
@@ -2553,6 +2561,7 @@ void Topology::AssignUBParams(ParmHolder<BondParmType> const& newBondParams) {
 void Topology::AssignAngleParm(ParmHolder<AngleParmType> const& newAngleParams,
                               AngleArray& angles)
 {
+  ParmHolder<int> currentTypes;
   for (AngleArray::iterator ang = angles.begin(); ang != angles.end(); ++ang) {
     TypeNameHolder types(3);
     types.AddName( atoms_[ang->A1()].Type() );
@@ -2560,16 +2569,27 @@ void Topology::AssignAngleParm(ParmHolder<AngleParmType> const& newAngleParams,
     types.AddName( atoms_[ang->A3()].Type() );
     bool found;
     // See if parameter is present.
-    int idx = -1;
-    AngleParmType ap = newAngleParams.FindParam( types, found );
+    int idx = currentTypes.FindParam( types, found );
     if (!found) {
-      mprintf("Warning: Angle parameter not found for angle %s-%s-%s (%s-%s-%s)\n",
-              TruncResAtomNameNum(ang->A1()).c_str(),
-              TruncResAtomNameNum(ang->A2()).c_str(),
-              TruncResAtomNameNum(ang->A3()).c_str(),
-              *types[0], *types[1], *types[3]);
+      idx = -1;
+      // Not yet present in current types
+      AngleParmType ap = newAngleParams.FindParam( types, found );
+      if (!found) {
+        mprintf("Warning: Angle parameter not found for angle %s-%s-%s (%s-%s-%s)\n",
+                TruncResAtomNameNum(ang->A1()).c_str(),
+                TruncResAtomNameNum(ang->A2()).c_str(),
+                TruncResAtomNameNum(ang->A3()).c_str(),
+                *types[0], *types[1], *types[2]);
+      } else {
+        //idx = addAngleParm( angleparm_, ap ); // TODO uncomment for array packing
+        idx = (int)angleparm_.size();
+        angleparm_.push_back( ap );
+        mprintf("DEBUG: New angle type for %s-%s-%s (Tk=%g Teq=%g) idx=%i\n", *types[0], *types[1], *types[2], ap.Tk(), ap.Teq(), idx);
+        currentTypes.AddParm(types, idx, false);
+      }
     } else {
-      idx = addAngleParm( angleparm_, ap );
+        AngleParmType const& ap = angleparm_[idx];
+        mprintf("DEBUG: Existing angle type for %s-%s-%s (Tk=%g Teq=%g) idx=%i\n", *types[0], *types[1], *types[2], ap.Tk(), ap.Teq(), idx);
     }
     ang->SetIdx( idx );
   }
@@ -2586,6 +2606,7 @@ void Topology::AssignAngleParams(ParmHolder<AngleParmType> const& newAngleParams
 void Topology::AssignImproperParm(ParmHolder<DihedralParmType> const& newImproperParams,
                                   DihedralArray& impropers)
 {
+  ParmHolder<int> currentTypes;
   for (DihedralArray::iterator imp = impropers.begin(); imp != impropers.end(); ++imp) {
     TypeNameHolder types(4);
     types.AddName( atoms_[imp->A1()].Type() );
@@ -2594,17 +2615,24 @@ void Topology::AssignImproperParm(ParmHolder<DihedralParmType> const& newImprope
     types.AddName( atoms_[imp->A4()].Type() );
     bool found;
     // See if parameter is present.
-    int idx = -1;
-    DihedralParmType ip = newImproperParams.FindParam( types, found );
+    int idx = currentTypes.FindParam( types, found );
     if (!found) {
-      mprintf("Warning: Parameter not found for improper %s-%s-%s-%s (%s-%s-%s-%s)\n",
-              TruncResAtomNameNum(imp->A1()).c_str(),
-              TruncResAtomNameNum(imp->A2()).c_str(),
-              TruncResAtomNameNum(imp->A3()).c_str(),
-              TruncResAtomNameNum(imp->A4()).c_str(),
-              *types[0], *types[1], *types[3], *types[4]);
-    } else {
-      idx = addTorsionParm( chamber_.SetImproperParm(), ip );
+      idx = -1;
+      // Not yet present in current types
+      DihedralParmType ip = newImproperParams.FindParam( types, found );
+      if (!found) {
+        mprintf("Warning: Parameter not found for improper %s-%s-%s-%s (%s-%s-%s-%s)\n",
+                TruncResAtomNameNum(imp->A1()).c_str(),
+                TruncResAtomNameNum(imp->A2()).c_str(),
+                TruncResAtomNameNum(imp->A3()).c_str(),
+                TruncResAtomNameNum(imp->A4()).c_str(),
+                *types[0], *types[1], *types[2], *types[3]);
+      } else {
+        //idx = addTorsionParm( chamber_.SetImproperParm(), ip ); // TODO handle array packing
+        idx = (int)chamber_.ImproperParm().size();
+        chamber_.SetImproperParm().push_back( ip );
+        currentTypes.AddParm(types, idx, false);
+      }
     }
     imp->SetIdx( idx );
   }
@@ -2644,6 +2672,7 @@ void Topology::AssignDihedralParm(DihedralParmHolder const& newDihedralParams,
     mprintf("DEBUG: %zu incoming dihedrals, %zu unique dihedrals.\n",
             dihedralsIn.size(), dihedrals.size());
 
+  ParmHolder< std::vector<int> > currentTypes;
   dihedralsIn.clear();
   // Keep track of 1-4 interactions
   typedef std::pair<int,int> Ipair;
@@ -2676,108 +2705,128 @@ void Topology::AssignDihedralParm(DihedralParmHolder const& newDihedralParams,
     bool found;
     if (isImproper) {
       // ----- This is actually an improper dihedral. ----------------
-      DihedralParmType ip = newImproperParams.FindParam( types, found );
-      int idx = -1;
+      std::vector<int> idxs = currentTypes.FindParam( types, found );
       if (!found) {
-        mprintf("Warning: Improper parameters not found for improper dihedral %s-%s-%s-%s (%s-%s-%s-%s)\n",
-                TruncResAtomNameNum(dih->A1()).c_str(),
-                TruncResAtomNameNum(dih->A2()).c_str(),
-                TruncResAtomNameNum(dih->A3()).c_str(),
-                TruncResAtomNameNum(dih->A4()).c_str(),
-                *types[0], *types[1], *types[2], *types[3]);
-      } else {
-        idx = addTorsionParm( dihedralparm_, ip );
+        // Not yet present in current types
+        DihedralParmType ip = newImproperParams.FindParam( types, found );
+        if (!found) {
+          idxs.push_back( -1 );
+          mprintf("Warning: Improper parameters not found for improper dihedral %s-%s-%s-%s (%s-%s-%s-%s)\n",
+                  TruncResAtomNameNum(dih->A1()).c_str(),
+                  TruncResAtomNameNum(dih->A2()).c_str(),
+                  TruncResAtomNameNum(dih->A3()).c_str(),
+                  TruncResAtomNameNum(dih->A4()).c_str(),
+                  *types[0], *types[1], *types[2], *types[3]);
+        } else {
+          //int idx = addTorsionParm( dihedralparm_, ip ); // TODO handle array packing
+          int idx = (int)dihedralparm_.size();
+          dihedralparm_.push_back( ip );
+          idxs.push_back( idx );
+          currentTypes.AddParm(types, idxs, false);
+        }
       }
       DihedralType mydih = *dih;
-      mydih.SetIdx( idx );
+      mydih.SetIdx( idxs.front() );
       mydih.SetImproper( true );
       // Always skip 1-4 for impropers
       mydih.SetSkip14( true );
       dihedralsIn.push_back( mydih );
     } else {
-      // -----Regular dihedral. See if parameter already present. ----
-      DihedralParmArray dpa = newDihedralParams.FindParam( types, found );
-      if (!found) {
-        mprintf("Warning: Dihedral parameters not found for dihedral %s-%s-%s-%s (%s-%s-%s-%s)\n",
-                TruncResAtomNameNum(dih->A1()).c_str(),
-                TruncResAtomNameNum(dih->A2()).c_str(),
-                TruncResAtomNameNum(dih->A3()).c_str(),
-                TruncResAtomNameNum(dih->A4()).c_str(),
-                *types[0], *types[1], *types[2], *types[3]);
-        DihedralType mydih = *dih;
-        mydih.SetIdx( -1 );
-        dihedralsIn.push_back( mydih );
-      } else {
-        // Actually add parameters for this dihedral.
-        // Determine if this is actually a 1-4 interaction by making
-        // sure that A4 isnt part of a bond or angle with A1.
-        bool skip14 = false;
-        for (Atom::bond_iterator bat1 = atoms_[dih->A1()].bondbegin();
-                                 bat1 != atoms_[dih->A1()].bondend(); ++bat1)
-        {
-          if (*bat1 != dih->A2()) {
-            if (*bat1 == dih->A4()) {
-              skip14 = true;
-              break;
-            }
-            // Loop over angles, dih->A1() - bat1 - bat2
-            for (Atom::bond_iterator bat2 = atoms_[*bat1].bondbegin();
-                                     bat2 != atoms_[*bat1].bondend(); ++bat2)
-            {
-              //if (dih->A1() == 442 && dih->A4() == 444) { // DEBUG
-              //  mprintf("DEBUG: %4i %4i %4i %4i Checking angle %4i %4i %4i\n", dih->A1()+1, dih->A2()+1, dih->A3()+1, dih->A4()+1, dih->A1()+1, *bat1 + 1, *bat2 + 1);
-              //}
-              if (*bat2 != *bat1) {
-                if (*bat2 == dih->A4()) {
-                  skip14 = true;
-                  break;
-                }
-              }
-            } // END loop over bat1 bonded atoms
-            if (skip14) break;
-          }
-        } // END loop over dih->A1() bonded atoms
-        if (!skip14) {
-          // Determine if 1-4 interaction already calculated by previous dihedral.
-          // Make the lower end atom first. 
-          Ipair pair14;
-          if (dih->A1() < dih->A4()) {
-            pair14.first = dih->A1();
-            pair14.second = dih->A4();
-          } else {
-            pair14.first = dih->A4();
-            pair14.second = dih->A1();
-          }
-          Imap::const_iterator it = PairMap.find( pair14 );
-          if (it == PairMap.end()) {
-            skip14 = false;
-            PairMap.insert( pair14 );
-          } else {
+      // -----Regular dihedral. --------------------------------------
+      // Determine if this is actually a 1-4 interaction by making
+      // sure that A4 isnt part of a bond or angle with A1.
+      bool skip14 = false;
+      for (Atom::bond_iterator bat1 = atoms_[dih->A1()].bondbegin();
+                               bat1 != atoms_[dih->A1()].bondend(); ++bat1)
+      {
+        if (*bat1 != dih->A2()) {
+          if (*bat1 == dih->A4()) {
             skip14 = true;
-            //mprintf("DEBUG: Prior 1-4 calc detected.\n");
+            break;
           }
+          // Loop over angles, dih->A1() - bat1 - bat2
+          for (Atom::bond_iterator bat2 = atoms_[*bat1].bondbegin();
+                                   bat2 != atoms_[*bat1].bondend(); ++bat2)
+          {
+            //if (dih->A1() == 442 && dih->A4() == 444) { // DEBUG
+            //  mprintf("DEBUG: %4i %4i %4i %4i Checking angle %4i %4i %4i\n", dih->A1()+1, dih->A2()+1, dih->A3()+1, dih->A4()+1, dih->A1()+1, *bat1 + 1, *bat2 + 1);
+            //}
+            if (*bat2 != *bat1) {
+              if (*bat2 == dih->A4()) {
+                skip14 = true;
+                break;
+              }
+            }
+          } // END loop over bat1 bonded atoms
+          if (skip14) break;
         }
-        // Loop over multiplicities
-        //if (dih->A1() == 442 && dih->A4() == 444) { // DEBUG
-        //  mprintf("DEBUG: Skip14= %i\n", (int)skip14);
-        //}
-        for (DihedralParmArray::const_iterator it = dpa.begin(); it != dpa.end(); ++it) {
-          DihedralType mydih = *dih;
-          int idx = addTorsionParm( dihedralparm_, *it );
-          // If there are multiple parameters for the same dihedral, all but
-          // one of the 1-4 calcs need to be skipped.
-          if (it == dpa.begin())
-            mydih.SetSkip14(skip14);
-          else
-            mydih.SetSkip14(true);
-          mydih.SetIdx( idx );
-          dihedralsIn.push_back( mydih );
-//          mprintf("DEBUG: Assigned %4i %4i %4i %4i (%2s %2s %2s %2s) isImproper=%i skip14=%i\n",
-//            mydih.A1()+1, mydih.A2()+1, mydih.A3()+1, mydih.A4()+1,
-//            *types[0], *types[1], *types[2], *types[3],
-//            (int)mydih.IsImproper(), (int)mydih.Skip14());
+      } // END loop over dih->A1() bonded atoms
+      if (!skip14) {
+        // Determine if 1-4 interaction already calculated by previous dihedral.
+        // Make the lower end atom first. 
+        Ipair pair14;
+        if (dih->A1() < dih->A4()) {
+          pair14.first = dih->A1();
+          pair14.second = dih->A4();
+        } else {
+          pair14.first = dih->A4();
+          pair14.second = dih->A1();
+        }
+        Imap::const_iterator it = PairMap.find( pair14 );
+        if (it == PairMap.end()) {
+          skip14 = false;
+          PairMap.insert( pair14 );
+        } else {
+          skip14 = true;
+          //mprintf("DEBUG: Prior 1-4 calc detected.\n");
         }
       }
+      //if (dih->A1() == 442 && dih->A4() == 444) { // DEBUG
+      //  mprintf("DEBUG: Skip14= %i\n", (int)skip14);
+      //}
+
+      // See if parameter already present. ----
+      std::vector<int> idxs = currentTypes.FindParam( types, found );
+      if (!found) {
+        // Not yet present in current types
+        DihedralParmArray dpa = newDihedralParams.FindParam( types, found );
+        if (!found) {
+          mprintf("Warning: Dihedral parameters not found for dihedral %s-%s-%s-%s (%s-%s-%s-%s)\n",
+                  TruncResAtomNameNum(dih->A1()).c_str(),
+                  TruncResAtomNameNum(dih->A2()).c_str(),
+                  TruncResAtomNameNum(dih->A3()).c_str(),
+                  TruncResAtomNameNum(dih->A4()).c_str(),
+                  *types[0], *types[1], *types[2], *types[3]);
+          idxs.push_back( -1 );
+        } else {
+          // Loop over multiplicities
+          for (DihedralParmArray::const_iterator it = dpa.begin(); it != dpa.end(); ++it) {
+            //int idx = addTorsionParm( dihedralparm_, *it ); // TODO handle array packing
+            int idx = (int)dihedralparm_.size();
+            dihedralparm_.push_back( *it );
+            idxs.push_back( idx );
+          } // END loop over dihedral multiplicities
+          currentTypes.AddParm(types, idxs, false);
+        } // END parameters found for this dihedral
+      }
+      // Actually add parameters for this dihedral.
+      for (std::vector<int>::const_iterator idx = idxs.begin(); idx != idxs.end(); ++idx)
+      {
+        DihedralType mydih = *dih;
+        mydih.SetImproper( false );
+        // If there are multiple parameters for the same dihedral, all but
+        // one of the 1-4 calcs need to be skipped.
+        if (idx == idxs.begin())
+          mydih.SetSkip14(skip14);
+        else
+          mydih.SetSkip14(true);
+        mydih.SetIdx( *idx );
+        dihedralsIn.push_back( mydih );
+//        mprintf("DEBUG: Assigned %4i %4i %4i %4i (%2s %2s %2s %2s) isImproper=%i skip14=%i\n",
+//                mydih.A1()+1, mydih.A2()+1, mydih.A3()+1, mydih.A4()+1,
+//                *types[0], *types[1], *types[2], *types[3],
+//                (int)mydih.IsImproper(), (int)mydih.Skip14());
+      } // END loop over dihedral parameter indices
     }
   } // END loop over all dihedrals
 }
@@ -2895,7 +2944,11 @@ void Topology::AssignNonbondParams(ParmHolder<AtomType> const& newTypes,
   }
 }
 
-/** Update/add to parameters in this topology with those from given set. */
+/** Update/add to parameters in this topology with those from given set.
+  * NOTE: This routine is separate from updateParams() to allow that
+  *       routine to be used by AppendTop() for testing the parameter
+  *       update code with topology appending.
+  */
 int Topology::UpdateParams(ParameterSet const& set1) {
   ParameterSet set0 = GetParameters();
   return updateParams(set0, set1);

From 3a546737998fddc9e525fc93d7b50bc58fa5deb5 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 12 Dec 2023 13:01:20 -0500
Subject: [PATCH 0156/1492] The first duplicated dihedral is used for 1-4
 instead of the last dihedral.

---
 test/Test_CharmmParams/test3.parm7.save | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/test/Test_CharmmParams/test3.parm7.save b/test/Test_CharmmParams/test3.parm7.save
index 85bd66be2f..f400305054 100644
--- a/test/Test_CharmmParams/test3.parm7.save
+++ b/test/Test_CharmmParams/test3.parm7.save
@@ -1,4 +1,4 @@
-%VERSION  VERSION_STAMP = V0001.000  DATE = 12/05/23 15:27:10                  
+%VERSION  VERSION_STAMP = V0001.000  DATE = 12/12/23 12:16:22                  
 %FLAG CTITLE                                                                    
 %FORMAT(a80)                                                                    
                                                                                 
@@ -352,20 +352,20 @@ LYS
       33      30      39      42      32      33      30      39      45      32
       33      30      39      48      33      36      30      39      42      32
       36      30      39      45      32      36      30      39      48      33
-      42      39      48      51      34      42      39      48      54      35
-      45      39      48      51      34      45      39      48      54      35
+      42      39      48      51      34      45      39      48      51      34
+      42      39      48      54      35      45      39      48      54      35
       51      48      54      57      36      51      48      54      60      36
 %FLAG DIHEDRALS_WITHOUT_HYDROGEN                                                
 %FORMAT(10I8)                                                                   
-       0       6     -12      21       1       0       6     -12      21       2
-       0       6      12      21       3       0       6      63      66       4
-       6      12     -21      30       5       6      12     -21      30       6
-       6      12      21      30       7      12       6      63      66       8
-      12      21     -30      39       9      12      21     -30      39      10
-      12      21      30      39      11      21      12      -6      63      12
-      21      12      -6      63      13      21      12       6      63      14
-      21      30      39      48      15      30      39     -48      54      16
-      30      39      48      54      17      39      48      54      57      18
+       0       6      12      21       1       0       6     -12      21       2
+       0       6     -12      21       3       0       6      63      66       4
+       6      12      21      30       5       6      12     -21      30       6
+       6      12     -21      30       7      12       6      63      66       8
+      12      21      30      39       9      12      21     -30      39      10
+      12      21     -30      39      11      21      12       6      63      12
+      21      12      -6      63      13      21      12      -6      63      14
+      21      30      39      48      15      30      39      48      54      16
+      30      39     -48      54      17      39      48      54      57      18
       39      48      54      60      18
 %FLAG EXCLUDED_ATOMS_LIST                                                       
 %FORMAT(10I8)                                                                   

From 8b9b6b145903db7a3dcb353f55f208ab67713fa4 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 13 Dec 2023 09:11:34 -0500
Subject: [PATCH 0157/1492] Add genangles keyword

---
 src/Exec_UpdateParameters.cpp | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/src/Exec_UpdateParameters.cpp b/src/Exec_UpdateParameters.cpp
index 329056f7f4..7f7414393e 100644
--- a/src/Exec_UpdateParameters.cpp
+++ b/src/Exec_UpdateParameters.cpp
@@ -2,13 +2,15 @@
 #include "CpptrajStdio.h"
 #include "DataSet_Parameters.h"
 #include "DataSet_Topology.h"
+#include "Structure/GenerateAngles.h"
 
 const char* Exec_UpdateParameters::disclaimer_ = "Warning: This command is provided for convenience only.\nWarning: For editing topology files, ParmEd is a much better alternative.\n";
 
 // Exec_UpdateParameters::Help()
 void Exec_UpdateParameters::Help() const
 {
-  mprintf("\t%s setname <parm set>\n", DataSetList::TopArgs);
+  mprintf("\tsetname <parmset> [genangles]\n"
+          "\t%s\n", DataSetList::TopArgs);
   mprintf("  Update parameters in specified topology with those from <parm set>.\n"
           "  <parm set> can either be a parameter set or a topology. If a\n"
           "  parameter from <parm set> does not exist in the topology it\n"
@@ -21,6 +23,7 @@ Exec::RetType Exec_UpdateParameters::Execute(CpptrajState& State, ArgList& argIn
 {
   mprintf("%s", disclaimer_);
   std::string dsname = argIn.GetStringKey("setname");
+  bool genAngles = argIn.hasKey("genangles");
   if (dsname.empty()) {
     mprinterr("Error: Specify parameter set.\n");
     return CpptrajState::ERR;
@@ -43,10 +46,19 @@ Exec::RetType Exec_UpdateParameters::Execute(CpptrajState& State, ArgList& argIn
 
   mprintf("\tUpdating parameters in topology '%s' using those in set '%s'\n",
           top.c_str(), ds->legend());
+  if (genAngles)
+    mprintf("\tWill attempt to generate angle/dihedral information from bonds.\n");
 
   // Sort topology bond arrays to be consistent with LEaP
   //top.SortBonds();
 
+  if (genAngles) {
+    if (Cpptraj::Structure::GenerateAngles( top )) {
+      mprinterr("Error: Could not generate angle/dihedral information.\n");
+      return CpptrajState::ERR;
+    }
+  }
+
   if (ds->Type() == DataSet::PARAMETERS)
     top.UpdateParams(static_cast<DataSet_Parameters const&>( *ds ));
   else if (ds->Type() == DataSet::TOPOLOGY) {

From fa3aebabded84f758f25460cb629da29fbc5b2f8 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 13 Dec 2023 10:20:03 -0500
Subject: [PATCH 0158/1492] Try a different way of appending; go back to using
 updateParams to make parameter assignment more consistent. Leap seems to pack
 dihedral arrays but not angles or bonds so go back to the old behavior for
 dihedrals to be consistent with leap.

---
 src/Topology.cpp | 356 ++++++++++++++++++++++++++++-------------------
 1 file changed, 211 insertions(+), 145 deletions(-)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index 101c8adc1f..35f5d064b5 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2156,6 +2156,10 @@ static inline void GetDihedralParams(DihedralParmHolder& DP, ParmHolder<Dihedral
       } else {
         ret = DP.AddParm( types, dpa[b->Idx()], false );
       }
+      // DEBUG
+      //if (ret == ParameterHolders::ADDED) {
+      //  mprintf("DEBUG: Added %s %s %s %s idx=%i isImproper=%i\n", *(types[0]), *(types[1]), *(types[2]), *(types[3]), b->Idx(), (int)b->IsImproper());
+      //}
       if (ret == ParameterHolders::ERR) {
         paramOverwriteWarning("dihedral");
         mprintf("Warning: Dihedral %s %s %s %s PK=%g PN=%g Phase=%g SCEE=%g SCNB=%g\n",
@@ -2360,6 +2364,46 @@ template <class T> class TopVecAppend {
     }
 };
 
+/// Add bonds to array with given atom offset
+static inline void addBondsWithOffset(BondArray& bondsOut, BondArray const& bondsIn, int atomOffset, std::vector<Atom>const& atoms) {
+  // By convention any hydrogen atom should come second
+  for (BondArray::const_iterator bond = bondsIn.begin(); bond != bondsIn.end(); ++bond)
+  {
+    int atom1 = bond->A1() + atomOffset;
+    int atom2 = bond->A2() + atomOffset;
+    bool a1H = (atoms[atom1].Element() == Atom::HYDROGEN);
+    //bool a2H = (atoms[atom2].Element() == Atom::HYDROGEN);
+    //mprintf("\t\t\tAdding bond %i to %i (isH=%i)\n",atom1+1,atom2+1,(int)isH);
+    if (a1H)
+      bondsOut.push_back( BondType(atom2, atom1, -1) );
+    else
+      bondsOut.push_back( BondType(atom1, atom2, -1) );
+    //if (a1H || a2H) {
+    //  if (a1H)
+    //    bondsh_.push_back( BondType(atom2, atom1, pidx) );
+    //  else
+    //    bondsh_.push_back( BondType(atom1, atom2, pidx) );
+    //} else
+    //  bonds_.push_back( BondType( atom1, atom2, pidx ) );
+    //bondsOut.push_back( BondType(bond->A1() + atomOffset, bond->A2() + atomOffset, -1) );
+  }
+}
+
+/// Add angles to array with given offset
+static inline void addAnglesWithOffset(AngleArray& anglesOut, AngleArray const& anglesIn, int atomOffset) {
+  for (AngleArray::const_iterator angle = anglesIn.begin(); angle != anglesIn.end(); ++angle)
+    anglesOut.push_back( AngleType(angle->A1() + atomOffset, angle->A2() + atomOffset, angle->A3() + atomOffset, -1) );
+}
+
+/// Add dihedrals to array with given offset
+static inline void addDihedralsWithOffset(DihedralArray& dihedralsOut, DihedralArray const& dihedralsIn, int atomOffset)
+{
+  for (DihedralArray::const_iterator dih = dihedralsIn.begin(); dih != dihedralsIn.end(); ++dih)
+    dihedralsOut.push_back( DihedralType( dih->A1() + atomOffset, dih->A2() + atomOffset,
+                                          dih->A3() + atomOffset, dih->A4() + atomOffset,
+                                          dih->Type(), -1 ) );
+}
+
 // Topology::AppendTop()
 int Topology::AppendTop(Topology const& NewTop) {
   int atomOffset = (int)atoms_.size();
@@ -2369,11 +2413,11 @@ int Topology::AppendTop(Topology const& NewTop) {
 // NOTE: Lines commented out with //# can be used to test appending via the
 //       parameter update functionality. This is slower, but is a good test
 //       that the parameter update function is working correctly.
-//#  // Save old parameters
-//#  mprintf("DEBUG: Getting old parameters.\n");
-//#  ParameterSet oldParams = GetParameters();
-//#  oldParams.Summary(); // DEBUG
-  // Save nonbonded parameters from each topology TODO LJ 10-12
+  // Save old parameters
+  mprintf("DEBUG: Getting old parameters.\n");
+  ParameterSet oldParams = GetParameters();
+  oldParams.Summary(); // DEBUG
+/*  // Save nonbonded parameters from each topology TODO LJ 10-12
   ParmHolder<AtomType> myAtomTypes, newAtomTypes;
   ParmHolder<NonbondType> myNB, newNB;
   //ParmHolder<HB_ParmType> myHB, newHB;
@@ -2381,7 +2425,7 @@ int Topology::AppendTop(Topology const& NewTop) {
   GetLJAtomTypes( newAtomTypes, newNB, NewTop.atoms_, NewTop.nonbond_, debug_ );
   int nAtomTypeUpdated = UpdateParameters< ParmHolder<AtomType> >( myAtomTypes, newAtomTypes, "atom type", 1 ); // TODO verbose 
   int nLJparamsUpdated = UpdateParameters< ParmHolder<NonbondType> >( myNB, newNB, "LJ A-B", 1 ); // TODO verbose
-  mprintf("\t%i atom types updated, %i LJ params updated.\n", nAtomTypeUpdated, nLJparamsUpdated);
+  mprintf("\t%i atom types updated, %i LJ params updated.\n", nAtomTypeUpdated, nLJparamsUpdated);*/
 
   // Append NewTop atoms to this topology.
   for (atom_iterator atom = NewTop.begin(); atom != NewTop.end(); ++atom)
@@ -2393,10 +2437,21 @@ int Topology::AppendTop(Topology const& NewTop) {
     Residue const& res = NewTop.Res( CurrentAtom.ResNum() );
     // Bonds need to be cleared and re-added.
     CurrentAtom.ClearBonds();
+    for (Atom::bond_iterator bat = atom->bondbegin(); bat != atom->bondend(); ++bat)
+      CurrentAtom.AddBondToIdx( *bat + atomOffset );
+
     AddTopAtom( CurrentAtom, Residue(res.Name(), res.OriginalResNum(),
                                      res.Icode(), res.ChainId()) );
   }
-//#  // Recreate bonds for the added atoms
+  // Recreate bonds for the added atoms
+  addBondsWithOffset( bonds_, NewTop.Bonds(), atomOffset, atoms_ );
+  addBondsWithOffset( bondsh_, NewTop.BondsH(), atomOffset, atoms_ );
+  addBondsWithOffset( chamber_.SetUB(), NewTop.chamber_.UB(), atomOffset, atoms_ );
+  addAnglesWithOffset( angles_, NewTop.Angles(), atomOffset );
+  addAnglesWithOffset( anglesh_, NewTop.AnglesH(), atomOffset );
+  addDihedralsWithOffset( dihedrals_, NewTop.Dihedrals(), atomOffset );
+  addDihedralsWithOffset( dihedralsh_, NewTop.DihedralsH(), atomOffset );
+  addDihedralsWithOffset( chamber_.SetImpropers(), NewTop.chamber_.Impropers(), atomOffset );
 //#  for (BondArray::const_iterator bond = NewTop.Bonds().begin(); bond != NewTop.Bonds().end(); ++bond)
 //#    AddBond( bond->A1() + atomOffset, bond->A2() + atomOffset );
 //#  for (BondArray::const_iterator bond = NewTop.BondsH().begin(); bond != NewTop.BondsH().end(); ++bond)
@@ -2415,9 +2470,9 @@ int Topology::AppendTop(Topology const& NewTop) {
 //#      AddDihedral( DihedralType( dih->A1() + atomOffset, dih->A2() + atomOffset,
 //#                                 dih->A3() + atomOffset, dih->A4() + atomOffset,
 //#                                 dih->Type() ) );
-//#  // Update parameters
-//#  mprintf("DEBUG: Updating with new parameters.\n");
-//#  updateParams( oldParams, NewTop.GetParameters() );
+  // Update parameters
+  mprintf("DEBUG: Updating with new parameters.\n");
+  updateParams( oldParams, NewTop.GetParameters() );
 
   // EXTRA ATOM INFO
   TopVecAppend<NameType> appendNameType;
@@ -2432,7 +2487,7 @@ int Topology::AppendTop(Topology const& NewTop) {
   appendFloat.Append( occupancy_, NewTop.occupancy_, NewTop.Natom() );
   appendFloat.Append( bfactor_, NewTop.bfactor_, NewTop.Natom() );
 
-  // BONDS
+/*  // BONDS
   AddBondArray(NewTop.Bonds(),  NewTop.BondParm(), atomOffset);
   AddBondArray(NewTop.BondsH(), NewTop.BondParm(), atomOffset);
   // ANGLES
@@ -2447,7 +2502,7 @@ int Topology::AppendTop(Topology const& NewTop) {
 
   // Need to regenerate nonbonded info TODO verbose TODO LJ 10-12
   mprintf("\tRegenerating nonbond parameters.\n");
-  AssignNonbondParams( myAtomTypes, myNB, ParmHolder<HB_ParmType>() ); //FIXME LJ 10-12
+  AssignNonbondParams( myAtomTypes, myNB, ParmHolder<HB_ParmType>() ); //FIXME LJ 10-12*/
 
   // TODO append missing stuff?
 
@@ -2506,6 +2561,25 @@ const
     }
     bnd->SetIdx( idx );
   }
+/*
+  for (BondArray::iterator bnd = bonds.begin(); bnd != bonds.end(); ++bnd) {
+    TypeNameHolder types(2);
+    types.AddName( atoms_[bnd->A1()].Type() );
+    types.AddName( atoms_[bnd->A2()].Type() );
+    bool found;
+    // See if parameter is present.
+    int idx = -1;
+    BondParmType bp = newBondParams.FindParam( types, found );
+    if (!found) {
+      mprintf("Warning: parameter not found for %s %s-%s (%s-%s)\n", desc,
+              TruncResAtomNameNum(bnd->A1()).c_str(),
+              TruncResAtomNameNum(bnd->A2()).c_str(),
+              *types[0], *types[1]);
+    } else {
+      idx = addBondParm( bpa, bp );
+    }
+    bnd->SetIdx( idx );
+  }*/
 }
 
 /** Replace any current bond parameters with given bond parameters. */
@@ -2584,15 +2658,33 @@ void Topology::AssignAngleParm(ParmHolder<AngleParmType> const& newAngleParams,
         //idx = addAngleParm( angleparm_, ap ); // TODO uncomment for array packing
         idx = (int)angleparm_.size();
         angleparm_.push_back( ap );
-        mprintf("DEBUG: New angle type for %s-%s-%s (Tk=%g Teq=%g) idx=%i\n", *types[0], *types[1], *types[2], ap.Tk(), ap.Teq(), idx);
+        //mprintf("DEBUG: New angle type for %s-%s-%s (Tk=%g Teq=%g) idx=%i\n", *types[0], *types[1], *types[2], ap.Tk(), ap.Teq(), idx);
         currentTypes.AddParm(types, idx, false);
       }
-    } else {
-        AngleParmType const& ap = angleparm_[idx];
-        mprintf("DEBUG: Existing angle type for %s-%s-%s (Tk=%g Teq=%g) idx=%i\n", *types[0], *types[1], *types[2], ap.Tk(), ap.Teq(), idx);
     }
     ang->SetIdx( idx );
   }
+/*
+  for (AngleArray::iterator ang = angles.begin(); ang != angles.end(); ++ang) {
+    TypeNameHolder types(3);
+    types.AddName( atoms_[ang->A1()].Type() );
+    types.AddName( atoms_[ang->A2()].Type() );
+    types.AddName( atoms_[ang->A3()].Type() );
+    bool found;
+    // See if parameter is present.
+    int idx = -1;
+    AngleParmType ap = newAngleParams.FindParam( types, found );
+    if (!found) {
+      mprintf("Warning: Angle parameter not found for angle %s-%s-%s (%s-%s-%s)\n",
+              TruncResAtomNameNum(ang->A1()).c_str(),
+              TruncResAtomNameNum(ang->A2()).c_str(),
+              TruncResAtomNameNum(ang->A3()).c_str(),
+              *types[0], *types[1], *types[3]);
+    } else {
+      idx = addAngleParm( angleparm_, ap );
+    }
+    ang->SetIdx( idx );
+  }*/
 }
 
 /** Replace any current angle parameters with given angle parameters. */
@@ -2606,7 +2698,6 @@ void Topology::AssignAngleParams(ParmHolder<AngleParmType> const& newAngleParams
 void Topology::AssignImproperParm(ParmHolder<DihedralParmType> const& newImproperParams,
                                   DihedralArray& impropers)
 {
-  ParmHolder<int> currentTypes;
   for (DihedralArray::iterator imp = impropers.begin(); imp != impropers.end(); ++imp) {
     TypeNameHolder types(4);
     types.AddName( atoms_[imp->A1()].Type() );
@@ -2615,24 +2706,17 @@ void Topology::AssignImproperParm(ParmHolder<DihedralParmType> const& newImprope
     types.AddName( atoms_[imp->A4()].Type() );
     bool found;
     // See if parameter is present.
-    int idx = currentTypes.FindParam( types, found );
+    int idx = -1;
+    DihedralParmType ip = newImproperParams.FindParam( types, found );
     if (!found) {
-      idx = -1;
-      // Not yet present in current types
-      DihedralParmType ip = newImproperParams.FindParam( types, found );
-      if (!found) {
-        mprintf("Warning: Parameter not found for improper %s-%s-%s-%s (%s-%s-%s-%s)\n",
-                TruncResAtomNameNum(imp->A1()).c_str(),
-                TruncResAtomNameNum(imp->A2()).c_str(),
-                TruncResAtomNameNum(imp->A3()).c_str(),
-                TruncResAtomNameNum(imp->A4()).c_str(),
-                *types[0], *types[1], *types[2], *types[3]);
-      } else {
-        //idx = addTorsionParm( chamber_.SetImproperParm(), ip ); // TODO handle array packing
-        idx = (int)chamber_.ImproperParm().size();
-        chamber_.SetImproperParm().push_back( ip );
-        currentTypes.AddParm(types, idx, false);
-      }
+      mprintf("Warning: Parameter not found for improper %s-%s-%s-%s (%s-%s-%s-%s)\n",
+              TruncResAtomNameNum(imp->A1()).c_str(),
+              TruncResAtomNameNum(imp->A2()).c_str(),
+              TruncResAtomNameNum(imp->A3()).c_str(),
+              TruncResAtomNameNum(imp->A4()).c_str(),
+              *types[0], *types[1], *types[3], *types[4]);
+    } else {
+      idx = addTorsionParm( chamber_.SetImproperParm(), ip );
     }
     imp->SetIdx( idx );
   }
@@ -2672,7 +2756,6 @@ void Topology::AssignDihedralParm(DihedralParmHolder const& newDihedralParams,
     mprintf("DEBUG: %zu incoming dihedrals, %zu unique dihedrals.\n",
             dihedralsIn.size(), dihedrals.size());
 
-  ParmHolder< std::vector<int> > currentTypes;
   dihedralsIn.clear();
   // Keep track of 1-4 interactions
   typedef std::pair<int,int> Ipair;
@@ -2705,128 +2788,108 @@ void Topology::AssignDihedralParm(DihedralParmHolder const& newDihedralParams,
     bool found;
     if (isImproper) {
       // ----- This is actually an improper dihedral. ----------------
-      std::vector<int> idxs = currentTypes.FindParam( types, found );
+      DihedralParmType ip = newImproperParams.FindParam( types, found );
+      int idx = -1;
       if (!found) {
-        // Not yet present in current types
-        DihedralParmType ip = newImproperParams.FindParam( types, found );
-        if (!found) {
-          idxs.push_back( -1 );
-          mprintf("Warning: Improper parameters not found for improper dihedral %s-%s-%s-%s (%s-%s-%s-%s)\n",
-                  TruncResAtomNameNum(dih->A1()).c_str(),
-                  TruncResAtomNameNum(dih->A2()).c_str(),
-                  TruncResAtomNameNum(dih->A3()).c_str(),
-                  TruncResAtomNameNum(dih->A4()).c_str(),
-                  *types[0], *types[1], *types[2], *types[3]);
-        } else {
-          //int idx = addTorsionParm( dihedralparm_, ip ); // TODO handle array packing
-          int idx = (int)dihedralparm_.size();
-          dihedralparm_.push_back( ip );
-          idxs.push_back( idx );
-          currentTypes.AddParm(types, idxs, false);
-        }
+        mprintf("Warning: Improper parameters not found for improper dihedral %s-%s-%s-%s (%s-%s-%s-%s)\n",
+                TruncResAtomNameNum(dih->A1()).c_str(),
+                TruncResAtomNameNum(dih->A2()).c_str(),
+                TruncResAtomNameNum(dih->A3()).c_str(),
+                TruncResAtomNameNum(dih->A4()).c_str(),
+                *types[0], *types[1], *types[2], *types[3]);
+      } else {
+        idx = addTorsionParm( dihedralparm_, ip );
       }
       DihedralType mydih = *dih;
-      mydih.SetIdx( idxs.front() );
+      mydih.SetIdx( idx );
       mydih.SetImproper( true );
       // Always skip 1-4 for impropers
       mydih.SetSkip14( true );
       dihedralsIn.push_back( mydih );
     } else {
-      // -----Regular dihedral. --------------------------------------
-      // Determine if this is actually a 1-4 interaction by making
-      // sure that A4 isnt part of a bond or angle with A1.
-      bool skip14 = false;
-      for (Atom::bond_iterator bat1 = atoms_[dih->A1()].bondbegin();
-                               bat1 != atoms_[dih->A1()].bondend(); ++bat1)
-      {
-        if (*bat1 != dih->A2()) {
-          if (*bat1 == dih->A4()) {
+      // -----Regular dihedral. See if parameter already present. ----
+      DihedralParmArray dpa = newDihedralParams.FindParam( types, found );
+      if (!found) {
+        mprintf("Warning: Dihedral parameters not found for dihedral %s-%s-%s-%s (%s-%s-%s-%s)\n",
+                TruncResAtomNameNum(dih->A1()).c_str(),
+                TruncResAtomNameNum(dih->A2()).c_str(),
+                TruncResAtomNameNum(dih->A3()).c_str(),
+                TruncResAtomNameNum(dih->A4()).c_str(),
+                *types[0], *types[1], *types[2], *types[3]);
+        DihedralType mydih = *dih;
+        mydih.SetIdx( -1 );
+        dihedralsIn.push_back( mydih );
+      } else {
+        // Actually add parameters for this dihedral.
+        // Determine if this is actually a 1-4 interaction by making
+        // sure that A4 isnt part of a bond or angle with A1.
+        bool skip14 = false;
+        for (Atom::bond_iterator bat1 = atoms_[dih->A1()].bondbegin();
+                                 bat1 != atoms_[dih->A1()].bondend(); ++bat1)
+        {
+          if (*bat1 != dih->A2()) {
+            if (*bat1 == dih->A4()) {
+              skip14 = true;
+              break;
+            }
+            // Loop over angles, dih->A1() - bat1 - bat2
+            for (Atom::bond_iterator bat2 = atoms_[*bat1].bondbegin();
+                                     bat2 != atoms_[*bat1].bondend(); ++bat2)
+            {
+              //if (dih->A1() == 442 && dih->A4() == 444) { // DEBUG
+              //  mprintf("DEBUG: %4i %4i %4i %4i Checking angle %4i %4i %4i\n", dih->A1()+1, dih->A2()+1, dih->A3()+1, dih->A4()+1, dih->A1()+1, *bat1 + 1, *bat2 + 1);
+              //}
+              if (*bat2 != *bat1) {
+                if (*bat2 == dih->A4()) {
+                  skip14 = true;
+                  break;
+                }
+              }
+            } // END loop over bat1 bonded atoms
+            if (skip14) break;
+          }
+        } // END loop over dih->A1() bonded atoms
+        if (!skip14) {
+          // Determine if 1-4 interaction already calculated by previous dihedral.
+          // Make the lower end atom first. 
+          Ipair pair14;
+          if (dih->A1() < dih->A4()) {
+            pair14.first = dih->A1();
+            pair14.second = dih->A4();
+          } else {
+            pair14.first = dih->A4();
+            pair14.second = dih->A1();
+          }
+          Imap::const_iterator it = PairMap.find( pair14 );
+          if (it == PairMap.end()) {
+            skip14 = false;
+            PairMap.insert( pair14 );
+          } else {
             skip14 = true;
-            break;
+            //mprintf("DEBUG: Prior 1-4 calc detected.\n");
           }
-          // Loop over angles, dih->A1() - bat1 - bat2
-          for (Atom::bond_iterator bat2 = atoms_[*bat1].bondbegin();
-                                   bat2 != atoms_[*bat1].bondend(); ++bat2)
-          {
-            //if (dih->A1() == 442 && dih->A4() == 444) { // DEBUG
-            //  mprintf("DEBUG: %4i %4i %4i %4i Checking angle %4i %4i %4i\n", dih->A1()+1, dih->A2()+1, dih->A3()+1, dih->A4()+1, dih->A1()+1, *bat1 + 1, *bat2 + 1);
-            //}
-            if (*bat2 != *bat1) {
-              if (*bat2 == dih->A4()) {
-                skip14 = true;
-                break;
-              }
-            }
-          } // END loop over bat1 bonded atoms
-          if (skip14) break;
-        }
-      } // END loop over dih->A1() bonded atoms
-      if (!skip14) {
-        // Determine if 1-4 interaction already calculated by previous dihedral.
-        // Make the lower end atom first. 
-        Ipair pair14;
-        if (dih->A1() < dih->A4()) {
-          pair14.first = dih->A1();
-          pair14.second = dih->A4();
-        } else {
-          pair14.first = dih->A4();
-          pair14.second = dih->A1();
         }
-        Imap::const_iterator it = PairMap.find( pair14 );
-        if (it == PairMap.end()) {
-          skip14 = false;
-          PairMap.insert( pair14 );
-        } else {
-          skip14 = true;
-          //mprintf("DEBUG: Prior 1-4 calc detected.\n");
+        // Loop over multiplicities
+        //if (dih->A1() == 442 && dih->A4() == 444) { // DEBUG
+        //  mprintf("DEBUG: Skip14= %i\n", (int)skip14);
+        //}
+        for (DihedralParmArray::const_iterator it = dpa.begin(); it != dpa.end(); ++it) {
+          DihedralType mydih = *dih;
+          int idx = addTorsionParm( dihedralparm_, *it );
+          // If there are multiple parameters for the same dihedral, all but
+          // one of the 1-4 calcs need to be skipped.
+          if (it == dpa.begin())
+            mydih.SetSkip14(skip14);
+          else
+            mydih.SetSkip14(true);
+          mydih.SetIdx( idx );
+          dihedralsIn.push_back( mydih );
+//          mprintf("DEBUG: Assigned %4i %4i %4i %4i (%2s %2s %2s %2s) isImproper=%i skip14=%i\n",
+//            mydih.A1()+1, mydih.A2()+1, mydih.A3()+1, mydih.A4()+1,
+//            *types[0], *types[1], *types[2], *types[3],
+//            (int)mydih.IsImproper(), (int)mydih.Skip14());
         }
       }
-      //if (dih->A1() == 442 && dih->A4() == 444) { // DEBUG
-      //  mprintf("DEBUG: Skip14= %i\n", (int)skip14);
-      //}
-
-      // See if parameter already present. ----
-      std::vector<int> idxs = currentTypes.FindParam( types, found );
-      if (!found) {
-        // Not yet present in current types
-        DihedralParmArray dpa = newDihedralParams.FindParam( types, found );
-        if (!found) {
-          mprintf("Warning: Dihedral parameters not found for dihedral %s-%s-%s-%s (%s-%s-%s-%s)\n",
-                  TruncResAtomNameNum(dih->A1()).c_str(),
-                  TruncResAtomNameNum(dih->A2()).c_str(),
-                  TruncResAtomNameNum(dih->A3()).c_str(),
-                  TruncResAtomNameNum(dih->A4()).c_str(),
-                  *types[0], *types[1], *types[2], *types[3]);
-          idxs.push_back( -1 );
-        } else {
-          // Loop over multiplicities
-          for (DihedralParmArray::const_iterator it = dpa.begin(); it != dpa.end(); ++it) {
-            //int idx = addTorsionParm( dihedralparm_, *it ); // TODO handle array packing
-            int idx = (int)dihedralparm_.size();
-            dihedralparm_.push_back( *it );
-            idxs.push_back( idx );
-          } // END loop over dihedral multiplicities
-          currentTypes.AddParm(types, idxs, false);
-        } // END parameters found for this dihedral
-      }
-      // Actually add parameters for this dihedral.
-      for (std::vector<int>::const_iterator idx = idxs.begin(); idx != idxs.end(); ++idx)
-      {
-        DihedralType mydih = *dih;
-        mydih.SetImproper( false );
-        // If there are multiple parameters for the same dihedral, all but
-        // one of the 1-4 calcs need to be skipped.
-        if (idx == idxs.begin())
-          mydih.SetSkip14(skip14);
-        else
-          mydih.SetSkip14(true);
-        mydih.SetIdx( *idx );
-        dihedralsIn.push_back( mydih );
-//        mprintf("DEBUG: Assigned %4i %4i %4i %4i (%2s %2s %2s %2s) isImproper=%i skip14=%i\n",
-//                mydih.A1()+1, mydih.A2()+1, mydih.A3()+1, mydih.A4()+1,
-//                *types[0], *types[1], *types[2], *types[3],
-//                (int)mydih.IsImproper(), (int)mydih.Skip14());
-      } // END loop over dihedral parameter indices
     }
   } // END loop over all dihedrals
 }
@@ -2956,7 +3019,7 @@ int Topology::UpdateParams(ParameterSet const& set1) {
 
 /** Update/add to parameters in this topology by combining those from given sets. */
 int Topology::updateParams(ParameterSet& set0, ParameterSet const& set1) {
-  set1.Summary(); // DEBUG
+  //set1.Summary(); // DEBUG
   // Check TODO is this necessary?
   if (set0.AT().size() < 1)
     mprintf("Warning: No atom type information in '%s'\n", c_str());
@@ -2971,6 +3034,9 @@ int Topology::updateParams(ParameterSet& set0, ParameterSet const& set1) {
               c_str(), set1.ParamSetName().c_str());
     return 1;
   }
+  mprintf("DEBUG: Updated parameters.\n");
+  set0.Summary();
+  //set0.Debug();
 
 //  unsigned int updateCount;
   // Bond parameters

From 67ca80f8a21181b99b723a250f51b4b8dd9dd502 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 13 Dec 2023 10:35:49 -0500
Subject: [PATCH 0159/1492] updateparameters now packs dihedral parameters

---
 test/Test_CharmmParams/test3.parm7.save | 76 +++++++++----------------
 1 file changed, 28 insertions(+), 48 deletions(-)

diff --git a/test/Test_CharmmParams/test3.parm7.save b/test/Test_CharmmParams/test3.parm7.save
index f400305054..3a34b026b1 100644
--- a/test/Test_CharmmParams/test3.parm7.save
+++ b/test/Test_CharmmParams/test3.parm7.save
@@ -1,11 +1,11 @@
-%VERSION  VERSION_STAMP = V0001.000  DATE = 12/12/23 12:16:22                  
+%VERSION  VERSION_STAMP = V0001.000  DATE = 12/13/23 10:09:59                  
 %FLAG CTITLE                                                                    
 %FORMAT(a80)                                                                    
                                                                                 
 %FLAG POINTERS                                                                  
 %FORMAT(10I8)                                                                   
       23      12      11      11      26      12      42      19       0       0
-     114       1      11      12      19      13      22      36      12       0
+     114       1      11      12      19      13      22      19      12       0
        0       0       0       0       0       0       0       1      23       0
        0
 %FLAG FORCE_FIELD_TYPE                                                          
@@ -123,51 +123,31 @@ LYS
   8.80000000E-01  0.00000000E+00  1.90000000E+00  0.00000000E+00  6.30000000E-01
   1.00000000E-02  1.50000000E-01  1.40000000E+00  1.00000000E-01  1.50000000E-01
   1.00000000E-01  3.50000000E-01  4.20000000E-01  1.91000000E+00  1.90000000E-01
-  1.10000000E+00  2.00000000E-01  2.20000000E+00  2.00000000E-01  0.00000000E+00
-  0.00000000E+00  0.00000000E+00  1.90000000E-01  2.00000000E-01  2.00000000E-01
-  0.00000000E+00  1.90000000E-01  2.00000000E-01  1.90000000E-01  1.90000000E-01
-  2.00000000E-01  1.90000000E-01  1.90000000E-01  0.00000000E+00  0.00000000E+00
-  1.92500000E+00
+  1.10000000E+00  2.00000000E-01  2.20000000E+00  1.92500000E+00
 %FLAG DIHEDRAL_PERIODICITY                                                      
 %FORMAT(5E16.8)                                                                 
   1.00000000E+00  2.00000000E+00  3.00000000E+00  1.00000000E+00  1.00000000E+00
   2.00000000E+00  3.00000000E+00  1.00000000E+00  2.00000000E+00  4.00000000E+00
   6.00000000E+00  1.00000000E+00  2.00000000E+00  3.00000000E+00  3.00000000E+00
-  1.00000000E+00  3.00000000E+00  2.00000000E+00  3.00000000E+00  1.00000000E+00
-  1.00000000E+00  1.00000000E+00  3.00000000E+00  3.00000000E+00  3.00000000E+00
-  1.00000000E+00  3.00000000E+00  3.00000000E+00  3.00000000E+00  3.00000000E+00
-  3.00000000E+00  3.00000000E+00  3.00000000E+00  1.00000000E+00  1.00000000E+00
-  2.00000000E+00
+  1.00000000E+00  3.00000000E+00  2.00000000E+00  2.00000000E+00
 %FLAG DIHEDRAL_PHASE                                                            
 %FORMAT(5E16.8)                                                                 
   3.14159265E+00  3.14159265E+00  0.00000000E+00  0.00000000E+00  3.14159265E+00
   0.00000000E+00  0.00000000E+00  0.00000000E+00  3.14159265E+00  0.00000000E+00
   3.14159265E+00  3.14159265E+00  3.14159265E+00  3.14159265E+00  0.00000000E+00
-  3.14159265E+00  0.00000000E+00  3.14159265E+00  0.00000000E+00  0.00000000E+00
-  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
-  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
-  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
-  3.14159265E+00
+  3.14159265E+00  0.00000000E+00  3.14159265E+00  3.14159265E+00
 %FLAG SCEE_SCALE_FACTOR                                                         
 %FORMAT(5E16.8)                                                                 
   1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00
   1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00
   1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00
-  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00
-  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00
-  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00
-  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00
-  1.00000000E+00
+  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00
 %FLAG SCNB_SCALE_FACTOR                                                         
 %FORMAT(5E16.8)                                                                 
   1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00
   1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00
   1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00
-  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00
-  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00
-  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00
-  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00
-  1.00000000E+00
+  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00
 %FLAG CHARMM_NUM_IMPROPERS                                                      
 %FORMAT(10I8)                                                                   
        1
@@ -334,27 +314,27 @@ LYS
       48      54      60       9      57      54      60      10
 %FLAG DIHEDRALS_INC_HYDROGEN                                                    
 %FORMAT(10I8)                                                                   
-       0       6      12      15      19       0       6      12      18      19
-       3       0       6       9      20       3       0       6      12      21
-       3       0       6      63      22       6      12      21      24      23
-       6      12      21      27      23       9       6      12      15      24
-       9       6      12      18      24       9       6      12      21      25
-       9       6      63      66      26      12      21      30      33      27
-      12      21      30      36      27      15      12       6      63      28
-      15      12      21      24      29      15      12      21      27      29
-      15      12      21      30      27      18      12       6      63      28
-      18      12      21      24      29      18      12      21      27      29
-      18      12      21      30      27      21      30      39      42      30
-      21      30      39      45      30      24      21      30      33      29
-      24      21      30      36      29      24      21      30      39      27
-      27      21      30      33      29      27      21      30      36      29
-      27      21      30      39      27      30      39      48      51      31
-      33      30      39      42      32      33      30      39      45      32
-      33      30      39      48      33      36      30      39      42      32
-      36      30      39      45      32      36      30      39      48      33
-      42      39      48      51      34      45      39      48      51      34
-      42      39      48      54      35      45      39      48      54      35
-      51      48      54      57      36      51      48      54      60      36
+       0       6      12      15      17       0       6      12      18      17
+       3       0       6       9       4       3       0       6      12       4
+       3       0       6      63       4       6      12      21      24      15
+       6      12      21      27      15       9       6      12      15      17
+       9       6      12      18      17       9       6      12      21      17
+       9       6      63      66       4      12      21      30      33      15
+      12      21      30      36      15      15      12       6      63      17
+      15      12      21      24      15      15      12      21      27      15
+      15      12      21      30      15      18      12       6      63      17
+      18      12      21      24      15      18      12      21      27      15
+      18      12      21      30      15      21      30      39      42      15
+      21      30      39      45      15      24      21      30      33      15
+      24      21      30      36      15      24      21      30      39      15
+      27      21      30      33      15      27      21      30      36      15
+      27      21      30      39      15      30      39      48      51      17
+      33      30      39      42      15      33      30      39      45      15
+      33      30      39      48      15      36      30      39      42      15
+      36      30      39      45      15      36      30      39      48      15
+      42      39      48      51       4      45      39      48      51       4
+      42      39      48      54       4      45      39      48      54       4
+      51      48      54      57      19      51      48      54      60      19
 %FLAG DIHEDRALS_WITHOUT_HYDROGEN                                                
 %FORMAT(10I8)                                                                   
        0       6      12      21       1       0       6     -12      21       2

From 729af660ee265ec3e3e4e60420b5b550679df9f8 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 13 Dec 2023 11:01:56 -0500
Subject: [PATCH 0160/1492] New topology with better parameter assignment

---
 test/Test_CombineCrd/combinedParm.parm7.save | 781 ++++++++++---------
 1 file changed, 402 insertions(+), 379 deletions(-)

diff --git a/test/Test_CombineCrd/combinedParm.parm7.save b/test/Test_CombineCrd/combinedParm.parm7.save
index f04e266dab..bd4a9fa073 100644
--- a/test/Test_CombineCrd/combinedParm.parm7.save
+++ b/test/Test_CombineCrd/combinedParm.parm7.save
@@ -1,11 +1,11 @@
-%VERSION  VERSION_STAMP = V0001.000  DATE = 08/18/20 18:40:07                  
+%VERSION  VERSION_STAMP = V0001.000  DATE = 12/13/23 10:11:18                  
 %FLAG TITLE                                                                     
 %FORMAT(20a4)                                                                   
 combinedParm                                                                    
 %FLAG POINTERS                                                                  
 %FORMAT(10I8)                                                                   
      244      14     111     141     246     194     511     408       0       0
-    1327      14     141     194     408      26      38      37       0       0
+    1327      14     141     194     408      37      75      37      27       0
        0       0       0       0       0       0       0       2      24       0
        0
 %FLAG ATOM_NAME                                                                 
@@ -238,39 +238,57 @@ SER TRP THR TRP GLU ASN GLY LYS TRP THR TRP LYS NHE TCS
 %FLAG BOND_FORCE_CONSTANT                                                       
 %FORMAT(5E16.8)                                                                 
   5.70000000E+02  4.90000000E+02  3.20000000E+02  3.10000000E+02  3.17000000E+02
-  3.67000000E+02  4.69000000E+02  4.69000000E+02  4.47000000E+02  4.28000000E+02
-  4.27000000E+02  5.46000000E+02  3.88000000E+02  3.17000000E+02  3.37000000E+02
-  6.56000000E+02  5.53000000E+02  3.40000000E+02  4.34000000E+02  3.67000000E+02
-  4.78400000E+02  3.22800000E+02  3.72400000E+02  3.86100000E+02  3.44300000E+02
-  3.69600000E+02
+  3.67000000E+02  4.69000000E+02  4.69000000E+02  4.69000000E+02  4.47000000E+02
+  4.28000000E+02  4.27000000E+02  5.46000000E+02  3.88000000E+02  3.17000000E+02
+  3.37000000E+02  3.10000000E+02  6.56000000E+02  3.17000000E+02  3.67000000E+02
+  4.78400000E+02  3.22800000E+02  3.72400000E+02  3.86100000E+02  5.53000000E+02
+  3.40000000E+02  3.40000000E+02  4.34000000E+02  3.67000000E+02  4.34000000E+02
+  3.67000000E+02  3.40000000E+02  3.40000000E+02  4.34000000E+02  3.40000000E+02
+  3.44300000E+02  3.69600000E+02
 %FLAG BOND_EQUIL_VALUE                                                          
 %FORMAT(5E16.8)                                                                 
   1.22900000E+00  1.33500000E+00  1.41000000E+00  1.52600000E+00  1.52200000E+00
-  1.47100000E+00  1.40400000E+00  1.40000000E+00  1.41900000E+00  1.38000000E+00
-  1.38100000E+00  1.35200000E+00  1.45900000E+00  1.49500000E+00  1.44900000E+00
-  1.25000000E+00  9.60000000E-01  1.09000000E+00  1.01000000E+00  1.08000000E+00
-  1.38700000E+00  1.72900000E+00  1.37300000E+00  1.36200000E+00  1.08700000E+00
-  9.74000000E-01
+  1.47100000E+00  1.40400000E+00  1.40000000E+00  1.40000000E+00  1.41900000E+00
+  1.38000000E+00  1.38100000E+00  1.35200000E+00  1.45900000E+00  1.49500000E+00
+  1.44900000E+00  1.52600000E+00  1.25000000E+00  1.52200000E+00  1.47100000E+00
+  1.38700000E+00  1.72900000E+00  1.37300000E+00  1.36200000E+00  9.60000000E-01
+  1.09000000E+00  1.09000000E+00  1.01000000E+00  1.08000000E+00  1.01000000E+00
+  1.08000000E+00  1.09000000E+00  1.09000000E+00  1.01000000E+00  1.09000000E+00
+  1.08700000E+00  9.74000000E-01
 %FLAG ANGLE_FORCE_CONSTANT                                                      
 %FORMAT(5E16.8)                                                                 
   8.00000000E+01  5.00000000E+01  6.30000000E+01  5.00000000E+01  8.00000000E+01
-  7.00000000E+01  8.00000000E+01  6.30000000E+01  6.30000000E+01  6.30000000E+01
-  7.00000000E+01  7.00000000E+01  6.30000000E+01  7.00000000E+01  7.00000000E+01
-  6.30000000E+01  6.30000000E+01  7.00000000E+01  7.00000000E+01  6.30000000E+01
-  8.00000000E+01  6.30000000E+01  4.00000000E+01  8.00000000E+01  7.00000000E+01
-  5.00000000E+01  3.50000000E+01  5.50000000E+01  5.00000000E+01  5.00000000E+01
-  3.50000000E+01  6.29200000E+01  6.71800000E+01  6.97900000E+01  6.98500000E+01
-  6.33100000E+01  4.84600000E+01  4.88500000E+01
+  7.00000000E+01  8.00000000E+01  8.00000000E+01  6.30000000E+01  6.30000000E+01
+  6.30000000E+01  6.30000000E+01  6.30000000E+01  7.00000000E+01  7.00000000E+01
+  6.30000000E+01  7.00000000E+01  7.00000000E+01  6.30000000E+01  6.30000000E+01
+  7.00000000E+01  7.00000000E+01  6.30000000E+01  8.00000000E+01  6.30000000E+01
+  5.00000000E+01  4.00000000E+01  8.00000000E+01  7.00000000E+01  6.30000000E+01
+  8.00000000E+01  7.00000000E+01  6.30000000E+01  8.00000000E+01  4.00000000E+01
+  6.29200000E+01  6.71800000E+01  6.97900000E+01  6.98500000E+01  6.33100000E+01
+  5.00000000E+01  5.00000000E+01  3.50000000E+01  5.50000000E+01  5.00000000E+01
+  5.00000000E+01  5.00000000E+01  5.00000000E+01  3.50000000E+01  5.00000000E+01
+  5.00000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01
+  5.00000000E+01  5.00000000E+01  5.00000000E+01  3.50000000E+01  5.00000000E+01
+  5.00000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01
+  5.00000000E+01  5.00000000E+01  3.50000000E+01  3.50000000E+01  5.00000000E+01
+  3.50000000E+01  5.00000000E+01  5.00000000E+01  4.84600000E+01  4.88500000E+01
 %FLAG ANGLE_EQUIL_VALUE                                                         
 %FORMAT(5E16.8)                                                                 
   2.14501057E+00  2.12755727E+00  1.93906163E+00  1.91113635E+00  2.10137732E+00
-  2.03505478E+00  1.94080696E+00  2.09439600E+00  2.14151991E+00  2.02807346E+00
-  2.31779824E+00  1.82212452E+00  1.85703112E+00  1.94778828E+00  1.89717371E+00
-  1.89891904E+00  2.35445017E+00  2.18166250E+00  2.24449438E+00  2.01760148E+00
-  1.91462701E+00  1.92160833E+00  1.91113635E+00  2.19911580E+00  2.04203610E+00
-  2.09439600E+00  1.91113635E+00  1.89368305E+00  2.14850123E+00  2.06018753E+00
-  2.09439600E+00  2.08392402E+00  2.09387240E+00  2.08043336E+00  2.09334880E+00
-  2.09352334E+00  2.09457053E+00  1.91061275E+00
+  2.03505478E+00  1.94080696E+00  1.94080696E+00  2.09439600E+00  2.09439600E+00
+  2.14151991E+00  2.09439600E+00  2.02807346E+00  2.31779824E+00  1.82212452E+00
+  1.85703112E+00  1.94778828E+00  1.89717371E+00  1.89891904E+00  2.35445017E+00
+  2.18166250E+00  2.24449438E+00  2.01760148E+00  1.91462701E+00  1.92160833E+00
+  1.91113635E+00  1.91113635E+00  2.19911580E+00  2.04203610E+00  1.93906163E+00
+  2.10137732E+00  2.03505478E+00  1.93906163E+00  1.94080696E+00  1.91113635E+00
+  2.08392402E+00  2.09387240E+00  2.08043336E+00  2.09334880E+00  2.09352334E+00
+  2.09439600E+00  1.91113635E+00  1.91113635E+00  1.89368305E+00  1.91113635E+00
+  1.91113635E+00  1.91113635E+00  1.91113635E+00  1.91113635E+00  1.91113635E+00
+  2.09439600E+00  2.09439600E+00  2.09439600E+00  2.14850123E+00  2.09439600E+00
+  2.09439600E+00  2.09439600E+00  1.91113635E+00  1.91113635E+00  1.91113635E+00
+  1.91113635E+00  1.91113635E+00  2.06018753E+00  1.91113635E+00  1.91113635E+00
+  1.91113635E+00  1.91113635E+00  2.09439600E+00  1.91113635E+00  1.91113635E+00
+  1.91113635E+00  1.91113635E+00  1.91113635E+00  2.09457053E+00  1.91061275E+00
 %FLAG DIHEDRAL_FORCE_CONSTANT                                                   
 %FORMAT(5E16.8)                                                                 
   2.50000000E+00  2.00000000E+00  2.00000000E+00  4.00000000E-01  0.00000000E+00
@@ -278,9 +296,9 @@ SER TRP THR TRP GLU ASN GLY LYS TRP THR TRP LYS NHE TCS
   2.00000000E-01  2.00000000E-01  3.62500000E+00  3.00000000E+00  3.50000000E+00
   6.52500000E+00  1.67500000E+00  1.52500000E+00  1.50000000E+00  4.50000000E-01
   1.58000000E+00  5.50000000E-01  2.00000000E-01  2.50000000E-01  1.80000000E-01
-  1.05000000E+01  1.10000000E+00  1.66666667E-01  2.50000000E-01  1.60000000E-01
-  8.00000000E-01  8.00000000E-02  0.00000000E+00  1.50000000E-01  1.00000000E+00
-  9.00000000E-01  1.10000000E+00
+  1.05000000E+01  1.10000000E+00  9.00000000E-01  1.10000000E+00  1.66666667E-01
+  2.50000000E-01  1.60000000E-01  8.00000000E-01  8.00000000E-02  0.00000000E+00
+  1.50000000E-01  1.00000000E+00
 %FLAG DIHEDRAL_PERIODICITY                                                      
 %FORMAT(5E16.8)                                                                 
   2.00000000E+00  1.00000000E+00  2.00000000E+00  3.00000000E+00  4.00000000E+00
@@ -288,9 +306,9 @@ SER TRP THR TRP GLU ASN GLY LYS TRP THR TRP LYS NHE TCS
   1.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
   2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  1.00000000E+00
   2.00000000E+00  3.00000000E+00  1.00000000E+00  2.00000000E+00  3.00000000E+00
-  2.00000000E+00  2.00000000E+00  3.00000000E+00  1.00000000E+00  3.00000000E+00
-  1.00000000E+00  3.00000000E+00  3.00000000E+00  3.00000000E+00  2.00000000E+00
-  2.00000000E+00  2.00000000E+00
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  3.00000000E+00
+  1.00000000E+00  3.00000000E+00  1.00000000E+00  3.00000000E+00  3.00000000E+00
+  3.00000000E+00  2.00000000E+00
 %FLAG DIHEDRAL_PHASE                                                            
 %FORMAT(5E16.8)                                                                 
   3.14159400E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
@@ -298,9 +316,9 @@ SER TRP THR TRP GLU ASN GLY LYS TRP THR TRP LYS NHE TCS
   0.00000000E+00  0.00000000E+00  3.14159400E+00  3.14159400E+00  3.14159400E+00
   3.14159400E+00  3.14159400E+00  3.14159400E+00  3.14159400E+00  3.14159400E+00
   3.14159400E+00  3.14159400E+00  3.14159400E+00  3.14159400E+00  0.00000000E+00
-  3.14159400E+00  3.14159400E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
-  0.00000000E+00  3.14159400E+00  0.00000000E+00  0.00000000E+00  3.14159400E+00
-  3.14159400E+00  3.14159400E+00
+  3.14159400E+00  3.14159400E+00  3.14159400E+00  3.14159400E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  3.14159400E+00  0.00000000E+00
+  0.00000000E+00  3.14159400E+00
 %FLAG SCEE_SCALE_FACTOR                                                         
 %FORMAT(5E16.8)                                                                 
   1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00
@@ -309,8 +327,8 @@ SER TRP THR TRP GLU ASN GLY LYS TRP THR TRP LYS NHE TCS
   1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00
   1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00
   0.00000000E+00  0.00000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00
-  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00  0.00000000E+00
-  1.20000000E+00  1.20000000E+00
+  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00
+  1.20000000E+00  0.00000000E+00
 %FLAG SCNB_SCALE_FACTOR                                                         
 %FORMAT(5E16.8)                                                                 
   2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
@@ -319,132 +337,137 @@ SER TRP THR TRP GLU ASN GLY LYS TRP THR TRP LYS NHE TCS
   2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
   2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
   0.00000000E+00  0.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
-  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  0.00000000E+00
-  2.00000000E+00  2.00000000E+00
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  2.00000000E+00  0.00000000E+00
 %FLAG SOLTY                                                                     
 %FORMAT(5E16.8)                                                                 
-
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00
 %FLAG LENNARD_JONES_ACOEF                                                       
 %FORMAT(5E16.8)                                                                 
   9.44293233E+05  2.12601181E+03  1.39982777E-01  9.95480466E+05  2.56678134E+03
   1.04308023E+06  2.01791425E+04  9.14716912E+00  2.27401052E+04  2.01823541E+02
   6.20665997E+04  5.94667300E+01  6.78771368E+04  8.79040886E+02  3.25969625E+03
-  7.44975864E+05  1.40467023E+03  7.91544157E+05  1.45985502E+04  4.66922514E+04
+  7.44975864E+05  1.40467023E+03  7.91544156E+05  1.45985502E+04  4.66922514E+04
   5.81803229E+05  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
-  0.00000000E+00  0.00000000E+00  0.00000000E+00  8.82619071E+05  2.27577561E+03
-  9.24822270E+05  2.01619733E+04  6.01816484E+04  7.01803794E+05  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  8.82619071E+05  2.27577560E+03
+  9.24822269E+05  2.01619733E+04  6.01816484E+04  7.01803794E+05  0.00000000E+00
   8.19971662E+05  6.06829342E+05  1.02595236E+03  6.47841731E+05  1.12780457E+04
   3.69471530E+04  4.71003287E+05  0.00000000E+00  5.74393458E+05  3.79876399E+05
   8.96776989E+04  1.07193646E+02  9.71708117E+04  1.41077189E+03  4.98586848E+03
   6.82786631E+04  0.00000000E+00  8.61541883E+04  5.44261042E+04  7.51607703E+03
   6.58473870E+04  6.63368273E+01  7.18621074E+04  9.55000044E+02  3.50301067E+03
-  4.96707306E+04  0.00000000E+00  6.37148278E+04  3.93690817E+04  5.34045360E+03
-  3.76169105E+03  7.91627154E+04  8.90987508E+01  8.59947003E+04  1.21014911E+03
-  4.33325458E+03  6.00750218E+04  0.00000000E+00  7.62451550E+04  4.77908183E+04
+  4.96707305E+04  0.00000000E+00  6.37148277E+04  3.93690817E+04  5.34045360E+03
+  3.76169105E+03  7.91627155E+04  8.90987508E+01  8.59947003E+04  1.21014911E+03
+  4.33325458E+03  6.00750218E+04  0.00000000E+00  7.62451550E+04  4.77908184E+04
   6.55825601E+03  4.64559155E+03  5.71629601E+03  5.89818288E+05  1.03954408E+03
   6.28541239E+05  1.11851919E+04  3.63097246E+04  4.58874091E+05  0.00000000E+00
   5.57281136E+05  3.70622491E+05  5.33379252E+04  3.86654992E+04  4.68711055E+04
   3.61397723E+05  1.76079018E+06  4.83020817E+03  1.83982239E+06  4.14717456E+04
   1.22102013E+05  1.40513595E+06  0.00000000E+00  1.63123475E+06  1.15256113E+06
-  1.74057868E+05  1.29147101E+05  1.54217682E+05  1.11729277E+06  3.24095688E+06
+  1.74057868E+05  1.29147101E+05  1.54217681E+05  1.11729277E+06  3.24095688E+06
 %FLAG LENNARD_JONES_BCOEF                                                       
 %FORMAT(5E16.8)                                                                 
   8.01323529E+02  2.09604198E+01  9.37598976E-02  7.36907417E+02  2.06278363E+01
   6.75612247E+02  6.45756063E+01  7.57919667E-01  6.13981767E+01  3.56012899E+00
   1.13252061E+02  1.93248820E+00  1.06076943E+02  7.42992380E+00  1.43076527E+01
-  7.50714425E+02  1.79702257E+01  6.93079947E+02  5.79323581E+01  1.03606917E+02
+  7.50714426E+02  1.79702257E+01  6.93079947E+02  5.79323582E+01  1.03606917E+02
   6.99746810E+02  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
   0.00000000E+00  0.00000000E+00  0.00000000E+00  6.53361429E+02  1.82891803E+01
-  5.99015525E+02  5.44372326E+01  9.40505980E+01  6.14502845E+02  0.00000000E+00
+  5.99015525E+02  5.44372327E+01  9.40505981E+01  6.14502845E+02  0.00000000E+00
   5.31102864E+02  6.77220874E+02  1.53505284E+01  6.26720080E+02  5.08951803E+01
-  9.21192136E+01  6.29300710E+02  0.00000000E+00  5.55666448E+02  5.64885984E+02
+  9.21192136E+01  6.29300711E+02  0.00000000E+00  5.55666449E+02  5.64885984E+02
   1.36131731E+02  2.59456373E+00  1.26919150E+02  9.41257003E+00  1.76949863E+01
-  1.25287818E+02  0.00000000E+00  1.12529845E+02  1.11805549E+02  2.17257828E+01
+  1.25287819E+02  0.00000000E+00  1.12529845E+02  1.11805549E+02  2.17257828E+01
   1.15327881E+02  2.01792524E+00  1.07908863E+02  7.65648470E+00  1.46638650E+01
-  1.05648788E+02  0.00000000E+00  9.56748258E+01  9.40124296E+01  1.81057616E+01
-  1.50233639E+01  1.26451907E+02  2.33864085E+00  1.18043746E+02  8.61880722E+00
+  1.05648788E+02  0.00000000E+00  9.56748257E+01  9.40124296E+01  1.81057616E+01
+  1.50233639E+01  1.26451907E+02  2.33864085E+00  1.18043747E+02  8.61880723E+00
   1.63092814E+01  1.16187983E+02  0.00000000E+00  1.04660679E+02  1.03580945E+02
   2.00642027E+01  1.66953734E+01  1.85196588E+01  6.33305958E+02  1.46567808E+01
   5.85549272E+02  4.80771660E+01  8.66220818E+01  5.89183300E+02  0.00000000E+00
-  5.19163331E+02  5.29252520E+02  1.04986921E+02  8.83744760E+01  9.73010753E+01
+  5.19163331E+02  5.29252520E+02  1.04986921E+02  8.83744760E+01  9.73010751E+01
   4.95732238E+02  1.22266505E+03  3.53019992E+01  1.11939598E+03  1.03440958E+02
   1.77491594E+02  1.15202544E+03  0.00000000E+00  9.92485818E+02  1.04286543E+03
   2.11915736E+02  1.80470661E+02  1.97211104E+02  9.73951183E+02  1.85348706E+03
 %FLAG BONDS_INC_HYDROGEN                                                        
 %FORMAT(10I8)                                                                   
-      27      30      17      18      21      18      18      24      18      12
-      15      18       0       3      19       0       6      19       0       9
-      19      96      99      20      90      93      20      84      87      20
-      78      81      20      69      72      19      63      66      20      51
-      54      18      51      57      18      45      48      18      39      42
-      19     141     144      17     129     132      18     129     135      18
-     129     138      18     123     126      18     117     120      18     111
-     114      19     210     213      20     204     207      20     198     201
-      20     192     195      20     183     186      19     177     180      20
-     165     168      18     165     171      18     159     162      18     153
-     156      19     246     249      18     246     252      18     237     240
-      18     237     243      18     231     234      18     225     228      19
-     297     300      19     297     303      19     282     285      18     282
-     288      18     276     279      18     270     273      19     318     321
-      18     318     324      18     312     315      19     381     384      19
-     381     387      19     381     390      19     372     375      18     372
-     378      18     363     366      18     363     369      18     354     357
-      18     354     360      18     345     348      18     345     351      18
-     339     342      18     333     336      19     456     459      20     450
-     453      20     444     447      20     438     441      20     429     432
-      19     423     426      20     411     414      18     411     417      18
-     405     408      18     399     402      19     501     504      17     489
-     492      18     489     495      18     489     498      18     483     486
-      18     477     480      18     471     474      19     570     573      20
-     564     567      20     558     561      20     552     555      20     543
-     546      19     537     540      20     525     528      18     525     531
-      18     519     522      18     513     516      19     633     636      19
-     633     639      19     633     642      19     624     627      18     624
-     630      18     615     618      18     615     621      18     606     609
-      18     606     612      18     597     600      18     597     603      18
-     591     594      18     585     588      19     651     654      19     651
-     657      19     699     729      25     696     726      25     690     723
-      25     681     720      26     675     717      25     672     714      25
-     666     711      25
+      27      30      25      18      21      26      18      24      26      12
+      15      27       0       3      28       0       6      28       0       9
+      28      96      99      29      90      93      29      84      87      29
+      78      81      29      69      72      30      63      66      31      51
+      54      32      51      57      32      45      48      33      39      42
+      34     141     144      25     129     132      32     129     135      32
+     129     138      32     123     126      26     117     120      33     111
+     114      34     210     213      29     204     207      29     198     201
+      29     192     195      29     183     186      30     177     180      31
+     165     168      32     165     171      32     159     162      33     153
+     156      34     246     249      32     246     252      32     237     240
+      32     237     243      32     231     234      33     225     228      34
+     297     300      34     297     303      34     282     285      32     282
+     288      32     276     279      33     270     273      34     318     321
+      33     318     324      33     312     315      34     381     384      28
+     381     387      28     381     390      28     372     375      35     372
+     378      35     363     366      32     363     369      32     354     357
+      32     354     360      32     345     348      32     345     351      32
+     339     342      33     333     336      34     456     459      29     450
+     453      29     444     447      29     438     441      29     429     432
+      30     423     426      31     411     414      32     411     417      32
+     405     408      33     399     402      34     501     504      25     489
+     492      32     489     495      32     489     498      32     483     486
+      26     477     480      33     471     474      34     570     573      29
+     564     567      29     558     561      29     552     555      29     543
+     546      30     537     540      31     525     528      32     525     531
+      32     519     522      33     513     516      34     633     636      28
+     633     639      28     633     642      28     624     627      35     624
+     630      35     615     618      32     615     621      32     606     609
+      32     606     612      32     597     600      32     597     603      32
+     591     594      33     585     588      34     651     654      34     651
+     657      34     699     729      36     696     726      36     690     723
+      36     681     720      37     675     717      36     672     714      36
+     666     711      36
 %FLAG BONDS_WITHOUT_HYDROGEN                                                    
 %FORMAT(10I8)                                                                   
       33      36       1      33      39       2      18      27       3      12
       18       4      12      33       5       0      12       6     105     108
        1     105     111       2      96     102       7      90      96       8
-      84      90       8      78      84       8      75      78       8      75
-     102       9      69      75      10      63      69      11      60      63
-      12      60     102      13      51      60      14      45      51       4
-      45     105       5      39      45      15     147     150       1     147
-     153       2     123     129       4     123     141       3     117     123
-       4     117     147       5     111     117      15     219     222       1
+      84      90       8      78      84       8      75      78       9      75
+     102      10      69      75      11      63      69      12      60      63
+      13      60     102      14      51      60      15      45      51       4
+      45     105       5      39      45      16     147     150       1     147
+     153       2     123     129      17     123     141       3     117     123
+       4     117     147       5     111     117      16     219     222       1
      219     225       2     210     216       7     204     210       8     198
-     204       8     192     198       8     189     192       8     189     216
-       9     183     189      10     177     183      11     174     177      12
-     174     216      13     165     174      14     159     165       4     159
-     219       5     153     159      15     264     267       1     264     270
-       2     255     258      16     255     261      16     246     255       5
-     237     246       4     231     237       4     231     264       5     225
-     231      15     306     309       1     306     312       2     291     294
-       1     291     297       2     282     291       5     276     282       4
-     276     306       5     270     276      15     327     330       1     327
-     333       2     318     327       5     312     318      15     393     396
-       1     393     399       2     372     381       6     363     372       4
-     354     363       4     345     354       4     339     345       4     339
-     393       5     333     339      15     465     468       1     465     471
+     204       8     192     198       8     189     192       9     189     216
+      10     183     189      11     177     183      12     174     177      13
+     174     216      14     165     174      15     159     165       4     159
+     219       5     153     159      16     264     267       1     264     270
+       2     255     258      18     255     261      18     246     255      19
+     237     246      17     231     237       4     231     264       5     225
+     231      16     306     309       1     306     312       2     291     294
+       1     291     297       2     282     291      19     276     282       4
+     276     306       5     270     276      16     327     330       1     327
+     333       2     318     327       5     312     318      16     393     396
+       1     393     399       2     372     381      20     363     372      17
+     354     363      17     345     354      17     339     345       4     339
+     393       5     333     339      16     465     468       1     465     471
        2     456     462       7     450     456       8     444     450       8
-     438     444       8     435     438       8     435     462       9     429
-     435      10     423     429      11     420     423      12     420     462
-      13     411     420      14     405     411       4     405     465       5
-     399     405      15     507     510       1     507     513       2     483
-     489       4     483     501       3     477     483       4     477     507
-       5     471     477      15     579     582       1     579     585       2
+     438     444       8     435     438       9     435     462      10     429
+     435      11     423     429      12     420     423      13     420     462
+      14     411     420      15     405     411       4     405     465       5
+     399     405      16     507     510       1     507     513       2     483
+     489      17     483     501       3     477     483       4     477     507
+       5     471     477      16     579     582       1     579     585       2
      570     576       7     564     570       8     558     564       8     552
-     558       8     549     552       8     549     576       9     543     549
-      10     537     543      11     534     537      12     534     576      13
-     525     534      14     519     525       4     519     579       5     513
-     519      15     645     648       1     645     651       2     624     633
-       6     615     624       4     606     615       4     597     606       4
-     591     597       4     591     645       5     585     591      15     696
+     558       8     549     552       9     549     576      10     543     549
+      11     537     543      12     534     537      13     534     576      14
+     525     534      15     519     525       4     519     579       5     513
+     519      16     645     648       1     645     651       2     624     633
+      20     615     624      17     606     615      17     597     606      17
+     591     597       4     591     645       5     585     591      16     696
      699      21     693     696      21     693     705      22     690     693
       21     687     690      21     687     702      22     684     687      21
      684     699      21     678     684      23     672     675      21     669
@@ -453,194 +476,194 @@ SER TRP THR TRP GLU ASN GLY LYS TRP THR TRP LYS NHE TCS
      660     678      23
 %FLAG ANGLES_INC_HYDROGEN                                                       
 %FORMAT(10I8)                                                                   
-      33      39      42      26      24      18      27       4      21      18
-      24      27      21      18      27       4      18      27      30      28
-      15      12      18       4      15      12      33       4      12      18
-      21       4      12      18      24       4       9       0      12       4
-       6       0       9      27       6       0      12       4       3       0
-       6      27       3       0       9      27       3       0      12       4
-       0      12      15       4     105     111     114      26      99      96
-     102      26      93      90      96      26      90      96      99      26
-      87      84      90      26      84      90      93      26      81      78
-      84      26      78      84      87      26      75      78      81      26
-      72      69      75      29      66      63      69      26      63      69
-      72      26      60      63      66      26      57      51      60       4
-      54      51      57      27      54      51      60       4      48      45
-      51       4      48      45     105       4      45      51      54       4
-      45      51      57       4      42      39      45      30      39      45
-      48       4     147     153     156      26     135     129     138      27
-     132     129     135      27     132     129     138      27     126     123
-     129       4     126     123     141       4     123     129     132       4
-     123     129     135       4     123     129     138       4     123     141
-     144      28     120     117     123       4     120     117     147       4
-     117     123     126       4     114     111     117      30     111     117
-     120       4     219     225     228      26     213     210     216      26
-     207     204     210      26     204     210     213      26     201     198
-     204      26     198     204     207      26     195     192     198      26
-     192     198     201      26     189     192     195      26     186     183
-     189      29     180     177     183      26     177     183     186      26
-     174     177     180      26     171     165     174       4     168     165
-     171      27     168     165     174       4     162     159     165       4
-     162     159     219       4     159     165     168       4     159     165
-     171       4     156     153     159      30     153     159     162       4
-     264     270     273      26     252     246     255       4     249     246
-     252      27     249     246     255       4     243     237     246       4
-     240     237     243      27     240     237     246       4     237     246
-     249       4     237     246     252       4     234     231     237       4
-     234     231     264       4     231     237     240       4     231     237
-     243       4     228     225     231      30     225     231     234       4
-     306     312     315      26     300     297     303      31     291     297
-     300      26     291     297     303      26     288     282     291       4
-     285     282     288      27     285     282     291       4     279     276
-     282       4     279     276     306       4     276     282     285       4
-     276     282     288       4     273     270     276      30     270     276
-     279       4     327     333     336      26     324     318     327       4
-     321     318     324      27     321     318     327       4     315     312
-     318      30     312     318     321       4     312     318     324       4
-     393     399     402      26     387     381     390      27     384     381
-     387      27     384     381     390      27     378     372     381       4
-     375     372     378      27     375     372     381       4     372     381
-     384       4     372     381     387       4     372     381     390       4
-     369     363     372       4     366     363     369      27     366     363
-     372       4     363     372     375       4     363     372     378       4
-     360     354     363       4     357     354     360      27     357     354
-     363       4     354     363     366       4     354     363     369       4
-     351     345     354       4     348     345     351      27     348     345
-     354       4     345     354     357       4     345     354     360       4
-     342     339     345       4     342     339     393       4     339     345
-     348       4     339     345     351       4     336     333     339      30
-     333     339     342       4     465     471     474      26     459     456
-     462      26     453     450     456      26     450     456     459      26
-     447     444     450      26     444     450     453      26     441     438
-     444      26     438     444     447      26     435     438     441      26
-     432     429     435      29     426     423     429      26     423     429
-     432      26     420     423     426      26     417     411     420       4
-     414     411     417      27     414     411     420       4     408     405
-     411       4     408     405     465       4     405     411     414       4
-     405     411     417       4     402     399     405      30     399     405
-     408       4     507     513     516      26     495     489     498      27
-     492     489     495      27     492     489     498      27     486     483
-     489       4     486     483     501       4     483     489     492       4
-     483     489     495       4     483     489     498       4     483     501
-     504      28     480     477     483       4     480     477     507       4
-     477     483     486       4     474     471     477      30     471     477
-     480       4     579     585     588      26     573     570     576      26
-     567     564     570      26     564     570     573      26     561     558
-     564      26     558     564     567      26     555     552     558      26
-     552     558     561      26     549     552     555      26     546     543
-     549      29     540     537     543      26     537     543     546      26
-     534     537     540      26     531     525     534       4     528     525
-     531      27     528     525     534       4     522     519     525       4
-     522     519     579       4     519     525     528       4     519     525
-     531       4     516     513     519      30     513     519     522       4
-     645     651     654      26     645     651     657      26     639     633
-     642      27     636     633     639      27     636     633     642      27
-     630     624     633       4     627     624     630      27     627     624
-     633       4     624     633     636       4     624     633     639       4
-     624     633     642       4     621     615     624       4     618     615
-     621      27     618     615     624       4     615     624     627       4
-     615     624     630       4     612     606     615       4     609     606
-     612      27     609     606     615       4     606     615     618       4
-     606     615     621       4     603     597     606       4     600     597
-     603      27     600     597     606       4     597     606     609       4
-     597     606     612       4     594     591     597       4     594     591
-     645       4     591     597     600       4     591     597     603       4
-     588     585     591      30     585     591     594       4     654     651
-     657      31     699     696     726      37     696     699     729      37
-     693     690     723      37     693     696     726      37     687     690
-     723      37     684     699     729      37     675     672     714      37
-     672     675     717      37     669     666     711      37     669     672
-     714      37     663     666     711      37     663     681     720      38
-     660     675     717      37
+      33      39      42      41      24      18      27      42      21      18
+      24      43      21      18      27      42      18      27      30      44
+      15      12      18      45      15      12      33      46      12      18
+      21      47      12      18      24      47       9       0      12      48
+       6       0       9      49       6       0      12      48       3       0
+       6      49       3       0       9      49       3       0      12      48
+       0      12      15      50     105     111     114      41      99      96
+     102      51      93      90      96      52      90      96      99      52
+      87      84      90      52      84      90      93      52      81      78
+      84      52      78      84      87      52      75      78      81      53
+      72      69      75      54      66      63      69      55      63      69
+      72      56      60      63      66      57      57      51      60      58
+      54      51      57      59      54      51      60      58      48      45
+      51      60      48      45     105      61      45      51      54      62
+      45      51      57      62      42      39      45      63      39      45
+      48      64     147     153     156      41     135     129     138      59
+     132     129     135      59     132     129     138      59     126     123
+     129      65     126     123     141      42     123     129     132      66
+     123     129     135      66     123     129     138      66     123     141
+     144      44     120     117     123      60     120     117     147      61
+     117     123     126      47     114     111     117      63     111     117
+     120      64     219     225     228      41     213     210     216      51
+     207     204     210      52     204     210     213      52     201     198
+     204      52     198     204     207      52     195     192     198      52
+     192     198     201      52     189     192     195      53     186     183
+     189      54     180     177     183      55     177     183     186      56
+     174     177     180      57     171     165     174      58     168     165
+     171      59     168     165     174      58     162     159     165      60
+     162     159     219      61     159     165     168      62     159     165
+     171      62     156     153     159      63     153     159     162      64
+     264     270     273      41     252     246     255      67     249     246
+     252      59     249     246     255      67     243     237     246      66
+     240     237     243      59     240     237     246      66     237     246
+     249      66     237     246     252      66     234     231     237      60
+     234     231     264      61     231     237     240      62     231     237
+     243      62     228     225     231      63     225     231     234      64
+     306     312     315      41     300     297     303      68     291     297
+     300      41     291     297     303      41     288     282     291      67
+     285     282     288      59     285     282     291      67     279     276
+     282      60     279     276     306      61     276     282     285      62
+     276     282     288      62     273     270     276      63     270     276
+     279      64     327     333     336      41     324     318     327      61
+     321     318     324      69     321     318     327      61     315     312
+     318      63     312     318     321      64     312     318     324      64
+     393     399     402      41     387     381     390      49     384     381
+     387      49     384     381     390      49     378     372     381      70
+     375     372     378      71     375     372     381      70     372     381
+     384      72     372     381     387      72     372     381     390      72
+     369     363     372      66     366     363     369      59     366     363
+     372      66     363     372     375      73     363     372     378      73
+     360     354     363      66     357     354     360      59     357     354
+     363      66     354     363     366      66     354     363     369      66
+     351     345     354      66     348     345     351      59     348     345
+     354      66     345     354     357      66     345     354     360      66
+     342     339     345      60     342     339     393      61     339     345
+     348      62     339     345     351      62     336     333     339      63
+     333     339     342      64     465     471     474      41     459     456
+     462      51     453     450     456      52     450     456     459      52
+     447     444     450      52     444     450     453      52     441     438
+     444      52     438     444     447      52     435     438     441      53
+     432     429     435      54     426     423     429      55     423     429
+     432      56     420     423     426      57     417     411     420      58
+     414     411     417      59     414     411     420      58     408     405
+     411      60     408     405     465      61     405     411     414      62
+     405     411     417      62     402     399     405      63     399     405
+     408      64     507     513     516      41     495     489     498      59
+     492     489     495      59     492     489     498      59     486     483
+     489      65     486     483     501      42     483     489     492      66
+     483     489     495      66     483     489     498      66     483     501
+     504      44     480     477     483      60     480     477     507      61
+     477     483     486      47     474     471     477      63     471     477
+     480      64     579     585     588      41     573     570     576      51
+     567     564     570      52     564     570     573      52     561     558
+     564      52     558     564     567      52     555     552     558      52
+     552     558     561      52     549     552     555      53     546     543
+     549      54     540     537     543      55     537     543     546      56
+     534     537     540      57     531     525     534      58     528     525
+     531      59     528     525     534      58     522     519     525      60
+     522     519     579      61     519     525     528      62     519     525
+     531      62     516     513     519      63     513     519     522      64
+     645     651     654      41     645     651     657      41     639     633
+     642      49     636     633     639      49     636     633     642      49
+     630     624     633      70     627     624     630      71     627     624
+     633      70     624     633     636      72     624     633     639      72
+     624     633     642      72     621     615     624      66     618     615
+     621      59     618     615     624      66     615     624     627      73
+     615     624     630      73     612     606     615      66     609     606
+     612      59     609     606     615      66     606     615     618      66
+     606     615     621      66     603     597     606      66     600     597
+     603      59     600     597     606      66     597     606     609      66
+     597     606     612      66     594     591     597      60     594     591
+     645      61     591     597     600      62     591     597     603      62
+     588     585     591      63     585     591     594      64     654     651
+     657      68     699     696     726      74     696     699     729      74
+     693     690     723      74     693     696     726      74     687     690
+     723      74     684     699     729      74     675     672     714      74
+     672     675     717      74     669     666     711      74     669     672
+     714      74     663     666     711      74     663     681     720      75
+     660     675     717      74
 %FLAG ANGLES_WITHOUT_HYDROGEN                                                   
 %FORMAT(10I8)                                                                   
       36      33      39       1      33      39      45       2      18      12
       33       3      12      18      27       4      12      33      36       5
       12      33      39       6       0      12      18       7       0      12
-      33       7     108     105     111       1     105     111     117       2
-      90      96     102       8      84      90      96       8      78      75
-     102       9      78      84      90       8      75      78      84       8
-      75     102      96      10      69      75      78      11      69      75
-     102      12      63      60     102      13      63      69      75      14
-      60      63      69      15      60     102      75      16      60     102
-      96      17      51      45     105       3      51      60      63      18
-      51      60     102      19      45      51      60      20      45     105
-     108       5      45     105     111       6      39      45      51      21
-      39      45     105      22     150     147     153       1     147     153
-     159       2     129     123     141       4     123     117     147       3
-     117     123     129      23     117     123     141       4     117     147
-     150       5     117     147     153       6     111     117     123      21
-     111     117     147      22     222     219     225       1     219     225
-     231       2     204     210     216       8     198     204     210       8
-     192     189     216       9     192     198     204       8     189     192
-     198       8     189     216     210      10     183     189     192      11
-     183     189     216      12     177     174     216      13     177     183
-     189      14     174     177     183      15     174     216     189      16
-     174     216     210      17     165     159     219       3     165     174
-     177      18     165     174     216      19     159     165     174      20
+      33       8     108     105     111       1     105     111     117       2
+      90      96     102       9      84      90      96      10      78      75
+     102      11      78      84      90      10      75      78      84      12
+      75     102      96      13      69      75      78      14      69      75
+     102      15      63      60     102      16      63      69      75      17
+      60      63      69      18      60     102      75      19      60     102
+      96      20      51      45     105       3      51      60      63      21
+      51      60     102      22      45      51      60      23      45     105
+     108       5      45     105     111       6      39      45      51      24
+      39      45     105      25     150     147     153       1     147     153
+     159       2     129     123     141      26     123     117     147       3
+     117     123     129      27     117     123     141       4     117     147
+     150       5     117     147     153       6     111     117     123      24
+     111     117     147      25     222     219     225       1     219     225
+     231       2     204     210     216       9     198     204     210      10
+     192     189     216      11     192     198     204      10     189     192
+     198      12     189     216     210      13     183     189     192      14
+     183     189     216      15     177     174     216      16     177     183
+     189      17     174     177     183      18     174     216     189      19
+     174     216     210      20     165     159     219       3     165     174
+     177      21     165     174     216      22     159     165     174      23
      159     219     222       5     159     219     225       6     153     159
-     165      21     153     159     219      22     267     264     270       1
-     264     270     276       2     258     255     261      24     246     255
-     258      25     246     255     261      25     237     231     264       3
-     237     246     255       3     231     237     246      23     231     264
-     267       5     231     264     270       6     225     231     237      21
-     225     231     264      22     309     306     312       1     306     312
+     165      24     153     159     219      25     267     264     270       1
+     264     270     276       2     258     255     261      28     246     255
+     258      29     246     255     261      29     237     231     264       3
+     237     246     255      30     231     237     246      27     231     264
+     267       5     231     264     270       6     225     231     237      24
+     225     231     264      25     309     306     312       1     306     312
      318       2     294     291     297       1     282     276     306       3
-     282     291     294       5     282     291     297       6     276     282
-     291       3     276     306     309       5     276     306     312       6
-     270     276     282      21     270     276     306      22     330     327
+     282     291     294      31     282     291     297      32     276     282
+     291      33     276     306     309       5     276     306     312       6
+     270     276     282      24     270     276     306      25     330     327
      333       1     327     333     339       2     318     327     330       5
-     318     327     333       6     312     318     327      22     396     393
-     399       1     393     399     405       2     363     372     381       7
-     354     363     372      23     345     339     393       3     345     354
-     363      23     339     345     354      23     339     393     396       5
-     339     393     399       6     333     339     345      21     333     339
-     393      22     468     465     471       1     465     471     477       2
-     450     456     462       8     444     450     456       8     438     435
-     462       9     438     444     450       8     435     438     444       8
-     435     462     456      10     429     435     438      11     429     435
-     462      12     423     420     462      13     423     429     435      14
-     420     423     429      15     420     462     435      16     420     462
-     456      17     411     405     465       3     411     420     423      18
-     411     420     462      19     405     411     420      20     405     465
-     468       5     405     465     471       6     399     405     411      21
-     399     405     465      22     510     507     513       1     507     513
-     519       2     489     483     501       4     483     477     507       3
-     477     483     489      23     477     483     501       4     477     507
-     510       5     477     507     513       6     471     477     483      21
-     471     477     507      22     582     579     585       1     579     585
-     591       2     564     570     576       8     558     564     570       8
-     552     549     576       9     552     558     564       8     549     552
-     558       8     549     576     570      10     543     549     552      11
-     543     549     576      12     537     534     576      13     537     543
-     549      14     534     537     543      15     534     576     549      16
-     534     576     570      17     525     519     579       3     525     534
-     537      18     525     534     576      19     519     525     534      20
+     318     327     333       6     312     318     327      25     396     393
+     399       1     393     399     405       2     363     372     381      34
+     354     363     372      35     345     339     393       3     345     354
+     363      35     339     345     354      27     339     393     396       5
+     339     393     399       6     333     339     345      24     333     339
+     393      25     468     465     471       1     465     471     477       2
+     450     456     462       9     444     450     456      10     438     435
+     462      11     438     444     450      10     435     438     444      12
+     435     462     456      13     429     435     438      14     429     435
+     462      15     423     420     462      16     423     429     435      17
+     420     423     429      18     420     462     435      19     420     462
+     456      20     411     405     465       3     411     420     423      21
+     411     420     462      22     405     411     420      23     405     465
+     468       5     405     465     471       6     399     405     411      24
+     399     405     465      25     510     507     513       1     507     513
+     519       2     489     483     501      26     483     477     507       3
+     477     483     489      27     477     483     501       4     477     507
+     510       5     477     507     513       6     471     477     483      24
+     471     477     507      25     582     579     585       1     579     585
+     591       2     564     570     576       9     558     564     570      10
+     552     549     576      11     552     558     564      10     549     552
+     558      12     549     576     570      13     543     549     552      14
+     543     549     576      15     537     534     576      16     537     543
+     549      17     534     537     543      18     534     576     549      19
+     534     576     570      20     525     519     579       3     525     534
+     537      21     525     534     576      22     519     525     534      23
      519     579     582       5     519     579     585       6     513     519
-     525      21     513     519     579      22     648     645     651       1
-     615     624     633       7     606     615     624      23     597     591
-     645       3     597     606     615      23     591     597     606      23
+     525      24     513     519     579      25     648     645     651       1
+     615     624     633      34     606     615     624      35     597     591
+     645       3     597     606     615      35     591     597     606      27
      591     645     648       5     591     645     651       6     585     591
-     597      21     585     591     645      22     696     693     705      32
-     693     696     699      33     690     687     702      32     690     693
-     696      33     690     693     705      32     687     684     699      33
-     687     690     693      33     684     687     690      33     684     687
-     702      32     684     699     696      33     678     684     687      34
-     678     684     699      34     675     660     678      34     672     669
-     708      32     669     672     675      33     666     663     681      35
-     666     669     672      33     666     669     708      32     663     660
-     675      33     663     660     678      34     663     666     669      33
-     660     663     666      33     660     663     681      35     660     675
-     672      33     660     678     684      36
+     597      24     585     591     645      25     696     693     705      36
+     693     696     699      37     690     687     702      36     690     693
+     696      37     690     693     705      36     687     684     699      37
+     687     690     693      37     684     687     690      37     684     687
+     702      36     684     699     696      37     678     684     687      38
+     678     684     699      38     675     660     678      38     672     669
+     708      36     669     672     675      37     666     663     681      39
+     666     669     672      37     666     669     708      36     663     660
+     675      37     663     660     678      38     663     666     669      37
+     660     663     666      37     660     663     681      39     660     675
+     672      37     660     678     684      40
 %FLAG DIHEDRALS_INC_HYDROGEN                                                    
 %FORMAT(10I8)                                                                   
       36      33      39      42       2      36      33     -39      42       1
       33      39      45      48      10      24      18      12      33       9
-      24      18      27      30      28      21      18      12      33       9
-      21      18      27      30      28      15      12      18      21       9
+      24      18      27      30      30      21      18      12      33       9
+      21      18      27      30      30      15      12      18      21       9
       15      12      18      24       9      15      12      18      27       9
       15      12      33      36      10      15      12      33      39      10
-      12      18      27      30      29      12      18     -27      30      30
+      12      18      27      30      31      12      18     -27      30      32
       12      33      39      42       1       9       0      12      15       9
        9       0      12      18       9       9       0      12      33       9
        6       0      12      15       9       6       0      12      18       9
@@ -663,26 +686,26 @@ SER TRP THR TRP GLU ASN GLY LYS TRP THR TRP LYS NHE TCS
       54      51      60      63      10      54      51      60     102      10
       51      60      63      66      16      48      45      51      54       9
       48      45      51      57       9      48      45      51      60       9
-      48      45     105     108      31      48      45    -105     108      10
-      48      45    -105     108      32      48      45     105     111      10
+      48      45     105     108      33      48      45    -105     108      10
+      48      45    -105     108      34      48      45     105     111      10
       45     105     111     114       1      42      39      45      48      10
       42      39      45      51      10      42      39      45     105      10
       39      45      51      54       9      39      45      51      57       9
      150     147     153     156       2     150     147    -153     156       1
-     147     153     159     162      10     138     129     123     141      29
-     138     129    -123     141      33     135     129     123     141      29
-     135     129    -123     141      33     132     129     123     141      29
-     132     129    -123     141      33     129     123     141     144      29
-     129     123    -141     144      30     126     123     117     147       9
+     147     153     159     162      10     138     129     123     141      31
+     138     129    -123     141      35     135     129     123     141      31
+     135     129    -123     141      35     132     129     123     141      31
+     132     129    -123     141      35     129     123     141     144      31
+     129     123    -141     144      32     126     123     117     147       9
      126     123     129     132       9     126     123     129     135       9
-     126     123     129     138       9     126     123     141     144      28
+     126     123     129     138       9     126     123     141     144      30
      120     117     123     126       9     120     117     123     129       9
-     120     117     123     141      29     120     117    -123     141      33
-     120     117     147     150      31     120     117    -147     150      10
-     120     117    -147     150      32     120     117     147     153      10
-     117     123     129     132      30     117     123     129     135      30
-     117     123     129     138      30     117     123     141     144      29
-     117     123    -141     144      30     117     147     153     156       1
+     120     117     123     141      31     120     117    -123     141      35
+     120     117     147     150      33     120     117    -147     150      10
+     120     117    -147     150      34     120     117     147     153      10
+     117     123     129     132      32     117     123     129     135      32
+     117     123     129     138      32     117     123     141     144      31
+     117     123    -141     144      32     117     147     153     156       1
      114     111     117     120      10     114     111     117     123      10
      114     111     117     147      10     111     117     123     126       9
      222     219     225     228       2     222     219    -225     228       1
@@ -701,8 +724,8 @@ SER TRP THR TRP GLU ASN GLY LYS TRP THR TRP LYS NHE TCS
      168     165     174     177      10     168     165     174     216      10
      165     174     177     180      16     162     159     165     168       9
      162     159     165     171       9     162     159     165     174       9
-     162     159     219     222      31     162     159    -219     222      10
-     162     159    -219     222      32     162     159     219     225      10
+     162     159     219     222      33     162     159    -219     222      10
+     162     159    -219     222      34     162     159     219     225      10
      159     219     225     228       1     156     153     159     162      10
      156     153     159     165      10     156     153     159     219      10
      153     159     165     168       9     153     159     165     171       9
@@ -710,14 +733,14 @@ SER TRP THR TRP GLU ASN GLY LYS TRP THR TRP LYS NHE TCS
      264     270     276     279      10     252     246     255     258      10
      252     246     255     261      10     249     246     255     258      10
      249     246     255     261      10     243     237     231     264       9
-     243     237     246     249      34     243     237     246     252      34
+     243     237     246     249      36     243     237     246     252      36
      243     237     246     255       9     240     237     231     264       9
-     240     237     246     249      34     240     237     246     252      34
+     240     237     246     249      36     240     237     246     252      36
      240     237     246     255       9     234     231     237     240       9
      234     231     237     243       9     234     231     237     246       9
-     234     231     264     267      31     234     231    -264     267      10
-     234     231    -264     267      32     234     231     264     270      10
-     231     237     246     249      30     231     237     246     252      30
+     234     231     264     267      33     234     231    -264     267      10
+     234     231    -264     267      34     234     231     264     270      10
+     231     237     246     249      32     231     237     246     252      32
      231     264     270     273       1     228     225     231     234      10
      228     225     231     237      10     228     225     231     264      10
      225     231     237     240       9     225     231     237     243       9
@@ -725,24 +748,24 @@ SER TRP THR TRP GLU ASN GLY LYS TRP THR TRP LYS NHE TCS
      306     312     318     321      10     306     312     318     324      10
      294     291     297     300       2     294     291    -297     300       1
      294     291     297     303       2     294     291    -297     303       1
-     288     282     276     306       9     288     282     291     294      31
-     288     282    -291     294      10     288     282    -291     294      32
+     288     282     276     306       9     288     282     291     294      33
+     288     282    -291     294      10     288     282    -291     294      34
      288     282     291     297      10     285     282     276     306       9
-     285     282     291     294      31     285     282    -291     294      10
-     285     282    -291     294      32     285     282     291     297      10
+     285     282     291     294      33     285     282    -291     294      10
+     285     282    -291     294      34     285     282     291     297      10
      282     291     297     300       1     282     291     297     303       1
      279     276     282     285       9     279     276     282     288       9
-     279     276     282     291       9     279     276     306     309      31
-     279     276    -306     309      10     279     276    -306     309      32
+     279     276     282     291       9     279     276     306     309      33
+     279     276    -306     309      10     279     276    -306     309      34
      279     276     306     312      10     276     306     312     315       1
      273     270     276     279      10     273     270     276     282      10
      273     270     276     306      10     270     276     282     285       9
      270     276     282     288       9     330     327     333     336       2
      330     327    -333     336       1     327     333     339     342      10
-     324     318     327     330      31     324     318    -327     330      10
-     324     318    -327     330      32     324     318     327     333      10
-     321     318     327     330      31     321     318    -327     330      10
-     321     318    -327     330      32     321     318     327     333      10
+     324     318     327     330      33     324     318    -327     330      10
+     324     318    -327     330      34     324     318     327     333      10
+     321     318     327     330      33     321     318    -327     330      10
+     321     318    -327     330      34     321     318     327     333      10
      318     327     333     336       1     315     312     318     321      10
      315     312     318     324      10     315     312     318     327      10
      396     393     399     402       2     396     393    -399     402       1
@@ -754,20 +777,20 @@ SER TRP THR TRP GLU ASN GLY LYS TRP THR TRP LYS NHE TCS
      366     363     372     375       9     366     363     372     378       9
      366     363     372     381       9     363     372     381     384       9
      363     372     381     387       9     363     372     381     390       9
-     360     354     363     366      34     360     354     363     369      34
-     360     354     363     372      30     357     354     363     366      34
-     357     354     363     369      34     357     354     363     372      30
+     360     354     363     366      36     360     354     363     369      36
+     360     354     363     372      32     357     354     363     366      36
+     357     354     363     369      36     357     354     363     372      32
      354     363     372     375       9     354     363     372     378       9
-     351     345     339     393       9     351     345     354     357      34
-     351     345     354     360      34     351     345     354     363      30
-     348     345     339     393       9     348     345     354     357      34
-     348     345     354     360      34     348     345     354     363      30
-     345     354     363     366      30     345     354     363     369      30
+     351     345     339     393       9     351     345     354     357      36
+     351     345     354     360      36     351     345     354     363      32
+     348     345     339     393       9     348     345     354     357      36
+     348     345     354     360      36     348     345     354     363      32
+     345     354     363     366      32     345     354     363     369      32
      342     339     345     348       9     342     339     345     351       9
-     342     339     345     354       9     342     339     393     396      31
-     342     339    -393     396      10     342     339    -393     396      32
-     342     339     393     399      10     339     345     354     357      30
-     339     345     354     360      30     339     393     399     402       1
+     342     339     345     354       9     342     339     393     396      33
+     342     339    -393     396      10     342     339    -393     396      34
+     342     339     393     399      10     339     345     354     357      32
+     339     345     354     360      32     339     393     399     402       1
      336     333     339     342      10     336     333     339     345      10
      336     333     339     393      10     333     339     345     348       9
      333     339     345     351       9     468     465     471     474       2
@@ -786,26 +809,26 @@ SER TRP THR TRP GLU ASN GLY LYS TRP THR TRP LYS NHE TCS
      414     411     405     465       9     414     411     420     423      10
      414     411     420     462      10     411     420     423     426      16
      408     405     411     414       9     408     405     411     417       9
-     408     405     411     420       9     408     405     465     468      31
-     408     405    -465     468      10     408     405    -465     468      32
+     408     405     411     420       9     408     405     465     468      33
+     408     405    -465     468      10     408     405    -465     468      34
      408     405     465     471      10     405     465     471     474       1
      402     399     405     408      10     402     399     405     411      10
      402     399     405     465      10     399     405     411     414       9
      399     405     411     417       9     510     507     513     516       2
      510     507    -513     516       1     507     513     519     522      10
-     498     489     483     501      29     498     489    -483     501      33
-     495     489     483     501      29     495     489    -483     501      33
-     492     489     483     501      29     492     489    -483     501      33
-     489     483     501     504      29     489     483    -501     504      30
+     498     489     483     501      31     498     489    -483     501      35
+     495     489     483     501      31     495     489    -483     501      35
+     492     489     483     501      31     492     489    -483     501      35
+     489     483     501     504      31     489     483    -501     504      32
      486     483     477     507       9     486     483     489     492       9
      486     483     489     495       9     486     483     489     498       9
-     486     483     501     504      28     480     477     483     486       9
-     480     477     483     489       9     480     477     483     501      29
-     480     477    -483     501      33     480     477     507     510      31
-     480     477    -507     510      10     480     477    -507     510      32
-     480     477     507     513      10     477     483     489     492      30
-     477     483     489     495      30     477     483     489     498      30
-     477     483     501     504      29     477     483    -501     504      30
+     486     483     501     504      30     480     477     483     486       9
+     480     477     483     489       9     480     477     483     501      31
+     480     477    -483     501      35     480     477     507     510      33
+     480     477    -507     510      10     480     477    -507     510      34
+     480     477     507     513      10     477     483     489     492      32
+     477     483     489     495      32     477     483     489     498      32
+     477     483     501     504      31     477     483    -501     504      32
      477     507     513     516       1     474     471     477     480      10
      474     471     477     483      10     474     471     477     507      10
      471     477     483     486       9     582     579     585     588       2
@@ -824,8 +847,8 @@ SER TRP THR TRP GLU ASN GLY LYS TRP THR TRP LYS NHE TCS
      528     525     519     579       9     528     525     534     537      10
      528     525     534     576      10     525     534     537     540      16
      522     519     525     528       9     522     519     525     531       9
-     522     519     525     534       9     522     519     579     582      31
-     522     519    -579     582      10     522     519    -579     582      32
+     522     519     525     534       9     522     519     579     582      33
+     522     519    -579     582      10     522     519    -579     582      34
      522     519     579     585      10     519     579     585     588       1
      516     513     519     522      10     516     513     519     525      10
      516     513     519     579      10     513     519     525     528       9
@@ -839,42 +862,42 @@ SER TRP THR TRP GLU ASN GLY LYS TRP THR TRP LYS NHE TCS
      618     615     624     627       9     618     615     624     630       9
      618     615     624     633       9     615     624     633     636       9
      615     624     633     639       9     615     624     633     642       9
-     612     606     615     618      34     612     606     615     621      34
-     612     606     615     624      30     609     606     615     618      34
-     609     606     615     621      34     609     606     615     624      30
+     612     606     615     618      36     612     606     615     621      36
+     612     606     615     624      32     609     606     615     618      36
+     609     606     615     621      36     609     606     615     624      32
      606     615     624     627       9     606     615     624     630       9
-     603     597     591     645       9     603     597     606     609      34
-     603     597     606     612      34     603     597     606     615      30
-     600     597     591     645       9     600     597     606     609      34
-     600     597     606     612      34     600     597     606     615      30
-     597     606     615     618      30     597     606     615     621      30
+     603     597     591     645       9     603     597     606     609      36
+     603     597     606     612      36     603     597     606     615      32
+     600     597     591     645       9     600     597     606     609      36
+     600     597     606     612      36     600     597     606     615      32
+     597     606     615     618      32     597     606     615     621      32
      594     591     597     600       9     594     591     597     603       9
-     594     591     597     606       9     594     591     645     648      31
-     594     591    -645     648      10     594     591    -645     648      32
-     594     591     645     651      10     591     597     606     609      30
-     591     597     606     612      30     591     645     651     654       1
+     594     591     597     606       9     594     591     645     648      33
+     594     591    -645     648      10     594     591    -645     648      34
+     594     591     645     651      10     591     597     606     609      32
+     591     597     606     612      32     591     645     651     654       1
      591     645     651     657       1     588     585     591     594      10
      588     585     591     597      10     588     585     591     645      10
      585     591     597     600       9     585     591     597     603       9
       90     102     -96     -99      27      84      96     -90     -93      27
       78      90     -84     -87      27      75      84     -78     -81      27
-      63      75     -69     -72      35      60      69     -63     -66      27
+      63      75     -69     -72      37      60      69     -63     -66      27
       33      45     -39     -42      27     105     117    -111    -114      27
      204     216    -210    -213      27     198     210    -204    -207      27
      192     204    -198    -201      27     189     198    -192    -195      27
-     177     189    -183    -186      35     174     183    -177    -180      27
+     177     189    -183    -186      37     174     183    -177    -180      27
      147     159    -153    -156      27     219     231    -225    -228      27
-     291     300    -297    -303      35     264     276    -270    -273      27
+     291     300    -297    -303      37     264     276    -270    -273      27
      306     318    -312    -315      27     327     339    -333    -336      27
      450     462    -456    -459      27     444     456    -450    -453      27
      438     450    -444    -447      27     435     444    -438    -441      27
-     423     435    -429    -432      35     420     429    -423    -426      27
+     423     435    -429    -432      37     420     429    -423    -426      27
      393     405    -399    -402      27     465     477    -471    -474      27
      564     576    -570    -573      27     558     570    -564    -567      27
      552     564    -558    -561      27     549     558    -552    -555      27
-     537     549    -543    -546      35     534     543    -537    -540      27
+     537     549    -543    -546      37     534     543    -537    -540      27
      507     519    -513    -516      27     579     591    -585    -588      27
-     645     654    -651    -657      35     726     696     699     729      13
+     645     654    -651    -657      37     726     696     699     729      13
      714     672     675     717      13     708     669     666     711      13
      708     669     672     714      13     705     693     690     723      13
      705     693     696     726      13     702     687     690     723      13
@@ -883,13 +906,13 @@ SER TRP THR TRP GLU ASN GLY LYS TRP THR TRP LYS NHE TCS
      684     687     690     723      13     684     699     696     726      13
      681     663     666     711      13     678     660     675     717      13
      678     684     699     729      13     672     669     666     711      13
-     669     672     675     717      13     666     663     681     720      36
+     669     672     675     717      13     666     663     681     720      28
      666     669     672     714      13     663     660     675     717      13
-     660     663     666     711      13     660     663     681     720      36
-     660     675     672     714      13     684     696    -699    -729      37
-     693     699    -696    -726      37     687     693    -690    -723      37
-     660     672    -675    -717      37     669     675    -672    -714      37
-     663     669    -666    -711      37
+     660     663     666     711      13     660     663     681     720      28
+     660     675     672     714      13     684     696    -699    -729      29
+     693     699    -696    -726      29     687     693    -690    -723      29
+     660     672    -675    -717      29     669     675    -672    -714      29
+     663     669    -666    -711      29
 %FLAG DIHEDRALS_WITHOUT_HYDROGEN                                                
 %FORMAT(10I8)                                                                   
       36      33      39      45       1      33      39      45      51       2
@@ -1085,17 +1108,17 @@ SER TRP THR TRP GLU ASN GLY LYS TRP THR TRP LYS NHE TCS
      684     687     690     693      13     684     699    -696     693      13
      678     660     663     681      13     678     684     687     690      13
      678     684     687     702      13     678     684     699     696      13
-     675     660     663     681      13     675     660     678     684      36
+     675     660     663     681      13     675     660     678     684      28
      675     672     669     708      13     672     675     660     678      13
      669     666     663     681      13     666     663     660     675      13
      666     663     660     678      13     666     669    -672     675      13
-     663     660     675     672      13     663     660     678     684      36
+     663     660     675     672      13     663     660     678     684      28
      663     666    -669     672      13     663     666     669     708      13
      660     663     666     669      13     660     675    -672     669      13
-     660     678     684     687      36     660     678     684     699      36
-     690     696    -693    -705      37     684     690    -687    -702      37
-     687     699    -684    -678      37     666     672    -669    -708      37
-     660     666    -663    -681      37     678     660    -675    -663      37
+     660     678     684     687      28     660     678     684     699      28
+     690     696    -693    -705      29     684     690    -687    -702      29
+     687     699    -684    -678      29     666     672    -669    -708      29
+     660     666    -663    -681      29     663     675    -660    -678      29
 %FLAG EXCLUDED_ATOMS_LIST                                                       
 %FORMAT(10I8)                                                                   
        2       3       4       5       6       7       8       9      10      12

From 859832583e5ec017fcd2efe1d002501003c5d021 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 13 Dec 2023 11:02:18 -0500
Subject: [PATCH 0161/1492] Add actual test save topology. Was previously
 writing out the unchanged topology and checking that. This topology produces
 the exact same energies as the previous.

---
 test/Test_CombineCrd/FabI.NDP.TCS.parm7.save | 20961 +++++++++++++++++
 1 file changed, 20961 insertions(+)
 create mode 100644 test/Test_CombineCrd/FabI.NDP.TCS.parm7.save

diff --git a/test/Test_CombineCrd/FabI.NDP.TCS.parm7.save b/test/Test_CombineCrd/FabI.NDP.TCS.parm7.save
new file mode 100644
index 0000000000..82b717ac5b
--- /dev/null
+++ b/test/Test_CombineCrd/FabI.NDP.TCS.parm7.save
@@ -0,0 +1,20961 @@
+%VERSION  VERSION_STAMP = V0001.000  DATE = 12/13/23 10:11:19                  
+%FLAG TITLE                                                                     
+%FORMAT(20a4)                                                                   
+combinedParm                                                                    
+%FLAG POINTERS                                                                  
+%FORMAT(10I8)                                                                   
+    4143      18    2060    2125    4682    2878    8776    7180       0       0
+   22768     270    2125    2878    7180      73     149      66      50       0
+       0       0       0       0       0       0       0       2      70       0
+       0
+%FLAG ATOM_NAME                                                                 
+%FORMAT(20a4)                                                                   
+N   H1  H2  H3  CA  HA  CB  HB2 HB3 CG  HG2 HG3 SD  CE  HE1 HE2 HE3 C   O   N   
+H   CA  HA2 HA3 C   O   N   H   CA  HA  CB  HB2 HB3 CG  CD1 HD1 CE1 HE1 CZ  HZ  
+CE2 HE2 CD2 HD2 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG  CD1 HD11HD12HD13CD2 
+HD21HD22HD23C   O   N   H   CA  HA  CB  HB1 HB2 HB3 C   O   N   H   CA  HA2 HA3 
+C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  HD2 HD3 CE  HE2 HE3 NZ  HZ1 
+HZ2 HZ3 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  HD2 HD3 CE  HE2 HE3 
+NZ  HZ1 HZ2 HZ3 C   O   N   H   CA  HA  CB  HB  CG2 HG21HG22HG23CG1 HG12HG13CD1 
+HD11HD12HD13C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG  CD1 HD11HD12HD13CD2 HD21
+HD22HD23C   O   N   H   CA  HA  CB  HB  CG2 HG21HG22HG23CG1 HG12HG13CD1 HD11HD12
+HD13C   O   N   H   CA  HA  CB  HB  CG2 HG21HG22HG23OG1 HG1 C   O   N   H   CA  
+HA2 HA3 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG  CD1 HD11HD12HD13CD2 HD21HD22
+HD23C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG  CD1 HD11HD12HD13CD2 HD21HD22HD23
+C   O   N   H   CA  HA  CB  HB2 HB3 OG  HG  C   O   N   H   CA  HA  CB  HB2 HB3 
+CG  OD1 ND2 HD21HD22C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  HD2 HD3 
+CE  HE2 HE3 NZ  HZ1 HZ2 HZ3 C   O   N   H   CA  HA  CB  HB2 HB3 OG  HG  C   O   
+N   H   CA  HA  CB  HB  CG2 HG21HG22HG23CG1 HG12HG13CD1 HD11HD12HD13C   O   N   
+H   CA  HA  CB  HB1 HB2 HB3 C   O   N   H   CA  HA  CB  HB2 HB3 CG  CD1 HD1 CE1 
+HE1 CZ  OH  HH  CE2 HE2 CD2 HD2 C   O   N   H   CA  HA2 HA3 C   O   N   H   CA  
+HA  CB  HB  CG2 HG21HG22HG23CG1 HG12HG13CD1 HD11HD12HD13C   O   N   H   CA  HA  
+CB  HB1 HB2 HB3 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  HD2 HD3 CE  
+HE2 HE3 NZ  HZ1 HZ2 HZ3 C   O   N   H   CA  HA  CB  HB1 HB2 HB3 C   O   N   H   
+CA  HA  CB  HB2 HB3 CG  HG2 HG3 SD  CE  HE1 HE2 HE3 C   O   N   H   CA  HA  CB  
+HB2 HB3 CG  ND1 CE1 HE1 NE2 HE2 CD2 HD2 C   O   N   H   CA  HA  CB  HB2 HB3 CG  
+HG2 HG3 CD  HD2 HD3 NE  HE  CZ  NH1 HH11HH12NH2 HH21HH22C   O   N   H   CA  HA  
+CB  HB2 HB3 CG  HG2 HG3 CD  OE1 OE2 C   O   N   H   CA  HA2 HA3 C   O   N   H   
+CA  HA  CB  HB1 HB2 HB3 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  OE1 
+OE2 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG  CD1 HD11HD12HD13CD2 HD21HD22HD23
+C   O   N   H   CA  HA  CB  HB1 HB2 HB3 C   O   N   H   CA  HA  CB  HB2 HB3 CG  
+CD1 HD1 CE1 HE1 CZ  HZ  CE2 HE2 CD2 HD2 C   O   N   H   CA  HA  CB  HB  CG2 HG21
+HG22HG23OG1 HG1 C   O   N   H   CA  HA  CB  HB2 HB3 CG  CD1 HD1 CE1 HE1 CZ  OH  
+HH  CE2 HE2 CD2 HD2 C   O   N   H   CA  HA  CB  HB  CG1 HG11HG12HG13CG2 HG21HG22
+HG23C   O   N   H   CA  HA2 HA3 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 
+CD  OE1 NE2 HE21HE22C   O   N   H   CA  HA  CB  HB2 HB3 CG  CD1 HD1 CE1 HE1 CZ  
+HZ  CE2 HE2 CD2 HD2 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  HD2 HD3 
+CE  HE2 HE3 NZ  HZ1 HZ2 HZ3 C   O   N   H   CA  HA  CB  HB2 HB3 CG  OD1 OD2 C   
+O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  HD2 HD3 NE  HE  CZ  NH1 HH11HH12
+NH2 HH21HH22C   O   N   H   CA  HA  CB  HB  CG1 HG11HG12HG13CG2 HG21HG22HG23C   
+O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  OE1 OE2 C   O   N   H   CA  HA  
+CB  HB2 HB3 CG  HG2 HG3 CD  HD2 HD3 CE  HE2 HE3 NZ  HZ1 HZ2 HZ3 C   O   N   H   
+CA  HA  CB  HB2 HB3 CG  HG  CD1 HD11HD12HD13CD2 HD21HD22HD23C   O   N   H   CA  
+HA  CB  HB2 HB3 SG  HG  C   O   N   H   CA  HA  CB  HB1 HB2 HB3 C   O   N   H   
+CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  OE1 OE2 C   O   N   H   CA  HA  CB  HB2 HB3 
+CG  CD1 HD1 CE1 HE1 CZ  HZ  CE2 HE2 CD2 HD2 C   O   N   H   CA  HA  CB  HB2 HB3 
+CG  OD1 ND2 HD21HD22C   O   N   CD  HD2 HD3 CG  HG2 HG3 CB  HB2 HB3 CA  HA  C   
+O   N   H   CA  HA  CB  HB1 HB2 HB3 C   O   N   H   CA  HA  CB  HB1 HB2 HB3 C   
+O   N   H   CA  HA  CB  HB  CG1 HG11HG12HG13CG2 HG21HG22HG23C   O   N   H   CA  
+HA  CB  HB2 HB3 CG  HG  CD1 HD11HD12HD13CD2 HD21HD22HD23C   O   N   CD  HD2 HD3 
+CG  HG2 HG3 CB  HB2 HB3 CA  HA  C   O   N   H   CA  HA  CB  HB2 HB3 SG  HG  C   
+O   N   H   CA  HA  CB  HB2 HB3 CG  OD1 OD2 C   O   N   H   CA  HA  CB  HB  CG1 
+HG11HG12HG13CG2 HG21HG22HG23C   O   N   H   CA  HA  CB  HB  CG2 HG21HG22HG23CG1 
+HG12HG13CD1 HD11HD12HD13C   O   N   H   CA  HA  CB  HB2 HB3 OG  HG  C   O   N   
+H   CA  HA  CB  HB2 HB3 CG  OD1 OD2 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 
+HG3 CD  OE1 NE2 HE21HE22C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  OE1 
+OE2 C   O   N   H   CA  HA  CB  HB  CG2 HG21HG22HG23CG1 HG12HG13CD1 HD11HD12HD13
+C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  HD2 HD3 CE  HE2 HE3 NZ  HZ1 
+HZ2 HZ3 C   O   N   H   CA  HA  CB  HB2 HB3 CG  OD1 OD2 C   O   N   H   CA  HA  
+CB  HB2 HB3 CG  HG  CD1 HD11HD12HD13CD2 HD21HD22HD23C   O   N   H   CA  HA  CB  
+HB2 HB3 CG  CD1 HD1 CE1 HE1 CZ  HZ  CE2 HE2 CD2 HD2 C   O   N   H   CA  HA  CB  
+HB  CG1 HG11HG12HG13CG2 HG21HG22HG23C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 
+HG3 CD  OE1 OE2 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG  CD1 HD11HD12HD13CD2 
+HD21HD22HD23C   O   N   H   CA  HA2 HA3 C   O   N   H   CA  HA  CB  HB2 HB3 CG  
+HG2 HG3 CD  HD2 HD3 CE  HE2 HE3 NZ  HZ1 HZ2 HZ3 C   O   N   H   CA  HA  CB  HB  
+CG1 HG11HG12HG13CG2 HG21HG22HG23C   O   N   H   CA  HA  CB  HB2 HB3 CG  CD1 HD1 
+NE1 HE1 CE2 CZ2 HZ2 CH2 HH2 CZ3 HZ3 CE3 HE3 CD2 C   O   N   H   CA  HA  CB  HB2 
+HB3 CG  OD1 OD2 C   O   N   H   CA  HA2 HA3 C   O   N   H   CA  HA  CB  HB2 HB3 
+CG  HG  CD1 HD11HD12HD13CD2 HD21HD22HD23C   O   N   H   CA  HA  CB  HB2 HB3 CG  
+OD1 OD2 C   O   N   H   CA  HA  CB  HB1 HB2 HB3 C   O   N   H   CA  HA  CB  HB  
+CG2 HG21HG22HG23CG1 HG12HG13CD1 HD11HD12HD13C   O   N   H   CA  HA  CB  HB  CG1 
+HG11HG12HG13CG2 HG21HG22HG23C   O   N   H   CA  HA  CB  HB2 HB3 CG  ND1 CE1 HE1 
+NE2 HE2 CD2 HD2 C   O   N   H   CA  HA  CB  HB2 HB3 OG  HG  C   O   N   H   CA  
+HA  CB  HB  CG2 HG21HG22HG23CG1 HG12HG13CD1 HD11HD12HD13C   O   N   H   CA  HA  
+CB  HB1 HB2 HB3 C   O   N   H   CA  HA  CB  HB2 HB3 CG  CD1 HD1 CE1 HE1 CZ  HZ  
+CE2 HE2 CD2 HD2 C   O   N   H   CA  HA  CB  HB1 HB2 HB3 C   O   N   CD  HD2 HD3 
+CG  HG2 HG3 CB  HB2 HB3 CA  HA  C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 
+CD  HD2 HD3 NE  HE  CZ  NH1 HH11HH12NH2 HH21HH22C   O   N   H   CA  HA  CB  HB2 
+HB3 CG  OD1 OD2 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  OE1 NE2 HE21
+HE22C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG  CD1 HD11HD12HD13CD2 HD21HD22HD23
+C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  OE1 OE2 C   O   N   H   CA  
+HA2 HA3 C   O   N   H   CA  HA  CB  HB2 HB3 CG  OD1 ND2 HD21HD22C   O   N   H   
+CA  HA  CB  HB2 HB3 CG  CD1 HD1 CE1 HE1 CZ  HZ  CE2 HE2 CD2 HD2 C   O   N   H   
+CA  HA  CB  HB  CG2 HG21HG22HG23CG1 HG12HG13CD1 HD11HD12HD13C   O   N   H   CA  
+HA  CB  HB2 HB3 CG  OD1 OD2 C   O   N   H   CA  HA  CB  HB2 HB3 SG  HG  C   O   
+N   H   CA  HA  CB  HB  CG1 HG11HG12HG13CG2 HG21HG22HG23C   O   N   H   CA  HA  
+CB  HB  CG2 HG21HG22HG23OG1 HG1 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 
+CD  HD2 HD3 NE  HE  CZ  NH1 HH11HH12NH2 HH21HH22C   O   N   H   CA  HA  CB  HB2 
+HB3 CG  HG2 HG3 CD  OE1 OE2 C   O   N   H   CA  HA2 HA3 C   O   N   H   CA  HA  
+CB  HB2 HB3 CG  CD1 HD1 CE1 HE1 CZ  HZ  CE2 HE2 CD2 HD2 C   O   N   H   CA  HA  
+CB  HB2 HB3 OG  HG  C   O   N   H   CA  HA  CB  HB  CG2 HG21HG22HG23CG1 HG12HG13
+CD1 HD11HD12HD13C   O   N   H   CA  HA  CB  HB1 HB2 HB3 C   O   N   H   CA  HA  
+CB  HB2 HB3 CG  ND1 CE1 HE1 NE2 HE2 CD2 HD2 C   O   N   H   CA  HA  CB  HB2 HB3 
+CG  OD1 OD2 C   O   N   H   CA  HA  CB  HB  CG2 HG21HG22HG23CG1 HG12HG13CD1 HD11
+HD12HD13C   O   N   H   CA  HA  CB  HB2 HB3 OG  HG  C   O   N   H   CA  HA  CB  
+HB1 HB2 HB3 C   O   N   H   CA  HA  CB  HB2 HB3 CG  CD1 HD1 CE1 HE1 CZ  OH  HH  
+CE2 HE2 CD2 HD2 C   O   N   H   CA  HA  CB  HB2 HB3 OG  HG  C   O   N   H   CA  
+HA  CB  HB2 HB3 CG  CD1 HD1 CE1 HE1 CZ  HZ  CE2 HE2 CD2 HD2 C   O   N   H   CA  
+HA  CB  HB1 HB2 HB3 C   O   N   H   CA  HA  CB  HB1 HB2 HB3 C   O   N   H   CA  
+HA  CB  HB2 HB3 CG  HG  CD1 HD11HD12HD13CD2 HD21HD22HD23C   O   N   H   CA  HA  
+CB  HB1 HB2 HB3 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  HD2 HD3 CE  
+HE2 HE3 NZ  HZ1 HZ2 HZ3 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  OE1 
+OE2 C   O   N   H   CA  HA2 HA3 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 
+CD  HD2 HD3 NE  HE  CZ  NH1 HH11HH12NH2 HH21HH22C   O   N   H   CA  HA  CB  HB2 
+HB3 OG  HG  C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 SD  CE  HE1 HE2 HE3 
+C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 SD  CE  HE1 HE2 HE3 C   O   N   
+H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  HD2 HD3 CE  HE2 HE3 NZ  HZ1 HZ2 HZ3 C   
+O   N   H   CA  HA  CB  HB2 HB3 CG  OD1 ND2 HD21HD22C   O   N   H   CA  HA  CB  
+HB2 HB3 CG  HG2 HG3 CD  HD2 HD3 NE  HE  CZ  NH1 HH11HH12NH2 HH21HH22C   O   N   
+H   CA  HA  CB  HB2 HB3 CG  OD1 ND2 HD21HD22C   O   N   H   CA  HA  CB  HB1 HB2 
+HB3 C   O   N   H   CA  HA  CB  HB2 HB3 OG  HG  C   O   N   H   CA  HA  CB  HB2 
+HB3 CG  HG2 HG3 SD  CE  HE1 HE2 HE3 C   O   N   H   CA  HA  CB  HB  CG1 HG11HG12
+HG13CG2 HG21HG22HG23C   O   N   H   CA  HA  CB  HB1 HB2 HB3 C   O   N   H   CA  
+HA  CB  HB2 HB3 CG  HG  CD1 HD11HD12HD13CD2 HD21HD22HD23C   O   N   H   CA  HA  
+CB  HB  CG2 HG21HG22HG23OG1 HG1 C   O   N   H   CA  HA  CB  HB2 HB3 CG  CD1 HD1 
+CE1 HE1 CZ  OH  HH  CE2 HE2 CD2 HD2 C   O   N   H   CA  HA  CB  HB  CG2 HG21HG22
+HG23CG1 HG12HG13CD1 HD11HD12HD13C   O   N   H   CA  HA2 HA3 C   O   N   H   CA  
+HA  CB  HB1 HB2 HB3 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  OE1 OE2 
+C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  HD2 HD3 CE  HE2 HE3 NZ  HZ1 
+HZ2 HZ3 C   O   N   H   CA  HA  CB  HB1 HB2 HB3 C   O   N   H   CA  HA  CB  HB2 
+HB3 CG  HG2 HG3 SD  CE  HE1 HE2 HE3 C   O   N   CD  HD2 HD3 CG  HG2 HG3 CB  HB2 
+HB3 CA  HA  C   O   N   H   CA  HA  CB  HB2 HB3 OG  HG  C   O   N   H   CA  HA  
+CB  HB2 HB3 CG  CD1 HD1 CE1 HE1 CZ  OH  HH  CE2 HE2 CD2 HD2 C   O   N   H   CA  
+HA  CB  HB2 HB3 CG  OD1 ND2 HD21HD22C   O   N   H   CA  HA  CB  HB  CG2 HG21HG22
+HG23OG1 HG1 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 SD  CE  HE1 HE2 HE3 
+C   O   N   H   CA  HA2 HA3 C   O   N   H   CA  HA  CB  HB  CG1 HG11HG12HG13CG2 
+HG21HG22HG23C   O   N   H   CA  HA  CB  HB1 HB2 HB3 C   O   N   H   CA  HA  CB  
+HB2 HB3 CG  HG2 HG3 CD  HD2 HD3 CE  HE2 HE3 NZ  HZ1 HZ2 HZ3 C   O   N   H   CA  
+HA  CB  HB1 HB2 HB3 C   O   N   H   CA  HA  CB  HB2 HB3 OG  HG  C   O   N   H   
+CA  HA  CB  HB2 HB3 CG  HG  CD1 HD11HD12HD13CD2 HD21HD22HD23C   O   N   H   CA  
+HA  CB  HB2 HB3 CG  HG2 HG3 CD  OE1 OE2 C   O   N   H   CA  HA  CB  HB1 HB2 HB3 
+C   O   N   H   CA  HA  CB  HB  CG2 HG21HG22HG23OG1 HG1 C   O   N   H   CA  HA  
+CB  HB  CG1 HG11HG12HG13CG2 HG21HG22HG23C   O   N   H   CA  HA  CB  HB2 HB3 CG  
+HG2 HG3 CD  HD2 HD3 NE  HE  CZ  NH1 HH11HH12NH2 HH21HH22C   O   N   H   CA  HA  
+CB  HB2 HB3 CG  CD1 HD1 CE1 HE1 CZ  OH  HH  CE2 HE2 CD2 HD2 C   O   N   H   CA  
+HA  CB  HB  CG2 HG21HG22HG23OG1 HG1 C   O   N   H   CA  HA  CB  HB1 HB2 HB3 C   
+O   N   H   CA  HA  CB  HB2 HB3 CG  HG  CD1 HD11HD12HD13CD2 HD21HD22HD23C   O   
+N   H   CA  HA  CB  HB1 HB2 HB3 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG  CD1 
+HD11HD12HD13CD2 HD21HD22HD23C   O   N   H   CA  HA2 HA3 C   O   N   H   CA  HA  
+CB  HB2 HB3 CG  HG2 HG3 CD  OE1 OE2 C   O   N   H   CA  HA  CB  HB2 HB3 CG  OD1 
+OD2 C   O   N   H   CA  HA2 HA3 C   O   N   H   CA  HA  CB  HB  CG2 HG21HG22HG23
+CG1 HG12HG13CD1 HD11HD12HD13C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  
+HD2 HD3 CE  HE2 HE3 NZ  HZ1 HZ2 HZ3 C   O   N   H   CA  HA  CB  HB  CG1 HG11HG12
+HG13CG2 HG21HG22HG23C   O   N   H   CA  HA  CB  HB2 HB3 CG  OD1 ND2 HD21HD22C   
+O   N   H   CA  HA  CB  HB1 HB2 HB3 C   O   N   H   CA  HA  CB  HB  CG1 HG11HG12
+HG13CG2 HG21HG22HG23C   O   N   H   CA  HA  CB  HB2 HB3 OG  HG  C   O   N   H   
+CA  HA  CB  HB1 HB2 HB3 C   O   N   H   CA  HA2 HA3 C   O   N   CD  HD2 HD3 CG  
+HG2 HG3 CB  HB2 HB3 CA  HA  C   O   N   H   CA  HA  CB  HB  CG2 HG21HG22HG23CG1 
+HG12HG13CD1 HD11HD12HD13C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  HD2 
+HD3 CE  HE2 HE3 NZ  HZ1 HZ2 HZ3 C   O   N   H   CA  HA  CB  HB  CG2 HG21HG22HG23
+OG1 HG1 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG  CD1 HD11HD12HD13CD2 HD21HD22
+HD23C   O   N   H   CA  HA  CB  HB1 HB2 HB3 C   O   N   H   CA  HA  CB  HB1 HB2 
+HB3 C   O   N   H   CA  HA  CB  HB2 HB3 OG  HG  C   O   N   H   CA  HA2 HA3 C   
+O   N   H   CA  HA  CB  HB  CG2 HG21HG22HG23CG1 HG12HG13CD1 HD11HD12HD13C   O   
+N   H   CA  HA  CB  HB2 HB3 OG  HG  C   O   N   H   CA  HA  CB  HB2 HB3 CG  OD1 
+ND2 HD21HD22C   O   N   H   CA  HA  CB  HB2 HB3 CG  CD1 HD1 CE1 HE1 CZ  HZ  CE2 
+HE2 CD2 HD2 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  HD2 HD3 CE  HE2 
+HE3 NZ  HZ1 HZ2 HZ3 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  HD2 HD3 
+CE  HE2 HE3 NZ  HZ1 HZ2 HZ3 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 SD  
+CE  HE1 HE2 HE3 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG  CD1 HD11HD12HD13CD2 
+HD21HD22HD23C   O   N   H   CA  HA  CB  HB2 HB3 CG  OD1 OD2 C   O   N   H   CA  
+HA  CB  HB2 HB3 CG  CD1 HD1 CE1 HE1 CZ  OH  HH  CE2 HE2 CD2 HD2 C   O   N   H   
+CA  HA  CB  HB2 HB3 CG  OD1 ND2 HD21HD22C   O   N   H   CA  HA  CB  HB1 HB2 HB3 
+C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 SD  CE  HE1 HE2 HE3 C   O   N   
+H   CA  HA  CB  HB  CG1 HG11HG12HG13CG2 HG21HG22HG23C   O   N   H   CA  HA  CB  
+HB2 HB3 OG  HG  C   O   N   CD  HD2 HD3 CG  HG2 HG3 CB  HB2 HB3 CA  HA  C   O   
+N   H   CA  HA  CB  HB2 HB3 CG  HG  CD1 HD11HD12HD13CD2 HD21HD22HD23C   O   N   
+H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  HD2 HD3 CE  HE2 HE3 NZ  HZ1 HZ2 HZ3 C   
+O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  HD2 HD3 CE  HE2 HE3 NZ  HZ1 HZ2 
+HZ3 C   O   N   H   CA  HA  CB  HB2 HB3 CG  OD1 ND2 HD21HD22C   O   N   H   CA  
+HA  CB  HB  CG1 HG11HG12HG13CG2 HG21HG22HG23C   O   N   H   CA  HA  CB  HB2 HB3 
+CG  OD1 OD2 C   O   N   H   CA  HA  CB  HB  CG2 HG21HG22HG23CG1 HG12HG13CD1 HD11
+HD12HD13C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 SD  CE  HE1 HE2 HE3 C   
+O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  OE1 OE2 C   O   N   H   CA  HA  
+CB  HB  CG1 HG11HG12HG13CG2 HG21HG22HG23C   O   N   H   CA  HA2 HA3 C   O   N   
+H   CA  HA  CB  HB2 HB3 CG  OD1 ND2 HD21HD22C   O   N   H   CA  HA  CB  HB  CG2 
+HG21HG22HG23OG1 HG1 C   O   N   H   CA  HA  CB  HB  CG1 HG11HG12HG13CG2 HG21HG22
+HG23C   O   N   H   CA  HA  CB  HB1 HB2 HB3 C   O   N   H   CA  HA  CB  HB2 HB3 
+CG  CD1 HD1 CE1 HE1 CZ  HZ  CE2 HE2 CD2 HD2 C   O   N   H   CA  HA  CB  HB2 HB3 
+CG  HG  CD1 HD11HD12HD13CD2 HD21HD22HD23C   O   N   H   CA  HA  CB  HB2 HB3 SG  
+HG  C   O   N   H   CA  HA  CB  HB2 HB3 OG  HG  C   O   N   H   CA  HA  CB  HB2 
+HB3 CG  OD1 OD2 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 SD  CE  HE1 HE2 
+HE3 C   O   N   H   CA  HA  CB  HB1 HB2 HB3 C   O   N   H   CA  HA  CB  HB  CG2 
+HG21HG22HG23OG1 HG1 C   O   N   H   CA  HA2 HA3 C   O   N   H   CA  HA  CB  HB  
+CG2 HG21HG22HG23CG1 HG12HG13CD1 HD11HD12HD13C   O   N   H   CA  HA  CB  HB  CG2 
+HG21HG22HG23OG1 HG1 C   O   N   H   CA  HA2 HA3 C   O   N   H   CA  HA  CB  HB2 
+HB3 CG  HG2 HG3 CD  OE1 OE2 C   O   N   H   CA  HA  CB  HB  CG1 HG11HG12HG13CG2 
+HG21HG22HG23C   O   N   H   CA  HA  CB  HB  CG1 HG11HG12HG13CG2 HG21HG22HG23C   
+O   N   H   CA  HA  CB  HB2 HB3 CG  ND1 CE1 HE1 NE2 HE2 CD2 HD2 C   O   N   H   
+CA  HA  CB  HB  CG1 HG11HG12HG13CG2 HG21HG22HG23C   O   N   H   CA  HA  CB  HB2 
+HB3 CG  OD1 OD2 C   O   N   H   CA  HA  CB  HB1 HB2 HB3 C   O   N   H   CA  HA2 
+HA3 C   O   N   H   CA  HA  CB  HB2 HB3 CG  CD1 HD1 CE1 HE1 CZ  OH  HH  CE2 HE2 
+CD2 HD2 C   O   N   H   CA  HA  CB  HB2 HB3 CG  ND1 CE1 HE1 NE2 HE2 CD2 HD2 C   
+O   N   H   CA  HA  CB  HB2 HB3 SG  HG  C   O   N   H   CA  HA  CB  HB  CG1 HG11
+HG12HG13CG2 HG21HG22HG23C   O   N   H   CA  HA  CB  HB2 HB3 OG  HG  C   O   N   
+H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 SD  CE  HE1 HE2 HE3 C   O   N   H   CA  HA2 
+HA3 C   O   N   H   CA  HA  CB  HB2 HB3 CG  OD1 ND2 HD21HD22C   O   N   H   CA  
+HA  CB  HB  CG1 HG11HG12HG13CG2 HG21HG22HG23C   O   N   H   CA  HA  CB  HB2 HB3 
+CG  HG  CD1 HD11HD12HD13CD2 HD21HD22HD23C   O   N   H   CA  HA  CB  HB2 HB3 CG  
+HG  CD1 HD11HD12HD13CD2 HD21HD22HD23C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 
+HG3 CD  OE1 OE2 C   O   N   H   CA  HA  CB  HB2 HB3 CG  ND1 CE1 HE1 NE2 HE2 CD2 
+HD2 C   O   N   H   CA  HA  CB  HB2 HB3 CG  ND1 CE1 HE1 NE2 HE2 CD2 HD2 C   O   
+N   H   CA  HA  CB  HB2 HB3 CG  ND1 CE1 HE1 NE2 HE2 CD2 HD2 C   O   N   H   CA  
+HA  CB  HB2 HB3 CG  ND1 CE1 HE1 NE2 HE2 CD2 HD2 C   O   N   H   CA  HA  CB  HB2 
+HB3 CG  ND1 CE1 HE1 NE2 HE2 CD2 HD2 C   O   N   H   CA  HA  CB  HB2 HB3 CG  ND1 
+CE1 HE1 NE2 HE2 CD2 HD2 C   O   OXT P1  O1  O2  O3  C1  C2  O4  C3  O5  C4  O6  
+C5  N1  C6  N2  C7  C8  N3  N4  C9  N5  C10 O7  P2  O8  O9  O10 C11 C12 O11 C13 
+O12 C14 O13 C15 N6  C16 C17 C18 O14 N7  C19 C20 C21 H51 H52 H53 H54 H55 H56 H57 
+H58 H60 H64 H65 H67 H73 H74 H75 H76 H77 H78 H79 H80 H92 H86 H87 H90 H89 H81 C1  
+C2  C3  C4  C5  C6  O1  O2  C7  C8  C9  C10 C11 C12 CL2 CL3 CL1 H18 H19 H20 H21 
+H22 H23 H24 
+%FLAG CHARGE                                                                    
+%FORMAT(5E16.8)                                                                 
+  2.90099016E+00  3.61530432E+00  3.61530432E+00  3.61530432E+00  4.02712830E-01
+  2.03360868E+00  1.57622895E+00  2.27778750E-01  2.27778750E-01  6.08624820E-01
+  5.32091160E-01  5.32091160E-01 -5.05486602E+00 -6.21380430E-01  1.08787131E+00
+  1.08787131E+00  1.08787131E+00  1.11575143E+01 -1.04104000E+01 -7.57501011E+00
+  4.95464337E+00 -4.59201960E-01  1.27191654E+00  1.27191654E+00  1.08841798E+01
+ -1.03484442E+01 -7.57501011E+00  4.95464337E+00 -4.37335200E-02  1.78214094E+00
+ -6.25024890E-01  5.37557850E-01  5.37557850E-01  2.15023140E-01 -2.28872088E+00
+  2.42356590E+00 -3.10507992E+00  2.60578890E+00 -1.95343056E+00  2.36343231E+00
+ -3.10507992E+00  2.60578890E+00 -2.28872088E+00  2.42356590E+00  1.08841798E+01
+ -1.03484442E+01 -7.57501011E+00  4.95464337E+00 -9.43915140E-01  1.68009606E+00
+ -2.00809746E+00  8.32759110E-01  8.32759110E-01  6.43429413E+00 -6.57825030E-01
+ -7.50940983E+00  1.82223000E+00  1.82223000E+00  1.82223000E+00 -7.50940983E+00
+  1.82223000E+00  1.82223000E+00  1.82223000E+00  1.08841798E+01 -1.03484442E+01
+ -7.57501011E+00  4.95464337E+00  6.14091510E-01  1.49969529E+00 -3.32556975E+00
+  1.09880469E+00  1.09880469E+00  1.09880469E+00  1.08841798E+01 -1.03484442E+01
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+  3.07978737E+00  4.06251601E+00  7.12209484E+00  7.12209484E+00  1.42758965E+00
+  2.01048458E+00  2.01048458E+00  1.44626751E+00  2.25555629E+00  8.14755478E+00
+  3.06460819E+00  7.84355215E+00  3.26388726E+00  2.69646306E+00  6.91802331E+00
+  6.91802331E+00  3.41894082E+00  3.34060315E+00  4.13908611E+00 -7.10669700E-02
+  2.60761113E+00 -2.71512270E+00  8.45514720E-01 -2.73334500E+00 -1.80400770E+00
+ -4.46810796E+00 -8.83963773E+00  2.02449753E+00  8.01781200E-02 -1.84045230E+00
+  2.55112200E-02 -1.74934080E+00 -2.97023490E+00 -1.04596002E+00 -1.44685062E+00
+ -1.46507292E+00  3.11601330E+00  2.82445650E+00  2.84267880E+00  8.03603430E+00
+  3.02490180E+00  2.84267880E+00  2.89734570E+00
+%FLAG ATOMIC_NUMBER                                                             
+%FORMAT(10I8)                                                                   
+       7       1       1       1       6       1       6       1       1       6
+       1       1      16       6       1       1       1       6       8       7
+       1       6       1       1       6       8       7       1       6       1
+       6       1       1       6       6       1       6       1       6       1
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+       1       1       1       6       8       7       1       6       1       6
+       1       1       1       6       8       7       1       6       1       1
+       6       8       7       1       6       1       6       1       1       6
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+       1       1       6       8       7       1       6       1       6       1
+       1       6       1       1       6       1       1       6       1       1
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+       1       1       1       6       8       7       1       6       1       6
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+       1       1       6       8       7       1       6       1       6       1
+       6       1       1       1       6       1       1       6       1       1
+       1       6       8       7       1       6       1       6       1       6
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+       1       6       1       6       1       1       1       6       1       1
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+       1       1       6       8       7       1       6       1       6       1
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+       1       6       1       6       1       1       6       7       6       1
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+       1       6       1       1       6       8       8       6       8       7
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+       6       1       1       1       6       8       7       1       6       1
+       6       1       1       6       7       6       1       7       1       6
+       1       6       8       7       1       6       1       6       1       1
+       6       8       8       6       8       7       1       6       1       6
+       1       6       1       1       1       6       1       1       6       1
+       1       1       6       8       7       1       6       1       6       1
+       1       8       1       6       8       7       1       6       1       6
+       1       1       1       6       8       7       1       6       1       6
+       1       1       6       6       1       6       1       6       8       1
+       6       1       6       1       6       8       7       1       6       1
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+       1       6       1       1       6       6       1       6       1       6
+       1       6       1       6       1       6       8       7       1       6
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+       1       6       1       1       1       6       8       7       1       6
+       1       6       1       1       6       1       6       1       1       1
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+       6       1       1       6       1       1       6       1       1       6
+       1       1       7       1       1       1       6       8       7       1
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+       1       8       1       6       8       7       1       6       1       6
+       1       1       6       1       1      16       6       1       1       1
+       6       8       7       1       6       1       6       1       1       6
+       1       1      16       6       1       1       1       6       8       7
+       1       6       1       6       1       1       6       1       1       6
+       1       1       6       1       1       7       1       1       1       6
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+       1       1       6       1       1       6       1       1       7       1
+       6       7       1       1       7       1       1       6       8       7
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+       1       6       8       7       1       6       1       6       1       1
+       1       6       8       7       1       6       1       6       1       1
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+       6       1       1       1       6       8       7       1       6       1
+       6       1       6       1       1       1       8       1       6       8
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+       6       1       6       8       1       6       1       6       1       6
+       8       7       1       6       1       6       1       6       1       1
+       1       6       1       1       6       1       1       1       6       8
+       7       1       6       1       1       6       8       7       1       6
+       1       6       1       1       1       6       8       7       1       6
+       1       6       1       1       6       1       1       6       8       8
+       6       8       7       1       6       1       6       1       1       6
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+       1       1       6       8       7       1       6       1       6       1
+       1       1       6       8       7       1       6       1       6       1
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+       1       6       1       6       8       7       1       6       1       6
+       1       1       8       1       6       8       7       1       6       1
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+       6       8       7       1       6       1       6       1       1       6
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+       8       6       8       7       1       6       1       1       6       8
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+%FLAG MASS                                                                      
+%FORMAT(5E16.8)                                                                 
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+%FLAG ATOM_TYPE_INDEX                                                           
+%FORMAT(10I8)                                                                   
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+       2       2       8       9       1       2       3       6       3       5
+       3       5       5       5       3       5       5       5       8       9
+       1       2       3       6       3       5       5       8       8      14
+       1       2       8       8      10       8      10       8      10       8
+      10       8       8       9       1       2       3       6       3       5
+       5       8       9       9       8       9       1       2       3       6
+       6       8       9       1       2       3       6       3       5       5
+       3       5       3       5       5       5       3       5       5       5
+       8       9       1       2       3       6       3       5       5       8
+       9       9       8       9       1       2       3       6       3       5
+       5       5       8       9       1       2       3       6       3       5
+       3       5       5       5       3       5       5       3       5       5
+       5       8       9       1       2       3       6       3       5       3
+       5       5       5       3       5       5       5       8       9       1
+       2       3       6       3       5       5       8       1       8      13
+       1       2       8      14       8       9       1       2       3       6
+       3       6       6      11      12       8       9       1       2       3
+       6       3       5       3       5       5       5       3       5       5
+       3       5       5       5       8       9       1       2       3       6
+       3       5       5       5       8       9       1       2       3       6
+       3       5       5       8       8      10       8      10       8      10
+       8      10       8      10       8       9       1       2       3       6
+       3       5       5       5       8       9       1       3       6       6
+       3       5       5       3       5       5       3       6       8       9
+       1       2       3       6       3       5       5       3       5       5
+       3       6       6       1       2       8       1       2       2       1
+       2       2       8       9       1       2       3       6       3       5
+       5       8       9       9       8       9       1       2       3       6
+       3       5       5       3       5       5       8       9       1       2
+       2       8       9       1       2       3       6       3       5       5
+       3       5       3       5       5       5       3       5       5       5
+       8       9       1       2       3       6       3       5       5       3
+       5       5       8       9       9       8       9       1       2       3
+       6       6       8       9       1       2       3       6       3       5
+       5       8       9       1       2       2       8       9       1       2
+       3       6       3       5       5       8       8      10       8      10
+       8      10       8      10       8      10       8       9       1       2
+       3       6       3       5       3       5       5       5       3       5
+       5       3       5       5       5       8       9       1       2       3
+       6       3       5       5       8       9       9       8       9       1
+       2       3       6       3       6       6       7       2       8       9
+       1       2       3       6       3       5       3       5       5       5
+       3       5       5       5       8       9       1       2       3       6
+       3       6       3       5       5       5      11      12       8       9
+       1       2       3       6       3       5       5       3       5       5
+       3       6       6       1       2       8       1       2       2       1
+       2       2       8       9       1       2       3       6       3       5
+       5       3       5       5       8       9       9       8       9       1
+       2       3       6       6       8       9       1       2       3       6
+       3       5       5       8       8      10       8      10       8      10
+       8      10       8      10       8       9       1       2       3       6
+       3       6       6      11      12       8       9       1       2       3
+       6       3       5       3       5       5       5       3       5       5
+       3       5       5       5       8       9       1       2       3       6
+       3       5       5       5       8       9       1       2       3       6
+       3       5       5       8       1       8      13       1       2       8
+      14       8       9       1       2       3       6       3       5       5
+       8       9       9       8       9       1       2       3       6       3
+       5       3       5       5       5       3       5       5       3       5
+       5       5       8       9       1       2       3       6       3       6
+       6      11      12       8       9       1       2       3       6       3
+       5       5       5       8       9       1       2       3       6       3
+       5       5       8       8      10       8      10       8      11      12
+       8      10       8      10       8       9       1       2       3       6
+       3       6       6      11      12       8       9       1       2       3
+       6       3       5       5       8       8      10       8      10       8
+      10       8      10       8      10       8       9       1       2       3
+       6       3       5       5       5       8       9       1       2       3
+       6       3       5       5       5       8       9       1       2       3
+       6       3       5       5       3       5       3       5       5       5
+       3       5       5       5       8       9       1       2       3       6
+       3       5       5       5       8       9       1       2       3       6
+       3       5       5       3       5       5       3       5       5       3
+       4       4       1       2       2       2       8       9       1       2
+       3       6       3       5       5       3       5       5       8       9
+       9       8       9       1       2       3       6       6       8       9
+       1       2       3       6       3       5       5       3       5       5
+       3       6       6       1       2       8       1       2       2       1
+       2       2       8       9       1       2       3       6       3       6
+       6      11      12       8       9       1       2       3       6       3
+       5       5       3       6       6       7       3       6       6       6
+       8       9       1       2       3       6       3       5       5       3
+       6       6       7       3       6       6       6       8       9       1
+       2       3       6       3       5       5       3       5       5       3
+       5       5       3       4       4       1       2       2       2       8
+       9       1       2       3       6       3       5       5       8       9
+       1       2       2       8       9       1       2       3       6       3
+       5       5       3       5       5       3       6       6       1       2
+       8       1       2       2       1       2       2       8       9       1
+       2       3       6       3       5       5       8       9       1       2
+       2       8       9       1       2       3       6       3       5       5
+       5       8       9       1       2       3       6       3       6       6
+      11      12       8       9       1       2       3       6       3       5
+       5       3       6       6       7       3       6       6       6       8
+       9       1       2       3       6       3       5       3       5       5
+       5       3       5       5       5       8       9       1       2       3
+       6       3       5       5       5       8       9       1       2       3
+       6       3       5       5       3       5       3       5       5       5
+       3       5       5       5       8       9       1       2       3       6
+       3       6       3       5       5       5      11      12       8       9
+       1       2       3       6       3       5       5       8       8      10
+       8      10       8      11      12       8      10       8      10       8
+       9       1       2       3       6       3       5       3       5       5
+       5       3       5       5       3       5       5       5       8       9
+       1       2       3       6       6       8       9       1       2       3
+       6       3       5       5       5       8       9       1       2       3
+       6       3       5       5       3       5       5       8       9       9
+       8       9       1       2       3       6       3       5       5       3
+       5       5       3       5       5       3       4       4       1       2
+       2       2       8       9       1       2       3       6       3       5
+       5       5       8       9       1       2       3       6       3       5
+       5       3       6       6       7       3       6       6       6       8
+       9       1       3       6       6       3       5       5       3       5
+       5       3       6       8       9       1       2       3       6       3
+       6       6      11      12       8       9       1       2       3       6
+       3       5       5       8       8      10       8      10       8      11
+      12       8      10       8      10       8       9       1       2       3
+       6       3       5       5       8       9       1       2       2       8
+       9       1       2       3       6       3       6       3       5       5
+       5      11      12       8       9       1       2       3       6       3
+       5       5       3       6       6       7       3       6       6       6
+       8       9       1       2       3       6       6       8       9       1
+       2       3       6       3       5       3       5       5       5       3
+       5       5       5       8       9       1       2       3       6       3
+       5       5       5       8       9       1       2       3       6       3
+       5       5       3       5       5       3       5       5       3       4
+       4       1       2       2       2       8       9       1       2       3
+       6       3       5       5       5       8       9       1       2       3
+       6       3       6       6      11      12       8       9       1       2
+       3       6       3       5       5       3       5       3       5       5
+       5       3       5       5       5       8       9       1       2       3
+       6       3       5       5       3       5       5       8       9       9
+       8       9       1       2       3       6       3       5       5       5
+       8       9       1       2       3       6       3       6       3       5
+       5       5      11      12       8       9       1       2       3       6
+       3       5       3       5       5       5       3       5       5       5
+       8       9       1       2       3       6       3       5       5       3
+       5       5       3       6       6       1       2       8       1       2
+       2       1       2       2       8       9       1       2       3       6
+       3       5       5       8       8      10       8      10       8      11
+      12       8      10       8      10       8       9       1       2       3
+       6       3       6       3       5       5       5      11      12       8
+       9       1       2       3       6       3       5       5       5       8
+       9       1       2       3       6       3       5       5       3       5
+       3       5       5       5       3       5       5       5       8       9
+       1       2       3       6       3       5       5       5       8       9
+       1       2       3       6       3       5       5       3       5       3
+       5       5       5       3       5       5       5       8       9       1
+       2       3       6       6       8       9       1       2       3       6
+       3       5       5       3       5       5       8       9       9       8
+       9       1       2       3       6       3       5       5       8       9
+       9       8       9       1       2       3       6       6       8       9
+       1       2       3       6       3       5       3       5       5       5
+       3       5       5       3       5       5       5       8       9       1
+       2       3       6       3       5       5       3       5       5       3
+       5       5       3       4       4       1       2       2       2       8
+       9       1       2       3       6       3       5       3       5       5
+       5       3       5       5       5       8       9       1       2       3
+       6       3       5       5       8       9       1       2       2       8
+       9       1       2       3       6       3       5       5       5       8
+       9       1       2       3       6       3       5       3       5       5
+       5       3       5       5       5       8       9       1       2       3
+       6       3       6       6      11      12       8       9       1       2
+       3       6       3       5       5       5       8       9       1       2
+       3       6       6       8       9       1       3       6       6       3
+       5       5       3       5       5       3       6       8       9       1
+       2       3       6       3       5       3       5       5       5       3
+       5       5       3       5       5       5       8       9       1       2
+       3       6       3       5       5       3       5       5       3       5
+       5       3       4       4       1       2       2       2       8       9
+       1       2       3       6       3       6       3       5       5       5
+      11      12       8       9       1       2       3       6       3       5
+       5       3       5       3       5       5       5       3       5       5
+       5       8       9       1       2       3       6       3       5       5
+       5       8       9       1       2       3       6       3       5       5
+       5       8       9       1       2       3       6       3       6       6
+      11      12       8       9       1       2       3       6       6       8
+       9       1       2       3       6       3       5       3       5       5
+       5       3       5       5       3       5       5       5       8       9
+       1       2       3       6       3       6       6      11      12       8
+       9       1       2       3       6       3       5       5       8       9
+       1       2       2       8       9       1       2       3       6       3
+       5       5       8       8      10       8      10       8      10       8
+      10       8      10       8       9       1       2       3       6       3
+       5       5       3       5       5       3       5       5       3       4
+       4       1       2       2       2       8       9       1       2       3
+       6       3       5       5       3       5       5       3       5       5
+       3       4       4       1       2       2       2       8       9       1
+       2       3       6       3       5       5       3       6       6       7
+       3       6       6       6       8       9       1       2       3       6
+       3       5       5       3       5       3       5       5       5       3
+       5       5       5       8       9       1       2       3       6       3
+       5       5       8       9       9       8       9       1       2       3
+       6       3       5       5       8       8      10       8      10       8
+      11      12       8      10       8      10       8       9       1       2
+       3       6       3       5       5       8       9       1       2       2
+       8       9       1       2       3       6       3       5       5       5
+       8       9       1       2       3       6       3       5       5       3
+       6       6       7       3       6       6       6       8       9       1
+       2       3       6       3       5       3       5       5       5       3
+       5       5       5       8       9       1       2       3       6       3
+       6       6      11      12       8       9       1       3       6       6
+       3       5       5       3       5       5       3       6       8       9
+       1       2       3       6       3       5       5       3       5       3
+       5       5       5       3       5       5       5       8       9       1
+       2       3       6       3       5       5       3       5       5       3
+       5       5       3       4       4       1       2       2       2       8
+       9       1       2       3       6       3       5       5       3       5
+       5       3       5       5       3       4       4       1       2       2
+       2       8       9       1       2       3       6       3       5       5
+       8       9       1       2       2       8       9       1       2       3
+       6       3       5       3       5       5       5       3       5       5
+       5       8       9       1       2       3       6       3       5       5
+       8       9       9       8       9       1       2       3       6       3
+       5       3       5       5       5       3       5       5       3       5
+       5       5       8       9       1       2       3       6       3       5
+       5       3       6       6       7       3       6       6       6       8
+       9       1       2       3       6       3       5       5       3       5
+       5       8       9       9       8       9       1       2       3       6
+       3       5       3       5       5       5       3       5       5       5
+       8       9       1       2       3       6       6       8       9       1
+       2       3       6       3       5       5       8       9       1       2
+       2       8       9       1       2       3       6       3       6       3
+       5       5       5      11      12       8       9       1       2       3
+       6       3       5       3       5       5       5       3       5       5
+       5       8       9       1       2       3       6       3       5       5
+       5       8       9       1       2       3       6       3       5       5
+       8       8      10       8      10       8      10       8      10       8
+      10       8       9       1       2       3       6       3       5       5
+       3       5       3       5       5       5       3       5       5       5
+       8       9       1       2       3       6       3       6       6       7
+       2       8       9       1       2       3       6       3       6       6
+      11      12       8       9       1       2       3       6       3       5
+       5       8       9       9       8       9       1       2       3       6
+       3       5       5       3       6       6       7       3       6       6
+       6       8       9       1       2       3       6       3       5       5
+       5       8       9       1       2       3       6       3       6       3
+       5       5       5      11      12       8       9       1       2       3
+       6       6       8       9       1       2       3       6       3       5
+       3       5       5       5       3       5       5       3       5       5
+       5       8       9       1       2       3       6       3       6       3
+       5       5       5      11      12       8       9       1       2       3
+       6       6       8       9       1       2       3       6       3       5
+       5       3       5       5       8       9       9       8       9       1
+       2       3       6       3       5       3       5       5       5       3
+       5       5       5       8       9       1       2       3       6       3
+       5       3       5       5       5       3       5       5       5       8
+       9       1       2       3       6       3       5       5       8       1
+       8      13       1       2       8      14       8       9       1       2
+       3       6       3       5       3       5       5       5       3       5
+       5       5       8       9       1       2       3       6       3       5
+       5       8       9       9       8       9       1       2       3       6
+       3       5       5       5       8       9       1       2       3       6
+       6       8       9       1       2       3       6       3       5       5
+       8       8      10       8      10       8      11      12       8      10
+       8      10       8       9       1       2       3       6       3       5
+       5       8       1       8      13       1       2       8      14       8
+       9       1       2       3       6       3       6       6       7       2
+       8       9       1       2       3       6       3       5       3       5
+       5       5       3       5       5       5       8       9       1       2
+       3       6       3       6       6      11      12       8       9       1
+       2       3       6       3       5       5       3       6       6       7
+       3       6       6       6       8       9       1       2       3       6
+       6       8       9       1       2       3       6       3       5       5
+       8       9       1       2       2       8       9       1       2       3
+       6       3       5       3       5       5       5       3       5       5
+       5       8       9       1       2       3       6       3       5       5
+       3       5       3       5       5       5       3       5       5       5
+       8       9       1       2       3       6       3       5       5       3
+       5       3       5       5       5       3       5       5       5       8
+       9       1       2       3       6       3       5       5       3       5
+       5       8       9       9       8       9       1       2       3       6
+       3       5       5       8       1       8      13       1       2       8
+      14       8       9       1       2       3       6       3       5       5
+       8       1       8      13       1       2       8      14       8       9
+       1       2       3       6       3       5       5       8       1       8
+      13       1       2       8      14       8       9       1       2       3
+       6       3       5       5       8       1       8      13       1       2
+       8      14       8       9       1       2       3       6       3       5
+       5       8       1       8      13       1       2       8      14       8
+       9       1       2       3       6       3       5       5       8       1
+       8      13       1       2       8      14       8       9       9      15
+       9       9      16       3       3      16       3      11       3      11
+       3       1       8       1       8       8       1       1       8       1
+       8      16      15       9       9      16       3       3      16       3
+      11       3      11       3       1       8       8       8       9       1
+       8       8       8       6       6       6       6      12       6      12
+      17      13       2       2      13       6       6       6       6      12
+       6      12      17      10       2       2      10      10      10       8
+       8       8       8       8       8      16      11       8       8       8
+       8       8       8      18      18      18      10      10      10      12
+      10      10      10
+%FLAG NUMBER_EXCLUDED_ATOMS                                                     
+%FORMAT(10I8)                                                                   
+      12       6       5       4      13       7      10       6       5       8
+       3       2       4       3       2       1       1       7       3       7
+       4       7       4       3       7       3      10       4      12       7
+      12       5       4      10       8       4       6       3       5       3
+       3       2       1       1       7       3      10       4      13       7
+      15       6       5      10       8       7       3       2       1       3
+       2       1       1       7       3      10       4      10       7       6
+       3       2       1       7       3       7       4       7       4       3
+       7       3      10       4      13       7      12       6       5      10
+       5       4       9       5       4       6       5       4       3       2
+       1       1       7       3      10       4      13       7      12       6
+       5      10       5       4       9       5       4       6       5       4
+       3       2       1       1       7       3      10       4      16       7
+      15       9       8       3       2       1       7       5       4       3
+       2       1       1       7       3      10       4      13       7      15
+       6       5      10       8       7       3       2       1       3       2
+       1       1       7       3      10       4      16       7      15       9
+       8       3       2       1       7       5       4       3       2       1
+       1       7       3      10       4      14       7      10       7       6
+       3       2       1       2       1       7       3       7       4       7
+       4       3       7       3      10       4      13       7      15       6
+       5      10       8       7       3       2       1       3       2       1
+       1       7       3      10       4      13       7      15       6       5
+      10       8       7       3       2       1       3       2       1       1
+       7       3      10       4      11       7       7       4       3       2
+       1       7       3      10       4      12       7      10       5       4
+       5       3       2       1       1       7       3      10       4      13
+       7      12       6       5      10       5       4       9       5       4
+       6       5       4       3       2       1       1       7       3      10
+       4      11       7       7       4       3       2       1       7       3
+      10       4      16       7      15       9       8       3       2       1
+       7       5       4       3       2       1       1       7       3      10
+       4      10       7       6       3       2       1       7       3      10
+       4      12       7      12       5       4      10       8       4       7
+       3       6       4       1       3       2       1       1       7       3
+       7       4       7       4       3       7       3      10       4      16
+       7      15       9       8       3       2       1       7       5       4
+       3       2       1       1       7       3      10       4      10       7
+       6       3       2       1       7       3      10       4      13       7
+      12       6       5      10       5       4       9       5       4       6
+       5       4       3       2       1       1       7       3      10       4
+      10       7       6       3       2       1       7       3      10       4
+      13       7      10       6       5       8       3       2       4       3
+       2       1       1       7       3      10       4      12       7      11
+       5       4       8       6       5       3       3       2       1       1
+       7       3      10       4      13       7      12       6       5       9
+       5       4       7       4       3       8       3       6       5       2
+       1       2       1       1       7       3      10       4      13       7
+      11       6       5       6       4       3       2       1       1       7
+       3       7       4       7       4       3       7       3      10       4
+      10       7       6       3       2       1       7       3      10       4
+      13       7      11       6       5       6       4       3       2       1
+       1       7       3      10       4      13       7      15       6       5
+      10       8       7       3       2       1       3       2       1       1
+       7       3      10       4      10       7       6       3       2       1
+       7       3      10       4      12       7      12       5       4      10
+       8       4       6       3       5       3       3       2       1       1
+       7       3      10       4      14       7      10       7       6       3
+       2       1       2       1       7       3      10       4      12       7
+      12       5       4      10       8       4       7       3       6       4
+       1       3       2       1       1       7       3      10       4      16
+       7      12       9       8       3       2       1       4       2       1
+       1       7       3       7       4       7       4       3       7       3
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+       4       3       2       1       1       7       3      10       4      12
+       7      12       5       4      10       8       4       6       3       5
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+       7      12       6       5      10       5       4       9       5       4
+       6       5       4       3       2       1       1       7       3      10
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+       3      10       4      13       7      12       6       5       9       5
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+       4       5       3       2       1       1       7       3      10       4
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+       5       3       3       2       1       1       7       3      10       4
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+       4       3       2       1       1       7       3      10       4      12
+       7       8       5       4       3       1       1       7       3      10
+       4      11       7       7       4       3       2       1       7       3
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+       4       2       1       1       7       3      10       4      14       7
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+      10       4      13       7      12       6       5       9       5       4
+       7       4       3       8       3       6       5       2       1       2
+       1       1       7       3      10       4      13       7      11       6
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+       4       7       4       3       7       3      10       4      12       7
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+       3       2       1       1       7       3      10       4      11       7
+       7       4       3       2       1       7       3      10       4      16
+       7      15       9       8       3       2       1       7       5       4
+       3       2       1       1       7       3      10       4      10       7
+       6       3       2       1       7       3      10       4      12       7
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+       1       7       3      10       4      12       7       8       5       4
+       3       1       1       7       3      10       4      16       7      15
+       9       8       3       2       1       7       5       4       3       2
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+       3       2       1       7       3      10       4      10       7       6
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+       5       4      10       8       4       7       3       6       4       1
+       3       2       1       1       7       3      10       4      11       7
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+       7      12       5       4      10       8       4       6       3       5
+       3       3       2       1       1       7       3      10       4      10
+       7       6       3       2       1       7       3      10       4      10
+       7       6       3       2       1       7       3      10       4      13
+       7      15       6       5      10       8       7       3       2       1
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+       7       4       7       4       3       7       3      10       4      10
+       7       6       3       2       1       7       3      10       4      13
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+       1       3       2       1       1       7       3      10       4      12
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+       1       2       1       7       3      10       4      13       7      10
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+       6       5      10       5       4       9       5       4       6       5
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+       7       6       3       2       1       7       3      10       4      11
+       7       7       4       3       2       1       7       3      10       4
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+       1       3       2       1       1       7       3      10       4      13
+       7      11       6       5       6       4       3       2       1       1
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+       7       3      10       4      14       7      10       7       6       3
+       2       1       2       1       7       3      10       4      16       7
+      12       9       8       3       2       1       4       2       1       1
+       7       3      10       4      13       7      12       6       5       9
+       5       4       7       4       3       8       3       6       5       2
+       1       2       1       1       7       3      10       4      12       7
+      12       5       4      10       8       4       7       3       6       4
+       1       3       2       1       1       7       3      10       4      14
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+       3      10       4      10       7       6       3       2       1       7
+       3      10       4      13       7      15       6       5      10       8
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+      10       4      10       7       6       3       2       1       7       3
+      10       4      13       7      15       6       5      10       8       7
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+       4       7       4       3       7       3      10       4      13       7
+      11       6       5       6       4       3       2       1       1       7
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+       1       7       3       7       4       7       4       3       7       3
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+       7       5       4       3       2       1       1       7       3      10
+       4      13       7      12       6       5      10       5       4       9
+       5       4       6       5       4       3       2       1       1       7
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+       1       4       2       1       1       7       3      10       4      12
+       7      10       5       4       5       3       2       1       1       7
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+       3      10       4      16       7      12       9       8       3       2
+       1       4       2       1       1       7       3      10       4      11
+       7       7       4       3       2       1       7       3      10       4
+      10       7       6       3       2       1       7       3       7       4
+       7       4       3      10       3      14      11       6       5       8
+       5       4       7       4       3       6       3       7       3      10
+       4      16       7      15       9       8       3       2       1       7
+       5       4       3       2       1       1       7       3      10       4
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+       4       6       5       4       3       2       1       1       7       3
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+       2       1       7       3      10       4      13       7      15       6
+       5      10       8       7       3       2       1       3       2       1
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+       1       7       3      10       4      11       7       7       4       3
+       2       1       7       3       7       4       7       4       3       7
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+       1       7       5       4       3       2       1       1       7       3
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+       3      10       4      12       7      10       5       4       5       3
+       2       1       1       7       3      10       4      12       7      12
+       5       4      10       8       4       6       3       5       3       3
+       2       1       1       7       3      10       4      13       7      12
+       6       5      10       5       4       9       5       4       6       5
+       4       3       2       1       1       7       3      10       4      13
+       7      12       6       5      10       5       4       9       5       4
+       6       5       4       3       2       1       1       7       3      10
+       4      13       7      10       6       5       8       3       2       4
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+      15       6       5      10       8       7       3       2       1       3
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+       5       4       3       1       1       7       3      10       4      12
+       7      12       5       4      10       8       4       7       3       6
+       4       1       3       2       1       1       7       3      10       4
+      12       7      10       5       4       5       3       2       1       1
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+       7       3      10       4      13       7      10       6       5       8
+       3       2       4       3       2       1       1       7       3      10
+       4      16       7      12       9       8       3       2       1       4
+       2       1       1       7       3      10       4      11       7       7
+       4       3       2       1      10       3      14      11       6       5
+       8       5       4       7       4       3       6       3       7       3
+      10       4      13       7      15       6       5      10       8       7
+       3       2       1       3       2       1       1       7       3      10
+       4      13       7      12       6       5      10       5       4       9
+       5       4       6       5       4       3       2       1       1       7
+       3      10       4      13       7      12       6       5      10       5
+       4       9       5       4       6       5       4       3       2       1
+       1       7       3      10       4      12       7      10       5       4
+       5       3       2       1       1       7       3      10       4      16
+       7      12       9       8       3       2       1       4       2       1
+       1       7       3      10       4      12       7       8       5       4
+       3       1       1       7       3      10       4      16       7      15
+       9       8       3       2       1       7       5       4       3       2
+       1       1       7       3      10       4      13       7      10       6
+       5       8       3       2       4       3       2       1       1       7
+       3      10       4      13       7      11       6       5       6       4
+       3       2       1       1       7       3      10       4      16       7
+      12       9       8       3       2       1       4       2       1       1
+       7       3       7       4       7       4       3       7       3      10
+       4      12       7      10       5       4       5       3       2       1
+       1       7       3      10       4      14       7      10       7       6
+       3       2       1       2       1       7       3      10       4      16
+       7      12       9       8       3       2       1       4       2       1
+       1       7       3      10       4      10       7       6       3       2
+       1       7       3      10       4      12       7      12       5       4
+      10       8       4       6       3       5       3       3       2       1
+       1       7       3      10       4      13       7      15       6       5
+      10       8       7       3       2       1       3       2       1       1
+       7       3      10       4      11       7       7       4       3       2
+       1       7       3      10       4      11       7       7       4       3
+       2       1       7       3      10       4      12       7       8       5
+       4       3       1       1       7       3      10       4      13       7
+      10       6       5       8       3       2       4       3       2       1
+       1       7       3      10       4      10       7       6       3       2
+       1       7       3      10       4      14       7      10       7       6
+       3       2       1       2       1       7       3       7       4       7
+       4       3       7       3      10       4      16       7      15       9
+       8       3       2       1       7       5       4       3       2       1
+       1       7       3      10       4      14       7      10       7       6
+       3       2       1       2       1       7       3       7       4       7
+       4       3       7       3      10       4      13       7      11       6
+       5       6       4       3       2       1       1       7       3      10
+       4      16       7      12       9       8       3       2       1       4
+       2       1       1       7       3      10       4      16       7      12
+       9       8       3       2       1       4       2       1       1       7
+       3      10       4      12       7      11       5       4       8       6
+       5       3       3       2       1       1       7       3      10       4
+      16       7      12       9       8       3       2       1       4       2
+       1       1       7       3      10       4      12       7       8       5
+       4       3       1       1       7       3      10       4      10       7
+       6       3       2       1       7       3       7       4       7       4
+       3       7       3      10       4      12       7      12       5       4
+      10       8       4       7       3       6       4       1       3       2
+       1       1       7       3      10       4      12       7      11       5
+       4       8       6       5       3       3       2       1       1       7
+       3      10       4      11       7       7       4       3       2       1
+       7       3      10       4      16       7      12       9       8       3
+       2       1       4       2       1       1       7       3      10       4
+      11       7       7       4       3       2       1       7       3      10
+       4      13       7      10       6       5       8       3       2       4
+       3       2       1       1       7       3       7       4       7       4
+       3       7       3      10       4      12       7      10       5       4
+       5       3       2       1       1       7       3      10       4      16
+       7      12       9       8       3       2       1       4       2       1
+       1       7       3      10       4      13       7      15       6       5
+      10       8       7       3       2       1       3       2       1       1
+       7       3      10       4      13       7      15       6       5      10
+       8       7       3       2       1       3       2       1       1       7
+       3      10       4      13       7      11       6       5       6       4
+       3       2       1       1       7       3      10       4      12       7
+      11       5       4       8       6       5       3       3       2       1
+       1       7       3      10       4      12       7      11       5       4
+       8       6       5       3       3       2       1       1       7       3
+      10       4      12       7      11       5       4       8       6       5
+       3       3       2       1       1       7       3      10       4      12
+       7      11       5       4       8       6       5       3       3       2
+       1       1       7       3      10       4      12       7      11       5
+       4       8       6       5       3       3       2       1       1       7
+       3      10       4      10       7      11       5       4       8       6
+       5       3       3       2       1       1       2       1       1      12
+       5       4       9      11      14      14      13       7      11       6
+      12      10       7       7       9       8       5       6       3       2
+       3       5       7       3       2       7      10      14      14      13
+       7      11       6      12      11      11      11       8       4       3
+       6       4       5       2       1       1       2       1       2       1
+       1       1       1       1       1       2       1       1       2       1
+       2       1       1       1       1       1       1       1       1      14
+      11       9       7       6       6       9       2       9       8       7
+       7       5       4       1       2       2       1       1       1       1
+       1       1       1
+%FLAG NONBONDED_PARM_INDEX                                                      
+%FORMAT(10I8)                                                                   
+       1       2       4       7      11      16      22      29      37      46
+      56      67      79      92     106     121     137     154       2       3
+       5       8      12      17      23      30      38      47      57      68
+      80      93     107     122     138     155       4       5       6       9
+      13      18      24      31      39      48      58      69      81      94
+     108     123     139     156       7       8       9      10      14      19
+      25      32      40      49      59      70      82      95     109     124
+     140     157      11      12      13      14      15      20      26      33
+      41      50      60      71      83      96     110     125     141     158
+      16      17      18      19      20      21      27      34      42      51
+      61      72      84      97     111     126     142     159      22      23
+      24      25      26      27      28      35      43      52      62      73
+      85      98     112     127     143     160      29      30      31      32
+      33      34      35      36      44      53      63      74      86      99
+     113     128     144     161      37      38      39      40      41      42
+      43      44      45      54      64      75      87     100     114     129
+     145     162      46      47      48      49      50      51      52      53
+      54      55      65      76      88     101     115     130     146     163
+      56      57      58      59      60      61      62      63      64      65
+      66      77      89     102     116     131     147     164      67      68
+      69      70      71      72      73      74      75      76      77      78
+      90     103     117     132     148     165      79      80      81      82
+      83      84      85      86      87      88      89      90      91     104
+     118     133     149     166      92      93      94      95      96      97
+      98      99     100     101     102     103     104     105     119     134
+     150     167     106     107     108     109     110     111     112     113
+     114     115     116     117     118     119     120     135     151     168
+     121     122     123     124     125     126     127     128     129     130
+     131     132     133     134     135     136     152     169     137     138
+     139     140     141     142     143     144     145     146     147     148
+     149     150     151     152     153     170     154     155     156     157
+     158     159     160     161     162     163     164     165     166     167
+     168     169     170     171
+%FLAG RESIDUE_LABEL                                                             
+%FORMAT(20a4)                                                                   
+MET GLY PHE LEU ALA GLY LYS LYS ILE LEU ILE THR GLY LEU LEU SER ASN LYS SER ILE 
+ALA TYR GLY ILE ALA LYS ALA MET HIE ARG GLU GLY ALA GLU LEU ALA PHE THR TYR VAL 
+GLY GLN PHE LYS ASP ARG VAL GLU LYS LEU CYS ALA GLU PHE ASN PRO ALA ALA VAL LEU 
+PRO CYS ASP VAL ILE SER ASP GLN GLU ILE LYS ASP LEU PHE VAL GLU LEU GLY LYS VAL 
+TRP ASP GLY LEU ASP ALA ILE VAL HIE SER ILE ALA PHE ALA PRO ARG ASP GLN LEU GLU 
+GLY ASN PHE ILE ASP CYS VAL THR ARG GLU GLY PHE SER ILE ALA HIE ASP ILE SER ALA 
+TYR SER PHE ALA ALA LEU ALA LYS GLU GLY ARG SER MET MET LYS ASN ARG ASN ALA SER 
+MET VAL ALA LEU THR TYR ILE GLY ALA GLU LYS ALA MET PRO SER TYR ASN THR MET GLY 
+VAL ALA LYS ALA SER LEU GLU ALA THR VAL ARG TYR THR ALA LEU ALA LEU GLY GLU ASP 
+GLY ILE LYS VAL ASN ALA VAL SER ALA GLY PRO ILE LYS THR LEU ALA ALA SER GLY ILE 
+SER ASN PHE LYS LYS MET LEU ASP TYR ASN ALA MET VAL SER PRO LEU LYS LYS ASN VAL 
+ASP ILE MET GLU VAL GLY ASN THR VAL ALA PHE LEU CYS SER ASP MET ALA THR GLY ILE 
+THR GLY GLU VAL VAL HIE VAL ASP ALA GLY TYR HIE CYS VAL SER MET GLY ASN VAL LEU 
+LEU GLU HIE HIE HIE HIE HIE HIE NDP TCS 
+%FLAG RESIDUE_POINTER                                                           
+%FORMAT(10I8)                                                                   
+       1      20      27      47      66      76      83     105     127     146
+     165     184     198     205     224     243     254     268     290     301
+     320     330     351     358     377     387     409     419     436     453
+     477     492     499     509     524     543     553     573     587     608
+     624     631     648     668     690     702     726     742     757     779
+     798     809     819     834     854     868     882     892     902     918
+     937     951     962     974     990    1009    1020    1032    1049    1064
+    1083    1105    1117    1136    1156    1172    1187    1206    1213    1235
+    1251    1275    1287    1294    1313    1325    1335    1354    1370    1387
+    1398    1417    1427    1447    1457    1471    1495    1507    1524    1543
+    1558    1565    1579    1599    1618    1630    1641    1657    1671    1695
+    1710    1717    1737    1748    1767    1777    1794    1806    1825    1836
+    1846    1867    1878    1898    1908    1918    1937    1947    1969    1984
+    1991    2015    2026    2043    2060    2082    2096    2120    2134    2144
+    2155    2172    2188    2198    2217    2231    2252    2271    2278    2288
+    2303    2325    2335    2352    2366    2377    2398    2412    2426    2443
+    2450    2466    2476    2498    2508    2519    2538    2553    2563    2577
+    2593    2617    2638    2652    2662    2681    2691    2710    2717    2732
+    2744    2751    2770    2792    2808    2822    2832    2848    2859    2869
+    2876    2890    2909    2931    2945    2964    2974    2984    2995    3002
+    3021    3032    3046    3066    3088    3110    3127    3146    3158    3179
+    3193    3203    3220    3236    3247    3261    3280    3302    3324    3338
+    3354    3366    3385    3402    3417    3433    3440    3454    3468    3484
+    3494    3514    3533    3544    3555    3567    3584    3594    3608    3615
+    3634    3648    3655    3670    3686    3702    3719    3735    3747    3757
+    3764    3785    3802    3813    3829    3840    3857    3864    3878    3894
+    3913    3932    3947    3964    3981    3998    4015    4032    4050    4120
+%FLAG BOND_FORCE_CONSTANT                                                       
+%FORMAT(5E16.8)                                                                 
+  5.70000000E+02  4.90000000E+02  2.27000000E+02  3.10000000E+02  3.17000000E+02
+  3.67000000E+02  3.37000000E+02  4.69000000E+02  3.17000000E+02  3.20000000E+02
+  4.50000000E+02  4.69000000E+02  4.27000000E+02  4.77000000E+02  4.88000000E+02
+  4.10000000E+02  5.18000000E+02  3.17000000E+02  4.81000000E+02  3.37000000E+02
+  6.56000000E+02  2.37000000E+02  4.69000000E+02  4.69000000E+02  4.47000000E+02
+  4.28000000E+02  5.46000000E+02  3.88000000E+02  3.17000000E+02  4.20000000E+02
+  4.50000000E+02  3.02000000E+02  8.60000000E+02  3.02000000E+02  4.20000000E+02
+  3.37000000E+02  3.20000000E+02  2.30000000E+02  5.25000000E+02  4.61000000E+02
+  5.02000000E+02  4.83000000E+02  5.20000000E+02  4.14000000E+02  5.29000000E+02
+  4.40000000E+02  4.36000000E+02  3.37000000E+02  4.78400000E+02  3.22800000E+02
+  3.72400000E+02  3.86100000E+02  3.40000000E+02  3.40000000E+02  3.40000000E+02
+  4.34000000E+02  4.34000000E+02  3.67000000E+02  5.53000000E+02  3.67000000E+02
+  4.34000000E+02  3.67000000E+02  4.34000000E+02  2.74000000E+02  3.50000000E+02
+  3.50000000E+02  3.50000000E+02  4.34000000E+02  3.40000000E+02  3.67000000E+02
+  3.67000000E+02  3.44300000E+02  3.69600000E+02
+%FLAG BOND_EQUIL_VALUE                                                          
+%FORMAT(5E16.8)                                                                 
+  1.22900000E+00  1.33500000E+00  1.81000000E+00  1.52600000E+00  1.52200000E+00
+  1.47100000E+00  1.44900000E+00  1.40000000E+00  1.51000000E+00  1.41000000E+00
+  1.36400000E+00  1.40900000E+00  1.38100000E+00  1.34300000E+00  1.33500000E+00
+  1.39400000E+00  1.37100000E+00  1.50400000E+00  1.34000000E+00  1.46300000E+00
+  1.25000000E+00  1.81000000E+00  1.40400000E+00  1.40000000E+00  1.41900000E+00
+  1.38000000E+00  1.35200000E+00  1.45900000E+00  1.49500000E+00  1.35000000E+00
+  1.36000000E+00  1.48000000E+00  1.23000000E+00  1.48000000E+00  1.31500000E+00
+  1.47500000E+00  1.41000000E+00  1.61000000E+00  1.48000000E+00  1.35400000E+00
+  1.32400000E+00  1.33900000E+00  1.37000000E+00  1.39100000E+00  1.30400000E+00
+  1.37100000E+00  1.37400000E+00  1.47500000E+00  1.38700000E+00  1.72900000E+00
+  1.37300000E+00  1.36200000E+00  1.09000000E+00  1.09000000E+00  1.09000000E+00
+  1.01000000E+00  1.01000000E+00  1.08000000E+00  9.60000000E-01  1.08000000E+00
+  1.01000000E+00  1.08000000E+00  1.01000000E+00  1.33600000E+00  1.09000000E+00
+  1.09000000E+00  1.09000000E+00  1.01000000E+00  1.09000000E+00  1.08000000E+00
+  1.08000000E+00  1.08700000E+00  9.74000000E-01
+%FLAG ANGLE_FORCE_CONSTANT                                                      
+%FORMAT(5E16.8)                                                                 
+  8.00000000E+01  5.00000000E+01  6.20000000E+01  6.30000000E+01  5.00000000E+01
+  4.00000000E+01  8.00000000E+01  7.00000000E+01  8.00000000E+01  8.00000000E+01
+  6.30000000E+01  6.30000000E+01  7.00000000E+01  6.30000000E+01  8.00000000E+01
+  5.00000000E+01  7.00000000E+01  6.30000000E+01  6.30000000E+01  7.00000000E+01
+  7.00000000E+01  7.00000000E+01  7.00000000E+01  7.00000000E+01  7.00000000E+01
+  7.00000000E+01  6.30000000E+01  7.00000000E+01  5.00000000E+01  8.00000000E+01
+  8.00000000E+01  7.00000000E+01  5.00000000E+01  5.00000000E+01  6.30000000E+01
+  6.30000000E+01  6.30000000E+01  6.30000000E+01  7.00000000E+01  7.00000000E+01
+  6.30000000E+01  7.00000000E+01  7.00000000E+01  6.30000000E+01  6.30000000E+01
+  7.00000000E+01  7.00000000E+01  6.30000000E+01  4.00000000E+01  8.50000000E+01
+  4.00000000E+01  8.50000000E+01  8.50000000E+01  5.00000000E+01  3.00000000E+01
+  1.00000000E+01  1.20000000E+02  7.00000000E+01  5.00000000E+01  5.00000000E+01
+  5.00000000E+01  6.00000000E+01  1.00000000E+02  1.40000000E+02  1.00000000E+02
+  4.50000000E+01  7.00000000E+01  7.00000000E+01  7.00000000E+01  6.30000000E+01
+  7.00000000E+01  7.00000000E+01  7.00000000E+01  7.00000000E+01  7.00000000E+01
+  7.00000000E+01  7.00000000E+01  7.00000000E+01  7.00000000E+01  7.00000000E+01
+  7.00000000E+01  7.00000000E+01  7.00000000E+01  5.00000000E+01  5.00000000E+01
+  1.00000000E+02  6.29200000E+01  6.71800000E+01  6.97900000E+01  6.98500000E+01
+  6.33100000E+01  5.00000000E+01  3.50000000E+01  5.00000000E+01  5.00000000E+01
+  3.50000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01
+  3.50000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01
+  5.00000000E+01  5.00000000E+01  3.50000000E+01  5.00000000E+01  5.50000000E+01
+  3.50000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01
+  5.00000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01
+  5.00000000E+01  3.50000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01
+  5.00000000E+01  4.30000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01
+  5.00000000E+01  5.00000000E+01  3.50000000E+01  3.00000000E+01  8.00000000E+01
+  8.00000000E+01  3.00000000E+01  3.50000000E+01  5.00000000E+01  8.00000000E+01
+  5.00000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01
+  5.00000000E+01  5.00000000E+01  4.84600000E+01  4.88500000E+01
+%FLAG ANGLE_EQUIL_VALUE                                                         
+%FORMAT(5E16.8)                                                                 
+  2.14501057E+00  2.12755727E+00  1.72613137E+00  1.93906163E+00  2.00189351E+00
+  1.91113635E+00  2.10137732E+00  2.03505478E+00  1.94080696E+00  1.94080696E+00
+  1.92160833E+00  2.09439600E+00  2.09439600E+00  1.98967620E+00  1.91462701E+00
+  1.91113635E+00  2.09439600E+00  2.09439600E+00  2.09439600E+00  2.09439600E+00
+  2.09439600E+00  2.09439600E+00  2.04203610E+00  2.09439600E+00  2.09439600E+00
+  2.09439600E+00  1.97396823E+00  2.09439600E+00  2.15024656E+00  1.94080696E+00
+  2.19911580E+00  2.04203610E+00  1.89542838E+00  2.05948940E+00  2.09439600E+00
+  2.14151991E+00  2.09439600E+00  2.02807346E+00  2.31779824E+00  1.82212452E+00
+  1.85703112E+00  1.94778828E+00  1.89717371E+00  1.89891904E+00  2.35445017E+00
+  2.18166250E+00  2.24449438E+00  2.01760148E+00  2.05948940E+00  2.24274905E+00
+  1.92335366E+00  1.97222290E+00  2.06821605E+00  2.05948940E+00  2.09439600E+00
+  2.30034494E+00  2.12930260E+00  2.12406661E+00  1.91113635E+00  1.91113635E+00
+  1.91113635E+00  1.91113635E+00  1.88897066E+00  2.09265067E+00  2.10312265E+00
+  1.79070858E+00  1.93731630E+00  2.25322103E+00  2.08217869E+00  2.04727209E+00
+  2.06996138E+00  2.22878641E+00  2.04727209E+00  2.15548255E+00  1.92684432E+00
+  2.31081692E+00  1.83957782E+00  1.81165254E+00  1.98793087E+00  1.85354046E+00
+  2.20260646E+00  2.24798504E+00  2.19562514E+00  1.91113635E+00  1.91113635E+00
+  2.10312265E+00  2.08392402E+00  2.09387240E+00  2.08043336E+00  2.09334880E+00
+  2.09352334E+00  2.09439600E+00  1.91113635E+00  1.91113635E+00  1.91113635E+00
+  1.91113635E+00  1.91113635E+00  1.91113635E+00  1.91113635E+00  1.91113635E+00
+  1.91113635E+00  1.91113635E+00  1.91113635E+00  2.06018753E+00  1.91113635E+00
+  2.09439600E+00  1.91113635E+00  1.91113635E+00  1.91113635E+00  1.89368305E+00
+  2.09439600E+00  1.91113635E+00  1.97222290E+00  2.09439600E+00  2.09439600E+00
+  2.09439600E+00  2.09439600E+00  2.09439600E+00  2.09439600E+00  2.09439600E+00
+  1.91113635E+00  2.09439600E+00  2.09439600E+00  1.91113635E+00  2.06647072E+00
+  1.91113635E+00  1.67551680E+00  2.09439600E+00  2.09439600E+00  2.14850123E+00
+  2.09439600E+00  1.91113635E+00  2.09439600E+00  2.12930260E+00  2.11184930E+00
+  2.10312265E+00  2.07694270E+00  2.09439600E+00  1.91113635E+00  2.05076275E+00
+  1.91113635E+00  1.91113635E+00  1.91113635E+00  2.01498349E+00  2.14762857E+00
+  1.91113635E+00  2.14762857E+00  2.09457053E+00  1.91061275E+00
+%FLAG DIHEDRAL_FORCE_CONSTANT                                                   
+%FORMAT(5E16.8)                                                                 
+  2.50000000E+00  0.00000000E+00  2.70000000E-01  4.20000000E-01  0.00000000E+00
+  1.55555556E-01  0.00000000E+00  2.00000000E-01  2.00000000E-01  4.00000000E-01
+  3.33333333E-01  2.00000000E+00  2.00000000E+00  4.50000000E-01  1.58000000E+00
+  5.50000000E-01  3.62500000E+00  2.00000000E-01  2.50000000E-01  1.80000000E-01
+  2.40000000E+00  5.37500000E+00  2.32500000E+00  5.00000000E+00  1.50000000E+00
+  0.00000000E+00  3.00000000E+00  3.50000000E+00  6.52500000E+00  1.67500000E+00
+  1.52500000E+00  1.05000000E+01  1.10000000E+00  1.00000000E+00  6.20000000E-01
+  2.38000000E+00  4.00000000E+00  6.00000000E+00  3.50000000E-01  7.00000000E+00
+  1.17500000E+00  1.44000000E-01  1.00000000E-01  3.83000000E-01  3.83333333E-01
+  2.50000000E-01  1.20000000E+00  6.80000000E+00  4.80000000E+00  5.45000000E+00
+  4.15000000E+00  1.70000000E+00  1.65000000E+00  2.55000000E+00  1.00000000E+01
+  2.50000000E+00  6.50000000E-01  9.00000000E-01  8.00000000E-01  8.00000000E-02
+  1.60000000E-01  1.50000000E-01  2.50000000E-01  1.66666667E-01  2.30000000E+00
+  2.00000000E+00
+%FLAG DIHEDRAL_PERIODICITY                                                      
+%FORMAT(5E16.8)                                                                 
+  2.00000000E+00  1.00000000E+00  2.00000000E+00  3.00000000E+00  4.00000000E+00
+  3.00000000E+00  2.00000000E+00  1.00000000E+00  2.00000000E+00  3.00000000E+00
+  3.00000000E+00  1.00000000E+00  2.00000000E+00  1.00000000E+00  2.00000000E+00
+  3.00000000E+00  2.00000000E+00  1.00000000E+00  2.00000000E+00  3.00000000E+00
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  3.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  1.00000000E+00  2.00000000E+00
+  2.00000000E+00  3.00000000E+00  2.00000000E+00  3.00000000E+00  3.00000000E+00
+  3.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  1.00000000E+00  2.00000000E+00  2.00000000E+00  1.00000000E+00  3.00000000E+00
+  3.00000000E+00  3.00000000E+00  1.00000000E+00  3.00000000E+00  2.00000000E+00
+  2.00000000E+00
+%FLAG DIHEDRAL_PHASE                                                            
+%FORMAT(5E16.8)                                                                 
+  3.14159400E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  3.14159400E+00  3.14159400E+00
+  3.14159400E+00  3.14159400E+00  3.14159400E+00  3.14159400E+00  0.00000000E+00
+  3.14159400E+00  3.14159400E+00  3.14159400E+00  3.14159400E+00  3.14159400E+00
+  0.00000000E+00  3.14159400E+00  3.14159400E+00  3.14159400E+00  3.14159400E+00
+  3.14159400E+00  3.14159400E+00  3.14159400E+00  3.14159400E+00  0.00000000E+00
+  3.14159400E+00  3.14159400E+00  3.14159400E+00  0.00000000E+00  3.14159400E+00
+  0.00000000E+00  0.00000000E+00  3.14159400E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  3.14159400E+00  3.14159400E+00  3.14159400E+00
+  3.14159400E+00  3.14159400E+00  3.14159400E+00  3.14159400E+00  3.14159400E+00
+  0.00000000E+00  0.00000000E+00  3.14159400E+00  0.00000000E+00  3.14159400E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  3.14159400E+00
+  3.14159400E+00
+%FLAG SCEE_SCALE_FACTOR                                                         
+%FORMAT(5E16.8)                                                                 
+  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00
+  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00
+  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00
+  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00
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+%FLAG SCNB_SCALE_FACTOR                                                         
+%FORMAT(5E16.8)                                                                 
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+%FLAG SOLTY                                                                     
+%FORMAT(5E16.8)                                                                 
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+%FLAG LENNARD_JONES_ACOEF                                                       
+%FORMAT(5E16.8)                                                                 
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+%FLAG LENNARD_JONES_BCOEF                                                       
+%FORMAT(5E16.8)                                                                 
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+%FLAG BONDS_INC_HYDROGEN                                                        
+%FORMAT(10I8)                                                                   
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+%FLAG BONDS_WITHOUT_HYDROGEN                                                    
+%FORMAT(10I8)                                                                   
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+%FLAG ANGLES_INC_HYDROGEN                                                       
+%FORMAT(10I8)                                                                   
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+   10494   10491   10497      96   10494   10491   10500     107   10488   10485
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+   10485   10491   10497      95   10482   10479   10485     104   10479   10485
+   10488     105   10590   10596   10599      92   10584   10578   10587      96
+   10581   10578   10584      96   10581   10578   10587      96   10572   10566
+   10575      96   10569   10566   10572      96   10569   10566   10575      96
+   10563   10560   10566      95   10563   10560   10578      95   10560   10566
+   10569      95   10560   10566   10572      95   10560   10566   10575      95
+   10560   10578   10581      95   10560   10578   10584      95   10560   10578
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+   10554   10551   10560      95   10551   10560   10563      95   10548   10545
+   10551      97   10548   10545   10590     103   10545   10551   10554      95
+   10545   10551   10557      95   10542   10539   10545     104   10539   10545
+   10548     105   10623   10629   10632      92   10614   10608   10617     126
+   10611   10608   10614      93   10611   10608   10617     126   10608   10617
+   10620     127   10605   10602   10608      97   10605   10602   10623     103
+   10602   10608   10611      97   10602   10608   10614      97   10599   10596
+   10602     104   10596   10602   10605     105   10656   10662   10665      92
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+   10638   10635   10656     103   10635   10641   10644      97   10635   10641
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+   10680      96   10677   10674   10683     112   10671   10668   10674      97
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+   10728      94   10722   10719   10725      93   10722   10719   10728      94
+   10716   10710   10719      95   10713   10710   10716      96   10713   10710
+   10719      95   10710   10719   10722      97   10710   10719   10725      97
+   10707   10704   10710      97   10707   10704   10743     103   10704   10710
+   10713      95   10704   10710   10716      95   10701   10698   10704     104
+   10698   10704   10707     105   10773   10779   10782      92   10767   10761
+   10770      96   10764   10761   10767      96   10764   10761   10770      96
+   10758   10755   10761      97   10758   10755   10773     103   10755   10761
+   10764      95   10755   10761   10767      95   10755   10761   10770      95
+   10752   10749   10755     104   10749   10755   10758     105   10815   10821
+   10824      92   10803   10797   10806      96   10800   10797   10803      96
+   10800   10797   10806      96   10794   10791   10797      97   10794   10791
+   10809     109   10791   10797   10800      95   10791   10797   10803      95
+   10791   10797   10806      95   10791   10809   10812     110   10788   10785
+   10791      97   10788   10785   10815     103   10785   10791   10794      97
+   10782   10779   10785     104   10779   10785   10788     105   10836   10842
+   10845      92   10833   10827   10836     103   10830   10827   10833      93
+   10830   10827   10836     103   10824   10821   10827     104   10821   10827
+   10830     105   10821   10827   10833     105   10893   10899   10902      92
+   10887   10881   10890      96   10884   10881   10887      96   10884   10881
+   10890      96   10878   10872   10881      95   10875   10872   10878      96
+   10875   10872   10881      95   10872   10881   10884      95   10872   10881
+   10887      95   10872   10881   10890      95   10866   10860   10869      96
+   10863   10860   10866      96   10863   10860   10869      96   10857   10854
+   10860      95   10857   10854   10872      95   10854   10860   10863      95
+   10854   10860   10866      95   10854   10860   10869      95   10854   10872
+   10875      95   10854   10872   10878      95   10851   10848   10854      97
+   10851   10848   10893     103   10848   10854   10857      95   10845   10842
+   10848     104   10842   10848   10851     105   10935   10941   10944      92
+   10923   10917   10926      96   10920   10917   10923      96   10920   10917
+   10926      96   10914   10911   10917      97   10914   10911   10929     109
+   10911   10917   10920      95   10911   10917   10923      95   10911   10917
+   10926      95   10911   10929   10932     110   10908   10905   10911      97
+   10908   10905   10935     103   10905   10911   10914      97   10902   10899
+   10905     104   10899   10905   10908     105   10956   10962   10965      92
+   10953   10947   10956     103   10950   10947   10953      93   10950   10947
+   10956     103   10944   10941   10947     104   10941   10947   10950     105
+   10941   10947   10953     105   11001   11007   11010      92   10989   10983
+   10992     112   10986   10983   10989      96   10986   10983   10992     112
+   10980   10974   10983      95   10977   10974   10980      96   10977   10974
+   10983      95   10974   10983   10986      95   10974   10983   10989      95
+   10971   10968   10974      97   10971   10968   11001     103   10968   10974
+   10977      95   10968   10974   10980      95   10965   10962   10968     104
+   10962   10968   10971     105   11049   11055   11058      92   11043   11037
+   11046      96   11040   11037   11043      96   11040   11037   11046      96
+   11031   11025   11034      96   11028   11025   11031      96   11028   11025
+   11034      96   11022   11019   11025      95   11022   11019   11037      95
+   11019   11025   11028      95   11019   11025   11031      95   11019   11025
+   11034      95   11019   11037   11040      95   11019   11037   11043      95
+   11019   11037   11046      95   11016   11013   11019      97   11016   11013
+   11049     103   11013   11019   11022      95   11010   11007   11013     104
+   11007   11013   11016     105   11097   11103   11106      92   11091   11085
+   11094      96   11088   11085   11091      96   11088   11085   11094      96
+   11079   11073   11082      96   11076   11073   11079      96   11076   11073
+   11082      96   11070   11067   11073      95   11070   11067   11085      95
+   11067   11073   11076      95   11067   11073   11079      95   11067   11073
+   11082      95   11067   11085   11088      95   11067   11085   11091      95
+   11067   11085   11094      95   11064   11061   11067      97   11064   11061
+   11097     103   11061   11067   11070      95   11058   11055   11061     104
+   11055   11061   11064     105   11148   11154   11157      92   11139   11136
+   11142     115   11136   11142   11145     116   11133   11130   11136     117
+   11130   11136   11139     118   11127   11130   11133     119   11124   11142
+   11145     120   11121   11115   11124     121   11118   11115   11121      96
+   11118   11115   11124     121   11112   11109   11115      97   11112   11109
+   11148     103   11109   11115   11118      95   11109   11115   11121      95
+   11106   11103   11109     104   11103   11109   11112     105   11196   11202
+   11205      92   11190   11184   11193      96   11187   11184   11190      96
+   11187   11184   11193      96   11178   11172   11181      96   11175   11172
+   11178      96   11175   11172   11181      96   11169   11166   11172      95
+   11169   11166   11184      95   11166   11172   11175      95   11166   11172
+   11178      95   11166   11172   11181      95   11166   11184   11187      95
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+   11166      97   11163   11160   11196     103   11160   11166   11169      95
+   11157   11154   11160     104   11154   11160   11163     105   11232   11238
+   11241      92   11220   11214   11223     112   11217   11214   11220      96
+   11217   11214   11223     112   11211   11208   11214      97   11211   11208
+   11232     103   11208   11214   11217      95   11208   11214   11220      95
+   11205   11202   11208     104   11202   11208   11211     105   11262   11268
+   11271      92   11256   11250   11259      96   11253   11250   11256      96
+   11253   11250   11259      96   11247   11244   11250      97   11247   11244
+   11262     103   11244   11250   11253      95   11244   11250   11256      95
+   11244   11250   11259      95   11241   11238   11244     104   11238   11244
+   11247     105   11283   11289   11292      92   11280   11274   11283     103
+   11277   11274   11280      93   11277   11274   11283     103   11271   11268
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+   11346   11352   11355      92   11337   11334   11340     106   11334   11340
+   11343     106   11325   11328   11331     113   11325   11334   11337     114
+   11322   11319   11325     114   11316   11313   11319     106   11313   11319
+   11322     106   11310   11313   11316     106   11310   11340   11343     106
+   11307   11301   11310     107   11304   11301   11307      96   11304   11301
+   11310     107   11298   11295   11301      97   11298   11295   11346     103
+   11295   11301   11304      95   11295   11301   11307      95   11292   11289
+   11295     104   11289   11295   11298     105   11397   11403   11406      92
+   11388   11385   11391     115   11385   11391   11394     116   11382   11379
+   11385     117   11379   11385   11388     118   11376   11379   11382     119
+   11373   11391   11394     120   11370   11364   11373     121   11367   11364
+   11370      96   11367   11364   11373     121   11361   11358   11364      97
+   11361   11358   11397     103   11358   11364   11367      95   11358   11364
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+   11430   11436   11439      92   11421   11415   11424     126   11418   11415
+   11421      93   11418   11415   11424     126   11415   11424   11427     127
+   11412   11409   11415      97   11412   11409   11430     103   11409   11415
+   11418      97   11409   11415   11421      97   11406   11403   11409     104
+   11403   11409   11412     105   11478   11484   11487      92   11472   11466
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+   11460   11454   11463      96   11457   11454   11460      96   11457   11454
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+   11448   11454   11457      95   11448   11454   11460      95   11448   11454
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+   11448   11466   11475      95   11445   11442   11448      97   11445   11442
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+   11496   11505   11508     110   11493   11490   11496      97   11493   11490
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+   11487   11484   11490     104   11484   11490   11493     105   11562   11568
+   11571      92   11556   11550   11559      93   11553   11550   11556      93
+   11553   11550   11559      93   11547   11550   11553      94   11547   11550
+   11556      94   11547   11550   11559      94   11544   11538   11547      94
+   11541   11538   11544      93   11541   11538   11547      94   11535   11529
+   11538      95   11532   11529   11535      96   11532   11529   11538      95
+   11529   11538   11541      97   11529   11538   11544      97   11526   11523
+   11529      97   11526   11523   11562     103   11523   11529   11532      95
+   11523   11529   11535      95   11520   11517   11523     104   11517   11523
+   11526     105   11583   11589   11592      92   11580   11574   11583     103
+   11577   11574   11580      93   11577   11574   11583     103   11571   11568
+   11574     104   11568   11574   11577     105   11568   11574   11580     105
+   11625   11631   11634      92   11619   11616   11622     111   11610   11616
+   11619      92   11610   11616   11622      92   11607   11601   11610     112
+   11604   11601   11607      96   11604   11601   11610     112   11598   11595
+   11601      97   11598   11595   11625     103   11595   11601   11604      95
+   11595   11601   11607      95   11592   11589   11595     104   11589   11595
+   11598     105   11673   11679   11682      92   11667   11661   11670      96
+   11664   11661   11667      96   11664   11661   11670      96   11655   11649
+   11658      96   11652   11649   11655      96   11652   11649   11658      96
+   11646   11643   11649      95   11646   11643   11661      95   11643   11649
+   11652      95   11643   11649   11655      95   11643   11649   11658      95
+   11643   11661   11664      95   11643   11661   11667      95   11643   11661
+   11670      95   11640   11637   11643      97   11640   11637   11673     103
+   11637   11643   11646      95   11634   11631   11637     104   11631   11637
+   11640     105   11730   11736   11739      92   11724   11718   11727      96
+   11721   11718   11724      96   11721   11718   11727      96   11712   11706
+   11715      96   11709   11706   11712      96   11709   11706   11715      96
+   11703   11700   11706      95   11703   11700   11718      95   11700   11706
+   11709      95   11700   11706   11712      95   11700   11706   11715      95
+   11700   11718   11721      95   11700   11718   11724      95   11700   11718
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+   11778   11775   11781      96   11778   11775   11784      96   11769   11763
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+   11805      97   11802   11799   11832     103   11799   11805   11808      95
+   11799   11805   11811      95   11796   11793   11799     104   11793   11799
+   11802     105   11883   11889   11892      92   11874   11871   11877     115
+   11871   11877   11880     116   11868   11865   11871     117   11865   11871
+   11874     118   11862   11865   11868     119   11859   11877   11880     120
+   11856   11850   11859     121   11853   11850   11856      96   11853   11850
+   11859     121   11847   11844   11850      97   11847   11844   11883     103
+   11844   11850   11853      95   11844   11850   11856      95   11841   11838
+   11844     104   11838   11844   11847     105   11934   11940   11943      92
+   11925   11922   11928     115   11922   11928   11931     116   11919   11916
+   11922     117   11916   11922   11925     118   11913   11916   11919     119
+   11910   11928   11931     120   11907   11901   11910     121   11904   11901
+   11907      96   11904   11901   11910     121   11898   11895   11901      97
+   11898   11895   11934     103   11895   11901   11904      95   11895   11901
+   11907      95   11892   11889   11895     104   11889   11895   11898     105
+   11985   11991   11994      92   11976   11973   11979     115   11973   11979
+   11982     116   11970   11967   11973     117   11967   11973   11976     118
+   11964   11967   11970     119   11961   11979   11982     120   11958   11952
+   11961     121   11955   11952   11958      96   11955   11952   11961     121
+   11949   11946   11952      97   11949   11946   11985     103   11946   11952
+   11955      95   11946   11952   11958      95   11943   11940   11946     104
+   11940   11946   11949     105   12036   12042   12045      92   12027   12024
+   12030     115   12024   12030   12033     116   12021   12018   12024     117
+   12018   12024   12027     118   12015   12018   12021     119   12012   12030
+   12033     120   12009   12003   12012     121   12006   12003   12009      96
+   12006   12003   12012     121   12000   11997   12003      97   12000   11997
+   12036     103   11997   12003   12006      95   11997   12003   12009      95
+   11994   11991   11997     104   11991   11997   12000     105   12087   12093
+   12096      92   12078   12075   12081     115   12075   12081   12084     116
+   12072   12069   12075     117   12069   12075   12078     118   12066   12069
+   12072     119   12063   12081   12084     120   12060   12054   12063     121
+   12057   12054   12060      96   12057   12054   12063     121   12051   12048
+   12054      97   12051   12048   12087     103   12048   12054   12057      95
+   12048   12054   12060      95   12045   12042   12048     104   12042   12048
+   12051     105   12129   12126   12132     115   12126   12132   12135     116
+   12123   12120   12126     117   12120   12126   12129     118   12117   12120
+   12123     119   12114   12132   12135     120   12111   12105   12114     121
+   12108   12105   12111      96   12108   12105   12114     121   12102   12099
+   12105      97   12102   12099   12138     103   12099   12105   12108      95
+   12099   12105   12111      95   12096   12093   12099     104   12093   12099
+   12102     105   12342   12267   12345     133   12315   12228   12318      93
+   12306   12198   12309     122   12279   12159   12282      93   12276   12273
+   12351     134   12273   12270   12348     135   12273   12276   12354     136
+   12270   12273   12351     137   12261   12267   12342     138   12261   12267
+   12345     138   12258   12255   12339     136   12258   12270   12348     135
+   12252   12249   12336     139   12252   12276   12354     140   12252   12255
+   12339     140   12249   12243   12330      97   12246   12243   12330     109
+   12243   12237   12324      97   12243   12249   12336     141   12243   12246
+   12333     110   12240   12237   12324     109   12237   12231   12321      97
+   12237   12243   12330      97   12237   12240   12327     110   12234   12231
+   12321     142   12234   12249   12336     143   12231   12228   12318      97
+   12231   12228   12315      97   12231   12237   12324      97   12228   12231
+   12321      97   12225   12228   12318     142   12225   12228   12315     142
+   12207   12204   12312     144   12201   12204   12312     144   12195   12198
+   12306     123   12195   12198   12309     123   12189   12186   12303     145
+   12183   12180   12300     146   12183   12186   12303     147   12180   12174
+   12294      97   12177   12174   12294     109   12174   12168   12288      97
+   12174   12180   12300     141   12174   12177   12297     110   12171   12168
+   12288     109   12168   12162   12285      97   12168   12174   12294      97
+   12168   12171   12291     110   12165   12162   12285     142   12165   12180
+   12300     143   12162   12159   12279      97   12162   12159   12282      97
+   12162   12168   12288      97   12159   12162   12285      97   12156   12159
+   12279     142   12156   12159   12282     142   12396   12393   12423     148
+   12393   12396   12426     148   12390   12387   12420     148   12390   12393
+   12423     148   12384   12387   12420     148   12381   12396   12426     148
+   12372   12369   12411     148   12369   12372   12414     148   12366   12363
+   12408     148   12366   12369   12411     148   12360   12363   12408     148
+   12360   12378   12417     149   12357   12372   12414     148
+%FLAG ANGLES_WITHOUT_HYDROGEN                                                   
+%FORMAT(10I8)                                                                   
+      54      51      57       1      51      57      63       2      27      36
+      39       3      18      12      51       4      18      27      36       5
+      12      18      27       6      12      51      54       7      12      51
+      57       8       0      12      18       9       0      12      51      10
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+%FLAG DIHEDRALS_INC_HYDROGEN                                                    
+%FORMAT(10I8)                                                                   
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+%FLAG DIHEDRALS_WITHOUT_HYDROGEN                                                
+%FORMAT(10I8)                                                                   
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+%FLAG EXCLUDED_ATOMS_LIST                                                       
+%FORMAT(10I8)                                                                   
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+    4111       0    4112    4113       0       0       0    4116       0    4118
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+    4142    4143    4134    4135    4142    4143    4141    4141    4142    4137
+    4138       0    4139       0       0       0    4143       0
+%FLAG HBOND_ACOEF                                                               
+%FORMAT(5E16.8)                                                                 
+
+%FLAG HBOND_BCOEF                                                               
+%FORMAT(5E16.8)                                                                 
+
+%FLAG HBCUT                                                                     
+%FORMAT(5E16.8)                                                                 
+
+%FLAG AMBER_ATOM_TYPE                                                           
+%FORMAT(20a4)                                                                   
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+%FORMAT(20a4)                                                                   
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+3   E   E   B   E   S   E   B   E   B   E   M   E   M   E   M   E   3   E   E   
+B   E   E   M   E   M   E   M   E   3   E   3   E   E   E   3   E   E   3   E   
+E   E   M   E   M   E   M   E   3   E   E   S   E   M   E   M   E   M   E   3   
+E   E   E   M   E   M   E   M   E   3   E   E   B   B   E   B   E   B   S   E   
+S   E   S   E   M   E   M   E   M   E   3   E   E   S   E   M   E   M   E   M   
+E   3   E   E   B   B   E   B   E   B   E   S   E   S   E   M   E   M   E   M   
+E   3   E   E   E   M   E   M   E   M   E   3   E   E   E   M   E   M   E   M   
+E   3   E   E   3   E   3   E   E   E   3   E   E   E   M   E   M   E   M   E   
+3   E   E   E   M   E   M   E   M   E   3   E   E   3   E   E   3   E   E   3   
+E   E   3   E   E   E   M   E   M   E   M   E   3   E   E   3   E   E   B   E   
+E   M   E   M   E   M   E   E   M   E   M   E   M   E   3   E   E   3   E   E   
+3   E   E   B   E   B   B   E   E   B   E   E   M   E   M   E   M   E   3   E   
+E   S   E   M   E   M   E   M   E   3   E   E   3   E   E   S   3   E   E   E   
+M   E   M   E   M   E   3   E   E   3   E   E   S   3   E   E   E   M   E   M   
+E   M   E   3   E   E   3   E   E   3   E   E   3   E   E   3   E   E   E   M   
+E   M   E   M   E   3   E   E   B   E   B   E   E   M   E   M   E   M   E   3   
+E   E   3   E   E   3   E   E   B   E   B   B   E   E   B   E   E   M   E   M   
+E   M   E   3   E   E   B   E   B   E   E   M   E   M   E   M   E   3   E   E   
+E   M   E   M   E   M   E   3   E   E   S   E   M   E   M   E   M   E   3   E   
+E   3   E   E   S   3   E   E   E   M   E   M   E   M   E   3   E   3   E   E   
+E   3   E   E   E   M   E   M   E   M   E   3   E   E   E   M   E   M   E   M   
+E   3   E   E   3   E   3   E   E   E   3   E   E   E   M   E   M   E   M   E   
+3   E   3   E   E   E   S   E   M   E   M   E   M   E   3   E   E   B   B   E   
+B   E   B   S   E   S   E   S   E   M   E   M   E   M   E   3   E   3   E   E   
+E   3   E   E   3   E   E   E   M   E   M   E   M   E   E   M   E   M   E   M   
+E   3   E   E   E   M   E   M   E   M   E   3   E   E   3   E   E   B   E   E   
+M   E   M   E   M   E   3   E   E   3   E   E   3   E   E   3   E   E   3   E   
+E   E   M   E   M   E   M   E   3   E   E   E   M   E   M   E   M   E   3   E   
+E   3   E   E   S   3   E   E   E   M   E   M   3   E   E   3   E   E   B   E   
+E   M   E   M   E   M   E   M   E   3   E   E   S   E   M   E   M   E   M   E   
+3   E   E   B   B   E   B   E   B   S   E   S   E   S   E   M   E   M   E   M   
+E   3   E   E   B   E   B   E   E   M   E   M   E   M   E   3   E   3   E   E   
+E   S   E   M   E   M   E   M   E   3   E   E   3   E   E   S   3   E   E   E   
+M   E   M   E   M   E   E   M   E   M   E   M   E   3   E   3   E   E   E   3   
+E   E   E   M   E   M   E   M   E   3   E   E   E   M   E   M   E   M   E   3   
+E   E   3   E   E   3   E   E   3   E   E   3   E   E   E   M   E   M   E   M   
+E   3   E   E   E   M   E   M   E   M   E   3   E   E   S   E   M   E   M   E   
+M   E   3   E   E   3   E   3   E   E   E   3   E   E   E   M   E   M   E   M   
+E   3   E   E   3   E   E   B   E   E   M   E   M   E   M   E   3   E   E   E   
+M   E   M   E   M   E   3   E   3   E   E   E   S   E   M   E   M   E   M   E   
+3   E   3   E   E   E   3   E   E   E   M   E   M   E   M   E   3   E   E   3   
+E   E   3   E   E   B   E   B   B   E   E   B   E   E   M   E   M   E   M   E   
+3   E   E   B   B   E   B   E   B   S   E   S   E   S   E   M   E   M   E   M   
+E   3   E   3   E   E   E   S   E   M   E   M   E   M   E   3   E   E   E   M   
+E   M   E   M   E   3   E   E   3   E   3   E   E   E   3   E   E   E   M   E   
+M   E   M   E   3   E   E   E   M   E   M   E   M   E   3   E   E   3   E   3   
+E   E   E   3   E   E   E   M   E   M   E   M   E   E   M   E   M   E   M   E   
+3   E   E   3   E   E   B   E   E   M   E   M   E   M   E   3   E   E   B   E   
+E   M   E   M   E   M   E   E   M   E   M   E   M   E   3   E   3   E   E   E   
+3   E   E   3   E   E   E   M   E   M   E   M   E   3   E   E   3   E   E   3   
+E   E   3   E   E   3   E   E   E   M   E   M   E   M   E   3   E   3   E   E   
+E   3   E   E   E   M   E   M   E   M   E   3   E   E   B   E   B   E   E   M   
+E   M   E   M   E   3   E   E   E   M   E   M   E   M   E   3   E   3   E   E   
+E   3   E   E   E   M   E   M   E   M   E   3   E   E   S   E   M   E   M   E   
+M   E   3   E   E   E   M   E   M   E   M   E   E   M   E   M   3   E   E   3   
+E   E   B   E   E   M   E   M   E   M   E   M   E   3   E   3   E   E   E   3   
+E   E   3   E   E   E   M   E   M   E   M   E   3   E   E   3   E   E   3   E   
+E   3   E   E   3   E   E   E   M   E   M   E   M   E   3   E   3   E   E   E   
+S   E   M   E   M   E   M   E   3   E   E   3   E   3   E   E   E   3   E   E   
+E   M   E   M   E   M   E   3   E   E   E   M   E   M   E   M   E   3   E   E   
+E   M   E   M   E   M   E   3   E   E   S   E   M   E   M   E   M   E   E   M   
+E   M   E   M   E   3   E   3   E   E   E   3   E   E   3   E   E   E   M   E   
+M   E   M   E   3   E   E   S   E   M   E   M   E   M   E   3   E   E   B   E   
+B   E   E   M   E   M   E   M   E   3   E   E   B   B   E   B   E   B   E   S   
+E   S   E   M   E   M   E   M   E   3   E   E   3   E   E   3   E   E   3   E   
+E   3   E   E   E   M   E   M   E   M   E   3   E   E   3   E   E   3   E   E   
+3   E   E   3   E   E   E   M   E   M   E   M   E   3   E   E   3   E   E   S   
+3   E   E   E   M   E   M   E   M   E   3   E   E   3   E   3   E   E   E   3   
+E   E   E   M   E   M   E   M   E   3   E   E   B   E   E   M   E   M   E   M   
+E   3   E   E   B   B   E   B   E   B   S   E   S   E   S   E   M   E   M   E   
+M   E   3   E   E   B   E   B   E   E   M   E   M   E   M   E   3   E   E   E   
+M   E   M   E   M   E   3   E   E   3   E   E   S   3   E   E   E   M   E   M   
+E   M   E   3   E   3   E   E   E   3   E   E   E   M   E   M   E   M   E   3   
+E   E   S   E   M   E   M   3   E   E   3   E   E   B   E   E   M   E   M   E   
+M   E   M   E   3   E   E   3   E   3   E   E   E   3   E   E   E   M   E   M   
+E   M   E   3   E   E   3   E   E   3   E   E   3   E   E   3   E   E   E   M   
+E   M   E   M   E   3   E   E   3   E   E   3   E   E   3   E   E   3   E   E   
+E   M   E   M   E   M   E   3   E   E   B   E   B   E   E   M   E   M   E   M   
+E   3   E   3   E   E   E   3   E   E   E   M   E   M   E   M   E   3   E   E   
+B   E   E   M   E   M   E   M   E   3   E   3   E   E   E   3   E   E   3   E   
+E   E   M   E   M   E   M   E   3   E   E   3   E   E   S   3   E   E   E   M   
+E   M   E   M   E   3   E   E   3   E   E   B   E   E   M   E   M   E   M   E   
+3   E   3   E   E   E   3   E   E   E   M   E   M   E   M   E   E   M   E   M   
+E   M   E   3   E   E   B   E   B   E   E   M   E   M   E   M   E   3   E   3   
+E   E   E   S   E   M   E   M   E   M   E   3   E   3   E   E   E   3   E   E   
+E   M   E   M   E   M   E   3   E   E   E   M   E   M   E   M   E   3   E   E   
+B   B   E   B   E   B   E   S   E   S   E   M   E   M   E   M   E   3   E   E   
+3   E   3   E   E   E   3   E   E   E   M   E   M   E   M   E   3   E   E   S   
+E   M   E   M   E   M   E   3   E   E   S   E   M   E   M   E   M   E   3   E   
+E   B   E   E   M   E   M   E   M   E   3   E   E   3   E   E   S   3   E   E   
+E   M   E   M   E   M   E   3   E   E   E   M   E   M   E   M   E   3   E   3   
+E   E   E   S   E   M   E   M   E   M   E   E   M   E   M   E   M   E   3   E   
+3   E   E   E   3   E   E   3   E   E   E   M   E   M   E   M   E   3   E   3   
+E   E   E   S   E   M   E   M   E   M   E   E   M   E   M   E   M   E   3   E   
+E   3   E   E   B   E   E   M   E   M   E   M   E   3   E   3   E   E   E   3   
+E   E   E   M   E   M   E   M   E   3   E   3   E   E   E   3   E   E   E   M   
+E   M   E   M   E   3   E   E   B   E   S   E   B   E   B   E   M   E   M   E   
+M   E   3   E   3   E   E   E   3   E   E   E   M   E   M   E   M   E   3   E   
+E   B   E   E   M   E   M   E   M   E   3   E   E   E   M   E   M   E   M   E   
+E   M   E   M   E   M   E   3   E   E   B   B   E   B   E   B   S   E   S   E   
+S   E   M   E   M   E   M   E   3   E   E   B   E   S   E   B   E   B   E   M   
+E   M   E   M   E   3   E   E   S   E   M   E   M   E   M   E   3   E   3   E   
+E   E   3   E   E   E   M   E   M   E   M   E   3   E   E   S   E   M   E   M   
+E   M   E   3   E   E   3   E   E   S   3   E   E   E   M   E   M   E   M   E   
+E   M   E   M   E   M   E   3   E   E   B   E   B   E   E   M   E   M   E   M   
+E   3   E   3   E   E   E   3   E   E   E   M   E   M   E   M   E   3   E   E   
+3   E   3   E   E   E   3   E   E   E   M   E   M   E   M   E   3   E   E   3   
+E   3   E   E   E   3   E   E   E   M   E   M   E   M   E   3   E   E   3   E   
+E   B   E   E   M   E   M   E   M   E   3   E   E   B   E   S   E   B   E   B   
+E   M   E   M   E   M   E   3   E   E   B   E   S   E   B   E   B   E   M   E   
+M   E   M   E   3   E   E   B   E   S   E   B   E   B   E   M   E   M   E   M   
+E   3   E   E   B   E   S   E   B   E   B   E   M   E   M   E   M   E   3   E   
+E   B   E   S   E   B   E   B   E   M   E   BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA 
+%FLAG JOIN_ARRAY                                                                
+%FORMAT(10I8)                                                                   
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
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+%FLAG IROTAT                                                                    
+%FORMAT(10I8)                                                                   
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+%FLAG SOLVENT_POINTERS                                                          
+%FORMAT(3I8)                                                                    
+     270       3       4
+%FLAG ATOMS_PER_MOLECULE                                                        
+%FORMAT(10I8)                                                                   
+    4049      70      24
+%FLAG BOX_DIMENSIONS                                                            
+%FORMAT(5E16.8)                                                                 
+  1.09471219E+02  8.62058016E+01  8.62058016E+01  8.62058016E+01
+%FLAG RADII                                                                     
+%FORMAT(5E16.8)                                                                 
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+%FORMAT(5E16.8)                                                                 
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+  7.20000000E-01  7.20000000E-01  7.20000000E-01  8.50000000E-01  7.90000000E-01
+  7.20000000E-01  7.20000000E-01  7.20000000E-01  8.50000000E-01  8.50000000E-01
+  8.50000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01
+  8.50000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01
+  8.50000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01
+  8.50000000E-01  8.50000000E-01  8.50000000E-01  8.00000000E-01  8.50000000E-01
+  8.50000000E-01  8.00000000E-01  8.00000000E-01  8.00000000E-01  7.20000000E-01
+  7.20000000E-01  7.20000000E-01  7.20000000E-01  7.20000000E-01  7.20000000E-01
+  8.50000000E-01  8.50000000E-01  7.20000000E-01  7.20000000E-01  7.20000000E-01
+  7.20000000E-01  7.20000000E-01  7.20000000E-01  8.00000000E-01  8.00000000E-01
+  8.00000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01
+  8.50000000E-01  8.50000000E-01  8.50000000E-01

From 216465950bb20c5696b46a33ecab89027e954dcc Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 13 Dec 2023 11:06:35 -0500
Subject: [PATCH 0162/1492] Actually compare against the correct save topology.

---
 test/Test_CombineCrd/RunTest.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/Test_CombineCrd/RunTest.sh b/test/Test_CombineCrd/RunTest.sh
index ed8b4e1fd4..cc4673187d 100755
--- a/test/Test_CombineCrd/RunTest.sh
+++ b/test/Test_CombineCrd/RunTest.sh
@@ -75,7 +75,7 @@ parmwrite out FabI.NDP.TCS.parm7 crdset combinedCrd
 EOF
   RunCpptraj "Split coords and recombine test."
   DoTest E1.dat E2.dat
-  DoTest ../FtuFabI.NAD.TCL.parm7 FabI.NDP.TCS.parm7 -I %VERSION
+  DoTest FabI.NDP.TCS.parm7.save FabI.NDP.TCS.parm7 -I %VERSION
 fi
 
 EndTest

From fbd6a9619caf54b1d46d1e3398e0ab84395ed68d Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 13 Dec 2023 11:15:47 -0500
Subject: [PATCH 0163/1492] Update dependencies

---
 src/cpptrajdepend | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index e465ed3ccb..3cfeb348ca 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -340,7 +340,7 @@ Exec_SplitCoords.o : Exec_SplitCoords.cpp Action.h ActionList.h ActionState.h An
 Exec_System.o : Exec_System.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_System.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Top.o : Exec_Top.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Top.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h TopInfo.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Traj.o : Exec_Traj.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Traj.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_UpdateParameters.o : Exec_UpdateParameters.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h DataSet_Topology.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_UpdateParameters.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_UpdateParameters.o : Exec_UpdateParameters.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h DataSet_Topology.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_UpdateParameters.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/GenerateAngles.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_ViewRst.o : Exec_ViewRst.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ViewRst.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h ViewRst.h
 Exec_Zmatrix.o : Exec_Zmatrix.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Zmatrix.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Zmatrix.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 ExtendedSimilarity.o : ExtendedSimilarity.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h ExtendedSimilarity.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
@@ -464,7 +464,7 @@ TextFormat.o : TextFormat.cpp StringRoutines.h TextFormat.h
 Timer.o : Timer.cpp CpptrajStdio.h Timer.h
 TinkerFile.o : TinkerFile.cpp ArgList.h Atom.h AtomMask.h Box.h BufferedLine.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TinkerFile.h Unit.h Vec3.h
 TopInfo.o : TopInfo.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h DistRoutines.h FileIO.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Mol.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h TopInfo.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Topology.o : Topology.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Topology.o : Topology.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h UpdateParameters.h Vec3.h
 TorsionRoutines.o : TorsionRoutines.cpp Constants.h TorsionRoutines.h Vec3.h
 TrajFrameCounter.o : TrajFrameCounter.cpp ArgList.h CpptrajStdio.h TrajFrameCounter.h
 TrajIOarray.o : TrajIOarray.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryFile.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h

From 1b14e6c2310130984a2e592cb6fd8f3ea280a0f9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 13 Dec 2023 11:16:44 -0500
Subject: [PATCH 0164/1492] Fix up depencies.

---
 src/Topology.cpp  | 1 -
 src/cpptrajdepend | 2 +-
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index 35f5d064b5..ec01226c49 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -7,7 +7,6 @@
 #include "AtomType.h"
 #include "AtomMask.h"
 #include "CharMask.h"
-#include "UpdateParameters.h"
 
 const NonbondType Topology::LJ_EMPTY = NonbondType();
 
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 3cfeb348ca..348356a862 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -464,7 +464,7 @@ TextFormat.o : TextFormat.cpp StringRoutines.h TextFormat.h
 Timer.o : Timer.cpp CpptrajStdio.h Timer.h
 TinkerFile.o : TinkerFile.cpp ArgList.h Atom.h AtomMask.h Box.h BufferedLine.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TinkerFile.h Unit.h Vec3.h
 TopInfo.o : TopInfo.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h DistRoutines.h FileIO.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Mol.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h TopInfo.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Topology.o : Topology.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h UpdateParameters.h Vec3.h
+Topology.o : Topology.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 TorsionRoutines.o : TorsionRoutines.cpp Constants.h TorsionRoutines.h Vec3.h
 TrajFrameCounter.o : TrajFrameCounter.cpp ArgList.h CpptrajStdio.h TrajFrameCounter.h
 TrajIOarray.o : TrajIOarray.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryFile.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h

From bd5cc20c945dba3ecd82df6847209d3f1b8f369a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 13 Dec 2023 13:22:12 -0500
Subject: [PATCH 0165/1492] Comment out some unused functions

---
 src/Topology.cpp | 4 +++-
 src/Topology.h   | 6 +++---
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index ec01226c49..9143404cd4 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2287,6 +2287,7 @@ ParameterSet Topology::GetParameters() const {
 }
 
 // -----------------------------------------------------------------------------
+/*
 // Topology::AddBondArray()
 void Topology::AddBondArray(BondArray const& barray, BondParmArray const& bp, int atomOffset) {
   if (bp.empty()) {
@@ -2334,7 +2335,7 @@ void Topology::AddDihArray(DihedralArray const& darray, DihedralParmArray const&
       AddDihedral( DihedralType( dih->A1() + atomOffset, dih->A2() + atomOffset,
                                  dih->A3() + atomOffset, dih->A4() + atomOffset,
                                  dih->Type() ), dp[dih->Idx()] );
-}
+}*/
 
 /** This template can be used when doing Append() on a generic std::vector array
   * of type T. The array will be appended to a given array of the same type.
@@ -2451,6 +2452,7 @@ int Topology::AppendTop(Topology const& NewTop) {
   addDihedralsWithOffset( dihedrals_, NewTop.Dihedrals(), atomOffset );
   addDihedralsWithOffset( dihedralsh_, NewTop.DihedralsH(), atomOffset );
   addDihedralsWithOffset( chamber_.SetImpropers(), NewTop.chamber_.Impropers(), atomOffset );
+  // TODO CMAP
 //#  for (BondArray::const_iterator bond = NewTop.Bonds().begin(); bond != NewTop.Bonds().end(); ++bond)
 //#    AddBond( bond->A1() + atomOffset, bond->A2() + atomOffset );
 //#  for (BondArray::const_iterator bond = NewTop.BondsH().begin(); bond != NewTop.BondsH().end(); ++bond)
diff --git a/src/Topology.h b/src/Topology.h
index 466de2d36d..8444bb58c1 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -288,9 +288,9 @@ class Topology {
     void StripDihedralParmArray(DihedralArray&, std::vector<int>&, DihedralParmArray&) const;
     void StripDihedralParmArray(DihedralArray&, std::vector<int>&, DihedralParmArray&,
                                 DihedralParmArray const&) const;
-    inline void AddBondArray(BondArray const&, BondParmArray const&, int);
-    inline void AddAngleArray(AngleArray const&, AngleParmArray const&, int);
-    inline void AddDihArray(DihedralArray const&, DihedralParmArray const&, int);
+//    inline void AddBondArray(BondArray const&, BondParmArray const&, int);
+//    inline void AddAngleArray(AngleArray const&, AngleParmArray const&, int);
+//    inline void AddDihArray(DihedralArray const&, DihedralParmArray const&, int);
 
     /// Update parameters in this Topology with those from combined sets.
     int updateParams(ParameterSet&, ParameterSet const&);

From 41f970cb539a6c6c924f772f1e68cbe186733b4b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 13 Dec 2023 13:34:51 -0500
Subject: [PATCH 0166/1492] Add noindices to help

---
 src/Exec_Top.cpp |  5 +++--
 src/TopInfo.cpp  | 10 ++++++++--
 2 files changed, 11 insertions(+), 4 deletions(-)

diff --git a/src/Exec_Top.cpp b/src/Exec_Top.cpp
index 89f40e53e1..0f32883631 100644
--- a/src/Exec_Top.cpp
+++ b/src/Exec_Top.cpp
@@ -10,8 +10,9 @@ void Exec_LoadParm::Help() const {
 }
 // -----------------------------------------------------------------------------
 void Exec_ParmInfo::Help() const {
-  mprintf("\t[%s] [<mask>]\n", DataSetList::TopIdxArgs);
-  mprintf("  Print information on specfied topology (first by default).\n");
+  mprintf("\t[%s] [<mask>] [noindices]\n", DataSetList::TopIdxArgs);
+  mprintf("  Print information on specfied topology (first by default).\n"
+          "  If 'noindices' is specified indices will not be printed for parameters.\n");
 }
 
 Exec::RetType Exec_ParmInfo::Execute(CpptrajState& State, ArgList& argIn) {
diff --git a/src/TopInfo.cpp b/src/TopInfo.cpp
index 8a54ebaeb5..d7e7e6172f 100644
--- a/src/TopInfo.cpp
+++ b/src/TopInfo.cpp
@@ -449,7 +449,10 @@ void TopInfo::PrintBonds(BondArray const& barray, BondParmArray const& bondparm,
         printBond = false;
     }
     if (printBond) {
-      outfile_->Printf("%*i", nw, nb);
+      if (printIndices_)
+        outfile_->Printf("%*i", nw, nb);
+      else
+        outfile_->Printf("%*c", nw, ' ');
       int bidx = batom->Idx();
       if ( bidx > -1 )
         outfile_->Printf(" %6.2f %6.3f", bondparm[bidx].Rk(), bondparm[bidx].Req());
@@ -534,7 +537,10 @@ void TopInfo::PrintAngles(AngleArray const& aarray, AngleParmArray const& anglep
                     mask1.AtomInCharMask(atom2) ||
                     mask1.AtomInCharMask(atom3));
     if (printAngle) {
-      outfile_->Printf("%*i", nw, na);
+      if (printIndices_)
+        outfile_->Printf("%*i", nw, na);
+      else
+        outfile_->Printf("%*c", nw, ' ');
       int aidx = aatom->Idx();
       if ( aidx > -1 )
         outfile_->Printf(" %6.3f %6.2f", angleparm[aidx].Tk(), 

From 452cfc76ed593879e99575e956ab6e5ab8db2178 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 13 Dec 2023 13:43:32 -0500
Subject: [PATCH 0167/1492] Add noindices/extra keywords to help and manual.

---
 doc/cpptraj.lyx  | 54 +++++++++++++++++++++++++++++++++++++++++-------
 src/Exec_Top.cpp | 26 +++++++++++++++--------
 2 files changed, 63 insertions(+), 17 deletions(-)

diff --git a/doc/cpptraj.lyx b/doc/cpptraj.lyx
index 71f72662f6..e78dcabe9c 100644
--- a/doc/cpptraj.lyx
+++ b/doc/cpptraj.lyx
@@ -14449,7 +14449,11 @@ angleinfo | angles | printangles
 \end_layout
 
 \begin_layout LyX-Code
-angleinfo [parm <name> | parmindex <#> | <#>] [<mask1>] [<mask2> <mask3>]
+angleinfo [parm <name> | parmindex <#> | <#>]
+\end_layout
+
+\begin_layout LyX-Code
+          [<mask1>] [<mask2> <mask3>] [noindices]
 \end_layout
 
 \begin_layout LyX-Code
@@ -14498,6 +14502,10 @@ parmindex
 <mask3>] If specified, angles must match all masks.
 \end_layout
 
+\begin_layout Description
+[noindices] Do not print angle indices.
+\end_layout
+
 \begin_layout Description
 [out
 \begin_inset space ~
@@ -14674,7 +14682,7 @@ bondinfo [parm <name> | parmindex <#> | <#>]
 \end_layout
 
 \begin_layout LyX-Code
-         [<mask1>] [<mask2>] [out <file>] [nointrares]
+         [<mask1>] [<mask2>] [out <file>] [nointrares] [noindices]
 \end_layout
 
 \begin_deeper
@@ -14727,6 +14735,10 @@ parmindex
 [nointrares] Do not print intra-residue bonds.
 \end_layout
 
+\begin_layout Description
+[noindices] Do not print bond indices.
+\end_layout
+
 \end_deeper
 \begin_layout Standard
 Print bond information for atoms in <mask> for selected topology (first
@@ -15331,12 +15343,15 @@ dihedralinfo | dihedrals | printdihedrals
 \end_layout
 
 \begin_layout LyX-Code
-dihedralinfo [parm <name> | parmindex <#> | <#>] [<mask1>] [<mask2> <mask3>
- <mask4>]
+dihedralinfo [parm <name> | parmindex <#> | <#>]
 \end_layout
 
 \begin_layout LyX-Code
-             [out <file>]
+             [<mask1>] [<mask2> <mask3> <mask4>] [noindices]
+\end_layout
+
+\begin_layout LyX-Code
+             [out <file>] [extra]
 \end_layout
 
 \begin_deeper
@@ -15385,6 +15400,10 @@ parmindex
 <mask4>] If specified, dihedrals must match all masks.
 \end_layout
 
+\begin_layout Description
+[noindices] Do not print dihedral indices.
+\end_layout
+
 \begin_layout Description
 [out
 \begin_inset space ~
@@ -15393,6 +15412,10 @@ parmindex
 <file>] File to print to (default STDOUT).
 \end_layout
 
+\begin_layout Description
+[extra] Print SCEE/SCNB info as well.
+\end_layout
+
 \end_deeper
 \begin_layout Standard
 Print dihedral information of atoms in <mask> for selected topology (first
@@ -15537,8 +15560,11 @@ improperinfo | impropers | printimpropers
 \end_layout
 
 \begin_layout LyX-Code
-improperinfo [parm <name> | parmindex <#> | <#>] [<mask1>] [<mask2> <mask3>
- <mask4>]
+improperinfo [parm <name> | parmindex <#> | <#>]
+\end_layout
+
+\begin_layout LyX-Code
+             [<mask1>] [<mask2> <mask3> <mask4>] [noindices]
 \end_layout
 
 \begin_layout LyX-Code
@@ -15591,6 +15617,10 @@ parmindex
 <mask4>] If specified, impropers must match all masks.
 \end_layout
 
+\begin_layout Description
+[noindices] Do not print improper indices.
+\end_layout
+
 \begin_layout Description
 [out
 \begin_inset space ~
@@ -16443,7 +16473,11 @@ printub | ubinfo
 \end_layout
 
 \begin_layout LyX-Code
-printub [parm <name> | parmindex <#> | <#>] [<mask1>] [<mask2>] [out <file>]
+printub [parm <name> | parmindex <#> | <#>]
+\end_layout
+
+\begin_layout LyX-Code
+        [<mask1>] [<mask2>] [out <file>] [noindices]
 \end_layout
 
 \begin_deeper
@@ -16492,6 +16526,10 @@ parmindex
 <file>] File to print to (default STDOUT).
 \end_layout
 
+\begin_layout Description
+[noindices] Do not print UB indices.
+\end_layout
+
 \end_deeper
 \begin_layout Standard
 For specified topology (first by default) either print CHARMM Urey-Bradley
diff --git a/src/Exec_Top.cpp b/src/Exec_Top.cpp
index 0f32883631..8980eff421 100644
--- a/src/Exec_Top.cpp
+++ b/src/Exec_Top.cpp
@@ -10,9 +10,8 @@ void Exec_LoadParm::Help() const {
 }
 // -----------------------------------------------------------------------------
 void Exec_ParmInfo::Help() const {
-  mprintf("\t[%s] [<mask>] [noindices]\n", DataSetList::TopIdxArgs);
-  mprintf("  Print information on specfied topology (first by default).\n"
-          "  If 'noindices' is specified indices will not be printed for parameters.\n");
+  mprintf("\t[%s] [<mask>]\n", DataSetList::TopIdxArgs);
+  mprintf("  Print information on specfied topology (first by default).\n");
 }
 
 Exec::RetType Exec_ParmInfo::Execute(CpptrajState& State, ArgList& argIn) {
@@ -55,7 +54,8 @@ static int CommonSetup(TopInfo& info, CpptrajState& State, ArgList& argIn, const
 
 // -----------------------------------------------------------------------------
 void Exec_BondInfo::Help() const {
-  mprintf("\t[%s] [<mask1>] [<mask2>] [out <file>] [nointrares]\n", DataSetList::TopIdxArgs);
+  mprintf("\t[%s]\n"
+          "\t[<mask1>] [<mask2>] [out <file>] [nointrares] [noindices]\n", DataSetList::TopIdxArgs);
   mprintf("  For specified topology (first by default) either print bond info for all\n"
           "  atoms in <mask1>, or print info for bonds with first atom in <mask1> and\n"
           "  second atom in <mask2>. If 'nointrares' is specified, only print bonds\n"
@@ -71,7 +71,8 @@ Exec::RetType Exec_BondInfo::Execute(CpptrajState& State, ArgList& argIn) {
 }
 // -----------------------------------------------------------------------------
 void Exec_UBInfo::Help() const {
-  mprintf("\t[%s] [<mask1>] [<mask2>] [out <file>]\n", DataSetList::TopIdxArgs);
+  mprintf("\t[%s]\n"
+          "\t[<mask1>] [<mask2>] [out <file>] [noindices]\n", DataSetList::TopIdxArgs);
   mprintf("  For specified topology (first by default) either print CHARMM Urey-Bradley\n"
           "  info for all atoms in <mask1>, or print info for bonds with first atom in\n"
           "  <mask1> and second atom in <mask2>.\n");
@@ -87,7 +88,9 @@ Exec::RetType Exec_UBInfo::Execute(CpptrajState& State, ArgList& argIn) {
 
 // -----------------------------------------------------------------------------
 void Exec_AngleInfo::Help() const {
-  mprintf("\t[%s] [<mask1>] [<mask2> <mask3>]\n\t[out <file>]\n", DataSetList::TopIdxArgs);
+  mprintf("\t[%s]\n"
+          "\t[<mask1>] [<mask2> <mask3>] [noindices]\n"
+          "\t[out <file>]\n", DataSetList::TopIdxArgs);
   mprintf("  For specified topology (first by default) either print angle info for all\n"
           "  atoms in <mask1>, or print info for angles with first atom in <mask1>,\n"
           "  second atom in <mask2>, and third atom in <mask3>.\n");
@@ -103,10 +106,13 @@ Exec::RetType Exec_AngleInfo::Execute(CpptrajState& State, ArgList& argIn) {
 }
 // -----------------------------------------------------------------------------
 void Exec_DihedralInfo::Help() const {
-  mprintf("\t[%s] [<mask1>] [<mask2> <mask3> <mask4>]\n\t[out <file>] [extra]\n", DataSetList::TopIdxArgs);
+  mprintf("\t[%s]\n"
+          "\t[<mask1>] [<mask2> <mask3> <mask4>] [noindices]\n"
+          "\t[out <file>] [extra]\n", DataSetList::TopIdxArgs);
   mprintf("  For specified topology (first by default) either print dihedral info for all\n"
           "  atoms in <mask1>, or print info for dihedrals with first atom in <mask1>,\n"
-          "  second atom in <mask2>, third atom in <mask3>, and fourth atom in <mask4>.\n");
+          "  second atom in <mask2>, third atom in <mask3>, and fourth atom in <mask4>.\n"
+          "  If 'extra' is specified, print SCEE and SCNB factors as well.\n");
 }
 
 Exec::RetType Exec_DihedralInfo::Execute(CpptrajState& State, ArgList& argIn) {
@@ -128,7 +134,9 @@ Exec::RetType Exec_DihedralInfo::Execute(CpptrajState& State, ArgList& argIn) {
 
 // -----------------------------------------------------------------------------
 void Exec_ImproperInfo::Help() const {
-  mprintf("\t[%s] [<mask1>] [<mask2> <mask3> <mask4>]\n\t[out <file>]\n", DataSetList::TopIdxArgs);
+  mprintf("\t[%s]\n"
+          "\t[<mask1>] [<mask2> <mask3> <mask4>] [noindices]\n"
+          "\t[out <file>]\n", DataSetList::TopIdxArgs);
   mprintf("  For specified topology (first by default) either print CHARMM improper info\n"
           "  for all atoms in <mask1>, or print info for dihedrals with first atom in <mask1>,\n"
           "  second atom in <mask2>, third atom in <mask3>, and fourth atom in <mask4>.\n");

From ab7980a4b76f369b304ed445cc5c4a79aa0b8e2e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 13 Dec 2023 13:59:28 -0500
Subject: [PATCH 0168/1492] Add script to find out if test dirs are missing
 from the test Makefile

---
 devtools/FindMissingTests.sh | 15 +++++++++++++++
 1 file changed, 15 insertions(+)
 create mode 100755 devtools/FindMissingTests.sh

diff --git a/devtools/FindMissingTests.sh b/devtools/FindMissingTests.sh
new file mode 100755
index 0000000000..af79c65774
--- /dev/null
+++ b/devtools/FindMissingTests.sh
@@ -0,0 +1,15 @@
+#!/bin/bash
+
+if [ ! -f 'Makefile' ] ; then
+  echo "Should be executed in directory where main test Makefile is."
+  exit 1
+fi
+
+for DIR in `ls -d Test_*` ; do
+  if [ -d "$DIR" ] ; then
+    IN_MAKEFILE=`grep $DIR Makefile`
+    if [ -z "$IN_MAKEFILE" ] ; then
+      echo "$DIR not in Makefile."
+    fi
+  fi
+done

From 4c705ccfa723e2fdfa191f3cb982e27067f63bd2 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 13 Dec 2023 14:03:03 -0500
Subject: [PATCH 0169/1492] Add missing tests

---
 test/Makefile | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/test/Makefile b/test/Makefile
index 5c97316457..f75f161bf1 100644
--- a/test/Makefile
+++ b/test/Makefile
@@ -539,6 +539,12 @@ test.readoff:
 test.sequence:
 	@-cd Test_Sequence && ./RunTest.sh $(OPT)
 
+test.refinetrajectory:
+	@-cd Test_RefineTrajectory && ./RunTest.sh $(OPT)
+
+test.readamberff:
+	@-cd Test_ReadAmberFF && ./RunTest.sh $(OPT)
+
 # Every test target should go here.
 COMPLETETESTS=test.general \
               test.strip \
@@ -709,7 +715,9 @@ COMPLETETESTS=test.general \
               test.readprep \
               test.zmatrix \
               test.readoff \
-              test.sequence
+              test.sequence \
+              test.refinetrajectory \
+              test.readamberff
 
 test.all:
 	$(MAKE) test.complete summary

From ae38483c761289972627289df7109ba8521fad3c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 13 Dec 2023 14:03:13 -0500
Subject: [PATCH 0170/1492] Convert radians to degrees in output

---
 src/ParameterSet.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/ParameterSet.cpp b/src/ParameterSet.cpp
index ff6dc6c5b7..70438dcd07 100644
--- a/src/ParameterSet.cpp
+++ b/src/ParameterSet.cpp
@@ -79,7 +79,7 @@ void ParameterSet::Print(CpptrajFile& Out) const {
     Out.Printf("Angle parameters:\n");
     Out.Printf("\t%6s %6s %6s : %12s %12s\n", "Type1", "Type2", "Type3", "Tk", "Teq");
     for (ParmHolder<AngleParmType>::const_iterator bp = angleParm_.begin(); bp != angleParm_.end(); ++bp)
-      Out.Printf("\t%6s %6s %6s : %12.4f %12.4f\n", *(bp->first[0]), *(bp->first[1]), *(bp->first[2]), bp->second.Tk(), bp->second.Teq());
+      Out.Printf("\t%6s %6s %6s : %12.4f %12.4f\n", *(bp->first[0]), *(bp->first[1]), *(bp->first[2]), bp->second.Tk(), bp->second.Teq()*Constants::RADDEG);
   }
   if (!ubParm_.empty()) {
     Out.Printf("UB parameters:\n");

From a96564e00820ed1c4f277092f41dfc3f86478d2a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 14 Dec 2023 14:18:16 -0500
Subject: [PATCH 0171/1492] Load residue templates.

---
 src/Exec_Build.cpp | 40 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index dee7222833..77d43cd28d 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -36,6 +36,46 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
   // Get modifiable topology
   Topology& topIn = *(coords.TopPtr());
 
+  // Get residue templates.
+  typedef std::vector<DataSet_Coords*> Carray;
+  Carray Templates;
+  std::string lib = argIn.GetStringKey("lib");
+  if (lib.empty()) {
+    mprintf("\tNo template(s) specified with 'lib'; using any loaded templates.\n");
+    DataSetList sets = State.DSL().SelectGroupSets( "*", DataSet::COORDINATES ); // TODO specific set type for units?
+    for (DataSetList::const_iterator it = sets.begin(); it != sets.end(); ++it)
+    {
+      // Should only be a single residue FIXME need new set type
+      DataSet_Coords const& ds = static_cast<DataSet_Coords const&>( *(*it) );
+      if ( ds.Top().Nres() == 1 )
+        Templates.push_back( (DataSet_Coords*)(*it) );
+    }
+  } else {
+    while (!lib.empty()) {
+      DataSetList sets = State.DSL().SelectGroupSets( lib, DataSet::COORDINATES ); // TODO specific set type for units?
+      if (sets.empty()) {
+        mprintf("Warning: No sets corresponding to '%s'\n", lib.c_str());
+      } else {
+        for (DataSetList::const_iterator it = sets.begin(); it != sets.end(); ++it)
+        {
+          // Should only be a single residue FIXME need new set type
+          DataSet_Coords const& ds = static_cast<DataSet_Coords const&>( *(*it) );
+          if ( ds.Top().Nres() == 1 )
+            Templates.push_back( (DataSet_Coords*)(*it) );
+        }
+      }
+      lib = argIn.GetStringKey("lib");
+    }
+  }
+  if (Templates.empty())
+    mprintf("Warning: No residue templates loaded.\n");
+  else {
+    mprintf("\t%zu residue templates found:", Templates.size());
+    for (std::vector<DataSet_Coords*>::const_iterator it = Templates.begin(); it != Templates.end(); ++it)
+      mprintf(" %s", (*it)->legend());
+    mprintf("\n");
+  }
+
   // Fill in atoms with templates
 
   // Generate angles/dihedrals

From 68e742b78a8c0980070011ed9eb2183b8eebc945 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 14 Dec 2023 15:12:14 -0500
Subject: [PATCH 0172/1492] Start filling in residues using templates.

---
 src/Exec_Build.cpp | 41 ++++++++++++++++++++++++++++++++++++++++-
 src/Exec_Build.h   |  7 +++++++
 2 files changed, 47 insertions(+), 1 deletion(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 77d43cd28d..8bab1477ed 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -3,6 +3,40 @@
 #include "DataSet_Parameters.h"
 #include "Structure/GenerateAngles.h"
 
+DataSet_Coords* Exec_Build::IdTemplateFromName(Carray const& Templates,
+                                               NameType const& rname)
+{
+  DataSet_Coords* out = 0;
+  // Assume Coords set aspect is what we need
+  for (Carray::const_iterator it = Templates.begin(); it != Templates.end(); ++it) {
+    if ( rname == NameType( (*it)->Meta().Aspect() ) ) {
+      out = *it;
+      break;
+    }
+  }
+  return out;
+}
+
+/** Use given templates to construct a final molecule. */
+int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
+                                       Carray const& Templates,
+                                       Topology const& topIn, Frame const& frameIn)
+{
+  for (int ires = 0; ires != topIn.Nres(); ires++)
+  {
+    // Identify a template based on the residue name.
+    DataSet_Coords* resTemplate = IdTemplateFromName(Templates, topIn.Res(ires).Name());
+    if (resTemplate == 0) {
+      mprintf("Warning: No template found for residue %s\n", topIn.TruncResNameNum(ires).c_str());
+    } else {
+      mprintf("\tTemplate %s being used for residue %s\n",
+              resTemplate->legend(), topIn.TruncResNameNum(ires).c_str());
+    }
+  }
+
+  return 0;
+}
+
 // Exec_Build::Help()
 void Exec_Build::Help() const
 {
@@ -37,7 +71,6 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
   Topology& topIn = *(coords.TopPtr());
 
   // Get residue templates.
-  typedef std::vector<DataSet_Coords*> Carray;
   Carray Templates;
   std::string lib = argIn.GetStringKey("lib");
   if (lib.empty()) {
@@ -77,6 +110,12 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
   }
 
   // Fill in atoms with templates
+  Topology topOut;
+  Frame frameOut;
+  if (FillAtomsWithTemplates(topOut, frameOut, Templates, topIn, frameIn)) {
+    mprinterr("Error: Could not fill in atoms using templates.\n");
+    return CpptrajState::ERR;
+  }
 
   // Generate angles/dihedrals
   if (Cpptraj::Structure::GenerateAngles(topIn)) {
diff --git a/src/Exec_Build.h b/src/Exec_Build.h
index 9225f7e3bf..102d1e849f 100644
--- a/src/Exec_Build.h
+++ b/src/Exec_Build.h
@@ -8,5 +8,12 @@ class Exec_Build : public Exec {
     void Help() const;
     DispatchObject* Alloc() const { return (DispatchObject*)new Exec_Build(); }
     RetType Execute(CpptrajState&, ArgList&);
+  private:
+    typedef std::vector<DataSet_Coords*> Carray;
+
+    /// Identify residue template from residue name
+    static DataSet_Coords* IdTemplateFromName(Carray const&, NameType const&);
+    /// Create new topology/frame using templates
+    static int FillAtomsWithTemplates(Topology&, Frame&, Carray const&, Topology const&, Frame const&);
 };
 #endif

From cdb2014a04f656cc965c801d2c4ceb248cb735a0 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 14 Dec 2023 15:23:13 -0500
Subject: [PATCH 0173/1492] Find atoms in templates

---
 src/Exec_Build.cpp | 33 +++++++++++++++++++++++++++++++++
 src/Exec_Build.h   |  2 ++
 2 files changed, 35 insertions(+)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 8bab1477ed..138658c9ac 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -17,6 +17,30 @@ DataSet_Coords* Exec_Build::IdTemplateFromName(Carray const& Templates,
   return out;
 }
 
+/** Map atoms in residue to template. */
+std::vector<int> Exec_Build::MapAtomsToTemplate(Topology const& topIn,
+                                                int rnum,
+                                                DataSet_Coords* resTemplate)
+{
+  std::vector<int> mapOut;
+  mapOut.reserve( resTemplate->Top().Natom() );
+  Residue const& resIn = topIn.Res(rnum);
+  for (int iref = 0; iref != resTemplate->Top().Natom(); iref++)
+  {
+    // Find this atom name in topIn
+    NameType const& refName = resTemplate->Top()[iref].Name();
+    int iat = -1;
+    for (int itgt = resIn.FirstAtom(); itgt != resIn.LastAtom(); itgt++) {
+      if ( refName == topIn[itgt].Name() ) {
+        iat = itgt;
+        break;
+      }
+    }
+    mapOut.push_back( iat );
+  }
+  return mapOut;
+}
+
 /** Use given templates to construct a final molecule. */
 int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
                                        Carray const& Templates,
@@ -31,6 +55,15 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
     } else {
       mprintf("\tTemplate %s being used for residue %s\n",
               resTemplate->legend(), topIn.TruncResNameNum(ires).c_str());
+      std::vector<int> map = MapAtomsToTemplate( topIn, ires, resTemplate );
+      mprintf("\t  Atom map:\n");
+      for (int iref = 0; iref != resTemplate->Top().Natom(); iref++) {
+        mprintf("\t\t%6i %6s =>", iref+1, *(resTemplate->Top()[iref].Name()));
+        if (map[iref] == -1)
+          mprintf(" No match\n");
+        else
+          mprintf(" %6i %6s\n", map[iref]+1, *(topIn[map[iref]].Name()));
+      }
     }
   }
 
diff --git a/src/Exec_Build.h b/src/Exec_Build.h
index 102d1e849f..c96aad7e69 100644
--- a/src/Exec_Build.h
+++ b/src/Exec_Build.h
@@ -15,5 +15,7 @@ class Exec_Build : public Exec {
     static DataSet_Coords* IdTemplateFromName(Carray const&, NameType const&);
     /// Create new topology/frame using templates
     static int FillAtomsWithTemplates(Topology&, Frame&, Carray const&, Topology const&, Frame const&);
+    /// Map atoms in topology to template
+    static std::vector<int> MapAtomsToTemplate(Topology const&, int, DataSet_Coords*);
 };
 #endif

From dc02bf5204a4f3860f23b49e4a8ddbd6b3ab9ce2 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 14 Dec 2023 16:31:02 -0500
Subject: [PATCH 0174/1492] Start trying to fill in missing atoms.

---
 src/Exec_Build.cpp | 45 +++++++++++++++++++++++++++++++++++++++++++++
 src/cpptrajdepend  |  2 +-
 2 files changed, 46 insertions(+), 1 deletion(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 138658c9ac..1a787ed5fe 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -2,6 +2,7 @@
 #include "CpptrajStdio.h"
 #include "DataSet_Parameters.h"
 #include "Structure/GenerateAngles.h"
+#include "Structure/Zmatrix.h"
 
 DataSet_Coords* Exec_Build::IdTemplateFromName(Carray const& Templates,
                                                NameType const& rname)
@@ -46,6 +47,9 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
                                        Carray const& Templates,
                                        Topology const& topIn, Frame const& frameIn)
 {
+  std::vector<Vec3> XYZ; // FIXME should use frameOut
+  Cpptraj::Structure::Zmatrix::Barray hasPosition;
+  int nAtomsMissing = 0;
   for (int ires = 0; ires != topIn.Nres(); ires++)
   {
     // Identify a template based on the residue name.
@@ -55,6 +59,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
     } else {
       mprintf("\tTemplate %s being used for residue %s\n",
               resTemplate->legend(), topIn.TruncResNameNum(ires).c_str());
+      // Map atoms to template atoms
       std::vector<int> map = MapAtomsToTemplate( topIn, ires, resTemplate );
       mprintf("\t  Atom map:\n");
       for (int iref = 0; iref != resTemplate->Top().Natom(); iref++) {
@@ -64,8 +69,48 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
         else
           mprintf(" %6i %6s\n", map[iref]+1, *(topIn[map[iref]].Name()));
       }
+      for (int iref = 0; iref != resTemplate->Top().Natom(); iref++) {
+        topOut.AddTopAtom( resTemplate->Top()[iref], topIn.Res(ires) );
+        if (map[iref] == -1) {
+          XYZ.push_back( Vec3(0.0) );
+          hasPosition.push_back( false );
+          nAtomsMissing++;
+        } else {
+          XYZ.push_back( Vec3(frameIn.XYZ(map[iref])) );
+          hasPosition.push_back( true );
+        }
+      }
+      // DEBUG
+      Frame templateFrame = resTemplate->AllocateFrame();
+      resTemplate->GetFrame( 0, templateFrame );
+      Cpptraj::Structure::Zmatrix zmatrix;
+      if (zmatrix.SetFromFrame( templateFrame, resTemplate->Top(), 0 )) {
+        mprinterr("Error: Could not set up residue template zmatrix.\n");
+        return 1;
+      }
+      zmatrix.print();
+      // If no atoms missing just fill in the residue
+/*      if (nAtomsMissing == 0) {
+        for (int iref = 0; iref != resTemplate->Top().Natom(); iref++) {
+          topOut.AddTopAtom( resTemplate->Top()[iref], topIn.Res(ires) );
+          XYZ.push_back( Vec3(frameIn.XYZ(map[iref])) );
+        }
+      } else {
+        mprintf("\tTrying to fill in missing atoms.\n");
+        // one or more atoms missing. Try to use Zmatrix to fill it in
+        
+         // DEBUG*/
+
     }
   }
+  mprintf("\t%i atoms missing.\n", nAtomsMissing);
+  for (int iat = 0; iat != topOut.Natom(); iat++)
+  {
+    Residue const& res = topOut.Res( topOut[iat].ResNum() );
+    mprintf("%6i %6s %6i %6s (%i) %g %g %g\n",
+            iat+1, *(topOut[iat].Name()), res.OriginalResNum(), *(res.Name()),
+            (int)hasPosition[iat], XYZ[iat][0], XYZ[iat][1], XYZ[iat][2]);
+  }
 
   return 0;
 }
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 348356a862..3f959374c5 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -288,7 +288,7 @@ Ewald_Regular.o : Ewald_Regular.cpp Atom.h AtomMask.h Box.h Constants.h Coordina
 ExclusionArray.o : ExclusionArray.cpp Atom.h AtomMask.h CharMask.h CpptrajStdio.h ExclusionArray.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Unit.h
 Exec_AddMissingRes.o : Exec_AddMissingRes.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CharMask.h CompactFrameArray.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_AddMissingRes.h Exec_AddMissingRes_Pres.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Analyze.o : Exec_Analyze.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Analyze.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Build.o : Exec_Build.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/GenerateAngles.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Build.o : Exec_Build.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/GenerateAngles.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Calc.o : Exec_Calc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Calc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_CatCrd.o : Exec_CatCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CatCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Change.o : Exec_Change.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Change.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h

From 8ad97a444f0dd574f0ded012d1133b94b4b05a38 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 14 Dec 2023 16:41:51 -0500
Subject: [PATCH 0175/1492] Allow ability to update IC indices according to
 maps.

---
 src/Exec_Build.cpp               | 1 +
 src/Structure/InternalCoords.cpp | 8 ++++++++
 src/Structure/InternalCoords.h   | 3 +++
 src/Structure/Zmatrix.cpp        | 6 ++++++
 src/Structure/Zmatrix.h          | 2 ++
 5 files changed, 20 insertions(+)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 1a787ed5fe..7ae235c81b 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -88,6 +88,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
         mprinterr("Error: Could not set up residue template zmatrix.\n");
         return 1;
       }
+      zmatrix.RemapIcIndices( map );
       zmatrix.print();
       // If no atoms missing just fill in the residue
 /*      if (nAtomsMissing == 0) {
diff --git a/src/Structure/InternalCoords.cpp b/src/Structure/InternalCoords.cpp
index 3161f023c7..d923fb22a2 100644
--- a/src/Structure/InternalCoords.cpp
+++ b/src/Structure/InternalCoords.cpp
@@ -67,3 +67,11 @@ void InternalCoords::printIC(Topology const& top) const {
           top.AtomMaskName(AtL()).c_str(),
           val_[0], val_[1], val_[2]);
 }
+
+/** Remap internal coords indices. */
+void InternalCoords::RemapIndices(std::vector<int> const& map) {
+  if (ati_    != NO_ATOM) ati_    = map[AtI()];
+  if (idx_[0] != NO_ATOM) idx_[0] = map[AtJ()];
+  if (idx_[1] != NO_ATOM) idx_[1] = map[AtK()];
+  if (idx_[2] != NO_ATOM) idx_[2] = map[AtL()];
+}
diff --git a/src/Structure/InternalCoords.h b/src/Structure/InternalCoords.h
index 3be154e9d8..b1ac7140ed 100644
--- a/src/Structure/InternalCoords.h
+++ b/src/Structure/InternalCoords.h
@@ -1,5 +1,6 @@
 #ifndef INC_STRUCTURE_INTERNALCOORDS_H
 #define INC_STRUCTURE_INTERNALCOORDS_H
+#include <vector>
 class Topology;
 namespace Cpptraj {
 namespace Structure {
@@ -38,6 +39,8 @@ class InternalCoords {
     static unsigned int sizeInBytes() { return (4*sizeof(int)) + (3*sizeof(double)); }
 
     void printIC(Topology const&) const;
+    /// Remap internal indices according to given map
+    void RemapIndices(std::vector<int> const&);
   private:
     int ati_;       ///< Atom I index
     int idx_[3];    ///< Atom indices for distance, angle, torsion
diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index 538564c2b9..d64be5f22e 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -120,6 +120,12 @@ void Zmatrix::print(Topology* topIn) const {
   }
 }
 
+/** Remap internal coordinate indices according to the given atom map. */
+void Zmatrix::RemapIcIndices(std::vector<int> const& map) {
+  for (ICarray::iterator it = IC_.begin(); it != IC_.end(); ++it)
+    it->RemapIndices(map);
+}
+
 /** \return True if all Cartesian seeds are set. */
 bool Zmatrix::HasCartSeeds() const {
   bool has_cart_seed = (seedAt0_ != InternalCoords::NO_ATOM &&
diff --git a/src/Structure/Zmatrix.h b/src/Structure/Zmatrix.h
index d778e34145..f2342c0a46 100644
--- a/src/Structure/Zmatrix.h
+++ b/src/Structure/Zmatrix.h
@@ -31,6 +31,8 @@ class Zmatrix {
     int AddIC(InternalCoords const&);
     /// Set specified IC
     void SetIC(unsigned int, InternalCoords const&);
+    /// Remap IC indices according to given map
+    void RemapIcIndices(std::vector<int> const&);
 
     /// Set seed atoms from frame/top
     int SetSeedPositions(Frame const&, Topology const&, int, int, int);

From df40d389b46390ea7ed8396944b5f11d830b72bc Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 18 Dec 2023 09:15:12 -0500
Subject: [PATCH 0176/1492] Add missing file

---
 test/Test_ReadAmberFF/toyrna.dat | 157 +++++++++++++++++++++++++++++++
 1 file changed, 157 insertions(+)
 create mode 100644 test/Test_ReadAmberFF/toyrna.dat

diff --git a/test/Test_ReadAmberFF/toyrna.dat b/test/Test_ReadAmberFF/toyrna.dat
new file mode 100644
index 0000000000..20b19ba4c1
--- /dev/null
+++ b/test/Test_ReadAmberFF/toyrna.dat
@@ -0,0 +1,157 @@
+toyrna force field
+CB 56.00         0.000               backbone C4'
+CS 43.00         0.000               sugar C1'
+G9 25.00         0.000               sp2 nitrogen in base
+G7 25.00         0.000               sp2 nitrogen in base
+G6 25.00         0.000               sp2 oxygen   in base
+G1 25.00         0.000               sp2 nitrogen in base
+G2 25.00         0.000               sp2 nitrogen in base
+G3 25.00         0.000               sp2 nitrogen in base
+A9 26.80         0.000               sp2 nitrogen in base
+A7 26.80         0.000               sp2 nitrogen in base
+A6 26.80         0.000               sp2 nitrogen in base
+A1 26.80         0.000               sp2 nitrogen in base
+A3 26.80         0.000               sp2 nitrogen in base
+U1 27.75         0.000               sp2 nitrogen in base
+U3 27.75         0.000               sp2 nitrogen in base
+U4 27.75         0.000               sp2 oxygen   in base
+U2 27.75         0.000               sp2 oxygen   in base
+C1 27.50         0.000               sp2 nitrogen in base
+C3 27.50         0.000               sp2 nitrogen in base
+C4 27.50         0.000               sp2 nitrogen in base
+C2 27.50         0.000               sp2 oxygen   in base
+P  95.00         0.000               phosphate,pol:JACS,112,8543,90,K.J.Miller
+
+
+P -CB  150.0    3.90
+CB-CS  100.0    2.35
+CS-G9  150.0    1.48
+CS-A9  150.0    1.48
+CS-U1  150.0    1.48
+CS-C1  150.0    1.48
+A9-A7  100.0    2.24
+A7-A6  100.0    3.08
+A6-A1  100.0    2.31
+A1-A3  100.0    2.39
+A3-A9  100.0    2.43
+G9-G7  100.0    2.25
+G7-G6  100.0    3.09
+G6-G1  100.0    2.27
+G1-G2  100.0    2.29
+G2-G3  100.0    2.31
+G3-G9  100.0    2.42
+U1-U4  100.0    4.04
+U4-U3  100.0    2.27
+U3-U2  100.0    2.28
+U2-U1  100.0    2.29
+C1-C4  100.0    4.04
+C4-C3  100.0    2.31
+C3-C2  100.0    2.26
+C2-C1  100.0    2.27
+
+CS-A9-A7     45.      160.9
+A9-A7-A6     50.      118.9
+A7-A6-A1     50.       85.4
+A6-A1-A3     50.      123.9
+A1-A3-A9     50.      112.1
+A3-A9-A7     50.       99.7
+CS-A9-A3     45.       99.1
+CS-G9-G7     45.      161.2
+G9-G7-G6     50.      117.7
+G7-G6-G1     50.       85.2
+G6-G1-G2     10.      175.1
+G1-G2-G3     50.       62.2
+G2-G3-G9     50.      169.6
+G3-G9-G7     50.      100.3
+CS-G9-G3     45.       97.9
+CS-U1-U4      0.      180.0
+U1-U4-U3     50.       29.5
+U4-U3-U2      0.      180.0
+U3-U2-U1     50.       61.8
+U2-U1-U4     50.       87.3
+CS-U1-U2     45.       90.8
+CS-C1-C4      0.      180.0
+C1-C4-C3     50.       30.0
+C4-C3-C2      0.      180.0
+C3-C2-C1     50.       62.3
+C2-C1-C4     50.       87.7
+CS-C1-C2     45.       89.2
+P -CB-P      22.       97.0
+CB-P -CB     30.      103.0
+P -CB-CS     30.      104.0
+CB-CS-G9     30.      122.5
+CB-CS-A9     30.      122.5
+CB-CS-U1     30.      122.5
+CB-CS-C1     30.      122.5
+
+X -CB-CS-X    1    7.50       -165.0             1.
+X -P -CB-X    1    0.0         180.0             2.
+X -CS-G9-X    1    0.0         180.0             2.
+X -CS-A9-X    1    0.0         180.0             2.
+X -CS-U1-X    1    0.0         180.0             2.
+X -CS-C1-X    1    0.0         180.0             2.
+X -A9-A7-X    1    0.0         180.0             2.
+X -A7-A6-X    1    0.0         180.0             2.
+X -A6-A1-X    1    0.0         180.0             2.
+X -A1-A3-X    1    0.0         180.0             2.
+X -A3-A9-X    1    0.0         180.0             2.
+X -G9-G7-X    1    0.0         180.0             2.
+X -G7-G6-X    1    0.0         180.0             2.
+X -G6-G1-X    1    0.0         180.0             2.
+X -G1-G2-X    1    0.0         180.0             2.
+X -G2-G3-X    1    0.0         180.0             2.
+X -G3-G9-X    1    0.0         180.0             2.
+X -U1-U4-X    1    0.0         180.0             2.
+X -U4-U3-X    1    0.0         180.0             2.
+X -U3-U2-X    1    0.0         180.0             2.
+X -U2-U1-X    1    0.0         180.0             2.
+X -C1-C4-X    1    0.0         180.0             2.
+X -C4-C3-X    1    0.0         180.0             2.
+X -C3-C2-X    1    0.0         180.0             2.
+X -C2-C1-X    1    0.0         180.0             2.
+CS-C1-C2-C3   1    2.0         180.0             2.
+C4-C1-C2-C3   1    2.0         180.0             2.
+CS-U1-U2-U3   1    2.0         180.0             2.
+U4-U1-U2-U3   1    2.0         180.0             2.
+CS-G9-G7-G6   1    2.0         180.0             2.
+G9-G7-G6-G1   1    2.0         180.0             2.
+CS-A9-A7-A6   1    2.0         180.0             2.
+A9-A7-A6-A1   1    2.0         180.0             2.
+CB-CS-C1-C2   1    2.0         180.0             2.
+CB-CS-U1-U2   1    2.0         180.0             2.
+CB-CS-G9-G3   1    2.0         180.0             2.
+CB-CS-A9-A3   1    2.0         180.0             2.
+
+
+  G6  C4   5.0     3.0                                   0.
+  G1  C3   5.0     3.0                                   0.
+  G2  C2   5.0     3.0                                   0.
+  A6  U4   5.0     3.0                                   0.
+  A1  U3   5.0     3.0                                   0.
+  G7  C4   5.0     6.0                                   0.
+  G3  C2   5.0     5.25                                  0.
+
+CB  CS
+G9  A9  U1  C1
+
+MOD4      RE
+  P           3.0000  0.2000
+  CB          2.0000  0.2000
+  G7          1.8000  0.2000
+  G6          1.8000  0.2000
+  G1          1.8000  0.2000
+  G2          1.8000  0.2000
+  G3          1.8000  0.2000
+  A7          1.8000  0.2000
+  A6          1.8000  0.2000
+  A1          1.8000  0.2000
+  A3          1.8000  0.2000
+  U4          1.8000  0.2000
+  U3          1.8000  0.2000
+  U2          1.8000  0.2000
+  C4          1.8000  0.2000
+  C3          1.8000  0.2000
+  C2          1.8000  0.2000
+  G9          1.8000  0.3000
+ 
+END

From 50d1c4be21f8a95b1d01eb19dc5e489059a0c677 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 18 Dec 2023 09:16:17 -0500
Subject: [PATCH 0177/1492] Add atom hybridization to AtomType

---
 src/AtomType.h | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/src/AtomType.h b/src/AtomType.h
index 659e84fc8e..e603f0361b 100644
--- a/src/AtomType.h
+++ b/src/AtomType.h
@@ -4,14 +4,16 @@
 /// Hold parameters for a unique atom type
 class AtomType {
   public:
+    /// Atom hybridization types
+    enum HybridizationType { SP = 0, SP2, SP3, UNKNOWN_HYBRIDIZATION };
     /// CONSTRUCTOR
-    AtomType() : mass_(0.0), polarizability_(0.0), oidx_(-1) {}
+    AtomType() : mass_(0.0), polarizability_(0.0), oidx_(-1), hybrid_(UNKNOWN_HYBRIDIZATION) {}
     /// CONSTRUCTOR - Mass only
-    AtomType(double m) : mass_(m), oidx_(-1) {}
+    AtomType(double m) : mass_(m), polarizability_(0.0), oidx_(-1), hybrid_(UNKNOWN_HYBRIDIZATION) {}
     /// CONSTRUCTOR - Mass, polarizability
-    AtomType(double m, double p) : mass_(m), polarizability_(p), oidx_(-1) {}
+    AtomType(double m, double p) : mass_(m), polarizability_(p), oidx_(-1), hybrid_(UNKNOWN_HYBRIDIZATION) {}
     /// CONSTRUCTOR - Radius, well depth, mass, polarizability
-    AtomType(double r, double d, double m, double p) : lj_(r, d), mass_(m), oidx_(-1) {}
+    AtomType(double r, double d, double m, double p) : lj_(r, d), mass_(m), oidx_(-1), hybrid_(UNKNOWN_HYBRIDIZATION) {}
     /// Set type index
     void SetTypeIdx(int i) { oidx_ = i; }
     /// \return default LJ parameters
@@ -22,6 +24,8 @@ class AtomType {
     double Polarizability() const { return polarizability_; }
     /// \return Original atom type index. Useful when checking for off-diagonal NB parameters.
     int OriginalIdx()       const { return oidx_; }
+    /// \return Atom hybridization
+    HybridizationType Hybridization() const { return hybrid_; }
     /// \return true if mass, polarizability, or LJ params are less than incoming
     bool operator<(AtomType const& rhs) const {
       if (FEQ(mass_, rhs.mass_)) {
@@ -49,5 +53,6 @@ class AtomType {
     double mass_;           ///< Mass in amu
     double polarizability_; ///< Atomic polarizability in Ang^3
     int oidx_;              ///< Original atom type index, for indexing nonbond parameters.
+    HybridizationType hybrid_; ///< Atom hybridization
 };
 #endif

From 05adf6c7b4c97a1426ced596af3fd2b07953359b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 19 Dec 2023 08:56:38 -0500
Subject: [PATCH 0178/1492] Find templates first to see how many atoms we
 expect

---
 src/Exec_Build.cpp | 120 ++++++++++++++++++++++++++++++++-------------
 1 file changed, 86 insertions(+), 34 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 7ae235c81b..2fc6793994 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -47,21 +47,57 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
                                        Carray const& Templates,
                                        Topology const& topIn, Frame const& frameIn)
 {
-  std::vector<Vec3> XYZ; // FIXME should use frameOut
-  Cpptraj::Structure::Zmatrix::Barray hasPosition;
-  int nAtomsMissing = 0;
+  // Array of templates for each residue
+  std::vector<DataSet_Coords*> ResTemplates;
+  ResTemplates.reserve( topIn.Nres() );
+  // Initial loop to try to match residues to templates
+  int newNatom = 0;
   for (int ires = 0; ires != topIn.Nres(); ires++)
   {
     // Identify a template based on the residue name.
-    DataSet_Coords* resTemplate = IdTemplateFromName(Templates, topIn.Res(ires).Name());
+    Residue const& currentRes = topIn.Res(ires);
+    DataSet_Coords* resTemplate = IdTemplateFromName(Templates, currentRes.Name());
     if (resTemplate == 0) {
       mprintf("Warning: No template found for residue %s\n", topIn.TruncResNameNum(ires).c_str());
+      newNatom += currentRes.NumAtoms();
     } else {
       mprintf("\tTemplate %s being used for residue %s\n",
               resTemplate->legend(), topIn.TruncResNameNum(ires).c_str());
-      // Map atoms to template atoms
+      newNatom += resTemplate->Top().Natom();
+    }
+    ResTemplates.push_back( resTemplate );
+  }
+  mprintf("\tFinal structure should have %i atoms.\n", newNatom);
+  frameOut.SetupFrame( newNatom );
+  // Clear frame so that AddXYZ can be used
+  frameOut.ClearAtoms();
+
+  // hasPosition - for each atom in topOut, status on whether atom in frameOut needs building
+  Cpptraj::Structure::Zmatrix::Barray hasPosition;
+  hasPosition.reserve( newNatom );
+  // Z-matrices for residues that have missing atoms
+  typedef std::vector<Cpptraj::Structure::Zmatrix*> Zarray;
+  Zarray ResZmatrices;
+  ResZmatrices.reserve( topIn.Nres() );
+  int nRefAtomsMissing = 0;
+  for (int ires = 0; ires != topIn.Nres(); ires++)
+  {
+    Residue const& currentRes = topIn.Res(ires);
+    DataSet_Coords* resTemplate = ResTemplates[ires];
+    if (resTemplate == 0) {
+      // No template. Just add the atoms.
+      for (int itgt = currentRes.FirstAtom(); itgt != currentRes.LastAtom(); ++itgt)
+      {
+        topOut.AddTopAtom( topIn[itgt], currentRes );
+        frameOut.AddVec3( Vec3(frameIn.XYZ(itgt)) );
+        hasPosition.push_back( true );
+      }
+    } else {
+      // A template exists for this residue.
+      // Map source atoms to template atoms.
       std::vector<int> map = MapAtomsToTemplate( topIn, ires, resTemplate );
       mprintf("\t  Atom map:\n");
+      // DEBUG - print map
       for (int iref = 0; iref != resTemplate->Top().Natom(); iref++) {
         mprintf("\t\t%6i %6s =>", iref+1, *(resTemplate->Top()[iref].Name()));
         if (map[iref] == -1)
@@ -69,50 +105,66 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
         else
           mprintf(" %6i %6s\n", map[iref]+1, *(topIn[map[iref]].Name()));
       }
+      // Map template atoms back to source atoms.
+      std::vector<int> pdb(currentRes.NumAtoms(), -1);
+      bool atomsNeedBuilding = false;
       for (int iref = 0; iref != resTemplate->Top().Natom(); iref++) {
-        topOut.AddTopAtom( resTemplate->Top()[iref], topIn.Res(ires) );
+        topOut.AddTopAtom( resTemplate->Top()[iref], currentRes );
         if (map[iref] == -1) {
-          XYZ.push_back( Vec3(0.0) );
+          frameOut.AddVec3( Vec3(0.0) );
           hasPosition.push_back( false );
-          nAtomsMissing++;
+          nRefAtomsMissing++;
+          atomsNeedBuilding = true;
         } else {
-          XYZ.push_back( Vec3(frameIn.XYZ(map[iref])) );
+          int itgt = map[iref];
+          frameOut.AddVec3( Vec3(frameIn.XYZ(itgt)) );
           hasPosition.push_back( true );
+          pdb[itgt-currentRes.FirstAtom()] = iref;
         }
       }
-      // DEBUG
-      Frame templateFrame = resTemplate->AllocateFrame();
-      resTemplate->GetFrame( 0, templateFrame );
-      Cpptraj::Structure::Zmatrix zmatrix;
-      if (zmatrix.SetFromFrame( templateFrame, resTemplate->Top(), 0 )) {
-        mprinterr("Error: Could not set up residue template zmatrix.\n");
-        return 1;
-      }
-      zmatrix.RemapIcIndices( map );
-      zmatrix.print();
-      // If no atoms missing just fill in the residue
-/*      if (nAtomsMissing == 0) {
-        for (int iref = 0; iref != resTemplate->Top().Natom(); iref++) {
-          topOut.AddTopAtom( resTemplate->Top()[iref], topIn.Res(ires) );
-          XYZ.push_back( Vec3(frameIn.XYZ(map[iref])) );
+      // See if any current atoms were not mapped to reference
+      int nTgtAtomsMissing = 0;
+      for (int itgt = 0; itgt != currentRes.NumAtoms(); itgt++)
+        if (pdb[itgt] == -1)
+          nTgtAtomsMissing++;
+      mprintf("\t%i source atoms not mapped to template.\n", nTgtAtomsMissing);
+      // Save zmatrix if atoms need to be built
+      if (atomsNeedBuilding) {
+        Frame templateFrame = resTemplate->AllocateFrame();
+        resTemplate->GetFrame( 0, templateFrame );
+        Cpptraj::Structure::Zmatrix* zmatrix = new Cpptraj::Structure::Zmatrix();
+        if (zmatrix->SetFromFrame( templateFrame, resTemplate->Top(), 0 )) {
+          mprinterr("Error: Could not set up residue template zmatrix.\n");
+          return 1;
         }
-      } else {
-        mprintf("\tTrying to fill in missing atoms.\n");
-        // one or more atoms missing. Try to use Zmatrix to fill it in
-        
-         // DEBUG*/
-
-    }
-  }
-  mprintf("\t%i atoms missing.\n", nAtomsMissing);
+        zmatrix->RemapIcIndices( map );
+        ResZmatrices.push_back( zmatrix );
+        //zmatrix->print();
+      } else
+        ResZmatrices.push_back( 0 );
+    } // END template exists
+  } // END loop over source residues
+  mprintf("\t%i template atoms missing in source.\n", nRefAtomsMissing);
   for (int iat = 0; iat != topOut.Natom(); iat++)
   {
     Residue const& res = topOut.Res( topOut[iat].ResNum() );
+    const double* XYZ = frameOut.XYZ(iat);
     mprintf("%6i %6s %6i %6s (%i) %g %g %g\n",
             iat+1, *(topOut[iat].Name()), res.OriginalResNum(), *(res.Name()),
-            (int)hasPosition[iat], XYZ[iat][0], XYZ[iat][1], XYZ[iat][2]);
+            (int)hasPosition[iat], XYZ[0], XYZ[1], XYZ[2]);
+  }
+
+  for (Zarray::const_iterator it = ResZmatrices.begin(); it != ResZmatrices.end(); ++it)
+  {
+    mprintf("DEBUG: Zmatrix for building residue %li\n", it - ResZmatrices.begin() + 1);
+    Cpptraj::Structure::Zmatrix* zmatrix = *it;
+    if (zmatrix != 0)
+      zmatrix->print();
   }
 
+  // Clean up zmatrices
+  for (Zarray::iterator it = ResZmatrices.begin(); it != ResZmatrices.end(); ++it)
+    delete *it;
   return 0;
 }
 

From 2292b6d14d84d754992b8bc35c96ddd312cce623 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 19 Dec 2023 09:18:08 -0500
Subject: [PATCH 0179/1492] Do initial missing atom build. Use offset instead
 of remap since not all atoms may be mapped.

---
 src/Exec_Build.cpp               | 39 +++++++++++++++++++++++---------
 src/Structure/InternalCoords.cpp | 10 +++++++-
 src/Structure/InternalCoords.h   |  4 +++-
 src/Structure/Zmatrix.cpp        |  8 ++++++-
 src/Structure/Zmatrix.h          |  4 +++-
 5 files changed, 50 insertions(+), 15 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 2fc6793994..5abc4f54c4 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -82,6 +82,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
   int nRefAtomsMissing = 0;
   for (int ires = 0; ires != topIn.Nres(); ires++)
   {
+    mprintf("\tAdding atoms for residue %s\n", topIn.TruncResNameNum(ires).c_str());
     Residue const& currentRes = topIn.Res(ires);
     DataSet_Coords* resTemplate = ResTemplates[ires];
     if (resTemplate == 0) {
@@ -108,6 +109,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
       // Map template atoms back to source atoms.
       std::vector<int> pdb(currentRes.NumAtoms(), -1);
       bool atomsNeedBuilding = false;
+      int atomOffset = topOut.Natom();
       for (int iref = 0; iref != resTemplate->Top().Natom(); iref++) {
         topOut.AddTopAtom( resTemplate->Top()[iref], currentRes );
         if (map[iref] == -1) {
@@ -137,14 +139,35 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
           mprinterr("Error: Could not set up residue template zmatrix.\n");
           return 1;
         }
-        zmatrix->RemapIcIndices( map );
+        zmatrix->print( resTemplate->TopPtr() );
+        zmatrix->OffsetIcIndices( atomOffset );
         ResZmatrices.push_back( zmatrix );
-        //zmatrix->print();
+        zmatrix->print( &topOut );
       } else
         ResZmatrices.push_back( 0 );
     } // END template exists
   } // END loop over source residues
   mprintf("\t%i template atoms missing in source.\n", nRefAtomsMissing);
+
+  // Build using internal coords if needed.
+  bool buildFailed = false;
+  for (Zarray::const_iterator it = ResZmatrices.begin(); it != ResZmatrices.end(); ++it)
+  {
+    Cpptraj::Structure::Zmatrix* zmatrix = *it;
+    if (zmatrix != 0) {
+      mprintf("DEBUG: Zmatrix for building residue %li %s\n", it - ResZmatrices.begin() + 1,
+              topOut.TruncResNameNum(it - ResZmatrices.begin()).c_str());
+      zmatrix->print(&topOut);
+      zmatrix->SetDebug( 1 ); // DEBUG
+      if (zmatrix->SetToFrame( frameOut, hasPosition )) {
+        mprinterr("Error: Building residue %s failed.\n",
+                  topOut.TruncResNameNum(it - ResZmatrices.begin()).c_str());
+        buildFailed = true;
+      }
+    }
+  }
+
+  // DEBUG - Print new top/coords
   for (int iat = 0; iat != topOut.Natom(); iat++)
   {
     Residue const& res = topOut.Res( topOut[iat].ResNum() );
@@ -154,17 +177,11 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
             (int)hasPosition[iat], XYZ[0], XYZ[1], XYZ[2]);
   }
 
-  for (Zarray::const_iterator it = ResZmatrices.begin(); it != ResZmatrices.end(); ++it)
-  {
-    mprintf("DEBUG: Zmatrix for building residue %li\n", it - ResZmatrices.begin() + 1);
-    Cpptraj::Structure::Zmatrix* zmatrix = *it;
-    if (zmatrix != 0)
-      zmatrix->print();
-  }
-
   // Clean up zmatrices
   for (Zarray::iterator it = ResZmatrices.begin(); it != ResZmatrices.end(); ++it)
-    delete *it;
+    if (*it != 0) delete *it;
+
+  if (buildFailed) return 1;
   return 0;
 }
 
diff --git a/src/Structure/InternalCoords.cpp b/src/Structure/InternalCoords.cpp
index d923fb22a2..08b65e39fe 100644
--- a/src/Structure/InternalCoords.cpp
+++ b/src/Structure/InternalCoords.cpp
@@ -69,9 +69,17 @@ void InternalCoords::printIC(Topology const& top) const {
 }
 
 /** Remap internal coords indices. */
-void InternalCoords::RemapIndices(std::vector<int> const& map) {
+/*void InternalCoords::RemapIndices(std::vector<int> const& map) {
   if (ati_    != NO_ATOM) ati_    = map[AtI()];
   if (idx_[0] != NO_ATOM) idx_[0] = map[AtJ()];
   if (idx_[1] != NO_ATOM) idx_[1] = map[AtK()];
   if (idx_[2] != NO_ATOM) idx_[2] = map[AtL()];
+}*/
+
+/** Offset internal coords indices. */
+void InternalCoords::OffsetIndices(int offset) {
+  if (ati_    != NO_ATOM) ati_    += offset;
+  if (idx_[0] != NO_ATOM) idx_[0] += offset;
+  if (idx_[1] != NO_ATOM) idx_[1] += offset;
+  if (idx_[2] != NO_ATOM) idx_[2] += offset;
 }
diff --git a/src/Structure/InternalCoords.h b/src/Structure/InternalCoords.h
index b1ac7140ed..7494d2f9d2 100644
--- a/src/Structure/InternalCoords.h
+++ b/src/Structure/InternalCoords.h
@@ -40,7 +40,9 @@ class InternalCoords {
 
     void printIC(Topology const&) const;
     /// Remap internal indices according to given map
-    void RemapIndices(std::vector<int> const&);
+    //void RemapIndices(std::vector<int> const&);
+    /// Offset internal indices by given offset
+    void OffsetIndices(int);
   private:
     int ati_;       ///< Atom I index
     int idx_[3];    ///< Atom indices for distance, angle, torsion
diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index d64be5f22e..8c03c97d39 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -121,9 +121,15 @@ void Zmatrix::print(Topology* topIn) const {
 }
 
 /** Remap internal coordinate indices according to the given atom map. */
-void Zmatrix::RemapIcIndices(std::vector<int> const& map) {
+/*void Zmatrix::RemapIcIndices(std::vector<int> const& map) {
   for (ICarray::iterator it = IC_.begin(); it != IC_.end(); ++it)
     it->RemapIndices(map);
+}*/
+
+/** Increment IC indices by given offset */
+void Zmatrix::OffsetIcIndices(int offset) {
+  for (ICarray::iterator it = IC_.begin(); it != IC_.end(); ++it)
+    it->OffsetIndices(offset);
 }
 
 /** \return True if all Cartesian seeds are set. */
diff --git a/src/Structure/Zmatrix.h b/src/Structure/Zmatrix.h
index f2342c0a46..8b53f03fe7 100644
--- a/src/Structure/Zmatrix.h
+++ b/src/Structure/Zmatrix.h
@@ -32,7 +32,9 @@ class Zmatrix {
     /// Set specified IC
     void SetIC(unsigned int, InternalCoords const&);
     /// Remap IC indices according to given map
-    void RemapIcIndices(std::vector<int> const&);
+    //void RemapIcIndices(std::vector<int> const&);
+    /// Offset IC indices by given value
+    void OffsetIcIndices(int);
 
     /// Set seed atoms from frame/top
     int SetSeedPositions(Frame const&, Topology const&, int, int, int);

From b27004f2c886de3ef6399dbe0a78948b76f1877d Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 19 Dec 2023 09:50:04 -0500
Subject: [PATCH 0180/1492] Require output COORDS be specified

---
 src/Exec_Build.cpp | 45 +++++++++++++++++++++++++++++++++++----------
 1 file changed, 35 insertions(+), 10 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 5abc4f54c4..6b1ac4cfeb 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -75,7 +75,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
   // hasPosition - for each atom in topOut, status on whether atom in frameOut needs building
   Cpptraj::Structure::Zmatrix::Barray hasPosition;
   hasPosition.reserve( newNatom );
-  // Z-matrices for residues that have missing atoms
+  // Hold Z-matrices for residues that have missing atoms
   typedef std::vector<Cpptraj::Structure::Zmatrix*> Zarray;
   Zarray ResZmatrices;
   ResZmatrices.reserve( topIn.Nres() );
@@ -185,10 +185,12 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
   return 0;
 }
 
+// -----------------------------------------------------------------------------
 // Exec_Build::Help()
 void Exec_Build::Help() const
 {
-  mprintf("\tcrdset <COORDS set> [frame <#>] [parmset <param set> ...]\n");
+  mprintf("\tname <output COORDS> crdset <COORDS set> [frame <#>]\n"
+          "\t[parmset <param set> ...] [lib <lib set> ...]\n");
 }
 
 // Exec_Build::Execute()
@@ -200,12 +202,13 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
     mprinterr("Error: Must specify input COORDS set with 'crdset'\n");
     return CpptrajState::ERR;
   }
-  DataSet* ds = State.DSL().FindSetOfGroup( crdset, DataSet::COORDINATES );
-  if (ds == 0) {
+  DataSet* inCrdPtr = State.DSL().FindSetOfGroup( crdset, DataSet::COORDINATES );
+  if (inCrdPtr == 0) {
     mprinterr("Error: No COORDS set found matching %s\n", crdset.c_str());
     return CpptrajState::ERR;
   }
-  DataSet_Coords& coords = static_cast<DataSet_Coords&>( *((DataSet_Coords*)ds) );
+  // TODO make it so this can be const (cant bc GetFrame)
+  DataSet_Coords& coords = static_cast<DataSet_Coords&>( *((DataSet_Coords*)inCrdPtr) );
   // Get frame from input coords
   int tgtframe = argIn.getKeyInt("frame", 1) - 1;
   mprintf("\tUsing frame %i from COORDS set %s\n", tgtframe+1, coords.legend());
@@ -216,7 +219,22 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
   Frame frameIn = coords.AllocateFrame();
   coords.GetFrame(tgtframe, frameIn);
   // Get modifiable topology
-  Topology& topIn = *(coords.TopPtr());
+  //Topology& topIn = *(coords.TopPtr());
+  Topology const& topIn = coords.Top();
+
+  // Output coords
+  std::string outset = argIn.GetStringKey("name");
+  if (outset.empty()) {
+    mprinterr("Error: Must specify output COORDS set with 'name'\n");
+    return CpptrajState::ERR;
+  }
+  DataSet* outCrdPtr = State.DSL().AddSet( DataSet::COORDS, outset );
+  if (outCrdPtr == 0) {
+    mprinterr("Error: Could not allocate output COORDS set with name '%s'\n", outset.c_str());
+    return CpptrajState::ERR;
+  }
+  DataSet_Coords& crdout = static_cast<DataSet_Coords&>( *((DataSet_Coords*)outCrdPtr) );
+  mprintf("\tOutput COORDS set: %s\n", crdout.legend());
 
   // Get residue templates.
   Carray Templates;
@@ -266,8 +284,8 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
   }
 
   // Generate angles/dihedrals
-  if (Cpptraj::Structure::GenerateAngles(topIn)) {
-    mprinterr("Error: Could not generate angles/dihedrals for '%s'\n", topIn.c_str());
+  if (Cpptraj::Structure::GenerateAngles(topOut)) {
+    mprinterr("Error: Could not generate angles/dihedrals for '%s'\n", topOut.c_str());
     return CpptrajState::ERR;
   }
 
@@ -319,12 +337,19 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
 
   // Update parameters
   Exec::RetType ret = CpptrajState::OK;
-  if ( topIn.UpdateParams( *mainParmSet  ) ) {
-    mprinterr("Error: Could not update parameters for '%s'.\n", topIn.c_str());
+  if ( topOut.UpdateParams( *mainParmSet  ) ) {
+    mprinterr("Error: Could not update parameters for '%s'.\n", topOut.c_str());
     ret = CpptrajState::ERR;
   }
 
   if (free_parmset_mem && mainParmSet != 0) delete mainParmSet;
 
+  // Update coords 
+  if (crdout.CoordsSetup( topOut, CoordinateInfo() )) { // FIXME better coordinate info
+    mprinterr("Error: Could not set up output COORDS.\n");
+    return CpptrajState::ERR;
+  }
+  crdout.SetCRD(0, frameOut);
+
   return ret;
 }

From a1909f8293cba78453782d17bef6575894859e0e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 19 Dec 2023 13:00:43 -0500
Subject: [PATCH 0181/1492] Add non-template intra-residue bonds

---
 src/Exec_Build.cpp | 23 +++++++++++++++++++++--
 1 file changed, 21 insertions(+), 2 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 6b1ac4cfeb..f7f81869aa 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -75,6 +75,9 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
   // hasPosition - for each atom in topOut, status on whether atom in frameOut needs building
   Cpptraj::Structure::Zmatrix::Barray hasPosition;
   hasPosition.reserve( newNatom );
+  // For holding bonded atom pairs
+  typedef std::pair<int,int> Ipair;
+  typedef std::vector<Ipair> IParray;
   // Hold Z-matrices for residues that have missing atoms
   typedef std::vector<Cpptraj::Structure::Zmatrix*> Zarray;
   Zarray ResZmatrices;
@@ -83,16 +86,33 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
   for (int ires = 0; ires != topIn.Nres(); ires++)
   {
     mprintf("\tAdding atoms for residue %s\n", topIn.TruncResNameNum(ires).c_str());
+    int atomOffset = topOut.Natom();
     Residue const& currentRes = topIn.Res(ires);
     DataSet_Coords* resTemplate = ResTemplates[ires];
     if (resTemplate == 0) {
       // No template. Just add the atoms.
+      IParray bondsToAdd;
       for (int itgt = currentRes.FirstAtom(); itgt != currentRes.LastAtom(); ++itgt)
       {
-        topOut.AddTopAtom( topIn[itgt], currentRes );
+        // Add intra-residue bonds
+        Atom currentAtom = topIn[itgt];
+        int at0 = itgt - currentRes.FirstAtom() + atomOffset;
+        for (Atom::bond_iterator bat = currentAtom.bondbegin(); bat != currentAtom.bondend(); ++bat) {
+          if ( topIn[*bat].ResNum() == ires ) {
+            int at1 = *bat - currentRes.FirstAtom() + atomOffset;
+            mprintf("Will add bond between %i and %i (original %i and %i)\n", at0+1, at1+1, itgt+1, *bat + 1);
+            bondsToAdd.push_back( Ipair(at0, at1) );
+            //topOut.AddBond(at0, at1);
+            // TODO inter-residue
+          }
+        }
+        currentAtom.ClearBonds();
+        topOut.AddTopAtom( currentAtom, currentRes );
         frameOut.AddVec3( Vec3(frameIn.XYZ(itgt)) );
         hasPosition.push_back( true );
       }
+      for (IParray::const_iterator it = bondsToAdd.begin(); it != bondsToAdd.end(); ++it)
+        topOut.AddBond(it->first, it->second);
     } else {
       // A template exists for this residue.
       // Map source atoms to template atoms.
@@ -109,7 +129,6 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
       // Map template atoms back to source atoms.
       std::vector<int> pdb(currentRes.NumAtoms(), -1);
       bool atomsNeedBuilding = false;
-      int atomOffset = topOut.Natom();
       for (int iref = 0; iref != resTemplate->Top().Natom(); iref++) {
         topOut.AddTopAtom( resTemplate->Top()[iref], currentRes );
         if (map[iref] == -1) {

From abec019459203184f71f4cb30ecf3afc918e0e97 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 19 Dec 2023 14:27:56 -0500
Subject: [PATCH 0182/1492] Change to intraResBonds

---
 src/Exec_Build.cpp | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index f7f81869aa..9d78cb1737 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -91,7 +91,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
     DataSet_Coords* resTemplate = ResTemplates[ires];
     if (resTemplate == 0) {
       // No template. Just add the atoms.
-      IParray bondsToAdd;
+      IParray intraResBonds;
       for (int itgt = currentRes.FirstAtom(); itgt != currentRes.LastAtom(); ++itgt)
       {
         // Add intra-residue bonds
@@ -101,17 +101,17 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
           if ( topIn[*bat].ResNum() == ires ) {
             int at1 = *bat - currentRes.FirstAtom() + atomOffset;
             mprintf("Will add bond between %i and %i (original %i and %i)\n", at0+1, at1+1, itgt+1, *bat + 1);
-            bondsToAdd.push_back( Ipair(at0, at1) );
+            intraResBonds.push_back( Ipair(at0, at1) );
             //topOut.AddBond(at0, at1);
             // TODO inter-residue
           }
         }
-        currentAtom.ClearBonds();
+        currentAtom.ClearBonds(); // FIXME AddTopAtom should clear bonds
         topOut.AddTopAtom( currentAtom, currentRes );
         frameOut.AddVec3( Vec3(frameIn.XYZ(itgt)) );
         hasPosition.push_back( true );
       }
-      for (IParray::const_iterator it = bondsToAdd.begin(); it != bondsToAdd.end(); ++it)
+      for (IParray::const_iterator it = intraResBonds.begin(); it != intraResBonds.end(); ++it)
         topOut.AddBond(it->first, it->second);
     } else {
       // A template exists for this residue.

From a29e395688f0f0efa77bde0486f1f7ae0b1c697c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 19 Dec 2023 15:06:45 -0500
Subject: [PATCH 0183/1492] Track intra-residue bonds for template residues as
 well

---
 src/Exec_Build.cpp | 22 +++++++++++++++++-----
 1 file changed, 17 insertions(+), 5 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 9d78cb1737..899d1b598e 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -89,12 +89,12 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
     int atomOffset = topOut.Natom();
     Residue const& currentRes = topIn.Res(ires);
     DataSet_Coords* resTemplate = ResTemplates[ires];
+    IParray intraResBonds;
     if (resTemplate == 0) {
       // No template. Just add the atoms.
-      IParray intraResBonds;
       for (int itgt = currentRes.FirstAtom(); itgt != currentRes.LastAtom(); ++itgt)
       {
-        // Add intra-residue bonds
+        // Track intra-residue bonds
         Atom currentAtom = topIn[itgt];
         int at0 = itgt - currentRes.FirstAtom() + atomOffset;
         for (Atom::bond_iterator bat = currentAtom.bondbegin(); bat != currentAtom.bondend(); ++bat) {
@@ -111,8 +111,6 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
         frameOut.AddVec3( Vec3(frameIn.XYZ(itgt)) );
         hasPosition.push_back( true );
       }
-      for (IParray::const_iterator it = intraResBonds.begin(); it != intraResBonds.end(); ++it)
-        topOut.AddBond(it->first, it->second);
     } else {
       // A template exists for this residue.
       // Map source atoms to template atoms.
@@ -130,7 +128,18 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
       std::vector<int> pdb(currentRes.NumAtoms(), -1);
       bool atomsNeedBuilding = false;
       for (int iref = 0; iref != resTemplate->Top().Natom(); iref++) {
-        topOut.AddTopAtom( resTemplate->Top()[iref], currentRes );
+        // Track intra-residue bonds
+        Atom currentAtom = resTemplate->Top()[iref];
+        int at0 = iref + atomOffset;
+        for (Atom::bond_iterator bat = currentAtom.bondbegin(); bat != currentAtom.bondend(); ++bat) {
+          if ( topIn[*bat].ResNum() == ires ) {
+            int at1 = *bat + atomOffset;
+            mprintf("Will add bond between %i and %i (original %i and %i)\n", at0+1, at1+1, iref+1, *bat + 1);
+            intraResBonds.push_back( Ipair(at0, at1) );
+          }
+        }
+        currentAtom.ClearBonds();
+        topOut.AddTopAtom( currentAtom, currentRes );
         if (map[iref] == -1) {
           frameOut.AddVec3( Vec3(0.0) );
           hasPosition.push_back( false );
@@ -165,6 +174,9 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
       } else
         ResZmatrices.push_back( 0 );
     } // END template exists
+    // Add intra-residue bonds
+    for (IParray::const_iterator it = intraResBonds.begin(); it != intraResBonds.end(); ++it)
+      topOut.AddBond(it->first, it->second);
   } // END loop over source residues
   mprintf("\t%i template atoms missing in source.\n", nRefAtomsMissing);
 

From f7c848c132b84e0521c5ff78a2684a61eb6ab712 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 19 Dec 2023 15:44:09 -0500
Subject: [PATCH 0184/1492] Fix intra-residue bonds for templates. Start
 inter-residue bonds.

---
 src/Exec_Build.cpp | 53 ++++++++++++++++++++++++++++++++++++----------
 1 file changed, 42 insertions(+), 11 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 899d1b598e..ce4dd2bd97 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -75,13 +75,19 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
   // hasPosition - for each atom in topOut, status on whether atom in frameOut needs building
   Cpptraj::Structure::Zmatrix::Barray hasPosition;
   hasPosition.reserve( newNatom );
-  // For holding bonded atom pairs
-  typedef std::pair<int,int> Ipair;
-  typedef std::vector<Ipair> IParray;
+
   // Hold Z-matrices for residues that have missing atoms
   typedef std::vector<Cpptraj::Structure::Zmatrix*> Zarray;
   Zarray ResZmatrices;
   ResZmatrices.reserve( topIn.Nres() );
+
+  // For inter-residue bonding, use residue # and atom name since
+  // atom numbering may change if atoms are added from templates.
+  typedef std::pair<int,NameType> ResAtPair;
+  typedef std::vector<ResAtPair> ResAtArray;
+  ResAtArray interResBonds;
+
+  // Loop for setting up atoms in the topology from residues or residue templates.
   int nRefAtomsMissing = 0;
   for (int ires = 0; ires != topIn.Nres(); ires++)
   {
@@ -89,6 +95,9 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
     int atomOffset = topOut.Natom();
     Residue const& currentRes = topIn.Res(ires);
     DataSet_Coords* resTemplate = ResTemplates[ires];
+    // For holding bonded atom pairs
+    typedef std::pair<int,int> Ipair;
+    typedef std::vector<Ipair> IParray;
     IParray intraResBonds;
     if (resTemplate == 0) {
       // No template. Just add the atoms.
@@ -100,10 +109,13 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
         for (Atom::bond_iterator bat = currentAtom.bondbegin(); bat != currentAtom.bondend(); ++bat) {
           if ( topIn[*bat].ResNum() == ires ) {
             int at1 = *bat - currentRes.FirstAtom() + atomOffset;
-            mprintf("Will add bond between %i and %i (original %i and %i)\n", at0+1, at1+1, itgt+1, *bat + 1);
-            intraResBonds.push_back( Ipair(at0, at1) );
-            //topOut.AddBond(at0, at1);
-            // TODO inter-residue
+            if (at1 > at0) {
+              mprintf("Will add bond between %i and %i (original %i and %i)\n", at0+1, at1+1, itgt+1, *bat + 1);
+              intraResBonds.push_back( Ipair(at0, at1) );
+            }
+          } else {
+            interResBonds.push_back( ResAtPair(ires, currentAtom.Name()) );
+            interResBonds.push_back( ResAtPair(topIn[*bat].ResNum(), topIn[*bat].Name()) );
           }
         }
         currentAtom.ClearBonds(); // FIXME AddTopAtom should clear bonds
@@ -132,12 +144,16 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
         Atom currentAtom = resTemplate->Top()[iref];
         int at0 = iref + atomOffset;
         for (Atom::bond_iterator bat = currentAtom.bondbegin(); bat != currentAtom.bondend(); ++bat) {
-          if ( topIn[*bat].ResNum() == ires ) {
+          //if ( resTemplate->Top()[*bat].ResNum() == ires ) {
             int at1 = *bat + atomOffset;
-            mprintf("Will add bond between %i and %i (original %i and %i)\n", at0+1, at1+1, iref+1, *bat + 1);
-            intraResBonds.push_back( Ipair(at0, at1) );
-          }
+            if (at1 > at0) {
+              mprintf("Will add bond between %i and %i (original %i and %i)\n", at0+1, at1+1, iref+1, *bat + 1);
+              intraResBonds.push_back( Ipair(at0, at1) );
+            }
+          //}
         }
+        // TODO connect atoms for inter-residue connections
+        // TODO check source atoms for inter-residue connections
         currentAtom.ClearBonds();
         topOut.AddTopAtom( currentAtom, currentRes );
         if (map[iref] == -1) {
@@ -176,8 +192,23 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
     } // END template exists
     // Add intra-residue bonds
     for (IParray::const_iterator it = intraResBonds.begin(); it != intraResBonds.end(); ++it)
+    {
+      mprintf("DEBUG: Intra-res bond: Res %s atom %s to res %s atom %s\n",
+              topOut.TruncResNameNum(topOut[it->first].ResNum()).c_str(), *(topOut[it->first].Name()),
+              topOut.TruncResNameNum(topOut[it->second].ResNum()).c_str(), *(topOut[it->second].Name()));
       topOut.AddBond(it->first, it->second);
+    }
   } // END loop over source residues
+  // Add inter-residue bonds
+  for (ResAtArray::const_iterator it = interResBonds.begin(); it != interResBonds.end(); ++it)
+  {
+    ResAtPair const& ra0 = *it;
+    ++it;
+    ResAtPair const& ra1 = *it;
+    mprintf("DEBUG: Inter-res bond: Res %i atom %s to res %i atom %s\n",
+            ra0.first+1, *(ra0.second),
+            ra1.first+1, *(ra1.second));
+  }
   mprintf("\t%i template atoms missing in source.\n", nRefAtomsMissing);
 
   // Build using internal coords if needed.

From 95e151cc16f8122ccca3546f759dc199cabd55f4 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 19 Dec 2023 15:52:25 -0500
Subject: [PATCH 0185/1492] Track existing inter-residue connections for
 templates

---
 src/Exec_Build.cpp | 27 +++++++++++++++++----------
 1 file changed, 17 insertions(+), 10 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index ce4dd2bd97..0b345f6982 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -104,9 +104,9 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
       for (int itgt = currentRes.FirstAtom(); itgt != currentRes.LastAtom(); ++itgt)
       {
         // Track intra-residue bonds
-        Atom currentAtom = topIn[itgt];
+        Atom sourceAtom = topIn[itgt];
         int at0 = itgt - currentRes.FirstAtom() + atomOffset;
-        for (Atom::bond_iterator bat = currentAtom.bondbegin(); bat != currentAtom.bondend(); ++bat) {
+        for (Atom::bond_iterator bat = sourceAtom.bondbegin(); bat != sourceAtom.bondend(); ++bat) {
           if ( topIn[*bat].ResNum() == ires ) {
             int at1 = *bat - currentRes.FirstAtom() + atomOffset;
             if (at1 > at0) {
@@ -114,12 +114,12 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
               intraResBonds.push_back( Ipair(at0, at1) );
             }
           } else {
-            interResBonds.push_back( ResAtPair(ires, currentAtom.Name()) );
+            interResBonds.push_back( ResAtPair(ires, sourceAtom.Name()) );
             interResBonds.push_back( ResAtPair(topIn[*bat].ResNum(), topIn[*bat].Name()) );
           }
         }
-        currentAtom.ClearBonds(); // FIXME AddTopAtom should clear bonds
-        topOut.AddTopAtom( currentAtom, currentRes );
+        sourceAtom.ClearBonds(); // FIXME AddTopAtom should clear bonds
+        topOut.AddTopAtom( sourceAtom, currentRes );
         frameOut.AddVec3( Vec3(frameIn.XYZ(itgt)) );
         hasPosition.push_back( true );
       }
@@ -141,9 +141,9 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
       bool atomsNeedBuilding = false;
       for (int iref = 0; iref != resTemplate->Top().Natom(); iref++) {
         // Track intra-residue bonds
-        Atom currentAtom = resTemplate->Top()[iref];
+        Atom templateAtom = resTemplate->Top()[iref];
         int at0 = iref + atomOffset;
-        for (Atom::bond_iterator bat = currentAtom.bondbegin(); bat != currentAtom.bondend(); ++bat) {
+        for (Atom::bond_iterator bat = templateAtom.bondbegin(); bat != templateAtom.bondend(); ++bat) {
           //if ( resTemplate->Top()[*bat].ResNum() == ires ) {
             int at1 = *bat + atomOffset;
             if (at1 > at0) {
@@ -153,9 +153,8 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
           //}
         }
         // TODO connect atoms for inter-residue connections
-        // TODO check source atoms for inter-residue connections
-        currentAtom.ClearBonds();
-        topOut.AddTopAtom( currentAtom, currentRes );
+        templateAtom.ClearBonds();
+        topOut.AddTopAtom( templateAtom, currentRes );
         if (map[iref] == -1) {
           frameOut.AddVec3( Vec3(0.0) );
           hasPosition.push_back( false );
@@ -166,6 +165,14 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
           frameOut.AddVec3( Vec3(frameIn.XYZ(itgt)) );
           hasPosition.push_back( true );
           pdb[itgt-currentRes.FirstAtom()] = iref;
+          // Check source atoms for inter-residue connections
+          Atom const& sourceAtom = topIn[itgt];
+          for (Atom::bond_iterator bat = sourceAtom.bondbegin(); bat != sourceAtom.bondend(); ++bat) {
+            if ( topIn[*bat].ResNum() != ires ) {
+              interResBonds.push_back( ResAtPair(ires, sourceAtom.Name()) );
+              interResBonds.push_back( ResAtPair(topIn[*bat].ResNum(), topIn[*bat].Name()) );
+            }
+          }
         }
       }
       // See if any current atoms were not mapped to reference

From d7910ece13189e1af865504481843aa36b35a53a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 19 Dec 2023 15:55:47 -0500
Subject: [PATCH 0186/1492] Try to avoid duplicate inter-residue bonds

---
 src/Exec_Build.cpp | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 0b345f6982..536d092edc 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -114,8 +114,10 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
               intraResBonds.push_back( Ipair(at0, at1) );
             }
           } else {
-            interResBonds.push_back( ResAtPair(ires, sourceAtom.Name()) );
-            interResBonds.push_back( ResAtPair(topIn[*bat].ResNum(), topIn[*bat].Name()) );
+            if (topIn[*bat].ResNum() > ires) {
+              interResBonds.push_back( ResAtPair(ires, sourceAtom.Name()) );
+              interResBonds.push_back( ResAtPair(topIn[*bat].ResNum(), topIn[*bat].Name()) );
+            }
           }
         }
         sourceAtom.ClearBonds(); // FIXME AddTopAtom should clear bonds
@@ -168,7 +170,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
           // Check source atoms for inter-residue connections
           Atom const& sourceAtom = topIn[itgt];
           for (Atom::bond_iterator bat = sourceAtom.bondbegin(); bat != sourceAtom.bondend(); ++bat) {
-            if ( topIn[*bat].ResNum() != ires ) {
+            if ( topIn[*bat].ResNum() > ires ) {
               interResBonds.push_back( ResAtPair(ires, sourceAtom.Name()) );
               interResBonds.push_back( ResAtPair(topIn[*bat].ResNum(), topIn[*bat].Name()) );
             }

From 9978117dbb909145b91892aefa14a2d9f6e00320 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 19 Dec 2023 16:02:46 -0500
Subject: [PATCH 0187/1492] Do the inter-residue bonds

---
 src/Exec_Build.cpp | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 536d092edc..0992ed984a 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -217,6 +217,17 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
     mprintf("DEBUG: Inter-res bond: Res %i atom %s to res %i atom %s\n",
             ra0.first+1, *(ra0.second),
             ra1.first+1, *(ra1.second));
+    int at0 = topOut.FindAtomInResidue(ra0.first, ra0.second);
+    if (at0 < 0) {
+      mprinterr("Error: Atom %s not found in residue %i\n", *(ra0.second), ra0.first);
+      return 1;
+    }
+    int at1 = topOut.FindAtomInResidue(ra1.first, ra1.second);
+    if (at1 < 0) {
+      mprinterr("Error: Atom %s not found in residue %i\n", *(ra1.second), ra1.first);
+      return 1;
+    }
+    topOut.AddBond(at0, at1);
   }
   mprintf("\t%i template atoms missing in source.\n", nRefAtomsMissing);
 
@@ -252,6 +263,10 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
   for (Zarray::iterator it = ResZmatrices.begin(); it != ResZmatrices.end(); ++it)
     if (*it != 0) delete *it;
 
+  // Finalize topology
+  topOut.CommonSetup(); // TODO dont assign default bond parameters here
+  topOut.Summary();
+
   if (buildFailed) return 1;
   return 0;
 }

From 14cc4522ab3950d1866d6dc1079e2455e1db9bb3 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 20 Dec 2023 14:47:54 -0500
Subject: [PATCH 0188/1492] Try to deal with dihedral/improper wildcard terms.
 Want to honor wildcards when searching, not when adding.

---
 src/AmberParamFile.cpp  |  9 ++++++--
 src/CharmmParamFile.cpp |  7 +++++-
 src/Exec_Change.cpp     |  2 +-
 src/ParameterHolders.h  | 36 +++++++++++++++++++++++------
 src/TypeNameHolder.h    | 51 +++++++++++++++++++++++++++++++++++++----
 5 files changed, 90 insertions(+), 15 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index f62d6bf329..f3030d00bc 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -375,7 +375,10 @@ int AmberParamFile::assign_offdiag(ParameterSet& prm, Oarray const& Offdiag) con
 /** Read parametrers from Amber frcmod file. */
 int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int debugIn) const
 {
- // Read title
+  // Set wildcard character for dihedrals and impropers
+  prm.DP().SetWildcard('X');
+  prm.IP().SetWildcard('X');
+  // Read title
   BufferedLine infile;
   if (infile.OpenFileRead( fname )) {
     mprinterr("Error: Could not open file '%s' as Amber FF.\n", fname.full());
@@ -455,7 +458,9 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int deb
 int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
                                std::string const& nbsetnameIn, int debugIn) const
 {
-
+  // Set wildcard character for dihedrals and impropers
+  prm.DP().SetWildcard('X');
+  prm.IP().SetWildcard('X');
   // For files with > 1 set of NB params
   typedef std::vector<NonbondSet> NbSetArrayType;
   NbSetArrayType NBsets;
diff --git a/src/CharmmParamFile.cpp b/src/CharmmParamFile.cpp
index f89f9fe086..5f635074d5 100644
--- a/src/CharmmParamFile.cpp
+++ b/src/CharmmParamFile.cpp
@@ -82,6 +82,10 @@ int CharmmParamFile::ReadParams(ParameterSet& prm, FileName const& nameIn, int d
   std::string currentResName;
   double currentResQ = 0.0;
 
+  // Set wildcard character for dihedrals and impropers
+  prm.DP().SetWildcard('X');
+  prm.IP().SetWildcard('X');
+
   while (ReadInput(input, infile)) {
     if (input.empty()) continue;
     if (input[0] == '*') {
@@ -220,7 +224,8 @@ int CharmmParamFile::ReadParams(ParameterSet& prm, FileName const& nameIn, int d
             if (args.Nargs() < 7)
               mprintf("Warning: Bad syntax for dihedral parameter on line %i: %s\n", infile.LineNumber(), line);
             else {
-              TypeNameHolder types(4, "X"); // X is wildcard character
+              //TypeNameHolder types(4, "X"); // X is wildcard character
+              TypeNameHolder types(4);
               types.AddName( args.GetStringNext() );
               types.AddName( args.GetStringNext() );
               types.AddName( args.GetStringNext() );
diff --git a/src/Exec_Change.cpp b/src/Exec_Change.cpp
index 254892c36f..ad71c1bab8 100644
--- a/src/Exec_Change.cpp
+++ b/src/Exec_Change.cpp
@@ -377,7 +377,7 @@ int Exec_Change::FindBondTypeIdx(Topology const& topIn, BondArray const& bonds,
     TypeNameHolder thisType(2);
     thisType.AddName( topIn[bnd->A1()].Type() );
     thisType.AddName( topIn[bnd->A2()].Type() );
-    if (thisType == tgtType) {
+    if (thisType.Match_NoWC( tgtType )) {
       bidx = bnd->Idx();
       break;
     }
diff --git a/src/ParameterHolders.h b/src/ParameterHolders.h
index cfbc83f4e1..a01ba6ce41 100644
--- a/src/ParameterHolders.h
+++ b/src/ParameterHolders.h
@@ -20,12 +20,14 @@ template <class T> class ParmHolder {
     void clear()              { bpmap_.clear(); }
     size_t size()       const { return bpmap_.size(); }
     bool empty()        const { return bpmap_.empty(); }
+    /// Set wildcard character
+    void SetWildcard(char wc) { wc_ = NameType(std::string(1, wc)); }
     /// Add (or update if allowed) given parameter to holder.
     ParameterHolders::RetType AddParm(TypeNameHolder const& types, T const& bp, bool allowUpdate) {
       // Check if parm for these types exist
       typename Bmap::iterator it = bpmap_.begin();
       for (; it != bpmap_.end(); ++it)
-        if (it->first == types) break;
+        if (it->first.Match_NoWC( types )) break;
       if (it == bpmap_.end()) {
         // New parm
         //mprintf("DEBUG: New parameter:");
@@ -71,20 +73,32 @@ template <class T> class ParmHolder {
     T FindParam(TypeNameHolder const& types, bool& found) const { // TODO only use GetParam()?
       found = true;
       for (const_iterator it = begin(); it != end(); ++it)
-        if (it->first == types) return it->second;
+        if (it->first.Match_NoWC( types )) return it->second;
+      if (wc_.len() > 0) {
+        for (const_iterator it = begin(); it != end(); ++it)
+          if (it->first.Match_WC( types, wc_)) return it->second;
+      }
       found = false;
       return T();
     }
     /// \return iterator to parameter matching the given types.
     iterator GetParam(TypeNameHolder const& types) {
       for (iterator it = bpmap_.begin(); it != bpmap_.end(); ++it)
-        if (it->first == types) return it;
+        if (it->first.Match_NoWC( types )) return it;
+      if (wc_.len() > 0) {
+        for (iterator it = bpmap_.begin(); it != bpmap_.end(); ++it)
+          if (it->first.Match_WC( types, wc_)) return it;
+      }
       return bpmap_.end();
     }
     /// \return const iterator to parameter matching the given types.
     const_iterator GetParam(TypeNameHolder const& types) const {
       for (const_iterator it = bpmap_.begin(); it != bpmap_.end(); ++it)
-        if (it->first == types) return it;
+        if (it->first.Match_NoWC( types )) return it;
+      if (wc_.len() > 0) {
+        for (const_iterator it = bpmap_.begin(); it != bpmap_.end(); ++it)
+          if (it->first.Match_WC( types, wc_)) return it;
+      }
       return bpmap_.end();
     }
     /// \return size in memory in bytes
@@ -98,6 +112,7 @@ template <class T> class ParmHolder {
     }
   private:
     Bmap bpmap_;
+    NameType wc_; ///< Wildcard character
 };
 
 // -----------------------------------------------------------------------------
@@ -115,6 +130,8 @@ class DihedralParmHolder {
     void clear()              { bpmap_.clear();        }
     size_t size()       const { return bpmap_.size();  }
     bool empty()        const { return bpmap_.empty(); }
+    /// Set wildcard character
+    void SetWildcard(char wc) { wc_ = NameType(std::string(1, wc)); }
     /** Add (or update) a single dihedral parameter for given atom types. */
     ParameterHolders::RetType
     AddParm(TypeNameHolder const& types, DihedralParmType const& dp, bool allowUpdate) {
@@ -122,7 +139,7 @@ class DihedralParmHolder {
       Bmap::iterator it0 = bpmap_.begin();
       for (; it0 != bpmap_.end(); ++it0)
       {
-        if (it0->first == types)
+        if (it0->first.Match_NoWC( types ))
           break;
       }
       if (it0 == bpmap_.end()) {
@@ -167,7 +184,7 @@ class DihedralParmHolder {
       Bmap::iterator it0 = bpmap_.begin();
       for (; it0 != bpmap_.end(); ++it0)
       {
-        if (it0->first == types)
+        if (it0->first.Match_NoWC( types ))
           break;
       }
       if (it0 == bpmap_.end()) {
@@ -204,7 +221,11 @@ class DihedralParmHolder {
     DihedralParmArray FindParam(TypeNameHolder const& types, bool& found) const {
       found = true;
       for (const_iterator it = begin(); it != end(); ++it)
-        if (it->first == types) return it->second;
+        if (it->first.Match_NoWC( types )) return it->second;
+      if (wc_.len() > 0) {
+        for (const_iterator it = begin(); it != end(); ++it)
+          if (it->first.Match_WC( types, wc_)) return it->second;
+      }
       found = false;
       return DihedralParmArray();
     }
@@ -219,5 +240,6 @@ class DihedralParmHolder {
     }
   private:
     Bmap bpmap_;
+    NameType wc_; ///< Wildcard character
 };
 #endif
diff --git a/src/TypeNameHolder.h b/src/TypeNameHolder.h
index be362f7c90..eb8b129e1a 100644
--- a/src/TypeNameHolder.h
+++ b/src/TypeNameHolder.h
@@ -14,8 +14,8 @@ class TypeNameHolder {
     TypeNameHolder(Narray const& namesIn) : types_(namesIn) {}
     /// CONSTRUCTOR - Reserve space for given number of type names
     TypeNameHolder(int size) { types_.clear(); types_.reserve(size); }
-    /// CONSTRUCTOR - Set wildcard name and reserve space for given number of type names.
-    TypeNameHolder(int size, NameType const& wc) : wildcard_(wc) { types_.clear(); types_.reserve(size); }
+/*    /// CONSTRUCTOR - Set wildcard name and reserve space for given number of type names.
+    TypeNameHolder(int size, NameType const& wc) : wildcard_(wc) { types_.clear(); types_.reserve(size); }*/
     /// Add atom type name.
     void AddName(NameType const& n) { types_.push_back( n ); }
     /// \return Iterator to beginning of type name array.
@@ -26,7 +26,50 @@ class TypeNameHolder {
     size_t Size() const { return types_.size(); }
     /// \return Type name at index
     NameType const& operator[](int idx) const { return types_[idx]; }
+    /// \return true if either direction is an exact match, no wildcard.
+    bool Match_NoWC(TypeNameHolder const& rhs) const {
+      if (types_.size() != rhs.types_.size()) return false;
+      // Forwards direction
+      bool match = true;
+      for (unsigned int idx = 0; idx != types_.size(); idx++)
+        if (types_[idx] != rhs.types_[idx]) {
+          match = false;
+          break;
+        }
+      if (match) return true;
+      // Reverse direction
+      match = true;
+      unsigned int idx2 = types_.size() - 1;
+      for (unsigned int idx = 0; idx != types_.size(); idx++, idx2--)
+        if (types_[idx] != rhs.types_[idx2]) {
+          match = false;
+          break;
+        }
+      return match;
+    }
     /// \return true if either direction is a match, taking into account wildcard.
+    bool Match_WC(TypeNameHolder const& rhs, NameType const& wildcard) const {
+      // Sanity check
+      if (types_.size() != rhs.types_.size()) return false;
+      // Forwards direction
+      bool match = true;
+      for (unsigned int idx = 0; idx != types_.size(); idx++)
+        if (types_[idx] != rhs.types_[idx] && types_[idx] != wildcard) {
+          match = false;
+          break;
+        }
+      if (match) return true;
+      // Reverse direction
+      match = true;
+      unsigned int idx2 = types_.size() - 1;
+      for (unsigned int idx = 0; idx != types_.size(); idx++, idx2--)
+        if (types_[idx] != rhs.types_[idx2] && types_[idx] != wildcard) {
+          match = false;
+          break;
+        }
+      return match;
+    }
+/*    /// \return true if either direction is a match, taking into account wildcard.
     bool operator==(TypeNameHolder const& rhs) const {
       // Sanity check
       if (types_.size() != rhs.types_.size()) return false;
@@ -47,7 +90,7 @@ class TypeNameHolder {
           break;
         }
       return match;
-    }
+    }*/
     /// Will sort by type names in ascending order.
     bool operator<(TypeNameHolder const& rhs) const {
       if (types_.size() != rhs.types_.size()) {
@@ -71,6 +114,6 @@ class TypeNameHolder {
     size_t DataSize() const { return (types_.size()*NameType::DataSize()) + NameType::DataSize(); }
   private:
     Narray types_;
-    NameType wildcard_;
+    //NameType wildcard_;
 };
 #endif

From a2ac2ed44c21a01110cd2b65d40b93dd29f504ec Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 20 Dec 2023 15:25:43 -0500
Subject: [PATCH 0189/1492] Dihedral phase should be stored internally in
 radians

---
 src/AmberParamFile.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index f3030d00bc..76cb3c8a74 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -203,7 +203,7 @@ const
   types.AddName( symbols[2] );
   types.AddName( symbols[3] );
   ParameterHolders::RetType ret =
-    prm.DP().AddParm(types, DihedralParmType(PK / (double)IDIVF, PN, PHASE, scee, scnb), true);
+    prm.DP().AddParm(types, DihedralParmType(PK / (double)IDIVF, PN, PHASE*Constants::DEGRAD, scee, scnb), true);
   if (ret == ParameterHolders::UPDATED) {
     mprintf("Warning: Redefining dihedral type %s - %s - %s - %s (PN=%g)\n",
             *(types[0]), *(types[1]), *(types[2]), *(types[3]), PN);
@@ -239,7 +239,7 @@ const
   types.AddName( symbols[2] );
   types.AddName( symbols[3] );
   ParameterHolders::RetType ret =
-    prm.IP().AddParm(types, DihedralParmType(PK, PN, PHASE), true);
+    prm.IP().AddParm(types, DihedralParmType(PK, PN, PHASE*Constants::DEGRAD), true);
   if (ret == ParameterHolders::UPDATED)
     mprintf("Warning: Redefining improper type %s - %s - %s - %s\n",
             *(types[0]), *(types[1]), *(types[2]), *(types[3]));

From 3f2c2f0a561123807a5d1feaf6f4c8ee922d767b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 21 Dec 2023 06:12:30 -0500
Subject: [PATCH 0190/1492] For debug only, set empty dihedral parameters and
 put a leading 'D' when printing regular dihedrals

---
 src/TopInfo.cpp  | 3 ++-
 src/Topology.cpp | 4 +++-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/src/TopInfo.cpp b/src/TopInfo.cpp
index d7e7e6172f..0293b7e8b1 100644
--- a/src/TopInfo.cpp
+++ b/src/TopInfo.cpp
@@ -622,7 +622,8 @@ void TopInfo::PrintDihedrals(DihedralArray const& darray, DihedralParmArray cons
                        mask1.AtomInCharMask(atom4));
     if (printDihedral) {
       // Determine dihedral type: 'E'nd, 'I'mproper, or 'B'oth
-      char type = ' ';
+      //char type = ' ';
+      char type = 'D'; // DEBUG
       if      (dih->Type() == DihedralType::END     ) type = 'E';
       else if (dih->Type() == DihedralType::IMPROPER) type = 'I';
       else if (dih->Type() == DihedralType::BOTH    ) type = 'B';
diff --git a/src/Topology.cpp b/src/Topology.cpp
index 9143404cd4..6e3b484ef1 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2818,7 +2818,9 @@ void Topology::AssignDihedralParm(DihedralParmHolder const& newDihedralParams,
                 TruncResAtomNameNum(dih->A4()).c_str(),
                 *types[0], *types[1], *types[2], *types[3]);
         DihedralType mydih = *dih;
-        mydih.SetIdx( -1 );
+        int idx = addTorsionParm( dihedralparm_, DihedralParmType() ); // DEBUG
+        mydih.SetIdx( idx ); // DEBUG
+        //mydih.SetIdx( -1 );
         dihedralsIn.push_back( mydih );
       } else {
         // Actually add parameters for this dihedral.

From 67ca1b2280df16a2afdf8a2347ebbf566701267e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 21 Dec 2023 09:14:52 -0500
Subject: [PATCH 0191/1492] Output phase in degrees

---
 src/ParameterSet.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/ParameterSet.cpp b/src/ParameterSet.cpp
index 70438dcd07..ad071ec51c 100644
--- a/src/ParameterSet.cpp
+++ b/src/ParameterSet.cpp
@@ -93,13 +93,13 @@ void ParameterSet::Print(CpptrajFile& Out) const {
     for (DihedralParmHolder::const_iterator it0 = dihParm_.begin(); it0 != dihParm_.end(); ++it0)
       for (DihedralParmArray::const_iterator it1 = it0->second.begin();
                                              it1 != it0->second.end(); ++it1)
-        Out.Printf("\t%6s %6s %6s %6s : %12.4f %12.4f %12.4f\n", *(it0->first[0]), *(it0->first[1]), *(it0->first[2]), *(it0->first[3]), it1->Pk(), it1->Pn(), it1->Phase());
+        Out.Printf("\t%6s %6s %6s %6s : %12.4f %12.4f %12.4f\n", *(it0->first[0]), *(it0->first[1]), *(it0->first[2]), *(it0->first[3]), it1->Pk(), it1->Pn(), it1->Phase()*Constants::RADDEG);
   }
   if (!impParm_.empty()) {
     Out.Printf("Improper parameters:\n");
     Out.Printf("\t%6s %6s %6s %6s %12s %12s %12s\n", "Type1", "Type2", "Type3", "Type4", "Pk", "Pn", "Phase");
     for (ParmHolder<DihedralParmType>::const_iterator bp = impParm_.begin(); bp != impParm_.end(); ++bp)
-      Out.Printf("\t%6s %6s %6s %6s : %12.4f %12.4f %12.4f\n", *(bp->first[0]), *(bp->first[1]), *(bp->first[2]), *(bp->first[3]), bp->second.Pk(), bp->second.Pn(), bp->second.Phase());
+      Out.Printf("\t%6s %6s %6s %6s : %12.4f %12.4f %12.4f\n", *(bp->first[0]), *(bp->first[1]), *(bp->first[2]), *(bp->first[3]), bp->second.Pk(), bp->second.Pn(), bp->second.Phase()*Constants::RADDEG);
   }
   if (!hydrophilicAtomTypes_.empty()) {
     Out.Printf("Hydrophilic atom types:");

From ac4ac50889f443c59b1e670869f663c6c5987e6f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 21 Dec 2023 09:17:03 -0500
Subject: [PATCH 0192/1492] For debug, if not printing indices print D for
 regular dihedrals

---
 src/TopInfo.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/TopInfo.cpp b/src/TopInfo.cpp
index 0293b7e8b1..b0738f65ce 100644
--- a/src/TopInfo.cpp
+++ b/src/TopInfo.cpp
@@ -622,8 +622,8 @@ void TopInfo::PrintDihedrals(DihedralArray const& darray, DihedralParmArray cons
                        mask1.AtomInCharMask(atom4));
     if (printDihedral) {
       // Determine dihedral type: 'E'nd, 'I'mproper, or 'B'oth
-      //char type = ' ';
-      char type = 'D'; // DEBUG
+      char type = ' ';
+      if (!printIndices_) type = 'D'; // DEBUG
       if      (dih->Type() == DihedralType::END     ) type = 'E';
       else if (dih->Type() == DihedralType::IMPROPER) type = 'I';
       else if (dih->Type() == DihedralType::BOTH    ) type = 'B';

From 72f2a0032affd678537254d783965090b5a52b4c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 21 Dec 2023 09:36:13 -0500
Subject: [PATCH 0193/1492] Properly handle negative PN

---
 src/AmberParamFile.cpp | 35 ++++++++++++++++++++++++-----------
 1 file changed, 24 insertions(+), 11 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 76cb3c8a74..b09d0f35a8 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -156,21 +156,27 @@ const
   return 0;
 }
 
-/** Read input for dihedral. */
+/** Read input for dihedral.
+  * IPT , JPT , KPT , LPT , IDIVF , PK , PHASE , PN
+  * FORMAT(A2,1X,A2,1X,A2,1X,A2,I4,3F15.2)
+  * If IPT .eq. 'X ' .and. LPT .eq. 'X ' then any dihedrals in the
+  * system involving the atoms "JPT" and and "KPT" are assigned 
+  * the same parameters.  This is called the general dihedral type
+  * and is of the form "X "-"JPT"-"KPT"-"X ".
+  * IDIVF is the factor by which the torsional barrier is divided.
+  * Consult Weiner, et al., JACS 106:765 (1984) p. 769 for
+  * details. Basically, the actual torsional potential is
+  *   (PK/IDIVF) * (1 + cos(PN*phi - PHASE))
+  * If PN .lt. 0.0 then the torsional potential is assumed to have more
+  * than one term, and the values of the rest of the terms are read from
+  * the next cards until a positive PN is encountered.  The negative value
+  * of pn is used only for identifying the existence of the next term and 
+  * only the absolute value of PN is kept.
+  */
 int AmberParamFile::read_dihedral(ParameterSet& prm, const char* ptr)
 const
 {
   // Dihedral parameters
-  // IPT , JPT , KPT , LPT , IDIVF , PK , PHASE , PN
-  // FORMAT(A2,1X,A2,1X,A2,1X,A2,I4,3F15.2)
-  // If IPT .eq. 'X ' .and. LPT .eq. 'X ' then any dihedrals in the
-  // system involving the atoms "JPT" and and "KPT" are assigned 
-  // the same parameters.  This is called the general dihedral type
-  // and is of the form "X "-"JPT"-"KPT"-"X ".
-  // IDIVF is the factor by which the torsional barrier is divided.
-  // Consult Weiner, et al., JACS 106:765 (1984) p. 769 for
-  // details. Basically, the actual torsional potential is
-  //   (PK/IDIVF) * (1 + cos(PN*phi - PHASE))
   if (debug_ > 1) mprintf("DEBUG: Dihedral: %s\n", ptr);
   std::vector<std::string> symbols(4);
   int pos = read_symbols(ptr, symbols, 4);
@@ -183,11 +189,13 @@ const
   double PK, PHASE, PN;
   char sSCEE[128];
   char sSCNB[128];
+  // TODO note when PN is negative and expect more terms?
   int nscan = sscanf(ptr+pos, "%i %lf %lf %lf %s %s", &IDIVF, &PK, &PHASE, &PN, sSCEE, sSCNB);
   if (nscan < 4) {
     mprinterr("Error: Expected IDIVF, PK, PHASE, PN, got only %i elements\n", nscan);
     return 1;
   }
+  if (PN < 0.0) PN = -PN;
   double scee = 1.2; // AMBER DEFAULT
   double scnb = 2.0; // AMBER DEFAULT
   if (nscan == 6) {
@@ -233,6 +241,11 @@ const
     mprinterr("Error: Expected PK, PHASE, PN, got only %i elements\n", nscan);
     return 1;
   }
+  if (PN < 0.0) {
+    mprintf("Warning: Improper for %s-%s-%s-%s has negative phase (%g)\n",
+            symbols[0].c_str(), symbols[1].c_str(), symbols[2].c_str(), symbols[3].c_str(), PN);
+    PN = -PN;
+  }
   TypeNameHolder types(4);
   types.AddName( symbols[0] );
   types.AddName( symbols[1] );

From 21c54d066cb29d4af92ff220864aaf7a4e07eed3 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 21 Dec 2023 09:52:35 -0500
Subject: [PATCH 0194/1492] Recognize residuesPdbSequenceNumber section in OFF
 files

---
 src/DataIO_AmberLib.cpp | 2 +-
 src/DataIO_AmberLib.h   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/DataIO_AmberLib.cpp b/src/DataIO_AmberLib.cpp
index 8088f022ea..3743a0800e 100644
--- a/src/DataIO_AmberLib.cpp
+++ b/src/DataIO_AmberLib.cpp
@@ -89,7 +89,7 @@ int DataIO_AmberLib::ReadData(FileName const& fname, DataSetList& dsl, std::stri
 const char* DataIO_AmberLib::sectionStr_[] = {
   "atoms", "atomspertinfo", "boundbox", "childsequence", "connect",
   "connectivity", "hierarchy", "name", "positions", "residueconnect",
-  "residues", "solventcap", "velocities", 0 };
+  "residues", "residuesPdbSequenceNumber", "solventcap", "velocities", 0 };
 
 /** \return Section type from entry line. */
 DataIO_AmberLib::SectionType DataIO_AmberLib::id_section(std::string const& line,
diff --git a/src/DataIO_AmberLib.h b/src/DataIO_AmberLib.h
index 9f8952fa37..6ea4d12b91 100644
--- a/src/DataIO_AmberLib.h
+++ b/src/DataIO_AmberLib.h
@@ -19,7 +19,7 @@ class DataIO_AmberLib : public DataIO {
     // Keep in sync with sectionStr_
     enum SectionType { ATOMTABLE = 0, PERTINFO, BOUNDBOX, CHILDSEQUENCE, CONNECT,
                        CONNECTIVITY, HIERARCHY, UNITNAME, POSITIONS, RESCONNECT,
-                       RESIDUES, SOLVENTCAP, VELOCITIES, UNKNOWN_SECTION };
+                       RESIDUES, RESPDBSEQUENCE, SOLVENTCAP, VELOCITIES, UNKNOWN_SECTION };
     /// Strings corresponding to section type
     static const char* sectionStr_[];
 

From 63dd4f86e633eacff890366192cdf6598da77f17 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 21 Dec 2023 11:46:30 -0500
Subject: [PATCH 0195/1492] Try to follow the apparent leap convention of
 having dihedral first atom always < last atom

---
 src/Structure/GenerateAngles.cpp | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/src/Structure/GenerateAngles.cpp b/src/Structure/GenerateAngles.cpp
index 61fabb25bf..f490071ec8 100644
--- a/src/Structure/GenerateAngles.cpp
+++ b/src/Structure/GenerateAngles.cpp
@@ -30,7 +30,11 @@ static inline void enumerateDihedrals(int at1, int at2, Topology& topIn) {
         for (Atom::bond_iterator bat2 = A2.bondbegin(); bat2 != A2.bondend(); ++bat2)
         {
           if (*bat2 != at1) {
-            topIn.AddDihedral(*bat1, at1, at2, *bat2);
+            // LEaP convention appears to be first atom less than last atom
+            if (*bat1 < *bat2)
+              topIn.AddDihedral(*bat1, at1, at2, *bat2);
+            else
+              topIn.AddDihedral(*bat2, at2, at1, *bat1);
             mprintf("%s - %s - %s - %s\n",
                     topIn.AtomMaskName(*bat1).c_str(),
                     topIn.AtomMaskName(at1).c_str(),

From 4dcaa2a0fd4e15ae6bb74c196cba7c915f9a1b6c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 21 Dec 2023 11:46:56 -0500
Subject: [PATCH 0196/1492] Try to follow leap convention of dihedral parms
 sorted by multiplicity in ascending order

---
 src/ParameterHolders.h | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/src/ParameterHolders.h b/src/ParameterHolders.h
index a01ba6ce41..b4da67ecff 100644
--- a/src/ParameterHolders.h
+++ b/src/ParameterHolders.h
@@ -159,7 +159,20 @@ class DihedralParmHolder {
           // Brand new multiplicity for this dihedral.
           //mprintf("DEBUG: Dihedral new mult: %s %s %s %s pk=%12.4f pn=%12.4f pp=%12.4f\n",
           //        *types[0], *types[1], *types[2], *types[3], dp.Pk(), dp.Pn(), dp.Phase());
-          it0->second.push_back( dp );
+          //it0->second.push_back( dp );
+          // Try to keep multiplicities in order.
+          DihedralParmArray sorted;
+          bool isInserted = false;
+          for (DihedralParmArray::const_iterator jt = it0->second.begin(); jt != it0->second.end(); ++jt) {
+            if (!isInserted) {
+              if (dp.Pn() < jt->Pn()) {
+                sorted.push_back( dp );
+                isInserted = true;
+              }
+            }
+            sorted.push_back( *jt );
+          }
+          it0->second = sorted;
         } else {
           if (dp < *it1 || *it1 < dp) {
             //mprintf("DEBUG: Attempt dihedral update mult (allow=%i): %s %s %s %s pk=%6.2f pn=%3.1f pp=%6.3f (orig pk=%6.2f pn=%3.1f pp=%6.3f )\n",

From 851076e643ba2103b77711741d43a0da2b580ea4 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 21 Dec 2023 11:47:36 -0500
Subject: [PATCH 0197/1492] Add an assign parameters function

---
 src/Exec_Build.cpp |  2 +-
 src/Topology.cpp   | 27 +++++++++++++++++++++++++++
 src/Topology.h     |  2 ++
 3 files changed, 30 insertions(+), 1 deletion(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 0992ed984a..d1b4214e67 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -423,7 +423,7 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
 
   // Update parameters
   Exec::RetType ret = CpptrajState::OK;
-  if ( topOut.UpdateParams( *mainParmSet  ) ) {
+  if ( topOut.AssignParams( *mainParmSet  ) ) {
     mprinterr("Error: Could not update parameters for '%s'.\n", topOut.c_str());
     ret = CpptrajState::ERR;
   }
diff --git a/src/Topology.cpp b/src/Topology.cpp
index 6e3b484ef1..9652e99b1e 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -3010,6 +3010,33 @@ void Topology::AssignNonbondParams(ParmHolder<AtomType> const& newTypes,
   }
 }
 
+/** Replace existing parameters with the given parameter set. */
+int Topology::AssignParams(ParameterSet const& set0) {
+  // Bond parameters
+  mprintf("\tRegenerating bond parameters.\n");
+  AssignBondParams( set0.BP() );
+  // Angle parameters
+  mprintf("\tRegenerating angle parameters.\n");
+  AssignAngleParams( set0.AP() );
+  // Dihedral parameters
+  mprintf("\tRegenerating dihedral parameters.\n");
+  AssignDihedralParams( set0.DP(), set0.IP() );
+  // Urey-Bradley
+  mprintf("\tRegenerating UB parameters.\n");
+  AssignUBParams( set0.UB() );
+  // Improper parameters
+  mprintf("\tRegenerating improper parameters.\n");
+  AssignImproperParams( set0.IP() );
+  // Atom types
+  mprintf("\tRegenerating atom type parameters.\n");
+  AssignAtomTypeParm( set0.AT() );
+  // LJ 6-12
+  mprintf("\tRegenerating nonbond parameters.\n");
+  AssignNonbondParams( set0.AT(), set0.NB(), set0.HB() );
+  // TODO LJ14
+  return 0;
+}
+
 /** Update/add to parameters in this topology with those from given set.
   * NOTE: This routine is separate from updateParams() to allow that
   *       routine to be used by AppendTop() for testing the parameter
diff --git a/src/Topology.h b/src/Topology.h
index 8444bb58c1..354fe9509e 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -198,6 +198,8 @@ class Topology {
     int SetSolvent(std::string const&);
     /// \return ParameterSet for this Topology
     ParameterSet GetParameters() const;
+    /// Replace existing parameters with those in given set.
+    int AssignParams(ParameterSet const&);
     /// Update parameters in this Topology with those in given set.
     int UpdateParams(ParameterSet const&);
     // ----- Print topology info -----------------

From 785060c98e7eb681fa27e10958c1ebd5def43df1 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 21 Dec 2023 12:14:05 -0500
Subject: [PATCH 0198/1492] Use FEQ to compare floating points. Handle case
 where existing DihedralParmArray is empty or the incoming multiplicity is
 already > than the last (i.e. already in order).

---
 src/ParameterHolders.h | 29 +++++++++++++++++------------
 1 file changed, 17 insertions(+), 12 deletions(-)

diff --git a/src/ParameterHolders.h b/src/ParameterHolders.h
index b4da67ecff..cb1d77ae9b 100644
--- a/src/ParameterHolders.h
+++ b/src/ParameterHolders.h
@@ -152,27 +152,32 @@ class DihedralParmHolder {
         DihedralParmArray::iterator it1 = it0->second.begin();
         for (; it1 != it0->second.end(); ++it1)
         {
-          if (it1->Pn() == dp.Pn())
+          if (FEQ(it1->Pn(), dp.Pn()))
             break;
         }
         if (it1 == it0->second.end()) {
           // Brand new multiplicity for this dihedral.
           //mprintf("DEBUG: Dihedral new mult: %s %s %s %s pk=%12.4f pn=%12.4f pp=%12.4f\n",
           //        *types[0], *types[1], *types[2], *types[3], dp.Pk(), dp.Pn(), dp.Phase());
-          //it0->second.push_back( dp );
-          // Try to keep multiplicities in order.
-          DihedralParmArray sorted;
-          bool isInserted = false;
-          for (DihedralParmArray::const_iterator jt = it0->second.begin(); jt != it0->second.end(); ++jt) {
-            if (!isInserted) {
-              if (dp.Pn() < jt->Pn()) {
-                sorted.push_back( dp );
-                isInserted = true;
+          if (it0->second.empty())
+            it0->second.push_back( dp );
+          else if (dp.Pn() > it0->second.back().Pn())
+            it0->second.push_back( dp );
+          else {
+            // Try to keep multiplicities in order.
+            DihedralParmArray sorted;
+            bool isInserted = false;
+            for (DihedralParmArray::const_iterator jt = it0->second.begin(); jt != it0->second.end(); ++jt) {
+              if (!isInserted) {
+                if (dp.Pn() < jt->Pn()) {
+                  sorted.push_back( dp );
+                  isInserted = true;
+                }
               }
+              sorted.push_back( *jt );
             }
-            sorted.push_back( *jt );
+            it0->second = sorted;
           }
-          it0->second = sorted;
         } else {
           if (dp < *it1 || *it1 < dp) {
             //mprintf("DEBUG: Attempt dihedral update mult (allow=%i): %s %s %s %s pk=%6.2f pn=%3.1f pp=%6.3f (orig pk=%6.2f pn=%3.1f pp=%6.3f )\n",

From 61cb8f3b4440e8dd044aa153f50c29c84ec7c023 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 21 Dec 2023 13:03:11 -0500
Subject: [PATCH 0199/1492] Function to guess atom hybridization

---
 src/GuessAtomHybridization.cpp | 58 ++++++++++++++++++++++++++++++++++
 src/GuessAtomHybridization.h   | 10 ++++++
 2 files changed, 68 insertions(+)
 create mode 100644 src/GuessAtomHybridization.cpp
 create mode 100644 src/GuessAtomHybridization.h

diff --git a/src/GuessAtomHybridization.cpp b/src/GuessAtomHybridization.cpp
new file mode 100644
index 0000000000..289cffd98f
--- /dev/null
+++ b/src/GuessAtomHybridization.cpp
@@ -0,0 +1,58 @@
+#include "GuessAtomHybridization.h"
+#include "Atom.h"
+#include "Topology.h"
+
+AtomType::HybridizationType Cpptraj::GuessAtomHybridization(Atom const& AJ, Topology const& topIn)
+{
+  AtomType::HybridizationType hybrid = AtomType::UNKNOWN_HYBRIDIZATION;
+  // Handle specific elements
+  switch (AJ.Element()) {
+    case Atom::CARBON :
+      switch (AJ.Nbonds()) {
+        case 2 : hybrid = AtomType::SP; break;
+        case 3 : hybrid = AtomType::SP2; break;
+        case 4 : hybrid = AtomType::SP3; break;
+      }
+      break;
+    case Atom::NITROGEN :
+      switch (AJ.Nbonds()) {
+        case 2 : hybrid = AtomType::SP2; break;
+        case 3 :
+          // Check for potential SP2. If only 1 of the bonded atoms is
+          // hydrogen, assume SP2. TODO actually check for aromaticity.
+          int n_hydrogens = 0;
+          for (Atom::bond_iterator bat = AJ.bondbegin(); bat != AJ.bondend(); ++bat)
+            if (topIn[*bat].Element() == Atom::HYDROGEN)
+              n_hydrogens++;
+          if (n_hydrogens == 1)
+            hybrid = AtomType::SP2;
+          else
+            hybrid = AtomType::SP3;
+          break;
+      }
+      break;
+    case Atom::OXYGEN :
+      switch (AJ.Nbonds()) {
+        case 2 : hybrid = AtomType::SP3; break;
+      }
+      break;
+    case Atom::SULFUR :
+      switch (AJ.Nbonds()) {
+        case 2 : hybrid = AtomType::SP3; break;
+      }
+      break;
+    default: hybrid = AtomType::UNKNOWN_HYBRIDIZATION; break;
+  }
+/*
+if (hybrid == AtomType::UNKNOWN_HYBRIDIZATION) {
+    // Assign a theta based on number of bonds 
+    switch (AJ.Nbonds()) {
+      case 4 : hybrid = AtomType::SP3; break;
+      case 3 : hybrid = AtomType::SP2; break;
+      case 2 : hybrid = AtomType::SP; break;
+      default : mprinterr("Internal Error: GuessAtomHybridization(): Unhandled # bonds for %s (%i)\n", topIn.AtomMaskName(aj).c_str(), AJ.Nbonds()); return 1;
+    }
+*/
+
+  return hybrid;
+}
diff --git a/src/GuessAtomHybridization.h b/src/GuessAtomHybridization.h
new file mode 100644
index 0000000000..dc7b84fe76
--- /dev/null
+++ b/src/GuessAtomHybridization.h
@@ -0,0 +1,10 @@
+#ifndef INC_GUESSATOMHYBRIDIZATION_H
+#define INC_GUESSATOMHYBRIDIZATION_H
+#include "AtomType.h" // for HybridizationType
+class Atom;
+class Topology;
+namespace Cpptraj {
+/// Guess atom hybridization type based on element/bonding
+AtomType::HybridizationType GuessAtomHybridization(Atom const&, Topology const&);
+}
+#endif

From c2f0627b6c0af6a832a252c5e5d17d1e349d097b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 21 Dec 2023 13:03:51 -0500
Subject: [PATCH 0200/1492] Update dependencies

---
 src/cpptrajdepend | 1 +
 src/cpptrajfiles  | 1 +
 2 files changed, 2 insertions(+)

diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 3f959374c5..2aef471f15 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -368,6 +368,7 @@ Gpu.o : Gpu.cpp Gpu.h
 GridAction.o : GridAction.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridAction.h GridBin.h GridMover.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 GridBin.o : GridBin.cpp Box.h CpptrajStdio.h GridBin.h Matrix_3x3.h Parallel.h Vec3.h
 GridMover.o : GridMover.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_3D.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h GridMover.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+GuessAtomHybridization.o : GuessAtomHybridization.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h FileName.h Frame.h GuessAtomHybridization.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 HistBin.o : HistBin.cpp Constants.h CpptrajStdio.h Dimension.h HistBin.h
 Hungarian.o : Hungarian.cpp ArrayIterator.h Constants.h CpptrajStdio.h Hungarian.h Matrix.h
 ImageRoutines.o : ImageRoutines.cpp Atom.h AtomMask.h Box.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h Frame.h ImageOption.h ImageRoutines.h ImageTypes.h Image_List.h Image_List_Mask.h Image_List_Pair.h Image_List_Pair_CoM.h Image_List_Pair_First.h Image_List_Pair_Geom.h Image_List_Unit.h Image_List_Unit_CoM.h Image_List_Unit_First.h Image_List_Unit_Geom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Unit.h Vec3.h
diff --git a/src/cpptrajfiles b/src/cpptrajfiles
index 7bcfb827aa..d0929dd54c 100644
--- a/src/cpptrajfiles
+++ b/src/cpptrajfiles
@@ -337,6 +337,7 @@ COMMON_SOURCES= \
         GridAction.cpp \
         GridMover.cpp \
         GridBin.cpp \
+        GuessAtomHybridization.cpp \
         HistBin.cpp \
         Hungarian.cpp \
         ImageRoutines.cpp \

From 14f15693fdfa6ab0ecb91e05c140a3d256e013bd Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 21 Dec 2023 13:04:15 -0500
Subject: [PATCH 0201/1492] Add note

---
 src/Structure/Model.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Structure/Model.cpp b/src/Structure/Model.cpp
index affbf21f06..d818e129ec 100644
--- a/src/Structure/Model.cpp
+++ b/src/Structure/Model.cpp
@@ -7,7 +7,7 @@
 
 /** Attempt to assign a reasonable value for theta internal coordinate for
   * atom i given that atoms j and k have known positions.
-  */
+  */ // FIXME use GuessAtomHybridization
 int Cpptraj::Structure::Model::AssignTheta(double& theta, int ai, int aj, int ak, Topology const& topIn, Frame const& frameIn, std::vector<bool> const& atomPositionKnown, int debug)
 {
   // Figure out hybridization and chirality of atom j.

From 839f4bccf6cadfce1c28f1dfd8cb0960fcef6c7e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 21 Dec 2023 13:13:51 -0500
Subject: [PATCH 0202/1492] Start generating impropers

---
 src/Exec_Build.cpp               |  6 ++++++
 src/Structure/GenerateAngles.cpp | 16 ++++++++++++++++
 src/Structure/GenerateAngles.h   |  2 ++
 src/cpptrajdepend                |  2 +-
 4 files changed, 25 insertions(+), 1 deletion(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index d1b4214e67..55d337bdde 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -375,6 +375,12 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
     return CpptrajState::ERR;
   }
 
+  // Generate impropers
+  if (Cpptraj::Structure::GenerateImpropers(topOut)) {
+    mprinterr("Error: Could not generate impropers for '%s'\n", topOut.c_str());
+    return CpptrajState::ERR;
+  }
+
   // Get parameter sets.
   typedef std::vector<DataSet_Parameters*> Parray;
   Parray ParamSets;
diff --git a/src/Structure/GenerateAngles.cpp b/src/Structure/GenerateAngles.cpp
index f490071ec8..8d2e05e07e 100644
--- a/src/Structure/GenerateAngles.cpp
+++ b/src/Structure/GenerateAngles.cpp
@@ -1,5 +1,6 @@
 #include "GenerateAngles.h"
 #include "../CpptrajStdio.h"
+#include "../GuessAtomHybridization.h"
 #include "../ParameterTypes.h"
 #include "../Topology.h"
 #include <algorithm> // std::sort
@@ -99,3 +100,18 @@ int Cpptraj::Structure::GenerateAngles(Topology& topIn) {
   }
   return 0;
 }
+
+/** Try to determine impropers for topology. */
+int Cpptraj::Structure::GenerateImpropers(Topology& topIn) {
+  for (int iat = 0; iat != topIn.Natom(); iat++) {
+    Atom const& AJ = topIn[iat];
+    if (AJ.Nbonds() == 3) { // TODO only 3 atoms OK?
+      // FIXME pass in atom types
+      AtomType::HybridizationType hybrid = Cpptraj::GuessAtomHybridization( AJ, topIn );
+      if (hybrid == AtomType::SP2) {
+        mprintf("DEBUG: Potential improper center: %s\n", topIn.AtomMaskName(iat).c_str());
+      }
+    }
+  }
+  return 0;
+}
diff --git a/src/Structure/GenerateAngles.h b/src/Structure/GenerateAngles.h
index b3e1c141c2..79abe86b4e 100644
--- a/src/Structure/GenerateAngles.h
+++ b/src/Structure/GenerateAngles.h
@@ -5,6 +5,8 @@ namespace Cpptraj {
 namespace Structure {
 /// Generate angles from bonds in a Topology
 int GenerateAngles(Topology&);
+/// Generate impropers
+int GenerateImpropers(Topology&);
 }
 }
 #endif
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 2aef471f15..8a2ed830b0 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -446,7 +446,7 @@ Structure/Chirality.o : Structure/Chirality.cpp Atom.h AtomMask.h AtomType.h Box
 Structure/Disulfide.o : Structure/Disulfide.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Disulfide.h Structure/ResStatArray.h Structure/StructureRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/FunctionalGroup.o : Structure/FunctionalGroup.cpp Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/FxnGroupBuilder.o : Structure/FxnGroupBuilder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h Structure/FxnGroupBuilder.h Structure/StructureRoutines.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Structure/GenerateAngles.o : Structure/GenerateAngles.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/GenerateAngles.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Structure/GenerateAngles.o : Structure/GenerateAngles.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h GuessAtomHybridization.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/GenerateAngles.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/HisProt.o : Structure/HisProt.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/HisProt.h Structure/StructureRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/InternalCoords.o : Structure/InternalCoords.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/InternalCoords.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/Model.o : Structure/Model.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/Model.h Structure/StructureEnum.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h

From a6a83e4038a27decf6c764a849b85257310d2ccd Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 21 Dec 2023 13:25:40 -0500
Subject: [PATCH 0203/1492] Use atom type info

---
 src/Exec_Build.cpp               | 12 ++++++------
 src/Structure/GenerateAngles.cpp | 11 ++++++++---
 src/Structure/GenerateAngles.h   |  4 +++-
 3 files changed, 17 insertions(+), 10 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 55d337bdde..4fee21d2fb 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -375,12 +375,6 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
     return CpptrajState::ERR;
   }
 
-  // Generate impropers
-  if (Cpptraj::Structure::GenerateImpropers(topOut)) {
-    mprinterr("Error: Could not generate impropers for '%s'\n", topOut.c_str());
-    return CpptrajState::ERR;
-  }
-
   // Get parameter sets.
   typedef std::vector<DataSet_Parameters*> Parray;
   Parray ParamSets;
@@ -427,6 +421,12 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
       mainParmSet->UpdateParamSet( *(*it), UC, State.Debug(), State.Debug() ); // FIXME verbose
   }
 
+  // Generate impropers
+  if (Cpptraj::Structure::GenerateImpropers(topOut, mainParmSet->AT())) {
+    mprinterr("Error: Could not generate impropers for '%s'\n", topOut.c_str());
+    return CpptrajState::ERR;
+  }
+
   // Update parameters
   Exec::RetType ret = CpptrajState::OK;
   if ( topOut.AssignParams( *mainParmSet  ) ) {
diff --git a/src/Structure/GenerateAngles.cpp b/src/Structure/GenerateAngles.cpp
index 8d2e05e07e..36c8584008 100644
--- a/src/Structure/GenerateAngles.cpp
+++ b/src/Structure/GenerateAngles.cpp
@@ -102,12 +102,17 @@ int Cpptraj::Structure::GenerateAngles(Topology& topIn) {
 }
 
 /** Try to determine impropers for topology. */
-int Cpptraj::Structure::GenerateImpropers(Topology& topIn) {
+int Cpptraj::Structure::GenerateImpropers(Topology& topIn, ParmHolder<AtomType> const& AT) {
   for (int iat = 0; iat != topIn.Natom(); iat++) {
     Atom const& AJ = topIn[iat];
     if (AJ.Nbonds() == 3) { // TODO only 3 atoms OK?
-      // FIXME pass in atom types
-      AtomType::HybridizationType hybrid = Cpptraj::GuessAtomHybridization( AJ, topIn );
+      AtomType::HybridizationType hybrid = AtomType::UNKNOWN_HYBRIDIZATION; 
+      bool found;
+      AtomType atype = AT.FindParam(TypeNameHolder(AJ.Type()), found);
+      if (found)
+        hybrid = atype.Hybridization();
+      if (hybrid == AtomType::UNKNOWN_HYBRIDIZATION)
+        hybrid = Cpptraj::GuessAtomHybridization( AJ, topIn );
       if (hybrid == AtomType::SP2) {
         mprintf("DEBUG: Potential improper center: %s\n", topIn.AtomMaskName(iat).c_str());
       }
diff --git a/src/Structure/GenerateAngles.h b/src/Structure/GenerateAngles.h
index 79abe86b4e..09bd38785b 100644
--- a/src/Structure/GenerateAngles.h
+++ b/src/Structure/GenerateAngles.h
@@ -1,12 +1,14 @@
 #ifndef INC_STRUCTURE_GENERATEANGLES_H
 #define INC_STRUCTURE_GENERATEANGLES_H
 class Topology;
+class AtomType;
+template <typename Type> class ParmHolder;
 namespace Cpptraj {
 namespace Structure {
 /// Generate angles from bonds in a Topology
 int GenerateAngles(Topology&);
 /// Generate impropers
-int GenerateImpropers(Topology&);
+int GenerateImpropers(Topology&, ParmHolder<AtomType> const&);
 }
 }
 #endif

From 6221799a3e92efd6bff667eeae4a085164e3f02c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 21 Dec 2023 13:30:14 -0500
Subject: [PATCH 0204/1492] Use GuessAtomHybridization in Model

---
 src/Structure/Model.cpp | 23 +++++++++++++----------
 src/cpptrajdepend       |  2 +-
 2 files changed, 14 insertions(+), 11 deletions(-)

diff --git a/src/Structure/Model.cpp b/src/Structure/Model.cpp
index d818e129ec..cdd914223d 100644
--- a/src/Structure/Model.cpp
+++ b/src/Structure/Model.cpp
@@ -1,6 +1,7 @@
 #include "Model.h"
 #include "BuildAtom.h"
 #include "../CpptrajStdio.h"
+#include "../GuessAtomHybridization.h"
 #include "../Topology.h"
 #include "../TorsionRoutines.h"
 #include "../Constants.h"
@@ -14,7 +15,7 @@ int Cpptraj::Structure::Model::AssignTheta(double& theta, int ai, int aj, int ak
   if (debug > 0)
     mprintf("DEBUG: AssignTheta for atom j : %s\n", topIn.AtomMaskName(aj).c_str());
 
-  enum HybridizationType { SP = 0, SP2, SP3, UNKNOWN_HYBRIDIZATION };
+  //enum HybridizationType { SP = 0, SP2, SP3, UNKNOWN_HYBRIDIZATION };
 
   Atom const& AJ = topIn[aj];
   if (debug > 0) {
@@ -27,7 +28,9 @@ int Cpptraj::Structure::Model::AssignTheta(double& theta, int ai, int aj, int ak
     mprinterr("Internal Error: AssignTheta() called for atom J %s with fewer than 2 bonds.\n", topIn.AtomMaskName(aj).c_str());
     return 1;
   }
-
+  // TODO pass in atom type info?
+  AtomType::HybridizationType hybrid = GuessAtomHybridization(AJ, topIn);
+/*
   HybridizationType hybrid = UNKNOWN_HYBRIDIZATION;
   // Handle specific elements
   switch (AJ.Element()) {
@@ -66,7 +69,7 @@ int Cpptraj::Structure::Model::AssignTheta(double& theta, int ai, int aj, int ak
       }
       break;
     default: hybrid = UNKNOWN_HYBRIDIZATION; break;
-  }
+  }*/
   // Fill in what values we can for known atoms
 /*  std::vector<double> knownTheta( AJ.Nbonds() );
   int knownIdx = -1;
@@ -82,20 +85,20 @@ int Cpptraj::Structure::Model::AssignTheta(double& theta, int ai, int aj, int ak
   }
   if (knownIdx == -1) {*/
     //mprintf("DEBUG:\t\tNo known theta.\n");
-  if (hybrid == UNKNOWN_HYBRIDIZATION) {
+  if (hybrid == AtomType::UNKNOWN_HYBRIDIZATION) {
     // Assign a theta based on number of bonds 
     switch (AJ.Nbonds()) {
-      case 4 : hybrid = SP3; break;
-      case 3 : hybrid = SP2; break;
-      case 2 : hybrid = SP; break;
+      case 4 : hybrid = AtomType::SP3; break;
+      case 3 : hybrid = AtomType::SP2; break;
+      case 2 : hybrid = AtomType::SP; break;
       default : mprinterr("Internal Error: AssignTheta(): Unhandled # bonds for %s (%i)\n", topIn.AtomMaskName(aj).c_str(), AJ.Nbonds()); return 1;
     }
   }
   // Assign a theta based on hybridization
   switch (hybrid) {
-    case SP3 : theta = 109.5 * Constants::DEGRAD; break;
-    case SP2 : theta = 120.0 * Constants::DEGRAD; break;
-    case SP  : theta = 180.0 * Constants::DEGRAD; break;
+    case AtomType::SP3 : theta = 109.5 * Constants::DEGRAD; break;
+    case AtomType::SP2 : theta = 120.0 * Constants::DEGRAD; break;
+    case AtomType::SP  : theta = 180.0 * Constants::DEGRAD; break;
     default : mprinterr("Internal Error: AssignTheta(): Unhandled hybridization for %s (%i)\n", topIn.AtomMaskName(aj).c_str(), AJ.Nbonds()); return 1;
   }/*
   } else {
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 8a2ed830b0..1515262f73 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -449,7 +449,7 @@ Structure/FxnGroupBuilder.o : Structure/FxnGroupBuilder.cpp Atom.h AtomMask.h At
 Structure/GenerateAngles.o : Structure/GenerateAngles.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h GuessAtomHybridization.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/GenerateAngles.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/HisProt.o : Structure/HisProt.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/HisProt.h Structure/StructureRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/InternalCoords.o : Structure/InternalCoords.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/InternalCoords.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Structure/Model.o : Structure/Model.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/Model.h Structure/StructureEnum.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Structure/Model.o : Structure/Model.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h GuessAtomHybridization.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/Model.h Structure/StructureEnum.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 Structure/StructureEnum.o : Structure/StructureEnum.cpp Structure/StructureEnum.h
 Structure/StructureRoutines.o : Structure/StructureRoutines.cpp Atom.h CpptrajStdio.h NameType.h Residue.h Structure/StructureRoutines.h SymbolExporting.h
 Structure/Sugar.o : Structure/Sugar.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h

From d291831128674637f9c4f1c17821e1b7c23646a7 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 21 Dec 2023 14:37:32 -0500
Subject: [PATCH 0205/1492] Add warning

---
 src/Structure/GenerateAngles.cpp | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/Structure/GenerateAngles.cpp b/src/Structure/GenerateAngles.cpp
index 36c8584008..e7f5ec6ed8 100644
--- a/src/Structure/GenerateAngles.cpp
+++ b/src/Structure/GenerateAngles.cpp
@@ -115,6 +115,9 @@ int Cpptraj::Structure::GenerateImpropers(Topology& topIn, ParmHolder<AtomType>
         hybrid = Cpptraj::GuessAtomHybridization( AJ, topIn );
       if (hybrid == AtomType::SP2) {
         mprintf("DEBUG: Potential improper center: %s\n", topIn.AtomMaskName(iat).c_str());
+      } else if (hybrid == AtomType::UNKNOWN_HYBRIDIZATION) {
+        mprintf("Warning: When searching for impropers could not determine hybridization of %s\n",
+                topIn.AtomMaskName(iat).c_str());
       }
     }
   }

From d0b428f3e0039a3f36580f239a38985ac206f138 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 21 Dec 2023 14:51:52 -0500
Subject: [PATCH 0206/1492] Actually add the improper. I think I'm doing the
 ordering the same as leap but not 100% certain.

---
 src/Structure/GenerateAngles.cpp | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/src/Structure/GenerateAngles.cpp b/src/Structure/GenerateAngles.cpp
index e7f5ec6ed8..990f54cfa5 100644
--- a/src/Structure/GenerateAngles.cpp
+++ b/src/Structure/GenerateAngles.cpp
@@ -48,8 +48,7 @@ static inline void enumerateDihedrals(int at1, int at2, Topology& topIn) {
   }
 }
 
-        
-
+/* Set angles and dihedrals in given topology based on current bond arrays. */
 int Cpptraj::Structure::GenerateAngles(Topology& topIn) {
   if (topIn.Nbonds() < 1) {
     mprintf("Warning: No bonds in '%s', no angles to generate.\n", topIn.c_str());
@@ -101,7 +100,7 @@ int Cpptraj::Structure::GenerateAngles(Topology& topIn) {
   return 0;
 }
 
-/** Try to determine impropers for topology. */
+/** Try to determine impropers for topology. */ // TODO option for charmm improper
 int Cpptraj::Structure::GenerateImpropers(Topology& topIn, ParmHolder<AtomType> const& AT) {
   for (int iat = 0; iat != topIn.Natom(); iat++) {
     Atom const& AJ = topIn[iat];
@@ -115,6 +114,14 @@ int Cpptraj::Structure::GenerateImpropers(Topology& topIn, ParmHolder<AtomType>
         hybrid = Cpptraj::GuessAtomHybridization( AJ, topIn );
       if (hybrid == AtomType::SP2) {
         mprintf("DEBUG: Potential improper center: %s\n", topIn.AtomMaskName(iat).c_str());
+        // iat is the central (3rd) atom.
+        // lowest bonded atom index is the 1st atom.
+        // highest bonded atom index is the second atom.
+        // remaining atom is the fourth atom.
+        Atom AJcopy = AJ;
+        AJcopy.SortBonds();
+        std::vector<int> const& bonds = AJcopy.BondIdxArray();
+        topIn.AddDihedral( DihedralType( bonds[0], bonds[2], iat, bonds[1], DihedralType::BOTH ) );
       } else if (hybrid == AtomType::UNKNOWN_HYBRIDIZATION) {
         mprintf("Warning: When searching for impropers could not determine hybridization of %s\n",
                 topIn.AtomMaskName(iat).c_str());

From f2ebefac9c8c2628fae734befeb55ab714ae938a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 24 Dec 2023 13:18:59 -0500
Subject: [PATCH 0207/1492] Add desc command for comparing to LEaP

---
 src/Exec_Desc.cpp | 79 +++++++++++++++++++++++++++++++++++++++++++++++
 src/Exec_Desc.h   | 14 +++++++++
 2 files changed, 93 insertions(+)
 create mode 100644 src/Exec_Desc.cpp
 create mode 100644 src/Exec_Desc.h

diff --git a/src/Exec_Desc.cpp b/src/Exec_Desc.cpp
new file mode 100644
index 0000000000..433f0306e8
--- /dev/null
+++ b/src/Exec_Desc.cpp
@@ -0,0 +1,79 @@
+#include "Exec_Desc.h"
+#include "CpptrajStdio.h"
+
+int Exec_Desc::desc_atom(Topology const& topIn, int iat) {
+  Atom const& AT = topIn[iat];
+
+  const int bondorder = 1; // FIXME
+  mprintf("ATOM\n");
+  mprintf("Name:         %-5s\n", *(AT.Name()));
+  mprintf("Type:         %-5s\n", *(AT.Type()));
+  mprintf("Charge:       %6.4f\n", AT.Charge());
+  mprintf("Polarization: %6.4f\n", 0.0); // FIXME
+  mprintf("Element:      %-5s\n", AT.ElementName());
+  if (AT.Nbonds() == 0)
+    mprintf("  NO BONDS\n");
+  else {
+    for (Atom::bond_iterator bat = AT.bondbegin(); bat != AT.bondend(); ++bat) {
+      mprintf("  Bonded to %s by a", topIn.AtomMaskName(*bat).c_str());
+      switch (bondorder) {
+        case 1 : mprintf(" single"); break;
+        case 2 : mprintf(" double"); break;
+        case 3 : mprintf(" triple"); break;
+        case 4 : mprintf(" n aromatic"); break;
+        default : mprintf(" ????"); break;
+      }
+      mprintf(" bond.\n");
+    }
+  }
+  return 0;
+}
+ 
+
+// Exec_Desc::Help()
+void Exec_Desc::Help() const
+{
+
+}
+
+// Exec_Desc::Execute()
+Exec::RetType Exec_Desc::Execute(CpptrajState& State, ArgList& argIn)
+{
+  // Get Topology
+  Topology* parm = State.DSL().GetTopByIndex( argIn );
+  if (parm == 0) {
+    mprinterr("Error: No topologies loaded.\n");
+    return CpptrajState::ERR;
+  }
+  mprintf("\tUsing topology: %s\n", parm->c_str());
+  // Get output file
+  std::string outname = argIn.GetStringKey("out");
+  CpptrajFile* outfile = State.DFL().AddCpptrajFile(outname, "Atom description",
+                                                    DataFileList::TEXT, true);
+  if (outfile == 0) return CpptrajState::ERR;
+  mprintf("\tOutput to '%s'\n", outfile->Filename().full());
+  // Get mask
+  std::string maskstr = argIn.GetMaskNext();
+  AtomMask mask;
+  if (mask.SetMaskString(maskstr)) {
+    mprinterr("Error: Invalid atom mask: %s\n", maskstr.c_str());
+    return CpptrajState::ERR;
+  }
+
+  // Set up mask
+  if (parm->SetupIntegerMask( mask )) {
+    mprinterr("Error: Could not set up mask '%s'\n", mask.MaskString());
+    return CpptrajState::ERR;
+  }
+  mask.MaskInfo();
+  if (mask.None()) {
+    mprintf("Warning: '%s' selects no atoms.\n", mask.MaskString());
+    return CpptrajState::OK;
+  }
+
+  // Loop over atoms
+  for (AtomMask::const_iterator at = mask.begin(); at != mask.end(); ++at)
+    desc_atom( *parm, *at );
+
+  return CpptrajState::OK;
+}
diff --git a/src/Exec_Desc.h b/src/Exec_Desc.h
new file mode 100644
index 0000000000..abf3a6bb18
--- /dev/null
+++ b/src/Exec_Desc.h
@@ -0,0 +1,14 @@
+#ifndef INC_EXEC_DESC_H
+#define INC_EXEC_DESC_H
+#include "Exec.h"
+/// <Enter description of Exec_Desc here>
+class Exec_Desc : public Exec {
+  public:
+    Exec_Desc() : Exec(GENERAL) {}
+    void Help() const;
+    DispatchObject* Alloc() const { return (DispatchObject*)new Exec_Desc(); }
+    RetType Execute(CpptrajState&, ArgList&);
+  private:
+    static int desc_atom(Topology const&, int);
+};
+#endif

From 1081cbbc2ffad74de63a9aa602d9405da3238dee Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 24 Dec 2023 13:36:53 -0500
Subject: [PATCH 0208/1492] Enable desc for comparing to leap

---
 src/Command.cpp   | 2 ++
 src/Exec_Desc.h   | 2 +-
 src/cpptrajdepend | 3 ++-
 src/cpptrajfiles  | 1 +
 4 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/src/Command.cpp b/src/Command.cpp
index 4b3e12aed2..6c905c66c2 100644
--- a/src/Command.cpp
+++ b/src/Command.cpp
@@ -72,6 +72,7 @@
 #include "Exec_ScaleDihedralK.h"
 #include "Exec_Top.h"
 #include "Exec_UpdateParameters.h"
+#include "Exec_Desc.h"
 // ----- ACTION ----------------------------------------------------------------
 #include "Action_Angle.h"
 #include "Action_Distance.h"
@@ -299,6 +300,7 @@ void Command::Init() {
   Command::AddCmd( new Exec_Change(),        Cmd::EXE, 1, "change" );
   Command::AddCmd( new Exec_ChargeInfo(),    Cmd::EXE, 1, "charge" );
   Command::AddCmd( new Exec_CompareTop(),    Cmd::EXE, 1, "comparetop" );
+  Command::AddCmd( new Exec_Desc(),          Cmd::EXE, 1, "desc" );
   Command::AddCmd( new Exec_DihedralInfo(),Cmd::EXE, 3,"dihedrals","dihedralinfo","printdihedrals");
   Command::AddCmd( new Exec_HmassRepartition(),Cmd::EXE, 1, "hmassrepartition" );
   Command::AddCmd( new Exec_ImproperInfo(),Cmd::EXE, 3,"impropers","improperinfo","printimpropers");
diff --git a/src/Exec_Desc.h b/src/Exec_Desc.h
index abf3a6bb18..2bf830a71d 100644
--- a/src/Exec_Desc.h
+++ b/src/Exec_Desc.h
@@ -4,7 +4,7 @@
 /// <Enter description of Exec_Desc here>
 class Exec_Desc : public Exec {
   public:
-    Exec_Desc() : Exec(GENERAL) {}
+    Exec_Desc() : Exec(PARM) {}
     void Help() const;
     DispatchObject* Alloc() const { return (DispatchObject*)new Exec_Desc(); }
     RetType Execute(CpptrajState&, ArgList&);
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 1515262f73..3e62c05a7d 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -187,7 +187,7 @@ ClusterMap.o : ClusterMap.cpp AssociatedData.h ClusterMap.h Constants.h CpptrajF
 Cmd.o : Cmd.cpp Cmd.h DispatchObject.h
 CmdInput.o : CmdInput.cpp CmdInput.h StringRoutines.h
 CmdList.o : CmdList.cpp Cmd.h CmdList.h DispatchObject.h
-Command.o : Command.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h ActionTopWriter.h Action_Align.h Action_Angle.h Action_AreaPerMol.h Action_AtomMap.h Action_AtomicCorr.h Action_AtomicFluct.h Action_AutoImage.h Action_Average.h Action_AvgBox.h Action_Bounds.h Action_Box.h Action_Center.h Action_Channel.h Action_CheckChirality.h Action_CheckStructure.h Action_Closest.h Action_ClusterDihedral.h Action_Contacts.h Action_CreateCrd.h Action_CreateReservoir.h Action_DNAionTracker.h Action_DSSP.h Action_Density.h Action_Diffusion.h Action_Dihedral.h Action_DihedralRMS.h Action_Dipole.h Action_DistRmsd.h Action_Distance.h Action_Energy.h Action_Esander.h Action_FilterByData.h Action_FixAtomOrder.h Action_FixImagedBonds.h Action_GIST.h Action_Grid.h Action_GridFreeEnergy.h Action_HydrogenBond.h Action_Image.h Action_InfraredSpectrum.h Action_Jcoupling.h Action_Keep.h Action_LESsplit.h Action_LIE.h Action_LipidOrder.h Action_MakeStructure.h Action_Mask.h Action_Matrix.h Action_MinImage.h Action_Molsurf.h Action_MultiDihedral.h Action_MultiPucker.h Action_MultiVector.h Action_NAstruct.h Action_NMRrst.h Action_NativeContacts.h Action_OrderParameter.h Action_Outtraj.h Action_PairDist.h Action_Pairwise.h Action_Principal.h Action_Projection.h Action_Pucker.h Action_Radgyr.h Action_Radial.h Action_RandomizeIons.h Action_Remap.h Action_ReplicateCell.h Action_Rmsd.h Action_Rotate.h Action_RunningAvg.h Action_STFC_Diffusion.h Action_Scale.h Action_SetVelocity.h Action_Spam.h Action_Strip.h Action_Surf.h Action_SymmetricRmsd.h Action_Temperature.h Action_Time.h Action_ToroidalDiffusion.h Action_Translate.h Action_Unstrip.h Action_Unwrap.h Action_Vector.h Action_VelocityAutoCorr.h Action_Volmap.h Action_Volume.h Action_Watershell.h Action_XtalSymm.h Analysis.h AnalysisList.h AnalysisState.h Analysis_AmdBias.h Analysis_AutoCorr.h Analysis_Average.h Analysis_CalcDiffusion.h Analysis_Clustering.h Analysis_ConstantPHStats.h Analysis_Corr.h Analysis_CrankShaft.h Analysis_CrdFluct.h Analysis_CrossCorr.h Analysis_CurveFit.h Analysis_Divergence.h Analysis_EvalPlateau.h Analysis_FFT.h Analysis_HausdorffDistance.h Analysis_Hist.h Analysis_IRED.h Analysis_Integrate.h Analysis_KDE.h Analysis_Lifetime.h Analysis_LowestCurve.h Analysis_Matrix.h Analysis_MeltCurve.h Analysis_Modes.h Analysis_MultiHist.h Analysis_Multicurve.h Analysis_Overlap.h Analysis_PhiPsi.h Analysis_Regression.h Analysis_RemLog.h Analysis_Rms2d.h Analysis_RmsAvgCorr.h Analysis_Rotdif.h Analysis_RunningAvg.h Analysis_Slope.h Analysis_Spline.h Analysis_State.h Analysis_Statistics.h Analysis_TI.h Analysis_TICA.h Analysis_Timecorr.h Analysis_VectorMath.h Analysis_Wavelet.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h AxisType.h BaseIOtype.h Box.h BoxArgs.h BufferedLine.h CharMask.h Cluster/Algorithm.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Control.h Cluster/DrawGraph.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Sieve.h Cluster/Silhouette.h ClusterMap.h Cmd.h CmdInput.h CmdList.h Command.h CompactFrameArray.h ComplexArray.h Constants.h Constraints.h ControlBlock.h ControlBlock_For.h CoordinateInfo.h Corr.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_RemLog.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h Deprecated.h DiffusionResults.h DihedralSearch.h Dimension.h DispatchObject.h Energy.h Energy_Sander.h EnsembleIn.h EnsembleOutList.h Ewald.h EwaldOptions.h Ewald_ParticleMesh.h ExclusionArray.h Exec.h Exec_AddMissingRes.h Exec_Analyze.h Exec_Build.h Exec_Calc.h Exec_CatCrd.h Exec_Change.h Exec_ClusterMap.h Exec_CombineCoords.h Exec_Commands.h Exec_CompareClusters.h Exec_CompareEnergy.h Exec_CompareTop.h Exec_CrdAction.h Exec_CrdOut.h Exec_CrdTransform.h Exec_CreateSet.h Exec_DataFile.h Exec_DataFilter.h Exec_DataSetCmd.h Exec_Emin.h Exec_ExtendedComparison.h Exec_Flatten.h Exec_GenerateAmberRst.h Exec_Graft.h Exec_Help.h Exec_HmassRepartition.h Exec_LoadCrd.h Exec_LoadTraj.h Exec_ParallelAnalysis.h Exec_ParmBox.h Exec_ParmSolvent.h Exec_ParmStrip.h Exec_ParmWrite.h Exec_ParseTiming.h Exec_PermuteDihedrals.h Exec_Precision.h Exec_PrepareForLeap.h Exec_PrintData.h Exec_Random.h Exec_ReadData.h Exec_ReadEnsembleData.h Exec_ReadInput.h Exec_RotateDihedral.h Exec_RunAnalysis.h Exec_ScaleDihedralK.h Exec_Sequence.h Exec_SequenceAlign.h Exec_Set.h Exec_Show.h Exec_SortEnsembleData.h Exec_SplitCoords.h Exec_System.h Exec_Top.h Exec_Traj.h Exec_UpdateParameters.h Exec_ViewRst.h Exec_Zmatrix.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h GIST_PME.h Grid.h GridAction.h GridBin.h GridMover.h HistBin.h Hungarian.h ImageOption.h ImageTypes.h InputTrajCommon.h MapAtom.h MaskArray.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h OnlineVarT.h OutputTrajCommon.h PDBfile.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PubFFT.h Pucker.h Pucker_PuckerMask.h Pucker_PuckerSearch.h Pucker_PuckerToken.h RPNcalc.h Random.h Range.h ReferenceAction.h ReferenceFrame.h RemdReservoirNC.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h SplineFxnTable.h StructureCheck.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h cuda_kernels/GistCudaSetup.cuh helpme_standalone.h molsurf.h
+Command.o : Command.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h ActionTopWriter.h Action_Align.h Action_Angle.h Action_AreaPerMol.h Action_AtomMap.h Action_AtomicCorr.h Action_AtomicFluct.h Action_AutoImage.h Action_Average.h Action_AvgBox.h Action_Bounds.h Action_Box.h Action_Center.h Action_Channel.h Action_CheckChirality.h Action_CheckStructure.h Action_Closest.h Action_ClusterDihedral.h Action_Contacts.h Action_CreateCrd.h Action_CreateReservoir.h Action_DNAionTracker.h Action_DSSP.h Action_Density.h Action_Diffusion.h Action_Dihedral.h Action_DihedralRMS.h Action_Dipole.h Action_DistRmsd.h Action_Distance.h Action_Energy.h Action_Esander.h Action_FilterByData.h Action_FixAtomOrder.h Action_FixImagedBonds.h Action_GIST.h Action_Grid.h Action_GridFreeEnergy.h Action_HydrogenBond.h Action_Image.h Action_InfraredSpectrum.h Action_Jcoupling.h Action_Keep.h Action_LESsplit.h Action_LIE.h Action_LipidOrder.h Action_MakeStructure.h Action_Mask.h Action_Matrix.h Action_MinImage.h Action_Molsurf.h Action_MultiDihedral.h Action_MultiPucker.h Action_MultiVector.h Action_NAstruct.h Action_NMRrst.h Action_NativeContacts.h Action_OrderParameter.h Action_Outtraj.h Action_PairDist.h Action_Pairwise.h Action_Principal.h Action_Projection.h Action_Pucker.h Action_Radgyr.h Action_Radial.h Action_RandomizeIons.h Action_Remap.h Action_ReplicateCell.h Action_Rmsd.h Action_Rotate.h Action_RunningAvg.h Action_STFC_Diffusion.h Action_Scale.h Action_SetVelocity.h Action_Spam.h Action_Strip.h Action_Surf.h Action_SymmetricRmsd.h Action_Temperature.h Action_Time.h Action_ToroidalDiffusion.h Action_Translate.h Action_Unstrip.h Action_Unwrap.h Action_Vector.h Action_VelocityAutoCorr.h Action_Volmap.h Action_Volume.h Action_Watershell.h Action_XtalSymm.h Analysis.h AnalysisList.h AnalysisState.h Analysis_AmdBias.h Analysis_AutoCorr.h Analysis_Average.h Analysis_CalcDiffusion.h Analysis_Clustering.h Analysis_ConstantPHStats.h Analysis_Corr.h Analysis_CrankShaft.h Analysis_CrdFluct.h Analysis_CrossCorr.h Analysis_CurveFit.h Analysis_Divergence.h Analysis_EvalPlateau.h Analysis_FFT.h Analysis_HausdorffDistance.h Analysis_Hist.h Analysis_IRED.h Analysis_Integrate.h Analysis_KDE.h Analysis_Lifetime.h Analysis_LowestCurve.h Analysis_Matrix.h Analysis_MeltCurve.h Analysis_Modes.h Analysis_MultiHist.h Analysis_Multicurve.h Analysis_Overlap.h Analysis_PhiPsi.h Analysis_Regression.h Analysis_RemLog.h Analysis_Rms2d.h Analysis_RmsAvgCorr.h Analysis_Rotdif.h Analysis_RunningAvg.h Analysis_Slope.h Analysis_Spline.h Analysis_State.h Analysis_Statistics.h Analysis_TI.h Analysis_TICA.h Analysis_Timecorr.h Analysis_VectorMath.h Analysis_Wavelet.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h AxisType.h BaseIOtype.h Box.h BoxArgs.h BufferedLine.h CharMask.h Cluster/Algorithm.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Control.h Cluster/DrawGraph.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Sieve.h Cluster/Silhouette.h ClusterMap.h Cmd.h CmdInput.h CmdList.h Command.h CompactFrameArray.h ComplexArray.h Constants.h Constraints.h ControlBlock.h ControlBlock_For.h CoordinateInfo.h Corr.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_RemLog.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h Deprecated.h DiffusionResults.h DihedralSearch.h Dimension.h DispatchObject.h Energy.h Energy_Sander.h EnsembleIn.h EnsembleOutList.h Ewald.h EwaldOptions.h Ewald_ParticleMesh.h ExclusionArray.h Exec.h Exec_AddMissingRes.h Exec_Analyze.h Exec_Build.h Exec_Calc.h Exec_CatCrd.h Exec_Change.h Exec_ClusterMap.h Exec_CombineCoords.h Exec_Commands.h Exec_CompareClusters.h Exec_CompareEnergy.h Exec_CompareTop.h Exec_CrdAction.h Exec_CrdOut.h Exec_CrdTransform.h Exec_CreateSet.h Exec_DataFile.h Exec_DataFilter.h Exec_DataSetCmd.h Exec_Desc.h Exec_Emin.h Exec_ExtendedComparison.h Exec_Flatten.h Exec_GenerateAmberRst.h Exec_Graft.h Exec_Help.h Exec_HmassRepartition.h Exec_LoadCrd.h Exec_LoadTraj.h Exec_ParallelAnalysis.h Exec_ParmBox.h Exec_ParmSolvent.h Exec_ParmStrip.h Exec_ParmWrite.h Exec_ParseTiming.h Exec_PermuteDihedrals.h Exec_Precision.h Exec_PrepareForLeap.h Exec_PrintData.h Exec_Random.h Exec_ReadData.h Exec_ReadEnsembleData.h Exec_ReadInput.h Exec_RotateDihedral.h Exec_RunAnalysis.h Exec_ScaleDihedralK.h Exec_Sequence.h Exec_SequenceAlign.h Exec_Set.h Exec_Show.h Exec_SortEnsembleData.h Exec_SplitCoords.h Exec_System.h Exec_Top.h Exec_Traj.h Exec_UpdateParameters.h Exec_ViewRst.h Exec_Zmatrix.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h GIST_PME.h Grid.h GridAction.h GridBin.h GridMover.h HistBin.h Hungarian.h ImageOption.h ImageTypes.h InputTrajCommon.h MapAtom.h MaskArray.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h OnlineVarT.h OutputTrajCommon.h PDBfile.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PubFFT.h Pucker.h Pucker_PuckerMask.h Pucker_PuckerSearch.h Pucker_PuckerToken.h RPNcalc.h Random.h Range.h ReferenceAction.h ReferenceFrame.h RemdReservoirNC.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h SplineFxnTable.h StructureCheck.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h cuda_kernels/GistCudaSetup.cuh helpme_standalone.h molsurf.h
 CompactFrameArray.o : CompactFrameArray.cpp Box.h CompactFrameArray.h CoordinateInfo.h CpptrajStdio.h Matrix_3x3.h Parallel.h ReplicaDimArray.h Vec3.h
 ComplexArray.o : ComplexArray.cpp ArrayIterator.h ComplexArray.h
 Constraints.o : Constraints.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
@@ -305,6 +305,7 @@ Exec_CreateSet.o : Exec_CreateSet.cpp Action.h ActionList.h ActionState.h Analys
 Exec_DataFile.o : Exec_DataFile.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_DataFile.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_DataFilter.o : Exec_DataFilter.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_DataFilter.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_DataSetCmd.o : Exec_DataSetCmd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h ArrayIterator.h AssociatedData.h AssociatedData_Connect.h AssociatedData_NOE.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_Mesh.h DataSet_Vector.h DataSet_string.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_DataSetCmd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Desc.o : Exec_Desc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Desc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Emin.o : Exec_Emin.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Emin.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_ExtendedComparison.o : Exec_ExtendedComparison.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ExtendedComparison.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Flatten.o : Exec_Flatten.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Flatten.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
diff --git a/src/cpptrajfiles b/src/cpptrajfiles
index d0929dd54c..11560b4aa0 100644
--- a/src/cpptrajfiles
+++ b/src/cpptrajfiles
@@ -275,6 +275,7 @@ COMMON_SOURCES= \
         Exec_DataFile.cpp \
         Exec_DataFilter.cpp \
         Exec_DataSetCmd.cpp \
+        Exec_Desc.cpp \
         Exec_Emin.cpp \
         Exec_ExtendedComparison.cpp \
         Exec_Flatten.cpp \

From ed84c21ae67c4d4dd22128e434476849d4dc36b3 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 24 Dec 2023 13:53:43 -0500
Subject: [PATCH 0209/1492] Move debug step to TopInfo

---
 src/TopInfo.cpp  | 5 +++++
 src/Topology.cpp | 4 +---
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/src/TopInfo.cpp b/src/TopInfo.cpp
index b0738f65ce..9fa244fa7f 100644
--- a/src/TopInfo.cpp
+++ b/src/TopInfo.cpp
@@ -637,6 +637,11 @@ void TopInfo::PrintDihedrals(DihedralArray const& darray, DihedralParmArray cons
                  dihedralparm[didx].Pn());
         if (printExtraInfo)
           outfile_->Printf(" %4.1f %4.1f", dihedralparm[didx].SCEE(), dihedralparm[didx].SCNB());
+      } else {
+        // DEBUG
+        outfile_->Printf(" %7s %5s %4s", "NONE", "NONE", "NONE");
+        if (printExtraInfo)
+          outfile_->Printf(" %4s %4s", "NONE", "NONE");
       }
       if ( !coords_.empty() )
         outfile_->Printf(" %7.2f", Torsion( coords_.XYZ(atom1),
diff --git a/src/Topology.cpp b/src/Topology.cpp
index 9652e99b1e..24a720c61b 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2818,9 +2818,7 @@ void Topology::AssignDihedralParm(DihedralParmHolder const& newDihedralParams,
                 TruncResAtomNameNum(dih->A4()).c_str(),
                 *types[0], *types[1], *types[2], *types[3]);
         DihedralType mydih = *dih;
-        int idx = addTorsionParm( dihedralparm_, DihedralParmType() ); // DEBUG
-        mydih.SetIdx( idx ); // DEBUG
-        //mydih.SetIdx( -1 );
+        mydih.SetIdx( -1 );
         dihedralsIn.push_back( mydih );
       } else {
         // Actually add parameters for this dihedral.

From 6b7fdaf4092c031341a0ad77f6d453beeb022d66 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 24 Dec 2023 16:24:39 -0500
Subject: [PATCH 0210/1492] Order improper atoms the same way leap does,
 alphabetically by atom type

---
 src/Structure/GenerateAngles.cpp | 129 +++++++++++++++++++++++++++++--
 1 file changed, 121 insertions(+), 8 deletions(-)

diff --git a/src/Structure/GenerateAngles.cpp b/src/Structure/GenerateAngles.cpp
index 990f54cfa5..078ded5a22 100644
--- a/src/Structure/GenerateAngles.cpp
+++ b/src/Structure/GenerateAngles.cpp
@@ -100,6 +100,113 @@ int Cpptraj::Structure::GenerateAngles(Topology& topIn) {
   return 0;
 }
 
+/** Try to order an improper the same way that LEaP does.
+  * LEaP has wild card names first, followed by atom types
+  * in alphabetical order. The third atom is always the central
+  * atom.
+  */
+static int order_improper_atoms(int* leapdih, int centralAt, Topology const& topIn)
+{
+  Atom const& Ak = topIn[centralAt];
+  std::vector<int> const& bonds = Ak.BondIdxArray();
+  int indices[3];
+  indices[0] = bonds[0];
+  indices[1] = bonds[1];
+  indices[2] = bonds[2];
+  if (topIn[indices[0]].Type() > topIn[indices[1]].Type()) std::swap( indices[0], indices[1] );
+  if (topIn[indices[1]].Type() > topIn[indices[2]].Type()) std::swap( indices[1], indices[2] );
+  if (topIn[indices[0]].Type() > topIn[indices[1]].Type()) std::swap( indices[0], indices[1] );
+  if (topIn[indices[1]].Type() > topIn[indices[2]].Type()) std::swap( indices[1], indices[2] );
+  leapdih[0] = indices[0];
+  leapdih[1] = indices[1];
+  leapdih[2] = centralAt;
+  leapdih[3] = indices[2];
+  return 0;
+}
+/*
+static int order_improper_atoms(int* indices, int centralAt, Topology const& topIn)
+{
+  indices[2] = centralAt;
+  Atom const& Ak = topIn[centralAt];
+  std::vector<int> const& bonds = Ak.BondIdxArray();
+  NameType const& a1 = topIn[bonds[0]].Type();
+  NameType const& a2 = topIn[bonds[1]].Type();
+  NameType const& a3 = topIn[bonds[2]].Type();
+  if (a1 < a2) {
+    if (a1 < a3) {
+      // a1 < a2 and a1 < a3
+      indices[0] = bonds[0];
+      if (a2 < a3) {
+        indices[1] = bonds[1];
+        indices[3] = bonds[2];
+      } else {
+        indices[1] = bonds[2];
+        indices[3] = bonds[1];
+      }
+    } else {
+      // a1 < a2 and a3 < a1
+      indices[0] = bonds[2];
+      indices[1] = bonds[0];
+      indices[3] = bonds[1];
+    }
+  } else {
+    if (a2 < a3) {
+      // a2 < a1 and a2 < a3
+      indices[0] = bonds[1];
+      if (a1 < a3) {
+        indices[1] = bonds[0];
+        indices[3] = bonds[2];
+      } else {
+        indices[1] = bonds[2];
+        indices[3] = bonds[0];
+      }
+    } else {
+      // a2 < a1 and a3 < a2
+      indices[0] = bonds[2];
+      indices[1] = bonds[1];
+      indices[3] = bonds[0];
+    }
+  }
+
+  return 0;
+}*/
+/*static int order_improper_atoms(int* oaObj, int iat, Topology const& topIn) {
+  int iIndex1 = 0;
+  int iIndex2 = 0;
+  int iIndex0 = 0;
+  for (int i = 0; i < 3; i++)
+    oaObj[i] = -1;
+
+  Atom const& AJ = topIn[iat];
+  int iAtomCoordination = AJ.Nbonds();
+
+  if ( iIndex1 <= iIndex0 )
+    iIndex1 = iIndex0+1;
+  if ( iIndex2 <= iIndex1 )
+    iIndex2 = iIndex1+1;
+  else iIndex2++;
+
+  if ( iIndex2 >= iAtomCoordination ) {
+      iIndex1++;
+      iIndex2 = iIndex1 + 1;
+      if ( iIndex2 >= iAtomCoordination ) {
+          iIndex0++;
+          iIndex1 = iIndex0 + 1;
+          iIndex2 = iIndex1 + 1;
+      }
+  }
+
+  if ( iIndex2 < (iAtomCoordination) ) {
+      mprintf("DEBUG: iIndex %i %i %i\n", iIndex0, iIndex1, iIndex2);
+      oaObj[2] = iat;
+      oaObj[0] = AJ.BondIdxArray()[iIndex0]; //(OBJEKT) aAtomBondedNeighbor( cCont, iIndex0 );
+      oaObj[1] = AJ.BondIdxArray()[iIndex1]; //(OBJEKT) aAtomBondedNeighbor( cCont, iIndex1 );
+      oaObj[3] = AJ.BondIdxArray()[iIndex2]; //(OBJEKT) aAtomBondedNeighbor( cCont, iIndex2 );
+      return 0;
+  }
+  return 1;
+}*/
+
 /** Try to determine impropers for topology. */ // TODO option for charmm improper
 int Cpptraj::Structure::GenerateImpropers(Topology& topIn, ParmHolder<AtomType> const& AT) {
   for (int iat = 0; iat != topIn.Natom(); iat++) {
@@ -114,14 +221,20 @@ int Cpptraj::Structure::GenerateImpropers(Topology& topIn, ParmHolder<AtomType>
         hybrid = Cpptraj::GuessAtomHybridization( AJ, topIn );
       if (hybrid == AtomType::SP2) {
         mprintf("DEBUG: Potential improper center: %s\n", topIn.AtomMaskName(iat).c_str());
-        // iat is the central (3rd) atom.
-        // lowest bonded atom index is the 1st atom.
-        // highest bonded atom index is the second atom.
-        // remaining atom is the fourth atom.
-        Atom AJcopy = AJ;
-        AJcopy.SortBonds();
-        std::vector<int> const& bonds = AJcopy.BondIdxArray();
-        topIn.AddDihedral( DihedralType( bonds[0], bonds[2], iat, bonds[1], DihedralType::BOTH ) );
+        int leapdih[4];
+        order_improper_atoms(leapdih, iat, topIn);
+        mprintf("DEBUG: Bond order %s : %i %i %i %i %s %s %s %s\n",
+                topIn.AtomMaskName(iat).c_str(),
+                AJ.BondIdxArray()[0]+1,
+                AJ.BondIdxArray()[1]+1,
+                iat+1,
+                AJ.BondIdxArray()[2]+1,
+                topIn.AtomMaskName(AJ.BondIdxArray()[0]).c_str(),
+                topIn.AtomMaskName(AJ.BondIdxArray()[1]).c_str(),
+                topIn.AtomMaskName(iat).c_str(),
+                topIn.AtomMaskName(AJ.BondIdxArray()[2]).c_str());
+        mprintf("DEBUG: Leap order: %i %i %i %i\n", leapdih[0]+1, leapdih[1]+1, leapdih[2]+1, leapdih[3]+1);
+        topIn.AddDihedral( DihedralType(leapdih[0], leapdih[1], leapdih[2], leapdih[3], DihedralType::BOTH) );
       } else if (hybrid == AtomType::UNKNOWN_HYBRIDIZATION) {
         mprintf("Warning: When searching for impropers could not determine hybridization of %s\n",
                 topIn.AtomMaskName(iat).c_str());

From 32cadce072912a6e760dd1d459d8342ab1e9cc8e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 26 Dec 2023 09:22:56 -0500
Subject: [PATCH 0211/1492] Add function to do improper type name sorting

---
 src/TypeNameHolder.h | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/src/TypeNameHolder.h b/src/TypeNameHolder.h
index eb8b129e1a..04a53508f8 100644
--- a/src/TypeNameHolder.h
+++ b/src/TypeNameHolder.h
@@ -4,6 +4,12 @@
 #include "NameType.h"
 /// Used to hold one or more atom type names.
 class TypeNameHolder {
+    // Swap NameTypes
+    static inline void tswap(NameType& n0, NameType& n1) {
+      NameType tmp = n1;
+      n1 = n0;
+      n0 = tmp;
+    }
   public:
     typedef std::vector<NameType> Narray;
     typedef Narray::const_iterator const_iterator;
@@ -110,6 +116,20 @@ class TypeNameHolder {
         tstr.append( " " + std::string( *(*it) ) );
       return tstr;
     }
+    /// Sort typenames alphabetically, preserving the 3rd position (for impropers)
+    void SortImproperByAlpha(NameType const& wc) {
+      if (types_.size() != 4) return;
+      if (wc.len() > 0) {
+        // Replace wildcards with spaces so they appear first
+        if (types_[0] == wc) types_[0] = NameType(" ");
+        if (types_[1] == wc) types_[1] = NameType(" ");
+        if (types_[3] == wc) types_[3] = NameType(" ");
+      }
+      if (types_[0] > types_[1]) tswap(types_[0], types_[1]);
+      if (types_[1] > types_[3]) tswap(types_[1], types_[3]);
+      if (types_[0] > types_[1]) tswap(types_[0], types_[1]);
+      if (types_[1] > types_[3]) tswap(types_[1], types_[3]);
+    }
     /// \return size in bytes
     size_t DataSize() const { return (types_.size()*NameType::DataSize()) + NameType::DataSize(); }
   private:

From b347abac99b021b64fc8e1c8a6a1ae7fce0cecdf Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 26 Dec 2023 09:26:32 -0500
Subject: [PATCH 0212/1492] Start adding TypeNameHolder unit test

---
 unitTests/TypeNameHolder/UnitTest.sh | 13 +++++++++++++
 unitTests/TypeNameHolder/main.cpp    | 26 ++++++++++++++++++++++++++
 2 files changed, 39 insertions(+)
 create mode 100755 unitTests/TypeNameHolder/UnitTest.sh
 create mode 100644 unitTests/TypeNameHolder/main.cpp

diff --git a/unitTests/TypeNameHolder/UnitTest.sh b/unitTests/TypeNameHolder/UnitTest.sh
new file mode 100755
index 0000000000..42b0fbe761
--- /dev/null
+++ b/unitTests/TypeNameHolder/UnitTest.sh
@@ -0,0 +1,13 @@
+#!/bin/bash
+
+. ../UnitMaster.sh
+
+CleanFiles Makefile main.o NameType.o a.out CpptrajStdio.o
+
+UNITSOURCES='NameType.cpp CpptrajStdio.cpp'
+
+CreateMakefile
+
+RunMake "TypeNameHolder class unit test."
+
+EndTest
diff --git a/unitTests/TypeNameHolder/main.cpp b/unitTests/TypeNameHolder/main.cpp
new file mode 100644
index 0000000000..b6a79a7199
--- /dev/null
+++ b/unitTests/TypeNameHolder/main.cpp
@@ -0,0 +1,26 @@
+// Unit test for NameType class
+#include <cstdio>
+#include <vector>
+#include <string>
+#include <algorithm>
+#include "TypeNameHolder.h"
+
+static const int Err(const char* msg) {
+  fprintf(stderr, "Error: %s\n", msg);
+  return 1;
+}
+
+/*struct reverseSort {
+  bool operator() (const NameType& lhs, const NameType& rhs) const {
+    return ( lhs > rhs );
+  }
+} reverseSortObj;*/
+
+int main() {
+  TypeNameHolder type1;
+  type1.AddName("CT");
+  TypeNameHolder type2("O");
+  bool ismatch = type1.Match_NoWC( type2 );
+  if (ismatch) return Err("TypeNameHolder single type match failed.");
+  return 0;
+}

From cc4e4ff3084124effb94be8dd4b4d0ba43fc9a94 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 26 Dec 2023 09:42:43 -0500
Subject: [PATCH 0213/1492] Ensure replaced wc names are restored

---
 src/TypeNameHolder.h | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/src/TypeNameHolder.h b/src/TypeNameHolder.h
index 04a53508f8..19ce1ce1ef 100644
--- a/src/TypeNameHolder.h
+++ b/src/TypeNameHolder.h
@@ -129,6 +129,12 @@ class TypeNameHolder {
       if (types_[1] > types_[3]) tswap(types_[1], types_[3]);
       if (types_[0] > types_[1]) tswap(types_[0], types_[1]);
       if (types_[1] > types_[3]) tswap(types_[1], types_[3]);
+      if (wc.len() > 0) {
+        // Restore wildcards
+        if (types_[0] == " ") types_[0] = wc;
+        if (types_[1] == " ") types_[1] = wc;
+        if (types_[3] == " ") types_[3] = wc;
+      }
     }
     /// \return size in bytes
     size_t DataSize() const { return (types_.size()*NameType::DataSize()) + NameType::DataSize(); }

From 0b8477c644285b145903fabcbcf9a8791ce28515 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 26 Dec 2023 09:48:31 -0500
Subject: [PATCH 0214/1492] Finish TypeNameHolder test

---
 unitTests/TypeNameHolder/main.cpp | 71 ++++++++++++++++++++++++++++++-
 1 file changed, 70 insertions(+), 1 deletion(-)

diff --git a/unitTests/TypeNameHolder/main.cpp b/unitTests/TypeNameHolder/main.cpp
index b6a79a7199..3b3f32609a 100644
--- a/unitTests/TypeNameHolder/main.cpp
+++ b/unitTests/TypeNameHolder/main.cpp
@@ -21,6 +21,75 @@ int main() {
   type1.AddName("CT");
   TypeNameHolder type2("O");
   bool ismatch = type1.Match_NoWC( type2 );
-  if (ismatch) return Err("TypeNameHolder single type match failed.");
+  if (ismatch) return Err("TypeNameHolder single type no match failed.");
+  TypeNameHolder type3("CT");
+  ismatch = type1.Match_NoWC( type3 );
+  if (!ismatch) return Err("TypeNameHolder single type match failed.");
+
+  TypeNameHolder bp1(2);
+  bp1.AddName("CT");
+  bp1.AddName("O");
+  TypeNameHolder bp2(2);
+  bp2.AddName("O");
+  bp2.AddName("CT");
+  ismatch = bp1.Match_NoWC( bp2 );
+  if (!ismatch) return Err("TypeNameHolder two type reverse match failed.");
+
+  TypeNameHolder ap1(3);
+  ap1.AddName("CT");
+  ap1.AddName("O");
+  ap1.AddName("HO");
+  TypeNameHolder ap2(3);
+  ap2.AddName("HO");
+  ap2.AddName("O");
+  ap2.AddName("CT");
+  ismatch = ap2.Match_NoWC( ap1 );
+  if (!ismatch) return Err("TypeNameHolder three type reverse match failed.");
+
+  TypeNameHolder dp1(4);
+  dp1.AddName("X");
+  dp1.AddName("CX");
+  dp1.AddName("O");
+  dp1.AddName("X");
+  TypeNameHolder dp2(4);
+  dp2.AddName("CT");
+  dp2.AddName("CX");
+  dp2.AddName("O");
+  dp2.AddName("HO");
+  ismatch = dp1.Match_NoWC( dp2 );
+  if (ismatch) return Err("TypeNameHolder four type no WC match failed.");
+  ismatch = dp1.Match_WC( dp2, "X" );
+  if (!ismatch) return Err("TypeNameHolder four type WC match failed.");
+
+  TypeNameHolder ip1(4);
+  ip1.AddName("O");
+  ip1.AddName("HO");
+  ip1.AddName("CT");
+  ip1.AddName("N");
+  ip1.SortImproperByAlpha("X");
+  if (ip1[0] != "HO") return Err("TypeNameHolder improper alpha sort failed (pos 0)");
+  if (ip1[1] != "N") return Err("TypeNameHolder improper alpha sort failed (pos 1)");
+  if (ip1[2] != "CT") return Err("TypeNameHolder improper alpha sort failed (pos 2)");
+  if (ip1[3] != "O") return Err("TypeNameHolder improper alpha sort failed (pos 3)");
+
+  TypeNameHolder ip2(4);
+  ip2.AddName("O");
+  ip2.AddName("X");
+  ip2.AddName("CT");
+  ip2.AddName("X");
+  ip2.SortImproperByAlpha("X");
+  if (ip2[0] != "X") return Err("TypeNameHolder improper2 alpha sort failed (pos 0)");
+  if (ip2[1] != "X") return Err("TypeNameHolder improper2 alpha sort failed (pos 1)");
+  if (ip2[2] != "CT") return Err("TypeNameHolder improper2 alpha sort failed (pos 2)");
+  if (ip2[3] != "O") return Err("TypeNameHolder improper2 alpha sort failed (pos 3)");
+
+  //printf("ip1 %s %s %s %s\n", *ip1[0], *ip1[1], *ip1[2], *ip1[3]);
+  //printf("ip2 %s %s %s %s\n", *ip2[0], *ip2[1], *ip2[2], *ip2[3]);
+
+  ismatch = ip2.Match_NoWC( ip1 );
+  if (ismatch) return Err("TypeNameHolder improper no WC match failed.");
+  ismatch = ip2.Match_WC( ip1, "X" );
+  if (!ismatch) return Err("TypeNameHolder improper WC match failed.");
+
   return 0;
 }

From 1934135fc4d979e32e5861f7d5a111e6b6ff5755 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 26 Dec 2023 09:49:57 -0500
Subject: [PATCH 0215/1492] Enable TypeNameHolder test

---
 unitTests/Makefile | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/unitTests/Makefile b/unitTests/Makefile
index 7a694a5cfa..a099ae2f00 100644
--- a/unitTests/Makefile
+++ b/unitTests/Makefile
@@ -19,13 +19,17 @@ unit.StringRoutines:
 unit.Range:
 	@-cd Range && ./UnitTest.sh $(OPT)
 
+unit.TypeNameHolder:
+	@-cd TypeNameHolder && ./UnitTest.sh $(OPT)
+
 # ----- Every unit test should go here -----------
 COMPLETETESTS= \
   unit.NameType \
   unit.ArgList \
   unit.GistEntropyUtils \
   unit.StringRoutines \
-  unit.Range
+  unit.Range \
+  unit.TypeNameHolder
 
 test.cpptraj: $(COMPLETETESTS)
 

From 447f57c14da245cfdae6d92afb5e0344eda271bb Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 26 Dec 2023 12:11:40 -0500
Subject: [PATCH 0216/1492] Fix the function call

---
 unitTests/GistEntropyUtils/main.cpp | 20 ++++++++++++--------
 1 file changed, 12 insertions(+), 8 deletions(-)

diff --git a/unitTests/GistEntropyUtils/main.cpp b/unitTests/GistEntropyUtils/main.cpp
index 3d33af708d..809f6c6421 100644
--- a/unitTests/GistEntropyUtils/main.cpp
+++ b/unitTests/GistEntropyUtils/main.cpp
@@ -111,22 +111,26 @@ int main() {
   int grid_Nz = 3;
   Vec3 grid_origin(0, 0, 0);
   double grid_spacing = 0.5;
+  float w4 = 0.0;
+  float x4 = 0.0;
+  float y4 = 0.0;
+  float z4 = 0.0;
   assertClose(searchGridNearestNeighbors6D(
-    Vec3(1, 0, 0), 0, 1, 0, 0, grid_crd, grid_Q, grid_Nx, grid_Ny, grid_Nz, grid_origin, grid_spacing, 2, -1).first,
+    Vec3(1, 0, 0), 0, 1, 0, w4, x4, y4, z4, grid_crd, grid_Q, grid_Nx, grid_Ny, grid_Nz, grid_spacing, 2, -1).first,
     GIST_HUGE, "Wrong trans. dist. with empty grid.");
 
   // after adding a point in the same voxel, it should be found.
   grid_crd[9].push_back(0.6); grid_crd[9].push_back(0); grid_crd[9].push_back(0);
   grid_Q[9].push_back(1); grid_Q[9].push_back(0); grid_Q[9].push_back(0); grid_Q[9].push_back(0);
   std::pair<double, double>nbrs;
-  nbrs = searchGridNearestNeighbors6D(Vec3(1, 0, 0), 0, 1, 0, 0, grid_crd, grid_Q, grid_Nx, grid_Ny, grid_Nz, grid_origin, grid_spacing, 1, -1);
+  nbrs = searchGridNearestNeighbors6D(Vec3(1, 0, 0), 0, 1, 0, w4, x4, y4, z4, grid_crd, grid_Q, grid_Nx, grid_Ny, grid_Nz, grid_spacing, 1, -1);
   assertClose(nbrs.first, 0.16, "Wrong trans. dist. with empty grid.");
   assertClose(nbrs.second, PI_SQR + 0.16, "Wrong trans. dist. with empty grid.");
   
-  nbrs = searchGridNearestNeighbors6D(Vec3(1, 0, 0), 0, 1, 0, 0, grid_crd, grid_Q, grid_Nx, grid_Ny, grid_Nz, grid_origin, grid_spacing, 0, -1);
+  nbrs = searchGridNearestNeighbors6D(Vec3(1, 0, 0), 0, 1, 0, w4, x4, y4, z4, grid_crd, grid_Q, grid_Nx, grid_Ny, grid_Nz, grid_spacing, 0, -1);
   assertClose(nbrs.first, GIST_HUGE, "Does not omit outer shells in NN search.");
 
-  nbrs = searchGridNearestNeighbors6D(Vec3(-1, 0, 0), 0, 1, 0, 0, grid_crd, grid_Q, grid_Nx, grid_Ny, grid_Nz, grid_origin, grid_spacing, 10, -1);
+  nbrs = searchGridNearestNeighbors6D(Vec3(-1, 0, 0), 0, 1, 0, w4, x4, y4, z4, grid_crd, grid_Q, grid_Nx, grid_Ny, grid_Nz, grid_spacing, 10, -1);
   assertClose(nbrs.first, 1.6*1.6, "Does not work for out of bounds center.");
 
   // add another point one voxel higher, with different rotation;
@@ -134,20 +138,20 @@ int main() {
   grid_crd[18].push_back(1.1); grid_crd[18].push_back(0); grid_crd[18].push_back(0);
   grid_Q[18].push_back(0); grid_Q[18].push_back(1); grid_Q[18].push_back(0); grid_Q[18].push_back(0);
 
-  nbrs = searchGridNearestNeighbors6D(Vec3(0.1, 0, 0), 0, 1, 0, 0, grid_crd, grid_Q, grid_Nx, grid_Ny, grid_Nz, grid_origin, grid_spacing, 2, -1);
+  nbrs = searchGridNearestNeighbors6D(Vec3(0.1, 0, 0), 0, 1, 0, w4, x4, y4, z4, grid_crd, grid_Q, grid_Nx, grid_Ny, grid_Nz, grid_spacing, 2, -1);
   assertClose(nbrs.first, 0.5 * 0.5, "Does not find correct trans NN.");
   assertClose(nbrs.second, 1.0 * 1.0, "Does not find correct six NN with n_layers=2.");
 
-  nbrs = searchGridNearestNeighbors6D(Vec3(0.1, 0, 0), 0, 1, 0, 0, grid_crd, grid_Q, grid_Nx, grid_Ny, grid_Nz, grid_origin, grid_spacing, 1, -1);
+  nbrs = searchGridNearestNeighbors6D(Vec3(0.1, 0, 0), 0, 1, 0, w4, x4, y4, z4, grid_crd, grid_Q, grid_Nx, grid_Ny, grid_Nz, grid_spacing, 1, -1);
   assertClose(nbrs.first, 0.5*0.5, "Does not find correct trans NN.");
   assertClose(nbrs.second, 0.5*0.5 + PI_SQR, "Does not find correct six NN with n_layers=1.");
 
   // test that a molecule can be omitted in the central voxel.
-  nbrs = searchGridNearestNeighbors6D(Vec3(0.6, 0, 0), 0, 1, 0, 0, grid_crd, grid_Q, grid_Nx, grid_Ny, grid_Nz, grid_origin, grid_spacing, 1, 0);
+  nbrs = searchGridNearestNeighbors6D(Vec3(0.6, 0, 0), 0, 1, 0, w4, x4, y4, z4, grid_crd, grid_Q, grid_Nx, grid_Ny, grid_Nz, grid_spacing, 1, 0);
   assertClose(nbrs.first, 0.5*0.5, "Does not find correct trans NN.");
 
   // test that no molecule is always omitted in the central voxel.
-  nbrs = searchGridNearestNeighbors6D(Vec3(0.6, 0, 0), 0, 1, 0, 0, grid_crd, grid_Q, grid_Nx, grid_Ny, grid_Nz, grid_origin, grid_spacing, 1, -1);
+  nbrs = searchGridNearestNeighbors6D(Vec3(0.6, 0, 0), 0, 1, 0, w4, x4, y4, z4, grid_crd, grid_Q, grid_Nx, grid_Ny, grid_Nz, grid_spacing, 1, -1);
   assertClose(nbrs.first, 0.0, "Does not find correct trans NN.");
 
   // Test quaternion distance with slightly non-normalized quaternions

From c73aca9ac19971653de66260e8977b25d9951caa Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 27 Dec 2023 08:30:04 -0500
Subject: [PATCH 0217/1492] Add some notes

---
 unitTests/GistEntropyUtils/main.cpp | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/unitTests/GistEntropyUtils/main.cpp b/unitTests/GistEntropyUtils/main.cpp
index 809f6c6421..e327011e4d 100644
--- a/unitTests/GistEntropyUtils/main.cpp
+++ b/unitTests/GistEntropyUtils/main.cpp
@@ -119,7 +119,8 @@ int main() {
     Vec3(1, 0, 0), 0, 1, 0, w4, x4, y4, z4, grid_crd, grid_Q, grid_Nx, grid_Ny, grid_Nz, grid_spacing, 2, -1).first,
     GIST_HUGE, "Wrong trans. dist. with empty grid.");
 
-  // after adding a point in the same voxel, it should be found.
+  // after adding a point in the same voxel, it should be foundi.
+  // grid index 9 corresponds to 1 0 0
   grid_crd[9].push_back(0.6); grid_crd[9].push_back(0); grid_crd[9].push_back(0);
   grid_Q[9].push_back(1); grid_Q[9].push_back(0); grid_Q[9].push_back(0); grid_Q[9].push_back(0);
   std::pair<double, double>nbrs;
@@ -135,6 +136,7 @@ int main() {
 
   // add another point one voxel higher, with different rotation;
   // Depending on rotation, this might be the NN. But might not be found if n_layers is < 2;
+  // grid index 18 corresponds to 2 0 0
   grid_crd[18].push_back(1.1); grid_crd[18].push_back(0); grid_crd[18].push_back(0);
   grid_Q[18].push_back(0); grid_Q[18].push_back(1); grid_Q[18].push_back(0); grid_Q[18].push_back(0);
 

From b9a8c22c222d59a4c0fa3891c5cab785d253d195 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 31 Dec 2023 09:17:48 -0500
Subject: [PATCH 0218/1492] First attempt at creating a dedicated improper
 holder

---
 src/ParameterHolders.h | 105 ++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 103 insertions(+), 2 deletions(-)

diff --git a/src/ParameterHolders.h b/src/ParameterHolders.h
index cb1d77ae9b..255b8794b2 100644
--- a/src/ParameterHolders.h
+++ b/src/ParameterHolders.h
@@ -127,6 +127,7 @@ class DihedralParmHolder {
     typedef std::vector<Bpair> Bmap;
   public:
     DihedralParmHolder() {}
+    virtual ~DihedralParmHolder() {} ///< Virtual since inherited
     void clear()              { bpmap_.clear();        }
     size_t size()       const { return bpmap_.size();  }
     bool empty()        const { return bpmap_.empty(); }
@@ -236,7 +237,7 @@ class DihedralParmHolder {
     const_iterator begin() const { return bpmap_.begin(); }
     const_iterator end()   const { return bpmap_.end();   }
     /// \return Array of dihedral parameters matching given atom types.
-    DihedralParmArray FindParam(TypeNameHolder const& types, bool& found) const {
+    virtual DihedralParmArray FindParam(TypeNameHolder const& types, bool& found) const {
       found = true;
       for (const_iterator it = begin(); it != end(); ++it)
         if (it->first.Match_NoWC( types )) return it->second;
@@ -256,8 +257,108 @@ class DihedralParmHolder {
              (bpmap_.size() * sizeof(DihedralParmArray)) +
              sizeof(Bmap);
     }
+  protected:
+    NameType wc_; ///< Wildcard character
   private:
     Bmap bpmap_;
-    NameType wc_; ///< Wildcard character
+};
+// -----------------------------------------------------------------------------
+/// Specialized class for associating atom types with improper parameters.
+/** Impropers are a little tricky in that by convention the third atom is
+  * the central atom, and all other atoms can be in any order.
+  * The Amber convention is usually (but not always) to have the non-central
+  * improper atom types sorted alphabetically, with wildcards given
+  * precedence, but this is not always the case and does not always work.
+  * For example, using straight up backwards/forwards matching, the wildcard
+  * type X-X-CW-H4 will not match the given alphabetized type C*-H4-CW-NA.
+  * All combinations of A1, A2, and A4 should be checked.
+  */
+class ImproperParmHolder : private DihedralParmHolder {
+    /// Function for matching wildcards (WildCard Match)
+    static inline bool wcm(NameType const& t0, NameType const& t1, NameType const& wc) {
+      return (t0 == wc || t0 == t1);
+    }
+  public:
+    ImproperParmHolder() {}
+    /** Add (or update) a single improper parameter for given atom types. */
+    ParameterHolders::RetType
+    AddParm(TypeNameHolder const& types, DihedralParmType const& dp, bool allowUpdate) {
+      return DihedralParmHolder::AddParm( types, dp, allowUpdate );
+    }
+    /// \return Array of improper parameters matching given atom types.
+    DihedralParmArray FindParam(TypeNameHolder const& types, bool& found) const {
+      found = true;
+      // First, no wildcard
+      for (const_iterator it = begin(); it != end(); ++it) {
+        TypeNameHolder const& myTypes = it->first;
+        // Central (third) type must match
+        if (myTypes[2] == types[2]) {
+          // Try all permutations
+          if (myTypes[0] == types[0]) {
+            if (myTypes[1] == types[1] && myTypes[3] == types[3]) {
+              // 0 1 2 3
+              return it->second;
+            } else if (myTypes[1] == types[3] && myTypes[3] == types[1]) {
+              // 0 3 2 1
+              return it->second;
+            }
+          } else if (myTypes[0] == types[1]) {
+            if (myTypes[1] == types[0] && myTypes[3] == types[3]) {
+              // 1 0 2 3
+              return it->second;
+            } else if (myTypes[1] == types[3] && myTypes[3] == types[0]) {
+              // 1 3 2 0
+              return it->second;
+            }
+          } else if (myTypes[0] == types[3]) {
+            if (myTypes[1] == types[0] && myTypes[3] == types[1]) {
+              // 3 0 2 1
+              return it->second;
+            } else if (myTypes[1] == types[1] && myTypes[3] == types[0]) {
+              // 3 1 2 0
+              return it->second;
+            }
+          }
+        }
+      } // END loop over parameters
+      // Wildcard if present
+      if (wc_.len() > 0) {
+        for (const_iterator it = begin(); it != end(); ++it) {
+          TypeNameHolder const& myTypes = it->first;
+          // Central (third) type must match
+          if (wcm(myTypes[2], types[2], wc_)) {
+            // Try all permutations
+            if (wcm(myTypes[0], types[0], wc_)) {
+              if (wcm(myTypes[1], types[1], wc_) && wcm(myTypes[3], types[3], wc_)) {
+                // 0 1 2 3
+                return it->second;
+              } else if (wcm(myTypes[1], types[3], wc_) && wcm(myTypes[3], types[1], wc_)) {
+                // 0 3 2 1
+                return it->second;
+              }
+            } else if (wcm(myTypes[0], types[1], wc_)) {
+              if (wcm(myTypes[1], types[0], wc_) && wcm(myTypes[3], types[3], wc_)) {
+                // 1 0 2 3
+                return it->second;
+              } else if (wcm(myTypes[1], types[3], wc_) && wcm(myTypes[3], types[0], wc_)) {
+                // 1 3 2 0
+                return it->second;
+              }
+            } else if (wcm(myTypes[0], types[3], wc_)) {
+              if (wcm(myTypes[1], types[0], wc_) && wcm(myTypes[3], types[1], wc_)) {
+                // 3 0 2 1
+                return it->second;
+              } else if (wcm(myTypes[1], types[1], wc_) && wcm(myTypes[3], types[0], wc_)) {
+                // 3 1 2 0
+                return it->second;
+              }
+            }
+          }
+        } // END loop over parameters
+      } // END wildcard matches
+      found = false;
+      return DihedralParmArray();
+    } // END FindParam()
+  private:
 };
 #endif

From 22bb0dddf1056781edec1b62fc44e67081db2dfc Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 31 Dec 2023 09:22:54 -0500
Subject: [PATCH 0219/1492] Start ImproperParmHolder unit test

---
 unitTests/ImproperParmHolder/UnitTest.sh | 13 +++++++++
 unitTests/ImproperParmHolder/main.cpp    | 35 ++++++++++++++++++++++++
 2 files changed, 48 insertions(+)
 create mode 100755 unitTests/ImproperParmHolder/UnitTest.sh
 create mode 100644 unitTests/ImproperParmHolder/main.cpp

diff --git a/unitTests/ImproperParmHolder/UnitTest.sh b/unitTests/ImproperParmHolder/UnitTest.sh
new file mode 100755
index 0000000000..0be03f5a67
--- /dev/null
+++ b/unitTests/ImproperParmHolder/UnitTest.sh
@@ -0,0 +1,13 @@
+#!/bin/bash
+
+. ../UnitMaster.sh
+
+CleanFiles Makefile main.o NameType.o a.out CpptrajStdio.o
+
+UNITSOURCES='NameType.cpp CpptrajStdio.cpp'
+
+CreateMakefile
+
+RunMake "ImproperParmHolder class unit test."
+
+EndTest
diff --git a/unitTests/ImproperParmHolder/main.cpp b/unitTests/ImproperParmHolder/main.cpp
new file mode 100644
index 0000000000..964b4089c0
--- /dev/null
+++ b/unitTests/ImproperParmHolder/main.cpp
@@ -0,0 +1,35 @@
+// Unit test for ImproperParmHolder class
+#include <cstdio>
+#include <vector>
+#include <string>
+#include <algorithm>
+#include "ParameterHolders.h"
+
+static const int Err(const char* msg) {
+  fprintf(stderr, "Error: %s\n", msg);
+  return 1;
+}
+
+int main() {
+  ImproperParmHolder IP;
+
+  TypeNameHolder ip1(4);
+  ip1.AddName("O");
+  ip1.AddName("HO");
+  ip1.AddName("CT");
+  ip1.AddName("N");
+  //ip1.SortImproperByAlpha("X");
+
+  TypeNameHolder ip2(4);
+  ip2.AddName("O");
+  ip2.AddName("X");
+  ip2.AddName("CT");
+  ip2.AddName("X");
+  //ip2.SortImproperByAlpha("X");
+  
+  //printf("ip1 %s %s %s %s\n", *ip1[0], *ip1[1], *ip1[2], *ip1[3]);
+  //printf("ip2 %s %s %s %s\n", *ip2[0], *ip2[1], *ip2[2], *ip2[3]);
+
+
+  return 0;
+}

From 57a9746859d0d13bad993c6d3f752cfefb7ed8cb Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 31 Dec 2023 09:23:19 -0500
Subject: [PATCH 0220/1492] Fix comment

---
 unitTests/TypeNameHolder/main.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/unitTests/TypeNameHolder/main.cpp b/unitTests/TypeNameHolder/main.cpp
index 3b3f32609a..2b84eb824a 100644
--- a/unitTests/TypeNameHolder/main.cpp
+++ b/unitTests/TypeNameHolder/main.cpp
@@ -1,4 +1,4 @@
-// Unit test for NameType class
+// Unit test for TypeNameHolder class
 #include <cstdio>
 #include <vector>
 #include <string>

From 935e8f0eed462e1813de0fb63f774a975dc5a55c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 31 Dec 2023 09:30:57 -0500
Subject: [PATCH 0221/1492] Try an actual test, doesnt work yet

---
 unitTests/ImproperParmHolder/main.cpp | 21 +++++++++++++++++++--
 1 file changed, 19 insertions(+), 2 deletions(-)

diff --git a/unitTests/ImproperParmHolder/main.cpp b/unitTests/ImproperParmHolder/main.cpp
index 964b4089c0..816854939c 100644
--- a/unitTests/ImproperParmHolder/main.cpp
+++ b/unitTests/ImproperParmHolder/main.cpp
@@ -13,6 +13,12 @@ static const int Err(const char* msg) {
 int main() {
   ImproperParmHolder IP;
 
+  TypeNameHolder ip0(4);
+  ip0.AddName("N*");
+  ip0.AddName("CX");
+  ip0.AddName("CT");
+  ip0.AddName("HN");
+
   TypeNameHolder ip1(4);
   ip1.AddName("O");
   ip1.AddName("HO");
@@ -21,15 +27,26 @@ int main() {
   //ip1.SortImproperByAlpha("X");
 
   TypeNameHolder ip2(4);
-  ip2.AddName("O");
   ip2.AddName("X");
-  ip2.AddName("CT");
   ip2.AddName("X");
+  ip2.AddName("CT");
+  ip2.AddName("O");
+  ParameterHolders::RetType ret = IP.AddParm( ip2, DihedralParmType( 2.0, 1.0, 3.14159/2.0 ), false );
+  if (ret == ParameterHolders::ERR) return Err("Could not add improper parameter");
   //ip2.SortImproperByAlpha("X");
   
   //printf("ip1 %s %s %s %s\n", *ip1[0], *ip1[1], *ip1[2], *ip1[3]);
   //printf("ip2 %s %s %s %s\n", *ip2[0], *ip2[1], *ip2[2], *ip2[3]);
 
+  bool found;
+  DihedralParmArray impropers = IP.FindParam( ip1, found );
+  if (!found) {
+    return Err("Improper parameter search with wildcard match failed.");
+  }
+  impropers = IP.FindParam( ip0, found );
+  if (found) {
+    return Err("Improper parameter search found something when it should not have.");
+  }
 
   return 0;
 }

From 29a909a8bd2ff8a99f04c94c7a9bef702f105d58 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 31 Dec 2023 09:33:37 -0500
Subject: [PATCH 0222/1492] Set wildcard

---
 unitTests/ImproperParmHolder/main.cpp | 1 +
 1 file changed, 1 insertion(+)

diff --git a/unitTests/ImproperParmHolder/main.cpp b/unitTests/ImproperParmHolder/main.cpp
index 816854939c..8866d0b0ca 100644
--- a/unitTests/ImproperParmHolder/main.cpp
+++ b/unitTests/ImproperParmHolder/main.cpp
@@ -12,6 +12,7 @@ static const int Err(const char* msg) {
 
 int main() {
   ImproperParmHolder IP;
+  IP.SetWildcard('X');
 
   TypeNameHolder ip0(4);
   ip0.AddName("N*");

From 092c89c9bf6c71202c3493d6cd76d15a928dcfb9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 31 Dec 2023 09:34:03 -0500
Subject: [PATCH 0223/1492] Add function to set wc

---
 src/ParameterHolders.h | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/ParameterHolders.h b/src/ParameterHolders.h
index 255b8794b2..c967b61f6e 100644
--- a/src/ParameterHolders.h
+++ b/src/ParameterHolders.h
@@ -280,6 +280,8 @@ class ImproperParmHolder : private DihedralParmHolder {
     }
   public:
     ImproperParmHolder() {}
+    /** Set Wildcard char */
+    void SetWildcard(char wc) { DihedralParmHolder::SetWildcard(wc); }
     /** Add (or update) a single improper parameter for given atom types. */
     ParameterHolders::RetType
     AddParm(TypeNameHolder const& types, DihedralParmType const& dp, bool allowUpdate) {

From 7bb9a58caae834ffc253a60d37e06ffb13d566ee Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 1 Jan 2024 09:43:37 -0500
Subject: [PATCH 0224/1492] Add some more tests

---
 unitTests/ImproperParmHolder/main.cpp | 40 +++++++++++++++------------
 1 file changed, 23 insertions(+), 17 deletions(-)

diff --git a/unitTests/ImproperParmHolder/main.cpp b/unitTests/ImproperParmHolder/main.cpp
index 8866d0b0ca..056d4c2d36 100644
--- a/unitTests/ImproperParmHolder/main.cpp
+++ b/unitTests/ImproperParmHolder/main.cpp
@@ -1,8 +1,5 @@
 // Unit test for ImproperParmHolder class
 #include <cstdio>
-#include <vector>
-#include <string>
-#include <algorithm>
 #include "ParameterHolders.h"
 
 static const int Err(const char* msg) {
@@ -11,9 +8,6 @@ static const int Err(const char* msg) {
 }
 
 int main() {
-  ImproperParmHolder IP;
-  IP.SetWildcard('X');
-
   TypeNameHolder ip0(4);
   ip0.AddName("N*");
   ip0.AddName("CX");
@@ -27,27 +21,39 @@ int main() {
   ip1.AddName("N");
   //ip1.SortImproperByAlpha("X");
 
+  TypeNameHolder ip1a(4);
+  ip1a.AddName("N");
+  ip1a.AddName("O");
+  ip1a.AddName("CT");
+  ip1a.AddName("HO");
+
+  ImproperParmHolder IP0;
+  ParameterHolders::RetType ret = IP0.AddParm( ip1, DihedralParmType( 3.0, 1.0, 0.0 ), false );
+  if (ret == ParameterHolders::ERR) return Err("Could not add improper parameter");
+  bool found;
+  DihedralParmArray impropers = IP0.FindParam( ip1a, found );
+  if (!found) return Err("Could not find improper parameter (no wildcards).");
+
   TypeNameHolder ip2(4);
   ip2.AddName("X");
   ip2.AddName("X");
   ip2.AddName("CT");
   ip2.AddName("O");
-  ParameterHolders::RetType ret = IP.AddParm( ip2, DihedralParmType( 2.0, 1.0, 3.14159/2.0 ), false );
+
+  ImproperParmHolder IP;
+  ret = IP.AddParm( ip2, DihedralParmType( 2.0, 1.0, 3.14159/2.0 ), false );
   if (ret == ParameterHolders::ERR) return Err("Could not add improper parameter");
   //ip2.SortImproperByAlpha("X");
   
-  //printf("ip1 %s %s %s %s\n", *ip1[0], *ip1[1], *ip1[2], *ip1[3]);
-  //printf("ip2 %s %s %s %s\n", *ip2[0], *ip2[1], *ip2[2], *ip2[3]);
+  impropers = IP.FindParam( ip1, found);
+  if (found) return Err("Improper parameter search before wildcard added failed.");
+
+  IP.SetWildcard('X');
+  impropers = IP.FindParam( ip1, found );
+  if (!found) return Err("Improper parameter search with wildcard match failed.");
 
-  bool found;
-  DihedralParmArray impropers = IP.FindParam( ip1, found );
-  if (!found) {
-    return Err("Improper parameter search with wildcard match failed.");
-  }
   impropers = IP.FindParam( ip0, found );
-  if (found) {
-    return Err("Improper parameter search found something when it should not have.");
-  }
+  if (found) return Err("Improper parameter search found something when it should not have.");
 
   return 0;
 }

From f067732dee8f456c445bca0e6b162f55fd2a6269 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 1 Jan 2024 09:44:00 -0500
Subject: [PATCH 0225/1492] Fix FindParam, add some debug info

---
 src/ParameterHolders.h | 42 +++++++++++++++++-------------------------
 1 file changed, 17 insertions(+), 25 deletions(-)

diff --git a/src/ParameterHolders.h b/src/ParameterHolders.h
index c967b61f6e..017289c4e0 100644
--- a/src/ParameterHolders.h
+++ b/src/ParameterHolders.h
@@ -4,7 +4,7 @@
 #include <utility> // std::pair
 #include "TypeNameHolder.h"
 #include "ParameterTypes.h"
-//#incl ude "CpptrajStdio.h" // DEBUG
+//#inc lude "CpptrajStdio.h" // DEBUG
 
 namespace ParameterHolders {
   enum RetType { ADDED = 0, SAME, UPDATED, ERR };
@@ -289,37 +289,35 @@ class ImproperParmHolder : private DihedralParmHolder {
     }
     /// \return Array of improper parameters matching given atom types.
     DihedralParmArray FindParam(TypeNameHolder const& types, bool& found) const {
+      //mprintf("DEBUG: FindParam wc=%s Inco=%s-%s-%s-%s\n",*wc_, *(types[0]), *(types[1]),   *(types[2]),   *(types[3]));
       found = true;
       // First, no wildcard
       for (const_iterator it = begin(); it != end(); ++it) {
         TypeNameHolder const& myTypes = it->first;
         // Central (third) type must match
         if (myTypes[2] == types[2]) {
+          //mprintf("DEBUG: FindParam (improper) central atom match %s", *(types[2]));
+          //mprintf(" This=%s-%s-%s-%s", *(myTypes[0]), *(myTypes[1]), *(myTypes[2]), *(myTypes[3]));
+          //mprintf(" Inco=%s-%s-%s-%s\n", *(types[0]), *(types[1]),   *(types[2]),   *(types[3]));
           // Try all permutations
-          if (myTypes[0] == types[0]) {
-            if (myTypes[1] == types[1] && myTypes[3] == types[3]) {
+          if (       myTypes[0] == types[0] && myTypes[1] == types[1] && myTypes[3] == types[3]) {
               // 0 1 2 3
               return it->second;
-            } else if (myTypes[1] == types[3] && myTypes[3] == types[1]) {
+          } else if (myTypes[0] == types[0] && myTypes[1] == types[3] && myTypes[3] == types[1]) {
               // 0 3 2 1
               return it->second;
-            }
-          } else if (myTypes[0] == types[1]) {
-            if (myTypes[1] == types[0] && myTypes[3] == types[3]) {
+          } else if (myTypes[0] == types[1] && myTypes[1] == types[0] && myTypes[3] == types[3]) {
               // 1 0 2 3
               return it->second;
-            } else if (myTypes[1] == types[3] && myTypes[3] == types[0]) {
+          } else if (myTypes[0] == types[1] && myTypes[1] == types[3] && myTypes[3] == types[0]) {
               // 1 3 2 0
               return it->second;
-            }
-          } else if (myTypes[0] == types[3]) {
-            if (myTypes[1] == types[0] && myTypes[3] == types[1]) {
+          } else if (myTypes[0] == types[3] && myTypes[1] == types[0] && myTypes[3] == types[1]) {
               // 3 0 2 1
               return it->second;
-            } else if (myTypes[1] == types[1] && myTypes[3] == types[0]) {
+          } else if (myTypes[0] == types[3] && myTypes[1] == types[1] && myTypes[3] == types[0]) {
               // 3 1 2 0
               return it->second;
-            }
           }
         }
       } // END loop over parameters
@@ -330,30 +328,24 @@ class ImproperParmHolder : private DihedralParmHolder {
           // Central (third) type must match
           if (wcm(myTypes[2], types[2], wc_)) {
             // Try all permutations
-            if (wcm(myTypes[0], types[0], wc_)) {
-              if (wcm(myTypes[1], types[1], wc_) && wcm(myTypes[3], types[3], wc_)) {
+            if (       wcm(myTypes[0], types[0], wc_) && wcm(myTypes[1], types[1], wc_) && wcm(myTypes[3], types[3], wc_)) {
                 // 0 1 2 3
                 return it->second;
-              } else if (wcm(myTypes[1], types[3], wc_) && wcm(myTypes[3], types[1], wc_)) {
+            } else if (wcm(myTypes[0], types[0], wc_) && wcm(myTypes[1], types[3], wc_) && wcm(myTypes[3], types[1], wc_)) {
                 // 0 3 2 1
                 return it->second;
-              }
-            } else if (wcm(myTypes[0], types[1], wc_)) {
-              if (wcm(myTypes[1], types[0], wc_) && wcm(myTypes[3], types[3], wc_)) {
+            } else if (wcm(myTypes[0], types[1], wc_) && wcm(myTypes[1], types[0], wc_) && wcm(myTypes[3], types[3], wc_)) {
                 // 1 0 2 3
                 return it->second;
-              } else if (wcm(myTypes[1], types[3], wc_) && wcm(myTypes[3], types[0], wc_)) {
+            } else if (wcm(myTypes[0], types[1], wc_) && wcm(myTypes[1], types[3], wc_) && wcm(myTypes[3], types[0], wc_)) {
                 // 1 3 2 0
                 return it->second;
-              }
-            } else if (wcm(myTypes[0], types[3], wc_)) {
-              if (wcm(myTypes[1], types[0], wc_) && wcm(myTypes[3], types[1], wc_)) {
+            } else if (wcm(myTypes[0], types[3], wc_) && wcm(myTypes[1], types[0], wc_) && wcm(myTypes[3], types[1], wc_)) {
                 // 3 0 2 1
                 return it->second;
-              } else if (wcm(myTypes[1], types[1], wc_) && wcm(myTypes[3], types[0], wc_)) {
+            } else if (wcm(myTypes[0], types[3], wc_) && wcm(myTypes[1], types[1], wc_) && wcm(myTypes[3], types[0], wc_)) {
                 // 3 1 2 0
                 return it->second;
-              }
             }
           }
         } // END loop over parameters

From a6324d53bdb1c2da609dac70d5458a4922904b34 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 1 Jan 2024 09:46:53 -0500
Subject: [PATCH 0226/1492] Add but dont yet enable sort

---
 src/AmberParamFile.cpp | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index b09d0f35a8..317f85ee96 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -251,6 +251,7 @@ const
   types.AddName( symbols[1] );
   types.AddName( symbols[2] );
   types.AddName( symbols[3] );
+  //types.SortImproperByAlpha("X"); // FIXME wildcard should be a static var
   ParameterHolders::RetType ret =
     prm.IP().AddParm(types, DihedralParmType(PK, PN, PHASE*Constants::DEGRAD), true);
   if (ret == ParameterHolders::UPDATED)

From 818069b7b11bb21d6499eeb04fd96bd5ad4f2d30 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 1 Jan 2024 14:42:16 -0500
Subject: [PATCH 0227/1492] Use ImproperParmHolder

---
 src/ParameterHolders.h | 16 ++++++++++++++++
 src/ParameterSet.cpp   |  8 +++++---
 src/ParameterSet.h     |  6 +++---
 src/Parm_CharmmPsf.cpp |  9 +++++++--
 src/Topology.cpp       | 26 ++++++++++++++++----------
 src/Topology.h         |  8 ++++----
 6 files changed, 51 insertions(+), 22 deletions(-)

diff --git a/src/ParameterHolders.h b/src/ParameterHolders.h
index 017289c4e0..0ceba700ba 100644
--- a/src/ParameterHolders.h
+++ b/src/ParameterHolders.h
@@ -280,6 +280,15 @@ class ImproperParmHolder : private DihedralParmHolder {
     }
   public:
     ImproperParmHolder() {}
+    /// \return Number of improper parameter sets
+    size_t size()       const { return DihedralParmHolder::size();  }
+    /// \return True if no parameters
+    bool empty()        const { return DihedralParmHolder::empty(); }
+
+    typedef typename DihedralParmHolder::const_iterator const_iterator;
+    const_iterator begin() const { return DihedralParmHolder::begin(); }
+    const_iterator end()   const { return DihedralParmHolder::end();   }
+
     /** Set Wildcard char */
     void SetWildcard(char wc) { DihedralParmHolder::SetWildcard(wc); }
     /** Add (or update) a single improper parameter for given atom types. */
@@ -287,6 +296,11 @@ class ImproperParmHolder : private DihedralParmHolder {
     AddParm(TypeNameHolder const& types, DihedralParmType const& dp, bool allowUpdate) {
       return DihedralParmHolder::AddParm( types, dp, allowUpdate );
     }
+    /** This version takes an array of dihedral parameters. */
+    ParameterHolders::RetType
+    AddParm(TypeNameHolder const& types, DihedralParmArray const& dpa, bool allowUpdate) {
+      return DihedralParmHolder::AddParm( types, dpa, allowUpdate );
+    }
     /// \return Array of improper parameters matching given atom types.
     DihedralParmArray FindParam(TypeNameHolder const& types, bool& found) const {
       //mprintf("DEBUG: FindParam wc=%s Inco=%s-%s-%s-%s\n",*wc_, *(types[0]), *(types[1]),   *(types[2]),   *(types[3]));
@@ -353,6 +367,8 @@ class ImproperParmHolder : private DihedralParmHolder {
       found = false;
       return DihedralParmArray();
     } // END FindParam()
+    /// \return size in memory in bytes
+    size_t DataSize() const { return DihedralParmHolder::DataSize(); }
   private:
 };
 #endif
diff --git a/src/ParameterSet.cpp b/src/ParameterSet.cpp
index ad071ec51c..4cb1039c8f 100644
--- a/src/ParameterSet.cpp
+++ b/src/ParameterSet.cpp
@@ -98,8 +98,10 @@ void ParameterSet::Print(CpptrajFile& Out) const {
   if (!impParm_.empty()) {
     Out.Printf("Improper parameters:\n");
     Out.Printf("\t%6s %6s %6s %6s %12s %12s %12s\n", "Type1", "Type2", "Type3", "Type4", "Pk", "Pn", "Phase");
-    for (ParmHolder<DihedralParmType>::const_iterator bp = impParm_.begin(); bp != impParm_.end(); ++bp)
-      Out.Printf("\t%6s %6s %6s %6s : %12.4f %12.4f %12.4f\n", *(bp->first[0]), *(bp->first[1]), *(bp->first[2]), *(bp->first[3]), bp->second.Pk(), bp->second.Pn(), bp->second.Phase()*Constants::RADDEG);
+    for (ImproperParmHolder::const_iterator it0 = impParm_.begin(); it0 != impParm_.end(); ++it0)
+      for (DihedralParmArray::const_iterator it1 = it0->second.begin();
+                                             it1 != it0->second.end(); ++it1)
+        Out.Printf("\t%6s %6s %6s %6s : %12.4f %12.4f %12.4f\n", *(it0->first[0]), *(it0->first[1]), *(it0->first[2]), *(it0->first[3]), it1->Pk(), it1->Pn(), it1->Phase()*Constants::RADDEG);
   }
   if (!hydrophilicAtomTypes_.empty()) {
     Out.Printf("Hydrophilic atom types:");
@@ -126,7 +128,7 @@ int ParameterSet::UpdateParamSet(ParameterSet const& set1, UpdateCount& uc, int
   // Dihedral/improper parameters
   uc.nDihedralsUpdated_ = UpdateParameters< DihedralParmHolder >(set0.DP(), set1.DP(), "dihedral", verbose);
   // Improper parameters
-  uc.nImpropersUpdated_ = UpdateParameters< ParmHolder<DihedralParmType> >(set0.IP(), set1.IP(), "improper", verbose);
+  uc.nImpropersUpdated_ = UpdateParameters< ImproperParmHolder >(set0.IP(), set1.IP(), "improper", verbose);
   // Urey-Bradley parameters
   uc.nUreyBradleyUpdated_ = UpdateParameters< ParmHolder<BondParmType> >(set0.UB(), set1.UB(), "Urey-Bradley", verbose);
   // Atom types
diff --git a/src/ParameterSet.h b/src/ParameterSet.h
index 072e4c598f..422ce2b345 100644
--- a/src/ParameterSet.h
+++ b/src/ParameterSet.h
@@ -15,7 +15,7 @@ class ParameterSet {
     ParmHolder<BondParmType>& BP()     { return bondParm_;  }
     ParmHolder<AngleParmType>& AP()    { return angleParm_; }
     ParmHolder<BondParmType>& UB()     { return ubParm_;    }
-    ParmHolder<DihedralParmType>& IP() { return impParm_;   }
+    ImproperParmHolder& IP()           { return impParm_;   }
     DihedralParmHolder& DP()           { return dihParm_;   }
     ParmHolder<HB_ParmType>& HB()      { return HBparm_;    }
 
@@ -28,7 +28,7 @@ class ParameterSet {
     ParmHolder<BondParmType> const& BP()     const { return bondParm_;  }
     ParmHolder<AngleParmType> const& AP()    const { return angleParm_; }
     ParmHolder<BondParmType> const& UB()     const { return ubParm_;    }
-    ParmHolder<DihedralParmType> const& IP() const { return impParm_;   }
+    ImproperParmHolder const& IP()           const { return impParm_;   }
     DihedralParmHolder const& DP()           const { return dihParm_;   }
     ParmHolder<HB_ParmType> const& HB()      const { return HBparm_;    }
     std::string const& NbParamName()         const { return NBname_;    }
@@ -83,7 +83,7 @@ class ParameterSet {
     ParmHolder<BondParmType> bondParm_;    ///< Hooke's law bond potential parameters
     ParmHolder<AngleParmType> angleParm_;  ///< Hooke's law angle potential parameters
     ParmHolder<BondParmType> ubParm_;      ///< Urey-Bradley parameters
-    ParmHolder<DihedralParmType> impParm_; ///< Improper dihedral parameters
+    ImproperParmHolder impParm_;           ///< Improper dihedral parameters
     DihedralParmHolder dihParm_;           ///< Cosine-series dihedral parameters
     ParmHolder<HB_ParmType> HBparm_;       ///< LJ 10-12 A-B parameters for hydrogen bonds
     NsetType hydrophilicAtomTypes_;        ///< Hold names of hydrophilic atom types
diff --git a/src/Parm_CharmmPsf.cpp b/src/Parm_CharmmPsf.cpp
index 0f59b32efb..b5c7702b15 100644
--- a/src/Parm_CharmmPsf.cpp
+++ b/src/Parm_CharmmPsf.cpp
@@ -113,8 +113,13 @@ int Parm_CharmmPsf::ReadDihedrals(BufferedLine& infile, int ndihedral, const cha
             }
           } else {
             // Charmm Improper. Expect only one paramter per type.
-            DihedralParmType ipt = params_.IP().FindParam( types, found );
-            parmOut.AddCharmmImproper( dih, ipt );
+            DihedralParmArray ipa = params_.IP().FindParam( types, found );
+            if (found) {
+              if (ipa.size() > 1)
+                mprintf("Warning: %zu improper parameters found for types %s - %s - %s - %s, expected only one."
+                        "Warning: Only using first parameter.\n", ipa.size(), *(types[0]), *(types[1]), *(types[2]), *(types[3]));
+              parmOut.AddCharmmImproper( dih, ipa.front() );
+            }
           } 
           if (!found) {
             mprintf("Warning: Parameters not found for %s %s - %s - %s - %s\n", typestr, parmOut.AtomMaskName(a1).c_str(), parmOut.AtomMaskName(a2).c_str(), parmOut.AtomMaskName(a3).c_str(), parmOut.AtomMaskName(a4).c_str());
diff --git a/src/Topology.cpp b/src/Topology.cpp
index 24a720c61b..af29e46fa3 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2119,7 +2119,7 @@ static inline void GetAngleParams(ParmHolder<AngleParmType>& AP, std::vector<Ato
 }
 
 // GetImproperParams()
-static inline void GetImproperParams(ParmHolder<DihedralParmType>& IP, std::vector<Atom> const& atoms, DihedralArray const& imp, DihedralParmArray const& ipa) {
+static inline void GetImproperParams(ImproperParmHolder& IP, std::vector<Atom> const& atoms, DihedralArray const& imp, DihedralParmArray const& ipa) {
   for (DihedralArray::const_iterator b = imp.begin(); b != imp.end(); ++b)
   {
     if (b->Idx() != -1) {
@@ -2136,7 +2136,7 @@ static inline void GetImproperParams(ParmHolder<DihedralParmType>& IP, std::vect
 }
 
 // GetDihedralParams()
-static inline void GetDihedralParams(DihedralParmHolder& DP, ParmHolder<DihedralParmType>& IP, std::vector<Atom> const& atoms, DihedralArray const& dih, DihedralParmArray const& dpa) {
+static inline void GetDihedralParams(DihedralParmHolder& DP, ImproperParmHolder& IP, std::vector<Atom> const& atoms, DihedralArray const& dih, DihedralParmArray const& dpa) {
   for (DihedralArray::const_iterator b = dih.begin(); b != dih.end(); ++b)
   {
     if (b->Idx() != -1) {
@@ -2696,7 +2696,7 @@ void Topology::AssignAngleParams(ParmHolder<AngleParmType> const& newAngleParams
 }
 
 /** Set parameters for improper dihedrals in given improper dihedral array. */
-void Topology::AssignImproperParm(ParmHolder<DihedralParmType> const& newImproperParams,
+void Topology::AssignImproperParm(ImproperParmHolder const& newImproperParams,
                                   DihedralArray& impropers)
 {
   for (DihedralArray::iterator imp = impropers.begin(); imp != impropers.end(); ++imp) {
@@ -2708,7 +2708,7 @@ void Topology::AssignImproperParm(ParmHolder<DihedralParmType> const& newImprope
     bool found;
     // See if parameter is present.
     int idx = -1;
-    DihedralParmType ip = newImproperParams.FindParam( types, found );
+    DihedralParmArray ipa = newImproperParams.FindParam( types, found );
     if (!found) {
       mprintf("Warning: Parameter not found for improper %s-%s-%s-%s (%s-%s-%s-%s)\n",
               TruncResAtomNameNum(imp->A1()).c_str(),
@@ -2717,14 +2717,17 @@ void Topology::AssignImproperParm(ParmHolder<DihedralParmType> const& newImprope
               TruncResAtomNameNum(imp->A4()).c_str(),
               *types[0], *types[1], *types[3], *types[4]);
     } else {
-      idx = addTorsionParm( chamber_.SetImproperParm(), ip );
+      if (ipa.size() > 1)
+        mprintf("Warning: %zu improper parameters found for types %s - %s - %s - %s, expected only one."
+                        "Warning: Only using first parameter.\n", ipa.size(), *(types[0]), *(types[1]), *(types[2]), *(types[3]));
+      idx = addTorsionParm( chamber_.SetImproperParm(), ipa.front() );
     }
     imp->SetIdx( idx );
   }
 }
 
 /** Replace any current improper parameters with given improper parameters. */
-void Topology::AssignImproperParams(ParmHolder<DihedralParmType> const& newImproperParams) {
+void Topology::AssignImproperParams(ImproperParmHolder const& newImproperParams) {
   chamber_.SetImproperParm().clear();
   AssignImproperParm( newImproperParams, chamber_.SetImpropers() );
 }
@@ -2734,7 +2737,7 @@ void Topology::AssignImproperParams(ParmHolder<DihedralParmType> const& newImpro
   * this function in order for improper and 1-4 detection to work.
   */
 void Topology::AssignDihedralParm(DihedralParmHolder const& newDihedralParams,
-                                  ParmHolder<DihedralParmType> const& newImproperParams,
+                                  ImproperParmHolder const& newImproperParams,
                                   DihedralArray& dihedralsIn)
 {
   // Dihedrals can be a bit of a pain since there can be multiple
@@ -2789,7 +2792,7 @@ void Topology::AssignDihedralParm(DihedralParmHolder const& newDihedralParams,
     bool found;
     if (isImproper) {
       // ----- This is actually an improper dihedral. ----------------
-      DihedralParmType ip = newImproperParams.FindParam( types, found );
+      DihedralParmArray ipa = newImproperParams.FindParam( types, found );
       int idx = -1;
       if (!found) {
         mprintf("Warning: Improper parameters not found for improper dihedral %s-%s-%s-%s (%s-%s-%s-%s)\n",
@@ -2799,7 +2802,10 @@ void Topology::AssignDihedralParm(DihedralParmHolder const& newDihedralParams,
                 TruncResAtomNameNum(dih->A4()).c_str(),
                 *types[0], *types[1], *types[2], *types[3]);
       } else {
-        idx = addTorsionParm( dihedralparm_, ip );
+        if (ipa.size() > 1)
+          mprintf("Warning: %zu improper parameters found for types %s - %s - %s - %s, expected only one."
+                  "Warning: Only using first parameter.\n", ipa.size(), *(types[0]), *(types[1]), *(types[2]), *(types[3]));
+        idx = addTorsionParm( dihedralparm_, ipa.front() );
       }
       DihedralType mydih = *dih;
       mydih.SetIdx( idx );
@@ -2896,7 +2902,7 @@ void Topology::AssignDihedralParm(DihedralParmHolder const& newDihedralParams,
 }
 
 /** Replace any current dihedral parameters with given dihedral parameters. */
-void Topology::AssignDihedralParams(DihedralParmHolder const& newDihedralParams, ParmHolder<DihedralParmType> const& newImproperParams) {
+void Topology::AssignDihedralParams(DihedralParmHolder const& newDihedralParams, ImproperParmHolder const& newImproperParams) {
   dihedralparm_.clear();
   AssignDihedralParm( newDihedralParams, newImproperParams, dihedrals_ );
   AssignDihedralParm( newDihedralParams, newImproperParams, dihedralsh_ );
diff --git a/src/Topology.h b/src/Topology.h
index 354fe9509e..8c049510a1 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -139,8 +139,8 @@ class Topology {
     void AddDihedral(int i, int j, int k, int l) { AddDihedral(DihedralType(i,j,k,l,-1), -1); }
     void AddDihedral(DihedralType const&, bool);
     void AddDihedral(DihedralType const&, DihedralParmType const&);
-    void AssignImproperParams(ParmHolder<DihedralParmType> const&);
-    void AssignDihedralParams(DihedralParmHolder const&, ParmHolder<DihedralParmType> const&);
+    void AssignImproperParams(ImproperParmHolder const&);
+    void AssignDihedralParams(DihedralParmHolder const&, ImproperParmHolder const&);
     // ----- CMAP-specific routines --------------
     bool                     HasCmap()      const { return !cmapGrid_.empty(); }
     CmapGridArray     const& CmapGrid()     const { return cmapGrid_;     }
@@ -300,8 +300,8 @@ class Topology {
     void AssignAtomTypeParm(ParmHolder<AtomType> const&);
     void AssignBondParm(ParmHolder<BondParmType> const&, BondArray&, BondParmArray&, const char*) const;
     void AssignAngleParm(ParmHolder<AngleParmType> const&, AngleArray&);
-    void AssignImproperParm(ParmHolder<DihedralParmType> const&, DihedralArray&);
-    void AssignDihedralParm(DihedralParmHolder const&, ParmHolder<DihedralParmType> const&, DihedralArray&);
+    void AssignImproperParm(ImproperParmHolder const&, DihedralArray&);
+    void AssignDihedralParm(DihedralParmHolder const&, ImproperParmHolder const&, DihedralArray&);
 
     static const NonbondType LJ_EMPTY;
     std::vector<Atom> atoms_;

From af62e6314ab56dac6356fc1055148e374d47ad91 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 1 Jan 2024 20:56:43 -0500
Subject: [PATCH 0228/1492] Save atom ordering

---
 src/ParameterHolders.h | 31 ++++++++++++++++++++++++++++---
 src/Topology.cpp       | 20 ++++++++++++++++++--
 2 files changed, 46 insertions(+), 5 deletions(-)

diff --git a/src/ParameterHolders.h b/src/ParameterHolders.h
index 0ceba700ba..898cc7a879 100644
--- a/src/ParameterHolders.h
+++ b/src/ParameterHolders.h
@@ -237,7 +237,7 @@ class DihedralParmHolder {
     const_iterator begin() const { return bpmap_.begin(); }
     const_iterator end()   const { return bpmap_.end();   }
     /// \return Array of dihedral parameters matching given atom types.
-    virtual DihedralParmArray FindParam(TypeNameHolder const& types, bool& found) const {
+    DihedralParmArray FindParam(TypeNameHolder const& types, bool& found) const {
       found = true;
       for (const_iterator it = begin(); it != end(); ++it)
         if (it->first.Match_NoWC( types )) return it->second;
@@ -279,12 +279,20 @@ class ImproperParmHolder : private DihedralParmHolder {
       return (t0 == wc || t0 == t1);
     }
   public:
+    /// Denote returned parameter atom type order
+    enum OrderType { O_013,
+                     O_031,
+                     O_103,
+                     O_130,
+                     O_301,
+                     O_310 };
     ImproperParmHolder() {}
     /// \return Number of improper parameter sets
     size_t size()       const { return DihedralParmHolder::size();  }
     /// \return True if no parameters
     bool empty()        const { return DihedralParmHolder::empty(); }
-
+    /// \return ordering of last type
+    //OrderType LastOrder() const { return lastOrder_; }
     typedef typename DihedralParmHolder::const_iterator const_iterator;
     const_iterator begin() const { return DihedralParmHolder::begin(); }
     const_iterator end()   const { return DihedralParmHolder::end();   }
@@ -301,8 +309,12 @@ class ImproperParmHolder : private DihedralParmHolder {
     AddParm(TypeNameHolder const& types, DihedralParmArray const& dpa, bool allowUpdate) {
       return DihedralParmHolder::AddParm( types, dpa, allowUpdate );
     }
-    /// \return Array of improper parameters matching given atom types.
     DihedralParmArray FindParam(TypeNameHolder const& types, bool& found) const {
+      OrderType lastOrder;
+      return FindParam(types, found, lastOrder);
+    }
+    /// \return Array of improper parameters matching given atom types.
+    DihedralParmArray FindParam(TypeNameHolder const& types, bool& found, OrderType& lastOrder_) const {
       //mprintf("DEBUG: FindParam wc=%s Inco=%s-%s-%s-%s\n",*wc_, *(types[0]), *(types[1]),   *(types[2]),   *(types[3]));
       found = true;
       // First, no wildcard
@@ -316,21 +328,27 @@ class ImproperParmHolder : private DihedralParmHolder {
           // Try all permutations
           if (       myTypes[0] == types[0] && myTypes[1] == types[1] && myTypes[3] == types[3]) {
               // 0 1 2 3
+              lastOrder_ = O_013;
               return it->second;
           } else if (myTypes[0] == types[0] && myTypes[1] == types[3] && myTypes[3] == types[1]) {
               // 0 3 2 1
+              lastOrder_ = O_031;
               return it->second;
           } else if (myTypes[0] == types[1] && myTypes[1] == types[0] && myTypes[3] == types[3]) {
               // 1 0 2 3
+              lastOrder_ = O_103;
               return it->second;
           } else if (myTypes[0] == types[1] && myTypes[1] == types[3] && myTypes[3] == types[0]) {
               // 1 3 2 0
+              lastOrder_ = O_130;
               return it->second;
           } else if (myTypes[0] == types[3] && myTypes[1] == types[0] && myTypes[3] == types[1]) {
               // 3 0 2 1
+              lastOrder_ = O_301;
               return it->second;
           } else if (myTypes[0] == types[3] && myTypes[1] == types[1] && myTypes[3] == types[0]) {
               // 3 1 2 0
+              lastOrder_ = O_310;
               return it->second;
           }
         }
@@ -344,21 +362,27 @@ class ImproperParmHolder : private DihedralParmHolder {
             // Try all permutations
             if (       wcm(myTypes[0], types[0], wc_) && wcm(myTypes[1], types[1], wc_) && wcm(myTypes[3], types[3], wc_)) {
                 // 0 1 2 3
+                lastOrder_ = O_013;
                 return it->second;
             } else if (wcm(myTypes[0], types[0], wc_) && wcm(myTypes[1], types[3], wc_) && wcm(myTypes[3], types[1], wc_)) {
                 // 0 3 2 1
+                lastOrder_ = O_031;
                 return it->second;
             } else if (wcm(myTypes[0], types[1], wc_) && wcm(myTypes[1], types[0], wc_) && wcm(myTypes[3], types[3], wc_)) {
                 // 1 0 2 3
+                lastOrder_ = O_103;
                 return it->second;
             } else if (wcm(myTypes[0], types[1], wc_) && wcm(myTypes[1], types[3], wc_) && wcm(myTypes[3], types[0], wc_)) {
                 // 1 3 2 0
+                lastOrder_ = O_130;
                 return it->second;
             } else if (wcm(myTypes[0], types[3], wc_) && wcm(myTypes[1], types[0], wc_) && wcm(myTypes[3], types[1], wc_)) {
                 // 3 0 2 1
+                lastOrder_ = O_301;
                 return it->second;
             } else if (wcm(myTypes[0], types[3], wc_) && wcm(myTypes[1], types[1], wc_) && wcm(myTypes[3], types[0], wc_)) {
                 // 3 1 2 0
+                lastOrder_ = O_310;
                 return it->second;
             }
           }
@@ -370,5 +394,6 @@ class ImproperParmHolder : private DihedralParmHolder {
     /// \return size in memory in bytes
     size_t DataSize() const { return DihedralParmHolder::DataSize(); }
   private:
+    //OrderType lastOrder_; ///< Atom ordering of the last returned parameter
 };
 #endif
diff --git a/src/Topology.cpp b/src/Topology.cpp
index af29e46fa3..f42ff00ea6 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2695,6 +2695,18 @@ void Topology::AssignAngleParams(ParmHolder<AngleParmType> const& newAngleParams
   AssignAngleParm( newAngleParams, anglesh_ );
 }
 
+/** Reorder improper atoms so that they match the parameter. */
+static void match_improper_to_parm(DihedralType& imp, TypeNameHolder const& types, ImproperParmHolder::OrderType order)
+{
+  mprintf("DEBUG: Improper types : %4s %4s %4s %4s (order %i)\n", *(types[0]), *(types[1]), *(types[2]), *(types[3]),
+          //*(atoms_[imp->A1()].Type()),
+          //*(atoms_[imp->A2()].Type()),
+          //*(atoms_[imp->A3()].Type()),
+          //*(atoms_[imp->A4()].Type()),
+          (int)order);
+  //mprintf("DEBUG: Parm types     : %4s %4s %4s %4s\n", 
+}
+
 /** Set parameters for improper dihedrals in given improper dihedral array. */
 void Topology::AssignImproperParm(ImproperParmHolder const& newImproperParams,
                                   DihedralArray& impropers)
@@ -2708,7 +2720,8 @@ void Topology::AssignImproperParm(ImproperParmHolder const& newImproperParams,
     bool found;
     // See if parameter is present.
     int idx = -1;
-    DihedralParmArray ipa = newImproperParams.FindParam( types, found );
+    ImproperParmHolder::OrderType lastOrder;
+    DihedralParmArray ipa = newImproperParams.FindParam( types, found, lastOrder );
     if (!found) {
       mprintf("Warning: Parameter not found for improper %s-%s-%s-%s (%s-%s-%s-%s)\n",
               TruncResAtomNameNum(imp->A1()).c_str(),
@@ -2720,6 +2733,7 @@ void Topology::AssignImproperParm(ImproperParmHolder const& newImproperParams,
       if (ipa.size() > 1)
         mprintf("Warning: %zu improper parameters found for types %s - %s - %s - %s, expected only one."
                         "Warning: Only using first parameter.\n", ipa.size(), *(types[0]), *(types[1]), *(types[2]), *(types[3]));
+      match_improper_to_parm( *imp, types, lastOrder );
       idx = addTorsionParm( chamber_.SetImproperParm(), ipa.front() );
     }
     imp->SetIdx( idx );
@@ -2792,7 +2806,8 @@ void Topology::AssignDihedralParm(DihedralParmHolder const& newDihedralParams,
     bool found;
     if (isImproper) {
       // ----- This is actually an improper dihedral. ----------------
-      DihedralParmArray ipa = newImproperParams.FindParam( types, found );
+      ImproperParmHolder::OrderType lastOrder;
+      DihedralParmArray ipa = newImproperParams.FindParam( types, found, lastOrder );
       int idx = -1;
       if (!found) {
         mprintf("Warning: Improper parameters not found for improper dihedral %s-%s-%s-%s (%s-%s-%s-%s)\n",
@@ -2805,6 +2820,7 @@ void Topology::AssignDihedralParm(DihedralParmHolder const& newDihedralParams,
         if (ipa.size() > 1)
           mprintf("Warning: %zu improper parameters found for types %s - %s - %s - %s, expected only one."
                   "Warning: Only using first parameter.\n", ipa.size(), *(types[0]), *(types[1]), *(types[2]), *(types[3]));
+        match_improper_to_parm( *dih, types, lastOrder );
         idx = addTorsionParm( dihedralparm_, ipa.front() );
       }
       DihedralType mydih = *dih;

From 4559bf94c4cb5eebd086d34d1643a0d85b6d5ad7 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 2 Jan 2024 11:57:57 -0500
Subject: [PATCH 0229/1492] Add function for reordering improper and a test

---
 src/ParameterHolders.h                | 13 +++++++++++
 src/ParameterTypes.h                  |  4 ++++
 unitTests/ImproperParmHolder/main.cpp | 31 +++++++++++++++++++++++++++
 3 files changed, 48 insertions(+)

diff --git a/src/ParameterHolders.h b/src/ParameterHolders.h
index 898cc7a879..610b1de79d 100644
--- a/src/ParameterHolders.h
+++ b/src/ParameterHolders.h
@@ -278,6 +278,8 @@ class ImproperParmHolder : private DihedralParmHolder {
     static inline bool wcm(NameType const& t0, NameType const& t1, NameType const& wc) {
       return (t0 == wc || t0 == t1);
     }
+    /// Function for swapping integers
+    static inline void swp(int& i1, int& i2) { int tmp = i1; i1 = i2; i2 = tmp; }
   public:
     /// Denote returned parameter atom type order
     enum OrderType { O_013,
@@ -313,6 +315,17 @@ class ImproperParmHolder : private DihedralParmHolder {
       OrderType lastOrder;
       return FindParam(types, found, lastOrder);
     }
+    /// Remap the given improper according to the desired order
+    static void ReorderImproper(DihedralType& imp, OrderType order) {
+      switch (order) {
+        case O_013 : break;
+        case O_031 : swp( imp.ChangeA2(), imp.ChangeA4() ); break;
+        case O_103 : swp( imp.ChangeA1(), imp.ChangeA2() ); break;
+        case O_130 : swp( imp.ChangeA1(), imp.ChangeA4() ); swp( imp.ChangeA1(), imp.ChangeA2() ); break;
+        case O_301 : swp( imp.ChangeA2(), imp.ChangeA4() ); swp( imp.ChangeA1(), imp.ChangeA2() ); break;
+        case O_310 : swp( imp.ChangeA1(), imp.ChangeA4() ); break;
+      }
+    }
     /// \return Array of improper parameters matching given atom types.
     DihedralParmArray FindParam(TypeNameHolder const& types, bool& found, OrderType& lastOrder_) const {
       //mprintf("DEBUG: FindParam wc=%s Inco=%s-%s-%s-%s\n",*wc_, *(types[0]), *(types[1]),   *(types[2]),   *(types[3]));
diff --git a/src/ParameterTypes.h b/src/ParameterTypes.h
index 9098f561a4..99dbd05568 100644
--- a/src/ParameterTypes.h
+++ b/src/ParameterTypes.h
@@ -233,6 +233,10 @@ class DihedralType {
     void SetIdx(int i)        { idx_ = i;      }
     void SetSkip14(bool b)    { skip14_ = b;   }
     void SetImproper(bool b)  { improper_ = b; }
+    int& ChangeA1() { return a1_; }
+    int& ChangeA2() { return a2_; }
+    int& ChangeA3() { return a3_; }
+    int& ChangeA4() { return a4_; }
     /// \return type based on skip 1-4 (end) and improper status
     inline Dtype Type() const {
       if (skip14_ && improper_) return BOTH;
diff --git a/unitTests/ImproperParmHolder/main.cpp b/unitTests/ImproperParmHolder/main.cpp
index 056d4c2d36..ef6bd4fa28 100644
--- a/unitTests/ImproperParmHolder/main.cpp
+++ b/unitTests/ImproperParmHolder/main.cpp
@@ -7,6 +7,10 @@ static const int Err(const char* msg) {
   return 1;
 }
 
+/*static void printImp(DihedralType const& imp) {
+  printf("%i %i %i %i\n", imp.A1(), imp.A2(), imp.A3(), imp.A4());
+}*/
+
 int main() {
   TypeNameHolder ip0(4);
   ip0.AddName("N*");
@@ -55,5 +59,32 @@ int main() {
   impropers = IP.FindParam( ip0, found );
   if (found) return Err("Improper parameter search found something when it should not have.");
 
+  DihedralType imp( 0, 1, 2, 3, -1 );
+  ImproperParmHolder::ReorderImproper( imp, ImproperParmHolder::O_013 );
+  if (imp.A1() != 0 || imp.A2() != 1 || imp.A3() != 2 || imp.A4() != 3)
+    return Err("Improper reorder failed (O_013).");
+  ImproperParmHolder::ReorderImproper( imp, ImproperParmHolder::O_031 );
+  if (imp.A1() != 0 || imp.A2() != 3 || imp.A3() != 2 || imp.A4() != 1)
+    return Err("Improper reorder failed (O_031).");
+  imp = DihedralType( 0, 1, 2, 3, -1 );
+  ImproperParmHolder::ReorderImproper( imp, ImproperParmHolder::O_103 );
+  if (imp.A1() != 1 || imp.A2() != 0 || imp.A3() != 2 || imp.A4() != 3)
+    return Err("Improper reorder failed (O_103).");
+  imp = DihedralType( 0, 1, 2, 3, -1 );
+  ImproperParmHolder::ReorderImproper( imp, ImproperParmHolder::O_130 );
+  //printImp(imp);
+  if (imp.A1() != 1 || imp.A2() != 3 || imp.A3() != 2 || imp.A4() != 0)
+    return Err("Improper reorder failed (O_130).");
+  imp = DihedralType( 0, 1, 2, 3, -1 );
+  ImproperParmHolder::ReorderImproper( imp, ImproperParmHolder::O_301 );
+  //printImp(imp);
+  if (imp.A1() != 3 || imp.A2() != 0 || imp.A3() != 2 || imp.A4() != 1)
+    return Err("Improper reorder failed (O_301).");
+  imp = DihedralType( 0, 1, 2, 3, -1 );
+  ImproperParmHolder::ReorderImproper( imp, ImproperParmHolder::O_310 );
+  //printImp(imp);
+  if (imp.A1() != 3 || imp.A2() != 1 || imp.A3() != 2 || imp.A4() != 0)
+    return Err("Improper reorder failed (O_310).");
+
   return 0;
 }

From 642690a3689af9e5b305018bb1d560462b225465 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 2 Jan 2024 16:08:49 -0500
Subject: [PATCH 0230/1492] Have improper FindParam do improper reordering

---
 src/ParameterHolders.h | 113 +++++++++++++++++++++++++++++++----------
 1 file changed, 87 insertions(+), 26 deletions(-)

diff --git a/src/ParameterHolders.h b/src/ParameterHolders.h
index 610b1de79d..433fd6a036 100644
--- a/src/ParameterHolders.h
+++ b/src/ParameterHolders.h
@@ -311,12 +311,9 @@ class ImproperParmHolder : private DihedralParmHolder {
     AddParm(TypeNameHolder const& types, DihedralParmArray const& dpa, bool allowUpdate) {
       return DihedralParmHolder::AddParm( types, dpa, allowUpdate );
     }
-    DihedralParmArray FindParam(TypeNameHolder const& types, bool& found) const {
-      OrderType lastOrder;
-      return FindParam(types, found, lastOrder);
-    }
-    /// Remap the given improper according to the desired order
-    static void ReorderImproper(DihedralType& imp, OrderType order) {
+  private:
+    /// Remap the given improper according to the desired order, correct for wildcards in given types
+    void ReorderImproper(DihedralType& imp, OrderType order, TypeNameHolder const& types) const {
       switch (order) {
         case O_013 : break;
         case O_031 : swp( imp.ChangeA2(), imp.ChangeA4() ); break;
@@ -325,13 +322,42 @@ class ImproperParmHolder : private DihedralParmHolder {
         case O_301 : swp( imp.ChangeA2(), imp.ChangeA4() ); swp( imp.ChangeA1(), imp.ChangeA2() ); break;
         case O_310 : swp( imp.ChangeA1(), imp.ChangeA4() ); break;
       }
+      if (wc_.len() > 0 && types.Size() > 0) {
+        // If there are wildcards, need to order matching types by atom index.
+        // General order of imp should now match types due to above swaps.
+        bool wc1 = (types[0] == wc_);
+        bool wc2 = (types[1] == wc_);
+        bool wc4 = (types[3] == wc_);
+        //mprintf("DEBUG: %s WC0=%i %s WC1=%i %s WC3=%i\n", *types[0], (int)wc1, *types[1], (int)wc2, *types[3], (int)wc4);
+        if (wc4 && wc2 && wc1) {
+          // All three wildcard - should be rare but need to check.
+          if (imp.A1() > imp.A2()) swp(imp.ChangeA1(), imp.ChangeA2());
+          if (imp.A2() > imp.A4()) swp(imp.ChangeA2(), imp.ChangeA4());
+          if (imp.A1() > imp.A2()) swp(imp.ChangeA1(), imp.ChangeA2());
+          if (imp.A2() > imp.A4()) swp(imp.ChangeA2(), imp.ChangeA4());
+        } else if (wc1 && wc2) {
+          if (imp.A1() > imp.A2()) swp(imp.ChangeA1(), imp.ChangeA2());
+        } else if (wc1 && wc4) {
+          if (imp.A1() > imp.A4()) swp(imp.ChangeA1(), imp.ChangeA4());
+        } else if (wc2 && wc4) {
+          if (imp.A2() > imp.A4()) swp(imp.ChangeA2(), imp.ChangeA4());
+        }
+      }
     }
-    /// \return Array of improper parameters matching given atom types.
-    DihedralParmArray FindParam(TypeNameHolder const& types, bool& found, OrderType& lastOrder_) const {
+  public:
+    /// Remap the given improper according to the desired order. Used by unit test to check that reordering works.
+    void ReorderImproper(DihedralType& imp, OrderType order) const {
+      ReorderImproper(imp, order, TypeNameHolder());
+    }
+    /// \return Array of improper parameters matching given atom types. Improper will be reordered to match parameter order.
+    DihedralParmArray FindParam(TypeNameHolder const& types, bool& found, DihedralType& imp, bool& reordered) const {
       //mprintf("DEBUG: FindParam wc=%s Inco=%s-%s-%s-%s\n",*wc_, *(types[0]), *(types[1]),   *(types[2]),   *(types[3]));
-      found = true;
+      found = false;
+      reordered = false;
       // First, no wildcard
-      for (const_iterator it = begin(); it != end(); ++it) {
+      const_iterator it = begin();
+      OrderType lastOrder_;
+      for (; it != end(); ++it) {
         TypeNameHolder const& myTypes = it->first;
         // Central (third) type must match
         if (myTypes[2] == types[2]) {
@@ -342,33 +368,46 @@ class ImproperParmHolder : private DihedralParmHolder {
           if (       myTypes[0] == types[0] && myTypes[1] == types[1] && myTypes[3] == types[3]) {
               // 0 1 2 3
               lastOrder_ = O_013;
-              return it->second;
+              found = true;
+              //return it->second;
+              break;
           } else if (myTypes[0] == types[0] && myTypes[1] == types[3] && myTypes[3] == types[1]) {
               // 0 3 2 1
               lastOrder_ = O_031;
-              return it->second;
+              found = true;
+              //return it->second;
+              break;
           } else if (myTypes[0] == types[1] && myTypes[1] == types[0] && myTypes[3] == types[3]) {
               // 1 0 2 3
               lastOrder_ = O_103;
-              return it->second;
+              found = true;
+              //return it->second;
+              break;
           } else if (myTypes[0] == types[1] && myTypes[1] == types[3] && myTypes[3] == types[0]) {
               // 1 3 2 0
               lastOrder_ = O_130;
-              return it->second;
+              found = true;
+              //return it->second;
+              break;
           } else if (myTypes[0] == types[3] && myTypes[1] == types[0] && myTypes[3] == types[1]) {
               // 3 0 2 1
               lastOrder_ = O_301;
-              return it->second;
+              found = true;
+              //return it->second;
+              break;
           } else if (myTypes[0] == types[3] && myTypes[1] == types[1] && myTypes[3] == types[0]) {
               // 3 1 2 0
               lastOrder_ = O_310;
-              return it->second;
+              found = true;
+              //return it->second;
+              break;
           }
         }
       } // END loop over parameters
       // Wildcard if present
-      if (wc_.len() > 0) {
-        for (const_iterator it = begin(); it != end(); ++it) {
+      if (!found && wc_.len() > 0) {
+        it = begin();
+        for (; it != end(); ++it) {
           TypeNameHolder const& myTypes = it->first;
           // Central (third) type must match
           if (wcm(myTypes[2], types[2], wc_)) {
@@ -376,34 +415,56 @@ class ImproperParmHolder : private DihedralParmHolder {
             if (       wcm(myTypes[0], types[0], wc_) && wcm(myTypes[1], types[1], wc_) && wcm(myTypes[3], types[3], wc_)) {
                 // 0 1 2 3
                 lastOrder_ = O_013;
-                return it->second;
+                found = true;
+                //return it->second;
+                break;
             } else if (wcm(myTypes[0], types[0], wc_) && wcm(myTypes[1], types[3], wc_) && wcm(myTypes[3], types[1], wc_)) {
                 // 0 3 2 1
                 lastOrder_ = O_031;
-                return it->second;
+                found = true;
+                //return it->second;
+                break;
             } else if (wcm(myTypes[0], types[1], wc_) && wcm(myTypes[1], types[0], wc_) && wcm(myTypes[3], types[3], wc_)) {
                 // 1 0 2 3
                 lastOrder_ = O_103;
-                return it->second;
+                found = true;
+                //return it->second;
+                break;
             } else if (wcm(myTypes[0], types[1], wc_) && wcm(myTypes[1], types[3], wc_) && wcm(myTypes[3], types[0], wc_)) {
                 // 1 3 2 0
                 lastOrder_ = O_130;
-                return it->second;
+                found = true;
+                //return it->second;
+                break;
             } else if (wcm(myTypes[0], types[3], wc_) && wcm(myTypes[1], types[0], wc_) && wcm(myTypes[3], types[1], wc_)) {
                 // 3 0 2 1
                 lastOrder_ = O_301;
-                return it->second;
+                found = true;
+                //return it->second;
+                break;
             } else if (wcm(myTypes[0], types[3], wc_) && wcm(myTypes[1], types[1], wc_) && wcm(myTypes[3], types[0], wc_)) {
                 // 3 1 2 0
                 lastOrder_ = O_310;
-                return it->second;
+                found = true;
+                //return it->second;
+                break;
             }
           }
         } // END loop over parameters
       } // END wildcard matches
-      found = false;
-      return DihedralParmArray();
+      //found = false;
+      if (!found) return DihedralParmArray();
+      // We have found a parameter. Do any reordering.
+      if (lastOrder_ != O_013) reordered = true;
+      ReorderImproper( imp, lastOrder_, it->first );
+      return it->second;
     } // END FindParam()
+    /// \return Dihedral parm array corresponding to types. Use by unit test.
+    DihedralParmArray FindParam(TypeNameHolder const& types, bool& found) const {
+      DihedralType blank;
+      bool reordered;
+      return FindParam(types, found, blank, reordered);
+    }
     /// \return size in memory in bytes
     size_t DataSize() const { return DihedralParmHolder::DataSize(); }
   private:

From 4bd249a305e9913cd7b553b1caaedd23f6cd3c85 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 2 Jan 2024 16:09:46 -0500
Subject: [PATCH 0231/1492] Enable unit test and update for updated FindParam

---
 unitTests/ImproperParmHolder/main.cpp | 12 ++++++------
 unitTests/Makefile                    |  6 +++++-
 2 files changed, 11 insertions(+), 7 deletions(-)

diff --git a/unitTests/ImproperParmHolder/main.cpp b/unitTests/ImproperParmHolder/main.cpp
index ef6bd4fa28..c19ebc547f 100644
--- a/unitTests/ImproperParmHolder/main.cpp
+++ b/unitTests/ImproperParmHolder/main.cpp
@@ -60,28 +60,28 @@ int main() {
   if (found) return Err("Improper parameter search found something when it should not have.");
 
   DihedralType imp( 0, 1, 2, 3, -1 );
-  ImproperParmHolder::ReorderImproper( imp, ImproperParmHolder::O_013 );
+  IP.ReorderImproper( imp, ImproperParmHolder::O_013 );
   if (imp.A1() != 0 || imp.A2() != 1 || imp.A3() != 2 || imp.A4() != 3)
     return Err("Improper reorder failed (O_013).");
-  ImproperParmHolder::ReorderImproper( imp, ImproperParmHolder::O_031 );
+  IP.ReorderImproper( imp, ImproperParmHolder::O_031 );
   if (imp.A1() != 0 || imp.A2() != 3 || imp.A3() != 2 || imp.A4() != 1)
     return Err("Improper reorder failed (O_031).");
   imp = DihedralType( 0, 1, 2, 3, -1 );
-  ImproperParmHolder::ReorderImproper( imp, ImproperParmHolder::O_103 );
+  IP.ReorderImproper( imp, ImproperParmHolder::O_103 );
   if (imp.A1() != 1 || imp.A2() != 0 || imp.A3() != 2 || imp.A4() != 3)
     return Err("Improper reorder failed (O_103).");
   imp = DihedralType( 0, 1, 2, 3, -1 );
-  ImproperParmHolder::ReorderImproper( imp, ImproperParmHolder::O_130 );
+  IP.ReorderImproper( imp, ImproperParmHolder::O_130 );
   //printImp(imp);
   if (imp.A1() != 1 || imp.A2() != 3 || imp.A3() != 2 || imp.A4() != 0)
     return Err("Improper reorder failed (O_130).");
   imp = DihedralType( 0, 1, 2, 3, -1 );
-  ImproperParmHolder::ReorderImproper( imp, ImproperParmHolder::O_301 );
+  IP.ReorderImproper( imp, ImproperParmHolder::O_301 );
   //printImp(imp);
   if (imp.A1() != 3 || imp.A2() != 0 || imp.A3() != 2 || imp.A4() != 1)
     return Err("Improper reorder failed (O_301).");
   imp = DihedralType( 0, 1, 2, 3, -1 );
-  ImproperParmHolder::ReorderImproper( imp, ImproperParmHolder::O_310 );
+  IP.ReorderImproper( imp, ImproperParmHolder::O_310 );
   //printImp(imp);
   if (imp.A1() != 3 || imp.A2() != 1 || imp.A3() != 2 || imp.A4() != 0)
     return Err("Improper reorder failed (O_310).");
diff --git a/unitTests/Makefile b/unitTests/Makefile
index a099ae2f00..4e1b304426 100644
--- a/unitTests/Makefile
+++ b/unitTests/Makefile
@@ -22,6 +22,9 @@ unit.Range:
 unit.TypeNameHolder:
 	@-cd TypeNameHolder && ./UnitTest.sh $(OPT)
 
+unit.ImproperParmHolder:
+	@-cd ImproperParmHolder && ./UnitTest.sh $(OPT)
+
 # ----- Every unit test should go here -----------
 COMPLETETESTS= \
   unit.NameType \
@@ -29,7 +32,8 @@ COMPLETETESTS= \
   unit.GistEntropyUtils \
   unit.StringRoutines \
   unit.Range \
-  unit.TypeNameHolder
+  unit.TypeNameHolder \
+  unit.ImproperParmHolder
 
 test.cpptraj: $(COMPLETETESTS)
 

From 9ffa4855ed7ba83d29691bc385f63ac7b84e931d Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 2 Jan 2024 16:17:42 -0500
Subject: [PATCH 0232/1492] FindParam does reordering. Just warn if reordering
 has occurred.

---
 src/Topology.cpp | 38 +++++++++++++++++++++++---------------
 src/Topology.h   |  1 +
 2 files changed, 24 insertions(+), 15 deletions(-)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index f42ff00ea6..0bcb9d694b 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2695,16 +2695,20 @@ void Topology::AssignAngleParams(ParmHolder<AngleParmType> const& newAngleParams
   AssignAngleParm( newAngleParams, anglesh_ );
 }
 
-/** Reorder improper atoms so that they match the parameter. */
-static void match_improper_to_parm(DihedralType& imp, TypeNameHolder const& types, ImproperParmHolder::OrderType order)
+/** Warn if improper atoms have been reordered so they match the parameter. */
+void Topology::warn_improper_reorder(DihedralType const& imp0, DihedralType const& imp)
+const
 {
-  mprintf("DEBUG: Improper types : %4s %4s %4s %4s (order %i)\n", *(types[0]), *(types[1]), *(types[2]), *(types[3]),
-          //*(atoms_[imp->A1()].Type()),
-          //*(atoms_[imp->A2()].Type()),
-          //*(atoms_[imp->A3()].Type()),
-          //*(atoms_[imp->A4()].Type()),
-          (int)order);
-  //mprintf("DEBUG: Parm types     : %4s %4s %4s %4s\n", 
+  mprintf("Warning: Improper types have been reordered from %4s %4s %4s %4s",
+          *(atoms_[imp0.A1()].Type()),
+          *(atoms_[imp0.A2()].Type()),
+          *(atoms_[imp0.A3()].Type()),
+          *(atoms_[imp0.A4()].Type()));
+  mprintf(" to %4s %4s %4s %4s to match improper parameter.\n",
+          *(atoms_[imp.A1()].Type()),
+          *(atoms_[imp.A2()].Type()),
+          *(atoms_[imp.A3()].Type()),
+          *(atoms_[imp.A4()].Type()));
 }
 
 /** Set parameters for improper dihedrals in given improper dihedral array. */
@@ -2720,8 +2724,10 @@ void Topology::AssignImproperParm(ImproperParmHolder const& newImproperParams,
     bool found;
     // See if parameter is present.
     int idx = -1;
-    ImproperParmHolder::OrderType lastOrder;
-    DihedralParmArray ipa = newImproperParams.FindParam( types, found, lastOrder );
+    //ImproperParmHolder::OrderType lastOrder;
+    DihedralType imp0 = *imp;
+    bool reordered;
+    DihedralParmArray ipa = newImproperParams.FindParam( types, found, *imp, reordered );
     if (!found) {
       mprintf("Warning: Parameter not found for improper %s-%s-%s-%s (%s-%s-%s-%s)\n",
               TruncResAtomNameNum(imp->A1()).c_str(),
@@ -2733,7 +2739,7 @@ void Topology::AssignImproperParm(ImproperParmHolder const& newImproperParams,
       if (ipa.size() > 1)
         mprintf("Warning: %zu improper parameters found for types %s - %s - %s - %s, expected only one."
                         "Warning: Only using first parameter.\n", ipa.size(), *(types[0]), *(types[1]), *(types[2]), *(types[3]));
-      match_improper_to_parm( *imp, types, lastOrder );
+      if (reordered) warn_improper_reorder( imp0, *imp );
       idx = addTorsionParm( chamber_.SetImproperParm(), ipa.front() );
     }
     imp->SetIdx( idx );
@@ -2806,8 +2812,10 @@ void Topology::AssignDihedralParm(DihedralParmHolder const& newDihedralParams,
     bool found;
     if (isImproper) {
       // ----- This is actually an improper dihedral. ----------------
-      ImproperParmHolder::OrderType lastOrder;
-      DihedralParmArray ipa = newImproperParams.FindParam( types, found, lastOrder );
+      //ImproperParmHolder::OrderType lastOrder;
+      DihedralType dih0 = *dih;
+      bool reordered;
+      DihedralParmArray ipa = newImproperParams.FindParam( types, found, *dih, reordered );
       int idx = -1;
       if (!found) {
         mprintf("Warning: Improper parameters not found for improper dihedral %s-%s-%s-%s (%s-%s-%s-%s)\n",
@@ -2820,7 +2828,7 @@ void Topology::AssignDihedralParm(DihedralParmHolder const& newDihedralParams,
         if (ipa.size() > 1)
           mprintf("Warning: %zu improper parameters found for types %s - %s - %s - %s, expected only one."
                   "Warning: Only using first parameter.\n", ipa.size(), *(types[0]), *(types[1]), *(types[2]), *(types[3]));
-        match_improper_to_parm( *dih, types, lastOrder );
+        if (reordered) warn_improper_reorder( dih0, *dih );
         idx = addTorsionParm( dihedralparm_, ipa.front() );
       }
       DihedralType mydih = *dih;
diff --git a/src/Topology.h b/src/Topology.h
index 8c049510a1..399c47f83d 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -300,6 +300,7 @@ class Topology {
     void AssignAtomTypeParm(ParmHolder<AtomType> const&);
     void AssignBondParm(ParmHolder<BondParmType> const&, BondArray&, BondParmArray&, const char*) const;
     void AssignAngleParm(ParmHolder<AngleParmType> const&, AngleArray&);
+    void warn_improper_reorder(DihedralType const&, DihedralType const&) const;
     void AssignImproperParm(ImproperParmHolder const&, DihedralArray&);
     void AssignDihedralParm(DihedralParmHolder const&, ImproperParmHolder const&, DihedralArray&);
 

From 0a2ae3ff34fe09be3c726f5f4708ec6311d592aa Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 3 Jan 2024 09:32:26 -0500
Subject: [PATCH 0233/1492] Remove function that will never be used

---
 src/Topology.cpp | 6 ------
 src/Topology.h   | 1 -
 2 files changed, 7 deletions(-)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index 0bcb9d694b..531a6cd17b 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -898,12 +898,6 @@ void Topology::AddBond(BondType const& bndIn, bool isH) {
   atoms_[bndIn.A2()].AddBondToIdx( bndIn.A1() );
 }
 
-/** Sort bond arrays. May want to do this to e.g. match LEAP bond ordering. */
-/*void Topology::SortBonds() {
-  std::sort(bonds_.begin(), bonds_.end());
-  std::sort(bondsh_.begin(), bondsh_.end());
-}*/
-
 /** Check if given angle parm exists in given angle parm array. Add if not.
   * \return Index in angle parm array.
   */
diff --git a/src/Topology.h b/src/Topology.h
index 399c47f83d..8c26c1cfb6 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -115,7 +115,6 @@ class Topology {
     void AddBond(BondType const&, bool);
     void AddBond(int, int, BondParmType const&);
     int RemoveBond(int, int);
-    //void SortBonds();
     void AssignBondParams(ParmHolder<BondParmType> const&);
     // ----- Angle-specific routines -------------
     size_t Nangles()                           const { return angles_.size()+anglesh_.size(); }

From 9bdab484d1b6a34c9d4ade1000420a71f832f914 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 3 Jan 2024 09:46:55 -0500
Subject: [PATCH 0234/1492] Rename file to better reflect what the functions do

---
 src/Structure/{GenerateAngles.cpp => GenerateConnectivity.cpp} | 0
 src/Structure/{GenerateAngles.h => GenerateConnectivity.h}     | 0
 2 files changed, 0 insertions(+), 0 deletions(-)
 rename src/Structure/{GenerateAngles.cpp => GenerateConnectivity.cpp} (100%)
 rename src/Structure/{GenerateAngles.h => GenerateConnectivity.h} (100%)

diff --git a/src/Structure/GenerateAngles.cpp b/src/Structure/GenerateConnectivity.cpp
similarity index 100%
rename from src/Structure/GenerateAngles.cpp
rename to src/Structure/GenerateConnectivity.cpp
diff --git a/src/Structure/GenerateAngles.h b/src/Structure/GenerateConnectivity.h
similarity index 100%
rename from src/Structure/GenerateAngles.h
rename to src/Structure/GenerateConnectivity.h

From 30039cd54a062fb8cbec20e1a4e2fffb2643d538 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 3 Jan 2024 09:52:20 -0500
Subject: [PATCH 0235/1492] Change names to better reflect what happens, remove
 old code.

---
 src/Structure/GenerateConnectivity.cpp | 42 +++++++++++++++++++-------
 src/Structure/GenerateConnectivity.h   | 10 +++---
 src/Structure/structuredepend          |  4 +--
 src/Structure/structurefiles           |  2 +-
 4 files changed, 39 insertions(+), 19 deletions(-)

diff --git a/src/Structure/GenerateConnectivity.cpp b/src/Structure/GenerateConnectivity.cpp
index 078ded5a22..cf795f8a36 100644
--- a/src/Structure/GenerateConnectivity.cpp
+++ b/src/Structure/GenerateConnectivity.cpp
@@ -1,9 +1,9 @@
-#include "GenerateAngles.h"
+#include "GenerateConnectivity.h"
 #include "../CpptrajStdio.h"
 #include "../GuessAtomHybridization.h"
 #include "../ParameterTypes.h"
 #include "../Topology.h"
-#include <algorithm> // std::sort
+#include <algorithm> // std::swap
 
 static inline void enumerateAngles(int at1, int at2, Topology& topIn) {
   Atom const& A2 = topIn[at2];
@@ -48,8 +48,12 @@ static inline void enumerateDihedrals(int at1, int at2, Topology& topIn) {
   }
 }
 
-/* Set angles and dihedrals in given topology based on current bond arrays. */
-int Cpptraj::Structure::GenerateAngles(Topology& topIn) {
+/* Set bonds, angles, and dihedral arrays for a given topology based on 
+ * current atom connectivity.
+ * This is done in the same manner as LEaP, which goes in increasing
+ * residue order but decreasing atom index.
+ */
+int Cpptraj::Structure::GenerateBondAngleTorsionArrays(Topology& topIn) {
   if (topIn.Nbonds() < 1) {
     mprintf("Warning: No bonds in '%s', no angles to generate.\n", topIn.c_str());
     return 0;
@@ -65,15 +69,31 @@ int Cpptraj::Structure::GenerateAngles(Topology& topIn) {
     //return 0;
   }
   if (has_angles && has_dihedrals) return 0;
+  // Clear existing bond information TODO clear angles and dihedrals?
+  topIn.ClearBondArrays();
   // Create a combined bonds array
   BondArray allBonds;
   allBonds.reserve(topIn.Nbonds());
 
-  for (BondArray::const_iterator it = topIn.Bonds().begin(); it != topIn.Bonds().end(); ++it)
-    allBonds.push_back( *it );
-  for (BondArray::const_iterator it = topIn.BondsH().begin(); it != topIn.BondsH().end(); ++it)
-    allBonds.push_back( *it );
-  std::sort( allBonds.begin(), allBonds.end() );
+  int bidx = 0;
+  for (int ires = 0; ires < topIn.Nres(); ires++)
+  {
+    Residue const& res = topIn.Res(ires);
+    for (int iat = res.LastAtom()-1; iat >= res.FirstAtom(); iat--)
+    {
+      Atom const& At = topIn[iat];
+      for (Atom::bond_iterator bat = At.bondbegin(); bat != At.bondend(); ++bat)
+      {
+        if (iat < *bat) {
+          mprintf("DEBUG: BOND  i= %i  %i - %i (%i %i)\n",  bidx++, iat+1, *bat+1, iat*3, *bat*3);
+          allBonds.push_back( BondType(iat, *bat, -1) );
+          topIn.AddToBondArrays( BondType(iat, *bat, -1) );
+        }
+        //else
+        //  mprintf("DEBUG: X    i= %i  %i - %i (%i %i)\n",   bidx++, iat+1, *bat+1, iat*3, *bat*3);
+      }
+    }
+  }
 
   mprintf("DEBUG: Sorted bonds:\n");
   for (BondArray::const_iterator it = allBonds.begin(); it != allBonds.end(); ++it)
@@ -82,8 +102,8 @@ int Cpptraj::Structure::GenerateAngles(Topology& topIn) {
             topIn.AtomMaskName(it->A2()).c_str());
 
   // Angles
-  AngleArray angles;
-  AngleArray anglesH;
+  //AngleArray angles;
+  //AngleArray anglesH;
   for (BondArray::const_iterator it = allBonds.begin(); it != allBonds.end(); ++it)
   {
     if (!has_angles) {
diff --git a/src/Structure/GenerateConnectivity.h b/src/Structure/GenerateConnectivity.h
index 09bd38785b..d56585b9dc 100644
--- a/src/Structure/GenerateConnectivity.h
+++ b/src/Structure/GenerateConnectivity.h
@@ -1,13 +1,13 @@
-#ifndef INC_STRUCTURE_GENERATEANGLES_H
-#define INC_STRUCTURE_GENERATEANGLES_H
+#ifndef INC_STRUCTURE_GENERATECONNECTIVITY_H
+#define INC_STRUCTURE_GENERATECONNECTIVITY_H
 class Topology;
 class AtomType;
 template <typename Type> class ParmHolder;
 namespace Cpptraj {
 namespace Structure {
-/// Generate angles from bonds in a Topology
-int GenerateAngles(Topology&);
-/// Generate impropers
+/// Generate bond/angle/torsion arrays from atom connectivity in a Topology
+int GenerateBondAngleTorsionArrays(Topology&);
+/// Generate impropers in a Topology
 int GenerateImpropers(Topology&, ParmHolder<AtomType> const&);
 }
 }
diff --git a/src/Structure/structuredepend b/src/Structure/structuredepend
index bd21185aeb..b99a9b01ec 100644
--- a/src/Structure/structuredepend
+++ b/src/Structure/structuredepend
@@ -3,10 +3,10 @@ Chirality.o : Chirality.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Co
 Disulfide.o : Disulfide.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Disulfide.h ResStatArray.h StructureRoutines.h
 FunctionalGroup.o : FunctionalGroup.cpp ../Atom.h ../AtomMap.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h FunctionalGroup.h
 FxnGroupBuilder.o : FxnGroupBuilder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h FunctionalGroup.h FxnGroupBuilder.h StructureRoutines.h Sugar.h SugarToken.h
-GenerateAngles.o : GenerateAngles.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h GenerateAngles.h
+GenerateConnectivity.o : GenerateConnectivity.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h GenerateConnectivity.h
 HisProt.o : HisProt.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h HisProt.h StructureRoutines.h
 InternalCoords.o : InternalCoords.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h InternalCoords.h
-Model.o : Model.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h Model.h StructureEnum.h
+Model.o : Model.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h Model.h StructureEnum.h
 StructureEnum.o : StructureEnum.cpp StructureEnum.h
 StructureRoutines.o : StructureRoutines.cpp ../Atom.h ../CpptrajStdio.h ../NameType.h ../Residue.h ../SymbolExporting.h StructureRoutines.h
 Sugar.o : Sugar.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Sugar.h SugarToken.h
diff --git a/src/Structure/structurefiles b/src/Structure/structurefiles
index a6449d535b..47dcb912e4 100644
--- a/src/Structure/structurefiles
+++ b/src/Structure/structurefiles
@@ -5,7 +5,7 @@ STRUCTURE_SOURCES= \
   Disulfide.cpp \
   FunctionalGroup.cpp \
   FxnGroupBuilder.cpp \
-  GenerateAngles.cpp \
+  GenerateConnectivity.cpp \
   HisProt.cpp \
   InternalCoords.cpp \
   Model.cpp \

From e8b71378f36052ab040321b764801d04fefb8d0a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 3 Jan 2024 09:52:35 -0500
Subject: [PATCH 0236/1492] Update CMakeLists

---
 src/Structure/CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Structure/CMakeLists.txt b/src/Structure/CMakeLists.txt
index c88fecfe3f..7350e7edca 100644
--- a/src/Structure/CMakeLists.txt
+++ b/src/Structure/CMakeLists.txt
@@ -5,7 +5,7 @@ target_sources(cpptraj_common_obj PRIVATE
   ${CMAKE_CURRENT_LIST_DIR}/Disulfide.cpp
   ${CMAKE_CURRENT_LIST_DIR}/FunctionalGroup.cpp
   ${CMAKE_CURRENT_LIST_DIR}/FxnGroupBuilder.cpp
-  ${CMAKE_CURRENT_LIST_DIR}/GenerateAngles.cpp
+  ${CMAKE_CURRENT_LIST_DIR}/GenerateConnectivity.cpp
   ${CMAKE_CURRENT_LIST_DIR}/HisProt.cpp
   ${CMAKE_CURRENT_LIST_DIR}/InternalCoords.cpp
   ${CMAKE_CURRENT_LIST_DIR}/Model.cpp

From f2d37bdbdd93573f3fa3146f75e6ac77126377f6 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 3 Jan 2024 09:58:42 -0500
Subject: [PATCH 0237/1492] Update for changed function name

---
 src/Exec_Build.cpp            |  4 ++--
 src/Exec_Sequence.cpp         |  4 ++--
 src/Exec_UpdateParameters.cpp |  4 ++--
 src/Topology.cpp              | 20 ++++++++++++++++++++
 src/Topology.h                |  4 ++++
 src/cpptrajdepend             |  8 ++++----
 6 files changed, 34 insertions(+), 10 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 4fee21d2fb..52e74efc33 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -1,7 +1,7 @@
 #include "Exec_Build.h"
 #include "CpptrajStdio.h"
 #include "DataSet_Parameters.h"
-#include "Structure/GenerateAngles.h"
+#include "Structure/GenerateConnectivity.h"
 #include "Structure/Zmatrix.h"
 
 DataSet_Coords* Exec_Build::IdTemplateFromName(Carray const& Templates,
@@ -370,7 +370,7 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
   }
 
   // Generate angles/dihedrals
-  if (Cpptraj::Structure::GenerateAngles(topOut)) {
+  if (Cpptraj::Structure::GenerateBondAngleTorsionArrays(topOut)) {
     mprinterr("Error: Could not generate angles/dihedrals for '%s'\n", topOut.c_str());
     return CpptrajState::ERR;
   }
diff --git a/src/Exec_Sequence.cpp b/src/Exec_Sequence.cpp
index 89fe0f823d..6b5356fd7b 100644
--- a/src/Exec_Sequence.cpp
+++ b/src/Exec_Sequence.cpp
@@ -2,7 +2,7 @@
 #include "CpptrajStdio.h"
 #include "AssociatedData_Connect.h"
 #include "Structure/Builder.h"
-#include "Structure/GenerateAngles.h"
+#include "Structure/GenerateConnectivity.h"
 
 /** Generate and build the specified sequence. */
 int Exec_Sequence::generate_sequence(DataSet_Coords* OUT,
@@ -117,7 +117,7 @@ const
 
   // Generate angles and dihedrals
  if (combinedTop.Nbonds() > 0) {
-   if (Cpptraj::Structure::GenerateAngles(combinedTop)) {
+   if (Cpptraj::Structure::GenerateBondAngleTorsionArrays(combinedTop)) {
      mprinterr("Error: Angle generation failed.\n");
      return 1;
    }
diff --git a/src/Exec_UpdateParameters.cpp b/src/Exec_UpdateParameters.cpp
index 7f7414393e..735cdcfd8a 100644
--- a/src/Exec_UpdateParameters.cpp
+++ b/src/Exec_UpdateParameters.cpp
@@ -2,7 +2,7 @@
 #include "CpptrajStdio.h"
 #include "DataSet_Parameters.h"
 #include "DataSet_Topology.h"
-#include "Structure/GenerateAngles.h"
+#include "Structure/GenerateConnectivity.h"
 
 const char* Exec_UpdateParameters::disclaimer_ = "Warning: This command is provided for convenience only.\nWarning: For editing topology files, ParmEd is a much better alternative.\n";
 
@@ -53,7 +53,7 @@ Exec::RetType Exec_UpdateParameters::Execute(CpptrajState& State, ArgList& argIn
   //top.SortBonds();
 
   if (genAngles) {
-    if (Cpptraj::Structure::GenerateAngles( top )) {
+    if (Cpptraj::Structure::GenerateBondAngleTorsionArrays( top )) {
       mprinterr("Error: Could not generate angle/dihedral information.\n");
       return CpptrajState::ERR;
     }
diff --git a/src/Topology.cpp b/src/Topology.cpp
index 531a6cd17b..7b83420bc2 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -898,6 +898,26 @@ void Topology::AddBond(BondType const& bndIn, bool isH) {
   atoms_[bndIn.A2()].AddBondToIdx( bndIn.A1() );
 }
 
+/** Clear bond arrays, but do not clear atom connectivity. Used
+  * when regenerating bond information from atom connectivity.
+  */
+void Topology::ClearBondArrays() {
+  bonds_.clear();
+  bondsh_.clear();
+}
+
+/** Add to bond arrays but do not update atom connectivity. Used
+  * when regenerating bond information from atom connectivity.
+  */
+void Topology::AddToBondArrays(BondType const& bnd) {
+  // TODO enforce H as second atom?
+  if (atoms_[bnd.A1()].Element() == Atom::HYDROGEN ||
+      atoms_[bnd.A2()].Element() == Atom::HYDROGEN)
+    bondsh_.push_back( bnd );
+  else
+    bonds_.push_back( bnd );
+}
+
 /** Check if given angle parm exists in given angle parm array. Add if not.
   * \return Index in angle parm array.
   */
diff --git a/src/Topology.h b/src/Topology.h
index 8c26c1cfb6..c34333f1d7 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -116,6 +116,10 @@ class Topology {
     void AddBond(int, int, BondParmType const&);
     int RemoveBond(int, int);
     void AssignBondParams(ParmHolder<BondParmType> const&);
+    /// Clear bond arrays but not atom connectivity
+    void ClearBondArrays();
+    /// Add to bond arrays but do not update atom connectivity
+    void AddToBondArrays(BondType const&);
     // ----- Angle-specific routines -------------
     size_t Nangles()                           const { return angles_.size()+anglesh_.size(); }
     AngleArray        const& Angles()       const { return angles_;       }
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 3e62c05a7d..db7c95c1c7 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -288,7 +288,7 @@ Ewald_Regular.o : Ewald_Regular.cpp Atom.h AtomMask.h Box.h Constants.h Coordina
 ExclusionArray.o : ExclusionArray.cpp Atom.h AtomMask.h CharMask.h CpptrajStdio.h ExclusionArray.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Unit.h
 Exec_AddMissingRes.o : Exec_AddMissingRes.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CharMask.h CompactFrameArray.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_AddMissingRes.h Exec_AddMissingRes_Pres.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Analyze.o : Exec_Analyze.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Analyze.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Build.o : Exec_Build.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/GenerateAngles.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Build.o : Exec_Build.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/GenerateConnectivity.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Calc.o : Exec_Calc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Calc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_CatCrd.o : Exec_CatCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CatCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Change.o : Exec_Change.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Change.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
@@ -332,7 +332,7 @@ Exec_ReadInput.o : Exec_ReadInput.cpp Action.h ActionList.h ActionState.h Analys
 Exec_RotateDihedral.o : Exec_RotateDihedral.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_RotateDihedral.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_RunAnalysis.o : Exec_RunAnalysis.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_RunAnalysis.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_ScaleDihedralK.o : Exec_ScaleDihedralK.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ScaleDihedralK.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Sequence.o : Exec_Sequence.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Sequence.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/GenerateAngles.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Sequence.o : Exec_Sequence.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Sequence.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/GenerateConnectivity.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_SequenceAlign.o : Exec_SequenceAlign.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SequenceAlign.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Set.o : Exec_Set.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_StringVar.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Set.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Show.o : Exec_Show.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_StringVar.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Show.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
@@ -341,7 +341,7 @@ Exec_SplitCoords.o : Exec_SplitCoords.cpp Action.h ActionList.h ActionState.h An
 Exec_System.o : Exec_System.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_System.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Top.o : Exec_Top.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Top.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h TopInfo.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Traj.o : Exec_Traj.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Traj.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_UpdateParameters.o : Exec_UpdateParameters.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h DataSet_Topology.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_UpdateParameters.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/GenerateAngles.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_UpdateParameters.o : Exec_UpdateParameters.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h DataSet_Topology.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_UpdateParameters.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/GenerateConnectivity.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_ViewRst.o : Exec_ViewRst.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ViewRst.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h ViewRst.h
 Exec_Zmatrix.o : Exec_Zmatrix.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Zmatrix.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Zmatrix.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 ExtendedSimilarity.o : ExtendedSimilarity.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h ExtendedSimilarity.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
@@ -447,7 +447,7 @@ Structure/Chirality.o : Structure/Chirality.cpp Atom.h AtomMask.h AtomType.h Box
 Structure/Disulfide.o : Structure/Disulfide.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Disulfide.h Structure/ResStatArray.h Structure/StructureRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/FunctionalGroup.o : Structure/FunctionalGroup.cpp Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/FxnGroupBuilder.o : Structure/FxnGroupBuilder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h Structure/FxnGroupBuilder.h Structure/StructureRoutines.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Structure/GenerateAngles.o : Structure/GenerateAngles.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h GuessAtomHybridization.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/GenerateAngles.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Structure/GenerateConnectivity.o : Structure/GenerateConnectivity.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h GuessAtomHybridization.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/GenerateConnectivity.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/HisProt.o : Structure/HisProt.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/HisProt.h Structure/StructureRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/InternalCoords.o : Structure/InternalCoords.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/InternalCoords.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/Model.o : Structure/Model.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h GuessAtomHybridization.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/Model.h Structure/StructureEnum.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h

From 858742f49489913d210170b138414e45e812f134 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 3 Jan 2024 10:39:35 -0500
Subject: [PATCH 0238/1492] Do Angles the same way as leap

---
 src/Structure/GenerateConnectivity.cpp | 66 ++++++++++++++++++--------
 1 file changed, 45 insertions(+), 21 deletions(-)

diff --git a/src/Structure/GenerateConnectivity.cpp b/src/Structure/GenerateConnectivity.cpp
index cf795f8a36..b01ae0d0aa 100644
--- a/src/Structure/GenerateConnectivity.cpp
+++ b/src/Structure/GenerateConnectivity.cpp
@@ -5,17 +5,18 @@
 #include "../Topology.h"
 #include <algorithm> // std::swap
 
-static inline void enumerateAngles(int at1, int at2, Topology& topIn) {
+static inline void enumerateAngles(int& aidx, int at1, int at2, Topology& topIn) {
   Atom const& A2 = topIn[at2];
   if (A2.Nbonds() > 1) {
     for (Atom::bond_iterator bat = A2.bondbegin(); bat != A2.bondend(); ++bat)
     {
       if (*bat != at1 && at1 < *bat) {
         topIn.AddAngle(at1, at2, *bat);
-        mprintf("%s - %s - %s\n",
-                topIn.AtomMaskName(at1).c_str(),
-                topIn.AtomMaskName(at2).c_str(),
-                topIn.AtomMaskName(*bat).c_str());
+        mprintf("DEBUG: ANGLE  i= %i  %i - %i - %i (%i %i %i)\n",  aidx++, at1+1, at2+1, *bat+1, at1*3, at2*3, *bat*3);
+        //mprintf("%s - %s - %s\n",
+        //        topIn.AtomMaskName(at1).c_str(),
+        //        topIn.AtomMaskName(at2).c_str(),
+        //        topIn.AtomMaskName(*bat).c_str());
       }
     }
   }
@@ -36,11 +37,11 @@ static inline void enumerateDihedrals(int at1, int at2, Topology& topIn) {
               topIn.AddDihedral(*bat1, at1, at2, *bat2);
             else
               topIn.AddDihedral(*bat2, at2, at1, *bat1);
-            mprintf("%s - %s - %s - %s\n",
-                    topIn.AtomMaskName(*bat1).c_str(),
-                    topIn.AtomMaskName(at1).c_str(),
-                    topIn.AtomMaskName(at2).c_str(),
-                    topIn.AtomMaskName(*bat2).c_str());
+            //mprintf("%s - %s - %s - %s\n",
+            //        topIn.AtomMaskName(*bat1).c_str(),
+            //        topIn.AtomMaskName(at1).c_str(),
+            //        topIn.AtomMaskName(at2).c_str(),
+            //        topIn.AtomMaskName(*bat2).c_str());
           }
         }
       }
@@ -95,23 +96,46 @@ int Cpptraj::Structure::GenerateBondAngleTorsionArrays(Topology& topIn) {
     }
   }
 
-  mprintf("DEBUG: Sorted bonds:\n");
-  for (BondArray::const_iterator it = allBonds.begin(); it != allBonds.end(); ++it)
-    mprintf("\t%s - %s\n",
-            topIn.AtomMaskName(it->A1()).c_str(),
-            topIn.AtomMaskName(it->A2()).c_str());
+  // ANGLES TODO combine above
+  int aidx = 0;
+  for (int ires = 0; ires < topIn.Nres(); ires++)
+  {
+    Residue const& res = topIn.Res(ires);
+    for (int iat1 = res.LastAtom()-1; iat1 >= res.FirstAtom(); iat1--)
+    {
+      Atom const& At1 = topIn[iat1];
+      for (int bidx1 = 0; bidx1 < At1.Nbonds(); bidx1++) {
+        int iat2 = At1.Bond(bidx1);
+        Atom const& At2 = topIn[iat2];
+        for (int bidx2 = 0; bidx2 < At2.Nbonds(); bidx2++) {
+          int iat3 = At2.Bond(bidx2);
+          if (iat1 < iat3) {
+            mprintf("DEBUG: ANGLE  i= %i  %i - %i - %i (%i %i %i)\n", aidx++, iat1+1, iat2+1, iat3+1, iat1*3, iat2*3, iat3*3);
+            topIn.AddAngle(iat1, iat2, iat3);
+          }
+        }
+      }
+    }
+  }
+
+  //mprintf("DEBUG: Sorted bonds:\n");
+  //for (BondArray::const_iterator it = allBonds.begin(); it != allBonds.end(); ++it)
+  //  mprintf("\t%s - %s\n",
+  //          topIn.AtomMaskName(it->A1()).c_str(),
+  //          topIn.AtomMaskName(it->A2()).c_str());
 
   // Angles
   //AngleArray angles;
   //AngleArray anglesH;
+  aidx = 0;
   for (BondArray::const_iterator it = allBonds.begin(); it != allBonds.end(); ++it)
   {
-    if (!has_angles) {
-      // Forward direction. A1-A2-X
-      enumerateAngles( it->A1(), it->A2(), topIn );
-      // Reverse direction. A2-A1-X
-      enumerateAngles( it->A2(), it->A1(), topIn );
-    }
+    //if (!has_angles) {
+    //  // Forward direction. A1-A2-X
+    //  enumerateAngles( aidx, it->A1(), it->A2(), topIn );
+    //  // Reverse direction. A2-A1-X
+    //  enumerateAngles( aidx, it->A2(), it->A1(), topIn );
+    //}
     if (!has_dihedrals) {
       // Dihedrals
       enumerateDihedrals( it->A1(), it->A2(), topIn );

From eba259917b41716192e62640909145381ecf4d59 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 3 Jan 2024 12:38:41 -0500
Subject: [PATCH 0239/1492] Move old way of generating angles/torsions to
 different routine

---
 src/Structure/GenerateConnectivity.cpp | 79 +++++++++++++++++---------
 src/Structure/GenerateConnectivity.h   |  2 +
 2 files changed, 54 insertions(+), 27 deletions(-)

diff --git a/src/Structure/GenerateConnectivity.cpp b/src/Structure/GenerateConnectivity.cpp
index b01ae0d0aa..e20a2f777b 100644
--- a/src/Structure/GenerateConnectivity.cpp
+++ b/src/Structure/GenerateConnectivity.cpp
@@ -49,6 +49,57 @@ static inline void enumerateDihedrals(int at1, int at2, Topology& topIn) {
   }
 }
 
+/* Set bonds, angles, and dihedral arrays for a given topology based on
+ * a sorted and combined version of the current bond arrays.
+ */
+int Cpptraj::Structure::GenerateAngleTorsionArrays(Topology& topIn) {
+  if (topIn.Nbonds() < 1) {
+    mprintf("Warning: No bonds in '%s', no angles to generate.\n", topIn.c_str());
+    return 0;
+  }
+  bool has_angles = topIn.Nangles() > 0;
+  if (has_angles) {
+    mprintf("Warning: Topology '%s' already has angle information.\n", topIn.c_str());
+    //return 0;
+  }
+  bool has_dihedrals = topIn.Ndihedrals() > 0;
+  if (has_dihedrals) {
+    mprintf("Warning: Topology '%s' already has dihedral information.\n", topIn.c_str());
+    //return 0;
+  }
+  if (has_angles && has_dihedrals) return 0;
+  // Create a combined bonds array
+  BondArray allBonds;
+  allBonds.reserve(topIn.Nbonds());
+  for (BondArray::const_iterator it = topIn.Bonds().begin(); it != topIn.Bonds().end(); ++it)
+    allBonds.push_back( *it );
+  for (BondArray::const_iterator it = topIn.BondsH().begin(); it != topIn.BondsH().end(); ++it)
+    allBonds.push_back( *it );
+  std::sort( allBonds.begin(), allBonds.end() );
+  mprintf("DEBUG: Sorted bonds:\n");
+  for (BondArray::const_iterator it = allBonds.begin(); it != allBonds.end(); ++it)
+    mprintf("\t%s - %s\n",
+            topIn.AtomMaskName(it->A1()).c_str(),
+            topIn.AtomMaskName(it->A2()).c_str());
+
+  // Angles and Torsiions
+  int aidx = 0;
+  for (BondArray::const_iterator it = allBonds.begin(); it != allBonds.end(); ++it)
+  {
+    if (!has_angles) {
+      // Forward direction. A1-A2-X
+      enumerateAngles( aidx, it->A1(), it->A2(), topIn );
+      // Reverse direction. A2-A1-X
+      enumerateAngles( aidx, it->A2(), it->A1(), topIn );
+    }
+    if (!has_dihedrals) {
+      // Dihedrals
+      enumerateDihedrals( it->A1(), it->A2(), topIn );
+    }
+  }
+  return 0;
+}
+
 /* Set bonds, angles, and dihedral arrays for a given topology based on 
  * current atom connectivity.
  * This is done in the same manner as LEaP, which goes in increasing
@@ -72,10 +123,8 @@ int Cpptraj::Structure::GenerateBondAngleTorsionArrays(Topology& topIn) {
   if (has_angles && has_dihedrals) return 0;
   // Clear existing bond information TODO clear angles and dihedrals?
   topIn.ClearBondArrays();
-  // Create a combined bonds array
-  BondArray allBonds;
-  allBonds.reserve(topIn.Nbonds());
 
+  // BONDS
   int bidx = 0;
   for (int ires = 0; ires < topIn.Nres(); ires++)
   {
@@ -87,7 +136,6 @@ int Cpptraj::Structure::GenerateBondAngleTorsionArrays(Topology& topIn) {
       {
         if (iat < *bat) {
           mprintf("DEBUG: BOND  i= %i  %i - %i (%i %i)\n",  bidx++, iat+1, *bat+1, iat*3, *bat*3);
-          allBonds.push_back( BondType(iat, *bat, -1) );
           topIn.AddToBondArrays( BondType(iat, *bat, -1) );
         }
         //else
@@ -118,29 +166,6 @@ int Cpptraj::Structure::GenerateBondAngleTorsionArrays(Topology& topIn) {
     }
   }
 
-  //mprintf("DEBUG: Sorted bonds:\n");
-  //for (BondArray::const_iterator it = allBonds.begin(); it != allBonds.end(); ++it)
-  //  mprintf("\t%s - %s\n",
-  //          topIn.AtomMaskName(it->A1()).c_str(),
-  //          topIn.AtomMaskName(it->A2()).c_str());
-
-  // Angles
-  //AngleArray angles;
-  //AngleArray anglesH;
-  aidx = 0;
-  for (BondArray::const_iterator it = allBonds.begin(); it != allBonds.end(); ++it)
-  {
-    //if (!has_angles) {
-    //  // Forward direction. A1-A2-X
-    //  enumerateAngles( aidx, it->A1(), it->A2(), topIn );
-    //  // Reverse direction. A2-A1-X
-    //  enumerateAngles( aidx, it->A2(), it->A1(), topIn );
-    //}
-    if (!has_dihedrals) {
-      // Dihedrals
-      enumerateDihedrals( it->A1(), it->A2(), topIn );
-    }
-  }
   return 0;
 }
 
diff --git a/src/Structure/GenerateConnectivity.h b/src/Structure/GenerateConnectivity.h
index d56585b9dc..8016cde261 100644
--- a/src/Structure/GenerateConnectivity.h
+++ b/src/Structure/GenerateConnectivity.h
@@ -5,6 +5,8 @@ class AtomType;
 template <typename Type> class ParmHolder;
 namespace Cpptraj {
 namespace Structure {
+/// Generate angle/torsion arrays from bond arrays in a Topology
+int GenerateAngleTorsionArrays(Topology&);
 /// Generate bond/angle/torsion arrays from atom connectivity in a Topology
 int GenerateBondAngleTorsionArrays(Topology&);
 /// Generate impropers in a Topology

From e7e53cc7cfcbe1ad84fe624bb05b235983d2f1fc Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 3 Jan 2024 12:58:25 -0500
Subject: [PATCH 0240/1492] Add torsion search that mimics leap

---
 src/Structure/GenerateConnectivity.cpp | 28 ++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/src/Structure/GenerateConnectivity.cpp b/src/Structure/GenerateConnectivity.cpp
index e20a2f777b..207aaf575f 100644
--- a/src/Structure/GenerateConnectivity.cpp
+++ b/src/Structure/GenerateConnectivity.cpp
@@ -166,6 +166,34 @@ int Cpptraj::Structure::GenerateBondAngleTorsionArrays(Topology& topIn) {
     }
   }
 
+  // TORSIONS TODO combine above
+  int didx = 0;
+  for (int ires = 0; ires < topIn.Nres(); ires++)
+  {
+    Residue const& res = topIn.Res(ires);
+    for (int iat1 = res.LastAtom()-1; iat1 >= res.FirstAtom(); iat1--)
+    {
+      Atom const& At1 = topIn[iat1];
+      for (int bidx1 = 0; bidx1 < At1.Nbonds(); bidx1++) {
+        int iat2 = At1.Bond(bidx1);
+        Atom const& At2 = topIn[iat2];
+        for (int bidx2 = 0; bidx2 < At2.Nbonds(); bidx2++) {
+          int iat3 = At2.Bond(bidx2);
+          if (iat3 != iat1) {
+            Atom const& At3 = topIn[iat3];
+            for (int bidx3 = 0; bidx3 < At3.Nbonds(); bidx3++) {
+              int iat4 = At3.Bond(bidx3);
+              if (iat4 != iat2 && iat1 < iat4) {
+                mprintf("DEBUG: DIHEDRAL  i= %i  %i - %i - %i - %i (%i %i %i %i)\n", didx++, iat1+1, iat2+1, iat3+1, iat4+1, iat1*3, iat2*3, iat3*3, iat4*3);
+                topIn.AddDihedral( iat1, iat2, iat3, iat4 );
+              }
+            }
+          }
+        }
+      }
+    }
+  }
+
   return 0;
 }
 

From 1e93a49c6ebd8a5fc443c2f4ff2f116c07fd64cc Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 3 Jan 2024 13:05:49 -0500
Subject: [PATCH 0241/1492] Switch order in which impropers are searched for to
 match leap

---
 src/Structure/GenerateConnectivity.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Structure/GenerateConnectivity.cpp b/src/Structure/GenerateConnectivity.cpp
index 207aaf575f..1b20a6c3b5 100644
--- a/src/Structure/GenerateConnectivity.cpp
+++ b/src/Structure/GenerateConnectivity.cpp
@@ -306,7 +306,7 @@ static int order_improper_atoms(int* indices, int centralAt, Topology const& top
 
 /** Try to determine impropers for topology. */ // TODO option for charmm improper
 int Cpptraj::Structure::GenerateImpropers(Topology& topIn, ParmHolder<AtomType> const& AT) {
-  for (int iat = 0; iat != topIn.Natom(); iat++) {
+  for (int iat = topIn.Natom()-1; iat >= 0; iat--) {
     Atom const& AJ = topIn[iat];
     if (AJ.Nbonds() == 3) { // TODO only 3 atoms OK?
       AtomType::HybridizationType hybrid = AtomType::UNKNOWN_HYBRIDIZATION; 

From d79b3e2714858386645506e2749ee141d807141c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 3 Jan 2024 14:28:10 -0500
Subject: [PATCH 0242/1492] Add function for generating a bond array in same
 order as leap. Created BondArray class so it can be forward declared.

---
 src/Exec_CompareEnergy.cpp             |  4 +--
 src/ParameterTypes.h                   | 41 +++++++++++++++++++++++++-
 src/Structure/GenerateConnectivity.cpp | 26 ++++++++++++++++
 src/Structure/GenerateConnectivity.h   |  3 ++
 4 files changed, 71 insertions(+), 3 deletions(-)

diff --git a/src/Exec_CompareEnergy.cpp b/src/Exec_CompareEnergy.cpp
index 5040fb092f..519b3a278b 100644
--- a/src/Exec_CompareEnergy.cpp
+++ b/src/Exec_CompareEnergy.cpp
@@ -146,8 +146,8 @@ const
 
   Eresults Ebond(bondDeltaE_, bondDeltaR_);
   CalcEnergy<BondType, BondParmType>(Ebond, bondout_,
-                                     frame0, commonBonds0_, top0.BondParm(),
-                                     frame1, commonBonds1_, top1.BondParm(),
+                                     frame0, commonBonds0_.Array(), top0.BondParm(),
+                                     frame1, commonBonds1_.Array(), top1.BondParm(),
                                      bondNames_, EBONDFXN);
   Ebond.Print( bondout_, "Bond" );
 }
diff --git a/src/ParameterTypes.h b/src/ParameterTypes.h
index 99dbd05568..611a350986 100644
--- a/src/ParameterTypes.h
+++ b/src/ParameterTypes.h
@@ -81,7 +81,46 @@ class BondType {
     int a2_;
     int idx_;
 };
-typedef std::vector<BondType> BondArray;
+/// Hold array of bond parameters
+class BondArray {
+    typedef std::vector<BondType> BArray;
+  public:
+    /// CONSTRUCTOR
+    BondArray() {}
+
+    /// iterator
+    typedef BArray::iterator iterator;
+    /// begin
+    iterator begin() { return bonds_.begin(); }
+    /// end
+    iterator end()   { return bonds_.end();   }
+    /// const iterator
+    typedef BArray::const_iterator const_iterator;
+    /// const begin
+    const_iterator begin() const { return bonds_.begin(); }
+    /// const end
+    const_iterator end()   const { return bonds_.end();   }
+
+    /// Reserve space for # of bonds
+    void reserve(size_t n) { bonds_.reserve(n); }
+    /// Add bond
+    void push_back(BondType const& b) { bonds_.push_back(b); }
+    /// Clear bonds
+    void clear() { bonds_.clear(); }
+    /// Erase given bond from array
+    void erase( iterator bnd ) { bonds_.erase( bnd ); }
+
+    /// \return true if no bonds
+    bool empty()  const { return bonds_.empty(); }
+    /// \return number of bonds
+    size_t size() const { return bonds_.size(); }
+    /// \return specified bond
+    BondType const& operator[](size_t idx) const { return bonds_[idx]; }
+    /// \return underlying array
+    std::vector<BondType> const& Array() const { return bonds_; }
+  private:
+    BArray bonds_;
+};
 /// Hold angle parameters
 class AngleParmType {
   public:
diff --git a/src/Structure/GenerateConnectivity.cpp b/src/Structure/GenerateConnectivity.cpp
index 1b20a6c3b5..31388ccc8e 100644
--- a/src/Structure/GenerateConnectivity.cpp
+++ b/src/Structure/GenerateConnectivity.cpp
@@ -100,6 +100,32 @@ int Cpptraj::Structure::GenerateAngleTorsionArrays(Topology& topIn) {
   return 0;
 }
 
+/** From atom connectivity, generate a bond array in the same order as LEaP. */ // TODO use in GenerateBAT
+BondArray Cpptraj::Structure::GenerateBondArray(Topology const& topIn)
+{
+  BondArray out;
+  // BONDS
+  int bidx = 0;
+  for (int ires = 0; ires < topIn.Nres(); ires++)
+  {
+    Residue const& res = topIn.Res(ires);
+    for (int iat = res.LastAtom()-1; iat >= res.FirstAtom(); iat--)
+    {
+      Atom const& At = topIn[iat];
+      for (Atom::bond_iterator bat = At.bondbegin(); bat != At.bondend(); ++bat)
+      {
+        if (iat < *bat) {
+          mprintf("DEBUG: BOND  i= %i  %i - %i (%i %i)\n",  bidx++, iat+1, *bat+1, iat*3, *bat*3);
+          out.push_back( BondType(iat, *bat, -1) );
+        }
+        //else
+        //  mprintf("DEBUG: X    i= %i  %i - %i (%i %i)\n",   bidx++, iat+1, *bat+1, iat*3, *bat*3);
+      }
+    }
+  }
+  return out;
+}
+
 /* Set bonds, angles, and dihedral arrays for a given topology based on 
  * current atom connectivity.
  * This is done in the same manner as LEaP, which goes in increasing
diff --git a/src/Structure/GenerateConnectivity.h b/src/Structure/GenerateConnectivity.h
index 8016cde261..38040e73ef 100644
--- a/src/Structure/GenerateConnectivity.h
+++ b/src/Structure/GenerateConnectivity.h
@@ -2,6 +2,7 @@
 #define INC_STRUCTURE_GENERATECONNECTIVITY_H
 class Topology;
 class AtomType;
+class BondArray;
 template <typename Type> class ParmHolder;
 namespace Cpptraj {
 namespace Structure {
@@ -11,6 +12,8 @@ int GenerateAngleTorsionArrays(Topology&);
 int GenerateBondAngleTorsionArrays(Topology&);
 /// Generate impropers in a Topology
 int GenerateImpropers(Topology&, ParmHolder<AtomType> const&);
+/// Generate bond array in same order as leap
+BondArray GenerateBondArray(Topology const&);
 }
 }
 #endif

From a8108e4f8a38c1f78c9d26f4f5cd3e14dcc3d64f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 3 Jan 2024 16:01:40 -0500
Subject: [PATCH 0243/1492] Add GenerateConnectivityArrays

---
 src/Structure/CMakeLists.txt                 |  1 +
 src/Structure/GenerateConnectivityArrays.cpp | 33 ++++++++++++++++++++
 src/Structure/GenerateConnectivityArrays.h   | 13 ++++++++
 src/Structure/structuredepend                |  1 +
 src/Structure/structurefiles                 |  1 +
 5 files changed, 49 insertions(+)
 create mode 100644 src/Structure/GenerateConnectivityArrays.cpp
 create mode 100644 src/Structure/GenerateConnectivityArrays.h

diff --git a/src/Structure/CMakeLists.txt b/src/Structure/CMakeLists.txt
index 7350e7edca..d04716f8bc 100644
--- a/src/Structure/CMakeLists.txt
+++ b/src/Structure/CMakeLists.txt
@@ -5,6 +5,7 @@ target_sources(cpptraj_common_obj PRIVATE
   ${CMAKE_CURRENT_LIST_DIR}/Disulfide.cpp
   ${CMAKE_CURRENT_LIST_DIR}/FunctionalGroup.cpp
   ${CMAKE_CURRENT_LIST_DIR}/FxnGroupBuilder.cpp
+  ${CMAKE_CURRENT_LIST_DIR}/GenerateConnectivityArrays.cpp
   ${CMAKE_CURRENT_LIST_DIR}/GenerateConnectivity.cpp
   ${CMAKE_CURRENT_LIST_DIR}/HisProt.cpp
   ${CMAKE_CURRENT_LIST_DIR}/InternalCoords.cpp
diff --git a/src/Structure/GenerateConnectivityArrays.cpp b/src/Structure/GenerateConnectivityArrays.cpp
new file mode 100644
index 0000000000..e19b0acd3c
--- /dev/null
+++ b/src/Structure/GenerateConnectivityArrays.cpp
@@ -0,0 +1,33 @@
+#include "GenerateConnectivityArrays.h"
+#include "../ParameterTypes.h"
+#include "../Atom.h"
+#include "../Residue.h"
+#include "../CpptrajStdio.h"
+
+/** From atom connectivity, generate a bond array in the same order as LEaP. */ // TODO use in GenerateBAT
+BondArray Cpptraj::Structure::GenerateBondArray(std::vector<Residue> const& residues,
+                                                std::vector<Atom> const& atoms)
+{
+  BondArray out;
+  // BONDS
+  int bidx = 0;
+  for (std::vector<Residue>::const_iterator res = residues.begin(); res != residues.end(); ++res)
+  {
+    for (int iat = res->LastAtom()-1; iat >= res->FirstAtom(); iat--)
+    {
+      Atom const& At = atoms[iat];
+      for (Atom::bond_iterator bat = At.bondbegin(); bat != At.bondend(); ++bat)
+      {
+        if (iat < *bat) {
+          mprintf("DEBUG: BOND  i= %i  %i - %i (%i %i)\n",  bidx++, iat+1, *bat+1, iat*3, *bat*3);
+          out.push_back( BondType(iat, *bat, -1) );
+        }
+        //else
+        //  mprintf("DEBUG: X    i= %i  %i - %i (%i %i)\n",   bidx++, iat+1, *bat+1, iat*3, *bat*3);
+      }
+    }
+  }
+  return out;
+}
+
+
diff --git a/src/Structure/GenerateConnectivityArrays.h b/src/Structure/GenerateConnectivityArrays.h
new file mode 100644
index 0000000000..b0503642f1
--- /dev/null
+++ b/src/Structure/GenerateConnectivityArrays.h
@@ -0,0 +1,13 @@
+#ifndef INC_STRUCTURE_GENERATECONNECTIVITYARRAYS_H
+#define INC_STRUCTURE_GENERATECONNECTIVITYARRAYS_H
+#include <vector>
+class BondArray;
+class Residue;
+class Atom;
+namespace Cpptraj {
+namespace Structure {
+/// Generate bond array in same order as leap
+BondArray GenerateBondArray(std::vector<Residue> const&, std::vector<Atom> const&);
+}
+}
+#endif
diff --git a/src/Structure/structuredepend b/src/Structure/structuredepend
index b99a9b01ec..eedc6f95c4 100644
--- a/src/Structure/structuredepend
+++ b/src/Structure/structuredepend
@@ -4,6 +4,7 @@ Disulfide.o : Disulfide.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Co
 FunctionalGroup.o : FunctionalGroup.cpp ../Atom.h ../AtomMap.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h FunctionalGroup.h
 FxnGroupBuilder.o : FxnGroupBuilder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h FunctionalGroup.h FxnGroupBuilder.h StructureRoutines.h Sugar.h SugarToken.h
 GenerateConnectivity.o : GenerateConnectivity.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h GenerateConnectivity.h
+GenerateConnectivityArrays.o : GenerateConnectivityArrays.cpp ../Atom.h ../Constants.h ../CpptrajStdio.h ../NameType.h ../ParameterTypes.h ../Residue.h ../SymbolExporting.h GenerateConnectivityArrays.h
 HisProt.o : HisProt.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h HisProt.h StructureRoutines.h
 InternalCoords.o : InternalCoords.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h InternalCoords.h
 Model.o : Model.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h Model.h StructureEnum.h
diff --git a/src/Structure/structurefiles b/src/Structure/structurefiles
index 47dcb912e4..6a6dd3da57 100644
--- a/src/Structure/structurefiles
+++ b/src/Structure/structurefiles
@@ -5,6 +5,7 @@ STRUCTURE_SOURCES= \
   Disulfide.cpp \
   FunctionalGroup.cpp \
   FxnGroupBuilder.cpp \
+  GenerateConnectivityArrays.cpp \
   GenerateConnectivity.cpp \
   HisProt.cpp \
   InternalCoords.cpp \

From 70cf575ce0dc607a0a333b82fb0be875e8fc4da4 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 3 Jan 2024 16:06:10 -0500
Subject: [PATCH 0244/1492] GenerateBondArray is now in a separate file so that
 Topology can use it

---
 src/Structure/GenerateConnectivity.cpp | 26 --------------------------
 src/Structure/GenerateConnectivity.h   |  3 ---
 2 files changed, 29 deletions(-)

diff --git a/src/Structure/GenerateConnectivity.cpp b/src/Structure/GenerateConnectivity.cpp
index 31388ccc8e..1b20a6c3b5 100644
--- a/src/Structure/GenerateConnectivity.cpp
+++ b/src/Structure/GenerateConnectivity.cpp
@@ -100,32 +100,6 @@ int Cpptraj::Structure::GenerateAngleTorsionArrays(Topology& topIn) {
   return 0;
 }
 
-/** From atom connectivity, generate a bond array in the same order as LEaP. */ // TODO use in GenerateBAT
-BondArray Cpptraj::Structure::GenerateBondArray(Topology const& topIn)
-{
-  BondArray out;
-  // BONDS
-  int bidx = 0;
-  for (int ires = 0; ires < topIn.Nres(); ires++)
-  {
-    Residue const& res = topIn.Res(ires);
-    for (int iat = res.LastAtom()-1; iat >= res.FirstAtom(); iat--)
-    {
-      Atom const& At = topIn[iat];
-      for (Atom::bond_iterator bat = At.bondbegin(); bat != At.bondend(); ++bat)
-      {
-        if (iat < *bat) {
-          mprintf("DEBUG: BOND  i= %i  %i - %i (%i %i)\n",  bidx++, iat+1, *bat+1, iat*3, *bat*3);
-          out.push_back( BondType(iat, *bat, -1) );
-        }
-        //else
-        //  mprintf("DEBUG: X    i= %i  %i - %i (%i %i)\n",   bidx++, iat+1, *bat+1, iat*3, *bat*3);
-      }
-    }
-  }
-  return out;
-}
-
 /* Set bonds, angles, and dihedral arrays for a given topology based on 
  * current atom connectivity.
  * This is done in the same manner as LEaP, which goes in increasing
diff --git a/src/Structure/GenerateConnectivity.h b/src/Structure/GenerateConnectivity.h
index 38040e73ef..8016cde261 100644
--- a/src/Structure/GenerateConnectivity.h
+++ b/src/Structure/GenerateConnectivity.h
@@ -2,7 +2,6 @@
 #define INC_STRUCTURE_GENERATECONNECTIVITY_H
 class Topology;
 class AtomType;
-class BondArray;
 template <typename Type> class ParmHolder;
 namespace Cpptraj {
 namespace Structure {
@@ -12,8 +11,6 @@ int GenerateAngleTorsionArrays(Topology&);
 int GenerateBondAngleTorsionArrays(Topology&);
 /// Generate impropers in a Topology
 int GenerateImpropers(Topology&, ParmHolder<AtomType> const&);
-/// Generate bond array in same order as leap
-BondArray GenerateBondArray(Topology const&);
 }
 }
 #endif

From 0030723030dfc2b6653d16758eab7667094739c4 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 3 Jan 2024 16:06:29 -0500
Subject: [PATCH 0245/1492] When assigning bond parameters, regenerate the bond
 arrays in a leap type order so parameter assignment happens the same way.

---
 src/Topology.cpp  | 12 ++++++++++--
 src/cpptrajdepend |  3 ++-
 2 files changed, 12 insertions(+), 3 deletions(-)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index 7b83420bc2..a6326c39a8 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -7,6 +7,7 @@
 #include "AtomType.h"
 #include "AtomMask.h"
 #include "CharMask.h"
+#include "Structure/GenerateConnectivityArrays.h"
 
 const NonbondType Topology::LJ_EMPTY = NonbondType();
 
@@ -2600,8 +2601,15 @@ const
 /** Replace any current bond parameters with given bond parameters. */
 void Topology::AssignBondParams(ParmHolder<BondParmType> const& newBondParams) {
   bondparm_.clear();
-  AssignBondParm( newBondParams, bonds_,  bondparm_, "bond" );
-  AssignBondParm( newBondParams, bondsh_, bondparm_, "bond" );
+  // Regenerate bond array in LEaP order
+  bonds_.clear();
+  bondsh_.clear();
+  BondArray allBonds = Cpptraj::Structure::GenerateBondArray(residues_, atoms_);
+  AssignBondParm( newBondParams, allBonds, bondparm_, "bond" );
+  for (BondArray::const_iterator bnd = allBonds.begin(); bnd != allBonds.end(); ++bnd)
+    AddToBondArrays( *bnd );
+//  AssignBondParm( newBondParams, bonds_,  bondparm_, "bond" );
+//  AssignBondParm( newBondParams, bondsh_, bondparm_, "bond" );
 /**  // Try to match leap bond ordering. Appears to be by index with priority
   // given to heavy atoms.
   BondArray tmpBonds;
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index db7c95c1c7..c1cdc06b6b 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -448,6 +448,7 @@ Structure/Disulfide.o : Structure/Disulfide.cpp Atom.h AtomMask.h AtomType.h Box
 Structure/FunctionalGroup.o : Structure/FunctionalGroup.cpp Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/FxnGroupBuilder.o : Structure/FxnGroupBuilder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h Structure/FxnGroupBuilder.h Structure/StructureRoutines.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/GenerateConnectivity.o : Structure/GenerateConnectivity.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h GuessAtomHybridization.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/GenerateConnectivity.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Structure/GenerateConnectivityArrays.o : Structure/GenerateConnectivityArrays.cpp Atom.h Constants.h CpptrajStdio.h NameType.h ParameterTypes.h Residue.h Structure/GenerateConnectivityArrays.h SymbolExporting.h
 Structure/HisProt.o : Structure/HisProt.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/HisProt.h Structure/StructureRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/InternalCoords.o : Structure/InternalCoords.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/InternalCoords.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/Model.o : Structure/Model.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h GuessAtomHybridization.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/Model.h Structure/StructureEnum.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
@@ -466,7 +467,7 @@ TextFormat.o : TextFormat.cpp StringRoutines.h TextFormat.h
 Timer.o : Timer.cpp CpptrajStdio.h Timer.h
 TinkerFile.o : TinkerFile.cpp ArgList.h Atom.h AtomMask.h Box.h BufferedLine.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TinkerFile.h Unit.h Vec3.h
 TopInfo.o : TopInfo.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h DistRoutines.h FileIO.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Mol.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h TopInfo.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Topology.o : Topology.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Topology.o : Topology.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/GenerateConnectivityArrays.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 TorsionRoutines.o : TorsionRoutines.cpp Constants.h TorsionRoutines.h Vec3.h
 TrajFrameCounter.o : TrajFrameCounter.cpp ArgList.h CpptrajStdio.h TrajFrameCounter.h
 TrajIOarray.o : TrajIOarray.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryFile.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h

From 284db71e69dad5bb7521d7be209cff6d07a4d8bf Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 3 Jan 2024 16:14:37 -0500
Subject: [PATCH 0246/1492] Generate angles same order as leap function

---
 src/ParameterTypes.h                         | 41 +++++++++++++++++++-
 src/Structure/GenerateConnectivityArrays.cpp | 28 ++++++++++++-
 src/Structure/GenerateConnectivityArrays.h   |  3 ++
 3 files changed, 70 insertions(+), 2 deletions(-)

diff --git a/src/ParameterTypes.h b/src/ParameterTypes.h
index 611a350986..7efdd13c77 100644
--- a/src/ParameterTypes.h
+++ b/src/ParameterTypes.h
@@ -175,7 +175,46 @@ class AngleType {
     int a3_;
     int idx_;
 };
-typedef std::vector<AngleType> AngleArray;
+/// Hold array of angle parameters
+class AngleArray {
+    typedef std::vector<AngleType> AArray;
+  public:
+    /// CONSTRUCTOR
+    AngleArray() {}
+
+    /// iterator
+    typedef AArray::iterator iterator;
+    /// begin
+    iterator begin() { return angles_.begin(); }
+    /// end
+    iterator end()   { return angles_.end();   }
+    /// const iterator
+    typedef AArray::const_iterator const_iterator;
+    /// const begin
+    const_iterator begin() const { return angles_.begin(); }
+    /// const end
+    const_iterator end()   const { return angles_.end();   }
+
+    /// Reserve space for # of angles
+    void reserve(size_t n) { angles_.reserve(n); }
+    /// Add angle
+    void push_back(AngleType const& b) { angles_.push_back(b); }
+    /// Clear angles
+    void clear() { angles_.clear(); }
+    /// Erase given angle from array
+    void erase( iterator bnd ) { angles_.erase( bnd ); }
+
+    /// \return true if no angles
+    bool empty()  const { return angles_.empty(); }
+    /// \return number of angles
+    size_t size() const { return angles_.size(); }
+    /// \return specified angle
+    AngleType const& operator[](size_t idx) const { return angles_[idx]; }
+    /// \return underlying array
+    std::vector<AngleType> const& Array() const { return angles_; }
+  private:
+    AArray angles_;
+};
 /// Hold dihedral parameters
 class DihedralParmType {
   public:
diff --git a/src/Structure/GenerateConnectivityArrays.cpp b/src/Structure/GenerateConnectivityArrays.cpp
index e19b0acd3c..88e973a91a 100644
--- a/src/Structure/GenerateConnectivityArrays.cpp
+++ b/src/Structure/GenerateConnectivityArrays.cpp
@@ -30,4 +30,30 @@ BondArray Cpptraj::Structure::GenerateBondArray(std::vector<Residue> const& resi
   return out;
 }
 
-
+/** From atom connectiviy, generate an angle array in the same order as LEaP. */ // TODO use in GenerateBAT
+AngleArray Cpptraj::Structure::GenerateAngleArray(std::vector<Residue> const& residues,
+                                                  std::vector<Atom> const& atoms)
+{
+  AngleArray out;
+  // ANGLES TODO combine above
+  int aidx = 0;
+  for (std::vector<Residue>::const_iterator res = residues.begin(); res != residues.end(); ++res)
+  {
+    for (int iat1 = res->LastAtom()-1; iat1 >= res->FirstAtom(); iat1--)
+    {
+      Atom const& At1 = atoms[iat1];
+      for (int bidx1 = 0; bidx1 < At1.Nbonds(); bidx1++) {
+        int iat2 = At1.Bond(bidx1);
+        Atom const& At2 = atoms[iat2];
+        for (int bidx2 = 0; bidx2 < At2.Nbonds(); bidx2++) {
+          int iat3 = At2.Bond(bidx2);
+          if (iat1 < iat3) {
+            mprintf("DEBUG: ANGLE  i= %i  %i - %i - %i (%i %i %i)\n", aidx++, iat1+1, iat2+1, iat3+1, iat1*3, iat2*3, iat3*3);
+            out.push_back( AngleType(iat1, iat2, iat3, -1) );
+          }
+        }
+      }
+    }
+  }
+  return out;
+}
diff --git a/src/Structure/GenerateConnectivityArrays.h b/src/Structure/GenerateConnectivityArrays.h
index b0503642f1..aaebff0cdf 100644
--- a/src/Structure/GenerateConnectivityArrays.h
+++ b/src/Structure/GenerateConnectivityArrays.h
@@ -2,12 +2,15 @@
 #define INC_STRUCTURE_GENERATECONNECTIVITYARRAYS_H
 #include <vector>
 class BondArray;
+class AngleArray;
 class Residue;
 class Atom;
 namespace Cpptraj {
 namespace Structure {
 /// Generate bond array in same order as leap
 BondArray GenerateBondArray(std::vector<Residue> const&, std::vector<Atom> const&);
+/// Generate angle array in same order as leap
+AngleArray GenerateAngleArray(std::vector<Residue> const&, std::vector<Atom> const&);
 }
 }
 #endif

From a92c819f2fdb4fc44ec8aa51cc8c600e04b1a3b4 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 3 Jan 2024 16:16:33 -0500
Subject: [PATCH 0247/1492] Add DihedralArray class

---
 src/ParameterTypes.h | 41 ++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 40 insertions(+), 1 deletion(-)

diff --git a/src/ParameterTypes.h b/src/ParameterTypes.h
index 7efdd13c77..380408b0b5 100644
--- a/src/ParameterTypes.h
+++ b/src/ParameterTypes.h
@@ -350,7 +350,46 @@ class DihedralType {
     bool skip14_; ///< If true the 1-4 interaction for this dihedral should be skipped.
     bool improper_; ///< If true this is an improper dihedral.
 };
-typedef std::vector<DihedralType> DihedralArray;
+/// Hold array of dihedral parameters
+class DihedralArray {
+    typedef std::vector<DihedralType> DArray;
+  public:
+    /// CONSTRUCTOR
+    DihedralArray() {}
+
+    /// iterator
+    typedef DArray::iterator iterator;
+    /// begin
+    iterator begin() { return dihedrals_.begin(); }
+    /// end
+    iterator end()   { return dihedrals_.end();   }
+    /// const iterator
+    typedef DArray::const_iterator const_iterator;
+    /// const begin
+    const_iterator begin() const { return dihedrals_.begin(); }
+    /// const end
+    const_iterator end()   const { return dihedrals_.end();   }
+
+    /// Reserve space for # of dihedrals
+    void reserve(size_t n) { dihedrals_.reserve(n); }
+    /// Add dihedral
+    void push_back(DihedralType const& b) { dihedrals_.push_back(b); }
+    /// Clear dihedrals
+    void clear() { dihedrals_.clear(); }
+    /// Erase given dihedral from array
+    void erase( iterator bnd ) { dihedrals_.erase( bnd ); }
+
+    /// \return true if no dihedrals
+    bool empty()  const { return dihedrals_.empty(); }
+    /// \return number of dihedrals
+    size_t size() const { return dihedrals_.size(); }
+    /// \return specified dihedral
+    DihedralType const& operator[](size_t idx) const { return dihedrals_[idx]; }
+    /// \return underlying array
+    std::vector<DihedralType> const& Array() const { return dihedrals_; }
+  private:
+    DArray dihedrals_;
+};
 // ----- NON-BONDED PARAMETERS -------------------------------------------------
 /// Hold LJ 10-12 hbond params
 class HB_ParmType {

From c025fcfad309c11950f5ddec3f056e77c6518265 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 3 Jan 2024 16:19:58 -0500
Subject: [PATCH 0248/1492] Generate dihedral array in same order as leap
 function

---
 src/Structure/GenerateConnectivityArrays.cpp | 34 ++++++++++++++++++++
 src/Structure/GenerateConnectivityArrays.h   |  3 ++
 2 files changed, 37 insertions(+)

diff --git a/src/Structure/GenerateConnectivityArrays.cpp b/src/Structure/GenerateConnectivityArrays.cpp
index 88e973a91a..8d5590893a 100644
--- a/src/Structure/GenerateConnectivityArrays.cpp
+++ b/src/Structure/GenerateConnectivityArrays.cpp
@@ -57,3 +57,37 @@ AngleArray Cpptraj::Structure::GenerateAngleArray(std::vector<Residue> const& re
   }
   return out;
 }
+
+/** From atom connectivity, generate a dihedral array in the same order as LEaP. */ // TODO use in GenerateBAT
+DihedralArray Cpptraj::Structure::GenerateDihedralArray(std::vector<Residue> const& residues,
+                                                        std::vector<Atom> const& atoms)
+{
+  DihedralArray out;
+  // TORSIONS TODO combine above
+  int didx = 0;
+  for (std::vector<Residue>::const_iterator res = residues.begin(); res != residues.end(); ++res)
+  {
+    for (int iat1 = res->LastAtom()-1; iat1 >= res->FirstAtom(); iat1--)
+    {
+      Atom const& At1 = atoms[iat1];
+      for (int bidx1 = 0; bidx1 < At1.Nbonds(); bidx1++) {
+        int iat2 = At1.Bond(bidx1);
+        Atom const& At2 = atoms[iat2];
+        for (int bidx2 = 0; bidx2 < At2.Nbonds(); bidx2++) {
+          int iat3 = At2.Bond(bidx2);
+          if (iat3 != iat1) {
+            Atom const& At3 = atoms[iat3];
+            for (int bidx3 = 0; bidx3 < At3.Nbonds(); bidx3++) {
+              int iat4 = At3.Bond(bidx3);
+              if (iat4 != iat2 && iat1 < iat4) {
+                mprintf("DEBUG: DIHEDRAL  i= %i  %i - %i - %i - %i (%i %i %i %i)\n", didx++, iat1+1, iat2+1, iat3+1, iat4+1, iat1*3, iat2*3, iat3*3, iat4*3);
+                out.push_back( DihedralType( iat1, iat2, iat3, iat4, -1 ) );
+              }
+            }
+          }
+        }
+      }
+    }
+  }
+  return out;
+}
diff --git a/src/Structure/GenerateConnectivityArrays.h b/src/Structure/GenerateConnectivityArrays.h
index aaebff0cdf..0119c0f391 100644
--- a/src/Structure/GenerateConnectivityArrays.h
+++ b/src/Structure/GenerateConnectivityArrays.h
@@ -3,6 +3,7 @@
 #include <vector>
 class BondArray;
 class AngleArray;
+class DihedralArray;
 class Residue;
 class Atom;
 namespace Cpptraj {
@@ -11,6 +12,8 @@ namespace Structure {
 BondArray GenerateBondArray(std::vector<Residue> const&, std::vector<Atom> const&);
 /// Generate angle array in same order as leap
 AngleArray GenerateAngleArray(std::vector<Residue> const&, std::vector<Atom> const&);
+/// Generate dihedral array in same order as leap
+DihedralArray GenerateDihedralArray(std::vector<Residue> const&, std::vector<Atom> const&);
 }
 }
 #endif

From ae6cda59e2b48a45ddee442aca5c39f98f5af773 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 3 Jan 2024 16:32:23 -0500
Subject: [PATCH 0249/1492] Update for new array types

---
 src/Exec_CompareEnergy.cpp | 8 ++++----
 src/ParameterTypes.h       | 2 ++
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/src/Exec_CompareEnergy.cpp b/src/Exec_CompareEnergy.cpp
index 519b3a278b..4b83e2015b 100644
--- a/src/Exec_CompareEnergy.cpp
+++ b/src/Exec_CompareEnergy.cpp
@@ -234,8 +234,8 @@ const
 
   Eresults Eangle(angleDeltaE_, angleDeltaR_);
   CalcEnergy<AngleType, AngleParmType>(Eangle, angleout_,
-                                     frame0, commonAngles0_, top0.AngleParm(),
-                                     frame1, commonAngles1_, top1.AngleParm(),
+                                     frame0, commonAngles0_.Array(), top0.AngleParm(),
+                                     frame1, commonAngles1_.Array(), top1.AngleParm(),
                                      angleNames_, EANGFXN);
   Eangle.Print( angleout_, "Angle" );
 }
@@ -324,8 +324,8 @@ const
 
   Eresults Edihedral(dihedralDeltaE_, dihedralDeltaR_);
   CalcEnergy<DihedralType, DihedralParmType>(Edihedral, dihedralout_,
-                                             frame0, commonDihedrals0_, top0.DihedralParm(),
-                                             frame1, commonDihedrals1_, top1.DihedralParm(),
+                                             frame0, commonDihedrals0_.Array(), top0.DihedralParm(),
+                                             frame1, commonDihedrals1_.Array(), top1.DihedralParm(),
                                              dihedralNames_, EDIHFXN);
   Edihedral.Print( dihedralout_, "Dihedral" );
 }
diff --git a/src/ParameterTypes.h b/src/ParameterTypes.h
index 380408b0b5..12ace1b869 100644
--- a/src/ParameterTypes.h
+++ b/src/ParameterTypes.h
@@ -385,6 +385,8 @@ class DihedralArray {
     size_t size() const { return dihedrals_.size(); }
     /// \return specified dihedral
     DihedralType const& operator[](size_t idx) const { return dihedrals_[idx]; }
+    /// \return last dihedral added
+    DihedralType const& back() const { return dihedrals_.back(); }
     /// \return underlying array
     std::vector<DihedralType> const& Array() const { return dihedrals_; }
   private:

From c5f2d52ded3e32abe21df72f3d4328ba6470af9e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 3 Jan 2024 16:40:46 -0500
Subject: [PATCH 0250/1492] Do angles the same way as leap

---
 src/Topology.cpp | 22 ++++++++++++++++++++--
 src/Topology.h   |  4 +++-
 2 files changed, 23 insertions(+), 3 deletions(-)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index a6326c39a8..864942e0be 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -980,6 +980,17 @@ void Topology::AddAngle(AngleType const& angIn, bool isH) {
     angles_.push_back( angIn );
 }
 
+/** Add to angle arrays. Used when regenerating angle information
+  * from atom connectivity.
+  */
+void Topology::AddToAngleArrays(AngleType const& ang) {
+  if (atoms_[ang.A1()].Element() == Atom::HYDROGEN ||
+      atoms_[ang.A2()].Element() == Atom::HYDROGEN ||
+      atoms_[ang.A3()].Element() == Atom::HYDROGEN)
+    anglesh_.push_back( ang );
+  else
+    angles_.push_back( ang );
+}
 // -----------------------------------------------
 /** Check if given dihedral parm exists in given dihedral parm array. Add if not.
   * \return Index in dihedral parm array.
@@ -2713,8 +2724,15 @@ void Topology::AssignAngleParm(ParmHolder<AngleParmType> const& newAngleParams,
 /** Replace any current angle parameters with given angle parameters. */
 void Topology::AssignAngleParams(ParmHolder<AngleParmType> const& newAngleParams) {
   angleparm_.clear();
-  AssignAngleParm( newAngleParams, angles_ );
-  AssignAngleParm( newAngleParams, anglesh_ );
+  // Regenerate angle array in LEaP order
+  angles_.clear();
+  anglesh_.clear();
+  AngleArray allAngles = Cpptraj::Structure::GenerateAngleArray(residues_, atoms_);
+  AssignAngleParm( newAngleParams, allAngles );
+  for (AngleArray::const_iterator ang = allAngles.begin(); ang != allAngles.end(); ++ang)
+    AddToAngleArrays( *ang );
+  //AssignAngleParm( newAngleParams, angles_ );
+  //AssignAngleParm( newAngleParams, anglesh_ );
 }
 
 /** Warn if improper atoms have been reordered so they match the parameter. */
diff --git a/src/Topology.h b/src/Topology.h
index c34333f1d7..4999fa28c4 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -129,7 +129,9 @@ class Topology {
     void AddAngle(int i, int j, int k)            { AddAngle(i, j, k, -1); }
     void AddAngle(int, int, int, int);
     void AddAngle(AngleType const&, bool);
-    void AddAngle(int, int, int, AngleParmType const&); 
+    void AddAngle(int, int, int, AngleParmType const&);
+    /// Add to angle arrays
+    void AddToAngleArrays(AngleType const&);
     void AssignAngleParams(ParmHolder<AngleParmType> const&);
     // ----- Dihedral-specific routines ----------
     size_t Ndihedrals()                        const { return dihedrals_.size()+dihedralsh_.size(); }

From 230d1e8b5448c4224d07d26918ab2ee882d337ce Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 4 Jan 2024 08:33:51 -0500
Subject: [PATCH 0251/1492] Only regenerate connectivity arrays when
 AssignParam is called

---
 src/Topology.cpp | 77 +++++++++++++-----------------------------------
 1 file changed, 21 insertions(+), 56 deletions(-)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index 864942e0be..5b2ab2679f 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2612,51 +2612,8 @@ const
 /** Replace any current bond parameters with given bond parameters. */
 void Topology::AssignBondParams(ParmHolder<BondParmType> const& newBondParams) {
   bondparm_.clear();
-  // Regenerate bond array in LEaP order
-  bonds_.clear();
-  bondsh_.clear();
-  BondArray allBonds = Cpptraj::Structure::GenerateBondArray(residues_, atoms_);
-  AssignBondParm( newBondParams, allBonds, bondparm_, "bond" );
-  for (BondArray::const_iterator bnd = allBonds.begin(); bnd != allBonds.end(); ++bnd)
-    AddToBondArrays( *bnd );
-//  AssignBondParm( newBondParams, bonds_,  bondparm_, "bond" );
-//  AssignBondParm( newBondParams, bondsh_, bondparm_, "bond" );
-/**  // Try to match leap bond ordering. Appears to be by index with priority
-  // given to heavy atoms.
-  BondArray tmpBonds;
-  tmpBonds.resize( bonds_.size() + bondsh_.size() );
-  std::copy( bonds_.begin(), bonds_.end(), tmpBonds.begin() );
-  std::copy( bondsh_.begin(), bondsh_.end(), tmpBonds.begin() + bonds_.size() );
-  std::sort( tmpBonds.begin(), tmpBonds.end() );**/
-/*
-  BondArray::iterator b1 = bonds_.begin();
-  BondArray::iterator b2 = bondsh_.begin();
-  while (b1 != bonds_.end() || b2 != bondsh_.end()) {
-    int iat = b1->A1();
-    tmpBonds.push_back( *b1 );
-    ++b1;
-    while (b1 != bonds_.end() && b1->A1() == iat) {
-      tmpBonds.push_back( *b1 );
-      ++b1;
-    }
-    while (b2 != bondsh_.end() && b2->A1() == iat) {
-      tmpBonds.push_back( *b2 );
-      ++b2;
-    }
-  }
-  if (tmpBonds.size() != bonds_.size() + bondsh_.size()) {
-    mprinterr("Internal Error: AssignBondParams: Size of temp. bonds array %zu != total # bonds %zu\n",
-              tmpBonds.size(), bonds_.size() + bondsh_.size());
-  }*/
-/**  AssignBondParm( newBondParams, tmpBonds, bondparm_, "bond" );
-  bonds_.clear();
-  bondsh_.clear();
-  for (BondArray::const_iterator it = tmpBonds.begin(); it != tmpBonds.end(); ++it)
-    if ( atoms_[it->A1()].Element() == Atom::HYDROGEN ||
-         atoms_[it->A2()].Element() == Atom::HYDROGEN)
-      bondsh_.push_back( *it );
-    else
-      bonds_.push_back( *it );**/
+  AssignBondParm( newBondParams, bonds_,  bondparm_, "bond" );
+  AssignBondParm( newBondParams, bondsh_, bondparm_, "bond" );
 }
 
 /** Replace any current Urey-Bradley parameters with given UB parameters. */
@@ -2724,15 +2681,8 @@ void Topology::AssignAngleParm(ParmHolder<AngleParmType> const& newAngleParams,
 /** Replace any current angle parameters with given angle parameters. */
 void Topology::AssignAngleParams(ParmHolder<AngleParmType> const& newAngleParams) {
   angleparm_.clear();
-  // Regenerate angle array in LEaP order
-  angles_.clear();
-  anglesh_.clear();
-  AngleArray allAngles = Cpptraj::Structure::GenerateAngleArray(residues_, atoms_);
-  AssignAngleParm( newAngleParams, allAngles );
-  for (AngleArray::const_iterator ang = allAngles.begin(); ang != allAngles.end(); ++ang)
-    AddToAngleArrays( *ang );
-  //AssignAngleParm( newAngleParams, angles_ );
-  //AssignAngleParm( newAngleParams, anglesh_ );
+  AssignAngleParm( newAngleParams, angles_ );
+  AssignAngleParm( newAngleParams, anglesh_ );
 }
 
 /** Warn if improper atoms have been reordered so they match the parameter. */
@@ -3080,12 +3030,27 @@ void Topology::AssignNonbondParams(ParmHolder<AtomType> const& newTypes,
 
 /** Replace existing parameters with the given parameter set. */
 int Topology::AssignParams(ParameterSet const& set0) {
+
   // Bond parameters
   mprintf("\tRegenerating bond parameters.\n");
-  AssignBondParams( set0.BP() );
+  bondparm_.clear();
+  // Regenerate bond array in LEaP order
+  bonds_.clear();
+  bondsh_.clear();
+  BondArray allBonds = Cpptraj::Structure::GenerateBondArray(residues_, atoms_);
+  AssignBondParm( set0.BP(), allBonds, bondparm_, "bond" );
+  for (BondArray::const_iterator bnd = allBonds.begin(); bnd != allBonds.end(); ++bnd)
+    AddToBondArrays( *bnd );
   // Angle parameters
   mprintf("\tRegenerating angle parameters.\n");
-  AssignAngleParams( set0.AP() );
+  angleparm_.clear();
+  // Regenerate angle array in LEaP order
+  angles_.clear();
+  anglesh_.clear();
+  AngleArray allAngles = Cpptraj::Structure::GenerateAngleArray(residues_, atoms_);
+  AssignAngleParm( set0.AP(), allAngles );
+  for (AngleArray::const_iterator ang = allAngles.begin(); ang != allAngles.end(); ++ang)
+    AddToAngleArrays( *ang );
   // Dihedral parameters
   mprintf("\tRegenerating dihedral parameters.\n");
   AssignDihedralParams( set0.DP(), set0.IP() );

From d7961c9f6a0a65b36fe8db759173a6e8353ea21b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 4 Jan 2024 08:54:43 -0500
Subject: [PATCH 0252/1492] Refactor dihedral parameter assignment so it can
 accept a passed-in array

---
 src/Topology.cpp | 68 +++++++++++++++++++++++++-----------------------
 src/Topology.h   |  3 ++-
 2 files changed, 38 insertions(+), 33 deletions(-)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index 5b2ab2679f..03d27bdd04 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2745,39 +2745,21 @@ void Topology::AssignImproperParams(ImproperParmHolder const& newImproperParams)
 /** Set parameters for dihedrals in given dihedral array.
   * Bond and angle information must be set up prior to calling
   * this function in order for improper and 1-4 detection to work.
+  * \param newDihedralParams New proper dihedral parameters.
+  * \param newImproperParams New improper dihedral parameters.
+  * \param dihedrals Array containing only unique dihedrals.
   */
-void Topology::AssignDihedralParm(DihedralParmHolder const& newDihedralParams,
-                                  ImproperParmHolder const& newImproperParams,
-                                  DihedralArray& dihedralsIn)
+DihedralArray Topology::AssignDihedralParm(DihedralParmHolder const& newDihedralParams,
+                                           ImproperParmHolder const& newImproperParams,
+                                           DihedralArray const& dihedrals)
 {
-  // Dihedrals can be a bit of a pain since there can be multiple
-  // multiplicities for a single dihedral type. In case multiplicities
-  // change, start with a fresh dihedral array containing only unique
-  // dihedrals.
-  //DihedralArray tmpdih = dihedralsIn;
-  //std::sort( tmpdih.begin(), tmpdih.end() );
-  // Assume dihedrals with multiple terms are consecutive already
-  DihedralArray dihedrals;
-  for (DihedralArray::const_iterator dih = dihedralsIn.begin(); dih != dihedralsIn.end(); ++dih) {
-    if (dihedrals.empty())
-      dihedrals.push_back( *dih );
-    else {
-      if ( *dih != dihedrals.back() )
-        dihedrals.push_back( *dih );
-    }
-  }
-  if (debug_ > 0)
-    mprintf("DEBUG: %zu incoming dihedrals, %zu unique dihedrals.\n",
-            dihedralsIn.size(), dihedrals.size());
-
-  dihedralsIn.clear();
+  DihedralArray dihedralsIn;
   // Keep track of 1-4 interactions
   typedef std::pair<int,int> Ipair;
   typedef std::set<Ipair> Imap;
   Imap PairMap;
   // Loop over all dihedrals
-  for (DihedralArray::iterator dih = dihedrals.begin(); dih != dihedrals.end(); ++dih) {
-
+  for (DihedralArray::const_iterator dih = dihedrals.begin(); dih != dihedrals.end(); ++dih) {
     TypeNameHolder types(4);
     types.AddName( atoms_[dih->A1()].Type() );
     types.AddName( atoms_[dih->A2()].Type() );
@@ -2803,9 +2785,9 @@ void Topology::AssignDihedralParm(DihedralParmHolder const& newDihedralParams,
     if (isImproper) {
       // ----- This is actually an improper dihedral. ----------------
       //ImproperParmHolder::OrderType lastOrder;
-      DihedralType dih0 = *dih;
+      DihedralType mydih = *dih;
       bool reordered;
-      DihedralParmArray ipa = newImproperParams.FindParam( types, found, *dih, reordered );
+      DihedralParmArray ipa = newImproperParams.FindParam( types, found, mydih, reordered );
       int idx = -1;
       if (!found) {
         mprintf("Warning: Improper parameters not found for improper dihedral %s-%s-%s-%s (%s-%s-%s-%s)\n",
@@ -2818,10 +2800,9 @@ void Topology::AssignDihedralParm(DihedralParmHolder const& newDihedralParams,
         if (ipa.size() > 1)
           mprintf("Warning: %zu improper parameters found for types %s - %s - %s - %s, expected only one."
                   "Warning: Only using first parameter.\n", ipa.size(), *(types[0]), *(types[1]), *(types[2]), *(types[3]));
-        if (reordered) warn_improper_reorder( dih0, *dih );
+        if (reordered) warn_improper_reorder( *dih, mydih );
         idx = addTorsionParm( dihedralparm_, ipa.front() );
       }
-      DihedralType mydih = *dih;
       mydih.SetIdx( idx );
       mydih.SetImproper( true );
       // Always skip 1-4 for impropers
@@ -2913,13 +2894,36 @@ void Topology::AssignDihedralParm(DihedralParmHolder const& newDihedralParams,
       }
     }
   } // END loop over all dihedrals
+  return dihedralsIn;
+}
+
+/** \return Array of only unique dihedrals (get rid of multiplicities) */
+DihedralArray Topology::get_unique_dihedrals(DihedralArray const& dihedralsIn) const {
+  // Assume dihedrals with multiple terms are consecutive already
+  DihedralArray dihedrals;
+  for (DihedralArray::const_iterator dih = dihedralsIn.begin(); dih != dihedralsIn.end(); ++dih) {
+    if (dihedrals.empty())
+      dihedrals.push_back( *dih );
+    else {
+      if ( *dih != dihedrals.back() )
+        dihedrals.push_back( *dih );
+    }
+  }
+  if (debug_ > 0)
+    mprintf("DEBUG: %zu incoming dihedrals, %zu unique dihedrals.\n",
+            dihedralsIn.size(), dihedrals.size());
+  return dihedrals;
 }
 
 /** Replace any current dihedral parameters with given dihedral parameters. */
 void Topology::AssignDihedralParams(DihedralParmHolder const& newDihedralParams, ImproperParmHolder const& newImproperParams) {
   dihedralparm_.clear();
-  AssignDihedralParm( newDihedralParams, newImproperParams, dihedrals_ );
-  AssignDihedralParm( newDihedralParams, newImproperParams, dihedralsh_ );
+  // Dihedrals can be a bit of a pain since there can be multiple
+  // multiplicities for a single dihedral type. In case multiplicities
+  // change, start with a fresh dihedral array containing only unique
+  // dihedrals.
+  dihedrals_  = AssignDihedralParm( newDihedralParams, newImproperParams, get_unique_dihedrals(dihedrals_)  );
+  dihedralsh_ = AssignDihedralParm( newDihedralParams, newImproperParams, get_unique_dihedrals(dihedralsh_) );
 }
 
 /** Replace current nonbond parameters with given nonbond parameters. */
diff --git a/src/Topology.h b/src/Topology.h
index 4999fa28c4..0d07077f3e 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -307,7 +307,8 @@ class Topology {
     void AssignAngleParm(ParmHolder<AngleParmType> const&, AngleArray&);
     void warn_improper_reorder(DihedralType const&, DihedralType const&) const;
     void AssignImproperParm(ImproperParmHolder const&, DihedralArray&);
-    void AssignDihedralParm(DihedralParmHolder const&, ImproperParmHolder const&, DihedralArray&);
+    inline DihedralArray get_unique_dihedrals(DihedralArray const&) const;
+    DihedralArray AssignDihedralParm(DihedralParmHolder const&, ImproperParmHolder const&, DihedralArray const&);
 
     static const NonbondType LJ_EMPTY;
     std::vector<Atom> atoms_;

From 361a71b2072a6c58df2f980fe66f1285b7401223 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 4 Jan 2024 09:06:11 -0500
Subject: [PATCH 0253/1492] Add dihedrals. Start working on impropers.

---
 src/Topology.cpp | 29 +++++++++++++++++++++++++----
 src/Topology.h   |  4 +++-
 2 files changed, 28 insertions(+), 5 deletions(-)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index 03d27bdd04..ee80430582 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -991,6 +991,7 @@ void Topology::AddToAngleArrays(AngleType const& ang) {
   else
     angles_.push_back( ang );
 }
+
 // -----------------------------------------------
 /** Check if given dihedral parm exists in given dihedral parm array. Add if not.
   * \return Index in dihedral parm array.
@@ -1074,6 +1075,19 @@ void Topology::AddDihedral(DihedralType const& dihIn, bool isH) {
     dihedrals_.push_back( dihIn );
 }
 
+/** Add to dihedral arrays. Used when regenerating dihedral information
+  * from atom connectivity.
+  */
+void Topology::AddToDihedralArrays(DihedralType const& dih) {
+  if (atoms_[dih.A1()].Element() == Atom::HYDROGEN ||
+      atoms_[dih.A4()].Element() == Atom::HYDROGEN ||
+      atoms_[dih.A2()].Element() == Atom::HYDROGEN ||
+      atoms_[dih.A3()].Element() == Atom::HYDROGEN)
+    dihedralsh_.push_back( dih );
+  else
+    dihedrals_.push_back( dih );
+}
+
 /** Add given Charmm improper with given improper parm to Charmm improper array. */
 void Topology::AddCharmmImproper(DihedralType const& imp, DihedralParmType const& IPin)
 {
@@ -2703,7 +2717,9 @@ const
 
 /** Set parameters for improper dihedrals in given improper dihedral array. */
 void Topology::AssignImproperParm(ImproperParmHolder const& newImproperParams,
-                                  DihedralArray& impropers)
+                                  DihedralArray& impropers,
+                                  DihedralParmArray& dpa)
+const
 {
   for (DihedralArray::iterator imp = impropers.begin(); imp != impropers.end(); ++imp) {
     TypeNameHolder types(4);
@@ -2730,7 +2746,7 @@ void Topology::AssignImproperParm(ImproperParmHolder const& newImproperParams,
         mprintf("Warning: %zu improper parameters found for types %s - %s - %s - %s, expected only one."
                         "Warning: Only using first parameter.\n", ipa.size(), *(types[0]), *(types[1]), *(types[2]), *(types[3]));
       if (reordered) warn_improper_reorder( imp0, *imp );
-      idx = addTorsionParm( chamber_.SetImproperParm(), ipa.front() );
+      idx = addTorsionParm( dpa, ipa.front() );
     }
     imp->SetIdx( idx );
   }
@@ -2739,7 +2755,7 @@ void Topology::AssignImproperParm(ImproperParmHolder const& newImproperParams,
 /** Replace any current improper parameters with given improper parameters. */
 void Topology::AssignImproperParams(ImproperParmHolder const& newImproperParams) {
   chamber_.SetImproperParm().clear();
-  AssignImproperParm( newImproperParams, chamber_.SetImpropers() );
+  AssignImproperParm( newImproperParams, chamber_.SetImpropers(), chamber_.SetImproperParm() );
 }
 
 /** Set parameters for dihedrals in given dihedral array.
@@ -3057,7 +3073,12 @@ int Topology::AssignParams(ParameterSet const& set0) {
     AddToAngleArrays( *ang );
   // Dihedral parameters
   mprintf("\tRegenerating dihedral parameters.\n");
-  AssignDihedralParams( set0.DP(), set0.IP() );
+  dihedrals_.clear();
+  dihedralsh_.clear();
+  DihedralArray allDihedrals = Cpptraj::Structure::GenerateDihedralArray(residues_, atoms_);
+  allDihedrals = AssignDihedralParm( set0.DP(), set0.IP(), allDihedrals );
+  for (DihedralArray::const_iterator dih = allDihedrals.begin(); dih != allDihedrals.end(); ++dih)
+    AddToDihedralArrays( *dih );
   // Urey-Bradley
   mprintf("\tRegenerating UB parameters.\n");
   AssignUBParams( set0.UB() );
diff --git a/src/Topology.h b/src/Topology.h
index 0d07077f3e..ec9d70981c 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -146,6 +146,8 @@ class Topology {
     void AddDihedral(DihedralType const&, DihedralParmType const&);
     void AssignImproperParams(ImproperParmHolder const&);
     void AssignDihedralParams(DihedralParmHolder const&, ImproperParmHolder const&);
+    /// Add to dihedral arrays
+    void AddToDihedralArrays(DihedralType const&);
     // ----- CMAP-specific routines --------------
     bool                     HasCmap()      const { return !cmapGrid_.empty(); }
     CmapGridArray     const& CmapGrid()     const { return cmapGrid_;     }
@@ -306,7 +308,7 @@ class Topology {
     void AssignBondParm(ParmHolder<BondParmType> const&, BondArray&, BondParmArray&, const char*) const;
     void AssignAngleParm(ParmHolder<AngleParmType> const&, AngleArray&);
     void warn_improper_reorder(DihedralType const&, DihedralType const&) const;
-    void AssignImproperParm(ImproperParmHolder const&, DihedralArray&);
+    void AssignImproperParm(ImproperParmHolder const&, DihedralArray&, DihedralParmArray&) const;
     inline DihedralArray get_unique_dihedrals(DihedralArray const&) const;
     DihedralArray AssignDihedralParm(DihedralParmHolder const&, ImproperParmHolder const&, DihedralArray const&);
 

From 5926a46378b34dad9ee6fdb78621bd6432c7c7e7 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 4 Jan 2024 10:08:25 -0500
Subject: [PATCH 0254/1492] Only the array of atoms is needed

---
 src/GuessAtomHybridization.cpp | 5 ++---
 src/GuessAtomHybridization.h   | 4 ++--
 2 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/src/GuessAtomHybridization.cpp b/src/GuessAtomHybridization.cpp
index 289cffd98f..249bb29a31 100644
--- a/src/GuessAtomHybridization.cpp
+++ b/src/GuessAtomHybridization.cpp
@@ -1,8 +1,7 @@
 #include "GuessAtomHybridization.h"
 #include "Atom.h"
-#include "Topology.h"
 
-AtomType::HybridizationType Cpptraj::GuessAtomHybridization(Atom const& AJ, Topology const& topIn)
+AtomType::HybridizationType Cpptraj::GuessAtomHybridization(Atom const& AJ, std::vector<Atom> const& atoms)
 {
   AtomType::HybridizationType hybrid = AtomType::UNKNOWN_HYBRIDIZATION;
   // Handle specific elements
@@ -22,7 +21,7 @@ AtomType::HybridizationType Cpptraj::GuessAtomHybridization(Atom const& AJ, Topo
           // hydrogen, assume SP2. TODO actually check for aromaticity.
           int n_hydrogens = 0;
           for (Atom::bond_iterator bat = AJ.bondbegin(); bat != AJ.bondend(); ++bat)
-            if (topIn[*bat].Element() == Atom::HYDROGEN)
+            if (atoms[*bat].Element() == Atom::HYDROGEN)
               n_hydrogens++;
           if (n_hydrogens == 1)
             hybrid = AtomType::SP2;
diff --git a/src/GuessAtomHybridization.h b/src/GuessAtomHybridization.h
index dc7b84fe76..a99bea9d32 100644
--- a/src/GuessAtomHybridization.h
+++ b/src/GuessAtomHybridization.h
@@ -1,10 +1,10 @@
 #ifndef INC_GUESSATOMHYBRIDIZATION_H
 #define INC_GUESSATOMHYBRIDIZATION_H
+#include <vector>
 #include "AtomType.h" // for HybridizationType
 class Atom;
-class Topology;
 namespace Cpptraj {
 /// Guess atom hybridization type based on element/bonding
-AtomType::HybridizationType GuessAtomHybridization(Atom const&, Topology const&);
+AtomType::HybridizationType GuessAtomHybridization(Atom const&, std::vector<Atom> const&);
 }
 #endif

From 1b99f5c02b082c4c0f0de8072d964fc9f5805e48 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 4 Jan 2024 10:08:53 -0500
Subject: [PATCH 0255/1492] Separate out function to find impropers

---
 src/Structure/GenerateImpropers.cpp | 83 +++++++++++++++++++++++++++++
 src/Structure/GenerateImpropers.h   | 14 +++++
 src/Structure/structuredepend       |  3 +-
 src/Structure/structurefiles        |  1 +
 4 files changed, 100 insertions(+), 1 deletion(-)
 create mode 100644 src/Structure/GenerateImpropers.cpp
 create mode 100644 src/Structure/GenerateImpropers.h

diff --git a/src/Structure/GenerateImpropers.cpp b/src/Structure/GenerateImpropers.cpp
new file mode 100644
index 0000000000..9db50929f2
--- /dev/null
+++ b/src/Structure/GenerateImpropers.cpp
@@ -0,0 +1,83 @@
+#include "GenerateImpropers.h"
+#include "../CpptrajStdio.h"
+#include "../Atom.h"
+#include "../AtomType.h"
+#include "../GuessAtomHybridization.h"
+#include "../ParameterTypes.h"
+#include "../ParameterHolders.h"
+#include <algorithm> // std::swap
+
+/** Try to order an improper the same way that LEaP does.
+  * LEaP has wild card names first, followed by atom types
+  * in alphabetical order. The third atom is always the central
+  * atom.
+  */
+static int order_improper_atoms(int* leapdih, int centralAt, std::vector<Atom> const& topIn)
+{
+  Atom const& Ak = topIn[centralAt];
+  std::vector<int> const& bonds = Ak.BondIdxArray();
+  int indices[3];
+  indices[0] = bonds[0];
+  indices[1] = bonds[1];
+  indices[2] = bonds[2];
+  if (topIn[indices[0]].Type() > topIn[indices[1]].Type()) std::swap( indices[0], indices[1] );
+  if (topIn[indices[1]].Type() > topIn[indices[2]].Type()) std::swap( indices[1], indices[2] );
+  if (topIn[indices[0]].Type() > topIn[indices[1]].Type()) std::swap( indices[0], indices[1] );
+  if (topIn[indices[1]].Type() > topIn[indices[2]].Type()) std::swap( indices[1], indices[2] );
+  leapdih[0] = indices[0];
+  leapdih[1] = indices[1];
+  leapdih[2] = centralAt;
+  leapdih[3] = indices[2];
+  return 0;
+}
+
+// DEBUG
+static inline void printName(Atom const& AJ) {
+  mprintf(" :%i@%s", AJ.ResNum()+1, AJ.Name().Truncated().c_str());
+}
+
+/** Try to determine impropers for topology. */ // TODO option for charmm improper
+DihedralArray Cpptraj::Structure::GenerateImproperArray(std::vector<Atom> const& atoms,
+                                                        ParmHolder<AtomType> const& AT)
+{
+  DihedralArray out;
+  long int atBegin = (long int)(atoms.size()) - 1;
+  for (long int iat = atBegin; iat >= 0; iat--) {
+    Atom const& AJ = atoms[iat];
+    if (AJ.Nbonds() == 3) { // TODO only 3 atoms OK?
+      AtomType::HybridizationType hybrid = AtomType::UNKNOWN_HYBRIDIZATION; 
+      bool found;
+      AtomType atype = AT.FindParam(TypeNameHolder(AJ.Type()), found);
+      if (found)
+        hybrid = atype.Hybridization();
+      if (hybrid == AtomType::UNKNOWN_HYBRIDIZATION)
+        hybrid = Cpptraj::GuessAtomHybridization( AJ, atoms );
+      if (hybrid == AtomType::SP2) {
+        mprintf("DEBUG: Potential improper center:");
+        printName(AJ);
+        mprintf("\n");
+        int leapdih[4];
+        order_improper_atoms(leapdih, iat, atoms);
+        mprintf("DEBUG: Bond order");
+        printName(AJ);
+        mprintf(": %i %i %i %i", 
+                AJ.BondIdxArray()[0]+1,
+                AJ.BondIdxArray()[1]+1,
+                iat+1,
+                AJ.BondIdxArray()[2]+1);
+        printName(atoms[AJ.BondIdxArray()[0]]);
+        printName(atoms[AJ.BondIdxArray()[1]]);
+        printName(AJ);
+        printName(atoms[AJ.BondIdxArray()[2]]);
+        mprintf("\n");
+        mprintf("DEBUG: Leap order: %i %i %i %i\n", leapdih[0]+1, leapdih[1]+1, leapdih[2]+1, leapdih[3]+1);
+        out.push_back( DihedralType(leapdih[0], leapdih[1], leapdih[2], leapdih[3], DihedralType::BOTH) );
+      } else if (hybrid == AtomType::UNKNOWN_HYBRIDIZATION) {
+        mprintf("Warning: When searching for impropers could not determine hybridization of");
+        printName(AJ);
+        mprintf("\n");
+      }
+    }
+  }
+  return out;
+}
diff --git a/src/Structure/GenerateImpropers.h b/src/Structure/GenerateImpropers.h
new file mode 100644
index 0000000000..8d47c42e05
--- /dev/null
+++ b/src/Structure/GenerateImpropers.h
@@ -0,0 +1,14 @@
+#ifndef INC_STRUCTURE_GENERATEIMPROPERS_H
+#define INC_STRUCTURE_GENERATEIMPROPERS_H
+#include <vector>
+class Atom;
+class AtomType;
+class DihedralArray;
+template <typename Type> class ParmHolder;
+namespace Cpptraj {
+namespace Structure {
+/// Generate improper dihedral array in same order as leap
+DihedralArray GenerateImproperArray(std::vector<Atom> const&, ParmHolder<AtomType> const&);
+}
+}
+#endif
diff --git a/src/Structure/structuredepend b/src/Structure/structuredepend
index eedc6f95c4..cb893b8f36 100644
--- a/src/Structure/structuredepend
+++ b/src/Structure/structuredepend
@@ -3,8 +3,9 @@ Chirality.o : Chirality.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Co
 Disulfide.o : Disulfide.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Disulfide.h ResStatArray.h StructureRoutines.h
 FunctionalGroup.o : FunctionalGroup.cpp ../Atom.h ../AtomMap.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h FunctionalGroup.h
 FxnGroupBuilder.o : FxnGroupBuilder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h FunctionalGroup.h FxnGroupBuilder.h StructureRoutines.h Sugar.h SugarToken.h
-GenerateConnectivity.o : GenerateConnectivity.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h GenerateConnectivity.h
+GenerateConnectivity.o : GenerateConnectivity.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h GenerateConnectivity.h
 GenerateConnectivityArrays.o : GenerateConnectivityArrays.cpp ../Atom.h ../Constants.h ../CpptrajStdio.h ../NameType.h ../ParameterTypes.h ../Residue.h ../SymbolExporting.h GenerateConnectivityArrays.h
+GenerateImpropers.o : GenerateImpropers.cpp ../Atom.h ../AtomType.h ../Constants.h ../CpptrajStdio.h ../GuessAtomHybridization.h ../NameType.h ../ParameterHolders.h ../ParameterTypes.h ../SymbolExporting.h ../TypeNameHolder.h GenerateImpropers.h
 HisProt.o : HisProt.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h HisProt.h StructureRoutines.h
 InternalCoords.o : InternalCoords.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h InternalCoords.h
 Model.o : Model.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h Model.h StructureEnum.h
diff --git a/src/Structure/structurefiles b/src/Structure/structurefiles
index 6a6dd3da57..825ca83eb0 100644
--- a/src/Structure/structurefiles
+++ b/src/Structure/structurefiles
@@ -7,6 +7,7 @@ STRUCTURE_SOURCES= \
   FxnGroupBuilder.cpp \
   GenerateConnectivityArrays.cpp \
   GenerateConnectivity.cpp \
+  GenerateImpropers.cpp \
   HisProt.cpp \
   InternalCoords.cpp \
   Model.cpp \

From 1b4688571e8bb0a3c8e1d1cac658e8eb2c6c40b3 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 4 Jan 2024 10:09:26 -0500
Subject: [PATCH 0256/1492] Make comment more specific

---
 src/Structure/GenerateConnectivityArrays.h | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Structure/GenerateConnectivityArrays.h b/src/Structure/GenerateConnectivityArrays.h
index 0119c0f391..8fac565a63 100644
--- a/src/Structure/GenerateConnectivityArrays.h
+++ b/src/Structure/GenerateConnectivityArrays.h
@@ -12,7 +12,7 @@ namespace Structure {
 BondArray GenerateBondArray(std::vector<Residue> const&, std::vector<Atom> const&);
 /// Generate angle array in same order as leap
 AngleArray GenerateAngleArray(std::vector<Residue> const&, std::vector<Atom> const&);
-/// Generate dihedral array in same order as leap
+/// Generate proper dihedral array in same order as leap
 DihedralArray GenerateDihedralArray(std::vector<Residue> const&, std::vector<Atom> const&);
 }
 }

From 8e5235a3fd12c555a96371164311ccd86971820c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 4 Jan 2024 10:09:38 -0500
Subject: [PATCH 0257/1492] Update CMakeLists

---
 src/Structure/CMakeLists.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/Structure/CMakeLists.txt b/src/Structure/CMakeLists.txt
index d04716f8bc..e0fa49b0e7 100644
--- a/src/Structure/CMakeLists.txt
+++ b/src/Structure/CMakeLists.txt
@@ -7,6 +7,7 @@ target_sources(cpptraj_common_obj PRIVATE
   ${CMAKE_CURRENT_LIST_DIR}/FxnGroupBuilder.cpp
   ${CMAKE_CURRENT_LIST_DIR}/GenerateConnectivityArrays.cpp
   ${CMAKE_CURRENT_LIST_DIR}/GenerateConnectivity.cpp
+  ${CMAKE_CURRENT_LIST_DIR}/GenerateImpropers.cpp
   ${CMAKE_CURRENT_LIST_DIR}/HisProt.cpp
   ${CMAKE_CURRENT_LIST_DIR}/InternalCoords.cpp
   ${CMAKE_CURRENT_LIST_DIR}/Model.cpp

From 81780ebf2c592e68a011e4309d84e027caf6feb8 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 4 Jan 2024 10:09:58 -0500
Subject: [PATCH 0258/1492] Update for how GuessHybridization should be called

---
 src/Structure/Model.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Structure/Model.cpp b/src/Structure/Model.cpp
index cdd914223d..33b99d4a16 100644
--- a/src/Structure/Model.cpp
+++ b/src/Structure/Model.cpp
@@ -29,7 +29,7 @@ int Cpptraj::Structure::Model::AssignTheta(double& theta, int ai, int aj, int ak
     return 1;
   }
   // TODO pass in atom type info?
-  AtomType::HybridizationType hybrid = GuessAtomHybridization(AJ, topIn);
+  AtomType::HybridizationType hybrid = GuessAtomHybridization(AJ, topIn.Atoms());
 /*
   HybridizationType hybrid = UNKNOWN_HYBRIDIZATION;
   // Handle specific elements

From d66a9e76430d179ce83150eeb4a9ebdfbec034a4 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 4 Jan 2024 10:11:38 -0500
Subject: [PATCH 0259/1492] Generate impropers is now in separate file. Update
 dependencies.

---
 src/Structure/GenerateConnectivity.cpp | 148 +------------------------
 src/Structure/GenerateConnectivity.h   |   4 -
 src/cpptrajdepend                      |   9 +-
 3 files changed, 6 insertions(+), 155 deletions(-)

diff --git a/src/Structure/GenerateConnectivity.cpp b/src/Structure/GenerateConnectivity.cpp
index 1b20a6c3b5..e303482902 100644
--- a/src/Structure/GenerateConnectivity.cpp
+++ b/src/Structure/GenerateConnectivity.cpp
@@ -1,9 +1,7 @@
 #include "GenerateConnectivity.h"
 #include "../CpptrajStdio.h"
-#include "../GuessAtomHybridization.h"
-#include "../ParameterTypes.h"
 #include "../Topology.h"
-#include <algorithm> // std::swap
+#include <algorithm> // std::sort
 
 static inline void enumerateAngles(int& aidx, int at1, int at2, Topology& topIn) {
   Atom const& A2 = topIn[at2];
@@ -196,147 +194,3 @@ int Cpptraj::Structure::GenerateBondAngleTorsionArrays(Topology& topIn) {
 
   return 0;
 }
-
-/** Try to order an improper the same way that LEaP does.
-  * LEaP has wild card names first, followed by atom types
-  * in alphabetical order. The third atom is always the central
-  * atom.
-  */
-static int order_improper_atoms(int* leapdih, int centralAt, Topology const& topIn)
-{
-  Atom const& Ak = topIn[centralAt];
-  std::vector<int> const& bonds = Ak.BondIdxArray();
-  int indices[3];
-  indices[0] = bonds[0];
-  indices[1] = bonds[1];
-  indices[2] = bonds[2];
-  if (topIn[indices[0]].Type() > topIn[indices[1]].Type()) std::swap( indices[0], indices[1] );
-  if (topIn[indices[1]].Type() > topIn[indices[2]].Type()) std::swap( indices[1], indices[2] );
-  if (topIn[indices[0]].Type() > topIn[indices[1]].Type()) std::swap( indices[0], indices[1] );
-  if (topIn[indices[1]].Type() > topIn[indices[2]].Type()) std::swap( indices[1], indices[2] );
-  leapdih[0] = indices[0];
-  leapdih[1] = indices[1];
-  leapdih[2] = centralAt;
-  leapdih[3] = indices[2];
-  return 0;
-}
-/*
-static int order_improper_atoms(int* indices, int centralAt, Topology const& topIn)
-{
-  indices[2] = centralAt;
-  Atom const& Ak = topIn[centralAt];
-  std::vector<int> const& bonds = Ak.BondIdxArray();
-  NameType const& a1 = topIn[bonds[0]].Type();
-  NameType const& a2 = topIn[bonds[1]].Type();
-  NameType const& a3 = topIn[bonds[2]].Type();
-  if (a1 < a2) {
-    if (a1 < a3) {
-      // a1 < a2 and a1 < a3
-      indices[0] = bonds[0];
-      if (a2 < a3) {
-        indices[1] = bonds[1];
-        indices[3] = bonds[2];
-      } else {
-        indices[1] = bonds[2];
-        indices[3] = bonds[1];
-      }
-    } else {
-      // a1 < a2 and a3 < a1
-      indices[0] = bonds[2];
-      indices[1] = bonds[0];
-      indices[3] = bonds[1];
-    }
-  } else {
-    if (a2 < a3) {
-      // a2 < a1 and a2 < a3
-      indices[0] = bonds[1];
-      if (a1 < a3) {
-        indices[1] = bonds[0];
-        indices[3] = bonds[2];
-      } else {
-        indices[1] = bonds[2];
-        indices[3] = bonds[0];
-      }
-    } else {
-      // a2 < a1 and a3 < a2
-      indices[0] = bonds[2];
-      indices[1] = bonds[1];
-      indices[3] = bonds[0];
-    }
-  }
-
-  return 0;
-}*/
-/*static int order_improper_atoms(int* oaObj, int iat, Topology const& topIn) {
-  int iIndex1 = 0;
-  int iIndex2 = 0;
-  int iIndex0 = 0;
-  for (int i = 0; i < 3; i++)
-    oaObj[i] = -1;
-
-  Atom const& AJ = topIn[iat];
-  int iAtomCoordination = AJ.Nbonds();
-
-  if ( iIndex1 <= iIndex0 )
-    iIndex1 = iIndex0+1;
-  if ( iIndex2 <= iIndex1 )
-    iIndex2 = iIndex1+1;
-  else iIndex2++;
-
-  if ( iIndex2 >= iAtomCoordination ) {
-      iIndex1++;
-      iIndex2 = iIndex1 + 1;
-      if ( iIndex2 >= iAtomCoordination ) {
-          iIndex0++;
-          iIndex1 = iIndex0 + 1;
-          iIndex2 = iIndex1 + 1;
-      }
-  }
-
-  if ( iIndex2 < (iAtomCoordination) ) {
-      mprintf("DEBUG: iIndex %i %i %i\n", iIndex0, iIndex1, iIndex2);
-      oaObj[2] = iat;
-      oaObj[0] = AJ.BondIdxArray()[iIndex0]; //(OBJEKT) aAtomBondedNeighbor( cCont, iIndex0 );
-      oaObj[1] = AJ.BondIdxArray()[iIndex1]; //(OBJEKT) aAtomBondedNeighbor( cCont, iIndex1 );
-      oaObj[3] = AJ.BondIdxArray()[iIndex2]; //(OBJEKT) aAtomBondedNeighbor( cCont, iIndex2 );
-      return 0;
-  }
-  return 1;
-}*/
-
-/** Try to determine impropers for topology. */ // TODO option for charmm improper
-int Cpptraj::Structure::GenerateImpropers(Topology& topIn, ParmHolder<AtomType> const& AT) {
-  for (int iat = topIn.Natom()-1; iat >= 0; iat--) {
-    Atom const& AJ = topIn[iat];
-    if (AJ.Nbonds() == 3) { // TODO only 3 atoms OK?
-      AtomType::HybridizationType hybrid = AtomType::UNKNOWN_HYBRIDIZATION; 
-      bool found;
-      AtomType atype = AT.FindParam(TypeNameHolder(AJ.Type()), found);
-      if (found)
-        hybrid = atype.Hybridization();
-      if (hybrid == AtomType::UNKNOWN_HYBRIDIZATION)
-        hybrid = Cpptraj::GuessAtomHybridization( AJ, topIn );
-      if (hybrid == AtomType::SP2) {
-        mprintf("DEBUG: Potential improper center: %s\n", topIn.AtomMaskName(iat).c_str());
-        int leapdih[4];
-        order_improper_atoms(leapdih, iat, topIn);
-        mprintf("DEBUG: Bond order %s : %i %i %i %i %s %s %s %s\n",
-                topIn.AtomMaskName(iat).c_str(),
-                AJ.BondIdxArray()[0]+1,
-                AJ.BondIdxArray()[1]+1,
-                iat+1,
-                AJ.BondIdxArray()[2]+1,
-                topIn.AtomMaskName(AJ.BondIdxArray()[0]).c_str(),
-                topIn.AtomMaskName(AJ.BondIdxArray()[1]).c_str(),
-                topIn.AtomMaskName(iat).c_str(),
-                topIn.AtomMaskName(AJ.BondIdxArray()[2]).c_str());
-        mprintf("DEBUG: Leap order: %i %i %i %i\n", leapdih[0]+1, leapdih[1]+1, leapdih[2]+1, leapdih[3]+1);
-        topIn.AddDihedral( DihedralType(leapdih[0], leapdih[1], leapdih[2], leapdih[3], DihedralType::BOTH) );
-      } else if (hybrid == AtomType::UNKNOWN_HYBRIDIZATION) {
-        mprintf("Warning: When searching for impropers could not determine hybridization of %s\n",
-                topIn.AtomMaskName(iat).c_str());
-      }
-    }
-  }
-  return 0;
-}
diff --git a/src/Structure/GenerateConnectivity.h b/src/Structure/GenerateConnectivity.h
index 8016cde261..dd4a150bfc 100644
--- a/src/Structure/GenerateConnectivity.h
+++ b/src/Structure/GenerateConnectivity.h
@@ -1,16 +1,12 @@
 #ifndef INC_STRUCTURE_GENERATECONNECTIVITY_H
 #define INC_STRUCTURE_GENERATECONNECTIVITY_H
 class Topology;
-class AtomType;
-template <typename Type> class ParmHolder;
 namespace Cpptraj {
 namespace Structure {
 /// Generate angle/torsion arrays from bond arrays in a Topology
 int GenerateAngleTorsionArrays(Topology&);
 /// Generate bond/angle/torsion arrays from atom connectivity in a Topology
 int GenerateBondAngleTorsionArrays(Topology&);
-/// Generate impropers in a Topology
-int GenerateImpropers(Topology&, ParmHolder<AtomType> const&);
 }
 }
 #endif
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index c1cdc06b6b..05ca2d63ae 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -288,7 +288,7 @@ Ewald_Regular.o : Ewald_Regular.cpp Atom.h AtomMask.h Box.h Constants.h Coordina
 ExclusionArray.o : ExclusionArray.cpp Atom.h AtomMask.h CharMask.h CpptrajStdio.h ExclusionArray.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Unit.h
 Exec_AddMissingRes.o : Exec_AddMissingRes.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CharMask.h CompactFrameArray.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_AddMissingRes.h Exec_AddMissingRes_Pres.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Analyze.o : Exec_Analyze.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Analyze.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Build.o : Exec_Build.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/GenerateConnectivity.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Build.o : Exec_Build.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Calc.o : Exec_Calc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Calc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_CatCrd.o : Exec_CatCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CatCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Change.o : Exec_Change.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Change.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
@@ -369,7 +369,7 @@ Gpu.o : Gpu.cpp Gpu.h
 GridAction.o : GridAction.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridAction.h GridBin.h GridMover.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 GridBin.o : GridBin.cpp Box.h CpptrajStdio.h GridBin.h Matrix_3x3.h Parallel.h Vec3.h
 GridMover.o : GridMover.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_3D.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h GridMover.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-GuessAtomHybridization.o : GuessAtomHybridization.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h FileName.h Frame.h GuessAtomHybridization.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+GuessAtomHybridization.o : GuessAtomHybridization.cpp Atom.h AtomType.h Constants.h GuessAtomHybridization.h NameType.h ParameterTypes.h SymbolExporting.h
 HistBin.o : HistBin.cpp Constants.h CpptrajStdio.h Dimension.h HistBin.h
 Hungarian.o : Hungarian.cpp ArrayIterator.h Constants.h CpptrajStdio.h Hungarian.h Matrix.h
 ImageRoutines.o : ImageRoutines.cpp Atom.h AtomMask.h Box.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h Frame.h ImageOption.h ImageRoutines.h ImageTypes.h Image_List.h Image_List_Mask.h Image_List_Pair.h Image_List_Pair_CoM.h Image_List_Pair_First.h Image_List_Pair_Geom.h Image_List_Unit.h Image_List_Unit_CoM.h Image_List_Unit_First.h Image_List_Unit_Geom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Unit.h Vec3.h
@@ -447,8 +447,9 @@ Structure/Chirality.o : Structure/Chirality.cpp Atom.h AtomMask.h AtomType.h Box
 Structure/Disulfide.o : Structure/Disulfide.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Disulfide.h Structure/ResStatArray.h Structure/StructureRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/FunctionalGroup.o : Structure/FunctionalGroup.cpp Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/FxnGroupBuilder.o : Structure/FxnGroupBuilder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h Structure/FxnGroupBuilder.h Structure/StructureRoutines.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Structure/GenerateConnectivity.o : Structure/GenerateConnectivity.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h GuessAtomHybridization.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/GenerateConnectivity.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Structure/GenerateConnectivity.o : Structure/GenerateConnectivity.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/GenerateConnectivity.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/GenerateConnectivityArrays.o : Structure/GenerateConnectivityArrays.cpp Atom.h Constants.h CpptrajStdio.h NameType.h ParameterTypes.h Residue.h Structure/GenerateConnectivityArrays.h SymbolExporting.h
+Structure/GenerateImpropers.o : Structure/GenerateImpropers.cpp Atom.h AtomType.h Constants.h CpptrajStdio.h GuessAtomHybridization.h NameType.h ParameterHolders.h ParameterTypes.h Structure/GenerateImpropers.h SymbolExporting.h TypeNameHolder.h
 Structure/HisProt.o : Structure/HisProt.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/HisProt.h Structure/StructureRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/InternalCoords.o : Structure/InternalCoords.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/InternalCoords.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/Model.o : Structure/Model.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h GuessAtomHybridization.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/Model.h Structure/StructureEnum.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
@@ -467,7 +468,7 @@ TextFormat.o : TextFormat.cpp StringRoutines.h TextFormat.h
 Timer.o : Timer.cpp CpptrajStdio.h Timer.h
 TinkerFile.o : TinkerFile.cpp ArgList.h Atom.h AtomMask.h Box.h BufferedLine.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TinkerFile.h Unit.h Vec3.h
 TopInfo.o : TopInfo.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h DistRoutines.h FileIO.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Mol.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h TopInfo.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Topology.o : Topology.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/GenerateConnectivityArrays.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Topology.o : Topology.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/GenerateConnectivityArrays.h Structure/GenerateImpropers.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 TorsionRoutines.o : TorsionRoutines.cpp Constants.h TorsionRoutines.h Vec3.h
 TrajFrameCounter.o : TrajFrameCounter.cpp ArgList.h CpptrajStdio.h TrajFrameCounter.h
 TrajIOarray.o : TrajIOarray.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryFile.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h

From daba3baaaeeaffdb0a1c06c93e19e651b8fc88d9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 4 Jan 2024 10:13:57 -0500
Subject: [PATCH 0260/1492] AssignParams in Topology builds the topology
 arrays, no need to do it explicitly.

---
 src/Exec_Build.cpp | 19 ++++---------------
 1 file changed, 4 insertions(+), 15 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 52e74efc33..1dc353dea6 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -1,7 +1,7 @@
 #include "Exec_Build.h"
 #include "CpptrajStdio.h"
 #include "DataSet_Parameters.h"
-#include "Structure/GenerateConnectivity.h"
+//#inc lude "Structure/GenerateConnectivity.h"
 #include "Structure/Zmatrix.h"
 
 DataSet_Coords* Exec_Build::IdTemplateFromName(Carray const& Templates,
@@ -369,12 +369,6 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
     return CpptrajState::ERR;
   }
 
-  // Generate angles/dihedrals
-  if (Cpptraj::Structure::GenerateBondAngleTorsionArrays(topOut)) {
-    mprinterr("Error: Could not generate angles/dihedrals for '%s'\n", topOut.c_str());
-    return CpptrajState::ERR;
-  }
-
   // Get parameter sets.
   typedef std::vector<DataSet_Parameters*> Parray;
   Parray ParamSets;
@@ -421,16 +415,11 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
       mainParmSet->UpdateParamSet( *(*it), UC, State.Debug(), State.Debug() ); // FIXME verbose
   }
 
-  // Generate impropers
-  if (Cpptraj::Structure::GenerateImpropers(topOut, mainParmSet->AT())) {
-    mprinterr("Error: Could not generate impropers for '%s'\n", topOut.c_str());
-    return CpptrajState::ERR;
-  }
-
-  // Update parameters
+  // Assign parameters. This will create the bond/angle/dihedral/improper
+  // arrays as well.
   Exec::RetType ret = CpptrajState::OK;
   if ( topOut.AssignParams( *mainParmSet  ) ) {
-    mprinterr("Error: Could not update parameters for '%s'.\n", topOut.c_str());
+    mprinterr("Error: Could not assign parameters for '%s'.\n", topOut.c_str());
     ret = CpptrajState::ERR;
   }
 

From f36c7a7c1405f75b1f0bdc6d96f75a8598f435ae Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 4 Jan 2024 10:14:38 -0500
Subject: [PATCH 0261/1492] Generate impropers

---
 src/Topology.cpp | 15 ++++++++++++---
 1 file changed, 12 insertions(+), 3 deletions(-)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index ee80430582..8bd0930fd3 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -8,6 +8,7 @@
 #include "AtomMask.h"
 #include "CharMask.h"
 #include "Structure/GenerateConnectivityArrays.h"
+#include "Structure/GenerateImpropers.h"
 
 const NonbondType Topology::LJ_EMPTY = NonbondType();
 
@@ -3080,11 +3081,19 @@ int Topology::AssignParams(ParameterSet const& set0) {
   for (DihedralArray::const_iterator dih = allDihedrals.begin(); dih != allDihedrals.end(); ++dih)
     AddToDihedralArrays( *dih );
   // Urey-Bradley
-  mprintf("\tRegenerating UB parameters.\n");
+  mprintf("\tRegenerating Urey-Bradley parameters.\n");
   AssignUBParams( set0.UB() );
   // Improper parameters
-  mprintf("\tRegenerating improper parameters.\n");
-  AssignImproperParams( set0.IP() );
+  if (!chamber_.Impropers().empty()) {
+    mprintf("\tRegenerating CHARMM improper parameters.\n");
+    AssignImproperParams( set0.IP() );
+  } else {
+    mprintf("\tRegenerating improper parameters.\n");
+    DihedralArray allImpropers = Cpptraj::Structure::GenerateImproperArray(atoms_, set0.AT());
+    allImpropers = AssignDihedralParm( set0.DP(), set0.IP(), allImpropers );
+    for (DihedralArray::const_iterator imp = allImpropers.begin(); imp != allImpropers.end(); ++imp)
+      AddToDihedralArrays( *imp );
+  }
   // Atom types
   mprintf("\tRegenerating atom type parameters.\n");
   AssignAtomTypeParm( set0.AT() );

From cd410233f30fe7eefc46078a716cca8c4d81496c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 4 Jan 2024 10:35:14 -0500
Subject: [PATCH 0262/1492] Start adding GB params

---
 src/Parm/CMakeLists.txt |  4 ++++
 src/Parm/GB_Params.cpp  | 36 ++++++++++++++++++++++++++++++++++++
 src/Parm/GB_Params.h    | 21 +++++++++++++++++++++
 src/Parm/Makefile       | 26 ++++++++++++++++++++++++++
 src/Parm/parmdepend     |  1 +
 src/Parm/parmfiles      |  3 +++
 6 files changed, 91 insertions(+)
 create mode 100644 src/Parm/CMakeLists.txt
 create mode 100644 src/Parm/GB_Params.cpp
 create mode 100644 src/Parm/GB_Params.h
 create mode 100644 src/Parm/Makefile
 create mode 100644 src/Parm/parmdepend
 create mode 100644 src/Parm/parmfiles

diff --git a/src/Parm/CMakeLists.txt b/src/Parm/CMakeLists.txt
new file mode 100644
index 0000000000..caeb638991
--- /dev/null
+++ b/src/Parm/CMakeLists.txt
@@ -0,0 +1,4 @@
+#CMake buildfile for CPPTRAJ Parm subdirectory.
+target_sources(cpptraj_common_obj PRIVATE
+  ${CMAKE_CURRENT_LIST_DIR}/GB_Params.cpp
+)
diff --git a/src/Parm/GB_Params.cpp b/src/Parm/GB_Params.cpp
new file mode 100644
index 0000000000..2b4a9958ca
--- /dev/null
+++ b/src/Parm/GB_Params.cpp
@@ -0,0 +1,36 @@
+#include "GB_Params.h"
+#include "../Topology.h"
+#include "../CpptrajStdio.h"
+
+static const char* GB_RadiiTypeStr_[] = {
+  "Bondi radii",
+  "Amber 6 modified Bondi radii",
+  "Modified Bondi radii",
+  "Radii optimized for Amber charges by Huo and Kollman",
+  "H(N)-modified Bondi radii",
+  "PARSE radii",
+  "ArgH and AspGluO modified Bondi2 radii",
+  "Unknown GB radii set"
+};
+
+static const char* GB_RadiiTypeKey_[] = {
+  "bondi",
+  "amber6",
+  "mbondi",
+  "pbamber",
+  "mbondi2",
+  "parse",
+  "mbondi3"
+};
+
+/** Assign GB radii and screening parameters based on the given radius set. */
+int Cpptraj::Parm::Assign_GB_Radii(Topology& top, GB_RadiiType radiiSet)
+{
+  if (radiiSet == UNKNOWN_GB) {
+    mprinterr("Error: Unknown GB radii set.\n");
+    return 1;
+  }
+  mprintf("\tUsing GB radii set: %s\n", GB_RadiiTypeStr_[radiiSet]);
+
+  return 0;
+}
diff --git a/src/Parm/GB_Params.h b/src/Parm/GB_Params.h
new file mode 100644
index 0000000000..8dc3e94a88
--- /dev/null
+++ b/src/Parm/GB_Params.h
@@ -0,0 +1,21 @@
+#ifndef INC_PARM_GBPARAMS_H
+#define INC_PARM_GBPARAMS_H
+class Topology;
+namespace Cpptraj {
+namespace Parm {
+/// Known radii types. KEEP SYNCED WITH GB_RadiiTypeStr[] in GB_Params.cpp
+enum GB_RadiiType { 
+  BONDI=0,          ///< 0, bondi, Bondi radii
+  BONDI_AMBER6,     ///< 1, amber6, Amber6 modified Bondi radii
+  MBONDI,           ///< 2, mbondi, Modified bondi radii
+  PB_AMBER,         ///< 3, pbamber, PB radii from Huo and Kollman, currently unused
+  MBONDI2,          ///< 6, mbondi2, H(N)-modified Bondi radii
+  PARSE,            ///< 7, parse, PARSE radii
+  MBONDI3,          ///< 8, ArgH and AspGluO modified Bondi2 radii
+  UNKNOWN_GB
+};
+/// Assign GB radii
+int Assign_GB_Radii(Topology&, GB_RadiiType);
+}
+}
+#endif 
diff --git a/src/Parm/Makefile b/src/Parm/Makefile
new file mode 100644
index 0000000000..0f070ffe50
--- /dev/null
+++ b/src/Parm/Makefile
@@ -0,0 +1,26 @@
+# Parm Makefile
+include ../../config.h
+
+include parmfiles
+
+DEL_FILE = /bin/rm -f
+
+# Objects
+OBJECTS=$(PARM_SOURCES:.cpp=.o)
+
+# Default target: objects
+all: $(OBJECTS)
+
+clean:
+	$(DEL_FILE) *.o
+
+uninstall: clean
+
+# Dependency targets
+../findDepend:
+	cd ../ && $(MAKE) findDepend
+
+depend: ../findDepend
+	../findDepend $(PARM_SOURCES) > parmdepend
+
+include parmdepend
diff --git a/src/Parm/parmdepend b/src/Parm/parmdepend
new file mode 100644
index 0000000000..3fb8667ee2
--- /dev/null
+++ b/src/Parm/parmdepend
@@ -0,0 +1 @@
+GB_Params.o : GB_Params.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h GB_Params.h
diff --git a/src/Parm/parmfiles b/src/Parm/parmfiles
new file mode 100644
index 0000000000..86a58ec097
--- /dev/null
+++ b/src/Parm/parmfiles
@@ -0,0 +1,3 @@
+# Files for Parm subdirectory.
+PARM_SOURCES= \
+  GB_Params.cpp

From f962370205ce640cfdc3daed8d88a5f5bb34bff3 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 4 Jan 2024 11:17:17 -0500
Subject: [PATCH 0263/1492] Finish initial GB radii function

---
 src/Parm/GB_Params.cpp | 264 +++++++++++++++++++++++++++++++++++++++--
 1 file changed, 257 insertions(+), 7 deletions(-)

diff --git a/src/Parm/GB_Params.cpp b/src/Parm/GB_Params.cpp
index 2b4a9958ca..496d9b9cd1 100644
--- a/src/Parm/GB_Params.cpp
+++ b/src/Parm/GB_Params.cpp
@@ -14,15 +14,263 @@ static const char* GB_RadiiTypeStr_[] = {
 };
 
 static const char* GB_RadiiTypeKey_[] = {
-  "bondi",
-  "amber6",
-  "mbondi",
-  "pbamber",
-  "mbondi2",
-  "parse",
-  "mbondi3"
+  "bondi",   // 0
+  "amber6",  // 1
+  "mbondi",  // 2
+  "pbamber", // 3
+  "mbondi2", // 6
+  "parse",   // 7
+  "mbondi3", // 8
+  0
 };
 
+/// These are the numeric iGBparm values used in LEaP
+static const int GB_RadiiTypeIGB_[] = {
+  0, // bondi
+  1, // amber6
+  2, // mbondi
+  3, // pbamber
+  6, // mbondi2
+  7, // parse
+  8, // mbondi3
+  999999
+};
+
+/** Assign GB radii. */
+static void assign_gb_radii(Topology& top, Cpptraj::Parm::GB_RadiiType radiiSet)
+{
+  int iGBparm = GB_RadiiTypeIGB_[radiiSet];
+  for (int iat = 0; iat != top.Natom(); iat++)
+  {
+    Atom const& currentAtom = top[iat];
+    Residue const& currentRes = top.Res(currentAtom.ResNum());
+    double dGBrad = 0.0;
+//    saPAtom = PVAI(uUnit->vaAtoms, SAVEATOMt, i);
+//    iIndex = iParmSetFindAtom(uUnit->psParameters, saPAtom->sType);
+//    ParmSetAtom(uUnit->psParameters, iIndex, sType, &dMass, &dPolar,
+//                &dEpsilon, &dRStar, &dEpsilon14, &dRStar14, &dScreenF,
+//                &iElement, &iHybridization, sDesc);
+    if (iGBparm < 3 || iGBparm == 6 || iGBparm == 8) {
+      // Bondi or modified Bondi radii
+      switch (currentAtom.Element()) {
+        case Atom::HYDROGEN:
+          dGBrad = 1.2;
+
+          // Make the modifications that hydrogen radii
+          // depend upon the atoms they are bonded to.  
+          // iGBparm=1 corresponds to Amber 6, JACS 122:2489 (2000);
+          // iGBparm=2 adds the update of Biopolymers 56: 275 (2001)   
+          if (currentAtom.Nbonds() > 0) {
+
+	    // For multiply bonded Hydrogen atoms use the first bond for
+            // determining modified GB radii.  WAT contains multiply bonded
+	    // Hydrogen atoms so do not emit a warning.
+            Atom const& aAtomA = top[currentAtom.Bond(0)];
+            if (iGBparm == 1 || iGBparm == 2) {
+              switch (aAtomA.Element()) {
+                case Atom::CARBON: dGBrad = 1.3; break;      // Carbon
+                case Atom::OXYGEN: dGBrad = 0.8; break;      // Oxygen
+                case Atom::SULFUR: dGBrad = 0.8; break;      // Sulfur
+                case Atom::NITROGEN:
+                  if (iGBparm == 2) {
+                    dGBrad = 1.3;
+                  }
+                  break;      // Nitrogen, mbondi
+                case Atom::HYDROGEN:        // Special case: water hydrogen
+                  if (aAtomA.Type() == "HW" || aAtomA.Type() == "hw") {
+                                dGBrad = 0.8;
+		  }
+                  break;
+                default : break;
+              }
+            }
+	    else if (iGBparm == 6 || iGBparm == 8) {
+
+              // Try Alexey's scheme
+              if (currentAtom.Element() == Atom::NITROGEN) {
+                dGBrad = 1.3;
+                if (iGBparm == 8) {
+
+                  // Update residue as appropriate
+                  //if (saPAtom->iResidueIndex != iResidueIndex) {
+                  //  iResidueIndex = saPAtom->iResidueIndex;
+                  //  cPTemp = PVAI(uUnit->vaResidues, SAVERESIDUEt,
+                  //                iResidueIndex - 1)->sName;
+                  //  if (strlen(cPTemp) > 3) {
+                  //    cPTemp += (strlen(cPTemp) - 3);
+		  //  }
+                  //}
+
+		  // Adjust Arg HH and HE
+                  if (currentRes.Name() == "ARG" && (currentAtom.Name().Match("HH*") || currentAtom.Name() == "HE"))
+                  {
+                  //if (!strcmp(cPTemp, "ARG") &&
+		  //    !(strncmp(sAtomName(saPAtom->aAtom), "HH", 2) &&
+                  //      strcmp(sAtomName(saPAtom->aAtom), "HE"))) {
+                    dGBrad = 1.17;
+                  }
+                }
+              }
+            }
+          }
+          else {
+            mprintf("Warning: Unbonded Hydrogen atom %s in %s.\n"
+                    " Cannot determine the requested GB radius for this atom.\n"
+                    " Writing the unmodified Bondi GB radius.\n",
+                    *(currentAtom.Name()),
+                    top.TruncResNameNum(currentAtom.ResNum()).c_str());
+          }
+          break;
+        case Atom::CARBON:
+
+	  // Use the mass of the carbon atom. We are testing for
+          // carbons here. C1 == CH, C2 == CH2, C3 == CH3. UA carbons
+          // have a larger radius (2.2), so we want to make sure that
+          // the C1, C2, and C3 atom types _really_ correspond to UA
+          // UA carbons. C1 atoms should have a mass of 12.01 + 1.01,
+          // C2 should be 12.01 + 2.02, and C3 should be 12.01 + 3.03.
+          // This mneumonic will not work for 13C named "C1". This is
+          // a (hopefully) temporary kludge. FIXME not sure this first line is right
+          //if (strncmp(sType, "C1", 2) && strncmp(sType, "C2", 2) && strncmp(sType, "C3", 2)) {
+	  if (currentAtom.Type() != "C1" && currentAtom.Type() != "C2" && currentAtom.Type() != "C3") {
+            dGBrad = 1.7;
+	  }
+          else if (currentAtom.Type() == "C1" && currentAtom.Mass() < 13.0) {
+            dGBrad = 1.7;
+	  }
+	  else if (currentAtom.Type() == "C2" && currentAtom.Mass() < 14.0) {
+	    dGBrad = 1.7;
+	  }
+	  else if (currentAtom.Type() == "C3" && currentAtom.Mass() < 15.0) {
+	    dGBrad = 1.7;
+	  }
+          else {
+            dGBrad = 2.2;
+	  }
+          break;
+        case Atom::NITROGEN:
+          dGBrad = 1.55;
+          break;
+        case Atom::OXYGEN:
+          dGBrad = 1.5;
+          if (iGBparm == 8) {
+
+            // Update residue as appropriate
+            //if (saPAtom->iResidueIndex != iResidueIndex) {
+            //  iResidueIndex = saPAtom->iResidueIndex;
+            //  cPTemp = PVAI(uUnit->vaResidues, SAVERESIDUEt, iResidueIndex - 1)->sName;
+            //  if (strlen(cPTemp) > 3) {
+            //    cPTemp += (strlen(cPTemp) - 3);
+	    //  }
+            //}
+	    
+            // Adjust Asp OD and Glu OE, and terminal OXT
+            if ( (currentRes.Name() == "ASP" && currentAtom.Name().Match("OD*")) ||
+                 (currentRes.Name() == "AS4" && currentAtom.Name().Match("OD*")) ||
+                 (currentRes.Name() == "GLU" && currentAtom.Name().Match("OE*")) ||
+                 (currentRes.Name() == "GL4" && currentAtom.Name().Match("OE*")) ||
+                 currentAtom.Name() == "OXT")
+            {
+            //if (!(strcmp(cPTemp, "ASP") || strncmp(sAtomName(saPAtom->aAtom), "OD", 2)) ||
+            //      !(strcmp(cPTemp, "AS4") || strncmp(sAtomName(saPAtom->aAtom), "OD", 2)) ||
+            //      !(strcmp(cPTemp, "GLU") || strncmp(sAtomName(saPAtom->aAtom), "OE", 2)) ||
+            //      !(strcmp(cPTemp, "GL4") || strncmp(sAtomName(saPAtom->aAtom), "OE", 2)) ||
+            //      (!strcmp(sAtomName(saPAtom->aAtom), "OXT") ||
+            //      (i + 1 < iVarArrayElementCount(uUnit->vaAtoms) &&
+            //       !strcmp(sAtomName(PVAI(uUnit->vaAtoms, SAVEATOMt, i + 1)->aAtom),
+            //      "OXT")))) {
+	      dGBrad = 1.4;
+	    }
+          }
+          break;
+        case Atom::FLUORINE:
+          dGBrad = 1.5;
+          break;
+        case Atom::SILICON:
+          dGBrad = 2.1;
+          break;
+        case Atom::PHOSPHORUS:
+          dGBrad = 1.85;
+          break;
+        case Atom::SULFUR:
+          dGBrad = 1.8;
+          break;
+        case Atom::CHLORINE:
+          dGBrad = 1.7;
+          break;
+        default:
+          dGBrad = 1.5;
+          break;
+      }
+    }
+    else if (iGBparm == 3) {
+
+      // Radii from Huo & Kollman
+      switch (currentAtom.Element()) {
+        case Atom::HYDROGEN:
+          dGBrad = 1.15;
+          break;
+        case Atom::CARBON:
+          dGBrad = 1.85;
+          break;
+        case Atom::NITROGEN:
+          dGBrad = 1.64;
+          break;
+        case Atom::OXYGEN:
+          dGBrad = 1.53;
+          break;
+        case Atom::FLUORINE:
+          dGBrad = 1.53;
+          break;
+        case Atom::PHOSPHORUS:
+          dGBrad = 2.02;
+          break;
+        case Atom::SULFUR:
+          dGBrad = 2.00;
+          break;
+        case Atom::CHLORINE:
+          dGBrad = 1.97;
+          break;
+        case Atom::BROMINE:
+          dGBrad = 2.03;
+          break;
+        case Atom::IODINE:
+          dGBrad = 2.10;
+          break;
+        default:
+          dGBrad = 1.5;
+          break;
+      }
+    }
+    else if (iGBparm == 7) {
+
+      // Parse radii
+      switch (currentAtom.Element()) {
+        case Atom::HYDROGEN:
+          dGBrad = 1.00;
+          break;
+        case Atom::CARBON:
+          dGBrad = 1.70;
+          break;
+        case Atom::NITROGEN:
+          dGBrad = 1.50;
+          break;
+        case Atom::OXYGEN:
+          dGBrad = 1.40;
+          break;
+        case Atom::SULFUR:
+          dGBrad = 1.85;
+          break;
+        default:
+          dGBrad = 1.50;
+          break;
+          // Radii from J. Phys. Chem. 1994, 98, 1978-1988
+      }
+    }
+    top.SetAtom(iat).SetGBradius( dGBrad );
+  } // END loop over atoms
+}
+
 /** Assign GB radii and screening parameters based on the given radius set. */
 int Cpptraj::Parm::Assign_GB_Radii(Topology& top, GB_RadiiType radiiSet)
 {
@@ -31,6 +279,8 @@ int Cpptraj::Parm::Assign_GB_Radii(Topology& top, GB_RadiiType radiiSet)
     return 1;
   }
   mprintf("\tUsing GB radii set: %s\n", GB_RadiiTypeStr_[radiiSet]);
+  top.SetGBradiiSet( std::string(GB_RadiiTypeStr_[radiiSet]) );
+  assign_gb_radii( top, radiiSet );
 
   return 0;
 }

From 73cc8ebc2b46a4005c4bdc58e8b8cd0e690c67a8 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 4 Jan 2024 11:21:19 -0500
Subject: [PATCH 0264/1492] Add Parm subdir to build

---
 src/CMakeLists.txt | 1 +
 src/Makefile       | 9 +++++++--
 src/cpptrajfiles   | 2 +-
 3 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 4977c05e15..4e4c3efb75 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -115,6 +115,7 @@ endif()
 add_library(cpptraj_common_obj OBJECT ${CPPTRAJ_COMMON_SOURCES})
 add_subdirectory(Cluster)
 add_subdirectory(Structure)
+add_subdirectory(Parm)
 make_pic_if_needed(cpptraj_common_obj)
 
 #normally this would be applied by target_link_libraries, but since we use that intermediary object library, we have to apply it manually
diff --git a/src/Makefile b/src/Makefile
index 625e87e043..d739bb6c59 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -8,9 +8,11 @@ include Cluster/clusterfiles
 CLUSTER_SOURCEFILES=$(CLUSTER_SOURCES:%.cpp=Cluster/%.cpp)
 include Structure/structurefiles
 STRUCTURE_SOURCEFILES=$(STRUCTURE_SOURCES:%.cpp=Structure/%.cpp)
+include Parm/parmfiles
+PARM_SOURCEFILES=$(PARM_SOURCES:%.cpp=Parm/%.cpp)
 
 # All object files
-OBJECTS=$(SOURCES:.cpp=.o) $(CSOURCES:.c=.o) $(CLUSTER_SOURCEFILES:.cpp=.o) $(STRUCTURE_SOURCEFILES:.cpp=.o)
+OBJECTS=$(SOURCES:.cpp=.o) $(CSOURCES:.c=.o) $(CLUSTER_SOURCEFILES:.cpp=.o) $(STRUCTURE_SOURCEFILES:.cpp=.o) $(PARM_SOURCEFILES:.cpp=.o)
 
 # General rules
 .cpp.o:
@@ -27,6 +29,7 @@ DEL_FILE = /bin/rm -f
 showsources:
 	@echo $(CLUSTER_SOURCEFILES)
 	@echo $(STRUCTURE_SOURCEFILES)
+	@echo $(PARM_SOURCEFILES)
 
 showobjects:
 	@echo $(OBJECTS)
@@ -137,7 +140,7 @@ findDepend: FindDepend.cpp FindDepend.o
 	$(CXX) -o findDepend FindDepend.o
 
 depend: findDepend
-	./findDepend $(SOURCES) $(CSOURCES) $(CLUSTER_SOURCEFILES) $(STRUCTURE_SOURCEFILES) > cpptrajdepend
+	./findDepend $(SOURCES) $(CSOURCES) $(CLUSTER_SOURCEFILES) $(STRUCTURE_SOURCEFILES) $(PARM_SOURCEFILES) > cpptrajdepend
 
 dependclean:
 	$(DEL_FILE) FindDepend.o findDepend
@@ -151,6 +154,7 @@ clean:
 	cd cuda_kernels && $(MAKE) clean
 	cd Cluster && $(MAKE) clean
 	cd Structure && $(MAKE) clean
+	cd Parm && $(MAKE) clean
 	cd tng && $(MAKE) clean
 
 uninstall_lib:
@@ -174,6 +178,7 @@ uninstall: uninstall_lib uninstall_inc
 	cd cuda_kernels && $(MAKE) uninstall
 	cd Cluster && $(MAKE) uninstall
 	cd Structure && $(MAKE) uninstall
+	cd Parm && $(MAKE) uninstall
 
 # Header dependencies
 include cpptrajdepend
diff --git a/src/cpptrajfiles b/src/cpptrajfiles
index 11560b4aa0..52ca7dce8c 100644
--- a/src/cpptrajfiles
+++ b/src/cpptrajfiles
@@ -478,7 +478,7 @@ SOURCES=$(COMMON_SOURCES) \
 # by libcpptraj. They MUST have the '.LIBCPPTRAJ.o' extension and will be
 # compiled with the '-DLIBCPPTRAJ' define.
 # NOTE: This variable MUST be in cpptrajfiles as the cmake build expects it.
-LIBCPPTRAJ_OBJECTS=$(COMMON_SOURCES:.cpp=.o) $(CSOURCES:.c=.o) $(CLUSTER_SOURCEFILES:.cpp=.o) $(STRUCTURE_SOURCEFILES:.cpp=.o) \
+LIBCPPTRAJ_OBJECTS=$(COMMON_SOURCES:.cpp=.o) $(CSOURCES:.c=.o) $(CLUSTER_SOURCEFILES:.cpp=.o) $(STRUCTURE_SOURCEFILES:.cpp=.o) $(PARM_SOURCEFILES:.cpp=.o) \
         Action_Esander.LIBCPPTRAJ.o \
         Command.LIBCPPTRAJ.o \
         Cpptraj.LIBCPPTRAJ.o \

From 8a5354b1fb830c6fdf2b9e4aab2c3b38bb8b91bd Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 4 Jan 2024 11:27:15 -0500
Subject: [PATCH 0265/1492] Get type from key

---
 src/Parm/GB_Params.cpp | 10 ++++++++++
 src/Parm/GB_Params.h   |  3 +++
 2 files changed, 13 insertions(+)

diff --git a/src/Parm/GB_Params.cpp b/src/Parm/GB_Params.cpp
index 496d9b9cd1..34203854b8 100644
--- a/src/Parm/GB_Params.cpp
+++ b/src/Parm/GB_Params.cpp
@@ -24,6 +24,16 @@ static const char* GB_RadiiTypeKey_[] = {
   0
 };
 
+/** \return GB_RadiiType corresponding to string. */
+Cpptraj::Parm::GB_RadiiType Cpptraj::Parm::GbTypeFromKey(std::string const& key) {
+  if (!key.empty()) {
+    for (int i = 0; i < (int)UNKNOWN_GB; i++) {
+      if ( key == std::string(GB_RadiiTypeKey_[i]) ) return (GB_RadiiType)i;
+    }
+  }
+  return UNKNOWN_GB;
+}
+
 /// These are the numeric iGBparm values used in LEaP
 static const int GB_RadiiTypeIGB_[] = {
   0, // bondi
diff --git a/src/Parm/GB_Params.h b/src/Parm/GB_Params.h
index 8dc3e94a88..ab07ac9b0b 100644
--- a/src/Parm/GB_Params.h
+++ b/src/Parm/GB_Params.h
@@ -1,5 +1,6 @@
 #ifndef INC_PARM_GBPARAMS_H
 #define INC_PARM_GBPARAMS_H
+#include <string>
 class Topology;
 namespace Cpptraj {
 namespace Parm {
@@ -14,6 +15,8 @@ enum GB_RadiiType {
   MBONDI3,          ///< 8, ArgH and AspGluO modified Bondi2 radii
   UNKNOWN_GB
 };
+/// \return GB radii type corresponding to string
+GB_RadiiType GbTypeFromKey(std::string const&);
 /// Assign GB radii
 int Assign_GB_Radii(Topology&, GB_RadiiType);
 }

From 92650dc0299be944991ad5ca74ad4abae6a7fb37 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 4 Jan 2024 11:30:39 -0500
Subject: [PATCH 0266/1492] Add function to return string corresponding to gb
 type

---
 src/Parm/GB_Params.cpp | 5 +++++
 src/Parm/GB_Params.h   | 2 ++
 2 files changed, 7 insertions(+)

diff --git a/src/Parm/GB_Params.cpp b/src/Parm/GB_Params.cpp
index 34203854b8..4c31f19a70 100644
--- a/src/Parm/GB_Params.cpp
+++ b/src/Parm/GB_Params.cpp
@@ -24,6 +24,11 @@ static const char* GB_RadiiTypeKey_[] = {
   0
 };
 
+/** \return char string corresponding to type. */
+std::string Cpptraj::Parm::GbTypeStr(GB_RadiiType t) {
+  return std::string(GB_RadiiTypeStr_[t]);
+}
+
 /** \return GB_RadiiType corresponding to string. */
 Cpptraj::Parm::GB_RadiiType Cpptraj::Parm::GbTypeFromKey(std::string const& key) {
   if (!key.empty()) {
diff --git a/src/Parm/GB_Params.h b/src/Parm/GB_Params.h
index ab07ac9b0b..97f24d11ff 100644
--- a/src/Parm/GB_Params.h
+++ b/src/Parm/GB_Params.h
@@ -15,6 +15,8 @@ enum GB_RadiiType {
   MBONDI3,          ///< 8, ArgH and AspGluO modified Bondi2 radii
   UNKNOWN_GB
 };
+/// \return string corresponding to gb radii set
+std::string GbTypeStr(GB_RadiiType);
 /// \return GB radii type corresponding to string
 GB_RadiiType GbTypeFromKey(std::string const&);
 /// Assign GB radii

From a7163fce16dd03fd44cc72c3a031cb9fdc90691e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 4 Jan 2024 11:34:46 -0500
Subject: [PATCH 0267/1492] Do gb radii assignment

---
 src/Exec_Build.cpp | 18 ++++++++++++++++++
 src/cpptrajdepend  |  3 ++-
 2 files changed, 20 insertions(+), 1 deletion(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 1dc353dea6..371d7058a2 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -3,6 +3,7 @@
 #include "DataSet_Parameters.h"
 //#inc lude "Structure/GenerateConnectivity.h"
 #include "Structure/Zmatrix.h"
+#include "Parm/GB_Params.h"
 
 DataSet_Coords* Exec_Build::IdTemplateFromName(Carray const& Templates,
                                                NameType const& rname)
@@ -322,6 +323,18 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
   DataSet_Coords& crdout = static_cast<DataSet_Coords&>( *((DataSet_Coords*)outCrdPtr) );
   mprintf("\tOutput COORDS set: %s\n", crdout.legend());
 
+  // GB radii set
+  Cpptraj::Parm::GB_RadiiType gbradii = Cpptraj::Parm::MBONDI; // Default
+  std::string gbset = argIn.GetStringKey("gb");
+  if (!gbset.empty()) {
+    gbradii = Cpptraj::Parm::GbTypeFromKey( gbset );
+    if (gbradii == Cpptraj::Parm::UNKNOWN_GB) {
+      mprinterr("Error: Unknown GB radii set: %s\n", gbset.c_str());
+      return CpptrajState::ERR;
+    }
+  }
+  mprintf("\tGB radii set: %s\n", Cpptraj::Parm::GbTypeStr(gbradii).c_str());
+
   // Get residue templates.
   Carray Templates;
   std::string lib = argIn.GetStringKey("lib");
@@ -422,6 +435,11 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
     mprinterr("Error: Could not assign parameters for '%s'.\n", topOut.c_str());
     ret = CpptrajState::ERR;
   }
+  // Assign GB parameters
+  if (Cpptraj::Parm::Assign_GB_Radii( topOut, gbradii )) {
+    mprinterr("Error: Could not assign GB parameters for '%s'\n", topOut.c_str());
+    ret = CpptrajState::ERR;
+  }
 
   if (free_parmset_mem && mainParmSet != 0) delete mainParmSet;
 
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 05ca2d63ae..5e3558a479 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -288,7 +288,7 @@ Ewald_Regular.o : Ewald_Regular.cpp Atom.h AtomMask.h Box.h Constants.h Coordina
 ExclusionArray.o : ExclusionArray.cpp Atom.h AtomMask.h CharMask.h CpptrajStdio.h ExclusionArray.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Unit.h
 Exec_AddMissingRes.o : Exec_AddMissingRes.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CharMask.h CompactFrameArray.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_AddMissingRes.h Exec_AddMissingRes_Pres.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Analyze.o : Exec_Analyze.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Analyze.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Build.o : Exec_Build.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Build.o : Exec_Build.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/GB_Params.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Calc.o : Exec_Calc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Calc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_CatCrd.o : Exec_CatCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CatCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Change.o : Exec_Change.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Change.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
@@ -399,6 +399,7 @@ PairList.o : PairList.cpp Atom.h AtomMask.h Box.h CoordinateInfo.h CpptrajStdio.
 Parallel.o : Parallel.cpp Parallel.h
 ParallelNetcdf.o : ParallelNetcdf.cpp CpptrajStdio.h Parallel.h ParallelNetcdf.h
 ParameterSet.o : ParameterSet.cpp AtomType.h Constants.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h TypeNameHolder.h UpdateParameters.h
+Parm/GB_Params.o : Parm/GB_Params.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/GB_Params.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 ParmFile.o : ParmFile.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h ParmIO.h Parm_Amber.h Parm_CIF.h Parm_CharmmPsf.h Parm_Gromacs.h Parm_Mol2.h Parm_PDB.h Parm_SDF.h Parm_Tinker.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Parm_Amber.o : Parm_Amber.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h ExclusionArray.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_Amber.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Parm_CIF.o : Parm_CIF.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h CIFfile.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_CIF.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h

From fe77b2f5e1613b32e3551447085cc7fa6b1af77b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 4 Jan 2024 11:47:29 -0500
Subject: [PATCH 0268/1492] Add gb screen params

---
 src/Parm/GB_Params.cpp | 107 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 107 insertions(+)

diff --git a/src/Parm/GB_Params.cpp b/src/Parm/GB_Params.cpp
index 4c31f19a70..65db247499 100644
--- a/src/Parm/GB_Params.cpp
+++ b/src/Parm/GB_Params.cpp
@@ -286,6 +286,112 @@ static void assign_gb_radii(Topology& top, Cpptraj::Parm::GB_RadiiType radiiSet)
   } // END loop over atoms
 }
 
+/** Assign GB screening parameters. */
+static void assign_gb_screen(Topology& top, Cpptraj::Parm::GB_RadiiType radiiSet)
+{
+  int iGBparm = GB_RadiiTypeIGB_[radiiSet];
+  for (int iat = 0; iat != top.Natom(); iat++)
+  {
+    Atom const& currentAtom = top[iat];
+    double dGBscreen = 0;
+    if (iGBparm < 4 || iGBparm == 6 || iGBparm == 8) {
+
+      // For now, hardwire the Bondi radii
+      switch (currentAtom.Element()) {
+        case Atom::HYDROGEN:
+          dGBscreen = 0.85;
+          break;
+        case Atom::CARBON:
+          dGBscreen = 0.72;
+          break;
+        case Atom::NITROGEN:
+          dGBscreen = 0.79;
+          break;
+        case Atom::OXYGEN:
+          dGBscreen = 0.85;
+          break;
+        case Atom::FLUORINE:
+          dGBscreen = 0.88;
+          break;
+        case Atom::PHOSPHORUS:
+          dGBscreen = 0.86;
+          break;
+        case Atom::SULFUR:
+          dGBscreen = 0.96;
+          break;
+        default:
+          dGBscreen = 0.8;
+          break;          // or should fail??
+      }
+    }
+    else if (iGBparm == 4) {    // param for Jayaram et al. 'GB'
+      switch (currentAtom.Element()) {
+        case Atom::HYDROGEN:
+          dGBscreen = 0.8461;
+          break;
+        case Atom::CARBON:
+          dGBscreen = 0.9615;
+          break;
+        case Atom::NITROGEN:
+          dGBscreen = 0.9343;
+          break;
+        case Atom::OXYGEN:
+          dGBscreen = 1.0088;
+          break;
+        case Atom::SODIUM:
+          dGBscreen = 1.0000;
+          break;
+        case Atom::MAGNESIUM:
+          dGBscreen = 1.0000;
+          break;          // Set by HG
+        case Atom::PHOSPHORUS:
+          dGBscreen = 1.0700;
+          break;
+        case Atom::SULFUR:
+          dGBscreen = 1.1733;
+          break;
+        default:
+          dGBscreen = 0.8000;
+          break;          // Set by HG
+      }
+    }
+    else if (iGBparm == 5) {
+
+      // Param for Jayaram et al. 'MGB'
+      switch (currentAtom.Element()) {
+        case Atom::HYDROGEN:
+          dGBscreen = 0.8846;
+          break;
+        case Atom::CARBON:
+          dGBscreen = 0.9186;
+          break;
+        case Atom::NITROGEN:
+          dGBscreen = 0.8733;
+          break;
+        case Atom::OXYGEN:
+          dGBscreen = 0.8836;
+          break;
+        case Atom::SODIUM:
+          dGBscreen = 1.0000;
+          break;
+        case Atom::MAGNESIUM:
+          dGBscreen = 1.0000;
+          break;          // Set by HG
+        case Atom::PHOSPHORUS:
+          dGBscreen = 0.9604;
+          break;
+        case Atom::SULFUR:
+          dGBscreen = 0.9323;
+          break;
+        default:
+          dGBscreen = 0.8000;
+          break;          // Set by HG
+      }
+    }
+    top.SetAtom(iat).SetGBscreen( dGBscreen );
+  } // END loop over atoms
+}
+
 /** Assign GB radii and screening parameters based on the given radius set. */
 int Cpptraj::Parm::Assign_GB_Radii(Topology& top, GB_RadiiType radiiSet)
 {
@@ -296,6 +402,7 @@ int Cpptraj::Parm::Assign_GB_Radii(Topology& top, GB_RadiiType radiiSet)
   mprintf("\tUsing GB radii set: %s\n", GB_RadiiTypeStr_[radiiSet]);
   top.SetGBradiiSet( std::string(GB_RadiiTypeStr_[radiiSet]) );
   assign_gb_radii( top, radiiSet );
+  assign_gb_screen( top, radiiSet );
 
   return 0;
 }

From 5a7cec41ab6ed020791eb2e6535c528c959239e9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 4 Jan 2024 15:15:13 -0500
Subject: [PATCH 0269/1492] Add note

---
 src/Topology.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index 8bd0930fd3..4a80add13b 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2769,7 +2769,7 @@ void Topology::AssignImproperParams(ImproperParmHolder const& newImproperParams)
 DihedralArray Topology::AssignDihedralParm(DihedralParmHolder const& newDihedralParams,
                                            ImproperParmHolder const& newImproperParams,
                                            DihedralArray const& dihedrals)
-{
+{ // TODO skip extra points
   DihedralArray dihedralsIn;
   // Keep track of 1-4 interactions
   typedef std::pair<int,int> Ipair;

From ac9caf7fb5713e185bde020bf1dfab14d58b411d Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 4 Jan 2024 20:26:29 -0500
Subject: [PATCH 0270/1492] Fix atom ordering in impropers. Still need to fix
 the sp2 checking

---
 src/Structure/GenerateImpropers.cpp | 15 ++++++++++++---
 src/Structure/GenerateImpropers.h   |  3 ++-
 src/Structure/structuredepend       |  2 +-
 src/Topology.cpp                    |  2 +-
 src/cpptrajdepend                   |  2 +-
 5 files changed, 17 insertions(+), 7 deletions(-)

diff --git a/src/Structure/GenerateImpropers.cpp b/src/Structure/GenerateImpropers.cpp
index 9db50929f2..2e7463d23f 100644
--- a/src/Structure/GenerateImpropers.cpp
+++ b/src/Structure/GenerateImpropers.cpp
@@ -2,6 +2,7 @@
 #include "../CpptrajStdio.h"
 #include "../Atom.h"
 #include "../AtomType.h"
+#include "../Residue.h"
 #include "../GuessAtomHybridization.h"
 #include "../ParameterTypes.h"
 #include "../ParameterHolders.h"
@@ -37,12 +38,19 @@ static inline void printName(Atom const& AJ) {
 }
 
 /** Try to determine impropers for topology. */ // TODO option for charmm improper
-DihedralArray Cpptraj::Structure::GenerateImproperArray(std::vector<Atom> const& atoms,
+DihedralArray Cpptraj::Structure::GenerateImproperArray(std::vector<Residue> const& residues,
+                                                        std::vector<Atom> const& atoms,
                                                         ParmHolder<AtomType> const& AT)
 {
   DihedralArray out;
-  long int atBegin = (long int)(atoms.size()) - 1;
-  for (long int iat = atBegin; iat >= 0; iat--) {
+  //int iidx = 0;
+  for (std::vector<Residue>::const_iterator res = residues.begin(); res != residues.end(); ++res)
+  {
+    for (int iat = res->LastAtom()-1; iat >= res->FirstAtom(); iat--)
+    {
+//
+//  long int atBegin = (long int)(atoms.size()) - 1;
+//  for (long int iat = atBegin; iat >= 0; iat--) {
     Atom const& AJ = atoms[iat];
     if (AJ.Nbonds() == 3) { // TODO only 3 atoms OK?
       AtomType::HybridizationType hybrid = AtomType::UNKNOWN_HYBRIDIZATION; 
@@ -78,6 +86,7 @@ DihedralArray Cpptraj::Structure::GenerateImproperArray(std::vector<Atom> const&
         mprintf("\n");
       }
     }
+    }
   }
   return out;
 }
diff --git a/src/Structure/GenerateImpropers.h b/src/Structure/GenerateImpropers.h
index 8d47c42e05..f88dbacf3d 100644
--- a/src/Structure/GenerateImpropers.h
+++ b/src/Structure/GenerateImpropers.h
@@ -2,13 +2,14 @@
 #define INC_STRUCTURE_GENERATEIMPROPERS_H
 #include <vector>
 class Atom;
+class Residue;
 class AtomType;
 class DihedralArray;
 template <typename Type> class ParmHolder;
 namespace Cpptraj {
 namespace Structure {
 /// Generate improper dihedral array in same order as leap
-DihedralArray GenerateImproperArray(std::vector<Atom> const&, ParmHolder<AtomType> const&);
+DihedralArray GenerateImproperArray(std::vector<Residue> const&, std::vector<Atom> const&, ParmHolder<AtomType> const&);
 }
 }
 #endif
diff --git a/src/Structure/structuredepend b/src/Structure/structuredepend
index cb893b8f36..a15da61fb8 100644
--- a/src/Structure/structuredepend
+++ b/src/Structure/structuredepend
@@ -5,7 +5,7 @@ FunctionalGroup.o : FunctionalGroup.cpp ../Atom.h ../AtomMap.h ../AtomMask.h ../
 FxnGroupBuilder.o : FxnGroupBuilder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h FunctionalGroup.h FxnGroupBuilder.h StructureRoutines.h Sugar.h SugarToken.h
 GenerateConnectivity.o : GenerateConnectivity.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h GenerateConnectivity.h
 GenerateConnectivityArrays.o : GenerateConnectivityArrays.cpp ../Atom.h ../Constants.h ../CpptrajStdio.h ../NameType.h ../ParameterTypes.h ../Residue.h ../SymbolExporting.h GenerateConnectivityArrays.h
-GenerateImpropers.o : GenerateImpropers.cpp ../Atom.h ../AtomType.h ../Constants.h ../CpptrajStdio.h ../GuessAtomHybridization.h ../NameType.h ../ParameterHolders.h ../ParameterTypes.h ../SymbolExporting.h ../TypeNameHolder.h GenerateImpropers.h
+GenerateImpropers.o : GenerateImpropers.cpp ../Atom.h ../AtomType.h ../Constants.h ../CpptrajStdio.h ../GuessAtomHybridization.h ../NameType.h ../ParameterHolders.h ../ParameterTypes.h ../Residue.h ../SymbolExporting.h ../TypeNameHolder.h GenerateImpropers.h
 HisProt.o : HisProt.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h HisProt.h StructureRoutines.h
 InternalCoords.o : InternalCoords.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h InternalCoords.h
 Model.o : Model.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h Model.h StructureEnum.h
diff --git a/src/Topology.cpp b/src/Topology.cpp
index 4a80add13b..ba7437212e 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -3089,7 +3089,7 @@ int Topology::AssignParams(ParameterSet const& set0) {
     AssignImproperParams( set0.IP() );
   } else {
     mprintf("\tRegenerating improper parameters.\n");
-    DihedralArray allImpropers = Cpptraj::Structure::GenerateImproperArray(atoms_, set0.AT());
+    DihedralArray allImpropers = Cpptraj::Structure::GenerateImproperArray(residues_, atoms_, set0.AT());
     allImpropers = AssignDihedralParm( set0.DP(), set0.IP(), allImpropers );
     for (DihedralArray::const_iterator imp = allImpropers.begin(); imp != allImpropers.end(); ++imp)
       AddToDihedralArrays( *imp );
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 5e3558a479..88a254f584 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -450,7 +450,7 @@ Structure/FunctionalGroup.o : Structure/FunctionalGroup.cpp Atom.h AtomMap.h Ato
 Structure/FxnGroupBuilder.o : Structure/FxnGroupBuilder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h Structure/FxnGroupBuilder.h Structure/StructureRoutines.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/GenerateConnectivity.o : Structure/GenerateConnectivity.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/GenerateConnectivity.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/GenerateConnectivityArrays.o : Structure/GenerateConnectivityArrays.cpp Atom.h Constants.h CpptrajStdio.h NameType.h ParameterTypes.h Residue.h Structure/GenerateConnectivityArrays.h SymbolExporting.h
-Structure/GenerateImpropers.o : Structure/GenerateImpropers.cpp Atom.h AtomType.h Constants.h CpptrajStdio.h GuessAtomHybridization.h NameType.h ParameterHolders.h ParameterTypes.h Structure/GenerateImpropers.h SymbolExporting.h TypeNameHolder.h
+Structure/GenerateImpropers.o : Structure/GenerateImpropers.cpp Atom.h AtomType.h Constants.h CpptrajStdio.h GuessAtomHybridization.h NameType.h ParameterHolders.h ParameterTypes.h Residue.h Structure/GenerateImpropers.h SymbolExporting.h TypeNameHolder.h
 Structure/HisProt.o : Structure/HisProt.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/HisProt.h Structure/StructureRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/InternalCoords.o : Structure/InternalCoords.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/InternalCoords.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/Model.o : Structure/Model.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h GuessAtomHybridization.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/Model.h Structure/StructureEnum.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h

From cf9b3a9b69d7cf99582835eeadf25c059523463a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 5 Jan 2024 10:16:32 -0500
Subject: [PATCH 0271/1492] New version of improper generation that is closer
 to what leap does

---
 src/Structure/GenerateConnectivityArrays.cpp | 66 ++++++++++++++++++++
 src/Structure/GenerateConnectivityArrays.h   |  2 +
 2 files changed, 68 insertions(+)

diff --git a/src/Structure/GenerateConnectivityArrays.cpp b/src/Structure/GenerateConnectivityArrays.cpp
index 8d5590893a..1bb7ddb5bb 100644
--- a/src/Structure/GenerateConnectivityArrays.cpp
+++ b/src/Structure/GenerateConnectivityArrays.cpp
@@ -91,3 +91,69 @@ DihedralArray Cpptraj::Structure::GenerateDihedralArray(std::vector<Residue> con
   }
   return out;
 }
+
+/** Try to order an improper the same way that LEaP does.
+  * LEaP has wild card names first, followed by atom types
+  * in alphabetical order.
+  */
+static void order_improper_atoms(int* indices, std::vector<Atom> const& atoms)
+{
+  if (atoms[indices[0]].Type() > atoms[indices[1]].Type()) std::swap( indices[0], indices[1] );
+  if (atoms[indices[1]].Type() > atoms[indices[2]].Type()) std::swap( indices[1], indices[2] );
+  if (atoms[indices[0]].Type() > atoms[indices[1]].Type()) std::swap( indices[0], indices[1] );
+  if (atoms[indices[1]].Type() > atoms[indices[2]].Type()) std::swap( indices[1], indices[2] );
+}
+
+// DEBUG
+static inline void printName(Atom const& AJ) {
+  mprintf(" :%i@%s", AJ.ResNum()+1, AJ.Name().Truncated().c_str());
+}
+
+/** From atom connectivity, generate an improper array in the same order as LEaP.
+  * No attempt is made to determine if this is an sp2 center; that is done
+  * during parameterization.
+  */
+DihedralArray Cpptraj::Structure::GenerateImproperArray(std::vector<Residue> const& residues,
+                                                        std::vector<Atom> const& atoms)
+{
+  DihedralArray out;
+  int iidx = 0;
+  for (std::vector<Residue>::const_iterator res = residues.begin(); res != residues.end(); ++res)
+  {
+    for (int iat3 = res->LastAtom()-1; iat3 >= res->FirstAtom(); iat3--)
+    {
+      Atom const& AJ = atoms[iat3];
+      if (AJ.Nbonds() >= 3) {
+        for (int bidx0 = 0; bidx0 < AJ.Nbonds(); bidx0++) {
+          for (int bidx1 = bidx0 + 1; bidx1 < AJ.Nbonds(); bidx1++) {
+            for (int bidx2 = bidx1 + 1; bidx2 < AJ.Nbonds(); bidx2++) {
+              int iat1 = AJ.BondIdxArray()[bidx0];
+              int iat2 = AJ.BondIdxArray()[bidx1];
+              int iat4 = AJ.BondIdxArray()[bidx2];
+              mprintf("DEBUG: IMPROPER  i= %i  %i - %i - %i - %i (%i %i %i %i)\n", iidx++, iat1+1, iat2+1, iat3+1, iat4+1, iat1*3, iat2*3, iat3*3, iat4*3);
+              int indices[3];
+              indices[0] = iat1;
+              indices[1] = iat2;
+              indices[2] = iat4;
+              order_improper_atoms(indices, atoms);
+              out.push_back( DihedralType(indices[0], indices[1], iat3, indices[2], DihedralType::BOTH) );
+              // DEBUG
+              mprintf("DEBUG:\tOriginal order :");
+              printName(atoms[iat1]);
+              printName(atoms[iat2]);
+              printName(atoms[iat3]);
+              printName(atoms[iat4]);
+              mprintf("\nDEBUG:\tLeap order     :");
+              printName(atoms[indices[0]]);
+              printName(atoms[indices[1]]);
+              printName(atoms[iat3]);
+              printName(atoms[indices[2]]);
+              mprintf("\n");
+            }
+          }
+        } // END outer loop over bond indices
+      }
+    } // END loop over residue atoms
+  } // END loop over residues
+  return out;
+}
diff --git a/src/Structure/GenerateConnectivityArrays.h b/src/Structure/GenerateConnectivityArrays.h
index 8fac565a63..27c6f5c647 100644
--- a/src/Structure/GenerateConnectivityArrays.h
+++ b/src/Structure/GenerateConnectivityArrays.h
@@ -14,6 +14,8 @@ BondArray GenerateBondArray(std::vector<Residue> const&, std::vector<Atom> const
 AngleArray GenerateAngleArray(std::vector<Residue> const&, std::vector<Atom> const&);
 /// Generate proper dihedral array in same order as leap
 DihedralArray GenerateDihedralArray(std::vector<Residue> const&, std::vector<Atom> const&);
+/// Generate improper dihedral array in same order as leap
+DihedralArray GenerateImproperArray(std::vector<Residue> const&, std::vector<Atom> const&);
 }
 }
 #endif

From 4651ed6f8df3c1d8f5e85a410b24da39fbf5e3ae Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 5 Jan 2024 10:17:54 -0500
Subject: [PATCH 0272/1492] Remove old routine

---
 src/Structure/GenerateImpropers.cpp | 92 -----------------------------
 src/Structure/GenerateImpropers.h   | 15 -----
 2 files changed, 107 deletions(-)
 delete mode 100644 src/Structure/GenerateImpropers.cpp
 delete mode 100644 src/Structure/GenerateImpropers.h

diff --git a/src/Structure/GenerateImpropers.cpp b/src/Structure/GenerateImpropers.cpp
deleted file mode 100644
index 2e7463d23f..0000000000
--- a/src/Structure/GenerateImpropers.cpp
+++ /dev/null
@@ -1,92 +0,0 @@
-#include "GenerateImpropers.h"
-#include "../CpptrajStdio.h"
-#include "../Atom.h"
-#include "../AtomType.h"
-#include "../Residue.h"
-#include "../GuessAtomHybridization.h"
-#include "../ParameterTypes.h"
-#include "../ParameterHolders.h"
-#include <algorithm> // std::swap
-
-/** Try to order an improper the same way that LEaP does.
-  * LEaP has wild card names first, followed by atom types
-  * in alphabetical order. The third atom is always the central
-  * atom.
-  */
-static int order_improper_atoms(int* leapdih, int centralAt, std::vector<Atom> const& topIn)
-{
-  Atom const& Ak = topIn[centralAt];
-  std::vector<int> const& bonds = Ak.BondIdxArray();
-  int indices[3];
-  indices[0] = bonds[0];
-  indices[1] = bonds[1];
-  indices[2] = bonds[2];
-  if (topIn[indices[0]].Type() > topIn[indices[1]].Type()) std::swap( indices[0], indices[1] );
-  if (topIn[indices[1]].Type() > topIn[indices[2]].Type()) std::swap( indices[1], indices[2] );
-  if (topIn[indices[0]].Type() > topIn[indices[1]].Type()) std::swap( indices[0], indices[1] );
-  if (topIn[indices[1]].Type() > topIn[indices[2]].Type()) std::swap( indices[1], indices[2] );
-  leapdih[0] = indices[0];
-  leapdih[1] = indices[1];
-  leapdih[2] = centralAt;
-  leapdih[3] = indices[2];
-  return 0;
-}
-
-// DEBUG
-static inline void printName(Atom const& AJ) {
-  mprintf(" :%i@%s", AJ.ResNum()+1, AJ.Name().Truncated().c_str());
-}
-
-/** Try to determine impropers for topology. */ // TODO option for charmm improper
-DihedralArray Cpptraj::Structure::GenerateImproperArray(std::vector<Residue> const& residues,
-                                                        std::vector<Atom> const& atoms,
-                                                        ParmHolder<AtomType> const& AT)
-{
-  DihedralArray out;
-  //int iidx = 0;
-  for (std::vector<Residue>::const_iterator res = residues.begin(); res != residues.end(); ++res)
-  {
-    for (int iat = res->LastAtom()-1; iat >= res->FirstAtom(); iat--)
-    {
-//
-//  long int atBegin = (long int)(atoms.size()) - 1;
-//  for (long int iat = atBegin; iat >= 0; iat--) {
-    Atom const& AJ = atoms[iat];
-    if (AJ.Nbonds() == 3) { // TODO only 3 atoms OK?
-      AtomType::HybridizationType hybrid = AtomType::UNKNOWN_HYBRIDIZATION; 
-      bool found;
-      AtomType atype = AT.FindParam(TypeNameHolder(AJ.Type()), found);
-      if (found)
-        hybrid = atype.Hybridization();
-      if (hybrid == AtomType::UNKNOWN_HYBRIDIZATION)
-        hybrid = Cpptraj::GuessAtomHybridization( AJ, atoms );
-      if (hybrid == AtomType::SP2) {
-        mprintf("DEBUG: Potential improper center:");
-        printName(AJ);
-        mprintf("\n");
-        int leapdih[4];
-        order_improper_atoms(leapdih, iat, atoms);
-        mprintf("DEBUG: Bond order");
-        printName(AJ);
-        mprintf(": %i %i %i %i", 
-                AJ.BondIdxArray()[0]+1,
-                AJ.BondIdxArray()[1]+1,
-                iat+1,
-                AJ.BondIdxArray()[2]+1);
-        printName(atoms[AJ.BondIdxArray()[0]]);
-        printName(atoms[AJ.BondIdxArray()[1]]);
-        printName(AJ);
-        printName(atoms[AJ.BondIdxArray()[2]]);
-        mprintf("\n");
-        mprintf("DEBUG: Leap order: %i %i %i %i\n", leapdih[0]+1, leapdih[1]+1, leapdih[2]+1, leapdih[3]+1);
-        out.push_back( DihedralType(leapdih[0], leapdih[1], leapdih[2], leapdih[3], DihedralType::BOTH) );
-      } else if (hybrid == AtomType::UNKNOWN_HYBRIDIZATION) {
-        mprintf("Warning: When searching for impropers could not determine hybridization of");
-        printName(AJ);
-        mprintf("\n");
-      }
-    }
-    }
-  }
-  return out;
-}
diff --git a/src/Structure/GenerateImpropers.h b/src/Structure/GenerateImpropers.h
deleted file mode 100644
index f88dbacf3d..0000000000
--- a/src/Structure/GenerateImpropers.h
+++ /dev/null
@@ -1,15 +0,0 @@
-#ifndef INC_STRUCTURE_GENERATEIMPROPERS_H
-#define INC_STRUCTURE_GENERATEIMPROPERS_H
-#include <vector>
-class Atom;
-class Residue;
-class AtomType;
-class DihedralArray;
-template <typename Type> class ParmHolder;
-namespace Cpptraj {
-namespace Structure {
-/// Generate improper dihedral array in same order as leap
-DihedralArray GenerateImproperArray(std::vector<Residue> const&, std::vector<Atom> const&, ParmHolder<AtomType> const&);
-}
-}
-#endif

From 0149fa7896df79a40faaa078227c0a06c4bb4fc8 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 5 Jan 2024 13:31:12 -0500
Subject: [PATCH 0273/1492] Assign impropers the same way as leap; do not add
 improper if no parameter is present, but warn if the central atom is sp2

---
 src/Structure/CMakeLists.txt                 |  1 -
 src/Structure/GenerateConnectivityArrays.cpp |  1 +
 src/Structure/structuredepend                |  1 -
 src/Structure/structurefiles                 |  1 -
 src/Topology.cpp                             | 48 ++++++++++++++------
 src/Topology.h                               |  5 +-
 src/cpptrajdepend                            |  3 +-
 7 files changed, 39 insertions(+), 21 deletions(-)

diff --git a/src/Structure/CMakeLists.txt b/src/Structure/CMakeLists.txt
index e0fa49b0e7..d04716f8bc 100644
--- a/src/Structure/CMakeLists.txt
+++ b/src/Structure/CMakeLists.txt
@@ -7,7 +7,6 @@ target_sources(cpptraj_common_obj PRIVATE
   ${CMAKE_CURRENT_LIST_DIR}/FxnGroupBuilder.cpp
   ${CMAKE_CURRENT_LIST_DIR}/GenerateConnectivityArrays.cpp
   ${CMAKE_CURRENT_LIST_DIR}/GenerateConnectivity.cpp
-  ${CMAKE_CURRENT_LIST_DIR}/GenerateImpropers.cpp
   ${CMAKE_CURRENT_LIST_DIR}/HisProt.cpp
   ${CMAKE_CURRENT_LIST_DIR}/InternalCoords.cpp
   ${CMAKE_CURRENT_LIST_DIR}/Model.cpp
diff --git a/src/Structure/GenerateConnectivityArrays.cpp b/src/Structure/GenerateConnectivityArrays.cpp
index 1bb7ddb5bb..8c2c01e261 100644
--- a/src/Structure/GenerateConnectivityArrays.cpp
+++ b/src/Structure/GenerateConnectivityArrays.cpp
@@ -3,6 +3,7 @@
 #include "../Atom.h"
 #include "../Residue.h"
 #include "../CpptrajStdio.h"
+#include <algorithm> // std::swap
 
 /** From atom connectivity, generate a bond array in the same order as LEaP. */ // TODO use in GenerateBAT
 BondArray Cpptraj::Structure::GenerateBondArray(std::vector<Residue> const& residues,
diff --git a/src/Structure/structuredepend b/src/Structure/structuredepend
index a15da61fb8..1cc597f095 100644
--- a/src/Structure/structuredepend
+++ b/src/Structure/structuredepend
@@ -5,7 +5,6 @@ FunctionalGroup.o : FunctionalGroup.cpp ../Atom.h ../AtomMap.h ../AtomMask.h ../
 FxnGroupBuilder.o : FxnGroupBuilder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h FunctionalGroup.h FxnGroupBuilder.h StructureRoutines.h Sugar.h SugarToken.h
 GenerateConnectivity.o : GenerateConnectivity.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h GenerateConnectivity.h
 GenerateConnectivityArrays.o : GenerateConnectivityArrays.cpp ../Atom.h ../Constants.h ../CpptrajStdio.h ../NameType.h ../ParameterTypes.h ../Residue.h ../SymbolExporting.h GenerateConnectivityArrays.h
-GenerateImpropers.o : GenerateImpropers.cpp ../Atom.h ../AtomType.h ../Constants.h ../CpptrajStdio.h ../GuessAtomHybridization.h ../NameType.h ../ParameterHolders.h ../ParameterTypes.h ../Residue.h ../SymbolExporting.h ../TypeNameHolder.h GenerateImpropers.h
 HisProt.o : HisProt.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h HisProt.h StructureRoutines.h
 InternalCoords.o : InternalCoords.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h InternalCoords.h
 Model.o : Model.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h Model.h StructureEnum.h
diff --git a/src/Structure/structurefiles b/src/Structure/structurefiles
index 825ca83eb0..6a6dd3da57 100644
--- a/src/Structure/structurefiles
+++ b/src/Structure/structurefiles
@@ -7,7 +7,6 @@ STRUCTURE_SOURCES= \
   FxnGroupBuilder.cpp \
   GenerateConnectivityArrays.cpp \
   GenerateConnectivity.cpp \
-  GenerateImpropers.cpp \
   HisProt.cpp \
   InternalCoords.cpp \
   Model.cpp \
diff --git a/src/Topology.cpp b/src/Topology.cpp
index ba7437212e..859a9901a2 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -7,8 +7,8 @@
 #include "AtomType.h"
 #include "AtomMask.h"
 #include "CharMask.h"
+#include "GuessAtomHybridization.h"
 #include "Structure/GenerateConnectivityArrays.h"
-#include "Structure/GenerateImpropers.h"
 
 const NonbondType Topology::LJ_EMPTY = NonbondType();
 
@@ -2768,6 +2768,7 @@ void Topology::AssignImproperParams(ImproperParmHolder const& newImproperParams)
   */
 DihedralArray Topology::AssignDihedralParm(DihedralParmHolder const& newDihedralParams,
                                            ImproperParmHolder const& newImproperParams,
+                                           ParmHolder<AtomType> const& AT,
                                            DihedralArray const& dihedrals)
 { // TODO skip extra points
   DihedralArray dihedralsIn;
@@ -2799,8 +2800,12 @@ DihedralArray Topology::AssignDihedralParm(DihedralParmHolder const& newDihedral
               (int)dih->IsImproper(), (int)isImproper);
     }
     bool found;
-    if (isImproper) {
+    if (dih->IsImproper()) {
       // ----- This is actually an improper dihedral. ----------------
+      // Impropers are treated differently than other topology types. If
+      // no parameter is found, do not add it to the list of dihedrals.
+      // However, if no parameter is found and the central atom is
+      // SP2, print a warning.
       //ImproperParmHolder::OrderType lastOrder;
       DihedralType mydih = *dih;
       bool reordered;
@@ -2813,18 +2818,31 @@ DihedralArray Topology::AssignDihedralParm(DihedralParmHolder const& newDihedral
                 TruncResAtomNameNum(dih->A3()).c_str(),
                 TruncResAtomNameNum(dih->A4()).c_str(),
                 *types[0], *types[1], *types[2], *types[3]);
+        // Central atom
+        Atom const& AJ = atoms_[dih->A3()];
+        AtomType::HybridizationType hybrid = AtomType::UNKNOWN_HYBRIDIZATION;
+        AtomType atype = AT.FindParam(TypeNameHolder(AJ.Type()), found);
+        if (found)
+          hybrid = atype.Hybridization();
+        if (hybrid == AtomType::UNKNOWN_HYBRIDIZATION) {
+          mprintf("Warning: Guessing hybridization for improper central atom %s\n", AtomMaskName(dih->A3()).c_str());
+          hybrid = Cpptraj::GuessAtomHybridization( AJ, atoms_ );
+        }
+        if (hybrid == AtomType::SP2) {
+          mprintf("Warning: No improper parameters for SP2 hybridized atom %s\n", AtomMaskName(dih->A3()).c_str());
+        }
       } else {
         if (ipa.size() > 1)
           mprintf("Warning: %zu improper parameters found for types %s - %s - %s - %s, expected only one."
                   "Warning: Only using first parameter.\n", ipa.size(), *(types[0]), *(types[1]), *(types[2]), *(types[3]));
         if (reordered) warn_improper_reorder( *dih, mydih );
         idx = addTorsionParm( dihedralparm_, ipa.front() );
+        mydih.SetIdx( idx );
+        mydih.SetImproper( true );
+        // Always skip 1-4 for impropers
+        mydih.SetSkip14( true );
+        dihedralsIn.push_back( mydih );
       }
-      mydih.SetIdx( idx );
-      mydih.SetImproper( true );
-      // Always skip 1-4 for impropers
-      mydih.SetSkip14( true );
-      dihedralsIn.push_back( mydih );
     } else {
       // -----Regular dihedral. See if parameter already present. ----
       DihedralParmArray dpa = newDihedralParams.FindParam( types, found );
@@ -2933,14 +2951,16 @@ DihedralArray Topology::get_unique_dihedrals(DihedralArray const& dihedralsIn) c
 }
 
 /** Replace any current dihedral parameters with given dihedral parameters. */
-void Topology::AssignDihedralParams(DihedralParmHolder const& newDihedralParams, ImproperParmHolder const& newImproperParams) {
+void Topology::AssignDihedralParams(DihedralParmHolder const& newDihedralParams, ImproperParmHolder const& newImproperParams,
+                                    ParmHolder<AtomType> const& AT)
+{
   dihedralparm_.clear();
   // Dihedrals can be a bit of a pain since there can be multiple
   // multiplicities for a single dihedral type. In case multiplicities
   // change, start with a fresh dihedral array containing only unique
   // dihedrals.
-  dihedrals_  = AssignDihedralParm( newDihedralParams, newImproperParams, get_unique_dihedrals(dihedrals_)  );
-  dihedralsh_ = AssignDihedralParm( newDihedralParams, newImproperParams, get_unique_dihedrals(dihedralsh_) );
+  dihedrals_  = AssignDihedralParm( newDihedralParams, newImproperParams, AT, get_unique_dihedrals(dihedrals_)  );
+  dihedralsh_ = AssignDihedralParm( newDihedralParams, newImproperParams, AT, get_unique_dihedrals(dihedralsh_) );
 }
 
 /** Replace current nonbond parameters with given nonbond parameters. */
@@ -3077,7 +3097,7 @@ int Topology::AssignParams(ParameterSet const& set0) {
   dihedrals_.clear();
   dihedralsh_.clear();
   DihedralArray allDihedrals = Cpptraj::Structure::GenerateDihedralArray(residues_, atoms_);
-  allDihedrals = AssignDihedralParm( set0.DP(), set0.IP(), allDihedrals );
+  allDihedrals = AssignDihedralParm( set0.DP(), set0.IP(), set0.AT(), allDihedrals );
   for (DihedralArray::const_iterator dih = allDihedrals.begin(); dih != allDihedrals.end(); ++dih)
     AddToDihedralArrays( *dih );
   // Urey-Bradley
@@ -3089,8 +3109,8 @@ int Topology::AssignParams(ParameterSet const& set0) {
     AssignImproperParams( set0.IP() );
   } else {
     mprintf("\tRegenerating improper parameters.\n");
-    DihedralArray allImpropers = Cpptraj::Structure::GenerateImproperArray(residues_, atoms_, set0.AT());
-    allImpropers = AssignDihedralParm( set0.DP(), set0.IP(), allImpropers );
+    DihedralArray allImpropers = Cpptraj::Structure::GenerateImproperArray(residues_, atoms_);
+    allImpropers = AssignDihedralParm( set0.DP(), set0.IP(), set0.AT(), allImpropers );
     for (DihedralArray::const_iterator imp = allImpropers.begin(); imp != allImpropers.end(); ++imp)
       AddToDihedralArrays( *imp );
   }
@@ -3152,7 +3172,7 @@ int Topology::updateParams(ParameterSet& set0, ParameterSet const& set1) {
 //  updateCount = UpdateParameters< DihedralParmHolder >(set0.DP(), set1.DP(), "dihedral");
   if (UC.nDihedralsUpdated_ > 0) {
     mprintf("\tRegenerating dihedral parameters.\n");
-    AssignDihedralParams( set0.DP(), set0.IP() );
+    AssignDihedralParams( set0.DP(), set0.IP(), set0.AT() );
   }
   // Urey-Bradley
 //  updateCount = UpdateParameters< ParmHolder<BondParmType> >(set0.UB(), set1.UB(), "Urey-Bradley");
diff --git a/src/Topology.h b/src/Topology.h
index ec9d70981c..6afa53dcc0 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -145,7 +145,7 @@ class Topology {
     void AddDihedral(DihedralType const&, bool);
     void AddDihedral(DihedralType const&, DihedralParmType const&);
     void AssignImproperParams(ImproperParmHolder const&);
-    void AssignDihedralParams(DihedralParmHolder const&, ImproperParmHolder const&);
+    void AssignDihedralParams(DihedralParmHolder const&, ImproperParmHolder const&, ParmHolder<AtomType> const&);
     /// Add to dihedral arrays
     void AddToDihedralArrays(DihedralType const&);
     // ----- CMAP-specific routines --------------
@@ -310,7 +310,8 @@ class Topology {
     void warn_improper_reorder(DihedralType const&, DihedralType const&) const;
     void AssignImproperParm(ImproperParmHolder const&, DihedralArray&, DihedralParmArray&) const;
     inline DihedralArray get_unique_dihedrals(DihedralArray const&) const;
-    DihedralArray AssignDihedralParm(DihedralParmHolder const&, ImproperParmHolder const&, DihedralArray const&);
+    DihedralArray AssignDihedralParm(DihedralParmHolder const&, ImproperParmHolder const&,
+                                     ParmHolder<AtomType> const&, DihedralArray const&);
 
     static const NonbondType LJ_EMPTY;
     std::vector<Atom> atoms_;
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 88a254f584..067c995755 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -450,7 +450,6 @@ Structure/FunctionalGroup.o : Structure/FunctionalGroup.cpp Atom.h AtomMap.h Ato
 Structure/FxnGroupBuilder.o : Structure/FxnGroupBuilder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h Structure/FxnGroupBuilder.h Structure/StructureRoutines.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/GenerateConnectivity.o : Structure/GenerateConnectivity.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/GenerateConnectivity.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/GenerateConnectivityArrays.o : Structure/GenerateConnectivityArrays.cpp Atom.h Constants.h CpptrajStdio.h NameType.h ParameterTypes.h Residue.h Structure/GenerateConnectivityArrays.h SymbolExporting.h
-Structure/GenerateImpropers.o : Structure/GenerateImpropers.cpp Atom.h AtomType.h Constants.h CpptrajStdio.h GuessAtomHybridization.h NameType.h ParameterHolders.h ParameterTypes.h Residue.h Structure/GenerateImpropers.h SymbolExporting.h TypeNameHolder.h
 Structure/HisProt.o : Structure/HisProt.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/HisProt.h Structure/StructureRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/InternalCoords.o : Structure/InternalCoords.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/InternalCoords.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/Model.o : Structure/Model.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h GuessAtomHybridization.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/Model.h Structure/StructureEnum.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
@@ -469,7 +468,7 @@ TextFormat.o : TextFormat.cpp StringRoutines.h TextFormat.h
 Timer.o : Timer.cpp CpptrajStdio.h Timer.h
 TinkerFile.o : TinkerFile.cpp ArgList.h Atom.h AtomMask.h Box.h BufferedLine.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TinkerFile.h Unit.h Vec3.h
 TopInfo.o : TopInfo.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h DistRoutines.h FileIO.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Mol.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h TopInfo.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Topology.o : Topology.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/GenerateConnectivityArrays.h Structure/GenerateImpropers.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Topology.o : Topology.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/GenerateConnectivityArrays.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 TorsionRoutines.o : TorsionRoutines.cpp Constants.h TorsionRoutines.h Vec3.h
 TrajFrameCounter.o : TrajFrameCounter.cpp ArgList.h CpptrajStdio.h TrajFrameCounter.h
 TrajIOarray.o : TrajIOarray.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryFile.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h

From c7a29afc7b90e015630d347e7bc9ba1e1b331533 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 5 Jan 2024 13:39:17 -0500
Subject: [PATCH 0274/1492] Create empty arrays

---
 src/Exec_Build.cpp | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 371d7058a2..886898776a 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -440,6 +440,10 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
     mprinterr("Error: Could not assign GB parameters for '%s'\n", topOut.c_str());
     ret = CpptrajState::ERR;
   }
+  // Create empty arrays for the TREE, JOIN, and IROTAT arrays
+  topOut.AllocTreeChainClassification( );
+  topOut.AllocJoinArray();
+  topOut.AllocRotateArray();
 
   if (free_parmset_mem && mainParmSet != 0) delete mainParmSet;
 

From 4a2dbf1becb49baaba592b805af1676c584afb42 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 5 Jan 2024 15:33:45 -0500
Subject: [PATCH 0275/1492] Start concept of atom scan direction

---
 src/Exec_Build.cpp                           | 18 ++++++++--
 src/Structure/GenerateConnectivityArrays.cpp | 36 ++++++++++++++++++--
 src/Structure/GenerateConnectivityArrays.h   |  4 +++
 3 files changed, 54 insertions(+), 4 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 886898776a..2060e77fa9 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -1,7 +1,7 @@
 #include "Exec_Build.h"
 #include "CpptrajStdio.h"
 #include "DataSet_Parameters.h"
-//#inc lude "Structure/GenerateConnectivity.h"
+#include "Structure/GenerateConnectivityArrays.h"
 #include "Structure/Zmatrix.h"
 #include "Parm/GB_Params.h"
 
@@ -277,12 +277,26 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
 void Exec_Build::Help() const
 {
   mprintf("\tname <output COORDS> crdset <COORDS set> [frame <#>]\n"
-          "\t[parmset <param set> ...] [lib <lib set> ...]\n");
+          "\t[parmset <param set> ...] [lib <lib set> ...]\n"
+          "\t[atomscandir {f|b}]\n"
+         );
 }
 
 // Exec_Build::Execute()
 Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
 {
+  // Atom scan direction
+  std::string atomscandir = argIn.GetStringKey("atomscandir");
+  if (!atomscandir.empty()) {
+    if (atomscandir == "f")
+      Cpptraj::Structure::SetAtomScanDirection(Cpptraj::Structure::SCAN_ATOMS_FORWARDS);
+    else if (atomscandir == "b")
+      Cpptraj::Structure::SetAtomScanDirection(Cpptraj::Structure::SCAN_ATOMS_BACKWARDS);
+    else {
+      mprinterr("Error: Unrecognized keyword for 'atomscandir' : %s\n", atomscandir.c_str());
+      return CpptrajState::ERR;
+    }
+  }
   // Get input coords
   std::string crdset = argIn.GetStringKey("crdset");
   if (crdset.empty()) {
diff --git a/src/Structure/GenerateConnectivityArrays.cpp b/src/Structure/GenerateConnectivityArrays.cpp
index 8c2c01e261..fc6e706d79 100644
--- a/src/Structure/GenerateConnectivityArrays.cpp
+++ b/src/Structure/GenerateConnectivityArrays.cpp
@@ -5,6 +5,32 @@
 #include "../CpptrajStdio.h"
 #include <algorithm> // std::swap
 
+/// The direction in which atoms in residues should be scanned
+static Cpptraj::Structure::AtomScanDirectionType CpptrajStructureAtomScanDirection_ = Cpptraj::Structure::SCAN_ATOMS_BACKWARDS;
+
+/** Set default atom scan direction. */
+void Cpptraj::Structure::SetAtomScanDirection( AtomScanDirectionType direction ) {
+  if (direction == SCAN_ATOMS_BACKWARDS)
+    mprintf("\tSetting atom scan direction to backwards.\n");
+  else
+    mprintf("\tSetting atom scan direction to forwards.\n");
+  CpptrajStructureAtomScanDirection_ = direction;
+}
+
+/// Set start and end atoms along with offset based on atom scan direction
+static inline void set_indices(int& start, int& end, int& offset, int firstatom, int lastatom)
+{
+  if (CpptrajStructureAtomScanDirection_ == Cpptraj::Structure::SCAN_ATOMS_BACKWARDS) {
+    start = lastatom - 1;
+    end = firstatom - 1;
+    offset = -1;
+  } else {
+    start = firstatom;
+    end = lastatom;
+    offset = 1;
+  }
+}
+
 /** From atom connectivity, generate a bond array in the same order as LEaP. */ // TODO use in GenerateBAT
 BondArray Cpptraj::Structure::GenerateBondArray(std::vector<Residue> const& residues,
                                                 std::vector<Atom> const& atoms)
@@ -14,7 +40,10 @@ BondArray Cpptraj::Structure::GenerateBondArray(std::vector<Residue> const& resi
   int bidx = 0;
   for (std::vector<Residue>::const_iterator res = residues.begin(); res != residues.end(); ++res)
   {
-    for (int iat = res->LastAtom()-1; iat >= res->FirstAtom(); iat--)
+    int start, end, offset;
+    set_indices(start, end, offset, res->FirstAtom(), res->LastAtom());
+    for (int iat = start; iat != end; iat += offset)
+    //for (int iat = res->LastAtom()-1; iat >= res->FirstAtom(); iat--)
     {
       Atom const& At = atoms[iat];
       for (Atom::bond_iterator bat = At.bondbegin(); bat != At.bondend(); ++bat)
@@ -40,7 +69,10 @@ AngleArray Cpptraj::Structure::GenerateAngleArray(std::vector<Residue> const& re
   int aidx = 0;
   for (std::vector<Residue>::const_iterator res = residues.begin(); res != residues.end(); ++res)
   {
-    for (int iat1 = res->LastAtom()-1; iat1 >= res->FirstAtom(); iat1--)
+    int start, end, offset;
+    set_indices(start, end, offset, res->FirstAtom(), res->LastAtom());
+    for (int iat1 = start; iat1 != end; iat1 += offset)
+    //for (int iat1 = res->LastAtom()-1; iat1 >= res->FirstAtom(); iat1--)
     {
       Atom const& At1 = atoms[iat1];
       for (int bidx1 = 0; bidx1 < At1.Nbonds(); bidx1++) {
diff --git a/src/Structure/GenerateConnectivityArrays.h b/src/Structure/GenerateConnectivityArrays.h
index 27c6f5c647..9975c3d83b 100644
--- a/src/Structure/GenerateConnectivityArrays.h
+++ b/src/Structure/GenerateConnectivityArrays.h
@@ -8,6 +8,10 @@ class Residue;
 class Atom;
 namespace Cpptraj {
 namespace Structure {
+/// Specify direction in which atoms in residues should be scanned
+enum AtomScanDirectionType { SCAN_ATOMS_BACKWARDS = 0, SCAN_ATOMS_FORWARDS };
+/// Set default atom scan direction
+void SetAtomScanDirection(AtomScanDirectionType);
 /// Generate bond array in same order as leap
 BondArray GenerateBondArray(std::vector<Residue> const&, std::vector<Atom> const&);
 /// Generate angle array in same order as leap

From 059f0e38378894e89b1b6b8230fec332ca2efe5b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 5 Jan 2024 15:37:56 -0500
Subject: [PATCH 0276/1492] Have dihedral and improper respect the atom scan
 direction

---
 src/Structure/GenerateConnectivityArrays.cpp | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/src/Structure/GenerateConnectivityArrays.cpp b/src/Structure/GenerateConnectivityArrays.cpp
index fc6e706d79..91c9c13127 100644
--- a/src/Structure/GenerateConnectivityArrays.cpp
+++ b/src/Structure/GenerateConnectivityArrays.cpp
@@ -100,7 +100,10 @@ DihedralArray Cpptraj::Structure::GenerateDihedralArray(std::vector<Residue> con
   int didx = 0;
   for (std::vector<Residue>::const_iterator res = residues.begin(); res != residues.end(); ++res)
   {
-    for (int iat1 = res->LastAtom()-1; iat1 >= res->FirstAtom(); iat1--)
+    int start, end, offset;
+    set_indices(start, end, offset, res->FirstAtom(), res->LastAtom());
+    for (int iat1 = start; iat1 != end; iat1 += offset)
+    //for (int iat1 = res->LastAtom()-1; iat1 >= res->FirstAtom(); iat1--)
     {
       Atom const& At1 = atoms[iat1];
       for (int bidx1 = 0; bidx1 < At1.Nbonds(); bidx1++) {
@@ -153,7 +156,10 @@ DihedralArray Cpptraj::Structure::GenerateImproperArray(std::vector<Residue> con
   int iidx = 0;
   for (std::vector<Residue>::const_iterator res = residues.begin(); res != residues.end(); ++res)
   {
-    for (int iat3 = res->LastAtom()-1; iat3 >= res->FirstAtom(); iat3--)
+    int start, end, offset;
+    set_indices(start, end, offset, res->FirstAtom(), res->LastAtom());
+    for (int iat3 = start; iat3 != end; iat3 += offset)
+    //for (int iat3 = res->LastAtom()-1; iat3 >= res->FirstAtom(); iat3--)
     {
       Atom const& AJ = atoms[iat3];
       if (AJ.Nbonds() >= 3) {

From 4354390d4b77268f914c8564e760fcf630c9dda5 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 5 Jan 2024 15:58:30 -0500
Subject: [PATCH 0277/1492] Print atom type as well for debugging

---
 src/Structure/GenerateConnectivityArrays.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Structure/GenerateConnectivityArrays.cpp b/src/Structure/GenerateConnectivityArrays.cpp
index 91c9c13127..e85be89015 100644
--- a/src/Structure/GenerateConnectivityArrays.cpp
+++ b/src/Structure/GenerateConnectivityArrays.cpp
@@ -142,7 +142,7 @@ static void order_improper_atoms(int* indices, std::vector<Atom> const& atoms)
 
 // DEBUG
 static inline void printName(Atom const& AJ) {
-  mprintf(" :%i@%s", AJ.ResNum()+1, AJ.Name().Truncated().c_str());
+  mprintf(" :%i@%s (%s)", AJ.ResNum()+1, AJ.Name().Truncated().c_str(), AJ.Type().Truncated().c_str());
 }
 
 /** From atom connectivity, generate an improper array in the same order as LEaP.

From 567a3bb39850d5b1bd824e737d66a11d932dca01 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 8 Jan 2024 09:39:26 -0500
Subject: [PATCH 0278/1492] Start adding ability to read leap rc file

---
 src/DataFile.cpp      |  3 ++
 src/DataFile.h        |  1 +
 src/DataIO_LeapRC.cpp | 81 +++++++++++++++++++++++++++++++++++++++++++
 src/DataIO_LeapRC.h   | 17 +++++++++
 src/cpptrajdepend     |  7 ++--
 src/cpptrajfiles      |  5 +--
 6 files changed, 109 insertions(+), 5 deletions(-)
 create mode 100644 src/DataIO_LeapRC.cpp
 create mode 100644 src/DataIO_LeapRC.h

diff --git a/src/DataFile.cpp b/src/DataFile.cpp
index 4403b0d6e9..b467763dc3 100644
--- a/src/DataFile.cpp
+++ b/src/DataFile.cpp
@@ -36,6 +36,7 @@
 #include "DataIO_AmberLib.h"
 #include "DataIO_AmberFF.h"
 #include "DataIO_AmberFrcmod.h"
+#include "DataIO_LeapRC.h"
 
 // CONSTRUCTOR
 DataFile::DataFile() :
@@ -93,6 +94,7 @@ const FileTypes::AllocToken DataFile::DF_AllocArray[] = {
   { "Amber OFF File",     0,                             0,            DataIO_AmberLib::Alloc},
   { "Amber Force Field",  DataIO_AmberFF::ReadHelp,      0,            DataIO_AmberFF::Alloc},
   { "Amber Frcmod File",  0,                             0,            DataIO_AmberFrcmod::Alloc},
+  { "Amber LEaP RC File", 0,                             0,            DataIO_LeapRC::Alloc},
   { "Unknown Data file",  0,                       0,                        0                    }
 };
 
@@ -124,6 +126,7 @@ const FileTypes::KeyToken DataFile::DF_KeyArray[] = {
   { AMBERLIB,     "off",          ".lib" },
   { AMBERFF,      "amberff",      ".parm" },
   { AMBERFRCMOD,  "frcmod",       ".frcmod" },
+  { AMBERLEAPRC,  "leaprc",       ".leaprc" },
   { UNKNOWN_DATA, 0,        0        }
 };
 
diff --git a/src/DataFile.h b/src/DataFile.h
index 7cd62360b7..814f057108 100644
--- a/src/DataFile.h
+++ b/src/DataFile.h
@@ -19,6 +19,7 @@ class DataFile {
       VECTRAJ, XVG, CCP4, CHARMMREPD, CHARMMFASTREP,
       CHARMMOUT, CPOUT, CHARMMRTFPRM, CMATRIX_BINARY, CMATRIX_NETCDF, PEAKS,
       NETCDFDATA, AMBERENE, NUMPY, AMBERPREP, AMBERLIB, AMBERFF, AMBERFRCMOD,
+      AMBERLEAPRC,
       UNKNOWN_DATA 
     };
     DataFile();
diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
new file mode 100644
index 0000000000..a0aaac40e4
--- /dev/null
+++ b/src/DataIO_LeapRC.cpp
@@ -0,0 +1,81 @@
+#include "DataIO_LeapRC.h"
+#include "CpptrajStdio.h"
+#include "BufferedLine.h"
+
+/// CONSTRUCTOR
+DataIO_LeapRC::DataIO_LeapRC()
+{
+
+}
+
+// DataIO_LeapRC::ID_DataFormat()
+bool DataIO_LeapRC::ID_DataFormat(CpptrajFile& infile)
+{
+  if (infile.OpenFile()) return false;
+  bool isLeaprc = false;
+  // Scan the first 5 non-blank non-comment lines
+  int nLinesScanned = 0;
+  while (nLinesScanned < 5 && !isLeaprc) {
+    const char* ptr = infile.NextLine();
+    if (ptr == 0) break;
+    if (ptr[0] == '\0' || ptr[0] == '#') continue;
+    nLinesScanned++;
+    ArgList line(ptr);
+    if (line.Nargs() > 0) {
+      if (line[0] == "logFile" || line[0] == "logfile")
+        isLeaprc = true;
+      else if (line[0] == "source")
+        isLeaprc = true;
+      else if (line[0] == "addAtomTypes" || line[0] == "addatomtypes")
+        isLeaprc = true;
+    }
+  }
+  infile.CloseFile();
+  return isLeaprc;
+}
+
+// DataIO_LeapRC::ReadHelp()
+void DataIO_LeapRC::ReadHelp()
+{
+
+}
+
+// DataIO_LeapRC::processReadArgs()
+int DataIO_LeapRC::processReadArgs(ArgList& argIn)
+{
+
+  return 0;
+}
+
+// DataIO_LeapRC::ReadData()
+int DataIO_LeapRC::ReadData(FileName const& fname, DataSetList& dsl, std::string const& dsname)
+{
+  BufferedLine infile;
+  if (infile.OpenFileRead(fname)) {
+    mprinterr("Error: Could not open leaprc file '%s'\n", fname.full());
+    return 1;
+  }
+
+  infile.CloseFile();
+  return 0;
+}
+
+// DataIO_LeapRC::WriteHelp()
+void DataIO_LeapRC::WriteHelp()
+{
+
+}
+
+// DataIO_LeapRC::processWriteArgs()
+int DataIO_LeapRC::processWriteArgs(ArgList& argIn)
+{
+
+  return 0;
+}
+
+// DataIO_LeapRC::WriteData()
+int DataIO_LeapRC::WriteData(FileName const& fname, DataSetList const& dsl)
+{
+
+  return 1;
+}
diff --git a/src/DataIO_LeapRC.h b/src/DataIO_LeapRC.h
new file mode 100644
index 0000000000..90344f89f8
--- /dev/null
+++ b/src/DataIO_LeapRC.h
@@ -0,0 +1,17 @@
+#ifndef INC_DATAIO_LEAPRC_H
+#define INC_DATAIO_LEAPRC_H
+#include "DataIO.h"
+/// Read parameters and units from a leap rc file 
+class DataIO_LeapRC : public DataIO {
+  public:
+    DataIO_LeapRC();
+    static void ReadHelp();
+    static void WriteHelp();
+    static BaseIOtype* Alloc() { return (BaseIOtype*)new DataIO_LeapRC(); }
+    int processReadArgs(ArgList&);
+    int ReadData(FileName const&, DataSetList&, std::string const&);
+    int processWriteArgs(ArgList&);
+    int WriteData(FileName const&, DataSetList const&);
+    bool ID_DataFormat(CpptrajFile&);
+};
+#endif
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 067c995755..1f0cfef939 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -200,7 +200,7 @@ CpptrajFile.o : CpptrajFile.cpp CpptrajFile.h CpptrajStdio.h FileIO.h FileIO_Bzi
 CpptrajState.o : CpptrajState.cpp Action.h ActionList.h ActionState.h Action_CreateCrd.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_Topology.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleNavigator.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 CpptrajStdio.o : CpptrajStdio.cpp Parallel.h
 CurveFit.o : CurveFit.cpp CurveFit.h
-DataFile.o : DataFile.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Cluster/Cframes.h Cluster/Cmatrix_NC.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataFile.h DataIO.h DataIO_AmberEne.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_CCP4.h DataIO_CharmmFastRep.h DataIO_CharmmOutput.h DataIO_CharmmRepLog.h DataIO_CharmmRtfPrm.h DataIO_Cmatrix_Binary.h DataIO_Cmatrix_NC.h DataIO_Cpout.h DataIO_Evecs.h DataIO_Gnuplot.h DataIO_Grace.h DataIO_Mdout.h DataIO_NetCDF.h DataIO_Numpy.h DataIO_OpenDx.h DataIO_Peaks.h DataIO_RemLog.h DataIO_Std.h DataIO_VecTraj.h DataIO_XVG.h DataIO_Xplor.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TypeNameHolder.h Unit.h Vec3.h
+DataFile.o : DataFile.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Cluster/Cframes.h Cluster/Cmatrix_NC.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataFile.h DataIO.h DataIO_AmberEne.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_CCP4.h DataIO_CharmmFastRep.h DataIO_CharmmOutput.h DataIO_CharmmRepLog.h DataIO_CharmmRtfPrm.h DataIO_Cmatrix_Binary.h DataIO_Cmatrix_NC.h DataIO_Cpout.h DataIO_Evecs.h DataIO_Gnuplot.h DataIO_Grace.h DataIO_LeapRC.h DataIO_Mdout.h DataIO_NetCDF.h DataIO_Numpy.h DataIO_OpenDx.h DataIO_Peaks.h DataIO_RemLog.h DataIO_Std.h DataIO_VecTraj.h DataIO_XVG.h DataIO_Xplor.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TypeNameHolder.h Unit.h Vec3.h
 DataFileList.o : DataFileList.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataFilter.o : DataFilter.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_integer.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO.o : DataIO.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
@@ -220,6 +220,7 @@ DataIO_Cpout.o : DataIO_Cpout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h A
 DataIO_Evecs.o : DataIO_Evecs.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Evecs.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Gnuplot.o : DataIO_Gnuplot.cpp ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Gnuplot.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Grace.o : DataIO_Grace.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Grace.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_string.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_LeapRC.o : DataIO_LeapRC.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Mdout.o : DataIO_Mdout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Mdout.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_NetCDF.o : DataIO_NetCDF.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/Cframes.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_NetCDF.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_Mesh.h DataSet_Modes.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_Vector.h DataSet_Vector_Scalar.h DataSet_string.h DataSet_unsignedInt.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h Version.h
 DataIO_Numpy.o : DataIO_Numpy.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Numpy.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h libnpy/npy.hpp
@@ -288,7 +289,7 @@ Ewald_Regular.o : Ewald_Regular.cpp Atom.h AtomMask.h Box.h Constants.h Coordina
 ExclusionArray.o : ExclusionArray.cpp Atom.h AtomMask.h CharMask.h CpptrajStdio.h ExclusionArray.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Unit.h
 Exec_AddMissingRes.o : Exec_AddMissingRes.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CharMask.h CompactFrameArray.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_AddMissingRes.h Exec_AddMissingRes_Pres.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Analyze.o : Exec_Analyze.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Analyze.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Build.o : Exec_Build.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/GB_Params.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Build.o : Exec_Build.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/GB_Params.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Calc.o : Exec_Calc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Calc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_CatCrd.o : Exec_CatCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CatCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Change.o : Exec_Change.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Change.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
@@ -468,7 +469,7 @@ TextFormat.o : TextFormat.cpp StringRoutines.h TextFormat.h
 Timer.o : Timer.cpp CpptrajStdio.h Timer.h
 TinkerFile.o : TinkerFile.cpp ArgList.h Atom.h AtomMask.h Box.h BufferedLine.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TinkerFile.h Unit.h Vec3.h
 TopInfo.o : TopInfo.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h DistRoutines.h FileIO.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Mol.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h TopInfo.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Topology.o : Topology.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/GenerateConnectivityArrays.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Topology.o : Topology.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h GuessAtomHybridization.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/GenerateConnectivityArrays.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 TorsionRoutines.o : TorsionRoutines.cpp Constants.h TorsionRoutines.h Vec3.h
 TrajFrameCounter.o : TrajFrameCounter.cpp ArgList.h CpptrajStdio.h TrajFrameCounter.h
 TrajIOarray.o : TrajIOarray.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryFile.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
diff --git a/src/cpptrajfiles b/src/cpptrajfiles
index 52ca7dce8c..fbf1907ef3 100644
--- a/src/cpptrajfiles
+++ b/src/cpptrajfiles
@@ -191,11 +191,12 @@ COMMON_SOURCES= \
         DataIO_Evecs.cpp \
         DataIO_Gnuplot.cpp \
         DataIO_Grace.cpp \
-        DataIO_OpenDx.cpp \
-        DataIO_Peaks.cpp \
+        DataIO_LeapRC.cpp \
         DataIO_Mdout.cpp \
         DataIO_NetCDF.cpp \
         DataIO_Numpy.cpp \
+        DataIO_OpenDx.cpp \
+        DataIO_Peaks.cpp \
         DataIO_RemLog.cpp \
         DataIO_Std.cpp \
         DataIO_VecTraj.cpp \

From ec42ca1d82c9c409d4d1fd112f42eb3438cd5d63 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 8 Jan 2024 10:06:18 -0500
Subject: [PATCH 0279/1492] Implement loadamberparams

---
 src/DataIO_LeapRC.cpp | 55 ++++++++++++++++++++++++++++++++++++++++---
 src/DataIO_LeapRC.h   |  4 ++++
 src/cpptrajdepend     |  2 +-
 3 files changed, 57 insertions(+), 4 deletions(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index a0aaac40e4..21440fffed 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -1,6 +1,9 @@
 #include "DataIO_LeapRC.h"
 #include "CpptrajStdio.h"
 #include "BufferedLine.h"
+#include "DataIO_AmberFF.h"
+#include "DataIO_AmberFrcmod.h"
+#include <cstdlib> //getenv
 
 /// CONSTRUCTOR
 DataIO_LeapRC::DataIO_LeapRC()
@@ -20,7 +23,7 @@ bool DataIO_LeapRC::ID_DataFormat(CpptrajFile& infile)
     if (ptr == 0) break;
     if (ptr[0] == '\0' || ptr[0] == '#') continue;
     nLinesScanned++;
-    ArgList line(ptr);
+    ArgList line(ptr, " \t");
     if (line.Nargs() > 0) {
       if (line[0] == "logFile" || line[0] == "logfile")
         isLeaprc = true;
@@ -47,17 +50,63 @@ int DataIO_LeapRC::processReadArgs(ArgList& argIn)
   return 0;
 }
 
+/** LEaP loadAmberParams command. */
+int DataIO_LeapRC::LoadAmberParams(std::string const& filename, DataSetList& dsl, std::string const& dsname) const {
+  // TODO detect this better
+  ArgList fargs( filename, "." );
+  if (fargs.hasKey("frcmod")) {
+    mprintf("\tLoading force field modifications from '%s'\n", filename.c_str());
+    DataIO_AmberFrcmod infile;
+    if (infile.ReadData(amberhome_ + "parm/" + filename, dsl, dsname)) {
+      mprinterr("Error: Could not load force field modifications from '%s'\n", filename.c_str());
+      return 1;
+    }
+  } else {
+    mprintf("\tLoading force field from '%s'\n", filename.c_str());
+    DataIO_AmberFF infile;
+    if (infile.ReadData(amberhome_ + "parm/" + filename, dsl, dsname)) {
+      mprinterr("Error: Could not load force field from '%s'\n", filename.c_str());
+      return 1;
+    }
+  }
+  return 0;
+}
+
 // DataIO_LeapRC::ReadData()
 int DataIO_LeapRC::ReadData(FileName const& fname, DataSetList& dsl, std::string const& dsname)
 {
+  // First, need to determine where the Amber FF files are
+  const char* env = getenv("AMBERHOME");
+  if (env != 0)
+    amberhome_ = std::string(env) + "/dat/leap/";
+  else {
+    mprintf("Warning: AMBERHOME is not set. Determining FF file location based on leaprc file.\n");
+    // Try to guess based on where the leaprc file is
+    FileName leapcmddir( fname.DirPrefix_NoSlash() );
+    amberhome_ = leapcmddir.DirPrefix();
+  }
+  mprintf("\tForce field files located in '%s'\n", amberhome_.c_str());
   BufferedLine infile;
   if (infile.OpenFileRead(fname)) {
     mprinterr("Error: Could not open leaprc file '%s'\n", fname.full());
     return 1;
   }
-
+  int err = 0;
+  const char* ptr = infile.Line();
+  while (ptr != 0) {
+    if (ptr[0] != '\0' && ptr[0] != '#') {
+      ArgList line( ptr, " \t" );
+      std::string param_fname;
+      if (line.Contains("loadAmberParams"))
+        err = LoadAmberParams( line.GetStringKey("loadAmberParams"), dsl, dsname );
+      else if (line.Contains("loadamberparams"))
+        err = LoadAmberParams( line.GetStringKey("loadamberparams"), dsl, dsname );
+    }
+    if (err != 0) break;
+    ptr = infile.Line();
+  }
   infile.CloseFile();
-  return 0;
+  return err;
 }
 
 // DataIO_LeapRC::WriteHelp()
diff --git a/src/DataIO_LeapRC.h b/src/DataIO_LeapRC.h
index 90344f89f8..1b28b2a7ef 100644
--- a/src/DataIO_LeapRC.h
+++ b/src/DataIO_LeapRC.h
@@ -13,5 +13,9 @@ class DataIO_LeapRC : public DataIO {
     int processWriteArgs(ArgList&);
     int WriteData(FileName const&, DataSetList const&);
     bool ID_DataFormat(CpptrajFile&);
+  private:
+    int LoadAmberParams(std::string const&, DataSetList&, std::string const&) const;
+
+    std::string amberhome_;
 };
 #endif
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 1f0cfef939..61340986e3 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -220,7 +220,7 @@ DataIO_Cpout.o : DataIO_Cpout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h A
 DataIO_Evecs.o : DataIO_Evecs.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Evecs.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Gnuplot.o : DataIO_Gnuplot.cpp ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Gnuplot.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Grace.o : DataIO_Grace.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Grace.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_string.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_LeapRC.o : DataIO_LeapRC.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_LeapRC.o : DataIO_LeapRC.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Mdout.o : DataIO_Mdout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Mdout.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_NetCDF.o : DataIO_NetCDF.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/Cframes.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_NetCDF.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_Mesh.h DataSet_Modes.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_Vector.h DataSet_Vector_Scalar.h DataSet_string.h DataSet_unsignedInt.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h Version.h
 DataIO_Numpy.o : DataIO_Numpy.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Numpy.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h libnpy/npy.hpp

From 5b5470ea69a41974a33c12074051646ea152d03b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 8 Jan 2024 10:11:05 -0500
Subject: [PATCH 0280/1492] Implement loadoff command

---
 src/DataIO_LeapRC.cpp | 15 +++++++++++++++
 src/DataIO_LeapRC.h   |  1 +
 src/cpptrajdepend     |  2 +-
 3 files changed, 17 insertions(+), 1 deletion(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 21440fffed..c7633c354d 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -3,6 +3,7 @@
 #include "BufferedLine.h"
 #include "DataIO_AmberFF.h"
 #include "DataIO_AmberFrcmod.h"
+#include "DataIO_AmberLib.h"
 #include <cstdlib> //getenv
 
 /// CONSTRUCTOR
@@ -72,6 +73,16 @@ int DataIO_LeapRC::LoadAmberParams(std::string const& filename, DataSetList& dsl
   return 0;
 }
 
+/** LEaP loadOff command. */
+int DataIO_LeapRC::LoadOFF(std::string const& filename, DataSetList& dsl, std::string const& dsname) const {
+  DataIO_AmberLib infile;
+  if (infile.ReadData(amberhome_ + "lib/" + filename, dsl, dsname)) {
+    mprinterr("Error: Could not load library file '%s'\n", filename.c_str());
+    return 1;
+  }
+  return 0;
+}
+
 // DataIO_LeapRC::ReadData()
 int DataIO_LeapRC::ReadData(FileName const& fname, DataSetList& dsl, std::string const& dsname)
 {
@@ -101,6 +112,10 @@ int DataIO_LeapRC::ReadData(FileName const& fname, DataSetList& dsl, std::string
         err = LoadAmberParams( line.GetStringKey("loadAmberParams"), dsl, dsname );
       else if (line.Contains("loadamberparams"))
         err = LoadAmberParams( line.GetStringKey("loadamberparams"), dsl, dsname );
+      else if (line.Contains("loadOff"))
+        err = LoadOFF( line.GetStringKey("loadOff"), dsl, dsname );
+      else if (line.Contains("loadoff"))
+        err = LoadOFF( line.GetStringKey("loadoff"), dsl, dsname );
     }
     if (err != 0) break;
     ptr = infile.Line();
diff --git a/src/DataIO_LeapRC.h b/src/DataIO_LeapRC.h
index 1b28b2a7ef..2142417e21 100644
--- a/src/DataIO_LeapRC.h
+++ b/src/DataIO_LeapRC.h
@@ -15,6 +15,7 @@ class DataIO_LeapRC : public DataIO {
     bool ID_DataFormat(CpptrajFile&);
   private:
     int LoadAmberParams(std::string const&, DataSetList&, std::string const&) const;
+    int LoadOFF(std::string const&, DataSetList&, std::string const&) const;
 
     std::string amberhome_;
 };
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 61340986e3..f6c1f3a166 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -220,7 +220,7 @@ DataIO_Cpout.o : DataIO_Cpout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h A
 DataIO_Evecs.o : DataIO_Evecs.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Evecs.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Gnuplot.o : DataIO_Gnuplot.cpp ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Gnuplot.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Grace.o : DataIO_Grace.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Grace.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_string.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_LeapRC.o : DataIO_LeapRC.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_LeapRC.o : DataIO_LeapRC.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Mdout.o : DataIO_Mdout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Mdout.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_NetCDF.o : DataIO_NetCDF.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/Cframes.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_NetCDF.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_Mesh.h DataSet_Modes.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_Vector.h DataSet_Vector_Scalar.h DataSet_string.h DataSet_unsignedInt.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h Version.h
 DataIO_Numpy.o : DataIO_Numpy.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Numpy.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h libnpy/npy.hpp

From 64586a2137b10ad7b675c1cf0efcbacd6a8bc48c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 8 Jan 2024 10:21:05 -0500
Subject: [PATCH 0281/1492] Read amber prep

---
 src/DataIO_LeapRC.cpp | 21 ++++++++++++++++++++-
 src/DataIO_LeapRC.h   |  1 +
 src/cpptrajdepend     |  2 +-
 3 files changed, 22 insertions(+), 2 deletions(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index c7633c354d..3ee24cd38e 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -4,6 +4,7 @@
 #include "DataIO_AmberFF.h"
 #include "DataIO_AmberFrcmod.h"
 #include "DataIO_AmberLib.h"
+#include "DataIO_AmberPrep.h"
 #include <cstdlib> //getenv
 
 /// CONSTRUCTOR
@@ -83,6 +84,16 @@ int DataIO_LeapRC::LoadOFF(std::string const& filename, DataSetList& dsl, std::s
   return 0;
 }
 
+/** LEaP loadAmberPrep command. */
+int DataIO_LeapRC::LoadAmberPrep(std::string const& filename, DataSetList& dsl, std::string const& dsname) const {
+  DataIO_AmberPrep infile;
+  if (infile.ReadData(amberhome_ + "lib/" + filename, dsl, dsname)) {
+    mprinterr("Error: Could not load prep file '%s'\n", filename.c_str());
+    return 1;
+  }
+  return 0;
+}
+
 // DataIO_LeapRC::ReadData()
 int DataIO_LeapRC::ReadData(FileName const& fname, DataSetList& dsl, std::string const& dsname)
 {
@@ -94,7 +105,11 @@ int DataIO_LeapRC::ReadData(FileName const& fname, DataSetList& dsl, std::string
     mprintf("Warning: AMBERHOME is not set. Determining FF file location based on leaprc file.\n");
     // Try to guess based on where the leaprc file is
     FileName leapcmddir( fname.DirPrefix_NoSlash() );
-    amberhome_ = leapcmddir.DirPrefix();
+    if (leapcmddir.Base() == "oldff") {
+      FileName leapcmddir2( leapcmddir.DirPrefix_NoSlash() );
+      amberhome_ = leapcmddir2.DirPrefix();
+    } else
+      amberhome_ = leapcmddir.DirPrefix();
   }
   mprintf("\tForce field files located in '%s'\n", amberhome_.c_str());
   BufferedLine infile;
@@ -116,6 +131,10 @@ int DataIO_LeapRC::ReadData(FileName const& fname, DataSetList& dsl, std::string
         err = LoadOFF( line.GetStringKey("loadOff"), dsl, dsname );
       else if (line.Contains("loadoff"))
         err = LoadOFF( line.GetStringKey("loadoff"), dsl, dsname );
+      else if (line.Contains("loadAmberPrep"))
+        err = LoadAmberPrep( line.GetStringKey("loadAmberPrep"), dsl, dsname );
+      else if (line.Contains("loadamberprep"))
+        err = LoadAmberPrep( line.GetStringKey("loadamberprep"), dsl, dsname );
     }
     if (err != 0) break;
     ptr = infile.Line();
diff --git a/src/DataIO_LeapRC.h b/src/DataIO_LeapRC.h
index 2142417e21..8a3aff3fb2 100644
--- a/src/DataIO_LeapRC.h
+++ b/src/DataIO_LeapRC.h
@@ -16,6 +16,7 @@ class DataIO_LeapRC : public DataIO {
   private:
     int LoadAmberParams(std::string const&, DataSetList&, std::string const&) const;
     int LoadOFF(std::string const&, DataSetList&, std::string const&) const;
+    int LoadAmberPrep(std::string const&, DataSetList&, std::string const&) const;
 
     std::string amberhome_;
 };
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index f6c1f3a166..61e5b64a01 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -220,7 +220,7 @@ DataIO_Cpout.o : DataIO_Cpout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h A
 DataIO_Evecs.o : DataIO_Evecs.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Evecs.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Gnuplot.o : DataIO_Gnuplot.cpp ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Gnuplot.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Grace.o : DataIO_Grace.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Grace.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_string.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_LeapRC.o : DataIO_LeapRC.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_LeapRC.o : DataIO_LeapRC.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Mdout.o : DataIO_Mdout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Mdout.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_NetCDF.o : DataIO_NetCDF.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/Cframes.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_NetCDF.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_Mesh.h DataSet_Modes.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_Vector.h DataSet_Vector_Scalar.h DataSet_string.h DataSet_unsignedInt.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h Version.h
 DataIO_Numpy.o : DataIO_Numpy.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Numpy.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h libnpy/npy.hpp

From 303581739ffd5d598f40b8e122a243a1448782d6 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 8 Jan 2024 11:14:00 -0500
Subject: [PATCH 0282/1492] Remove sequence check. Use residue name from
 residues section.

---
 src/DataIO_AmberLib.cpp | 25 ++++++++++++++++++++-----
 1 file changed, 20 insertions(+), 5 deletions(-)

diff --git a/src/DataIO_AmberLib.cpp b/src/DataIO_AmberLib.cpp
index 3743a0800e..82c467adc0 100644
--- a/src/DataIO_AmberLib.cpp
+++ b/src/DataIO_AmberLib.cpp
@@ -137,17 +137,18 @@ int DataIO_AmberLib::read_atoms(Topology& topOut, std::string const& line, std::
     return 1;
   }
   // Sanity check
-  if (seq-1 != topOut.Natom()) {
-    mprinterr("Error: For unit %s expected sequence %i, got %i\n", unitName.c_str(), topOut.Natom()+1, seq);
-    return 1;
-  }
+  //if (seq-1 != topOut.Natom()) {
+  //  mprinterr("Error: For unit %s expected sequence %i, got %i\n", unitName.c_str(), topOut.Natom()+1, seq);
+  //  return 1;
+  //}
   Atom atm;
   atm.SetName( NameType(noquotes(aname)) );
   atm.SetTypeName( NameType(noquotes(atype)) );
   atm.DetermineElement( elt );
   atm.SetMassFromElement();
   atm.SetCharge( charge );
-  Residue res( unitName, resx, ' ', ' ' );
+  // We dont know the actual residue name yet
+  Residue res( "TMP", resx, ' ', ' ' );
   topOut.AddTopAtom( atm, res );
   return 0;
 }
@@ -210,6 +211,7 @@ const
   top.SetParmName( unitName, FileName() );
   std::vector<Vec3> positions;
   Frame frm;
+  int ridx = 0;
 
   bool readUnit = true;
   while (readUnit) {
@@ -243,6 +245,19 @@ const
         if (read_positions(positions, Line)) return 1;
       } else if (currentSection == CONNECT) {
         if (read_connect(ConnectAtoms, Line)) return 1;
+      } else if (currentSection == RESIDUES) {
+        // Rely on ArgList to remove quotes
+        ArgList tmpArg( Line );
+        if (tmpArg.Nargs() < 1) {
+          mprinterr("Error: Could not read residue from residues section.\n");
+          mprinterr("Error: Line: %s\n", Line);
+          return 1;
+        }
+        if (ridx >= top.Nres()) {
+          mprinterr("Error: Too many residues in residues section, or residues section before atom table.\n");
+          return 1;
+        }
+        top.SetRes( ridx++ ).SetName( tmpArg[0] );
       }
     }
   }

From 7c7a1698622b78cda91d18a86183740519ab5500 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 8 Jan 2024 11:27:49 -0500
Subject: [PATCH 0283/1492] Do not try to set up bond parms for units

---
 src/DataIO_AmberLib.cpp | 11 +++++++----
 src/DataIO_AmberLib.h   |  2 +-
 src/Topology.cpp        | 15 +++++++++++++--
 src/Topology.h          |  4 +++-
 4 files changed, 24 insertions(+), 8 deletions(-)

diff --git a/src/DataIO_AmberLib.cpp b/src/DataIO_AmberLib.cpp
index 82c467adc0..32ff816b45 100644
--- a/src/DataIO_AmberLib.cpp
+++ b/src/DataIO_AmberLib.cpp
@@ -177,7 +177,7 @@ int DataIO_AmberLib::read_bonds(Topology& topOut, std::string const& line) {
 }
 
 /** Read connections line */
-int DataIO_AmberLib::read_connect(AssociatedData_Connect& ConnectAtoms, std::string const& line) {
+int DataIO_AmberLib::read_connect(AssociatedData_Connect& ConnectAtoms, std::string const& line) const {
   int connectAtom = -1;
   if (sscanf(line.c_str(), "%i", &connectAtom) != 1) {
     mprinterr("Error: Expected 1 column for connect line: %s\n", line.c_str());
@@ -185,7 +185,9 @@ int DataIO_AmberLib::read_connect(AssociatedData_Connect& ConnectAtoms, std::str
   }
   // Amber lib atoms start from 1
   if (connectAtom < 1) {
-    mprintf("Warning: Atom index < 1 in connect line: %s\n", line.c_str());
+    // This may be legit when only one connect atom
+    if (debug_ > 0)
+      mprintf("Warning: Atom index < 1 in connect line: %s\n", line.c_str());
   }
   ConnectAtoms.AddConnectAtom( connectAtom-1 );
   return 0;
@@ -261,7 +263,8 @@ const
       }
     }
   }
-  top.CommonSetup();
+  // Set up topology; determine molecules, but no residue renumber or bond parm determination
+  top.CommonSetup(true, false, false);
   if (debug_ > 1) top.Summary();
   frm.SetupFrameV( top.Atoms(), CoordinateInfo() );
   frm.ClearAtoms();
@@ -272,7 +275,7 @@ const
   crd->AddFrame( frm );
   crd->AssociateData( &ConnectAtoms );
   if (debug_ > 1) ConnectAtoms.Ainfo();
-  mprintf("\n");
+  if (debug_ > 0) mprintf("\n");
   
   return 0;
 }
diff --git a/src/DataIO_AmberLib.h b/src/DataIO_AmberLib.h
index 6ea4d12b91..6db1b509cd 100644
--- a/src/DataIO_AmberLib.h
+++ b/src/DataIO_AmberLib.h
@@ -31,6 +31,6 @@ class DataIO_AmberLib : public DataIO {
     static int read_atoms(Topology&, std::string const&, std::string const&);
     static int read_bonds(Topology&, std::string const&);
     static int read_positions(std::vector<Vec3>&, std::string const&);
-    static int read_connect(AssociatedData_Connect&, std::string const&);
+    int read_connect(AssociatedData_Connect&, std::string const&) const;
 };
 #endif
diff --git a/src/Topology.cpp b/src/Topology.cpp
index 859a9901a2..4304d2b430 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -497,12 +497,23 @@ const
 }
 
 // Topology::CommonSetup()
-/** Set up common to all topologies.
+/** Set up common to all topologies. Assign bond lengths if none are present.
   * \param molsearch If true, determine molecules based on bond info.
   * \param renumberResidues If true, renumber residues if any residue is part of more than 1 molecule
   *        e.g. when alternate locations are present.
   */
 int Topology::CommonSetup(bool molsearch, bool renumberResidues)
+{
+  return CommonSetup(molsearch, renumberResidues, true);
+}
+
+/** Set up common to all topologies.
+  * \param molsearch If true, determine molecules based on bond info.
+  * \param renumberResidues If true, renumber residues if any residue is part of more than 1 molecule
+  *        e.g. when alternate locations are present.
+  * \param assignBondParm If true, assign default bond lengths if no parameters present.
+  */
+int Topology::CommonSetup(bool molsearch, bool renumberResidues, bool assignBondParm)
 {
   // Check the size of any "extra" arrays
   if (CheckExtraSize(tree_.size(), "Amber tree")) return 1;
@@ -514,7 +525,7 @@ int Topology::CommonSetup(bool molsearch, bool renumberResidues)
   if (CheckExtraSize(pdbSerialNum_.size(), "PDB serial #")) return 1;
   // TODO: Make bond parm assignment / molecule search optional?
   // Assign default lengths if necessary (for e.g. CheckStructure)
-  if (bondparm_.empty())
+  if (assignBondParm && bondparm_.empty())
     generateBondParameters();
   if (molsearch) {
     // Determine molecule info from bonds
diff --git a/src/Topology.h b/src/Topology.h
index 6afa53dcc0..b023e31f1d 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -221,7 +221,9 @@ class Topology {
     //void StartNewMol();
     /// Perform common final setup: optional molecule determination, renumber residues by molecules
     int CommonSetup(bool, bool);
-    /// Perform common final setup with molecule determination on, renumber residues off.
+    /// Perform common final setup: optional molecule determination, renumber residues by molecules, assign bond parameters
+    int CommonSetup(bool, bool, bool);
+    /// Perform common final setup with molecule determination on, renumber residues off, assign bond parameters on.
     int CommonSetup() { return CommonSetup(true, false); }
     /// Set up with no residue info TODO deprecate in favor of routine in CommonSetup?
     int Setup_NoResInfo();

From 06322fc409a9a7cbebde9a7f648a09399e39c35d Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 8 Jan 2024 11:28:20 -0500
Subject: [PATCH 0284/1492] Dont set up bond parms for prep units

---
 src/DataIO_AmberPrep.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/DataIO_AmberPrep.cpp b/src/DataIO_AmberPrep.cpp
index 1424ec29cd..c5f87ee327 100644
--- a/src/DataIO_AmberPrep.cpp
+++ b/src/DataIO_AmberPrep.cpp
@@ -294,7 +294,7 @@ const
     bondSearch.FindBonds( top, BondSearch::SEARCH_REGULAR, frm, 0.2, debug_ );
   }
   // Set up topology
-  top.CommonSetup(true, false);
+  top.CommonSetup(true, false, false);
   if (debug_ > 0)
     top.Summary();
   if (debug_ > 1)

From 0b52498eff9f28f5503624faef7015db65d7475c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 8 Jan 2024 14:23:59 -0500
Subject: [PATCH 0285/1492] Only warn on missing improper parameter if debug
 level is up

---
 src/Topology.cpp | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index 4304d2b430..653d722873 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2823,12 +2823,13 @@ DihedralArray Topology::AssignDihedralParm(DihedralParmHolder const& newDihedral
       DihedralParmArray ipa = newImproperParams.FindParam( types, found, mydih, reordered );
       int idx = -1;
       if (!found) {
-        mprintf("Warning: Improper parameters not found for improper dihedral %s-%s-%s-%s (%s-%s-%s-%s)\n",
-                TruncResAtomNameNum(dih->A1()).c_str(),
-                TruncResAtomNameNum(dih->A2()).c_str(),
-                TruncResAtomNameNum(dih->A3()).c_str(),
-                TruncResAtomNameNum(dih->A4()).c_str(),
-                *types[0], *types[1], *types[2], *types[3]);
+        if (debug_ > 0)
+          mprintf("Warning: Improper parameters not found for improper dihedral %s-%s-%s-%s (%s-%s-%s-%s)\n",
+                  TruncResAtomNameNum(dih->A1()).c_str(),
+                  TruncResAtomNameNum(dih->A2()).c_str(),
+                  TruncResAtomNameNum(dih->A3()).c_str(),
+                  TruncResAtomNameNum(dih->A4()).c_str(),
+                  *types[0], *types[1], *types[2], *types[3]);
         // Central atom
         Atom const& AJ = atoms_[dih->A3()];
         AtomType::HybridizationType hybrid = AtomType::UNKNOWN_HYBRIDIZATION;

From 2eba157ff64e1fda40fde6cca1156bd212a79c7f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 8 Jan 2024 14:31:18 -0500
Subject: [PATCH 0286/1492] Add GetParam() for ImproperParmArray

---
 src/ParameterHolders.h | 85 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 85 insertions(+)

diff --git a/src/ParameterHolders.h b/src/ParameterHolders.h
index 433fd6a036..a12c33a790 100644
--- a/src/ParameterHolders.h
+++ b/src/ParameterHolders.h
@@ -349,6 +349,91 @@ class ImproperParmHolder : private DihedralParmHolder {
     void ReorderImproper(DihedralType& imp, OrderType order) const {
       ReorderImproper(imp, order, TypeNameHolder());
     }
+    /// Get improper parameters matching given atom types. If found, improper will be reordered to match parameter order.
+    const_iterator GetParam(TypeNameHolder const& types, DihedralType& imp, bool& reordered) const {
+      //mprintf("DEBUG: FindParam wc=%s Inco=%s-%s-%s-%s\n",*wc_, *(types[0]), *(types[1]),   *(types[2]),   *(types[3]));
+      reordered = false;
+      // First, no wildcard
+      const_iterator it = begin();
+      OrderType lastOrder_;
+      for (; it != end(); ++it) {
+        TypeNameHolder const& myTypes = it->first;
+        // Central (third) type must match
+        if (myTypes[2] == types[2]) {
+          //mprintf("DEBUG: FindParam (improper) central atom match %s", *(types[2]));
+          //mprintf(" This=%s-%s-%s-%s", *(myTypes[0]), *(myTypes[1]), *(myTypes[2]), *(myTypes[3]));
+          //mprintf(" Inco=%s-%s-%s-%s\n", *(types[0]), *(types[1]),   *(types[2]),   *(types[3]));
+          // Try all permutations
+          if (       myTypes[0] == types[0] && myTypes[1] == types[1] && myTypes[3] == types[3]) {
+              // 0 1 2 3
+              lastOrder_ = O_013;
+              break;
+          } else if (myTypes[0] == types[0] && myTypes[1] == types[3] && myTypes[3] == types[1]) {
+              // 0 3 2 1
+              lastOrder_ = O_031;
+              break;
+          } else if (myTypes[0] == types[1] && myTypes[1] == types[0] && myTypes[3] == types[3]) {
+              // 1 0 2 3
+              lastOrder_ = O_103;
+              break;
+          } else if (myTypes[0] == types[1] && myTypes[1] == types[3] && myTypes[3] == types[0]) {
+              // 1 3 2 0
+              lastOrder_ = O_130;
+              break;
+          } else if (myTypes[0] == types[3] && myTypes[1] == types[0] && myTypes[3] == types[1]) {
+              // 3 0 2 1
+              lastOrder_ = O_301;
+              break;
+          } else if (myTypes[0] == types[3] && myTypes[1] == types[1] && myTypes[3] == types[0]) {
+              // 3 1 2 0
+              lastOrder_ = O_310;
+              break;
+          }
+        }
+      } // END loop over parameters
+      // Wildcard if present
+      if (it == end() && wc_.len() > 0) {
+        it = begin();
+        for (; it != end(); ++it) {
+          TypeNameHolder const& myTypes = it->first;
+          // Central (third) type must match
+          if (wcm(myTypes[2], types[2], wc_)) {
+            // Try all permutations
+            if (       wcm(myTypes[0], types[0], wc_) && wcm(myTypes[1], types[1], wc_) && wcm(myTypes[3], types[3], wc_)) {
+                // 0 1 2 3
+                lastOrder_ = O_013;
+                break;
+            } else if (wcm(myTypes[0], types[0], wc_) && wcm(myTypes[1], types[3], wc_) && wcm(myTypes[3], types[1], wc_)) {
+                // 0 3 2 1
+                lastOrder_ = O_031;
+                break;
+            } else if (wcm(myTypes[0], types[1], wc_) && wcm(myTypes[1], types[0], wc_) && wcm(myTypes[3], types[3], wc_)) {
+                // 1 0 2 3
+                lastOrder_ = O_103;
+                break;
+            } else if (wcm(myTypes[0], types[1], wc_) && wcm(myTypes[1], types[3], wc_) && wcm(myTypes[3], types[0], wc_)) {
+                // 1 3 2 0
+                lastOrder_ = O_130;
+                break;
+            } else if (wcm(myTypes[0], types[3], wc_) && wcm(myTypes[1], types[0], wc_) && wcm(myTypes[3], types[1], wc_)) {
+                // 3 0 2 1
+                lastOrder_ = O_301;
+                break;
+            } else if (wcm(myTypes[0], types[3], wc_) && wcm(myTypes[1], types[1], wc_) && wcm(myTypes[3], types[0], wc_)) {
+                // 3 1 2 0
+                lastOrder_ = O_310;
+                break;
+            }
+          }
+        } // END loop over parameters
+      } // END wildcard matches
+      if (it != end()) {
+        // We have found a parameter. Do any reordering.
+        if (lastOrder_ != O_013) reordered = true;
+        ReorderImproper( imp, lastOrder_, it->first );
+      }
+      return it;
+    } // END GetParam()
     /// \return Array of improper parameters matching given atom types. Improper will be reordered to match parameter order.
     DihedralParmArray FindParam(TypeNameHolder const& types, bool& found, DihedralType& imp, bool& reordered) const {
       //mprintf("DEBUG: FindParam wc=%s Inco=%s-%s-%s-%s\n",*wc_, *(types[0]), *(types[1]),   *(types[2]),   *(types[3]));

From d747a004b91a04f53e92df4458daa17d244f3664 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 8 Jan 2024 14:37:27 -0500
Subject: [PATCH 0287/1492] Start improper cache

---
 src/Topology.cpp | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index 653d722873..07a4529ae3 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2783,6 +2783,8 @@ DihedralArray Topology::AssignDihedralParm(DihedralParmHolder const& newDihedral
                                            DihedralArray const& dihedrals)
 { // TODO skip extra points
   DihedralArray dihedralsIn;
+  // Improper cache
+  ImproperParmHolder improperCache;
   // Keep track of 1-4 interactions
   typedef std::pair<int,int> Ipair;
   typedef std::set<Ipair> Imap;
@@ -2820,7 +2822,13 @@ DihedralArray Topology::AssignDihedralParm(DihedralParmHolder const& newDihedral
       //ImproperParmHolder::OrderType lastOrder;
       DihedralType mydih = *dih;
       bool reordered;
-      DihedralParmArray ipa = newImproperParams.FindParam( types, found, mydih, reordered );
+      DihedralParmArray ipa;
+      ImproperParmHolder::const_iterator impit = improperCache.GetParam( types, mydih, reordered );
+      if (impit == improperCache.end()) {
+        ipa = newImproperParams.FindParam( types, found, mydih, reordered );
+      } else {
+        ipa = impit->second;
+      }
       int idx = -1;
       if (!found) {
         if (debug_ > 0)

From c42239c07ba06e0dbdc25e4cd570d0870f0f5c2b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 8 Jan 2024 14:47:11 -0500
Subject: [PATCH 0288/1492] Start using improper cache

---
 src/Topology.cpp | 17 ++++++++++++++++-
 1 file changed, 16 insertions(+), 1 deletion(-)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index 07a4529ae3..6bd296db58 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2820,14 +2820,29 @@ DihedralArray Topology::AssignDihedralParm(DihedralParmHolder const& newDihedral
       // However, if no parameter is found and the central atom is
       // SP2, print a warning.
       //ImproperParmHolder::OrderType lastOrder;
+      found = false;
       DihedralType mydih = *dih;
       bool reordered;
       DihedralParmArray ipa;
+      TypeNameHolder paramTypes;
       ImproperParmHolder::const_iterator impit = improperCache.GetParam( types, mydih, reordered );
       if (impit == improperCache.end()) {
-        ipa = newImproperParams.FindParam( types, found, mydih, reordered );
+        impit = newImproperParams.GetParam( types, mydih, reordered );
+        if (impit != newImproperParams.end()) {
+          paramTypes = impit->first;
+          ipa = impit->second;
+          found = true;
+          mprintf("DEBUG: Found new value for improper %2s %2s %2s %2s (%2s %2s %2s %2s)\n",
+                  *types[0], *types[1], *types[2], *types[3],
+                  *paramTypes[0], *paramTypes[1], *paramTypes[2], *paramTypes[3]);
+        }
       } else {
+        paramTypes = impit->first;
         ipa = impit->second;
+        found = true;
+        mprintf("DEBUG: Using cached value for improper %2s %2s %2s %2s (%2s %2s %2s %2s)\n",
+                *types[0], *types[1], *types[2], *types[3],
+                  *paramTypes[0], *paramTypes[1], *paramTypes[2], *paramTypes[3]);
       }
       int idx = -1;
       if (!found) {

From f00e9edb93dcbbcaf8afdb2b937d9e050efdabeb Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 8 Jan 2024 14:59:40 -0500
Subject: [PATCH 0289/1492] In order to match leap behavior, make sure that
 cached improper parameters are sorted alphabetically by type.

---
 src/ParameterHolders.h |  4 ++++
 src/Topology.cpp       | 10 ++++++++++
 2 files changed, 14 insertions(+)

diff --git a/src/ParameterHolders.h b/src/ParameterHolders.h
index a12c33a790..53d66055fc 100644
--- a/src/ParameterHolders.h
+++ b/src/ParameterHolders.h
@@ -293,6 +293,8 @@ class ImproperParmHolder : private DihedralParmHolder {
     size_t size()       const { return DihedralParmHolder::size();  }
     /// \return True if no parameters
     bool empty()        const { return DihedralParmHolder::empty(); }
+    /// \return Wildcard
+    NameType const& Wildcard() const { return wc_; }
     /// \return ordering of last type
     //OrderType LastOrder() const { return lastOrder_; }
     typedef typename DihedralParmHolder::const_iterator const_iterator;
@@ -301,6 +303,8 @@ class ImproperParmHolder : private DihedralParmHolder {
 
     /** Set Wildcard char */
     void SetWildcard(char wc) { DihedralParmHolder::SetWildcard(wc); }
+    /** Set Wildcard */
+    void SetWildcard(NameType const& wc) { wc_ = wc; }
     /** Add (or update) a single improper parameter for given atom types. */
     ParameterHolders::RetType
     AddParm(TypeNameHolder const& types, DihedralParmType const& dp, bool allowUpdate) {
diff --git a/src/Topology.cpp b/src/Topology.cpp
index 6bd296db58..d08c672fc0 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2785,6 +2785,7 @@ DihedralArray Topology::AssignDihedralParm(DihedralParmHolder const& newDihedral
   DihedralArray dihedralsIn;
   // Improper cache
   ImproperParmHolder improperCache;
+  improperCache.SetWildcard( newImproperParams.Wildcard() );
   // Keep track of 1-4 interactions
   typedef std::pair<int,int> Ipair;
   typedef std::set<Ipair> Imap;
@@ -2823,12 +2824,14 @@ DihedralArray Topology::AssignDihedralParm(DihedralParmHolder const& newDihedral
       found = false;
       DihedralType mydih = *dih;
       bool reordered;
+      bool is_new_improper = false;
       DihedralParmArray ipa;
       TypeNameHolder paramTypes;
       ImproperParmHolder::const_iterator impit = improperCache.GetParam( types, mydih, reordered );
       if (impit == improperCache.end()) {
         impit = newImproperParams.GetParam( types, mydih, reordered );
         if (impit != newImproperParams.end()) {
+          is_new_improper = true;
           paramTypes = impit->first;
           ipa = impit->second;
           found = true;
@@ -2877,6 +2880,13 @@ DihedralArray Topology::AssignDihedralParm(DihedralParmHolder const& newDihedral
         // Always skip 1-4 for impropers
         mydih.SetSkip14( true );
         dihedralsIn.push_back( mydih );
+        // Add to the cache
+        if (is_new_improper) {
+          // To match leap behavior, make sure paramTypes are sorted alphabetically.
+          mprintf("DEBUG: Improper wildcard: %s\n", *(newImproperParams.Wildcard()));
+          paramTypes.SortImproperByAlpha( newImproperParams.Wildcard() );
+          improperCache.AddParm( paramTypes, ipa.front(), false );
+        }
       }
     } else {
       // -----Regular dihedral. See if parameter already present. ----

From c9339df31a007e26cdc1dbd47a5b2131a0c64af2 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 8 Jan 2024 15:09:17 -0500
Subject: [PATCH 0290/1492] Use GetParam in FindParam

---
 src/ParameterHolders.h | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/src/ParameterHolders.h b/src/ParameterHolders.h
index 53d66055fc..4b8b21d306 100644
--- a/src/ParameterHolders.h
+++ b/src/ParameterHolders.h
@@ -440,6 +440,15 @@ class ImproperParmHolder : private DihedralParmHolder {
     } // END GetParam()
     /// \return Array of improper parameters matching given atom types. Improper will be reordered to match parameter order.
     DihedralParmArray FindParam(TypeNameHolder const& types, bool& found, DihedralType& imp, bool& reordered) const {
+      const_iterator it = GetParam( types, imp, reordered );
+      if (it == end()) {
+        found = false;
+        return DihedralParmArray();
+      } else {
+        found = true;
+        return it->second;
+      }
+/*
       //mprintf("DEBUG: FindParam wc=%s Inco=%s-%s-%s-%s\n",*wc_, *(types[0]), *(types[1]),   *(types[2]),   *(types[3]));
       found = false;
       reordered = false;
@@ -547,6 +556,7 @@ class ImproperParmHolder : private DihedralParmHolder {
       if (lastOrder_ != O_013) reordered = true;
       ReorderImproper( imp, lastOrder_, it->first );
       return it->second;
+*/
     } // END FindParam()
     /// \return Dihedral parm array corresponding to types. Use by unit test.
     DihedralParmArray FindParam(TypeNameHolder const& types, bool& found) const {

From 0e09aee5e22e8e41403f8e8f3d89219f1f075063 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 8 Jan 2024 15:20:58 -0500
Subject: [PATCH 0291/1492] Remove old code

---
 src/ParameterHolders.h | 112 -----------------------------------------
 src/Topology.cpp       |   2 -
 2 files changed, 114 deletions(-)

diff --git a/src/ParameterHolders.h b/src/ParameterHolders.h
index 4b8b21d306..440c04d9cc 100644
--- a/src/ParameterHolders.h
+++ b/src/ParameterHolders.h
@@ -295,8 +295,6 @@ class ImproperParmHolder : private DihedralParmHolder {
     bool empty()        const { return DihedralParmHolder::empty(); }
     /// \return Wildcard
     NameType const& Wildcard() const { return wc_; }
-    /// \return ordering of last type
-    //OrderType LastOrder() const { return lastOrder_; }
     typedef typename DihedralParmHolder::const_iterator const_iterator;
     const_iterator begin() const { return DihedralParmHolder::begin(); }
     const_iterator end()   const { return DihedralParmHolder::end();   }
@@ -448,115 +446,6 @@ class ImproperParmHolder : private DihedralParmHolder {
         found = true;
         return it->second;
       }
-/*
-      //mprintf("DEBUG: FindParam wc=%s Inco=%s-%s-%s-%s\n",*wc_, *(types[0]), *(types[1]),   *(types[2]),   *(types[3]));
-      found = false;
-      reordered = false;
-      // First, no wildcard
-      const_iterator it = begin();
-      OrderType lastOrder_;
-      for (; it != end(); ++it) {
-        TypeNameHolder const& myTypes = it->first;
-        // Central (third) type must match
-        if (myTypes[2] == types[2]) {
-          //mprintf("DEBUG: FindParam (improper) central atom match %s", *(types[2]));
-          //mprintf(" This=%s-%s-%s-%s", *(myTypes[0]), *(myTypes[1]), *(myTypes[2]), *(myTypes[3]));
-          //mprintf(" Inco=%s-%s-%s-%s\n", *(types[0]), *(types[1]),   *(types[2]),   *(types[3]));
-          // Try all permutations
-          if (       myTypes[0] == types[0] && myTypes[1] == types[1] && myTypes[3] == types[3]) {
-              // 0 1 2 3
-              lastOrder_ = O_013;
-              found = true;
-              //return it->second;
-              break;
-          } else if (myTypes[0] == types[0] && myTypes[1] == types[3] && myTypes[3] == types[1]) {
-              // 0 3 2 1
-              lastOrder_ = O_031;
-              found = true;
-              //return it->second;
-              break;
-          } else if (myTypes[0] == types[1] && myTypes[1] == types[0] && myTypes[3] == types[3]) {
-              // 1 0 2 3
-              lastOrder_ = O_103;
-              found = true;
-              //return it->second;
-              break;
-          } else if (myTypes[0] == types[1] && myTypes[1] == types[3] && myTypes[3] == types[0]) {
-              // 1 3 2 0
-              lastOrder_ = O_130;
-              found = true;
-              //return it->second;
-              break;
-          } else if (myTypes[0] == types[3] && myTypes[1] == types[0] && myTypes[3] == types[1]) {
-              // 3 0 2 1
-              lastOrder_ = O_301;
-              found = true;
-              //return it->second;
-              break;
-          } else if (myTypes[0] == types[3] && myTypes[1] == types[1] && myTypes[3] == types[0]) {
-              // 3 1 2 0
-              lastOrder_ = O_310;
-              found = true;
-              //return it->second;
-              break;
-          }
-        }
-      } // END loop over parameters
-      // Wildcard if present
-      if (!found && wc_.len() > 0) {
-        it = begin();
-        for (; it != end(); ++it) {
-          TypeNameHolder const& myTypes = it->first;
-          // Central (third) type must match
-          if (wcm(myTypes[2], types[2], wc_)) {
-            // Try all permutations
-            if (       wcm(myTypes[0], types[0], wc_) && wcm(myTypes[1], types[1], wc_) && wcm(myTypes[3], types[3], wc_)) {
-                // 0 1 2 3
-                lastOrder_ = O_013;
-                found = true;
-                //return it->second;
-                break;
-            } else if (wcm(myTypes[0], types[0], wc_) && wcm(myTypes[1], types[3], wc_) && wcm(myTypes[3], types[1], wc_)) {
-                // 0 3 2 1
-                lastOrder_ = O_031;
-                found = true;
-                //return it->second;
-                break;
-            } else if (wcm(myTypes[0], types[1], wc_) && wcm(myTypes[1], types[0], wc_) && wcm(myTypes[3], types[3], wc_)) {
-                // 1 0 2 3
-                lastOrder_ = O_103;
-                found = true;
-                //return it->second;
-                break;
-            } else if (wcm(myTypes[0], types[1], wc_) && wcm(myTypes[1], types[3], wc_) && wcm(myTypes[3], types[0], wc_)) {
-                // 1 3 2 0
-                lastOrder_ = O_130;
-                found = true;
-                //return it->second;
-                break;
-            } else if (wcm(myTypes[0], types[3], wc_) && wcm(myTypes[1], types[0], wc_) && wcm(myTypes[3], types[1], wc_)) {
-                // 3 0 2 1
-                lastOrder_ = O_301;
-                found = true;
-                //return it->second;
-                break;
-            } else if (wcm(myTypes[0], types[3], wc_) && wcm(myTypes[1], types[1], wc_) && wcm(myTypes[3], types[0], wc_)) {
-                // 3 1 2 0
-                lastOrder_ = O_310;
-                found = true;
-                //return it->second;
-                break;
-            }
-          }
-        } // END loop over parameters
-      } // END wildcard matches
-      //found = false;
-      if (!found) return DihedralParmArray();
-      // We have found a parameter. Do any reordering.
-      if (lastOrder_ != O_013) reordered = true;
-      ReorderImproper( imp, lastOrder_, it->first );
-      return it->second;
-*/
     } // END FindParam()
     /// \return Dihedral parm array corresponding to types. Use by unit test.
     DihedralParmArray FindParam(TypeNameHolder const& types, bool& found) const {
@@ -567,6 +456,5 @@ class ImproperParmHolder : private DihedralParmHolder {
     /// \return size in memory in bytes
     size_t DataSize() const { return DihedralParmHolder::DataSize(); }
   private:
-    //OrderType lastOrder_; ///< Atom ordering of the last returned parameter
 };
 #endif
diff --git a/src/Topology.cpp b/src/Topology.cpp
index d08c672fc0..5dac6abdf0 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2742,7 +2742,6 @@ const
     bool found;
     // See if parameter is present.
     int idx = -1;
-    //ImproperParmHolder::OrderType lastOrder;
     DihedralType imp0 = *imp;
     bool reordered;
     DihedralParmArray ipa = newImproperParams.FindParam( types, found, *imp, reordered );
@@ -2820,7 +2819,6 @@ DihedralArray Topology::AssignDihedralParm(DihedralParmHolder const& newDihedral
       // no parameter is found, do not add it to the list of dihedrals.
       // However, if no parameter is found and the central atom is
       // SP2, print a warning.
-      //ImproperParmHolder::OrderType lastOrder;
       found = false;
       DihedralType mydih = *dih;
       bool reordered;

From a17f34f928125dbbd0e0c8a4d1e3164d9b6b29c9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 8 Jan 2024 16:07:39 -0500
Subject: [PATCH 0292/1492] Only sort types in cache when assigning to mimic
 new leap behavior.

---
 src/Topology.cpp | 30 ++++++++++++++++--------------
 src/Topology.h   |  2 +-
 2 files changed, 17 insertions(+), 15 deletions(-)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index 5dac6abdf0..917827126c 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2775,11 +2775,13 @@ void Topology::AssignImproperParams(ImproperParmHolder const& newImproperParams)
   * \param newDihedralParams New proper dihedral parameters.
   * \param newImproperParams New improper dihedral parameters.
   * \param dihedrals Array containing only unique dihedrals.
+  * \param sort_improper_cache If true, sort improper types in cache (to match current leap behavior)
   */
 DihedralArray Topology::AssignDihedralParm(DihedralParmHolder const& newDihedralParams,
                                            ImproperParmHolder const& newImproperParams,
                                            ParmHolder<AtomType> const& AT,
-                                           DihedralArray const& dihedrals)
+                                           DihedralArray const& dihedrals,
+                                           bool sort_improper_cache)
 { // TODO skip extra points
   DihedralArray dihedralsIn;
   // Improper cache
@@ -2882,7 +2884,7 @@ DihedralArray Topology::AssignDihedralParm(DihedralParmHolder const& newDihedral
         if (is_new_improper) {
           // To match leap behavior, make sure paramTypes are sorted alphabetically.
           mprintf("DEBUG: Improper wildcard: %s\n", *(newImproperParams.Wildcard()));
-          paramTypes.SortImproperByAlpha( newImproperParams.Wildcard() );
+          if (sort_improper_cache) paramTypes.SortImproperByAlpha( newImproperParams.Wildcard() );
           improperCache.AddParm( paramTypes, ipa.front(), false );
         }
       }
@@ -3002,8 +3004,8 @@ void Topology::AssignDihedralParams(DihedralParmHolder const& newDihedralParams,
   // multiplicities for a single dihedral type. In case multiplicities
   // change, start with a fresh dihedral array containing only unique
   // dihedrals.
-  dihedrals_  = AssignDihedralParm( newDihedralParams, newImproperParams, AT, get_unique_dihedrals(dihedrals_)  );
-  dihedralsh_ = AssignDihedralParm( newDihedralParams, newImproperParams, AT, get_unique_dihedrals(dihedralsh_) );
+  dihedrals_  = AssignDihedralParm( newDihedralParams, newImproperParams, AT, get_unique_dihedrals(dihedrals_), false  );
+  dihedralsh_ = AssignDihedralParm( newDihedralParams, newImproperParams, AT, get_unique_dihedrals(dihedralsh_), false );
 }
 
 /** Replace current nonbond parameters with given nonbond parameters. */
@@ -3116,7 +3118,7 @@ void Topology::AssignNonbondParams(ParmHolder<AtomType> const& newTypes,
 int Topology::AssignParams(ParameterSet const& set0) {
 
   // Bond parameters
-  mprintf("\tRegenerating bond parameters.\n");
+  mprintf("\tAssigning bond parameters.\n");
   bondparm_.clear();
   // Regenerate bond array in LEaP order
   bonds_.clear();
@@ -3126,7 +3128,7 @@ int Topology::AssignParams(ParameterSet const& set0) {
   for (BondArray::const_iterator bnd = allBonds.begin(); bnd != allBonds.end(); ++bnd)
     AddToBondArrays( *bnd );
   // Angle parameters
-  mprintf("\tRegenerating angle parameters.\n");
+  mprintf("\tAssigning angle parameters.\n");
   angleparm_.clear();
   // Regenerate angle array in LEaP order
   angles_.clear();
@@ -3136,32 +3138,32 @@ int Topology::AssignParams(ParameterSet const& set0) {
   for (AngleArray::const_iterator ang = allAngles.begin(); ang != allAngles.end(); ++ang)
     AddToAngleArrays( *ang );
   // Dihedral parameters
-  mprintf("\tRegenerating dihedral parameters.\n");
+  mprintf("\tAssigning dihedral parameters.\n");
   dihedrals_.clear();
   dihedralsh_.clear();
   DihedralArray allDihedrals = Cpptraj::Structure::GenerateDihedralArray(residues_, atoms_);
-  allDihedrals = AssignDihedralParm( set0.DP(), set0.IP(), set0.AT(), allDihedrals );
+  allDihedrals = AssignDihedralParm( set0.DP(), set0.IP(), set0.AT(), allDihedrals, false );
   for (DihedralArray::const_iterator dih = allDihedrals.begin(); dih != allDihedrals.end(); ++dih)
     AddToDihedralArrays( *dih );
   // Urey-Bradley
-  mprintf("\tRegenerating Urey-Bradley parameters.\n");
+  mprintf("\tAssigning Urey-Bradley parameters.\n");
   AssignUBParams( set0.UB() );
   // Improper parameters
   if (!chamber_.Impropers().empty()) {
-    mprintf("\tRegenerating CHARMM improper parameters.\n");
+    mprintf("\tAssigning CHARMM improper parameters.\n");
     AssignImproperParams( set0.IP() );
   } else {
-    mprintf("\tRegenerating improper parameters.\n");
+    mprintf("\tAssigning improper parameters.\n");
     DihedralArray allImpropers = Cpptraj::Structure::GenerateImproperArray(residues_, atoms_);
-    allImpropers = AssignDihedralParm( set0.DP(), set0.IP(), set0.AT(), allImpropers );
+    allImpropers = AssignDihedralParm( set0.DP(), set0.IP(), set0.AT(), allImpropers, true );
     for (DihedralArray::const_iterator imp = allImpropers.begin(); imp != allImpropers.end(); ++imp)
       AddToDihedralArrays( *imp );
   }
   // Atom types
-  mprintf("\tRegenerating atom type parameters.\n");
+  mprintf("\tAssigning atom type parameters.\n");
   AssignAtomTypeParm( set0.AT() );
   // LJ 6-12
-  mprintf("\tRegenerating nonbond parameters.\n");
+  mprintf("\tAssigning nonbond parameters.\n");
   AssignNonbondParams( set0.AT(), set0.NB(), set0.HB() );
   // TODO LJ14
   return 0;
diff --git a/src/Topology.h b/src/Topology.h
index b023e31f1d..825ed4cc50 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -313,7 +313,7 @@ class Topology {
     void AssignImproperParm(ImproperParmHolder const&, DihedralArray&, DihedralParmArray&) const;
     inline DihedralArray get_unique_dihedrals(DihedralArray const&) const;
     DihedralArray AssignDihedralParm(DihedralParmHolder const&, ImproperParmHolder const&,
-                                     ParmHolder<AtomType> const&, DihedralArray const&);
+                                     ParmHolder<AtomType> const&, DihedralArray const&, bool);
 
     static const NonbondType LJ_EMPTY;
     std::vector<Atom> atoms_;

From 16771edf14d3307232dde8aa9718b4d110ada7ab Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 9 Jan 2024 08:34:26 -0500
Subject: [PATCH 0293/1492] Comment out wildcard for regular parameter holder.
 Add variable to require exact matching for impropers.

---
 src/ParameterHolders.h | 181 +++++++++++++++++++++--------------------
 1 file changed, 92 insertions(+), 89 deletions(-)

diff --git a/src/ParameterHolders.h b/src/ParameterHolders.h
index 440c04d9cc..573c6a598f 100644
--- a/src/ParameterHolders.h
+++ b/src/ParameterHolders.h
@@ -16,12 +16,16 @@ template <class T> class ParmHolder {
     typedef std::pair<TypeNameHolder,T> Bpair;
     typedef std::vector<Bpair> Bmap;
   public:
+    /// CONSTRUCTOR
     ParmHolder() {}
+    /// Clear all parameters
     void clear()              { bpmap_.clear(); }
+    /// \return Number of parameters
     size_t size()       const { return bpmap_.size(); }
+    /// \return true if no parameters
     bool empty()        const { return bpmap_.empty(); }
     /// Set wildcard character
-    void SetWildcard(char wc) { wc_ = NameType(std::string(1, wc)); }
+    //void SetWildcard(char wc) { wc_ = NameType(std::string(1, wc)); }
     /// Add (or update if allowed) given parameter to holder.
     ParameterHolders::RetType AddParm(TypeNameHolder const& types, T const& bp, bool allowUpdate) {
       // Check if parm for these types exist
@@ -74,10 +78,10 @@ template <class T> class ParmHolder {
       found = true;
       for (const_iterator it = begin(); it != end(); ++it)
         if (it->first.Match_NoWC( types )) return it->second;
-      if (wc_.len() > 0) {
-        for (const_iterator it = begin(); it != end(); ++it)
-          if (it->first.Match_WC( types, wc_)) return it->second;
-      }
+      //if (wc_.len() > 0) {
+      //  for (const_iterator it = begin(); it != end(); ++it)
+      //    if (it->first.Match_WC( types, wc_)) return it->second;
+      //}
       found = false;
       return T();
     }
@@ -85,20 +89,20 @@ template <class T> class ParmHolder {
     iterator GetParam(TypeNameHolder const& types) {
       for (iterator it = bpmap_.begin(); it != bpmap_.end(); ++it)
         if (it->first.Match_NoWC( types )) return it;
-      if (wc_.len() > 0) {
-        for (iterator it = bpmap_.begin(); it != bpmap_.end(); ++it)
-          if (it->first.Match_WC( types, wc_)) return it;
-      }
+      //if (wc_.len() > 0) {
+      //  for (iterator it = bpmap_.begin(); it != bpmap_.end(); ++it)
+      //    if (it->first.Match_WC( types, wc_)) return it;
+      //}
       return bpmap_.end();
     }
     /// \return const iterator to parameter matching the given types.
     const_iterator GetParam(TypeNameHolder const& types) const {
       for (const_iterator it = bpmap_.begin(); it != bpmap_.end(); ++it)
         if (it->first.Match_NoWC( types )) return it;
-      if (wc_.len() > 0) {
-        for (const_iterator it = bpmap_.begin(); it != bpmap_.end(); ++it)
-          if (it->first.Match_WC( types, wc_)) return it;
-      }
+      //if (wc_.len() > 0) {
+      //  for (const_iterator it = bpmap_.begin(); it != bpmap_.end(); ++it)
+      //    if (it->first.Match_WC( types, wc_)) return it;
+      //}
       return bpmap_.end();
     }
     /// \return size in memory in bytes
@@ -112,7 +116,7 @@ template <class T> class ParmHolder {
     }
   private:
     Bmap bpmap_;
-    NameType wc_; ///< Wildcard character
+    //NameType wc_; ///< Wildcard character
 };
 
 // -----------------------------------------------------------------------------
@@ -126,14 +130,19 @@ class DihedralParmHolder {
     typedef std::pair<TypeNameHolder,DihedralParmArray> Bpair;
     typedef std::vector<Bpair> Bmap;
   public:
+    /// CONSTRUCTOR
     DihedralParmHolder() {}
-    virtual ~DihedralParmHolder() {} ///< Virtual since inherited
+    /// DESTRUCTOR - virtual since inherited
+    virtual ~DihedralParmHolder() {}
+    /// Clear dihedral parameters
     void clear()              { bpmap_.clear();        }
+    /// \return Number of dihedral parameters
     size_t size()       const { return bpmap_.size();  }
+    /// \return true if no dihedral parameters
     bool empty()        const { return bpmap_.empty(); }
     /// Set wildcard character
     void SetWildcard(char wc) { wc_ = NameType(std::string(1, wc)); }
-    /** Add (or update) a single dihedral parameter for given atom types. */
+    /// Add (or update) a single dihedral parameter for given atom types.
     ParameterHolders::RetType
     AddParm(TypeNameHolder const& types, DihedralParmType const& dp, bool allowUpdate) {
       // Check if parm for these types exist
@@ -195,8 +204,7 @@ class DihedralParmHolder {
       }
       return ParameterHolders::ADDED;
     }
-
-    /** This version takes an array of dihedral parameters. */
+    /// Add array of dihedral parameters with unique multiplicities
     ParameterHolders::RetType
     AddParm(TypeNameHolder const& types, DihedralParmArray const& dpa, bool allowUpdate) {
       // Check if parm for these types exist
@@ -232,9 +240,11 @@ class DihedralParmHolder {
       }
       return ParameterHolders::ADDED;
     }
-
+    /// Const iterator
     typedef typename Bmap::const_iterator const_iterator;
+    /// \return const iterator to beginning
     const_iterator begin() const { return bpmap_.begin(); }
+    /// \return const iterator to end
     const_iterator end()   const { return bpmap_.end();   }
     /// \return Array of dihedral parameters matching given atom types.
     DihedralParmArray FindParam(TypeNameHolder const& types, bool& found) const {
@@ -288,27 +298,31 @@ class ImproperParmHolder : private DihedralParmHolder {
                      O_130,
                      O_301,
                      O_310 };
-    ImproperParmHolder() {}
+    ImproperParmHolder() : require_exact_match_(false) {}
     /// \return Number of improper parameter sets
     size_t size()       const { return DihedralParmHolder::size();  }
     /// \return True if no parameters
     bool empty()        const { return DihedralParmHolder::empty(); }
     /// \return Wildcard
     NameType const& Wildcard() const { return wc_; }
+    /// const iterator
     typedef typename DihedralParmHolder::const_iterator const_iterator;
+    /// const iterator to beginning of parameters
     const_iterator begin() const { return DihedralParmHolder::begin(); }
+    /// const iterator to end of parameters
     const_iterator end()   const { return DihedralParmHolder::end();   }
-
-    /** Set Wildcard char */
+    /// Set Wildcard char
     void SetWildcard(char wc) { DihedralParmHolder::SetWildcard(wc); }
-    /** Set Wildcard */
+    /// Set Wildcard
     void SetWildcard(NameType const& wc) { wc_ = wc; }
-    /** Add (or update) a single improper parameter for given atom types. */
+    /// Indicate whether exact type matches are required
+    void SetRequireExactMatch(bool b) { require_exact_match_ = b; }
+    /// Add (or update) a single improper parameter for given atom types.
     ParameterHolders::RetType
     AddParm(TypeNameHolder const& types, DihedralParmType const& dp, bool allowUpdate) {
       return DihedralParmHolder::AddParm( types, dp, allowUpdate );
     }
-    /** This version takes an array of dihedral parameters. */
+    /// Add array of improper parameters, one for each multiplicity.
     ParameterHolders::RetType
     AddParm(TypeNameHolder const& types, DihedralParmArray const& dpa, bool allowUpdate) {
       return DihedralParmHolder::AddParm( types, dpa, allowUpdate );
@@ -355,80 +369,68 @@ class ImproperParmHolder : private DihedralParmHolder {
     const_iterator GetParam(TypeNameHolder const& types, DihedralType& imp, bool& reordered) const {
       //mprintf("DEBUG: FindParam wc=%s Inco=%s-%s-%s-%s\n",*wc_, *(types[0]), *(types[1]),   *(types[2]),   *(types[3]));
       reordered = false;
-      // First, no wildcard
+      OrderType lastOrder_ = O_013;
       const_iterator it = begin();
-      OrderType lastOrder_;
-      for (; it != end(); ++it) {
-        TypeNameHolder const& myTypes = it->first;
-        // Central (third) type must match
-        if (myTypes[2] == types[2]) {
-          //mprintf("DEBUG: FindParam (improper) central atom match %s", *(types[2]));
-          //mprintf(" This=%s-%s-%s-%s", *(myTypes[0]), *(myTypes[1]), *(myTypes[2]), *(myTypes[3]));
-          //mprintf(" Inco=%s-%s-%s-%s\n", *(types[0]), *(types[1]),   *(types[2]),   *(types[3]));
-          // Try all permutations
-          if (       myTypes[0] == types[0] && myTypes[1] == types[1] && myTypes[3] == types[3]) {
-              // 0 1 2 3
-              lastOrder_ = O_013;
-              break;
-          } else if (myTypes[0] == types[0] && myTypes[1] == types[3] && myTypes[3] == types[1]) {
-              // 0 3 2 1
-              lastOrder_ = O_031;
-              break;
-          } else if (myTypes[0] == types[1] && myTypes[1] == types[0] && myTypes[3] == types[3]) {
-              // 1 0 2 3
-              lastOrder_ = O_103;
-              break;
-          } else if (myTypes[0] == types[1] && myTypes[1] == types[3] && myTypes[3] == types[0]) {
-              // 1 3 2 0
-              lastOrder_ = O_130;
-              break;
-          } else if (myTypes[0] == types[3] && myTypes[1] == types[0] && myTypes[3] == types[1]) {
-              // 3 0 2 1
-              lastOrder_ = O_301;
-              break;
-          } else if (myTypes[0] == types[3] && myTypes[1] == types[1] && myTypes[3] == types[0]) {
-              // 3 1 2 0
-              lastOrder_ = O_310;
-              break;
+      // If we require an exact match, look for that first.
+      if (require_exact_match_) {
+        for (; it != end(); ++it) {
+          TypeNameHolder const& myTypes = it->first;
+          if (myTypes[2] == types[2] && myTypes[0] == types[0] &&
+              myTypes[1] == types[1] && myTypes[3] == types[3])
+          {
+            break;
           }
         }
-      } // END loop over parameters
-      // Wildcard if present
-      if (it == end() && wc_.len() > 0) {
-        it = begin();
+      } else {
+        // Inexact match. First, no wildcard
         for (; it != end(); ++it) {
           TypeNameHolder const& myTypes = it->first;
           // Central (third) type must match
-          if (wcm(myTypes[2], types[2], wc_)) {
+          if (myTypes[2] == types[2]) {
+            //mprintf("DEBUG: FindParam (improper) central atom match %s", *(types[2]));
+            //mprintf(" This=%s-%s-%s-%s", *(myTypes[0]), *(myTypes[1]), *(myTypes[2]), *(myTypes[3]));
+            //mprintf(" Inco=%s-%s-%s-%s\n", *(types[0]), *(types[1]),   *(types[2]),   *(types[3]));
             // Try all permutations
-            if (       wcm(myTypes[0], types[0], wc_) && wcm(myTypes[1], types[1], wc_) && wcm(myTypes[3], types[3], wc_)) {
-                // 0 1 2 3
-                lastOrder_ = O_013;
-                break;
-            } else if (wcm(myTypes[0], types[0], wc_) && wcm(myTypes[1], types[3], wc_) && wcm(myTypes[3], types[1], wc_)) {
-                // 0 3 2 1
-                lastOrder_ = O_031;
-                break;
-            } else if (wcm(myTypes[0], types[1], wc_) && wcm(myTypes[1], types[0], wc_) && wcm(myTypes[3], types[3], wc_)) {
-                // 1 0 2 3
-                lastOrder_ = O_103;
-                break;
-            } else if (wcm(myTypes[0], types[1], wc_) && wcm(myTypes[1], types[3], wc_) && wcm(myTypes[3], types[0], wc_)) {
-                // 1 3 2 0
-                lastOrder_ = O_130;
-                break;
-            } else if (wcm(myTypes[0], types[3], wc_) && wcm(myTypes[1], types[0], wc_) && wcm(myTypes[3], types[1], wc_)) {
-                // 3 0 2 1
-                lastOrder_ = O_301;
-                break;
-            } else if (wcm(myTypes[0], types[3], wc_) && wcm(myTypes[1], types[1], wc_) && wcm(myTypes[3], types[0], wc_)) {
-                // 3 1 2 0
-                lastOrder_ = O_310;
-                break;
+            if (       myTypes[0] == types[0] && myTypes[1] == types[1] && myTypes[3] == types[3]) { // 0 1 2 3
+                lastOrder_ = O_013; break;
+            } else if (myTypes[0] == types[0] && myTypes[1] == types[3] && myTypes[3] == types[1]) { // 0 3 2 1
+                lastOrder_ = O_031; break;
+            } else if (myTypes[0] == types[1] && myTypes[1] == types[0] && myTypes[3] == types[3]) { // 1 0 2 3
+                lastOrder_ = O_103; break;
+            } else if (myTypes[0] == types[1] && myTypes[1] == types[3] && myTypes[3] == types[0]) { // 1 3 2 0
+                lastOrder_ = O_130; break;
+            } else if (myTypes[0] == types[3] && myTypes[1] == types[0] && myTypes[3] == types[1]) { // 3 0 2 1
+                lastOrder_ = O_301; break;
+            } else if (myTypes[0] == types[3] && myTypes[1] == types[1] && myTypes[3] == types[0]) { // 3 1 2 0
+                lastOrder_ = O_310; break;
             }
           }
         } // END loop over parameters
-      } // END wildcard matches
+        // Second, do wildcard matches if wildcard is set.
+        if (it == end() && wc_.len() > 0) {
+          it = begin();
+          for (; it != end(); ++it) {
+            TypeNameHolder const& myTypes = it->first;
+            // Central (third) type must match
+            if (wcm(myTypes[2], types[2], wc_)) {
+              // Try all permutations
+              if (       wcm(myTypes[0], types[0], wc_) && wcm(myTypes[1], types[1], wc_) && wcm(myTypes[3], types[3], wc_)) { // 0 1 2 3
+                  lastOrder_ = O_013; break;
+              } else if (wcm(myTypes[0], types[0], wc_) && wcm(myTypes[1], types[3], wc_) && wcm(myTypes[3], types[1], wc_)) { // 0 3 2 1
+                  lastOrder_ = O_031; break;
+              } else if (wcm(myTypes[0], types[1], wc_) && wcm(myTypes[1], types[0], wc_) && wcm(myTypes[3], types[3], wc_)) { // 1 0 2 3
+                  lastOrder_ = O_103; break;
+              } else if (wcm(myTypes[0], types[1], wc_) && wcm(myTypes[1], types[3], wc_) && wcm(myTypes[3], types[0], wc_)) { // 1 3 2 0
+                  lastOrder_ = O_130; break;
+              } else if (wcm(myTypes[0], types[3], wc_) && wcm(myTypes[1], types[0], wc_) && wcm(myTypes[3], types[1], wc_)) { // 3 0 2 1
+                  lastOrder_ = O_301; break;
+              } else if (wcm(myTypes[0], types[3], wc_) && wcm(myTypes[1], types[1], wc_) && wcm(myTypes[3], types[0], wc_)) { // 3 1 2 0
+                  lastOrder_ = O_310; break;
+              }
+            }
+          } // END loop over parameters
+        } // END wildcard matches
+      } // END require exact match
       if (it != end()) {
         // We have found a parameter. Do any reordering.
         if (lastOrder_ != O_013) reordered = true;
@@ -456,5 +458,6 @@ class ImproperParmHolder : private DihedralParmHolder {
     /// \return size in memory in bytes
     size_t DataSize() const { return DihedralParmHolder::DataSize(); }
   private:
+    bool require_exact_match_; ///< If true, types must match in exact order
 };
 #endif

From 80956e05cbce7a36431c038480672586fad8f74e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 9 Jan 2024 09:12:34 -0500
Subject: [PATCH 0294/1492] If incoming improper parameters require an exact
 match, have the improper cache require an exact match

---
 src/ParameterHolders.h | 14 ++++++++------
 src/Topology.cpp       |  3 +++
 2 files changed, 11 insertions(+), 6 deletions(-)

diff --git a/src/ParameterHolders.h b/src/ParameterHolders.h
index 573c6a598f..ee08d281b3 100644
--- a/src/ParameterHolders.h
+++ b/src/ParameterHolders.h
@@ -300,22 +300,24 @@ class ImproperParmHolder : private DihedralParmHolder {
                      O_310 };
     ImproperParmHolder() : require_exact_match_(false) {}
     /// \return Number of improper parameter sets
-    size_t size()       const { return DihedralParmHolder::size();  }
+    size_t size()              const { return DihedralParmHolder::size();  }
     /// \return True if no parameters
-    bool empty()        const { return DihedralParmHolder::empty(); }
+    bool empty()               const { return DihedralParmHolder::empty(); }
     /// \return Wildcard
     NameType const& Wildcard() const { return wc_; }
+    /// \return True if an exact match is required to find a parameter
+    bool RequireExactMatch()   const { return require_exact_match_; }
     /// const iterator
     typedef typename DihedralParmHolder::const_iterator const_iterator;
     /// const iterator to beginning of parameters
-    const_iterator begin() const { return DihedralParmHolder::begin(); }
+    const_iterator begin()     const { return DihedralParmHolder::begin(); }
     /// const iterator to end of parameters
-    const_iterator end()   const { return DihedralParmHolder::end();   }
+    const_iterator end()       const { return DihedralParmHolder::end();   }
     /// Set Wildcard char
     void SetWildcard(char wc) { DihedralParmHolder::SetWildcard(wc); }
     /// Set Wildcard
     void SetWildcard(NameType const& wc) { wc_ = wc; }
-    /// Indicate whether exact type matches are required
+    /// Indicate whether exact type matches are required to find parameters
     void SetRequireExactMatch(bool b) { require_exact_match_ = b; }
     /// Add (or update) a single improper parameter for given atom types.
     ParameterHolders::RetType
@@ -458,6 +460,6 @@ class ImproperParmHolder : private DihedralParmHolder {
     /// \return size in memory in bytes
     size_t DataSize() const { return DihedralParmHolder::DataSize(); }
   private:
-    bool require_exact_match_; ///< If true, types must match in exact order
+    bool require_exact_match_; ///< If true, types must match in exact order when finding parameters
 };
 #endif
diff --git a/src/Topology.cpp b/src/Topology.cpp
index 917827126c..f504aa29b5 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2172,6 +2172,7 @@ static inline void GetAngleParams(ParmHolder<AngleParmType>& AP, std::vector<Ato
 
 // GetImproperParams()
 static inline void GetImproperParams(ImproperParmHolder& IP, std::vector<Atom> const& atoms, DihedralArray const& imp, DihedralParmArray const& ipa) {
+  IP.SetRequireExactMatch(true);
   for (DihedralArray::const_iterator b = imp.begin(); b != imp.end(); ++b)
   {
     if (b->Idx() != -1) {
@@ -2189,6 +2190,7 @@ static inline void GetImproperParams(ImproperParmHolder& IP, std::vector<Atom> c
 
 // GetDihedralParams()
 static inline void GetDihedralParams(DihedralParmHolder& DP, ImproperParmHolder& IP, std::vector<Atom> const& atoms, DihedralArray const& dih, DihedralParmArray const& dpa) {
+  IP.SetRequireExactMatch(true);
   for (DihedralArray::const_iterator b = dih.begin(); b != dih.end(); ++b)
   {
     if (b->Idx() != -1) {
@@ -2787,6 +2789,7 @@ DihedralArray Topology::AssignDihedralParm(DihedralParmHolder const& newDihedral
   // Improper cache
   ImproperParmHolder improperCache;
   improperCache.SetWildcard( newImproperParams.Wildcard() );
+  improperCache.SetRequireExactMatch( newImproperParams.RequireExactMatch() );
   // Keep track of 1-4 interactions
   typedef std::pair<int,int> Ipair;
   typedef std::set<Ipair> Imap;

From b8ef8c0603394f79ab2f9780f9c38d95da8c1c3c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 9 Jan 2024 09:34:55 -0500
Subject: [PATCH 0295/1492] Add function for generating angles/torsions from
 bond array

---
 src/Structure/GenerateConnectivityArrays.cpp | 56 ++++++++++++++++++++
 src/Structure/GenerateConnectivityArrays.h   |  2 +
 2 files changed, 58 insertions(+)

diff --git a/src/Structure/GenerateConnectivityArrays.cpp b/src/Structure/GenerateConnectivityArrays.cpp
index e85be89015..0b7dd8e6c8 100644
--- a/src/Structure/GenerateConnectivityArrays.cpp
+++ b/src/Structure/GenerateConnectivityArrays.cpp
@@ -196,3 +196,59 @@ DihedralArray Cpptraj::Structure::GenerateImproperArray(std::vector<Residue> con
   } // END loop over residues
   return out;
 }
+
+/// Given 2 bonded atoms at1 and at2, get all angles at1-at2-X
+static inline void enumerateAngles(AngleArray& angles, int at1, int at2, std::vector<Atom> const& atoms)
+{
+  Atom const& A2 = atoms[at2];
+  if (A2.Nbonds() > 1) {
+    for (Atom::bond_iterator bat = A2.bondbegin(); bat != A2.bondend(); ++bat)
+    {
+      if (*bat != at1 && at1 < *bat) {
+        mprintf("DEBUG: ANGLE  i= %zu  %i - %i - %i (%i %i %i)\n",  angles.size(), at1+1, at2+1, *bat+1, at1*3, at2*3, *bat*3);
+        angles.push_back( AngleType(at1, at2, *bat, -1) );
+      }
+    }
+  }
+}
+
+/// Given 2 bonded atoms at1 and at2, get all torsions X-at1-at2-Y
+static inline void enumerateDihedrals(DihedralArray& dihedrals, int at1, int at2, std::vector<Atom> const& atoms)
+{
+  Atom const& A1 = atoms[at1];
+  Atom const& A2 = atoms[at2];
+  if (A1.Nbonds() > 1 && A2.Nbonds() > 1) {
+    for (Atom::bond_iterator bat1 = A1.bondbegin(); bat1 != A1.bondend(); ++bat1)
+    {
+      if (*bat1 != at2) {
+        for (Atom::bond_iterator bat2 = A2.bondbegin(); bat2 != A2.bondend(); ++bat2)
+        {
+          if (*bat2 != at1) {
+            // LEaP convention appears to be first atom less than last atom
+            if (*bat1 < *bat2)
+              dihedrals.push_back( DihedralType(*bat1, at1, at2, *bat2, -1) );
+            else
+              dihedrals.push_back( DihedralType(*bat2, at2, at1, *bat1, -1) );
+          }
+        }
+      }
+    }
+  }
+}
+
+/** Generate angle and torsion arrays from given bond array. */
+void Cpptraj::Structure::GenerateAngleAndTorsionArraysFromBonds(AngleArray& angles,
+                                                                DihedralArray& dihedrals,
+                                                                std::vector<Atom> const& atoms,
+                                                                BondArray const& allBonds)
+{
+  for (BondArray::const_iterator it = allBonds.begin(); it != allBonds.end(); ++it)
+  {
+    // Forward direction. A1-A2-X
+    enumerateAngles( angles, it->A1(), it->A2(), atoms );
+    // Reverse direction. A2-A1-X
+    enumerateAngles( angles, it->A2(), it->A1(), atoms );
+    // Dihedrals
+    enumerateDihedrals( dihedrals, it->A1(), it->A2(), atoms );
+  }
+}
diff --git a/src/Structure/GenerateConnectivityArrays.h b/src/Structure/GenerateConnectivityArrays.h
index 9975c3d83b..b0bc6f8bc2 100644
--- a/src/Structure/GenerateConnectivityArrays.h
+++ b/src/Structure/GenerateConnectivityArrays.h
@@ -20,6 +20,8 @@ AngleArray GenerateAngleArray(std::vector<Residue> const&, std::vector<Atom> con
 DihedralArray GenerateDihedralArray(std::vector<Residue> const&, std::vector<Atom> const&);
 /// Generate improper dihedral array in same order as leap
 DihedralArray GenerateImproperArray(std::vector<Residue> const&, std::vector<Atom> const&);
+/// Generate angle and torsion arrays from bonds
+void GenerateAngleAndTorsionArraysFromBonds(AngleArray&, DihedralArray&, std::vector<Atom> const&, BondArray const&);
 }
 }
 #endif

From 6003019da555c44107a1db16556c9c5f26fe052b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 9 Jan 2024 09:36:49 -0500
Subject: [PATCH 0296/1492] Remove old connectivity generation

---
 src/Structure/GenerateConnectivity.cpp | 196 -------------------------
 src/Structure/GenerateConnectivity.h   |  12 --
 2 files changed, 208 deletions(-)
 delete mode 100644 src/Structure/GenerateConnectivity.cpp
 delete mode 100644 src/Structure/GenerateConnectivity.h

diff --git a/src/Structure/GenerateConnectivity.cpp b/src/Structure/GenerateConnectivity.cpp
deleted file mode 100644
index e303482902..0000000000
--- a/src/Structure/GenerateConnectivity.cpp
+++ /dev/null
@@ -1,196 +0,0 @@
-#include "GenerateConnectivity.h"
-#include "../CpptrajStdio.h"
-#include "../Topology.h"
-#include <algorithm> // std::sort
-
-static inline void enumerateAngles(int& aidx, int at1, int at2, Topology& topIn) {
-  Atom const& A2 = topIn[at2];
-  if (A2.Nbonds() > 1) {
-    for (Atom::bond_iterator bat = A2.bondbegin(); bat != A2.bondend(); ++bat)
-    {
-      if (*bat != at1 && at1 < *bat) {
-        topIn.AddAngle(at1, at2, *bat);
-        mprintf("DEBUG: ANGLE  i= %i  %i - %i - %i (%i %i %i)\n",  aidx++, at1+1, at2+1, *bat+1, at1*3, at2*3, *bat*3);
-        //mprintf("%s - %s - %s\n",
-        //        topIn.AtomMaskName(at1).c_str(),
-        //        topIn.AtomMaskName(at2).c_str(),
-        //        topIn.AtomMaskName(*bat).c_str());
-      }
-    }
-  }
-}
-
-static inline void enumerateDihedrals(int at1, int at2, Topology& topIn) {
-  Atom const& A1 = topIn[at1];
-  Atom const& A2 = topIn[at2];
-  if (A1.Nbonds() > 1 && A2.Nbonds() > 1) {
-    for (Atom::bond_iterator bat1 = A1.bondbegin(); bat1 != A1.bondend(); ++bat1)
-    {
-      if (*bat1 != at2) {
-        for (Atom::bond_iterator bat2 = A2.bondbegin(); bat2 != A2.bondend(); ++bat2)
-        {
-          if (*bat2 != at1) {
-            // LEaP convention appears to be first atom less than last atom
-            if (*bat1 < *bat2)
-              topIn.AddDihedral(*bat1, at1, at2, *bat2);
-            else
-              topIn.AddDihedral(*bat2, at2, at1, *bat1);
-            //mprintf("%s - %s - %s - %s\n",
-            //        topIn.AtomMaskName(*bat1).c_str(),
-            //        topIn.AtomMaskName(at1).c_str(),
-            //        topIn.AtomMaskName(at2).c_str(),
-            //        topIn.AtomMaskName(*bat2).c_str());
-          }
-        }
-      }
-    }
-  }
-}
-
-/* Set bonds, angles, and dihedral arrays for a given topology based on
- * a sorted and combined version of the current bond arrays.
- */
-int Cpptraj::Structure::GenerateAngleTorsionArrays(Topology& topIn) {
-  if (topIn.Nbonds() < 1) {
-    mprintf("Warning: No bonds in '%s', no angles to generate.\n", topIn.c_str());
-    return 0;
-  }
-  bool has_angles = topIn.Nangles() > 0;
-  if (has_angles) {
-    mprintf("Warning: Topology '%s' already has angle information.\n", topIn.c_str());
-    //return 0;
-  }
-  bool has_dihedrals = topIn.Ndihedrals() > 0;
-  if (has_dihedrals) {
-    mprintf("Warning: Topology '%s' already has dihedral information.\n", topIn.c_str());
-    //return 0;
-  }
-  if (has_angles && has_dihedrals) return 0;
-  // Create a combined bonds array
-  BondArray allBonds;
-  allBonds.reserve(topIn.Nbonds());
-  for (BondArray::const_iterator it = topIn.Bonds().begin(); it != topIn.Bonds().end(); ++it)
-    allBonds.push_back( *it );
-  for (BondArray::const_iterator it = topIn.BondsH().begin(); it != topIn.BondsH().end(); ++it)
-    allBonds.push_back( *it );
-  std::sort( allBonds.begin(), allBonds.end() );
-  mprintf("DEBUG: Sorted bonds:\n");
-  for (BondArray::const_iterator it = allBonds.begin(); it != allBonds.end(); ++it)
-    mprintf("\t%s - %s\n",
-            topIn.AtomMaskName(it->A1()).c_str(),
-            topIn.AtomMaskName(it->A2()).c_str());
-
-  // Angles and Torsiions
-  int aidx = 0;
-  for (BondArray::const_iterator it = allBonds.begin(); it != allBonds.end(); ++it)
-  {
-    if (!has_angles) {
-      // Forward direction. A1-A2-X
-      enumerateAngles( aidx, it->A1(), it->A2(), topIn );
-      // Reverse direction. A2-A1-X
-      enumerateAngles( aidx, it->A2(), it->A1(), topIn );
-    }
-    if (!has_dihedrals) {
-      // Dihedrals
-      enumerateDihedrals( it->A1(), it->A2(), topIn );
-    }
-  }
-  return 0;
-}
-
-/* Set bonds, angles, and dihedral arrays for a given topology based on 
- * current atom connectivity.
- * This is done in the same manner as LEaP, which goes in increasing
- * residue order but decreasing atom index.
- */
-int Cpptraj::Structure::GenerateBondAngleTorsionArrays(Topology& topIn) {
-  if (topIn.Nbonds() < 1) {
-    mprintf("Warning: No bonds in '%s', no angles to generate.\n", topIn.c_str());
-    return 0;
-  }
-  bool has_angles = topIn.Nangles() > 0;
-  if (has_angles) {
-    mprintf("Warning: Topology '%s' already has angle information.\n", topIn.c_str());
-    //return 0;
-  }
-  bool has_dihedrals = topIn.Ndihedrals() > 0;
-  if (has_dihedrals) {
-    mprintf("Warning: Topology '%s' already has dihedral information.\n", topIn.c_str());
-    //return 0;
-  }
-  if (has_angles && has_dihedrals) return 0;
-  // Clear existing bond information TODO clear angles and dihedrals?
-  topIn.ClearBondArrays();
-
-  // BONDS
-  int bidx = 0;
-  for (int ires = 0; ires < topIn.Nres(); ires++)
-  {
-    Residue const& res = topIn.Res(ires);
-    for (int iat = res.LastAtom()-1; iat >= res.FirstAtom(); iat--)
-    {
-      Atom const& At = topIn[iat];
-      for (Atom::bond_iterator bat = At.bondbegin(); bat != At.bondend(); ++bat)
-      {
-        if (iat < *bat) {
-          mprintf("DEBUG: BOND  i= %i  %i - %i (%i %i)\n",  bidx++, iat+1, *bat+1, iat*3, *bat*3);
-          topIn.AddToBondArrays( BondType(iat, *bat, -1) );
-        }
-        //else
-        //  mprintf("DEBUG: X    i= %i  %i - %i (%i %i)\n",   bidx++, iat+1, *bat+1, iat*3, *bat*3);
-      }
-    }
-  }
-
-  // ANGLES TODO combine above
-  int aidx = 0;
-  for (int ires = 0; ires < topIn.Nres(); ires++)
-  {
-    Residue const& res = topIn.Res(ires);
-    for (int iat1 = res.LastAtom()-1; iat1 >= res.FirstAtom(); iat1--)
-    {
-      Atom const& At1 = topIn[iat1];
-      for (int bidx1 = 0; bidx1 < At1.Nbonds(); bidx1++) {
-        int iat2 = At1.Bond(bidx1);
-        Atom const& At2 = topIn[iat2];
-        for (int bidx2 = 0; bidx2 < At2.Nbonds(); bidx2++) {
-          int iat3 = At2.Bond(bidx2);
-          if (iat1 < iat3) {
-            mprintf("DEBUG: ANGLE  i= %i  %i - %i - %i (%i %i %i)\n", aidx++, iat1+1, iat2+1, iat3+1, iat1*3, iat2*3, iat3*3);
-            topIn.AddAngle(iat1, iat2, iat3);
-          }
-        }
-      }
-    }
-  }
-
-  // TORSIONS TODO combine above
-  int didx = 0;
-  for (int ires = 0; ires < topIn.Nres(); ires++)
-  {
-    Residue const& res = topIn.Res(ires);
-    for (int iat1 = res.LastAtom()-1; iat1 >= res.FirstAtom(); iat1--)
-    {
-      Atom const& At1 = topIn[iat1];
-      for (int bidx1 = 0; bidx1 < At1.Nbonds(); bidx1++) {
-        int iat2 = At1.Bond(bidx1);
-        Atom const& At2 = topIn[iat2];
-        for (int bidx2 = 0; bidx2 < At2.Nbonds(); bidx2++) {
-          int iat3 = At2.Bond(bidx2);
-          if (iat3 != iat1) {
-            Atom const& At3 = topIn[iat3];
-            for (int bidx3 = 0; bidx3 < At3.Nbonds(); bidx3++) {
-              int iat4 = At3.Bond(bidx3);
-              if (iat4 != iat2 && iat1 < iat4) {
-                mprintf("DEBUG: DIHEDRAL  i= %i  %i - %i - %i - %i (%i %i %i %i)\n", didx++, iat1+1, iat2+1, iat3+1, iat4+1, iat1*3, iat2*3, iat3*3, iat4*3);
-                topIn.AddDihedral( iat1, iat2, iat3, iat4 );
-              }
-            }
-          }
-        }
-      }
-    }
-  }
-
-  return 0;
-}
diff --git a/src/Structure/GenerateConnectivity.h b/src/Structure/GenerateConnectivity.h
deleted file mode 100644
index dd4a150bfc..0000000000
--- a/src/Structure/GenerateConnectivity.h
+++ /dev/null
@@ -1,12 +0,0 @@
-#ifndef INC_STRUCTURE_GENERATECONNECTIVITY_H
-#define INC_STRUCTURE_GENERATECONNECTIVITY_H
-class Topology;
-namespace Cpptraj {
-namespace Structure {
-/// Generate angle/torsion arrays from bond arrays in a Topology
-int GenerateAngleTorsionArrays(Topology&);
-/// Generate bond/angle/torsion arrays from atom connectivity in a Topology
-int GenerateBondAngleTorsionArrays(Topology&);
-}
-}
-#endif

From fe128563802740b49da225aeb811caca6019970e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 9 Jan 2024 10:28:10 -0500
Subject: [PATCH 0297/1492] Remove obsolete bond/angle/torsion generation

---
 src/Exec_Sequence.cpp         | 27 +++++++++++++++++++--------
 src/Exec_UpdateParameters.cpp | 24 ++++++++++--------------
 src/Structure/CMakeLists.txt  |  1 -
 src/Structure/structuredepend |  1 -
 src/Structure/structurefiles  |  1 -
 src/Topology.cpp              |  2 ++
 src/cpptrajdepend             |  5 ++---
 7 files changed, 33 insertions(+), 28 deletions(-)

diff --git a/src/Exec_Sequence.cpp b/src/Exec_Sequence.cpp
index 6b5356fd7b..4bc95592d0 100644
--- a/src/Exec_Sequence.cpp
+++ b/src/Exec_Sequence.cpp
@@ -2,7 +2,6 @@
 #include "CpptrajStdio.h"
 #include "AssociatedData_Connect.h"
 #include "Structure/Builder.h"
-#include "Structure/GenerateConnectivity.h"
 
 /** Generate and build the specified sequence. */
 int Exec_Sequence::generate_sequence(DataSet_Coords* OUT,
@@ -91,7 +90,6 @@ const
   Frame CombinedFrame = Units.front()->AllocateFrame();
   Units.front()->GetFrame(0, CombinedFrame);
 
-
   using namespace Cpptraj::Structure;
   Builder builder;
   for (unsigned int idx = 1; idx < Units.size(); idx++) {
@@ -116,12 +114,12 @@ const
   }
 
   // Generate angles and dihedrals
- if (combinedTop.Nbonds() > 0) {
-   if (Cpptraj::Structure::GenerateBondAngleTorsionArrays(combinedTop)) {
-     mprinterr("Error: Angle generation failed.\n");
-     return 1;
-   }
- }
+  //if (combinedTop.Nbonds() > 0) {
+  //  if (Cpptraj::Structure::GenerateBondAngleTorsionArrays(combinedTop)) {
+  //    mprinterr("Error: Angle generation failed.\n");
+  //    return 1;
+  //  }
+  //}
 
   OUT->CoordsSetup(combinedTop, CombinedFrame.CoordsInfo());
   OUT->AddFrame( CombinedFrame );
@@ -142,6 +140,19 @@ void Exec_Sequence::Help() const
 Exec::RetType Exec_Sequence::Execute(CpptrajState& State, ArgList& argIn)
 {
   debug_ = State.Debug();
+  // Atom scan direction TODO add to help
+/*    Cpptraj::Structure::SetAtomScanDirection(Cpptraj::Structure::SCAN_ATOMS_FORWARDS);
+  std::string atomscandir = argIn.GetStringKey("atomscandir");
+  if (!atomscandir.empty()) {
+    if (atomscandir == "f")
+      Cpptraj::Structure::SetAtomScanDirection(Cpptraj::Structure::SCAN_ATOMS_FORWARDS);
+    else if (atomscandir == "b")
+      Cpptraj::Structure::SetAtomScanDirection(Cpptraj::Structure::SCAN_ATOMS_BACKWARDS);
+    else {
+      mprinterr("Error: Unrecognized keyword for 'atomscandir' : %s\n", atomscandir.c_str());
+      return CpptrajState::ERR;
+    }
+  }*/
   // Args
   Sarray LibSetNames;
   std::string libsetname = argIn.GetStringKey("libset");
diff --git a/src/Exec_UpdateParameters.cpp b/src/Exec_UpdateParameters.cpp
index 735cdcfd8a..68b4b0e101 100644
--- a/src/Exec_UpdateParameters.cpp
+++ b/src/Exec_UpdateParameters.cpp
@@ -2,14 +2,13 @@
 #include "CpptrajStdio.h"
 #include "DataSet_Parameters.h"
 #include "DataSet_Topology.h"
-#include "Structure/GenerateConnectivity.h"
 
 const char* Exec_UpdateParameters::disclaimer_ = "Warning: This command is provided for convenience only.\nWarning: For editing topology files, ParmEd is a much better alternative.\n";
 
 // Exec_UpdateParameters::Help()
 void Exec_UpdateParameters::Help() const
 {
-  mprintf("\tsetname <parmset> [genangles]\n"
+  mprintf("\tsetname <parmset>\n"
           "\t%s\n", DataSetList::TopArgs);
   mprintf("  Update parameters in specified topology with those from <parm set>.\n"
           "  <parm set> can either be a parameter set or a topology. If a\n"
@@ -23,7 +22,7 @@ Exec::RetType Exec_UpdateParameters::Execute(CpptrajState& State, ArgList& argIn
 {
   mprintf("%s", disclaimer_);
   std::string dsname = argIn.GetStringKey("setname");
-  bool genAngles = argIn.hasKey("genangles");
+  //bool genAngles = argIn.hasKey("genangles");
   if (dsname.empty()) {
     mprinterr("Error: Specify parameter set.\n");
     return CpptrajState::ERR;
@@ -46,18 +45,15 @@ Exec::RetType Exec_UpdateParameters::Execute(CpptrajState& State, ArgList& argIn
 
   mprintf("\tUpdating parameters in topology '%s' using those in set '%s'\n",
           top.c_str(), ds->legend());
-  if (genAngles)
-    mprintf("\tWill attempt to generate angle/dihedral information from bonds.\n");
+  //if (genAngles)
+  //  mprintf("\tWill attempt to generate angle/dihedral information from bonds.\n");
 
-  // Sort topology bond arrays to be consistent with LEaP
-  //top.SortBonds();
-
-  if (genAngles) {
-    if (Cpptraj::Structure::GenerateBondAngleTorsionArrays( top )) {
-      mprinterr("Error: Could not generate angle/dihedral information.\n");
-      return CpptrajState::ERR;
-    }
-  }
+  //if (genAngles) {
+  //  if (Cpptraj::Structure::GenerateBondAngleTorsionArrays( top )) {
+  //    mprinterr("Error: Could not generate angle/dihedral information.\n");
+  //    return CpptrajState::ERR;
+  //  }
+  //}
 
   if (ds->Type() == DataSet::PARAMETERS)
     top.UpdateParams(static_cast<DataSet_Parameters const&>( *ds ));
diff --git a/src/Structure/CMakeLists.txt b/src/Structure/CMakeLists.txt
index d04716f8bc..f6ec6cc9f6 100644
--- a/src/Structure/CMakeLists.txt
+++ b/src/Structure/CMakeLists.txt
@@ -6,7 +6,6 @@ target_sources(cpptraj_common_obj PRIVATE
   ${CMAKE_CURRENT_LIST_DIR}/FunctionalGroup.cpp
   ${CMAKE_CURRENT_LIST_DIR}/FxnGroupBuilder.cpp
   ${CMAKE_CURRENT_LIST_DIR}/GenerateConnectivityArrays.cpp
-  ${CMAKE_CURRENT_LIST_DIR}/GenerateConnectivity.cpp
   ${CMAKE_CURRENT_LIST_DIR}/HisProt.cpp
   ${CMAKE_CURRENT_LIST_DIR}/InternalCoords.cpp
   ${CMAKE_CURRENT_LIST_DIR}/Model.cpp
diff --git a/src/Structure/structuredepend b/src/Structure/structuredepend
index 1cc597f095..b11ad9e7ba 100644
--- a/src/Structure/structuredepend
+++ b/src/Structure/structuredepend
@@ -3,7 +3,6 @@ Chirality.o : Chirality.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Co
 Disulfide.o : Disulfide.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Disulfide.h ResStatArray.h StructureRoutines.h
 FunctionalGroup.o : FunctionalGroup.cpp ../Atom.h ../AtomMap.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h FunctionalGroup.h
 FxnGroupBuilder.o : FxnGroupBuilder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h FunctionalGroup.h FxnGroupBuilder.h StructureRoutines.h Sugar.h SugarToken.h
-GenerateConnectivity.o : GenerateConnectivity.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h GenerateConnectivity.h
 GenerateConnectivityArrays.o : GenerateConnectivityArrays.cpp ../Atom.h ../Constants.h ../CpptrajStdio.h ../NameType.h ../ParameterTypes.h ../Residue.h ../SymbolExporting.h GenerateConnectivityArrays.h
 HisProt.o : HisProt.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h HisProt.h StructureRoutines.h
 InternalCoords.o : InternalCoords.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h InternalCoords.h
diff --git a/src/Structure/structurefiles b/src/Structure/structurefiles
index 6a6dd3da57..d5c54bfca2 100644
--- a/src/Structure/structurefiles
+++ b/src/Structure/structurefiles
@@ -6,7 +6,6 @@ STRUCTURE_SOURCES= \
   FunctionalGroup.cpp \
   FxnGroupBuilder.cpp \
   GenerateConnectivityArrays.cpp \
-  GenerateConnectivity.cpp \
   HisProt.cpp \
   InternalCoords.cpp \
   Model.cpp \
diff --git a/src/Topology.cpp b/src/Topology.cpp
index f504aa29b5..051e6b3d42 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -3142,6 +3142,8 @@ int Topology::AssignParams(ParameterSet const& set0) {
     AddToAngleArrays( *ang );
   // Dihedral parameters
   mprintf("\tAssigning dihedral parameters.\n");
+  dihedralparm_.clear();
+  // Regenerate dihedral array in LEaP order
   dihedrals_.clear();
   dihedralsh_.clear();
   DihedralArray allDihedrals = Cpptraj::Structure::GenerateDihedralArray(residues_, atoms_);
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 61e5b64a01..7ef4cb6e0b 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -333,7 +333,7 @@ Exec_ReadInput.o : Exec_ReadInput.cpp Action.h ActionList.h ActionState.h Analys
 Exec_RotateDihedral.o : Exec_RotateDihedral.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_RotateDihedral.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_RunAnalysis.o : Exec_RunAnalysis.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_RunAnalysis.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_ScaleDihedralK.o : Exec_ScaleDihedralK.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ScaleDihedralK.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Sequence.o : Exec_Sequence.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Sequence.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/GenerateConnectivity.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Sequence.o : Exec_Sequence.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Sequence.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_SequenceAlign.o : Exec_SequenceAlign.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SequenceAlign.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Set.o : Exec_Set.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_StringVar.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Set.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Show.o : Exec_Show.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_StringVar.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Show.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
@@ -342,7 +342,7 @@ Exec_SplitCoords.o : Exec_SplitCoords.cpp Action.h ActionList.h ActionState.h An
 Exec_System.o : Exec_System.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_System.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Top.o : Exec_Top.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Top.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h TopInfo.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Traj.o : Exec_Traj.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Traj.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_UpdateParameters.o : Exec_UpdateParameters.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h DataSet_Topology.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_UpdateParameters.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/GenerateConnectivity.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_UpdateParameters.o : Exec_UpdateParameters.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h DataSet_Topology.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_UpdateParameters.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_ViewRst.o : Exec_ViewRst.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ViewRst.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h ViewRst.h
 Exec_Zmatrix.o : Exec_Zmatrix.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Zmatrix.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Zmatrix.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 ExtendedSimilarity.o : ExtendedSimilarity.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h ExtendedSimilarity.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
@@ -449,7 +449,6 @@ Structure/Chirality.o : Structure/Chirality.cpp Atom.h AtomMask.h AtomType.h Box
 Structure/Disulfide.o : Structure/Disulfide.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Disulfide.h Structure/ResStatArray.h Structure/StructureRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/FunctionalGroup.o : Structure/FunctionalGroup.cpp Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/FxnGroupBuilder.o : Structure/FxnGroupBuilder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h Structure/FxnGroupBuilder.h Structure/StructureRoutines.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Structure/GenerateConnectivity.o : Structure/GenerateConnectivity.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/GenerateConnectivity.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/GenerateConnectivityArrays.o : Structure/GenerateConnectivityArrays.cpp Atom.h Constants.h CpptrajStdio.h NameType.h ParameterTypes.h Residue.h Structure/GenerateConnectivityArrays.h SymbolExporting.h
 Structure/HisProt.o : Structure/HisProt.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/HisProt.h Structure/StructureRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/InternalCoords.o : Structure/InternalCoords.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/InternalCoords.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h

From 433fa2f4b95f217b28aa28617e312e7748fa6e5a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 9 Jan 2024 10:36:18 -0500
Subject: [PATCH 0298/1492] Actually set polarizability in constructor

---
 src/AtomType.h | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/AtomType.h b/src/AtomType.h
index e603f0361b..0af047fc74 100644
--- a/src/AtomType.h
+++ b/src/AtomType.h
@@ -13,7 +13,7 @@ class AtomType {
     /// CONSTRUCTOR - Mass, polarizability
     AtomType(double m, double p) : mass_(m), polarizability_(p), oidx_(-1), hybrid_(UNKNOWN_HYBRIDIZATION) {}
     /// CONSTRUCTOR - Radius, well depth, mass, polarizability
-    AtomType(double r, double d, double m, double p) : lj_(r, d), mass_(m), oidx_(-1), hybrid_(UNKNOWN_HYBRIDIZATION) {}
+    AtomType(double r, double d, double m, double p) : lj_(r, d), mass_(m), polarizability_(p), oidx_(-1), hybrid_(UNKNOWN_HYBRIDIZATION) {}
     /// Set type index
     void SetTypeIdx(int i) { oidx_ = i; }
     /// \return default LJ parameters

From 2c5322aad65f5de141bbfb1fe60d671efee43a45 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 9 Jan 2024 12:00:56 -0500
Subject: [PATCH 0299/1492] Add seed set routine that takes into account known
 positions

---
 src/Structure/Zmatrix.cpp | 104 +++++++++++++++++++++++++++++++++++---
 src/Structure/Zmatrix.h   |   4 +-
 2 files changed, 100 insertions(+), 8 deletions(-)

diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index 8c03c97d39..f161eea714 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -192,6 +192,91 @@ void Zmatrix::addIc(int at0, int at1, int at2, int at3,
                                 Torsion(xyz0, xyz1, xyz2, xyz3) * Constants::RADDEG) );
 }
 
+/** Set seeds as 3 consecutive atoms for which positions are known. */
+int Zmatrix::autoSetSeeds_withPositions(Frame const& frameIn, Topology const& topIn, Molecule const& mol, Barray const& positionKnown)
+{
+  seedAt0_ = InternalCoords::NO_ATOM;
+  seedAt1_ = InternalCoords::NO_ATOM;
+  seedAt2_ = InternalCoords::NO_ATOM;
+
+  if (positionKnown.empty()) {
+    mprinterr("InternalError: Zmatrix::autoSetSeeds_withPositions() called with an empty known position array.\n");
+    return 1;
+  }
+  if (mol.NumAtoms() < 1) {
+    mprinterr("Internal Error: Zmatrix::autoSetSeeds_withPositions() called with an empty molecule.\n");
+    return 1;
+  }
+  // Special cases
+  if (mol.NumAtoms() == 1) {
+    seedAt0_ = mol.MolUnit().Front();
+    seed0Pos_ = Vec3(frameIn.XYZ(seedAt0_));
+    return 0;
+  } else if (mol.NumAtoms() == 2) {
+    seedAt0_ = mol.MolUnit().Front();
+    seed0Pos_ = Vec3(frameIn.XYZ(seedAt0_));
+    if (topIn[seedAt0_].Nbonds() != 1) {
+      mprinterr("Internal Error: Zmatrix::autoSetSeeds_simple(): 2 atoms but no bonds.\n");
+      return 1;
+    }
+    seedAt1_ = topIn[seedAt0_].Bond(0);
+    seed1Pos_ = Vec3(frameIn.XYZ(seedAt1_));
+    return 0;
+  }
+  // Loop over atoms in the molecule
+  int numS2bonds = -1;
+  for (Unit::const_iterator seg = mol.MolUnit().segBegin();
+                            seg != mol.MolUnit().segEnd(); ++seg)
+  {
+    for (int at = seg->Begin(); at != seg->End(); ++at) {
+      if (positionKnown[at]) {
+        Atom const& AJ = topIn[at];
+        if (AJ.Nbonds() > 1) {
+          for (int bidx1 = 0; bidx1 < AJ.Nbonds(); bidx1++) {
+            for (int bidx2 = bidx1 + 1; bidx2 < AJ.Nbonds(); bidx2++) {
+              int bat1 = AJ.Bond(bidx1);
+              int bat2 = AJ.Bond(bidx2);
+              if (positionKnown[bat1] && positionKnown[bat2]) {
+                int s1 = at;
+                int s0, s2;
+                // b1 - AJ - b2
+                Atom const& b1 = topIn[bat1];
+                Atom const& b2 = topIn[bat2];
+                // The atom with more bonds should be AK (seed 2)
+                if (b1.Nbonds() > b2.Nbonds()) {
+                  s0 = bat2;
+                  s2 = bat1;
+                } else {
+                  s0 = bat1;
+                  s2 = bat2;
+                }
+                if (numS2bonds == -1 || topIn[s2].Nbonds() > numS2bonds) {
+                  seedAt0_ = s0;
+                  seedAt1_ = s1;
+                  seedAt2_ = s2;
+                  numS2bonds = topIn[s2].Nbonds();
+                }
+              }
+            } // END inner loop over bonded atoms
+          } // END outer loop over bonded atoms
+        } // END AJ bonds > 1
+      } // END position of AJ is known
+    } // END loop over segment atoms
+  } // END loop over segments
+
+  if (seedAt0_ == InternalCoords::NO_ATOM ||
+      seedAt1_ == InternalCoords::NO_ATOM ||
+      seedAt2_ == InternalCoords::NO_ATOM)
+  {
+    mprinterr("Error: No suitable seed atoms with known positions could be found.\n");
+    return 1;
+  }
+  seed0Pos_ = Vec3(frameIn.XYZ(seedAt0_));
+  seed1Pos_ = Vec3(frameIn.XYZ(seedAt1_));
+  seed2Pos_ = Vec3(frameIn.XYZ(seedAt2_));
+  return 0;
+}
+
 /** Simple automatic setting of seeds for a molecule.
   * seed0 - seed1 - seed 2
   * Prefer that seed1 has only exactly 2 bonds. It cannot have 1.
@@ -202,11 +287,11 @@ int Zmatrix::autoSetSeeds_simple(Frame const& frameIn, Topology const& topIn, Mo
   seedAt1_ = InternalCoords::NO_ATOM;
   seedAt2_ = InternalCoords::NO_ATOM;
 
-  // Handle special cases
   if (mol.NumAtoms() < 1) {
     mprinterr("Internal Error: Zmatrix::autoSetSeeds_simple() called with an empty molecule.\n");
     return 1;
   }
+  // Handle special cases
   if (mol.NumAtoms() == 1) {
     seedAt0_ = mol.MolUnit().Front();
     seed0Pos_ = Vec3(frameIn.XYZ(seedAt0_));
@@ -450,7 +535,8 @@ int Zmatrix::traceMol(int atL0, int atK0, int atJ0,
   * This algorithm attempts to "trace" the molecule in a manner that
   * should make internal coordinate assignment more "natural".
   */
-int Zmatrix::SetFromFrame_Trace(Frame const& frameIn, Topology const& topIn, int molnum)
+int Zmatrix::SetFromFrame_Trace(Frame const& frameIn, Topology const& topIn, int molnum,
+                                Barray const& knownPositions)
 {
   if (molnum < 0) {
     mprinterr("Internal Error: Zmatrix::SetFromFrame(): Negative molecule index.\n");
@@ -470,13 +556,17 @@ int Zmatrix::SetFromFrame_Trace(Frame const& frameIn, Topology const& topIn, int
 
   // See if we need to assign seed atoms
   if (!HasCartSeeds()) {
-    // First seed atom will just be first atom TODO lowest index heavy atom?
-    if (autoSetSeeds_simple(frameIn, topIn, currentMol)) {
+    int seedErr = 0;
+    if (knownPositions.empty())
+      // First seed atom will just be first atom TODO lowest index heavy atom?
+      seedErr = autoSetSeeds_simple(frameIn, topIn, currentMol);
+    else
+      seedErr = autoSetSeeds_withPositions(frameIn, topIn, currentMol, knownPositions);
+    if (seedErr != 0) {
     //if (autoSetSeeds(frameIn, topIn, maxnatom, currentMol.MolUnit().Front())) {
       mprinterr("Error: Could not automatically determine seed atoms.\n");
       return 1;
     }
-
   } else {
     // Seed atoms already set
     if (debug_ > 0)
@@ -542,13 +632,13 @@ int Zmatrix::SetFromFrame_Trace(Frame const& frameIn, Topology const& topIn, int
 
 /** Setup Zmatrix from Cartesian coordinates/topology. */
 int Zmatrix::SetFromFrame(Frame const& frameIn, Topology const& topIn) {
-  return SetFromFrame_Trace(frameIn, topIn, 0);
+  return SetFromFrame_Trace(frameIn, topIn, 0, Barray());
 }
 
 /** Setup Zmatrix from Cartesian coordinates/topology. */
 int Zmatrix::SetFromFrame(Frame const& frameIn, Topology const& topIn, int molnum)
 {
-  return SetFromFrame_Trace(frameIn, topIn, molnum);
+  return SetFromFrame_Trace(frameIn, topIn, molnum, Barray());
 }
 
 /** Given two bonded atoms A and B, where B has a depth of at least 2
diff --git a/src/Structure/Zmatrix.h b/src/Structure/Zmatrix.h
index 8b53f03fe7..89f20007b7 100644
--- a/src/Structure/Zmatrix.h
+++ b/src/Structure/Zmatrix.h
@@ -71,6 +71,8 @@ class Zmatrix {
     static Vec3 AtomIposition(InternalCoords const&, Frame const&);
   private:
     typedef std::vector<int> Iarray;
+    /// Set seeds as 3 consecutive atoms with known positions
+    int autoSetSeeds_withPositions(Frame const&, Topology const&, Molecule const&, Barray const&);
     /// Simple version of auto set seeds based on connectivity only
     int autoSetSeeds_simple(Frame const&, Topology const&, Molecule const&);
     /// Calculate and add an internal coordinate given indices and Cartesian coords.
@@ -78,7 +80,7 @@ class Zmatrix {
     /// Add internal coordiantes by tracing a molecule
     int traceMol(int, int, int, Frame const&, Topology const&, unsigned int, unsigned int&, Barray&);
     /// Convert from Cartesian to minimal Zmatrix by tracing a molecule
-    int SetFromFrame_Trace(Frame const&, Topology const&, int);
+    int SetFromFrame_Trace(Frame const&, Topology const&, int, Barray const&);
     /// \return True if IC seeds are set
     //bool HasICSeeds() const;
     /// \return True if Cartesian seeds are set

From aef619ac6c2ba100280fcc4a30f2944553ba46d4 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 9 Jan 2024 12:27:43 -0500
Subject: [PATCH 0300/1492] Start new way to properly set up seeds so that
 residues actually get built.

---
 src/Exec_Build.cpp        | 20 +++++++++++------
 src/Structure/Zmatrix.cpp | 45 ++++++++++++++++++++++-----------------
 src/Structure/Zmatrix.h   |  6 ++++--
 3 files changed, 43 insertions(+), 28 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 2060e77fa9..5c749363ed 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -238,14 +238,20 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
   {
     Cpptraj::Structure::Zmatrix* zmatrix = *it;
     if (zmatrix != 0) {
-      mprintf("DEBUG: Zmatrix for building residue %li %s\n", it - ResZmatrices.begin() + 1,
-              topOut.TruncResNameNum(it - ResZmatrices.begin()).c_str());
-      zmatrix->print(&topOut);
-      zmatrix->SetDebug( 1 ); // DEBUG
-      if (zmatrix->SetToFrame( frameOut, hasPosition )) {
-        mprinterr("Error: Building residue %s failed.\n",
-                  topOut.TruncResNameNum(it - ResZmatrices.begin()).c_str());
+      // Update zmatrix seeds
+      if (zmatrix->AutoSetSeedsWithPositions( frameOut, topOut, it - ResZmatrices.begin(), hasPosition )) {
+        mprinterr("Error: Could not set up seed atoms for Zmatrix.\n");
         buildFailed = true;
+      } else {
+        mprintf("DEBUG: Zmatrix for building residue %li %s\n", it - ResZmatrices.begin() + 1,
+                topOut.TruncResNameNum(it - ResZmatrices.begin()).c_str());
+        zmatrix->print(&topOut);
+        zmatrix->SetDebug( 1 ); // DEBUG
+        if (zmatrix->SetToFrame( frameOut, hasPosition )) {
+          mprinterr("Error: Building residue %s failed.\n",
+                    topOut.TruncResNameNum(it - ResZmatrices.begin()).c_str());
+          buildFailed = true;
+        }
       }
     }
   }
diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index f161eea714..760c8e20f2 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -192,8 +192,14 @@ void Zmatrix::addIc(int at0, int at1, int at2, int at3,
                                 Torsion(xyz0, xyz1, xyz2, xyz3) * Constants::RADDEG) );
 }
 
+/** Set seeds as 3 consecutive atoms from mol 0 for which positions are known. */
+int Zmatrix::AutoSetSeedsWithPositions(Frame const& frameIn, Topology const& topIn, int ires, Barray const& positionKnown)
+{
+  return autoSetSeeds_withPositions(frameIn, topIn, topIn.Res(ires).FirstAtom(), topIn.Res(ires).LastAtom(), positionKnown);
+}
+
 /** Set seeds as 3 consecutive atoms for which positions are known. */
-int Zmatrix::autoSetSeeds_withPositions(Frame const& frameIn, Topology const& topIn, Molecule const& mol, Barray const& positionKnown)
+int Zmatrix::autoSetSeeds_withPositions(Frame const& frameIn, Topology const& topIn, int startAtom, int endAtom, Barray const& positionKnown)
 {
   seedAt0_ = InternalCoords::NO_ATOM;
   seedAt1_ = InternalCoords::NO_ATOM;
@@ -203,17 +209,18 @@ int Zmatrix::autoSetSeeds_withPositions(Frame const& frameIn, Topology const& to
     mprinterr("InternalError: Zmatrix::autoSetSeeds_withPositions() called with an empty known position array.\n");
     return 1;
   }
-  if (mol.NumAtoms() < 1) {
-    mprinterr("Internal Error: Zmatrix::autoSetSeeds_withPositions() called with an empty molecule.\n");
+  int numAtoms = endAtom - startAtom;
+  if (numAtoms < 1) {
+    mprinterr("Internal Error: Zmatrix::autoSetSeeds_withPositions() called with start <= end atom.\n");
     return 1;
   }
   // Special cases
-  if (mol.NumAtoms() == 1) {
-    seedAt0_ = mol.MolUnit().Front();
+  if (numAtoms == 1) {
+    seedAt0_ = startAtom;
     seed0Pos_ = Vec3(frameIn.XYZ(seedAt0_));
     return 0;
-  } else if (mol.NumAtoms() == 2) {
-    seedAt0_ = mol.MolUnit().Front();
+  } else if (numAtoms == 2) {
+    seedAt0_ = startAtom;
     seed0Pos_ = Vec3(frameIn.XYZ(seedAt0_));
     if (topIn[seedAt0_].Nbonds() != 1) {
       mprinterr("Internal Error: Zmatrix::autoSetSeeds_simple(): 2 atoms but no bonds.\n");
@@ -225,10 +232,11 @@ int Zmatrix::autoSetSeeds_withPositions(Frame const& frameIn, Topology const& to
   }
   // Loop over atoms in the molecule
   int numS2bonds = -1;
-  for (Unit::const_iterator seg = mol.MolUnit().segBegin();
-                            seg != mol.MolUnit().segEnd(); ++seg)
-  {
-    for (int at = seg->Begin(); at != seg->End(); ++at) {
+  for (int at = startAtom; at < endAtom; at++) {
+//  for (Unit::const_iterator seg = mol.MolUnit().segBegin();
+//                            seg != mol.MolUnit().segEnd(); ++seg)
+//  {
+//    for (int at = seg->Begin(); at != seg->End(); ++at) {
       if (positionKnown[at]) {
         Atom const& AJ = topIn[at];
         if (AJ.Nbonds() > 1) {
@@ -261,7 +269,7 @@ int Zmatrix::autoSetSeeds_withPositions(Frame const& frameIn, Topology const& to
           } // END outer loop over bonded atoms
         } // END AJ bonds > 1
       } // END position of AJ is known
-    } // END loop over segment atoms
+    //} // END loop over segment atoms
   } // END loop over segments
 
   if (seedAt0_ == InternalCoords::NO_ATOM ||
@@ -535,8 +543,7 @@ int Zmatrix::traceMol(int atL0, int atK0, int atJ0,
   * This algorithm attempts to "trace" the molecule in a manner that
   * should make internal coordinate assignment more "natural".
   */
-int Zmatrix::SetFromFrame_Trace(Frame const& frameIn, Topology const& topIn, int molnum,
-                                Barray const& knownPositions)
+int Zmatrix::SetFromFrame_Trace(Frame const& frameIn, Topology const& topIn, int molnum)
 {
   if (molnum < 0) {
     mprinterr("Internal Error: Zmatrix::SetFromFrame(): Negative molecule index.\n");
@@ -557,11 +564,11 @@ int Zmatrix::SetFromFrame_Trace(Frame const& frameIn, Topology const& topIn, int
   // See if we need to assign seed atoms
   if (!HasCartSeeds()) {
     int seedErr = 0;
-    if (knownPositions.empty())
+    //if (knownPositions.empty())
       // First seed atom will just be first atom TODO lowest index heavy atom?
       seedErr = autoSetSeeds_simple(frameIn, topIn, currentMol);
-    else
-      seedErr = autoSetSeeds_withPositions(frameIn, topIn, currentMol, knownPositions);
+    //else
+    //  seedErr = autoSetSeeds_withPositions(frameIn, topIn, currentMol, knownPositions);
     if (seedErr != 0) {
     //if (autoSetSeeds(frameIn, topIn, maxnatom, currentMol.MolUnit().Front())) {
       mprinterr("Error: Could not automatically determine seed atoms.\n");
@@ -632,13 +639,13 @@ int Zmatrix::SetFromFrame_Trace(Frame const& frameIn, Topology const& topIn, int
 
 /** Setup Zmatrix from Cartesian coordinates/topology. */
 int Zmatrix::SetFromFrame(Frame const& frameIn, Topology const& topIn) {
-  return SetFromFrame_Trace(frameIn, topIn, 0, Barray());
+  return SetFromFrame_Trace(frameIn, topIn, 0);
 }
 
 /** Setup Zmatrix from Cartesian coordinates/topology. */
 int Zmatrix::SetFromFrame(Frame const& frameIn, Topology const& topIn, int molnum)
 {
-  return SetFromFrame_Trace(frameIn, topIn, molnum, Barray());
+  return SetFromFrame_Trace(frameIn, topIn, molnum);
 }
 
 /** Given two bonded atoms A and B, where B has a depth of at least 2
diff --git a/src/Structure/Zmatrix.h b/src/Structure/Zmatrix.h
index 89f20007b7..608a4b26b5 100644
--- a/src/Structure/Zmatrix.h
+++ b/src/Structure/Zmatrix.h
@@ -38,6 +38,8 @@ class Zmatrix {
 
     /// Set seed atoms from frame/top
     int SetSeedPositions(Frame const&, Topology const&, int, int, int);
+    /// Set seed atoms as 3 consecutive atoms with known positions for specified residue # 
+    int AutoSetSeedsWithPositions(Frame const&, Topology const&, int, Barray const&);
 
     /// Convert specifed molecule of Frame/Topology to internal coordinates array
     int SetFromFrame(Frame const&, Topology const&, int);
@@ -72,7 +74,7 @@ class Zmatrix {
   private:
     typedef std::vector<int> Iarray;
     /// Set seeds as 3 consecutive atoms with known positions
-    int autoSetSeeds_withPositions(Frame const&, Topology const&, Molecule const&, Barray const&);
+    int autoSetSeeds_withPositions(Frame const&, Topology const&, int, int, Barray const&);
     /// Simple version of auto set seeds based on connectivity only
     int autoSetSeeds_simple(Frame const&, Topology const&, Molecule const&);
     /// Calculate and add an internal coordinate given indices and Cartesian coords.
@@ -80,7 +82,7 @@ class Zmatrix {
     /// Add internal coordiantes by tracing a molecule
     int traceMol(int, int, int, Frame const&, Topology const&, unsigned int, unsigned int&, Barray&);
     /// Convert from Cartesian to minimal Zmatrix by tracing a molecule
-    int SetFromFrame_Trace(Frame const&, Topology const&, int, Barray const&);
+    int SetFromFrame_Trace(Frame const&, Topology const&, int);
     /// \return True if IC seeds are set
     //bool HasICSeeds() const;
     /// \return True if Cartesian seeds are set

From 53382bf7b29fa024cf64b861a8842fc83ea9bcd0 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 9 Jan 2024 17:23:59 -0500
Subject: [PATCH 0301/1492] Add full internal coordinates for seed atoms

---
 src/Structure/Zmatrix.cpp | 85 +++++++++++++++++++++++++++++++++++----
 src/Structure/Zmatrix.h   |  5 ++-
 2 files changed, 81 insertions(+), 9 deletions(-)

diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index 760c8e20f2..18327e4f7f 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -539,6 +539,47 @@ int Zmatrix::traceMol(int atL0, int atK0, int atJ0,
   return 0;
 }
 
+/** Add IC for the given atom. */
+int Zmatrix::addInternalCoordForAtom(int iat, Frame const& frameIn, Topology const& topIn)
+{
+  int maxScore = -1;
+  int maxAtj = -1;
+  int maxAtk = -1;
+  int maxAtl = -1;
+  Atom const& atomI = topIn[iat];
+  for (Atom::bond_iterator jat = atomI.bondbegin(); jat != atomI.bondend(); ++jat) {
+    Atom const& atomJ = topIn[*jat];
+    for (Atom::bond_iterator kat = atomJ.bondbegin(); kat != atomJ.bondend(); ++kat) {
+      if (*kat != iat) {
+        Atom const& atomK = topIn[*kat];
+        for (Atom::bond_iterator lat = atomK.bondbegin(); lat != atomK.bondend(); ++lat) {
+          if (*lat != *jat && *lat != iat) {
+            int nbondScore = topIn[*lat].Nbonds();
+            if (maxScore == -1 || nbondScore > maxScore) {
+              maxScore = nbondScore;
+              maxAtj = *jat;
+              maxAtk = *kat;
+              maxAtl = *lat;
+            }
+            mprintf("DEBUG: Potential IC for %s [ %s - %s - %s ] score= %i\n",
+                    topIn.AtomMaskName(iat).c_str(),
+                    topIn.AtomMaskName(*jat).c_str(),
+                    topIn.AtomMaskName(*kat).c_str(),
+                    topIn.AtomMaskName(*lat).c_str(),
+                    nbondScore);
+          }
+        }
+      }
+    }
+  }
+  if (maxScore == -1) {
+    mprintf("Warning: Unable to define IC for atom %s\n", topIn.AtomMaskName(iat).c_str());
+  } else {
+      addIc( iat, maxAtj, maxAtk, maxAtl, frameIn.XYZ(iat), frameIn.XYZ(maxAtj), frameIn.XYZ(maxAtk), frameIn.XYZ(maxAtl) );
+  }
+  return 0;
+}
+
 /** Set up Zmatrix from Cartesian coordinates and topology.
   * This algorithm attempts to "trace" the molecule in a manner that
   * should make internal coordinate assignment more "natural".
@@ -582,7 +623,7 @@ int Zmatrix::SetFromFrame_Trace(Frame const& frameIn, Topology const& topIn, int
               topIn.AtomMaskName(seedAt1_).c_str(),
               topIn.AtomMaskName(seedAt2_).c_str());
   }
-  // Add IC seeds
+  // Add basic ICs for seeds
   if (seedAt0_ != InternalCoords::NO_ATOM)
     AddIC( InternalCoords(seedAt0_, InternalCoords::NO_ATOM, InternalCoords::NO_ATOM, InternalCoords::NO_ATOM,
                               0, 0, 0) );
@@ -633,7 +674,28 @@ int Zmatrix::SetFromFrame_Trace(Frame const& frameIn, Topology const& topIn, int
   if (nHasIC < maxnatom) {
     mprintf("Warning: Not all atoms have an associated internal coordinate.\n");
   }
-
+  // Add ICs for seeds
+  if (maxnatom > 3) {
+    //Atom const& SA0 = topIn[seedAt0_];
+    //Atom const& SA1 = topIn[seedAt1_];
+    //Atom const& SA2 = topIn[seedAt2_];
+    // Seed 0; 0-1-2-X
+    addInternalCoordForAtom(seedAt0_, frameIn, topIn);
+    addInternalCoordForAtom(seedAt1_, frameIn, topIn);
+    addInternalCoordForAtom(seedAt2_, frameIn, topIn);
+/*    if (SA2.Nbonds() < 2)
+      mprintf("Warning: Third seed atom has only one bond. Cannot create full IC for seed 0.\n");
+    else {
+      int at3;
+      for (Atom::bond_iterator bat = SA2.bondbegin(); bat != SA2.bondend(); ++bat) {
+        if (*bat != seedAt1_ && *bat != seedAt0_) {
+          at3 = *bat;
+          break;
+        }
+      }
+      addIc( seedAt0_, seedAt1_, seedAt2_, at3, frameIn.XYZ(seedAt0_), frameIn.XYZ(seedAt1_), frameIn.XYZ(seedAt2_), frameIn.XYZ(at3) );
+    }*/
+  }
   return 0;
 }
 
@@ -923,6 +985,7 @@ int Zmatrix::SetToFrame(Frame& frameOut, Barray& hasPosition) const {
   Barray isUsed( IC_.size(), false );
   unsigned int Nused = 0;
   if (HasCartSeeds()) {
+    mprintf("DEBUG: Has Cartesian seeds.\n");
     if (icseed0_ != InternalCoords::NO_ATOM) MARK(icseed0_, isUsed, Nused);
     if (icseed1_ != InternalCoords::NO_ATOM) MARK(icseed1_, isUsed, Nused);
     if (icseed2_ != InternalCoords::NO_ATOM) MARK(icseed2_, isUsed, Nused);
@@ -968,17 +1031,21 @@ int Zmatrix::SetToFrame(Frame& frameOut, Barray& hasPosition) const {
   } // END Does not have Cart. seeds
   // Find the lowest unused IC
   unsigned int lowestUnusedIC = 0;
-  for (; lowestUnusedIC < IC_.size(); ++lowestUnusedIC)
-    if (!isUsed[lowestUnusedIC]) break;
-  if (debug_ > 0) mprintf("DEBUG: Lowest unused IC: %u\n", lowestUnusedIC+1);
+//  for (; lowestUnusedIC < IC_.size(); ++lowestUnusedIC)
+//    if (!isUsed[lowestUnusedIC]) break;
+//  if (debug_ > 0) mprintf("DEBUG: Lowest unused IC: %u\n", lowestUnusedIC+1);
 
   // Loop over remaining ICs 
   while (Nused < IC_.size()) {
     // Find the next IC that is not yet used.
-    unsigned int idx = lowestUnusedIC;
+//    unsigned int idx = lowestUnusedIC;
+    unsigned int idx = 0;
     bool findNextIC = true;
     while (findNextIC) {
-      while (idx < IC_.size() && isUsed[idx]) idx++;
+      while (idx < IC_.size() && isUsed[idx]) {
+        mprintf("DEBUG:\t\tIC %u is used\n", idx+1);
+        idx++;
+      }
       if (idx >= IC_.size()) {
         mprinterr("Error: Could not find next IC to use.\n");
         return 1;
@@ -989,8 +1056,10 @@ int Zmatrix::SetToFrame(Frame& frameOut, Barray& hasPosition) const {
           hasPosition[ IC_[idx].AtL() ])
       {
         findNextIC = false;
-      } else
+      } else {
+        mprintf("DEBUG:\t\tIC %u is missing atoms.\n", idx+1);
         idx++;
+      }
     } // END loop finding next atom to set
     if (debug_ > 0) mprintf("DEBUG: Next IC to use is %u\n", idx+1);
 
diff --git a/src/Structure/Zmatrix.h b/src/Structure/Zmatrix.h
index 608a4b26b5..3fb70d5c28 100644
--- a/src/Structure/Zmatrix.h
+++ b/src/Structure/Zmatrix.h
@@ -79,8 +79,11 @@ class Zmatrix {
     int autoSetSeeds_simple(Frame const&, Topology const&, Molecule const&);
     /// Calculate and add an internal coordinate given indices and Cartesian coords.
     void addIc(int,int,int,int,const double*,const double*,const double*,const double*);
-    /// Add internal coordiantes by tracing a molecule
+    /// Add internal coordinates by tracing a molecule
     int traceMol(int, int, int, Frame const&, Topology const&, unsigned int, unsigned int&, Barray&);
+    /// Add internal coordinate for given atom
+    int addInternalCoordForAtom(int, Frame const&, Topology const&);
+
     /// Convert from Cartesian to minimal Zmatrix by tracing a molecule
     int SetFromFrame_Trace(Frame const&, Topology const&, int);
     /// \return True if IC seeds are set

From a891538c0823eded714f07798e4cb45bb32c0f92 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 10 Jan 2024 10:24:50 -0500
Subject: [PATCH 0302/1492] Only set positions for atoms without positions

---
 src/Structure/Zmatrix.cpp | 43 +++++++++++++++++++++++++++++++++++++--
 1 file changed, 41 insertions(+), 2 deletions(-)

diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index 18327e4f7f..c48335ccea 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -1030,11 +1030,50 @@ int Zmatrix::SetToFrame(Frame& frameOut, Barray& hasPosition) const {
     } // END seed atom 0
   } // END Does not have Cart. seeds
   // Find the lowest unused IC
-  unsigned int lowestUnusedIC = 0;
+//  unsigned int lowestUnusedIC = 0;
 //  for (; lowestUnusedIC < IC_.size(); ++lowestUnusedIC)
 //    if (!isUsed[lowestUnusedIC]) break;
 //  if (debug_ > 0) mprintf("DEBUG: Lowest unused IC: %u\n", lowestUnusedIC+1);
 
+  // Out of the remaining ICs, count which ones do not have positions set.
+  unsigned int remainingPositionsToSet = 0;
+  for (unsigned int icIdx = 0; icIdx != IC_.size(); ++icIdx) {
+    if (!isUsed[icIdx] && !hasPosition[IC_[icIdx].AtI()])
+      remainingPositionsToSet++;
+  }
+  mprintf("DEBUG: %u positions to set.\n", remainingPositionsToSet);
+
+  while (remainingPositionsToSet > 0 && Nused < IC_.size()) {
+    // Get the next IC with a position to set
+    int icIdx = -1;
+    for (unsigned int idx = 0; idx != IC_.size(); ++idx) {
+      if (!isUsed[idx] && !hasPosition[IC_[idx].AtI()]) {
+        // All 3 of the connecting atoms must be set
+        if (hasPosition[ IC_[idx].AtJ() ] &&
+            hasPosition[ IC_[idx].AtK() ] &&
+            hasPosition[ IC_[idx].AtL() ])
+        {
+          icIdx = (int)idx;
+          break;
+        } else {
+          mprintf("DEBUG:\t\tIC %u is missing atoms.\n", idx+1);
+        }
+      }
+    }
+    if (icIdx < 0) {
+      mprinterr("Error: Could not find next IC to use.\n");
+      return 1;
+    }
+    if (debug_ > 0) mprintf("DEBUG: Next IC to use is %i\n", icIdx+1);
+    InternalCoords const& ic = IC_[icIdx];
+    Vec3 posI = AtomIposition(ic, frameOut);
+
+    frameOut.SetXYZ( ic.AtI(), posI );
+    hasPosition[ ic.AtI() ] = true;
+    remainingPositionsToSet--;
+    MARK(icIdx, isUsed, Nused);
+  } // END loop over remaining positions
+/*
   // Loop over remaining ICs 
   while (Nused < IC_.size()) {
     // Find the next IC that is not yet used.
@@ -1077,6 +1116,6 @@ int Zmatrix::SetToFrame(Frame& frameOut, Barray& hasPosition) const {
 
     //break; // DEBUG
   } // END loop over internal coordinates
-
+*/
   return 0;
 }

From bef5095df7729a9143c678812016021f128388b4 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 10 Jan 2024 15:41:55 -0500
Subject: [PATCH 0303/1492] Use the exact same strings that are in leap

---
 src/Parm/GB_Params.cpp | 18 +++++++++++++++++-
 src/Parm/GB_Params.h   |  2 ++
 2 files changed, 19 insertions(+), 1 deletion(-)

diff --git a/src/Parm/GB_Params.cpp b/src/Parm/GB_Params.cpp
index 65db247499..2205ee853b 100644
--- a/src/Parm/GB_Params.cpp
+++ b/src/Parm/GB_Params.cpp
@@ -24,11 +24,27 @@ static const char* GB_RadiiTypeKey_[] = {
   0
 };
 
+static const char* GB_RadiiAmberFlag_[] = {
+  "Bondi radii (bondi)",                              // 0
+  "amber6 modified Bondi radii (amber6)",             // 1
+  "modified Bondi radii (mbondi)",                    // 2
+  "Huo and Kollman optimized radii (pbamber)",        // 3
+  "H(N)-modified Bondi radii (mbondi2)",              // 6
+  "Parse radii (parse)",                              // 7
+  "ArgH and AspGluO modified Bondi2 radii (mbondi3)", // 8
+  "Unknown radius set (leap needs to be modified!)"
+};
+
 /** \return char string corresponding to type. */
 std::string Cpptraj::Parm::GbTypeStr(GB_RadiiType t) {
   return std::string(GB_RadiiTypeStr_[t]);
 }
 
+/** \return Amber topology FLAG */
+std::string Cpptraj::Parm::GbAmberFlag(GB_RadiiType t) {
+  return std::string(GB_RadiiAmberFlag_[t]);
+}
+
 /** \return GB_RadiiType corresponding to string. */
 Cpptraj::Parm::GB_RadiiType Cpptraj::Parm::GbTypeFromKey(std::string const& key) {
   if (!key.empty()) {
@@ -400,7 +416,7 @@ int Cpptraj::Parm::Assign_GB_Radii(Topology& top, GB_RadiiType radiiSet)
     return 1;
   }
   mprintf("\tUsing GB radii set: %s\n", GB_RadiiTypeStr_[radiiSet]);
-  top.SetGBradiiSet( std::string(GB_RadiiTypeStr_[radiiSet]) );
+  top.SetGBradiiSet( std::string(GB_RadiiAmberFlag_[radiiSet]) );
   assign_gb_radii( top, radiiSet );
   assign_gb_screen( top, radiiSet );
 
diff --git a/src/Parm/GB_Params.h b/src/Parm/GB_Params.h
index 97f24d11ff..6067d2f6ee 100644
--- a/src/Parm/GB_Params.h
+++ b/src/Parm/GB_Params.h
@@ -15,6 +15,8 @@ enum GB_RadiiType {
   MBONDI3,          ///< 8, ArgH and AspGluO modified Bondi2 radii
   UNKNOWN_GB
 };
+/// \return string corresponding to Amber Radii Flag
+std::string GbAmberFlag(GB_RadiiType);
 /// \return string corresponding to gb radii set
 std::string GbTypeStr(GB_RadiiType);
 /// \return GB radii type corresponding to string

From ba8c30c9ce180a3a60e64250616753d8cf6ef86e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 10 Jan 2024 18:55:18 -0500
Subject: [PATCH 0304/1492] Detect terminal residues

---
 src/Exec_Build.cpp | 42 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 5c749363ed..32aff5eb8e 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -48,6 +48,48 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
                                        Carray const& Templates,
                                        Topology const& topIn, Frame const& frameIn)
 {
+  // Determine which residues are terminal
+  typedef std::vector<int> Iarray;
+  typedef std::vector<Iarray> IIarray;
+  IIarray terminalResidues( topIn.Nmol() );
+  for (int ires = 0; ires != topIn.Nres(); ires++)
+  {
+    Residue const& currentRes = topIn.Res(ires);
+    int n_connections = 0;
+    for (int at = currentRes.FirstAtom(); at != currentRes.LastAtom(); at++)
+    {
+      if (topIn[at].Element() != Atom::HYDROGEN && topIn[at].Nbonds() > 1) {
+        for (Atom::bond_iterator bat = topIn[at].bondbegin(); bat != topIn[at].bondend(); ++bat)
+        {
+          if (topIn[*bat].ResNum() != topIn[at].ResNum())
+            n_connections++;
+        }
+      }
+    }
+    mprintf("DEBUG: Res %s has %i connections.\n", topIn.TruncResNameNum(ires).c_str(), n_connections);
+    if (n_connections == 1) {
+      int molnum = topIn[currentRes.FirstAtom()].MolNum();
+      terminalResidues[ molnum ].push_back( ires );
+    }
+  }
+  enum TermType { BEG_TERMINAL = 0, REGULAR, END_TERMINAL };
+  typedef std::vector<TermType> Tarray;
+  Tarray residueTerminalStatus( topIn.Nres(), REGULAR );
+  mprintf("\tTerminal residues:\n");
+  for (IIarray::const_iterator mit = terminalResidues.begin(); mit != terminalResidues.end(); ++mit)
+  {
+    mprintf("\t\tMol %li:", mit - terminalResidues.begin() + 1);
+    for (Iarray::const_iterator it = mit->begin(); it != mit->end(); ++it) {
+      mprintf(" %s", topIn.TruncResNameNum( *it ).c_str());
+      if (it == mit->begin())
+        residueTerminalStatus[*it] = BEG_TERMINAL;
+      else
+        residueTerminalStatus[*it] = END_TERMINAL;
+      mprintf("(%i)", (int)residueTerminalStatus[*it]);
+    }
+    mprintf("\n");
+  }
+
   // Array of templates for each residue
   std::vector<DataSet_Coords*> ResTemplates;
   ResTemplates.reserve( topIn.Nres() );

From 3963744ff26367f888ae970c97fae970cf4660ee Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 11 Jan 2024 09:48:05 -0500
Subject: [PATCH 0305/1492] Track residue connections

---
 src/Exec_Build.cpp        | 28 ++++++++++++++++++++++------
 src/Structure/Zmatrix.cpp |  4 +++-
 2 files changed, 25 insertions(+), 7 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 32aff5eb8e..fdc2e70c25 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -48,10 +48,12 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
                                        Carray const& Templates,
                                        Topology const& topIn, Frame const& frameIn)
 {
-  // Determine which residues are terminal
   typedef std::vector<int> Iarray;
   typedef std::vector<Iarray> IIarray;
-  IIarray terminalResidues( topIn.Nmol() );
+  // Determine which residues are terminal
+  IIarray molTermResidues( topIn.Nmol() );
+  // Track residue connections
+  IIarray resConnections( topIn.Nres() );
   for (int ires = 0; ires != topIn.Nres(); ires++)
   {
     Residue const& currentRes = topIn.Res(ires);
@@ -61,24 +63,36 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
       if (topIn[at].Element() != Atom::HYDROGEN && topIn[at].Nbonds() > 1) {
         for (Atom::bond_iterator bat = topIn[at].bondbegin(); bat != topIn[at].bondend(); ++bat)
         {
-          if (topIn[*bat].ResNum() != topIn[at].ResNum())
+          if (topIn[*bat].ResNum() != topIn[at].ResNum()) {
             n_connections++;
+            resConnections[ ires ].push_back( topIn[*bat].ResNum() );
+          }
         }
       }
     }
     mprintf("DEBUG: Res %s has %i connections.\n", topIn.TruncResNameNum(ires).c_str(), n_connections);
     if (n_connections == 1) {
       int molnum = topIn[currentRes.FirstAtom()].MolNum();
-      terminalResidues[ molnum ].push_back( ires );
+      molTermResidues[ molnum ].push_back( ires );
     }
   }
+  // DEBUG Print residue connections
+  mprintf("DEBUG: Residue connections:\n");
+  for (IIarray::const_iterator rit = resConnections.begin(); rit != resConnections.end(); ++rit)
+  {
+    mprintf("DEBUG:\t\t%s to", topIn.TruncResNameNum(rit-resConnections.begin()).c_str());
+    for (Iarray::const_iterator it = rit->begin(); it != rit->end(); ++it)
+      mprintf(" %s", topIn.TruncResNameNum( *it ).c_str());
+    mprintf("\n");
+  }
+  // Set residue terminal status
   enum TermType { BEG_TERMINAL = 0, REGULAR, END_TERMINAL };
   typedef std::vector<TermType> Tarray;
   Tarray residueTerminalStatus( topIn.Nres(), REGULAR );
   mprintf("\tTerminal residues:\n");
-  for (IIarray::const_iterator mit = terminalResidues.begin(); mit != terminalResidues.end(); ++mit)
+  for (IIarray::const_iterator mit = molTermResidues.begin(); mit != molTermResidues.end(); ++mit)
   {
-    mprintf("\t\tMol %li:", mit - terminalResidues.begin() + 1);
+    mprintf("\t\tMol %li:", mit - molTermResidues.begin() + 1);
     for (Iarray::const_iterator it = mit->begin(); it != mit->end(); ++it) {
       mprintf(" %s", topIn.TruncResNameNum( *it ).c_str());
       if (it == mit->begin())
@@ -280,6 +294,8 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
   {
     Cpptraj::Structure::Zmatrix* zmatrix = *it;
     if (zmatrix != 0) {
+      // Create zmatrix with previous residue if needed
+      
       // Update zmatrix seeds
       if (zmatrix->AutoSetSeedsWithPositions( frameOut, topOut, it - ResZmatrices.begin(), hasPosition )) {
         mprinterr("Error: Could not set up seed atoms for Zmatrix.\n");
diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index c48335ccea..bc92235e18 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -1038,8 +1038,10 @@ int Zmatrix::SetToFrame(Frame& frameOut, Barray& hasPosition) const {
   // Out of the remaining ICs, count which ones do not have positions set.
   unsigned int remainingPositionsToSet = 0;
   for (unsigned int icIdx = 0; icIdx != IC_.size(); ++icIdx) {
-    if (!isUsed[icIdx] && !hasPosition[IC_[icIdx].AtI()])
+    if (!isUsed[icIdx] && !hasPosition[IC_[icIdx].AtI()]) {
       remainingPositionsToSet++;
+      mprintf("DEBUG:\t\tAtom %i needs its position set.\n", IC_[icIdx].AtI());
+    }
   }
   mprintf("DEBUG: %u positions to set.\n", remainingPositionsToSet);
 

From 412a1fe59c092d6a4269609bc03ad0455f195857 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 11 Jan 2024 10:26:02 -0500
Subject: [PATCH 0306/1492] Make const

---
 src/Structure/Zmatrix.cpp | 2 +-
 src/Structure/Zmatrix.h   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index bc92235e18..09ad074ab7 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -93,7 +93,7 @@ std::vector<int> Zmatrix::AtomI_indices(int atomi) const {
 }
 
 /** Print to stdout */
-void Zmatrix::print(Topology* topIn) const {
+void Zmatrix::print(Topology const* topIn) const {
   mprintf("%zu internal coords.\n", IC_.size());
   mprintf("Seed IC indices    : %i %i %i\n", icseed0_+1, icseed1_+1, icseed2_+1);
   mprintf("Seed Cart. indices : %i %i %i\n", seedAt0_+1, seedAt1_+1, seedAt2_+1);
diff --git a/src/Structure/Zmatrix.h b/src/Structure/Zmatrix.h
index 3fb70d5c28..f177758dad 100644
--- a/src/Structure/Zmatrix.h
+++ b/src/Structure/Zmatrix.h
@@ -19,7 +19,7 @@ class Zmatrix {
     /// Set debug level
     void SetDebug(int d) { debug_ = d; }
     /// Print to stdout
-    void print(Topology*) const;
+    void print(Topology const*) const;
     /// Print to stdout, no atom names
     void print() const { print(0); }
 

From c43ddc80c719f351bf1be88cb89aae113b8bac3a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 11 Jan 2024 10:49:50 -0500
Subject: [PATCH 0307/1492] Add some debug info

---
 src/Structure/Zmatrix.cpp | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index 09ad074ab7..c47e55eb15 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -721,9 +721,10 @@ int Zmatrix::SetupICsAroundBond(int atA, int atB, Frame const& frameIn, Topology
                                 BuildAtom const& AtomA, BuildAtom const& AtomB)
 {
   if (debug_ > 0)
-    mprintf("DEBUG: SetupICsAroundBond: atA= %s (%i)  atB= %s (%i)\n",
+    mprintf("DEBUG: SetupICsAroundBond: atA= %s (%i)  atB= %s (%i) total # atoms %i\n",
             topIn.AtomMaskName(atA).c_str(), atA+1,
-            topIn.AtomMaskName(atB).c_str(), atB+1);
+            topIn.AtomMaskName(atB).c_str(), atB+1,
+            topIn.Natom());
   IC_.clear();
 
   Barray hasIC( topIn.Natom(), false );
@@ -732,6 +733,7 @@ int Zmatrix::SetupICsAroundBond(int atA, int atB, Frame const& frameIn, Topology
   for (std::vector<bool>::const_iterator it = atomPositionKnown.begin();
                                          it != atomPositionKnown.end(); ++it)
   {
+    //mprintf("DEBUG: MARKING KNOWN ATOMS. %li\n", it - atomPositionKnown.begin());
     if (*it) MARK( it - atomPositionKnown.begin(), hasIC, nHasIC );
   }
 

From ff3bcb0a7f76d91d17952fe0bb940dc93e28a057 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 11 Jan 2024 10:54:21 -0500
Subject: [PATCH 0308/1492] Dont check # of bonds in case there are 1 atom
 residues

---
 src/Exec_Build.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index fdc2e70c25..8dc5677a9e 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -60,7 +60,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
     int n_connections = 0;
     for (int at = currentRes.FirstAtom(); at != currentRes.LastAtom(); at++)
     {
-      if (topIn[at].Element() != Atom::HYDROGEN && topIn[at].Nbonds() > 1) {
+      //if (topIn[at].Element() != Atom::HYDROGEN && topIn[at].Nbonds() > 1) {
         for (Atom::bond_iterator bat = topIn[at].bondbegin(); bat != topIn[at].bondend(); ++bat)
         {
           if (topIn[*bat].ResNum() != topIn[at].ResNum()) {
@@ -68,7 +68,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
             resConnections[ ires ].push_back( topIn[*bat].ResNum() );
           }
         }
-      }
+      //}
     }
     mprintf("DEBUG: Res %s has %i connections.\n", topIn.TruncResNameNum(ires).c_str(), n_connections);
     if (n_connections == 1) {

From 9cb0b2b899c5f2d37332237de1164d04d6c64cf9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 11 Jan 2024 10:55:12 -0500
Subject: [PATCH 0309/1492] Hide some debug info

---
 src/Exec_Build.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 8dc5677a9e..30087529fc 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -249,10 +249,10 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
           mprinterr("Error: Could not set up residue template zmatrix.\n");
           return 1;
         }
-        zmatrix->print( resTemplate->TopPtr() );
+        //zmatrix->print( resTemplate->TopPtr() );
         zmatrix->OffsetIcIndices( atomOffset );
         ResZmatrices.push_back( zmatrix );
-        zmatrix->print( &topOut );
+        //zmatrix->print( &topOut );
       } else
         ResZmatrices.push_back( 0 );
     } // END template exists

From 1e6b6104891444d9269270e64ccc30cfdd5f1d61 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 11 Jan 2024 10:57:07 -0500
Subject: [PATCH 0310/1492] Calculate residue index once

---
 src/Exec_Build.cpp | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 30087529fc..20c40864ee 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -292,22 +292,21 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
   bool buildFailed = false;
   for (Zarray::const_iterator it = ResZmatrices.begin(); it != ResZmatrices.end(); ++it)
   {
+    long int ires = it-ResZmatrices.begin();
     Cpptraj::Structure::Zmatrix* zmatrix = *it;
     if (zmatrix != 0) {
-      // Create zmatrix with previous residue if needed
-      
       // Update zmatrix seeds
-      if (zmatrix->AutoSetSeedsWithPositions( frameOut, topOut, it - ResZmatrices.begin(), hasPosition )) {
+      if (zmatrix->AutoSetSeedsWithPositions( frameOut, topOut, ires, hasPosition )) {
         mprinterr("Error: Could not set up seed atoms for Zmatrix.\n");
         buildFailed = true;
       } else {
-        mprintf("DEBUG: Zmatrix for building residue %li %s\n", it - ResZmatrices.begin() + 1,
-                topOut.TruncResNameNum(it - ResZmatrices.begin()).c_str());
+        mprintf("DEBUG: Zmatrix for building residue %li %s\n", ires + 1,
+                topOut.TruncResNameNum(ires).c_str());
         zmatrix->print(&topOut);
         zmatrix->SetDebug( 1 ); // DEBUG
         if (zmatrix->SetToFrame( frameOut, hasPosition )) {
           mprinterr("Error: Building residue %s failed.\n",
-                    topOut.TruncResNameNum(it - ResZmatrices.begin()).c_str());
+                    topOut.TruncResNameNum(ires).c_str());
           buildFailed = true;
         }
       }

From 11dc044eea873663c079b2c8756fe686836ab467 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 11 Jan 2024 10:58:24 -0500
Subject: [PATCH 0311/1492] Add some debug info

---
 src/Exec_Build.cpp | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 20c40864ee..7c065c3b38 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -295,6 +295,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
     long int ires = it-ResZmatrices.begin();
     Cpptraj::Structure::Zmatrix* zmatrix = *it;
     if (zmatrix != 0) {
+      mprintf("DEBUG: BUILD residue %li %s\n", ires + 1, topOut.TruncResNameNum(ires).c_str());
       // Update zmatrix seeds
       if (zmatrix->AutoSetSeedsWithPositions( frameOut, topOut, ires, hasPosition )) {
         mprinterr("Error: Could not set up seed atoms for Zmatrix.\n");

From ba1a2691e4573ffcb791c9b10781474dfb2987b7 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 11 Jan 2024 11:12:13 -0500
Subject: [PATCH 0312/1492] Hide some debug info

---
 src/Structure/Zmatrix.cpp | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index c47e55eb15..8d2c74eeae 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -561,12 +561,12 @@ int Zmatrix::addInternalCoordForAtom(int iat, Frame const& frameIn, Topology con
               maxAtk = *kat;
               maxAtl = *lat;
             }
-            mprintf("DEBUG: Potential IC for %s [ %s - %s - %s ] score= %i\n",
-                    topIn.AtomMaskName(iat).c_str(),
-                    topIn.AtomMaskName(*jat).c_str(),
-                    topIn.AtomMaskName(*kat).c_str(),
-                    topIn.AtomMaskName(*lat).c_str(),
-                    nbondScore);
+            //mprintf("DEBUG: Potential IC for %s [ %s - %s - %s ] score= %i\n",
+            //        topIn.AtomMaskName(iat).c_str(),
+            //        topIn.AtomMaskName(*jat).c_str(),
+            //        topIn.AtomMaskName(*kat).c_str(),
+            //        topIn.AtomMaskName(*lat).c_str(),
+            //        nbondScore);
           }
         }
       }

From 125dd0a144209932e764178c458c39b113ca131c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 11 Jan 2024 11:42:26 -0500
Subject: [PATCH 0313/1492] Fix atom offset in debug message, add another debug
 message

---
 src/Structure/Zmatrix.cpp | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index 8d2c74eeae..b6759bd1b0 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -214,6 +214,7 @@ int Zmatrix::autoSetSeeds_withPositions(Frame const& frameIn, Topology const& to
     mprinterr("Internal Error: Zmatrix::autoSetSeeds_withPositions() called with start <= end atom.\n");
     return 1;
   }
+  mprintf("DEBUG: autoSetSeeds_withPositions from atoms %s to %s\n", topIn.AtomMaskName(startAtom).c_str(), topIn.AtomMaskName(endAtom-1).c_str());
   // Special cases
   if (numAtoms == 1) {
     seedAt0_ = startAtom;
@@ -1042,7 +1043,7 @@ int Zmatrix::SetToFrame(Frame& frameOut, Barray& hasPosition) const {
   for (unsigned int icIdx = 0; icIdx != IC_.size(); ++icIdx) {
     if (!isUsed[icIdx] && !hasPosition[IC_[icIdx].AtI()]) {
       remainingPositionsToSet++;
-      mprintf("DEBUG:\t\tAtom %i needs its position set.\n", IC_[icIdx].AtI());
+      mprintf("DEBUG:\t\tAtom %i needs its position set.\n", IC_[icIdx].AtI()+1);
     }
   }
   mprintf("DEBUG: %u positions to set.\n", remainingPositionsToSet);

From 4293dba4bfe5b23704651d5c646e9b550dc7c6d0 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 11 Jan 2024 11:42:57 -0500
Subject: [PATCH 0314/1492] Use TruncResNameOnumId to get original residue
 numbers. Ensure blank build zmatrix inserted when residue does not have a
 template.

---
 src/Exec_Build.cpp | 41 ++++++++++++++++++++++++++---------------
 1 file changed, 26 insertions(+), 15 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 7c065c3b38..c5cef5e957 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -70,7 +70,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
         }
       //}
     }
-    mprintf("DEBUG: Res %s has %i connections.\n", topIn.TruncResNameNum(ires).c_str(), n_connections);
+    mprintf("DEBUG: Res %s has %i connections.\n", topIn.TruncResNameOnumId(ires).c_str(), n_connections);
     if (n_connections == 1) {
       int molnum = topIn[currentRes.FirstAtom()].MolNum();
       molTermResidues[ molnum ].push_back( ires );
@@ -80,9 +80,9 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
   mprintf("DEBUG: Residue connections:\n");
   for (IIarray::const_iterator rit = resConnections.begin(); rit != resConnections.end(); ++rit)
   {
-    mprintf("DEBUG:\t\t%s to", topIn.TruncResNameNum(rit-resConnections.begin()).c_str());
+    mprintf("DEBUG:\t\t%s to", topIn.TruncResNameOnumId(rit-resConnections.begin()).c_str());
     for (Iarray::const_iterator it = rit->begin(); it != rit->end(); ++it)
-      mprintf(" %s", topIn.TruncResNameNum( *it ).c_str());
+      mprintf(" %s", topIn.TruncResNameOnumId( *it ).c_str());
     mprintf("\n");
   }
   // Set residue terminal status
@@ -94,7 +94,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
   {
     mprintf("\t\tMol %li:", mit - molTermResidues.begin() + 1);
     for (Iarray::const_iterator it = mit->begin(); it != mit->end(); ++it) {
-      mprintf(" %s", topIn.TruncResNameNum( *it ).c_str());
+      mprintf(" %s", topIn.TruncResNameOnumId( *it ).c_str());
       if (it == mit->begin())
         residueTerminalStatus[*it] = BEG_TERMINAL;
       else
@@ -115,11 +115,11 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
     Residue const& currentRes = topIn.Res(ires);
     DataSet_Coords* resTemplate = IdTemplateFromName(Templates, currentRes.Name());
     if (resTemplate == 0) {
-      mprintf("Warning: No template found for residue %s\n", topIn.TruncResNameNum(ires).c_str());
+      mprintf("Warning: No template found for residue %s\n", topIn.TruncResNameOnumId(ires).c_str());
       newNatom += currentRes.NumAtoms();
     } else {
       mprintf("\tTemplate %s being used for residue %s\n",
-              resTemplate->legend(), topIn.TruncResNameNum(ires).c_str());
+              resTemplate->legend(), topIn.TruncResNameOnumId(ires).c_str());
       newNatom += resTemplate->Top().Natom();
     }
     ResTemplates.push_back( resTemplate );
@@ -148,8 +148,9 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
   int nRefAtomsMissing = 0;
   for (int ires = 0; ires != topIn.Nres(); ires++)
   {
-    mprintf("\tAdding atoms for residue %s\n", topIn.TruncResNameNum(ires).c_str());
+    mprintf("\tAdding atoms for residue %s\n", topIn.TruncResNameOnumId(ires).c_str());
     int atomOffset = topOut.Natom();
+    mprintf("DEBUG: atom offset is %i\n", atomOffset);
     Residue const& currentRes = topIn.Res(ires);
     DataSet_Coords* resTemplate = ResTemplates[ires];
     // For holding bonded atom pairs
@@ -158,6 +159,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
     IParray intraResBonds;
     if (resTemplate == 0) {
       // No template. Just add the atoms.
+      ResZmatrices.push_back( 0 );
       for (int itgt = currentRes.FirstAtom(); itgt != currentRes.LastAtom(); ++itgt)
       {
         // Track intra-residue bonds
@@ -249,19 +251,24 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
           mprinterr("Error: Could not set up residue template zmatrix.\n");
           return 1;
         }
-        //zmatrix->print( resTemplate->TopPtr() );
+        zmatrix->print( resTemplate->TopPtr() );
         zmatrix->OffsetIcIndices( atomOffset );
         ResZmatrices.push_back( zmatrix );
-        //zmatrix->print( &topOut );
+        zmatrix->print( &topOut );
+        for (Iarray::const_iterator jres = resConnections[ires].begin();
+                                    jres != resConnections[ires].end(); ++jres)
+        {
+          mprintf("DEBUG:\t\tConnected residue %s\n", topIn.TruncResNameOnumId(*jres).c_str());
+        }
       } else
         ResZmatrices.push_back( 0 );
     } // END template exists
     // Add intra-residue bonds
     for (IParray::const_iterator it = intraResBonds.begin(); it != intraResBonds.end(); ++it)
     {
-      mprintf("DEBUG: Intra-res bond: Res %s atom %s to res %s atom %s\n",
-              topOut.TruncResNameNum(topOut[it->first].ResNum()).c_str(), *(topOut[it->first].Name()),
-              topOut.TruncResNameNum(topOut[it->second].ResNum()).c_str(), *(topOut[it->second].Name()));
+      //mprintf("DEBUG: Intra-res bond: Res %s atom %s to res %s atom %s\n",
+      //        topOut.TruncResNameOnumId(topOut[it->first].ResNum()).c_str(), *(topOut[it->first].Name()),
+      //        topOut.TruncResNameOnumId(topOut[it->second].ResNum()).c_str(), *(topOut[it->second].Name()));
       topOut.AddBond(it->first, it->second);
     }
   } // END loop over source residues
@@ -287,6 +294,10 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
     topOut.AddBond(at0, at1);
   }
   mprintf("\t%i template atoms missing in source.\n", nRefAtomsMissing);
+  if (hasPosition.size() != (unsigned int)newNatom) {
+    mprinterr("Internal Error: hasPosition size %zu != newNatom size %i\n", hasPosition.size(), newNatom);
+    return 1;
+  }
 
   // Build using internal coords if needed.
   bool buildFailed = false;
@@ -295,19 +306,19 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
     long int ires = it-ResZmatrices.begin();
     Cpptraj::Structure::Zmatrix* zmatrix = *it;
     if (zmatrix != 0) {
-      mprintf("DEBUG: BUILD residue %li %s\n", ires + 1, topOut.TruncResNameNum(ires).c_str());
+      mprintf("DEBUG: BUILD residue %li %s\n", ires + 1, topOut.TruncResNameOnumId(ires).c_str());
       // Update zmatrix seeds
       if (zmatrix->AutoSetSeedsWithPositions( frameOut, topOut, ires, hasPosition )) {
         mprinterr("Error: Could not set up seed atoms for Zmatrix.\n");
         buildFailed = true;
       } else {
         mprintf("DEBUG: Zmatrix for building residue %li %s\n", ires + 1,
-                topOut.TruncResNameNum(ires).c_str());
+                topOut.TruncResNameOnumId(ires).c_str());
         zmatrix->print(&topOut);
         zmatrix->SetDebug( 1 ); // DEBUG
         if (zmatrix->SetToFrame( frameOut, hasPosition )) {
           mprinterr("Error: Building residue %s failed.\n",
-                    topOut.TruncResNameNum(ires).c_str());
+                    topOut.TruncResNameOnumId(ires).c_str());
           buildFailed = true;
         }
       }

From ce7e96eadaf33ec35e04a6ec470298c1a8dfe5d9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 11 Jan 2024 11:45:17 -0500
Subject: [PATCH 0315/1492] Add a new check

---
 src/Exec_Build.cpp | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index c5cef5e957..6310c4b18c 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -298,6 +298,10 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
     mprinterr("Internal Error: hasPosition size %zu != newNatom size %i\n", hasPosition.size(), newNatom);
     return 1;
   }
+  if (ResZmatrices.size() != (unsigned int)topOut.Nres()) {
+    mprinterr("Internal Error: ResZmatrices size %zu != newNres size %i\n", ResZmatrices.size(), topOut.Nres());
+    return 1;
+  }
 
   // Build using internal coords if needed.
   bool buildFailed = false;

From 57294f1e31e9e609b5d9251c9510871cb34057b1 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 11 Jan 2024 15:30:34 -0500
Subject: [PATCH 0316/1492] Simplify addIc routine. Add routine to generate
 complete list of potential ICs from all possible torsions. Modify SetToFrame
 to deal with multiple potential ICs per atom.

---
 src/Structure/Zmatrix.cpp | 133 ++++++++++++++++++++++++++++++--------
 src/Structure/Zmatrix.h   |   8 ++-
 2 files changed, 111 insertions(+), 30 deletions(-)

diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index b6759bd1b0..14b29f6c2d 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -192,6 +192,10 @@ void Zmatrix::addIc(int at0, int at1, int at2, int at3,
                                 Torsion(xyz0, xyz1, xyz2, xyz3) * Constants::RADDEG) );
 }
 
+void Zmatrix::addIc(int at0, int at1, int at2, int at3, Frame const& frameIn) {
+  addIc(at0, at1, at2, at3, frameIn.XYZ(at0), frameIn.XYZ(at1), frameIn.XYZ(at2), frameIn.XYZ(at3));
+}
+
 /** Set seeds as 3 consecutive atoms from mol 0 for which positions are known. */
 int Zmatrix::AutoSetSeedsWithPositions(Frame const& frameIn, Topology const& topIn, int ires, Barray const& positionKnown)
 {
@@ -436,7 +440,7 @@ int Zmatrix::traceMol(int atL0, int atK0, int atJ0,
     }
     // Create ICs for 1 bond atoms
     for (Iarray::const_iterator atI = OneBondAtoms.begin(); atI != OneBondAtoms.end(); ++atI) {
-      addIc(*atI, atJ, atK, atL, frameIn.XYZ(*atI), frameIn.XYZ(atJ), frameIn.XYZ(atK), frameIn.XYZ(atL));
+      addIc(*atI, atJ, atK, atL, frameIn);
       if (debug_ > 1) {
         mprintf("DEBUG: Added (1 atom) ");
         IC_.back().printIC(topIn);
@@ -463,7 +467,7 @@ int Zmatrix::traceMol(int atL0, int atK0, int atJ0,
                   topIn.AtomMaskName(p.al_).c_str());
         }
         if (!hasIC[p.ai_]) {
-          addIc(p.ai_, p.aj_, p.ak_, p.al_, frameIn.XYZ(p.ai_), frameIn.XYZ(p.aj_), frameIn.XYZ(p.ak_), frameIn.XYZ(p.al_));
+          addIc(p.ai_, p.aj_, p.ak_, p.al_, frameIn);
           if (debug_ > 1) {
             mprintf("DEBUG: Added (stack) ");
             IC_.back().printIC(topIn);
@@ -501,7 +505,7 @@ int Zmatrix::traceMol(int atL0, int atK0, int atJ0,
       }
       // Add lowest index as IC
       if (!hasIC[atI]) {
-        addIc(atI, atJ, atK, atL, frameIn.XYZ(atI), frameIn.XYZ(atJ), frameIn.XYZ(atK), frameIn.XYZ(atL));
+        addIc(atI, atJ, atK, atL, frameIn);
         if (debug_ > 1) {
           mprintf("DEBUG: Added (next) ");
           IC_.back().printIC(topIn);
@@ -576,11 +580,60 @@ int Zmatrix::addInternalCoordForAtom(int iat, Frame const& frameIn, Topology con
   if (maxScore == -1) {
     mprintf("Warning: Unable to define IC for atom %s\n", topIn.AtomMaskName(iat).c_str());
   } else {
-      addIc( iat, maxAtj, maxAtk, maxAtl, frameIn.XYZ(iat), frameIn.XYZ(maxAtj), frameIn.XYZ(maxAtk), frameIn.XYZ(maxAtl) );
+      addIc( iat, maxAtj, maxAtk, maxAtl, frameIn );
   }
   return 0;
 }
 
+/** Set up Zmatrix from Cartesian coordinates and topology.
+  * Use torsions based on bonds to create a complete set of ICs.
+  */
+int Zmatrix::SetFromFrameAndBonds(Frame const& frameIn, Topology const& topIn, int molnum)
+{
+  if (molnum < 0) {
+    mprinterr("Internal Error: Zmatrix::SetFromFrame(): Negative molecule index.\n");
+    return 1;
+  }
+  if (topIn.Nmol() < 1) {
+    mprinterr("Internal Error: Zmatrix::SetFromFrame(): No molecules.\n");
+    return 1;
+  }
+  clear();
+
+  IC_.clear();
+  Molecule const& currentMol = topIn.Mol(molnum);
+
+  for (Unit::const_iterator seg = currentMol.MolUnit().segBegin();
+                            seg != currentMol.MolUnit().segEnd(); ++seg)
+  {
+    for (int iat1 = seg->Begin(); iat1 != seg->End(); ++iat1)
+    {
+      Atom const& At1 = topIn[iat1];
+      for (int bidx1 = 0; bidx1 < At1.Nbonds(); bidx1++) {
+        int iat2 = At1.Bond(bidx1);
+        Atom const& At2 = topIn[iat2];
+        for (int bidx2 = 0; bidx2 < At2.Nbonds(); bidx2++) {
+          int iat3 = At2.Bond(bidx2);
+          if (iat3 != iat1) {
+            Atom const& At3 = topIn[iat3];
+            for (int bidx3 = 0; bidx3 < At3.Nbonds(); bidx3++) {
+              int iat4 = At3.Bond(bidx3);
+              if (iat4 != iat2 && iat1 < iat4) {
+                mprintf("DEBUG: DIHEDRAL  %i - %i - %i - %i (%i %i %i %i)\n", iat1+1, iat2+1, iat3+1, iat4+1, iat1*3, iat2*3, iat3*3, iat4*3);
+                //out.push_back( DihedralType( iat1, iat2, iat3, iat4, -1 ) );
+                addIc(iat1, iat2, iat3, iat4, frameIn);
+                addIc(iat4, iat3, iat2, iat1, frameIn);
+              }
+            }
+          }
+        }
+      }
+    }
+  }
+
+  return 0;
+}
+
 /** Set up Zmatrix from Cartesian coordinates and topology.
   * This algorithm attempts to "trace" the molecule in a manner that
   * should make internal coordinate assignment more "natural".
@@ -663,7 +716,7 @@ int Zmatrix::SetFromFrame_Trace(Frame const& frameIn, Topology const& topIn, int
           //     I
           //     |
           // L - K - J
-          addIc(*bat, seedAt2_, seedAt1_, seedAt0_, frameIn.XYZ(*bat), frameIn.XYZ(seedAt2_), frameIn.XYZ(seedAt1_), frameIn.XYZ(seedAt0_));
+          addIc(*bat, seedAt2_, seedAt1_, seedAt0_, frameIn);
           MARK(*bat, hasIC, nHasIC);
           // Follow improper branch if needed: L - K - I - ?
           if (traceMol(seedAt0_, seedAt1_, *bat, frameIn, topIn, maxnatom, nHasIC, hasIC)) return 1;
@@ -676,7 +729,7 @@ int Zmatrix::SetFromFrame_Trace(Frame const& frameIn, Topology const& topIn, int
     mprintf("Warning: Not all atoms have an associated internal coordinate.\n");
   }
   // Add ICs for seeds
-  if (maxnatom > 3) {
+  /*if (maxnatom > 3) {
     //Atom const& SA0 = topIn[seedAt0_];
     //Atom const& SA1 = topIn[seedAt1_];
     //Atom const& SA2 = topIn[seedAt2_];
@@ -684,19 +737,7 @@ int Zmatrix::SetFromFrame_Trace(Frame const& frameIn, Topology const& topIn, int
     addInternalCoordForAtom(seedAt0_, frameIn, topIn);
     addInternalCoordForAtom(seedAt1_, frameIn, topIn);
     addInternalCoordForAtom(seedAt2_, frameIn, topIn);
-/*    if (SA2.Nbonds() < 2)
-      mprintf("Warning: Third seed atom has only one bond. Cannot create full IC for seed 0.\n");
-    else {
-      int at3;
-      for (Atom::bond_iterator bat = SA2.bondbegin(); bat != SA2.bondend(); ++bat) {
-        if (*bat != seedAt1_ && *bat != seedAt0_) {
-          at3 = *bat;
-          break;
-        }
-      }
-      addIc( seedAt0_, seedAt1_, seedAt2_, at3, frameIn.XYZ(seedAt0_), frameIn.XYZ(seedAt1_), frameIn.XYZ(seedAt2_), frameIn.XYZ(at3) );
-    }*/
-  }
+  }*/
   return 0;
 }
 
@@ -1039,16 +1080,45 @@ int Zmatrix::SetToFrame(Frame& frameOut, Barray& hasPosition) const {
 //  if (debug_ > 0) mprintf("DEBUG: Lowest unused IC: %u\n", lowestUnusedIC+1);
 
   // Out of the remaining ICs, count which ones do not have positions set.
-  unsigned int remainingPositionsToSet = 0;
+  Iarray positionsToSet;
+  //unsigned int remainingPositionsToSet = 0;
   for (unsigned int icIdx = 0; icIdx != IC_.size(); ++icIdx) {
     if (!isUsed[icIdx] && !hasPosition[IC_[icIdx].AtI()]) {
-      remainingPositionsToSet++;
-      mprintf("DEBUG:\t\tAtom %i needs its position set.\n", IC_[icIdx].AtI()+1);
+      Iarray::const_iterator it = std::find(positionsToSet.begin(), positionsToSet.end(), IC_[icIdx].AtI());
+      if (it == positionsToSet.end()) {
+        positionsToSet.push_back( IC_[icIdx].AtI() );
+        mprintf("DEBUG:\t\tAtom %i needs its position set.\n", IC_[icIdx].AtI()+1);
+      }
     }
   }
-  mprintf("DEBUG: %u positions to set.\n", remainingPositionsToSet);
+  mprintf("DEBUG: %zu positions to set.\n", positionsToSet.size());
 
-  while (remainingPositionsToSet > 0 && Nused < IC_.size()) {
+  //while (remainingPositionsToSet > 0 && Nused < IC_.size()) {
+  Iarray::const_iterator at_with_unset_pos = positionsToSet.begin();
+  while (Nused < IC_.size()) {
+    // Get next atom that needs its position set
+    for (; at_with_unset_pos != positionsToSet.end(); ++at_with_unset_pos)
+      if (!hasPosition[*at_with_unset_pos]) break;
+    if (at_with_unset_pos == positionsToSet.end()) {
+      mprintf("DEBUG: No more positions to set.\n");
+      break;
+    }
+    mprintf("DEBUG: Setting position of atom %i\n", (*at_with_unset_pos) + 1);
+    // Get IC that corresponds to this atom
+    int icIdx = -1;
+    for (unsigned int idx = 0; idx != IC_.size(); ++idx) {
+      if (IC_[idx].AtI() == *at_with_unset_pos) {
+        // All 3 of the connecting atoms must be set
+        if (hasPosition[ IC_[idx].AtJ() ] &&
+            hasPosition[ IC_[idx].AtK() ] &&
+            hasPosition[ IC_[idx].AtL() ])
+        {
+          icIdx = (int)idx;
+          break;
+        }
+      }
+    }
+/*
     // Get the next IC with a position to set
     int icIdx = -1;
     for (unsigned int idx = 0; idx != IC_.size(); ++idx) {
@@ -1064,10 +1134,15 @@ int Zmatrix::SetToFrame(Frame& frameOut, Barray& hasPosition) const {
           mprintf("DEBUG:\t\tIC %u is missing atoms.\n", idx+1);
         }
       }
-    }
+    }*/
     if (icIdx < 0) {
-      mprinterr("Error: Could not find next IC to use.\n");
-      return 1;
+      mprintf("DEBUG: Could not find complete IC yet.\n");
+      ++at_with_unset_pos;
+      if (at_with_unset_pos == positionsToSet.end()) {
+        mprinterr("Error: Could not find next IC to use.\n");
+        return 1;
+      }
+      continue; // FIXME
     }
     if (debug_ > 0) mprintf("DEBUG: Next IC to use is %i\n", icIdx+1);
     InternalCoords const& ic = IC_[icIdx];
@@ -1075,8 +1150,10 @@ int Zmatrix::SetToFrame(Frame& frameOut, Barray& hasPosition) const {
 
     frameOut.SetXYZ( ic.AtI(), posI );
     hasPosition[ ic.AtI() ] = true;
-    remainingPositionsToSet--;
+    //remainingPositionsToSet--;
     MARK(icIdx, isUsed, Nused);
+    // Go back to start, new ICs may now be enabled
+    at_with_unset_pos = positionsToSet.begin();
   } // END loop over remaining positions
 /*
   // Loop over remaining ICs 
diff --git a/src/Structure/Zmatrix.h b/src/Structure/Zmatrix.h
index f177758dad..3fbbf56f95 100644
--- a/src/Structure/Zmatrix.h
+++ b/src/Structure/Zmatrix.h
@@ -38,9 +38,11 @@ class Zmatrix {
 
     /// Set seed atoms from frame/top
     int SetSeedPositions(Frame const&, Topology const&, int, int, int);
-    /// Set seed atoms as 3 consecutive atoms with known positions for specified residue # 
+    /// Set seed atoms as 3 consecutive atoms with known positions for specified residue # TODO deprecate?
     int AutoSetSeedsWithPositions(Frame const&, Topology const&, int, Barray const&);
 
+    /// Try to generate complete ICs from bonds
+    int SetFromFrameAndBonds(Frame const&, Topology const&, int);
     /// Convert specifed molecule of Frame/Topology to internal coordinates array
     int SetFromFrame(Frame const&, Topology const&, int);
     /// Convert molecule 0 of Frame/Topology to internal coordinates array
@@ -78,7 +80,9 @@ class Zmatrix {
     /// Simple version of auto set seeds based on connectivity only
     int autoSetSeeds_simple(Frame const&, Topology const&, Molecule const&);
     /// Calculate and add an internal coordinate given indices and Cartesian coords.
-    void addIc(int,int,int,int,const double*,const double*,const double*,const double*);
+    inline void addIc(int,int,int,int,const double*,const double*,const double*,const double*);
+    /// Calculate and add an internal coordinate given indices and Cartesian coords.
+    inline void addIc(int,int,int,int,Frame const&);
     /// Add internal coordinates by tracing a molecule
     int traceMol(int, int, int, Frame const&, Topology const&, unsigned int, unsigned int&, Barray&);
     /// Add internal coordinate for given atom

From e65d3144da5f66b84ec62d6349dc92c62d222836 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 11 Jan 2024 15:33:35 -0500
Subject: [PATCH 0317/1492] Set zmatrix from bonds/torsions. Do not bother
 setting seeds

---
 src/Exec_Build.cpp | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 6310c4b18c..aeb7e99c1c 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -247,7 +247,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
         Frame templateFrame = resTemplate->AllocateFrame();
         resTemplate->GetFrame( 0, templateFrame );
         Cpptraj::Structure::Zmatrix* zmatrix = new Cpptraj::Structure::Zmatrix();
-        if (zmatrix->SetFromFrame( templateFrame, resTemplate->Top(), 0 )) {
+        if (zmatrix->SetFromFrameAndBonds( templateFrame, resTemplate->Top(), 0 )) {
           mprinterr("Error: Could not set up residue template zmatrix.\n");
           return 1;
         }
@@ -312,10 +312,10 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
     if (zmatrix != 0) {
       mprintf("DEBUG: BUILD residue %li %s\n", ires + 1, topOut.TruncResNameOnumId(ires).c_str());
       // Update zmatrix seeds
-      if (zmatrix->AutoSetSeedsWithPositions( frameOut, topOut, ires, hasPosition )) {
-        mprinterr("Error: Could not set up seed atoms for Zmatrix.\n");
-        buildFailed = true;
-      } else {
+      //if (zmatrix->AutoSetSeedsWithPositions( frameOut, topOut, ires, hasPosition )) {
+      //  mprinterr("Error: Could not set up seed atoms for Zmatrix.\n");
+      //  buildFailed = true;
+      //} else {
         mprintf("DEBUG: Zmatrix for building residue %li %s\n", ires + 1,
                 topOut.TruncResNameOnumId(ires).c_str());
         zmatrix->print(&topOut);
@@ -325,7 +325,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
                     topOut.TruncResNameOnumId(ires).c_str());
           buildFailed = true;
         }
-      }
+      //}
     }
   }
 

From 413a040ae4447fca45b98a6a092eda19f6c91515 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 12 Jan 2024 09:08:53 -0500
Subject: [PATCH 0318/1492] Protect against invalid NB params in amber topology

---
 src/Parm_Amber.cpp | 18 +++++++++++++++---
 src/Parm_Amber.h   |  2 ++
 2 files changed, 17 insertions(+), 3 deletions(-)

diff --git a/src/Parm_Amber.cpp b/src/Parm_Amber.cpp
index 9552a3e141..40b8d68ea1 100644
--- a/src/Parm_Amber.cpp
+++ b/src/Parm_Amber.cpp
@@ -167,7 +167,8 @@ Parm_Amber::Parm_Amber() :
   N_impTerms_(0),
   writeChamber_(true),
   writeEmptyArrays_(false),
-  writePdbInfo_(true)
+  writePdbInfo_(true),
+  has_valid_nonbond_params_(true)
 {
   UB_count_[0] = 0;
   UB_count_[1] = 0;
@@ -248,6 +249,11 @@ int Parm_Amber::ReadParm(FileName const& fname, Topology& TopIn ) {
   else
     err = ReadNewParm( TopIn );
   if (err != 0) return 1;
+  // If nonbond info is invalid, clear it
+  if (!has_valid_nonbond_params_) {
+    mprintf("Warning: Topology '%s' has invalid nonbond parameters. Clearing.\n", fname.full());
+    TopIn.SetNonbond().Clear();
+  }
   // Determine Atom elements
   if (atomicNums_.empty()) {
     mprintf("\tThis Amber topology does not include atomic numbers.\n"
@@ -737,8 +743,14 @@ int Parm_Amber::ReadAtomicMass(Topology& TopIn, FortranData const& FMT) {
   */
 int Parm_Amber::ReadAtomTypeIndex(Topology& TopIn, FortranData const& FMT) {
   if (SetupBuffer(F_ATYPEIDX, values_[NATOM], FMT)) return 1;
-  for (int idx = 0; idx != values_[NATOM]; idx++)
-    TopIn.SetAtom(idx).SetTypeIndex( atoi(file_.NextElement()) - 1 );
+  for (int idx = 0; idx != values_[NATOM]; idx++) {
+    int atypeIdx = atoi(file_.NextElement());
+    if (atypeIdx < 1) {
+      mprintf("Warning: Bad atom type index < 1 (%i) for atom %i\n", atypeIdx, idx+1);
+      has_valid_nonbond_params_ = false;
+    }
+    TopIn.SetAtom(idx).SetTypeIndex( atypeIdx - 1 );
+  }
   return 0;
 }
 
diff --git a/src/Parm_Amber.h b/src/Parm_Amber.h
index 7a6332ac4d..443fe1a2c1 100644
--- a/src/Parm_Amber.h
+++ b/src/Parm_Amber.h
@@ -191,6 +191,8 @@ class Parm_Amber : public ParmIO {
     bool writeChamber_;     ///< If true write CHAMBER info
     bool writeEmptyArrays_; ///< If true try to write TREE, IROTATE, JOIN even if not present 
     bool writePdbInfo_;     ///< If true write chain IDs etc
+
+    bool has_valid_nonbond_params_; ///< Will set to false if invalid nonbonds detected on read
 };
 // -----------------------------------------------------------------------------
 class Parm_Amber::FortranData {

From 538ac941ee1cc57ee7f10147420d2a74806cb145 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 12 Jan 2024 09:31:31 -0500
Subject: [PATCH 0319/1492] Do not rely on connectivity to determine terminal
 status, may not be accurate, especially for PDBs

---
 src/Exec_Build.cpp | 51 ++++++++++++++++++++++++++++++++++------------
 1 file changed, 38 insertions(+), 13 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index aeb7e99c1c..19916768dc 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -48,10 +48,14 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
                                        Carray const& Templates,
                                        Topology const& topIn, Frame const& frameIn)
 {
-  typedef std::vector<int> Iarray;
-  typedef std::vector<Iarray> IIarray;
-  // Determine which residues are terminal
-  IIarray molTermResidues( topIn.Nmol() );
+  // Residue terminal status
+  enum TermType { BEG_TERMINAL = 0, REGULAR, END_TERMINAL };
+
+  // Track which residues are terminal
+  //typedef std::vector<int> Iarray;
+  //typedef std::vector<Iarray> IIarray;
+  //IIarray molTermResidues;
+/*
   // Track residue connections
   IIarray resConnections( topIn.Nres() );
   for (int ires = 0; ires != topIn.Nres(); ires++)
@@ -85,8 +89,6 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
       mprintf(" %s", topIn.TruncResNameOnumId( *it ).c_str());
     mprintf("\n");
   }
-  // Set residue terminal status
-  enum TermType { BEG_TERMINAL = 0, REGULAR, END_TERMINAL };
   typedef std::vector<TermType> Tarray;
   Tarray residueTerminalStatus( topIn.Nres(), REGULAR );
   mprintf("\tTerminal residues:\n");
@@ -103,7 +105,8 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
     }
     mprintf("\n");
   }
-
+*/
+  // -----------------------------------
   // Array of templates for each residue
   std::vector<DataSet_Coords*> ResTemplates;
   ResTemplates.reserve( topIn.Nres() );
@@ -111,8 +114,26 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
   int newNatom = 0;
   for (int ires = 0; ires != topIn.Nres(); ires++)
   {
-    // Identify a template based on the residue name.
     Residue const& currentRes = topIn.Res(ires);
+    mprintf("DEBUG: ---------- Processing Residue %s ---------- \n", topIn.TruncResNameNum(ires).c_str());
+    int pres = ires - 1;
+    int nres = ires + 1;
+    // Determine if this is a terminal residue
+    TermType resTermType;
+    if (ires == 0 && topIn.Nres() > 1) {
+      resTermType = BEG_TERMINAL;
+    } else if (currentRes.IsTerminal()) {
+      resTermType = END_TERMINAL;
+    } else if (pres > -1 && topIn.Res(pres).IsTerminal()) {
+      resTermType = BEG_TERMINAL;
+    } else if (nres < topIn.Nres() && topIn.Res(nres).ChainId() != currentRes.ChainId()) {
+      resTermType = END_TERMINAL;
+    } else {
+      resTermType = REGULAR;
+    }
+    static const char* TermTypeStr[] = { "Begin", "Regular", "End" };
+    mprintf("DEBUG: Residue type: %s\n", TermTypeStr[resTermType]);
+    // Identify a template based on the residue name.
     DataSet_Coords* resTemplate = IdTemplateFromName(Templates, currentRes.Name());
     if (resTemplate == 0) {
       mprintf("Warning: No template found for residue %s\n", topIn.TruncResNameOnumId(ires).c_str());
@@ -129,6 +150,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
   // Clear frame so that AddXYZ can be used
   frameOut.ClearAtoms();
 
+  // -----------------------------------
   // hasPosition - for each atom in topOut, status on whether atom in frameOut needs building
   Cpptraj::Structure::Zmatrix::Barray hasPosition;
   hasPosition.reserve( newNatom );
@@ -255,11 +277,11 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
         zmatrix->OffsetIcIndices( atomOffset );
         ResZmatrices.push_back( zmatrix );
         zmatrix->print( &topOut );
-        for (Iarray::const_iterator jres = resConnections[ires].begin();
-                                    jres != resConnections[ires].end(); ++jres)
-        {
-          mprintf("DEBUG:\t\tConnected residue %s\n", topIn.TruncResNameOnumId(*jres).c_str());
-        }
+        //for (Iarray::const_iterator jres = resConnections[ires].begin();
+        //                            jres != resConnections[ires].end(); ++jres)
+        //{
+        //  mprintf("DEBUG:\t\tConnected residue %s\n", topIn.TruncResNameOnumId(*jres).c_str());
+        //}
       } else
         ResZmatrices.push_back( 0 );
     } // END template exists
@@ -272,6 +294,8 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
       topOut.AddBond(it->first, it->second);
     }
   } // END loop over source residues
+
+  // -----------------------------------
   // Add inter-residue bonds
   for (ResAtArray::const_iterator it = interResBonds.begin(); it != interResBonds.end(); ++it)
   {
@@ -303,6 +327,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
     return 1;
   }
 
+  // -----------------------------------
   // Build using internal coords if needed.
   bool buildFailed = false;
   for (Zarray::const_iterator it = ResZmatrices.begin(); it != ResZmatrices.end(); ++it)

From 12f295655472aa997f080e07cd2c3e18180bb2b3 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 12 Jan 2024 09:57:25 -0500
Subject: [PATCH 0320/1492] Read hybridizations from addAtomTypes

---
 src/DataIO_LeapRC.cpp | 70 +++++++++++++++++++++++++++++++++++++++++++
 src/DataIO_LeapRC.h   |  5 ++++
 2 files changed, 75 insertions(+)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 3ee24cd38e..ee56fafad6 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -94,6 +94,73 @@ int DataIO_LeapRC::LoadAmberPrep(std::string const& filename, DataSetList& dsl,
   return 0;
 }
 
+/** LEaP addAtomTypes command. */
+int DataIO_LeapRC::AddAtomTypes(NHarrayType& atomHybridizations, BufferedLine& infile)
+const
+{
+  int bracketCount = 0;
+  // First line should contain the command
+  const char* line = infile.CurrentLine();
+  while (line != 0) {
+    // Process the line
+    std::string tmp;
+    for (const char* ptr = line; *ptr != '\0'; ++ptr)
+    {
+      if (*ptr == '{')
+        bracketCount++;
+      else if (*ptr == '}') {
+        bracketCount--;
+        if (bracketCount == 1) {
+          mprintf("DEBUG: addAtomTypes: %s\n", tmp.c_str());
+          ArgList aline( tmp );
+          // Some entries (like LP and EP) are not required to have elements.
+          // Set the hybridization index to 1 or 2.
+          int hidx;
+          if (aline.Nargs() == 3)
+            hidx = 2;
+          else if (aline.Nargs() == 2)
+            hidx = 1;
+          else {
+            mprinterr("Error: Malformed addAtomTypes entry %s\n", tmp.c_str());
+            return 1;
+          }
+          AtomType::HybridizationType ht;
+          if (aline[hidx] == "sp3")
+            ht = AtomType::SP3;
+          else if (aline[hidx] == "sp2")
+            ht = AtomType::SP2;
+          else if (aline[hidx] == "sp")
+            ht = AtomType::SP;
+          else {
+            mprintf("Warning: Unknown hybridization in addAtomTypes entry %s\n", tmp.c_str());
+            ht = AtomType::UNKNOWN_HYBRIDIZATION;
+          }
+          atomHybridizations.push_back( NHpairType(aline[0], ht) );
+          tmp.clear();
+        }
+      } else {
+        if (bracketCount == 2)
+          tmp += *ptr;
+      }
+    }
+    if (bracketCount < 0) {
+      mprinterr("Error: Too many close brackets '}' in addAtomTypes command.\n");
+      return 1;
+    } else if (bracketCount == 0) {
+      break;
+    } //else {
+      //mprintf("DEBUG: addAtomTypes: %s\n", tmp.c_str());
+    //}
+    line = infile.Line();
+  }
+  if (bracketCount != 0) {
+    mprinterr("Error: Not enough close brackets '}' in addAtomTypes command.\n");
+    return 1;
+  }
+  mprintf("\tRead %zu atom hybridizations.\n", atomHybridizations.size());
+  return 0;
+}
+
 // DataIO_LeapRC::ReadData()
 int DataIO_LeapRC::ReadData(FileName const& fname, DataSetList& dsl, std::string const& dsname)
 {
@@ -117,6 +184,7 @@ int DataIO_LeapRC::ReadData(FileName const& fname, DataSetList& dsl, std::string
     mprinterr("Error: Could not open leaprc file '%s'\n", fname.full());
     return 1;
   }
+  NHarrayType atomHybridizations;
   int err = 0;
   const char* ptr = infile.Line();
   while (ptr != 0) {
@@ -135,6 +203,8 @@ int DataIO_LeapRC::ReadData(FileName const& fname, DataSetList& dsl, std::string
         err = LoadAmberPrep( line.GetStringKey("loadAmberPrep"), dsl, dsname );
       else if (line.Contains("loadamberprep"))
         err = LoadAmberPrep( line.GetStringKey("loadamberprep"), dsl, dsname );
+      else if (line.Contains("addAtomTypes") || line.Contains("addatomtypes"))
+        err = AddAtomTypes(atomHybridizations, infile);
     }
     if (err != 0) break;
     ptr = infile.Line();
diff --git a/src/DataIO_LeapRC.h b/src/DataIO_LeapRC.h
index 8a3aff3fb2..ca6cec6f26 100644
--- a/src/DataIO_LeapRC.h
+++ b/src/DataIO_LeapRC.h
@@ -1,6 +1,7 @@
 #ifndef INC_DATAIO_LEAPRC_H
 #define INC_DATAIO_LEAPRC_H
 #include "DataIO.h"
+class BufferedLine;
 /// Read parameters and units from a leap rc file 
 class DataIO_LeapRC : public DataIO {
   public:
@@ -14,9 +15,13 @@ class DataIO_LeapRC : public DataIO {
     int WriteData(FileName const&, DataSetList const&);
     bool ID_DataFormat(CpptrajFile&);
   private:
+    typedef std::pair<NameType, AtomType::HybridizationType> NHpairType;
+    typedef std::vector<NHpairType> NHarrayType;
+
     int LoadAmberParams(std::string const&, DataSetList&, std::string const&) const;
     int LoadOFF(std::string const&, DataSetList&, std::string const&) const;
     int LoadAmberPrep(std::string const&, DataSetList&, std::string const&) const;
+    int AddAtomTypes(NHarrayType&, BufferedLine&) const;
 
     std::string amberhome_;
 };

From 6dd85623bed00a0f5cc21444b4fac9ce774f525f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 12 Jan 2024 10:17:25 -0500
Subject: [PATCH 0321/1492] Handle duplicate types.

---
 src/DataIO_LeapRC.cpp | 14 +++++++++++++-
 src/DataIO_LeapRC.h   |  3 ++-
 2 files changed, 15 insertions(+), 2 deletions(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index ee56fafad6..dd4449b6c8 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -135,7 +135,19 @@ const
             mprintf("Warning: Unknown hybridization in addAtomTypes entry %s\n", tmp.c_str());
             ht = AtomType::UNKNOWN_HYBRIDIZATION;
           }
-          atomHybridizations.push_back( NHpairType(aline[0], ht) );
+          NameType atype(aline[0]);
+          NHarrayType::iterator it = atomHybridizations.lower_bound( atype );
+          if (it == atomHybridizations.end() || it->first != atype) {
+            it = atomHybridizations.insert( it, NHpairType(atype, ht) );
+          } else {
+            mprintf("Warning: Duplicate entry for '%s' in addAtomTypes.", *atype);
+            if (it->second != ht) {
+              mprintf(" Overwriting.\n");
+              mprintf("Warning: Line is %s\n", tmp.c_str());
+              it->second = ht;
+            } else
+              mprintf("\n");
+          }
           tmp.clear();
         }
       } else {
diff --git a/src/DataIO_LeapRC.h b/src/DataIO_LeapRC.h
index ca6cec6f26..e93972e11e 100644
--- a/src/DataIO_LeapRC.h
+++ b/src/DataIO_LeapRC.h
@@ -1,6 +1,7 @@
 #ifndef INC_DATAIO_LEAPRC_H
 #define INC_DATAIO_LEAPRC_H
 #include "DataIO.h"
+#include <map>
 class BufferedLine;
 /// Read parameters and units from a leap rc file 
 class DataIO_LeapRC : public DataIO {
@@ -16,7 +17,7 @@ class DataIO_LeapRC : public DataIO {
     bool ID_DataFormat(CpptrajFile&);
   private:
     typedef std::pair<NameType, AtomType::HybridizationType> NHpairType;
-    typedef std::vector<NHpairType> NHarrayType;
+    typedef std::map<NameType, AtomType::HybridizationType> NHarrayType;
 
     int LoadAmberParams(std::string const&, DataSetList&, std::string const&) const;
     int LoadOFF(std::string const&, DataSetList&, std::string const&) const;

From aeb5ef8b5ee94775ee859b5611b94340205ed2c9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 12 Jan 2024 13:03:06 -0500
Subject: [PATCH 0322/1492] Load param/unit sets into separate datasetlists
 before adding to main

---
 src/DataIO_LeapRC.cpp | 36 ++++++++++++++++++++++++++++++------
 1 file changed, 30 insertions(+), 6 deletions(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index dd4449b6c8..3f10f08e00 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -173,6 +173,22 @@ const
   return 0;
 }
 
+/// Move sets from paramDSL to dsl
+static inline int addSetsToList(DataSetList& dsl, DataSetList& paramDSL)
+{
+  // Add data sets to the main data set list
+  for (DataSetList::const_iterator ds = paramDSL.begin(); ds != paramDSL.end(); ++ds) {
+    DataSet* dtmp = dsl.CheckForSet( (*ds)->Meta() );
+    if (dtmp != 0) {
+      mprinterr("Error: Set '%s' already exists.\n", (*ds)->legend());
+      return 1;
+    }
+    dsl.AddSet( *ds );
+  }
+  paramDSL.SetHasCopies( true );
+  return 0;
+}
+
 // DataIO_LeapRC::ReadData()
 int DataIO_LeapRC::ReadData(FileName const& fname, DataSetList& dsl, std::string const& dsname)
 {
@@ -196,6 +212,8 @@ int DataIO_LeapRC::ReadData(FileName const& fname, DataSetList& dsl, std::string
     mprinterr("Error: Could not open leaprc file '%s'\n", fname.full());
     return 1;
   }
+  DataSetList paramDSL;
+  DataSetList unitDSL;
   NHarrayType atomHybridizations;
   int err = 0;
   const char* ptr = infile.Line();
@@ -204,17 +222,17 @@ int DataIO_LeapRC::ReadData(FileName const& fname, DataSetList& dsl, std::string
       ArgList line( ptr, " \t" );
       std::string param_fname;
       if (line.Contains("loadAmberParams"))
-        err = LoadAmberParams( line.GetStringKey("loadAmberParams"), dsl, dsname );
+        err = LoadAmberParams( line.GetStringKey("loadAmberParams"), paramDSL, dsname );
       else if (line.Contains("loadamberparams"))
-        err = LoadAmberParams( line.GetStringKey("loadamberparams"), dsl, dsname );
+        err = LoadAmberParams( line.GetStringKey("loadamberparams"), paramDSL, dsname );
       else if (line.Contains("loadOff"))
-        err = LoadOFF( line.GetStringKey("loadOff"), dsl, dsname );
+        err = LoadOFF( line.GetStringKey("loadOff"), unitDSL, dsname );
       else if (line.Contains("loadoff"))
-        err = LoadOFF( line.GetStringKey("loadoff"), dsl, dsname );
+        err = LoadOFF( line.GetStringKey("loadoff"), unitDSL, dsname );
       else if (line.Contains("loadAmberPrep"))
-        err = LoadAmberPrep( line.GetStringKey("loadAmberPrep"), dsl, dsname );
+        err = LoadAmberPrep( line.GetStringKey("loadAmberPrep"), unitDSL, dsname );
       else if (line.Contains("loadamberprep"))
-        err = LoadAmberPrep( line.GetStringKey("loadamberprep"), dsl, dsname );
+        err = LoadAmberPrep( line.GetStringKey("loadamberprep"), unitDSL, dsname );
       else if (line.Contains("addAtomTypes") || line.Contains("addatomtypes"))
         err = AddAtomTypes(atomHybridizations, infile);
     }
@@ -222,6 +240,12 @@ int DataIO_LeapRC::ReadData(FileName const& fname, DataSetList& dsl, std::string
     ptr = infile.Line();
   }
   infile.CloseFile();
+
+  // Add data sets to the main data set list
+  if (addSetsToList(dsl, paramDSL)) return err+1;
+
+  if (addSetsToList(dsl, unitDSL)) return err+1;
+
   return err;
 }
 

From 115c7192d852eb7d44a26b880770cd27d2ba8d6b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 12 Jan 2024 14:26:40 -0500
Subject: [PATCH 0323/1492] Set atom hybridizations from leap rc file

---
 src/AtomType.h        |  2 ++
 src/DataIO_LeapRC.cpp | 19 +++++++++++++++++++
 2 files changed, 21 insertions(+)

diff --git a/src/AtomType.h b/src/AtomType.h
index 0af047fc74..7ac4295c71 100644
--- a/src/AtomType.h
+++ b/src/AtomType.h
@@ -46,6 +46,8 @@ class AtomType {
     }
     /// Used to modify LJ params
     LJparmType& SetLJ() { return lj_; }
+    /// Set atom hybridization
+    void SetHybridization(HybridizationType h) { hybrid_ = h; }
     /// \return data size  (2 double for LJparmType)
     static size_t DataSize() { return (4*sizeof(double)) + sizeof(int); }
   private:
diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 3f10f08e00..d95594d8bc 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -5,6 +5,7 @@
 #include "DataIO_AmberFrcmod.h"
 #include "DataIO_AmberLib.h"
 #include "DataIO_AmberPrep.h"
+#include "DataSet_Parameters.h"
 #include <cstdlib> //getenv
 
 /// CONSTRUCTOR
@@ -241,6 +242,24 @@ int DataIO_LeapRC::ReadData(FileName const& fname, DataSetList& dsl, std::string
   }
   infile.CloseFile();
 
+  // Update hybridizations for parameter atom types
+  for (DataSetList::const_iterator ds = paramDSL.begin(); ds != paramDSL.end(); ++ds)
+  {
+    if ( (*ds)->Type() == DataSet::PARAMETERS ) {
+      DataSet_Parameters& param = static_cast<DataSet_Parameters&>( *(*ds) );
+      mprintf("\tUpdating atom hybridizations in set %s\n", param.legend());
+      for (ParmHolder<AtomType>::iterator it = param.AT().begin();
+                                          it != param.AT().end(); ++it)
+      {
+        NHarrayType::const_iterator ah = atomHybridizations.find( it->first[0] );
+        if (ah == atomHybridizations.end())
+          mprintf("Warning: No hybridization set for atom type '%s'\n", *(it->first[0]));
+        else
+          it->second.SetHybridization( ah->second );
+      }
+    }
+  }
+
   // Add data sets to the main data set list
   if (addSetsToList(dsl, paramDSL)) return err+1;
 

From 86717d23f249668e7e916b7b892e4c662b1073aa Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 12 Jan 2024 15:01:47 -0500
Subject: [PATCH 0324/1492] Start addpdbresmap command support

---
 src/DataIO_LeapRC.cpp | 45 +++++++++++++++++++++++++++++++++++++++++++
 src/DataIO_LeapRC.h   |  1 +
 2 files changed, 46 insertions(+)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index d95594d8bc..6b511f3c59 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -174,6 +174,49 @@ const
   return 0;
 }
 
+/** LEaP addPdbResMap command. */
+int DataIO_LeapRC::AddPdbResMap(BufferedLine& infile)
+const
+{
+  int bracketCount = 0;
+  // First line should contain the command
+  const char* line = infile.CurrentLine();
+  while (line != 0) {
+    // Process the line
+    std::string tmp;
+    for (const char* ptr = line; *ptr != '\0'; ++ptr)
+    {
+      if (*ptr == '{')
+        bracketCount++;
+      else if (*ptr == '}') {
+        bracketCount--;
+        if (bracketCount == 1) {
+          mprintf("DEBUG: addPdbResMap: %s\n", tmp.c_str());
+          ArgList aline( tmp );
+          tmp.clear();
+        }
+      } else {
+        if (bracketCount == 2)
+          tmp += *ptr;
+      }
+    }
+    if (bracketCount < 0) {
+      mprinterr("Error: Too many close brackets '}' in addPdbResMap command.\n");
+      return 1;
+    } else if (bracketCount == 0) {
+      break;
+    } //else {
+      //mprintf("DEBUG: addPdbResMap: %s\n", tmp.c_str());
+    //}
+    line = infile.Line();
+  }
+  if (bracketCount != 0) {
+    mprinterr("Error: Not enough close brackets '}' in addPdbResMap command.\n");
+    return 1;
+  }
+  return 0;
+}
+
 /// Move sets from paramDSL to dsl
 static inline int addSetsToList(DataSetList& dsl, DataSetList& paramDSL)
 {
@@ -236,6 +279,8 @@ int DataIO_LeapRC::ReadData(FileName const& fname, DataSetList& dsl, std::string
         err = LoadAmberPrep( line.GetStringKey("loadamberprep"), unitDSL, dsname );
       else if (line.Contains("addAtomTypes") || line.Contains("addatomtypes"))
         err = AddAtomTypes(atomHybridizations, infile);
+      else if (line.Contains("addPdbResMap") || line.Contains("addpdbresmap"))
+        err = AddPdbResMap(infile);
     }
     if (err != 0) break;
     ptr = infile.Line();
diff --git a/src/DataIO_LeapRC.h b/src/DataIO_LeapRC.h
index e93972e11e..06e95135a1 100644
--- a/src/DataIO_LeapRC.h
+++ b/src/DataIO_LeapRC.h
@@ -23,6 +23,7 @@ class DataIO_LeapRC : public DataIO {
     int LoadOFF(std::string const&, DataSetList&, std::string const&) const;
     int LoadAmberPrep(std::string const&, DataSetList&, std::string const&) const;
     int AddAtomTypes(NHarrayType&, BufferedLine&) const;
+    int AddPdbResMap(BufferedLine&) const;
 
     std::string amberhome_;
 };

From 262a0c3620998f6849bedf847ab0c8262886ac26 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 12 Jan 2024 15:24:32 -0500
Subject: [PATCH 0325/1492] Move terminal type to Structure namespace

---
 src/Exec_Build.cpp              | 18 ++++++++----------
 src/Structure/StructureEnum.cpp | 10 ++++++++++
 src/Structure/StructureEnum.h   |  5 +++++
 3 files changed, 23 insertions(+), 10 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 19916768dc..3fd57358fe 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -49,8 +49,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
                                        Topology const& topIn, Frame const& frameIn)
 {
   // Residue terminal status
-  enum TermType { BEG_TERMINAL = 0, REGULAR, END_TERMINAL };
-
+  
   // Track which residues are terminal
   //typedef std::vector<int> Iarray;
   //typedef std::vector<Iarray> IIarray;
@@ -119,20 +118,19 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
     int pres = ires - 1;
     int nres = ires + 1;
     // Determine if this is a terminal residue
-    TermType resTermType;
+    Cpptraj::Structure::TerminalType resTermType;
     if (ires == 0 && topIn.Nres() > 1) {
-      resTermType = BEG_TERMINAL;
+      resTermType = Cpptraj::Structure::BEG_TERMINAL;
     } else if (currentRes.IsTerminal()) {
-      resTermType = END_TERMINAL;
+      resTermType = Cpptraj::Structure::END_TERMINAL;
     } else if (pres > -1 && topIn.Res(pres).IsTerminal()) {
-      resTermType = BEG_TERMINAL;
+      resTermType = Cpptraj::Structure::BEG_TERMINAL;
     } else if (nres < topIn.Nres() && topIn.Res(nres).ChainId() != currentRes.ChainId()) {
-      resTermType = END_TERMINAL;
+      resTermType = Cpptraj::Structure::END_TERMINAL;
     } else {
-      resTermType = REGULAR;
+      resTermType = Cpptraj::Structure::NON_TERMINAL;
     }
-    static const char* TermTypeStr[] = { "Begin", "Regular", "End" };
-    mprintf("DEBUG: Residue type: %s\n", TermTypeStr[resTermType]);
+    mprintf("DEBUG: Residue type: %s\n", Cpptraj::Structure::terminalStr(resTermType));
     // Identify a template based on the residue name.
     DataSet_Coords* resTemplate = IdTemplateFromName(Templates, currentRes.Name());
     if (resTemplate == 0) {
diff --git a/src/Structure/StructureEnum.cpp b/src/Structure/StructureEnum.cpp
index 1ef86d24f8..17e4711c7e 100644
--- a/src/Structure/StructureEnum.cpp
+++ b/src/Structure/StructureEnum.cpp
@@ -10,3 +10,13 @@ const char* Cpptraj::Structure::chiralStr(ChiralType ct) {
   }
   return 0;
 }
+
+/** return string corresponding to TerminalType */
+const char* Cpptraj::Structure::terminalStr(TerminalType tt) {
+  switch (tt) {
+    case BEG_TERMINAL : return "Begin";
+    case NON_TERMINAL : return "Non";
+    case END_TERMINAL : return "End";
+  }
+  return 0;
+}
diff --git a/src/Structure/StructureEnum.h b/src/Structure/StructureEnum.h
index 311767921a..3014a56b0b 100644
--- a/src/Structure/StructureEnum.h
+++ b/src/Structure/StructureEnum.h
@@ -7,6 +7,11 @@ enum ChiralType { CHIRALITY_ERR = 0, IS_S, IS_R, IS_UNKNOWN_CHIRALITY };
 /// \return String corresponding to ChiralType
 const char* chiralStr(ChiralType);
 
+/// Residue terminal type
+enum TerminalType { BEG_TERMINAL = 0, NON_TERMINAL, END_TERMINAL };
+/// \return String corresponding to TerminalType
+const char* terminalStr(TerminalType);
+
 }
 }
 #endif

From ed9f76d3e79208c7a5c8304a3d91c02248693502 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 12 Jan 2024 15:40:11 -0500
Subject: [PATCH 0326/1492] Save the pdb res map

---
 src/DataIO_LeapRC.cpp | 32 +++++++++++++++++++++++++++++---
 src/DataIO_LeapRC.h   | 10 +++++++++-
 src/cpptrajdepend     |  4 ++--
 3 files changed, 40 insertions(+), 6 deletions(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 6b511f3c59..c36cd0212b 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -175,7 +175,7 @@ const
 }
 
 /** LEaP addPdbResMap command. */
-int DataIO_LeapRC::AddPdbResMap(BufferedLine& infile)
+int DataIO_LeapRC::AddPdbResMap(PdbResMapArray& pdbResMap, BufferedLine& infile)
 const
 {
   int bracketCount = 0;
@@ -193,6 +193,25 @@ const
         if (bracketCount == 1) {
           mprintf("DEBUG: addPdbResMap: %s\n", tmp.c_str());
           ArgList aline( tmp );
+          // 3 tokens: terminal type (0=beg 1=end), PDB name, unit name
+          if (aline.Nargs() != 3) {
+            mprinterr("Error: Malformed entry in addPdbResMap: %s\n", tmp.c_str());
+            return 1;
+          }
+          Cpptraj::Structure::TerminalType termType = Cpptraj::Structure::NON_TERMINAL;
+          if (aline[0] == "0")
+            termType = Cpptraj::Structure::BEG_TERMINAL;
+          else if (aline[0] == "1")
+            termType = Cpptraj::Structure::END_TERMINAL;
+          else
+            mprintf("Warning: Unrecognized terminal type in addPdbResMap: %s\n", aline[0].c_str());
+          if (termType != Cpptraj::Structure::NON_TERMINAL) {
+            PdbResMapType prm;
+            prm.termType_ = termType;
+            prm.pdbName_ = aline[1];
+            prm.unitName_ = aline[2];
+            pdbResMap.push_back( prm );
+          }
           tmp.clear();
         }
       } else {
@@ -259,6 +278,7 @@ int DataIO_LeapRC::ReadData(FileName const& fname, DataSetList& dsl, std::string
   DataSetList paramDSL;
   DataSetList unitDSL;
   NHarrayType atomHybridizations;
+  PdbResMapArray pdbResMap;
   int err = 0;
   const char* ptr = infile.Line();
   while (ptr != 0) {
@@ -280,7 +300,7 @@ int DataIO_LeapRC::ReadData(FileName const& fname, DataSetList& dsl, std::string
       else if (line.Contains("addAtomTypes") || line.Contains("addatomtypes"))
         err = AddAtomTypes(atomHybridizations, infile);
       else if (line.Contains("addPdbResMap") || line.Contains("addpdbresmap"))
-        err = AddPdbResMap(infile);
+        err = AddPdbResMap(pdbResMap, infile);
     }
     if (err != 0) break;
     ptr = infile.Line();
@@ -304,7 +324,13 @@ int DataIO_LeapRC::ReadData(FileName const& fname, DataSetList& dsl, std::string
       }
     }
   }
-
+//            // Find the unit in unit DSL
+//            DataSet* ds = unitDSL.CheckForSet( MetaData(dsname, aline[2]) );
+//            if (ds == 0) {
+//             mprintf("Warning: Unit '%s' was not found among loaded units.\n", aline[2].c_str());
+//            } else {
+//              mprintf("DEBUG: Found unit %s\n", ds->legend());
+//            }
   // Add data sets to the main data set list
   if (addSetsToList(dsl, paramDSL)) return err+1;
 
diff --git a/src/DataIO_LeapRC.h b/src/DataIO_LeapRC.h
index 06e95135a1..f7fa009bd4 100644
--- a/src/DataIO_LeapRC.h
+++ b/src/DataIO_LeapRC.h
@@ -1,6 +1,7 @@
 #ifndef INC_DATAIO_LEAPRC_H
 #define INC_DATAIO_LEAPRC_H
 #include "DataIO.h"
+#include "Structure/StructureEnum.h"
 #include <map>
 class BufferedLine;
 /// Read parameters and units from a leap rc file 
@@ -19,11 +20,18 @@ class DataIO_LeapRC : public DataIO {
     typedef std::pair<NameType, AtomType::HybridizationType> NHpairType;
     typedef std::map<NameType, AtomType::HybridizationType> NHarrayType;
 
+    struct PdbResMapType {
+      std::string unitName_;
+      NameType pdbName_;
+      Cpptraj::Structure::TerminalType termType_;
+    };
+    typedef std::vector<PdbResMapType> PdbResMapArray;
+
     int LoadAmberParams(std::string const&, DataSetList&, std::string const&) const;
     int LoadOFF(std::string const&, DataSetList&, std::string const&) const;
     int LoadAmberPrep(std::string const&, DataSetList&, std::string const&) const;
     int AddAtomTypes(NHarrayType&, BufferedLine&) const;
-    int AddPdbResMap(BufferedLine&) const;
+    int AddPdbResMap(PdbResMapArray&, BufferedLine&) const;
 
     std::string amberhome_;
 };
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 7ef4cb6e0b..92c176089c 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -200,7 +200,7 @@ CpptrajFile.o : CpptrajFile.cpp CpptrajFile.h CpptrajStdio.h FileIO.h FileIO_Bzi
 CpptrajState.o : CpptrajState.cpp Action.h ActionList.h ActionState.h Action_CreateCrd.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_Topology.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleNavigator.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 CpptrajStdio.o : CpptrajStdio.cpp Parallel.h
 CurveFit.o : CurveFit.cpp CurveFit.h
-DataFile.o : DataFile.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Cluster/Cframes.h Cluster/Cmatrix_NC.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataFile.h DataIO.h DataIO_AmberEne.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_CCP4.h DataIO_CharmmFastRep.h DataIO_CharmmOutput.h DataIO_CharmmRepLog.h DataIO_CharmmRtfPrm.h DataIO_Cmatrix_Binary.h DataIO_Cmatrix_NC.h DataIO_Cpout.h DataIO_Evecs.h DataIO_Gnuplot.h DataIO_Grace.h DataIO_LeapRC.h DataIO_Mdout.h DataIO_NetCDF.h DataIO_Numpy.h DataIO_OpenDx.h DataIO_Peaks.h DataIO_RemLog.h DataIO_Std.h DataIO_VecTraj.h DataIO_XVG.h DataIO_Xplor.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TypeNameHolder.h Unit.h Vec3.h
+DataFile.o : DataFile.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Cluster/Cframes.h Cluster/Cmatrix_NC.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataFile.h DataIO.h DataIO_AmberEne.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_CCP4.h DataIO_CharmmFastRep.h DataIO_CharmmOutput.h DataIO_CharmmRepLog.h DataIO_CharmmRtfPrm.h DataIO_Cmatrix_Binary.h DataIO_Cmatrix_NC.h DataIO_Cpout.h DataIO_Evecs.h DataIO_Gnuplot.h DataIO_Grace.h DataIO_LeapRC.h DataIO_Mdout.h DataIO_NetCDF.h DataIO_Numpy.h DataIO_OpenDx.h DataIO_Peaks.h DataIO_RemLog.h DataIO_Std.h DataIO_VecTraj.h DataIO_XVG.h DataIO_Xplor.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TypeNameHolder.h Unit.h Vec3.h
 DataFileList.o : DataFileList.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataFilter.o : DataFilter.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_integer.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO.o : DataIO.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
@@ -220,7 +220,7 @@ DataIO_Cpout.o : DataIO_Cpout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h A
 DataIO_Evecs.o : DataIO_Evecs.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Evecs.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Gnuplot.o : DataIO_Gnuplot.cpp ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Gnuplot.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Grace.o : DataIO_Grace.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Grace.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_string.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_LeapRC.o : DataIO_LeapRC.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_LeapRC.o : DataIO_LeapRC.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Mdout.o : DataIO_Mdout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Mdout.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_NetCDF.o : DataIO_NetCDF.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/Cframes.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_NetCDF.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_Mesh.h DataSet_Modes.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_Vector.h DataSet_Vector_Scalar.h DataSet_string.h DataSet_unsignedInt.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h Version.h
 DataIO_Numpy.o : DataIO_Numpy.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Numpy.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h libnpy/npy.hpp

From 95ebd435c662bb6cdb98cf8e9e33c162d16ce578 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 12 Jan 2024 15:46:34 -0500
Subject: [PATCH 0327/1492] Identify equals sign

---
 src/DataIO_LeapRC.cpp | 18 +++++++++++++++++-
 1 file changed, 17 insertions(+), 1 deletion(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index c36cd0212b..f14af36dab 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -284,7 +284,6 @@ int DataIO_LeapRC::ReadData(FileName const& fname, DataSetList& dsl, std::string
   while (ptr != 0) {
     if (ptr[0] != '\0' && ptr[0] != '#') {
       ArgList line( ptr, " \t" );
-      std::string param_fname;
       if (line.Contains("loadAmberParams"))
         err = LoadAmberParams( line.GetStringKey("loadAmberParams"), paramDSL, dsname );
       else if (line.Contains("loadamberparams"))
@@ -301,6 +300,23 @@ int DataIO_LeapRC::ReadData(FileName const& fname, DataSetList& dsl, std::string
         err = AddAtomTypes(atomHybridizations, infile);
       else if (line.Contains("addPdbResMap") || line.Contains("addpdbresmap"))
         err = AddPdbResMap(pdbResMap, infile);
+      else {
+        // Does this line contain an equals sign?
+        bool has_equals = false;
+        for (const char* p = ptr; *p != '\0'; ++p) {
+          if (*p == '=') {
+            has_equals = true;
+            break;
+          }
+        }
+        // See if this is a unit alias
+        if (has_equals) {
+          ArgList equals(ptr, " =\t");
+          if (equals.Nargs() == 2) {
+            mprintf("DEBUG: %s = %s\n", equals[0].c_str(), equals[1].c_str());
+          }
+        }
+      }
     }
     if (err != 0) break;
     ptr = infile.Line();

From 5baa967fe858f15a0df3b7c5d9b1782646b2d45e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 13 Jan 2024 14:08:16 -0500
Subject: [PATCH 0328/1492] Add AssociatedData_ResId class

---
 src/AssociatedData_ResId.cpp | 15 +++++++++++++++
 src/AssociatedData_ResId.h   | 22 ++++++++++++++++++++++
 2 files changed, 37 insertions(+)
 create mode 100644 src/AssociatedData_ResId.cpp
 create mode 100644 src/AssociatedData_ResId.h

diff --git a/src/AssociatedData_ResId.cpp b/src/AssociatedData_ResId.cpp
new file mode 100644
index 0000000000..7cf3205f1a
--- /dev/null
+++ b/src/AssociatedData_ResId.cpp
@@ -0,0 +1,15 @@
+#include "AssociatedData_ResId.h"
+#include "CpptrajStdio.h"
+
+/** Help text */
+const char* AssociatedData_ResId::HelpText = "\0";
+
+/** Process Args */
+int AssociatedData_ResId::ProcessAdataArgs(ArgList& argIn) {
+  return 0;
+}
+
+/** Print info */
+void AssociatedData_ResId::Ainfo() const {
+  mprintf(" (Res name %s termType %s)", *resName_, Cpptraj::Structure::terminalStr(termType_));
+}
diff --git a/src/AssociatedData_ResId.h b/src/AssociatedData_ResId.h
new file mode 100644
index 0000000000..300891e5e4
--- /dev/null
+++ b/src/AssociatedData_ResId.h
@@ -0,0 +1,22 @@
+#ifndef INC_ASSOCIATEDDATA_RESID_H
+#define INC_ASSOCIATEDDATA_RESID_H
+#include "AssociatedData.h"
+#include "NameType.h"
+#include "Structure/StructureEnum.h"
+class NameType;
+/// Used to identify what residues a residue template matches
+class AssociatedData_ResId : public AssociatedData {
+  public:
+    /// CONSTRUCTOR
+    AssociatedData_ResId() : AssociatedData(RESID), termType_(Cpptraj::Structure::NON_TERMINAL) {}
+    // ----- Inherited functions -------
+    static const char* HelpText;
+    int ProcessAdataArgs(ArgList&);
+    AssociatedData* Copy() const { return new AssociatedData_ResId(*this); }
+    void Ainfo() const;
+    // ---------------------------------
+  private:
+    NameType resName_;                          ///< Target residue name
+    Cpptraj::Structure::TerminalType termType_; ///< Target residue terminal type
+};
+#endif

From 933160e281c959dda329b26f87f5c98e0002f9b3 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 13 Jan 2024 14:14:22 -0500
Subject: [PATCH 0329/1492] Update depends

---
 src/AssociatedData.h | 2 +-
 src/cpptrajdepend    | 1 +
 src/cpptrajfiles     | 1 +
 3 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/AssociatedData.h b/src/AssociatedData.h
index f37af22d7c..9341769c49 100644
--- a/src/AssociatedData.h
+++ b/src/AssociatedData.h
@@ -6,7 +6,7 @@ class AssociatedData {
     /// Destructor. Virtual since this class is inherited.
     virtual ~AssociatedData() {}
     /// Associated data types
-    enum AssociatedType { NOE = 0, CONNECT };
+    enum AssociatedType { NOE = 0, CONNECT, RESID };
     /// CONSTRUCTOR - take associated data type
     AssociatedData(AssociatedType t) : type_(t) {}
     /// \return Associated data type
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 92c176089c..a17b23d1ed 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -140,6 +140,7 @@ ArgList.o : ArgList.cpp ArgList.h CpptrajStdio.h StringRoutines.h
 Array1D.o : Array1D.cpp ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 AssociatedData_Connect.o : AssociatedData_Connect.cpp ArgList.h AssociatedData.h AssociatedData_Connect.h CpptrajStdio.h
 AssociatedData_NOE.o : AssociatedData_NOE.cpp ArgList.h AssociatedData.h AssociatedData_NOE.h CpptrajStdio.h
+AssociatedData_ResId.o : AssociatedData_ResId.cpp AssociatedData.h AssociatedData_ResId.h CpptrajStdio.h NameType.h Structure/StructureEnum.h
 Atom.o : Atom.cpp Atom.h CpptrajStdio.h NameType.h SymbolExporting.h
 AtomMap.o : AtomMap.cpp Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 AtomMask.o : AtomMask.cpp Atom.h AtomMask.h CpptrajStdio.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h SymbolExporting.h Unit.h
diff --git a/src/cpptrajfiles b/src/cpptrajfiles
index fbf1907ef3..31eeeb7ad4 100644
--- a/src/cpptrajfiles
+++ b/src/cpptrajfiles
@@ -143,6 +143,7 @@ COMMON_SOURCES= \
         Array1D.cpp \
         AssociatedData_Connect.cpp \
         AssociatedData_NOE.cpp \
+        AssociatedData_ResId.cpp \
         Atom.cpp \
         AtomMap.cpp \
         AtomMask.cpp \

From 454078460d7af915f700bf62ebc7993491ec2b88 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 13 Jan 2024 14:20:49 -0500
Subject: [PATCH 0330/1492] Save unit aliases

---
 src/DataIO_LeapRC.cpp | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index f14af36dab..03788fc7db 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -279,6 +279,9 @@ int DataIO_LeapRC::ReadData(FileName const& fname, DataSetList& dsl, std::string
   DataSetList unitDSL;
   NHarrayType atomHybridizations;
   PdbResMapArray pdbResMap;
+  typedef std::pair<std::string, std::string> AUpair;
+  typedef std::vector<AUpair> AUarray;
+  AUarray unitAliases;
   int err = 0;
   const char* ptr = infile.Line();
   while (ptr != 0) {
@@ -309,11 +312,12 @@ int DataIO_LeapRC::ReadData(FileName const& fname, DataSetList& dsl, std::string
             break;
           }
         }
-        // See if this is a unit alias
+        // See if this is a unit alias (interpret as 'alias = unit')
         if (has_equals) {
           ArgList equals(ptr, " =\t");
           if (equals.Nargs() == 2) {
             mprintf("DEBUG: %s = %s\n", equals[0].c_str(), equals[1].c_str());
+            unitAliases.push_back( AUpair(equals[0], equals[1]) );
           }
         }
       }

From 94401461e2a1e0ab95f413e10190761079365aca Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 13 Jan 2024 15:42:05 -0500
Subject: [PATCH 0331/1492] Actually copy the units to match leap behavior.
 Ensure associated data is copied.

---
 src/DataIO_LeapRC.cpp | 30 ++++++++++++++++++++++++++----
 src/DataSet.cpp       |  7 +++++++
 src/DataSet.h         |  2 ++
 3 files changed, 35 insertions(+), 4 deletions(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 03788fc7db..bd9564c00c 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -279,9 +279,6 @@ int DataIO_LeapRC::ReadData(FileName const& fname, DataSetList& dsl, std::string
   DataSetList unitDSL;
   NHarrayType atomHybridizations;
   PdbResMapArray pdbResMap;
-  typedef std::pair<std::string, std::string> AUpair;
-  typedef std::vector<AUpair> AUarray;
-  AUarray unitAliases;
   int err = 0;
   const char* ptr = infile.Line();
   while (ptr != 0) {
@@ -317,7 +314,32 @@ int DataIO_LeapRC::ReadData(FileName const& fname, DataSetList& dsl, std::string
           ArgList equals(ptr, " =\t");
           if (equals.Nargs() == 2) {
             mprintf("DEBUG: %s = %s\n", equals[0].c_str(), equals[1].c_str());
-            unitAliases.push_back( AUpair(equals[0], equals[1]) );
+            // Find the unit to make a copy of
+            DataSet* ds0 = unitDSL.CheckForSet( MetaData(dsname, equals[1]) );
+            if (ds0 == 0) {
+              mprinterr("Error: Could not find unit '%s' to copy to '%s'\n", equals[1].c_str(), equals[0].c_str());
+              return 1;
+            }
+            DataSet_Coords& crd0 = static_cast<DataSet_Coords&>( *ds0 );
+            // Allocate copy
+            DataSet* ds1 = unitDSL.AddSet( DataSet::COORDS, MetaData(dsname, equals[0]) );
+            if (ds1 == 0) {
+              mprinterr("Error: Could not allocate unit '%s' for '%s'\n", equals[0].c_str(), equals[1].c_str());
+              return 1;
+            }
+            DataSet_Coords& crd1 = static_cast<DataSet_Coords&>( *ds1 );
+            if (crd1.CoordsSetup( crd0.Top(), crd0.CoordsInfo() )) {
+              mprinterr("Error: Could not set up unit '%s' for '%s'\n", equals[0].c_str(), equals[1].c_str());
+              return 1;
+            }
+            crd1.Allocate( DataSet::SizeArray(1, 1) );
+            // Copy
+            Frame tmpFrm = crd0.AllocateFrame();
+            crd0.GetFrame(0, tmpFrm);
+            crd1.SetCRD(0, tmpFrm );
+            // Copy associated data
+            crd1.CopyAssociatedDataFrom( crd0 );
+            mprintf("DEBUG: Created unit set %s\n", crd1.legend());
           }
         }
       }
diff --git a/src/DataSet.cpp b/src/DataSet.cpp
index b9e0d5b797..54f1f11372 100644
--- a/src/DataSet.cpp
+++ b/src/DataSet.cpp
@@ -89,6 +89,13 @@ void DataSet::ClearAssociatedData() {
   associatedData_.clear();
 }
 
+/** Copy all assocated data from the given data set. */
+void DataSet::CopyAssociatedDataFrom(DataSet const& dsIn) {
+  for (AdataArray::const_iterator ad = dsIn.associatedData_.begin();
+                                  ad != dsIn.associatedData_.end(); ++ad)
+    associatedData_.push_back( (*ad)->Copy() );
+}
+
 // DESTRUCTOR
 DataSet::~DataSet() { ClearAssociatedData(); }
 
diff --git a/src/DataSet.h b/src/DataSet.h
index f619652f4d..9413d8d33a 100644
--- a/src/DataSet.h
+++ b/src/DataSet.h
@@ -86,6 +86,8 @@ class DataSet {
     // -----------------------------------------------------
     /// Associate additional data with this set.
     void AssociateData(AssociatedData const* a) { associatedData_.push_back( a->Copy() ); }
+    /// Copy associated data from given set to this set.
+    void CopyAssociatedDataFrom(DataSet const&);
     /// Set DataSet MetaData
     int SetMeta(MetaData const&);
     /// Set DataSet ensemble number.

From a1318704d3557195f16760bebba3f31dd87d0600 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 13 Jan 2024 15:47:25 -0500
Subject: [PATCH 0332/1492] Start finding units for pdb res map

---
 src/DataIO_LeapRC.cpp | 24 +++++++++++++++++-------
 1 file changed, 17 insertions(+), 7 deletions(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index bd9564c00c..f6a11420c6 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -366,13 +366,23 @@ int DataIO_LeapRC::ReadData(FileName const& fname, DataSetList& dsl, std::string
       }
     }
   }
-//            // Find the unit in unit DSL
-//            DataSet* ds = unitDSL.CheckForSet( MetaData(dsname, aline[2]) );
-//            if (ds == 0) {
-//             mprintf("Warning: Unit '%s' was not found among loaded units.\n", aline[2].c_str());
-//            } else {
-//              mprintf("DEBUG: Found unit %s\n", ds->legend());
-//            }
+  // Update units with pdb residue map info
+  //for (DataSetList::const_iterator ds = unitDSL.begin(); ds != paramDSL.end(); ++ds)
+  //{
+  //  if ( (*ds)->Group() == DataSet::COORDINATES ) {
+  //    DataSet_Coords& crd = static_cast<DataSet_Coords&>( *(*ds) );
+  for (PdbResMapArray::const_iterator it = pdbResMap.begin();
+                                      it != pdbResMap.end(); ++it)
+  {
+    // Find the unit in unit DSL
+    DataSet* ds = unitDSL.CheckForSet( MetaData(dsname, it->unitName_) );
+    if (ds == 0) {
+      mprintf("Warning: Unit '%s' was not found among loaded units.\n", it->unitName_.c_str());
+    } else {
+      mprintf("DEBUG: Found unit %s\n", ds->legend());
+    }
+  }
+
   // Add data sets to the main data set list
   if (addSetsToList(dsl, paramDSL)) return err+1;
 

From f843076b80d10de19be1152b7a76e92784519049 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 13 Jan 2024 15:53:23 -0500
Subject: [PATCH 0333/1492] Associate pdb res map info with appropriate unit
 set

---
 src/AssociatedData_ResId.h | 3 +++
 src/DataIO_LeapRC.cpp      | 9 +++++++--
 src/cpptrajdepend          | 2 +-
 3 files changed, 11 insertions(+), 3 deletions(-)

diff --git a/src/AssociatedData_ResId.h b/src/AssociatedData_ResId.h
index 300891e5e4..192e6ed9c4 100644
--- a/src/AssociatedData_ResId.h
+++ b/src/AssociatedData_ResId.h
@@ -9,6 +9,9 @@ class AssociatedData_ResId : public AssociatedData {
   public:
     /// CONSTRUCTOR
     AssociatedData_ResId() : AssociatedData(RESID), termType_(Cpptraj::Structure::NON_TERMINAL) {}
+    /// CONSTRUCTOR - Pdb name, terminal type
+    AssociatedData_ResId(NameType const& n, Cpptraj::Structure::TerminalType t) :
+      AssociatedData(RESID), resName_(n), termType_(t) {}
     // ----- Inherited functions -------
     static const char* HelpText;
     int ProcessAdataArgs(ArgList&);
diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index f6a11420c6..724a2c8388 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -1,4 +1,5 @@
 #include "DataIO_LeapRC.h"
+#include "AssociatedData_ResId.h"
 #include "CpptrajStdio.h"
 #include "BufferedLine.h"
 #include "DataIO_AmberFF.h"
@@ -370,7 +371,6 @@ int DataIO_LeapRC::ReadData(FileName const& fname, DataSetList& dsl, std::string
   //for (DataSetList::const_iterator ds = unitDSL.begin(); ds != paramDSL.end(); ++ds)
   //{
   //  if ( (*ds)->Group() == DataSet::COORDINATES ) {
-  //    DataSet_Coords& crd = static_cast<DataSet_Coords&>( *(*ds) );
   for (PdbResMapArray::const_iterator it = pdbResMap.begin();
                                       it != pdbResMap.end(); ++it)
   {
@@ -379,7 +379,12 @@ int DataIO_LeapRC::ReadData(FileName const& fname, DataSetList& dsl, std::string
     if (ds == 0) {
       mprintf("Warning: Unit '%s' was not found among loaded units.\n", it->unitName_.c_str());
     } else {
-      mprintf("DEBUG: Found unit %s\n", ds->legend());
+      DataSet_Coords& crd = static_cast<DataSet_Coords&>( *ds );
+      AssociatedData_ResId resid( it->pdbName_, it->termType_ );
+      crd.AssociateData( &resid );
+      mprintf("DEBUG: Found unit %s", crd.legend());
+      resid.Ainfo();
+      mprintf("\n");
     }
   }
 
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index a17b23d1ed..06237af11d 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -221,7 +221,7 @@ DataIO_Cpout.o : DataIO_Cpout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h A
 DataIO_Evecs.o : DataIO_Evecs.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Evecs.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Gnuplot.o : DataIO_Gnuplot.cpp ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Gnuplot.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Grace.o : DataIO_Grace.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Grace.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_string.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_LeapRC.o : DataIO_LeapRC.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_LeapRC.o : DataIO_LeapRC.cpp ArgList.h AssociatedData.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Mdout.o : DataIO_Mdout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Mdout.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_NetCDF.o : DataIO_NetCDF.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/Cframes.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_NetCDF.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_Mesh.h DataSet_Modes.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_Vector.h DataSet_Vector_Scalar.h DataSet_string.h DataSet_unsignedInt.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h Version.h
 DataIO_Numpy.o : DataIO_Numpy.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Numpy.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h libnpy/npy.hpp

From 40ce0191b4cb527659f7d4dcdf1b0ced7a9c2187 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 13 Jan 2024 16:02:30 -0500
Subject: [PATCH 0334/1492] ID terminal templates

---
 src/AssociatedData_ResId.h |  2 ++
 src/Exec_Build.cpp         | 34 +++++++++++++++++++++++++++-------
 src/Exec_Build.h           |  3 ++-
 src/cpptrajdepend          |  4 ++--
 4 files changed, 33 insertions(+), 10 deletions(-)

diff --git a/src/AssociatedData_ResId.h b/src/AssociatedData_ResId.h
index 192e6ed9c4..a46aea9d45 100644
--- a/src/AssociatedData_ResId.h
+++ b/src/AssociatedData_ResId.h
@@ -18,6 +18,8 @@ class AssociatedData_ResId : public AssociatedData {
     AssociatedData* Copy() const { return new AssociatedData_ResId(*this); }
     void Ainfo() const;
     // ---------------------------------
+    NameType const& ResName() const { return resName_; }
+    Cpptraj::Structure::TerminalType TermType() const { return termType_; }
   private:
     NameType resName_;                          ///< Target residue name
     Cpptraj::Structure::TerminalType termType_; ///< Target residue terminal type
diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 3fd57358fe..315e738300 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -4,18 +4,38 @@
 #include "Structure/GenerateConnectivityArrays.h"
 #include "Structure/Zmatrix.h"
 #include "Parm/GB_Params.h"
+#include "AssociatedData_ResId.h"
 
+/** Try to identify residue template DataSet from the given residue
+  * name (from e.g. the PDB/Mol2/etc file).
+  */
 DataSet_Coords* Exec_Build::IdTemplateFromName(Carray const& Templates,
-                                               NameType const& rname)
+                                               NameType const& rname,
+                                               Cpptraj::Structure::TerminalType termType)
 {
   DataSet_Coords* out = 0;
-  // Assume Coords set aspect is what we need
-  for (Carray::const_iterator it = Templates.begin(); it != Templates.end(); ++it) {
-    if ( rname == NameType( (*it)->Meta().Aspect() ) ) {
-      out = *it;
-      break;
+  if (termType == Cpptraj::Structure::NON_TERMINAL) {
+    // Assume Coords set aspect is what we need
+    for (Carray::const_iterator it = Templates.begin(); it != Templates.end(); ++it) {
+      if ( rname == NameType( (*it)->Meta().Aspect() ) ) {
+        out = *it;
+        break;
+      }
+    }
+  } else {
+    // Looking for a terminal residue. Need to get sets with AssociatedData_ResId
+    for (Carray::const_iterator it = Templates.begin(); it != Templates.end(); ++it) {
+      AssociatedData* ad = (*it)->GetAssociatedData( AssociatedData::RESID );
+      if (ad != 0) {
+        AssociatedData_ResId const& resid = static_cast<AssociatedData_ResId const&>( *ad );
+        if (rname == resid.ResName() && termType == resid.TermType()) {
+          out = *it;
+          break;
+        }
+      }
     }
   }
+
   return out;
 }
 
@@ -132,7 +152,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
     }
     mprintf("DEBUG: Residue type: %s\n", Cpptraj::Structure::terminalStr(resTermType));
     // Identify a template based on the residue name.
-    DataSet_Coords* resTemplate = IdTemplateFromName(Templates, currentRes.Name());
+    DataSet_Coords* resTemplate = IdTemplateFromName(Templates, currentRes.Name(), resTermType);
     if (resTemplate == 0) {
       mprintf("Warning: No template found for residue %s\n", topIn.TruncResNameOnumId(ires).c_str());
       newNatom += currentRes.NumAtoms();
diff --git a/src/Exec_Build.h b/src/Exec_Build.h
index c96aad7e69..d25edf4b24 100644
--- a/src/Exec_Build.h
+++ b/src/Exec_Build.h
@@ -1,6 +1,7 @@
 #ifndef INC_EXEC_BUILD_H
 #define INC_EXEC_BUILD_H
 #include "Exec.h"
+#include "Structure/StructureEnum.h"
 /// Used to build a structure 
 class Exec_Build : public Exec {
   public:
@@ -12,7 +13,7 @@ class Exec_Build : public Exec {
     typedef std::vector<DataSet_Coords*> Carray;
 
     /// Identify residue template from residue name
-    static DataSet_Coords* IdTemplateFromName(Carray const&, NameType const&);
+    static DataSet_Coords* IdTemplateFromName(Carray const&, NameType const&, Cpptraj::Structure::TerminalType);
     /// Create new topology/frame using templates
     static int FillAtomsWithTemplates(Topology&, Frame&, Carray const&, Topology const&, Frame const&);
     /// Map atoms in topology to template
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 06237af11d..ee25a9af47 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -188,7 +188,7 @@ ClusterMap.o : ClusterMap.cpp AssociatedData.h ClusterMap.h Constants.h CpptrajF
 Cmd.o : Cmd.cpp Cmd.h DispatchObject.h
 CmdInput.o : CmdInput.cpp CmdInput.h StringRoutines.h
 CmdList.o : CmdList.cpp Cmd.h CmdList.h DispatchObject.h
-Command.o : Command.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h ActionTopWriter.h Action_Align.h Action_Angle.h Action_AreaPerMol.h Action_AtomMap.h Action_AtomicCorr.h Action_AtomicFluct.h Action_AutoImage.h Action_Average.h Action_AvgBox.h Action_Bounds.h Action_Box.h Action_Center.h Action_Channel.h Action_CheckChirality.h Action_CheckStructure.h Action_Closest.h Action_ClusterDihedral.h Action_Contacts.h Action_CreateCrd.h Action_CreateReservoir.h Action_DNAionTracker.h Action_DSSP.h Action_Density.h Action_Diffusion.h Action_Dihedral.h Action_DihedralRMS.h Action_Dipole.h Action_DistRmsd.h Action_Distance.h Action_Energy.h Action_Esander.h Action_FilterByData.h Action_FixAtomOrder.h Action_FixImagedBonds.h Action_GIST.h Action_Grid.h Action_GridFreeEnergy.h Action_HydrogenBond.h Action_Image.h Action_InfraredSpectrum.h Action_Jcoupling.h Action_Keep.h Action_LESsplit.h Action_LIE.h Action_LipidOrder.h Action_MakeStructure.h Action_Mask.h Action_Matrix.h Action_MinImage.h Action_Molsurf.h Action_MultiDihedral.h Action_MultiPucker.h Action_MultiVector.h Action_NAstruct.h Action_NMRrst.h Action_NativeContacts.h Action_OrderParameter.h Action_Outtraj.h Action_PairDist.h Action_Pairwise.h Action_Principal.h Action_Projection.h Action_Pucker.h Action_Radgyr.h Action_Radial.h Action_RandomizeIons.h Action_Remap.h Action_ReplicateCell.h Action_Rmsd.h Action_Rotate.h Action_RunningAvg.h Action_STFC_Diffusion.h Action_Scale.h Action_SetVelocity.h Action_Spam.h Action_Strip.h Action_Surf.h Action_SymmetricRmsd.h Action_Temperature.h Action_Time.h Action_ToroidalDiffusion.h Action_Translate.h Action_Unstrip.h Action_Unwrap.h Action_Vector.h Action_VelocityAutoCorr.h Action_Volmap.h Action_Volume.h Action_Watershell.h Action_XtalSymm.h Analysis.h AnalysisList.h AnalysisState.h Analysis_AmdBias.h Analysis_AutoCorr.h Analysis_Average.h Analysis_CalcDiffusion.h Analysis_Clustering.h Analysis_ConstantPHStats.h Analysis_Corr.h Analysis_CrankShaft.h Analysis_CrdFluct.h Analysis_CrossCorr.h Analysis_CurveFit.h Analysis_Divergence.h Analysis_EvalPlateau.h Analysis_FFT.h Analysis_HausdorffDistance.h Analysis_Hist.h Analysis_IRED.h Analysis_Integrate.h Analysis_KDE.h Analysis_Lifetime.h Analysis_LowestCurve.h Analysis_Matrix.h Analysis_MeltCurve.h Analysis_Modes.h Analysis_MultiHist.h Analysis_Multicurve.h Analysis_Overlap.h Analysis_PhiPsi.h Analysis_Regression.h Analysis_RemLog.h Analysis_Rms2d.h Analysis_RmsAvgCorr.h Analysis_Rotdif.h Analysis_RunningAvg.h Analysis_Slope.h Analysis_Spline.h Analysis_State.h Analysis_Statistics.h Analysis_TI.h Analysis_TICA.h Analysis_Timecorr.h Analysis_VectorMath.h Analysis_Wavelet.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h AxisType.h BaseIOtype.h Box.h BoxArgs.h BufferedLine.h CharMask.h Cluster/Algorithm.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Control.h Cluster/DrawGraph.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Sieve.h Cluster/Silhouette.h ClusterMap.h Cmd.h CmdInput.h CmdList.h Command.h CompactFrameArray.h ComplexArray.h Constants.h Constraints.h ControlBlock.h ControlBlock_For.h CoordinateInfo.h Corr.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_RemLog.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h Deprecated.h DiffusionResults.h DihedralSearch.h Dimension.h DispatchObject.h Energy.h Energy_Sander.h EnsembleIn.h EnsembleOutList.h Ewald.h EwaldOptions.h Ewald_ParticleMesh.h ExclusionArray.h Exec.h Exec_AddMissingRes.h Exec_Analyze.h Exec_Build.h Exec_Calc.h Exec_CatCrd.h Exec_Change.h Exec_ClusterMap.h Exec_CombineCoords.h Exec_Commands.h Exec_CompareClusters.h Exec_CompareEnergy.h Exec_CompareTop.h Exec_CrdAction.h Exec_CrdOut.h Exec_CrdTransform.h Exec_CreateSet.h Exec_DataFile.h Exec_DataFilter.h Exec_DataSetCmd.h Exec_Desc.h Exec_Emin.h Exec_ExtendedComparison.h Exec_Flatten.h Exec_GenerateAmberRst.h Exec_Graft.h Exec_Help.h Exec_HmassRepartition.h Exec_LoadCrd.h Exec_LoadTraj.h Exec_ParallelAnalysis.h Exec_ParmBox.h Exec_ParmSolvent.h Exec_ParmStrip.h Exec_ParmWrite.h Exec_ParseTiming.h Exec_PermuteDihedrals.h Exec_Precision.h Exec_PrepareForLeap.h Exec_PrintData.h Exec_Random.h Exec_ReadData.h Exec_ReadEnsembleData.h Exec_ReadInput.h Exec_RotateDihedral.h Exec_RunAnalysis.h Exec_ScaleDihedralK.h Exec_Sequence.h Exec_SequenceAlign.h Exec_Set.h Exec_Show.h Exec_SortEnsembleData.h Exec_SplitCoords.h Exec_System.h Exec_Top.h Exec_Traj.h Exec_UpdateParameters.h Exec_ViewRst.h Exec_Zmatrix.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h GIST_PME.h Grid.h GridAction.h GridBin.h GridMover.h HistBin.h Hungarian.h ImageOption.h ImageTypes.h InputTrajCommon.h MapAtom.h MaskArray.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h OnlineVarT.h OutputTrajCommon.h PDBfile.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PubFFT.h Pucker.h Pucker_PuckerMask.h Pucker_PuckerSearch.h Pucker_PuckerToken.h RPNcalc.h Random.h Range.h ReferenceAction.h ReferenceFrame.h RemdReservoirNC.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h SplineFxnTable.h StructureCheck.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h cuda_kernels/GistCudaSetup.cuh helpme_standalone.h molsurf.h
+Command.o : Command.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h ActionTopWriter.h Action_Align.h Action_Angle.h Action_AreaPerMol.h Action_AtomMap.h Action_AtomicCorr.h Action_AtomicFluct.h Action_AutoImage.h Action_Average.h Action_AvgBox.h Action_Bounds.h Action_Box.h Action_Center.h Action_Channel.h Action_CheckChirality.h Action_CheckStructure.h Action_Closest.h Action_ClusterDihedral.h Action_Contacts.h Action_CreateCrd.h Action_CreateReservoir.h Action_DNAionTracker.h Action_DSSP.h Action_Density.h Action_Diffusion.h Action_Dihedral.h Action_DihedralRMS.h Action_Dipole.h Action_DistRmsd.h Action_Distance.h Action_Energy.h Action_Esander.h Action_FilterByData.h Action_FixAtomOrder.h Action_FixImagedBonds.h Action_GIST.h Action_Grid.h Action_GridFreeEnergy.h Action_HydrogenBond.h Action_Image.h Action_InfraredSpectrum.h Action_Jcoupling.h Action_Keep.h Action_LESsplit.h Action_LIE.h Action_LipidOrder.h Action_MakeStructure.h Action_Mask.h Action_Matrix.h Action_MinImage.h Action_Molsurf.h Action_MultiDihedral.h Action_MultiPucker.h Action_MultiVector.h Action_NAstruct.h Action_NMRrst.h Action_NativeContacts.h Action_OrderParameter.h Action_Outtraj.h Action_PairDist.h Action_Pairwise.h Action_Principal.h Action_Projection.h Action_Pucker.h Action_Radgyr.h Action_Radial.h Action_RandomizeIons.h Action_Remap.h Action_ReplicateCell.h Action_Rmsd.h Action_Rotate.h Action_RunningAvg.h Action_STFC_Diffusion.h Action_Scale.h Action_SetVelocity.h Action_Spam.h Action_Strip.h Action_Surf.h Action_SymmetricRmsd.h Action_Temperature.h Action_Time.h Action_ToroidalDiffusion.h Action_Translate.h Action_Unstrip.h Action_Unwrap.h Action_Vector.h Action_VelocityAutoCorr.h Action_Volmap.h Action_Volume.h Action_Watershell.h Action_XtalSymm.h Analysis.h AnalysisList.h AnalysisState.h Analysis_AmdBias.h Analysis_AutoCorr.h Analysis_Average.h Analysis_CalcDiffusion.h Analysis_Clustering.h Analysis_ConstantPHStats.h Analysis_Corr.h Analysis_CrankShaft.h Analysis_CrdFluct.h Analysis_CrossCorr.h Analysis_CurveFit.h Analysis_Divergence.h Analysis_EvalPlateau.h Analysis_FFT.h Analysis_HausdorffDistance.h Analysis_Hist.h Analysis_IRED.h Analysis_Integrate.h Analysis_KDE.h Analysis_Lifetime.h Analysis_LowestCurve.h Analysis_Matrix.h Analysis_MeltCurve.h Analysis_Modes.h Analysis_MultiHist.h Analysis_Multicurve.h Analysis_Overlap.h Analysis_PhiPsi.h Analysis_Regression.h Analysis_RemLog.h Analysis_Rms2d.h Analysis_RmsAvgCorr.h Analysis_Rotdif.h Analysis_RunningAvg.h Analysis_Slope.h Analysis_Spline.h Analysis_State.h Analysis_Statistics.h Analysis_TI.h Analysis_TICA.h Analysis_Timecorr.h Analysis_VectorMath.h Analysis_Wavelet.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h AxisType.h BaseIOtype.h Box.h BoxArgs.h BufferedLine.h CharMask.h Cluster/Algorithm.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Control.h Cluster/DrawGraph.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Sieve.h Cluster/Silhouette.h ClusterMap.h Cmd.h CmdInput.h CmdList.h Command.h CompactFrameArray.h ComplexArray.h Constants.h Constraints.h ControlBlock.h ControlBlock_For.h CoordinateInfo.h Corr.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_RemLog.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h Deprecated.h DiffusionResults.h DihedralSearch.h Dimension.h DispatchObject.h Energy.h Energy_Sander.h EnsembleIn.h EnsembleOutList.h Ewald.h EwaldOptions.h Ewald_ParticleMesh.h ExclusionArray.h Exec.h Exec_AddMissingRes.h Exec_Analyze.h Exec_Build.h Exec_Calc.h Exec_CatCrd.h Exec_Change.h Exec_ClusterMap.h Exec_CombineCoords.h Exec_Commands.h Exec_CompareClusters.h Exec_CompareEnergy.h Exec_CompareTop.h Exec_CrdAction.h Exec_CrdOut.h Exec_CrdTransform.h Exec_CreateSet.h Exec_DataFile.h Exec_DataFilter.h Exec_DataSetCmd.h Exec_Desc.h Exec_Emin.h Exec_ExtendedComparison.h Exec_Flatten.h Exec_GenerateAmberRst.h Exec_Graft.h Exec_Help.h Exec_HmassRepartition.h Exec_LoadCrd.h Exec_LoadTraj.h Exec_ParallelAnalysis.h Exec_ParmBox.h Exec_ParmSolvent.h Exec_ParmStrip.h Exec_ParmWrite.h Exec_ParseTiming.h Exec_PermuteDihedrals.h Exec_Precision.h Exec_PrepareForLeap.h Exec_PrintData.h Exec_Random.h Exec_ReadData.h Exec_ReadEnsembleData.h Exec_ReadInput.h Exec_RotateDihedral.h Exec_RunAnalysis.h Exec_ScaleDihedralK.h Exec_Sequence.h Exec_SequenceAlign.h Exec_Set.h Exec_Show.h Exec_SortEnsembleData.h Exec_SplitCoords.h Exec_System.h Exec_Top.h Exec_Traj.h Exec_UpdateParameters.h Exec_ViewRst.h Exec_Zmatrix.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h GIST_PME.h Grid.h GridAction.h GridBin.h GridMover.h HistBin.h Hungarian.h ImageOption.h ImageTypes.h InputTrajCommon.h MapAtom.h MaskArray.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h OnlineVarT.h OutputTrajCommon.h PDBfile.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PubFFT.h Pucker.h Pucker_PuckerMask.h Pucker_PuckerSearch.h Pucker_PuckerToken.h RPNcalc.h Random.h Range.h ReferenceAction.h ReferenceFrame.h RemdReservoirNC.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h SplineFxnTable.h Structure/StructureEnum.h StructureCheck.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h cuda_kernels/GistCudaSetup.cuh helpme_standalone.h molsurf.h
 CompactFrameArray.o : CompactFrameArray.cpp Box.h CompactFrameArray.h CoordinateInfo.h CpptrajStdio.h Matrix_3x3.h Parallel.h ReplicaDimArray.h Vec3.h
 ComplexArray.o : ComplexArray.cpp ArrayIterator.h ComplexArray.h
 Constraints.o : Constraints.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
@@ -290,7 +290,7 @@ Ewald_Regular.o : Ewald_Regular.cpp Atom.h AtomMask.h Box.h Constants.h Coordina
 ExclusionArray.o : ExclusionArray.cpp Atom.h AtomMask.h CharMask.h CpptrajStdio.h ExclusionArray.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Unit.h
 Exec_AddMissingRes.o : Exec_AddMissingRes.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CharMask.h CompactFrameArray.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_AddMissingRes.h Exec_AddMissingRes_Pres.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Analyze.o : Exec_Analyze.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Analyze.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Build.o : Exec_Build.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/GB_Params.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Build.o : Exec_Build.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/GB_Params.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Calc.o : Exec_Calc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Calc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_CatCrd.o : Exec_CatCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CatCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Change.o : Exec_Change.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Change.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h

From 6e9e67eba8094a7bcd29f0502c17c65391457ade Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 13 Jan 2024 19:06:21 -0500
Subject: [PATCH 0335/1492] If a specific terminal version of a res is not
 found, fall back to regular res

---
 src/Exec_Build.cpp | 22 +++++++++++++---------
 1 file changed, 13 insertions(+), 9 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 315e738300..0731d67377 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -14,15 +14,7 @@ DataSet_Coords* Exec_Build::IdTemplateFromName(Carray const& Templates,
                                                Cpptraj::Structure::TerminalType termType)
 {
   DataSet_Coords* out = 0;
-  if (termType == Cpptraj::Structure::NON_TERMINAL) {
-    // Assume Coords set aspect is what we need
-    for (Carray::const_iterator it = Templates.begin(); it != Templates.end(); ++it) {
-      if ( rname == NameType( (*it)->Meta().Aspect() ) ) {
-        out = *it;
-        break;
-      }
-    }
-  } else {
+  if (termType != Cpptraj::Structure::NON_TERMINAL) {
     // Looking for a terminal residue. Need to get sets with AssociatedData_ResId
     for (Carray::const_iterator it = Templates.begin(); it != Templates.end(); ++it) {
       AssociatedData* ad = (*it)->GetAssociatedData( AssociatedData::RESID );
@@ -35,6 +27,18 @@ DataSet_Coords* Exec_Build::IdTemplateFromName(Carray const& Templates,
       }
     }
   }
+  if (out == 0) {
+    // Terminal residue not found or non-terminal residue.
+    if (termType != Cpptraj::Structure::NON_TERMINAL)
+      mprintf("Warning: No terminal residue found for '%s'\n", *rname);
+    // Assume Coords set aspect is what we need
+    for (Carray::const_iterator it = Templates.begin(); it != Templates.end(); ++it) {
+      if ( rname == NameType( (*it)->Meta().Aspect() ) ) {
+        out = *it;
+        break;
+      }
+    }
+  }
 
   return out;
 }

From 5f991a71e57604e37e9e40ef5b71029396f76872 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 14 Jan 2024 15:06:04 -0500
Subject: [PATCH 0336/1492] Leap turns the dihedral around when k or l == 0
 even for "normal" dihedrals

---
 src/Parm_Amber.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Parm_Amber.cpp b/src/Parm_Amber.cpp
index 40b8d68ea1..c012e2278a 100644
--- a/src/Parm_Amber.cpp
+++ b/src/Parm_Amber.cpp
@@ -1630,7 +1630,7 @@ int Parm_Amber::WriteDihedrals(FlagType flag, DihedralArray const& DIH) {
   if (BufferAlloc(flag, DIH.size()*5)) return 1;
   for (DihedralArray::const_iterator it = DIH.begin(); it != DIH.end(); ++it) {
     int dihIdxs[4];
-    if (it->Type() != DihedralType::NORMAL && (it->A3() == 0 || it->A4() == 0)) {
+    if (it->A3() == 0 || it->A4() == 0) {
       mprintf("Warning: Had to turn torsion around to avoid K,L == 0\n");
       mprintf("Warning: Old order (i j k l): %i %i %i %i\n", it->A1(), it->A2(), it->A3(), it->A4());
       dihIdxs[0] = it->A4()*3;

From 41583eb26f2502dc412d43d519da399425d92b3a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 15 Jan 2024 10:16:35 -0500
Subject: [PATCH 0337/1492] Start function to update ICs

---
 src/Structure/Zmatrix.cpp | 35 ++++++++++++++++++++++++++++-------
 src/Structure/Zmatrix.h   |  8 +++++---
 2 files changed, 33 insertions(+), 10 deletions(-)

diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index 14b29f6c2d..c9231782fd 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -179,21 +179,24 @@ static inline void MARK(int i, std::vector<bool>& isUsed, unsigned int& Nused) {
   }
 }
 
-/** Calculate and add an internal coordinate given atom indices
+/** Calculate an internal coordinate given atom indices
   * and corresponding Cartesian coordinates.
   */
-void Zmatrix::addIc(int at0, int at1, int at2, int at3,
+static inline InternalCoords calcIc(int at0, int at1, int at2, int at3,
                    const double* xyz0, const double* xyz1,
                    const double* xyz2, const double* xyz3)
 {
-  IC_.push_back( InternalCoords(at0, at1, at2, at3,
+  return InternalCoords(at0, at1, at2, at3,
                                 sqrt(DIST2_NoImage(xyz0, xyz1)),
                                 CalcAngle(xyz0, xyz1, xyz2) * Constants::RADDEG,
-                                Torsion(xyz0, xyz1, xyz2, xyz3) * Constants::RADDEG) );
+                                Torsion(xyz0, xyz1, xyz2, xyz3) * Constants::RADDEG);
 }
 
+/** Calculate and add an internal coordinate given atom indices
+  * and corresponding Cartesian coordinates.
+  */
 void Zmatrix::addIc(int at0, int at1, int at2, int at3, Frame const& frameIn) {
-  addIc(at0, at1, at2, at3, frameIn.XYZ(at0), frameIn.XYZ(at1), frameIn.XYZ(at2), frameIn.XYZ(at3));
+  IC_.push_back( calcIc(at0, at1, at2, at3, frameIn.XYZ(at0), frameIn.XYZ(at1), frameIn.XYZ(at2), frameIn.XYZ(at3)) );
 }
 
 /** Set seeds as 3 consecutive atoms from mol 0 for which positions are known. */
@@ -585,10 +588,28 @@ int Zmatrix::addInternalCoordForAtom(int iat, Frame const& frameIn, Topology con
   return 0;
 }
 
+/** For existing torsions, see if all coordinates in that torsion
+  * exist. If so, update the IC from the existing coordinates.
+  */
+int Zmatrix::UpdateICsFromFrame(Frame const& frameIn, Barray const& hasPosition)
+{
+  for (ICarray::iterator ic = IC_.begin(); ic != IC_.end(); ++ic)
+  {
+    if (hasPosition[ic->AtI()] &&
+        hasPosition[ic->AtJ()] &&
+        hasPosition[ic->AtK()] &&
+        hasPosition[ic->AtL()])
+    {
+      mprintf("DEBUG: Updating IC %i %i %i %i\n", ic->AtI()+1, ic->AtJ()+1, ic->AtK()+1, ic->AtL()+1);
+    }
+  }
+  return 0;
+} 
+
 /** Set up Zmatrix from Cartesian coordinates and topology.
-  * Use torsions based on bonds to create a complete set of ICs.
+  * Use torsions based on connectivity to create a complete set of ICs.
   */
-int Zmatrix::SetFromFrameAndBonds(Frame const& frameIn, Topology const& topIn, int molnum)
+int Zmatrix::SetFromFrameAndConnect(Frame const& frameIn, Topology const& topIn, int molnum)
 {
   if (molnum < 0) {
     mprinterr("Internal Error: Zmatrix::SetFromFrame(): Negative molecule index.\n");
diff --git a/src/Structure/Zmatrix.h b/src/Structure/Zmatrix.h
index 3fbbf56f95..5c9a0d0c3e 100644
--- a/src/Structure/Zmatrix.h
+++ b/src/Structure/Zmatrix.h
@@ -41,8 +41,10 @@ class Zmatrix {
     /// Set seed atoms as 3 consecutive atoms with known positions for specified residue # TODO deprecate?
     int AutoSetSeedsWithPositions(Frame const&, Topology const&, int, Barray const&);
 
-    /// Try to generate complete ICs from bonds
-    int SetFromFrameAndBonds(Frame const&, Topology const&, int);
+    /// Try to generate complete ICs from atom connectivity
+    int SetFromFrameAndConnect(Frame const&, Topology const&, int);
+    /// Update ICs from existing coords
+    int UpdateICsFromFrame(Frame const&, Barray const&);
     /// Convert specifed molecule of Frame/Topology to internal coordinates array
     int SetFromFrame(Frame const&, Topology const&, int);
     /// Convert molecule 0 of Frame/Topology to internal coordinates array
@@ -80,7 +82,7 @@ class Zmatrix {
     /// Simple version of auto set seeds based on connectivity only
     int autoSetSeeds_simple(Frame const&, Topology const&, Molecule const&);
     /// Calculate and add an internal coordinate given indices and Cartesian coords.
-    inline void addIc(int,int,int,int,const double*,const double*,const double*,const double*);
+    //inline void addIc(int,int,int,int,const double*,const double*,const double*,const double*);
     /// Calculate and add an internal coordinate given indices and Cartesian coords.
     inline void addIc(int,int,int,int,Frame const&);
     /// Add internal coordinates by tracing a molecule

From c8d3e8cbe1d52cb7d8ba5da49fc07565fa4fc3ac Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 15 Jan 2024 10:18:54 -0500
Subject: [PATCH 0338/1492] Update the IC

---
 src/Structure/Zmatrix.cpp | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index c9231782fd..03d2d0e853 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -601,6 +601,7 @@ int Zmatrix::UpdateICsFromFrame(Frame const& frameIn, Barray const& hasPosition)
         hasPosition[ic->AtL()])
     {
       mprintf("DEBUG: Updating IC %i %i %i %i\n", ic->AtI()+1, ic->AtJ()+1, ic->AtK()+1, ic->AtL()+1);
+      *ic = calcIc(ic->AtI(), ic->AtJ(), ic->AtK(), ic->AtL(), frameIn.XYZ(ic->AtI()), frameIn.XYZ(ic->AtJ()), frameIn.XYZ(ic->AtK()), frameIn.XYZ(ic->AtL()));
     }
   }
   return 0;

From 2162e8647aef49a503d9d7294e3076dcfca5a0bd Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 15 Jan 2024 13:55:06 -0500
Subject: [PATCH 0339/1492] Rework the function so it is looking at all ICs
 that share a central bond. Pass in topology for debugging.

---
 src/Exec_Build.cpp        |  7 ++++-
 src/Structure/Zmatrix.cpp | 55 +++++++++++++++++++++++++++++++--------
 src/Structure/Zmatrix.h   |  2 +-
 3 files changed, 51 insertions(+), 13 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 0731d67377..cb0579ce12 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -291,7 +291,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
         Frame templateFrame = resTemplate->AllocateFrame();
         resTemplate->GetFrame( 0, templateFrame );
         Cpptraj::Structure::Zmatrix* zmatrix = new Cpptraj::Structure::Zmatrix();
-        if (zmatrix->SetFromFrameAndBonds( templateFrame, resTemplate->Top(), 0 )) {
+        if (zmatrix->SetFromFrameAndConnect( templateFrame, resTemplate->Top(), 0 )) {
           mprinterr("Error: Could not set up residue template zmatrix.\n");
           return 1;
         }
@@ -358,6 +358,11 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
     Cpptraj::Structure::Zmatrix* zmatrix = *it;
     if (zmatrix != 0) {
       mprintf("DEBUG: BUILD residue %li %s\n", ires + 1, topOut.TruncResNameOnumId(ires).c_str());
+      // Update internal coords from known positions
+      if (zmatrix->UpdateICsFromFrame( frameOut, topOut, hasPosition )) {
+        mprinterr("Error: Failed to update Zmatrix with values from existing positions.\n");
+        return 1;
+      }
       // Update zmatrix seeds
       //if (zmatrix->AutoSetSeedsWithPositions( frameOut, topOut, ires, hasPosition )) {
       //  mprinterr("Error: Could not set up seed atoms for Zmatrix.\n");
diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index 03d2d0e853..6b1f024874 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -591,19 +591,52 @@ int Zmatrix::addInternalCoordForAtom(int iat, Frame const& frameIn, Topology con
 /** For existing torsions, see if all coordinates in that torsion
   * exist. If so, update the IC from the existing coordinates.
   */
-int Zmatrix::UpdateICsFromFrame(Frame const& frameIn, Barray const& hasPosition)
+int Zmatrix::UpdateICsFromFrame(Frame const& frameIn, Topology const& topIn, Barray const& hasPosition)
 {
-  for (ICarray::iterator ic = IC_.begin(); ic != IC_.end(); ++ic)
-  {
-    if (hasPosition[ic->AtI()] &&
-        hasPosition[ic->AtJ()] &&
-        hasPosition[ic->AtK()] &&
-        hasPosition[ic->AtL()])
-    {
-      mprintf("DEBUG: Updating IC %i %i %i %i\n", ic->AtI()+1, ic->AtJ()+1, ic->AtK()+1, ic->AtL()+1);
-      *ic = calcIc(ic->AtI(), ic->AtJ(), ic->AtK(), ic->AtL(), frameIn.XYZ(ic->AtI()), frameIn.XYZ(ic->AtJ()), frameIn.XYZ(ic->AtK()), frameIn.XYZ(ic->AtL()));
+  Barray isUsed( IC_.size(), false );
+  unsigned int Nused = 0;
+  while (Nused < IC_.size()) {
+    unsigned int idx = 0;
+    while (idx < IC_.size() && isUsed[idx]) idx++;
+    if (idx >= IC_.size()) break;
+    // Unused IC. Find all other ICs that share atoms J-K
+    MARK(idx, isUsed, Nused);
+    Iarray bondICs(1, idx);
+    for (unsigned int jdx = idx + 1; jdx < IC_.size(); jdx++) {
+      if ( IC_[idx].AtJ() == IC_[jdx].AtJ() &&
+           IC_[idx].AtK() == IC_[jdx].AtK() )
+      {
+        bondICs.push_back( jdx );
+        MARK(jdx, isUsed, Nused);
+      }
     }
-  }
+    mprintf("DEBUG: Looking at %zu ICs involving %s - %s\n", bondICs.size(),
+            topIn.AtomMaskName(IC_[idx].AtJ()).c_str(),
+            topIn.AtomMaskName(IC_[idx].AtK()).c_str());
+    bool needsUpdate = false;
+    double tDiff = 0;
+    for (Iarray::const_iterator it = bondICs.begin(); it != bondICs.end(); ++it)
+    {
+      InternalCoords const& thisIc = IC_[*it];
+      if (hasPosition[thisIc.AtI()] &&
+          hasPosition[thisIc.AtJ()] &&
+          hasPosition[thisIc.AtK()] &&
+          hasPosition[thisIc.AtL()])
+      {
+        mprintf("DEBUG:\tMeasuring torsion of fixed atoms: %s - %s - %s - %s\n",
+                topIn.AtomMaskName(thisIc.AtI()).c_str(),
+                topIn.AtomMaskName(thisIc.AtJ()).c_str(),
+                topIn.AtomMaskName(thisIc.AtK()).c_str(),
+                topIn.AtomMaskName(thisIc.AtL()).c_str());
+        InternalCoords frameIc = calcIc(thisIc.AtI(), thisIc.AtJ(), thisIc.AtK(), thisIc.AtL(),
+                                        frameIn.XYZ(thisIc.AtI()), frameIn.XYZ(thisIc.AtJ()),
+                                        frameIn.XYZ(thisIc.AtK()), frameIn.XYZ(thisIc.AtL()));
+        mprintf("DEBUG:\tdTorsion= %f  dInternalValue= %f\n", frameIc.Phi(), thisIc.Phi());
+        tDiff = frameIc.Phi() - thisIc.Phi();
+        needsUpdate = true;
+      }
+    } // END loop over ICs sharing J-K bond
+  } // END loop over ICs
   return 0;
 } 
 
diff --git a/src/Structure/Zmatrix.h b/src/Structure/Zmatrix.h
index 5c9a0d0c3e..a02743285d 100644
--- a/src/Structure/Zmatrix.h
+++ b/src/Structure/Zmatrix.h
@@ -44,7 +44,7 @@ class Zmatrix {
     /// Try to generate complete ICs from atom connectivity
     int SetFromFrameAndConnect(Frame const&, Topology const&, int);
     /// Update ICs from existing coords
-    int UpdateICsFromFrame(Frame const&, Barray const&);
+    int UpdateICsFromFrame(Frame const&, Topology const&, Barray const&);
     /// Convert specifed molecule of Frame/Topology to internal coordinates array
     int SetFromFrame(Frame const&, Topology const&, int);
     /// Convert molecule 0 of Frame/Topology to internal coordinates array

From 548f0a31eea022cc2f477f7b793a0b48c1267875 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 15 Jan 2024 14:23:59 -0500
Subject: [PATCH 0340/1492] Try to update internals

---
 src/Structure/InternalCoords.h |  2 ++
 src/Structure/Zmatrix.cpp      | 27 ++++++++++++++++++++++++---
 2 files changed, 26 insertions(+), 3 deletions(-)

diff --git a/src/Structure/InternalCoords.h b/src/Structure/InternalCoords.h
index 7494d2f9d2..e655ce94a5 100644
--- a/src/Structure/InternalCoords.h
+++ b/src/Structure/InternalCoords.h
@@ -43,6 +43,8 @@ class InternalCoords {
     //void RemapIndices(std::vector<int> const&);
     /// Offset internal indices by given offset
     void OffsetIndices(int);
+    /// Set the value of Phi
+    void SetPhi(double p) { val_[2] = p; }
   private:
     int ati_;       ///< Atom I index
     int idx_[3];    ///< Atom indices for distance, angle, torsion
diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index 6b1f024874..c4a59960fc 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -631,11 +631,32 @@ int Zmatrix::UpdateICsFromFrame(Frame const& frameIn, Topology const& topIn, Bar
         InternalCoords frameIc = calcIc(thisIc.AtI(), thisIc.AtJ(), thisIc.AtK(), thisIc.AtL(),
                                         frameIn.XYZ(thisIc.AtI()), frameIn.XYZ(thisIc.AtJ()),
                                         frameIn.XYZ(thisIc.AtK()), frameIn.XYZ(thisIc.AtL()));
-        mprintf("DEBUG:\tdTorsion= %f  dInternalValue= %f\n", frameIc.Phi(), thisIc.Phi());
-        tDiff = frameIc.Phi() - thisIc.Phi();
+        double dTorsion = frameIc.Phi() * Constants::DEGRAD;
+        double dInternalValue = thisIc.Phi() * Constants::DEGRAD;
+        mprintf("DEBUG:\tdTorsion= %f  dInternalValue= %f\n", dTorsion, dInternalValue);
+        tDiff = (dTorsion - dInternalValue) * Constants::RADDEG;
         needsUpdate = true;
       }
-    } // END loop over ICs sharing J-K bond
+    } // END calc loop over ICs sharing J-K bond
+    // If any difference was found, shift all of the torsions
+    if (needsUpdate) {
+      mprintf("DEBUG: Twisting torsions centered on %s - %s by %f degrees\n",
+              topIn.AtomMaskName(IC_[idx].AtJ()).c_str(),
+              topIn.AtomMaskName(IC_[idx].AtK()).c_str(),
+              tDiff);
+      for (Iarray::const_iterator it = bondICs.begin(); it != bondICs.end(); ++it)
+      {
+        InternalCoords& thisIc = IC_[*it];
+        double dNew = thisIc.Phi() + tDiff;
+        mprintf("DEBUG:\tTwisting torsion for atoms: %s-%s-%s-%s\n",
+                topIn.AtomMaskName(thisIc.AtI()).c_str(),
+                topIn.AtomMaskName(thisIc.AtJ()).c_str(),
+                topIn.AtomMaskName(thisIc.AtK()).c_str(),
+                topIn.AtomMaskName(thisIc.AtL()).c_str());
+        mprintf("DEBUG:\t------- From %f to %f\n", thisIc.Phi(), dNew);
+        thisIc.SetPhi( dNew );
+      }
+    }
   } // END loop over ICs
   return 0;
 } 

From c2abc9efed02ad647d47e8fd9596fd7f0b66be40 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 16 Jan 2024 18:53:12 -0500
Subject: [PATCH 0341/1492] Start new code to update internals in same order as
 leap

---
 src/Exec_Build.cpp        |  2 +-
 src/Structure/Zmatrix.cpp | 85 +++++++++++++++++++++++++++++++++++----
 src/Structure/Zmatrix.h   |  2 +-
 3 files changed, 79 insertions(+), 10 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index cb0579ce12..d6e9ab12d5 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -359,7 +359,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
     if (zmatrix != 0) {
       mprintf("DEBUG: BUILD residue %li %s\n", ires + 1, topOut.TruncResNameOnumId(ires).c_str());
       // Update internal coords from known positions
-      if (zmatrix->UpdateICsFromFrame( frameOut, topOut, hasPosition )) {
+      if (zmatrix->UpdateICsFromFrame( frameOut, ires, topOut, hasPosition )) {
         mprinterr("Error: Failed to update Zmatrix with values from existing positions.\n");
         return 1;
       }
diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index c4a59960fc..d14b567a17 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -6,6 +6,7 @@
 #include "Zmatrix.h"
 #include "BuildAtom.h"
 #include "Model.h"
+#include "GenerateConnectivityArrays.h"
 #include "../Frame.h"
 #include "../CpptrajStdio.h"
 #include "../Constants.h"
@@ -591,8 +592,71 @@ int Zmatrix::addInternalCoordForAtom(int iat, Frame const& frameIn, Topology con
 /** For existing torsions, see if all coordinates in that torsion
   * exist. If so, update the IC from the existing coordinates.
   */
-int Zmatrix::UpdateICsFromFrame(Frame const& frameIn, Topology const& topIn, Barray const& hasPosition)
+int Zmatrix::UpdateICsFromFrame(Frame const& frameIn, int ires, Topology const& topIn, Barray const& hasPosition)
 {
+  Barray isUsed( IC_.size(), false );
+  unsigned int Nused = 0;
+  // Get list of bonds 
+  BondArray myBonds = GenerateBondArray( std::vector<Residue>(1, topIn.Res(ires)), topIn.Atoms() );
+  for (BondArray::const_iterator bnd = myBonds.begin(); bnd != myBonds.end(); ++bnd) {
+    if (topIn[bnd->A1()].ResNum() == ires && topIn[bnd->A2()].ResNum() == ires) {
+      mprintf("DEBUG: Looking at torsions around: %s - %s\n", topIn.AtomMaskName(bnd->A1()).c_str(), topIn.AtomMaskName(bnd->A2()).c_str());    // Find all ICs that share atoms 1 and 2 (J and K)
+      Iarray bondICs;
+      bool needsUpdate = false;
+      double tDiff = 0;
+      for (unsigned int idx = 0; idx != IC_.size(); idx++)
+      {
+        if (!isUsed[idx]) {
+          InternalCoords& thisIc = IC_[idx];
+          if (bnd->A1() == thisIc.AtJ() && bnd->A2() == thisIc.AtK()) {
+            // This IC has this bond at the center
+            bondICs.push_back( idx );
+            MARK(idx, isUsed, Nused);
+            if (hasPosition[thisIc.AtI()] &&
+                hasPosition[thisIc.AtJ()] &&
+                hasPosition[thisIc.AtK()] &&
+                hasPosition[thisIc.AtL()])
+            {
+              mprintf("DEBUG:\tMeasuring torsion of fixed atoms: %s - %s - %s - %s\n",
+                      topIn.AtomMaskName(thisIc.AtI()).c_str(),
+                      topIn.AtomMaskName(thisIc.AtJ()).c_str(),
+                      topIn.AtomMaskName(thisIc.AtK()).c_str(),
+                      topIn.AtomMaskName(thisIc.AtL()).c_str());
+              InternalCoords frameIc = calcIc(thisIc.AtI(), thisIc.AtJ(), thisIc.AtK(), thisIc.AtL(),
+                                              frameIn.XYZ(thisIc.AtI()), frameIn.XYZ(thisIc.AtJ()),
+                                              frameIn.XYZ(thisIc.AtK()), frameIn.XYZ(thisIc.AtL()));
+              double dTorsion = frameIc.Phi() * Constants::DEGRAD;
+              double dInternalValue = thisIc.Phi() * Constants::DEGRAD;
+              tDiff = (dTorsion - dInternalValue) * Constants::RADDEG;
+              mprintf("DEBUG:\tdTorsion= %f  dInternalValue= %f\n", dTorsion, dInternalValue);
+              thisIc = frameIc;
+              needsUpdate = true;
+            } // END all IC coords present
+          } // END this IC matches current bond
+        } // END IC is not used
+      } // END loop searching for ICs matching current bond
+      // If any difference was found, shift all of the torsions
+      if (needsUpdate) {
+        mprintf("DEBUG: Twisting torsions centered on %s - %s by %f degrees\n",
+                topIn.AtomMaskName(bnd->A1()).c_str(),
+                topIn.AtomMaskName(bnd->A2()).c_str(),
+                tDiff);
+        for (Iarray::const_iterator it = bondICs.begin(); it != bondICs.end(); ++it)
+        {
+          InternalCoords& thisIc = IC_[*it];
+          double dNew = thisIc.Phi() + tDiff;
+          mprintf("DEBUG:\tTwisting torsion for atoms: %s-%s-%s-%s\n",
+                  topIn.AtomMaskName(thisIc.AtI()).c_str(),
+                  topIn.AtomMaskName(thisIc.AtJ()).c_str(),
+                  topIn.AtomMaskName(thisIc.AtK()).c_str(),
+                  topIn.AtomMaskName(thisIc.AtL()).c_str());
+          mprintf("DEBUG:\t------- From %f to %f\n", thisIc.Phi(), dNew);
+          thisIc.SetPhi( dNew );
+        }
+      } // END ICs need update
+    } // END both bond atoms belong to this residue
+  } // END loop over bonds
+/*
   Barray isUsed( IC_.size(), false );
   unsigned int Nused = 0;
   while (Nused < IC_.size()) {
@@ -614,10 +678,12 @@ int Zmatrix::UpdateICsFromFrame(Frame const& frameIn, Topology const& topIn, Bar
             topIn.AtomMaskName(IC_[idx].AtJ()).c_str(),
             topIn.AtomMaskName(IC_[idx].AtK()).c_str());
     bool needsUpdate = false;
+    Iarray toUpdate;
+    toUpdate.reserve( bondICs.size() );
     double tDiff = 0;
-    for (Iarray::const_iterator it = bondICs.begin(); it != bondICs.end(); ++it)
+    for (Iarray::iterator it = bondICs.begin(); it != bondICs.end(); ++it)
     {
-      InternalCoords const& thisIc = IC_[*it];
+      InternalCoords& thisIc = IC_[*it];
       if (hasPosition[thisIc.AtI()] &&
           hasPosition[thisIc.AtJ()] &&
           hasPosition[thisIc.AtK()] &&
@@ -633,9 +699,12 @@ int Zmatrix::UpdateICsFromFrame(Frame const& frameIn, Topology const& topIn, Bar
                                         frameIn.XYZ(thisIc.AtK()), frameIn.XYZ(thisIc.AtL()));
         double dTorsion = frameIc.Phi() * Constants::DEGRAD;
         double dInternalValue = thisIc.Phi() * Constants::DEGRAD;
-        mprintf("DEBUG:\tdTorsion= %f  dInternalValue= %f\n", dTorsion, dInternalValue);
         tDiff = (dTorsion - dInternalValue) * Constants::RADDEG;
+        mprintf("DEBUG:\tdTorsion= %f  dInternalValue= %f\n", dTorsion, dInternalValue);
+        thisIc = frameIc;
         needsUpdate = true;
+      } else {
+        toUpdate.push_back( *it );
       }
     } // END calc loop over ICs sharing J-K bond
     // If any difference was found, shift all of the torsions
@@ -644,7 +713,7 @@ int Zmatrix::UpdateICsFromFrame(Frame const& frameIn, Topology const& topIn, Bar
               topIn.AtomMaskName(IC_[idx].AtJ()).c_str(),
               topIn.AtomMaskName(IC_[idx].AtK()).c_str(),
               tDiff);
-      for (Iarray::const_iterator it = bondICs.begin(); it != bondICs.end(); ++it)
+      for (Iarray::const_iterator it = toUpdate.begin(); it != toUpdate.end(); ++it)
       {
         InternalCoords& thisIc = IC_[*it];
         double dNew = thisIc.Phi() + tDiff;
@@ -657,7 +726,7 @@ int Zmatrix::UpdateICsFromFrame(Frame const& frameIn, Topology const& topIn, Bar
         thisIc.SetPhi( dNew );
       }
     }
-  } // END loop over ICs
+  } // END loop over ICs*/
   return 0;
 } 
 
@@ -695,10 +764,10 @@ int Zmatrix::SetFromFrameAndConnect(Frame const& frameIn, Topology const& topIn,
             for (int bidx3 = 0; bidx3 < At3.Nbonds(); bidx3++) {
               int iat4 = At3.Bond(bidx3);
               if (iat4 != iat2 && iat1 < iat4) {
-                mprintf("DEBUG: DIHEDRAL  %i - %i - %i - %i (%i %i %i %i)\n", iat1+1, iat2+1, iat3+1, iat4+1, iat1*3, iat2*3, iat3*3, iat4*3);
+                //mprintf("DEBUG: DIHEDRAL  %i - %i - %i - %i (%i %i %i %i)\n", iat1+1, iat2+1, iat3+1, iat4+1, iat1*3, iat2*3, iat3*3, iat4*3);
                 //out.push_back( DihedralType( iat1, iat2, iat3, iat4, -1 ) );
                 addIc(iat1, iat2, iat3, iat4, frameIn);
-                addIc(iat4, iat3, iat2, iat1, frameIn);
+                addIc(iat4, iat3, iat2, iat1, frameIn); // FIXME should the reverse one be put in?
               }
             }
           }
diff --git a/src/Structure/Zmatrix.h b/src/Structure/Zmatrix.h
index a02743285d..0788df4a74 100644
--- a/src/Structure/Zmatrix.h
+++ b/src/Structure/Zmatrix.h
@@ -44,7 +44,7 @@ class Zmatrix {
     /// Try to generate complete ICs from atom connectivity
     int SetFromFrameAndConnect(Frame const&, Topology const&, int);
     /// Update ICs from existing coords
-    int UpdateICsFromFrame(Frame const&, Topology const&, Barray const&);
+    int UpdateICsFromFrame(Frame const&, int, Topology const&, Barray const&);
     /// Convert specifed molecule of Frame/Topology to internal coordinates array
     int SetFromFrame(Frame const&, Topology const&, int);
     /// Convert molecule 0 of Frame/Topology to internal coordinates array

From d8b9596d493647ebfa78275388c0d8dd69478743 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 17 Jan 2024 16:23:13 -0500
Subject: [PATCH 0342/1492] Start building ICs the same way as leap

---
 src/Exec_Build.cpp        |  26 ++++--
 src/Exec_Build.h          |   2 +-
 src/Structure/Model.cpp   | 167 ++++++++++++++++++++++++++++++++++++++
 src/Structure/Model.h     |   8 ++
 src/Structure/Zmatrix.cpp |  40 +++++++++
 src/Structure/Zmatrix.h   |   3 +
 6 files changed, 236 insertions(+), 10 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index d6e9ab12d5..6417433e9e 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -70,7 +70,8 @@ std::vector<int> Exec_Build::MapAtomsToTemplate(Topology const& topIn,
 /** Use given templates to construct a final molecule. */
 int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
                                        Carray const& Templates,
-                                       Topology const& topIn, Frame const& frameIn)
+                                       Topology const& topIn, Frame const& frameIn,
+                                       ParameterSet const& mainParmSet)
 {
   // Residue terminal status
   
@@ -358,6 +359,12 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
     Cpptraj::Structure::Zmatrix* zmatrix = *it;
     if (zmatrix != 0) {
       mprintf("DEBUG: BUILD residue %li %s\n", ires + 1, topOut.TruncResNameOnumId(ires).c_str());
+      // TEST FIXME
+      Cpptraj::Structure::Zmatrix testZ;
+      if (testZ.BuildZmatrixFromTop(frameOut, topOut, ires, mainParmSet.AT(), hasPosition)) {
+        mprinterr("Error: Failed to create zmatrix from topology.\n");
+        return 1;
+      }
       // Update internal coords from known positions
       if (zmatrix->UpdateICsFromFrame( frameOut, ires, topOut, hasPosition )) {
         mprinterr("Error: Failed to update Zmatrix with values from existing positions.\n");
@@ -519,14 +526,6 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
     mprintf("\n");
   }
 
-  // Fill in atoms with templates
-  Topology topOut;
-  Frame frameOut;
-  if (FillAtomsWithTemplates(topOut, frameOut, Templates, topIn, frameIn)) {
-    mprinterr("Error: Could not fill in atoms using templates.\n");
-    return CpptrajState::ERR;
-  }
-
   // Get parameter sets.
   typedef std::vector<DataSet_Parameters*> Parray;
   Parray ParamSets;
@@ -573,6 +572,15 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
       mainParmSet->UpdateParamSet( *(*it), UC, State.Debug(), State.Debug() ); // FIXME verbose
   }
 
+  // Fill in atoms with templates
+  Topology topOut;
+  Frame frameOut;
+  if (FillAtomsWithTemplates(topOut, frameOut, Templates, topIn, frameIn, *mainParmSet)) {
+    mprinterr("Error: Could not fill in atoms using templates.\n");
+    return CpptrajState::ERR;
+  }
+
+
   // Assign parameters. This will create the bond/angle/dihedral/improper
   // arrays as well.
   Exec::RetType ret = CpptrajState::OK;
diff --git a/src/Exec_Build.h b/src/Exec_Build.h
index d25edf4b24..4e9b793bf1 100644
--- a/src/Exec_Build.h
+++ b/src/Exec_Build.h
@@ -15,7 +15,7 @@ class Exec_Build : public Exec {
     /// Identify residue template from residue name
     static DataSet_Coords* IdTemplateFromName(Carray const&, NameType const&, Cpptraj::Structure::TerminalType);
     /// Create new topology/frame using templates
-    static int FillAtomsWithTemplates(Topology&, Frame&, Carray const&, Topology const&, Frame const&);
+    static int FillAtomsWithTemplates(Topology&, Frame&, Carray const&, Topology const&, Frame const&, ParameterSet const&);
     /// Map atoms in topology to template
     static std::vector<int> MapAtomsToTemplate(Topology const&, int, DataSet_Coords*);
 };
diff --git a/src/Structure/Model.cpp b/src/Structure/Model.cpp
index 33b99d4a16..21c7705fb8 100644
--- a/src/Structure/Model.cpp
+++ b/src/Structure/Model.cpp
@@ -1,5 +1,6 @@
 #include "Model.h"
 #include "BuildAtom.h"
+#include "Chirality.h"
 #include "../CpptrajStdio.h"
 #include "../GuessAtomHybridization.h"
 #include "../Topology.h"
@@ -259,3 +260,169 @@ int Cpptraj::Structure::Model::AssignPhi(double& phi, int ai, int aj, int ak, in
 
   return 0;
 }
+
+/** Attempt to assign a reasonable values for phi internal coordinates for
+  * atoms around a central bond j and k.
+  */
+int Cpptraj::Structure::Model::AssignPhiAroundBond(std::vector<InternalCoords>& IC,
+                                                   ParmHolder<AtomType> const& AT,
+                                                   int ax, int ay,
+                                                   Topology const& topIn, Frame const& frameIn,
+                                                   std::vector<bool> const& atomPositionKnown,
+                                                   int debug)
+{
+  // Figure out hybridization and chirality of atom j.
+  //if (debug > 0)
+    mprintf("DEBUG: AssignPhi for bond %s - %s\n", topIn.AtomMaskName(ax).c_str(), topIn.AtomMaskName(ay).c_str());
+
+  // Both need to have more than 1 bond
+  if (topIn[ax].Nbonds() < 2 || topIn[ay].Nbonds() < 2) {
+    mprintf("DEBUG: Not possible to make a torsion (%i bonds, %i bonds)\n", topIn[ax].Nbonds(), topIn[ay].Nbonds());
+    return 0;
+  }
+  // Get hybridization of atoms x and y
+  ParmHolder<AtomType>::const_iterator atx = AT.GetParam( TypeNameHolder(topIn[ax].Type()) );
+  ParmHolder<AtomType>::const_iterator aty = AT.GetParam( TypeNameHolder(topIn[ay].Type()) );
+  AtomType::HybridizationType hx, hy;
+  if (atx != AT.end() && atx->second.Hybridization() == AtomType::UNKNOWN_HYBRIDIZATION)
+    hx = GuessAtomHybridization( topIn[ax], topIn.Atoms() );
+  else
+    hx = atx->second.Hybridization();
+  if (aty != AT.end() && aty->second.Hybridization() == AtomType::UNKNOWN_HYBRIDIZATION)
+    hy = GuessAtomHybridization( topIn[ax], topIn.Atoms() );
+  else
+    hy = aty->second.Hybridization();
+
+  int aj, ak;
+  // Ensure hybridization of atom X is > atom Y
+  if (hx < hy) {
+    aj = ay;
+    ak = ax;
+  } else {
+    aj = ax;
+    ak = ay;
+  }
+  mprintf("DEBUG: In hybridization order: %s - %s (%i - %i)\n", topIn.AtomMaskName(aj).c_str(), topIn.AtomMaskName(ak).c_str(),
+          (int)hx, (int)hy);
+
+  Atom const& AJ = topIn[aj];
+  Atom const& AK = topIn[ak];
+
+/*
+  BuildAtom AtomJ;
+  if (AJ.Nbonds() > 2) {
+    Cpptraj::Structure::SetPriority(AtomJ.ModifyPriority(), aj, topIn, frameIn, 0); // FIXME chiralityDebug
+  }
+
+
+//  if (debug > 0) mprintf("DEBUG:\t\tNbonds: %i\n", AJ.Nbonds());
+//  // If atom J only has 2 bonds, ai-aj-ak-al is the only possibility.
+//  if (AJ.Nbonds() < 3) {
+//    if (debug > 0)
+//      mprintf("DEBUG:\t\tFewer than 3 bonds. Setting phi to -180.\n");
+//    phi = -180 * Constants::DEGRAD;
+//    return 0;
+//  }
+
+  // TODO check that atom i actually ends up on the list?
+  std::vector<int> const& priority = AtomJ.Priority();
+  int ai = 
+  if (debug > 0) {
+    mprintf("DEBUG: Original chirality around J %s is %s\n", topIn.AtomMaskName(aj).c_str(), chiralStr(AtomJ.Chirality()));
+    mprintf("DEBUG:\t\tPriority around J %s(%i):", 
+            topIn.AtomMaskName(aj).c_str(), (int)atomPositionKnown[aj]);
+    for (int idx = 0; idx < AJ.Nbonds(); idx++)
+      mprintf(" %s(%i)", topIn.AtomMaskName(priority[idx]).c_str(), (int)atomPositionKnown[priority[idx]]);
+    mprintf("\n");
+  }
+
+  // Fill in what values we can for known atoms
+  std::vector<double> knownPhi( AJ.Nbonds() );
+  int knownIdx = -1;
+  for (int idx = 0; idx < AJ.Nbonds(); idx++) {
+    int atnum = priority[idx];
+    if (atnum != ak && atomPositionKnown[atnum] &&
+                       atomPositionKnown[aj] &&
+                       atomPositionKnown[ak] &&
+                       atomPositionKnown[al])
+    {
+      knownPhi[idx] = Torsion(frameIn.XYZ(atnum),
+                              frameIn.XYZ(aj),
+                              frameIn.XYZ(ak),
+                              frameIn.XYZ(al));
+      if (debug > 0)
+        mprintf("DEBUG:\t\tKnown phi for %s = %g\n", topIn.AtomMaskName(atnum).c_str(), knownPhi[idx]*Constants::RADDEG);
+      if (knownIdx == -1) knownIdx = idx; // FIXME handle more than 1 known
+    }
+  }
+
+  // If we have to assign an initial phi, make trans the longer branch
+  if (knownIdx == -1) {
+    std::vector<bool> visited = atomPositionKnown;
+    // TODO: Ensure bonded atoms are not yet visited?
+    visited[aj] = true;
+    visited[ak] = true;
+    std::vector<int> depth( AJ.Nbonds() );
+    for (int idx = 0; idx < AJ.Nbonds(); idx++) {
+      int atnum = priority[idx];
+      if (atnum != ak) {
+        int currentDepth = 0;
+        depth[idx] = atom_depth(currentDepth, atnum, topIn, visited, 10);
+        if (debug > 0)
+          mprintf("DEBUG:\t\tAJ %s depth from %s is %i\n",
+                  topIn.AtomMaskName(aj).c_str(), topIn.AtomMaskName(atnum).c_str(), depth[idx]);
+        if (knownIdx == -1 && depth[idx] < 3) {
+          knownIdx = idx;
+          knownPhi[idx] = 0;
+        }
+      }
+    }
+  }
+
+  // The interval will be 360 / (number of bonds - 1)
+  double interval = Constants::TWOPI / (AJ.Nbonds() - 1);
+
+  double startPhi;
+  if (knownIdx == -1) {
+    startPhi = -180*Constants::DEGRAD;
+    if (debug > 0) mprintf("DEBUG:\t\tNo known phi. Setting to %g.\n", startPhi*Constants::RADDEG);
+    knownIdx = 0;
+  } else
+    startPhi = knownPhi[knownIdx];
+
+  if (AtomJ.Chirality() == IS_R) {
+    startPhi = -startPhi;
+    interval = -interval;
+  }
+  if (debug > 0) {
+    mprintf("DEBUG:\t\tStart phi is %g degrees\n", startPhi*Constants::RADDEG);
+    mprintf("DEBUG:\t\tInterval is %g degrees\n", interval * Constants::RADDEG);
+  }
+    
+  // Forward direction
+  double currentPhi = startPhi;
+  for (int idx = knownIdx; idx < AJ.Nbonds(); idx++) {
+    int atnum = priority[idx];
+    if (atnum != ak) {
+      if (atnum == ai) phi = currentPhi;
+      if (debug > 0)
+        mprintf("DEBUG:\t\t\t%s phi= %g\n", topIn.AtomMaskName(atnum).c_str(), currentPhi*Constants::RADDEG);
+      currentPhi += interval;
+      currentPhi = wrap360(currentPhi);
+    }
+  }
+  // Reverse direction
+  currentPhi = startPhi - interval;
+  for (int idx = knownIdx - 1; idx > -1; idx--) {
+    int atnum = priority[idx];
+    if (atnum != ak) {
+      if (atnum == ai) phi = currentPhi;
+      if (debug > 0)
+        mprintf("DEBUG:\t\t\t%s phi= %g\n", topIn.AtomMaskName(atnum).c_str(), currentPhi*Constants::RADDEG);
+      currentPhi -= interval;
+      currentPhi = wrap360(currentPhi);
+    }
+  }
+*/
+  return 0;
+}
diff --git a/src/Structure/Model.h b/src/Structure/Model.h
index 240e64875e..0f58f6f260 100644
--- a/src/Structure/Model.h
+++ b/src/Structure/Model.h
@@ -4,9 +4,12 @@
 #include "StructureEnum.h"
 class Topology;
 class Frame;
+class AtomType;
+template <typename T> class ParmHolder;
 namespace Cpptraj {
 namespace Structure {
 class BuildAtom;
+class InternalCoords;
 /// Routines to generate model parameters
 namespace Model {
 /// Given atoms J K and L, attempt to assign a reasonable value for phi for atom I
@@ -14,6 +17,11 @@ int AssignPhi(double&, int, int, int, int, Topology const&, Frame const&, std::v
 /// Given atoms J and K, attempt to assign a reasonable value for theta for atom I
 int AssignTheta(double&, int, int, int, Topology const&, Frame const&, std::vector<bool> const&, int);
 
+int AssignPhiAroundBond(std::vector<InternalCoords>&, ParmHolder<AtomType> const&,
+                        int, int, Topology const&, Frame const&,
+                        std::vector<bool> const&, int);
+
+
 } // END namespace Model
 } // END namespace Structure
 } // END namespace Cpptraj
diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index d14b567a17..f36f15b693 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -730,6 +730,46 @@ int Zmatrix::UpdateICsFromFrame(Frame const& frameIn, int ires, Topology const&
   return 0;
 } 
 
+/** Set up Zmatrix in a manner similar to leap. */
+int Zmatrix::BuildZmatrixFromTop(Frame const& frameIn, Topology const& topIn, int ires, ParmHolder<AtomType> const& AT,
+                                 Barray const& hasPosition)
+{
+  if (ires < 0) {
+    mprinterr("Internal Error: Zmatrix::BuildZmatrixFromTop(): Negative residue index.\n");
+    return 1;
+  }         
+  //if (topIn.Nmol() < 1) {
+  //  mprinterr("Internal Error: Zmatrix::SetFromFrame(): No molecules.\n");
+  //  return 1;
+  //}
+  clear(); 
+  
+  IC_.clear();
+  //Molecule const& currentMol = topIn.Mol(molnum);
+  //std::vector<Residue> residues;
+  //for (Unit::const_iterator seg = currentMol.MolUnit().segBegin();
+  //                          seg != currentMol.MolUnit().segEnd(); ++seg)
+  //{
+  //  int r0 = topIn[seg->Begin()].ResNum();
+  //  int r1 = topIn[seg->End()].ResNum();
+  //  for (int ridx = r0; ridx <= r1; ridx++)
+  //    residues.push_back( topIn.Res(ridx) );
+  //}
+  BondArray myBonds = GenerateBondArray( std::vector<Residue>(1, topIn.Res(ires)), topIn.Atoms() );
+  for (BondArray::const_iterator bnd = myBonds.begin(); bnd != myBonds.end(); ++bnd)
+  {
+    if (Cpptraj::Structure::Model::AssignPhiAroundBond(IC_, AT, bnd->A1(), bnd->A2(), topIn, frameIn, hasPosition, debug_))
+    {
+      mprinterr("Error: Assigning phi around bond %s - %s failed.\n",
+                topIn.AtomMaskName(bnd->A1()).c_str(),
+                topIn.AtomMaskName(bnd->A2()).c_str());
+      return 1;
+    }
+  }
+
+  return 0;
+}
+
 /** Set up Zmatrix from Cartesian coordinates and topology.
   * Use torsions based on connectivity to create a complete set of ICs.
   */
diff --git a/src/Structure/Zmatrix.h b/src/Structure/Zmatrix.h
index 0788df4a74..1ebdbcaec2 100644
--- a/src/Structure/Zmatrix.h
+++ b/src/Structure/Zmatrix.h
@@ -6,6 +6,8 @@
 class Frame;
 class Topology;
 class Molecule;
+template <typename T> class ParmHolder;
+class AtomType;
 namespace Cpptraj {
 namespace Structure {
 class BuildAtom;
@@ -43,6 +45,7 @@ class Zmatrix {
 
     /// Try to generate complete ICs from atom connectivity
     int SetFromFrameAndConnect(Frame const&, Topology const&, int);
+    int BuildZmatrixFromTop(Frame const&, Topology const&, int, ParmHolder<AtomType> const&, Barray const&);
     /// Update ICs from existing coords
     int UpdateICsFromFrame(Frame const&, int, Topology const&, Barray const&);
     /// Convert specifed molecule of Frame/Topology to internal coordinates array

From 9b56062e9aaca32859e0e44d8023a42773ccdb6d Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 18 Jan 2024 08:25:31 -0500
Subject: [PATCH 0343/1492] More debug

---
 src/Exec_Build.cpp | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 6417433e9e..727ecf7101 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -296,10 +296,10 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
           mprinterr("Error: Could not set up residue template zmatrix.\n");
           return 1;
         }
-        zmatrix->print( resTemplate->TopPtr() );
+//        zmatrix->print( resTemplate->TopPtr() );
         zmatrix->OffsetIcIndices( atomOffset );
         ResZmatrices.push_back( zmatrix );
-        zmatrix->print( &topOut );
+//        zmatrix->print( &topOut );
         //for (Iarray::const_iterator jres = resConnections[ires].begin();
         //                            jres != resConnections[ires].end(); ++jres)
         //{
@@ -360,11 +360,14 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
     if (zmatrix != 0) {
       mprintf("DEBUG: BUILD residue %li %s\n", ires + 1, topOut.TruncResNameOnumId(ires).c_str());
       // TEST FIXME
-      Cpptraj::Structure::Zmatrix testZ;
-      if (testZ.BuildZmatrixFromTop(frameOut, topOut, ires, mainParmSet.AT(), hasPosition)) {
-        mprinterr("Error: Failed to create zmatrix from topology.\n");
-        return 1;
-      }
+//      Cpptraj::Structure::Zmatrix testZ;
+//      if (testZ.BuildZmatrixFromTop(frameOut, topOut, ires, mainParmSet.AT(), hasPosition)) {
+//        mprinterr("Error: Failed to create zmatrix from topology.\n");
+//        return 1;
+//      }
+      mprintf("DEBUG: Zmatrix for building residue %li %s\n", ires + 1,
+              topOut.TruncResNameOnumId(ires).c_str());
+      zmatrix->print(&topOut);
       // Update internal coords from known positions
       if (zmatrix->UpdateICsFromFrame( frameOut, ires, topOut, hasPosition )) {
         mprinterr("Error: Failed to update Zmatrix with values from existing positions.\n");
@@ -375,9 +378,6 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
       //  mprinterr("Error: Could not set up seed atoms for Zmatrix.\n");
       //  buildFailed = true;
       //} else {
-        mprintf("DEBUG: Zmatrix for building residue %li %s\n", ires + 1,
-                topOut.TruncResNameOnumId(ires).c_str());
-        zmatrix->print(&topOut);
         zmatrix->SetDebug( 1 ); // DEBUG
         if (zmatrix->SetToFrame( frameOut, hasPosition )) {
           mprinterr("Error: Building residue %s failed.\n",

From ee59020d1c8159b67d4bde2d05f95a79db6fd47d Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 18 Jan 2024 09:21:32 -0500
Subject: [PATCH 0344/1492] Get rid of BuildZmatrixFromTop

---
 src/Structure/Zmatrix.cpp | 49 ++++++---------------------------------
 src/Structure/Zmatrix.h   |  3 ---
 2 files changed, 7 insertions(+), 45 deletions(-)

diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index f36f15b693..89f5916188 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -608,7 +608,9 @@ int Zmatrix::UpdateICsFromFrame(Frame const& frameIn, int ires, Topology const&
       {
         if (!isUsed[idx]) {
           InternalCoords& thisIc = IC_[idx];
-          if (bnd->A1() == thisIc.AtJ() && bnd->A2() == thisIc.AtK()) {
+          if ( (bnd->A1() == thisIc.AtJ() && bnd->A2() == thisIc.AtK()) ||
+               (bnd->A2() == thisIc.AtJ() && bnd->A1() == thisIc.AtK()) )
+          {
             // This IC has this bond at the center
             bondICs.push_back( idx );
             MARK(idx, isUsed, Nused);
@@ -730,46 +732,6 @@ int Zmatrix::UpdateICsFromFrame(Frame const& frameIn, int ires, Topology const&
   return 0;
 } 
 
-/** Set up Zmatrix in a manner similar to leap. */
-int Zmatrix::BuildZmatrixFromTop(Frame const& frameIn, Topology const& topIn, int ires, ParmHolder<AtomType> const& AT,
-                                 Barray const& hasPosition)
-{
-  if (ires < 0) {
-    mprinterr("Internal Error: Zmatrix::BuildZmatrixFromTop(): Negative residue index.\n");
-    return 1;
-  }         
-  //if (topIn.Nmol() < 1) {
-  //  mprinterr("Internal Error: Zmatrix::SetFromFrame(): No molecules.\n");
-  //  return 1;
-  //}
-  clear(); 
-  
-  IC_.clear();
-  //Molecule const& currentMol = topIn.Mol(molnum);
-  //std::vector<Residue> residues;
-  //for (Unit::const_iterator seg = currentMol.MolUnit().segBegin();
-  //                          seg != currentMol.MolUnit().segEnd(); ++seg)
-  //{
-  //  int r0 = topIn[seg->Begin()].ResNum();
-  //  int r1 = topIn[seg->End()].ResNum();
-  //  for (int ridx = r0; ridx <= r1; ridx++)
-  //    residues.push_back( topIn.Res(ridx) );
-  //}
-  BondArray myBonds = GenerateBondArray( std::vector<Residue>(1, topIn.Res(ires)), topIn.Atoms() );
-  for (BondArray::const_iterator bnd = myBonds.begin(); bnd != myBonds.end(); ++bnd)
-  {
-    if (Cpptraj::Structure::Model::AssignPhiAroundBond(IC_, AT, bnd->A1(), bnd->A2(), topIn, frameIn, hasPosition, debug_))
-    {
-      mprinterr("Error: Assigning phi around bond %s - %s failed.\n",
-                topIn.AtomMaskName(bnd->A1()).c_str(),
-                topIn.AtomMaskName(bnd->A2()).c_str());
-      return 1;
-    }
-  }
-
-  return 0;
-}
-
 /** Set up Zmatrix from Cartesian coordinates and topology.
   * Use torsions based on connectivity to create a complete set of ICs.
   */
@@ -1329,8 +1291,11 @@ int Zmatrix::SetToFrame(Frame& frameOut, Barray& hasPosition) const {
       }
       continue; // FIXME
     }
-    if (debug_ > 0) mprintf("DEBUG: Next IC to use is %i\n", icIdx+1);
     InternalCoords const& ic = IC_[icIdx];
+    if (debug_ > 0)
+      mprintf("DEBUG: Next IC to use is %i : %i %i %i %i r=%g theta=%g phi=%g\n",
+              icIdx+1, ic.AtI()+1, ic.AtJ()+1, ic.AtK()+1, ic.AtL()+1,
+              ic.Dist(), ic.Theta(), ic.Phi());
     Vec3 posI = AtomIposition(ic, frameOut);
 
     frameOut.SetXYZ( ic.AtI(), posI );
diff --git a/src/Structure/Zmatrix.h b/src/Structure/Zmatrix.h
index 1ebdbcaec2..0788df4a74 100644
--- a/src/Structure/Zmatrix.h
+++ b/src/Structure/Zmatrix.h
@@ -6,8 +6,6 @@
 class Frame;
 class Topology;
 class Molecule;
-template <typename T> class ParmHolder;
-class AtomType;
 namespace Cpptraj {
 namespace Structure {
 class BuildAtom;
@@ -45,7 +43,6 @@ class Zmatrix {
 
     /// Try to generate complete ICs from atom connectivity
     int SetFromFrameAndConnect(Frame const&, Topology const&, int);
-    int BuildZmatrixFromTop(Frame const&, Topology const&, int, ParmHolder<AtomType> const&, Barray const&);
     /// Update ICs from existing coords
     int UpdateICsFromFrame(Frame const&, int, Topology const&, Barray const&);
     /// Convert specifed molecule of Frame/Topology to internal coordinates array

From 844b573d640dba9157caf25e8dc225a1b3afa54c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 18 Jan 2024 09:27:37 -0500
Subject: [PATCH 0345/1492] Add complete keyword

---
 src/Exec_Zmatrix.cpp | 23 +++++++++++++++++------
 src/Exec_Zmatrix.h   |  2 +-
 2 files changed, 18 insertions(+), 7 deletions(-)

diff --git a/src/Exec_Zmatrix.cpp b/src/Exec_Zmatrix.cpp
index 16b643c408..feaa976432 100644
--- a/src/Exec_Zmatrix.cpp
+++ b/src/Exec_Zmatrix.cpp
@@ -7,14 +7,18 @@ using namespace Cpptraj::Structure;
 
 /** Get Zmatrix for specified molecule at specified frame number. */
 int Exec_Zmatrix::getZmatrix(DataSet_Coords* CRD, int molnum, int frmidx,
-                             std::string const& dsname, DataFile* outfile, CpptrajState& State)
+                             std::string const& dsname, DataFile* outfile, CpptrajState& State,
+                             bool complete_zmatrix)
 const
 {
  if (CRD == 0) {
     mprinterr("Error: No COORDS set specified.\n");
     return CpptrajState::ERR;
   }
-  mprintf("\tGetting Z-matrix from set '%s'\n", CRD->legend());
+  if (complete_zmatrix)
+    mprintf("\tGetting complete Z-matrix from set '%s'\n", CRD->legend());
+  else
+    mprintf("\tGetting minimal Z-matrix from set '%s'\n", CRD->legend());
   if (CRD->Size() < 1) {
     mprinterr("Error: Set '%s' is empty.\n", CRD->legend());
     return 1; 
@@ -41,7 +45,11 @@ const
   Zmatrix& zmatrix = *(zset->Zptr());
 
   zmatrix.SetDebug( State.Debug() );
-  int errStat = zmatrix.SetFromFrame( frmIn, CRD->Top(), molnum );
+  int errStat;
+  if (complete_zmatrix)
+    errStat = zmatrix.SetFromFrameAndConnect(frmIn, CRD->Top(), molnum);
+  else
+    errStat = zmatrix.SetFromFrame( frmIn, CRD->Top(), molnum );
   if (debug_ > 0) zmatrix.print(); // DEBUG
   return errStat;
 }
@@ -108,11 +116,13 @@ const
 void Exec_Zmatrix::Help() const
 {
   mprintf("\t<COORDS set name> [name <output set name>]\n"
-          "\t{ zset <input zmatrix set> [parm <top>|parmindex <#>] |\n"
+          "\t{ zset <input zmatrix set> [parm <top>|parmindex <#>] [complete]|\n"
           "\t  [molnum <mol#>] [frame <frame#>] [out <zmatrix file>] }\n"
           "  If 'zset' is specified, use Z-matrix to generate coordinates using\n"
           "  a specified topology or topology from specified COORDS set;\n"
-          "  output is a new COORDS set.\n"
+          "  output is a new COORDS set. If 'complete is specified, generate\n"
+          "  as many internal coordinates as possible, otherwise a minimal\n"
+          "  set (1 internal coordinate per atom) will be generated.\n"
           "  Otherwise calculate Zmatrix for specified molecule/frame of\n"
           "  specified COORDS set; output is a Z-matrix set.\n");
 }
@@ -123,6 +133,7 @@ Exec::RetType Exec_Zmatrix::Execute(CpptrajState& State, ArgList& argIn)
   debug_ = State.Debug();
   std::string dsname = argIn.GetStringKey("name");
   std::string zsetname = argIn.GetStringKey("zset");
+  bool complete_zmatrix = argIn.hasKey("complete");
   int molnum = -1;
   int frmidx = -1;
   DataFile* outfile = 0;
@@ -151,7 +162,7 @@ Exec::RetType Exec_Zmatrix::Execute(CpptrajState& State, ArgList& argIn)
   if (!zsetname.empty()) {
     errStat = putZmatrix(CRD, topIn, zsetname, dsname, State);
   } else {
-    errStat = getZmatrix(CRD, molnum, frmidx, dsname, outfile, State);
+    errStat = getZmatrix(CRD, molnum, frmidx, dsname, outfile, State, complete_zmatrix);
   }
 
   if (errStat != 0) return CpptrajState::ERR;
diff --git a/src/Exec_Zmatrix.h b/src/Exec_Zmatrix.h
index 0b89547724..3be172520f 100644
--- a/src/Exec_Zmatrix.h
+++ b/src/Exec_Zmatrix.h
@@ -9,7 +9,7 @@ class Exec_Zmatrix : public Exec {
     DispatchObject* Alloc() const { return (DispatchObject*)new Exec_Zmatrix(); }
     RetType Execute(CpptrajState&, ArgList&);
   private:
-    int getZmatrix(DataSet_Coords*, int, int, std::string const&, DataFile*, CpptrajState&) const;
+    int getZmatrix(DataSet_Coords*, int, int, std::string const&, DataFile*, CpptrajState&,bool) const;
     int putZmatrix(DataSet_Coords*, Topology*, std::string const&, std::string const&, CpptrajState&) const;
 
     int debug_;

From 851fc163920a76d81ef586c546d2d781bb6bfed9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 18 Jan 2024 09:27:48 -0500
Subject: [PATCH 0346/1492] Remove code

---
 src/Structure/Model.cpp | 167 ----------------------------------------
 src/Structure/Model.h   |   9 ---
 2 files changed, 176 deletions(-)

diff --git a/src/Structure/Model.cpp b/src/Structure/Model.cpp
index 21c7705fb8..33b99d4a16 100644
--- a/src/Structure/Model.cpp
+++ b/src/Structure/Model.cpp
@@ -1,6 +1,5 @@
 #include "Model.h"
 #include "BuildAtom.h"
-#include "Chirality.h"
 #include "../CpptrajStdio.h"
 #include "../GuessAtomHybridization.h"
 #include "../Topology.h"
@@ -260,169 +259,3 @@ int Cpptraj::Structure::Model::AssignPhi(double& phi, int ai, int aj, int ak, in
 
   return 0;
 }
-
-/** Attempt to assign a reasonable values for phi internal coordinates for
-  * atoms around a central bond j and k.
-  */
-int Cpptraj::Structure::Model::AssignPhiAroundBond(std::vector<InternalCoords>& IC,
-                                                   ParmHolder<AtomType> const& AT,
-                                                   int ax, int ay,
-                                                   Topology const& topIn, Frame const& frameIn,
-                                                   std::vector<bool> const& atomPositionKnown,
-                                                   int debug)
-{
-  // Figure out hybridization and chirality of atom j.
-  //if (debug > 0)
-    mprintf("DEBUG: AssignPhi for bond %s - %s\n", topIn.AtomMaskName(ax).c_str(), topIn.AtomMaskName(ay).c_str());
-
-  // Both need to have more than 1 bond
-  if (topIn[ax].Nbonds() < 2 || topIn[ay].Nbonds() < 2) {
-    mprintf("DEBUG: Not possible to make a torsion (%i bonds, %i bonds)\n", topIn[ax].Nbonds(), topIn[ay].Nbonds());
-    return 0;
-  }
-  // Get hybridization of atoms x and y
-  ParmHolder<AtomType>::const_iterator atx = AT.GetParam( TypeNameHolder(topIn[ax].Type()) );
-  ParmHolder<AtomType>::const_iterator aty = AT.GetParam( TypeNameHolder(topIn[ay].Type()) );
-  AtomType::HybridizationType hx, hy;
-  if (atx != AT.end() && atx->second.Hybridization() == AtomType::UNKNOWN_HYBRIDIZATION)
-    hx = GuessAtomHybridization( topIn[ax], topIn.Atoms() );
-  else
-    hx = atx->second.Hybridization();
-  if (aty != AT.end() && aty->second.Hybridization() == AtomType::UNKNOWN_HYBRIDIZATION)
-    hy = GuessAtomHybridization( topIn[ax], topIn.Atoms() );
-  else
-    hy = aty->second.Hybridization();
-
-  int aj, ak;
-  // Ensure hybridization of atom X is > atom Y
-  if (hx < hy) {
-    aj = ay;
-    ak = ax;
-  } else {
-    aj = ax;
-    ak = ay;
-  }
-  mprintf("DEBUG: In hybridization order: %s - %s (%i - %i)\n", topIn.AtomMaskName(aj).c_str(), topIn.AtomMaskName(ak).c_str(),
-          (int)hx, (int)hy);
-
-  Atom const& AJ = topIn[aj];
-  Atom const& AK = topIn[ak];
-
-/*
-  BuildAtom AtomJ;
-  if (AJ.Nbonds() > 2) {
-    Cpptraj::Structure::SetPriority(AtomJ.ModifyPriority(), aj, topIn, frameIn, 0); // FIXME chiralityDebug
-  }
-
-
-//  if (debug > 0) mprintf("DEBUG:\t\tNbonds: %i\n", AJ.Nbonds());
-//  // If atom J only has 2 bonds, ai-aj-ak-al is the only possibility.
-//  if (AJ.Nbonds() < 3) {
-//    if (debug > 0)
-//      mprintf("DEBUG:\t\tFewer than 3 bonds. Setting phi to -180.\n");
-//    phi = -180 * Constants::DEGRAD;
-//    return 0;
-//  }
-
-  // TODO check that atom i actually ends up on the list?
-  std::vector<int> const& priority = AtomJ.Priority();
-  int ai = 
-  if (debug > 0) {
-    mprintf("DEBUG: Original chirality around J %s is %s\n", topIn.AtomMaskName(aj).c_str(), chiralStr(AtomJ.Chirality()));
-    mprintf("DEBUG:\t\tPriority around J %s(%i):", 
-            topIn.AtomMaskName(aj).c_str(), (int)atomPositionKnown[aj]);
-    for (int idx = 0; idx < AJ.Nbonds(); idx++)
-      mprintf(" %s(%i)", topIn.AtomMaskName(priority[idx]).c_str(), (int)atomPositionKnown[priority[idx]]);
-    mprintf("\n");
-  }
-
-  // Fill in what values we can for known atoms
-  std::vector<double> knownPhi( AJ.Nbonds() );
-  int knownIdx = -1;
-  for (int idx = 0; idx < AJ.Nbonds(); idx++) {
-    int atnum = priority[idx];
-    if (atnum != ak && atomPositionKnown[atnum] &&
-                       atomPositionKnown[aj] &&
-                       atomPositionKnown[ak] &&
-                       atomPositionKnown[al])
-    {
-      knownPhi[idx] = Torsion(frameIn.XYZ(atnum),
-                              frameIn.XYZ(aj),
-                              frameIn.XYZ(ak),
-                              frameIn.XYZ(al));
-      if (debug > 0)
-        mprintf("DEBUG:\t\tKnown phi for %s = %g\n", topIn.AtomMaskName(atnum).c_str(), knownPhi[idx]*Constants::RADDEG);
-      if (knownIdx == -1) knownIdx = idx; // FIXME handle more than 1 known
-    }
-  }
-
-  // If we have to assign an initial phi, make trans the longer branch
-  if (knownIdx == -1) {
-    std::vector<bool> visited = atomPositionKnown;
-    // TODO: Ensure bonded atoms are not yet visited?
-    visited[aj] = true;
-    visited[ak] = true;
-    std::vector<int> depth( AJ.Nbonds() );
-    for (int idx = 0; idx < AJ.Nbonds(); idx++) {
-      int atnum = priority[idx];
-      if (atnum != ak) {
-        int currentDepth = 0;
-        depth[idx] = atom_depth(currentDepth, atnum, topIn, visited, 10);
-        if (debug > 0)
-          mprintf("DEBUG:\t\tAJ %s depth from %s is %i\n",
-                  topIn.AtomMaskName(aj).c_str(), topIn.AtomMaskName(atnum).c_str(), depth[idx]);
-        if (knownIdx == -1 && depth[idx] < 3) {
-          knownIdx = idx;
-          knownPhi[idx] = 0;
-        }
-      }
-    }
-  }
-
-  // The interval will be 360 / (number of bonds - 1)
-  double interval = Constants::TWOPI / (AJ.Nbonds() - 1);
-
-  double startPhi;
-  if (knownIdx == -1) {
-    startPhi = -180*Constants::DEGRAD;
-    if (debug > 0) mprintf("DEBUG:\t\tNo known phi. Setting to %g.\n", startPhi*Constants::RADDEG);
-    knownIdx = 0;
-  } else
-    startPhi = knownPhi[knownIdx];
-
-  if (AtomJ.Chirality() == IS_R) {
-    startPhi = -startPhi;
-    interval = -interval;
-  }
-  if (debug > 0) {
-    mprintf("DEBUG:\t\tStart phi is %g degrees\n", startPhi*Constants::RADDEG);
-    mprintf("DEBUG:\t\tInterval is %g degrees\n", interval * Constants::RADDEG);
-  }
-    
-  // Forward direction
-  double currentPhi = startPhi;
-  for (int idx = knownIdx; idx < AJ.Nbonds(); idx++) {
-    int atnum = priority[idx];
-    if (atnum != ak) {
-      if (atnum == ai) phi = currentPhi;
-      if (debug > 0)
-        mprintf("DEBUG:\t\t\t%s phi= %g\n", topIn.AtomMaskName(atnum).c_str(), currentPhi*Constants::RADDEG);
-      currentPhi += interval;
-      currentPhi = wrap360(currentPhi);
-    }
-  }
-  // Reverse direction
-  currentPhi = startPhi - interval;
-  for (int idx = knownIdx - 1; idx > -1; idx--) {
-    int atnum = priority[idx];
-    if (atnum != ak) {
-      if (atnum == ai) phi = currentPhi;
-      if (debug > 0)
-        mprintf("DEBUG:\t\t\t%s phi= %g\n", topIn.AtomMaskName(atnum).c_str(), currentPhi*Constants::RADDEG);
-      currentPhi -= interval;
-      currentPhi = wrap360(currentPhi);
-    }
-  }
-*/
-  return 0;
-}
diff --git a/src/Structure/Model.h b/src/Structure/Model.h
index 0f58f6f260..0ceea95c3e 100644
--- a/src/Structure/Model.h
+++ b/src/Structure/Model.h
@@ -4,24 +4,15 @@
 #include "StructureEnum.h"
 class Topology;
 class Frame;
-class AtomType;
-template <typename T> class ParmHolder;
 namespace Cpptraj {
 namespace Structure {
 class BuildAtom;
-class InternalCoords;
 /// Routines to generate model parameters
 namespace Model {
 /// Given atoms J K and L, attempt to assign a reasonable value for phi for atom I
 int AssignPhi(double&, int, int, int, int, Topology const&, Frame const&, std::vector<bool> const&, BuildAtom const&, int);
 /// Given atoms J and K, attempt to assign a reasonable value for theta for atom I
 int AssignTheta(double&, int, int, int, Topology const&, Frame const&, std::vector<bool> const&, int);
-
-int AssignPhiAroundBond(std::vector<InternalCoords>&, ParmHolder<AtomType> const&,
-                        int, int, Topology const&, Frame const&,
-                        std::vector<bool> const&, int);
-
-
 } // END namespace Model
 } // END namespace Structure
 } // END namespace Cpptraj

From c1e307d9c09297fb11c1fc764abb308221ed282a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 18 Jan 2024 09:28:14 -0500
Subject: [PATCH 0347/1492] Update dependencies

---
 src/Structure/structuredepend | 2 +-
 src/cpptrajdepend             | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/Structure/structuredepend b/src/Structure/structuredepend
index b11ad9e7ba..84e708f424 100644
--- a/src/Structure/structuredepend
+++ b/src/Structure/structuredepend
@@ -13,4 +13,4 @@ Sugar.o : Sugar.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.
 SugarBuilder.o : SugarBuilder.cpp ../ArgList.h ../Atom.h ../AtomMap.h ../AtomMask.h ../AtomType.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DistRoutines.h ../FileIO.h ../FileName.h ../Frame.h ../ImageOption.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Chirality.h FunctionalGroup.h FxnGroupBuilder.h LinkAtom.h ResStatArray.h StructureEnum.h StructureRoutines.h Sugar.h SugarBuilder.h SugarLinkAtoms.h SugarToken.h
 SugarLinkAtoms.o : SugarLinkAtoms.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../StringRoutines.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h LinkAtom.h SugarLinkAtoms.h
 SugarToken.o : SugarToken.cpp ../ArgList.h ../CpptrajStdio.h SugarToken.h
-Zmatrix.o : Zmatrix.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h InternalCoords.h Model.h StructureEnum.h Zmatrix.h
+Zmatrix.o : Zmatrix.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h GenerateConnectivityArrays.h InternalCoords.h Model.h StructureEnum.h Zmatrix.h
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index ee25a9af47..7a037c2ed9 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -460,7 +460,7 @@ Structure/Sugar.o : Structure/Sugar.cpp Atom.h AtomMask.h AtomType.h Box.h Const
 Structure/SugarBuilder.o : Structure/SugarBuilder.cpp ArgList.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DistRoutines.h FileIO.h FileName.h Frame.h ImageOption.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Chirality.h Structure/FunctionalGroup.h Structure/FxnGroupBuilder.h Structure/LinkAtom.h Structure/ResStatArray.h Structure/StructureEnum.h Structure/StructureRoutines.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarLinkAtoms.h Structure/SugarToken.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 Structure/SugarLinkAtoms.o : Structure/SugarLinkAtoms.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/LinkAtom.h Structure/SugarLinkAtoms.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/SugarToken.o : Structure/SugarToken.cpp ArgList.h CpptrajStdio.h Structure/SugarToken.h
-Structure/Zmatrix.o : Structure/Zmatrix.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/InternalCoords.h Structure/Model.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Structure/Zmatrix.o : Structure/Zmatrix.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/Model.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 StructureCheck.o : StructureCheck.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h ExclusionArray.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StructureCheck.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 StructureMapper.o : StructureMapper.cpp AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StructureMapper.h SymbolExporting.h TextFormat.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 SymmetricRmsdCalc.o : SymmetricRmsdCalc.cpp ArrayIterator.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h Hungarian.h ImageOption.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h Topology.h TypeNameHolder.h Unit.h Vec3.h

From dff7ceeac20962fd5511fac0a71b48ec9372d6fe Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 18 Jan 2024 11:28:17 -0500
Subject: [PATCH 0348/1492] Save residue terminal status. Add some comments.
 Hide some debug.

---
 src/Exec_Build.cpp | 20 ++++++++++++++------
 1 file changed, 14 insertions(+), 6 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 727ecf7101..cd88dbeba0 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -134,6 +134,8 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
   // Array of templates for each residue
   std::vector<DataSet_Coords*> ResTemplates;
   ResTemplates.reserve( topIn.Nres() );
+  std::vector<Cpptraj::Structure::TerminalType> ResTypes;
+  ResTypes.reserve( topIn.Nres() );
   // Initial loop to try to match residues to templates
   int newNatom = 0;
   for (int ires = 0; ires != topIn.Nres(); ires++)
@@ -156,6 +158,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
       resTermType = Cpptraj::Structure::NON_TERMINAL;
     }
     mprintf("DEBUG: Residue type: %s\n", Cpptraj::Structure::terminalStr(resTermType));
+    ResTypes.push_back( resTermType );
     // Identify a template based on the residue name.
     DataSet_Coords* resTemplate = IdTemplateFromName(Templates, currentRes.Name(), resTermType);
     if (resTemplate == 0) {
@@ -203,7 +206,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
     typedef std::vector<Ipair> IParray;
     IParray intraResBonds;
     if (resTemplate == 0) {
-      // No template. Just add the atoms.
+      // ----- No template. Just add the atoms. ------------
       ResZmatrices.push_back( 0 );
       for (int itgt = currentRes.FirstAtom(); itgt != currentRes.LastAtom(); ++itgt)
       {
@@ -212,12 +215,14 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
         int at0 = itgt - currentRes.FirstAtom() + atomOffset;
         for (Atom::bond_iterator bat = sourceAtom.bondbegin(); bat != sourceAtom.bondend(); ++bat) {
           if ( topIn[*bat].ResNum() == ires ) {
+            // Intra-residue
             int at1 = *bat - currentRes.FirstAtom() + atomOffset;
             if (at1 > at0) {
-              mprintf("Will add bond between %i and %i (original %i and %i)\n", at0+1, at1+1, itgt+1, *bat + 1);
+              //mprintf("Will add bond between %i and %i (original %i and %i)\n", at0+1, at1+1, itgt+1, *bat + 1);
               intraResBonds.push_back( Ipair(at0, at1) );
             }
           } else {
+            // Inter-residue. Only record if bonding to the next residue.
             if (topIn[*bat].ResNum() > ires) {
               interResBonds.push_back( ResAtPair(ires, sourceAtom.Name()) );
               interResBonds.push_back( ResAtPair(topIn[*bat].ResNum(), topIn[*bat].Name()) );
@@ -230,7 +235,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
         hasPosition.push_back( true );
       }
     } else {
-      // A template exists for this residue.
+      // ----- A template exists for this residue. ---------
       // Map source atoms to template atoms.
       std::vector<int> map = MapAtomsToTemplate( topIn, ires, resTemplate );
       mprintf("\t  Atom map:\n");
@@ -253,13 +258,13 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
           //if ( resTemplate->Top()[*bat].ResNum() == ires ) {
             int at1 = *bat + atomOffset;
             if (at1 > at0) {
-              mprintf("Will add bond between %i and %i (original %i and %i)\n", at0+1, at1+1, iref+1, *bat + 1);
+              //mprintf("Will add bond between %i and %i (original %i and %i)\n", at0+1, at1+1, iref+1, *bat + 1);
               intraResBonds.push_back( Ipair(at0, at1) );
             }
           //}
         }
         // TODO connect atoms for inter-residue connections
-        templateAtom.ClearBonds();
+        templateAtom.ClearBonds(); // FIXME AddTopAtom should clear bonds
         topOut.AddTopAtom( templateAtom, currentRes );
         if (map[iref] == -1) {
           frameOut.AddVec3( Vec3(0.0) );
@@ -317,6 +322,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
       topOut.AddBond(it->first, it->second);
     }
   } // END loop over source residues
+  mprintf("\t%i template atoms missing in source.\n", nRefAtomsMissing);
 
   // -----------------------------------
   // Add inter-residue bonds
@@ -340,7 +346,9 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
     }
     topOut.AddBond(at0, at1);
   }
-  mprintf("\t%i template atoms missing in source.\n", nRefAtomsMissing);
+
+  // -----------------------------------
+  // Do some error checking
   if (hasPosition.size() != (unsigned int)newNatom) {
     mprinterr("Internal Error: hasPosition size %zu != newNatom size %i\n", hasPosition.size(), newNatom);
     return 1;

From 4a7bc8fb0b1f71222082741af61cf8498f216d25 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 18 Jan 2024 11:50:09 -0500
Subject: [PATCH 0349/1492] Report residue type during build

---
 src/Exec_Build.cpp | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index cd88dbeba0..a9f721f84a 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -134,7 +134,8 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
   // Array of templates for each residue
   std::vector<DataSet_Coords*> ResTemplates;
   ResTemplates.reserve( topIn.Nres() );
-  std::vector<Cpptraj::Structure::TerminalType> ResTypes;
+  typedef std::vector<Cpptraj::Structure::TerminalType> TermTypeArray;
+  TermTypeArray ResTypes;
   ResTypes.reserve( topIn.Nres() );
   // Initial loop to try to match residues to templates
   int newNatom = 0;
@@ -361,12 +362,14 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
   // -----------------------------------
   // Build using internal coords if needed.
   bool buildFailed = false;
-  for (Zarray::const_iterator it = ResZmatrices.begin(); it != ResZmatrices.end(); ++it)
+  TermTypeArray::const_iterator termType = ResTypes.begin();
+  for (Zarray::const_iterator it = ResZmatrices.begin(); it != ResZmatrices.end(); ++it, ++termType)
   {
     long int ires = it-ResZmatrices.begin();
     Cpptraj::Structure::Zmatrix* zmatrix = *it;
     if (zmatrix != 0) {
       mprintf("DEBUG: BUILD residue %li %s\n", ires + 1, topOut.TruncResNameOnumId(ires).c_str());
+      mprintf("DEBUG: Residue type: %s terminal\n", Cpptraj::Structure::terminalStr(*termType));
       // TEST FIXME
 //      Cpptraj::Structure::Zmatrix testZ;
 //      if (testZ.BuildZmatrixFromTop(frameOut, topOut, ires, mainParmSet.AT(), hasPosition)) {

From 913f83b3f0745126a725ac0468468a7f3e7fd032 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 18 Jan 2024 14:58:47 -0500
Subject: [PATCH 0350/1492] Remove FIXME

---
 src/Structure/Model.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Structure/Model.cpp b/src/Structure/Model.cpp
index 33b99d4a16..658bfb66f8 100644
--- a/src/Structure/Model.cpp
+++ b/src/Structure/Model.cpp
@@ -8,7 +8,7 @@
 
 /** Attempt to assign a reasonable value for theta internal coordinate for
   * atom i given that atoms j and k have known positions.
-  */ // FIXME use GuessAtomHybridization
+  */
 int Cpptraj::Structure::Model::AssignTheta(double& theta, int ai, int aj, int ak, Topology const& topIn, Frame const& frameIn, std::vector<bool> const& atomPositionKnown, int debug)
 {
   // Figure out hybridization and chirality of atom j.

From 2ba3a02574e563dc2185f7b3d351a92d9367f709 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 18 Jan 2024 15:27:56 -0500
Subject: [PATCH 0351/1492] Create zmatrix for link between residues

---
 src/Exec_Build.cpp            | 32 +++++++++++++-
 src/Structure/Builder.cpp     | 82 +++++++++++++++++++++++++++++++++++
 src/Structure/Builder.h       |  6 ++-
 src/Structure/Model.cpp       | 13 ++++++
 src/Structure/Model.h         |  2 +
 src/Structure/Zmatrix.cpp     | 16 +++++--
 src/Structure/structuredepend |  2 +-
 src/cpptrajdepend             |  4 +-
 8 files changed, 147 insertions(+), 10 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index a9f721f84a..9e8de1ba66 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -1,6 +1,7 @@
 #include "Exec_Build.h"
 #include "CpptrajStdio.h"
 #include "DataSet_Parameters.h"
+#include "Structure/Builder.h"
 #include "Structure/GenerateConnectivityArrays.h"
 #include "Structure/Zmatrix.h"
 #include "Parm/GB_Params.h"
@@ -361,6 +362,15 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
 
   // -----------------------------------
   // Build using internal coords if needed.
+  std::vector<bool> resIsBuilt; // TODO is this needed?
+  resIsBuilt.reserve( ResZmatrices.size() );
+  for (Zarray::const_iterator it = ResZmatrices.begin(); it != ResZmatrices.end(); ++it) {
+    if ( *it == 0 )
+      resIsBuilt.push_back( true );
+    else
+      resIsBuilt.push_back( false );
+  }
+  
   bool buildFailed = false;
   TermTypeArray::const_iterator termType = ResTypes.begin();
   for (Zarray::const_iterator it = ResZmatrices.begin(); it != ResZmatrices.end(); ++it, ++termType)
@@ -370,6 +380,25 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
     if (zmatrix != 0) {
       mprintf("DEBUG: BUILD residue %li %s\n", ires + 1, topOut.TruncResNameOnumId(ires).c_str());
       mprintf("DEBUG: Residue type: %s terminal\n", Cpptraj::Structure::terminalStr(*termType));
+      // Is this residue connected to an earlier residue?
+      if ( *termType != Cpptraj::Structure::BEG_TERMINAL ) {
+        for (int at = topOut.Res(ires).FirstAtom(); at != topOut.Res(ires).LastAtom(); ++at)
+        {
+          for (Atom::bond_iterator bat = topOut[at].bondbegin(); bat != topOut[at].bondend(); ++bat)
+          {
+            if ((long int)topOut[*bat].ResNum() < ires) {
+              mprintf("DEBUG: Connected to residue %i\n", topOut[*bat].ResNum());
+              Cpptraj::Structure::Builder linkBuilder;
+              linkBuilder.SetDebug( 1 ); // FIXME
+              if (linkBuilder.ModelCoordsAroundBond(frameOut, topOut, at, *bat, hasPosition)) {
+                mprinterr("Error: Model coords around bond failed between %s and %s\n",
+                          topOut.AtomMaskName(at).c_str(), topOut.AtomMaskName(*bat).c_str());
+                return 1;
+              }
+            }
+          }
+        }
+      }
       // TEST FIXME
 //      Cpptraj::Structure::Zmatrix testZ;
 //      if (testZ.BuildZmatrixFromTop(frameOut, topOut, ires, mainParmSet.AT(), hasPosition)) {
@@ -394,7 +423,8 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
           mprinterr("Error: Building residue %s failed.\n",
                     topOut.TruncResNameOnumId(ires).c_str());
           buildFailed = true;
-        }
+        } else
+          resIsBuilt[ires] = true;
       //}
     }
   }
diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 4b09556d77..5646d0006d 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -18,6 +18,7 @@ Builder::Builder() :
 int Builder::Combine(Topology&       frag0Top, Frame&       frag0frm,
                      Topology const& frag1Top, Frame const& frag1frm,
                      int bondAt0, int bondAt1)
+const
 {
   int natom0 = frag0Top.Natom();
   int newNatom = natom0 + frag1Top.Natom();
@@ -107,3 +108,84 @@ int Builder::Combine(Topology&       frag0Top, Frame&       frag0frm,
 
   return 0;
 }
+
+static inline int known_count(int ires, Topology const& topIn, std::vector<bool> const& hasPosition)
+{
+  int count = 0;
+  for (int at = topIn.Res(ires).FirstAtom(); at != topIn.Res(ires).LastAtom(); at++)
+    if (hasPosition[at])
+      count++;
+  return count;
+}
+
+/** Model the coordinates around a bond */
+int Builder::ModelCoordsAroundBond(Frame& frameIn, Topology const& topIn, int bondAt0, int bondAt1, Barray& hasPosition) const {
+  mprintf("DEBUG: Model coords around bond %s - %s\n", topIn.AtomMaskName(bondAt0).c_str(), topIn.AtomMaskName(bondAt1).c_str());
+  int res0 = topIn[bondAt0].ResNum();
+  int res1 = topIn[bondAt1].ResNum();
+  if (res0 == res1) {
+    mprinterr("Internal Error: ModelCoordsAroundBond(): Atoms are in the same residue.\n");
+    return 1;
+  }
+  // Determine which "direction" we will be combining the fragments.
+  // Make atA belong to the less-known fragment. atB fragment will be "known".
+  int known0 = known_count(res0, topIn, hasPosition);
+  int known1 = known_count(res1, topIn, hasPosition);
+  int atA, atB;
+
+  if (known0 < known1) {
+    // Fragment 1 is better-known 
+    atA = bondAt0;
+    atB = bondAt1;
+  } else {
+    // Fragment 0 is better or equally known 
+    atA = bondAt1;
+    atB = bondAt0;
+  }
+
+  mprintf("DEBUG: More well-known atom: %s\n", topIn.AtomMaskName(atB).c_str());
+  mprintf("DEBUG: Less well-known atom: %s\n", topIn.AtomMaskName(atA).c_str());
+
+  int chiralityDebug;
+  if (debug_ < 1)
+    chiralityDebug = 0;
+  else
+    chiralityDebug = debug_ - 1;
+
+  // Get the chirality around each atom before the bond is added.
+  // Determine priorities
+  BuildAtom AtomA;
+  if (topIn[atA].Nbonds() > 2) {
+    AtomA.SetChirality( DetermineChirality(atA, topIn, frameIn, chiralityDebug) );
+    SetPriority(AtomA.ModifyPriority(), atA, topIn, frameIn, chiralityDebug);
+  }
+  if (debug_ > 0)
+    mprintf("DEBUG:\tAtom %4s chirality %6s\n", topIn.AtomMaskName(atA).c_str(), chiralStr(AtomA.Chirality()));
+  BuildAtom AtomB;
+  if (topIn[atB].Nbonds() > 2) {
+    AtomB.SetChirality( DetermineChirality(atB, topIn, frameIn, chiralityDebug) );
+    SetPriority(AtomB.ModifyPriority(), atB, topIn, frameIn, chiralityDebug);
+  }
+  if (debug_ > 0)
+    mprintf("DEBUG:\tAtom %4s chirality %6s\n", topIn.AtomMaskName(atB).c_str(), chiralStr(AtomB.Chirality()));
+
+  // Generate Zmatrix only for ICs involving bonded atoms
+  Zmatrix bondZmatrix;
+
+  bondZmatrix.SetDebug( debug_ );
+  if (bondZmatrix.SetupICsAroundBond(atA, atB, frameIn, topIn, hasPosition, AtomA, AtomB)) {
+    mprinterr("Error: Zmatrix setup for ICs around %s and %s failed.\n",
+              topIn.AtomMaskName(atA).c_str(),
+              topIn.AtomMaskName(atB).c_str());
+    return 1;
+  }
+  if (debug_ > 0)
+    bondZmatrix.print(&topIn);
+  if (bondZmatrix.SetToFrame( frameIn, hasPosition )) {
+    mprinterr("Error: Conversion from bondZmatrix to Cartesian coords failed.\n");
+    return 1;
+  }
+
+  return 0;
+}
+
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index 86087d0bec..705902f005 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -7,15 +7,17 @@ namespace Cpptraj {
 namespace Structure {
 /// Used to attach different topology/frame combos using internal coordinates
 class Builder {
+    typedef std::vector<bool> Barray;
   public:
     /// CONSTRUCTOR
     Builder();
     /// Combine second fragment into first fragment and bond
-    int Combine(Topology&, Frame&, Topology const&, Frame const&, int, int);
+    int Combine(Topology&, Frame&, Topology const&, Frame const&, int, int) const;
+    /// Model the coordinates around a bond given only some coordinates are known
+    int ModelCoordsAroundBond(Frame&, Topology const&, int, int, Barray&) const;
     /// Set debug
     void SetDebug(int d) { debug_ = d; }
   private:
-    typedef std::vector<bool> Barray;
 
     int debug_;
 };
diff --git a/src/Structure/Model.cpp b/src/Structure/Model.cpp
index 658bfb66f8..4a0067e2d7 100644
--- a/src/Structure/Model.cpp
+++ b/src/Structure/Model.cpp
@@ -4,7 +4,20 @@
 #include "../GuessAtomHybridization.h"
 #include "../Topology.h"
 #include "../TorsionRoutines.h"
+#include "../DistRoutines.h"
 #include "../Constants.h"
+#include <cmath>
+
+/** Assign reasonable value for bond distance. */
+int Cpptraj::Structure::Model::AssignLength(double& dist, int ai, int aj, Topology const& topIn, Frame const& frameIn, std::vector<bool> const& atomPositionKnown, int debug)
+{
+  if (atomPositionKnown[ai] && atomPositionKnown[aj])
+    dist = sqrt( DIST2_NoImage( frameIn.XYZ(ai), frameIn.XYZ(aj) ) );
+  else
+    // One or both positions unknown. Use bond length. TODO use parameters
+    dist = Atom::GetBondLength( topIn[ai].Element(), topIn[aj].Element() );
+  return 0;
+}
 
 /** Attempt to assign a reasonable value for theta internal coordinate for
   * atom i given that atoms j and k have known positions.
diff --git a/src/Structure/Model.h b/src/Structure/Model.h
index 0ceea95c3e..9a6452d53f 100644
--- a/src/Structure/Model.h
+++ b/src/Structure/Model.h
@@ -9,6 +9,8 @@ namespace Structure {
 class BuildAtom;
 /// Routines to generate model parameters
 namespace Model {
+/// Assign a reasonable value for bond distance given 2 atoms whose position may or may not be known
+int AssignLength(double&, int, int, Topology const&, Frame const&, std::vector<bool> const&, int);
 /// Given atoms J K and L, attempt to assign a reasonable value for phi for atom I
 int AssignPhi(double&, int, int, int, int, Topology const&, Frame const&, std::vector<bool> const&, BuildAtom const&, int);
 /// Given atoms J and K, attempt to assign a reasonable value for theta for atom I
diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index 89f5916188..932741398c 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -977,7 +977,11 @@ int Zmatrix::SetupICsAroundBond(int atA, int atB, Frame const& frameIn, Topology
   // ---- I J: Set dist, theta, phi for atA atB K L internal coord ---
   if (debug_ > 0)
     mprintf("DEBUG: IC (i j) %i - %i - %i - %i\n", atA+1, atB+1, atk0+1, atl0+1);
-  double newDist = Atom::GetBondLength( topIn[atA].Element(), topIn[atB].Element() );
+  double newDist = 0;
+  if (Cpptraj::Structure::Model::AssignLength(newDist, atA, atB, topIn, frameIn, atomPositionKnown, modelDebug)) {
+    mprinterr("Error: length (i j) assignment failed.\n");
+    return 1;
+  }
   if (debug_ > 0) mprintf("DEBUG:\t\tnewDist= %g\n", newDist);
   double newTheta = 0;
   if (Cpptraj::Structure::Model::AssignTheta(newTheta, atA, atB, atk0, topIn, frameIn, atomPositionKnown, modelDebug)) {
@@ -1008,8 +1012,11 @@ int Zmatrix::SetupICsAroundBond(int atA, int atB, Frame const& frameIn, Topology
   {
     if (*iat != atB) {
       if (ati == -1) ati = *iat;
-      // Use existing dist
-      newDist = sqrt( DIST2_NoImage(frameIn.XYZ(*iat), frameIn.XYZ(atA)) );
+      // Set bond dist
+      if (Cpptraj::Structure::Model::AssignLength(newDist, *iat, atA, topIn, frameIn, atomPositionKnown, modelDebug)) {
+        mprinterr("Error: length (j k) assignment failed.\n");
+        return 1;
+      }
       // Set theta for I atA atB
       newTheta = 0;
       if (Cpptraj::Structure::Model::AssignTheta(newTheta, *iat, atA, atB, topIn, frameIn, atomPositionKnown, modelDebug)) {
@@ -1062,6 +1069,7 @@ int Zmatrix::SetupICsAroundBond(int atA, int atB, Frame const& frameIn, Topology
       } */
     }
   }
+/*
   // Handle remaining atoms.
   if (AJ1.Nbonds() > 1) {
     if (AJ1.Nbonds() == 2) {
@@ -1099,7 +1107,7 @@ int Zmatrix::SetupICsAroundBond(int atA, int atB, Frame const& frameIn, Topology
       }
     }
   }
-
+*/
   return 0;
 }
 
diff --git a/src/Structure/structuredepend b/src/Structure/structuredepend
index 84e708f424..ccf6cce6e9 100644
--- a/src/Structure/structuredepend
+++ b/src/Structure/structuredepend
@@ -6,7 +6,7 @@ FxnGroupBuilder.o : FxnGroupBuilder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ..
 GenerateConnectivityArrays.o : GenerateConnectivityArrays.cpp ../Atom.h ../Constants.h ../CpptrajStdio.h ../NameType.h ../ParameterTypes.h ../Residue.h ../SymbolExporting.h GenerateConnectivityArrays.h
 HisProt.o : HisProt.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h HisProt.h StructureRoutines.h
 InternalCoords.o : InternalCoords.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h InternalCoords.h
-Model.o : Model.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h Model.h StructureEnum.h
+Model.o : Model.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h Model.h StructureEnum.h
 StructureEnum.o : StructureEnum.cpp StructureEnum.h
 StructureRoutines.o : StructureRoutines.cpp ../Atom.h ../CpptrajStdio.h ../NameType.h ../Residue.h ../SymbolExporting.h StructureRoutines.h
 Sugar.o : Sugar.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Sugar.h SugarToken.h
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 7a037c2ed9..a9da180829 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -290,7 +290,7 @@ Ewald_Regular.o : Ewald_Regular.cpp Atom.h AtomMask.h Box.h Constants.h Coordina
 ExclusionArray.o : ExclusionArray.cpp Atom.h AtomMask.h CharMask.h CpptrajStdio.h ExclusionArray.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Unit.h
 Exec_AddMissingRes.o : Exec_AddMissingRes.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CharMask.h CompactFrameArray.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_AddMissingRes.h Exec_AddMissingRes_Pres.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Analyze.o : Exec_Analyze.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Analyze.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Build.o : Exec_Build.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/GB_Params.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Build.o : Exec_Build.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/GB_Params.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Calc.o : Exec_Calc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Calc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_CatCrd.o : Exec_CatCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CatCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Change.o : Exec_Change.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Change.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
@@ -453,7 +453,7 @@ Structure/FxnGroupBuilder.o : Structure/FxnGroupBuilder.cpp Atom.h AtomMask.h At
 Structure/GenerateConnectivityArrays.o : Structure/GenerateConnectivityArrays.cpp Atom.h Constants.h CpptrajStdio.h NameType.h ParameterTypes.h Residue.h Structure/GenerateConnectivityArrays.h SymbolExporting.h
 Structure/HisProt.o : Structure/HisProt.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/HisProt.h Structure/StructureRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/InternalCoords.o : Structure/InternalCoords.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/InternalCoords.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Structure/Model.o : Structure/Model.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h GuessAtomHybridization.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/Model.h Structure/StructureEnum.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Structure/Model.o : Structure/Model.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h GuessAtomHybridization.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/Model.h Structure/StructureEnum.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 Structure/StructureEnum.o : Structure/StructureEnum.cpp Structure/StructureEnum.h
 Structure/StructureRoutines.o : Structure/StructureRoutines.cpp Atom.h CpptrajStdio.h NameType.h Residue.h Structure/StructureRoutines.h SymbolExporting.h
 Structure/Sugar.o : Structure/Sugar.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h

From f17c846ce1178e91db16f1cc9c680614ee32e82b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 19 Jan 2024 09:00:49 -0500
Subject: [PATCH 0352/1492] Change into a class

---
 src/Structure/Model.cpp | 30 +++++++++++++++---------------
 src/Structure/Model.h   | 26 ++++++++++++++++----------
 2 files changed, 31 insertions(+), 25 deletions(-)

diff --git a/src/Structure/Model.cpp b/src/Structure/Model.cpp
index 4a0067e2d7..ea268652c3 100644
--- a/src/Structure/Model.cpp
+++ b/src/Structure/Model.cpp
@@ -9,7 +9,7 @@
 #include <cmath>
 
 /** Assign reasonable value for bond distance. */
-int Cpptraj::Structure::Model::AssignLength(double& dist, int ai, int aj, Topology const& topIn, Frame const& frameIn, std::vector<bool> const& atomPositionKnown, int debug)
+int Cpptraj::Structure::Model::AssignLength(double& dist, int ai, int aj, Topology const& topIn, Frame const& frameIn, std::vector<bool> const& atomPositionKnown)
 {
   if (atomPositionKnown[ai] && atomPositionKnown[aj])
     dist = sqrt( DIST2_NoImage( frameIn.XYZ(ai), frameIn.XYZ(aj) ) );
@@ -22,16 +22,16 @@ int Cpptraj::Structure::Model::AssignLength(double& dist, int ai, int aj, Topolo
 /** Attempt to assign a reasonable value for theta internal coordinate for
   * atom i given that atoms j and k have known positions.
   */
-int Cpptraj::Structure::Model::AssignTheta(double& theta, int ai, int aj, int ak, Topology const& topIn, Frame const& frameIn, std::vector<bool> const& atomPositionKnown, int debug)
+int Cpptraj::Structure::Model::AssignTheta(double& theta, int ai, int aj, int ak, Topology const& topIn, Frame const& frameIn, std::vector<bool> const& atomPositionKnown)
 {
   // Figure out hybridization and chirality of atom j.
-  if (debug > 0)
+  if (debug_ > 0)
     mprintf("DEBUG: AssignTheta for atom j : %s\n", topIn.AtomMaskName(aj).c_str());
 
   //enum HybridizationType { SP = 0, SP2, SP3, UNKNOWN_HYBRIDIZATION };
 
   Atom const& AJ = topIn[aj];
-  if (debug > 0) {
+  if (debug_ > 0) {
     mprintf("DEBUG:\t\tI %s Nbonds: %i\n", topIn[ai].ElementName(), topIn[ai].Nbonds());
     mprintf("DEBUG:\t\tJ %s Nbonds: %i\n", AJ.ElementName(), AJ.Nbonds());
     mprintf("DEBUG:\t\tK %s Nbonds: %i\n", topIn[ak].ElementName(), topIn[ak].Nbonds());
@@ -155,17 +155,17 @@ static inline double wrap360(double phi) {
 int Cpptraj::Structure::Model::AssignPhi(double& phi, int ai, int aj, int ak, int al,
                                          Topology const& topIn, Frame const& frameIn,
                                          std::vector<bool> const& atomPositionKnown,
-                                         BuildAtom const& AtomJ, int debug)
+                                         BuildAtom const& AtomJ)
 {
   // Figure out hybridization and chirality of atom j.
-  if (debug > 0)
+  if (debug_ > 0)
     mprintf("DEBUG: AssignPhi for atom j : %s\n", topIn.AtomMaskName(aj).c_str());
 
   Atom const& AJ = topIn[aj];
-  if (debug > 0) mprintf("DEBUG:\t\tNbonds: %i\n", AJ.Nbonds());
+  if (debug_ > 0) mprintf("DEBUG:\t\tNbonds: %i\n", AJ.Nbonds());
   // If atom J only has 2 bonds, ai-aj-ak-al is the only possibility.
   if (AJ.Nbonds() < 3) {
-    if (debug > 0)
+    if (debug_ > 0)
       mprintf("DEBUG:\t\tFewer than 3 bonds. Setting phi to -180.\n");
     phi = -180 * Constants::DEGRAD;
     return 0;
@@ -173,7 +173,7 @@ int Cpptraj::Structure::Model::AssignPhi(double& phi, int ai, int aj, int ak, in
 
   // TODO check that atom i actually ends up on the list?
   std::vector<int> const& priority = AtomJ.Priority();
-  if (debug > 0) {
+  if (debug_ > 0) {
     mprintf("DEBUG: Original chirality around J %s is %s\n", topIn.AtomMaskName(aj).c_str(), chiralStr(AtomJ.Chirality()));
     mprintf("DEBUG:\t\tPriority around J %s(%i):", 
             topIn.AtomMaskName(aj).c_str(), (int)atomPositionKnown[aj]);
@@ -196,7 +196,7 @@ int Cpptraj::Structure::Model::AssignPhi(double& phi, int ai, int aj, int ak, in
                               frameIn.XYZ(aj),
                               frameIn.XYZ(ak),
                               frameIn.XYZ(al));
-      if (debug > 0)
+      if (debug_ > 0)
         mprintf("DEBUG:\t\tKnown phi for %s = %g\n", topIn.AtomMaskName(atnum).c_str(), knownPhi[idx]*Constants::RADDEG);
       if (knownIdx == -1) knownIdx = idx; // FIXME handle more than 1 known
     }
@@ -214,7 +214,7 @@ int Cpptraj::Structure::Model::AssignPhi(double& phi, int ai, int aj, int ak, in
       if (atnum != ak) {
         int currentDepth = 0;
         depth[idx] = atom_depth(currentDepth, atnum, topIn, visited, 10);
-        if (debug > 0)
+        if (debug_ > 0)
           mprintf("DEBUG:\t\tAJ %s depth from %s is %i\n",
                   topIn.AtomMaskName(aj).c_str(), topIn.AtomMaskName(atnum).c_str(), depth[idx]);
         if (knownIdx == -1 && depth[idx] < 3) {
@@ -231,7 +231,7 @@ int Cpptraj::Structure::Model::AssignPhi(double& phi, int ai, int aj, int ak, in
   double startPhi;
   if (knownIdx == -1) {
     startPhi = -180*Constants::DEGRAD;
-    if (debug > 0) mprintf("DEBUG:\t\tNo known phi. Setting to %g.\n", startPhi*Constants::RADDEG);
+    if (debug_ > 0) mprintf("DEBUG:\t\tNo known phi. Setting to %g.\n", startPhi*Constants::RADDEG);
     knownIdx = 0;
   } else
     startPhi = knownPhi[knownIdx];
@@ -240,7 +240,7 @@ int Cpptraj::Structure::Model::AssignPhi(double& phi, int ai, int aj, int ak, in
     startPhi = -startPhi;
     interval = -interval;
   }
-  if (debug > 0) {
+  if (debug_ > 0) {
     mprintf("DEBUG:\t\tStart phi is %g degrees\n", startPhi*Constants::RADDEG);
     mprintf("DEBUG:\t\tInterval is %g degrees\n", interval * Constants::RADDEG);
   }
@@ -251,7 +251,7 @@ int Cpptraj::Structure::Model::AssignPhi(double& phi, int ai, int aj, int ak, in
     int atnum = priority[idx];
     if (atnum != ak) {
       if (atnum == ai) phi = currentPhi;
-      if (debug > 0)
+      if (debug_ > 0)
         mprintf("DEBUG:\t\t\t%s phi= %g\n", topIn.AtomMaskName(atnum).c_str(), currentPhi*Constants::RADDEG);
       currentPhi += interval;
       currentPhi = wrap360(currentPhi);
@@ -263,7 +263,7 @@ int Cpptraj::Structure::Model::AssignPhi(double& phi, int ai, int aj, int ak, in
     int atnum = priority[idx];
     if (atnum != ak) {
       if (atnum == ai) phi = currentPhi;
-      if (debug > 0)
+      if (debug_ > 0)
         mprintf("DEBUG:\t\t\t%s phi= %g\n", topIn.AtomMaskName(atnum).c_str(), currentPhi*Constants::RADDEG);
       currentPhi -= interval;
       currentPhi = wrap360(currentPhi);
diff --git a/src/Structure/Model.h b/src/Structure/Model.h
index 9a6452d53f..30befeda63 100644
--- a/src/Structure/Model.h
+++ b/src/Structure/Model.h
@@ -1,21 +1,27 @@
 #ifndef INC_STRUCTURE_MODEL_H
 #define INC_STRUCTURE_MODEL_H
 #include <vector>
-#include "StructureEnum.h"
+//#incl ude "StructureEnum.h"
 class Topology;
 class Frame;
 namespace Cpptraj {
 namespace Structure {
 class BuildAtom;
-/// Routines to generate model parameters
-namespace Model {
-/// Assign a reasonable value for bond distance given 2 atoms whose position may or may not be known
-int AssignLength(double&, int, int, Topology const&, Frame const&, std::vector<bool> const&, int);
-/// Given atoms J K and L, attempt to assign a reasonable value for phi for atom I
-int AssignPhi(double&, int, int, int, int, Topology const&, Frame const&, std::vector<bool> const&, BuildAtom const&, int);
-/// Given atoms J and K, attempt to assign a reasonable value for theta for atom I
-int AssignTheta(double&, int, int, int, Topology const&, Frame const&, std::vector<bool> const&, int);
-} // END namespace Model
+/// Routines to create a model for missing bond/angle/torsion parameters
+class Model {
+  public:
+    Model() : debug_(0) {}
+    /// Set debug level
+    void SetDebug(int d) { debug_ = d; }
+    /// Assign a reasonable value for bond distance given 2 atoms whose position may or may not be known
+    int AssignLength(double&, int, int, Topology const&, Frame const&, std::vector<bool> const&);
+    /// Given atoms J and K, attempt to assign a reasonable value for theta for atom I
+    int AssignTheta(double&, int, int, int, Topology const&, Frame const&, std::vector<bool> const&);
+    /// Given atoms J K and L, attempt to assign a reasonable value for phi for atom I
+    int AssignPhi(double&, int, int, int, int, Topology const&, Frame const&, std::vector<bool> const&, BuildAtom const&);
+  private:
+    int debug_;
+};
 } // END namespace Structure
 } // END namespace Cpptraj
 #endif

From e61964fdc034e29dd73bdbbc71266037280d8eae Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 19 Jan 2024 09:01:12 -0500
Subject: [PATCH 0353/1492] Update depends

---
 src/Structure/structuredepend | 2 +-
 src/cpptrajdepend             | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/Structure/structuredepend b/src/Structure/structuredepend
index ccf6cce6e9..ed0a465379 100644
--- a/src/Structure/structuredepend
+++ b/src/Structure/structuredepend
@@ -13,4 +13,4 @@ Sugar.o : Sugar.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.
 SugarBuilder.o : SugarBuilder.cpp ../ArgList.h ../Atom.h ../AtomMap.h ../AtomMask.h ../AtomType.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DistRoutines.h ../FileIO.h ../FileName.h ../Frame.h ../ImageOption.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Chirality.h FunctionalGroup.h FxnGroupBuilder.h LinkAtom.h ResStatArray.h StructureEnum.h StructureRoutines.h Sugar.h SugarBuilder.h SugarLinkAtoms.h SugarToken.h
 SugarLinkAtoms.o : SugarLinkAtoms.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../StringRoutines.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h LinkAtom.h SugarLinkAtoms.h
 SugarToken.o : SugarToken.cpp ../ArgList.h ../CpptrajStdio.h SugarToken.h
-Zmatrix.o : Zmatrix.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h GenerateConnectivityArrays.h InternalCoords.h Model.h StructureEnum.h Zmatrix.h
+Zmatrix.o : Zmatrix.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h Chirality.h GenerateConnectivityArrays.h InternalCoords.h Model.h StructureEnum.h Zmatrix.h
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index a9da180829..dc4ddeb557 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -460,7 +460,7 @@ Structure/Sugar.o : Structure/Sugar.cpp Atom.h AtomMask.h AtomType.h Box.h Const
 Structure/SugarBuilder.o : Structure/SugarBuilder.cpp ArgList.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DistRoutines.h FileIO.h FileName.h Frame.h ImageOption.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Chirality.h Structure/FunctionalGroup.h Structure/FxnGroupBuilder.h Structure/LinkAtom.h Structure/ResStatArray.h Structure/StructureEnum.h Structure/StructureRoutines.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarLinkAtoms.h Structure/SugarToken.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 Structure/SugarLinkAtoms.o : Structure/SugarLinkAtoms.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/LinkAtom.h Structure/SugarLinkAtoms.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/SugarToken.o : Structure/SugarToken.cpp ArgList.h CpptrajStdio.h Structure/SugarToken.h
-Structure/Zmatrix.o : Structure/Zmatrix.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/Model.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Structure/Zmatrix.o : Structure/Zmatrix.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/Chirality.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/Model.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 StructureCheck.o : StructureCheck.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h ExclusionArray.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StructureCheck.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 StructureMapper.o : StructureMapper.cpp AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StructureMapper.h SymbolExporting.h TextFormat.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 SymmetricRmsdCalc.o : SymmetricRmsdCalc.cpp ArrayIterator.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h Hungarian.h ImageOption.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h Topology.h TypeNameHolder.h Unit.h Vec3.h

From 412b20578365d78c42780fbff483dae5b9ad70bc Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 19 Jan 2024 09:04:49 -0500
Subject: [PATCH 0354/1492] SetFromFrameAndConnect now does all atoms. Test
 some code for determining KL pair parameters around bond IJ.

---
 src/Structure/Zmatrix.cpp | 123 +++++++++++++++++++++++++++++---------
 src/Structure/Zmatrix.h   |   2 +-
 2 files changed, 96 insertions(+), 29 deletions(-)

diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index 932741398c..b1e1ad4665 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -7,6 +7,7 @@
 #include "BuildAtom.h"
 #include "Model.h"
 #include "GenerateConnectivityArrays.h"
+#include "Chirality.h"
 #include "../Frame.h"
 #include "../CpptrajStdio.h"
 #include "../Constants.h"
@@ -735,25 +736,26 @@ int Zmatrix::UpdateICsFromFrame(Frame const& frameIn, int ires, Topology const&
 /** Set up Zmatrix from Cartesian coordinates and topology.
   * Use torsions based on connectivity to create a complete set of ICs.
   */
-int Zmatrix::SetFromFrameAndConnect(Frame const& frameIn, Topology const& topIn, int molnum)
+int Zmatrix::SetFromFrameAndConnect(Frame const& frameIn, Topology const& topIn) //, int molnum)
 {
-  if (molnum < 0) {
-    mprinterr("Internal Error: Zmatrix::SetFromFrame(): Negative molecule index.\n");
-    return 1;
-  }
-  if (topIn.Nmol() < 1) {
-    mprinterr("Internal Error: Zmatrix::SetFromFrame(): No molecules.\n");
-    return 1;
-  }
+//  if (molnum < 0) {
+//    mprinterr("Internal Error: Zmatrix::SetFromFrame(): Negative molecule index.\n");
+//    return 1;
+//  }
+//  if (topIn.Nmol() < 1) {
+//    mprinterr("Internal Error: Zmatrix::SetFromFrame(): No molecules.\n");
+//    return 1;
+//  }
   clear();
 
   IC_.clear();
-  Molecule const& currentMol = topIn.Mol(molnum);
+//  Molecule const& currentMol = topIn.Mol(molnum);
 
-  for (Unit::const_iterator seg = currentMol.MolUnit().segBegin();
-                            seg != currentMol.MolUnit().segEnd(); ++seg)
-  {
-    for (int iat1 = seg->Begin(); iat1 != seg->End(); ++iat1)
+//  for (Unit::const_iterator seg = currentMol.MolUnit().segBegin();
+//                            seg != currentMol.MolUnit().segEnd(); ++seg)
+//  {
+//    for (int iat1 = seg->Begin(); iat1 != seg->End(); ++iat1)
+    for (int iat1 = 0; iat1 < topIn.Natom(); iat1++)
     {
       Atom const& At1 = topIn[iat1];
       for (int bidx1 = 0; bidx1 < At1.Nbonds(); bidx1++) {
@@ -776,6 +778,49 @@ int Zmatrix::SetFromFrameAndConnect(Frame const& frameIn, Topology const& topIn,
         }
       }
     }
+  //}
+  if (IC_.empty()) {
+    // Either 4-5 atoms in a tetrahedral configuration or else
+    // some other strange configuration.
+    mprintf("Warning: No ICs created for %s\n", topIn.c_str());
+/*
+    // Create ICs using 1st 3 heaviest atoms.
+    if (topIn.Natom() > 3) {
+      typedef std::pair<double,int> MIpair;
+      // Used to sort mass descending).
+      struct MassCmp {
+        inline bool operator()(MIpair const& lhs, MIpair const& rhs) const {
+          if (lhs.first == rhs.first)
+            return lhs.second < rhs.second;
+          else
+            return lhs.first > rhs.first;
+        }
+      };
+
+      std::vector<MIpair> MassIndices;
+      MassIndices.reserve( topIn.Natom() );
+      for (int iat = 0; iat < topIn.Natom(); iat++)
+        MassIndices.push_back( MIpair(topIn[iat].Mass(), iat) );
+      // Sort by mass
+      std::sort( MassIndices.begin(), MassIndices.end(), MassCmp() );
+      mprintf("Sorted:");
+      for (std::vector<MIpair>::const_iterator it = MassIndices.begin(); it != MassIndices.end(); ++it)
+        mprintf(" %s", topIn.AtomMaskName(it->second).c_str());
+      mprintf("\n");
+      // Set up ICs
+      for (int iat1 = 0; iat1 < topIn.Natom(); iat1++) {
+        std::vector<int> iats;
+        iats.reserve(3);
+        for (std::vector<MIpair>::const_iterator it = MassIndices.begin(); it != MassIndices.end(); ++it)
+        {
+          if (it->second != iat1)
+            iats.push_back( it->second );
+          if (iats.size() == 3) break;
+        }
+        addIc(iat1, iats[0], iats[1], iats[2], frameIn);
+      }
+    }
+*/
   }
 
   return 0;
@@ -1042,31 +1087,53 @@ int Zmatrix::SetupICsAroundBond(int atA, int atB, Frame const& frameIn, Topology
       }
       MARK( *iat, hasIC, nHasIC );
       // ----- K L: Set up ICs for X iat atA atB ---------------------
-      /*Atom const& AJ2 = topIn[*iat];
+      Atom const& AJ2 = topIn[*iat];
       for (Atom::bond_iterator i2at = AJ2.bondbegin(); i2at != AJ2.bondend(); ++i2at)
       {
         if (*i2at != atA && *i2at != atB && !hasIC[*i2at]) {
-          // Use existing dist and theta
-          newDist = sqrt( DIST2_NoImage(frameIn.XYZ(*i2at), frameIn.XYZ(*iat)) );
-          newTheta = CalcAngle( frameIn.XYZ(*i2at), frameIn.XYZ(*iat), frameIn.XYZ(atA) );
+          mprintf("DEBUG: MODEL K L IC: %s %s %s %s %i %i %i %i\n",
+                  topIn.AtomMaskName(*i2at).c_str(),
+                  topIn.AtomMaskName(*iat).c_str(),
+                  topIn.AtomMaskName(atA).c_str(),
+                  topIn.AtomMaskName(atB).c_str(),
+                  *i2at+1, *iat+1, atA+1, atB+1);
+          if (Cpptraj::Structure::Model::AssignLength(newDist, *i2at, *iat, topIn, frameIn, atomPositionKnown, modelDebug)) {
+            mprinterr("Error: length (k l) assignment failed.\n");
+            return 1;
+          }
+          mprintf("DEBUG: K L distance= %g\n", newDist);
+          //newTheta = CalcAngle( frameIn.XYZ(*i2at), frameIn.XYZ(*iat), frameIn.XYZ(atA) );
+          if (Cpptraj::Structure::Model::AssignTheta(newTheta, *iat, atA, atB, topIn, frameIn, atomPositionKnown, modelDebug)) {
+            mprinterr("Error: theta (k l) assignment failed.\n");
+            return 1;
+          }
+          mprintf("DEBUG: K L angle= %g\n", newTheta*Constants::RADDEG);
           // Set phi for X iat atA atB
+          BuildAtom AtomC;
+          if (topIn[*iat].Nbonds() > 2) {
+            AtomC.SetChirality( DetermineChirality(*iat, topIn, frameIn, modelDebug) );
+            SetPriority(AtomC.ModifyPriority(), *iat, topIn, frameIn, modelDebug);
+          }
           newPhi = 0;
-          if (Cpptraj::Structure::Model::AssignPhi(newPhi, *i2at, *iat, atA, atB, topIn, frameIn, atomPositionKnown, atomChirality)) {
+          if (Cpptraj::Structure::Model::AssignPhi(newPhi, *i2at, *iat, atA, atB, topIn, frameIn,
+                                                   atomPositionKnown, AtomC, 1)) // FIXME debug level
+          {
             mprinterr("Error: phi (k l) assignment failed.\n");
             return 1;
           }
-          mprintf("DEBUG:\t\tnewPhi = %g\n", newPhi*Constants::RADDEG);
-          IC_.push_back(InternalCoords( *i2at, *iat, atA, atB, newDist, newTheta*Constants::RADDEG, newPhi*Constants::RADDEG ));
-          mprintf("DEBUG: MODEL K L IC: ");
-          IC_.back().printIC(topIn);
-          MARK( *i2at, hasIC, nHasIC );
+          mprintf("DEBUG: K L Phi = %g\n", newPhi*Constants::RADDEG);
+          //IC_.push_back(InternalCoords( *i2at, *iat, atA, atB, newDist, newTheta*Constants::RADDEG, newPhi*Constants::RADDEG ));
+          //mprintf("DEBUG: MODEL K L IC: ");
+          //IC_.back().printIC(topIn);
+          //MARK( *i2at, hasIC, nHasIC );
           // Trace from atA *iat *i2at outwards
-          ToTrace.push_back(atA);
-          ToTrace.push_back(*iat);
-          ToTrace.push_back(*i2at);
+          //ToTrace.push_back(atA);
+          //ToTrace.push_back(*iat);
+          //ToTrace.push_back(*i2at);
           //if (traceMol(atA, *iat, *i2at, frameIn, topIn, topIn.Natom(), nHasIC, hasIC)) return 1;
+
         }
-      } */
+      } 
     }
   }
 /*
diff --git a/src/Structure/Zmatrix.h b/src/Structure/Zmatrix.h
index 0788df4a74..d60ff50ddd 100644
--- a/src/Structure/Zmatrix.h
+++ b/src/Structure/Zmatrix.h
@@ -42,7 +42,7 @@ class Zmatrix {
     int AutoSetSeedsWithPositions(Frame const&, Topology const&, int, Barray const&);
 
     /// Try to generate complete ICs from atom connectivity
-    int SetFromFrameAndConnect(Frame const&, Topology const&, int);
+    int SetFromFrameAndConnect(Frame const&, Topology const&);//, int);
     /// Update ICs from existing coords
     int UpdateICsFromFrame(Frame const&, int, Topology const&, Barray const&);
     /// Convert specifed molecule of Frame/Topology to internal coordinates array

From c5988f7bcccb2835a5f223d26ca0c9467e312506 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 19 Jan 2024 09:06:02 -0500
Subject: [PATCH 0355/1492] No need to specify molecule number to
 SetFromFrameAndConnect

---
 src/Exec_Build.cpp   | 2 +-
 src/Exec_Zmatrix.cpp | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 9e8de1ba66..39afa8a282 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -299,7 +299,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
         Frame templateFrame = resTemplate->AllocateFrame();
         resTemplate->GetFrame( 0, templateFrame );
         Cpptraj::Structure::Zmatrix* zmatrix = new Cpptraj::Structure::Zmatrix();
-        if (zmatrix->SetFromFrameAndConnect( templateFrame, resTemplate->Top(), 0 )) {
+        if (zmatrix->SetFromFrameAndConnect( templateFrame, resTemplate->Top() )) {
           mprinterr("Error: Could not set up residue template zmatrix.\n");
           return 1;
         }
diff --git a/src/Exec_Zmatrix.cpp b/src/Exec_Zmatrix.cpp
index feaa976432..c4e8158e9e 100644
--- a/src/Exec_Zmatrix.cpp
+++ b/src/Exec_Zmatrix.cpp
@@ -47,7 +47,7 @@ const
   zmatrix.SetDebug( State.Debug() );
   int errStat;
   if (complete_zmatrix)
-    errStat = zmatrix.SetFromFrameAndConnect(frmIn, CRD->Top(), molnum);
+    errStat = zmatrix.SetFromFrameAndConnect(frmIn, CRD->Top());
   else
     errStat = zmatrix.SetFromFrame( frmIn, CRD->Top(), molnum );
   if (debug_ > 0) zmatrix.print(); // DEBUG

From 4758054590d43241a4f1a4fb5c47c3d4849bab78 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 19 Jan 2024 09:23:59 -0500
Subject: [PATCH 0356/1492] Start new assign phi routine

---
 src/Structure/Model.cpp | 41 +++++++++++++++++++++++++++++++++++++++++
 src/Structure/Model.h   | 10 +++++++---
 2 files changed, 48 insertions(+), 3 deletions(-)

diff --git a/src/Structure/Model.cpp b/src/Structure/Model.cpp
index ea268652c3..afe3073e68 100644
--- a/src/Structure/Model.cpp
+++ b/src/Structure/Model.cpp
@@ -10,6 +10,7 @@
 
 /** Assign reasonable value for bond distance. */
 int Cpptraj::Structure::Model::AssignLength(double& dist, int ai, int aj, Topology const& topIn, Frame const& frameIn, std::vector<bool> const& atomPositionKnown)
+const
 {
   if (atomPositionKnown[ai] && atomPositionKnown[aj])
     dist = sqrt( DIST2_NoImage( frameIn.XYZ(ai), frameIn.XYZ(aj) ) );
@@ -23,6 +24,7 @@ int Cpptraj::Structure::Model::AssignLength(double& dist, int ai, int aj, Topolo
   * atom i given that atoms j and k have known positions.
   */
 int Cpptraj::Structure::Model::AssignTheta(double& theta, int ai, int aj, int ak, Topology const& topIn, Frame const& frameIn, std::vector<bool> const& atomPositionKnown)
+const
 {
   // Figure out hybridization and chirality of atom j.
   if (debug_ > 0)
@@ -156,6 +158,7 @@ int Cpptraj::Structure::Model::AssignPhi(double& phi, int ai, int aj, int ak, in
                                          Topology const& topIn, Frame const& frameIn,
                                          std::vector<bool> const& atomPositionKnown,
                                          BuildAtom const& AtomJ)
+const
 {
   // Figure out hybridization and chirality of atom j.
   if (debug_ > 0)
@@ -272,3 +275,41 @@ int Cpptraj::Structure::Model::AssignPhi(double& phi, int ai, int aj, int ak, in
 
   return 0;
 }
+
+static inline AtomType::HybridizationType getAtomHybridization(ParmHolder<AtomType> const& AT, Topology const& topIn, int ix)
+{
+  AtomType::HybridizationType hx;
+  ParmHolder<AtomType>::const_iterator itx = AT.GetParam( TypeNameHolder( topIn[ix].Type() ) );
+  if (itx == AT.end())
+    hx = Cpptraj::GuessAtomHybridization(topIn[ix], topIn.Atoms());
+  else
+    hx = itx->second.Hybridization();
+  return hx;
+}
+
+/** Assign phi values around a bond. */
+int Cpptraj::Structure::Model::AssignPhiAroundBond(int ix, int iy, Topology const& topIn, Frame const& frameIn,
+                                                   std::vector<bool> const& atomPositionKnown,
+                                                   ParmHolder<AtomType> const& AT)
+const
+{
+  // Order atoms by hybridization; AX > AY
+  int ax, ay;
+  AtomType::HybridizationType hx = getAtomHybridization(AT, topIn, ix);
+  AtomType::HybridizationType hy = getAtomHybridization(AT, topIn, iy);
+  if (hx < hy) {
+    ax = iy;
+    ay = ix;
+  } else {
+    ax = ix;
+    ay = iy;
+  }
+  mprintf("DEBUG: Assign torsions around %s (%i) - %s (%i)\n",
+          topIn.AtomMaskName(ix).c_str(), (int)hx,
+          topIn.AtomMaskName(iy).c_str(), (int)hy);
+  mprintf("DEBUG: Ordered by hybridization: %s %s\n", 
+          topIn.AtomMaskName(ax).c_str(),
+          topIn.AtomMaskName(ay).c_str());
+ 
+  return 0;
+}
diff --git a/src/Structure/Model.h b/src/Structure/Model.h
index 30befeda63..d93d1bc24b 100644
--- a/src/Structure/Model.h
+++ b/src/Structure/Model.h
@@ -4,6 +4,8 @@
 //#incl ude "StructureEnum.h"
 class Topology;
 class Frame;
+template <typename T> class ParmHolder;
+class AtomType;
 namespace Cpptraj {
 namespace Structure {
 class BuildAtom;
@@ -14,11 +16,13 @@ class Model {
     /// Set debug level
     void SetDebug(int d) { debug_ = d; }
     /// Assign a reasonable value for bond distance given 2 atoms whose position may or may not be known
-    int AssignLength(double&, int, int, Topology const&, Frame const&, std::vector<bool> const&);
+    int AssignLength(double&, int, int, Topology const&, Frame const&, std::vector<bool> const&) const;
     /// Given atoms J and K, attempt to assign a reasonable value for theta for atom I
-    int AssignTheta(double&, int, int, int, Topology const&, Frame const&, std::vector<bool> const&);
+    int AssignTheta(double&, int, int, int, Topology const&, Frame const&, std::vector<bool> const&) const;
     /// Given atoms J K and L, attempt to assign a reasonable value for phi for atom I
-    int AssignPhi(double&, int, int, int, int, Topology const&, Frame const&, std::vector<bool> const&, BuildAtom const&);
+    int AssignPhi(double&, int, int, int, int, Topology const&, Frame const&, std::vector<bool> const&, BuildAtom const&) const;
+    /// Assign phi around bond
+    int AssignPhiAroundBond(int, int, Topology const&, Frame const&, std::vector<bool> const&, ParmHolder<AtomType> const&) const;
   private:
     int debug_;
 };

From a72a343465b9f2dd67afa50875b6db32258bd487 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 19 Jan 2024 09:27:42 -0500
Subject: [PATCH 0357/1492] Use class instead of namespace

---
 src/Structure/Zmatrix.cpp | 26 ++++++++++++++------------
 1 file changed, 14 insertions(+), 12 deletions(-)

diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index b1e1ad4665..9ad2fbdd9c 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -1019,24 +1019,26 @@ int Zmatrix::SetupICsAroundBond(int atA, int atB, Frame const& frameIn, Topology
               topIn.AtomMaskName(atl0).c_str());
     modelDebug = debug_ - 1;
   }
+  Cpptraj::Structure::Model model;
+  model.SetDebug( modelDebug );
   // ---- I J: Set dist, theta, phi for atA atB K L internal coord ---
   if (debug_ > 0)
     mprintf("DEBUG: IC (i j) %i - %i - %i - %i\n", atA+1, atB+1, atk0+1, atl0+1);
   double newDist = 0;
-  if (Cpptraj::Structure::Model::AssignLength(newDist, atA, atB, topIn, frameIn, atomPositionKnown, modelDebug)) {
+  if (model.AssignLength(newDist, atA, atB, topIn, frameIn, atomPositionKnown)) {
     mprinterr("Error: length (i j) assignment failed.\n");
     return 1;
   }
   if (debug_ > 0) mprintf("DEBUG:\t\tnewDist= %g\n", newDist);
   double newTheta = 0;
-  if (Cpptraj::Structure::Model::AssignTheta(newTheta, atA, atB, atk0, topIn, frameIn, atomPositionKnown, modelDebug)) {
+  if (model.AssignTheta(newTheta, atA, atB, atk0, topIn, frameIn, atomPositionKnown)) {
     mprinterr("Error: theta (i j) assignment failed.\n");
     return 1;
   }
   if (debug_ > 0) mprintf("DEBUG:\t\tnewTheta = %g\n", newTheta*Constants::RADDEG);
   double newPhi = 0;
-  if (Cpptraj::Structure::Model::AssignPhi(newPhi, atA, atB, atk0, atl0, topIn, frameIn,
-                                           atomPositionKnown, AtomB, modelDebug))
+  if (model.AssignPhi(newPhi, atA, atB, atk0, atl0, topIn, frameIn,
+                                           atomPositionKnown, AtomB))
   {
     mprinterr("Error: phi (i j) assignment failed.\n");
     return 1;
@@ -1058,13 +1060,13 @@ int Zmatrix::SetupICsAroundBond(int atA, int atB, Frame const& frameIn, Topology
     if (*iat != atB) {
       if (ati == -1) ati = *iat;
       // Set bond dist
-      if (Cpptraj::Structure::Model::AssignLength(newDist, *iat, atA, topIn, frameIn, atomPositionKnown, modelDebug)) {
+      if (model.AssignLength(newDist, *iat, atA, topIn, frameIn, atomPositionKnown)) {
         mprinterr("Error: length (j k) assignment failed.\n");
         return 1;
       }
       // Set theta for I atA atB
       newTheta = 0;
-      if (Cpptraj::Structure::Model::AssignTheta(newTheta, *iat, atA, atB, topIn, frameIn, atomPositionKnown, modelDebug)) {
+      if (model.AssignTheta(newTheta, *iat, atA, atB, topIn, frameIn, atomPositionKnown)) {
         mprinterr("Error: theta (j k) assignment failed.\n");
         return 1;
       }
@@ -1072,8 +1074,8 @@ int Zmatrix::SetupICsAroundBond(int atA, int atB, Frame const& frameIn, Topology
         mprintf("DEBUG:\t\tnewTheta = %g\n", newTheta*Constants::RADDEG);
       // Set phi for I atA atB K
       newPhi = 0;
-      if (Cpptraj::Structure::Model::AssignPhi(newPhi, *iat, atA, atB, atk0, topIn, frameIn,
-                                               atomPositionKnown, AtomA, modelDebug))
+      if (model.AssignPhi(newPhi, *iat, atA, atB, atk0, topIn, frameIn,
+                                               atomPositionKnown, AtomA))
       {
         mprinterr("Error: phi (j k) assignment failed.\n");
         return 1;
@@ -1097,13 +1099,13 @@ int Zmatrix::SetupICsAroundBond(int atA, int atB, Frame const& frameIn, Topology
                   topIn.AtomMaskName(atA).c_str(),
                   topIn.AtomMaskName(atB).c_str(),
                   *i2at+1, *iat+1, atA+1, atB+1);
-          if (Cpptraj::Structure::Model::AssignLength(newDist, *i2at, *iat, topIn, frameIn, atomPositionKnown, modelDebug)) {
+          if (model.AssignLength(newDist, *i2at, *iat, topIn, frameIn, atomPositionKnown)) {
             mprinterr("Error: length (k l) assignment failed.\n");
             return 1;
           }
           mprintf("DEBUG: K L distance= %g\n", newDist);
           //newTheta = CalcAngle( frameIn.XYZ(*i2at), frameIn.XYZ(*iat), frameIn.XYZ(atA) );
-          if (Cpptraj::Structure::Model::AssignTheta(newTheta, *iat, atA, atB, topIn, frameIn, atomPositionKnown, modelDebug)) {
+          if (model.AssignTheta(newTheta, *iat, atA, atB, topIn, frameIn, atomPositionKnown)) {
             mprinterr("Error: theta (k l) assignment failed.\n");
             return 1;
           }
@@ -1115,8 +1117,8 @@ int Zmatrix::SetupICsAroundBond(int atA, int atB, Frame const& frameIn, Topology
             SetPriority(AtomC.ModifyPriority(), *iat, topIn, frameIn, modelDebug);
           }
           newPhi = 0;
-          if (Cpptraj::Structure::Model::AssignPhi(newPhi, *i2at, *iat, atA, atB, topIn, frameIn,
-                                                   atomPositionKnown, AtomC, 1)) // FIXME debug level
+          if (model.AssignPhi(newPhi, *i2at, *iat, atA, atB, topIn, frameIn,
+                                                   atomPositionKnown, AtomC)) // FIXME debug level
           {
             mprinterr("Error: phi (k l) assignment failed.\n");
             return 1;

From 8ea683d90dd34cbc5d7a7f06db3c0388f9d7fe15 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 19 Jan 2024 09:41:24 -0500
Subject: [PATCH 0358/1492] Try using SetFromFrameAndConnect

---
 src/Structure/Builder.cpp | 17 +++++++++++++++--
 1 file changed, 15 insertions(+), 2 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 5646d0006d..3f65896a84 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -20,6 +20,9 @@ int Builder::Combine(Topology&       frag0Top, Frame&       frag0frm,
                      int bondAt0, int bondAt1)
 const
 {
+  mprintf("DEBUG: Calling COMBINE between %s and %s\n",
+          frag0Top.AtomMaskName(bondAt0).c_str(),
+          frag1Top.AtomMaskName(bondAt1).c_str());
   int natom0 = frag0Top.Natom();
   int newNatom = natom0 + frag1Top.Natom();
 
@@ -28,23 +31,28 @@ const
   // Ensure atB index is what it will be after fragments are combined.
   Barray posKnown( newNatom, false );
   int atA, atB;
+  Zmatrix zmatrixA;
   if (frag0Top.HeavyAtomCount() < frag1Top.HeavyAtomCount()) {
     // Fragment 1 is larger
     atA = bondAt0;
     atB = bondAt1 + natom0;
     for (int at = frag0Top.Natom(); at != newNatom; at++)
       posKnown[at] = true;
+    zmatrixA.SetFromFrameAndConnect( frag0frm, frag0Top );
   } else {
     // Fragment 0 is larger or equal
     atA = bondAt1 + natom0;
     atB = bondAt0;
     for (int at = 0; at != natom0; at++)
      posKnown[at] = true;
+    zmatrixA.SetFromFrameAndConnect( frag1frm, frag1Top );
+    zmatrixA.OffsetIcIndices( natom0 );
   }
 
   // Combine fragment1 into fragment 0 topology
   Topology& combinedTop = frag0Top;
   combinedTop.AppendTop( frag1Top );
+  zmatrixA.print( &combinedTop );
   // Combined fragment1 into fragment 0 coords.
   // Need to save the original coords in frame0 since SetupFrameV does not preserve.
   double* tmpcrd0 = new double[natom0*3];
@@ -92,19 +100,24 @@ const
   // Generate Zmatrix only for ICs involving bonded atoms
   Zmatrix bondZmatrix;
 
-  bondZmatrix.SetDebug( debug_ );
+  //bondZmatrix.SetDebug( debug_ );
+  bondZmatrix.SetDebug( 1 ); // FIXME
   if (bondZmatrix.SetupICsAroundBond(atA, atB, CombinedFrame, combinedTop, posKnown, AtomA, AtomB)) {
     mprinterr("Error: Zmatrix setup for ICs around %s and %s failed.\n",
               combinedTop.AtomMaskName(atA).c_str(),
               combinedTop.AtomMaskName(atB).c_str());
     return 1;
   }
-  if (debug_ > 0)
+  //if (debug_ > 0)
     bondZmatrix.print(&combinedTop);
   if (bondZmatrix.SetToFrame( CombinedFrame, posKnown )) {
     mprinterr("Error: Conversion from bondZmatrix to Cartesian coords failed.\n");
     return 1;
   }
+  if (zmatrixA.SetToFrame( CombinedFrame, posKnown )) {
+    mprinterr("Error: Conversion from zmatrixA to Cartesian coords failed.\n");
+    return 1;
+  }
 
   return 0;
 }

From af5e3d04595d3b820b18d83a6dd373444bd32b5f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 19 Jan 2024 14:23:05 -0500
Subject: [PATCH 0359/1492] Fix assigning phi with priority

---
 src/Structure/Model.cpp | 85 ++++++++++++++++++++++++++++++++---------
 src/Structure/Model.h   |  6 +--
 2 files changed, 71 insertions(+), 20 deletions(-)

diff --git a/src/Structure/Model.cpp b/src/Structure/Model.cpp
index afe3073e68..e47d45473d 100644
--- a/src/Structure/Model.cpp
+++ b/src/Structure/Model.cpp
@@ -178,7 +178,7 @@ const
   std::vector<int> const& priority = AtomJ.Priority();
   if (debug_ > 0) {
     mprintf("DEBUG: Original chirality around J %s is %s\n", topIn.AtomMaskName(aj).c_str(), chiralStr(AtomJ.Chirality()));
-    mprintf("DEBUG:\t\tPriority around J %s(%i):", 
+    mprintf("DEBUG:\t\tPriority around J %s(%i) is", 
             topIn.AtomMaskName(aj).c_str(), (int)atomPositionKnown[aj]);
     for (int idx = 0; idx < AJ.Nbonds(); idx++)
       mprintf(" %s(%i)", topIn.AtomMaskName(priority[idx]).c_str(), (int)atomPositionKnown[priority[idx]]);
@@ -187,6 +187,7 @@ const
 
   // Fill in what values we can for known atoms
   std::vector<double> knownPhi( AJ.Nbonds() );
+  std::vector<bool> isKnown( AJ.Nbonds(), false );
   int knownIdx = -1;
   for (int idx = 0; idx < AJ.Nbonds(); idx++) {
     int atnum = priority[idx];
@@ -199,8 +200,9 @@ const
                               frameIn.XYZ(aj),
                               frameIn.XYZ(ak),
                               frameIn.XYZ(al));
+      isKnown[idx] = true;
       if (debug_ > 0)
-        mprintf("DEBUG:\t\tKnown phi for %s = %g\n", topIn.AtomMaskName(atnum).c_str(), knownPhi[idx]*Constants::RADDEG);
+        mprintf("DEBUG:\t\tKnown phi for %s (pos=%i) = %g\n", topIn.AtomMaskName(atnum).c_str(), idx, knownPhi[idx]*Constants::RADDEG);
       if (knownIdx == -1) knownIdx = idx; // FIXME handle more than 1 known
     }
   }
@@ -211,26 +213,79 @@ const
     // TODO: Ensure bonded atoms are not yet visited?
     visited[aj] = true;
     visited[ak] = true;
-    std::vector<int> depth( AJ.Nbonds() );
+    //std::vector<int> depth( AJ.Nbonds() );
+    int max_depth = 0;
+    int max_idx = -1;
     for (int idx = 0; idx < AJ.Nbonds(); idx++) {
       int atnum = priority[idx];
       if (atnum != ak) {
         int currentDepth = 0;
-        depth[idx] = atom_depth(currentDepth, atnum, topIn, visited, 10);
+        //depth[idx] = atom_depth(currentDepth, atnum, topIn, visited, 10);
+        int depth = atom_depth(currentDepth, atnum, topIn, visited, 10);
         if (debug_ > 0)
           mprintf("DEBUG:\t\tAJ %s depth from %s is %i\n",
-                  topIn.AtomMaskName(aj).c_str(), topIn.AtomMaskName(atnum).c_str(), depth[idx]);
-        if (knownIdx == -1 && depth[idx] < 3) {
-          knownIdx = idx;
-          knownPhi[idx] = 0;
+                  topIn.AtomMaskName(aj).c_str(), topIn.AtomMaskName(atnum).c_str(), depth);
+        //if (knownIdx == -1 && depth[idx] < 3) {
+        //  knownIdx = idx;
+        //  knownPhi[idx] = 0;
+        //}
+        if (max_idx == -1 || depth > max_depth) {
+          max_depth = depth;
+          max_idx = idx;
         }
       }
     }
+    mprintf("DEBUG:\t\tLongest depth is for atom %s (%i)\n", topIn.AtomMaskName(priority[max_idx]).c_str(), max_depth);
+    knownIdx = max_idx;
+    knownPhi[max_idx] = -180 * Constants::DEGRAD;
+    isKnown[max_idx] = true;
+  }
+
+  // Sanity check
+  if (knownIdx < 0) {
+    mprinterr("Internal Error: AssignPhi(): knownIdx is < 0\n");
+    return 1;
   }
 
   // The interval will be 360 / (number of bonds - 1)
   double interval = Constants::TWOPI / (AJ.Nbonds() - 1);
+  if (AtomJ.Chirality() == IS_S || AtomJ.Chirality() == IS_UNKNOWN_CHIRALITY)
+    interval = -interval;
+
+  if (debug_ > 0) {
+    mprintf("DEBUG:\t\tStart phi is %g degrees\n", knownPhi[knownIdx]*Constants::RADDEG);
+    mprintf("DEBUG:\t\tInterval is %g, chirality around J is %s\n", interval*Constants::RADDEG, chiralStr(AtomJ.Chirality()));
+  }
 
+  // Forwards from the known index
+  double currentPhi = knownPhi[knownIdx];
+  for (int idx = knownIdx; idx < AJ.Nbonds(); idx++) {
+    int atnum = priority[idx];
+    if (atnum != ak) {
+      if (isKnown[idx])
+        currentPhi = knownPhi[idx];
+      else
+        currentPhi = wrap360(currentPhi + interval);
+      if (atnum == ai) phi = currentPhi;
+      if (debug_ > 0)
+        mprintf("DEBUG:\t\t\t%s (at# %i) phi= %g\n", topIn.AtomMaskName(atnum).c_str(), atnum+1, currentPhi*Constants::RADDEG);
+    }
+  }
+  // Backwards from the known index
+  currentPhi = knownPhi[knownIdx];
+  for (int idx = knownIdx - 1; idx > -1; idx--) {
+    int atnum = priority[idx];
+    if (atnum != ak) {
+      if (isKnown[idx])
+        currentPhi = knownPhi[idx];
+      else
+        currentPhi = wrap360(currentPhi - interval);
+      if (atnum == ai) phi = currentPhi;
+      if (debug_ > 0)
+        mprintf("DEBUG:\t\t\t%s (at# %i) phi= %g\n", topIn.AtomMaskName(atnum).c_str(), atnum+1, currentPhi*Constants::RADDEG);
+    }
+  }
+/*
   double startPhi;
   if (knownIdx == -1) {
     startPhi = -180*Constants::DEGRAD;
@@ -243,10 +298,6 @@ const
     startPhi = -startPhi;
     interval = -interval;
   }
-  if (debug_ > 0) {
-    mprintf("DEBUG:\t\tStart phi is %g degrees\n", startPhi*Constants::RADDEG);
-    mprintf("DEBUG:\t\tInterval is %g degrees\n", interval * Constants::RADDEG);
-  }
     
   // Forward direction
   double currentPhi = startPhi;
@@ -272,10 +323,10 @@ const
       currentPhi = wrap360(currentPhi);
     }
   }
-
+*/
   return 0;
 }
-
+/*
 static inline AtomType::HybridizationType getAtomHybridization(ParmHolder<AtomType> const& AT, Topology const& topIn, int ix)
 {
   AtomType::HybridizationType hx;
@@ -286,9 +337,9 @@ static inline AtomType::HybridizationType getAtomHybridization(ParmHolder<AtomTy
     hx = itx->second.Hybridization();
   return hx;
 }
-
+*/
 /** Assign phi values around a bond. */
-int Cpptraj::Structure::Model::AssignPhiAroundBond(int ix, int iy, Topology const& topIn, Frame const& frameIn,
+/*int Cpptraj::Structure::Model::AssignPhiAroundBond(int ix, int iy, Topology const& topIn, Frame const& frameIn,
                                                    std::vector<bool> const& atomPositionKnown,
                                                    ParmHolder<AtomType> const& AT)
 const
@@ -312,4 +363,4 @@ const
           topIn.AtomMaskName(ay).c_str());
  
   return 0;
-}
+}*/
diff --git a/src/Structure/Model.h b/src/Structure/Model.h
index d93d1bc24b..b46d863815 100644
--- a/src/Structure/Model.h
+++ b/src/Structure/Model.h
@@ -4,8 +4,8 @@
 //#incl ude "StructureEnum.h"
 class Topology;
 class Frame;
-template <typename T> class ParmHolder;
-class AtomType;
+//template <typename T> class ParmHolder;
+//class AtomType;
 namespace Cpptraj {
 namespace Structure {
 class BuildAtom;
@@ -22,7 +22,7 @@ class Model {
     /// Given atoms J K and L, attempt to assign a reasonable value for phi for atom I
     int AssignPhi(double&, int, int, int, int, Topology const&, Frame const&, std::vector<bool> const&, BuildAtom const&) const;
     /// Assign phi around bond
-    int AssignPhiAroundBond(int, int, Topology const&, Frame const&, std::vector<bool> const&, ParmHolder<AtomType> const&) const;
+    //int AssignPhiAroundBond(int, int, Topology const&, Frame const&, std::vector<bool> const&, ParmHolder<AtomType> const&) const;
   private:
     int debug_;
 };

From 92a7018ed68586c6ffaa2d92e084656ab1d10044 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 19 Jan 2024 14:42:51 -0500
Subject: [PATCH 0360/1492] Start refactoring AssignPhi so it can be called
 once for a group of 3 connected atoms and chirality does not have to be
 passed in.

---
 src/Structure/Model.cpp | 36 ++++++++++++++++++++++++++++--------
 src/Structure/Model.h   |  2 ++
 2 files changed, 30 insertions(+), 8 deletions(-)

diff --git a/src/Structure/Model.cpp b/src/Structure/Model.cpp
index e47d45473d..23ea3e3452 100644
--- a/src/Structure/Model.cpp
+++ b/src/Structure/Model.cpp
@@ -1,5 +1,7 @@
 #include "Model.h"
 #include "BuildAtom.h"
+#include "InternalCoords.h"
+#include "Chirality.h"
 #include "../CpptrajStdio.h"
 #include "../GuessAtomHybridization.h"
 #include "../Topology.h"
@@ -148,36 +150,52 @@ static inline double wrap360(double phi) {
     return phi;
 }
 
-/** Attempt to assign a reasonable value for phi internal coordinate for atom i
-  * given that atoms j k and l have known positions.
+/** Attempt to assign reasonable values for phi internal coordinates for atoms
+  * bonded to atom j given that atoms j k and l have known positions.
   *   j - k
   *  /     \
   * i       l
   */
+//int Cpptraj::Structure::Model::AssignPhi(std::vector<InternalCoords>& IC, int aj, int ak, int al,
 int Cpptraj::Structure::Model::AssignPhi(double& phi, int ai, int aj, int ak, int al,
                                          Topology const& topIn, Frame const& frameIn,
                                          std::vector<bool> const& atomPositionKnown,
                                          BuildAtom const& AtomJ)
 const
 {
+  Atom const& AJ = topIn[aj];
+  // If atom J has only 1 bond this is not needed.
+  if (AJ.Nbonds() < 2) return 0;
+
   // Figure out hybridization and chirality of atom j.
   if (debug_ > 0)
     mprintf("DEBUG: AssignPhi for atom j : %s\n", topIn.AtomMaskName(aj).c_str());
+  std::vector<int> priority;
+  int chiralDebug = debug_;
+  if (chiralDebug > 0)
+    chiralDebug--;
+  ChiralType chirality = SetPriority(priority, aj, topIn, frameIn, chiralDebug);
 
-  Atom const& AJ = topIn[aj];
   if (debug_ > 0) mprintf("DEBUG:\t\tNbonds: %i\n", AJ.Nbonds());
   // If atom J only has 2 bonds, ai-aj-ak-al is the only possibility.
   if (AJ.Nbonds() < 3) {
     if (debug_ > 0)
       mprintf("DEBUG:\t\tFewer than 3 bonds. Setting phi to -180.\n");
-    phi = -180 * Constants::DEGRAD;
+    double currentPhi = -180 * Constants::DEGRAD;
+    for (int idx = 0; idx < AJ.Nbonds(); idx++) {
+      if (AJ.Bond(idx) != ak) {
+        //IC.push_back( InternalCoords(AJ.Bond(idx), aj, ak, al, 0, 0, currentPhi) );
+        phi = currentPhi;
+        break;
+       }
+    }
     return 0;
   }
 
   // TODO check that atom i actually ends up on the list?
-  std::vector<int> const& priority = AtomJ.Priority();
+  //std::vector<int> const& priority = AtomJ.Priority();
   if (debug_ > 0) {
-    mprintf("DEBUG: Original chirality around J %s is %s\n", topIn.AtomMaskName(aj).c_str(), chiralStr(AtomJ.Chirality()));
+    mprintf("DEBUG: Original chirality around J %s is %s\n", topIn.AtomMaskName(aj).c_str(), chiralStr(chirality));
     mprintf("DEBUG:\t\tPriority around J %s(%i) is", 
             topIn.AtomMaskName(aj).c_str(), (int)atomPositionKnown[aj]);
     for (int idx = 0; idx < AJ.Nbonds(); idx++)
@@ -249,12 +267,12 @@ const
 
   // The interval will be 360 / (number of bonds - 1)
   double interval = Constants::TWOPI / (AJ.Nbonds() - 1);
-  if (AtomJ.Chirality() == IS_S || AtomJ.Chirality() == IS_UNKNOWN_CHIRALITY)
+  if (chirality == IS_S || chirality == IS_UNKNOWN_CHIRALITY)
     interval = -interval;
 
   if (debug_ > 0) {
     mprintf("DEBUG:\t\tStart phi is %g degrees\n", knownPhi[knownIdx]*Constants::RADDEG);
-    mprintf("DEBUG:\t\tInterval is %g, chirality around J is %s\n", interval*Constants::RADDEG, chiralStr(AtomJ.Chirality()));
+    mprintf("DEBUG:\t\tInterval is %g, chirality around J is %s\n", interval*Constants::RADDEG, chiralStr(chirality));
   }
 
   // Forwards from the known index
@@ -267,6 +285,7 @@ const
       else
         currentPhi = wrap360(currentPhi + interval);
       if (atnum == ai) phi = currentPhi;
+      //IC.push_back( InternalCoords(atnum, aj, ak, al, 0, 0, currentPhi) );
       if (debug_ > 0)
         mprintf("DEBUG:\t\t\t%s (at# %i) phi= %g\n", topIn.AtomMaskName(atnum).c_str(), atnum+1, currentPhi*Constants::RADDEG);
     }
@@ -281,6 +300,7 @@ const
       else
         currentPhi = wrap360(currentPhi - interval);
       if (atnum == ai) phi = currentPhi;
+      //IC.push_back( InternalCoords(atnum, aj, ak, al, 0, 0, currentPhi) );
       if (debug_ > 0)
         mprintf("DEBUG:\t\t\t%s (at# %i) phi= %g\n", topIn.AtomMaskName(atnum).c_str(), atnum+1, currentPhi*Constants::RADDEG);
     }
diff --git a/src/Structure/Model.h b/src/Structure/Model.h
index b46d863815..d820c5e1e3 100644
--- a/src/Structure/Model.h
+++ b/src/Structure/Model.h
@@ -9,6 +9,7 @@ class Frame;
 namespace Cpptraj {
 namespace Structure {
 class BuildAtom;
+class InternalCoords;
 /// Routines to create a model for missing bond/angle/torsion parameters
 class Model {
   public:
@@ -20,6 +21,7 @@ class Model {
     /// Given atoms J and K, attempt to assign a reasonable value for theta for atom I
     int AssignTheta(double&, int, int, int, Topology const&, Frame const&, std::vector<bool> const&) const;
     /// Given atoms J K and L, attempt to assign a reasonable value for phi for atom I
+    //int AssignPhi(std::vector<InternalCoords>&, int, int, int, Topology const&, Frame const&, std::vector<bool> const&, BuildAtom const&) const;
     int AssignPhi(double&, int, int, int, int, Topology const&, Frame const&, std::vector<bool> const&, BuildAtom const&) const;
     /// Assign phi around bond
     //int AssignPhiAroundBond(int, int, Topology const&, Frame const&, std::vector<bool> const&, ParmHolder<AtomType> const&) const;

From 5fac17cc8ff8f60071af00cadbb5c984b6d4d286 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 19 Jan 2024 15:17:02 -0500
Subject: [PATCH 0361/1492] No need to figure out chirality when less than 3
 bonds

---
 src/Structure/Model.cpp | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/src/Structure/Model.cpp b/src/Structure/Model.cpp
index 23ea3e3452..d2d6c1670f 100644
--- a/src/Structure/Model.cpp
+++ b/src/Structure/Model.cpp
@@ -167,15 +167,6 @@ const
   // If atom J has only 1 bond this is not needed.
   if (AJ.Nbonds() < 2) return 0;
 
-  // Figure out hybridization and chirality of atom j.
-  if (debug_ > 0)
-    mprintf("DEBUG: AssignPhi for atom j : %s\n", topIn.AtomMaskName(aj).c_str());
-  std::vector<int> priority;
-  int chiralDebug = debug_;
-  if (chiralDebug > 0)
-    chiralDebug--;
-  ChiralType chirality = SetPriority(priority, aj, topIn, frameIn, chiralDebug);
-
   if (debug_ > 0) mprintf("DEBUG:\t\tNbonds: %i\n", AJ.Nbonds());
   // If atom J only has 2 bonds, ai-aj-ak-al is the only possibility.
   if (AJ.Nbonds() < 3) {
@@ -191,6 +182,15 @@ const
     }
     return 0;
   }
+  // Figure out hybridization and chirality of atom j.
+  if (debug_ > 0)
+    mprintf("DEBUG: AssignPhi for atom j : %s\n", topIn.AtomMaskName(aj).c_str());
+  std::vector<int> priority;
+  int chiralDebug = debug_;
+  if (chiralDebug > 0)
+    chiralDebug--;
+  ChiralType chirality = SetPriority(priority, aj, topIn, frameIn, chiralDebug);
+
 
   // TODO check that atom i actually ends up on the list?
   //std::vector<int> const& priority = AtomJ.Priority();

From 31c0eea1a1f552de46f876960ceca84319915cbc Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 19 Jan 2024 15:26:36 -0500
Subject: [PATCH 0362/1492] Use passed-in priority for now

---
 src/Structure/Model.cpp | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/src/Structure/Model.cpp b/src/Structure/Model.cpp
index d2d6c1670f..626ee482a6 100644
--- a/src/Structure/Model.cpp
+++ b/src/Structure/Model.cpp
@@ -185,15 +185,16 @@ const
   // Figure out hybridization and chirality of atom j.
   if (debug_ > 0)
     mprintf("DEBUG: AssignPhi for atom j : %s\n", topIn.AtomMaskName(aj).c_str());
-  std::vector<int> priority;
-  int chiralDebug = debug_;
-  if (chiralDebug > 0)
-    chiralDebug--;
-  ChiralType chirality = SetPriority(priority, aj, topIn, frameIn, chiralDebug);
+//  std::vector<int> priority;
+//  int chiralDebug = debug_;
+//  if (chiralDebug > 0)
+//    chiralDebug--;
+//  ChiralType chirality = SetPriority(priority, aj, topIn, frameIn, chiralDebug);
 
 
   // TODO check that atom i actually ends up on the list?
-  //std::vector<int> const& priority = AtomJ.Priority();
+  std::vector<int> const& priority = AtomJ.Priority();
+  ChiralType chirality = AtomJ.Chirality();
   if (debug_ > 0) {
     mprintf("DEBUG: Original chirality around J %s is %s\n", topIn.AtomMaskName(aj).c_str(), chiralStr(chirality));
     mprintf("DEBUG:\t\tPriority around J %s(%i) is", 

From 4f1351d0823bd1b7ddf118d24ddd7fd9b599c201 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 19 Jan 2024 15:27:29 -0500
Subject: [PATCH 0363/1492] Comment out unused includes

---
 src/Structure/Model.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/Structure/Model.cpp b/src/Structure/Model.cpp
index 626ee482a6..e2befb15f7 100644
--- a/src/Structure/Model.cpp
+++ b/src/Structure/Model.cpp
@@ -1,7 +1,7 @@
 #include "Model.h"
 #include "BuildAtom.h"
-#include "InternalCoords.h"
-#include "Chirality.h"
+//#incl ude "InternalCoords.h"
+//#incl ude "Chirality.h"
 #include "../CpptrajStdio.h"
 #include "../GuessAtomHybridization.h"
 #include "../Topology.h"

From b48137e08ca43ace1b929366123c04538d6b6bf9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 19 Jan 2024 15:29:50 -0500
Subject: [PATCH 0364/1492] Enable adding IC for K L around bond I J

---
 src/Structure/Zmatrix.cpp | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index 9ad2fbdd9c..ddddcf2566 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -1117,17 +1117,18 @@ int Zmatrix::SetupICsAroundBond(int atA, int atB, Frame const& frameIn, Topology
             SetPriority(AtomC.ModifyPriority(), *iat, topIn, frameIn, modelDebug);
           }
           newPhi = 0;
+          //model.SetDebug( 1 ); // FIXME
           if (model.AssignPhi(newPhi, *i2at, *iat, atA, atB, topIn, frameIn,
-                                                   atomPositionKnown, AtomC)) // FIXME debug level
+                                                   atomPositionKnown, AtomC))
           {
             mprinterr("Error: phi (k l) assignment failed.\n");
             return 1;
           }
           mprintf("DEBUG: K L Phi = %g\n", newPhi*Constants::RADDEG);
-          //IC_.push_back(InternalCoords( *i2at, *iat, atA, atB, newDist, newTheta*Constants::RADDEG, newPhi*Constants::RADDEG ));
-          //mprintf("DEBUG: MODEL K L IC: ");
-          //IC_.back().printIC(topIn);
-          //MARK( *i2at, hasIC, nHasIC );
+          IC_.push_back(InternalCoords( *i2at, *iat, atA, atB, newDist, newTheta*Constants::RADDEG, newPhi*Constants::RADDEG ));
+          mprintf("DEBUG: MODEL K L IC: ");
+          IC_.back().printIC(topIn);
+          MARK( *i2at, hasIC, nHasIC );
           // Trace from atA *iat *i2at outwards
           //ToTrace.push_back(atA);
           //ToTrace.push_back(*iat);

From 0fa1aee0d8818b8054967bd0c8533caa3bd7f50f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 19 Jan 2024 16:39:47 -0500
Subject: [PATCH 0365/1492] Try to handle cases where a known interval can be
 calculated

---
 src/Structure/Model.cpp | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/src/Structure/Model.cpp b/src/Structure/Model.cpp
index e2befb15f7..32162bb204 100644
--- a/src/Structure/Model.cpp
+++ b/src/Structure/Model.cpp
@@ -208,6 +208,8 @@ const
   std::vector<double> knownPhi( AJ.Nbonds() );
   std::vector<bool> isKnown( AJ.Nbonds(), false );
   int knownIdx = -1;
+  double knownInterval = 0;
+  bool hasKnownInterval = false;
   for (int idx = 0; idx < AJ.Nbonds(); idx++) {
     int atnum = priority[idx];
     if (atnum != ak && atomPositionKnown[atnum] &&
@@ -223,8 +225,14 @@ const
       if (debug_ > 0)
         mprintf("DEBUG:\t\tKnown phi for %s (pos=%i) = %g\n", topIn.AtomMaskName(atnum).c_str(), idx, knownPhi[idx]*Constants::RADDEG);
       if (knownIdx == -1) knownIdx = idx; // FIXME handle more than 1 known
+      if (idx > 0 && isKnown[idx-1] && isKnown[idx]) {
+        knownInterval = wrap360(knownPhi[idx] - knownPhi[idx-1]);
+        hasKnownInterval = true;
+      }
     }
   }
+  if (hasKnownInterval)
+    mprintf("DEBUG:\t\tKnown interval = %g\n", knownInterval * Constants::RADDEG);
 
   // If we have to assign an initial phi, make trans the longer branch
   if (knownIdx == -1) {
@@ -268,8 +276,24 @@ const
 
   // The interval will be 360 / (number of bonds - 1)
   double interval = Constants::TWOPI / (AJ.Nbonds() - 1);
+  if (hasKnownInterval) {
+    if (chirality == IS_UNKNOWN_CHIRALITY) {
+      mprintf("DEBUG: Setting chirality from known interval.\n");
+      if (knownInterval < 0)
+        chirality = IS_S;
+      else
+        chirality = IS_R;
+    } else if (chirality == IS_S) {
+      if (knownInterval > 0)
+        mprinterr("Error: Detected chirality S does not match known interval %g\n", knownInterval*Constants::RADDEG);
+    } else if (chirality == IS_R) {
+      if (knownInterval < 0)
+        mprinterr("Error: Detected chriality R does not match known interval %g\n", knownInterval*Constants::RADDEG);
+    }
+  }
   if (chirality == IS_S || chirality == IS_UNKNOWN_CHIRALITY)
     interval = -interval;
+ 
 
   if (debug_ > 0) {
     mprintf("DEBUG:\t\tStart phi is %g degrees\n", knownPhi[knownIdx]*Constants::RADDEG);

From 607978361fe54a40366682eb05ae95c188f70513 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 21 Jan 2024 15:19:58 -0500
Subject: [PATCH 0366/1492] Add some debug code

---
 src/Action_CheckChirality.cpp | 9 +++++++++
 src/Action_CheckChirality.h   | 1 +
 2 files changed, 10 insertions(+)

diff --git a/src/Action_CheckChirality.cpp b/src/Action_CheckChirality.cpp
index b877d305b0..10ce49e645 100644
--- a/src/Action_CheckChirality.cpp
+++ b/src/Action_CheckChirality.cpp
@@ -2,6 +2,7 @@
 #include "CpptrajStdio.h"
 #include "TorsionRoutines.h"
 #include "DataSet_Mesh.h"
+//#inc lude "Structure/Chirality.h" // DEBUG
 
 void Action_CheckChirality::Help() const {
   mprintf("\t[<name>] [<mask1>] [out <filename>]\n"
@@ -48,6 +49,7 @@ Action::RetType Action_CheckChirality::Init(ArgList& actionArgs, ActionInit& ini
 // Action_CheckChirality::Setup()
 /** Set angle up for this parmtop. Get masks etc. */
 Action::RetType Action_CheckChirality::Setup(ActionSetup& setup) {
+//  top_ = setup.TopAddress(); // DEBUG
   if (setup.Top().SetupCharMask(Mask1_)) return Action::ERR;
   if (Mask1_.None()) {
     mprinterr("Warning: Mask '%s' selects no atoms.\n", Mask1_.MaskString());
@@ -139,6 +141,13 @@ Action::RetType Action_CheckChirality::DoAction(int frameNum, ActionFrame& frm)
       ri->N_L_++;
     else
       ri->N_D_++;
+//    DEBUG
+//    int at = ri->ca_ / 3;
+//    Cpptraj::Structure::ChiralType chirality = Cpptraj::Structure::IS_UNKNOWN_CHIRALITY;
+//    if (top_->Atoms()[at].Nbonds() > 2)
+//      chirality = Cpptraj::Structure::DetermineChirality(at, *top_, frm.Frm(), 0);
+//    mprintf("Chirality around %s is %s\n", top_->AtomMaskName(at).c_str(), Cpptraj::Structure::chiralStr(chirality));
+//    DEBUG
   }
 
   return Action::OK;
diff --git a/src/Action_CheckChirality.h b/src/Action_CheckChirality.h
index b145703501..861f3801d3 100644
--- a/src/Action_CheckChirality.h
+++ b/src/Action_CheckChirality.h
@@ -36,5 +36,6 @@ class Action_CheckChirality: public Action {
     DataSet* data_D_;     ///< Hold number of times each residue was D
     std::string setname_; ///< Data set name
     ActionInit Init_;     ///< Master DSL/DFL
+//    Topology* top_; // DEBUG
 };
 #endif

From e804e8dad3488b55a407f24848cba612090e7026 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 22 Jan 2024 09:40:14 -0500
Subject: [PATCH 0367/1492] Update test save with new modeled coords

---
 test/Test_Sequence/Mol.mol2.save | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/test/Test_Sequence/Mol.mol2.save b/test/Test_Sequence/Mol.mol2.save
index d15e8643b6..482c8198c5 100644
--- a/test/Test_Sequence/Mol.mol2.save
+++ b/test/Test_Sequence/Mol.mol2.save
@@ -6,10 +6,10 @@ USER_CHARGES
 
 
 @<TRIPOS>ATOM
-      1 C1         -1.8623   -1.2984   -0.5952 CT         1 MOC      1.387300
-      2 H2         -2.2353   -2.1775   -1.1026 H1         1 MOC     -0.288000
-      3 H3         -2.2811   -0.4130   -1.0709 H1         1 MOC     -0.288000
-      4 H4         -2.1956   -1.3220    0.4412 H1         1 MOC     -0.288000
+      1 C1         -1.9010   -1.2979   -0.5927 CT         1 MOC      1.387300
+      2 H2         -2.3121   -2.1475   -1.1378 H1         1 MOC     -0.288000
+      3 H3         -2.2811   -0.3718   -1.0240 H1         1 MOC     -0.288000
+      4 H4         -2.1989   -1.3598    0.4539 H1         1 MOC     -0.288000
       5 O5         -0.4741   -1.3169   -0.6848 OS         1 MOC     -0.523200
       6 N           0.0540   -0.2256    0.0153 N          2 CNALA   -0.570310
       7 H          -0.4149    0.5139    0.5357 H          2 CNALA    0.364710

From 272edf0344437dda6e39ac2ea8553f650dbd7311 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 22 Jan 2024 10:29:55 -0500
Subject: [PATCH 0368/1492] Start refactoring chiral routines.

---
 src/Structure/BuildAtom.h   | 35 ++++++++++++++++--------
 src/Structure/Builder.cpp   | 12 ++++-----
 src/Structure/Chirality.cpp | 53 ++++++++++++++++++++++++++-----------
 src/Structure/Chirality.h   | 12 +++++----
 4 files changed, 74 insertions(+), 38 deletions(-)

diff --git a/src/Structure/BuildAtom.h b/src/Structure/BuildAtom.h
index 1515d2ce9f..b576290058 100644
--- a/src/Structure/BuildAtom.h
+++ b/src/Structure/BuildAtom.h
@@ -1,28 +1,41 @@
 #ifndef INC_STRUCTURE_BUILDATOM_H
 #define INC_STRUCTURE_BUILDATOM_H
 #include "StructureEnum.h"
+#include <vector>
 namespace Cpptraj {
 namespace Structure {
-/// Hold information for an atom used when building/modelling new coordinates.
+/// Hold chirality/orientation information for an atom. Used when building/modelling new coordinates.
 class BuildAtom {
   public:
-    BuildAtom() : ctype_(IS_UNKNOWN_CHIRALITY) {}
+    /// Blank constructor 
+    BuildAtom() : tors_(0), ctype_(IS_UNKNOWN_CHIRALITY), orientation_(IS_UNKNOWN_CHIRALITY) {}
+    /// CONSTRUCTOR - Take only chiral type. Usually used to indicate an error
+    BuildAtom(ChiralType e) : tors_(0), ctype_(e), orientation_(e) {}
+    /// CONSTRUCTOR - torsion, chirality, orientation, priority array
+    BuildAtom(double t, ChiralType c, ChiralType o, std::vector<int> const& p) :
+                  tors_(t), ctype_(c), orientation_(o), priority_(p) {}
+    /// Update the priority array
+    void SetPriority(std::vector<int> const& p) { priority_ = p; }
     /// Set chirality
-    void SetChirality(ChiralType c) { ctype_ = c; }
-    /// Set size of priority array based on number of bonds
-    //void SetNbonds(int n) { priority_.assign(n, -1); }
-    /// \return Pointer to priority array
-    //int* PriorityPtr() { return &(priority_[0]); }
+    //void SetChirality(ChiralType c) { ctype_ = c; }
     /// Used to modify the priority array
-    std::vector<int>& ModifyPriority() { return priority_; }
+    //std::vector<int>& ModifyPriority() { return priority_; }
 
     /// \return Atom chirality
-    ChiralType Chirality() const { return ctype_; }
+    ChiralType Chirality()             const { return ctype_; }
+    /// \return Orientation around atom
+    ChiralType Orientation()           const { return orientation_; }
     /// \return Priority array
     std::vector<int> const& Priority() const { return priority_; }
+    /// \return Value of the orientation torsion around atom (in radians).
+    double TorsionVal()                const { return tors_; }
+    /// \return True if an error occurred determining chirality
+    bool ChiralError()                 const { return (ctype_ == CHIRALITY_ERR) || priority_.empty(); }
   private:
-    ChiralType ctype_;          ///< Chirality around atom
-    std::vector<int> priority_; ///< Indices of bonded atoms, sorted by priority
+    double tors_;               ///< Torsion around the atom in radians (via priority, 1-2-3-0, where 0 is this atom).
+    ChiralType ctype_;          ///< Chirality around atom.
+    ChiralType orientation_;    ///< Orientation when chirality cannot be determined.
+    std::vector<int> priority_; ///< Indices of bonded atoms, sorted by priority.
 };
 }
 }
diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 3f65896a84..c4cb4305af 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -71,12 +71,12 @@ const
   // Get the chirality around each atom before the bond is added.
   BuildAtom AtomA;
   if (combinedTop[atA].Nbonds() > 2)
-    AtomA.SetChirality( DetermineChirality(atA, combinedTop, CombinedFrame, chiralityDebug) );
+    AtomA = DetermineChirality(atA, combinedTop, CombinedFrame, chiralityDebug);
   if (debug_ > 0)
     mprintf("DEBUG:\tAtom %4s chirality %6s\n", combinedTop.AtomMaskName(atA).c_str(), chiralStr(AtomA.Chirality()));
   BuildAtom AtomB;
   if (combinedTop[atB].Nbonds() > 2)
-    AtomB.SetChirality( DetermineChirality(atB, combinedTop, CombinedFrame, chiralityDebug) );
+    AtomB = DetermineChirality(atB, combinedTop, CombinedFrame, chiralityDebug);
   if (debug_ > 0)
     mprintf("DEBUG:\tAtom %4s chirality %6s\n", combinedTop.AtomMaskName(atB).c_str(), chiralStr(AtomB.Chirality()));
 
@@ -87,7 +87,7 @@ const
   // // Regenerate the molecule info FIXME should Topology just do this?
   if (combinedTop.DetermineMolecules()) return 1;
 
-  // Determine priorities
+  // Determine new priorities around atoms that were just bonded
   if (combinedTop[atA].Nbonds() > 2) {
     //AtomA.SetNbonds(combinedTop[atA].Nbonds());
     SetPriority(AtomA.ModifyPriority(), atA, combinedTop, CombinedFrame, chiralityDebug);
@@ -169,15 +169,13 @@ int Builder::ModelCoordsAroundBond(Frame& frameIn, Topology const& topIn, int bo
   // Determine priorities
   BuildAtom AtomA;
   if (topIn[atA].Nbonds() > 2) {
-    AtomA.SetChirality( DetermineChirality(atA, topIn, frameIn, chiralityDebug) );
-    SetPriority(AtomA.ModifyPriority(), atA, topIn, frameIn, chiralityDebug);
+    AtomA = DetermineChirality(atA, topIn, frameIn, chiralityDebug);
   }
   if (debug_ > 0)
     mprintf("DEBUG:\tAtom %4s chirality %6s\n", topIn.AtomMaskName(atA).c_str(), chiralStr(AtomA.Chirality()));
   BuildAtom AtomB;
   if (topIn[atB].Nbonds() > 2) {
-    AtomB.SetChirality( DetermineChirality(atB, topIn, frameIn, chiralityDebug) );
-    SetPriority(AtomB.ModifyPriority(), atB, topIn, frameIn, chiralityDebug);
+    AtomB = DetermineChirality(atB, topIn, frameIn, chiralityDebug);
   }
   if (debug_ > 0)
     mprintf("DEBUG:\tAtom %4s chirality %6s\n", topIn.AtomMaskName(atB).c_str(), chiralStr(AtomB.Chirality()));
diff --git a/src/Structure/Chirality.cpp b/src/Structure/Chirality.cpp
index c7da6d0b62..10ea534a79 100644
--- a/src/Structure/Chirality.cpp
+++ b/src/Structure/Chirality.cpp
@@ -1,4 +1,5 @@
 #include "Chirality.h"
+#include "BuildAtom.h"
 #include "../Constants.h"
 #include "../CpptrajStdio.h"
 #include "../Frame.h"
@@ -76,24 +77,24 @@ class priority_element {
   *   1-2-3-0
   * where 0 is the chiral center. Negative is S, positive is R.
   */
-Cpptraj::Structure::ChiralType
-  Cpptraj::Structure::DetermineChirality(double& tors, int* AtomIndices,
+Cpptraj::Structure::BuildAtom
+  Cpptraj::Structure::DetermineChirality(//double& tors, int* AtomIndices,
                                          int atnum,
                                          Topology const& topIn,
                                          Frame const& frameIn, int debugIn)
 {
-  tors = 0.0;
   Atom const& atom = topIn[atnum];
   if (atom.Nbonds() < 3) {
     mprinterr("Error: CalcChiralAtomTorsion called for atom %s with less than 3 bonds.\n",
               topIn.AtomMaskName(atnum).c_str());
-    return CHIRALITY_ERR;
+    return BuildAtom(CHIRALITY_ERR);
   }
   // Calculate a priority score for each bonded atom.
   // First just use the atomic number.
   if (debugIn > 0)
     mprintf("DEBUG: Determining priorities around atom %s\n", topIn.AtomMaskName(atnum).c_str());
   std::vector<priority_element> priority;
+  priority.reserve( atom.Nbonds() );
   for (int idx = 0; idx != atom.Nbonds(); idx++) {
     priority.push_back( priority_element(atom.Bond(idx), topIn[atom.Bond(idx)].AtomicNumber()) );
     if (debugIn > 0)
@@ -144,18 +145,20 @@ Cpptraj::Structure::ChiralType
     mprintf("\n");
   }
 
-  if (AtomIndices != 0) {
+  std::vector<int> AtomIndices( atom.Nbonds() );
+  //if (AtomIndices != 0) {
     for (unsigned int ip = 0; ip != priority.size(); ++ip)
       AtomIndices[ip] = priority[ip].AtNum();
-  }
-  if (depth_limit_hit) return IS_UNKNOWN_CHIRALITY;
+  //}
+  //if (depth_limit_hit) return IS_UNKNOWN_CHIRALITY;
 
-  tors = Torsion( frameIn.XYZ(priority[0].AtNum()),
-                  frameIn.XYZ(priority[1].AtNum()),
-                  frameIn.XYZ(priority[2].AtNum()),
-                  frameIn.XYZ(atnum) );
+  double tors = Torsion( frameIn.XYZ(priority[0].AtNum()),
+                         frameIn.XYZ(priority[1].AtNum()),
+                         frameIn.XYZ(priority[2].AtNum()),
+                         frameIn.XYZ(atnum) );
   if (debugIn > 0)
     mprintf("DEBUG: Torsion around '%s' is %f",  topIn.AtomMaskName(atnum).c_str(), tors*Constants::RADDEG);
+
   ChiralType ret;
   if (tors < 0) {
     ret = IS_S;
@@ -164,21 +167,29 @@ Cpptraj::Structure::ChiralType
     ret = IS_R;
     if (debugIn > 0) mprintf(" (R)\n");
   }
-  return ret;
+  BuildAtom out;
+  if (depth_limit_hit) {
+    // No real chirality; just store orientation.
+    out = BuildAtom(tors, IS_UNKNOWN_CHIRALITY, ret, AtomIndices);
+  } else {
+    // Chirality determined.
+    out = BuildAtom(tors, ret, ret, AtomIndices);
+  }
+  return out;
 }
 
 /** Determine chirality around specified atom. */
-Cpptraj::Structure::ChiralType
+/*Cpptraj::Structure::ChiralType
   Cpptraj::Structure::DetermineChirality(int atnum,
                                          Topology const& topIn,
                                          Frame const& frameIn, int debugIn)
 {
   double tors;
   return DetermineChirality(tors, 0, atnum, topIn, frameIn, debugIn);
-}
+}*/
 
 /** Set priority around a specified atom. */
-Cpptraj::Structure::ChiralType
+/*Cpptraj::Structure::ChiralType
   Cpptraj::Structure::SetPriority(std::vector<int>& priority,
                                   int atnum, Topology const& topIn,
                                   Frame const& frameIn, int debugIn)
@@ -186,4 +197,16 @@ Cpptraj::Structure::ChiralType
   priority.resize( topIn[atnum].Nbonds() );
   double tors;
   return DetermineChirality(tors, &priority[0], atnum, topIn, frameIn, debugIn);
+}*/
+
+/** Only set the priority around a specified atom. */
+int Cpptraj::Structure::UpdatePriority(BuildAtom& atomIn, int atnum, Topology const& topIn, Frame const& frameIn, int debugIn)
+{
+  BuildAtom tmpAtom = DetermineChirality(atnum, topIn, frameIn, debugIn);
+  if (tmpAtom.ChiralError()) {
+    mprinterr("Error: Could not update priority for atom %s\n", topIn.AtomMaskName(atnum).c_str());
+    return 1;
+  }
+  atomIn.SetPriority( tmpAtom.Priority() );
+  return 0;
 }
diff --git a/src/Structure/Chirality.h b/src/Structure/Chirality.h
index e895352409..2fafd960f5 100644
--- a/src/Structure/Chirality.h
+++ b/src/Structure/Chirality.h
@@ -1,18 +1,20 @@
 #ifndef INC_STRUCTURE_CHIRALITY_H
 #define INC_STRUCTURE_CHIRALITY_H
-#include <vector>
 #include "StructureEnum.h"
 class Topology;
 class Frame;
 namespace Cpptraj {
 namespace Structure {
-
+class BuildAtom;
 /// \return Chirality at specified atom, set torsion value
-ChiralType DetermineChirality(double&, int*, int, Topology const&, Frame const&, int);
+BuildAtom DetermineChirality(int, Topology const&, Frame const&, int);
+//ChiralType DetermineChirality(double&, int*, int, Topology const&, Frame const&, int);
 /// \return Chirality at specified atom
-ChiralType DetermineChirality(int, Topology const&, Frame const&, int);
+//ChiralType DetermineChirality(int, Topology const&, Frame const&, int);
 /// \return Chirality at specified atom, set priority
-ChiralType SetPriority(std::vector<int>&, int, Topology const&, Frame const&, int);
+//ChiralType SetPriority(std::vector<int>&, int, Topology const&, Frame const&, int);
+/// Only update priority around atom. Useful when orientation around atom is not known/correct.
+int UpdatePriority(BuildAtom&, int, Topology const&, Frame const&, int);
 }
 }
 #endif

From ef2ffdba9a8f708588c6bc56e3bf8d66844e8eab Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 22 Jan 2024 10:55:54 -0500
Subject: [PATCH 0369/1492] Move chirality routines into BuildAtom

---
 src/Structure/BuildAtom.cpp   | 193 ++++++++++++++++++++++++++++++++++
 src/Structure/BuildAtom.h     |  19 ++--
 src/Structure/CMakeLists.txt  |   1 +
 src/Structure/structuredepend |   3 +-
 src/Structure/structurefiles  |   1 +
 5 files changed, 209 insertions(+), 8 deletions(-)
 create mode 100644 src/Structure/BuildAtom.cpp

diff --git a/src/Structure/BuildAtom.cpp b/src/Structure/BuildAtom.cpp
new file mode 100644
index 0000000000..2bfb86527e
--- /dev/null
+++ b/src/Structure/BuildAtom.cpp
@@ -0,0 +1,193 @@
+#include "BuildAtom.h"
+#include "../Constants.h"
+#include "../CpptrajStdio.h"
+#include "../Frame.h"
+#include "../Topology.h"
+#include "../TorsionRoutines.h"
+#include <algorithm> // std::sort
+
+/// \return Total priority (i.e. sum of atomic numbers) of atoms bonded to given atom.
+int Cpptraj::Structure::BuildAtom::totalPriority(Topology const& topIn, int atnum, int rnum,
+                                                int depth, int tgtdepth, std::vector<bool>& Visited)
+{
+  if (Visited[atnum] || depth == tgtdepth) return 0;
+  Visited[atnum] = true;
+  if (topIn[atnum].ResNum() != rnum) {
+    if (depth == 0)
+      // Atom in another residue bonded to chiral atom (e.g. O to C1)
+      return topIn[atnum].AtomicNumber();
+    else
+      // Atom in another residue bonded to atom bonded to chiral atom
+      return 0;
+  }
+  int sum = 0;
+  Atom const& atom = topIn[atnum];
+  for (Atom::bond_iterator bat = atom.bondbegin(); bat != atom.bondend(); ++bat)
+    sum += topIn[*bat].AtomicNumber() + totalPriority(topIn, *bat, rnum, depth+1, tgtdepth, Visited);
+  return sum;
+}
+
+/// Used to determine priority of moieties bonded to an atom
+class priority_element {
+  public:
+    /// CONSTRUCT from atom number and initial priority
+    priority_element(int a, int p1) : atnum_(a), priority1_(p1), priority2_(-1) {}
+    /// Set priority 2
+    void SetPriority2(int p2) { priority2_ = p2; }
+    /// \return Atom number
+    int AtNum() const { return atnum_; }
+    /// \return Priority 1
+    int Priority1() const { return priority1_; }
+    /// \return Priority 2
+    int Priority2() const { return priority2_; }
+    /// Sort on priority 1, then priority 2
+    bool operator<(const priority_element& rhs) const {
+      if (*this != rhs) {
+        if (priority1_ == rhs.priority1_) {
+          return (priority2_ > rhs.priority2_);
+        } else {
+          return (priority1_ > rhs.priority1_);
+        }
+      } else
+        return false;
+    }
+    /// \return true if priorities are identical
+    bool operator==(const priority_element& rhs) const {
+      return (priority1_ == rhs.priority1_) && (priority2_ == rhs.priority2_);
+    }
+    /// \return true if priorities are not equal
+    bool operator!=(const priority_element& rhs) const {
+      if (priority2_ != rhs.priority2_ ||
+          priority1_ != rhs.priority1_) return true;
+      return false;
+    }
+  private:
+    int atnum_;
+    int priority1_;
+    int priority2_;
+};
+
+/** Given an atom that is a chiral center, attempt to calculate a
+  * torsion that will help determine R vs S. Priorities will be 
+  * assigned to bonded atoms as 1, 2, 3, and optionally 4. The
+  * torsion will then be calculated as
+  *   1-2-3-0
+  * where 0 is the chiral center. Negative is S, positive is R.
+  */
+int Cpptraj::Structure::BuildAtom::determineChirality(int atnum, Topology const& topIn,
+                                                      Frame const& frameIn, int debugIn,
+                                                      bool set_priority_only)
+{
+  priority_.clear();
+  Atom const& atom = topIn[atnum];
+  if (atom.Nbonds() < 3) {
+    mprinterr("Error: CalcChiralAtomTorsion called for atom %s with less than 3 bonds.\n",
+              topIn.AtomMaskName(atnum).c_str());
+    ctype_ = CHIRALITY_ERR;
+    orientation_ = CHIRALITY_ERR;
+    return 1;
+  }
+//  ctype_ = IS_UNKNOWN_CHIRALITY;
+//  orientation_ = IS_UNKNOWN_CHIRALITY;
+//  tors_ = 0;
+  // Calculate a priority score for each bonded atom.
+  // First just use the atomic number.
+  if (debugIn > 0)
+    mprintf("DEBUG: Determining priorities around atom %s\n", topIn.AtomMaskName(atnum).c_str());
+  std::vector<priority_element> atomPriorities;
+  atomPriorities.reserve( atom.Nbonds() );
+  for (int idx = 0; idx != atom.Nbonds(); idx++) {
+    atomPriorities.push_back( priority_element(atom.Bond(idx), topIn[atom.Bond(idx)].AtomicNumber()) );
+    if (debugIn > 0)
+      mprintf("DEBUG:\t\t%i Priority for %s is %i\n", idx, topIn.AtomMaskName(atom.Bond(idx)).c_str(), atomPriorities.back().Priority1());
+  }
+  // For any identical priorities, need to check who they are bonded to.
+  bool depth_limit_hit = false;
+  for (int idx1 = 0; idx1 != atom.Nbonds(); idx1++) {
+    for (int idx2 = idx1+1; idx2 != atom.Nbonds(); idx2++) {
+      if (atomPriorities[idx1] == atomPriorities[idx2]) {
+        bool identical_priorities = true;
+        int depth = 1;
+        while (identical_priorities) {
+          if (debugIn > 0)
+            mprintf("DEBUG: Priority of index %i == %i, depth %i\n", idx1, idx2, depth);
+          std::vector<bool> Visited(topIn.Natom(), false);
+          Visited[atnum] = true;
+          atomPriorities[idx1].SetPriority2(totalPriority(topIn, atom.Bond(idx1), atom.ResNum(), 0, depth, Visited));
+          if (debugIn > 0)
+            mprintf("DEBUG:\tPriority2 of %i is %i\n", idx1, atomPriorities[idx1].Priority2());
+
+          Visited.assign(topIn.Natom(), false);
+          Visited[atnum] = true;
+          atomPriorities[idx2].SetPriority2(totalPriority(topIn, atom.Bond(idx2), atom.ResNum(), 0, depth, Visited));
+          if (debugIn > 0)
+            mprintf("DEBUG:\tPriority2 of %i is %i\n", idx2, atomPriorities[idx2].Priority2());
+          if (atomPriorities[idx1] != atomPriorities[idx2]) {
+            identical_priorities = false;
+            break;
+          }
+          if (depth == 10) {
+            mprintf("Warning: Could not determine priority around '%s'\n",
+                      topIn.AtomMaskName(atnum).c_str());
+            depth_limit_hit = true;
+            break;
+          }
+          depth++;
+        } // END while identical priorities
+      }
+    }
+  }
+  std::sort(atomPriorities.begin(), atomPriorities.end());
+  if (debugIn > 0) {
+    mprintf("DEBUG: Sorted by priority:");
+    for (std::vector<priority_element>::const_iterator it = atomPriorities.begin();
+                                                       it != atomPriorities.end(); ++it)
+      mprintf(" %s", topIn.AtomMaskName(it->AtNum()).c_str());
+    mprintf("\n");
+  }
+
+  priority_ = std::vector<int>( atom.Nbonds() );
+  for (unsigned int ip = 0; ip != atomPriorities.size(); ++ip)
+    priority_[ip] = atomPriorities[ip].AtNum();
+
+  if (set_priority_only) return 0;
+
+  tors_ = Torsion( frameIn.XYZ(atomPriorities[0].AtNum()),
+                   frameIn.XYZ(atomPriorities[1].AtNum()),
+                   frameIn.XYZ(atomPriorities[2].AtNum()),
+                   frameIn.XYZ(atnum) );
+  if (debugIn > 0)
+    mprintf("DEBUG: Torsion around '%s' is %f",  topIn.AtomMaskName(atnum).c_str(), tors_*Constants::RADDEG);
+
+  ChiralType ret;
+  if (tors_ < 0) {
+    ret = IS_S;
+    if (debugIn > 0) mprintf(" (S)\n");
+  } else {
+    ret = IS_R;
+    if (debugIn > 0) mprintf(" (R)\n");
+  }
+  if (depth_limit_hit) {
+    // No real chirality; just store orientation.
+    orientation_ = ret;
+  } else {
+    // Chirality determined.
+    ctype_ = ret;
+    orientation_ = ret;
+  }
+  return 0;
+}
+
+/** Determine chirality and priority around an atom. */
+int Cpptraj::Structure::BuildAtom::DetermineChirality(int atnum, Topology const& topIn,
+                                                      Frame const& frameIn, int debugIn)
+{
+  return determineChirality(atnum, topIn, frameIn, debugIn, false);
+}
+
+/** Determine only priority around an atom. */
+int Cpptraj::Structure::BuildAtom::SetPriority(int atnum, Topology const& topIn,
+                                               Frame const& frameIn, int debugIn)
+{
+  return determineChirality(atnum, topIn, frameIn, debugIn, true);
+}
diff --git a/src/Structure/BuildAtom.h b/src/Structure/BuildAtom.h
index b576290058..891c578fac 100644
--- a/src/Structure/BuildAtom.h
+++ b/src/Structure/BuildAtom.h
@@ -2,6 +2,8 @@
 #define INC_STRUCTURE_BUILDATOM_H
 #include "StructureEnum.h"
 #include <vector>
+class Topology;
+class Frame;
 namespace Cpptraj {
 namespace Structure {
 /// Hold chirality/orientation information for an atom. Used when building/modelling new coordinates.
@@ -14,12 +16,10 @@ class BuildAtom {
     /// CONSTRUCTOR - torsion, chirality, orientation, priority array
     BuildAtom(double t, ChiralType c, ChiralType o, std::vector<int> const& p) :
                   tors_(t), ctype_(c), orientation_(o), priority_(p) {}
-    /// Update the priority array
-    void SetPriority(std::vector<int> const& p) { priority_ = p; }
-    /// Set chirality
-    //void SetChirality(ChiralType c) { ctype_ = c; }
-    /// Used to modify the priority array
-    //std::vector<int>& ModifyPriority() { return priority_; }
+    /// Set chirality, orientation, and priority around specified atom
+    int DetermineChirality(int, Topology const&, Frame const&, int);
+    /// Only set the priority around specified atom
+    int SetPriority(int, Topology const&, Frame const&, int);
 
     /// \return Atom chirality
     ChiralType Chirality()             const { return ctype_; }
@@ -30,8 +30,13 @@ class BuildAtom {
     /// \return Value of the orientation torsion around atom (in radians).
     double TorsionVal()                const { return tors_; }
     /// \return True if an error occurred determining chirality
-    bool ChiralError()                 const { return (ctype_ == CHIRALITY_ERR) || priority_.empty(); }
+    bool ChiralError()                 const { return (ctype_ == CHIRALITY_ERR);}
   private:
+    /// Total priority (i.e. sum of atomic numbers) of atoms bonded to given atom.
+    static int totalPriority(Topology const&, int, int, int, int, std::vector<bool>&);
+    /// Determine priority and optionally chirality as well
+    int determineChirality(int, Topology const&, Frame const&, int, bool);
+
     double tors_;               ///< Torsion around the atom in radians (via priority, 1-2-3-0, where 0 is this atom).
     ChiralType ctype_;          ///< Chirality around atom.
     ChiralType orientation_;    ///< Orientation when chirality cannot be determined.
diff --git a/src/Structure/CMakeLists.txt b/src/Structure/CMakeLists.txt
index f6ec6cc9f6..5f8b3a9644 100644
--- a/src/Structure/CMakeLists.txt
+++ b/src/Structure/CMakeLists.txt
@@ -1,5 +1,6 @@
 #CMake buildfile for CPPTRAJ Structure subdirectory.
 target_sources(cpptraj_common_obj PRIVATE
+  ${CMAKE_CURRENT_LIST_DIR}/BuildAtom.cpp
   ${CMAKE_CURRENT_LIST_DIR}/Builder.cpp
   ${CMAKE_CURRENT_LIST_DIR}/Chirality.cpp
   ${CMAKE_CURRENT_LIST_DIR}/Disulfide.cpp
diff --git a/src/Structure/structuredepend b/src/Structure/structuredepend
index ed0a465379..3aaad0dfd4 100644
--- a/src/Structure/structuredepend
+++ b/src/Structure/structuredepend
@@ -1,5 +1,6 @@
+BuildAtom.o : BuildAtom.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h StructureEnum.h
 Builder.o : Builder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h Builder.h Chirality.h InternalCoords.h StructureEnum.h Zmatrix.h
-Chirality.o : Chirality.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Chirality.h StructureEnum.h
+Chirality.o : Chirality.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h Chirality.h StructureEnum.h
 Disulfide.o : Disulfide.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Disulfide.h ResStatArray.h StructureRoutines.h
 FunctionalGroup.o : FunctionalGroup.cpp ../Atom.h ../AtomMap.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h FunctionalGroup.h
 FxnGroupBuilder.o : FxnGroupBuilder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h FunctionalGroup.h FxnGroupBuilder.h StructureRoutines.h Sugar.h SugarToken.h
diff --git a/src/Structure/structurefiles b/src/Structure/structurefiles
index d5c54bfca2..39f1222bf8 100644
--- a/src/Structure/structurefiles
+++ b/src/Structure/structurefiles
@@ -1,5 +1,6 @@
 # Files for Structure subdirectory.
 STRUCTURE_SOURCES= \
+  BuildAtom.cpp \
   Builder.cpp \
   Chirality.cpp \
   Disulfide.cpp \

From ecfa5cf4b77db7dbd36d3b7f5b8400cbeedf03df Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 22 Jan 2024 10:59:49 -0500
Subject: [PATCH 0370/1492] Get rid of CHIRALITY_ERR since
 DetermineChirality/SetPriority return an int now

---
 src/Structure/BuildAtom.cpp     | 2 --
 src/Structure/BuildAtom.h       | 2 --
 src/Structure/StructureEnum.cpp | 1 -
 src/Structure/StructureEnum.h   | 2 +-
 4 files changed, 1 insertion(+), 6 deletions(-)

diff --git a/src/Structure/BuildAtom.cpp b/src/Structure/BuildAtom.cpp
index 2bfb86527e..b53b7b58b4 100644
--- a/src/Structure/BuildAtom.cpp
+++ b/src/Structure/BuildAtom.cpp
@@ -83,8 +83,6 @@ int Cpptraj::Structure::BuildAtom::determineChirality(int atnum, Topology const&
   if (atom.Nbonds() < 3) {
     mprinterr("Error: CalcChiralAtomTorsion called for atom %s with less than 3 bonds.\n",
               topIn.AtomMaskName(atnum).c_str());
-    ctype_ = CHIRALITY_ERR;
-    orientation_ = CHIRALITY_ERR;
     return 1;
   }
 //  ctype_ = IS_UNKNOWN_CHIRALITY;
diff --git a/src/Structure/BuildAtom.h b/src/Structure/BuildAtom.h
index 891c578fac..ae9583ce7a 100644
--- a/src/Structure/BuildAtom.h
+++ b/src/Structure/BuildAtom.h
@@ -29,8 +29,6 @@ class BuildAtom {
     std::vector<int> const& Priority() const { return priority_; }
     /// \return Value of the orientation torsion around atom (in radians).
     double TorsionVal()                const { return tors_; }
-    /// \return True if an error occurred determining chirality
-    bool ChiralError()                 const { return (ctype_ == CHIRALITY_ERR);}
   private:
     /// Total priority (i.e. sum of atomic numbers) of atoms bonded to given atom.
     static int totalPriority(Topology const&, int, int, int, int, std::vector<bool>&);
diff --git a/src/Structure/StructureEnum.cpp b/src/Structure/StructureEnum.cpp
index 17e4711c7e..b158ff2838 100644
--- a/src/Structure/StructureEnum.cpp
+++ b/src/Structure/StructureEnum.cpp
@@ -3,7 +3,6 @@
 /** \return string corresponding to ChiralType */
 const char* Cpptraj::Structure::chiralStr(ChiralType ct) {
   switch (ct) {
-    case CHIRALITY_ERR : return "Error";
     case IS_S : return "S";
     case IS_R : return "R";
     case IS_UNKNOWN_CHIRALITY : return "Unknown";
diff --git a/src/Structure/StructureEnum.h b/src/Structure/StructureEnum.h
index 3014a56b0b..9063a4ed91 100644
--- a/src/Structure/StructureEnum.h
+++ b/src/Structure/StructureEnum.h
@@ -3,7 +3,7 @@
 namespace Cpptraj {
 namespace Structure {
 
-enum ChiralType { CHIRALITY_ERR = 0, IS_S, IS_R, IS_UNKNOWN_CHIRALITY };
+enum ChiralType { IS_S = 0, IS_R, IS_UNKNOWN_CHIRALITY };
 /// \return String corresponding to ChiralType
 const char* chiralStr(ChiralType);
 

From 3c9e813fbceb84c63be64370ddb81f3a8bdc9f3f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 22 Jan 2024 11:00:55 -0500
Subject: [PATCH 0371/1492] Remove Chirality routines which have been moved
 into BuildAtom

---
 src/Structure/CMakeLists.txt  |   1 -
 src/Structure/Chirality.cpp   | 212 ----------------------------------
 src/Structure/Chirality.h     |  20 ----
 src/Structure/structuredepend |   3 +-
 src/Structure/structurefiles  |   1 -
 5 files changed, 1 insertion(+), 236 deletions(-)
 delete mode 100644 src/Structure/Chirality.cpp
 delete mode 100644 src/Structure/Chirality.h

diff --git a/src/Structure/CMakeLists.txt b/src/Structure/CMakeLists.txt
index 5f8b3a9644..ffdd80270f 100644
--- a/src/Structure/CMakeLists.txt
+++ b/src/Structure/CMakeLists.txt
@@ -2,7 +2,6 @@
 target_sources(cpptraj_common_obj PRIVATE
   ${CMAKE_CURRENT_LIST_DIR}/BuildAtom.cpp
   ${CMAKE_CURRENT_LIST_DIR}/Builder.cpp
-  ${CMAKE_CURRENT_LIST_DIR}/Chirality.cpp
   ${CMAKE_CURRENT_LIST_DIR}/Disulfide.cpp
   ${CMAKE_CURRENT_LIST_DIR}/FunctionalGroup.cpp
   ${CMAKE_CURRENT_LIST_DIR}/FxnGroupBuilder.cpp
diff --git a/src/Structure/Chirality.cpp b/src/Structure/Chirality.cpp
deleted file mode 100644
index 10ea534a79..0000000000
--- a/src/Structure/Chirality.cpp
+++ /dev/null
@@ -1,212 +0,0 @@
-#include "Chirality.h"
-#include "BuildAtom.h"
-#include "../Constants.h"
-#include "../CpptrajStdio.h"
-#include "../Frame.h"
-#include "../Topology.h"
-#include "../TorsionRoutines.h"
-#include <vector>
-#include <algorithm> // sort
-
-/// \return Total priority (i.e. sum of atomic numbers) of atoms bonded to given atom.
-static int totalPriority(Topology const& topIn, int atnum, int rnum,
-                         int depth, int tgtdepth, std::vector<bool>& Visited)
-{
-  if (Visited[atnum] || depth == tgtdepth) return 0;
-  Visited[atnum] = true;
-  if (topIn[atnum].ResNum() != rnum) {
-    if (depth == 0)
-      // Atom in another residue bonded to chiral atom (e.g. O to C1)
-      return topIn[atnum].AtomicNumber();
-    else
-      // Atom in another residue bonded to atom bonded to chiral atom
-      return 0;
-  }
-  int sum = 0;
-  Atom const& atom = topIn[atnum];
-  for (Atom::bond_iterator bat = atom.bondbegin(); bat != atom.bondend(); ++bat)
-    sum += topIn[*bat].AtomicNumber() + totalPriority(topIn, *bat, rnum, depth+1, tgtdepth, Visited);
-  return sum;
-}
-
-/// Used to determine priority of moieties bonded to an atom
-class priority_element {
-  public:
-    /// CONSTRUCT from atom number and initial priority
-    priority_element(int a, int p1) : atnum_(a), priority1_(p1), priority2_(-1) {}
-    /// Set priority 2
-    void SetPriority2(int p2) { priority2_ = p2; }
-    /// \return Atom number
-    int AtNum() const { return atnum_; }
-    /// \return Priority 1
-    int Priority1() const { return priority1_; }
-    /// \return Priority 2
-    int Priority2() const { return priority2_; }
-    /// Sort on priority 1, then priority 2
-    bool operator<(const priority_element& rhs) const {
-      if (*this != rhs) {
-        if (priority1_ == rhs.priority1_) {
-          return (priority2_ > rhs.priority2_);
-        } else {
-          return (priority1_ > rhs.priority1_);
-        }
-      } else
-        return false;
-    }
-    /// \return true if priorities are identical
-    bool operator==(const priority_element& rhs) const {
-      return (priority1_ == rhs.priority1_) && (priority2_ == rhs.priority2_);
-    }
-    /// \return true if priorities are not equal
-    bool operator!=(const priority_element& rhs) const {
-      if (priority2_ != rhs.priority2_ ||
-          priority1_ != rhs.priority1_) return true;
-      return false;
-    }
-  private:
-    int atnum_;
-    int priority1_;
-    int priority2_;
-};
-
-
-/** Given an atom that is a chiral center, attempt to calculate a
-  * torsion that will help determine R vs S. Priorities will be 
-  * assigned to bonded atoms as 1, 2, 3, and optionally 4. The
-  * torsion will then be calculated as
-  *   1-2-3-0
-  * where 0 is the chiral center. Negative is S, positive is R.
-  */
-Cpptraj::Structure::BuildAtom
-  Cpptraj::Structure::DetermineChirality(//double& tors, int* AtomIndices,
-                                         int atnum,
-                                         Topology const& topIn,
-                                         Frame const& frameIn, int debugIn)
-{
-  Atom const& atom = topIn[atnum];
-  if (atom.Nbonds() < 3) {
-    mprinterr("Error: CalcChiralAtomTorsion called for atom %s with less than 3 bonds.\n",
-              topIn.AtomMaskName(atnum).c_str());
-    return BuildAtom(CHIRALITY_ERR);
-  }
-  // Calculate a priority score for each bonded atom.
-  // First just use the atomic number.
-  if (debugIn > 0)
-    mprintf("DEBUG: Determining priorities around atom %s\n", topIn.AtomMaskName(atnum).c_str());
-  std::vector<priority_element> priority;
-  priority.reserve( atom.Nbonds() );
-  for (int idx = 0; idx != atom.Nbonds(); idx++) {
-    priority.push_back( priority_element(atom.Bond(idx), topIn[atom.Bond(idx)].AtomicNumber()) );
-    if (debugIn > 0)
-      mprintf("DEBUG:\t\t%i Priority for %s is %i\n", idx, topIn.AtomMaskName(atom.Bond(idx)).c_str(), priority.back().Priority1());
-  }
-  // For any identical priorities, need to check who they are bonded to.
-  bool depth_limit_hit = false;
-  for (int idx1 = 0; idx1 != atom.Nbonds(); idx1++) {
-    for (int idx2 = idx1+1; idx2 != atom.Nbonds(); idx2++) {
-      if (priority[idx1] == priority[idx2]) {
-        bool identical_priorities = true;
-        int depth = 1;
-        while (identical_priorities) {
-          if (debugIn > 0)
-            mprintf("DEBUG: Priority of index %i == %i, depth %i\n", idx1, idx2, depth);
-          std::vector<bool> Visited(topIn.Natom(), false);
-          Visited[atnum] = true;
-          priority[idx1].SetPriority2(totalPriority(topIn, atom.Bond(idx1), atom.ResNum(), 0, depth, Visited));
-          if (debugIn > 0)
-            mprintf("DEBUG:\tPriority2 of %i is %i\n", idx1, priority[idx1].Priority2());
-
-          Visited.assign(topIn.Natom(), false);
-          Visited[atnum] = true;
-          priority[idx2].SetPriority2(totalPriority(topIn, atom.Bond(idx2), atom.ResNum(), 0, depth, Visited));
-          if (debugIn > 0)
-            mprintf("DEBUG:\tPriority2 of %i is %i\n", idx2, priority[idx2].Priority2());
-          if (priority[idx1] != priority[idx2]) {
-            identical_priorities = false;
-            break;
-          }
-          if (depth == 10) {
-            mprintf("Warning: Could not determine priority around '%s'\n",
-                      topIn.AtomMaskName(atnum).c_str());
-            depth_limit_hit = true;
-            break;
-          }
-          depth++;
-        } // END while identical priorities
-      }
-    }
-  }
-  std::sort(priority.begin(), priority.end());
-  if (debugIn > 0) {
-    mprintf("DEBUG: Sorted by priority:");
-    for (std::vector<priority_element>::const_iterator it = priority.begin();
-                                                       it != priority.end(); ++it)
-      mprintf(" %s", topIn.AtomMaskName(it->AtNum()).c_str());
-    mprintf("\n");
-  }
-
-  std::vector<int> AtomIndices( atom.Nbonds() );
-  //if (AtomIndices != 0) {
-    for (unsigned int ip = 0; ip != priority.size(); ++ip)
-      AtomIndices[ip] = priority[ip].AtNum();
-  //}
-  //if (depth_limit_hit) return IS_UNKNOWN_CHIRALITY;
-
-  double tors = Torsion( frameIn.XYZ(priority[0].AtNum()),
-                         frameIn.XYZ(priority[1].AtNum()),
-                         frameIn.XYZ(priority[2].AtNum()),
-                         frameIn.XYZ(atnum) );
-  if (debugIn > 0)
-    mprintf("DEBUG: Torsion around '%s' is %f",  topIn.AtomMaskName(atnum).c_str(), tors*Constants::RADDEG);
-
-  ChiralType ret;
-  if (tors < 0) {
-    ret = IS_S;
-    if (debugIn > 0) mprintf(" (S)\n");
-  } else {
-    ret = IS_R;
-    if (debugIn > 0) mprintf(" (R)\n");
-  }
-  BuildAtom out;
-  if (depth_limit_hit) {
-    // No real chirality; just store orientation.
-    out = BuildAtom(tors, IS_UNKNOWN_CHIRALITY, ret, AtomIndices);
-  } else {
-    // Chirality determined.
-    out = BuildAtom(tors, ret, ret, AtomIndices);
-  }
-  return out;
-}
-
-/** Determine chirality around specified atom. */
-/*Cpptraj::Structure::ChiralType
-  Cpptraj::Structure::DetermineChirality(int atnum,
-                                         Topology const& topIn,
-                                         Frame const& frameIn, int debugIn)
-{
-  double tors;
-  return DetermineChirality(tors, 0, atnum, topIn, frameIn, debugIn);
-}*/
-
-/** Set priority around a specified atom. */
-/*Cpptraj::Structure::ChiralType
-  Cpptraj::Structure::SetPriority(std::vector<int>& priority,
-                                  int atnum, Topology const& topIn,
-                                  Frame const& frameIn, int debugIn)
-{
-  priority.resize( topIn[atnum].Nbonds() );
-  double tors;
-  return DetermineChirality(tors, &priority[0], atnum, topIn, frameIn, debugIn);
-}*/
-
-/** Only set the priority around a specified atom. */
-int Cpptraj::Structure::UpdatePriority(BuildAtom& atomIn, int atnum, Topology const& topIn, Frame const& frameIn, int debugIn)
-{
-  BuildAtom tmpAtom = DetermineChirality(atnum, topIn, frameIn, debugIn);
-  if (tmpAtom.ChiralError()) {
-    mprinterr("Error: Could not update priority for atom %s\n", topIn.AtomMaskName(atnum).c_str());
-    return 1;
-  }
-  atomIn.SetPriority( tmpAtom.Priority() );
-  return 0;
-}
diff --git a/src/Structure/Chirality.h b/src/Structure/Chirality.h
deleted file mode 100644
index 2fafd960f5..0000000000
--- a/src/Structure/Chirality.h
+++ /dev/null
@@ -1,20 +0,0 @@
-#ifndef INC_STRUCTURE_CHIRALITY_H
-#define INC_STRUCTURE_CHIRALITY_H
-#include "StructureEnum.h"
-class Topology;
-class Frame;
-namespace Cpptraj {
-namespace Structure {
-class BuildAtom;
-/// \return Chirality at specified atom, set torsion value
-BuildAtom DetermineChirality(int, Topology const&, Frame const&, int);
-//ChiralType DetermineChirality(double&, int*, int, Topology const&, Frame const&, int);
-/// \return Chirality at specified atom
-//ChiralType DetermineChirality(int, Topology const&, Frame const&, int);
-/// \return Chirality at specified atom, set priority
-//ChiralType SetPriority(std::vector<int>&, int, Topology const&, Frame const&, int);
-/// Only update priority around atom. Useful when orientation around atom is not known/correct.
-int UpdatePriority(BuildAtom&, int, Topology const&, Frame const&, int);
-}
-}
-#endif
diff --git a/src/Structure/structuredepend b/src/Structure/structuredepend
index 3aaad0dfd4..cd95014981 100644
--- a/src/Structure/structuredepend
+++ b/src/Structure/structuredepend
@@ -1,6 +1,5 @@
 BuildAtom.o : BuildAtom.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h StructureEnum.h
 Builder.o : Builder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h Builder.h Chirality.h InternalCoords.h StructureEnum.h Zmatrix.h
-Chirality.o : Chirality.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h Chirality.h StructureEnum.h
 Disulfide.o : Disulfide.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Disulfide.h ResStatArray.h StructureRoutines.h
 FunctionalGroup.o : FunctionalGroup.cpp ../Atom.h ../AtomMap.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h FunctionalGroup.h
 FxnGroupBuilder.o : FxnGroupBuilder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h FunctionalGroup.h FxnGroupBuilder.h StructureRoutines.h Sugar.h SugarToken.h
@@ -11,7 +10,7 @@ Model.o : Model.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.
 StructureEnum.o : StructureEnum.cpp StructureEnum.h
 StructureRoutines.o : StructureRoutines.cpp ../Atom.h ../CpptrajStdio.h ../NameType.h ../Residue.h ../SymbolExporting.h StructureRoutines.h
 Sugar.o : Sugar.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Sugar.h SugarToken.h
-SugarBuilder.o : SugarBuilder.cpp ../ArgList.h ../Atom.h ../AtomMap.h ../AtomMask.h ../AtomType.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DistRoutines.h ../FileIO.h ../FileName.h ../Frame.h ../ImageOption.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Chirality.h FunctionalGroup.h FxnGroupBuilder.h LinkAtom.h ResStatArray.h StructureEnum.h StructureRoutines.h Sugar.h SugarBuilder.h SugarLinkAtoms.h SugarToken.h
+SugarBuilder.o : SugarBuilder.cpp ../ArgList.h ../Atom.h ../AtomMap.h ../AtomMask.h ../AtomType.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DistRoutines.h ../FileIO.h ../FileName.h ../Frame.h ../ImageOption.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Chirality.h FunctionalGroup.h FxnGroupBuilder.h LinkAtom.h ResStatArray.h StructureRoutines.h Sugar.h SugarBuilder.h SugarLinkAtoms.h SugarToken.h
 SugarLinkAtoms.o : SugarLinkAtoms.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../StringRoutines.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h LinkAtom.h SugarLinkAtoms.h
 SugarToken.o : SugarToken.cpp ../ArgList.h ../CpptrajStdio.h SugarToken.h
 Zmatrix.o : Zmatrix.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h Chirality.h GenerateConnectivityArrays.h InternalCoords.h Model.h StructureEnum.h Zmatrix.h
diff --git a/src/Structure/structurefiles b/src/Structure/structurefiles
index 39f1222bf8..d609540255 100644
--- a/src/Structure/structurefiles
+++ b/src/Structure/structurefiles
@@ -2,7 +2,6 @@
 STRUCTURE_SOURCES= \
   BuildAtom.cpp \
   Builder.cpp \
-  Chirality.cpp \
   Disulfide.cpp \
   FunctionalGroup.cpp \
   FxnGroupBuilder.cpp \

From 9e97630c3853f64210040eafb83259ba672464c3 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 22 Jan 2024 11:04:53 -0500
Subject: [PATCH 0372/1492] Fix debug messages. Ensure unknown chirality is
 set.

---
 src/Structure/BuildAtom.cpp | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/src/Structure/BuildAtom.cpp b/src/Structure/BuildAtom.cpp
index b53b7b58b4..7f0295d570 100644
--- a/src/Structure/BuildAtom.cpp
+++ b/src/Structure/BuildAtom.cpp
@@ -158,20 +158,21 @@ int Cpptraj::Structure::BuildAtom::determineChirality(int atnum, Topology const&
     mprintf("DEBUG: Torsion around '%s' is %f",  topIn.AtomMaskName(atnum).c_str(), tors_*Constants::RADDEG);
 
   ChiralType ret;
-  if (tors_ < 0) {
+  if (tors_ < 0)
     ret = IS_S;
-    if (debugIn > 0) mprintf(" (S)\n");
-  } else {
+  else
     ret = IS_R;
-    if (debugIn > 0) mprintf(" (R)\n");
-  }
+ 
   if (depth_limit_hit) {
     // No real chirality; just store orientation.
+    ctype_ = IS_UNKNOWN_CHIRALITY;
     orientation_ = ret;
+    if (debugIn > 0) mprintf(", orientation is (%s)\n", chiralStr(ret));
   } else {
     // Chirality determined.
     ctype_ = ret;
     orientation_ = ret;
+    if (debugIn > 0) mprintf(", chirality is (%s)\n", chiralStr(ret));
   }
   return 0;
 }

From 7914bd0a0d8b0abe15cc6ee523ef783a1e915092 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 22 Jan 2024 11:07:43 -0500
Subject: [PATCH 0373/1492] Remove dependence on old Chirality

---
 src/Structure/Builder.cpp     | 21 ++++++++++-----------
 src/Structure/structuredepend |  2 +-
 2 files changed, 11 insertions(+), 12 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index c4cb4305af..cb52e25591 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1,6 +1,5 @@
 #include "Builder.h"
 #include "BuildAtom.h"
-#include "Chirality.h"
 #include "Zmatrix.h"
 #include "../CpptrajStdio.h"
 #include "../Frame.h"
@@ -70,13 +69,15 @@ const
     chiralityDebug = debug_ - 1;
   // Get the chirality around each atom before the bond is added.
   BuildAtom AtomA;
-  if (combinedTop[atA].Nbonds() > 2)
-    AtomA = DetermineChirality(atA, combinedTop, CombinedFrame, chiralityDebug);
+  if (combinedTop[atA].Nbonds() > 2) {
+    if (AtomA.DetermineChirality(atA, combinedTop, CombinedFrame, chiralityDebug)) return 1;
+  }
   if (debug_ > 0)
     mprintf("DEBUG:\tAtom %4s chirality %6s\n", combinedTop.AtomMaskName(atA).c_str(), chiralStr(AtomA.Chirality()));
   BuildAtom AtomB;
-  if (combinedTop[atB].Nbonds() > 2)
-    AtomB = DetermineChirality(atB, combinedTop, CombinedFrame, chiralityDebug);
+  if (combinedTop[atB].Nbonds() > 2) {
+    if (AtomB.DetermineChirality(atB, combinedTop, CombinedFrame, chiralityDebug)) return 1;
+  }
   if (debug_ > 0)
     mprintf("DEBUG:\tAtom %4s chirality %6s\n", combinedTop.AtomMaskName(atB).c_str(), chiralStr(AtomB.Chirality()));
 
@@ -89,12 +90,10 @@ const
 
   // Determine new priorities around atoms that were just bonded
   if (combinedTop[atA].Nbonds() > 2) {
-    //AtomA.SetNbonds(combinedTop[atA].Nbonds());
-    SetPriority(AtomA.ModifyPriority(), atA, combinedTop, CombinedFrame, chiralityDebug);
+    if (AtomA.SetPriority(atA, combinedTop, CombinedFrame, chiralityDebug)) return 1;
   }
   if (combinedTop[atB].Nbonds() > 2) {
-    //AtomB.SetNbonds(combinedTop[atB].Nbonds());
-    SetPriority(AtomB.ModifyPriority(), atB, combinedTop, CombinedFrame, chiralityDebug);
+    if (AtomB.SetPriority(atB, combinedTop, CombinedFrame, chiralityDebug)) return 1;
   }
 
   // Generate Zmatrix only for ICs involving bonded atoms
@@ -169,13 +168,13 @@ int Builder::ModelCoordsAroundBond(Frame& frameIn, Topology const& topIn, int bo
   // Determine priorities
   BuildAtom AtomA;
   if (topIn[atA].Nbonds() > 2) {
-    AtomA = DetermineChirality(atA, topIn, frameIn, chiralityDebug);
+    if (AtomA.DetermineChirality(atA, topIn, frameIn, chiralityDebug)) return 1;
   }
   if (debug_ > 0)
     mprintf("DEBUG:\tAtom %4s chirality %6s\n", topIn.AtomMaskName(atA).c_str(), chiralStr(AtomA.Chirality()));
   BuildAtom AtomB;
   if (topIn[atB].Nbonds() > 2) {
-    AtomB = DetermineChirality(atB, topIn, frameIn, chiralityDebug);
+    if (AtomB.DetermineChirality(atB, topIn, frameIn, chiralityDebug)) return 1;
   }
   if (debug_ > 0)
     mprintf("DEBUG:\tAtom %4s chirality %6s\n", topIn.AtomMaskName(atB).c_str(), chiralStr(AtomB.Chirality()));
diff --git a/src/Structure/structuredepend b/src/Structure/structuredepend
index cd95014981..bf8442e82f 100644
--- a/src/Structure/structuredepend
+++ b/src/Structure/structuredepend
@@ -1,5 +1,5 @@
 BuildAtom.o : BuildAtom.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h StructureEnum.h
-Builder.o : Builder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h Builder.h Chirality.h InternalCoords.h StructureEnum.h Zmatrix.h
+Builder.o : Builder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h Builder.h InternalCoords.h StructureEnum.h Zmatrix.h
 Disulfide.o : Disulfide.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Disulfide.h ResStatArray.h StructureRoutines.h
 FunctionalGroup.o : FunctionalGroup.cpp ../Atom.h ../AtomMap.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h FunctionalGroup.h
 FxnGroupBuilder.o : FxnGroupBuilder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h FunctionalGroup.h FxnGroupBuilder.h StructureRoutines.h Sugar.h SugarToken.h

From b3798aaf5e0d83d346a9fa71bd168ac4b12c65ef Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 22 Jan 2024 11:12:33 -0500
Subject: [PATCH 0374/1492] Remove dependence on old Chirality routines

---
 src/Structure/SugarBuilder.cpp | 14 +++++++++-----
 src/Structure/structuredepend  |  2 +-
 2 files changed, 10 insertions(+), 6 deletions(-)

diff --git a/src/Structure/SugarBuilder.cpp b/src/Structure/SugarBuilder.cpp
index 1d805996cb..60378df809 100644
--- a/src/Structure/SugarBuilder.cpp
+++ b/src/Structure/SugarBuilder.cpp
@@ -1,5 +1,5 @@
 #include "SugarBuilder.h"
-#include "Chirality.h"
+#include "BuildAtom.h"
 #include "FxnGroupBuilder.h"
 #include "ResStatArray.h"
 #include "StructureRoutines.h"
@@ -1113,8 +1113,10 @@ const
     cdebug = 1;
   else
     cdebug = 0;
-  ChiralType ctypeR = DetermineChirality(sugar.HighestStereocenter(), topIn, frameIn, cdebug);
-  if (ctypeR == CHIRALITY_ERR || ctypeR == IS_UNKNOWN_CHIRALITY) {
+  BuildAtom atomR;
+  int cerr = atomR.DetermineChirality(sugar.HighestStereocenter(), topIn, frameIn, cdebug);
+  ChiralType ctypeR = atomR.Chirality();
+  if (cerr != 0 || ctypeR == IS_UNKNOWN_CHIRALITY) {
     mprinterr("Error: Could not determine configuration for furanose.\n"); // TODO warn?
     return 1;
   }
@@ -1123,8 +1125,10 @@ const
   else
     stoken.SetChirality(SugarToken::IS_L);
 
-  ChiralType ctypeA = DetermineChirality(sugar.AnomericAtom(), topIn, frameIn, cdebug);
-  if (ctypeA == CHIRALITY_ERR || ctypeA == IS_UNKNOWN_CHIRALITY) {
+  BuildAtom atomA;
+  cerr = atomA.DetermineChirality(sugar.AnomericAtom(), topIn, frameIn, cdebug);
+  ChiralType ctypeA = atomA.Chirality();
+  if (cerr != 0 || ctypeA == IS_UNKNOWN_CHIRALITY) {
     mprinterr("Error: Could not determine chirality around anomeric atom for furanose.\n"); // TODO warn?
     return 1;
   }
diff --git a/src/Structure/structuredepend b/src/Structure/structuredepend
index bf8442e82f..a5b95b1fe3 100644
--- a/src/Structure/structuredepend
+++ b/src/Structure/structuredepend
@@ -10,7 +10,7 @@ Model.o : Model.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.
 StructureEnum.o : StructureEnum.cpp StructureEnum.h
 StructureRoutines.o : StructureRoutines.cpp ../Atom.h ../CpptrajStdio.h ../NameType.h ../Residue.h ../SymbolExporting.h StructureRoutines.h
 Sugar.o : Sugar.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Sugar.h SugarToken.h
-SugarBuilder.o : SugarBuilder.cpp ../ArgList.h ../Atom.h ../AtomMap.h ../AtomMask.h ../AtomType.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DistRoutines.h ../FileIO.h ../FileName.h ../Frame.h ../ImageOption.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Chirality.h FunctionalGroup.h FxnGroupBuilder.h LinkAtom.h ResStatArray.h StructureRoutines.h Sugar.h SugarBuilder.h SugarLinkAtoms.h SugarToken.h
+SugarBuilder.o : SugarBuilder.cpp ../ArgList.h ../Atom.h ../AtomMap.h ../AtomMask.h ../AtomType.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DistRoutines.h ../FileIO.h ../FileName.h ../Frame.h ../ImageOption.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h FunctionalGroup.h FxnGroupBuilder.h LinkAtom.h ResStatArray.h StructureEnum.h StructureRoutines.h Sugar.h SugarBuilder.h SugarLinkAtoms.h SugarToken.h
 SugarLinkAtoms.o : SugarLinkAtoms.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../StringRoutines.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h LinkAtom.h SugarLinkAtoms.h
 SugarToken.o : SugarToken.cpp ../ArgList.h ../CpptrajStdio.h SugarToken.h
 Zmatrix.o : Zmatrix.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h Chirality.h GenerateConnectivityArrays.h InternalCoords.h Model.h StructureEnum.h Zmatrix.h

From ece6b12979b8e0aea7bb0e0ae153c62bf3ff3090 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 22 Jan 2024 11:16:28 -0500
Subject: [PATCH 0375/1492] Remove dependence on old Chirality routines. Update
 dependencies

---
 src/Structure/Zmatrix.cpp     | 4 +---
 src/Structure/structuredepend | 2 +-
 src/cpptrajdepend             | 8 ++++----
 3 files changed, 6 insertions(+), 8 deletions(-)

diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index ddddcf2566..93e3638281 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -7,7 +7,6 @@
 #include "BuildAtom.h"
 #include "Model.h"
 #include "GenerateConnectivityArrays.h"
-#include "Chirality.h"
 #include "../Frame.h"
 #include "../CpptrajStdio.h"
 #include "../Constants.h"
@@ -1113,8 +1112,7 @@ int Zmatrix::SetupICsAroundBond(int atA, int atB, Frame const& frameIn, Topology
           // Set phi for X iat atA atB
           BuildAtom AtomC;
           if (topIn[*iat].Nbonds() > 2) {
-            AtomC.SetChirality( DetermineChirality(*iat, topIn, frameIn, modelDebug) );
-            SetPriority(AtomC.ModifyPriority(), *iat, topIn, frameIn, modelDebug);
+            if (AtomC.DetermineChirality(*iat, topIn, frameIn, modelDebug)) return 1;
           }
           newPhi = 0;
           //model.SetDebug( 1 ); // FIXME
diff --git a/src/Structure/structuredepend b/src/Structure/structuredepend
index a5b95b1fe3..55eb7e12ff 100644
--- a/src/Structure/structuredepend
+++ b/src/Structure/structuredepend
@@ -13,4 +13,4 @@ Sugar.o : Sugar.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.
 SugarBuilder.o : SugarBuilder.cpp ../ArgList.h ../Atom.h ../AtomMap.h ../AtomMask.h ../AtomType.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DistRoutines.h ../FileIO.h ../FileName.h ../Frame.h ../ImageOption.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h FunctionalGroup.h FxnGroupBuilder.h LinkAtom.h ResStatArray.h StructureEnum.h StructureRoutines.h Sugar.h SugarBuilder.h SugarLinkAtoms.h SugarToken.h
 SugarLinkAtoms.o : SugarLinkAtoms.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../StringRoutines.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h LinkAtom.h SugarLinkAtoms.h
 SugarToken.o : SugarToken.cpp ../ArgList.h ../CpptrajStdio.h SugarToken.h
-Zmatrix.o : Zmatrix.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h Chirality.h GenerateConnectivityArrays.h InternalCoords.h Model.h StructureEnum.h Zmatrix.h
+Zmatrix.o : Zmatrix.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h GenerateConnectivityArrays.h InternalCoords.h Model.h StructureEnum.h Zmatrix.h
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index dc4ddeb557..644477756d 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -445,8 +445,8 @@ SpaceGroup.o : SpaceGroup.cpp Matrix_3x3.h Parallel.h SpaceGroup.h Vec3.h
 Spline.o : Spline.cpp CpptrajStdio.h Spline.h
 SplineFxnTable.o : SplineFxnTable.cpp Constants.h CpptrajStdio.h Spline.h SplineFxnTable.h StringRoutines.h
 StringRoutines.o : StringRoutines.cpp CpptrajStdio.h StringRoutines.h
-Structure/Builder.o : Structure/Builder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/Builder.h Structure/Chirality.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Structure/Chirality.o : Structure/Chirality.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Chirality.h Structure/StructureEnum.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Structure/BuildAtom.o : Structure/BuildAtom.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/StructureEnum.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Structure/Builder.o : Structure/Builder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/Builder.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/Disulfide.o : Structure/Disulfide.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Disulfide.h Structure/ResStatArray.h Structure/StructureRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/FunctionalGroup.o : Structure/FunctionalGroup.cpp Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/FxnGroupBuilder.o : Structure/FxnGroupBuilder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h Structure/FxnGroupBuilder.h Structure/StructureRoutines.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
@@ -457,10 +457,10 @@ Structure/Model.o : Structure/Model.cpp Atom.h AtomMask.h AtomType.h Box.h Const
 Structure/StructureEnum.o : Structure/StructureEnum.cpp Structure/StructureEnum.h
 Structure/StructureRoutines.o : Structure/StructureRoutines.cpp Atom.h CpptrajStdio.h NameType.h Residue.h Structure/StructureRoutines.h SymbolExporting.h
 Structure/Sugar.o : Structure/Sugar.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Structure/SugarBuilder.o : Structure/SugarBuilder.cpp ArgList.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DistRoutines.h FileIO.h FileName.h Frame.h ImageOption.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Chirality.h Structure/FunctionalGroup.h Structure/FxnGroupBuilder.h Structure/LinkAtom.h Structure/ResStatArray.h Structure/StructureEnum.h Structure/StructureRoutines.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarLinkAtoms.h Structure/SugarToken.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Structure/SugarBuilder.o : Structure/SugarBuilder.cpp ArgList.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DistRoutines.h FileIO.h FileName.h Frame.h ImageOption.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/FunctionalGroup.h Structure/FxnGroupBuilder.h Structure/LinkAtom.h Structure/ResStatArray.h Structure/StructureEnum.h Structure/StructureRoutines.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarLinkAtoms.h Structure/SugarToken.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 Structure/SugarLinkAtoms.o : Structure/SugarLinkAtoms.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/LinkAtom.h Structure/SugarLinkAtoms.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/SugarToken.o : Structure/SugarToken.cpp ArgList.h CpptrajStdio.h Structure/SugarToken.h
-Structure/Zmatrix.o : Structure/Zmatrix.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/Chirality.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/Model.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Structure/Zmatrix.o : Structure/Zmatrix.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/Model.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 StructureCheck.o : StructureCheck.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h ExclusionArray.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StructureCheck.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 StructureMapper.o : StructureMapper.cpp AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StructureMapper.h SymbolExporting.h TextFormat.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 SymmetricRmsdCalc.o : SymmetricRmsdCalc.cpp ArrayIterator.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h Hungarian.h ImageOption.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h Topology.h TypeNameHolder.h Unit.h Vec3.h

From c3d00f03f94dea9285735ab578e3651da07ff11c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 22 Jan 2024 11:31:48 -0500
Subject: [PATCH 0376/1492] If chirality not available, use orientation

---
 src/Structure/Model.cpp | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/src/Structure/Model.cpp b/src/Structure/Model.cpp
index 32162bb204..ba543c620b 100644
--- a/src/Structure/Model.cpp
+++ b/src/Structure/Model.cpp
@@ -195,6 +195,11 @@ const
   // TODO check that atom i actually ends up on the list?
   std::vector<int> const& priority = AtomJ.Priority();
   ChiralType chirality = AtomJ.Chirality();
+  if (chirality == IS_UNKNOWN_CHIRALITY) {
+    chirality = AtomJ.Orientation();
+    mprintf("Warning: Unknown chirality around %s; using detected orientation of %s\n",
+            topIn.AtomMaskName(aj).c_str(), chiralStr(chirality));
+  }
   if (debug_ > 0) {
     mprintf("DEBUG: Original chirality around J %s is %s\n", topIn.AtomMaskName(aj).c_str(), chiralStr(chirality));
     mprintf("DEBUG:\t\tPriority around J %s(%i) is", 

From a8633b5e6d81701360fa25ba280298edaaa06547 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 22 Jan 2024 11:47:43 -0500
Subject: [PATCH 0377/1492] Ensure builder debug is set

---
 src/Exec_Sequence.cpp | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/Exec_Sequence.cpp b/src/Exec_Sequence.cpp
index 4bc95592d0..47e2b737a2 100644
--- a/src/Exec_Sequence.cpp
+++ b/src/Exec_Sequence.cpp
@@ -92,6 +92,7 @@ const
 
   using namespace Cpptraj::Structure;
   Builder builder;
+  builder.SetDebug( debug_ );
   for (unsigned int idx = 1; idx < Units.size(); idx++) {
     mprintf("\tConnect %s atom %i to %s atom %i\n",
             Units[idx-1]->legend(), connectAt1[idx-1]+1,

From 24b564a3dc877df06bfb1797a112eb3b9ec8b465 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 22 Jan 2024 11:47:58 -0500
Subject: [PATCH 0378/1492] Change warning to debug message. Not being able to
 determine absolute priority isnt always a problem.

---
 src/Structure/BuildAtom.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/Structure/BuildAtom.cpp b/src/Structure/BuildAtom.cpp
index 7f0295d570..a2fdc26ec4 100644
--- a/src/Structure/BuildAtom.cpp
+++ b/src/Structure/BuildAtom.cpp
@@ -125,8 +125,8 @@ int Cpptraj::Structure::BuildAtom::determineChirality(int atnum, Topology const&
             break;
           }
           if (depth == 10) {
-            mprintf("Warning: Could not determine priority around '%s'\n",
-                      topIn.AtomMaskName(atnum).c_str());
+            if (debugIn > 0) mprintf("DEBUG: Could not determine priority around '%s'\n",
+                                     topIn.AtomMaskName(atnum).c_str());
             depth_limit_hit = true;
             break;
           }

From 037f5ca5906f171d3f4895aa1e40933035ad31fa Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 24 Jan 2024 12:38:00 -0500
Subject: [PATCH 0379/1492] Improve error message

---
 src/Structure/Builder.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index cb52e25591..d7066cc435 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -73,13 +73,13 @@ const
     if (AtomA.DetermineChirality(atA, combinedTop, CombinedFrame, chiralityDebug)) return 1;
   }
   if (debug_ > 0)
-    mprintf("DEBUG:\tAtom %4s chirality %6s\n", combinedTop.AtomMaskName(atA).c_str(), chiralStr(AtomA.Chirality()));
+    mprintf("DEBUG:\tAtom %4s chirality before bonding is %6s\n", combinedTop.AtomMaskName(atA).c_str(), chiralStr(AtomA.Chirality()));
   BuildAtom AtomB;
   if (combinedTop[atB].Nbonds() > 2) {
     if (AtomB.DetermineChirality(atB, combinedTop, CombinedFrame, chiralityDebug)) return 1;
   }
   if (debug_ > 0)
-    mprintf("DEBUG:\tAtom %4s chirality %6s\n", combinedTop.AtomMaskName(atB).c_str(), chiralStr(AtomB.Chirality()));
+    mprintf("DEBUG:\tAtom %4s chirality before bonding is %6s\n", combinedTop.AtomMaskName(atB).c_str(), chiralStr(AtomB.Chirality()));
 
   // Create the bond
   if (debug_ > 0)

From b1964b5360e29a1371aa3159df2c65f05c9061c4 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 24 Jan 2024 18:42:27 -0500
Subject: [PATCH 0380/1492] FIXME - Temporarily increase the default model
 debug level

---
 src/Structure/Zmatrix.cpp | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index 93e3638281..9fbd4ebda3 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -1019,7 +1019,8 @@ int Zmatrix::SetupICsAroundBond(int atA, int atB, Frame const& frameIn, Topology
     modelDebug = debug_ - 1;
   }
   Cpptraj::Structure::Model model;
-  model.SetDebug( modelDebug );
+  //model.SetDebug( modelDebug ); //FIXME
+  model.SetDebug( 1 );
   // ---- I J: Set dist, theta, phi for atA atB K L internal coord ---
   if (debug_ > 0)
     mprintf("DEBUG: IC (i j) %i - %i - %i - %i\n", atA+1, atB+1, atk0+1, atl0+1);

From a5853f86342cc990da8266802f682d7214f54ef3 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 25 Jan 2024 09:42:13 -0500
Subject: [PATCH 0381/1492] Fix printf issue

---
 src/DataIO_AmberLib.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/DataIO_AmberLib.cpp b/src/DataIO_AmberLib.cpp
index 32ff816b45..e4f0cf46d4 100644
--- a/src/DataIO_AmberLib.cpp
+++ b/src/DataIO_AmberLib.cpp
@@ -252,7 +252,7 @@ const
         ArgList tmpArg( Line );
         if (tmpArg.Nargs() < 1) {
           mprinterr("Error: Could not read residue from residues section.\n");
-          mprinterr("Error: Line: %s\n", Line);
+          mprinterr("Error: Line: %s\n", Line.c_str());
           return 1;
         }
         if (ridx >= top.Nres()) {

From 6f4f2226bbb26c4efd6a19aeffc0acf5ac177441 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 25 Jan 2024 10:29:34 -0500
Subject: [PATCH 0382/1492] Add 'byatom' keyword to checkchirality to allow
 printing of chirality at any atom

---
 src/Action_CheckChirality.cpp | 279 ++++++++++++++++++++++------------
 src/Action_CheckChirality.h   |   7 +-
 src/cpptrajdepend             |   2 +-
 3 files changed, 187 insertions(+), 101 deletions(-)

diff --git a/src/Action_CheckChirality.cpp b/src/Action_CheckChirality.cpp
index 10ce49e645..a8d1003074 100644
--- a/src/Action_CheckChirality.cpp
+++ b/src/Action_CheckChirality.cpp
@@ -2,43 +2,65 @@
 #include "CpptrajStdio.h"
 #include "TorsionRoutines.h"
 #include "DataSet_Mesh.h"
-//#inc lude "Structure/Chirality.h" // DEBUG
+//#incl ude "Constants.h"
+#include "Structure/BuildAtom.h"
 
 void Action_CheckChirality::Help() const {
-  mprintf("\t[<name>] [<mask1>] [out <filename>]\n"
-          "  Check the chirality of AA residues in <mask1>.\n");
+  mprintf("\t[<name>] [<mask1>] [out <filename>] [byatom]\n"
+          "  Check the chirality of amino acid residues in <mask1>.\n"
+          "  If 'byatom' is specified, check the chirality of any atoms in\n"
+          "  <mask1> that are chiral centers.\n");
 }
 
+/** CONSTRUCTOR */
+Action_CheckChirality::Action_CheckChirality() :
+  data_L_(0),
+  data_D_(0),
+  outfile_(0),
+  byatom_(false),
+  currentTop_(0),
+  debug_(0)
+{}
+
 // Action_CheckChirality::Init()
 Action::RetType Action_CheckChirality::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
 {
+  debug_ = debugIn;
   // Get keywords
-  DataFile* outfile = init.DFL().AddDataFile( actionArgs.GetStringKey("out"), actionArgs );
+  outfile_ = init.DFL().AddDataFile( actionArgs.GetStringKey("out"), actionArgs );
+  byatom_ = actionArgs.hasKey("byatom");
   // Get Masks
   if (Mask1_.SetMaskString( actionArgs.GetMaskNext() )) return Action::ERR;
   // Set up DataSets
   setname_ = actionArgs.GetStringNext();
   if (setname_.empty())
     setname_ = init.DSL().GenerateDefaultName("CHIRAL");
-  MetaData md(setname_, "L", MetaData::NOT_TS);
-  data_L_ = init.DSL().AddSet( DataSet::XYMESH, md);
-  md.SetAspect("D");
-  data_D_ = init.DSL().AddSet( DataSet::XYMESH, md); 
-  if (data_L_ == 0 || data_D_ == 0) return Action::ERR;
-  data_L_->SetupFormat().SetFormatWidthPrecision( 8, 0 );
-  data_D_->SetupFormat().SetFormatWidthPrecision( 8, 0 );
-  if (outfile != 0) {
-    outfile->AddDataSet( data_L_ );
-    outfile->AddDataSet( data_D_ );
+  if (!byatom_) {
+    MetaData md(setname_, "L", MetaData::NOT_TS);
+    data_L_ = init.DSL().AddSet( DataSet::XYMESH, md);
+    md.SetAspect("D");
+    data_D_ = init.DSL().AddSet( DataSet::XYMESH, md); 
+    if (data_L_ == 0 || data_D_ == 0) return Action::ERR;
+    data_L_->SetupFormat().SetFormatWidthPrecision( 8, 0 );
+    data_D_->SetupFormat().SetFormatWidthPrecision( 8, 0 );
+    if (outfile_ != 0) {
+      outfile_->AddDataSet( data_L_ );
+      outfile_->AddDataSet( data_D_ );
+    }
+#   ifdef MPI
+    data_L_->SetNeedsSync( false );
+    data_D_->SetNeedsSync( false );
+#   endif
+  }
+  if (!byatom_) {
+    mprintf("    CHECKCHIRALITY: Check chirality for AA residues in mask '%s'\n",
+            Mask1_.MaskString());
+  } else {
+    mprintf("    CHECKCHIRALITY: Check chirality for atoms in mask '%s'\n",
+            Mask1_.MaskString());
   }
-# ifdef MPI
-  data_L_->SetNeedsSync( false );
-  data_D_->SetNeedsSync( false );
-# endif
-  mprintf("    CHECKCHIRALITY: Check chirality for AA residues in mask '%s'\n",
-          Mask1_.MaskString());
-  if (outfile != 0)
-    mprintf("\tOutput to file %s\n", outfile->DataFilename().full());
+  if (outfile_ != 0)
+    mprintf("\tOutput to file %s\n", outfile_->DataFilename().full());
   if (!setname_.empty())
     mprintf("\tData set name: %s\n", setname_.c_str());
   Init_ = init;
@@ -55,92 +77,148 @@ Action::RetType Action_CheckChirality::Setup(ActionSetup& setup) {
     mprinterr("Warning: Mask '%s' selects no atoms.\n", Mask1_.MaskString());
     return Action::SKIP;
   }
-  // Reset any existing ResidueInfos to inactive
-  for (Rarray::iterator ri = resInfo_.begin(); ri != resInfo_.end(); ++ri)
-    ri->isActive_ = 0;
-  int Nactive = 0;
-  // Loop over all non-solvent residues
-  int resnum = 0;
-  std::vector<std::string> NotFound;
-  for (Topology::res_iterator res = setup.Top().ResStart();
-                              res != setup.Top().ResEnd(); ++res, ++resnum)
-  {
-    int firstAtom = res->FirstAtom();
-    int molnum = setup.Top()[firstAtom].MolNum();
-    // Skip solvent
-    if (!setup.Top().Mol(molnum).IsSolvent())
-    {
-      if (Mask1_.AtomsInCharMask( firstAtom, res->LastAtom() ))
-      { 
-        int n_atom = setup.Top().FindAtomInResidue(resnum, "N");
-        int ca_atom = setup.Top().FindAtomInResidue(resnum, "CA");
-        int c_atom = setup.Top().FindAtomInResidue(resnum, "C");
-        int cb_atom = setup.Top().FindAtomInResidue(resnum, "CB");
-        if (n_atom == -1 || ca_atom == -1 || c_atom == -1 || cb_atom == -1)
-        {
-          NotFound.push_back( setup.Top().TruncResNameNum(resnum) );
-          continue;
-        }
-        Nactive++;
-        // See if a data set is already present
-        Rarray::iterator rinfo = resInfo_.end();
-        for (Rarray::iterator ri = resInfo_.begin(); ri != resInfo_.end(); ++ri)
-          if (resnum == ri->num_) {
-            rinfo = ri;
-            break;
+  if (byatom_) {
+    currentTop_ = setup.TopAddress();
+    if (atomChiralitySets_.empty()) {
+      // First time
+      atomChiralitySets_.assign( setup.Top().Natom(), 0 );
+    } else if ((unsigned int)setup.Top().Natom() > atomChiralitySets_.size()) {
+      atomChiralitySets_.resize( setup.Top().Natom(), 0 );
+    }
+    // For each selected atom, create a set
+    for (int at = 0; at != setup.Top().Natom(); ++at) {
+      if (Mask1_.AtomInCharMask(at)) {
+        std::string legend = setup.Top().AtomMaskName(at);
+        if ( atomChiralitySets_[at] == 0 ) {
+          if (setup.Top()[at].Nbonds() < 3) {
+            mprintf("Warning: Atom %s has < 3 bonds, not checking for chirality.\n", legend.c_str());
+          } else {
+            // Initial set up
+            //atomChiralitySets_[at] = Init_.DSL().AddSet( DataSet::FLOAT, MetaData(setname_, at+1) );
+            atomChiralitySets_[at] = Init_.DSL().AddSet( DataSet::STRING, MetaData(setname_, at+1) );
+            if (atomChiralitySets_[at] == 0) {
+              mprinterr("Error: Could not allocate set for atom '%s'\n", legend.c_str());
+              return Action::ERR;
+            }
+            atomChiralitySets_[at]->SetLegend( legend );
+            if (outfile_ != 0) outfile_->AddDataSet( atomChiralitySets_[at] );
           }
-        if (rinfo != resInfo_.end()) {
-          // Update coord indices in ResidueInfo
-          rinfo->isActive_ = 1;
-          rinfo->n_ = n_atom * 3;
-          rinfo->ca_ = ca_atom * 3;
-          rinfo->c_ = c_atom * 3;
-          rinfo->cb_ = cb_atom * 3;
         } else {
-          // New ResidueInfo
-          ResidueInfo RI;
-          RI.num_ = resnum;
-          RI.isActive_ = 1;
-          RI.n_ = n_atom * 3;
-          RI.ca_ = ca_atom * 3;
-          RI.c_ = c_atom * 3;
-          RI.cb_ = cb_atom * 3;
-          RI.N_L_ = 0;
-          RI.N_D_ = 0;
-          resInfo_.push_back( RI );
+          // Check an already set up dataset
+          if (legend != atomChiralitySets_[at]->Meta().Legend()) {
+            mprintf("Warning: After topology change, atom %i has changed from %s to %s\n",
+                    at+1, atomChiralitySets_[at]->legend(), legend.c_str());
+          }
         }
-      } // END atoms in mask
-    } // END not solvent
-  } // END loop over residues
+      } // END atom is selected
+    } // END loop over atoms
+    mprintf("\tChecking chirality for %i atoms.\n", Mask1_.Nselected());
+  } else {
+    // Reset any existing ResidueInfos to inactive
+    for (Rarray::iterator ri = resInfo_.begin(); ri != resInfo_.end(); ++ri)
+      ri->isActive_ = 0;
+    int Nactive = 0;
+    // Loop over all non-solvent residues
+    int resnum = 0;
+    std::vector<std::string> NotFound;
+    for (Topology::res_iterator res = setup.Top().ResStart();
+                                res != setup.Top().ResEnd(); ++res, ++resnum)
+    {
+      int firstAtom = res->FirstAtom();
+      int molnum = setup.Top()[firstAtom].MolNum();
+      // Skip solvent
+      if (!setup.Top().Mol(molnum).IsSolvent())
+      {
+        if (Mask1_.AtomsInCharMask( firstAtom, res->LastAtom() ))
+        { 
+          int n_atom = setup.Top().FindAtomInResidue(resnum, "N");
+          int ca_atom = setup.Top().FindAtomInResidue(resnum, "CA");
+          int c_atom = setup.Top().FindAtomInResidue(resnum, "C");
+          int cb_atom = setup.Top().FindAtomInResidue(resnum, "CB");
+          if (n_atom == -1 || ca_atom == -1 || c_atom == -1 || cb_atom == -1)
+          {
+            NotFound.push_back( setup.Top().TruncResNameNum(resnum) );
+            continue;
+          }
+          Nactive++;
+          // See if a data set is already present
+          Rarray::iterator rinfo = resInfo_.end();
+          for (Rarray::iterator ri = resInfo_.begin(); ri != resInfo_.end(); ++ri)
+            if (resnum == ri->num_) {
+              rinfo = ri;
+              break;
+            }
+          if (rinfo != resInfo_.end()) {
+            // Update coord indices in ResidueInfo
+            rinfo->isActive_ = 1;
+            rinfo->n_ = n_atom * 3;
+            rinfo->ca_ = ca_atom * 3;
+            rinfo->c_ = c_atom * 3;
+            rinfo->cb_ = cb_atom * 3;
+          } else {
+            // New ResidueInfo
+            ResidueInfo RI;
+            RI.num_ = resnum;
+            RI.isActive_ = 1;
+            RI.n_ = n_atom * 3;
+            RI.ca_ = ca_atom * 3;
+            RI.c_ = c_atom * 3;
+            RI.cb_ = cb_atom * 3;
+            RI.N_L_ = 0;
+            RI.N_D_ = 0;
+            resInfo_.push_back( RI );
+          }
+        } // END atoms in mask
+      } // END not solvent
+    } // END loop over residues
 
-  if (Nactive == 0) {
-    mprintf("Warning: No valid residues selected from '%s'\n", setup.Top().c_str());
-    return Action::SKIP;
-  }
-  mprintf("\tChecking chirality for %i residues\n", Nactive);
-  if (!NotFound.empty()) {
-    mprintf("\tSome atoms not found for %zu residues (this is expected for e.g. GLY)\n\t",
-            NotFound.size());
-    for (std::vector<std::string>::const_iterator rn = NotFound.begin();
-                                                  rn != NotFound.end(); ++rn)
-      mprintf(" %s", rn->c_str());
-    mprintf("\n");
-  }
+    if (Nactive == 0) {
+      mprintf("Warning: No valid residues selected from '%s'\n", setup.Top().c_str());
+      return Action::SKIP;
+    }
+    mprintf("\tChecking chirality for %i residues\n", Nactive);
+    if (!NotFound.empty()) {
+      mprintf("\tSome atoms not found for %zu residues (this is expected for e.g. GLY)\n\t",
+              NotFound.size());
+      for (std::vector<std::string>::const_iterator rn = NotFound.begin();
+                                                    rn != NotFound.end(); ++rn)
+        mprintf(" %s", rn->c_str());
+      mprintf("\n");
+    }
+  } // END residue setup
   return Action::OK;
 }
 
 // Action_CheckChirality::DoAction()
 Action::RetType Action_CheckChirality::DoAction(int frameNum, ActionFrame& frm) {
-  for (Rarray::iterator ri = resInfo_.begin(); ri != resInfo_.end(); ++ri)
-  {
-    double torsion = Torsion( frm.Frm().CRD(ri->n_),
-                              frm.Frm().CRD(ri->ca_),
-                              frm.Frm().CRD(ri->c_),
-                              frm.Frm().CRD(ri->cb_) );
-    if (torsion < 0.0)
-      ri->N_L_++;
-    else
-      ri->N_D_++;
+  if (byatom_) {
+    for (std::vector<DataSet*>::const_iterator it = atomChiralitySets_.begin();
+                                               it != atomChiralitySets_.end(); ++it)
+    {
+      if (*it != 0) {
+        DataSet* ds = *it;
+        int iat = ds->Meta().Idx() - 1;
+        Cpptraj::Structure::BuildAtom AtomC;
+        if (AtomC.DetermineChirality(iat, *currentTop_, frm.Frm(), debug_))
+          return Action::ERR;
+        //double tval_degrees = AtomC.TorsionVal() * Constants::RADDEG;
+        //float ftval = (float)tval_degrees;
+        //ds->Add( frameNum, &ftval );
+        const char* chiralstr = Cpptraj::Structure::chiralStr( AtomC.Chirality() );
+        ds->Add( frameNum, chiralstr );
+      }
+    }
+  } else {
+    for (Rarray::iterator ri = resInfo_.begin(); ri != resInfo_.end(); ++ri)
+    {
+      double torsion = Torsion( frm.Frm().CRD(ri->n_),
+                                frm.Frm().CRD(ri->ca_),
+                                frm.Frm().CRD(ri->c_),
+                                frm.Frm().CRD(ri->cb_) );
+      if (torsion < 0.0)
+        ri->N_L_++;
+      else
+        ri->N_D_++;
 //    DEBUG
 //    int at = ri->ca_ / 3;
 //    Cpptraj::Structure::ChiralType chirality = Cpptraj::Structure::IS_UNKNOWN_CHIRALITY;
@@ -148,6 +226,7 @@ Action::RetType Action_CheckChirality::DoAction(int frameNum, ActionFrame& frm)
 //      chirality = Cpptraj::Structure::DetermineChirality(at, *top_, frm.Frm(), 0);
 //    mprintf("Chirality around %s is %s\n", top_->AtomMaskName(at).c_str(), Cpptraj::Structure::chiralStr(chirality));
 //    DEBUG
+    }
   }
 
   return Action::OK;
@@ -155,6 +234,7 @@ Action::RetType Action_CheckChirality::DoAction(int frameNum, ActionFrame& frm)
 
 #ifdef MPI
 int Action_CheckChirality::SyncAction() {
+  if (byatom_) return 0;
   int total_L, total_D;
   for (Rarray::iterator ri = resInfo_.begin(); ri != resInfo_.end(); ++ri) {
     Init_.TrajComm().ReduceMaster( &total_L, &(ri->N_L_), 1, MPI_INT, MPI_SUM );
@@ -169,6 +249,7 @@ int Action_CheckChirality::SyncAction() {
 #endif
 
 void Action_CheckChirality::Print() {
+  if (byatom_) return;
   data_L_->ModifyDim(Dimension::X).SetLabel("Res");
   data_D_->ModifyDim(Dimension::X).SetLabel("Res");
   DataSet_Mesh& dsetL = static_cast<DataSet_Mesh&>( *data_L_ );
diff --git a/src/Action_CheckChirality.h b/src/Action_CheckChirality.h
index 861f3801d3..3e3a1b0599 100644
--- a/src/Action_CheckChirality.h
+++ b/src/Action_CheckChirality.h
@@ -5,7 +5,7 @@
 /// Determine if amino acids are D or L 
 class Action_CheckChirality: public Action {
   public:
-    Action_CheckChirality() {}
+    Action_CheckChirality();
     DispatchObject* Alloc() const { return (DispatchObject*)new Action_CheckChirality(); }
     void Help() const;
   private:
@@ -35,7 +35,12 @@ class Action_CheckChirality: public Action {
     DataSet* data_L_;     ///< Hold number of times each residue was L
     DataSet* data_D_;     ///< Hold number of times each residue was D
     std::string setname_; ///< Data set name
+    DataFile* outfile_;   ///< Output file
+    std::vector<DataSet*> atomChiralitySets_; ///< For each atom, hold chirality each frame
     ActionInit Init_;     ///< Master DSL/DFL
+    bool byatom_;
+    Topology* currentTop_;
+    int debug_;
 //    Topology* top_; // DEBUG
 };
 #endif
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 57187e3768..18fa7492c2 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -14,7 +14,7 @@ Action_Bounds.o : Action_Bounds.cpp Action.h ActionState.h Action_Bounds.h ArgLi
 Action_Box.o : Action_Box.cpp Action.h ActionState.h Action_Box.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BoxArgs.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Action_Center.o : Action_Center.cpp Action.h ActionState.h Action_Center.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Action_Channel.o : Action_Channel.cpp Action.h ActionState.h Action_Channel.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_CheckChirality.o : Action_CheckChirality.cpp Action.h ActionState.h Action_CheckChirality.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Action_CheckChirality.o : Action_CheckChirality.cpp Action.h ActionState.h Action_CheckChirality.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h Structure/BuildAtom.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 Action_CheckStructure.o : Action_CheckStructure.cpp Action.h ActionState.h Action_CheckStructure.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_integer.h DataSet_string.h Dimension.h DispatchObject.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Action_Closest.o : Action_Closest.cpp Action.h ActionState.h ActionTopWriter.h Action_Closest.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h ImageRoutines.h ImageTypes.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h cuda_kernels/kernel_wrappers.cuh
 Action_ClusterDihedral.o : Action_ClusterDihedral.cpp Action.h ActionState.h Action_ClusterDihedral.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_integer.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h

From c753bb8786f348c58799042da2e5c5f9770a61fc Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 25 Jan 2024 14:11:04 -0500
Subject: [PATCH 0383/1492] Start new phi assignment

---
 src/Structure/Model.cpp | 65 +++++++++++++++++++++++++++++++++++++++--
 src/Structure/Model.h   |  7 +++--
 2 files changed, 68 insertions(+), 4 deletions(-)

diff --git a/src/Structure/Model.cpp b/src/Structure/Model.cpp
index ba543c620b..8a7b6fa45f 100644
--- a/src/Structure/Model.cpp
+++ b/src/Structure/Model.cpp
@@ -1,7 +1,6 @@
 #include "Model.h"
 #include "BuildAtom.h"
-//#incl ude "InternalCoords.h"
-//#incl ude "Chirality.h"
+#include "InternalCoords.h"
 #include "../CpptrajStdio.h"
 #include "../GuessAtomHybridization.h"
 #include "../Topology.h"
@@ -31,6 +30,11 @@ const
   // Figure out hybridization and chirality of atom j.
   if (debug_ > 0)
     mprintf("DEBUG: AssignTheta for atom j : %s\n", topIn.AtomMaskName(aj).c_str());
+  if (atomPositionKnown[ai] && atomPositionKnown[aj] && atomPositionKnown[ak])
+  {
+    theta = CalcAngle(frameIn.XYZ(ai), frameIn.XYZ(aj), frameIn.XYZ(ak));
+    return 0;
+  }
 
   //enum HybridizationType { SP = 0, SP2, SP3, UNKNOWN_HYBRIDIZATION };
 
@@ -376,6 +380,63 @@ const
 */
   return 0;
 }
+
+/** Assign internal coordinates for atoms I for torsions around J-K-L. */
+int Cpptraj::Structure::Model::AssignICsAroundBond(std::vector<InternalCoords>& IC,
+                                                   int aj, int ak, int al,
+                                                   Topology const& topIn, Frame const& frameIn,
+                                                   std::vector<bool> const& atomPositionKnown,
+                                                   BuildAtom const& AtomJ)
+const
+{
+  // Atoms J K and L should be known
+  if (!atomPositionKnown[aj] ||
+      !atomPositionKnown[ak] ||
+      !atomPositionKnown[al])
+  {
+    mprinterr("Internal Error: AssignIcAroundBond(): Not all atom positions known.\n"
+              "Internal Error: %i (%i), %i (%i), %i (%i)\n",
+              aj+1, (int)atomPositionKnown[aj],
+              ak+1, (int)atomPositionKnown[ak],
+              al+1, (int)atomPositionKnown[al]);
+    return 1;
+  }
+  Atom const& AJ = topIn[aj];
+  // If atom J has only 1 bond this is not needed.
+  if (AJ.Nbonds() < 2) return 0;
+  
+
+  if (debug_ > 0) mprintf("DEBUG:\t\tNbonds: %i\n", AJ.Nbonds());
+  // If atom J only has 2 bonds, ai-aj-ak-al is the only possibility.
+  if (AJ.Nbonds() < 3) {
+    if (debug_ > 0)
+      mprintf("DEBUG:\t\tFewer than 3 bonds. Setting phi to -180.\n");
+    double newPhi = -180 * Constants::DEGRAD;
+    for (int idx = 0; idx < AJ.Nbonds(); idx++) {
+      if (AJ.Bond(idx) != ak) {
+        int ai = AJ.Bond(idx);
+        double newDist = 0;
+        if (AssignLength(newDist, ai, aj, topIn, frameIn, atomPositionKnown)) {
+          mprinterr("Error: AssignLength failed for %s - %s \n",
+                    topIn.AtomMaskName(ai).c_str(), topIn.AtomMaskName(aj).c_str());
+          return 1;
+        }
+        double newTheta = 0;
+        if (AssignTheta(newTheta, ai, aj, ak, topIn, frameIn, atomPositionKnown)) {
+          mprinterr("Error: AssignTheta failed for %s - %s - %s\n",
+                    topIn.AtomMaskName(ai).c_str(),
+                    topIn.AtomMaskName(aj).c_str(),
+                    topIn.AtomMaskName(ak).c_str());
+        }
+        IC.push_back( InternalCoords(ai, aj, ak, al, newDist, newTheta, newPhi) );
+        break;
+      }
+    }
+    return 0;
+  } // END only 2 bonds
+
+  return 0;
+}
 /*
 static inline AtomType::HybridizationType getAtomHybridization(ParmHolder<AtomType> const& AT, Topology const& topIn, int ix)
 {
diff --git a/src/Structure/Model.h b/src/Structure/Model.h
index d820c5e1e3..b43613b027 100644
--- a/src/Structure/Model.h
+++ b/src/Structure/Model.h
@@ -22,9 +22,12 @@ class Model {
     int AssignTheta(double&, int, int, int, Topology const&, Frame const&, std::vector<bool> const&) const;
     /// Given atoms J K and L, attempt to assign a reasonable value for phi for atom I
     //int AssignPhi(std::vector<InternalCoords>&, int, int, int, Topology const&, Frame const&, std::vector<bool> const&, BuildAtom const&) const;
+    /// Given atoms I J K and L, attempt to assign a reasonable value for phi for atom I
     int AssignPhi(double&, int, int, int, int, Topology const&, Frame const&, std::vector<bool> const&, BuildAtom const&) const;
-    /// Assign phi around bond
-    //int AssignPhiAroundBond(int, int, Topology const&, Frame const&, std::vector<bool> const&, ParmHolder<AtomType> const&) const;
+    /// Assign internal coordinates for atoms I for torsions around J-K-L.
+    int AssignICsAroundBond(std::vector<InternalCoords>&, int, int, int,
+                           Topology const&, Frame const&, std::vector<bool> const&,
+                           BuildAtom const&) const;
   private:
     int debug_;
 };

From 992a45ee7d8992fb240b92b4ec6cdea98cdfe3f2 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 25 Jan 2024 14:35:06 -0500
Subject: [PATCH 0384/1492] Add known phi calc

---
 src/Structure/Model.cpp   | 64 ++++++++++++++++++++++++++++++++++++---
 src/Structure/Zmatrix.cpp |  7 +++++
 2 files changed, 67 insertions(+), 4 deletions(-)

diff --git a/src/Structure/Model.cpp b/src/Structure/Model.cpp
index 8a7b6fa45f..4f148f570d 100644
--- a/src/Structure/Model.cpp
+++ b/src/Structure/Model.cpp
@@ -389,17 +389,22 @@ int Cpptraj::Structure::Model::AssignICsAroundBond(std::vector<InternalCoords>&
                                                    BuildAtom const& AtomJ)
 const
 {
-  // Atoms J K and L should be known
+  mprintf("DEBUG: AssignICsAroundBond: X - %s - %s - %s  %i - %i - %i\n",
+          topIn.AtomMaskName(aj).c_str(),
+          topIn.AtomMaskName(ak).c_str(),
+          topIn.AtomMaskName(al).c_str(),
+          aj+1, ak+1, al+1);
+  // Ideally, atoms J K and L should be known
   if (!atomPositionKnown[aj] ||
       !atomPositionKnown[ak] ||
       !atomPositionKnown[al])
   {
-    mprinterr("Internal Error: AssignIcAroundBond(): Not all atom positions known.\n"
-              "Internal Error: %i (%i), %i (%i), %i (%i)\n",
+    mprintf("Warning: AssignICsAroundBond(): Not all atom positions known.\n"
+            "Warning: %i (%i), %i (%i), %i (%i)\n",
               aj+1, (int)atomPositionKnown[aj],
               ak+1, (int)atomPositionKnown[ak],
               al+1, (int)atomPositionKnown[al]);
-    return 1;
+    //return 1;
   }
   Atom const& AJ = topIn[aj];
   // If atom J has only 1 bond this is not needed.
@@ -435,6 +440,57 @@ const
     return 0;
   } // END only 2 bonds
 
+  // 3 or more bonds.
+  std::vector<int> const& priority = AtomJ.Priority();
+  ChiralType chirality = AtomJ.Chirality();
+  //if (chirality == IS_UNKNOWN_CHIRALITY) {
+  //  chirality = AtomJ.Orientation();
+  //  mprintf("Warning: Unknown chirality around %s; using detected orientation of %s\n",
+  //          topIn.AtomMaskName(aj).c_str(), chiralStr(chirality));
+  //}
+  if (debug_ > 0) {
+    mprintf("DEBUG: Original chirality around J %s is %s\n", topIn.AtomMaskName(aj).c_str(), chiralStr(chirality));
+    mprintf("DEBUG:\t\tPriority around J %s(%i) is", 
+            topIn.AtomMaskName(aj).c_str(), (int)atomPositionKnown[aj]);
+    for (int idx = 0; idx < AJ.Nbonds(); idx++)
+      mprintf(" %s(%i)", topIn.AtomMaskName(priority[idx]).c_str(), (int)atomPositionKnown[priority[idx]]);
+    mprintf("\n");
+  }
+
+  // Fill in what values we can for known atoms
+  std::vector<double> knownPhi( AJ.Nbonds() );
+  std::vector<bool> isKnown( AJ.Nbonds(), false );
+  int knownIdx = -1;
+  double knownInterval = 0;
+  bool hasKnownInterval = false;
+  for (int idx = 0; idx < AJ.Nbonds(); idx++) {
+    int atnum = priority[idx];
+    if (atnum != ak && atomPositionKnown[atnum] &&
+                       atomPositionKnown[aj] &&
+                       atomPositionKnown[ak] &&
+                       atomPositionKnown[al])
+    {
+      knownPhi[idx] = Torsion(frameIn.XYZ(atnum),
+                              frameIn.XYZ(aj),
+                              frameIn.XYZ(ak),
+                              frameIn.XYZ(al));
+      isKnown[idx] = true;
+      if (debug_ > 0)
+        mprintf("DEBUG:\t\tKnown phi for %s (pos=%i) = %g\n", topIn.AtomMaskName(atnum).c_str(), idx, knownPhi[idx]*Constants::RADDEG);
+      if (knownIdx == -1) knownIdx = idx; // FIXME handle more than 1 known
+      if (idx > 0 && isKnown[idx-1] && isKnown[idx]) {
+        knownInterval = wrap360(knownPhi[idx] - knownPhi[idx-1]);
+        hasKnownInterval = true;
+      }
+    }
+  }
+  if (hasKnownInterval)
+    mprintf("DEBUG:\t\tKnown interval = %g\n", knownInterval * Constants::RADDEG);
+
+//  for (int idx = 0; idx < AJ.Nbonds(); idx++) {
+//    if (AJ.Bond(idx) != ak) {
+//      int ai = AJ.Bond(idx);
+
   return 0;
 }
 /*
diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index 9fbd4ebda3..36d9e7e5ac 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -1021,6 +1021,13 @@ int Zmatrix::SetupICsAroundBond(int atA, int atB, Frame const& frameIn, Topology
   Cpptraj::Structure::Model model;
   //model.SetDebug( modelDebug ); //FIXME
   model.SetDebug( 1 );
+  // FIXME
+  std::vector<InternalCoords> tmpic;
+  if (model.AssignICsAroundBond(tmpic, atB, atk0, atl0, topIn, frameIn, atomPositionKnown, AtomB)) {
+    mprinterr("Error: AssignICsAroundBond failed.\n");
+    return 1;
+  }
+  // FIXME
   // ---- I J: Set dist, theta, phi for atA atB K L internal coord ---
   if (debug_ > 0)
     mprintf("DEBUG: IC (i j) %i - %i - %i - %i\n", atA+1, atB+1, atk0+1, atl0+1);

From 1277b434521c394211b8171eded5cd0bb92dcc4e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 25 Jan 2024 17:42:04 -0500
Subject: [PATCH 0385/1492] Print final ICs

---
 src/Structure/Zmatrix.cpp | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index 36d9e7e5ac..026ecb2795 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -1027,6 +1027,9 @@ int Zmatrix::SetupICsAroundBond(int atA, int atB, Frame const& frameIn, Topology
     mprinterr("Error: AssignICsAroundBond failed.\n");
     return 1;
   }
+  for (std::vector<InternalCoords>::const_iterator it = tmpic.begin(); it != tmpic.end(); ++it)
+    it->printIC( topIn );
+  mprintf("DEBUG: END AssignICsAroundBond ------------------------\n");
   // FIXME
   // ---- I J: Set dist, theta, phi for atA atB K L internal coord ---
   if (debug_ > 0)

From 24617b0cd5cac075e4d8a8daf48d39b1ad633ff1 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 26 Jan 2024 12:05:02 -0500
Subject: [PATCH 0386/1492] Add ParameterSet to model for hybridization. Finish
 initial incarnation of the new Assign phi routine

---
 src/Structure/Model.cpp       | 204 +++++++++++++++++++++++++++++++---
 src/Structure/Model.h         |   7 +-
 src/Structure/structuredepend |   2 +-
 src/cpptrajdepend             |   2 +-
 4 files changed, 197 insertions(+), 18 deletions(-)

diff --git a/src/Structure/Model.cpp b/src/Structure/Model.cpp
index 4f148f570d..13bece2f81 100644
--- a/src/Structure/Model.cpp
+++ b/src/Structure/Model.cpp
@@ -7,8 +7,24 @@
 #include "../TorsionRoutines.h"
 #include "../DistRoutines.h"
 #include "../Constants.h"
+#include "../ParameterSet.h"
 #include <cmath>
 
+/** CONSTRUCTOR */
+Cpptraj::Structure::Model::Model() :
+  debug_(0),
+  params_(0)
+{}
+
+/** Set optional parameter set. */
+void Cpptraj::Structure::Model::SetParameters(ParameterSet const* paramsIn) {
+  if (paramsIn == 0) {
+    mprinterr("Internal Error: Model::SetParmaters called with null set.\n");
+    return;
+  }
+  params_ = paramsIn;
+}
+
 /** Assign reasonable value for bond distance. */
 int Cpptraj::Structure::Model::AssignLength(double& dist, int ai, int aj, Topology const& topIn, Frame const& frameIn, std::vector<bool> const& atomPositionKnown)
 const
@@ -36,8 +52,6 @@ const
     return 0;
   }
 
-  //enum HybridizationType { SP = 0, SP2, SP3, UNKNOWN_HYBRIDIZATION };
-
   Atom const& AJ = topIn[aj];
   if (debug_ > 0) {
     mprintf("DEBUG:\t\tI %s Nbonds: %i\n", topIn[ai].ElementName(), topIn[ai].Nbonds());
@@ -49,8 +63,14 @@ const
     mprinterr("Internal Error: AssignTheta() called for atom J %s with fewer than 2 bonds.\n", topIn.AtomMaskName(aj).c_str());
     return 1;
   }
-  // TODO pass in atom type info?
-  AtomType::HybridizationType hybrid = GuessAtomHybridization(AJ, topIn.Atoms());
+  AtomType::HybridizationType hybrid = AtomType::UNKNOWN_HYBRIDIZATION;
+  if (params_ != 0) {
+    ParmHolder<AtomType>::const_iterator it = params_->AT().GetParam( TypeNameHolder(AJ.Type()) );
+    if (it != params_->AT().end())
+      hybrid = it->second.Hybridization();
+  }
+  if (hybrid == AtomType::UNKNOWN_HYBRIDIZATION)
+    hybrid = GuessAtomHybridization(AJ, topIn.Atoms());
 /*
   HybridizationType hybrid = UNKNOWN_HYBRIDIZATION;
   // Handle specific elements
@@ -283,8 +303,27 @@ const
     return 1;
   }
 
-  // The interval will be 360 / (number of bonds - 1)
-  double interval = Constants::TWOPI / (AJ.Nbonds() - 1);
+  bool intervalIsSet = false;
+  double interval = 0;
+  if (params_ != 0) {
+    ParmHolder<AtomType>::const_iterator it = params_->AT().GetParam( TypeNameHolder(AJ.Type()) );
+    if (it != params_->AT().end()) {
+      if (it->second.Hybridization() == AtomType::SP2) {
+        interval = 180 * Constants::DEGRAD;
+        intervalIsSet = true;
+      } else if (it->second.Hybridization() == AtomType::SP3) {
+        interval = 120 * Constants::DEGRAD;
+        intervalIsSet = true;
+      }
+    }
+    if (intervalIsSet) mprintf("DEBUG: Interval was set from atom J hybridization.\n");
+  }
+  if (!intervalIsSet) {
+    // The interval will be 360 / (number of bonds - 1)
+    interval = Constants::TWOPI / (AJ.Nbonds() - 1);
+    mprintf("DEBUG: Interval was set from number of bonds.\n");
+  }
+
   if (hasKnownInterval) {
     if (chirality == IS_UNKNOWN_CHIRALITY) {
       mprintf("DEBUG: Setting chirality from known interval.\n");
@@ -389,6 +428,7 @@ int Cpptraj::Structure::Model::AssignICsAroundBond(std::vector<InternalCoords>&
                                                    BuildAtom const& AtomJ)
 const
 {
+  mprintf("DEBUG: ------------------------------------------------\n");
   mprintf("DEBUG: AssignICsAroundBond: X - %s - %s - %s  %i - %i - %i\n",
           topIn.AtomMaskName(aj).c_str(),
           topIn.AtomMaskName(ak).c_str(),
@@ -443,13 +483,13 @@ const
   // 3 or more bonds.
   std::vector<int> const& priority = AtomJ.Priority();
   ChiralType chirality = AtomJ.Chirality();
-  //if (chirality == IS_UNKNOWN_CHIRALITY) {
-  //  chirality = AtomJ.Orientation();
-  //  mprintf("Warning: Unknown chirality around %s; using detected orientation of %s\n",
-  //          topIn.AtomMaskName(aj).c_str(), chiralStr(chirality));
-  //}
+  if (chirality == IS_UNKNOWN_CHIRALITY) {
+    chirality = AtomJ.Orientation();
+    mprintf("Warning: Unknown chirality around %s; using detected orientation of %s\n",
+            topIn.AtomMaskName(aj).c_str(), chiralStr(chirality));
+  }
   if (debug_ > 0) {
-    mprintf("DEBUG: Original chirality around J %s is %s\n", topIn.AtomMaskName(aj).c_str(), chiralStr(chirality));
+    mprintf("DEBUG:\t\tOriginal chirality around J %s is %s\n", topIn.AtomMaskName(aj).c_str(), chiralStr(chirality));
     mprintf("DEBUG:\t\tPriority around J %s(%i) is", 
             topIn.AtomMaskName(aj).c_str(), (int)atomPositionKnown[aj]);
     for (int idx = 0; idx < AJ.Nbonds(); idx++)
@@ -457,6 +497,21 @@ const
     mprintf("\n");
   }
 
+  // Get index of atom K in the priority list, starting from least priority.
+  int kPriorityIdx = -1;
+  for (int idx = AJ.Nbonds()-1; idx > -1; idx--) {
+    if (priority[idx] == ak) {
+      kPriorityIdx = AJ.Nbonds() - 1 - idx;
+      break;
+    }
+  }
+  mprintf("DEBUG:\t\tK priority index is %i\n", kPriorityIdx);
+  if (kPriorityIdx < 0) {
+    mprinterr("Error: Could not find atom K %s in atom J %s bond list.\n",
+              topIn.AtomMaskName(ak).c_str(), topIn.AtomMaskName(aj).c_str());
+    return 1;
+  }
+
   // Fill in what values we can for known atoms
   std::vector<double> knownPhi( AJ.Nbonds() );
   std::vector<bool> isKnown( AJ.Nbonds(), false );
@@ -487,9 +542,128 @@ const
   if (hasKnownInterval)
     mprintf("DEBUG:\t\tKnown interval = %g\n", knownInterval * Constants::RADDEG);
 
-//  for (int idx = 0; idx < AJ.Nbonds(); idx++) {
-//    if (AJ.Bond(idx) != ak) {
-//      int ai = AJ.Bond(idx);
+  // If we have to assign an initial phi, make trans the longer branch
+  if (knownIdx == -1) {
+    std::vector<bool> visited = atomPositionKnown;
+    // TODO: Ensure bonded atoms are not yet visited?
+    visited[aj] = true;
+    visited[ak] = true;
+    //std::vector<int> depth( AJ.Nbonds() );
+    int max_depth = 0;
+    int max_idx = -1;
+    for (int idx = 0; idx < AJ.Nbonds(); idx++) {
+      int atnum = priority[idx];
+      if (atnum != ak) {
+        int currentDepth = 0;
+        //depth[idx] = atom_depth(currentDepth, atnum, topIn, visited, 10);
+        int depth = atom_depth(currentDepth, atnum, topIn, visited, 10);
+        if (debug_ > 0)
+          mprintf("DEBUG:\t\tAJ %s depth from %s is %i\n",
+                  topIn.AtomMaskName(aj).c_str(), topIn.AtomMaskName(atnum).c_str(), depth);
+        //if (knownIdx == -1 && depth[idx] < 3) {
+        //  knownIdx = idx;
+        //  knownPhi[idx] = 0;
+        //}
+        if (max_idx == -1 || depth > max_depth) {
+          max_depth = depth;
+          max_idx = idx;
+        }
+      }
+    }
+    mprintf("DEBUG:\t\tLongest depth is for atom %s (%i)\n", topIn.AtomMaskName(priority[max_idx]).c_str(), max_depth);
+    knownIdx = max_idx;
+    knownPhi[max_idx] = -180 * Constants::DEGRAD;
+    isKnown[max_idx] = true;
+  }
+
+  // Sanity check
+  if (knownIdx < 0) {
+    mprinterr("Internal Error: AssignPhi(): knownIdx is < 0\n");
+    return 1;
+  }
+
+  // Determine the interval
+  bool intervalIsSet = false;
+  double interval = 0;
+  if (params_ != 0) {
+    ParmHolder<AtomType>::const_iterator it = params_->AT().GetParam( TypeNameHolder(AJ.Type()) );
+    if (it != params_->AT().end()) {
+      if (it->second.Hybridization() == AtomType::SP2) {
+        interval = 180 * Constants::DEGRAD;
+        intervalIsSet = true;
+      } else if (it->second.Hybridization() == AtomType::SP3) {
+        interval = 120 * Constants::DEGRAD;
+        intervalIsSet = true;
+      }
+    }
+    if (intervalIsSet) mprintf("DEBUG:\t\tInterval was set from atom J hybridization.\n");
+  }
+  if (!intervalIsSet) {
+    // The interval will be 360 / (number of bonds - 1)
+    interval = Constants::TWOPI / (AJ.Nbonds() - 1);
+    mprintf("DEBUG:\t\tInterval was set from number of bonds.\n");
+  }
+
+  // Check known interval if set
+  if (hasKnownInterval) {
+    if (chirality == IS_UNKNOWN_CHIRALITY) {
+      mprintf("DEBUG:\t\tSetting chirality from known interval.\n");
+      if (knownInterval < 0)
+        chirality = IS_S;
+      else
+        chirality = IS_R;
+    } else if (chirality == IS_S) {
+      if (knownInterval > 0)
+        mprinterr("Error: Detected chirality S does not match known interval %g\n", knownInterval*Constants::RADDEG);
+    } else if (chirality == IS_R) {
+      if (knownInterval < 0)
+        mprinterr("Error: Detected chriality R does not match known interval %g\n", knownInterval*Constants::RADDEG);
+    }
+  }
+
+  // Adjust interval based on chirality and priority of the k atom
+  if (chirality == IS_S || chirality == IS_UNKNOWN_CHIRALITY)
+    interval = -interval;
+  if ( kPriorityIdx%2 ) {
+    mprintf("DEBUG:\t\tFlipping interval based on priority index of %i\n", kPriorityIdx);
+    interval = -interval;
+  }
+
+  if (debug_ > 0) {
+    mprintf("DEBUG:\t\tStart phi is %g degrees\n", knownPhi[knownIdx]*Constants::RADDEG);
+    mprintf("DEBUG:\t\tInterval is %g, chirality around J is %s\n", interval*Constants::RADDEG, chiralStr(chirality));
+  }
+
+  // Forwards from the known index
+  double currentPhi = knownPhi[knownIdx];
+  for (int idx = knownIdx; idx < AJ.Nbonds(); idx++) {
+    int atnum = priority[idx];
+    if (atnum != ak) {
+      if (isKnown[idx])
+        currentPhi = knownPhi[idx];
+      else
+        currentPhi = wrap360(currentPhi + interval);
+      //if (atnum == ai) phi = currentPhi;
+      //IC.push_back( InternalCoords(atnum, aj, ak, al, 0, 0, currentPhi) );
+      if (debug_ > 0)
+        mprintf("DEBUG:\t\t\t%s (at# %i) phi= %g\n", topIn.AtomMaskName(atnum).c_str(), atnum+1, currentPhi*Constants::RADDEG);
+    }
+  }
+  // Backwards from the known index
+  currentPhi = knownPhi[knownIdx];
+  for (int idx = knownIdx - 1; idx > -1; idx--) {
+    int atnum = priority[idx];
+    if (atnum != ak) {
+      if (isKnown[idx])
+        currentPhi = knownPhi[idx];
+      else
+        currentPhi = wrap360(currentPhi - interval);
+      //if (atnum == ai) phi = currentPhi;
+      //IC.push_back( InternalCoords(atnum, aj, ak, al, 0, 0, currentPhi) );
+      if (debug_ > 0)
+        mprintf("DEBUG:\t\t\t%s (at# %i) phi= %g\n", topIn.AtomMaskName(atnum).c_str(), atnum+1, currentPhi*Constants::RADDEG);
+    }
+  }
 
   return 0;
 }
diff --git a/src/Structure/Model.h b/src/Structure/Model.h
index b43613b027..f57d9c1875 100644
--- a/src/Structure/Model.h
+++ b/src/Structure/Model.h
@@ -4,6 +4,7 @@
 //#incl ude "StructureEnum.h"
 class Topology;
 class Frame;
+class ParameterSet;
 //template <typename T> class ParmHolder;
 //class AtomType;
 namespace Cpptraj {
@@ -13,9 +14,12 @@ class InternalCoords;
 /// Routines to create a model for missing bond/angle/torsion parameters
 class Model {
   public:
-    Model() : debug_(0) {}
+    /// CONSTRUCTOR
+    Model();
     /// Set debug level
     void SetDebug(int d) { debug_ = d; }
+    /// Set optional parameter set
+    void SetParameters(ParameterSet const*);
     /// Assign a reasonable value for bond distance given 2 atoms whose position may or may not be known
     int AssignLength(double&, int, int, Topology const&, Frame const&, std::vector<bool> const&) const;
     /// Given atoms J and K, attempt to assign a reasonable value for theta for atom I
@@ -30,6 +34,7 @@ class Model {
                            BuildAtom const&) const;
   private:
     int debug_;
+    ParameterSet const* params_;
 };
 } // END namespace Structure
 } // END namespace Cpptraj
diff --git a/src/Structure/structuredepend b/src/Structure/structuredepend
index 55eb7e12ff..b944b35e4c 100644
--- a/src/Structure/structuredepend
+++ b/src/Structure/structuredepend
@@ -6,7 +6,7 @@ FxnGroupBuilder.o : FxnGroupBuilder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ..
 GenerateConnectivityArrays.o : GenerateConnectivityArrays.cpp ../Atom.h ../Constants.h ../CpptrajStdio.h ../NameType.h ../ParameterTypes.h ../Residue.h ../SymbolExporting.h GenerateConnectivityArrays.h
 HisProt.o : HisProt.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h HisProt.h StructureRoutines.h
 InternalCoords.o : InternalCoords.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h InternalCoords.h
-Model.o : Model.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h Model.h StructureEnum.h
+Model.o : Model.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h InternalCoords.h Model.h StructureEnum.h
 StructureEnum.o : StructureEnum.cpp StructureEnum.h
 StructureRoutines.o : StructureRoutines.cpp ../Atom.h ../CpptrajStdio.h ../NameType.h ../Residue.h ../SymbolExporting.h StructureRoutines.h
 Sugar.o : Sugar.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Sugar.h SugarToken.h
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 18fa7492c2..c3666e4073 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -453,7 +453,7 @@ Structure/FxnGroupBuilder.o : Structure/FxnGroupBuilder.cpp Atom.h AtomMask.h At
 Structure/GenerateConnectivityArrays.o : Structure/GenerateConnectivityArrays.cpp Atom.h Constants.h CpptrajStdio.h NameType.h ParameterTypes.h Residue.h Structure/GenerateConnectivityArrays.h SymbolExporting.h
 Structure/HisProt.o : Structure/HisProt.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/HisProt.h Structure/StructureRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/InternalCoords.o : Structure/InternalCoords.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/InternalCoords.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Structure/Model.o : Structure/Model.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h GuessAtomHybridization.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/Model.h Structure/StructureEnum.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Structure/Model.o : Structure/Model.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h GuessAtomHybridization.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/InternalCoords.h Structure/Model.h Structure/StructureEnum.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 Structure/StructureEnum.o : Structure/StructureEnum.cpp Structure/StructureEnum.h
 Structure/StructureRoutines.o : Structure/StructureRoutines.cpp Atom.h CpptrajStdio.h NameType.h Residue.h Structure/StructureRoutines.h SymbolExporting.h
 Structure/Sugar.o : Structure/Sugar.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h

From 9f8cf56a8727a4c8efed56cb5a6fe2f775b1e899 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 26 Jan 2024 12:25:10 -0500
Subject: [PATCH 0387/1492] Do J K ICs. Set unknown starting phi to interval.
 Improve debug messages

---
 src/Structure/Model.cpp   | 91 +++++++++++++++++++--------------------
 src/Structure/Zmatrix.cpp | 10 ++++-
 2 files changed, 54 insertions(+), 47 deletions(-)

diff --git a/src/Structure/Model.cpp b/src/Structure/Model.cpp
index 13bece2f81..55c0339fe9 100644
--- a/src/Structure/Model.cpp
+++ b/src/Structure/Model.cpp
@@ -428,7 +428,6 @@ int Cpptraj::Structure::Model::AssignICsAroundBond(std::vector<InternalCoords>&
                                                    BuildAtom const& AtomJ)
 const
 {
-  mprintf("DEBUG: ------------------------------------------------\n");
   mprintf("DEBUG: AssignICsAroundBond: X - %s - %s - %s  %i - %i - %i\n",
           topIn.AtomMaskName(aj).c_str(),
           topIn.AtomMaskName(ak).c_str(),
@@ -440,10 +439,10 @@ const
       !atomPositionKnown[al])
   {
     mprintf("Warning: AssignICsAroundBond(): Not all atom positions known.\n"
-            "Warning: %i (%i), %i (%i), %i (%i)\n",
-              aj+1, (int)atomPositionKnown[aj],
-              ak+1, (int)atomPositionKnown[ak],
-              al+1, (int)atomPositionKnown[al]);
+            "Warning: %i %s (%i) - %i %s (%i) - %i %s (%i)\n",
+              aj+1, topIn.AtomMaskName(aj).c_str(), (int)atomPositionKnown[aj],
+              ak+1, topIn.AtomMaskName(ak).c_str(), (int)atomPositionKnown[ak],
+              al+1, topIn.AtomMaskName(al).c_str(), (int)atomPositionKnown[al]);
     //return 1;
   }
   Atom const& AJ = topIn[aj];
@@ -542,6 +541,45 @@ const
   if (hasKnownInterval)
     mprintf("DEBUG:\t\tKnown interval = %g\n", knownInterval * Constants::RADDEG);
 
+  // Check known interval if set
+  if (hasKnownInterval) {
+    if (chirality == IS_UNKNOWN_CHIRALITY) {
+      mprintf("DEBUG:\t\tSetting chirality from known interval.\n");
+      if (knownInterval < 0)
+        chirality = IS_S;
+      else
+        chirality = IS_R;
+    } else if (chirality == IS_S) {
+      if (knownInterval > 0)
+        mprinterr("Error: Detected chirality S does not match known interval %g\n", knownInterval*Constants::RADDEG);
+    } else if (chirality == IS_R) {
+      if (knownInterval < 0)
+        mprinterr("Error: Detected chriality R does not match known interval %g\n", knownInterval*Constants::RADDEG);
+    }
+  }
+
+  // Determine the interval
+  bool intervalIsSet = false;
+  double interval = 0;
+  if (params_ != 0) {
+    ParmHolder<AtomType>::const_iterator it = params_->AT().GetParam( TypeNameHolder(AJ.Type()) );
+    if (it != params_->AT().end()) {
+      if (it->second.Hybridization() == AtomType::SP2) {
+        interval = 180 * Constants::DEGRAD;
+        intervalIsSet = true;
+      } else if (it->second.Hybridization() == AtomType::SP3) {
+        interval = 120 * Constants::DEGRAD;
+        intervalIsSet = true;
+      }
+    }
+    if (intervalIsSet) mprintf("DEBUG:\t\tInterval was set from atom J hybridization.\n");
+  }
+  if (!intervalIsSet) {
+    // The interval will be 360 / (number of bonds - 1)
+    interval = Constants::TWOPI / (AJ.Nbonds() - 1);
+    mprintf("DEBUG:\t\tInterval was set from number of bonds.\n");
+  }
+
   // If we have to assign an initial phi, make trans the longer branch
   if (knownIdx == -1) {
     std::vector<bool> visited = atomPositionKnown;
@@ -572,7 +610,7 @@ const
     }
     mprintf("DEBUG:\t\tLongest depth is for atom %s (%i)\n", topIn.AtomMaskName(priority[max_idx]).c_str(), max_depth);
     knownIdx = max_idx;
-    knownPhi[max_idx] = -180 * Constants::DEGRAD;
+    knownPhi[max_idx] = interval;// -180 * Constants::DEGRAD;
     isKnown[max_idx] = true;
   }
 
@@ -582,49 +620,10 @@ const
     return 1;
   }
 
-  // Determine the interval
-  bool intervalIsSet = false;
-  double interval = 0;
-  if (params_ != 0) {
-    ParmHolder<AtomType>::const_iterator it = params_->AT().GetParam( TypeNameHolder(AJ.Type()) );
-    if (it != params_->AT().end()) {
-      if (it->second.Hybridization() == AtomType::SP2) {
-        interval = 180 * Constants::DEGRAD;
-        intervalIsSet = true;
-      } else if (it->second.Hybridization() == AtomType::SP3) {
-        interval = 120 * Constants::DEGRAD;
-        intervalIsSet = true;
-      }
-    }
-    if (intervalIsSet) mprintf("DEBUG:\t\tInterval was set from atom J hybridization.\n");
-  }
-  if (!intervalIsSet) {
-    // The interval will be 360 / (number of bonds - 1)
-    interval = Constants::TWOPI / (AJ.Nbonds() - 1);
-    mprintf("DEBUG:\t\tInterval was set from number of bonds.\n");
-  }
-
-  // Check known interval if set
-  if (hasKnownInterval) {
-    if (chirality == IS_UNKNOWN_CHIRALITY) {
-      mprintf("DEBUG:\t\tSetting chirality from known interval.\n");
-      if (knownInterval < 0)
-        chirality = IS_S;
-      else
-        chirality = IS_R;
-    } else if (chirality == IS_S) {
-      if (knownInterval > 0)
-        mprinterr("Error: Detected chirality S does not match known interval %g\n", knownInterval*Constants::RADDEG);
-    } else if (chirality == IS_R) {
-      if (knownInterval < 0)
-        mprinterr("Error: Detected chriality R does not match known interval %g\n", knownInterval*Constants::RADDEG);
-    }
-  }
-
   // Adjust interval based on chirality and priority of the k atom
   if (chirality == IS_S || chirality == IS_UNKNOWN_CHIRALITY)
     interval = -interval;
-  if ( kPriorityIdx%2 ) {
+  if ( (kPriorityIdx%2) == 0 ) {
     mprintf("DEBUG:\t\tFlipping interval based on priority index of %i\n", kPriorityIdx);
     interval = -interval;
   }
diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index 026ecb2795..4d9fbbfbe3 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -1022,11 +1022,19 @@ int Zmatrix::SetupICsAroundBond(int atA, int atB, Frame const& frameIn, Topology
   //model.SetDebug( modelDebug ); //FIXME
   model.SetDebug( 1 );
   // FIXME
+  mprintf("DEBUG: ------------------------------------------------\n");
   std::vector<InternalCoords> tmpic;
+  // I J: Set up ICs for X atB K L
   if (model.AssignICsAroundBond(tmpic, atB, atk0, atl0, topIn, frameIn, atomPositionKnown, AtomB)) {
-    mprinterr("Error: AssignICsAroundBond failed.\n");
+    mprinterr("Error: AssignICsAroundBond (I J) failed.\n");
     return 1;
   }
+  // J K: Set up ICs for X atA atB K
+  if (model.AssignICsAroundBond(tmpic, atA, atB, atk0, topIn, frameIn, atomPositionKnown, AtomA)) {
+    mprinterr("Error: AssignICsAroundBond (J K) failed.\n");
+    return 1;
+  }
+  // Print ICs
   for (std::vector<InternalCoords>::const_iterator it = tmpic.begin(); it != tmpic.end(); ++it)
     it->printIC( topIn );
   mprintf("DEBUG: END AssignICsAroundBond ------------------------\n");

From b6a90519b73f0288e66c6079a71aeabd3017a0b5 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 26 Jan 2024 12:41:05 -0500
Subject: [PATCH 0388/1492] Actually add ICs

---
 src/Structure/Model.cpp | 35 +++++++++++++++++++++++++++++++++--
 src/Structure/Model.h   |  4 ++++
 2 files changed, 37 insertions(+), 2 deletions(-)

diff --git a/src/Structure/Model.cpp b/src/Structure/Model.cpp
index 55c0339fe9..f9af0becde 100644
--- a/src/Structure/Model.cpp
+++ b/src/Structure/Model.cpp
@@ -420,6 +420,34 @@ const
   return 0;
 }
 
+int Cpptraj::Structure::Model::insertIc(std::vector<InternalCoords>& IC,
+                                        int ai, int aj, int ak, int al, double newPhi,
+                                        Topology const& topIn, Frame const& frameIn,
+                                        std::vector<bool> const& atomPositionKnown)
+const
+{
+  if (atomPositionKnown[ai]) {
+    mprintf("DEBUG: Atom position already known for %s, skipping IC.\n", topIn.AtomMaskName(ai).c_str());
+    return 0;
+  }
+  double newDist = 0;
+  if (AssignLength(newDist, ai, aj, topIn, frameIn, atomPositionKnown)) {
+    mprinterr("Error: AssignLength failed for %s - %s \n",
+              topIn.AtomMaskName(ai).c_str(), topIn.AtomMaskName(aj).c_str());
+    return 1;
+  }
+  double newTheta = 0;
+  if (AssignTheta(newTheta, ai, aj, ak, topIn, frameIn, atomPositionKnown)) {
+    mprinterr("Error: AssignTheta failed for %s - %s - %s\n",
+              topIn.AtomMaskName(ai).c_str(),
+              topIn.AtomMaskName(aj).c_str(),
+              topIn.AtomMaskName(ak).c_str());
+    return 1;
+  }
+  IC.push_back( InternalCoords(ai, aj, ak, al, newDist, newTheta*Constants::RADDEG, newPhi*Constants::RADDEG) );
+  return 0;
+}
+
 /** Assign internal coordinates for atoms I for torsions around J-K-L. */
 int Cpptraj::Structure::Model::AssignICsAroundBond(std::vector<InternalCoords>& IC,
                                                    int aj, int ak, int al,
@@ -459,7 +487,8 @@ const
     for (int idx = 0; idx < AJ.Nbonds(); idx++) {
       if (AJ.Bond(idx) != ak) {
         int ai = AJ.Bond(idx);
-        double newDist = 0;
+        if (insertIc(IC, ai, aj, ak, al, newPhi, topIn, frameIn, atomPositionKnown)) return 1;
+/*        double newDist = 0;
         if (AssignLength(newDist, ai, aj, topIn, frameIn, atomPositionKnown)) {
           mprinterr("Error: AssignLength failed for %s - %s \n",
                     topIn.AtomMaskName(ai).c_str(), topIn.AtomMaskName(aj).c_str());
@@ -472,7 +501,7 @@ const
                     topIn.AtomMaskName(aj).c_str(),
                     topIn.AtomMaskName(ak).c_str());
         }
-        IC.push_back( InternalCoords(ai, aj, ak, al, newDist, newTheta, newPhi) );
+        IC.push_back( InternalCoords(ai, aj, ak, al, newDist, newTheta, newPhi) );*/
         break;
       }
     }
@@ -644,6 +673,7 @@ const
         currentPhi = wrap360(currentPhi + interval);
       //if (atnum == ai) phi = currentPhi;
       //IC.push_back( InternalCoords(atnum, aj, ak, al, 0, 0, currentPhi) );
+      if (insertIc(IC, atnum, aj, ak, al, currentPhi, topIn, frameIn, atomPositionKnown)) return 1;
       if (debug_ > 0)
         mprintf("DEBUG:\t\t\t%s (at# %i) phi= %g\n", topIn.AtomMaskName(atnum).c_str(), atnum+1, currentPhi*Constants::RADDEG);
     }
@@ -659,6 +689,7 @@ const
         currentPhi = wrap360(currentPhi - interval);
       //if (atnum == ai) phi = currentPhi;
       //IC.push_back( InternalCoords(atnum, aj, ak, al, 0, 0, currentPhi) );
+      if (insertIc(IC, atnum, aj, ak, al, currentPhi, topIn, frameIn, atomPositionKnown)) return 1;
       if (debug_ > 0)
         mprintf("DEBUG:\t\t\t%s (at# %i) phi= %g\n", topIn.AtomMaskName(atnum).c_str(), atnum+1, currentPhi*Constants::RADDEG);
     }
diff --git a/src/Structure/Model.h b/src/Structure/Model.h
index f57d9c1875..77044818eb 100644
--- a/src/Structure/Model.h
+++ b/src/Structure/Model.h
@@ -33,6 +33,10 @@ class Model {
                            Topology const&, Frame const&, std::vector<bool> const&,
                            BuildAtom const&) const;
   private:
+    int insertIc(std::vector<InternalCoords>&, int, int, int, int, double,
+                 Topology const&, Frame const&, std::vector<bool> const&) const;
+
+
     int debug_;
     ParameterSet const* params_;
 };

From 517eb5d488a863970b888f84d20dd1879f57a81c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 26 Jan 2024 12:53:06 -0500
Subject: [PATCH 0389/1492] Actually assign ICs, do K L ICs

---
 src/Structure/Zmatrix.cpp | 38 +++++++++++++++++++++++++++++---------
 1 file changed, 29 insertions(+), 9 deletions(-)

diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index 4d9fbbfbe3..a0a5a8ab93 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -1023,24 +1023,41 @@ int Zmatrix::SetupICsAroundBond(int atA, int atB, Frame const& frameIn, Topology
   model.SetDebug( 1 );
   // FIXME
   mprintf("DEBUG: ------------------------------------------------\n");
-  std::vector<InternalCoords> tmpic;
+  //std::vector<InternalCoords> tmpic;
   // I J: Set up ICs for X atB K L
-  if (model.AssignICsAroundBond(tmpic, atB, atk0, atl0, topIn, frameIn, atomPositionKnown, AtomB)) {
+  if (model.AssignICsAroundBond(IC_, atB, atk0, atl0, topIn, frameIn, atomPositionKnown, AtomB)) {
     mprinterr("Error: AssignICsAroundBond (I J) failed.\n");
     return 1;
   }
   // J K: Set up ICs for X atA atB K
-  if (model.AssignICsAroundBond(tmpic, atA, atB, atk0, topIn, frameIn, atomPositionKnown, AtomA)) {
+  if (model.AssignICsAroundBond(IC_, atA, atB, atk0, topIn, frameIn, atomPositionKnown, AtomA)) {
     mprinterr("Error: AssignICsAroundBond (J K) failed.\n");
     return 1;
   }
-  // Print ICs
-  for (std::vector<InternalCoords>::const_iterator it = tmpic.begin(); it != tmpic.end(); ++it)
-    it->printIC( topIn );
+  // K L: Set up ICs for X iat atA atB
+  Atom const& AJ1 = topIn[atA];
+  for (Atom::bond_iterator iat = AJ1.bondbegin(); iat != AJ1.bondend(); ++iat)
+  {
+    if (*iat != atB) {
+      BuildAtom AtomC;
+      if (topIn[*iat].Nbonds() > 2) {
+        if (AtomC.DetermineChirality(*iat, topIn, frameIn, modelDebug)) return 1;
+      }
+      if (model.AssignICsAroundBond(IC_, *iat, atA, atB, topIn, frameIn, atomPositionKnown, AtomC)) {
+        mprinterr("Error: AssignICsAroundBond (K L) failed.\n");
+        return 1;
+      }
+    }
+  }
+  // Mark/Print ICs
+  for (std::vector<InternalCoords>::const_iterator it = IC_.begin(); it != IC_.end(); ++it) {
+    it->printIC( topIn ); // DEBUG
+    MARK( it->AtI(), hasIC, nHasIC );
+  }
   mprintf("DEBUG: END AssignICsAroundBond ------------------------\n");
   // FIXME
   // ---- I J: Set dist, theta, phi for atA atB K L internal coord ---
-  if (debug_ > 0)
+/*  if (debug_ > 0)
     mprintf("DEBUG: IC (i j) %i - %i - %i - %i\n", atA+1, atB+1, atk0+1, atl0+1);
   double newDist = 0;
   if (model.AssignLength(newDist, atA, atB, topIn, frameIn, atomPositionKnown)) {
@@ -1067,7 +1084,8 @@ int Zmatrix::SetupICsAroundBond(int atA, int atB, Frame const& frameIn, Topology
     mprintf("DEBUG: MODEL I J IC: ");
     IC_.back().printIC(topIn);
   }
-  MARK( atA, hasIC, nHasIC );
+  MARK( atA, hasIC, nHasIC );*/
+/*
   // ----- J K: Set up ICs for X atA atB K ---------------------------
   Atom const& AJ1 = topIn[atA];
   int ati = -1;
@@ -1077,7 +1095,7 @@ int Zmatrix::SetupICsAroundBond(int atA, int atB, Frame const& frameIn, Topology
   {
     if (*iat != atB) {
       if (ati == -1) ati = *iat;
-      // Set bond dist
+/      // Set bond dist
       if (model.AssignLength(newDist, *iat, atA, topIn, frameIn, atomPositionKnown)) {
         mprinterr("Error: length (j k) assignment failed.\n");
         return 1;
@@ -1156,6 +1174,8 @@ int Zmatrix::SetupICsAroundBond(int atA, int atB, Frame const& frameIn, Topology
       } 
     }
   }
+*/
+
 /*
   // Handle remaining atoms.
   if (AJ1.Nbonds() > 1) {

From d50caaa3b61cf573e0a3fef42976402fe836721f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 27 Jan 2024 15:52:27 -0500
Subject: [PATCH 0390/1492] Try using known interval

---
 src/Structure/Model.cpp | 41 ++++++++++++++++++++---------------------
 1 file changed, 20 insertions(+), 21 deletions(-)

diff --git a/src/Structure/Model.cpp b/src/Structure/Model.cpp
index f9af0becde..c57338d3df 100644
--- a/src/Structure/Model.cpp
+++ b/src/Structure/Model.cpp
@@ -420,6 +420,7 @@ const
   return 0;
 }
 
+/** Insert internal coordinates with bond i-j, angle i-j-k, and torsion i-j-k-l. */
 int Cpptraj::Structure::Model::insertIc(std::vector<InternalCoords>& IC,
                                         int ai, int aj, int ak, int al, double newPhi,
                                         Topology const& topIn, Frame const& frameIn,
@@ -488,20 +489,6 @@ const
       if (AJ.Bond(idx) != ak) {
         int ai = AJ.Bond(idx);
         if (insertIc(IC, ai, aj, ak, al, newPhi, topIn, frameIn, atomPositionKnown)) return 1;
-/*        double newDist = 0;
-        if (AssignLength(newDist, ai, aj, topIn, frameIn, atomPositionKnown)) {
-          mprinterr("Error: AssignLength failed for %s - %s \n",
-                    topIn.AtomMaskName(ai).c_str(), topIn.AtomMaskName(aj).c_str());
-          return 1;
-        }
-        double newTheta = 0;
-        if (AssignTheta(newTheta, ai, aj, ak, topIn, frameIn, atomPositionKnown)) {
-          mprinterr("Error: AssignTheta failed for %s - %s - %s\n",
-                    topIn.AtomMaskName(ai).c_str(),
-                    topIn.AtomMaskName(aj).c_str(),
-                    topIn.AtomMaskName(ak).c_str());
-        }
-        IC.push_back( InternalCoords(ai, aj, ak, al, newDist, newTheta, newPhi) );*/
         break;
       }
     }
@@ -511,17 +498,15 @@ const
   // 3 or more bonds.
   std::vector<int> const& priority = AtomJ.Priority();
   ChiralType chirality = AtomJ.Chirality();
-  if (chirality == IS_UNKNOWN_CHIRALITY) {
-    chirality = AtomJ.Orientation();
-    mprintf("Warning: Unknown chirality around %s; using detected orientation of %s\n",
-            topIn.AtomMaskName(aj).c_str(), chiralStr(chirality));
-  }
+
   if (debug_ > 0) {
     mprintf("DEBUG:\t\tOriginal chirality around J %s is %s\n", topIn.AtomMaskName(aj).c_str(), chiralStr(chirality));
     mprintf("DEBUG:\t\tPriority around J %s(%i) is", 
             topIn.AtomMaskName(aj).c_str(), (int)atomPositionKnown[aj]);
     for (int idx = 0; idx < AJ.Nbonds(); idx++)
       mprintf(" %s(%i)", topIn.AtomMaskName(priority[idx]).c_str(), (int)atomPositionKnown[priority[idx]]);
+    for (int idx = 0; idx < AJ.Nbonds(); idx++)
+      mprintf(" %i", priority[idx]);
     mprintf("\n");
   }
 
@@ -567,11 +552,10 @@ const
       }
     }
   }
-  if (hasKnownInterval)
-    mprintf("DEBUG:\t\tKnown interval = %g\n", knownInterval * Constants::RADDEG);
 
   // Check known interval if set
   if (hasKnownInterval) {
+    mprintf("DEBUG:\t\tKnown interval = %g\n", knownInterval * Constants::RADDEG);
     if (chirality == IS_UNKNOWN_CHIRALITY) {
       mprintf("DEBUG:\t\tSetting chirality from known interval.\n");
       if (knownInterval < 0)
@@ -587,6 +571,13 @@ const
     }
   }
 
+  // If still no chirality use the detected orientation
+  if (chirality == IS_UNKNOWN_CHIRALITY) {
+    chirality = AtomJ.Orientation();
+    mprintf("Warning: Unknown chirality around %s; using detected orientation of %s\n",
+            topIn.AtomMaskName(aj).c_str(), chiralStr(chirality));
+  }
+
   // Determine the interval
   bool intervalIsSet = false;
   double interval = 0;
@@ -609,6 +600,14 @@ const
     mprintf("DEBUG:\t\tInterval was set from number of bonds.\n");
   }
 
+  // If there is a known interval, compare it to the determined one.
+  if (hasKnownInterval) {
+    double deltaInterval = fabs(interval - knownInterval);
+    mprintf("DEBUG:\t\tDetermined interval %g, known interval %g, delta %g\n",
+            interval*Constants::RADDEG, knownInterval*Constants::RADDEG, deltaInterval*Constants::RADDEG);
+    interval = fabs(knownInterval);
+  }
+
   // If we have to assign an initial phi, make trans the longer branch
   if (knownIdx == -1) {
     std::vector<bool> visited = atomPositionKnown;

From 45999894877270369aa84067dc009754f695aa70 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 27 Jan 2024 16:03:09 -0500
Subject: [PATCH 0391/1492] Adjust interval before know interval is used

---
 src/Structure/Model.cpp | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/Structure/Model.cpp b/src/Structure/Model.cpp
index c57338d3df..5f1cbbd336 100644
--- a/src/Structure/Model.cpp
+++ b/src/Structure/Model.cpp
@@ -600,6 +600,14 @@ const
     mprintf("DEBUG:\t\tInterval was set from number of bonds.\n");
   }
 
+  // Adjust interval based on chirality and priority of the k atom
+  if (chirality == IS_S || chirality == IS_UNKNOWN_CHIRALITY)
+    interval = -interval;
+  if ( (kPriorityIdx%2) == 0 ) {
+    mprintf("DEBUG:\t\tFlipping interval based on priority index of %i\n", kPriorityIdx);
+    interval = -interval;
+  }
+
   // If there is a known interval, compare it to the determined one.
   if (hasKnownInterval) {
     double deltaInterval = fabs(interval - knownInterval);
@@ -648,14 +656,6 @@ const
     return 1;
   }
 
-  // Adjust interval based on chirality and priority of the k atom
-  if (chirality == IS_S || chirality == IS_UNKNOWN_CHIRALITY)
-    interval = -interval;
-  if ( (kPriorityIdx%2) == 0 ) {
-    mprintf("DEBUG:\t\tFlipping interval based on priority index of %i\n", kPriorityIdx);
-    interval = -interval;
-  }
-
   if (debug_ > 0) {
     mprintf("DEBUG:\t\tStart phi is %g degrees\n", knownPhi[knownIdx]*Constants::RADDEG);
     mprintf("DEBUG:\t\tInterval is %g, chirality around J is %s\n", interval*Constants::RADDEG, chiralStr(chirality));

From e70ebecbee907135dd5e9f3844277fd8c9f6dd96 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 28 Jan 2024 15:47:37 -0500
Subject: [PATCH 0392/1492] Only set K L IC if another IC does not cover it

---
 src/Structure/Builder.cpp | 14 +++++++++++---
 src/Structure/Zmatrix.cpp | 27 +++++++++++++++++++++++----
 src/Structure/Zmatrix.h   |  3 ++-
 3 files changed, 36 insertions(+), 8 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index d7066cc435..2a2d0cdc4f 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -51,7 +51,6 @@ const
   // Combine fragment1 into fragment 0 topology
   Topology& combinedTop = frag0Top;
   combinedTop.AppendTop( frag1Top );
-  zmatrixA.print( &combinedTop );
   // Combined fragment1 into fragment 0 coords.
   // Need to save the original coords in frame0 since SetupFrameV does not preserve.
   double* tmpcrd0 = new double[natom0*3];
@@ -99,20 +98,28 @@ const
   // Generate Zmatrix only for ICs involving bonded atoms
   Zmatrix bondZmatrix;
 
+  // Note which atoms already have an IC in zmatrixA
+  std::vector<bool> hasIC(combinedTop.Natom(), false);
+  for (Zmatrix::const_iterator it = zmatrixA.begin(); it != zmatrixA.end(); ++it)
+    hasIC[it->AtI()] = true;
+
   //bondZmatrix.SetDebug( debug_ );
   bondZmatrix.SetDebug( 1 ); // FIXME
-  if (bondZmatrix.SetupICsAroundBond(atA, atB, CombinedFrame, combinedTop, posKnown, AtomA, AtomB)) {
+  if (bondZmatrix.SetupICsAroundBond(atA, atB, CombinedFrame, combinedTop, posKnown, hasIC, AtomA, AtomB)) {
     mprinterr("Error: Zmatrix setup for ICs around %s and %s failed.\n",
               combinedTop.AtomMaskName(atA).c_str(),
               combinedTop.AtomMaskName(atB).c_str());
     return 1;
   }
+  mprintf("DEBUG: CONVERT WITH bondZmatrix.\n");
   //if (debug_ > 0)
     bondZmatrix.print(&combinedTop);
   if (bondZmatrix.SetToFrame( CombinedFrame, posKnown )) {
     mprinterr("Error: Conversion from bondZmatrix to Cartesian coords failed.\n");
     return 1;
   }
+  mprintf("DEBUG: CONVERT WITH zmatrixA.\n");
+  zmatrixA.print( &combinedTop );
   if (zmatrixA.SetToFrame( CombinedFrame, posKnown )) {
     mprinterr("Error: Conversion from zmatrixA to Cartesian coords failed.\n");
     return 1;
@@ -183,7 +190,8 @@ int Builder::ModelCoordsAroundBond(Frame& frameIn, Topology const& topIn, int bo
   Zmatrix bondZmatrix;
 
   bondZmatrix.SetDebug( debug_ );
-  if (bondZmatrix.SetupICsAroundBond(atA, atB, frameIn, topIn, hasPosition, AtomA, AtomB)) {
+  std::vector<bool> hasIC(topIn.Natom(), false); // FIXME
+  if (bondZmatrix.SetupICsAroundBond(atA, atB, frameIn, topIn, hasPosition, hasIC, AtomA, AtomB)) {
     mprinterr("Error: Zmatrix setup for ICs around %s and %s failed.\n",
               topIn.AtomMaskName(atA).c_str(),
               topIn.AtomMaskName(atB).c_str());
diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index a0a5a8ab93..0be0bd2c45 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -951,6 +951,7 @@ int Zmatrix::SetFromFrame(Frame const& frameIn, Topology const& topIn, int molnu
   */
 int Zmatrix::SetupICsAroundBond(int atA, int atB, Frame const& frameIn, Topology const& topIn,
                                 std::vector<bool> const& atomPositionKnown,
+                                std::vector<bool> const& hasICin,
                                 BuildAtom const& AtomA, BuildAtom const& AtomB)
 {
   if (debug_ > 0)
@@ -960,8 +961,15 @@ int Zmatrix::SetupICsAroundBond(int atA, int atB, Frame const& frameIn, Topology
             topIn.Natom());
   IC_.clear();
 
-  Barray hasIC( topIn.Natom(), false );
+  //Barray hasIC( topIn.Natom(), false );
+  Barray hasIC = hasICin;
   unsigned int nHasIC = 0;
+  for (std::vector<bool>::const_iterator it = hasIC.begin(); it != hasIC.end(); ++it) {
+    if (*it) {
+      nHasIC++;
+      mprintf("DEBUG:\tAtom %s already has an IC.\n", topIn.AtomMaskName(it-hasIC.begin()).c_str());
+    }
+  }
   // Mark known atoms as already having IC
   for (std::vector<bool>::const_iterator it = atomPositionKnown.begin();
                                          it != atomPositionKnown.end(); ++it)
@@ -1043,9 +1051,20 @@ int Zmatrix::SetupICsAroundBond(int atA, int atB, Frame const& frameIn, Topology
       if (topIn[*iat].Nbonds() > 2) {
         if (AtomC.DetermineChirality(*iat, topIn, frameIn, modelDebug)) return 1;
       }
-      if (model.AssignICsAroundBond(IC_, *iat, atA, atB, topIn, frameIn, atomPositionKnown, AtomC)) {
-        mprinterr("Error: AssignICsAroundBond (K L) failed.\n");
-        return 1;
+      // Only do this if one or more of the atoms bonded to iat does not
+      // already have an IC.
+      unsigned int needsKLic = 0;
+      for (Atom::bond_iterator bat = topIn[*iat].bondbegin(); bat != topIn[*iat].bondend(); ++bat)
+        if ( *bat != atA && !hasIC[*bat] )
+          needsKLic++;
+      if (needsKLic > 0) {
+        mprintf("DEBUG: K L IC needed.\n");
+        if (model.AssignICsAroundBond(IC_, *iat, atA, atB, topIn, frameIn, atomPositionKnown, AtomC)) {
+          mprinterr("Error: AssignICsAroundBond (K L) failed.\n");
+          return 1;
+        }
+      } else {
+        mprintf("DEBUG: K L IC not needed.\n");
       }
     }
   }
diff --git a/src/Structure/Zmatrix.h b/src/Structure/Zmatrix.h
index d60ff50ddd..80ba9d61af 100644
--- a/src/Structure/Zmatrix.h
+++ b/src/Structure/Zmatrix.h
@@ -51,7 +51,8 @@ class Zmatrix {
     int SetFromFrame(Frame const&, Topology const&);
     /// Get internal coordinates around bond in one direction.
     int SetupICsAroundBond(int, int, Frame const&, Topology const&,
-                           std::vector<bool> const&, BuildAtom const&, BuildAtom const&);
+                           std::vector<bool> const&, std::vector<bool> const&,
+                           BuildAtom const&, BuildAtom const&);
 
     /// Set Frame from internal coords
     int SetToFrame(Frame&) const;

From 36da8acd8ac4db77d9e2443e3e356601c650e35e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 29 Jan 2024 10:05:17 -0500
Subject: [PATCH 0393/1492] Add debug info. Note which atoms have an IC
 associated and do not need an IC when modeling ICs around a bond.

---
 src/Exec_Build.cpp        | 15 +++++++++------
 src/Structure/Builder.cpp | 22 ++++++++++++++++++----
 src/Structure/Builder.h   |  3 ++-
 src/Structure/Model.cpp   |  2 +-
 src/Structure/Zmatrix.cpp | 11 +++++++----
 5 files changed, 37 insertions(+), 16 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 39afa8a282..5dee723fad 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -380,17 +380,23 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
     if (zmatrix != 0) {
       mprintf("DEBUG: BUILD residue %li %s\n", ires + 1, topOut.TruncResNameOnumId(ires).c_str());
       mprintf("DEBUG: Residue type: %s terminal\n", Cpptraj::Structure::terminalStr(*termType));
+      mprintf("DEBUG: Zmatrix for building residue %li %s\n", ires + 1,
+              topOut.TruncResNameOnumId(ires).c_str());
+      zmatrix->print(&topOut);
       // Is this residue connected to an earlier residue?
       if ( *termType != Cpptraj::Structure::BEG_TERMINAL ) {
         for (int at = topOut.Res(ires).FirstAtom(); at != topOut.Res(ires).LastAtom(); ++at)
         {
           for (Atom::bond_iterator bat = topOut[at].bondbegin(); bat != topOut[at].bondend(); ++bat)
           {
-            if ((long int)topOut[*bat].ResNum() < ires) {
-              mprintf("DEBUG: Connected to residue %i\n", topOut[*bat].ResNum());
+            long int jres = (long int)topOut[*bat].ResNum();
+            if (jres < ires) {
+              mprintf("DEBUG: Connected to residue %s\n", topOut.TruncResNameNum(jres).c_str());
               Cpptraj::Structure::Builder linkBuilder;
               linkBuilder.SetDebug( 1 ); // FIXME
-              if (linkBuilder.ModelCoordsAroundBond(frameOut, topOut, at, *bat, hasPosition)) {
+              if (linkBuilder.ModelCoordsAroundBond(frameOut, topOut, at, *bat,
+                                                    zmatrix, ResZmatrices[jres], hasPosition))
+              {
                 mprinterr("Error: Model coords around bond failed between %s and %s\n",
                           topOut.AtomMaskName(at).c_str(), topOut.AtomMaskName(*bat).c_str());
                 return 1;
@@ -405,9 +411,6 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
 //        mprinterr("Error: Failed to create zmatrix from topology.\n");
 //        return 1;
 //      }
-      mprintf("DEBUG: Zmatrix for building residue %li %s\n", ires + 1,
-              topOut.TruncResNameOnumId(ires).c_str());
-      zmatrix->print(&topOut);
       // Update internal coords from known positions
       if (zmatrix->UpdateICsFromFrame( frameOut, ires, topOut, hasPosition )) {
         mprinterr("Error: Failed to update Zmatrix with values from existing positions.\n");
diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 2a2d0cdc4f..27713b5c1b 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -128,6 +128,7 @@ const
   return 0;
 }
 
+/// \return The total number of atoms whose position is known for the specified residue
 static inline int known_count(int ires, Topology const& topIn, std::vector<bool> const& hasPosition)
 {
   int count = 0;
@@ -138,7 +139,10 @@ static inline int known_count(int ires, Topology const& topIn, std::vector<bool>
 }
 
 /** Model the coordinates around a bond */
-int Builder::ModelCoordsAroundBond(Frame& frameIn, Topology const& topIn, int bondAt0, int bondAt1, Barray& hasPosition) const {
+int Builder::ModelCoordsAroundBond(Frame& frameIn, Topology const& topIn, int bondAt0, int bondAt1,
+                                   Zmatrix const* zmatrix0, Zmatrix const* zmatrix1, Barray& hasPosition)
+const
+{
   mprintf("DEBUG: Model coords around bond %s - %s\n", topIn.AtomMaskName(bondAt0).c_str(), topIn.AtomMaskName(bondAt1).c_str());
   int res0 = topIn[bondAt0].ResNum();
   int res1 = topIn[bondAt1].ResNum();
@@ -151,19 +155,23 @@ int Builder::ModelCoordsAroundBond(Frame& frameIn, Topology const& topIn, int bo
   int known0 = known_count(res0, topIn, hasPosition);
   int known1 = known_count(res1, topIn, hasPosition);
   int atA, atB;
-
+  Zmatrix const* zA;
   if (known0 < known1) {
     // Fragment 1 is better-known 
     atA = bondAt0;
     atB = bondAt1;
+    zA  = zmatrix0;
+    //zB  = zmatrix1;
   } else {
     // Fragment 0 is better or equally known 
     atA = bondAt1;
     atB = bondAt0;
+    zA  = zmatrix1;
+    //zB  = zmatrix0;
   }
 
   mprintf("DEBUG: More well-known atom: %s\n", topIn.AtomMaskName(atB).c_str());
-  mprintf("DEBUG: Less well-known atom: %s\n", topIn.AtomMaskName(atA).c_str());
+  mprintf("DEBUG: Less well-known atom: %s  has zmatrix= %i\n", topIn.AtomMaskName(atA).c_str(), (int)(zA != 0));
 
   int chiralityDebug;
   if (debug_ < 1)
@@ -189,8 +197,14 @@ int Builder::ModelCoordsAroundBond(Frame& frameIn, Topology const& topIn, int bo
   // Generate Zmatrix only for ICs involving bonded atoms
   Zmatrix bondZmatrix;
 
+  // Note which atoms already have an IC in zmatrix A
+  std::vector<bool> hasIC(topIn.Natom(), false);
+  if (zA != 0) {
+    for (Zmatrix::const_iterator it = zA->begin(); it != zA->end(); ++it)
+      hasIC[it->AtI()] = true;
+  }
+
   bondZmatrix.SetDebug( debug_ );
-  std::vector<bool> hasIC(topIn.Natom(), false); // FIXME
   if (bondZmatrix.SetupICsAroundBond(atA, atB, frameIn, topIn, hasPosition, hasIC, AtomA, AtomB)) {
     mprinterr("Error: Zmatrix setup for ICs around %s and %s failed.\n",
               topIn.AtomMaskName(atA).c_str(),
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index 705902f005..bb82d47af7 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -5,6 +5,7 @@ class Topology;
 class Frame;
 namespace Cpptraj {
 namespace Structure {
+class Zmatrix;
 /// Used to attach different topology/frame combos using internal coordinates
 class Builder {
     typedef std::vector<bool> Barray;
@@ -14,7 +15,7 @@ class Builder {
     /// Combine second fragment into first fragment and bond
     int Combine(Topology&, Frame&, Topology const&, Frame const&, int, int) const;
     /// Model the coordinates around a bond given only some coordinates are known
-    int ModelCoordsAroundBond(Frame&, Topology const&, int, int, Barray&) const;
+    int ModelCoordsAroundBond(Frame&, Topology const&, int, int, Zmatrix const*, Zmatrix const*, Barray&) const;
     /// Set debug
     void SetDebug(int d) { debug_ = d; }
   private:
diff --git a/src/Structure/Model.cpp b/src/Structure/Model.cpp
index 5f1cbbd336..50f700a506 100644
--- a/src/Structure/Model.cpp
+++ b/src/Structure/Model.cpp
@@ -428,7 +428,7 @@ int Cpptraj::Structure::Model::insertIc(std::vector<InternalCoords>& IC,
 const
 {
   if (atomPositionKnown[ai]) {
-    mprintf("DEBUG: Atom position already known for %s, skipping IC.\n", topIn.AtomMaskName(ai).c_str());
+    mprintf("DEBUG:\tAtom position already known for %s, skipping IC.\n", topIn.AtomMaskName(ai).c_str());
     return 0;
   }
   double newDist = 0;
diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index 0be0bd2c45..a5ac85a720 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -1054,17 +1054,20 @@ int Zmatrix::SetupICsAroundBond(int atA, int atB, Frame const& frameIn, Topology
       // Only do this if one or more of the atoms bonded to iat does not
       // already have an IC.
       unsigned int needsKLic = 0;
-      for (Atom::bond_iterator bat = topIn[*iat].bondbegin(); bat != topIn[*iat].bondend(); ++bat)
-        if ( *bat != atA && !hasIC[*bat] )
+      for (Atom::bond_iterator bat = topIn[*iat].bondbegin(); bat != topIn[*iat].bondend(); ++bat) {
+        if ( *bat != atA && !hasIC[*bat] ) {
+          mprintf("DEBUG:\tAtom %s around %s has no IC.\n", topIn.AtomMaskName(*bat).c_str(), topIn.AtomMaskName(*iat).c_str());
           needsKLic++;
+        }
+      }
       if (needsKLic > 0) {
-        mprintf("DEBUG: K L IC needed.\n");
+        mprintf("DEBUG: K L IC needed for %s.\n", topIn.AtomMaskName(*iat).c_str());
         if (model.AssignICsAroundBond(IC_, *iat, atA, atB, topIn, frameIn, atomPositionKnown, AtomC)) {
           mprinterr("Error: AssignICsAroundBond (K L) failed.\n");
           return 1;
         }
       } else {
-        mprintf("DEBUG: K L IC not needed.\n");
+        mprintf("DEBUG: K L IC not needed for %s.\n", topIn.AtomMaskName(*iat).c_str());
       }
     }
   }

From de37f18f16c483b3fe8be701e3323b8d2de906e4 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 29 Jan 2024 10:21:14 -0500
Subject: [PATCH 0394/1492] Update again, fixed KL IC behavior

---
 test/Test_Sequence/Mol.mol2.save | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/test/Test_Sequence/Mol.mol2.save b/test/Test_Sequence/Mol.mol2.save
index 482c8198c5..c1b6440f8a 100644
--- a/test/Test_Sequence/Mol.mol2.save
+++ b/test/Test_Sequence/Mol.mol2.save
@@ -7,9 +7,9 @@ USER_CHARGES
 
 @<TRIPOS>ATOM
       1 C1         -1.9010   -1.2979   -0.5927 CT         1 MOC      1.387300
-      2 H2         -2.3121   -2.1475   -1.1378 H1         1 MOC     -0.288000
-      3 H3         -2.2811   -0.3718   -1.0240 H1         1 MOC     -0.288000
-      4 H4         -2.1989   -1.3598    0.4539 H1         1 MOC     -0.288000
+      2 H2         -2.2470   -2.2143   -0.1146 H1         1 MOC     -0.288000
+      3 H3         -2.3292   -1.2263   -1.5925 H1         1 MOC     -0.288000
+      4 H4         -2.2160   -0.4385   -0.0008 H1         1 MOC     -0.288000
       5 O5         -0.4741   -1.3169   -0.6848 OS         1 MOC     -0.523200
       6 N           0.0540   -0.2256    0.0153 N          2 CNALA   -0.570310
       7 H          -0.4149    0.5139    0.5357 H          2 CNALA    0.364710

From 1f7209f68649c3c3a1428db9549b296ae4edcdfe Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 29 Jan 2024 11:04:25 -0500
Subject: [PATCH 0395/1492] Make sequence search more expansive

---
 src/Exec_Sequence.cpp     | 7 ++++++-
 src/Structure/Zmatrix.cpp | 2 +-
 2 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/src/Exec_Sequence.cpp b/src/Exec_Sequence.cpp
index 47e2b737a2..89127f23cb 100644
--- a/src/Exec_Sequence.cpp
+++ b/src/Exec_Sequence.cpp
@@ -25,7 +25,12 @@ const
     DataSet_Coords* unit = 0;
     if (LibSetNames.empty()) {
       // Look for name
-      unit = (DataSet_Coords*)DSL.FindSetOfGroup( *it, DataSet::COORDINATES );
+      unit = (DataSet_Coords*)DSL.FindSetOfGroup( *it, DataSet::COORDINATES ); // FIXME need new set type
+      if (unit == 0) {
+        // Look for *[name]
+        std::string searchStr("*[" + *it + "]");
+        unit = (DataSet_Coords*)DSL.FindSetOfGroup( searchStr, DataSet::COORDINATES ); // FIXME need new set type
+      }
     } else {
       // Look for name[aspect]
       DataSet* ds = 0;
diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index a5ac85a720..2029906dda 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -1429,7 +1429,7 @@ int Zmatrix::SetToFrame(Frame& frameOut, Barray& hasPosition) const {
       continue; // FIXME
     }
     InternalCoords const& ic = IC_[icIdx];
-    if (debug_ > 0)
+    //if (debug_ > 0)
       mprintf("DEBUG: Next IC to use is %i : %i %i %i %i r=%g theta=%g phi=%g\n",
               icIdx+1, ic.AtI()+1, ic.AtJ()+1, ic.AtK()+1, ic.AtL()+1,
               ic.Dist(), ic.Theta(), ic.Phi());

From 8d4d77a45022bd98f3fbc63a97a612f4841cc629 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 29 Jan 2024 13:13:55 -0500
Subject: [PATCH 0396/1492] Add HasType function

---
 src/Atom.h         | 1 +
 src/Parm_Amber.cpp | 2 +-
 src/Topology.cpp   | 6 +++---
 3 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/src/Atom.h b/src/Atom.h
index ddc79dad78..8d6432508e 100644
--- a/src/Atom.h
+++ b/src/Atom.h
@@ -81,6 +81,7 @@ class Atom {
     inline double ElementRadius()      const { return AtomicElementRadius_[element_]; }
     inline const NameType& Name()      const { return aname_; }
     inline const NameType& Type()      const { return atype_; }
+    inline bool HasType()              const { return (atype_.len() > 0); }
     inline int TypeIndex()             const { return atype_index_; }
     inline int MolNum()                const { return mol_; }
     inline int Nbonds()                const { return (int)bonds_.size(); }
diff --git a/src/Parm_Amber.cpp b/src/Parm_Amber.cpp
index c012e2278a..9f2b903bfb 100644
--- a/src/Parm_Amber.cpp
+++ b/src/Parm_Amber.cpp
@@ -2174,7 +2174,7 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
   // Check that atoms actually have a type.
   int NemptyTypes = 0;
   for (Topology::atom_iterator atm = TopOut.begin(); atm != TopOut.end(); ++atm) {
-    if (atm->Type().len() < 1) ++NemptyTypes;
+    if (!atm->HasType()) ++NemptyTypes;
     file_.CharToBuffer( *(atm->Type()) );
   }
   file_.FlushBuffer();
diff --git a/src/Topology.cpp b/src/Topology.cpp
index 051e6b3d42..121e038b80 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -53,7 +53,7 @@ unsigned int Topology::NuniqueAtomTypes() const {
   ParmHolder<int> currentAtomTypes;
   for (std::vector<Atom>::const_iterator atm = atoms_.begin(); atm != atoms_.end(); ++atm)
   {
-    if (atm->Type().len() > 0) {
+    if (atm->HasType()) {
       TypeNameHolder atype( atm->Type() );
       // Find in currentAtomTypes.
       bool found;
@@ -2310,7 +2310,7 @@ static inline void GetLJAtomTypes( ParmHolder<AtomType>& atomTypes, ParmHolder<N
     mprintf("DEBUG: Topology does not have nonbond parameters.\n");
     // No nonbonded parameters. Just save mass/polarizability.
     for (std::vector<Atom>::const_iterator atm = atoms.begin(); atm != atoms.end(); ++atm)
-      if (atm->Type().len() > 0)
+      if (atm->HasType() > 0)
         atomTypes.AddParm( TypeNameHolder(atm->Type()), AtomType(atm->Mass(), atm->Polar()), true );
   }
 }
@@ -3022,7 +3022,7 @@ void Topology::AssignNonbondParams(ParmHolder<AtomType> const& newTypes,
   ParmHolder<AtomType> currentAtomTypes;
   for (std::vector<Atom>::const_iterator atm = atoms_.begin(); atm != atoms_.end(); ++atm)
   {
-    if (atm->Type().len() > 0) {
+    if (atm->HasType()) {
       TypeNameHolder types(1);
       types.AddName(atm->Type());
       // Find in newTypes.

From 083ffd54314385c2bb78cc08948e953f63e849df Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 29 Jan 2024 14:04:07 -0500
Subject: [PATCH 0397/1492] Add code to get bond lengths from parameters if
 they are present. Only calc AtomC chirality if actually doing K L IC

---
 src/Structure/Model.cpp   | 23 ++++++++++++++++++++---
 src/Structure/Zmatrix.cpp |  8 ++++----
 2 files changed, 24 insertions(+), 7 deletions(-)

diff --git a/src/Structure/Model.cpp b/src/Structure/Model.cpp
index 50f700a506..9629b791dd 100644
--- a/src/Structure/Model.cpp
+++ b/src/Structure/Model.cpp
@@ -31,9 +31,26 @@ const
 {
   if (atomPositionKnown[ai] && atomPositionKnown[aj])
     dist = sqrt( DIST2_NoImage( frameIn.XYZ(ai), frameIn.XYZ(aj) ) );
-  else
-    // One or both positions unknown. Use bond length. TODO use parameters
-    dist = Atom::GetBondLength( topIn[ai].Element(), topIn[aj].Element() );
+  else {
+    // One or both positions unknown. Use estimated bond length or parameters.
+    bool foundParam = false;
+    if (params_ != 0 && topIn[ai].HasType() && topIn[aj].HasType()) {
+      TypeNameHolder btypes(2);
+      btypes.AddName( topIn[ai].Type() );
+      btypes.AddName( topIn[aj].Type() );
+      ParmHolder<BondParmType>::const_iterator it = params_->BP().GetParam( btypes );
+      if (it != params_->BP().end()) {
+        dist = it->second.Req();
+        foundParam = true;
+        mprintf("DEBUG: Found bond parameter for %s (%s) - %s (%s): req=%g rk=%g\n",
+                topIn.AtomMaskName(ai).c_str(), *(topIn[ai].Type()),
+                topIn.AtomMaskName(aj).c_str(), *(topIn[aj].Type()),
+                it->second.Req(), it->second.Rk());
+      }
+    }
+    if (!foundParam)
+      dist = Atom::GetBondLength( topIn[ai].Element(), topIn[aj].Element() );
+  }
   return 0;
 }
 
diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index 2029906dda..f623d82374 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -1047,10 +1047,6 @@ int Zmatrix::SetupICsAroundBond(int atA, int atB, Frame const& frameIn, Topology
   for (Atom::bond_iterator iat = AJ1.bondbegin(); iat != AJ1.bondend(); ++iat)
   {
     if (*iat != atB) {
-      BuildAtom AtomC;
-      if (topIn[*iat].Nbonds() > 2) {
-        if (AtomC.DetermineChirality(*iat, topIn, frameIn, modelDebug)) return 1;
-      }
       // Only do this if one or more of the atoms bonded to iat does not
       // already have an IC.
       unsigned int needsKLic = 0;
@@ -1061,6 +1057,10 @@ int Zmatrix::SetupICsAroundBond(int atA, int atB, Frame const& frameIn, Topology
         }
       }
       if (needsKLic > 0) {
+        BuildAtom AtomC;
+        if (topIn[*iat].Nbonds() > 2) {
+          if (AtomC.DetermineChirality(*iat, topIn, frameIn, modelDebug)) return 1;
+        }
         mprintf("DEBUG: K L IC needed for %s.\n", topIn.AtomMaskName(*iat).c_str());
         if (model.AssignICsAroundBond(IC_, *iat, atA, atB, topIn, frameIn, atomPositionKnown, AtomC)) {
           mprinterr("Error: AssignICsAroundBond (K L) failed.\n");

From daa8bd64e7812edeec67462ef3f046d7901711e2 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 29 Jan 2024 15:10:27 -0500
Subject: [PATCH 0398/1492] Add parameter set var

---
 src/Structure/Builder.cpp | 3 ++-
 src/Structure/Builder.h   | 4 ++++
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 27713b5c1b..10fe1b6341 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -10,7 +10,8 @@ using namespace Cpptraj::Structure;
 
 /** CONSTRUCTOR */
 Builder::Builder() :
-  debug_(0)
+  debug_(0),
+  params_(0)
 {}
 
 /** Combine two units. Fragment 1 will be merged into Fragment 0 and bonded. */
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index bb82d47af7..4f596662af 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -3,6 +3,7 @@
 #include <vector>
 class Topology;
 class Frame;
+class ParameterSet;
 namespace Cpptraj {
 namespace Structure {
 class Zmatrix;
@@ -18,9 +19,12 @@ class Builder {
     int ModelCoordsAroundBond(Frame&, Topology const&, int, int, Zmatrix const*, Zmatrix const*, Barray&) const;
     /// Set debug
     void SetDebug(int d) { debug_ = d; }
+    /// Set optional parameter set
+    void SetParameters(ParameterSet const*);
   private:
 
     int debug_;
+    ParameterSet const* params_;
 };
 }
 }

From 285bdf5a06ecb044244d73075fb959bbee2faefe Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 29 Jan 2024 15:30:24 -0500
Subject: [PATCH 0399/1492] Move SetupICsAroundBond into Builder

---
 src/Structure/Builder.cpp     | 307 +++++++++++++++++++++++++++++++++-
 src/Structure/Builder.h       |   4 +
 src/Structure/Model.cpp       |  14 +-
 src/Structure/Model.h         |   6 +-
 src/Structure/Zmatrix.cpp     | 302 +--------------------------------
 src/Structure/Zmatrix.h       |   6 -
 src/Structure/structuredepend |   6 +-
 src/cpptrajdepend             |   6 +-
 8 files changed, 326 insertions(+), 325 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 10fe1b6341..1465ec7fff 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1,5 +1,6 @@
 #include "Builder.h"
 #include "BuildAtom.h"
+#include "Model.h"
 #include "Zmatrix.h"
 #include "../CpptrajStdio.h"
 #include "../Frame.h"
@@ -106,7 +107,7 @@ const
 
   //bondZmatrix.SetDebug( debug_ );
   bondZmatrix.SetDebug( 1 ); // FIXME
-  if (bondZmatrix.SetupICsAroundBond(atA, atB, CombinedFrame, combinedTop, posKnown, hasIC, AtomA, AtomB)) {
+  if (SetupICsAroundBond(bondZmatrix, atA, atB, CombinedFrame, combinedTop, posKnown, hasIC, AtomA, AtomB)) {
     mprinterr("Error: Zmatrix setup for ICs around %s and %s failed.\n",
               combinedTop.AtomMaskName(atA).c_str(),
               combinedTop.AtomMaskName(atB).c_str());
@@ -206,7 +207,7 @@ const
   }
 
   bondZmatrix.SetDebug( debug_ );
-  if (bondZmatrix.SetupICsAroundBond(atA, atB, frameIn, topIn, hasPosition, hasIC, AtomA, AtomB)) {
+  if (SetupICsAroundBond(bondZmatrix, atA, atB, frameIn, topIn, hasPosition, hasIC, AtomA, AtomB)) {
     mprinterr("Error: Zmatrix setup for ICs around %s and %s failed.\n",
               topIn.AtomMaskName(atA).c_str(),
               topIn.AtomMaskName(atB).c_str());
@@ -222,3 +223,305 @@ const
   return 0;
 }
 
+/** Given two bonded atoms A and B, where B has a depth of at least 2
+  * (i.e., it is possible to have B be atom J where we can form J-K-L),
+  * set up a complete set of internal coordinates involving A and B in the
+  * direction of atom A. This means all internal coordinates with A and B
+  * as I and J (should be only 1), as J and K, and as K and L.
+  */
+int Builder::SetupICsAroundBond(Zmatrix& zmatrix,
+                                int atA, int atB, Frame const& frameIn, Topology const& topIn,
+                                std::vector<bool> const& atomPositionKnown,
+                                std::vector<bool> const& hasICin,
+                                BuildAtom const& AtomA, BuildAtom const& AtomB)
+const
+{
+  if (debug_ > 0)
+    mprintf("DEBUG: SetupICsAroundBond: atA= %s (%i)  atB= %s (%i) total # atoms %i\n",
+            topIn.AtomMaskName(atA).c_str(), atA+1,
+            topIn.AtomMaskName(atB).c_str(), atB+1,
+            topIn.Natom());
+  zmatrix.clear();
+
+  //Barray hasIC( topIn.Natom(), false );
+  Barray hasIC = hasICin;
+  unsigned int nHasIC = 0;
+  for (std::vector<bool>::const_iterator it = hasIC.begin(); it != hasIC.end(); ++it) {
+    if (*it) {
+      nHasIC++;
+      mprintf("DEBUG:\tAtom %s already has an IC.\n", topIn.AtomMaskName(it-hasIC.begin()).c_str());
+    }
+  }
+  // Mark known atoms as already having IC
+  for (std::vector<bool>::const_iterator it = atomPositionKnown.begin();
+                                         it != atomPositionKnown.end(); ++it)
+  {
+    //mprintf("DEBUG: MARKING KNOWN ATOMS. %li\n", it - atomPositionKnown.begin());
+    if (*it) { //MARK( it - atomPositionKnown.begin(), hasIC, nHasIC );
+      hasIC[it - atomPositionKnown.begin()] = true;
+      nHasIC++;
+    }
+  }
+
+  // First, make sure atom B as a bond depth of at least 2.
+  // Choose K and L atoms given atA is I and atB is J.
+  Atom const& AJ = topIn[atB];
+  typedef std::pair<int,int> Apair;
+  std::vector<Apair> KLpairs;
+  for (Atom::bond_iterator kat = AJ.bondbegin(); kat != AJ.bondend(); ++kat)
+  {
+    if (*kat != atA) {
+      //mprintf("DEBUG: kat= %s\n", topIn.AtomMaskName(*kat).c_str());
+      Atom const& AK = topIn[*kat];
+      for (Atom::bond_iterator lat = AK.bondbegin(); lat != AK.bondend(); ++lat)
+      {
+        if (*lat != atB && *lat != atA) {
+          //mprintf("DEBUG: lat= %s\n", topIn.AtomMaskName(*lat).c_str());
+          KLpairs.push_back( Apair(*kat, *lat) );
+        }
+      }
+    }
+  }
+  if (debug_ > 0) {
+    for (std::vector<Apair>::const_iterator it = KLpairs.begin();
+                                            it != KLpairs.end(); ++it)
+      mprintf("DEBUG:\t\tKL pair %s - %s\n", topIn.AtomMaskName(it->first).c_str(),
+              topIn.AtomMaskName(it->second).c_str());
+  }
+  if (KLpairs.empty()) {
+    mprinterr("Error: SetFromFrameAroundBond(): Could not find an atom pair bonded to atom %s\n",
+              topIn.AtomMaskName(atB).c_str());
+    return 1;
+  }
+  // TODO be smarter about how K and L are selected?
+  double maxMass = topIn[KLpairs[0].first].Mass() + topIn[KLpairs[0].second].Mass();
+  unsigned int maxIdx = 0;
+  for (unsigned int idx = 1; idx < KLpairs.size(); idx++) {
+    double sumMass = topIn[KLpairs[idx].first].Mass() + topIn[KLpairs[idx].second].Mass();
+    if (sumMass > maxMass) {
+      maxMass = sumMass;
+      maxIdx = idx;
+    }
+  }
+  int atk0 = KLpairs[maxIdx].first;
+  int atl0 = KLpairs[maxIdx].second;
+  int modelDebug = 0;
+  if (debug_ > 0) {
+    mprintf("DEBUG: Chosen KL pair: %s - %s\n",topIn.AtomMaskName(atk0).c_str(),
+              topIn.AtomMaskName(atl0).c_str());
+    modelDebug = debug_ - 1;
+  }
+  Cpptraj::Structure::Model model;
+  //model.SetDebug( modelDebug ); //FIXME
+  model.SetDebug( 1 );
+  // FIXME
+  mprintf("DEBUG: ------------------------------------------------\n");
+  //std::vector<InternalCoords> tmpic;
+  // I J: Set up ICs for X atB K L
+  if (model.AssignICsAroundBond(zmatrix, atB, atk0, atl0, topIn, frameIn, atomPositionKnown, AtomB)) {
+    mprinterr("Error: AssignICsAroundBond (I J) failed.\n");
+    return 1;
+  }
+  // J K: Set up ICs for X atA atB K
+  if (model.AssignICsAroundBond(zmatrix, atA, atB, atk0, topIn, frameIn, atomPositionKnown, AtomA)) {
+    mprinterr("Error: AssignICsAroundBond (J K) failed.\n");
+    return 1;
+  }
+  // K L: Set up ICs for X iat atA atB
+  Atom const& AJ1 = topIn[atA];
+  for (Atom::bond_iterator iat = AJ1.bondbegin(); iat != AJ1.bondend(); ++iat)
+  {
+    if (*iat != atB) {
+      // Only do this if one or more of the atoms bonded to iat does not
+      // already have an IC.
+      unsigned int needsKLic = 0;
+      for (Atom::bond_iterator bat = topIn[*iat].bondbegin(); bat != topIn[*iat].bondend(); ++bat) {
+        if ( *bat != atA && !hasIC[*bat] ) {
+          mprintf("DEBUG:\tAtom %s around %s has no IC.\n", topIn.AtomMaskName(*bat).c_str(), topIn.AtomMaskName(*iat).c_str());
+          needsKLic++;
+        }
+      }
+      if (needsKLic > 0) {
+        BuildAtom AtomC;
+        if (topIn[*iat].Nbonds() > 2) {
+          if (AtomC.DetermineChirality(*iat, topIn, frameIn, modelDebug)) return 1;
+        }
+        mprintf("DEBUG: K L IC needed for %s.\n", topIn.AtomMaskName(*iat).c_str());
+        if (model.AssignICsAroundBond(zmatrix, *iat, atA, atB, topIn, frameIn, atomPositionKnown, AtomC)) {
+          mprinterr("Error: AssignICsAroundBond (K L) failed.\n");
+          return 1;
+        }
+      } else {
+        mprintf("DEBUG: K L IC not needed for %s.\n", topIn.AtomMaskName(*iat).c_str());
+      }
+    }
+  }
+  // Mark/Print ICs
+  for (Zmatrix::const_iterator it = zmatrix.begin(); it != zmatrix.end(); ++it) {
+    it->printIC( topIn ); // DEBUG
+    //MARK( it->AtI(), hasIC, nHasIC );
+  }
+  mprintf("DEBUG: END AssignICsAroundBond ------------------------\n");
+  // FIXME
+  // ---- I J: Set dist, theta, phi for atA atB K L internal coord ---
+/*  if (debug_ > 0)
+    mprintf("DEBUG: IC (i j) %i - %i - %i - %i\n", atA+1, atB+1, atk0+1, atl0+1);
+  double newDist = 0;
+  if (model.AssignLength(newDist, atA, atB, topIn, frameIn, atomPositionKnown)) {
+    mprinterr("Error: length (i j) assignment failed.\n");
+    return 1;
+  }
+  if (debug_ > 0) mprintf("DEBUG:\t\tnewDist= %g\n", newDist);
+  double newTheta = 0;
+  if (model.AssignTheta(newTheta, atA, atB, atk0, topIn, frameIn, atomPositionKnown)) {
+    mprinterr("Error: theta (i j) assignment failed.\n");
+    return 1;
+  }
+  if (debug_ > 0) mprintf("DEBUG:\t\tnewTheta = %g\n", newTheta*Constants::RADDEG);
+  double newPhi = 0;
+  if (model.AssignPhi(newPhi, atA, atB, atk0, atl0, topIn, frameIn,
+                                           atomPositionKnown, AtomB))
+  {
+    mprinterr("Error: phi (i j) assignment failed.\n");
+    return 1;
+  }
+  if (debug_ > 0) mprintf("DEBUG:\t\tnewPhi = %g\n", newPhi*Constants::RADDEG);
+  IC_.push_back(InternalCoords( atA, atB, atk0, atl0, newDist, newTheta*Constants::RADDEG, newPhi*Constants::RADDEG ));
+  if (debug_ > 0) {
+    mprintf("DEBUG: MODEL I J IC: ");
+    IC_.back().printIC(topIn);
+  }
+  MARK( atA, hasIC, nHasIC );*/
+/*
+  // ----- J K: Set up ICs for X atA atB K ---------------------------
+  Atom const& AJ1 = topIn[atA];
+  int ati = -1;
+  //Atom const& AK1 = topIn[atB];
+  //Atom const& AL1 = topIn[atk0];
+  for (Atom::bond_iterator iat = AJ1.bondbegin(); iat != AJ1.bondend(); ++iat)
+  {
+    if (*iat != atB) {
+      if (ati == -1) ati = *iat;
+/      // Set bond dist
+      if (model.AssignLength(newDist, *iat, atA, topIn, frameIn, atomPositionKnown)) {
+        mprinterr("Error: length (j k) assignment failed.\n");
+        return 1;
+      }
+      // Set theta for I atA atB
+      newTheta = 0;
+      if (model.AssignTheta(newTheta, *iat, atA, atB, topIn, frameIn, atomPositionKnown)) {
+        mprinterr("Error: theta (j k) assignment failed.\n");
+        return 1;
+      }
+      if (debug_ > 0)
+        mprintf("DEBUG:\t\tnewTheta = %g\n", newTheta*Constants::RADDEG);
+      // Set phi for I atA atB K
+      newPhi = 0;
+      if (model.AssignPhi(newPhi, *iat, atA, atB, atk0, topIn, frameIn,
+                                               atomPositionKnown, AtomA))
+      {
+        mprinterr("Error: phi (j k) assignment failed.\n");
+        return 1;
+      }
+      if (debug_ > 0)
+        mprintf("DEBUG:\t\tnewPhi = %g\n", newPhi*Constants::RADDEG);
+      IC_.push_back(InternalCoords( *iat, atA, atB, atk0, newDist, newTheta*Constants::RADDEG, newPhi*Constants::RADDEG ));
+      if (debug_ > 0) {
+        mprintf("DEBUG: MODEL J K IC: ");
+        IC_.back().printIC(topIn);
+      }
+      MARK( *iat, hasIC, nHasIC );
+      // ----- K L: Set up ICs for X iat atA atB ---------------------
+      Atom const& AJ2 = topIn[*iat];
+      for (Atom::bond_iterator i2at = AJ2.bondbegin(); i2at != AJ2.bondend(); ++i2at)
+      {
+        if (*i2at != atA && *i2at != atB && !hasIC[*i2at]) {
+          mprintf("DEBUG: MODEL K L IC: %s %s %s %s %i %i %i %i\n",
+                  topIn.AtomMaskName(*i2at).c_str(),
+                  topIn.AtomMaskName(*iat).c_str(),
+                  topIn.AtomMaskName(atA).c_str(),
+                  topIn.AtomMaskName(atB).c_str(),
+                  *i2at+1, *iat+1, atA+1, atB+1);
+          if (model.AssignLength(newDist, *i2at, *iat, topIn, frameIn, atomPositionKnown)) {
+            mprinterr("Error: length (k l) assignment failed.\n");
+            return 1;
+          }
+          mprintf("DEBUG: K L distance= %g\n", newDist);
+          //newTheta = CalcAngle( frameIn.XYZ(*i2at), frameIn.XYZ(*iat), frameIn.XYZ(atA) );
+          if (model.AssignTheta(newTheta, *iat, atA, atB, topIn, frameIn, atomPositionKnown)) {
+            mprinterr("Error: theta (k l) assignment failed.\n");
+            return 1;
+          }
+          mprintf("DEBUG: K L angle= %g\n", newTheta*Constants::RADDEG);
+          // Set phi for X iat atA atB
+          BuildAtom AtomC;
+          if (topIn[*iat].Nbonds() > 2) {
+            if (AtomC.DetermineChirality(*iat, topIn, frameIn, modelDebug)) return 1;
+          }
+          newPhi = 0;
+          //model.SetDebug( 1 ); // FIXME
+          if (model.AssignPhi(newPhi, *i2at, *iat, atA, atB, topIn, frameIn,
+                                                   atomPositionKnown, AtomC))
+          {
+            mprinterr("Error: phi (k l) assignment failed.\n");
+            return 1;
+          }
+          mprintf("DEBUG: K L Phi = %g\n", newPhi*Constants::RADDEG);
+          IC_.push_back(InternalCoords( *i2at, *iat, atA, atB, newDist, newTheta*Constants::RADDEG, newPhi*Constants::RADDEG ));
+          mprintf("DEBUG: MODEL K L IC: ");
+          IC_.back().printIC(topIn);
+          MARK( *i2at, hasIC, nHasIC );
+          // Trace from atA *iat *i2at outwards
+          //ToTrace.push_back(atA);
+          //ToTrace.push_back(*iat);
+          //ToTrace.push_back(*i2at);
+          //if (traceMol(atA, *iat, *i2at, frameIn, topIn, topIn.Natom(), nHasIC, hasIC)) return 1;
+
+        }
+      } 
+    }
+  }
+*/
+
+/*
+  // Handle remaining atoms.
+  if (AJ1.Nbonds() > 1) {
+    if (AJ1.Nbonds() == 2) {
+      if (debug_ > 0) mprintf("DEBUG: 2 bonds to %s.\n", topIn.AtomMaskName(atA).c_str());
+      if (traceMol(atB, atA, ati, frameIn, topIn, topIn.Natom(), nHasIC, hasIC))
+        return 1;
+    } else {
+      // 3 or more bonds
+      std::vector<int> const& priority = AtomA.Priority();
+      int at0 = -1;
+      int at1 = -1;
+      std::vector<int> remainingAtoms;
+      if (debug_ > 0) mprintf("DEBUG: %i bonds to %s\n", AJ1.Nbonds(), topIn.AtomMaskName(atA).c_str());
+      for (std::vector<int>::const_iterator it = priority.begin(); it != priority.end(); ++it) {
+        if (*it != atB) {
+          if (debug_ > 0) mprintf("DEBUG:\t\t%s\n", topIn.AtomMaskName(*it).c_str());
+          if (at0 == -1)
+            at0 = *it;
+          else if (at1 == -1)
+            at1 = *it;
+          else
+            remainingAtoms.push_back( *it );
+        }
+      }
+      // at0 atA at1
+      if (traceMol(at1, atA, at0, frameIn, topIn, topIn.Natom(), nHasIC, hasIC))
+        return 1;
+      // at1 atA, at0
+      if (traceMol(at0, atA, at1, frameIn, topIn, topIn.Natom(), nHasIC, hasIC))
+        return 1;
+      // Remaining atoms.
+      for (std::vector<int>::const_iterator it = remainingAtoms.begin(); it != remainingAtoms.end(); ++it) {
+        if (traceMol(at0, atA, *it, frameIn, topIn, topIn.Natom(), nHasIC, hasIC))
+          return 1;
+      }
+    }
+  }
+*/
+  return 0;
+}
+
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index 4f596662af..d8336dedb6 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -6,6 +6,7 @@ class Frame;
 class ParameterSet;
 namespace Cpptraj {
 namespace Structure {
+class BuildAtom;
 class Zmatrix;
 /// Used to attach different topology/frame combos using internal coordinates
 class Builder {
@@ -22,6 +23,9 @@ class Builder {
     /// Set optional parameter set
     void SetParameters(ParameterSet const*);
   private:
+    int SetupICsAroundBond(Zmatrix&, int, int, Frame const&, Topology const&,
+                           std::vector<bool> const&, std::vector<bool> const&,
+                           BuildAtom const&, BuildAtom const&) const;
 
     int debug_;
     ParameterSet const* params_;
diff --git a/src/Structure/Model.cpp b/src/Structure/Model.cpp
index 9629b791dd..a0d560964f 100644
--- a/src/Structure/Model.cpp
+++ b/src/Structure/Model.cpp
@@ -1,6 +1,6 @@
 #include "Model.h"
 #include "BuildAtom.h"
-#include "InternalCoords.h"
+#include "Zmatrix.h"
 #include "../CpptrajStdio.h"
 #include "../GuessAtomHybridization.h"
 #include "../Topology.h"
@@ -438,7 +438,7 @@ const
 }
 
 /** Insert internal coordinates with bond i-j, angle i-j-k, and torsion i-j-k-l. */
-int Cpptraj::Structure::Model::insertIc(std::vector<InternalCoords>& IC,
+int Cpptraj::Structure::Model::insertIc(Zmatrix& zmatrix,
                                         int ai, int aj, int ak, int al, double newPhi,
                                         Topology const& topIn, Frame const& frameIn,
                                         std::vector<bool> const& atomPositionKnown)
@@ -462,12 +462,12 @@ const
               topIn.AtomMaskName(ak).c_str());
     return 1;
   }
-  IC.push_back( InternalCoords(ai, aj, ak, al, newDist, newTheta*Constants::RADDEG, newPhi*Constants::RADDEG) );
+  zmatrix.AddIC( InternalCoords(ai, aj, ak, al, newDist, newTheta*Constants::RADDEG, newPhi*Constants::RADDEG) );
   return 0;
 }
 
 /** Assign internal coordinates for atoms I for torsions around J-K-L. */
-int Cpptraj::Structure::Model::AssignICsAroundBond(std::vector<InternalCoords>& IC,
+int Cpptraj::Structure::Model::AssignICsAroundBond(Zmatrix& zmatrix,
                                                    int aj, int ak, int al,
                                                    Topology const& topIn, Frame const& frameIn,
                                                    std::vector<bool> const& atomPositionKnown,
@@ -505,7 +505,7 @@ const
     for (int idx = 0; idx < AJ.Nbonds(); idx++) {
       if (AJ.Bond(idx) != ak) {
         int ai = AJ.Bond(idx);
-        if (insertIc(IC, ai, aj, ak, al, newPhi, topIn, frameIn, atomPositionKnown)) return 1;
+        if (insertIc(zmatrix, ai, aj, ak, al, newPhi, topIn, frameIn, atomPositionKnown)) return 1;
         break;
       }
     }
@@ -689,7 +689,7 @@ const
         currentPhi = wrap360(currentPhi + interval);
       //if (atnum == ai) phi = currentPhi;
       //IC.push_back( InternalCoords(atnum, aj, ak, al, 0, 0, currentPhi) );
-      if (insertIc(IC, atnum, aj, ak, al, currentPhi, topIn, frameIn, atomPositionKnown)) return 1;
+      if (insertIc(zmatrix, atnum, aj, ak, al, currentPhi, topIn, frameIn, atomPositionKnown)) return 1;
       if (debug_ > 0)
         mprintf("DEBUG:\t\t\t%s (at# %i) phi= %g\n", topIn.AtomMaskName(atnum).c_str(), atnum+1, currentPhi*Constants::RADDEG);
     }
@@ -705,7 +705,7 @@ const
         currentPhi = wrap360(currentPhi - interval);
       //if (atnum == ai) phi = currentPhi;
       //IC.push_back( InternalCoords(atnum, aj, ak, al, 0, 0, currentPhi) );
-      if (insertIc(IC, atnum, aj, ak, al, currentPhi, topIn, frameIn, atomPositionKnown)) return 1;
+      if (insertIc(zmatrix, atnum, aj, ak, al, currentPhi, topIn, frameIn, atomPositionKnown)) return 1;
       if (debug_ > 0)
         mprintf("DEBUG:\t\t\t%s (at# %i) phi= %g\n", topIn.AtomMaskName(atnum).c_str(), atnum+1, currentPhi*Constants::RADDEG);
     }
diff --git a/src/Structure/Model.h b/src/Structure/Model.h
index 77044818eb..f73f711579 100644
--- a/src/Structure/Model.h
+++ b/src/Structure/Model.h
@@ -10,7 +10,7 @@ class ParameterSet;
 namespace Cpptraj {
 namespace Structure {
 class BuildAtom;
-class InternalCoords;
+class Zmatrix; 
 /// Routines to create a model for missing bond/angle/torsion parameters
 class Model {
   public:
@@ -29,11 +29,11 @@ class Model {
     /// Given atoms I J K and L, attempt to assign a reasonable value for phi for atom I
     int AssignPhi(double&, int, int, int, int, Topology const&, Frame const&, std::vector<bool> const&, BuildAtom const&) const;
     /// Assign internal coordinates for atoms I for torsions around J-K-L.
-    int AssignICsAroundBond(std::vector<InternalCoords>&, int, int, int,
+    int AssignICsAroundBond(Zmatrix&, int, int, int,
                            Topology const&, Frame const&, std::vector<bool> const&,
                            BuildAtom const&) const;
   private:
-    int insertIc(std::vector<InternalCoords>&, int, int, int, int, double,
+    int insertIc(Zmatrix&, int, int, int, int, double,
                  Topology const&, Frame const&, std::vector<bool> const&) const;
 
 
diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index f623d82374..0eae2717b9 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -1,11 +1,8 @@
 #include <vector>
-#include <algorithm> // std::sort, std::min, std::max
+#include <algorithm> // std::sort, std::min, std::max, std::find
 #include <stack>
 #include <cmath> // cos
-#include <utility> // std::pair
 #include "Zmatrix.h"
-#include "BuildAtom.h"
-#include "Model.h"
 #include "GenerateConnectivityArrays.h"
 #include "../Frame.h"
 #include "../CpptrajStdio.h"
@@ -943,303 +940,6 @@ int Zmatrix::SetFromFrame(Frame const& frameIn, Topology const& topIn, int molnu
   return SetFromFrame_Trace(frameIn, topIn, molnum);
 }
 
-/** Given two bonded atoms A and B, where B has a depth of at least 2
-  * (i.e., it is possible to have B be atom J where we can form J-K-L),
-  * set up a complete set of internal coordinates involving A and B in the
-  * direction of atom A. This means all internal coordinates with A and B
-  * as I and J (should be only 1), as J and K, and as K and L.
-  */
-int Zmatrix::SetupICsAroundBond(int atA, int atB, Frame const& frameIn, Topology const& topIn,
-                                std::vector<bool> const& atomPositionKnown,
-                                std::vector<bool> const& hasICin,
-                                BuildAtom const& AtomA, BuildAtom const& AtomB)
-{
-  if (debug_ > 0)
-    mprintf("DEBUG: SetupICsAroundBond: atA= %s (%i)  atB= %s (%i) total # atoms %i\n",
-            topIn.AtomMaskName(atA).c_str(), atA+1,
-            topIn.AtomMaskName(atB).c_str(), atB+1,
-            topIn.Natom());
-  IC_.clear();
-
-  //Barray hasIC( topIn.Natom(), false );
-  Barray hasIC = hasICin;
-  unsigned int nHasIC = 0;
-  for (std::vector<bool>::const_iterator it = hasIC.begin(); it != hasIC.end(); ++it) {
-    if (*it) {
-      nHasIC++;
-      mprintf("DEBUG:\tAtom %s already has an IC.\n", topIn.AtomMaskName(it-hasIC.begin()).c_str());
-    }
-  }
-  // Mark known atoms as already having IC
-  for (std::vector<bool>::const_iterator it = atomPositionKnown.begin();
-                                         it != atomPositionKnown.end(); ++it)
-  {
-    //mprintf("DEBUG: MARKING KNOWN ATOMS. %li\n", it - atomPositionKnown.begin());
-    if (*it) MARK( it - atomPositionKnown.begin(), hasIC, nHasIC );
-  }
-
-  // First, make sure atom B as a bond depth of at least 2.
-  // Choose K and L atoms given atA is I and atB is J.
-  Atom const& AJ = topIn[atB];
-  typedef std::pair<int,int> Apair;
-  std::vector<Apair> KLpairs;
-  for (Atom::bond_iterator kat = AJ.bondbegin(); kat != AJ.bondend(); ++kat)
-  {
-    if (*kat != atA) {
-      //mprintf("DEBUG: kat= %s\n", topIn.AtomMaskName(*kat).c_str());
-      Atom const& AK = topIn[*kat];
-      for (Atom::bond_iterator lat = AK.bondbegin(); lat != AK.bondend(); ++lat)
-      {
-        if (*lat != atB && *lat != atA) {
-          //mprintf("DEBUG: lat= %s\n", topIn.AtomMaskName(*lat).c_str());
-          KLpairs.push_back( Apair(*kat, *lat) );
-        }
-      }
-    }
-  }
-  if (debug_ > 0) {
-    for (std::vector<Apair>::const_iterator it = KLpairs.begin();
-                                            it != KLpairs.end(); ++it)
-      mprintf("DEBUG:\t\tKL pair %s - %s\n", topIn.AtomMaskName(it->first).c_str(),
-              topIn.AtomMaskName(it->second).c_str());
-  }
-  if (KLpairs.empty()) {
-    mprinterr("Error: SetFromFrameAroundBond(): Could not find an atom pair bonded to atom %s\n",
-              topIn.AtomMaskName(atB).c_str());
-    return 1;
-  }
-  // TODO be smarter about how K and L are selected?
-  double maxMass = topIn[KLpairs[0].first].Mass() + topIn[KLpairs[0].second].Mass();
-  unsigned int maxIdx = 0;
-  for (unsigned int idx = 1; idx < KLpairs.size(); idx++) {
-    double sumMass = topIn[KLpairs[idx].first].Mass() + topIn[KLpairs[idx].second].Mass();
-    if (sumMass > maxMass) {
-      maxMass = sumMass;
-      maxIdx = idx;
-    }
-  }
-  int atk0 = KLpairs[maxIdx].first;
-  int atl0 = KLpairs[maxIdx].second;
-  int modelDebug = 0;
-  if (debug_ > 0) {
-    mprintf("DEBUG: Chosen KL pair: %s - %s\n",topIn.AtomMaskName(atk0).c_str(),
-              topIn.AtomMaskName(atl0).c_str());
-    modelDebug = debug_ - 1;
-  }
-  Cpptraj::Structure::Model model;
-  //model.SetDebug( modelDebug ); //FIXME
-  model.SetDebug( 1 );
-  // FIXME
-  mprintf("DEBUG: ------------------------------------------------\n");
-  //std::vector<InternalCoords> tmpic;
-  // I J: Set up ICs for X atB K L
-  if (model.AssignICsAroundBond(IC_, atB, atk0, atl0, topIn, frameIn, atomPositionKnown, AtomB)) {
-    mprinterr("Error: AssignICsAroundBond (I J) failed.\n");
-    return 1;
-  }
-  // J K: Set up ICs for X atA atB K
-  if (model.AssignICsAroundBond(IC_, atA, atB, atk0, topIn, frameIn, atomPositionKnown, AtomA)) {
-    mprinterr("Error: AssignICsAroundBond (J K) failed.\n");
-    return 1;
-  }
-  // K L: Set up ICs for X iat atA atB
-  Atom const& AJ1 = topIn[atA];
-  for (Atom::bond_iterator iat = AJ1.bondbegin(); iat != AJ1.bondend(); ++iat)
-  {
-    if (*iat != atB) {
-      // Only do this if one or more of the atoms bonded to iat does not
-      // already have an IC.
-      unsigned int needsKLic = 0;
-      for (Atom::bond_iterator bat = topIn[*iat].bondbegin(); bat != topIn[*iat].bondend(); ++bat) {
-        if ( *bat != atA && !hasIC[*bat] ) {
-          mprintf("DEBUG:\tAtom %s around %s has no IC.\n", topIn.AtomMaskName(*bat).c_str(), topIn.AtomMaskName(*iat).c_str());
-          needsKLic++;
-        }
-      }
-      if (needsKLic > 0) {
-        BuildAtom AtomC;
-        if (topIn[*iat].Nbonds() > 2) {
-          if (AtomC.DetermineChirality(*iat, topIn, frameIn, modelDebug)) return 1;
-        }
-        mprintf("DEBUG: K L IC needed for %s.\n", topIn.AtomMaskName(*iat).c_str());
-        if (model.AssignICsAroundBond(IC_, *iat, atA, atB, topIn, frameIn, atomPositionKnown, AtomC)) {
-          mprinterr("Error: AssignICsAroundBond (K L) failed.\n");
-          return 1;
-        }
-      } else {
-        mprintf("DEBUG: K L IC not needed for %s.\n", topIn.AtomMaskName(*iat).c_str());
-      }
-    }
-  }
-  // Mark/Print ICs
-  for (std::vector<InternalCoords>::const_iterator it = IC_.begin(); it != IC_.end(); ++it) {
-    it->printIC( topIn ); // DEBUG
-    MARK( it->AtI(), hasIC, nHasIC );
-  }
-  mprintf("DEBUG: END AssignICsAroundBond ------------------------\n");
-  // FIXME
-  // ---- I J: Set dist, theta, phi for atA atB K L internal coord ---
-/*  if (debug_ > 0)
-    mprintf("DEBUG: IC (i j) %i - %i - %i - %i\n", atA+1, atB+1, atk0+1, atl0+1);
-  double newDist = 0;
-  if (model.AssignLength(newDist, atA, atB, topIn, frameIn, atomPositionKnown)) {
-    mprinterr("Error: length (i j) assignment failed.\n");
-    return 1;
-  }
-  if (debug_ > 0) mprintf("DEBUG:\t\tnewDist= %g\n", newDist);
-  double newTheta = 0;
-  if (model.AssignTheta(newTheta, atA, atB, atk0, topIn, frameIn, atomPositionKnown)) {
-    mprinterr("Error: theta (i j) assignment failed.\n");
-    return 1;
-  }
-  if (debug_ > 0) mprintf("DEBUG:\t\tnewTheta = %g\n", newTheta*Constants::RADDEG);
-  double newPhi = 0;
-  if (model.AssignPhi(newPhi, atA, atB, atk0, atl0, topIn, frameIn,
-                                           atomPositionKnown, AtomB))
-  {
-    mprinterr("Error: phi (i j) assignment failed.\n");
-    return 1;
-  }
-  if (debug_ > 0) mprintf("DEBUG:\t\tnewPhi = %g\n", newPhi*Constants::RADDEG);
-  IC_.push_back(InternalCoords( atA, atB, atk0, atl0, newDist, newTheta*Constants::RADDEG, newPhi*Constants::RADDEG ));
-  if (debug_ > 0) {
-    mprintf("DEBUG: MODEL I J IC: ");
-    IC_.back().printIC(topIn);
-  }
-  MARK( atA, hasIC, nHasIC );*/
-/*
-  // ----- J K: Set up ICs for X atA atB K ---------------------------
-  Atom const& AJ1 = topIn[atA];
-  int ati = -1;
-  //Atom const& AK1 = topIn[atB];
-  //Atom const& AL1 = topIn[atk0];
-  for (Atom::bond_iterator iat = AJ1.bondbegin(); iat != AJ1.bondend(); ++iat)
-  {
-    if (*iat != atB) {
-      if (ati == -1) ati = *iat;
-/      // Set bond dist
-      if (model.AssignLength(newDist, *iat, atA, topIn, frameIn, atomPositionKnown)) {
-        mprinterr("Error: length (j k) assignment failed.\n");
-        return 1;
-      }
-      // Set theta for I atA atB
-      newTheta = 0;
-      if (model.AssignTheta(newTheta, *iat, atA, atB, topIn, frameIn, atomPositionKnown)) {
-        mprinterr("Error: theta (j k) assignment failed.\n");
-        return 1;
-      }
-      if (debug_ > 0)
-        mprintf("DEBUG:\t\tnewTheta = %g\n", newTheta*Constants::RADDEG);
-      // Set phi for I atA atB K
-      newPhi = 0;
-      if (model.AssignPhi(newPhi, *iat, atA, atB, atk0, topIn, frameIn,
-                                               atomPositionKnown, AtomA))
-      {
-        mprinterr("Error: phi (j k) assignment failed.\n");
-        return 1;
-      }
-      if (debug_ > 0)
-        mprintf("DEBUG:\t\tnewPhi = %g\n", newPhi*Constants::RADDEG);
-      IC_.push_back(InternalCoords( *iat, atA, atB, atk0, newDist, newTheta*Constants::RADDEG, newPhi*Constants::RADDEG ));
-      if (debug_ > 0) {
-        mprintf("DEBUG: MODEL J K IC: ");
-        IC_.back().printIC(topIn);
-      }
-      MARK( *iat, hasIC, nHasIC );
-      // ----- K L: Set up ICs for X iat atA atB ---------------------
-      Atom const& AJ2 = topIn[*iat];
-      for (Atom::bond_iterator i2at = AJ2.bondbegin(); i2at != AJ2.bondend(); ++i2at)
-      {
-        if (*i2at != atA && *i2at != atB && !hasIC[*i2at]) {
-          mprintf("DEBUG: MODEL K L IC: %s %s %s %s %i %i %i %i\n",
-                  topIn.AtomMaskName(*i2at).c_str(),
-                  topIn.AtomMaskName(*iat).c_str(),
-                  topIn.AtomMaskName(atA).c_str(),
-                  topIn.AtomMaskName(atB).c_str(),
-                  *i2at+1, *iat+1, atA+1, atB+1);
-          if (model.AssignLength(newDist, *i2at, *iat, topIn, frameIn, atomPositionKnown)) {
-            mprinterr("Error: length (k l) assignment failed.\n");
-            return 1;
-          }
-          mprintf("DEBUG: K L distance= %g\n", newDist);
-          //newTheta = CalcAngle( frameIn.XYZ(*i2at), frameIn.XYZ(*iat), frameIn.XYZ(atA) );
-          if (model.AssignTheta(newTheta, *iat, atA, atB, topIn, frameIn, atomPositionKnown)) {
-            mprinterr("Error: theta (k l) assignment failed.\n");
-            return 1;
-          }
-          mprintf("DEBUG: K L angle= %g\n", newTheta*Constants::RADDEG);
-          // Set phi for X iat atA atB
-          BuildAtom AtomC;
-          if (topIn[*iat].Nbonds() > 2) {
-            if (AtomC.DetermineChirality(*iat, topIn, frameIn, modelDebug)) return 1;
-          }
-          newPhi = 0;
-          //model.SetDebug( 1 ); // FIXME
-          if (model.AssignPhi(newPhi, *i2at, *iat, atA, atB, topIn, frameIn,
-                                                   atomPositionKnown, AtomC))
-          {
-            mprinterr("Error: phi (k l) assignment failed.\n");
-            return 1;
-          }
-          mprintf("DEBUG: K L Phi = %g\n", newPhi*Constants::RADDEG);
-          IC_.push_back(InternalCoords( *i2at, *iat, atA, atB, newDist, newTheta*Constants::RADDEG, newPhi*Constants::RADDEG ));
-          mprintf("DEBUG: MODEL K L IC: ");
-          IC_.back().printIC(topIn);
-          MARK( *i2at, hasIC, nHasIC );
-          // Trace from atA *iat *i2at outwards
-          //ToTrace.push_back(atA);
-          //ToTrace.push_back(*iat);
-          //ToTrace.push_back(*i2at);
-          //if (traceMol(atA, *iat, *i2at, frameIn, topIn, topIn.Natom(), nHasIC, hasIC)) return 1;
-
-        }
-      } 
-    }
-  }
-*/
-
-/*
-  // Handle remaining atoms.
-  if (AJ1.Nbonds() > 1) {
-    if (AJ1.Nbonds() == 2) {
-      if (debug_ > 0) mprintf("DEBUG: 2 bonds to %s.\n", topIn.AtomMaskName(atA).c_str());
-      if (traceMol(atB, atA, ati, frameIn, topIn, topIn.Natom(), nHasIC, hasIC))
-        return 1;
-    } else {
-      // 3 or more bonds
-      std::vector<int> const& priority = AtomA.Priority();
-      int at0 = -1;
-      int at1 = -1;
-      std::vector<int> remainingAtoms;
-      if (debug_ > 0) mprintf("DEBUG: %i bonds to %s\n", AJ1.Nbonds(), topIn.AtomMaskName(atA).c_str());
-      for (std::vector<int>::const_iterator it = priority.begin(); it != priority.end(); ++it) {
-        if (*it != atB) {
-          if (debug_ > 0) mprintf("DEBUG:\t\t%s\n", topIn.AtomMaskName(*it).c_str());
-          if (at0 == -1)
-            at0 = *it;
-          else if (at1 == -1)
-            at1 = *it;
-          else
-            remainingAtoms.push_back( *it );
-        }
-      }
-      // at0 atA at1
-      if (traceMol(at1, atA, at0, frameIn, topIn, topIn.Natom(), nHasIC, hasIC))
-        return 1;
-      // at1 atA, at0
-      if (traceMol(at0, atA, at1, frameIn, topIn, topIn.Natom(), nHasIC, hasIC))
-        return 1;
-      // Remaining atoms.
-      for (std::vector<int>::const_iterator it = remainingAtoms.begin(); it != remainingAtoms.end(); ++it) {
-        if (traceMol(at0, atA, *it, frameIn, topIn, topIn.Natom(), nHasIC, hasIC))
-          return 1;
-      }
-    }
-  }
-*/
-  return 0;
-}
-
 // -----------------------------------------------------------------------------
 /** \return Position of atom I from given internal coordinate. */
 Vec3 Zmatrix::AtomIposition(InternalCoords const& ic, Frame const& frameOut)
diff --git a/src/Structure/Zmatrix.h b/src/Structure/Zmatrix.h
index 80ba9d61af..165d5c661e 100644
--- a/src/Structure/Zmatrix.h
+++ b/src/Structure/Zmatrix.h
@@ -1,14 +1,12 @@
 #ifndef INC_STRUCTURE_ZMATRIX_H
 #define INC_STRUCTURE_ZMATRIX_H
 #include "InternalCoords.h"
-#include "StructureEnum.h"
 #include "../Vec3.h"
 class Frame;
 class Topology;
 class Molecule;
 namespace Cpptraj {
 namespace Structure {
-class BuildAtom;
 /// Hold internal coordinates for a system.
 class Zmatrix {
     typedef std::vector<InternalCoords> ICarray;
@@ -49,10 +47,6 @@ class Zmatrix {
     int SetFromFrame(Frame const&, Topology const&, int);
     /// Convert molecule 0 of Frame/Topology to internal coordinates array
     int SetFromFrame(Frame const&, Topology const&);
-    /// Get internal coordinates around bond in one direction.
-    int SetupICsAroundBond(int, int, Frame const&, Topology const&,
-                           std::vector<bool> const&, std::vector<bool> const&,
-                           BuildAtom const&, BuildAtom const&);
 
     /// Set Frame from internal coords
     int SetToFrame(Frame&) const;
diff --git a/src/Structure/structuredepend b/src/Structure/structuredepend
index b944b35e4c..0c7b220ea1 100644
--- a/src/Structure/structuredepend
+++ b/src/Structure/structuredepend
@@ -1,16 +1,16 @@
 BuildAtom.o : BuildAtom.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h StructureEnum.h
-Builder.o : Builder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h Builder.h InternalCoords.h StructureEnum.h Zmatrix.h
+Builder.o : Builder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h Builder.h InternalCoords.h Model.h StructureEnum.h Zmatrix.h
 Disulfide.o : Disulfide.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Disulfide.h ResStatArray.h StructureRoutines.h
 FunctionalGroup.o : FunctionalGroup.cpp ../Atom.h ../AtomMap.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h FunctionalGroup.h
 FxnGroupBuilder.o : FxnGroupBuilder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h FunctionalGroup.h FxnGroupBuilder.h StructureRoutines.h Sugar.h SugarToken.h
 GenerateConnectivityArrays.o : GenerateConnectivityArrays.cpp ../Atom.h ../Constants.h ../CpptrajStdio.h ../NameType.h ../ParameterTypes.h ../Residue.h ../SymbolExporting.h GenerateConnectivityArrays.h
 HisProt.o : HisProt.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h HisProt.h StructureRoutines.h
 InternalCoords.o : InternalCoords.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h InternalCoords.h
-Model.o : Model.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h InternalCoords.h Model.h StructureEnum.h
+Model.o : Model.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h InternalCoords.h Model.h StructureEnum.h Zmatrix.h
 StructureEnum.o : StructureEnum.cpp StructureEnum.h
 StructureRoutines.o : StructureRoutines.cpp ../Atom.h ../CpptrajStdio.h ../NameType.h ../Residue.h ../SymbolExporting.h StructureRoutines.h
 Sugar.o : Sugar.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Sugar.h SugarToken.h
 SugarBuilder.o : SugarBuilder.cpp ../ArgList.h ../Atom.h ../AtomMap.h ../AtomMask.h ../AtomType.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DistRoutines.h ../FileIO.h ../FileName.h ../Frame.h ../ImageOption.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h FunctionalGroup.h FxnGroupBuilder.h LinkAtom.h ResStatArray.h StructureEnum.h StructureRoutines.h Sugar.h SugarBuilder.h SugarLinkAtoms.h SugarToken.h
 SugarLinkAtoms.o : SugarLinkAtoms.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../StringRoutines.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h LinkAtom.h SugarLinkAtoms.h
 SugarToken.o : SugarToken.cpp ../ArgList.h ../CpptrajStdio.h SugarToken.h
-Zmatrix.o : Zmatrix.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h GenerateConnectivityArrays.h InternalCoords.h Model.h StructureEnum.h Zmatrix.h
+Zmatrix.o : Zmatrix.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h GenerateConnectivityArrays.h InternalCoords.h StructureEnum.h Zmatrix.h
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index c3666e4073..f58b379a6f 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -446,21 +446,21 @@ Spline.o : Spline.cpp CpptrajStdio.h Spline.h
 SplineFxnTable.o : SplineFxnTable.cpp Constants.h CpptrajStdio.h Spline.h SplineFxnTable.h StringRoutines.h
 StringRoutines.o : StringRoutines.cpp CpptrajStdio.h StringRoutines.h
 Structure/BuildAtom.o : Structure/BuildAtom.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/StructureEnum.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Structure/Builder.o : Structure/Builder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/Builder.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Structure/Builder.o : Structure/Builder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/Builder.h Structure/InternalCoords.h Structure/Model.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/Disulfide.o : Structure/Disulfide.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Disulfide.h Structure/ResStatArray.h Structure/StructureRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/FunctionalGroup.o : Structure/FunctionalGroup.cpp Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/FxnGroupBuilder.o : Structure/FxnGroupBuilder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h Structure/FxnGroupBuilder.h Structure/StructureRoutines.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/GenerateConnectivityArrays.o : Structure/GenerateConnectivityArrays.cpp Atom.h Constants.h CpptrajStdio.h NameType.h ParameterTypes.h Residue.h Structure/GenerateConnectivityArrays.h SymbolExporting.h
 Structure/HisProt.o : Structure/HisProt.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/HisProt.h Structure/StructureRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/InternalCoords.o : Structure/InternalCoords.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/InternalCoords.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Structure/Model.o : Structure/Model.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h GuessAtomHybridization.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/InternalCoords.h Structure/Model.h Structure/StructureEnum.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Structure/Model.o : Structure/Model.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h GuessAtomHybridization.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/InternalCoords.h Structure/Model.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 Structure/StructureEnum.o : Structure/StructureEnum.cpp Structure/StructureEnum.h
 Structure/StructureRoutines.o : Structure/StructureRoutines.cpp Atom.h CpptrajStdio.h NameType.h Residue.h Structure/StructureRoutines.h SymbolExporting.h
 Structure/Sugar.o : Structure/Sugar.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/SugarBuilder.o : Structure/SugarBuilder.cpp ArgList.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DistRoutines.h FileIO.h FileName.h Frame.h ImageOption.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/FunctionalGroup.h Structure/FxnGroupBuilder.h Structure/LinkAtom.h Structure/ResStatArray.h Structure/StructureEnum.h Structure/StructureRoutines.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarLinkAtoms.h Structure/SugarToken.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 Structure/SugarLinkAtoms.o : Structure/SugarLinkAtoms.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/LinkAtom.h Structure/SugarLinkAtoms.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/SugarToken.o : Structure/SugarToken.cpp ArgList.h CpptrajStdio.h Structure/SugarToken.h
-Structure/Zmatrix.o : Structure/Zmatrix.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/Model.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Structure/Zmatrix.o : Structure/Zmatrix.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 StructureCheck.o : StructureCheck.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h ExclusionArray.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StructureCheck.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 StructureMapper.o : StructureMapper.cpp AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StructureMapper.h SymbolExporting.h TextFormat.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 SymmetricRmsdCalc.o : SymmetricRmsdCalc.cpp ArrayIterator.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h Hungarian.h ImageOption.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h Topology.h TypeNameHolder.h Unit.h Vec3.h

From 3aed3f0ef8bc60360d508e445af3b90fe19d44a1 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 29 Jan 2024 15:33:51 -0500
Subject: [PATCH 0400/1492] Add SetParameters

---
 src/Structure/Builder.cpp | 9 +++++++++
 src/Structure/Builder.h   | 9 +++++----
 2 files changed, 14 insertions(+), 4 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 1465ec7fff..3dcbf1cff6 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -15,6 +15,15 @@ Builder::Builder() :
   params_(0)
 {}
 
+/** Set optional parameter set. */
+void Cpptraj::Structure::Builder::SetParameters(ParameterSet const* paramsIn) {
+  if (paramsIn == 0) {
+    mprinterr("Internal Error: Builder::SetParmaters called with null set.\n");
+    return;
+  }
+  params_ = paramsIn;
+}
+
 /** Combine two units. Fragment 1 will be merged into Fragment 0 and bonded. */
 int Builder::Combine(Topology&       frag0Top, Frame&       frag0frm,
                      Topology const& frag1Top, Frame const& frag1frm,
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index d8336dedb6..020f677c69 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -14,14 +14,15 @@ class Builder {
   public:
     /// CONSTRUCTOR
     Builder();
-    /// Combine second fragment into first fragment and bond
-    int Combine(Topology&, Frame&, Topology const&, Frame const&, int, int) const;
-    /// Model the coordinates around a bond given only some coordinates are known
-    int ModelCoordsAroundBond(Frame&, Topology const&, int, int, Zmatrix const*, Zmatrix const*, Barray&) const;
     /// Set debug
     void SetDebug(int d) { debug_ = d; }
     /// Set optional parameter set
     void SetParameters(ParameterSet const*);
+
+    /// Combine second fragment into first fragment and bond
+    int Combine(Topology&, Frame&, Topology const&, Frame const&, int, int) const;
+    /// Model the coordinates around a bond given only some coordinates are known
+    int ModelCoordsAroundBond(Frame&, Topology const&, int, int, Zmatrix const*, Zmatrix const*, Barray&) const;
   private:
     int SetupICsAroundBond(Zmatrix&, int, int, Frame const&, Topology const&,
                            std::vector<bool> const&, std::vector<bool> const&,

From cd20b708bb673c3b945fd4d452dbae41ccf25765 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 29 Jan 2024 15:35:52 -0500
Subject: [PATCH 0401/1492] Copy AssignLengths to Builder

---
 src/Structure/Builder.cpp | 32 ++++++++++++++++++++++++++++++++
 src/Structure/Builder.h   |  3 +++
 2 files changed, 35 insertions(+)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 3dcbf1cff6..78b33cc8f5 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -3,6 +3,7 @@
 #include "Model.h"
 #include "Zmatrix.h"
 #include "../CpptrajStdio.h"
+#include "../DistRoutines.h"
 #include "../Frame.h"
 #include "../Topology.h"
 #include <algorithm> // std::copy
@@ -24,6 +25,37 @@ void Cpptraj::Structure::Builder::SetParameters(ParameterSet const* paramsIn) {
   params_ = paramsIn;
 }
 
+// -----------------------------------------------------------------------------
+/** Assign reasonable value for bond distance. */
+int Cpptraj::Structure::Builder::AssignLength(double& dist, int ai, int aj, Topology const& topIn, Frame const& frameIn, std::vector<bool> const& atomPositionKnown)
+const
+{
+  if (atomPositionKnown[ai] && atomPositionKnown[aj])
+    dist = sqrt( DIST2_NoImage( frameIn.XYZ(ai), frameIn.XYZ(aj) ) );
+  else {
+    // One or both positions unknown. Use estimated bond length or parameters.
+    bool foundParam = false;
+    if (params_ != 0 && topIn[ai].HasType() && topIn[aj].HasType()) {
+      TypeNameHolder btypes(2);
+      btypes.AddName( topIn[ai].Type() );
+      btypes.AddName( topIn[aj].Type() );
+      ParmHolder<BondParmType>::const_iterator it = params_->BP().GetParam( btypes );
+      if (it != params_->BP().end()) {
+        dist = it->second.Req();
+        foundParam = true;
+        mprintf("DEBUG: Found bond parameter for %s (%s) - %s (%s): req=%g rk=%g\n",
+                topIn.AtomMaskName(ai).c_str(), *(topIn[ai].Type()),
+                topIn.AtomMaskName(aj).c_str(), *(topIn[aj].Type()),
+                it->second.Req(), it->second.Rk());
+      }
+    }
+    if (!foundParam)
+      dist = Atom::GetBondLength( topIn[ai].Element(), topIn[aj].Element() );
+  }
+  return 0;
+}
+
+// -----------------------------------------------------------------------------
 /** Combine two units. Fragment 1 will be merged into Fragment 0 and bonded. */
 int Builder::Combine(Topology&       frag0Top, Frame&       frag0frm,
                      Topology const& frag1Top, Frame const& frag1frm,
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index 020f677c69..fd4baf304a 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -24,6 +24,9 @@ class Builder {
     /// Model the coordinates around a bond given only some coordinates are known
     int ModelCoordsAroundBond(Frame&, Topology const&, int, int, Zmatrix const*, Zmatrix const*, Barray&) const;
   private:
+    /// Assign a reasonable value for bond distance given 2 atoms whose position may or may not be known
+    int AssignLength(double&, int, int, Topology const&, Frame const&, std::vector<bool> const&) const;
+
     int SetupICsAroundBond(Zmatrix&, int, int, Frame const&, Topology const&,
                            std::vector<bool> const&, std::vector<bool> const&,
                            BuildAtom const&, BuildAtom const&) const;

From 475387f34fd7fe44e27f09245235cdb55778d2be Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 29 Jan 2024 15:38:00 -0500
Subject: [PATCH 0402/1492] Copy AssignTheta to Builder

---
 src/Structure/Builder.cpp | 115 ++++++++++++++++++++++++++++++++++++++
 src/Structure/Builder.h   |   3 +
 2 files changed, 118 insertions(+)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 78b33cc8f5..3ca3be6258 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -2,10 +2,13 @@
 #include "BuildAtom.h"
 #include "Model.h"
 #include "Zmatrix.h"
+#include "../Constants.h"
 #include "../CpptrajStdio.h"
 #include "../DistRoutines.h"
 #include "../Frame.h"
+#include "../GuessAtomHybridization.h"
 #include "../Topology.h"
+#include "../TorsionRoutines.h"
 #include <algorithm> // std::copy
 
 using namespace Cpptraj::Structure;
@@ -55,6 +58,118 @@ const
   return 0;
 }
 
+/** Attempt to assign a reasonable value for theta internal coordinate for
+  * atom i given that atoms j and k have known positions.
+  */
+int Cpptraj::Structure::Builder::AssignTheta(double& theta, int ai, int aj, int ak, Topology const& topIn, Frame const& frameIn, std::vector<bool> const& atomPositionKnown)
+const
+{
+  // Figure out hybridization and chirality of atom j.
+  if (debug_ > 0)
+    mprintf("DEBUG: AssignTheta for atom j : %s\n", topIn.AtomMaskName(aj).c_str());
+  if (atomPositionKnown[ai] && atomPositionKnown[aj] && atomPositionKnown[ak])
+  {
+    theta = CalcAngle(frameIn.XYZ(ai), frameIn.XYZ(aj), frameIn.XYZ(ak));
+    return 0;
+  }
+
+  Atom const& AJ = topIn[aj];
+  if (debug_ > 0) {
+    mprintf("DEBUG:\t\tI %s Nbonds: %i\n", topIn[ai].ElementName(), topIn[ai].Nbonds());
+    mprintf("DEBUG:\t\tJ %s Nbonds: %i\n", AJ.ElementName(), AJ.Nbonds());
+    mprintf("DEBUG:\t\tK %s Nbonds: %i\n", topIn[ak].ElementName(), topIn[ak].Nbonds());
+  }
+  // Sanity check
+  if (AJ.Nbonds() < 2) {
+    mprinterr("Internal Error: AssignTheta() called for atom J %s with fewer than 2 bonds.\n", topIn.AtomMaskName(aj).c_str());
+    return 1;
+  }
+  AtomType::HybridizationType hybrid = AtomType::UNKNOWN_HYBRIDIZATION;
+  if (params_ != 0) {
+    ParmHolder<AtomType>::const_iterator it = params_->AT().GetParam( TypeNameHolder(AJ.Type()) );
+    if (it != params_->AT().end())
+      hybrid = it->second.Hybridization();
+  }
+  if (hybrid == AtomType::UNKNOWN_HYBRIDIZATION)
+    hybrid = GuessAtomHybridization(AJ, topIn.Atoms());
+/*
+  HybridizationType hybrid = UNKNOWN_HYBRIDIZATION;
+  // Handle specific elements
+  switch (AJ.Element()) {
+    case Atom::CARBON :
+      switch (AJ.Nbonds()) {
+        case 2 : hybrid = SP; break;
+        case 3 : hybrid = SP2; break;
+        case 4 : hybrid = SP3; break;
+      }
+      break;
+    case Atom::NITROGEN :
+      switch (AJ.Nbonds()) {
+        case 2 : hybrid = SP2; break;
+        case 3 :
+          // Check for potential SP2. If only 1 of the bonded atoms is
+          // hydrogen, assume SP2. TODO actually check for aromaticity.
+          int n_hydrogens = 0;
+          for (Atom::bond_iterator bat = AJ.bondbegin(); bat != AJ.bondend(); ++bat)
+            if (topIn[*bat].Element() == Atom::HYDROGEN)
+              n_hydrogens++;
+          if (n_hydrogens == 1)
+            hybrid = SP2;
+          else
+            hybrid = SP3;
+          break;
+      }
+      break;
+    case Atom::OXYGEN :
+      switch (AJ.Nbonds()) {
+        case 2 : hybrid = SP3; break;
+      }
+      break;
+    case Atom::SULFUR :
+      switch (AJ.Nbonds()) {
+        case 2 : hybrid = SP3; break;
+      }
+      break;
+    default: hybrid = UNKNOWN_HYBRIDIZATION; break;
+  }*/
+  // Fill in what values we can for known atoms
+/*  std::vector<double> knownTheta( AJ.Nbonds() );
+  int knownIdx = -1;
+  for (int idx = 0; idx < AJ.Nbonds(); idx++) {
+    int atnum = AJ.Bond(idx);
+    if (atnum != ak && atomPositionKnown[atnum]) {
+      knownTheta[idx] = CalcAngle(frameIn.XYZ(atnum),
+                                  frameIn.XYZ(aj),
+                                  frameIn.XYZ(ak));
+      mprintf("DEBUG:\t\tKnown theta for %s = %g\n", topIn.AtomMaskName(atnum).c_str(), knownTheta[idx]*Constants::RADDEG);
+      if (knownIdx == -1) knownIdx = idx; // FIXME handle more than 1 known
+    }
+  }
+  if (knownIdx == -1) {*/
+    //mprintf("DEBUG:\t\tNo known theta.\n");
+  if (hybrid == AtomType::UNKNOWN_HYBRIDIZATION) {
+    // Assign a theta based on number of bonds 
+    switch (AJ.Nbonds()) {
+      case 4 : hybrid = AtomType::SP3; break;
+      case 3 : hybrid = AtomType::SP2; break;
+      case 2 : hybrid = AtomType::SP; break;
+      default : mprinterr("Internal Error: AssignTheta(): Unhandled # bonds for %s (%i)\n", topIn.AtomMaskName(aj).c_str(), AJ.Nbonds()); return 1;
+    }
+  }
+  // Assign a theta based on hybridization
+  switch (hybrid) {
+    case AtomType::SP3 : theta = 109.5 * Constants::DEGRAD; break;
+    case AtomType::SP2 : theta = 120.0 * Constants::DEGRAD; break;
+    case AtomType::SP  : theta = 180.0 * Constants::DEGRAD; break;
+    default : mprinterr("Internal Error: AssignTheta(): Unhandled hybridization for %s (%i)\n", topIn.AtomMaskName(aj).c_str(), AJ.Nbonds()); return 1;
+  }/*
+  } else {
+    theta = knownTheta[knownIdx]; // TODO just use above guess via hybrid?
+  }*/
+
+  return 0;
+}
+
 // -----------------------------------------------------------------------------
 /** Combine two units. Fragment 1 will be merged into Fragment 0 and bonded. */
 int Builder::Combine(Topology&       frag0Top, Frame&       frag0frm,
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index fd4baf304a..297cda10bd 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -26,7 +26,10 @@ class Builder {
   private:
     /// Assign a reasonable value for bond distance given 2 atoms whose position may or may not be known
     int AssignLength(double&, int, int, Topology const&, Frame const&, std::vector<bool> const&) const;
+    /// Given atoms J and K, attempt to assign a reasonable value for theta for atom I
+    int AssignTheta(double&, int, int, int, Topology const&, Frame const&, std::vector<bool> const&) const;
 
+    /// Model coordinates around a bond
     int SetupICsAroundBond(Zmatrix&, int, int, Frame const&, Topology const&,
                            std::vector<bool> const&, std::vector<bool> const&,
                            BuildAtom const&, BuildAtom const&) const;

From d2ad854cf50416d6752184ba938ae755e94c1afe Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 29 Jan 2024 15:42:03 -0500
Subject: [PATCH 0403/1492] Copy AssignICsAroundBond to Builder

---
 src/Structure/Builder.cpp | 302 ++++++++++++++++++++++++++++++++++++++
 src/Structure/Builder.h   |   7 +
 2 files changed, 309 insertions(+)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 3ca3be6258..a170ff40b4 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -169,6 +169,308 @@ const
 
   return 0;
 }
+/** Insert internal coordinates with bond i-j, angle i-j-k, and torsion i-j-k-l. */
+int Cpptraj::Structure::Builder::insertIc(Zmatrix& zmatrix,
+                                        int ai, int aj, int ak, int al, double newPhi,
+                                        Topology const& topIn, Frame const& frameIn,
+                                        std::vector<bool> const& atomPositionKnown)
+const
+{
+  if (atomPositionKnown[ai]) {
+    mprintf("DEBUG:\tAtom position already known for %s, skipping IC.\n", topIn.AtomMaskName(ai).c_str());
+    return 0;
+  }
+  double newDist = 0;
+  if (AssignLength(newDist, ai, aj, topIn, frameIn, atomPositionKnown)) {
+    mprinterr("Error: AssignLength failed for %s - %s \n",
+              topIn.AtomMaskName(ai).c_str(), topIn.AtomMaskName(aj).c_str());
+    return 1;
+  }
+  double newTheta = 0;
+  if (AssignTheta(newTheta, ai, aj, ak, topIn, frameIn, atomPositionKnown)) {
+    mprinterr("Error: AssignTheta failed for %s - %s - %s\n",
+              topIn.AtomMaskName(ai).c_str(),
+              topIn.AtomMaskName(aj).c_str(),
+              topIn.AtomMaskName(ak).c_str());
+    return 1;
+  }
+  zmatrix.AddIC( InternalCoords(ai, aj, ak, al, newDist, newTheta*Constants::RADDEG, newPhi*Constants::RADDEG) );
+  return 0;
+}
+
+/// Recursive function to return depth from an atom along bonds
+static int atom_depth(int& depth,
+                      int at, Topology const& topIn, std::vector<bool>& visited, int maxdepth)
+{
+  if (depth == maxdepth) return 0;
+  depth++;
+  visited[at] = true;
+  int depthFromHere = 1;
+  for (Atom::bond_iterator bat = topIn[at].bondbegin(); bat != topIn[at].bondend(); ++bat)
+  {
+    if (!visited[*bat])
+      depthFromHere += atom_depth( depth, *bat, topIn, visited, maxdepth );
+  }
+  return depthFromHere;
+}
+
+/// Wrap given value between -PI and PI
+static inline double wrap360(double phi) {
+  if (phi > Constants::PI)
+    return phi - Constants::TWOPI;
+  else if (phi < -Constants::PI)
+    return phi + Constants::TWOPI;
+  else
+    return phi;
+}
+
+/** Assign internal coordinates for atoms I for torsions around J-K-L. */
+int Cpptraj::Structure::Builder::AssignICsAroundBond(Zmatrix& zmatrix,
+                                                   int aj, int ak, int al,
+                                                   Topology const& topIn, Frame const& frameIn,
+                                                   std::vector<bool> const& atomPositionKnown,
+                                                   BuildAtom const& AtomJ)
+const
+{
+  mprintf("DEBUG: AssignICsAroundBond: X - %s - %s - %s  %i - %i - %i\n",
+          topIn.AtomMaskName(aj).c_str(),
+          topIn.AtomMaskName(ak).c_str(),
+          topIn.AtomMaskName(al).c_str(),
+          aj+1, ak+1, al+1);
+  // Ideally, atoms J K and L should be known
+  if (!atomPositionKnown[aj] ||
+      !atomPositionKnown[ak] ||
+      !atomPositionKnown[al])
+  {
+    mprintf("Warning: AssignICsAroundBond(): Not all atom positions known.\n"
+            "Warning: %i %s (%i) - %i %s (%i) - %i %s (%i)\n",
+              aj+1, topIn.AtomMaskName(aj).c_str(), (int)atomPositionKnown[aj],
+              ak+1, topIn.AtomMaskName(ak).c_str(), (int)atomPositionKnown[ak],
+              al+1, topIn.AtomMaskName(al).c_str(), (int)atomPositionKnown[al]);
+    //return 1;
+  }
+  Atom const& AJ = topIn[aj];
+  // If atom J has only 1 bond this is not needed.
+  if (AJ.Nbonds() < 2) return 0;
+  
+
+  if (debug_ > 0) mprintf("DEBUG:\t\tNbonds: %i\n", AJ.Nbonds());
+  // If atom J only has 2 bonds, ai-aj-ak-al is the only possibility.
+  if (AJ.Nbonds() < 3) {
+    if (debug_ > 0)
+      mprintf("DEBUG:\t\tFewer than 3 bonds. Setting phi to -180.\n");
+    double newPhi = -180 * Constants::DEGRAD;
+    for (int idx = 0; idx < AJ.Nbonds(); idx++) {
+      if (AJ.Bond(idx) != ak) {
+        int ai = AJ.Bond(idx);
+        if (insertIc(zmatrix, ai, aj, ak, al, newPhi, topIn, frameIn, atomPositionKnown)) return 1;
+        break;
+      }
+    }
+    return 0;
+  } // END only 2 bonds
+
+  // 3 or more bonds.
+  std::vector<int> const& priority = AtomJ.Priority();
+  ChiralType chirality = AtomJ.Chirality();
+
+  if (debug_ > 0) {
+    mprintf("DEBUG:\t\tOriginal chirality around J %s is %s\n", topIn.AtomMaskName(aj).c_str(), chiralStr(chirality));
+    mprintf("DEBUG:\t\tPriority around J %s(%i) is", 
+            topIn.AtomMaskName(aj).c_str(), (int)atomPositionKnown[aj]);
+    for (int idx = 0; idx < AJ.Nbonds(); idx++)
+      mprintf(" %s(%i)", topIn.AtomMaskName(priority[idx]).c_str(), (int)atomPositionKnown[priority[idx]]);
+    for (int idx = 0; idx < AJ.Nbonds(); idx++)
+      mprintf(" %i", priority[idx]);
+    mprintf("\n");
+  }
+
+  // Get index of atom K in the priority list, starting from least priority.
+  int kPriorityIdx = -1;
+  for (int idx = AJ.Nbonds()-1; idx > -1; idx--) {
+    if (priority[idx] == ak) {
+      kPriorityIdx = AJ.Nbonds() - 1 - idx;
+      break;
+    }
+  }
+  mprintf("DEBUG:\t\tK priority index is %i\n", kPriorityIdx);
+  if (kPriorityIdx < 0) {
+    mprinterr("Error: Could not find atom K %s in atom J %s bond list.\n",
+              topIn.AtomMaskName(ak).c_str(), topIn.AtomMaskName(aj).c_str());
+    return 1;
+  }
+
+  // Fill in what values we can for known atoms
+  std::vector<double> knownPhi( AJ.Nbonds() );
+  std::vector<bool> isKnown( AJ.Nbonds(), false );
+  int knownIdx = -1;
+  double knownInterval = 0;
+  bool hasKnownInterval = false;
+  for (int idx = 0; idx < AJ.Nbonds(); idx++) {
+    int atnum = priority[idx];
+    if (atnum != ak && atomPositionKnown[atnum] &&
+                       atomPositionKnown[aj] &&
+                       atomPositionKnown[ak] &&
+                       atomPositionKnown[al])
+    {
+      knownPhi[idx] = Torsion(frameIn.XYZ(atnum),
+                              frameIn.XYZ(aj),
+                              frameIn.XYZ(ak),
+                              frameIn.XYZ(al));
+      isKnown[idx] = true;
+      if (debug_ > 0)
+        mprintf("DEBUG:\t\tKnown phi for %s (pos=%i) = %g\n", topIn.AtomMaskName(atnum).c_str(), idx, knownPhi[idx]*Constants::RADDEG);
+      if (knownIdx == -1) knownIdx = idx; // FIXME handle more than 1 known
+      if (idx > 0 && isKnown[idx-1] && isKnown[idx]) {
+        knownInterval = wrap360(knownPhi[idx] - knownPhi[idx-1]);
+        hasKnownInterval = true;
+      }
+    }
+  }
+
+  // Check known interval if set
+  if (hasKnownInterval) {
+    mprintf("DEBUG:\t\tKnown interval = %g\n", knownInterval * Constants::RADDEG);
+    if (chirality == IS_UNKNOWN_CHIRALITY) {
+      mprintf("DEBUG:\t\tSetting chirality from known interval.\n");
+      if (knownInterval < 0)
+        chirality = IS_S;
+      else
+        chirality = IS_R;
+    } else if (chirality == IS_S) {
+      if (knownInterval > 0)
+        mprinterr("Error: Detected chirality S does not match known interval %g\n", knownInterval*Constants::RADDEG);
+    } else if (chirality == IS_R) {
+      if (knownInterval < 0)
+        mprinterr("Error: Detected chriality R does not match known interval %g\n", knownInterval*Constants::RADDEG);
+    }
+  }
+
+  // If still no chirality use the detected orientation
+  if (chirality == IS_UNKNOWN_CHIRALITY) {
+    chirality = AtomJ.Orientation();
+    mprintf("Warning: Unknown chirality around %s; using detected orientation of %s\n",
+            topIn.AtomMaskName(aj).c_str(), chiralStr(chirality));
+  }
+
+  // Determine the interval
+  bool intervalIsSet = false;
+  double interval = 0;
+  if (params_ != 0) {
+    ParmHolder<AtomType>::const_iterator it = params_->AT().GetParam( TypeNameHolder(AJ.Type()) );
+    if (it != params_->AT().end()) {
+      if (it->second.Hybridization() == AtomType::SP2) {
+        interval = 180 * Constants::DEGRAD;
+        intervalIsSet = true;
+      } else if (it->second.Hybridization() == AtomType::SP3) {
+        interval = 120 * Constants::DEGRAD;
+        intervalIsSet = true;
+      }
+    }
+    if (intervalIsSet) mprintf("DEBUG:\t\tInterval was set from atom J hybridization.\n");
+  }
+  if (!intervalIsSet) {
+    // The interval will be 360 / (number of bonds - 1)
+    interval = Constants::TWOPI / (AJ.Nbonds() - 1);
+    mprintf("DEBUG:\t\tInterval was set from number of bonds.\n");
+  }
+
+  // Adjust interval based on chirality and priority of the k atom
+  if (chirality == IS_S || chirality == IS_UNKNOWN_CHIRALITY)
+    interval = -interval;
+  if ( (kPriorityIdx%2) == 0 ) {
+    mprintf("DEBUG:\t\tFlipping interval based on priority index of %i\n", kPriorityIdx);
+    interval = -interval;
+  }
+
+  // If there is a known interval, compare it to the determined one.
+  if (hasKnownInterval) {
+    double deltaInterval = fabs(interval - knownInterval);
+    mprintf("DEBUG:\t\tDetermined interval %g, known interval %g, delta %g\n",
+            interval*Constants::RADDEG, knownInterval*Constants::RADDEG, deltaInterval*Constants::RADDEG);
+    interval = fabs(knownInterval);
+  }
+
+  // If we have to assign an initial phi, make trans the longer branch
+  if (knownIdx == -1) {
+    std::vector<bool> visited = atomPositionKnown;
+    // TODO: Ensure bonded atoms are not yet visited?
+    visited[aj] = true;
+    visited[ak] = true;
+    //std::vector<int> depth( AJ.Nbonds() );
+    int max_depth = 0;
+    int max_idx = -1;
+    for (int idx = 0; idx < AJ.Nbonds(); idx++) {
+      int atnum = priority[idx];
+      if (atnum != ak) {
+        int currentDepth = 0;
+        //depth[idx] = atom_depth(currentDepth, atnum, topIn, visited, 10);
+        int depth = atom_depth(currentDepth, atnum, topIn, visited, 10);
+        if (debug_ > 0)
+          mprintf("DEBUG:\t\tAJ %s depth from %s is %i\n",
+                  topIn.AtomMaskName(aj).c_str(), topIn.AtomMaskName(atnum).c_str(), depth);
+        //if (knownIdx == -1 && depth[idx] < 3) {
+        //  knownIdx = idx;
+        //  knownPhi[idx] = 0;
+        //}
+        if (max_idx == -1 || depth > max_depth) {
+          max_depth = depth;
+          max_idx = idx;
+        }
+      }
+    }
+    mprintf("DEBUG:\t\tLongest depth is for atom %s (%i)\n", topIn.AtomMaskName(priority[max_idx]).c_str(), max_depth);
+    knownIdx = max_idx;
+    knownPhi[max_idx] = interval;// -180 * Constants::DEGRAD;
+    isKnown[max_idx] = true;
+  }
+
+  // Sanity check
+  if (knownIdx < 0) {
+    mprinterr("Internal Error: AssignPhi(): knownIdx is < 0\n");
+    return 1;
+  }
+
+  if (debug_ > 0) {
+    mprintf("DEBUG:\t\tStart phi is %g degrees\n", knownPhi[knownIdx]*Constants::RADDEG);
+    mprintf("DEBUG:\t\tInterval is %g, chirality around J is %s\n", interval*Constants::RADDEG, chiralStr(chirality));
+  }
+
+  // Forwards from the known index
+  double currentPhi = knownPhi[knownIdx];
+  for (int idx = knownIdx; idx < AJ.Nbonds(); idx++) {
+    int atnum = priority[idx];
+    if (atnum != ak) {
+      if (isKnown[idx])
+        currentPhi = knownPhi[idx];
+      else
+        currentPhi = wrap360(currentPhi + interval);
+      //if (atnum == ai) phi = currentPhi;
+      //IC.push_back( InternalCoords(atnum, aj, ak, al, 0, 0, currentPhi) );
+      if (insertIc(zmatrix, atnum, aj, ak, al, currentPhi, topIn, frameIn, atomPositionKnown)) return 1;
+      if (debug_ > 0)
+        mprintf("DEBUG:\t\t\t%s (at# %i) phi= %g\n", topIn.AtomMaskName(atnum).c_str(), atnum+1, currentPhi*Constants::RADDEG);
+    }
+  }
+  // Backwards from the known index
+  currentPhi = knownPhi[knownIdx];
+  for (int idx = knownIdx - 1; idx > -1; idx--) {
+    int atnum = priority[idx];
+    if (atnum != ak) {
+      if (isKnown[idx])
+        currentPhi = knownPhi[idx];
+      else
+        currentPhi = wrap360(currentPhi - interval);
+      //if (atnum == ai) phi = currentPhi;
+      //IC.push_back( InternalCoords(atnum, aj, ak, al, 0, 0, currentPhi) );
+      if (insertIc(zmatrix, atnum, aj, ak, al, currentPhi, topIn, frameIn, atomPositionKnown)) return 1;
+      if (debug_ > 0)
+        mprintf("DEBUG:\t\t\t%s (at# %i) phi= %g\n", topIn.AtomMaskName(atnum).c_str(), atnum+1, currentPhi*Constants::RADDEG);
+    }
+  }
+
+  return 0;
+}
 
 // -----------------------------------------------------------------------------
 /** Combine two units. Fragment 1 will be merged into Fragment 0 and bonded. */
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index 297cda10bd..3b2055b837 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -28,6 +28,13 @@ class Builder {
     int AssignLength(double&, int, int, Topology const&, Frame const&, std::vector<bool> const&) const;
     /// Given atoms J and K, attempt to assign a reasonable value for theta for atom I
     int AssignTheta(double&, int, int, int, Topology const&, Frame const&, std::vector<bool> const&) const;
+    /// Insert an internal coord into a zmatrix
+    int insertIc(Zmatrix&, int, int, int, int, double,
+                 Topology const&, Frame const&, std::vector<bool> const&) const;
+    /// Assign internal coordinates for atoms I for torsions around J-K-L.
+    int AssignICsAroundBond(Zmatrix&, int, int, int,
+                           Topology const&, Frame const&, std::vector<bool> const&,
+                           BuildAtom const&) const;
 
     /// Model coordinates around a bond
     int SetupICsAroundBond(Zmatrix&, int, int, Frame const&, Topology const&,

From f0e2f3612ea73ebe2f107afa40b3d526b57e69e7 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 30 Jan 2024 08:04:55 -0500
Subject: [PATCH 0404/1492] Remove Model class; functionality moved to Builder
 class.

---
 src/Structure/Builder.cpp     |  11 +-
 src/Structure/CMakeLists.txt  |   1 -
 src/Structure/Model.cpp       | 753 ----------------------------------
 src/Structure/Model.h         |  45 --
 src/Structure/structuredepend |   5 +-
 src/Structure/structurefiles  |   1 -
 src/cpptrajdepend             |  11 +-
 7 files changed, 12 insertions(+), 815 deletions(-)
 delete mode 100644 src/Structure/Model.cpp
 delete mode 100644 src/Structure/Model.h

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index a170ff40b4..02cbb2664b 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1,6 +1,5 @@
 #include "Builder.h"
 #include "BuildAtom.h"
-#include "Model.h"
 #include "Zmatrix.h"
 #include "../Constants.h"
 #include "../CpptrajStdio.h"
@@ -769,19 +768,19 @@ const
               topIn.AtomMaskName(atl0).c_str());
     modelDebug = debug_ - 1;
   }
-  Cpptraj::Structure::Model model;
+  //Cpptraj::Structure::Model model;
   //model.SetDebug( modelDebug ); //FIXME
-  model.SetDebug( 1 );
+  //model.SetDebug( 1 );
   // FIXME
   mprintf("DEBUG: ------------------------------------------------\n");
   //std::vector<InternalCoords> tmpic;
   // I J: Set up ICs for X atB K L
-  if (model.AssignICsAroundBond(zmatrix, atB, atk0, atl0, topIn, frameIn, atomPositionKnown, AtomB)) {
+  if (AssignICsAroundBond(zmatrix, atB, atk0, atl0, topIn, frameIn, atomPositionKnown, AtomB)) {
     mprinterr("Error: AssignICsAroundBond (I J) failed.\n");
     return 1;
   }
   // J K: Set up ICs for X atA atB K
-  if (model.AssignICsAroundBond(zmatrix, atA, atB, atk0, topIn, frameIn, atomPositionKnown, AtomA)) {
+  if (AssignICsAroundBond(zmatrix, atA, atB, atk0, topIn, frameIn, atomPositionKnown, AtomA)) {
     mprinterr("Error: AssignICsAroundBond (J K) failed.\n");
     return 1;
   }
@@ -805,7 +804,7 @@ const
           if (AtomC.DetermineChirality(*iat, topIn, frameIn, modelDebug)) return 1;
         }
         mprintf("DEBUG: K L IC needed for %s.\n", topIn.AtomMaskName(*iat).c_str());
-        if (model.AssignICsAroundBond(zmatrix, *iat, atA, atB, topIn, frameIn, atomPositionKnown, AtomC)) {
+        if (AssignICsAroundBond(zmatrix, *iat, atA, atB, topIn, frameIn, atomPositionKnown, AtomC)) {
           mprinterr("Error: AssignICsAroundBond (K L) failed.\n");
           return 1;
         }
diff --git a/src/Structure/CMakeLists.txt b/src/Structure/CMakeLists.txt
index ffdd80270f..a7cebdea51 100644
--- a/src/Structure/CMakeLists.txt
+++ b/src/Structure/CMakeLists.txt
@@ -8,7 +8,6 @@ target_sources(cpptraj_common_obj PRIVATE
   ${CMAKE_CURRENT_LIST_DIR}/GenerateConnectivityArrays.cpp
   ${CMAKE_CURRENT_LIST_DIR}/HisProt.cpp
   ${CMAKE_CURRENT_LIST_DIR}/InternalCoords.cpp
-  ${CMAKE_CURRENT_LIST_DIR}/Model.cpp
   ${CMAKE_CURRENT_LIST_DIR}/StructureEnum.cpp
   ${CMAKE_CURRENT_LIST_DIR}/StructureRoutines.cpp
   ${CMAKE_CURRENT_LIST_DIR}/SugarBuilder.cpp
diff --git a/src/Structure/Model.cpp b/src/Structure/Model.cpp
deleted file mode 100644
index a0d560964f..0000000000
--- a/src/Structure/Model.cpp
+++ /dev/null
@@ -1,753 +0,0 @@
-#include "Model.h"
-#include "BuildAtom.h"
-#include "Zmatrix.h"
-#include "../CpptrajStdio.h"
-#include "../GuessAtomHybridization.h"
-#include "../Topology.h"
-#include "../TorsionRoutines.h"
-#include "../DistRoutines.h"
-#include "../Constants.h"
-#include "../ParameterSet.h"
-#include <cmath>
-
-/** CONSTRUCTOR */
-Cpptraj::Structure::Model::Model() :
-  debug_(0),
-  params_(0)
-{}
-
-/** Set optional parameter set. */
-void Cpptraj::Structure::Model::SetParameters(ParameterSet const* paramsIn) {
-  if (paramsIn == 0) {
-    mprinterr("Internal Error: Model::SetParmaters called with null set.\n");
-    return;
-  }
-  params_ = paramsIn;
-}
-
-/** Assign reasonable value for bond distance. */
-int Cpptraj::Structure::Model::AssignLength(double& dist, int ai, int aj, Topology const& topIn, Frame const& frameIn, std::vector<bool> const& atomPositionKnown)
-const
-{
-  if (atomPositionKnown[ai] && atomPositionKnown[aj])
-    dist = sqrt( DIST2_NoImage( frameIn.XYZ(ai), frameIn.XYZ(aj) ) );
-  else {
-    // One or both positions unknown. Use estimated bond length or parameters.
-    bool foundParam = false;
-    if (params_ != 0 && topIn[ai].HasType() && topIn[aj].HasType()) {
-      TypeNameHolder btypes(2);
-      btypes.AddName( topIn[ai].Type() );
-      btypes.AddName( topIn[aj].Type() );
-      ParmHolder<BondParmType>::const_iterator it = params_->BP().GetParam( btypes );
-      if (it != params_->BP().end()) {
-        dist = it->second.Req();
-        foundParam = true;
-        mprintf("DEBUG: Found bond parameter for %s (%s) - %s (%s): req=%g rk=%g\n",
-                topIn.AtomMaskName(ai).c_str(), *(topIn[ai].Type()),
-                topIn.AtomMaskName(aj).c_str(), *(topIn[aj].Type()),
-                it->second.Req(), it->second.Rk());
-      }
-    }
-    if (!foundParam)
-      dist = Atom::GetBondLength( topIn[ai].Element(), topIn[aj].Element() );
-  }
-  return 0;
-}
-
-/** Attempt to assign a reasonable value for theta internal coordinate for
-  * atom i given that atoms j and k have known positions.
-  */
-int Cpptraj::Structure::Model::AssignTheta(double& theta, int ai, int aj, int ak, Topology const& topIn, Frame const& frameIn, std::vector<bool> const& atomPositionKnown)
-const
-{
-  // Figure out hybridization and chirality of atom j.
-  if (debug_ > 0)
-    mprintf("DEBUG: AssignTheta for atom j : %s\n", topIn.AtomMaskName(aj).c_str());
-  if (atomPositionKnown[ai] && atomPositionKnown[aj] && atomPositionKnown[ak])
-  {
-    theta = CalcAngle(frameIn.XYZ(ai), frameIn.XYZ(aj), frameIn.XYZ(ak));
-    return 0;
-  }
-
-  Atom const& AJ = topIn[aj];
-  if (debug_ > 0) {
-    mprintf("DEBUG:\t\tI %s Nbonds: %i\n", topIn[ai].ElementName(), topIn[ai].Nbonds());
-    mprintf("DEBUG:\t\tJ %s Nbonds: %i\n", AJ.ElementName(), AJ.Nbonds());
-    mprintf("DEBUG:\t\tK %s Nbonds: %i\n", topIn[ak].ElementName(), topIn[ak].Nbonds());
-  }
-  // Sanity check
-  if (AJ.Nbonds() < 2) {
-    mprinterr("Internal Error: AssignTheta() called for atom J %s with fewer than 2 bonds.\n", topIn.AtomMaskName(aj).c_str());
-    return 1;
-  }
-  AtomType::HybridizationType hybrid = AtomType::UNKNOWN_HYBRIDIZATION;
-  if (params_ != 0) {
-    ParmHolder<AtomType>::const_iterator it = params_->AT().GetParam( TypeNameHolder(AJ.Type()) );
-    if (it != params_->AT().end())
-      hybrid = it->second.Hybridization();
-  }
-  if (hybrid == AtomType::UNKNOWN_HYBRIDIZATION)
-    hybrid = GuessAtomHybridization(AJ, topIn.Atoms());
-/*
-  HybridizationType hybrid = UNKNOWN_HYBRIDIZATION;
-  // Handle specific elements
-  switch (AJ.Element()) {
-    case Atom::CARBON :
-      switch (AJ.Nbonds()) {
-        case 2 : hybrid = SP; break;
-        case 3 : hybrid = SP2; break;
-        case 4 : hybrid = SP3; break;
-      }
-      break;
-    case Atom::NITROGEN :
-      switch (AJ.Nbonds()) {
-        case 2 : hybrid = SP2; break;
-        case 3 :
-          // Check for potential SP2. If only 1 of the bonded atoms is
-          // hydrogen, assume SP2. TODO actually check for aromaticity.
-          int n_hydrogens = 0;
-          for (Atom::bond_iterator bat = AJ.bondbegin(); bat != AJ.bondend(); ++bat)
-            if (topIn[*bat].Element() == Atom::HYDROGEN)
-              n_hydrogens++;
-          if (n_hydrogens == 1)
-            hybrid = SP2;
-          else
-            hybrid = SP3;
-          break;
-      }
-      break;
-    case Atom::OXYGEN :
-      switch (AJ.Nbonds()) {
-        case 2 : hybrid = SP3; break;
-      }
-      break;
-    case Atom::SULFUR :
-      switch (AJ.Nbonds()) {
-        case 2 : hybrid = SP3; break;
-      }
-      break;
-    default: hybrid = UNKNOWN_HYBRIDIZATION; break;
-  }*/
-  // Fill in what values we can for known atoms
-/*  std::vector<double> knownTheta( AJ.Nbonds() );
-  int knownIdx = -1;
-  for (int idx = 0; idx < AJ.Nbonds(); idx++) {
-    int atnum = AJ.Bond(idx);
-    if (atnum != ak && atomPositionKnown[atnum]) {
-      knownTheta[idx] = CalcAngle(frameIn.XYZ(atnum),
-                                  frameIn.XYZ(aj),
-                                  frameIn.XYZ(ak));
-      mprintf("DEBUG:\t\tKnown theta for %s = %g\n", topIn.AtomMaskName(atnum).c_str(), knownTheta[idx]*Constants::RADDEG);
-      if (knownIdx == -1) knownIdx = idx; // FIXME handle more than 1 known
-    }
-  }
-  if (knownIdx == -1) {*/
-    //mprintf("DEBUG:\t\tNo known theta.\n");
-  if (hybrid == AtomType::UNKNOWN_HYBRIDIZATION) {
-    // Assign a theta based on number of bonds 
-    switch (AJ.Nbonds()) {
-      case 4 : hybrid = AtomType::SP3; break;
-      case 3 : hybrid = AtomType::SP2; break;
-      case 2 : hybrid = AtomType::SP; break;
-      default : mprinterr("Internal Error: AssignTheta(): Unhandled # bonds for %s (%i)\n", topIn.AtomMaskName(aj).c_str(), AJ.Nbonds()); return 1;
-    }
-  }
-  // Assign a theta based on hybridization
-  switch (hybrid) {
-    case AtomType::SP3 : theta = 109.5 * Constants::DEGRAD; break;
-    case AtomType::SP2 : theta = 120.0 * Constants::DEGRAD; break;
-    case AtomType::SP  : theta = 180.0 * Constants::DEGRAD; break;
-    default : mprinterr("Internal Error: AssignTheta(): Unhandled hybridization for %s (%i)\n", topIn.AtomMaskName(aj).c_str(), AJ.Nbonds()); return 1;
-  }/*
-  } else {
-    theta = knownTheta[knownIdx]; // TODO just use above guess via hybrid?
-  }*/
-
-  return 0;
-}
-
-/// Recursive function to return depth from an atom along bonds
-static int atom_depth(int& depth,
-                      int at, Topology const& topIn, std::vector<bool>& visited, int maxdepth)
-{
-  if (depth == maxdepth) return 0;
-  depth++;
-  visited[at] = true;
-  int depthFromHere = 1;
-  for (Atom::bond_iterator bat = topIn[at].bondbegin(); bat != topIn[at].bondend(); ++bat)
-  {
-    if (!visited[*bat])
-      depthFromHere += atom_depth( depth, *bat, topIn, visited, maxdepth );
-  }
-  return depthFromHere;
-}
-
-static inline double wrap360(double phi) {
-  if (phi > Constants::PI)
-    return phi - Constants::TWOPI;
-  else if (phi < -Constants::PI)
-    return phi + Constants::TWOPI;
-  else
-    return phi;
-}
-
-/** Attempt to assign reasonable values for phi internal coordinates for atoms
-  * bonded to atom j given that atoms j k and l have known positions.
-  *   j - k
-  *  /     \
-  * i       l
-  */
-//int Cpptraj::Structure::Model::AssignPhi(std::vector<InternalCoords>& IC, int aj, int ak, int al,
-int Cpptraj::Structure::Model::AssignPhi(double& phi, int ai, int aj, int ak, int al,
-                                         Topology const& topIn, Frame const& frameIn,
-                                         std::vector<bool> const& atomPositionKnown,
-                                         BuildAtom const& AtomJ)
-const
-{
-  Atom const& AJ = topIn[aj];
-  // If atom J has only 1 bond this is not needed.
-  if (AJ.Nbonds() < 2) return 0;
-
-  if (debug_ > 0) mprintf("DEBUG:\t\tNbonds: %i\n", AJ.Nbonds());
-  // If atom J only has 2 bonds, ai-aj-ak-al is the only possibility.
-  if (AJ.Nbonds() < 3) {
-    if (debug_ > 0)
-      mprintf("DEBUG:\t\tFewer than 3 bonds. Setting phi to -180.\n");
-    double currentPhi = -180 * Constants::DEGRAD;
-    for (int idx = 0; idx < AJ.Nbonds(); idx++) {
-      if (AJ.Bond(idx) != ak) {
-        //IC.push_back( InternalCoords(AJ.Bond(idx), aj, ak, al, 0, 0, currentPhi) );
-        phi = currentPhi;
-        break;
-       }
-    }
-    return 0;
-  }
-  // Figure out hybridization and chirality of atom j.
-  if (debug_ > 0)
-    mprintf("DEBUG: AssignPhi for atom j : %s\n", topIn.AtomMaskName(aj).c_str());
-//  std::vector<int> priority;
-//  int chiralDebug = debug_;
-//  if (chiralDebug > 0)
-//    chiralDebug--;
-//  ChiralType chirality = SetPriority(priority, aj, topIn, frameIn, chiralDebug);
-
-
-  // TODO check that atom i actually ends up on the list?
-  std::vector<int> const& priority = AtomJ.Priority();
-  ChiralType chirality = AtomJ.Chirality();
-  if (chirality == IS_UNKNOWN_CHIRALITY) {
-    chirality = AtomJ.Orientation();
-    mprintf("Warning: Unknown chirality around %s; using detected orientation of %s\n",
-            topIn.AtomMaskName(aj).c_str(), chiralStr(chirality));
-  }
-  if (debug_ > 0) {
-    mprintf("DEBUG: Original chirality around J %s is %s\n", topIn.AtomMaskName(aj).c_str(), chiralStr(chirality));
-    mprintf("DEBUG:\t\tPriority around J %s(%i) is", 
-            topIn.AtomMaskName(aj).c_str(), (int)atomPositionKnown[aj]);
-    for (int idx = 0; idx < AJ.Nbonds(); idx++)
-      mprintf(" %s(%i)", topIn.AtomMaskName(priority[idx]).c_str(), (int)atomPositionKnown[priority[idx]]);
-    mprintf("\n");
-  }
-
-  // Fill in what values we can for known atoms
-  std::vector<double> knownPhi( AJ.Nbonds() );
-  std::vector<bool> isKnown( AJ.Nbonds(), false );
-  int knownIdx = -1;
-  double knownInterval = 0;
-  bool hasKnownInterval = false;
-  for (int idx = 0; idx < AJ.Nbonds(); idx++) {
-    int atnum = priority[idx];
-    if (atnum != ak && atomPositionKnown[atnum] &&
-                       atomPositionKnown[aj] &&
-                       atomPositionKnown[ak] &&
-                       atomPositionKnown[al])
-    {
-      knownPhi[idx] = Torsion(frameIn.XYZ(atnum),
-                              frameIn.XYZ(aj),
-                              frameIn.XYZ(ak),
-                              frameIn.XYZ(al));
-      isKnown[idx] = true;
-      if (debug_ > 0)
-        mprintf("DEBUG:\t\tKnown phi for %s (pos=%i) = %g\n", topIn.AtomMaskName(atnum).c_str(), idx, knownPhi[idx]*Constants::RADDEG);
-      if (knownIdx == -1) knownIdx = idx; // FIXME handle more than 1 known
-      if (idx > 0 && isKnown[idx-1] && isKnown[idx]) {
-        knownInterval = wrap360(knownPhi[idx] - knownPhi[idx-1]);
-        hasKnownInterval = true;
-      }
-    }
-  }
-  if (hasKnownInterval)
-    mprintf("DEBUG:\t\tKnown interval = %g\n", knownInterval * Constants::RADDEG);
-
-  // If we have to assign an initial phi, make trans the longer branch
-  if (knownIdx == -1) {
-    std::vector<bool> visited = atomPositionKnown;
-    // TODO: Ensure bonded atoms are not yet visited?
-    visited[aj] = true;
-    visited[ak] = true;
-    //std::vector<int> depth( AJ.Nbonds() );
-    int max_depth = 0;
-    int max_idx = -1;
-    for (int idx = 0; idx < AJ.Nbonds(); idx++) {
-      int atnum = priority[idx];
-      if (atnum != ak) {
-        int currentDepth = 0;
-        //depth[idx] = atom_depth(currentDepth, atnum, topIn, visited, 10);
-        int depth = atom_depth(currentDepth, atnum, topIn, visited, 10);
-        if (debug_ > 0)
-          mprintf("DEBUG:\t\tAJ %s depth from %s is %i\n",
-                  topIn.AtomMaskName(aj).c_str(), topIn.AtomMaskName(atnum).c_str(), depth);
-        //if (knownIdx == -1 && depth[idx] < 3) {
-        //  knownIdx = idx;
-        //  knownPhi[idx] = 0;
-        //}
-        if (max_idx == -1 || depth > max_depth) {
-          max_depth = depth;
-          max_idx = idx;
-        }
-      }
-    }
-    mprintf("DEBUG:\t\tLongest depth is for atom %s (%i)\n", topIn.AtomMaskName(priority[max_idx]).c_str(), max_depth);
-    knownIdx = max_idx;
-    knownPhi[max_idx] = -180 * Constants::DEGRAD;
-    isKnown[max_idx] = true;
-  }
-
-  // Sanity check
-  if (knownIdx < 0) {
-    mprinterr("Internal Error: AssignPhi(): knownIdx is < 0\n");
-    return 1;
-  }
-
-  bool intervalIsSet = false;
-  double interval = 0;
-  if (params_ != 0) {
-    ParmHolder<AtomType>::const_iterator it = params_->AT().GetParam( TypeNameHolder(AJ.Type()) );
-    if (it != params_->AT().end()) {
-      if (it->second.Hybridization() == AtomType::SP2) {
-        interval = 180 * Constants::DEGRAD;
-        intervalIsSet = true;
-      } else if (it->second.Hybridization() == AtomType::SP3) {
-        interval = 120 * Constants::DEGRAD;
-        intervalIsSet = true;
-      }
-    }
-    if (intervalIsSet) mprintf("DEBUG: Interval was set from atom J hybridization.\n");
-  }
-  if (!intervalIsSet) {
-    // The interval will be 360 / (number of bonds - 1)
-    interval = Constants::TWOPI / (AJ.Nbonds() - 1);
-    mprintf("DEBUG: Interval was set from number of bonds.\n");
-  }
-
-  if (hasKnownInterval) {
-    if (chirality == IS_UNKNOWN_CHIRALITY) {
-      mprintf("DEBUG: Setting chirality from known interval.\n");
-      if (knownInterval < 0)
-        chirality = IS_S;
-      else
-        chirality = IS_R;
-    } else if (chirality == IS_S) {
-      if (knownInterval > 0)
-        mprinterr("Error: Detected chirality S does not match known interval %g\n", knownInterval*Constants::RADDEG);
-    } else if (chirality == IS_R) {
-      if (knownInterval < 0)
-        mprinterr("Error: Detected chriality R does not match known interval %g\n", knownInterval*Constants::RADDEG);
-    }
-  }
-  if (chirality == IS_S || chirality == IS_UNKNOWN_CHIRALITY)
-    interval = -interval;
- 
-
-  if (debug_ > 0) {
-    mprintf("DEBUG:\t\tStart phi is %g degrees\n", knownPhi[knownIdx]*Constants::RADDEG);
-    mprintf("DEBUG:\t\tInterval is %g, chirality around J is %s\n", interval*Constants::RADDEG, chiralStr(chirality));
-  }
-
-  // Forwards from the known index
-  double currentPhi = knownPhi[knownIdx];
-  for (int idx = knownIdx; idx < AJ.Nbonds(); idx++) {
-    int atnum = priority[idx];
-    if (atnum != ak) {
-      if (isKnown[idx])
-        currentPhi = knownPhi[idx];
-      else
-        currentPhi = wrap360(currentPhi + interval);
-      if (atnum == ai) phi = currentPhi;
-      //IC.push_back( InternalCoords(atnum, aj, ak, al, 0, 0, currentPhi) );
-      if (debug_ > 0)
-        mprintf("DEBUG:\t\t\t%s (at# %i) phi= %g\n", topIn.AtomMaskName(atnum).c_str(), atnum+1, currentPhi*Constants::RADDEG);
-    }
-  }
-  // Backwards from the known index
-  currentPhi = knownPhi[knownIdx];
-  for (int idx = knownIdx - 1; idx > -1; idx--) {
-    int atnum = priority[idx];
-    if (atnum != ak) {
-      if (isKnown[idx])
-        currentPhi = knownPhi[idx];
-      else
-        currentPhi = wrap360(currentPhi - interval);
-      if (atnum == ai) phi = currentPhi;
-      //IC.push_back( InternalCoords(atnum, aj, ak, al, 0, 0, currentPhi) );
-      if (debug_ > 0)
-        mprintf("DEBUG:\t\t\t%s (at# %i) phi= %g\n", topIn.AtomMaskName(atnum).c_str(), atnum+1, currentPhi*Constants::RADDEG);
-    }
-  }
-/*
-  double startPhi;
-  if (knownIdx == -1) {
-    startPhi = -180*Constants::DEGRAD;
-    if (debug_ > 0) mprintf("DEBUG:\t\tNo known phi. Setting to %g.\n", startPhi*Constants::RADDEG);
-    knownIdx = 0;
-  } else
-    startPhi = knownPhi[knownIdx];
-
-  if (AtomJ.Chirality() == IS_R) {
-    startPhi = -startPhi;
-    interval = -interval;
-  }
-    
-  // Forward direction
-  double currentPhi = startPhi;
-  for (int idx = knownIdx; idx < AJ.Nbonds(); idx++) {
-    int atnum = priority[idx];
-    if (atnum != ak) {
-      if (atnum == ai) phi = currentPhi;
-      if (debug_ > 0)
-        mprintf("DEBUG:\t\t\t%s phi= %g\n", topIn.AtomMaskName(atnum).c_str(), currentPhi*Constants::RADDEG);
-      currentPhi += interval;
-      currentPhi = wrap360(currentPhi);
-    }
-  }
-  // Reverse direction
-  currentPhi = startPhi - interval;
-  for (int idx = knownIdx - 1; idx > -1; idx--) {
-    int atnum = priority[idx];
-    if (atnum != ak) {
-      if (atnum == ai) phi = currentPhi;
-      if (debug_ > 0)
-        mprintf("DEBUG:\t\t\t%s phi= %g\n", topIn.AtomMaskName(atnum).c_str(), currentPhi*Constants::RADDEG);
-      currentPhi -= interval;
-      currentPhi = wrap360(currentPhi);
-    }
-  }
-*/
-  return 0;
-}
-
-/** Insert internal coordinates with bond i-j, angle i-j-k, and torsion i-j-k-l. */
-int Cpptraj::Structure::Model::insertIc(Zmatrix& zmatrix,
-                                        int ai, int aj, int ak, int al, double newPhi,
-                                        Topology const& topIn, Frame const& frameIn,
-                                        std::vector<bool> const& atomPositionKnown)
-const
-{
-  if (atomPositionKnown[ai]) {
-    mprintf("DEBUG:\tAtom position already known for %s, skipping IC.\n", topIn.AtomMaskName(ai).c_str());
-    return 0;
-  }
-  double newDist = 0;
-  if (AssignLength(newDist, ai, aj, topIn, frameIn, atomPositionKnown)) {
-    mprinterr("Error: AssignLength failed for %s - %s \n",
-              topIn.AtomMaskName(ai).c_str(), topIn.AtomMaskName(aj).c_str());
-    return 1;
-  }
-  double newTheta = 0;
-  if (AssignTheta(newTheta, ai, aj, ak, topIn, frameIn, atomPositionKnown)) {
-    mprinterr("Error: AssignTheta failed for %s - %s - %s\n",
-              topIn.AtomMaskName(ai).c_str(),
-              topIn.AtomMaskName(aj).c_str(),
-              topIn.AtomMaskName(ak).c_str());
-    return 1;
-  }
-  zmatrix.AddIC( InternalCoords(ai, aj, ak, al, newDist, newTheta*Constants::RADDEG, newPhi*Constants::RADDEG) );
-  return 0;
-}
-
-/** Assign internal coordinates for atoms I for torsions around J-K-L. */
-int Cpptraj::Structure::Model::AssignICsAroundBond(Zmatrix& zmatrix,
-                                                   int aj, int ak, int al,
-                                                   Topology const& topIn, Frame const& frameIn,
-                                                   std::vector<bool> const& atomPositionKnown,
-                                                   BuildAtom const& AtomJ)
-const
-{
-  mprintf("DEBUG: AssignICsAroundBond: X - %s - %s - %s  %i - %i - %i\n",
-          topIn.AtomMaskName(aj).c_str(),
-          topIn.AtomMaskName(ak).c_str(),
-          topIn.AtomMaskName(al).c_str(),
-          aj+1, ak+1, al+1);
-  // Ideally, atoms J K and L should be known
-  if (!atomPositionKnown[aj] ||
-      !atomPositionKnown[ak] ||
-      !atomPositionKnown[al])
-  {
-    mprintf("Warning: AssignICsAroundBond(): Not all atom positions known.\n"
-            "Warning: %i %s (%i) - %i %s (%i) - %i %s (%i)\n",
-              aj+1, topIn.AtomMaskName(aj).c_str(), (int)atomPositionKnown[aj],
-              ak+1, topIn.AtomMaskName(ak).c_str(), (int)atomPositionKnown[ak],
-              al+1, topIn.AtomMaskName(al).c_str(), (int)atomPositionKnown[al]);
-    //return 1;
-  }
-  Atom const& AJ = topIn[aj];
-  // If atom J has only 1 bond this is not needed.
-  if (AJ.Nbonds() < 2) return 0;
-  
-
-  if (debug_ > 0) mprintf("DEBUG:\t\tNbonds: %i\n", AJ.Nbonds());
-  // If atom J only has 2 bonds, ai-aj-ak-al is the only possibility.
-  if (AJ.Nbonds() < 3) {
-    if (debug_ > 0)
-      mprintf("DEBUG:\t\tFewer than 3 bonds. Setting phi to -180.\n");
-    double newPhi = -180 * Constants::DEGRAD;
-    for (int idx = 0; idx < AJ.Nbonds(); idx++) {
-      if (AJ.Bond(idx) != ak) {
-        int ai = AJ.Bond(idx);
-        if (insertIc(zmatrix, ai, aj, ak, al, newPhi, topIn, frameIn, atomPositionKnown)) return 1;
-        break;
-      }
-    }
-    return 0;
-  } // END only 2 bonds
-
-  // 3 or more bonds.
-  std::vector<int> const& priority = AtomJ.Priority();
-  ChiralType chirality = AtomJ.Chirality();
-
-  if (debug_ > 0) {
-    mprintf("DEBUG:\t\tOriginal chirality around J %s is %s\n", topIn.AtomMaskName(aj).c_str(), chiralStr(chirality));
-    mprintf("DEBUG:\t\tPriority around J %s(%i) is", 
-            topIn.AtomMaskName(aj).c_str(), (int)atomPositionKnown[aj]);
-    for (int idx = 0; idx < AJ.Nbonds(); idx++)
-      mprintf(" %s(%i)", topIn.AtomMaskName(priority[idx]).c_str(), (int)atomPositionKnown[priority[idx]]);
-    for (int idx = 0; idx < AJ.Nbonds(); idx++)
-      mprintf(" %i", priority[idx]);
-    mprintf("\n");
-  }
-
-  // Get index of atom K in the priority list, starting from least priority.
-  int kPriorityIdx = -1;
-  for (int idx = AJ.Nbonds()-1; idx > -1; idx--) {
-    if (priority[idx] == ak) {
-      kPriorityIdx = AJ.Nbonds() - 1 - idx;
-      break;
-    }
-  }
-  mprintf("DEBUG:\t\tK priority index is %i\n", kPriorityIdx);
-  if (kPriorityIdx < 0) {
-    mprinterr("Error: Could not find atom K %s in atom J %s bond list.\n",
-              topIn.AtomMaskName(ak).c_str(), topIn.AtomMaskName(aj).c_str());
-    return 1;
-  }
-
-  // Fill in what values we can for known atoms
-  std::vector<double> knownPhi( AJ.Nbonds() );
-  std::vector<bool> isKnown( AJ.Nbonds(), false );
-  int knownIdx = -1;
-  double knownInterval = 0;
-  bool hasKnownInterval = false;
-  for (int idx = 0; idx < AJ.Nbonds(); idx++) {
-    int atnum = priority[idx];
-    if (atnum != ak && atomPositionKnown[atnum] &&
-                       atomPositionKnown[aj] &&
-                       atomPositionKnown[ak] &&
-                       atomPositionKnown[al])
-    {
-      knownPhi[idx] = Torsion(frameIn.XYZ(atnum),
-                              frameIn.XYZ(aj),
-                              frameIn.XYZ(ak),
-                              frameIn.XYZ(al));
-      isKnown[idx] = true;
-      if (debug_ > 0)
-        mprintf("DEBUG:\t\tKnown phi for %s (pos=%i) = %g\n", topIn.AtomMaskName(atnum).c_str(), idx, knownPhi[idx]*Constants::RADDEG);
-      if (knownIdx == -1) knownIdx = idx; // FIXME handle more than 1 known
-      if (idx > 0 && isKnown[idx-1] && isKnown[idx]) {
-        knownInterval = wrap360(knownPhi[idx] - knownPhi[idx-1]);
-        hasKnownInterval = true;
-      }
-    }
-  }
-
-  // Check known interval if set
-  if (hasKnownInterval) {
-    mprintf("DEBUG:\t\tKnown interval = %g\n", knownInterval * Constants::RADDEG);
-    if (chirality == IS_UNKNOWN_CHIRALITY) {
-      mprintf("DEBUG:\t\tSetting chirality from known interval.\n");
-      if (knownInterval < 0)
-        chirality = IS_S;
-      else
-        chirality = IS_R;
-    } else if (chirality == IS_S) {
-      if (knownInterval > 0)
-        mprinterr("Error: Detected chirality S does not match known interval %g\n", knownInterval*Constants::RADDEG);
-    } else if (chirality == IS_R) {
-      if (knownInterval < 0)
-        mprinterr("Error: Detected chriality R does not match known interval %g\n", knownInterval*Constants::RADDEG);
-    }
-  }
-
-  // If still no chirality use the detected orientation
-  if (chirality == IS_UNKNOWN_CHIRALITY) {
-    chirality = AtomJ.Orientation();
-    mprintf("Warning: Unknown chirality around %s; using detected orientation of %s\n",
-            topIn.AtomMaskName(aj).c_str(), chiralStr(chirality));
-  }
-
-  // Determine the interval
-  bool intervalIsSet = false;
-  double interval = 0;
-  if (params_ != 0) {
-    ParmHolder<AtomType>::const_iterator it = params_->AT().GetParam( TypeNameHolder(AJ.Type()) );
-    if (it != params_->AT().end()) {
-      if (it->second.Hybridization() == AtomType::SP2) {
-        interval = 180 * Constants::DEGRAD;
-        intervalIsSet = true;
-      } else if (it->second.Hybridization() == AtomType::SP3) {
-        interval = 120 * Constants::DEGRAD;
-        intervalIsSet = true;
-      }
-    }
-    if (intervalIsSet) mprintf("DEBUG:\t\tInterval was set from atom J hybridization.\n");
-  }
-  if (!intervalIsSet) {
-    // The interval will be 360 / (number of bonds - 1)
-    interval = Constants::TWOPI / (AJ.Nbonds() - 1);
-    mprintf("DEBUG:\t\tInterval was set from number of bonds.\n");
-  }
-
-  // Adjust interval based on chirality and priority of the k atom
-  if (chirality == IS_S || chirality == IS_UNKNOWN_CHIRALITY)
-    interval = -interval;
-  if ( (kPriorityIdx%2) == 0 ) {
-    mprintf("DEBUG:\t\tFlipping interval based on priority index of %i\n", kPriorityIdx);
-    interval = -interval;
-  }
-
-  // If there is a known interval, compare it to the determined one.
-  if (hasKnownInterval) {
-    double deltaInterval = fabs(interval - knownInterval);
-    mprintf("DEBUG:\t\tDetermined interval %g, known interval %g, delta %g\n",
-            interval*Constants::RADDEG, knownInterval*Constants::RADDEG, deltaInterval*Constants::RADDEG);
-    interval = fabs(knownInterval);
-  }
-
-  // If we have to assign an initial phi, make trans the longer branch
-  if (knownIdx == -1) {
-    std::vector<bool> visited = atomPositionKnown;
-    // TODO: Ensure bonded atoms are not yet visited?
-    visited[aj] = true;
-    visited[ak] = true;
-    //std::vector<int> depth( AJ.Nbonds() );
-    int max_depth = 0;
-    int max_idx = -1;
-    for (int idx = 0; idx < AJ.Nbonds(); idx++) {
-      int atnum = priority[idx];
-      if (atnum != ak) {
-        int currentDepth = 0;
-        //depth[idx] = atom_depth(currentDepth, atnum, topIn, visited, 10);
-        int depth = atom_depth(currentDepth, atnum, topIn, visited, 10);
-        if (debug_ > 0)
-          mprintf("DEBUG:\t\tAJ %s depth from %s is %i\n",
-                  topIn.AtomMaskName(aj).c_str(), topIn.AtomMaskName(atnum).c_str(), depth);
-        //if (knownIdx == -1 && depth[idx] < 3) {
-        //  knownIdx = idx;
-        //  knownPhi[idx] = 0;
-        //}
-        if (max_idx == -1 || depth > max_depth) {
-          max_depth = depth;
-          max_idx = idx;
-        }
-      }
-    }
-    mprintf("DEBUG:\t\tLongest depth is for atom %s (%i)\n", topIn.AtomMaskName(priority[max_idx]).c_str(), max_depth);
-    knownIdx = max_idx;
-    knownPhi[max_idx] = interval;// -180 * Constants::DEGRAD;
-    isKnown[max_idx] = true;
-  }
-
-  // Sanity check
-  if (knownIdx < 0) {
-    mprinterr("Internal Error: AssignPhi(): knownIdx is < 0\n");
-    return 1;
-  }
-
-  if (debug_ > 0) {
-    mprintf("DEBUG:\t\tStart phi is %g degrees\n", knownPhi[knownIdx]*Constants::RADDEG);
-    mprintf("DEBUG:\t\tInterval is %g, chirality around J is %s\n", interval*Constants::RADDEG, chiralStr(chirality));
-  }
-
-  // Forwards from the known index
-  double currentPhi = knownPhi[knownIdx];
-  for (int idx = knownIdx; idx < AJ.Nbonds(); idx++) {
-    int atnum = priority[idx];
-    if (atnum != ak) {
-      if (isKnown[idx])
-        currentPhi = knownPhi[idx];
-      else
-        currentPhi = wrap360(currentPhi + interval);
-      //if (atnum == ai) phi = currentPhi;
-      //IC.push_back( InternalCoords(atnum, aj, ak, al, 0, 0, currentPhi) );
-      if (insertIc(zmatrix, atnum, aj, ak, al, currentPhi, topIn, frameIn, atomPositionKnown)) return 1;
-      if (debug_ > 0)
-        mprintf("DEBUG:\t\t\t%s (at# %i) phi= %g\n", topIn.AtomMaskName(atnum).c_str(), atnum+1, currentPhi*Constants::RADDEG);
-    }
-  }
-  // Backwards from the known index
-  currentPhi = knownPhi[knownIdx];
-  for (int idx = knownIdx - 1; idx > -1; idx--) {
-    int atnum = priority[idx];
-    if (atnum != ak) {
-      if (isKnown[idx])
-        currentPhi = knownPhi[idx];
-      else
-        currentPhi = wrap360(currentPhi - interval);
-      //if (atnum == ai) phi = currentPhi;
-      //IC.push_back( InternalCoords(atnum, aj, ak, al, 0, 0, currentPhi) );
-      if (insertIc(zmatrix, atnum, aj, ak, al, currentPhi, topIn, frameIn, atomPositionKnown)) return 1;
-      if (debug_ > 0)
-        mprintf("DEBUG:\t\t\t%s (at# %i) phi= %g\n", topIn.AtomMaskName(atnum).c_str(), atnum+1, currentPhi*Constants::RADDEG);
-    }
-  }
-
-  return 0;
-}
-/*
-static inline AtomType::HybridizationType getAtomHybridization(ParmHolder<AtomType> const& AT, Topology const& topIn, int ix)
-{
-  AtomType::HybridizationType hx;
-  ParmHolder<AtomType>::const_iterator itx = AT.GetParam( TypeNameHolder( topIn[ix].Type() ) );
-  if (itx == AT.end())
-    hx = Cpptraj::GuessAtomHybridization(topIn[ix], topIn.Atoms());
-  else
-    hx = itx->second.Hybridization();
-  return hx;
-}
-*/
-/** Assign phi values around a bond. */
-/*int Cpptraj::Structure::Model::AssignPhiAroundBond(int ix, int iy, Topology const& topIn, Frame const& frameIn,
-                                                   std::vector<bool> const& atomPositionKnown,
-                                                   ParmHolder<AtomType> const& AT)
-const
-{
-  // Order atoms by hybridization; AX > AY
-  int ax, ay;
-  AtomType::HybridizationType hx = getAtomHybridization(AT, topIn, ix);
-  AtomType::HybridizationType hy = getAtomHybridization(AT, topIn, iy);
-  if (hx < hy) {
-    ax = iy;
-    ay = ix;
-  } else {
-    ax = ix;
-    ay = iy;
-  }
-  mprintf("DEBUG: Assign torsions around %s (%i) - %s (%i)\n",
-          topIn.AtomMaskName(ix).c_str(), (int)hx,
-          topIn.AtomMaskName(iy).c_str(), (int)hy);
-  mprintf("DEBUG: Ordered by hybridization: %s %s\n", 
-          topIn.AtomMaskName(ax).c_str(),
-          topIn.AtomMaskName(ay).c_str());
- 
-  return 0;
-}*/
diff --git a/src/Structure/Model.h b/src/Structure/Model.h
deleted file mode 100644
index f73f711579..0000000000
--- a/src/Structure/Model.h
+++ /dev/null
@@ -1,45 +0,0 @@
-#ifndef INC_STRUCTURE_MODEL_H
-#define INC_STRUCTURE_MODEL_H
-#include <vector>
-//#incl ude "StructureEnum.h"
-class Topology;
-class Frame;
-class ParameterSet;
-//template <typename T> class ParmHolder;
-//class AtomType;
-namespace Cpptraj {
-namespace Structure {
-class BuildAtom;
-class Zmatrix; 
-/// Routines to create a model for missing bond/angle/torsion parameters
-class Model {
-  public:
-    /// CONSTRUCTOR
-    Model();
-    /// Set debug level
-    void SetDebug(int d) { debug_ = d; }
-    /// Set optional parameter set
-    void SetParameters(ParameterSet const*);
-    /// Assign a reasonable value for bond distance given 2 atoms whose position may or may not be known
-    int AssignLength(double&, int, int, Topology const&, Frame const&, std::vector<bool> const&) const;
-    /// Given atoms J and K, attempt to assign a reasonable value for theta for atom I
-    int AssignTheta(double&, int, int, int, Topology const&, Frame const&, std::vector<bool> const&) const;
-    /// Given atoms J K and L, attempt to assign a reasonable value for phi for atom I
-    //int AssignPhi(std::vector<InternalCoords>&, int, int, int, Topology const&, Frame const&, std::vector<bool> const&, BuildAtom const&) const;
-    /// Given atoms I J K and L, attempt to assign a reasonable value for phi for atom I
-    int AssignPhi(double&, int, int, int, int, Topology const&, Frame const&, std::vector<bool> const&, BuildAtom const&) const;
-    /// Assign internal coordinates for atoms I for torsions around J-K-L.
-    int AssignICsAroundBond(Zmatrix&, int, int, int,
-                           Topology const&, Frame const&, std::vector<bool> const&,
-                           BuildAtom const&) const;
-  private:
-    int insertIc(Zmatrix&, int, int, int, int, double,
-                 Topology const&, Frame const&, std::vector<bool> const&) const;
-
-
-    int debug_;
-    ParameterSet const* params_;
-};
-} // END namespace Structure
-} // END namespace Cpptraj
-#endif
diff --git a/src/Structure/structuredepend b/src/Structure/structuredepend
index 0c7b220ea1..772844a3da 100644
--- a/src/Structure/structuredepend
+++ b/src/Structure/structuredepend
@@ -1,16 +1,15 @@
 BuildAtom.o : BuildAtom.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h StructureEnum.h
-Builder.o : Builder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h Builder.h InternalCoords.h Model.h StructureEnum.h Zmatrix.h
+Builder.o : Builder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h Builder.h InternalCoords.h StructureEnum.h Zmatrix.h
 Disulfide.o : Disulfide.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Disulfide.h ResStatArray.h StructureRoutines.h
 FunctionalGroup.o : FunctionalGroup.cpp ../Atom.h ../AtomMap.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h FunctionalGroup.h
 FxnGroupBuilder.o : FxnGroupBuilder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h FunctionalGroup.h FxnGroupBuilder.h StructureRoutines.h Sugar.h SugarToken.h
 GenerateConnectivityArrays.o : GenerateConnectivityArrays.cpp ../Atom.h ../Constants.h ../CpptrajStdio.h ../NameType.h ../ParameterTypes.h ../Residue.h ../SymbolExporting.h GenerateConnectivityArrays.h
 HisProt.o : HisProt.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h HisProt.h StructureRoutines.h
 InternalCoords.o : InternalCoords.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h InternalCoords.h
-Model.o : Model.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h InternalCoords.h Model.h StructureEnum.h Zmatrix.h
 StructureEnum.o : StructureEnum.cpp StructureEnum.h
 StructureRoutines.o : StructureRoutines.cpp ../Atom.h ../CpptrajStdio.h ../NameType.h ../Residue.h ../SymbolExporting.h StructureRoutines.h
 Sugar.o : Sugar.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Sugar.h SugarToken.h
 SugarBuilder.o : SugarBuilder.cpp ../ArgList.h ../Atom.h ../AtomMap.h ../AtomMask.h ../AtomType.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DistRoutines.h ../FileIO.h ../FileName.h ../Frame.h ../ImageOption.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h FunctionalGroup.h FxnGroupBuilder.h LinkAtom.h ResStatArray.h StructureEnum.h StructureRoutines.h Sugar.h SugarBuilder.h SugarLinkAtoms.h SugarToken.h
 SugarLinkAtoms.o : SugarLinkAtoms.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../StringRoutines.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h LinkAtom.h SugarLinkAtoms.h
 SugarToken.o : SugarToken.cpp ../ArgList.h ../CpptrajStdio.h SugarToken.h
-Zmatrix.o : Zmatrix.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h GenerateConnectivityArrays.h InternalCoords.h StructureEnum.h Zmatrix.h
+Zmatrix.o : Zmatrix.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h GenerateConnectivityArrays.h InternalCoords.h Zmatrix.h
diff --git a/src/Structure/structurefiles b/src/Structure/structurefiles
index d609540255..1e7c8a3f12 100644
--- a/src/Structure/structurefiles
+++ b/src/Structure/structurefiles
@@ -8,7 +8,6 @@ STRUCTURE_SOURCES= \
   GenerateConnectivityArrays.cpp \
   HisProt.cpp \
   InternalCoords.cpp \
-  Model.cpp \
   StructureEnum.cpp \
   StructureRoutines.cpp \
   SugarBuilder.cpp \
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index f58b379a6f..93baffd806 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -209,7 +209,7 @@ DataIO_AmberEne.o : DataIO_AmberEne.cpp ArgList.h AssociatedData.h Atom.h AtomMa
 DataIO_AmberFF.o : DataIO_AmberFF.cpp AmberParamFile.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberFF.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_AmberFrcmod.o : DataIO_AmberFrcmod.cpp AmberParamFile.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberFrcmod.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_AmberLib.o : DataIO_AmberLib.cpp ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberLib.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_AmberPrep.o : DataIO_AmberPrep.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberPrep.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_AmberPrep.o : DataIO_AmberPrep.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberPrep.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_CCP4.o : DataIO_CCP4.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ByteRoutines.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CCP4.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_CharmmFastRep.o : DataIO_CharmmFastRep.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmFastRep.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_CharmmOutput.o : DataIO_CharmmOutput.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmOutput.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
@@ -260,7 +260,7 @@ DataSet_Tensor.o : DataSet_Tensor.cpp AssociatedData.h CpptrajFile.h DataSet.h D
 DataSet_Topology.o : DataSet_Topology.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Topology.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataSet_Vector.o : DataSet_Vector.cpp ArrayIterator.h AssociatedData.h ComplexArray.h Constants.h Corr.h CpptrajFile.h DataSet.h DataSet_1D.h DataSet_Vector.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h PubFFT.h Range.h SymbolExporting.h TextFormat.h Vec3.h
 DataSet_Vector_Scalar.o : DataSet_Vector_Scalar.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Vector_Scalar.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h Vec3.h
-DataSet_Zmatrix.o : DataSet_Zmatrix.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Zmatrix.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h TextFormat.h Vec3.h
+DataSet_Zmatrix.o : DataSet_Zmatrix.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Zmatrix.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h Structure/InternalCoords.h Structure/Zmatrix.h TextFormat.h Vec3.h
 DataSet_double.o : DataSet_double.cpp AssociatedData.h CpptrajFile.h DataSet.h DataSet_1D.h DataSet_double.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
 DataSet_float.o : DataSet_float.cpp AssociatedData.h CpptrajFile.h DataSet.h DataSet_1D.h DataSet_float.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
 DataSet_integer_disk.o : DataSet_integer_disk.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_integer.h DataSet_integer_disk.h Dimension.h FileIO.h FileName.h File_TempName.h MetaData.h NC_Routines.h Parallel.h Range.h TextFormat.h
@@ -345,7 +345,7 @@ Exec_Top.o : Exec_Top.cpp Action.h ActionList.h ActionState.h Analysis.h Analysi
 Exec_Traj.o : Exec_Traj.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Traj.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_UpdateParameters.o : Exec_UpdateParameters.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h DataSet_Topology.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_UpdateParameters.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_ViewRst.o : Exec_ViewRst.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ViewRst.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h ViewRst.h
-Exec_Zmatrix.o : Exec_Zmatrix.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Zmatrix.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Zmatrix.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Zmatrix.o : Exec_Zmatrix.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Zmatrix.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Zmatrix.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 ExtendedSimilarity.o : ExtendedSimilarity.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h ExtendedSimilarity.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 ExternalFxn.o : ExternalFxn.cpp Random.h
 FileIO_Bzip2.o : FileIO_Bzip2.cpp CpptrajStdio.h FileIO.h FileIO_Bzip2.h
@@ -446,21 +446,20 @@ Spline.o : Spline.cpp CpptrajStdio.h Spline.h
 SplineFxnTable.o : SplineFxnTable.cpp Constants.h CpptrajStdio.h Spline.h SplineFxnTable.h StringRoutines.h
 StringRoutines.o : StringRoutines.cpp CpptrajStdio.h StringRoutines.h
 Structure/BuildAtom.o : Structure/BuildAtom.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/StructureEnum.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Structure/Builder.o : Structure/Builder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/Builder.h Structure/InternalCoords.h Structure/Model.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Structure/Builder.o : Structure/Builder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h GuessAtomHybridization.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/Builder.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 Structure/Disulfide.o : Structure/Disulfide.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Disulfide.h Structure/ResStatArray.h Structure/StructureRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/FunctionalGroup.o : Structure/FunctionalGroup.cpp Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/FxnGroupBuilder.o : Structure/FxnGroupBuilder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h Structure/FxnGroupBuilder.h Structure/StructureRoutines.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/GenerateConnectivityArrays.o : Structure/GenerateConnectivityArrays.cpp Atom.h Constants.h CpptrajStdio.h NameType.h ParameterTypes.h Residue.h Structure/GenerateConnectivityArrays.h SymbolExporting.h
 Structure/HisProt.o : Structure/HisProt.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/HisProt.h Structure/StructureRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/InternalCoords.o : Structure/InternalCoords.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/InternalCoords.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Structure/Model.o : Structure/Model.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h GuessAtomHybridization.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/InternalCoords.h Structure/Model.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 Structure/StructureEnum.o : Structure/StructureEnum.cpp Structure/StructureEnum.h
 Structure/StructureRoutines.o : Structure/StructureRoutines.cpp Atom.h CpptrajStdio.h NameType.h Residue.h Structure/StructureRoutines.h SymbolExporting.h
 Structure/Sugar.o : Structure/Sugar.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/SugarBuilder.o : Structure/SugarBuilder.cpp ArgList.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DistRoutines.h FileIO.h FileName.h Frame.h ImageOption.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/FunctionalGroup.h Structure/FxnGroupBuilder.h Structure/LinkAtom.h Structure/ResStatArray.h Structure/StructureEnum.h Structure/StructureRoutines.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarLinkAtoms.h Structure/SugarToken.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 Structure/SugarLinkAtoms.o : Structure/SugarLinkAtoms.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/LinkAtom.h Structure/SugarLinkAtoms.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/SugarToken.o : Structure/SugarToken.cpp ArgList.h CpptrajStdio.h Structure/SugarToken.h
-Structure/Zmatrix.o : Structure/Zmatrix.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Structure/Zmatrix.o : Structure/Zmatrix.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 StructureCheck.o : StructureCheck.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h ExclusionArray.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StructureCheck.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 StructureMapper.o : StructureMapper.cpp AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StructureMapper.h SymbolExporting.h TextFormat.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 SymmetricRmsdCalc.o : SymmetricRmsdCalc.cpp ArrayIterator.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h Hungarian.h ImageOption.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h Topology.h TypeNameHolder.h Unit.h Vec3.h

From c54d6d2f67338cc87b61fbd7bcd11fd3162ddc8f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 30 Jan 2024 08:13:41 -0500
Subject: [PATCH 0405/1492] Look for angle parameters

---
 src/Structure/Builder.cpp | 65 +++++++++++++++------------------------
 1 file changed, 24 insertions(+), 41 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 02cbb2664b..ee439d63f1 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -63,7 +63,6 @@ const
 int Cpptraj::Structure::Builder::AssignTheta(double& theta, int ai, int aj, int ak, Topology const& topIn, Frame const& frameIn, std::vector<bool> const& atomPositionKnown)
 const
 {
-  // Figure out hybridization and chirality of atom j.
   if (debug_ > 0)
     mprintf("DEBUG: AssignTheta for atom j : %s\n", topIn.AtomMaskName(aj).c_str());
   if (atomPositionKnown[ai] && atomPositionKnown[aj] && atomPositionKnown[ak])
@@ -72,6 +71,28 @@ const
     return 0;
   }
 
+  if (params_ != 0 &&
+      topIn[ai].HasType() &&
+      topIn[aj].HasType() &&
+      topIn[ak].HasType())
+  {
+    TypeNameHolder atypes(3);
+    atypes.AddName( topIn[ai].Type() );
+    atypes.AddName( topIn[aj].Type() );
+    atypes.AddName( topIn[ak].Type() );
+    ParmHolder<AngleParmType>::const_iterator it = params_->AP().GetParam( atypes );
+    if (it != params_->AP().end()) {
+      theta = it->second.Teq();
+      mprintf("DEBUG: Found angle parameter for %s (%s) - %s (%s) - %s (%s): teq=%g tk=%g\n",
+                topIn.AtomMaskName(ai).c_str(), *(topIn[ai].Type()),
+                topIn.AtomMaskName(aj).c_str(), *(topIn[aj].Type()),
+                topIn.AtomMaskName(ak).c_str(), *(topIn[ak].Type()),
+                it->second.Teq()*Constants::RADDEG, it->second.Tk());
+      return 0;
+    }
+  }
+
+  // Figure out hybridization and chirality of atom j.
   Atom const& AJ = topIn[aj];
   if (debug_ > 0) {
     mprintf("DEBUG:\t\tI %s Nbonds: %i\n", topIn[ai].ElementName(), topIn[ai].Nbonds());
@@ -91,46 +112,7 @@ const
   }
   if (hybrid == AtomType::UNKNOWN_HYBRIDIZATION)
     hybrid = GuessAtomHybridization(AJ, topIn.Atoms());
-/*
-  HybridizationType hybrid = UNKNOWN_HYBRIDIZATION;
-  // Handle specific elements
-  switch (AJ.Element()) {
-    case Atom::CARBON :
-      switch (AJ.Nbonds()) {
-        case 2 : hybrid = SP; break;
-        case 3 : hybrid = SP2; break;
-        case 4 : hybrid = SP3; break;
-      }
-      break;
-    case Atom::NITROGEN :
-      switch (AJ.Nbonds()) {
-        case 2 : hybrid = SP2; break;
-        case 3 :
-          // Check for potential SP2. If only 1 of the bonded atoms is
-          // hydrogen, assume SP2. TODO actually check for aromaticity.
-          int n_hydrogens = 0;
-          for (Atom::bond_iterator bat = AJ.bondbegin(); bat != AJ.bondend(); ++bat)
-            if (topIn[*bat].Element() == Atom::HYDROGEN)
-              n_hydrogens++;
-          if (n_hydrogens == 1)
-            hybrid = SP2;
-          else
-            hybrid = SP3;
-          break;
-      }
-      break;
-    case Atom::OXYGEN :
-      switch (AJ.Nbonds()) {
-        case 2 : hybrid = SP3; break;
-      }
-      break;
-    case Atom::SULFUR :
-      switch (AJ.Nbonds()) {
-        case 2 : hybrid = SP3; break;
-      }
-      break;
-    default: hybrid = UNKNOWN_HYBRIDIZATION; break;
-  }*/
+
   // Fill in what values we can for known atoms
 /*  std::vector<double> knownTheta( AJ.Nbonds() );
   int knownIdx = -1;
@@ -168,6 +150,7 @@ const
 
   return 0;
 }
+
 /** Insert internal coordinates with bond i-j, angle i-j-k, and torsion i-j-k-l. */
 int Cpptraj::Structure::Builder::insertIc(Zmatrix& zmatrix,
                                         int ai, int aj, int ak, int al, double newPhi,

From 5772f89cfb4d5a73cc864a6069f10efd758a8d86 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 30 Jan 2024 08:25:25 -0500
Subject: [PATCH 0406/1492] Set up the main parameter set

---
 src/Exec_Build.cpp | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 5dee723fad..77e094dcbf 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -394,6 +394,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
               mprintf("DEBUG: Connected to residue %s\n", topOut.TruncResNameNum(jres).c_str());
               Cpptraj::Structure::Builder linkBuilder;
               linkBuilder.SetDebug( 1 ); // FIXME
+              linkBuilder.SetParameters( &mainParmSet );
               if (linkBuilder.ModelCoordsAroundBond(frameOut, topOut, at, *bat,
                                                     zmatrix, ResZmatrices[jres], hasPosition))
               {

From 1c4ea3014d7e3db60a4081a9692c85ccf9decc9d Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 30 Jan 2024 09:03:31 -0500
Subject: [PATCH 0407/1492] Move UpdateICsFromFrame to Builder

---
 src/Exec_Build.cpp            |  10 +--
 src/Structure/Builder.cpp     | 157 ++++++++++++++++++++++++++++++++++
 src/Structure/Builder.h       |   6 ++
 src/Structure/Zmatrix.cpp     | 144 -------------------------------
 src/Structure/Zmatrix.h       |   4 +-
 src/Structure/structuredepend |   4 +-
 src/cpptrajdepend             |   4 +-
 7 files changed, 174 insertions(+), 155 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 77e094dcbf..2b02cdd930 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -370,7 +370,10 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
     else
       resIsBuilt.push_back( false );
   }
-  
+
+  Cpptraj::Structure::Builder linkBuilder;
+  linkBuilder.SetDebug( 1 ); // FIXME
+  linkBuilder.SetParameters( &mainParmSet );
   bool buildFailed = false;
   TermTypeArray::const_iterator termType = ResTypes.begin();
   for (Zarray::const_iterator it = ResZmatrices.begin(); it != ResZmatrices.end(); ++it, ++termType)
@@ -392,9 +395,6 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
             long int jres = (long int)topOut[*bat].ResNum();
             if (jres < ires) {
               mprintf("DEBUG: Connected to residue %s\n", topOut.TruncResNameNum(jres).c_str());
-              Cpptraj::Structure::Builder linkBuilder;
-              linkBuilder.SetDebug( 1 ); // FIXME
-              linkBuilder.SetParameters( &mainParmSet );
               if (linkBuilder.ModelCoordsAroundBond(frameOut, topOut, at, *bat,
                                                     zmatrix, ResZmatrices[jres], hasPosition))
               {
@@ -413,7 +413,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
 //        return 1;
 //      }
       // Update internal coords from known positions
-      if (zmatrix->UpdateICsFromFrame( frameOut, ires, topOut, hasPosition )) {
+      if (linkBuilder.UpdateICsFromFrame( *zmatrix, frameOut, ires, topOut, hasPosition )) {
         mprinterr("Error: Failed to update Zmatrix with values from existing positions.\n");
         return 1;
       }
diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index ee439d63f1..2630191210 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1,5 +1,6 @@
 #include "Builder.h"
 #include "BuildAtom.h"
+#include "GenerateConnectivityArrays.h"
 #include "Zmatrix.h"
 #include "../Constants.h"
 #include "../CpptrajStdio.h"
@@ -151,6 +152,20 @@ const
   return 0;
 }
 
+/** Calculate internal coordinate for atoms i j k l with known positions. */
+Cpptraj::Structure::InternalCoords Builder::calcKnownAtomIc(int ai, int aj, int ak, int al, Frame const& frameIn)
+{
+  double newDist = DIST2_NoImage(frameIn.XYZ(ai), frameIn.XYZ(aj));
+
+  double newTheta = CalcAngle( frameIn.XYZ(ai), frameIn.XYZ(aj), frameIn.XYZ(ak) );
+
+  double newPhi = Torsion( frameIn.XYZ(ai),
+                           frameIn.XYZ(aj),
+                           frameIn.XYZ(ak),
+                           frameIn.XYZ(al) );
+  return InternalCoords(ai, aj, ak, al, newDist, newTheta*Constants::RADDEG, newPhi*Constants::RADDEG);
+}
+
 /** Insert internal coordinates with bond i-j, angle i-j-k, and torsion i-j-k-l. */
 int Cpptraj::Structure::Builder::insertIc(Zmatrix& zmatrix,
                                         int ai, int aj, int ak, int al, double newPhi,
@@ -965,3 +980,145 @@ const
   return 0;
 }
 
+/** For existing torsions, see if all coordinates in that torsion
+  * exist. If so, update the IC from the existing coordinates.
+  */
+int Builder::UpdateICsFromFrame(Zmatrix& zmatrix, Frame const& frameIn, int ires, Topology const& topIn, Barray const& hasPosition)
+const
+{
+  Barray isUsed( zmatrix.N_IC(), false );
+  //unsigned int Nused = 0;
+  // Get list of bonds 
+  BondArray myBonds = GenerateBondArray( std::vector<Residue>(1, topIn.Res(ires)), topIn.Atoms() );
+  for (BondArray::const_iterator bnd = myBonds.begin(); bnd != myBonds.end(); ++bnd) {
+    if (topIn[bnd->A1()].ResNum() == ires && topIn[bnd->A2()].ResNum() == ires) {
+      mprintf("DEBUG: Looking at torsions around: %s - %s\n", topIn.AtomMaskName(bnd->A1()).c_str(), topIn.AtomMaskName(bnd->A2()).c_str());    // Find all ICs that share atoms 1 and 2 (J and K)
+      Iarray bondICs;
+      bool needsUpdate = false;
+      double tDiff = 0;
+      for (unsigned int idx = 0; idx != zmatrix.N_IC(); idx++)
+      {
+        if (!isUsed[idx]) {
+          InternalCoords& thisIc = zmatrix.ModifyIC(idx);
+          if ( (bnd->A1() == thisIc.AtJ() && bnd->A2() == thisIc.AtK()) ||
+               (bnd->A2() == thisIc.AtJ() && bnd->A1() == thisIc.AtK()) )
+          {
+            // This IC has this bond at the center
+            bondICs.push_back( idx );
+            isUsed[idx] = true;
+            //MARK(idx, isUsed, Nused);
+            if (hasPosition[thisIc.AtI()] &&
+                hasPosition[thisIc.AtJ()] &&
+                hasPosition[thisIc.AtK()] &&
+                hasPosition[thisIc.AtL()])
+            {
+              mprintf("DEBUG:\tMeasuring torsion of fixed atoms: %s - %s - %s - %s\n",
+                      topIn.AtomMaskName(thisIc.AtI()).c_str(),
+                      topIn.AtomMaskName(thisIc.AtJ()).c_str(),
+                      topIn.AtomMaskName(thisIc.AtK()).c_str(),
+                      topIn.AtomMaskName(thisIc.AtL()).c_str());
+              InternalCoords frameIc = calcKnownAtomIc(thisIc.AtI(), thisIc.AtJ(), thisIc.AtK(), thisIc.AtL(), frameIn);
+              double dTorsion = frameIc.Phi() * Constants::DEGRAD;
+              double dInternalValue = thisIc.Phi() * Constants::DEGRAD;
+              tDiff = (dTorsion - dInternalValue) * Constants::RADDEG;
+              mprintf("DEBUG:\tdTorsion= %f  dInternalValue= %f\n", dTorsion, dInternalValue);
+              thisIc = frameIc;
+              needsUpdate = true;
+            } // END all IC coords present
+          } // END this IC matches current bond
+        } // END IC is not used
+      } // END loop searching for ICs matching current bond
+      // If any difference was found, shift all of the torsions
+      if (needsUpdate) {
+        mprintf("DEBUG: Twisting torsions centered on %s - %s by %f degrees\n",
+                topIn.AtomMaskName(bnd->A1()).c_str(),
+                topIn.AtomMaskName(bnd->A2()).c_str(),
+                tDiff);
+        for (Iarray::const_iterator it = bondICs.begin(); it != bondICs.end(); ++it)
+        {
+          InternalCoords& thisIc = zmatrix.ModifyIC(*it);
+          double dNew = thisIc.Phi() + tDiff;
+          mprintf("DEBUG:\tTwisting torsion for atoms: %s-%s-%s-%s\n",
+                  topIn.AtomMaskName(thisIc.AtI()).c_str(),
+                  topIn.AtomMaskName(thisIc.AtJ()).c_str(),
+                  topIn.AtomMaskName(thisIc.AtK()).c_str(),
+                  topIn.AtomMaskName(thisIc.AtL()).c_str());
+          mprintf("DEBUG:\t------- From %f to %f\n", thisIc.Phi(), dNew);
+          thisIc.SetPhi( dNew );
+        }
+      } // END ICs need update
+    } // END both bond atoms belong to this residue
+  } // END loop over bonds
+/*
+  Barray isUsed( IC_.size(), false );
+  unsigned int Nused = 0;
+  while (Nused < IC_.size()) {
+    unsigned int idx = 0;
+    while (idx < IC_.size() && isUsed[idx]) idx++;
+    if (idx >= IC_.size()) break;
+    // Unused IC. Find all other ICs that share atoms J-K
+    MARK(idx, isUsed, Nused);
+    Iarray bondICs(1, idx);
+    for (unsigned int jdx = idx + 1; jdx < IC_.size(); jdx++) {
+      if ( IC_[idx].AtJ() == IC_[jdx].AtJ() &&
+           IC_[idx].AtK() == IC_[jdx].AtK() )
+      {
+        bondICs.push_back( jdx );
+        MARK(jdx, isUsed, Nused);
+      }
+    }
+    mprintf("DEBUG: Looking at %zu ICs involving %s - %s\n", bondICs.size(),
+            topIn.AtomMaskName(IC_[idx].AtJ()).c_str(),
+            topIn.AtomMaskName(IC_[idx].AtK()).c_str());
+    bool needsUpdate = false;
+    Iarray toUpdate;
+    toUpdate.reserve( bondICs.size() );
+    double tDiff = 0;
+    for (Iarray::iterator it = bondICs.begin(); it != bondICs.end(); ++it)
+    {
+      InternalCoords& thisIc = IC_[*it];
+      if (hasPosition[thisIc.AtI()] &&
+          hasPosition[thisIc.AtJ()] &&
+          hasPosition[thisIc.AtK()] &&
+          hasPosition[thisIc.AtL()])
+      {
+        mprintf("DEBUG:\tMeasuring torsion of fixed atoms: %s - %s - %s - %s\n",
+                topIn.AtomMaskName(thisIc.AtI()).c_str(),
+                topIn.AtomMaskName(thisIc.AtJ()).c_str(),
+                topIn.AtomMaskName(thisIc.AtK()).c_str(),
+                topIn.AtomMaskName(thisIc.AtL()).c_str());
+        InternalCoords frameIc = calcIc(thisIc.AtI(), thisIc.AtJ(), thisIc.AtK(), thisIc.AtL(),
+                                        frameIn.XYZ(thisIc.AtI()), frameIn.XYZ(thisIc.AtJ()),
+                                        frameIn.XYZ(thisIc.AtK()), frameIn.XYZ(thisIc.AtL()));
+        double dTorsion = frameIc.Phi() * Constants::DEGRAD;
+        double dInternalValue = thisIc.Phi() * Constants::DEGRAD;
+        tDiff = (dTorsion - dInternalValue) * Constants::RADDEG;
+        mprintf("DEBUG:\tdTorsion= %f  dInternalValue= %f\n", dTorsion, dInternalValue);
+        thisIc = frameIc;
+        needsUpdate = true;
+      } else {
+        toUpdate.push_back( *it );
+      }
+    } // END calc loop over ICs sharing J-K bond
+    // If any difference was found, shift all of the torsions
+    if (needsUpdate) {
+      mprintf("DEBUG: Twisting torsions centered on %s - %s by %f degrees\n",
+              topIn.AtomMaskName(IC_[idx].AtJ()).c_str(),
+              topIn.AtomMaskName(IC_[idx].AtK()).c_str(),
+              tDiff);
+      for (Iarray::const_iterator it = toUpdate.begin(); it != toUpdate.end(); ++it)
+      {
+        InternalCoords& thisIc = IC_[*it];
+        double dNew = thisIc.Phi() + tDiff;
+        mprintf("DEBUG:\tTwisting torsion for atoms: %s-%s-%s-%s\n",
+                topIn.AtomMaskName(thisIc.AtI()).c_str(),
+                topIn.AtomMaskName(thisIc.AtJ()).c_str(),
+                topIn.AtomMaskName(thisIc.AtK()).c_str(),
+                topIn.AtomMaskName(thisIc.AtL()).c_str());
+        mprintf("DEBUG:\t------- From %f to %f\n", thisIc.Phi(), dNew);
+        thisIc.SetPhi( dNew );
+      }
+    }
+  } // END loop over ICs*/
+  return 0;
+} 
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index 3b2055b837..f2fc696a7d 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -8,6 +8,7 @@ namespace Cpptraj {
 namespace Structure {
 class BuildAtom;
 class Zmatrix;
+class InternalCoords;
 /// Used to attach different topology/frame combos using internal coordinates
 class Builder {
     typedef std::vector<bool> Barray;
@@ -23,11 +24,16 @@ class Builder {
     int Combine(Topology&, Frame&, Topology const&, Frame const&, int, int) const;
     /// Model the coordinates around a bond given only some coordinates are known
     int ModelCoordsAroundBond(Frame&, Topology const&, int, int, Zmatrix const*, Zmatrix const*, Barray&) const;
+    /// Update the internal coordinates in given Zmatrix with values from Frame/Parameters
+    int UpdateICsFromFrame(Zmatrix&, Frame const&, int, Topology const&, Barray const&) const;
   private:
+    typedef std::vector<int> Iarray;
     /// Assign a reasonable value for bond distance given 2 atoms whose position may or may not be known
     int AssignLength(double&, int, int, Topology const&, Frame const&, std::vector<bool> const&) const;
     /// Given atoms J and K, attempt to assign a reasonable value for theta for atom I
     int AssignTheta(double&, int, int, int, Topology const&, Frame const&, std::vector<bool> const&) const;
+    /// Calculate an internal coordinate for known atoms
+    static inline InternalCoords calcKnownAtomIc(int, int, int, int, Frame const&);
     /// Insert an internal coord into a zmatrix
     int insertIc(Zmatrix&, int, int, int, int, double,
                  Topology const&, Frame const&, std::vector<bool> const&) const;
diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index 0eae2717b9..5e91740f47 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -3,7 +3,6 @@
 #include <stack>
 #include <cmath> // cos
 #include "Zmatrix.h"
-#include "GenerateConnectivityArrays.h"
 #include "../Frame.h"
 #include "../CpptrajStdio.h"
 #include "../Constants.h"
@@ -586,149 +585,6 @@ int Zmatrix::addInternalCoordForAtom(int iat, Frame const& frameIn, Topology con
   return 0;
 }
 
-/** For existing torsions, see if all coordinates in that torsion
-  * exist. If so, update the IC from the existing coordinates.
-  */
-int Zmatrix::UpdateICsFromFrame(Frame const& frameIn, int ires, Topology const& topIn, Barray const& hasPosition)
-{
-  Barray isUsed( IC_.size(), false );
-  unsigned int Nused = 0;
-  // Get list of bonds 
-  BondArray myBonds = GenerateBondArray( std::vector<Residue>(1, topIn.Res(ires)), topIn.Atoms() );
-  for (BondArray::const_iterator bnd = myBonds.begin(); bnd != myBonds.end(); ++bnd) {
-    if (topIn[bnd->A1()].ResNum() == ires && topIn[bnd->A2()].ResNum() == ires) {
-      mprintf("DEBUG: Looking at torsions around: %s - %s\n", topIn.AtomMaskName(bnd->A1()).c_str(), topIn.AtomMaskName(bnd->A2()).c_str());    // Find all ICs that share atoms 1 and 2 (J and K)
-      Iarray bondICs;
-      bool needsUpdate = false;
-      double tDiff = 0;
-      for (unsigned int idx = 0; idx != IC_.size(); idx++)
-      {
-        if (!isUsed[idx]) {
-          InternalCoords& thisIc = IC_[idx];
-          if ( (bnd->A1() == thisIc.AtJ() && bnd->A2() == thisIc.AtK()) ||
-               (bnd->A2() == thisIc.AtJ() && bnd->A1() == thisIc.AtK()) )
-          {
-            // This IC has this bond at the center
-            bondICs.push_back( idx );
-            MARK(idx, isUsed, Nused);
-            if (hasPosition[thisIc.AtI()] &&
-                hasPosition[thisIc.AtJ()] &&
-                hasPosition[thisIc.AtK()] &&
-                hasPosition[thisIc.AtL()])
-            {
-              mprintf("DEBUG:\tMeasuring torsion of fixed atoms: %s - %s - %s - %s\n",
-                      topIn.AtomMaskName(thisIc.AtI()).c_str(),
-                      topIn.AtomMaskName(thisIc.AtJ()).c_str(),
-                      topIn.AtomMaskName(thisIc.AtK()).c_str(),
-                      topIn.AtomMaskName(thisIc.AtL()).c_str());
-              InternalCoords frameIc = calcIc(thisIc.AtI(), thisIc.AtJ(), thisIc.AtK(), thisIc.AtL(),
-                                              frameIn.XYZ(thisIc.AtI()), frameIn.XYZ(thisIc.AtJ()),
-                                              frameIn.XYZ(thisIc.AtK()), frameIn.XYZ(thisIc.AtL()));
-              double dTorsion = frameIc.Phi() * Constants::DEGRAD;
-              double dInternalValue = thisIc.Phi() * Constants::DEGRAD;
-              tDiff = (dTorsion - dInternalValue) * Constants::RADDEG;
-              mprintf("DEBUG:\tdTorsion= %f  dInternalValue= %f\n", dTorsion, dInternalValue);
-              thisIc = frameIc;
-              needsUpdate = true;
-            } // END all IC coords present
-          } // END this IC matches current bond
-        } // END IC is not used
-      } // END loop searching for ICs matching current bond
-      // If any difference was found, shift all of the torsions
-      if (needsUpdate) {
-        mprintf("DEBUG: Twisting torsions centered on %s - %s by %f degrees\n",
-                topIn.AtomMaskName(bnd->A1()).c_str(),
-                topIn.AtomMaskName(bnd->A2()).c_str(),
-                tDiff);
-        for (Iarray::const_iterator it = bondICs.begin(); it != bondICs.end(); ++it)
-        {
-          InternalCoords& thisIc = IC_[*it];
-          double dNew = thisIc.Phi() + tDiff;
-          mprintf("DEBUG:\tTwisting torsion for atoms: %s-%s-%s-%s\n",
-                  topIn.AtomMaskName(thisIc.AtI()).c_str(),
-                  topIn.AtomMaskName(thisIc.AtJ()).c_str(),
-                  topIn.AtomMaskName(thisIc.AtK()).c_str(),
-                  topIn.AtomMaskName(thisIc.AtL()).c_str());
-          mprintf("DEBUG:\t------- From %f to %f\n", thisIc.Phi(), dNew);
-          thisIc.SetPhi( dNew );
-        }
-      } // END ICs need update
-    } // END both bond atoms belong to this residue
-  } // END loop over bonds
-/*
-  Barray isUsed( IC_.size(), false );
-  unsigned int Nused = 0;
-  while (Nused < IC_.size()) {
-    unsigned int idx = 0;
-    while (idx < IC_.size() && isUsed[idx]) idx++;
-    if (idx >= IC_.size()) break;
-    // Unused IC. Find all other ICs that share atoms J-K
-    MARK(idx, isUsed, Nused);
-    Iarray bondICs(1, idx);
-    for (unsigned int jdx = idx + 1; jdx < IC_.size(); jdx++) {
-      if ( IC_[idx].AtJ() == IC_[jdx].AtJ() &&
-           IC_[idx].AtK() == IC_[jdx].AtK() )
-      {
-        bondICs.push_back( jdx );
-        MARK(jdx, isUsed, Nused);
-      }
-    }
-    mprintf("DEBUG: Looking at %zu ICs involving %s - %s\n", bondICs.size(),
-            topIn.AtomMaskName(IC_[idx].AtJ()).c_str(),
-            topIn.AtomMaskName(IC_[idx].AtK()).c_str());
-    bool needsUpdate = false;
-    Iarray toUpdate;
-    toUpdate.reserve( bondICs.size() );
-    double tDiff = 0;
-    for (Iarray::iterator it = bondICs.begin(); it != bondICs.end(); ++it)
-    {
-      InternalCoords& thisIc = IC_[*it];
-      if (hasPosition[thisIc.AtI()] &&
-          hasPosition[thisIc.AtJ()] &&
-          hasPosition[thisIc.AtK()] &&
-          hasPosition[thisIc.AtL()])
-      {
-        mprintf("DEBUG:\tMeasuring torsion of fixed atoms: %s - %s - %s - %s\n",
-                topIn.AtomMaskName(thisIc.AtI()).c_str(),
-                topIn.AtomMaskName(thisIc.AtJ()).c_str(),
-                topIn.AtomMaskName(thisIc.AtK()).c_str(),
-                topIn.AtomMaskName(thisIc.AtL()).c_str());
-        InternalCoords frameIc = calcIc(thisIc.AtI(), thisIc.AtJ(), thisIc.AtK(), thisIc.AtL(),
-                                        frameIn.XYZ(thisIc.AtI()), frameIn.XYZ(thisIc.AtJ()),
-                                        frameIn.XYZ(thisIc.AtK()), frameIn.XYZ(thisIc.AtL()));
-        double dTorsion = frameIc.Phi() * Constants::DEGRAD;
-        double dInternalValue = thisIc.Phi() * Constants::DEGRAD;
-        tDiff = (dTorsion - dInternalValue) * Constants::RADDEG;
-        mprintf("DEBUG:\tdTorsion= %f  dInternalValue= %f\n", dTorsion, dInternalValue);
-        thisIc = frameIc;
-        needsUpdate = true;
-      } else {
-        toUpdate.push_back( *it );
-      }
-    } // END calc loop over ICs sharing J-K bond
-    // If any difference was found, shift all of the torsions
-    if (needsUpdate) {
-      mprintf("DEBUG: Twisting torsions centered on %s - %s by %f degrees\n",
-              topIn.AtomMaskName(IC_[idx].AtJ()).c_str(),
-              topIn.AtomMaskName(IC_[idx].AtK()).c_str(),
-              tDiff);
-      for (Iarray::const_iterator it = toUpdate.begin(); it != toUpdate.end(); ++it)
-      {
-        InternalCoords& thisIc = IC_[*it];
-        double dNew = thisIc.Phi() + tDiff;
-        mprintf("DEBUG:\tTwisting torsion for atoms: %s-%s-%s-%s\n",
-                topIn.AtomMaskName(thisIc.AtI()).c_str(),
-                topIn.AtomMaskName(thisIc.AtJ()).c_str(),
-                topIn.AtomMaskName(thisIc.AtK()).c_str(),
-                topIn.AtomMaskName(thisIc.AtL()).c_str());
-        mprintf("DEBUG:\t------- From %f to %f\n", thisIc.Phi(), dNew);
-        thisIc.SetPhi( dNew );
-      }
-    }
-  } // END loop over ICs*/
-  return 0;
-} 
-
 /** Set up Zmatrix from Cartesian coordinates and topology.
   * Use torsions based on connectivity to create a complete set of ICs.
   */
diff --git a/src/Structure/Zmatrix.h b/src/Structure/Zmatrix.h
index 165d5c661e..7d27d471cc 100644
--- a/src/Structure/Zmatrix.h
+++ b/src/Structure/Zmatrix.h
@@ -41,12 +41,12 @@ class Zmatrix {
 
     /// Try to generate complete ICs from atom connectivity
     int SetFromFrameAndConnect(Frame const&, Topology const&);//, int);
-    /// Update ICs from existing coords
-    int UpdateICsFromFrame(Frame const&, int, Topology const&, Barray const&);
     /// Convert specifed molecule of Frame/Topology to internal coordinates array
     int SetFromFrame(Frame const&, Topology const&, int);
     /// Convert molecule 0 of Frame/Topology to internal coordinates array
     int SetFromFrame(Frame const&, Topology const&);
+    /// \return Modifable reference to specified IC
+    InternalCoords& ModifyIC(unsigned int idx) { return IC_[idx]; }
 
     /// Set Frame from internal coords
     int SetToFrame(Frame&) const;
diff --git a/src/Structure/structuredepend b/src/Structure/structuredepend
index 772844a3da..c2874b3e7e 100644
--- a/src/Structure/structuredepend
+++ b/src/Structure/structuredepend
@@ -1,5 +1,5 @@
 BuildAtom.o : BuildAtom.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h StructureEnum.h
-Builder.o : Builder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h Builder.h InternalCoords.h StructureEnum.h Zmatrix.h
+Builder.o : Builder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h Builder.h GenerateConnectivityArrays.h InternalCoords.h StructureEnum.h Zmatrix.h
 Disulfide.o : Disulfide.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Disulfide.h ResStatArray.h StructureRoutines.h
 FunctionalGroup.o : FunctionalGroup.cpp ../Atom.h ../AtomMap.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h FunctionalGroup.h
 FxnGroupBuilder.o : FxnGroupBuilder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h FunctionalGroup.h FxnGroupBuilder.h StructureRoutines.h Sugar.h SugarToken.h
@@ -12,4 +12,4 @@ Sugar.o : Sugar.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.
 SugarBuilder.o : SugarBuilder.cpp ../ArgList.h ../Atom.h ../AtomMap.h ../AtomMask.h ../AtomType.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DistRoutines.h ../FileIO.h ../FileName.h ../Frame.h ../ImageOption.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h FunctionalGroup.h FxnGroupBuilder.h LinkAtom.h ResStatArray.h StructureEnum.h StructureRoutines.h Sugar.h SugarBuilder.h SugarLinkAtoms.h SugarToken.h
 SugarLinkAtoms.o : SugarLinkAtoms.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../StringRoutines.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h LinkAtom.h SugarLinkAtoms.h
 SugarToken.o : SugarToken.cpp ../ArgList.h ../CpptrajStdio.h SugarToken.h
-Zmatrix.o : Zmatrix.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h GenerateConnectivityArrays.h InternalCoords.h Zmatrix.h
+Zmatrix.o : Zmatrix.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h InternalCoords.h Zmatrix.h
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 93baffd806..8ee99a7068 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -446,7 +446,7 @@ Spline.o : Spline.cpp CpptrajStdio.h Spline.h
 SplineFxnTable.o : SplineFxnTable.cpp Constants.h CpptrajStdio.h Spline.h SplineFxnTable.h StringRoutines.h
 StringRoutines.o : StringRoutines.cpp CpptrajStdio.h StringRoutines.h
 Structure/BuildAtom.o : Structure/BuildAtom.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/StructureEnum.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Structure/Builder.o : Structure/Builder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h GuessAtomHybridization.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/Builder.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Structure/Builder.o : Structure/Builder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h GuessAtomHybridization.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/Builder.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 Structure/Disulfide.o : Structure/Disulfide.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Disulfide.h Structure/ResStatArray.h Structure/StructureRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/FunctionalGroup.o : Structure/FunctionalGroup.cpp Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/FxnGroupBuilder.o : Structure/FxnGroupBuilder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h Structure/FxnGroupBuilder.h Structure/StructureRoutines.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
@@ -459,7 +459,7 @@ Structure/Sugar.o : Structure/Sugar.cpp Atom.h AtomMask.h AtomType.h Box.h Const
 Structure/SugarBuilder.o : Structure/SugarBuilder.cpp ArgList.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DistRoutines.h FileIO.h FileName.h Frame.h ImageOption.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/FunctionalGroup.h Structure/FxnGroupBuilder.h Structure/LinkAtom.h Structure/ResStatArray.h Structure/StructureEnum.h Structure/StructureRoutines.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarLinkAtoms.h Structure/SugarToken.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 Structure/SugarLinkAtoms.o : Structure/SugarLinkAtoms.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/LinkAtom.h Structure/SugarLinkAtoms.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/SugarToken.o : Structure/SugarToken.cpp ArgList.h CpptrajStdio.h Structure/SugarToken.h
-Structure/Zmatrix.o : Structure/Zmatrix.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Structure/Zmatrix.o : Structure/Zmatrix.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 StructureCheck.o : StructureCheck.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h ExclusionArray.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StructureCheck.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 StructureMapper.o : StructureMapper.cpp AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StructureMapper.h SymbolExporting.h TextFormat.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 SymmetricRmsdCalc.o : SymmetricRmsdCalc.cpp ArrayIterator.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h Hungarian.h ImageOption.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h Topology.h TypeNameHolder.h Unit.h Vec3.h

From 27319edf32bf9976bd6d3536926d7d6c0c368776 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 30 Jan 2024 09:05:12 -0500
Subject: [PATCH 0408/1492] Remove unused code

---
 src/Structure/Builder.cpp | 71 ---------------------------------------
 1 file changed, 71 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 2630191210..ee91d3d1ef 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1049,76 +1049,5 @@ const
       } // END ICs need update
     } // END both bond atoms belong to this residue
   } // END loop over bonds
-/*
-  Barray isUsed( IC_.size(), false );
-  unsigned int Nused = 0;
-  while (Nused < IC_.size()) {
-    unsigned int idx = 0;
-    while (idx < IC_.size() && isUsed[idx]) idx++;
-    if (idx >= IC_.size()) break;
-    // Unused IC. Find all other ICs that share atoms J-K
-    MARK(idx, isUsed, Nused);
-    Iarray bondICs(1, idx);
-    for (unsigned int jdx = idx + 1; jdx < IC_.size(); jdx++) {
-      if ( IC_[idx].AtJ() == IC_[jdx].AtJ() &&
-           IC_[idx].AtK() == IC_[jdx].AtK() )
-      {
-        bondICs.push_back( jdx );
-        MARK(jdx, isUsed, Nused);
-      }
-    }
-    mprintf("DEBUG: Looking at %zu ICs involving %s - %s\n", bondICs.size(),
-            topIn.AtomMaskName(IC_[idx].AtJ()).c_str(),
-            topIn.AtomMaskName(IC_[idx].AtK()).c_str());
-    bool needsUpdate = false;
-    Iarray toUpdate;
-    toUpdate.reserve( bondICs.size() );
-    double tDiff = 0;
-    for (Iarray::iterator it = bondICs.begin(); it != bondICs.end(); ++it)
-    {
-      InternalCoords& thisIc = IC_[*it];
-      if (hasPosition[thisIc.AtI()] &&
-          hasPosition[thisIc.AtJ()] &&
-          hasPosition[thisIc.AtK()] &&
-          hasPosition[thisIc.AtL()])
-      {
-        mprintf("DEBUG:\tMeasuring torsion of fixed atoms: %s - %s - %s - %s\n",
-                topIn.AtomMaskName(thisIc.AtI()).c_str(),
-                topIn.AtomMaskName(thisIc.AtJ()).c_str(),
-                topIn.AtomMaskName(thisIc.AtK()).c_str(),
-                topIn.AtomMaskName(thisIc.AtL()).c_str());
-        InternalCoords frameIc = calcIc(thisIc.AtI(), thisIc.AtJ(), thisIc.AtK(), thisIc.AtL(),
-                                        frameIn.XYZ(thisIc.AtI()), frameIn.XYZ(thisIc.AtJ()),
-                                        frameIn.XYZ(thisIc.AtK()), frameIn.XYZ(thisIc.AtL()));
-        double dTorsion = frameIc.Phi() * Constants::DEGRAD;
-        double dInternalValue = thisIc.Phi() * Constants::DEGRAD;
-        tDiff = (dTorsion - dInternalValue) * Constants::RADDEG;
-        mprintf("DEBUG:\tdTorsion= %f  dInternalValue= %f\n", dTorsion, dInternalValue);
-        thisIc = frameIc;
-        needsUpdate = true;
-      } else {
-        toUpdate.push_back( *it );
-      }
-    } // END calc loop over ICs sharing J-K bond
-    // If any difference was found, shift all of the torsions
-    if (needsUpdate) {
-      mprintf("DEBUG: Twisting torsions centered on %s - %s by %f degrees\n",
-              topIn.AtomMaskName(IC_[idx].AtJ()).c_str(),
-              topIn.AtomMaskName(IC_[idx].AtK()).c_str(),
-              tDiff);
-      for (Iarray::const_iterator it = toUpdate.begin(); it != toUpdate.end(); ++it)
-      {
-        InternalCoords& thisIc = IC_[*it];
-        double dNew = thisIc.Phi() + tDiff;
-        mprintf("DEBUG:\tTwisting torsion for atoms: %s-%s-%s-%s\n",
-                topIn.AtomMaskName(thisIc.AtI()).c_str(),
-                topIn.AtomMaskName(thisIc.AtJ()).c_str(),
-                topIn.AtomMaskName(thisIc.AtK()).c_str(),
-                topIn.AtomMaskName(thisIc.AtL()).c_str());
-        mprintf("DEBUG:\t------- From %f to %f\n", thisIc.Phi(), dNew);
-        thisIc.SetPhi( dNew );
-      }
-    }
-  } // END loop over ICs*/
   return 0;
 } 

From 7b033a8b63ec262a28481ecfa3398627864a2513 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 30 Jan 2024 09:14:34 -0500
Subject: [PATCH 0409/1492] Separate out finding length parameters

---
 src/Structure/Builder.cpp | 68 +++++++++++++++++++++++++++------------
 src/Structure/Builder.h   |  2 ++
 2 files changed, 50 insertions(+), 20 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index ee91d3d1ef..02e42bcd68 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -29,32 +29,57 @@ void Cpptraj::Structure::Builder::SetParameters(ParameterSet const* paramsIn) {
 }
 
 // -----------------------------------------------------------------------------
+/** Get length from parameter set if present.
+  * \return 1 if a length parameter was found.
+  */
+int Cpptraj::Structure::Builder::getLengthParam(double& dist, int ai, int aj, Topology const& topIn)
+const
+{
+  if (params_ != 0 && topIn[ai].HasType() && topIn[aj].HasType()) {
+    TypeNameHolder btypes(2);
+    btypes.AddName( topIn[ai].Type() );
+    btypes.AddName( topIn[aj].Type() );
+    ParmHolder<BondParmType>::const_iterator it = params_->BP().GetParam( btypes );
+    if (it != params_->BP().end()) {
+      dist = it->second.Req();
+      mprintf("DEBUG: Found bond parameter for %s (%s) - %s (%s): req=%g rk=%g\n",
+              topIn.AtomMaskName(ai).c_str(), *(topIn[ai].Type()),
+              topIn.AtomMaskName(aj).c_str(), *(topIn[aj].Type()),
+              it->second.Req(), it->second.Rk());
+      return 1;
+    }
+  }
+  return 0;
+}
+
 /** Assign reasonable value for bond distance. */
 int Cpptraj::Structure::Builder::AssignLength(double& dist, int ai, int aj, Topology const& topIn, Frame const& frameIn, std::vector<bool> const& atomPositionKnown)
 const
 {
-  if (atomPositionKnown[ai] && atomPositionKnown[aj])
+  if (atomPositionKnown[ai] && atomPositionKnown[aj]) {
     dist = sqrt( DIST2_NoImage( frameIn.XYZ(ai), frameIn.XYZ(aj) ) );
-  else {
-    // One or both positions unknown. Use estimated bond length or parameters.
-    bool foundParam = false;
-    if (params_ != 0 && topIn[ai].HasType() && topIn[aj].HasType()) {
-      TypeNameHolder btypes(2);
-      btypes.AddName( topIn[ai].Type() );
-      btypes.AddName( topIn[aj].Type() );
-      ParmHolder<BondParmType>::const_iterator it = params_->BP().GetParam( btypes );
-      if (it != params_->BP().end()) {
-        dist = it->second.Req();
-        foundParam = true;
-        mprintf("DEBUG: Found bond parameter for %s (%s) - %s (%s): req=%g rk=%g\n",
-                topIn.AtomMaskName(ai).c_str(), *(topIn[ai].Type()),
-                topIn.AtomMaskName(aj).c_str(), *(topIn[aj].Type()),
-                it->second.Req(), it->second.Rk());
-      }
-    }
-    if (!foundParam)
-      dist = Atom::GetBondLength( topIn[ai].Element(), topIn[aj].Element() );
+    return 0;
   }
+
+  // One or both positions unknown. Use estimated bond length or parameters.
+  if (getLengthParam(dist, ai, aj, topIn)) return 0;
+/*  if (params_ != 0 && topIn[ai].HasType() && topIn[aj].HasType()) {
+    TypeNameHolder btypes(2);
+    btypes.AddName( topIn[ai].Type() );
+    btypes.AddName( topIn[aj].Type() );
+    ParmHolder<BondParmType>::const_iterator it = params_->BP().GetParam( btypes );
+    if (it != params_->BP().end()) {
+      dist = it->second.Req();
+      mprintf("DEBUG: Found bond parameter for %s (%s) - %s (%s): req=%g rk=%g\n",
+              topIn.AtomMaskName(ai).c_str(), *(topIn[ai].Type()),
+              topIn.AtomMaskName(aj).c_str(), *(topIn[aj].Type()),
+              it->second.Req(), it->second.Rk());
+      return 0;
+    }
+  }*/
+
+  // Default to bond length based on elements
+  dist = Atom::GetBondLength( topIn[ai].Element(), topIn[aj].Element() );
   return 0;
 }
 
@@ -986,6 +1011,9 @@ const
 int Builder::UpdateICsFromFrame(Zmatrix& zmatrix, Frame const& frameIn, int ires, Topology const& topIn, Barray const& hasPosition)
 const
 {
+  // Update bond/angle values for atoms with no position.
+  
+  // Update torsions
   Barray isUsed( zmatrix.N_IC(), false );
   //unsigned int Nused = 0;
   // Get list of bonds 
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index f2fc696a7d..dbc3795639 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -28,6 +28,8 @@ class Builder {
     int UpdateICsFromFrame(Zmatrix&, Frame const&, int, Topology const&, Barray const&) const;
   private:
     typedef std::vector<int> Iarray;
+    /// Get length parameter for atoms
+    int getLengthParam(double&, int, int, Topology const&) const;
     /// Assign a reasonable value for bond distance given 2 atoms whose position may or may not be known
     int AssignLength(double&, int, int, Topology const&, Frame const&, std::vector<bool> const&) const;
     /// Given atoms J and K, attempt to assign a reasonable value for theta for atom I

From df9e57e15d1748e190dbcb1a4739536ea918ab76 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 30 Jan 2024 14:27:58 -0500
Subject: [PATCH 0410/1492] Separate out getting angle parameter

---
 src/Structure/Builder.cpp | 33 ++++++++++++++++++++++++++++++++-
 src/Structure/Builder.h   |  2 ++
 2 files changed, 34 insertions(+), 1 deletion(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 02e42bcd68..3d921bea4f 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -83,6 +83,35 @@ const
   return 0;
 }
 
+/** Get angle parameter if present.
+  * \return 1 if parameter found.
+  */
+int Cpptraj::Structure::Builder::getAngleParam(double& theta, int ai, int aj, int ak, Topology const& topIn)
+const
+{
+  if (params_ != 0 &&
+      topIn[ai].HasType() &&
+      topIn[aj].HasType() &&
+      topIn[ak].HasType())
+  {
+    TypeNameHolder atypes(3);
+    atypes.AddName( topIn[ai].Type() );
+    atypes.AddName( topIn[aj].Type() );
+    atypes.AddName( topIn[ak].Type() );
+    ParmHolder<AngleParmType>::const_iterator it = params_->AP().GetParam( atypes );
+    if (it != params_->AP().end()) {
+      theta = it->second.Teq();
+      mprintf("DEBUG: Found angle parameter for %s (%s) - %s (%s) - %s (%s): teq=%g tk=%g\n",
+                topIn.AtomMaskName(ai).c_str(), *(topIn[ai].Type()),
+                topIn.AtomMaskName(aj).c_str(), *(topIn[aj].Type()),
+                topIn.AtomMaskName(ak).c_str(), *(topIn[ak].Type()),
+                it->second.Teq()*Constants::RADDEG, it->second.Tk());
+      return 1;
+    }
+  }
+  return 0;
+}
+
 /** Attempt to assign a reasonable value for theta internal coordinate for
   * atom i given that atoms j and k have known positions.
   */
@@ -97,6 +126,8 @@ const
     return 0;
   }
 
+  if (getAngleParam(theta, ai, aj, ak, topIn)) return 0;
+/*
   if (params_ != 0 &&
       topIn[ai].HasType() &&
       topIn[aj].HasType() &&
@@ -117,7 +148,7 @@ const
       return 0;
     }
   }
-
+*/
   // Figure out hybridization and chirality of atom j.
   Atom const& AJ = topIn[aj];
   if (debug_ > 0) {
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index dbc3795639..c912d0651b 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -32,6 +32,8 @@ class Builder {
     int getLengthParam(double&, int, int, Topology const&) const;
     /// Assign a reasonable value for bond distance given 2 atoms whose position may or may not be known
     int AssignLength(double&, int, int, Topology const&, Frame const&, std::vector<bool> const&) const;
+    /// Get angle parameter for atoms.
+    int getAngleParam(double&, int, int, int, Topology const&) const;
     /// Given atoms J and K, attempt to assign a reasonable value for theta for atom I
     int AssignTheta(double&, int, int, int, Topology const&, Frame const&, std::vector<bool> const&) const;
     /// Calculate an internal coordinate for known atoms

From 018810211362e30838815fd4793e9426e182d0de Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 30 Jan 2024 14:41:10 -0500
Subject: [PATCH 0411/1492] Add but do not yet enable ability to update ICs
 with values from parameter set

---
 src/Structure/Builder.cpp      | 23 ++++++++++++++++++++++-
 src/Structure/InternalCoords.h |  4 ++++
 2 files changed, 26 insertions(+), 1 deletion(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 3d921bea4f..7b2c9ac8b1 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1043,7 +1043,28 @@ int Builder::UpdateICsFromFrame(Zmatrix& zmatrix, Frame const& frameIn, int ires
 const
 {
   // Update bond/angle values for atoms with no position.
-  
+/*  for (unsigned int idx = 0; idx != zmatrix.N_IC(); idx++)
+  {
+    InternalCoords& thisIc = zmatrix.ModifyIC(idx);
+    if (!hasPosition[thisIc.AtI()]) {
+      double dist = 0;
+      if (getLengthParam( dist, thisIc.AtI(), thisIc.AtJ(), topIn )) {
+        mprintf("DEBUG: Replacing existing bond length %g for %s - %s with parameter %g\n",
+                thisIc.Dist(), topIn.AtomMaskName(thisIc.AtI()).c_str(),
+                topIn.AtomMaskName(thisIc.AtJ()).c_str(), dist);
+        thisIc.SetDist( dist );
+      }
+      double theta = 0;
+      if (getAngleParam( theta, thisIc.AtI(), thisIc.AtJ(), thisIc.AtK(), topIn)) {
+        theta *= Constants::RADDEG;
+        mprintf("DEBUG: Replacing existing angle %g for %s - %s - %s with parameter %g\n",
+                thisIc.Theta(), topIn.AtomMaskName(thisIc.AtI()).c_str(),
+                topIn.AtomMaskName(thisIc.AtJ()).c_str(), topIn.AtomMaskName(thisIc.AtK()).c_str(),
+                theta);
+        thisIc.SetTheta( theta );
+      }
+    }
+  }*/
   // Update torsions
   Barray isUsed( zmatrix.N_IC(), false );
   //unsigned int Nused = 0;
diff --git a/src/Structure/InternalCoords.h b/src/Structure/InternalCoords.h
index e655ce94a5..acf02face1 100644
--- a/src/Structure/InternalCoords.h
+++ b/src/Structure/InternalCoords.h
@@ -45,6 +45,10 @@ class InternalCoords {
     void OffsetIndices(int);
     /// Set the value of Phi
     void SetPhi(double p) { val_[2] = p; }
+    /// Set the value of theta
+    void SetTheta(double t) { val_[1] = t; }
+    /// Set the value of distance
+    void SetDist(double d) { val_[0] = d; }
   private:
     int ati_;       ///< Atom I index
     int idx_[3];    ///< Atom indices for distance, angle, torsion

From 468cf7d9380279cd0775621623fc0495141154b9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 30 Jan 2024 15:50:38 -0500
Subject: [PATCH 0412/1492] No need to update ICs for atoms that have
 coordinates set.

---
 src/Structure/Builder.cpp | 30 ++++++++++++++++++++++++++----
 1 file changed, 26 insertions(+), 4 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 7b2c9ac8b1..a423674729 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1043,9 +1043,30 @@ int Builder::UpdateICsFromFrame(Zmatrix& zmatrix, Frame const& frameIn, int ires
 const
 {
   // Update bond/angle values for atoms with no position.
-/*  for (unsigned int idx = 0; idx != zmatrix.N_IC(); idx++)
-  {
-    InternalCoords& thisIc = zmatrix.ModifyIC(idx);
+//  for (unsigned int idx = 0; idx != zmatrix.N_IC(); idx++)
+//  {
+/*    InternalCoords& thisIc = zmatrix.ModifyIC(idx);
+    if (hasPosition[thisIc.AtI()] && hasPosition[thisIc.AtJ()]) {
+      // Bond exists.
+      double dist = DIST2_NoImage( frameIn.XYZ(thisIc.AtI()), frameIn.XYZ(thisIc.AtJ()) );
+      mprintf("DEBUG: Replacing existing bond length %g for %s - %s with existing length %g\n",
+              thisIc.Dist(), topIn.AtomMaskName(thisIc.AtI()).c_str(),
+              topIn.AtomMaskName(thisIc.AtJ()).c_str(), dist);
+      thisIc.SetDist( dist );
+      if (hasPosition[thisIc.AtK()]) {
+        // Angle also exists
+        double theta = CalcAngle(frameIn.XYZ(thisIc.AtI()),
+                                 frameIn.XYZ(thisIc.AtJ()),
+                                 frameIn.XYZ(thisIc.AtK()));
+        theta *= Constants::RADDEG;
+        mprintf("DEBUG: Replacing existing angle %g for %s - %s - %s with existing angle %g\n",
+                thisIc.Theta(), topIn.AtomMaskName(thisIc.AtI()).c_str(),
+                topIn.AtomMaskName(thisIc.AtJ()).c_str(), topIn.AtomMaskName(thisIc.AtK()).c_str(),
+                theta);
+        thisIc.SetTheta( theta );
+    }
+  }*/
+/*
     if (!hasPosition[thisIc.AtI()]) {
       double dist = 0;
       if (getLengthParam( dist, thisIc.AtI(), thisIc.AtJ(), topIn )) {
@@ -1064,7 +1085,8 @@ const
         thisIc.SetTheta( theta );
       }
     }
-  }*/
+*/
+//  } // END loop over zmatrix ICs
   // Update torsions
   Barray isUsed( zmatrix.N_IC(), false );
   //unsigned int Nused = 0;

From 227aa974c0c9efefc03e99d73e0362290923af72 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 31 Jan 2024 09:02:14 -0500
Subject: [PATCH 0413/1492] Remove old code

---
 src/Structure/Zmatrix.cpp | 53 +++++++++++++--------------------------
 1 file changed, 18 insertions(+), 35 deletions(-)

diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index 5e91740f47..c76eb9ed2f 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -590,47 +590,30 @@ int Zmatrix::addInternalCoordForAtom(int iat, Frame const& frameIn, Topology con
   */
 int Zmatrix::SetFromFrameAndConnect(Frame const& frameIn, Topology const& topIn) //, int molnum)
 {
-//  if (molnum < 0) {
-//    mprinterr("Internal Error: Zmatrix::SetFromFrame(): Negative molecule index.\n");
-//    return 1;
-//  }
-//  if (topIn.Nmol() < 1) {
-//    mprinterr("Internal Error: Zmatrix::SetFromFrame(): No molecules.\n");
-//    return 1;
-//  }
   clear();
-
-  IC_.clear();
-//  Molecule const& currentMol = topIn.Mol(molnum);
-
-//  for (Unit::const_iterator seg = currentMol.MolUnit().segBegin();
-//                            seg != currentMol.MolUnit().segEnd(); ++seg)
-//  {
-//    for (int iat1 = seg->Begin(); iat1 != seg->End(); ++iat1)
-    for (int iat1 = 0; iat1 < topIn.Natom(); iat1++)
-    {
-      Atom const& At1 = topIn[iat1];
-      for (int bidx1 = 0; bidx1 < At1.Nbonds(); bidx1++) {
-        int iat2 = At1.Bond(bidx1);
-        Atom const& At2 = topIn[iat2];
-        for (int bidx2 = 0; bidx2 < At2.Nbonds(); bidx2++) {
-          int iat3 = At2.Bond(bidx2);
-          if (iat3 != iat1) {
-            Atom const& At3 = topIn[iat3];
-            for (int bidx3 = 0; bidx3 < At3.Nbonds(); bidx3++) {
-              int iat4 = At3.Bond(bidx3);
-              if (iat4 != iat2 && iat1 < iat4) {
-                //mprintf("DEBUG: DIHEDRAL  %i - %i - %i - %i (%i %i %i %i)\n", iat1+1, iat2+1, iat3+1, iat4+1, iat1*3, iat2*3, iat3*3, iat4*3);
-                //out.push_back( DihedralType( iat1, iat2, iat3, iat4, -1 ) );
-                addIc(iat1, iat2, iat3, iat4, frameIn);
-                addIc(iat4, iat3, iat2, iat1, frameIn); // FIXME should the reverse one be put in?
-              }
+  for (int iat1 = 0; iat1 < topIn.Natom(); iat1++)
+  {
+    Atom const& At1 = topIn[iat1];
+    for (int bidx1 = 0; bidx1 < At1.Nbonds(); bidx1++) {
+      int iat2 = At1.Bond(bidx1);
+      Atom const& At2 = topIn[iat2];
+      for (int bidx2 = 0; bidx2 < At2.Nbonds(); bidx2++) {
+        int iat3 = At2.Bond(bidx2);
+        if (iat3 != iat1) {
+          Atom const& At3 = topIn[iat3];
+          for (int bidx3 = 0; bidx3 < At3.Nbonds(); bidx3++) {
+            int iat4 = At3.Bond(bidx3);
+            if (iat4 != iat2 && iat1 < iat4) {
+              //mprintf("DEBUG: DIHEDRAL  %i - %i - %i - %i (%i %i %i %i)\n", iat1+1, iat2+1, iat3+1, iat4+1, iat1*3, iat2*3, iat3*3, iat4*3);
+              //out.push_back( DihedralType( iat1, iat2, iat3, iat4, -1 ) );
+              addIc(iat1, iat2, iat3, iat4, frameIn);
+              addIc(iat4, iat3, iat2, iat1, frameIn); // FIXME should the reverse one be put in?
             }
           }
         }
       }
     }
-  //}
+  }
   if (IC_.empty()) {
     // Either 4-5 atoms in a tetrahedral configuration or else
     // some other strange configuration.

From 590822e109c38ee6d0deafd1a4b1dc2277986688 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 31 Jan 2024 09:44:28 -0500
Subject: [PATCH 0414/1492] Start trying to build internals in the same order
 as leap

---
 src/Structure/GenerateConnectivityArrays.cpp | 26 ++++++++++++++++++++
 src/Structure/GenerateConnectivityArrays.h   |  2 ++
 src/Structure/Zmatrix.cpp                    |  4 +++
 src/Topology.h                               |  1 +
 4 files changed, 33 insertions(+)

diff --git a/src/Structure/GenerateConnectivityArrays.cpp b/src/Structure/GenerateConnectivityArrays.cpp
index 0b7dd8e6c8..edf57535bc 100644
--- a/src/Structure/GenerateConnectivityArrays.cpp
+++ b/src/Structure/GenerateConnectivityArrays.cpp
@@ -252,3 +252,29 @@ void Cpptraj::Structure::GenerateAngleAndTorsionArraysFromBonds(AngleArray& angl
     enumerateDihedrals( dihedrals, it->A1(), it->A2(), atoms );
   }
 }
+
+/** Generate dihedral array in the same order as LEaP's
+  * BuildInternalsForContainer/ModelAssignTorsionsAround.
+  */
+DihedralArray Cpptraj::Structure::GenerateInternals(std::vector<Residue> const& residues,
+                                                    std::vector<Atom> const& atoms)
+{
+  // First generate the bond array
+  BondArray bonds = GenerateBondArray( residues, atoms );
+  // Loop over bonds
+  for (BondArray::const_iterator bnd = bonds.begin(); bnd != bonds.end(); ++bnd)
+  {
+    Atom const& A2 = atoms[bnd->A1()];
+    Atom const& A3 = atoms[bnd->A2()];
+    if (A2.Nbonds() > 1 && A3.Nbonds() > 1) {
+      Residue const& R2 = residues[A2.ResNum()];
+      Residue const& R3 = residues[A3.ResNum()];
+      mprintf("Building torsion INTERNALs around: .R<%s %i>.A<%s %i> - .R<%s %i>.A<%s %i>\n",
+              *(R2.Name()), A2.ResNum()+1, *(A2.Name()), bnd->A1()+1, 
+              *(R3.Name()), A3.ResNum()+1, *(A3.Name()), bnd->A2()+1 );
+    }
+  }
+
+  DihedralArray out;
+  return out;
+}
diff --git a/src/Structure/GenerateConnectivityArrays.h b/src/Structure/GenerateConnectivityArrays.h
index b0bc6f8bc2..43eed2f57f 100644
--- a/src/Structure/GenerateConnectivityArrays.h
+++ b/src/Structure/GenerateConnectivityArrays.h
@@ -22,6 +22,8 @@ DihedralArray GenerateDihedralArray(std::vector<Residue> const&, std::vector<Ato
 DihedralArray GenerateImproperArray(std::vector<Residue> const&, std::vector<Atom> const&);
 /// Generate angle and torsion arrays from bonds
 void GenerateAngleAndTorsionArraysFromBonds(AngleArray&, DihedralArray&, std::vector<Atom> const&, BondArray const&);
+/// Generate array of dihedrals to be used as internal coordinates
+DihedralArray GenerateInternals(std::vector<Residue> const&, std::vector<Atom> const&);
 }
 }
 #endif
diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index c76eb9ed2f..275c87e9df 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -3,6 +3,7 @@
 #include <stack>
 #include <cmath> // cos
 #include "Zmatrix.h"
+#include "GenerateConnectivityArrays.h"
 #include "../Frame.h"
 #include "../CpptrajStdio.h"
 #include "../Constants.h"
@@ -591,6 +592,9 @@ int Zmatrix::addInternalCoordForAtom(int iat, Frame const& frameIn, Topology con
 int Zmatrix::SetFromFrameAndConnect(Frame const& frameIn, Topology const& topIn) //, int molnum)
 {
   clear();
+  // DEBUG
+  DihedralArray internals = GenerateInternals(topIn.Residues(), topIn.Atoms());
+  // DEBUG
   for (int iat1 = 0; iat1 < topIn.Natom(); iat1++)
   {
     Atom const& At1 = topIn[iat1];
diff --git a/src/Topology.h b/src/Topology.h
index 825ed4cc50..b193af71e2 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -89,6 +89,7 @@ class Topology {
     inline res_iterator ResEnd()   const { return residues_.end();   }
     const Residue& Res(int idx)    const { return residues_[idx];    }
     Residue& SetRes(int idx)             { return residues_[idx];    }
+    std::vector<Residue> const& Residues() const { return residues_; }
     Range SoluteResidues() const;
     /// Merge residues in given range
     int MergeResidues(int, int);

From 50be3d1af483a1d1be9cd47206f359c838c3bc75 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 31 Jan 2024 10:56:42 -0500
Subject: [PATCH 0415/1492] Move the leap-like internal coord generation scheme
 to inside zmatrix

---
 src/Structure/GenerateConnectivityArrays.cpp | 26 ------
 src/Structure/GenerateConnectivityArrays.h   |  2 -
 src/Structure/Zmatrix.cpp                    | 88 +++++++++++++++++++-
 src/Structure/Zmatrix.h                      |  2 +
 4 files changed, 88 insertions(+), 30 deletions(-)

diff --git a/src/Structure/GenerateConnectivityArrays.cpp b/src/Structure/GenerateConnectivityArrays.cpp
index edf57535bc..0b7dd8e6c8 100644
--- a/src/Structure/GenerateConnectivityArrays.cpp
+++ b/src/Structure/GenerateConnectivityArrays.cpp
@@ -252,29 +252,3 @@ void Cpptraj::Structure::GenerateAngleAndTorsionArraysFromBonds(AngleArray& angl
     enumerateDihedrals( dihedrals, it->A1(), it->A2(), atoms );
   }
 }
-
-/** Generate dihedral array in the same order as LEaP's
-  * BuildInternalsForContainer/ModelAssignTorsionsAround.
-  */
-DihedralArray Cpptraj::Structure::GenerateInternals(std::vector<Residue> const& residues,
-                                                    std::vector<Atom> const& atoms)
-{
-  // First generate the bond array
-  BondArray bonds = GenerateBondArray( residues, atoms );
-  // Loop over bonds
-  for (BondArray::const_iterator bnd = bonds.begin(); bnd != bonds.end(); ++bnd)
-  {
-    Atom const& A2 = atoms[bnd->A1()];
-    Atom const& A3 = atoms[bnd->A2()];
-    if (A2.Nbonds() > 1 && A3.Nbonds() > 1) {
-      Residue const& R2 = residues[A2.ResNum()];
-      Residue const& R3 = residues[A3.ResNum()];
-      mprintf("Building torsion INTERNALs around: .R<%s %i>.A<%s %i> - .R<%s %i>.A<%s %i>\n",
-              *(R2.Name()), A2.ResNum()+1, *(A2.Name()), bnd->A1()+1, 
-              *(R3.Name()), A3.ResNum()+1, *(A3.Name()), bnd->A2()+1 );
-    }
-  }
-
-  DihedralArray out;
-  return out;
-}
diff --git a/src/Structure/GenerateConnectivityArrays.h b/src/Structure/GenerateConnectivityArrays.h
index 43eed2f57f..b0bc6f8bc2 100644
--- a/src/Structure/GenerateConnectivityArrays.h
+++ b/src/Structure/GenerateConnectivityArrays.h
@@ -22,8 +22,6 @@ DihedralArray GenerateDihedralArray(std::vector<Residue> const&, std::vector<Ato
 DihedralArray GenerateImproperArray(std::vector<Residue> const&, std::vector<Atom> const&);
 /// Generate angle and torsion arrays from bonds
 void GenerateAngleAndTorsionArraysFromBonds(AngleArray&, DihedralArray&, std::vector<Atom> const&, BondArray const&);
-/// Generate array of dihedrals to be used as internal coordinates
-DihedralArray GenerateInternals(std::vector<Residue> const&, std::vector<Atom> const&);
 }
 }
 #endif
diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index 275c87e9df..401be123b5 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -1,5 +1,5 @@
 #include <vector>
-#include <algorithm> // std::sort, std::min, std::max, std::find
+#include <algorithm> // std::sort, std::min, std::max, std::find, std::swap
 #include <stack>
 #include <cmath> // cos
 #include "Zmatrix.h"
@@ -586,6 +586,90 @@ int Zmatrix::addInternalCoordForAtom(int iat, Frame const& frameIn, Topology con
   return 0;
 }
 
+// -----------------------------------------------
+/** \return the LEaP 'weight' of an atom.
+  * Originally used to force the 'heaviest' atoms around a torsion trans to
+  * each other. The 'weight' of an atom is defined as its element number,
+  * unless the atom is CARBON, then it is 1000, making it the 'heaviest' atom.
+  */
+static int LeapAtomWeight(Atom const& At)
+{
+  if ( At.Element() == Atom::CARBON )
+    return 1000;
+  return At.AtomicNumber();
+}
+
+/** Order atoms bonded to the given atom in a manner similar to LEaP's
+  * zModelOrderAtoms. In that routine, first atoms were sorted into
+  * known position > unknown position. Then the heaviest atom in each
+  * subgroup was swapped with the first element of that list. Since at this
+  * point we assume all positions are known, we are just shifting the
+  * heaviest atom to the front of the list.
+  * The ignore atom is the index of the atom this atom is bonded to that
+  * forms the torsion we are interested in.
+  */
+static inline std::vector<int> SortBondedAtomsLikeLeap(Atom const& At, Topology const& topIn, int ignoreAtom)
+{
+  std::vector<int> out;
+  out.reserve( At.Nbonds() );
+  // Find the index of the heaviest atom
+  int iHighest = 0;
+  int iPos = 0;
+  for (int idx = 0; idx < At.Nbonds(); idx++) {
+    int bat = At.Bond(idx);
+    if (bat != ignoreAtom) {
+      out.push_back( bat );
+      int iWeight = LeapAtomWeight( topIn[bat] );
+      if ( iHighest < iWeight ) {
+        iHighest = iWeight;
+        iPos = (int)out.size()-1;
+      }
+    }
+  }
+  // If highest weight atom not already in front, swap it there.
+  if (iPos != 0) std::swap( out[0], out[iPos] );
+
+  return out;
+}
+
+/** Set up Zmatrix from Cartesian coordinates and topology in the same
+  * manner as LEaP's BuildInternalsForContainer/ModelAssignTorsionsAround.
+  * Currently assumes all positions are known.
+  */
+int Zmatrix::GenerateInternals(Frame const& frameIn, Topology const& topIn)
+{
+  // First generate the bond array
+  BondArray bonds = GenerateBondArray( topIn.Residues(), topIn.Atoms() );
+  // Loop over bonds
+  for (BondArray::const_iterator bnd = bonds.begin(); bnd != bonds.end(); ++bnd)
+  {
+    Atom const& A2 = topIn[bnd->A1()];
+    Atom const& A3 = topIn[bnd->A2()];
+    if (A2.Nbonds() > 1 && A3.Nbonds() > 1) {
+      Residue const& R2 = topIn.Res(A2.ResNum());
+      Residue const& R3 = topIn.Res(A3.ResNum());
+      mprintf("Building torsion INTERNALs around: .R<%s %i>.A<%s %i> - .R<%s %i>.A<%s %i>\n",
+              *(R2.Name()), A2.ResNum()+1, *(A2.Name()), bnd->A1()+1, 
+              *(R3.Name()), A3.ResNum()+1, *(A3.Name()), bnd->A2()+1 );
+      Iarray sorted_a2 = SortBondedAtomsLikeLeap(A2, topIn, bnd->A2());
+      Iarray sorted_a3 = SortBondedAtomsLikeLeap(A3, topIn, bnd->A1());
+      mprintf("Orientation around: %s {", *(A2.Name()));
+      for (Atom::bond_iterator bat = A2.bondbegin(); bat != A2.bondend(); ++bat) mprintf(" %s", *(topIn[*bat].Name()));
+      mprintf("}\n");
+      for (Iarray::const_iterator it = sorted_a2.begin(); it != sorted_a2.end(); ++it)
+        mprintf("Atom %li: %s\n", it - sorted_a2.begin(), *(topIn[*it].Name()));
+      mprintf("Orientation around: %s {", *(A3.Name()));
+      for (Atom::bond_iterator bat = A3.bondbegin(); bat != A3.bondend(); ++bat) mprintf(" %s", *(topIn[*bat].Name()));
+      mprintf("}\n");
+      for (Iarray::const_iterator it = sorted_a3.begin(); it != sorted_a3.end(); ++it)
+        mprintf("Atom %li: %s\n", it - sorted_a3.begin(), *(topIn[*it].Name()));
+
+    }
+  }
+  return 0;
+}
+
+// -----------------------------------------------
 /** Set up Zmatrix from Cartesian coordinates and topology.
   * Use torsions based on connectivity to create a complete set of ICs.
   */
@@ -593,7 +677,7 @@ int Zmatrix::SetFromFrameAndConnect(Frame const& frameIn, Topology const& topIn)
 {
   clear();
   // DEBUG
-  DihedralArray internals = GenerateInternals(topIn.Residues(), topIn.Atoms());
+  GenerateInternals(frameIn, topIn);
   // DEBUG
   for (int iat1 = 0; iat1 < topIn.Natom(); iat1++)
   {
diff --git a/src/Structure/Zmatrix.h b/src/Structure/Zmatrix.h
index 7d27d471cc..d6cb710759 100644
--- a/src/Structure/Zmatrix.h
+++ b/src/Structure/Zmatrix.h
@@ -39,6 +39,8 @@ class Zmatrix {
     /// Set seed atoms as 3 consecutive atoms with known positions for specified residue # TODO deprecate?
     int AutoSetSeedsWithPositions(Frame const&, Topology const&, int, Barray const&);
 
+    /// Try to generate complete ICs in same manner as LEaP
+    int GenerateInternals(Frame const&, Topology const&);
     /// Try to generate complete ICs from atom connectivity
     int SetFromFrameAndConnect(Frame const&, Topology const&);//, int);
     /// Convert specifed molecule of Frame/Topology to internal coordinates array

From 6dd31d48b26415e1e4b3f6b343e2a1d92b552cce Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 31 Jan 2024 11:34:50 -0500
Subject: [PATCH 0416/1492] Create a dedicated leap format name function for
 easier debugging

---
 src/Structure/Zmatrix.cpp | 9 ++++-----
 src/Topology.cpp          | 8 ++++++++
 src/Topology.h            | 2 ++
 3 files changed, 14 insertions(+), 5 deletions(-)

diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index 401be123b5..8647f0469e 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -646,11 +646,10 @@ int Zmatrix::GenerateInternals(Frame const& frameIn, Topology const& topIn)
     Atom const& A2 = topIn[bnd->A1()];
     Atom const& A3 = topIn[bnd->A2()];
     if (A2.Nbonds() > 1 && A3.Nbonds() > 1) {
-      Residue const& R2 = topIn.Res(A2.ResNum());
-      Residue const& R3 = topIn.Res(A3.ResNum());
-      mprintf("Building torsion INTERNALs around: .R<%s %i>.A<%s %i> - .R<%s %i>.A<%s %i>\n",
-              *(R2.Name()), A2.ResNum()+1, *(A2.Name()), bnd->A1()+1, 
-              *(R3.Name()), A3.ResNum()+1, *(A3.Name()), bnd->A2()+1 );
+      //Residue const& R2 = topIn.Res(A2.ResNum());
+      //Residue const& R3 = topIn.Res(A3.ResNum());
+      mprintf("Building torsion INTERNALs around: %s - %s\n",
+              topIn.LeapName(bnd->A1()).c_str(), topIn.LeapName(bnd->A2()).c_str());
       Iarray sorted_a2 = SortBondedAtomsLikeLeap(A2, topIn, bnd->A2());
       Iarray sorted_a3 = SortBondedAtomsLikeLeap(A3, topIn, bnd->A1());
       mprintf("Orientation around: %s {", *(A2.Name()));
diff --git a/src/Topology.cpp b/src/Topology.cpp
index 121e038b80..48046ba4ac 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -334,6 +334,14 @@ std::string Topology::TruncAtomNameNum(int atom) const {
   return atom_name;
 }
 
+/** Given an atom number, return a string in LEaP-style format. */
+std::string Topology::LeapName(int at) const {
+  int rnum = atoms_[at].ResNum();
+  std::string out( ".R<" + residues_[rnum].Name().Truncated() + " " + integerToString(rnum+1) +
+                  ">.A<" + atoms_[at].Name().Truncated()      + " " + integerToString(at+1) + ">");
+  return out;
+}
+
 // Topology::TruncResNameNum()
 /** Given a residue index (starting from 0), return a string containing 
   * residue name and number (starting from 1) with format: 
diff --git a/src/Topology.h b/src/Topology.h
index b193af71e2..804c734f1c 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -196,6 +196,8 @@ class Topology {
     std::string AtomMaskName(int) const;
     /// Format: <atom name>_<atom num>
     std::string TruncAtomNameNum(int) const;
+    /// LEaP Format: R<res #>.A<at #>
+    std::string LeapName(int) const;
     /// Format: <res name>:<res num> 
     std::string TruncResNameNum(int) const;
     /// Format: <res name>_<onum>[_<id>]

From 410e182195ce37f4ada23f3f285d16c3d84a9692 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 31 Jan 2024 12:06:08 -0500
Subject: [PATCH 0417/1492] Use leap ordering for internal coordinates. Getting
 closer!

---
 src/Exec_Build.cpp        |  3 ++-
 src/Structure/Zmatrix.cpp | 22 ++++++++++++++++++----
 2 files changed, 20 insertions(+), 5 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 2b02cdd930..3dd6016afc 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -299,7 +299,8 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
         Frame templateFrame = resTemplate->AllocateFrame();
         resTemplate->GetFrame( 0, templateFrame );
         Cpptraj::Structure::Zmatrix* zmatrix = new Cpptraj::Structure::Zmatrix();
-        if (zmatrix->SetFromFrameAndConnect( templateFrame, resTemplate->Top() )) {
+        //if (zmatrix->SetFromFrameAndConnect( templateFrame, resTemplate->Top() )) {
+        if (zmatrix->GenerateInternals( templateFrame, resTemplate->Top() )) {
           mprinterr("Error: Could not set up residue template zmatrix.\n");
           return 1;
         }
diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index 8647f0469e..31ead01817 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -638,6 +638,7 @@ static inline std::vector<int> SortBondedAtomsLikeLeap(Atom const& At, Topology
   */
 int Zmatrix::GenerateInternals(Frame const& frameIn, Topology const& topIn)
 {
+  clear();
   // First generate the bond array
   BondArray bonds = GenerateBondArray( topIn.Residues(), topIn.Atoms() );
   // Loop over bonds
@@ -662,7 +663,22 @@ int Zmatrix::GenerateInternals(Frame const& frameIn, Topology const& topIn)
       mprintf("}\n");
       for (Iarray::const_iterator it = sorted_a3.begin(); it != sorted_a3.end(); ++it)
         mprintf("Atom %li: %s\n", it - sorted_a3.begin(), *(topIn[*it].Name()));
-
+      // Build the torsions
+      int aj = bnd->A1();
+      int ak = bnd->A2();
+      for (Iarray::const_iterator ai = sorted_a2.begin(); ai != sorted_a2.end(); ++ai) {
+        for (Iarray::const_iterator al = sorted_a3.begin(); al != sorted_a3.end(); ++al) {
+          //double dval = Torsion(frameIn.XYZ(*ai), frameIn.XYZ(aj), frameIn.XYZ(ak), frameIn.XYZ(*al));
+          addIc(*ai, aj, ak, *al, frameIn);
+          mprintf("++++Torsion INTERNAL: %f to %s - %s - %s - %s\n",
+                  IC_.back().Phi() * Constants::RADDEG,
+                  topIn.LeapName(*ai).c_str(),
+                  topIn.LeapName(aj).c_str(),
+                  topIn.LeapName(ak).c_str(),
+                  topIn.LeapName(*al).c_str());
+          addIc(*al, ak, aj, *ai, frameIn);
+        }
+      }
     }
   }
   return 0;
@@ -675,9 +691,7 @@ int Zmatrix::GenerateInternals(Frame const& frameIn, Topology const& topIn)
 int Zmatrix::SetFromFrameAndConnect(Frame const& frameIn, Topology const& topIn) //, int molnum)
 {
   clear();
-  // DEBUG
-  GenerateInternals(frameIn, topIn);
-  // DEBUG
+
   for (int iat1 = 0; iat1 < topIn.Natom(); iat1++)
   {
     Atom const& At1 = topIn[iat1];

From 41fc28c2dceced6430519eef4eb199ffe7d9e79d Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 31 Jan 2024 12:26:09 -0500
Subject: [PATCH 0418/1492] Use LeapName in more places

---
 src/Structure/Builder.cpp | 12 ++++++------
 src/Structure/Zmatrix.cpp |  2 +-
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index a423674729..99a9eba09a 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1115,10 +1115,10 @@ const
                 hasPosition[thisIc.AtL()])
             {
               mprintf("DEBUG:\tMeasuring torsion of fixed atoms: %s - %s - %s - %s\n",
-                      topIn.AtomMaskName(thisIc.AtI()).c_str(),
-                      topIn.AtomMaskName(thisIc.AtJ()).c_str(),
-                      topIn.AtomMaskName(thisIc.AtK()).c_str(),
-                      topIn.AtomMaskName(thisIc.AtL()).c_str());
+                      topIn.LeapName(thisIc.AtI()).c_str(),
+                      topIn.LeapName(thisIc.AtJ()).c_str(),
+                      topIn.LeapName(thisIc.AtK()).c_str(),
+                      topIn.LeapName(thisIc.AtL()).c_str());
               InternalCoords frameIc = calcKnownAtomIc(thisIc.AtI(), thisIc.AtJ(), thisIc.AtK(), thisIc.AtL(), frameIn);
               double dTorsion = frameIc.Phi() * Constants::DEGRAD;
               double dInternalValue = thisIc.Phi() * Constants::DEGRAD;
@@ -1133,8 +1133,8 @@ const
       // If any difference was found, shift all of the torsions
       if (needsUpdate) {
         mprintf("DEBUG: Twisting torsions centered on %s - %s by %f degrees\n",
-                topIn.AtomMaskName(bnd->A1()).c_str(),
-                topIn.AtomMaskName(bnd->A2()).c_str(),
+                topIn.LeapName(bnd->A1()).c_str(),
+                topIn.LeapName(bnd->A2()).c_str(),
                 tDiff);
         for (Iarray::const_iterator it = bondICs.begin(); it != bondICs.end(); ++it)
         {
diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index 31ead01817..8acb53f49e 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -671,7 +671,7 @@ int Zmatrix::GenerateInternals(Frame const& frameIn, Topology const& topIn)
           //double dval = Torsion(frameIn.XYZ(*ai), frameIn.XYZ(aj), frameIn.XYZ(ak), frameIn.XYZ(*al));
           addIc(*ai, aj, ak, *al, frameIn);
           mprintf("++++Torsion INTERNAL: %f to %s - %s - %s - %s\n",
-                  IC_.back().Phi() * Constants::RADDEG,
+                  IC_.back().Phi(),
                   topIn.LeapName(*ai).c_str(),
                   topIn.LeapName(aj).c_str(),
                   topIn.LeapName(ak).c_str(),

From 2db89609a6a4d5479632c09649366fc6a0d589f7 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 1 Feb 2024 10:08:40 -0500
Subject: [PATCH 0419/1492] Add <, ==, and != operators

---
 src/Structure/InternalCoords.h | 36 +++++++++++++++++++++++++++++++++-
 1 file changed, 35 insertions(+), 1 deletion(-)

diff --git a/src/Structure/InternalCoords.h b/src/Structure/InternalCoords.h
index acf02face1..7dc8f1c3a0 100644
--- a/src/Structure/InternalCoords.h
+++ b/src/Structure/InternalCoords.h
@@ -24,7 +24,41 @@ class InternalCoords {
     InternalCoords(InternalCoords const&);
     /// ASSIGNMENT
     InternalCoords& operator=(InternalCoords const&);
-
+    /// Less than another IC using AI < AL < AK < AJ
+    bool operator<(InternalCoords const& rhs) const {
+      if (ati_ == rhs.ati_) {
+        if (idx_[2] == rhs.idx_[2]) { // Atom L
+          if (idx_[1] == rhs.idx_[1]) { // Atom K
+            if (idx_[0] == rhs.idx_[0]) { // Atom J
+              return false; // Equal
+            } else {
+              return (idx_[0] < rhs.idx_[0]);
+            }
+          } else {
+            return (idx_[1] < rhs.idx_[1]);
+          }
+        } else {
+          return (idx_[2] < rhs.idx_[2]);
+        }
+      } else {
+        return (ati_ < rhs.ati_);
+      }
+    }
+    /// \return True if all indices are equal
+    bool operator==(InternalCoords const& rhs) const {
+      return ( ati_ == rhs.ati_ &&
+               idx_[0] == rhs.idx_[0] &&
+               idx_[1] == rhs.idx_[1] &&
+               idx_[2] == rhs.idx_[2] );
+    }
+    /// \return True if any index is not equal
+    bool operator!=(InternalCoords const& rhs) const {
+      return ( ati_ != rhs.ati_ ||
+               idx_[0] != rhs.idx_[0] ||
+               idx_[1] != rhs.idx_[1] ||
+               idx_[2] != rhs.idx_[2] );
+    }
+    /// Indictaes no atom set
     static const int NO_ATOM;
 
     double Dist() const { return val_[0]; }

From f765f178f798b0de01a63b6062518e36ea7fa377 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 1 Feb 2024 10:20:58 -0500
Subject: [PATCH 0420/1492] Have ModelCoordsAroundBond add IC to existing
 Zmatrix instead of actually setting the coordinates.

---
 src/Exec_Build.cpp        |  2 +-
 src/Structure/Builder.cpp | 72 ++++++++++++++++++++++++---------------
 src/Structure/Builder.h   |  2 +-
 src/Structure/Zmatrix.cpp |  5 +++
 src/Structure/Zmatrix.h   |  2 ++
 5 files changed, 53 insertions(+), 30 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 3dd6016afc..a8499759cd 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -397,7 +397,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
             if (jres < ires) {
               mprintf("DEBUG: Connected to residue %s\n", topOut.TruncResNameNum(jres).c_str());
               if (linkBuilder.ModelCoordsAroundBond(frameOut, topOut, at, *bat,
-                                                    zmatrix, ResZmatrices[jres], hasPosition))
+                                                    *zmatrix, hasPosition))
               {
                 mprinterr("Error: Model coords around bond failed between %s and %s\n",
                           topOut.AtomMaskName(at).c_str(), topOut.AtomMaskName(*bat).c_str());
diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 99a9eba09a..8926c601bd 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -642,18 +642,21 @@ const
 }
 
 /// \return The total number of atoms whose position is known for the specified residue
-static inline int known_count(int ires, Topology const& topIn, std::vector<bool> const& hasPosition)
+/*static inline int known_count(int ires, Topology const& topIn, std::vector<bool> const& hasPosition)
 {
   int count = 0;
   for (int at = topIn.Res(ires).FirstAtom(); at != topIn.Res(ires).LastAtom(); at++)
     if (hasPosition[at])
       count++;
   return count;
-}
+}*/
 
-/** Model the coordinates around a bond */
-int Builder::ModelCoordsAroundBond(Frame& frameIn, Topology const& topIn, int bondAt0, int bondAt1,
-                                   Zmatrix const* zmatrix0, Zmatrix const* zmatrix1, Barray& hasPosition)
+/** Model the internal coordinates around a bond between two residues defined
+  * by bondAt0 (in residue0) and bondAt1 in (residue1).
+  *
+  */
+int Builder::ModelCoordsAroundBond(Frame const& frameIn, Topology const& topIn, int bondAt0, int bondAt1,
+                                   Zmatrix& zmatrix0, Barray const& hasPosition)
 const
 {
   mprintf("DEBUG: Model coords around bond %s - %s\n", topIn.AtomMaskName(bondAt0).c_str(), topIn.AtomMaskName(bondAt1).c_str());
@@ -664,24 +667,33 @@ const
     return 1;
   }
   // Determine which "direction" we will be combining the fragments.
-  // Make atA belong to the less-known fragment. atB fragment will be "known".
-  int known0 = known_count(res0, topIn, hasPosition);
-  int known1 = known_count(res1, topIn, hasPosition);
-  int atA, atB;
-  Zmatrix const* zA;
-  if (known0 < known1) {
-    // Fragment 1 is better-known 
-    atA = bondAt0;
-    atB = bondAt1;
-    zA  = zmatrix0;
-    //zB  = zmatrix1;
-  } else {
-    // Fragment 0 is better or equally known 
-    atA = bondAt1;
-    atB = bondAt0;
-    zA  = zmatrix1;
-    //zB  = zmatrix0;
-  }
+  // Ensure atA belongs to the less-known fragment. atB fragment will be "known".
+//  int known0 = known_count(res0, topIn, hasPosition);
+//  int known1 = known_count(res1, topIn, hasPosition);
+////  int atA, atB;
+//  if (known0 > known1) {
+//    mprinterr("Internal Error: ModelCoordsAroundBond(): Residue0 '%s' is more well-known than Residue1 '%s'\n",
+//              topIn.TruncResNameNum( topIn[bondAt0].ResNum() ).c_str(),
+//              topIn.TruncResNameNum( topIn[bondAt1].ResNum() ).c_str());
+//    return 1;
+//  }
+  int atA = bondAt0;
+  int atB = bondAt1;
+  Zmatrix* zA = &zmatrix0; // FIXME
+//  Zmatrix const* zA;
+//  if (known0 < known1) {
+//    // Fragment 1 is better-known 
+//    atA = bondAt0;
+//    atB = bondAt1;
+//    zA  = zmatrix0;
+//    //zB  = zmatrix1;
+//  } else {
+//    // Fragment 0 is better or equally known 
+//    atA = bondAt1;
+//    atB = bondAt0;
+//    zA  = zmatrix1;
+//    //zB  = zmatrix0;
+//  }
 
   mprintf("DEBUG: More well-known atom: %s\n", topIn.AtomMaskName(atB).c_str());
   mprintf("DEBUG: Less well-known atom: %s  has zmatrix= %i\n", topIn.AtomMaskName(atA).c_str(), (int)(zA != 0));
@@ -724,12 +736,16 @@ const
               topIn.AtomMaskName(atB).c_str());
     return 1;
   }
+  // Add the remaining ICs FIXME check for duplicates
+  for (Zmatrix::const_iterator it = zmatrix0.begin(); it != zmatrix0.end(); ++it)
+    bondZmatrix.AddIC( *it );
   if (debug_ > 0)
     bondZmatrix.print(&topIn);
-  if (bondZmatrix.SetToFrame( frameIn, hasPosition )) {
-    mprinterr("Error: Conversion from bondZmatrix to Cartesian coords failed.\n");
-    return 1;
-  }
+  zmatrix0 = bondZmatrix;
+//  if (bondZmatrix.SetToFrame( frameIn, hasPosition )) {
+//    mprinterr("Error: Conversion from bondZmatrix to Cartesian coords failed.\n");
+//    return 1;
+//  }
 
   return 0;
 }
@@ -752,7 +768,7 @@ const
             topIn.AtomMaskName(atA).c_str(), atA+1,
             topIn.AtomMaskName(atB).c_str(), atB+1,
             topIn.Natom());
-  zmatrix.clear();
+//  zmatrix.clear();
 
   //Barray hasIC( topIn.Natom(), false );
   Barray hasIC = hasICin;
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index c912d0651b..13e285ab48 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -23,7 +23,7 @@ class Builder {
     /// Combine second fragment into first fragment and bond
     int Combine(Topology&, Frame&, Topology const&, Frame const&, int, int) const;
     /// Model the coordinates around a bond given only some coordinates are known
-    int ModelCoordsAroundBond(Frame&, Topology const&, int, int, Zmatrix const*, Zmatrix const*, Barray&) const;
+    int ModelCoordsAroundBond(Frame const&, Topology const&, int, int, Zmatrix&, Barray const&) const;
     /// Update the internal coordinates in given Zmatrix with values from Frame/Parameters
     int UpdateICsFromFrame(Zmatrix&, Frame const&, int, Topology const&, Barray const&) const;
   private:
diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index 8acb53f49e..e76a05a68e 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -41,6 +41,11 @@ void Zmatrix::clear() {
   seedAt2_ = InternalCoords::NO_ATOM;
 }
 
+/** Sort ICs. */
+void Zmatrix::sort() {
+  std::sort( IC_.begin(), IC_.end() );
+}
+
 /// Error message for seed already set
 static inline int seed_err(int iseed) {
   mprinterr("Internal Error: Internal coord seed %i is already set.\n", iseed);
diff --git a/src/Structure/Zmatrix.h b/src/Structure/Zmatrix.h
index d6cb710759..fbd921d84c 100644
--- a/src/Structure/Zmatrix.h
+++ b/src/Structure/Zmatrix.h
@@ -25,6 +25,8 @@ class Zmatrix {
     void reserve(unsigned int n) { IC_.reserve( n ); }
     /// Clear the Zmatrix
     void clear();
+    /// Sort ICs by atom index (I < L < K < J)
+    void sort();
     /// Add internal coordinate
     int AddIC(InternalCoords const&);
     /// Set specified IC

From 1ec5ae84cf6eccfa666f934f0a2d915bb0377bf9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 1 Feb 2024 11:10:22 -0500
Subject: [PATCH 0421/1492] For atoms with 3 bonds, determine the angle if the
 2 other angles are known via known atoms/ICs

---
 src/Exec_Build.cpp        |   1 +
 src/Structure/Builder.cpp | 152 ++++++++++++++++++++++----------------
 src/Structure/Builder.h   |   3 +
 3 files changed, 94 insertions(+), 62 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index a8499759cd..5462530b60 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -387,6 +387,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
       mprintf("DEBUG: Zmatrix for building residue %li %s\n", ires + 1,
               topOut.TruncResNameOnumId(ires).c_str());
       zmatrix->print(&topOut);
+      linkBuilder.SetZmatrix( zmatrix );
       // Is this residue connected to an earlier residue?
       if ( *termType != Cpptraj::Structure::BEG_TERMINAL ) {
         for (int at = topOut.Res(ires).FirstAtom(); at != topOut.Res(ires).LastAtom(); ++at)
diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 8926c601bd..9c5ad8224e 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -16,7 +16,8 @@ using namespace Cpptraj::Structure;
 /** CONSTRUCTOR */
 Builder::Builder() :
   debug_(0),
-  params_(0)
+  params_(0),
+  currentZmatrix_(0)
 {}
 
 /** Set optional parameter set. */
@@ -28,6 +29,15 @@ void Cpptraj::Structure::Builder::SetParameters(ParameterSet const* paramsIn) {
   params_ = paramsIn;
 }
 
+/** Set optional Zmatrix. */
+void Cpptraj::Structure::Builder::SetZmatrix(Zmatrix const* zmatrixIn) {
+  if (zmatrixIn == 0) {
+    mprinterr("Internal Error: Builder::SetZmatrix called with null set.\n");
+    return;
+  }
+  currentZmatrix_ = zmatrixIn;
+}
+
 // -----------------------------------------------------------------------------
 /** Get length from parameter set if present.
   * \return 1 if a length parameter was found.
@@ -63,20 +73,6 @@ const
 
   // One or both positions unknown. Use estimated bond length or parameters.
   if (getLengthParam(dist, ai, aj, topIn)) return 0;
-/*  if (params_ != 0 && topIn[ai].HasType() && topIn[aj].HasType()) {
-    TypeNameHolder btypes(2);
-    btypes.AddName( topIn[ai].Type() );
-    btypes.AddName( topIn[aj].Type() );
-    ParmHolder<BondParmType>::const_iterator it = params_->BP().GetParam( btypes );
-    if (it != params_->BP().end()) {
-      dist = it->second.Req();
-      mprintf("DEBUG: Found bond parameter for %s (%s) - %s (%s): req=%g rk=%g\n",
-              topIn.AtomMaskName(ai).c_str(), *(topIn[ai].Type()),
-              topIn.AtomMaskName(aj).c_str(), *(topIn[aj].Type()),
-              it->second.Req(), it->second.Rk());
-      return 0;
-    }
-  }*/
 
   // Default to bond length based on elements
   dist = Atom::GetBondLength( topIn[ai].Element(), topIn[aj].Element() );
@@ -120,73 +116,107 @@ const
 {
   if (debug_ > 0)
     mprintf("DEBUG: AssignTheta for atom j : %s\n", topIn.AtomMaskName(aj).c_str());
+  Atom const& AJ = topIn[aj];
+
+  // Sanity check
+  if (AJ.Nbonds() < 2) {
+    mprinterr("Internal Error: AssignTheta() called for atom J %s with fewer than 2 bonds.\n", topIn.AtomMaskName(aj).c_str());
+    return 1;
+  }
+
+  // Check if all positions are already known
   if (atomPositionKnown[ai] && atomPositionKnown[aj] && atomPositionKnown[ak])
   {
     theta = CalcAngle(frameIn.XYZ(ai), frameIn.XYZ(aj), frameIn.XYZ(ak));
     return 0;
   }
 
-  if (getAngleParam(theta, ai, aj, ak, topIn)) return 0;
-/*
-  if (params_ != 0 &&
-      topIn[ai].HasType() &&
-      topIn[aj].HasType() &&
-      topIn[ak].HasType())
-  {
-    TypeNameHolder atypes(3);
-    atypes.AddName( topIn[ai].Type() );
-    atypes.AddName( topIn[aj].Type() );
-    atypes.AddName( topIn[ak].Type() );
-    ParmHolder<AngleParmType>::const_iterator it = params_->AP().GetParam( atypes );
-    if (it != params_->AP().end()) {
-      theta = it->second.Teq();
-      mprintf("DEBUG: Found angle parameter for %s (%s) - %s (%s) - %s (%s): teq=%g tk=%g\n",
-                topIn.AtomMaskName(ai).c_str(), *(topIn[ai].Type()),
-                topIn.AtomMaskName(aj).c_str(), *(topIn[aj].Type()),
-                topIn.AtomMaskName(ak).c_str(), *(topIn[ak].Type()),
-                it->second.Teq()*Constants::RADDEG, it->second.Tk());
+  // Figure out angles from known atoms + ICs
+  int nAngles = (AJ.Nbonds() * (AJ.Nbonds()-1)) / 2;
+  if (nAngles == 3) {
+    mprintf("DEBUG: Expect %i angles around AJ.\n", nAngles);
+    std::vector<double> thetaVals;
+    int tgtIdx = -1;
+    int numKnown = 0;
+    for (int idx0 = 0; idx0 < AJ.Nbonds(); idx0++) {
+      int atomi = AJ.Bond(idx0);
+      for (int idx1 = idx0 + 1; idx1 < AJ.Nbonds(); idx1++) {
+        int atomk = AJ.Bond(idx1);
+        mprintf("DEBUG: AssignTheta(): Angle %zu atoms %i - %i - %i\n", thetaVals.size(), atomi+1, aj+1, atomk+1);
+        if (ai == atomi && ak == atomk)
+          tgtIdx = (int)thetaVals.size();
+        double ajTheta = 0;
+        if (atomPositionKnown[atomi] && atomPositionKnown[aj] && atomPositionKnown[atomk]) {
+          ajTheta = CalcAngle(frameIn.XYZ(atomi), frameIn.XYZ(aj), frameIn.XYZ(atomk));
+          numKnown++;
+          mprintf("DEBUG: AssignTheta(): Known angle centered on atom J: %s - %s - %s = %g\n",
+                  topIn.LeapName(atomi).c_str(), 
+                  topIn.LeapName(aj).c_str(), 
+                  topIn.LeapName(atomk).c_str(),
+                  ajTheta * Constants::RADDEG);
+        } else if (currentZmatrix_ != 0) { // FIXME faster search?
+          for (Zmatrix::const_iterator ic = currentZmatrix_->begin(); ic != currentZmatrix_->end(); ++ic) {
+            if (ic->AtI() == atomi && ic->AtJ() == aj && ic->AtK() == atomk) {
+              // TODO: Check that repeats are equal?
+              ajTheta = ic->Theta() * Constants::DEGRAD;
+              numKnown++;
+              mprintf("DEBUG: AssignTheta(): IC angle centered on atomJ: %s - %s - %s = %g\n",
+                      topIn.LeapName(atomi).c_str(), 
+                      topIn.LeapName(aj).c_str(), 
+                      topIn.LeapName(atomk).c_str(),
+                      ic->Theta());
+              break;
+            }
+          }
+        }
+        thetaVals.push_back( ajTheta );
+      } // END inner loop over bonds to AJ
+    } // END outer loop over bonds to AJ
+    mprintf("DEBUG: AssignTheta(): thetaVals=");
+    for (std::vector<double>::const_iterator it = thetaVals.begin(); it != thetaVals.end(); ++it) {
+      mprintf(" %g", *it * Constants::RADDEG);
+      if (tgtIdx == it - thetaVals.begin()) mprintf("*");
+    }
+    mprintf("\n");
+    if (tgtIdx != -1 && numKnown >= 2) {
+      double sumTheta = 0;
+      for (std::vector<double>::const_iterator it = thetaVals.begin(); it != thetaVals.end(); ++it) {
+        if (it - thetaVals.begin() != tgtIdx) {
+          double tval = *it;
+          if (tval < 0)
+            tval += Constants::TWOPI;
+          else if (tval > Constants::TWOPI)
+            tval -= Constants::TWOPI;
+          sumTheta += tval;
+        }
+      }
+      theta = Constants::TWOPI - sumTheta;
+      mprintf("DEBUG: AssignTheta(): Setting from existing atoms/ICs: %g\n", theta * Constants::RADDEG);
       return 0;
     }
   }
-*/
+
+  // See if a parameter is defined for these atom types
+  if (getAngleParam(theta, ai, aj, ak, topIn)) return 0;
+
   // Figure out hybridization and chirality of atom j.
-  Atom const& AJ = topIn[aj];
   if (debug_ > 0) {
     mprintf("DEBUG:\t\tI %s Nbonds: %i\n", topIn[ai].ElementName(), topIn[ai].Nbonds());
     mprintf("DEBUG:\t\tJ %s Nbonds: %i\n", AJ.ElementName(), AJ.Nbonds());
     mprintf("DEBUG:\t\tK %s Nbonds: %i\n", topIn[ak].ElementName(), topIn[ak].Nbonds());
   }
-  // Sanity check
-  if (AJ.Nbonds() < 2) {
-    mprinterr("Internal Error: AssignTheta() called for atom J %s with fewer than 2 bonds.\n", topIn.AtomMaskName(aj).c_str());
-    return 1;
-  }
   AtomType::HybridizationType hybrid = AtomType::UNKNOWN_HYBRIDIZATION;
+  // Check params for hybrid
   if (params_ != 0) {
     ParmHolder<AtomType>::const_iterator it = params_->AT().GetParam( TypeNameHolder(AJ.Type()) );
     if (it != params_->AT().end())
       hybrid = it->second.Hybridization();
   }
+  // Guess hybrid if needed
   if (hybrid == AtomType::UNKNOWN_HYBRIDIZATION)
     hybrid = GuessAtomHybridization(AJ, topIn.Atoms());
-
-  // Fill in what values we can for known atoms
-/*  std::vector<double> knownTheta( AJ.Nbonds() );
-  int knownIdx = -1;
-  for (int idx = 0; idx < AJ.Nbonds(); idx++) {
-    int atnum = AJ.Bond(idx);
-    if (atnum != ak && atomPositionKnown[atnum]) {
-      knownTheta[idx] = CalcAngle(frameIn.XYZ(atnum),
-                                  frameIn.XYZ(aj),
-                                  frameIn.XYZ(ak));
-      mprintf("DEBUG:\t\tKnown theta for %s = %g\n", topIn.AtomMaskName(atnum).c_str(), knownTheta[idx]*Constants::RADDEG);
-      if (knownIdx == -1) knownIdx = idx; // FIXME handle more than 1 known
-    }
-  }
-  if (knownIdx == -1) {*/
-    //mprintf("DEBUG:\t\tNo known theta.\n");
+  // Set from number of bonds if still unknown. This is a pretty crude guess.
   if (hybrid == AtomType::UNKNOWN_HYBRIDIZATION) {
-    // Assign a theta based on number of bonds 
     switch (AJ.Nbonds()) {
       case 4 : hybrid = AtomType::SP3; break;
       case 3 : hybrid = AtomType::SP2; break;
@@ -194,16 +224,14 @@ const
       default : mprinterr("Internal Error: AssignTheta(): Unhandled # bonds for %s (%i)\n", topIn.AtomMaskName(aj).c_str(), AJ.Nbonds()); return 1;
     }
   }
+
   // Assign a theta based on hybridization
   switch (hybrid) {
     case AtomType::SP3 : theta = 109.5 * Constants::DEGRAD; break;
     case AtomType::SP2 : theta = 120.0 * Constants::DEGRAD; break;
     case AtomType::SP  : theta = 180.0 * Constants::DEGRAD; break;
     default : mprinterr("Internal Error: AssignTheta(): Unhandled hybridization for %s (%i)\n", topIn.AtomMaskName(aj).c_str(), AJ.Nbonds()); return 1;
-  }/*
-  } else {
-    theta = knownTheta[knownIdx]; // TODO just use above guess via hybrid?
-  }*/
+  }
 
   return 0;
 }
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index 13e285ab48..c8f346d9f8 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -19,6 +19,8 @@ class Builder {
     void SetDebug(int d) { debug_ = d; }
     /// Set optional parameter set
     void SetParameters(ParameterSet const*);
+    /// Set optional Zmatrix with current ICs
+    void SetZmatrix(Zmatrix const*);
 
     /// Combine second fragment into first fragment and bond
     int Combine(Topology&, Frame&, Topology const&, Frame const&, int, int) const;
@@ -53,6 +55,7 @@ class Builder {
 
     int debug_;
     ParameterSet const* params_;
+    Zmatrix const* currentZmatrix_; ///< Any existing internal coordinates
 };
 }
 }

From 9939cdd5d1c99c575bfdd937baa6377bc7220b07 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 2 Feb 2024 08:42:51 -0500
Subject: [PATCH 0422/1492] Start moving GenerateInternals routine to Builder.
 Change std::vector<bool> to Barray

---
 src/Structure/Builder.cpp | 123 ++++++++++++++++++++++++++++++++++----
 src/Structure/Builder.h   |  13 ++--
 2 files changed, 117 insertions(+), 19 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 9c5ad8224e..07c254726c 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -63,7 +63,7 @@ const
 }
 
 /** Assign reasonable value for bond distance. */
-int Cpptraj::Structure::Builder::AssignLength(double& dist, int ai, int aj, Topology const& topIn, Frame const& frameIn, std::vector<bool> const& atomPositionKnown)
+int Cpptraj::Structure::Builder::AssignLength(double& dist, int ai, int aj, Topology const& topIn, Frame const& frameIn, Barray const& atomPositionKnown)
 const
 {
   if (atomPositionKnown[ai] && atomPositionKnown[aj]) {
@@ -111,7 +111,7 @@ const
 /** Attempt to assign a reasonable value for theta internal coordinate for
   * atom i given that atoms j and k have known positions.
   */
-int Cpptraj::Structure::Builder::AssignTheta(double& theta, int ai, int aj, int ak, Topology const& topIn, Frame const& frameIn, std::vector<bool> const& atomPositionKnown)
+int Cpptraj::Structure::Builder::AssignTheta(double& theta, int ai, int aj, int ak, Topology const& topIn, Frame const& frameIn, Barray const& atomPositionKnown)
 const
 {
   if (debug_ > 0)
@@ -254,7 +254,7 @@ Cpptraj::Structure::InternalCoords Builder::calcKnownAtomIc(int ai, int aj, int
 int Cpptraj::Structure::Builder::insertIc(Zmatrix& zmatrix,
                                         int ai, int aj, int ak, int al, double newPhi,
                                         Topology const& topIn, Frame const& frameIn,
-                                        std::vector<bool> const& atomPositionKnown)
+                                        Barray const& atomPositionKnown)
 const
 {
   if (atomPositionKnown[ai]) {
@@ -309,7 +309,7 @@ static inline double wrap360(double phi) {
 int Cpptraj::Structure::Builder::AssignICsAroundBond(Zmatrix& zmatrix,
                                                    int aj, int ak, int al,
                                                    Topology const& topIn, Frame const& frameIn,
-                                                   std::vector<bool> const& atomPositionKnown,
+                                                   Barray const& atomPositionKnown,
                                                    BuildAtom const& AtomJ)
 const
 {
@@ -383,7 +383,7 @@ const
 
   // Fill in what values we can for known atoms
   std::vector<double> knownPhi( AJ.Nbonds() );
-  std::vector<bool> isKnown( AJ.Nbonds(), false );
+  Barray isKnown( AJ.Nbonds(), false );
   int knownIdx = -1;
   double knownInterval = 0;
   bool hasKnownInterval = false;
@@ -474,7 +474,7 @@ const
 
   // If we have to assign an initial phi, make trans the longer branch
   if (knownIdx == -1) {
-    std::vector<bool> visited = atomPositionKnown;
+    Barray visited = atomPositionKnown;
     // TODO: Ensure bonded atoms are not yet visited?
     visited[aj] = true;
     visited[ak] = true;
@@ -640,7 +640,7 @@ const
   Zmatrix bondZmatrix;
 
   // Note which atoms already have an IC in zmatrixA
-  std::vector<bool> hasIC(combinedTop.Natom(), false);
+  Barray hasIC(combinedTop.Natom(), false);
   for (Zmatrix::const_iterator it = zmatrixA.begin(); it != zmatrixA.end(); ++it)
     hasIC[it->AtI()] = true;
 
@@ -751,7 +751,7 @@ const
   Zmatrix bondZmatrix;
 
   // Note which atoms already have an IC in zmatrix A
-  std::vector<bool> hasIC(topIn.Natom(), false);
+  Barray hasIC(topIn.Natom(), false);
   if (zA != 0) {
     for (Zmatrix::const_iterator it = zA->begin(); it != zA->end(); ++it)
       hasIC[it->AtI()] = true;
@@ -786,8 +786,8 @@ const
   */
 int Builder::SetupICsAroundBond(Zmatrix& zmatrix,
                                 int atA, int atB, Frame const& frameIn, Topology const& topIn,
-                                std::vector<bool> const& atomPositionKnown,
-                                std::vector<bool> const& hasICin,
+                                Barray const& atomPositionKnown,
+                                Barray const& hasICin,
                                 BuildAtom const& AtomA, BuildAtom const& AtomB)
 const
 {
@@ -801,14 +801,14 @@ const
   //Barray hasIC( topIn.Natom(), false );
   Barray hasIC = hasICin;
   unsigned int nHasIC = 0;
-  for (std::vector<bool>::const_iterator it = hasIC.begin(); it != hasIC.end(); ++it) {
+  for (Barray::const_iterator it = hasIC.begin(); it != hasIC.end(); ++it) {
     if (*it) {
       nHasIC++;
       mprintf("DEBUG:\tAtom %s already has an IC.\n", topIn.AtomMaskName(it-hasIC.begin()).c_str());
     }
   }
   // Mark known atoms as already having IC
-  for (std::vector<bool>::const_iterator it = atomPositionKnown.begin();
+  for (Barray::const_iterator it = atomPositionKnown.begin();
                                          it != atomPositionKnown.end(); ++it)
   {
     //mprintf("DEBUG: MARKING KNOWN ATOMS. %li\n", it - atomPositionKnown.begin());
@@ -1196,4 +1196,101 @@ const
     } // END both bond atoms belong to this residue
   } // END loop over bonds
   return 0;
-} 
+}
+// -----------------------------------------------
+/** \return the LEaP 'weight' of an atom.
+  * Originally used to force the 'heaviest' atoms around a torsion trans to
+  * each other. The 'weight' of an atom is defined as its element number,
+  * unless the atom is CARBON, then it is 1000, making it the 'heaviest' atom.
+  */
+static int LeapAtomWeight(Atom const& At)
+{
+  if ( At.Element() == Atom::CARBON )
+    return 1000;
+  return At.AtomicNumber();
+}
+
+/** Order atoms bonded to the given atom in a manner similar to LEaP's
+  * zModelOrderAtoms. In that routine, first atoms were sorted into
+  * known position > unknown position. Then the heaviest atom in each
+  * subgroup was swapped with the first element of that list. Since at this
+  * point we assume all positions are known, we are just shifting the
+  * heaviest atom to the front of the list.
+  * The ignore atom is the index of the atom this atom is bonded to that
+  * forms the torsion we are interested in.
+  */
+static inline std::vector<int> SortBondedAtomsLikeLeap(Atom const& At, Topology const& topIn, int ignoreAtom)
+{
+  std::vector<int> out;
+  out.reserve( At.Nbonds() );
+  // Find the index of the heaviest atom
+  int iHighest = 0;
+  int iPos = 0;
+  for (int idx = 0; idx < At.Nbonds(); idx++) {
+    int bat = At.Bond(idx);
+    if (bat != ignoreAtom) {
+      out.push_back( bat );
+      int iWeight = LeapAtomWeight( topIn[bat] );
+      if ( iHighest < iWeight ) {
+        iHighest = iWeight;
+        iPos = (int)out.size()-1;
+      }
+    }
+  }
+  // If highest weight atom not already in front, swap it there.
+  if (iPos != 0) std::swap( out[0], out[iPos] );
+
+  return out;
+}
+
+/** Generate internal coordinates in the same
+  * manner as LEaP's BuildInternalsForContainer/ModelAssignTorsionsAround.
+  */
+int Builder::GenerateInternals(Zmatrix& zmatrix, Frame const& frameIn, Topology const& topIn, Barray const& hasPosition)
+{
+  zmatrix.clear();
+  // First generate the bond array
+  BondArray bonds = GenerateBondArray( topIn.Residues(), topIn.Atoms() );
+  // Loop over bonds
+  for (BondArray::const_iterator bnd = bonds.begin(); bnd != bonds.end(); ++bnd)
+  {
+    Atom const& A2 = topIn[bnd->A1()];
+    Atom const& A3 = topIn[bnd->A2()];
+    if (A2.Nbonds() > 1 && A3.Nbonds() > 1) {
+      //Residue const& R2 = topIn.Res(A2.ResNum());
+      //Residue const& R3 = topIn.Res(A3.ResNum());
+      mprintf("Building torsion INTERNALs around: %s - %s\n",
+              topIn.LeapName(bnd->A1()).c_str(), topIn.LeapName(bnd->A2()).c_str());
+      Iarray sorted_a2 = SortBondedAtomsLikeLeap(A2, topIn, bnd->A2());
+      Iarray sorted_a3 = SortBondedAtomsLikeLeap(A3, topIn, bnd->A1());
+      mprintf("Orientation around: %s {", *(A2.Name()));
+      for (Atom::bond_iterator bat = A2.bondbegin(); bat != A2.bondend(); ++bat) mprintf(" %s", *(topIn[*bat].Name()));
+      mprintf("}\n");
+      for (Iarray::const_iterator it = sorted_a2.begin(); it != sorted_a2.end(); ++it)
+        mprintf("Atom %li: %s\n", it - sorted_a2.begin(), *(topIn[*it].Name()));
+      mprintf("Orientation around: %s {", *(A3.Name()));
+      for (Atom::bond_iterator bat = A3.bondbegin(); bat != A3.bondend(); ++bat) mprintf(" %s", *(topIn[*bat].Name()));
+      mprintf("}\n");
+      for (Iarray::const_iterator it = sorted_a3.begin(); it != sorted_a3.end(); ++it)
+        mprintf("Atom %li: %s\n", it - sorted_a3.begin(), *(topIn[*it].Name()));
+      // Build the torsions
+      int aj = bnd->A1();
+      int ak = bnd->A2();
+      for (Iarray::const_iterator ai = sorted_a2.begin(); ai != sorted_a2.end(); ++ai) {
+        for (Iarray::const_iterator al = sorted_a3.begin(); al != sorted_a3.end(); ++al) {
+          //double dval = Torsion(frameIn.XYZ(*ai), frameIn.XYZ(aj), frameIn.XYZ(ak), frameIn.XYZ(*al));
+          addIc(*ai, aj, ak, *al, frameIn);
+          mprintf("++++Torsion INTERNAL: %f to %s - %s - %s - %s\n",
+                  IC_.back().Phi(),
+                  topIn.LeapName(*ai).c_str(),
+                  topIn.LeapName(aj).c_str(),
+                  topIn.LeapName(ak).c_str(),
+                  topIn.LeapName(*al).c_str());
+          addIc(*al, ak, aj, *ai, frameIn);
+        }
+      }
+    }
+  }
+  return 0;
+}
+ 
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index c8f346d9f8..b2873d4b19 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -33,26 +33,27 @@ class Builder {
     /// Get length parameter for atoms
     int getLengthParam(double&, int, int, Topology const&) const;
     /// Assign a reasonable value for bond distance given 2 atoms whose position may or may not be known
-    int AssignLength(double&, int, int, Topology const&, Frame const&, std::vector<bool> const&) const;
+    int AssignLength(double&, int, int, Topology const&, Frame const&, Barray const&) const;
     /// Get angle parameter for atoms.
     int getAngleParam(double&, int, int, int, Topology const&) const;
     /// Given atoms J and K, attempt to assign a reasonable value for theta for atom I
-    int AssignTheta(double&, int, int, int, Topology const&, Frame const&, std::vector<bool> const&) const;
+    int AssignTheta(double&, int, int, int, Topology const&, Frame const&, Barray const&) const;
     /// Calculate an internal coordinate for known atoms
     static inline InternalCoords calcKnownAtomIc(int, int, int, int, Frame const&);
     /// Insert an internal coord into a zmatrix
     int insertIc(Zmatrix&, int, int, int, int, double,
-                 Topology const&, Frame const&, std::vector<bool> const&) const;
+                 Topology const&, Frame const&, Barray const&) const;
     /// Assign internal coordinates for atoms I for torsions around J-K-L.
     int AssignICsAroundBond(Zmatrix&, int, int, int,
-                           Topology const&, Frame const&, std::vector<bool> const&,
+                           Topology const&, Frame const&, Barray const&,
                            BuildAtom const&) const;
 
     /// Model coordinates around a bond
     int SetupICsAroundBond(Zmatrix&, int, int, Frame const&, Topology const&,
-                           std::vector<bool> const&, std::vector<bool> const&,
+                           Barray const&, Barray const&,
                            BuildAtom const&, BuildAtom const&) const;
-
+    /// Generate internal coordinates in the same manner as LEaP
+    int GenerateInternals(Zmatrix&, Frame const&, Topology const&, Barray const&);
     int debug_;
     ParameterSet const* params_;
     Zmatrix const* currentZmatrix_; ///< Any existing internal coordinates

From f8ab3ffc4f1b588d9cbe2c85a2fcf5d8cb754a21 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 2 Feb 2024 08:49:37 -0500
Subject: [PATCH 0423/1492] Finish adding GenerateInternals to Builder

---
 src/Structure/Builder.cpp |  6 +++---
 src/Structure/Builder.h   |  1 +
 src/Structure/Zmatrix.cpp | 12 ++++++------
 src/Structure/Zmatrix.h   |  6 ++++--
 4 files changed, 14 insertions(+), 11 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 07c254726c..f045208677 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1279,14 +1279,14 @@ int Builder::GenerateInternals(Zmatrix& zmatrix, Frame const& frameIn, Topology
       for (Iarray::const_iterator ai = sorted_a2.begin(); ai != sorted_a2.end(); ++ai) {
         for (Iarray::const_iterator al = sorted_a3.begin(); al != sorted_a3.end(); ++al) {
           //double dval = Torsion(frameIn.XYZ(*ai), frameIn.XYZ(aj), frameIn.XYZ(ak), frameIn.XYZ(*al));
-          addIc(*ai, aj, ak, *al, frameIn);
+          zmatrix.AddIC(*ai, aj, ak, *al, frameIn);
           mprintf("++++Torsion INTERNAL: %f to %s - %s - %s - %s\n",
-                  IC_.back().Phi(),
+                  zmatrix.back().Phi(),
                   topIn.LeapName(*ai).c_str(),
                   topIn.LeapName(aj).c_str(),
                   topIn.LeapName(ak).c_str(),
                   topIn.LeapName(*al).c_str());
-          addIc(*al, ak, aj, *ai, frameIn);
+          zmatrix.AddIC(*al, ak, aj, *ai, frameIn);
         }
       }
     }
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index b2873d4b19..9cf7b05af3 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -54,6 +54,7 @@ class Builder {
                            BuildAtom const&, BuildAtom const&) const;
     /// Generate internal coordinates in the same manner as LEaP
     int GenerateInternals(Zmatrix&, Frame const&, Topology const&, Barray const&);
+
     int debug_;
     ParameterSet const* params_;
     Zmatrix const* currentZmatrix_; ///< Any existing internal coordinates
diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index e76a05a68e..89dbbda772 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -80,6 +80,12 @@ int Zmatrix::AddIC(InternalCoords const& ic) {
   return 0;
 }
 
+/** Calculate and add internal coordinate from frame. */
+int Zmatrix::AddIC(int ai, int aj, int ak, int al, Frame const& frameIn) {
+  addIc(ai, aj, ak, al, frameIn);
+  return 0;
+}
+
 /** Set IC at specified position. */ // TODO check if seed?
 void Zmatrix::SetIC(unsigned int idx, InternalCoords const& ic) {
   IC_[idx] = ic;
@@ -123,12 +129,6 @@ void Zmatrix::print(Topology const* topIn) const {
   }
 }
 
-/** Remap internal coordinate indices according to the given atom map. */
-/*void Zmatrix::RemapIcIndices(std::vector<int> const& map) {
-  for (ICarray::iterator it = IC_.begin(); it != IC_.end(); ++it)
-    it->RemapIndices(map);
-}*/
-
 /** Increment IC indices by given offset */
 void Zmatrix::OffsetIcIndices(int offset) {
   for (ICarray::iterator it = IC_.begin(); it != IC_.end(); ++it)
diff --git a/src/Structure/Zmatrix.h b/src/Structure/Zmatrix.h
index fbd921d84c..a727b771f0 100644
--- a/src/Structure/Zmatrix.h
+++ b/src/Structure/Zmatrix.h
@@ -27,12 +27,14 @@ class Zmatrix {
     void clear();
     /// Sort ICs by atom index (I < L < K < J)
     void sort();
+    /// \return the last added IC
+    InternalCoords const& back() const { return IC_.back(); }
     /// Add internal coordinate
     int AddIC(InternalCoords const&);
+    /// Calculate and add internal coordinate for specified atoms
+    int AddIC(int,int,int,int,Frame const&);
     /// Set specified IC
     void SetIC(unsigned int, InternalCoords const&);
-    /// Remap IC indices according to given map
-    //void RemapIcIndices(std::vector<int> const&);
     /// Offset IC indices by given value
     void OffsetIcIndices(int);
 

From 5118d800bf04eba0e1b89bdd98c10e6d6bf5b2a2 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 2 Feb 2024 09:59:42 -0500
Subject: [PATCH 0424/1492] Start testing new code. Order by hybdridization

---
 src/Exec_Build.cpp        | 10 ++++++
 src/Structure/Builder.cpp | 69 ++++++++++++++++++++++++++++++++++++++-
 src/Structure/Builder.h   |  9 +++--
 3 files changed, 85 insertions(+), 3 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 5462530b60..49be97a84b 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -194,6 +194,10 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
   typedef std::vector<ResAtPair> ResAtArray;
   ResAtArray interResBonds;
 
+  Cpptraj::Structure::Builder structureBuilder;
+  structureBuilder.SetDebug( 1 );
+  structureBuilder.SetParameters( &mainParmSet );
+
   // Loop for setting up atoms in the topology from residues or residue templates.
   int nRefAtomsMissing = 0;
   for (int ires = 0; ires != topIn.Nres(); ires++)
@@ -307,6 +311,12 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
 //        zmatrix->print( resTemplate->TopPtr() );
         zmatrix->OffsetIcIndices( atomOffset );
         ResZmatrices.push_back( zmatrix );
+        // FIXME DEBUG
+        Cpptraj::Structure::Zmatrix tmpz;
+        if (structureBuilder.GenerateInternals( tmpz, templateFrame, resTemplate->Top(), std::vector<bool>(resTemplate->Top().Natom(), true) )) {
+          mprinterr("Error: Generate internals for template failed.\n");
+          return 1;
+        }
 //        zmatrix->print( &topOut );
         //for (Iarray::const_iterator jres = resConnections[ires].begin();
         //                            jres != resConnections[ires].end(); ++jres)
diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index f045208677..80ae60d3b4 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1243,17 +1243,83 @@ static inline std::vector<int> SortBondedAtomsLikeLeap(Atom const& At, Topology
   return out;
 }
 
+/** Assign torsions around bonded atoms in manner similar to LEaP's ModelAssignTorsionsAround. */
+int Builder::assignTorsionsAroundBond(int a1, int a2, Frame const& frameIn, Topology const& topIn, Barray const& hasPosition)
+{
+  // No need to do this if either atom only has 1 bond.
+  if (topIn[a1].Nbonds() < 2 || topIn[a2].Nbonds() < 2)
+    return 0;
+  // Get atom hybridizations
+  AtomType::HybridizationType H1 = AtomType::UNKNOWN_HYBRIDIZATION;
+  AtomType::HybridizationType H2 = AtomType::UNKNOWN_HYBRIDIZATION;
+  if (params_ != 0) {
+    ParmHolder<AtomType>::const_iterator it;
+    if (topIn[a1].HasType()) {
+      it = params_->AT().GetParam( TypeNameHolder(topIn[a1].Type()) );
+      if (it != params_->AT().end())
+        H1 = it->second.Hybridization();
+    }
+    if (topIn[a2].HasType()) {
+      it = params_->AT().GetParam( TypeNameHolder(topIn[a2].Type()) );
+      if (it != params_->AT().end())
+        H2 = it->second.Hybridization();
+    }
+  }
+  if (H1 == AtomType::UNKNOWN_HYBRIDIZATION)
+    H1 = GuessAtomHybridization(topIn[a1], topIn.Atoms());
+  if (H2 == AtomType::UNKNOWN_HYBRIDIZATION)
+    H2 = GuessAtomHybridization(topIn[a2], topIn.Atoms());
+  if (H1 == AtomType::UNKNOWN_HYBRIDIZATION)
+    mprintf("Warning: No hybridization set for atom %s\n", topIn.AtomMaskName(a1).c_str());
+  if (H2 == AtomType::UNKNOWN_HYBRIDIZATION)
+    mprintf("Warning: No hybridization set for atom %s\n", topIn.AtomMaskName(a2).c_str());
+  // Ensure the hybridization of ax is > ay
+  int ax, ay;
+  AtomType::HybridizationType Hx, Hy; // DEBUG
+  if (H1 == AtomType::UNKNOWN_HYBRIDIZATION || H2 == AtomType::UNKNOWN_HYBRIDIZATION) {
+    // Do not try to sort.
+    ax = a1;
+    ay = a2;
+    Hx = H1;
+    Hy = H2;
+  } else if (H1 < H2) {
+    ax = a2;
+    ay = a1;
+    Hx = H2;
+    Hy = H1;
+  } else {
+    ax = a1;
+    ay = a2;
+    Hx = H1;
+    Hy = H2;
+  }
+  static const char* hstr[] = { "SP", "SP2", "SP3", "Unknown" };
+  mprintf("DEBUG: assignTorsionsAroundBond: AX= %s (%s)  AY= %s (%s)\n",
+          topIn.AtomMaskName(ax).c_str(), hstr[Hx],
+          topIn.AtomMaskName(ay).c_str(), hstr[Hy]);
+
+  return 0;
+}
+
 /** Generate internal coordinates in the same
   * manner as LEaP's BuildInternalsForContainer/ModelAssignTorsionsAround.
   */
 int Builder::GenerateInternals(Zmatrix& zmatrix, Frame const& frameIn, Topology const& topIn, Barray const& hasPosition)
 {
+  mprintf("DEBUG: ----- Entering Builder::GenerateInternals. -----\n");
   zmatrix.clear();
   // First generate the bond array
   BondArray bonds = GenerateBondArray( topIn.Residues(), topIn.Atoms() );
   // Loop over bonds
   for (BondArray::const_iterator bnd = bonds.begin(); bnd != bonds.end(); ++bnd)
   {
+    if (assignTorsionsAroundBond( bnd->A1(), bnd->A2(), frameIn, topIn, hasPosition )) {
+      mprinterr("Error Assign torsions around bond %s - %s failed.\n",
+                topIn.AtomMaskName(bnd->A1()).c_str(),
+                topIn.AtomMaskName(bnd->A2()).c_str());
+      return 1;
+    }
+/*
     Atom const& A2 = topIn[bnd->A1()];
     Atom const& A3 = topIn[bnd->A2()];
     if (A2.Nbonds() > 1 && A3.Nbonds() > 1) {
@@ -1289,8 +1355,9 @@ int Builder::GenerateInternals(Zmatrix& zmatrix, Frame const& frameIn, Topology
           zmatrix.AddIC(*al, ak, aj, *ai, frameIn);
         }
       }
-    }
+    }*/
   }
+  mprintf("DEBUG: ----- Leaving Builder::GenerateInternals. ------\n");
   return 0;
 }
  
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index 9cf7b05af3..f8efefc2b7 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -28,6 +28,10 @@ class Builder {
     int ModelCoordsAroundBond(Frame const&, Topology const&, int, int, Zmatrix&, Barray const&) const;
     /// Update the internal coordinates in given Zmatrix with values from Frame/Parameters
     int UpdateICsFromFrame(Zmatrix&, Frame const&, int, Topology const&, Barray const&) const;
+
+    /// Generate internal coordinates in the same manner as LEaP
+    int GenerateInternals(Zmatrix&, Frame const&, Topology const&, Barray const&);
+
   private:
     typedef std::vector<int> Iarray;
     /// Get length parameter for atoms
@@ -52,8 +56,9 @@ class Builder {
     int SetupICsAroundBond(Zmatrix&, int, int, Frame const&, Topology const&,
                            Barray const&, Barray const&,
                            BuildAtom const&, BuildAtom const&) const;
-    /// Generate internal coordinates in the same manner as LEaP
-    int GenerateInternals(Zmatrix&, Frame const&, Topology const&, Barray const&);
+
+    /// Model torsions around a bond in the same manner as LEaP
+    int assignTorsionsAroundBond(int, int, Frame const&, Topology const&, Barray const&);
 
     int debug_;
     ParameterSet const* params_;

From 6cef130c689544eaa38014eef4096bbaebc8252a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 2 Feb 2024 10:27:55 -0500
Subject: [PATCH 0425/1492] Do the sifting by known/unknown

---
 src/Structure/Builder.cpp | 77 ++++++++++++++++++++++++++++++++++++---
 1 file changed, 71 insertions(+), 6 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 80ae60d3b4..221fdcc9f5 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1210,24 +1210,45 @@ static int LeapAtomWeight(Atom const& At)
   return At.AtomicNumber();
 }
 
+/** Place atoms with known position ahead of atoms with no known position.
+  * \param firstUnknownIdx Position in output array of the first unknown atom.
+  * \param At The atom to sift.
+  * \param hasPosition Array indicating whether atoms have position.
+  */
+static inline std::vector<int> SiftBondedAtomsLikeLeap(unsigned int& firstUnknownIdx, Atom const& At, std::vector<bool> const& hasPosition)
+{
+  std::vector<int> out;
+  out.reserve( At.Nbonds() );
+  for (Atom::bond_iterator bat = At.bondbegin(); bat != At.bondend(); ++bat)
+    if (hasPosition[*bat])
+      out.push_back( *bat );
+  firstUnknownIdx = out.size();
+  for (Atom::bond_iterator bat = At.bondbegin(); bat != At.bondend(); ++bat)
+    if (!hasPosition[*bat])
+      out.push_back( *bat );
+  return out;
+}
+
 /** Order atoms bonded to the given atom in a manner similar to LEaP's
   * zModelOrderAtoms. In that routine, first atoms were sorted into
   * known position > unknown position. Then the heaviest atom in each
-  * subgroup was swapped with the first element of that list. Since at this
-  * point we assume all positions are known, we are just shifting the
-  * heaviest atom to the front of the list.
+  * subgroup was swapped with the first element of that list. 
   * The ignore atom is the index of the atom this atom is bonded to that
   * forms the torsion we are interested in.
   */
-static inline std::vector<int> SortBondedAtomsLikeLeap(Atom const& At, Topology const& topIn, int ignoreAtom)
+static inline std::vector<int> SortBondedAtomsLikeLeap(unsigned int& firstUnknownIdx,
+                                                       Atom const& At, Topology const& topIn,
+                                                       int ignoreAtom, std::vector<bool> const& hasPosition)
 {
   std::vector<int> out;
   out.reserve( At.Nbonds() );
+  // Sift so that atoms with known position are at the front
+  std::vector<int> bondedAtoms = SiftBondedAtomsLikeLeap(firstUnknownIdx, At, hasPosition);
   // Find the index of the heaviest atom
   int iHighest = 0;
   int iPos = 0;
-  for (int idx = 0; idx < At.Nbonds(); idx++) {
-    int bat = At.Bond(idx);
+  for (unsigned int idx = 0; idx < bondedAtoms.size(); idx++) {
+    int bat = bondedAtoms[idx];
     if (bat != ignoreAtom) {
       out.push_back( bat );
       int iWeight = LeapAtomWeight( topIn[bat] );
@@ -1297,6 +1318,50 @@ int Builder::assignTorsionsAroundBond(int a1, int a2, Frame const& frameIn, Topo
   mprintf("DEBUG: assignTorsionsAroundBond: AX= %s (%s)  AY= %s (%s)\n",
           topIn.AtomMaskName(ax).c_str(), hstr[Hx],
           topIn.AtomMaskName(ay).c_str(), hstr[Hy]);
+  // Check if there is at least one atom on either side of the ax-ay pair
+  // whose position is known.
+  Atom const& AX = topIn[ax];
+  Atom const& AY = topIn[ay];
+  bool axHasKnownAtoms = false;
+  for (Atom::bond_iterator bat = AX.bondbegin(); bat != AX.bondend(); ++bat) {
+    if (*bat != ay && hasPosition[*bat]) {
+      axHasKnownAtoms = true;
+      break;
+    }
+  }
+  bool ayHasKnownAtoms = false;
+  for (Atom::bond_iterator bat = AY.bondbegin(); bat != AY.bondend(); ++bat) {
+    if (*bat != ax && hasPosition[*bat]) {
+      ayHasKnownAtoms = true;
+      break;
+    }
+  }
+
+  if (!axHasKnownAtoms && !ayHasKnownAtoms) {
+    mprinterr("Internal Error: assignTorsionsAroundBond both not known not yet implemented.\n");
+    return 1;
+  } else {
+    mprintf("DEBUG: Using externals to fit new torsions around: %s - %s\n",
+            topIn.LeapName(ax).c_str(),
+            topIn.LeapName(ay).c_str());
+    // Sort AX bonds
+    unsigned int firstUnknownIdxX = 0;
+    Iarray sorted_ax = SortBondedAtomsLikeLeap(firstUnknownIdxX, AX, topIn, ay, hasPosition);
+    mprintf("Orientation around: %s {", *(AX.Name()));
+    for (Atom::bond_iterator bat = AX.bondbegin(); bat != AX.bondend(); ++bat) mprintf(" %s", *(topIn[*bat].Name()));
+    mprintf("}\n");
+    for (Iarray::const_iterator it = sorted_ax.begin(); it != sorted_ax.end(); ++it)
+        mprintf("Atom %li: %s\n", it - sorted_ax.begin(), *(topIn[*it].Name()));
+    // Sort AY bonds
+    unsigned int firstUnknownIdxY = 0;
+    Iarray sorted_ay = SortBondedAtomsLikeLeap(firstUnknownIdxY, AY, topIn, ax, hasPosition);
+    mprintf("Orientation around: %s {", *(AY.Name()));
+    for (Atom::bond_iterator bat = AY.bondbegin(); bat != AY.bondend(); ++bat) mprintf(" %s", *(topIn[*bat].Name()));
+    mprintf("}\n");
+    for (Iarray::const_iterator it = sorted_ay.begin(); it != sorted_ay.end(); ++it)
+        mprintf("Atom %li: %s\n", it - sorted_ay.begin(), *(topIn[*it].Name()));
+
+  }
 
   return 0;
 }

From 0d44caf3020cad95320c8941fe5dfac434e472a3 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 2 Feb 2024 10:50:25 -0500
Subject: [PATCH 0426/1492] Get orientation

---
 src/Structure/Builder.cpp | 68 ++++++++++++++++++++++++++++++++++-----
 1 file changed, 60 insertions(+), 8 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 221fdcc9f5..50ab68e9b3 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1264,6 +1264,47 @@ static inline std::vector<int> SortBondedAtomsLikeLeap(unsigned int& firstUnknow
   return out;
 }
 
+/** LEaP routine for determining atom chirality.
+  * This is done by crossing A to B and then dotting the
+  * result with C. TODO use Chirality in BuildAtom?
+  * The chirality of the vectors is determined by the sign of
+  * the result, which is determined by whether or not C has
+  * a component in the direction AxB or in the opposite direction.
+  */
+static inline double VectorAtomChirality(Vec3 const& Center, Vec3 const& A, Vec3 const& B, Vec3 const& C)
+{
+  Vec3 vA = A - Center;
+  Vec3 vB = B - Center;
+  Vec3 vC = C - Center;
+  Vec3 vCross = vA.Cross( vB );
+  double dot = vCross * vC;
+  if (dot > 0)
+    return 1.0;
+  else if (dot < 0)
+    return -1.0;
+  return 0.0;
+}
+
+/** Assuming atoms have been ordered with SortBondedAtomsLikeLeap,
+  * calculate the orientation of the iB atom with respect to the
+  * triangle (iA, iX, iY). This orientation will be used by the
+  * CreateSpXSpX routines to determine which torsion values to use.
+  */
+static inline double calculateOrientation(int iX, int iA, int iY, int iB, Frame const& frameIn, std::vector<bool> const& hasPosition)
+{
+  double dOrientation = 1.0;
+  if (hasPosition[iX] &&
+      hasPosition[iA] &&
+      hasPosition[iY] &&
+      hasPosition[iB])
+  {
+    dOrientation = VectorAtomChirality( frameIn.XYZ(iX), frameIn.XYZ(iA), frameIn.XYZ(iY), frameIn.XYZ(iB) );
+  } else {
+    mprinterr("Internal Error: Builder::calculateOrientation not yet set up for unknown positions.\n");
+  }
+  return dOrientation;
+}
+
 /** Assign torsions around bonded atoms in manner similar to LEaP's ModelAssignTorsionsAround. */
 int Builder::assignTorsionsAroundBond(int a1, int a2, Frame const& frameIn, Topology const& topIn, Barray const& hasPosition)
 {
@@ -1347,17 +1388,28 @@ int Builder::assignTorsionsAroundBond(int a1, int a2, Frame const& frameIn, Topo
     // Sort AX bonds
     unsigned int firstUnknownIdxX = 0;
     Iarray sorted_ax = SortBondedAtomsLikeLeap(firstUnknownIdxX, AX, topIn, ay, hasPosition);
-    mprintf("Orientation around: %s {", *(AX.Name()));
-    for (Atom::bond_iterator bat = AX.bondbegin(); bat != AX.bondend(); ++bat) mprintf(" %s", *(topIn[*bat].Name()));
-    mprintf("}\n");
-    for (Iarray::const_iterator it = sorted_ax.begin(); it != sorted_ax.end(); ++it)
-        mprintf("Atom %li: %s\n", it - sorted_ax.begin(), *(topIn[*it].Name()));
     // Sort AY bonds
     unsigned int firstUnknownIdxY = 0;
     Iarray sorted_ay = SortBondedAtomsLikeLeap(firstUnknownIdxY, AY, topIn, ax, hasPosition);
-    mprintf("Orientation around: %s {", *(AY.Name()));
-    for (Atom::bond_iterator bat = AY.bondbegin(); bat != AY.bondend(); ++bat) mprintf(" %s", *(topIn[*bat].Name()));
-    mprintf("}\n");
+    // Calculate the chirality around atom X
+    double Xorientation = 0;
+    if (Hx == AtomType::SP3) {
+      Xorientation = calculateOrientation( ax, sorted_ax[0], ay, sorted_ax[1], frameIn, hasPosition );
+    }
+    // Calculate the chirality around atom Y
+    double Yorientation = 0;
+    if (Hy == AtomType::SP3) {
+      Yorientation = calculateOrientation( ay, sorted_ay[0], ax, sorted_ay[1], frameIn, hasPosition );
+    }
+    // DEBUG
+    mprintf("Orientation around: %s = %f\n", *(AX.Name()), Xorientation);
+    //for (Atom::bond_iterator bat = AX.bondbegin(); bat != AX.bondend(); ++bat) mprintf(" %s", *(topIn[*bat].Name()));
+    //mprintf("}\n");
+    for (Iarray::const_iterator it = sorted_ax.begin(); it != sorted_ax.end(); ++it)
+        mprintf("Atom %li: %s\n", it - sorted_ax.begin(), *(topIn[*it].Name()));
+    mprintf("Orientation around: %s = %f\n", *(AY.Name()), Yorientation);
+    //for (Atom::bond_iterator bat = AY.bondbegin(); bat != AY.bondend(); ++bat) mprintf(" %s", *(topIn[*bat].Name()));
+    //mprintf("}\n");
     for (Iarray::const_iterator it = sorted_ay.begin(); it != sorted_ay.end(); ++it)
         mprintf("Atom %li: %s\n", it - sorted_ay.begin(), *(topIn[*it].Name()));
 

From eadfb43829e6deecc4fb4463c3886a629709ff6f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 2 Feb 2024 11:00:39 -0500
Subject: [PATCH 0427/1492] Calculate absolute torsion

---
 src/Structure/Builder.cpp | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 50ab68e9b3..30bedf598a 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1412,7 +1412,21 @@ int Builder::assignTorsionsAroundBond(int a1, int a2, Frame const& frameIn, Topo
     //mprintf("}\n");
     for (Iarray::const_iterator it = sorted_ay.begin(); it != sorted_ay.end(); ++it)
         mprintf("Atom %li: %s\n", it - sorted_ay.begin(), *(topIn[*it].Name()));
-
+    // Calculate the actual torsion angle between A-X-Y-D
+    double dAbsolute;
+    if (hasPosition[sorted_ax[0]] &&
+        hasPosition[ax] &&
+        hasPosition[ay] &&
+        hasPosition[sorted_ay[0]])
+    {
+      dAbsolute = Torsion( frameIn.XYZ(sorted_ax[0]),
+                           frameIn.XYZ(ax),
+                           frameIn.XYZ(ay),
+                           frameIn.XYZ(sorted_ay[0]) );
+    } else {
+      dAbsolute = 180.0 * Constants::DEGRAD;
+    }
+    mprintf("DABSOLUTE= %g\n", dAbsolute);
   }
 
   return 0;

From ff463a4a9bbf72f7439befc19a0f0c4af8011b26 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 2 Feb 2024 11:09:33 -0500
Subject: [PATCH 0428/1492] Start routines for modelling in torsions

---
 src/Structure/Builder.cpp | 32 ++++++++++++++++++++++++++++++++
 src/Structure/Builder.h   |  4 ++++
 2 files changed, 36 insertions(+)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 30bedf598a..f48d449aa0 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1305,6 +1305,18 @@ static inline double calculateOrientation(int iX, int iA, int iY, int iB, Frame
   return dOrientation;
 }
 
+void Builder::createSp3Sp3Torsions() {
+  return;
+}
+
+void Builder::createSp3Sp2Torsions() {
+  return;
+}
+
+void Builder::createSp2Sp2Torsions() {
+  return;
+}
+
 /** Assign torsions around bonded atoms in manner similar to LEaP's ModelAssignTorsionsAround. */
 int Builder::assignTorsionsAroundBond(int a1, int a2, Frame const& frameIn, Topology const& topIn, Barray const& hasPosition)
 {
@@ -1427,6 +1439,26 @@ int Builder::assignTorsionsAroundBond(int a1, int a2, Frame const& frameIn, Topo
       dAbsolute = 180.0 * Constants::DEGRAD;
     }
     mprintf("DABSOLUTE= %g\n", dAbsolute);
+    // Build the new internals
+    if (Hx == AtomType::SP3 && Hy == AtomType::SP3) {
+      mprintf("SP3 SP3\n");
+      createSp3Sp3Torsions();
+    } else if (Hx == AtomType::SP3 && Hy == AtomType::SP2) {
+      mprintf("SP3 SP2\n");
+      createSp3Sp2Torsions();
+    } else if (Hx == AtomType::SP2 && Hy == AtomType::SP2) {
+      mprintf("SP2 SP2\n");
+      createSp2Sp2Torsions();
+    } else {
+      mprinterr("Error: Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported\n"
+                "Error: ---Tried to superimpose torsions for: *-%s-%s-*\n"
+                "Error: --- With %s - %s\n"
+                "Error: --- Sp0 probably means a new atom type is involved\n"
+                "Error: --- which needs to be defined prior to this routine.\n",
+                topIn.AtomMaskName(ax).c_str(), topIn.AtomMaskName(ay).c_str(),
+                hstr[Hx], hstr[Hy]);
+     return 1;
+    }
   }
 
   return 0;
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index f8efefc2b7..26ed0bc39c 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -60,6 +60,10 @@ class Builder {
     /// Model torsions around a bond in the same manner as LEaP
     int assignTorsionsAroundBond(int, int, Frame const&, Topology const&, Barray const&);
 
+    void createSp3Sp3Torsions();
+    void createSp3Sp2Torsions();
+    void createSp2Sp2Torsions();
+
     int debug_;
     ParameterSet const* params_;
     Zmatrix const* currentZmatrix_; ///< Any existing internal coordinates

From 480ebac8de91ad3b12eb4a30c087a647f87bb862 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 2 Feb 2024 11:21:10 -0500
Subject: [PATCH 0429/1492] Start ModelTorsion class

---
 src/Structure/Builder.cpp | 49 +++++++++++++++++++++++++--------------
 src/Structure/Builder.h   |  4 ++++
 2 files changed, 36 insertions(+), 17 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index f48d449aa0..9cd81a23ef 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1197,6 +1197,18 @@ const
   } // END loop over bonds
   return 0;
 }
+
+// ------------------------------------------------------------------------------
+/** Store info for modelling torsions around X-Y */
+class Cpptraj::Structure::Builder::ModelTorsion {
+  public:
+    int ax_; ///< Atom X
+    int ay_; ///< Atom Y
+    Iarray sorted_ax_; ///< Hold the leap-sorted bonds for atom X
+    Iarray sorted_ay_; ///< Hold the leap-sorted bonds for atom Y
+    double dAbsolute_; ///< Hold the value of the A-X-Y-D torsion in radians
+};
+    
 // -----------------------------------------------
 /** \return the LEaP 'weight' of an atom.
   * Originally used to force the 'heaviest' atoms around a torsion trans to
@@ -1305,6 +1317,7 @@ static inline double calculateOrientation(int iX, int iA, int iY, int iB, Frame
   return dOrientation;
 }
 
+/** Create torsions around SP3-SP3. */
 void Builder::createSp3Sp3Torsions() {
   return;
 }
@@ -1397,48 +1410,50 @@ int Builder::assignTorsionsAroundBond(int a1, int a2, Frame const& frameIn, Topo
     mprintf("DEBUG: Using externals to fit new torsions around: %s - %s\n",
             topIn.LeapName(ax).c_str(),
             topIn.LeapName(ay).c_str());
+    ModelTorsion mT;
+    mT.ax_ = ax;
+    mT.ay_ = ay;
     // Sort AX bonds
     unsigned int firstUnknownIdxX = 0;
-    Iarray sorted_ax = SortBondedAtomsLikeLeap(firstUnknownIdxX, AX, topIn, ay, hasPosition);
+    mT.sorted_ax_ = SortBondedAtomsLikeLeap(firstUnknownIdxX, AX, topIn, ay, hasPosition);
     // Sort AY bonds
     unsigned int firstUnknownIdxY = 0;
-    Iarray sorted_ay = SortBondedAtomsLikeLeap(firstUnknownIdxY, AY, topIn, ax, hasPosition);
+    mT.sorted_ay_ = SortBondedAtomsLikeLeap(firstUnknownIdxY, AY, topIn, ax, hasPosition);
     // Calculate the chirality around atom X
     double Xorientation = 0;
     if (Hx == AtomType::SP3) {
-      Xorientation = calculateOrientation( ax, sorted_ax[0], ay, sorted_ax[1], frameIn, hasPosition );
+      Xorientation = calculateOrientation( ax, mT.sorted_ax_[0], ay, mT.sorted_ax_[1], frameIn, hasPosition );
     }
     // Calculate the chirality around atom Y
     double Yorientation = 0;
     if (Hy == AtomType::SP3) {
-      Yorientation = calculateOrientation( ay, sorted_ay[0], ax, sorted_ay[1], frameIn, hasPosition );
+      Yorientation = calculateOrientation( ay, mT.sorted_ay_[0], ax, mT.sorted_ay_[1], frameIn, hasPosition );
     }
     // DEBUG
     mprintf("Orientation around: %s = %f\n", *(AX.Name()), Xorientation);
     //for (Atom::bond_iterator bat = AX.bondbegin(); bat != AX.bondend(); ++bat) mprintf(" %s", *(topIn[*bat].Name()));
     //mprintf("}\n");
-    for (Iarray::const_iterator it = sorted_ax.begin(); it != sorted_ax.end(); ++it)
-        mprintf("Atom %li: %s\n", it - sorted_ax.begin(), *(topIn[*it].Name()));
+    for (Iarray::const_iterator it = mT.sorted_ax_.begin(); it != mT.sorted_ax_.end(); ++it)
+        mprintf("Atom %li: %s\n", it - mT.sorted_ax_.begin(), *(topIn[*it].Name()));
     mprintf("Orientation around: %s = %f\n", *(AY.Name()), Yorientation);
     //for (Atom::bond_iterator bat = AY.bondbegin(); bat != AY.bondend(); ++bat) mprintf(" %s", *(topIn[*bat].Name()));
     //mprintf("}\n");
-    for (Iarray::const_iterator it = sorted_ay.begin(); it != sorted_ay.end(); ++it)
-        mprintf("Atom %li: %s\n", it - sorted_ay.begin(), *(topIn[*it].Name()));
+    for (Iarray::const_iterator it = mT.sorted_ay_.begin(); it != mT.sorted_ay_.end(); ++it)
+        mprintf("Atom %li: %s\n", it - mT.sorted_ay_.begin(), *(topIn[*it].Name()));
     // Calculate the actual torsion angle between A-X-Y-D
-    double dAbsolute;
-    if (hasPosition[sorted_ax[0]] &&
+    if (hasPosition[mT.sorted_ax_[0]] &&
         hasPosition[ax] &&
         hasPosition[ay] &&
-        hasPosition[sorted_ay[0]])
+        hasPosition[mT.sorted_ay_[0]])
     {
-      dAbsolute = Torsion( frameIn.XYZ(sorted_ax[0]),
-                           frameIn.XYZ(ax),
-                           frameIn.XYZ(ay),
-                           frameIn.XYZ(sorted_ay[0]) );
+      mT.dAbsolute_ = Torsion( frameIn.XYZ(mT.sorted_ax_[0]),
+                               frameIn.XYZ(ax),
+                               frameIn.XYZ(ay),
+                               frameIn.XYZ(mT.sorted_ay_[0]) );
     } else {
-      dAbsolute = 180.0 * Constants::DEGRAD;
+      mT.dAbsolute_ = 180.0 * Constants::DEGRAD;
     }
-    mprintf("DABSOLUTE= %g\n", dAbsolute);
+    mprintf("DABSOLUTE= %g\n", mT.dAbsolute_);
     // Build the new internals
     if (Hx == AtomType::SP3 && Hy == AtomType::SP3) {
       mprintf("SP3 SP3\n");
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index 26ed0bc39c..6cd9e62eba 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -34,6 +34,10 @@ class Builder {
 
   private:
     typedef std::vector<int> Iarray;
+
+    /// Used to hold parameters for modeling a torsion
+    class ModelTorsion;
+
     /// Get length parameter for atoms
     int getLengthParam(double&, int, int, Topology const&) const;
     /// Assign a reasonable value for bond distance given 2 atoms whose position may or may not be known

From 3cecb6b5c98567a5d3aed1c25c2021f45765914a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 2 Feb 2024 14:12:46 -0500
Subject: [PATCH 0430/1492] Place functions inside ModelTorsion

---
 src/Structure/Builder.cpp | 155 +++++++++++++++++++++++++-------------
 1 file changed, 101 insertions(+), 54 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 9cd81a23ef..4bb0c1c42f 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1202,20 +1202,34 @@ const
 /** Store info for modelling torsions around X-Y */
 class Cpptraj::Structure::Builder::ModelTorsion {
   public:
-    int ax_; ///< Atom X
-    int ay_; ///< Atom Y
-    Iarray sorted_ax_; ///< Hold the leap-sorted bonds for atom X
-    Iarray sorted_ay_; ///< Hold the leap-sorted bonds for atom Y
-    double dAbsolute_; ///< Hold the value of the A-X-Y-D torsion in radians
+    /// CONSTRUCTOR
+    ModelTorsion() : ax_(-1), ay_(-1), dAbsolute_(0), Xorientation_(0), Yorientation_(0) {}
+    /// Set up torsions around bonded atoms
+    int SetupTorsion(int, int, AtomType::HybridizationType, AtomType::HybridizationType,
+                     Frame const&, Topology const&, std::vector<bool> const&);
+
+  private:
+    static int LeapAtomWeight(Atom const&);
+    static inline std::vector<int> SiftBondedAtomsLikeLeap(unsigned int&, Atom const&, std::vector<bool> const&);
+    static inline std::vector<int> SortBondedAtomsLikeLeap(unsigned int&, Atom const&,
+                                                           Topology const& topIn, int ignoreAtom,
+                                                           std::vector<bool> const& hasPosition);
+
+    int ax_;              ///< Atom X
+    int ay_;              ///< Atom Y
+    Iarray sorted_ax_;    ///< Hold the leap-sorted bonds for atom X
+    Iarray sorted_ay_;    ///< Hold the leap-sorted bonds for atom Y
+    double dAbsolute_;    ///< Hold the value of the A-X-Y-D torsion in radians
+    double Xorientation_; ///< Orientation around the X atom TODO make an enum?
+    double Yorientation_; ///< Orientation around the Y atoms
 };
     
-// -----------------------------------------------
 /** \return the LEaP 'weight' of an atom.
   * Originally used to force the 'heaviest' atoms around a torsion trans to
   * each other. The 'weight' of an atom is defined as its element number,
   * unless the atom is CARBON, then it is 1000, making it the 'heaviest' atom.
   */
-static int LeapAtomWeight(Atom const& At)
+int Cpptraj::Structure::Builder::ModelTorsion::LeapAtomWeight(Atom const& At)
 {
   if ( At.Element() == Atom::CARBON )
     return 1000;
@@ -1227,7 +1241,10 @@ static int LeapAtomWeight(Atom const& At)
   * \param At The atom to sift.
   * \param hasPosition Array indicating whether atoms have position.
   */
-static inline std::vector<int> SiftBondedAtomsLikeLeap(unsigned int& firstUnknownIdx, Atom const& At, std::vector<bool> const& hasPosition)
+std::vector<int> 
+  Cpptraj::Structure::Builder::ModelTorsion::SiftBondedAtomsLikeLeap(unsigned int& firstUnknownIdx,
+                                                                     Atom const& At,
+                                                                     std::vector<bool> const& hasPosition)
 {
   std::vector<int> out;
   out.reserve( At.Nbonds() );
@@ -1248,9 +1265,11 @@ static inline std::vector<int> SiftBondedAtomsLikeLeap(unsigned int& firstUnknow
   * The ignore atom is the index of the atom this atom is bonded to that
   * forms the torsion we are interested in.
   */
-static inline std::vector<int> SortBondedAtomsLikeLeap(unsigned int& firstUnknownIdx,
-                                                       Atom const& At, Topology const& topIn,
-                                                       int ignoreAtom, std::vector<bool> const& hasPosition)
+std::vector<int>
+  Cpptraj::Structure::Builder::ModelTorsion::SortBondedAtomsLikeLeap(unsigned int& firstUnknownIdx,
+                                                                     Atom const& At, Topology const& topIn,
+                                                                     int ignoreAtom,
+                                                                     std::vector<bool> const& hasPosition)
 {
   std::vector<int> out;
   out.reserve( At.Nbonds() );
@@ -1317,6 +1336,69 @@ static inline double calculateOrientation(int iX, int iA, int iY, int iB, Frame
   return dOrientation;
 }
 
+/** Set up model torsion for bonded atoms. */
+int Cpptraj::Structure::Builder::ModelTorsion::SetupTorsion(int ax, int ay,
+                                                            AtomType::HybridizationType Hx,
+                                                            AtomType::HybridizationType Hy,
+                                                            Frame const& frameIn,
+                                                            Topology const& topIn,
+                                                            std::vector<bool> const& hasPosition)
+{
+  if (Hx != AtomType::UNKNOWN_HYBRIDIZATION && Hy != AtomType::UNKNOWN_HYBRIDIZATION) {
+    if (Hy > Hx) {
+      mprinterr("Internal Error: :ModelTorsion::SetupTorsion() called with AX hybrid > AY hybrid.\n");
+      return 1;
+    }
+  }
+  ax_ = ax;
+  ay_ = ay;
+  Atom const& AX = topIn[ax];
+  Atom const& AY = topIn[ay];
+  // Sort AX bonds
+  unsigned int firstUnknownIdxX = 0;
+  sorted_ax_ = SortBondedAtomsLikeLeap(firstUnknownIdxX, AX, topIn, ay, hasPosition);
+  // Sort AY bonds
+  unsigned int firstUnknownIdxY = 0;
+  sorted_ay_ = SortBondedAtomsLikeLeap(firstUnknownIdxY, AY, topIn, ax, hasPosition);
+  // Calculate the chirality around atom X
+  Xorientation_ = 0;
+  if (Hx == AtomType::SP3) {
+    Xorientation_ = calculateOrientation( ax, sorted_ax_[0], ay, sorted_ax_[1], frameIn, hasPosition );
+  }
+  // Calculate the chirality around atom Y
+  Yorientation_ = 0;
+  if (Hy == AtomType::SP3) {
+    Yorientation_ = calculateOrientation( ay, sorted_ay_[0], ax, sorted_ay_[1], frameIn, hasPosition );
+  }
+  // DEBUG
+  mprintf("Orientation around: %s = %f\n", *(AX.Name()), Xorientation_);
+  //for (Atom::bond_iterator bat = AX.bondbegin(); bat != AX.bondend(); ++bat) mprintf(" %s", *(topIn[*bat].Name()));
+  //mprintf("}\n");
+  for (Iarray::const_iterator it = sorted_ax_.begin(); it != sorted_ax_.end(); ++it)
+      mprintf("Atom %li: %s\n", it - sorted_ax_.begin(), *(topIn[*it].Name()));
+  mprintf("Orientation around: %s = %f\n", *(AY.Name()), Yorientation_);
+  //for (Atom::bond_iterator bat = AY.bondbegin(); bat != AY.bondend(); ++bat) mprintf(" %s", *(topIn[*bat].Name()));
+  //mprintf("}\n");
+  for (Iarray::const_iterator it = sorted_ay_.begin(); it != sorted_ay_.end(); ++it)
+      mprintf("Atom %li: %s\n", it - sorted_ay_.begin(), *(topIn[*it].Name()));
+  // Calculate the actual torsion angle between A-X-Y-D
+  if (hasPosition[sorted_ax_[0]] &&
+      hasPosition[ax] &&
+      hasPosition[ay] &&
+      hasPosition[sorted_ay_[0]])
+  {
+    dAbsolute_ = Torsion( frameIn.XYZ(sorted_ax_[0]),
+                          frameIn.XYZ(ax),
+                          frameIn.XYZ(ay),
+                          frameIn.XYZ(sorted_ay_[0]) );
+  } else {
+    dAbsolute_ = 180.0 * Constants::DEGRAD;
+  }
+  mprintf("DABSOLUTE= %g\n", dAbsolute_);
+  return 0;
+}
+
+// -----------------------------------------------
 /** Create torsions around SP3-SP3. */
 void Builder::createSp3Sp3Torsions() {
   return;
@@ -1410,50 +1492,15 @@ int Builder::assignTorsionsAroundBond(int a1, int a2, Frame const& frameIn, Topo
     mprintf("DEBUG: Using externals to fit new torsions around: %s - %s\n",
             topIn.LeapName(ax).c_str(),
             topIn.LeapName(ay).c_str());
+
     ModelTorsion mT;
-    mT.ax_ = ax;
-    mT.ay_ = ay;
-    // Sort AX bonds
-    unsigned int firstUnknownIdxX = 0;
-    mT.sorted_ax_ = SortBondedAtomsLikeLeap(firstUnknownIdxX, AX, topIn, ay, hasPosition);
-    // Sort AY bonds
-    unsigned int firstUnknownIdxY = 0;
-    mT.sorted_ay_ = SortBondedAtomsLikeLeap(firstUnknownIdxY, AY, topIn, ax, hasPosition);
-    // Calculate the chirality around atom X
-    double Xorientation = 0;
-    if (Hx == AtomType::SP3) {
-      Xorientation = calculateOrientation( ax, mT.sorted_ax_[0], ay, mT.sorted_ax_[1], frameIn, hasPosition );
-    }
-    // Calculate the chirality around atom Y
-    double Yorientation = 0;
-    if (Hy == AtomType::SP3) {
-      Yorientation = calculateOrientation( ay, mT.sorted_ay_[0], ax, mT.sorted_ay_[1], frameIn, hasPosition );
-    }
-    // DEBUG
-    mprintf("Orientation around: %s = %f\n", *(AX.Name()), Xorientation);
-    //for (Atom::bond_iterator bat = AX.bondbegin(); bat != AX.bondend(); ++bat) mprintf(" %s", *(topIn[*bat].Name()));
-    //mprintf("}\n");
-    for (Iarray::const_iterator it = mT.sorted_ax_.begin(); it != mT.sorted_ax_.end(); ++it)
-        mprintf("Atom %li: %s\n", it - mT.sorted_ax_.begin(), *(topIn[*it].Name()));
-    mprintf("Orientation around: %s = %f\n", *(AY.Name()), Yorientation);
-    //for (Atom::bond_iterator bat = AY.bondbegin(); bat != AY.bondend(); ++bat) mprintf(" %s", *(topIn[*bat].Name()));
-    //mprintf("}\n");
-    for (Iarray::const_iterator it = mT.sorted_ay_.begin(); it != mT.sorted_ay_.end(); ++it)
-        mprintf("Atom %li: %s\n", it - mT.sorted_ay_.begin(), *(topIn[*it].Name()));
-    // Calculate the actual torsion angle between A-X-Y-D
-    if (hasPosition[mT.sorted_ax_[0]] &&
-        hasPosition[ax] &&
-        hasPosition[ay] &&
-        hasPosition[mT.sorted_ay_[0]])
-    {
-      mT.dAbsolute_ = Torsion( frameIn.XYZ(mT.sorted_ax_[0]),
-                               frameIn.XYZ(ax),
-                               frameIn.XYZ(ay),
-                               frameIn.XYZ(mT.sorted_ay_[0]) );
-    } else {
-      mT.dAbsolute_ = 180.0 * Constants::DEGRAD;
-    }
-    mprintf("DABSOLUTE= %g\n", mT.dAbsolute_);
+    if (mT.SetupTorsion(ax, ay, Hx, Hy, frameIn, topIn, hasPosition)) {
+      mprinterr("Error: Could not set up torsions around %s - %s\n",
+                topIn.LeapName(ax).c_str(),
+                topIn.LeapName(ay).c_str());
+      return 1;
+    } 
+
     // Build the new internals
     if (Hx == AtomType::SP3 && Hy == AtomType::SP3) {
       mprintf("SP3 SP3\n");

From 924b79fe71d003123be7c65e2201ac5c457c0a69 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 2 Feb 2024 14:31:23 -0500
Subject: [PATCH 0431/1492] Change class to TorsionModel. Start adding
 ModelTorsion routines

---
 src/Structure/Builder.cpp | 99 +++++++++++++++++++++++++++++++++++----
 src/Structure/Builder.h   |  6 ++-
 2 files changed, 93 insertions(+), 12 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 4bb0c1c42f..c9ba6d4a1b 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1200,14 +1200,24 @@ const
 
 // ------------------------------------------------------------------------------
 /** Store info for modelling torsions around X-Y */
-class Cpptraj::Structure::Builder::ModelTorsion {
+class Cpptraj::Structure::Builder::TorsionModel {
   public:
     /// CONSTRUCTOR
-    ModelTorsion() : ax_(-1), ay_(-1), dAbsolute_(0), Xorientation_(0), Yorientation_(0) {}
+    TorsionModel() : ax_(-1), ay_(-1), dAbsolute_(0), Xorientation_(0), Yorientation_(0) {}
     /// Set up torsions around bonded atoms
     int SetupTorsion(int, int, AtomType::HybridizationType, AtomType::HybridizationType,
                      Frame const&, Topology const&, std::vector<bool> const&);
 
+    /// \return Value of A-X-Y-D torsion in radians
+    double Absolute() const { return dAbsolute_; }
+    /// \return Value of orientation around X
+    double XOrientation() const { return Xorientation_; }
+    /// \return Value of orientation around Y
+    double YOrientation() const { return Yorientation_; }
+    /// \return Sorted atoms bonded to X excluding Y
+    std::vector<int> const& SortedAx() const { return sorted_ax_; }
+    /// \return Sorted atoms bonded to Y excluding X
+    std::vector<int> const& SortedAy() const { return sorted_ay_; }
   private:
     static int LeapAtomWeight(Atom const&);
     static inline std::vector<int> SiftBondedAtomsLikeLeap(unsigned int&, Atom const&, std::vector<bool> const&);
@@ -1229,7 +1239,7 @@ class Cpptraj::Structure::Builder::ModelTorsion {
   * each other. The 'weight' of an atom is defined as its element number,
   * unless the atom is CARBON, then it is 1000, making it the 'heaviest' atom.
   */
-int Cpptraj::Structure::Builder::ModelTorsion::LeapAtomWeight(Atom const& At)
+int Cpptraj::Structure::Builder::TorsionModel::LeapAtomWeight(Atom const& At)
 {
   if ( At.Element() == Atom::CARBON )
     return 1000;
@@ -1242,7 +1252,7 @@ int Cpptraj::Structure::Builder::ModelTorsion::LeapAtomWeight(Atom const& At)
   * \param hasPosition Array indicating whether atoms have position.
   */
 std::vector<int> 
-  Cpptraj::Structure::Builder::ModelTorsion::SiftBondedAtomsLikeLeap(unsigned int& firstUnknownIdx,
+  Cpptraj::Structure::Builder::TorsionModel::SiftBondedAtomsLikeLeap(unsigned int& firstUnknownIdx,
                                                                      Atom const& At,
                                                                      std::vector<bool> const& hasPosition)
 {
@@ -1266,7 +1276,7 @@ std::vector<int>
   * forms the torsion we are interested in.
   */
 std::vector<int>
-  Cpptraj::Structure::Builder::ModelTorsion::SortBondedAtomsLikeLeap(unsigned int& firstUnknownIdx,
+  Cpptraj::Structure::Builder::TorsionModel::SortBondedAtomsLikeLeap(unsigned int& firstUnknownIdx,
                                                                      Atom const& At, Topology const& topIn,
                                                                      int ignoreAtom,
                                                                      std::vector<bool> const& hasPosition)
@@ -1337,7 +1347,7 @@ static inline double calculateOrientation(int iX, int iA, int iY, int iB, Frame
 }
 
 /** Set up model torsion for bonded atoms. */
-int Cpptraj::Structure::Builder::ModelTorsion::SetupTorsion(int ax, int ay,
+int Cpptraj::Structure::Builder::TorsionModel::SetupTorsion(int ax, int ay,
                                                             AtomType::HybridizationType Hx,
                                                             AtomType::HybridizationType Hy,
                                                             Frame const& frameIn,
@@ -1346,7 +1356,7 @@ int Cpptraj::Structure::Builder::ModelTorsion::SetupTorsion(int ax, int ay,
 {
   if (Hx != AtomType::UNKNOWN_HYBRIDIZATION && Hy != AtomType::UNKNOWN_HYBRIDIZATION) {
     if (Hy > Hx) {
-      mprinterr("Internal Error: :ModelTorsion::SetupTorsion() called with AX hybrid > AY hybrid.\n");
+      mprinterr("Internal Error: TorsionModel::SetupTorsion() called with AX hybrid > AY hybrid.\n");
       return 1;
     }
   }
@@ -1399,8 +1409,77 @@ int Cpptraj::Structure::Builder::ModelTorsion::SetupTorsion(int ax, int ay,
 }
 
 // -----------------------------------------------
+/** Model torsion */
+void Builder::ModelTorsion(TorsionModel const& MT, unsigned int iBondX, unsigned int iBondY, double dval)
+{
+  if (iBondX >= MT.SortedAx().size()) {
+    mprinterr("Internal Error: Builder::ModelTorsion: iBondX %u is >= # sorted bonds %zu\n", iBondX, MT.SortedAx().size());
+    return;
+  }
+  if (iBondY >= MT.SortedAy().size()) {
+    mprinterr("Internal Error: Builder::ModelTorsion: iBondY %u is >= # sorted bonds %zu\n", iBondY, MT.SortedAy().size());
+    return;
+  }
+
+}
+
 /** Create torsions around SP3-SP3. */
-void Builder::createSp3Sp3Torsions() {
+void Builder::createSp3Sp3Torsions(TorsionModel const& MT) {
+  // First twist the torsion so that the AD torsion has
+  // the same absolute angle that is measured
+  // and twist all the others with it.
+  static const double PIOVER3 = Constants::PI / 3.0;
+  double dADOffset = MT.Absolute() - Constants::PI;
+  double d180      = Constants::PI + dADOffset;
+  double dm60      = -PIOVER3      + dADOffset;
+  double d60       =  PIOVER3      + dADOffset;
+
+  if ( MT.XOrientation() > 0.0 ) {
+    if ( MT.YOrientation() > 0.0 ) {
+      ModelTorsion( MT, 0, 0, d180 );
+      ModelTorsion( MT, 0, 1, dm60 );
+      ModelTorsion( MT, 0, 2, d60 );
+      ModelTorsion( MT, 1, 0, dm60 );
+      ModelTorsion( MT, 1, 1, d60 );
+      ModelTorsion( MT, 1, 2, d180 );
+      ModelTorsion( MT, 2, 0, d60 );
+      ModelTorsion( MT, 2, 1, d180 );
+      ModelTorsion( MT, 2, 2, dm60 );
+    } else {
+      ModelTorsion( MT, 0, 0,  d180 );
+      ModelTorsion( MT, 0, 1,  d60 );
+      ModelTorsion( MT, 0, 2,  dm60 );
+      ModelTorsion( MT, 1, 0,  dm60 );
+      ModelTorsion( MT, 1, 1,  d180 );
+      ModelTorsion( MT, 1, 2,  d60 );
+      ModelTorsion( MT, 2, 0,  d60 );
+      ModelTorsion( MT, 2, 1,  dm60 );
+      ModelTorsion( MT, 2, 2,  d180 );
+    }
+  } else {
+    if ( MT.YOrientation() > 0.0 ) {
+      ModelTorsion( MT, 0, 0, d180 );
+      ModelTorsion( MT, 0, 1, dm60 );
+      ModelTorsion( MT, 0, 2, d60 );
+      ModelTorsion( MT, 1, 0, d60 );
+      ModelTorsion( MT, 1, 1, d180 );
+      ModelTorsion( MT, 1, 2, dm60 );
+      ModelTorsion( MT, 2, 0, dm60 );
+      ModelTorsion( MT, 2, 1, d60 );
+      ModelTorsion( MT, 2, 2, d180 );
+    } else {
+      ModelTorsion( MT, 0, 0, d180 );
+      ModelTorsion( MT, 0, 1, d60 );
+      ModelTorsion( MT, 0, 2, dm60 );
+      ModelTorsion( MT, 1, 0, d60 );
+      ModelTorsion( MT, 1, 1, dm60 );
+      ModelTorsion( MT, 1, 2, d180 );
+      ModelTorsion( MT, 2, 0, dm60 );
+      ModelTorsion( MT, 2, 1, d180 );
+      ModelTorsion( MT, 2, 2, d60 );
+    }
+  }
+
   return;
 }
 
@@ -1493,7 +1572,7 @@ int Builder::assignTorsionsAroundBond(int a1, int a2, Frame const& frameIn, Topo
             topIn.LeapName(ax).c_str(),
             topIn.LeapName(ay).c_str());
 
-    ModelTorsion mT;
+    TorsionModel mT;
     if (mT.SetupTorsion(ax, ay, Hx, Hy, frameIn, topIn, hasPosition)) {
       mprinterr("Error: Could not set up torsions around %s - %s\n",
                 topIn.LeapName(ax).c_str(),
@@ -1504,7 +1583,7 @@ int Builder::assignTorsionsAroundBond(int a1, int a2, Frame const& frameIn, Topo
     // Build the new internals
     if (Hx == AtomType::SP3 && Hy == AtomType::SP3) {
       mprintf("SP3 SP3\n");
-      createSp3Sp3Torsions();
+      createSp3Sp3Torsions(mT);
     } else if (Hx == AtomType::SP3 && Hy == AtomType::SP2) {
       mprintf("SP3 SP2\n");
       createSp3Sp2Torsions();
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index 6cd9e62eba..5f64e30175 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -36,7 +36,7 @@ class Builder {
     typedef std::vector<int> Iarray;
 
     /// Used to hold parameters for modeling a torsion
-    class ModelTorsion;
+    class TorsionModel;
 
     /// Get length parameter for atoms
     int getLengthParam(double&, int, int, Topology const&) const;
@@ -64,7 +64,9 @@ class Builder {
     /// Model torsions around a bond in the same manner as LEaP
     int assignTorsionsAroundBond(int, int, Frame const&, Topology const&, Barray const&);
 
-    void createSp3Sp3Torsions();
+    void ModelTorsion(TorsionModel const&, unsigned int, unsigned int, double);
+
+    void createSp3Sp3Torsions(TorsionModel const&);
     void createSp3Sp2Torsions();
     void createSp2Sp2Torsions();
 

From f6870f3e03badaf194c1411c1a1525bc2617b52b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 2 Feb 2024 14:55:13 -0500
Subject: [PATCH 0432/1492] Do SP3 SP3 and SP3 SP2

---
 src/Structure/Builder.cpp | 145 ++++++++++++++++++++++++++------------
 src/Structure/Builder.h   |   6 +-
 2 files changed, 101 insertions(+), 50 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index c9ba6d4a1b..d1c9d8e61e 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1218,6 +1218,10 @@ class Cpptraj::Structure::Builder::TorsionModel {
     std::vector<int> const& SortedAx() const { return sorted_ax_; }
     /// \return Sorted atoms bonded to Y excluding X
     std::vector<int> const& SortedAy() const { return sorted_ay_; }
+    /// \return Index of atom X
+    int AtX() const { return ax_; }
+    /// \return Index of atom Y
+    int AtY() const { return ay_; }
   private:
     static int LeapAtomWeight(Atom const&);
     static inline std::vector<int> SiftBondedAtomsLikeLeap(unsigned int&, Atom const&, std::vector<bool> const&);
@@ -1410,21 +1414,38 @@ int Cpptraj::Structure::Builder::TorsionModel::SetupTorsion(int ax, int ay,
 
 // -----------------------------------------------
 /** Model torsion */
-void Builder::ModelTorsion(TorsionModel const& MT, unsigned int iBondX, unsigned int iBondY, double dval)
+void Builder::ModelTorsion(TorsionModel const& MT, unsigned int iBondX, unsigned int iBondY, double dvalIn, Frame const& frameIn, Barray const& hasPosition)
 {
-  if (iBondX >= MT.SortedAx().size()) {
-    mprinterr("Internal Error: Builder::ModelTorsion: iBondX %u is >= # sorted bonds %zu\n", iBondX, MT.SortedAx().size());
-    return;
-  }
-  if (iBondY >= MT.SortedAy().size()) {
-    mprinterr("Internal Error: Builder::ModelTorsion: iBondY %u is >= # sorted bonds %zu\n", iBondY, MT.SortedAy().size());
+  if (iBondX >= MT.SortedAx().size() ||
+      iBondY >= MT.SortedAy().size())
     return;
+
+  int aa = MT.SortedAx()[iBondX];
+  int ax = MT.AtX();
+  int ay = MT.AtY();
+  int ad = MT.SortedAy()[iBondY];
+  // If the coordinates for the atoms are defined then
+  // measure the torsion angle between them and use that for
+  // the internal.
+  double dval = dvalIn;
+  if (hasPosition[aa] &&
+      hasPosition[ax] &&
+      hasPosition[ay] &&
+      hasPosition[ad])
+  {
+    dval = Torsion( frameIn.XYZ(aa),
+                    frameIn.XYZ(ax),
+                    frameIn.XYZ(ay),
+                    frameIn.XYZ(ad) );
+  } else {
+    mprinterr("Internal Error: Need to implement torsion lookup.\n");
   }
+  mprintf( "++++Torsion INTERNAL: %f to %i - %i - %i - %i\n", dval*Constants::RADDEG, aa+1, ax+1, ay+1, ad+1);
 
 }
 
 /** Create torsions around SP3-SP3. */
-void Builder::createSp3Sp3Torsions(TorsionModel const& MT) {
+void Builder::createSp3Sp3Torsions(TorsionModel const& MT, Frame const& frameIn, Barray const& hasPosition) {
   // First twist the torsion so that the AD torsion has
   // the same absolute angle that is measured
   // and twist all the others with it.
@@ -1436,54 +1457,84 @@ void Builder::createSp3Sp3Torsions(TorsionModel const& MT) {
 
   if ( MT.XOrientation() > 0.0 ) {
     if ( MT.YOrientation() > 0.0 ) {
-      ModelTorsion( MT, 0, 0, d180 );
-      ModelTorsion( MT, 0, 1, dm60 );
-      ModelTorsion( MT, 0, 2, d60 );
-      ModelTorsion( MT, 1, 0, dm60 );
-      ModelTorsion( MT, 1, 1, d60 );
-      ModelTorsion( MT, 1, 2, d180 );
-      ModelTorsion( MT, 2, 0, d60 );
-      ModelTorsion( MT, 2, 1, d180 );
-      ModelTorsion( MT, 2, 2, dm60 );
+      ModelTorsion( MT, 0, 0, d180, frameIn, hasPosition);
+      ModelTorsion( MT, 0, 1, dm60, frameIn, hasPosition);
+      ModelTorsion( MT, 0, 2, d60, frameIn, hasPosition);
+      ModelTorsion( MT, 1, 0, dm60, frameIn, hasPosition);
+      ModelTorsion( MT, 1, 1, d60, frameIn, hasPosition);
+      ModelTorsion( MT, 1, 2, d180, frameIn, hasPosition);
+      ModelTorsion( MT, 2, 0, d60, frameIn, hasPosition);
+      ModelTorsion( MT, 2, 1, d180, frameIn, hasPosition);
+      ModelTorsion( MT, 2, 2, dm60, frameIn, hasPosition);
     } else {
-      ModelTorsion( MT, 0, 0,  d180 );
-      ModelTorsion( MT, 0, 1,  d60 );
-      ModelTorsion( MT, 0, 2,  dm60 );
-      ModelTorsion( MT, 1, 0,  dm60 );
-      ModelTorsion( MT, 1, 1,  d180 );
-      ModelTorsion( MT, 1, 2,  d60 );
-      ModelTorsion( MT, 2, 0,  d60 );
-      ModelTorsion( MT, 2, 1,  dm60 );
-      ModelTorsion( MT, 2, 2,  d180 );
+      ModelTorsion( MT, 0, 0,  d180, frameIn, hasPosition);
+      ModelTorsion( MT, 0, 1,  d60, frameIn, hasPosition);
+      ModelTorsion( MT, 0, 2,  dm60, frameIn, hasPosition);
+      ModelTorsion( MT, 1, 0,  dm60, frameIn, hasPosition);
+      ModelTorsion( MT, 1, 1,  d180, frameIn, hasPosition);
+      ModelTorsion( MT, 1, 2,  d60, frameIn, hasPosition);
+      ModelTorsion( MT, 2, 0,  d60, frameIn, hasPosition);
+      ModelTorsion( MT, 2, 1,  dm60, frameIn, hasPosition);
+      ModelTorsion( MT, 2, 2,  d180, frameIn, hasPosition);
     }
   } else {
     if ( MT.YOrientation() > 0.0 ) {
-      ModelTorsion( MT, 0, 0, d180 );
-      ModelTorsion( MT, 0, 1, dm60 );
-      ModelTorsion( MT, 0, 2, d60 );
-      ModelTorsion( MT, 1, 0, d60 );
-      ModelTorsion( MT, 1, 1, d180 );
-      ModelTorsion( MT, 1, 2, dm60 );
-      ModelTorsion( MT, 2, 0, dm60 );
-      ModelTorsion( MT, 2, 1, d60 );
-      ModelTorsion( MT, 2, 2, d180 );
+      ModelTorsion( MT, 0, 0, d180, frameIn, hasPosition);
+      ModelTorsion( MT, 0, 1, dm60, frameIn, hasPosition);
+      ModelTorsion( MT, 0, 2, d60, frameIn, hasPosition);
+      ModelTorsion( MT, 1, 0, d60, frameIn, hasPosition);
+      ModelTorsion( MT, 1, 1, d180, frameIn, hasPosition);
+      ModelTorsion( MT, 1, 2, dm60, frameIn, hasPosition);
+      ModelTorsion( MT, 2, 0, dm60, frameIn, hasPosition);
+      ModelTorsion( MT, 2, 1, d60, frameIn, hasPosition);
+      ModelTorsion( MT, 2, 2, d180, frameIn, hasPosition);
     } else {
-      ModelTorsion( MT, 0, 0, d180 );
-      ModelTorsion( MT, 0, 1, d60 );
-      ModelTorsion( MT, 0, 2, dm60 );
-      ModelTorsion( MT, 1, 0, d60 );
-      ModelTorsion( MT, 1, 1, dm60 );
-      ModelTorsion( MT, 1, 2, d180 );
-      ModelTorsion( MT, 2, 0, dm60 );
-      ModelTorsion( MT, 2, 1, d180 );
-      ModelTorsion( MT, 2, 2, d60 );
+      ModelTorsion( MT, 0, 0, d180, frameIn, hasPosition);
+      ModelTorsion( MT, 0, 1, d60, frameIn, hasPosition);
+      ModelTorsion( MT, 0, 2, dm60, frameIn, hasPosition);
+      ModelTorsion( MT, 1, 0, d60, frameIn, hasPosition);
+      ModelTorsion( MT, 1, 1, dm60, frameIn, hasPosition);
+      ModelTorsion( MT, 1, 2, d180, frameIn, hasPosition);
+      ModelTorsion( MT, 2, 0, dm60, frameIn, hasPosition);
+      ModelTorsion( MT, 2, 1, d180, frameIn, hasPosition);
+      ModelTorsion( MT, 2, 2, d60, frameIn, hasPosition);
     }
   }
 
   return;
 }
 
-void Builder::createSp3Sp2Torsions() {
+/** Create torsions around SP3-SP2. */
+void Builder::createSp3Sp2Torsions(TorsionModel const& MT, Frame const& frameIn, Barray const& hasPosition) {
+  // First twist the torsion so that the AD torsion has
+  // the same absolute angle that is measured
+  // and twist all the others with it.
+  static const double PIOVER3   = Constants::PI / 3.0;
+  static const double PIOVER3x2 = PIOVER3 * 2.0;
+  double dADOffset = MT.Absolute() - Constants::PI;
+  double   d180    = Constants::PI + dADOffset;
+  double   dm60    = -PIOVER3      + dADOffset;
+  double   d60     =  PIOVER3      + dADOffset;
+  double  dm120    = -PIOVER3x2    + dADOffset;
+  double  d120     =  PIOVER3x2    + dADOffset;
+  double  d0       =                 dADOffset;
+
+  if ( MT.XOrientation() > 0.0 ) {
+    ModelTorsion( MT, 0, 0, d180, frameIn, hasPosition);
+    ModelTorsion( MT, 0, 1, d0, frameIn, hasPosition);
+    ModelTorsion( MT, 1, 0, dm60, frameIn, hasPosition);
+    ModelTorsion( MT, 1, 1, d120, frameIn, hasPosition);
+    ModelTorsion( MT, 2, 0, d60, frameIn, hasPosition);
+    ModelTorsion( MT, 2, 1, dm120, frameIn, hasPosition);
+  } else {
+    ModelTorsion( MT, 0, 0, d180, frameIn, hasPosition);
+    ModelTorsion( MT, 0, 1, d0, frameIn, hasPosition);
+    ModelTorsion( MT, 1, 0, d60, frameIn, hasPosition);
+    ModelTorsion( MT, 1, 1, dm120, frameIn, hasPosition);
+    ModelTorsion( MT, 2, 0, dm60, frameIn, hasPosition);
+    ModelTorsion( MT, 2, 1, d120, frameIn, hasPosition);
+  }
+
   return;
 }
 
@@ -1583,10 +1634,10 @@ int Builder::assignTorsionsAroundBond(int a1, int a2, Frame const& frameIn, Topo
     // Build the new internals
     if (Hx == AtomType::SP3 && Hy == AtomType::SP3) {
       mprintf("SP3 SP3\n");
-      createSp3Sp3Torsions(mT);
+      createSp3Sp3Torsions(mT, frameIn, hasPosition);
     } else if (Hx == AtomType::SP3 && Hy == AtomType::SP2) {
       mprintf("SP3 SP2\n");
-      createSp3Sp2Torsions();
+      createSp3Sp2Torsions(mT, frameIn, hasPosition);
     } else if (Hx == AtomType::SP2 && Hy == AtomType::SP2) {
       mprintf("SP2 SP2\n");
       createSp2Sp2Torsions();
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index 5f64e30175..c0c0ccef0f 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -64,10 +64,10 @@ class Builder {
     /// Model torsions around a bond in the same manner as LEaP
     int assignTorsionsAroundBond(int, int, Frame const&, Topology const&, Barray const&);
 
-    void ModelTorsion(TorsionModel const&, unsigned int, unsigned int, double);
+    void ModelTorsion(TorsionModel const&, unsigned int, unsigned int, double, Frame const&, Barray const&);
 
-    void createSp3Sp3Torsions(TorsionModel const&);
-    void createSp3Sp2Torsions();
+    void createSp3Sp3Torsions(TorsionModel const&, Frame const&, Barray const&);
+    void createSp3Sp2Torsions(TorsionModel const&, Frame const&, Barray const&);
     void createSp2Sp2Torsions();
 
     int debug_;

From 4f3e5add6efa170813a723b07764578ac67ab81a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 2 Feb 2024 15:04:16 -0500
Subject: [PATCH 0433/1492] Do SP2 SP2

---
 src/Structure/Builder.cpp | 15 +++++++++++++--
 src/Structure/Builder.h   |  2 +-
 2 files changed, 14 insertions(+), 3 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index d1c9d8e61e..84aaa0ab1d 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1538,7 +1538,18 @@ void Builder::createSp3Sp2Torsions(TorsionModel const& MT, Frame const& frameIn,
   return;
 }
 
-void Builder::createSp2Sp2Torsions() {
+void Builder::createSp2Sp2Torsions(TorsionModel const& MT, Frame const& frameIn, Barray const& hasPosition) {
+  // First twist the torsion so that the AD torsion has
+  // the same absolute angle that is measured
+  // and twist all the others with it.
+  double dADOffset = MT.Absolute() - Constants::PI;
+  double d180      = Constants::PI + dADOffset;
+  double d0        =                 dADOffset;
+
+  ModelTorsion( MT, 0, 0, d180, frameIn, hasPosition );
+  ModelTorsion( MT, 0, 1, d0, frameIn, hasPosition );
+  ModelTorsion( MT, 1, 0, d0, frameIn, hasPosition );
+  ModelTorsion( MT, 1, 1, d180, frameIn, hasPosition );
   return;
 }
 
@@ -1640,7 +1651,7 @@ int Builder::assignTorsionsAroundBond(int a1, int a2, Frame const& frameIn, Topo
       createSp3Sp2Torsions(mT, frameIn, hasPosition);
     } else if (Hx == AtomType::SP2 && Hy == AtomType::SP2) {
       mprintf("SP2 SP2\n");
-      createSp2Sp2Torsions();
+      createSp2Sp2Torsions(mT, frameIn, hasPosition);
     } else {
       mprinterr("Error: Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported\n"
                 "Error: ---Tried to superimpose torsions for: *-%s-%s-*\n"
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index c0c0ccef0f..c44cf723e7 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -68,7 +68,7 @@ class Builder {
 
     void createSp3Sp3Torsions(TorsionModel const&, Frame const&, Barray const&);
     void createSp3Sp2Torsions(TorsionModel const&, Frame const&, Barray const&);
-    void createSp2Sp2Torsions();
+    void createSp2Sp2Torsions(TorsionModel const&, Frame const&, Barray const&);
 
     int debug_;
     ParameterSet const* params_;

From 9563a15936beefba4098d1815b436b5bee14477d Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 3 Feb 2024 08:55:39 -0500
Subject: [PATCH 0434/1492] Put common vars in the class

---
 src/Structure/Builder.cpp | 133 ++++++++++++++++++++------------------
 src/Structure/Builder.h   |   6 +-
 2 files changed, 75 insertions(+), 64 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 84aaa0ab1d..ca4232ee06 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1414,7 +1414,7 @@ int Cpptraj::Structure::Builder::TorsionModel::SetupTorsion(int ax, int ay,
 
 // -----------------------------------------------
 /** Model torsion */
-void Builder::ModelTorsion(TorsionModel const& MT, unsigned int iBondX, unsigned int iBondY, double dvalIn, Frame const& frameIn, Barray const& hasPosition)
+void Builder::ModelTorsion(TorsionModel const& MT, unsigned int iBondX, unsigned int iBondY, double dvalIn)
 {
   if (iBondX >= MT.SortedAx().size() ||
       iBondY >= MT.SortedAy().size())
@@ -1428,20 +1428,23 @@ void Builder::ModelTorsion(TorsionModel const& MT, unsigned int iBondX, unsigned
   // measure the torsion angle between them and use that for
   // the internal.
   double dval = dvalIn;
-  if (hasPosition[aa] &&
-      hasPosition[ax] &&
-      hasPosition[ay] &&
-      hasPosition[ad])
+  if ((*hasPosition_)[aa] &&
+      (*hasPosition_)[ax] &&
+      (*hasPosition_)[ay] &&
+      (*hasPosition_)[ad])
   {
-    dval = Torsion( frameIn.XYZ(aa),
-                    frameIn.XYZ(ax),
-                    frameIn.XYZ(ay),
-                    frameIn.XYZ(ad) );
+    dval = Torsion( currentFrm_->XYZ(aa),
+                    currentFrm_->XYZ(ax),
+                    currentFrm_->XYZ(ay),
+                    currentFrm_->XYZ(ad) );
   } else {
     mprinterr("Internal Error: Need to implement torsion lookup.\n");
   }
-  mprintf( "++++Torsion INTERNAL: %f to %i - %i - %i - %i\n", dval*Constants::RADDEG, aa+1, ax+1, ay+1, ad+1);
-
+  mprintf("++++Torsion INTERNAL: %f to %s - %s - %s - %s\n", dval*Constants::RADDEG,
+          currentTop_->LeapName(aa).c_str(),
+          currentTop_->LeapName(ax).c_str(),
+          currentTop_->LeapName(ay).c_str(),
+          currentTop_->LeapName(ad).c_str());
 }
 
 /** Create torsions around SP3-SP3. */
@@ -1457,47 +1460,47 @@ void Builder::createSp3Sp3Torsions(TorsionModel const& MT, Frame const& frameIn,
 
   if ( MT.XOrientation() > 0.0 ) {
     if ( MT.YOrientation() > 0.0 ) {
-      ModelTorsion( MT, 0, 0, d180, frameIn, hasPosition);
-      ModelTorsion( MT, 0, 1, dm60, frameIn, hasPosition);
-      ModelTorsion( MT, 0, 2, d60, frameIn, hasPosition);
-      ModelTorsion( MT, 1, 0, dm60, frameIn, hasPosition);
-      ModelTorsion( MT, 1, 1, d60, frameIn, hasPosition);
-      ModelTorsion( MT, 1, 2, d180, frameIn, hasPosition);
-      ModelTorsion( MT, 2, 0, d60, frameIn, hasPosition);
-      ModelTorsion( MT, 2, 1, d180, frameIn, hasPosition);
-      ModelTorsion( MT, 2, 2, dm60, frameIn, hasPosition);
+      ModelTorsion( MT, 0, 0, d180);
+      ModelTorsion( MT, 0, 1, dm60);
+      ModelTorsion( MT, 0, 2, d60);
+      ModelTorsion( MT, 1, 0, dm60);
+      ModelTorsion( MT, 1, 1, d60);
+      ModelTorsion( MT, 1, 2, d180);
+      ModelTorsion( MT, 2, 0, d60);
+      ModelTorsion( MT, 2, 1, d180);
+      ModelTorsion( MT, 2, 2, dm60);
     } else {
-      ModelTorsion( MT, 0, 0,  d180, frameIn, hasPosition);
-      ModelTorsion( MT, 0, 1,  d60, frameIn, hasPosition);
-      ModelTorsion( MT, 0, 2,  dm60, frameIn, hasPosition);
-      ModelTorsion( MT, 1, 0,  dm60, frameIn, hasPosition);
-      ModelTorsion( MT, 1, 1,  d180, frameIn, hasPosition);
-      ModelTorsion( MT, 1, 2,  d60, frameIn, hasPosition);
-      ModelTorsion( MT, 2, 0,  d60, frameIn, hasPosition);
-      ModelTorsion( MT, 2, 1,  dm60, frameIn, hasPosition);
-      ModelTorsion( MT, 2, 2,  d180, frameIn, hasPosition);
+      ModelTorsion( MT, 0, 0,  d180);
+      ModelTorsion( MT, 0, 1,  d60);
+      ModelTorsion( MT, 0, 2,  dm60);
+      ModelTorsion( MT, 1, 0,  dm60);
+      ModelTorsion( MT, 1, 1,  d180);
+      ModelTorsion( MT, 1, 2,  d60);
+      ModelTorsion( MT, 2, 0,  d60);
+      ModelTorsion( MT, 2, 1,  dm60);
+      ModelTorsion( MT, 2, 2,  d180);
     }
   } else {
     if ( MT.YOrientation() > 0.0 ) {
-      ModelTorsion( MT, 0, 0, d180, frameIn, hasPosition);
-      ModelTorsion( MT, 0, 1, dm60, frameIn, hasPosition);
-      ModelTorsion( MT, 0, 2, d60, frameIn, hasPosition);
-      ModelTorsion( MT, 1, 0, d60, frameIn, hasPosition);
-      ModelTorsion( MT, 1, 1, d180, frameIn, hasPosition);
-      ModelTorsion( MT, 1, 2, dm60, frameIn, hasPosition);
-      ModelTorsion( MT, 2, 0, dm60, frameIn, hasPosition);
-      ModelTorsion( MT, 2, 1, d60, frameIn, hasPosition);
-      ModelTorsion( MT, 2, 2, d180, frameIn, hasPosition);
+      ModelTorsion( MT, 0, 0, d180);
+      ModelTorsion( MT, 0, 1, dm60);
+      ModelTorsion( MT, 0, 2, d60);
+      ModelTorsion( MT, 1, 0, d60);
+      ModelTorsion( MT, 1, 1, d180);
+      ModelTorsion( MT, 1, 2, dm60);
+      ModelTorsion( MT, 2, 0, dm60);
+      ModelTorsion( MT, 2, 1, d60);
+      ModelTorsion( MT, 2, 2, d180);
     } else {
-      ModelTorsion( MT, 0, 0, d180, frameIn, hasPosition);
-      ModelTorsion( MT, 0, 1, d60, frameIn, hasPosition);
-      ModelTorsion( MT, 0, 2, dm60, frameIn, hasPosition);
-      ModelTorsion( MT, 1, 0, d60, frameIn, hasPosition);
-      ModelTorsion( MT, 1, 1, dm60, frameIn, hasPosition);
-      ModelTorsion( MT, 1, 2, d180, frameIn, hasPosition);
-      ModelTorsion( MT, 2, 0, dm60, frameIn, hasPosition);
-      ModelTorsion( MT, 2, 1, d180, frameIn, hasPosition);
-      ModelTorsion( MT, 2, 2, d60, frameIn, hasPosition);
+      ModelTorsion( MT, 0, 0, d180);
+      ModelTorsion( MT, 0, 1, d60);
+      ModelTorsion( MT, 0, 2, dm60);
+      ModelTorsion( MT, 1, 0, d60);
+      ModelTorsion( MT, 1, 1, dm60);
+      ModelTorsion( MT, 1, 2, d180);
+      ModelTorsion( MT, 2, 0, dm60);
+      ModelTorsion( MT, 2, 1, d180);
+      ModelTorsion( MT, 2, 2, d60);
     }
   }
 
@@ -1520,19 +1523,19 @@ void Builder::createSp3Sp2Torsions(TorsionModel const& MT, Frame const& frameIn,
   double  d0       =                 dADOffset;
 
   if ( MT.XOrientation() > 0.0 ) {
-    ModelTorsion( MT, 0, 0, d180, frameIn, hasPosition);
-    ModelTorsion( MT, 0, 1, d0, frameIn, hasPosition);
-    ModelTorsion( MT, 1, 0, dm60, frameIn, hasPosition);
-    ModelTorsion( MT, 1, 1, d120, frameIn, hasPosition);
-    ModelTorsion( MT, 2, 0, d60, frameIn, hasPosition);
-    ModelTorsion( MT, 2, 1, dm120, frameIn, hasPosition);
+    ModelTorsion( MT, 0, 0, d180);
+    ModelTorsion( MT, 0, 1, d0);
+    ModelTorsion( MT, 1, 0, dm60);
+    ModelTorsion( MT, 1, 1, d120);
+    ModelTorsion( MT, 2, 0, d60);
+    ModelTorsion( MT, 2, 1, dm120);
   } else {
-    ModelTorsion( MT, 0, 0, d180, frameIn, hasPosition);
-    ModelTorsion( MT, 0, 1, d0, frameIn, hasPosition);
-    ModelTorsion( MT, 1, 0, d60, frameIn, hasPosition);
-    ModelTorsion( MT, 1, 1, dm120, frameIn, hasPosition);
-    ModelTorsion( MT, 2, 0, dm60, frameIn, hasPosition);
-    ModelTorsion( MT, 2, 1, d120, frameIn, hasPosition);
+    ModelTorsion( MT, 0, 0, d180);
+    ModelTorsion( MT, 0, 1, d0);
+    ModelTorsion( MT, 1, 0, d60);
+    ModelTorsion( MT, 1, 1, dm120);
+    ModelTorsion( MT, 2, 0, dm60);
+    ModelTorsion( MT, 2, 1, d120);
   }
 
   return;
@@ -1546,16 +1549,20 @@ void Builder::createSp2Sp2Torsions(TorsionModel const& MT, Frame const& frameIn,
   double d180      = Constants::PI + dADOffset;
   double d0        =                 dADOffset;
 
-  ModelTorsion( MT, 0, 0, d180, frameIn, hasPosition );
-  ModelTorsion( MT, 0, 1, d0, frameIn, hasPosition );
-  ModelTorsion( MT, 1, 0, d0, frameIn, hasPosition );
-  ModelTorsion( MT, 1, 1, d180, frameIn, hasPosition );
+  ModelTorsion( MT, 0, 0, d180 );
+  ModelTorsion( MT, 0, 1, d0 );
+  ModelTorsion( MT, 1, 0, d0 );
+  ModelTorsion( MT, 1, 1, d180 );
   return;
 }
 
 /** Assign torsions around bonded atoms in manner similar to LEaP's ModelAssignTorsionsAround. */
 int Builder::assignTorsionsAroundBond(int a1, int a2, Frame const& frameIn, Topology const& topIn, Barray const& hasPosition)
 {
+  // Save addresses of frame, topology, and hasPosition
+  currentFrm_ = &frameIn;
+  currentTop_ = &topIn;
+  hasPosition_ = &hasPosition;
   // No need to do this if either atom only has 1 bond.
   if (topIn[a1].Nbonds() < 2 || topIn[a2].Nbonds() < 2)
     return 0;
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index c44cf723e7..b393d554c7 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -64,7 +64,7 @@ class Builder {
     /// Model torsions around a bond in the same manner as LEaP
     int assignTorsionsAroundBond(int, int, Frame const&, Topology const&, Barray const&);
 
-    void ModelTorsion(TorsionModel const&, unsigned int, unsigned int, double, Frame const&, Barray const&);
+    void ModelTorsion(TorsionModel const&, unsigned int, unsigned int, double);
 
     void createSp3Sp3Torsions(TorsionModel const&, Frame const&, Barray const&);
     void createSp3Sp2Torsions(TorsionModel const&, Frame const&, Barray const&);
@@ -73,6 +73,10 @@ class Builder {
     int debug_;
     ParameterSet const* params_;
     Zmatrix const* currentZmatrix_; ///< Any existing internal coordinates
+
+    Topology const* currentTop_; ///< Topology for the createSpXSpXTorsions/ModelTorsion routines
+    Frame const* currentFrm_;    ///< Frame for the createSpXSpXTorsions routines
+    Barray const* hasPosition_;  ///< Array indicating which atoms have position for createSpXSpXTorsions/ModelTorsion routines
 };
 }
 }

From 87e9a42f1d762acf98ba42762045065644c416f2 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 3 Feb 2024 09:03:49 -0500
Subject: [PATCH 0435/1492] No need to pass in frame or hasPosition anymore.
 Save address of current Zmatrix

---
 src/Structure/Builder.cpp | 57 ++++++++-------------------------------
 src/Structure/Builder.h   |  8 +++---
 2 files changed, 15 insertions(+), 50 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index ca4232ee06..647ebb1bd0 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1448,7 +1448,7 @@ void Builder::ModelTorsion(TorsionModel const& MT, unsigned int iBondX, unsigned
 }
 
 /** Create torsions around SP3-SP3. */
-void Builder::createSp3Sp3Torsions(TorsionModel const& MT, Frame const& frameIn, Barray const& hasPosition) {
+void Builder::createSp3Sp3Torsions(TorsionModel const& MT) {
   // First twist the torsion so that the AD torsion has
   // the same absolute angle that is measured
   // and twist all the others with it.
@@ -1508,7 +1508,7 @@ void Builder::createSp3Sp3Torsions(TorsionModel const& MT, Frame const& frameIn,
 }
 
 /** Create torsions around SP3-SP2. */
-void Builder::createSp3Sp2Torsions(TorsionModel const& MT, Frame const& frameIn, Barray const& hasPosition) {
+void Builder::createSp3Sp2Torsions(TorsionModel const& MT) {
   // First twist the torsion so that the AD torsion has
   // the same absolute angle that is measured
   // and twist all the others with it.
@@ -1541,7 +1541,7 @@ void Builder::createSp3Sp2Torsions(TorsionModel const& MT, Frame const& frameIn,
   return;
 }
 
-void Builder::createSp2Sp2Torsions(TorsionModel const& MT, Frame const& frameIn, Barray const& hasPosition) {
+void Builder::createSp2Sp2Torsions(TorsionModel const& MT) {
   // First twist the torsion so that the AD torsion has
   // the same absolute angle that is measured
   // and twist all the others with it.
@@ -1557,9 +1557,11 @@ void Builder::createSp2Sp2Torsions(TorsionModel const& MT, Frame const& frameIn,
 }
 
 /** Assign torsions around bonded atoms in manner similar to LEaP's ModelAssignTorsionsAround. */
-int Builder::assignTorsionsAroundBond(int a1, int a2, Frame const& frameIn, Topology const& topIn, Barray const& hasPosition)
+int Builder::assignTorsionsAroundBond(Zmatrix& zmatrix, int a1, int a2, Frame const& frameIn, Topology const& topIn, Barray const& hasPosition)
 {
-  // Save addresses of frame, topology, and hasPosition
+  // Save addresses of zmatrix, frame, topology, and hasPosition.
+  // These are required for the createSpXSpX routines.
+  currentZmatrix_ = &zmatrix;
   currentFrm_ = &frameIn;
   currentTop_ = &topIn;
   hasPosition_ = &hasPosition;
@@ -1652,13 +1654,13 @@ int Builder::assignTorsionsAroundBond(int a1, int a2, Frame const& frameIn, Topo
     // Build the new internals
     if (Hx == AtomType::SP3 && Hy == AtomType::SP3) {
       mprintf("SP3 SP3\n");
-      createSp3Sp3Torsions(mT, frameIn, hasPosition);
+      createSp3Sp3Torsions(mT);
     } else if (Hx == AtomType::SP3 && Hy == AtomType::SP2) {
       mprintf("SP3 SP2\n");
-      createSp3Sp2Torsions(mT, frameIn, hasPosition);
+      createSp3Sp2Torsions(mT);
     } else if (Hx == AtomType::SP2 && Hy == AtomType::SP2) {
       mprintf("SP2 SP2\n");
-      createSp2Sp2Torsions(mT, frameIn, hasPosition);
+      createSp2Sp2Torsions(mT);
     } else {
       mprinterr("Error: Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported\n"
                 "Error: ---Tried to superimpose torsions for: *-%s-%s-*\n"
@@ -1686,49 +1688,12 @@ int Builder::GenerateInternals(Zmatrix& zmatrix, Frame const& frameIn, Topology
   // Loop over bonds
   for (BondArray::const_iterator bnd = bonds.begin(); bnd != bonds.end(); ++bnd)
   {
-    if (assignTorsionsAroundBond( bnd->A1(), bnd->A2(), frameIn, topIn, hasPosition )) {
+    if (assignTorsionsAroundBond( zmatrix, bnd->A1(), bnd->A2(), frameIn, topIn, hasPosition )) {
       mprinterr("Error Assign torsions around bond %s - %s failed.\n",
                 topIn.AtomMaskName(bnd->A1()).c_str(),
                 topIn.AtomMaskName(bnd->A2()).c_str());
       return 1;
     }
-/*
-    Atom const& A2 = topIn[bnd->A1()];
-    Atom const& A3 = topIn[bnd->A2()];
-    if (A2.Nbonds() > 1 && A3.Nbonds() > 1) {
-      //Residue const& R2 = topIn.Res(A2.ResNum());
-      //Residue const& R3 = topIn.Res(A3.ResNum());
-      mprintf("Building torsion INTERNALs around: %s - %s\n",
-              topIn.LeapName(bnd->A1()).c_str(), topIn.LeapName(bnd->A2()).c_str());
-      Iarray sorted_a2 = SortBondedAtomsLikeLeap(A2, topIn, bnd->A2());
-      Iarray sorted_a3 = SortBondedAtomsLikeLeap(A3, topIn, bnd->A1());
-      mprintf("Orientation around: %s {", *(A2.Name()));
-      for (Atom::bond_iterator bat = A2.bondbegin(); bat != A2.bondend(); ++bat) mprintf(" %s", *(topIn[*bat].Name()));
-      mprintf("}\n");
-      for (Iarray::const_iterator it = sorted_a2.begin(); it != sorted_a2.end(); ++it)
-        mprintf("Atom %li: %s\n", it - sorted_a2.begin(), *(topIn[*it].Name()));
-      mprintf("Orientation around: %s {", *(A3.Name()));
-      for (Atom::bond_iterator bat = A3.bondbegin(); bat != A3.bondend(); ++bat) mprintf(" %s", *(topIn[*bat].Name()));
-      mprintf("}\n");
-      for (Iarray::const_iterator it = sorted_a3.begin(); it != sorted_a3.end(); ++it)
-        mprintf("Atom %li: %s\n", it - sorted_a3.begin(), *(topIn[*it].Name()));
-      // Build the torsions
-      int aj = bnd->A1();
-      int ak = bnd->A2();
-      for (Iarray::const_iterator ai = sorted_a2.begin(); ai != sorted_a2.end(); ++ai) {
-        for (Iarray::const_iterator al = sorted_a3.begin(); al != sorted_a3.end(); ++al) {
-          //double dval = Torsion(frameIn.XYZ(*ai), frameIn.XYZ(aj), frameIn.XYZ(ak), frameIn.XYZ(*al));
-          zmatrix.AddIC(*ai, aj, ak, *al, frameIn);
-          mprintf("++++Torsion INTERNAL: %f to %s - %s - %s - %s\n",
-                  zmatrix.back().Phi(),
-                  topIn.LeapName(*ai).c_str(),
-                  topIn.LeapName(aj).c_str(),
-                  topIn.LeapName(ak).c_str(),
-                  topIn.LeapName(*al).c_str());
-          zmatrix.AddIC(*al, ak, aj, *ai, frameIn);
-        }
-      }
-    }*/
   }
   mprintf("DEBUG: ----- Leaving Builder::GenerateInternals. ------\n");
   return 0;
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index b393d554c7..711d1fb547 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -62,13 +62,13 @@ class Builder {
                            BuildAtom const&, BuildAtom const&) const;
 
     /// Model torsions around a bond in the same manner as LEaP
-    int assignTorsionsAroundBond(int, int, Frame const&, Topology const&, Barray const&);
+    int assignTorsionsAroundBond(Zmatrix&, int, int, Frame const&, Topology const&, Barray const&);
 
     void ModelTorsion(TorsionModel const&, unsigned int, unsigned int, double);
 
-    void createSp3Sp3Torsions(TorsionModel const&, Frame const&, Barray const&);
-    void createSp3Sp2Torsions(TorsionModel const&, Frame const&, Barray const&);
-    void createSp2Sp2Torsions(TorsionModel const&, Frame const&, Barray const&);
+    void createSp3Sp3Torsions(TorsionModel const&);
+    void createSp3Sp2Torsions(TorsionModel const&);
+    void createSp2Sp2Torsions(TorsionModel const&);
 
     int debug_;
     ParameterSet const* params_;

From 88b3239579b6bc0677c0ce60fa4097f5e5b40531 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 3 Feb 2024 14:03:21 -0500
Subject: [PATCH 0436/1492] Add the ICs to Zmatrix

---
 src/Structure/Builder.cpp | 47 +++++++++++++++++++++++++++++++++------
 src/Structure/Builder.h   |  4 ++--
 2 files changed, 42 insertions(+), 9 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 647ebb1bd0..9c32dc3ebb 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -30,7 +30,7 @@ void Cpptraj::Structure::Builder::SetParameters(ParameterSet const* paramsIn) {
 }
 
 /** Set optional Zmatrix. */
-void Cpptraj::Structure::Builder::SetZmatrix(Zmatrix const* zmatrixIn) {
+void Cpptraj::Structure::Builder::SetZmatrix(Zmatrix* zmatrixIn) {
   if (zmatrixIn == 0) {
     mprinterr("Internal Error: Builder::SetZmatrix called with null set.\n");
     return;
@@ -1424,27 +1424,59 @@ void Builder::ModelTorsion(TorsionModel const& MT, unsigned int iBondX, unsigned
   int ax = MT.AtX();
   int ay = MT.AtY();
   int ad = MT.SortedAy()[iBondY];
+  // Get bond lengths
+  double l0, l1;
+  if (AssignLength(l0, aa, ax, *currentTop_, *currentFrm_, *hasPosition_)) {
+    mprinterr("Error: Could not assign length between %s and %s\n",
+              currentTop_->AtomMaskName(aa).c_str(),
+              currentTop_->AtomMaskName(ax).c_str());
+    return;
+  }
+  if (AssignLength(l1, ad, ay, *currentTop_, *currentFrm_, *hasPosition_)) {
+    mprinterr("Error: Could not assign length between %s and %s\n",
+              currentTop_->AtomMaskName(ad).c_str(),
+              currentTop_->AtomMaskName(ay).c_str());
+    return;
+  }
+  // Get angles
+  double t0, t1;
+  if (AssignTheta(t0, aa, ax, ay, *currentTop_, *currentFrm_, *hasPosition_)) {
+    mprinterr("Error: Could not assign angle between %s and %s and %s\n",
+              currentTop_->AtomMaskName(aa).c_str(),
+              currentTop_->AtomMaskName(ax).c_str(),
+              currentTop_->AtomMaskName(ay).c_str());
+    return;
+  }
+  if (AssignTheta(t1, ad, ay, ax, *currentTop_, *currentFrm_, *hasPosition_)) {
+    mprinterr("Error: Could not assign angle between %s and %s and %s\n",
+              currentTop_->AtomMaskName(ad).c_str(),
+              currentTop_->AtomMaskName(ay).c_str(),
+              currentTop_->AtomMaskName(ax).c_str());
+    return;
+  }
   // If the coordinates for the atoms are defined then
   // measure the torsion angle between them and use that for
   // the internal.
-  double dval = dvalIn;
+  double phiVal = dvalIn;
   if ((*hasPosition_)[aa] &&
       (*hasPosition_)[ax] &&
       (*hasPosition_)[ay] &&
       (*hasPosition_)[ad])
   {
-    dval = Torsion( currentFrm_->XYZ(aa),
-                    currentFrm_->XYZ(ax),
-                    currentFrm_->XYZ(ay),
-                    currentFrm_->XYZ(ad) );
+    phiVal = Torsion( currentFrm_->XYZ(aa),
+                      currentFrm_->XYZ(ax),
+                      currentFrm_->XYZ(ay),
+                      currentFrm_->XYZ(ad) );
   } else {
     mprinterr("Internal Error: Need to implement torsion lookup.\n");
   }
-  mprintf("++++Torsion INTERNAL: %f to %s - %s - %s - %s\n", dval*Constants::RADDEG,
+  mprintf("++++Torsion INTERNAL: %f to %s - %s - %s - %s\n", phiVal*Constants::RADDEG,
           currentTop_->LeapName(aa).c_str(),
           currentTop_->LeapName(ax).c_str(),
           currentTop_->LeapName(ay).c_str(),
           currentTop_->LeapName(ad).c_str());
+  currentZmatrix_->AddIC( InternalCoords(aa, ax, ay, ad, l0, t0*Constants::RADDEG, phiVal*Constants::RADDEG) );
+  currentZmatrix_->AddIC( InternalCoords(ad, ay, ax, aa, l1, t1*Constants::RADDEG, phiVal*Constants::RADDEG) );
 }
 
 /** Create torsions around SP3-SP3. */
@@ -1695,6 +1727,7 @@ int Builder::GenerateInternals(Zmatrix& zmatrix, Frame const& frameIn, Topology
       return 1;
     }
   }
+  zmatrix.print( &topIn );
   mprintf("DEBUG: ----- Leaving Builder::GenerateInternals. ------\n");
   return 0;
 }
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index 711d1fb547..eb61bf763b 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -20,7 +20,7 @@ class Builder {
     /// Set optional parameter set
     void SetParameters(ParameterSet const*);
     /// Set optional Zmatrix with current ICs
-    void SetZmatrix(Zmatrix const*);
+    void SetZmatrix(Zmatrix*);
 
     /// Combine second fragment into first fragment and bond
     int Combine(Topology&, Frame&, Topology const&, Frame const&, int, int) const;
@@ -72,7 +72,7 @@ class Builder {
 
     int debug_;
     ParameterSet const* params_;
-    Zmatrix const* currentZmatrix_; ///< Any existing internal coordinates
+    Zmatrix* currentZmatrix_; ///< Any existing internal coordinates
 
     Topology const* currentTop_; ///< Topology for the createSpXSpXTorsions/ModelTorsion routines
     Frame const* currentFrm_;    ///< Frame for the createSpXSpXTorsions routines

From a446ffd61fe9f9fc6adacdcab56c650ded162950 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 3 Feb 2024 14:08:43 -0500
Subject: [PATCH 0437/1492] Use new generate routine

---
 src/Exec_Build.cpp        | 16 ++++++++--------
 src/Structure/Builder.cpp |  2 +-
 2 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 49be97a84b..b2b878f5af 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -304,19 +304,19 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
         resTemplate->GetFrame( 0, templateFrame );
         Cpptraj::Structure::Zmatrix* zmatrix = new Cpptraj::Structure::Zmatrix();
         //if (zmatrix->SetFromFrameAndConnect( templateFrame, resTemplate->Top() )) {
-        if (zmatrix->GenerateInternals( templateFrame, resTemplate->Top() )) {
-          mprinterr("Error: Could not set up residue template zmatrix.\n");
+//        if (zmatrix->GenerateInternals( templateFrame, resTemplate->Top() )) {
+//          mprinterr("Error: Could not set up residue template zmatrix.\n");
+//          return 1;
+//        }
+        if (structureBuilder.GenerateInternals(*zmatrix, templateFrame, resTemplate->Top(),
+                                               std::vector<bool>(resTemplate->Top().Natom(), true)))
+        {
+          mprinterr("Error: Generate internals for residue template failed.\n");
           return 1;
         }
 //        zmatrix->print( resTemplate->TopPtr() );
         zmatrix->OffsetIcIndices( atomOffset );
         ResZmatrices.push_back( zmatrix );
-        // FIXME DEBUG
-        Cpptraj::Structure::Zmatrix tmpz;
-        if (structureBuilder.GenerateInternals( tmpz, templateFrame, resTemplate->Top(), std::vector<bool>(resTemplate->Top().Natom(), true) )) {
-          mprinterr("Error: Generate internals for template failed.\n");
-          return 1;
-        }
 //        zmatrix->print( &topOut );
         //for (Iarray::const_iterator jres = resConnections[ires].begin();
         //                            jres != resConnections[ires].end(); ++jres)
diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 9c32dc3ebb..c2aa4e2e35 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1727,7 +1727,7 @@ int Builder::GenerateInternals(Zmatrix& zmatrix, Frame const& frameIn, Topology
       return 1;
     }
   }
-  zmatrix.print( &topIn );
+  //zmatrix.print( &topIn );
   mprintf("DEBUG: ----- Leaving Builder::GenerateInternals. ------\n");
   return 0;
 }

From b2af45d6b14a6e6d1ce0999b5dd649a3a92810d4 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 3 Feb 2024 14:46:29 -0500
Subject: [PATCH 0438/1492] Test using the new torsion modeller to assign
 torsions around a residue link. Not yet working.

---
 src/Exec_Build.cpp        | 10 ++++++++++
 src/Structure/Builder.cpp | 38 +++++++++++++++++++-------------------
 src/Structure/Builder.h   |  6 +++---
 3 files changed, 32 insertions(+), 22 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index b2b878f5af..853dd111ab 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -414,6 +414,16 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
                           topOut.AtomMaskName(at).c_str(), topOut.AtomMaskName(*bat).c_str());
                 return 1;
               }
+              // FIXME DEBUG
+              Cpptraj::Structure::Zmatrix tmpz;
+              if (structureBuilder.AssignTorsionsAroundBond(tmpz, at, *bat, frameOut, topOut,
+                                                            hasPosition))
+              {
+                mprinterr("Error: Assign torsions around inter-residue bond %s - %s failed.\n",
+                          topOut.AtomMaskName(at).c_str(), topOut.AtomMaskName(*bat).c_str());
+                return 1;
+              }
+              tmpz.print(&topOut);
             }
           }
         }
diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index c2aa4e2e35..d4ab7ac1e3 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1485,10 +1485,10 @@ void Builder::createSp3Sp3Torsions(TorsionModel const& MT) {
   // the same absolute angle that is measured
   // and twist all the others with it.
   static const double PIOVER3 = Constants::PI / 3.0;
-  double dADOffset = MT.Absolute() - Constants::PI;
-  double d180      = Constants::PI + dADOffset;
-  double dm60      = -PIOVER3      + dADOffset;
-  double d60       =  PIOVER3      + dADOffset;
+  double dADOffset = wrap360(MT.Absolute() - Constants::PI);
+  double d180      = wrap360(Constants::PI + dADOffset    );
+  double dm60      = wrap360(-PIOVER3      + dADOffset    );
+  double d60       = wrap360( PIOVER3      + dADOffset    );
 
   if ( MT.XOrientation() > 0.0 ) {
     if ( MT.YOrientation() > 0.0 ) {
@@ -1546,13 +1546,13 @@ void Builder::createSp3Sp2Torsions(TorsionModel const& MT) {
   // and twist all the others with it.
   static const double PIOVER3   = Constants::PI / 3.0;
   static const double PIOVER3x2 = PIOVER3 * 2.0;
-  double dADOffset = MT.Absolute() - Constants::PI;
-  double   d180    = Constants::PI + dADOffset;
-  double   dm60    = -PIOVER3      + dADOffset;
-  double   d60     =  PIOVER3      + dADOffset;
-  double  dm120    = -PIOVER3x2    + dADOffset;
-  double  d120     =  PIOVER3x2    + dADOffset;
-  double  d0       =                 dADOffset;
+  double dADOffset = wrap360(MT.Absolute() - Constants::PI);
+  double   d180    = wrap360(Constants::PI + dADOffset    );
+  double   dm60    = wrap360(-PIOVER3      + dADOffset    );
+  double   d60     = wrap360( PIOVER3      + dADOffset    );
+  double  dm120    = wrap360(-PIOVER3x2    + dADOffset    );
+  double  d120     = wrap360( PIOVER3x2    + dADOffset    );
+  double  d0       =                         dADOffset     ;
 
   if ( MT.XOrientation() > 0.0 ) {
     ModelTorsion( MT, 0, 0, d180);
@@ -1577,9 +1577,9 @@ void Builder::createSp2Sp2Torsions(TorsionModel const& MT) {
   // First twist the torsion so that the AD torsion has
   // the same absolute angle that is measured
   // and twist all the others with it.
-  double dADOffset = MT.Absolute() - Constants::PI;
-  double d180      = Constants::PI + dADOffset;
-  double d0        =                 dADOffset;
+  double dADOffset = wrap360(MT.Absolute() - Constants::PI);
+  double d180      = wrap360(Constants::PI + dADOffset    );
+  double d0        =                 dADOffset             ;
 
   ModelTorsion( MT, 0, 0, d180 );
   ModelTorsion( MT, 0, 1, d0 );
@@ -1589,10 +1589,10 @@ void Builder::createSp2Sp2Torsions(TorsionModel const& MT) {
 }
 
 /** Assign torsions around bonded atoms in manner similar to LEaP's ModelAssignTorsionsAround. */
-int Builder::assignTorsionsAroundBond(Zmatrix& zmatrix, int a1, int a2, Frame const& frameIn, Topology const& topIn, Barray const& hasPosition)
+int Builder::AssignTorsionsAroundBond(Zmatrix& zmatrix, int a1, int a2, Frame const& frameIn, Topology const& topIn, Barray const& hasPosition)
 {
   // Save addresses of zmatrix, frame, topology, and hasPosition.
-  // These are required for the createSpXSpX routines.
+  // These are required for the createSpXSpX routines. TODO zero them at the end?
   currentZmatrix_ = &zmatrix;
   currentFrm_ = &frameIn;
   currentTop_ = &topIn;
@@ -1645,7 +1645,7 @@ int Builder::assignTorsionsAroundBond(Zmatrix& zmatrix, int a1, int a2, Frame co
     Hy = H2;
   }
   static const char* hstr[] = { "SP", "SP2", "SP3", "Unknown" };
-  mprintf("DEBUG: assignTorsionsAroundBond: AX= %s (%s)  AY= %s (%s)\n",
+  mprintf("DEBUG: AssignTorsionsAroundBond: AX= %s (%s)  AY= %s (%s)\n",
           topIn.AtomMaskName(ax).c_str(), hstr[Hx],
           topIn.AtomMaskName(ay).c_str(), hstr[Hy]);
   // Check if there is at least one atom on either side of the ax-ay pair
@@ -1668,7 +1668,7 @@ int Builder::assignTorsionsAroundBond(Zmatrix& zmatrix, int a1, int a2, Frame co
   }
 
   if (!axHasKnownAtoms && !ayHasKnownAtoms) {
-    mprinterr("Internal Error: assignTorsionsAroundBond both not known not yet implemented.\n");
+    mprinterr("Internal Error: AssignTorsionsAroundBond both not known not yet implemented.\n");
     return 1;
   } else {
     mprintf("DEBUG: Using externals to fit new torsions around: %s - %s\n",
@@ -1720,7 +1720,7 @@ int Builder::GenerateInternals(Zmatrix& zmatrix, Frame const& frameIn, Topology
   // Loop over bonds
   for (BondArray::const_iterator bnd = bonds.begin(); bnd != bonds.end(); ++bnd)
   {
-    if (assignTorsionsAroundBond( zmatrix, bnd->A1(), bnd->A2(), frameIn, topIn, hasPosition )) {
+    if (AssignTorsionsAroundBond( zmatrix, bnd->A1(), bnd->A2(), frameIn, topIn, hasPosition )) {
       mprinterr("Error Assign torsions around bond %s - %s failed.\n",
                 topIn.AtomMaskName(bnd->A1()).c_str(),
                 topIn.AtomMaskName(bnd->A2()).c_str());
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index eb61bf763b..7a5b72218b 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -31,6 +31,8 @@ class Builder {
 
     /// Generate internal coordinates in the same manner as LEaP
     int GenerateInternals(Zmatrix&, Frame const&, Topology const&, Barray const&);
+    /// Model torsions around a bond in the same manner as LEaP
+    int AssignTorsionsAroundBond(Zmatrix&, int, int, Frame const&, Topology const&, Barray const&);
 
   private:
     typedef std::vector<int> Iarray;
@@ -61,9 +63,7 @@ class Builder {
                            Barray const&, Barray const&,
                            BuildAtom const&, BuildAtom const&) const;
 
-    /// Model torsions around a bond in the same manner as LEaP
-    int assignTorsionsAroundBond(Zmatrix&, int, int, Frame const&, Topology const&, Barray const&);
-
+    /// Create IC for a torsion
     void ModelTorsion(TorsionModel const&, unsigned int, unsigned int, double);
 
     void createSp3Sp3Torsions(TorsionModel const&);

From ad36ceac2ae333a28cb24f478e34288cb3ca3e2b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 3 Feb 2024 19:32:39 -0500
Subject: [PATCH 0439/1492] Fix boolean

---
 src/Structure/Builder.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index d4ab7ac1e3..bafb66fe52 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1667,7 +1667,7 @@ int Builder::AssignTorsionsAroundBond(Zmatrix& zmatrix, int a1, int a2, Frame co
     }
   }
 
-  if (!axHasKnownAtoms && !ayHasKnownAtoms) {
+  if (!(axHasKnownAtoms && ayHasKnownAtoms)) {
     mprinterr("Internal Error: AssignTorsionsAroundBond both not known not yet implemented.\n");
     return 1;
   } else {

From 6e2570c55a09d1380cff3949f2eda90c5cd95791 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 4 Feb 2024 09:50:43 -0500
Subject: [PATCH 0440/1492] Have currentZmatrix be any existing ICs, and
 newZmatrix be ICs that we set

---
 src/Exec_Build.cpp        |  1 +
 src/Structure/Builder.cpp | 14 +++++++++-----
 src/Structure/Builder.h   |  5 +++--
 3 files changed, 13 insertions(+), 7 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 853dd111ab..035e7a2fec 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -416,6 +416,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
               }
               // FIXME DEBUG
               Cpptraj::Structure::Zmatrix tmpz;
+              structureBuilder.SetZmatrix( zmatrix );
               if (structureBuilder.AssignTorsionsAroundBond(tmpz, at, *bat, frameOut, topOut,
                                                             hasPosition))
               {
diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index bafb66fe52..9ebe277f72 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -17,7 +17,11 @@ using namespace Cpptraj::Structure;
 Builder::Builder() :
   debug_(0),
   params_(0),
-  currentZmatrix_(0)
+  currentZmatrix_(0),
+  currentTop_(0),
+  currentFrm_(0),
+  hasPosition_(0),
+  newZmatrix_(0)
 {}
 
 /** Set optional parameter set. */
@@ -30,7 +34,7 @@ void Cpptraj::Structure::Builder::SetParameters(ParameterSet const* paramsIn) {
 }
 
 /** Set optional Zmatrix. */
-void Cpptraj::Structure::Builder::SetZmatrix(Zmatrix* zmatrixIn) {
+void Cpptraj::Structure::Builder::SetZmatrix(Zmatrix const* zmatrixIn) {
   if (zmatrixIn == 0) {
     mprinterr("Internal Error: Builder::SetZmatrix called with null set.\n");
     return;
@@ -1475,8 +1479,8 @@ void Builder::ModelTorsion(TorsionModel const& MT, unsigned int iBondX, unsigned
           currentTop_->LeapName(ax).c_str(),
           currentTop_->LeapName(ay).c_str(),
           currentTop_->LeapName(ad).c_str());
-  currentZmatrix_->AddIC( InternalCoords(aa, ax, ay, ad, l0, t0*Constants::RADDEG, phiVal*Constants::RADDEG) );
-  currentZmatrix_->AddIC( InternalCoords(ad, ay, ax, aa, l1, t1*Constants::RADDEG, phiVal*Constants::RADDEG) );
+  newZmatrix_->AddIC( InternalCoords(aa, ax, ay, ad, l0, t0*Constants::RADDEG, phiVal*Constants::RADDEG) );
+  newZmatrix_->AddIC( InternalCoords(ad, ay, ax, aa, l1, t1*Constants::RADDEG, phiVal*Constants::RADDEG) );
 }
 
 /** Create torsions around SP3-SP3. */
@@ -1593,7 +1597,7 @@ int Builder::AssignTorsionsAroundBond(Zmatrix& zmatrix, int a1, int a2, Frame co
 {
   // Save addresses of zmatrix, frame, topology, and hasPosition.
   // These are required for the createSpXSpX routines. TODO zero them at the end?
-  currentZmatrix_ = &zmatrix;
+  newZmatrix_ = &zmatrix;
   currentFrm_ = &frameIn;
   currentTop_ = &topIn;
   hasPosition_ = &hasPosition;
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index 7a5b72218b..3d31ef6059 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -20,7 +20,7 @@ class Builder {
     /// Set optional parameter set
     void SetParameters(ParameterSet const*);
     /// Set optional Zmatrix with current ICs
-    void SetZmatrix(Zmatrix*);
+    void SetZmatrix(Zmatrix const*);
 
     /// Combine second fragment into first fragment and bond
     int Combine(Topology&, Frame&, Topology const&, Frame const&, int, int) const;
@@ -72,11 +72,12 @@ class Builder {
 
     int debug_;
     ParameterSet const* params_;
-    Zmatrix* currentZmatrix_; ///< Any existing internal coordinates
+    Zmatrix const* currentZmatrix_; ///< Any existing internal coordinates
 
     Topology const* currentTop_; ///< Topology for the createSpXSpXTorsions/ModelTorsion routines
     Frame const* currentFrm_;    ///< Frame for the createSpXSpXTorsions routines
     Barray const* hasPosition_;  ///< Array indicating which atoms have position for createSpXSpXTorsions/ModelTorsion routines
+    Zmatrix* newZmatrix_;        ///< Hold output ICs from AssignTorsionsAroundBond
 };
 }
 }

From 41b318365e18a83a54581ad8ae03114a945e0ee7 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 4 Feb 2024 13:59:16 -0500
Subject: [PATCH 0441/1492] Start code for when not all atoms are known

---
 src/Structure/Builder.cpp | 22 +++++++++++++++++++---
 1 file changed, 19 insertions(+), 3 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 9ebe277f72..453c37dbf8 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1670,11 +1670,27 @@ int Builder::AssignTorsionsAroundBond(Zmatrix& zmatrix, int a1, int a2, Frame co
       break;
     }
   }
-
+  mprintf("bKnownX=%i  bKnownY=%i\n", (int)axHasKnownAtoms, (int)ayHasKnownAtoms);
   if (!(axHasKnownAtoms && ayHasKnownAtoms)) {
-    mprinterr("Internal Error: AssignTorsionsAroundBond both not known not yet implemented.\n");
-    return 1;
+    // Find any existing internal coords around ax-ay
+    std::vector<InternalCoords> iTorsions;
+    if (currentZmatrix_ != 0) {
+      for (Zmatrix::const_iterator it = currentZmatrix_->begin(); it != currentZmatrix_->end(); ++it)
+      {
+        if (it->AtJ() == ax && it->AtK() == ay) {
+          iTorsions.push_back( *it );
+        }
+      }
+    }
+    if (!iTorsions.empty()) {
+      mprintf("Using INTERNALs to fit new torsions around: %s - %s\n",
+              topIn.LeapName(ax).c_str(), topIn.LeapName(ay).c_str());
+    } else {
+      mprintf("Completely free in assigning new torsions for: %s - %s\n",
+              topIn.LeapName(ax).c_str(), topIn.LeapName(ay).c_str());
+    }
   } else {
+    // Use existing atoms to determine torsions
     mprintf("DEBUG: Using externals to fit new torsions around: %s - %s\n",
             topIn.LeapName(ax).c_str(),
             topIn.LeapName(ay).c_str());

From 68682aeeb6733fb8d2a4250d71f181bd4dbe4100 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 5 Feb 2024 10:38:35 -0500
Subject: [PATCH 0442/1492] Hide debug

---
 src/Structure/GenerateConnectivityArrays.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/Structure/GenerateConnectivityArrays.cpp b/src/Structure/GenerateConnectivityArrays.cpp
index 0b7dd8e6c8..60285efc1c 100644
--- a/src/Structure/GenerateConnectivityArrays.cpp
+++ b/src/Structure/GenerateConnectivityArrays.cpp
@@ -37,7 +37,7 @@ BondArray Cpptraj::Structure::GenerateBondArray(std::vector<Residue> const& resi
 {
   BondArray out;
   // BONDS
-  int bidx = 0;
+  //int bidx = 0; // DEBUG
   for (std::vector<Residue>::const_iterator res = residues.begin(); res != residues.end(); ++res)
   {
     int start, end, offset;
@@ -49,7 +49,7 @@ BondArray Cpptraj::Structure::GenerateBondArray(std::vector<Residue> const& resi
       for (Atom::bond_iterator bat = At.bondbegin(); bat != At.bondend(); ++bat)
       {
         if (iat < *bat) {
-          mprintf("DEBUG: BOND  i= %i  %i - %i (%i %i)\n",  bidx++, iat+1, *bat+1, iat*3, *bat*3);
+          //mprintf("DEBUG: BOND  i= %i  %i - %i (%i %i)\n",  bidx++, iat+1, *bat+1, iat*3, *bat*3);
           out.push_back( BondType(iat, *bat, -1) );
         }
         //else

From a3bd8fc24a7224c8d8a4764363942d894354ab24 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 5 Feb 2024 10:39:32 -0500
Subject: [PATCH 0443/1492] Remove wrap360 for now to be consistent with leap
 internally. Start new code for generating the ICs around a linkage

---
 src/Exec_Build.cpp        |  7 ++--
 src/Structure/Builder.cpp | 76 ++++++++++++++++++++++++++++++---------
 src/Structure/Builder.h   | 12 ++++---
 3 files changed, 72 insertions(+), 23 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 035e7a2fec..63bb3e1c96 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -392,7 +392,8 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
     long int ires = it-ResZmatrices.begin();
     Cpptraj::Structure::Zmatrix* zmatrix = *it;
     if (zmatrix != 0) {
-      mprintf("DEBUG: BUILD residue %li %s\n", ires + 1, topOut.TruncResNameOnumId(ires).c_str());
+      mprintf("DEBUG: ***** BUILD residue %li %s *****\n", ires + 1,
+              topOut.TruncResNameOnumId(ires).c_str());
       mprintf("DEBUG: Residue type: %s terminal\n", Cpptraj::Structure::terminalStr(*termType));
       mprintf("DEBUG: Zmatrix for building residue %li %s\n", ires + 1,
               topOut.TruncResNameOnumId(ires).c_str());
@@ -417,8 +418,8 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
               // FIXME DEBUG
               Cpptraj::Structure::Zmatrix tmpz;
               structureBuilder.SetZmatrix( zmatrix );
-              if (structureBuilder.AssignTorsionsAroundBond(tmpz, at, *bat, frameOut, topOut,
-                                                            hasPosition))
+              if (structureBuilder.GenerateInternalsAroundLink(tmpz, at, *bat, frameOut, topOut,
+                                                               hasPosition))
               {
                 mprinterr("Error: Assign torsions around inter-residue bond %s - %s failed.\n",
                           topOut.AtomMaskName(at).c_str(), topOut.AtomMaskName(*bat).c_str());
diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 453c37dbf8..d3f42f84fe 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1423,7 +1423,7 @@ void Builder::ModelTorsion(TorsionModel const& MT, unsigned int iBondX, unsigned
   if (iBondX >= MT.SortedAx().size() ||
       iBondY >= MT.SortedAy().size())
     return;
-
+  mprintf("CALLING ModelTorsion for iBondX=%u iBondY=%u dVal=%g\n",iBondX,iBondY,dvalIn*Constants::RADDEG);
   int aa = MT.SortedAx()[iBondX];
   int ax = MT.AtX();
   int ay = MT.AtY();
@@ -1489,10 +1489,10 @@ void Builder::createSp3Sp3Torsions(TorsionModel const& MT) {
   // the same absolute angle that is measured
   // and twist all the others with it.
   static const double PIOVER3 = Constants::PI / 3.0;
-  double dADOffset = wrap360(MT.Absolute() - Constants::PI);
-  double d180      = wrap360(Constants::PI + dADOffset    );
-  double dm60      = wrap360(-PIOVER3      + dADOffset    );
-  double d60       = wrap360( PIOVER3      + dADOffset    );
+  double dADOffset =         MT.Absolute() - Constants::PI ;
+  double d180      =         Constants::PI + dADOffset     ;
+  double dm60      =         -PIOVER3      + dADOffset     ;
+  double d60       =          PIOVER3      + dADOffset     ;
 
   if ( MT.XOrientation() > 0.0 ) {
     if ( MT.YOrientation() > 0.0 ) {
@@ -1550,12 +1550,12 @@ void Builder::createSp3Sp2Torsions(TorsionModel const& MT) {
   // and twist all the others with it.
   static const double PIOVER3   = Constants::PI / 3.0;
   static const double PIOVER3x2 = PIOVER3 * 2.0;
-  double dADOffset = wrap360(MT.Absolute() - Constants::PI);
-  double   d180    = wrap360(Constants::PI + dADOffset    );
-  double   dm60    = wrap360(-PIOVER3      + dADOffset    );
-  double   d60     = wrap360( PIOVER3      + dADOffset    );
-  double  dm120    = wrap360(-PIOVER3x2    + dADOffset    );
-  double  d120     = wrap360( PIOVER3x2    + dADOffset    );
+  double dADOffset =         MT.Absolute() - Constants::PI ;
+  double   d180    =         Constants::PI + dADOffset     ;
+  double   dm60    =         -PIOVER3      + dADOffset     ;
+  double   d60     =          PIOVER3      + dADOffset     ;
+  double  dm120    =         -PIOVER3x2    + dADOffset     ;
+  double  d120     =          PIOVER3x2    + dADOffset     ;
   double  d0       =                         dADOffset     ;
 
   if ( MT.XOrientation() > 0.0 ) {
@@ -1581,9 +1581,14 @@ void Builder::createSp2Sp2Torsions(TorsionModel const& MT) {
   // First twist the torsion so that the AD torsion has
   // the same absolute angle that is measured
   // and twist all the others with it.
-  double dADOffset = wrap360(MT.Absolute() - Constants::PI);
-  double d180      = wrap360(Constants::PI + dADOffset    );
+  double dADOffset =         MT.Absolute() - Constants::PI ;
+  double d180      =         Constants::PI + dADOffset     ;
   double d0        =                 dADOffset             ;
+  mprintf("In ModelCreateSp2Sp2Torsions, dAbsolute is %g, dADOffset= %g, d180= %g, d0= %g\n",
+          MT.Absolute()*Constants::RADDEG,
+          dADOffset * Constants::RADDEG,
+          d180 * Constants::RADDEG,
+          d0 * Constants::RADDEG);
 
   ModelTorsion( MT, 0, 0, d180 );
   ModelTorsion( MT, 0, 1, d0 );
@@ -1593,7 +1598,7 @@ void Builder::createSp2Sp2Torsions(TorsionModel const& MT) {
 }
 
 /** Assign torsions around bonded atoms in manner similar to LEaP's ModelAssignTorsionsAround. */
-int Builder::AssignTorsionsAroundBond(Zmatrix& zmatrix, int a1, int a2, Frame const& frameIn, Topology const& topIn, Barray const& hasPosition)
+int Builder::assignTorsionsAroundBond(Zmatrix& zmatrix, int a1, int a2, Frame const& frameIn, Topology const& topIn, Barray const& hasPosition)
 {
   // Save addresses of zmatrix, frame, topology, and hasPosition.
   // These are required for the createSpXSpX routines. TODO zero them at the end?
@@ -1649,7 +1654,7 @@ int Builder::AssignTorsionsAroundBond(Zmatrix& zmatrix, int a1, int a2, Frame co
     Hy = H2;
   }
   static const char* hstr[] = { "SP", "SP2", "SP3", "Unknown" };
-  mprintf("DEBUG: AssignTorsionsAroundBond: AX= %s (%s)  AY= %s (%s)\n",
+  mprintf("DEBUG: assignTorsionsAroundBond: AX= %s (%s)  AY= %s (%s)\n",
           topIn.AtomMaskName(ax).c_str(), hstr[Hx],
           topIn.AtomMaskName(ay).c_str(), hstr[Hy]);
   // Check if there is at least one atom on either side of the ax-ay pair
@@ -1685,6 +1690,8 @@ int Builder::AssignTorsionsAroundBond(Zmatrix& zmatrix, int a1, int a2, Frame co
     if (!iTorsions.empty()) {
       mprintf("Using INTERNALs to fit new torsions around: %s - %s\n",
               topIn.LeapName(ax).c_str(), topIn.LeapName(ay).c_str());
+      for (std::vector<InternalCoords>::const_iterator ic = iTorsions.begin(); ic != iTorsions.end(); ++ic)
+        ic->printIC( topIn );
     } else {
       mprintf("Completely free in assigning new torsions for: %s - %s\n",
               topIn.LeapName(ax).c_str(), topIn.LeapName(ay).c_str());
@@ -1740,7 +1747,7 @@ int Builder::GenerateInternals(Zmatrix& zmatrix, Frame const& frameIn, Topology
   // Loop over bonds
   for (BondArray::const_iterator bnd = bonds.begin(); bnd != bonds.end(); ++bnd)
   {
-    if (AssignTorsionsAroundBond( zmatrix, bnd->A1(), bnd->A2(), frameIn, topIn, hasPosition )) {
+    if (assignTorsionsAroundBond( zmatrix, bnd->A1(), bnd->A2(), frameIn, topIn, hasPosition )) {
       mprinterr("Error Assign torsions around bond %s - %s failed.\n",
                 topIn.AtomMaskName(bnd->A1()).c_str(),
                 topIn.AtomMaskName(bnd->A2()).c_str());
@@ -1752,3 +1759,40 @@ int Builder::GenerateInternals(Zmatrix& zmatrix, Frame const& frameIn, Topology
   return 0;
 }
  
+/** Generate internal coordinates around a bond linking two residues
+  * in the same manner as LEaP.
+  * \param zmatrix Hold output ICs
+  * \param at0 Atom in residue we are linking to.
+  * \param at1 Atom in resiude we are linking from.
+  */
+int Builder::GenerateInternalsAroundLink(Zmatrix& zmatrix, int at0, int at1,
+                                         Frame const& frameIn, Topology const& topIn,
+                                         Barray const& hasPosition)
+{
+  mprintf("DEBUG: ----- Entering Builder::GenerateInternalsAroundLink. -----\n");
+  // Sanity check
+  Atom const& A0 = topIn[at0];
+  Atom const& A1 = topIn[at1];
+  if (A0.ResNum() == A1.ResNum()) {
+    mprinterr("Internal Error: Builder::GenerateInternalsAroundLink(): Atoms are in the same residue.\n");
+    return 1;
+  }
+  // Create a temporary has position array marking atoms in at0 residue
+  // (except at0) as unknown.
+  //Residue const& R0 = topIn.Res(A0.ResNum());
+  //Barray tmpHasPosition = hasPosition;
+  //for (int at = R0.FirstAtom(); at != R0.LastAtom(); at++)
+  //{
+  //  if (at != at0)
+  //    tmpHasPosition[at] = false;
+  //}
+  // Create torsions around the link
+  if (assignTorsionsAroundBond( zmatrix, at0, at1, frameIn, topIn, hasPosition )) {
+    mprinterr("Error Assign torsions around link %s - %s failed.\n",
+              topIn.AtomMaskName(at0).c_str(),
+              topIn.AtomMaskName(at1).c_str());
+    return 1;
+  }
+  mprintf("DEBUG: ----- Leaving Builder::GenerateInternalsAroundLink. -----\n");
+  return 0;
+}
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index 3d31ef6059..c8e613d5ef 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -31,8 +31,8 @@ class Builder {
 
     /// Generate internal coordinates in the same manner as LEaP
     int GenerateInternals(Zmatrix&, Frame const&, Topology const&, Barray const&);
-    /// Model torsions around a bond in the same manner as LEaP
-    int AssignTorsionsAroundBond(Zmatrix&, int, int, Frame const&, Topology const&, Barray const&);
+    /// Generate internal coordinates around a link between residues in same manner as LEaP
+    int GenerateInternalsAroundLink(Zmatrix&, int, int, Frame const&, Topology const&, Barray const&);
 
   private:
     typedef std::vector<int> Iarray;
@@ -65,10 +65,14 @@ class Builder {
 
     /// Create IC for a torsion
     void ModelTorsion(TorsionModel const&, unsigned int, unsigned int, double);
-
+    /// Create ICs around SP3-SP3 linkage
     void createSp3Sp3Torsions(TorsionModel const&);
+    /// Create ICs around SP3-SP2 linkage
     void createSp3Sp2Torsions(TorsionModel const&);
+    /// Create ICs around SP2-SP2 linkage
     void createSp2Sp2Torsions(TorsionModel const&);
+    /// Model torsions around a bond in the same manner as LEaP
+    int assignTorsionsAroundBond(Zmatrix&, int, int, Frame const&, Topology const&, Barray const&);
 
     int debug_;
     ParameterSet const* params_;
@@ -77,7 +81,7 @@ class Builder {
     Topology const* currentTop_; ///< Topology for the createSpXSpXTorsions/ModelTorsion routines
     Frame const* currentFrm_;    ///< Frame for the createSpXSpXTorsions routines
     Barray const* hasPosition_;  ///< Array indicating which atoms have position for createSpXSpXTorsions/ModelTorsion routines
-    Zmatrix* newZmatrix_;        ///< Hold output ICs from AssignTorsionsAroundBond
+    Zmatrix* newZmatrix_;        ///< Hold output ICs from assignTorsionsAroundBond
 };
 }
 }

From 8421c7f9e64e79a8fdcf0fa93241d9a48c9d10e0 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 5 Feb 2024 13:34:22 -0500
Subject: [PATCH 0444/1492] New function to generate spanning tree atoms

---
 src/Structure/Builder.cpp                    |  5 +++
 src/Structure/GenerateConnectivityArrays.cpp | 40 ++++++++++++++++++++
 src/Structure/GenerateConnectivityArrays.h   |  2 +
 3 files changed, 47 insertions(+)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index d3f42f84fe..64d65037c3 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1777,6 +1777,11 @@ int Builder::GenerateInternalsAroundLink(Zmatrix& zmatrix, int at0, int at1,
     mprinterr("Internal Error: Builder::GenerateInternalsAroundLink(): Atoms are in the same residue.\n");
     return 1;
   }
+  // Create spanning tree across the link
+  std::vector<int> span_atoms = GenerateSpanningTree(at0, at1, 4, topIn.Atoms());
+  for (std::vector<int>::const_iterator it = span_atoms.begin(); 
+                                        it != span_atoms.end(); ++it)
+    mprintf("SPANNING TREE ATOM: %s\n", topIn.LeapName(*it).c_str());
   // Create a temporary has position array marking atoms in at0 residue
   // (except at0) as unknown.
   //Residue const& R0 = topIn.Res(A0.ResNum());
diff --git a/src/Structure/GenerateConnectivityArrays.cpp b/src/Structure/GenerateConnectivityArrays.cpp
index 60285efc1c..9dada227b4 100644
--- a/src/Structure/GenerateConnectivityArrays.cpp
+++ b/src/Structure/GenerateConnectivityArrays.cpp
@@ -60,6 +60,46 @@ BondArray Cpptraj::Structure::GenerateBondArray(std::vector<Residue> const& resi
   return out;
 }
 
+static inline void visit_tree_atom(std::vector<int>& out,
+                                   int at, int targetDepth, int currentDepth,
+                                   std::vector<bool>& atomSeen,
+                                   std::vector<Atom> const& atoms)
+{
+  if (currentDepth == targetDepth) return;
+  if (!atomSeen[at]) {
+    out.push_back( at );
+    atomSeen[at] = true;
+  }
+  for (Atom::bond_iterator bat = atoms[at].bondbegin();
+                           bat != atoms[at].bondend();
+                         ++bat)
+  {
+    if (!atomSeen[*bat]) {
+      out.push_back( *bat );
+      atomSeen[*bat] = true;
+    }
+  }
+  for (Atom::bond_iterator bat = atoms[at].bondbegin();
+                           bat != atoms[at].bondend();
+                         ++bat)
+  {
+    if (atoms[*bat].Nbonds() > 1)
+      visit_tree_atom(out, *bat, targetDepth, currentDepth+1, atomSeen, atoms);
+  }
+}
+
+std::vector<int> Cpptraj::Structure::GenerateSpanningTree(int at0, int at1, int targetDepth,
+                                                          std::vector<Atom> const& atoms)
+{
+  std::vector<int> out;
+
+  std::vector<bool> atomSeen(atoms.size(), false);
+
+  visit_tree_atom(out, at0, targetDepth, 0, atomSeen, atoms);
+
+  return out;
+}
+
 /** From atom connectiviy, generate an angle array in the same order as LEaP. */ // TODO use in GenerateBAT
 AngleArray Cpptraj::Structure::GenerateAngleArray(std::vector<Residue> const& residues,
                                                   std::vector<Atom> const& atoms)
diff --git a/src/Structure/GenerateConnectivityArrays.h b/src/Structure/GenerateConnectivityArrays.h
index b0bc6f8bc2..9fe70514e7 100644
--- a/src/Structure/GenerateConnectivityArrays.h
+++ b/src/Structure/GenerateConnectivityArrays.h
@@ -14,6 +14,8 @@ enum AtomScanDirectionType { SCAN_ATOMS_BACKWARDS = 0, SCAN_ATOMS_FORWARDS };
 void SetAtomScanDirection(AtomScanDirectionType);
 /// Generate bond array in same order as leap
 BondArray GenerateBondArray(std::vector<Residue> const&, std::vector<Atom> const&);
+/// Generate a spanning tree
+std::vector<int> GenerateSpanningTree(int, int, int, std::vector<Atom> const&);
 /// Generate angle array in same order as leap
 AngleArray GenerateAngleArray(std::vector<Residue> const&, std::vector<Atom> const&);
 /// Generate proper dihedral array in same order as leap

From bc4e6872f7a349caad0f2eaa0ff3378c020e9420 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 5 Feb 2024 14:58:58 -0500
Subject: [PATCH 0445/1492] Start generateAtomInternals

---
 src/Structure/Builder.cpp | 53 ++++++++++++++++++++++++++++++++++++---
 src/Structure/Builder.h   |  3 +++
 2 files changed, 52 insertions(+), 4 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 64d65037c3..b482823218 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1597,6 +1597,20 @@ void Builder::createSp2Sp2Torsions(TorsionModel const& MT) {
   return;
 }
 
+/** Find any existing internal coords around ax-ay. */
+std::vector<InternalCoords> Builder::getExistingInternals(int ax, int ay) const {
+  std::vector<InternalCoords> iTorsions;
+  if (currentZmatrix_ != 0) {
+    for (Zmatrix::const_iterator it = currentZmatrix_->begin(); it != currentZmatrix_->end(); ++it)
+    {
+      if (it->AtJ() == ax && it->AtK() == ay) {
+        iTorsions.push_back( *it );
+      }
+    }
+  }
+  return iTorsions;
+}
+
 /** Assign torsions around bonded atoms in manner similar to LEaP's ModelAssignTorsionsAround. */
 int Builder::assignTorsionsAroundBond(Zmatrix& zmatrix, int a1, int a2, Frame const& frameIn, Topology const& topIn, Barray const& hasPosition)
 {
@@ -1678,15 +1692,15 @@ int Builder::assignTorsionsAroundBond(Zmatrix& zmatrix, int a1, int a2, Frame co
   mprintf("bKnownX=%i  bKnownY=%i\n", (int)axHasKnownAtoms, (int)ayHasKnownAtoms);
   if (!(axHasKnownAtoms && ayHasKnownAtoms)) {
     // Find any existing internal coords around ax-ay
-    std::vector<InternalCoords> iTorsions;
-    if (currentZmatrix_ != 0) {
+    std::vector<InternalCoords> iTorsions = getExistingInternals(ax, ay);
+/*    if (currentZmatrix_ != 0) {
       for (Zmatrix::const_iterator it = currentZmatrix_->begin(); it != currentZmatrix_->end(); ++it)
       {
         if (it->AtJ() == ax && it->AtK() == ay) {
           iTorsions.push_back( *it );
         }
       }
-    }
+    }*/
     if (!iTorsions.empty()) {
       mprintf("Using INTERNALs to fit new torsions around: %s - %s\n",
               topIn.LeapName(ax).c_str(), topIn.LeapName(ay).c_str());
@@ -1758,6 +1772,34 @@ int Builder::GenerateInternals(Zmatrix& zmatrix, Frame const& frameIn, Topology
   mprintf("DEBUG: ----- Leaving Builder::GenerateInternals. ------\n");
   return 0;
 }
+
+/** Build internal coordinates around an atom. */
+int Builder::generateAtomInternals(int at, Frame const& frameIn, Topology const& topIn, Barray const& hasPosition)
+{
+  mprintf( "Building internals for: %s\n", topIn.LeapName(at).c_str());
+  Atom const& AtA = topIn[at];
+  for (Atom::bond_iterator bat = AtA.bondbegin(); bat != AtA.bondend(); ++bat) {
+    Atom const& AtB = topIn[*bat];
+    for (Atom::bond_iterator cat = AtB.bondbegin(); cat != AtB.bondend(); ++cat) {
+      if (*cat != at) {
+        Atom const& AtC = topIn[*cat];
+        mprintf("Building torsion INTERNALs for: %s  around: %s - %s\n",
+               topIn.LeapName(at).c_str(),
+               topIn.LeapName(*bat).c_str(),
+               topIn.LeapName(*cat).c_str());
+        std::vector<InternalCoords> iTorsions = getExistingInternals(*bat, *cat);
+        int iShouldBe = (AtB.Nbonds() - 1) * (AtC.Nbonds() - 1);
+        mprintf("ISHOULDBE= %i ITORSIONS= %zu\n", iShouldBe, iTorsions.size());
+        if (iShouldBe != (int)iTorsions.size()) {
+          Zmatrix tmpz; // FIXME
+          assignTorsionsAroundBond(tmpz, *bat, *cat, frameIn, topIn, hasPosition);
+        }
+      }
+    }
+  }
+
+  return 0;
+}
  
 /** Generate internal coordinates around a bond linking two residues
   * in the same manner as LEaP.
@@ -1781,7 +1823,10 @@ int Builder::GenerateInternalsAroundLink(Zmatrix& zmatrix, int at0, int at1,
   std::vector<int> span_atoms = GenerateSpanningTree(at0, at1, 4, topIn.Atoms());
   for (std::vector<int>::const_iterator it = span_atoms.begin(); 
                                         it != span_atoms.end(); ++it)
-    mprintf("SPANNING TREE ATOM: %s\n", topIn.LeapName(*it).c_str());
+  {
+    //mprintf("SPANNING TREE ATOM: %s\n", topIn.LeapName(*it).c_str());
+    generateAtomInternals(*it, frameIn, topIn, hasPosition);
+  }
   // Create a temporary has position array marking atoms in at0 residue
   // (except at0) as unknown.
   //Residue const& R0 = topIn.Res(A0.ResNum());
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index c8e613d5ef..1a794a4145 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -74,6 +74,9 @@ class Builder {
     /// Model torsions around a bond in the same manner as LEaP
     int assignTorsionsAroundBond(Zmatrix&, int, int, Frame const&, Topology const&, Barray const&);
 
+    std::vector<InternalCoords> getExistingInternals(int, int) const;
+    int generateAtomInternals(int, Frame const&, Topology const&, Barray const&);
+
     int debug_;
     ParameterSet const* params_;
     Zmatrix const* currentZmatrix_; ///< Any existing internal coordinates

From a968de5e2b1bcd89c459cf6387b783a3135bdd63 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 5 Feb 2024 15:21:20 -0500
Subject: [PATCH 0446/1492] Save residue bonding atoms

---
 src/Exec_Build.cpp | 19 ++++++++++++++++---
 1 file changed, 16 insertions(+), 3 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 63bb3e1c96..0c6a7c8c6c 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -198,6 +198,10 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
   structureBuilder.SetDebug( 1 );
   structureBuilder.SetParameters( &mainParmSet );
 
+  // For holding bonded atom pairs
+  typedef std::pair<int,int> Ipair;
+  typedef std::vector<Ipair> IParray;
+
   // Loop for setting up atoms in the topology from residues or residue templates.
   int nRefAtomsMissing = 0;
   for (int ires = 0; ires != topIn.Nres(); ires++)
@@ -207,9 +211,6 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
     mprintf("DEBUG: atom offset is %i\n", atomOffset);
     Residue const& currentRes = topIn.Res(ires);
     DataSet_Coords* resTemplate = ResTemplates[ires];
-    // For holding bonded atom pairs
-    typedef std::pair<int,int> Ipair;
-    typedef std::vector<Ipair> IParray;
     IParray intraResBonds;
     if (resTemplate == 0) {
       // ----- No template. Just add the atoms. ------------
@@ -339,6 +340,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
 
   // -----------------------------------
   // Add inter-residue bonds
+  std::vector<IParray> resBondingAtoms(topOut.Nres());
   for (ResAtArray::const_iterator it = interResBonds.begin(); it != interResBonds.end(); ++it)
   {
     ResAtPair const& ra0 = *it;
@@ -358,6 +360,17 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
       return 1;
     }
     topOut.AddBond(at0, at1);
+    // Save bonding atoms
+    resBondingAtoms[ra0.first].push_back( Ipair(at0, at1) );
+    resBondingAtoms[ra1.first].push_back( Ipair(at1, at0) );
+  }
+  // DEBUG print residue bonding atoms
+  for (std::vector<IParray>::const_iterator rit = resBondingAtoms.begin();
+                                            rit != resBondingAtoms.end(); ++rit)
+  {
+    mprintf("\tResidue %s bonding atoms.\n", topOut.TruncResNameNum(rit-resBondingAtoms.begin()).c_str());
+    for (IParray::const_iterator it = rit->begin(); it != rit->end(); ++it)
+      mprintf("\t\t%s - %s\n", topOut.AtomMaskName(it->first).c_str(), topOut.AtomMaskName(it->second).c_str());
   }
 
   // -----------------------------------

From b10a5d91307f4f91f70c6b302dfa36caaf5975de Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 5 Feb 2024 15:38:51 -0500
Subject: [PATCH 0447/1492] Start using resBondedAtoms

---
 src/Exec_Build.cpp | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 0c6a7c8c6c..7851bf4689 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -399,7 +399,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
   linkBuilder.SetDebug( 1 ); // FIXME
   linkBuilder.SetParameters( &mainParmSet );
   bool buildFailed = false;
-  TermTypeArray::const_iterator termType = ResTypes.begin();
+  TermTypeArray::const_iterator termType = ResTypes.begin(); // FIXME is termType needed?
   for (Zarray::const_iterator it = ResZmatrices.begin(); it != ResZmatrices.end(); ++it, ++termType)
   {
     long int ires = it-ResZmatrices.begin();
@@ -413,6 +413,15 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
       zmatrix->print(&topOut);
       linkBuilder.SetZmatrix( zmatrix );
       // Is this residue connected to an earlier residue?
+      for (IParray::const_iterator resBonds = resBondingAtoms[ires].begin();
+                                   resBonds != resBondingAtoms[ires].end(); ++resBonds)
+      {
+        if (resBonds->second < resBonds->first) {
+          mprintf("\t\tResidue connection: %s - %s\n",
+                  topOut.AtomMaskName(resBonds->first).c_str(),
+                  topOut.AtomMaskName(resBonds->second).c_str());
+        }
+      }
       if ( *termType != Cpptraj::Structure::BEG_TERMINAL ) {
         for (int at = topOut.Res(ires).FirstAtom(); at != topOut.Res(ires).LastAtom(); ++at)
         {

From 91d611271e808aa27bb130af363be1761a647c79 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 6 Feb 2024 08:55:33 -0500
Subject: [PATCH 0448/1492] Start creating inter-residue links like leap.

---
 src/Exec_Build.cpp        | 28 +++++++++++++++------------
 src/Structure/Builder.cpp | 40 +++++++++++++++++++++------------------
 2 files changed, 38 insertions(+), 30 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 7851bf4689..b2ed9419aa 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -359,7 +359,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
       mprinterr("Error: Atom %s not found in residue %i\n", *(ra1.second), ra1.first);
       return 1;
     }
-    topOut.AddBond(at0, at1);
+    //topOut.AddBond(at0, at1);
     // Save bonding atoms
     resBondingAtoms[ra0.first].push_back( Ipair(at0, at1) );
     resBondingAtoms[ra1.first].push_back( Ipair(at1, at0) );
@@ -420,8 +420,21 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
           mprintf("\t\tResidue connection: %s - %s\n",
                   topOut.AtomMaskName(resBonds->first).c_str(),
                   topOut.AtomMaskName(resBonds->second).c_str());
+          topOut.AddBond(resBonds->first, resBonds->second);
+          // FIXME DEBUG
+          structureBuilder.SetZmatrix( zmatrix );
+          if (structureBuilder.GenerateInternalsAroundLink(*zmatrix, resBonds->first, resBonds->second,
+                                                           frameOut, topOut, hasPosition))
+          {
+            mprinterr("Error: Assign torsions around inter-residue link %s - %s failed.\n",
+                      topOut.AtomMaskName(resBonds->first).c_str(),
+                      topOut.AtomMaskName(resBonds->second).c_str());
+            return 1;
+          }
+          //tmpz.print(&topOut);
         }
       }
+/*
       if ( *termType != Cpptraj::Structure::BEG_TERMINAL ) {
         for (int at = topOut.Res(ires).FirstAtom(); at != topOut.Res(ires).LastAtom(); ++at)
         {
@@ -437,21 +450,12 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
                           topOut.AtomMaskName(at).c_str(), topOut.AtomMaskName(*bat).c_str());
                 return 1;
               }
-              // FIXME DEBUG
-              Cpptraj::Structure::Zmatrix tmpz;
-              structureBuilder.SetZmatrix( zmatrix );
-              if (structureBuilder.GenerateInternalsAroundLink(tmpz, at, *bat, frameOut, topOut,
-                                                               hasPosition))
-              {
-                mprinterr("Error: Assign torsions around inter-residue bond %s - %s failed.\n",
-                          topOut.AtomMaskName(at).c_str(), topOut.AtomMaskName(*bat).c_str());
-                return 1;
-              }
-              tmpz.print(&topOut);
+              
             }
           }
         }
       }
+*/
       // TEST FIXME
 //      Cpptraj::Structure::Zmatrix testZ;
 //      if (testZ.BuildZmatrixFromTop(frameOut, topOut, ires, mainParmSet.AT(), hasPosition)) {
diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index b482823218..862a741acb 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1804,7 +1804,7 @@ int Builder::generateAtomInternals(int at, Frame const& frameIn, Topology const&
 /** Generate internal coordinates around a bond linking two residues
   * in the same manner as LEaP.
   * \param zmatrix Hold output ICs
-  * \param at0 Atom in residue we are linking to.
+  * \param at0 Atom in residue we are linking to (i.e. the current residue).
   * \param at1 Atom in resiude we are linking from.
   */
 int Builder::GenerateInternalsAroundLink(Zmatrix& zmatrix, int at0, int at1,
@@ -1819,30 +1819,34 @@ int Builder::GenerateInternalsAroundLink(Zmatrix& zmatrix, int at0, int at1,
     mprinterr("Internal Error: Builder::GenerateInternalsAroundLink(): Atoms are in the same residue.\n");
     return 1;
   }
+  // In order to mimic the way LEaP does things, mark all atoms before
+  // this residue as having position, the first known atom of this residue
+  // has having position, and all other atoms as not having position.
+  Residue const& R0 = topIn.Res(A0.ResNum());
+  Barray tmpHasPosition( topIn.Natom(), false );
+  for (int at = 0; at < R0.FirstAtom(); at++)
+    tmpHasPosition[at] = true;
+  for (int at = R0.FirstAtom(); at != R0.LastAtom(); at++) {
+    if (hasPosition[at]) {
+      tmpHasPosition[at] = true;
+      break;
+    }
+  }
   // Create spanning tree across the link
   std::vector<int> span_atoms = GenerateSpanningTree(at0, at1, 4, topIn.Atoms());
   for (std::vector<int>::const_iterator it = span_atoms.begin(); 
                                         it != span_atoms.end(); ++it)
   {
     //mprintf("SPANNING TREE ATOM: %s\n", topIn.LeapName(*it).c_str());
-    generateAtomInternals(*it, frameIn, topIn, hasPosition);
-  }
-  // Create a temporary has position array marking atoms in at0 residue
-  // (except at0) as unknown.
-  //Residue const& R0 = topIn.Res(A0.ResNum());
-  //Barray tmpHasPosition = hasPosition;
-  //for (int at = R0.FirstAtom(); at != R0.LastAtom(); at++)
-  //{
-  //  if (at != at0)
-  //    tmpHasPosition[at] = false;
-  //}
-  // Create torsions around the link
-  if (assignTorsionsAroundBond( zmatrix, at0, at1, frameIn, topIn, hasPosition )) {
-    mprinterr("Error Assign torsions around link %s - %s failed.\n",
-              topIn.AtomMaskName(at0).c_str(),
-              topIn.AtomMaskName(at1).c_str());
-    return 1;
+    generateAtomInternals(*it, frameIn, topIn, tmpHasPosition);
   }
+  // Create torsions around the link
+  //if (assignTorsionsAroundBond( zmatrix, at0, at1, frameIn, topIn, hasPosition )) {
+  //  mprinterr("Error Assign torsions around link %s - %s failed.\n",
+  //            topIn.AtomMaskName(at0).c_str(),
+  //            topIn.AtomMaskName(at1).c_str());
+  //  return 1;
+  //}
   mprintf("DEBUG: ----- Leaving Builder::GenerateInternalsAroundLink. -----\n");
   return 0;
 }

From 3391916f0bac47952d33f5f256bd5c86e1b1e991 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 6 Feb 2024 09:21:30 -0500
Subject: [PATCH 0449/1492] Start building mock coords

---
 src/Structure/Builder.cpp | 29 ++++++++++++++++++++++++++++-
 src/Structure/Builder.h   |  5 ++++-
 2 files changed, 32 insertions(+), 2 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 862a741acb..a237b9f873 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1208,6 +1208,8 @@ class Cpptraj::Structure::Builder::TorsionModel {
   public:
     /// CONSTRUCTOR
     TorsionModel() : ax_(-1), ay_(-1), dAbsolute_(0), Xorientation_(0), Yorientation_(0) {}
+    /// CONSTRUCTOR - AX and AY atom indices
+    TorsionModel(int ax, int ay) : ax_(ax), ay_(ay),  dAbsolute_(0), Xorientation_(0), Yorientation_(0) {}
     /// Set up torsions around bonded atoms
     int SetupTorsion(int, int, AtomType::HybridizationType, AtomType::HybridizationType,
                      Frame const&, Topology const&, std::vector<bool> const&);
@@ -1611,6 +1613,22 @@ std::vector<InternalCoords> Builder::getExistingInternals(int ax, int ay) const
   return iTorsions;
 }
 
+/** Build mock external coordinates around the given torsion using 
+  * the given internal coordinates.
+  */
+int Builder::buildMockExternals(TorsionModel& mT, std::vector<InternalCoords> const& iaTorsions)
+const
+{
+  if (iaTorsions.empty()) {
+    mprinterr("Internal Error: Builder::buildMockExternals() called with no internal torsions.\n");
+    return 1;
+  }
+  InternalCoords const& iInt = iaTorsions.front();
+  mprintf("=======  Started mock coords from: %s\n", currentTop_->LeapName(iInt.AtI()).c_str());
+
+  return 0;
+}
+
 /** Assign torsions around bonded atoms in manner similar to LEaP's ModelAssignTorsionsAround. */
 int Builder::assignTorsionsAroundBond(Zmatrix& zmatrix, int a1, int a2, Frame const& frameIn, Topology const& topIn, Barray const& hasPosition)
 {
@@ -1706,6 +1724,12 @@ int Builder::assignTorsionsAroundBond(Zmatrix& zmatrix, int a1, int a2, Frame co
               topIn.LeapName(ax).c_str(), topIn.LeapName(ay).c_str());
       for (std::vector<InternalCoords>::const_iterator ic = iTorsions.begin(); ic != iTorsions.end(); ++ic)
         ic->printIC( topIn );
+      TorsionModel mT(ax, ay);
+      if (buildMockExternals(mT, iTorsions)) {
+        mprinterr("Error: Building mock externals around %s - %s failed.\n",
+                  topIn.AtomMaskName(ax).c_str(), topIn.AtomMaskName(ay).c_str());
+        return 1;
+      }
     } else {
       mprintf("Completely free in assigning new torsions for: %s - %s\n",
               topIn.LeapName(ax).c_str(), topIn.LeapName(ay).c_str());
@@ -1838,7 +1862,10 @@ int Builder::GenerateInternalsAroundLink(Zmatrix& zmatrix, int at0, int at1,
                                         it != span_atoms.end(); ++it)
   {
     //mprintf("SPANNING TREE ATOM: %s\n", topIn.LeapName(*it).c_str());
-    generateAtomInternals(*it, frameIn, topIn, tmpHasPosition);
+    if (generateAtomInternals(*it, frameIn, topIn, tmpHasPosition)) {
+      mprinterr("Error: Could not generate internals for atom %s\n", topIn.AtomMaskName(*it).c_str());
+      return 1;
+    }
   }
   // Create torsions around the link
   //if (assignTorsionsAroundBond( zmatrix, at0, at1, frameIn, topIn, hasPosition )) {
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index 1a794a4145..8897d5f6f4 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -73,8 +73,11 @@ class Builder {
     void createSp2Sp2Torsions(TorsionModel const&);
     /// Model torsions around a bond in the same manner as LEaP
     int assignTorsionsAroundBond(Zmatrix&, int, int, Frame const&, Topology const&, Barray const&);
-
+    /// Get any existing internal coords from currentZmatrix around specified atoms
     std::vector<InternalCoords> getExistingInternals(int, int) const;
+    /// Build mock coordinates around given torsion
+    int buildMockExternals(TorsionModel& MT, std::vector<InternalCoords> const& iaTorsions) const;
+    /// Generate internal coords for a given atom
     int generateAtomInternals(int, Frame const&, Topology const&, Barray const&);
 
     int debug_;

From 6073c9559677dac0a3a50fc4e1951ef57e9ecbc3 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 6 Feb 2024 11:28:49 -0500
Subject: [PATCH 0450/1492] Finish up initial code for building mock externals

---
 src/Structure/Builder.cpp | 142 ++++++++++++++++++++++++++++++++++----
 src/Structure/Zmatrix.cpp |  35 +++++++---
 src/Structure/Zmatrix.h   |   3 +-
 3 files changed, 159 insertions(+), 21 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index a237b9f873..59d9d36ec1 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1613,8 +1613,38 @@ std::vector<InternalCoords> Builder::getExistingInternals(int ax, int ay) const
   return iTorsions;
 }
 
+/// Used to track atoms for mock externals
+class MockAtom {
+  public:
+    /// CONSTRUCTOR - index, position
+    MockAtom(int idx, Vec3 const& pos) : idx_(idx), pos_(pos), known_(true) {}
+    /// CONSTRUCTOR - index, unknown position
+    MockAtom(int idx) : idx_(idx), pos_(0.0), known_(false) {}
+    /// Set position
+    void SetPos(Vec3 const& p) { pos_ = p; known_ = true; }
+
+    int Idx() const { return idx_; }
+    Vec3 const& Pos() const { return pos_; }
+    bool Known() const { return known_; }
+  private:
+    int idx_; ///< Atom index
+    Vec3 pos_; ///< Atom mock position
+    bool known_; ///< True if atom position is known
+};
+
+/// Used to find mock atom
+static inline std::vector<MockAtom>::iterator find_mock_atom(std::vector<MockAtom>& outerAtoms, int idx)
+{
+  std::vector<MockAtom>::iterator it = outerAtoms.begin();
+  for (; it != outerAtoms.end(); ++it)
+    if (it->Idx() == idx) return it;
+  return outerAtoms.end();
+}
+
 /** Build mock external coordinates around the given torsion using 
   * the given internal coordinates.
+  * By definition, the two central atoms will be the same for each
+  * IC in iaTorsions.
   */
 int Builder::buildMockExternals(TorsionModel& mT, std::vector<InternalCoords> const& iaTorsions)
 const
@@ -1623,8 +1653,104 @@ const
     mprinterr("Internal Error: Builder::buildMockExternals() called with no internal torsions.\n");
     return 1;
   }
-  InternalCoords const& iInt = iaTorsions.front();
-  mprintf("=======  Started mock coords from: %s\n", currentTop_->LeapName(iInt.AtI()).c_str());
+  mprintf("=======  Started mock coords from: %s\n", currentTop_->LeapName(iaTorsions.front().AtI()).c_str());
+
+  for (std::vector<InternalCoords>::const_iterator ic = iaTorsions.begin();
+                                                   ic != iaTorsions.end(); ++ic)
+    mprintf("------- Known torsion: %s - %s - %s - %s  %f\n",
+            currentTop_->LeapName(ic->AtI()).c_str(),
+            currentTop_->LeapName(ic->AtJ()).c_str(),
+            currentTop_->LeapName(ic->AtK()).c_str(),
+            currentTop_->LeapName(ic->AtL()).c_str(),
+            ic->Phi());
+
+  // Define coordinates for the central atoms.
+  Vec3 posX(0, 0, 0);
+  Vec3 posY(1, 0, 0);
+
+  // Hold info on X-Y outer atoms
+  typedef std::vector<MockAtom> Marray;
+  Marray outerAtoms;
+
+  // Define outer atoms
+  for (std::vector<InternalCoords>::const_iterator ic = iaTorsions.begin();
+                                                   ic != iaTorsions.end(); ++ic)
+  {
+    if (ic == iaTorsions.begin()) {
+      // Define first outer atom as being in the XY plane
+      outerAtoms.push_back( MockAtom(ic->AtI(), Vec3(1, 1, 0)) );
+    } else {
+      Marray::iterator mi = find_mock_atom( outerAtoms, ic->AtI() );
+      if (mi == outerAtoms.end())
+        outerAtoms.push_back( MockAtom(ic->AtI()) );
+    }
+    Marray::iterator ml = find_mock_atom( outerAtoms, ic->AtL() );
+    if (ml == outerAtoms.end())
+      outerAtoms.push_back( MockAtom(ic->AtL()) );
+  }
+  mprintf("DEBUG: Outer atoms:\n");
+  for (Marray::const_iterator it = outerAtoms.begin(); it != outerAtoms.end(); ++it)
+    mprintf("DEBUG:\t\t%i %4s (%i) {%f %f %f}\n", it->Idx()+1, currentTop_->AtomMaskName(it->Idx()).c_str(),
+            (int)it->Known(), it->Pos()[0], it->Pos()[1], it->Pos()[2]);
+
+  // Loop through the known torsions looking for those that
+  // have one position defined, then build coords for the
+  // other atom and mark the torsion as used.
+  std::vector<bool> used( iaTorsions.size(), false );
+  unsigned int nused = 0;
+  for (unsigned int idx = 0; idx != iaTorsions.size(); idx++) {
+    //bool gotOne = false;
+    for (unsigned int jdx = 0; jdx != iaTorsions.size(); jdx++) {
+      if (!used[jdx]) {
+        InternalCoords const& iInt = iaTorsions[jdx];
+        Marray::iterator tmpAt1 = find_mock_atom(outerAtoms, iInt.AtI());
+        Marray::iterator tmpAt4 = find_mock_atom(outerAtoms, iInt.AtL());
+        if (tmpAt1 == outerAtoms.end()) {
+          mprinterr("Internal Error: Builder::buildMockExternals(): Outer atom I %i not found.\n", iInt.AtI()+1);
+          return 1;
+        }
+        if (tmpAt4 == outerAtoms.end()) {
+          mprinterr("Internal Error: Builder::buildMockExternals(): Outer atom L %i not found.\n", iInt.AtL()+1);
+          return 1;
+        }
+        Vec3 maPC1, maPC2;
+        Marray::iterator tgt = outerAtoms.end();
+        Marray::iterator knownAt = outerAtoms.end();
+        if (tmpAt4->Known()) {
+          tgt     = tmpAt1;
+          maPC1   = posX;
+          maPC2   = posY;
+          knownAt = tmpAt4;
+        } else if (tmpAt1->Known()) {
+          //gotOne = true; // FIXME needed?
+          tgt     = tmpAt4;
+          maPC1   = posY;
+          maPC2   = posX;
+          knownAt = tmpAt1;
+        }
+        if (tgt != outerAtoms.end()) {
+          //gotOne = true;
+          mprintf("======= Building mock coord for: %s\n", currentTop_->LeapName(tgt->Idx()).c_str());
+          mprintf("======= Using torsion: %s - %s - %s - %s (p1known= %i, p4known= %i)\n",
+                   currentTop_->LeapName(iInt.AtI()).c_str(),
+                   currentTop_->LeapName(iInt.AtJ()).c_str(),
+                   currentTop_->LeapName(iInt.AtK()).c_str(),
+                   currentTop_->LeapName(iInt.AtL()).c_str(),
+                   (int)tmpAt1->Known(), (int)tmpAt4->Known());
+          // Now build the coordinate for the target atom
+          tgt->SetPos( Zmatrix::AtomIposition(maPC1, maPC2, knownAt->Pos(), 1.0, 90.0, iInt.Phi()) );
+          mprintf("ZMatrixAll:  %f,%f,%f\n", tgt->Pos()[0], tgt->Pos()[1], tgt->Pos()[2]);
+          used[jdx] = true;
+          nused++;
+          break;
+        }
+      } // END IC not yet used
+    } // END inner loop over ICs
+  } // END outer loop over ICs
+  if (nused < used.size()) {
+    mprinterr("Error: There are %u torsions left over for mock coords.\n", used.size() - nused);
+    return 1;
+  }
 
   return 0;
 }
@@ -1711,19 +1837,11 @@ int Builder::assignTorsionsAroundBond(Zmatrix& zmatrix, int a1, int a2, Frame co
   if (!(axHasKnownAtoms && ayHasKnownAtoms)) {
     // Find any existing internal coords around ax-ay
     std::vector<InternalCoords> iTorsions = getExistingInternals(ax, ay);
-/*    if (currentZmatrix_ != 0) {
-      for (Zmatrix::const_iterator it = currentZmatrix_->begin(); it != currentZmatrix_->end(); ++it)
-      {
-        if (it->AtJ() == ax && it->AtK() == ay) {
-          iTorsions.push_back( *it );
-        }
-      }
-    }*/
     if (!iTorsions.empty()) {
       mprintf("Using INTERNALs to fit new torsions around: %s - %s\n",
               topIn.LeapName(ax).c_str(), topIn.LeapName(ay).c_str());
-      for (std::vector<InternalCoords>::const_iterator ic = iTorsions.begin(); ic != iTorsions.end(); ++ic)
-        ic->printIC( topIn );
+      //for (std::vector<InternalCoords>::const_iterator ic = iTorsions.begin(); ic != iTorsions.end(); ++ic)
+      //  ic->printIC( topIn );
       TorsionModel mT(ax, ay);
       if (buildMockExternals(mT, iTorsions)) {
         mprinterr("Error: Building mock externals around %s - %s failed.\n",
diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index 89dbbda772..15aba9eb12 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -886,12 +886,16 @@ int Zmatrix::SetFromFrame(Frame const& frameIn, Topology const& topIn, int molnu
 }
 
 // -----------------------------------------------------------------------------
-/** \return Position of atom I from given internal coordinate. */
-Vec3 Zmatrix::AtomIposition(InternalCoords const& ic, Frame const& frameOut)
+/** \return Position of atom I from positions of atoms J, K, and L,
+  *         and corresponding distance (in Ang) and angle/torsion
+  *         values (in degrees).
+  */
+Vec3 Zmatrix::AtomIposition(Vec3 const& posJ, Vec3 const& posK, Vec3 const& posL,
+                            double rdist, double theta, double phi)
 {
-    double rdist = ic.Dist();
-    double theta = ic.Theta();
-    double phi   = ic.Phi();
+//    double rdist = ic.Dist();
+//    double theta = ic.Theta();
+//    double phi   = ic.Phi();
 
     double sinTheta = sin(theta * Constants::DEGRAD);
     double cosTheta = cos(theta * Constants::DEGRAD);
@@ -903,9 +907,9 @@ Vec3 Zmatrix::AtomIposition(InternalCoords const& ic, Frame const& frameOut)
                 rdist * cosPhi * sinTheta,
                 rdist * sinPhi * sinTheta );
 
-    Vec3 posL = Vec3( frameOut.XYZ( ic.AtL()) );
-    Vec3 posK = Vec3( frameOut.XYZ( ic.AtK()) );
-    Vec3 posJ = Vec3( frameOut.XYZ( ic.AtJ()) );
+//    Vec3 posL = Vec3( frameOut.XYZ( ic.AtL()) );
+//    Vec3 posK = Vec3( frameOut.XYZ( ic.AtK()) );
+//    Vec3 posJ = Vec3( frameOut.XYZ( ic.AtJ()) );
 
     Vec3 LK = posK - posL;
     Vec3 KJ = posJ - posK;
@@ -923,6 +927,21 @@ Vec3 Zmatrix::AtomIposition(InternalCoords const& ic, Frame const& frameOut)
   return posI;
 }
 
+/** \return Position of atom I from given internal coordinate and Frame. */
+Vec3 Zmatrix::AtomIposition(InternalCoords const& ic, Frame const& frameOut)
+{
+    double rdist = ic.Dist();
+    double theta = ic.Theta();
+    double phi   = ic.Phi();
+
+    Vec3 posJ = Vec3( frameOut.XYZ( ic.AtJ()) );
+    Vec3 posK = Vec3( frameOut.XYZ( ic.AtK()) );
+    Vec3 posL = Vec3( frameOut.XYZ( ic.AtL()) );
+
+    return AtomIposition(posJ, posK, posL, rdist, theta, phi);
+}
+
+
 /** Set Cartesian coordinates in Frame from internal coordinates.
   * Assume none of the positions in frameOut can be used initially.
   */
diff --git a/src/Structure/Zmatrix.h b/src/Structure/Zmatrix.h
index a727b771f0..9c9b627f71 100644
--- a/src/Structure/Zmatrix.h
+++ b/src/Structure/Zmatrix.h
@@ -73,7 +73,8 @@ class Zmatrix {
     unsigned int sizeInBytes() const { return (7*sizeof(int)) +
                                               (9*sizeof(double)) + // 3 Vec3
                                               (IC_.size() * InternalCoords::sizeInBytes()); }
-
+    /// \return XYZ position of atom I using positions of atoms J/K/L and distance/angle/torsion (deg)
+    static Vec3 AtomIposition(Vec3 const&, Vec3 const&, Vec3 const&, double, double, double);
     /// \return XYZ position of atom I for given internal coordinate
     static Vec3 AtomIposition(InternalCoords const&, Frame const&);
   private:

From 9acf1a0559801283a7b0c194df6a6b1431bad10a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 6 Feb 2024 15:19:01 -0500
Subject: [PATCH 0451/1492] Start reworking the model routines so that all the
 information needed is in TorsionModel

---
 src/Structure/Builder.cpp | 628 +++++++++++++++++++++-----------------
 1 file changed, 349 insertions(+), 279 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 59d9d36ec1..42110cd58c 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1203,16 +1203,51 @@ const
 }
 
 // ------------------------------------------------------------------------------
+/// Used to track atoms for mock externals
+class MockAtom {
+  public:
+    /// CONSTRUCTOR
+    MockAtom() : idx_(-1), pos_(0.0), known_(false) {}
+    /// CONSTRUCTOR - index, position
+    MockAtom(int idx, Vec3 const& pos) : idx_(idx), pos_(pos), known_(true) {}
+    /// CONSTRUCTOR - index, unknown position
+    MockAtom(int idx) : idx_(idx), pos_(0.0), known_(false) {}
+    /// Set position
+    void SetPos(Vec3 const& p) { pos_ = p; known_ = true; }
+
+    int Idx()         const { return idx_; }
+    Vec3 const& Pos() const { return pos_; }
+    bool Known()      const { return known_; }
+  private:
+    int idx_;    ///< Atom index
+    Vec3 pos_;   ///< Atom position
+    bool known_; ///< True if atom position is known
+};
+
+/// Used to find mock atom
+static inline std::vector<MockAtom>::iterator find_mock_atom(std::vector<MockAtom>& outerAtoms, int idx)
+{
+  std::vector<MockAtom>::iterator it = outerAtoms.begin();
+  for (; it != outerAtoms.end(); ++it)
+    if (it->Idx() == idx) return it;
+  return outerAtoms.end();
+}
+
+// -----------------------------------------------
 /** Store info for modelling torsions around X-Y */
 class Cpptraj::Structure::Builder::TorsionModel {
   public:
+    typedef std::vector<MockAtom> Marray;
     /// CONSTRUCTOR
-    TorsionModel() : ax_(-1), ay_(-1), dAbsolute_(0), Xorientation_(0), Yorientation_(0) {}
+    TorsionModel() : dAbsolute_(0), Xorientation_(0), Yorientation_(0), axHasKnownAtoms_(false), ayHasKnownAtoms_(false) {}
     /// CONSTRUCTOR - AX and AY atom indices
-    TorsionModel(int ax, int ay) : ax_(ax), ay_(ay),  dAbsolute_(0), Xorientation_(0), Yorientation_(0) {}
+    //TorsionModel(int ax, int ay) : ax_(ax), ay_(ay),  dAbsolute_(0), Xorientation_(0), Yorientation_(0) {}
+    /// Initialize torsions around bonded atoms
+    int InitTorsion(int, int, Frame const&, Topology const&, std::vector<bool> const&);
     /// Set up torsions around bonded atoms
-    int SetupTorsion(int, int, AtomType::HybridizationType, AtomType::HybridizationType,
-                     Frame const&, Topology const&, std::vector<bool> const&);
+    int SetupTorsion(AtomType::HybridizationType, AtomType::HybridizationType, Topology const& topIn);
+    /// Build mock externals from given internals
+    int BuildMockExternals(std::vector<InternalCoords> const&, Topology const&);
 
     /// \return Value of A-X-Y-D torsion in radians
     double Absolute() const { return dAbsolute_; }
@@ -1221,27 +1256,32 @@ class Cpptraj::Structure::Builder::TorsionModel {
     /// \return Value of orientation around Y
     double YOrientation() const { return Yorientation_; }
     /// \return Sorted atoms bonded to X excluding Y
-    std::vector<int> const& SortedAx() const { return sorted_ax_; }
+    Marray const& SortedAx() const { return sorted_ax_; }
     /// \return Sorted atoms bonded to Y excluding X
-    std::vector<int> const& SortedAy() const { return sorted_ay_; }
-    /// \return Index of atom X
-    int AtX() const { return ax_; }
-    /// \return Index of atom Y
-    int AtY() const { return ay_; }
+    Marray const& SortedAy() const { return sorted_ay_; }
+    /// \return Atom X
+    MockAtom const& AtX() const { return atX_; }
+    /// \return Atom Y
+    MockAtom const& AtY() const { return atY_; }
+    /// \return True if AX has known bonded atoms
+    bool AxHasKnownAtoms() const { return axHasKnownAtoms_; }
+    /// \return True if AY has known bonded atoms
+    bool AyHasKnownAtoms() const { return ayHasKnownAtoms_; }
   private:
     static int LeapAtomWeight(Atom const&);
-    static inline std::vector<int> SiftBondedAtomsLikeLeap(unsigned int&, Atom const&, std::vector<bool> const&);
-    static inline std::vector<int> SortBondedAtomsLikeLeap(unsigned int&, Atom const&,
-                                                           Topology const& topIn, int ignoreAtom,
-                                                           std::vector<bool> const& hasPosition);
-
-    int ax_;              ///< Atom X
-    int ay_;              ///< Atom Y
-    Iarray sorted_ax_;    ///< Hold the leap-sorted bonds for atom X
-    Iarray sorted_ay_;    ///< Hold the leap-sorted bonds for atom Y
+    //static inline std::vector<int> SiftBondedAtomsLikeLeap(unsigned int&, Atom const&, std::vector<bool> const&);
+    static inline Marray SortBondedAtomsLikeLeap(unsigned int&, Topology const& topIn, Marray const&);
+    static inline void swap_heaviest(Marray&, Topology const&);
+
+    MockAtom atX_;              ///< Atom X
+    MockAtom atY_;              ///< Atom Y
+    Marray sorted_ax_;    ///< Hold the leap-sorted bonded atoms for atom X
+    Marray sorted_ay_;    ///< Hold the leap-sorted bonded atoms for atom Y
     double dAbsolute_;    ///< Hold the value of the A-X-Y-D torsion in radians
     double Xorientation_; ///< Orientation around the X atom TODO make an enum?
     double Yorientation_; ///< Orientation around the Y atoms
+    bool axHasKnownAtoms_; ///< True if any atom around ax (other than ay) is known
+    bool ayHasKnownAtoms_; ///< True if any atom around ay (other than ax) is known
 };
     
 /** \return the LEaP 'weight' of an atom.
@@ -1261,7 +1301,7 @@ int Cpptraj::Structure::Builder::TorsionModel::LeapAtomWeight(Atom const& At)
   * \param At The atom to sift.
   * \param hasPosition Array indicating whether atoms have position.
   */
-std::vector<int> 
+/*std::vector<int> 
   Cpptraj::Structure::Builder::TorsionModel::SiftBondedAtomsLikeLeap(unsigned int& firstUnknownIdx,
                                                                      Atom const& At,
                                                                      std::vector<bool> const& hasPosition)
@@ -1276,6 +1316,29 @@ std::vector<int>
     if (!hasPosition[*bat])
       out.push_back( *bat );
   return out;
+}*/
+
+static inline void swap_mock_atom(MockAtom& lhs, MockAtom& rhs) {
+  MockAtom tmp = lhs;
+  lhs = rhs;
+  rhs = tmp;
+}
+
+void Cpptraj::Structure::Builder::TorsionModel::swap_heaviest(Marray& bondedAtoms, Topology const& topIn)
+{
+  // Find the index of the heaviest atom
+  int iHighest = 0;
+  int iPos = 0;
+  for (Marray::const_iterator it = bondedAtoms.begin(); it != bondedAtoms.end(); ++it)
+  {
+    int iWeight = LeapAtomWeight( topIn[it->Idx()] );
+    if ( iHighest < iWeight ) {
+      iHighest = iWeight;
+      iPos = (int)(it - bondedAtoms.begin());
+    }
+  }
+  // If highest weight atom not already in front, swap it there.
+  if (iPos != 0) swap_mock_atom( bondedAtoms[0], bondedAtoms[iPos] );
 }
 
 /** Order atoms bonded to the given atom in a manner similar to LEaP's
@@ -1285,34 +1348,32 @@ std::vector<int>
   * The ignore atom is the index of the atom this atom is bonded to that
   * forms the torsion we are interested in.
   */
-std::vector<int>
+std::vector<MockAtom>
   Cpptraj::Structure::Builder::TorsionModel::SortBondedAtomsLikeLeap(unsigned int& firstUnknownIdx,
-                                                                     Atom const& At, Topology const& topIn,
-                                                                     int ignoreAtom,
-                                                                     std::vector<bool> const& hasPosition)
+                                                                     Topology const& topIn,
+                                                                     std::vector<MockAtom> const& bondedAtoms)
 {
-  std::vector<int> out;
-  out.reserve( At.Nbonds() );
+  typedef std::vector<MockAtom> Marray;
+  Marray known_out;
+  known_out.reserve( bondedAtoms.size() );
   // Sift so that atoms with known position are at the front
-  std::vector<int> bondedAtoms = SiftBondedAtomsLikeLeap(firstUnknownIdx, At, hasPosition);
-  // Find the index of the heaviest atom
-  int iHighest = 0;
-  int iPos = 0;
-  for (unsigned int idx = 0; idx < bondedAtoms.size(); idx++) {
-    int bat = bondedAtoms[idx];
-    if (bat != ignoreAtom) {
-      out.push_back( bat );
-      int iWeight = LeapAtomWeight( topIn[bat] );
-      if ( iHighest < iWeight ) {
-        iHighest = iWeight;
-        iPos = (int)out.size()-1;
-      }
-    }
-  }
-  // If highest weight atom not already in front, swap it there.
-  if (iPos != 0) std::swap( out[0], out[iPos] );
-
-  return out;
+  for (Marray::const_iterator it = bondedAtoms.begin(); it != bondedAtoms.end(); ++it)
+    if (it->Known())
+      known_out.push_back( *it );
+  firstUnknownIdx = known_out.size();
+  swap_heaviest(known_out, topIn);
+  // Unknown atoms go at the back
+  Marray unknown_out;
+  unknown_out.reserve(bondedAtoms.size() - known_out.size() + 1);
+  for (Marray::const_iterator it = bondedAtoms.begin(); it != bondedAtoms.end(); ++it)
+    if (!it->Known())
+      unknown_out.push_back( *it );
+  swap_heaviest(unknown_out, topIn);
+
+  for (Marray::const_iterator it = unknown_out.begin(); it != unknown_out.end(); ++it)
+    known_out.push_back( *it );
+
+  return known_out;
 }
 
 /** LEaP routine for determining atom chirality.
@@ -1341,28 +1402,70 @@ static inline double VectorAtomChirality(Vec3 const& Center, Vec3 const& A, Vec3
   * triangle (iA, iX, iY). This orientation will be used by the
   * CreateSpXSpX routines to determine which torsion values to use.
   */
-static inline double calculateOrientation(int iX, int iA, int iY, int iB, Frame const& frameIn, std::vector<bool> const& hasPosition)
+static inline double calculateOrientation(MockAtom const& iX, MockAtom const& iA, MockAtom const& iY, MockAtom const& iB)
 {
   double dOrientation = 1.0;
-  if (hasPosition[iX] &&
-      hasPosition[iA] &&
-      hasPosition[iY] &&
-      hasPosition[iB])
+  if (iX.Known() &&
+      iA.Known() &&
+      iY.Known() &&
+      iB.Known())
   {
-    dOrientation = VectorAtomChirality( frameIn.XYZ(iX), frameIn.XYZ(iA), frameIn.XYZ(iY), frameIn.XYZ(iB) );
+    dOrientation = VectorAtomChirality( iX.Pos(), iA.Pos(), iY.Pos(), iB.Pos() );
   } else {
     mprinterr("Internal Error: Builder::calculateOrientation not yet set up for unknown positions.\n");
   }
   return dOrientation;
 }
 
+/** Initialize model torsion for bonded atoms. */
+int Cpptraj::Structure::Builder::TorsionModel::InitTorsion(int ax, int ay,
+                                                           Frame const& frameIn,
+                                                           Topology const& topIn,
+                                                           std::vector<bool> const& hasPosition)
+{
+  if (hasPosition[ax])
+    atX_ = MockAtom(ax, frameIn.XYZ(ax));
+  else
+    atX_ = MockAtom(ax);
+  if (hasPosition[ay])
+    atY_ = MockAtom(ay, frameIn.XYZ(ay));
+  else
+    atY_ = MockAtom(ay);
+  Atom const& AX = topIn[ax];
+  Atom const& AY = topIn[ay];
+  // Create array of AX bonded atoms
+  axHasKnownAtoms_ = false;
+  sorted_ax_.clear();
+  sorted_ax_.reserve( AX.Nbonds() - 1 );
+  for (Atom::bond_iterator bat = AX.bondbegin(); bat != AX.bondend(); ++bat) {
+    if (*bat != ay) {
+      if (hasPosition[*bat]) {
+        axHasKnownAtoms_ = true;
+        sorted_ax_.push_back( MockAtom(*bat, frameIn.XYZ(*bat)) );
+      } else
+        sorted_ax_.push_back( MockAtom(*bat) );
+    }
+  }
+  // Create array of AY bonded atoms
+  ayHasKnownAtoms_ = false;
+  sorted_ay_.clear();
+  sorted_ay_.reserve( AY.Nbonds() - 1 );
+  for (Atom::bond_iterator bat = AY.bondbegin(); bat != AY.bondend(); ++bat) {
+    if (*bat != ax) {
+      if (hasPosition[*bat]) {
+        ayHasKnownAtoms_ = true;
+        sorted_ay_.push_back( MockAtom(*bat, frameIn.XYZ(*bat)) );
+      } else
+        sorted_ay_.push_back( MockAtom(*bat) );
+    }
+  }
+  return 0;
+}
+
 /** Set up model torsion for bonded atoms. */
-int Cpptraj::Structure::Builder::TorsionModel::SetupTorsion(int ax, int ay,
-                                                            AtomType::HybridizationType Hx,
+int Cpptraj::Structure::Builder::TorsionModel::SetupTorsion(AtomType::HybridizationType Hx,
                                                             AtomType::HybridizationType Hy,
-                                                            Frame const& frameIn,
-                                                            Topology const& topIn,
-                                                            std::vector<bool> const& hasPosition)
+                                                            Topology const& topIn)
 {
   if (Hx != AtomType::UNKNOWN_HYBRIDIZATION && Hy != AtomType::UNKNOWN_HYBRIDIZATION) {
     if (Hy > Hx) {
@@ -1370,47 +1473,45 @@ int Cpptraj::Structure::Builder::TorsionModel::SetupTorsion(int ax, int ay,
       return 1;
     }
   }
-  ax_ = ax;
-  ay_ = ay;
-  Atom const& AX = topIn[ax];
-  Atom const& AY = topIn[ay];
   // Sort AX bonds
   unsigned int firstUnknownIdxX = 0;
-  sorted_ax_ = SortBondedAtomsLikeLeap(firstUnknownIdxX, AX, topIn, ay, hasPosition);
+  sorted_ax_ = SortBondedAtomsLikeLeap(firstUnknownIdxX, topIn, sorted_ax_);
   // Sort AY bonds
   unsigned int firstUnknownIdxY = 0;
-  sorted_ay_ = SortBondedAtomsLikeLeap(firstUnknownIdxY, AY, topIn, ax, hasPosition);
+  sorted_ay_ = SortBondedAtomsLikeLeap(firstUnknownIdxY, topIn, sorted_ay_);
   // Calculate the chirality around atom X
   Xorientation_ = 0;
   if (Hx == AtomType::SP3) {
-    Xorientation_ = calculateOrientation( ax, sorted_ax_[0], ay, sorted_ax_[1], frameIn, hasPosition );
+    Xorientation_ = calculateOrientation( atX_, sorted_ax_[0], atY_, sorted_ax_[1] );
   }
   // Calculate the chirality around atom Y
   Yorientation_ = 0;
   if (Hy == AtomType::SP3) {
-    Yorientation_ = calculateOrientation( ay, sorted_ay_[0], ax, sorted_ay_[1], frameIn, hasPosition );
+    Yorientation_ = calculateOrientation( atY_, sorted_ay_[0], atX_, sorted_ay_[1] );
   }
   // DEBUG
+  Atom const& AX = topIn[atX_.Idx()];
+  Atom const& AY = topIn[atY_.Idx()];
   mprintf("Orientation around: %s = %f\n", *(AX.Name()), Xorientation_);
   //for (Atom::bond_iterator bat = AX.bondbegin(); bat != AX.bondend(); ++bat) mprintf(" %s", *(topIn[*bat].Name()));
   //mprintf("}\n");
-  for (Iarray::const_iterator it = sorted_ax_.begin(); it != sorted_ax_.end(); ++it)
-      mprintf("Atom %li: %s\n", it - sorted_ax_.begin(), *(topIn[*it].Name()));
+  for (Marray::const_iterator it = sorted_ax_.begin(); it != sorted_ax_.end(); ++it)
+      mprintf("Atom %li: %s\n", it - sorted_ax_.begin(), *(topIn[it->Idx()].Name()));
   mprintf("Orientation around: %s = %f\n", *(AY.Name()), Yorientation_);
   //for (Atom::bond_iterator bat = AY.bondbegin(); bat != AY.bondend(); ++bat) mprintf(" %s", *(topIn[*bat].Name()));
   //mprintf("}\n");
-  for (Iarray::const_iterator it = sorted_ay_.begin(); it != sorted_ay_.end(); ++it)
-      mprintf("Atom %li: %s\n", it - sorted_ay_.begin(), *(topIn[*it].Name()));
+  for (Marray::const_iterator it = sorted_ay_.begin(); it != sorted_ay_.end(); ++it)
+      mprintf("Atom %li: %s\n", it - sorted_ay_.begin(), *(topIn[it->Idx()].Name()));
   // Calculate the actual torsion angle between A-X-Y-D
-  if (hasPosition[sorted_ax_[0]] &&
-      hasPosition[ax] &&
-      hasPosition[ay] &&
-      hasPosition[sorted_ay_[0]])
+  if (sorted_ax_[0].Known() &&
+      atX_.Known() &&
+      atY_.Known() &&
+      sorted_ay_[0].Known())
   {
-    dAbsolute_ = Torsion( frameIn.XYZ(sorted_ax_[0]),
-                          frameIn.XYZ(ax),
-                          frameIn.XYZ(ay),
-                          frameIn.XYZ(sorted_ay_[0]) );
+    dAbsolute_ = Torsion( sorted_ax_[0].Pos().Dptr(),
+                          atX_.Pos().Dptr(),
+                          atY_.Pos().Dptr(),
+                          sorted_ay_[0].Pos().Dptr() );
   } else {
     dAbsolute_ = 180.0 * Constants::DEGRAD;
   }
@@ -1418,7 +1519,121 @@ int Cpptraj::Structure::Builder::TorsionModel::SetupTorsion(int ax, int ay,
   return 0;
 }
 
-// -----------------------------------------------
+/** Build mock external coordinates around the given torsion using 
+  * the given internal coordinates.
+  * By definition, the two central atoms will be the same for each
+  * IC in iaTorsions.
+  */
+int Cpptraj::Structure::Builder::TorsionModel::BuildMockExternals(std::vector<InternalCoords> const& iaTorsions,
+                                                                  Topology const& topIn) // DEBUG topIn for debug only
+{
+  if (iaTorsions.empty()) {
+    mprinterr("Internal Error: Builder::buildMockExternals() called with no internal torsions.\n");
+    return 1;
+  }
+  mprintf("=======  Started mock coords from: %s\n", topIn.LeapName(iaTorsions.front().AtI()).c_str());
+
+  for (std::vector<InternalCoords>::const_iterator ic = iaTorsions.begin();
+                                                   ic != iaTorsions.end(); ++ic)
+    mprintf("------- Known torsion: %s - %s - %s - %s  %f\n",
+            topIn.LeapName(ic->AtI()).c_str(),
+            topIn.LeapName(ic->AtJ()).c_str(),
+            topIn.LeapName(ic->AtK()).c_str(),
+            topIn.LeapName(ic->AtL()).c_str(),
+            ic->Phi());
+
+  // Define coordinates for the central atoms.
+  Vec3 posX(0, 0, 0);
+  Vec3 posY(1, 0, 0);
+
+  // Hold info on X-Y outer atoms
+  typedef std::vector<MockAtom> Marray;
+  Marray outerAtoms;
+
+  // Define outer atoms
+  for (std::vector<InternalCoords>::const_iterator ic = iaTorsions.begin();
+                                                   ic != iaTorsions.end(); ++ic)
+  {
+    if (ic == iaTorsions.begin()) {
+      // Define first outer atom as being in the XY plane
+      outerAtoms.push_back( MockAtom(ic->AtI(), Vec3(1, 1, 0)) );
+    } else {
+      Marray::iterator mi = find_mock_atom( outerAtoms, ic->AtI() );
+      if (mi == outerAtoms.end())
+        outerAtoms.push_back( MockAtom(ic->AtI()) );
+    }
+    Marray::iterator ml = find_mock_atom( outerAtoms, ic->AtL() );
+    if (ml == outerAtoms.end())
+      outerAtoms.push_back( MockAtom(ic->AtL()) );
+  }
+  mprintf("DEBUG: Outer atoms:\n");
+  for (Marray::const_iterator it = outerAtoms.begin(); it != outerAtoms.end(); ++it)
+    mprintf("DEBUG:\t\t%i %4s (%i) {%f %f %f}\n", it->Idx()+1, topIn.AtomMaskName(it->Idx()).c_str(),
+            (int)it->Known(), it->Pos()[0], it->Pos()[1], it->Pos()[2]);
+
+  // Loop through the known torsions looking for those that
+  // have one position defined, then build coords for the
+  // other atom and mark the torsion as used.
+  std::vector<bool> used( iaTorsions.size(), false );
+  unsigned int nused = 0;
+  for (unsigned int idx = 0; idx != iaTorsions.size(); idx++) {
+    //bool gotOne = false;
+    for (unsigned int jdx = 0; jdx != iaTorsions.size(); jdx++) {
+      if (!used[jdx]) {
+        InternalCoords const& iInt = iaTorsions[jdx];
+        Marray::iterator tmpAt1 = find_mock_atom(outerAtoms, iInt.AtI());
+        Marray::iterator tmpAt4 = find_mock_atom(outerAtoms, iInt.AtL());
+        if (tmpAt1 == outerAtoms.end()) {
+          mprinterr("Internal Error: Builder::buildMockExternals(): Outer atom I %i not found.\n", iInt.AtI()+1);
+          return 1;
+        }
+        if (tmpAt4 == outerAtoms.end()) {
+          mprinterr("Internal Error: Builder::buildMockExternals(): Outer atom L %i not found.\n", iInt.AtL()+1);
+          return 1;
+        }
+        Vec3 maPC1, maPC2;
+        Marray::iterator tgt = outerAtoms.end();
+        Marray::iterator knownAt = outerAtoms.end();
+        if (tmpAt4->Known()) {
+          tgt     = tmpAt1;
+          maPC1   = posX;
+          maPC2   = posY;
+          knownAt = tmpAt4;
+        } else if (tmpAt1->Known()) {
+          //gotOne = true; // FIXME needed?
+          tgt     = tmpAt4;
+          maPC1   = posY;
+          maPC2   = posX;
+          knownAt = tmpAt1;
+        }
+        if (tgt != outerAtoms.end()) {
+          //gotOne = true;
+          mprintf("======= Building mock coord for: %s\n", topIn.LeapName(tgt->Idx()).c_str());
+          mprintf("======= Using torsion: %s - %s - %s - %s (p1known= %i, p4known= %i)\n",
+                   topIn.LeapName(iInt.AtI()).c_str(),
+                   topIn.LeapName(iInt.AtJ()).c_str(),
+                   topIn.LeapName(iInt.AtK()).c_str(),
+                   topIn.LeapName(iInt.AtL()).c_str(),
+                   (int)tmpAt1->Known(), (int)tmpAt4->Known());
+          // Now build the coordinate for the target atom
+          tgt->SetPos( Zmatrix::AtomIposition(maPC1, maPC2, knownAt->Pos(), 1.0, 90.0, iInt.Phi()) );
+          mprintf("ZMatrixAll:  %f,%f,%f\n", tgt->Pos()[0], tgt->Pos()[1], tgt->Pos()[2]);
+          used[jdx] = true;
+          nused++;
+          break;
+        }
+      } // END IC not yet used
+    } // END inner loop over ICs
+  } // END outer loop over ICs
+  if (nused < used.size()) {
+    mprinterr("Error: There are %u torsions left over for mock coords.\n", used.size() - nused);
+    return 1;
+  }
+
+  return 0;
+}
+
+// -----------------------------------------------------------------------------
 /** Model torsion */
 void Builder::ModelTorsion(TorsionModel const& MT, unsigned int iBondX, unsigned int iBondY, double dvalIn)
 {
@@ -1426,11 +1641,11 @@ void Builder::ModelTorsion(TorsionModel const& MT, unsigned int iBondX, unsigned
       iBondY >= MT.SortedAy().size())
     return;
   mprintf("CALLING ModelTorsion for iBondX=%u iBondY=%u dVal=%g\n",iBondX,iBondY,dvalIn*Constants::RADDEG);
-  int aa = MT.SortedAx()[iBondX];
-  int ax = MT.AtX();
-  int ay = MT.AtY();
-  int ad = MT.SortedAy()[iBondY];
-  // Get bond lengths
+  int aa = MT.SortedAx()[iBondX].Idx();
+  int ax = MT.AtX().Idx();
+  int ay = MT.AtY().Idx();
+  int ad = MT.SortedAy()[iBondY].Idx();
+  // Get bond lengths FIXME deal with unknown positions
   double l0, l1;
   if (AssignLength(l0, aa, ax, *currentTop_, *currentFrm_, *hasPosition_)) {
     mprinterr("Error: Could not assign length between %s and %s\n",
@@ -1463,16 +1678,21 @@ void Builder::ModelTorsion(TorsionModel const& MT, unsigned int iBondX, unsigned
   // If the coordinates for the atoms are defined then
   // measure the torsion angle between them and use that for
   // the internal.
+  MockAtom const& AA = MT.SortedAx()[iBondX];
+  MockAtom const& AX = MT.AtX();
+  MockAtom const& AY = MT.AtY();
+  MockAtom const& AD = MT.SortedAy()[iBondY];
+
   double phiVal = dvalIn;
-  if ((*hasPosition_)[aa] &&
-      (*hasPosition_)[ax] &&
-      (*hasPosition_)[ay] &&
-      (*hasPosition_)[ad])
+  if (AA.Known() &&
+      AX.Known() &&
+      AY.Known() &&
+      AD.Known())
   {
-    phiVal = Torsion( currentFrm_->XYZ(aa),
-                      currentFrm_->XYZ(ax),
-                      currentFrm_->XYZ(ay),
-                      currentFrm_->XYZ(ad) );
+    phiVal = Torsion( AA.Pos().Dptr(),
+                      AX.Pos().Dptr(),
+                      AY.Pos().Dptr(),
+                      AD.Pos().Dptr() );
   } else {
     mprinterr("Internal Error: Need to implement torsion lookup.\n");
   }
@@ -1613,147 +1833,6 @@ std::vector<InternalCoords> Builder::getExistingInternals(int ax, int ay) const
   return iTorsions;
 }
 
-/// Used to track atoms for mock externals
-class MockAtom {
-  public:
-    /// CONSTRUCTOR - index, position
-    MockAtom(int idx, Vec3 const& pos) : idx_(idx), pos_(pos), known_(true) {}
-    /// CONSTRUCTOR - index, unknown position
-    MockAtom(int idx) : idx_(idx), pos_(0.0), known_(false) {}
-    /// Set position
-    void SetPos(Vec3 const& p) { pos_ = p; known_ = true; }
-
-    int Idx() const { return idx_; }
-    Vec3 const& Pos() const { return pos_; }
-    bool Known() const { return known_; }
-  private:
-    int idx_; ///< Atom index
-    Vec3 pos_; ///< Atom mock position
-    bool known_; ///< True if atom position is known
-};
-
-/// Used to find mock atom
-static inline std::vector<MockAtom>::iterator find_mock_atom(std::vector<MockAtom>& outerAtoms, int idx)
-{
-  std::vector<MockAtom>::iterator it = outerAtoms.begin();
-  for (; it != outerAtoms.end(); ++it)
-    if (it->Idx() == idx) return it;
-  return outerAtoms.end();
-}
-
-/** Build mock external coordinates around the given torsion using 
-  * the given internal coordinates.
-  * By definition, the two central atoms will be the same for each
-  * IC in iaTorsions.
-  */
-int Builder::buildMockExternals(TorsionModel& mT, std::vector<InternalCoords> const& iaTorsions)
-const
-{
-  if (iaTorsions.empty()) {
-    mprinterr("Internal Error: Builder::buildMockExternals() called with no internal torsions.\n");
-    return 1;
-  }
-  mprintf("=======  Started mock coords from: %s\n", currentTop_->LeapName(iaTorsions.front().AtI()).c_str());
-
-  for (std::vector<InternalCoords>::const_iterator ic = iaTorsions.begin();
-                                                   ic != iaTorsions.end(); ++ic)
-    mprintf("------- Known torsion: %s - %s - %s - %s  %f\n",
-            currentTop_->LeapName(ic->AtI()).c_str(),
-            currentTop_->LeapName(ic->AtJ()).c_str(),
-            currentTop_->LeapName(ic->AtK()).c_str(),
-            currentTop_->LeapName(ic->AtL()).c_str(),
-            ic->Phi());
-
-  // Define coordinates for the central atoms.
-  Vec3 posX(0, 0, 0);
-  Vec3 posY(1, 0, 0);
-
-  // Hold info on X-Y outer atoms
-  typedef std::vector<MockAtom> Marray;
-  Marray outerAtoms;
-
-  // Define outer atoms
-  for (std::vector<InternalCoords>::const_iterator ic = iaTorsions.begin();
-                                                   ic != iaTorsions.end(); ++ic)
-  {
-    if (ic == iaTorsions.begin()) {
-      // Define first outer atom as being in the XY plane
-      outerAtoms.push_back( MockAtom(ic->AtI(), Vec3(1, 1, 0)) );
-    } else {
-      Marray::iterator mi = find_mock_atom( outerAtoms, ic->AtI() );
-      if (mi == outerAtoms.end())
-        outerAtoms.push_back( MockAtom(ic->AtI()) );
-    }
-    Marray::iterator ml = find_mock_atom( outerAtoms, ic->AtL() );
-    if (ml == outerAtoms.end())
-      outerAtoms.push_back( MockAtom(ic->AtL()) );
-  }
-  mprintf("DEBUG: Outer atoms:\n");
-  for (Marray::const_iterator it = outerAtoms.begin(); it != outerAtoms.end(); ++it)
-    mprintf("DEBUG:\t\t%i %4s (%i) {%f %f %f}\n", it->Idx()+1, currentTop_->AtomMaskName(it->Idx()).c_str(),
-            (int)it->Known(), it->Pos()[0], it->Pos()[1], it->Pos()[2]);
-
-  // Loop through the known torsions looking for those that
-  // have one position defined, then build coords for the
-  // other atom and mark the torsion as used.
-  std::vector<bool> used( iaTorsions.size(), false );
-  unsigned int nused = 0;
-  for (unsigned int idx = 0; idx != iaTorsions.size(); idx++) {
-    //bool gotOne = false;
-    for (unsigned int jdx = 0; jdx != iaTorsions.size(); jdx++) {
-      if (!used[jdx]) {
-        InternalCoords const& iInt = iaTorsions[jdx];
-        Marray::iterator tmpAt1 = find_mock_atom(outerAtoms, iInt.AtI());
-        Marray::iterator tmpAt4 = find_mock_atom(outerAtoms, iInt.AtL());
-        if (tmpAt1 == outerAtoms.end()) {
-          mprinterr("Internal Error: Builder::buildMockExternals(): Outer atom I %i not found.\n", iInt.AtI()+1);
-          return 1;
-        }
-        if (tmpAt4 == outerAtoms.end()) {
-          mprinterr("Internal Error: Builder::buildMockExternals(): Outer atom L %i not found.\n", iInt.AtL()+1);
-          return 1;
-        }
-        Vec3 maPC1, maPC2;
-        Marray::iterator tgt = outerAtoms.end();
-        Marray::iterator knownAt = outerAtoms.end();
-        if (tmpAt4->Known()) {
-          tgt     = tmpAt1;
-          maPC1   = posX;
-          maPC2   = posY;
-          knownAt = tmpAt4;
-        } else if (tmpAt1->Known()) {
-          //gotOne = true; // FIXME needed?
-          tgt     = tmpAt4;
-          maPC1   = posY;
-          maPC2   = posX;
-          knownAt = tmpAt1;
-        }
-        if (tgt != outerAtoms.end()) {
-          //gotOne = true;
-          mprintf("======= Building mock coord for: %s\n", currentTop_->LeapName(tgt->Idx()).c_str());
-          mprintf("======= Using torsion: %s - %s - %s - %s (p1known= %i, p4known= %i)\n",
-                   currentTop_->LeapName(iInt.AtI()).c_str(),
-                   currentTop_->LeapName(iInt.AtJ()).c_str(),
-                   currentTop_->LeapName(iInt.AtK()).c_str(),
-                   currentTop_->LeapName(iInt.AtL()).c_str(),
-                   (int)tmpAt1->Known(), (int)tmpAt4->Known());
-          // Now build the coordinate for the target atom
-          tgt->SetPos( Zmatrix::AtomIposition(maPC1, maPC2, knownAt->Pos(), 1.0, 90.0, iInt.Phi()) );
-          mprintf("ZMatrixAll:  %f,%f,%f\n", tgt->Pos()[0], tgt->Pos()[1], tgt->Pos()[2]);
-          used[jdx] = true;
-          nused++;
-          break;
-        }
-      } // END IC not yet used
-    } // END inner loop over ICs
-  } // END outer loop over ICs
-  if (nused < used.size()) {
-    mprinterr("Error: There are %u torsions left over for mock coords.\n", used.size() - nused);
-    return 1;
-  }
-
-  return 0;
-}
 
 /** Assign torsions around bonded atoms in manner similar to LEaP's ModelAssignTorsionsAround. */
 int Builder::assignTorsionsAroundBond(Zmatrix& zmatrix, int a1, int a2, Frame const& frameIn, Topology const& topIn, Barray const& hasPosition)
@@ -1815,26 +1894,17 @@ int Builder::assignTorsionsAroundBond(Zmatrix& zmatrix, int a1, int a2, Frame co
   mprintf("DEBUG: assignTorsionsAroundBond: AX= %s (%s)  AY= %s (%s)\n",
           topIn.AtomMaskName(ax).c_str(), hstr[Hx],
           topIn.AtomMaskName(ay).c_str(), hstr[Hy]);
+  TorsionModel mT;
+  if (mT.InitTorsion( ax, ay, frameIn, topIn, hasPosition )) {
+    mprinterr("Error: Could not init model torsion.\n");
+    return 1;
+  }
   // Check if there is at least one atom on either side of the ax-ay pair
   // whose position is known.
-  Atom const& AX = topIn[ax];
-  Atom const& AY = topIn[ay];
-  bool axHasKnownAtoms = false;
-  for (Atom::bond_iterator bat = AX.bondbegin(); bat != AX.bondend(); ++bat) {
-    if (*bat != ay && hasPosition[*bat]) {
-      axHasKnownAtoms = true;
-      break;
-    }
-  }
-  bool ayHasKnownAtoms = false;
-  for (Atom::bond_iterator bat = AY.bondbegin(); bat != AY.bondend(); ++bat) {
-    if (*bat != ax && hasPosition[*bat]) {
-      ayHasKnownAtoms = true;
-      break;
-    }
-  }
-  mprintf("bKnownX=%i  bKnownY=%i\n", (int)axHasKnownAtoms, (int)ayHasKnownAtoms);
-  if (!(axHasKnownAtoms && ayHasKnownAtoms)) {
+  //Atom const& AX = topIn[ax];
+  //Atom const& AY = topIn[ay];
+  mprintf("bKnownX=%i  bKnownY=%i\n", (int)mT.AxHasKnownAtoms(), (int)mT.AyHasKnownAtoms());
+  if (!(mT.AxHasKnownAtoms() && mT.AyHasKnownAtoms())) {
     // Find any existing internal coords around ax-ay
     std::vector<InternalCoords> iTorsions = getExistingInternals(ax, ay);
     if (!iTorsions.empty()) {
@@ -1842,50 +1912,50 @@ int Builder::assignTorsionsAroundBond(Zmatrix& zmatrix, int a1, int a2, Frame co
               topIn.LeapName(ax).c_str(), topIn.LeapName(ay).c_str());
       //for (std::vector<InternalCoords>::const_iterator ic = iTorsions.begin(); ic != iTorsions.end(); ++ic)
       //  ic->printIC( topIn );
-      TorsionModel mT(ax, ay);
-      if (buildMockExternals(mT, iTorsions)) {
+      if (mT.BuildMockExternals(iTorsions, topIn)) {
         mprinterr("Error: Building mock externals around %s - %s failed.\n",
                   topIn.AtomMaskName(ax).c_str(), topIn.AtomMaskName(ay).c_str());
         return 1;
       }
+      return 0; // FIXME DEBUG 
     } else {
       mprintf("Completely free in assigning new torsions for: %s - %s\n",
               topIn.LeapName(ax).c_str(), topIn.LeapName(ay).c_str());
+      return 0; // FIXME DEBUG 
     }
   } else {
     // Use existing atoms to determine torsions
     mprintf("DEBUG: Using externals to fit new torsions around: %s - %s\n",
             topIn.LeapName(ax).c_str(),
             topIn.LeapName(ay).c_str());
+  }
 
-    TorsionModel mT;
-    if (mT.SetupTorsion(ax, ay, Hx, Hy, frameIn, topIn, hasPosition)) {
-      mprinterr("Error: Could not set up torsions around %s - %s\n",
-                topIn.LeapName(ax).c_str(),
-                topIn.LeapName(ay).c_str());
-      return 1;
-    } 
-
-    // Build the new internals
-    if (Hx == AtomType::SP3 && Hy == AtomType::SP3) {
-      mprintf("SP3 SP3\n");
-      createSp3Sp3Torsions(mT);
-    } else if (Hx == AtomType::SP3 && Hy == AtomType::SP2) {
-      mprintf("SP3 SP2\n");
-      createSp3Sp2Torsions(mT);
-    } else if (Hx == AtomType::SP2 && Hy == AtomType::SP2) {
-      mprintf("SP2 SP2\n");
-      createSp2Sp2Torsions(mT);
-    } else {
-      mprinterr("Error: Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported\n"
-                "Error: ---Tried to superimpose torsions for: *-%s-%s-*\n"
-                "Error: --- With %s - %s\n"
-                "Error: --- Sp0 probably means a new atom type is involved\n"
-                "Error: --- which needs to be defined prior to this routine.\n",
-                topIn.AtomMaskName(ax).c_str(), topIn.AtomMaskName(ay).c_str(),
-                hstr[Hx], hstr[Hy]);
-     return 1;
-    }
+  if (mT.SetupTorsion(Hx, Hy, topIn)) {
+    mprinterr("Error: Could not set up torsions around %s - %s\n",
+              topIn.LeapName(ax).c_str(),
+              topIn.LeapName(ay).c_str());
+    return 1;
+  } 
+
+  // Build the new internals
+  if (Hx == AtomType::SP3 && Hy == AtomType::SP3) {
+    mprintf("SP3 SP3\n");
+    createSp3Sp3Torsions(mT);
+  } else if (Hx == AtomType::SP3 && Hy == AtomType::SP2) {
+    mprintf("SP3 SP2\n");
+    createSp3Sp2Torsions(mT);
+  } else if (Hx == AtomType::SP2 && Hy == AtomType::SP2) {
+    mprintf("SP2 SP2\n");
+    createSp2Sp2Torsions(mT);
+  } else {
+    mprinterr("Error: Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported\n"
+              "Error: ---Tried to superimpose torsions for: *-%s-%s-*\n"
+              "Error: --- With %s - %s\n"
+              "Error: --- Sp0 probably means a new atom type is involved\n"
+              "Error: --- which needs to be defined prior to this routine.\n",
+              topIn.AtomMaskName(ax).c_str(), topIn.AtomMaskName(ay).c_str(),
+              hstr[Hx], hstr[Hy]);
+   return 1;
   }
 
   return 0;

From 94fe32591fe59a4915147f4ea90ae7591330e314 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 6 Feb 2024 16:23:48 -0500
Subject: [PATCH 0452/1492] Set outer atom positions unknown

---
 src/Structure/Builder.cpp | 38 +++++++++++++++++++++++++-------------
 1 file changed, 25 insertions(+), 13 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 42110cd58c..22886d03ca 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1214,6 +1214,8 @@ class MockAtom {
     MockAtom(int idx) : idx_(idx), pos_(0.0), known_(false) {}
     /// Set position
     void SetPos(Vec3 const& p) { pos_ = p; known_ = true; }
+    /// Set unknown
+    void SetUnknown() { pos_ = Vec3(0.0); known_ = false; }
 
     int Idx()         const { return idx_; }
     Vec3 const& Pos() const { return pos_; }
@@ -1224,15 +1226,6 @@ class MockAtom {
     bool known_; ///< True if atom position is known
 };
 
-/// Used to find mock atom
-static inline std::vector<MockAtom>::iterator find_mock_atom(std::vector<MockAtom>& outerAtoms, int idx)
-{
-  std::vector<MockAtom>::iterator it = outerAtoms.begin();
-  for (; it != outerAtoms.end(); ++it)
-    if (it->Idx() == idx) return it;
-  return outerAtoms.end();
-}
-
 // -----------------------------------------------
 /** Store info for modelling torsions around X-Y */
 class Cpptraj::Structure::Builder::TorsionModel {
@@ -1519,6 +1512,15 @@ int Cpptraj::Structure::Builder::TorsionModel::SetupTorsion(AtomType::Hybridizat
   return 0;
 }
 
+/// Used to find mock atom
+static inline std::vector<MockAtom>::iterator find_mock_atom(std::vector<MockAtom>& outerAtoms, int idx)
+{
+  std::vector<MockAtom>::iterator it = outerAtoms.begin();
+  for (; it != outerAtoms.end(); ++it)
+    if (it->Idx() == idx) return it;
+  return outerAtoms.end();
+}
+
 /** Build mock external coordinates around the given torsion using 
   * the given internal coordinates.
   * By definition, the two central atoms will be the same for each
@@ -1543,10 +1545,20 @@ int Cpptraj::Structure::Builder::TorsionModel::BuildMockExternals(std::vector<In
             ic->Phi());
 
   // Define coordinates for the central atoms.
-  Vec3 posX(0, 0, 0);
-  Vec3 posY(1, 0, 0);
-
-  // Hold info on X-Y outer atoms
+  //Vec3 posX(0, 0, 0);
+  //Vec3 posY(1, 0, 0);
+  atX_.SetPos( Vec3(0, 0, 0) );
+  atY_.SetPos( Vec3(1, 0, 0) );
+  Vec3 const& posX = atX_.Pos();
+  Vec3 const& posY = atY_.Pos();
+
+  // Tell the outer atoms they do not have defined positions.
+  for (Marray::iterator it = sorted_ax_.begin(); it != sorted_ax_.end(); ++it)
+    it->SetUnknown();
+  for (Marray::iterator it = sorted_ay_.begin(); it != sorted_ay_.end(); ++it)
+    it->SetUnknown();
+
+//  // Hold info on X-Y outer atoms
   typedef std::vector<MockAtom> Marray;
   Marray outerAtoms;
 

From 8c7fd1af617f1666c63a70a9e87326718326c72f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 6 Feb 2024 16:31:49 -0500
Subject: [PATCH 0453/1492] Add code to update the outer atoms of the
 TorsionModel

---
 src/Structure/Builder.cpp | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 22886d03ca..6668b9b0fc 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1641,6 +1641,24 @@ int Cpptraj::Structure::Builder::TorsionModel::BuildMockExternals(std::vector<In
     mprinterr("Error: There are %u torsions left over for mock coords.\n", used.size() - nused);
     return 1;
   }
+  // Update the outer atoms for this torsion
+  mprintf("DEBUG: Final outer atoms:\n");
+  for (Marray::const_iterator it = outerAtoms.begin(); it != outerAtoms.end(); ++it) {
+    mprintf("DEBUG:\t\t%i %4s (%i) {%f %f %f}\n", it->Idx()+1, topIn.AtomMaskName(it->Idx()).c_str(),
+            (int)it->Known(), it->Pos()[0], it->Pos()[1], it->Pos()[2]);
+    Marray::iterator itx = find_mock_atom(sorted_ax_, it->Idx());
+    if (itx != sorted_ax_.end()) {
+      *itx = *it;
+    } else {
+      itx = find_mock_atom(sorted_ay_, it->Idx());
+      if (itx != sorted_ay_.end()) {
+        *itx = *it;
+      } else {
+        mprinterr("Internal Error: TorsionModel::BuildMockExternals(): Could not update mock atom.\n");
+        return 1;
+      }
+    }
+  }
 
   return 0;
 }

From af6a010b22de91b878681797657d6d5a2b34aba1 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 6 Feb 2024 16:40:00 -0500
Subject: [PATCH 0454/1492] Test the model coords

---
 src/Structure/Builder.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 6668b9b0fc..401da3643f 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1947,7 +1947,7 @@ int Builder::assignTorsionsAroundBond(Zmatrix& zmatrix, int a1, int a2, Frame co
                   topIn.AtomMaskName(ax).c_str(), topIn.AtomMaskName(ay).c_str());
         return 1;
       }
-      return 0; // FIXME DEBUG 
+      //return 0; // FIXME DEBUG 
     } else {
       mprintf("Completely free in assigning new torsions for: %s - %s\n",
               topIn.LeapName(ax).c_str(), topIn.LeapName(ay).c_str());

From 9b754d9b1716b059cdd998134391ce1bc5f94850 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 6 Feb 2024 16:44:57 -0500
Subject: [PATCH 0455/1492] Start code for restricting which atoms get ICs
 assigned

---
 src/Structure/Builder.cpp | 10 +++++-----
 src/Structure/Builder.h   |  2 +-
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 401da3643f..e524130edd 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1865,7 +1865,7 @@ std::vector<InternalCoords> Builder::getExistingInternals(int ax, int ay) const
 
 
 /** Assign torsions around bonded atoms in manner similar to LEaP's ModelAssignTorsionsAround. */
-int Builder::assignTorsionsAroundBond(Zmatrix& zmatrix, int a1, int a2, Frame const& frameIn, Topology const& topIn, Barray const& hasPosition)
+int Builder::assignTorsionsAroundBond(Zmatrix& zmatrix, int a1, int a2, Frame const& frameIn, Topology const& topIn, Barray const& hasPosition, int aAtomIdx)
 {
   // Save addresses of zmatrix, frame, topology, and hasPosition.
   // These are required for the createSpXSpX routines. TODO zero them at the end?
@@ -1921,9 +1921,9 @@ int Builder::assignTorsionsAroundBond(Zmatrix& zmatrix, int a1, int a2, Frame co
     Hy = H2;
   }
   static const char* hstr[] = { "SP", "SP2", "SP3", "Unknown" };
-  mprintf("DEBUG: assignTorsionsAroundBond: AX= %s (%s)  AY= %s (%s)\n",
+  mprintf("DEBUG: assignTorsionsAroundBond: AX= %s (%s)  AY= %s (%s), aAtomIdx= %i\n",
           topIn.AtomMaskName(ax).c_str(), hstr[Hx],
-          topIn.AtomMaskName(ay).c_str(), hstr[Hy]);
+          topIn.AtomMaskName(ay).c_str(), hstr[Hy], aAtomIdx);
   TorsionModel mT;
   if (mT.InitTorsion( ax, ay, frameIn, topIn, hasPosition )) {
     mprinterr("Error: Could not init model torsion.\n");
@@ -2003,7 +2003,7 @@ int Builder::GenerateInternals(Zmatrix& zmatrix, Frame const& frameIn, Topology
   // Loop over bonds
   for (BondArray::const_iterator bnd = bonds.begin(); bnd != bonds.end(); ++bnd)
   {
-    if (assignTorsionsAroundBond( zmatrix, bnd->A1(), bnd->A2(), frameIn, topIn, hasPosition )) {
+    if (assignTorsionsAroundBond( zmatrix, bnd->A1(), bnd->A2(), frameIn, topIn, hasPosition, -1 )) {
       mprinterr("Error Assign torsions around bond %s - %s failed.\n",
                 topIn.AtomMaskName(bnd->A1()).c_str(),
                 topIn.AtomMaskName(bnd->A2()).c_str());
@@ -2034,7 +2034,7 @@ int Builder::generateAtomInternals(int at, Frame const& frameIn, Topology const&
         mprintf("ISHOULDBE= %i ITORSIONS= %zu\n", iShouldBe, iTorsions.size());
         if (iShouldBe != (int)iTorsions.size()) {
           Zmatrix tmpz; // FIXME
-          assignTorsionsAroundBond(tmpz, *bat, *cat, frameIn, topIn, hasPosition);
+          assignTorsionsAroundBond(tmpz, *bat, *cat, frameIn, topIn, hasPosition, at);
         }
       }
     }
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index 8897d5f6f4..d2ae985d9c 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -72,7 +72,7 @@ class Builder {
     /// Create ICs around SP2-SP2 linkage
     void createSp2Sp2Torsions(TorsionModel const&);
     /// Model torsions around a bond in the same manner as LEaP
-    int assignTorsionsAroundBond(Zmatrix&, int, int, Frame const&, Topology const&, Barray const&);
+    int assignTorsionsAroundBond(Zmatrix&, int, int, Frame const&, Topology const&, Barray const&, int);
     /// Get any existing internal coords from currentZmatrix around specified atoms
     std::vector<InternalCoords> getExistingInternals(int, int) const;
     /// Build mock coordinates around given torsion

From 88fbcaaf1a5804ce24e33504621d0de26bcf1821 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 7 Feb 2024 09:50:34 -0500
Subject: [PATCH 0456/1492] Implement search for existing torsions. Indicate
 whether internals actually need to be built for atoms or not.

---
 src/Structure/Builder.cpp | 194 ++++++++++++++++++++++----------------
 src/Structure/Builder.h   |   2 +
 2 files changed, 113 insertions(+), 83 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index e524130edd..db85441237 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1207,23 +1207,27 @@ const
 class MockAtom {
   public:
     /// CONSTRUCTOR
-    MockAtom() : idx_(-1), pos_(0.0), known_(false) {}
+    MockAtom() : idx_(-1), pos_(0.0), known_(false), buildInternals_(false) {}
     /// CONSTRUCTOR - index, position
-    MockAtom(int idx, Vec3 const& pos) : idx_(idx), pos_(pos), known_(true) {}
+    MockAtom(int idx, Vec3 const& pos) : idx_(idx), pos_(pos), known_(true), buildInternals_(false) {}
     /// CONSTRUCTOR - index, unknown position
-    MockAtom(int idx) : idx_(idx), pos_(0.0), known_(false) {}
+    MockAtom(int idx) : idx_(idx), pos_(0.0), known_(false), buildInternals_(false) {}
     /// Set position
     void SetPos(Vec3 const& p) { pos_ = p; known_ = true; }
-    /// Set unknown
+    /// Set position status to unknown
     void SetUnknown() { pos_ = Vec3(0.0); known_ = false; }
+    /// Set build internals status
+    void SetBuildInternals(bool b) { buildInternals_ = b; }
 
     int Idx()         const { return idx_; }
     Vec3 const& Pos() const { return pos_; }
     bool Known()      const { return known_; }
+    bool BuildInternals() const { return buildInternals_; }
   private:
     int idx_;    ///< Atom index
     Vec3 pos_;   ///< Atom position
     bool known_; ///< True if atom position is known
+    bool buildInternals_; ///< True if internals should be built for this atom
 };
 
 // -----------------------------------------------
@@ -1236,7 +1240,7 @@ class Cpptraj::Structure::Builder::TorsionModel {
     /// CONSTRUCTOR - AX and AY atom indices
     //TorsionModel(int ax, int ay) : ax_(ax), ay_(ay),  dAbsolute_(0), Xorientation_(0), Yorientation_(0) {}
     /// Initialize torsions around bonded atoms
-    int InitTorsion(int, int, Frame const&, Topology const&, std::vector<bool> const&);
+    int InitTorsion(int, int, Frame const&, Topology const&, std::vector<bool> const&, int);
     /// Set up torsions around bonded atoms
     int SetupTorsion(AtomType::HybridizationType, AtomType::HybridizationType, Topology const& topIn);
     /// Build mock externals from given internals
@@ -1414,7 +1418,8 @@ static inline double calculateOrientation(MockAtom const& iX, MockAtom const& iA
 int Cpptraj::Structure::Builder::TorsionModel::InitTorsion(int ax, int ay,
                                                            Frame const& frameIn,
                                                            Topology const& topIn,
-                                                           std::vector<bool> const& hasPosition)
+                                                           std::vector<bool> const& hasPosition,
+                                                           int aAtomIdx)
 {
   if (hasPosition[ax])
     atX_ = MockAtom(ax, frameIn.XYZ(ax));
@@ -1437,6 +1442,7 @@ int Cpptraj::Structure::Builder::TorsionModel::InitTorsion(int ax, int ay,
         sorted_ax_.push_back( MockAtom(*bat, frameIn.XYZ(*bat)) );
       } else
         sorted_ax_.push_back( MockAtom(*bat) );
+      sorted_ax_.back().SetBuildInternals( (aAtomIdx == -1 || aAtomIdx == *bat) );
     }
   }
   // Create array of AY bonded atoms
@@ -1450,6 +1456,7 @@ int Cpptraj::Structure::Builder::TorsionModel::InitTorsion(int ax, int ay,
         sorted_ay_.push_back( MockAtom(*bat, frameIn.XYZ(*bat)) );
       } else
         sorted_ay_.push_back( MockAtom(*bat) );
+      sorted_ay_.back().SetBuildInternals( (aAtomIdx == -1 || aAtomIdx == *bat) );
     }
   }
   return 0;
@@ -1489,12 +1496,12 @@ int Cpptraj::Structure::Builder::TorsionModel::SetupTorsion(AtomType::Hybridizat
   //for (Atom::bond_iterator bat = AX.bondbegin(); bat != AX.bondend(); ++bat) mprintf(" %s", *(topIn[*bat].Name()));
   //mprintf("}\n");
   for (Marray::const_iterator it = sorted_ax_.begin(); it != sorted_ax_.end(); ++it)
-      mprintf("Atom %li: %s\n", it - sorted_ax_.begin(), *(topIn[it->Idx()].Name()));
+      mprintf("Atom %li: %s (%i) (build=%i)\n", it - sorted_ax_.begin(), *(topIn[it->Idx()].Name()), (int)it->Known(), (int)it->BuildInternals());
   mprintf("Orientation around: %s = %f\n", *(AY.Name()), Yorientation_);
   //for (Atom::bond_iterator bat = AY.bondbegin(); bat != AY.bondend(); ++bat) mprintf(" %s", *(topIn[*bat].Name()));
   //mprintf("}\n");
   for (Marray::const_iterator it = sorted_ay_.begin(); it != sorted_ay_.end(); ++it)
-      mprintf("Atom %li: %s\n", it - sorted_ay_.begin(), *(topIn[it->Idx()].Name()));
+      mprintf("Atom %li: %s (%i) (build=%i)\n", it - sorted_ay_.begin(), *(topIn[it->Idx()].Name()), (int)it->Known(), (int)it->BuildInternals());
   // Calculate the actual torsion angle between A-X-Y-D
   if (sorted_ax_[0].Known() &&
       atX_.Known() &&
@@ -1641,18 +1648,18 @@ int Cpptraj::Structure::Builder::TorsionModel::BuildMockExternals(std::vector<In
     mprinterr("Error: There are %u torsions left over for mock coords.\n", used.size() - nused);
     return 1;
   }
-  // Update the outer atoms for this torsion
+  // Update the outer atom positions for this torsion
   mprintf("DEBUG: Final outer atoms:\n");
   for (Marray::const_iterator it = outerAtoms.begin(); it != outerAtoms.end(); ++it) {
     mprintf("DEBUG:\t\t%i %4s (%i) {%f %f %f}\n", it->Idx()+1, topIn.AtomMaskName(it->Idx()).c_str(),
             (int)it->Known(), it->Pos()[0], it->Pos()[1], it->Pos()[2]);
     Marray::iterator itx = find_mock_atom(sorted_ax_, it->Idx());
     if (itx != sorted_ax_.end()) {
-      *itx = *it;
+      itx->SetPos( it->Pos() );
     } else {
       itx = find_mock_atom(sorted_ay_, it->Idx());
       if (itx != sorted_ay_.end()) {
-        *itx = *it;
+        itx->SetPos( it->Pos() );
       } else {
         mprinterr("Internal Error: TorsionModel::BuildMockExternals(): Could not update mock atom.\n");
         return 1;
@@ -1664,6 +1671,37 @@ int Cpptraj::Structure::Builder::TorsionModel::BuildMockExternals(std::vector<In
 }
 
 // -----------------------------------------------------------------------------
+/** Find any existing internal coords around ax-ay. */ // TODO put in Zmatrix?
+std::vector<InternalCoords> Builder::getExistingInternals(int ax, int ay) const {
+  std::vector<InternalCoords> iTorsions;
+  if (currentZmatrix_ != 0) {
+    for (Zmatrix::const_iterator it = currentZmatrix_->begin(); it != currentZmatrix_->end(); ++it)
+    {
+      if (it->AtJ() == ax && it->AtK() == ay) {
+        iTorsions.push_back( *it );
+      }
+    }
+  }
+  return iTorsions;
+}
+
+/** \return index of internal coords matching the 4 given atoms, -1 for no match. */ // TODO put in Zmatrix?
+int Builder::getExistingInternalIdx(int ai, int aj, int ak, int al) const {
+  int idx = -1;
+  if (currentZmatrix_ != 0) {
+    for (Zmatrix::const_iterator it = currentZmatrix_->begin(); it != currentZmatrix_->end(); ++it)
+    {
+      if ( (it->AtI() == ai && it->AtJ() == aj && it->AtK() == ak && it->AtL() == al) ||
+           (it->AtI() == al && it->AtJ() == ak && it->AtK() == aj && it->AtL() == ai) )
+      {
+        idx = (int)(currentZmatrix_->begin() - it);
+        break;
+      }
+    }
+  }
+  return idx;
+}
+
 /** Model torsion */
 void Builder::ModelTorsion(TorsionModel const& MT, unsigned int iBondX, unsigned int iBondY, double dvalIn)
 {
@@ -1671,48 +1709,21 @@ void Builder::ModelTorsion(TorsionModel const& MT, unsigned int iBondX, unsigned
       iBondY >= MT.SortedAy().size())
     return;
   mprintf("CALLING ModelTorsion for iBondX=%u iBondY=%u dVal=%g\n",iBondX,iBondY,dvalIn*Constants::RADDEG);
-  int aa = MT.SortedAx()[iBondX].Idx();
-  int ax = MT.AtX().Idx();
-  int ay = MT.AtY().Idx();
-  int ad = MT.SortedAy()[iBondY].Idx();
-  // Get bond lengths FIXME deal with unknown positions
-  double l0, l1;
-  if (AssignLength(l0, aa, ax, *currentTop_, *currentFrm_, *hasPosition_)) {
-    mprinterr("Error: Could not assign length between %s and %s\n",
-              currentTop_->AtomMaskName(aa).c_str(),
-              currentTop_->AtomMaskName(ax).c_str());
-    return;
-  }
-  if (AssignLength(l1, ad, ay, *currentTop_, *currentFrm_, *hasPosition_)) {
-    mprinterr("Error: Could not assign length between %s and %s\n",
-              currentTop_->AtomMaskName(ad).c_str(),
-              currentTop_->AtomMaskName(ay).c_str());
-    return;
-  }
-  // Get angles
-  double t0, t1;
-  if (AssignTheta(t0, aa, ax, ay, *currentTop_, *currentFrm_, *hasPosition_)) {
-    mprinterr("Error: Could not assign angle between %s and %s and %s\n",
-              currentTop_->AtomMaskName(aa).c_str(),
-              currentTop_->AtomMaskName(ax).c_str(),
-              currentTop_->AtomMaskName(ay).c_str());
-    return;
-  }
-  if (AssignTheta(t1, ad, ay, ax, *currentTop_, *currentFrm_, *hasPosition_)) {
-    mprinterr("Error: Could not assign angle between %s and %s and %s\n",
-              currentTop_->AtomMaskName(ad).c_str(),
-              currentTop_->AtomMaskName(ay).c_str(),
-              currentTop_->AtomMaskName(ax).c_str());
+  MockAtom const& AA = MT.SortedAx()[iBondX];
+  MockAtom const& AX = MT.AtX();
+  MockAtom const& AY = MT.AtY();
+  MockAtom const& AD = MT.SortedAy()[iBondY];
+  if ( !(AA.BuildInternals() || AD.BuildInternals()) ) {
+    mprintf("%s does not need internals.\n", *((*currentTop_)[AA.Idx()].Name()));
     return;
   }
+  int aa = AA.Idx();
+  int ax = AX.Idx();
+  int ay = AY.Idx();
+  int ad = AD.Idx();
   // If the coordinates for the atoms are defined then
   // measure the torsion angle between them and use that for
   // the internal.
-  MockAtom const& AA = MT.SortedAx()[iBondX];
-  MockAtom const& AX = MT.AtX();
-  MockAtom const& AY = MT.AtY();
-  MockAtom const& AD = MT.SortedAy()[iBondY];
-
   double phiVal = dvalIn;
   if (AA.Known() &&
       AX.Known() &&
@@ -1723,16 +1734,52 @@ void Builder::ModelTorsion(TorsionModel const& MT, unsigned int iBondX, unsigned
                       AX.Pos().Dptr(),
                       AY.Pos().Dptr(),
                       AD.Pos().Dptr() );
+    mprintf(" %s replacing dval with %f\n", currentTop_->LeapName(aa).c_str(), phiVal*Constants::RADDEG);
+  }
+  // Look for an existing internal
+  int icIdx = getExistingInternalIdx( aa, ax, ay, ad );
+  if (icIdx < 0) {
+    // Get bond lengths FIXME deal with unknown positions
+    double l0, l1;
+    if (AssignLength(l0, aa, ax, *currentTop_, *currentFrm_, *hasPosition_)) {
+      mprinterr("Error: Could not assign length between %s and %s\n",
+                currentTop_->AtomMaskName(aa).c_str(),
+                currentTop_->AtomMaskName(ax).c_str());
+      return;
+    }
+    if (AssignLength(l1, ad, ay, *currentTop_, *currentFrm_, *hasPosition_)) {
+      mprinterr("Error: Could not assign length between %s and %s\n",
+                currentTop_->AtomMaskName(ad).c_str(),
+                currentTop_->AtomMaskName(ay).c_str());
+      return;
+    }
+    // Get angles
+    double t0, t1;
+    if (AssignTheta(t0, aa, ax, ay, *currentTop_, *currentFrm_, *hasPosition_)) {
+      mprinterr("Error: Could not assign angle between %s and %s and %s\n",
+                currentTop_->AtomMaskName(aa).c_str(),
+                currentTop_->AtomMaskName(ax).c_str(),
+                currentTop_->AtomMaskName(ay).c_str());
+      return;
+    }
+    if (AssignTheta(t1, ad, ay, ax, *currentTop_, *currentFrm_, *hasPosition_)) {
+      mprinterr("Error: Could not assign angle between %s and %s and %s\n",
+                currentTop_->AtomMaskName(ad).c_str(),
+                currentTop_->AtomMaskName(ay).c_str(),
+                currentTop_->AtomMaskName(ax).c_str());
+      return;
+    }
+
+    mprintf("++++Torsion INTERNAL: %f to %s - %s - %s - %s\n", phiVal*Constants::RADDEG,
+            currentTop_->LeapName(aa).c_str(),
+            currentTop_->LeapName(ax).c_str(),
+            currentTop_->LeapName(ay).c_str(),
+            currentTop_->LeapName(ad).c_str());
+    newZmatrix_->AddIC( InternalCoords(aa, ax, ay, ad, l0, t0*Constants::RADDEG, phiVal*Constants::RADDEG) );
+    newZmatrix_->AddIC( InternalCoords(ad, ay, ax, aa, l1, t1*Constants::RADDEG, phiVal*Constants::RADDEG) );
   } else {
-    mprinterr("Internal Error: Need to implement torsion lookup.\n");
-  }
-  mprintf("++++Torsion INTERNAL: %f to %s - %s - %s - %s\n", phiVal*Constants::RADDEG,
-          currentTop_->LeapName(aa).c_str(),
-          currentTop_->LeapName(ax).c_str(),
-          currentTop_->LeapName(ay).c_str(),
-          currentTop_->LeapName(ad).c_str());
-  newZmatrix_->AddIC( InternalCoords(aa, ax, ay, ad, l0, t0*Constants::RADDEG, phiVal*Constants::RADDEG) );
-  newZmatrix_->AddIC( InternalCoords(ad, ay, ax, aa, l1, t1*Constants::RADDEG, phiVal*Constants::RADDEG) );
+    mprintf( "Torsional INTERNAL already exists\n" );
+  }
 }
 
 /** Create torsions around SP3-SP3. */
@@ -1849,21 +1896,6 @@ void Builder::createSp2Sp2Torsions(TorsionModel const& MT) {
   return;
 }
 
-/** Find any existing internal coords around ax-ay. */
-std::vector<InternalCoords> Builder::getExistingInternals(int ax, int ay) const {
-  std::vector<InternalCoords> iTorsions;
-  if (currentZmatrix_ != 0) {
-    for (Zmatrix::const_iterator it = currentZmatrix_->begin(); it != currentZmatrix_->end(); ++it)
-    {
-      if (it->AtJ() == ax && it->AtK() == ay) {
-        iTorsions.push_back( *it );
-      }
-    }
-  }
-  return iTorsions;
-}
-
-
 /** Assign torsions around bonded atoms in manner similar to LEaP's ModelAssignTorsionsAround. */
 int Builder::assignTorsionsAroundBond(Zmatrix& zmatrix, int a1, int a2, Frame const& frameIn, Topology const& topIn, Barray const& hasPosition, int aAtomIdx)
 {
@@ -1921,11 +1953,13 @@ int Builder::assignTorsionsAroundBond(Zmatrix& zmatrix, int a1, int a2, Frame co
     Hy = H2;
   }
   static const char* hstr[] = { "SP", "SP2", "SP3", "Unknown" };
-  mprintf("DEBUG: assignTorsionsAroundBond: AX= %s (%s)  AY= %s (%s), aAtomIdx= %i\n",
+  mprintf("DEBUG: assignTorsionsAroundBond: AX= %s (%s)  AY= %s (%s), aAtomIdx= %i",
           topIn.AtomMaskName(ax).c_str(), hstr[Hx],
-          topIn.AtomMaskName(ay).c_str(), hstr[Hy], aAtomIdx);
+          topIn.AtomMaskName(ay).c_str(), hstr[Hy], aAtomIdx+1);
+  if (aAtomIdx != -1) mprintf(" %s", topIn.AtomMaskName(aAtomIdx).c_str()); // DEBUG
+  mprintf("\n"); // DEBUG
   TorsionModel mT;
-  if (mT.InitTorsion( ax, ay, frameIn, topIn, hasPosition )) {
+  if (mT.InitTorsion( ax, ay, frameIn, topIn, hasPosition, aAtomIdx )) {
     mprinterr("Error: Could not init model torsion.\n");
     return 1;
   }
@@ -2062,18 +2096,12 @@ int Builder::GenerateInternalsAroundLink(Zmatrix& zmatrix, int at0, int at1,
     return 1;
   }
   // In order to mimic the way LEaP does things, mark all atoms before
-  // this residue as having position, the first known atom of this residue
-  // has having position, and all other atoms as not having position.
+  // this residue as having position, and all other atoms as not having
+  // position.
   Residue const& R0 = topIn.Res(A0.ResNum());
   Barray tmpHasPosition( topIn.Natom(), false );
   for (int at = 0; at < R0.FirstAtom(); at++)
     tmpHasPosition[at] = true;
-  for (int at = R0.FirstAtom(); at != R0.LastAtom(); at++) {
-    if (hasPosition[at]) {
-      tmpHasPosition[at] = true;
-      break;
-    }
-  }
   // Create spanning tree across the link
   std::vector<int> span_atoms = GenerateSpanningTree(at0, at1, 4, topIn.Atoms());
   for (std::vector<int>::const_iterator it = span_atoms.begin(); 
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index d2ae985d9c..8c40d5a179 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -75,6 +75,8 @@ class Builder {
     int assignTorsionsAroundBond(Zmatrix&, int, int, Frame const&, Topology const&, Barray const&, int);
     /// Get any existing internal coords from currentZmatrix around specified atoms
     std::vector<InternalCoords> getExistingInternals(int, int) const;
+    /// Get specific internal coords from currentZmatrix
+    int getExistingInternalIdx(int, int, int, int) const;
     /// Build mock coordinates around given torsion
     int buildMockExternals(TorsionModel& MT, std::vector<InternalCoords> const& iaTorsions) const;
     /// Generate internal coords for a given atom

From e00896e690f74de1f0ea90c2625dbc22d9d2ae24 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 7 Feb 2024 10:47:45 -0500
Subject: [PATCH 0457/1492] Add more debug

---
 src/Structure/Builder.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index db85441237..9060386c5a 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1778,7 +1778,7 @@ void Builder::ModelTorsion(TorsionModel const& MT, unsigned int iBondX, unsigned
     newZmatrix_->AddIC( InternalCoords(aa, ax, ay, ad, l0, t0*Constants::RADDEG, phiVal*Constants::RADDEG) );
     newZmatrix_->AddIC( InternalCoords(ad, ay, ax, aa, l1, t1*Constants::RADDEG, phiVal*Constants::RADDEG) );
   } else {
-    mprintf( "Torsional INTERNAL already exists\n" );
+    mprintf( "Torsional INTERNAL already exists: %f\n", (*currentZmatrix_)[icIdx].Phi() );
   }
 }
 
@@ -1985,7 +1985,7 @@ int Builder::assignTorsionsAroundBond(Zmatrix& zmatrix, int a1, int a2, Frame co
     } else {
       mprintf("Completely free in assigning new torsions for: %s - %s\n",
               topIn.LeapName(ax).c_str(), topIn.LeapName(ay).c_str());
-      return 0; // FIXME DEBUG 
+      //return 0; // FIXME DEBUG 
     }
   } else {
     // Use existing atoms to determine torsions

From a6dc13fd6e54ac579ba82ce13cb6e78729ae9b6a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 7 Feb 2024 11:12:52 -0500
Subject: [PATCH 0458/1492] Generate spanning tree in exactly the same way as
 leap (without the recursion)

---
 src/Structure/GenerateConnectivityArrays.cpp | 53 +++++++++-----------
 1 file changed, 24 insertions(+), 29 deletions(-)

diff --git a/src/Structure/GenerateConnectivityArrays.cpp b/src/Structure/GenerateConnectivityArrays.cpp
index 9dada227b4..d81ccc13d0 100644
--- a/src/Structure/GenerateConnectivityArrays.cpp
+++ b/src/Structure/GenerateConnectivityArrays.cpp
@@ -60,34 +60,7 @@ BondArray Cpptraj::Structure::GenerateBondArray(std::vector<Residue> const& resi
   return out;
 }
 
-static inline void visit_tree_atom(std::vector<int>& out,
-                                   int at, int targetDepth, int currentDepth,
-                                   std::vector<bool>& atomSeen,
-                                   std::vector<Atom> const& atoms)
-{
-  if (currentDepth == targetDepth) return;
-  if (!atomSeen[at]) {
-    out.push_back( at );
-    atomSeen[at] = true;
-  }
-  for (Atom::bond_iterator bat = atoms[at].bondbegin();
-                           bat != atoms[at].bondend();
-                         ++bat)
-  {
-    if (!atomSeen[*bat]) {
-      out.push_back( *bat );
-      atomSeen[*bat] = true;
-    }
-  }
-  for (Atom::bond_iterator bat = atoms[at].bondbegin();
-                           bat != atoms[at].bondend();
-                         ++bat)
-  {
-    if (atoms[*bat].Nbonds() > 1)
-      visit_tree_atom(out, *bat, targetDepth, currentDepth+1, atomSeen, atoms);
-  }
-}
-
+/** Generate a spanning tree around two atoms in the same manner as LEaP. */ // FIXME at1 not strictly needed
 std::vector<int> Cpptraj::Structure::GenerateSpanningTree(int at0, int at1, int targetDepth,
                                                           std::vector<Atom> const& atoms)
 {
@@ -95,7 +68,29 @@ std::vector<int> Cpptraj::Structure::GenerateSpanningTree(int at0, int at1, int
 
   std::vector<bool> atomSeen(atoms.size(), false);
 
-  visit_tree_atom(out, at0, targetDepth, 0, atomSeen, atoms);
+  std::vector<int> queue;
+  std::vector<int> depth;
+
+  out.push_back( at0 );
+  queue.push_back( at0 );
+  depth.push_back( 0 );
+  atomSeen[at0] = true;
+  unsigned int idx = 0;
+  while (idx < queue.size()) {
+    Atom const& currentAt = atoms[queue[idx]];
+    for (Atom::bond_iterator bat = currentAt.bondbegin(); bat != currentAt.bondend(); ++bat)
+    {
+      if (!atomSeen[*bat]) {
+        out.push_back( *bat );
+        atomSeen[*bat] = true;
+        if (depth[idx] + 1 < targetDepth && atoms[*bat].Nbonds() > 1) {
+          queue.push_back( *bat );
+          depth.push_back( depth[idx]+1 );
+        }
+      }
+    }
+    idx++;
+  }
 
   return out;
 }

From 91979ececb10b2562ed066203301931469fc80d1 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 7 Feb 2024 13:26:16 -0500
Subject: [PATCH 0459/1492] Only use structureBuilder

---
 src/Exec_Build.cpp | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index b2ed9419aa..3e73ffdce7 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -395,9 +395,9 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
       resIsBuilt.push_back( false );
   }
 
-  Cpptraj::Structure::Builder linkBuilder;
-  linkBuilder.SetDebug( 1 ); // FIXME
-  linkBuilder.SetParameters( &mainParmSet );
+//  Cpptraj::Structure::Builder linkBuilder;
+//  linkBuilder.SetDebug( 1 ); // FIXME
+//  linkBuilder.SetParameters( &mainParmSet );
   bool buildFailed = false;
   TermTypeArray::const_iterator termType = ResTypes.begin(); // FIXME is termType needed?
   for (Zarray::const_iterator it = ResZmatrices.begin(); it != ResZmatrices.end(); ++it, ++termType)
@@ -411,7 +411,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
       mprintf("DEBUG: Zmatrix for building residue %li %s\n", ires + 1,
               topOut.TruncResNameOnumId(ires).c_str());
       zmatrix->print(&topOut);
-      linkBuilder.SetZmatrix( zmatrix );
+//      linkBuilder.SetZmatrix( zmatrix );
       // Is this residue connected to an earlier residue?
       for (IParray::const_iterator resBonds = resBondingAtoms[ires].begin();
                                    resBonds != resBondingAtoms[ires].end(); ++resBonds)
@@ -463,7 +463,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
 //        return 1;
 //      }
       // Update internal coords from known positions
-      if (linkBuilder.UpdateICsFromFrame( *zmatrix, frameOut, ires, topOut, hasPosition )) {
+      if (structureBuilder.UpdateICsFromFrame( *zmatrix, frameOut, ires, topOut, hasPosition )) {
         mprinterr("Error: Failed to update Zmatrix with values from existing positions.\n");
         return 1;
       }

From ca03b6ab46697b6c6cf443eef018f2118f54a4a5 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 7 Feb 2024 13:27:09 -0500
Subject: [PATCH 0460/1492] Do a better search for existing internals. Dont add
 to the temp Zmatrix

---
 src/Structure/Builder.cpp | 25 +++++++++++++++++++++----
 src/Structure/Builder.h   |  2 +-
 2 files changed, 22 insertions(+), 5 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 9060386c5a..46ea20ae9a 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1681,6 +1681,24 @@ std::vector<InternalCoords> Builder::getExistingInternals(int ax, int ay) const
         iTorsions.push_back( *it );
       }
     }
+    for (Zmatrix::const_iterator it = currentZmatrix_->begin(); it != currentZmatrix_->end(); ++it)
+    {
+      if (it->AtJ() == ay && it->AtK() == ax) {
+        // Avoid duplicates FIXME just track torsions eventually not the whole zmatrix
+        bool duplicate = false;
+        for (std::vector<InternalCoords>::const_iterator jt = iTorsions.begin(); jt != iTorsions.end(); ++jt) {
+          if (jt->AtI() == it->AtL() &&
+              jt->AtJ() == it->AtK() &&
+              jt->AtK() == it->AtJ() &&
+              jt->AtL() == it->AtI())
+          {
+            duplicate = true;
+            break;
+          }
+        }
+        if (!duplicate) iTorsions.push_back( *it );
+      }
+    }
   }
   return iTorsions;
 }
@@ -2050,7 +2068,7 @@ int Builder::GenerateInternals(Zmatrix& zmatrix, Frame const& frameIn, Topology
 }
 
 /** Build internal coordinates around an atom. */
-int Builder::generateAtomInternals(int at, Frame const& frameIn, Topology const& topIn, Barray const& hasPosition)
+int Builder::generateAtomInternals(Zmatrix& zmatrix, int at, Frame const& frameIn, Topology const& topIn, Barray const& hasPosition)
 {
   mprintf( "Building internals for: %s\n", topIn.LeapName(at).c_str());
   Atom const& AtA = topIn[at];
@@ -2067,8 +2085,7 @@ int Builder::generateAtomInternals(int at, Frame const& frameIn, Topology const&
         int iShouldBe = (AtB.Nbonds() - 1) * (AtC.Nbonds() - 1);
         mprintf("ISHOULDBE= %i ITORSIONS= %zu\n", iShouldBe, iTorsions.size());
         if (iShouldBe != (int)iTorsions.size()) {
-          Zmatrix tmpz; // FIXME
-          assignTorsionsAroundBond(tmpz, *bat, *cat, frameIn, topIn, hasPosition, at);
+          assignTorsionsAroundBond(zmatrix, *bat, *cat, frameIn, topIn, hasPosition, at);
         }
       }
     }
@@ -2108,7 +2125,7 @@ int Builder::GenerateInternalsAroundLink(Zmatrix& zmatrix, int at0, int at1,
                                         it != span_atoms.end(); ++it)
   {
     //mprintf("SPANNING TREE ATOM: %s\n", topIn.LeapName(*it).c_str());
-    if (generateAtomInternals(*it, frameIn, topIn, tmpHasPosition)) {
+    if (generateAtomInternals(zmatrix, *it, frameIn, topIn, tmpHasPosition)) {
       mprinterr("Error: Could not generate internals for atom %s\n", topIn.AtomMaskName(*it).c_str());
       return 1;
     }
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index 8c40d5a179..ffe6d47ac0 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -80,7 +80,7 @@ class Builder {
     /// Build mock coordinates around given torsion
     int buildMockExternals(TorsionModel& MT, std::vector<InternalCoords> const& iaTorsions) const;
     /// Generate internal coords for a given atom
-    int generateAtomInternals(int, Frame const&, Topology const&, Barray const&);
+    int generateAtomInternals(Zmatrix&, int, Frame const&, Topology const&, Barray const&);
 
     int debug_;
     ParameterSet const* params_;

From 9a40eba79b9d2d24a4c0eb6f2bab3992056b69cd Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 7 Feb 2024 14:29:47 -0500
Subject: [PATCH 0461/1492] Start reformatting for saving internals

---
 src/Exec_Build.cpp        |  39 +++---
 src/Structure/Builder.cpp | 261 +++++++++++++-------------------------
 src/Structure/Builder.h   |  63 ++++++---
 3 files changed, 159 insertions(+), 204 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 3e73ffdce7..942821ddf6 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -184,7 +184,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
   hasPosition.reserve( newNatom );
 
   // Hold Z-matrices for residues that have missing atoms
-  typedef std::vector<Cpptraj::Structure::Zmatrix*> Zarray;
+  typedef std::vector<Cpptraj::Structure::Builder*> Zarray;
   Zarray ResZmatrices;
   ResZmatrices.reserve( topIn.Nres() );
 
@@ -194,9 +194,9 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
   typedef std::vector<ResAtPair> ResAtArray;
   ResAtArray interResBonds;
 
-  Cpptraj::Structure::Builder structureBuilder;
-  structureBuilder.SetDebug( 1 );
-  structureBuilder.SetParameters( &mainParmSet );
+  //Cpptraj::Structure::Builder structureBuilder;
+  //structureBuilder.SetDebug( 1 );
+  //structureBuilder.SetParameters( &mainParmSet );
 
   // For holding bonded atom pairs
   typedef std::pair<int,int> Ipair;
@@ -303,21 +303,23 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
       if (atomsNeedBuilding) {
         Frame templateFrame = resTemplate->AllocateFrame();
         resTemplate->GetFrame( 0, templateFrame );
-        Cpptraj::Structure::Zmatrix* zmatrix = new Cpptraj::Structure::Zmatrix();
+        Cpptraj::Structure::Builder* structureBuilder = new Cpptraj::Structure::Builder();
+        structureBuilder->SetDebug( 1 ); // DEBUG FIXME
+        structureBuilder->SetParameters( &mainParmSet );
         //if (zmatrix->SetFromFrameAndConnect( templateFrame, resTemplate->Top() )) {
 //        if (zmatrix->GenerateInternals( templateFrame, resTemplate->Top() )) {
 //          mprinterr("Error: Could not set up residue template zmatrix.\n");
 //          return 1;
 //        }
-        if (structureBuilder.GenerateInternals(*zmatrix, templateFrame, resTemplate->Top(),
+        if (structureBuilder->GenerateInternals(templateFrame, resTemplate->Top(),
                                                std::vector<bool>(resTemplate->Top().Natom(), true)))
         {
           mprinterr("Error: Generate internals for residue template failed.\n");
           return 1;
         }
 //        zmatrix->print( resTemplate->TopPtr() );
-        zmatrix->OffsetIcIndices( atomOffset );
-        ResZmatrices.push_back( zmatrix );
+        structureBuilder->UpdateIndicesWithOffset( atomOffset );
+        ResZmatrices.push_back( structureBuilder );
 //        zmatrix->print( &topOut );
         //for (Iarray::const_iterator jres = resConnections[ires].begin();
         //                            jres != resConnections[ires].end(); ++jres)
@@ -403,14 +405,14 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
   for (Zarray::const_iterator it = ResZmatrices.begin(); it != ResZmatrices.end(); ++it, ++termType)
   {
     long int ires = it-ResZmatrices.begin();
-    Cpptraj::Structure::Zmatrix* zmatrix = *it;
-    if (zmatrix != 0) {
+    Cpptraj::Structure::Builder* structureBuilder = *it;
+    if (structureBuilder != 0) {
       mprintf("DEBUG: ***** BUILD residue %li %s *****\n", ires + 1,
               topOut.TruncResNameOnumId(ires).c_str());
       mprintf("DEBUG: Residue type: %s terminal\n", Cpptraj::Structure::terminalStr(*termType));
-      mprintf("DEBUG: Zmatrix for building residue %li %s\n", ires + 1,
-              topOut.TruncResNameOnumId(ires).c_str());
-      zmatrix->print(&topOut);
+      //mprintf("DEBUG: Zmatrix for building residue %li %s\n", ires + 1,
+      //        topOut.TruncResNameOnumId(ires).c_str());
+      //zmatrix->print(&topOut);
 //      linkBuilder.SetZmatrix( zmatrix );
       // Is this residue connected to an earlier residue?
       for (IParray::const_iterator resBonds = resBondingAtoms[ires].begin();
@@ -422,8 +424,8 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
                   topOut.AtomMaskName(resBonds->second).c_str());
           topOut.AddBond(resBonds->first, resBonds->second);
           // FIXME DEBUG
-          structureBuilder.SetZmatrix( zmatrix );
-          if (structureBuilder.GenerateInternalsAroundLink(*zmatrix, resBonds->first, resBonds->second,
+          //structureBuilder.SetZmatrix( zmatrix );
+          if (structureBuilder->GenerateInternalsAroundLink(resBonds->first, resBonds->second,
                                                            frameOut, topOut, hasPosition))
           {
             mprinterr("Error: Assign torsions around inter-residue link %s - %s failed.\n",
@@ -463,7 +465,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
 //        return 1;
 //      }
       // Update internal coords from known positions
-      if (structureBuilder.UpdateICsFromFrame( *zmatrix, frameOut, ires, topOut, hasPosition )) {
+      if (structureBuilder->UpdateICsFromFrame( frameOut, ires, topOut, hasPosition )) {
         mprinterr("Error: Failed to update Zmatrix with values from existing positions.\n");
         return 1;
       }
@@ -472,8 +474,9 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
       //  mprinterr("Error: Could not set up seed atoms for Zmatrix.\n");
       //  buildFailed = true;
       //} else {
-        zmatrix->SetDebug( 1 ); // DEBUG
-        if (zmatrix->SetToFrame( frameOut, hasPosition )) {
+        Cpptraj::Structure::Zmatrix tmpz; // FIXME
+        tmpz.SetDebug( 1 ); // DEBUG
+        if (tmpz.SetToFrame( frameOut, hasPosition )) {
           mprinterr("Error: Building residue %s failed.\n",
                     topOut.TruncResNameOnumId(ires).c_str());
           buildFailed = true;
diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 46ea20ae9a..669fe56490 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -17,11 +17,9 @@ using namespace Cpptraj::Structure;
 Builder::Builder() :
   debug_(0),
   params_(0),
-  currentZmatrix_(0),
   currentTop_(0),
   currentFrm_(0),
-  hasPosition_(0),
-  newZmatrix_(0)
+  hasPosition_(0)
 {}
 
 /** Set optional parameter set. */
@@ -33,15 +31,6 @@ void Cpptraj::Structure::Builder::SetParameters(ParameterSet const* paramsIn) {
   params_ = paramsIn;
 }
 
-/** Set optional Zmatrix. */
-void Cpptraj::Structure::Builder::SetZmatrix(Zmatrix const* zmatrixIn) {
-  if (zmatrixIn == 0) {
-    mprinterr("Internal Error: Builder::SetZmatrix called with null set.\n");
-    return;
-  }
-  currentZmatrix_ = zmatrixIn;
-}
-
 // -----------------------------------------------------------------------------
 /** Get length from parameter set if present.
   * \return 1 if a length parameter was found.
@@ -158,7 +147,9 @@ const
                   topIn.LeapName(aj).c_str(), 
                   topIn.LeapName(atomk).c_str(),
                   ajTheta * Constants::RADDEG);
-        } else if (currentZmatrix_ != 0) { // FIXME faster search?
+         } else {
+           mprinterr("Internal Error: Implement angle lookup.\n");
+        /*} else if (currentZmatrix_ != 0) { // FIXME faster search?
           for (Zmatrix::const_iterator ic = currentZmatrix_->begin(); ic != currentZmatrix_->end(); ++ic) {
             if (ic->AtI() == atomi && ic->AtJ() == aj && ic->AtK() == atomk) {
               // TODO: Check that repeats are equal?
@@ -171,7 +162,7 @@ const
                       ic->Theta());
               break;
             }
-          }
+          }*/
         }
         thetaVals.push_back( ajTheta );
       } // END inner loop over bonds to AJ
@@ -1087,114 +1078,58 @@ const
 /** For existing torsions, see if all coordinates in that torsion
   * exist. If so, update the IC from the existing coordinates.
   */
-int Builder::UpdateICsFromFrame(Zmatrix& zmatrix, Frame const& frameIn, int ires, Topology const& topIn, Barray const& hasPosition)
-const
+int Builder::UpdateICsFromFrame(Frame const& frameIn, int ires, Topology const& topIn, Barray const& hasPosition)
 {
-  // Update bond/angle values for atoms with no position.
-//  for (unsigned int idx = 0; idx != zmatrix.N_IC(); idx++)
-//  {
-/*    InternalCoords& thisIc = zmatrix.ModifyIC(idx);
-    if (hasPosition[thisIc.AtI()] && hasPosition[thisIc.AtJ()]) {
-      // Bond exists.
-      double dist = DIST2_NoImage( frameIn.XYZ(thisIc.AtI()), frameIn.XYZ(thisIc.AtJ()) );
-      mprintf("DEBUG: Replacing existing bond length %g for %s - %s with existing length %g\n",
-              thisIc.Dist(), topIn.AtomMaskName(thisIc.AtI()).c_str(),
-              topIn.AtomMaskName(thisIc.AtJ()).c_str(), dist);
-      thisIc.SetDist( dist );
-      if (hasPosition[thisIc.AtK()]) {
-        // Angle also exists
-        double theta = CalcAngle(frameIn.XYZ(thisIc.AtI()),
-                                 frameIn.XYZ(thisIc.AtJ()),
-                                 frameIn.XYZ(thisIc.AtK()));
-        theta *= Constants::RADDEG;
-        mprintf("DEBUG: Replacing existing angle %g for %s - %s - %s with existing angle %g\n",
-                thisIc.Theta(), topIn.AtomMaskName(thisIc.AtI()).c_str(),
-                topIn.AtomMaskName(thisIc.AtJ()).c_str(), topIn.AtomMaskName(thisIc.AtK()).c_str(),
-                theta);
-        thisIc.SetTheta( theta );
-    }
-  }*/
-/*
-    if (!hasPosition[thisIc.AtI()]) {
-      double dist = 0;
-      if (getLengthParam( dist, thisIc.AtI(), thisIc.AtJ(), topIn )) {
-        mprintf("DEBUG: Replacing existing bond length %g for %s - %s with parameter %g\n",
-                thisIc.Dist(), topIn.AtomMaskName(thisIc.AtI()).c_str(),
-                topIn.AtomMaskName(thisIc.AtJ()).c_str(), dist);
-        thisIc.SetDist( dist );
-      }
-      double theta = 0;
-      if (getAngleParam( theta, thisIc.AtI(), thisIc.AtJ(), thisIc.AtK(), topIn)) {
-        theta *= Constants::RADDEG;
-        mprintf("DEBUG: Replacing existing angle %g for %s - %s - %s with parameter %g\n",
-                thisIc.Theta(), topIn.AtomMaskName(thisIc.AtI()).c_str(),
-                topIn.AtomMaskName(thisIc.AtJ()).c_str(), topIn.AtomMaskName(thisIc.AtK()).c_str(),
-                theta);
-        thisIc.SetTheta( theta );
-      }
-    }
-*/
-//  } // END loop over zmatrix ICs
-  // Update torsions
-  Barray isUsed( zmatrix.N_IC(), false );
-  //unsigned int Nused = 0;
-  // Get list of bonds 
+  // Update torsions.
+  // Get list of bonds.
   BondArray myBonds = GenerateBondArray( std::vector<Residue>(1, topIn.Res(ires)), topIn.Atoms() );
   for (BondArray::const_iterator bnd = myBonds.begin(); bnd != myBonds.end(); ++bnd) {
     if (topIn[bnd->A1()].ResNum() == ires && topIn[bnd->A2()].ResNum() == ires) {
-      mprintf("DEBUG: Looking at torsions around: %s - %s\n", topIn.AtomMaskName(bnd->A1()).c_str(), topIn.AtomMaskName(bnd->A2()).c_str());    // Find all ICs that share atoms 1 and 2 (J and K)
-      Iarray bondICs;
+      mprintf("DEBUG: Looking at torsions around: %s - %s\n", topIn.AtomMaskName(bnd->A1()).c_str(), topIn.AtomMaskName(bnd->A2()).c_str());
+      // Find all ICs that share atoms 1 and 2 (J and K)
       bool needsUpdate = false;
       double tDiff = 0;
-      for (unsigned int idx = 0; idx != zmatrix.N_IC(); idx++)
+      Tarray iTorsions = getExistingTorsions(bnd->A1(), bnd->A2());
+      for (unsigned int idx = 0; idx != iTorsions.size(); idx++)
       {
-        if (!isUsed[idx]) {
-          InternalCoords& thisIc = zmatrix.ModifyIC(idx);
-          if ( (bnd->A1() == thisIc.AtJ() && bnd->A2() == thisIc.AtK()) ||
-               (bnd->A2() == thisIc.AtJ() && bnd->A1() == thisIc.AtK()) )
-          {
-            // This IC has this bond at the center
-            bondICs.push_back( idx );
-            isUsed[idx] = true;
-            //MARK(idx, isUsed, Nused);
-            if (hasPosition[thisIc.AtI()] &&
-                hasPosition[thisIc.AtJ()] &&
-                hasPosition[thisIc.AtK()] &&
-                hasPosition[thisIc.AtL()])
-            {
-              mprintf("DEBUG:\tMeasuring torsion of fixed atoms: %s - %s - %s - %s\n",
-                      topIn.LeapName(thisIc.AtI()).c_str(),
-                      topIn.LeapName(thisIc.AtJ()).c_str(),
-                      topIn.LeapName(thisIc.AtK()).c_str(),
-                      topIn.LeapName(thisIc.AtL()).c_str());
-              InternalCoords frameIc = calcKnownAtomIc(thisIc.AtI(), thisIc.AtJ(), thisIc.AtK(), thisIc.AtL(), frameIn);
-              double dTorsion = frameIc.Phi() * Constants::DEGRAD;
-              double dInternalValue = thisIc.Phi() * Constants::DEGRAD;
-              tDiff = (dTorsion - dInternalValue) * Constants::RADDEG;
-              mprintf("DEBUG:\tdTorsion= %f  dInternalValue= %f\n", dTorsion, dInternalValue);
-              thisIc = frameIc;
-              needsUpdate = true;
-            } // END all IC coords present
-          } // END this IC matches current bond
-        } // END IC is not used
-      } // END loop searching for ICs matching current bond
+        InternalTorsion const& thisIc = internalTorsions_[idx];
+        if (hasPosition[thisIc.AtI()] &&
+            hasPosition[thisIc.AtJ()] &&
+            hasPosition[thisIc.AtK()] &&
+            hasPosition[thisIc.AtL()])
+        {
+          mprintf("DEBUG:\tMeasuring torsion of fixed atoms: %s - %s - %s - %s\n",
+                  topIn.LeapName(thisIc.AtI()).c_str(),
+                  topIn.LeapName(thisIc.AtJ()).c_str(),
+                  topIn.LeapName(thisIc.AtK()).c_str(),
+                  topIn.LeapName(thisIc.AtL()).c_str());
+          double dTorsion = Torsion(frameIn.XYZ(thisIc.AtI()),
+                                    frameIn.XYZ(thisIc.AtJ()),
+                                    frameIn.XYZ(thisIc.AtK()),
+                                    frameIn.XYZ(thisIc.AtL()));
+          double dInternalValue = thisIc.PhiVal();
+          tDiff = (dTorsion - dInternalValue);
+          mprintf("DEBUG:\tdTorsion= %f  dInternalValue= %f\n", dTorsion*Constants::RADDEG, dInternalValue*Constants::RADDEG);
+          needsUpdate = true;
+        } // END all coords present
+      } // END loop over torsions matching current bond
       // If any difference was found, shift all of the torsions
       if (needsUpdate) {
         mprintf("DEBUG: Twisting torsions centered on %s - %s by %f degrees\n",
                 topIn.LeapName(bnd->A1()).c_str(),
                 topIn.LeapName(bnd->A2()).c_str(),
                 tDiff);
-        for (Iarray::const_iterator it = bondICs.begin(); it != bondICs.end(); ++it)
-        {
-          InternalCoords& thisIc = zmatrix.ModifyIC(*it);
-          double dNew = thisIc.Phi() + tDiff;
-          mprintf("DEBUG:\tTwisting torsion for atoms: %s-%s-%s-%s\n",
-                  topIn.AtomMaskName(thisIc.AtI()).c_str(),
-                  topIn.AtomMaskName(thisIc.AtJ()).c_str(),
-                  topIn.AtomMaskName(thisIc.AtK()).c_str(),
-                  topIn.AtomMaskName(thisIc.AtL()).c_str());
-          mprintf("DEBUG:\t------- From %f to %f\n", thisIc.Phi(), dNew);
-          thisIc.SetPhi( dNew );
+      for (unsigned int idx = 0; idx != iTorsions.size(); idx++)
+      {
+        InternalTorsion& thisIc = internalTorsions_[idx];
+        double dNew = thisIc.PhiVal() + tDiff;
+        mprintf("DEBUG:\tTwisting torsion for atoms: %s-%s-%s-%s\n",
+                topIn.AtomMaskName(thisIc.AtI()).c_str(),
+                topIn.AtomMaskName(thisIc.AtJ()).c_str(),
+                topIn.AtomMaskName(thisIc.AtK()).c_str(),
+                topIn.AtomMaskName(thisIc.AtL()).c_str());
+          mprintf("DEBUG:\t------- From %f to %f\n", thisIc.PhiVal()*Constants::RADDEG, dNew*Constants::RADDEG);
+          thisIc.SetPhiVal( dNew );
         }
       } // END ICs need update
     } // END both bond atoms belong to this residue
@@ -1244,7 +1179,7 @@ class Cpptraj::Structure::Builder::TorsionModel {
     /// Set up torsions around bonded atoms
     int SetupTorsion(AtomType::HybridizationType, AtomType::HybridizationType, Topology const& topIn);
     /// Build mock externals from given internals
-    int BuildMockExternals(std::vector<InternalCoords> const&, Topology const&);
+    int BuildMockExternals(Tarray const&, Topology const&);
 
     /// \return Value of A-X-Y-D torsion in radians
     double Absolute() const { return dAbsolute_; }
@@ -1533,7 +1468,7 @@ static inline std::vector<MockAtom>::iterator find_mock_atom(std::vector<MockAto
   * By definition, the two central atoms will be the same for each
   * IC in iaTorsions.
   */
-int Cpptraj::Structure::Builder::TorsionModel::BuildMockExternals(std::vector<InternalCoords> const& iaTorsions,
+int Cpptraj::Structure::Builder::TorsionModel::BuildMockExternals(Tarray const& iaTorsions,
                                                                   Topology const& topIn) // DEBUG topIn for debug only
 {
   if (iaTorsions.empty()) {
@@ -1542,14 +1477,13 @@ int Cpptraj::Structure::Builder::TorsionModel::BuildMockExternals(std::vector<In
   }
   mprintf("=======  Started mock coords from: %s\n", topIn.LeapName(iaTorsions.front().AtI()).c_str());
 
-  for (std::vector<InternalCoords>::const_iterator ic = iaTorsions.begin();
-                                                   ic != iaTorsions.end(); ++ic)
+  for (Tarray::const_iterator ic = iaTorsions.begin(); ic != iaTorsions.end(); ++ic)
     mprintf("------- Known torsion: %s - %s - %s - %s  %f\n",
             topIn.LeapName(ic->AtI()).c_str(),
             topIn.LeapName(ic->AtJ()).c_str(),
             topIn.LeapName(ic->AtK()).c_str(),
             topIn.LeapName(ic->AtL()).c_str(),
-            ic->Phi());
+            ic->PhiVal()*Constants::RADDEG);
 
   // Define coordinates for the central atoms.
   //Vec3 posX(0, 0, 0);
@@ -1570,8 +1504,7 @@ int Cpptraj::Structure::Builder::TorsionModel::BuildMockExternals(std::vector<In
   Marray outerAtoms;
 
   // Define outer atoms
-  for (std::vector<InternalCoords>::const_iterator ic = iaTorsions.begin();
-                                                   ic != iaTorsions.end(); ++ic)
+  for (Tarray::const_iterator ic = iaTorsions.begin(); ic != iaTorsions.end(); ++ic)
   {
     if (ic == iaTorsions.begin()) {
       // Define first outer atom as being in the XY plane
@@ -1599,7 +1532,7 @@ int Cpptraj::Structure::Builder::TorsionModel::BuildMockExternals(std::vector<In
     //bool gotOne = false;
     for (unsigned int jdx = 0; jdx != iaTorsions.size(); jdx++) {
       if (!used[jdx]) {
-        InternalCoords const& iInt = iaTorsions[jdx];
+        InternalTorsion const& iInt = iaTorsions[jdx];
         Marray::iterator tmpAt1 = find_mock_atom(outerAtoms, iInt.AtI());
         Marray::iterator tmpAt4 = find_mock_atom(outerAtoms, iInt.AtL());
         if (tmpAt1 == outerAtoms.end()) {
@@ -1635,7 +1568,7 @@ int Cpptraj::Structure::Builder::TorsionModel::BuildMockExternals(std::vector<In
                    topIn.LeapName(iInt.AtL()).c_str(),
                    (int)tmpAt1->Known(), (int)tmpAt4->Known());
           // Now build the coordinate for the target atom
-          tgt->SetPos( Zmatrix::AtomIposition(maPC1, maPC2, knownAt->Pos(), 1.0, 90.0, iInt.Phi()) );
+          tgt->SetPos( Zmatrix::AtomIposition(maPC1, maPC2, knownAt->Pos(), 1.0, 90.0, iInt.PhiVal()*Constants::RADDEG) );
           mprintf("ZMatrixAll:  %f,%f,%f\n", tgt->Pos()[0], tgt->Pos()[1], tgt->Pos()[2]);
           used[jdx] = true;
           nused++;
@@ -1671,50 +1604,36 @@ int Cpptraj::Structure::Builder::TorsionModel::BuildMockExternals(std::vector<In
 }
 
 // -----------------------------------------------------------------------------
-/** Find any existing internal coords around ax-ay. */ // TODO put in Zmatrix?
-std::vector<InternalCoords> Builder::getExistingInternals(int ax, int ay) const {
-  std::vector<InternalCoords> iTorsions;
-  if (currentZmatrix_ != 0) {
-    for (Zmatrix::const_iterator it = currentZmatrix_->begin(); it != currentZmatrix_->end(); ++it)
-    {
-      if (it->AtJ() == ax && it->AtK() == ay) {
-        iTorsions.push_back( *it );
-      }
-    }
-    for (Zmatrix::const_iterator it = currentZmatrix_->begin(); it != currentZmatrix_->end(); ++it)
+/** Update all indices in internals according to the given offset. */
+void Builder::UpdateIndicesWithOffset(int atomOffset) {
+  for (Tarray::iterator it = internalTorsions_.begin(); it != internalTorsions_.end(); ++it)
+    it->OffsetIndices( atomOffset );
+}
+
+/** Find any existing torsions around ax-ay. */
+Builder::Tarray Builder::getExistingTorsions(int ax, int ay) const {
+  Tarray iTorsions;
+  for (Tarray::const_iterator it = internalTorsions_.begin(); it != internalTorsions_.end(); ++it)
+  {
+    if ((it->AtJ() == ax && it->AtK() == ay) ||
+        (it->AtJ() == ay && it->AtJ() == ax))
     {
-      if (it->AtJ() == ay && it->AtK() == ax) {
-        // Avoid duplicates FIXME just track torsions eventually not the whole zmatrix
-        bool duplicate = false;
-        for (std::vector<InternalCoords>::const_iterator jt = iTorsions.begin(); jt != iTorsions.end(); ++jt) {
-          if (jt->AtI() == it->AtL() &&
-              jt->AtJ() == it->AtK() &&
-              jt->AtK() == it->AtJ() &&
-              jt->AtL() == it->AtI())
-          {
-            duplicate = true;
-            break;
-          }
-        }
-        if (!duplicate) iTorsions.push_back( *it );
-      }
+      iTorsions.push_back( *it );
     }
   }
   return iTorsions;
 }
 
-/** \return index of internal coords matching the 4 given atoms, -1 for no match. */ // TODO put in Zmatrix?
-int Builder::getExistingInternalIdx(int ai, int aj, int ak, int al) const {
+/** \return index of existing torsion matching the 4 given atoms, -1 for no match. */
+int Builder::getExistingTorsionIdx(int ai, int aj, int ak, int al) const {
   int idx = -1;
-  if (currentZmatrix_ != 0) {
-    for (Zmatrix::const_iterator it = currentZmatrix_->begin(); it != currentZmatrix_->end(); ++it)
+  for (Tarray::const_iterator it = internalTorsions_.begin(); it != internalTorsions_.end(); ++it)
+  {
+    if ( (it->AtI() == ai && it->AtJ() == aj && it->AtK() == ak && it->AtL() == al) ||
+         (it->AtI() == al && it->AtJ() == ak && it->AtK() == aj && it->AtL() == ai) )
     {
-      if ( (it->AtI() == ai && it->AtJ() == aj && it->AtK() == ak && it->AtL() == al) ||
-           (it->AtI() == al && it->AtJ() == ak && it->AtK() == aj && it->AtL() == ai) )
-      {
-        idx = (int)(currentZmatrix_->begin() - it);
-        break;
-      }
+      idx = (int)(internalTorsions_.begin() - it);
+      break;
     }
   }
   return idx;
@@ -1755,9 +1674,9 @@ void Builder::ModelTorsion(TorsionModel const& MT, unsigned int iBondX, unsigned
     mprintf(" %s replacing dval with %f\n", currentTop_->LeapName(aa).c_str(), phiVal*Constants::RADDEG);
   }
   // Look for an existing internal
-  int icIdx = getExistingInternalIdx( aa, ax, ay, ad );
+  int icIdx = getExistingTorsionIdx( aa, ax, ay, ad );
   if (icIdx < 0) {
-    // Get bond lengths FIXME deal with unknown positions
+/*    // Get bond lengths FIXME deal with unknown positions
     double l0, l1;
     if (AssignLength(l0, aa, ax, *currentTop_, *currentFrm_, *hasPosition_)) {
       mprinterr("Error: Could not assign length between %s and %s\n",
@@ -1786,17 +1705,18 @@ void Builder::ModelTorsion(TorsionModel const& MT, unsigned int iBondX, unsigned
                 currentTop_->AtomMaskName(ay).c_str(),
                 currentTop_->AtomMaskName(ax).c_str());
       return;
-    }
+    }*/
 
     mprintf("++++Torsion INTERNAL: %f to %s - %s - %s - %s\n", phiVal*Constants::RADDEG,
             currentTop_->LeapName(aa).c_str(),
             currentTop_->LeapName(ax).c_str(),
             currentTop_->LeapName(ay).c_str(),
             currentTop_->LeapName(ad).c_str());
-    newZmatrix_->AddIC( InternalCoords(aa, ax, ay, ad, l0, t0*Constants::RADDEG, phiVal*Constants::RADDEG) );
-    newZmatrix_->AddIC( InternalCoords(ad, ay, ax, aa, l1, t1*Constants::RADDEG, phiVal*Constants::RADDEG) );
+    internalTorsions_.push_back( InternalTorsion(aa, ax, ay, ad, phiVal) );
+    //newZmatrix_->AddIC( InternalCoords(aa, ax, ay, ad, l0, t0*Constants::RADDEG, phiVal*Constants::RADDEG) );
+    //newZmatrix_->AddIC( InternalCoords(ad, ay, ax, aa, l1, t1*Constants::RADDEG, phiVal*Constants::RADDEG) );
   } else {
-    mprintf( "Torsional INTERNAL already exists: %f\n", (*currentZmatrix_)[icIdx].Phi() );
+    mprintf( "Torsional INTERNAL already exists: %f\n", internalTorsions_[icIdx].PhiVal()*Constants::RADDEG );
   }
 }
 
@@ -1915,11 +1835,10 @@ void Builder::createSp2Sp2Torsions(TorsionModel const& MT) {
 }
 
 /** Assign torsions around bonded atoms in manner similar to LEaP's ModelAssignTorsionsAround. */
-int Builder::assignTorsionsAroundBond(Zmatrix& zmatrix, int a1, int a2, Frame const& frameIn, Topology const& topIn, Barray const& hasPosition, int aAtomIdx)
+int Builder::assignTorsionsAroundBond(int a1, int a2, Frame const& frameIn, Topology const& topIn, Barray const& hasPosition, int aAtomIdx)
 {
   // Save addresses of zmatrix, frame, topology, and hasPosition.
   // These are required for the createSpXSpX routines. TODO zero them at the end?
-  newZmatrix_ = &zmatrix;
   currentFrm_ = &frameIn;
   currentTop_ = &topIn;
   hasPosition_ = &hasPosition;
@@ -1988,7 +1907,7 @@ int Builder::assignTorsionsAroundBond(Zmatrix& zmatrix, int a1, int a2, Frame co
   mprintf("bKnownX=%i  bKnownY=%i\n", (int)mT.AxHasKnownAtoms(), (int)mT.AyHasKnownAtoms());
   if (!(mT.AxHasKnownAtoms() && mT.AyHasKnownAtoms())) {
     // Find any existing internal coords around ax-ay
-    std::vector<InternalCoords> iTorsions = getExistingInternals(ax, ay);
+    Tarray iTorsions = getExistingTorsions(ax, ay);
     if (!iTorsions.empty()) {
       mprintf("Using INTERNALs to fit new torsions around: %s - %s\n",
               topIn.LeapName(ax).c_str(), topIn.LeapName(ay).c_str());
@@ -2046,16 +1965,16 @@ int Builder::assignTorsionsAroundBond(Zmatrix& zmatrix, int a1, int a2, Frame co
 /** Generate internal coordinates in the same
   * manner as LEaP's BuildInternalsForContainer/ModelAssignTorsionsAround.
   */
-int Builder::GenerateInternals(Zmatrix& zmatrix, Frame const& frameIn, Topology const& topIn, Barray const& hasPosition)
+int Builder::GenerateInternals(Frame const& frameIn, Topology const& topIn, Barray const& hasPosition)
 {
   mprintf("DEBUG: ----- Entering Builder::GenerateInternals. -----\n");
-  zmatrix.clear();
+//  zmatrix.clear();
   // First generate the bond array
   BondArray bonds = GenerateBondArray( topIn.Residues(), topIn.Atoms() );
   // Loop over bonds
   for (BondArray::const_iterator bnd = bonds.begin(); bnd != bonds.end(); ++bnd)
   {
-    if (assignTorsionsAroundBond( zmatrix, bnd->A1(), bnd->A2(), frameIn, topIn, hasPosition, -1 )) {
+    if (assignTorsionsAroundBond( bnd->A1(), bnd->A2(), frameIn, topIn, hasPosition, -1 )) {
       mprinterr("Error Assign torsions around bond %s - %s failed.\n",
                 topIn.AtomMaskName(bnd->A1()).c_str(),
                 topIn.AtomMaskName(bnd->A2()).c_str());
@@ -2068,7 +1987,7 @@ int Builder::GenerateInternals(Zmatrix& zmatrix, Frame const& frameIn, Topology
 }
 
 /** Build internal coordinates around an atom. */
-int Builder::generateAtomInternals(Zmatrix& zmatrix, int at, Frame const& frameIn, Topology const& topIn, Barray const& hasPosition)
+int Builder::generateAtomInternals(int at, Frame const& frameIn, Topology const& topIn, Barray const& hasPosition)
 {
   mprintf( "Building internals for: %s\n", topIn.LeapName(at).c_str());
   Atom const& AtA = topIn[at];
@@ -2081,11 +2000,11 @@ int Builder::generateAtomInternals(Zmatrix& zmatrix, int at, Frame const& frameI
                topIn.LeapName(at).c_str(),
                topIn.LeapName(*bat).c_str(),
                topIn.LeapName(*cat).c_str());
-        std::vector<InternalCoords> iTorsions = getExistingInternals(*bat, *cat);
+        Tarray iTorsions = getExistingTorsions(*bat, *cat);
         int iShouldBe = (AtB.Nbonds() - 1) * (AtC.Nbonds() - 1);
         mprintf("ISHOULDBE= %i ITORSIONS= %zu\n", iShouldBe, iTorsions.size());
         if (iShouldBe != (int)iTorsions.size()) {
-          assignTorsionsAroundBond(zmatrix, *bat, *cat, frameIn, topIn, hasPosition, at);
+          assignTorsionsAroundBond(*bat, *cat, frameIn, topIn, hasPosition, at);
         }
       }
     }
@@ -2100,7 +2019,7 @@ int Builder::generateAtomInternals(Zmatrix& zmatrix, int at, Frame const& frameI
   * \param at0 Atom in residue we are linking to (i.e. the current residue).
   * \param at1 Atom in resiude we are linking from.
   */
-int Builder::GenerateInternalsAroundLink(Zmatrix& zmatrix, int at0, int at1,
+int Builder::GenerateInternalsAroundLink(int at0, int at1,
                                          Frame const& frameIn, Topology const& topIn,
                                          Barray const& hasPosition)
 {
@@ -2125,7 +2044,7 @@ int Builder::GenerateInternalsAroundLink(Zmatrix& zmatrix, int at0, int at1,
                                         it != span_atoms.end(); ++it)
   {
     //mprintf("SPANNING TREE ATOM: %s\n", topIn.LeapName(*it).c_str());
-    if (generateAtomInternals(zmatrix, *it, frameIn, topIn, tmpHasPosition)) {
+    if (generateAtomInternals(*it, frameIn, topIn, tmpHasPosition)) {
       mprinterr("Error: Could not generate internals for atom %s\n", topIn.AtomMaskName(*it).c_str());
       return 1;
     }
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index ffe6d47ac0..bc9ff7b8b3 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -19,26 +19,30 @@ class Builder {
     void SetDebug(int d) { debug_ = d; }
     /// Set optional parameter set
     void SetParameters(ParameterSet const*);
-    /// Set optional Zmatrix with current ICs
-    void SetZmatrix(Zmatrix const*);
 
     /// Combine second fragment into first fragment and bond
     int Combine(Topology&, Frame&, Topology const&, Frame const&, int, int) const;
     /// Model the coordinates around a bond given only some coordinates are known
     int ModelCoordsAroundBond(Frame const&, Topology const&, int, int, Zmatrix&, Barray const&) const;
-    /// Update the internal coordinates in given Zmatrix with values from Frame/Parameters
-    int UpdateICsFromFrame(Zmatrix&, Frame const&, int, Topology const&, Barray const&) const;
 
+
+    /// Update the internal coordinates in given Zmatrix with values from Frame/Parameters
+    int UpdateICsFromFrame(Frame const&, int, Topology const&, Barray const&);
     /// Generate internal coordinates in the same manner as LEaP
-    int GenerateInternals(Zmatrix&, Frame const&, Topology const&, Barray const&);
+    int GenerateInternals(Frame const&, Topology const&, Barray const&);
     /// Generate internal coordinates around a link between residues in same manner as LEaP
-    int GenerateInternalsAroundLink(Zmatrix&, int, int, Frame const&, Topology const&, Barray const&);
-
+    int GenerateInternalsAroundLink(int, int, Frame const&, Topology const&, Barray const&);
+    /// Update existing indices with given offset
+    void UpdateIndicesWithOffset(int);
   private:
     typedef std::vector<int> Iarray;
 
     /// Used to hold parameters for modeling a torsion
     class TorsionModel;
+    /// Hold torsion
+    class InternalTorsion;
+
+    typedef std::vector<InternalTorsion> Tarray;
 
     /// Get length parameter for atoms
     int getLengthParam(double&, int, int, Topology const&) const;
@@ -72,24 +76,53 @@ class Builder {
     /// Create ICs around SP2-SP2 linkage
     void createSp2Sp2Torsions(TorsionModel const&);
     /// Model torsions around a bond in the same manner as LEaP
-    int assignTorsionsAroundBond(Zmatrix&, int, int, Frame const&, Topology const&, Barray const&, int);
-    /// Get any existing internal coords from currentZmatrix around specified atoms
-    std::vector<InternalCoords> getExistingInternals(int, int) const;
-    /// Get specific internal coords from currentZmatrix
-    int getExistingInternalIdx(int, int, int, int) const;
+    int assignTorsionsAroundBond(int, int, Frame const&, Topology const&, Barray const&, int);
+    /// Get any existing internal coords from internalTorsions_ around specified atoms
+    Tarray getExistingTorsions(int, int) const;
+    /// Get specific internal coords from internalTorsions_
+    int getExistingTorsionIdx(int, int, int, int) const;
     /// Build mock coordinates around given torsion
     int buildMockExternals(TorsionModel& MT, std::vector<InternalCoords> const& iaTorsions) const;
     /// Generate internal coords for a given atom
-    int generateAtomInternals(Zmatrix&, int, Frame const&, Topology const&, Barray const&);
+    int generateAtomInternals(int, Frame const&, Topology const&, Barray const&);
 
     int debug_;
     ParameterSet const* params_;
-    Zmatrix const* currentZmatrix_; ///< Any existing internal coordinates
 
     Topology const* currentTop_; ///< Topology for the createSpXSpXTorsions/ModelTorsion routines
     Frame const* currentFrm_;    ///< Frame for the createSpXSpXTorsions routines
     Barray const* hasPosition_;  ///< Array indicating which atoms have position for createSpXSpXTorsions/ModelTorsion routines
-    Zmatrix* newZmatrix_;        ///< Hold output ICs from assignTorsionsAroundBond
+    Tarray internalTorsions_;
+};
+/// ----- Hold torsion internal ------------------
+class Cpptraj::Structure::Builder::InternalTorsion {
+  public:
+    /// CONSTRUCTOR
+    InternalTorsion() : ai_(-1), aj_(-1), ak_(-1), al_(-1), phi_(0) {}
+    /// CONSTRUCTOR
+    InternalTorsion(int i, int j, int k, int l, double p) :
+      ai_(i), aj_(j), ak_(k), al_(l), phi_(p) {}
+    /// Set the phi value in radians
+    void SetPhiVal(double p) { phi_ = p; }
+    /// Offset indices by given value
+    void OffsetIndices(int o) {
+      ai_ += 0;
+      aj_ += 0;
+      ak_ += 0;
+      al_ += 0;
+    }
+
+    int AtI() const { return ai_; }
+    int AtJ() const { return aj_; }
+    int AtK() const { return ak_; }
+    int AtL() const { return al_; }
+    double PhiVal() const { return phi_; }
+  private:
+    int ai_;
+    int aj_;
+    int ak_;
+    int al_;
+    double phi_;
 };
 }
 }

From 45ce40613c3aa2cb30f4129fdf7d30281421ab56 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 7 Feb 2024 15:00:13 -0500
Subject: [PATCH 0462/1492] Angle internals

---
 src/Structure/Builder.cpp                    | 63 ++++++++++++++++++++
 src/Structure/Builder.h                      | 33 ++++++++++
 src/Structure/GenerateConnectivityArrays.cpp | 12 ++--
 3 files changed, 102 insertions(+), 6 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 669fe56490..08952082b2 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1639,6 +1639,50 @@ int Builder::getExistingTorsionIdx(int ai, int aj, int ak, int al) const {
   return idx;
 }
 
+/** Mode angle */
+double Builder::ModelBondAngle(int ai, int aj, int ak, Topology const& topIn) const {
+  // First look up parameter
+  double theta = 0;
+  if (getAngleParam(theta, ai, aj, ak, topIn)) {
+    return theta;
+  }
+  Atom const& AJ = topIn[aj];
+  // Figure out hybridization and chirality of atom j.
+  if (debug_ > 0) {
+    mprintf("DEBUG:\t\tI %s Nbonds: %i\n", topIn[ai].ElementName(), topIn[ai].Nbonds());
+    mprintf("DEBUG:\t\tJ %s Nbonds: %i\n", AJ.ElementName(), AJ.Nbonds());
+    mprintf("DEBUG:\t\tK %s Nbonds: %i\n", topIn[ak].ElementName(), topIn[ak].Nbonds());
+  }
+  AtomType::HybridizationType hybrid = AtomType::UNKNOWN_HYBRIDIZATION;
+  // Check params for hybrid
+  if (params_ != 0) {
+    ParmHolder<AtomType>::const_iterator it = params_->AT().GetParam( TypeNameHolder(AJ.Type()) );
+    if (it != params_->AT().end())
+      hybrid = it->second.Hybridization();
+  }
+  // Guess hybrid if needed
+  if (hybrid == AtomType::UNKNOWN_HYBRIDIZATION)
+    hybrid = GuessAtomHybridization(AJ, topIn.Atoms());
+  // Set from number of bonds if still unknown. This is a pretty crude guess.
+  if (hybrid == AtomType::UNKNOWN_HYBRIDIZATION) {
+    switch (AJ.Nbonds()) {
+      case 4 : hybrid = AtomType::SP3; break;
+      case 3 : hybrid = AtomType::SP2; break;
+      case 2 : hybrid = AtomType::SP; break;
+      default : mprinterr("Internal Error: AssignTheta(): Unhandled # bonds for %s (%i)\n", topIn.AtomMaskName(aj).c_str(), AJ.Nbonds()); return 1;
+    }
+  }
+
+  // Assign a theta based on hybridization
+  switch (hybrid) {
+    case AtomType::SP3 : theta = 109.5 * Constants::DEGRAD; break;
+    case AtomType::SP2 : theta = 120.0 * Constants::DEGRAD; break;
+    case AtomType::SP  : theta = 180.0 * Constants::DEGRAD; break;
+    default : mprinterr("Internal Error: AssignTheta(): Unhandled hybridization for %s (%i)\n", topIn.AtomMaskName(aj).c_str(), AJ.Nbonds()); return 1;
+  }
+  return theta;
+}
+
 /** Model torsion */
 void Builder::ModelTorsion(TorsionModel const& MT, unsigned int iBondX, unsigned int iBondY, double dvalIn)
 {
@@ -1981,6 +2025,25 @@ int Builder::GenerateInternals(Frame const& frameIn, Topology const& topIn, Barr
       return 1;
     }
   }
+  // Loop over angles
+  AngleArray angles = GenerateAngleArray( topIn.Residues(), topIn.Atoms() );
+  for (AngleArray::const_iterator ang = angles.begin(); ang != angles.end(); ++ang)
+  {
+    double dValue = 0;
+    if (hasPosition[ang->A1()] &&
+        hasPosition[ang->A2()] &&
+        hasPosition[ang->A3()])
+    {
+      dValue = CalcAngle( frameIn.XYZ(ang->A1()), frameIn.XYZ(ang->A2()), frameIn.XYZ(ang->A3()) );
+    } else {
+      dValue = ModelBondAngle( ang->A1(), ang->A2(), ang->A3(), topIn );
+    }
+    internalAngles_.push_back( InternalAngle(ang->A1(), ang->A2(), ang->A3(), dValue) );
+    mprintf("++++Angle INTERNAL: %f  for %s - %s - %s\n", dValue*Constants::RADDEG,
+            topIn.LeapName(ang->A1()).c_str(),
+            topIn.LeapName(ang->A2()).c_str(),
+            topIn.LeapName(ang->A3()).c_str());
+  }
   //zmatrix.print( &topIn );
   mprintf("DEBUG: ----- Leaving Builder::GenerateInternals. ------\n");
   return 0;
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index bc9ff7b8b3..562393e026 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -41,8 +41,11 @@ class Builder {
     class TorsionModel;
     /// Hold torsion
     class InternalTorsion;
+    /// Hold angle
+    class InternalAngle;
 
     typedef std::vector<InternalTorsion> Tarray;
+    typedef std::vector<InternalAngle> Aarray;
 
     /// Get length parameter for atoms
     int getLengthParam(double&, int, int, Topology const&) const;
@@ -69,6 +72,8 @@ class Builder {
 
     /// Create IC for a torsion
     void ModelTorsion(TorsionModel const&, unsigned int, unsigned int, double);
+    /// Get angle value
+    double ModelBondAngle(int, int, int, Topology const&) const;
     /// Create ICs around SP3-SP3 linkage
     void createSp3Sp3Torsions(TorsionModel const&);
     /// Create ICs around SP3-SP2 linkage
@@ -93,6 +98,7 @@ class Builder {
     Frame const* currentFrm_;    ///< Frame for the createSpXSpXTorsions routines
     Barray const* hasPosition_;  ///< Array indicating which atoms have position for createSpXSpXTorsions/ModelTorsion routines
     Tarray internalTorsions_;
+    Aarray internalAngles_;
 };
 /// ----- Hold torsion internal ------------------
 class Cpptraj::Structure::Builder::InternalTorsion {
@@ -124,6 +130,33 @@ class Cpptraj::Structure::Builder::InternalTorsion {
     int al_;
     double phi_;
 };
+// ----- Hold angle internal ---------------------
+class Cpptraj::Structure::Builder::InternalAngle {
+  public:
+    /// CONSTRUCTOR
+    InternalAngle() : ai_(-1), aj_(-1), ak_(-1), theta_(0) {}
+    /// CONSTRUCTOR
+    InternalAngle(int i, int j, int k, double t) :
+      ai_(i), aj_(j), ak_(k), theta_(t) {}
+    /// Set the phi value in radians
+    void SetThetaVal(double t) { theta_ = t; }
+    /// Offset indices by given value
+    void OffsetIndices(int o) {
+      ai_ += 0;
+      aj_ += 0;
+      ak_ += 0;
+    }
+
+    int AtI() const { return ai_; }
+    int AtJ() const { return aj_; }
+    int AtK() const { return ak_; }
+    double ThetaVal() const { return theta_; }
+  private:
+    int ai_;
+    int aj_;
+    int ak_;
+    double theta_;
+};
 }
 }
 #endif
diff --git a/src/Structure/GenerateConnectivityArrays.cpp b/src/Structure/GenerateConnectivityArrays.cpp
index d81ccc13d0..0cdc011937 100644
--- a/src/Structure/GenerateConnectivityArrays.cpp
+++ b/src/Structure/GenerateConnectivityArrays.cpp
@@ -101,7 +101,7 @@ AngleArray Cpptraj::Structure::GenerateAngleArray(std::vector<Residue> const& re
 {
   AngleArray out;
   // ANGLES TODO combine above
-  int aidx = 0;
+//  int aidx = 0;
   for (std::vector<Residue>::const_iterator res = residues.begin(); res != residues.end(); ++res)
   {
     int start, end, offset;
@@ -116,7 +116,7 @@ AngleArray Cpptraj::Structure::GenerateAngleArray(std::vector<Residue> const& re
         for (int bidx2 = 0; bidx2 < At2.Nbonds(); bidx2++) {
           int iat3 = At2.Bond(bidx2);
           if (iat1 < iat3) {
-            mprintf("DEBUG: ANGLE  i= %i  %i - %i - %i (%i %i %i)\n", aidx++, iat1+1, iat2+1, iat3+1, iat1*3, iat2*3, iat3*3);
+            //mprintf("DEBUG: ANGLE  i= %i  %i - %i - %i (%i %i %i)\n", aidx++, iat1+1, iat2+1, iat3+1, iat1*3, iat2*3, iat3*3);
             out.push_back( AngleType(iat1, iat2, iat3, -1) );
           }
         }
@@ -132,7 +132,7 @@ DihedralArray Cpptraj::Structure::GenerateDihedralArray(std::vector<Residue> con
 {
   DihedralArray out;
   // TORSIONS TODO combine above
-  int didx = 0;
+//  int didx = 0;
   for (std::vector<Residue>::const_iterator res = residues.begin(); res != residues.end(); ++res)
   {
     int start, end, offset;
@@ -151,7 +151,7 @@ DihedralArray Cpptraj::Structure::GenerateDihedralArray(std::vector<Residue> con
             for (int bidx3 = 0; bidx3 < At3.Nbonds(); bidx3++) {
               int iat4 = At3.Bond(bidx3);
               if (iat4 != iat2 && iat1 < iat4) {
-                mprintf("DEBUG: DIHEDRAL  i= %i  %i - %i - %i - %i (%i %i %i %i)\n", didx++, iat1+1, iat2+1, iat3+1, iat4+1, iat1*3, iat2*3, iat3*3, iat4*3);
+                //mprintf("DEBUG: DIHEDRAL  i= %i  %i - %i - %i - %i (%i %i %i %i)\n", didx++, iat1+1, iat2+1, iat3+1, iat4+1, iat1*3, iat2*3, iat3*3, iat4*3);
                 out.push_back( DihedralType( iat1, iat2, iat3, iat4, -1 ) );
               }
             }
@@ -188,7 +188,7 @@ DihedralArray Cpptraj::Structure::GenerateImproperArray(std::vector<Residue> con
                                                         std::vector<Atom> const& atoms)
 {
   DihedralArray out;
-  int iidx = 0;
+//  int iidx = 0;
   for (std::vector<Residue>::const_iterator res = residues.begin(); res != residues.end(); ++res)
   {
     int start, end, offset;
@@ -204,7 +204,7 @@ DihedralArray Cpptraj::Structure::GenerateImproperArray(std::vector<Residue> con
               int iat1 = AJ.BondIdxArray()[bidx0];
               int iat2 = AJ.BondIdxArray()[bidx1];
               int iat4 = AJ.BondIdxArray()[bidx2];
-              mprintf("DEBUG: IMPROPER  i= %i  %i - %i - %i - %i (%i %i %i %i)\n", iidx++, iat1+1, iat2+1, iat3+1, iat4+1, iat1*3, iat2*3, iat3*3, iat4*3);
+              //mprintf("DEBUG: IMPROPER  i= %i  %i - %i - %i - %i (%i %i %i %i)\n", iidx++, iat1+1, iat2+1, iat3+1, iat4+1, iat1*3, iat2*3, iat3*3, iat4*3);
               int indices[3];
               indices[0] = iat1;
               indices[1] = iat2;

From cd46874372395a91729f9c7fd99d5c5b110d1fc0 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 7 Feb 2024 15:21:47 -0500
Subject: [PATCH 0463/1492] Bond internals

---
 src/Structure/Builder.cpp | 74 +++++++++++++++++++++++++++++++++++++--
 src/Structure/Builder.h   | 31 ++++++++++++++++
 2 files changed, 103 insertions(+), 2 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 08952082b2..716b7b7da3 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1075,6 +1075,7 @@ const
   return 0;
 }
 
+// ==============================================================================
 /** For existing torsions, see if all coordinates in that torsion
   * exist. If so, update the IC from the existing coordinates.
   */
@@ -1137,7 +1138,6 @@ int Builder::UpdateICsFromFrame(Frame const& frameIn, int ires, Topology const&
   return 0;
 }
 
-// ------------------------------------------------------------------------------
 /// Used to track atoms for mock externals
 class MockAtom {
   public:
@@ -1639,7 +1639,60 @@ int Builder::getExistingTorsionIdx(int ai, int aj, int ak, int al) const {
   return idx;
 }
 
-/** Mode angle */
+/** Model bond */
+double Builder::ModelBondLength(int ai, int aj, Topology const& topIn) const {
+  // First look up parameter
+  double dist = 0;
+  if (getLengthParam(dist, ai, aj, topIn)) {
+    return dist;
+  }
+  Atom const& AI = topIn[ai];
+  Atom const& AJ = topIn[aj];
+  AtomType::HybridizationType hybridI = AtomType::UNKNOWN_HYBRIDIZATION;
+  AtomType::HybridizationType hybridJ = AtomType::UNKNOWN_HYBRIDIZATION;
+  // Check params for hybrid
+  if (params_ != 0) {
+    ParmHolder<AtomType>::const_iterator it = params_->AT().GetParam( TypeNameHolder(AI.Type()) );
+    if (it != params_->AT().end())
+      hybridI = it->second.Hybridization();
+    it = params_->AT().GetParam( TypeNameHolder(AJ.Type()) );
+    if (it != params_->AT().end())
+      hybridJ = it->second.Hybridization();
+  }
+  if (hybridI == AtomType::UNKNOWN_HYBRIDIZATION ||
+      hybridJ == AtomType::UNKNOWN_HYBRIDIZATION)
+  {
+    // Default to bond length based on elements
+    dist = Atom::GetBondLength( AI.Element(), AJ.Element() );
+  } else {
+    // Use leap method based on atom hybridization
+    AtomType::HybridizationType hybrid1, hybrid2;
+    if (hybridI < hybridJ) {
+      hybrid1 = hybridI;
+      hybrid2 = hybridJ;
+    } else {
+      hybrid1 = hybridJ;
+      hybrid2 = hybridI;
+    }
+    if (hybrid1 == AtomType::SP3 && hybrid2 == AtomType::SP3)
+      dist = 1.5;
+    else if (hybrid1 == AtomType::SP2 && hybrid2 == AtomType::SP3)
+      dist = 1.4;
+    else if (hybrid1 == AtomType::SP && hybrid2 == AtomType::SP3)
+      dist = 1.3;
+    else if (hybrid1 == AtomType::SP2 && hybrid2 == AtomType::SP2)
+      dist = 1.35;
+    else if (hybrid1 == AtomType::SP && hybrid2 == AtomType::SP2)
+      dist = 1.3;
+    else if (hybrid1 == AtomType::SP && hybrid2 == AtomType::SP)
+      dist = 1.1;
+    else
+      dist =  Atom::GetBondLength( AI.Element(), AJ.Element() );
+  }
+  return dist;
+}
+
+/** Model angle */
 double Builder::ModelBondAngle(int ai, int aj, int ak, Topology const& topIn) const {
   // First look up parameter
   double theta = 0;
@@ -2044,6 +2097,23 @@ int Builder::GenerateInternals(Frame const& frameIn, Topology const& topIn, Barr
             topIn.LeapName(ang->A2()).c_str(),
             topIn.LeapName(ang->A3()).c_str());
   }
+  // Loop over bonds
+  for (BondArray::const_iterator bnd = bonds.begin(); bnd != bonds.end(); ++bnd)
+  {
+    double dValue = 0;
+    if (hasPosition[bnd->A1()] &&
+        hasPosition[bnd->A2()])
+    {
+      dValue = sqrt(DIST2_NoImage( frameIn.XYZ(bnd->A1()), frameIn.XYZ(bnd->A2()) ) );
+    } else {
+      dValue = ModelBondLength( bnd->A1(), bnd->A2(), topIn );
+    }
+    internalBonds_.push_back( InternalBond(bnd->A1(), bnd->A2(), dValue) );
+    mprintf("++++Bond INTERNAL: %f  for %s - %s\n", dValue,
+            topIn.LeapName(bnd->A1()).c_str(),
+            topIn.LeapName(bnd->A2()).c_str());
+  }
+
   //zmatrix.print( &topIn );
   mprintf("DEBUG: ----- Leaving Builder::GenerateInternals. ------\n");
   return 0;
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index 562393e026..6932c677f5 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -43,9 +43,12 @@ class Builder {
     class InternalTorsion;
     /// Hold angle
     class InternalAngle;
+    /// Hold bond
+    class InternalBond;
 
     typedef std::vector<InternalTorsion> Tarray;
     typedef std::vector<InternalAngle> Aarray;
+    typedef std::vector<InternalBond> Larray;
 
     /// Get length parameter for atoms
     int getLengthParam(double&, int, int, Topology const&) const;
@@ -74,6 +77,8 @@ class Builder {
     void ModelTorsion(TorsionModel const&, unsigned int, unsigned int, double);
     /// Get angle value
     double ModelBondAngle(int, int, int, Topology const&) const;
+    /// Get bond length
+    double ModelBondLength(int, int, Topology const&) const;
     /// Create ICs around SP3-SP3 linkage
     void createSp3Sp3Torsions(TorsionModel const&);
     /// Create ICs around SP3-SP2 linkage
@@ -99,6 +104,7 @@ class Builder {
     Barray const* hasPosition_;  ///< Array indicating which atoms have position for createSpXSpXTorsions/ModelTorsion routines
     Tarray internalTorsions_;
     Aarray internalAngles_;
+    Larray internalBonds_;
 };
 /// ----- Hold torsion internal ------------------
 class Cpptraj::Structure::Builder::InternalTorsion {
@@ -157,6 +163,31 @@ class Cpptraj::Structure::Builder::InternalAngle {
     int ak_;
     double theta_;
 };
+// ----- Hold bond internal ----------------------
+class Cpptraj::Structure::Builder::InternalBond {
+  public:
+    /// CONSTRUCTOR
+    InternalBond() : ai_(-1), aj_(-1), dist_(0) {}
+    /// CONSTRUCTOR
+    InternalBond(int i, int j, double d) :
+      ai_(i), aj_(j), dist_(d) {}
+    /// Set the distance value in angstroms
+    void SetDistVal(double d) { dist_ = d; }
+    /// Offset indices by given value
+    void OffsetIndices(int o) {
+      ai_ += 0;
+      aj_ += 0;
+    }
+
+    int AtI() const { return ai_; }
+    int AtJ() const { return aj_; }
+    double DistVal() const { return dist_; }
+  private:
+    int ai_;
+    int aj_;
+    double dist_;
+};
+
 }
 }
 #endif

From b174a5e343ab6e112b934a0c4792ac51e187308f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 7 Feb 2024 15:28:13 -0500
Subject: [PATCH 0464/1492] Fix offset updates

---
 src/Structure/Builder.cpp |  4 ++++
 src/Structure/Builder.h   | 18 +++++++++---------
 2 files changed, 13 insertions(+), 9 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 716b7b7da3..9493a6a87e 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1608,6 +1608,10 @@ int Cpptraj::Structure::Builder::TorsionModel::BuildMockExternals(Tarray const&
 void Builder::UpdateIndicesWithOffset(int atomOffset) {
   for (Tarray::iterator it = internalTorsions_.begin(); it != internalTorsions_.end(); ++it)
     it->OffsetIndices( atomOffset );
+  for (Aarray::iterator it = internalAngles_.begin(); it != internalAngles_.end(); ++it)
+    it->OffsetIndices( atomOffset );
+  for (Larray::iterator it = internalBonds_.begin(); it != internalBonds_.end(); ++it)
+    it->OffsetIndices( atomOffset );
 }
 
 /** Find any existing torsions around ax-ay. */
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index 6932c677f5..9da6196161 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -118,10 +118,10 @@ class Cpptraj::Structure::Builder::InternalTorsion {
     void SetPhiVal(double p) { phi_ = p; }
     /// Offset indices by given value
     void OffsetIndices(int o) {
-      ai_ += 0;
-      aj_ += 0;
-      ak_ += 0;
-      al_ += 0;
+      ai_ += o;
+      aj_ += o;
+      ak_ += o;
+      al_ += o;
     }
 
     int AtI() const { return ai_; }
@@ -148,9 +148,9 @@ class Cpptraj::Structure::Builder::InternalAngle {
     void SetThetaVal(double t) { theta_ = t; }
     /// Offset indices by given value
     void OffsetIndices(int o) {
-      ai_ += 0;
-      aj_ += 0;
-      ak_ += 0;
+      ai_ += o;
+      aj_ += o;
+      ak_ += o;
     }
 
     int AtI() const { return ai_; }
@@ -175,8 +175,8 @@ class Cpptraj::Structure::Builder::InternalBond {
     void SetDistVal(double d) { dist_ = d; }
     /// Offset indices by given value
     void OffsetIndices(int o) {
-      ai_ += 0;
-      aj_ += 0;
+      ai_ += o;
+      aj_ += o;
     }
 
     int AtI() const { return ai_; }

From 1fcbea59cf682233d0fa57631b5a38f3c50c2441 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 7 Feb 2024 15:56:42 -0500
Subject: [PATCH 0465/1492] Fix index

---
 src/Structure/Builder.cpp | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 9493a6a87e..78e5a67750 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1620,7 +1620,7 @@ Builder::Tarray Builder::getExistingTorsions(int ax, int ay) const {
   for (Tarray::const_iterator it = internalTorsions_.begin(); it != internalTorsions_.end(); ++it)
   {
     if ((it->AtJ() == ax && it->AtK() == ay) ||
-        (it->AtJ() == ay && it->AtJ() == ax))
+        (it->AtJ() == ay && it->AtK() == ax))
     {
       iTorsions.push_back( *it );
     }
@@ -1630,13 +1630,16 @@ Builder::Tarray Builder::getExistingTorsions(int ax, int ay) const {
 
 /** \return index of existing torsion matching the 4 given atoms, -1 for no match. */
 int Builder::getExistingTorsionIdx(int ai, int aj, int ak, int al) const {
+  //mprintf("SEARCHING FOR %i %i %i %i\n", ai, aj, ak, al);
   int idx = -1;
   for (Tarray::const_iterator it = internalTorsions_.begin(); it != internalTorsions_.end(); ++it)
   {
+    //mprintf("\t\t%i %i %i %i\n", it->AtI(), it->AtJ(), it->AtK(), it->AtL());
     if ( (it->AtI() == ai && it->AtJ() == aj && it->AtK() == ak && it->AtL() == al) ||
          (it->AtI() == al && it->AtJ() == ak && it->AtK() == aj && it->AtL() == ai) )
     {
-      idx = (int)(internalTorsions_.begin() - it);
+      idx = (int)(it - internalTorsions_.begin());
+      //mprintf("FOUND at index %i\n", idx);
       break;
     }
   }
@@ -2140,6 +2143,15 @@ int Builder::generateAtomInternals(int at, Frame const& frameIn, Topology const&
         Tarray iTorsions = getExistingTorsions(*bat, *cat);
         int iShouldBe = (AtB.Nbonds() - 1) * (AtC.Nbonds() - 1);
         mprintf("ISHOULDBE= %i ITORSIONS= %zu\n", iShouldBe, iTorsions.size());
+        if (iShouldBe == 6 && iTorsions.size() == 6) { // FIXME DEBUG
+          for (Tarray::const_iterator it = iTorsions.begin(); it != iTorsions.end(); ++it)
+            mprintf("*** %s - %s - %s - %s : %f\n",
+                    topIn.LeapName(it->AtI()).c_str(),
+                    topIn.LeapName(it->AtJ()).c_str(),
+                    topIn.LeapName(it->AtK()).c_str(),
+                    topIn.LeapName(it->AtL()).c_str(),
+                    it->PhiVal()*Constants::RADDEG);
+        }
         if (iShouldBe != (int)iTorsions.size()) {
           assignTorsionsAroundBond(*bat, *cat, frameIn, topIn, hasPosition, at);
         }

From a5ed820823a913d27703078fe20f2af743d3e006 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 8 Feb 2024 09:23:44 -0500
Subject: [PATCH 0466/1492] Generate angle internals for one atom

---
 src/Structure/Builder.cpp | 49 +++++++++++++++++++++++++++++++++++++++
 src/Structure/Builder.h   | 26 ++++++++++++---------
 2 files changed, 64 insertions(+), 11 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 78e5a67750..ca8b28bf50 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1646,6 +1646,21 @@ int Builder::getExistingTorsionIdx(int ai, int aj, int ak, int al) const {
   return idx;
 }
 
+/** \return Index of existing angle matching the 3 given atoms, -1 for no match. */
+int Builder::getExistingAngleIdx(int ai, int aj, int ak) const {
+  int idx = -1;
+  for (Aarray::const_iterator it = internalAngles_.begin(); it != internalAngles_.end(); ++it)
+  {
+    if ((it->AtI() == ai && it->AtJ() == aj && it->AtK() == ak) ||
+        (it->AtI() == ak && it->AtJ() == aj && it->AtK() == ai))
+    {
+      idx = (int)(it - internalAngles_.begin());
+      break;
+    }
+  }
+  return idx;
+}
+
 /** Model bond */
 double Builder::ModelBondLength(int ai, int aj, Topology const& topIn) const {
   // First look up parameter
@@ -2130,6 +2145,7 @@ int Builder::GenerateInternals(Frame const& frameIn, Topology const& topIn, Barr
 int Builder::generateAtomInternals(int at, Frame const& frameIn, Topology const& topIn, Barray const& hasPosition)
 {
   mprintf( "Building internals for: %s\n", topIn.LeapName(at).c_str());
+  // Torsions
   Atom const& AtA = topIn[at];
   for (Atom::bond_iterator bat = AtA.bondbegin(); bat != AtA.bondend(); ++bat) {
     Atom const& AtB = topIn[*bat];
@@ -2158,6 +2174,39 @@ int Builder::generateAtomInternals(int at, Frame const& frameIn, Topology const&
       }
     }
   }
+  // Angles
+  for (Atom::bond_iterator bat = AtA.bondbegin(); bat != AtA.bondend(); ++bat) {
+    Atom const& AtB = topIn[*bat];
+    for (Atom::bond_iterator cat = AtB.bondbegin(); cat != AtB.bondend(); ++cat) {
+      if (*cat != at) {
+        mprintf("Building angle INTERNAL for: %s - %s - %s\n",
+                topIn.LeapName(at).c_str(),
+                topIn.LeapName(*bat).c_str(),
+                topIn.LeapName(*cat).c_str());
+        int aidx = getExistingAngleIdx(at, *bat, *cat);
+        if (aidx < 0) {
+          double dValue = 0;
+          if (hasPosition[at] &&
+              hasPosition[*bat] &&
+              hasPosition[*cat])
+          {
+            mprintf("Got bond angle from externals\n");
+            dValue = CalcAngle(frameIn.XYZ(at), frameIn.XYZ(*bat), frameIn.XYZ(*cat));
+          } else {
+            mprintf("Got bond angle from model builder\n");
+            dValue = ModelBondAngle(at, *bat, *cat, topIn);
+          }
+          mprintf("++++Angle INTERNAL: %f  for %s - %s - %s\n", dValue*Constants::RADDEG,
+                  topIn.LeapName(at).c_str(),
+                  topIn.LeapName(*bat).c_str(),
+                  topIn.LeapName(*cat).c_str());
+          internalAngles_.push_back(InternalAngle(at, *bat, *cat, dValue));
+        } else {
+          mprintf("Angle INTERNAL was already defined\n");
+        }
+      }
+    } // END loop over atoms bonded to B
+  } // END loop over atoms bonded to A
 
   return 0;
 }
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index 9da6196161..1b784bb05e 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -52,10 +52,12 @@ class Builder {
 
     /// Get length parameter for atoms
     int getLengthParam(double&, int, int, Topology const&) const;
-    /// Assign a reasonable value for bond distance given 2 atoms whose position may or may not be known
-    int AssignLength(double&, int, int, Topology const&, Frame const&, Barray const&) const;
     /// Get angle parameter for atoms.
     int getAngleParam(double&, int, int, int, Topology const&) const;
+
+    // ===========================================
+    /// Assign a reasonable value for bond distance given 2 atoms whose position may or may not be known
+    int AssignLength(double&, int, int, Topology const&, Frame const&, Barray const&) const;
     /// Given atoms J and K, attempt to assign a reasonable value for theta for atom I
     int AssignTheta(double&, int, int, int, Topology const&, Frame const&, Barray const&) const;
     /// Calculate an internal coordinate for known atoms
@@ -72,25 +74,27 @@ class Builder {
     int SetupICsAroundBond(Zmatrix&, int, int, Frame const&, Topology const&,
                            Barray const&, Barray const&,
                            BuildAtom const&, BuildAtom const&) const;
-
-    /// Create IC for a torsion
+    // ===========================================
+    /// Calculte phi value for a torsion in a TorsionModel
     void ModelTorsion(TorsionModel const&, unsigned int, unsigned int, double);
-    /// Get angle value
+    /// Get angle parameter/model an angle value
     double ModelBondAngle(int, int, int, Topology const&) const;
-    /// Get bond length
+    /// Get bond parameter/model a bond length
     double ModelBondLength(int, int, Topology const&) const;
-    /// Create ICs around SP3-SP3 linkage
+    /// Create torsion around SP3-SP3 linkage
     void createSp3Sp3Torsions(TorsionModel const&);
-    /// Create ICs around SP3-SP2 linkage
+    /// Create torsion around SP3-SP2 linkage
     void createSp3Sp2Torsions(TorsionModel const&);
-    /// Create ICs around SP2-SP2 linkage
+    /// Create torsion around SP2-SP2 linkage
     void createSp2Sp2Torsions(TorsionModel const&);
     /// Model torsions around a bond in the same manner as LEaP
     int assignTorsionsAroundBond(int, int, Frame const&, Topology const&, Barray const&, int);
-    /// Get any existing internal coords from internalTorsions_ around specified atoms
+    /// Get any existing internal torsion around specified atoms
     Tarray getExistingTorsions(int, int) const;
-    /// Get specific internal coords from internalTorsions_
+    /// Get specific internal torsion
     int getExistingTorsionIdx(int, int, int, int) const;
+    /// Get specific internal angle
+    int getExistingAngleIdx(int, int, int) const;
     /// Build mock coordinates around given torsion
     int buildMockExternals(TorsionModel& MT, std::vector<InternalCoords> const& iaTorsions) const;
     /// Generate internal coords for a given atom

From 0f9f0302cd4a9e3777d574281764e788f51ac8e0 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 8 Feb 2024 09:35:28 -0500
Subject: [PATCH 0467/1492] Bond internals for one atom

---
 src/Structure/Builder.cpp | 40 +++++++++++++++++++++++++++++++++++++++
 src/Structure/Builder.h   |  2 ++
 2 files changed, 42 insertions(+)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index ca8b28bf50..b6fcf155c9 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1661,6 +1661,21 @@ int Builder::getExistingAngleIdx(int ai, int aj, int ak) const {
   return idx;
 }
 
+/** \return Index of existing bond matching the 2 given atoms, -1 for no match. */
+int Builder::getExistingBondIdx(int ai, int aj) const {
+  int idx = -1;
+  for (Larray::const_iterator it = internalBonds_.begin(); it != internalBonds_.end(); ++it)
+  {
+    if ((it->AtI() == ai && it->AtJ() == aj) ||
+        (it->AtI() == aj && it->AtJ() == ai))
+    {
+      idx = (int)(it - internalBonds_.begin());
+      break;
+    }
+  }
+  return idx;
+}
+
 /** Model bond */
 double Builder::ModelBondLength(int ai, int aj, Topology const& topIn) const {
   // First look up parameter
@@ -2207,6 +2222,31 @@ int Builder::generateAtomInternals(int at, Frame const& frameIn, Topology const&
       }
     } // END loop over atoms bonded to B
   } // END loop over atoms bonded to A
+  // Bonds
+  for (Atom::bond_iterator bat = AtA.bondbegin(); bat != AtA.bondend(); ++bat) {
+    mprintf("Building bond INTERNAL for: %s - %s\n",
+            topIn.LeapName(at).c_str(),
+            topIn.LeapName(*bat).c_str());
+    int bidx = getExistingBondIdx(at, *bat);
+    if (bidx < 0) {
+      double dValue = 0;
+      if (hasPosition[at] &&
+          hasPosition[*bat])
+      {
+        mprintf("Got bond length from externals\n");
+        dValue = sqrt(DIST2_NoImage(frameIn.XYZ(at), frameIn.XYZ(*bat)));
+      } else {
+        mprintf("Got bond length from the model builder\n");
+        dValue = ModelBondLength(at, *bat, topIn);
+      }
+      mprintf("++++Bond INTERNAL: %f  for %s - %s\n", dValue,
+              topIn.LeapName(at).c_str(),
+              topIn.LeapName(*bat).c_str());
+      internalBonds_.push_back(InternalBond(at, *bat, dValue));
+    } else {
+      mprintf( "Bond length INTERNAL already defined\n" );
+    }
+  } // END loop over atoms bonded to A
 
   return 0;
 }
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index 1b784bb05e..d44b332d22 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -95,6 +95,8 @@ class Builder {
     int getExistingTorsionIdx(int, int, int, int) const;
     /// Get specific internal angle
     int getExistingAngleIdx(int, int, int) const;
+    /// Get specific internal bond
+    int getExistingBondIdx(int, int) const;
     /// Build mock coordinates around given torsion
     int buildMockExternals(TorsionModel& MT, std::vector<InternalCoords> const& iaTorsions) const;
     /// Generate internal coords for a given atom

From 5246dbe97bd86ec9e3763a3d0f0551d4430e235b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 8 Feb 2024 09:50:18 -0500
Subject: [PATCH 0468/1492] Create zmatrix from internals

---
 src/Structure/Builder.cpp | 54 ++++++++++++++++++++++++++++++++++++---
 src/Structure/Builder.h   |  2 ++
 2 files changed, 53 insertions(+), 3 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index b6fcf155c9..3e9f84fa10 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -2096,8 +2096,8 @@ int Builder::assignTorsionsAroundBond(int a1, int a2, Frame const& frameIn, Topo
   return 0;
 }
 
-/** Generate internal coordinates in the same
-  * manner as LEaP's BuildInternalsForContainer/ModelAssignTorsionsAround.
+/** Generate internal coordinates in the same manner as LEaP's
+  * BuildInternalsForContainer.
   */
 int Builder::GenerateInternals(Frame const& frameIn, Topology const& topIn, Barray const& hasPosition)
 {
@@ -2150,7 +2150,7 @@ int Builder::GenerateInternals(Frame const& frameIn, Topology const& topIn, Barr
             topIn.LeapName(bnd->A1()).c_str(),
             topIn.LeapName(bnd->A2()).c_str());
   }
-
+  // FIXME do chirality
   //zmatrix.print( &topIn );
   mprintf("DEBUG: ----- Leaving Builder::GenerateInternals. ------\n");
   return 0;
@@ -2247,6 +2247,7 @@ int Builder::generateAtomInternals(int at, Frame const& frameIn, Topology const&
       mprintf( "Bond length INTERNAL already defined\n" );
     }
   } // END loop over atoms bonded to A
+  // FIXME do chirality
 
   return 0;
 }
@@ -2297,3 +2298,50 @@ int Builder::GenerateInternalsAroundLink(int at0, int at1,
   mprintf("DEBUG: ----- Leaving Builder::GenerateInternalsAroundLink. -----\n");
   return 0;
 }
+
+/** Generate a Zmatrix from the current internals. TODO only for atoms that need it? */
+int Builder::GetZmatrixFromInternals(Zmatrix& zmatrix, Topology const& topIn) const {
+  zmatrix.clear();
+
+  for (Tarray::const_iterator dih = internalTorsions_.begin(); dih != internalTorsions_.end(); ++dih)
+  {
+    // Get angles i-j-k and j-k-l
+    int aidx0 = getExistingAngleIdx(dih->AtI(), dih->AtJ(), dih->AtK());
+    int aidx1 = getExistingAngleIdx(dih->AtJ(), dih->AtK(), dih->AtL());
+    if (aidx0 < 0) {
+      mprinterr("Error: Missing angle internal for %s - %s - %s\n",
+                topIn.AtomMaskName(dih->AtI()).c_str(),
+                topIn.AtomMaskName(dih->AtJ()).c_str(),
+                topIn.AtomMaskName(dih->AtK()).c_str());
+      return 1;
+    }
+    if (aidx1 < 0) {
+      mprinterr("Error: Missing angle internal for %s - %s - %s\n",
+                topIn.AtomMaskName(dih->AtJ()).c_str(),
+                topIn.AtomMaskName(dih->AtK()).c_str(),
+                topIn.AtomMaskName(dih->AtL()).c_str());
+      return 1;
+    }
+    // Get Bonds i-j and k-l
+    int bidx0 = getExistingBondIdx(dih->AtI(), dih->AtJ());
+    int bidx1 = getExistingBondIdx(dih->AtK(), dih->AtL());
+    if (bidx0 < 0) {
+      mprinterr("Error: Missing bond internal for %s - %s\n",
+                topIn.AtomMaskName(dih->AtI()).c_str(),
+                topIn.AtomMaskName(dih->AtJ()).c_str());
+    }
+    if (bidx1 < 0) {
+    mprinterr("Error: Missing bond internal for %s - %s\n",
+                topIn.AtomMaskName(dih->AtK()).c_str(),
+                topIn.AtomMaskName(dih->AtL()).c_str());
+    }
+    // Add internal coordinates
+    zmatrix.AddIC( InternalCoords(dih->AtI(), dih->AtJ(), dih->AtK(), dih->AtL(), dih->PhiVal()*Constants::RADDEG,
+                                  internalAngles_[aidx0].ThetaVal()*Constants::RADDEG,
+                                  internalBonds_[bidx0].DistVal()) );
+    zmatrix.AddIC( InternalCoords(dih->AtL(), dih->AtK(), dih->AtJ(), dih->AtI(), dih->PhiVal()*Constants::RADDEG,
+                                  internalAngles_[aidx1].ThetaVal()*Constants::RADDEG,
+                                  internalBonds_[bidx1].DistVal()) );
+  } // END loop over internal torsions
+  return 0;
+}
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index d44b332d22..739e916579 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -34,6 +34,8 @@ class Builder {
     int GenerateInternalsAroundLink(int, int, Frame const&, Topology const&, Barray const&);
     /// Update existing indices with given offset
     void UpdateIndicesWithOffset(int);
+    /// \return Zmatrix from current internals
+    int GetZmatrixFromInternals(Zmatrix&, Topology const&) const;
   private:
     typedef std::vector<int> Iarray;
 

From f637ac5791c986ad13d2ba163360dcb3552a63bf Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 8 Feb 2024 10:38:53 -0500
Subject: [PATCH 0469/1492] Try to actually build coords. Seems to fail
 miserably

---
 src/Exec_Build.cpp        |  6 +++-
 src/Structure/Builder.cpp | 71 +++++++++++++++++++++++++++++++++++----
 src/Structure/Builder.h   |  4 +++
 3 files changed, 74 insertions(+), 7 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 942821ddf6..181e8b2f8f 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -474,8 +474,12 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
       //  mprinterr("Error: Could not set up seed atoms for Zmatrix.\n");
       //  buildFailed = true;
       //} else {
-        Cpptraj::Structure::Zmatrix tmpz; // FIXME
+        Cpptraj::Structure::Zmatrix tmpz;
         tmpz.SetDebug( 1 ); // DEBUG
+        if (structureBuilder->GetZmatrixFromInternals(tmpz, topOut)) {
+          mprinterr("Error: Could not get Zmatrix from internals.\n");
+          return 1;
+        }
         if (tmpz.SetToFrame( frameOut, hasPosition )) {
           mprinterr("Error: Building residue %s failed.\n",
                     topOut.TruncResNameOnumId(ires).c_str());
diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 3e9f84fa10..ccd7df49db 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -2096,6 +2096,45 @@ int Builder::assignTorsionsAroundBond(int a1, int a2, Frame const& frameIn, Topo
   return 0;
 }
 
+/** Build angle internal. */
+void Builder::buildAngleInternal(int a1, int a2, int a3, Frame const& frameIn, Topology const& topIn,
+                                 Barray const& hasPosition)
+{
+    double dValue = 0;
+    if (hasPosition[a1] &&
+        hasPosition[a2] &&
+        hasPosition[a3])
+    {
+      dValue = CalcAngle( frameIn.XYZ(a1), frameIn.XYZ(a2), frameIn.XYZ(a3) );
+    } else {
+      dValue = ModelBondAngle( a1, a2, a3, topIn );
+    }
+    internalAngles_.push_back( InternalAngle(a1, a2, a3, dValue) );
+    mprintf("++++Angle INTERNAL: %f  for %s - %s - %s\n", dValue*Constants::RADDEG,
+            topIn.LeapName(a1).c_str(),
+            topIn.LeapName(a2).c_str(),
+            topIn.LeapName(a3).c_str());
+}
+
+/** Build bond internal. */
+void Builder::buildBondInternal(int a1, int a2, Frame const& frameIn, Topology const& topIn,
+                                Barray const& hasPosition)
+{
+    double dValue = 0;
+    if (hasPosition[a1] &&
+        hasPosition[a2])
+    {
+      dValue = sqrt(DIST2_NoImage( frameIn.XYZ(a1), frameIn.XYZ(a2) ) );
+    } else {
+      dValue = ModelBondLength( a1, a2, topIn );
+    }
+    internalBonds_.push_back( InternalBond(a1, a2, dValue) );
+    mprintf("++++Bond INTERNAL: %f  for %s - %s\n", dValue,
+            topIn.LeapName(a1).c_str(),
+            topIn.LeapName(a2).c_str());
+}
+
+
 /** Generate internal coordinates in the same manner as LEaP's
   * BuildInternalsForContainer.
   */
@@ -2295,12 +2334,26 @@ int Builder::GenerateInternalsAroundLink(int at0, int at1,
   //            topIn.AtomMaskName(at1).c_str());
   //  return 1;
   //}
+  // FIXME this is a hack to make certain we have all the angle/bond terms we need
+  for (Tarray::const_iterator dih = internalTorsions_.begin(); dih != internalTorsions_.end(); ++dih)
+  {
+    int idx = getExistingAngleIdx(dih->AtI(), dih->AtJ(), dih->AtK());
+    if (idx < 0) buildAngleInternal( dih->AtI(), dih->AtJ(), dih->AtK(), frameIn, topIn, hasPosition );
+    idx = getExistingAngleIdx(dih->AtJ(), dih->AtK(), dih->AtL());
+    if (idx < 0) buildAngleInternal( dih->AtJ(), dih->AtK(), dih->AtL(), frameIn, topIn, hasPosition );
+    idx = getExistingBondIdx(dih->AtI(), dih->AtJ());
+    if (idx < 0) buildBondInternal( dih->AtI(), dih->AtJ(), frameIn, topIn, hasPosition );
+    idx = getExistingBondIdx(dih->AtK(), dih->AtL());
+    if (idx < 0) buildBondInternal( dih->AtK(), dih->AtL(), frameIn, topIn, hasPosition );
+  }
+
   mprintf("DEBUG: ----- Leaving Builder::GenerateInternalsAroundLink. -----\n");
   return 0;
 }
 
 /** Generate a Zmatrix from the current internals. TODO only for atoms that need it? */
 int Builder::GetZmatrixFromInternals(Zmatrix& zmatrix, Topology const& topIn) const {
+  mprintf("DEBUG: ----- Enter GetZmatrixFromInternals -----\n");
   zmatrix.clear();
 
   for (Tarray::const_iterator dih = internalTorsions_.begin(); dih != internalTorsions_.end(); ++dih)
@@ -2309,14 +2362,14 @@ int Builder::GetZmatrixFromInternals(Zmatrix& zmatrix, Topology const& topIn) co
     int aidx0 = getExistingAngleIdx(dih->AtI(), dih->AtJ(), dih->AtK());
     int aidx1 = getExistingAngleIdx(dih->AtJ(), dih->AtK(), dih->AtL());
     if (aidx0 < 0) {
-      mprinterr("Error: Missing angle internal for %s - %s - %s\n",
+      mprinterr("Error: Missing angle0 internal for %s - %s - %s\n",
                 topIn.AtomMaskName(dih->AtI()).c_str(),
                 topIn.AtomMaskName(dih->AtJ()).c_str(),
                 topIn.AtomMaskName(dih->AtK()).c_str());
       return 1;
     }
     if (aidx1 < 0) {
-      mprinterr("Error: Missing angle internal for %s - %s - %s\n",
+      mprinterr("Error: Missing angle1 internal for %s - %s - %s\n",
                 topIn.AtomMaskName(dih->AtJ()).c_str(),
                 topIn.AtomMaskName(dih->AtK()).c_str(),
                 topIn.AtomMaskName(dih->AtL()).c_str());
@@ -2326,12 +2379,17 @@ int Builder::GetZmatrixFromInternals(Zmatrix& zmatrix, Topology const& topIn) co
     int bidx0 = getExistingBondIdx(dih->AtI(), dih->AtJ());
     int bidx1 = getExistingBondIdx(dih->AtK(), dih->AtL());
     if (bidx0 < 0) {
-      mprinterr("Error: Missing bond internal for %s - %s\n",
-                topIn.AtomMaskName(dih->AtI()).c_str(),
-                topIn.AtomMaskName(dih->AtJ()).c_str());
+      mprinterr("Error: Missing bond0 internal for %s - %s\n",
+                topIn.LeapName(dih->AtI()).c_str(),
+                topIn.LeapName(dih->AtJ()).c_str());
+      //mprintf("DEBUG: Internal %s - %s - %s - %s\n",
+      //        topIn.LeapName(dih->AtI()).c_str(),
+      //        topIn.LeapName(dih->AtJ()).c_str(),
+      //        topIn.LeapName(dih->AtK()).c_str(),
+      //        topIn.LeapName(dih->AtL()).c_str());
     }
     if (bidx1 < 0) {
-    mprinterr("Error: Missing bond internal for %s - %s\n",
+    mprinterr("Error: Missing bond1 internal for %s - %s\n",
                 topIn.AtomMaskName(dih->AtK()).c_str(),
                 topIn.AtomMaskName(dih->AtL()).c_str());
     }
@@ -2343,5 +2401,6 @@ int Builder::GetZmatrixFromInternals(Zmatrix& zmatrix, Topology const& topIn) co
                                   internalAngles_[aidx1].ThetaVal()*Constants::RADDEG,
                                   internalBonds_[bidx1].DistVal()) );
   } // END loop over internal torsions
+  mprintf("DEBUG: ----- Exit GetZmatrixFromInternals -----\n");
   return 0;
 }
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index 739e916579..74169e534b 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -101,6 +101,10 @@ class Builder {
     int getExistingBondIdx(int, int) const;
     /// Build mock coordinates around given torsion
     int buildMockExternals(TorsionModel& MT, std::vector<InternalCoords> const& iaTorsions) const;
+    /// Build angle internal
+    void buildAngleInternal(int, int, int, Frame const&, Topology const&, Barray const&);
+    /// Build bond internal
+    void buildBondInternal(int, int, Frame const&, Topology const&, Barray const&);
     /// Generate internal coords for a given atom
     int generateAtomInternals(int, Frame const&, Topology const&, Barray const&);
 

From e330a262900ef84564862f6be1e5a9d0e886fdb1 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 8 Feb 2024 10:41:40 -0500
Subject: [PATCH 0470/1492] Use buildX routines

---
 src/Structure/Builder.cpp | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index ccd7df49db..23f80d3306 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -2158,7 +2158,8 @@ int Builder::GenerateInternals(Frame const& frameIn, Topology const& topIn, Barr
   AngleArray angles = GenerateAngleArray( topIn.Residues(), topIn.Atoms() );
   for (AngleArray::const_iterator ang = angles.begin(); ang != angles.end(); ++ang)
   {
-    double dValue = 0;
+    buildAngleInternal(ang->A1(), ang->A2(), ang->A3(), frameIn, topIn, hasPosition);
+/*    double dValue = 0;
     if (hasPosition[ang->A1()] &&
         hasPosition[ang->A2()] &&
         hasPosition[ang->A3()])
@@ -2171,12 +2172,13 @@ int Builder::GenerateInternals(Frame const& frameIn, Topology const& topIn, Barr
     mprintf("++++Angle INTERNAL: %f  for %s - %s - %s\n", dValue*Constants::RADDEG,
             topIn.LeapName(ang->A1()).c_str(),
             topIn.LeapName(ang->A2()).c_str(),
-            topIn.LeapName(ang->A3()).c_str());
+            topIn.LeapName(ang->A3()).c_str());*/
   }
   // Loop over bonds
   for (BondArray::const_iterator bnd = bonds.begin(); bnd != bonds.end(); ++bnd)
   {
-    double dValue = 0;
+    buildBondInternal(bnd->A1(), bnd->A2(), frameIn, topIn, hasPosition);
+/*    double dValue = 0;
     if (hasPosition[bnd->A1()] &&
         hasPosition[bnd->A2()])
     {
@@ -2187,7 +2189,7 @@ int Builder::GenerateInternals(Frame const& frameIn, Topology const& topIn, Barr
     internalBonds_.push_back( InternalBond(bnd->A1(), bnd->A2(), dValue) );
     mprintf("++++Bond INTERNAL: %f  for %s - %s\n", dValue,
             topIn.LeapName(bnd->A1()).c_str(),
-            topIn.LeapName(bnd->A2()).c_str());
+            topIn.LeapName(bnd->A2()).c_str());*/
   }
   // FIXME do chirality
   //zmatrix.print( &topIn );

From 636320fc4376f48386e0ecfab0bd15b698a7bf46 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 8 Feb 2024 12:08:22 -0500
Subject: [PATCH 0471/1492] Add debug messages for comparing to leap

---
 src/Structure/Zmatrix.cpp | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index 15aba9eb12..beb03c7f5a 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -1097,6 +1097,9 @@ int Zmatrix::SetToFrame(Frame& frameOut, Barray& hasPosition) const {
       mprintf("DEBUG: Next IC to use is %i : %i %i %i %i r=%g theta=%g phi=%g\n",
               icIdx+1, ic.AtI()+1, ic.AtJ()+1, ic.AtK()+1, ic.AtL()+1,
               ic.Dist(), ic.Theta(), ic.Phi());
+    mprintf( "Torsion = %f\n", ic.Phi() );
+    mprintf( "Angle   = %f\n", ic.Theta() );
+    mprintf( "Bond    = %f\n", ic.Dist() );
     Vec3 posI = AtomIposition(ic, frameOut);
 
     frameOut.SetXYZ( ic.AtI(), posI );

From 49c634031fd2438ddcd7edee007390b82d157042 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 8 Feb 2024 12:09:16 -0500
Subject: [PATCH 0472/1492] Fix values passed into InternalCoords (was
 flipped). When searching for existing torsion internals around a bond, return
 indices into torsionInternals instead of copies since we want to modify them
 sometimes.

---
 src/Structure/Builder.cpp | 137 ++++++++++++++++++--------------------
 src/Structure/Builder.h   |   4 +-
 2 files changed, 68 insertions(+), 73 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 23f80d3306..cd7430c045 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1086,51 +1086,51 @@ int Builder::UpdateICsFromFrame(Frame const& frameIn, int ires, Topology const&
   BondArray myBonds = GenerateBondArray( std::vector<Residue>(1, topIn.Res(ires)), topIn.Atoms() );
   for (BondArray::const_iterator bnd = myBonds.begin(); bnd != myBonds.end(); ++bnd) {
     if (topIn[bnd->A1()].ResNum() == ires && topIn[bnd->A2()].ResNum() == ires) {
-      mprintf("DEBUG: Looking at torsions around: %s - %s\n", topIn.AtomMaskName(bnd->A1()).c_str(), topIn.AtomMaskName(bnd->A2()).c_str());
+      mprintf("Looking at torsions around: %s - %s\n", topIn.LeapName(bnd->A1()).c_str(), topIn.LeapName(bnd->A2()).c_str());
       // Find all ICs that share atoms 1 and 2 (J and K)
       bool needsUpdate = false;
       double tDiff = 0;
-      Tarray iTorsions = getExistingTorsions(bnd->A1(), bnd->A2());
-      for (unsigned int idx = 0; idx != iTorsions.size(); idx++)
+      Iarray iTorsions = getExistingTorsionIdxs(bnd->A1(), bnd->A2());
+      for (Iarray::const_iterator idx = iTorsions.begin(); idx != iTorsions.end(); ++idx)
       {
-        InternalTorsion const& thisIc = internalTorsions_[idx];
-        if (hasPosition[thisIc.AtI()] &&
-            hasPosition[thisIc.AtJ()] &&
-            hasPosition[thisIc.AtK()] &&
-            hasPosition[thisIc.AtL()])
+        InternalTorsion const& dih = internalTorsions_[*idx];
+        if (hasPosition[dih.AtI()] &&
+            hasPosition[dih.AtJ()] &&
+            hasPosition[dih.AtK()] &&
+            hasPosition[dih.AtL()])
         {
-          mprintf("DEBUG:\tMeasuring torsion of fixed atoms: %s - %s - %s - %s\n",
-                  topIn.LeapName(thisIc.AtI()).c_str(),
-                  topIn.LeapName(thisIc.AtJ()).c_str(),
-                  topIn.LeapName(thisIc.AtK()).c_str(),
-                  topIn.LeapName(thisIc.AtL()).c_str());
-          double dTorsion = Torsion(frameIn.XYZ(thisIc.AtI()),
-                                    frameIn.XYZ(thisIc.AtJ()),
-                                    frameIn.XYZ(thisIc.AtK()),
-                                    frameIn.XYZ(thisIc.AtL()));
-          double dInternalValue = thisIc.PhiVal();
+          mprintf("Measuring torsion of fixed atoms: %s - %s - %s - %s\n",
+                  topIn.LeapName(dih.AtI()).c_str(),
+                  topIn.LeapName(dih.AtJ()).c_str(),
+                  topIn.LeapName(dih.AtK()).c_str(),
+                  topIn.LeapName(dih.AtL()).c_str());
+          double dTorsion = Torsion(frameIn.XYZ(dih.AtI()),
+                                    frameIn.XYZ(dih.AtJ()),
+                                    frameIn.XYZ(dih.AtK()),
+                                    frameIn.XYZ(dih.AtL()));
+          double dInternalValue = dih.PhiVal();
           tDiff = (dTorsion - dInternalValue);
-          mprintf("DEBUG:\tdTorsion= %f  dInternalValue= %f\n", dTorsion*Constants::RADDEG, dInternalValue*Constants::RADDEG);
+          mprintf("\tdTorsion= %f  dInternalValue= %f\n", dTorsion, dInternalValue);
           needsUpdate = true;
         } // END all coords present
       } // END loop over torsions matching current bond
       // If any difference was found, shift all of the torsions
       if (needsUpdate) {
-        mprintf("DEBUG: Twisting torsions centered on %s - %s by %f degrees\n",
+        mprintf("Twisting torsions centered on %s - %s by %f degrees\n",
                 topIn.LeapName(bnd->A1()).c_str(),
                 topIn.LeapName(bnd->A2()).c_str(),
-                tDiff);
-      for (unsigned int idx = 0; idx != iTorsions.size(); idx++)
-      {
-        InternalTorsion& thisIc = internalTorsions_[idx];
-        double dNew = thisIc.PhiVal() + tDiff;
-        mprintf("DEBUG:\tTwisting torsion for atoms: %s-%s-%s-%s\n",
-                topIn.AtomMaskName(thisIc.AtI()).c_str(),
-                topIn.AtomMaskName(thisIc.AtJ()).c_str(),
-                topIn.AtomMaskName(thisIc.AtK()).c_str(),
-                topIn.AtomMaskName(thisIc.AtL()).c_str());
-          mprintf("DEBUG:\t------- From %f to %f\n", thisIc.PhiVal()*Constants::RADDEG, dNew*Constants::RADDEG);
-          thisIc.SetPhiVal( dNew );
+                tDiff*Constants::RADDEG);
+        for (Iarray::const_iterator idx = iTorsions.begin(); idx != iTorsions.end(); ++idx)
+        {
+          InternalTorsion& dih = internalTorsions_[*idx];
+          double dNew = dih.PhiVal() + tDiff;
+          mprintf("Twisting torsion for atoms: %s-%s-%s-%s\n",
+                  *(topIn[dih.AtI()].Name()),
+                  *(topIn[dih.AtJ()].Name()),
+                  *(topIn[dih.AtK()].Name()),
+                  *(topIn[dih.AtL()].Name()));
+          mprintf("------- From %f to %f\n", dih.PhiVal()*Constants::RADDEG, dNew*Constants::RADDEG);
+          dih.SetPhiVal( dNew );
         }
       } // END ICs need update
     } // END both bond atoms belong to this residue
@@ -1179,7 +1179,7 @@ class Cpptraj::Structure::Builder::TorsionModel {
     /// Set up torsions around bonded atoms
     int SetupTorsion(AtomType::HybridizationType, AtomType::HybridizationType, Topology const& topIn);
     /// Build mock externals from given internals
-    int BuildMockExternals(Tarray const&, Topology const&);
+    int BuildMockExternals(Iarray const&, Tarray const&, Topology const&);
 
     /// \return Value of A-X-Y-D torsion in radians
     double Absolute() const { return dAbsolute_; }
@@ -1468,22 +1468,25 @@ static inline std::vector<MockAtom>::iterator find_mock_atom(std::vector<MockAto
   * By definition, the two central atoms will be the same for each
   * IC in iaTorsions.
   */
-int Cpptraj::Structure::Builder::TorsionModel::BuildMockExternals(Tarray const& iaTorsions,
+int Cpptraj::Structure::Builder::TorsionModel::BuildMockExternals(Iarray const& iaTorsions,
+                                                                  Tarray const& internalTorsionsIn,
                                                                   Topology const& topIn) // DEBUG topIn for debug only
 {
   if (iaTorsions.empty()) {
     mprinterr("Internal Error: Builder::buildMockExternals() called with no internal torsions.\n");
     return 1;
   }
-  mprintf("=======  Started mock coords from: %s\n", topIn.LeapName(iaTorsions.front().AtI()).c_str());
+  mprintf("=======  Started mock coords from: %s\n", topIn.LeapName(internalTorsionsIn[iaTorsions.front()].AtI()).c_str());
 
-  for (Tarray::const_iterator ic = iaTorsions.begin(); ic != iaTorsions.end(); ++ic)
+  for (Iarray::const_iterator idx = iaTorsions.begin(); idx != iaTorsions.end(); ++idx) {
+    InternalTorsion const& ic = internalTorsionsIn[*idx];
     mprintf("------- Known torsion: %s - %s - %s - %s  %f\n",
-            topIn.LeapName(ic->AtI()).c_str(),
-            topIn.LeapName(ic->AtJ()).c_str(),
-            topIn.LeapName(ic->AtK()).c_str(),
-            topIn.LeapName(ic->AtL()).c_str(),
-            ic->PhiVal()*Constants::RADDEG);
+            topIn.LeapName(ic.AtI()).c_str(),
+            topIn.LeapName(ic.AtJ()).c_str(),
+            topIn.LeapName(ic.AtK()).c_str(),
+            topIn.LeapName(ic.AtL()).c_str(),
+            ic.PhiVal()*Constants::RADDEG);
+  }
 
   // Define coordinates for the central atoms.
   //Vec3 posX(0, 0, 0);
@@ -1504,19 +1507,20 @@ int Cpptraj::Structure::Builder::TorsionModel::BuildMockExternals(Tarray const&
   Marray outerAtoms;
 
   // Define outer atoms
-  for (Tarray::const_iterator ic = iaTorsions.begin(); ic != iaTorsions.end(); ++ic)
+  for (Iarray::const_iterator idx = iaTorsions.begin(); idx != iaTorsions.end(); ++idx)
   {
-    if (ic == iaTorsions.begin()) {
+    InternalTorsion const& ic = internalTorsionsIn[*idx];
+    if (idx == iaTorsions.begin()) {
       // Define first outer atom as being in the XY plane
-      outerAtoms.push_back( MockAtom(ic->AtI(), Vec3(1, 1, 0)) );
+      outerAtoms.push_back( MockAtom(ic.AtI(), Vec3(1, 1, 0)) );
     } else {
-      Marray::iterator mi = find_mock_atom( outerAtoms, ic->AtI() );
+      Marray::iterator mi = find_mock_atom( outerAtoms, ic.AtI() );
       if (mi == outerAtoms.end())
-        outerAtoms.push_back( MockAtom(ic->AtI()) );
+        outerAtoms.push_back( MockAtom(ic.AtI()) );
     }
-    Marray::iterator ml = find_mock_atom( outerAtoms, ic->AtL() );
+    Marray::iterator ml = find_mock_atom( outerAtoms, ic.AtL() );
     if (ml == outerAtoms.end())
-      outerAtoms.push_back( MockAtom(ic->AtL()) );
+      outerAtoms.push_back( MockAtom(ic.AtL()) );
   }
   mprintf("DEBUG: Outer atoms:\n");
   for (Marray::const_iterator it = outerAtoms.begin(); it != outerAtoms.end(); ++it)
@@ -1532,7 +1536,7 @@ int Cpptraj::Structure::Builder::TorsionModel::BuildMockExternals(Tarray const&
     //bool gotOne = false;
     for (unsigned int jdx = 0; jdx != iaTorsions.size(); jdx++) {
       if (!used[jdx]) {
-        InternalTorsion const& iInt = iaTorsions[jdx];
+        InternalTorsion const& iInt = internalTorsionsIn[iaTorsions[jdx]];
         Marray::iterator tmpAt1 = find_mock_atom(outerAtoms, iInt.AtI());
         Marray::iterator tmpAt4 = find_mock_atom(outerAtoms, iInt.AtL());
         if (tmpAt1 == outerAtoms.end()) {
@@ -1615,14 +1619,14 @@ void Builder::UpdateIndicesWithOffset(int atomOffset) {
 }
 
 /** Find any existing torsions around ax-ay. */
-Builder::Tarray Builder::getExistingTorsions(int ax, int ay) const {
-  Tarray iTorsions;
+Builder::Iarray Builder::getExistingTorsionIdxs(int ax, int ay) const {
+  Iarray iTorsions;
   for (Tarray::const_iterator it = internalTorsions_.begin(); it != internalTorsions_.end(); ++it)
   {
     if ((it->AtJ() == ax && it->AtK() == ay) ||
         (it->AtJ() == ay && it->AtK() == ax))
     {
-      iTorsions.push_back( *it );
+      iTorsions.push_back( it - internalTorsions_.begin() );
     }
   }
   return iTorsions;
@@ -1805,7 +1809,7 @@ void Builder::ModelTorsion(TorsionModel const& MT, unsigned int iBondX, unsigned
                       AX.Pos().Dptr(),
                       AY.Pos().Dptr(),
                       AD.Pos().Dptr() );
-    mprintf(" %s replacing dval with %f\n", currentTop_->LeapName(aa).c_str(), phiVal*Constants::RADDEG);
+    mprintf(" %s replacing dval with %f\n", *((*currentTop_)[aa].Name()), phiVal*Constants::RADDEG);
   }
   // Look for an existing internal
   int icIdx = getExistingTorsionIdx( aa, ax, ay, ad );
@@ -2041,13 +2045,11 @@ int Builder::assignTorsionsAroundBond(int a1, int a2, Frame const& frameIn, Topo
   mprintf("bKnownX=%i  bKnownY=%i\n", (int)mT.AxHasKnownAtoms(), (int)mT.AyHasKnownAtoms());
   if (!(mT.AxHasKnownAtoms() && mT.AyHasKnownAtoms())) {
     // Find any existing internal coords around ax-ay
-    Tarray iTorsions = getExistingTorsions(ax, ay);
+    Iarray iTorsions = getExistingTorsionIdxs(ax, ay);
     if (!iTorsions.empty()) {
       mprintf("Using INTERNALs to fit new torsions around: %s - %s\n",
               topIn.LeapName(ax).c_str(), topIn.LeapName(ay).c_str());
-      //for (std::vector<InternalCoords>::const_iterator ic = iTorsions.begin(); ic != iTorsions.end(); ++ic)
-      //  ic->printIC( topIn );
-      if (mT.BuildMockExternals(iTorsions, topIn)) {
+      if (mT.BuildMockExternals(iTorsions, internalTorsions_, topIn)) {
         mprinterr("Error: Building mock externals around %s - %s failed.\n",
                   topIn.AtomMaskName(ax).c_str(), topIn.AtomMaskName(ay).c_str());
         return 1;
@@ -2212,18 +2214,9 @@ int Builder::generateAtomInternals(int at, Frame const& frameIn, Topology const&
                topIn.LeapName(at).c_str(),
                topIn.LeapName(*bat).c_str(),
                topIn.LeapName(*cat).c_str());
-        Tarray iTorsions = getExistingTorsions(*bat, *cat);
+        Iarray iTorsions = getExistingTorsionIdxs(*bat, *cat);
         int iShouldBe = (AtB.Nbonds() - 1) * (AtC.Nbonds() - 1);
         mprintf("ISHOULDBE= %i ITORSIONS= %zu\n", iShouldBe, iTorsions.size());
-        if (iShouldBe == 6 && iTorsions.size() == 6) { // FIXME DEBUG
-          for (Tarray::const_iterator it = iTorsions.begin(); it != iTorsions.end(); ++it)
-            mprintf("*** %s - %s - %s - %s : %f\n",
-                    topIn.LeapName(it->AtI()).c_str(),
-                    topIn.LeapName(it->AtJ()).c_str(),
-                    topIn.LeapName(it->AtK()).c_str(),
-                    topIn.LeapName(it->AtL()).c_str(),
-                    it->PhiVal()*Constants::RADDEG);
-        }
         if (iShouldBe != (int)iTorsions.size()) {
           assignTorsionsAroundBond(*bat, *cat, frameIn, topIn, hasPosition, at);
         }
@@ -2396,12 +2389,14 @@ int Builder::GetZmatrixFromInternals(Zmatrix& zmatrix, Topology const& topIn) co
                 topIn.AtomMaskName(dih->AtL()).c_str());
     }
     // Add internal coordinates
-    zmatrix.AddIC( InternalCoords(dih->AtI(), dih->AtJ(), dih->AtK(), dih->AtL(), dih->PhiVal()*Constants::RADDEG,
+    zmatrix.AddIC( InternalCoords(dih->AtI(), dih->AtJ(), dih->AtK(), dih->AtL(),
+                                  internalBonds_[bidx0].DistVal(),
                                   internalAngles_[aidx0].ThetaVal()*Constants::RADDEG,
-                                  internalBonds_[bidx0].DistVal()) );
-    zmatrix.AddIC( InternalCoords(dih->AtL(), dih->AtK(), dih->AtJ(), dih->AtI(), dih->PhiVal()*Constants::RADDEG,
+                                  dih->PhiVal()*Constants::RADDEG) );
+    zmatrix.AddIC( InternalCoords(dih->AtL(), dih->AtK(), dih->AtJ(), dih->AtI(),
+                                  internalBonds_[bidx1].DistVal(),
                                   internalAngles_[aidx1].ThetaVal()*Constants::RADDEG,
-                                  internalBonds_[bidx1].DistVal()) );
+                                  dih->PhiVal()*Constants::RADDEG) );
   } // END loop over internal torsions
   mprintf("DEBUG: ----- Exit GetZmatrixFromInternals -----\n");
   return 0;
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index 74169e534b..2ad3005720 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -91,8 +91,8 @@ class Builder {
     void createSp2Sp2Torsions(TorsionModel const&);
     /// Model torsions around a bond in the same manner as LEaP
     int assignTorsionsAroundBond(int, int, Frame const&, Topology const&, Barray const&, int);
-    /// Get any existing internal torsion around specified atoms
-    Tarray getExistingTorsions(int, int) const;
+    /// Get any existing internal torsion indices around specified atoms
+    Iarray getExistingTorsionIdxs(int, int) const;
     /// Get specific internal torsion
     int getExistingTorsionIdx(int, int, int, int) const;
     /// Get specific internal angle

From bbffa76b35d196dbfee8c378fc629b222635fcbc Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 8 Feb 2024 12:16:26 -0500
Subject: [PATCH 0473/1492] Add message so we know when we are looking for
 extra params

---
 src/Structure/Builder.cpp | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index cd7430c045..7a0c333b27 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -2330,6 +2330,7 @@ int Builder::GenerateInternalsAroundLink(int at0, int at1,
   //  return 1;
   //}
   // FIXME this is a hack to make certain we have all the angle/bond terms we need
+  mprintf("DEBUG: LOOKING FOR MISSING ANGLE/BOND PARAMS.\n");
   for (Tarray::const_iterator dih = internalTorsions_.begin(); dih != internalTorsions_.end(); ++dih)
   {
     int idx = getExistingAngleIdx(dih->AtI(), dih->AtJ(), dih->AtK());

From 276090d8e16cb1bd3abb0b91817f856ca9de81be Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 8 Feb 2024 12:17:03 -0500
Subject: [PATCH 0474/1492] Rework the order in which things are done so that
 internals are only generated for each residue as it is being built. This
 should keep memory costs under control.

---
 src/Exec_Build.cpp | 135 +++++++++++++++++++--------------------------
 1 file changed, 57 insertions(+), 78 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 181e8b2f8f..a14c9e83c8 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -184,9 +184,13 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
   hasPosition.reserve( newNatom );
 
   // Hold Z-matrices for residues that have missing atoms
-  typedef std::vector<Cpptraj::Structure::Builder*> Zarray;
-  Zarray ResZmatrices;
-  ResZmatrices.reserve( topIn.Nres() );
+//  typedef std::vector<Cpptraj::Structure::Builder*> Zarray;
+//  Zarray ResZmatrices;
+//  ResZmatrices.reserve( topIn.Nres() );
+  // Hold atom offsets needed when building residues
+  typedef std::vector<int> Iarray;
+  Iarray AtomOffsets;
+  AtomOffsets.reserve( topIn.Nres() );
 
   // For inter-residue bonding, use residue # and atom name since
   // atom numbering may change if atoms are added from templates.
@@ -214,7 +218,8 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
     IParray intraResBonds;
     if (resTemplate == 0) {
       // ----- No template. Just add the atoms. ------------
-      ResZmatrices.push_back( 0 );
+      //ResZmatrices.push_back( 0 );
+      AtomOffsets.push_back( -1 );
       for (int itgt = currentRes.FirstAtom(); itgt != currentRes.LastAtom(); ++itgt)
       {
         // Track intra-residue bonds
@@ -301,25 +306,16 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
       mprintf("\t%i source atoms not mapped to template.\n", nTgtAtomsMissing);
       // Save zmatrix if atoms need to be built
       if (atomsNeedBuilding) {
-        Frame templateFrame = resTemplate->AllocateFrame();
-        resTemplate->GetFrame( 0, templateFrame );
-        Cpptraj::Structure::Builder* structureBuilder = new Cpptraj::Structure::Builder();
-        structureBuilder->SetDebug( 1 ); // DEBUG FIXME
-        structureBuilder->SetParameters( &mainParmSet );
+        AtomOffsets.push_back( atomOffset );
+
         //if (zmatrix->SetFromFrameAndConnect( templateFrame, resTemplate->Top() )) {
 //        if (zmatrix->GenerateInternals( templateFrame, resTemplate->Top() )) {
 //          mprinterr("Error: Could not set up residue template zmatrix.\n");
 //          return 1;
 //        }
-        if (structureBuilder->GenerateInternals(templateFrame, resTemplate->Top(),
-                                               std::vector<bool>(resTemplate->Top().Natom(), true)))
-        {
-          mprinterr("Error: Generate internals for residue template failed.\n");
-          return 1;
-        }
+
 //        zmatrix->print( resTemplate->TopPtr() );
-        structureBuilder->UpdateIndicesWithOffset( atomOffset );
-        ResZmatrices.push_back( structureBuilder );
+//        ResZmatrices.push_back( structureBuilder );
 //        zmatrix->print( &topOut );
         //for (Iarray::const_iterator jres = resConnections[ires].begin();
         //                            jres != resConnections[ires].end(); ++jres)
@@ -327,7 +323,8 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
         //  mprintf("DEBUG:\t\tConnected residue %s\n", topIn.TruncResNameOnumId(*jres).c_str());
         //}
       } else
-        ResZmatrices.push_back( 0 );
+        AtomOffsets.push_back( -1 );
+//        ResZmatrices.push_back( 0 );
     } // END template exists
     // Add intra-residue bonds
     for (IParray::const_iterator it = intraResBonds.begin(); it != intraResBonds.end(); ++it)
@@ -381,17 +378,17 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
     mprinterr("Internal Error: hasPosition size %zu != newNatom size %i\n", hasPosition.size(), newNatom);
     return 1;
   }
-  if (ResZmatrices.size() != (unsigned int)topOut.Nres()) {
-    mprinterr("Internal Error: ResZmatrices size %zu != newNres size %i\n", ResZmatrices.size(), topOut.Nres());
+  if (AtomOffsets.size() != (unsigned int)topOut.Nres()) {
+    mprinterr("Internal Error: AtomOffsets size %zu != newNres size %i\n", AtomOffsets.size(), topOut.Nres());
     return 1;
   }
 
   // -----------------------------------
   // Build using internal coords if needed.
   std::vector<bool> resIsBuilt; // TODO is this needed?
-  resIsBuilt.reserve( ResZmatrices.size() );
-  for (Zarray::const_iterator it = ResZmatrices.begin(); it != ResZmatrices.end(); ++it) {
-    if ( *it == 0 )
+  resIsBuilt.reserve( AtomOffsets.size() );
+  for (Iarray::const_iterator it = AtomOffsets.begin(); it != AtomOffsets.end(); ++it) {
+    if ( *it < 0 )
       resIsBuilt.push_back( true );
     else
       resIsBuilt.push_back( false );
@@ -402,11 +399,26 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
 //  linkBuilder.SetParameters( &mainParmSet );
   bool buildFailed = false;
   TermTypeArray::const_iterator termType = ResTypes.begin(); // FIXME is termType needed?
-  for (Zarray::const_iterator it = ResZmatrices.begin(); it != ResZmatrices.end(); ++it, ++termType)
+  //for (Zarray::const_iterator it = ResZmatrices.begin(); it != ResZmatrices.end(); ++it, ++termType)
+  for (Iarray::const_iterator it = AtomOffsets.begin(); it != AtomOffsets.end(); ++it)
   {
-    long int ires = it-ResZmatrices.begin();
-    Cpptraj::Structure::Builder* structureBuilder = *it;
-    if (structureBuilder != 0) {
+    long int ires = it-AtomOffsets.begin();
+    //Cpptraj::Structure::Builder* structureBuilder = *it;
+    if (*it > -1) {
+      Cpptraj::Structure::Builder* structureBuilder = new Cpptraj::Structure::Builder();
+      structureBuilder->SetDebug( 1 ); // DEBUG FIXME
+      structureBuilder->SetParameters( &mainParmSet );
+      DataSet_Coords* resTemplate = ResTemplates[ires];
+      Frame templateFrame = resTemplate->AllocateFrame();
+      resTemplate->GetFrame( 0, templateFrame );
+      if (structureBuilder->GenerateInternals(templateFrame, resTemplate->Top(),
+                                             std::vector<bool>(resTemplate->Top().Natom(), true)))
+      {
+        mprinterr("Error: Generate internals for residue template failed.\n");
+        return 1;
+      }
+      structureBuilder->UpdateIndicesWithOffset( *it );
+
       mprintf("DEBUG: ***** BUILD residue %li %s *****\n", ires + 1,
               topOut.TruncResNameOnumId(ires).c_str());
       mprintf("DEBUG: Residue type: %s terminal\n", Cpptraj::Structure::terminalStr(*termType));
@@ -423,10 +435,9 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
                   topOut.AtomMaskName(resBonds->first).c_str(),
                   topOut.AtomMaskName(resBonds->second).c_str());
           topOut.AddBond(resBonds->first, resBonds->second);
-          // FIXME DEBUG
-          //structureBuilder.SetZmatrix( zmatrix );
+          // Generate internals around the link
           if (structureBuilder->GenerateInternalsAroundLink(resBonds->first, resBonds->second,
-                                                           frameOut, topOut, hasPosition))
+                                                            frameOut, topOut, hasPosition))
           {
             mprinterr("Error: Assign torsions around inter-residue link %s - %s failed.\n",
                       topOut.AtomMaskName(resBonds->first).c_str(),
@@ -436,57 +447,25 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
           //tmpz.print(&topOut);
         }
       }
-/*
-      if ( *termType != Cpptraj::Structure::BEG_TERMINAL ) {
-        for (int at = topOut.Res(ires).FirstAtom(); at != topOut.Res(ires).LastAtom(); ++at)
-        {
-          for (Atom::bond_iterator bat = topOut[at].bondbegin(); bat != topOut[at].bondend(); ++bat)
-          {
-            long int jres = (long int)topOut[*bat].ResNum();
-            if (jres < ires) {
-              mprintf("DEBUG: Connected to residue %s\n", topOut.TruncResNameNum(jres).c_str());
-              if (linkBuilder.ModelCoordsAroundBond(frameOut, topOut, at, *bat,
-                                                    *zmatrix, hasPosition))
-              {
-                mprinterr("Error: Model coords around bond failed between %s and %s\n",
-                          topOut.AtomMaskName(at).c_str(), topOut.AtomMaskName(*bat).c_str());
-                return 1;
-              }
-              
-            }
-          }
-        }
-      }
-*/
-      // TEST FIXME
-//      Cpptraj::Structure::Zmatrix testZ;
-//      if (testZ.BuildZmatrixFromTop(frameOut, topOut, ires, mainParmSet.AT(), hasPosition)) {
-//        mprinterr("Error: Failed to create zmatrix from topology.\n");
-//        return 1;
-//      }
       // Update internal coords from known positions
       if (structureBuilder->UpdateICsFromFrame( frameOut, ires, topOut, hasPosition )) {
         mprinterr("Error: Failed to update Zmatrix with values from existing positions.\n");
         return 1;
       }
-      // Update zmatrix seeds
-      //if (zmatrix->AutoSetSeedsWithPositions( frameOut, topOut, ires, hasPosition )) {
-      //  mprinterr("Error: Could not set up seed atoms for Zmatrix.\n");
-      //  buildFailed = true;
-      //} else {
-        Cpptraj::Structure::Zmatrix tmpz;
-        tmpz.SetDebug( 1 ); // DEBUG
-        if (structureBuilder->GetZmatrixFromInternals(tmpz, topOut)) {
-          mprinterr("Error: Could not get Zmatrix from internals.\n");
-          return 1;
-        }
-        if (tmpz.SetToFrame( frameOut, hasPosition )) {
-          mprinterr("Error: Building residue %s failed.\n",
-                    topOut.TruncResNameOnumId(ires).c_str());
-          buildFailed = true;
-        } else
-          resIsBuilt[ires] = true;
-      //}
+      // Convert to Zmatrix and assign missing atom positions
+      Cpptraj::Structure::Zmatrix tmpz;
+      tmpz.SetDebug( 1 ); // DEBUG
+      if (structureBuilder->GetZmatrixFromInternals(tmpz, topOut)) {
+        mprinterr("Error: Could not get Zmatrix from internals.\n");
+        return 1;
+      }
+      if (tmpz.SetToFrame( frameOut, hasPosition )) {
+        mprinterr("Error: Building residue %s failed.\n",
+                  topOut.TruncResNameOnumId(ires).c_str());
+        buildFailed = true;
+      } else
+        resIsBuilt[ires] = true;
+      delete structureBuilder;
     }
   }
 
@@ -501,8 +480,8 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
   }
 
   // Clean up zmatrices
-  for (Zarray::iterator it = ResZmatrices.begin(); it != ResZmatrices.end(); ++it)
-    if (*it != 0) delete *it;
+  //for (Zarray::iterator it = ResZmatrices.begin(); it != ResZmatrices.end(); ++it)
+  //  if (*it != 0) delete *it;
 
   // Finalize topology
   topOut.CommonSetup(); // TODO dont assign default bond parameters here

From 4ceda1bcdb9aac264f026e8264341f0cd418e501 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 8 Feb 2024 12:32:31 -0500
Subject: [PATCH 0475/1492] Get rid of old code. Dont try to assign default
 bond parameters to built topology

---
 src/Exec_Build.cpp | 142 +++++++--------------------------------------
 1 file changed, 22 insertions(+), 120 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index a14c9e83c8..ab5f2200f6 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -74,64 +74,6 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
                                        Topology const& topIn, Frame const& frameIn,
                                        ParameterSet const& mainParmSet)
 {
-  // Residue terminal status
-  
-  // Track which residues are terminal
-  //typedef std::vector<int> Iarray;
-  //typedef std::vector<Iarray> IIarray;
-  //IIarray molTermResidues;
-/*
-  // Track residue connections
-  IIarray resConnections( topIn.Nres() );
-  for (int ires = 0; ires != topIn.Nres(); ires++)
-  {
-    Residue const& currentRes = topIn.Res(ires);
-    int n_connections = 0;
-    for (int at = currentRes.FirstAtom(); at != currentRes.LastAtom(); at++)
-    {
-      //if (topIn[at].Element() != Atom::HYDROGEN && topIn[at].Nbonds() > 1) {
-        for (Atom::bond_iterator bat = topIn[at].bondbegin(); bat != topIn[at].bondend(); ++bat)
-        {
-          if (topIn[*bat].ResNum() != topIn[at].ResNum()) {
-            n_connections++;
-            resConnections[ ires ].push_back( topIn[*bat].ResNum() );
-          }
-        }
-      //}
-    }
-    mprintf("DEBUG: Res %s has %i connections.\n", topIn.TruncResNameOnumId(ires).c_str(), n_connections);
-    if (n_connections == 1) {
-      int molnum = topIn[currentRes.FirstAtom()].MolNum();
-      molTermResidues[ molnum ].push_back( ires );
-    }
-  }
-  // DEBUG Print residue connections
-  mprintf("DEBUG: Residue connections:\n");
-  for (IIarray::const_iterator rit = resConnections.begin(); rit != resConnections.end(); ++rit)
-  {
-    mprintf("DEBUG:\t\t%s to", topIn.TruncResNameOnumId(rit-resConnections.begin()).c_str());
-    for (Iarray::const_iterator it = rit->begin(); it != rit->end(); ++it)
-      mprintf(" %s", topIn.TruncResNameOnumId( *it ).c_str());
-    mprintf("\n");
-  }
-  typedef std::vector<TermType> Tarray;
-  Tarray residueTerminalStatus( topIn.Nres(), REGULAR );
-  mprintf("\tTerminal residues:\n");
-  for (IIarray::const_iterator mit = molTermResidues.begin(); mit != molTermResidues.end(); ++mit)
-  {
-    mprintf("\t\tMol %li:", mit - molTermResidues.begin() + 1);
-    for (Iarray::const_iterator it = mit->begin(); it != mit->end(); ++it) {
-      mprintf(" %s", topIn.TruncResNameOnumId( *it ).c_str());
-      if (it == mit->begin())
-        residueTerminalStatus[*it] = BEG_TERMINAL;
-      else
-        residueTerminalStatus[*it] = END_TERMINAL;
-      mprintf("(%i)", (int)residueTerminalStatus[*it]);
-    }
-    mprintf("\n");
-  }
-*/
-  // -----------------------------------
   // Array of templates for each residue
   std::vector<DataSet_Coords*> ResTemplates;
   ResTemplates.reserve( topIn.Nres() );
@@ -159,8 +101,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
     } else {
       resTermType = Cpptraj::Structure::NON_TERMINAL;
     }
-    mprintf("DEBUG: Residue type: %s\n", Cpptraj::Structure::terminalStr(resTermType));
-    ResTypes.push_back( resTermType );
+    mprintf("DEBUG: Residue type: %s terminal\n", Cpptraj::Structure::terminalStr(resTermType));
     // Identify a template based on the residue name.
     DataSet_Coords* resTemplate = IdTemplateFromName(Templates, currentRes.Name(), resTermType);
     if (resTemplate == 0) {
@@ -183,10 +124,6 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
   Cpptraj::Structure::Zmatrix::Barray hasPosition;
   hasPosition.reserve( newNatom );
 
-  // Hold Z-matrices for residues that have missing atoms
-//  typedef std::vector<Cpptraj::Structure::Builder*> Zarray;
-//  Zarray ResZmatrices;
-//  ResZmatrices.reserve( topIn.Nres() );
   // Hold atom offsets needed when building residues
   typedef std::vector<int> Iarray;
   Iarray AtomOffsets;
@@ -198,10 +135,6 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
   typedef std::vector<ResAtPair> ResAtArray;
   ResAtArray interResBonds;
 
-  //Cpptraj::Structure::Builder structureBuilder;
-  //structureBuilder.SetDebug( 1 );
-  //structureBuilder.SetParameters( &mainParmSet );
-
   // For holding bonded atom pairs
   typedef std::pair<int,int> Ipair;
   typedef std::vector<Ipair> IParray;
@@ -218,7 +151,6 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
     IParray intraResBonds;
     if (resTemplate == 0) {
       // ----- No template. Just add the atoms. ------------
-      //ResZmatrices.push_back( 0 );
       AtomOffsets.push_back( -1 );
       for (int itgt = currentRes.FirstAtom(); itgt != currentRes.LastAtom(); ++itgt)
       {
@@ -275,7 +207,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
             }
           //}
         }
-        // TODO connect atoms for inter-residue connections
+        // TODO check connect atoms for inter-residue connections
         templateAtom.ClearBonds(); // FIXME AddTopAtom should clear bonds
         topOut.AddTopAtom( templateAtom, currentRes );
         if (map[iref] == -1) {
@@ -304,27 +236,11 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
         if (pdb[itgt] == -1)
           nTgtAtomsMissing++;
       mprintf("\t%i source atoms not mapped to template.\n", nTgtAtomsMissing);
-      // Save zmatrix if atoms need to be built
-      if (atomsNeedBuilding) {
+      // Save atom offset if atoms need to be built
+      if (atomsNeedBuilding)
         AtomOffsets.push_back( atomOffset );
-
-        //if (zmatrix->SetFromFrameAndConnect( templateFrame, resTemplate->Top() )) {
-//        if (zmatrix->GenerateInternals( templateFrame, resTemplate->Top() )) {
-//          mprinterr("Error: Could not set up residue template zmatrix.\n");
-//          return 1;
-//        }
-
-//        zmatrix->print( resTemplate->TopPtr() );
-//        ResZmatrices.push_back( structureBuilder );
-//        zmatrix->print( &topOut );
-        //for (Iarray::const_iterator jres = resConnections[ires].begin();
-        //                            jres != resConnections[ires].end(); ++jres)
-        //{
-        //  mprintf("DEBUG:\t\tConnected residue %s\n", topIn.TruncResNameOnumId(*jres).c_str());
-        //}
-      } else
+      else
         AtomOffsets.push_back( -1 );
-//        ResZmatrices.push_back( 0 );
     } // END template exists
     // Add intra-residue bonds
     for (IParray::const_iterator it = intraResBonds.begin(); it != intraResBonds.end(); ++it)
@@ -338,7 +254,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
   mprintf("\t%i template atoms missing in source.\n", nRefAtomsMissing);
 
   // -----------------------------------
-  // Add inter-residue bonds
+  // Check inter-residue bonds
   std::vector<IParray> resBondingAtoms(topOut.Nres());
   for (ResAtArray::const_iterator it = interResBonds.begin(); it != interResBonds.end(); ++it)
   {
@@ -358,7 +274,6 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
       mprinterr("Error: Atom %s not found in residue %i\n", *(ra1.second), ra1.first);
       return 1;
     }
-    //topOut.AddBond(at0, at1);
     // Save bonding atoms
     resBondingAtoms[ra0.first].push_back( Ipair(at0, at1) );
     resBondingAtoms[ra1.first].push_back( Ipair(at1, at0) );
@@ -385,29 +300,25 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
 
   // -----------------------------------
   // Build using internal coords if needed.
-  std::vector<bool> resIsBuilt; // TODO is this needed?
-  resIsBuilt.reserve( AtomOffsets.size() );
-  for (Iarray::const_iterator it = AtomOffsets.begin(); it != AtomOffsets.end(); ++it) {
-    if ( *it < 0 )
-      resIsBuilt.push_back( true );
-    else
-      resIsBuilt.push_back( false );
-  }
+//  std::vector<bool> resIsBuilt; // TODO is this needed?
+//  resIsBuilt.reserve( AtomOffsets.size() );
+//  for (Iarray::const_iterator it = AtomOffsets.begin(); it != AtomOffsets.end(); ++it) {
+//    if ( *it < 0 )
+//      resIsBuilt.push_back( true );
+//    else
+//      resIsBuilt.push_back( false );
+//  }
 
-//  Cpptraj::Structure::Builder linkBuilder;
-//  linkBuilder.SetDebug( 1 ); // FIXME
-//  linkBuilder.SetParameters( &mainParmSet );
   bool buildFailed = false;
-  TermTypeArray::const_iterator termType = ResTypes.begin(); // FIXME is termType needed?
-  //for (Zarray::const_iterator it = ResZmatrices.begin(); it != ResZmatrices.end(); ++it, ++termType)
   for (Iarray::const_iterator it = AtomOffsets.begin(); it != AtomOffsets.end(); ++it)
   {
     long int ires = it-AtomOffsets.begin();
-    //Cpptraj::Structure::Builder* structureBuilder = *it;
     if (*it > -1) {
+      // Residue has atom offset which indicates it needs something built.
       Cpptraj::Structure::Builder* structureBuilder = new Cpptraj::Structure::Builder();
       structureBuilder->SetDebug( 1 ); // DEBUG FIXME
       structureBuilder->SetParameters( &mainParmSet );
+      // Generate internals from the template, update indices to this topology.
       DataSet_Coords* resTemplate = ResTemplates[ires];
       Frame templateFrame = resTemplate->AllocateFrame();
       resTemplate->GetFrame( 0, templateFrame );
@@ -421,11 +332,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
 
       mprintf("DEBUG: ***** BUILD residue %li %s *****\n", ires + 1,
               topOut.TruncResNameOnumId(ires).c_str());
-      mprintf("DEBUG: Residue type: %s terminal\n", Cpptraj::Structure::terminalStr(*termType));
-      //mprintf("DEBUG: Zmatrix for building residue %li %s\n", ires + 1,
-      //        topOut.TruncResNameOnumId(ires).c_str());
-      //zmatrix->print(&topOut);
-//      linkBuilder.SetZmatrix( zmatrix );
+      //mprintf("DEBUG: Residue type: %s terminal\n", Cpptraj::Structure::terminalStr(*termType));
       // Is this residue connected to an earlier residue?
       for (IParray::const_iterator resBonds = resBondingAtoms[ires].begin();
                                    resBonds != resBondingAtoms[ires].end(); ++resBonds)
@@ -444,7 +351,6 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
                       topOut.AtomMaskName(resBonds->second).c_str());
             return 1;
           }
-          //tmpz.print(&topOut);
         }
       }
       // Update internal coords from known positions
@@ -463,11 +369,11 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
         mprinterr("Error: Building residue %s failed.\n",
                   topOut.TruncResNameOnumId(ires).c_str());
         buildFailed = true;
-      } else
-        resIsBuilt[ires] = true;
+      }// else
+       // resIsBuilt[ires] = true;
       delete structureBuilder;
     }
-  }
+  } // END loop over atom offsets
 
   // DEBUG - Print new top/coords
   for (int iat = 0; iat != topOut.Natom(); iat++)
@@ -479,12 +385,8 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
             (int)hasPosition[iat], XYZ[0], XYZ[1], XYZ[2]);
   }
 
-  // Clean up zmatrices
-  //for (Zarray::iterator it = ResZmatrices.begin(); it != ResZmatrices.end(); ++it)
-  //  if (*it != 0) delete *it;
-
-  // Finalize topology
-  topOut.CommonSetup(); // TODO dont assign default bond parameters here
+  // Finalize topology - determine molecules, dont renumber residues, dont assign default bond params
+  topOut.CommonSetup(true, false, false);
   topOut.Summary();
 
   if (buildFailed) return 1;

From 024a9127409b7292a079681f5e60bc78baa9a952 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 8 Feb 2024 12:38:32 -0500
Subject: [PATCH 0476/1492] Add comment line

---
 src/Structure/Builder.cpp | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 7a0c333b27..5b578f0af7 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -101,6 +101,7 @@ const
   return 0;
 }
 
+// -----------------------------------------------------------------------------
 /** Attempt to assign a reasonable value for theta internal coordinate for
   * atom i given that atoms j and k have known positions.
   */

From 1c777e6af3e5cf524200247c8e6f5922ce27288f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 8 Feb 2024 12:58:29 -0500
Subject: [PATCH 0477/1492] Start new sequnce

---
 src/Exec_Sequence.cpp | 69 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 69 insertions(+)

diff --git a/src/Exec_Sequence.cpp b/src/Exec_Sequence.cpp
index 89127f23cb..768cfc5e0b 100644
--- a/src/Exec_Sequence.cpp
+++ b/src/Exec_Sequence.cpp
@@ -2,6 +2,7 @@
 #include "CpptrajStdio.h"
 #include "AssociatedData_Connect.h"
 #include "Structure/Builder.h"
+#include "Structure/Zmatrix.h"
 
 /** Generate and build the specified sequence. */
 int Exec_Sequence::generate_sequence(DataSet_Coords* OUT,
@@ -85,6 +86,74 @@ const
   for (unsigned int idx = 0; idx < Units.size(); idx++)
     mprintf("\tUnit %s HEAD %i TAIL %i\n", Units[idx]->legend(), connectAt0[idx]+1, connectAt1[idx]+1);
 
+  Topology topOut;
+  Frame frameOut;
+  mprintf("\tFinal structure should have %i atoms.\n", total_natom);
+  frameOut.SetupFrame( total_natom );
+  // Clear frame so that AddXYZ can be used
+  frameOut.ClearAtoms();
+
+  // hasPosition - for each atom in topOut, status on whether atom in frameOut needs building
+  Cpptraj::Structure::Zmatrix::Barray hasPosition;
+  hasPosition.reserve( total_natom );
+
+  // Hold atom offsets needed when building residues
+  typedef std::vector<int> Iarray;
+  Iarray AtomOffsets;
+  AtomOffsets.reserve( Units.size() ); // FIXME assuming 1 residue per unit
+
+  // For holding bonded atom pairs
+  typedef std::pair<int,int> Ipair;
+  typedef std::vector<Ipair> IParray;
+
+  // Loop for setting up atoms in the topology from units
+  for (unsigned int idx = 0; idx < Units.size(); idx++)
+  {
+    DataSet_Coords* unit = Units[idx];
+    mprintf("\tAdding atoms for unit %s\n", unit->legend());
+    Residue const& currentRes = unit->Top().Res(0); // FIXME assuming 1 unit
+    int atomOffset = topOut.Natom();
+    mprintf("DEBUG: atom offset is %i\n", atomOffset);
+    // Add the unit atoms. Only the first unit has known position.
+    bool atomPosKnown = (idx == 0);
+    Frame unitFrm = unit->AllocateFrame();
+    unit->GetFrame(0, unitFrm);
+    IParray intraResBonds;
+    for (int itgt = 0; itgt < unit->Top().Natom(); itgt++)
+    {
+      Atom sourceAtom = unit->Top()[itgt];
+      // Save the bonds
+      int at0 = itgt + atomOffset;
+      for (Atom::bond_iterator bat = sourceAtom.bondbegin(); bat != sourceAtom.bondend(); ++bat) {
+        int at1 = *bat + atomOffset;
+        if (at1 > at0) {
+          mprintf("Will add bond between %i and %i (original %i and %i)\n", at0+1, at1+1, itgt+1, *bat + 1);
+          intraResBonds.push_back( Ipair(at0, at1) );
+        }
+      }
+      sourceAtom.ClearBonds(); // FIXME AddTopAtom should clear bonds
+      topOut.AddTopAtom( sourceAtom, currentRes );
+      frameOut.AddVec3( Vec3(unitFrm.XYZ(itgt)) );
+      hasPosition.push_back( atomPosKnown );
+    }
+    // Add the bonds
+    // Add intra-residue bonds
+    for (IParray::const_iterator it = intraResBonds.begin(); it != intraResBonds.end(); ++it)
+    {
+      //mprintf("DEBUG: Intra-res bond: Res %s atom %s to res %s atom %s\n",
+      //        topOut.TruncResNameOnumId(topOut[it->first].ResNum()).c_str(), *(topOut[it->first].Name()),
+      //        topOut.TruncResNameOnumId(topOut[it->second].ResNum()).c_str(), *(topOut[it->second].Name()));
+      topOut.AddBond(it->first, it->second);
+    }
+
+    // All units after the first need building
+    if (atomPosKnown)
+      AtomOffsets.push_back( -1 );
+    else
+      AtomOffsets.push_back( atomOffset );
+  } // END loop over units
+
+
   Topology combinedTop;
   combinedTop.SetDebug( debug_ );
   combinedTop.SetParmName( OUT->Meta().Name(), FileName() );

From b309d3bfd283da4b4e50f99e8e02730279f4601e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 8 Feb 2024 13:01:16 -0500
Subject: [PATCH 0478/1492] Fix comments

---
 src/Exec_Sequence.cpp | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/Exec_Sequence.cpp b/src/Exec_Sequence.cpp
index 768cfc5e0b..f1b5d591e6 100644
--- a/src/Exec_Sequence.cpp
+++ b/src/Exec_Sequence.cpp
@@ -122,7 +122,7 @@ const
     for (int itgt = 0; itgt < unit->Top().Natom(); itgt++)
     {
       Atom sourceAtom = unit->Top()[itgt];
-      // Save the bonds
+      // Save the intra-residue bonds
       int at0 = itgt + atomOffset;
       for (Atom::bond_iterator bat = sourceAtom.bondbegin(); bat != sourceAtom.bondend(); ++bat) {
         int at1 = *bat + atomOffset;
@@ -136,7 +136,6 @@ const
       frameOut.AddVec3( Vec3(unitFrm.XYZ(itgt)) );
       hasPosition.push_back( atomPosKnown );
     }
-    // Add the bonds
     // Add intra-residue bonds
     for (IParray::const_iterator it = intraResBonds.begin(); it != intraResBonds.end(); ++it)
     {

From bb15f5498887238d0cbc8ddbf3e9ff40cac231c4 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 8 Feb 2024 13:28:23 -0500
Subject: [PATCH 0479/1492] Do the inter-residue bonds

---
 src/Exec_DataSetCmd.cpp |  2 ++
 src/Exec_Sequence.cpp   | 29 +++++++++++++++++++++++++++--
 2 files changed, 29 insertions(+), 2 deletions(-)

diff --git a/src/Exec_DataSetCmd.cpp b/src/Exec_DataSetCmd.cpp
index 9d60c346f8..93778e6b48 100644
--- a/src/Exec_DataSetCmd.cpp
+++ b/src/Exec_DataSetCmd.cpp
@@ -385,6 +385,8 @@ Exec::RetType Exec_DataSetCmd::SetConnect(CpptrajState& State, ArgList& argIn) {
         mprinterr("Error: Neither head atom nor tail atom could be set via mask.\n");
         return CpptrajState::ERR;
       }
+      if (head > -1) mprintf("\tHead atom# %i\n", head+1);
+      if (tail > -1) mprintf("\tTail atom# %i\n", tail+1);
       connect = AssociatedData_Connect(head, tail);
     }
     // Check for existing associated data
diff --git a/src/Exec_Sequence.cpp b/src/Exec_Sequence.cpp
index f1b5d591e6..10774e9aa9 100644
--- a/src/Exec_Sequence.cpp
+++ b/src/Exec_Sequence.cpp
@@ -107,12 +107,26 @@ const
   typedef std::vector<Ipair> IParray;
 
   // Loop for setting up atoms in the topology from units
+  int prevTailAtom = -1;
   for (unsigned int idx = 0; idx < Units.size(); idx++)
   {
+    int atomOffset = topOut.Natom();
     DataSet_Coords* unit = Units[idx];
-    mprintf("\tAdding atoms for unit %s\n", unit->legend());
+    // Needs to have connect associated data
+    AssociatedData* ad = unit->GetAssociatedData(AssociatedData::CONNECT);
+    if (ad == 0) {
+      mprinterr("Error: Unit '%s' does not have CONNECT data.\n", unit->legend());
+      return 1;
+    }
+    AssociatedData_Connect const& CONN = static_cast<AssociatedData_Connect const&>( *ad );
+    if (CONN.NconnectAtoms() < 2) {
+      mprinterr("Error: Not enough connect atoms in unit '%s'\n", unit->legend());
+      return 1;
+    }
+    int headAtom = CONN.Connect()[0] + atomOffset;
+    int tailAtom = CONN.Connect()[1] + atomOffset;
+    mprintf("\tAdding atoms for unit %s (head %i tail %i)\n", unit->legend(), headAtom+1, tailAtom+1);
     Residue const& currentRes = unit->Top().Res(0); // FIXME assuming 1 unit
-    int atomOffset = topOut.Natom();
     mprintf("DEBUG: atom offset is %i\n", atomOffset);
     // Add the unit atoms. Only the first unit has known position.
     bool atomPosKnown = (idx == 0);
@@ -144,6 +158,17 @@ const
       //        topOut.TruncResNameOnumId(topOut[it->second].ResNum()).c_str(), *(topOut[it->second].Name()));
       topOut.AddBond(it->first, it->second);
     }
+    // Connect HEAD atom of this residue to TAIL of previous residue
+    if (idx > 0) {
+      if (prevTailAtom < 0 || headAtom < 0) {
+        mprinterr("Error: Could not find connect atoms for previous residue (%i) and/or this residue (%i)\n",
+                  prevTailAtom+1, headAtom+1);
+        return 1;
+      }
+      mprintf("Will add bond between %i and %i\n", prevTailAtom+1, headAtom+1);
+      topOut.AddBond(prevTailAtom, headAtom);
+    }
+    prevTailAtom = tailAtom;
 
     // All units after the first need building
     if (atomPosKnown)

From 8a6333feb863c5e0056fd24505e8eb96026b2f2b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 8 Feb 2024 13:41:38 -0500
Subject: [PATCH 0480/1492] Start using new build routines in sequence

---
 src/Exec_Sequence.cpp | 67 +++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 64 insertions(+), 3 deletions(-)

diff --git a/src/Exec_Sequence.cpp b/src/Exec_Sequence.cpp
index 10774e9aa9..9c63ebfbc5 100644
--- a/src/Exec_Sequence.cpp
+++ b/src/Exec_Sequence.cpp
@@ -107,6 +107,7 @@ const
   typedef std::vector<Ipair> IParray;
 
   // Loop for setting up atoms in the topology from units
+  IParray interResBonds;
   int prevTailAtom = -1;
   for (unsigned int idx = 0; idx < Units.size(); idx++)
   {
@@ -130,7 +131,7 @@ const
     mprintf("DEBUG: atom offset is %i\n", atomOffset);
     // Add the unit atoms. Only the first unit has known position.
     bool atomPosKnown = (idx == 0);
-    Frame unitFrm = unit->AllocateFrame();
+    Frame unitFrm = unit->AllocateFrame(); // FIXME only first res
     unit->GetFrame(0, unitFrm);
     IParray intraResBonds;
     for (int itgt = 0; itgt < unit->Top().Natom(); itgt++)
@@ -166,8 +167,10 @@ const
         return 1;
       }
       mprintf("Will add bond between %i and %i\n", prevTailAtom+1, headAtom+1);
-      topOut.AddBond(prevTailAtom, headAtom);
-    }
+      interResBonds.push_back( Ipair(prevTailAtom, headAtom) );
+    } else
+      // Placeholder
+      interResBonds.push_back( Ipair(-1, -1) );
     prevTailAtom = tailAtom;
 
     // All units after the first need building
@@ -177,6 +180,64 @@ const
       AtomOffsets.push_back( atomOffset );
   } // END loop over units
 
+  // Build
+  bool buildFailed = false;
+  for (Iarray::const_iterator it = AtomOffsets.begin(); it != AtomOffsets.end(); ++it)
+  {
+    long int ires = it-AtomOffsets.begin();
+    if (*it > -1) {
+      // Residue has atom offset which indicates it needs something built.
+      Cpptraj::Structure::Builder* structureBuilder = new Cpptraj::Structure::Builder();
+      structureBuilder->SetDebug( 1 ); // DEBUG FIXME
+      //structureBuilder->SetParameters( &mainParmSet ); TODO import parameters?
+      // Generate internals from the template, update indices to this topology.
+      DataSet_Coords* unit = Units[ires];
+      Frame unitFrm = unit->AllocateFrame();
+      unit->GetFrame(0, unitFrm);
+      if (structureBuilder->GenerateInternals(unitFrm, unit->Top(),
+                                              std::vector<bool>(unit->Top().Natom(), true)))
+      {
+        mprinterr("Error: Generate internals for unit failed.\n");
+        return 1;
+      }
+      structureBuilder->UpdateIndicesWithOffset( *it );
+
+      mprintf("DEBUG: ***** BUILD unit %li %s *****\n", ires + 1,
+              topOut.TruncResNameOnumId(ires).c_str());
+
+      // Connect unit
+      topOut.AddBond( interResBonds[ires].first, interResBonds[ires].second );
+      // Generate internals around the link
+      if (structureBuilder->GenerateInternalsAroundLink(interResBonds[ires].first, interResBonds[ires].second,
+                                                        frameOut, topOut, hasPosition))
+      {
+        mprinterr("Error: Assign torsions around inter-unit link %s - %s failed.\n",
+                  topOut.AtomMaskName(interResBonds[ires].first).c_str(),
+                  topOut.AtomMaskName(interResBonds[ires].second).c_str());
+        return 1;
+      }
+      // Update internal coords from known positions
+      if (structureBuilder->UpdateICsFromFrame( frameOut, ires, topOut, hasPosition )) {
+        mprinterr("Error: Failed to update Zmatrix with values from existing positions.\n");
+        return 1;
+      }
+      // Convert to Zmatrix and assign missing atom positions
+      Cpptraj::Structure::Zmatrix tmpz;
+      tmpz.SetDebug( 1 ); // DEBUG
+      if (structureBuilder->GetZmatrixFromInternals(tmpz, topOut)) {
+        mprinterr("Error: Could not get Zmatrix from internals.\n");
+        return 1;
+      }
+      if (tmpz.SetToFrame( frameOut, hasPosition )) {
+        mprinterr("Error: Building residue %s failed.\n",
+                  topOut.TruncResNameOnumId(ires).c_str());
+        buildFailed = true;
+      }
+      delete structureBuilder;
+    }
+  }
+
+
 
   Topology combinedTop;
   combinedTop.SetDebug( debug_ );

From b714d0b97ac23ee66c9d3cf4e35597f2899e774c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 8 Feb 2024 15:10:38 -0500
Subject: [PATCH 0481/1492] Add some debug info

---
 src/Exec_Sequence.cpp | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/Exec_Sequence.cpp b/src/Exec_Sequence.cpp
index 9c63ebfbc5..ea2fc78c3f 100644
--- a/src/Exec_Sequence.cpp
+++ b/src/Exec_Sequence.cpp
@@ -206,6 +206,9 @@ const
               topOut.TruncResNameOnumId(ires).c_str());
 
       // Connect unit
+      mprintf("DEBUG: Linking atoms %s and %s\n",
+              topOut.AtomMaskName(interResBonds[ires].first).c_str(),
+              topOut.AtomMaskName(interResBonds[ires].second).c_str());
       topOut.AddBond( interResBonds[ires].first, interResBonds[ires].second );
       // Generate internals around the link
       if (structureBuilder->GenerateInternalsAroundLink(interResBonds[ires].first, interResBonds[ires].second,

From 60cef5da2b8fde8e7a71b9e53f484709ca169b6d Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 8 Feb 2024 15:37:14 -0500
Subject: [PATCH 0482/1492] Determine chirality around atom

---
 src/Structure/Builder.cpp | 35 ++++++++++++++++++++++++++++++++++-
 src/Structure/Builder.h   |  2 ++
 2 files changed, 36 insertions(+), 1 deletion(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 5b578f0af7..1267cc1750 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -2137,6 +2137,35 @@ void Builder::buildBondInternal(int a1, int a2, Frame const& frameIn, Topology c
             topIn.LeapName(a2).c_str());
 }
 
+/** Determine chirality around a single atom. */
+int Builder::determineChirality(int at, Frame const& frameIn, Topology const& topIn, Barray const& hasPosition)
+{
+  BuildAtom bldAt;
+  if (topIn[at].Nbonds() > 2 && hasPosition[at]) {
+    // All bonded atoms must have position
+    bool bonded_atoms_have_position = true;
+    for (Atom::bond_iterator bat = topIn[at].bondbegin(); bat != topIn[at].bondend(); ++bat)
+    {
+      if (!hasPosition[*bat]) {
+        bonded_atoms_have_position = false;
+        break;
+      }
+    }
+    if (bonded_atoms_have_position) {
+      if (bldAt.DetermineChirality(at, topIn, frameIn, 0)) {// FIXME debug level
+        mprinterr("Error: Problem determining chirality of atom %s\n",
+                  topIn.AtomMaskName(at).c_str());
+        return 1;
+      }
+    }
+    mprintf("Got chirality from external coordinates\n" );
+    mprintf("++++Chirality INTERNAL: %f  for %s\n", bldAt.TorsionVal()*Constants::RADDEG,
+            topIn.LeapName(at).c_str());
+  } else {
+    mprintf("Left chirality undefined for %s\n",topIn.LeapName(at).c_str() );
+  }
+  return 0;
+}
 
 /** Generate internal coordinates in the same manner as LEaP's
   * BuildInternalsForContainer.
@@ -2194,7 +2223,11 @@ int Builder::GenerateInternals(Frame const& frameIn, Topology const& topIn, Barr
             topIn.LeapName(bnd->A1()).c_str(),
             topIn.LeapName(bnd->A2()).c_str());*/
   }
-  // FIXME do chirality
+  // Chirality
+  for (int at = 0; at != topIn.Natom(); ++at) {
+    if (determineChirality(at, frameIn, topIn, hasPosition))
+      return 1;
+  }
   //zmatrix.print( &topIn );
   mprintf("DEBUG: ----- Leaving Builder::GenerateInternals. ------\n");
   return 0;
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index 2ad3005720..80b0ef850e 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -105,6 +105,8 @@ class Builder {
     void buildAngleInternal(int, int, int, Frame const&, Topology const&, Barray const&);
     /// Build bond internal
     void buildBondInternal(int, int, Frame const&, Topology const&, Barray const&);
+    /// Determine chirality around an atom
+    int determineChirality(int, Frame const&, Topology const&, Barray const&);
     /// Generate internal coords for a given atom
     int generateAtomInternals(int, Frame const&, Topology const&, Barray const&);
 

From 63c7a262061e70f50f41675bac1045db112c2a0f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 9 Feb 2024 09:27:08 -0500
Subject: [PATCH 0483/1492] Add leap chirality calc

---
 src/Structure/Builder.cpp | 153 ++++++++++++++++++++++++++++++++++++--
 src/Structure/Builder.h   |   9 ++-
 2 files changed, 155 insertions(+), 7 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 1267cc1750..396d822dc8 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1311,7 +1311,7 @@ std::vector<MockAtom>
 
 /** LEaP routine for determining atom chirality.
   * This is done by crossing A to B and then dotting the
-  * result with C. TODO use Chirality in BuildAtom?
+  * result with C. TODO use Chirality in BuildAtom? Use an Enum?
   * The chirality of the vectors is determined by the sign of
   * the result, which is determined by whether or not C has
   * a component in the direction AxB or in the opposite direction.
@@ -1330,6 +1330,56 @@ static inline double VectorAtomChirality(Vec3 const& Center, Vec3 const& A, Vec3
   return 0.0;
 }
 
+/** LEaP routine for determining atom chirality when positions may or
+  * may not be defined. Currently the criteria for chirality is 
+  * absolute orientation of the vectors joining this atom to its neighbors.
+  * The neighbors are passed as vPA, vPB, vPC, vPD and bA, bB, bC, bD
+  * define whether or not the position is defined.
+  *
+  * This routine calculates the chirality using the defined vectors and
+  * then flips the sign depending on which vectors were used to calculate
+  * the chirality. If the ATOMs have (fKnown) set then their coordinate
+  * is considered to be known.
+  */
+static inline double VectorAtomNormalizedChirality(Vec3 const& Center,
+                                                   Vec3 const& vPA, bool bA,
+                                                   Vec3 const& vPB, bool bB,
+                                                   Vec3 const& vPC, bool bC,
+                                                   Vec3 const& vPD, bool bD)
+{
+  double dChi = 0;
+  
+  if (!bA) {
+    // If A is not known then use B,C,D to calc chirality.
+    // The chirality calculated will be negative w.r.t. the
+    // correct chirality.
+    if (!bB || !bC || !bD) return dChi;
+    dChi = -VectorAtomChirality( Center, vPB, vPC, vPD );
+    return dChi;
+  }
+
+  if (!bB) {
+    // If B is not known then use A,C,D to calc chirality.
+    // The chirality calculated will be correct.
+    if (!bB || !bD) return dChi;
+    dChi = VectorAtomChirality( Center, vPA, vPC, vPD );
+    return dChi;
+  }
+
+  if (!bC) {
+    // If C is not known then use A,B,D to calc chirality.
+    // The chirality calculated will be negative w.r.t. the
+    // correct chirality.
+    if (!bD) return dChi;
+    dChi = -VectorAtomChirality( Center, vPA, vPB, vPD );
+    return dChi;
+  }
+
+  dChi = VectorAtomChirality( Center, vPA, vPB, vPC );
+
+  return dChi;
+}
+
 /** Assuming atoms have been ordered with SortBondedAtomsLikeLeap,
   * calculate the orientation of the iB atom with respect to the
   * triangle (iA, iX, iY). This orientation will be used by the
@@ -2137,9 +2187,94 @@ void Builder::buildBondInternal(int a1, int a2, Frame const& frameIn, Topology c
             topIn.LeapName(a2).c_str());
 }
 
-/** Determine chirality around a single atom. */
-int Builder::determineChirality(int at, Frame const& frameIn, Topology const& topIn, Barray const& hasPosition)
+/** \return index of atom less than all others but larger than aLast */
+int Builder::findLeastLargerThan(Atom const& aAtom, int aLast)
+{
+  int aSmall = -1;
+  for (Atom::bond_iterator aCur = aAtom.bondbegin(); aCur != aAtom.bondend(); ++aCur)
+  {
+    if (aLast != -1) {
+      if (aLast >= *aCur) continue;
+    }
+    if (aSmall == -1)
+      aSmall = *aCur;
+    else if ( *aCur < aSmall )
+      aSmall = *aCur;
+  }
+  return aSmall;
+}
+
+/** Sort neighbors of given atom in the same manner as LEaP. */
+void Builder::chiralityOrderNeighbors(Atom const& aAtom,
+                                      int& aPAtomA, int& aPAtomB,
+                                      int& aPAtomC, int& aPAtomD)
 {
+  aPAtomA = -1;
+  aPAtomB = -1;
+  aPAtomC = -1;
+  aPAtomD = -1;
+
+  if (aAtom.Nbonds() < 1) return;
+
+  aPAtomA = findLeastLargerThan(aAtom, -1);
+  if (aAtom.Nbonds() < 2) return;
+
+  aPAtomB = findLeastLargerThan(aAtom, aPAtomA);
+  if (aAtom.Nbonds() < 3) return;
+
+  aPAtomC = findLeastLargerThan(aAtom, aPAtomB);
+  if (aAtom.Nbonds() < 4) return;
+
+  aPAtomD = findLeastLargerThan(aAtom, aPAtomC);
+}
+
+/** Determine chirality around a single atom.
+  * \return 1 if chirality was determined, 0 if left undefined.
+  */
+int Builder::determineChirality(double& dChi, int at, Frame const& frameIn, Topology const& topIn, Barray const& hasPosition)
+{
+  dChi = 0.0;
+  if (!hasPosition[at]) {
+    return 0;
+  }
+  // Only check atoms with 3 or 4 bonds
+  Atom const& A0 = topIn[at];
+  mprintf("CHIRALITY CALCULATION FOR %s (nbonds= %i)\n", *(A0.Name()), A0.Nbonds());
+  for (Atom::bond_iterator bat = A0.bondbegin(); bat != A0.bondend(); ++bat)
+    mprintf("\tneighbor %s (id= %i) [%i]\n", *(topIn[*bat].Name()), *bat, (int)hasPosition[*bat]);
+  if ( A0.Nbonds() == 3 ||
+       A0.Nbonds() == 4 )
+  {
+    int aAtomA = -1;
+    int aAtomB = -1;
+    int aAtomC = -1;
+    int aAtomD = -1;
+    chiralityOrderNeighbors(A0, aAtomA, aAtomB, aAtomC, aAtomD);
+
+    bool knowA = (aAtomA != -1 && hasPosition[aAtomA]);
+    bool knowB = (aAtomB != -1 && hasPosition[aAtomB]);
+    bool knowC = (aAtomC != -1 && hasPosition[aAtomC]);
+    bool knowD = (aAtomD != -1 && hasPosition[aAtomD]);
+
+    if (knowA) mprintf("Chirality order A %s %i\n", *(topIn[aAtomA].Name()), aAtomA);
+    if (knowB) mprintf("Chirality order B %s %i\n", *(topIn[aAtomB].Name()), aAtomB);
+    if (knowC) mprintf("Chirality order C %s %i\n", *(topIn[aAtomC].Name()), aAtomC);
+    if (knowD) mprintf("Chirality order D %s %i\n", *(topIn[aAtomD].Name()), aAtomD);
+
+    Vec3 vPA, vPB, vPC, vPD;
+    if (knowA) vPA = Vec3(frameIn.XYZ(aAtomA));
+    if (knowB) vPB = Vec3(frameIn.XYZ(aAtomB));
+    if (knowC) vPC = Vec3(frameIn.XYZ(aAtomC));
+    if (knowD) vPD = Vec3(frameIn.XYZ(aAtomD));
+
+    dChi = VectorAtomNormalizedChirality( Vec3(frameIn.XYZ(at)),
+                                          vPA, knowA,
+                                          vPB, knowB,
+                                          vPC, knowC,
+                                          vPD, knowD );
+    return 1;
+  }
+/*
   BuildAtom bldAt;
   if (topIn[at].Nbonds() > 2 && hasPosition[at]) {
     // All bonded atoms must have position
@@ -2163,7 +2298,7 @@ int Builder::determineChirality(int at, Frame const& frameIn, Topology const& to
             topIn.LeapName(at).c_str());
   } else {
     mprintf("Left chirality undefined for %s\n",topIn.LeapName(at).c_str() );
-  }
+  }*/
   return 0;
 }
 
@@ -2225,8 +2360,14 @@ int Builder::GenerateInternals(Frame const& frameIn, Topology const& topIn, Barr
   }
   // Chirality
   for (int at = 0; at != topIn.Natom(); ++at) {
-    if (determineChirality(at, frameIn, topIn, hasPosition))
-      return 1;
+    double dValue = 0;
+    if (determineChirality(dValue, at, frameIn, topIn, hasPosition)) {
+      mprintf("Got chirality from external coordinates\n" );
+      mprintf("++++Chirality INTERNAL: %f  for %s\n", dValue,
+              topIn.LeapName(at).c_str());
+    } else {
+      mprintf("Left chirality undefined for %s\n",topIn.LeapName(at).c_str() );
+    }
   }
   //zmatrix.print( &topIn );
   mprintf("DEBUG: ----- Leaving Builder::GenerateInternals. ------\n");
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index 80b0ef850e..b0503d37ca 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -1,6 +1,7 @@
 #ifndef INC_STRUCTURE_BUILDER_H
 #define INC_STRUCTURE_BUILDER_H
 #include <vector>
+class Atom;
 class Topology;
 class Frame;
 class ParameterSet;
@@ -105,8 +106,14 @@ class Builder {
     void buildAngleInternal(int, int, int, Frame const&, Topology const&, Barray const&);
     /// Build bond internal
     void buildBondInternal(int, int, Frame const&, Topology const&, Barray const&);
+
+    /// Find index of bonded atom less than all others but larger than last
+    static inline int findLeastLargerThan(Atom const&, int);
+    /// Sort neighbors of atom. Used in determineChirality
+    static void chiralityOrderNeighbors(Atom const&, int&, int&, int&, int&);
     /// Determine chirality around an atom
-    int determineChirality(int, Frame const&, Topology const&, Barray const&);
+    int determineChirality(double&, int, Frame const&, Topology const&, Barray const&);
+
     /// Generate internal coords for a given atom
     int generateAtomInternals(int, Frame const&, Topology const&, Barray const&);
 

From 6291a8d13b7323a85a91162a766764c12d65baf0 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 9 Feb 2024 10:10:24 -0500
Subject: [PATCH 0484/1492] Store chiralities from template. Check against
 calculated values

---
 src/Structure/Builder.cpp | 72 ++++++++++++++++++++++-----------------
 src/Structure/Builder.h   | 38 +++++++++++++++++++++
 2 files changed, 78 insertions(+), 32 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 396d822dc8..b0416cd132 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1667,6 +1667,8 @@ void Builder::UpdateIndicesWithOffset(int atomOffset) {
     it->OffsetIndices( atomOffset );
   for (Larray::iterator it = internalBonds_.begin(); it != internalBonds_.end(); ++it)
     it->OffsetIndices( atomOffset );
+  for (Carray::iterator it = internalChirality_.begin(); it != internalChirality_.end(); ++it)
+    it->OffsetIndices( atomOffset );
 }
 
 /** Find any existing torsions around ax-ay. */
@@ -1731,6 +1733,19 @@ int Builder::getExistingBondIdx(int ai, int aj) const {
   return idx;
 }
 
+/** \return Index of existing chirality value matching given atom, 1 for no match. */
+int Builder::getExistingChiralityIdx(int ai) const {
+  int idx = -1;
+  for (Carray::const_iterator it = internalChirality_.begin(); it != internalChirality_.end(); ++it)
+  {
+    if (it->AtI() == ai) {
+      idx = (int)(it - internalChirality_.begin());
+      break;
+    }
+  }
+  return idx;
+}
+
 /** Model bond */
 double Builder::ModelBondLength(int ai, int aj, Topology const& topIn) const {
   // First look up parameter
@@ -2308,10 +2323,9 @@ int Builder::determineChirality(double& dChi, int at, Frame const& frameIn, Topo
 int Builder::GenerateInternals(Frame const& frameIn, Topology const& topIn, Barray const& hasPosition)
 {
   mprintf("DEBUG: ----- Entering Builder::GenerateInternals. -----\n");
-//  zmatrix.clear();
-  // First generate the bond array
+  // First generate the bond array for use in determining torsions.
   BondArray bonds = GenerateBondArray( topIn.Residues(), topIn.Atoms() );
-  // Loop over bonds
+  // Loop over bonds to determine torsions.
   for (BondArray::const_iterator bnd = bonds.begin(); bnd != bonds.end(); ++bnd)
   {
     if (assignTorsionsAroundBond( bnd->A1(), bnd->A2(), frameIn, topIn, hasPosition, -1 )) {
@@ -2321,42 +2335,16 @@ int Builder::GenerateInternals(Frame const& frameIn, Topology const& topIn, Barr
       return 1;
     }
   }
-  // Loop over angles
+  // Loop over angles.
   AngleArray angles = GenerateAngleArray( topIn.Residues(), topIn.Atoms() );
   for (AngleArray::const_iterator ang = angles.begin(); ang != angles.end(); ++ang)
   {
     buildAngleInternal(ang->A1(), ang->A2(), ang->A3(), frameIn, topIn, hasPosition);
-/*    double dValue = 0;
-    if (hasPosition[ang->A1()] &&
-        hasPosition[ang->A2()] &&
-        hasPosition[ang->A3()])
-    {
-      dValue = CalcAngle( frameIn.XYZ(ang->A1()), frameIn.XYZ(ang->A2()), frameIn.XYZ(ang->A3()) );
-    } else {
-      dValue = ModelBondAngle( ang->A1(), ang->A2(), ang->A3(), topIn );
-    }
-    internalAngles_.push_back( InternalAngle(ang->A1(), ang->A2(), ang->A3(), dValue) );
-    mprintf("++++Angle INTERNAL: %f  for %s - %s - %s\n", dValue*Constants::RADDEG,
-            topIn.LeapName(ang->A1()).c_str(),
-            topIn.LeapName(ang->A2()).c_str(),
-            topIn.LeapName(ang->A3()).c_str());*/
   }
   // Loop over bonds
   for (BondArray::const_iterator bnd = bonds.begin(); bnd != bonds.end(); ++bnd)
   {
     buildBondInternal(bnd->A1(), bnd->A2(), frameIn, topIn, hasPosition);
-/*    double dValue = 0;
-    if (hasPosition[bnd->A1()] &&
-        hasPosition[bnd->A2()])
-    {
-      dValue = sqrt(DIST2_NoImage( frameIn.XYZ(bnd->A1()), frameIn.XYZ(bnd->A2()) ) );
-    } else {
-      dValue = ModelBondLength( bnd->A1(), bnd->A2(), topIn );
-    }
-    internalBonds_.push_back( InternalBond(bnd->A1(), bnd->A2(), dValue) );
-    mprintf("++++Bond INTERNAL: %f  for %s - %s\n", dValue,
-            topIn.LeapName(bnd->A1()).c_str(),
-            topIn.LeapName(bnd->A2()).c_str());*/
   }
   // Chirality
   for (int at = 0; at != topIn.Natom(); ++at) {
@@ -2368,8 +2356,8 @@ int Builder::GenerateInternals(Frame const& frameIn, Topology const& topIn, Barr
     } else {
       mprintf("Left chirality undefined for %s\n",topIn.LeapName(at).c_str() );
     }
+    internalChirality_.push_back( InternalChirality(at, dValue) );
   }
-  //zmatrix.print( &topIn );
   mprintf("DEBUG: ----- Leaving Builder::GenerateInternals. ------\n");
   return 0;
 }
@@ -2456,7 +2444,27 @@ int Builder::generateAtomInternals(int at, Frame const& frameIn, Topology const&
       mprintf( "Bond length INTERNAL already defined\n" );
     }
   } // END loop over atoms bonded to A
-  // FIXME do chirality
+  // Chirality
+  double dChi = 0;
+  int cidx = getExistingChiralityIdx(at);
+  if (determineChirality(dChi, at, frameIn, topIn, hasPosition)) {
+    mprintf("Got chirality from external coordinates\n" );
+    mprintf("++++Chirality INTERNAL: %f  for %s\n", dChi,
+              topIn.LeapName(at).c_str());
+    if (cidx == -1)
+      internalChirality_.push_back( InternalChirality(at, dChi) );
+    else {
+      // Check that this chirality matches previously determine chirality
+      if (!internalChirality_[cidx].ChiralityMatches(dChi))
+        mprintf("Warning: Atom %s chirality (%f) does not match previous chirality (%f)\n",
+                topIn.AtomMaskName(at).c_str(), dChi, internalChirality_[cidx].ChiralVal());
+    }
+  } else {
+    if (cidx == -1)
+      mprintf("Left chirality undefined for %s\n",topIn.LeapName(at).c_str() );
+    else
+      mprintf("Using already-defined chirality (%f).\n", internalChirality_[cidx].ChiralVal());
+  }
 
   return 0;
 }
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index b0503d37ca..18ab848aaf 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -48,10 +48,13 @@ class Builder {
     class InternalAngle;
     /// Hold bond
     class InternalBond;
+    /// Hold chirality
+    class InternalChirality;
 
     typedef std::vector<InternalTorsion> Tarray;
     typedef std::vector<InternalAngle> Aarray;
     typedef std::vector<InternalBond> Larray;
+    typedef std::vector<InternalChirality> Carray;
 
     /// Get length parameter for atoms
     int getLengthParam(double&, int, int, Topology const&) const;
@@ -100,6 +103,8 @@ class Builder {
     int getExistingAngleIdx(int, int, int) const;
     /// Get specific internal bond
     int getExistingBondIdx(int, int) const;
+    /// Get specific chirality
+    int getExistingChiralityIdx(int) const;
     /// Build mock coordinates around given torsion
     int buildMockExternals(TorsionModel& MT, std::vector<InternalCoords> const& iaTorsions) const;
     /// Build angle internal
@@ -126,6 +131,7 @@ class Builder {
     Tarray internalTorsions_;
     Aarray internalAngles_;
     Larray internalBonds_;
+    Carray internalChirality_;
 };
 /// ----- Hold torsion internal ------------------
 class Cpptraj::Structure::Builder::InternalTorsion {
@@ -208,7 +214,39 @@ class Cpptraj::Structure::Builder::InternalBond {
     int aj_;
     double dist_;
 };
+// ----- Hold chirality value --------------------
+class Cpptraj::Structure::Builder::InternalChirality {
+  public:
+    /// CONSTRUCTOR
+    InternalChirality() : ai_(-1), dChi_(0) {}
+    /// CONSTRUCTOR
+    InternalChirality(int i, double d) : ai_(i), dChi_(d) {}
+    /// Set the chirality value TODO use enum?
+    void SetChiralVal(double d) { dChi_ = d; }
+    /// Offset indices by given value
+    void OffsetIndices(int o) { ai_ += o; }
+
+    /// \return true if given chirality matches this one
+    bool ChiralityMatches(double d) const {
+      int thisC = 0;
+      if (dChi_ > 0)
+        thisC = 1;
+      else if (dChi_ < 0)
+        thisC = -1;
+      int otherC = 0;
+      if (d > 0)
+        otherC = 1;
+      else if (d < 0)
+        otherC = -1;
+      return (thisC == otherC);
+    }
 
+    int AtI() const { return ai_; }
+    double ChiralVal() const { return dChi_; }
+  private:
+    int ai_;
+    double dChi_;
+};
 }
 }
 #endif

From 47c9896678939a9c10718c4f6f1a41b0c940bd0f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 9 Feb 2024 10:50:24 -0500
Subject: [PATCH 0485/1492] Pass in chi values if they exist

---
 src/Structure/Builder.cpp | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index b0416cd132..f33998f407 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1178,7 +1178,7 @@ class Cpptraj::Structure::Builder::TorsionModel {
     /// Initialize torsions around bonded atoms
     int InitTorsion(int, int, Frame const&, Topology const&, std::vector<bool> const&, int);
     /// Set up torsions around bonded atoms
-    int SetupTorsion(AtomType::HybridizationType, AtomType::HybridizationType, Topology const& topIn);
+    int SetupTorsion(AtomType::HybridizationType, AtomType::HybridizationType, Topology const& topIn, double, double);
     /// Build mock externals from given internals
     int BuildMockExternals(Iarray const&, Tarray const&, Topology const&);
 
@@ -1451,7 +1451,8 @@ int Cpptraj::Structure::Builder::TorsionModel::InitTorsion(int ax, int ay,
 /** Set up model torsion for bonded atoms. */
 int Cpptraj::Structure::Builder::TorsionModel::SetupTorsion(AtomType::HybridizationType Hx,
                                                             AtomType::HybridizationType Hy,
-                                                            Topology const& topIn)
+                                                            Topology const& topIn,
+                                                            double chiX, double chiY)
 {
   if (Hx != AtomType::UNKNOWN_HYBRIDIZATION && Hy != AtomType::UNKNOWN_HYBRIDIZATION) {
     if (Hy > Hx) {
@@ -2132,8 +2133,15 @@ int Builder::assignTorsionsAroundBond(int a1, int a2, Frame const& frameIn, Topo
             topIn.LeapName(ax).c_str(),
             topIn.LeapName(ay).c_str());
   }
-
-  if (mT.SetupTorsion(Hx, Hy, topIn)) {
+  // Get chiralities around X and Y if they exist
+  double chiX = 0;
+  int Xcidx = getExistingChiralityIdx( ax );
+  if (Xcidx != -1) chiX = internalChirality_[Xcidx].ChiralVal();
+  double chiY = 0;
+  int Ycidx = getExistingChiralityIdx( ay );
+  if (Ycidx != -1) chiY = internalChirality_[Ycidx].ChiralVal();
+  // Set up the torsion model
+  if (mT.SetupTorsion(Hx, Hy, topIn, chiX, chiY)) {
     mprinterr("Error: Could not set up torsions around %s - %s\n",
               topIn.LeapName(ax).c_str(),
               topIn.LeapName(ay).c_str());

From a78388f77b9020b43ecaf38124d29b9f186945af Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 9 Feb 2024 10:51:57 -0500
Subject: [PATCH 0486/1492] Pass in chi values to calculateOrientation

---
 src/Structure/Builder.cpp | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index f33998f407..9551d11443 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1385,7 +1385,7 @@ static inline double VectorAtomNormalizedChirality(Vec3 const& Center,
   * triangle (iA, iX, iY). This orientation will be used by the
   * CreateSpXSpX routines to determine which torsion values to use.
   */
-static inline double calculateOrientation(MockAtom const& iX, MockAtom const& iA, MockAtom const& iY, MockAtom const& iB)
+static inline double calculateOrientation(MockAtom const& iX, double chiX, MockAtom const& iA, MockAtom const& iY, MockAtom const& iB)
 {
   double dOrientation = 1.0;
   if (iX.Known() &&
@@ -1469,12 +1469,12 @@ int Cpptraj::Structure::Builder::TorsionModel::SetupTorsion(AtomType::Hybridizat
   // Calculate the chirality around atom X
   Xorientation_ = 0;
   if (Hx == AtomType::SP3) {
-    Xorientation_ = calculateOrientation( atX_, sorted_ax_[0], atY_, sorted_ax_[1] );
+    Xorientation_ = calculateOrientation( atX_, chiX, sorted_ax_[0], atY_, sorted_ax_[1] );
   }
   // Calculate the chirality around atom Y
   Yorientation_ = 0;
   if (Hy == AtomType::SP3) {
-    Yorientation_ = calculateOrientation( atY_, sorted_ay_[0], atX_, sorted_ay_[1] );
+    Yorientation_ = calculateOrientation( atY_, chiY, sorted_ay_[0], atX_, sorted_ay_[1] );
   }
   // DEBUG
   Atom const& AX = topIn[atX_.Idx()];

From 2775ba9a2bb0768239c513d5e3f6f79c84117649 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 9 Feb 2024 10:54:37 -0500
Subject: [PATCH 0487/1492] Report chi values

---
 src/Structure/Builder.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 9551d11443..d878c9ceae 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1479,12 +1479,12 @@ int Cpptraj::Structure::Builder::TorsionModel::SetupTorsion(AtomType::Hybridizat
   // DEBUG
   Atom const& AX = topIn[atX_.Idx()];
   Atom const& AY = topIn[atY_.Idx()];
-  mprintf("Orientation around: %s = %f\n", *(AX.Name()), Xorientation_);
+  mprintf("Orientation around: %s = %f (chiX= %f)\n", *(AX.Name()), Xorientation_, chiX);
   //for (Atom::bond_iterator bat = AX.bondbegin(); bat != AX.bondend(); ++bat) mprintf(" %s", *(topIn[*bat].Name()));
   //mprintf("}\n");
   for (Marray::const_iterator it = sorted_ax_.begin(); it != sorted_ax_.end(); ++it)
       mprintf("Atom %li: %s (%i) (build=%i)\n", it - sorted_ax_.begin(), *(topIn[it->Idx()].Name()), (int)it->Known(), (int)it->BuildInternals());
-  mprintf("Orientation around: %s = %f\n", *(AY.Name()), Yorientation_);
+  mprintf("Orientation around: %s = %f (chiY= %f)\n", *(AY.Name()), Yorientation_, chiY);
   //for (Atom::bond_iterator bat = AY.bondbegin(); bat != AY.bondend(); ++bat) mprintf(" %s", *(topIn[*bat].Name()));
   //mprintf("}\n");
   for (Marray::const_iterator it = sorted_ay_.begin(); it != sorted_ay_.end(); ++it)

From c75b6bbb795706e44124aeb0b669704c68769124 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 9 Feb 2024 10:57:44 -0500
Subject: [PATCH 0488/1492] Make static

---
 src/Structure/Builder.cpp | 81 ++++++++++++++++++++-------------------
 src/Structure/Builder.h   |  4 +-
 2 files changed, 43 insertions(+), 42 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index d878c9ceae..c96319f68f 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1380,6 +1380,47 @@ static inline double VectorAtomNormalizedChirality(Vec3 const& Center,
   return dChi;
 }
 
+/** \return index of atom less than all others but larger than aLast */
+static inline int findLeastLargerThan(Atom const& aAtom, int aLast)
+{
+  int aSmall = -1;
+  for (Atom::bond_iterator aCur = aAtom.bondbegin(); aCur != aAtom.bondend(); ++aCur)
+  {
+    if (aLast != -1) {
+      if (aLast >= *aCur) continue;
+    }
+    if (aSmall == -1)
+      aSmall = *aCur;
+    else if ( *aCur < aSmall )
+      aSmall = *aCur;
+  }
+  return aSmall;
+}
+
+/** Sort neighbors of given atom in the same manner as LEaP. */
+static inline void chiralityOrderNeighbors(Atom const& aAtom,
+                                      int& aPAtomA, int& aPAtomB,
+                                      int& aPAtomC, int& aPAtomD)
+{
+  aPAtomA = -1;
+  aPAtomB = -1;
+  aPAtomC = -1;
+  aPAtomD = -1;
+
+  if (aAtom.Nbonds() < 1) return;
+
+  aPAtomA = findLeastLargerThan(aAtom, -1);
+  if (aAtom.Nbonds() < 2) return;
+
+  aPAtomB = findLeastLargerThan(aAtom, aPAtomA);
+  if (aAtom.Nbonds() < 3) return;
+
+  aPAtomC = findLeastLargerThan(aAtom, aPAtomB);
+  if (aAtom.Nbonds() < 4) return;
+
+  aPAtomD = findLeastLargerThan(aAtom, aPAtomC);
+}
+
 /** Assuming atoms have been ordered with SortBondedAtomsLikeLeap,
   * calculate the orientation of the iB atom with respect to the
   * triangle (iA, iX, iY). This orientation will be used by the
@@ -2210,46 +2251,6 @@ void Builder::buildBondInternal(int a1, int a2, Frame const& frameIn, Topology c
             topIn.LeapName(a2).c_str());
 }
 
-/** \return index of atom less than all others but larger than aLast */
-int Builder::findLeastLargerThan(Atom const& aAtom, int aLast)
-{
-  int aSmall = -1;
-  for (Atom::bond_iterator aCur = aAtom.bondbegin(); aCur != aAtom.bondend(); ++aCur)
-  {
-    if (aLast != -1) {
-      if (aLast >= *aCur) continue;
-    }
-    if (aSmall == -1)
-      aSmall = *aCur;
-    else if ( *aCur < aSmall )
-      aSmall = *aCur;
-  }
-  return aSmall;
-}
-
-/** Sort neighbors of given atom in the same manner as LEaP. */
-void Builder::chiralityOrderNeighbors(Atom const& aAtom,
-                                      int& aPAtomA, int& aPAtomB,
-                                      int& aPAtomC, int& aPAtomD)
-{
-  aPAtomA = -1;
-  aPAtomB = -1;
-  aPAtomC = -1;
-  aPAtomD = -1;
-
-  if (aAtom.Nbonds() < 1) return;
-
-  aPAtomA = findLeastLargerThan(aAtom, -1);
-  if (aAtom.Nbonds() < 2) return;
-
-  aPAtomB = findLeastLargerThan(aAtom, aPAtomA);
-  if (aAtom.Nbonds() < 3) return;
-
-  aPAtomC = findLeastLargerThan(aAtom, aPAtomB);
-  if (aAtom.Nbonds() < 4) return;
-
-  aPAtomD = findLeastLargerThan(aAtom, aPAtomC);
-}
 
 /** Determine chirality around a single atom.
   * \return 1 if chirality was determined, 0 if left undefined.
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index 18ab848aaf..282df5c974 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -113,9 +113,9 @@ class Builder {
     void buildBondInternal(int, int, Frame const&, Topology const&, Barray const&);
 
     /// Find index of bonded atom less than all others but larger than last
-    static inline int findLeastLargerThan(Atom const&, int);
+    //static inline int findLeastLargerThan(Atom const&, int);
     /// Sort neighbors of atom. Used in determineChirality
-    static void chiralityOrderNeighbors(Atom const&, int&, int&, int&, int&);
+    //static void chiralityOrderNeighbors(Atom const&, int&, int&, int&, int&);
     /// Determine chirality around an atom
     int determineChirality(double&, int, Frame const&, Topology const&, Barray const&);
 

From 641b1eb0a3da05061a22ae3a0cc8f73090debe84 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 9 Feb 2024 11:15:12 -0500
Subject: [PATCH 0489/1492] Add 2 new chirality routines.

---
 src/Structure/Builder.cpp | 73 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 73 insertions(+)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index c96319f68f..c27ad6a0bd 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -10,6 +10,7 @@
 #include "../Topology.h"
 #include "../TorsionRoutines.h"
 #include <algorithm> // std::copy
+#include <cmath> // fabs
 
 using namespace Cpptraj::Structure;
 
@@ -1421,6 +1422,78 @@ static inline void chiralityOrderNeighbors(Atom const& aAtom,
   aPAtomD = findLeastLargerThan(aAtom, aPAtomC);
 }
 
+/** Transform the orientation that has been measured with 
+ *      respect to the ordering in aaOrig[4] to the ordering
+ *      in aaNew[4].  Return the result.
+ *
+ *      The transformation is done by swapping ATOMs in aaOrig until
+ *      the order matches that of aaNew, each time two ATOMs are swapped,
+ *      flip the sign of the orientation.
+ *
+ *      SIDE EFFECT:   The order in aaOrig is changed.
+  */
+static inline void chiralityTransformOrientation(double dOrig, int* aaOrig, double& dPNew, const int* aaNew)
+{
+  dPNew = dOrig;
+  for (int i=0; i<4; i++ ) {
+    int j = i;
+    for ( ; j<4; j++ ) {
+      if ( aaOrig[j] == aaNew[i] )
+        break;
+    }
+    if ( j >= 4 ) {
+      mprinterr("Error: Comparing atoms %i %i %i aand %i to atoms %i %i %i and %i.\n",
+                aaOrig[0]+1, aaOrig[1]+1, aaOrig[2]+1, aaOrig[3]+1,
+                aaNew[0]+1, aaNew[1]+1, aaNew[2]+1, aaNew[3]+1);
+      mprinterr("Error: This error may be due to faulty Connection atoms.\n");
+      // TODO fatal
+    }
+    // Swap elements and flip sign
+    if ( j != i ) {
+      std::swap( aaOrig[j], aaOrig[i] );
+      dPNew = -dPNew;
+    }
+  }
+}
+
+/** Transform the chirality which has been measured with
+ *  respect to ATOM ID ordering to an arbitrary ordering.
+ */
+static inline double chiralityToOrientation(double dChirality, Atom const& aCenter,
+                                            int aAtomA, int aAtomB, int aAtomC, int aAtomD)
+{
+  if (fabs(dChirality) < Constants::SMALL) return 0.0;
+
+  int aaOrig[4];
+  chiralityOrderNeighbors( aCenter, aaOrig[0], aaOrig[1], aaOrig[2], aaOrig[3] );
+
+  int aaNew[4];
+  aaNew[0] = aAtomA;
+  aaNew[1] = aAtomB;
+  aaNew[2] = aAtomC;
+  aaNew[3] = aAtomD;
+
+  bool newNull = (aaNew[3] == -1);
+  bool origNull = (aaOrig[3] == -1);
+  if (newNull && !origNull) {
+    for (int i = 0; i < 4; i++) {
+      bool found = false;
+      for (int j=0; j<3; j++) found |= (aaOrig[i] == aaNew[j]);
+      if ( !found ) {
+        aaNew[3] = aaOrig[i];
+        break;
+      }
+    }
+  } else if (!newNull && origNull) {
+    mprinterr("Error: Only three neighbors around: aCenter, but orientation has 4\n");
+  }
+
+  double dOrient;
+  chiralityTransformOrientation( dChirality, aaOrig, dOrient, aaNew );
+
+  return dOrient;
+}
+
 /** Assuming atoms have been ordered with SortBondedAtomsLikeLeap,
   * calculate the orientation of the iB atom with respect to the
   * triangle (iA, iX, iY). This orientation will be used by the

From 4b69c9c06a500d78df160f616a412fb3de821e71 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 9 Feb 2024 11:56:24 -0500
Subject: [PATCH 0490/1492] Get orientation when unknown positions are present

---
 src/Structure/Builder.cpp | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index c27ad6a0bd..c812f2851c 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1499,7 +1499,7 @@ static inline double chiralityToOrientation(double dChirality, Atom const& aCent
   * triangle (iA, iX, iY). This orientation will be used by the
   * CreateSpXSpX routines to determine which torsion values to use.
   */
-static inline double calculateOrientation(MockAtom const& iX, double chiX, MockAtom const& iA, MockAtom const& iY, MockAtom const& iB)
+static inline double calculateOrientation(MockAtom const& iX, double chiX, Atom const& AX, MockAtom const& iA, MockAtom const& iY, MockAtom const& iB)
 {
   double dOrientation = 1.0;
   if (iX.Known() &&
@@ -1509,7 +1509,12 @@ static inline double calculateOrientation(MockAtom const& iX, double chiX, MockA
   {
     dOrientation = VectorAtomChirality( iX.Pos(), iA.Pos(), iY.Pos(), iB.Pos() );
   } else {
-    mprinterr("Internal Error: Builder::calculateOrientation not yet set up for unknown positions.\n");
+    double dChi = chiX;
+    if (fabs(dChi) < Constants::SMALL) {
+      mprintf("default chirality on\n");
+      dChi = 1.0;
+    }
+    dOrientation = chiralityToOrientation(dChi, AX, iA.Idx(), iY.Idx(), iB.Idx(), -1);
   }
   return dOrientation;
 }
@@ -1583,12 +1588,12 @@ int Cpptraj::Structure::Builder::TorsionModel::SetupTorsion(AtomType::Hybridizat
   // Calculate the chirality around atom X
   Xorientation_ = 0;
   if (Hx == AtomType::SP3) {
-    Xorientation_ = calculateOrientation( atX_, chiX, sorted_ax_[0], atY_, sorted_ax_[1] );
+    Xorientation_ = calculateOrientation( atX_, chiX, topIn[atX_.Idx()], sorted_ax_[0], atY_, sorted_ax_[1] );
   }
   // Calculate the chirality around atom Y
   Yorientation_ = 0;
   if (Hy == AtomType::SP3) {
-    Yorientation_ = calculateOrientation( atY_, chiY, sorted_ay_[0], atX_, sorted_ay_[1] );
+    Yorientation_ = calculateOrientation( atY_, chiY, topIn[atY_.Idx()], sorted_ay_[0], atX_, sorted_ay_[1] );
   }
   // DEBUG
   Atom const& AX = topIn[atX_.Idx()];

From dde8d85de42dfe06ea4a02e641175275a8cb5163 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 9 Feb 2024 12:37:24 -0500
Subject: [PATCH 0491/1492] Determine chirality same way as leap

---
 src/Structure/Builder.cpp | 44 ++++++++++++++++++++++++++++++++++-----
 src/Structure/Builder.h   |  3 +++
 2 files changed, 42 insertions(+), 5 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index c812f2851c..5baca3cd5f 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -2158,6 +2158,40 @@ void Builder::createSp2Sp2Torsions(TorsionModel const& MT) {
   return;
 }
 
+/** Determine hybridization in the same manner as leap */
+AtomType::HybridizationType Builder::getAtomHybridization(Atom const& aAtom) const {
+  AtomType::HybridizationType H1 = AtomType::UNKNOWN_HYBRIDIZATION;
+  if (params_ != 0) {
+    ParmHolder<AtomType>::const_iterator it;
+    if (aAtom.HasType()) {
+      it = params_->AT().GetParam( TypeNameHolder(aAtom.Type()) );
+      if (it != params_->AT().end())
+        H1 = it->second.Hybridization();
+    }
+  }
+  if (H1 == AtomType::UNKNOWN_HYBRIDIZATION) {
+    // TODO bond orders?
+    int iSingle = 0;
+    int iDouble = 0;
+    int iTriple = 0;
+    int iAromatic = 0;
+    for (int i = 0; i < aAtom.Nbonds(); i++)
+      iSingle++;
+    //printf("iAtomHybridization: %s isingle=%i\n", iSingle);
+    if ( iAromatic != 0 )       H1 = AtomType::SP2;
+                // one or more triple bonds makes the atom SP1
+    else if ( iTriple != 0 )    H1 = AtomType::SP;
+                // Two or more double bonds makes the atom linear, SP1
+    else if ( iDouble >= 2 )    H1 = AtomType::SP;
+                // One double bond makes the atom SP2
+    else if ( iDouble != 0 )    H1 = AtomType::SP2;
+                // Otherwise the atom is SP3
+    else                        H1 = AtomType::SP3;
+  }
+
+  return H1;
+}
+
 /** Assign torsions around bonded atoms in manner similar to LEaP's ModelAssignTorsionsAround. */
 int Builder::assignTorsionsAroundBond(int a1, int a2, Frame const& frameIn, Topology const& topIn, Barray const& hasPosition, int aAtomIdx)
 {
@@ -2170,9 +2204,9 @@ int Builder::assignTorsionsAroundBond(int a1, int a2, Frame const& frameIn, Topo
   if (topIn[a1].Nbonds() < 2 || topIn[a2].Nbonds() < 2)
     return 0;
   // Get atom hybridizations
-  AtomType::HybridizationType H1 = AtomType::UNKNOWN_HYBRIDIZATION;
-  AtomType::HybridizationType H2 = AtomType::UNKNOWN_HYBRIDIZATION;
-  if (params_ != 0) {
+  AtomType::HybridizationType H1 = getAtomHybridization( topIn[a1] );
+  AtomType::HybridizationType H2 = getAtomHybridization( topIn[a2] );//AtomType::UNKNOWN_HYBRIDIZATION;
+/*  if (params_ != 0) {
     ParmHolder<AtomType>::const_iterator it;
     if (topIn[a1].HasType()) {
       it = params_->AT().GetParam( TypeNameHolder(topIn[a1].Type()) );
@@ -2188,7 +2222,7 @@ int Builder::assignTorsionsAroundBond(int a1, int a2, Frame const& frameIn, Topo
   if (H1 == AtomType::UNKNOWN_HYBRIDIZATION)
     H1 = GuessAtomHybridization(topIn[a1], topIn.Atoms());
   if (H2 == AtomType::UNKNOWN_HYBRIDIZATION)
-    H2 = GuessAtomHybridization(topIn[a2], topIn.Atoms());
+    H2 = GuessAtomHybridization(topIn[a2], topIn.Atoms());*/
   if (H1 == AtomType::UNKNOWN_HYBRIDIZATION)
     mprintf("Warning: No hybridization set for atom %s\n", topIn.AtomMaskName(a1).c_str());
   if (H2 == AtomType::UNKNOWN_HYBRIDIZATION)
@@ -2248,7 +2282,7 @@ int Builder::assignTorsionsAroundBond(int a1, int a2, Frame const& frameIn, Topo
     }
   } else {
     // Use existing atoms to determine torsions
-    mprintf("DEBUG: Using externals to fit new torsions around: %s - %s\n",
+    mprintf("Using externals to fit new torsions around: %s - %s\n",
             topIn.LeapName(ax).c_str(),
             topIn.LeapName(ay).c_str());
   }
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index 282df5c974..6493737708 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -1,6 +1,7 @@
 #ifndef INC_STRUCTURE_BUILDER_H
 #define INC_STRUCTURE_BUILDER_H
 #include <vector>
+#include "../AtomType.h"
 class Atom;
 class Topology;
 class Frame;
@@ -93,6 +94,8 @@ class Builder {
     void createSp3Sp2Torsions(TorsionModel const&);
     /// Create torsion around SP2-SP2 linkage
     void createSp2Sp2Torsions(TorsionModel const&);
+    /// Dtermine atom hybridization in the same way as leap
+    AtomType::HybridizationType getAtomHybridization(Atom const&) const;
     /// Model torsions around a bond in the same manner as LEaP
     int assignTorsionsAroundBond(int, int, Frame const&, Topology const&, Barray const&, int);
     /// Get any existing internal torsion indices around specified atoms

From d297c8afd2924a595a2b4384f2da1e61624eb9aa Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 9 Feb 2024 15:10:06 -0500
Subject: [PATCH 0492/1492] Fix orientation calc when not enough bonded atoms

---
 src/Exec_Sequence.cpp     |  9 ++++++++-
 src/Structure/Builder.cpp | 12 ++++++++++--
 2 files changed, 18 insertions(+), 3 deletions(-)

diff --git a/src/Exec_Sequence.cpp b/src/Exec_Sequence.cpp
index ea2fc78c3f..4dd327205d 100644
--- a/src/Exec_Sequence.cpp
+++ b/src/Exec_Sequence.cpp
@@ -240,8 +240,15 @@ const
     }
   }
 
+  // Finalize topology - determine molecules, dont renumber residues, assign default bond params
+  topOut.CommonSetup(true, false, true);
+  topOut.Summary();
 
+  OUT->CoordsSetup(topOut, frameOut.CoordsInfo());
+  OUT->AddFrame( frameOut );
 
+  if (buildFailed) return 1;
+/*
   Topology combinedTop;
   combinedTop.SetDebug( debug_ );
   combinedTop.SetParmName( OUT->Meta().Name(), FileName() );
@@ -285,7 +292,7 @@ const
   //}
 
   OUT->CoordsSetup(combinedTop, CombinedFrame.CoordsInfo());
-  OUT->AddFrame( CombinedFrame );
+  OUT->AddFrame( CombinedFrame );*/
 
   return 0;
 }
diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 5baca3cd5f..a78c8235ff 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1508,12 +1508,14 @@ static inline double calculateOrientation(MockAtom const& iX, double chiX, Atom
       iB.Known())
   {
     dOrientation = VectorAtomChirality( iX.Pos(), iA.Pos(), iY.Pos(), iB.Pos() );
+    mprintf("ORIENTATION: known = %f\n", dOrientation);
   } else {
     double dChi = chiX;
     if (fabs(dChi) < Constants::SMALL) {
       mprintf("default chirality on\n");
       dChi = 1.0;
     }
+    mprintf("ORIENTATION: Chirality %f\n", dChi);
     dOrientation = chiralityToOrientation(dChi, AX, iA.Idx(), iY.Idx(), iB.Idx(), -1);
   }
   return dOrientation;
@@ -1588,12 +1590,18 @@ int Cpptraj::Structure::Builder::TorsionModel::SetupTorsion(AtomType::Hybridizat
   // Calculate the chirality around atom X
   Xorientation_ = 0;
   if (Hx == AtomType::SP3) {
-    Xorientation_ = calculateOrientation( atX_, chiX, topIn[atX_.Idx()], sorted_ax_[0], atY_, sorted_ax_[1] );
+    if (sorted_ax_.size() < 2)
+      Xorientation_ = 1.0;
+    else
+      Xorientation_ = calculateOrientation( atX_, chiX, topIn[atX_.Idx()], sorted_ax_[0], atY_, sorted_ax_[1] );
   }
   // Calculate the chirality around atom Y
   Yorientation_ = 0;
   if (Hy == AtomType::SP3) {
-    Yorientation_ = calculateOrientation( atY_, chiY, topIn[atY_.Idx()], sorted_ay_[0], atX_, sorted_ay_[1] );
+    if (sorted_ay_.size() < 2)
+      Yorientation_ = 1.0;
+    else
+      Yorientation_ = calculateOrientation( atY_, chiY, topIn[atY_.Idx()], sorted_ay_[0], atX_, sorted_ay_[1] );
   }
   // DEBUG
   Atom const& AX = topIn[atX_.Idx()];

From 77ba3086437c9cbd7220849be6fcc11b55b18332 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 9 Feb 2024 15:34:40 -0500
Subject: [PATCH 0493/1492] Use leap guess hybridization in model angle/bond

---
 src/Exec_Sequence.cpp     |   3 +-
 src/Structure/Builder.cpp | 112 ++++++++++++++------------------------
 2 files changed, 43 insertions(+), 72 deletions(-)

diff --git a/src/Exec_Sequence.cpp b/src/Exec_Sequence.cpp
index 4dd327205d..f51d3aec7e 100644
--- a/src/Exec_Sequence.cpp
+++ b/src/Exec_Sequence.cpp
@@ -167,7 +167,8 @@ const
         return 1;
       }
       mprintf("Will add bond between %i and %i\n", prevTailAtom+1, headAtom+1);
-      interResBonds.push_back( Ipair(prevTailAtom, headAtom) );
+      // To preserve compat. with LEaP, make first atom the head atom.
+      interResBonds.push_back( Ipair(headAtom, prevTailAtom) );
     } else
       // Placeholder
       interResBonds.push_back( Ipair(-1, -1) );
diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index a78c8235ff..181c8cc856 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1874,6 +1874,40 @@ int Builder::getExistingChiralityIdx(int ai) const {
   return idx;
 }
 
+/** Determine hybridization in the same manner as leap */
+AtomType::HybridizationType Builder::getAtomHybridization(Atom const& aAtom) const {
+  AtomType::HybridizationType H1 = AtomType::UNKNOWN_HYBRIDIZATION;
+  if (params_ != 0) {
+    ParmHolder<AtomType>::const_iterator it;
+    if (aAtom.HasType()) {
+      it = params_->AT().GetParam( TypeNameHolder(aAtom.Type()) );
+      if (it != params_->AT().end())
+        H1 = it->second.Hybridization();
+    }
+  }
+  if (H1 == AtomType::UNKNOWN_HYBRIDIZATION) {
+    // TODO bond orders?
+    int iSingle = 0;
+    int iDouble = 0;
+    int iTriple = 0;
+    int iAromatic = 0;
+    for (int i = 0; i < aAtom.Nbonds(); i++)
+      iSingle++;
+    //printf("iAtomHybridization: %s isingle=%i\n", iSingle);
+    if ( iAromatic != 0 )       H1 = AtomType::SP2;
+                // one or more triple bonds makes the atom SP1
+    else if ( iTriple != 0 )    H1 = AtomType::SP;
+                // Two or more double bonds makes the atom linear, SP1
+    else if ( iDouble >= 2 )    H1 = AtomType::SP;
+                // One double bond makes the atom SP2
+    else if ( iDouble != 0 )    H1 = AtomType::SP2;
+                // Otherwise the atom is SP3
+    else                        H1 = AtomType::SP3;
+  }
+
+  return H1;
+}
+
 /** Model bond */
 double Builder::ModelBondLength(int ai, int aj, Topology const& topIn) const {
   // First look up parameter
@@ -1883,17 +1917,9 @@ double Builder::ModelBondLength(int ai, int aj, Topology const& topIn) const {
   }
   Atom const& AI = topIn[ai];
   Atom const& AJ = topIn[aj];
-  AtomType::HybridizationType hybridI = AtomType::UNKNOWN_HYBRIDIZATION;
-  AtomType::HybridizationType hybridJ = AtomType::UNKNOWN_HYBRIDIZATION;
-  // Check params for hybrid
-  if (params_ != 0) {
-    ParmHolder<AtomType>::const_iterator it = params_->AT().GetParam( TypeNameHolder(AI.Type()) );
-    if (it != params_->AT().end())
-      hybridI = it->second.Hybridization();
-    it = params_->AT().GetParam( TypeNameHolder(AJ.Type()) );
-    if (it != params_->AT().end())
-      hybridJ = it->second.Hybridization();
-  }
+  AtomType::HybridizationType hybridI = getAtomHybridization( AI );
+  AtomType::HybridizationType hybridJ = getAtomHybridization( AJ );
+
   if (hybridI == AtomType::UNKNOWN_HYBRIDIZATION ||
       hybridJ == AtomType::UNKNOWN_HYBRIDIZATION)
   {
@@ -1941,16 +1967,11 @@ double Builder::ModelBondAngle(int ai, int aj, int ak, Topology const& topIn) co
     mprintf("DEBUG:\t\tJ %s Nbonds: %i\n", AJ.ElementName(), AJ.Nbonds());
     mprintf("DEBUG:\t\tK %s Nbonds: %i\n", topIn[ak].ElementName(), topIn[ak].Nbonds());
   }
-  AtomType::HybridizationType hybrid = AtomType::UNKNOWN_HYBRIDIZATION;
-  // Check params for hybrid
-  if (params_ != 0) {
-    ParmHolder<AtomType>::const_iterator it = params_->AT().GetParam( TypeNameHolder(AJ.Type()) );
-    if (it != params_->AT().end())
-      hybrid = it->second.Hybridization();
-  }
+  AtomType::HybridizationType hybrid = getAtomHybridization( AJ );
+
   // Guess hybrid if needed
-  if (hybrid == AtomType::UNKNOWN_HYBRIDIZATION)
-    hybrid = GuessAtomHybridization(AJ, topIn.Atoms());
+  //if (hybrid == AtomType::UNKNOWN_HYBRIDIZATION)
+  //  hybrid = GuessAtomHybridization(AJ, topIn.Atoms());
   // Set from number of bonds if still unknown. This is a pretty crude guess.
   if (hybrid == AtomType::UNKNOWN_HYBRIDIZATION) {
     switch (AJ.Nbonds()) {
@@ -2166,40 +2187,6 @@ void Builder::createSp2Sp2Torsions(TorsionModel const& MT) {
   return;
 }
 
-/** Determine hybridization in the same manner as leap */
-AtomType::HybridizationType Builder::getAtomHybridization(Atom const& aAtom) const {
-  AtomType::HybridizationType H1 = AtomType::UNKNOWN_HYBRIDIZATION;
-  if (params_ != 0) {
-    ParmHolder<AtomType>::const_iterator it;
-    if (aAtom.HasType()) {
-      it = params_->AT().GetParam( TypeNameHolder(aAtom.Type()) );
-      if (it != params_->AT().end())
-        H1 = it->second.Hybridization();
-    }
-  }
-  if (H1 == AtomType::UNKNOWN_HYBRIDIZATION) {
-    // TODO bond orders?
-    int iSingle = 0;
-    int iDouble = 0;
-    int iTriple = 0;
-    int iAromatic = 0;
-    for (int i = 0; i < aAtom.Nbonds(); i++)
-      iSingle++;
-    //printf("iAtomHybridization: %s isingle=%i\n", iSingle);
-    if ( iAromatic != 0 )       H1 = AtomType::SP2;
-                // one or more triple bonds makes the atom SP1
-    else if ( iTriple != 0 )    H1 = AtomType::SP;
-                // Two or more double bonds makes the atom linear, SP1
-    else if ( iDouble >= 2 )    H1 = AtomType::SP;
-                // One double bond makes the atom SP2
-    else if ( iDouble != 0 )    H1 = AtomType::SP2;
-                // Otherwise the atom is SP3
-    else                        H1 = AtomType::SP3;
-  }
-
-  return H1;
-}
-
 /** Assign torsions around bonded atoms in manner similar to LEaP's ModelAssignTorsionsAround. */
 int Builder::assignTorsionsAroundBond(int a1, int a2, Frame const& frameIn, Topology const& topIn, Barray const& hasPosition, int aAtomIdx)
 {
@@ -2214,23 +2201,6 @@ int Builder::assignTorsionsAroundBond(int a1, int a2, Frame const& frameIn, Topo
   // Get atom hybridizations
   AtomType::HybridizationType H1 = getAtomHybridization( topIn[a1] );
   AtomType::HybridizationType H2 = getAtomHybridization( topIn[a2] );//AtomType::UNKNOWN_HYBRIDIZATION;
-/*  if (params_ != 0) {
-    ParmHolder<AtomType>::const_iterator it;
-    if (topIn[a1].HasType()) {
-      it = params_->AT().GetParam( TypeNameHolder(topIn[a1].Type()) );
-      if (it != params_->AT().end())
-        H1 = it->second.Hybridization();
-    }
-    if (topIn[a2].HasType()) {
-      it = params_->AT().GetParam( TypeNameHolder(topIn[a2].Type()) );
-      if (it != params_->AT().end())
-        H2 = it->second.Hybridization();
-    }
-  }
-  if (H1 == AtomType::UNKNOWN_HYBRIDIZATION)
-    H1 = GuessAtomHybridization(topIn[a1], topIn.Atoms());
-  if (H2 == AtomType::UNKNOWN_HYBRIDIZATION)
-    H2 = GuessAtomHybridization(topIn[a2], topIn.Atoms());*/
   if (H1 == AtomType::UNKNOWN_HYBRIDIZATION)
     mprintf("Warning: No hybridization set for atom %s\n", topIn.AtomMaskName(a1).c_str());
   if (H2 == AtomType::UNKNOWN_HYBRIDIZATION)

From 96209684d22f1256b2b9cec43b0aa724338ea2ae Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 10 Feb 2024 08:02:00 -0500
Subject: [PATCH 0494/1492] This is much closer to what leap produces

---
 test/Test_Sequence/Mol.mol2.save | 36 ++++++++++++++++----------------
 1 file changed, 18 insertions(+), 18 deletions(-)

diff --git a/test/Test_Sequence/Mol.mol2.save b/test/Test_Sequence/Mol.mol2.save
index c1b6440f8a..23ccbc3d64 100644
--- a/test/Test_Sequence/Mol.mol2.save
+++ b/test/Test_Sequence/Mol.mol2.save
@@ -6,23 +6,23 @@ USER_CHARGES
 
 
 @<TRIPOS>ATOM
-      1 C1         -1.9010   -1.2979   -0.5927 CT         1 MOC      1.387300
-      2 H2         -2.2470   -2.2143   -0.1146 H1         1 MOC     -0.288000
-      3 H3         -2.3292   -1.2263   -1.5925 H1         1 MOC     -0.288000
-      4 H4         -2.2160   -0.4385   -0.0008 H1         1 MOC     -0.288000
-      5 O5         -0.4741   -1.3169   -0.6848 OS         1 MOC     -0.523200
-      6 N           0.0540   -0.2256    0.0153 N          2 CNALA   -0.570310
-      7 H          -0.4149    0.5139    0.5357 H          2 CNALA    0.364710
-      8 CA          1.5127   -0.0215    0.0706 CX         2 CNALA    0.118030
-      9 HA          1.9976   -0.8599   -0.4376 H1         2 CNALA    0.105630
-     10 CB          1.8871    1.2873   -0.6522 CT         2 CNALA   -0.214290
-     11 HB1         1.5308    1.2705   -1.6848 HC         2 CNALA    0.081710
-     12 HB2         1.4452    2.1491   -0.1463 HC         2 CNALA    0.081710
-     13 HB3         2.9715    1.4185   -0.6703 HC         2 CNALA    0.081710
-     14 C           2.0167   -0.0042    1.5042 C          2 CNALA    0.597740
-     15 O           1.3510    0.3674    2.4498 O          2 CNALA   -0.533510
-     16 OXT         3.2954   -0.2516    1.6078 OH         2 CNALA   -0.566290
-     17 HXT         3.6319   -0.4443    0.7168 HO         2 CNALA    0.453160
+      1 C1         -1.1655    0.1889   -0.0001 CT         1 MOC      1.387300
+      2 H2         -2.0028   -0.4954   -0.0001 H1         1 MOC     -0.288000
+      3 H3         -1.2286    0.8227   -0.8832 H1         1 MOC     -0.288000
+      4 H4         -1.2287    0.8227    0.8831 H1         1 MOC     -0.288000
+      5 O5          0.0000   -0.5708    0.0000 OS         1 MOC     -0.523200
+      6 N           1.1916    0.3403    0.0000 N          2 CNALA   -0.570310
+      7 H           1.1430    0.8923   -0.8547 H          2 CNALA    0.364710
+      8 CA          2.4264   -0.4645    0.0001 CX         2 CNALA    0.118030
+      9 HA          2.4901   -0.9979    0.9529 H1         2 CNALA    0.105630
+     10 CB          2.3829   -1.4921   -1.1479 CT         2 CNALA   -0.214290
+     11 HB1         1.4987   -2.1277   -1.0603 HC         2 CNALA    0.081710
+     12 HB2         2.3542   -0.9887   -2.1172 HC         2 CNALA    0.081710
+     13 HB3         3.2659   -2.1348   -1.1206 HC         2 CNALA    0.081710
+     14 C           3.6613    0.4137   -0.1142 C          2 CNALA    0.597740
+     15 O           3.6774    1.4856   -0.6854 O          2 CNALA   -0.533510
+     16 OXT         4.7542   -0.1713    0.2984 OH         2 CNALA   -0.566290
+     17 HXT         4.5091   -1.0471    0.6406 HO         2 CNALA    0.453160
 @<TRIPOS>BOND
     1     1     5 1
     2     6     8 1
@@ -30,7 +30,7 @@ USER_CHARGES
     4     8    14 1
     5    14    15 1
     6    14    16 1
-    7     5     6 1
+    7     6     5 1
     8     1     2 1
     9     1     3 1
    10     1     4 1

From 72f11c351f7b0939a21e37cf48aebdccb201736c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 11 Feb 2024 13:45:16 -0500
Subject: [PATCH 0495/1492] Dont use new

---
 src/Exec_Build.cpp | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index ab5f2200f6..49fff328e5 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -315,20 +315,20 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
     long int ires = it-AtomOffsets.begin();
     if (*it > -1) {
       // Residue has atom offset which indicates it needs something built.
-      Cpptraj::Structure::Builder* structureBuilder = new Cpptraj::Structure::Builder();
-      structureBuilder->SetDebug( 1 ); // DEBUG FIXME
-      structureBuilder->SetParameters( &mainParmSet );
+      Cpptraj::Structure::Builder structureBuilder;// = new Cpptraj::Structure::Builder();
+      structureBuilder.SetDebug( 1 ); // DEBUG FIXME
+      structureBuilder.SetParameters( &mainParmSet );
       // Generate internals from the template, update indices to this topology.
       DataSet_Coords* resTemplate = ResTemplates[ires];
       Frame templateFrame = resTemplate->AllocateFrame();
       resTemplate->GetFrame( 0, templateFrame );
-      if (structureBuilder->GenerateInternals(templateFrame, resTemplate->Top(),
+      if (structureBuilder.GenerateInternals(templateFrame, resTemplate->Top(),
                                              std::vector<bool>(resTemplate->Top().Natom(), true)))
       {
         mprinterr("Error: Generate internals for residue template failed.\n");
         return 1;
       }
-      structureBuilder->UpdateIndicesWithOffset( *it );
+      structureBuilder.UpdateIndicesWithOffset( *it );
 
       mprintf("DEBUG: ***** BUILD residue %li %s *****\n", ires + 1,
               topOut.TruncResNameOnumId(ires).c_str());
@@ -343,7 +343,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
                   topOut.AtomMaskName(resBonds->second).c_str());
           topOut.AddBond(resBonds->first, resBonds->second);
           // Generate internals around the link
-          if (structureBuilder->GenerateInternalsAroundLink(resBonds->first, resBonds->second,
+          if (structureBuilder.GenerateInternalsAroundLink(resBonds->first, resBonds->second,
                                                             frameOut, topOut, hasPosition))
           {
             mprinterr("Error: Assign torsions around inter-residue link %s - %s failed.\n",
@@ -354,14 +354,14 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
         }
       }
       // Update internal coords from known positions
-      if (structureBuilder->UpdateICsFromFrame( frameOut, ires, topOut, hasPosition )) {
+      if (structureBuilder.UpdateICsFromFrame( frameOut, ires, topOut, hasPosition )) {
         mprinterr("Error: Failed to update Zmatrix with values from existing positions.\n");
         return 1;
       }
       // Convert to Zmatrix and assign missing atom positions
       Cpptraj::Structure::Zmatrix tmpz;
       tmpz.SetDebug( 1 ); // DEBUG
-      if (structureBuilder->GetZmatrixFromInternals(tmpz, topOut)) {
+      if (structureBuilder.GetZmatrixFromInternals(tmpz, topOut)) {
         mprinterr("Error: Could not get Zmatrix from internals.\n");
         return 1;
       }
@@ -371,7 +371,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
         buildFailed = true;
       }// else
        // resIsBuilt[ires] = true;
-      delete structureBuilder;
+      //delete structureBuilder;
     }
   } // END loop over atom offsets
 

From accc6b276987028f559cf3615d2f8e7925648d73 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 11 Feb 2024 13:45:42 -0500
Subject: [PATCH 0496/1492] Use Builder

---
 src/Exec_Sequence.cpp | 56 +++++++++++++++++++++----------------------
 1 file changed, 28 insertions(+), 28 deletions(-)

diff --git a/src/Exec_Sequence.cpp b/src/Exec_Sequence.cpp
index f51d3aec7e..1d96f2cf55 100644
--- a/src/Exec_Sequence.cpp
+++ b/src/Exec_Sequence.cpp
@@ -15,10 +15,10 @@ const
   typedef std::vector<DataSet_Coords*> Uarray;
   Uarray Units;
   Units.reserve( main_sequence.size() );
-  typedef std::vector<int> Iarray;
-  Iarray connectAt0, connectAt1;
-  connectAt0.reserve( Units.size() );
-  connectAt1.reserve( Units.size() );
+//  typedef std::vector<int> Iarray;
+//  Iarray connectAt0, connectAt1;
+//  connectAt0.reserve( Units.size() );
+//  connectAt1.reserve( Units.size() );
   int total_natom = 0;
 
   for (Sarray::const_iterator it = main_sequence.begin(); it != main_sequence.end(); ++it)
@@ -61,20 +61,20 @@ const
       mprintf("Warning: Unit '%s' has more than 1 frame. Only using first frame.\n", unit->legend());
     }
     // Needs to have connect associated data
-    AssociatedData* ad = unit->GetAssociatedData(AssociatedData::CONNECT);
-    if (ad == 0) {
-      mprinterr("Error: Unit '%s' does not have CONNECT data.\n", unit->legend());
-      return 1;
-    }
-    AssociatedData_Connect const& C = static_cast<AssociatedData_Connect const&>( *ad );
-    if (C.NconnectAtoms() < 2) {
-      mprinterr("Error: Not enough connect atoms in unit '%s'\n", unit->legend());
-      return 1;
-    }
-    // Update connect atom 1 indices based on their position in the sequence.
-    // Do not update connect atom 0 indices since they will not yet be connected.
-    connectAt0.push_back( C.Connect()[0] );
-    connectAt1.push_back( C.Connect()[1] + total_natom );
+//    AssociatedData* ad = unit->GetAssociatedData(AssociatedData::CONNECT);
+//    if (ad == 0) {
+//      mprinterr("Error: Unit '%s' does not have CONNECT data.\n", unit->legend());
+//      return 1;
+//    }
+//    AssociatedData_Connect const& C = static_cast<AssociatedData_Connect const&>( *ad );
+//    if (C.NconnectAtoms() < 2) {
+//      mprinterr("Error: Not enough connect atoms in unit '%s'\n", unit->legend());
+//      return 1;
+//    }
+//    // Update connect atom 1 indices based on their position in the sequence.
+//    // Do not update connect atom 0 indices since they will not yet be connected.
+//    connectAt0.push_back( C.Connect()[0] );
+//    connectAt1.push_back( C.Connect()[1] + total_natom );
     Units.push_back( unit );
     total_natom += unit->Top().Natom();
   } // END loop over sequence
@@ -83,8 +83,8 @@ const
     mprinterr("Error: No units.\n");
     return 1;
   }
-  for (unsigned int idx = 0; idx < Units.size(); idx++)
-    mprintf("\tUnit %s HEAD %i TAIL %i\n", Units[idx]->legend(), connectAt0[idx]+1, connectAt1[idx]+1);
+//  for (unsigned int idx = 0; idx < Units.size(); idx++)
+//    mprintf("\tUnit %s HEAD %i TAIL %i\n", Units[idx]->legend(), connectAt0[idx]+1, connectAt1[idx]+1);
 
   Topology topOut;
   Frame frameOut;
@@ -188,20 +188,20 @@ const
     long int ires = it-AtomOffsets.begin();
     if (*it > -1) {
       // Residue has atom offset which indicates it needs something built.
-      Cpptraj::Structure::Builder* structureBuilder = new Cpptraj::Structure::Builder();
-      structureBuilder->SetDebug( 1 ); // DEBUG FIXME
+      Cpptraj::Structure::Builder structureBuilder;// = new Cpptraj::Structure::Builder();
+      structureBuilder.SetDebug( 1 ); // DEBUG FIXME
       //structureBuilder->SetParameters( &mainParmSet ); TODO import parameters?
       // Generate internals from the template, update indices to this topology.
       DataSet_Coords* unit = Units[ires];
       Frame unitFrm = unit->AllocateFrame();
       unit->GetFrame(0, unitFrm);
-      if (structureBuilder->GenerateInternals(unitFrm, unit->Top(),
+      if (structureBuilder.GenerateInternals(unitFrm, unit->Top(),
                                               std::vector<bool>(unit->Top().Natom(), true)))
       {
         mprinterr("Error: Generate internals for unit failed.\n");
         return 1;
       }
-      structureBuilder->UpdateIndicesWithOffset( *it );
+      structureBuilder.UpdateIndicesWithOffset( *it );
 
       mprintf("DEBUG: ***** BUILD unit %li %s *****\n", ires + 1,
               topOut.TruncResNameOnumId(ires).c_str());
@@ -212,7 +212,7 @@ const
               topOut.AtomMaskName(interResBonds[ires].second).c_str());
       topOut.AddBond( interResBonds[ires].first, interResBonds[ires].second );
       // Generate internals around the link
-      if (structureBuilder->GenerateInternalsAroundLink(interResBonds[ires].first, interResBonds[ires].second,
+      if (structureBuilder.GenerateInternalsAroundLink(interResBonds[ires].first, interResBonds[ires].second,
                                                         frameOut, topOut, hasPosition))
       {
         mprinterr("Error: Assign torsions around inter-unit link %s - %s failed.\n",
@@ -221,14 +221,14 @@ const
         return 1;
       }
       // Update internal coords from known positions
-      if (structureBuilder->UpdateICsFromFrame( frameOut, ires, topOut, hasPosition )) {
+      if (structureBuilder.UpdateICsFromFrame( frameOut, ires, topOut, hasPosition )) {
         mprinterr("Error: Failed to update Zmatrix with values from existing positions.\n");
         return 1;
       }
       // Convert to Zmatrix and assign missing atom positions
       Cpptraj::Structure::Zmatrix tmpz;
       tmpz.SetDebug( 1 ); // DEBUG
-      if (structureBuilder->GetZmatrixFromInternals(tmpz, topOut)) {
+      if (structureBuilder.GetZmatrixFromInternals(tmpz, topOut)) {
         mprinterr("Error: Could not get Zmatrix from internals.\n");
         return 1;
       }
@@ -237,7 +237,7 @@ const
                   topOut.TruncResNameOnumId(ires).c_str());
         buildFailed = true;
       }
-      delete structureBuilder;
+      //delete structureBuilder;
     }
   }
 

From c97ff999a00a99b944e121546630b7fcd68d5c17 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 12 Feb 2024 08:46:46 -0500
Subject: [PATCH 0497/1492] Add some more debug info

---
 src/Structure/Builder.cpp | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 181c8cc856..26d6940071 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1442,7 +1442,7 @@ static inline void chiralityTransformOrientation(double dOrig, int* aaOrig, doub
         break;
     }
     if ( j >= 4 ) {
-      mprinterr("Error: Comparing atoms %i %i %i aand %i to atoms %i %i %i and %i.\n",
+      mprinterr("Error: Comparing atoms %i %i %i and %i to atoms %i %i %i and %i.\n",
                 aaOrig[0]+1, aaOrig[1]+1, aaOrig[2]+1, aaOrig[3]+1,
                 aaNew[0]+1, aaNew[1]+1, aaNew[2]+1, aaNew[3]+1);
       mprinterr("Error: This error may be due to faulty Connection atoms.\n");
@@ -2579,12 +2579,13 @@ int Builder::GenerateInternalsAroundLink(int at0, int at1,
                                          Barray const& hasPosition)
 {
   mprintf("DEBUG: ----- Entering Builder::GenerateInternalsAroundLink. -----\n");
+  mprintf("DEBUG: Link: %s to %s\n", topIn.AtomMaskName(at0).c_str(), topIn.AtomMaskName(at1).c_str());
   // Sanity check
   Atom const& A0 = topIn[at0];
   Atom const& A1 = topIn[at1];
   if (A0.ResNum() == A1.ResNum()) {
-    mprinterr("Internal Error: Builder::GenerateInternalsAroundLink(): Atoms are in the same residue.\n");
-    return 1;
+    mprintf("Warning: Builder::GenerateInternalsAroundLink(): Atoms are in the same residue.\n");
+    //return 1;
   }
   // In order to mimic the way LEaP does things, mark all atoms before
   // this residue as having position, and all other atoms as not having

From 69c98ac0d159eff548a9ef4baabd07b7a2f95eba Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 12 Feb 2024 08:51:36 -0500
Subject: [PATCH 0498/1492] Use builder in graft

---
 src/Exec_Graft.cpp | 118 ++++++++++++++++++++++++++++++++++++++++++++-
 src/cpptrajdepend  |   6 +--
 2 files changed, 119 insertions(+), 5 deletions(-)

diff --git a/src/Exec_Graft.cpp b/src/Exec_Graft.cpp
index be97ea5c0c..207dbae367 100644
--- a/src/Exec_Graft.cpp
+++ b/src/Exec_Graft.cpp
@@ -2,7 +2,9 @@
 #include "CpptrajStdio.h"
 #include "DataSet_Coords.h"
 #include "Structure/Builder.h"
+#include "Structure/Zmatrix.h"
 #include <algorithm> // std::copy
+#include <utility> // std::pair
 
 using namespace Cpptraj::Structure;
 
@@ -297,7 +299,119 @@ const
     return 1;
   }
 
-  // Combine topologies.
+  for (int at = 0; at != mol0Top.Natom(); at++)
+    mprintf("\t%6i %s %s\n", at+1, mol0Top.AtomMaskName(at).c_str(), *(mol0Top.Res(mol0Top[at].ResNum()).Name()));
+  mprintf("BOND ATOM 0 %i\n", bondat0+1);
+  for (int at = 0; at != mol1Top.Natom(); at++)
+    mprintf("\t%6i %s %s\n", at+1, mol1Top.AtomMaskName(at).c_str(), *(mol1Top.Res(mol1Top[at].ResNum()).Name()));
+  mprintf("BOND ATOM 1 %i\n", bondat1+1);
+
+  // Combine topologies. TODO save original chiralities
+  Topology topOut;
+  Frame frameOut;
+  int total_natom = mol0Top.Natom() + mol1Top.Natom();
+  frameOut.SetupFrame( total_natom );
+  // Clear frame so that AddXYZ can be used
+  frameOut.ClearAtoms();
+  // hasPosition - for each atom in topOut, status on whether atom in frameOut needs building
+  Cpptraj::Structure::Zmatrix::Barray hasPosition;
+  hasPosition.reserve( total_natom );
+  // For saving intra-res bonds
+  typedef std::pair<int,int> Ipair;
+  typedef std::vector<Ipair> IParray;
+  IParray intraResBonds;
+  // Add mol0 atoms to topology
+  topOut.SetDebug( debug_ );
+  topOut.SetParmName( outCoords->Meta().Name(), FileName() );
+  topOut.SetParmBox( mol0frm.BoxCrd() );
+  for (int at = 0; at < mol0Top.Natom(); at++) {
+    Atom sourceAtom = mol0Top[at];
+    for (Atom::bond_iterator bat = sourceAtom.bondbegin(); bat != sourceAtom.bondend(); ++bat) {
+      if (*bat > at) {
+        mprintf("Will add bond between %i and %i\n", at+1, *bat+1);
+        intraResBonds.push_back( Ipair(at, *bat) );
+      }
+    }
+    sourceAtom.ClearBonds(); // FIXME AddTopAtom should clear bonds
+    topOut.AddTopAtom( sourceAtom, mol0Top.Res(mol0Top[at].ResNum()) );
+    frameOut.AddVec3( Vec3(mol0frm.XYZ(at)) );
+    hasPosition.push_back( true );
+  }
+  // Add mol1 atoms
+  int atomOffset = mol0Top.Natom();
+  mprintf("DEBUG: Atom offset is %i\n", atomOffset);
+  for (int itgt = 0; itgt < mol1Top.Natom(); itgt++) {
+    Atom sourceAtom = mol1Top[itgt];
+    int at0 = itgt + atomOffset;
+    for (Atom::bond_iterator bat = sourceAtom.bondbegin(); bat != sourceAtom.bondend(); ++bat) {
+      int at1 = *bat + atomOffset;
+      if (at1 > at0) {
+        mprintf("Will add bond between %i and %i (original %i and %i)\n", at0+1, at1+1, itgt+1, *bat + 1);
+        intraResBonds.push_back( Ipair(at0, at1) );
+      }
+    }
+    sourceAtom.ClearBonds(); // FIXME AddTopAtom should clear bonds
+    topOut.AddTopAtom( sourceAtom, mol1Top.Res(mol1Top[itgt].ResNum()) );
+    frameOut.AddVec3( Vec3(mol1frm.XYZ(itgt)) );
+    hasPosition.push_back( false );
+  }
+  //Add intra-residue bonds
+  for (IParray::const_iterator it = intraResBonds.begin(); it != intraResBonds.end(); ++it)
+  {
+    //mprintf("DEBUG: Intra-res bond: Res %s atom %s to res %s atom %s\n",
+    //        topOut.TruncResNameOnumId(topOut[it->first].ResNum()).c_str(), *(topOut[it->first].Name()),
+    //        topOut.TruncResNameOnumId(topOut[it->second].ResNum()).c_str(), *(topOut[it->second].Name()));
+    topOut.AddBond(it->first, it->second);
+  }
+  // FIXME
+  for (int at = 0; at != topOut.Natom(); at++)
+    mprintf("\t%6i %s %s\n", at+1, topOut.AtomMaskName(at).c_str(), *(topOut.Res(topOut[at].ResNum()).Name()));
+  // Build
+  Cpptraj::Structure::Builder structureBuilder;
+  structureBuilder.SetDebug( 1 ); // DEBUG FIXME
+  if (structureBuilder.GenerateInternals( mol1frm, mol1Top,
+                                          std::vector<bool>(mol1Top.Natom(), true) ))
+  {
+    mprinterr("Error: Generate internals for %s failed.\n", mol1Top.c_str());
+    return 1;
+  }
+  structureBuilder.UpdateIndicesWithOffset( atomOffset );
+  // Connect unit. Head atom of second unit comes first to match LEaP.
+  mprintf("\tConnect %s (%i) and %s (%i, original %s and %s)\n",
+          topOut.AtomMaskName(bondat1+atomOffset).c_str(), bondat1+atomOffset+1,
+          topOut.AtomMaskName(bondat0).c_str(), bondat0+1,
+          mol1Top.AtomMaskName(bondat1).c_str(),
+          mol0Top.AtomMaskName(bondat0).c_str());
+  topOut.AddBond( bondat1 + atomOffset, bondat0 );
+  // Generate internals around the link
+  if (structureBuilder.GenerateInternalsAroundLink( bondat1 + atomOffset,
+                                                    bondat0,
+                                                    frameOut, topOut, hasPosition ) )
+  {
+    mprinterr("Error: Assign torsions around graft bond atoms %s - %s failed.\n",
+              topOut.AtomMaskName(bondat1 + atomOffset).c_str(),
+              topOut.AtomMaskName(bondat0).c_str());
+    return 1;
+  }
+  // Convert to Zmatrix and assign missing atom positions
+  Cpptraj::Structure::Zmatrix tmpz;
+  tmpz.SetDebug( 1 ); // DEBUG
+  if (structureBuilder.GetZmatrixFromInternals(tmpz, topOut)) {
+    mprinterr("Error: Could not get Zmatrix from internals.\n");
+    return 1;
+  }
+  if (tmpz.SetToFrame( frameOut, hasPosition )) {
+    mprinterr("Error: Grafting %s with %s build from internals failed.\n",
+              mol0Top.c_str(), mol1Top.c_str());
+    return 1;
+  }
+  // Finalize topology - determine molecules, dont renumber residues, assign default bond params
+  topOut.CommonSetup(true, false, true);
+  topOut.Summary();
+  // Add to output data set
+  if (outCoords->CoordsSetup(topOut, frameOut.CoordsInfo())) return 1;
+  outCoords->AddFrame( frameOut );
+/*
   Topology combinedTop;
   combinedTop.SetDebug( debug_ );
   combinedTop.SetParmName( outCoords->Meta().Name(), FileName() );
@@ -318,7 +432,7 @@ const
   if (outCoords->CoordsSetup(combinedTop, CombinedFrame.CoordsInfo())) return 1;
 
   // Add frame to the output data set
-  outCoords->AddFrame( CombinedFrame );
+  outCoords->AddFrame( CombinedFrame );*/
 
   return 0;
 }
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 8ee99a7068..87b530f95e 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -312,7 +312,7 @@ Exec_Emin.o : Exec_Emin.cpp Action.h ActionList.h ActionState.h Analysis.h Analy
 Exec_ExtendedComparison.o : Exec_ExtendedComparison.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ExtendedComparison.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Flatten.o : Exec_Flatten.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Flatten.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_GenerateAmberRst.o : Exec_GenerateAmberRst.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_GenerateAmberRst.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Graft.o : Exec_Graft.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Graft.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Graft.o : Exec_Graft.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Graft.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Help.o : Exec_Help.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Help.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_HmassRepartition.o : Exec_HmassRepartition.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_HmassRepartition.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_LoadCrd.o : Exec_LoadCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_LoadCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
@@ -334,7 +334,7 @@ Exec_ReadInput.o : Exec_ReadInput.cpp Action.h ActionList.h ActionState.h Analys
 Exec_RotateDihedral.o : Exec_RotateDihedral.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_RotateDihedral.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_RunAnalysis.o : Exec_RunAnalysis.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_RunAnalysis.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_ScaleDihedralK.o : Exec_ScaleDihedralK.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ScaleDihedralK.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Sequence.o : Exec_Sequence.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Sequence.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Sequence.o : Exec_Sequence.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Sequence.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_SequenceAlign.o : Exec_SequenceAlign.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SequenceAlign.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Set.o : Exec_Set.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_StringVar.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Set.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Show.o : Exec_Show.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_StringVar.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Show.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
@@ -459,7 +459,7 @@ Structure/Sugar.o : Structure/Sugar.cpp Atom.h AtomMask.h AtomType.h Box.h Const
 Structure/SugarBuilder.o : Structure/SugarBuilder.cpp ArgList.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DistRoutines.h FileIO.h FileName.h Frame.h ImageOption.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/FunctionalGroup.h Structure/FxnGroupBuilder.h Structure/LinkAtom.h Structure/ResStatArray.h Structure/StructureEnum.h Structure/StructureRoutines.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarLinkAtoms.h Structure/SugarToken.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 Structure/SugarLinkAtoms.o : Structure/SugarLinkAtoms.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/LinkAtom.h Structure/SugarLinkAtoms.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/SugarToken.o : Structure/SugarToken.cpp ArgList.h CpptrajStdio.h Structure/SugarToken.h
-Structure/Zmatrix.o : Structure/Zmatrix.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Structure/Zmatrix.o : Structure/Zmatrix.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 StructureCheck.o : StructureCheck.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h ExclusionArray.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StructureCheck.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 StructureMapper.o : StructureMapper.cpp AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StructureMapper.h SymbolExporting.h TextFormat.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 SymmetricRmsdCalc.o : SymmetricRmsdCalc.cpp ArrayIterator.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h Hungarian.h ImageOption.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h Topology.h TypeNameHolder.h Unit.h Vec3.h

From 6953052c739f92c0cabd0560a9c064550576ed3b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 12 Feb 2024 09:01:45 -0500
Subject: [PATCH 0499/1492] Comment out unused code

---
 src/Structure/Builder.cpp | 410 +++++++++++++++++++-------------------
 src/Structure/Builder.h   |  26 +--
 2 files changed, 218 insertions(+), 218 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 26d6940071..0daf80510d 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -56,23 +56,6 @@ const
   return 0;
 }
 
-/** Assign reasonable value for bond distance. */
-int Cpptraj::Structure::Builder::AssignLength(double& dist, int ai, int aj, Topology const& topIn, Frame const& frameIn, Barray const& atomPositionKnown)
-const
-{
-  if (atomPositionKnown[ai] && atomPositionKnown[aj]) {
-    dist = sqrt( DIST2_NoImage( frameIn.XYZ(ai), frameIn.XYZ(aj) ) );
-    return 0;
-  }
-
-  // One or both positions unknown. Use estimated bond length or parameters.
-  if (getLengthParam(dist, ai, aj, topIn)) return 0;
-
-  // Default to bond length based on elements
-  dist = Atom::GetBondLength( topIn[ai].Element(), topIn[aj].Element() );
-  return 0;
-}
-
 /** Get angle parameter if present.
   * \return 1 if parameter found.
   */
@@ -103,10 +86,27 @@ const
 }
 
 // -----------------------------------------------------------------------------
+/** Assign reasonable value for bond distance. */
+/*int Cpptraj::Structure::Builder::AssignLength(double& dist, int ai, int aj, Topology const& topIn, Frame const& frameIn, Barray const& atomPositionKnown)
+const
+{
+  if (atomPositionKnown[ai] && atomPositionKnown[aj]) {
+    dist = sqrt( DIST2_NoImage( frameIn.XYZ(ai), frameIn.XYZ(aj) ) );
+    return 0;
+  }
+
+  // One or both positions unknown. Use estimated bond length or parameters.
+  if (getLengthParam(dist, ai, aj, topIn)) return 0;
+
+  // Default to bond length based on elements
+  dist = Atom::GetBondLength( topIn[ai].Element(), topIn[aj].Element() );
+  return 0;
+}*/
+
 /** Attempt to assign a reasonable value for theta internal coordinate for
   * atom i given that atoms j and k have known positions.
   */
-int Cpptraj::Structure::Builder::AssignTheta(double& theta, int ai, int aj, int ak, Topology const& topIn, Frame const& frameIn, Barray const& atomPositionKnown)
+/*int Cpptraj::Structure::Builder::AssignTheta(double& theta, int ai, int aj, int ak, Topology const& topIn, Frame const& frameIn, Barray const& atomPositionKnown)
 const
 {
   if (debug_ > 0)
@@ -151,20 +151,20 @@ const
                   ajTheta * Constants::RADDEG);
          } else {
            mprinterr("Internal Error: Implement angle lookup.\n");
-        /*} else if (currentZmatrix_ != 0) { // FIXME faster search?
-          for (Zmatrix::const_iterator ic = currentZmatrix_->begin(); ic != currentZmatrix_->end(); ++ic) {
-            if (ic->AtI() == atomi && ic->AtJ() == aj && ic->AtK() == atomk) {
-              // TODO: Check that repeats are equal?
-              ajTheta = ic->Theta() * Constants::DEGRAD;
-              numKnown++;
-              mprintf("DEBUG: AssignTheta(): IC angle centered on atomJ: %s - %s - %s = %g\n",
-                      topIn.LeapName(atomi).c_str(), 
-                      topIn.LeapName(aj).c_str(), 
-                      topIn.LeapName(atomk).c_str(),
-                      ic->Theta());
-              break;
-            }
-          }*/
+        //} else if (currentZmatrix_ != 0) { // FIXME faster search?
+        //  for (Zmatrix::const_iterator ic = currentZmatrix_->begin(); ic != currentZmatrix_->end(); ++ic) {
+        //    if (ic->AtI() == atomi && ic->AtJ() == aj && ic->AtK() == atomk) {
+        //      // TODO: Check that repeats are equal?
+        //      ajTheta = ic->Theta() * Constants::DEGRAD;
+        //      numKnown++;
+        //      mprintf("DEBUG: AssignTheta(): IC angle centered on atomJ: %s - %s - %s = %g\n",
+        //              topIn.LeapName(atomi).c_str(), 
+        //              topIn.LeapName(aj).c_str(), 
+        //              topIn.LeapName(atomk).c_str(),
+        //              ic->Theta());
+        //      break;
+        //    }
+        //  }
         }
         thetaVals.push_back( ajTheta );
       } // END inner loop over bonds to AJ
@@ -231,10 +231,10 @@ const
   }
 
   return 0;
-}
+}*/
 
 /** Calculate internal coordinate for atoms i j k l with known positions. */
-Cpptraj::Structure::InternalCoords Builder::calcKnownAtomIc(int ai, int aj, int ak, int al, Frame const& frameIn)
+/*Cpptraj::Structure::InternalCoords Builder::calcKnownAtomIc(int ai, int aj, int ak, int al, Frame const& frameIn)
 {
   double newDist = DIST2_NoImage(frameIn.XYZ(ai), frameIn.XYZ(aj));
 
@@ -245,10 +245,10 @@ Cpptraj::Structure::InternalCoords Builder::calcKnownAtomIc(int ai, int aj, int
                            frameIn.XYZ(ak),
                            frameIn.XYZ(al) );
   return InternalCoords(ai, aj, ak, al, newDist, newTheta*Constants::RADDEG, newPhi*Constants::RADDEG);
-}
+}*/
 
 /** Insert internal coordinates with bond i-j, angle i-j-k, and torsion i-j-k-l. */
-int Cpptraj::Structure::Builder::insertIc(Zmatrix& zmatrix,
+/*int Cpptraj::Structure::Builder::insertIc(Zmatrix& zmatrix,
                                         int ai, int aj, int ak, int al, double newPhi,
                                         Topology const& topIn, Frame const& frameIn,
                                         Barray const& atomPositionKnown)
@@ -274,10 +274,10 @@ const
   }
   zmatrix.AddIC( InternalCoords(ai, aj, ak, al, newDist, newTheta*Constants::RADDEG, newPhi*Constants::RADDEG) );
   return 0;
-}
+}*/
 
 /// Recursive function to return depth from an atom along bonds
-static int atom_depth(int& depth,
+/*static int atom_depth(int& depth,
                       int at, Topology const& topIn, std::vector<bool>& visited, int maxdepth)
 {
   if (depth == maxdepth) return 0;
@@ -290,20 +290,20 @@ static int atom_depth(int& depth,
       depthFromHere += atom_depth( depth, *bat, topIn, visited, maxdepth );
   }
   return depthFromHere;
-}
+}*/
 
 /// Wrap given value between -PI and PI
-static inline double wrap360(double phi) {
+/*static inline double wrap360(double phi) {
   if (phi > Constants::PI)
     return phi - Constants::TWOPI;
   else if (phi < -Constants::PI)
     return phi + Constants::TWOPI;
   else
     return phi;
-}
+}*/
 
 /** Assign internal coordinates for atoms I for torsions around J-K-L. */
-int Cpptraj::Structure::Builder::AssignICsAroundBond(Zmatrix& zmatrix,
+/*int Cpptraj::Structure::Builder::AssignICsAroundBond(Zmatrix& zmatrix,
                                                    int aj, int ak, int al,
                                                    Topology const& topIn, Frame const& frameIn,
                                                    Barray const& atomPositionKnown,
@@ -548,11 +548,11 @@ const
   }
 
   return 0;
-}
+}*/
 
 // -----------------------------------------------------------------------------
 /** Combine two units. Fragment 1 will be merged into Fragment 0 and bonded. */
-int Builder::Combine(Topology&       frag0Top, Frame&       frag0frm,
+/*int Builder::Combine(Topology&       frag0Top, Frame&       frag0frm,
                      Topology const& frag1Top, Frame const& frag1frm,
                      int bondAt0, int bondAt1)
 const
@@ -664,7 +664,7 @@ const
   }
 
   return 0;
-}
+}*/
 
 /// \return The total number of atoms whose position is known for the specified residue
 /*static inline int known_count(int ires, Topology const& topIn, std::vector<bool> const& hasPosition)
@@ -680,7 +680,7 @@ const
   * by bondAt0 (in residue0) and bondAt1 in (residue1).
   *
   */
-int Builder::ModelCoordsAroundBond(Frame const& frameIn, Topology const& topIn, int bondAt0, int bondAt1,
+/*int Builder::ModelCoordsAroundBond(Frame const& frameIn, Topology const& topIn, int bondAt0, int bondAt1,
                                    Zmatrix& zmatrix0, Barray const& hasPosition)
 const
 {
@@ -773,7 +773,7 @@ const
 //  }
 
   return 0;
-}
+}*/
 
 /** Given two bonded atoms A and B, where B has a depth of at least 2
   * (i.e., it is possible to have B be atom J where we can form J-K-L),
@@ -781,7 +781,7 @@ const
   * direction of atom A. This means all internal coordinates with A and B
   * as I and J (should be only 1), as J and K, and as K and L.
   */
-int Builder::SetupICsAroundBond(Zmatrix& zmatrix,
+/*int Builder::SetupICsAroundBond(Zmatrix& zmatrix,
                                 int atA, int atB, Frame const& frameIn, Topology const& topIn,
                                 Barray const& atomPositionKnown,
                                 Barray const& hasICin,
@@ -916,166 +916,166 @@ const
   mprintf("DEBUG: END AssignICsAroundBond ------------------------\n");
   // FIXME
   // ---- I J: Set dist, theta, phi for atA atB K L internal coord ---
-/*  if (debug_ > 0)
-    mprintf("DEBUG: IC (i j) %i - %i - %i - %i\n", atA+1, atB+1, atk0+1, atl0+1);
-  double newDist = 0;
-  if (model.AssignLength(newDist, atA, atB, topIn, frameIn, atomPositionKnown)) {
-    mprinterr("Error: length (i j) assignment failed.\n");
-    return 1;
-  }
-  if (debug_ > 0) mprintf("DEBUG:\t\tnewDist= %g\n", newDist);
-  double newTheta = 0;
-  if (model.AssignTheta(newTheta, atA, atB, atk0, topIn, frameIn, atomPositionKnown)) {
-    mprinterr("Error: theta (i j) assignment failed.\n");
-    return 1;
-  }
-  if (debug_ > 0) mprintf("DEBUG:\t\tnewTheta = %g\n", newTheta*Constants::RADDEG);
-  double newPhi = 0;
-  if (model.AssignPhi(newPhi, atA, atB, atk0, atl0, topIn, frameIn,
-                                           atomPositionKnown, AtomB))
-  {
-    mprinterr("Error: phi (i j) assignment failed.\n");
-    return 1;
-  }
-  if (debug_ > 0) mprintf("DEBUG:\t\tnewPhi = %g\n", newPhi*Constants::RADDEG);
-  IC_.push_back(InternalCoords( atA, atB, atk0, atl0, newDist, newTheta*Constants::RADDEG, newPhi*Constants::RADDEG ));
-  if (debug_ > 0) {
-    mprintf("DEBUG: MODEL I J IC: ");
-    IC_.back().printIC(topIn);
-  }
-  MARK( atA, hasIC, nHasIC );*/
-/*
-  // ----- J K: Set up ICs for X atA atB K ---------------------------
-  Atom const& AJ1 = topIn[atA];
-  int ati = -1;
-  //Atom const& AK1 = topIn[atB];
-  //Atom const& AL1 = topIn[atk0];
-  for (Atom::bond_iterator iat = AJ1.bondbegin(); iat != AJ1.bondend(); ++iat)
-  {
-    if (*iat != atB) {
-      if (ati == -1) ati = *iat;
-/      // Set bond dist
-      if (model.AssignLength(newDist, *iat, atA, topIn, frameIn, atomPositionKnown)) {
-        mprinterr("Error: length (j k) assignment failed.\n");
-        return 1;
-      }
-      // Set theta for I atA atB
-      newTheta = 0;
-      if (model.AssignTheta(newTheta, *iat, atA, atB, topIn, frameIn, atomPositionKnown)) {
-        mprinterr("Error: theta (j k) assignment failed.\n");
-        return 1;
-      }
-      if (debug_ > 0)
-        mprintf("DEBUG:\t\tnewTheta = %g\n", newTheta*Constants::RADDEG);
-      // Set phi for I atA atB K
-      newPhi = 0;
-      if (model.AssignPhi(newPhi, *iat, atA, atB, atk0, topIn, frameIn,
-                                               atomPositionKnown, AtomA))
-      {
-        mprinterr("Error: phi (j k) assignment failed.\n");
-        return 1;
-      }
-      if (debug_ > 0)
-        mprintf("DEBUG:\t\tnewPhi = %g\n", newPhi*Constants::RADDEG);
-      IC_.push_back(InternalCoords( *iat, atA, atB, atk0, newDist, newTheta*Constants::RADDEG, newPhi*Constants::RADDEG ));
-      if (debug_ > 0) {
-        mprintf("DEBUG: MODEL J K IC: ");
-        IC_.back().printIC(topIn);
-      }
-      MARK( *iat, hasIC, nHasIC );
-      // ----- K L: Set up ICs for X iat atA atB ---------------------
-      Atom const& AJ2 = topIn[*iat];
-      for (Atom::bond_iterator i2at = AJ2.bondbegin(); i2at != AJ2.bondend(); ++i2at)
-      {
-        if (*i2at != atA && *i2at != atB && !hasIC[*i2at]) {
-          mprintf("DEBUG: MODEL K L IC: %s %s %s %s %i %i %i %i\n",
-                  topIn.AtomMaskName(*i2at).c_str(),
-                  topIn.AtomMaskName(*iat).c_str(),
-                  topIn.AtomMaskName(atA).c_str(),
-                  topIn.AtomMaskName(atB).c_str(),
-                  *i2at+1, *iat+1, atA+1, atB+1);
-          if (model.AssignLength(newDist, *i2at, *iat, topIn, frameIn, atomPositionKnown)) {
-            mprinterr("Error: length (k l) assignment failed.\n");
-            return 1;
-          }
-          mprintf("DEBUG: K L distance= %g\n", newDist);
-          //newTheta = CalcAngle( frameIn.XYZ(*i2at), frameIn.XYZ(*iat), frameIn.XYZ(atA) );
-          if (model.AssignTheta(newTheta, *iat, atA, atB, topIn, frameIn, atomPositionKnown)) {
-            mprinterr("Error: theta (k l) assignment failed.\n");
-            return 1;
-          }
-          mprintf("DEBUG: K L angle= %g\n", newTheta*Constants::RADDEG);
-          // Set phi for X iat atA atB
-          BuildAtom AtomC;
-          if (topIn[*iat].Nbonds() > 2) {
-            if (AtomC.DetermineChirality(*iat, topIn, frameIn, modelDebug)) return 1;
-          }
-          newPhi = 0;
-          //model.SetDebug( 1 ); // FIXME
-          if (model.AssignPhi(newPhi, *i2at, *iat, atA, atB, topIn, frameIn,
-                                                   atomPositionKnown, AtomC))
-          {
-            mprinterr("Error: phi (k l) assignment failed.\n");
-            return 1;
-          }
-          mprintf("DEBUG: K L Phi = %g\n", newPhi*Constants::RADDEG);
-          IC_.push_back(InternalCoords( *i2at, *iat, atA, atB, newDist, newTheta*Constants::RADDEG, newPhi*Constants::RADDEG ));
-          mprintf("DEBUG: MODEL K L IC: ");
-          IC_.back().printIC(topIn);
-          MARK( *i2at, hasIC, nHasIC );
-          // Trace from atA *iat *i2at outwards
-          //ToTrace.push_back(atA);
-          //ToTrace.push_back(*iat);
-          //ToTrace.push_back(*i2at);
-          //if (traceMol(atA, *iat, *i2at, frameIn, topIn, topIn.Natom(), nHasIC, hasIC)) return 1;
+//  if (debug_ > 0)
+//    mprintf("DEBUG: IC (i j) %i - %i - %i - %i\n", atA+1, atB+1, atk0+1, atl0+1);
+//  double newDist = 0;
+//  if (model.AssignLength(newDist, atA, atB, topIn, frameIn, atomPositionKnown)) {
+//    mprinterr("Error: length (i j) assignment failed.\n");
+//    return 1;
+//  }
+//  if (debug_ > 0) mprintf("DEBUG:\t\tnewDist= %g\n", newDist);
+//  double newTheta = 0;
+//  if (model.AssignTheta(newTheta, atA, atB, atk0, topIn, frameIn, atomPositionKnown)) {
+//    mprinterr("Error: theta (i j) assignment failed.\n");
+//    return 1;
+//  }
+//  if (debug_ > 0) mprintf("DEBUG:\t\tnewTheta = %g\n", newTheta*Constants::RADDEG);
+//  double newPhi = 0;
+//  if (model.AssignPhi(newPhi, atA, atB, atk0, atl0, topIn, frameIn,
+//                                           atomPositionKnown, AtomB))
+//  {
+//    mprinterr("Error: phi (i j) assignment failed.\n");
+//    return 1;
+//  }
+//  if (debug_ > 0) mprintf("DEBUG:\t\tnewPhi = %g\n", newPhi*Constants::RADDEG);
+//  IC_.push_back(InternalCoords( atA, atB, atk0, atl0, newDist, newTheta*Constants::RADDEG, newPhi*Constants::RADDEG ));
+//  if (debug_ > 0) {
+//    mprintf("DEBUG: MODEL I J IC: ");
+//    IC_.back().printIC(topIn);
+//  }
+//  MARK( atA, hasIC, nHasIC );
+//
+//  // ----- J K: Set up ICs for X atA atB K ---------------------------
+//  Atom const& AJ1 = topIn[atA];
+//  int ati = -1;
+//  //Atom const& AK1 = topIn[atB];
+//  //Atom const& AL1 = topIn[atk0];
+//  for (Atom::bond_iterator iat = AJ1.bondbegin(); iat != AJ1.bondend(); ++iat)
+//  {
+//    if (*iat != atB) {
+//      if (ati == -1) ati = *iat;
+//      // Set bond dist
+//      if (model.AssignLength(newDist, *iat, atA, topIn, frameIn, atomPositionKnown)) {
+//        mprinterr("Error: length (j k) assignment failed.\n");
+//        return 1;
+//      }
+//      // Set theta for I atA atB
+//      newTheta = 0;
+//      if (model.AssignTheta(newTheta, *iat, atA, atB, topIn, frameIn, atomPositionKnown)) {
+//        mprinterr("Error: theta (j k) assignment failed.\n");
+//        return 1;
+//      }
+//      if (debug_ > 0)
+//        mprintf("DEBUG:\t\tnewTheta = %g\n", newTheta*Constants::RADDEG);
+//      // Set phi for I atA atB K
+//      newPhi = 0;
+//      if (model.AssignPhi(newPhi, *iat, atA, atB, atk0, topIn, frameIn,
+//                                               atomPositionKnown, AtomA))
+//      {
+//        mprinterr("Error: phi (j k) assignment failed.\n");
+//        return 1;
+//      }
+//      if (debug_ > 0)
+//        mprintf("DEBUG:\t\tnewPhi = %g\n", newPhi*Constants::RADDEG);
+//      IC_.push_back(InternalCoords( *iat, atA, atB, atk0, newDist, newTheta*Constants::RADDEG, newPhi*Constants::RADDEG ));
+//      if (debug_ > 0) {
+//        mprintf("DEBUG: MODEL J K IC: ");
+//        IC_.back().printIC(topIn);
+//      }
+//      MARK( *iat, hasIC, nHasIC );
+//      // ----- K L: Set up ICs for X iat atA atB ---------------------
+//      Atom const& AJ2 = topIn[*iat];
+//      for (Atom::bond_iterator i2at = AJ2.bondbegin(); i2at != AJ2.bondend(); ++i2at)
+//      {
+//        if (*i2at != atA && *i2at != atB && !hasIC[*i2at]) {
+//          mprintf("DEBUG: MODEL K L IC: %s %s %s %s %i %i %i %i\n",
+//                  topIn.AtomMaskName(*i2at).c_str(),
+//                  topIn.AtomMaskName(*iat).c_str(),
+//                  topIn.AtomMaskName(atA).c_str(),
+//                  topIn.AtomMaskName(atB).c_str(),
+//                  *i2at+1, *iat+1, atA+1, atB+1);
+//          if (model.AssignLength(newDist, *i2at, *iat, topIn, frameIn, atomPositionKnown)) {
+//            mprinterr("Error: length (k l) assignment failed.\n");
+//            return 1;
+//          }
+//          mprintf("DEBUG: K L distance= %g\n", newDist);
+//          //newTheta = CalcAngle( frameIn.XYZ(*i2at), frameIn.XYZ(*iat), frameIn.XYZ(atA) );
+//          if (model.AssignTheta(newTheta, *iat, atA, atB, topIn, frameIn, atomPositionKnown)) {
+//            mprinterr("Error: theta (k l) assignment failed.\n");
+//            return 1;
+//          }
+//          mprintf("DEBUG: K L angle= %g\n", newTheta*Constants::RADDEG);
+//          // Set phi for X iat atA atB
+//          BuildAtom AtomC;
+//          if (topIn[*iat].Nbonds() > 2) {
+//            if (AtomC.DetermineChirality(*iat, topIn, frameIn, modelDebug)) return 1;
+//          }
+//          newPhi = 0;
+//          //model.SetDebug( 1 ); // FIXME
+//          if (model.AssignPhi(newPhi, *i2at, *iat, atA, atB, topIn, frameIn,
+//                                                   atomPositionKnown, AtomC))
+//          {
+//            mprinterr("Error: phi (k l) assignment failed.\n");
+//            return 1;
+//          }
+//          mprintf("DEBUG: K L Phi = %g\n", newPhi*Constants::RADDEG);
+//          IC_.push_back(InternalCoords( *i2at, *iat, atA, atB, newDist, newTheta*Constants::RADDEG, newPhi*Constants::RADDEG ));
+//          mprintf("DEBUG: MODEL K L IC: ");
+//          IC_.back().printIC(topIn);
+//          MARK( *i2at, hasIC, nHasIC );
+//          // Trace from atA *iat *i2at outwards
+//          //ToTrace.push_back(atA);
+//          //ToTrace.push_back(*iat);
+//          //ToTrace.push_back(*i2at);
+//          //if (traceMol(atA, *iat, *i2at, frameIn, topIn, topIn.Natom(), nHasIC, hasIC)) return 1;
+//
+//        }
+//      } 
+//    }
+//  }
 
-        }
-      } 
-    }
-  }
-*/
 
-/*
-  // Handle remaining atoms.
-  if (AJ1.Nbonds() > 1) {
-    if (AJ1.Nbonds() == 2) {
-      if (debug_ > 0) mprintf("DEBUG: 2 bonds to %s.\n", topIn.AtomMaskName(atA).c_str());
-      if (traceMol(atB, atA, ati, frameIn, topIn, topIn.Natom(), nHasIC, hasIC))
-        return 1;
-    } else {
-      // 3 or more bonds
-      std::vector<int> const& priority = AtomA.Priority();
-      int at0 = -1;
-      int at1 = -1;
-      std::vector<int> remainingAtoms;
-      if (debug_ > 0) mprintf("DEBUG: %i bonds to %s\n", AJ1.Nbonds(), topIn.AtomMaskName(atA).c_str());
-      for (std::vector<int>::const_iterator it = priority.begin(); it != priority.end(); ++it) {
-        if (*it != atB) {
-          if (debug_ > 0) mprintf("DEBUG:\t\t%s\n", topIn.AtomMaskName(*it).c_str());
-          if (at0 == -1)
-            at0 = *it;
-          else if (at1 == -1)
-            at1 = *it;
-          else
-            remainingAtoms.push_back( *it );
-        }
-      }
-      // at0 atA at1
-      if (traceMol(at1, atA, at0, frameIn, topIn, topIn.Natom(), nHasIC, hasIC))
-        return 1;
-      // at1 atA, at0
-      if (traceMol(at0, atA, at1, frameIn, topIn, topIn.Natom(), nHasIC, hasIC))
-        return 1;
-      // Remaining atoms.
-      for (std::vector<int>::const_iterator it = remainingAtoms.begin(); it != remainingAtoms.end(); ++it) {
-        if (traceMol(at0, atA, *it, frameIn, topIn, topIn.Natom(), nHasIC, hasIC))
-          return 1;
-      }
-    }
-  }
-*/
+//
+//// Handle remaining atoms.
+//if (AJ1.Nbonds() > 1) {
+//  if (AJ1.Nbonds() == 2) {
+//    if (debug_ > 0) mprintf("DEBUG: 2 bonds to %s.\n", topIn.AtomMaskName(atA).c_str());
+//    if (traceMol(atB, atA, ati, frameIn, topIn, topIn.Natom(), nHasIC, hasIC))
+//      return 1;
+//  } else {
+//    // 3 or more bonds
+//    std::vector<int> const& priority = AtomA.Priority();
+//    int at0 = -1;
+//    int at1 = -1;
+//    std::vector<int> remainingAtoms;
+//    if (debug_ > 0) mprintf("DEBUG: %i bonds to %s\n", AJ1.Nbonds(), topIn.AtomMaskName(atA).c_str());
+//    for (std::vector<int>::const_iterator it = priority.begin(); it != priority.end(); ++it) {
+//      if (*it != atB) {
+//        if (debug_ > 0) mprintf("DEBUG:\t\t%s\n", topIn.AtomMaskName(*it).c_str());
+//        if (at0 == -1)
+//          at0 = *it;
+//        else if (at1 == -1)
+//          at1 = *it;
+//        else
+//          remainingAtoms.push_back( *it );
+//      }
+//    }
+//    // at0 atA at1
+//    if (traceMol(at1, atA, at0, frameIn, topIn, topIn.Natom(), nHasIC, hasIC))
+//      return 1;
+//    // at1 atA, at0
+//    if (traceMol(at0, atA, at1, frameIn, topIn, topIn.Natom(), nHasIC, hasIC))
+//      return 1;
+//    // Remaining atoms.
+//    for (std::vector<int>::const_iterator it = remainingAtoms.begin(); it != remainingAtoms.end(); ++it) {
+//      if (traceMol(at0, atA, *it, frameIn, topIn, topIn.Natom(), nHasIC, hasIC))
+//        return 1;
+//    }
+//  }
+//}
+//
   return 0;
-}
+}*/
 
 // ==============================================================================
 /** For existing torsions, see if all coordinates in that torsion
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index 6493737708..a168684f17 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -23,9 +23,9 @@ class Builder {
     void SetParameters(ParameterSet const*);
 
     /// Combine second fragment into first fragment and bond
-    int Combine(Topology&, Frame&, Topology const&, Frame const&, int, int) const;
+//    int Combine(Topology&, Frame&, Topology const&, Frame const&, int, int) const;
     /// Model the coordinates around a bond given only some coordinates are known
-    int ModelCoordsAroundBond(Frame const&, Topology const&, int, int, Zmatrix&, Barray const&) const;
+//    int ModelCoordsAroundBond(Frame const&, Topology const&, int, int, Zmatrix&, Barray const&) const;
 
 
     /// Update the internal coordinates in given Zmatrix with values from Frame/Parameters
@@ -64,23 +64,23 @@ class Builder {
 
     // ===========================================
     /// Assign a reasonable value for bond distance given 2 atoms whose position may or may not be known
-    int AssignLength(double&, int, int, Topology const&, Frame const&, Barray const&) const;
+//    int AssignLength(double&, int, int, Topology const&, Frame const&, Barray const&) const;
     /// Given atoms J and K, attempt to assign a reasonable value for theta for atom I
-    int AssignTheta(double&, int, int, int, Topology const&, Frame const&, Barray const&) const;
+//    int AssignTheta(double&, int, int, int, Topology const&, Frame const&, Barray const&) const;
     /// Calculate an internal coordinate for known atoms
-    static inline InternalCoords calcKnownAtomIc(int, int, int, int, Frame const&);
+//    static inline InternalCoords calcKnownAtomIc(int, int, int, int, Frame const&);
     /// Insert an internal coord into a zmatrix
-    int insertIc(Zmatrix&, int, int, int, int, double,
-                 Topology const&, Frame const&, Barray const&) const;
+//    int insertIc(Zmatrix&, int, int, int, int, double,
+//                 Topology const&, Frame const&, Barray const&) const;
     /// Assign internal coordinates for atoms I for torsions around J-K-L.
-    int AssignICsAroundBond(Zmatrix&, int, int, int,
-                           Topology const&, Frame const&, Barray const&,
-                           BuildAtom const&) const;
+//    int AssignICsAroundBond(Zmatrix&, int, int, int,
+//                           Topology const&, Frame const&, Barray const&,
+//                           BuildAtom const&) const;
 
     /// Model coordinates around a bond
-    int SetupICsAroundBond(Zmatrix&, int, int, Frame const&, Topology const&,
-                           Barray const&, Barray const&,
-                           BuildAtom const&, BuildAtom const&) const;
+//    int SetupICsAroundBond(Zmatrix&, int, int, Frame const&, Topology const&,
+//                           Barray const&, Barray const&,
+//                           BuildAtom const&, BuildAtom const&) const;
     // ===========================================
     /// Calculte phi value for a torsion in a TorsionModel
     void ModelTorsion(TorsionModel const&, unsigned int, unsigned int, double);

From ff13e3ae36d5c5efa7633d9f0ae0cb4caaffaa4c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 12 Feb 2024 09:08:12 -0500
Subject: [PATCH 0500/1492] Get rid of old code

---
 src/Structure/Builder.cpp     | 998 +---------------------------------
 src/Structure/Builder.h       |  30 +-
 src/Structure/structuredepend |   4 +-
 src/cpptrajdepend             |   2 +-
 4 files changed, 6 insertions(+), 1028 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 0daf80510d..06c639abfc 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1,5 +1,4 @@
 #include "Builder.h"
-#include "BuildAtom.h"
 #include "GenerateConnectivityArrays.h"
 #include "Zmatrix.h"
 #include "../Constants.h"
@@ -32,7 +31,6 @@ void Cpptraj::Structure::Builder::SetParameters(ParameterSet const* paramsIn) {
   params_ = paramsIn;
 }
 
-// -----------------------------------------------------------------------------
 /** Get length from parameter set if present.
   * \return 1 if a length parameter was found.
   */
@@ -85,999 +83,6 @@ const
   return 0;
 }
 
-// -----------------------------------------------------------------------------
-/** Assign reasonable value for bond distance. */
-/*int Cpptraj::Structure::Builder::AssignLength(double& dist, int ai, int aj, Topology const& topIn, Frame const& frameIn, Barray const& atomPositionKnown)
-const
-{
-  if (atomPositionKnown[ai] && atomPositionKnown[aj]) {
-    dist = sqrt( DIST2_NoImage( frameIn.XYZ(ai), frameIn.XYZ(aj) ) );
-    return 0;
-  }
-
-  // One or both positions unknown. Use estimated bond length or parameters.
-  if (getLengthParam(dist, ai, aj, topIn)) return 0;
-
-  // Default to bond length based on elements
-  dist = Atom::GetBondLength( topIn[ai].Element(), topIn[aj].Element() );
-  return 0;
-}*/
-
-/** Attempt to assign a reasonable value for theta internal coordinate for
-  * atom i given that atoms j and k have known positions.
-  */
-/*int Cpptraj::Structure::Builder::AssignTheta(double& theta, int ai, int aj, int ak, Topology const& topIn, Frame const& frameIn, Barray const& atomPositionKnown)
-const
-{
-  if (debug_ > 0)
-    mprintf("DEBUG: AssignTheta for atom j : %s\n", topIn.AtomMaskName(aj).c_str());
-  Atom const& AJ = topIn[aj];
-
-  // Sanity check
-  if (AJ.Nbonds() < 2) {
-    mprinterr("Internal Error: AssignTheta() called for atom J %s with fewer than 2 bonds.\n", topIn.AtomMaskName(aj).c_str());
-    return 1;
-  }
-
-  // Check if all positions are already known
-  if (atomPositionKnown[ai] && atomPositionKnown[aj] && atomPositionKnown[ak])
-  {
-    theta = CalcAngle(frameIn.XYZ(ai), frameIn.XYZ(aj), frameIn.XYZ(ak));
-    return 0;
-  }
-
-  // Figure out angles from known atoms + ICs
-  int nAngles = (AJ.Nbonds() * (AJ.Nbonds()-1)) / 2;
-  if (nAngles == 3) {
-    mprintf("DEBUG: Expect %i angles around AJ.\n", nAngles);
-    std::vector<double> thetaVals;
-    int tgtIdx = -1;
-    int numKnown = 0;
-    for (int idx0 = 0; idx0 < AJ.Nbonds(); idx0++) {
-      int atomi = AJ.Bond(idx0);
-      for (int idx1 = idx0 + 1; idx1 < AJ.Nbonds(); idx1++) {
-        int atomk = AJ.Bond(idx1);
-        mprintf("DEBUG: AssignTheta(): Angle %zu atoms %i - %i - %i\n", thetaVals.size(), atomi+1, aj+1, atomk+1);
-        if (ai == atomi && ak == atomk)
-          tgtIdx = (int)thetaVals.size();
-        double ajTheta = 0;
-        if (atomPositionKnown[atomi] && atomPositionKnown[aj] && atomPositionKnown[atomk]) {
-          ajTheta = CalcAngle(frameIn.XYZ(atomi), frameIn.XYZ(aj), frameIn.XYZ(atomk));
-          numKnown++;
-          mprintf("DEBUG: AssignTheta(): Known angle centered on atom J: %s - %s - %s = %g\n",
-                  topIn.LeapName(atomi).c_str(), 
-                  topIn.LeapName(aj).c_str(), 
-                  topIn.LeapName(atomk).c_str(),
-                  ajTheta * Constants::RADDEG);
-         } else {
-           mprinterr("Internal Error: Implement angle lookup.\n");
-        //} else if (currentZmatrix_ != 0) { // FIXME faster search?
-        //  for (Zmatrix::const_iterator ic = currentZmatrix_->begin(); ic != currentZmatrix_->end(); ++ic) {
-        //    if (ic->AtI() == atomi && ic->AtJ() == aj && ic->AtK() == atomk) {
-        //      // TODO: Check that repeats are equal?
-        //      ajTheta = ic->Theta() * Constants::DEGRAD;
-        //      numKnown++;
-        //      mprintf("DEBUG: AssignTheta(): IC angle centered on atomJ: %s - %s - %s = %g\n",
-        //              topIn.LeapName(atomi).c_str(), 
-        //              topIn.LeapName(aj).c_str(), 
-        //              topIn.LeapName(atomk).c_str(),
-        //              ic->Theta());
-        //      break;
-        //    }
-        //  }
-        }
-        thetaVals.push_back( ajTheta );
-      } // END inner loop over bonds to AJ
-    } // END outer loop over bonds to AJ
-    mprintf("DEBUG: AssignTheta(): thetaVals=");
-    for (std::vector<double>::const_iterator it = thetaVals.begin(); it != thetaVals.end(); ++it) {
-      mprintf(" %g", *it * Constants::RADDEG);
-      if (tgtIdx == it - thetaVals.begin()) mprintf("*");
-    }
-    mprintf("\n");
-    if (tgtIdx != -1 && numKnown >= 2) {
-      double sumTheta = 0;
-      for (std::vector<double>::const_iterator it = thetaVals.begin(); it != thetaVals.end(); ++it) {
-        if (it - thetaVals.begin() != tgtIdx) {
-          double tval = *it;
-          if (tval < 0)
-            tval += Constants::TWOPI;
-          else if (tval > Constants::TWOPI)
-            tval -= Constants::TWOPI;
-          sumTheta += tval;
-        }
-      }
-      theta = Constants::TWOPI - sumTheta;
-      mprintf("DEBUG: AssignTheta(): Setting from existing atoms/ICs: %g\n", theta * Constants::RADDEG);
-      return 0;
-    }
-  }
-
-  // See if a parameter is defined for these atom types
-  if (getAngleParam(theta, ai, aj, ak, topIn)) return 0;
-
-  // Figure out hybridization and chirality of atom j.
-  if (debug_ > 0) {
-    mprintf("DEBUG:\t\tI %s Nbonds: %i\n", topIn[ai].ElementName(), topIn[ai].Nbonds());
-    mprintf("DEBUG:\t\tJ %s Nbonds: %i\n", AJ.ElementName(), AJ.Nbonds());
-    mprintf("DEBUG:\t\tK %s Nbonds: %i\n", topIn[ak].ElementName(), topIn[ak].Nbonds());
-  }
-  AtomType::HybridizationType hybrid = AtomType::UNKNOWN_HYBRIDIZATION;
-  // Check params for hybrid
-  if (params_ != 0) {
-    ParmHolder<AtomType>::const_iterator it = params_->AT().GetParam( TypeNameHolder(AJ.Type()) );
-    if (it != params_->AT().end())
-      hybrid = it->second.Hybridization();
-  }
-  // Guess hybrid if needed
-  if (hybrid == AtomType::UNKNOWN_HYBRIDIZATION)
-    hybrid = GuessAtomHybridization(AJ, topIn.Atoms());
-  // Set from number of bonds if still unknown. This is a pretty crude guess.
-  if (hybrid == AtomType::UNKNOWN_HYBRIDIZATION) {
-    switch (AJ.Nbonds()) {
-      case 4 : hybrid = AtomType::SP3; break;
-      case 3 : hybrid = AtomType::SP2; break;
-      case 2 : hybrid = AtomType::SP; break;
-      default : mprinterr("Internal Error: AssignTheta(): Unhandled # bonds for %s (%i)\n", topIn.AtomMaskName(aj).c_str(), AJ.Nbonds()); return 1;
-    }
-  }
-
-  // Assign a theta based on hybridization
-  switch (hybrid) {
-    case AtomType::SP3 : theta = 109.5 * Constants::DEGRAD; break;
-    case AtomType::SP2 : theta = 120.0 * Constants::DEGRAD; break;
-    case AtomType::SP  : theta = 180.0 * Constants::DEGRAD; break;
-    default : mprinterr("Internal Error: AssignTheta(): Unhandled hybridization for %s (%i)\n", topIn.AtomMaskName(aj).c_str(), AJ.Nbonds()); return 1;
-  }
-
-  return 0;
-}*/
-
-/** Calculate internal coordinate for atoms i j k l with known positions. */
-/*Cpptraj::Structure::InternalCoords Builder::calcKnownAtomIc(int ai, int aj, int ak, int al, Frame const& frameIn)
-{
-  double newDist = DIST2_NoImage(frameIn.XYZ(ai), frameIn.XYZ(aj));
-
-  double newTheta = CalcAngle( frameIn.XYZ(ai), frameIn.XYZ(aj), frameIn.XYZ(ak) );
-
-  double newPhi = Torsion( frameIn.XYZ(ai),
-                           frameIn.XYZ(aj),
-                           frameIn.XYZ(ak),
-                           frameIn.XYZ(al) );
-  return InternalCoords(ai, aj, ak, al, newDist, newTheta*Constants::RADDEG, newPhi*Constants::RADDEG);
-}*/
-
-/** Insert internal coordinates with bond i-j, angle i-j-k, and torsion i-j-k-l. */
-/*int Cpptraj::Structure::Builder::insertIc(Zmatrix& zmatrix,
-                                        int ai, int aj, int ak, int al, double newPhi,
-                                        Topology const& topIn, Frame const& frameIn,
-                                        Barray const& atomPositionKnown)
-const
-{
-  if (atomPositionKnown[ai]) {
-    mprintf("DEBUG:\tAtom position already known for %s, skipping IC.\n", topIn.AtomMaskName(ai).c_str());
-    return 0;
-  }
-  double newDist = 0;
-  if (AssignLength(newDist, ai, aj, topIn, frameIn, atomPositionKnown)) {
-    mprinterr("Error: AssignLength failed for %s - %s \n",
-              topIn.AtomMaskName(ai).c_str(), topIn.AtomMaskName(aj).c_str());
-    return 1;
-  }
-  double newTheta = 0;
-  if (AssignTheta(newTheta, ai, aj, ak, topIn, frameIn, atomPositionKnown)) {
-    mprinterr("Error: AssignTheta failed for %s - %s - %s\n",
-              topIn.AtomMaskName(ai).c_str(),
-              topIn.AtomMaskName(aj).c_str(),
-              topIn.AtomMaskName(ak).c_str());
-    return 1;
-  }
-  zmatrix.AddIC( InternalCoords(ai, aj, ak, al, newDist, newTheta*Constants::RADDEG, newPhi*Constants::RADDEG) );
-  return 0;
-}*/
-
-/// Recursive function to return depth from an atom along bonds
-/*static int atom_depth(int& depth,
-                      int at, Topology const& topIn, std::vector<bool>& visited, int maxdepth)
-{
-  if (depth == maxdepth) return 0;
-  depth++;
-  visited[at] = true;
-  int depthFromHere = 1;
-  for (Atom::bond_iterator bat = topIn[at].bondbegin(); bat != topIn[at].bondend(); ++bat)
-  {
-    if (!visited[*bat])
-      depthFromHere += atom_depth( depth, *bat, topIn, visited, maxdepth );
-  }
-  return depthFromHere;
-}*/
-
-/// Wrap given value between -PI and PI
-/*static inline double wrap360(double phi) {
-  if (phi > Constants::PI)
-    return phi - Constants::TWOPI;
-  else if (phi < -Constants::PI)
-    return phi + Constants::TWOPI;
-  else
-    return phi;
-}*/
-
-/** Assign internal coordinates for atoms I for torsions around J-K-L. */
-/*int Cpptraj::Structure::Builder::AssignICsAroundBond(Zmatrix& zmatrix,
-                                                   int aj, int ak, int al,
-                                                   Topology const& topIn, Frame const& frameIn,
-                                                   Barray const& atomPositionKnown,
-                                                   BuildAtom const& AtomJ)
-const
-{
-  mprintf("DEBUG: AssignICsAroundBond: X - %s - %s - %s  %i - %i - %i\n",
-          topIn.AtomMaskName(aj).c_str(),
-          topIn.AtomMaskName(ak).c_str(),
-          topIn.AtomMaskName(al).c_str(),
-          aj+1, ak+1, al+1);
-  // Ideally, atoms J K and L should be known
-  if (!atomPositionKnown[aj] ||
-      !atomPositionKnown[ak] ||
-      !atomPositionKnown[al])
-  {
-    mprintf("Warning: AssignICsAroundBond(): Not all atom positions known.\n"
-            "Warning: %i %s (%i) - %i %s (%i) - %i %s (%i)\n",
-              aj+1, topIn.AtomMaskName(aj).c_str(), (int)atomPositionKnown[aj],
-              ak+1, topIn.AtomMaskName(ak).c_str(), (int)atomPositionKnown[ak],
-              al+1, topIn.AtomMaskName(al).c_str(), (int)atomPositionKnown[al]);
-    //return 1;
-  }
-  Atom const& AJ = topIn[aj];
-  // If atom J has only 1 bond this is not needed.
-  if (AJ.Nbonds() < 2) return 0;
-  
-
-  if (debug_ > 0) mprintf("DEBUG:\t\tNbonds: %i\n", AJ.Nbonds());
-  // If atom J only has 2 bonds, ai-aj-ak-al is the only possibility.
-  if (AJ.Nbonds() < 3) {
-    if (debug_ > 0)
-      mprintf("DEBUG:\t\tFewer than 3 bonds. Setting phi to -180.\n");
-    double newPhi = -180 * Constants::DEGRAD;
-    for (int idx = 0; idx < AJ.Nbonds(); idx++) {
-      if (AJ.Bond(idx) != ak) {
-        int ai = AJ.Bond(idx);
-        if (insertIc(zmatrix, ai, aj, ak, al, newPhi, topIn, frameIn, atomPositionKnown)) return 1;
-        break;
-      }
-    }
-    return 0;
-  } // END only 2 bonds
-
-  // 3 or more bonds.
-  std::vector<int> const& priority = AtomJ.Priority();
-  ChiralType chirality = AtomJ.Chirality();
-
-  if (debug_ > 0) {
-    mprintf("DEBUG:\t\tOriginal chirality around J %s is %s\n", topIn.AtomMaskName(aj).c_str(), chiralStr(chirality));
-    mprintf("DEBUG:\t\tPriority around J %s(%i) is", 
-            topIn.AtomMaskName(aj).c_str(), (int)atomPositionKnown[aj]);
-    for (int idx = 0; idx < AJ.Nbonds(); idx++)
-      mprintf(" %s(%i)", topIn.AtomMaskName(priority[idx]).c_str(), (int)atomPositionKnown[priority[idx]]);
-    for (int idx = 0; idx < AJ.Nbonds(); idx++)
-      mprintf(" %i", priority[idx]);
-    mprintf("\n");
-  }
-
-  // Get index of atom K in the priority list, starting from least priority.
-  int kPriorityIdx = -1;
-  for (int idx = AJ.Nbonds()-1; idx > -1; idx--) {
-    if (priority[idx] == ak) {
-      kPriorityIdx = AJ.Nbonds() - 1 - idx;
-      break;
-    }
-  }
-  mprintf("DEBUG:\t\tK priority index is %i\n", kPriorityIdx);
-  if (kPriorityIdx < 0) {
-    mprinterr("Error: Could not find atom K %s in atom J %s bond list.\n",
-              topIn.AtomMaskName(ak).c_str(), topIn.AtomMaskName(aj).c_str());
-    return 1;
-  }
-
-  // Fill in what values we can for known atoms
-  std::vector<double> knownPhi( AJ.Nbonds() );
-  Barray isKnown( AJ.Nbonds(), false );
-  int knownIdx = -1;
-  double knownInterval = 0;
-  bool hasKnownInterval = false;
-  for (int idx = 0; idx < AJ.Nbonds(); idx++) {
-    int atnum = priority[idx];
-    if (atnum != ak && atomPositionKnown[atnum] &&
-                       atomPositionKnown[aj] &&
-                       atomPositionKnown[ak] &&
-                       atomPositionKnown[al])
-    {
-      knownPhi[idx] = Torsion(frameIn.XYZ(atnum),
-                              frameIn.XYZ(aj),
-                              frameIn.XYZ(ak),
-                              frameIn.XYZ(al));
-      isKnown[idx] = true;
-      if (debug_ > 0)
-        mprintf("DEBUG:\t\tKnown phi for %s (pos=%i) = %g\n", topIn.AtomMaskName(atnum).c_str(), idx, knownPhi[idx]*Constants::RADDEG);
-      if (knownIdx == -1) knownIdx = idx; // FIXME handle more than 1 known
-      if (idx > 0 && isKnown[idx-1] && isKnown[idx]) {
-        knownInterval = wrap360(knownPhi[idx] - knownPhi[idx-1]);
-        hasKnownInterval = true;
-      }
-    }
-  }
-
-  // Check known interval if set
-  if (hasKnownInterval) {
-    mprintf("DEBUG:\t\tKnown interval = %g\n", knownInterval * Constants::RADDEG);
-    if (chirality == IS_UNKNOWN_CHIRALITY) {
-      mprintf("DEBUG:\t\tSetting chirality from known interval.\n");
-      if (knownInterval < 0)
-        chirality = IS_S;
-      else
-        chirality = IS_R;
-    } else if (chirality == IS_S) {
-      if (knownInterval > 0)
-        mprinterr("Error: Detected chirality S does not match known interval %g\n", knownInterval*Constants::RADDEG);
-    } else if (chirality == IS_R) {
-      if (knownInterval < 0)
-        mprinterr("Error: Detected chriality R does not match known interval %g\n", knownInterval*Constants::RADDEG);
-    }
-  }
-
-  // If still no chirality use the detected orientation
-  if (chirality == IS_UNKNOWN_CHIRALITY) {
-    chirality = AtomJ.Orientation();
-    mprintf("Warning: Unknown chirality around %s; using detected orientation of %s\n",
-            topIn.AtomMaskName(aj).c_str(), chiralStr(chirality));
-  }
-
-  // Determine the interval
-  bool intervalIsSet = false;
-  double interval = 0;
-  if (params_ != 0) {
-    ParmHolder<AtomType>::const_iterator it = params_->AT().GetParam( TypeNameHolder(AJ.Type()) );
-    if (it != params_->AT().end()) {
-      if (it->second.Hybridization() == AtomType::SP2) {
-        interval = 180 * Constants::DEGRAD;
-        intervalIsSet = true;
-      } else if (it->second.Hybridization() == AtomType::SP3) {
-        interval = 120 * Constants::DEGRAD;
-        intervalIsSet = true;
-      }
-    }
-    if (intervalIsSet) mprintf("DEBUG:\t\tInterval was set from atom J hybridization.\n");
-  }
-  if (!intervalIsSet) {
-    // The interval will be 360 / (number of bonds - 1)
-    interval = Constants::TWOPI / (AJ.Nbonds() - 1);
-    mprintf("DEBUG:\t\tInterval was set from number of bonds.\n");
-  }
-
-  // Adjust interval based on chirality and priority of the k atom
-  if (chirality == IS_S || chirality == IS_UNKNOWN_CHIRALITY)
-    interval = -interval;
-  if ( (kPriorityIdx%2) == 0 ) {
-    mprintf("DEBUG:\t\tFlipping interval based on priority index of %i\n", kPriorityIdx);
-    interval = -interval;
-  }
-
-  // If there is a known interval, compare it to the determined one.
-  if (hasKnownInterval) {
-    double deltaInterval = fabs(interval - knownInterval);
-    mprintf("DEBUG:\t\tDetermined interval %g, known interval %g, delta %g\n",
-            interval*Constants::RADDEG, knownInterval*Constants::RADDEG, deltaInterval*Constants::RADDEG);
-    interval = fabs(knownInterval);
-  }
-
-  // If we have to assign an initial phi, make trans the longer branch
-  if (knownIdx == -1) {
-    Barray visited = atomPositionKnown;
-    // TODO: Ensure bonded atoms are not yet visited?
-    visited[aj] = true;
-    visited[ak] = true;
-    //std::vector<int> depth( AJ.Nbonds() );
-    int max_depth = 0;
-    int max_idx = -1;
-    for (int idx = 0; idx < AJ.Nbonds(); idx++) {
-      int atnum = priority[idx];
-      if (atnum != ak) {
-        int currentDepth = 0;
-        //depth[idx] = atom_depth(currentDepth, atnum, topIn, visited, 10);
-        int depth = atom_depth(currentDepth, atnum, topIn, visited, 10);
-        if (debug_ > 0)
-          mprintf("DEBUG:\t\tAJ %s depth from %s is %i\n",
-                  topIn.AtomMaskName(aj).c_str(), topIn.AtomMaskName(atnum).c_str(), depth);
-        //if (knownIdx == -1 && depth[idx] < 3) {
-        //  knownIdx = idx;
-        //  knownPhi[idx] = 0;
-        //}
-        if (max_idx == -1 || depth > max_depth) {
-          max_depth = depth;
-          max_idx = idx;
-        }
-      }
-    }
-    mprintf("DEBUG:\t\tLongest depth is for atom %s (%i)\n", topIn.AtomMaskName(priority[max_idx]).c_str(), max_depth);
-    knownIdx = max_idx;
-    knownPhi[max_idx] = interval;// -180 * Constants::DEGRAD;
-    isKnown[max_idx] = true;
-  }
-
-  // Sanity check
-  if (knownIdx < 0) {
-    mprinterr("Internal Error: AssignPhi(): knownIdx is < 0\n");
-    return 1;
-  }
-
-  if (debug_ > 0) {
-    mprintf("DEBUG:\t\tStart phi is %g degrees\n", knownPhi[knownIdx]*Constants::RADDEG);
-    mprintf("DEBUG:\t\tInterval is %g, chirality around J is %s\n", interval*Constants::RADDEG, chiralStr(chirality));
-  }
-
-  // Forwards from the known index
-  double currentPhi = knownPhi[knownIdx];
-  for (int idx = knownIdx; idx < AJ.Nbonds(); idx++) {
-    int atnum = priority[idx];
-    if (atnum != ak) {
-      if (isKnown[idx])
-        currentPhi = knownPhi[idx];
-      else
-        currentPhi = wrap360(currentPhi + interval);
-      //if (atnum == ai) phi = currentPhi;
-      //IC.push_back( InternalCoords(atnum, aj, ak, al, 0, 0, currentPhi) );
-      if (insertIc(zmatrix, atnum, aj, ak, al, currentPhi, topIn, frameIn, atomPositionKnown)) return 1;
-      if (debug_ > 0)
-        mprintf("DEBUG:\t\t\t%s (at# %i) phi= %g\n", topIn.AtomMaskName(atnum).c_str(), atnum+1, currentPhi*Constants::RADDEG);
-    }
-  }
-  // Backwards from the known index
-  currentPhi = knownPhi[knownIdx];
-  for (int idx = knownIdx - 1; idx > -1; idx--) {
-    int atnum = priority[idx];
-    if (atnum != ak) {
-      if (isKnown[idx])
-        currentPhi = knownPhi[idx];
-      else
-        currentPhi = wrap360(currentPhi - interval);
-      //if (atnum == ai) phi = currentPhi;
-      //IC.push_back( InternalCoords(atnum, aj, ak, al, 0, 0, currentPhi) );
-      if (insertIc(zmatrix, atnum, aj, ak, al, currentPhi, topIn, frameIn, atomPositionKnown)) return 1;
-      if (debug_ > 0)
-        mprintf("DEBUG:\t\t\t%s (at# %i) phi= %g\n", topIn.AtomMaskName(atnum).c_str(), atnum+1, currentPhi*Constants::RADDEG);
-    }
-  }
-
-  return 0;
-}*/
-
-// -----------------------------------------------------------------------------
-/** Combine two units. Fragment 1 will be merged into Fragment 0 and bonded. */
-/*int Builder::Combine(Topology&       frag0Top, Frame&       frag0frm,
-                     Topology const& frag1Top, Frame const& frag1frm,
-                     int bondAt0, int bondAt1)
-const
-{
-  mprintf("DEBUG: Calling COMBINE between %s and %s\n",
-          frag0Top.AtomMaskName(bondAt0).c_str(),
-          frag1Top.AtomMaskName(bondAt1).c_str());
-  int natom0 = frag0Top.Natom();
-  int newNatom = natom0 + frag1Top.Natom();
-
-  // Determine which "direction" we will be combining the fragments.
-  // Make atA belong to the smaller fragment. atB fragment will be "known".
-  // Ensure atB index is what it will be after fragments are combined.
-  Barray posKnown( newNatom, false );
-  int atA, atB;
-  Zmatrix zmatrixA;
-  if (frag0Top.HeavyAtomCount() < frag1Top.HeavyAtomCount()) {
-    // Fragment 1 is larger
-    atA = bondAt0;
-    atB = bondAt1 + natom0;
-    for (int at = frag0Top.Natom(); at != newNatom; at++)
-      posKnown[at] = true;
-    zmatrixA.SetFromFrameAndConnect( frag0frm, frag0Top );
-  } else {
-    // Fragment 0 is larger or equal
-    atA = bondAt1 + natom0;
-    atB = bondAt0;
-    for (int at = 0; at != natom0; at++)
-     posKnown[at] = true;
-    zmatrixA.SetFromFrameAndConnect( frag1frm, frag1Top );
-    zmatrixA.OffsetIcIndices( natom0 );
-  }
-
-  // Combine fragment1 into fragment 0 topology
-  Topology& combinedTop = frag0Top;
-  combinedTop.AppendTop( frag1Top );
-  // Combined fragment1 into fragment 0 coords.
-  // Need to save the original coords in frame0 since SetupFrameV does not preserve.
-  double* tmpcrd0 = new double[natom0*3];
-  std::copy( frag0frm.xAddress(), frag0frm.xAddress()+frag0frm.size(), tmpcrd0 );
-  frag0frm.SetupFrameV( combinedTop.Atoms(), CoordinateInfo(frag0frm.BoxCrd(), false, false, false));
-  std::copy( tmpcrd0, tmpcrd0+natom0*3, frag0frm.xAddress() );
-  std::copy( frag1frm.xAddress(), frag1frm.xAddress()+frag1frm.size(), frag0frm.xAddress()+natom0*3 );
-  Frame& CombinedFrame = frag0frm;
-  delete[] tmpcrd0;
-
-  int chiralityDebug;
-  if (debug_ < 1)
-    chiralityDebug = 0;
-  else
-    chiralityDebug = debug_ - 1;
-  // Get the chirality around each atom before the bond is added.
-  BuildAtom AtomA;
-  if (combinedTop[atA].Nbonds() > 2) {
-    if (AtomA.DetermineChirality(atA, combinedTop, CombinedFrame, chiralityDebug)) return 1;
-  }
-  if (debug_ > 0)
-    mprintf("DEBUG:\tAtom %4s chirality before bonding is %6s\n", combinedTop.AtomMaskName(atA).c_str(), chiralStr(AtomA.Chirality()));
-  BuildAtom AtomB;
-  if (combinedTop[atB].Nbonds() > 2) {
-    if (AtomB.DetermineChirality(atB, combinedTop, CombinedFrame, chiralityDebug)) return 1;
-  }
-  if (debug_ > 0)
-    mprintf("DEBUG:\tAtom %4s chirality before bonding is %6s\n", combinedTop.AtomMaskName(atB).c_str(), chiralStr(AtomB.Chirality()));
-
-  // Create the bond
-  if (debug_ > 0)
-    mprintf("DEBUG: Bonding atom %s to %s\n", combinedTop.AtomMaskName(atA).c_str(), combinedTop.AtomMaskName(atB).c_str());
-  combinedTop.AddBond( atA, atB ); // TODO pseudo-parameter?
-  // // Regenerate the molecule info FIXME should Topology just do this?
-  if (combinedTop.DetermineMolecules()) return 1;
-
-  // Determine new priorities around atoms that were just bonded
-  if (combinedTop[atA].Nbonds() > 2) {
-    if (AtomA.SetPriority(atA, combinedTop, CombinedFrame, chiralityDebug)) return 1;
-  }
-  if (combinedTop[atB].Nbonds() > 2) {
-    if (AtomB.SetPriority(atB, combinedTop, CombinedFrame, chiralityDebug)) return 1;
-  }
-
-  // Generate Zmatrix only for ICs involving bonded atoms
-  Zmatrix bondZmatrix;
-
-  // Note which atoms already have an IC in zmatrixA
-  Barray hasIC(combinedTop.Natom(), false);
-  for (Zmatrix::const_iterator it = zmatrixA.begin(); it != zmatrixA.end(); ++it)
-    hasIC[it->AtI()] = true;
-
-  //bondZmatrix.SetDebug( debug_ );
-  bondZmatrix.SetDebug( 1 ); // FIXME
-  if (SetupICsAroundBond(bondZmatrix, atA, atB, CombinedFrame, combinedTop, posKnown, hasIC, AtomA, AtomB)) {
-    mprinterr("Error: Zmatrix setup for ICs around %s and %s failed.\n",
-              combinedTop.AtomMaskName(atA).c_str(),
-              combinedTop.AtomMaskName(atB).c_str());
-    return 1;
-  }
-  mprintf("DEBUG: CONVERT WITH bondZmatrix.\n");
-  //if (debug_ > 0)
-    bondZmatrix.print(&combinedTop);
-  if (bondZmatrix.SetToFrame( CombinedFrame, posKnown )) {
-    mprinterr("Error: Conversion from bondZmatrix to Cartesian coords failed.\n");
-    return 1;
-  }
-  mprintf("DEBUG: CONVERT WITH zmatrixA.\n");
-  zmatrixA.print( &combinedTop );
-  if (zmatrixA.SetToFrame( CombinedFrame, posKnown )) {
-    mprinterr("Error: Conversion from zmatrixA to Cartesian coords failed.\n");
-    return 1;
-  }
-
-  return 0;
-}*/
-
-/// \return The total number of atoms whose position is known for the specified residue
-/*static inline int known_count(int ires, Topology const& topIn, std::vector<bool> const& hasPosition)
-{
-  int count = 0;
-  for (int at = topIn.Res(ires).FirstAtom(); at != topIn.Res(ires).LastAtom(); at++)
-    if (hasPosition[at])
-      count++;
-  return count;
-}*/
-
-/** Model the internal coordinates around a bond between two residues defined
-  * by bondAt0 (in residue0) and bondAt1 in (residue1).
-  *
-  */
-/*int Builder::ModelCoordsAroundBond(Frame const& frameIn, Topology const& topIn, int bondAt0, int bondAt1,
-                                   Zmatrix& zmatrix0, Barray const& hasPosition)
-const
-{
-  mprintf("DEBUG: Model coords around bond %s - %s\n", topIn.AtomMaskName(bondAt0).c_str(), topIn.AtomMaskName(bondAt1).c_str());
-  int res0 = topIn[bondAt0].ResNum();
-  int res1 = topIn[bondAt1].ResNum();
-  if (res0 == res1) {
-    mprinterr("Internal Error: ModelCoordsAroundBond(): Atoms are in the same residue.\n");
-    return 1;
-  }
-  // Determine which "direction" we will be combining the fragments.
-  // Ensure atA belongs to the less-known fragment. atB fragment will be "known".
-//  int known0 = known_count(res0, topIn, hasPosition);
-//  int known1 = known_count(res1, topIn, hasPosition);
-////  int atA, atB;
-//  if (known0 > known1) {
-//    mprinterr("Internal Error: ModelCoordsAroundBond(): Residue0 '%s' is more well-known than Residue1 '%s'\n",
-//              topIn.TruncResNameNum( topIn[bondAt0].ResNum() ).c_str(),
-//              topIn.TruncResNameNum( topIn[bondAt1].ResNum() ).c_str());
-//    return 1;
-//  }
-  int atA = bondAt0;
-  int atB = bondAt1;
-  Zmatrix* zA = &zmatrix0; // FIXME
-//  Zmatrix const* zA;
-//  if (known0 < known1) {
-//    // Fragment 1 is better-known 
-//    atA = bondAt0;
-//    atB = bondAt1;
-//    zA  = zmatrix0;
-//    //zB  = zmatrix1;
-//  } else {
-//    // Fragment 0 is better or equally known 
-//    atA = bondAt1;
-//    atB = bondAt0;
-//    zA  = zmatrix1;
-//    //zB  = zmatrix0;
-//  }
-
-  mprintf("DEBUG: More well-known atom: %s\n", topIn.AtomMaskName(atB).c_str());
-  mprintf("DEBUG: Less well-known atom: %s  has zmatrix= %i\n", topIn.AtomMaskName(atA).c_str(), (int)(zA != 0));
-
-  int chiralityDebug;
-  if (debug_ < 1)
-    chiralityDebug = 0;
-  else
-    chiralityDebug = debug_ - 1;
-
-  // Get the chirality around each atom before the bond is added.
-  // Determine priorities
-  BuildAtom AtomA;
-  if (topIn[atA].Nbonds() > 2) {
-    if (AtomA.DetermineChirality(atA, topIn, frameIn, chiralityDebug)) return 1;
-  }
-  if (debug_ > 0)
-    mprintf("DEBUG:\tAtom %4s chirality %6s\n", topIn.AtomMaskName(atA).c_str(), chiralStr(AtomA.Chirality()));
-  BuildAtom AtomB;
-  if (topIn[atB].Nbonds() > 2) {
-    if (AtomB.DetermineChirality(atB, topIn, frameIn, chiralityDebug)) return 1;
-  }
-  if (debug_ > 0)
-    mprintf("DEBUG:\tAtom %4s chirality %6s\n", topIn.AtomMaskName(atB).c_str(), chiralStr(AtomB.Chirality()));
-
-  // Generate Zmatrix only for ICs involving bonded atoms
-  Zmatrix bondZmatrix;
-
-  // Note which atoms already have an IC in zmatrix A
-  Barray hasIC(topIn.Natom(), false);
-  if (zA != 0) {
-    for (Zmatrix::const_iterator it = zA->begin(); it != zA->end(); ++it)
-      hasIC[it->AtI()] = true;
-  }
-
-  bondZmatrix.SetDebug( debug_ );
-  if (SetupICsAroundBond(bondZmatrix, atA, atB, frameIn, topIn, hasPosition, hasIC, AtomA, AtomB)) {
-    mprinterr("Error: Zmatrix setup for ICs around %s and %s failed.\n",
-              topIn.AtomMaskName(atA).c_str(),
-              topIn.AtomMaskName(atB).c_str());
-    return 1;
-  }
-  // Add the remaining ICs FIXME check for duplicates
-  for (Zmatrix::const_iterator it = zmatrix0.begin(); it != zmatrix0.end(); ++it)
-    bondZmatrix.AddIC( *it );
-  if (debug_ > 0)
-    bondZmatrix.print(&topIn);
-  zmatrix0 = bondZmatrix;
-//  if (bondZmatrix.SetToFrame( frameIn, hasPosition )) {
-//    mprinterr("Error: Conversion from bondZmatrix to Cartesian coords failed.\n");
-//    return 1;
-//  }
-
-  return 0;
-}*/
-
-/** Given two bonded atoms A and B, where B has a depth of at least 2
-  * (i.e., it is possible to have B be atom J where we can form J-K-L),
-  * set up a complete set of internal coordinates involving A and B in the
-  * direction of atom A. This means all internal coordinates with A and B
-  * as I and J (should be only 1), as J and K, and as K and L.
-  */
-/*int Builder::SetupICsAroundBond(Zmatrix& zmatrix,
-                                int atA, int atB, Frame const& frameIn, Topology const& topIn,
-                                Barray const& atomPositionKnown,
-                                Barray const& hasICin,
-                                BuildAtom const& AtomA, BuildAtom const& AtomB)
-const
-{
-  if (debug_ > 0)
-    mprintf("DEBUG: SetupICsAroundBond: atA= %s (%i)  atB= %s (%i) total # atoms %i\n",
-            topIn.AtomMaskName(atA).c_str(), atA+1,
-            topIn.AtomMaskName(atB).c_str(), atB+1,
-            topIn.Natom());
-//  zmatrix.clear();
-
-  //Barray hasIC( topIn.Natom(), false );
-  Barray hasIC = hasICin;
-  unsigned int nHasIC = 0;
-  for (Barray::const_iterator it = hasIC.begin(); it != hasIC.end(); ++it) {
-    if (*it) {
-      nHasIC++;
-      mprintf("DEBUG:\tAtom %s already has an IC.\n", topIn.AtomMaskName(it-hasIC.begin()).c_str());
-    }
-  }
-  // Mark known atoms as already having IC
-  for (Barray::const_iterator it = atomPositionKnown.begin();
-                                         it != atomPositionKnown.end(); ++it)
-  {
-    //mprintf("DEBUG: MARKING KNOWN ATOMS. %li\n", it - atomPositionKnown.begin());
-    if (*it) { //MARK( it - atomPositionKnown.begin(), hasIC, nHasIC );
-      hasIC[it - atomPositionKnown.begin()] = true;
-      nHasIC++;
-    }
-  }
-
-  // First, make sure atom B as a bond depth of at least 2.
-  // Choose K and L atoms given atA is I and atB is J.
-  Atom const& AJ = topIn[atB];
-  typedef std::pair<int,int> Apair;
-  std::vector<Apair> KLpairs;
-  for (Atom::bond_iterator kat = AJ.bondbegin(); kat != AJ.bondend(); ++kat)
-  {
-    if (*kat != atA) {
-      //mprintf("DEBUG: kat= %s\n", topIn.AtomMaskName(*kat).c_str());
-      Atom const& AK = topIn[*kat];
-      for (Atom::bond_iterator lat = AK.bondbegin(); lat != AK.bondend(); ++lat)
-      {
-        if (*lat != atB && *lat != atA) {
-          //mprintf("DEBUG: lat= %s\n", topIn.AtomMaskName(*lat).c_str());
-          KLpairs.push_back( Apair(*kat, *lat) );
-        }
-      }
-    }
-  }
-  if (debug_ > 0) {
-    for (std::vector<Apair>::const_iterator it = KLpairs.begin();
-                                            it != KLpairs.end(); ++it)
-      mprintf("DEBUG:\t\tKL pair %s - %s\n", topIn.AtomMaskName(it->first).c_str(),
-              topIn.AtomMaskName(it->second).c_str());
-  }
-  if (KLpairs.empty()) {
-    mprinterr("Error: SetFromFrameAroundBond(): Could not find an atom pair bonded to atom %s\n",
-              topIn.AtomMaskName(atB).c_str());
-    return 1;
-  }
-  // TODO be smarter about how K and L are selected?
-  double maxMass = topIn[KLpairs[0].first].Mass() + topIn[KLpairs[0].second].Mass();
-  unsigned int maxIdx = 0;
-  for (unsigned int idx = 1; idx < KLpairs.size(); idx++) {
-    double sumMass = topIn[KLpairs[idx].first].Mass() + topIn[KLpairs[idx].second].Mass();
-    if (sumMass > maxMass) {
-      maxMass = sumMass;
-      maxIdx = idx;
-    }
-  }
-  int atk0 = KLpairs[maxIdx].first;
-  int atl0 = KLpairs[maxIdx].second;
-  int modelDebug = 0;
-  if (debug_ > 0) {
-    mprintf("DEBUG: Chosen KL pair: %s - %s\n",topIn.AtomMaskName(atk0).c_str(),
-              topIn.AtomMaskName(atl0).c_str());
-    modelDebug = debug_ - 1;
-  }
-  //Cpptraj::Structure::Model model;
-  //model.SetDebug( modelDebug ); //FIXME
-  //model.SetDebug( 1 );
-  // FIXME
-  mprintf("DEBUG: ------------------------------------------------\n");
-  //std::vector<InternalCoords> tmpic;
-  // I J: Set up ICs for X atB K L
-  if (AssignICsAroundBond(zmatrix, atB, atk0, atl0, topIn, frameIn, atomPositionKnown, AtomB)) {
-    mprinterr("Error: AssignICsAroundBond (I J) failed.\n");
-    return 1;
-  }
-  // J K: Set up ICs for X atA atB K
-  if (AssignICsAroundBond(zmatrix, atA, atB, atk0, topIn, frameIn, atomPositionKnown, AtomA)) {
-    mprinterr("Error: AssignICsAroundBond (J K) failed.\n");
-    return 1;
-  }
-  // K L: Set up ICs for X iat atA atB
-  Atom const& AJ1 = topIn[atA];
-  for (Atom::bond_iterator iat = AJ1.bondbegin(); iat != AJ1.bondend(); ++iat)
-  {
-    if (*iat != atB) {
-      // Only do this if one or more of the atoms bonded to iat does not
-      // already have an IC.
-      unsigned int needsKLic = 0;
-      for (Atom::bond_iterator bat = topIn[*iat].bondbegin(); bat != topIn[*iat].bondend(); ++bat) {
-        if ( *bat != atA && !hasIC[*bat] ) {
-          mprintf("DEBUG:\tAtom %s around %s has no IC.\n", topIn.AtomMaskName(*bat).c_str(), topIn.AtomMaskName(*iat).c_str());
-          needsKLic++;
-        }
-      }
-      if (needsKLic > 0) {
-        BuildAtom AtomC;
-        if (topIn[*iat].Nbonds() > 2) {
-          if (AtomC.DetermineChirality(*iat, topIn, frameIn, modelDebug)) return 1;
-        }
-        mprintf("DEBUG: K L IC needed for %s.\n", topIn.AtomMaskName(*iat).c_str());
-        if (AssignICsAroundBond(zmatrix, *iat, atA, atB, topIn, frameIn, atomPositionKnown, AtomC)) {
-          mprinterr("Error: AssignICsAroundBond (K L) failed.\n");
-          return 1;
-        }
-      } else {
-        mprintf("DEBUG: K L IC not needed for %s.\n", topIn.AtomMaskName(*iat).c_str());
-      }
-    }
-  }
-  // Mark/Print ICs
-  for (Zmatrix::const_iterator it = zmatrix.begin(); it != zmatrix.end(); ++it) {
-    it->printIC( topIn ); // DEBUG
-    //MARK( it->AtI(), hasIC, nHasIC );
-  }
-  mprintf("DEBUG: END AssignICsAroundBond ------------------------\n");
-  // FIXME
-  // ---- I J: Set dist, theta, phi for atA atB K L internal coord ---
-//  if (debug_ > 0)
-//    mprintf("DEBUG: IC (i j) %i - %i - %i - %i\n", atA+1, atB+1, atk0+1, atl0+1);
-//  double newDist = 0;
-//  if (model.AssignLength(newDist, atA, atB, topIn, frameIn, atomPositionKnown)) {
-//    mprinterr("Error: length (i j) assignment failed.\n");
-//    return 1;
-//  }
-//  if (debug_ > 0) mprintf("DEBUG:\t\tnewDist= %g\n", newDist);
-//  double newTheta = 0;
-//  if (model.AssignTheta(newTheta, atA, atB, atk0, topIn, frameIn, atomPositionKnown)) {
-//    mprinterr("Error: theta (i j) assignment failed.\n");
-//    return 1;
-//  }
-//  if (debug_ > 0) mprintf("DEBUG:\t\tnewTheta = %g\n", newTheta*Constants::RADDEG);
-//  double newPhi = 0;
-//  if (model.AssignPhi(newPhi, atA, atB, atk0, atl0, topIn, frameIn,
-//                                           atomPositionKnown, AtomB))
-//  {
-//    mprinterr("Error: phi (i j) assignment failed.\n");
-//    return 1;
-//  }
-//  if (debug_ > 0) mprintf("DEBUG:\t\tnewPhi = %g\n", newPhi*Constants::RADDEG);
-//  IC_.push_back(InternalCoords( atA, atB, atk0, atl0, newDist, newTheta*Constants::RADDEG, newPhi*Constants::RADDEG ));
-//  if (debug_ > 0) {
-//    mprintf("DEBUG: MODEL I J IC: ");
-//    IC_.back().printIC(topIn);
-//  }
-//  MARK( atA, hasIC, nHasIC );
-//
-//  // ----- J K: Set up ICs for X atA atB K ---------------------------
-//  Atom const& AJ1 = topIn[atA];
-//  int ati = -1;
-//  //Atom const& AK1 = topIn[atB];
-//  //Atom const& AL1 = topIn[atk0];
-//  for (Atom::bond_iterator iat = AJ1.bondbegin(); iat != AJ1.bondend(); ++iat)
-//  {
-//    if (*iat != atB) {
-//      if (ati == -1) ati = *iat;
-//      // Set bond dist
-//      if (model.AssignLength(newDist, *iat, atA, topIn, frameIn, atomPositionKnown)) {
-//        mprinterr("Error: length (j k) assignment failed.\n");
-//        return 1;
-//      }
-//      // Set theta for I atA atB
-//      newTheta = 0;
-//      if (model.AssignTheta(newTheta, *iat, atA, atB, topIn, frameIn, atomPositionKnown)) {
-//        mprinterr("Error: theta (j k) assignment failed.\n");
-//        return 1;
-//      }
-//      if (debug_ > 0)
-//        mprintf("DEBUG:\t\tnewTheta = %g\n", newTheta*Constants::RADDEG);
-//      // Set phi for I atA atB K
-//      newPhi = 0;
-//      if (model.AssignPhi(newPhi, *iat, atA, atB, atk0, topIn, frameIn,
-//                                               atomPositionKnown, AtomA))
-//      {
-//        mprinterr("Error: phi (j k) assignment failed.\n");
-//        return 1;
-//      }
-//      if (debug_ > 0)
-//        mprintf("DEBUG:\t\tnewPhi = %g\n", newPhi*Constants::RADDEG);
-//      IC_.push_back(InternalCoords( *iat, atA, atB, atk0, newDist, newTheta*Constants::RADDEG, newPhi*Constants::RADDEG ));
-//      if (debug_ > 0) {
-//        mprintf("DEBUG: MODEL J K IC: ");
-//        IC_.back().printIC(topIn);
-//      }
-//      MARK( *iat, hasIC, nHasIC );
-//      // ----- K L: Set up ICs for X iat atA atB ---------------------
-//      Atom const& AJ2 = topIn[*iat];
-//      for (Atom::bond_iterator i2at = AJ2.bondbegin(); i2at != AJ2.bondend(); ++i2at)
-//      {
-//        if (*i2at != atA && *i2at != atB && !hasIC[*i2at]) {
-//          mprintf("DEBUG: MODEL K L IC: %s %s %s %s %i %i %i %i\n",
-//                  topIn.AtomMaskName(*i2at).c_str(),
-//                  topIn.AtomMaskName(*iat).c_str(),
-//                  topIn.AtomMaskName(atA).c_str(),
-//                  topIn.AtomMaskName(atB).c_str(),
-//                  *i2at+1, *iat+1, atA+1, atB+1);
-//          if (model.AssignLength(newDist, *i2at, *iat, topIn, frameIn, atomPositionKnown)) {
-//            mprinterr("Error: length (k l) assignment failed.\n");
-//            return 1;
-//          }
-//          mprintf("DEBUG: K L distance= %g\n", newDist);
-//          //newTheta = CalcAngle( frameIn.XYZ(*i2at), frameIn.XYZ(*iat), frameIn.XYZ(atA) );
-//          if (model.AssignTheta(newTheta, *iat, atA, atB, topIn, frameIn, atomPositionKnown)) {
-//            mprinterr("Error: theta (k l) assignment failed.\n");
-//            return 1;
-//          }
-//          mprintf("DEBUG: K L angle= %g\n", newTheta*Constants::RADDEG);
-//          // Set phi for X iat atA atB
-//          BuildAtom AtomC;
-//          if (topIn[*iat].Nbonds() > 2) {
-//            if (AtomC.DetermineChirality(*iat, topIn, frameIn, modelDebug)) return 1;
-//          }
-//          newPhi = 0;
-//          //model.SetDebug( 1 ); // FIXME
-//          if (model.AssignPhi(newPhi, *i2at, *iat, atA, atB, topIn, frameIn,
-//                                                   atomPositionKnown, AtomC))
-//          {
-//            mprinterr("Error: phi (k l) assignment failed.\n");
-//            return 1;
-//          }
-//          mprintf("DEBUG: K L Phi = %g\n", newPhi*Constants::RADDEG);
-//          IC_.push_back(InternalCoords( *i2at, *iat, atA, atB, newDist, newTheta*Constants::RADDEG, newPhi*Constants::RADDEG ));
-//          mprintf("DEBUG: MODEL K L IC: ");
-//          IC_.back().printIC(topIn);
-//          MARK( *i2at, hasIC, nHasIC );
-//          // Trace from atA *iat *i2at outwards
-//          //ToTrace.push_back(atA);
-//          //ToTrace.push_back(*iat);
-//          //ToTrace.push_back(*i2at);
-//          //if (traceMol(atA, *iat, *i2at, frameIn, topIn, topIn.Natom(), nHasIC, hasIC)) return 1;
-//
-//        }
-//      } 
-//    }
-//  }
-
-
-//
-//// Handle remaining atoms.
-//if (AJ1.Nbonds() > 1) {
-//  if (AJ1.Nbonds() == 2) {
-//    if (debug_ > 0) mprintf("DEBUG: 2 bonds to %s.\n", topIn.AtomMaskName(atA).c_str());
-//    if (traceMol(atB, atA, ati, frameIn, topIn, topIn.Natom(), nHasIC, hasIC))
-//      return 1;
-//  } else {
-//    // 3 or more bonds
-//    std::vector<int> const& priority = AtomA.Priority();
-//    int at0 = -1;
-//    int at1 = -1;
-//    std::vector<int> remainingAtoms;
-//    if (debug_ > 0) mprintf("DEBUG: %i bonds to %s\n", AJ1.Nbonds(), topIn.AtomMaskName(atA).c_str());
-//    for (std::vector<int>::const_iterator it = priority.begin(); it != priority.end(); ++it) {
-//      if (*it != atB) {
-//        if (debug_ > 0) mprintf("DEBUG:\t\t%s\n", topIn.AtomMaskName(*it).c_str());
-//        if (at0 == -1)
-//          at0 = *it;
-//        else if (at1 == -1)
-//          at1 = *it;
-//        else
-//          remainingAtoms.push_back( *it );
-//      }
-//    }
-//    // at0 atA at1
-//    if (traceMol(at1, atA, at0, frameIn, topIn, topIn.Natom(), nHasIC, hasIC))
-//      return 1;
-//    // at1 atA, at0
-//    if (traceMol(at0, atA, at1, frameIn, topIn, topIn.Natom(), nHasIC, hasIC))
-//      return 1;
-//    // Remaining atoms.
-//    for (std::vector<int>::const_iterator it = remainingAtoms.begin(); it != remainingAtoms.end(); ++it) {
-//      if (traceMol(at0, atA, *it, frameIn, topIn, topIn.Natom(), nHasIC, hasIC))
-//        return 1;
-//    }
-//  }
-//}
-//
-  return 0;
-}*/
-
-// ==============================================================================
 /** For existing torsions, see if all coordinates in that torsion
   * exist. If so, update the IC from the existing coordinates.
   */
@@ -1140,6 +145,7 @@ int Builder::UpdateICsFromFrame(Frame const& frameIn, int ires, Topology const&
   return 0;
 }
 
+// -----------------------------------------------------------------------------
 /// Used to track atoms for mock externals
 class MockAtom {
   public:
@@ -1167,7 +173,7 @@ class MockAtom {
     bool buildInternals_; ///< True if internals should be built for this atom
 };
 
-// -----------------------------------------------
+// -----------------------------------------------------------------------------
 /** Store info for modelling torsions around X-Y */
 class Cpptraj::Structure::Builder::TorsionModel {
   public:
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index a168684f17..5a1c17eb5f 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -8,7 +8,6 @@ class Frame;
 class ParameterSet;
 namespace Cpptraj {
 namespace Structure {
-class BuildAtom;
 class Zmatrix;
 class InternalCoords;
 /// Used to attach different topology/frame combos using internal coordinates
@@ -21,13 +20,6 @@ class Builder {
     void SetDebug(int d) { debug_ = d; }
     /// Set optional parameter set
     void SetParameters(ParameterSet const*);
-
-    /// Combine second fragment into first fragment and bond
-//    int Combine(Topology&, Frame&, Topology const&, Frame const&, int, int) const;
-    /// Model the coordinates around a bond given only some coordinates are known
-//    int ModelCoordsAroundBond(Frame const&, Topology const&, int, int, Zmatrix&, Barray const&) const;
-
-
     /// Update the internal coordinates in given Zmatrix with values from Frame/Parameters
     int UpdateICsFromFrame(Frame const&, int, Topology const&, Barray const&);
     /// Generate internal coordinates in the same manner as LEaP
@@ -36,6 +28,7 @@ class Builder {
     int GenerateInternalsAroundLink(int, int, Frame const&, Topology const&, Barray const&);
     /// Update existing indices with given offset
     void UpdateIndicesWithOffset(int);
+
     /// \return Zmatrix from current internals
     int GetZmatrixFromInternals(Zmatrix&, Topology const&) const;
   private:
@@ -61,27 +54,6 @@ class Builder {
     int getLengthParam(double&, int, int, Topology const&) const;
     /// Get angle parameter for atoms.
     int getAngleParam(double&, int, int, int, Topology const&) const;
-
-    // ===========================================
-    /// Assign a reasonable value for bond distance given 2 atoms whose position may or may not be known
-//    int AssignLength(double&, int, int, Topology const&, Frame const&, Barray const&) const;
-    /// Given atoms J and K, attempt to assign a reasonable value for theta for atom I
-//    int AssignTheta(double&, int, int, int, Topology const&, Frame const&, Barray const&) const;
-    /// Calculate an internal coordinate for known atoms
-//    static inline InternalCoords calcKnownAtomIc(int, int, int, int, Frame const&);
-    /// Insert an internal coord into a zmatrix
-//    int insertIc(Zmatrix&, int, int, int, int, double,
-//                 Topology const&, Frame const&, Barray const&) const;
-    /// Assign internal coordinates for atoms I for torsions around J-K-L.
-//    int AssignICsAroundBond(Zmatrix&, int, int, int,
-//                           Topology const&, Frame const&, Barray const&,
-//                           BuildAtom const&) const;
-
-    /// Model coordinates around a bond
-//    int SetupICsAroundBond(Zmatrix&, int, int, Frame const&, Topology const&,
-//                           Barray const&, Barray const&,
-//                           BuildAtom const&, BuildAtom const&) const;
-    // ===========================================
     /// Calculte phi value for a torsion in a TorsionModel
     void ModelTorsion(TorsionModel const&, unsigned int, unsigned int, double);
     /// Get angle parameter/model an angle value
diff --git a/src/Structure/structuredepend b/src/Structure/structuredepend
index c2874b3e7e..0343bb0aa9 100644
--- a/src/Structure/structuredepend
+++ b/src/Structure/structuredepend
@@ -1,5 +1,5 @@
 BuildAtom.o : BuildAtom.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h StructureEnum.h
-Builder.o : Builder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h Builder.h GenerateConnectivityArrays.h InternalCoords.h StructureEnum.h Zmatrix.h
+Builder.o : Builder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Builder.h GenerateConnectivityArrays.h InternalCoords.h Zmatrix.h
 Disulfide.o : Disulfide.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Disulfide.h ResStatArray.h StructureRoutines.h
 FunctionalGroup.o : FunctionalGroup.cpp ../Atom.h ../AtomMap.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h FunctionalGroup.h
 FxnGroupBuilder.o : FxnGroupBuilder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h FunctionalGroup.h FxnGroupBuilder.h StructureRoutines.h Sugar.h SugarToken.h
@@ -12,4 +12,4 @@ Sugar.o : Sugar.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.
 SugarBuilder.o : SugarBuilder.cpp ../ArgList.h ../Atom.h ../AtomMap.h ../AtomMask.h ../AtomType.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DistRoutines.h ../FileIO.h ../FileName.h ../Frame.h ../ImageOption.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h FunctionalGroup.h FxnGroupBuilder.h LinkAtom.h ResStatArray.h StructureEnum.h StructureRoutines.h Sugar.h SugarBuilder.h SugarLinkAtoms.h SugarToken.h
 SugarLinkAtoms.o : SugarLinkAtoms.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../StringRoutines.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h LinkAtom.h SugarLinkAtoms.h
 SugarToken.o : SugarToken.cpp ../ArgList.h ../CpptrajStdio.h SugarToken.h
-Zmatrix.o : Zmatrix.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h InternalCoords.h Zmatrix.h
+Zmatrix.o : Zmatrix.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h GenerateConnectivityArrays.h InternalCoords.h Zmatrix.h
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 87b530f95e..2a8695bccc 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -446,7 +446,7 @@ Spline.o : Spline.cpp CpptrajStdio.h Spline.h
 SplineFxnTable.o : SplineFxnTable.cpp Constants.h CpptrajStdio.h Spline.h SplineFxnTable.h StringRoutines.h
 StringRoutines.o : StringRoutines.cpp CpptrajStdio.h StringRoutines.h
 Structure/BuildAtom.o : Structure/BuildAtom.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/StructureEnum.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Structure/Builder.o : Structure/Builder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h GuessAtomHybridization.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/Builder.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Structure/Builder.o : Structure/Builder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h GuessAtomHybridization.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Builder.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 Structure/Disulfide.o : Structure/Disulfide.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Disulfide.h Structure/ResStatArray.h Structure/StructureRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/FunctionalGroup.o : Structure/FunctionalGroup.cpp Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/FxnGroupBuilder.o : Structure/FxnGroupBuilder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h Structure/FxnGroupBuilder.h Structure/StructureRoutines.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h

From 3a7f5316a5edbaeb5c20f31892fa46761ae64938 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 12 Feb 2024 09:24:45 -0500
Subject: [PATCH 0501/1492] Try and use CPPTRAJ guess at hybridization if
 parameter not defined. If it comes back with SP, incremement to SP2

---
 src/Structure/Builder.cpp | 23 ++++++++++++++++-------
 src/Structure/Builder.h   |  2 +-
 2 files changed, 17 insertions(+), 8 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 06c639abfc..2763ac310f 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -881,8 +881,9 @@ int Builder::getExistingChiralityIdx(int ai) const {
 }
 
 /** Determine hybridization in the same manner as leap */
-AtomType::HybridizationType Builder::getAtomHybridization(Atom const& aAtom) const {
+AtomType::HybridizationType Builder::getAtomHybridization(Atom const& aAtom, std::vector<Atom> const& atoms) const {
   AtomType::HybridizationType H1 = AtomType::UNKNOWN_HYBRIDIZATION;
+  // Check if hybridization is defined in the parameter set.
   if (params_ != 0) {
     ParmHolder<AtomType>::const_iterator it;
     if (aAtom.HasType()) {
@@ -891,6 +892,14 @@ AtomType::HybridizationType Builder::getAtomHybridization(Atom const& aAtom) con
         H1 = it->second.Hybridization();
     }
   }
+  // Use the cpptraj guess.
+  H1 = GuessAtomHybridization(aAtom, atoms);
+  // FIXME this is a bit of a hack. If we get an SP type here its likely we
+  //       are generating internals for a fragment that has not been bonded
+  //       yet. Do SP2 instead.
+  if (H1 == AtomType::SP)
+    H1 = AtomType::SP2;
+  // Guess in the same way leap does
   if (H1 == AtomType::UNKNOWN_HYBRIDIZATION) {
     // TODO bond orders?
     int iSingle = 0;
@@ -923,8 +932,8 @@ double Builder::ModelBondLength(int ai, int aj, Topology const& topIn) const {
   }
   Atom const& AI = topIn[ai];
   Atom const& AJ = topIn[aj];
-  AtomType::HybridizationType hybridI = getAtomHybridization( AI );
-  AtomType::HybridizationType hybridJ = getAtomHybridization( AJ );
+  AtomType::HybridizationType hybridI = getAtomHybridization( AI, topIn.Atoms() );
+  AtomType::HybridizationType hybridJ = getAtomHybridization( AJ, topIn.Atoms() );
 
   if (hybridI == AtomType::UNKNOWN_HYBRIDIZATION ||
       hybridJ == AtomType::UNKNOWN_HYBRIDIZATION)
@@ -973,7 +982,7 @@ double Builder::ModelBondAngle(int ai, int aj, int ak, Topology const& topIn) co
     mprintf("DEBUG:\t\tJ %s Nbonds: %i\n", AJ.ElementName(), AJ.Nbonds());
     mprintf("DEBUG:\t\tK %s Nbonds: %i\n", topIn[ak].ElementName(), topIn[ak].Nbonds());
   }
-  AtomType::HybridizationType hybrid = getAtomHybridization( AJ );
+  AtomType::HybridizationType hybrid = getAtomHybridization( AJ, topIn.Atoms() );
 
   // Guess hybrid if needed
   //if (hybrid == AtomType::UNKNOWN_HYBRIDIZATION)
@@ -1205,8 +1214,8 @@ int Builder::assignTorsionsAroundBond(int a1, int a2, Frame const& frameIn, Topo
   if (topIn[a1].Nbonds() < 2 || topIn[a2].Nbonds() < 2)
     return 0;
   // Get atom hybridizations
-  AtomType::HybridizationType H1 = getAtomHybridization( topIn[a1] );
-  AtomType::HybridizationType H2 = getAtomHybridization( topIn[a2] );//AtomType::UNKNOWN_HYBRIDIZATION;
+  AtomType::HybridizationType H1 = getAtomHybridization( topIn[a1], topIn.Atoms() );
+  AtomType::HybridizationType H2 = getAtomHybridization( topIn[a2], topIn.Atoms() );//AtomType::UNKNOWN_HYBRIDIZATION;
   if (H1 == AtomType::UNKNOWN_HYBRIDIZATION)
     mprintf("Warning: No hybridization set for atom %s\n", topIn.AtomMaskName(a1).c_str());
   if (H2 == AtomType::UNKNOWN_HYBRIDIZATION)
@@ -1231,7 +1240,7 @@ int Builder::assignTorsionsAroundBond(int a1, int a2, Frame const& frameIn, Topo
     Hx = H1;
     Hy = H2;
   }
-  static const char* hstr[] = { "SP", "SP2", "SP3", "Unknown" };
+  static const char* hstr[] = { "SP1", "SP2", "SP3", "Unknown" };
   mprintf("DEBUG: assignTorsionsAroundBond: AX= %s (%s)  AY= %s (%s), aAtomIdx= %i",
           topIn.AtomMaskName(ax).c_str(), hstr[Hx],
           topIn.AtomMaskName(ay).c_str(), hstr[Hy], aAtomIdx+1);
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index 5a1c17eb5f..fcdabd2886 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -67,7 +67,7 @@ class Builder {
     /// Create torsion around SP2-SP2 linkage
     void createSp2Sp2Torsions(TorsionModel const&);
     /// Dtermine atom hybridization in the same way as leap
-    AtomType::HybridizationType getAtomHybridization(Atom const&) const;
+    AtomType::HybridizationType getAtomHybridization(Atom const&, std::vector<Atom> const&) const;
     /// Model torsions around a bond in the same manner as LEaP
     int assignTorsionsAroundBond(int, int, Frame const&, Topology const&, Barray const&, int);
     /// Get any existing internal torsion indices around specified atoms

From e087ea39117fcd70c09917f917841a95f032122f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 12 Feb 2024 09:36:37 -0500
Subject: [PATCH 0502/1492] Update for new IC handling

---
 test/Test_Graft/IC.Final.graft.mol2.save | 70 ++++++++++++------------
 1 file changed, 35 insertions(+), 35 deletions(-)

diff --git a/test/Test_Graft/IC.Final.graft.mol2.save b/test/Test_Graft/IC.Final.graft.mol2.save
index e4af61be0c..0355474365 100644
--- a/test/Test_Graft/IC.Final.graft.mol2.save
+++ b/test/Test_Graft/IC.Final.graft.mol2.save
@@ -6,40 +6,40 @@ USER_CHARGES
 
 
 @<TRIPOS>ATOM
-      1 N           5.0262    1.0605    2.4857 N          1 TYR     -0.415700
-      2 H           4.3432    1.6530    2.9356 H          1 TYR      0.271900
-      3 CA          5.5045    1.4387    1.1713 CX         1 TYR     -0.001400
-      4 HA          6.5833    1.5906    1.2064 H1         1 TYR      0.087600
-      5 CB          5.1981    0.3552    0.1428 CT         1 TYR     -0.015200
-      6 HB2         5.6866   -0.5735    0.4378 HC         1 TYR      0.029500
-      7 HB3         5.5697    0.6663   -0.8336 HC         1 TYR      0.029500
-      8 C           4.8470    2.7276    0.6990 C          1 TYR      0.597300
-      9 O           4.0264    3.3055    1.4083 O          1 TYR     -0.567900
-     10 C2          3.6760    0.1340    0.0670 CA         2 PRY      0.033204
-     11 C3          3.1370   -1.1220    0.3590 CA         2 PRY     -0.149016
-     12 H4          3.7940   -1.9290    0.6360 HA         2 PRY      0.153372
-     13 C4          1.7830   -1.3560    0.3010 CA         2 PRY     -0.336291
-     14 H5          1.3750   -2.3240    0.5260 HA         2 PRY      0.167425
-     15 C5          0.9070   -0.3310   -0.0550 CA         2 PRY      0.423974
-     16 O1         -0.4020   -0.6590   -0.0810 OS         2 PRY     -0.391815
-     17 C6          1.4180    0.9200   -0.3470 CA         2 PRY     -0.336291
-     18 H6          0.7760    1.7340   -0.6230 HA         2 PRY      0.167425
-     19 C7          2.7930    1.1360   -0.2830 CA         2 PRY     -0.149016
-     20 H7          3.1680    2.1180   -0.5140 HA         2 PRY      0.153372
-     21 C8         -1.3580    0.3020   -0.4580 CT         2 PRY      0.358047
-     22 C9         -2.6930   -0.3810   -0.4700 CM         2 PRY     -0.496680
-     23 C10        -3.8370    0.0490    0.0400 CM         2 PRY      0.317549
-     24 C11        -5.0960   -0.7730   -0.1000 CT         2 PRY     -0.394216
-     25 C12        -4.0350    1.3480    0.7820 CT         2 PRY     -0.394216
-     26 H8         -1.1210    0.6720   -1.4540 H1         2 PRY      0.001584
-     27 H9         -1.3270    1.1410    0.2250 H1         2 PRY      0.001584
-     28 H10        -2.6800   -1.3290   -0.9820 HA         2 PRY      0.192041
-     29 H11        -5.8660   -0.2140   -0.6260 HC         2 PRY      0.110363
-     30 H12        -5.5010   -1.0240    0.8780 HC         2 PRY      0.110363
-     31 H13        -4.9190   -1.6950   -0.6400 HC         2 PRY      0.110363
-     32 H14        -4.7240    1.9910    0.2380 HC         2 PRY      0.110363
-     33 H15        -3.1210    1.9030    0.9400 HC         2 PRY      0.110363
-     34 H16        -4.4820    1.1590    1.7540 HC         2 PRY      0.110363
+      1 N           3.3258    1.5479   -0.0000 N          1 TYR     -0.415700
+      2 H           3.9094    0.7236   -0.0000 H          1 TYR      0.271900
+      3 CA          3.9700    2.8458   -0.0000 CX         1 TYR     -0.001400
+      4 HA          3.6717    3.4001   -0.8898 H1         1 TYR      0.087600
+      5 CB          3.5770    3.6538    1.2321 CT         1 TYR     -0.015200
+      6 HB2         2.4970    3.8011    1.2414 HC         1 TYR      0.029500
+      7 HB3         3.8775    3.1158    2.1312 HC         1 TYR      0.029500
+      8 C           5.4855    2.7052   -0.0000 C          1 TYR      0.597300
+      9 O           6.0088    1.5932   -0.0000 O          1 TYR     -0.567900
+     10 C2          4.2167    4.8987    1.1983 CA         2 PRY      0.033204
+     11 C3          4.0500    5.8609    2.1981 CA         2 PRY     -0.149016
+     12 H4          3.4057    5.6495    3.0346 HA         2 PRY      0.153372
+     13 C4          4.6895    7.0771    2.1412 CA         2 PRY     -0.336291
+     14 H5          4.5566    7.8128    2.9127 HA         2 PRY      0.167425
+     15 C5          5.5298    7.3802    1.0703 CA         2 PRY      0.423974
+     16 O1          6.1127    8.5970    1.1066 OS         2 PRY     -0.391815
+     17 C6          5.7104    6.4428    0.0703 CA         2 PRY     -0.336291
+     18 H6          6.3501    6.6384   -0.7684 HA         2 PRY      0.167425
+     19 C7          5.0526    5.2168    0.1465 CA         2 PRY     -0.149016
+     20 H7          5.2076    4.5030   -0.6439 HA         2 PRY      0.153372
+     21 C8          6.9535    9.0030    0.0541 CT         2 PRY      0.358047
+     22 C9          7.3730   10.4140    0.3402 CM         2 PRY     -0.496680
+     23 C10         8.5864   10.9389    0.2629 CM         2 PRY      0.317549
+     24 C11         8.8094   12.4021    0.5624 CT         2 PRY     -0.394216
+     25 C12         9.8424   10.1956   -0.1206 CT         2 PRY     -0.394216
+     26 H8          6.4004    8.9625   -0.8827 H1         2 PRY      0.001584
+     27 H9          7.7956    8.3279   -0.0270 H1         2 PRY      0.001584
+     28 H10         6.5519   11.0514    0.6242 HA         2 PRY      0.192041
+     29 H11         9.2372   12.9117   -0.2975 HC         2 PRY      0.110363
+     30 H12         9.5134   12.5228    1.3829 HC         2 PRY      0.110363
+     31 H13         7.8882   12.9051    0.8297 HC         2 PRY      0.110363
+     32 H14        10.2558   10.6045   -1.0404 HC         2 PRY      0.110363
+     33 H15         9.6929    9.1354   -0.2690 HC         2 PRY      0.110363
+     34 H16        10.6002   10.3206    0.6478 HC         2 PRY      0.110363
 @<TRIPOS>BOND
     1     1     3 1
     2     3     5 1
@@ -57,7 +57,7 @@ USER_CHARGES
    14    22    23 1
    15    23    24 1
    16    23    25 1
-   17     5    10 1
+   17    10     5 1
    18     1     2 1
    19     3     4 1
    20     5     6 1

From 21a2eded99d4bcc6ee5d9d280680e620eb83d156 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 12 Feb 2024 10:23:01 -0500
Subject: [PATCH 0503/1492] Add function for getting internal coords that can
 be used to construct an atom.

---
 src/Structure/Builder.cpp | 53 +++++++++++++++++++++++++++++++++++++++
 src/Structure/Builder.h   |  2 ++
 2 files changed, 55 insertions(+)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 2763ac310f..6e2d33e7b8 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1645,6 +1645,59 @@ int Builder::GenerateInternalsAroundLink(int at0, int at1,
   return 0;
 }
 
+/** Find internal coordinates for given atom.
+  * Find torsion that contains this atom as one of the end atoms. The other
+  * three atoms must have known position.
+  * There must be a bond and angle that lie on the torsion and include
+  * the given atom as a terminal atom.
+  * \return 1 if complete internal coords were found, 0 if not.
+  */
+int Builder::getIcFromInternals(InternalCoords& icOut, int at, Barray const& hasPosition) const
+{
+  for (Tarray::const_iterator dih = internalTorsions_.begin(); dih != internalTorsions_.end(); ++dih)
+  {
+    if (at == dih->AtI()) {
+      if (hasPosition[dih->AtJ()] &&
+          hasPosition[dih->AtK()] &&
+          hasPosition[dih->AtL()])
+      {
+        int bidx = getExistingBondIdx(dih->AtI(), dih->AtJ());
+        if (bidx > -1) {
+          int aidx = getExistingAngleIdx(dih->AtI(), dih->AtJ(), dih->AtK());
+          if (aidx > -1) {
+            icOut = InternalCoords(dih->AtI(), dih->AtJ(), dih->AtK(), dih->AtL(),
+                                   internalBonds_[bidx].DistVal(),
+                                   internalAngles_[aidx].ThetaVal()*Constants::RADDEG,
+                                   dih->PhiVal()*Constants::RADDEG);
+            return 1;
+          }
+        }
+      }
+    } else if (at == dih->AtL()) {
+      if (hasPosition[dih->AtK()] &&
+          hasPosition[dih->AtJ()] &&
+          hasPosition[dih->AtI()])
+      {
+        int bidx = getExistingBondIdx(dih->AtL(), dih->AtK());
+        if (bidx > -1) {
+          int aidx = getExistingAngleIdx(dih->AtL(), dih->AtK(), dih->AtJ());
+          if (aidx > -1) {
+            icOut = InternalCoords(dih->AtL(), dih->AtK(), dih->AtJ(), dih->AtI(),
+                                   internalBonds_[bidx].DistVal(),
+                                   internalAngles_[aidx].ThetaVal()*Constants::RADDEG,
+                                   dih->PhiVal()*Constants::RADDEG);
+            return 1;
+          }
+        }
+      }
+    }
+  } // END loop over internal torsions
+  return 0;
+}
+ 
+
+//int Builder::BuildFromInternals
+
 /** Generate a Zmatrix from the current internals. TODO only for atoms that need it? */
 int Builder::GetZmatrixFromInternals(Zmatrix& zmatrix, Topology const& topIn) const {
   mprintf("DEBUG: ----- Enter GetZmatrixFromInternals -----\n");
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index fcdabd2886..0f300f815a 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -96,6 +96,8 @@ class Builder {
 
     /// Generate internal coords for a given atom
     int generateAtomInternals(int, Frame const&, Topology const&, Barray const&);
+    /// Get complete internal coords that can be used to construct specified atom
+    int getIcFromInternals(InternalCoords&, int, Barray const&) const;
 
     int debug_;
     ParameterSet const* params_;

From 652901ca5a28f954a8caaca1629673049f404c3f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 12 Feb 2024 10:47:38 -0500
Subject: [PATCH 0504/1492] Add function to build from internals

---
 src/Structure/Builder.cpp | 70 +++++++++++++++++++++++++++++++++++++--
 src/Structure/Builder.h   |  3 ++
 2 files changed, 71 insertions(+), 2 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 6e2d33e7b8..4098c8f9a5 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1694,9 +1694,75 @@ int Builder::getIcFromInternals(InternalCoords& icOut, int at, Barray const& has
   } // END loop over internal torsions
   return 0;
 }
- 
 
-//int Builder::BuildFromInternals
+/** Build coordinates for any atom of the specified residue that does
+  * not have its position set.
+  */ 
+int Builder::BuildFromInternals(Frame& frameOut, int ires, Topology const& topIn, Barray& hasPosition)
+const
+{
+  Residue const& currentRes = topIn.Res(ires);
+  // Count how many atoms need their positions set
+  unsigned int nAtomsThatNeedPositions = 0;
+  for (int at = currentRes.FirstAtom(); at != currentRes.LastAtom(); ++at)
+    if (!hasPosition[at])
+      nAtomsThatNeedPositions++;
+  mprintf("DEBUG: %u atoms need positions in residue %s\n", nAtomsThatNeedPositions, topIn.TruncResNameNum(ires).c_str());
+  if (nAtomsThatNeedPositions == 0) return 0;
+
+  // Loop over residue atoms
+  while (nAtomsThatNeedPositions > 0) {
+    unsigned int nAtomsBuilt = 0;
+    for (int at = currentRes.FirstAtom(); at != currentRes.LastAtom(); ++at)
+    {
+      int atToBuildAround = -1;
+      if (!hasPosition[at]) {
+        // Position of atom is not known.
+        mprintf("BUILD: Position of %s is not known.\n", *(topIn[at].Name()));
+        // Is this bonded to an atom with known position?
+        for (Atom::bond_iterator bat = topIn[at].bondbegin(); bat != topIn[at].bondend(); ++bat) {
+          if (hasPosition[*bat]) {
+            atToBuildAround = *bat;
+            break;
+          }
+        }
+      } else {
+        // Position of atom is known.
+        mprintf("BUILD: Position of %s is known.\n", *(topIn[at].Name()));
+        atToBuildAround = at;
+      }
+      // Build unknown positions around known atom
+      if (atToBuildAround != -1) {
+        mprintf("Building externals from %s\n", topIn.LeapName(atToBuildAround).c_str());
+        Atom const& bAtom = topIn[atToBuildAround];
+        for (Atom::bond_iterator bat = bAtom.bondbegin(); bat != bAtom.bondend(); ++bat)
+        {
+          if (!hasPosition[*bat]) {
+            // Find an internal coordinate.
+            InternalCoords ic;
+            if (getIcFromInternals(ic, *bat, hasPosition)) {
+              mprintf("Building atom %s using torsion/angle/bond\n", topIn.LeapName(*bat).c_str());
+              mprintf( "Torsion = %f\n", ic.Phi() );
+              mprintf( "Angle   = %f\n", ic.Theta() );
+              mprintf( "Bond    = %f\n", ic.Dist() );
+              Vec3 posI = Zmatrix::AtomIposition(ic, frameOut);
+              frameOut.SetXYZ( ic.AtI(), posI );
+              hasPosition[ ic.AtI() ] = true;
+              nAtomsBuilt++;
+              nAtomsThatNeedPositions--;
+            }
+          }
+        } // END loop over atoms bonded to atom with known position
+      }
+    } // END loop over residue atoms
+    // If we built no atoms this is a problem
+    if (nAtomsBuilt < 1) {
+      mprinterr("Error: No more atoms could be built for residue %s\n", topIn.TruncResNameNum(ires).c_str());
+      return 1;
+    }
+  } // END loop while atoms need position
+  return 0;
+}
 
 /** Generate a Zmatrix from the current internals. TODO only for atoms that need it? */
 int Builder::GetZmatrixFromInternals(Zmatrix& zmatrix, Topology const& topIn) const {
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index 0f300f815a..774757517f 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -29,6 +29,9 @@ class Builder {
     /// Update existing indices with given offset
     void UpdateIndicesWithOffset(int);
 
+    /// Build position from internals for any atom in residue with unset position
+    int BuildFromInternals(Frame&, int, Topology const&, Barray&) const;
+
     /// \return Zmatrix from current internals
     int GetZmatrixFromInternals(Zmatrix&, Topology const&) const;
   private:

From fa2aae51bd9a8dd943176a36f24d36baa1a2ee72 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 12 Feb 2024 11:02:04 -0500
Subject: [PATCH 0505/1492] This should build things in the exact same order as
 leap

---
 src/Exec_Build.cpp                           | 15 ++++++++-------
 src/Structure/Builder.cpp                    | 11 ++++++++++-
 src/Structure/GenerateConnectivityArrays.cpp | 15 +++++++++++++++
 src/Structure/GenerateConnectivityArrays.h   |  2 ++
 4 files changed, 35 insertions(+), 8 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 49fff328e5..343a73c497 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -359,13 +359,14 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
         return 1;
       }
       // Convert to Zmatrix and assign missing atom positions
-      Cpptraj::Structure::Zmatrix tmpz;
-      tmpz.SetDebug( 1 ); // DEBUG
-      if (structureBuilder.GetZmatrixFromInternals(tmpz, topOut)) {
-        mprinterr("Error: Could not get Zmatrix from internals.\n");
-        return 1;
-      }
-      if (tmpz.SetToFrame( frameOut, hasPosition )) {
+      //Cpptraj::Structure::Zmatrix tmpz;
+      //tmpz.SetDebug( 1 ); // DEBUG
+      //if (structureBuilder.GetZmatrixFromInternals(tmpz, topOut)) {
+      //  mprinterr("Error: Could not get Zmatrix from internals.\n");
+      //  return 1;
+      //}
+      //if (tmpz.SetToFrame( frameOut, hasPosition )) {
+      if (structureBuilder.BuildFromInternals(frameOut, ires, topOut, hasPosition)) {
         mprinterr("Error: Building residue %s failed.\n",
                   topOut.TruncResNameOnumId(ires).c_str());
         buildFailed = true;
diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 4098c8f9a5..3756424f1c 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1710,11 +1710,16 @@ const
   mprintf("DEBUG: %u atoms need positions in residue %s\n", nAtomsThatNeedPositions, topIn.TruncResNameNum(ires).c_str());
   if (nAtomsThatNeedPositions == 0) return 0;
 
+  // Generate array over residue in same order that leap would do
+  std::vector<int> resIndices = GenerateAtomArray(std::vector<Residue>(1, topIn.Res(ires)), topIn.Atoms());
+
   // Loop over residue atoms
   while (nAtomsThatNeedPositions > 0) {
     unsigned int nAtomsBuilt = 0;
-    for (int at = currentRes.FirstAtom(); at != currentRes.LastAtom(); ++at)
+    for (std::vector<int>::const_iterator idx = resIndices.begin();
+                                          idx != resIndices.end(); ++idx)
     {
+      int at = *idx;
       int atToBuildAround = -1;
       if (!hasPosition[at]) {
         // Position of atom is not known.
@@ -1742,6 +1747,10 @@ const
             InternalCoords ic;
             if (getIcFromInternals(ic, *bat, hasPosition)) {
               mprintf("Building atom %s using torsion/angle/bond\n", topIn.LeapName(*bat).c_str());
+              mprintf("Using - %s - %s - %s\n",
+                      topIn.LeapName(ic.AtJ()).c_str(),
+                      topIn.LeapName(ic.AtK()).c_str(),
+                      topIn.LeapName(ic.AtL()).c_str());
               mprintf( "Torsion = %f\n", ic.Phi() );
               mprintf( "Angle   = %f\n", ic.Theta() );
               mprintf( "Bond    = %f\n", ic.Dist() );
diff --git a/src/Structure/GenerateConnectivityArrays.cpp b/src/Structure/GenerateConnectivityArrays.cpp
index 0cdc011937..2366ea616a 100644
--- a/src/Structure/GenerateConnectivityArrays.cpp
+++ b/src/Structure/GenerateConnectivityArrays.cpp
@@ -31,6 +31,21 @@ static inline void set_indices(int& start, int& end, int& offset, int firstatom,
   }
 }
 
+/** Generate atom array in same order as LEaP. */
+std::vector<int> Cpptraj::Structure::GenerateAtomArray(std::vector<Residue> const& residues,
+                                                       std::vector<Atom> const& atoms)
+{
+  std::vector<int> out;
+  for (std::vector<Residue>::const_iterator res = residues.begin(); res != residues.end(); ++res)
+  {
+    int start, end, offset;
+    set_indices(start, end, offset, res->FirstAtom(), res->LastAtom());
+    for (int iat = start; iat != end; iat += offset)
+      out.push_back( iat );
+  }
+  return out;
+}
+
 /** From atom connectivity, generate a bond array in the same order as LEaP. */ // TODO use in GenerateBAT
 BondArray Cpptraj::Structure::GenerateBondArray(std::vector<Residue> const& residues,
                                                 std::vector<Atom> const& atoms)
diff --git a/src/Structure/GenerateConnectivityArrays.h b/src/Structure/GenerateConnectivityArrays.h
index 9fe70514e7..7efd766dc8 100644
--- a/src/Structure/GenerateConnectivityArrays.h
+++ b/src/Structure/GenerateConnectivityArrays.h
@@ -12,6 +12,8 @@ namespace Structure {
 enum AtomScanDirectionType { SCAN_ATOMS_BACKWARDS = 0, SCAN_ATOMS_FORWARDS };
 /// Set default atom scan direction
 void SetAtomScanDirection(AtomScanDirectionType);
+/// Generate array of atom indices in same order as leap
+std::vector<int> GenerateAtomArray(std::vector<Residue> const&, std::vector<Atom> const&);
 /// Generate bond array in same order as leap
 BondArray GenerateBondArray(std::vector<Residue> const&, std::vector<Atom> const&);
 /// Generate a spanning tree

From 1ac8e820642a63b7f9b0f08bf497feddd2a9afeb Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 12 Feb 2024 14:12:31 -0500
Subject: [PATCH 0506/1492] Do not do per residue since units might have more
 than 1 residue

---
 src/Exec_Build.cpp        |  2 +-
 src/Exec_Graft.cpp        | 19 ++++++++++------
 src/Structure/Builder.cpp | 47 +++++++++++++++++++++++++++++----------
 src/Structure/Builder.h   |  4 ++--
 4 files changed, 50 insertions(+), 22 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 343a73c497..a9453040a3 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -366,7 +366,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
       //  return 1;
       //}
       //if (tmpz.SetToFrame( frameOut, hasPosition )) {
-      if (structureBuilder.BuildFromInternals(frameOut, ires, topOut, hasPosition)) {
+      if (structureBuilder.BuildFromInternals(frameOut, topOut, hasPosition)) {
         mprinterr("Error: Building residue %s failed.\n",
                   topOut.TruncResNameOnumId(ires).c_str());
         buildFailed = true;
diff --git a/src/Exec_Graft.cpp b/src/Exec_Graft.cpp
index 207dbae367..23ed2a8e58 100644
--- a/src/Exec_Graft.cpp
+++ b/src/Exec_Graft.cpp
@@ -394,17 +394,22 @@ const
     return 1;
   }
   // Convert to Zmatrix and assign missing atom positions
-  Cpptraj::Structure::Zmatrix tmpz;
-  tmpz.SetDebug( 1 ); // DEBUG
-  if (structureBuilder.GetZmatrixFromInternals(tmpz, topOut)) {
-    mprinterr("Error: Could not get Zmatrix from internals.\n");
-    return 1;
-  }
-  if (tmpz.SetToFrame( frameOut, hasPosition )) {
+  if (structureBuilder.BuildFromInternals(frameOut, topOut, hasPosition)) {
     mprinterr("Error: Grafting %s with %s build from internals failed.\n",
               mol0Top.c_str(), mol1Top.c_str());
     return 1;
   }
+//  Cpptraj::Structure::Zmatrix tmpz;
+//  tmpz.SetDebug( 1 ); // DEBUG
+//  if (structureBuilder.GetZmatrixFromInternals(tmpz, topOut)) {
+//    mprinterr("Error: Could not get Zmatrix from internals.\n");
+//    return 1;
+//  }
+//  if (tmpz.SetToFrame( frameOut, hasPosition )) {
+//    mprinterr("Error: Grafting %s with %s build from internals failed.\n",
+//              mol0Top.c_str(), mol1Top.c_str());
+//    return 1;
+//  }
   // Finalize topology - determine molecules, dont renumber residues, assign default bond params
   topOut.CommonSetup(true, false, true);
   topOut.Summary();
diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 3756424f1c..ce1ce28886 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1695,29 +1695,52 @@ int Builder::getIcFromInternals(InternalCoords& icOut, int at, Barray const& has
   return 0;
 }
 
-/** Build coordinates for any atom of the specified residue that does
+/** Build coordinates for any atom with an internal that does
   * not have its position set.
   */ 
-int Builder::BuildFromInternals(Frame& frameOut, int ires, Topology const& topIn, Barray& hasPosition)
+int Builder::BuildFromInternals(Frame& frameOut, Topology const& topIn, Barray& hasPosition)
 const
 {
-  Residue const& currentRes = topIn.Res(ires);
+  // Create a list of residues that have atoms that need positions
+  std::vector<Residue> residues;
+  std::vector<int> Rnums;
+  for (Tarray::const_iterator dih = internalTorsions_.begin();
+                              dih != internalTorsions_.end(); ++dih)
+  {
+    if (!hasPosition[dih->AtI()]) {
+      int rnum = topIn[dih->AtI()].ResNum();
+      bool has_rnum = false;
+      for (std::vector<int>::const_iterator it = Rnums.begin(); it != Rnums.end(); ++it) {
+        if (*it == rnum) {
+          has_rnum = true;
+          break;
+        }
+      }
+      if (!has_rnum) {
+        mprintf("DEBUG: Need to build for residue %s\n", topIn.TruncResNameNum(rnum).c_str());
+        residues.push_back( topIn.Res(rnum) );
+        Rnums.push_back(rnum);
+      }
+    }
+  }
+  // Generate array over residue in same order that leap would do
+  std::vector<int> atomIndices = GenerateAtomArray(residues, topIn.Atoms());
+  residues.clear();
+  Rnums.clear();
   // Count how many atoms need their positions set
   unsigned int nAtomsThatNeedPositions = 0;
-  for (int at = currentRes.FirstAtom(); at != currentRes.LastAtom(); ++at)
-    if (!hasPosition[at])
+  for (std::vector<int>::const_iterator it = atomIndices.begin();
+                                        it != atomIndices.end(); ++it)
+    if (!hasPosition[*it])
       nAtomsThatNeedPositions++;
-  mprintf("DEBUG: %u atoms need positions in residue %s\n", nAtomsThatNeedPositions, topIn.TruncResNameNum(ires).c_str());
+  mprintf("DEBUG: %u atoms need positions.\n", nAtomsThatNeedPositions);
   if (nAtomsThatNeedPositions == 0) return 0;
 
-  // Generate array over residue in same order that leap would do
-  std::vector<int> resIndices = GenerateAtomArray(std::vector<Residue>(1, topIn.Res(ires)), topIn.Atoms());
-
   // Loop over residue atoms
   while (nAtomsThatNeedPositions > 0) {
     unsigned int nAtomsBuilt = 0;
-    for (std::vector<int>::const_iterator idx = resIndices.begin();
-                                          idx != resIndices.end(); ++idx)
+    for (std::vector<int>::const_iterator idx = atomIndices.begin();
+                                          idx != atomIndices.end(); ++idx)
     {
       int at = *idx;
       int atToBuildAround = -1;
@@ -1766,7 +1789,7 @@ const
     } // END loop over residue atoms
     // If we built no atoms this is a problem
     if (nAtomsBuilt < 1) {
-      mprinterr("Error: No more atoms could be built for residue %s\n", topIn.TruncResNameNum(ires).c_str());
+      mprinterr("Error: No more atoms could be built for %s\n", topIn.c_str());
       return 1;
     }
   } // END loop while atoms need position
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index 774757517f..0df4b17291 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -29,8 +29,8 @@ class Builder {
     /// Update existing indices with given offset
     void UpdateIndicesWithOffset(int);
 
-    /// Build position from internals for any atom in residue with unset position
-    int BuildFromInternals(Frame&, int, Topology const&, Barray&) const;
+    /// Build position from internals for any atom with unset position
+    int BuildFromInternals(Frame&, Topology const&, Barray&) const;
 
     /// \return Zmatrix from current internals
     int GetZmatrixFromInternals(Zmatrix&, Topology const&) const;

From aa62a76f471f90317863f54f797b3028375ff688 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 12 Feb 2024 14:34:30 -0500
Subject: [PATCH 0507/1492] Print all internals when building atoms for
 debugging. Make leap name closer to what leap actually puts

---
 src/Exec_Sequence.cpp     | 15 ++++++++-------
 src/Structure/Builder.cpp | 33 +++++++++++++++++++++++++++++++++
 src/Structure/Builder.h   |  2 ++
 src/Topology.cpp          |  3 ++-
 4 files changed, 45 insertions(+), 8 deletions(-)

diff --git a/src/Exec_Sequence.cpp b/src/Exec_Sequence.cpp
index 1d96f2cf55..192753eca6 100644
--- a/src/Exec_Sequence.cpp
+++ b/src/Exec_Sequence.cpp
@@ -226,13 +226,14 @@ const
         return 1;
       }
       // Convert to Zmatrix and assign missing atom positions
-      Cpptraj::Structure::Zmatrix tmpz;
-      tmpz.SetDebug( 1 ); // DEBUG
-      if (structureBuilder.GetZmatrixFromInternals(tmpz, topOut)) {
-        mprinterr("Error: Could not get Zmatrix from internals.\n");
-        return 1;
-      }
-      if (tmpz.SetToFrame( frameOut, hasPosition )) {
+      //Cpptraj::Structure::Zmatrix tmpz;
+      //tmpz.SetDebug( 1 ); // DEBUG
+      //if (structureBuilder.GetZmatrixFromInternals(tmpz, topOut)) {
+      //  mprinterr("Error: Could not get Zmatrix from internals.\n");
+      //  return 1;
+      //}
+      //if (tmpz.SetToFrame( frameOut, hasPosition )) {
+      if (structureBuilder.BuildFromInternals(frameOut, topOut, hasPosition)) {
         mprinterr("Error: Building residue %s failed.\n",
                   topOut.TruncResNameOnumId(ires).c_str());
         buildFailed = true;
diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index ce1ce28886..6874eba012 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1645,6 +1645,37 @@ int Builder::GenerateInternalsAroundLink(int at0, int at1,
   return 0;
 }
 
+void Builder::printAllInternalsForAtom(int at, Topology const& topIn, Barray const& hasPosition) const
+{
+  mprintf("DEBUG: All internals for atom %s\n", topIn.LeapName(at).c_str());
+  for (Tarray::const_iterator dih = internalTorsions_.begin(); dih != internalTorsions_.end(); ++dih)
+  {
+    if (at == dih->AtI()) {
+      if (hasPosition[dih->AtJ()] &&
+          hasPosition[dih->AtK()] &&
+          hasPosition[dih->AtL()])
+      {
+        mprintf("DEBUG:\t\t%s - %s - %s Phi= %f\n",
+                topIn.LeapName(dih->AtJ()).c_str(),
+                topIn.LeapName(dih->AtK()).c_str(),
+                topIn.LeapName(dih->AtL()).c_str(),
+                dih->PhiVal()*Constants::RADDEG);
+      }
+    } else if (at == dih->AtL()) {
+      if (hasPosition[dih->AtK()] &&
+          hasPosition[dih->AtJ()] &&
+          hasPosition[dih->AtI()])
+      {
+        mprintf("DEBUG:\t\t%s - %s - %s Phi= %f\n",
+                topIn.LeapName(dih->AtK()).c_str(),
+                topIn.LeapName(dih->AtJ()).c_str(),
+                topIn.LeapName(dih->AtI()).c_str(),
+                dih->PhiVal()*Constants::RADDEG);
+      }
+    }
+  }
+}
+
 /** Find internal coordinates for given atom.
   * Find torsion that contains this atom as one of the end atoms. The other
   * three atoms must have known position.
@@ -1769,6 +1800,8 @@ const
             // Find an internal coordinate.
             InternalCoords ic;
             if (getIcFromInternals(ic, *bat, hasPosition)) {
+              printAllInternalsForAtom(*bat, topIn, hasPosition); // DEBUG
+
               mprintf("Building atom %s using torsion/angle/bond\n", topIn.LeapName(*bat).c_str());
               mprintf("Using - %s - %s - %s\n",
                       topIn.LeapName(ic.AtJ()).c_str(),
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index 0df4b17291..51805c7dda 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -101,6 +101,8 @@ class Builder {
     int generateAtomInternals(int, Frame const&, Topology const&, Barray const&);
     /// Get complete internal coords that can be used to construct specified atom
     int getIcFromInternals(InternalCoords&, int, Barray const&) const;
+    // For debug
+    void printAllInternalsForAtom(int, Topology const&, Barray const&) const;
 
     int debug_;
     ParameterSet const* params_;
diff --git a/src/Topology.cpp b/src/Topology.cpp
index 48046ba4ac..79a884f402 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -337,8 +337,9 @@ std::string Topology::TruncAtomNameNum(int atom) const {
 /** Given an atom number, return a string in LEaP-style format. */
 std::string Topology::LeapName(int at) const {
   int rnum = atoms_[at].ResNum();
+  int idx = at - residues_[rnum].FirstAtom() + 1;
   std::string out( ".R<" + residues_[rnum].Name().Truncated() + " " + integerToString(rnum+1) +
-                  ">.A<" + atoms_[at].Name().Truncated()      + " " + integerToString(at+1) + ">");
+                  ">.A<" + atoms_[at].Name().Truncated()      + " " + integerToString(idx) + ">");
   return out;
 }
 

From 631b620f6333f48d3b8bebd03ab868e5d43fef32 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 12 Feb 2024 15:01:07 -0500
Subject: [PATCH 0508/1492] Get rid of unused vars

---
 src/Structure/Builder.cpp | 41 +++------------------------------------
 src/Structure/Builder.h   |  2 --
 2 files changed, 3 insertions(+), 40 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 6874eba012..5d08f5efba 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -17,9 +17,7 @@ using namespace Cpptraj::Structure;
 Builder::Builder() :
   debug_(0),
   params_(0),
-  currentTop_(0),
-  currentFrm_(0),
-  hasPosition_(0)
+  currentTop_(0)
 {}
 
 /** Set optional parameter set. */
@@ -1044,37 +1042,6 @@ void Builder::ModelTorsion(TorsionModel const& MT, unsigned int iBondX, unsigned
   // Look for an existing internal
   int icIdx = getExistingTorsionIdx( aa, ax, ay, ad );
   if (icIdx < 0) {
-/*    // Get bond lengths FIXME deal with unknown positions
-    double l0, l1;
-    if (AssignLength(l0, aa, ax, *currentTop_, *currentFrm_, *hasPosition_)) {
-      mprinterr("Error: Could not assign length between %s and %s\n",
-                currentTop_->AtomMaskName(aa).c_str(),
-                currentTop_->AtomMaskName(ax).c_str());
-      return;
-    }
-    if (AssignLength(l1, ad, ay, *currentTop_, *currentFrm_, *hasPosition_)) {
-      mprinterr("Error: Could not assign length between %s and %s\n",
-                currentTop_->AtomMaskName(ad).c_str(),
-                currentTop_->AtomMaskName(ay).c_str());
-      return;
-    }
-    // Get angles
-    double t0, t1;
-    if (AssignTheta(t0, aa, ax, ay, *currentTop_, *currentFrm_, *hasPosition_)) {
-      mprinterr("Error: Could not assign angle between %s and %s and %s\n",
-                currentTop_->AtomMaskName(aa).c_str(),
-                currentTop_->AtomMaskName(ax).c_str(),
-                currentTop_->AtomMaskName(ay).c_str());
-      return;
-    }
-    if (AssignTheta(t1, ad, ay, ax, *currentTop_, *currentFrm_, *hasPosition_)) {
-      mprinterr("Error: Could not assign angle between %s and %s and %s\n",
-                currentTop_->AtomMaskName(ad).c_str(),
-                currentTop_->AtomMaskName(ay).c_str(),
-                currentTop_->AtomMaskName(ax).c_str());
-      return;
-    }*/
-
     mprintf("++++Torsion INTERNAL: %f to %s - %s - %s - %s\n", phiVal*Constants::RADDEG,
             currentTop_->LeapName(aa).c_str(),
             currentTop_->LeapName(ax).c_str(),
@@ -1205,11 +1172,9 @@ void Builder::createSp2Sp2Torsions(TorsionModel const& MT) {
 /** Assign torsions around bonded atoms in manner similar to LEaP's ModelAssignTorsionsAround. */
 int Builder::assignTorsionsAroundBond(int a1, int a2, Frame const& frameIn, Topology const& topIn, Barray const& hasPosition, int aAtomIdx)
 {
-  // Save addresses of zmatrix, frame, topology, and hasPosition.
-  // These are required for the createSpXSpX routines. TODO zero them at the end?
-  currentFrm_ = &frameIn;
+  // Save address of current topology.
+  // These are required for the ModelTorsion routine. TODO zero at the end?
   currentTop_ = &topIn;
-  hasPosition_ = &hasPosition;
   // No need to do this if either atom only has 1 bond.
   if (topIn[a1].Nbonds() < 2 || topIn[a2].Nbonds() < 2)
     return 0;
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index 51805c7dda..7fa3fc2791 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -108,8 +108,6 @@ class Builder {
     ParameterSet const* params_;
 
     Topology const* currentTop_; ///< Topology for the createSpXSpXTorsions/ModelTorsion routines
-    Frame const* currentFrm_;    ///< Frame for the createSpXSpXTorsions routines
-    Barray const* hasPosition_;  ///< Array indicating which atoms have position for createSpXSpXTorsions/ModelTorsion routines
     Tarray internalTorsions_;
     Aarray internalAngles_;
     Larray internalBonds_;

From 6849c64b2587503a365950a61d6dae4b0551b46b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 12 Feb 2024 15:16:51 -0500
Subject: [PATCH 0509/1492] Make UpdateICsFromFrame not depend on residue
 number

---
 src/Exec_Build.cpp        |  2 +-
 src/Exec_Graft.cpp        |  5 +++++
 src/Exec_Sequence.cpp     |  2 +-
 src/Structure/Builder.cpp | 36 +++++++++++++++++++++++++++---------
 src/Structure/Builder.h   |  7 ++++---
 5 files changed, 38 insertions(+), 14 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index a9453040a3..e92251914a 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -354,7 +354,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
         }
       }
       // Update internal coords from known positions
-      if (structureBuilder.UpdateICsFromFrame( frameOut, ires, topOut, hasPosition )) {
+      if (structureBuilder.UpdateICsFromFrame( frameOut, topOut, hasPosition )) {
         mprinterr("Error: Failed to update Zmatrix with values from existing positions.\n");
         return 1;
       }
diff --git a/src/Exec_Graft.cpp b/src/Exec_Graft.cpp
index 23ed2a8e58..e1b33151fb 100644
--- a/src/Exec_Graft.cpp
+++ b/src/Exec_Graft.cpp
@@ -393,6 +393,11 @@ const
               topOut.AtomMaskName(bondat0).c_str());
     return 1;
   }
+  // Update internal coords from known positions
+  if (structureBuilder.UpdateICsFromFrame( frameOut, topOut, hasPosition )) {
+    mprinterr("Error: Failed to update Zmatrix with values from existing positions.\n");
+    return 1;
+  }
   // Convert to Zmatrix and assign missing atom positions
   if (structureBuilder.BuildFromInternals(frameOut, topOut, hasPosition)) {
     mprinterr("Error: Grafting %s with %s build from internals failed.\n",
diff --git a/src/Exec_Sequence.cpp b/src/Exec_Sequence.cpp
index 192753eca6..eaa5c7840a 100644
--- a/src/Exec_Sequence.cpp
+++ b/src/Exec_Sequence.cpp
@@ -221,7 +221,7 @@ const
         return 1;
       }
       // Update internal coords from known positions
-      if (structureBuilder.UpdateICsFromFrame( frameOut, ires, topOut, hasPosition )) {
+      if (structureBuilder.UpdateICsFromFrame( frameOut, topOut, hasPosition )) {
         mprinterr("Error: Failed to update Zmatrix with values from existing positions.\n");
         return 1;
       }
diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 5d08f5efba..24254687a7 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -82,15 +82,34 @@ const
 }
 
 /** For existing torsions, see if all coordinates in that torsion
-  * exist. If so, update the IC from the existing coordinates.
+  * exist. If so, update the torsion from the existing coordinates.
   */
-int Builder::UpdateICsFromFrame(Frame const& frameIn, int ires, Topology const& topIn, Barray const& hasPosition)
+int Builder::UpdateICsFromFrame(Frame const& frameIn, Topology const& topIn, Barray const& hasPosition)
 {
-  // Update torsions.
+  // Create a list of residues that have atoms with internals 
+  std::vector<Residue> residues;
+  std::vector<int> Rnums;
+  for (Tarray::const_iterator dih = internalTorsions_.begin();
+                              dih != internalTorsions_.end(); ++dih)
+  {
+    int rnum = topIn[dih->AtI()].ResNum();
+    bool has_rnum = false;
+    for (std::vector<int>::const_iterator it = Rnums.begin(); it != Rnums.end(); ++it) {
+      if (*it == rnum) {
+        has_rnum = true;
+        break;
+      }
+    }
+    if (!has_rnum) {
+      mprintf("DEBUG: Residue %s has internals.\n", topIn.TruncResNameNum(rnum).c_str());
+      residues.push_back( topIn.Res(rnum) );
+      Rnums.push_back(rnum);
+    }
+  }
   // Get list of bonds.
-  BondArray myBonds = GenerateBondArray( std::vector<Residue>(1, topIn.Res(ires)), topIn.Atoms() );
+  BondArray myBonds = GenerateBondArray( residues, topIn.Atoms() );
   for (BondArray::const_iterator bnd = myBonds.begin(); bnd != myBonds.end(); ++bnd) {
-    if (topIn[bnd->A1()].ResNum() == ires && topIn[bnd->A2()].ResNum() == ires) {
+    //if (topIn[bnd->A1()].ResNum() == ires && topIn[bnd->A2()].ResNum() == ires) {
       mprintf("Looking at torsions around: %s - %s\n", topIn.LeapName(bnd->A1()).c_str(), topIn.LeapName(bnd->A2()).c_str());
       // Find all ICs that share atoms 1 and 2 (J and K)
       bool needsUpdate = false;
@@ -138,7 +157,7 @@ int Builder::UpdateICsFromFrame(Frame const& frameIn, int ires, Topology const&
           dih.SetPhiVal( dNew );
         }
       } // END ICs need update
-    } // END both bond atoms belong to this residue
+    //} // END both bond atoms belong to this residue
   } // END loop over bonds
   return 0;
 }
@@ -1048,8 +1067,6 @@ void Builder::ModelTorsion(TorsionModel const& MT, unsigned int iBondX, unsigned
             currentTop_->LeapName(ay).c_str(),
             currentTop_->LeapName(ad).c_str());
     internalTorsions_.push_back( InternalTorsion(aa, ax, ay, ad, phiVal) );
-    //newZmatrix_->AddIC( InternalCoords(aa, ax, ay, ad, l0, t0*Constants::RADDEG, phiVal*Constants::RADDEG) );
-    //newZmatrix_->AddIC( InternalCoords(ad, ay, ax, aa, l1, t1*Constants::RADDEG, phiVal*Constants::RADDEG) );
   } else {
     mprintf( "Torsional INTERNAL already exists: %f\n", internalTorsions_[icIdx].PhiVal()*Constants::RADDEG );
   }
@@ -1795,6 +1812,7 @@ const
 }
 
 /** Generate a Zmatrix from the current internals. TODO only for atoms that need it? */
+/*
 int Builder::GetZmatrixFromInternals(Zmatrix& zmatrix, Topology const& topIn) const {
   mprintf("DEBUG: ----- Enter GetZmatrixFromInternals -----\n");
   zmatrix.clear();
@@ -1848,4 +1866,4 @@ int Builder::GetZmatrixFromInternals(Zmatrix& zmatrix, Topology const& topIn) co
   } // END loop over internal torsions
   mprintf("DEBUG: ----- Exit GetZmatrixFromInternals -----\n");
   return 0;
-}
+}*/
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index 7fa3fc2791..e1a15cdbeb 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -20,8 +20,8 @@ class Builder {
     void SetDebug(int d) { debug_ = d; }
     /// Set optional parameter set
     void SetParameters(ParameterSet const*);
-    /// Update the internal coordinates in given Zmatrix with values from Frame/Parameters
-    int UpdateICsFromFrame(Frame const&, int, Topology const&, Barray const&);
+    /// Update the internal coordinates in given Zmatrix with values from Frame/Parameters TODO combine into BuildFromInternals?
+    int UpdateICsFromFrame(Frame const&, Topology const&, Barray const&);
     /// Generate internal coordinates in the same manner as LEaP
     int GenerateInternals(Frame const&, Topology const&, Barray const&);
     /// Generate internal coordinates around a link between residues in same manner as LEaP
@@ -33,7 +33,7 @@ class Builder {
     int BuildFromInternals(Frame&, Topology const&, Barray&) const;
 
     /// \return Zmatrix from current internals
-    int GetZmatrixFromInternals(Zmatrix&, Topology const&) const;
+    //int GetZmatrixFromInternals(Zmatrix&, Topology const&) const;
   private:
     typedef std::vector<int> Iarray;
 
@@ -112,6 +112,7 @@ class Builder {
     Aarray internalAngles_;
     Larray internalBonds_;
     Carray internalChirality_;
+    Iarray Rnums_;               ///< Hold residue indices pertaining to current internals
 };
 /// ----- Hold torsion internal ------------------
 class Cpptraj::Structure::Builder::InternalTorsion {

From cd378e01db81817a0a6b17f743bacb34bcb68099 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 13 Feb 2024 08:58:49 -0500
Subject: [PATCH 0510/1492] Move leap chirality routines into a separate file

---
 src/Structure/Builder.cpp     | 187 +-------------------------------
 src/Structure/CMakeLists.txt  |   1 +
 src/Structure/Chirality.cpp   | 193 ++++++++++++++++++++++++++++++++++
 src/Structure/Chirality.h     |  23 ++++
 src/Structure/structuredepend |   3 +-
 src/Structure/structurefiles  |   1 +
 src/cpptrajdepend             |   3 +-
 7 files changed, 225 insertions(+), 186 deletions(-)
 create mode 100644 src/Structure/Chirality.cpp
 create mode 100644 src/Structure/Chirality.h

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 24254687a7..b40e1a7e0e 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1,4 +1,5 @@
 #include "Builder.h"
+#include "Chirality.h"
 #include "GenerateConnectivityArrays.h"
 #include "Zmatrix.h"
 #include "../Constants.h"
@@ -333,190 +334,6 @@ std::vector<MockAtom>
   return known_out;
 }
 
-/** LEaP routine for determining atom chirality.
-  * This is done by crossing A to B and then dotting the
-  * result with C. TODO use Chirality in BuildAtom? Use an Enum?
-  * The chirality of the vectors is determined by the sign of
-  * the result, which is determined by whether or not C has
-  * a component in the direction AxB or in the opposite direction.
-  */
-static inline double VectorAtomChirality(Vec3 const& Center, Vec3 const& A, Vec3 const& B, Vec3 const& C)
-{
-  Vec3 vA = A - Center;
-  Vec3 vB = B - Center;
-  Vec3 vC = C - Center;
-  Vec3 vCross = vA.Cross( vB );
-  double dot = vCross * vC;
-  if (dot > 0)
-    return 1.0;
-  else if (dot < 0)
-    return -1.0;
-  return 0.0;
-}
-
-/** LEaP routine for determining atom chirality when positions may or
-  * may not be defined. Currently the criteria for chirality is 
-  * absolute orientation of the vectors joining this atom to its neighbors.
-  * The neighbors are passed as vPA, vPB, vPC, vPD and bA, bB, bC, bD
-  * define whether or not the position is defined.
-  *
-  * This routine calculates the chirality using the defined vectors and
-  * then flips the sign depending on which vectors were used to calculate
-  * the chirality. If the ATOMs have (fKnown) set then their coordinate
-  * is considered to be known.
-  */
-static inline double VectorAtomNormalizedChirality(Vec3 const& Center,
-                                                   Vec3 const& vPA, bool bA,
-                                                   Vec3 const& vPB, bool bB,
-                                                   Vec3 const& vPC, bool bC,
-                                                   Vec3 const& vPD, bool bD)
-{
-  double dChi = 0;
-  
-  if (!bA) {
-    // If A is not known then use B,C,D to calc chirality.
-    // The chirality calculated will be negative w.r.t. the
-    // correct chirality.
-    if (!bB || !bC || !bD) return dChi;
-    dChi = -VectorAtomChirality( Center, vPB, vPC, vPD );
-    return dChi;
-  }
-
-  if (!bB) {
-    // If B is not known then use A,C,D to calc chirality.
-    // The chirality calculated will be correct.
-    if (!bB || !bD) return dChi;
-    dChi = VectorAtomChirality( Center, vPA, vPC, vPD );
-    return dChi;
-  }
-
-  if (!bC) {
-    // If C is not known then use A,B,D to calc chirality.
-    // The chirality calculated will be negative w.r.t. the
-    // correct chirality.
-    if (!bD) return dChi;
-    dChi = -VectorAtomChirality( Center, vPA, vPB, vPD );
-    return dChi;
-  }
-
-  dChi = VectorAtomChirality( Center, vPA, vPB, vPC );
-
-  return dChi;
-}
-
-/** \return index of atom less than all others but larger than aLast */
-static inline int findLeastLargerThan(Atom const& aAtom, int aLast)
-{
-  int aSmall = -1;
-  for (Atom::bond_iterator aCur = aAtom.bondbegin(); aCur != aAtom.bondend(); ++aCur)
-  {
-    if (aLast != -1) {
-      if (aLast >= *aCur) continue;
-    }
-    if (aSmall == -1)
-      aSmall = *aCur;
-    else if ( *aCur < aSmall )
-      aSmall = *aCur;
-  }
-  return aSmall;
-}
-
-/** Sort neighbors of given atom in the same manner as LEaP. */
-static inline void chiralityOrderNeighbors(Atom const& aAtom,
-                                      int& aPAtomA, int& aPAtomB,
-                                      int& aPAtomC, int& aPAtomD)
-{
-  aPAtomA = -1;
-  aPAtomB = -1;
-  aPAtomC = -1;
-  aPAtomD = -1;
-
-  if (aAtom.Nbonds() < 1) return;
-
-  aPAtomA = findLeastLargerThan(aAtom, -1);
-  if (aAtom.Nbonds() < 2) return;
-
-  aPAtomB = findLeastLargerThan(aAtom, aPAtomA);
-  if (aAtom.Nbonds() < 3) return;
-
-  aPAtomC = findLeastLargerThan(aAtom, aPAtomB);
-  if (aAtom.Nbonds() < 4) return;
-
-  aPAtomD = findLeastLargerThan(aAtom, aPAtomC);
-}
-
-/** Transform the orientation that has been measured with 
- *      respect to the ordering in aaOrig[4] to the ordering
- *      in aaNew[4].  Return the result.
- *
- *      The transformation is done by swapping ATOMs in aaOrig until
- *      the order matches that of aaNew, each time two ATOMs are swapped,
- *      flip the sign of the orientation.
- *
- *      SIDE EFFECT:   The order in aaOrig is changed.
-  */
-static inline void chiralityTransformOrientation(double dOrig, int* aaOrig, double& dPNew, const int* aaNew)
-{
-  dPNew = dOrig;
-  for (int i=0; i<4; i++ ) {
-    int j = i;
-    for ( ; j<4; j++ ) {
-      if ( aaOrig[j] == aaNew[i] )
-        break;
-    }
-    if ( j >= 4 ) {
-      mprinterr("Error: Comparing atoms %i %i %i and %i to atoms %i %i %i and %i.\n",
-                aaOrig[0]+1, aaOrig[1]+1, aaOrig[2]+1, aaOrig[3]+1,
-                aaNew[0]+1, aaNew[1]+1, aaNew[2]+1, aaNew[3]+1);
-      mprinterr("Error: This error may be due to faulty Connection atoms.\n");
-      // TODO fatal
-    }
-    // Swap elements and flip sign
-    if ( j != i ) {
-      std::swap( aaOrig[j], aaOrig[i] );
-      dPNew = -dPNew;
-    }
-  }
-}
-
-/** Transform the chirality which has been measured with
- *  respect to ATOM ID ordering to an arbitrary ordering.
- */
-static inline double chiralityToOrientation(double dChirality, Atom const& aCenter,
-                                            int aAtomA, int aAtomB, int aAtomC, int aAtomD)
-{
-  if (fabs(dChirality) < Constants::SMALL) return 0.0;
-
-  int aaOrig[4];
-  chiralityOrderNeighbors( aCenter, aaOrig[0], aaOrig[1], aaOrig[2], aaOrig[3] );
-
-  int aaNew[4];
-  aaNew[0] = aAtomA;
-  aaNew[1] = aAtomB;
-  aaNew[2] = aAtomC;
-  aaNew[3] = aAtomD;
-
-  bool newNull = (aaNew[3] == -1);
-  bool origNull = (aaOrig[3] == -1);
-  if (newNull && !origNull) {
-    for (int i = 0; i < 4; i++) {
-      bool found = false;
-      for (int j=0; j<3; j++) found |= (aaOrig[i] == aaNew[j]);
-      if ( !found ) {
-        aaNew[3] = aaOrig[i];
-        break;
-      }
-    }
-  } else if (!newNull && origNull) {
-    mprinterr("Error: Only three neighbors around: aCenter, but orientation has 4\n");
-  }
-
-  double dOrient;
-  chiralityTransformOrientation( dChirality, aaOrig, dOrient, aaNew );
-
-  return dOrient;
-}
-
 /** Assuming atoms have been ordered with SortBondedAtomsLikeLeap,
   * calculate the orientation of the iB atom with respect to the
   * triangle (iA, iX, iY). This orientation will be used by the
@@ -524,6 +341,7 @@ static inline double chiralityToOrientation(double dChirality, Atom const& aCent
   */
 static inline double calculateOrientation(MockAtom const& iX, double chiX, Atom const& AX, MockAtom const& iA, MockAtom const& iY, MockAtom const& iB)
 {
+  using namespace Cpptraj::Structure::Chirality;
   double dOrientation = 1.0;
   if (iX.Known() &&
       iA.Known() &&
@@ -1344,6 +1162,7 @@ void Builder::buildBondInternal(int a1, int a2, Frame const& frameIn, Topology c
   */
 int Builder::determineChirality(double& dChi, int at, Frame const& frameIn, Topology const& topIn, Barray const& hasPosition)
 {
+  using namespace Cpptraj::Structure::Chirality;
   dChi = 0.0;
   if (!hasPosition[at]) {
     return 0;
diff --git a/src/Structure/CMakeLists.txt b/src/Structure/CMakeLists.txt
index a7cebdea51..b434c765d1 100644
--- a/src/Structure/CMakeLists.txt
+++ b/src/Structure/CMakeLists.txt
@@ -2,6 +2,7 @@
 target_sources(cpptraj_common_obj PRIVATE
   ${CMAKE_CURRENT_LIST_DIR}/BuildAtom.cpp
   ${CMAKE_CURRENT_LIST_DIR}/Builder.cpp
+  ${CMAKE_CURRENT_LIST_DIR}/Chirality.cpp
   ${CMAKE_CURRENT_LIST_DIR}/Disulfide.cpp
   ${CMAKE_CURRENT_LIST_DIR}/FunctionalGroup.cpp
   ${CMAKE_CURRENT_LIST_DIR}/FxnGroupBuilder.cpp
diff --git a/src/Structure/Chirality.cpp b/src/Structure/Chirality.cpp
new file mode 100644
index 0000000000..96b6c5c653
--- /dev/null
+++ b/src/Structure/Chirality.cpp
@@ -0,0 +1,193 @@
+#include "Chirality.h"
+#include "../Atom.h"
+#include "../Constants.h"
+#include "../CpptrajStdio.h"
+#include "../Vec3.h"
+#include <cmath> // fabs
+
+/** LEaP routine for determining atom chirality.
+  * This is done by crossing A to B and then dotting the
+  * result with C. TODO use Chirality in BuildAtom? Use an Enum?
+  * The chirality of the vectors is determined by the sign of
+  * the result, which is determined by whether or not C has
+  * a component in the direction AxB or in the opposite direction.
+  */
+double Cpptraj::Structure::Chirality::VectorAtomChirality(Vec3 const& Center,
+                                                          Vec3 const& A, Vec3 const& B, Vec3 const& C)
+{
+  Vec3 vA = A - Center;
+  Vec3 vB = B - Center;
+  Vec3 vC = C - Center;
+  Vec3 vCross = vA.Cross( vB );
+  double dot = vCross * vC;
+  if (dot > 0)
+    return 1.0;
+  else if (dot < 0)
+    return -1.0;
+  return 0.0;
+}
+
+/** LEaP routine for determining atom chirality when positions may or
+  * may not be defined. Currently the criteria for chirality is 
+  * absolute orientation of the vectors joining this atom to its neighbors.
+  * The neighbors are passed as vPA, vPB, vPC, vPD and bA, bB, bC, bD
+  * define whether or not the position is defined.
+  *
+  * This routine calculates the chirality using the defined vectors and
+  * then flips the sign depending on which vectors were used to calculate
+  * the chirality. If the ATOMs have (fKnown) set then their coordinate
+  * is considered to be known.
+  */
+double Cpptraj::Structure::Chirality::VectorAtomNormalizedChirality(Vec3 const& Center,
+                                                                    Vec3 const& vPA, bool bA,
+                                                                    Vec3 const& vPB, bool bB,
+                                                                    Vec3 const& vPC, bool bC,
+                                                                    Vec3 const& vPD, bool bD)
+{
+  double dChi = 0;
+  
+  if (!bA) {
+    // If A is not known then use B,C,D to calc chirality.
+    // The chirality calculated will be negative w.r.t. the
+    // correct chirality.
+    if (!bB || !bC || !bD) return dChi;
+    dChi = -VectorAtomChirality( Center, vPB, vPC, vPD );
+    return dChi;
+  }
+
+  if (!bB) {
+    // If B is not known then use A,C,D to calc chirality.
+    // The chirality calculated will be correct.
+    if (!bB || !bD) return dChi;
+    dChi = VectorAtomChirality( Center, vPA, vPC, vPD );
+    return dChi;
+  }
+
+  if (!bC) {
+    // If C is not known then use A,B,D to calc chirality.
+    // The chirality calculated will be negative w.r.t. the
+    // correct chirality.
+    if (!bD) return dChi;
+    dChi = -VectorAtomChirality( Center, vPA, vPB, vPD );
+    return dChi;
+  }
+
+  dChi = VectorAtomChirality( Center, vPA, vPB, vPC );
+
+  return dChi;
+}
+
+/** \return index of atom less than all others but larger than aLast */
+static inline int findLeastLargerThan(Atom const& aAtom, int aLast)
+{
+  int aSmall = -1;
+  for (Atom::bond_iterator aCur = aAtom.bondbegin(); aCur != aAtom.bondend(); ++aCur)
+  {
+    if (aLast != -1) {
+      if (aLast >= *aCur) continue;
+    }
+    if (aSmall == -1)
+      aSmall = *aCur;
+    else if ( *aCur < aSmall )
+      aSmall = *aCur;
+  }
+  return aSmall;
+}
+
+/** Transform the orientation that has been measured with 
+ *      respect to the ordering in aaOrig[4] to the ordering
+ *      in aaNew[4].  Return the result.
+ *
+ *      The transformation is done by swapping ATOMs in aaOrig until
+ *      the order matches that of aaNew, each time two ATOMs are swapped,
+ *      flip the sign of the orientation.
+ *
+ *      SIDE EFFECT:   The order in aaOrig is changed.
+  */
+static inline void chiralityTransformOrientation(double dOrig, int* aaOrig, double& dPNew, const int* aaNew)
+{
+  dPNew = dOrig;
+  for (int i=0; i<4; i++ ) {
+    int j = i;
+    for ( ; j<4; j++ ) {
+      if ( aaOrig[j] == aaNew[i] )
+        break;
+    }
+    if ( j >= 4 ) {
+      mprinterr("Error: Comparing atoms %i %i %i and %i to atoms %i %i %i and %i.\n",
+                aaOrig[0]+1, aaOrig[1]+1, aaOrig[2]+1, aaOrig[3]+1,
+                aaNew[0]+1, aaNew[1]+1, aaNew[2]+1, aaNew[3]+1);
+      mprinterr("Error: This error may be due to faulty Connection atoms.\n");
+      // TODO fatal
+    }
+    // Swap elements and flip sign
+    if ( j != i ) {
+      std::swap( aaOrig[j], aaOrig[i] );
+      dPNew = -dPNew;
+    }
+  }
+}
+
+/** Sort neighbors of given atom in the same manner as LEaP. */
+void Cpptraj::Structure::Chirality::chiralityOrderNeighbors(Atom const& aAtom,
+                                                            int& aPAtomA, int& aPAtomB,
+                                                            int& aPAtomC, int& aPAtomD)
+{
+  aPAtomA = -1;
+  aPAtomB = -1;
+  aPAtomC = -1;
+  aPAtomD = -1;
+
+  if (aAtom.Nbonds() < 1) return;
+
+  aPAtomA = findLeastLargerThan(aAtom, -1);
+  if (aAtom.Nbonds() < 2) return;
+
+  aPAtomB = findLeastLargerThan(aAtom, aPAtomA);
+  if (aAtom.Nbonds() < 3) return;
+
+  aPAtomC = findLeastLargerThan(aAtom, aPAtomB);
+  if (aAtom.Nbonds() < 4) return;
+
+  aPAtomD = findLeastLargerThan(aAtom, aPAtomC);
+}
+
+/** Transform the chirality which has been measured with
+ *  respect to ATOM ID ordering to an arbitrary ordering.
+ */
+double Cpptraj::Structure::Chirality::chiralityToOrientation(double dChirality, Atom const& aCenter,
+                                            int aAtomA, int aAtomB, int aAtomC, int aAtomD)
+{
+  if (fabs(dChirality) < Constants::SMALL) return 0.0;
+
+  int aaOrig[4];
+  chiralityOrderNeighbors( aCenter, aaOrig[0], aaOrig[1], aaOrig[2], aaOrig[3] );
+
+  int aaNew[4];
+  aaNew[0] = aAtomA;
+  aaNew[1] = aAtomB;
+  aaNew[2] = aAtomC;
+  aaNew[3] = aAtomD;
+
+  bool newNull = (aaNew[3] == -1);
+  bool origNull = (aaOrig[3] == -1);
+  if (newNull && !origNull) {
+    for (int i = 0; i < 4; i++) {
+      bool found = false;
+      for (int j=0; j<3; j++) found |= (aaOrig[i] == aaNew[j]);
+      if ( !found ) {
+        aaNew[3] = aaOrig[i];
+        break;
+      }
+    }
+  } else if (!newNull && origNull) {
+    mprinterr("Error: Only three neighbors around: aCenter, but orientation has 4\n");
+  }
+
+  double dOrient;
+  chiralityTransformOrientation( dChirality, aaOrig, dOrient, aaNew );
+
+  return dOrient;
+}
+
+
diff --git a/src/Structure/Chirality.h b/src/Structure/Chirality.h
new file mode 100644
index 0000000000..569218e417
--- /dev/null
+++ b/src/Structure/Chirality.h
@@ -0,0 +1,23 @@
+#ifndef INC_STRUCTURE_CHIRALITY_H
+#define INC_STRUCTURE_CHIRALITY_H
+class Atom;
+class Vec3;
+namespace Cpptraj {
+namespace Structure {
+namespace Chirality {
+
+/// Calculate chirality in same manner as LEaP. All atom positions should be known.
+double VectorAtomChirality(Vec3 const&, Vec3 const&, Vec3 const&, Vec3 const&);
+/// Calculate chirality in same manner as LEaP. Some atom positions may not be known.
+double VectorAtomNormalizedChirality(Vec3 const&,
+                                     Vec3 const&, bool, Vec3 const&, bool,
+                                     Vec3 const&, bool, Vec3 const&, bool);
+/// Order atoms for chirality calculation like LEaP
+void chiralityOrderNeighbors(Atom const&, int&, int&, int&, int&);
+/// Transform given chirality to an orientation
+double chiralityToOrientation(double, Atom const&, int, int, int, int);
+
+}
+}
+}
+#endif
diff --git a/src/Structure/structuredepend b/src/Structure/structuredepend
index 0343bb0aa9..8038bb531b 100644
--- a/src/Structure/structuredepend
+++ b/src/Structure/structuredepend
@@ -1,5 +1,6 @@
 BuildAtom.o : BuildAtom.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h StructureEnum.h
-Builder.o : Builder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Builder.h GenerateConnectivityArrays.h InternalCoords.h Zmatrix.h
+Builder.o : Builder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Builder.h Chirality.h GenerateConnectivityArrays.h InternalCoords.h Zmatrix.h
+Chirality.o : Chirality.cpp ../Atom.h ../Constants.h ../CpptrajStdio.h ../NameType.h ../SymbolExporting.h ../Vec3.h Chirality.h
 Disulfide.o : Disulfide.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Disulfide.h ResStatArray.h StructureRoutines.h
 FunctionalGroup.o : FunctionalGroup.cpp ../Atom.h ../AtomMap.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h FunctionalGroup.h
 FxnGroupBuilder.o : FxnGroupBuilder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h FunctionalGroup.h FxnGroupBuilder.h StructureRoutines.h Sugar.h SugarToken.h
diff --git a/src/Structure/structurefiles b/src/Structure/structurefiles
index 1e7c8a3f12..d00e816504 100644
--- a/src/Structure/structurefiles
+++ b/src/Structure/structurefiles
@@ -2,6 +2,7 @@
 STRUCTURE_SOURCES= \
   BuildAtom.cpp \
   Builder.cpp \
+  Chirality.cpp \
   Disulfide.cpp \
   FunctionalGroup.cpp \
   FxnGroupBuilder.cpp \
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 2a8695bccc..2059dc510f 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -446,7 +446,8 @@ Spline.o : Spline.cpp CpptrajStdio.h Spline.h
 SplineFxnTable.o : SplineFxnTable.cpp Constants.h CpptrajStdio.h Spline.h SplineFxnTable.h StringRoutines.h
 StringRoutines.o : StringRoutines.cpp CpptrajStdio.h StringRoutines.h
 Structure/BuildAtom.o : Structure/BuildAtom.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/StructureEnum.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Structure/Builder.o : Structure/Builder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h GuessAtomHybridization.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Builder.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Structure/Builder.o : Structure/Builder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h GuessAtomHybridization.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Builder.h Structure/Chirality.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Structure/Chirality.o : Structure/Chirality.cpp Atom.h Constants.h CpptrajStdio.h NameType.h Structure/Chirality.h SymbolExporting.h Vec3.h
 Structure/Disulfide.o : Structure/Disulfide.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Disulfide.h Structure/ResStatArray.h Structure/StructureRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/FunctionalGroup.o : Structure/FunctionalGroup.cpp Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/FxnGroupBuilder.o : Structure/FxnGroupBuilder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h Structure/FxnGroupBuilder.h Structure/StructureRoutines.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h

From 1aec22d705a4982dc1926d0ea80ddfe8d2b58327 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 13 Feb 2024 09:17:08 -0500
Subject: [PATCH 0511/1492] Do not use cpptraj guess if a hybridization
 parameter was found.

---
 src/Structure/Builder.cpp | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index b40e1a7e0e..d434c43448 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -728,13 +728,15 @@ AtomType::HybridizationType Builder::getAtomHybridization(Atom const& aAtom, std
     }
   }
   // Use the cpptraj guess.
-  H1 = GuessAtomHybridization(aAtom, atoms);
-  // FIXME this is a bit of a hack. If we get an SP type here its likely we
-  //       are generating internals for a fragment that has not been bonded
-  //       yet. Do SP2 instead.
-  if (H1 == AtomType::SP)
-    H1 = AtomType::SP2;
-  // Guess in the same way leap does
+  if (H1 == AtomType::UNKNOWN_HYBRIDIZATION) {
+    H1 = GuessAtomHybridization(aAtom, atoms);
+    // FIXME this is a bit of a hack. If we get an SP type here its likely we
+    //       are generating internals for a fragment that has not been bonded
+    //       yet. Do SP2 instead.
+    if (H1 == AtomType::SP)
+      H1 = AtomType::SP2;
+  }
+  // If still unknown, guess in the same way leap does.
   if (H1 == AtomType::UNKNOWN_HYBRIDIZATION) {
     // TODO bond orders?
     int iSingle = 0;

From 96f4e4cd67dfac06358e84d687b865cd74ff3547 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 13 Feb 2024 10:42:44 -0500
Subject: [PATCH 0512/1492] Standalone routine to calculate orientation around
 an atom

---
 src/Structure/Builder.cpp | 34 +++++++++++++++++++++++++++++++++-
 src/Structure/Builder.h   |  2 ++
 2 files changed, 35 insertions(+), 1 deletion(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index d434c43448..cfdf69fe01 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -225,10 +225,11 @@ class Cpptraj::Structure::Builder::TorsionModel {
     bool AxHasKnownAtoms() const { return axHasKnownAtoms_; }
     /// \return True if AY has known bonded atoms
     bool AyHasKnownAtoms() const { return ayHasKnownAtoms_; }
+    /// Sort an array of MockAtoms the way that LEaP does
+    static Marray SortBondedAtomsLikeLeap(unsigned int&, Topology const& topIn, Marray const&);
   private:
     static int LeapAtomWeight(Atom const&);
     //static inline std::vector<int> SiftBondedAtomsLikeLeap(unsigned int&, Atom const&, std::vector<bool> const&);
-    static inline Marray SortBondedAtomsLikeLeap(unsigned int&, Topology const& topIn, Marray const&);
     static inline void swap_heaviest(Marray&, Topology const&);
 
     MockAtom atX_;              ///< Atom X
@@ -628,6 +629,37 @@ int Cpptraj::Structure::Builder::TorsionModel::BuildMockExternals(Iarray const&
 }
 
 // -----------------------------------------------------------------------------
+/** Calculate the orientation around a single atom. Assume all positions are known. */
+void Builder::CalculateOrientationAroundAtom(int ax, int ay, Frame const& frameIn, Topology const& topIn) {
+  using namespace Cpptraj::Structure::Chirality;
+
+  Vec3 iXPos( frameIn.XYZ(ax) );
+  Vec3 iYPos( frameIn.XYZ(ay) );
+  // Create array of AX bonded atoms
+  Atom const& AX = topIn[ax];
+  std::vector<MockAtom> sorted_ax;
+  sorted_ax.reserve( AX.Nbonds() - 1 );
+  for (Atom::bond_iterator bat = AX.bondbegin(); bat != AX.bondend(); ++bat) {
+    if (*bat != ay) {
+      sorted_ax.push_back( MockAtom(*bat, frameIn.XYZ(*bat)) );
+      sorted_ax.back().SetBuildInternals( true );
+    }
+  }
+  // Sort AX bonds
+  unsigned int firstUnknownIdxX = 0;
+  sorted_ax = TorsionModel::SortBondedAtomsLikeLeap(firstUnknownIdxX, topIn, sorted_ax);
+  // Calculate the chirality around atom X
+  double Xorientation = 0;
+  if (sorted_ax.size() < 2)
+    Xorientation = 1.0;
+  else
+    Xorientation = VectorAtomChirality( iXPos, sorted_ax[0].Pos(), iYPos, sorted_ax[1].Pos() );
+  mprintf("ORIENTATION: around atom %s (- %s) = %f\n",
+          topIn.LeapName(ax).c_str(),
+          topIn.LeapName(ay).c_str(),
+          Xorientation);
+}
+
 /** Update all indices in internals according to the given offset. */
 void Builder::UpdateIndicesWithOffset(int atomOffset) {
   for (Tarray::iterator it = internalTorsions_.begin(); it != internalTorsions_.end(); ++it)
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index e1a15cdbeb..8a8a631dde 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -29,6 +29,8 @@ class Builder {
     /// Update existing indices with given offset
     void UpdateIndicesWithOffset(int);
 
+    void CalculateOrientationAroundAtom(int, int, Frame const&, Topology const&); // TODO const?
+
     /// Build position from internals for any atom with unset position
     int BuildFromInternals(Frame&, Topology const&, Barray&) const;
 

From d63e6e91972fbd4230bce50c7d0cc3d0d94f63b7 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 13 Feb 2024 10:46:51 -0500
Subject: [PATCH 0513/1492] Make static

---
 src/Structure/Builder.h | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index 8a8a631dde..718de2e1ac 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -92,12 +92,8 @@ class Builder {
     /// Build bond internal
     void buildBondInternal(int, int, Frame const&, Topology const&, Barray const&);
 
-    /// Find index of bonded atom less than all others but larger than last
-    //static inline int findLeastLargerThan(Atom const&, int);
-    /// Sort neighbors of atom. Used in determineChirality
-    //static void chiralityOrderNeighbors(Atom const&, int&, int&, int&, int&);
     /// Determine chirality around an atom
-    int determineChirality(double&, int, Frame const&, Topology const&, Barray const&);
+    static int determineChirality(double&, int, Frame const&, Topology const&, Barray const&);
 
     /// Generate internal coords for a given atom
     int generateAtomInternals(int, Frame const&, Topology const&, Barray const&);

From 6d37afa14846b212b885407204e29e103e74cf45 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 13 Feb 2024 10:48:25 -0500
Subject: [PATCH 0514/1492] Make static, return orientation

---
 src/Structure/Builder.cpp | 3 ++-
 src/Structure/Builder.h   | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index cfdf69fe01..b77f21eefe 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -630,7 +630,7 @@ int Cpptraj::Structure::Builder::TorsionModel::BuildMockExternals(Iarray const&
 
 // -----------------------------------------------------------------------------
 /** Calculate the orientation around a single atom. Assume all positions are known. */
-void Builder::CalculateOrientationAroundAtom(int ax, int ay, Frame const& frameIn, Topology const& topIn) {
+double Builder::CalculateOrientationAroundAtom(int ax, int ay, Frame const& frameIn, Topology const& topIn) {
   using namespace Cpptraj::Structure::Chirality;
 
   Vec3 iXPos( frameIn.XYZ(ax) );
@@ -658,6 +658,7 @@ void Builder::CalculateOrientationAroundAtom(int ax, int ay, Frame const& frameI
           topIn.LeapName(ax).c_str(),
           topIn.LeapName(ay).c_str(),
           Xorientation);
+  return Xorientation;
 }
 
 /** Update all indices in internals according to the given offset. */
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index 718de2e1ac..6f4cf47cce 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -29,7 +29,7 @@ class Builder {
     /// Update existing indices with given offset
     void UpdateIndicesWithOffset(int);
 
-    void CalculateOrientationAroundAtom(int, int, Frame const&, Topology const&); // TODO const?
+    static double CalculateOrientationAroundAtom(int, int, Frame const&, Topology const&); // TODO const?
 
     /// Build position from internals for any atom with unset position
     int BuildFromInternals(Frame&, Topology const&, Barray&) const;

From 87190c98a31c1c4efef72fe4b6d39b695a03a53f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 13 Feb 2024 10:57:31 -0500
Subject: [PATCH 0515/1492] Add code for saving atom orientations

---
 src/Structure/Builder.cpp | 25 +++++++++++++++++++++++++
 src/Structure/Builder.h   |  5 +++++
 2 files changed, 30 insertions(+)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index b77f21eefe..6edd5157b3 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -30,6 +30,18 @@ void Cpptraj::Structure::Builder::SetParameters(ParameterSet const* paramsIn) {
   params_ = paramsIn;
 }
 
+/** Set an atoms orientation */
+void Cpptraj::Structure::Builder::SetAtomOrientation(int at, double orient) {
+  int oidx = getExistingOrientationIdx(at);
+  if (oidx == -1) {
+    internalOrientation_.push_back( InternalChirality(at, orient) );
+  } else {
+    mprintf("Warning: Overriding existing orientation %f for atom %i with %f\n",
+            internalOrientation_[oidx].ChiralVal(), at+1, orient);
+    internalOrientation_[oidx].SetChiralVal( orient );
+  }
+}
+
 /** Get length from parameter set if present.
   * \return 1 if a length parameter was found.
   */
@@ -748,6 +760,19 @@ int Builder::getExistingChiralityIdx(int ai) const {
   return idx;
 }
 
+/** \return Index of existing orientation value matching given atom, 1 for no match. */
+int Builder::getExistingOrientationIdx(int ai) const {
+  int idx = -1;
+  for (Carray::const_iterator it = internalOrientation_.begin(); it != internalOrientation_.end(); ++it)
+  {
+    if (it->AtI() == ai) {
+      idx = (int)(it - internalOrientation_.begin());
+      break;
+    }
+  }
+  return idx;
+}
+
 /** Determine hybridization in the same manner as leap */
 AtomType::HybridizationType Builder::getAtomHybridization(Atom const& aAtom, std::vector<Atom> const& atoms) const {
   AtomType::HybridizationType H1 = AtomType::UNKNOWN_HYBRIDIZATION;
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index 6f4cf47cce..d20fdd252b 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -20,6 +20,8 @@ class Builder {
     void SetDebug(int d) { debug_ = d; }
     /// Set optional parameter set
     void SetParameters(ParameterSet const*);
+    /// Set atom orientation
+    void SetAtomOrientation(int, double);
     /// Update the internal coordinates in given Zmatrix with values from Frame/Parameters TODO combine into BuildFromInternals?
     int UpdateICsFromFrame(Frame const&, Topology const&, Barray const&);
     /// Generate internal coordinates in the same manner as LEaP
@@ -85,6 +87,8 @@ class Builder {
     int getExistingBondIdx(int, int) const;
     /// Get specific chirality
     int getExistingChiralityIdx(int) const;
+    /// Get specific orientation
+    int getExistingOrientationIdx(int) const;
     /// Build mock coordinates around given torsion
     int buildMockExternals(TorsionModel& MT, std::vector<InternalCoords> const& iaTorsions) const;
     /// Build angle internal
@@ -110,6 +114,7 @@ class Builder {
     Aarray internalAngles_;
     Larray internalBonds_;
     Carray internalChirality_;
+    Carray internalOrientation_;
     Iarray Rnums_;               ///< Hold residue indices pertaining to current internals
 };
 /// ----- Hold torsion internal ------------------

From af9591a47829391138b22819b0331ff4ff48d849 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 13 Feb 2024 11:03:13 -0500
Subject: [PATCH 0516/1492] Start looking for existing orientations

---
 src/Structure/Builder.cpp | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 6edd5157b3..e5655fbc7e 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1146,6 +1146,11 @@ int Builder::assignTorsionsAroundBond(int a1, int a2, Frame const& frameIn, Topo
   double chiY = 0;
   int Ycidx = getExistingChiralityIdx( ay );
   if (Ycidx != -1) chiY = internalChirality_[Ycidx].ChiralVal();
+  // See if orientations exist
+  int Xoidx = getExistingOrientationIdx( ax );
+  if (Xoidx != -1) mprintf("DEBUG: Existing orientation for %s : %f\n", topIn.LeapName(ax).c_str(), internalOrientation_[Xoidx].ChiralVal());
+  int Yoidx = getExistingOrientationIdx( ay );
+  if (Yoidx != -1) mprintf("DEBUG: Existing orientation for %s : %f\n", topIn.LeapName(ay).c_str(), internalOrientation_[Yoidx].ChiralVal());
   // Set up the torsion model
   if (mT.SetupTorsion(Hx, Hy, topIn, chiX, chiY)) {
     mprinterr("Error: Could not set up torsions around %s - %s\n",

From 8b9b588e54e92fd449f70f3e1b1bceb1ec788e7c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 13 Feb 2024 11:55:46 -0500
Subject: [PATCH 0517/1492] Skip comment lines. Handle non-terminal pdb maps

---
 src/DataIO_LeapRC.cpp | 40 ++++++++++++++++++++++++++--------------
 1 file changed, 26 insertions(+), 14 deletions(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 724a2c8388..2180645cde 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -108,7 +108,10 @@ const
     std::string tmp;
     for (const char* ptr = line; *ptr != '\0'; ++ptr)
     {
-      if (*ptr == '{')
+      if (*ptr == '#') {
+        // Comment - skip everything else
+        break;
+      } else if (*ptr == '{')
         bracketCount++;
       else if (*ptr == '}') {
         bracketCount--;
@@ -187,7 +190,10 @@ const
     std::string tmp;
     for (const char* ptr = line; *ptr != '\0'; ++ptr)
     {
-      if (*ptr == '{')
+      if (*ptr == '#') {
+        // Comment - skip everything else
+        break;
+      } else if (*ptr == '{')
         bracketCount++;
       else if (*ptr == '}') {
         bracketCount--;
@@ -195,24 +201,30 @@ const
           mprintf("DEBUG: addPdbResMap: %s\n", tmp.c_str());
           ArgList aline( tmp );
           // 3 tokens: terminal type (0=beg 1=end), PDB name, unit name
-          if (aline.Nargs() != 3) {
+          if (aline.Nargs() < 2 || aline.Nargs() > 3) {
             mprinterr("Error: Malformed entry in addPdbResMap: %s\n", tmp.c_str());
             return 1;
           }
           Cpptraj::Structure::TerminalType termType = Cpptraj::Structure::NON_TERMINAL;
-          if (aline[0] == "0")
-            termType = Cpptraj::Structure::BEG_TERMINAL;
-          else if (aline[0] == "1")
-            termType = Cpptraj::Structure::END_TERMINAL;
-          else
-            mprintf("Warning: Unrecognized terminal type in addPdbResMap: %s\n", aline[0].c_str());
-          if (termType != Cpptraj::Structure::NON_TERMINAL) {
+          int pdbidx = 0;
+          int unitidx = 1;
+          if (aline.Nargs() == 3) {
+            if (aline[0] == "0")
+              termType = Cpptraj::Structure::BEG_TERMINAL;
+            else if (aline[0] == "1")
+              termType = Cpptraj::Structure::END_TERMINAL;
+            else
+              mprintf("Warning: Unrecognized terminal type in addPdbResMap: %s\n", aline[0].c_str());
+            pdbidx = 1;
+            unitidx = 2;
+          }
+          //if (termType != Cpptraj::Structure::NON_TERMINAL) {
             PdbResMapType prm;
             prm.termType_ = termType;
-            prm.pdbName_ = aline[1];
-            prm.unitName_ = aline[2];
+            prm.pdbName_ = aline[pdbidx];
+            prm.unitName_ = aline[unitidx];
             pdbResMap.push_back( prm );
-          }
+          //}
           tmp.clear();
         }
       } else {
@@ -226,7 +238,7 @@ const
     } else if (bracketCount == 0) {
       break;
     } //else {
-      //mprintf("DEBUG: addPdbResMap: %s\n", tmp.c_str());
+    //mprintf("DEBUG: END OF LINE: addPdbResMap: %s\n", tmp.c_str());
     //}
     line = infile.Line();
   }

From 7eeb190397c4adf5640a1d4f4a3b1f4701acd4db Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 13 Feb 2024 14:35:09 -0500
Subject: [PATCH 0518/1492] Save original chirality to use when grafting. Seems
 to be enough to save this and not orientation since we can get orientation
 using chirality

---
 src/Exec_Graft.cpp        | 86 +++++++++++++++++++++++++++++++++++-
 src/Exec_Graft.h          |  9 ++++
 src/Structure/Builder.cpp | 91 ++++++++++++++++++++++++++++-----------
 src/Structure/Builder.h   | 11 +++--
 4 files changed, 167 insertions(+), 30 deletions(-)

diff --git a/src/Exec_Graft.cpp b/src/Exec_Graft.cpp
index e1b33151fb..4c07198e93 100644
--- a/src/Exec_Graft.cpp
+++ b/src/Exec_Graft.cpp
@@ -3,6 +3,7 @@
 #include "DataSet_Coords.h"
 #include "Structure/Builder.h"
 #include "Structure/Zmatrix.h"
+#include "CharMask.h"
 #include <algorithm> // std::copy
 #include <utility> // std::pair
 
@@ -13,7 +14,13 @@ Exec_Graft::Exec_Graft() :
   Exec(COORDS),
   debug_(0),
   newMol0Top_(0),
-  newMol1Top_(0)
+  newMol1Top_(0),
+  hasOrient0_(false),
+  hasOrient1_(false),
+//  orient0_(0),
+//  orient1_(0),
+  chi0_(0),
+  chi1_(0)
 {}
 
 /** DESTRUCTOR */
@@ -224,6 +231,12 @@ Exec::RetType Exec_Graft::Execute(CpptrajState& State, ArgList& argIn)
     mol1frm.Trans_Rot_Trans( Trans, Rot, refTrans );
   }
 
+  if (use_ic) {
+    // Get internals for both topologies before they are modified.
+    get_original_orientations(mol0crd->Top(), mol0frm, mol1crd->Top(), mol1frm,
+                              mol0Mask, mol1Mask, bond0ArgStrings, bond1ArgStrings);
+  }
+
   // Modify the target (mol0) topology
   if (newMol0Top_ != 0) delete newMol0Top_;
   newMol0Top_ = 0;
@@ -271,6 +284,70 @@ Exec::RetType Exec_Graft::Execute(CpptrajState& State, ArgList& argIn)
   return CpptrajState::OK;
 }
 
+/** Get internals for molecules before modification. */
+int Exec_Graft::get_original_orientations(Topology const& mol0Top, Frame const& mol0frm,
+                                          Topology const& mol1Top, Frame const& mol1frm,
+                                          AtomMask const& mol0mask, AtomMask const& mol1mask,
+                                          Sarray const& bond0Atoms, Sarray const& bond1Atoms)
+{
+  // Get bonding atom masks
+  if (bond0Atoms.size() != 1 || bond1Atoms.size() != 1) {
+    mprinterr("Error: Graft with internal coordinates only works with 1 bond.\n");
+    return 1;
+  }
+  std::string const& tgtbondmask = bond0Atoms[0];
+  std::string const& srcbondmask = bond1Atoms[0];
+
+  // Select bond atom indices
+  int bondat0 = select_bond_idx(tgtbondmask, mol0Top);
+  if (bondat0 < 0) {
+    mprinterr("Error: Could not select target bond atom '%s'\n", tgtbondmask.c_str());
+    return 1;
+  }
+  int bondat1 = select_bond_idx(srcbondmask, mol1Top);
+  if (bondat1 < 0) {
+    mprinterr("Error: Could not select source bond atom '%s'\n", srcbondmask.c_str());
+    return 1;
+  }
+
+  // Will an atom bonded to this atom disappear?
+//  orient0_ = 0.0;
+  Atom const& At0 = mol0Top[bondat0];
+  CharMask cmask0( mol0mask.ConvertToCharMask(), mol0mask.Nselected() );
+  int vanish0idx = -1;
+  for (Atom::bond_iterator bat = At0.bondbegin(); bat != At0.bondend(); ++bat) {
+    if (!cmask0.AtomInCharMask( *bat )) { // TODO check multiple disappearing atoms
+      mprintf("DEBUG: Atom0 %s will vanish.\n", mol0Top.AtomMaskName(*bat).c_str());
+      if (vanish0idx == -1) vanish0idx = *bat;
+    }
+  }
+  if (vanish0idx != -1) {
+    hasOrient0_ = true;
+    chi0_    = Builder::DetermineChiralityAroundAtom(bondat0, mol0frm, mol0Top);
+    mprintf("DEBUG: Chirality around %s is %f\n", mol0Top.LeapName(bondat0).c_str(), chi0_);
+//    orient0_ = Builder::CalculateOrientationAroundAtom(bondat0, vanish0idx, mol0frm, mol0Top);
+  }
+
+//  orient1_ = 0.0;
+  Atom const& At1 = mol1Top[bondat1];
+  CharMask cmask1( mol1mask.ConvertToCharMask(), mol1mask.Nselected() );
+  int vanish1idx = -1;
+  for (Atom::bond_iterator bat = At1.bondbegin(); bat != At1.bondend(); ++bat) {
+    if (!cmask1.AtomInCharMask( *bat )) { // TODO check multiple disappearing atoms
+      mprintf("DEBUG: Atom1 %s will vanish.\n", mol1Top.AtomMaskName(*bat).c_str());
+      if (vanish1idx == -1) vanish1idx = *bat;
+    }
+  }
+  if (vanish1idx != -1) {
+    hasOrient1_ = true;
+    chi1_    = Builder::DetermineChiralityAroundAtom(bondat1, mol1frm, mol1Top);
+    mprintf("DEBUG: Chirality around %s is %f\n", mol1Top.LeapName(bondat1).c_str(), chi1_);
+//    orient1_ = Builder::CalculateOrientationAroundAtom(bondat1, vanish1idx, mol1frm, mol1Top);
+  }
+
+  return 0;
+}
+
 
 /** Graft using internal coordinates to build the final structure. */
 int Exec_Graft::graft_ic(DataSet_Coords* outCoords,
@@ -383,6 +460,13 @@ const
           mol1Top.AtomMaskName(bondat1).c_str(),
           mol0Top.AtomMaskName(bondat0).c_str());
   topOut.AddBond( bondat1 + atomOffset, bondat0 );
+  // Set any saved orientations
+  if (hasOrient0_ && hasOrient1_) {
+//    structureBuilder.SetAtomOrientation(bondat0, orient0_);
+    structureBuilder.SetAtomChirality(bondat0, chi0_);
+//    structureBuilder.SetAtomOrientation(bondat1 + atomOffset, orient1_);
+    structureBuilder.SetAtomChirality(bondat1 + atomOffset, chi1_);
+  }
   // Generate internals around the link
   if (structureBuilder.GenerateInternalsAroundLink( bondat1 + atomOffset,
                                                     bondat0,
diff --git a/src/Exec_Graft.h b/src/Exec_Graft.h
index ea7443a609..80732d7314 100644
--- a/src/Exec_Graft.h
+++ b/src/Exec_Graft.h
@@ -23,8 +23,17 @@ class Exec_Graft : public Exec {
     /// Graft assuming structures have been rms fit
     int graft_rms(DataSet_Coords*, Topology const&, Frame const&, Topology const&, Frame const&, Sarray const&, Sarray const&) const;
 
+    int get_original_orientations(Topology const&, Frame const&, Topology const&, Frame const&,
+                                  AtomMask const&, AtomMask const&,
+                                  Sarray const&, Sarray const&);
     int debug_;
     Topology* newMol0Top_; ///< Hold target topology if modified.
     Topology* newMol1Top_; ///< Hold source topology if modified.
+    bool hasOrient0_;
+    bool hasOrient1_;
+//    double orient0_; ///< When using IC, record original orientation around bonding atom 0
+//    double orient1_; ///< When using IC, record original orientation around bonding atom 1
+    double chi0_;    ///< When using IC, record original chirality around bonding atom 0
+    double chi1_;    ///< When using IC, record original chirality around bonding atom 1
 };
 #endif
diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index e5655fbc7e..44e6cd2520 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -31,7 +31,7 @@ void Cpptraj::Structure::Builder::SetParameters(ParameterSet const* paramsIn) {
 }
 
 /** Set an atoms orientation */
-void Cpptraj::Structure::Builder::SetAtomOrientation(int at, double orient) {
+/*void Cpptraj::Structure::Builder::SetAtomOrientation(int at, double orient) {
   int oidx = getExistingOrientationIdx(at);
   if (oidx == -1) {
     internalOrientation_.push_back( InternalChirality(at, orient) );
@@ -40,6 +40,18 @@ void Cpptraj::Structure::Builder::SetAtomOrientation(int at, double orient) {
             internalOrientation_[oidx].ChiralVal(), at+1, orient);
     internalOrientation_[oidx].SetChiralVal( orient );
   }
+}*/
+
+/** Set an atoms chirality */
+void Cpptraj::Structure::Builder::SetAtomChirality(int at, double chi) {
+  int cidx = getExistingChiralityIdx(at);
+  if (cidx == -1) {
+    internalChirality_.push_back( InternalChirality(at, chi) );
+  } else {
+    mprintf("Warning: Overriding existing chirality %f for atom %i with %f\n",
+            internalChirality_[cidx].ChiralVal(), at+1, chi);
+    internalChirality_[cidx].SetChiralVal( chi );
+  }
 }
 
 /** Get length from parameter set if present.
@@ -216,6 +228,7 @@ class Cpptraj::Structure::Builder::TorsionModel {
     int InitTorsion(int, int, Frame const&, Topology const&, std::vector<bool> const&, int);
     /// Set up torsions around bonded atoms
     int SetupTorsion(AtomType::HybridizationType, AtomType::HybridizationType, Topology const& topIn, double, double);
+    //int SetupTorsion(AtomType::HybridizationType, AtomType::HybridizationType, Topology const& topIn, double, double, double, double);
     /// Build mock externals from given internals
     int BuildMockExternals(Iarray const&, Tarray const&, Topology const&);
 
@@ -428,6 +441,7 @@ int Cpptraj::Structure::Builder::TorsionModel::SetupTorsion(AtomType::Hybridizat
                                                             AtomType::HybridizationType Hy,
                                                             Topology const& topIn,
                                                             double chiX, double chiY)
+//                                                            double orientX, double orientY)
 {
   if (Hx != AtomType::UNKNOWN_HYBRIDIZATION && Hy != AtomType::UNKNOWN_HYBRIDIZATION) {
     if (Hy > Hx) {
@@ -441,22 +455,31 @@ int Cpptraj::Structure::Builder::TorsionModel::SetupTorsion(AtomType::Hybridizat
   // Sort AY bonds
   unsigned int firstUnknownIdxY = 0;
   sorted_ay_ = SortBondedAtomsLikeLeap(firstUnknownIdxY, topIn, sorted_ay_);
-  // Calculate the chirality around atom X
-  Xorientation_ = 0;
-  if (Hx == AtomType::SP3) {
-    if (sorted_ax_.size() < 2)
-      Xorientation_ = 1.0;
-    else
-      Xorientation_ = calculateOrientation( atX_, chiX, topIn[atX_.Idx()], sorted_ax_[0], atY_, sorted_ax_[1] );
-  }
-  // Calculate the chirality around atom Y
-  Yorientation_ = 0;
-  if (Hy == AtomType::SP3) {
-    if (sorted_ay_.size() < 2)
-      Yorientation_ = 1.0;
-    else
-      Yorientation_ = calculateOrientation( atY_, chiY, topIn[atY_.Idx()], sorted_ay_[0], atX_, sorted_ay_[1] );
-  }
+  // If both orientations exist, use those. Otherwise calculate.
+//  bool existingOrientationX = (orientX > 0 || orientX < 0);
+//  bool existingOrientationY = (orientY > 0 || orientY < 0);
+//  if (existingOrientationX && existingOrientationY) {
+//    //Xorientation_ = orientX;
+//    //Yorientation_ = orientY;
+//    mprintf("DEBUG: ExistingOrientationX= %f  ExistingOrientationY= %f\n", orientX, orientY);
+//  }// else {
+    // Calculate the chirality around atom X
+    Xorientation_ = 0;
+    if (Hx == AtomType::SP3) {
+      if (sorted_ax_.size() < 2)
+        Xorientation_ = 1.0;
+      else
+        Xorientation_ = calculateOrientation( atX_, chiX, topIn[atX_.Idx()], sorted_ax_[0], atY_, sorted_ax_[1] );
+    }
+    // Calculate the chirality around atom Y
+    Yorientation_ = 0;
+    if (Hy == AtomType::SP3) {
+      if (sorted_ay_.size() < 2)
+        Yorientation_ = 1.0;
+      else
+        Yorientation_ = calculateOrientation( atY_, chiY, topIn[atY_.Idx()], sorted_ay_[0], atX_, sorted_ay_[1] );
+    }
+  //}
   // DEBUG
   Atom const& AX = topIn[atX_.Idx()];
   Atom const& AY = topIn[atY_.Idx()];
@@ -642,7 +665,7 @@ int Cpptraj::Structure::Builder::TorsionModel::BuildMockExternals(Iarray const&
 
 // -----------------------------------------------------------------------------
 /** Calculate the orientation around a single atom. Assume all positions are known. */
-double Builder::CalculateOrientationAroundAtom(int ax, int ay, Frame const& frameIn, Topology const& topIn) {
+/*double Builder::CalculateOrientationAroundAtom(int ax, int ay, Frame const& frameIn, Topology const& topIn) {
   using namespace Cpptraj::Structure::Chirality;
 
   Vec3 iXPos( frameIn.XYZ(ax) );
@@ -671,6 +694,14 @@ double Builder::CalculateOrientationAroundAtom(int ax, int ay, Frame const& fram
           topIn.LeapName(ay).c_str(),
           Xorientation);
   return Xorientation;
+}*/
+
+/** Determine the chirality around a single atom. Assume all positions are known. */
+double Builder::DetermineChiralityAroundAtom(int at, Frame const& frameIn, Topology const& topIn)
+{
+  double dChi = 0;
+  determineChirality(dChi, at, frameIn, topIn, std::vector<bool>(topIn.Natom(), true));
+  return dChi;
 }
 
 /** Update all indices in internals according to the given offset. */
@@ -761,7 +792,7 @@ int Builder::getExistingChiralityIdx(int ai) const {
 }
 
 /** \return Index of existing orientation value matching given atom, 1 for no match. */
-int Builder::getExistingOrientationIdx(int ai) const {
+/*int Builder::getExistingOrientationIdx(int ai) const {
   int idx = -1;
   for (Carray::const_iterator it = internalOrientation_.begin(); it != internalOrientation_.end(); ++it)
   {
@@ -771,7 +802,7 @@ int Builder::getExistingOrientationIdx(int ai) const {
     }
   }
   return idx;
-}
+}*/
 
 /** Determine hybridization in the same manner as leap */
 AtomType::HybridizationType Builder::getAtomHybridization(Atom const& aAtom, std::vector<Atom> const& atoms) const {
@@ -1147,12 +1178,22 @@ int Builder::assignTorsionsAroundBond(int a1, int a2, Frame const& frameIn, Topo
   int Ycidx = getExistingChiralityIdx( ay );
   if (Ycidx != -1) chiY = internalChirality_[Ycidx].ChiralVal();
   // See if orientations exist
-  int Xoidx = getExistingOrientationIdx( ax );
-  if (Xoidx != -1) mprintf("DEBUG: Existing orientation for %s : %f\n", topIn.LeapName(ax).c_str(), internalOrientation_[Xoidx].ChiralVal());
-  int Yoidx = getExistingOrientationIdx( ay );
-  if (Yoidx != -1) mprintf("DEBUG: Existing orientation for %s : %f\n", topIn.LeapName(ay).c_str(), internalOrientation_[Yoidx].ChiralVal());
+//  double orientX = 0;
+//  int Xoidx = getExistingOrientationIdx( ax );
+//  if (Xoidx != -1) {
+//    orientX = internalOrientation_[Xoidx].ChiralVal();
+//    mprintf("DEBUG: Existing orientation for %s : %f\n", topIn.LeapName(ax).c_str(), orientX);
+//  }
+//  double orientY = 0;
+//  int Yoidx = getExistingOrientationIdx( ay );
+//  if (Yoidx != -1) {
+//    orientY = internalOrientation_[Yoidx].ChiralVal();
+//    mprintf("DEBUG: Existing orientation for %s : %f\n", topIn.LeapName(ay).c_str(), orientY);
+//  }
   // Set up the torsion model
-  if (mT.SetupTorsion(Hx, Hy, topIn, chiX, chiY)) {
+  //if (mT.SetupTorsion(Hx, Hy, topIn, chiX, chiY, orientX, orientY))
+  if (mT.SetupTorsion(Hx, Hy, topIn, chiX, chiY))
+  {
     mprinterr("Error: Could not set up torsions around %s - %s\n",
               topIn.LeapName(ax).c_str(),
               topIn.LeapName(ay).c_str());
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index d20fdd252b..996a0ba647 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -21,7 +21,9 @@ class Builder {
     /// Set optional parameter set
     void SetParameters(ParameterSet const*);
     /// Set atom orientation
-    void SetAtomOrientation(int, double);
+//    void SetAtomOrientation(int, double);
+    /// Set atom chirality
+    void SetAtomChirality(int, double);
     /// Update the internal coordinates in given Zmatrix with values from Frame/Parameters TODO combine into BuildFromInternals?
     int UpdateICsFromFrame(Frame const&, Topology const&, Barray const&);
     /// Generate internal coordinates in the same manner as LEaP
@@ -31,7 +33,8 @@ class Builder {
     /// Update existing indices with given offset
     void UpdateIndicesWithOffset(int);
 
-    static double CalculateOrientationAroundAtom(int, int, Frame const&, Topology const&); // TODO const?
+//    static double CalculateOrientationAroundAtom(int, int, Frame const&, Topology const&); // TODO const?
+    static double DetermineChiralityAroundAtom(int, Frame const&, Topology const&);
 
     /// Build position from internals for any atom with unset position
     int BuildFromInternals(Frame&, Topology const&, Barray&) const;
@@ -88,7 +91,7 @@ class Builder {
     /// Get specific chirality
     int getExistingChiralityIdx(int) const;
     /// Get specific orientation
-    int getExistingOrientationIdx(int) const;
+//    int getExistingOrientationIdx(int) const;
     /// Build mock coordinates around given torsion
     int buildMockExternals(TorsionModel& MT, std::vector<InternalCoords> const& iaTorsions) const;
     /// Build angle internal
@@ -114,7 +117,7 @@ class Builder {
     Aarray internalAngles_;
     Larray internalBonds_;
     Carray internalChirality_;
-    Carray internalOrientation_;
+//    Carray internalOrientation_;
     Iarray Rnums_;               ///< Hold residue indices pertaining to current internals
 };
 /// ----- Hold torsion internal ------------------

From 9178fcb32d8ac3006a4558e647328457c4d6e314 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 13 Feb 2024 15:06:46 -0500
Subject: [PATCH 0519/1492] Update save for latest IC change

---
 test/Test_Graft/IC.Final.graft.mol2.save | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/test/Test_Graft/IC.Final.graft.mol2.save b/test/Test_Graft/IC.Final.graft.mol2.save
index 0355474365..c87c8124e7 100644
--- a/test/Test_Graft/IC.Final.graft.mol2.save
+++ b/test/Test_Graft/IC.Final.graft.mol2.save
@@ -16,8 +16,8 @@ USER_CHARGES
       8 C           5.4855    2.7052   -0.0000 C          1 TYR      0.597300
       9 O           6.0088    1.5932   -0.0000 O          1 TYR     -0.567900
      10 C2          4.2167    4.8987    1.1983 CA         2 PRY      0.033204
-     11 C3          4.0500    5.8609    2.1981 CA         2 PRY     -0.149016
-     12 H4          3.4057    5.6495    3.0346 HA         2 PRY      0.153372
+     11 C3          4.0092    5.8193    2.2292 CA         2 PRY     -0.149016
+     12 H4          3.3701    5.6304    3.0751 HA         2 PRY      0.153372
      13 C4          4.6895    7.0771    2.1412 CA         2 PRY     -0.336291
      14 H5          4.5566    7.8128    2.9127 HA         2 PRY      0.167425
      15 C5          5.5298    7.3802    1.0703 CA         2 PRY      0.423974
@@ -25,7 +25,7 @@ USER_CHARGES
      17 C6          5.7104    6.4428    0.0703 CA         2 PRY     -0.336291
      18 H6          6.3501    6.6384   -0.7684 HA         2 PRY      0.167425
      19 C7          5.0526    5.2168    0.1465 CA         2 PRY     -0.149016
-     20 H7          5.2076    4.5030   -0.6439 HA         2 PRY      0.153372
+     20 H7          5.2087    4.5024   -0.6431 HA         2 PRY      0.153372
      21 C8          6.9535    9.0030    0.0541 CT         2 PRY      0.358047
      22 C9          7.3730   10.4140    0.3402 CM         2 PRY     -0.496680
      23 C10         8.5864   10.9389    0.2629 CM         2 PRY      0.317549

From 66299862953f26c80b865e554189cc2d910c8e45 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 13 Feb 2024 15:22:55 -0500
Subject: [PATCH 0520/1492] Update for recent changes

---
 test/Test_Sequence/Mol.mol2.save | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/test/Test_Sequence/Mol.mol2.save b/test/Test_Sequence/Mol.mol2.save
index 23ccbc3d64..5f9908d9e1 100644
--- a/test/Test_Sequence/Mol.mol2.save
+++ b/test/Test_Sequence/Mol.mol2.save
@@ -11,18 +11,18 @@ USER_CHARGES
       3 H3         -1.2286    0.8227   -0.8832 H1         1 MOC     -0.288000
       4 H4         -1.2287    0.8227    0.8831 H1         1 MOC     -0.288000
       5 O5          0.0000   -0.5708    0.0000 OS         1 MOC     -0.523200
-      6 N           1.1916    0.3403    0.0000 N          2 CNALA   -0.570310
-      7 H           1.1430    0.8923   -0.8547 H          2 CNALA    0.364710
-      8 CA          2.4264   -0.4645    0.0001 CX         2 CNALA    0.118030
-      9 HA          2.4901   -0.9979    0.9529 H1         2 CNALA    0.105630
-     10 CB          2.3829   -1.4921   -1.1479 CT         2 CNALA   -0.214290
-     11 HB1         1.4987   -2.1277   -1.0603 HC         2 CNALA    0.081710
-     12 HB2         2.3542   -0.9887   -2.1172 HC         2 CNALA    0.081710
-     13 HB3         3.2659   -2.1348   -1.1206 HC         2 CNALA    0.081710
-     14 C           3.6613    0.4137   -0.1142 C          2 CNALA    0.597740
-     15 O           3.6774    1.4856   -0.6854 O          2 CNALA   -0.533510
-     16 OXT         4.7542   -0.1713    0.2984 OH         2 CNALA   -0.566290
-     17 HXT         4.5091   -1.0471    0.6406 HO         2 CNALA    0.453160
+      6 N           1.1121    0.2796    0.0000 N          2 CNALA   -0.570310
+      7 H           0.9809    1.2897   -0.0001 H          2 CNALA    0.364710
+      8 CA          2.4729   -0.2868    0.0001 CX         2 CNALA    0.118030
+      9 HA          2.3931   -1.3756    0.0659 H1         2 CNALA    0.105630
+     10 CB          3.1959    0.0847   -1.3094 CT         2 CNALA   -0.214290
+     11 HB1         2.6253   -0.2619   -2.1741 HC         2 CNALA    0.081710
+     12 HB2         3.3226    1.1672   -1.3882 HC         2 CNALA    0.081710
+     13 HB3         4.1837   -0.3803   -1.3471 HC         2 CNALA    0.081710
+     14 C           3.2705    0.1855    1.2044 C          2 CNALA    0.597740
+     15 O           3.0963    1.2554    1.7526 O          2 CNALA   -0.533510
+     16 OXT         4.2882   -0.5835    1.4869 OH         2 CNALA   -0.566290
+     17 HXT         4.2716   -1.3337    0.8695 HO         2 CNALA    0.453160
 @<TRIPOS>BOND
     1     1     5 1
     2     6     8 1

From 875b106119a06e90beaaa87a6988821d8b6c5d48 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 14 Feb 2024 08:33:00 -0500
Subject: [PATCH 0521/1492] Code cleanup

---
 src/Structure/Builder.cpp | 122 +++++++-------------------------------
 src/Structure/Builder.h   |  13 +---
 2 files changed, 22 insertions(+), 113 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 44e6cd2520..802c31be7c 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -30,18 +30,6 @@ void Cpptraj::Structure::Builder::SetParameters(ParameterSet const* paramsIn) {
   params_ = paramsIn;
 }
 
-/** Set an atoms orientation */
-/*void Cpptraj::Structure::Builder::SetAtomOrientation(int at, double orient) {
-  int oidx = getExistingOrientationIdx(at);
-  if (oidx == -1) {
-    internalOrientation_.push_back( InternalChirality(at, orient) );
-  } else {
-    mprintf("Warning: Overriding existing orientation %f for atom %i with %f\n",
-            internalOrientation_[oidx].ChiralVal(), at+1, orient);
-    internalOrientation_[oidx].SetChiralVal( orient );
-  }
-}*/
-
 /** Set an atoms chirality */
 void Cpptraj::Structure::Builder::SetAtomChirality(int at, double chi) {
   int cidx = getExistingChiralityIdx(at);
@@ -222,13 +210,10 @@ class Cpptraj::Structure::Builder::TorsionModel {
     typedef std::vector<MockAtom> Marray;
     /// CONSTRUCTOR
     TorsionModel() : dAbsolute_(0), Xorientation_(0), Yorientation_(0), axHasKnownAtoms_(false), ayHasKnownAtoms_(false) {}
-    /// CONSTRUCTOR - AX and AY atom indices
-    //TorsionModel(int ax, int ay) : ax_(ax), ay_(ay),  dAbsolute_(0), Xorientation_(0), Yorientation_(0) {}
     /// Initialize torsions around bonded atoms
     int InitTorsion(int, int, Frame const&, Topology const&, std::vector<bool> const&, int);
     /// Set up torsions around bonded atoms
     int SetupTorsion(AtomType::HybridizationType, AtomType::HybridizationType, Topology const& topIn, double, double);
-    //int SetupTorsion(AtomType::HybridizationType, AtomType::HybridizationType, Topology const& topIn, double, double, double, double);
     /// Build mock externals from given internals
     int BuildMockExternals(Iarray const&, Tarray const&, Topology const&);
 
@@ -455,31 +440,22 @@ int Cpptraj::Structure::Builder::TorsionModel::SetupTorsion(AtomType::Hybridizat
   // Sort AY bonds
   unsigned int firstUnknownIdxY = 0;
   sorted_ay_ = SortBondedAtomsLikeLeap(firstUnknownIdxY, topIn, sorted_ay_);
-  // If both orientations exist, use those. Otherwise calculate.
-//  bool existingOrientationX = (orientX > 0 || orientX < 0);
-//  bool existingOrientationY = (orientY > 0 || orientY < 0);
-//  if (existingOrientationX && existingOrientationY) {
-//    //Xorientation_ = orientX;
-//    //Yorientation_ = orientY;
-//    mprintf("DEBUG: ExistingOrientationX= %f  ExistingOrientationY= %f\n", orientX, orientY);
-//  }// else {
-    // Calculate the chirality around atom X
-    Xorientation_ = 0;
-    if (Hx == AtomType::SP3) {
-      if (sorted_ax_.size() < 2)
-        Xorientation_ = 1.0;
-      else
-        Xorientation_ = calculateOrientation( atX_, chiX, topIn[atX_.Idx()], sorted_ax_[0], atY_, sorted_ax_[1] );
-    }
-    // Calculate the chirality around atom Y
-    Yorientation_ = 0;
-    if (Hy == AtomType::SP3) {
-      if (sorted_ay_.size() < 2)
-        Yorientation_ = 1.0;
-      else
-        Yorientation_ = calculateOrientation( atY_, chiY, topIn[atY_.Idx()], sorted_ay_[0], atX_, sorted_ay_[1] );
-    }
-  //}
+  // Calculate the chirality around atom X
+  Xorientation_ = 0;
+  if (Hx == AtomType::SP3) {
+    if (sorted_ax_.size() < 2)
+      Xorientation_ = 1.0;
+    else
+      Xorientation_ = calculateOrientation( atX_, chiX, topIn[atX_.Idx()], sorted_ax_[0], atY_, sorted_ax_[1] );
+  }
+  // Calculate the chirality around atom Y
+  Yorientation_ = 0;
+  if (Hy == AtomType::SP3) {
+    if (sorted_ay_.size() < 2)
+      Yorientation_ = 1.0;
+    else
+      Yorientation_ = calculateOrientation( atY_, chiY, topIn[atY_.Idx()], sorted_ay_[0], atX_, sorted_ay_[1] );
+  }
   // DEBUG
   Atom const& AX = topIn[atX_.Idx()];
   Atom const& AY = topIn[atY_.Idx()];
@@ -529,7 +505,7 @@ int Cpptraj::Structure::Builder::TorsionModel::BuildMockExternals(Iarray const&
                                                                   Topology const& topIn) // DEBUG topIn for debug only
 {
   if (iaTorsions.empty()) {
-    mprinterr("Internal Error: Builder::buildMockExternals() called with no internal torsions.\n");
+    mprinterr("Internal Error: TorsionModel::BuildMockExternals() called with no internal torsions.\n");
     return 1;
   }
   mprintf("=======  Started mock coords from: %s\n", topIn.LeapName(internalTorsionsIn[iaTorsions.front()].AtI()).c_str());
@@ -596,11 +572,11 @@ int Cpptraj::Structure::Builder::TorsionModel::BuildMockExternals(Iarray const&
         Marray::iterator tmpAt1 = find_mock_atom(outerAtoms, iInt.AtI());
         Marray::iterator tmpAt4 = find_mock_atom(outerAtoms, iInt.AtL());
         if (tmpAt1 == outerAtoms.end()) {
-          mprinterr("Internal Error: Builder::buildMockExternals(): Outer atom I %i not found.\n", iInt.AtI()+1);
+          mprinterr("Internal Error: TorsionModel::BuildMockExternals(): Outer atom I %i not found.\n", iInt.AtI()+1);
           return 1;
         }
         if (tmpAt4 == outerAtoms.end()) {
-          mprinterr("Internal Error: Builder::buildMockExternals(): Outer atom L %i not found.\n", iInt.AtL()+1);
+          mprinterr("Internal Error: TorsionModel::BuildMockExternals(): Outer atom L %i not found.\n", iInt.AtL()+1);
           return 1;
         }
         Vec3 maPC1, maPC2;
@@ -664,38 +640,6 @@ int Cpptraj::Structure::Builder::TorsionModel::BuildMockExternals(Iarray const&
 }
 
 // -----------------------------------------------------------------------------
-/** Calculate the orientation around a single atom. Assume all positions are known. */
-/*double Builder::CalculateOrientationAroundAtom(int ax, int ay, Frame const& frameIn, Topology const& topIn) {
-  using namespace Cpptraj::Structure::Chirality;
-
-  Vec3 iXPos( frameIn.XYZ(ax) );
-  Vec3 iYPos( frameIn.XYZ(ay) );
-  // Create array of AX bonded atoms
-  Atom const& AX = topIn[ax];
-  std::vector<MockAtom> sorted_ax;
-  sorted_ax.reserve( AX.Nbonds() - 1 );
-  for (Atom::bond_iterator bat = AX.bondbegin(); bat != AX.bondend(); ++bat) {
-    if (*bat != ay) {
-      sorted_ax.push_back( MockAtom(*bat, frameIn.XYZ(*bat)) );
-      sorted_ax.back().SetBuildInternals( true );
-    }
-  }
-  // Sort AX bonds
-  unsigned int firstUnknownIdxX = 0;
-  sorted_ax = TorsionModel::SortBondedAtomsLikeLeap(firstUnknownIdxX, topIn, sorted_ax);
-  // Calculate the chirality around atom X
-  double Xorientation = 0;
-  if (sorted_ax.size() < 2)
-    Xorientation = 1.0;
-  else
-    Xorientation = VectorAtomChirality( iXPos, sorted_ax[0].Pos(), iYPos, sorted_ax[1].Pos() );
-  mprintf("ORIENTATION: around atom %s (- %s) = %f\n",
-          topIn.LeapName(ax).c_str(),
-          topIn.LeapName(ay).c_str(),
-          Xorientation);
-  return Xorientation;
-}*/
-
 /** Determine the chirality around a single atom. Assume all positions are known. */
 double Builder::DetermineChiralityAroundAtom(int at, Frame const& frameIn, Topology const& topIn)
 {
@@ -791,19 +735,6 @@ int Builder::getExistingChiralityIdx(int ai) const {
   return idx;
 }
 
-/** \return Index of existing orientation value matching given atom, 1 for no match. */
-/*int Builder::getExistingOrientationIdx(int ai) const {
-  int idx = -1;
-  for (Carray::const_iterator it = internalOrientation_.begin(); it != internalOrientation_.end(); ++it)
-  {
-    if (it->AtI() == ai) {
-      idx = (int)(it - internalOrientation_.begin());
-      break;
-    }
-  }
-  return idx;
-}*/
-
 /** Determine hybridization in the same manner as leap */
 AtomType::HybridizationType Builder::getAtomHybridization(Atom const& aAtom, std::vector<Atom> const& atoms) const {
   AtomType::HybridizationType H1 = AtomType::UNKNOWN_HYBRIDIZATION;
@@ -1177,21 +1108,7 @@ int Builder::assignTorsionsAroundBond(int a1, int a2, Frame const& frameIn, Topo
   double chiY = 0;
   int Ycidx = getExistingChiralityIdx( ay );
   if (Ycidx != -1) chiY = internalChirality_[Ycidx].ChiralVal();
-  // See if orientations exist
-//  double orientX = 0;
-//  int Xoidx = getExistingOrientationIdx( ax );
-//  if (Xoidx != -1) {
-//    orientX = internalOrientation_[Xoidx].ChiralVal();
-//    mprintf("DEBUG: Existing orientation for %s : %f\n", topIn.LeapName(ax).c_str(), orientX);
-//  }
-//  double orientY = 0;
-//  int Yoidx = getExistingOrientationIdx( ay );
-//  if (Yoidx != -1) {
-//    orientY = internalOrientation_[Yoidx].ChiralVal();
-//    mprintf("DEBUG: Existing orientation for %s : %f\n", topIn.LeapName(ay).c_str(), orientY);
-//  }
   // Set up the torsion model
-  //if (mT.SetupTorsion(Hx, Hy, topIn, chiX, chiY, orientX, orientY))
   if (mT.SetupTorsion(Hx, Hy, topIn, chiX, chiY))
   {
     mprinterr("Error: Could not set up torsions around %s - %s\n",
@@ -1552,6 +1469,7 @@ int Builder::GenerateInternalsAroundLink(int at0, int at1,
   return 0;
 }
 
+/** For debugging, print all the complete internals associated with the given atom. */
 void Builder::printAllInternalsForAtom(int at, Topology const& topIn, Barray const& hasPosition) const
 {
   mprintf("DEBUG: All internals for atom %s\n", topIn.LeapName(at).c_str());
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index 996a0ba647..155740dde2 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -16,12 +16,10 @@ class Builder {
   public:
     /// CONSTRUCTOR
     Builder();
-    /// Set debug
+    /// Set debug level
     void SetDebug(int d) { debug_ = d; }
     /// Set optional parameter set
     void SetParameters(ParameterSet const*);
-    /// Set atom orientation
-//    void SetAtomOrientation(int, double);
     /// Set atom chirality
     void SetAtomChirality(int, double);
     /// Update the internal coordinates in given Zmatrix with values from Frame/Parameters TODO combine into BuildFromInternals?
@@ -33,12 +31,10 @@ class Builder {
     /// Update existing indices with given offset
     void UpdateIndicesWithOffset(int);
 
-//    static double CalculateOrientationAroundAtom(int, int, Frame const&, Topology const&); // TODO const?
+    /// \return LEaP chirality value around given atom
     static double DetermineChiralityAroundAtom(int, Frame const&, Topology const&);
-
     /// Build position from internals for any atom with unset position
     int BuildFromInternals(Frame&, Topology const&, Barray&) const;
-
     /// \return Zmatrix from current internals
     //int GetZmatrixFromInternals(Zmatrix&, Topology const&) const;
   private:
@@ -90,10 +86,6 @@ class Builder {
     int getExistingBondIdx(int, int) const;
     /// Get specific chirality
     int getExistingChiralityIdx(int) const;
-    /// Get specific orientation
-//    int getExistingOrientationIdx(int) const;
-    /// Build mock coordinates around given torsion
-    int buildMockExternals(TorsionModel& MT, std::vector<InternalCoords> const& iaTorsions) const;
     /// Build angle internal
     void buildAngleInternal(int, int, int, Frame const&, Topology const&, Barray const&);
     /// Build bond internal
@@ -117,7 +109,6 @@ class Builder {
     Aarray internalAngles_;
     Larray internalBonds_;
     Carray internalChirality_;
-//    Carray internalOrientation_;
     Iarray Rnums_;               ///< Hold residue indices pertaining to current internals
 };
 /// ----- Hold torsion internal ------------------

From d68e77ef702e756eb16a05ca5bdaa318e0dfee54 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 14 Feb 2024 09:11:20 -0500
Subject: [PATCH 0522/1492] When grafting, adjust torsion around link so
 longest depth has trans

---
 src/Exec_Graft.cpp        | 12 +++--
 src/Structure/Builder.cpp | 92 +++++++++++++++++++++++++++++++++++++++
 src/Structure/Builder.h   |  6 ++-
 3 files changed, 105 insertions(+), 5 deletions(-)

diff --git a/src/Exec_Graft.cpp b/src/Exec_Graft.cpp
index 4c07198e93..ab8f20c758 100644
--- a/src/Exec_Graft.cpp
+++ b/src/Exec_Graft.cpp
@@ -461,12 +461,10 @@ const
           mol0Top.AtomMaskName(bondat0).c_str());
   topOut.AddBond( bondat1 + atomOffset, bondat0 );
   // Set any saved orientations
-  if (hasOrient0_ && hasOrient1_) {
-//    structureBuilder.SetAtomOrientation(bondat0, orient0_);
+  if (hasOrient0_)
     structureBuilder.SetAtomChirality(bondat0, chi0_);
-//    structureBuilder.SetAtomOrientation(bondat1 + atomOffset, orient1_);
+  if (hasOrient1_)
     structureBuilder.SetAtomChirality(bondat1 + atomOffset, chi1_);
-  }
   // Generate internals around the link
   if (structureBuilder.GenerateInternalsAroundLink( bondat1 + atomOffset,
                                                     bondat0,
@@ -477,6 +475,12 @@ const
               topOut.AtomMaskName(bondat0).c_str());
     return 1;
   }
+  // Adjust torsions around link so that longest 'path' is trans
+  if (structureBuilder.AdjustIcAroundLink(bondat0, bondat1 + atomOffset, frameOut, topOut))
+  {
+    mprinterr("Error: Failed to adjust internal coords around the link.\n");
+    return 1;
+  }
   // Update internal coords from known positions
   if (structureBuilder.UpdateICsFromFrame( frameOut, topOut, hasPosition )) {
     mprinterr("Error: Failed to update Zmatrix with values from existing positions.\n");
diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 802c31be7c..b1b0ca0150 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -94,6 +94,98 @@ const
   return 0;
 }
 
+/// Recursive function to return depth from an atom along bonds
+static int atom_depth(int& depth,
+                      int at, Topology const& topIn, std::vector<bool>& visited, int maxdepth)
+{
+  if (depth == maxdepth) return 0;
+  depth++;
+  visited[at] = true;
+  int depthFromHere = 1;
+  for (Atom::bond_iterator bat = topIn[at].bondbegin(); bat != topIn[at].bondend(); ++bat)
+  {
+    if (!visited[*bat])
+      depthFromHere += atom_depth( depth, *bat, topIn, visited, maxdepth );
+  }
+  return depthFromHere;
+}
+
+/** \return Index of atom with longest 'depth' around an atom, ignoring one bonded atom. */
+int Builder::get_depths_around_atom(int at0, int at1, Topology const& topIn) {
+  int largest_depth = 0;
+  int largest_depth_idx = -1;
+  Atom const& Atm0 = topIn[at0];
+  mprintf("DEBUG: Depths around %s\n", topIn.AtomMaskName(at0).c_str());
+  for (Atom::bond_iterator bat = Atm0.bondbegin(); bat != Atm0.bondend(); ++bat)
+  {
+    if (*bat != at1) {
+      Barray visited(topIn.Natom(), false);
+      visited[at0] = true;
+      visited[at1] = true;
+      // Get depth from here
+      int currentDepth = 0;
+      int depth = atom_depth(currentDepth, *bat, topIn, visited, 10);
+      mprintf("DEBUG:\t\t%s = %i\n", topIn.AtomMaskName(*bat).c_str(), depth);
+      if (depth > largest_depth) {
+        largest_depth = depth;
+        largest_depth_idx = *bat;
+      }
+    }
+  }
+  return largest_depth_idx;
+}
+
+/** Adjust internals around a link so that atoms with longest 'depth' are trans. */
+int Builder::AdjustIcAroundLink(int at0, int at1, Frame const& frameIn, Topology const& topIn)
+{
+  int atA = get_depths_around_atom(at0, at1, topIn);
+  int atD = get_depths_around_atom(at1, at0, topIn);
+  if (atA < 0 || atD < 0) return 0;
+  mprintf("DEBUG: Highest depth torsion is %s - %s - %s - %s\n",
+          topIn.AtomMaskName(atA).c_str(),
+          topIn.AtomMaskName(at0).c_str(),
+          topIn.AtomMaskName(at1).c_str(),
+          topIn.AtomMaskName(atD).c_str());
+  // Get that torsion
+  int tidx = getExistingTorsionIdx(atA, at0, at1, atD);
+  if (tidx < 0) {
+    mprintf("Warning: Could not adjust internal torsion %s - %s - %s - %s, not present.\n",
+          topIn.AtomMaskName(atA).c_str(),
+          topIn.AtomMaskName(at0).c_str(),
+          topIn.AtomMaskName(at1).c_str(),
+          topIn.AtomMaskName(atD).c_str());
+    return 0;
+  }
+  // Figure out the delta from 180
+  double dTorsion = 180.0 * Constants::DEGRAD;
+  double dInternalValue = internalTorsions_[tidx].PhiVal();
+  double tDiff = (dTorsion - dInternalValue);
+  mprintf("\tdTorsion= %f  dInternalValue= %f  tDiff= %f\n",
+          dTorsion*Constants::RADDEG, dInternalValue*Constants::RADDEG, tDiff*Constants::RADDEG);
+  if (fabs(tDiff) > Constants::SMALL) {
+    // Find all ICs that share atoms 1 and 2 (J and K)
+    Iarray iTorsions = getExistingTorsionIdxs(at0, at1);
+    mprintf("Twisting torsions centered on %s - %s by %f degrees\n",
+            topIn.LeapName(at0).c_str(),
+            topIn.LeapName(at1).c_str(),
+            tDiff*Constants::RADDEG);
+    for (Iarray::const_iterator idx = iTorsions.begin(); idx != iTorsions.end(); ++idx)
+    {
+      InternalTorsion& dih = internalTorsions_[*idx];
+      double dNew = dih.PhiVal() + tDiff;
+      mprintf("Twisting torsion for atoms: %s-%s-%s-%s\n",
+              *(topIn[dih.AtI()].Name()),
+              *(topIn[dih.AtJ()].Name()),
+              *(topIn[dih.AtK()].Name()),
+              *(topIn[dih.AtL()].Name()));
+      mprintf("------- From %f to %f\n", dih.PhiVal()*Constants::RADDEG, dNew*Constants::RADDEG);
+      dih.SetPhiVal( dNew );
+    }
+  }
+
+  return 0;
+}
+
 /** For existing torsions, see if all coordinates in that torsion
   * exist. If so, update the torsion from the existing coordinates.
   */
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index 155740dde2..5788d51ef7 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -37,6 +37,8 @@ class Builder {
     int BuildFromInternals(Frame&, Topology const&, Barray&) const;
     /// \return Zmatrix from current internals
     //int GetZmatrixFromInternals(Zmatrix&, Topology const&) const;
+    /// Adjust torsion around a bond so that atoms with longest 'depth' are trans
+    int AdjustIcAroundLink(int, int, Frame const&, Topology const&);
   private:
     typedef std::vector<int> Iarray;
 
@@ -98,8 +100,10 @@ class Builder {
     int generateAtomInternals(int, Frame const&, Topology const&, Barray const&);
     /// Get complete internal coords that can be used to construct specified atom
     int getIcFromInternals(InternalCoords&, int, Barray const&) const;
-    // For debug
+    /// For debug, print all valid internals associated with an atom
     void printAllInternalsForAtom(int, Topology const&, Barray const&) const;
+    /// \\return index of atom with longest 'depth' bonded to a given atom (ignoring one bonded atom).
+    static int get_depths_around_atom(int, int, Topology const&);
 
     int debug_;
     ParameterSet const* params_;

From 4745f1908a6c013446454f279d11b270b7200c71 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 14 Feb 2024 09:26:47 -0500
Subject: [PATCH 0523/1492] Fixed with link adjusted to trans

---
 test/Test_Graft/IC.Nucleotide.pdb.save | 34 +++++++++++++-------------
 1 file changed, 17 insertions(+), 17 deletions(-)

diff --git a/test/Test_Graft/IC.Nucleotide.pdb.save b/test/Test_Graft/IC.Nucleotide.pdb.save
index 59b95bddc8..47c7f549ad 100644
--- a/test/Test_Graft/IC.Nucleotide.pdb.save
+++ b/test/Test_Graft/IC.Nucleotide.pdb.save
@@ -12,22 +12,22 @@ ATOM     11  C2   DA     1       5.285  -2.520   5.935  1.00  0.00           C
 ATOM     12  H2   DA     1       5.498  -2.482   6.993  1.00  0.00           H  
 ATOM     13  N3   DA     1       5.073  -1.309   5.456  1.00  0.00           N  
 ATOM     14  C4   DA     1       4.806  -1.356   4.133  1.00  0.00           C  
-ATOM     15  C5'  DA     1       1.109   1.452   3.145  1.00  0.00           C  
-ATOM     16  H5'  DA     1       0.981   0.812   4.017  1.00  0.00           H  
-ATOM     17 H5''  DA     1       0.230   2.087   3.028  1.00  0.00           H  
-ATOM     18  C4'  DA     1       2.335   2.328   3.343  1.00  0.00           C  
-ATOM     19  H4'  DA     1       2.082   3.168   3.988  1.00  0.00           H  
-ATOM     20  O4'  DA     1       3.334   1.576   4.098  1.00  0.00           O  
-ATOM     21  C1'  DA     1       4.385   1.163   3.237  1.00  0.00           C  
-ATOM     22  H1'  DA     1       5.314   1.643   3.542  1.00  0.00           H  
-ATOM     23  C3'  DA     1       3.063   2.753   2.066  1.00  0.00           C  
-ATOM     24  H3'  DA     1       2.348   2.823   1.246  1.00  0.00           H  
-ATOM     25  C2'  DA     1       4.053   1.564   1.798  1.00  0.00           C  
-ATOM     26  H2'  DA     1       3.856   1.107   0.829  1.00  0.00           H  
-ATOM     27  O3'  DA     1       3.851   3.932   2.147  1.00  0.00           O  
-ATOM     28  P    DA     1      -0.042  -0.302   1.764  0.00  0.00           P  
-ATOM     29  O1P  DA     1      -1.186   0.613   1.641  0.00  0.00           O  
-ATOM     30  O2P  DA     1       0.290  -1.365   0.804  0.00  0.00           O  
-ATOM     31  O5'  DA     1       1.283   0.644   1.978  0.00  0.00           O  
+ATOM     15  C5'  DA     1       4.531   3.163   5.051  1.00  0.00           C  
+ATOM     16  H5'  DA     1       4.258   2.516   5.885  1.00  0.00           H  
+ATOM     17 H5''  DA     1       4.648   4.186   5.409  1.00  0.00           H  
+ATOM     18  C4'  DA     1       5.847   2.687   4.459  1.00  0.00           C  
+ATOM     19  H4'  DA     1       6.672   3.026   5.084  1.00  0.00           H  
+ATOM     20  O4'  DA     1       5.901   1.230   4.542  1.00  0.00           O  
+ATOM     21  C1'  DA     1       5.692   0.661   3.257  1.00  0.00           C  
+ATOM     22  H1'  DA     1       6.590   0.129   2.945  1.00  0.00           H  
+ATOM     23  C3'  DA     1       6.045   2.985   2.908  1.00  0.00           C  
+ATOM     24  H3'  DA     1       5.511   3.890   2.619  1.00  0.00           H  
+ATOM     25  C2'  DA     1       5.383   1.772   2.252  1.00  0.00           C  
+ATOM     26  H2'  DA     1       4.562   2.104   1.616  1.00  0.00           H  
+ATOM     27  O3'  DA     1       7.391   3.030   2.458  1.00  0.00           O  
+ATOM     28  P    DA     1       2.039   3.624   4.641  1.00  0.00           P  
+ATOM     29  O1P  DA     1       1.047   3.543   3.559  1.00  0.00           O  
+ATOM     30  O2P  DA     1       1.683   2.744   5.764  1.00  0.00           O  
+ATOM     31  O5'  DA     1       3.461   3.109   4.001  1.00  0.00           O  
 TER      32       DA     1 
 END   

From a18baab31c075d96203ce6a9274b8614767cf014 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 14 Feb 2024 12:43:45 -0500
Subject: [PATCH 0524/1492] Record template head/tail atoms

---
 src/Exec_Build.cpp | 33 ++++++++++++++++++++++++++++++++-
 src/cpptrajdepend  |  4 ++--
 2 files changed, 34 insertions(+), 3 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index e92251914a..2a04ace165 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -6,6 +6,7 @@
 #include "Structure/Zmatrix.h"
 #include "Parm/GB_Params.h"
 #include "AssociatedData_ResId.h"
+#include "AssociatedData_Connect.h"
 
 /** Try to identify residue template DataSet from the given residue
   * name (from e.g. the PDB/Mol2/etc file).
@@ -74,6 +75,12 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
                                        Topology const& topIn, Frame const& frameIn,
                                        ParameterSet const& mainParmSet)
 {
+  // Array of head/tail connect atoms for each residue
+  typedef std::vector<int> Iarray;
+  Iarray resHeadAtoms;
+  Iarray resTailAtoms;
+  resHeadAtoms.reserve( topIn.Nres() );
+  resTailAtoms.reserve( topIn.Nres() );
   // Array of templates for each residue
   std::vector<DataSet_Coords*> ResTemplates;
   ResTemplates.reserve( topIn.Nres() );
@@ -107,9 +114,26 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
     if (resTemplate == 0) {
       mprintf("Warning: No template found for residue %s\n", topIn.TruncResNameOnumId(ires).c_str());
       newNatom += currentRes.NumAtoms();
+      // Head and tail atoms are blank
+      resHeadAtoms.push_back( -1 );
+      resTailAtoms.push_back( -1 );
     } else {
       mprintf("\tTemplate %s being used for residue %s\n",
               resTemplate->legend(), topIn.TruncResNameOnumId(ires).c_str());
+      // Save the head and tail atoms
+      AssociatedData* ad = resTemplate->GetAssociatedData(AssociatedData::CONNECT);
+      if (ad == 0) {
+        mprintf("Warning: Unit '%s' does not have CONNECT data.\n", resTemplate->legend());
+      } else {
+        AssociatedData_Connect const& CONN = static_cast<AssociatedData_Connect const&>( *ad );
+        if (CONN.NconnectAtoms() < 2) {
+          mprinterr("Error: Not enough connect atoms in unit '%s'\n", resTemplate->legend());
+          return 1;
+        }
+        resHeadAtoms.push_back( CONN.Connect()[0] + newNatom );
+        resTailAtoms.push_back( CONN.Connect()[1] + newNatom );
+      }
+      // Update # of atoms
       newNatom += resTemplate->Top().Natom();
     }
     ResTemplates.push_back( resTemplate );
@@ -125,7 +149,6 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
   hasPosition.reserve( newNatom );
 
   // Hold atom offsets needed when building residues
-  typedef std::vector<int> Iarray;
   Iarray AtomOffsets;
   AtomOffsets.reserve( topIn.Nres() );
 
@@ -254,6 +277,14 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
   mprintf("\t%i template atoms missing in source.\n", nRefAtomsMissing);
 
   // -----------------------------------
+  for (unsigned int idx = 0; idx != ResTemplates.size(); idx++) {
+    if (ResTemplates[idx] != 0) {
+      mprintf("DEBUG: Template %s", ResTemplates[idx]->legend());
+      if (resHeadAtoms[idx] > -1) mprintf(" head %s", topOut.AtomMaskName(resHeadAtoms[idx]).c_str());
+      if (resTailAtoms[idx] > -1) mprintf(" tail %s", topOut.AtomMaskName(resTailAtoms[idx]).c_str());
+      mprintf("\n");
+    }
+  }
   // Check inter-residue bonds
   std::vector<IParray> resBondingAtoms(topOut.Nres());
   for (ResAtArray::const_iterator it = interResBonds.begin(); it != interResBonds.end(); ++it)
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 2059dc510f..f33234614a 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -290,7 +290,7 @@ Ewald_Regular.o : Ewald_Regular.cpp Atom.h AtomMask.h Box.h Constants.h Coordina
 ExclusionArray.o : ExclusionArray.cpp Atom.h AtomMask.h CharMask.h CpptrajStdio.h ExclusionArray.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Unit.h
 Exec_AddMissingRes.o : Exec_AddMissingRes.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CharMask.h CompactFrameArray.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_AddMissingRes.h Exec_AddMissingRes_Pres.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Analyze.o : Exec_Analyze.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Analyze.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Build.o : Exec_Build.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/GB_Params.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Build.o : Exec_Build.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/GB_Params.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Calc.o : Exec_Calc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Calc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_CatCrd.o : Exec_CatCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CatCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Change.o : Exec_Change.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Change.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
@@ -312,7 +312,7 @@ Exec_Emin.o : Exec_Emin.cpp Action.h ActionList.h ActionState.h Analysis.h Analy
 Exec_ExtendedComparison.o : Exec_ExtendedComparison.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ExtendedComparison.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Flatten.o : Exec_Flatten.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Flatten.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_GenerateAmberRst.o : Exec_GenerateAmberRst.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_GenerateAmberRst.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Graft.o : Exec_Graft.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Graft.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Graft.o : Exec_Graft.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Graft.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Help.o : Exec_Help.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Help.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_HmassRepartition.o : Exec_HmassRepartition.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_HmassRepartition.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_LoadCrd.o : Exec_LoadCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_LoadCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h

From dac790764f70f2c56bfba1f223130c366b5deca1 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 14 Feb 2024 12:46:54 -0500
Subject: [PATCH 0525/1492] Make final residue end-terminal by default

---
 src/Exec_Build.cpp | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 2a04ace165..68cc452d15 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -105,6 +105,8 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
       resTermType = Cpptraj::Structure::BEG_TERMINAL;
     } else if (nres < topIn.Nres() && topIn.Res(nres).ChainId() != currentRes.ChainId()) {
       resTermType = Cpptraj::Structure::END_TERMINAL;
+    } else if (nres == topIn.Nres()) {
+      resTermType = Cpptraj::Structure::END_TERMINAL;
     } else {
       resTermType = Cpptraj::Structure::NON_TERMINAL;
     }

From ceca343c9156690519dcd4300e9a181129b1aee5 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 14 Feb 2024 13:09:20 -0500
Subject: [PATCH 0526/1492] Check head/tail atoms

---
 src/Exec_Build.cpp | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 68cc452d15..ea3fe4eff7 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -311,6 +311,36 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
     resBondingAtoms[ra0.first].push_back( Ipair(at0, at1) );
     resBondingAtoms[ra1.first].push_back( Ipair(at1, at0) );
   }
+  // For each residue bonding atom pair, check that they match expected
+  // head/tail atoms.
+  for (std::vector<IParray>::const_iterator rit = resBondingAtoms.begin();
+                                            rit != resBondingAtoms.end(); ++rit)
+  {
+    long int ires = rit - resBondingAtoms.begin();
+    for (IParray::const_iterator atPair = rit->begin(); atPair != rit->end(); ++atPair)
+    {
+      long int jres = topOut[atPair->second].ResNum();
+      if (atPair->first == resHeadAtoms[ires]) {
+        // HEAD atom. Should connect to other residue TAIL atom.
+        if (atPair->second != resTailAtoms[jres]) {
+          mprintf("Warning: Detected inter-res bond %s - %s HEAD does not match TAIL.\n",
+                  topOut.AtomMaskName(atPair->first).c_str(),
+                  topOut.AtomMaskName(atPair->second).c_str());
+        }
+      } else if (atPair->first == resTailAtoms[ires]) {
+        // TAIL atom. Should connect to other residue HEAD atom.
+        if (atPair->second != resHeadAtoms[jres]) {
+          mprintf("Warning: Detected inter-res bond %s - %s TAIL does not match HEAD.\n",
+                  topOut.AtomMaskName(atPair->first).c_str(),
+                  topOut.AtomMaskName(atPair->second).c_str());
+        }
+      } else {
+        mprintf("Warning: Atom %s is not a HEAD or TAIL atom.\n",
+                topOut.AtomMaskName(atPair->first).c_str());
+      }
+    } // END loop over inter-residue bond pairs for this residue
+  } // END loop over residues
+
   // DEBUG print residue bonding atoms
   for (std::vector<IParray>::const_iterator rit = resBondingAtoms.begin();
                                             rit != resBondingAtoms.end(); ++rit)

From 00f33c0d3e2be68b687ad93d4cd20019e72532aa Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 14 Feb 2024 13:26:28 -0500
Subject: [PATCH 0527/1492] Fix when template has no HEAD or has no TAIL.
 Report unused HEAD/TAIL atoms.

---
 src/Exec_Build.cpp | 32 ++++++++++++++++++++++++++++++--
 1 file changed, 30 insertions(+), 2 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index ea3fe4eff7..b020c41fbe 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -132,8 +132,14 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
           mprinterr("Error: Not enough connect atoms in unit '%s'\n", resTemplate->legend());
           return 1;
         }
-        resHeadAtoms.push_back( CONN.Connect()[0] + newNatom );
-        resTailAtoms.push_back( CONN.Connect()[1] + newNatom );
+        if (CONN.Connect()[0] > -1)
+          resHeadAtoms.push_back( CONN.Connect()[0] + newNatom );
+        else
+          resHeadAtoms.push_back( -1 );
+        if (CONN.Connect()[1] > -1)
+          resTailAtoms.push_back( CONN.Connect()[1] + newNatom );
+        else
+          resTailAtoms.push_back( -1 );
       }
       // Update # of atoms
       newNatom += resTemplate->Top().Natom();
@@ -341,6 +347,28 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
     } // END loop over inter-residue bond pairs for this residue
   } // END loop over residues
 
+  // Mark used HEAD/TAIL atoms
+  for (std::vector<IParray>::const_iterator rit = resBondingAtoms.begin();
+                                            rit != resBondingAtoms.end(); ++rit)
+  {
+    long int ires = rit - resBondingAtoms.begin();
+    for (IParray::const_iterator atPair = rit->begin(); atPair != rit->end(); ++atPair)
+    {
+      if (atPair->first == resHeadAtoms[ires])
+        resHeadAtoms[ires] = -1;
+      else if (atPair->first == resTailAtoms[ires])
+        resTailAtoms[ires] = -1;
+    }
+  }
+
+  // Report unused HEAD/TAIL atoms
+  for (int ires = 0; ires != topOut.Nres(); ires++) { // TODO should be topIn?
+    if (resHeadAtoms[ires] != -1)
+      mprintf("Warning: Unused head atom %s\n", topOut.AtomMaskName(resHeadAtoms[ires]).c_str());
+    if (resTailAtoms[ires] != -1)
+      mprintf("Warning: Unused tail atom %s\n", topOut.AtomMaskName(resTailAtoms[ires]).c_str());
+  }
+
   // DEBUG print residue bonding atoms
   for (std::vector<IParray>::const_iterator rit = resBondingAtoms.begin();
                                             rit != resBondingAtoms.end(); ++rit)

From 8993ba948cd439af954b5ff07745a9fa85cfacd8 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 15 Feb 2024 08:59:26 -0500
Subject: [PATCH 0528/1492] No longer needs to depend on zmatrix

---
 src/Exec_Build.cpp      | 17 +++--------------
 src/Structure/Builder.h |  2 +-
 src/cpptrajdepend       |  2 +-
 3 files changed, 5 insertions(+), 16 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index b020c41fbe..b8a00e8bd5 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -3,7 +3,6 @@
 #include "DataSet_Parameters.h"
 #include "Structure/Builder.h"
 #include "Structure/GenerateConnectivityArrays.h"
-#include "Structure/Zmatrix.h"
 #include "Parm/GB_Params.h"
 #include "AssociatedData_ResId.h"
 #include "AssociatedData_Connect.h"
@@ -153,7 +152,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
 
   // -----------------------------------
   // hasPosition - for each atom in topOut, status on whether atom in frameOut needs building
-  Cpptraj::Structure::Zmatrix::Barray hasPosition;
+  Cpptraj::Structure::Builder::Barray hasPosition;
   hasPosition.reserve( newNatom );
 
   // Hold atom offsets needed when building residues
@@ -446,24 +445,14 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
       }
       // Update internal coords from known positions
       if (structureBuilder.UpdateICsFromFrame( frameOut, topOut, hasPosition )) {
-        mprinterr("Error: Failed to update Zmatrix with values from existing positions.\n");
+        mprinterr("Error: Failed to update internals with values from existing positions.\n");
         return 1;
       }
-      // Convert to Zmatrix and assign missing atom positions
-      //Cpptraj::Structure::Zmatrix tmpz;
-      //tmpz.SetDebug( 1 ); // DEBUG
-      //if (structureBuilder.GetZmatrixFromInternals(tmpz, topOut)) {
-      //  mprinterr("Error: Could not get Zmatrix from internals.\n");
-      //  return 1;
-      //}
-      //if (tmpz.SetToFrame( frameOut, hasPosition )) {
       if (structureBuilder.BuildFromInternals(frameOut, topOut, hasPosition)) {
         mprinterr("Error: Building residue %s failed.\n",
                   topOut.TruncResNameOnumId(ires).c_str());
         buildFailed = true;
-      }// else
-       // resIsBuilt[ires] = true;
-      //delete structureBuilder;
+      }
     }
   } // END loop over atom offsets
 
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index 5788d51ef7..a2d94a4b2a 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -12,8 +12,8 @@ class Zmatrix;
 class InternalCoords;
 /// Used to attach different topology/frame combos using internal coordinates
 class Builder {
-    typedef std::vector<bool> Barray;
   public:
+    typedef std::vector<bool> Barray;
     /// CONSTRUCTOR
     Builder();
     /// Set debug level
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index f33234614a..d376b56682 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -290,7 +290,7 @@ Ewald_Regular.o : Ewald_Regular.cpp Atom.h AtomMask.h Box.h Constants.h Coordina
 ExclusionArray.o : ExclusionArray.cpp Atom.h AtomMask.h CharMask.h CpptrajStdio.h ExclusionArray.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Unit.h
 Exec_AddMissingRes.o : Exec_AddMissingRes.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CharMask.h CompactFrameArray.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_AddMissingRes.h Exec_AddMissingRes_Pres.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Analyze.o : Exec_Analyze.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Analyze.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Build.o : Exec_Build.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/GB_Params.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Build.o : Exec_Build.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/GB_Params.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/GenerateConnectivityArrays.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Calc.o : Exec_Calc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Calc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_CatCrd.o : Exec_CatCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CatCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Change.o : Exec_Change.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Change.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h

From 6669749304432ad4d1db4e306efd3df4019c24d9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 15 Feb 2024 09:11:05 -0500
Subject: [PATCH 0529/1492] Connect unused HEAD atoms to unused TAIL atoms of
 prior residues

---
 src/Exec_Build.cpp | 28 +++++++++++++++++++++++-----
 1 file changed, 23 insertions(+), 5 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index b8a00e8bd5..af00c82de9 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -292,7 +292,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
       mprintf("\n");
     }
   }
-  // Check inter-residue bonds
+  // Check detected inter-residue bonds
   std::vector<IParray> resBondingAtoms(topOut.Nres());
   for (ResAtArray::const_iterator it = interResBonds.begin(); it != interResBonds.end(); ++it)
   {
@@ -312,11 +312,13 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
       mprinterr("Error: Atom %s not found in residue %i\n", *(ra1.second), ra1.first);
       return 1;
     }
-    // Save bonding atoms
+    // Save inter-residue bonding atoms; convention is atom belonging to
+    // the residue is first.
     resBondingAtoms[ra0.first].push_back( Ipair(at0, at1) );
     resBondingAtoms[ra1.first].push_back( Ipair(at1, at0) );
   }
-  // For each residue bonding atom pair, check that they match expected
+
+  // For each inter-residue bonding atom pair, check that they match expected
   // head/tail atoms.
   for (std::vector<IParray>::const_iterator rit = resBondingAtoms.begin();
                                             rit != resBondingAtoms.end(); ++rit)
@@ -346,7 +348,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
     } // END loop over inter-residue bond pairs for this residue
   } // END loop over residues
 
-  // Mark used HEAD/TAIL atoms
+  // Mark used HEAD/TAIL atoms in existing inter-residue bonds.
   for (std::vector<IParray>::const_iterator rit = resBondingAtoms.begin();
                                             rit != resBondingAtoms.end(); ++rit)
   {
@@ -360,6 +362,22 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
     }
   }
 
+  // Try to connect unused HEAD atoms to previous unused TAIL atoms
+  for (int ires = 1; ires < topOut.Nres(); ires++) {
+    int pres = ires - 1;
+    if (resHeadAtoms[ires] != -1) {
+      if (resTailAtoms[pres] != -1) {
+        mprintf("DEBUG: Connecting unused HEAD atom %s to unused tail atom %s\n",
+                topOut.AtomMaskName(resHeadAtoms[ires]).c_str(),
+                topOut.AtomMaskName(resTailAtoms[pres]).c_str());
+        resBondingAtoms[ires].push_back( Ipair(resHeadAtoms[ires], resTailAtoms[pres]) );
+        resBondingAtoms[pres].push_back( Ipair(resTailAtoms[pres], resHeadAtoms[ires]) );
+        resHeadAtoms[ires] = -1;
+        resTailAtoms[pres] = -1;
+      }
+    }
+  }
+
   // Report unused HEAD/TAIL atoms
   for (int ires = 0; ires != topOut.Nres(); ires++) { // TODO should be topIn?
     if (resHeadAtoms[ires] != -1)
@@ -368,7 +386,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
       mprintf("Warning: Unused tail atom %s\n", topOut.AtomMaskName(resTailAtoms[ires]).c_str());
   }
 
-  // DEBUG print residue bonding atoms
+  // DEBUG print inter-residue bonding atoms
   for (std::vector<IParray>::const_iterator rit = resBondingAtoms.begin();
                                             rit != resBondingAtoms.end(); ++rit)
   {

From b8dd9782cac8b77b0a65dddcf07248e56038c0f7 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 15 Feb 2024 09:25:48 -0500
Subject: [PATCH 0530/1492] Start new creator class

---
 src/Structure/CMakeLists.txt  |  1 +
 src/Structure/Creator.cpp     | 80 +++++++++++++++++++++++++++++++++++
 src/Structure/Creator.h       | 26 ++++++++++++
 src/Structure/structuredepend |  1 +
 src/Structure/structurefiles  |  1 +
 5 files changed, 109 insertions(+)
 create mode 100644 src/Structure/Creator.cpp
 create mode 100644 src/Structure/Creator.h

diff --git a/src/Structure/CMakeLists.txt b/src/Structure/CMakeLists.txt
index b434c765d1..18f46a3c1e 100644
--- a/src/Structure/CMakeLists.txt
+++ b/src/Structure/CMakeLists.txt
@@ -3,6 +3,7 @@ target_sources(cpptraj_common_obj PRIVATE
   ${CMAKE_CURRENT_LIST_DIR}/BuildAtom.cpp
   ${CMAKE_CURRENT_LIST_DIR}/Builder.cpp
   ${CMAKE_CURRENT_LIST_DIR}/Chirality.cpp
+  ${CMAKE_CURRENT_LIST_DIR}/Creator.cpp
   ${CMAKE_CURRENT_LIST_DIR}/Disulfide.cpp
   ${CMAKE_CURRENT_LIST_DIR}/FunctionalGroup.cpp
   ${CMAKE_CURRENT_LIST_DIR}/FxnGroupBuilder.cpp
diff --git a/src/Structure/Creator.cpp b/src/Structure/Creator.cpp
new file mode 100644
index 0000000000..2b9fa2c2f1
--- /dev/null
+++ b/src/Structure/Creator.cpp
@@ -0,0 +1,80 @@
+#include "Creator.h"
+#include "../ArgList.h"
+#include "../CpptrajStdio.h"
+#include "../DataSet_Parameters.h"
+#include "../DataSetList.h"
+
+using namespace Cpptraj::Structure;
+
+/** CONSTRUCTOR */
+Creator::Creator() :
+  mainParmSet_(0),
+  debug_(0),
+  free_parmset_mem_(false)
+{}
+
+/** DESTRUCTOR */
+Creator::~Creator() {
+  if (mainParmSet_ != 0)
+    delete mainParmSet_;
+}
+
+const char* Creator::keywords_ = "parmset <parameter set>";
+
+/** Initialize */
+int Creator::InitCreator(ArgList& argIn, DataSetList const& DSL, int debugIn)
+{
+  debug_ = debugIn;
+  // Get parameter sets.
+  typedef std::vector<DataSet_Parameters*> Parray;
+  Parray ParamSets;
+  std::string parmset = argIn.GetStringKey("parmset");
+  if (parmset.empty()) {
+    mprintf("\tNo parameter set(s) specified with 'parmset'; using any loaded sets.\n");
+    // See if there are any parameter sets.
+    DataSetList sets = DSL.GetSetsOfType( "*", DataSet::PARAMETERS );
+    for (DataSetList::const_iterator it = sets.begin(); it != sets.end(); ++it)
+      ParamSets.push_back( (DataSet_Parameters*)(*it) );
+  } else {
+    while (!parmset.empty()) {
+      DataSetList sets = DSL.GetSetsOfType( parmset, DataSet::PARAMETERS );
+      if (sets.empty()) {
+        mprintf("Warning: No parameter sets corresponding to '%s'\n", parmset.c_str());
+      } else {
+        for (DataSetList::const_iterator it = sets.begin(); it != sets.end(); ++it)
+          ParamSets.push_back( (DataSet_Parameters*)(*it) );
+      }
+      parmset = argIn.GetStringKey("parmset");
+    }
+  }
+  //if (ParamSets.empty()) {
+  //  mprinterr("Error: No parameter sets.\n");
+  //  return CpptrajState::ERR;
+  //}
+  if (!ParamSets.empty()) {
+    mprintf("\tParameter sets:\n");
+    for (Parray::const_iterator it = ParamSets.begin(); it != ParamSets.end(); ++it)
+      mprintf("\t  %s\n", (*it)->legend());
+
+    // Combine parameters if needed
+    if (mainParmSet_ != 0) {
+      if (free_parmset_mem_) delete mainParmSet_;
+    }
+    mainParmSet_ = 0;
+    free_parmset_mem_ = false;
+    if (ParamSets.size() == 1)
+      mainParmSet_ = ParamSets.front();
+    else {
+      free_parmset_mem_ = true;
+      mprintf("\tCombining parameter sets.\n");
+      Parray::const_iterator it = ParamSets.begin();
+      mainParmSet_ = new DataSet_Parameters( *(*it) );
+      ++it;
+      ParameterSet::UpdateCount UC;
+      for (; it != ParamSets.end(); ++it)
+        mainParmSet_->UpdateParamSet( *(*it), UC, debug_, debug_ ); // FIXME verbose
+    }
+  }
+  return 0;
+}
+
diff --git a/src/Structure/Creator.h b/src/Structure/Creator.h
new file mode 100644
index 0000000000..b4ce0571d2
--- /dev/null
+++ b/src/Structure/Creator.h
@@ -0,0 +1,26 @@
+#ifndef INC_STRUCTURE_CREATOR_H
+#define INC_STRUCTURE_CREATOR_H
+class ArgList;
+class DataSet_Parameters;
+class DataSetList;
+namespace Cpptraj {
+namespace Structure {
+/// Used to create a system from individual units
+class Creator {
+  public:
+    /// CONSTRUCTOR
+    Creator();
+    /// DESTRUCTOR
+    ~Creator();
+    /// Associated keywords for InitCreator
+    static const char* keywords_;
+    /// Initialize the Creator
+    int InitCreator(ArgList&, DataSetList const&, int);
+  private:
+    DataSet_Parameters* mainParmSet_; ///< Hold optional parameter set.
+    int debug_;                       ///< Debug level
+    bool free_parmset_mem_;           ///< True if main parm set is combined and should be freed
+};
+}
+}
+#endif
diff --git a/src/Structure/structuredepend b/src/Structure/structuredepend
index 8038bb531b..a41b2cd8d1 100644
--- a/src/Structure/structuredepend
+++ b/src/Structure/structuredepend
@@ -1,6 +1,7 @@
 BuildAtom.o : BuildAtom.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h StructureEnum.h
 Builder.o : Builder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Builder.h Chirality.h GenerateConnectivityArrays.h InternalCoords.h Zmatrix.h
 Chirality.o : Chirality.cpp ../Atom.h ../Constants.h ../CpptrajStdio.h ../NameType.h ../SymbolExporting.h ../Vec3.h Chirality.h
+Creator.o : Creator.cpp ../AssociatedData.h ../AtomType.h ../Constants.h ../CpptrajFile.h ../DataSet.h ../DataSet_Parameters.h ../Dimension.h ../FileIO.h ../FileName.h ../MetaData.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../TextFormat.h ../TypeNameHolder.h Creator.h
 Disulfide.o : Disulfide.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Disulfide.h ResStatArray.h StructureRoutines.h
 FunctionalGroup.o : FunctionalGroup.cpp ../Atom.h ../AtomMap.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h FunctionalGroup.h
 FxnGroupBuilder.o : FxnGroupBuilder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h FunctionalGroup.h FxnGroupBuilder.h StructureRoutines.h Sugar.h SugarToken.h
diff --git a/src/Structure/structurefiles b/src/Structure/structurefiles
index d00e816504..00491304ea 100644
--- a/src/Structure/structurefiles
+++ b/src/Structure/structurefiles
@@ -3,6 +3,7 @@ STRUCTURE_SOURCES= \
   BuildAtom.cpp \
   Builder.cpp \
   Chirality.cpp \
+  Creator.cpp \
   Disulfide.cpp \
   FunctionalGroup.cpp \
   FxnGroupBuilder.cpp \

From bc561f356ef668605a1b02106be6b13f44c8072a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 15 Feb 2024 09:41:32 -0500
Subject: [PATCH 0531/1492] Put in separate function

---
 src/Structure/Creator.cpp | 21 +++++++++++++++------
 src/Structure/Creator.h   |  6 ++++++
 2 files changed, 21 insertions(+), 6 deletions(-)

diff --git a/src/Structure/Creator.cpp b/src/Structure/Creator.cpp
index 2b9fa2c2f1..0cd76c4e09 100644
--- a/src/Structure/Creator.cpp
+++ b/src/Structure/Creator.cpp
@@ -25,7 +25,20 @@ const char* Creator::keywords_ = "parmset <parameter set>";
 int Creator::InitCreator(ArgList& argIn, DataSetList const& DSL, int debugIn)
 {
   debug_ = debugIn;
-  // Get parameter sets.
+  if (getParameterSets(argIn, DSL)) return 1;
+
+  return 0;
+}
+
+/** Get parameter sets. */
+int Creator::getParameterSets(ArgList& argIn, DataSetList const& DSL) {
+  // Clear any existing set
+  if (mainParmSet_ != 0) {
+    if (free_parmset_mem_) delete mainParmSet_;
+  }
+  mainParmSet_ = 0;
+  free_parmset_mem_ = false;
+  // Look for parmset args
   typedef std::vector<DataSet_Parameters*> Parray;
   Parray ParamSets;
   std::string parmset = argIn.GetStringKey("parmset");
@@ -57,11 +70,7 @@ int Creator::InitCreator(ArgList& argIn, DataSetList const& DSL, int debugIn)
       mprintf("\t  %s\n", (*it)->legend());
 
     // Combine parameters if needed
-    if (mainParmSet_ != 0) {
-      if (free_parmset_mem_) delete mainParmSet_;
-    }
-    mainParmSet_ = 0;
-    free_parmset_mem_ = false;
+
     if (ParamSets.size() == 1)
       mainParmSet_ = ParamSets.front();
     else {
diff --git a/src/Structure/Creator.h b/src/Structure/Creator.h
index b4ce0571d2..3d8ae7b0e8 100644
--- a/src/Structure/Creator.h
+++ b/src/Structure/Creator.h
@@ -16,7 +16,13 @@ class Creator {
     static const char* keywords_;
     /// Initialize the Creator
     int InitCreator(ArgList&, DataSetList const&, int);
+
+    /// \return True if a parameter set is defined
+    bool HasMainParmSet() const { return (mainParmSet_ != 0); }
   private:
+    /// Get parameter sets
+    int getParameterSets(ArgList&, DataSetList const&);
+
     DataSet_Parameters* mainParmSet_; ///< Hold optional parameter set.
     int debug_;                       ///< Debug level
     bool free_parmset_mem_;           ///< True if main parm set is combined and should be freed

From df17ecc14a8db043a86c5918edbd316e73b68956 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 15 Feb 2024 11:22:15 -0500
Subject: [PATCH 0532/1492] Fix memory issue in destructor. Start using creator
 in build.

---
 src/Exec_Build.cpp            | 18 ++++++++++++++----
 src/Structure/Creator.cpp     |  2 +-
 src/Structure/Creator.h       |  2 ++
 src/Structure/structuredepend |  2 +-
 src/cpptrajdepend             |  3 ++-
 5 files changed, 20 insertions(+), 7 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index af00c82de9..f7992964ea 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -2,6 +2,7 @@
 #include "CpptrajStdio.h"
 #include "DataSet_Parameters.h"
 #include "Structure/Builder.h"
+#include "Structure/Creator.h"
 #include "Structure/GenerateConnectivityArrays.h"
 #include "Parm/GB_Params.h"
 #include "AssociatedData_ResId.h"
@@ -609,6 +610,15 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
   }
 
   // Get parameter sets.
+  Cpptraj::Structure::Creator creator;
+  if (creator.InitCreator(argIn, State.DSL(), State.Debug())) {
+    return CpptrajState::ERR;
+  }
+  if (!creator.HasMainParmSet()) {
+    mprinterr("Error: No parameter sets.\n");
+    return CpptrajState::ERR;
+  }
+/*
   typedef std::vector<DataSet_Parameters*> Parray;
   Parray ParamSets;
   std::string parmset = argIn.GetStringKey("parmset");
@@ -652,12 +662,12 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
     ParameterSet::UpdateCount UC;
     for (; it != ParamSets.end(); ++it)
       mainParmSet->UpdateParamSet( *(*it), UC, State.Debug(), State.Debug() ); // FIXME verbose
-  }
+  }*/
 
   // Fill in atoms with templates
   Topology topOut;
   Frame frameOut;
-  if (FillAtomsWithTemplates(topOut, frameOut, Templates, topIn, frameIn, *mainParmSet)) {
+  if (FillAtomsWithTemplates(topOut, frameOut, Templates, topIn, frameIn, creator.MainParmSet())) {
     mprinterr("Error: Could not fill in atoms using templates.\n");
     return CpptrajState::ERR;
   }
@@ -666,7 +676,7 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
   // Assign parameters. This will create the bond/angle/dihedral/improper
   // arrays as well.
   Exec::RetType ret = CpptrajState::OK;
-  if ( topOut.AssignParams( *mainParmSet  ) ) {
+  if ( topOut.AssignParams( creator.MainParmSet()  ) ) {
     mprinterr("Error: Could not assign parameters for '%s'.\n", topOut.c_str());
     ret = CpptrajState::ERR;
   }
@@ -680,7 +690,7 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
   topOut.AllocJoinArray();
   topOut.AllocRotateArray();
 
-  if (free_parmset_mem && mainParmSet != 0) delete mainParmSet;
+  //if (free_parmset_mem && mainParmSet != 0) delete mainParmSet;
 
   // Update coords 
   if (crdout.CoordsSetup( topOut, CoordinateInfo() )) { // FIXME better coordinate info
diff --git a/src/Structure/Creator.cpp b/src/Structure/Creator.cpp
index 0cd76c4e09..ae0ff6a8fa 100644
--- a/src/Structure/Creator.cpp
+++ b/src/Structure/Creator.cpp
@@ -15,7 +15,7 @@ Creator::Creator() :
 
 /** DESTRUCTOR */
 Creator::~Creator() {
-  if (mainParmSet_ != 0)
+  if (mainParmSet_ != 0 && free_parmset_mem_)
     delete mainParmSet_;
 }
 
diff --git a/src/Structure/Creator.h b/src/Structure/Creator.h
index 3d8ae7b0e8..358f918473 100644
--- a/src/Structure/Creator.h
+++ b/src/Structure/Creator.h
@@ -19,6 +19,8 @@ class Creator {
 
     /// \return True if a parameter set is defined
     bool HasMainParmSet() const { return (mainParmSet_ != 0); }
+    /// \return Main parm set
+    DataSet_Parameters const& MainParmSet() const { return *mainParmSet_; }
   private:
     /// Get parameter sets
     int getParameterSets(ArgList&, DataSetList const&);
diff --git a/src/Structure/structuredepend b/src/Structure/structuredepend
index a41b2cd8d1..c81f6828ae 100644
--- a/src/Structure/structuredepend
+++ b/src/Structure/structuredepend
@@ -1,7 +1,7 @@
 BuildAtom.o : BuildAtom.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h StructureEnum.h
 Builder.o : Builder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Builder.h Chirality.h GenerateConnectivityArrays.h InternalCoords.h Zmatrix.h
 Chirality.o : Chirality.cpp ../Atom.h ../Constants.h ../CpptrajStdio.h ../NameType.h ../SymbolExporting.h ../Vec3.h Chirality.h
-Creator.o : Creator.cpp ../AssociatedData.h ../AtomType.h ../Constants.h ../CpptrajFile.h ../DataSet.h ../DataSet_Parameters.h ../Dimension.h ../FileIO.h ../FileName.h ../MetaData.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../TextFormat.h ../TypeNameHolder.h Creator.h
+Creator.o : Creator.cpp ../ArgList.h ../AssociatedData.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../DataSet_Parameters.h ../Dimension.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Creator.h
 Disulfide.o : Disulfide.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Disulfide.h ResStatArray.h StructureRoutines.h
 FunctionalGroup.o : FunctionalGroup.cpp ../Atom.h ../AtomMap.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h FunctionalGroup.h
 FxnGroupBuilder.o : FxnGroupBuilder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h FunctionalGroup.h FxnGroupBuilder.h StructureRoutines.h Sugar.h SugarToken.h
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index d376b56682..0592e8acb4 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -290,7 +290,7 @@ Ewald_Regular.o : Ewald_Regular.cpp Atom.h AtomMask.h Box.h Constants.h Coordina
 ExclusionArray.o : ExclusionArray.cpp Atom.h AtomMask.h CharMask.h CpptrajStdio.h ExclusionArray.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Unit.h
 Exec_AddMissingRes.o : Exec_AddMissingRes.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CharMask.h CompactFrameArray.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_AddMissingRes.h Exec_AddMissingRes_Pres.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Analyze.o : Exec_Analyze.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Analyze.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Build.o : Exec_Build.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/GB_Params.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/GenerateConnectivityArrays.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Build.o : Exec_Build.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/GB_Params.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/Creator.h Structure/GenerateConnectivityArrays.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Calc.o : Exec_Calc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Calc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_CatCrd.o : Exec_CatCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CatCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Change.o : Exec_Change.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Change.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
@@ -448,6 +448,7 @@ StringRoutines.o : StringRoutines.cpp CpptrajStdio.h StringRoutines.h
 Structure/BuildAtom.o : Structure/BuildAtom.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/StructureEnum.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 Structure/Builder.o : Structure/Builder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h GuessAtomHybridization.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Builder.h Structure/Chirality.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 Structure/Chirality.o : Structure/Chirality.cpp Atom.h Constants.h CpptrajStdio.h NameType.h Structure/Chirality.h SymbolExporting.h Vec3.h
+Structure/Creator.o : Structure/Creator.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/Creator.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/Disulfide.o : Structure/Disulfide.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Disulfide.h Structure/ResStatArray.h Structure/StructureRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/FunctionalGroup.o : Structure/FunctionalGroup.cpp Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/FxnGroupBuilder.o : Structure/FxnGroupBuilder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h Structure/FxnGroupBuilder.h Structure/StructureRoutines.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h

From 0331f33a001c65a1c8c41ac10283957be47784ed Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 15 Feb 2024 11:34:28 -0500
Subject: [PATCH 0533/1492] Code to get templates

---
 src/Structure/Creator.cpp | 47 ++++++++++++++++++++++++++++++++++++++-
 src/Structure/Creator.h   | 14 ++++++++++--
 2 files changed, 58 insertions(+), 3 deletions(-)

diff --git a/src/Structure/Creator.cpp b/src/Structure/Creator.cpp
index ae0ff6a8fa..4afbc98f5d 100644
--- a/src/Structure/Creator.cpp
+++ b/src/Structure/Creator.cpp
@@ -1,6 +1,7 @@
 #include "Creator.h"
 #include "../ArgList.h"
 #include "../CpptrajStdio.h"
+#include "../DataSet_Coords.h" // TODO new coords type
 #include "../DataSet_Parameters.h"
 #include "../DataSetList.h"
 
@@ -19,7 +20,9 @@ Creator::~Creator() {
     delete mainParmSet_;
 }
 
-const char* Creator::keywords_ = "parmset <parameter set>";
+const char* Creator::parm_keywords_ = "parmset <parameter setname>";
+
+const char* Creator::template_keywords_ = "lib <template setname>";
 
 /** Initialize */
 int Creator::InitCreator(ArgList& argIn, DataSetList const& DSL, int debugIn)
@@ -30,6 +33,48 @@ int Creator::InitCreator(ArgList& argIn, DataSetList const& DSL, int debugIn)
   return 0;
 }
 
+/** Get templates */
+int Creator::getTemplates(ArgList& argIn, DataSetList const& DSL) {
+  // Clear existing templates
+  Templates_.clear();
+  std::string lib = argIn.GetStringKey("lib");
+  if (lib.empty()) {
+    mprintf("\tNo template(s) specified with 'lib'; using any loaded templates.\n");
+    DataSetList sets = DSL.SelectGroupSets( "*", DataSet::COORDINATES ); // TODO specific set type for units?
+    for (DataSetList::const_iterator it = sets.begin(); it != sets.end(); ++it)
+    {
+      // Should only be a single residue FIXME need new set type
+      DataSet_Coords const& ds = static_cast<DataSet_Coords const&>( *(*it) );
+      if ( ds.Top().Nres() == 1 )
+        Templates_.push_back( (DataSet_Coords*)(*it) );
+    }
+  } else {
+    while (!lib.empty()) {
+      DataSetList sets = DSL.SelectGroupSets( lib, DataSet::COORDINATES ); // TODO specific set type for units?
+      if (sets.empty()) {
+        mprintf("Warning: No sets corresponding to '%s'\n", lib.c_str());
+      } else {
+        for (DataSetList::const_iterator it = sets.begin(); it != sets.end(); ++it)
+        {
+          // Should only be a single residue FIXME need new set type
+          //DataSet_Coords const& ds = static_cast<DataSet_Coords const&>( *(*it) );
+          //if ( ds.Top().Nres() == 1 )
+            Templates_.push_back( (DataSet_Coords*)(*it) );
+        }
+      }
+      lib = argIn.GetStringKey("lib");
+    }
+  }
+  if (!Templates_.empty()) {
+    mprintf("\t%zu residue templates found:", Templates_.size());
+    for (Carray::const_iterator it = Templates_.begin(); it != Templates_.end(); ++it)
+      mprintf(" %s", (*it)->legend());
+    mprintf("\n");
+  }
+
+  return 0;
+}
+
 /** Get parameter sets. */
 int Creator::getParameterSets(ArgList& argIn, DataSetList const& DSL) {
   // Clear any existing set
diff --git a/src/Structure/Creator.h b/src/Structure/Creator.h
index 358f918473..05e2c5f864 100644
--- a/src/Structure/Creator.h
+++ b/src/Structure/Creator.h
@@ -1,19 +1,24 @@
 #ifndef INC_STRUCTURE_CREATOR_H
 #define INC_STRUCTURE_CREATOR_H
+#include <vector>
 class ArgList;
+class DataSet_Coords;
 class DataSet_Parameters;
 class DataSetList;
 namespace Cpptraj {
 namespace Structure {
 /// Used to create a system from individual units
 class Creator {
+    typedef std::vector<DataSet_Coords*> Carray;
   public:
     /// CONSTRUCTOR
     Creator();
     /// DESTRUCTOR
     ~Creator();
-    /// Associated keywords for InitCreator
-    static const char* keywords_;
+    /// Associated parameter keywords for InitCreator
+    static const char* parm_keywords_;
+    /// Associated templtae keywords for InitCreator
+    static const char* template_keywords_;
     /// Initialize the Creator
     int InitCreator(ArgList&, DataSetList const&, int);
 
@@ -21,11 +26,16 @@ class Creator {
     bool HasMainParmSet() const { return (mainParmSet_ != 0); }
     /// \return Main parm set
     DataSet_Parameters const& MainParmSet() const { return *mainParmSet_; }
+    /// \return True if there are templates
+    bool HasTemplates() const { return (!Templates_.empty()); }
   private:
+    /// Get templates
+    int getTemplates(ArgList&, DataSetList const&);
     /// Get parameter sets
     int getParameterSets(ArgList&, DataSetList const&);
 
     DataSet_Parameters* mainParmSet_; ///< Hold optional parameter set.
+    Carray Templates_;                ///< Hold unit templates.
     int debug_;                       ///< Debug level
     bool free_parmset_mem_;           ///< True if main parm set is combined and should be freed
 };

From a21fba89ae41d6391d2ceccae4909c14f07d6e2e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 15 Feb 2024 11:35:15 -0500
Subject: [PATCH 0534/1492] Call in InitCreator

---
 src/Structure/Creator.cpp | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/Structure/Creator.cpp b/src/Structure/Creator.cpp
index 4afbc98f5d..cdd3cb876f 100644
--- a/src/Structure/Creator.cpp
+++ b/src/Structure/Creator.cpp
@@ -28,6 +28,7 @@ const char* Creator::template_keywords_ = "lib <template setname>";
 int Creator::InitCreator(ArgList& argIn, DataSetList const& DSL, int debugIn)
 {
   debug_ = debugIn;
+  if (getTemplates(argIn, DSL)) return 1;
   if (getParameterSets(argIn, DSL)) return 1;
 
   return 0;

From 1df9bb0a789ca21ec29ebbb7665988502255f693 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 15 Feb 2024 11:41:12 -0500
Subject: [PATCH 0535/1492] Add code to get template from name

---
 src/Structure/Creator.cpp     | 38 +++++++++++++++++++++++++++++++++++
 src/Structure/Creator.h       |  4 ++++
 src/Structure/structuredepend |  2 +-
 src/cpptrajdepend             |  4 ++--
 4 files changed, 45 insertions(+), 3 deletions(-)

diff --git a/src/Structure/Creator.cpp b/src/Structure/Creator.cpp
index cdd3cb876f..a944b538de 100644
--- a/src/Structure/Creator.cpp
+++ b/src/Structure/Creator.cpp
@@ -1,5 +1,6 @@
 #include "Creator.h"
 #include "../ArgList.h"
+#include "../AssociatedData_ResId.h"
 #include "../CpptrajStdio.h"
 #include "../DataSet_Coords.h" // TODO new coords type
 #include "../DataSet_Parameters.h"
@@ -34,6 +35,43 @@ int Creator::InitCreator(ArgList& argIn, DataSetList const& DSL, int debugIn)
   return 0;
 }
 
+/** Try to identify residue template DataSet from the given residue
+  * name (from e.g. the PDB/Mol2/etc file).
+  */
+DataSet_Coords* Creator::IdTemplateFromName(NameType const& rname,
+                                            TerminalType termType)
+const
+{
+  DataSet_Coords* out = 0;
+  if (termType != Cpptraj::Structure::NON_TERMINAL) {
+    // Looking for a terminal residue. Need to get sets with AssociatedData_ResId
+    for (Carray::const_iterator it = Templates_.begin(); it != Templates_.end(); ++it) {
+      AssociatedData* ad = (*it)->GetAssociatedData( AssociatedData::RESID );
+      if (ad != 0) {
+        AssociatedData_ResId const& resid = static_cast<AssociatedData_ResId const&>( *ad );
+        if (rname == resid.ResName() && termType == resid.TermType()) {
+          out = *it;
+          break;
+        }
+      }
+    }
+  }
+  if (out == 0) {
+    // Terminal residue not found or non-terminal residue.
+    if (termType != Cpptraj::Structure::NON_TERMINAL)
+      mprintf("Warning: No terminal residue found for '%s'\n", *rname);
+    // Assume Coords set aspect is what we need
+    for (Carray::const_iterator it = Templates_.begin(); it != Templates_.end(); ++it) {
+      if ( rname == NameType( (*it)->Meta().Aspect() ) ) {
+        out = *it;
+        break;
+      }
+    }
+  }
+
+  return out;
+}
+
 /** Get templates */
 int Creator::getTemplates(ArgList& argIn, DataSetList const& DSL) {
   // Clear existing templates
diff --git a/src/Structure/Creator.h b/src/Structure/Creator.h
index 05e2c5f864..a926052a4f 100644
--- a/src/Structure/Creator.h
+++ b/src/Structure/Creator.h
@@ -1,10 +1,12 @@
 #ifndef INC_STRUCTURE_CREATOR_H
 #define INC_STRUCTURE_CREATOR_H
 #include <vector>
+#include "StructureEnum.h" // TerminalType
 class ArgList;
 class DataSet_Coords;
 class DataSet_Parameters;
 class DataSetList;
+class NameType;
 namespace Cpptraj {
 namespace Structure {
 /// Used to create a system from individual units
@@ -28,6 +30,8 @@ class Creator {
     DataSet_Parameters const& MainParmSet() const { return *mainParmSet_; }
     /// \return True if there are templates
     bool HasTemplates() const { return (!Templates_.empty()); }
+    /// Identify residue template from residue name
+    DataSet_Coords* IdTemplateFromName(NameType const&, TerminalType) const;
   private:
     /// Get templates
     int getTemplates(ArgList&, DataSetList const&);
diff --git a/src/Structure/structuredepend b/src/Structure/structuredepend
index c81f6828ae..47a309d5cc 100644
--- a/src/Structure/structuredepend
+++ b/src/Structure/structuredepend
@@ -1,7 +1,7 @@
 BuildAtom.o : BuildAtom.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h StructureEnum.h
 Builder.o : Builder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Builder.h Chirality.h GenerateConnectivityArrays.h InternalCoords.h Zmatrix.h
 Chirality.o : Chirality.cpp ../Atom.h ../Constants.h ../CpptrajStdio.h ../NameType.h ../SymbolExporting.h ../Vec3.h Chirality.h
-Creator.o : Creator.cpp ../ArgList.h ../AssociatedData.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../DataSet_Parameters.h ../Dimension.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Creator.h
+Creator.o : Creator.cpp ../ArgList.h ../AssociatedData.h ../AssociatedData_ResId.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../DataSet_Parameters.h ../Dimension.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/StructureEnum.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Creator.h StructureEnum.h
 Disulfide.o : Disulfide.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Disulfide.h ResStatArray.h StructureRoutines.h
 FunctionalGroup.o : FunctionalGroup.cpp ../Atom.h ../AtomMap.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h FunctionalGroup.h
 FxnGroupBuilder.o : FxnGroupBuilder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h FunctionalGroup.h FxnGroupBuilder.h StructureRoutines.h Sugar.h SugarToken.h
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 0592e8acb4..9ffa727a27 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -188,7 +188,7 @@ ClusterMap.o : ClusterMap.cpp AssociatedData.h ClusterMap.h Constants.h CpptrajF
 Cmd.o : Cmd.cpp Cmd.h DispatchObject.h
 CmdInput.o : CmdInput.cpp CmdInput.h StringRoutines.h
 CmdList.o : CmdList.cpp Cmd.h CmdList.h DispatchObject.h
-Command.o : Command.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h ActionTopWriter.h Action_Align.h Action_Angle.h Action_AreaPerMol.h Action_AtomMap.h Action_AtomicCorr.h Action_AtomicFluct.h Action_AutoImage.h Action_Average.h Action_AvgBox.h Action_Bounds.h Action_Box.h Action_Center.h Action_Channel.h Action_CheckChirality.h Action_CheckStructure.h Action_Closest.h Action_ClusterDihedral.h Action_Contacts.h Action_CreateCrd.h Action_CreateReservoir.h Action_DNAionTracker.h Action_DSSP.h Action_Density.h Action_Diffusion.h Action_Dihedral.h Action_DihedralRMS.h Action_Dipole.h Action_DistRmsd.h Action_Distance.h Action_Energy.h Action_Esander.h Action_FilterByData.h Action_FixAtomOrder.h Action_FixImagedBonds.h Action_GIST.h Action_Grid.h Action_GridFreeEnergy.h Action_HydrogenBond.h Action_Image.h Action_InfraredSpectrum.h Action_Jcoupling.h Action_Keep.h Action_LESsplit.h Action_LIE.h Action_LipidOrder.h Action_MakeStructure.h Action_Mask.h Action_Matrix.h Action_MinImage.h Action_Molsurf.h Action_MultiDihedral.h Action_MultiPucker.h Action_MultiVector.h Action_NAstruct.h Action_NMRrst.h Action_NativeContacts.h Action_OrderParameter.h Action_Outtraj.h Action_PairDist.h Action_Pairwise.h Action_Principal.h Action_Projection.h Action_Pucker.h Action_Radgyr.h Action_Radial.h Action_RandomizeIons.h Action_Remap.h Action_ReplicateCell.h Action_Rmsd.h Action_Rotate.h Action_RunningAvg.h Action_STFC_Diffusion.h Action_Scale.h Action_SetVelocity.h Action_Spam.h Action_Strip.h Action_Surf.h Action_SymmetricRmsd.h Action_Temperature.h Action_Time.h Action_ToroidalDiffusion.h Action_Translate.h Action_Unstrip.h Action_Unwrap.h Action_Vector.h Action_VelocityAutoCorr.h Action_Volmap.h Action_Volume.h Action_Watershell.h Action_XtalSymm.h Analysis.h AnalysisList.h AnalysisState.h Analysis_AmdBias.h Analysis_AutoCorr.h Analysis_Average.h Analysis_CalcDiffusion.h Analysis_Clustering.h Analysis_ConstantPHStats.h Analysis_Corr.h Analysis_CrankShaft.h Analysis_CrdFluct.h Analysis_CrossCorr.h Analysis_CurveFit.h Analysis_Divergence.h Analysis_EvalPlateau.h Analysis_FFT.h Analysis_HausdorffDistance.h Analysis_Hist.h Analysis_IRED.h Analysis_Integrate.h Analysis_KDE.h Analysis_Lifetime.h Analysis_LowestCurve.h Analysis_Matrix.h Analysis_MeltCurve.h Analysis_Modes.h Analysis_MultiHist.h Analysis_Multicurve.h Analysis_Overlap.h Analysis_PhiPsi.h Analysis_Regression.h Analysis_RemLog.h Analysis_Rms2d.h Analysis_RmsAvgCorr.h Analysis_Rotdif.h Analysis_RunningAvg.h Analysis_Slope.h Analysis_Spline.h Analysis_State.h Analysis_Statistics.h Analysis_TI.h Analysis_TICA.h Analysis_Timecorr.h Analysis_VectorMath.h Analysis_Wavelet.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h AxisType.h BaseIOtype.h Box.h BoxArgs.h BufferedLine.h CharMask.h Cluster/Algorithm.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Control.h Cluster/DrawGraph.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Sieve.h Cluster/Silhouette.h ClusterMap.h Cmd.h CmdInput.h CmdList.h Command.h CompactFrameArray.h ComplexArray.h Constants.h Constraints.h ControlBlock.h ControlBlock_For.h CoordinateInfo.h Corr.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_RemLog.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h Deprecated.h DiffusionResults.h DihedralSearch.h Dimension.h DispatchObject.h Energy.h Energy_Sander.h EnsembleIn.h EnsembleOutList.h Ewald.h EwaldOptions.h Ewald_ParticleMesh.h ExclusionArray.h Exec.h Exec_AddMissingRes.h Exec_Analyze.h Exec_Build.h Exec_Calc.h Exec_CatCrd.h Exec_Change.h Exec_ClusterMap.h Exec_CombineCoords.h Exec_Commands.h Exec_CompareClusters.h Exec_CompareEnergy.h Exec_CompareTop.h Exec_CrdAction.h Exec_CrdOut.h Exec_CrdTransform.h Exec_CreateSet.h Exec_DataFile.h Exec_DataFilter.h Exec_DataSetCmd.h Exec_Desc.h Exec_Emin.h Exec_ExtendedComparison.h Exec_Flatten.h Exec_GenerateAmberRst.h Exec_Graft.h Exec_Help.h Exec_HmassRepartition.h Exec_LoadCrd.h Exec_LoadTraj.h Exec_ParallelAnalysis.h Exec_ParmBox.h Exec_ParmSolvent.h Exec_ParmStrip.h Exec_ParmWrite.h Exec_ParseTiming.h Exec_PermuteDihedrals.h Exec_Precision.h Exec_PrepareForLeap.h Exec_PrintData.h Exec_Random.h Exec_ReadData.h Exec_ReadEnsembleData.h Exec_ReadInput.h Exec_RotateDihedral.h Exec_RunAnalysis.h Exec_ScaleDihedralK.h Exec_Sequence.h Exec_SequenceAlign.h Exec_Set.h Exec_Show.h Exec_SortEnsembleData.h Exec_SplitCoords.h Exec_System.h Exec_Top.h Exec_Traj.h Exec_UpdateParameters.h Exec_ViewRst.h Exec_Zmatrix.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h GIST_PME.h Grid.h GridAction.h GridBin.h GridMover.h HistBin.h Hungarian.h ImageOption.h ImageTypes.h InputTrajCommon.h MapAtom.h MaskArray.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h OnlineVarT.h OutputTrajCommon.h PDBfile.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PubFFT.h Pucker.h Pucker_PuckerMask.h Pucker_PuckerSearch.h Pucker_PuckerToken.h RPNcalc.h Random.h Range.h ReferenceAction.h ReferenceFrame.h RemdReservoirNC.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h SplineFxnTable.h Structure/StructureEnum.h StructureCheck.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h cuda_kernels/GistCudaSetup.cuh helpme_standalone.h molsurf.h
+Command.o : Command.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h ActionTopWriter.h Action_Align.h Action_Angle.h Action_AreaPerMol.h Action_AtomMap.h Action_AtomicCorr.h Action_AtomicFluct.h Action_AutoImage.h Action_Average.h Action_AvgBox.h Action_Bounds.h Action_Box.h Action_Center.h Action_Channel.h Action_CheckChirality.h Action_CheckStructure.h Action_Closest.h Action_ClusterDihedral.h Action_Contacts.h Action_CreateCrd.h Action_CreateReservoir.h Action_DNAionTracker.h Action_DSSP.h Action_Density.h Action_Diffusion.h Action_Dihedral.h Action_DihedralRMS.h Action_Dipole.h Action_DistRmsd.h Action_Distance.h Action_Energy.h Action_Esander.h Action_FilterByData.h Action_FixAtomOrder.h Action_FixImagedBonds.h Action_GIST.h Action_Grid.h Action_GridFreeEnergy.h Action_HydrogenBond.h Action_Image.h Action_InfraredSpectrum.h Action_Jcoupling.h Action_Keep.h Action_LESsplit.h Action_LIE.h Action_LipidOrder.h Action_MakeStructure.h Action_Mask.h Action_Matrix.h Action_MinImage.h Action_Molsurf.h Action_MultiDihedral.h Action_MultiPucker.h Action_MultiVector.h Action_NAstruct.h Action_NMRrst.h Action_NativeContacts.h Action_OrderParameter.h Action_Outtraj.h Action_PairDist.h Action_Pairwise.h Action_Principal.h Action_Projection.h Action_Pucker.h Action_Radgyr.h Action_Radial.h Action_RandomizeIons.h Action_Remap.h Action_ReplicateCell.h Action_Rmsd.h Action_Rotate.h Action_RunningAvg.h Action_STFC_Diffusion.h Action_Scale.h Action_SetVelocity.h Action_Spam.h Action_Strip.h Action_Surf.h Action_SymmetricRmsd.h Action_Temperature.h Action_Time.h Action_ToroidalDiffusion.h Action_Translate.h Action_Unstrip.h Action_Unwrap.h Action_Vector.h Action_VelocityAutoCorr.h Action_Volmap.h Action_Volume.h Action_Watershell.h Action_XtalSymm.h Analysis.h AnalysisList.h AnalysisState.h Analysis_AmdBias.h Analysis_AutoCorr.h Analysis_Average.h Analysis_CalcDiffusion.h Analysis_Clustering.h Analysis_ConstantPHStats.h Analysis_Corr.h Analysis_CrankShaft.h Analysis_CrdFluct.h Analysis_CrossCorr.h Analysis_CurveFit.h Analysis_Divergence.h Analysis_EvalPlateau.h Analysis_FFT.h Analysis_HausdorffDistance.h Analysis_Hist.h Analysis_IRED.h Analysis_Integrate.h Analysis_KDE.h Analysis_Lifetime.h Analysis_LowestCurve.h Analysis_Matrix.h Analysis_MeltCurve.h Analysis_Modes.h Analysis_MultiHist.h Analysis_Multicurve.h Analysis_Overlap.h Analysis_PhiPsi.h Analysis_Regression.h Analysis_RemLog.h Analysis_Rms2d.h Analysis_RmsAvgCorr.h Analysis_Rotdif.h Analysis_RunningAvg.h Analysis_Slope.h Analysis_Spline.h Analysis_State.h Analysis_Statistics.h Analysis_TI.h Analysis_TICA.h Analysis_Timecorr.h Analysis_VectorMath.h Analysis_Wavelet.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h AxisType.h BaseIOtype.h Box.h BoxArgs.h BufferedLine.h CharMask.h Cluster/Algorithm.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Control.h Cluster/DrawGraph.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Sieve.h Cluster/Silhouette.h ClusterMap.h Cmd.h CmdInput.h CmdList.h Command.h CompactFrameArray.h ComplexArray.h Constants.h Constraints.h ControlBlock.h ControlBlock_For.h CoordinateInfo.h Corr.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_RemLog.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h Deprecated.h DiffusionResults.h DihedralSearch.h Dimension.h DispatchObject.h Energy.h Energy_Sander.h EnsembleIn.h EnsembleOutList.h Ewald.h EwaldOptions.h Ewald_ParticleMesh.h ExclusionArray.h Exec.h Exec_AddMissingRes.h Exec_Analyze.h Exec_Build.h Exec_Calc.h Exec_CatCrd.h Exec_Change.h Exec_ClusterMap.h Exec_CombineCoords.h Exec_Commands.h Exec_CompareClusters.h Exec_CompareEnergy.h Exec_CompareTop.h Exec_CrdAction.h Exec_CrdOut.h Exec_CrdTransform.h Exec_CreateSet.h Exec_DataFile.h Exec_DataFilter.h Exec_DataSetCmd.h Exec_Desc.h Exec_Emin.h Exec_ExtendedComparison.h Exec_Flatten.h Exec_GenerateAmberRst.h Exec_Graft.h Exec_Help.h Exec_HmassRepartition.h Exec_LoadCrd.h Exec_LoadTraj.h Exec_ParallelAnalysis.h Exec_ParmBox.h Exec_ParmSolvent.h Exec_ParmStrip.h Exec_ParmWrite.h Exec_ParseTiming.h Exec_PermuteDihedrals.h Exec_Precision.h Exec_PrepareForLeap.h Exec_PrintData.h Exec_Random.h Exec_ReadData.h Exec_ReadEnsembleData.h Exec_ReadInput.h Exec_RotateDihedral.h Exec_RunAnalysis.h Exec_ScaleDihedralK.h Exec_Sequence.h Exec_SequenceAlign.h Exec_Set.h Exec_Show.h Exec_SortEnsembleData.h Exec_SplitCoords.h Exec_System.h Exec_Top.h Exec_Traj.h Exec_UpdateParameters.h Exec_ViewRst.h Exec_Zmatrix.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h GIST_PME.h Grid.h GridAction.h GridBin.h GridMover.h HistBin.h Hungarian.h ImageOption.h ImageTypes.h InputTrajCommon.h MapAtom.h MaskArray.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h OnlineVarT.h OutputTrajCommon.h PDBfile.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PubFFT.h Pucker.h Pucker_PuckerMask.h Pucker_PuckerSearch.h Pucker_PuckerToken.h RPNcalc.h Random.h Range.h ReferenceAction.h ReferenceFrame.h RemdReservoirNC.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h SplineFxnTable.h StructureCheck.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h cuda_kernels/GistCudaSetup.cuh helpme_standalone.h molsurf.h
 CompactFrameArray.o : CompactFrameArray.cpp Box.h CompactFrameArray.h CoordinateInfo.h CpptrajStdio.h Matrix_3x3.h Parallel.h ReplicaDimArray.h Vec3.h
 ComplexArray.o : ComplexArray.cpp ArrayIterator.h ComplexArray.h
 Constraints.o : Constraints.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
@@ -448,7 +448,7 @@ StringRoutines.o : StringRoutines.cpp CpptrajStdio.h StringRoutines.h
 Structure/BuildAtom.o : Structure/BuildAtom.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/StructureEnum.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 Structure/Builder.o : Structure/Builder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h GuessAtomHybridization.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Builder.h Structure/Chirality.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 Structure/Chirality.o : Structure/Chirality.cpp Atom.h Constants.h CpptrajStdio.h NameType.h Structure/Chirality.h SymbolExporting.h Vec3.h
-Structure/Creator.o : Structure/Creator.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/Creator.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Structure/Creator.o : Structure/Creator.cpp ArgList.h AssociatedData.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/Creator.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/Disulfide.o : Structure/Disulfide.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Disulfide.h Structure/ResStatArray.h Structure/StructureRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/FunctionalGroup.o : Structure/FunctionalGroup.cpp Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/FxnGroupBuilder.o : Structure/FxnGroupBuilder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h Structure/FxnGroupBuilder.h Structure/StructureRoutines.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h

From bbba5d0e2a63c14b31efe14870a2c10dbe4b2764 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 15 Feb 2024 11:52:20 -0500
Subject: [PATCH 0536/1492] Add atomscandir keyword

---
 src/Structure/Creator.cpp     | 17 +++++++++++++++++
 src/Structure/Creator.h       |  6 ++++--
 src/Structure/structuredepend |  2 +-
 src/cpptrajdepend             |  4 ++--
 4 files changed, 24 insertions(+), 5 deletions(-)

diff --git a/src/Structure/Creator.cpp b/src/Structure/Creator.cpp
index a944b538de..b634ad736d 100644
--- a/src/Structure/Creator.cpp
+++ b/src/Structure/Creator.cpp
@@ -1,4 +1,5 @@
 #include "Creator.h"
+#include "GenerateConnectivityArrays.h" // For setting atom scan direction
 #include "../ArgList.h"
 #include "../AssociatedData_ResId.h"
 #include "../CpptrajStdio.h"
@@ -25,10 +26,26 @@ const char* Creator::parm_keywords_ = "parmset <parameter setname>";
 
 const char* Creator::template_keywords_ = "lib <template setname>";
 
+const char* Creator::other_keywords_ = "atomscandir {f|b}";
+
 /** Initialize */
 int Creator::InitCreator(ArgList& argIn, DataSetList const& DSL, int debugIn)
 {
   debug_ = debugIn;
+
+  // Atom scan direction
+  std::string atomscandir = argIn.GetStringKey("atomscandir");
+  if (!atomscandir.empty()) {
+    if (atomscandir == "f")
+      Cpptraj::Structure::SetAtomScanDirection(Cpptraj::Structure::SCAN_ATOMS_FORWARDS);
+    else if (atomscandir == "b")
+      Cpptraj::Structure::SetAtomScanDirection(Cpptraj::Structure::SCAN_ATOMS_BACKWARDS);
+    else {
+      mprinterr("Error: Unrecognized keyword for 'atomscandir' : %s\n", atomscandir.c_str());
+      return 1;
+    }
+  }
+
   if (getTemplates(argIn, DSL)) return 1;
   if (getParameterSets(argIn, DSL)) return 1;
 
diff --git a/src/Structure/Creator.h b/src/Structure/Creator.h
index a926052a4f..4309c67978 100644
--- a/src/Structure/Creator.h
+++ b/src/Structure/Creator.h
@@ -19,15 +19,17 @@ class Creator {
     ~Creator();
     /// Associated parameter keywords for InitCreator
     static const char* parm_keywords_;
-    /// Associated templtae keywords for InitCreator
+    /// Associated template keywords for InitCreator
     static const char* template_keywords_;
+    /// Other keywords for InitCreator
+    static const char* other_keywords_;
     /// Initialize the Creator
     int InitCreator(ArgList&, DataSetList const&, int);
 
     /// \return True if a parameter set is defined
     bool HasMainParmSet() const { return (mainParmSet_ != 0); }
     /// \return Main parm set
-    DataSet_Parameters const& MainParmSet() const { return *mainParmSet_; }
+    DataSet_Parameters const* MainParmSetPtr() const { return mainParmSet_; }
     /// \return True if there are templates
     bool HasTemplates() const { return (!Templates_.empty()); }
     /// Identify residue template from residue name
diff --git a/src/Structure/structuredepend b/src/Structure/structuredepend
index 47a309d5cc..c4e06a854c 100644
--- a/src/Structure/structuredepend
+++ b/src/Structure/structuredepend
@@ -1,7 +1,7 @@
 BuildAtom.o : BuildAtom.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h StructureEnum.h
 Builder.o : Builder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Builder.h Chirality.h GenerateConnectivityArrays.h InternalCoords.h Zmatrix.h
 Chirality.o : Chirality.cpp ../Atom.h ../Constants.h ../CpptrajStdio.h ../NameType.h ../SymbolExporting.h ../Vec3.h Chirality.h
-Creator.o : Creator.cpp ../ArgList.h ../AssociatedData.h ../AssociatedData_ResId.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../DataSet_Parameters.h ../Dimension.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/StructureEnum.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Creator.h StructureEnum.h
+Creator.o : Creator.cpp ../ArgList.h ../AssociatedData.h ../AssociatedData_ResId.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../DataSet_Parameters.h ../Dimension.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/StructureEnum.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Creator.h GenerateConnectivityArrays.h StructureEnum.h
 Disulfide.o : Disulfide.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Disulfide.h ResStatArray.h StructureRoutines.h
 FunctionalGroup.o : FunctionalGroup.cpp ../Atom.h ../AtomMap.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h FunctionalGroup.h
 FxnGroupBuilder.o : FxnGroupBuilder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h FunctionalGroup.h FxnGroupBuilder.h StructureRoutines.h Sugar.h SugarToken.h
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 9ffa727a27..4dfe731677 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -290,7 +290,7 @@ Ewald_Regular.o : Ewald_Regular.cpp Atom.h AtomMask.h Box.h Constants.h Coordina
 ExclusionArray.o : ExclusionArray.cpp Atom.h AtomMask.h CharMask.h CpptrajStdio.h ExclusionArray.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Unit.h
 Exec_AddMissingRes.o : Exec_AddMissingRes.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CharMask.h CompactFrameArray.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_AddMissingRes.h Exec_AddMissingRes_Pres.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Analyze.o : Exec_Analyze.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Analyze.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Build.o : Exec_Build.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/GB_Params.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/Creator.h Structure/GenerateConnectivityArrays.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Build.o : Exec_Build.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/GB_Params.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/Creator.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Calc.o : Exec_Calc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Calc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_CatCrd.o : Exec_CatCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CatCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Change.o : Exec_Change.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Change.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
@@ -448,7 +448,7 @@ StringRoutines.o : StringRoutines.cpp CpptrajStdio.h StringRoutines.h
 Structure/BuildAtom.o : Structure/BuildAtom.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/StructureEnum.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 Structure/Builder.o : Structure/Builder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h GuessAtomHybridization.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Builder.h Structure/Chirality.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 Structure/Chirality.o : Structure/Chirality.cpp Atom.h Constants.h CpptrajStdio.h NameType.h Structure/Chirality.h SymbolExporting.h Vec3.h
-Structure/Creator.o : Structure/Creator.cpp ArgList.h AssociatedData.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/Creator.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Structure/Creator.o : Structure/Creator.cpp ArgList.h AssociatedData.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/Creator.h Structure/GenerateConnectivityArrays.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/Disulfide.o : Structure/Disulfide.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Disulfide.h Structure/ResStatArray.h Structure/StructureRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/FunctionalGroup.o : Structure/FunctionalGroup.cpp Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/FxnGroupBuilder.o : Structure/FxnGroupBuilder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h Structure/FxnGroupBuilder.h Structure/StructureRoutines.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h

From f17e740a69a4109efc5d8079d853248a80ecd2d3 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 15 Feb 2024 11:56:44 -0500
Subject: [PATCH 0537/1492] Use creator

---
 src/Exec_Build.cpp | 71 +++++++++++-----------------------------------
 src/Exec_Build.h   | 12 ++++----
 2 files changed, 23 insertions(+), 60 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index f7992964ea..d9b42291b2 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -1,49 +1,10 @@
 #include "Exec_Build.h"
+#include "AssociatedData_Connect.h"
 #include "CpptrajStdio.h"
-#include "DataSet_Parameters.h"
+#include "DataSet_Parameters.h" // For casting DataSet_Parameters to ParameterSet
+#include "Parm/GB_Params.h"
 #include "Structure/Builder.h"
 #include "Structure/Creator.h"
-#include "Structure/GenerateConnectivityArrays.h"
-#include "Parm/GB_Params.h"
-#include "AssociatedData_ResId.h"
-#include "AssociatedData_Connect.h"
-
-/** Try to identify residue template DataSet from the given residue
-  * name (from e.g. the PDB/Mol2/etc file).
-  */
-DataSet_Coords* Exec_Build::IdTemplateFromName(Carray const& Templates,
-                                               NameType const& rname,
-                                               Cpptraj::Structure::TerminalType termType)
-{
-  DataSet_Coords* out = 0;
-  if (termType != Cpptraj::Structure::NON_TERMINAL) {
-    // Looking for a terminal residue. Need to get sets with AssociatedData_ResId
-    for (Carray::const_iterator it = Templates.begin(); it != Templates.end(); ++it) {
-      AssociatedData* ad = (*it)->GetAssociatedData( AssociatedData::RESID );
-      if (ad != 0) {
-        AssociatedData_ResId const& resid = static_cast<AssociatedData_ResId const&>( *ad );
-        if (rname == resid.ResName() && termType == resid.TermType()) {
-          out = *it;
-          break;
-        }
-      }
-    }
-  }
-  if (out == 0) {
-    // Terminal residue not found or non-terminal residue.
-    if (termType != Cpptraj::Structure::NON_TERMINAL)
-      mprintf("Warning: No terminal residue found for '%s'\n", *rname);
-    // Assume Coords set aspect is what we need
-    for (Carray::const_iterator it = Templates.begin(); it != Templates.end(); ++it) {
-      if ( rname == NameType( (*it)->Meta().Aspect() ) ) {
-        out = *it;
-        break;
-      }
-    }
-  }
-
-  return out;
-}
 
 /** Map atoms in residue to template. */
 std::vector<int> Exec_Build::MapAtomsToTemplate(Topology const& topIn,
@@ -71,9 +32,8 @@ std::vector<int> Exec_Build::MapAtomsToTemplate(Topology const& topIn,
 
 /** Use given templates to construct a final molecule. */
 int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
-                                       Carray const& Templates,
                                        Topology const& topIn, Frame const& frameIn,
-                                       ParameterSet const& mainParmSet)
+                                       Cpptraj::Structure::Creator const& creator)
 {
   // Array of head/tail connect atoms for each residue
   typedef std::vector<int> Iarray;
@@ -112,7 +72,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
     }
     mprintf("DEBUG: Residue type: %s terminal\n", Cpptraj::Structure::terminalStr(resTermType));
     // Identify a template based on the residue name.
-    DataSet_Coords* resTemplate = IdTemplateFromName(Templates, currentRes.Name(), resTermType);
+    DataSet_Coords* resTemplate = creator.IdTemplateFromName(currentRes.Name(), resTermType);
     if (resTemplate == 0) {
       mprintf("Warning: No template found for residue %s\n", topIn.TruncResNameOnumId(ires).c_str());
       newNatom += currentRes.NumAtoms();
@@ -426,7 +386,8 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
       // Residue has atom offset which indicates it needs something built.
       Cpptraj::Structure::Builder structureBuilder;// = new Cpptraj::Structure::Builder();
       structureBuilder.SetDebug( 1 ); // DEBUG FIXME
-      structureBuilder.SetParameters( &mainParmSet );
+      if (creator.HasMainParmSet())
+        structureBuilder.SetParameters( creator.MainParmSetPtr() );
       // Generate internals from the template, update indices to this topology.
       DataSet_Coords* resTemplate = ResTemplates[ires];
       Frame templateFrame = resTemplate->AllocateFrame();
@@ -506,7 +467,7 @@ void Exec_Build::Help() const
 // Exec_Build::Execute()
 Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
 {
-  // Atom scan direction
+/*  // Atom scan direction
   std::string atomscandir = argIn.GetStringKey("atomscandir");
   if (!atomscandir.empty()) {
     if (atomscandir == "f")
@@ -517,7 +478,7 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
       mprinterr("Error: Unrecognized keyword for 'atomscandir' : %s\n", atomscandir.c_str());
       return CpptrajState::ERR;
     }
-  }
+  }*/
   // Get input coords
   std::string crdset = argIn.GetStringKey("crdset");
   if (crdset.empty()) {
@@ -570,8 +531,7 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
   }
   mprintf("\tGB radii set: %s\n", Cpptraj::Parm::GbTypeStr(gbradii).c_str());
 
-  // Get residue templates.
-  Carray Templates;
+/*  Carray Templates;
   std::string lib = argIn.GetStringKey("lib");
   if (lib.empty()) {
     mprintf("\tNo template(s) specified with 'lib'; using any loaded templates.\n");
@@ -607,13 +567,16 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
     for (std::vector<DataSet_Coords*>::const_iterator it = Templates.begin(); it != Templates.end(); ++it)
       mprintf(" %s", (*it)->legend());
     mprintf("\n");
-  }
+  }*/
 
-  // Get parameter sets.
+  // Get templates and parameter sets.
   Cpptraj::Structure::Creator creator;
   if (creator.InitCreator(argIn, State.DSL(), State.Debug())) {
     return CpptrajState::ERR;
   }
+  if (!creator.HasTemplates()) {
+    mprintf("Warning: No residue templates loaded.\n");
+  }
   if (!creator.HasMainParmSet()) {
     mprinterr("Error: No parameter sets.\n");
     return CpptrajState::ERR;
@@ -667,7 +630,7 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
   // Fill in atoms with templates
   Topology topOut;
   Frame frameOut;
-  if (FillAtomsWithTemplates(topOut, frameOut, Templates, topIn, frameIn, creator.MainParmSet())) {
+  if (FillAtomsWithTemplates(topOut, frameOut, topIn, frameIn, creator)) {
     mprinterr("Error: Could not fill in atoms using templates.\n");
     return CpptrajState::ERR;
   }
@@ -676,7 +639,7 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
   // Assign parameters. This will create the bond/angle/dihedral/improper
   // arrays as well.
   Exec::RetType ret = CpptrajState::OK;
-  if ( topOut.AssignParams( creator.MainParmSet()  ) ) {
+  if ( topOut.AssignParams( *(creator.MainParmSetPtr())  ) ) {
     mprinterr("Error: Could not assign parameters for '%s'.\n", topOut.c_str());
     ret = CpptrajState::ERR;
   }
diff --git a/src/Exec_Build.h b/src/Exec_Build.h
index 4e9b793bf1..38464c106c 100644
--- a/src/Exec_Build.h
+++ b/src/Exec_Build.h
@@ -1,7 +1,11 @@
 #ifndef INC_EXEC_BUILD_H
 #define INC_EXEC_BUILD_H
 #include "Exec.h"
-#include "Structure/StructureEnum.h"
+namespace Cpptraj {
+namespace Structure {
+class Creator;
+}
+}
 /// Used to build a structure 
 class Exec_Build : public Exec {
   public:
@@ -10,12 +14,8 @@ class Exec_Build : public Exec {
     DispatchObject* Alloc() const { return (DispatchObject*)new Exec_Build(); }
     RetType Execute(CpptrajState&, ArgList&);
   private:
-    typedef std::vector<DataSet_Coords*> Carray;
-
-    /// Identify residue template from residue name
-    static DataSet_Coords* IdTemplateFromName(Carray const&, NameType const&, Cpptraj::Structure::TerminalType);
     /// Create new topology/frame using templates
-    static int FillAtomsWithTemplates(Topology&, Frame&, Carray const&, Topology const&, Frame const&, ParameterSet const&);
+    static int FillAtomsWithTemplates(Topology&, Frame&, Topology const&, Frame const&, Cpptraj::Structure::Creator const&);
     /// Map atoms in topology to template
     static std::vector<int> MapAtomsToTemplate(Topology const&, int, DataSet_Coords*);
 };

From 882960592a4d4467200ee5161cedc8ea8b51351f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 15 Feb 2024 13:46:14 -0500
Subject: [PATCH 0538/1492] Need 2 ID functions, one from data set name, one
 from residue associated data name

---
 src/Structure/Creator.cpp | 21 +++++++++++++++++++--
 src/Structure/Creator.h   |  5 ++++-
 2 files changed, 23 insertions(+), 3 deletions(-)

diff --git a/src/Structure/Creator.cpp b/src/Structure/Creator.cpp
index b634ad736d..d2c0abd4b2 100644
--- a/src/Structure/Creator.cpp
+++ b/src/Structure/Creator.cpp
@@ -52,11 +52,28 @@ int Creator::InitCreator(ArgList& argIn, DataSetList const& DSL, int debugIn)
   return 0;
 }
 
+/** Try to identify residue template DataSet from the given name;
+  * could be data set name or residue name.
+  */
+DataSet_Coords* Creator::IdTemplateFromName(std::string const& nameIn)
+const
+{
+  MetaData::SearchString search( nameIn );
+  for (Carray::const_iterator it = Templates_.begin(); it != Templates_.end(); ++it) {
+    if ((*it)->Meta().Match_WildCard(search)) {
+      return *it;
+    }
+  }
+  // No aspect. Convert to NameType TODO check for truncation
+  NameType rname( nameIn );
+  return IdTemplateFromResname( NameType(nameIn), Cpptraj::Structure::NON_TERMINAL );
+}
+
 /** Try to identify residue template DataSet from the given residue
   * name (from e.g. the PDB/Mol2/etc file).
   */
-DataSet_Coords* Creator::IdTemplateFromName(NameType const& rname,
-                                            TerminalType termType)
+DataSet_Coords* Creator::IdTemplateFromResname(NameType const& rname,
+                                              TerminalType termType)
 const
 {
   DataSet_Coords* out = 0;
diff --git a/src/Structure/Creator.h b/src/Structure/Creator.h
index 4309c67978..c1a98515c4 100644
--- a/src/Structure/Creator.h
+++ b/src/Structure/Creator.h
@@ -1,6 +1,7 @@
 #ifndef INC_STRUCTURE_CREATOR_H
 #define INC_STRUCTURE_CREATOR_H
 #include <vector>
+#include <string>
 #include "StructureEnum.h" // TerminalType
 class ArgList;
 class DataSet_Coords;
@@ -32,8 +33,10 @@ class Creator {
     DataSet_Parameters const* MainParmSetPtr() const { return mainParmSet_; }
     /// \return True if there are templates
     bool HasTemplates() const { return (!Templates_.empty()); }
+    /// Identify residue template from name
+    DataSet_Coords* IdTemplateFromName(std::string const&) const;
     /// Identify residue template from residue name
-    DataSet_Coords* IdTemplateFromName(NameType const&, TerminalType) const;
+    DataSet_Coords* IdTemplateFromResname(NameType const&, TerminalType) const;
   private:
     /// Get templates
     int getTemplates(ArgList&, DataSetList const&);

From e4d0a4622c16b396ca257b98a920c50c8d357c1f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 15 Feb 2024 13:47:41 -0500
Subject: [PATCH 0539/1492] Use Creator in sequence. Update dependencies. Use
 correct ID function in build.

---
 src/Exec_Build.cpp    |  2 +-
 src/Exec_Sequence.cpp | 88 +++++++++++--------------------------------
 src/Exec_Sequence.h   |  7 +++-
 src/cpptrajdepend     |  2 +-
 4 files changed, 29 insertions(+), 70 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index d9b42291b2..c8c02c5cf7 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -72,7 +72,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
     }
     mprintf("DEBUG: Residue type: %s terminal\n", Cpptraj::Structure::terminalStr(resTermType));
     // Identify a template based on the residue name.
-    DataSet_Coords* resTemplate = creator.IdTemplateFromName(currentRes.Name(), resTermType);
+    DataSet_Coords* resTemplate = creator.IdTemplateFromResname(currentRes.Name(), resTermType);
     if (resTemplate == 0) {
       mprintf("Warning: No template found for residue %s\n", topIn.TruncResNameOnumId(ires).c_str());
       newNatom += currentRes.NumAtoms();
diff --git a/src/Exec_Sequence.cpp b/src/Exec_Sequence.cpp
index eaa5c7840a..dd128e59bc 100644
--- a/src/Exec_Sequence.cpp
+++ b/src/Exec_Sequence.cpp
@@ -1,54 +1,28 @@
 #include "Exec_Sequence.h"
-#include "CpptrajStdio.h"
 #include "AssociatedData_Connect.h"
+#include "CpptrajStdio.h"
+#include "DataSet_Parameters.h" // For casting DataSet_Parameters to ParameterSet
 #include "Structure/Builder.h"
-#include "Structure/Zmatrix.h"
+#include "Structure/Creator.h"
 
 /** Generate and build the specified sequence. */
 int Exec_Sequence::generate_sequence(DataSet_Coords* OUT,
                                      DataSetList const& DSL,
                                      Sarray const& main_sequence,
-                                     Sarray const& LibSetNames)
+                                     Cpptraj::Structure::Creator const& creator)
 const
 {
   // First, get all units in order.
   typedef std::vector<DataSet_Coords*> Uarray;
   Uarray Units;
   Units.reserve( main_sequence.size() );
-//  typedef std::vector<int> Iarray;
-//  Iarray connectAt0, connectAt1;
-//  connectAt0.reserve( Units.size() );
-//  connectAt1.reserve( Units.size() );
+
   int total_natom = 0;
 
   for (Sarray::const_iterator it = main_sequence.begin(); it != main_sequence.end(); ++it)
   {
-    DataSet_Coords* unit = 0;
-    if (LibSetNames.empty()) {
-      // Look for name
-      unit = (DataSet_Coords*)DSL.FindSetOfGroup( *it, DataSet::COORDINATES ); // FIXME need new set type
-      if (unit == 0) {
-        // Look for *[name]
-        std::string searchStr("*[" + *it + "]");
-        unit = (DataSet_Coords*)DSL.FindSetOfGroup( searchStr, DataSet::COORDINATES ); // FIXME need new set type
-      }
-    } else {
-      // Look for name[aspect]
-      DataSet* ds = 0;
-      for (Sarray::const_iterator name = LibSetNames.begin(); name != LibSetNames.end(); ++name)
-      {
-        MetaData meta(*name, *it);
-        ds = DSL.CheckForSet( meta );
-        if (ds != 0) break;
-      }
-      if (ds != 0) {
-        if (ds->Group() != DataSet::COORDINATES) {
-          mprinterr("Error: Set '%s' is not of type Coordinates.\n", ds->legend());
-          return 1;
-        }
-        unit = (DataSet_Coords*)ds;
-      }
-    }
+    DataSet_Coords* unit = creator.IdTemplateFromName( *it );
+
     if (unit == 0) {
       mprinterr("Error: Unit '%s' not found.\n", it->c_str());
       return 1;
@@ -60,21 +34,6 @@ const
     if (unit->Size() > 1) {
       mprintf("Warning: Unit '%s' has more than 1 frame. Only using first frame.\n", unit->legend());
     }
-    // Needs to have connect associated data
-//    AssociatedData* ad = unit->GetAssociatedData(AssociatedData::CONNECT);
-//    if (ad == 0) {
-//      mprinterr("Error: Unit '%s' does not have CONNECT data.\n", unit->legend());
-//      return 1;
-//    }
-//    AssociatedData_Connect const& C = static_cast<AssociatedData_Connect const&>( *ad );
-//    if (C.NconnectAtoms() < 2) {
-//      mprinterr("Error: Not enough connect atoms in unit '%s'\n", unit->legend());
-//      return 1;
-//    }
-//    // Update connect atom 1 indices based on their position in the sequence.
-//    // Do not update connect atom 0 indices since they will not yet be connected.
-//    connectAt0.push_back( C.Connect()[0] );
-//    connectAt1.push_back( C.Connect()[1] + total_natom );
     Units.push_back( unit );
     total_natom += unit->Top().Natom();
   } // END loop over sequence
@@ -94,7 +53,7 @@ const
   frameOut.ClearAtoms();
 
   // hasPosition - for each atom in topOut, status on whether atom in frameOut needs building
-  Cpptraj::Structure::Zmatrix::Barray hasPosition;
+  Cpptraj::Structure::Builder::Barray hasPosition;
   hasPosition.reserve( total_natom );
 
   // Hold atom offsets needed when building residues
@@ -190,7 +149,8 @@ const
       // Residue has atom offset which indicates it needs something built.
       Cpptraj::Structure::Builder structureBuilder;// = new Cpptraj::Structure::Builder();
       structureBuilder.SetDebug( 1 ); // DEBUG FIXME
-      //structureBuilder->SetParameters( &mainParmSet ); TODO import parameters?
+      if (creator.HasMainParmSet())
+        structureBuilder.SetParameters( creator.MainParmSetPtr() );
       // Generate internals from the template, update indices to this topology.
       DataSet_Coords* unit = Units[ires];
       Frame unitFrm = unit->AllocateFrame();
@@ -312,26 +272,20 @@ void Exec_Sequence::Help() const
 Exec::RetType Exec_Sequence::Execute(CpptrajState& State, ArgList& argIn)
 {
   debug_ = State.Debug();
-  // Atom scan direction TODO add to help
-/*    Cpptraj::Structure::SetAtomScanDirection(Cpptraj::Structure::SCAN_ATOMS_FORWARDS);
-  std::string atomscandir = argIn.GetStringKey("atomscandir");
-  if (!atomscandir.empty()) {
-    if (atomscandir == "f")
-      Cpptraj::Structure::SetAtomScanDirection(Cpptraj::Structure::SCAN_ATOMS_FORWARDS);
-    else if (atomscandir == "b")
-      Cpptraj::Structure::SetAtomScanDirection(Cpptraj::Structure::SCAN_ATOMS_BACKWARDS);
-    else {
-      mprinterr("Error: Unrecognized keyword for 'atomscandir' : %s\n", atomscandir.c_str());
-      return CpptrajState::ERR;
-    }
-  }*/
+
   // Args
+  Cpptraj::Structure::Creator creator;
+  if (creator.InitCreator(argIn, State.DSL(), debug_)) {
+    return CpptrajState::ERR;
+  }
+
+/*
   Sarray LibSetNames;
   std::string libsetname = argIn.GetStringKey("libset");
   while (!libsetname.empty()) {
     LibSetNames.push_back( libsetname );
     libsetname = argIn.GetStringKey("libset");
-  }
+  } */
   std::string dsname = argIn.GetStringKey("name");
   if (dsname.empty()) {
     mprinterr("Error: No output set name specified with 'name'\n");
@@ -357,12 +311,12 @@ Exec::RetType Exec_Sequence::Execute(CpptrajState& State, ArgList& argIn)
   }
 
   // Info
-  if (!LibSetNames.empty()) {
+/*  if (!LibSetNames.empty()) {
     mprintf("\tLibrary set names:");
     for (Sarray::const_iterator it = LibSetNames.begin(); it != LibSetNames.end(); ++it)
       mprintf(" %s", it->c_str());
     mprintf("\n");
-  }
+  }*/
   mprintf("\tMain sequence:");
   for (Sarray::const_iterator it = main_sequence.begin(); it != main_sequence.end(); ++it)
     mprintf(" %s", it->c_str());
@@ -370,7 +324,7 @@ Exec::RetType Exec_Sequence::Execute(CpptrajState& State, ArgList& argIn)
   mprintf("\tOutput set name : %s\n", OUT->legend());
 
   // Execute
-  if (generate_sequence(OUT, State.DSL(), main_sequence, LibSetNames)) {
+  if (generate_sequence(OUT, State.DSL(), main_sequence, creator)) {
     mprinterr("Error: Could not generate sequence.\n");
     return CpptrajState::ERR;
   }
diff --git a/src/Exec_Sequence.h b/src/Exec_Sequence.h
index 148cf4e1af..12c71db23b 100644
--- a/src/Exec_Sequence.h
+++ b/src/Exec_Sequence.h
@@ -1,6 +1,11 @@
 #ifndef INC_EXEC_SEQUENCE_H
 #define INC_EXEC_SEQUENCE_H
 #include "Exec.h"
+namespace Cpptraj {
+namespace Structure { 
+class Creator;
+}
+}
 /// Create a molecule from a sequence of units 
 class Exec_Sequence : public Exec {
   public:
@@ -12,7 +17,7 @@ class Exec_Sequence : public Exec {
     typedef std::vector<std::string> Sarray;
 
     int generate_sequence(DataSet_Coords*, DataSetList const&,
-                          Sarray const&, Sarray const&) const;
+                          Sarray const&, Cpptraj::Structure::Creator const&) const;
 
     int debug_;
 };
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 4dfe731677..06cc182792 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -334,7 +334,7 @@ Exec_ReadInput.o : Exec_ReadInput.cpp Action.h ActionList.h ActionState.h Analys
 Exec_RotateDihedral.o : Exec_RotateDihedral.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_RotateDihedral.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_RunAnalysis.o : Exec_RunAnalysis.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_RunAnalysis.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_ScaleDihedralK.o : Exec_ScaleDihedralK.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ScaleDihedralK.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Sequence.o : Exec_Sequence.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Sequence.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Sequence.o : Exec_Sequence.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Sequence.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/Creator.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_SequenceAlign.o : Exec_SequenceAlign.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SequenceAlign.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Set.o : Exec_Set.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_StringVar.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Set.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Show.o : Exec_Show.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_StringVar.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Show.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h

From 2f7436b201ed2e9cbb04ed0044704fd453c9695e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 15 Feb 2024 13:48:38 -0500
Subject: [PATCH 0540/1492] libset is deprecated

---
 test/Test_Sequence/RunTest.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/Test_Sequence/RunTest.sh b/test/Test_Sequence/RunTest.sh
index 36935c1ed8..cacf3e9a90 100755
--- a/test/Test_Sequence/RunTest.sh
+++ b/test/Test_Sequence/RunTest.sh
@@ -17,7 +17,7 @@ list
 sequence CAPS[MOC] A15[CNALA] name Mol
 crdout Mol Mol.mol2
 
-sequence libset A15 libset CAPS MOC CNALA name Mol2
+sequence MOC CNALA name Mol2
 crdout Mol2 Mol2.mol2
 
 crdout CAPS[MOC] MOC.mol2

From 6855a331370c778147624bc81643e6442c325400 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 15 Feb 2024 13:53:16 -0500
Subject: [PATCH 0541/1492] Fix up help

---
 src/Exec_Build.cpp    | 10 +++++++---
 src/Exec_Sequence.cpp |  9 +++++++--
 2 files changed, 14 insertions(+), 5 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index c8c02c5cf7..a5fc83eee7 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -459,9 +459,13 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
 void Exec_Build::Help() const
 {
   mprintf("\tname <output COORDS> crdset <COORDS set> [frame <#>]\n"
-          "\t[parmset <param set> ...] [lib <lib set> ...]\n"
-          "\t[atomscandir {f|b}]\n"
-         );
+          "\t[%s]\n"
+          "\t[{%s} ...]\n"
+          "\t[{%s} ...]\n"
+          "  Build complete topology and parameters from given crdset.\n",
+          Cpptraj::Structure::Creator::other_keywords_,
+          Cpptraj::Structure::Creator::template_keywords_,
+          Cpptraj::Structure::Creator::parm_keywords_);
 }
 
 // Exec_Build::Execute()
diff --git a/src/Exec_Sequence.cpp b/src/Exec_Sequence.cpp
index dd128e59bc..fa5d195980 100644
--- a/src/Exec_Sequence.cpp
+++ b/src/Exec_Sequence.cpp
@@ -263,8 +263,13 @@ const
 void Exec_Sequence::Help() const
 {
   mprintf("\tname <output set name> <unit0> <unit1> ...\n"
-          "\t[{libset <libsetname>} ...]\n"
-          "  Create a molecule from a sequence of units.\n");
+          "\t[%s]\n"
+          "\t[{%s} ...]\n"
+          "\t[{%s} ...]\n"
+          "  Create a molecule from a sequence of units.\n",
+          Cpptraj::Structure::Creator::other_keywords_,
+          Cpptraj::Structure::Creator::template_keywords_,
+          Cpptraj::Structure::Creator::parm_keywords_);
 }
 
 

From 8e5fe25b321b25f7e7f07c286550f47ca1968d98 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 16 Feb 2024 09:04:46 -0500
Subject: [PATCH 0542/1492] Hide some debug info

---
 src/DataIO_LeapRC.cpp | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 2180645cde..003780be66 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -116,7 +116,7 @@ const
       else if (*ptr == '}') {
         bracketCount--;
         if (bracketCount == 1) {
-          mprintf("DEBUG: addAtomTypes: %s\n", tmp.c_str());
+          if (debug_ > 0) mprintf("DEBUG: addAtomTypes: %s\n", tmp.c_str());
           ArgList aline( tmp );
           // Some entries (like LP and EP) are not required to have elements.
           // Set the hybridization index to 1 or 2.
@@ -198,7 +198,7 @@ const
       else if (*ptr == '}') {
         bracketCount--;
         if (bracketCount == 1) {
-          mprintf("DEBUG: addPdbResMap: %s\n", tmp.c_str());
+          if (debug_ > 0) mprintf("DEBUG: addPdbResMap: %s\n", tmp.c_str());
           ArgList aline( tmp );
           // 3 tokens: terminal type (0=beg 1=end), PDB name, unit name
           if (aline.Nargs() < 2 || aline.Nargs() > 3) {
@@ -394,9 +394,11 @@ int DataIO_LeapRC::ReadData(FileName const& fname, DataSetList& dsl, std::string
       DataSet_Coords& crd = static_cast<DataSet_Coords&>( *ds );
       AssociatedData_ResId resid( it->pdbName_, it->termType_ );
       crd.AssociateData( &resid );
-      mprintf("DEBUG: Found unit %s", crd.legend());
-      resid.Ainfo();
-      mprintf("\n");
+      if (debug_ > 0) {
+        mprintf("DEBUG: Found unit %s", crd.legend());
+        resid.Ainfo();
+        mprintf("\n");
+      }
     }
   }
 

From 8b40cc975fe36ff81d4a5725d52c9d67b65bec27 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 16 Feb 2024 09:20:46 -0500
Subject: [PATCH 0543/1492] Make debug info match leap a little closer

---
 src/Exec_Sequence.cpp     |  6 ++++--
 src/Structure/Builder.cpp | 12 +++---------
 2 files changed, 7 insertions(+), 11 deletions(-)

diff --git a/src/Exec_Sequence.cpp b/src/Exec_Sequence.cpp
index fa5d195980..5b5db3735d 100644
--- a/src/Exec_Sequence.cpp
+++ b/src/Exec_Sequence.cpp
@@ -101,7 +101,8 @@ const
       for (Atom::bond_iterator bat = sourceAtom.bondbegin(); bat != sourceAtom.bondend(); ++bat) {
         int at1 = *bat + atomOffset;
         if (at1 > at0) {
-          mprintf("Will add bond between %i and %i (original %i and %i)\n", at0+1, at1+1, itgt+1, *bat + 1);
+          if (debug_ > 1)
+            mprintf("Will add bond between %i and %i (original %i and %i)\n", at0+1, at1+1, itgt+1, *bat + 1);
           intraResBonds.push_back( Ipair(at0, at1) );
         }
       }
@@ -125,7 +126,8 @@ const
                   prevTailAtom+1, headAtom+1);
         return 1;
       }
-      mprintf("Will add bond between %i and %i\n", prevTailAtom+1, headAtom+1);
+      if (debug_ > 1)
+        mprintf("Will add bond between %i and %i\n", prevTailAtom+1, headAtom+1);
       // To preserve compat. with LEaP, make first atom the head atom.
       interResBonds.push_back( Ipair(headAtom, prevTailAtom) );
     } else
diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index b1b0ca0150..890a259b17 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1156,8 +1156,8 @@ int Builder::assignTorsionsAroundBond(int a1, int a2, Frame const& frameIn, Topo
   }
   static const char* hstr[] = { "SP1", "SP2", "SP3", "Unknown" };
   mprintf("DEBUG: assignTorsionsAroundBond: AX= %s (%s)  AY= %s (%s), aAtomIdx= %i",
-          topIn.AtomMaskName(ax).c_str(), hstr[Hx],
-          topIn.AtomMaskName(ay).c_str(), hstr[Hy], aAtomIdx+1);
+          *(topIn[ax].Name()), hstr[Hx],
+          *(topIn[ay].Name()), hstr[Hy], aAtomIdx+1);
   if (aAtomIdx != -1) mprintf(" %s", topIn.AtomMaskName(aAtomIdx).c_str()); // DEBUG
   mprintf("\n"); // DEBUG
   TorsionModel mT;
@@ -1358,6 +1358,7 @@ int Builder::GenerateInternals(Frame const& frameIn, Topology const& topIn, Barr
   // Loop over bonds to determine torsions.
   for (BondArray::const_iterator bnd = bonds.begin(); bnd != bonds.end(); ++bnd)
   {
+    if (topIn[bnd->A1()].Nbonds() > 1 && topIn[bnd->A2()].Nbonds() > 1) mprintf("Building torsion INTERNALs around: %s - %s\n", topIn.LeapName(bnd->A1()).c_str(), topIn.LeapName(bnd->A2()).c_str()); // DEBUG
     if (assignTorsionsAroundBond( bnd->A1(), bnd->A2(), frameIn, topIn, hasPosition, -1 )) {
       mprinterr("Error Assign torsions around bond %s - %s failed.\n",
                 topIn.AtomMaskName(bnd->A1()).c_str(),
@@ -1536,13 +1537,6 @@ int Builder::GenerateInternalsAroundLink(int at0, int at1,
       return 1;
     }
   }
-  // Create torsions around the link
-  //if (assignTorsionsAroundBond( zmatrix, at0, at1, frameIn, topIn, hasPosition )) {
-  //  mprinterr("Error Assign torsions around link %s - %s failed.\n",
-  //            topIn.AtomMaskName(at0).c_str(),
-  //            topIn.AtomMaskName(at1).c_str());
-  //  return 1;
-  //}
   // FIXME this is a hack to make certain we have all the angle/bond terms we need
   mprintf("DEBUG: LOOKING FOR MISSING ANGLE/BOND PARAMS.\n");
   for (Tarray::const_iterator dih = internalTorsions_.begin(); dih != internalTorsions_.end(); ++dih)

From 6c531309e0b4787545783e1d903edd7680889449 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 16 Feb 2024 09:26:48 -0500
Subject: [PATCH 0544/1492] Add some debug. Do not try to update internals from
 externals during sequence since there are no externals.

---
 src/Exec_Sequence.cpp     | 13 +++----------
 src/Structure/Builder.cpp |  1 +
 2 files changed, 4 insertions(+), 10 deletions(-)

diff --git a/src/Exec_Sequence.cpp b/src/Exec_Sequence.cpp
index 5b5db3735d..1d20efbcd3 100644
--- a/src/Exec_Sequence.cpp
+++ b/src/Exec_Sequence.cpp
@@ -183,18 +183,11 @@ const
         return 1;
       }
       // Update internal coords from known positions
-      if (structureBuilder.UpdateICsFromFrame( frameOut, topOut, hasPosition )) {
-        mprinterr("Error: Failed to update Zmatrix with values from existing positions.\n");
-        return 1;
-      }
-      // Convert to Zmatrix and assign missing atom positions
-      //Cpptraj::Structure::Zmatrix tmpz;
-      //tmpz.SetDebug( 1 ); // DEBUG
-      //if (structureBuilder.GetZmatrixFromInternals(tmpz, topOut)) {
-      //  mprinterr("Error: Could not get Zmatrix from internals.\n");
+      // NOTE: By defintion, there are no known positions.
+      //if (structureBuilder.UpdateICsFromFrame( frameOut, topOut, hasPosition )) {
+      //  mprinterr("Error: Failed to update Zmatrix with values from existing positions.\n");
       //  return 1;
       //}
-      //if (tmpz.SetToFrame( frameOut, hasPosition )) {
       if (structureBuilder.BuildFromInternals(frameOut, topOut, hasPosition)) {
         mprinterr("Error: Building residue %s failed.\n",
                   topOut.TruncResNameOnumId(ires).c_str());
diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 890a259b17..3775b1a756 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1722,6 +1722,7 @@ const
               mprintf( "Angle   = %f\n", ic.Theta() );
               mprintf( "Bond    = %f\n", ic.Dist() );
               Vec3 posI = Zmatrix::AtomIposition(ic, frameOut);
+              mprintf( "ZMatrixAll:  %f,%f,%f\n", posI[0], posI[1], posI[2]);
               frameOut.SetXYZ( ic.AtI(), posI );
               hasPosition[ ic.AtI() ] = true;
               nAtomsBuilt++;

From d188853021b757b42405c9c704995d2539dd8997 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 16 Feb 2024 09:37:32 -0500
Subject: [PATCH 0545/1492] Hide some debug info

---
 src/Structure/Builder.cpp | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 3775b1a756..46ead345ea 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -646,11 +646,12 @@ int Cpptraj::Structure::Builder::TorsionModel::BuildMockExternals(Iarray const&
     if (ml == outerAtoms.end())
       outerAtoms.push_back( MockAtom(ic.AtL()) );
   }
+# ifdef CPPTRAJ_DEBUG_BUILDER
   mprintf("DEBUG: Outer atoms:\n");
   for (Marray::const_iterator it = outerAtoms.begin(); it != outerAtoms.end(); ++it)
     mprintf("DEBUG:\t\t%i %4s (%i) {%f %f %f}\n", it->Idx()+1, topIn.AtomMaskName(it->Idx()).c_str(),
             (int)it->Known(), it->Pos()[0], it->Pos()[1], it->Pos()[2]);
-
+# endif
   // Loop through the known torsions looking for those that
   // have one position defined, then build coords for the
   // other atom and mark the torsion as used.
@@ -709,11 +710,15 @@ int Cpptraj::Structure::Builder::TorsionModel::BuildMockExternals(Iarray const&
     mprinterr("Error: There are %u torsions left over for mock coords.\n", used.size() - nused);
     return 1;
   }
-  // Update the outer atom positions for this torsion
+# ifdef CPPTRAJ_DEBUG_BUILDER
   mprintf("DEBUG: Final outer atoms:\n");
   for (Marray::const_iterator it = outerAtoms.begin(); it != outerAtoms.end(); ++it) {
     mprintf("DEBUG:\t\t%i %4s (%i) {%f %f %f}\n", it->Idx()+1, topIn.AtomMaskName(it->Idx()).c_str(),
             (int)it->Known(), it->Pos()[0], it->Pos()[1], it->Pos()[2]);
+  }
+# endif
+  // Update the outer atom positions for this torsion
+  for (Marray::const_iterator it = outerAtoms.begin(); it != outerAtoms.end(); ++it) {
     Marray::iterator itx = find_mock_atom(sorted_ax_, it->Idx());
     if (itx != sorted_ax_.end()) {
       itx->SetPos( it->Pos() );

From 5e1831e7fbe96040bd291cac1bcebc10e9b0a6f7 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 17 Feb 2024 08:26:47 -0500
Subject: [PATCH 0546/1492] Fix differences in spanning tree usage between
 cpptraj and leap. The full spanning tree is only used when reading in
 existing coords from e.g. a PDB file.

---
 src/Exec_Build.cpp                           |  2 +-
 src/Exec_Graft.cpp                           |  2 +-
 src/Exec_Sequence.cpp                        |  2 +-
 src/Structure/Builder.cpp                    | 24 +++++++++++++-------
 src/Structure/Builder.h                      |  2 +-
 src/Structure/GenerateConnectivityArrays.cpp |  7 ++++--
 6 files changed, 25 insertions(+), 14 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index a5fc83eee7..83214e5437 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -414,7 +414,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
           topOut.AddBond(resBonds->first, resBonds->second);
           // Generate internals around the link
           if (structureBuilder.GenerateInternalsAroundLink(resBonds->first, resBonds->second,
-                                                            frameOut, topOut, hasPosition))
+                                                            frameOut, topOut, hasPosition, true))
           {
             mprinterr("Error: Assign torsions around inter-residue link %s - %s failed.\n",
                       topOut.AtomMaskName(resBonds->first).c_str(),
diff --git a/src/Exec_Graft.cpp b/src/Exec_Graft.cpp
index ab8f20c758..87069acec7 100644
--- a/src/Exec_Graft.cpp
+++ b/src/Exec_Graft.cpp
@@ -468,7 +468,7 @@ const
   // Generate internals around the link
   if (structureBuilder.GenerateInternalsAroundLink( bondat1 + atomOffset,
                                                     bondat0,
-                                                    frameOut, topOut, hasPosition ) )
+                                                    frameOut, topOut, hasPosition, false ) )
   {
     mprinterr("Error: Assign torsions around graft bond atoms %s - %s failed.\n",
               topOut.AtomMaskName(bondat1 + atomOffset).c_str(),
diff --git a/src/Exec_Sequence.cpp b/src/Exec_Sequence.cpp
index 1d20efbcd3..6c1fd59c6b 100644
--- a/src/Exec_Sequence.cpp
+++ b/src/Exec_Sequence.cpp
@@ -175,7 +175,7 @@ const
       topOut.AddBond( interResBonds[ires].first, interResBonds[ires].second );
       // Generate internals around the link
       if (structureBuilder.GenerateInternalsAroundLink(interResBonds[ires].first, interResBonds[ires].second,
-                                                        frameOut, topOut, hasPosition))
+                                                        frameOut, topOut, hasPosition, false))
       {
         mprinterr("Error: Assign torsions around inter-unit link %s - %s failed.\n",
                   topOut.AtomMaskName(interResBonds[ires].first).c_str(),
diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 46ead345ea..66d99eb0a9 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -551,12 +551,14 @@ int Cpptraj::Structure::Builder::TorsionModel::SetupTorsion(AtomType::Hybridizat
   // DEBUG
   Atom const& AX = topIn[atX_.Idx()];
   Atom const& AY = topIn[atY_.Idx()];
-  mprintf("Orientation around: %s = %f (chiX= %f)\n", *(AX.Name()), Xorientation_, chiX);
+  //mprintf("Orientation around: %s = %f (chiX= %f)\n", *(AX.Name()), Xorientation_, chiX);
+  mprintf("Orientation around: %s = %f\n", *(AX.Name()), Xorientation_);
   //for (Atom::bond_iterator bat = AX.bondbegin(); bat != AX.bondend(); ++bat) mprintf(" %s", *(topIn[*bat].Name()));
   //mprintf("}\n");
   for (Marray::const_iterator it = sorted_ax_.begin(); it != sorted_ax_.end(); ++it)
       mprintf("Atom %li: %s (%i) (build=%i)\n", it - sorted_ax_.begin(), *(topIn[it->Idx()].Name()), (int)it->Known(), (int)it->BuildInternals());
-  mprintf("Orientation around: %s = %f (chiY= %f)\n", *(AY.Name()), Yorientation_, chiY);
+  //mprintf("Orientation around: %s = %f (chiY= %f)\n", *(AY.Name()), Yorientation_, chiY);
+  mprintf("Orientation around: %s = %f\n", *(AY.Name()), Yorientation_);
   //for (Atom::bond_iterator bat = AY.bondbegin(); bat != AY.bondend(); ++bat) mprintf(" %s", *(topIn[*bat].Name()));
   //mprintf("}\n");
   for (Marray::const_iterator it = sorted_ay_.begin(); it != sorted_ay_.end(); ++it)
@@ -1110,7 +1112,7 @@ void Builder::createSp2Sp2Torsions(TorsionModel const& MT) {
   double dADOffset =         MT.Absolute() - Constants::PI ;
   double d180      =         Constants::PI + dADOffset     ;
   double d0        =                 dADOffset             ;
-  mprintf("In ModelCreateSp2Sp2Torsions, dAbsolute is %g, dADOffset= %g, d180= %g, d0= %g\n",
+  mprintf("In ModelCreateSp2Sp2Torsions, dAbsolute= %g, dADOffset= %g, d180= %g, d0= %g\n",
           MT.Absolute()*Constants::RADDEG,
           dADOffset * Constants::RADDEG,
           d180 * Constants::RADDEG,
@@ -1513,7 +1515,8 @@ int Builder::generateAtomInternals(int at, Frame const& frameIn, Topology const&
   */
 int Builder::GenerateInternalsAroundLink(int at0, int at1,
                                          Frame const& frameIn, Topology const& topIn,
-                                         Barray const& hasPosition)
+                                         Barray const& hasPosition,
+                                         bool fullTree)
 {
   mprintf("DEBUG: ----- Entering Builder::GenerateInternalsAroundLink. -----\n");
   mprintf("DEBUG: Link: %s to %s\n", topIn.AtomMaskName(at0).c_str(), topIn.AtomMaskName(at1).c_str());
@@ -1532,11 +1535,16 @@ int Builder::GenerateInternalsAroundLink(int at0, int at1,
   for (int at = 0; at < R0.FirstAtom(); at++)
     tmpHasPosition[at] = true;
   // Create spanning tree across the link
-  std::vector<int> span_atoms = GenerateSpanningTree(at0, at1, 4, topIn.Atoms());
+  int actualAt1;
+  if (fullTree)
+    actualAt1 = -1;
+  else
+    actualAt1 = at1;
+  std::vector<int> span_atoms = GenerateSpanningTree(at0, actualAt1, 4, topIn.Atoms());
   for (std::vector<int>::const_iterator it = span_atoms.begin(); 
                                         it != span_atoms.end(); ++it)
   {
-    //mprintf("SPANNING TREE ATOM: %s\n", topIn.LeapName(*it).c_str());
+    mprintf("SPANNING TREE ATOM: %s\n", *(topIn[*it].Name()));
     if (generateAtomInternals(*it, frameIn, topIn, tmpHasPosition)) {
       mprinterr("Error: Could not generate internals for atom %s\n", topIn.AtomMaskName(*it).c_str());
       return 1;
@@ -1693,7 +1701,7 @@ const
       int atToBuildAround = -1;
       if (!hasPosition[at]) {
         // Position of atom is not known.
-        mprintf("BUILD: Position of %s is not known.\n", *(topIn[at].Name()));
+        //mprintf("BUILD: Position of %s is not known.\n", *(topIn[at].Name()));
         // Is this bonded to an atom with known position?
         for (Atom::bond_iterator bat = topIn[at].bondbegin(); bat != topIn[at].bondend(); ++bat) {
           if (hasPosition[*bat]) {
@@ -1703,7 +1711,7 @@ const
         }
       } else {
         // Position of atom is known.
-        mprintf("BUILD: Position of %s is known.\n", *(topIn[at].Name()));
+        //mprintf("BUILD: Position of %s is known.\n", *(topIn[at].Name()));
         atToBuildAround = at;
       }
       // Build unknown positions around known atom
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index a2d94a4b2a..25c4233852 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -27,7 +27,7 @@ class Builder {
     /// Generate internal coordinates in the same manner as LEaP
     int GenerateInternals(Frame const&, Topology const&, Barray const&);
     /// Generate internal coordinates around a link between residues in same manner as LEaP
-    int GenerateInternalsAroundLink(int, int, Frame const&, Topology const&, Barray const&);
+    int GenerateInternalsAroundLink(int, int, Frame const&, Topology const&, Barray const&, bool);
     /// Update existing indices with given offset
     void UpdateIndicesWithOffset(int);
 
diff --git a/src/Structure/GenerateConnectivityArrays.cpp b/src/Structure/GenerateConnectivityArrays.cpp
index 2366ea616a..0f07c85d88 100644
--- a/src/Structure/GenerateConnectivityArrays.cpp
+++ b/src/Structure/GenerateConnectivityArrays.cpp
@@ -75,7 +75,10 @@ BondArray Cpptraj::Structure::GenerateBondArray(std::vector<Residue> const& resi
   return out;
 }
 
-/** Generate a spanning tree around two atoms in the same manner as LEaP. */ // FIXME at1 not strictly needed
+/** Generate a spanning tree around two atoms in the same manner as LEaP.
+  * If at1 is -1, get the full tree. Otherwise, just get the tree in 
+  * the direction of at0.
+  */
 std::vector<int> Cpptraj::Structure::GenerateSpanningTree(int at0, int at1, int targetDepth,
                                                           std::vector<Atom> const& atoms)
 {
@@ -95,7 +98,7 @@ std::vector<int> Cpptraj::Structure::GenerateSpanningTree(int at0, int at1, int
     Atom const& currentAt = atoms[queue[idx]];
     for (Atom::bond_iterator bat = currentAt.bondbegin(); bat != currentAt.bondend(); ++bat)
     {
-      if (!atomSeen[*bat]) {
+      if (*bat != at1 && !atomSeen[*bat]) {
         out.push_back( *bat );
         atomSeen[*bat] = true;
         if (depth[idx] + 1 < targetDepth && atoms[*bat].Nbonds() > 1) {

From 5dee7e351fae9d4deed9bd4d2c2a40287afda448 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 18 Feb 2024 09:36:09 -0500
Subject: [PATCH 0547/1492] Try to make sequence behave like it does in leap;
 in leap, sequence uses a spanning tree when building the next residue instead
 of just the atoms of the next residue (like when building from pdb).

---
 src/Exec_Build.cpp                           |  2 +-
 src/Exec_Graft.cpp                           |  2 +-
 src/Exec_Sequence.cpp                        |  7 +-
 src/Structure/Builder.cpp                    | 87 ++++++++++++++++----
 src/Structure/Builder.h                      | 16 +++-
 src/Structure/GenerateConnectivityArrays.cpp | 13 ++-
 6 files changed, 103 insertions(+), 24 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 83214e5437..0bd7601dac 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -414,7 +414,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
           topOut.AddBond(resBonds->first, resBonds->second);
           // Generate internals around the link
           if (structureBuilder.GenerateInternalsAroundLink(resBonds->first, resBonds->second,
-                                                            frameOut, topOut, hasPosition, true))
+                                                            frameOut, topOut, hasPosition, Cpptraj::Structure::Builder::BUILD))
           {
             mprinterr("Error: Assign torsions around inter-residue link %s - %s failed.\n",
                       topOut.AtomMaskName(resBonds->first).c_str(),
diff --git a/src/Exec_Graft.cpp b/src/Exec_Graft.cpp
index 87069acec7..09cb7f3459 100644
--- a/src/Exec_Graft.cpp
+++ b/src/Exec_Graft.cpp
@@ -468,7 +468,7 @@ const
   // Generate internals around the link
   if (structureBuilder.GenerateInternalsAroundLink( bondat1 + atomOffset,
                                                     bondat0,
-                                                    frameOut, topOut, hasPosition, false ) )
+                                                    frameOut, topOut, hasPosition, Cpptraj::Structure::Builder::SEQUENCE ) )
   {
     mprinterr("Error: Assign torsions around graft bond atoms %s - %s failed.\n",
               topOut.AtomMaskName(bondat1 + atomOffset).c_str(),
diff --git a/src/Exec_Sequence.cpp b/src/Exec_Sequence.cpp
index 6c1fd59c6b..ac60506543 100644
--- a/src/Exec_Sequence.cpp
+++ b/src/Exec_Sequence.cpp
@@ -175,7 +175,7 @@ const
       topOut.AddBond( interResBonds[ires].first, interResBonds[ires].second );
       // Generate internals around the link
       if (structureBuilder.GenerateInternalsAroundLink(interResBonds[ires].first, interResBonds[ires].second,
-                                                        frameOut, topOut, hasPosition, false))
+                                                        frameOut, topOut, hasPosition, Cpptraj::Structure::Builder::SEQUENCE))
       {
         mprinterr("Error: Assign torsions around inter-unit link %s - %s failed.\n",
                   topOut.AtomMaskName(interResBonds[ires].first).c_str(),
@@ -188,7 +188,10 @@ const
       //  mprinterr("Error: Failed to update Zmatrix with values from existing positions.\n");
       //  return 1;
       //}
-      if (structureBuilder.BuildFromInternals(frameOut, topOut, hasPosition)) {
+      if (structureBuilder.BuildSequenceFromInternals(frameOut, topOut, hasPosition,
+                                                      interResBonds[ires].first,
+                                                      interResBonds[ires].second))
+      {
         mprinterr("Error: Building residue %s failed.\n",
                   topOut.TruncResNameOnumId(ires).c_str());
         buildFailed = true;
diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 66d99eb0a9..7c88bec29e 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -603,7 +603,7 @@ int Cpptraj::Structure::Builder::TorsionModel::BuildMockExternals(Iarray const&
     return 1;
   }
   mprintf("=======  Started mock coords from: %s\n", topIn.LeapName(internalTorsionsIn[iaTorsions.front()].AtI()).c_str());
-
+  mprintf("========  %zu Torsions to build mock coords from:\n", iaTorsions.size());
   for (Iarray::const_iterator idx = iaTorsions.begin(); idx != iaTorsions.end(); ++idx) {
     InternalTorsion const& ic = internalTorsionsIn[*idx];
     mprintf("------- Known torsion: %s - %s - %s - %s  %f\n",
@@ -1385,7 +1385,10 @@ int Builder::GenerateInternals(Frame const& frameIn, Topology const& topIn, Barr
     buildBondInternal(bnd->A1(), bnd->A2(), frameIn, topIn, hasPosition);
   }
   // Chirality
-  for (int at = 0; at != topIn.Natom(); ++at) {
+  Iarray atomIdxs = GenerateAtomArray(topIn.Residues(), topIn.Atoms());
+  for (Iarray::const_iterator it = atomIdxs.begin(); it != atomIdxs.end(); ++it) {
+    int at = *it; // FIXME just use *it
+  //for (int at = 0; at != topIn.Natom(); ++at) {
     double dValue = 0;
     if (determineChirality(dValue, at, frameIn, topIn, hasPosition)) {
       mprintf("Got chirality from external coordinates\n" );
@@ -1516,7 +1519,7 @@ int Builder::generateAtomInternals(int at, Frame const& frameIn, Topology const&
 int Builder::GenerateInternalsAroundLink(int at0, int at1,
                                          Frame const& frameIn, Topology const& topIn,
                                          Barray const& hasPosition,
-                                         bool fullTree)
+                                         BuildType btype)
 {
   mprintf("DEBUG: ----- Entering Builder::GenerateInternalsAroundLink. -----\n");
   mprintf("DEBUG: Link: %s to %s\n", topIn.AtomMaskName(at0).c_str(), topIn.AtomMaskName(at1).c_str());
@@ -1536,13 +1539,14 @@ int Builder::GenerateInternalsAroundLink(int at0, int at1,
     tmpHasPosition[at] = true;
   // Create spanning tree across the link
   int actualAt1;
-  if (fullTree)
+  if (btype == BUILD)
+    // Want the full tree
     actualAt1 = -1;
   else
+    // Only want the 'forward' tree
     actualAt1 = at1;
-  std::vector<int> span_atoms = GenerateSpanningTree(at0, actualAt1, 4, topIn.Atoms());
-  for (std::vector<int>::const_iterator it = span_atoms.begin(); 
-                                        it != span_atoms.end(); ++it)
+  Iarray span_atoms = GenerateSpanningTree(at0, actualAt1, 4, topIn.Atoms());
+  for (Iarray::const_iterator it = span_atoms.begin(); it != span_atoms.end(); ++it)
   {
     mprintf("SPANNING TREE ATOM: %s\n", *(topIn[*it].Name()));
     if (generateAtomInternals(*it, frameIn, topIn, tmpHasPosition)) {
@@ -1650,13 +1654,11 @@ int Builder::getIcFromInternals(InternalCoords& icOut, int at, Barray const& has
   return 0;
 }
 
-/** Build coordinates for any atom with an internal that does
-  * not have its position set.
-  */ 
-int Builder::BuildFromInternals(Frame& frameOut, Topology const& topIn, Barray& hasPosition)
+/** \return Array of residues with atoms that need positions. */
+std::vector<Residue> Builder::residuesThatNeedPositions(Topology const& topIn,
+                                                        Barray const& hasPosition)
 const
 {
-  // Create a list of residues that have atoms that need positions
   std::vector<Residue> residues;
   std::vector<int> Rnums;
   for (Tarray::const_iterator dih = internalTorsions_.begin();
@@ -1678,10 +1680,65 @@ const
       }
     }
   }
+  return residues;
+} 
+
+/** Build coordinates for any atom with an internal that does
+  * not have its position set. Use same atom order as leap sequence.
+  */
+int Builder::BuildSequenceFromInternals(Frame& frameOut, Topology const& topIn,
+                                        Barray& hasPosition, int at0, int at1)
+const
+{
+  // Create a list of residues that have atoms that need positions
+  //std::vector<Residue> residues = residuesThatNeedPositions(topIn, hasPosition);
+  Iarray atomIndices = GenerateSpanningTree(at0, at1, -1, topIn.Atoms());
+
+  return buildExternalsForAtoms( atomIndices, frameOut, topIn, hasPosition ); 
+  return 0;
+}
+
+/** Build coordinates for any atom with an internal that does
+  * not have its position set.
+  */ 
+int Builder::BuildFromInternals(Frame& frameOut, Topology const& topIn, Barray& hasPosition)
+const
+{
+  // Create a list of residues that have atoms that need positions
+  std::vector<Residue> residues = residuesThatNeedPositions(topIn, hasPosition);
+//  std::vector<int> Rnums;
+//  for (Tarray::const_iterator dih = internalTorsions_.begin();
+//                              dih != internalTorsions_.end(); ++dih)
+//  {
+//    if (!hasPosition[dih->AtI()]) {
+//      int rnum = topIn[dih->AtI()].ResNum();
+//      bool has_rnum = false;
+//      for (std::vector<int>::const_iterator it = Rnums.begin(); it != Rnums.end(); ++it) {
+//        if (*it == rnum) {
+//          has_rnum = true;
+//          break;
+//        }
+//      }
+//      if (!has_rnum) {
+//        mprintf("DEBUG: Need to build for residue %s\n", topIn.TruncResNameNum(rnum).c_str());
+//        residues.push_back( topIn.Res(rnum) );
+//        Rnums.push_back(rnum);
+//      }
+//    }
+//  }
   // Generate array over residue in same order that leap would do
-  std::vector<int> atomIndices = GenerateAtomArray(residues, topIn.Atoms());
+  Iarray atomIndices = GenerateAtomArray(residues, topIn.Atoms());
   residues.clear();
-  Rnums.clear();
+//  Rnums.clear();
+  return buildExternalsForAtoms( atomIndices, frameOut, topIn, hasPosition ); 
+}
+
+/** Build externals for atoms in the given array using internals. */
+int Builder::buildExternalsForAtoms(Iarray const& atomIndices,
+                                    Frame& frameOut, Topology const& topIn,
+                                    Barray& hasPosition)
+const
+{
   // Count how many atoms need their positions set
   unsigned int nAtomsThatNeedPositions = 0;
   for (std::vector<int>::const_iterator it = atomIndices.begin();
@@ -1724,7 +1781,7 @@ const
             // Find an internal coordinate.
             InternalCoords ic;
             if (getIcFromInternals(ic, *bat, hasPosition)) {
-              printAllInternalsForAtom(*bat, topIn, hasPosition); // DEBUG
+              //printAllInternalsForAtom(*bat, topIn, hasPosition); // DEBUG
 
               mprintf("Building atom %s using torsion/angle/bond\n", topIn.LeapName(*bat).c_str());
               mprintf("Using - %s - %s - %s\n",
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index 25c4233852..5579afda02 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -6,6 +6,7 @@ class Atom;
 class Topology;
 class Frame;
 class ParameterSet;
+class Residue;
 namespace Cpptraj {
 namespace Structure {
 class Zmatrix;
@@ -14,6 +15,11 @@ class InternalCoords;
 class Builder {
   public:
     typedef std::vector<bool> Barray;
+    /// Build type
+    enum BuildType {
+      BUILD = 0, ///< For cases where some external coordinates may already be known.
+      SEQUENCE   ///< For cases where no external coordinates are known.
+    };
     /// CONSTRUCTOR
     Builder();
     /// Set debug level
@@ -27,14 +33,16 @@ class Builder {
     /// Generate internal coordinates in the same manner as LEaP
     int GenerateInternals(Frame const&, Topology const&, Barray const&);
     /// Generate internal coordinates around a link between residues in same manner as LEaP
-    int GenerateInternalsAroundLink(int, int, Frame const&, Topology const&, Barray const&, bool);
+    int GenerateInternalsAroundLink(int, int, Frame const&, Topology const&, Barray const&, BuildType);
     /// Update existing indices with given offset
     void UpdateIndicesWithOffset(int);
 
     /// \return LEaP chirality value around given atom
     static double DetermineChiralityAroundAtom(int, Frame const&, Topology const&);
-    /// Build position from internals for any atom with unset position
+    /// Build position from internals for any atom with unset position; some positions may be known.
     int BuildFromInternals(Frame&, Topology const&, Barray&) const;
+    /// Build position from internals for any atom with unset position
+    int BuildSequenceFromInternals(Frame&, Topology const&, Barray&, int, int) const;
     /// \return Zmatrix from current internals
     //int GetZmatrixFromInternals(Zmatrix&, Topology const&) const;
     /// Adjust torsion around a bond so that atoms with longest 'depth' are trans
@@ -104,6 +112,10 @@ class Builder {
     void printAllInternalsForAtom(int, Topology const&, Barray const&) const;
     /// \\return index of atom with longest 'depth' bonded to a given atom (ignoring one bonded atom).
     static int get_depths_around_atom(int, int, Topology const&);
+    /// \return array containing all residues with atoms that need positions
+    std::vector<Residue> residuesThatNeedPositions(Topology const&, Barray const&) const;
+    /// Build externals for atoms in the given array using internals.
+    int buildExternalsForAtoms(Iarray const&, Frame&, Topology const&, Barray&) const;
 
     int debug_;
     ParameterSet const* params_;
diff --git a/src/Structure/GenerateConnectivityArrays.cpp b/src/Structure/GenerateConnectivityArrays.cpp
index 0f07c85d88..de89fe5474 100644
--- a/src/Structure/GenerateConnectivityArrays.cpp
+++ b/src/Structure/GenerateConnectivityArrays.cpp
@@ -101,9 +101,16 @@ std::vector<int> Cpptraj::Structure::GenerateSpanningTree(int at0, int at1, int
       if (*bat != at1 && !atomSeen[*bat]) {
         out.push_back( *bat );
         atomSeen[*bat] = true;
-        if (depth[idx] + 1 < targetDepth && atoms[*bat].Nbonds() > 1) {
-          queue.push_back( *bat );
-          depth.push_back( depth[idx]+1 );
+        if (targetDepth < 1) {
+          if (atoms[*bat].Nbonds() > 1) {
+            queue.push_back( *bat );
+            depth.push_back( depth[idx]+1 );
+          }
+        } else {
+          if (depth[idx] + 1 < targetDepth && atoms[*bat].Nbonds() > 1) {
+            queue.push_back( *bat );
+            depth.push_back( depth[idx]+1 );
+          }
         }
       }
     }

From 5985bc1ee13f920ddfdf8205511ab3d50cdd26e6 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 20 Feb 2024 08:53:59 -0500
Subject: [PATCH 0548/1492] Exactly match behavior of Sift in leap

---
 src/Structure/Builder.cpp | 22 ++++++++++++----------
 1 file changed, 12 insertions(+), 10 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 7c88bec29e..8712ae211e 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -399,7 +399,7 @@ void Cpptraj::Structure::Builder::TorsionModel::swap_heaviest(Marray& bondedAtom
     }
   }
   // If highest weight atom not already in front, swap it there.
-  if (iPos != 0) swap_mock_atom( bondedAtoms[0], bondedAtoms[iPos] );
+  if (iHighest != 0) swap_mock_atom( bondedAtoms[0], bondedAtoms[iPos] );
 }
 
 /** Order atoms bonded to the given atom in a manner similar to LEaP's
@@ -423,14 +423,16 @@ std::vector<MockAtom>
       known_out.push_back( *it );
   firstUnknownIdx = known_out.size();
   swap_heaviest(known_out, topIn);
-  // Unknown atoms go at the back
+  // Unknown atoms go at the back.
+  // In order to match the way LEaP performs sifting, known atoms are
+  // added in order, but unknown atoms are added in reverse order.
   Marray unknown_out;
   unknown_out.reserve(bondedAtoms.size() - known_out.size() + 1);
-  for (Marray::const_iterator it = bondedAtoms.begin(); it != bondedAtoms.end(); ++it)
+  for (Marray::const_reverse_iterator it = bondedAtoms.rbegin(); it != bondedAtoms.rend(); ++it)
     if (!it->Known())
       unknown_out.push_back( *it );
   swap_heaviest(unknown_out, topIn);
-
+  // Append unknown array to known array and return
   for (Marray::const_iterator it = unknown_out.begin(); it != unknown_out.end(); ++it)
     known_out.push_back( *it );
 
@@ -552,15 +554,15 @@ int Cpptraj::Structure::Builder::TorsionModel::SetupTorsion(AtomType::Hybridizat
   Atom const& AX = topIn[atX_.Idx()];
   Atom const& AY = topIn[atY_.Idx()];
   //mprintf("Orientation around: %s = %f (chiX= %f)\n", *(AX.Name()), Xorientation_, chiX);
-  mprintf("Orientation around: %s = %f\n", *(AX.Name()), Xorientation_);
-  //for (Atom::bond_iterator bat = AX.bondbegin(); bat != AX.bondend(); ++bat) mprintf(" %s", *(topIn[*bat].Name()));
-  //mprintf("}\n");
+  mprintf("Orientation around: %s = %f {", *(AX.Name()), Xorientation_);
+  for (Atom::bond_iterator bat = AX.bondbegin(); bat != AX.bondend(); ++bat) mprintf(" %s", *(topIn[*bat].Name()));
+  mprintf("}\n");
   for (Marray::const_iterator it = sorted_ax_.begin(); it != sorted_ax_.end(); ++it)
       mprintf("Atom %li: %s (%i) (build=%i)\n", it - sorted_ax_.begin(), *(topIn[it->Idx()].Name()), (int)it->Known(), (int)it->BuildInternals());
   //mprintf("Orientation around: %s = %f (chiY= %f)\n", *(AY.Name()), Yorientation_, chiY);
-  mprintf("Orientation around: %s = %f\n", *(AY.Name()), Yorientation_);
-  //for (Atom::bond_iterator bat = AY.bondbegin(); bat != AY.bondend(); ++bat) mprintf(" %s", *(topIn[*bat].Name()));
-  //mprintf("}\n");
+  mprintf("Orientation around: %s = %f {", *(AY.Name()), Yorientation_);
+  for (Atom::bond_iterator bat = AY.bondbegin(); bat != AY.bondend(); ++bat) mprintf(" %s", *(topIn[*bat].Name()));
+  mprintf("}\n");
   for (Marray::const_iterator it = sorted_ay_.begin(); it != sorted_ay_.end(); ++it)
       mprintf("Atom %li: %s (%i) (build=%i)\n", it - sorted_ay_.begin(), *(topIn[it->Idx()].Name()), (int)it->Known(), (int)it->BuildInternals());
   // Calculate the actual torsion angle between A-X-Y-D

From 5772c0f3e59a1034c5c0fabdffd11e77d469004e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 20 Feb 2024 09:12:29 -0500
Subject: [PATCH 0549/1492] Do exact same atom ordering during sequence as leap

---
 src/Structure/Builder.cpp | 74 ++++++++++++++++++++++++++++++++++-----
 src/Structure/Builder.h   |  2 ++
 2 files changed, 68 insertions(+), 8 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 8712ae211e..c8c74502b1 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -554,15 +554,17 @@ int Cpptraj::Structure::Builder::TorsionModel::SetupTorsion(AtomType::Hybridizat
   Atom const& AX = topIn[atX_.Idx()];
   Atom const& AY = topIn[atY_.Idx()];
   //mprintf("Orientation around: %s = %f (chiX= %f)\n", *(AX.Name()), Xorientation_, chiX);
-  mprintf("Orientation around: %s = %f {", *(AX.Name()), Xorientation_);
-  for (Atom::bond_iterator bat = AX.bondbegin(); bat != AX.bondend(); ++bat) mprintf(" %s", *(topIn[*bat].Name()));
-  mprintf("}\n");
+  mprintf("Orientation around: %s = %f\n", *(AX.Name()), Xorientation_);
+  //mprintf("Orientation around: %s = %f {", *(AX.Name()), Xorientation_);
+  //for (Atom::bond_iterator bat = AX.bondbegin(); bat != AX.bondend(); ++bat) mprintf(" %s", *(topIn[*bat].Name()));
+  //mprintf("}\n");
   for (Marray::const_iterator it = sorted_ax_.begin(); it != sorted_ax_.end(); ++it)
       mprintf("Atom %li: %s (%i) (build=%i)\n", it - sorted_ax_.begin(), *(topIn[it->Idx()].Name()), (int)it->Known(), (int)it->BuildInternals());
   //mprintf("Orientation around: %s = %f (chiY= %f)\n", *(AY.Name()), Yorientation_, chiY);
-  mprintf("Orientation around: %s = %f {", *(AY.Name()), Yorientation_);
-  for (Atom::bond_iterator bat = AY.bondbegin(); bat != AY.bondend(); ++bat) mprintf(" %s", *(topIn[*bat].Name()));
-  mprintf("}\n");
+  mprintf("Orientation around: %s = %f\n", *(AY.Name()), Yorientation_);
+  //mprintf("Orientation around: %s = %f {", *(AY.Name()), Yorientation_);
+  //for (Atom::bond_iterator bat = AY.bondbegin(); bat != AY.bondend(); ++bat) mprintf(" %s", *(topIn[*bat].Name()));
+  //mprintf("}\n");
   for (Marray::const_iterator it = sorted_ay_.begin(); it != sorted_ay_.end(); ++it)
       mprintf("Atom %li: %s (%i) (build=%i)\n", it - sorted_ay_.begin(), *(topIn[it->Idx()].Name()), (int)it->Known(), (int)it->BuildInternals());
   // Calculate the actual torsion angle between A-X-Y-D
@@ -1685,6 +1687,33 @@ const
   return residues;
 } 
 
+/** Build coordinates for an atom from internals.
+  * \return 1 if atom was built, 0 otherwise.
+  */
+int Builder::buildCoordsForAtom(int at, Frame& frameOut, Topology const& topIn, Barray const& hasPosition)
+const
+{
+  // Find an internal coordinate for the atom.
+  InternalCoords ic;
+  if (getIcFromInternals(ic, at, hasPosition)) {
+    printAllInternalsForAtom(at, topIn, hasPosition); // DEBUG
+
+    mprintf("Building atom %s using torsion/angle/bond\n", topIn.LeapName(at).c_str());
+    mprintf("Using - %s - %s - %s\n",
+            topIn.LeapName(ic.AtJ()).c_str(),
+            topIn.LeapName(ic.AtK()).c_str(),
+            topIn.LeapName(ic.AtL()).c_str());
+    mprintf( "Torsion = %f\n", ic.Phi() );
+    mprintf( "Angle   = %f\n", ic.Theta() );
+    mprintf( "Bond    = %f\n", ic.Dist() );
+    Vec3 posI = Zmatrix::AtomIposition(ic, frameOut);
+    mprintf( "ZMatrixAll:  %f,%f,%f\n", posI[0], posI[1], posI[2]);
+    frameOut.SetXYZ( ic.AtI(), posI );
+    return 1;
+  }
+  return 0;
+}
+
 /** Build coordinates for any atom with an internal that does
   * not have its position set. Use same atom order as leap sequence.
   */
@@ -1696,7 +1725,36 @@ const
   //std::vector<Residue> residues = residuesThatNeedPositions(topIn, hasPosition);
   Iarray atomIndices = GenerateSpanningTree(at0, at1, -1, topIn.Atoms());
 
-  return buildExternalsForAtoms( atomIndices, frameOut, topIn, hasPosition ); 
+//  return buildExternalsForAtoms( atomIndices, frameOut, topIn, hasPosition ); 
+  // Count how many atoms need their positions set
+  unsigned int nAtomsThatNeedPositions = 0;
+  for (std::vector<int>::const_iterator it = atomIndices.begin();
+                                        it != atomIndices.end(); ++it)
+    if (!hasPosition[*it])
+      nAtomsThatNeedPositions++;
+  mprintf("DEBUG: %u atoms need positions.\n", nAtomsThatNeedPositions);
+  if (nAtomsThatNeedPositions == 0) return 0;
+
+  // Loop over residue atoms
+  while (nAtomsThatNeedPositions > 0) {
+    unsigned int nAtomsBuilt = 0;
+    for (std::vector<int>::const_iterator idx = atomIndices.begin();
+                                          idx != atomIndices.end(); ++idx)
+    {
+      if (!hasPosition[*idx]) {
+        if (buildCoordsForAtom(*idx, frameOut, topIn, hasPosition)) {
+          hasPosition[ *idx ] = true;
+          nAtomsBuilt++;
+          nAtomsThatNeedPositions--;
+        }
+      }
+    } // END loop over atom indices
+    // If we built no atoms this is a problem
+    if (nAtomsBuilt < 1) {
+      mprinterr("Error: No more atoms could be built in sequence for %s\n", topIn.c_str());
+      return 1;
+    }
+  } // END atoms need positions
   return 0;
 }
 
@@ -1783,7 +1841,7 @@ const
             // Find an internal coordinate.
             InternalCoords ic;
             if (getIcFromInternals(ic, *bat, hasPosition)) {
-              //printAllInternalsForAtom(*bat, topIn, hasPosition); // DEBUG
+              printAllInternalsForAtom(*bat, topIn, hasPosition); // DEBUG
 
               mprintf("Building atom %s using torsion/angle/bond\n", topIn.LeapName(*bat).c_str());
               mprintf("Using - %s - %s - %s\n",
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index 5579afda02..4062398d3c 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -114,6 +114,8 @@ class Builder {
     static int get_depths_around_atom(int, int, Topology const&);
     /// \return array containing all residues with atoms that need positions
     std::vector<Residue> residuesThatNeedPositions(Topology const&, Barray const&) const;
+    /// Build XYZ coords for an atom if internals are available
+    int buildCoordsForAtom(int, Frame&, Topology const&, Barray const&) const;
     /// Build externals for atoms in the given array using internals.
     int buildExternalsForAtoms(Iarray const&, Frame&, Topology const&, Barray&) const;
 

From e71af524e32539015ab842167a7e432d37f6f292 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 20 Feb 2024 09:15:56 -0500
Subject: [PATCH 0550/1492] No longer needs to be a separate function

---
 src/Structure/Builder.cpp | 15 ++-------------
 src/Structure/Builder.h   |  2 --
 2 files changed, 2 insertions(+), 15 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index c8c74502b1..e87247093b 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1658,7 +1658,7 @@ int Builder::getIcFromInternals(InternalCoords& icOut, int at, Barray const& has
   return 0;
 }
 
-/** \return Array of residues with atoms that need positions. */
+/** \return Array of residues with atoms that need positions. */ // TODO does this need to be separate
 std::vector<Residue> Builder::residuesThatNeedPositions(Topology const& topIn,
                                                         Barray const& hasPosition)
 const
@@ -1721,11 +1721,9 @@ int Builder::BuildSequenceFromInternals(Frame& frameOut, Topology const& topIn,
                                         Barray& hasPosition, int at0, int at1)
 const
 {
-  // Create a list of residues that have atoms that need positions
-  //std::vector<Residue> residues = residuesThatNeedPositions(topIn, hasPosition);
+  // Create a list of atoms that may need positions
   Iarray atomIndices = GenerateSpanningTree(at0, at1, -1, topIn.Atoms());
 
-//  return buildExternalsForAtoms( atomIndices, frameOut, topIn, hasPosition ); 
   // Count how many atoms need their positions set
   unsigned int nAtomsThatNeedPositions = 0;
   for (std::vector<int>::const_iterator it = atomIndices.begin();
@@ -1789,16 +1787,7 @@ const
   // Generate array over residue in same order that leap would do
   Iarray atomIndices = GenerateAtomArray(residues, topIn.Atoms());
   residues.clear();
-//  Rnums.clear();
-  return buildExternalsForAtoms( atomIndices, frameOut, topIn, hasPosition ); 
-}
 
-/** Build externals for atoms in the given array using internals. */
-int Builder::buildExternalsForAtoms(Iarray const& atomIndices,
-                                    Frame& frameOut, Topology const& topIn,
-                                    Barray& hasPosition)
-const
-{
   // Count how many atoms need their positions set
   unsigned int nAtomsThatNeedPositions = 0;
   for (std::vector<int>::const_iterator it = atomIndices.begin();
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index 4062398d3c..dcf07bda22 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -116,8 +116,6 @@ class Builder {
     std::vector<Residue> residuesThatNeedPositions(Topology const&, Barray const&) const;
     /// Build XYZ coords for an atom if internals are available
     int buildCoordsForAtom(int, Frame&, Topology const&, Barray const&) const;
-    /// Build externals for atoms in the given array using internals.
-    int buildExternalsForAtoms(Iarray const&, Frame&, Topology const&, Barray&) const;
 
     int debug_;
     ParameterSet const* params_;

From 4e840780809d56a4670ddf347b69ddbb21906609 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 20 Feb 2024 09:22:11 -0500
Subject: [PATCH 0551/1492] Use buildCoordsForAtom

---
 src/Structure/Builder.cpp | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index e87247093b..4f0f2eef73 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1696,7 +1696,7 @@ const
   // Find an internal coordinate for the atom.
   InternalCoords ic;
   if (getIcFromInternals(ic, at, hasPosition)) {
-    printAllInternalsForAtom(at, topIn, hasPosition); // DEBUG
+    //printAllInternalsForAtom(at, topIn, hasPosition); // DEBUG
 
     mprintf("Building atom %s using torsion/angle/bond\n", topIn.LeapName(at).c_str());
     mprintf("Using - %s - %s - %s\n",
@@ -1827,7 +1827,8 @@ const
         for (Atom::bond_iterator bat = bAtom.bondbegin(); bat != bAtom.bondend(); ++bat)
         {
           if (!hasPosition[*bat]) {
-            // Find an internal coordinate.
+            if (buildCoordsForAtom(*bat, frameOut, topIn, hasPosition)) {
+/*            // Find an internal coordinate.
             InternalCoords ic;
             if (getIcFromInternals(ic, *bat, hasPosition)) {
               printAllInternalsForAtom(*bat, topIn, hasPosition); // DEBUG
@@ -1842,8 +1843,8 @@ const
               mprintf( "Bond    = %f\n", ic.Dist() );
               Vec3 posI = Zmatrix::AtomIposition(ic, frameOut);
               mprintf( "ZMatrixAll:  %f,%f,%f\n", posI[0], posI[1], posI[2]);
-              frameOut.SetXYZ( ic.AtI(), posI );
-              hasPosition[ ic.AtI() ] = true;
+              frameOut.SetXYZ( ic.AtI(), posI );*/
+              hasPosition[ *bat ] = true;
               nAtomsBuilt++;
               nAtomsThatNeedPositions--;
             }

From d54d113648cd3630eb4e473a9f5663f80d0f4251 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 20 Feb 2024 09:36:47 -0500
Subject: [PATCH 0552/1492] Fix residue numbering in sequence

---
 src/Exec_Sequence.cpp | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/src/Exec_Sequence.cpp b/src/Exec_Sequence.cpp
index ac60506543..aeada226a5 100644
--- a/src/Exec_Sequence.cpp
+++ b/src/Exec_Sequence.cpp
@@ -71,6 +71,7 @@ const
   for (unsigned int idx = 0; idx < Units.size(); idx++)
   {
     int atomOffset = topOut.Natom();
+    int resOffset = topOut.Nres();
     DataSet_Coords* unit = Units[idx];
     // Needs to have connect associated data
     AssociatedData* ad = unit->GetAssociatedData(AssociatedData::CONNECT);
@@ -86,16 +87,17 @@ const
     int headAtom = CONN.Connect()[0] + atomOffset;
     int tailAtom = CONN.Connect()[1] + atomOffset;
     mprintf("\tAdding atoms for unit %s (head %i tail %i)\n", unit->legend(), headAtom+1, tailAtom+1);
-    Residue const& currentRes = unit->Top().Res(0); // FIXME assuming 1 unit
-    mprintf("DEBUG: atom offset is %i\n", atomOffset);
+    //mprintf("DEBUG: atom offset is %i\n", atomOffset);
     // Add the unit atoms. Only the first unit has known position.
     bool atomPosKnown = (idx == 0);
-    Frame unitFrm = unit->AllocateFrame(); // FIXME only first res
+    Frame unitFrm = unit->AllocateFrame();
     unit->GetFrame(0, unitFrm);
     IParray intraResBonds;
     for (int itgt = 0; itgt < unit->Top().Natom(); itgt++)
     {
       Atom sourceAtom = unit->Top()[itgt];
+      Residue currentRes = unit->Top().Res( sourceAtom.ResNum() );
+      currentRes.SetOriginalNum( currentRes.OriginalResNum() + resOffset );
       // Save the intra-residue bonds
       int at0 = itgt + atomOffset;
       for (Atom::bond_iterator bat = sourceAtom.bondbegin(); bat != sourceAtom.bondend(); ++bat) {

From 4314e735af7fd09e296f86081a8e9ed2ab2f1694 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 20 Feb 2024 09:40:35 -0500
Subject: [PATCH 0553/1492] Fix saving residue info in graft

---
 src/Exec_Graft.cpp | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/src/Exec_Graft.cpp b/src/Exec_Graft.cpp
index 09cb7f3459..21d3c1ce7b 100644
--- a/src/Exec_Graft.cpp
+++ b/src/Exec_Graft.cpp
@@ -383,7 +383,7 @@ const
     mprintf("\t%6i %s %s\n", at+1, mol1Top.AtomMaskName(at).c_str(), *(mol1Top.Res(mol1Top[at].ResNum()).Name()));
   mprintf("BOND ATOM 1 %i\n", bondat1+1);
 
-  // Combine topologies. TODO save original chiralities
+  // Combine topologies.
   Topology topOut;
   Frame frameOut;
   int total_natom = mol0Top.Natom() + mol1Top.Natom();
@@ -403,6 +403,7 @@ const
   topOut.SetParmBox( mol0frm.BoxCrd() );
   for (int at = 0; at < mol0Top.Natom(); at++) {
     Atom sourceAtom = mol0Top[at];
+    // Save the intra-residue bonds.
     for (Atom::bond_iterator bat = sourceAtom.bondbegin(); bat != sourceAtom.bondend(); ++bat) {
       if (*bat > at) {
         mprintf("Will add bond between %i and %i\n", at+1, *bat+1);
@@ -416,9 +417,13 @@ const
   }
   // Add mol1 atoms
   int atomOffset = mol0Top.Natom();
+  int resOffset = topOut.Nres();
   mprintf("DEBUG: Atom offset is %i\n", atomOffset);
   for (int itgt = 0; itgt < mol1Top.Natom(); itgt++) {
     Atom sourceAtom = mol1Top[itgt];
+    Residue currentRes = mol1Top.Res(sourceAtom.ResNum());
+    currentRes.SetOriginalNum( currentRes.OriginalResNum() + resOffset );
+    // Save the intra-residue bonds.
     int at0 = itgt + atomOffset;
     for (Atom::bond_iterator bat = sourceAtom.bondbegin(); bat != sourceAtom.bondend(); ++bat) {
       int at1 = *bat + atomOffset;
@@ -428,7 +433,7 @@ const
       }
     }
     sourceAtom.ClearBonds(); // FIXME AddTopAtom should clear bonds
-    topOut.AddTopAtom( sourceAtom, mol1Top.Res(mol1Top[itgt].ResNum()) );
+    topOut.AddTopAtom( sourceAtom, currentRes );
     frameOut.AddVec3( Vec3(mol1frm.XYZ(itgt)) );
     hasPosition.push_back( false );
   }

From 44f4014bbfa00913e1c0be846c94640b7fce7d93 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 20 Feb 2024 09:46:21 -0500
Subject: [PATCH 0554/1492] Update for fixed sequence builder

---
 test/Test_Graft/IC.Final.graft.mol2.save | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/test/Test_Graft/IC.Final.graft.mol2.save b/test/Test_Graft/IC.Final.graft.mol2.save
index c87c8124e7..ece3f0415e 100644
--- a/test/Test_Graft/IC.Final.graft.mol2.save
+++ b/test/Test_Graft/IC.Final.graft.mol2.save
@@ -17,28 +17,28 @@ USER_CHARGES
       9 O           6.0088    1.5932   -0.0000 O          1 TYR     -0.567900
      10 C2          4.2167    4.8987    1.1983 CA         2 PRY      0.033204
      11 C3          4.0092    5.8193    2.2292 CA         2 PRY     -0.149016
-     12 H4          3.3701    5.6304    3.0751 HA         2 PRY      0.153372
-     13 C4          4.6895    7.0771    2.1412 CA         2 PRY     -0.336291
-     14 H5          4.5566    7.8128    2.9127 HA         2 PRY      0.167425
+     12 H4          3.3555    5.5622    3.0454 HA         2 PRY      0.153372
+     13 C4          4.6204    7.0513    2.2286 CA         2 PRY     -0.336291
+     14 H5          4.4870    7.7865    3.0004 HA         2 PRY      0.167425
      15 C5          5.5298    7.3802    1.0703 CA         2 PRY      0.423974
      16 O1          6.1127    8.5970    1.1066 OS         2 PRY     -0.391815
      17 C6          5.7104    6.4428    0.0703 CA         2 PRY     -0.336291
      18 H6          6.3501    6.6384   -0.7684 HA         2 PRY      0.167425
      19 C7          5.0526    5.2168    0.1465 CA         2 PRY     -0.149016
      20 H7          5.2087    4.5024   -0.6431 HA         2 PRY      0.153372
-     21 C8          6.9535    9.0030    0.0541 CT         2 PRY      0.358047
+     21 C8          6.9536    9.0030    0.0541 CT         2 PRY      0.358047
      22 C9          7.3730   10.4140    0.3402 CM         2 PRY     -0.496680
-     23 C10         8.5864   10.9389    0.2629 CM         2 PRY      0.317549
+     23 C10         8.5864   10.9389    0.2630 CM         2 PRY      0.317549
      24 C11         8.8094   12.4021    0.5624 CT         2 PRY     -0.394216
-     25 C12         9.8424   10.1956   -0.1206 CT         2 PRY     -0.394216
-     26 H8          6.4004    8.9625   -0.8827 H1         2 PRY      0.001584
-     27 H9          7.7956    8.3279   -0.0270 H1         2 PRY      0.001584
-     28 H10         6.5519   11.0514    0.6242 HA         2 PRY      0.192041
+     25 C12         9.8424   10.1955   -0.1205 CT         2 PRY     -0.394216
+     26 H8          6.4005    8.9625   -0.8827 H1         2 PRY      0.001584
+     27 H9          7.7956    8.3279   -0.0269 H1         2 PRY      0.001584
+     28 H10         6.5520   11.0514    0.6242 HA         2 PRY      0.192041
      29 H11         9.2372   12.9117   -0.2975 HC         2 PRY      0.110363
-     30 H12         9.5134   12.5228    1.3829 HC         2 PRY      0.110363
+     30 H12         9.5134   12.5228    1.3830 HC         2 PRY      0.110363
      31 H13         7.8882   12.9051    0.8297 HC         2 PRY      0.110363
-     32 H14        10.2558   10.6045   -1.0404 HC         2 PRY      0.110363
-     33 H15         9.6929    9.1354   -0.2690 HC         2 PRY      0.110363
+     32 H14        10.2558   10.6044   -1.0403 HC         2 PRY      0.110363
+     33 H15         9.6929    9.1353   -0.2689 HC         2 PRY      0.110363
      34 H16        10.6002   10.3206    0.6478 HC         2 PRY      0.110363
 @<TRIPOS>BOND
     1     1     3 1

From 253c9bc82a9e1961ef0876f2ba09e9e65ad42a5f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 20 Feb 2024 09:46:36 -0500
Subject: [PATCH 0555/1492] Have graft use the sequence builder

---
 src/Exec_Graft.cpp    | 32 +++++++++++++-------------------
 src/Exec_Sequence.cpp |  3 ++-
 2 files changed, 15 insertions(+), 20 deletions(-)

diff --git a/src/Exec_Graft.cpp b/src/Exec_Graft.cpp
index 21d3c1ce7b..dd88844705 100644
--- a/src/Exec_Graft.cpp
+++ b/src/Exec_Graft.cpp
@@ -471,9 +471,9 @@ const
   if (hasOrient1_)
     structureBuilder.SetAtomChirality(bondat1 + atomOffset, chi1_);
   // Generate internals around the link
-  if (structureBuilder.GenerateInternalsAroundLink( bondat1 + atomOffset,
-                                                    bondat0,
-                                                    frameOut, topOut, hasPosition, Cpptraj::Structure::Builder::SEQUENCE ) )
+  if (structureBuilder.GenerateInternalsAroundLink(bondat1 + atomOffset, bondat0,
+                                                   frameOut, topOut, hasPosition,
+                                                   Cpptraj::Structure::Builder::SEQUENCE) )
   {
     mprinterr("Error: Assign torsions around graft bond atoms %s - %s failed.\n",
               topOut.AtomMaskName(bondat1 + atomOffset).c_str(),
@@ -487,27 +487,21 @@ const
     return 1;
   }
   // Update internal coords from known positions
-  if (structureBuilder.UpdateICsFromFrame( frameOut, topOut, hasPosition )) {
-    mprinterr("Error: Failed to update Zmatrix with values from existing positions.\n");
-    return 1;
-  }
+  // NOTE: By definition, there are no known positions
+  //if (structureBuilder.UpdateICsFromFrame( frameOut, topOut, hasPosition )) {
+  //  mprinterr("Error: Failed to update Zmatrix with values from existing positions.\n");
+  //  return 1;
+  //}
   // Convert to Zmatrix and assign missing atom positions
-  if (structureBuilder.BuildFromInternals(frameOut, topOut, hasPosition)) {
+  if (structureBuilder.BuildSequenceFromInternals(frameOut, topOut, hasPosition,
+                                                  bondat1 + atomOffset,
+                                                  bondat0))
+  {
     mprinterr("Error: Grafting %s with %s build from internals failed.\n",
               mol0Top.c_str(), mol1Top.c_str());
     return 1;
   }
-//  Cpptraj::Structure::Zmatrix tmpz;
-//  tmpz.SetDebug( 1 ); // DEBUG
-//  if (structureBuilder.GetZmatrixFromInternals(tmpz, topOut)) {
-//    mprinterr("Error: Could not get Zmatrix from internals.\n");
-//    return 1;
-//  }
-//  if (tmpz.SetToFrame( frameOut, hasPosition )) {
-//    mprinterr("Error: Grafting %s with %s build from internals failed.\n",
-//              mol0Top.c_str(), mol1Top.c_str());
-//    return 1;
-//  }
+
   // Finalize topology - determine molecules, dont renumber residues, assign default bond params
   topOut.CommonSetup(true, false, true);
   topOut.Summary();
diff --git a/src/Exec_Sequence.cpp b/src/Exec_Sequence.cpp
index aeada226a5..ff5a787563 100644
--- a/src/Exec_Sequence.cpp
+++ b/src/Exec_Sequence.cpp
@@ -177,7 +177,8 @@ const
       topOut.AddBond( interResBonds[ires].first, interResBonds[ires].second );
       // Generate internals around the link
       if (structureBuilder.GenerateInternalsAroundLink(interResBonds[ires].first, interResBonds[ires].second,
-                                                        frameOut, topOut, hasPosition, Cpptraj::Structure::Builder::SEQUENCE))
+                                                       frameOut, topOut, hasPosition,
+                                                       Cpptraj::Structure::Builder::SEQUENCE))
       {
         mprinterr("Error: Assign torsions around inter-unit link %s - %s failed.\n",
                   topOut.AtomMaskName(interResBonds[ires].first).c_str(),

From 30648faaf93592b267ca0c08bd1b2d9982a92859 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 20 Feb 2024 09:48:23 -0500
Subject: [PATCH 0556/1492] Update for fixed sequence builder

---
 test/Test_Graft/IC.Nucleotide.pdb.save | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/Test_Graft/IC.Nucleotide.pdb.save b/test/Test_Graft/IC.Nucleotide.pdb.save
index 47c7f549ad..909bdbb338 100644
--- a/test/Test_Graft/IC.Nucleotide.pdb.save
+++ b/test/Test_Graft/IC.Nucleotide.pdb.save
@@ -26,8 +26,8 @@ ATOM     25  C2'  DA     1       5.383   1.772   2.252  1.00  0.00           C
 ATOM     26  H2'  DA     1       4.562   2.104   1.616  1.00  0.00           H  
 ATOM     27  O3'  DA     1       7.391   3.030   2.458  1.00  0.00           O  
 ATOM     28  P    DA     1       2.039   3.624   4.641  1.00  0.00           P  
-ATOM     29  O1P  DA     1       1.047   3.543   3.559  1.00  0.00           O  
-ATOM     30  O2P  DA     1       1.683   2.744   5.764  1.00  0.00           O  
+ATOM     29  O1P  DA     1       2.266   5.005   5.093  1.00  0.00           O  
+ATOM     30  O2P  DA     1       1.005   3.564   3.598  1.00  0.00           O  
 ATOM     31  O5'  DA     1       3.461   3.109   4.001  1.00  0.00           O  
 TER      32       DA     1 
 END   

From 91e44cce990db9ba114df2270e5d27cefd5c4260 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 20 Feb 2024 09:57:01 -0500
Subject: [PATCH 0557/1492] Add test save with wrong chirality around base
 sugar linkage; only used for regression test at this point

---
 ...leotide.wrongChirality.ic.charge.mol2.save | 83 +++++++++++++++++++
 test/Test_Sequence/RunTest.sh                 | 10 ++-
 2 files changed, 91 insertions(+), 2 deletions(-)
 create mode 100644 test/Test_Sequence/Nucleotide.wrongChirality.ic.charge.mol2.save

diff --git a/test/Test_Sequence/Nucleotide.wrongChirality.ic.charge.mol2.save b/test/Test_Sequence/Nucleotide.wrongChirality.ic.charge.mol2.save
new file mode 100644
index 0000000000..e965bd8f41
--- /dev/null
+++ b/test/Test_Sequence/Nucleotide.wrongChirality.ic.charge.mol2.save
@@ -0,0 +1,83 @@
+@<TRIPOS>MOLECULE
+Cpptraj Generated mol2 file.
+   34    36     3     0     0
+SMALL
+USER_CHARGES
+
+
+@<TRIPOS>ATOM
+      1 N1         -1.7830   -0.1470   -0.0030 N*         1 ADD     -0.148886
+      2 C2         -1.5590   -1.5030    0.0010 CK         1 ADD      0.127127
+      3 H2         -2.3800   -2.1940    0.0030 H5         1 ADD      0.171612
+      4 N2         -0.3010   -1.8360   -0.0000 NB         1 ADD     -0.519773
+      5 C3          0.3630   -0.6210   -0.0050 CB         1 ADD     -0.084209
+      6 C4          1.7210   -0.2690   -0.0050 CA         1 ADD      0.860405
+      7 N3          2.7060   -1.1900   -0.0320 N2         1 ADD     -0.911090
+      8 H3          3.6400   -0.8830    0.1180 H          1 ADD      0.439926
+      9 H4          2.4860   -2.1470    0.1200 H          1 ADD      0.439926
+     10 N4          2.0450    1.0240    0.0040 NC         1 ADD     -0.782117
+     11 C5          1.0670    1.9280    0.0020 CQ         1 ADD      0.650264
+     12 H5          1.3920    2.9540    0.0070 H5         1 ADD      0.059220
+     13 N5         -0.2370    1.7300   -0.0020 NC         1 ADD     -0.751966
+     14 C6         -0.5410    0.4290   -0.0040 CB         1 ADD      0.565561
+     15 C1         -1.4030    1.1595    4.3469 CT         2 DDD      0.257703
+     16 H2         -1.2516    0.2160    4.8537 H1         2 DDD      0.015048
+     17 H3         -0.7109    1.8823    4.7767 H1         2 DDD      0.015048
+     18 C2         -1.0861    0.9657    2.8717 CT         2 DDD      0.233200
+     19 H4         -0.0242    0.7374    2.7879 H1         2 DDD     -0.002355
+     20 O2         -1.8298   -0.1171    2.3762 OS         2 DDD     -0.421059
+     21 C3         -2.5628    0.2353    1.2200 CT         2 DDD      0.589631
+     22 H5         -3.5149   -0.2886    1.2217 H1         2 DDD     -0.011915
+     23 C5         -1.5270    2.2751    1.8280 CT         2 DDD      0.329642
+     24 H9         -1.6604    3.2377    2.3180 H1         2 DDD      0.001219
+     25 C6         -2.8115    1.7412    1.2156 CT         2 DDD     -0.228214
+     26 H10        -3.6473    1.9297    1.8794 HC         2 DDD      0.093721
+     27 O3         -0.5861    2.4017    0.7905 OH         2 DDD     -0.578369
+     28 P1         -3.1597    1.8046    6.0424 P          3 MP1      0.672814
+     29 C2         -4.8803    2.3221    5.9787 CT         3 MP1     -0.603494
+     30 O2         -3.0028    0.6180    6.8648 O2         3 MP1     -1.029416
+     31 O3         -2.8282    1.6018    4.4990 OS         3 MP1     -0.644721
+     32 H7         -5.4834    1.4923    5.6307 HC         3 MP1      0.065172
+     33 H8         -5.0263    3.1602    5.3092 HC         3 MP1      0.065172
+     34 H9         -5.2096    2.5963    6.9743 HC         3 MP1      0.065172
+@<TRIPOS>BOND
+    1     1     2 1
+    2     1    14 1
+    3     2     4 1
+    4     4     5 1
+    5     5     6 1
+    6     5    14 1
+    7     6     7 1
+    8     6    10 1
+    9    10    11 1
+   10    11    13 1
+   11    13    14 1
+   12    15    18 1
+   13    18    20 1
+   14    18    23 1
+   15    20    21 1
+   16    21    25 1
+   17    23    25 1
+   18    23    27 1
+   19    28    29 1
+   20    28    30 1
+   21    28    31 1
+   22    21     1 1
+   23    31    15 1
+   24     2     3 1
+   25     7     8 1
+   26     7     9 1
+   27    11    12 1
+   28    15    16 1
+   29    15    17 1
+   30    18    19 1
+   31    21    22 1
+   32    23    24 1
+   33    25    26 1
+   34    29    32 1
+   35    29    33 1
+   36    29    34 1
+@<TRIPOS>SUBSTRUCTURE
+      1 ADD               1 ****               0 ****  **** 
+      2 DDD              15 ****               0 ****  **** 
+      3 MP1              28 ****               0 ****  **** 
diff --git a/test/Test_Sequence/RunTest.sh b/test/Test_Sequence/RunTest.sh
index cacf3e9a90..3b75d54222 100755
--- a/test/Test_Sequence/RunTest.sh
+++ b/test/Test_Sequence/RunTest.sh
@@ -49,8 +49,13 @@ EOF
 }
 
 # Link nucleic acid base + sugar + phosphate, IC, fix charges.
+# NOTE: This is not really how something like this should be
+#       constructed since after atoms are stripped from the sugar
+#       the original chirality is lost; sequence then builds in a
+#       default chirality which is not correct for nucleic acids.
+#       This test is purely a regression test.
 DNAic_charge() {
-  UNITNAME="$TESTNAME, Construct Nucleic Acid, IC, fix charges"
+  UNITNAME="$TESTNAME, Construct fake Nucleic Acid, IC, fix charges"
   CheckFor maxthreads 1
   if [ $? -eq 0 ] ; then
     cat > cpptraj.in <<EOF
@@ -75,7 +80,8 @@ charge crdset MyMol *
 crdout MyMol Nucleotide.ic.charge.mol2
 EOF
     RunCpptraj "$UNITNAME"
-    DoTest Nucleotide.ic.charge.mol2.save Nucleotide.ic.charge.mol2
+    #DoTest Nucleotide.ic.charge.mol2.save Nucleotide.ic.charge.mol2
+    DoTest Nucleotide.wrongChirality.ic.charge.mol2.save Nucleotide.ic.charge.mol2
   fi
 }
 

From cc5eb0f1ec51aa86d8b535fa0340fd16b793641d Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 20 Feb 2024 09:57:25 -0500
Subject: [PATCH 0558/1492] Remove unused code

---
 src/Exec_Graft.cpp        | 22 ----------------------
 src/Structure/Builder.cpp | 16 ----------------
 2 files changed, 38 deletions(-)

diff --git a/src/Exec_Graft.cpp b/src/Exec_Graft.cpp
index dd88844705..3de6547096 100644
--- a/src/Exec_Graft.cpp
+++ b/src/Exec_Graft.cpp
@@ -508,28 +508,6 @@ const
   // Add to output data set
   if (outCoords->CoordsSetup(topOut, frameOut.CoordsInfo())) return 1;
   outCoords->AddFrame( frameOut );
-/*
-  Topology combinedTop;
-  combinedTop.SetDebug( debug_ );
-  combinedTop.SetParmName( outCoords->Meta().Name(), FileName() );
-  combinedTop.AppendTop( mol0Top );
-  combinedTop.SetParmBox( mol0frm.BoxCrd() );
-  if (debug_ > 0)
-    combinedTop.Brief("Grafted parm:");
-
-  Frame CombinedFrame = mol0frm;
-  Builder builder;
-  builder.SetDebug( debug_ );
-  if (builder.Combine( combinedTop, CombinedFrame, mol1Top, mol1frm, bondat0, bondat1 )) {
-    mprinterr("Error: Fragment combine failed.\n");
-    return 1;
-  }
-
-  // Add topology to output COORDS set
-  if (outCoords->CoordsSetup(combinedTop, CombinedFrame.CoordsInfo())) return 1;
-
-  // Add frame to the output data set
-  outCoords->AddFrame( CombinedFrame );*/
 
   return 0;
 }
diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 4f0f2eef73..4c9733570e 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1828,22 +1828,6 @@ const
         {
           if (!hasPosition[*bat]) {
             if (buildCoordsForAtom(*bat, frameOut, topIn, hasPosition)) {
-/*            // Find an internal coordinate.
-            InternalCoords ic;
-            if (getIcFromInternals(ic, *bat, hasPosition)) {
-              printAllInternalsForAtom(*bat, topIn, hasPosition); // DEBUG
-
-              mprintf("Building atom %s using torsion/angle/bond\n", topIn.LeapName(*bat).c_str());
-              mprintf("Using - %s - %s - %s\n",
-                      topIn.LeapName(ic.AtJ()).c_str(),
-                      topIn.LeapName(ic.AtK()).c_str(),
-                      topIn.LeapName(ic.AtL()).c_str());
-              mprintf( "Torsion = %f\n", ic.Phi() );
-              mprintf( "Angle   = %f\n", ic.Theta() );
-              mprintf( "Bond    = %f\n", ic.Dist() );
-              Vec3 posI = Zmatrix::AtomIposition(ic, frameOut);
-              mprintf( "ZMatrixAll:  %f,%f,%f\n", posI[0], posI[1], posI[2]);
-              frameOut.SetXYZ( ic.AtI(), posI );*/
               hasPosition[ *bat ] = true;
               nAtomsBuilt++;
               nAtomsThatNeedPositions--;

From 7d13adc03d45f9c304bd0a867a3c491640a024d8 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 20 Feb 2024 10:25:24 -0500
Subject: [PATCH 0559/1492] Hide some debug info

---
 src/Structure/Builder.cpp | 36 ++++++++++++++++++++++++++----------
 1 file changed, 26 insertions(+), 10 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 4c9733570e..fb45a249a5 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -606,6 +606,7 @@ int Cpptraj::Structure::Builder::TorsionModel::BuildMockExternals(Iarray const&
     mprinterr("Internal Error: TorsionModel::BuildMockExternals() called with no internal torsions.\n");
     return 1;
   }
+# ifdef CPPTRAJ_DEBUG_BUILDER
   mprintf("=======  Started mock coords from: %s\n", topIn.LeapName(internalTorsionsIn[iaTorsions.front()].AtI()).c_str());
   mprintf("========  %zu Torsions to build mock coords from:\n", iaTorsions.size());
   for (Iarray::const_iterator idx = iaTorsions.begin(); idx != iaTorsions.end(); ++idx) {
@@ -617,7 +618,7 @@ int Cpptraj::Structure::Builder::TorsionModel::BuildMockExternals(Iarray const&
             topIn.LeapName(ic.AtL()).c_str(),
             ic.PhiVal()*Constants::RADDEG);
   }
-
+# endif
   // Define coordinates for the central atoms.
   //Vec3 posX(0, 0, 0);
   //Vec3 posY(1, 0, 0);
@@ -695,6 +696,7 @@ int Cpptraj::Structure::Builder::TorsionModel::BuildMockExternals(Iarray const&
         }
         if (tgt != outerAtoms.end()) {
           //gotOne = true;
+#         ifdef CPPTRAJ_DEBUG_BUILDER
           mprintf("======= Building mock coord for: %s\n", topIn.LeapName(tgt->Idx()).c_str());
           mprintf("======= Using torsion: %s - %s - %s - %s (p1known= %i, p4known= %i)\n",
                    topIn.LeapName(iInt.AtI()).c_str(),
@@ -702,9 +704,12 @@ int Cpptraj::Structure::Builder::TorsionModel::BuildMockExternals(Iarray const&
                    topIn.LeapName(iInt.AtK()).c_str(),
                    topIn.LeapName(iInt.AtL()).c_str(),
                    (int)tmpAt1->Known(), (int)tmpAt4->Known());
+#         endif
           // Now build the coordinate for the target atom
           tgt->SetPos( Zmatrix::AtomIposition(maPC1, maPC2, knownAt->Pos(), 1.0, 90.0, iInt.PhiVal()*Constants::RADDEG) );
+#         ifdef CPPTRAJ_DEBUG_BUILDER
           mprintf("ZMatrixAll:  %f,%f,%f\n", tgt->Pos()[0], tgt->Pos()[1], tgt->Pos()[2]);
+#         endif
           used[jdx] = true;
           nused++;
           break;
@@ -1166,11 +1171,13 @@ int Builder::assignTorsionsAroundBond(int a1, int a2, Frame const& frameIn, Topo
     Hy = H2;
   }
   static const char* hstr[] = { "SP1", "SP2", "SP3", "Unknown" };
-  mprintf("DEBUG: assignTorsionsAroundBond: AX= %s (%s)  AY= %s (%s), aAtomIdx= %i",
-          *(topIn[ax].Name()), hstr[Hx],
-          *(topIn[ay].Name()), hstr[Hy], aAtomIdx+1);
-  if (aAtomIdx != -1) mprintf(" %s", topIn.AtomMaskName(aAtomIdx).c_str()); // DEBUG
-  mprintf("\n"); // DEBUG
+  if (debug_ > 0) {
+    mprintf("DEBUG: assignTorsionsAroundBond: AX= %s (%s)  AY= %s (%s), aAtomIdx= %i",
+            *(topIn[ax].Name()), hstr[Hx],
+            *(topIn[ay].Name()), hstr[Hy], aAtomIdx+1);
+    if (aAtomIdx != -1) mprintf(" %s", topIn.AtomMaskName(aAtomIdx).c_str()); // DEBUG
+    mprintf("\n"); // DEBUG
+  }
   TorsionModel mT;
   if (mT.InitTorsion( ax, ay, frameIn, topIn, hasPosition, aAtomIdx )) {
     mprinterr("Error: Could not init model torsion.\n");
@@ -1180,30 +1187,39 @@ int Builder::assignTorsionsAroundBond(int a1, int a2, Frame const& frameIn, Topo
   // whose position is known.
   //Atom const& AX = topIn[ax];
   //Atom const& AY = topIn[ay];
+# ifdef CPPTRAJ_DEBUG_BUILDER
   mprintf("bKnownX=%i  bKnownY=%i\n", (int)mT.AxHasKnownAtoms(), (int)mT.AyHasKnownAtoms());
+# endif
   if (!(mT.AxHasKnownAtoms() && mT.AyHasKnownAtoms())) {
     // Find any existing internal coords around ax-ay
     Iarray iTorsions = getExistingTorsionIdxs(ax, ay);
     if (!iTorsions.empty()) {
+#     ifdef CPPTRAJ_DEBUG_BUILDER
       mprintf("Using INTERNALs to fit new torsions around: %s - %s\n",
               topIn.LeapName(ax).c_str(), topIn.LeapName(ay).c_str());
+#     endif
       if (mT.BuildMockExternals(iTorsions, internalTorsions_, topIn)) {
         mprinterr("Error: Building mock externals around %s - %s failed.\n",
                   topIn.AtomMaskName(ax).c_str(), topIn.AtomMaskName(ay).c_str());
         return 1;
       }
-      //return 0; // FIXME DEBUG 
-    } else {
+    } 
+#   ifdef CPPTRAJ_DEBUG_BUILDER
+      else {
       mprintf("Completely free in assigning new torsions for: %s - %s\n",
               topIn.LeapName(ax).c_str(), topIn.LeapName(ay).c_str());
-      //return 0; // FIXME DEBUG 
     }
-  } else {
+#   endif
+  }
+
+# ifdef CPPTRAJ_DEBUG_BUILDER
+    else {
     // Use existing atoms to determine torsions
     mprintf("Using externals to fit new torsions around: %s - %s\n",
             topIn.LeapName(ax).c_str(),
             topIn.LeapName(ay).c_str());
   }
+# endif
   // Get chiralities around X and Y if they exist
   double chiX = 0;
   int Xcidx = getExistingChiralityIdx( ax );

From 071b6c72fc1e9ff4a94f0c217de6dbec835d5841 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 20 Feb 2024 10:32:10 -0500
Subject: [PATCH 0560/1492] Hide more debug info

---
 src/Structure/Builder.cpp | 23 ++++++++++++++++++++++-
 1 file changed, 22 insertions(+), 1 deletion(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index fb45a249a5..5fa8e0a289 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -454,14 +454,20 @@ static inline double calculateOrientation(MockAtom const& iX, double chiX, Atom
       iB.Known())
   {
     dOrientation = VectorAtomChirality( iX.Pos(), iA.Pos(), iY.Pos(), iB.Pos() );
+#   ifdef CPPTRAJ_DEBUG_BUILDER
     mprintf("ORIENTATION: known = %f\n", dOrientation);
+#   endif
   } else {
     double dChi = chiX;
     if (fabs(dChi) < Constants::SMALL) {
+#     ifdef CPPTRAJ_DEBUG_BUILDER
       mprintf("default chirality on\n");
+#     endif
       dChi = 1.0;
     }
+#   ifdef CPPTRAJ_DEBUG_BUILDER
     mprintf("ORIENTATION: Chirality %f\n", dChi);
+#   endif
     dOrientation = chiralityToOrientation(dChi, AX, iA.Idx(), iY.Idx(), iB.Idx(), -1);
   }
   return dOrientation;
@@ -550,6 +556,7 @@ int Cpptraj::Structure::Builder::TorsionModel::SetupTorsion(AtomType::Hybridizat
     else
       Yorientation_ = calculateOrientation( atY_, chiY, topIn[atY_.Idx()], sorted_ay_[0], atX_, sorted_ay_[1] );
   }
+# ifdef CPPTRAJ_DEBUG_BUILDER
   // DEBUG
   Atom const& AX = topIn[atX_.Idx()];
   Atom const& AY = topIn[atY_.Idx()];
@@ -567,6 +574,7 @@ int Cpptraj::Structure::Builder::TorsionModel::SetupTorsion(AtomType::Hybridizat
   //mprintf("}\n");
   for (Marray::const_iterator it = sorted_ay_.begin(); it != sorted_ay_.end(); ++it)
       mprintf("Atom %li: %s (%i) (build=%i)\n", it - sorted_ay_.begin(), *(topIn[it->Idx()].Name()), (int)it->Known(), (int)it->BuildInternals());
+# endif
   // Calculate the actual torsion angle between A-X-Y-D
   if (sorted_ax_[0].Known() &&
       atX_.Known() &&
@@ -580,7 +588,9 @@ int Cpptraj::Structure::Builder::TorsionModel::SetupTorsion(AtomType::Hybridizat
   } else {
     dAbsolute_ = 180.0 * Constants::DEGRAD;
   }
+# ifdef CPPTRAJ_DEBUG_BUILDER
   mprintf("DABSOLUTE= %g\n", dAbsolute_);
+# endif
   return 0;
 }
 
@@ -978,13 +988,17 @@ void Builder::ModelTorsion(TorsionModel const& MT, unsigned int iBondX, unsigned
   if (iBondX >= MT.SortedAx().size() ||
       iBondY >= MT.SortedAy().size())
     return;
+# ifdef CPPTRAJ_DEBUG_BUILDER
   mprintf("CALLING ModelTorsion for iBondX=%u iBondY=%u dVal=%g\n",iBondX,iBondY,dvalIn*Constants::RADDEG);
+# endif
   MockAtom const& AA = MT.SortedAx()[iBondX];
   MockAtom const& AX = MT.AtX();
   MockAtom const& AY = MT.AtY();
   MockAtom const& AD = MT.SortedAy()[iBondY];
   if ( !(AA.BuildInternals() || AD.BuildInternals()) ) {
+#   ifdef CPPTRAJ_DEBUG_BUILDER
     mprintf("%s does not need internals.\n", *((*currentTop_)[AA.Idx()].Name()));
+#   endif
     return;
   }
   int aa = AA.Idx();
@@ -1004,7 +1018,9 @@ void Builder::ModelTorsion(TorsionModel const& MT, unsigned int iBondX, unsigned
                       AX.Pos().Dptr(),
                       AY.Pos().Dptr(),
                       AD.Pos().Dptr() );
+#   ifdef CPPTRAJ_DEBUG_BUILDER
     mprintf(" %s replacing dval with %f\n", *((*currentTop_)[aa].Name()), phiVal*Constants::RADDEG);
+#   endif
   }
   // Look for an existing internal
   int icIdx = getExistingTorsionIdx( aa, ax, ay, ad );
@@ -1211,7 +1227,6 @@ int Builder::assignTorsionsAroundBond(int a1, int a2, Frame const& frameIn, Topo
     }
 #   endif
   }
-
 # ifdef CPPTRAJ_DEBUG_BUILDER
     else {
     // Use existing atoms to determine torsions
@@ -1238,13 +1253,19 @@ int Builder::assignTorsionsAroundBond(int a1, int a2, Frame const& frameIn, Topo
 
   // Build the new internals
   if (Hx == AtomType::SP3 && Hy == AtomType::SP3) {
+#   ifdef CPPTRAJ_DEBUG_BUILDER
     mprintf("SP3 SP3\n");
+#   endif
     createSp3Sp3Torsions(mT);
   } else if (Hx == AtomType::SP3 && Hy == AtomType::SP2) {
+#   ifdef CPPTRAJ_DEBUG_BUILDER
     mprintf("SP3 SP2\n");
+#   endif
     createSp3Sp2Torsions(mT);
   } else if (Hx == AtomType::SP2 && Hy == AtomType::SP2) {
+#   ifdef CPPTRAJ_DEBUG_BUILDER
     mprintf("SP2 SP2\n");
+#   endif
     createSp2Sp2Torsions(mT);
   } else {
     mprinterr("Error: Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported\n"

From 852b60f8b111ac10a45fdfa12673e3b83d171972 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 20 Feb 2024 10:36:03 -0500
Subject: [PATCH 0561/1492] Hide more debug info

---
 src/Structure/Builder.cpp | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 5fa8e0a289..7c1ba94ffb 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1332,9 +1332,11 @@ int Builder::determineChirality(double& dChi, int at, Frame const& frameIn, Topo
   }
   // Only check atoms with 3 or 4 bonds
   Atom const& A0 = topIn[at];
+# ifdef CPPTRAJ_DEBUG_BUILDER
   mprintf("CHIRALITY CALCULATION FOR %s (nbonds= %i)\n", *(A0.Name()), A0.Nbonds());
   for (Atom::bond_iterator bat = A0.bondbegin(); bat != A0.bondend(); ++bat)
     mprintf("\tneighbor %s (id= %i) [%i]\n", *(topIn[*bat].Name()), *bat, (int)hasPosition[*bat]);
+# endif
   if ( A0.Nbonds() == 3 ||
        A0.Nbonds() == 4 )
   {
@@ -1348,12 +1350,12 @@ int Builder::determineChirality(double& dChi, int at, Frame const& frameIn, Topo
     bool knowB = (aAtomB != -1 && hasPosition[aAtomB]);
     bool knowC = (aAtomC != -1 && hasPosition[aAtomC]);
     bool knowD = (aAtomD != -1 && hasPosition[aAtomD]);
-
+#   ifdef CPPTRAJ_DEBUG_BUILDER
     if (knowA) mprintf("Chirality order A %s %i\n", *(topIn[aAtomA].Name()), aAtomA);
     if (knowB) mprintf("Chirality order B %s %i\n", *(topIn[aAtomB].Name()), aAtomB);
     if (knowC) mprintf("Chirality order C %s %i\n", *(topIn[aAtomC].Name()), aAtomC);
     if (knowD) mprintf("Chirality order D %s %i\n", *(topIn[aAtomD].Name()), aAtomD);
-
+#   endif
     Vec3 vPA, vPB, vPC, vPD;
     if (knowA) vPA = Vec3(frameIn.XYZ(aAtomA));
     if (knowB) vPB = Vec3(frameIn.XYZ(aAtomB));
@@ -1461,7 +1463,9 @@ int Builder::generateAtomInternals(int at, Frame const& frameIn, Topology const&
                topIn.LeapName(*cat).c_str());
         Iarray iTorsions = getExistingTorsionIdxs(*bat, *cat);
         int iShouldBe = (AtB.Nbonds() - 1) * (AtC.Nbonds() - 1);
+#       ifdef CPPTRAJ_DEBUG_BUILDER
         mprintf("ISHOULDBE= %i ITORSIONS= %zu\n", iShouldBe, iTorsions.size());
+#       endif
         if (iShouldBe != (int)iTorsions.size()) {
           assignTorsionsAroundBond(*bat, *cat, frameIn, topIn, hasPosition, at);
         }

From dbdda7103e67898e4032cc4a8ece80f1c77c10ae Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 20 Feb 2024 11:19:59 -0500
Subject: [PATCH 0562/1492] Set proper debug levels. Hide more debug info.

---
 src/Exec_Build.cpp        |  6 ++++--
 src/Exec_Build.h          |  6 ++++--
 src/Exec_Graft.cpp        |  8 ++++----
 src/Exec_Sequence.cpp     |  2 +-
 src/Structure/Builder.cpp | 32 ++++++++++++++++++--------------
 5 files changed, 31 insertions(+), 23 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 0bd7601dac..03337251a9 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -34,6 +34,7 @@ std::vector<int> Exec_Build::MapAtomsToTemplate(Topology const& topIn,
 int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
                                        Topology const& topIn, Frame const& frameIn,
                                        Cpptraj::Structure::Creator const& creator)
+const
 {
   // Array of head/tail connect atoms for each residue
   typedef std::vector<int> Iarray;
@@ -385,7 +386,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
     if (*it > -1) {
       // Residue has atom offset which indicates it needs something built.
       Cpptraj::Structure::Builder structureBuilder;// = new Cpptraj::Structure::Builder();
-      structureBuilder.SetDebug( 1 ); // DEBUG FIXME
+      structureBuilder.SetDebug( debug_ );
       if (creator.HasMainParmSet())
         structureBuilder.SetParameters( creator.MainParmSetPtr() );
       // Generate internals from the template, update indices to this topology.
@@ -471,6 +472,7 @@ void Exec_Build::Help() const
 // Exec_Build::Execute()
 Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
 {
+  debug_ = State.Debug();
 /*  // Atom scan direction
   std::string atomscandir = argIn.GetStringKey("atomscandir");
   if (!atomscandir.empty()) {
@@ -575,7 +577,7 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
 
   // Get templates and parameter sets.
   Cpptraj::Structure::Creator creator;
-  if (creator.InitCreator(argIn, State.DSL(), State.Debug())) {
+  if (creator.InitCreator(argIn, State.DSL(), debug_)) {
     return CpptrajState::ERR;
   }
   if (!creator.HasTemplates()) {
diff --git a/src/Exec_Build.h b/src/Exec_Build.h
index 38464c106c..f6dd1f4090 100644
--- a/src/Exec_Build.h
+++ b/src/Exec_Build.h
@@ -9,14 +9,16 @@ class Creator;
 /// Used to build a structure 
 class Exec_Build : public Exec {
   public:
-    Exec_Build() : Exec(GENERAL) {}
+    Exec_Build() : Exec(GENERAL), debug_() {}
     void Help() const;
     DispatchObject* Alloc() const { return (DispatchObject*)new Exec_Build(); }
     RetType Execute(CpptrajState&, ArgList&);
   private:
     /// Create new topology/frame using templates
-    static int FillAtomsWithTemplates(Topology&, Frame&, Topology const&, Frame const&, Cpptraj::Structure::Creator const&);
+    int FillAtomsWithTemplates(Topology&, Frame&, Topology const&, Frame const&, Cpptraj::Structure::Creator const&) const;
     /// Map atoms in topology to template
     static std::vector<int> MapAtomsToTemplate(Topology const&, int, DataSet_Coords*);
+
+    int debug_;
 };
 #endif
diff --git a/src/Exec_Graft.cpp b/src/Exec_Graft.cpp
index 3de6547096..e165f2da9a 100644
--- a/src/Exec_Graft.cpp
+++ b/src/Exec_Graft.cpp
@@ -445,12 +445,12 @@ const
     //        topOut.TruncResNameOnumId(topOut[it->second].ResNum()).c_str(), *(topOut[it->second].Name()));
     topOut.AddBond(it->first, it->second);
   }
-  // FIXME
-  for (int at = 0; at != topOut.Natom(); at++)
-    mprintf("\t%6i %s %s\n", at+1, topOut.AtomMaskName(at).c_str(), *(topOut.Res(topOut[at].ResNum()).Name()));
+  // DEBUG
+  //for (int at = 0; at != topOut.Natom(); at++)
+  //  mprintf("\t%6i %s %s\n", at+1, topOut.AtomMaskName(at).c_str(), *(topOut.Res(topOut[at].ResNum()).Name()));
   // Build
   Cpptraj::Structure::Builder structureBuilder;
-  structureBuilder.SetDebug( 1 ); // DEBUG FIXME
+  structureBuilder.SetDebug( debug_ );
   if (structureBuilder.GenerateInternals( mol1frm, mol1Top,
                                           std::vector<bool>(mol1Top.Natom(), true) ))
   {
diff --git a/src/Exec_Sequence.cpp b/src/Exec_Sequence.cpp
index ff5a787563..22b1158530 100644
--- a/src/Exec_Sequence.cpp
+++ b/src/Exec_Sequence.cpp
@@ -152,7 +152,7 @@ const
     if (*it > -1) {
       // Residue has atom offset which indicates it needs something built.
       Cpptraj::Structure::Builder structureBuilder;// = new Cpptraj::Structure::Builder();
-      structureBuilder.SetDebug( 1 ); // DEBUG FIXME
+      structureBuilder.SetDebug( debug_ );
       if (creator.HasMainParmSet())
         structureBuilder.SetParameters( creator.MainParmSetPtr() );
       // Generate internals from the template, update indices to this topology.
diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 7c1ba94ffb..526f977010 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1593,7 +1593,7 @@ int Builder::GenerateInternalsAroundLink(int at0, int at1,
   Iarray span_atoms = GenerateSpanningTree(at0, actualAt1, 4, topIn.Atoms());
   for (Iarray::const_iterator it = span_atoms.begin(); it != span_atoms.end(); ++it)
   {
-    mprintf("SPANNING TREE ATOM: %s\n", *(topIn[*it].Name()));
+    //mprintf("SPANNING TREE ATOM: %s\n", *(topIn[*it].Name()));
     if (generateAtomInternals(*it, frameIn, topIn, tmpHasPosition)) {
       mprinterr("Error: Could not generate internals for atom %s\n", topIn.AtomMaskName(*it).c_str());
       return 1;
@@ -1738,17 +1738,18 @@ const
   InternalCoords ic;
   if (getIcFromInternals(ic, at, hasPosition)) {
     //printAllInternalsForAtom(at, topIn, hasPosition); // DEBUG
-
-    mprintf("Building atom %s using torsion/angle/bond\n", topIn.LeapName(at).c_str());
-    mprintf("Using - %s - %s - %s\n",
-            topIn.LeapName(ic.AtJ()).c_str(),
-            topIn.LeapName(ic.AtK()).c_str(),
-            topIn.LeapName(ic.AtL()).c_str());
-    mprintf( "Torsion = %f\n", ic.Phi() );
-    mprintf( "Angle   = %f\n", ic.Theta() );
-    mprintf( "Bond    = %f\n", ic.Dist() );
     Vec3 posI = Zmatrix::AtomIposition(ic, frameOut);
-    mprintf( "ZMatrixAll:  %f,%f,%f\n", posI[0], posI[1], posI[2]);
+    if (debug_ > 1) {
+      mprintf("Building atom %s using torsion/angle/bond\n", topIn.LeapName(at).c_str());
+      mprintf("Using - %s - %s - %s\n",
+              topIn.LeapName(ic.AtJ()).c_str(),
+              topIn.LeapName(ic.AtK()).c_str(),
+              topIn.LeapName(ic.AtL()).c_str());
+      mprintf( "Torsion = %f\n", ic.Phi() );
+      mprintf( "Angle   = %f\n", ic.Theta() );
+      mprintf( "Bond    = %f\n", ic.Dist() );
+      mprintf( "ZMatrixAll:  %f,%f,%f\n", posI[0], posI[1], posI[2]);
+    }
     frameOut.SetXYZ( ic.AtI(), posI );
     return 1;
   }
@@ -1771,7 +1772,8 @@ const
                                         it != atomIndices.end(); ++it)
     if (!hasPosition[*it])
       nAtomsThatNeedPositions++;
-  mprintf("DEBUG: %u atoms need positions.\n", nAtomsThatNeedPositions);
+  if (debug_ > 0)
+    mprintf("DEBUG: %u atoms need positions.\n", nAtomsThatNeedPositions);
   if (nAtomsThatNeedPositions == 0) return 0;
 
   // Loop over residue atoms
@@ -1835,7 +1837,8 @@ const
                                         it != atomIndices.end(); ++it)
     if (!hasPosition[*it])
       nAtomsThatNeedPositions++;
-  mprintf("DEBUG: %u atoms need positions.\n", nAtomsThatNeedPositions);
+  if (debug_ > 0)
+    mprintf("DEBUG: %u atoms need positions.\n", nAtomsThatNeedPositions);
   if (nAtomsThatNeedPositions == 0) return 0;
 
   // Loop over residue atoms
@@ -1863,7 +1866,8 @@ const
       }
       // Build unknown positions around known atom
       if (atToBuildAround != -1) {
-        mprintf("Building externals from %s\n", topIn.LeapName(atToBuildAround).c_str());
+        if (debug_ > 0)
+          mprintf("Building externals from %s\n", topIn.LeapName(atToBuildAround).c_str());
         Atom const& bAtom = topIn[atToBuildAround];
         for (Atom::bond_iterator bat = bAtom.bondbegin(); bat != bAtom.bondend(); ++bat)
         {

From d6f60831509e9ac622a4ace6ae7ff696d9f6d007 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 20 Feb 2024 11:29:16 -0500
Subject: [PATCH 0563/1492] Hide more debug info. Replace unneeded extra
 variable

---
 src/Structure/Builder.cpp | 116 +++++++++++++++++++++-----------------
 1 file changed, 63 insertions(+), 53 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 526f977010..29545e61d4 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -191,7 +191,7 @@ int Builder::AdjustIcAroundLink(int at0, int at1, Frame const& frameIn, Topology
   */
 int Builder::UpdateICsFromFrame(Frame const& frameIn, Topology const& topIn, Barray const& hasPosition)
 {
-  // Create a list of residues that have atoms with internals 
+  // Create a list of residues that have atoms with internals TODO combine with residuesThatNeedPositions()?
   std::vector<Residue> residues;
   std::vector<int> Rnums;
   for (Tarray::const_iterator dih = internalTorsions_.begin();
@@ -206,7 +206,8 @@ int Builder::UpdateICsFromFrame(Frame const& frameIn, Topology const& topIn, Bar
       }
     }
     if (!has_rnum) {
-      mprintf("DEBUG: Residue %s has internals.\n", topIn.TruncResNameNum(rnum).c_str());
+      if (debug_ > 0)
+        mprintf("DEBUG: Residue %s has internals.\n", topIn.TruncResNameNum(rnum).c_str());
       residues.push_back( topIn.Res(rnum) );
       Rnums.push_back(rnum);
     }
@@ -214,55 +215,59 @@ int Builder::UpdateICsFromFrame(Frame const& frameIn, Topology const& topIn, Bar
   // Get list of bonds.
   BondArray myBonds = GenerateBondArray( residues, topIn.Atoms() );
   for (BondArray::const_iterator bnd = myBonds.begin(); bnd != myBonds.end(); ++bnd) {
-    //if (topIn[bnd->A1()].ResNum() == ires && topIn[bnd->A2()].ResNum() == ires) {
+    if (debug_ > 1)
       mprintf("Looking at torsions around: %s - %s\n", topIn.LeapName(bnd->A1()).c_str(), topIn.LeapName(bnd->A2()).c_str());
-      // Find all ICs that share atoms 1 and 2 (J and K)
-      bool needsUpdate = false;
-      double tDiff = 0;
-      Iarray iTorsions = getExistingTorsionIdxs(bnd->A1(), bnd->A2());
-      for (Iarray::const_iterator idx = iTorsions.begin(); idx != iTorsions.end(); ++idx)
+    // Find all ICs that share atoms 1 and 2 (J and K)
+    bool needsUpdate = false;
+    double tDiff = 0;
+    Iarray iTorsions = getExistingTorsionIdxs(bnd->A1(), bnd->A2());
+    for (Iarray::const_iterator idx = iTorsions.begin(); idx != iTorsions.end(); ++idx)
+    {
+      InternalTorsion const& dih = internalTorsions_[*idx];
+      if (hasPosition[dih.AtI()] &&
+          hasPosition[dih.AtJ()] &&
+          hasPosition[dih.AtK()] &&
+          hasPosition[dih.AtL()])
       {
-        InternalTorsion const& dih = internalTorsions_[*idx];
-        if (hasPosition[dih.AtI()] &&
-            hasPosition[dih.AtJ()] &&
-            hasPosition[dih.AtK()] &&
-            hasPosition[dih.AtL()])
-        {
+        if (debug_ > 1)
           mprintf("Measuring torsion of fixed atoms: %s - %s - %s - %s\n",
                   topIn.LeapName(dih.AtI()).c_str(),
                   topIn.LeapName(dih.AtJ()).c_str(),
                   topIn.LeapName(dih.AtK()).c_str(),
                   topIn.LeapName(dih.AtL()).c_str());
-          double dTorsion = Torsion(frameIn.XYZ(dih.AtI()),
-                                    frameIn.XYZ(dih.AtJ()),
-                                    frameIn.XYZ(dih.AtK()),
-                                    frameIn.XYZ(dih.AtL()));
-          double dInternalValue = dih.PhiVal();
-          tDiff = (dTorsion - dInternalValue);
+        double dTorsion = Torsion(frameIn.XYZ(dih.AtI()),
+                                  frameIn.XYZ(dih.AtJ()),
+                                  frameIn.XYZ(dih.AtK()),
+                                  frameIn.XYZ(dih.AtL()));
+        double dInternalValue = dih.PhiVal();
+        tDiff = (dTorsion - dInternalValue);
+        if (debug_ > 1)
           mprintf("\tdTorsion= %f  dInternalValue= %f\n", dTorsion, dInternalValue);
-          needsUpdate = true;
-        } // END all coords present
-      } // END loop over torsions matching current bond
-      // If any difference was found, shift all of the torsions
-      if (needsUpdate) {
+        needsUpdate = true;
+      } // END all coords present
+    } // END loop over torsions matching current bond
+    // If any difference was found, shift all of the torsions
+    if (needsUpdate) {
+      if (debug_ > 1)
         mprintf("Twisting torsions centered on %s - %s by %f degrees\n",
                 topIn.LeapName(bnd->A1()).c_str(),
                 topIn.LeapName(bnd->A2()).c_str(),
                 tDiff*Constants::RADDEG);
-        for (Iarray::const_iterator idx = iTorsions.begin(); idx != iTorsions.end(); ++idx)
-        {
-          InternalTorsion& dih = internalTorsions_[*idx];
-          double dNew = dih.PhiVal() + tDiff;
+      for (Iarray::const_iterator idx = iTorsions.begin(); idx != iTorsions.end(); ++idx)
+      {
+        InternalTorsion& dih = internalTorsions_[*idx];
+        double dNew = dih.PhiVal() + tDiff;
+        if (debug_ > 1) {
           mprintf("Twisting torsion for atoms: %s-%s-%s-%s\n",
                   *(topIn[dih.AtI()].Name()),
                   *(topIn[dih.AtJ()].Name()),
                   *(topIn[dih.AtK()].Name()),
                   *(topIn[dih.AtL()].Name()));
           mprintf("------- From %f to %f\n", dih.PhiVal()*Constants::RADDEG, dNew*Constants::RADDEG);
-          dih.SetPhiVal( dNew );
         }
-      } // END ICs need update
-    //} // END both bond atoms belong to this residue
+        dih.SetPhiVal( dNew );
+      }
+    } // END ICs need update
   } // END loop over bonds
   return 0;
 }
@@ -1025,14 +1030,16 @@ void Builder::ModelTorsion(TorsionModel const& MT, unsigned int iBondX, unsigned
   // Look for an existing internal
   int icIdx = getExistingTorsionIdx( aa, ax, ay, ad );
   if (icIdx < 0) {
-    mprintf("++++Torsion INTERNAL: %f to %s - %s - %s - %s\n", phiVal*Constants::RADDEG,
-            currentTop_->LeapName(aa).c_str(),
-            currentTop_->LeapName(ax).c_str(),
-            currentTop_->LeapName(ay).c_str(),
-            currentTop_->LeapName(ad).c_str());
+    if (debug_ > 1)
+      mprintf("++++Torsion INTERNAL: %f to %s - %s - %s - %s\n", phiVal*Constants::RADDEG,
+              currentTop_->LeapName(aa).c_str(),
+              currentTop_->LeapName(ax).c_str(),
+              currentTop_->LeapName(ay).c_str(),
+              currentTop_->LeapName(ad).c_str());
     internalTorsions_.push_back( InternalTorsion(aa, ax, ay, ad, phiVal) );
   } else {
-    mprintf( "Torsional INTERNAL already exists: %f\n", internalTorsions_[icIdx].PhiVal()*Constants::RADDEG );
+    if (debug_ > 1)
+      mprintf( "Torsional INTERNAL already exists: %f\n", internalTorsions_[icIdx].PhiVal()*Constants::RADDEG );
   }
 }
 
@@ -1295,10 +1302,11 @@ void Builder::buildAngleInternal(int a1, int a2, int a3, Frame const& frameIn, T
       dValue = ModelBondAngle( a1, a2, a3, topIn );
     }
     internalAngles_.push_back( InternalAngle(a1, a2, a3, dValue) );
-    mprintf("++++Angle INTERNAL: %f  for %s - %s - %s\n", dValue*Constants::RADDEG,
-            topIn.LeapName(a1).c_str(),
-            topIn.LeapName(a2).c_str(),
-            topIn.LeapName(a3).c_str());
+    if (debug_ > 1)
+      mprintf("++++Angle INTERNAL: %f  for %s - %s - %s\n", dValue*Constants::RADDEG,
+              topIn.LeapName(a1).c_str(),
+              topIn.LeapName(a2).c_str(),
+              topIn.LeapName(a3).c_str());
 }
 
 /** Build bond internal. */
@@ -1314,9 +1322,10 @@ void Builder::buildBondInternal(int a1, int a2, Frame const& frameIn, Topology c
       dValue = ModelBondLength( a1, a2, topIn );
     }
     internalBonds_.push_back( InternalBond(a1, a2, dValue) );
-    mprintf("++++Bond INTERNAL: %f  for %s - %s\n", dValue,
-            topIn.LeapName(a1).c_str(),
-            topIn.LeapName(a2).c_str());
+    if (debug_ > 1)
+      mprintf("++++Bond INTERNAL: %f  for %s - %s\n", dValue,
+              topIn.LeapName(a1).c_str(),
+              topIn.LeapName(a2).c_str());
 }
 
 
@@ -1430,17 +1439,18 @@ int Builder::GenerateInternals(Frame const& frameIn, Topology const& topIn, Barr
   // Chirality
   Iarray atomIdxs = GenerateAtomArray(topIn.Residues(), topIn.Atoms());
   for (Iarray::const_iterator it = atomIdxs.begin(); it != atomIdxs.end(); ++it) {
-    int at = *it; // FIXME just use *it
-  //for (int at = 0; at != topIn.Natom(); ++at) {
     double dValue = 0;
-    if (determineChirality(dValue, at, frameIn, topIn, hasPosition)) {
-      mprintf("Got chirality from external coordinates\n" );
-      mprintf("++++Chirality INTERNAL: %f  for %s\n", dValue,
-              topIn.LeapName(at).c_str());
+    if (determineChirality(dValue, *it, frameIn, topIn, hasPosition)) {
+      if (debug_ > 1) {
+        mprintf("Got chirality from external coordinates\n" );
+        mprintf("++++Chirality INTERNAL: %f  for %s\n", dValue,
+                topIn.LeapName(*it).c_str());
+      }
     } else {
-      mprintf("Left chirality undefined for %s\n",topIn.LeapName(at).c_str() );
+      if (debug_ > 1)
+        mprintf("Left chirality undefined for %s\n",topIn.LeapName(*it).c_str() );
     }
-    internalChirality_.push_back( InternalChirality(at, dValue) );
+    internalChirality_.push_back( InternalChirality(*it, dValue) );
   }
   mprintf("DEBUG: ----- Leaving Builder::GenerateInternals. ------\n");
   return 0;

From 7473f76b3221f52d2695e03b46983caed07e62eb Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 20 Feb 2024 11:34:46 -0500
Subject: [PATCH 0564/1492] Hide more debug

---
 src/Structure/Builder.cpp | 101 +++++++++++++++++++++-----------------
 1 file changed, 56 insertions(+), 45 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 29545e61d4..401f649760 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -55,10 +55,11 @@ const
     ParmHolder<BondParmType>::const_iterator it = params_->BP().GetParam( btypes );
     if (it != params_->BP().end()) {
       dist = it->second.Req();
-      mprintf("DEBUG: Found bond parameter for %s (%s) - %s (%s): req=%g rk=%g\n",
-              topIn.AtomMaskName(ai).c_str(), *(topIn[ai].Type()),
-              topIn.AtomMaskName(aj).c_str(), *(topIn[aj].Type()),
-              it->second.Req(), it->second.Rk());
+      if (debug_ > 1)
+        mprintf("DEBUG: Found bond parameter for %s (%s) - %s (%s): req=%g rk=%g\n",
+                topIn.AtomMaskName(ai).c_str(), *(topIn[ai].Type()),
+                topIn.AtomMaskName(aj).c_str(), *(topIn[aj].Type()),
+                it->second.Req(), it->second.Rk());
       return 1;
     }
   }
@@ -83,11 +84,12 @@ const
     ParmHolder<AngleParmType>::const_iterator it = params_->AP().GetParam( atypes );
     if (it != params_->AP().end()) {
       theta = it->second.Teq();
-      mprintf("DEBUG: Found angle parameter for %s (%s) - %s (%s) - %s (%s): teq=%g tk=%g\n",
-                topIn.AtomMaskName(ai).c_str(), *(topIn[ai].Type()),
-                topIn.AtomMaskName(aj).c_str(), *(topIn[aj].Type()),
-                topIn.AtomMaskName(ak).c_str(), *(topIn[ak].Type()),
-                it->second.Teq()*Constants::RADDEG, it->second.Tk());
+      if (debug_ > 1)
+        mprintf("DEBUG: Found angle parameter for %s (%s) - %s (%s) - %s (%s): teq=%g tk=%g\n",
+                  topIn.AtomMaskName(ai).c_str(), *(topIn[ai].Type()),
+                  topIn.AtomMaskName(aj).c_str(), *(topIn[aj].Type()),
+                  topIn.AtomMaskName(ak).c_str(), *(topIn[ak].Type()),
+                  it->second.Teq()*Constants::RADDEG, it->second.Tk());
       return 1;
     }
   }
@@ -1144,11 +1146,11 @@ void Builder::createSp2Sp2Torsions(TorsionModel const& MT) {
   double dADOffset =         MT.Absolute() - Constants::PI ;
   double d180      =         Constants::PI + dADOffset     ;
   double d0        =                 dADOffset             ;
-  mprintf("In ModelCreateSp2Sp2Torsions, dAbsolute= %g, dADOffset= %g, d180= %g, d0= %g\n",
-          MT.Absolute()*Constants::RADDEG,
-          dADOffset * Constants::RADDEG,
-          d180 * Constants::RADDEG,
-          d0 * Constants::RADDEG);
+  //mprintf("In ModelCreateSp2Sp2Torsions, dAbsolute= %g, dADOffset= %g, d180= %g, d0= %g\n",
+  //        MT.Absolute()*Constants::RADDEG,
+  //        dADOffset * Constants::RADDEG,
+  //        d180 * Constants::RADDEG,
+  //        d0 * Constants::RADDEG);
 
   ModelTorsion( MT, 0, 0, d180 );
   ModelTorsion( MT, 0, 1, d0 );
@@ -1467,10 +1469,11 @@ int Builder::generateAtomInternals(int at, Frame const& frameIn, Topology const&
     for (Atom::bond_iterator cat = AtB.bondbegin(); cat != AtB.bondend(); ++cat) {
       if (*cat != at) {
         Atom const& AtC = topIn[*cat];
-        mprintf("Building torsion INTERNALs for: %s  around: %s - %s\n",
-               topIn.LeapName(at).c_str(),
-               topIn.LeapName(*bat).c_str(),
-               topIn.LeapName(*cat).c_str());
+        if (debug_ > 1)
+          mprintf("Building torsion INTERNALs for: %s  around: %s - %s\n",
+                 topIn.LeapName(at).c_str(),
+                 topIn.LeapName(*bat).c_str(),
+                 topIn.LeapName(*cat).c_str());
         Iarray iTorsions = getExistingTorsionIdxs(*bat, *cat);
         int iShouldBe = (AtB.Nbonds() - 1) * (AtC.Nbonds() - 1);
 #       ifdef CPPTRAJ_DEBUG_BUILDER
@@ -1487,10 +1490,11 @@ int Builder::generateAtomInternals(int at, Frame const& frameIn, Topology const&
     Atom const& AtB = topIn[*bat];
     for (Atom::bond_iterator cat = AtB.bondbegin(); cat != AtB.bondend(); ++cat) {
       if (*cat != at) {
-        mprintf("Building angle INTERNAL for: %s - %s - %s\n",
-                topIn.LeapName(at).c_str(),
-                topIn.LeapName(*bat).c_str(),
-                topIn.LeapName(*cat).c_str());
+        if (debug_ > 1)
+          mprintf("Building angle INTERNAL for: %s - %s - %s\n",
+                  topIn.LeapName(at).c_str(),
+                  topIn.LeapName(*bat).c_str(),
+                  topIn.LeapName(*cat).c_str());
         int aidx = getExistingAngleIdx(at, *bat, *cat);
         if (aidx < 0) {
           double dValue = 0;
@@ -1498,55 +1502,60 @@ int Builder::generateAtomInternals(int at, Frame const& frameIn, Topology const&
               hasPosition[*bat] &&
               hasPosition[*cat])
           {
-            mprintf("Got bond angle from externals\n");
+            if (debug_ > 1) mprintf("Got bond angle from externals\n");
             dValue = CalcAngle(frameIn.XYZ(at), frameIn.XYZ(*bat), frameIn.XYZ(*cat));
           } else {
-            mprintf("Got bond angle from model builder\n");
+            if (debug_ > 1) mprintf("Got bond angle from model builder\n");
             dValue = ModelBondAngle(at, *bat, *cat, topIn);
           }
-          mprintf("++++Angle INTERNAL: %f  for %s - %s - %s\n", dValue*Constants::RADDEG,
-                  topIn.LeapName(at).c_str(),
-                  topIn.LeapName(*bat).c_str(),
-                  topIn.LeapName(*cat).c_str());
+          if (debug_ > 1)
+            mprintf("++++Angle INTERNAL: %f  for %s - %s - %s\n", dValue*Constants::RADDEG,
+                    topIn.LeapName(at).c_str(),
+                    topIn.LeapName(*bat).c_str(),
+                    topIn.LeapName(*cat).c_str());
           internalAngles_.push_back(InternalAngle(at, *bat, *cat, dValue));
         } else {
-          mprintf("Angle INTERNAL was already defined\n");
+          if (debug_ > 1) mprintf("Angle INTERNAL was already defined\n");
         }
       }
     } // END loop over atoms bonded to B
   } // END loop over atoms bonded to A
   // Bonds
   for (Atom::bond_iterator bat = AtA.bondbegin(); bat != AtA.bondend(); ++bat) {
-    mprintf("Building bond INTERNAL for: %s - %s\n",
-            topIn.LeapName(at).c_str(),
-            topIn.LeapName(*bat).c_str());
+    if (debug_ > 1)
+      mprintf("Building bond INTERNAL for: %s - %s\n",
+              topIn.LeapName(at).c_str(),
+              topIn.LeapName(*bat).c_str());
     int bidx = getExistingBondIdx(at, *bat);
     if (bidx < 0) {
       double dValue = 0;
       if (hasPosition[at] &&
           hasPosition[*bat])
       {
-        mprintf("Got bond length from externals\n");
+        if (debug_ > 1) mprintf("Got bond length from externals\n");
         dValue = sqrt(DIST2_NoImage(frameIn.XYZ(at), frameIn.XYZ(*bat)));
       } else {
-        mprintf("Got bond length from the model builder\n");
+        if (debug_ > 1) mprintf("Got bond length from the model builder\n");
         dValue = ModelBondLength(at, *bat, topIn);
       }
-      mprintf("++++Bond INTERNAL: %f  for %s - %s\n", dValue,
-              topIn.LeapName(at).c_str(),
-              topIn.LeapName(*bat).c_str());
+      if (debug_ > 1)
+        mprintf("++++Bond INTERNAL: %f  for %s - %s\n", dValue,
+                topIn.LeapName(at).c_str(),
+                topIn.LeapName(*bat).c_str());
       internalBonds_.push_back(InternalBond(at, *bat, dValue));
     } else {
-      mprintf( "Bond length INTERNAL already defined\n" );
+      if (debug_ > 1) mprintf( "Bond length INTERNAL already defined\n" );
     }
   } // END loop over atoms bonded to A
   // Chirality
   double dChi = 0;
   int cidx = getExistingChiralityIdx(at);
   if (determineChirality(dChi, at, frameIn, topIn, hasPosition)) {
-    mprintf("Got chirality from external coordinates\n" );
-    mprintf("++++Chirality INTERNAL: %f  for %s\n", dChi,
-              topIn.LeapName(at).c_str());
+    if (debug_ > 1) {
+      mprintf("Got chirality from external coordinates\n" );
+      mprintf("++++Chirality INTERNAL: %f  for %s\n", dChi,
+                topIn.LeapName(at).c_str());
+    }
     if (cidx == -1)
       internalChirality_.push_back( InternalChirality(at, dChi) );
     else {
@@ -1556,10 +1565,12 @@ int Builder::generateAtomInternals(int at, Frame const& frameIn, Topology const&
                 topIn.AtomMaskName(at).c_str(), dChi, internalChirality_[cidx].ChiralVal());
     }
   } else {
-    if (cidx == -1)
-      mprintf("Left chirality undefined for %s\n",topIn.LeapName(at).c_str() );
-    else
-      mprintf("Using already-defined chirality (%f).\n", internalChirality_[cidx].ChiralVal());
+    if (debug_ > 1) {
+      if (cidx == -1)
+        mprintf("Left chirality undefined for %s\n",topIn.LeapName(at).c_str() );
+      else
+        mprintf("Using already-defined chirality (%f).\n", internalChirality_[cidx].ChiralVal());
+    }
   }
 
   return 0;

From e45939478d097ed62d70146ca5734c694d11cae6 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 20 Feb 2024 11:37:49 -0500
Subject: [PATCH 0565/1492] Hide more debug

---
 src/Structure/Builder.cpp | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 401f649760..87343d0bde 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1419,7 +1419,11 @@ int Builder::GenerateInternals(Frame const& frameIn, Topology const& topIn, Barr
   // Loop over bonds to determine torsions.
   for (BondArray::const_iterator bnd = bonds.begin(); bnd != bonds.end(); ++bnd)
   {
-    if (topIn[bnd->A1()].Nbonds() > 1 && topIn[bnd->A2()].Nbonds() > 1) mprintf("Building torsion INTERNALs around: %s - %s\n", topIn.LeapName(bnd->A1()).c_str(), topIn.LeapName(bnd->A2()).c_str()); // DEBUG
+    if (debug_ > 0) {
+      if (topIn[bnd->A1()].Nbonds() > 1 && topIn[bnd->A2()].Nbonds() > 1)
+        mprintf("Building torsion INTERNALs around: %s - %s\n",
+                topIn.LeapName(bnd->A1()).c_str(), topIn.LeapName(bnd->A2()).c_str()); // DEBUG
+    }
     if (assignTorsionsAroundBond( bnd->A1(), bnd->A2(), frameIn, topIn, hasPosition, -1 )) {
       mprinterr("Error Assign torsions around bond %s - %s failed.\n",
                 topIn.AtomMaskName(bnd->A1()).c_str(),
@@ -1461,7 +1465,8 @@ int Builder::GenerateInternals(Frame const& frameIn, Topology const& topIn, Barr
 /** Build internal coordinates around an atom. */
 int Builder::generateAtomInternals(int at, Frame const& frameIn, Topology const& topIn, Barray const& hasPosition)
 {
-  mprintf( "Building internals for: %s\n", topIn.LeapName(at).c_str());
+  if (debug_ > 0)
+    mprintf( "Building internals for: %s\n", topIn.LeapName(at).c_str());
   // Torsions
   Atom const& AtA = topIn[at];
   for (Atom::bond_iterator bat = AtA.bondbegin(); bat != AtA.bondend(); ++bat) {

From 5d579f19fe91638b6167bbdba6a27c47ac39bd29 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 20 Feb 2024 11:42:51 -0500
Subject: [PATCH 0566/1492] Fix order of debug info. Hide some more

---
 src/Exec_Build.cpp        | 5 ++---
 src/Structure/Builder.cpp | 2 +-
 2 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 03337251a9..c046153948 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -384,6 +384,8 @@ const
   {
     long int ires = it-AtomOffsets.begin();
     if (*it > -1) {
+      mprintf("DEBUG: ***** BUILD residue %li %s *****\n", ires + 1,
+              topOut.TruncResNameOnumId(ires).c_str());
       // Residue has atom offset which indicates it needs something built.
       Cpptraj::Structure::Builder structureBuilder;// = new Cpptraj::Structure::Builder();
       structureBuilder.SetDebug( debug_ );
@@ -400,9 +402,6 @@ const
         return 1;
       }
       structureBuilder.UpdateIndicesWithOffset( *it );
-
-      mprintf("DEBUG: ***** BUILD residue %li %s *****\n", ires + 1,
-              topOut.TruncResNameOnumId(ires).c_str());
       //mprintf("DEBUG: Residue type: %s terminal\n", Cpptraj::Structure::terminalStr(*termType));
       // Is this residue connected to an earlier residue?
       for (IParray::const_iterator resBonds = resBondingAtoms[ires].begin();
diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 87343d0bde..4f4240aee7 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1745,7 +1745,7 @@ const
         }
       }
       if (!has_rnum) {
-        mprintf("DEBUG: Need to build for residue %s\n", topIn.TruncResNameNum(rnum).c_str());
+        if (debug_ > 0) mprintf("DEBUG: Need to build for residue %s\n", topIn.TruncResNameNum(rnum).c_str());
         residues.push_back( topIn.Res(rnum) );
         Rnums.push_back(rnum);
       }

From 958366f72f116c8daa98e0b97a4349b22d32572b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 20 Feb 2024 11:45:29 -0500
Subject: [PATCH 0567/1492] Finish hiding debug info in Builder

---
 src/Structure/Builder.cpp | 19 ++++++++++++-------
 1 file changed, 12 insertions(+), 7 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 4f4240aee7..b031edd4f0 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1413,7 +1413,8 @@ int Builder::determineChirality(double& dChi, int at, Frame const& frameIn, Topo
   */
 int Builder::GenerateInternals(Frame const& frameIn, Topology const& topIn, Barray const& hasPosition)
 {
-  mprintf("DEBUG: ----- Entering Builder::GenerateInternals. -----\n");
+  if (debug_ > 0)
+    mprintf("DEBUG: ----- Entering Builder::GenerateInternals. -----\n");
   // First generate the bond array for use in determining torsions.
   BondArray bonds = GenerateBondArray( topIn.Residues(), topIn.Atoms() );
   // Loop over bonds to determine torsions.
@@ -1458,7 +1459,8 @@ int Builder::GenerateInternals(Frame const& frameIn, Topology const& topIn, Barr
     }
     internalChirality_.push_back( InternalChirality(*it, dValue) );
   }
-  mprintf("DEBUG: ----- Leaving Builder::GenerateInternals. ------\n");
+  if (debug_ > 0)
+    mprintf("DEBUG: ----- Leaving Builder::GenerateInternals. ------\n");
   return 0;
 }
 
@@ -1592,8 +1594,10 @@ int Builder::GenerateInternalsAroundLink(int at0, int at1,
                                          Barray const& hasPosition,
                                          BuildType btype)
 {
-  mprintf("DEBUG: ----- Entering Builder::GenerateInternalsAroundLink. -----\n");
-  mprintf("DEBUG: Link: %s to %s\n", topIn.AtomMaskName(at0).c_str(), topIn.AtomMaskName(at1).c_str());
+  if (debug_ > 0) {
+    mprintf("DEBUG: ----- Entering Builder::GenerateInternalsAroundLink. -----\n");
+    mprintf("DEBUG: Link: %s to %s\n", topIn.AtomMaskName(at0).c_str(), topIn.AtomMaskName(at1).c_str());
+  }
   // Sanity check
   Atom const& A0 = topIn[at0];
   Atom const& A1 = topIn[at1];
@@ -1626,7 +1630,8 @@ int Builder::GenerateInternalsAroundLink(int at0, int at1,
     }
   }
   // FIXME this is a hack to make certain we have all the angle/bond terms we need
-  mprintf("DEBUG: LOOKING FOR MISSING ANGLE/BOND PARAMS.\n");
+  if (debug_ > 0)
+    mprintf("DEBUG: LOOKING FOR MISSING ANGLE/BOND PARAMS.\n");
   for (Tarray::const_iterator dih = internalTorsions_.begin(); dih != internalTorsions_.end(); ++dih)
   {
     int idx = getExistingAngleIdx(dih->AtI(), dih->AtJ(), dih->AtK());
@@ -1638,8 +1643,8 @@ int Builder::GenerateInternalsAroundLink(int at0, int at1,
     idx = getExistingBondIdx(dih->AtK(), dih->AtL());
     if (idx < 0) buildBondInternal( dih->AtK(), dih->AtL(), frameIn, topIn, hasPosition );
   }
-
-  mprintf("DEBUG: ----- Leaving Builder::GenerateInternalsAroundLink. -----\n");
+  if (debug_ > 0)
+    mprintf("DEBUG: ----- Leaving Builder::GenerateInternalsAroundLink. -----\n");
   return 0;
 }
 

From 06dc82a89d0d947eaad39c97154ded2006f67eb6 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 20 Feb 2024 11:57:31 -0500
Subject: [PATCH 0568/1492] Hide atom map and final atoms

---
 src/Exec_Build.cpp | 34 +++++++++++++++++++---------------
 1 file changed, 19 insertions(+), 15 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index c046153948..83c7bbb9dd 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -174,14 +174,16 @@ const
       // ----- A template exists for this residue. ---------
       // Map source atoms to template atoms.
       std::vector<int> map = MapAtomsToTemplate( topIn, ires, resTemplate );
-      mprintf("\t  Atom map:\n");
-      // DEBUG - print map
-      for (int iref = 0; iref != resTemplate->Top().Natom(); iref++) {
-        mprintf("\t\t%6i %6s =>", iref+1, *(resTemplate->Top()[iref].Name()));
-        if (map[iref] == -1)
-          mprintf(" No match\n");
-        else
-          mprintf(" %6i %6s\n", map[iref]+1, *(topIn[map[iref]].Name()));
+      if (debug_ > 1) {
+        mprintf("\t  Atom map:\n");
+        // DEBUG - print map
+        for (int iref = 0; iref != resTemplate->Top().Natom(); iref++) {
+          mprintf("\t\t%6i %6s =>", iref+1, *(resTemplate->Top()[iref].Name()));
+          if (map[iref] == -1)
+            mprintf(" No match\n");
+          else
+            mprintf(" %6i %6s\n", map[iref]+1, *(topIn[map[iref]].Name()));
+        }
       }
       // Map template atoms back to source atoms.
       std::vector<int> pdb(currentRes.NumAtoms(), -1);
@@ -437,13 +439,15 @@ const
   } // END loop over atom offsets
 
   // DEBUG - Print new top/coords
-  for (int iat = 0; iat != topOut.Natom(); iat++)
-  {
-    Residue const& res = topOut.Res( topOut[iat].ResNum() );
-    const double* XYZ = frameOut.XYZ(iat);
-    mprintf("%6i %6s %6i %6s (%i) %g %g %g\n",
-            iat+1, *(topOut[iat].Name()), res.OriginalResNum(), *(res.Name()),
-            (int)hasPosition[iat], XYZ[0], XYZ[1], XYZ[2]);
+  if (debug_ > 1) {
+    for (int iat = 0; iat != topOut.Natom(); iat++)
+    {
+      Residue const& res = topOut.Res( topOut[iat].ResNum() );
+      const double* XYZ = frameOut.XYZ(iat);
+      mprintf("%6i %6s %6i %6s (%i) %g %g %g\n",
+              iat+1, *(topOut[iat].Name()), res.OriginalResNum(), *(res.Name()),
+              (int)hasPosition[iat], XYZ[0], XYZ[1], XYZ[2]);
+    }
   }
 
   // Finalize topology - determine molecules, dont renumber residues, dont assign default bond params

From 9dcbad76f702944ea3809df7230f1104dc816a5e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 20 Feb 2024 11:59:34 -0500
Subject: [PATCH 0569/1492] Hide debug info

---
 src/Structure/GenerateConnectivityArrays.cpp | 22 ++++++++++----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/src/Structure/GenerateConnectivityArrays.cpp b/src/Structure/GenerateConnectivityArrays.cpp
index de89fe5474..ed5f33ffa6 100644
--- a/src/Structure/GenerateConnectivityArrays.cpp
+++ b/src/Structure/GenerateConnectivityArrays.cpp
@@ -237,17 +237,17 @@ DihedralArray Cpptraj::Structure::GenerateImproperArray(std::vector<Residue> con
               order_improper_atoms(indices, atoms);
               out.push_back( DihedralType(indices[0], indices[1], iat3, indices[2], DihedralType::BOTH) );
               // DEBUG
-              mprintf("DEBUG:\tOriginal order :");
-              printName(atoms[iat1]);
-              printName(atoms[iat2]);
-              printName(atoms[iat3]);
-              printName(atoms[iat4]);
-              mprintf("\nDEBUG:\tLeap order     :");
-              printName(atoms[indices[0]]);
-              printName(atoms[indices[1]]);
-              printName(atoms[iat3]);
-              printName(atoms[indices[2]]);
-              mprintf("\n");
+              //mprintf("DEBUG:\tOriginal order :");
+              //printName(atoms[iat1]);
+              //printName(atoms[iat2]);
+              //printName(atoms[iat3]);
+              //printName(atoms[iat4]);
+              //mprintf("\nDEBUG:\tLeap order     :");
+              //printName(atoms[indices[0]]);
+              //printName(atoms[indices[1]]);
+              //printName(atoms[iat3]);
+              //printName(atoms[indices[2]]);
+              //mprintf("\n");
             }
           }
         } // END outer loop over bond indices

From 72434a9aa71c24493c8674118902ed7dae5be688 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 20 Feb 2024 12:22:26 -0500
Subject: [PATCH 0570/1492] Hide debug info

---
 src/Topology.cpp | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index 79a884f402..abf3dc73a4 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2847,16 +2847,18 @@ DihedralArray Topology::AssignDihedralParm(DihedralParmHolder const& newDihedral
           paramTypes = impit->first;
           ipa = impit->second;
           found = true;
-          mprintf("DEBUG: Found new value for improper %2s %2s %2s %2s (%2s %2s %2s %2s)\n",
-                  *types[0], *types[1], *types[2], *types[3],
-                  *paramTypes[0], *paramTypes[1], *paramTypes[2], *paramTypes[3]);
+          if (debug_ > 1)
+            mprintf("DEBUG: Found new value for improper %2s %2s %2s %2s (%2s %2s %2s %2s)\n",
+                    *types[0], *types[1], *types[2], *types[3],
+                    *paramTypes[0], *paramTypes[1], *paramTypes[2], *paramTypes[3]);
         }
       } else {
         paramTypes = impit->first;
         ipa = impit->second;
         found = true;
-        mprintf("DEBUG: Using cached value for improper %2s %2s %2s %2s (%2s %2s %2s %2s)\n",
-                *types[0], *types[1], *types[2], *types[3],
+        if (debug_ > 1)
+          mprintf("DEBUG: Using cached value for improper %2s %2s %2s %2s (%2s %2s %2s %2s)\n",
+                  *types[0], *types[1], *types[2], *types[3],
                   *paramTypes[0], *paramTypes[1], *paramTypes[2], *paramTypes[3]);
       }
       int idx = -1;
@@ -2895,7 +2897,7 @@ DihedralArray Topology::AssignDihedralParm(DihedralParmHolder const& newDihedral
         // Add to the cache
         if (is_new_improper) {
           // To match leap behavior, make sure paramTypes are sorted alphabetically.
-          mprintf("DEBUG: Improper wildcard: %s\n", *(newImproperParams.Wildcard()));
+          //mprintf("DEBUG: Improper wildcard: %s\n", *(newImproperParams.Wildcard()));
           if (sort_improper_cache) paramTypes.SortImproperByAlpha( newImproperParams.Wildcard() );
           improperCache.AddParm( paramTypes, ipa.front(), false );
         }

From 0f2c787735ec906f9ec2d234ff8972224a24be67 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 20 Feb 2024 13:31:57 -0500
Subject: [PATCH 0571/1492] For debug, print residue ids for template residues

---
 src/Structure/Creator.cpp | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/src/Structure/Creator.cpp b/src/Structure/Creator.cpp
index d2c0abd4b2..9e86e62299 100644
--- a/src/Structure/Creator.cpp
+++ b/src/Structure/Creator.cpp
@@ -140,9 +140,16 @@ int Creator::getTemplates(ArgList& argIn, DataSetList const& DSL) {
   }
   if (!Templates_.empty()) {
     mprintf("\t%zu residue templates found:", Templates_.size());
-    for (Carray::const_iterator it = Templates_.begin(); it != Templates_.end(); ++it)
+    for (Carray::const_iterator it = Templates_.begin(); it != Templates_.end(); ++it) {
       mprintf(" %s", (*it)->legend());
-    mprintf("\n");
+      AssociatedData* ad = (*it)->GetAssociatedData( AssociatedData::RESID );
+      if (ad != 0) {
+        AssociatedData_ResId const& resid = static_cast<AssociatedData_ResId const&>( *ad );
+        resid.Ainfo();
+      }
+      mprintf("\n");
+    }
+    //mprintf("\n");
   }
 
   return 0;

From 68e1478312e053ce4606dd5306a0906e67ac6594 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 20 Feb 2024 15:33:06 -0500
Subject: [PATCH 0572/1492] For SugarBuilder and FunctionalGroup, only need the
 unique atom IDs, not the counts (which can be very long for large things), so
 create a separate function to just assign unique IDs.

---
 src/AtomMap.cpp                   | 18 ++++++++++++------
 src/AtomMap.h                     |  3 +++
 src/Structure/FunctionalGroup.cpp |  2 +-
 src/Structure/SugarBuilder.cpp    |  2 +-
 4 files changed, 17 insertions(+), 8 deletions(-)

diff --git a/src/AtomMap.cpp b/src/AtomMap.cpp
index fe1548494a..283646bd48 100644
--- a/src/AtomMap.cpp
+++ b/src/AtomMap.cpp
@@ -123,16 +123,13 @@ bool AtomMap::BondIsRepeated(int atom, int bondedAtom) const {
   return false;
 }
 
-// AtomMap::DetermineAtomIDs()
 /** Give each atom an identifier (atomID) based on what atoms are bonded to 
   * it. The first part of the atomID is the atom itself, followed by an 
   * alphabetized list of bonded atoms. So C in O=C-H2 would be CHHO.
   * Then create a 'unique string' comprised of this atomID and the 
-  * atomIDs of all bonded atoms (sorted). Once that is done determine
-  * which unique strings are actually unique (i.e. they are not repeated
-  * in this map). 
+  * atomIDs of all bonded atoms (sorted).
   */
-void AtomMap::DetermineAtomIDs() {
+void AtomMap::AssignUniqueAtomIDs() {
   // Determine self IDs
   if (debug_>0) mprintf("ATOM IDs:\n");
   unsigned int anum = 1;
@@ -187,6 +184,15 @@ void AtomMap::DetermineAtomIDs() {
     // NOTE: SetUnique also resets the duplicated counter.
     matom.SetUnique( unique );
   }
+}
+
+// AtomMap::DetermineAtomIDs()
+/** Assign each atom a unique ID. Once that is done determine
+  * which unique strings are actually unique (i.e. they are not repeated
+  * in this map). 
+  */
+void AtomMap::DetermineAtomIDs() {
+  AssignUniqueAtomIDs();
 
   // Determine which unique IDs are duplicated - set isUnique flag
   for (unsigned int i = 0; i < mapatoms_.size()-1; i++) {
@@ -202,7 +208,7 @@ void AtomMap::DetermineAtomIDs() {
   // DEBUG
   if (debug_ > 0) {
     mprintf("UNIQUE IDs:\n");
-    anum = 1;
+    unsigned int anum = 1;
     for (Marray::const_iterator matom = mapatoms_.begin();
                                 matom != mapatoms_.end(); ++matom)
     {
diff --git a/src/AtomMap.h b/src/AtomMap.h
index 3705fc6aaa..f39287d4c5 100644
--- a/src/AtomMap.h
+++ b/src/AtomMap.h
@@ -22,6 +22,9 @@ class AtomMap {
     /// Clear the map
     void ClearMap();
     bool BondIsRepeated(int,int) const;
+    /// Assign unique atom IDs
+    void AssignUniqueAtomIDs();
+    /// Assign unique atom IDs and determine which ones are duplicated
     void DetermineAtomIDs();
     void MarkAtomComplete(int,bool);
     void CheckForCompleteAtoms();
diff --git a/src/Structure/FunctionalGroup.cpp b/src/Structure/FunctionalGroup.cpp
index 3522d2ad8f..6caae8b56b 100644
--- a/src/Structure/FunctionalGroup.cpp
+++ b/src/Structure/FunctionalGroup.cpp
@@ -46,7 +46,7 @@ int FunctionalGroup::SetupFromTop(Topology const& groupTop, Atom::AtomicElementT
   AtomMap groupmap;
   //groupmap.SetDebug(10); // DEBUG
   groupmap.Setup( groupTop, Frame() );
-  groupmap.DetermineAtomIDs();
+  groupmap.AssignUniqueAtomIDs();
 
   for (int idx = 0; idx != groupmap.Natom(); idx++)
     AddAtom( groupmap[idx].Name(), groupmap[idx].Unique() );
diff --git a/src/Structure/SugarBuilder.cpp b/src/Structure/SugarBuilder.cpp
index 60378df809..cd250631af 100644
--- a/src/Structure/SugarBuilder.cpp
+++ b/src/Structure/SugarBuilder.cpp
@@ -1790,7 +1790,7 @@ int SugarBuilder::FixSugarsStructure(Topology& topIn, Frame& frameIn,
     mprinterr("Internal Error: FixSugarsStructure: Atom map setup failed.\n");
     return 1;
   }
-  myMap_.DetermineAtomIDs();
+  myMap_.AssignUniqueAtomIDs();
 
   Sugars_.clear();
   AtomMask sugarMask(sugarmaskstr_);

From 79fc7eaace03cc9cd3ceea8e681a169b0b7d03e0 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 21 Feb 2024 08:42:34 -0500
Subject: [PATCH 0573/1492] If insertion code changes, different residue

---
 src/Exec_Build.cpp | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 83c7bbb9dd..8b4c41479f 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -64,7 +64,9 @@ const
       resTermType = Cpptraj::Structure::END_TERMINAL;
     } else if (pres > -1 && topIn.Res(pres).IsTerminal()) {
       resTermType = Cpptraj::Structure::BEG_TERMINAL;
-    } else if (nres < topIn.Nres() && topIn.Res(nres).ChainId() != currentRes.ChainId()) {
+    } else if (nres < topIn.Nres() && (topIn.Res(nres).ChainId() != currentRes.ChainId() ||
+                                       topIn.Res(nres).Icode()   != currentRes.Icode()))
+    {
       resTermType = Cpptraj::Structure::END_TERMINAL;
     } else if (nres == topIn.Nres()) {
       resTermType = Cpptraj::Structure::END_TERMINAL;

From 9bf661ba04ab1245951a55b81008d53f81a85c2b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 21 Feb 2024 09:09:13 -0500
Subject: [PATCH 0574/1492] Give priority to connections from templates

---
 src/Exec_Build.cpp | 140 ++++++++++++++++++++++++++-------------------
 src/Exec_Build.h   |   7 +++
 2 files changed, 87 insertions(+), 60 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 8b4c41479f..835c47dcbb 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -30,6 +30,13 @@ std::vector<int> Exec_Build::MapAtomsToTemplate(Topology const& topIn,
   return mapOut;
 }
 
+/** Search in array of atom bonding pairs for given bonding pair. */
+bool Exec_Build::hasBondingPair(IParray const& bpairs, Ipair const& bpair) {
+  for (IParray::const_iterator it = bpairs.begin(); it != bpairs.end(); ++it)
+    if (*it == bpair) return true;
+  return false;
+}
+
 /** Use given templates to construct a final molecule. */
 int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
                                        Topology const& topIn, Frame const& frameIn,
@@ -37,7 +44,6 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
 const
 {
   // Array of head/tail connect atoms for each residue
-  typedef std::vector<int> Iarray;
   Iarray resHeadAtoms;
   Iarray resTailAtoms;
   resHeadAtoms.reserve( topIn.Nres() );
@@ -45,9 +51,9 @@ const
   // Array of templates for each residue
   std::vector<DataSet_Coords*> ResTemplates;
   ResTemplates.reserve( topIn.Nres() );
-  typedef std::vector<Cpptraj::Structure::TerminalType> TermTypeArray;
-  TermTypeArray ResTypes;
-  ResTypes.reserve( topIn.Nres() );
+  //typedef std::vector<Cpptraj::Structure::TerminalType> TermTypeArray;
+  //TermTypeArray ResTypes;
+  //ResTypes.reserve( topIn.Nres() );
   // Initial loop to try to match residues to templates
   int newNatom = 0;
   for (int ires = 0; ires != topIn.Nres(); ires++)
@@ -123,15 +129,11 @@ const
   Iarray AtomOffsets;
   AtomOffsets.reserve( topIn.Nres() );
 
-  // For inter-residue bonding, use residue # and atom name since
+  // For existing inter-residue bonding, use residue # and atom name since
   // atom numbering may change if atoms are added from templates.
   typedef std::pair<int,NameType> ResAtPair;
   typedef std::vector<ResAtPair> ResAtArray;
-  ResAtArray interResBonds;
-
-  // For holding bonded atom pairs
-  typedef std::pair<int,int> Ipair;
-  typedef std::vector<Ipair> IParray;
+  ResAtArray detectedInterResBonds;
 
   // Loop for setting up atoms in the topology from residues or residue templates.
   int nRefAtomsMissing = 0;
@@ -139,7 +141,7 @@ const
   {
     mprintf("\tAdding atoms for residue %s\n", topIn.TruncResNameOnumId(ires).c_str());
     int atomOffset = topOut.Natom();
-    mprintf("DEBUG: atom offset is %i\n", atomOffset);
+    //mprintf("DEBUG: atom offset is %i\n", atomOffset);
     Residue const& currentRes = topIn.Res(ires);
     DataSet_Coords* resTemplate = ResTemplates[ires];
     IParray intraResBonds;
@@ -160,10 +162,10 @@ const
               intraResBonds.push_back( Ipair(at0, at1) );
             }
           } else {
-            // Inter-residue. Only record if bonding to the next residue.
-            if (topIn[*bat].ResNum() > ires) {
-              interResBonds.push_back( ResAtPair(ires, sourceAtom.Name()) );
-              interResBonds.push_back( ResAtPair(topIn[*bat].ResNum(), topIn[*bat].Name()) );
+            // Inter-residue. Only record if bonding to a previous residue.
+            if (topIn[*bat].ResNum() < ires) {
+              detectedInterResBonds.push_back( ResAtPair(ires, sourceAtom.Name()) );
+              detectedInterResBonds.push_back( ResAtPair(topIn[*bat].ResNum(), topIn[*bat].Name()) );
             }
           }
         }
@@ -191,37 +193,36 @@ const
       std::vector<int> pdb(currentRes.NumAtoms(), -1);
       bool atomsNeedBuilding = false;
       for (int iref = 0; iref != resTemplate->Top().Natom(); iref++) {
-        // Track intra-residue bonds
+        // Track intra-residue bonds from the template.
         Atom templateAtom = resTemplate->Top()[iref];
         int at0 = iref + atomOffset;
         for (Atom::bond_iterator bat = templateAtom.bondbegin(); bat != templateAtom.bondend(); ++bat) {
-          //if ( resTemplate->Top()[*bat].ResNum() == ires ) {
-            int at1 = *bat + atomOffset;
-            if (at1 > at0) {
-              //mprintf("Will add bond between %i and %i (original %i and %i)\n", at0+1, at1+1, iref+1, *bat + 1);
-              intraResBonds.push_back( Ipair(at0, at1) );
-            }
-          //}
+          int at1 = *bat + atomOffset;
+          if (at1 > at0) {
+            //mprintf("Will add bond between %i and %i (original %i and %i)\n", at0+1, at1+1, iref+1, *bat + 1);
+            intraResBonds.push_back( Ipair(at0, at1) );
+          }
         }
-        // TODO check connect atoms for inter-residue connections
         templateAtom.ClearBonds(); // FIXME AddTopAtom should clear bonds
         topOut.AddTopAtom( templateAtom, currentRes );
         if (map[iref] == -1) {
+          // Template atom not in input structure.
           frameOut.AddVec3( Vec3(0.0) );
           hasPosition.push_back( false );
           nRefAtomsMissing++;
           atomsNeedBuilding = true;
         } else {
+          // Template atom was in input structure.
           int itgt = map[iref];
           frameOut.AddVec3( Vec3(frameIn.XYZ(itgt)) );
           hasPosition.push_back( true );
           pdb[itgt-currentRes.FirstAtom()] = iref;
-          // Check source atoms for inter-residue connections
+          // Check source atoms for inter-residue connections.
           Atom const& sourceAtom = topIn[itgt];
           for (Atom::bond_iterator bat = sourceAtom.bondbegin(); bat != sourceAtom.bondend(); ++bat) {
-            if ( topIn[*bat].ResNum() > ires ) {
-              interResBonds.push_back( ResAtPair(ires, sourceAtom.Name()) );
-              interResBonds.push_back( ResAtPair(topIn[*bat].ResNum(), topIn[*bat].Name()) );
+            if ( topIn[*bat].ResNum() < ires ) {
+              detectedInterResBonds.push_back( ResAtPair(ires, sourceAtom.Name()) );
+              detectedInterResBonds.push_back( ResAtPair(topIn[*bat].ResNum(), topIn[*bat].Name()) );
             }
           }
         }
@@ -250,6 +251,7 @@ const
   mprintf("\t%i template atoms missing in source.\n", nRefAtomsMissing);
 
   // -----------------------------------
+  // DEBUG - Print primary connection atoms
   for (unsigned int idx = 0; idx != ResTemplates.size(); idx++) {
     if (ResTemplates[idx] != 0) {
       mprintf("DEBUG: Template %s", ResTemplates[idx]->legend());
@@ -258,9 +260,41 @@ const
       mprintf("\n");
     }
   }
-  // Check detected inter-residue bonds
+
+  // Keep track of which residues are connected.
+  typedef std::vector<Iarray> ResConnectArray;
+  ResConnectArray ResidueConnections( topOut.Nres() );
+
+  // Try to connect HEAD atoms to previous residue TAIL atoms.
   std::vector<IParray> resBondingAtoms(topOut.Nres());
-  for (ResAtArray::const_iterator it = interResBonds.begin(); it != interResBonds.end(); ++it)
+  for (int ires = 1; ires < topOut.Nres(); ires++) {
+    int pres = ires - 1;
+    if (resHeadAtoms[ires] != -1) {
+      if (resTailAtoms[pres] != -1) {
+        mprintf("DEBUG: Connecting HEAD atom %s to tail atom %s\n",
+                topOut.AtomMaskName(resHeadAtoms[ires]).c_str(),
+                topOut.AtomMaskName(resTailAtoms[pres]).c_str());
+        resBondingAtoms[ires].push_back( Ipair(resHeadAtoms[ires], resTailAtoms[pres]) );
+        resBondingAtoms[pres].push_back( Ipair(resTailAtoms[pres], resHeadAtoms[ires]) );
+        resHeadAtoms[ires] = -1;
+        resTailAtoms[pres] = -1;
+        ResidueConnections[ires].push_back( pres );
+        ResidueConnections[pres].push_back( ires );
+      }
+    }
+  }
+
+  // Report unused HEAD/TAIL atoms
+  for (int ires = 0; ires != topOut.Nres(); ires++) { // TODO should be topIn?
+    if (resHeadAtoms[ires] != -1)
+      mprintf("Warning: Unused head atom %s\n", topOut.AtomMaskName(resHeadAtoms[ires]).c_str());
+    if (resTailAtoms[ires] != -1)
+      mprintf("Warning: Unused tail atom %s\n", topOut.AtomMaskName(resTailAtoms[ires]).c_str());
+  }
+
+  // Check detected inter-residue bonds
+  for (ResAtArray::const_iterator it = detectedInterResBonds.begin();
+                                  it != detectedInterResBonds.end(); ++it)
   {
     ResAtPair const& ra0 = *it;
     ++it;
@@ -280,13 +314,23 @@ const
     }
     // Save inter-residue bonding atoms; convention is atom belonging to
     // the residue is first.
-    resBondingAtoms[ra0.first].push_back( Ipair(at0, at1) );
-    resBondingAtoms[ra1.first].push_back( Ipair(at1, at0) );
+    if (!hasBondingPair(resBondingAtoms[ra0.first], Ipair(at0, at1)))
+      resBondingAtoms[ra0.first].push_back( Ipair(at0, at1) );
+    else
+      mprintf("DEBUG: Detected bond %s - %s already present.\n",
+              topOut.AtomMaskName(at0).c_str(),
+              topOut.AtomMaskName(at1).c_str());
+    if (!hasBondingPair(resBondingAtoms[ra1.first], Ipair(at1, at0)))
+      resBondingAtoms[ra1.first].push_back( Ipair(at1, at0) );
+    else
+      mprintf("DEBUG: Detected bond %s - %s already present.\n",
+              topOut.AtomMaskName(at1).c_str(),
+              topOut.AtomMaskName(at0).c_str());
   }
 
   // For each inter-residue bonding atom pair, check that they match expected
   // head/tail atoms.
-  for (std::vector<IParray>::const_iterator rit = resBondingAtoms.begin();
+/*  for (std::vector<IParray>::const_iterator rit = resBondingAtoms.begin();
                                             rit != resBondingAtoms.end(); ++rit)
   {
     long int ires = rit - resBondingAtoms.begin();
@@ -312,10 +356,10 @@ const
                 topOut.AtomMaskName(atPair->first).c_str());
       }
     } // END loop over inter-residue bond pairs for this residue
-  } // END loop over residues
+  } // END loop over residues*/
 
   // Mark used HEAD/TAIL atoms in existing inter-residue bonds.
-  for (std::vector<IParray>::const_iterator rit = resBondingAtoms.begin();
+/*  for (std::vector<IParray>::const_iterator rit = resBondingAtoms.begin();
                                             rit != resBondingAtoms.end(); ++rit)
   {
     long int ires = rit - resBondingAtoms.begin();
@@ -326,31 +370,7 @@ const
       else if (atPair->first == resTailAtoms[ires])
         resTailAtoms[ires] = -1;
     }
-  }
-
-  // Try to connect unused HEAD atoms to previous unused TAIL atoms
-  for (int ires = 1; ires < topOut.Nres(); ires++) {
-    int pres = ires - 1;
-    if (resHeadAtoms[ires] != -1) {
-      if (resTailAtoms[pres] != -1) {
-        mprintf("DEBUG: Connecting unused HEAD atom %s to unused tail atom %s\n",
-                topOut.AtomMaskName(resHeadAtoms[ires]).c_str(),
-                topOut.AtomMaskName(resTailAtoms[pres]).c_str());
-        resBondingAtoms[ires].push_back( Ipair(resHeadAtoms[ires], resTailAtoms[pres]) );
-        resBondingAtoms[pres].push_back( Ipair(resTailAtoms[pres], resHeadAtoms[ires]) );
-        resHeadAtoms[ires] = -1;
-        resTailAtoms[pres] = -1;
-      }
-    }
-  }
-
-  // Report unused HEAD/TAIL atoms
-  for (int ires = 0; ires != topOut.Nres(); ires++) { // TODO should be topIn?
-    if (resHeadAtoms[ires] != -1)
-      mprintf("Warning: Unused head atom %s\n", topOut.AtomMaskName(resHeadAtoms[ires]).c_str());
-    if (resTailAtoms[ires] != -1)
-      mprintf("Warning: Unused tail atom %s\n", topOut.AtomMaskName(resTailAtoms[ires]).c_str());
-  }
+  }*/
 
   // DEBUG print inter-residue bonding atoms
   for (std::vector<IParray>::const_iterator rit = resBondingAtoms.begin();
diff --git a/src/Exec_Build.h b/src/Exec_Build.h
index f6dd1f4090..1016faf61e 100644
--- a/src/Exec_Build.h
+++ b/src/Exec_Build.h
@@ -14,6 +14,13 @@ class Exec_Build : public Exec {
     DispatchObject* Alloc() const { return (DispatchObject*)new Exec_Build(); }
     RetType Execute(CpptrajState&, ArgList&);
   private:
+    typedef std::vector<int> Iarray;
+    // For holding bonded atom pairs.
+    typedef std::pair<int,int> Ipair;
+    typedef std::vector<Ipair> IParray;
+
+    /// \return true if given IParray has the given Ipair
+    static inline bool hasBondingPair(IParray const&, Ipair const&);
     /// Create new topology/frame using templates
     int FillAtomsWithTemplates(Topology&, Frame&, Topology const&, Frame const&, Cpptraj::Structure::Creator const&) const;
     /// Map atoms in topology to template

From c04f17ea08c703fd4e6b97b19281cd0f1da7f82e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 21 Feb 2024 09:28:39 -0500
Subject: [PATCH 0575/1492] Only add a detected non-template inter-residue
 connection if an inter-residue connection is not already present.

---
 src/Exec_Build.cpp | 54 +++++++++++++++++++++++++++++++++-------------
 src/Exec_Build.h   |  4 ++++
 2 files changed, 43 insertions(+), 15 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 835c47dcbb..f1d17ad580 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -37,6 +37,13 @@ bool Exec_Build::hasBondingPair(IParray const& bpairs, Ipair const& bpair) {
   return false;
 }
 
+/** \return True if target residue is in array of residue connections. */
+bool Exec_Build::resIsConnected(Iarray const& resConnections, int tgtRes) {
+  for (Iarray::const_iterator it = resConnections.begin(); it != resConnections.end(); ++it)
+    if (*it == tgtRes) return true;
+  return false;
+}
+
 /** Use given templates to construct a final molecule. */
 int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
                                        Topology const& topIn, Frame const& frameIn,
@@ -262,7 +269,6 @@ const
   }
 
   // Keep track of which residues are connected.
-  typedef std::vector<Iarray> ResConnectArray;
   ResConnectArray ResidueConnections( topOut.Nres() );
 
   // Try to connect HEAD atoms to previous residue TAIL atoms.
@@ -312,20 +318,38 @@ const
       mprinterr("Error: Atom %s not found in residue %i\n", *(ra1.second), ra1.first);
       return 1;
     }
-    // Save inter-residue bonding atoms; convention is atom belonging to
-    // the residue is first.
-    if (!hasBondingPair(resBondingAtoms[ra0.first], Ipair(at0, at1)))
-      resBondingAtoms[ra0.first].push_back( Ipair(at0, at1) );
-    else
-      mprintf("DEBUG: Detected bond %s - %s already present.\n",
-              topOut.AtomMaskName(at0).c_str(),
-              topOut.AtomMaskName(at1).c_str());
-    if (!hasBondingPair(resBondingAtoms[ra1.first], Ipair(at1, at0)))
-      resBondingAtoms[ra1.first].push_back( Ipair(at1, at0) );
-    else
-      mprintf("DEBUG: Detected bond %s - %s already present.\n",
-              topOut.AtomMaskName(at1).c_str(),
-              topOut.AtomMaskName(at0).c_str());
+    // Save detected inter-residue bonding atoms if not already added via
+    // template connect atoms. Convention is atom belonging to the current
+    // residue is first.
+    // NOTE: Only checking at0/at1 here, which should be fine.
+    if (!hasBondingPair(resBondingAtoms[ra0.first], Ipair(at0, at1))) {
+      // Check if we already have a connection from ra0 to ra1.
+      if (resIsConnected(ResidueConnections[ra0.first], ra1.first)) {
+        mprintf("Warning: Residue %s already connected to residue %s; ignoring\n"
+                "Warning: potential detected bond %s - %s\n",
+                topOut.TruncResNameNum(ra0.first).c_str(),
+                topOut.TruncResNameNum(ra1.first).c_str(),
+                topOut.AtomMaskName(at0).c_str(),
+                topOut.AtomMaskName(at1).c_str());
+      } else {
+        mprintf("\tAdding non-template bond %s - %s\n",
+                topOut.AtomMaskName(at0).c_str(),
+                topOut.AtomMaskName(at1).c_str());
+        resBondingAtoms[ra0.first].push_back( Ipair(at0, at1) );
+        resBondingAtoms[ra1.first].push_back( Ipair(at1, at0) );
+        ResidueConnections[ra0.first].push_back( ra1.first );
+        ResidueConnections[ra1.first].push_back( ra0.first );
+      }
+    } //else
+      //mprintf("DEBUG: Detected bond %s - %s already present.\n",
+      //        topOut.AtomMaskName(at0).c_str(),
+      //        topOut.AtomMaskName(at1).c_str());
+    //if (!hasBondingPair(resBondingAtoms[ra1.first], Ipair(at1, at0)))
+    //  resBondingAtoms[ra1.first].push_back( Ipair(at1, at0) );
+    //else
+    //  mprintf("DEBUG: Detected bond %s - %s already present.\n",
+    //          topOut.AtomMaskName(at1).c_str(),
+    //          topOut.AtomMaskName(at0).c_str());
   }
 
   // For each inter-residue bonding atom pair, check that they match expected
diff --git a/src/Exec_Build.h b/src/Exec_Build.h
index 1016faf61e..a8e7d7e124 100644
--- a/src/Exec_Build.h
+++ b/src/Exec_Build.h
@@ -15,12 +15,16 @@ class Exec_Build : public Exec {
     RetType Execute(CpptrajState&, ArgList&);
   private:
     typedef std::vector<int> Iarray;
+    // Keep track of which residues are connected to each other
+    typedef std::vector<Iarray> ResConnectArray;
     // For holding bonded atom pairs.
     typedef std::pair<int,int> Ipair;
     typedef std::vector<Ipair> IParray;
 
     /// \return true if given IParray has the given Ipair
     static inline bool hasBondingPair(IParray const&, Ipair const&);
+    /// \return true if given array of residue connections has target residue index.
+    static inline bool resIsConnected(Iarray const&, int);
     /// Create new topology/frame using templates
     int FillAtomsWithTemplates(Topology&, Frame&, Topology const&, Frame const&, Cpptraj::Structure::Creator const&) const;
     /// Map atoms in topology to template

From 1f44c7a83ab3c158118147c20855d20f09add737 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 21 Feb 2024 11:09:04 -0500
Subject: [PATCH 0576/1492] Since different leaprc files can load the same
 parameter file, keep track of which parameter files are loaded so that
 parameters do not end up overwritten.

---
 src/DataIO_AmberLib.cpp |  2 +-
 src/DataIO_LeapRC.cpp   | 54 +++++++++++++++++++++++++++++++----------
 src/DataIO_LeapRC.h     |  5 ++++
 3 files changed, 47 insertions(+), 14 deletions(-)

diff --git a/src/DataIO_AmberLib.cpp b/src/DataIO_AmberLib.cpp
index e4f0cf46d4..9011b9ed61 100644
--- a/src/DataIO_AmberLib.cpp
+++ b/src/DataIO_AmberLib.cpp
@@ -80,7 +80,7 @@ int DataIO_AmberLib::ReadData(FileName const& fname, DataSetList& dsl, std::stri
       return 1;
     }
   }
-  mprintf("\tRead %zu units from Amber OFF file.\n", UnitNames.size());
+  mprintf("\tRead %zu units from Amber OFF file %s.\n", UnitNames.size(), fname.base());
 
   return 0;
 }
diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 003780be66..39712b7bdd 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -15,6 +15,12 @@ DataIO_LeapRC::DataIO_LeapRC()
 
 }
 
+/** Track already loaded parm files. */
+DataIO_LeapRC::Sarray DataIO_LeapRC::paramFiles_ = Sarray();
+
+/** Track already loaded lib/prep files. */
+DataIO_LeapRC::Sarray DataIO_LeapRC::libFiles_ = Sarray();
+
 // DataIO_LeapRC::ID_DataFormat()
 bool DataIO_LeapRC::ID_DataFormat(CpptrajFile& infile)
 {
@@ -54,6 +60,13 @@ int DataIO_LeapRC::processReadArgs(ArgList& argIn)
   return 0;
 }
 
+/** Check if file already loaded. */
+bool DataIO_LeapRC::check_already_loaded(Sarray const& files, std::string const& filename) {
+  for (Sarray::const_iterator it = files.begin(); it != files.end(); ++it)
+    if (*it == filename) return true;
+  return false;
+}
+
 /** LEaP loadAmberParams command. */
 int DataIO_LeapRC::LoadAmberParams(std::string const& filename, DataSetList& dsl, std::string const& dsname) const {
   // TODO detect this better
@@ -66,11 +79,16 @@ int DataIO_LeapRC::LoadAmberParams(std::string const& filename, DataSetList& dsl
       return 1;
     }
   } else {
-    mprintf("\tLoading force field from '%s'\n", filename.c_str());
-    DataIO_AmberFF infile;
-    if (infile.ReadData(amberhome_ + "parm/" + filename, dsl, dsname)) {
-      mprinterr("Error: Could not load force field from '%s'\n", filename.c_str());
-      return 1;
+    if (check_already_loaded(paramFiles_, filename)) {
+      mprintf("Warning: Force field %s has already been loaded, skipping.\n", filename.c_str());
+    } else {
+      mprintf("\tLoading force field from '%s'\n", filename.c_str());
+      DataIO_AmberFF infile;
+      if (infile.ReadData(amberhome_ + "parm/" + filename, dsl, dsname)) {
+        mprinterr("Error: Could not load force field from '%s'\n", filename.c_str());
+        return 1;
+      }
+      paramFiles_.push_back( filename );
     }
   }
   return 0;
@@ -78,20 +96,30 @@ int DataIO_LeapRC::LoadAmberParams(std::string const& filename, DataSetList& dsl
 
 /** LEaP loadOff command. */
 int DataIO_LeapRC::LoadOFF(std::string const& filename, DataSetList& dsl, std::string const& dsname) const {
-  DataIO_AmberLib infile;
-  if (infile.ReadData(amberhome_ + "lib/" + filename, dsl, dsname)) {
-    mprinterr("Error: Could not load library file '%s'\n", filename.c_str());
-    return 1;
+  if (check_already_loaded(libFiles_, filename)) {
+    mprintf("Warning: Library %s has already been loaded, skipping.\n", filename.c_str());
+  } else {
+    DataIO_AmberLib infile;
+    if (infile.ReadData(amberhome_ + "lib/" + filename, dsl, dsname)) {
+      mprinterr("Error: Could not load library file '%s'\n", filename.c_str());
+      return 1;
+    }
+    libFiles_.push_back( filename );
   }
   return 0;
 }
 
 /** LEaP loadAmberPrep command. */
 int DataIO_LeapRC::LoadAmberPrep(std::string const& filename, DataSetList& dsl, std::string const& dsname) const {
-  DataIO_AmberPrep infile;
-  if (infile.ReadData(amberhome_ + "lib/" + filename, dsl, dsname)) {
-    mprinterr("Error: Could not load prep file '%s'\n", filename.c_str());
-    return 1;
+  if (check_already_loaded(libFiles_, filename)) {
+    mprintf("Warning: Prep file %s has already been loaded, skipping.\n", filename.c_str());
+  } else {
+    DataIO_AmberPrep infile;
+    if (infile.ReadData(amberhome_ + "lib/" + filename, dsl, dsname)) {
+      mprinterr("Error: Could not load prep file '%s'\n", filename.c_str());
+      return 1;
+    }
+    libFiles_.push_back( filename );
   }
   return 0;
 }
diff --git a/src/DataIO_LeapRC.h b/src/DataIO_LeapRC.h
index f7fa009bd4..5e7f5e2a83 100644
--- a/src/DataIO_LeapRC.h
+++ b/src/DataIO_LeapRC.h
@@ -19,6 +19,7 @@ class DataIO_LeapRC : public DataIO {
   private:
     typedef std::pair<NameType, AtomType::HybridizationType> NHpairType;
     typedef std::map<NameType, AtomType::HybridizationType> NHarrayType;
+    typedef std::vector<std::string> Sarray;
 
     struct PdbResMapType {
       std::string unitName_;
@@ -32,7 +33,11 @@ class DataIO_LeapRC : public DataIO {
     int LoadAmberPrep(std::string const&, DataSetList&, std::string const&) const;
     int AddAtomTypes(NHarrayType&, BufferedLine&) const;
     int AddPdbResMap(PdbResMapArray&, BufferedLine&) const;
+    /// Used to check if a parm/lib file was already loaded.
+    static inline bool check_already_loaded(Sarray const&, std::string const&);
 
     std::string amberhome_;
+    static Sarray paramFiles_; ///< Track amber FF param files loaded from leaprc files
+    static Sarray libFiles_;   ///< Track amber library/prep files loaded from leaprc files
 };
 #endif

From 0b382e8fb04fdd4c46f56460b1d30cb0dc19bef2 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 21 Feb 2024 12:54:03 -0500
Subject: [PATCH 0577/1492] Fix residue naming in build

---
 src/Exec_Build.cpp | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index f1d17ad580..e3d07e8b40 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -149,11 +149,11 @@ const
     mprintf("\tAdding atoms for residue %s\n", topIn.TruncResNameOnumId(ires).c_str());
     int atomOffset = topOut.Natom();
     //mprintf("DEBUG: atom offset is %i\n", atomOffset);
-    Residue const& currentRes = topIn.Res(ires);
     DataSet_Coords* resTemplate = ResTemplates[ires];
     IParray intraResBonds;
     if (resTemplate == 0) {
       // ----- No template. Just add the atoms. ------------
+      Residue const& currentRes = topIn.Res(ires);
       AtomOffsets.push_back( -1 );
       for (int itgt = currentRes.FirstAtom(); itgt != currentRes.LastAtom(); ++itgt)
       {
@@ -183,6 +183,15 @@ const
       }
     } else {
       // ----- A template exists for this residue. ---------
+      Residue currentRes = topIn.Res(ires);
+      // Use template residue name.
+      // To match LEaP behavior, if the template name is > 3 characters,
+      // truncate to the last 3 characters.
+      NameType const& templateResName = resTemplate->Top().Res(0).Name();
+      if (templateResName.len() < 4)
+        currentRes.SetName( templateResName );
+      else
+        currentRes.SetName( NameType( (*templateResName) + ( templateResName.len() - 3) ) );
       // Map source atoms to template atoms.
       std::vector<int> map = MapAtomsToTemplate( topIn, ires, resTemplate );
       if (debug_ > 1) {

From 0cd83a60e12fab98bc7a6a91f126f205af52110e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 21 Feb 2024 13:21:25 -0500
Subject: [PATCH 0578/1492] Add -leappi configure flag to make cpptraj use
 LEaPs value of PI for converting radians/degrees to more directly compare
 output topologies

---
 configure       |  7 +++++++
 src/Constants.h | 19 ++++++++++++++-----
 2 files changed, 21 insertions(+), 5 deletions(-)

diff --git a/configure b/configure
index 38282377c9..8d5be32139 100755
--- a/configure
+++ b/configure
@@ -102,6 +102,7 @@ UsageFull() {
   echo "    -gprofile         : Use Gnu compiler GLIBC profiling (>= V4.5)*"
   echo "    -vtune            : Enable options for use with Intel Vtune."
   echo "    -single-ensemble  : Enable support for reading/writing single ensemble trajectories."
+  echo "    -leappi           : Use LEaP's value of PI for converting radians/degrees."
   echo ""
   echo "*NOTE: -profile and -gprofile are mutually exclusive."
   echo ""
@@ -198,6 +199,7 @@ BUILD_MPI=''      # If not empty, attempt to download and build specified mpi di
 
 USE_SINGLEENSEMBLE=0 # Enable support for single ensemble trajectories
 USE_CPPTRAJDEBUG=0   # Enable internal cpptraj debug flags
+USE_LEAP_PI=0        # Use LEaP's value of PI for converting radians/degrees
 
 CLEAN='yes'          # yes = clean after configure, no = do not
 PERFORM_CHECKS='yes' # yes = Check compilers/libraries, no = do not
@@ -1257,6 +1259,7 @@ SetupFinalFlags() {
       DIRECTIVES="$DIRECTIVES -DLIBPME -DHAVE_FFTWD=1"
     fi
   fi
+  if [ $USE_LEAP_PI -eq 1 ] ; then DIRECTIVES="$DIRECTIVES -DCPPTRAJ_USE_LEAP_PI" ; fi
   # Determine if this is a GitHub or AmberTools build
   if [ ! -z "$AMBERHOME" ] ; then
     AMBCFGDIR=`pwd | grep "AmberTools/src"`
@@ -2597,6 +2600,7 @@ while [ ! -z "$1" ] ; do
     '-nolfs'           ) LFS='' ;;
     '-single-ensemble' ) USE_SINGLEENSEMBLE=1 ;;
     '-debugon'         ) USE_CPPTRAJDEBUG=1 ;;
+    '-leappi'          ) USE_LEAP_PI=1 ;;
     # Code profiling
     '-profile'  ) USE_PROFILE=1 ;;
     '-gprofile' ) USE_PROFILE=2 ;;
@@ -2812,6 +2816,9 @@ if [ $USE_STATIC -eq 1 ] ; then
 elif [ $USE_STATIC -eq 2 ] ; then
   echo "  Specified libraries will be linked statically if possible."
 fi
+if [ $USE_LEAP_PI -eq 1 ] ; then
+  echo "  Using LEaP's value of PI for converting radians/degrees."
+fi
 #echo DIRECTIVES $DIRECTIVES
 #echo CFLAGS $CFLAGS
 #echo CXXFLAGS $CXXFLAGS
diff --git a/src/Constants.h b/src/Constants.h
index 2fc72e1f0e..ce4facaeaa 100644
--- a/src/Constants.h
+++ b/src/Constants.h
@@ -12,16 +12,25 @@
  */
 namespace Constants {
   // Various incarnations of PI
-  const double PI           = 3.141592653589793; 
+# ifdef CPPTRAJ_USE_LEAP_PI
+  // NOTE: This lower-precision value of PI is ONLY for comparing results
+  //       directly to LEaP output. It is obtained from LEaP's DEGTORAD
+  //       constant 0.0174533 * 180.
+  const double PI           = 3.141594;
+  const double DEGRAD       = 0.0174533;
+  const double RADDEG       = 1 / DEGRAD;
+# else
+  const double PI           = 3.141592653589793;
+   /// Convert degrees to radians
+  const double DEGRAD       = 0.017453292519943295; // may have precision loss 
+  /// Convert radians to degrees
+  const double RADDEG       =   57.29577951308232;  // may have precision loss
+# endif
   const double TWOPI        = 6.283185307179586;  // may have precision loss
   const double FOURPI       = 12.566370614359172; // may have precision loss
   const double FOURTHIRDSPI = 4.1887902047863909; // may have precision loss 
   const double FOURFIFTHSPI = 2.5132741228718345; // may have precision loss
   const double PIOVER2      = 1.5707963267948966; // may have precision loss 
-  /// Convert degrees to radians
-  const double DEGRAD       = 0.017453292519943295; // may have precision loss 
-  /// Convert radians to degrees
-  const double RADDEG       =   57.29577951308232;  // may have precision loss
   /// For checking floating point zero
   const double SMALL        = 0.00000000000001;
   /// Gas constant in J/mol*K

From 7a6a87c7699b57fd162735b824906aefba780f58 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 21 Feb 2024 13:29:37 -0500
Subject: [PATCH 0579/1492] Only warn about improper reorder if debug level is
 set

---
 src/Topology.cpp | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index abf3dc73a4..0825936d40 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2726,6 +2726,7 @@ void Topology::AssignAngleParams(ParmHolder<AngleParmType> const& newAngleParams
 void Topology::warn_improper_reorder(DihedralType const& imp0, DihedralType const& imp)
 const
 {
+  if (debug_ < 1) return;
   mprintf("Warning: Improper types have been reordered from %4s %4s %4s %4s",
           *(atoms_[imp0.A1()].Type()),
           *(atoms_[imp0.A2()].Type()),

From 083a583498094a796c63f7ae2b267108c102a1e7 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 21 Feb 2024 13:39:01 -0500
Subject: [PATCH 0580/1492] Hide more debug info

---
 src/Exec_Build.cpp | 71 +++++++++++++++++++++++++++-------------------
 src/Parm_Amber.cpp |  9 ++++--
 2 files changed, 48 insertions(+), 32 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index e3d07e8b40..3282e1668b 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -66,7 +66,8 @@ const
   for (int ires = 0; ires != topIn.Nres(); ires++)
   {
     Residue const& currentRes = topIn.Res(ires);
-    mprintf("DEBUG: ---------- Processing Residue %s ---------- \n", topIn.TruncResNameNum(ires).c_str());
+    if (debug_ > 0)
+      mprintf("DEBUG: ---------- Processing Residue %s ---------- \n", topIn.TruncResNameNum(ires).c_str());
     int pres = ires - 1;
     int nres = ires + 1;
     // Determine if this is a terminal residue
@@ -86,7 +87,8 @@ const
     } else {
       resTermType = Cpptraj::Structure::NON_TERMINAL;
     }
-    mprintf("DEBUG: Residue type: %s terminal\n", Cpptraj::Structure::terminalStr(resTermType));
+    if (debug_ > 0)
+      mprintf("DEBUG: Residue type: %s terminal\n", Cpptraj::Structure::terminalStr(resTermType));
     // Identify a template based on the residue name.
     DataSet_Coords* resTemplate = creator.IdTemplateFromResname(currentRes.Name(), resTermType);
     if (resTemplate == 0) {
@@ -96,8 +98,9 @@ const
       resHeadAtoms.push_back( -1 );
       resTailAtoms.push_back( -1 );
     } else {
-      mprintf("\tTemplate %s being used for residue %s\n",
-              resTemplate->legend(), topIn.TruncResNameOnumId(ires).c_str());
+      if (debug_ > 0)
+        mprintf("\tTemplate %s being used for residue %s\n",
+                resTemplate->legend(), topIn.TruncResNameOnumId(ires).c_str());
       // Save the head and tail atoms
       AssociatedData* ad = resTemplate->GetAssociatedData(AssociatedData::CONNECT);
       if (ad == 0) {
@@ -146,7 +149,8 @@ const
   int nRefAtomsMissing = 0;
   for (int ires = 0; ires != topIn.Nres(); ires++)
   {
-    mprintf("\tAdding atoms for residue %s\n", topIn.TruncResNameOnumId(ires).c_str());
+    if (debug_ > 0)
+      mprintf("\tAdding atoms for residue %s\n", topIn.TruncResNameOnumId(ires).c_str());
     int atomOffset = topOut.Natom();
     //mprintf("DEBUG: atom offset is %i\n", atomOffset);
     DataSet_Coords* resTemplate = ResTemplates[ires];
@@ -248,7 +252,8 @@ const
       for (int itgt = 0; itgt != currentRes.NumAtoms(); itgt++)
         if (pdb[itgt] == -1)
           nTgtAtomsMissing++;
-      mprintf("\t%i source atoms not mapped to template.\n", nTgtAtomsMissing);
+      if (nTgtAtomsMissing > 0)
+        mprintf("\t%i source atoms not mapped to template.\n", nTgtAtomsMissing);
       // Save atom offset if atoms need to be built
       if (atomsNeedBuilding)
         AtomOffsets.push_back( atomOffset );
@@ -268,12 +273,14 @@ const
 
   // -----------------------------------
   // DEBUG - Print primary connection atoms
-  for (unsigned int idx = 0; idx != ResTemplates.size(); idx++) {
-    if (ResTemplates[idx] != 0) {
-      mprintf("DEBUG: Template %s", ResTemplates[idx]->legend());
-      if (resHeadAtoms[idx] > -1) mprintf(" head %s", topOut.AtomMaskName(resHeadAtoms[idx]).c_str());
-      if (resTailAtoms[idx] > -1) mprintf(" tail %s", topOut.AtomMaskName(resTailAtoms[idx]).c_str());
-      mprintf("\n");
+  if (debug_ > 0) {
+    for (unsigned int idx = 0; idx != ResTemplates.size(); idx++) {
+      if (ResTemplates[idx] != 0) {
+        mprintf("DEBUG: Template %s", ResTemplates[idx]->legend());
+        if (resHeadAtoms[idx] > -1) mprintf(" head %s", topOut.AtomMaskName(resHeadAtoms[idx]).c_str());
+        if (resTailAtoms[idx] > -1) mprintf(" tail %s", topOut.AtomMaskName(resTailAtoms[idx]).c_str());
+        mprintf("\n");
+      }
     }
   }
 
@@ -286,9 +293,10 @@ const
     int pres = ires - 1;
     if (resHeadAtoms[ires] != -1) {
       if (resTailAtoms[pres] != -1) {
-        mprintf("DEBUG: Connecting HEAD atom %s to tail atom %s\n",
-                topOut.AtomMaskName(resHeadAtoms[ires]).c_str(),
-                topOut.AtomMaskName(resTailAtoms[pres]).c_str());
+        if (debug_ > 0)
+          mprintf("DEBUG: Connecting HEAD atom %s to tail atom %s\n",
+                  topOut.AtomMaskName(resHeadAtoms[ires]).c_str(),
+                  topOut.AtomMaskName(resTailAtoms[pres]).c_str());
         resBondingAtoms[ires].push_back( Ipair(resHeadAtoms[ires], resTailAtoms[pres]) );
         resBondingAtoms[pres].push_back( Ipair(resTailAtoms[pres], resHeadAtoms[ires]) );
         resHeadAtoms[ires] = -1;
@@ -314,9 +322,10 @@ const
     ResAtPair const& ra0 = *it;
     ++it;
     ResAtPair const& ra1 = *it;
-    mprintf("DEBUG: Inter-res bond: Res %i atom %s to res %i atom %s\n",
-            ra0.first+1, *(ra0.second),
-            ra1.first+1, *(ra1.second));
+    if (debug_ > 1)
+      mprintf("DEBUG: Inter-res bond: Res %i atom %s to res %i atom %s\n",
+              ra0.first+1, *(ra0.second),
+              ra1.first+1, *(ra1.second));
     int at0 = topOut.FindAtomInResidue(ra0.first, ra0.second);
     if (at0 < 0) {
       mprinterr("Error: Atom %s not found in residue %i\n", *(ra0.second), ra0.first);
@@ -406,12 +415,14 @@ const
   }*/
 
   // DEBUG print inter-residue bonding atoms
-  for (std::vector<IParray>::const_iterator rit = resBondingAtoms.begin();
-                                            rit != resBondingAtoms.end(); ++rit)
-  {
-    mprintf("\tResidue %s bonding atoms.\n", topOut.TruncResNameNum(rit-resBondingAtoms.begin()).c_str());
-    for (IParray::const_iterator it = rit->begin(); it != rit->end(); ++it)
-      mprintf("\t\t%s - %s\n", topOut.AtomMaskName(it->first).c_str(), topOut.AtomMaskName(it->second).c_str());
+  if (debug_ > 0) {
+    for (std::vector<IParray>::const_iterator rit = resBondingAtoms.begin();
+                                              rit != resBondingAtoms.end(); ++rit)
+    {
+      mprintf("\tResidue %s bonding atoms.\n", topOut.TruncResNameNum(rit-resBondingAtoms.begin()).c_str());
+      for (IParray::const_iterator it = rit->begin(); it != rit->end(); ++it)
+        mprintf("\t\t%s - %s\n", topOut.AtomMaskName(it->first).c_str(), topOut.AtomMaskName(it->second).c_str());
+    }
   }
 
   // -----------------------------------
@@ -441,8 +452,9 @@ const
   {
     long int ires = it-AtomOffsets.begin();
     if (*it > -1) {
-      mprintf("DEBUG: ***** BUILD residue %li %s *****\n", ires + 1,
-              topOut.TruncResNameOnumId(ires).c_str());
+      if (debug_ > 0)
+        mprintf("DEBUG: ***** BUILD residue %li %s *****\n", ires + 1,
+                topOut.TruncResNameOnumId(ires).c_str());
       // Residue has atom offset which indicates it needs something built.
       Cpptraj::Structure::Builder structureBuilder;// = new Cpptraj::Structure::Builder();
       structureBuilder.SetDebug( debug_ );
@@ -465,9 +477,10 @@ const
                                    resBonds != resBondingAtoms[ires].end(); ++resBonds)
       {
         if (resBonds->second < resBonds->first) {
-          mprintf("\t\tResidue connection: %s - %s\n",
-                  topOut.AtomMaskName(resBonds->first).c_str(),
-                  topOut.AtomMaskName(resBonds->second).c_str());
+          if (debug_ > 0)
+            mprintf("\t\tResidue connection: %s - %s\n",
+                    topOut.AtomMaskName(resBonds->first).c_str(),
+                    topOut.AtomMaskName(resBonds->second).c_str());
           topOut.AddBond(resBonds->first, resBonds->second);
           // Generate internals around the link
           if (structureBuilder.GenerateInternalsAroundLink(resBonds->first, resBonds->second,
diff --git a/src/Parm_Amber.cpp b/src/Parm_Amber.cpp
index 9f2b903bfb..f705b73995 100644
--- a/src/Parm_Amber.cpp
+++ b/src/Parm_Amber.cpp
@@ -1631,13 +1631,16 @@ int Parm_Amber::WriteDihedrals(FlagType flag, DihedralArray const& DIH) {
   for (DihedralArray::const_iterator it = DIH.begin(); it != DIH.end(); ++it) {
     int dihIdxs[4];
     if (it->A3() == 0 || it->A4() == 0) {
-      mprintf("Warning: Had to turn torsion around to avoid K,L == 0\n");
-      mprintf("Warning: Old order (i j k l): %i %i %i %i\n", it->A1(), it->A2(), it->A3(), it->A4());
+      if (debug_ > 0) {
+        mprintf("Warning: Had to turn torsion around to avoid K,L == 0\n");
+        mprintf("Warning: Old order (i j k l): %i %i %i %i\n", it->A1(), it->A2(), it->A3(), it->A4());
+      }
       dihIdxs[0] = it->A4()*3;
       dihIdxs[1] = it->A3()*3;
       dihIdxs[2] = it->A2()*3;
       dihIdxs[3] = it->A1()*3;
-      mprintf("Warning: New order (i j k l): %i %i %i %i\n", it->A4(), it->A3(), it->A2(), it->A1());
+      if (debug_ > 0)
+        mprintf("Warning: New order (i j k l): %i %i %i %i\n", it->A4(), it->A3(), it->A2(), it->A1());
     } else {
       dihIdxs[0] = it->A1()*3;
       dihIdxs[1] = it->A2()*3;

From a3ac7795da238e0912c4a158d1613b93280d4cb9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 21 Feb 2024 13:42:00 -0500
Subject: [PATCH 0581/1492] Set topology name and debug

---
 src/Exec_Sequence.cpp | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/Exec_Sequence.cpp b/src/Exec_Sequence.cpp
index 22b1158530..70ac5167d6 100644
--- a/src/Exec_Sequence.cpp
+++ b/src/Exec_Sequence.cpp
@@ -46,6 +46,8 @@ const
 //    mprintf("\tUnit %s HEAD %i TAIL %i\n", Units[idx]->legend(), connectAt0[idx]+1, connectAt1[idx]+1);
 
   Topology topOut;
+  topOut.SetDebug( debug_ );
+  topOut.SetParmName( OUT->Meta().Name(), FileName() );
   Frame frameOut;
   mprintf("\tFinal structure should have %i atoms.\n", total_natom);
   frameOut.SetupFrame( total_natom );
@@ -214,7 +216,6 @@ const
 /*
   Topology combinedTop;
   combinedTop.SetDebug( debug_ );
-  combinedTop.SetParmName( OUT->Meta().Name(), FileName() );
   combinedTop.AppendTop( Units.front()->Top() );
   //combinedTop.SetParmBox( Units // TODO
   combinedTop.Brief("Sequence topology:");

From 9a85b50885da3a49139ed93ead765b75db0ff7df Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 21 Feb 2024 13:47:35 -0500
Subject: [PATCH 0582/1492] Add title keyword

---
 src/Exec_Build.cpp | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 3282e1668b..63e16fea37 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -531,6 +531,7 @@ const
 void Exec_Build::Help() const
 {
   mprintf("\tname <output COORDS> crdset <COORDS set> [frame <#>]\n"
+          "\t[title <title>]\n"
           "\t[%s]\n"
           "\t[{%s} ...]\n"
           "\t[{%s} ...]\n"
@@ -544,6 +545,7 @@ void Exec_Build::Help() const
 Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
 {
   debug_ = State.Debug();
+  std::string title = argIn.GetStringKey("title");
 /*  // Atom scan direction
   std::string atomscandir = argIn.GetStringKey("atomscandir");
   if (!atomscandir.empty()) {
@@ -706,6 +708,11 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
 
   // Fill in atoms with templates
   Topology topOut;
+  topOut.SetDebug( debug_ );
+  // TODO better default
+  if (title.empty())
+    title.assign( topIn.c_str() );
+  topOut.SetParmName( title, FileName() );
   Frame frameOut;
   if (FillAtomsWithTemplates(topOut, frameOut, topIn, frameIn, creator)) {
     mprinterr("Error: Could not fill in atoms using templates.\n");

From 5e07aca7a1763908427c0f7346c806acd1b2aa71 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 21 Feb 2024 13:48:53 -0500
Subject: [PATCH 0583/1492] Fix message

---
 src/Exec_Build.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 63e16fea37..aca73da1d0 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -344,7 +344,7 @@ const
       // Check if we already have a connection from ra0 to ra1.
       if (resIsConnected(ResidueConnections[ra0.first], ra1.first)) {
         mprintf("Warning: Residue %s already connected to residue %s; ignoring\n"
-                "Warning: potential detected bond %s - %s\n",
+                "Warning:   potential detected bond %s - %s\n",
                 topOut.TruncResNameNum(ra0.first).c_str(),
                 topOut.TruncResNameNum(ra1.first).c_str(),
                 topOut.AtomMaskName(at0).c_str(),

From bdaa392d5e97ce4161e7bd9f87f2ac3d140c62f3 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 21 Feb 2024 14:49:24 -0500
Subject: [PATCH 0584/1492] Start the PdbCleaner class

---
 src/Structure/PdbCleaner.cpp | 37 ++++++++++++++++++++++++++++++++++++
 src/Structure/PdbCleaner.h   | 25 ++++++++++++++++++++++++
 2 files changed, 62 insertions(+)
 create mode 100644 src/Structure/PdbCleaner.cpp
 create mode 100644 src/Structure/PdbCleaner.h

diff --git a/src/Structure/PdbCleaner.cpp b/src/Structure/PdbCleaner.cpp
new file mode 100644
index 0000000000..3f2477ef24
--- /dev/null
+++ b/src/Structure/PdbCleaner.cpp
@@ -0,0 +1,37 @@
+#include "PdbCleaner.h"
+#include "../ArgList.h"
+#include "../CpptrajStdio.h"
+
+using namespace Cpptraj::Structure;
+
+/** CONSTRUCTOR */
+PdbCleaner::PdbCleaner() :
+  remove_water_(false),
+  remove_h_(false)
+{}
+
+/** Initialize */
+int PdbCleaner::InitPdbCleaner(ArgList& argIn, std::string const& solventResNameIn,
+                               Iarray const& pdbResToRemoveIn)
+{
+  resnumsToRemove_ = pdbResToRemoveIn;
+  remove_water_ = argIn.hasKey("nowat");
+  if (solventResNameIn.empty())
+    waterMask_ = ":HOH";
+  else
+    waterMask_ = argIn.GetStringKey("watermask", ":" + solventResNameIn);
+  remove_h_ = argIn.hasKey("noh");
+  altLocArg_ = argIn.GetStringKey("keepaltloc");
+  if (!altLocArg_.empty()) {
+    if (altLocArg_ != "highestocc" &&
+        altLocArg_.size() > 1)
+    {
+      mprinterr("Error: Invalid keyword for 'keepaltloc' '%s'; must be 'highestocc' or 1 character.\n",
+                altLocArg_.c_str());
+      return 1;
+    }
+  }
+  stripMask_ = argIn.GetStringKey("stripmask");
+
+  return 0;
+}
diff --git a/src/Structure/PdbCleaner.h b/src/Structure/PdbCleaner.h
new file mode 100644
index 0000000000..69aaeb7ce4
--- /dev/null
+++ b/src/Structure/PdbCleaner.h
@@ -0,0 +1,25 @@
+#ifndef INC_STRUCTURE_PDBCLEANER_H
+#define INC_STRUCTURE_PDBCLEANER_H
+#include <vector>
+#include <string>
+class ArgList;
+namespace Cpptraj {
+namespace Structure {
+/// Used to clean up structures read from a PDB
+class PdbCleaner {
+    typedef std::vector<int> Iarray;
+  public:
+    PdbCleaner();
+    /// Initialize
+    int InitPdbCleaner(ArgList&, std::string const&, Iarray const&);
+  private:
+    bool remove_water_;      ///< If true, remove any water.
+    bool remove_h_;          ///< If true, remove hydrogen atoms.
+    std::string waterMask_;  ///< Mask expression for selecting water.
+    std::string altLocArg_;  ///< Only keep atoms with this alternate location identifier.
+    std::string stripMask_;  ///< General mask for removing atoms.
+    Iarray resnumsToRemove_; ///< Other residue numbers to remove.
+};
+}
+}
+#endif

From f2bb6a709c129bd7f979b0f5a01169922bd1b767 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 21 Feb 2024 15:03:13 -0500
Subject: [PATCH 0585/1492] Add setup, info, and modification routines.

---
 src/Structure/PdbCleaner.cpp | 206 +++++++++++++++++++++++++++++++++++
 src/Structure/PdbCleaner.h   |   9 ++
 2 files changed, 215 insertions(+)

diff --git a/src/Structure/PdbCleaner.cpp b/src/Structure/PdbCleaner.cpp
index 3f2477ef24..f40c2498ae 100644
--- a/src/Structure/PdbCleaner.cpp
+++ b/src/Structure/PdbCleaner.cpp
@@ -1,11 +1,14 @@
 #include "PdbCleaner.h"
 #include "../ArgList.h"
 #include "../CpptrajStdio.h"
+#include "../Topology.h"
+#include <map>
 
 using namespace Cpptraj::Structure;
 
 /** CONSTRUCTOR */
 PdbCleaner::PdbCleaner() :
+  debug_(0),
   remove_water_(false),
   remove_h_(false)
 {}
@@ -35,3 +38,206 @@ int PdbCleaner::InitPdbCleaner(ArgList& argIn, std::string const& solventResName
 
   return 0;
 }
+
+/** Setup */
+int PdbCleaner::SetupPdbCleaner(Topology const& topIn) {
+  // If keeping highest alt loc, check that alt locs and occupancies are present.
+  if (altLocArg_ == "highestocc") {
+    if (topIn.AtomAltLoc().empty()) {
+      mprintf("Warning: 'highestocc' specified but no atom alternate location info.\n");
+      altLocArg_.clear();
+    } else if (topIn.Occupancy().empty()) {
+      mprintf("Warning: 'highestocc' specified but no atom occupancy info.\n");
+      altLocArg_.clear();
+    }
+  }
+  // Check if alternate atom location IDs are present 
+  if (!topIn.AtomAltLoc().empty()) {
+    // For LEaP, must have only 1 atom alternate location
+    char firstAltLoc = ' ';
+    for (std::vector<char>::const_iterator altLocId = topIn.AtomAltLoc().begin();
+                                           altLocId != topIn.AtomAltLoc().end();
+                                         ++altLocId)
+    {
+      if (firstAltLoc == ' ') {
+        // Find first non-blank alternate location ID
+        if (*altLocId != ' ')
+          firstAltLoc = *altLocId;
+      } else if (*altLocId != ' ' && *altLocId != firstAltLoc) {
+        // Choose a default if necessary
+        if (altLocArg_.empty()) {
+          altLocArg_.assign(1, firstAltLoc);
+          mprintf("Warning: '%s' has atoms with multiple alternate location IDs.\n"
+                  "Warning: Keeping only '%s'.\n"
+                  "Warning: To choose a specific location to keep use the 'keepaltloc <char>'\n"
+                  "Warning:  keyword.\n", topIn.c_str(), altLocArg_.c_str());
+         }
+         break;
+      }
+    }
+  }
+  return 0;
+}
+
+/** Print info to stdout. */
+void PdbCleaner::PdbCleanerInfo() const {
+  if (remove_water_)
+    mprintf("\tRemoving solvent. Solvent mask= '%s'\n", waterMask_.c_str());
+  if (remove_h_)
+    mprintf("\tRemoving hydrogens.\n");
+  if (!altLocArg_.empty())
+    mprintf("\tIf present, keeping only alternate atom locations denoted by '%s'\n", altLocArg_.c_str());
+  if (!stripMask_.empty())
+    mprintf("\tRemoving atoms in mask '%s'\n", stripMask_.c_str());
+}
+
+/** Modify coords according to user wishes. */
+int PdbCleaner::ModifyCoords( Topology& topIn, Frame& frameIn )
+const
+{
+  // Create a mask denoting which atoms will be kept.
+  std::vector<bool> atomsToKeep( topIn.Natom(), true );
+  // Previously-determined array of residues to remove
+  for (Iarray::const_iterator rnum = resnumsToRemove_.begin();
+                              rnum != resnumsToRemove_.end(); ++rnum)
+  {
+    Residue const& res = topIn.Res( *rnum );
+    mprintf("\tRemoving %s\n", topIn.TruncResNameOnumId( *rnum ).c_str());
+    for (int at = res.FirstAtom(); at != res.LastAtom(); at++)
+      atomsToKeep[at] = false;
+  }
+  // User-specified strip mask
+  if (!stripMask_.empty()) {
+    AtomMask mask;
+    if (mask.SetMaskString( stripMask_ )) {
+      mprinterr("Error: Invalid mask string '%s'\n", stripMask_.c_str());
+      return 1;
+    }
+    if (topIn.SetupIntegerMask( mask )) return 1;
+    mask.MaskInfo();
+    if (!mask.None()) {
+      for (AtomMask::const_iterator atm = mask.begin(); atm != mask.end(); ++atm)
+        atomsToKeep[*atm] = false;
+    }
+  }
+  if (remove_water_) {
+    // Do not use cpptraj definition of solvent in case we have e.g. bound HOH
+    AtomMask mask;
+    if (mask.SetMaskString( waterMask_ )) {
+      mprinterr("Error: Invalid solvent mask string '%s'\n", waterMask_.c_str());
+      return 1;
+    }
+    if (topIn.SetupIntegerMask( mask )) return 1;
+    mask.MaskInfo();
+    if (!mask.None()) {
+      for (AtomMask::const_iterator atm = mask.begin(); atm != mask.end(); ++atm)
+        atomsToKeep[*atm] = false;
+    }
+
+  }
+  // Identify alternate atom location groups.
+  if (!altLocArg_.empty()) {
+    if (topIn.AtomAltLoc().empty()) {
+      mprintf("\tNo alternate atom locations.\n");
+    } else {
+      // Map atom name to atom indices
+      typedef std::map<NameType, std::vector<int>> AlocMapType;
+      AlocMapType alocMap;
+      for (int rnum = 0; rnum != topIn.Nres(); rnum++) {
+        alocMap.clear();
+        for (int at = topIn.Res(rnum).FirstAtom(); at != topIn.Res(rnum).LastAtom(); at++) {
+          if (topIn.AtomAltLoc()[at] != ' ') {
+            AlocMapType::iterator it = alocMap.find( topIn[at].Name() );
+            if (it == alocMap.end()) {
+              alocMap.insert( std::pair<NameType, std::vector<int>>( topIn[at].Name(),
+                                                                     std::vector<int>(1, at) ));
+            } else {
+              it->second.push_back( at );
+            }
+          }
+        } // END loop over atoms in residue
+        if (!alocMap.empty()) {
+          if (debug_ > 0)
+            mprintf("DEBUG: Alternate loc. for %s\n", topIn.TruncResNameOnumId(rnum).c_str());
+          // Loop over atoms with alternate locations
+          for (AlocMapType::const_iterator it = alocMap.begin(); it != alocMap.end(); ++it) {
+            if (debug_ > 0) {
+              // Print all alternate atoms
+              mprintf("\t'%s'", *(it->first));
+              for (std::vector<int>::const_iterator at = it->second.begin();
+                                                    at != it->second.end(); ++at)
+                mprintf(" %s[%c]", *(topIn[*at].Name()), topIn.AtomAltLoc()[*at]);
+              mprintf("\n");
+            }
+            // For each, choose which location to keep.
+            if (altLocArg_.size() == 1) {
+              // Keep only specified character
+              char altLocChar = altLocArg_[0];
+              for (std::vector<int>::const_iterator at = it->second.begin();
+                                                    at != it->second.end(); ++at)
+                if (topIn.AtomAltLoc()[*at] != altLocChar)
+                  atomsToKeep[*at] = false;
+            } else {
+              // Keep highest occupancy
+              if (topIn.Occupancy().empty()) {
+                mprintf("\tNo occupancy.\n"); // TODO error?
+              } else {
+                int highestOccAt = -1;
+                float highestOcc = 0;
+                for (std::vector<int>::const_iterator at = it->second.begin();
+                                                      at != it->second.end(); ++at)
+                {
+                  if (highestOccAt == -1) {
+                    highestOccAt = *at;
+                    highestOcc = topIn.Occupancy()[*at];
+                  } else if (topIn.Occupancy()[*at] > highestOcc) {
+                    highestOccAt = *at;
+                    highestOcc = topIn.Occupancy()[*at];
+                  }
+                }
+                // Set everything beside highest occ to false
+                for (std::vector<int>::const_iterator at = it->second.begin();
+                                                      at != it->second.end(); ++at)
+                  if (*at != highestOccAt)
+                    atomsToKeep[*at] = false;
+              }
+            }
+          } // END loop over atoms with alternate locations
+        }
+      } // END loop over residue numbers
+    }
+  }
+  // Denote hydrogens if removing
+  if (remove_h_) {
+    for (int at = 0; at != topIn.Natom(); at++)
+      if (topIn[at].Element() == Atom::HYDROGEN)
+        atomsToKeep[at] = false;
+  }
+
+  // Set up mask of only kept atoms.
+  AtomMask keptAtoms;
+  keptAtoms.SetNatoms( topIn.Natom() );
+  for (int idx = 0; idx != topIn.Natom(); idx++) {
+    if (atomsToKeep[idx])
+      keptAtoms.AddSelectedAtom(idx);
+  }
+  if (keptAtoms.Nselected() == topIn.Natom())
+    // Keeping everything, no modifications
+    return 0;
+  // Modify top/frame
+  Topology* newTop = topIn.modifyStateByMask( keptAtoms );
+  if (newTop == 0) {
+    mprinterr("Error: Could not create new topology.\n");
+    return 1;
+  }
+  newTop->Brief("After removing atoms:");
+  Frame newFrame;
+  newFrame.SetupFrameV(newTop->Atoms(), frameIn.CoordsInfo());
+  newFrame.SetFrame(frameIn, keptAtoms);
+
+  topIn = *newTop;
+  frameIn = newFrame;
+  delete newTop;
+
+  return 0;
+}
diff --git a/src/Structure/PdbCleaner.h b/src/Structure/PdbCleaner.h
index 69aaeb7ce4..8455ab0759 100644
--- a/src/Structure/PdbCleaner.h
+++ b/src/Structure/PdbCleaner.h
@@ -3,6 +3,8 @@
 #include <vector>
 #include <string>
 class ArgList;
+class Frame;
+class Topology;
 namespace Cpptraj {
 namespace Structure {
 /// Used to clean up structures read from a PDB
@@ -12,7 +14,14 @@ class PdbCleaner {
     PdbCleaner();
     /// Initialize
     int InitPdbCleaner(ArgList&, std::string const&, Iarray const&);
+    /// Setup
+    int SetupPdbCleaner(Topology const&);
+    /// Info
+    void PdbCleanerInfo() const;
+    /// Modify top/frame
+    int ModifyCoords(Topology&, Frame&) const;
   private:
+    int debug_;
     bool remove_water_;      ///< If true, remove any water.
     bool remove_h_;          ///< If true, remove hydrogen atoms.
     std::string waterMask_;  ///< Mask expression for selecting water.

From 5cfbdff2c2b880f9a2b15e22ed9253974a1adc10 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 21 Feb 2024 15:05:16 -0500
Subject: [PATCH 0586/1492] Add help text function

---
 src/Structure/PdbCleaner.cpp | 7 +++++++
 src/Structure/PdbCleaner.h   | 2 ++
 2 files changed, 9 insertions(+)

diff --git a/src/Structure/PdbCleaner.cpp b/src/Structure/PdbCleaner.cpp
index f40c2498ae..6554e89275 100644
--- a/src/Structure/PdbCleaner.cpp
+++ b/src/Structure/PdbCleaner.cpp
@@ -13,6 +13,13 @@ PdbCleaner::PdbCleaner() :
   remove_h_(false)
 {}
 
+/** Print help text. */
+void PdbCleaner::Help() {
+  mprintf("\t[nowat [watermask <watermask>] [noh]\n"
+          "\t[keepaltloc {<alt loc ID>|highestocc}]\n"
+          "\t[stripmask <stripmask>]\n");
+}
+
 /** Initialize */
 int PdbCleaner::InitPdbCleaner(ArgList& argIn, std::string const& solventResNameIn,
                                Iarray const& pdbResToRemoveIn)
diff --git a/src/Structure/PdbCleaner.h b/src/Structure/PdbCleaner.h
index 8455ab0759..9e9e1c2bac 100644
--- a/src/Structure/PdbCleaner.h
+++ b/src/Structure/PdbCleaner.h
@@ -12,6 +12,8 @@ class PdbCleaner {
     typedef std::vector<int> Iarray;
   public:
     PdbCleaner();
+    /// Help text
+    static void Help();
     /// Initialize
     int InitPdbCleaner(ArgList&, std::string const&, Iarray const&);
     /// Setup

From 38d9ba963e583c3372216b8692227ccdcac409e1 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 21 Feb 2024 15:05:51 -0500
Subject: [PATCH 0587/1492] Add to build

---
 src/Structure/CMakeLists.txt  | 1 +
 src/Structure/structuredepend | 1 +
 src/Structure/structurefiles  | 1 +
 3 files changed, 3 insertions(+)

diff --git a/src/Structure/CMakeLists.txt b/src/Structure/CMakeLists.txt
index 18f46a3c1e..d4287c6e3c 100644
--- a/src/Structure/CMakeLists.txt
+++ b/src/Structure/CMakeLists.txt
@@ -10,6 +10,7 @@ target_sources(cpptraj_common_obj PRIVATE
   ${CMAKE_CURRENT_LIST_DIR}/GenerateConnectivityArrays.cpp
   ${CMAKE_CURRENT_LIST_DIR}/HisProt.cpp
   ${CMAKE_CURRENT_LIST_DIR}/InternalCoords.cpp
+  ${CMAKE_CURRENT_LIST_DIR}/PdbCleaner.cpp
   ${CMAKE_CURRENT_LIST_DIR}/StructureEnum.cpp
   ${CMAKE_CURRENT_LIST_DIR}/StructureRoutines.cpp
   ${CMAKE_CURRENT_LIST_DIR}/SugarBuilder.cpp
diff --git a/src/Structure/structuredepend b/src/Structure/structuredepend
index c4e06a854c..70320f83f0 100644
--- a/src/Structure/structuredepend
+++ b/src/Structure/structuredepend
@@ -8,6 +8,7 @@ FxnGroupBuilder.o : FxnGroupBuilder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ..
 GenerateConnectivityArrays.o : GenerateConnectivityArrays.cpp ../Atom.h ../Constants.h ../CpptrajStdio.h ../NameType.h ../ParameterTypes.h ../Residue.h ../SymbolExporting.h GenerateConnectivityArrays.h
 HisProt.o : HisProt.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h HisProt.h StructureRoutines.h
 InternalCoords.o : InternalCoords.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h InternalCoords.h
+PdbCleaner.o : PdbCleaner.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h PdbCleaner.h
 StructureEnum.o : StructureEnum.cpp StructureEnum.h
 StructureRoutines.o : StructureRoutines.cpp ../Atom.h ../CpptrajStdio.h ../NameType.h ../Residue.h ../SymbolExporting.h StructureRoutines.h
 Sugar.o : Sugar.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Sugar.h SugarToken.h
diff --git a/src/Structure/structurefiles b/src/Structure/structurefiles
index 00491304ea..48693161e5 100644
--- a/src/Structure/structurefiles
+++ b/src/Structure/structurefiles
@@ -10,6 +10,7 @@ STRUCTURE_SOURCES= \
   GenerateConnectivityArrays.cpp \
   HisProt.cpp \
   InternalCoords.cpp \
+  PdbCleaner.cpp \
   StructureEnum.cpp \
   StructureRoutines.cpp \
   SugarBuilder.cpp \

From de3670230f228488a8991dea2d03263eb6a26772 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 21 Feb 2024 15:19:35 -0500
Subject: [PATCH 0588/1492] Incorporate the pdb cleaner into build

---
 src/Exec_Build.cpp         | 19 ++++++++++++++++++-
 src/Structure/PdbCleaner.h |  1 +
 src/cpptrajdepend          |  3 ++-
 3 files changed, 21 insertions(+), 2 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index aca73da1d0..f57e0f4f15 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -5,6 +5,7 @@
 #include "Parm/GB_Params.h"
 #include "Structure/Builder.h"
 #include "Structure/Creator.h"
+#include "Structure/PdbCleaner.h"
 
 /** Map atoms in residue to template. */
 std::vector<int> Exec_Build::MapAtomsToTemplate(Topology const& topIn,
@@ -582,7 +583,23 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
   coords.GetFrame(tgtframe, frameIn);
   // Get modifiable topology
   //Topology& topIn = *(coords.TopPtr());
-  Topology const& topIn = coords.Top();
+  //Topology const& topIn = coords.Top();
+  Topology topIn = coords.Top(); // FIXME do not work on the copy, work on the top itself
+  Cpptraj::Structure::PdbCleaner pdbCleaner;
+  pdbCleaner.SetDebug( debug_ );
+  if (pdbCleaner.InitPdbCleaner( argIn, "HOH", std::vector<int>() )) {
+    mprinterr("Error: Could not init PDB cleaner.\n");
+    return CpptrajState::ERR;
+  }
+  if (pdbCleaner.SetupPdbCleaner( topIn )) {
+    mprinterr("Error: Could not set up PDB cleaner.\n");
+    return CpptrajState::ERR;
+  }
+  pdbCleaner.PdbCleanerInfo();
+  if (pdbCleaner.ModifyCoords(topIn, frameIn)) {
+    mprinterr("Error: Could not clean PDB.\n");
+    return CpptrajState::ERR;
+  }
 
   // Output coords
   std::string outset = argIn.GetStringKey("name");
diff --git a/src/Structure/PdbCleaner.h b/src/Structure/PdbCleaner.h
index 9e9e1c2bac..d375cd8aef 100644
--- a/src/Structure/PdbCleaner.h
+++ b/src/Structure/PdbCleaner.h
@@ -12,6 +12,7 @@ class PdbCleaner {
     typedef std::vector<int> Iarray;
   public:
     PdbCleaner();
+    void SetDebug(int d) { debug_ = d; }
     /// Help text
     static void Help();
     /// Initialize
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 06cc182792..c7c9805ec5 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -290,7 +290,7 @@ Ewald_Regular.o : Ewald_Regular.cpp Atom.h AtomMask.h Box.h Constants.h Coordina
 ExclusionArray.o : ExclusionArray.cpp Atom.h AtomMask.h CharMask.h CpptrajStdio.h ExclusionArray.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Unit.h
 Exec_AddMissingRes.o : Exec_AddMissingRes.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CharMask.h CompactFrameArray.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_AddMissingRes.h Exec_AddMissingRes_Pres.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Analyze.o : Exec_Analyze.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Analyze.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Build.o : Exec_Build.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/GB_Params.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/Creator.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Build.o : Exec_Build.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/GB_Params.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/Creator.h Structure/PdbCleaner.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Calc.o : Exec_Calc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Calc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_CatCrd.o : Exec_CatCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CatCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Change.o : Exec_Change.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Change.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
@@ -455,6 +455,7 @@ Structure/FxnGroupBuilder.o : Structure/FxnGroupBuilder.cpp Atom.h AtomMask.h At
 Structure/GenerateConnectivityArrays.o : Structure/GenerateConnectivityArrays.cpp Atom.h Constants.h CpptrajStdio.h NameType.h ParameterTypes.h Residue.h Structure/GenerateConnectivityArrays.h SymbolExporting.h
 Structure/HisProt.o : Structure/HisProt.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/HisProt.h Structure/StructureRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/InternalCoords.o : Structure/InternalCoords.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/InternalCoords.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Structure/PdbCleaner.o : Structure/PdbCleaner.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/PdbCleaner.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/StructureEnum.o : Structure/StructureEnum.cpp Structure/StructureEnum.h
 Structure/StructureRoutines.o : Structure/StructureRoutines.cpp Atom.h CpptrajStdio.h NameType.h Residue.h Structure/StructureRoutines.h SymbolExporting.h
 Structure/Sugar.o : Structure/Sugar.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h

From ba4ee3393390b44330571298c03d349282539069 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 21 Feb 2024 18:33:28 -0500
Subject: [PATCH 0589/1492] Use PdbCleaner

---
 src/Exec_PrepareForLeap.cpp | 79 ++++++++++++++++++++++---------------
 src/Structure/PdbCleaner.h  |  2 +
 src/cpptrajdepend           |  2 +-
 3 files changed, 51 insertions(+), 32 deletions(-)

diff --git a/src/Exec_PrepareForLeap.cpp b/src/Exec_PrepareForLeap.cpp
index 82020e049b..9efd062d0a 100644
--- a/src/Exec_PrepareForLeap.cpp
+++ b/src/Exec_PrepareForLeap.cpp
@@ -8,6 +8,7 @@
 #include "StringRoutines.h"
 #include "Structure/Disulfide.h"
 #include "Structure/HisProt.h"
+#include "Structure/PdbCleaner.h"
 #include "Structure/ResStatArray.h"
 #include "Structure/SugarBuilder.h"
 #include "Structure/Sugar.h"
@@ -875,6 +876,33 @@ Exec::RetType Exec_PrepareForLeap::Execute(CpptrajState& State, ArgList& argIn)
     }
   }
 
+  // Do histidine detection before H atoms are removed
+  if (!argIn.hasKey("nohisdetect")) {
+    std::string nd1name = argIn.GetStringKey("nd1", "ND1");
+    std::string ne2name = argIn.GetStringKey("ne2", "NE2");
+    std::string hisname = argIn.GetStringKey("hisname", "HIS");
+    std::string hiename = argIn.GetStringKey("hiename", "HIE");
+    std::string hidname = argIn.GetStringKey("hidname", "HID");
+    std::string hipname = argIn.GetStringKey("hipname", "HIP");
+    mprintf("\tHistidine protonation detection:\n");
+    mprintf("\t\tND1 atom name                   : %s\n", nd1name.c_str());
+    mprintf("\t\tNE2 atom name                   : %s\n", ne2name.c_str());
+    mprintf("\t\tHistidine original residue name : %s\n", hisname.c_str());
+    mprintf("\t\tEpsilon-protonated residue name : %s\n", hiename.c_str());
+    mprintf("\t\tDelta-protonated residue name   : %s\n", hidname.c_str());
+    mprintf("\t\tDoubly-protonated residue name  : %s\n", hipname.c_str());
+    // Add epsilon, delta, and double-protonated names as recognized.
+    pdb_res_names_.insert( hiename );
+    pdb_res_names_.insert( hidname );
+    pdb_res_names_.insert( hipname );
+    if (DetermineHisProt( topIn,
+                          nd1name, ne2name,
+                          hisname, hiename, hidname, hipname)) {
+      mprinterr("Error: HIS protonation detection failed.\n");
+      return CpptrajState::ERR;
+    }
+  }
+
   Iarray pdbResToRemove;
   std::string removeArg = argIn.GetStringKey("remove");
   if (!removeArg.empty()) {
@@ -891,8 +919,24 @@ Exec::RetType Exec_PrepareForLeap::Execute(CpptrajState& State, ArgList& argIn)
     }
   }
 
+  Cpptraj::Structure::PdbCleaner pdbCleaner;
+  pdbCleaner.SetDebug( debug_ );
+  if (pdbCleaner.InitPdbCleaner( argIn, solventResName_, pdbResToRemove )) {
+    mprinterr("Error: Could not init PDB cleaner.\n");
+    return CpptrajState::ERR;
+  }
+  if (pdbCleaner.SetupPdbCleaner( topIn )) {
+    mprinterr("Error: Could not set up PDB cleaner.\n");
+    return CpptrajState::ERR;
+  }
+  pdbCleaner.PdbCleanerInfo();
+  if (pdbCleaner.ModifyCoords(topIn, frameIn)) {
+    mprinterr("Error: Could not clean PDB.\n");
+    return CpptrajState::ERR;
+  }
+
   // Deal with any coordinate modifications
-  bool remove_water     = argIn.hasKey("nowat");
+/*  bool remove_water     = argIn.hasKey("nowat");
   std::string waterMask = argIn.GetStringKey("watermask", ":" + solventResName_);
   bool remove_h         = argIn.hasKey("noh");
   std::string altLocArg = argIn.GetStringKey("keepaltloc");
@@ -957,38 +1001,11 @@ Exec::RetType Exec_PrepareForLeap::Execute(CpptrajState& State, ArgList& argIn)
     return CpptrajState::ERR;
   }
 
-  // Do histidine detection before H atoms are removed
-  if (!argIn.hasKey("nohisdetect")) {
-    std::string nd1name = argIn.GetStringKey("nd1", "ND1");
-    std::string ne2name = argIn.GetStringKey("ne2", "NE2");
-    std::string hisname = argIn.GetStringKey("hisname", "HIS");
-    std::string hiename = argIn.GetStringKey("hiename", "HIE");
-    std::string hidname = argIn.GetStringKey("hidname", "HID");
-    std::string hipname = argIn.GetStringKey("hipname", "HIP");
-    mprintf("\tHistidine protonation detection:\n");
-    mprintf("\t\tND1 atom name                   : %s\n", nd1name.c_str());
-    mprintf("\t\tNE2 atom name                   : %s\n", ne2name.c_str());
-    mprintf("\t\tHistidine original residue name : %s\n", hisname.c_str());
-    mprintf("\t\tEpsilon-protonated residue name : %s\n", hiename.c_str());
-    mprintf("\t\tDelta-protonated residue name   : %s\n", hidname.c_str());
-    mprintf("\t\tDoubly-protonated residue name  : %s\n", hipname.c_str());
-    // Add epsilon, delta, and double-protonated names as recognized.
-    pdb_res_names_.insert( hiename );
-    pdb_res_names_.insert( hidname );
-    pdb_res_names_.insert( hipname );
-    if (DetermineHisProt( topIn,
-                          nd1name, ne2name,
-                          hisname, hiename, hidname, hipname)) {
-      mprinterr("Error: HIS protonation detection failed.\n");
-      return CpptrajState::ERR;
-    }
-  }
-
   // Remove hydrogens
   if (remove_h) {
     if (RemoveHydrogens(topIn, frameIn)) return CpptrajState::ERR;
   }
-
+*/
   // If preparing sugars, need to set up an atom map and potentially
   // search for terminal sugars/missing bonds. Do this here after all atom
   // modifications have been done.
@@ -1112,7 +1129,7 @@ Exec::RetType Exec_PrepareForLeap::Execute(CpptrajState& State, ArgList& argIn)
   {
     NameType const& residueName = topIn.Res(it-resStat.begin()).Name();
     // Skip water if not removing water
-    if (!remove_water && residueName == solvName) continue;
+    if (!pdbCleaner.RemoveWater() && residueName == solvName) continue;
     // If status is unknown, see if this is a common residue name
     if ( *it == ResStatArray::UNKNOWN ) {
       SetType::const_iterator pname = pdb_res_names_.find( residueName );
@@ -1161,7 +1178,7 @@ Exec::RetType Exec_PrepareForLeap::Execute(CpptrajState& State, ArgList& argIn)
     outfile->Printf("%s\n", Cpptraj::LeapInterface::LeapBond(bnd->A1(), bnd->A2(), leapunitname_, topIn).c_str());
 
   // Count any solvent molecules
-  if (!remove_water) {
+  if (!pdbCleaner.RemoveWater()) {
     unsigned int nsolvent = 0;
     for (Topology::res_iterator res = topIn.ResStart(); res != topIn.ResEnd(); ++res) {
       if ( res->Name() == solvName) {
diff --git a/src/Structure/PdbCleaner.h b/src/Structure/PdbCleaner.h
index d375cd8aef..87ae1d763f 100644
--- a/src/Structure/PdbCleaner.h
+++ b/src/Structure/PdbCleaner.h
@@ -23,6 +23,8 @@ class PdbCleaner {
     void PdbCleanerInfo() const;
     /// Modify top/frame
     int ModifyCoords(Topology&, Frame&) const;
+    /// \return True if option to remove water is set
+    bool RemoveWater() const { return remove_water_; }
   private:
     int debug_;
     bool remove_water_;      ///< If true, remove any water.
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index c7c9805ec5..a2d23b9444 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -325,7 +325,7 @@ Exec_ParmWrite.o : Exec_ParmWrite.cpp Action.h ActionList.h ActionState.h Analys
 Exec_ParseTiming.o : Exec_ParseTiming.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParseTiming.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_PermuteDihedrals.o : Exec_PermuteDihedrals.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h DistRoutines.h EnsembleIn.h EnsembleOutList.h ExclusionArray.h Exec.h Exec_PermuteDihedrals.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Precision.o : Exec_Precision.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Precision.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_PrepareForLeap.o : Exec_PrepareForLeap.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_PrepareForLeap.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h LeapInterface.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h Remote.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/Disulfide.h Structure/HisProt.h Structure/ResStatArray.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Exec_PrepareForLeap.o : Exec_PrepareForLeap.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_PrepareForLeap.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h LeapInterface.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h Remote.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/Disulfide.h Structure/HisProt.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Exec_PrintData.o : Exec_PrintData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_PrintData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Random.o : Exec_Random.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Random.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_ReadData.o : Exec_ReadData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ReadData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h

From 27a3ca4e631feafe4fc40d6208076e14cee288d5 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 21 Feb 2024 18:34:47 -0500
Subject: [PATCH 0590/1492] Comment out old functions

---
 src/Exec_PrepareForLeap.cpp | 8 ++++----
 src/Exec_PrepareForLeap.h   | 6 +++---
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/Exec_PrepareForLeap.cpp b/src/Exec_PrepareForLeap.cpp
index 9efd062d0a..7aeb668e01 100644
--- a/src/Exec_PrepareForLeap.cpp
+++ b/src/Exec_PrepareForLeap.cpp
@@ -277,7 +277,7 @@ const
 // -----------------------------------------------------------------------------
 
 /** Modify coords according to user wishes. */
-int Exec_PrepareForLeap::ModifyCoords( Topology& topIn, Frame& frameIn,
+/*int Exec_PrepareForLeap::ModifyCoords( Topology& topIn, Frame& frameIn,
                                        bool remove_water,
                                        std::string const& altLocStr, std::string const& stripMask,
                                        std::string const& waterMask,
@@ -423,13 +423,13 @@ const
   delete newTop;
 
   return 0;
-}
+}*/
 
 /** Remove any hydrogen atoms. This is done separately from ModifyCoords
   * so that hydrogen atom info can be used to e.g. ID histidine
   * protonation.
   */
-int Exec_PrepareForLeap::RemoveHydrogens(Topology& topIn, Frame& frameIn) const {
+/*int Exec_PrepareForLeap::RemoveHydrogens(Topology& topIn, Frame& frameIn) const {
   AtomMask keptAtoms;
   keptAtoms.SetNatoms( topIn.Natom() );
   for (int idx = 0; idx != topIn.Natom(); idx++)
@@ -456,7 +456,7 @@ int Exec_PrepareForLeap::RemoveHydrogens(Topology& topIn, Frame& frameIn) const
   delete newTop;
 
   return 0;
-}
+}*/
 
 // -----------------------------------------------------------------------------
 
diff --git a/src/Exec_PrepareForLeap.h b/src/Exec_PrepareForLeap.h
index eb163c31f8..044992a5c4 100644
--- a/src/Exec_PrepareForLeap.h
+++ b/src/Exec_PrepareForLeap.h
@@ -37,10 +37,10 @@ class Exec_PrepareForLeap : public Exec {
     int FindTerByBonds(Topology&, CharMask const&) const;
 
     /// Remove specified atoms
-    int ModifyCoords(Topology&, Frame&, bool, std::string const&, std::string const&,
-                     std::string const&, Iarray const&) const;
+    //int ModifyCoords(Topology&, Frame&, bool, std::string const&, std::string const&,
+    //                 std::string const&, Iarray const&) const;
     /// Remove hydrogen atoms
-    int RemoveHydrogens(Topology&, Frame&) const;
+    //int RemoveHydrogens(Topology&, Frame&) const;
 
     /// Run leap to generate topology, perform any modifications
     int RunLeap(std::string const&, std::string const&) const;

From 5c657ebb619100d973948a9ec0974ab5fc5338cb Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 22 Feb 2024 20:31:18 -0500
Subject: [PATCH 0591/1492] Start NameMap dataset class

---
 src/DataSet_NameMap.cpp |  8 ++++++++
 src/DataSet_NameMap.h   | 28 ++++++++++++++++++++++++++++
 2 files changed, 36 insertions(+)
 create mode 100644 src/DataSet_NameMap.cpp
 create mode 100644 src/DataSet_NameMap.h

diff --git a/src/DataSet_NameMap.cpp b/src/DataSet_NameMap.cpp
new file mode 100644
index 0000000000..9ae598678a
--- /dev/null
+++ b/src/DataSet_NameMap.cpp
@@ -0,0 +1,8 @@
+#include "DataSet_NameMap.h"
+#include "CpptrajStdio.h"
+
+/// CONSTRUCTOR
+DataSet_NameMap::DataSet_NameMap()
+{
+
+}
diff --git a/src/DataSet_NameMap.h b/src/DataSet_NameMap.h
new file mode 100644
index 0000000000..fab29fea4a
--- /dev/null
+++ b/src/DataSet_NameMap.h
@@ -0,0 +1,28 @@
+#ifndef INC_DATASET_NAMEMAP_H
+#define INC_DATASET_NAMEMAP_H
+#include "DataSet.h"
+#include "NameType.h"
+#include <map>
+/// Used to map old atom names to new atom names 
+class DataSet_NameMap : public DataSet {
+  public:
+    DataSet_NameMap();
+    static DataSet* Alloc() { return (DataSet*)new DataSet_NameMap(); }
+    // ----- DataSet functions -------------------
+    size_t Size()                                    const { return 0; }
+    void Info()                                      const { return; }
+    int Allocate(SizeArray const&)                         { return 1; }
+    void Add(size_t, const void*)                          { return; }
+    void WriteBuffer(CpptrajFile&, SizeArray const&) const { return; }
+    int Append(DataSet*)                                   { return 1; }
+    size_t MemUsageInBytes()                         const { return 0; }
+#   ifdef MPI
+    int Sync(size_t, std::vector<int> const&, Parallel::Comm const&) { return 1; }
+#   endif
+    // -------------------------------------------
+  private:
+    typedef std::pair<NameType,NameType> AmapPair;
+    typedef std::map<NameType,NameType> AmapType;
+    AmapType nameMap_;
+};
+#endif

From 06fb3f81bfae079bc8e0dec62276c0a7d2adae8a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 22 Feb 2024 20:54:36 -0500
Subject: [PATCH 0592/1492] Start saving pdb atom name map

---
 src/DataIO_LeapRC.cpp | 64 +++++++++++++++++++++++++++++++++++++++++++
 src/DataIO_LeapRC.h   |  1 +
 src/DataSet.cpp       |  1 +
 src/DataSet.h         |  2 +-
 src/DataSetList.cpp   |  2 ++
 src/DataSet_NameMap.h |  7 +++--
 src/Parm_Amber.cpp    | 33 ++++++++++++++++++----
 src/Parm_Amber.h      |  2 ++
 src/cpptrajdepend     |  5 ++--
 src/cpptrajfiles      |  1 +
 10 files changed, 108 insertions(+), 10 deletions(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 39712b7bdd..6fc8c2017b 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -6,6 +6,7 @@
 #include "DataIO_AmberFrcmod.h"
 #include "DataIO_AmberLib.h"
 #include "DataIO_AmberPrep.h"
+#include "DataSet_NameMap.h"
 #include "DataSet_Parameters.h"
 #include <cstdlib> //getenv
 
@@ -276,6 +277,67 @@ const
   }
   return 0;
 }
+/** LEaP addPdbAtomMap command. */
+int DataIO_LeapRC::AddPdbAtomMap(std::string const& dsname, DataSetList& DSL, BufferedLine& infile)
+const
+{
+  MetaData meta(dsname, "atommap");
+  DataSet* ds = DSL.CheckForSet(meta);
+  if (ds == 0) {
+    ds = DSL.AddSet(DataSet::NAMEMAP, meta);
+    if (ds == 0) return 1;
+  }
+  DataSet_NameMap& namemap = static_cast<DataSet_NameMap&>( *ds );
+  mprintf("DEBUG: Name map set: %s\n", namemap.legend());
+  int bracketCount = 0;
+  // First line should contain the command
+  const char* line = infile.CurrentLine();
+  while (line != 0) {
+    // Process the line
+    std::string tmp;
+    for (const char* ptr = line; *ptr != '\0'; ++ptr)
+    {
+      if (*ptr == '#') {
+        // Comment - skip everything else
+        break;
+      } else if (*ptr == '{')
+        bracketCount++;
+      else if (*ptr == '}') {
+        bracketCount--;
+        if (bracketCount == 1) {
+          //if (debug_ > 0)
+            mprintf("DEBUG: addPdbAtomMap: %s\n", tmp.c_str());
+          ArgList aline( tmp );
+          // 2 tokens: Old name, new name
+          if (aline.Nargs() != 2) {
+            mprinterr("Error: Malformed entry in addPdbAtomMap: %s\n", tmp.c_str());
+            return 1;
+          }
+          mprintf("DEBUG: old= %s  new= %s\n", aline[0].c_str(), aline[1].c_str());
+          tmp.clear();
+        }
+      } else {
+        if (bracketCount == 2)
+          tmp += *ptr;
+      }
+    }
+    if (bracketCount < 0) {
+      mprinterr("Error: Too many close brackets '}' in addPdbAtomMap command.\n");
+      return 1;
+    } else if (bracketCount == 0) {
+      break;
+    } //else {
+    //mprintf("DEBUG: END OF LINE: addPdbResMap: %s\n", tmp.c_str());
+    //}
+    line = infile.Line();
+  }
+  if (bracketCount != 0) {
+    mprinterr("Error: Not enough close brackets '}' in addPdbAtomMap command.\n");
+    return 1;
+  }
+  return 0;
+}
+
 
 /// Move sets from paramDSL to dsl
 static inline int addSetsToList(DataSetList& dsl, DataSetList& paramDSL)
@@ -341,6 +403,8 @@ int DataIO_LeapRC::ReadData(FileName const& fname, DataSetList& dsl, std::string
         err = AddAtomTypes(atomHybridizations, infile);
       else if (line.Contains("addPdbResMap") || line.Contains("addpdbresmap"))
         err = AddPdbResMap(pdbResMap, infile);
+      else if (line.Contains("addPdbAtomMap") || line.Contains("addpdbatommap"))
+        err = AddPdbAtomMap(dsname, dsl, infile);
       else {
         // Does this line contain an equals sign?
         bool has_equals = false;
diff --git a/src/DataIO_LeapRC.h b/src/DataIO_LeapRC.h
index 5e7f5e2a83..9035379a01 100644
--- a/src/DataIO_LeapRC.h
+++ b/src/DataIO_LeapRC.h
@@ -33,6 +33,7 @@ class DataIO_LeapRC : public DataIO {
     int LoadAmberPrep(std::string const&, DataSetList&, std::string const&) const;
     int AddAtomTypes(NHarrayType&, BufferedLine&) const;
     int AddPdbResMap(PdbResMapArray&, BufferedLine&) const;
+    int AddPdbAtomMap(std::string const&, DataSetList&, BufferedLine&) const;
     /// Used to check if a parm/lib file was already loaded.
     static inline bool check_already_loaded(Sarray const&, std::string const&);
 
diff --git a/src/DataSet.cpp b/src/DataSet.cpp
index 54f1f11372..ab62cdf44c 100644
--- a/src/DataSet.cpp
+++ b/src/DataSet.cpp
@@ -33,6 +33,7 @@ const char* DataSet::Descriptions_[] = {
   "unsigned integer",           // UNSIGNED_INTEGER
   "frames",                     // FRAMES
   "zmatrix",                    // ZMATRIX
+  "name map",                   // NAMEMAP
   "unknown"                     // UNKNOWN_DATA
 };
 
diff --git a/src/DataSet.h b/src/DataSet.h
index 9413d8d33a..f061258afb 100644
--- a/src/DataSet.h
+++ b/src/DataSet.h
@@ -29,7 +29,7 @@ class DataSet {
       COORDS, VECTOR, MODES, GRID_FLT, GRID_DBL, REMLOG, XYMESH, TRAJ, REF_FRAME,
       MAT3X3, TOPOLOGY, PH, PH_EXPL, PH_IMPL,
       PARAMETERS, PMATRIX_MEM, PMATRIX_NC, TENSOR, STRINGVAR, VECTOR_SCALAR, UNSIGNED_INTEGER,
-      FRAMES, ZMATRIX,
+      FRAMES, ZMATRIX, NAMEMAP,
       UNKNOWN_DATA
     };
     /// Group DataSet belongs to.
diff --git a/src/DataSetList.cpp b/src/DataSetList.cpp
index a6662da59e..5ff99485d2 100644
--- a/src/DataSetList.cpp
+++ b/src/DataSetList.cpp
@@ -36,6 +36,7 @@
 #include "DataSet_unsignedInt.h"
 #include "DataSet_Coords_FRM.h"
 #include "DataSet_Zmatrix.h"
+#include "DataSet_NameMap.h"
 
 bool DataSetList::useDiskCache_ = false;
 
@@ -95,6 +96,7 @@ DataSet* DataSetList::NewSet(DataSet::DataType typeIn) {
     case DataSet::STRINGVAR     : ds = DataSet_StringVar::Alloc(); break;
     case DataSet::VECTOR_SCALAR : ds = DataSet_Vector_Scalar::Alloc(); break;
     case DataSet::ZMATRIX       : ds = DataSet_Zmatrix::Alloc(); break;
+    case DataSet::NAMEMAP       : ds = DataSet_NameMap::Alloc(); break;
     // Sanity check
     default:
       mprinterr("Internal Error: No allocator for DataSet type '%s'\n",
diff --git a/src/DataSet_NameMap.h b/src/DataSet_NameMap.h
index fab29fea4a..b702318c10 100644
--- a/src/DataSet_NameMap.h
+++ b/src/DataSet_NameMap.h
@@ -5,6 +5,8 @@
 #include <map>
 /// Used to map old atom names to new atom names 
 class DataSet_NameMap : public DataSet {
+    typedef std::pair<NameType,NameType> AmapPair;
+    typedef std::map<NameType,NameType> AmapType;
   public:
     DataSet_NameMap();
     static DataSet* Alloc() { return (DataSet*)new DataSet_NameMap(); }
@@ -20,9 +22,10 @@ class DataSet_NameMap : public DataSet {
     int Sync(size_t, std::vector<int> const&, Parallel::Comm const&) { return 1; }
 #   endif
     // -------------------------------------------
+    void AddNameMap(NameType const& oldName, NameType const& newName) {
+      nameMap_.insert( AmapPair(oldName, newName) );
+    }
   private:
-    typedef std::pair<NameType,NameType> AmapPair;
-    typedef std::map<NameType,NameType> AmapType;
     AmapType nameMap_;
 };
 #endif
diff --git a/src/Parm_Amber.cpp b/src/Parm_Amber.cpp
index f705b73995..e45315faa3 100644
--- a/src/Parm_Amber.cpp
+++ b/src/Parm_Amber.cpp
@@ -165,10 +165,12 @@ Parm_Amber::Parm_Amber() :
   atProblemFlag_(false),
   N_impropers_(0),
   N_impTerms_(0),
+  ncoords_(0),
   writeChamber_(true),
   writeEmptyArrays_(false),
   writePdbInfo_(true),
-  has_valid_nonbond_params_(true)
+  has_valid_nonbond_params_(true),
+  hasBadDihedrals_(false)
 {
   UB_count_[0] = 0;
   UB_count_[1] = 0;
@@ -675,6 +677,7 @@ int Parm_Amber::ReadPointers(int Npointers, Topology& TopIn, FortranData const&
   TopIn.SetNonbond().SetupLJforNtypes( values_[NTYPES] );
   numLJparm_ = TopIn.Nonbond().NBarray().size();
   TopIn.SetNonbond().SetNHBterms( values_[NPHB] );
+  ncoords_ = values_[NATOM] * 3;
   //TopIn.SetNatyp( values_[NATYP] );
   return 0;
 }
@@ -972,6 +975,14 @@ DihedralType Parm_Amber::GetDihedral() {
   int a3 = atoi(file_.NextElement());
   int a4 = atoi(file_.NextElement());
   int didx = atoi(file_.NextElement());
+  if (a1 < 0 || a1 >= ncoords_ ||
+      a2 < 0 || a2 >= ncoords_ ||
+      a3 < 0 || a3 >= ncoords_ ||
+      a4 < 0 || a4 >= ncoords_ ||
+      didx < 0 || didx - 1 >= values_[NPTRA])
+  {
+    hasBadDihedrals_ = true;
+  }
   return DihedralType( a1 / 3, a2 / 3, a3 / 3, a4 / 3, didx - 1 );
 }
 
@@ -979,8 +990,14 @@ DihedralType Parm_Amber::GetDihedral() {
 int Parm_Amber::ReadDihedralsH(Topology& TopIn, FortranData const& FMT) {
   int nvals = values_[NPHIH]*5;
   if (SetupBuffer(F_DIHH, nvals, FMT)) return 1;
-  for (int idx = 0; idx != nvals; idx += 5)
-    TopIn.AddDihedral( GetDihedral(), true );
+  for (int idx = 0; idx != nvals; idx += 5) {
+    DihedralType dih = GetDihedral();
+    if (hasBadDihedrals_) {
+      mprintf("Warning: Dihedrals including hydrogen have bad atom or parm indices, skipping.\n");
+      break;
+    }
+    TopIn.AddDihedral( dih, true );
+  }
   return 0;
 }
 
@@ -988,8 +1005,14 @@ int Parm_Amber::ReadDihedralsH(Topology& TopIn, FortranData const& FMT) {
 int Parm_Amber::ReadDihedrals(Topology& TopIn, FortranData const& FMT) {
   int nvals = values_[MPHIA]*5;
   if (SetupBuffer(F_DIH, nvals, FMT)) return 1;
-  for (int idx = 0; idx != nvals; idx += 5)
-    TopIn.AddDihedral( GetDihedral(), false );
+  for (int idx = 0; idx != nvals; idx += 5) {
+    DihedralType dih = GetDihedral();
+    if (hasBadDihedrals_) {
+      mprintf("Warning: Dihedrals not including hydrogen have bad atom or parm indices, skipping.\n");
+      break;
+    }
+    TopIn.AddDihedral( dih, false );
+  }
   return 0;
 }
 
diff --git a/src/Parm_Amber.h b/src/Parm_Amber.h
index 443fe1a2c1..dc4d6d50a6 100644
--- a/src/Parm_Amber.h
+++ b/src/Parm_Amber.h
@@ -181,6 +181,7 @@ class Parm_Amber : public ParmIO {
     int UB_count_[2];   ///< Urey-Bradley count: # bonds (x3), # parameters
     int N_impropers_;   ///< Number of impropers (x5)
     int N_impTerms_;    ///< Number of improper terms
+    int ncoords_;       ///< Number of coordinates (# atoms * 3)
     int n_cmap_terms_;  ///< Number of CMAP terms
     int n_cmap_grids_;  ///< Number of CMAP grids
 
@@ -193,6 +194,7 @@ class Parm_Amber : public ParmIO {
     bool writePdbInfo_;     ///< If true write chain IDs etc
 
     bool has_valid_nonbond_params_; ///< Will set to false if invalid nonbonds detected on read
+    bool hasBadDihedrals_; ///< Set to true if bad dihedrals detected on read
 };
 // -----------------------------------------------------------------------------
 class Parm_Amber::FortranData {
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index a2d23b9444..345e0f1c9f 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -221,7 +221,7 @@ DataIO_Cpout.o : DataIO_Cpout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h A
 DataIO_Evecs.o : DataIO_Evecs.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Evecs.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Gnuplot.o : DataIO_Gnuplot.cpp ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Gnuplot.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Grace.o : DataIO_Grace.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Grace.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_string.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_LeapRC.o : DataIO_LeapRC.cpp ArgList.h AssociatedData.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_LeapRC.o : DataIO_LeapRC.cpp ArgList.h AssociatedData.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Mdout.o : DataIO_Mdout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Mdout.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_NetCDF.o : DataIO_NetCDF.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/Cframes.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_NetCDF.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_Mesh.h DataSet_Modes.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_Vector.h DataSet_Vector_Scalar.h DataSet_string.h DataSet_unsignedInt.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h Version.h
 DataIO_Numpy.o : DataIO_Numpy.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Numpy.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h libnpy/npy.hpp
@@ -233,7 +233,7 @@ DataIO_VecTraj.o : DataIO_VecTraj.cpp ActionFrameCounter.h ArgList.h ArrayIterat
 DataIO_XVG.o : DataIO_XVG.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_XVG.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Xplor.o : DataIO_Xplor.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Xplor.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataSet.o : DataSet.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
-DataSetList.o : DataSetList.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Cluster/Cframes.h Cluster/Cmatrix_NC.h CompactFrameArray.h ComplexArray.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_FRM.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_GridDbl.h DataSet_GridFlt.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h DataSet_PHREMD_Implicit.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_PairwiseCache_NC.h DataSet_Parameters.h DataSet_RemLog.h DataSet_StringVar.h DataSet_Tensor.h DataSet_Topology.h DataSet_Vector.h DataSet_Vector_Scalar.h DataSet_Zmatrix.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_disk.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h DataSet_unsignedInt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h InputTrajCommon.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h SymmetricTensor.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TypeNameHolder.h Unit.h Vec3.h
+DataSetList.o : DataSetList.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Cluster/Cframes.h Cluster/Cmatrix_NC.h CompactFrameArray.h ComplexArray.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_FRM.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_GridDbl.h DataSet_GridFlt.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_NameMap.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h DataSet_PHREMD_Implicit.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_PairwiseCache_NC.h DataSet_Parameters.h DataSet_RemLog.h DataSet_StringVar.h DataSet_Tensor.h DataSet_Topology.h DataSet_Vector.h DataSet_Vector_Scalar.h DataSet_Zmatrix.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_disk.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h DataSet_unsignedInt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h InputTrajCommon.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h SymmetricTensor.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TypeNameHolder.h Unit.h Vec3.h
 DataSet_1D.o : DataSet_1D.cpp ArrayIterator.h AssociatedData.h ComplexArray.h Constants.h Corr.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h PubFFT.h Range.h TextFormat.h
 DataSet_3D.o : DataSet_3D.cpp AssociatedData.h Box.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_3D.h Dimension.h FileIO.h FileName.h GridBin.h Matrix_3x3.h MetaData.h Parallel.h Range.h TextFormat.h Vec3.h
 DataSet_Coords.o : DataSet_Coords.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
@@ -248,6 +248,7 @@ DataSet_MatrixDbl.o : DataSet_MatrixDbl.cpp ArrayIterator.h AssociatedData.h Cpp
 DataSet_MatrixFlt.o : DataSet_MatrixFlt.cpp ArrayIterator.h AssociatedData.h CpptrajFile.h DataSet.h DataSet_2D.h DataSet_MatrixFlt.h Dimension.h FileIO.h FileName.h Matrix.h MetaData.h Parallel.h Range.h TextFormat.h
 DataSet_Mesh.o : DataSet_Mesh.cpp AssociatedData.h Constants.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_Mesh.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h Spline.h TextFormat.h
 DataSet_Modes.o : DataSet_Modes.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_2D.h DataSet_MatrixDbl.h DataSet_Modes.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Unit.h Vec3.h
+DataSet_NameMap.o : DataSet_NameMap.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_NameMap.h Dimension.h FileIO.h FileName.h MetaData.h NameType.h Parallel.h Range.h TextFormat.h
 DataSet_PHREMD_Explicit.o : DataSet_PHREMD_Explicit.cpp AssociatedData.h Cph.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h Dimension.h FileIO.h FileName.h MetaData.h NameType.h Parallel.h Range.h TextFormat.h
 DataSet_PHREMD_Implicit.o : DataSet_PHREMD_Implicit.cpp AssociatedData.h Cph.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_PHREMD.h DataSet_PHREMD_Implicit.h Dimension.h FileIO.h FileName.h MetaData.h NameType.h Parallel.h Range.h TextFormat.h
 DataSet_PairwiseCache.o : DataSet_PairwiseCache.cpp AssociatedData.h Cluster/Cframes.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_PairwiseCache.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
diff --git a/src/cpptrajfiles b/src/cpptrajfiles
index 31eeeb7ad4..c674a57869 100644
--- a/src/cpptrajfiles
+++ b/src/cpptrajfiles
@@ -219,6 +219,7 @@ COMMON_SOURCES= \
         DataSet_MatrixFlt.cpp \
         DataSet_Mesh.cpp \
         DataSet_Modes.cpp \
+        DataSet_NameMap.cpp \
         DataSet_PairwiseCache.cpp \
         DataSet_PairwiseCache_MEM.cpp \
         DataSet_PairwiseCache_NC.cpp \

From 3575ad1d6b7123e86a2cc01d7562dd080404bae5 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 22 Feb 2024 20:56:14 -0500
Subject: [PATCH 0593/1492] Actually populate the map

---
 src/DataIO_LeapRC.cpp | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 6fc8c2017b..d7e4dd3962 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -314,6 +314,7 @@ const
             return 1;
           }
           mprintf("DEBUG: old= %s  new= %s\n", aline[0].c_str(), aline[1].c_str());
+          namemap.AddNameMap( aline[0], aline[1] );
           tmp.clear();
         }
       } else {

From 972edfe51f94091eca1d821bdddfbec34e2bd133 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 22 Feb 2024 21:01:51 -0500
Subject: [PATCH 0594/1492] Save name maps

---
 src/Structure/Creator.cpp | 7 +++++++
 src/Structure/Creator.h   | 3 +++
 src/cpptrajdepend         | 2 +-
 3 files changed, 11 insertions(+), 1 deletion(-)

diff --git a/src/Structure/Creator.cpp b/src/Structure/Creator.cpp
index 9e86e62299..8a65751508 100644
--- a/src/Structure/Creator.cpp
+++ b/src/Structure/Creator.cpp
@@ -4,6 +4,7 @@
 #include "../AssociatedData_ResId.h"
 #include "../CpptrajStdio.h"
 #include "../DataSet_Coords.h" // TODO new coords type
+#include "../DataSet_NameMap.h"
 #include "../DataSet_Parameters.h"
 #include "../DataSetList.h"
 
@@ -49,6 +50,12 @@ int Creator::InitCreator(ArgList& argIn, DataSetList const& DSL, int debugIn)
   if (getTemplates(argIn, DSL)) return 1;
   if (getParameterSets(argIn, DSL)) return 1;
 
+  // Get any atom name maps
+  DataSetList nameMapSets = DSL.GetSetsOfType("*", DataSet::NAMEMAP);
+  for (DataSetList::const_iterator ds = nameMapSets.begin();
+                                   ds != nameMapSets.end(); ++ds)
+    NameMaps_.push_back( static_cast<DataSet_NameMap*>( *ds ) );
+
   return 0;
 }
 
diff --git a/src/Structure/Creator.h b/src/Structure/Creator.h
index c1a98515c4..77ef507750 100644
--- a/src/Structure/Creator.h
+++ b/src/Structure/Creator.h
@@ -5,6 +5,7 @@
 #include "StructureEnum.h" // TerminalType
 class ArgList;
 class DataSet_Coords;
+class DataSet_NameMap;
 class DataSet_Parameters;
 class DataSetList;
 class NameType;
@@ -13,6 +14,7 @@ namespace Structure {
 /// Used to create a system from individual units
 class Creator {
     typedef std::vector<DataSet_Coords*> Carray;
+    typedef std::vector<DataSet_NameMap*> Narray;
   public:
     /// CONSTRUCTOR
     Creator();
@@ -45,6 +47,7 @@ class Creator {
 
     DataSet_Parameters* mainParmSet_; ///< Hold optional parameter set.
     Carray Templates_;                ///< Hold unit templates.
+    Narray NameMaps_;                 ///< Hold atom name maps.
     int debug_;                       ///< Debug level
     bool free_parmset_mem_;           ///< True if main parm set is combined and should be freed
 };
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 345e0f1c9f..8c80a90af5 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -449,7 +449,7 @@ StringRoutines.o : StringRoutines.cpp CpptrajStdio.h StringRoutines.h
 Structure/BuildAtom.o : Structure/BuildAtom.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/StructureEnum.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 Structure/Builder.o : Structure/Builder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h GuessAtomHybridization.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Builder.h Structure/Chirality.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 Structure/Chirality.o : Structure/Chirality.cpp Atom.h Constants.h CpptrajStdio.h NameType.h Structure/Chirality.h SymbolExporting.h Vec3.h
-Structure/Creator.o : Structure/Creator.cpp ArgList.h AssociatedData.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/Creator.h Structure/GenerateConnectivityArrays.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Structure/Creator.o : Structure/Creator.cpp ArgList.h AssociatedData.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/Creator.h Structure/GenerateConnectivityArrays.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/Disulfide.o : Structure/Disulfide.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Disulfide.h Structure/ResStatArray.h Structure/StructureRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/FunctionalGroup.o : Structure/FunctionalGroup.cpp Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/FxnGroupBuilder.o : Structure/FxnGroupBuilder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h Structure/FxnGroupBuilder.h Structure/StructureRoutines.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h

From 6a83c4914b8dd9f22cdab67df9368f061ff74595 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 22 Feb 2024 22:30:37 -0500
Subject: [PATCH 0595/1492] Start looking for aliases

---
 src/DataSet_NameMap.cpp   |  3 ++-
 src/DataSet_NameMap.h     |  6 ++++++
 src/Exec_Build.cpp        | 19 +++++++++++++++++--
 src/Exec_Build.h          |  2 +-
 src/Structure/Creator.cpp | 14 ++++++++++++++
 src/Structure/Creator.h   |  2 ++
 6 files changed, 42 insertions(+), 4 deletions(-)

diff --git a/src/DataSet_NameMap.cpp b/src/DataSet_NameMap.cpp
index 9ae598678a..91c08221be 100644
--- a/src/DataSet_NameMap.cpp
+++ b/src/DataSet_NameMap.cpp
@@ -2,7 +2,8 @@
 #include "CpptrajStdio.h"
 
 /// CONSTRUCTOR
-DataSet_NameMap::DataSet_NameMap()
+DataSet_NameMap::DataSet_NameMap() :
+  DataSet(NAMEMAP, GENERIC, TextFormat(), 0)
 {
 
 }
diff --git a/src/DataSet_NameMap.h b/src/DataSet_NameMap.h
index b702318c10..8c88253c4f 100644
--- a/src/DataSet_NameMap.h
+++ b/src/DataSet_NameMap.h
@@ -25,6 +25,12 @@ class DataSet_NameMap : public DataSet {
     void AddNameMap(NameType const& oldName, NameType const& newName) {
       nameMap_.insert( AmapPair(oldName, newName) );
     }
+    bool GetName(NameType& newName, NameType const& oldName) const {
+      AmapType::const_iterator it = nameMap_.find( oldName );
+      if (it == nameMap_.end()) return false;
+      newName = it->second;
+      return true;
+    }
   private:
     AmapType nameMap_;
 };
diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index f57e0f4f15..2e0b484024 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -10,11 +10,25 @@
 /** Map atoms in residue to template. */
 std::vector<int> Exec_Build::MapAtomsToTemplate(Topology const& topIn,
                                                 int rnum,
-                                                DataSet_Coords* resTemplate)
+                                                DataSet_Coords* resTemplate,
+                                                Cpptraj::Structure::Creator const& creator)
 {
   std::vector<int> mapOut;
   mapOut.reserve( resTemplate->Top().Natom() );
   Residue const& resIn = topIn.Res(rnum);
+  // For each atom in topIn, find a template atom
+  for (int itgt = resIn.FirstAtom(); itgt != resIn.LastAtom(); itgt++)
+  {
+    mprintf("DEBUG: Search for atom %s\n", *(topIn[itgt].Name()));
+    // Did this atom have an alias
+    NameType alias;
+    if (creator.GetAlias( alias, topIn[itgt].Name() )) {
+      mprintf("DEBUG: Atom %s alias is %s\n",
+              *(topIn[itgt].Name()),
+              *alias);
+    }
+  }
+
   for (int iref = 0; iref != resTemplate->Top().Natom(); iref++)
   {
     // Find this atom name in topIn
@@ -26,6 +40,7 @@ std::vector<int> Exec_Build::MapAtomsToTemplate(Topology const& topIn,
         break;
       }
     }
+    
     mapOut.push_back( iat );
   }
   return mapOut;
@@ -198,7 +213,7 @@ const
       else
         currentRes.SetName( NameType( (*templateResName) + ( templateResName.len() - 3) ) );
       // Map source atoms to template atoms.
-      std::vector<int> map = MapAtomsToTemplate( topIn, ires, resTemplate );
+      std::vector<int> map = MapAtomsToTemplate( topIn, ires, resTemplate, creator );
       if (debug_ > 1) {
         mprintf("\t  Atom map:\n");
         // DEBUG - print map
diff --git a/src/Exec_Build.h b/src/Exec_Build.h
index a8e7d7e124..5c45bd4243 100644
--- a/src/Exec_Build.h
+++ b/src/Exec_Build.h
@@ -28,7 +28,7 @@ class Exec_Build : public Exec {
     /// Create new topology/frame using templates
     int FillAtomsWithTemplates(Topology&, Frame&, Topology const&, Frame const&, Cpptraj::Structure::Creator const&) const;
     /// Map atoms in topology to template
-    static std::vector<int> MapAtomsToTemplate(Topology const&, int, DataSet_Coords*);
+    static std::vector<int> MapAtomsToTemplate(Topology const&, int, DataSet_Coords*, Cpptraj::Structure::Creator const&);
 
     int debug_;
 };
diff --git a/src/Structure/Creator.cpp b/src/Structure/Creator.cpp
index 8a65751508..ac41637895 100644
--- a/src/Structure/Creator.cpp
+++ b/src/Structure/Creator.cpp
@@ -54,7 +54,10 @@ int Creator::InitCreator(ArgList& argIn, DataSetList const& DSL, int debugIn)
   DataSetList nameMapSets = DSL.GetSetsOfType("*", DataSet::NAMEMAP);
   for (DataSetList::const_iterator ds = nameMapSets.begin();
                                    ds != nameMapSets.end(); ++ds)
+  {
     NameMaps_.push_back( static_cast<DataSet_NameMap*>( *ds ) );
+    mprintf("DEBUG: Atom name map: %s\n", NameMaps_.back()->legend());
+  }
 
   return 0;
 }
@@ -219,3 +222,14 @@ int Creator::getParameterSets(ArgList& argIn, DataSetList const& DSL) {
   return 0;
 }
 
+/** Get alias if present */
+bool Creator::GetAlias(NameType& newName, NameType const& oldName)
+const
+{
+  for (Narray::const_iterator it = NameMaps_.begin(); it != NameMaps_.end(); ++it)
+  {
+    if ((*it)->GetName( newName, oldName ))
+      return true;
+  }
+  return false;
+}
diff --git a/src/Structure/Creator.h b/src/Structure/Creator.h
index 77ef507750..dc42ed2505 100644
--- a/src/Structure/Creator.h
+++ b/src/Structure/Creator.h
@@ -39,6 +39,8 @@ class Creator {
     DataSet_Coords* IdTemplateFromName(std::string const&) const;
     /// Identify residue template from residue name
     DataSet_Coords* IdTemplateFromResname(NameType const&, TerminalType) const;
+    /// Get name map if its present
+    bool GetAlias(NameType&, NameType const&) const;
   private:
     /// Get templates
     int getTemplates(ArgList&, DataSetList const&);

From 6b6daf952a39ab0ef9908627a5d23949b01241ee Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 22 Feb 2024 22:40:33 -0500
Subject: [PATCH 0596/1492] Use aliases

---
 src/Exec_Build.cpp | 23 ++++++++++++++++-------
 1 file changed, 16 insertions(+), 7 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 2e0b484024..c272b00488 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -13,22 +13,31 @@ std::vector<int> Exec_Build::MapAtomsToTemplate(Topology const& topIn,
                                                 DataSet_Coords* resTemplate,
                                                 Cpptraj::Structure::Creator const& creator)
 {
-  std::vector<int> mapOut;
+  std::vector<int> mapOut(resTemplate->Top().Natom(), -1);
   mapOut.reserve( resTemplate->Top().Natom() );
   Residue const& resIn = topIn.Res(rnum);
   // For each atom in topIn, find a template atom
   for (int itgt = resIn.FirstAtom(); itgt != resIn.LastAtom(); itgt++)
   {
-    mprintf("DEBUG: Search for atom %s\n", *(topIn[itgt].Name()));
+    NameType const& tgtName = topIn[itgt].Name();
+    mprintf("DEBUG: Search for atom %s\n", *tgtName);
     // Did this atom have an alias
     NameType alias;
-    if (creator.GetAlias( alias, topIn[itgt].Name() )) {
+    if (creator.GetAlias( alias, tgtName )) {
       mprintf("DEBUG: Atom %s alias is %s\n",
-              *(topIn[itgt].Name()),
-              *alias);
+              *tgtName, *alias);
+    }
+    // See if tgtName or alias matches a reference atom
+    for (int iref = 0; iref != resTemplate->Top().Natom(); iref++)
+    {
+      NameType const& refName = resTemplate->Top()[iref].Name();
+      if (refName == tgtName || refName == alias) {
+        mapOut[iref] = itgt;
+        break;
+      }
     }
   }
-
+/*
   for (int iref = 0; iref != resTemplate->Top().Natom(); iref++)
   {
     // Find this atom name in topIn
@@ -42,7 +51,7 @@ std::vector<int> Exec_Build::MapAtomsToTemplate(Topology const& topIn,
     }
     
     mapOut.push_back( iat );
-  }
+  }*/
   return mapOut;
 }
 

From 5622cef49577485583a250e65532d7b9d1896569 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 22 Feb 2024 22:54:04 -0500
Subject: [PATCH 0597/1492] Only look for alias if there isnt a match

---
 src/Exec_Build.cpp | 29 +++++++++++++++++++++--------
 1 file changed, 21 insertions(+), 8 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index c272b00488..7d4f284ffd 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -20,22 +20,35 @@ std::vector<int> Exec_Build::MapAtomsToTemplate(Topology const& topIn,
   for (int itgt = resIn.FirstAtom(); itgt != resIn.LastAtom(); itgt++)
   {
     NameType const& tgtName = topIn[itgt].Name();
-    mprintf("DEBUG: Search for atom %s\n", *tgtName);
-    // Did this atom have an alias
-    NameType alias;
-    if (creator.GetAlias( alias, tgtName )) {
-      mprintf("DEBUG: Atom %s alias is %s\n",
-              *tgtName, *alias);
-    }
+    //mprintf("DEBUG: Search for atom %s\n", *tgtName);
+
     // See if tgtName or alias matches a reference atom
+    int iat = -1;
     for (int iref = 0; iref != resTemplate->Top().Natom(); iref++)
     {
       NameType const& refName = resTemplate->Top()[iref].Name();
-      if (refName == tgtName || refName == alias) {
+      if (refName == tgtName) {
         mapOut[iref] = itgt;
+        iat = itgt;
         break;
       }
     }
+    if (iat == -1) {
+      // Did this atom have an alias
+      NameType alias;
+      if (creator.GetAlias( alias, tgtName )) {
+        mprintf("DEBUG: Atom %s alias is %s\n", *tgtName, *alias);
+        for (int iref = 0; iref != resTemplate->Top().Natom(); iref++)
+        {
+          NameType const& refName = resTemplate->Top()[iref].Name();
+          if (refName == alias) {
+            mapOut[iref] = itgt;
+            iat = itgt;
+            break;
+          }
+        }
+      }
+    }
   }
 /*
   for (int iref = 0; iref != resTemplate->Top().Natom(); iref++)

From f96f2a237a8fadf945a293feaccac382c193b30d Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 22 Feb 2024 22:56:17 -0500
Subject: [PATCH 0598/1492] Remove the last commit

---
 src/Exec_Build.cpp | 29 ++++++++---------------------
 1 file changed, 8 insertions(+), 21 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 7d4f284ffd..c272b00488 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -20,35 +20,22 @@ std::vector<int> Exec_Build::MapAtomsToTemplate(Topology const& topIn,
   for (int itgt = resIn.FirstAtom(); itgt != resIn.LastAtom(); itgt++)
   {
     NameType const& tgtName = topIn[itgt].Name();
-    //mprintf("DEBUG: Search for atom %s\n", *tgtName);
-
+    mprintf("DEBUG: Search for atom %s\n", *tgtName);
+    // Did this atom have an alias
+    NameType alias;
+    if (creator.GetAlias( alias, tgtName )) {
+      mprintf("DEBUG: Atom %s alias is %s\n",
+              *tgtName, *alias);
+    }
     // See if tgtName or alias matches a reference atom
-    int iat = -1;
     for (int iref = 0; iref != resTemplate->Top().Natom(); iref++)
     {
       NameType const& refName = resTemplate->Top()[iref].Name();
-      if (refName == tgtName) {
+      if (refName == tgtName || refName == alias) {
         mapOut[iref] = itgt;
-        iat = itgt;
         break;
       }
     }
-    if (iat == -1) {
-      // Did this atom have an alias
-      NameType alias;
-      if (creator.GetAlias( alias, tgtName )) {
-        mprintf("DEBUG: Atom %s alias is %s\n", *tgtName, *alias);
-        for (int iref = 0; iref != resTemplate->Top().Natom(); iref++)
-        {
-          NameType const& refName = resTemplate->Top()[iref].Name();
-          if (refName == alias) {
-            mapOut[iref] = itgt;
-            iat = itgt;
-            break;
-          }
-        }
-      }
-    }
   }
 /*
   for (int iref = 0; iref != resTemplate->Top().Natom(); iref++)

From 6fad55e7aead580a682e0ceea4c2f14ffcfc6b77 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 23 Feb 2024 08:50:44 -0500
Subject: [PATCH 0599/1492] Use template atom names for detected interresidue
 bonds

---
 src/Exec_Build.cpp | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index c272b00488..26ba145924 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -20,7 +20,7 @@ std::vector<int> Exec_Build::MapAtomsToTemplate(Topology const& topIn,
   for (int itgt = resIn.FirstAtom(); itgt != resIn.LastAtom(); itgt++)
   {
     NameType const& tgtName = topIn[itgt].Name();
-    mprintf("DEBUG: Search for atom %s\n", *tgtName);
+    //mprintf("DEBUG: Search for atom %s\n", *tgtName);
     // Did this atom have an alias
     NameType alias;
     if (creator.GetAlias( alias, tgtName )) {
@@ -236,6 +236,10 @@ const
       }
       // Map template atoms back to source atoms.
       std::vector<int> pdb(currentRes.NumAtoms(), -1);
+      for (int iref = 0; iref != resTemplate->Top().Natom(); iref++) {
+        if (map[iref] != -1)
+          pdb[map[iref]-currentRes.FirstAtom()] = iref;
+      }
       bool atomsNeedBuilding = false;
       for (int iref = 0; iref != resTemplate->Top().Natom(); iref++) {
         // Track intra-residue bonds from the template.
@@ -261,13 +265,15 @@ const
           int itgt = map[iref];
           frameOut.AddVec3( Vec3(frameIn.XYZ(itgt)) );
           hasPosition.push_back( true );
-          pdb[itgt-currentRes.FirstAtom()] = iref;
+          //pdb[itgt-currentRes.FirstAtom()] = iref;
           // Check source atoms for inter-residue connections.
           Atom const& sourceAtom = topIn[itgt];
           for (Atom::bond_iterator bat = sourceAtom.bondbegin(); bat != sourceAtom.bondend(); ++bat) {
             if ( topIn[*bat].ResNum() < ires ) {
-              detectedInterResBonds.push_back( ResAtPair(ires, sourceAtom.Name()) );
-              detectedInterResBonds.push_back( ResAtPair(topIn[*bat].ResNum(), topIn[*bat].Name()) );
+              // Use template atom names
+              NameType const& bondAtomName = resTemplate->Top()[pdb[itgt-currentRes.FirstAtom()]].Name();
+              detectedInterResBonds.push_back( ResAtPair(ires, templateAtom.Name()) );
+              detectedInterResBonds.push_back( ResAtPair(topIn[*bat].ResNum(), bondAtomName) );
             }
           }
         }

From 361dcff4edbd392bfcd070acae963a3e5779bead Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 23 Feb 2024 10:11:30 -0500
Subject: [PATCH 0600/1492] Save source atom names; we dont want to use alias
 name if it wasnt actually used in the source.

---
 src/Exec_Build.cpp | 39 +++++++++++++++++++++++++++------------
 src/Exec_Build.h   |  2 +-
 2 files changed, 28 insertions(+), 13 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 26ba145924..cb0b973f2a 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -11,7 +11,8 @@
 std::vector<int> Exec_Build::MapAtomsToTemplate(Topology const& topIn,
                                                 int rnum,
                                                 DataSet_Coords* resTemplate,
-                                                Cpptraj::Structure::Creator const& creator)
+                                                Cpptraj::Structure::Creator const& creator,
+                                                std::vector<NameType>& sourceAtomNames)
 {
   std::vector<int> mapOut(resTemplate->Top().Natom(), -1);
   mapOut.reserve( resTemplate->Top().Natom() );
@@ -21,17 +22,22 @@ std::vector<int> Exec_Build::MapAtomsToTemplate(Topology const& topIn,
   {
     NameType const& tgtName = topIn[itgt].Name();
     //mprintf("DEBUG: Search for atom %s\n", *tgtName);
-    // Did this atom have an alias
+    // Check if this atom has an alias.
     NameType alias;
-    if (creator.GetAlias( alias, tgtName )) {
-      mprintf("DEBUG: Atom %s alias is %s\n",
-              *tgtName, *alias);
-    }
-    // See if tgtName or alias matches a reference atom
+    creator.GetAlias( alias, tgtName );
+//    if (creator.GetAlias( alias, tgtName )) {
+//      mprintf("DEBUG: Atom %s alias is %s\n", *tgtName, *alias);
+//    }
+    // See if tgtName or alias matches a reference (template) atom name.
     for (int iref = 0; iref != resTemplate->Top().Natom(); iref++)
     {
       NameType const& refName = resTemplate->Top()[iref].Name();
-      if (refName == tgtName || refName == alias) {
+      if (refName == tgtName) {
+        sourceAtomNames.push_back( tgtName );
+        mapOut[iref] = itgt;
+        break;
+      } else if (refName == alias) {
+        sourceAtomNames.push_back( alias );
         mapOut[iref] = itgt;
         break;
       }
@@ -170,6 +176,11 @@ const
   typedef std::vector<ResAtPair> ResAtArray;
   ResAtArray detectedInterResBonds;
 
+  // Hold template atom names corressponding to source atom names.
+  typedef std::vector<NameType> NameArray;
+  NameArray SourceAtomNames;
+  SourceAtomNames.reserve( topIn.Natom() );
+
   // Loop for setting up atoms in the topology from residues or residue templates.
   int nRefAtomsMissing = 0;
   for (int ires = 0; ires != topIn.Nres(); ires++)
@@ -188,6 +199,7 @@ const
       {
         // Track intra-residue bonds
         Atom sourceAtom = topIn[itgt];
+        SourceAtomNames.push_back( sourceAtom.Name() );
         int at0 = itgt - currentRes.FirstAtom() + atomOffset;
         for (Atom::bond_iterator bat = sourceAtom.bondbegin(); bat != sourceAtom.bondend(); ++bat) {
           if ( topIn[*bat].ResNum() == ires ) {
@@ -222,7 +234,7 @@ const
       else
         currentRes.SetName( NameType( (*templateResName) + ( templateResName.len() - 3) ) );
       // Map source atoms to template atoms.
-      std::vector<int> map = MapAtomsToTemplate( topIn, ires, resTemplate, creator );
+      std::vector<int> map = MapAtomsToTemplate( topIn, ires, resTemplate, creator, SourceAtomNames );
       if (debug_ > 1) {
         mprintf("\t  Atom map:\n");
         // DEBUG - print map
@@ -270,10 +282,9 @@ const
           Atom const& sourceAtom = topIn[itgt];
           for (Atom::bond_iterator bat = sourceAtom.bondbegin(); bat != sourceAtom.bondend(); ++bat) {
             if ( topIn[*bat].ResNum() < ires ) {
-              // Use template atom names
-              NameType const& bondAtomName = resTemplate->Top()[pdb[itgt-currentRes.FirstAtom()]].Name();
+              // Use template atom names. Use saved names in case source name had an alias.
               detectedInterResBonds.push_back( ResAtPair(ires, templateAtom.Name()) );
-              detectedInterResBonds.push_back( ResAtPair(topIn[*bat].ResNum(), bondAtomName) );
+              detectedInterResBonds.push_back( ResAtPair(topIn[*bat].ResNum(), SourceAtomNames[*bat]) );
             }
           }
         }
@@ -466,6 +477,10 @@ const
     mprinterr("Internal Error: AtomOffsets size %zu != newNres size %i\n", AtomOffsets.size(), topOut.Nres());
     return 1;
   }
+  if (SourceAtomNames.size() != (unsigned int)topIn.Natom()) {
+    mprinterr("Internal Error: Source atom names length %zu != # input atoms %i\n", SourceAtomNames.size(), topIn.Natom());
+    return 1;
+  }
 
   // -----------------------------------
   // Build using internal coords if needed.
diff --git a/src/Exec_Build.h b/src/Exec_Build.h
index 5c45bd4243..bea970cabc 100644
--- a/src/Exec_Build.h
+++ b/src/Exec_Build.h
@@ -28,7 +28,7 @@ class Exec_Build : public Exec {
     /// Create new topology/frame using templates
     int FillAtomsWithTemplates(Topology&, Frame&, Topology const&, Frame const&, Cpptraj::Structure::Creator const&) const;
     /// Map atoms in topology to template
-    static std::vector<int> MapAtomsToTemplate(Topology const&, int, DataSet_Coords*, Cpptraj::Structure::Creator const&);
+    static std::vector<int> MapAtomsToTemplate(Topology const&, int, DataSet_Coords*, Cpptraj::Structure::Creator const&, std::vector<NameType>&);
 
     int debug_;
 };

From 429ed57d39d80e5a0da3b640c5cc28d5db37df29 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 23 Feb 2024 10:17:04 -0500
Subject: [PATCH 0601/1492] Only search for an alias if the template name was
 not found.

---
 src/Exec_Build.cpp | 22 ++++++++++++++++------
 1 file changed, 16 insertions(+), 6 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index cb0b973f2a..bb04967eeb 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -22,26 +22,36 @@ std::vector<int> Exec_Build::MapAtomsToTemplate(Topology const& topIn,
   {
     NameType const& tgtName = topIn[itgt].Name();
     //mprintf("DEBUG: Search for atom %s\n", *tgtName);
+    bool found = false;
     // Check if this atom has an alias.
     NameType alias;
-    creator.GetAlias( alias, tgtName );
+    bool has_alias = creator.GetAlias( alias, tgtName );
 //    if (creator.GetAlias( alias, tgtName )) {
 //      mprintf("DEBUG: Atom %s alias is %s\n", *tgtName, *alias);
 //    }
-    // See if tgtName or alias matches a reference (template) atom name.
+    // See if tgtName matches a reference (template) atom name.
     for (int iref = 0; iref != resTemplate->Top().Natom(); iref++)
     {
       NameType const& refName = resTemplate->Top()[iref].Name();
       if (refName == tgtName) {
         sourceAtomNames.push_back( tgtName );
         mapOut[iref] = itgt;
-        break;
-      } else if (refName == alias) {
-        sourceAtomNames.push_back( alias );
-        mapOut[iref] = itgt;
+        found = true;
         break;
       }
     }
+    if (!found && has_alias) {
+      // See if alias matches a reference (template) atom name.
+      for (int iref = 0; iref != resTemplate->Top().Natom(); iref++) {
+        NameType const& refName = resTemplate->Top()[iref].Name();
+        if (refName == alias) {
+          sourceAtomNames.push_back( alias );
+          mapOut[iref] = itgt;
+          found = true;
+          break;
+        }
+      } // END search template for alias
+    } // END do alias search
   }
 /*
   for (int iref = 0; iref != resTemplate->Top().Natom(); iref++)

From 70ec52a932e7cf38c3d0be2b89a5bbb7bf51b62e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 23 Feb 2024 10:21:59 -0500
Subject: [PATCH 0602/1492] Only warn about not finding an aliased terminal
 resdidue if debug is set; could just be the terminal name itself is being
 used.

---
 src/Structure/Creator.cpp | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/Structure/Creator.cpp b/src/Structure/Creator.cpp
index ac41637895..15d6db1f10 100644
--- a/src/Structure/Creator.cpp
+++ b/src/Structure/Creator.cpp
@@ -101,9 +101,9 @@ const
     }
   }
   if (out == 0) {
-    // Terminal residue not found or non-terminal residue.
-    if (termType != Cpptraj::Structure::NON_TERMINAL)
-      mprintf("Warning: No terminal residue found for '%s'\n", *rname);
+    // Terminal residue with alias not found or non-terminal residue.
+    if (debug_ > 0 && termType != Cpptraj::Structure::NON_TERMINAL)
+      mprintf("DEBUG: No aliased terminal residue found for '%s'\n", *rname);
     // Assume Coords set aspect is what we need
     for (Carray::const_iterator it = Templates_.begin(); it != Templates_.end(); ++it) {
       if ( rname == NameType( (*it)->Meta().Aspect() ) ) {

From 032babe4a425a6c69508c93243a20c283fe8aa43 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 23 Feb 2024 11:43:11 -0500
Subject: [PATCH 0603/1492] Make missing atom types fatal

---
 src/Exec_Build.cpp | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index bb04967eeb..24bb289acf 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -193,6 +193,7 @@ const
 
   // Loop for setting up atoms in the topology from residues or residue templates.
   int nRefAtomsMissing = 0;
+  int nAtomsMissingTypes = 0;
   for (int ires = 0; ires != topIn.Nres(); ires++)
   {
     if (debug_ > 0)
@@ -209,6 +210,8 @@ const
       {
         // Track intra-residue bonds
         Atom sourceAtom = topIn[itgt];
+        if (sourceAtom.Type().len() < 1)
+          nAtomsMissingTypes++;
         SourceAtomNames.push_back( sourceAtom.Name() );
         int at0 = itgt - currentRes.FirstAtom() + atomOffset;
         for (Atom::bond_iterator bat = sourceAtom.bondbegin(); bat != sourceAtom.bondend(); ++bat) {
@@ -322,6 +325,12 @@ const
     }
   } // END loop over source residues
   mprintf("\t%i template atoms missing in source.\n", nRefAtomsMissing);
+  if (nAtomsMissingTypes > 0) {
+    mprinterr("Error: %i atoms are missing types, either because they did not have\n"
+              "Error:  one initially or they could not be matched to a template.\n"
+              "Error:  Build cannot proceed unless all atoms have a type.\n");
+    return 1;
+  }
 
   // -----------------------------------
   // DEBUG - Print primary connection atoms

From ed6dc895afeecf10f8c183d686de8f3147369091 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 23 Feb 2024 13:44:31 -0500
Subject: [PATCH 0604/1492] Handle cases where dihedrals do not have symbols
 and need to use the previous symbols

---
 src/AmberParamFile.cpp | 38 ++++++++++++++++++++++++++++++--------
 src/AmberParamFile.h   |  2 +-
 2 files changed, 31 insertions(+), 9 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 317f85ee96..efd45edd6f 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -173,16 +173,31 @@ const
   * of pn is used only for identifying the existence of the next term and 
   * only the absolute value of PN is kept.
   */
-int AmberParamFile::read_dihedral(ParameterSet& prm, const char* ptr)
+int AmberParamFile::read_dihedral(ParameterSet& prm, const char* ptr,
+                                  std::vector<std::string>& last_symbols,
+                                  bool first_char_is_space)
 const
 {
   // Dihedral parameters
-  if (debug_ > 1) mprintf("DEBUG: Dihedral: %s\n", ptr);
+  //if (debug_ > 1)
+    mprintf("DEBUG: Dihedral: %s\n", ptr);
   std::vector<std::string> symbols(4);
-  int pos = read_symbols(ptr, symbols, 4);
-  if (pos < 0) {
-    mprinterr("Error: Could not read symbols for dihedral from %s\n", ptr);
-    return 1;
+  int pos = 0;
+  if (first_char_is_space) {
+    // Assume no symbols on this line. Use previous symbols.
+    if (last_symbols.empty()) {
+      mprinterr("Error: No symbols in dihedral line: %s\n", ptr);
+      return 1;
+    }
+    symbols = last_symbols;
+    // Advance past the whitespace
+    while (ptr[pos] == ' ') pos++;
+  } else {
+    pos = read_symbols(ptr, symbols, 4);
+    if (pos < 0) {
+      mprinterr("Error: Could not read symbols for dihedral from %s\n", ptr);
+      return 1;
+    }
   }
   //mprintf("DEBUG: %s %s %s %s '%s'\n", symbols[0].c_str(), symbols[1].c_str(), symbols[2].c_str(), symbols[3].c_str(), ptr+pos);
   int IDIVF;
@@ -217,6 +232,7 @@ const
             *(types[0]), *(types[1]), *(types[2]), *(types[3]), PN);
     //mprintf("DEBUG: %s\n", ptr);
   }
+  last_symbols = symbols;
   return 0;
 }
 
@@ -403,6 +419,8 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int deb
     mprinterr("Error: Could not read anything from Amber FF file %s\n", fname.full());
     return 1;
   }
+  std::vector<std::string> last_symbols;
+  last_symbols.reserve(4);
   std::string title(ptr);
   mprintf("\tTitle: %s\n", title.c_str());
   prm.SetParamSetName( title );
@@ -412,6 +430,7 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int deb
   SectionType section = UNKNOWN;
   ptr = infile.Line();
   while (ptr != 0) {
+    bool first_char_is_space = (*ptr == ' ');
     // Advance to first non-space char
     while (*ptr == ' ' && *ptr != '\0') ++ptr;
     // Is this a recognized section keyword?
@@ -440,7 +459,7 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int deb
         else if (section == ANGLE)
           err = read_angle(prm, ptr);
         else if (section == DIHEDRAL)
-          err = read_dihedral(prm, ptr);
+          err = read_dihedral(prm, ptr, last_symbols, first_char_is_space);
         else if (section == IMPROPER)
           err = read_improper(prm, ptr);
         else if (section == LJ1012)
@@ -499,10 +518,13 @@ int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
   std::string title(ptr);
   mprintf("\tTitle: %s\n", title.c_str());
   prm.SetParamSetName( title );
+  std::vector<std::string> last_symbols;
+  last_symbols.reserve(4);
   // Read file
   SectionType section = ATYPE;
   ptr = infile.Line();
   while (ptr != 0) {
+    bool first_char_is_space = (*ptr == ' ');
     // Advance to first non-space char
     while (*ptr == ' ' && *ptr != '\0') ++ptr;
     //mprintf("DEBUG: First char: %c (%i)\n", *ptr, (int)*ptr);
@@ -571,7 +593,7 @@ int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
     } else if (section == ANGLE) {
       read_err = read_angle(prm, ptr);
     } else if (section == DIHEDRAL) {
-      read_err = read_dihedral(prm, ptr);
+      read_err = read_dihedral(prm, ptr, last_symbols, first_char_is_space);
     } else if (section == IMPROPER) {
       read_err = read_improper(prm, ptr);
     } else if (section == LJ1012) {
diff --git a/src/AmberParamFile.h b/src/AmberParamFile.h
index 8a3cff620a..c88de68cfc 100644
--- a/src/AmberParamFile.h
+++ b/src/AmberParamFile.h
@@ -35,7 +35,7 @@ class AmberParamFile {
     /// Read angle line
     int read_angle(ParameterSet&, const char*) const;
     /// Read dihedral line
-    int read_dihedral(ParameterSet&, const char*) const;
+    int read_dihedral(ParameterSet&, const char*, std::vector<std::string>&, bool) const;
     /// Read improper line
     int read_improper(ParameterSet&, const char*) const;
     /// Read LJ 10-12 hbond line

From b75fda227fa145bf6b5e240ffa0c7bdd30d27858 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 23 Feb 2024 14:01:05 -0500
Subject: [PATCH 0605/1492] If no connect info, put -1 for head and tail

---
 src/Exec_Build.cpp | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index bb04967eeb..8d35325446 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -146,6 +146,8 @@ const
       AssociatedData* ad = resTemplate->GetAssociatedData(AssociatedData::CONNECT);
       if (ad == 0) {
         mprintf("Warning: Unit '%s' does not have CONNECT data.\n", resTemplate->legend());
+        resHeadAtoms.push_back( -1 );
+        resTailAtoms.push_back( -1 );
       } else {
         AssociatedData_Connect const& CONN = static_cast<AssociatedData_Connect const&>( *ad );
         if (CONN.NconnectAtoms() < 2) {

From 247962b3c7697f7fd562bdedd0bcbed098fe7e8a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 23 Feb 2024 14:10:18 -0500
Subject: [PATCH 0606/1492] Hide debug

---
 src/Structure/Zmatrix.cpp | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index beb03c7f5a..5105df826c 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -1035,11 +1035,11 @@ int Zmatrix::SetToFrame(Frame& frameOut, Barray& hasPosition) const {
       Iarray::const_iterator it = std::find(positionsToSet.begin(), positionsToSet.end(), IC_[icIdx].AtI());
       if (it == positionsToSet.end()) {
         positionsToSet.push_back( IC_[icIdx].AtI() );
-        mprintf("DEBUG:\t\tAtom %i needs its position set.\n", IC_[icIdx].AtI()+1);
+        if (debug_ > 1) mprintf("DEBUG:\t\tAtom %i needs its position set.\n", IC_[icIdx].AtI()+1);
       }
     }
   }
-  mprintf("DEBUG: %zu positions to set.\n", positionsToSet.size());
+  if (debug_ > 0) mprintf("DEBUG: %zu positions to set.\n", positionsToSet.size());
 
   //while (remainingPositionsToSet > 0 && Nused < IC_.size()) {
   Iarray::const_iterator at_with_unset_pos = positionsToSet.begin();
@@ -1048,10 +1048,10 @@ int Zmatrix::SetToFrame(Frame& frameOut, Barray& hasPosition) const {
     for (; at_with_unset_pos != positionsToSet.end(); ++at_with_unset_pos)
       if (!hasPosition[*at_with_unset_pos]) break;
     if (at_with_unset_pos == positionsToSet.end()) {
-      mprintf("DEBUG: No more positions to set.\n");
+      if (debug_ > 0) mprintf("DEBUG: No more positions to set.\n");
       break;
     }
-    mprintf("DEBUG: Setting position of atom %i\n", (*at_with_unset_pos) + 1);
+    if (debug_ > 1) mprintf("DEBUG: Setting position of atom %i\n", (*at_with_unset_pos) + 1);
     // Get IC that corresponds to this atom
     int icIdx = -1;
     for (unsigned int idx = 0; idx != IC_.size(); ++idx) {
@@ -1093,13 +1093,14 @@ int Zmatrix::SetToFrame(Frame& frameOut, Barray& hasPosition) const {
       continue; // FIXME
     }
     InternalCoords const& ic = IC_[icIdx];
-    //if (debug_ > 0)
+    if (debug_ > 0) {
       mprintf("DEBUG: Next IC to use is %i : %i %i %i %i r=%g theta=%g phi=%g\n",
               icIdx+1, ic.AtI()+1, ic.AtJ()+1, ic.AtK()+1, ic.AtL()+1,
               ic.Dist(), ic.Theta(), ic.Phi());
-    mprintf( "Torsion = %f\n", ic.Phi() );
-    mprintf( "Angle   = %f\n", ic.Theta() );
-    mprintf( "Bond    = %f\n", ic.Dist() );
+      mprintf( "Torsion = %f\n", ic.Phi() );
+      mprintf( "Angle   = %f\n", ic.Theta() );
+      mprintf( "Bond    = %f\n", ic.Dist() );
+    }
     Vec3 posI = AtomIposition(ic, frameOut);
 
     frameOut.SetXYZ( ic.AtI(), posI );

From 15b8cdac2751657208beeb6e5bfdf9505f96f9ea Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 23 Feb 2024 14:10:33 -0500
Subject: [PATCH 0607/1492] Set debug levels

---
 src/DataIO_LeapRC.cpp | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index d7e4dd3962..274c7384a8 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -75,6 +75,7 @@ int DataIO_LeapRC::LoadAmberParams(std::string const& filename, DataSetList& dsl
   if (fargs.hasKey("frcmod")) {
     mprintf("\tLoading force field modifications from '%s'\n", filename.c_str());
     DataIO_AmberFrcmod infile;
+    infile.SetDebug( debug_ );
     if (infile.ReadData(amberhome_ + "parm/" + filename, dsl, dsname)) {
       mprinterr("Error: Could not load force field modifications from '%s'\n", filename.c_str());
       return 1;
@@ -101,6 +102,7 @@ int DataIO_LeapRC::LoadOFF(std::string const& filename, DataSetList& dsl, std::s
     mprintf("Warning: Library %s has already been loaded, skipping.\n", filename.c_str());
   } else {
     DataIO_AmberLib infile;
+    infile.SetDebug( debug_ );
     if (infile.ReadData(amberhome_ + "lib/" + filename, dsl, dsname)) {
       mprinterr("Error: Could not load library file '%s'\n", filename.c_str());
       return 1;
@@ -116,7 +118,8 @@ int DataIO_LeapRC::LoadAmberPrep(std::string const& filename, DataSetList& dsl,
     mprintf("Warning: Prep file %s has already been loaded, skipping.\n", filename.c_str());
   } else {
     DataIO_AmberPrep infile;
-    if (infile.ReadData(amberhome_ + "lib/" + filename, dsl, dsname)) {
+    infile.SetDebug( debug_ );
+    if (infile.ReadData(amberhome_ + "prep/" + filename, dsl, dsname)) {
       mprinterr("Error: Could not load prep file '%s'\n", filename.c_str());
       return 1;
     }

From bc980b62ab0b7346efb10d151a2606a8846ee573 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 23 Feb 2024 14:25:18 -0500
Subject: [PATCH 0608/1492] Add option to lib to allow overwrite of previous
 coord

---
 src/AmberParamFile.cpp   |  2 +-
 src/DataFile.cpp         |  2 +-
 src/DataIO_AmberLib.cpp  | 21 +++++++++++++++++----
 src/DataIO_AmberLib.h    |  2 ++
 src/DataIO_AmberPrep.cpp |  2 +-
 src/DataIO_LeapRC.cpp    |  3 +++
 6 files changed, 25 insertions(+), 7 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index efd45edd6f..4bc932debd 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -179,7 +179,7 @@ int AmberParamFile::read_dihedral(ParameterSet& prm, const char* ptr,
 const
 {
   // Dihedral parameters
-  //if (debug_ > 1)
+  if (debug_ > 1)
     mprintf("DEBUG: Dihedral: %s\n", ptr);
   std::vector<std::string> symbols(4);
   int pos = 0;
diff --git a/src/DataFile.cpp b/src/DataFile.cpp
index b467763dc3..1427bd0102 100644
--- a/src/DataFile.cpp
+++ b/src/DataFile.cpp
@@ -91,7 +91,7 @@ const FileTypes::AllocToken DataFile::DF_AllocArray[] = {
   { "Amber Energy File",  0,                             0,            DataIO_AmberEne::Alloc},
   { "Numpy array",        0,                             0,            DataIO_Numpy::Alloc},
   { "Amber Prep File",    DataIO_AmberPrep::ReadHelp,    0,            DataIO_AmberPrep::Alloc},
-  { "Amber OFF File",     0,                             0,            DataIO_AmberLib::Alloc},
+  { "Amber OFF File",     DataIO_AmberLib::ReadHelp,     0,            DataIO_AmberLib::Alloc},
   { "Amber Force Field",  DataIO_AmberFF::ReadHelp,      0,            DataIO_AmberFF::Alloc},
   { "Amber Frcmod File",  0,                             0,            DataIO_AmberFrcmod::Alloc},
   { "Amber LEaP RC File", 0,                             0,            DataIO_LeapRC::Alloc},
diff --git a/src/DataIO_AmberLib.cpp b/src/DataIO_AmberLib.cpp
index 9011b9ed61..3382fee7ea 100644
--- a/src/DataIO_AmberLib.cpp
+++ b/src/DataIO_AmberLib.cpp
@@ -4,7 +4,8 @@
 #include "AssociatedData_Connect.h"
 
 /// CONSTRUCTOR
-DataIO_AmberLib::DataIO_AmberLib()
+DataIO_AmberLib::DataIO_AmberLib() :
+  allowOverwrite_(false)
 {
 
 }
@@ -23,13 +24,13 @@ bool DataIO_AmberLib::ID_DataFormat(CpptrajFile& infile)
 // DataIO_AmberLib::ReadHelp()
 void DataIO_AmberLib::ReadHelp()
 {
-
+  mprintf("\tallowoverwrite : Allow existing sets to be overwritten.\n");
 }
 
 // DataIO_AmberLib::processReadArgs()
 int DataIO_AmberLib::processReadArgs(ArgList& argIn)
 {
-
+  allowOverwrite_ = argIn.hasKey("allowoverwrite");
   return 0;
 }
 
@@ -70,7 +71,19 @@ int DataIO_AmberLib::ReadData(FileName const& fname, DataSetList& dsl, std::stri
       mprinterr("Error: Expected '%s', got '%s'\n", entryColumn.c_str(), line.c_str());
       return 1;
     }
-    DataSet_Coords* ds = (DataSet_Coords*)dsl.AddSet( DataSet::COORDS, MetaData(dsname, *it) );
+    DataSet_Coords* ds = 0;
+    MetaData meta(dsname, *it);
+    DataSet* set = dsl.CheckForSet( meta );
+    if (set == 0) {
+      ds = (DataSet_Coords*)dsl.AddSet( DataSet::COORDS, meta );
+    } else if (allowOverwrite_) {
+      mprintf("Warning: Overwriting existing set %s\n", set->legend());
+      dsl.RemoveSet( set );
+      ds = (DataSet_Coords*)dsl.AddSet( DataSet::COORDS, meta );
+    } else {
+      mprinterr("Error: Set %s already exists and 'allowoverwrite' not specified.\n");
+      return 1;
+    }
     if (ds == 0) {
       mprinterr("Error: Could not create data set for unit %s\n", it->c_str());
       return 1;
diff --git a/src/DataIO_AmberLib.h b/src/DataIO_AmberLib.h
index 6db1b509cd..42f13152f0 100644
--- a/src/DataIO_AmberLib.h
+++ b/src/DataIO_AmberLib.h
@@ -32,5 +32,7 @@ class DataIO_AmberLib : public DataIO {
     static int read_bonds(Topology&, std::string const&);
     static int read_positions(std::vector<Vec3>&, std::string const&);
     int read_connect(AssociatedData_Connect&, std::string const&) const;
+
+    bool allowOverwrite_; ///< If true, allow existing sets to be overwritten
 };
 #endif
diff --git a/src/DataIO_AmberPrep.cpp b/src/DataIO_AmberPrep.cpp
index c5f87ee327..9062d96175 100644
--- a/src/DataIO_AmberPrep.cpp
+++ b/src/DataIO_AmberPrep.cpp
@@ -116,7 +116,7 @@ const
   std::string resName = args.GetStringNext();
   std::string coordFlag = args.GetStringNext();
   int kform = args.getNextInteger(-1);
-  if (debug_ > 0)
+//  if (debug_ > 0)
     mprintf("DEBUG: %s %s %i\n", resName.c_str(), coordFlag.c_str(), kform);
   // 6 - IFIXC , IOMIT , ISYMDU , IPOS
   // FORMAT (4A)
diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 274c7384a8..86a407366a 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -103,6 +103,9 @@ int DataIO_LeapRC::LoadOFF(std::string const& filename, DataSetList& dsl, std::s
   } else {
     DataIO_AmberLib infile;
     infile.SetDebug( debug_ );
+    // Allow lib to overwrite e.g. something from previous prep
+    ArgList tmpArgs("allowoverwrite");
+    infile.processReadArgs(tmpArgs);
     if (infile.ReadData(amberhome_ + "lib/" + filename, dsl, dsname)) {
       mprinterr("Error: Could not load library file '%s'\n", filename.c_str());
       return 1;

From 39da822b4202cb7bc4fca2ecaee4fe2e1437950b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 23 Feb 2024 14:40:16 -0500
Subject: [PATCH 0609/1492] Cannot assume units are in the same order they are
 initially listed in lib file

---
 src/DataIO_AmberLib.cpp | 41 ++++++++++++++++++++++++++++++-----------
 1 file changed, 30 insertions(+), 11 deletions(-)

diff --git a/src/DataIO_AmberLib.cpp b/src/DataIO_AmberLib.cpp
index 3382fee7ea..bf0dbfe43a 100644
--- a/src/DataIO_AmberLib.cpp
+++ b/src/DataIO_AmberLib.cpp
@@ -61,18 +61,36 @@ int DataIO_AmberLib::ReadData(FileName const& fname, DataSetList& dsl, std::stri
     line = infile.GetLine();
   }
   // Now should be at first unit
-  if (debug_ > 0) mprintf("DEBUG: Units:\n");
-  for (Sarray::const_iterator it = UnitNames.begin(); it != UnitNames.end(); ++it)
+  unsigned int units_read = 0;
+  if (debug_ > 0) {
+    mprintf("DEBUG: Units:");
+    for (Sarray::const_iterator it = UnitNames.begin(); it != UnitNames.end(); ++it)
+      mprintf(" %s", it->c_str());
+    mprintf("\n");
+  }
+  while (units_read < UnitNames.size())
   {
-    if (debug_ > 0) mprintf("DEBUG: Reading unit %s\n", it->c_str());
-    std::string entryColumn = "!entry." + *it + ".unit.atoms";
-    ArgList tmparg( line );
-    if (tmparg.Nargs() < 1 || tmparg[0] != entryColumn) {
-      mprinterr("Error: Expected '%s', got '%s'\n", entryColumn.c_str(), line.c_str());
+    // Which unit are we reading: !entry.<name>.unit.atoms most likely
+    ArgList tmparg( line, " !." );
+    std::string currentName = tmparg.GetStringKey("entry");
+    if (debug_ > 0)
+       mprintf("DEBUG: Reading unit %s\n", currentName.c_str());
+    // Ensure this is in the list of units
+    bool found = false;
+    for (Sarray::const_iterator it = UnitNames.begin(); it != UnitNames.end(); ++it) {
+      if (*it == currentName) {
+        found = true;
+        break;
+      }
+    }
+    if (!found) {
+      mprinterr("Error: Unit %s was not found in the initial list of names in lib file.\n",
+                currentName.c_str());
       return 1;
     }
+
     DataSet_Coords* ds = 0;
-    MetaData meta(dsname, *it);
+    MetaData meta(dsname, currentName);
     DataSet* set = dsl.CheckForSet( meta );
     if (set == 0) {
       ds = (DataSet_Coords*)dsl.AddSet( DataSet::COORDS, meta );
@@ -85,13 +103,14 @@ int DataIO_AmberLib::ReadData(FileName const& fname, DataSetList& dsl, std::stri
       return 1;
     }
     if (ds == 0) {
-      mprinterr("Error: Could not create data set for unit %s\n", it->c_str());
+      mprinterr("Error: Could not create data set for unit %s\n", currentName.c_str());
       return 1;
     }
-    if (read_unit( ds, infile, line, *it )) {
-      mprinterr("Error: Reading unit '%s'\n", it->c_str());
+    if (read_unit( ds, infile, line, currentName )) {
+      mprinterr("Error: Reading unit '%s'\n", currentName.c_str());
       return 1;
     }
+    units_read++;
   }
   mprintf("\tRead %zu units from Amber OFF file %s.\n", UnitNames.size(), fname.base());
 

From 3611cb66b2327ee5aa45d06cb130a241dca62e20 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 23 Feb 2024 14:46:48 -0500
Subject: [PATCH 0610/1492] Print SCEE and SCNB for dihedral parms

---
 src/ParameterSet.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/ParameterSet.cpp b/src/ParameterSet.cpp
index 4cb1039c8f..147f9dbcbe 100644
--- a/src/ParameterSet.cpp
+++ b/src/ParameterSet.cpp
@@ -89,11 +89,11 @@ void ParameterSet::Print(CpptrajFile& Out) const {
   }
   if (!dihParm_.empty()) {
     Out.Printf("Dihedral parameters:\n");
-    Out.Printf("\t%6s %6s %6s %6s %12s %12s %12s\n", "Type1", "Type2", "Type3", "Type4", "Pk", "Pn", "Phase");
+    Out.Printf("\t%6s %6s %6s %6s %12s %4s %6s %6s %6s\n", "Type1", "Type2", "Type3", "Type4", "Pk", "Pn", "Phase", "SCEE", "SCNB");
     for (DihedralParmHolder::const_iterator it0 = dihParm_.begin(); it0 != dihParm_.end(); ++it0)
       for (DihedralParmArray::const_iterator it1 = it0->second.begin();
                                              it1 != it0->second.end(); ++it1)
-        Out.Printf("\t%6s %6s %6s %6s : %12.4f %12.4f %12.4f\n", *(it0->first[0]), *(it0->first[1]), *(it0->first[2]), *(it0->first[3]), it1->Pk(), it1->Pn(), it1->Phase()*Constants::RADDEG);
+        Out.Printf("\t%6s %6s %6s %6s : %12.4f %4.1f %6.2f %6.2f %6.2f\n", *(it0->first[0]), *(it0->first[1]), *(it0->first[2]), *(it0->first[3]), it1->Pk(), it1->Pn(), it1->Phase()*Constants::RADDEG, it1->SCEE(), it1->SCNB());
   }
   if (!impParm_.empty()) {
     Out.Printf("Improper parameters:\n");

From 249c93412caa234177eac0be81027016f9201234 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 23 Feb 2024 15:04:45 -0500
Subject: [PATCH 0611/1492] Fix up missing atom types error message

---
 src/Exec_Build.cpp | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 3abd026fd0..8894464e67 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -330,7 +330,16 @@ const
   if (nAtomsMissingTypes > 0) {
     mprinterr("Error: %i atoms are missing types, either because they did not have\n"
               "Error:  one initially or they could not be matched to a template.\n"
-              "Error:  Build cannot proceed unless all atoms have a type.\n");
+              "Error:  Build cannot proceed unless all atoms have a type:\n",
+              nAtomsMissingTypes);
+    for (int ires = 0; ires != topOut.Nres(); ires++) {
+      std::string missingTypes;
+      for (int at = topOut.Res(ires).FirstAtom(); at != topOut.Res(ires).LastAtom(); ++at)
+        if ( topOut[at].Type().len() < 1 )
+          missingTypes.append(" " + topOut[at].Name().Truncated() );
+      if (!missingTypes.empty())
+        mprinterr("Error:\t%s missing types for%s\n", topOut.TruncResNameNum(ires).c_str(), missingTypes.c_str());
+    }
     return 1;
   }
 

From 03bf6f7487ff68a01f354a141b72dab765c22a89 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 23 Feb 2024 15:13:47 -0500
Subject: [PATCH 0612/1492] Start adding sugar prep

---
 src/Exec_Build.cpp | 36 ++++++++++++++++++++++++++++++++++++
 src/Exec_Build.h   |  5 ++++-
 src/cpptrajdepend  |  2 +-
 3 files changed, 41 insertions(+), 2 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 8894464e67..0c5ccf6164 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -6,6 +6,21 @@
 #include "Structure/Builder.h"
 #include "Structure/Creator.h"
 #include "Structure/PdbCleaner.h"
+#include "Structure/SugarBuilder.h"
+#include "Structure/Sugar.h"
+
+/** CONSTRUCTOR */
+Exec_Build::Exec_Build() :
+  Exec(GENERAL),
+  debug_(0),
+  sugarBuilder_(0)
+{}
+
+/** DESTRUCTOR */
+Exec_Build::~Exec_Build() {
+  if (sugarBuilder_ != 0)
+    delete sugarBuilder_;
+}
 
 /** Map atoms in residue to template. */
 std::vector<int> Exec_Build::MapAtomsToTemplate(Topology const& topIn,
@@ -798,6 +813,27 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
       mainParmSet->UpdateParamSet( *(*it), UC, State.Debug(), State.Debug() ); // FIXME verbose
   }*/
 
+  // Load PDB to glycam residue name map
+  bool prepare_sugars = !argIn.hasKey("nosugars");
+  if (!prepare_sugars)
+    mprintf("\tNot attempting to prepare sugars.\n");
+  else
+    mprintf("\tWill attempt to prepare sugars.\n");
+  if (sugarBuilder_ != 0) delete sugarBuilder_;
+  sugarBuilder_ = 0;
+  if (prepare_sugars) {
+    sugarBuilder_ = new Cpptraj::Structure::SugarBuilder(debug_);
+    // Init options
+    if (sugarBuilder_->InitOptions( argIn.hasKey("hasglycam"),
+                                    argIn.GetStringKey("sugarmask"),
+                                    argIn.GetStringKey("determinesugarsby", "geometry"),
+                                    argIn.GetStringKey("resmapfile") ))
+    {
+      mprinterr("Error: Sugar options init failed.\n");
+      return CpptrajState::ERR;
+    }
+  }
+
   // Fill in atoms with templates
   Topology topOut;
   topOut.SetDebug( debug_ );
diff --git a/src/Exec_Build.h b/src/Exec_Build.h
index bea970cabc..53d5d7829c 100644
--- a/src/Exec_Build.h
+++ b/src/Exec_Build.h
@@ -4,12 +4,14 @@
 namespace Cpptraj {
 namespace Structure {
 class Creator;
+class SugarBuilder;
 }
 }
 /// Used to build a structure 
 class Exec_Build : public Exec {
   public:
-    Exec_Build() : Exec(GENERAL), debug_() {}
+    Exec_Build();
+    ~Exec_Build();
     void Help() const;
     DispatchObject* Alloc() const { return (DispatchObject*)new Exec_Build(); }
     RetType Execute(CpptrajState&, ArgList&);
@@ -31,5 +33,6 @@ class Exec_Build : public Exec {
     static std::vector<int> MapAtomsToTemplate(Topology const&, int, DataSet_Coords*, Cpptraj::Structure::Creator const&, std::vector<NameType>&);
 
     int debug_;
+    Cpptraj::Structure::SugarBuilder* sugarBuilder_;
 };
 #endif
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 8c80a90af5..07798c22af 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -291,7 +291,7 @@ Ewald_Regular.o : Ewald_Regular.cpp Atom.h AtomMask.h Box.h Constants.h Coordina
 ExclusionArray.o : ExclusionArray.cpp Atom.h AtomMask.h CharMask.h CpptrajStdio.h ExclusionArray.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Unit.h
 Exec_AddMissingRes.o : Exec_AddMissingRes.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CharMask.h CompactFrameArray.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_AddMissingRes.h Exec_AddMissingRes_Pres.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Analyze.o : Exec_Analyze.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Analyze.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Build.o : Exec_Build.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/GB_Params.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/Creator.h Structure/PdbCleaner.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Build.o : Exec_Build.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/GB_Params.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/Creator.h Structure/PdbCleaner.h Structure/StructureEnum.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Calc.o : Exec_Calc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Calc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_CatCrd.o : Exec_CatCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CatCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Change.o : Exec_Change.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Change.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h

From 046c106de3c8c8684711d06f6ac2e98ac6be95b4 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 23 Feb 2024 15:37:39 -0500
Subject: [PATCH 0613/1492] Add in fix sugar structure

---
 src/Exec_Build.cpp | 28 +++++++++++++++++++++++++++-
 1 file changed, 27 insertions(+), 1 deletion(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 0c5ccf6164..e63bd1384c 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -675,9 +675,14 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
   //Topology& topIn = *(coords.TopPtr());
   //Topology const& topIn = coords.Top();
   Topology topIn = coords.Top(); // FIXME do not work on the copy, work on the top itself
+
+  std::string solventResName = argIn.GetStringKey("solventresname", "HOH");
+  mprintf("\tSolvent residue name: %s\n", solventResName.c_str());
+
+  // Clean up structure
   Cpptraj::Structure::PdbCleaner pdbCleaner;
   pdbCleaner.SetDebug( debug_ );
-  if (pdbCleaner.InitPdbCleaner( argIn, "HOH", std::vector<int>() )) {
+  if (pdbCleaner.InitPdbCleaner( argIn, solventResName, std::vector<int>() )) {
     mprinterr("Error: Could not init PDB cleaner.\n");
     return CpptrajState::ERR;
   }
@@ -832,6 +837,27 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
       mprinterr("Error: Sugar options init failed.\n");
       return CpptrajState::ERR;
     }
+    bool splitres = !argIn.hasKey("nosplitres");
+    if (splitres)
+      mprintf("\tWill split off recognized sugar functional groups into separate residues.\n");
+    else
+      mprintf("\tNot splitting recognized sugar functional groups into separate residues.\n");
+    bool c1bondsearch = !argIn.hasKey("noc1search");
+    if (c1bondsearch)
+      mprintf("\tWill search for missing bonds to sugar anomeric atoms.\n");
+    else
+      mprintf("\tNot searching for missing bonds to sugar anomeric atoms.\n");
+    // May need to modify sugar structure/topology, either by splitting
+    // C1 hydroxyls of terminal sugars into ROH residues, and/or by
+    // adding missing bonds to C1 atoms.
+    // This is done before any identification takes place since we want
+    // to identify based on the most up-to-date topology.
+    if (sugarBuilder_->FixSugarsStructure(topIn, frameIn,
+                                          c1bondsearch, splitres, solventResName))
+    {
+      mprinterr("Error: Sugar structure modification failed.\n");
+      return CpptrajState::ERR;
+    }
   }
 
   // Fill in atoms with templates

From bae5731e03ddc05ff1f8d48b226fe3fb39dab540 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 23 Feb 2024 15:43:48 -0500
Subject: [PATCH 0614/1492] Setting each sugar as terminal only needed for
 prepareforleap

---
 src/Exec_PrepareForLeap.cpp    |  1 +
 src/Structure/SugarBuilder.cpp | 23 +++++++++++++++--------
 src/Structure/SugarBuilder.h   |  2 ++
 3 files changed, 18 insertions(+), 8 deletions(-)

diff --git a/src/Exec_PrepareForLeap.cpp b/src/Exec_PrepareForLeap.cpp
index 7aeb668e01..cd39297f50 100644
--- a/src/Exec_PrepareForLeap.cpp
+++ b/src/Exec_PrepareForLeap.cpp
@@ -1118,6 +1118,7 @@ Exec::RetType Exec_PrepareForLeap::Execute(CpptrajState& State, ArgList& argIn)
       mprinterr("Error: Sugar preparation failed.\n");
       return CpptrajState::ERR;
     }
+    sugarBuilder.SetEachSugarAsTerminal(topIn);
   } else {
     mprintf("\tNot preparing sugars.\n");
   }
diff --git a/src/Structure/SugarBuilder.cpp b/src/Structure/SugarBuilder.cpp
index cd250631af..cc1eb58e1a 100644
--- a/src/Structure/SugarBuilder.cpp
+++ b/src/Structure/SugarBuilder.cpp
@@ -1947,14 +1947,21 @@ int SugarBuilder::PrepareSugars(bool errorsAreFatal,
     }
     // Bonds to sugars have been removed, so regenerate molecule info
     topIn.DetermineMolecules();
-    // Set each sugar as terminal
-    for (std::vector<Sugar>::const_iterator sugar = Sugars_.begin(); sugar != Sugars_.end(); ++sugar)
-    {
-      int rnum = sugar->ResNum(topIn);
-      topIn.SetRes(rnum).SetTerminal(true);
-      if (rnum - 1 > -1)
-        topIn.SetRes(rnum-1).SetTerminal(true);
-    }
+
   }
   return 0;
 }
+
+/** When being used in prepareforleap, this is used to set each sugar as
+  * terminal, which LEaP needs.
+  */
+void SugarBuilder::SetEachSugarAsTerminal(Topology& topIn) const {
+  // Set each sugar as terminal
+  for (std::vector<Sugar>::const_iterator sugar = Sugars_.begin(); sugar != Sugars_.end(); ++sugar)
+  {
+    int rnum = sugar->ResNum(topIn);
+    topIn.SetRes(rnum).SetTerminal(true);
+    if (rnum - 1 > -1)
+      topIn.SetRes(rnum-1).SetTerminal(true);
+  }
+}
diff --git a/src/Structure/SugarBuilder.h b/src/Structure/SugarBuilder.h
index 49e2421bb3..41eeb8786b 100644
--- a/src/Structure/SugarBuilder.h
+++ b/src/Structure/SugarBuilder.h
@@ -26,6 +26,8 @@ class SugarBuilder {
                            bool, bool, NameType const&);
     /// Identify sugars, do renaming, remove bonds, generate leap input
     int PrepareSugars(bool, ResStatArray&, Topology&, Frame const&, std::vector<BondType>&);
+    /// Set each sugar as a terminal residue
+    void SetEachSugarAsTerminal(Topology&) const;
   private:
     typedef std::vector<int> Iarray;
 

From 67e5b357dcc7b43d9f7e42bd1128de7d627ffe06 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 24 Feb 2024 14:18:43 -0500
Subject: [PATCH 0615/1492] Only remove bonds when using prepareforleap

---
 src/Exec_Build.cpp             |  8 ++++++++
 src/Exec_PrepareForLeap.cpp    | 15 ++++++++++++++-
 src/Structure/SugarBuilder.cpp |  7 +++----
 3 files changed, 25 insertions(+), 5 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index e63bd1384c..8e866860d0 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -6,6 +6,7 @@
 #include "Structure/Builder.h"
 #include "Structure/Creator.h"
 #include "Structure/PdbCleaner.h"
+#include "Structure/ResStatArray.h"
 #include "Structure/SugarBuilder.h"
 #include "Structure/Sugar.h"
 
@@ -858,6 +859,13 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
       mprinterr("Error: Sugar structure modification failed.\n");
       return CpptrajState::ERR;
     }
+    std::vector<BondType> LeapBonds;
+    Cpptraj::Structure::ResStatArray resStat( topIn.Nres() );
+    if (sugarBuilder_->PrepareSugars(true, resStat, topIn, frameIn, LeapBonds))
+    {
+      mprinterr("Error: Sugar preparation failed.\n");
+      return CpptrajState::ERR;
+    }
   }
 
   // Fill in atoms with templates
diff --git a/src/Exec_PrepareForLeap.cpp b/src/Exec_PrepareForLeap.cpp
index cd39297f50..e5a77e6911 100644
--- a/src/Exec_PrepareForLeap.cpp
+++ b/src/Exec_PrepareForLeap.cpp
@@ -1113,11 +1113,24 @@ Exec::RetType Exec_PrepareForLeap::Execute(CpptrajState& State, ArgList& argIn)
 
   // Prepare sugars
   if (prepare_sugars) {
-    if (sugarBuilder.PrepareSugars(errorsAreFatal_, resStat, topIn, frameIn, LeapBonds))
+    std::vector<BondType> SugarBonds; 
+    if (sugarBuilder.PrepareSugars(errorsAreFatal_, resStat, topIn, frameIn, SugarBonds))
     {
       mprinterr("Error: Sugar preparation failed.\n");
       return CpptrajState::ERR;
     }
+    // Remove bonds to sugar
+    if (!SugarBonds.empty()) {
+      for (std::vector<BondType>::const_iterator it = SugarBonds.begin();
+                                                 it != SugarBonds.end(); ++it)
+      {
+        LeapBonds.push_back( *it );
+        topIn.RemoveBond(it->A1(), it->A2());
+      }
+      // Bonds to sugars have been removed, so regenerate molecule info
+      topIn.DetermineMolecules();
+    }
+    // Set each sugar residue as a terminal residue
     sugarBuilder.SetEachSugarAsTerminal(topIn);
   } else {
     mprintf("\tNot preparing sugars.\n");
diff --git a/src/Structure/SugarBuilder.cpp b/src/Structure/SugarBuilder.cpp
index cc1eb58e1a..739612ea92 100644
--- a/src/Structure/SugarBuilder.cpp
+++ b/src/Structure/SugarBuilder.cpp
@@ -1935,7 +1935,7 @@ int SugarBuilder::PrepareSugars(bool errorsAreFatal,
     {
       //outfile->Printf("%s\n", LeapInterface::LeapBond(bnd->A1(), bnd->A2(), leapunitname, topIn).c_str());
       LeapBonds.push_back( *bnd );
-      topIn.RemoveBond(bnd->A1(), bnd->A2());
+      //topIn.RemoveBond(bnd->A1(), bnd->A2());
     }
     // Remove bonds between sugars
     for (std::set<BondType>::const_iterator bnd = sugarBondsToRemove.begin();
@@ -1943,11 +1943,10 @@ int SugarBuilder::PrepareSugars(bool errorsAreFatal,
     {
       //outfile->Printf("%s\n", LeapInterface::LeapBond(bnd->A1(), bnd->A2(), leapunitname, topIn).c_str());
       LeapBonds.push_back( *bnd );
-      topIn.RemoveBond(bnd->A1(), bnd->A2());
+      //topIn.RemoveBond(bnd->A1(), bnd->A2());
     }
     // Bonds to sugars have been removed, so regenerate molecule info
-    topIn.DetermineMolecules();
-
+    //topIn.DetermineMolecules();
   }
   return 0;
 }

From 86b24e02603f7db71078bbb5bd9b0fc340b93393 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 26 Feb 2024 10:02:21 -0500
Subject: [PATCH 0616/1492] Return max size of a name

---
 src/NameType.h | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/NameType.h b/src/NameType.h
index 35d50d8727..cb8cc9deeb 100644
--- a/src/NameType.h
+++ b/src/NameType.h
@@ -35,6 +35,8 @@ class NameType {
     std::string Formatted(int) const;
     /// \return non-space length of name
     int len() const;
+    /// \return max size of a name
+    static unsigned int max() { return (ArraySize_); }
     /// \return true if name comes before given name alphabetically
     bool operator<(NameType const& rhs) const {
       for (unsigned int i = 0; i != ArraySize_; i++)

From a68655b353a8bbec07ab3ef5b0efc5c3731792ef Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 26 Feb 2024 10:02:38 -0500
Subject: [PATCH 0617/1492] Look for aspect/name, but only if the name is short
 enough

---
 src/Structure/Creator.cpp | 19 ++++++++++++++++---
 1 file changed, 16 insertions(+), 3 deletions(-)

diff --git a/src/Structure/Creator.cpp b/src/Structure/Creator.cpp
index 15d6db1f10..84332392c8 100644
--- a/src/Structure/Creator.cpp
+++ b/src/Structure/Creator.cpp
@@ -106,9 +106,22 @@ const
       mprintf("DEBUG: No aliased terminal residue found for '%s'\n", *rname);
     // Assume Coords set aspect is what we need
     for (Carray::const_iterator it = Templates_.begin(); it != Templates_.end(); ++it) {
-      if ( rname == NameType( (*it)->Meta().Aspect() ) ) {
-        out = *it;
-        break;
+      if ( (*it)->Meta().Aspect().size() < NameType::max() ) {
+        if ( rname == NameType( (*it)->Meta().Aspect() ) ) {
+          out = *it;
+          break;
+        }
+      }
+    }
+  }
+  if (out == 0) {
+    // As a final attempt, just look for the name
+    for (Carray::const_iterator it = Templates_.begin(); it != Templates_.end(); ++it) {
+      if ( (*it)->Meta().Name().size() < NameType::max() ) {
+        if ( rname == NameType( (*it)->Meta().Name() ) ) {
+          out = *it;
+          break;
+        }
       }
     }
   }

From 5c274f31a100ed44cc83805227e1e5a36b1c54fe Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 26 Feb 2024 10:04:06 -0500
Subject: [PATCH 0618/1492] Indices for atoms 3 and 4 are allowed to be
 negative (of course)

---
 src/Parm_Amber.cpp | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/src/Parm_Amber.cpp b/src/Parm_Amber.cpp
index e45315faa3..8f3b207083 100644
--- a/src/Parm_Amber.cpp
+++ b/src/Parm_Amber.cpp
@@ -969,6 +969,9 @@ int Parm_Amber::ReadAngles(Topology& TopIn, FortranData const& FMT) {
 }
 
 // Parm_Amber::GetDihedral()
+/** Indices for atoms 3/4 are allowed to be negative, indicates end/improper
+  * dihedral respectively.
+  */
 DihedralType Parm_Amber::GetDihedral() {
   int a1 = atoi(file_.NextElement());
   int a2 = atoi(file_.NextElement());
@@ -977,8 +980,8 @@ DihedralType Parm_Amber::GetDihedral() {
   int didx = atoi(file_.NextElement());
   if (a1 < 0 || a1 >= ncoords_ ||
       a2 < 0 || a2 >= ncoords_ ||
-      a3 < 0 || a3 >= ncoords_ ||
-      a4 < 0 || a4 >= ncoords_ ||
+                a3 >= ncoords_ ||
+                a4 >= ncoords_ ||
       didx < 0 || didx - 1 >= values_[NPTRA])
   {
     hasBadDihedrals_ = true;

From 822f2aaec23f6dfd8ffc668669ab5897bd55d10f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 27 Feb 2024 10:40:34 -0500
Subject: [PATCH 0619/1492] Turn into a stand-alone class

---
 src/Structure/HisProt.cpp | 43 ++++++++++++++++++++++++++++++++++++++-
 src/Structure/HisProt.h   | 37 +++++++++++++++++++++++++++++----
 2 files changed, 75 insertions(+), 5 deletions(-)

diff --git a/src/Structure/HisProt.cpp b/src/Structure/HisProt.cpp
index 61de9d23a7..d197e76f3a 100644
--- a/src/Structure/HisProt.cpp
+++ b/src/Structure/HisProt.cpp
@@ -1,11 +1,52 @@
 #include "HisProt.h"
 #include "StructureRoutines.h"
+#include "../ArgList.h"
 #include "../CpptrajStdio.h"
 #include "../NameType.h"
 #include "../Topology.h"
 
 using namespace Cpptraj::Structure;
 
+/// Warn if name length greater than NameType max
+static inline void warn_length(std::string const& nameIn) {
+  if (nameIn.size() >= NameType::max())
+    mprintf("Warning: Name '%s' is too large and will be truncated.\n", nameIn.c_str());
+}
+
+/** Initialize from args. Get atom/residue names. */
+int HisProt::InitHisProt(ArgList& argIn, int debugIn) {
+  nd1name_ = argIn.GetStringKey("nd1", "ND1");
+  ne2name_ = argIn.GetStringKey("ne2", "NE2");
+  hisname_ = argIn.GetStringKey("hisname", "HIS");
+  hiename_ = argIn.GetStringKey("hiename", "HIE");
+  hidname_ = argIn.GetStringKey("hidname", "HID");
+  hipname_ = argIn.GetStringKey("hipname", "HIP");
+  warn_length(nd1name_);
+  warn_length(ne2name_);
+  warn_length(hisname_);
+  warn_length(hiename_);
+  warn_length(hidname_);
+  warn_length(hipname_);
+  return 0;
+}
+
+/** Print info to stdout. */
+void HisProt::HisProtInfo() const {
+  mprintf("\tHistidine protonation detection:\n");
+  mprintf("\t\tND1 atom name                   : %s\n", nd1name_.c_str());
+  mprintf("\t\tNE2 atom name                   : %s\n", ne2name_.c_str());
+  mprintf("\t\tHistidine original residue name : %s\n", hisname_.c_str());
+  mprintf("\t\tEpsilon-protonated residue name : %s\n", hiename_.c_str());
+  mprintf("\t\tDelta-protonated residue name   : %s\n", hidname_.c_str());
+  mprintf("\t\tDoubly-protonated residue name  : %s\n", hipname_.c_str());
+}
+
+/** Determine histidine protonation from hydrogens. */
+int HisProt::DetermineHisProt(Topology& topIn) const {
+  return determineHisProt(topIn, nd1name_, ne2name_, hisname_,
+                          hiename_, hiename_, hipname_);
+}
+
 /** Try to determine histidine protonation from existing hydrogens.
   * Change residue names as appropriate.
   * \param topIn Input topology.
@@ -16,7 +57,7 @@ using namespace Cpptraj::Structure;
   * \param HidName Name for delta-protonated His.
   * \param HipName Name for doubly-protonated His.
   */
-int Cpptraj::Structure::DetermineHisProt( Topology& topIn,
+int HisProt::determineHisProt( Topology& topIn,
                                            NameType const& ND1,
                                            NameType const& NE2,
                                            NameType const& HisName,
diff --git a/src/Structure/HisProt.h b/src/Structure/HisProt.h
index f9e9539454..3e6e61fe7f 100644
--- a/src/Structure/HisProt.h
+++ b/src/Structure/HisProt.h
@@ -1,13 +1,42 @@
 #ifndef INC_STRUCTURE_HISPROT_H
 #define INC_STRUCTURE_HISPROT_H
+#include <string>
+class ArgList;
 class Topology;
 class NameType;
 namespace Cpptraj {
 namespace Structure {
-/// Try to determine protonation state of histidines from any hydrogens present.
-int DetermineHisProt(Topology&,
-                     NameType const&, NameType const&,
-                     NameType const&, NameType const&, NameType const&, NameType const&);
+/// For determining Histidine protonation
+class HisProt {
+  public:
+    /// CONSTRUCTOR
+    HisProt();
+    /// Initialize
+    int InitHisProt(ArgList&, int);
+    /// Print info to stdout
+    void HisProtInfo() const;
+    /// \return Epsilon-protonated name
+    std::string const& EpsilonProtHisName() const { return hiename_; }
+    /// \return Delta-protonated name
+    std::string const& DeltaProtHisName() const { return hidname_; }
+    /// \return Doubly-protonated name
+    std::string const& DoubleProtHisName() const { return hipname_; }
+    /// Determine histidine protonation from hydrogen atom placement
+    int DetermineHisProt(Topology&) const;
+  private:
+    /// Try to determine protonation state of histidines from any hydrogens present.
+    static int determineHisProt(Topology&,
+                                NameType const&, NameType const&,
+                                NameType const&, NameType const&,
+                                NameType const&, NameType const&);
+
+    std::string nd1name_; ///< Delta nitrogen atom name
+    std::string ne2name_; ///< Epsilon nitrogen atom name
+    std::string hisname_; ///< Histidine original residue name
+    std::string hiename_; ///< Epsilon-protonated residue name
+    std::string hidname_; ///< Delta-protonated residue name
+    std::string hipname_; ///< Doubly-protonated residue name
+};
 }
 }
 #endif

From 130100d7c63ad4326466acfe131a8bf12e1b79cd Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 27 Feb 2024 10:47:04 -0500
Subject: [PATCH 0620/1492] Use new HisProt class

---
 src/Exec_PrepareForLeap.cpp | 29 ++++++++++-------------------
 src/Structure/HisProt.cpp   |  3 +++
 2 files changed, 13 insertions(+), 19 deletions(-)

diff --git a/src/Exec_PrepareForLeap.cpp b/src/Exec_PrepareForLeap.cpp
index e5a77e6911..5aa5500dc6 100644
--- a/src/Exec_PrepareForLeap.cpp
+++ b/src/Exec_PrepareForLeap.cpp
@@ -878,26 +878,17 @@ Exec::RetType Exec_PrepareForLeap::Execute(CpptrajState& State, ArgList& argIn)
 
   // Do histidine detection before H atoms are removed
   if (!argIn.hasKey("nohisdetect")) {
-    std::string nd1name = argIn.GetStringKey("nd1", "ND1");
-    std::string ne2name = argIn.GetStringKey("ne2", "NE2");
-    std::string hisname = argIn.GetStringKey("hisname", "HIS");
-    std::string hiename = argIn.GetStringKey("hiename", "HIE");
-    std::string hidname = argIn.GetStringKey("hidname", "HID");
-    std::string hipname = argIn.GetStringKey("hipname", "HIP");
-    mprintf("\tHistidine protonation detection:\n");
-    mprintf("\t\tND1 atom name                   : %s\n", nd1name.c_str());
-    mprintf("\t\tNE2 atom name                   : %s\n", ne2name.c_str());
-    mprintf("\t\tHistidine original residue name : %s\n", hisname.c_str());
-    mprintf("\t\tEpsilon-protonated residue name : %s\n", hiename.c_str());
-    mprintf("\t\tDelta-protonated residue name   : %s\n", hidname.c_str());
-    mprintf("\t\tDoubly-protonated residue name  : %s\n", hipname.c_str());
+    Cpptraj::Structure::HisProt hisProt;
+    if (hisProt.InitHisProt( argIn, debug_ )) {
+      mprinterr("Error: Could not initialize histidine detection.\n");
+      return CpptrajState::ERR;
+    }
+    hisProt.HisProtInfo();
     // Add epsilon, delta, and double-protonated names as recognized.
-    pdb_res_names_.insert( hiename );
-    pdb_res_names_.insert( hidname );
-    pdb_res_names_.insert( hipname );
-    if (DetermineHisProt( topIn,
-                          nd1name, ne2name,
-                          hisname, hiename, hidname, hipname)) {
+    pdb_res_names_.insert( hisProt.EpsilonProtHisName() );
+    pdb_res_names_.insert( hisProt.DeltaProtHisName() );
+    pdb_res_names_.insert( hisProt.DoubleProtHisName() );
+    if (hisProt.DetermineHisProt( topIn )) {
       mprinterr("Error: HIS protonation detection failed.\n");
       return CpptrajState::ERR;
     }
diff --git a/src/Structure/HisProt.cpp b/src/Structure/HisProt.cpp
index d197e76f3a..037e817344 100644
--- a/src/Structure/HisProt.cpp
+++ b/src/Structure/HisProt.cpp
@@ -7,6 +7,9 @@
 
 using namespace Cpptraj::Structure;
 
+/** CONSTRUCTOR */
+HisProt::HisProt() {}
+
 /// Warn if name length greater than NameType max
 static inline void warn_length(std::string const& nameIn) {
   if (nameIn.size() >= NameType::max())

From 3df97aac33e89fbfb9535c11cb6bbb06c831a6c0 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 27 Feb 2024 10:51:19 -0500
Subject: [PATCH 0621/1492] Add to build

---
 src/Exec_Build.cpp        | 15 +++++++++++++++
 src/Structure/HisProt.cpp |  5 +++++
 src/Structure/HisProt.h   |  2 ++
 3 files changed, 22 insertions(+)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 8e866860d0..eb9b9901c2 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -5,6 +5,7 @@
 #include "Parm/GB_Params.h"
 #include "Structure/Builder.h"
 #include "Structure/Creator.h"
+#include "Structure/HisProt.h"
 #include "Structure/PdbCleaner.h"
 #include "Structure/ResStatArray.h"
 #include "Structure/SugarBuilder.h"
@@ -680,6 +681,20 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
   std::string solventResName = argIn.GetStringKey("solventresname", "HOH");
   mprintf("\tSolvent residue name: %s\n", solventResName.c_str());
 
+  // Do histidine detection before H atoms are removed
+  if (!argIn.hasKey("nohisdetect")) {
+    Cpptraj::Structure::HisProt hisProt;
+    if (hisProt.InitHisProt( argIn, debug_ )) {
+      mprinterr("Error: Could not initialize histidine detection.\n");
+      return CpptrajState::ERR;
+    }
+    hisProt.HisProtInfo();
+    if (hisProt.DetermineHisProt( topIn )) {
+      mprinterr("Error: HIS protonation detection failed.\n");
+      return CpptrajState::ERR;
+    }
+  }
+
   // Clean up structure
   Cpptraj::Structure::PdbCleaner pdbCleaner;
   pdbCleaner.SetDebug( debug_ );
diff --git a/src/Structure/HisProt.cpp b/src/Structure/HisProt.cpp
index 037e817344..52af8e17b8 100644
--- a/src/Structure/HisProt.cpp
+++ b/src/Structure/HisProt.cpp
@@ -16,6 +16,11 @@ static inline void warn_length(std::string const& nameIn) {
     mprintf("Warning: Name '%s' is too large and will be truncated.\n", nameIn.c_str());
 }
 
+const char* HisProt::keywords_ =
+  "\t[{nohisdetect |\n"
+  "\t  [nd1 <nd1>] [ne2 <ne2] [hisname <his>] [hiename <hie>]\n"
+  "\t  [hidname <hid>] [hipname <hip]}]\n";
+
 /** Initialize from args. Get atom/residue names. */
 int HisProt::InitHisProt(ArgList& argIn, int debugIn) {
   nd1name_ = argIn.GetStringKey("nd1", "ND1");
diff --git a/src/Structure/HisProt.h b/src/Structure/HisProt.h
index 3e6e61fe7f..023790933b 100644
--- a/src/Structure/HisProt.h
+++ b/src/Structure/HisProt.h
@@ -11,6 +11,8 @@ class HisProt {
   public:
     /// CONSTRUCTOR
     HisProt();
+    /// \return keywords recognized by init
+    static const char* keywords_;
     /// Initialize
     int InitHisProt(ArgList&, int);
     /// Print info to stdout

From b4e0329e49f78f307f8152e41a52fd0c1668de36 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 27 Feb 2024 10:53:33 -0500
Subject: [PATCH 0622/1492] Add the keywords into help text

---
 src/Exec_Build.cpp          | 4 +++-
 src/Exec_PrepareForLeap.cpp | 7 +++----
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index eb9b9901c2..f59a95ffad 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -628,10 +628,12 @@ void Exec_Build::Help() const
           "\t[%s]\n"
           "\t[{%s} ...]\n"
           "\t[{%s} ...]\n"
+          "%s"
           "  Build complete topology and parameters from given crdset.\n",
           Cpptraj::Structure::Creator::other_keywords_,
           Cpptraj::Structure::Creator::template_keywords_,
-          Cpptraj::Structure::Creator::parm_keywords_);
+          Cpptraj::Structure::Creator::parm_keywords_,
+          Cpptraj::Structure::HisProt::keywords_);
 }
 
 // Exec_Build::Execute()
diff --git a/src/Exec_PrepareForLeap.cpp b/src/Exec_PrepareForLeap.cpp
index 5aa5500dc6..64d15c7a97 100644
--- a/src/Exec_PrepareForLeap.cpp
+++ b/src/Exec_PrepareForLeap.cpp
@@ -715,9 +715,7 @@ void Exec_PrepareForLeap::Help() const
           "\t[keepaltloc {<alt loc ID>|highestocc}]\n"
           "\t[stripmask <stripmask>] [solventresname <solventresname>]\n"
           "\t[molmask <molmask> ...] [determinemolmask <mask>]\n"
-          "\t[{nohisdetect |\n"
-          "\t  [nd1 <nd1>] [ne2 <ne2] [hisname <his>] [hiename <hie>]\n"
-          "\t  [hidname <hid>] [hipname <hip]}]\n"
+          "%s"
           "\t[{nodisulfides |\n"
           "\t  existingdisulfides |\n"
           "\t  [cysmask <cysmask>] [disulfidecut <cut>] [newcysname <name>]}]\n"
@@ -736,7 +734,8 @@ void Exec_PrepareForLeap::Help() const
           "  input to add the bonds back once the structure has been loaded\n"
           "  into LEaP will be written to <leap input file>.\n"
           "  The command will attempt to download parameters for unknown\n"
-          "  residues unless 'nodlparams' is specified.\n"
+          "  residues unless 'nodlparams' is specified.\n",
+          HisProt::keywords_
          );
 }
 

From 3915b8b6d7e20d3e59626f35f777c8027a3c1f43 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 27 Feb 2024 11:00:19 -0500
Subject: [PATCH 0623/1492] Get rid of old code

---
 src/Exec_Build.cpp | 101 +--------------------------------------------
 1 file changed, 2 insertions(+), 99 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index f59a95ffad..e534f3edec 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -641,18 +641,7 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
 {
   debug_ = State.Debug();
   std::string title = argIn.GetStringKey("title");
-/*  // Atom scan direction
-  std::string atomscandir = argIn.GetStringKey("atomscandir");
-  if (!atomscandir.empty()) {
-    if (atomscandir == "f")
-      Cpptraj::Structure::SetAtomScanDirection(Cpptraj::Structure::SCAN_ATOMS_FORWARDS);
-    else if (atomscandir == "b")
-      Cpptraj::Structure::SetAtomScanDirection(Cpptraj::Structure::SCAN_ATOMS_BACKWARDS);
-    else {
-      mprinterr("Error: Unrecognized keyword for 'atomscandir' : %s\n", atomscandir.c_str());
-      return CpptrajState::ERR;
-    }
-  }*/
+
   // Get input coords
   std::string crdset = argIn.GetStringKey("crdset");
   if (crdset.empty()) {
@@ -714,7 +703,7 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
     return CpptrajState::ERR;
   }
 
-  // Output coords
+  // Set up Output coords
   std::string outset = argIn.GetStringKey("name");
   if (outset.empty()) {
     mprinterr("Error: Must specify output COORDS set with 'name'\n");
@@ -740,44 +729,6 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
   }
   mprintf("\tGB radii set: %s\n", Cpptraj::Parm::GbTypeStr(gbradii).c_str());
 
-/*  Carray Templates;
-  std::string lib = argIn.GetStringKey("lib");
-  if (lib.empty()) {
-    mprintf("\tNo template(s) specified with 'lib'; using any loaded templates.\n");
-    DataSetList sets = State.DSL().SelectGroupSets( "*", DataSet::COORDINATES ); // TODO specific set type for units?
-    for (DataSetList::const_iterator it = sets.begin(); it != sets.end(); ++it)
-    {
-      // Should only be a single residue FIXME need new set type
-      DataSet_Coords const& ds = static_cast<DataSet_Coords const&>( *(*it) );
-      if ( ds.Top().Nres() == 1 )
-        Templates.push_back( (DataSet_Coords*)(*it) );
-    }
-  } else {
-    while (!lib.empty()) {
-      DataSetList sets = State.DSL().SelectGroupSets( lib, DataSet::COORDINATES ); // TODO specific set type for units?
-      if (sets.empty()) {
-        mprintf("Warning: No sets corresponding to '%s'\n", lib.c_str());
-      } else {
-        for (DataSetList::const_iterator it = sets.begin(); it != sets.end(); ++it)
-        {
-          // Should only be a single residue FIXME need new set type
-          DataSet_Coords const& ds = static_cast<DataSet_Coords const&>( *(*it) );
-          if ( ds.Top().Nres() == 1 )
-            Templates.push_back( (DataSet_Coords*)(*it) );
-        }
-      }
-      lib = argIn.GetStringKey("lib");
-    }
-  }
-  if (Templates.empty())
-    mprintf("Warning: No residue templates loaded.\n");
-  else {
-    mprintf("\t%zu residue templates found:", Templates.size());
-    for (std::vector<DataSet_Coords*>::const_iterator it = Templates.begin(); it != Templates.end(); ++it)
-      mprintf(" %s", (*it)->legend());
-    mprintf("\n");
-  }*/
-
   // Get templates and parameter sets.
   Cpptraj::Structure::Creator creator;
   if (creator.InitCreator(argIn, State.DSL(), debug_)) {
@@ -790,51 +741,6 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
     mprinterr("Error: No parameter sets.\n");
     return CpptrajState::ERR;
   }
-/*
-  typedef std::vector<DataSet_Parameters*> Parray;
-  Parray ParamSets;
-  std::string parmset = argIn.GetStringKey("parmset");
-  if (parmset.empty()) {
-    mprintf("\tNo parameter set(s) specified with 'parmset'; using any loaded sets.\n");
-    // See if there are any parameter sets.
-    DataSetList sets = State.DSL().GetSetsOfType( "*", DataSet::PARAMETERS );
-    for (DataSetList::const_iterator it = sets.begin(); it != sets.end(); ++it)
-      ParamSets.push_back( (DataSet_Parameters*)(*it) );
-  } else {
-    while (!parmset.empty()) {
-      DataSetList sets = State.DSL().GetSetsOfType( parmset, DataSet::PARAMETERS );
-      if (sets.empty()) {
-        mprintf("Warning: No parameter sets corresponding to '%s'\n", parmset.c_str());
-      } else {
-        for (DataSetList::const_iterator it = sets.begin(); it != sets.end(); ++it)
-          ParamSets.push_back( (DataSet_Parameters*)(*it) );
-      }
-      parmset = argIn.GetStringKey("parmset");
-    }
-  }
-  if (ParamSets.empty()) {
-    mprinterr("Error: No parameter sets.\n");
-    return CpptrajState::ERR;
-  }
-  mprintf("\tParameter sets:\n");
-  for (Parray::const_iterator it = ParamSets.begin(); it != ParamSets.end(); ++it)
-    mprintf("\t  %s\n", (*it)->legend());
-
-  // Combine parameters if needed
-  DataSet_Parameters* mainParmSet = 0;
-  bool free_parmset_mem = false;
-  if (ParamSets.size() == 1)
-    mainParmSet = ParamSets.front();
-  else {
-    free_parmset_mem = true;
-    mprintf("\tCombining parameter sets.\n");
-    Parray::const_iterator it = ParamSets.begin();
-    mainParmSet = new DataSet_Parameters( *(*it) );
-    ++it;
-    ParameterSet::UpdateCount UC;
-    for (; it != ParamSets.end(); ++it)
-      mainParmSet->UpdateParamSet( *(*it), UC, State.Debug(), State.Debug() ); // FIXME verbose
-  }*/
 
   // Load PDB to glycam residue name map
   bool prepare_sugars = !argIn.hasKey("nosugars");
@@ -898,7 +804,6 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
     return CpptrajState::ERR;
   }
 
-
   // Assign parameters. This will create the bond/angle/dihedral/improper
   // arrays as well.
   Exec::RetType ret = CpptrajState::OK;
@@ -916,8 +821,6 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
   topOut.AllocJoinArray();
   topOut.AllocRotateArray();
 
-  //if (free_parmset_mem && mainParmSet != 0) delete mainParmSet;
-
   // Update coords 
   if (crdout.CoordsSetup( topOut, CoordinateInfo() )) { // FIXME better coordinate info
     mprinterr("Error: Could not set up output COORDS.\n");

From a432ddf5752ef5e15e6ff3f8689dc418e3b7d0c3 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 27 Feb 2024 14:15:18 -0500
Subject: [PATCH 0624/1492] Remove old code

---
 src/Exec_Build.cpp          |   3 +-
 src/Exec_PrepareForLeap.cpp | 257 +-----------------------------------
 src/Exec_PrepareForLeap.h   |   6 -
 3 files changed, 3 insertions(+), 263 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index e534f3edec..b9366e54cb 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -742,7 +742,8 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
     return CpptrajState::ERR;
   }
 
-  // Load PDB to glycam residue name map
+  // Handle sugars.
+  // TODO should be on a residue by residue basis in FillAtomsWithTemplates
   bool prepare_sugars = !argIn.hasKey("nosugars");
   if (!prepare_sugars)
     mprintf("\tNot attempting to prepare sugars.\n");
diff --git a/src/Exec_PrepareForLeap.cpp b/src/Exec_PrepareForLeap.cpp
index 64d15c7a97..72f747a011 100644
--- a/src/Exec_PrepareForLeap.cpp
+++ b/src/Exec_PrepareForLeap.cpp
@@ -276,190 +276,6 @@ const
 
 // -----------------------------------------------------------------------------
 
-/** Modify coords according to user wishes. */
-/*int Exec_PrepareForLeap::ModifyCoords( Topology& topIn, Frame& frameIn,
-                                       bool remove_water,
-                                       std::string const& altLocStr, std::string const& stripMask,
-                                       std::string const& waterMask,
-                                       Iarray const& resnumsToRemove )
-const
-{
-  // Create a mask denoting which atoms will be kept.
-  std::vector<bool> atomsToKeep( topIn.Natom(), true );
-  // Previously-determined array of residues to remove
-  for (Iarray::const_iterator rnum = resnumsToRemove.begin();
-                              rnum != resnumsToRemove.end(); ++rnum)
-  {
-    Residue const& res = topIn.Res( *rnum );
-    mprintf("\tRemoving %s\n", topIn.TruncResNameOnumId( *rnum ).c_str());
-    for (int at = res.FirstAtom(); at != res.LastAtom(); at++)
-      atomsToKeep[at] = false;
-  }
-  // User-specified strip mask
-  if (!stripMask.empty()) {
-    AtomMask mask;
-    if (mask.SetMaskString( stripMask )) {
-      mprinterr("Error: Invalid mask string '%s'\n", stripMask.c_str());
-      return 1;
-    }
-    if (topIn.SetupIntegerMask( mask )) return 1;
-    mask.MaskInfo();
-    if (!mask.None()) {
-      for (AtomMask::const_iterator atm = mask.begin(); atm != mask.end(); ++atm)
-        atomsToKeep[*atm] = false;
-    }
-  }
-  if (remove_water) {
-    // Do not use cpptraj definition of solvent in case we have e.g. bound HOH
-    AtomMask mask;
-    if (mask.SetMaskString( waterMask )) {
-      mprinterr("Error: Invalid solvent mask string '%s'\n", waterMask.c_str());
-      return 1;
-    }
-    if (topIn.SetupIntegerMask( mask )) return 1;
-    mask.MaskInfo();
-    if (!mask.None()) {
-      for (AtomMask::const_iterator atm = mask.begin(); atm != mask.end(); ++atm)
-        atomsToKeep[*atm] = false;
-    }
-
-  }
-  // Identify alternate atom location groups.
-  if (!altLocStr.empty()) {
-    if (topIn.AtomAltLoc().empty()) {
-      mprintf("\tNo alternate atom locations.\n");
-    } else {
-      // Map atom name to atom indices
-      typedef std::map<NameType, std::vector<int>> AlocMapType;
-      AlocMapType alocMap;
-      for (int rnum = 0; rnum != topIn.Nres(); rnum++) {
-        alocMap.clear();
-        for (int at = topIn.Res(rnum).FirstAtom(); at != topIn.Res(rnum).LastAtom(); at++) {
-          if (topIn.AtomAltLoc()[at] != ' ') {
-            AlocMapType::iterator it = alocMap.find( topIn[at].Name() );
-            if (it == alocMap.end()) {
-              alocMap.insert( std::pair<NameType, std::vector<int>>( topIn[at].Name(),
-                                                                     std::vector<int>(1, at) ));
-            } else {
-              it->second.push_back( at );
-            }
-          }
-        } // END loop over atoms in residue
-        if (!alocMap.empty()) {
-          if (debug_ > 0)
-            mprintf("DEBUG: Alternate loc. for %s\n", topIn.TruncResNameOnumId(rnum).c_str());
-          // Loop over atoms with alternate locations
-          for (AlocMapType::const_iterator it = alocMap.begin(); it != alocMap.end(); ++it) {
-            if (debug_ > 0) {
-              // Print all alternate atoms
-              mprintf("\t'%s'", *(it->first));
-              for (std::vector<int>::const_iterator at = it->second.begin();
-                                                    at != it->second.end(); ++at)
-                mprintf(" %s[%c]", *(topIn[*at].Name()), topIn.AtomAltLoc()[*at]);
-              mprintf("\n");
-            }
-            // For each, choose which location to keep.
-            if (altLocStr.size() == 1) {
-              // Keep only specified character
-              char altLocChar = altLocStr[0];
-              for (std::vector<int>::const_iterator at = it->second.begin();
-                                                    at != it->second.end(); ++at)
-                if (topIn.AtomAltLoc()[*at] != altLocChar)
-                  atomsToKeep[*at] = false;
-            } else {
-              // Keep highest occupancy
-              if (topIn.Occupancy().empty()) {
-                mprintf("\tNo occupancy.\n"); // TODO error?
-              } else {
-                int highestOccAt = -1;
-                float highestOcc = 0;
-                for (std::vector<int>::const_iterator at = it->second.begin();
-                                                      at != it->second.end(); ++at)
-                {
-                  if (highestOccAt == -1) {
-                    highestOccAt = *at;
-                    highestOcc = topIn.Occupancy()[*at];
-                  } else if (topIn.Occupancy()[*at] > highestOcc) {
-                    highestOccAt = *at;
-                    highestOcc = topIn.Occupancy()[*at];
-                  }
-                }
-                // Set everything beside highest occ to false
-                for (std::vector<int>::const_iterator at = it->second.begin();
-                                                      at != it->second.end(); ++at)
-                  if (*at != highestOccAt)
-                    atomsToKeep[*at] = false;
-              }
-            }
-          } // END loop over atoms with alternate locations
-        }
-      } // END loop over residue numbers
-    }
-  }
-
-  // Set up mask of only kept atoms.
-  AtomMask keptAtoms;
-  keptAtoms.SetNatoms( topIn.Natom() );
-  for (int idx = 0; idx != topIn.Natom(); idx++) {
-    if (atomsToKeep[idx])
-      keptAtoms.AddSelectedAtom(idx);
-  }
-  if (keptAtoms.Nselected() == topIn.Natom())
-    // Keeping everything, no modifications
-    return 0;
-  // Modify top/frame
-  Topology* newTop = topIn.modifyStateByMask( keptAtoms );
-  if (newTop == 0) {
-    mprinterr("Error: Could not create new topology.\n");
-    return 1;
-  }
-  newTop->Brief("After removing atoms:");
-  Frame newFrame;
-  newFrame.SetupFrameV(newTop->Atoms(), frameIn.CoordsInfo());
-  newFrame.SetFrame(frameIn, keptAtoms);
-
-  topIn = *newTop;
-  frameIn = newFrame;
-  delete newTop;
-
-  return 0;
-}*/
-
-/** Remove any hydrogen atoms. This is done separately from ModifyCoords
-  * so that hydrogen atom info can be used to e.g. ID histidine
-  * protonation.
-  */
-/*int Exec_PrepareForLeap::RemoveHydrogens(Topology& topIn, Frame& frameIn) const {
-  AtomMask keptAtoms;
-  keptAtoms.SetNatoms( topIn.Natom() );
-  for (int idx = 0; idx != topIn.Natom(); idx++)
-  {
-    if (topIn[idx].Element() != Atom::HYDROGEN)
-      keptAtoms.AddSelectedAtom(idx);
-  }
-  if (keptAtoms.Nselected() == topIn.Natom())
-    // Keeping everything, no modification
-    return 0;
-  // Modify top/frame
-  Topology* newTop = topIn.modifyStateByMask( keptAtoms );
-  if (newTop == 0) {
-    mprinterr("Error: Could not create new topology with no hydrogens.\n");
-    return 1;
-  }
-  newTop->Brief("After removing hydrogen atoms:");
-  Frame newFrame;
-  newFrame.SetupFrameV(newTop->Atoms(), frameIn.CoordsInfo());
-  newFrame.SetFrame(frameIn, keptAtoms);
-
-  topIn = *newTop;
-  frameIn = newFrame;
-  delete newTop;
-
-  return 0;
-}*/
-
-// -----------------------------------------------------------------------------
-
 /// \return index of oxygen atom bonded to this atom but not in same residue
 static inline int getLinkOxygenIdx(Topology const& leaptop, int at, int rnum) {
   int o_idx = -1;
@@ -776,7 +592,6 @@ Exec::RetType Exec_PrepareForLeap::Execute(CpptrajState& State, ArgList& argIn)
   Frame frameIn = coords.AllocateFrame();
   coords.GetFrame(tgtframe, frameIn);
 
-
   // Copy input topology, may be modified.
   Topology topIn = coords.Top();
 
@@ -909,6 +724,7 @@ Exec::RetType Exec_PrepareForLeap::Execute(CpptrajState& State, ArgList& argIn)
     }
   }
 
+  // Deal with any coordinate modifications
   Cpptraj::Structure::PdbCleaner pdbCleaner;
   pdbCleaner.SetDebug( debug_ );
   if (pdbCleaner.InitPdbCleaner( argIn, solventResName_, pdbResToRemove )) {
@@ -925,77 +741,6 @@ Exec::RetType Exec_PrepareForLeap::Execute(CpptrajState& State, ArgList& argIn)
     return CpptrajState::ERR;
   }
 
-  // Deal with any coordinate modifications
-/*  bool remove_water     = argIn.hasKey("nowat");
-  std::string waterMask = argIn.GetStringKey("watermask", ":" + solventResName_);
-  bool remove_h         = argIn.hasKey("noh");
-  std::string altLocArg = argIn.GetStringKey("keepaltloc");
-  if (!altLocArg.empty()) {
-    if (altLocArg != "highestocc" &&
-        altLocArg.size() > 1)
-    {
-      mprinterr("Error: Invalid keyword for 'keepaltloc' '%s'; must be 'highestocc' or 1 character.\n",
-                altLocArg.c_str());
-      return CpptrajState::ERR;
-    }
-  }
-  std::string stripMask = argIn.GetStringKey("stripmask");
-
-  // If keeping highest alt loc, check that alt locs and occupancies are present.
-  if (altLocArg == "highestocc") {
-    if (topIn.AtomAltLoc().empty()) {
-      mprintf("Warning: 'highestocc' specified but no atom alternate location info.\n");
-      altLocArg.clear();
-    } else if (topIn.Occupancy().empty()) {
-      mprintf("Warning: 'highestocc' specified but no atom occupancy info.\n");
-      altLocArg.clear();
-    }
-  }
-  // Check if alternate atom location IDs are present 
-  if (!topIn.AtomAltLoc().empty()) {
-    // For LEaP, must have only 1 atom alternate location
-    char firstAltLoc = ' ';
-    for (std::vector<char>::const_iterator altLocId = topIn.AtomAltLoc().begin();
-                                           altLocId != topIn.AtomAltLoc().end();
-                                         ++altLocId)
-    {
-      if (firstAltLoc == ' ') {
-        // Find first non-blank alternate location ID
-        if (*altLocId != ' ')
-          firstAltLoc = *altLocId;
-      } else if (*altLocId != ' ' && *altLocId != firstAltLoc) {
-        // Choose a default if necessary
-        if (altLocArg.empty()) {
-          altLocArg.assign(1, firstAltLoc);
-          mprintf("Warning: '%s' has atoms with multiple alternate location IDs, which\n"
-                  "Warning:  are not supported by LEaP. Keeping only '%s'.\n"
-                  "Warning: To choose a specific location to keep use the 'keepaltloc <char>'\n"
-                  "Warning:  keyword.\n", coords.legend(), altLocArg.c_str());
-         }
-         break;
-      }
-    }
-  }
-
-  if (remove_water)
-    mprintf("\tRemoving solvent. Solvent mask= '%s'\n", waterMask.c_str());
-  if (remove_h)
-    mprintf("\tRemoving hydrogens.\n");
-  if (!altLocArg.empty())
-    mprintf("\tIf present, keeping only alternate atom locations denoted by '%s'\n", altLocArg.c_str());
-  if (!stripMask.empty())
-    mprintf("\tRemoving atoms in mask '%s'\n", stripMask.c_str());
-  if (ModifyCoords(topIn, frameIn, remove_water, altLocArg, stripMask, waterMask, pdbResToRemove))
-  {
-    mprinterr("Error: Modification of '%s' failed.\n", coords.legend());
-    return CpptrajState::ERR;
-  }
-
-  // Remove hydrogens
-  if (remove_h) {
-    if (RemoveHydrogens(topIn, frameIn)) return CpptrajState::ERR;
-  }
-*/
   // If preparing sugars, need to set up an atom map and potentially
   // search for terminal sugars/missing bonds. Do this here after all atom
   // modifications have been done.
diff --git a/src/Exec_PrepareForLeap.h b/src/Exec_PrepareForLeap.h
index 044992a5c4..bb3a43509c 100644
--- a/src/Exec_PrepareForLeap.h
+++ b/src/Exec_PrepareForLeap.h
@@ -36,12 +36,6 @@ class Exec_PrepareForLeap : public Exec {
     /// Try to determine where TER cards should be placed based on bonds
     int FindTerByBonds(Topology&, CharMask const&) const;
 
-    /// Remove specified atoms
-    //int ModifyCoords(Topology&, Frame&, bool, std::string const&, std::string const&,
-    //                 std::string const&, Iarray const&) const;
-    /// Remove hydrogen atoms
-    //int RemoveHydrogens(Topology&, Frame&) const;
-
     /// Run leap to generate topology, perform any modifications
     int RunLeap(std::string const&, std::string const&) const;
     /// Print a warning for residues that will need modification after leap

From da9c05baa6517164d16f5e5fd4b857f3ce891311 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 27 Feb 2024 14:28:06 -0500
Subject: [PATCH 0625/1492] Change to class

---
 src/Structure/Disulfide.cpp   | 34 +++++++++++++++++++++++++++++++++-
 src/Structure/Disulfide.h     | 23 +++++++++++++++++++++--
 src/Structure/structuredepend |  6 +++---
 src/cpptrajdepend             |  6 +++---
 4 files changed, 60 insertions(+), 9 deletions(-)

diff --git a/src/Structure/Disulfide.cpp b/src/Structure/Disulfide.cpp
index 4b42a3b746..1f5c4f6055 100644
--- a/src/Structure/Disulfide.cpp
+++ b/src/Structure/Disulfide.cpp
@@ -1,6 +1,7 @@
 #include "Disulfide.h"
 #include "ResStatArray.h"
 #include "StructureRoutines.h"
+#include "../ArgList.h"
 #include "../CpptrajStdio.h"
 #include "../DistRoutines.h"
 #include "../Frame.h"
@@ -9,8 +10,39 @@
 
 using namespace Cpptraj::Structure;
 
+/** CONSTRUCTOR */
+Disulfide::Disulfide() :
+  disulfidecut_(2.5),
+  searchForNewDisulfides_(true)
+{}
+
+/** Init with args */
+int Disulfide::InitDisulfide(ArgList& argIn, int debugIn)
+{
+  disulfidecut_ = argIn.getKeyDouble("disulfidecut", 2.5);
+  newcysnamestr_ = argIn.GetStringKey("newcysname", "CYX");
+  cysmaskstr_ = argIn.GetStringKey("cysmask", ":CYS@SG");
+  searchForNewDisulfides_ = !argIn.hasKey("existingdisulfides");
+  return 0;
+}
+
+/** Print info to stdout. */
+//void Disulfide::DisulfideInfo() const {
+
+
+/** Search for disulfide bonds. */
+int Disulfide::SearchForDisulfides(ResStatArray& resStat, Topology& topIn,
+                                   Frame const& frameIn,
+                                   std::vector<BondType>& LeapBonds)
+const
+{
+  return searchForDisulfides(resStat, disulfidecut_, newcysnamestr_,
+                             cysmaskstr_, searchForNewDisulfides_,
+                             topIn, frameIn, LeapBonds);
+}
+
 /** Search for disulfide bonds. */
-int Cpptraj::Structure::SearchForDisulfides(ResStatArray& resStat,
+int Disulfide::searchForDisulfides(ResStatArray& resStat,
                                              double disulfidecut,
                                              std::string const& newcysnamestr,
                                              std::string const& cysmaskstr,
diff --git a/src/Structure/Disulfide.h b/src/Structure/Disulfide.h
index c89bea4ec4..61bc7c9c9e 100644
--- a/src/Structure/Disulfide.h
+++ b/src/Structure/Disulfide.h
@@ -2,6 +2,7 @@
 #define INC_STRUCTURE_DISULFIDE_H
 #include <string>
 #include <vector>
+class ArgList;
 class BondType;
 class CpptrajFile;
 class Frame;
@@ -9,10 +10,28 @@ class Topology;
 namespace Cpptraj {
 namespace Structure {
 class ResStatArray;
-/// Search for disulfide bonds
-int SearchForDisulfides(ResStatArray&,
+/// Used to search for disulfide bonds and rename residues appropriately
+class Disulfide {
+  public:
+    /// Constructor
+    Disulfide();
+    /// Init from args
+    int InitDisulfide(ArgList&, int);
+    /// Print info to stdout
+    //void DisulfideInfo() const;
+    /// Search for disulfide bonds
+    int SearchForDisulfides(ResStatArray&, Topology&, Frame const&, std::vector<BondType>&) const;
+  private:
+    /// Search for disulfide bonds
+    static int searchForDisulfides(ResStatArray&,
                         double, std::string const&, std::string const&, bool,
                         Topology&, Frame const&, std::vector<BondType>&);
+
+    double disulfidecut_; ///< Distance cutoff for disulfide bonds in Ang.
+    std::string newcysnamestr_; ///< Name of cysteine residues involved in disulfide bonds
+    std::string cysmaskstr_;    ///< Cysteine mask string
+    bool searchForNewDisulfides_; ///< If true, look for new disulfides in addition to existing bonds
+};
 }
 }
 #endif
diff --git a/src/Structure/structuredepend b/src/Structure/structuredepend
index 70320f83f0..bb1bca6bd3 100644
--- a/src/Structure/structuredepend
+++ b/src/Structure/structuredepend
@@ -1,12 +1,12 @@
 BuildAtom.o : BuildAtom.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h StructureEnum.h
 Builder.o : Builder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Builder.h Chirality.h GenerateConnectivityArrays.h InternalCoords.h Zmatrix.h
 Chirality.o : Chirality.cpp ../Atom.h ../Constants.h ../CpptrajStdio.h ../NameType.h ../SymbolExporting.h ../Vec3.h Chirality.h
-Creator.o : Creator.cpp ../ArgList.h ../AssociatedData.h ../AssociatedData_ResId.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../DataSet_Parameters.h ../Dimension.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/StructureEnum.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Creator.h GenerateConnectivityArrays.h StructureEnum.h
-Disulfide.o : Disulfide.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Disulfide.h ResStatArray.h StructureRoutines.h
+Creator.o : Creator.cpp ../ArgList.h ../AssociatedData.h ../AssociatedData_ResId.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../DataSet_NameMap.h ../DataSet_Parameters.h ../Dimension.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/StructureEnum.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Creator.h GenerateConnectivityArrays.h StructureEnum.h
+Disulfide.o : Disulfide.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Disulfide.h ResStatArray.h StructureRoutines.h
 FunctionalGroup.o : FunctionalGroup.cpp ../Atom.h ../AtomMap.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h FunctionalGroup.h
 FxnGroupBuilder.o : FxnGroupBuilder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h FunctionalGroup.h FxnGroupBuilder.h StructureRoutines.h Sugar.h SugarToken.h
 GenerateConnectivityArrays.o : GenerateConnectivityArrays.cpp ../Atom.h ../Constants.h ../CpptrajStdio.h ../NameType.h ../ParameterTypes.h ../Residue.h ../SymbolExporting.h GenerateConnectivityArrays.h
-HisProt.o : HisProt.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h HisProt.h StructureRoutines.h
+HisProt.o : HisProt.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h HisProt.h StructureRoutines.h
 InternalCoords.o : InternalCoords.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h InternalCoords.h
 PdbCleaner.o : PdbCleaner.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h PdbCleaner.h
 StructureEnum.o : StructureEnum.cpp StructureEnum.h
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 07798c22af..a5ed7d0997 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -291,7 +291,7 @@ Ewald_Regular.o : Ewald_Regular.cpp Atom.h AtomMask.h Box.h Constants.h Coordina
 ExclusionArray.o : ExclusionArray.cpp Atom.h AtomMask.h CharMask.h CpptrajStdio.h ExclusionArray.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Unit.h
 Exec_AddMissingRes.o : Exec_AddMissingRes.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CharMask.h CompactFrameArray.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_AddMissingRes.h Exec_AddMissingRes_Pres.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Analyze.o : Exec_Analyze.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Analyze.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Build.o : Exec_Build.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/GB_Params.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/Creator.h Structure/PdbCleaner.h Structure/StructureEnum.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Build.o : Exec_Build.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/GB_Params.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/Creator.h Structure/HisProt.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/StructureEnum.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Calc.o : Exec_Calc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Calc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_CatCrd.o : Exec_CatCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CatCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Change.o : Exec_Change.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Change.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
@@ -450,11 +450,11 @@ Structure/BuildAtom.o : Structure/BuildAtom.cpp Atom.h AtomMask.h AtomType.h Box
 Structure/Builder.o : Structure/Builder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h GuessAtomHybridization.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Builder.h Structure/Chirality.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 Structure/Chirality.o : Structure/Chirality.cpp Atom.h Constants.h CpptrajStdio.h NameType.h Structure/Chirality.h SymbolExporting.h Vec3.h
 Structure/Creator.o : Structure/Creator.cpp ArgList.h AssociatedData.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/Creator.h Structure/GenerateConnectivityArrays.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Structure/Disulfide.o : Structure/Disulfide.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Disulfide.h Structure/ResStatArray.h Structure/StructureRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Structure/Disulfide.o : Structure/Disulfide.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Disulfide.h Structure/ResStatArray.h Structure/StructureRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/FunctionalGroup.o : Structure/FunctionalGroup.cpp Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/FxnGroupBuilder.o : Structure/FxnGroupBuilder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h Structure/FxnGroupBuilder.h Structure/StructureRoutines.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/GenerateConnectivityArrays.o : Structure/GenerateConnectivityArrays.cpp Atom.h Constants.h CpptrajStdio.h NameType.h ParameterTypes.h Residue.h Structure/GenerateConnectivityArrays.h SymbolExporting.h
-Structure/HisProt.o : Structure/HisProt.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/HisProt.h Structure/StructureRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Structure/HisProt.o : Structure/HisProt.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/HisProt.h Structure/StructureRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/InternalCoords.o : Structure/InternalCoords.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/InternalCoords.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/PdbCleaner.o : Structure/PdbCleaner.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/PdbCleaner.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/StructureEnum.o : Structure/StructureEnum.cpp Structure/StructureEnum.h

From 479e88d25c1190c378950925f300c87a7bc3b0c5 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 27 Feb 2024 14:33:18 -0500
Subject: [PATCH 0626/1492] Use Disulfide class

---
 src/Exec_PrepareForLeap.cpp | 19 +++++++++----------
 src/Structure/Disulfide.cpp |  6 ++++++
 src/Structure/Disulfide.h   |  2 ++
 3 files changed, 17 insertions(+), 10 deletions(-)

diff --git a/src/Exec_PrepareForLeap.cpp b/src/Exec_PrepareForLeap.cpp
index 72f747a011..c7fe52224e 100644
--- a/src/Exec_PrepareForLeap.cpp
+++ b/src/Exec_PrepareForLeap.cpp
@@ -532,9 +532,7 @@ void Exec_PrepareForLeap::Help() const
           "\t[stripmask <stripmask>] [solventresname <solventresname>]\n"
           "\t[molmask <molmask> ...] [determinemolmask <mask>]\n"
           "%s"
-          "\t[{nodisulfides |\n"
-          "\t  existingdisulfides |\n"
-          "\t  [cysmask <cysmask>] [disulfidecut <cut>] [newcysname <name>]}]\n"
+          "%s"
           "\t[{nosugars |\n"
           "\t  sugarmask <sugarmask> [noc1search] [nosplitres]\n"
           "\t  [resmapfile <file>]\n"
@@ -551,7 +549,8 @@ void Exec_PrepareForLeap::Help() const
           "  into LEaP will be written to <leap input file>.\n"
           "  The command will attempt to download parameters for unknown\n"
           "  residues unless 'nodlparams' is specified.\n",
-          HisProt::keywords_
+          HisProt::keywords_,
+          Disulfide::keywords_
          );
 }
 
@@ -832,12 +831,12 @@ Exec::RetType Exec_PrepareForLeap::Execute(CpptrajState& State, ArgList& argIn)
 
   // Disulfide search
   if (!argIn.hasKey("nodisulfides")) {
-    if (SearchForDisulfides( resStat,
-                             argIn.getKeyDouble("disulfidecut", 2.5),
-                             argIn.GetStringKey("newcysname", "CYX"),
-                             argIn.GetStringKey("cysmask", ":CYS@SG"),
-                            !argIn.hasKey("existingdisulfides"),
-                             topIn, frameIn, LeapBonds ))
+    Cpptraj::Structure::Disulfide disulfide;
+    if (disulfide.InitDisulfide( argIn, debug_ )) {
+      mprinterr("Error: Could not init disulfide search.\n");
+      return CpptrajState::ERR;
+    }
+    if (disulfide.SearchForDisulfides( resStat, topIn, frameIn, LeapBonds ))
     {
       mprinterr("Error: Disulfide search failed.\n");
       return CpptrajState::ERR;
diff --git a/src/Structure/Disulfide.cpp b/src/Structure/Disulfide.cpp
index 1f5c4f6055..8ee8c94286 100644
--- a/src/Structure/Disulfide.cpp
+++ b/src/Structure/Disulfide.cpp
@@ -16,6 +16,12 @@ Disulfide::Disulfide() :
   searchForNewDisulfides_(true)
 {}
 
+/** Keywords recognized by InitDisulfide */
+const char* Disulfide::keywords_ =
+  "\t[{nodisulfides |\n"
+  "\t  existingdisulfides |\n"
+  "\t  [cysmask <cysmask>] [disulfidecut <cut>] [newcysname <name>]}]\n";
+
 /** Init with args */
 int Disulfide::InitDisulfide(ArgList& argIn, int debugIn)
 {
diff --git a/src/Structure/Disulfide.h b/src/Structure/Disulfide.h
index 61bc7c9c9e..bbf7971ee3 100644
--- a/src/Structure/Disulfide.h
+++ b/src/Structure/Disulfide.h
@@ -15,6 +15,8 @@ class Disulfide {
   public:
     /// Constructor
     Disulfide();
+    /// Keywords recognized by InitDisulfide
+    static const char* keywords_;
     /// Init from args
     int InitDisulfide(ArgList&, int);
     /// Print info to stdout

From fd84ba10e3f09201dc7204998954799ea9fea05a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 27 Feb 2024 14:40:14 -0500
Subject: [PATCH 0627/1492] Add option to add newly detected disulfide bonds

---
 src/Structure/Disulfide.cpp | 13 +++++++++----
 src/Structure/Disulfide.h   |  7 +++++--
 2 files changed, 14 insertions(+), 6 deletions(-)

diff --git a/src/Structure/Disulfide.cpp b/src/Structure/Disulfide.cpp
index 8ee8c94286..7268dc9481 100644
--- a/src/Structure/Disulfide.cpp
+++ b/src/Structure/Disulfide.cpp
@@ -13,7 +13,8 @@ using namespace Cpptraj::Structure;
 /** CONSTRUCTOR */
 Disulfide::Disulfide() :
   disulfidecut_(2.5),
-  searchForNewDisulfides_(true)
+  searchForNewDisulfides_(true),
+  addNewBonds_(NO_ADD_BONDS)
 {}
 
 /** Keywords recognized by InitDisulfide */
@@ -23,8 +24,9 @@ const char* Disulfide::keywords_ =
   "\t  [cysmask <cysmask>] [disulfidecut <cut>] [newcysname <name>]}]\n";
 
 /** Init with args */
-int Disulfide::InitDisulfide(ArgList& argIn, int debugIn)
+int Disulfide::InitDisulfide(ArgList& argIn, AddType addTypeIn, int debugIn)
 {
+  addNewBonds_ = addTypeIn;
   disulfidecut_ = argIn.getKeyDouble("disulfidecut", 2.5);
   newcysnamestr_ = argIn.GetStringKey("newcysname", "CYX");
   cysmaskstr_ = argIn.GetStringKey("cysmask", ":CYS@SG");
@@ -44,7 +46,7 @@ const
 {
   return searchForDisulfides(resStat, disulfidecut_, newcysnamestr_,
                              cysmaskstr_, searchForNewDisulfides_,
-                             topIn, frameIn, LeapBonds);
+                             topIn, frameIn, LeapBonds, addNewBonds_);
 }
 
 /** Search for disulfide bonds. */
@@ -54,7 +56,8 @@ int Disulfide::searchForDisulfides(ResStatArray& resStat,
                                              std::string const& cysmaskstr,
                                              bool searchForNewDisulfides,
                                              Topology& topIn, Frame const& frameIn,
-                                             std::vector<BondType>& LeapBonds)
+                                             std::vector<BondType>& LeapBonds,
+                                             AddType addNewBonds)
 {
   // Disulfide search
   typedef std::vector<int> Iarray;
@@ -175,6 +178,8 @@ int Disulfide::searchForDisulfides(ResStatArray& resStat,
                     topIn.ResNameNumAtomNameNum(at2).c_str(), sqrt(it->first));
             disulfidePartner[it->second.first ] = it->second.second;
             disulfidePartner[it->second.second] = it->second.first;
+            if (addNewBonds == ADD_BONDS)
+              topIn.AddBond( at1, at2 );
           }
         } // END loop over sorted distances
       } // END s_idxs not empty()
diff --git a/src/Structure/Disulfide.h b/src/Structure/Disulfide.h
index bbf7971ee3..9f5df092c8 100644
--- a/src/Structure/Disulfide.h
+++ b/src/Structure/Disulfide.h
@@ -17,8 +17,10 @@ class Disulfide {
     Disulfide();
     /// Keywords recognized by InitDisulfide
     static const char* keywords_;
+    /// Will indicate whether we want to add newly detected disulfide bonds to Topology
+    enum AddType { ADD_BONDS = 0, NO_ADD_BONDS };
     /// Init from args
-    int InitDisulfide(ArgList&, int);
+    int InitDisulfide(ArgList&, AddType, int);
     /// Print info to stdout
     //void DisulfideInfo() const;
     /// Search for disulfide bonds
@@ -27,12 +29,13 @@ class Disulfide {
     /// Search for disulfide bonds
     static int searchForDisulfides(ResStatArray&,
                         double, std::string const&, std::string const&, bool,
-                        Topology&, Frame const&, std::vector<BondType>&);
+                        Topology&, Frame const&, std::vector<BondType>&, AddType);
 
     double disulfidecut_; ///< Distance cutoff for disulfide bonds in Ang.
     std::string newcysnamestr_; ///< Name of cysteine residues involved in disulfide bonds
     std::string cysmaskstr_;    ///< Cysteine mask string
     bool searchForNewDisulfides_; ///< If true, look for new disulfides in addition to existing bonds
+    AddType addNewBonds_; ///< Indicate whether newly detected disulfides should be added to Topology
 };
 }
 }

From 04e6444462f14697b7a960ce64bc53e95c5c7a87 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 27 Feb 2024 14:41:23 -0500
Subject: [PATCH 0628/1492] prepareforleap does not want disulfides added

---
 src/Exec_PrepareForLeap.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Exec_PrepareForLeap.cpp b/src/Exec_PrepareForLeap.cpp
index c7fe52224e..70bbe5f55d 100644
--- a/src/Exec_PrepareForLeap.cpp
+++ b/src/Exec_PrepareForLeap.cpp
@@ -832,7 +832,7 @@ Exec::RetType Exec_PrepareForLeap::Execute(CpptrajState& State, ArgList& argIn)
   // Disulfide search
   if (!argIn.hasKey("nodisulfides")) {
     Cpptraj::Structure::Disulfide disulfide;
-    if (disulfide.InitDisulfide( argIn, debug_ )) {
+    if (disulfide.InitDisulfide( argIn, Disulfide::NO_ADD_BONDS, debug_ )) {
       mprinterr("Error: Could not init disulfide search.\n");
       return CpptrajState::ERR;
     }

From a8b4e1dfb6c1d655864f9f1ab21f78574f3bf9c3 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 27 Feb 2024 14:45:36 -0500
Subject: [PATCH 0629/1492] Add disulfide search

---
 src/Exec_Build.cpp | 27 +++++++++++++++++++++++++--
 src/cpptrajdepend  |  2 +-
 2 files changed, 26 insertions(+), 3 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index b9366e54cb..ba719aa448 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -5,6 +5,7 @@
 #include "Parm/GB_Params.h"
 #include "Structure/Builder.h"
 #include "Structure/Creator.h"
+#include "Structure/Disulfide.h"
 #include "Structure/HisProt.h"
 #include "Structure/PdbCleaner.h"
 #include "Structure/ResStatArray.h"
@@ -629,11 +630,14 @@ void Exec_Build::Help() const
           "\t[{%s} ...]\n"
           "\t[{%s} ...]\n"
           "%s"
+          "%s"
           "  Build complete topology and parameters from given crdset.\n",
           Cpptraj::Structure::Creator::other_keywords_,
           Cpptraj::Structure::Creator::template_keywords_,
           Cpptraj::Structure::Creator::parm_keywords_,
-          Cpptraj::Structure::HisProt::keywords_);
+          Cpptraj::Structure::HisProt::keywords_,
+          Cpptraj::Structure::Disulfide::keywords_
+         );
 }
 
 // Exec_Build::Execute()
@@ -742,6 +746,26 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
     return CpptrajState::ERR;
   }
 
+  // All residues start unknown
+  Cpptraj::Structure::ResStatArray resStat( topIn.Nres() );
+
+  // Disulfide search
+  if (!argIn.hasKey("nodisulfides")) {
+    Cpptraj::Structure::Disulfide disulfide;
+    if (disulfide.InitDisulfide( argIn, Cpptraj::Structure::Disulfide::ADD_BONDS, debug_ )) {
+      mprinterr("Error: Could not init disulfide search.\n");
+      return CpptrajState::ERR;
+    }
+    std::vector<BondType> LeapBonds;
+    if (disulfide.SearchForDisulfides( resStat, topIn, frameIn, LeapBonds ))
+    {
+      mprinterr("Error: Disulfide search failed.\n");
+      return CpptrajState::ERR;
+    }
+  } else {
+    mprintf("\tNot searching for disulfides.\n");
+  }
+
   // Handle sugars.
   // TODO should be on a residue by residue basis in FillAtomsWithTemplates
   bool prepare_sugars = !argIn.hasKey("nosugars");
@@ -784,7 +808,6 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
       return CpptrajState::ERR;
     }
     std::vector<BondType> LeapBonds;
-    Cpptraj::Structure::ResStatArray resStat( topIn.Nres() );
     if (sugarBuilder_->PrepareSugars(true, resStat, topIn, frameIn, LeapBonds))
     {
       mprinterr("Error: Sugar preparation failed.\n");
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index a5ed7d0997..3e5591e4ba 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -291,7 +291,7 @@ Ewald_Regular.o : Ewald_Regular.cpp Atom.h AtomMask.h Box.h Constants.h Coordina
 ExclusionArray.o : ExclusionArray.cpp Atom.h AtomMask.h CharMask.h CpptrajStdio.h ExclusionArray.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Unit.h
 Exec_AddMissingRes.o : Exec_AddMissingRes.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CharMask.h CompactFrameArray.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_AddMissingRes.h Exec_AddMissingRes_Pres.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Analyze.o : Exec_Analyze.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Analyze.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Build.o : Exec_Build.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/GB_Params.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/Creator.h Structure/HisProt.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/StructureEnum.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Build.o : Exec_Build.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/GB_Params.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/Creator.h Structure/Disulfide.h Structure/HisProt.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/StructureEnum.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Calc.o : Exec_Calc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Calc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_CatCrd.o : Exec_CatCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CatCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Change.o : Exec_Change.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Change.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h

From 0172ad698905a2f19f8e6ac06eb856e25cb96f1c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 28 Feb 2024 09:12:09 -0500
Subject: [PATCH 0630/1492] Add some debug

---
 src/Action_CheckStructure.cpp | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/Action_CheckStructure.cpp b/src/Action_CheckStructure.cpp
index deb38aca38..ba95e9c600 100644
--- a/src/Action_CheckStructure.cpp
+++ b/src/Action_CheckStructure.cpp
@@ -138,6 +138,10 @@ Action::RetType Action_CheckStructure::Init(ArgList& actionArgs, ActionInit& ini
 // Action_CheckStructure::Setup()
 Action::RetType Action_CheckStructure::Setup(ActionSetup& setup) {
   CurrentParm_ = setup.TopAddress();
+  if (check_.Debug() > 0) {
+    if (setup.CoordInfo().HasBox())
+      setup.CoordInfo().TrajBox().PrintInfo();
+  }
   if (check_.Setup( setup.Top(), setup.CoordInfo().TrajBox() )) return Action::ERR;
   check_.Mask1().MaskInfo();
   if (check_.Mask2().MaskStringSet())

From bab2aa9c8e248339054c3c0d3eaa92d7714ba38b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 28 Feb 2024 09:12:20 -0500
Subject: [PATCH 0631/1492] Return debug level

---
 src/StructureCheck.h | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/StructureCheck.h b/src/StructureCheck.h
index ea5a452913..0c2b8680c1 100644
--- a/src/StructureCheck.h
+++ b/src/StructureCheck.h
@@ -31,6 +31,7 @@ class StructureCheck {
     double NonBondCut2()        const { return nonbondcut2_; }
     double PairListCut()        const { return plcut_; }
     unsigned int Nbonds()       const { return bondList_.size(); }
+    int Debug()                 const { return debug_; }
 #   ifdef _OPENMP
     unsigned int Nthreads()     const { return thread_problemAtoms_.size(); }
 #   endif

From 4243d4cb567b79aacc5293e3c6fd6f317c3f419d Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 28 Feb 2024 09:12:48 -0500
Subject: [PATCH 0632/1492] If modifying a coords set with box info, ensure box
 info in associated CoordinateInfo is updated as well.

---
 src/Exec_CrdAction.cpp | 22 ++++++++++++++++++++--
 1 file changed, 20 insertions(+), 2 deletions(-)

diff --git a/src/Exec_CrdAction.cpp b/src/Exec_CrdAction.cpp
index 73e530a74f..f60a6d77d9 100644
--- a/src/Exec_CrdAction.cpp
+++ b/src/Exec_CrdAction.cpp
@@ -33,6 +33,7 @@ Exec::RetType Exec_CrdAction::DoCrdAction(CpptrajState& State, ArgList& actionar
     return CpptrajState::ERR;
   // If the topology was modified, we will need a new COORDS set.
   DataSet_Coords* crdOut = 0;
+  bool box_needs_update = false;
   if ( setup_ret == Action::MODIFY_TOPOLOGY ) {
     // This will not work for a TRJ set.
     switch ( CRD->Type() ) {
@@ -47,6 +48,12 @@ Exec::RetType Exec_CrdAction::DoCrdAction(CpptrajState& State, ArgList& actionar
     if (frameCount.TotalReadFrames() != (int)CRD->Size())
       mprintf("Info: crdaction: Previous size= %zu, new size is %i\n",
               CRD->Size(), frameCount.TotalReadFrames());
+    // Note if we will have to update the coordinate info box data
+    if (originalSetup.CoordInfo().HasBox()) {
+      if (State.Debug() > 0)
+        mprintf("DEBUG: Need up update box info in COORDS set.\n");
+      box_needs_update = true;
+    }
     // Set up set, copy original metadata
     crdOut->SetMeta( CRD->Meta() );
     if (crdOut->CoordsSetup( originalSetup.Top(), originalSetup.CoordInfo() ))
@@ -60,8 +67,9 @@ Exec::RetType Exec_CrdAction::DoCrdAction(CpptrajState& State, ArgList& actionar
       return CpptrajState::ERR;
     }
   }
-    
+
   // Loop over all frames in COORDS.
+  Box updateBox;
   ProgressBar* progress = 0;
   if (State.ShowProgress())
     progress = new ProgressBar( frameCount.TotalReadFrames() );
@@ -85,6 +93,8 @@ Exec::RetType Exec_CrdAction::DoCrdAction(CpptrajState& State, ArgList& actionar
       else
         CRD->SetCRD( frame, frm.Frm() );
     }
+    if (frame == frameCount.Start() && box_needs_update)
+      updateBox = frm.Frm().BoxCrd();
   } 
   if (progress != 0) delete progress;
 # ifdef MPI
@@ -96,7 +106,15 @@ Exec::RetType Exec_CrdAction::DoCrdAction(CpptrajState& State, ArgList& actionar
             CRD->legend(), actionargs.Command());
     State.DSL().RemoveSet( CRD );
     State.DSL().AddSet( crdOut );
-  } 
+  }
+  // Update CoordinateInfo box if needed
+  if (box_needs_update) {
+    crdOut->UpdateCoordsInfoBox( updateBox );
+    mprintf("Info: crdaction: Box for '%s' was modified by action '%s'\n",
+            CRD->legend(), actionargs.Command());
+    if (State.Debug() > 0)
+      crdOut->CoordsInfo().TrajBox().PrintInfo();
+  }
   act->Print();
   State.MasterDataFileWrite();
   total_time.Stop();

From 0886df7a347e6597b2e63eeb33458ec7a128cb36 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 28 Feb 2024 09:13:16 -0500
Subject: [PATCH 0633/1492] Add function to update box in CoordinateInfo

---
 src/DataSet_Coords.cpp | 5 +++++
 src/DataSet_Coords.h   | 2 ++
 2 files changed, 7 insertions(+)

diff --git a/src/DataSet_Coords.cpp b/src/DataSet_Coords.cpp
index a573d2ab63..4c95ae0ce9 100644
--- a/src/DataSet_Coords.cpp
+++ b/src/DataSet_Coords.cpp
@@ -12,3 +12,8 @@ void DataSet_Coords::CommonInfo() const {
   if (cInfo_.HasVel()) mprintf(" Velocities,");
   mprintf(" %i atoms", top_.Natom());
 }
+
+/** Update coords info box */
+void DataSet_Coords::UpdateCoordsInfoBox( Box const& boxIn ) {
+  cInfo_.SetBox( boxIn );
+}
diff --git a/src/DataSet_Coords.h b/src/DataSet_Coords.h
index bcc2192e02..68f44e0784 100644
--- a/src/DataSet_Coords.h
+++ b/src/DataSet_Coords.h
@@ -32,6 +32,8 @@ class DataSet_Coords : public DataSet {
     inline Topology* TopPtr() { return &top_; }
     /// \return CoordinateInfo associated with these COORDS
     inline CoordinateInfo const& CoordsInfo() const { return cInfo_; }
+    /// Used to modify box in coords info
+    void UpdateCoordsInfoBox(Box const&);
   protected:
     void CommonInfo() const;
     Topology top_;         ///< Topology corresponding to coordinates.

From 8e3efeb73ff0950b530f19e2616a94d9e5c21254 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 28 Feb 2024 10:28:26 -0500
Subject: [PATCH 0634/1492] Change structure check default pairlist cutoff to 8
 ang

---
 src/Action_CheckStructure.cpp | 2 +-
 src/Exec_PermuteDihedrals.cpp | 2 +-
 src/StructureCheck.cpp        | 4 +---
 3 files changed, 3 insertions(+), 5 deletions(-)

diff --git a/src/Action_CheckStructure.cpp b/src/Action_CheckStructure.cpp
index ba95e9c600..f1d3e9e4a8 100644
--- a/src/Action_CheckStructure.cpp
+++ b/src/Action_CheckStructure.cpp
@@ -60,7 +60,7 @@ Action::RetType Action_CheckStructure::Init(ArgList& actionArgs, ActionInit& ini
     nonbondcut,
     actionArgs.getKeyDouble("offset",1.15),
     actionArgs.getKeyDouble("minoffset", 0.5),
-    actionArgs.getKeyDouble("plcut", std::max(4.0, nonbondcut))
+    actionArgs.getKeyDouble("plcut", std::max(8.0, nonbondcut))
   );
   if (err != 0) return Action::ERR;
   // Remaining keywords
diff --git a/src/Exec_PermuteDihedrals.cpp b/src/Exec_PermuteDihedrals.cpp
index a99426f5e1..646a5c474d 100644
--- a/src/Exec_PermuteDihedrals.cpp
+++ b/src/Exec_PermuteDihedrals.cpp
@@ -197,7 +197,7 @@ Exec::RetType Exec_PermuteDihedrals::Execute(CpptrajState& State, ArgList& argIn
     // Increment backtrack by 1 since we need to skip over current res
     ++backtrack_;
     // Initialize CheckStructure
-    if (checkStructure_.SetOptions( false, false, false, State.Debug(), "*", "", 0.8, 1.15, 0.5, 4.0 )) {
+    if (checkStructure_.SetOptions( false, false, false, State.Debug(), "*", "", 0.8, 1.15, 0.5, 8.0 )) {
       mprinterr("Error: Could not set up structure check.\n");
       return CpptrajState::ERR;
     }
diff --git a/src/StructureCheck.cpp b/src/StructureCheck.cpp
index 49aadcd8b0..ce573b6dae 100644
--- a/src/StructureCheck.cpp
+++ b/src/StructureCheck.cpp
@@ -14,9 +14,7 @@ StructureCheck::StructureCheck() :
   bondoffset_(1.15),
   bondMinOffset_(0.50),
   nonbondcut2_(0.64), // 0.8^2
-  // NOTE: Default of 4.0 Ang for cutoff is from trial and error; seems
-  //       to give a good balance between speed and grid size.
-  plcut_(4.0),
+  plcut_(8.0),
   checkType_(NO_PL_1_MASK),
   debug_(0),
   bondcheck_(true),

From 2333aa860e2cc547609981dee6873bda783062aa Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 28 Feb 2024 16:28:08 -0500
Subject: [PATCH 0635/1492] Use a heuristic to estimate pairlist cutoff during
 structure check to ensure memory requirements do not get out of control.

---
 src/Action_CheckStructure.cpp |  6 ++++--
 src/StructureCheck.cpp        | 17 +++++++++++++++++
 2 files changed, 21 insertions(+), 2 deletions(-)

diff --git a/src/Action_CheckStructure.cpp b/src/Action_CheckStructure.cpp
index f1d3e9e4a8..4b75461250 100644
--- a/src/Action_CheckStructure.cpp
+++ b/src/Action_CheckStructure.cpp
@@ -48,7 +48,9 @@ Action::RetType Action_CheckStructure::Init(ArgList& actionArgs, ActionInit& ini
                                          "Structure check", DataFileList::TEXT, true);
   else
     outfile_ = 0;
-  double nonbondcut =  actionArgs.getKeyDouble("cut",0.8);
+  double nonbondcut = actionArgs.getKeyDouble("cut",0.8);
+  double plcut      = actionArgs.getKeyDouble("plcut", -1);
+  //  actionArgs.getKeyDouble("plcut", std::max(8.0, nonbondcut))
   // Structure checker setup
   int err = check_.SetOptions(
     !(actionArgs.hasKey("noimage")),
@@ -60,7 +62,7 @@ Action::RetType Action_CheckStructure::Init(ArgList& actionArgs, ActionInit& ini
     nonbondcut,
     actionArgs.getKeyDouble("offset",1.15),
     actionArgs.getKeyDouble("minoffset", 0.5),
-    actionArgs.getKeyDouble("plcut", std::max(8.0, nonbondcut))
+    plcut
   );
   if (err != 0) return Action::ERR;
   // Remaining keywords
diff --git a/src/StructureCheck.cpp b/src/StructureCheck.cpp
index ce573b6dae..a71ca9c169 100644
--- a/src/StructureCheck.cpp
+++ b/src/StructureCheck.cpp
@@ -124,6 +124,23 @@ int StructureCheck::Setup(Topology const& topIn, Box const& boxIn)
   ExclusionArray::ListOpt ex_list_opt = ExclusionArray::ONLY_GREATER_IDX;
   if (imageOpt_.ImagingEnabled() && !Mask2_.MaskStringSet()) {
     mprintf("\tUsing pair list.\n");
+    // If pairlist cutoff < 0 try to use a heuristic to estimate.
+    if (plcut_ < 0) {
+      // Get the minimum dimension length
+      double minDimLen = boxIn.Param(Box::X);
+      if (boxIn.Param(Box::Y) < minDimLen)
+        minDimLen = boxIn.Param(Box::Y);
+      if (boxIn.Param(Box::Z) < minDimLen)
+        minDimLen = boxIn.Param(Box::Z);
+      // Have cutoff be sqrt of min dim len
+      plcut_ = sqrt(minDimLen);
+      if (plcut_ < 8.0) {
+        plcut_ = 8.0;
+        mprintf("\tSet pairlist cutoff to default of %f Ang.\n", plcut_);
+      } else
+        mprintf("\tSet pairlist cutoff to %f Ang. based on minimum box dimension %f Ang.\n",
+                plcut_, minDimLen);
+    }
     if (pairList_.InitPairList( plcut_, 0.1, debug_ )) {
       mprinterr("Error: StructureCheck: Could not init pair list.\n");
       return 1;

From 2e602729fec0df6f1d7d75f1fcfaf892737838c3 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 29 Feb 2024 08:44:30 -0500
Subject: [PATCH 0636/1492] Fix message

---
 src/Action_CheckStructure.cpp | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/Action_CheckStructure.cpp b/src/Action_CheckStructure.cpp
index 4b75461250..601435e893 100644
--- a/src/Action_CheckStructure.cpp
+++ b/src/Action_CheckStructure.cpp
@@ -130,7 +130,10 @@ Action::RetType Action_CheckStructure::Init(ArgList& actionArgs, ActionInit& ini
   }
   if (silent_)
     mprintf("\tStructure warning messages will be suppressed.\n");
-  mprintf("\tCutoff for building pair list is %f Ang.\n", check_.PairListCut());
+  if ( check_.PairListCut() < 0.0 )
+    mprintf("\tPair list cutoff will be determined from system size.\n");
+  else
+    mprintf("\tCutoff for building pair list is %f Ang.\n", check_.PairListCut());
 # ifdef _OPENMP
   mprintf("\tParallelizing calculation with %u threads.\n", check_.Nthreads());
 # endif

From c36fce70f54fc9bf670cfb2ca2ce0362218e2711 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 29 Feb 2024 14:33:40 -0500
Subject: [PATCH 0637/1492] Use HasType

---
 src/Exec_Build.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index ba719aa448..554866f2ac 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -230,7 +230,7 @@ const
       {
         // Track intra-residue bonds
         Atom sourceAtom = topIn[itgt];
-        if (sourceAtom.Type().len() < 1)
+        if (!sourceAtom.HasType())
           nAtomsMissingTypes++;
         SourceAtomNames.push_back( sourceAtom.Name() );
         int at0 = itgt - currentRes.FirstAtom() + atomOffset;
@@ -353,7 +353,7 @@ const
     for (int ires = 0; ires != topOut.Nres(); ires++) {
       std::string missingTypes;
       for (int at = topOut.Res(ires).FirstAtom(); at != topOut.Res(ires).LastAtom(); ++at)
-        if ( topOut[at].Type().len() < 1 )
+        if ( !topOut[at].HasType() )
           missingTypes.append(" " + topOut[at].Name().Truncated() );
       if (!missingTypes.empty())
         mprinterr("Error:\t%s missing types for%s\n", topOut.TruncResNameNum(ires).c_str(), missingTypes.c_str());

From 685678ff48dadcfcfce8038ada2c0bad7547468a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 29 Feb 2024 15:16:13 -0500
Subject: [PATCH 0638/1492] Start source command

---
 src/Command.cpp     |  2 ++
 src/Exec_Source.cpp | 39 +++++++++++++++++++++++++++++++++++++++
 src/Exec_Source.h   | 12 ++++++++++++
 src/cpptrajdepend   |  3 ++-
 src/cpptrajfiles    |  1 +
 5 files changed, 56 insertions(+), 1 deletion(-)
 create mode 100644 src/Exec_Source.cpp
 create mode 100644 src/Exec_Source.h

diff --git a/src/Command.cpp b/src/Command.cpp
index 6c905c66c2..12bc2f08fb 100644
--- a/src/Command.cpp
+++ b/src/Command.cpp
@@ -33,6 +33,7 @@
 #include "Exec_ReadInput.h"
 #include "Exec_RunAnalysis.h"
 #include "Exec_SortEnsembleData.h"
+#include "Exec_Source.h"
 #include "Exec_SequenceAlign.h"
 #include "Exec_ViewRst.h"
 #include "Exec_Set.h"
@@ -261,6 +262,7 @@ void Command::Init() {
   Command::AddCmd( new Exec_SilenceActions(),  Cmd::EXE, 1, "silenceactions" );
   Command::AddCmd( new Exec_SequenceAlign(),   Cmd::EXE, 1, "sequencealign" ); // hidden
   Command::AddCmd( new Exec_SortEnsembleData(),Cmd::EXE, 1, "sortensembledata" );
+  Command::AddCmd( new Exec_Source(),          Cmd::EXE, 1, "source" );
   Command::AddCmd( new Exec_WriteDataFile(),   Cmd::EXE, 2, "write", "writedata" );
   Command::AddCmd( new Exec_UseDiskCache(),    Cmd::EXE, 1, "usediskcache" );
   Command::AddCmd( new Exec_ViewRst(),         Cmd::EXE, 1, "viewrst" ); // hidden
diff --git a/src/Exec_Source.cpp b/src/Exec_Source.cpp
new file mode 100644
index 0000000000..3578222c1d
--- /dev/null
+++ b/src/Exec_Source.cpp
@@ -0,0 +1,39 @@
+#include "Exec_Source.h"
+#include "CpptrajStdio.h"
+
+// Exec_Source::Help()
+void Exec_Source::Help() const
+{
+
+}
+
+// Exec_Source::Execute()
+Exec::RetType Exec_Source::Execute(CpptrajState& State, ArgList& argIn)
+{
+  // source <file>
+  std::string fname = argIn.GetStringNext();
+  if (fname.empty()) {
+    mprinterr("Error: No filename given for 'source'.\n");
+    return CpptrajState::ERR;
+  }
+  // If file is in this dir, read it.
+  // Otherwise, prepend AMBERHOME/dat/leap/cmd
+  std::string fileName;
+  if ( File::Exists( fname ) ) {
+    fileName = fname;
+  } else {
+    const char* env = getenv("AMBERHOME");
+    if (env == 0) {
+      mprinterr("Error: %s not found and AMBERHOME is not set.\n", fname.c_str());
+      return CpptrajState::ERR;
+    }
+    fileName = std::string(env) + "/dat/leap/cmd/" + fname;
+    if (!File::Exists(fileName)) {
+      mprinterr("Error: %s not found.\n", fileName.c_str());
+      return CpptrajState::ERR;
+    }
+  }
+  mprintf("\tReading %s\n", fileName.c_str());
+
+  return CpptrajState::OK;
+}
diff --git a/src/Exec_Source.h b/src/Exec_Source.h
new file mode 100644
index 0000000000..ea20f3c979
--- /dev/null
+++ b/src/Exec_Source.h
@@ -0,0 +1,12 @@
+#ifndef INC_EXEC_SOURCE_H
+#define INC_EXEC_SOURCE_H
+#include "Exec.h"
+/// Replicate LEaPs source command 
+class Exec_Source : public Exec {
+  public:
+    Exec_Source() : Exec(GENERAL) {}
+    void Help() const;
+    DispatchObject* Alloc() const { return (DispatchObject*)new Exec_Source(); }
+    RetType Execute(CpptrajState&, ArgList&);
+};
+#endif
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 3e5591e4ba..f19f6c242b 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -188,7 +188,7 @@ ClusterMap.o : ClusterMap.cpp AssociatedData.h ClusterMap.h Constants.h CpptrajF
 Cmd.o : Cmd.cpp Cmd.h DispatchObject.h
 CmdInput.o : CmdInput.cpp CmdInput.h StringRoutines.h
 CmdList.o : CmdList.cpp Cmd.h CmdList.h DispatchObject.h
-Command.o : Command.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h ActionTopWriter.h Action_Align.h Action_Angle.h Action_AreaPerMol.h Action_AtomMap.h Action_AtomicCorr.h Action_AtomicFluct.h Action_AutoImage.h Action_Average.h Action_AvgBox.h Action_Bounds.h Action_Box.h Action_Center.h Action_Channel.h Action_CheckChirality.h Action_CheckStructure.h Action_Closest.h Action_ClusterDihedral.h Action_Contacts.h Action_CreateCrd.h Action_CreateReservoir.h Action_DNAionTracker.h Action_DSSP.h Action_Density.h Action_Diffusion.h Action_Dihedral.h Action_DihedralRMS.h Action_Dipole.h Action_DistRmsd.h Action_Distance.h Action_Energy.h Action_Esander.h Action_FilterByData.h Action_FixAtomOrder.h Action_FixImagedBonds.h Action_GIST.h Action_Grid.h Action_GridFreeEnergy.h Action_HydrogenBond.h Action_Image.h Action_InfraredSpectrum.h Action_Jcoupling.h Action_Keep.h Action_LESsplit.h Action_LIE.h Action_LipidOrder.h Action_MakeStructure.h Action_Mask.h Action_Matrix.h Action_MinImage.h Action_Molsurf.h Action_MultiDihedral.h Action_MultiPucker.h Action_MultiVector.h Action_NAstruct.h Action_NMRrst.h Action_NativeContacts.h Action_OrderParameter.h Action_Outtraj.h Action_PairDist.h Action_Pairwise.h Action_Principal.h Action_Projection.h Action_Pucker.h Action_Radgyr.h Action_Radial.h Action_RandomizeIons.h Action_Remap.h Action_ReplicateCell.h Action_Rmsd.h Action_Rotate.h Action_RunningAvg.h Action_STFC_Diffusion.h Action_Scale.h Action_SetVelocity.h Action_Spam.h Action_Strip.h Action_Surf.h Action_SymmetricRmsd.h Action_Temperature.h Action_Time.h Action_ToroidalDiffusion.h Action_Translate.h Action_Unstrip.h Action_Unwrap.h Action_Vector.h Action_VelocityAutoCorr.h Action_Volmap.h Action_Volume.h Action_Watershell.h Action_XtalSymm.h Analysis.h AnalysisList.h AnalysisState.h Analysis_AmdBias.h Analysis_AutoCorr.h Analysis_Average.h Analysis_CalcDiffusion.h Analysis_Clustering.h Analysis_ConstantPHStats.h Analysis_Corr.h Analysis_CrankShaft.h Analysis_CrdFluct.h Analysis_CrossCorr.h Analysis_CurveFit.h Analysis_Divergence.h Analysis_EvalPlateau.h Analysis_FFT.h Analysis_HausdorffDistance.h Analysis_Hist.h Analysis_IRED.h Analysis_Integrate.h Analysis_KDE.h Analysis_Lifetime.h Analysis_LowestCurve.h Analysis_Matrix.h Analysis_MeltCurve.h Analysis_Modes.h Analysis_MultiHist.h Analysis_Multicurve.h Analysis_Overlap.h Analysis_PhiPsi.h Analysis_Regression.h Analysis_RemLog.h Analysis_Rms2d.h Analysis_RmsAvgCorr.h Analysis_Rotdif.h Analysis_RunningAvg.h Analysis_Slope.h Analysis_Spline.h Analysis_State.h Analysis_Statistics.h Analysis_TI.h Analysis_TICA.h Analysis_Timecorr.h Analysis_VectorMath.h Analysis_Wavelet.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h AxisType.h BaseIOtype.h Box.h BoxArgs.h BufferedLine.h CharMask.h Cluster/Algorithm.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Control.h Cluster/DrawGraph.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Sieve.h Cluster/Silhouette.h ClusterMap.h Cmd.h CmdInput.h CmdList.h Command.h CompactFrameArray.h ComplexArray.h Constants.h Constraints.h ControlBlock.h ControlBlock_For.h CoordinateInfo.h Corr.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_RemLog.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h Deprecated.h DiffusionResults.h DihedralSearch.h Dimension.h DispatchObject.h Energy.h Energy_Sander.h EnsembleIn.h EnsembleOutList.h Ewald.h EwaldOptions.h Ewald_ParticleMesh.h ExclusionArray.h Exec.h Exec_AddMissingRes.h Exec_Analyze.h Exec_Build.h Exec_Calc.h Exec_CatCrd.h Exec_Change.h Exec_ClusterMap.h Exec_CombineCoords.h Exec_Commands.h Exec_CompareClusters.h Exec_CompareEnergy.h Exec_CompareTop.h Exec_CrdAction.h Exec_CrdOut.h Exec_CrdTransform.h Exec_CreateSet.h Exec_DataFile.h Exec_DataFilter.h Exec_DataSetCmd.h Exec_Desc.h Exec_Emin.h Exec_ExtendedComparison.h Exec_Flatten.h Exec_GenerateAmberRst.h Exec_Graft.h Exec_Help.h Exec_HmassRepartition.h Exec_LoadCrd.h Exec_LoadTraj.h Exec_ParallelAnalysis.h Exec_ParmBox.h Exec_ParmSolvent.h Exec_ParmStrip.h Exec_ParmWrite.h Exec_ParseTiming.h Exec_PermuteDihedrals.h Exec_Precision.h Exec_PrepareForLeap.h Exec_PrintData.h Exec_Random.h Exec_ReadData.h Exec_ReadEnsembleData.h Exec_ReadInput.h Exec_RotateDihedral.h Exec_RunAnalysis.h Exec_ScaleDihedralK.h Exec_Sequence.h Exec_SequenceAlign.h Exec_Set.h Exec_Show.h Exec_SortEnsembleData.h Exec_SplitCoords.h Exec_System.h Exec_Top.h Exec_Traj.h Exec_UpdateParameters.h Exec_ViewRst.h Exec_Zmatrix.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h GIST_PME.h Grid.h GridAction.h GridBin.h GridMover.h HistBin.h Hungarian.h ImageOption.h ImageTypes.h InputTrajCommon.h MapAtom.h MaskArray.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h OnlineVarT.h OutputTrajCommon.h PDBfile.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PubFFT.h Pucker.h Pucker_PuckerMask.h Pucker_PuckerSearch.h Pucker_PuckerToken.h RPNcalc.h Random.h Range.h ReferenceAction.h ReferenceFrame.h RemdReservoirNC.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h SplineFxnTable.h StructureCheck.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h cuda_kernels/GistCudaSetup.cuh helpme_standalone.h molsurf.h
+Command.o : Command.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h ActionTopWriter.h Action_Align.h Action_Angle.h Action_AreaPerMol.h Action_AtomMap.h Action_AtomicCorr.h Action_AtomicFluct.h Action_AutoImage.h Action_Average.h Action_AvgBox.h Action_Bounds.h Action_Box.h Action_Center.h Action_Channel.h Action_CheckChirality.h Action_CheckStructure.h Action_Closest.h Action_ClusterDihedral.h Action_Contacts.h Action_CreateCrd.h Action_CreateReservoir.h Action_DNAionTracker.h Action_DSSP.h Action_Density.h Action_Diffusion.h Action_Dihedral.h Action_DihedralRMS.h Action_Dipole.h Action_DistRmsd.h Action_Distance.h Action_Energy.h Action_Esander.h Action_FilterByData.h Action_FixAtomOrder.h Action_FixImagedBonds.h Action_GIST.h Action_Grid.h Action_GridFreeEnergy.h Action_HydrogenBond.h Action_Image.h Action_InfraredSpectrum.h Action_Jcoupling.h Action_Keep.h Action_LESsplit.h Action_LIE.h Action_LipidOrder.h Action_MakeStructure.h Action_Mask.h Action_Matrix.h Action_MinImage.h Action_Molsurf.h Action_MultiDihedral.h Action_MultiPucker.h Action_MultiVector.h Action_NAstruct.h Action_NMRrst.h Action_NativeContacts.h Action_OrderParameter.h Action_Outtraj.h Action_PairDist.h Action_Pairwise.h Action_Principal.h Action_Projection.h Action_Pucker.h Action_Radgyr.h Action_Radial.h Action_RandomizeIons.h Action_Remap.h Action_ReplicateCell.h Action_Rmsd.h Action_Rotate.h Action_RunningAvg.h Action_STFC_Diffusion.h Action_Scale.h Action_SetVelocity.h Action_Spam.h Action_Strip.h Action_Surf.h Action_SymmetricRmsd.h Action_Temperature.h Action_Time.h Action_ToroidalDiffusion.h Action_Translate.h Action_Unstrip.h Action_Unwrap.h Action_Vector.h Action_VelocityAutoCorr.h Action_Volmap.h Action_Volume.h Action_Watershell.h Action_XtalSymm.h Analysis.h AnalysisList.h AnalysisState.h Analysis_AmdBias.h Analysis_AutoCorr.h Analysis_Average.h Analysis_CalcDiffusion.h Analysis_Clustering.h Analysis_ConstantPHStats.h Analysis_Corr.h Analysis_CrankShaft.h Analysis_CrdFluct.h Analysis_CrossCorr.h Analysis_CurveFit.h Analysis_Divergence.h Analysis_EvalPlateau.h Analysis_FFT.h Analysis_HausdorffDistance.h Analysis_Hist.h Analysis_IRED.h Analysis_Integrate.h Analysis_KDE.h Analysis_Lifetime.h Analysis_LowestCurve.h Analysis_Matrix.h Analysis_MeltCurve.h Analysis_Modes.h Analysis_MultiHist.h Analysis_Multicurve.h Analysis_Overlap.h Analysis_PhiPsi.h Analysis_Regression.h Analysis_RemLog.h Analysis_Rms2d.h Analysis_RmsAvgCorr.h Analysis_Rotdif.h Analysis_RunningAvg.h Analysis_Slope.h Analysis_Spline.h Analysis_State.h Analysis_Statistics.h Analysis_TI.h Analysis_TICA.h Analysis_Timecorr.h Analysis_VectorMath.h Analysis_Wavelet.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h AxisType.h BaseIOtype.h Box.h BoxArgs.h BufferedLine.h CharMask.h Cluster/Algorithm.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Control.h Cluster/DrawGraph.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Sieve.h Cluster/Silhouette.h ClusterMap.h Cmd.h CmdInput.h CmdList.h Command.h CompactFrameArray.h ComplexArray.h Constants.h Constraints.h ControlBlock.h ControlBlock_For.h CoordinateInfo.h Corr.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_RemLog.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h Deprecated.h DiffusionResults.h DihedralSearch.h Dimension.h DispatchObject.h Energy.h Energy_Sander.h EnsembleIn.h EnsembleOutList.h Ewald.h EwaldOptions.h Ewald_ParticleMesh.h ExclusionArray.h Exec.h Exec_AddMissingRes.h Exec_Analyze.h Exec_Build.h Exec_Calc.h Exec_CatCrd.h Exec_Change.h Exec_ClusterMap.h Exec_CombineCoords.h Exec_Commands.h Exec_CompareClusters.h Exec_CompareEnergy.h Exec_CompareTop.h Exec_CrdAction.h Exec_CrdOut.h Exec_CrdTransform.h Exec_CreateSet.h Exec_DataFile.h Exec_DataFilter.h Exec_DataSetCmd.h Exec_Desc.h Exec_Emin.h Exec_ExtendedComparison.h Exec_Flatten.h Exec_GenerateAmberRst.h Exec_Graft.h Exec_Help.h Exec_HmassRepartition.h Exec_LoadCrd.h Exec_LoadTraj.h Exec_ParallelAnalysis.h Exec_ParmBox.h Exec_ParmSolvent.h Exec_ParmStrip.h Exec_ParmWrite.h Exec_ParseTiming.h Exec_PermuteDihedrals.h Exec_Precision.h Exec_PrepareForLeap.h Exec_PrintData.h Exec_Random.h Exec_ReadData.h Exec_ReadEnsembleData.h Exec_ReadInput.h Exec_RotateDihedral.h Exec_RunAnalysis.h Exec_ScaleDihedralK.h Exec_Sequence.h Exec_SequenceAlign.h Exec_Set.h Exec_Show.h Exec_SortEnsembleData.h Exec_Source.h Exec_SplitCoords.h Exec_System.h Exec_Top.h Exec_Traj.h Exec_UpdateParameters.h Exec_ViewRst.h Exec_Zmatrix.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h GIST_PME.h Grid.h GridAction.h GridBin.h GridMover.h HistBin.h Hungarian.h ImageOption.h ImageTypes.h InputTrajCommon.h MapAtom.h MaskArray.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h OnlineVarT.h OutputTrajCommon.h PDBfile.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PubFFT.h Pucker.h Pucker_PuckerMask.h Pucker_PuckerSearch.h Pucker_PuckerToken.h RPNcalc.h Random.h Range.h ReferenceAction.h ReferenceFrame.h RemdReservoirNC.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h SplineFxnTable.h StructureCheck.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h cuda_kernels/GistCudaSetup.cuh helpme_standalone.h molsurf.h
 CompactFrameArray.o : CompactFrameArray.cpp Box.h CompactFrameArray.h CoordinateInfo.h CpptrajStdio.h Matrix_3x3.h Parallel.h ReplicaDimArray.h Vec3.h
 ComplexArray.o : ComplexArray.cpp ArrayIterator.h ComplexArray.h
 Constraints.o : Constraints.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
@@ -340,6 +340,7 @@ Exec_SequenceAlign.o : Exec_SequenceAlign.cpp Action.h ActionFrameCounter.h Acti
 Exec_Set.o : Exec_Set.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_StringVar.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Set.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Show.o : Exec_Show.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_StringVar.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Show.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_SortEnsembleData.o : Exec_SortEnsembleData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h DataSet_PHREMD_Implicit.h DataSet_pH.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SortEnsembleData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Source.o : Exec_Source.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Source.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_SplitCoords.o : Exec_SplitCoords.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SplitCoords.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_System.o : Exec_System.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_System.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Top.o : Exec_Top.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Top.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h TopInfo.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
diff --git a/src/cpptrajfiles b/src/cpptrajfiles
index c674a57869..e1a86128b2 100644
--- a/src/cpptrajfiles
+++ b/src/cpptrajfiles
@@ -310,6 +310,7 @@ COMMON_SOURCES= \
         Exec_SequenceAlign.cpp \
         Exec_Show.cpp \
         Exec_SortEnsembleData.cpp \
+        Exec_Source.cpp \
         Exec_SplitCoords.cpp \
         Exec_System.cpp \
         Exec_Top.cpp \

From 08ef4899dacd89f9f970188b042720c9d50785cb Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 29 Feb 2024 15:27:18 -0500
Subject: [PATCH 0639/1492] Finish the source command

---
 src/Exec_Source.cpp | 27 ++++++++++++++++++++++-----
 src/cpptrajdepend   |  2 +-
 2 files changed, 23 insertions(+), 6 deletions(-)

diff --git a/src/Exec_Source.cpp b/src/Exec_Source.cpp
index 3578222c1d..fbd2d5c6b1 100644
--- a/src/Exec_Source.cpp
+++ b/src/Exec_Source.cpp
@@ -1,5 +1,6 @@
 #include "Exec_Source.h"
 #include "CpptrajStdio.h"
+#include "DataIO_LeapRC.h"
 
 // Exec_Source::Help()
 void Exec_Source::Help() const
@@ -18,22 +19,38 @@ Exec::RetType Exec_Source::Execute(CpptrajState& State, ArgList& argIn)
   }
   // If file is in this dir, read it.
   // Otherwise, prepend AMBERHOME/dat/leap/cmd
-  std::string fileName;
+  FileName fileName;
   if ( File::Exists( fname ) ) {
-    fileName = fname;
+    fileName.SetFileName( fname );
   } else {
     const char* env = getenv("AMBERHOME");
     if (env == 0) {
       mprinterr("Error: %s not found and AMBERHOME is not set.\n", fname.c_str());
       return CpptrajState::ERR;
     }
-    fileName = std::string(env) + "/dat/leap/cmd/" + fname;
+    fileName.SetFileName( std::string(env) + "/dat/leap/cmd/" + fname );
     if (!File::Exists(fileName)) {
-      mprinterr("Error: %s not found.\n", fileName.c_str());
+      mprinterr("Error: %s not found.\n", fileName.full());
       return CpptrajState::ERR;
     }
   }
-  mprintf("\tReading %s\n", fileName.c_str());
+  mprintf("\tReading %s\n", fileName.full());
+
+  DataIO_LeapRC infile;
+  CpptrajFile tmp;
+  tmp.SetupRead( fileName, State.Debug() );
+  if (!infile.ID_DataFormat( tmp )) {
+    mprinterr("Error: %s does not appear to be a leaprc file.\n", fileName.full());
+    return CpptrajState::ERR;
+  }
+  if (infile.processReadArgs( argIn )) {
+    mprinterr("Error: Could not process read args for leaprc file %s\n", fileName.full());
+    return CpptrajState::ERR;
+  }
+  if (infile.ReadData(fileName, State.DSL(), fileName.Base())) {
+    mprinterr("Error: Could not read leaprc file %s\n", fileName.full());
+    return CpptrajState::ERR;
+  }
 
   return CpptrajState::OK;
 }
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index f19f6c242b..860f562838 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -340,7 +340,7 @@ Exec_SequenceAlign.o : Exec_SequenceAlign.cpp Action.h ActionFrameCounter.h Acti
 Exec_Set.o : Exec_Set.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_StringVar.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Set.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Show.o : Exec_Show.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_StringVar.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Show.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_SortEnsembleData.o : Exec_SortEnsembleData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h DataSet_PHREMD_Implicit.h DataSet_pH.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SortEnsembleData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Source.o : Exec_Source.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Source.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Source.o : Exec_Source.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Source.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_SplitCoords.o : Exec_SplitCoords.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SplitCoords.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_System.o : Exec_System.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_System.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Top.o : Exec_Top.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Top.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h TopInfo.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h

From 08838d741e0349f1b56761b2814233f4c39fbe18 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 29 Feb 2024 15:31:41 -0500
Subject: [PATCH 0640/1492] Fix name map sizes

---
 src/DataSet_NameMap.h | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/DataSet_NameMap.h b/src/DataSet_NameMap.h
index 8c88253c4f..3760c73f10 100644
--- a/src/DataSet_NameMap.h
+++ b/src/DataSet_NameMap.h
@@ -11,13 +11,13 @@ class DataSet_NameMap : public DataSet {
     DataSet_NameMap();
     static DataSet* Alloc() { return (DataSet*)new DataSet_NameMap(); }
     // ----- DataSet functions -------------------
-    size_t Size()                                    const { return 0; }
+    size_t Size()                                    const { return nameMap_.size(); }
     void Info()                                      const { return; }
     int Allocate(SizeArray const&)                         { return 1; }
     void Add(size_t, const void*)                          { return; }
     void WriteBuffer(CpptrajFile&, SizeArray const&) const { return; }
     int Append(DataSet*)                                   { return 1; }
-    size_t MemUsageInBytes()                         const { return 0; }
+    size_t MemUsageInBytes()                         const { return Size() * (2*NameType::max()); }
 #   ifdef MPI
     int Sync(size_t, std::vector<int> const&, Parallel::Comm const&) { return 1; }
 #   endif

From f98fbdeed4caeea946fb44a881b44359b94274c0 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 29 Feb 2024 16:45:58 -0500
Subject: [PATCH 0641/1492] Hide some debug info

---
 src/DataIO_LeapRC.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 86a407366a..f94f510457 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -311,7 +311,7 @@ const
       else if (*ptr == '}') {
         bracketCount--;
         if (bracketCount == 1) {
-          //if (debug_ > 0)
+          if (debug_ > 0)
             mprintf("DEBUG: addPdbAtomMap: %s\n", tmp.c_str());
           ArgList aline( tmp );
           // 2 tokens: Old name, new name
@@ -319,7 +319,7 @@ const
             mprinterr("Error: Malformed entry in addPdbAtomMap: %s\n", tmp.c_str());
             return 1;
           }
-          mprintf("DEBUG: old= %s  new= %s\n", aline[0].c_str(), aline[1].c_str());
+          if (debug_ > 0) mprintf("DEBUG: old= %s  new= %s\n", aline[0].c_str(), aline[1].c_str());
           namemap.AddNameMap( aline[0], aline[1] );
           tmp.clear();
         }

From 5140a53b4eeace5ade50456fd5b4dc3a7891eb88 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 29 Feb 2024 16:57:48 -0500
Subject: [PATCH 0642/1492] Hide some debug info

---
 src/Exec_Build.cpp        |  2 +-
 src/Exec_Sequence.cpp     |  2 +-
 src/Structure/Creator.cpp | 26 +++++++++++++++++---------
 src/Structure/Creator.h   |  2 ++
 4 files changed, 21 insertions(+), 11 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 554866f2ac..a63a9fd4d1 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -734,7 +734,7 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
   mprintf("\tGB radii set: %s\n", Cpptraj::Parm::GbTypeStr(gbradii).c_str());
 
   // Get templates and parameter sets.
-  Cpptraj::Structure::Creator creator;
+  Cpptraj::Structure::Creator creator( debug_ );
   if (creator.InitCreator(argIn, State.DSL(), debug_)) {
     return CpptrajState::ERR;
   }
diff --git a/src/Exec_Sequence.cpp b/src/Exec_Sequence.cpp
index 70ac5167d6..955d7baca9 100644
--- a/src/Exec_Sequence.cpp
+++ b/src/Exec_Sequence.cpp
@@ -281,7 +281,7 @@ Exec::RetType Exec_Sequence::Execute(CpptrajState& State, ArgList& argIn)
   debug_ = State.Debug();
 
   // Args
-  Cpptraj::Structure::Creator creator;
+  Cpptraj::Structure::Creator creator(debug_);
   if (creator.InitCreator(argIn, State.DSL(), debug_)) {
     return CpptrajState::ERR;
   }
diff --git a/src/Structure/Creator.cpp b/src/Structure/Creator.cpp
index 84332392c8..a80833f499 100644
--- a/src/Structure/Creator.cpp
+++ b/src/Structure/Creator.cpp
@@ -17,6 +17,13 @@ Creator::Creator() :
   free_parmset_mem_(false)
 {}
 
+/** CONSTRUCTOR */
+Creator::Creator(int d) :
+  mainParmSet_(0),
+  debug_(d),
+  free_parmset_mem_(false)
+{}
+
 /** DESTRUCTOR */
 Creator::~Creator() {
   if (mainParmSet_ != 0 && free_parmset_mem_)
@@ -162,17 +169,18 @@ int Creator::getTemplates(ArgList& argIn, DataSetList const& DSL) {
     }
   }
   if (!Templates_.empty()) {
-    mprintf("\t%zu residue templates found:", Templates_.size());
-    for (Carray::const_iterator it = Templates_.begin(); it != Templates_.end(); ++it) {
-      mprintf(" %s", (*it)->legend());
-      AssociatedData* ad = (*it)->GetAssociatedData( AssociatedData::RESID );
-      if (ad != 0) {
-        AssociatedData_ResId const& resid = static_cast<AssociatedData_ResId const&>( *ad );
-        resid.Ainfo();
+    mprintf("\t%zu residue templates found:\n", Templates_.size());
+    if (debug_ > 0) {
+      for (Carray::const_iterator it = Templates_.begin(); it != Templates_.end(); ++it) {
+        mprintf("\t%s", (*it)->legend());
+        AssociatedData* ad = (*it)->GetAssociatedData( AssociatedData::RESID );
+        if (ad != 0) {
+          AssociatedData_ResId const& resid = static_cast<AssociatedData_ResId const&>( *ad );
+          resid.Ainfo();
+        }
+        mprintf("\n");
       }
-      mprintf("\n");
     }
-    //mprintf("\n");
   }
 
   return 0;
diff --git a/src/Structure/Creator.h b/src/Structure/Creator.h
index dc42ed2505..21d4e7c61d 100644
--- a/src/Structure/Creator.h
+++ b/src/Structure/Creator.h
@@ -18,6 +18,8 @@ class Creator {
   public:
     /// CONSTRUCTOR
     Creator();
+    /// CONSTRUCTOR - debug level
+    Creator(int);
     /// DESTRUCTOR
     ~Creator();
     /// Associated parameter keywords for InitCreator

From 8a90b839bc66cb2d32b9f985f4dd35eb96f51e92 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 1 Mar 2024 08:43:57 -0500
Subject: [PATCH 0643/1492] Recognize CMAP section

---
 src/AmberParamFile.cpp | 1 +
 src/AmberParamFile.h   | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 4bc932debd..499061f53b 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -442,6 +442,7 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int deb
       else if (line.compare(0, 4, "DIHE") == 0) section = DIHEDRAL;
       else if (line.compare(0, 4, "IMPR") == 0) section = IMPROPER;
       else if (line.compare(0, 4, "HBON") == 0) section = LJ1012;
+      else if (line.compare(0, 4, "CMAP") == 0) section = CMAP;
       else if (line.compare(0, 6, "LJEDIT") == 0) {
         section = LJEDIT;
         prm.SetHasLJparams( true );
diff --git a/src/AmberParamFile.h b/src/AmberParamFile.h
index c88de68cfc..1cdbbb5368 100644
--- a/src/AmberParamFile.h
+++ b/src/AmberParamFile.h
@@ -21,7 +21,7 @@ class AmberParamFile {
     static const int MAXSYMLEN;
 
     enum SectionType { ATYPE = 0, HYDROPHILIC, BOND, ANGLE, DIHEDRAL, IMPROPER, 
-                       LJ1012, NB_EQUIV, NONBOND, LJEDIT, UNKNOWN };
+                       LJ1012, NB_EQUIV, NONBOND, LJEDIT, CMAP, UNKNOWN };
 
     class NonbondSet;
     class OffdiagNB;

From 52ee85d0c15e82cc7b66c4ade0ef46c42630db97 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 1 Mar 2024 09:04:28 -0500
Subject: [PATCH 0644/1492] Start CMAP section read

---
 src/AmberParamFile.cpp | 27 +++++++++++++++++++++++++++
 src/AmberParamFile.h   |  3 +++
 2 files changed, 30 insertions(+)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 499061f53b..c5d44c2c73 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -359,6 +359,30 @@ const
   return 0;
 }
 
+/** Read CMAP section */
+int AmberParamFile::read_cmap(CmapType& currentCmapFlag, std::string const& line) const {
+  //if (ptr[0] == '%' && ptr[1] == 'F' && ptr[2] == 'L' &&
+  //    ptr[3] == 'A' && ptr[4] == 'G')
+  ArgList argline(line);
+  if (argline.Nargs() > 1)
+  {
+    if (argline[0] == "%FLAG") {
+      if (argline[1] == "CMAP_COUNT") {
+        int cmapcount = argline.getKeyInt("CMAP_COUNT", -1);
+        mprintf("DEBUG: Cmap count: %i\n", cmapcount);
+      } else if (argline[1] == "CMAP_TITLE")
+        currentCmapFlag = CMAP_TITLE;
+      else if (argline[1] == "CMAP_RESLIST")
+        currentCmapFlag = CMAP_RESLIST;
+      else if (argline[1] == "CMAP_RESOLUTION") {
+        int cmapres = argline.getKeyInt("CMAP_RESOLUTION", -1);
+        mprintf("DEBUG: Cmap res: %i\n", cmapres);
+      } else if (argline[1] == "CMAP_PARAMETER")
+        currentCmapFlag = CMAP_PARAMETER;
+    }
+  }
+  return 0;
+}
 
 /** Assign nonbond parameters from a NonbondSet to ParameterSet */
 int AmberParamFile::assign_nb(ParameterSet& prm, NonbondSet const& nbset) const {
@@ -428,6 +452,7 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int deb
   Oarray Offdiag;
   // Read file
   SectionType section = UNKNOWN;
+  CmapType currentCmapFlag = CMAP_INITIAL;
   ptr = infile.Line();
   while (ptr != 0) {
     bool first_char_is_space = (*ptr == ' ');
@@ -469,6 +494,8 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int deb
           err = read_nb_RE(nbset, ptr);
         else if (section == LJEDIT)
           err = read_ljedit(Offdiag, ptr);
+        else if (section == CMAP)
+          err = read_cmap(currentCmapFlag, line);
         if (err != 0) {
           mprinterr("Error: Reading line: %s\n", ptr);
           return 1;
diff --git a/src/AmberParamFile.h b/src/AmberParamFile.h
index 1cdbbb5368..8bebed1c58 100644
--- a/src/AmberParamFile.h
+++ b/src/AmberParamFile.h
@@ -22,6 +22,7 @@ class AmberParamFile {
 
     enum SectionType { ATYPE = 0, HYDROPHILIC, BOND, ANGLE, DIHEDRAL, IMPROPER, 
                        LJ1012, NB_EQUIV, NONBOND, LJEDIT, CMAP, UNKNOWN };
+    enum CmapType { CMAP_INITIAL, CMAP_TITLE, CMAP_RESLIST, CMAP_PARAMETER };
 
     class NonbondSet;
     class OffdiagNB;
@@ -44,6 +45,8 @@ class AmberParamFile {
     int read_nb_RE(NonbondSet&, const char*) const;
     /// Read LJ 6-12 off-diagonal modifications
     int read_ljedit(Oarray&, const char*) const;
+    /// Read CMAP section
+    int read_cmap(CmapType&, std::string const&) const;
     /// Assign parameters from NonbondSet to ParameterSet
     int assign_nb(ParameterSet&, NonbondSet const&) const;
     /// Assign parameters from OffdiagNB array to ParameterSet

From 9d2585768e296bc45387466e866e62f678291c4f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 1 Mar 2024 09:23:24 -0500
Subject: [PATCH 0645/1492] Add CMAP to ParameterSet

---
 src/ParameterSet.cpp | 4 ++++
 src/ParameterSet.h   | 9 +++++++--
 src/ParameterTypes.h | 1 +
 3 files changed, 12 insertions(+), 2 deletions(-)

diff --git a/src/ParameterSet.cpp b/src/ParameterSet.cpp
index 147f9dbcbe..9db0f705e2 100644
--- a/src/ParameterSet.cpp
+++ b/src/ParameterSet.cpp
@@ -5,6 +5,9 @@
 #include "UpdateParameters.h"
 
 size_t ParameterSet::DataSize() const {
+  unsigned int cmapsize = 0;
+  for (CmapGridArray::const_iterator it = CMAP_.begin(); it != CMAP_.end(); ++it)
+    cmapsize += it->DataSize();
   return (atomTypes_.DataSize() +
           bondParm_.DataSize() +
           angleParm_.DataSize() +
@@ -12,6 +15,7 @@ size_t ParameterSet::DataSize() const {
           dihParm_.DataSize() +
           impParm_.DataSize() +
           HBparm_.DataSize() +
+          cmapsize +
           (hydrophilicAtomTypes_.size() * NameType::DataSize()));
 }
 
diff --git a/src/ParameterSet.h b/src/ParameterSet.h
index 422ce2b345..6152657e70 100644
--- a/src/ParameterSet.h
+++ b/src/ParameterSet.h
@@ -18,6 +18,7 @@ class ParameterSet {
     ImproperParmHolder& IP()           { return impParm_;   }
     DihedralParmHolder& DP()           { return dihParm_;   }
     ParmHolder<HB_ParmType>& HB()      { return HBparm_;    }
+    CmapGridArray& CMAP()              { return CMAP_;      }
 
     void SetHasLJparams(bool b) { hasLJparams_ = b; }
     bool HasLJparams() const { return hasLJparams_; }
@@ -31,8 +32,10 @@ class ParameterSet {
     ImproperParmHolder const& IP()           const { return impParm_;   }
     DihedralParmHolder const& DP()           const { return dihParm_;   }
     ParmHolder<HB_ParmType> const& HB()      const { return HBparm_;    }
+    CmapGridArray const& CMAP()              const { return CMAP_;      }
     std::string const& NbParamName()         const { return NBname_;    }
-    std::string ParamSetName()               const;
+    /// \return Parameter set names as a single line
+    std::string ParamSetName()        const;
     /// Write parameters to file with given name
     void Debug(const char*) const;
     /// Write parameters to stdout
@@ -49,7 +52,7 @@ class ParameterSet {
                         nDihedralsUpdated_(0), nImpropersUpdated_(0),
                         nUreyBradleyUpdated_(0), nAtomTypeUpdated_(0),
                         nLJparamsUpdated_(0), nLJ14paramsUpdated_(0),
-                        nHBparamsUpdated_(0) {}
+                        nHBparamsUpdated_(0), nCmapUpdated_(0) {}
         unsigned int nBondsUpdated_;
         unsigned int nAnglesUpdated_;
         unsigned int nDihedralsUpdated_;
@@ -59,6 +62,7 @@ class ParameterSet {
         unsigned int nLJparamsUpdated_;
         unsigned int nLJ14paramsUpdated_;
         unsigned int nHBparamsUpdated_;
+        unsigned int nCmapUpdated_;
     };
     /// Update this set with parameters from given set
     int UpdateParamSet(ParameterSet const&, UpdateCount&, int, int);
@@ -86,6 +90,7 @@ class ParameterSet {
     ImproperParmHolder impParm_;           ///< Improper dihedral parameters
     DihedralParmHolder dihParm_;           ///< Cosine-series dihedral parameters
     ParmHolder<HB_ParmType> HBparm_;       ///< LJ 10-12 A-B parameters for hydrogen bonds
+    CmapGridArray CMAP_;                   ///< CMAP parameters; unlike others, not indexed by atom type
     NsetType hydrophilicAtomTypes_;        ///< Hold names of hydrophilic atom types
     bool hasLJparams_;
 };
diff --git a/src/ParameterTypes.h b/src/ParameterTypes.h
index 12ace1b869..ca339fa88a 100644
--- a/src/ParameterTypes.h
+++ b/src/ParameterTypes.h
@@ -718,6 +718,7 @@ class CmapGridType {
     inline std::vector<double> const& Grid() const { return grid_;             }
     inline int Size()                        const { return (int)grid_.size(); }
     void SetGridPt(int idx, double d)              { grid_[idx] = d;           }
+    unsigned int DataSize()                  const { return (sizeof(int) + (grid_.size()*sizeof(double))); }
   private:
     int resolution_;           ///< Number of steps along each phi/psi CMAP axis
     std::vector<double> grid_; ///< CMAP grid (size is resolution_*resolution_)

From cc6274a3f07f13bf20705adac33da9f17abdee16 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 1 Mar 2024 10:11:40 -0500
Subject: [PATCH 0646/1492] Finish reading in cmap grids, do some error
 checking

---
 src/AmberParamFile.cpp | 47 ++++++++++++++++++++++++++++++++++++------
 src/AmberParamFile.h   |  2 +-
 src/ParameterTypes.h   | 28 +++++++++++++++++++------
 src/Parm_Amber.cpp     |  2 +-
 4 files changed, 65 insertions(+), 14 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index c5d44c2c73..be4e626b62 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -360,25 +360,60 @@ const
 }
 
 /** Read CMAP section */
-int AmberParamFile::read_cmap(CmapType& currentCmapFlag, std::string const& line) const {
+int AmberParamFile::read_cmap(ParameterSet& prm, CmapType& currentCmapFlag, std::string const& line) const {
   //if (ptr[0] == '%' && ptr[1] == 'F' && ptr[2] == 'L' &&
   //    ptr[3] == 'A' && ptr[4] == 'G')
+  int currentCmapIdx;
+  if (prm.CMAP().empty())
+    currentCmapIdx = -1;
+  else
+    currentCmapIdx = prm.CMAP().size() - 1;
   ArgList argline(line);
   if (argline.Nargs() > 1)
   {
     if (argline[0] == "%FLAG") {
       if (argline[1] == "CMAP_COUNT") {
+        // New CMAP term. Ignore the index for now. If a previous CMAP
+        // was read make sure its OK.
+        if (currentCmapIdx > -1) {
+          if (!prm.CMAP()[currentCmapIdx].CmapIsValid()) {
+            mprinterr("Error: Previous CMAP term is not valid.\n");
+            return 1;
+          }
+        }
         int cmapcount = argline.getKeyInt("CMAP_COUNT", -1);
         mprintf("DEBUG: Cmap count: %i\n", cmapcount);
-      } else if (argline[1] == "CMAP_TITLE")
+        prm.CMAP().push_back( CmapGridType() );
+        if ( cmapcount != (int)prm.CMAP().size() )
+          mprintf("Warning: CMAP term is not in numerical order. CMAP_COUNT %i, expected %zu\n",
+                  cmapcount, prm.CMAP().size());
+        return 0;
+      } else if (argline[1] == "CMAP_TITLE") {
         currentCmapFlag = CMAP_TITLE;
-      else if (argline[1] == "CMAP_RESLIST")
+        return 0;
+      } else if (argline[1] == "CMAP_RESLIST") {
         currentCmapFlag = CMAP_RESLIST;
-      else if (argline[1] == "CMAP_RESOLUTION") {
+        return 0;
+      } else if (argline[1] == "CMAP_RESOLUTION") {
         int cmapres = argline.getKeyInt("CMAP_RESOLUTION", -1);
         mprintf("DEBUG: Cmap res: %i\n", cmapres);
-      } else if (argline[1] == "CMAP_PARAMETER")
+        prm.CMAP()[currentCmapIdx].SetResolution( cmapres );
+        return 0;
+      } else if (argline[1] == "CMAP_PARAMETER") {
         currentCmapFlag = CMAP_PARAMETER;
+        return 0;
+      }
+    }
+  }
+
+  if (currentCmapFlag == CMAP_PARAMETER) {
+    double terms[8];
+    int nterms = sscanf(line.c_str(), "%lf %lf %lf %lf %lf %lf %lf %lf",
+                        terms, terms+1, terms+2, terms+3,
+                        terms+4, terms+5, terms+6, terms+7);
+    for (int i = 0; i != nterms; i++) {
+      //mprintf("DEBUG: cmap term %f\n", terms[i] );
+      prm.CMAP()[currentCmapIdx].AddToGrid( terms[i] );
     }
   }
   return 0;
@@ -495,7 +530,7 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int deb
         else if (section == LJEDIT)
           err = read_ljedit(Offdiag, ptr);
         else if (section == CMAP)
-          err = read_cmap(currentCmapFlag, line);
+          err = read_cmap(prm, currentCmapFlag, line);
         if (err != 0) {
           mprinterr("Error: Reading line: %s\n", ptr);
           return 1;
diff --git a/src/AmberParamFile.h b/src/AmberParamFile.h
index 8bebed1c58..820822e973 100644
--- a/src/AmberParamFile.h
+++ b/src/AmberParamFile.h
@@ -46,7 +46,7 @@ class AmberParamFile {
     /// Read LJ 6-12 off-diagonal modifications
     int read_ljedit(Oarray&, const char*) const;
     /// Read CMAP section
-    int read_cmap(CmapType&, std::string const&) const;
+    int read_cmap(ParameterSet&, CmapType&, std::string const&) const;
     /// Assign parameters from NonbondSet to ParameterSet
     int assign_nb(ParameterSet&, NonbondSet const&) const;
     /// Assign parameters from OffdiagNB array to ParameterSet
diff --git a/src/ParameterTypes.h b/src/ParameterTypes.h
index ca339fa88a..524b32cc88 100644
--- a/src/ParameterTypes.h
+++ b/src/ParameterTypes.h
@@ -713,14 +713,30 @@ class CapParmType {
 class CmapGridType {
   public:
     CmapGridType() : resolution_(0) {}
-    CmapGridType(unsigned int r) : resolution_(r), grid_((size_t)r*(size_t)r, 0.0) {}
-    inline int Resolution()                  const { return resolution_;       }
-    inline std::vector<double> const& Grid() const { return grid_;             }
-    inline int Size()                        const { return (int)grid_.size(); }
+    CmapGridType(unsigned int r) : resolution_(r), grid_(r*r, 0.0) {}
+    unsigned int Resolution()                const { return resolution_;       }
+    std::vector<double> const& Grid()        const { return grid_;             }
+    /// \return Grid size as integer, used for topology write
+    int Size()                               const { return (int)grid_.size(); }
+    unsigned int DataSize()                  const { return (sizeof(unsigned int) + (grid_.size()*sizeof(double))); }
+    /// Set specified grid point
     void SetGridPt(int idx, double d)              { grid_[idx] = d;           }
-    unsigned int DataSize()                  const { return (sizeof(int) + (grid_.size()*sizeof(double))); }
+    /// Prepare grid for given resolution
+    void SetResolution(unsigned int r) {
+      grid_.clear();
+      grid_.reserve( r*r );
+      resolution_ = r;
+    }
+    /// Add value to the grid
+    void AddToGrid(double d) { grid_.push_back( d ); }
+    /// \return True if the CMAP is valid
+    bool CmapIsValid() const {
+      if (resolution_*resolution_ != grid_.size())
+        return false;
+      return true;
+    }
   private:
-    int resolution_;           ///< Number of steps along each phi/psi CMAP axis
+    unsigned int resolution_;  ///< Number of steps along each phi/psi CMAP axis
     std::vector<double> grid_; ///< CMAP grid (size is resolution_*resolution_)
 };
 typedef std::vector<CmapGridType> CmapGridArray;
diff --git a/src/Parm_Amber.cpp b/src/Parm_Amber.cpp
index 8f3b207083..4a27de153c 100644
--- a/src/Parm_Amber.cpp
+++ b/src/Parm_Amber.cpp
@@ -2229,7 +2229,7 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
     if (BufferAlloc(f_grid_res, TopOut.CmapGrid().size())) return 1;
     for (CmapGridArray::const_iterator grid = TopOut.CmapGrid().begin();
                                        grid != TopOut.CmapGrid().end(); ++grid)
-      file_.IntToBuffer( grid->Resolution() );
+      file_.IntToBuffer( (int)grid->Resolution() );
     file_.FlushBuffer();
     // CMAP GRIDS
     int ngrid = 1;

From 20a5ae7e15388d4effee9f2ef7ebc7f773c1892e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 1 Mar 2024 11:13:25 -0500
Subject: [PATCH 0647/1492] Read cmap title and residue names

---
 src/AmberParamFile.cpp | 25 +++++++++++++++++++++++++
 src/ParameterTypes.h   | 28 ++++++++++++++++++++++++++--
 2 files changed, 51 insertions(+), 2 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index be4e626b62..fe401c3f61 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -380,6 +380,12 @@ int AmberParamFile::read_cmap(ParameterSet& prm, CmapType& currentCmapFlag, std:
             mprinterr("Error: Previous CMAP term is not valid.\n");
             return 1;
           }
+          if (!prm.CMAP()[currentCmapIdx].CmapNresIsValid()) {
+            mprintf("Warning: # expected CMAP %i residue names %i not equal to actual number %zu\n",
+                    currentCmapIdx+1,
+                    prm.CMAP()[currentCmapIdx].NcmapResNames(),
+                    prm.CMAP()[currentCmapIdx].ResNames().size());
+          }
         }
         int cmapcount = argline.getKeyInt("CMAP_COUNT", -1);
         mprintf("DEBUG: Cmap count: %i\n", cmapcount);
@@ -393,10 +399,20 @@ int AmberParamFile::read_cmap(ParameterSet& prm, CmapType& currentCmapFlag, std:
         return 0;
       } else if (argline[1] == "CMAP_RESLIST") {
         currentCmapFlag = CMAP_RESLIST;
+        int nres = argline.getKeyInt("CMAP_RESLIST", -1);
+        if (nres < 1) {
+          mprinterr("Error: Bad CMAP # residues: %s\n", line.c_str());
+          return 1;
+        }
+        prm.CMAP()[currentCmapIdx].SetNumCmapRes( nres );
         return 0;
       } else if (argline[1] == "CMAP_RESOLUTION") {
         int cmapres = argline.getKeyInt("CMAP_RESOLUTION", -1);
         mprintf("DEBUG: Cmap res: %i\n", cmapres);
+        if (cmapres < 1) {
+          mprinterr("Error: Bad CMAP resolution: %s\n", line.c_str());
+          return 1;
+        }
         prm.CMAP()[currentCmapIdx].SetResolution( cmapres );
         return 0;
       } else if (argline[1] == "CMAP_PARAMETER") {
@@ -415,6 +431,15 @@ int AmberParamFile::read_cmap(ParameterSet& prm, CmapType& currentCmapFlag, std:
       //mprintf("DEBUG: cmap term %f\n", terms[i] );
       prm.CMAP()[currentCmapIdx].AddToGrid( terms[i] );
     }
+  } else if (currentCmapFlag == CMAP_RESLIST) {
+    ArgList resnames( line );
+    std::string rn = resnames.GetStringNext();
+    while (!rn.empty()) {
+      prm.CMAP()[currentCmapIdx].AddResName( rn );
+      rn = resnames.GetStringNext();
+    }
+  } else if (currentCmapFlag == CMAP_TITLE) {
+    prm.CMAP()[currentCmapIdx].SetTitle( line );
   }
   return 0;
 }
diff --git a/src/ParameterTypes.h b/src/ParameterTypes.h
index 524b32cc88..a78510b680 100644
--- a/src/ParameterTypes.h
+++ b/src/ParameterTypes.h
@@ -712,12 +712,17 @@ class CapParmType {
 /// Hold CMAP grid parameters
 class CmapGridType {
   public:
-    CmapGridType() : resolution_(0) {}
-    CmapGridType(unsigned int r) : resolution_(r), grid_(r*r, 0.0) {}
+    CmapGridType() : nCmapRes_(0), resolution_(0) {}
+    CmapGridType(unsigned int r) : nCmapRes_(0), resolution_(r), grid_(r*r, 0.0) {}
     unsigned int Resolution()                const { return resolution_;       }
     std::vector<double> const& Grid()        const { return grid_;             }
+    /// \return array of residue names this CMAP applies to
+    std::vector<std::string> ResNames()      const { return resNames_; }
+    /// \return Expected number of CMAP residue names
+    int NcmapResNames()                      const { return nCmapRes_; }
     /// \return Grid size as integer, used for topology write
     int Size()                               const { return (int)grid_.size(); }
+    /// Size of the CMAP grid in bytes
     unsigned int DataSize()                  const { return (sizeof(unsigned int) + (grid_.size()*sizeof(double))); }
     /// Set specified grid point
     void SetGridPt(int idx, double d)              { grid_[idx] = d;           }
@@ -729,15 +734,34 @@ class CmapGridType {
     }
     /// Add value to the grid
     void AddToGrid(double d) { grid_.push_back( d ); }
+    /// Set CMAP title
+    void SetTitle(std::string const& t) { title_ = t; }
+    /// Number of residues this CMAP will be applied to
+    void SetNumCmapRes(int n) {
+      resNames_.clear();
+      resNames_.reserve( n );
+      nCmapRes_ = n;
+    }
+    /// Add residue name this CMAP will apply to
+    void AddResName(std::string const& n) { resNames_.push_back( n ); }
     /// \return True if the CMAP is valid
     bool CmapIsValid() const {
       if (resolution_*resolution_ != grid_.size())
         return false;
       return true;
     }
+    /// \return True if CMAP # res names matches expected.
+    bool CmapNresIsValid() const {
+      if (nCmapRes_ != (int)resNames_.size())
+        return false;
+      return true;
+    }
   private:
+    int nCmapRes_;             ///< Number of expected residues this CMAP will apply to
     unsigned int resolution_;  ///< Number of steps along each phi/psi CMAP axis
     std::vector<double> grid_; ///< CMAP grid (size is resolution_*resolution_)
+    std::string title_;        ///< CMAP title (from parameter file)
+    std::vector<std::string> resNames_; ///< Residue names this CMAP will apply to
 };
 typedef std::vector<CmapGridType> CmapGridArray;
 /// Hold CMAP atom indices and corresponding grid index

From 25744a75e89512593d3adb246c4478b715e66bb0 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 1 Mar 2024 11:49:03 -0500
Subject: [PATCH 0648/1492] Add more check for valid cmap. Change printed debug
 info

---
 src/AmberParamFile.cpp | 39 +++++++++++++++++++++++++++------------
 src/ParameterTypes.h   |  4 +++-
 2 files changed, 30 insertions(+), 13 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index fe401c3f61..eb3d8ac7e2 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -359,6 +359,26 @@ const
   return 0;
 }
 
+static inline int check_cmap(int currentCmapIdx, CmapGridType const& cmap) {
+  mprintf("DEBUG: Cmap %i '%s' (gridSize= %i) %zu res:",
+          currentCmapIdx, cmap.Title().c_str(), cmap.Size(), cmap.ResNames().size());
+  for (std::vector<std::string>::const_iterator it = cmap.ResNames().begin();
+                                                it != cmap.ResNames().end(); ++it)
+    mprintf(" %s", it->c_str());
+  mprintf("\n");
+  if (!cmap.CmapIsValid()) {
+    mprinterr("Error: Previous CMAP term is not valid.\n");
+    return 1;
+  }
+  if (!cmap.CmapNresIsValid()) {
+    mprintf("Warning: # expected CMAP %i residue names %i not equal to actual number %zu\n",
+            currentCmapIdx,
+            cmap.NcmapResNames(),
+            cmap.ResNames().size());
+  }
+  return 0;
+}
+
 /** Read CMAP section */
 int AmberParamFile::read_cmap(ParameterSet& prm, CmapType& currentCmapFlag, std::string const& line) const {
   //if (ptr[0] == '%' && ptr[1] == 'F' && ptr[2] == 'L' &&
@@ -376,19 +396,10 @@ int AmberParamFile::read_cmap(ParameterSet& prm, CmapType& currentCmapFlag, std:
         // New CMAP term. Ignore the index for now. If a previous CMAP
         // was read make sure its OK.
         if (currentCmapIdx > -1) {
-          if (!prm.CMAP()[currentCmapIdx].CmapIsValid()) {
-            mprinterr("Error: Previous CMAP term is not valid.\n");
-            return 1;
-          }
-          if (!prm.CMAP()[currentCmapIdx].CmapNresIsValid()) {
-            mprintf("Warning: # expected CMAP %i residue names %i not equal to actual number %zu\n",
-                    currentCmapIdx+1,
-                    prm.CMAP()[currentCmapIdx].NcmapResNames(),
-                    prm.CMAP()[currentCmapIdx].ResNames().size());
-          }
+          if (check_cmap(currentCmapIdx+1, prm.CMAP()[currentCmapIdx])) return 1;
         }
         int cmapcount = argline.getKeyInt("CMAP_COUNT", -1);
-        mprintf("DEBUG: Cmap count: %i\n", cmapcount);
+        //mprintf("DEBUG: Cmap count: %i\n", cmapcount);
         prm.CMAP().push_back( CmapGridType() );
         if ( cmapcount != (int)prm.CMAP().size() )
           mprintf("Warning: CMAP term is not in numerical order. CMAP_COUNT %i, expected %zu\n",
@@ -408,7 +419,7 @@ int AmberParamFile::read_cmap(ParameterSet& prm, CmapType& currentCmapFlag, std:
         return 0;
       } else if (argline[1] == "CMAP_RESOLUTION") {
         int cmapres = argline.getKeyInt("CMAP_RESOLUTION", -1);
-        mprintf("DEBUG: Cmap res: %i\n", cmapres);
+        //mprintf("DEBUG: Cmap res: %i\n", cmapres);
         if (cmapres < 1) {
           mprinterr("Error: Bad CMAP resolution: %s\n", line.c_str());
           return 1;
@@ -564,6 +575,10 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int deb
     }
     ptr = infile.Line();
   }
+  // Check last cmap
+  if (!prm.CMAP().empty()) {
+    if (check_cmap(prm.CMAP().size(), prm.CMAP().back())) return 1;
+  }
   // Nonbonds
   if (assign_nb(prm, nbset)) return 1;
   // Off-diagonal NB modifications
diff --git a/src/ParameterTypes.h b/src/ParameterTypes.h
index a78510b680..26352352db 100644
--- a/src/ParameterTypes.h
+++ b/src/ParameterTypes.h
@@ -717,11 +717,13 @@ class CmapGridType {
     unsigned int Resolution()                const { return resolution_;       }
     std::vector<double> const& Grid()        const { return grid_;             }
     /// \return array of residue names this CMAP applies to
-    std::vector<std::string> ResNames()      const { return resNames_; }
+    std::vector<std::string> const& ResNames() const { return resNames_; }
     /// \return Expected number of CMAP residue names
     int NcmapResNames()                      const { return nCmapRes_; }
     /// \return Grid size as integer, used for topology write
     int Size()                               const { return (int)grid_.size(); }
+    /// \return CMAP title
+    std::string const& Title()               const { return title_; }
     /// Size of the CMAP grid in bytes
     unsigned int DataSize()                  const { return (sizeof(unsigned int) + (grid_.size()*sizeof(double))); }
     /// Set specified grid point

From 9a5b6a8397c7030cf5acbaf70fb2935e132de88b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 2 Mar 2024 08:11:54 -0500
Subject: [PATCH 0649/1492] Add to print

---
 src/ParameterSet.cpp | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/src/ParameterSet.cpp b/src/ParameterSet.cpp
index 9db0f705e2..c6bef667f3 100644
--- a/src/ParameterSet.cpp
+++ b/src/ParameterSet.cpp
@@ -42,6 +42,7 @@ void ParameterSet::Summary() const {
   mprintf("\t  %zu UB parameters.\n", ubParm_.size());
   mprintf("\t  %zu dihedral parameters.\n", dihParm_.size());
   mprintf("\t  %zu improper parameters.\n", impParm_.size());
+  mprintf("\t  %zu CMAP parameters.\n", CMAP_.size());
 }
 
 /** Write parameters out to given file. */
@@ -113,6 +114,17 @@ void ParameterSet::Print(CpptrajFile& Out) const {
       Out.Printf(" %s", it->Truncated().c_str());
     Out.Printf("\n");
   }
+  if (!CMAP_.empty()) {
+    Out.Printf("CMAP parameters:\n");
+    for (CmapGridArray::const_iterator it = CMAP_.begin(); it != CMAP_.end(); ++it) {
+      Out.Printf("\tCMAP %li '%s' (resolution %u) residues:",
+              it - CMAP_.begin(), it->Title().c_str(), it->Resolution());
+      for (std::vector<std::string>::const_iterator rn = it->ResNames().begin();
+                                                    rn != it->ResNames().end(); ++rn)
+        Out.Printf(" %s", rn->c_str());
+      Out.Printf("\n");
+    }
+  }
 }
 
 /** Update/add to parameters in this topology with those from given set. */

From 9adfb2c9f3010d8bb0d89d374f6b7573bef3d5f9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 2 Mar 2024 08:20:43 -0500
Subject: [PATCH 0650/1492] Print the grid

---
 src/ParameterSet.cpp | 17 ++++++++++++++++-
 1 file changed, 16 insertions(+), 1 deletion(-)

diff --git a/src/ParameterSet.cpp b/src/ParameterSet.cpp
index c6bef667f3..3db76fcad6 100644
--- a/src/ParameterSet.cpp
+++ b/src/ParameterSet.cpp
@@ -118,11 +118,26 @@ void ParameterSet::Print(CpptrajFile& Out) const {
     Out.Printf("CMAP parameters:\n");
     for (CmapGridArray::const_iterator it = CMAP_.begin(); it != CMAP_.end(); ++it) {
       Out.Printf("\tCMAP %li '%s' (resolution %u) residues:",
-              it - CMAP_.begin(), it->Title().c_str(), it->Resolution());
+              it - CMAP_.begin() + 1, it->Title().c_str(), it->Resolution());
       for (std::vector<std::string>::const_iterator rn = it->ResNames().begin();
                                                     rn != it->ResNames().end(); ++rn)
         Out.Printf(" %s", rn->c_str());
       Out.Printf("\n");
+      int col = 0;
+      for (std::vector<double>::const_iterator gp = it->Grid().begin();
+                                               gp != it->Grid().end(); ++gp)
+      {
+        if (col == 0)
+          Out.Printf("%9.5f", *gp);
+        else
+          Out.Printf(" %9.5f", *gp);
+        col++;
+        if (col == 8) {
+          Out.Printf("\n");
+          col = 0;
+        }
+      }
+      if (col != 0) Out.Printf("\n");
     }
   }
 }

From ebc1ea6f6ed3971bfc1259c41781868956cb8bbc Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 2 Mar 2024 09:00:33 -0500
Subject: [PATCH 0651/1492] Start adding CMAP term update, but may need a
 separate class.

---
 src/ParameterSet.cpp | 54 ++++++++++++++++++++++++++++++++++++++++++++
 src/ParameterSet.h   |  3 +++
 2 files changed, 57 insertions(+)

diff --git a/src/ParameterSet.cpp b/src/ParameterSet.cpp
index 3db76fcad6..8cd936e1ad 100644
--- a/src/ParameterSet.cpp
+++ b/src/ParameterSet.cpp
@@ -142,6 +142,58 @@ void ParameterSet::Print(CpptrajFile& Out) const {
   }
 }
 
+/** Update/add to CMAP parameters.
+  * CMAP terms are different in that they are applied via residue name instead
+  * of atom type, hence the separate routine.
+  * \return The number of CMAP terms updated.
+  */
+int ParameterSet::updateCmapTerms(ParameterSet const& set1, int debugIn, int verbose) {
+  typedef std::vector<std::string> Sarray;
+  enum ResMatchType { NO_MATCH = 0, FULL_MATCH, PARTIAL_MATCH };
+  // Loop over the incoming CMAPs
+  for (CmapGridArray::const_iterator it = set1.CMAP().begin(); it != set1.CMAP().end(); ++it)
+  {
+    // Does a CMAP for any of the residues exist?
+    ResMatchType mtype = NO_MATCH;
+    CmapGridArray::iterator currentCmap = CMAP_.end();
+    for (CmapGridArray::iterator jt = CMAP_.begin(); jt != CMAP_.end(); ++jt)
+    {
+      int nMatch = 0;
+      for (Sarray::const_iterator rni = it->ResNames().begin(); rni != it->ResNames().end(); ++rni)
+      {
+        for (Sarray::const_iterator rnj = jt->ResNames().begin(); rnj != jt->ResNames().end(); ++rnj)
+        {
+          if (*rni == *rnj) {
+            nMatch++;
+            break;
+          }
+        } // END loop over cmap j res names
+      } // END loop over cmap i res names
+      if (nMatch == (int)jt->ResNames().size()) {
+        mtype = FULL_MATCH;
+        currentCmap = jt;
+        break;
+      } else if (nMatch > 0) {
+        mtype = PARTIAL_MATCH;
+        currentCmap = jt;
+        break;
+      }
+    } // END loop over existing CMAP terms
+    if (mtype == PARTIAL_MATCH) {
+      mprinterr("Internal Error: Partial match between new CMAP '%s' and existing CMAP '%s'\n"
+                "Internal Error:   Not yet set up to handle this kind of parameter update.\n",
+                it->Title().c_str(), currentCmap->Title().c_str());
+      return -1;
+    } else if (mtype == FULL_MATCH) {
+      mprintf("DEBUG: Match between new CMAP '%s' and existing CMAP '%s'\n",
+              it->Title().c_str(), currentCmap->Title().c_str());
+    } else if (mtype == NO_MATCH) {
+      mprintf("DEBUG: CMAP '%s' is a new CMAP.\n", it->Title().c_str());
+    }
+  } // END loop over new CMAP terms
+  return 0;
+}
+
 /** Update/add to parameters in this topology with those from given set. */
 int ParameterSet::UpdateParamSet(ParameterSet const& set1, UpdateCount& uc, int debugIn, int verbose) {
   ParameterSet& set0 = *this;
@@ -170,6 +222,8 @@ int ParameterSet::UpdateParamSet(ParameterSet const& set1, UpdateCount& uc, int
   uc.nLJ14paramsUpdated_ = UpdateParameters< ParmHolder<NonbondType> >(set0.NB14(), set1.NB14(), "LJ A-B 1-4", verbose);
   // HB LJ 10-12 Pairs
   uc.nHBparamsUpdated_ = UpdateParameters< ParmHolder<HB_ParmType> >(set0.HB(), set1.HB(), "LJ HB 10-12", verbose);
+  // CMAP
+  uc.nCmapUpdated_ = updateCmapTerms(set1, debugIn, verbose);
 
   if (debugIn > 0) set0.Debug("newp.dat");
   return 0;
diff --git a/src/ParameterSet.h b/src/ParameterSet.h
index 6152657e70..6cf8dbbed9 100644
--- a/src/ParameterSet.h
+++ b/src/ParameterSet.h
@@ -78,6 +78,9 @@ class ParameterSet {
     typedef std::vector<NameType> NsetType;
     typedef std::vector<std::string> Sarray;
 
+    /// Update CMAP terms
+    int updateCmapTerms(ParameterSet const&, int, int);
+
     Sarray name_;                          ///< Parameter set name(s)
     std::string NBname_;                   ///< Nonbond set name
 

From 2f1d0f301c46cb6a37144b7bfd600d7ccbc8f0fb Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 2 Mar 2024 09:09:40 -0500
Subject: [PATCH 0652/1492] Start CmapParmHolder

---
 src/Parm/CmapParmHolder.cpp |  7 +++++++
 src/Parm/CmapParmHolder.h   | 17 +++++++++++++++++
 2 files changed, 24 insertions(+)
 create mode 100644 src/Parm/CmapParmHolder.cpp
 create mode 100644 src/Parm/CmapParmHolder.h

diff --git a/src/Parm/CmapParmHolder.cpp b/src/Parm/CmapParmHolder.cpp
new file mode 100644
index 0000000000..895e0049bb
--- /dev/null
+++ b/src/Parm/CmapParmHolder.cpp
@@ -0,0 +1,7 @@
+#include "CmapParmHolder.h"
+#include "../ParameterTypes.h"
+
+using namespace Cpptraj::Parm;
+
+/** CONSTRUCTOR */
+CmapParmHolder::CmapParmHolder() {}
diff --git a/src/Parm/CmapParmHolder.h b/src/Parm/CmapParmHolder.h
new file mode 100644
index 0000000000..d4772fb3e6
--- /dev/null
+++ b/src/Parm/CmapParmHolder.h
@@ -0,0 +1,17 @@
+#ifndef INC_PARM_CMAPPARMHOLDER_H
+#define INC_PARM_CMAPPARMHOLDER_H
+class CmapGridType;
+#include <vector>
+namespace Cpptraj {
+namespace Parm {
+/// Hold CMAP terms
+class CmapParmHolder {
+  public:
+    CmapParmHolder();
+  private:
+    typedef std::vector<CmapGridType> Carray;
+    Carray CMAP_;
+};
+}
+}
+#endif

From 28a6c11df3092409e949225951cb8ac1e1f70806 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 2 Mar 2024 10:03:06 -0500
Subject: [PATCH 0653/1492] Start using the CmapParmHolder

---
 src/ParameterSet.cpp          |  54 +--
 src/ParameterSet.h            |  10 +-
 src/Parm/CMakeLists.txt       |   1 +
 src/Parm/CmapParmHolder.cpp   |  55 +++
 src/Parm/CmapParmHolder.h     |  21 +-
 src/Parm/parmdepend           |   3 +-
 src/Parm/parmfiles            |   1 +
 src/Structure/structuredepend |  26 +-
 src/cpptrajdepend             | 713 +++++++++++++++++-----------------
 9 files changed, 454 insertions(+), 430 deletions(-)

diff --git a/src/ParameterSet.cpp b/src/ParameterSet.cpp
index 8cd936e1ad..8f41bc4b29 100644
--- a/src/ParameterSet.cpp
+++ b/src/ParameterSet.cpp
@@ -142,58 +142,6 @@ void ParameterSet::Print(CpptrajFile& Out) const {
   }
 }
 
-/** Update/add to CMAP parameters.
-  * CMAP terms are different in that they are applied via residue name instead
-  * of atom type, hence the separate routine.
-  * \return The number of CMAP terms updated.
-  */
-int ParameterSet::updateCmapTerms(ParameterSet const& set1, int debugIn, int verbose) {
-  typedef std::vector<std::string> Sarray;
-  enum ResMatchType { NO_MATCH = 0, FULL_MATCH, PARTIAL_MATCH };
-  // Loop over the incoming CMAPs
-  for (CmapGridArray::const_iterator it = set1.CMAP().begin(); it != set1.CMAP().end(); ++it)
-  {
-    // Does a CMAP for any of the residues exist?
-    ResMatchType mtype = NO_MATCH;
-    CmapGridArray::iterator currentCmap = CMAP_.end();
-    for (CmapGridArray::iterator jt = CMAP_.begin(); jt != CMAP_.end(); ++jt)
-    {
-      int nMatch = 0;
-      for (Sarray::const_iterator rni = it->ResNames().begin(); rni != it->ResNames().end(); ++rni)
-      {
-        for (Sarray::const_iterator rnj = jt->ResNames().begin(); rnj != jt->ResNames().end(); ++rnj)
-        {
-          if (*rni == *rnj) {
-            nMatch++;
-            break;
-          }
-        } // END loop over cmap j res names
-      } // END loop over cmap i res names
-      if (nMatch == (int)jt->ResNames().size()) {
-        mtype = FULL_MATCH;
-        currentCmap = jt;
-        break;
-      } else if (nMatch > 0) {
-        mtype = PARTIAL_MATCH;
-        currentCmap = jt;
-        break;
-      }
-    } // END loop over existing CMAP terms
-    if (mtype == PARTIAL_MATCH) {
-      mprinterr("Internal Error: Partial match between new CMAP '%s' and existing CMAP '%s'\n"
-                "Internal Error:   Not yet set up to handle this kind of parameter update.\n",
-                it->Title().c_str(), currentCmap->Title().c_str());
-      return -1;
-    } else if (mtype == FULL_MATCH) {
-      mprintf("DEBUG: Match between new CMAP '%s' and existing CMAP '%s'\n",
-              it->Title().c_str(), currentCmap->Title().c_str());
-    } else if (mtype == NO_MATCH) {
-      mprintf("DEBUG: CMAP '%s' is a new CMAP.\n", it->Title().c_str());
-    }
-  } // END loop over new CMAP terms
-  return 0;
-}
-
 /** Update/add to parameters in this topology with those from given set. */
 int ParameterSet::UpdateParamSet(ParameterSet const& set1, UpdateCount& uc, int debugIn, int verbose) {
   ParameterSet& set0 = *this;
@@ -223,7 +171,7 @@ int ParameterSet::UpdateParamSet(ParameterSet const& set1, UpdateCount& uc, int
   // HB LJ 10-12 Pairs
   uc.nHBparamsUpdated_ = UpdateParameters< ParmHolder<HB_ParmType> >(set0.HB(), set1.HB(), "LJ HB 10-12", verbose);
   // CMAP
-  uc.nCmapUpdated_ = updateCmapTerms(set1, debugIn, verbose);
+  //uc.nCmapUpdated_ = updateCmapTerms(set1, debugIn, verbose);
 
   if (debugIn > 0) set0.Debug("newp.dat");
   return 0;
diff --git a/src/ParameterSet.h b/src/ParameterSet.h
index 6cf8dbbed9..4d44639827 100644
--- a/src/ParameterSet.h
+++ b/src/ParameterSet.h
@@ -2,6 +2,7 @@
 #define INC_PARAMETERSET_H
 #include "ParameterTypes.h"
 #include "ParameterHolders.h"
+#include "Parm/CmapParmHolder.h"
 #include "AtomType.h"
 class CpptrajFile;
 /// Hold a set of parameters for atom types, bonds, angles, etc.
@@ -18,7 +19,7 @@ class ParameterSet {
     ImproperParmHolder& IP()           { return impParm_;   }
     DihedralParmHolder& DP()           { return dihParm_;   }
     ParmHolder<HB_ParmType>& HB()      { return HBparm_;    }
-    CmapGridArray& CMAP()              { return CMAP_;      }
+    Cpptraj::Parm::CmapParmHolder& CMAP() { return CMAP_;      }
 
     void SetHasLJparams(bool b) { hasLJparams_ = b; }
     bool HasLJparams() const { return hasLJparams_; }
@@ -32,7 +33,7 @@ class ParameterSet {
     ImproperParmHolder const& IP()           const { return impParm_;   }
     DihedralParmHolder const& DP()           const { return dihParm_;   }
     ParmHolder<HB_ParmType> const& HB()      const { return HBparm_;    }
-    CmapGridArray const& CMAP()              const { return CMAP_;      }
+    Cpptraj::Parm::CmapParmHolder const& CMAP() const { return CMAP_;      }
     std::string const& NbParamName()         const { return NBname_;    }
     /// \return Parameter set names as a single line
     std::string ParamSetName()        const;
@@ -78,9 +79,6 @@ class ParameterSet {
     typedef std::vector<NameType> NsetType;
     typedef std::vector<std::string> Sarray;
 
-    /// Update CMAP terms
-    int updateCmapTerms(ParameterSet const&, int, int);
-
     Sarray name_;                          ///< Parameter set name(s)
     std::string NBname_;                   ///< Nonbond set name
 
@@ -93,7 +91,7 @@ class ParameterSet {
     ImproperParmHolder impParm_;           ///< Improper dihedral parameters
     DihedralParmHolder dihParm_;           ///< Cosine-series dihedral parameters
     ParmHolder<HB_ParmType> HBparm_;       ///< LJ 10-12 A-B parameters for hydrogen bonds
-    CmapGridArray CMAP_;                   ///< CMAP parameters; unlike others, not indexed by atom type
+    Cpptraj::Parm::CmapParmHolder CMAP_;   ///< CMAP parameters; unlike others, not indexed by atom type
     NsetType hydrophilicAtomTypes_;        ///< Hold names of hydrophilic atom types
     bool hasLJparams_;
 };
diff --git a/src/Parm/CMakeLists.txt b/src/Parm/CMakeLists.txt
index caeb638991..bc34003868 100644
--- a/src/Parm/CMakeLists.txt
+++ b/src/Parm/CMakeLists.txt
@@ -1,4 +1,5 @@
 #CMake buildfile for CPPTRAJ Parm subdirectory.
 target_sources(cpptraj_common_obj PRIVATE
+  ${CMAKE_CURRENT_LIST_DIR}/CmapParmHolder.cpp
   ${CMAKE_CURRENT_LIST_DIR}/GB_Params.cpp
 )
diff --git a/src/Parm/CmapParmHolder.cpp b/src/Parm/CmapParmHolder.cpp
index 895e0049bb..593b3482db 100644
--- a/src/Parm/CmapParmHolder.cpp
+++ b/src/Parm/CmapParmHolder.cpp
@@ -1,7 +1,62 @@
 #include "CmapParmHolder.h"
+#include "../CpptrajStdio.h"
 #include "../ParameterTypes.h"
 
 using namespace Cpptraj::Parm;
 
 /** CONSTRUCTOR */
 CmapParmHolder::CmapParmHolder() {}
+
+/** Update/add to CMAP parameters.
+  * CMAP terms are different in that they are applied via residue name instead
+  * of atom type, hence the separate routine.
+  */
+ParameterHolders::RetType CmapParmHolder::AddParm(CmapGridType const& cmap1, bool allowUpdate) {
+  typedef std::vector<std::string> Sarray;
+  enum ResMatchType { NO_MATCH = 0, FULL_MATCH, PARTIAL_MATCH };
+  // Does a CMAP for any of the residues exist?
+  ResMatchType mtype = NO_MATCH;
+  CmapGridArray::iterator currentCmap = CMAP_.end();
+  for (CmapGridArray::iterator jt = CMAP_.begin(); jt != CMAP_.end(); ++jt)
+  {
+    int nMatch = 0;
+    for (Sarray::const_iterator rni = cmap1.ResNames().begin(); rni != cmap1.ResNames().end(); ++rni)
+    {
+      for (Sarray::const_iterator rnj = jt->ResNames().begin(); rnj != jt->ResNames().end(); ++rnj)
+      {
+        if (*rni == *rnj) {
+          nMatch++;
+          break;
+        }
+      } // END loop over cmap j res names
+    } // END loop over cmap i res names
+    if (nMatch == (int)jt->ResNames().size()) {
+      mtype = FULL_MATCH;
+      currentCmap = jt;
+      break;
+    } else if (nMatch > 0) {
+      mtype = PARTIAL_MATCH;
+      currentCmap = jt;
+      break;
+    }
+  } // END loop over existing CMAP terms
+  if (mtype == PARTIAL_MATCH) {
+    mprinterr("Internal Error: Partial match between new CMAP '%s' and existing CMAP '%s'\n"
+              "Internal Error:   Not yet set up to handle this kind of parameter update.\n",
+              cmap1.Title().c_str(), currentCmap->Title().c_str());
+    return ParameterHolders::ERR;
+  } else if (mtype == FULL_MATCH) {
+    mprintf("DEBUG: Match between new CMAP '%s' and existing CMAP '%s'\n",
+            cmap1.Title().c_str(), currentCmap->Title().c_str());
+    if (allowUpdate) {
+      *currentCmap = cmap1;
+      return ParameterHolders::UPDATED;
+    } else
+      return ParameterHolders::ERR;
+  }
+  // NO_MATCH
+  mprintf("DEBUG: CMAP '%s' is a new CMAP.\n", cmap1.Title().c_str());
+  CMAP_.push_back( cmap1 );
+  return ParameterHolders::ADDED;
+}
+
diff --git a/src/Parm/CmapParmHolder.h b/src/Parm/CmapParmHolder.h
index d4772fb3e6..dff1f51860 100644
--- a/src/Parm/CmapParmHolder.h
+++ b/src/Parm/CmapParmHolder.h
@@ -2,14 +2,33 @@
 #define INC_PARM_CMAPPARMHOLDER_H
 class CmapGridType;
 #include <vector>
+#include "../ParameterHolders.h" // TODO fix the includes
 namespace Cpptraj {
 namespace Parm {
 /// Hold CMAP terms
 class CmapParmHolder {
+    typedef std::vector<CmapGridType> Carray;
   public:
     CmapParmHolder();
+
+    /// const iterator
+    typedef Carray::const_iterator const_iterator;
+    /// const begin iterator
+    const_iterator begin() const { return CMAP_.begin(); }
+    /// const end iterator
+    const_iterator end() const { return CMAP_.end(); }
+    /// \return Number of CMAP terms
+    Carray::size_type size() const { return CMAP_.size(); }
+    /// \return true if no CMAP terms
+    bool empty() const { return CMAP_.empty(); }
+    /// \return CMAP at index
+    //CmapGridType const& operator[](int idx) const { return CMAP_[idx]; }
+
+    /// \return Modifiable CMAP at index
+    
+    /// Add/update cmap term
+    ParameterHolders::RetType AddParm(CmapGridType const&, bool);
   private:
-    typedef std::vector<CmapGridType> Carray;
     Carray CMAP_;
 };
 }
diff --git a/src/Parm/parmdepend b/src/Parm/parmdepend
index 3fb8667ee2..de2147e82d 100644
--- a/src/Parm/parmdepend
+++ b/src/Parm/parmdepend
@@ -1 +1,2 @@
-GB_Params.o : GB_Params.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h GB_Params.h
+CmapParmHolder.o : CmapParmHolder.cpp ../Constants.h ../CpptrajStdio.h ../NameType.h ../ParameterHolders.h ../ParameterTypes.h ../TypeNameHolder.h CmapParmHolder.h
+GB_Params.o : GB_Params.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Parm/../Constants.h ../Parm/../NameType.h ../Parm/../ParameterHolders.h ../Parm/../ParameterTypes.h ../Parm/../TypeNameHolder.h ../Parm/CmapParmHolder.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h GB_Params.h
diff --git a/src/Parm/parmfiles b/src/Parm/parmfiles
index 86a58ec097..f556a1a93e 100644
--- a/src/Parm/parmfiles
+++ b/src/Parm/parmfiles
@@ -1,3 +1,4 @@
 # Files for Parm subdirectory.
 PARM_SOURCES= \
+  CmapParmHolder.cpp \
   GB_Params.cpp
diff --git a/src/Structure/structuredepend b/src/Structure/structuredepend
index bb1bca6bd3..a37d6d11b7 100644
--- a/src/Structure/structuredepend
+++ b/src/Structure/structuredepend
@@ -1,18 +1,18 @@
-BuildAtom.o : BuildAtom.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h StructureEnum.h
-Builder.o : Builder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Builder.h Chirality.h GenerateConnectivityArrays.h InternalCoords.h Zmatrix.h
+BuildAtom.o : BuildAtom.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Parm/../Constants.h ../Parm/../NameType.h ../Parm/../ParameterHolders.h ../Parm/../ParameterTypes.h ../Parm/../TypeNameHolder.h ../Parm/CmapParmHolder.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h StructureEnum.h
+Builder.o : Builder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Parm/../Constants.h ../Parm/../NameType.h ../Parm/../ParameterHolders.h ../Parm/../ParameterTypes.h ../Parm/../TypeNameHolder.h ../Parm/CmapParmHolder.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Builder.h Chirality.h GenerateConnectivityArrays.h InternalCoords.h Zmatrix.h
 Chirality.o : Chirality.cpp ../Atom.h ../Constants.h ../CpptrajStdio.h ../NameType.h ../SymbolExporting.h ../Vec3.h Chirality.h
-Creator.o : Creator.cpp ../ArgList.h ../AssociatedData.h ../AssociatedData_ResId.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../DataSet_NameMap.h ../DataSet_Parameters.h ../Dimension.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/StructureEnum.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Creator.h GenerateConnectivityArrays.h StructureEnum.h
-Disulfide.o : Disulfide.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Disulfide.h ResStatArray.h StructureRoutines.h
-FunctionalGroup.o : FunctionalGroup.cpp ../Atom.h ../AtomMap.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h FunctionalGroup.h
-FxnGroupBuilder.o : FxnGroupBuilder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h FunctionalGroup.h FxnGroupBuilder.h StructureRoutines.h Sugar.h SugarToken.h
+Creator.o : Creator.cpp ../ArgList.h ../AssociatedData.h ../AssociatedData_ResId.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../DataSet_NameMap.h ../DataSet_Parameters.h ../Dimension.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Parm/../Constants.h ../Parm/../NameType.h ../Parm/../ParameterHolders.h ../Parm/../ParameterTypes.h ../Parm/../TypeNameHolder.h ../Parm/CmapParmHolder.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/StructureEnum.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Creator.h GenerateConnectivityArrays.h StructureEnum.h
+Disulfide.o : Disulfide.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Parm/../Constants.h ../Parm/../NameType.h ../Parm/../ParameterHolders.h ../Parm/../ParameterTypes.h ../Parm/../TypeNameHolder.h ../Parm/CmapParmHolder.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Disulfide.h ResStatArray.h StructureRoutines.h
+FunctionalGroup.o : FunctionalGroup.cpp ../Atom.h ../AtomMap.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Parm/../Constants.h ../Parm/../NameType.h ../Parm/../ParameterHolders.h ../Parm/../ParameterTypes.h ../Parm/../TypeNameHolder.h ../Parm/CmapParmHolder.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h FunctionalGroup.h
+FxnGroupBuilder.o : FxnGroupBuilder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Parm/../Constants.h ../Parm/../NameType.h ../Parm/../ParameterHolders.h ../Parm/../ParameterTypes.h ../Parm/../TypeNameHolder.h ../Parm/CmapParmHolder.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h FunctionalGroup.h FxnGroupBuilder.h StructureRoutines.h Sugar.h SugarToken.h
 GenerateConnectivityArrays.o : GenerateConnectivityArrays.cpp ../Atom.h ../Constants.h ../CpptrajStdio.h ../NameType.h ../ParameterTypes.h ../Residue.h ../SymbolExporting.h GenerateConnectivityArrays.h
-HisProt.o : HisProt.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h HisProt.h StructureRoutines.h
-InternalCoords.o : InternalCoords.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h InternalCoords.h
-PdbCleaner.o : PdbCleaner.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h PdbCleaner.h
+HisProt.o : HisProt.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Parm/../Constants.h ../Parm/../NameType.h ../Parm/../ParameterHolders.h ../Parm/../ParameterTypes.h ../Parm/../TypeNameHolder.h ../Parm/CmapParmHolder.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h HisProt.h StructureRoutines.h
+InternalCoords.o : InternalCoords.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Parm/../Constants.h ../Parm/../NameType.h ../Parm/../ParameterHolders.h ../Parm/../ParameterTypes.h ../Parm/../TypeNameHolder.h ../Parm/CmapParmHolder.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h InternalCoords.h
+PdbCleaner.o : PdbCleaner.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Parm/../Constants.h ../Parm/../NameType.h ../Parm/../ParameterHolders.h ../Parm/../ParameterTypes.h ../Parm/../TypeNameHolder.h ../Parm/CmapParmHolder.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h PdbCleaner.h
 StructureEnum.o : StructureEnum.cpp StructureEnum.h
 StructureRoutines.o : StructureRoutines.cpp ../Atom.h ../CpptrajStdio.h ../NameType.h ../Residue.h ../SymbolExporting.h StructureRoutines.h
-Sugar.o : Sugar.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Sugar.h SugarToken.h
-SugarBuilder.o : SugarBuilder.cpp ../ArgList.h ../Atom.h ../AtomMap.h ../AtomMask.h ../AtomType.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DistRoutines.h ../FileIO.h ../FileName.h ../Frame.h ../ImageOption.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h FunctionalGroup.h FxnGroupBuilder.h LinkAtom.h ResStatArray.h StructureEnum.h StructureRoutines.h Sugar.h SugarBuilder.h SugarLinkAtoms.h SugarToken.h
-SugarLinkAtoms.o : SugarLinkAtoms.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../StringRoutines.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h LinkAtom.h SugarLinkAtoms.h
+Sugar.o : Sugar.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Parm/../Constants.h ../Parm/../NameType.h ../Parm/../ParameterHolders.h ../Parm/../ParameterTypes.h ../Parm/../TypeNameHolder.h ../Parm/CmapParmHolder.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Sugar.h SugarToken.h
+SugarBuilder.o : SugarBuilder.cpp ../ArgList.h ../Atom.h ../AtomMap.h ../AtomMask.h ../AtomType.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DistRoutines.h ../FileIO.h ../FileName.h ../Frame.h ../ImageOption.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Parm/../Constants.h ../Parm/../NameType.h ../Parm/../ParameterHolders.h ../Parm/../ParameterTypes.h ../Parm/../TypeNameHolder.h ../Parm/CmapParmHolder.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h FunctionalGroup.h FxnGroupBuilder.h LinkAtom.h ResStatArray.h StructureEnum.h StructureRoutines.h Sugar.h SugarBuilder.h SugarLinkAtoms.h SugarToken.h
+SugarLinkAtoms.o : SugarLinkAtoms.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Parm/../Constants.h ../Parm/../NameType.h ../Parm/../ParameterHolders.h ../Parm/../ParameterTypes.h ../Parm/../TypeNameHolder.h ../Parm/CmapParmHolder.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../StringRoutines.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h LinkAtom.h SugarLinkAtoms.h
 SugarToken.o : SugarToken.cpp ../ArgList.h ../CpptrajStdio.h SugarToken.h
-Zmatrix.o : Zmatrix.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h GenerateConnectivityArrays.h InternalCoords.h Zmatrix.h
+Zmatrix.o : Zmatrix.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Parm/../Constants.h ../Parm/../NameType.h ../Parm/../ParameterHolders.h ../Parm/../ParameterTypes.h ../Parm/../TypeNameHolder.h ../Parm/CmapParmHolder.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h GenerateConnectivityArrays.h InternalCoords.h Zmatrix.h
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 860f562838..91dd35e684 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -1,151 +1,151 @@
 ActionFrameCounter.o : ActionFrameCounter.cpp ActionFrameCounter.h ArgList.h CpptrajStdio.h
-ActionList.o : ActionList.cpp Action.h ActionList.h ActionState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-ActionTopWriter.o : ActionTopWriter.cpp ActionState.h ActionTopWriter.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Align.o : Action_Align.cpp Action.h ActionState.h Action_Align.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Angle.o : Action_Angle.cpp Action.h ActionState.h Action_Angle.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Action_AreaPerMol.o : Action_AreaPerMol.cpp Action.h ActionState.h Action_AreaPerMol.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_AtomMap.o : Action_AtomMap.cpp Action.h ActionState.h Action_AtomMap.h ArgList.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h StructureMapper.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_AtomicCorr.o : Action_AtomicCorr.cpp Action.h ActionState.h Action_AtomicCorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_AtomicFluct.o : Action_AtomicFluct.cpp Action.h ActionFrameCounter.h ActionState.h Action_AtomicFluct.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_AutoImage.o : Action_AutoImage.cpp Action.h ActionState.h Action_AutoImage.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h ImageRoutines.h ImageTypes.h Image_List.h Image_List_Unit.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Average.o : Action_Average.cpp Action.h ActionFrameCounter.h ActionState.h Action_Average.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-Action_AvgBox.o : Action_AvgBox.cpp Action.h ActionState.h Action_AvgBox.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Bounds.o : Action_Bounds.cpp Action.h ActionState.h Action_Bounds.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Box.o : Action_Box.cpp Action.h ActionState.h Action_Box.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BoxArgs.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Center.o : Action_Center.cpp Action.h ActionState.h Action_Center.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Channel.o : Action_Channel.cpp Action.h ActionState.h Action_Channel.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_CheckChirality.o : Action_CheckChirality.cpp Action.h ActionState.h Action_CheckChirality.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h Structure/BuildAtom.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Action_CheckStructure.o : Action_CheckStructure.cpp Action.h ActionState.h Action_CheckStructure.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_integer.h DataSet_string.h Dimension.h DispatchObject.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Closest.o : Action_Closest.cpp Action.h ActionState.h ActionTopWriter.h Action_Closest.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h ImageRoutines.h ImageTypes.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h cuda_kernels/kernel_wrappers.cuh
-Action_ClusterDihedral.o : Action_ClusterDihedral.cpp Action.h ActionState.h Action_ClusterDihedral.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_integer.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Action_Contacts.o : Action_Contacts.cpp Action.h ActionState.h Action_Contacts.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_CreateCrd.o : Action_CreateCrd.cpp Action.h ActionState.h Action_CreateCrd.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_CreateReservoir.o : Action_CreateReservoir.cpp Action.h ActionState.h Action_CreateReservoir.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h RemdReservoirNC.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_DNAionTracker.o : Action_DNAionTracker.cpp Action.h ActionState.h Action_DNAionTracker.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_DSSP.o : Action_DSSP.cpp Action.h ActionState.h Action_DSSP.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Density.o : Action_Density.cpp Action.h ActionState.h Action_Density.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Diffusion.o : Action_Diffusion.cpp Action.h ActionState.h Action_Diffusion.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_double.h DiffusionResults.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Dihedral.o : Action_Dihedral.cpp Action.h ActionState.h Action_Dihedral.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Action_DihedralRMS.o : Action_DihedralRMS.cpp Action.h ActionState.h Action_DihedralRMS.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Action_Dipole.o : Action_Dipole.cpp Action.h ActionState.h Action_Dipole.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridAction.h GridBin.h GridMover.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_DistRmsd.o : Action_DistRmsd.cpp Action.h ActionState.h Action_DistRmsd.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Distance.o : Action_Distance.cpp Action.h ActionState.h Action_Distance.h ArgList.h AssociatedData.h AssociatedData_NOE.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Energy.o : Action_Energy.cpp Action.h ActionState.h Action_Energy.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h Energy.h EnergyArray.h Ewald.h EwaldOptions.h Ewald_ParticleMesh.h Ewald_Regular.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h helpme_standalone.h
-Action_Esander.o : Action_Esander.cpp Action.h ActionState.h Action_Esander.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h Energy_Sander.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_FilterByData.o : Action_FilterByData.cpp Action.h ActionState.h Action_FilterByData.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_FixAtomOrder.o : Action_FixAtomOrder.cpp Action.h ActionState.h ActionTopWriter.h Action_FixAtomOrder.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomTopType.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_FixImagedBonds.o : Action_FixImagedBonds.cpp Action.h ActionState.h Action_FixImagedBonds.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_GIST.o : Action_GIST.cpp Action.h ActionState.h Action_GIST.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridDbl.h DataSet_GridFlt.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h DistRoutines.h Ewald.h EwaldOptions.h Ewald_ParticleMesh.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h GIST_PME.h GistEntropyUtils.h Grid.h GridBin.h GridMover.h ImageOption.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h cuda_kernels/GistCudaSetup.cuh helpme_standalone.h
-Action_Grid.o : Action_Grid.cpp Action.h ActionState.h Action_Grid.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridAction.h GridBin.h GridMover.h MaskArray.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_GridFreeEnergy.o : Action_GridFreeEnergy.cpp Action.h ActionState.h Action_GridFreeEnergy.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridAction.h GridBin.h GridMover.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_HydrogenBond.o : Action_HydrogenBond.cpp Action.h ActionState.h Action_HydrogenBond.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_integer.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Action_Image.o : Action_Image.cpp Action.h ActionState.h Action_Image.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h ImageRoutines.h ImageTypes.h Image_List.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_InfraredSpectrum.o : Action_InfraredSpectrum.cpp Action.h ActionState.h Action_InfraredSpectrum.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Jcoupling.o : Action_Jcoupling.cpp Action.h ActionState.h Action_Jcoupling.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Action_Keep.o : Action_Keep.cpp Action.h ActionState.h ActionTopWriter.h Action_Keep.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_string.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_LESsplit.o : Action_LESsplit.cpp Action.h ActionFrameCounter.h ActionState.h Action_LESsplit.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-Action_LIE.o : Action_LIE.cpp Action.h ActionState.h Action_LIE.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_LipidOrder.o : Action_LipidOrder.cpp Action.h ActionState.h Action_LipidOrder.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_MakeStructure.o : Action_MakeStructure.cpp Action.h ActionState.h Action_MakeStructure.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Action_Mask.o : Action_Mask.cpp Action.h ActionFrameCounter.h ActionState.h Action_Mask.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-Action_Matrix.o : Action_Matrix.cpp Action.h ActionFrameCounter.h ActionState.h Action_Matrix.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Vector.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_MinImage.o : Action_MinImage.cpp Action.h ActionState.h Action_MinImage.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Molsurf.o : Action_Molsurf.cpp Action.h ActionState.h Action_Molsurf.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h molsurf.h
-Action_MultiDihedral.o : Action_MultiDihedral.cpp Action.h ActionState.h Action_MultiDihedral.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DihedralSearch.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Action_MultiPucker.o : Action_MultiPucker.cpp Action.h ActionState.h Action_MultiPucker.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Pucker.h Pucker_PuckerMask.h Pucker_PuckerSearch.h Pucker_PuckerToken.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Action_MultiVector.o : Action_MultiVector.cpp Action.h ActionState.h Action_MultiVector.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_NAstruct.o : Action_NAstruct.cpp Action.h ActionFrameCounter.h ActionState.h Action_NAstruct.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h AxisType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_float.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-Action_NMRrst.o : Action_NMRrst.cpp Action.h ActionState.h Action_NMRrst.h ArgList.h AssociatedData.h AssociatedData_NOE.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_float.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h ViewRst.h
-Action_NativeContacts.o : Action_NativeContacts.cpp Action.h ActionState.h Action_NativeContacts.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_integer.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_OrderParameter.o : Action_OrderParameter.cpp Action.h ActionState.h Action_OrderParameter.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Outtraj.o : Action_Outtraj.cpp Action.h ActionFrameCounter.h ActionState.h Action_Outtraj.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-Action_PairDist.o : Action_PairDist.cpp Action.h ActionState.h Action_PairDist.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Pairwise.o : Action_Pairwise.cpp Action.h ActionFrameCounter.h ActionState.h Action_Pairwise.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h Dimension.h DispatchObject.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-Action_Principal.o : Action_Principal.cpp Action.h ActionState.h Action_Principal.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Projection.o : Action_Projection.cpp Action.h ActionFrameCounter.h ActionState.h Action_Projection.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Pucker.o : Action_Pucker.cpp Action.h ActionState.h Action_Pucker.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Action_Radgyr.o : Action_Radgyr.cpp Action.h ActionState.h Action_Radgyr.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Radial.o : Action_Radial.cpp Action.h ActionState.h Action_Radial.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h Gpu.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h cuda_kernels/kernel_rdf.cuh
-Action_RandomizeIons.o : Action_RandomizeIons.cpp Action.h ActionState.h Action_RandomizeIons.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Remap.o : Action_Remap.cpp Action.h ActionState.h ActionTopWriter.h Action_Remap.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_ReplicateCell.o : Action_ReplicateCell.cpp Action.h ActionFrameCounter.h ActionState.h ActionTopWriter.h Action_ReplicateCell.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-Action_Rmsd.o : Action_Rmsd.cpp Action.h ActionState.h Action_Rmsd.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Rotate.o : Action_Rotate.cpp Action.h ActionState.h Action_Rotate.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_RunningAvg.o : Action_RunningAvg.cpp Action.h ActionState.h Action_RunningAvg.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_STFC_Diffusion.o : Action_STFC_Diffusion.cpp Action.h ActionState.h Action_STFC_Diffusion.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Scale.o : Action_Scale.cpp Action.h ActionState.h Action_Scale.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_SetVelocity.o : Action_SetVelocity.cpp Action.h ActionState.h Action_SetVelocity.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Spam.o : Action_Spam.cpp Action.h ActionState.h Action_Spam.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_Peaks.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h DataSet_Vector_Scalar.h DataSet_double.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h HistBin.h ImageOption.h KDE.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Strip.o : Action_Strip.cpp Action.h ActionState.h ActionTopWriter.h Action_Strip.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Surf.o : Action_Surf.cpp Action.h ActionState.h Action_Surf.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_SymmetricRmsd.o : Action_SymmetricRmsd.cpp Action.h ActionState.h Action_SymmetricRmsd.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h Hungarian.h ImageOption.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Temperature.o : Action_Temperature.cpp Action.h ActionState.h Action_Temperature.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Time.o : Action_Time.cpp Action.h ActionState.h Action_Time.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_ToroidalDiffusion.o : Action_ToroidalDiffusion.cpp Action.h ActionState.h Action_ToroidalDiffusion.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DiffusionResults.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Translate.o : Action_Translate.cpp Action.h ActionState.h Action_Translate.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Unstrip.o : Action_Unstrip.cpp Action.h ActionState.h Action_Unstrip.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Unwrap.o : Action_Unwrap.cpp Action.h ActionState.h Action_Unwrap.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h ImageRoutines.h ImageTypes.h Image_List.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Vector.o : Action_Vector.cpp Action.h ActionState.h Action_Vector.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h GridBin.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_VelocityAutoCorr.o : Action_VelocityAutoCorr.cpp Action.h ActionState.h Action_VelocityAutoCorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Volmap.o : Action_Volmap.cpp Action.h ActionState.h Action_Volmap.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridDbl.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Volume.o : Action_Volume.cpp Action.h ActionState.h Action_Volume.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Watershell.o : Action_Watershell.cpp Action.h ActionState.h Action_Watershell.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h ImageRoutines.h ImageTypes.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h cuda_kernels/kernel_wrappers.cuh
-Action_XtalSymm.o : Action_XtalSymm.cpp Action.h ActionState.h Action_XtalSymm.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SpaceGroup.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-AmberParamFile.o : AmberParamFile.cpp AmberParamFile.h ArgList.h AtomType.h BufferedLine.h Constants.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h StringRoutines.h TypeNameHolder.h
-AnalysisList.o : AnalysisList.cpp ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_AmdBias.o : Analysis_AmdBias.cpp ActionState.h Analysis.h AnalysisState.h Analysis_AmdBias.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_AutoCorr.o : Analysis_AutoCorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_AutoCorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Average.o : Analysis_Average.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Average.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_CalcDiffusion.o : Analysis_CalcDiffusion.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CalcDiffusion.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_double.h DiffusionResults.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Clustering.o : Analysis_Clustering.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Clustering.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/Algorithm.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Control.h Cluster/DrawGraph.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Sieve.h Cluster/Silhouette.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_ConstantPHStats.o : Analysis_ConstantPHStats.cpp ActionState.h Analysis.h AnalysisState.h Analysis_ConstantPHStats.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h DataSet_pH.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Corr.o : Analysis_Corr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Corr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_CrankShaft.o : Analysis_CrankShaft.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CrankShaft.h Analysis_Statistics.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_float.h DataSet_integer.h DataSet_string.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_CrdFluct.o : Analysis_CrdFluct.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CrdFluct.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_CrossCorr.o : Analysis_CrossCorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CrossCorr.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_CurveFit.o : Analysis_CurveFit.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CurveFit.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h CurveFit.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Divergence.o : Analysis_Divergence.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Divergence.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_EvalPlateau.o : Analysis_EvalPlateau.cpp ActionState.h Analysis.h AnalysisState.h Analysis_EvalPlateau.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h CurveFit.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_FFT.o : Analysis_FFT.cpp ActionState.h Analysis.h AnalysisState.h Analysis_FFT.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_HausdorffDistance.o : Analysis_HausdorffDistance.cpp ActionState.h Analysis.h AnalysisState.h Analysis_HausdorffDistance.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Hist.o : Analysis_Hist.cpp ActionFrameCounter.h ActionState.h Analysis.h AnalysisState.h Analysis_Hist.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridBin.h HistBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_IRED.o : Analysis_IRED.cpp ActionState.h Analysis.h AnalysisState.h Analysis_IRED.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Integrate.o : Analysis_Integrate.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Integrate.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_KDE.o : Analysis_KDE.cpp ActionState.h Analysis.h AnalysisState.h Analysis_KDE.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h HistBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Lifetime.o : Analysis_Lifetime.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Lifetime.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_LowestCurve.o : Analysis_LowestCurve.cpp ActionState.h Analysis.h AnalysisState.h Analysis_LowestCurve.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h HistBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Matrix.o : Analysis_Matrix.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Matrix.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_MeltCurve.o : Analysis_MeltCurve.cpp ActionState.h Analysis.h AnalysisState.h Analysis_MeltCurve.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Modes.o : Analysis_Modes.cpp ActionFrameCounter.h ActionState.h Analysis.h AnalysisState.h Analysis_Modes.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_MultiHist.o : Analysis_MultiHist.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Hist.h Analysis_KDE.h Analysis_MultiHist.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h HistBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Multicurve.o : Analysis_Multicurve.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CurveFit.h Analysis_Multicurve.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Overlap.o : Analysis_Overlap.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Overlap.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_PhiPsi.o : Analysis_PhiPsi.cpp ActionState.h Analysis.h AnalysisState.h Analysis_PhiPsi.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Regression.o : Analysis_Regression.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Regression.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_RemLog.o : Analysis_RemLog.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Lifetime.h Analysis_RemLog.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h DataSet_RemLog.h DataSet_integer.h DataSet_integer_mem.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Rms2d.o : Analysis_Rms2d.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Rms2d.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Hungarian.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h QuaternionRMSD.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_RmsAvgCorr.o : Analysis_RmsAvgCorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_RmsAvgCorr.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Rotdif.o : Analysis_Rotdif.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Rotdif.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h CurveFit.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_Mesh.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h PubFFT.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SimplexMin.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_RunningAvg.o : Analysis_RunningAvg.cpp ActionState.h Analysis.h AnalysisState.h Analysis_RunningAvg.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Slope.o : Analysis_Slope.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Slope.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Spline.o : Analysis_Spline.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Spline.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_State.o : Analysis_State.cpp ActionState.h Analysis.h AnalysisState.h Analysis_State.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Statistics.o : Analysis_Statistics.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Statistics.h ArgList.h Array1D.h AssociatedData.h AssociatedData_NOE.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_float.h DataSet_integer.h DataSet_string.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_TI.o : Analysis_TI.cpp ActionState.h Analysis.h AnalysisState.h Analysis_TI.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_TICA.o : Analysis_TICA.cpp ActionState.h Analysis.h AnalysisState.h Analysis_TICA.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Timecorr.o : Analysis_Timecorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Timecorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_VectorMath.o : Analysis_VectorMath.cpp ActionState.h Analysis.h AnalysisState.h Analysis_VectorMath.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Wavelet.o : Analysis_Wavelet.cpp ActionFrameCounter.h ActionState.h Analysis.h AnalysisState.h Analysis_Wavelet.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ClusterMap.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h ProgressBar.h ProgressTimer.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+ActionList.o : ActionList.cpp Action.h ActionList.h ActionState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+ActionTopWriter.o : ActionTopWriter.cpp ActionState.h ActionTopWriter.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Align.o : Action_Align.cpp Action.h ActionState.h Action_Align.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Angle.o : Action_Angle.cpp Action.h ActionState.h Action_Angle.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Action_AreaPerMol.o : Action_AreaPerMol.cpp Action.h ActionState.h Action_AreaPerMol.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_AtomMap.o : Action_AtomMap.cpp Action.h ActionState.h Action_AtomMap.h ArgList.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h StructureMapper.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_AtomicCorr.o : Action_AtomicCorr.cpp Action.h ActionState.h Action_AtomicCorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_AtomicFluct.o : Action_AtomicFluct.cpp Action.h ActionFrameCounter.h ActionState.h Action_AtomicFluct.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_AutoImage.o : Action_AutoImage.cpp Action.h ActionState.h Action_AutoImage.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h ImageRoutines.h ImageTypes.h Image_List.h Image_List_Unit.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Average.o : Action_Average.cpp Action.h ActionFrameCounter.h ActionState.h Action_Average.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Action_AvgBox.o : Action_AvgBox.cpp Action.h ActionState.h Action_AvgBox.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Bounds.o : Action_Bounds.cpp Action.h ActionState.h Action_Bounds.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Box.o : Action_Box.cpp Action.h ActionState.h Action_Box.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BoxArgs.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Center.o : Action_Center.cpp Action.h ActionState.h Action_Center.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Channel.o : Action_Channel.cpp Action.h ActionState.h Action_Channel.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_CheckChirality.o : Action_CheckChirality.cpp Action.h ActionState.h Action_CheckChirality.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h Structure/BuildAtom.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Action_CheckStructure.o : Action_CheckStructure.cpp Action.h ActionState.h Action_CheckStructure.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_integer.h DataSet_string.h Dimension.h DispatchObject.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Closest.o : Action_Closest.cpp Action.h ActionState.h ActionTopWriter.h Action_Closest.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h ImageRoutines.h ImageTypes.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h cuda_kernels/kernel_wrappers.cuh
+Action_ClusterDihedral.o : Action_ClusterDihedral.cpp Action.h ActionState.h Action_ClusterDihedral.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_integer.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Action_Contacts.o : Action_Contacts.cpp Action.h ActionState.h Action_Contacts.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_CreateCrd.o : Action_CreateCrd.cpp Action.h ActionState.h Action_CreateCrd.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_CreateReservoir.o : Action_CreateReservoir.cpp Action.h ActionState.h Action_CreateReservoir.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h RemdReservoirNC.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_DNAionTracker.o : Action_DNAionTracker.cpp Action.h ActionState.h Action_DNAionTracker.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_DSSP.o : Action_DSSP.cpp Action.h ActionState.h Action_DSSP.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Density.o : Action_Density.cpp Action.h ActionState.h Action_Density.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Diffusion.o : Action_Diffusion.cpp Action.h ActionState.h Action_Diffusion.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_double.h DiffusionResults.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Dihedral.o : Action_Dihedral.cpp Action.h ActionState.h Action_Dihedral.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Action_DihedralRMS.o : Action_DihedralRMS.cpp Action.h ActionState.h Action_DihedralRMS.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Action_Dipole.o : Action_Dipole.cpp Action.h ActionState.h Action_Dipole.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridAction.h GridBin.h GridMover.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_DistRmsd.o : Action_DistRmsd.cpp Action.h ActionState.h Action_DistRmsd.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Distance.o : Action_Distance.cpp Action.h ActionState.h Action_Distance.h ArgList.h AssociatedData.h AssociatedData_NOE.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Energy.o : Action_Energy.cpp Action.h ActionState.h Action_Energy.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h Energy.h EnergyArray.h Ewald.h EwaldOptions.h Ewald_ParticleMesh.h Ewald_Regular.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h helpme_standalone.h
+Action_Esander.o : Action_Esander.cpp Action.h ActionState.h Action_Esander.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h Energy_Sander.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_FilterByData.o : Action_FilterByData.cpp Action.h ActionState.h Action_FilterByData.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_FixAtomOrder.o : Action_FixAtomOrder.cpp Action.h ActionState.h ActionTopWriter.h Action_FixAtomOrder.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomTopType.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_FixImagedBonds.o : Action_FixImagedBonds.cpp Action.h ActionState.h Action_FixImagedBonds.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_GIST.o : Action_GIST.cpp Action.h ActionState.h Action_GIST.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridDbl.h DataSet_GridFlt.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h DistRoutines.h Ewald.h EwaldOptions.h Ewald_ParticleMesh.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h GIST_PME.h GistEntropyUtils.h Grid.h GridBin.h GridMover.h ImageOption.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h cuda_kernels/GistCudaSetup.cuh helpme_standalone.h
+Action_Grid.o : Action_Grid.cpp Action.h ActionState.h Action_Grid.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridAction.h GridBin.h GridMover.h MaskArray.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_GridFreeEnergy.o : Action_GridFreeEnergy.cpp Action.h ActionState.h Action_GridFreeEnergy.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridAction.h GridBin.h GridMover.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_HydrogenBond.o : Action_HydrogenBond.cpp Action.h ActionState.h Action_HydrogenBond.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_integer.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Action_Image.o : Action_Image.cpp Action.h ActionState.h Action_Image.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h ImageRoutines.h ImageTypes.h Image_List.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_InfraredSpectrum.o : Action_InfraredSpectrum.cpp Action.h ActionState.h Action_InfraredSpectrum.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ProgressBar.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Jcoupling.o : Action_Jcoupling.cpp Action.h ActionState.h Action_Jcoupling.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Action_Keep.o : Action_Keep.cpp Action.h ActionState.h ActionTopWriter.h Action_Keep.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_string.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_LESsplit.o : Action_LESsplit.cpp Action.h ActionFrameCounter.h ActionState.h Action_LESsplit.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Action_LIE.o : Action_LIE.cpp Action.h ActionState.h Action_LIE.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_LipidOrder.o : Action_LipidOrder.cpp Action.h ActionState.h Action_LipidOrder.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_MakeStructure.o : Action_MakeStructure.cpp Action.h ActionState.h Action_MakeStructure.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Action_Mask.o : Action_Mask.cpp Action.h ActionFrameCounter.h ActionState.h Action_Mask.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Action_Matrix.o : Action_Matrix.cpp Action.h ActionFrameCounter.h ActionState.h Action_Matrix.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Vector.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_MinImage.o : Action_MinImage.cpp Action.h ActionState.h Action_MinImage.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Molsurf.o : Action_Molsurf.cpp Action.h ActionState.h Action_Molsurf.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h molsurf.h
+Action_MultiDihedral.o : Action_MultiDihedral.cpp Action.h ActionState.h Action_MultiDihedral.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DihedralSearch.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Action_MultiPucker.o : Action_MultiPucker.cpp Action.h ActionState.h Action_MultiPucker.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Pucker.h Pucker_PuckerMask.h Pucker_PuckerSearch.h Pucker_PuckerToken.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Action_MultiVector.o : Action_MultiVector.cpp Action.h ActionState.h Action_MultiVector.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_NAstruct.o : Action_NAstruct.cpp Action.h ActionFrameCounter.h ActionState.h Action_NAstruct.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h AxisType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_float.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Action_NMRrst.o : Action_NMRrst.cpp Action.h ActionState.h Action_NMRrst.h ArgList.h AssociatedData.h AssociatedData_NOE.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_float.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h ViewRst.h
+Action_NativeContacts.o : Action_NativeContacts.cpp Action.h ActionState.h Action_NativeContacts.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_integer.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_OrderParameter.o : Action_OrderParameter.cpp Action.h ActionState.h Action_OrderParameter.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Outtraj.o : Action_Outtraj.cpp Action.h ActionFrameCounter.h ActionState.h Action_Outtraj.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Action_PairDist.o : Action_PairDist.cpp Action.h ActionState.h Action_PairDist.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Pairwise.o : Action_Pairwise.cpp Action.h ActionFrameCounter.h ActionState.h Action_Pairwise.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h Dimension.h DispatchObject.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Action_Principal.o : Action_Principal.cpp Action.h ActionState.h Action_Principal.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Projection.o : Action_Projection.cpp Action.h ActionFrameCounter.h ActionState.h Action_Projection.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Pucker.o : Action_Pucker.cpp Action.h ActionState.h Action_Pucker.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Action_Radgyr.o : Action_Radgyr.cpp Action.h ActionState.h Action_Radgyr.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Radial.o : Action_Radial.cpp Action.h ActionState.h Action_Radial.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h Gpu.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h cuda_kernels/kernel_rdf.cuh
+Action_RandomizeIons.o : Action_RandomizeIons.cpp Action.h ActionState.h Action_RandomizeIons.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Remap.o : Action_Remap.cpp Action.h ActionState.h ActionTopWriter.h Action_Remap.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_ReplicateCell.o : Action_ReplicateCell.cpp Action.h ActionFrameCounter.h ActionState.h ActionTopWriter.h Action_ReplicateCell.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Action_Rmsd.o : Action_Rmsd.cpp Action.h ActionState.h Action_Rmsd.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Rotate.o : Action_Rotate.cpp Action.h ActionState.h Action_Rotate.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_RunningAvg.o : Action_RunningAvg.cpp Action.h ActionState.h Action_RunningAvg.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_STFC_Diffusion.o : Action_STFC_Diffusion.cpp Action.h ActionState.h Action_STFC_Diffusion.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Scale.o : Action_Scale.cpp Action.h ActionState.h Action_Scale.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_SetVelocity.o : Action_SetVelocity.cpp Action.h ActionState.h Action_SetVelocity.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Spam.o : Action_Spam.cpp Action.h ActionState.h Action_Spam.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_Peaks.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h DataSet_Vector_Scalar.h DataSet_double.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h HistBin.h ImageOption.h KDE.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Strip.o : Action_Strip.cpp Action.h ActionState.h ActionTopWriter.h Action_Strip.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Surf.o : Action_Surf.cpp Action.h ActionState.h Action_Surf.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_SymmetricRmsd.o : Action_SymmetricRmsd.cpp Action.h ActionState.h Action_SymmetricRmsd.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h Hungarian.h ImageOption.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Temperature.o : Action_Temperature.cpp Action.h ActionState.h Action_Temperature.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Time.o : Action_Time.cpp Action.h ActionState.h Action_Time.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_ToroidalDiffusion.o : Action_ToroidalDiffusion.cpp Action.h ActionState.h Action_ToroidalDiffusion.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DiffusionResults.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Translate.o : Action_Translate.cpp Action.h ActionState.h Action_Translate.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Unstrip.o : Action_Unstrip.cpp Action.h ActionState.h Action_Unstrip.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Unwrap.o : Action_Unwrap.cpp Action.h ActionState.h Action_Unwrap.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h ImageRoutines.h ImageTypes.h Image_List.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Vector.o : Action_Vector.cpp Action.h ActionState.h Action_Vector.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h GridBin.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_VelocityAutoCorr.o : Action_VelocityAutoCorr.cpp Action.h ActionState.h Action_VelocityAutoCorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ProgressBar.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Volmap.o : Action_Volmap.cpp Action.h ActionState.h Action_Volmap.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridDbl.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Volume.o : Action_Volume.cpp Action.h ActionState.h Action_Volume.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Watershell.o : Action_Watershell.cpp Action.h ActionState.h Action_Watershell.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h ImageRoutines.h ImageTypes.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h cuda_kernels/kernel_wrappers.cuh
+Action_XtalSymm.o : Action_XtalSymm.cpp Action.h ActionState.h Action_XtalSymm.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SpaceGroup.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+AmberParamFile.o : AmberParamFile.cpp AmberParamFile.h ArgList.h AtomType.h BufferedLine.h Constants.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h StringRoutines.h TypeNameHolder.h
+AnalysisList.o : AnalysisList.cpp ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_AmdBias.o : Analysis_AmdBias.cpp ActionState.h Analysis.h AnalysisState.h Analysis_AmdBias.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_AutoCorr.o : Analysis_AutoCorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_AutoCorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_Average.o : Analysis_Average.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Average.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_CalcDiffusion.o : Analysis_CalcDiffusion.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CalcDiffusion.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_double.h DiffusionResults.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_Clustering.o : Analysis_Clustering.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Clustering.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/Algorithm.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Control.h Cluster/DrawGraph.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Sieve.h Cluster/Silhouette.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_ConstantPHStats.o : Analysis_ConstantPHStats.cpp ActionState.h Analysis.h AnalysisState.h Analysis_ConstantPHStats.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h DataSet_pH.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_Corr.o : Analysis_Corr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Corr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_CrankShaft.o : Analysis_CrankShaft.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CrankShaft.h Analysis_Statistics.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_float.h DataSet_integer.h DataSet_string.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_CrdFluct.o : Analysis_CrdFluct.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CrdFluct.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_CrossCorr.o : Analysis_CrossCorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CrossCorr.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_CurveFit.o : Analysis_CurveFit.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CurveFit.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h CurveFit.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_Divergence.o : Analysis_Divergence.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Divergence.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_EvalPlateau.o : Analysis_EvalPlateau.cpp ActionState.h Analysis.h AnalysisState.h Analysis_EvalPlateau.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h CurveFit.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_FFT.o : Analysis_FFT.cpp ActionState.h Analysis.h AnalysisState.h Analysis_FFT.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_HausdorffDistance.o : Analysis_HausdorffDistance.cpp ActionState.h Analysis.h AnalysisState.h Analysis_HausdorffDistance.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_Hist.o : Analysis_Hist.cpp ActionFrameCounter.h ActionState.h Analysis.h AnalysisState.h Analysis_Hist.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridBin.h HistBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_IRED.o : Analysis_IRED.cpp ActionState.h Analysis.h AnalysisState.h Analysis_IRED.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_Integrate.o : Analysis_Integrate.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Integrate.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_KDE.o : Analysis_KDE.cpp ActionState.h Analysis.h AnalysisState.h Analysis_KDE.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h HistBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_Lifetime.o : Analysis_Lifetime.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Lifetime.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_LowestCurve.o : Analysis_LowestCurve.cpp ActionState.h Analysis.h AnalysisState.h Analysis_LowestCurve.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h HistBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_Matrix.o : Analysis_Matrix.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Matrix.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_MeltCurve.o : Analysis_MeltCurve.cpp ActionState.h Analysis.h AnalysisState.h Analysis_MeltCurve.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_Modes.o : Analysis_Modes.cpp ActionFrameCounter.h ActionState.h Analysis.h AnalysisState.h Analysis_Modes.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_MultiHist.o : Analysis_MultiHist.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Hist.h Analysis_KDE.h Analysis_MultiHist.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h HistBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_Multicurve.o : Analysis_Multicurve.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CurveFit.h Analysis_Multicurve.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_Overlap.o : Analysis_Overlap.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Overlap.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_PhiPsi.o : Analysis_PhiPsi.cpp ActionState.h Analysis.h AnalysisState.h Analysis_PhiPsi.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_Regression.o : Analysis_Regression.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Regression.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_RemLog.o : Analysis_RemLog.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Lifetime.h Analysis_RemLog.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h DataSet_RemLog.h DataSet_integer.h DataSet_integer_mem.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_Rms2d.o : Analysis_Rms2d.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Rms2d.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Hungarian.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ProgressBar.h QuaternionRMSD.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_RmsAvgCorr.o : Analysis_RmsAvgCorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_RmsAvgCorr.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_Rotdif.o : Analysis_Rotdif.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Rotdif.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h CurveFit.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_Mesh.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ProgressBar.h PubFFT.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SimplexMin.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_RunningAvg.o : Analysis_RunningAvg.cpp ActionState.h Analysis.h AnalysisState.h Analysis_RunningAvg.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_Slope.o : Analysis_Slope.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Slope.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_Spline.o : Analysis_Spline.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Spline.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_State.o : Analysis_State.cpp ActionState.h Analysis.h AnalysisState.h Analysis_State.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_Statistics.o : Analysis_Statistics.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Statistics.h ArgList.h Array1D.h AssociatedData.h AssociatedData_NOE.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_float.h DataSet_integer.h DataSet_string.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_TI.o : Analysis_TI.cpp ActionState.h Analysis.h AnalysisState.h Analysis_TI.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_TICA.o : Analysis_TICA.cpp ActionState.h Analysis.h AnalysisState.h Analysis_TICA.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_Timecorr.o : Analysis_Timecorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Timecorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_VectorMath.o : Analysis_VectorMath.cpp ActionState.h Analysis.h AnalysisState.h Analysis_VectorMath.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_Wavelet.o : Analysis_Wavelet.cpp ActionFrameCounter.h ActionState.h Analysis.h AnalysisState.h Analysis_Wavelet.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ClusterMap.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ParmFile.h ProgressBar.h ProgressTimer.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 ArgList.o : ArgList.cpp ArgList.h CpptrajStdio.h StringRoutines.h
-Array1D.o : Array1D.cpp ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Array1D.o : Array1D.cpp ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 AssociatedData_Connect.o : AssociatedData_Connect.cpp ArgList.h AssociatedData.h AssociatedData_Connect.h CpptrajStdio.h
 AssociatedData_NOE.o : AssociatedData_NOE.cpp ArgList.h AssociatedData.h AssociatedData_NOE.h CpptrajStdio.h
 AssociatedData_ResId.o : AssociatedData_ResId.cpp AssociatedData.h AssociatedData_ResId.h CpptrajStdio.h NameType.h Structure/StructureEnum.h
 Atom.o : Atom.cpp Atom.h CpptrajStdio.h NameType.h SymbolExporting.h
-AtomMap.o : AtomMap.cpp Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+AtomMap.o : AtomMap.cpp Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 AtomMask.o : AtomMask.cpp Atom.h AtomMask.h CpptrajStdio.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h SymbolExporting.h Unit.h
-AxisType.o : AxisType.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h AxisType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-BondSearch.o : BondSearch.cpp Atom.h AtomMask.h AtomType.h BondSearch.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+AxisType.o : AxisType.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h AxisType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+BondSearch.o : BondSearch.cpp Atom.h AtomMask.h AtomType.h BondSearch.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Box.o : Box.cpp Box.h Constants.h CpptrajStdio.h Matrix_3x3.h Parallel.h Vec3.h
 BoxArgs.o : BoxArgs.cpp ArgList.h Box.h BoxArgs.h CpptrajStdio.h Matrix_3x3.h Parallel.h Vec3.h
 BufferedFrame.o : BufferedFrame.cpp BufferedFrame.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Parallel.h TextFormat.h
@@ -153,9 +153,9 @@ BufferedLine.o : BufferedLine.cpp BufferedLine.h CpptrajFile.h CpptrajStdio.h Fi
 ByteRoutines.o : ByteRoutines.cpp
 CIFfile.o : CIFfile.cpp ArgList.h Atom.h BufferedLine.h CIFfile.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h SymbolExporting.h
 CharMask.o : CharMask.cpp Atom.h CharMask.h CpptrajStdio.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h SymbolExporting.h Unit.h
-CharmmParamFile.o : CharmmParamFile.cpp ArgList.h AtomType.h BufferedLine.h CharmmParamFile.h Constants.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h StringRoutines.h TypeNameHolder.h
+CharmmParamFile.o : CharmmParamFile.cpp ArgList.h AtomType.h BufferedLine.h CharmmParamFile.h Constants.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h StringRoutines.h TypeNameHolder.h
 Cluster/Algorithm.o : Cluster/Algorithm.cpp Cluster/Algorithm.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h CpptrajStdio.h
-Cluster/Algorithm_DBscan.o : Cluster/Algorithm_DBscan.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/Algorithm.h Cluster/Algorithm_DBscan.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Cluster/Algorithm_DBscan.o : Cluster/Algorithm_DBscan.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/Algorithm.h Cluster/Algorithm_DBscan.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Cluster/Algorithm_DPeaks.o : Cluster/Algorithm_DPeaks.cpp ArgList.h AssociatedData.h Cluster/Algorithm.h Cluster/Algorithm_DPeaks.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_Mesh.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h ProgressBar.h Range.h Spline.h TextFormat.h
 Cluster/Algorithm_HierAgglo.o : Cluster/Algorithm_HierAgglo.cpp ArgList.h ArrayIterator.h Cluster/Algorithm.h Cluster/Algorithm_HierAgglo.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/DynamicMatrix.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Matrix.h Parallel.h ProgressBar.h Timer.h
 Cluster/Algorithm_Kmeans.o : Cluster/Algorithm_Kmeans.cpp ArgList.h Cluster/Algorithm.h Cluster/Algorithm_Kmeans.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Parallel.h ProgressBar.h Random.h
@@ -165,82 +165,82 @@ Cluster/Centroid_Coord.o : Cluster/Centroid_Coord.cpp Atom.h AtomMask.h Box.h Cl
 Cluster/Cframes.o : Cluster/Cframes.cpp Cluster/Cframes.h
 Cluster/Cmatrix_Binary.o : Cluster/Cmatrix_Binary.cpp Cluster/Cframes.h Cluster/Cmatrix_Binary.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Parallel.h
 Cluster/Cmatrix_NC.o : Cluster/Cmatrix_NC.cpp Cluster/Cframes.h Cluster/Cmatrix_NC.h CpptrajStdio.h FileName.h NC_Routines.h
-Cluster/Control.o : Cluster/Control.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Cluster/Algorithm.h Cluster/Algorithm_DBscan.h Cluster/Algorithm_DPeaks.h Cluster/Algorithm_HierAgglo.h Cluster/Algorithm_Kmeans.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Control.h Cluster/DBI.h Cluster/DrawGraph.h Cluster/DynamicMatrix.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Output.h Cluster/PseudoF.h Cluster/Results.h Cluster/Results_Coords.h Cluster/Sieve.h Cluster/Silhouette.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_float.h DataSet_integer.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TypeNameHolder.h Unit.h Vec3.h
+Cluster/Control.o : Cluster/Control.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Cluster/Algorithm.h Cluster/Algorithm_DBscan.h Cluster/Algorithm_DPeaks.h Cluster/Algorithm_HierAgglo.h Cluster/Algorithm_Kmeans.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Control.h Cluster/DBI.h Cluster/DrawGraph.h Cluster/DynamicMatrix.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Output.h Cluster/PseudoF.h Cluster/Results.h Cluster/Results_Coords.h Cluster/Sieve.h Cluster/Silhouette.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_float.h DataSet_integer.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TypeNameHolder.h Unit.h Vec3.h
 Cluster/DBI.o : Cluster/DBI.cpp Cluster/CentroidArray.h Cluster/Cframes.h Cluster/DBI.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h
 Cluster/DrawGraph.o : Cluster/DrawGraph.cpp AssociatedData.h Atom.h Cluster/Cframes.h Cluster/DrawGraph.h Cluster/Metric.h Cluster/MetricArray.h Constants.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h Dimension.h FileIO.h FileName.h MetaData.h NameType.h PDBfile.h Parallel.h Range.h Residue.h SymbolExporting.h TextFormat.h Vec3.h
 Cluster/DynamicMatrix.o : Cluster/DynamicMatrix.cpp ArrayIterator.h Cluster/DynamicMatrix.h CpptrajStdio.h Matrix.h
 Cluster/List.o : Cluster/List.cpp AssociatedData.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_integer.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h ProgressBar.h Range.h TextFormat.h
-Cluster/MetricArray.o : Cluster/MetricArray.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Metric_DME.h Cluster/Metric_QuatRMSD.h Cluster/Metric_RMS.h Cluster/Metric_SRMSD.h Cluster/Metric_Scalar.h Cluster/Metric_Torsion.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h QuaternionRMSD.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Cluster/Metric_DME.o : Cluster/Metric_DME.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Cluster/Centroid.h Cluster/Centroid_Coord.h Cluster/Cframes.h Cluster/Metric.h Cluster/Metric_DME.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Cluster/MetricArray.o : Cluster/MetricArray.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Metric_DME.h Cluster/Metric_QuatRMSD.h Cluster/Metric_RMS.h Cluster/Metric_SRMSD.h Cluster/Metric_Scalar.h Cluster/Metric_Torsion.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ProgressBar.h QuaternionRMSD.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Cluster/Metric_DME.o : Cluster/Metric_DME.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Cluster/Centroid.h Cluster/Centroid_Coord.h Cluster/Cframes.h Cluster/Metric.h Cluster/Metric_DME.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Cluster/Metric_Matrix2D.o : Cluster/Metric_Matrix2D.cpp AssociatedData.h Cluster/Metric.h Cluster/Metric_Matrix2D.h CpptrajFile.h DataSet.h DataSet_2D.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
-Cluster/Metric_QuatRMSD.o : Cluster/Metric_QuatRMSD.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Cluster/Centroid.h Cluster/Centroid_Coord.h Cluster/Cframes.h Cluster/Metric.h Cluster/Metric_QuatRMSD.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h QuaternionRMSD.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Cluster/Metric_RMS.o : Cluster/Metric_RMS.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Cluster/Centroid.h Cluster/Centroid_Coord.h Cluster/Cframes.h Cluster/Metric.h Cluster/Metric_RMS.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Cluster/Metric_SRMSD.o : Cluster/Metric_SRMSD.cpp ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Cluster/Centroid.h Cluster/Centroid_Coord.h Cluster/Cframes.h Cluster/Metric.h Cluster/Metric_SRMSD.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Cluster/Metric_QuatRMSD.o : Cluster/Metric_QuatRMSD.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Cluster/Centroid.h Cluster/Centroid_Coord.h Cluster/Cframes.h Cluster/Metric.h Cluster/Metric_QuatRMSD.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h QuaternionRMSD.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Cluster/Metric_RMS.o : Cluster/Metric_RMS.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Cluster/Centroid.h Cluster/Centroid_Coord.h Cluster/Cframes.h Cluster/Metric.h Cluster/Metric_RMS.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Cluster/Metric_SRMSD.o : Cluster/Metric_SRMSD.cpp ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Cluster/Centroid.h Cluster/Centroid_Coord.h Cluster/Cframes.h Cluster/Metric.h Cluster/Metric_SRMSD.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Cluster/Metric_Scalar.o : Cluster/Metric_Scalar.cpp AssociatedData.h Cluster/Centroid.h Cluster/Centroid_Num.h Cluster/Cframes.h Cluster/Metric.h Cluster/Metric_Scalar.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
 Cluster/Metric_Torsion.o : Cluster/Metric_Torsion.cpp AssociatedData.h Cluster/Centroid.h Cluster/Centroid_Num.h Cluster/Cframes.h Cluster/Metric.h Cluster/Metric_Torsion.h Constants.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
 Cluster/Node.o : Cluster/Node.cpp AssociatedData.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h CpptrajFile.h DataSet.h DataSet_1D.h DataSet_float.h DataSet_integer.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
 Cluster/Output.o : Cluster/Output.cpp ArrayIterator.h Cluster/Algorithm.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Output.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Matrix.h Parallel.h Timer.h
 Cluster/PseudoF.o : Cluster/PseudoF.cpp Cluster/CentroidArray.h Cluster/Cframes.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/PseudoF.h Constants.h CpptrajStdio.h
-Cluster/Results_Coords.o : Cluster/Results_Coords.cpp ActionFrameCounter.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Metric_DME.h Cluster/Metric_RMS.h Cluster/Metric_SRMSD.h Cluster/Node.h Cluster/Results.h Cluster/Results_Coords.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Cluster/Results_Coords.o : Cluster/Results_Coords.cpp ActionFrameCounter.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Metric_DME.h Cluster/Metric_RMS.h Cluster/Metric_SRMSD.h Cluster/Node.h Cluster/Results.h Cluster/Results_Coords.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Cluster/Sieve.o : Cluster/Sieve.cpp AssociatedData.h Cluster/Cframes.h Cluster/Sieve.h CpptrajFile.h DataSet.h DataSet_PairwiseCache.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Random.h Range.h TextFormat.h
 Cluster/Silhouette.o : Cluster/Silhouette.cpp Cluster/CentroidArray.h Cluster/Cframes.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Silhouette.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h OnlineVarT.h Parallel.h
 ClusterMap.o : ClusterMap.cpp AssociatedData.h ClusterMap.h Constants.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_2D.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h ProgressBar.h ProgressTimer.h Range.h TextFormat.h Timer.h
 Cmd.o : Cmd.cpp Cmd.h DispatchObject.h
 CmdInput.o : CmdInput.cpp CmdInput.h StringRoutines.h
 CmdList.o : CmdList.cpp Cmd.h CmdList.h DispatchObject.h
-Command.o : Command.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h ActionTopWriter.h Action_Align.h Action_Angle.h Action_AreaPerMol.h Action_AtomMap.h Action_AtomicCorr.h Action_AtomicFluct.h Action_AutoImage.h Action_Average.h Action_AvgBox.h Action_Bounds.h Action_Box.h Action_Center.h Action_Channel.h Action_CheckChirality.h Action_CheckStructure.h Action_Closest.h Action_ClusterDihedral.h Action_Contacts.h Action_CreateCrd.h Action_CreateReservoir.h Action_DNAionTracker.h Action_DSSP.h Action_Density.h Action_Diffusion.h Action_Dihedral.h Action_DihedralRMS.h Action_Dipole.h Action_DistRmsd.h Action_Distance.h Action_Energy.h Action_Esander.h Action_FilterByData.h Action_FixAtomOrder.h Action_FixImagedBonds.h Action_GIST.h Action_Grid.h Action_GridFreeEnergy.h Action_HydrogenBond.h Action_Image.h Action_InfraredSpectrum.h Action_Jcoupling.h Action_Keep.h Action_LESsplit.h Action_LIE.h Action_LipidOrder.h Action_MakeStructure.h Action_Mask.h Action_Matrix.h Action_MinImage.h Action_Molsurf.h Action_MultiDihedral.h Action_MultiPucker.h Action_MultiVector.h Action_NAstruct.h Action_NMRrst.h Action_NativeContacts.h Action_OrderParameter.h Action_Outtraj.h Action_PairDist.h Action_Pairwise.h Action_Principal.h Action_Projection.h Action_Pucker.h Action_Radgyr.h Action_Radial.h Action_RandomizeIons.h Action_Remap.h Action_ReplicateCell.h Action_Rmsd.h Action_Rotate.h Action_RunningAvg.h Action_STFC_Diffusion.h Action_Scale.h Action_SetVelocity.h Action_Spam.h Action_Strip.h Action_Surf.h Action_SymmetricRmsd.h Action_Temperature.h Action_Time.h Action_ToroidalDiffusion.h Action_Translate.h Action_Unstrip.h Action_Unwrap.h Action_Vector.h Action_VelocityAutoCorr.h Action_Volmap.h Action_Volume.h Action_Watershell.h Action_XtalSymm.h Analysis.h AnalysisList.h AnalysisState.h Analysis_AmdBias.h Analysis_AutoCorr.h Analysis_Average.h Analysis_CalcDiffusion.h Analysis_Clustering.h Analysis_ConstantPHStats.h Analysis_Corr.h Analysis_CrankShaft.h Analysis_CrdFluct.h Analysis_CrossCorr.h Analysis_CurveFit.h Analysis_Divergence.h Analysis_EvalPlateau.h Analysis_FFT.h Analysis_HausdorffDistance.h Analysis_Hist.h Analysis_IRED.h Analysis_Integrate.h Analysis_KDE.h Analysis_Lifetime.h Analysis_LowestCurve.h Analysis_Matrix.h Analysis_MeltCurve.h Analysis_Modes.h Analysis_MultiHist.h Analysis_Multicurve.h Analysis_Overlap.h Analysis_PhiPsi.h Analysis_Regression.h Analysis_RemLog.h Analysis_Rms2d.h Analysis_RmsAvgCorr.h Analysis_Rotdif.h Analysis_RunningAvg.h Analysis_Slope.h Analysis_Spline.h Analysis_State.h Analysis_Statistics.h Analysis_TI.h Analysis_TICA.h Analysis_Timecorr.h Analysis_VectorMath.h Analysis_Wavelet.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h AxisType.h BaseIOtype.h Box.h BoxArgs.h BufferedLine.h CharMask.h Cluster/Algorithm.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Control.h Cluster/DrawGraph.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Sieve.h Cluster/Silhouette.h ClusterMap.h Cmd.h CmdInput.h CmdList.h Command.h CompactFrameArray.h ComplexArray.h Constants.h Constraints.h ControlBlock.h ControlBlock_For.h CoordinateInfo.h Corr.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_RemLog.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h Deprecated.h DiffusionResults.h DihedralSearch.h Dimension.h DispatchObject.h Energy.h Energy_Sander.h EnsembleIn.h EnsembleOutList.h Ewald.h EwaldOptions.h Ewald_ParticleMesh.h ExclusionArray.h Exec.h Exec_AddMissingRes.h Exec_Analyze.h Exec_Build.h Exec_Calc.h Exec_CatCrd.h Exec_Change.h Exec_ClusterMap.h Exec_CombineCoords.h Exec_Commands.h Exec_CompareClusters.h Exec_CompareEnergy.h Exec_CompareTop.h Exec_CrdAction.h Exec_CrdOut.h Exec_CrdTransform.h Exec_CreateSet.h Exec_DataFile.h Exec_DataFilter.h Exec_DataSetCmd.h Exec_Desc.h Exec_Emin.h Exec_ExtendedComparison.h Exec_Flatten.h Exec_GenerateAmberRst.h Exec_Graft.h Exec_Help.h Exec_HmassRepartition.h Exec_LoadCrd.h Exec_LoadTraj.h Exec_ParallelAnalysis.h Exec_ParmBox.h Exec_ParmSolvent.h Exec_ParmStrip.h Exec_ParmWrite.h Exec_ParseTiming.h Exec_PermuteDihedrals.h Exec_Precision.h Exec_PrepareForLeap.h Exec_PrintData.h Exec_Random.h Exec_ReadData.h Exec_ReadEnsembleData.h Exec_ReadInput.h Exec_RotateDihedral.h Exec_RunAnalysis.h Exec_ScaleDihedralK.h Exec_Sequence.h Exec_SequenceAlign.h Exec_Set.h Exec_Show.h Exec_SortEnsembleData.h Exec_Source.h Exec_SplitCoords.h Exec_System.h Exec_Top.h Exec_Traj.h Exec_UpdateParameters.h Exec_ViewRst.h Exec_Zmatrix.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h GIST_PME.h Grid.h GridAction.h GridBin.h GridMover.h HistBin.h Hungarian.h ImageOption.h ImageTypes.h InputTrajCommon.h MapAtom.h MaskArray.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h OnlineVarT.h OutputTrajCommon.h PDBfile.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PubFFT.h Pucker.h Pucker_PuckerMask.h Pucker_PuckerSearch.h Pucker_PuckerToken.h RPNcalc.h Random.h Range.h ReferenceAction.h ReferenceFrame.h RemdReservoirNC.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h SplineFxnTable.h StructureCheck.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h cuda_kernels/GistCudaSetup.cuh helpme_standalone.h molsurf.h
+Command.o : Command.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h ActionTopWriter.h Action_Align.h Action_Angle.h Action_AreaPerMol.h Action_AtomMap.h Action_AtomicCorr.h Action_AtomicFluct.h Action_AutoImage.h Action_Average.h Action_AvgBox.h Action_Bounds.h Action_Box.h Action_Center.h Action_Channel.h Action_CheckChirality.h Action_CheckStructure.h Action_Closest.h Action_ClusterDihedral.h Action_Contacts.h Action_CreateCrd.h Action_CreateReservoir.h Action_DNAionTracker.h Action_DSSP.h Action_Density.h Action_Diffusion.h Action_Dihedral.h Action_DihedralRMS.h Action_Dipole.h Action_DistRmsd.h Action_Distance.h Action_Energy.h Action_Esander.h Action_FilterByData.h Action_FixAtomOrder.h Action_FixImagedBonds.h Action_GIST.h Action_Grid.h Action_GridFreeEnergy.h Action_HydrogenBond.h Action_Image.h Action_InfraredSpectrum.h Action_Jcoupling.h Action_Keep.h Action_LESsplit.h Action_LIE.h Action_LipidOrder.h Action_MakeStructure.h Action_Mask.h Action_Matrix.h Action_MinImage.h Action_Molsurf.h Action_MultiDihedral.h Action_MultiPucker.h Action_MultiVector.h Action_NAstruct.h Action_NMRrst.h Action_NativeContacts.h Action_OrderParameter.h Action_Outtraj.h Action_PairDist.h Action_Pairwise.h Action_Principal.h Action_Projection.h Action_Pucker.h Action_Radgyr.h Action_Radial.h Action_RandomizeIons.h Action_Remap.h Action_ReplicateCell.h Action_Rmsd.h Action_Rotate.h Action_RunningAvg.h Action_STFC_Diffusion.h Action_Scale.h Action_SetVelocity.h Action_Spam.h Action_Strip.h Action_Surf.h Action_SymmetricRmsd.h Action_Temperature.h Action_Time.h Action_ToroidalDiffusion.h Action_Translate.h Action_Unstrip.h Action_Unwrap.h Action_Vector.h Action_VelocityAutoCorr.h Action_Volmap.h Action_Volume.h Action_Watershell.h Action_XtalSymm.h Analysis.h AnalysisList.h AnalysisState.h Analysis_AmdBias.h Analysis_AutoCorr.h Analysis_Average.h Analysis_CalcDiffusion.h Analysis_Clustering.h Analysis_ConstantPHStats.h Analysis_Corr.h Analysis_CrankShaft.h Analysis_CrdFluct.h Analysis_CrossCorr.h Analysis_CurveFit.h Analysis_Divergence.h Analysis_EvalPlateau.h Analysis_FFT.h Analysis_HausdorffDistance.h Analysis_Hist.h Analysis_IRED.h Analysis_Integrate.h Analysis_KDE.h Analysis_Lifetime.h Analysis_LowestCurve.h Analysis_Matrix.h Analysis_MeltCurve.h Analysis_Modes.h Analysis_MultiHist.h Analysis_Multicurve.h Analysis_Overlap.h Analysis_PhiPsi.h Analysis_Regression.h Analysis_RemLog.h Analysis_Rms2d.h Analysis_RmsAvgCorr.h Analysis_Rotdif.h Analysis_RunningAvg.h Analysis_Slope.h Analysis_Spline.h Analysis_State.h Analysis_Statistics.h Analysis_TI.h Analysis_TICA.h Analysis_Timecorr.h Analysis_VectorMath.h Analysis_Wavelet.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h AxisType.h BaseIOtype.h Box.h BoxArgs.h BufferedLine.h CharMask.h Cluster/Algorithm.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Control.h Cluster/DrawGraph.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Sieve.h Cluster/Silhouette.h ClusterMap.h Cmd.h CmdInput.h CmdList.h Command.h CompactFrameArray.h ComplexArray.h Constants.h Constraints.h ControlBlock.h ControlBlock_For.h CoordinateInfo.h Corr.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_RemLog.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h Deprecated.h DiffusionResults.h DihedralSearch.h Dimension.h DispatchObject.h Energy.h Energy_Sander.h EnsembleIn.h EnsembleOutList.h Ewald.h EwaldOptions.h Ewald_ParticleMesh.h ExclusionArray.h Exec.h Exec_AddMissingRes.h Exec_Analyze.h Exec_Build.h Exec_Calc.h Exec_CatCrd.h Exec_Change.h Exec_ClusterMap.h Exec_CombineCoords.h Exec_Commands.h Exec_CompareClusters.h Exec_CompareEnergy.h Exec_CompareTop.h Exec_CrdAction.h Exec_CrdOut.h Exec_CrdTransform.h Exec_CreateSet.h Exec_DataFile.h Exec_DataFilter.h Exec_DataSetCmd.h Exec_Desc.h Exec_Emin.h Exec_ExtendedComparison.h Exec_Flatten.h Exec_GenerateAmberRst.h Exec_Graft.h Exec_Help.h Exec_HmassRepartition.h Exec_LoadCrd.h Exec_LoadTraj.h Exec_ParallelAnalysis.h Exec_ParmBox.h Exec_ParmSolvent.h Exec_ParmStrip.h Exec_ParmWrite.h Exec_ParseTiming.h Exec_PermuteDihedrals.h Exec_Precision.h Exec_PrepareForLeap.h Exec_PrintData.h Exec_Random.h Exec_ReadData.h Exec_ReadEnsembleData.h Exec_ReadInput.h Exec_RotateDihedral.h Exec_RunAnalysis.h Exec_ScaleDihedralK.h Exec_Sequence.h Exec_SequenceAlign.h Exec_Set.h Exec_Show.h Exec_SortEnsembleData.h Exec_Source.h Exec_SplitCoords.h Exec_System.h Exec_Top.h Exec_Traj.h Exec_UpdateParameters.h Exec_ViewRst.h Exec_Zmatrix.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h GIST_PME.h Grid.h GridAction.h GridBin.h GridMover.h HistBin.h Hungarian.h ImageOption.h ImageTypes.h InputTrajCommon.h MapAtom.h MaskArray.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h OnlineVarT.h OutputTrajCommon.h PDBfile.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h PubFFT.h Pucker.h Pucker_PuckerMask.h Pucker_PuckerSearch.h Pucker_PuckerToken.h RPNcalc.h Random.h Range.h ReferenceAction.h ReferenceFrame.h RemdReservoirNC.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h SplineFxnTable.h StructureCheck.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h cuda_kernels/GistCudaSetup.cuh helpme_standalone.h molsurf.h
 CompactFrameArray.o : CompactFrameArray.cpp Box.h CompactFrameArray.h CoordinateInfo.h CpptrajStdio.h Matrix_3x3.h Parallel.h ReplicaDimArray.h Vec3.h
 ComplexArray.o : ComplexArray.cpp ArrayIterator.h ComplexArray.h
-Constraints.o : Constraints.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-ControlBlock_For.o : ControlBlock_For.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h ControlBlock.h ControlBlock_For.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_dataSetBlocks.h ForLoop_inData.h ForLoop_integer.h ForLoop_list.h ForLoop_mask.h ForLoop_overSets.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Constraints.o : Constraints.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+ControlBlock_For.o : ControlBlock_For.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h ControlBlock.h ControlBlock_For.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_dataSetBlocks.h ForLoop_inData.h ForLoop_integer.h ForLoop_list.h ForLoop_mask.h ForLoop_overSets.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 CoordinateInfo.o : CoordinateInfo.cpp Box.h CoordinateInfo.h CpptrajStdio.h Matrix_3x3.h Parallel.h ReplicaDimArray.h Vec3.h
 Corr.o : Corr.cpp ArrayIterator.h ComplexArray.h Corr.h PubFFT.h
 Cph.o : Cph.cpp Cph.h NameType.h
-Cpptraj.o : Cpptraj.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdInput.h CmdList.h Command.h Constants.h CoordinateInfo.h Cpptraj.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h Gpu.h HipDefinitions.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NDiff.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReadLine.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h TopInfo.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h Version.h
+Cpptraj.o : Cpptraj.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdInput.h CmdList.h Command.h Constants.h CoordinateInfo.h Cpptraj.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h Gpu.h HipDefinitions.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NDiff.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ParmFile.h Range.h ReadLine.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h TopInfo.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h Version.h
 CpptrajFile.o : CpptrajFile.cpp CpptrajFile.h CpptrajStdio.h FileIO.h FileIO_Bzip2.h FileIO_Gzip.h FileIO_Mpi.h FileIO_MpiShared.h FileIO_Std.h FileName.h Parallel.h StringRoutines.h
-CpptrajState.o : CpptrajState.cpp Action.h ActionList.h ActionState.h Action_CreateCrd.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_Topology.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleNavigator.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+CpptrajState.o : CpptrajState.cpp Action.h ActionList.h ActionState.h Action_CreateCrd.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_Topology.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleNavigator.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ProgressBar.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 CpptrajStdio.o : CpptrajStdio.cpp Parallel.h
 CurveFit.o : CurveFit.cpp CurveFit.h
-DataFile.o : DataFile.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Cluster/Cframes.h Cluster/Cmatrix_NC.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataFile.h DataIO.h DataIO_AmberEne.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_CCP4.h DataIO_CharmmFastRep.h DataIO_CharmmOutput.h DataIO_CharmmRepLog.h DataIO_CharmmRtfPrm.h DataIO_Cmatrix_Binary.h DataIO_Cmatrix_NC.h DataIO_Cpout.h DataIO_Evecs.h DataIO_Gnuplot.h DataIO_Grace.h DataIO_LeapRC.h DataIO_Mdout.h DataIO_NetCDF.h DataIO_Numpy.h DataIO_OpenDx.h DataIO_Peaks.h DataIO_RemLog.h DataIO_Std.h DataIO_VecTraj.h DataIO_XVG.h DataIO_Xplor.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TypeNameHolder.h Unit.h Vec3.h
-DataFileList.o : DataFileList.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataFilter.o : DataFilter.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_integer.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO.o : DataIO.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_AmberEne.o : DataIO_AmberEne.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberEne.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_AmberFF.o : DataIO_AmberFF.cpp AmberParamFile.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberFF.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_AmberFrcmod.o : DataIO_AmberFrcmod.cpp AmberParamFile.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberFrcmod.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_AmberLib.o : DataIO_AmberLib.cpp ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberLib.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_AmberPrep.o : DataIO_AmberPrep.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberPrep.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_CCP4.o : DataIO_CCP4.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ByteRoutines.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CCP4.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_CharmmFastRep.o : DataIO_CharmmFastRep.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmFastRep.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_CharmmOutput.o : DataIO_CharmmOutput.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmOutput.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_CharmmRepLog.o : DataIO_CharmmRepLog.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmRepLog.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_CharmmRtfPrm.o : DataIO_CharmmRtfPrm.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharmmParamFile.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmRtfPrm.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h DataSet_Topology.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_Cmatrix_Binary.o : DataIO_Cmatrix_Binary.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/Cframes.h Cluster/Cmatrix_Binary.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Cmatrix_Binary.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_Cmatrix_NC.o : DataIO_Cmatrix_NC.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/Cframes.h Cluster/Cmatrix_NC.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Cmatrix_NC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_Cpout.o : DataIO_Cpout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Cpout.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h DataSet_PHREMD_Implicit.h DataSet_pH.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_Evecs.o : DataIO_Evecs.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Evecs.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_Gnuplot.o : DataIO_Gnuplot.cpp ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Gnuplot.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_Grace.o : DataIO_Grace.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Grace.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_string.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_LeapRC.o : DataIO_LeapRC.cpp ArgList.h AssociatedData.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_Mdout.o : DataIO_Mdout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Mdout.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_NetCDF.o : DataIO_NetCDF.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/Cframes.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_NetCDF.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_Mesh.h DataSet_Modes.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_Vector.h DataSet_Vector_Scalar.h DataSet_string.h DataSet_unsignedInt.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h Version.h
-DataIO_Numpy.o : DataIO_Numpy.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Numpy.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h libnpy/npy.hpp
-DataIO_OpenDx.o : DataIO_OpenDx.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_OpenDx.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridDbl.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_Peaks.o : DataIO_Peaks.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Peaks.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector_Scalar.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_RemLog.o : DataIO_RemLog.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_RemLog.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_Std.o : DataIO_Std.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Cluster/Cframes.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Std.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_Parameters.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_string.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_VecTraj.o : DataIO_VecTraj.cpp ActionFrameCounter.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_VecTraj.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_XVG.o : DataIO_XVG.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_XVG.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_Xplor.o : DataIO_Xplor.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Xplor.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataFile.o : DataFile.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Cluster/Cframes.h Cluster/Cmatrix_NC.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataFile.h DataIO.h DataIO_AmberEne.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_CCP4.h DataIO_CharmmFastRep.h DataIO_CharmmOutput.h DataIO_CharmmRepLog.h DataIO_CharmmRtfPrm.h DataIO_Cmatrix_Binary.h DataIO_Cmatrix_NC.h DataIO_Cpout.h DataIO_Evecs.h DataIO_Gnuplot.h DataIO_Grace.h DataIO_LeapRC.h DataIO_Mdout.h DataIO_NetCDF.h DataIO_Numpy.h DataIO_OpenDx.h DataIO_Peaks.h DataIO_RemLog.h DataIO_Std.h DataIO_VecTraj.h DataIO_XVG.h DataIO_Xplor.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TypeNameHolder.h Unit.h Vec3.h
+DataFileList.o : DataFileList.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataFilter.o : DataFilter.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_integer.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO.o : DataIO.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_AmberEne.o : DataIO_AmberEne.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberEne.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_AmberFF.o : DataIO_AmberFF.cpp AmberParamFile.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberFF.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_AmberFrcmod.o : DataIO_AmberFrcmod.cpp AmberParamFile.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberFrcmod.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_AmberLib.o : DataIO_AmberLib.cpp ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberLib.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_AmberPrep.o : DataIO_AmberPrep.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberPrep.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_CCP4.o : DataIO_CCP4.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ByteRoutines.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CCP4.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_CharmmFastRep.o : DataIO_CharmmFastRep.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmFastRep.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_CharmmOutput.o : DataIO_CharmmOutput.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmOutput.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_CharmmRepLog.o : DataIO_CharmmRepLog.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmRepLog.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_CharmmRtfPrm.o : DataIO_CharmmRtfPrm.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharmmParamFile.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmRtfPrm.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h DataSet_Topology.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_Cmatrix_Binary.o : DataIO_Cmatrix_Binary.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/Cframes.h Cluster/Cmatrix_Binary.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Cmatrix_Binary.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_Cmatrix_NC.o : DataIO_Cmatrix_NC.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/Cframes.h Cluster/Cmatrix_NC.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Cmatrix_NC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_Cpout.o : DataIO_Cpout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Cpout.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h DataSet_PHREMD_Implicit.h DataSet_pH.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_Evecs.o : DataIO_Evecs.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Evecs.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_Gnuplot.o : DataIO_Gnuplot.cpp ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Gnuplot.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_Grace.o : DataIO_Grace.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Grace.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_string.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_LeapRC.o : DataIO_LeapRC.cpp ArgList.h AssociatedData.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_Mdout.o : DataIO_Mdout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Mdout.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_NetCDF.o : DataIO_NetCDF.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/Cframes.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_NetCDF.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_Mesh.h DataSet_Modes.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_Vector.h DataSet_Vector_Scalar.h DataSet_string.h DataSet_unsignedInt.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h Version.h
+DataIO_Numpy.o : DataIO_Numpy.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Numpy.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h libnpy/npy.hpp
+DataIO_OpenDx.o : DataIO_OpenDx.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_OpenDx.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridDbl.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_Peaks.o : DataIO_Peaks.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Peaks.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector_Scalar.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_RemLog.o : DataIO_RemLog.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_RemLog.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_Std.o : DataIO_Std.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Cluster/Cframes.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Std.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_Parameters.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_string.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_VecTraj.o : DataIO_VecTraj.cpp ActionFrameCounter.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_VecTraj.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_XVG.o : DataIO_XVG.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_XVG.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_Xplor.o : DataIO_Xplor.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Xplor.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataSet.o : DataSet.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
-DataSetList.o : DataSetList.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Cluster/Cframes.h Cluster/Cmatrix_NC.h CompactFrameArray.h ComplexArray.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_FRM.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_GridDbl.h DataSet_GridFlt.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_NameMap.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h DataSet_PHREMD_Implicit.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_PairwiseCache_NC.h DataSet_Parameters.h DataSet_RemLog.h DataSet_StringVar.h DataSet_Tensor.h DataSet_Topology.h DataSet_Vector.h DataSet_Vector_Scalar.h DataSet_Zmatrix.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_disk.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h DataSet_unsignedInt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h InputTrajCommon.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h SymmetricTensor.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TypeNameHolder.h Unit.h Vec3.h
+DataSetList.o : DataSetList.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Cluster/Cframes.h Cluster/Cmatrix_NC.h CompactFrameArray.h ComplexArray.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_FRM.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_GridDbl.h DataSet_GridFlt.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_NameMap.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h DataSet_PHREMD_Implicit.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_PairwiseCache_NC.h DataSet_Parameters.h DataSet_RemLog.h DataSet_StringVar.h DataSet_Tensor.h DataSet_Topology.h DataSet_Vector.h DataSet_Vector_Scalar.h DataSet_Zmatrix.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_disk.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h DataSet_unsignedInt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h InputTrajCommon.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h SymmetricTensor.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TypeNameHolder.h Unit.h Vec3.h
 DataSet_1D.o : DataSet_1D.cpp ArrayIterator.h AssociatedData.h ComplexArray.h Constants.h Corr.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h PubFFT.h Range.h TextFormat.h
 DataSet_3D.o : DataSet_3D.cpp AssociatedData.h Box.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_3D.h Dimension.h FileIO.h FileName.h GridBin.h Matrix_3x3.h MetaData.h Parallel.h Range.h TextFormat.h Vec3.h
-DataSet_Coords.o : DataSet_Coords.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataSet_Coords_CRD.o : DataSet_Coords_CRD.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_CRD.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataSet_Coords_FRM.o : DataSet_Coords_FRM.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_FRM.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataSet_Coords_REF.o : DataSet_Coords_REF.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TrajFrameCounter.h Trajin.h Trajin_Single.h TypeNameHolder.h Unit.h Vec3.h
-DataSet_Coords_TRJ.o : DataSet_Coords_TRJ.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_TRJ.h Dimension.h FileIO.h FileName.h Frame.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h Trajin_Single.h TypeNameHolder.h Unit.h Vec3.h
+DataSet_Coords.o : DataSet_Coords.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataSet_Coords_CRD.o : DataSet_Coords_CRD.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_CRD.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataSet_Coords_FRM.o : DataSet_Coords_FRM.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_FRM.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataSet_Coords_REF.o : DataSet_Coords_REF.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TrajFrameCounter.h Trajin.h Trajin_Single.h TypeNameHolder.h Unit.h Vec3.h
+DataSet_Coords_TRJ.o : DataSet_Coords_TRJ.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_TRJ.h Dimension.h FileIO.h FileName.h Frame.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h Trajin_Single.h TypeNameHolder.h Unit.h Vec3.h
 DataSet_GridDbl.o : DataSet_GridDbl.cpp ArrayIterator.h AssociatedData.h Box.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_3D.h DataSet_GridDbl.h Dimension.h FileIO.h FileName.h Grid.h GridBin.h Matrix_3x3.h MetaData.h Parallel.h Range.h StringRoutines.h TextFormat.h Vec3.h
 DataSet_GridFlt.o : DataSet_GridFlt.cpp ArrayIterator.h AssociatedData.h Box.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_3D.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Grid.h GridBin.h Matrix_3x3.h MetaData.h Parallel.h Range.h StringRoutines.h TextFormat.h Vec3.h
 DataSet_Mat3x3.o : DataSet_Mat3x3.cpp AssociatedData.h CpptrajFile.h DataSet.h DataSet_Mat3x3.h Dimension.h FileIO.h FileName.h Matrix_3x3.h MetaData.h Parallel.h Range.h TextFormat.h Vec3.h
@@ -254,11 +254,11 @@ DataSet_PHREMD_Implicit.o : DataSet_PHREMD_Implicit.cpp AssociatedData.h Cph.h C
 DataSet_PairwiseCache.o : DataSet_PairwiseCache.cpp AssociatedData.h Cluster/Cframes.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_PairwiseCache.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
 DataSet_PairwiseCache_MEM.o : DataSet_PairwiseCache_MEM.cpp ArrayIterator.h AssociatedData.h Cluster/Cframes.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h Dimension.h FileIO.h FileName.h Matrix.h MetaData.h Parallel.h Range.h StringRoutines.h TextFormat.h
 DataSet_PairwiseCache_NC.o : DataSet_PairwiseCache_NC.cpp AssociatedData.h Cluster/Cframes.h Cluster/Cmatrix_NC.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_PairwiseCache.h DataSet_PairwiseCache_NC.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h StringRoutines.h TextFormat.h
-DataSet_Parameters.o : DataSet_Parameters.cpp AssociatedData.h AtomType.h Constants.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h MetaData.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h TextFormat.h TypeNameHolder.h
+DataSet_Parameters.o : DataSet_Parameters.cpp AssociatedData.h AtomType.h Constants.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h MetaData.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h TextFormat.h TypeNameHolder.h
 DataSet_RemLog.o : DataSet_RemLog.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h ReplicaDimArray.h TextFormat.h
 DataSet_StringVar.o : DataSet_StringVar.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_StringVar.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
 DataSet_Tensor.o : DataSet_Tensor.cpp AssociatedData.h CpptrajFile.h DataSet.h DataSet_Tensor.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h SymmetricTensor.h TextFormat.h
-DataSet_Topology.o : DataSet_Topology.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Topology.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataSet_Topology.o : DataSet_Topology.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Topology.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ParmFile.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataSet_Vector.o : DataSet_Vector.cpp ArrayIterator.h AssociatedData.h ComplexArray.h Constants.h Corr.h CpptrajFile.h DataSet.h DataSet_1D.h DataSet_Vector.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h PubFFT.h Range.h SymbolExporting.h TextFormat.h Vec3.h
 DataSet_Vector_Scalar.o : DataSet_Vector_Scalar.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Vector_Scalar.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h Vec3.h
 DataSet_Zmatrix.o : DataSet_Zmatrix.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Zmatrix.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h Structure/InternalCoords.h Structure/Zmatrix.h TextFormat.h Vec3.h
@@ -270,85 +270,85 @@ DataSet_pH.o : DataSet_pH.cpp AssociatedData.h Cph.h CpptrajFile.h CpptrajStdio.
 DataSet_string.o : DataSet_string.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_string.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
 DataSet_unsignedInt.o : DataSet_unsignedInt.cpp AssociatedData.h CpptrajFile.h DataSet.h DataSet_1D.h DataSet_unsignedInt.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
 Deprecated.o : Deprecated.cpp CpptrajStdio.h Deprecated.h DispatchObject.h
-DiffusionResults.o : DiffusionResults.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DiffusionResults.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DihedralSearch.o : DihedralSearch.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DihedralSearch.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DiffusionResults.o : DiffusionResults.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DiffusionResults.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DihedralSearch.o : DihedralSearch.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DihedralSearch.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DistRoutines.o : DistRoutines.cpp Box.h DistRoutines.h ImageOption.h Matrix_3x3.h Parallel.h Vec3.h
-Energy.o : Energy.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h Energy.h Energy/Ene_Angle.h Energy/Ene_Bond.h Energy/Kernel_Harmonic.h ExclusionArray.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Energy.o : Energy.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h Energy.h Energy/Ene_Angle.h Energy/Ene_Bond.h Energy/Kernel_Harmonic.h ExclusionArray.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 EnergyArray.o : EnergyArray.cpp CpptrajFile.h CpptrajStdio.h EnergyArray.h FileIO.h FileName.h Parallel.h
-Energy_Sander.o : Energy_Sander.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy_Sander.h FileName.h FileTypes.h File_TempName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Energy_Sander.o : Energy_Sander.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy_Sander.h FileName.h FileTypes.h File_TempName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ParmFile.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 EnsembleIn.o : EnsembleIn.cpp Atom.h AtomMask.h Box.h CoordinateInfo.h CpptrajStdio.h EnsembleIn.h FileName.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h Timer.h TrajFrameCounter.h Unit.h Vec3.h
-EnsembleIn_Multi.o : EnsembleIn_Multi.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h EnsembleIn.h EnsembleIn_Multi.h FileIO.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-EnsembleIn_Single.o : EnsembleIn_Single.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h EnsembleIn.h EnsembleIn_Single.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+EnsembleIn_Multi.o : EnsembleIn_Multi.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h EnsembleIn.h EnsembleIn_Multi.h FileIO.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+EnsembleIn_Single.o : EnsembleIn_Single.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h EnsembleIn.h EnsembleIn_Single.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
 EnsembleNavigator.o : EnsembleNavigator.cpp Atom.h AtomMask.h Box.h CoordinateInfo.h CpptrajStdio.h EnsembleIn.h EnsembleNavigator.h FileName.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h Timer.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TrajinList.h Unit.h Vec3.h
 EnsembleOut.o : EnsembleOut.cpp ActionFrameCounter.h BaseIOtype.h Box.h CoordinateInfo.h CpptrajStdio.h EnsembleOut.h FileName.h FileTypes.h FramePtrArray.h Matrix_3x3.h OutputTrajCommon.h Parallel.h Range.h ReplicaDimArray.h TrajectoryFile.h Vec3.h
-EnsembleOutList.o : EnsembleOutList.cpp ActionFrameCounter.h ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h EnsembleOut.h EnsembleOutList.h EnsembleOut_Multi.h EnsembleOut_Single.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TrajectoryFile.h TypeNameHolder.h Unit.h Vec3.h
-EnsembleOut_Multi.o : EnsembleOut_Multi.cpp ActionFrameCounter.h ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h EnsembleOut.h EnsembleOut_Multi.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-EnsembleOut_Single.o : EnsembleOut_Single.cpp ActionFrameCounter.h ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h EnsembleOut.h EnsembleOut_Single.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Ewald.o : Ewald.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h EnergyKernel_Adjust.h EnergyKernel_Nonbond.h Ewald.h ExclusionArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h PairListLoop.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Spline.h SplineFxnTable.h StringRoutines.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+EnsembleOutList.o : EnsembleOutList.cpp ActionFrameCounter.h ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h EnsembleOut.h EnsembleOutList.h EnsembleOut_Multi.h EnsembleOut_Single.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TrajectoryFile.h TypeNameHolder.h Unit.h Vec3.h
+EnsembleOut_Multi.o : EnsembleOut_Multi.cpp ActionFrameCounter.h ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h EnsembleOut.h EnsembleOut_Multi.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+EnsembleOut_Single.o : EnsembleOut_Single.cpp ActionFrameCounter.h ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h EnsembleOut.h EnsembleOut_Single.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+Ewald.o : Ewald.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h EnergyKernel_Adjust.h EnergyKernel_Nonbond.h Ewald.h ExclusionArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h PairListLoop.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h Spline.h SplineFxnTable.h StringRoutines.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 EwaldOptions.o : EwaldOptions.cpp ArgList.h CpptrajStdio.h EwaldOptions.h
 Ewald_ParticleMesh.o : Ewald_ParticleMesh.cpp Atom.h AtomMask.h Box.h CoordinateInfo.h CpptrajStdio.h Ewald.h EwaldOptions.h Ewald_ParticleMesh.h ExclusionArray.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h Timer.h Unit.h Vec3.h helpme_standalone.h
 Ewald_Regular.o : Ewald_Regular.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Ewald.h EwaldOptions.h Ewald_Regular.h ExclusionArray.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h StringRoutines.h SymbolExporting.h Timer.h Unit.h Vec3.h
 ExclusionArray.o : ExclusionArray.cpp Atom.h AtomMask.h CharMask.h CpptrajStdio.h ExclusionArray.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Unit.h
-Exec_AddMissingRes.o : Exec_AddMissingRes.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CharMask.h CompactFrameArray.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_AddMissingRes.h Exec_AddMissingRes_Pres.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Analyze.o : Exec_Analyze.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Analyze.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Build.o : Exec_Build.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/GB_Params.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/Creator.h Structure/Disulfide.h Structure/HisProt.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/StructureEnum.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Calc.o : Exec_Calc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Calc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_CatCrd.o : Exec_CatCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CatCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Change.o : Exec_Change.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Change.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_ClusterMap.o : Exec_ClusterMap.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ClusterMap.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ClusterMap.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_CombineCoords.o : Exec_CombineCoords.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CombineCoords.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Commands.o : Exec_Commands.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Commands.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_CompareClusters.o : Exec_CompareClusters.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CompareClusters.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_CompareEnergy.o : Exec_CompareEnergy.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h Energy/Kernel_Fourier.h Energy/Kernel_Harmonic.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CompareEnergy.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_CompareTop.o : Exec_CompareTop.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CompareTop.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_CrdAction.o : Exec_CrdAction.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CrdAction.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_CrdOut.o : Exec_CrdOut.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CrdOut.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-Exec_CrdTransform.o : Exec_CrdTransform.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CrdTransform.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_CreateSet.o : Exec_CreateSet.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CreateSet.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_DataFile.o : Exec_DataFile.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_DataFile.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_DataFilter.o : Exec_DataFilter.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_DataFilter.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_DataSetCmd.o : Exec_DataSetCmd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h ArrayIterator.h AssociatedData.h AssociatedData_Connect.h AssociatedData_NOE.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_Mesh.h DataSet_Vector.h DataSet_string.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_DataSetCmd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Desc.o : Exec_Desc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Desc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Emin.o : Exec_Emin.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Emin.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_ExtendedComparison.o : Exec_ExtendedComparison.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ExtendedComparison.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Flatten.o : Exec_Flatten.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Flatten.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_GenerateAmberRst.o : Exec_GenerateAmberRst.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_GenerateAmberRst.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Graft.o : Exec_Graft.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Graft.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Help.o : Exec_Help.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Help.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_HmassRepartition.o : Exec_HmassRepartition.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_HmassRepartition.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_LoadCrd.o : Exec_LoadCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_LoadCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_LoadTraj.o : Exec_LoadTraj.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_LoadTraj.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_ParallelAnalysis.o : Exec_ParallelAnalysis.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParallelAnalysis.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_ParmBox.o : Exec_ParmBox.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BoxArgs.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmBox.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_ParmSolvent.o : Exec_ParmSolvent.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmSolvent.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_ParmStrip.o : Exec_ParmStrip.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmStrip.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_ParmWrite.o : Exec_ParmWrite.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmWrite.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_ParseTiming.o : Exec_ParseTiming.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParseTiming.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_PermuteDihedrals.o : Exec_PermuteDihedrals.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h DistRoutines.h EnsembleIn.h EnsembleOutList.h ExclusionArray.h Exec.h Exec_PermuteDihedrals.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Precision.o : Exec_Precision.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Precision.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_PrepareForLeap.o : Exec_PrepareForLeap.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_PrepareForLeap.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h LeapInterface.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h Remote.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/Disulfide.h Structure/HisProt.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-Exec_PrintData.o : Exec_PrintData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_PrintData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Random.o : Exec_Random.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Random.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_ReadData.o : Exec_ReadData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ReadData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_ReadEnsembleData.o : Exec_ReadEnsembleData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ReadEnsembleData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_ReadInput.o : Exec_ReadInput.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ReadInput.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_RotateDihedral.o : Exec_RotateDihedral.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_RotateDihedral.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_RunAnalysis.o : Exec_RunAnalysis.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_RunAnalysis.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_ScaleDihedralK.o : Exec_ScaleDihedralK.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ScaleDihedralK.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Sequence.o : Exec_Sequence.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Sequence.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/Creator.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_SequenceAlign.o : Exec_SequenceAlign.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SequenceAlign.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Set.o : Exec_Set.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_StringVar.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Set.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Show.o : Exec_Show.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_StringVar.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Show.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_SortEnsembleData.o : Exec_SortEnsembleData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h DataSet_PHREMD_Implicit.h DataSet_pH.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SortEnsembleData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Source.o : Exec_Source.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Source.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_SplitCoords.o : Exec_SplitCoords.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SplitCoords.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_System.o : Exec_System.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_System.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Top.o : Exec_Top.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Top.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h TopInfo.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Traj.o : Exec_Traj.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Traj.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_UpdateParameters.o : Exec_UpdateParameters.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h DataSet_Topology.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_UpdateParameters.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_ViewRst.o : Exec_ViewRst.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ViewRst.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h ViewRst.h
-Exec_Zmatrix.o : Exec_Zmatrix.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Zmatrix.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Zmatrix.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-ExtendedSimilarity.o : ExtendedSimilarity.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h ExtendedSimilarity.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Exec_AddMissingRes.o : Exec_AddMissingRes.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CharMask.h CompactFrameArray.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_AddMissingRes.h Exec_AddMissingRes_Pres.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ParmFile.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Analyze.o : Exec_Analyze.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Analyze.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Build.o : Exec_Build.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Parm/GB_Params.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/Creator.h Structure/Disulfide.h Structure/HisProt.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/StructureEnum.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Calc.o : Exec_Calc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Calc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_CatCrd.o : Exec_CatCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CatCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Change.o : Exec_Change.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Change.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_ClusterMap.o : Exec_ClusterMap.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ClusterMap.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ClusterMap.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_CombineCoords.o : Exec_CombineCoords.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CombineCoords.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Commands.o : Exec_Commands.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Commands.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_CompareClusters.o : Exec_CompareClusters.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CompareClusters.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_CompareEnergy.o : Exec_CompareEnergy.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h Energy/Kernel_Fourier.h Energy/Kernel_Harmonic.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CompareEnergy.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_CompareTop.o : Exec_CompareTop.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CompareTop.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_CrdAction.o : Exec_CrdAction.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CrdAction.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_CrdOut.o : Exec_CrdOut.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CrdOut.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Exec_CrdTransform.o : Exec_CrdTransform.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CrdTransform.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_CreateSet.o : Exec_CreateSet.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CreateSet.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_DataFile.o : Exec_DataFile.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_DataFile.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_DataFilter.o : Exec_DataFilter.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_DataFilter.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_DataSetCmd.o : Exec_DataSetCmd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h ArrayIterator.h AssociatedData.h AssociatedData_Connect.h AssociatedData_NOE.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_Mesh.h DataSet_Vector.h DataSet_string.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_DataSetCmd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Desc.o : Exec_Desc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Desc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Emin.o : Exec_Emin.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Emin.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_ExtendedComparison.o : Exec_ExtendedComparison.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ExtendedComparison.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Flatten.o : Exec_Flatten.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Flatten.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_GenerateAmberRst.o : Exec_GenerateAmberRst.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_GenerateAmberRst.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Graft.o : Exec_Graft.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Graft.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Help.o : Exec_Help.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Help.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_HmassRepartition.o : Exec_HmassRepartition.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_HmassRepartition.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_LoadCrd.o : Exec_LoadCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_LoadCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_LoadTraj.o : Exec_LoadTraj.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_LoadTraj.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_ParallelAnalysis.o : Exec_ParallelAnalysis.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParallelAnalysis.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_ParmBox.o : Exec_ParmBox.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BoxArgs.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmBox.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_ParmSolvent.o : Exec_ParmSolvent.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmSolvent.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_ParmStrip.o : Exec_ParmStrip.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmStrip.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_ParmWrite.o : Exec_ParmWrite.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmWrite.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_ParseTiming.o : Exec_ParseTiming.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParseTiming.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_PermuteDihedrals.o : Exec_PermuteDihedrals.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h DistRoutines.h EnsembleIn.h EnsembleOutList.h ExclusionArray.h Exec.h Exec_PermuteDihedrals.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Precision.o : Exec_Precision.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Precision.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_PrepareForLeap.o : Exec_PrepareForLeap.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_PrepareForLeap.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h LeapInterface.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ParmFile.h Range.h ReferenceFrame.h Remote.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/Disulfide.h Structure/HisProt.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Exec_PrintData.o : Exec_PrintData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_PrintData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Random.o : Exec_Random.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Random.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_ReadData.o : Exec_ReadData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ReadData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_ReadEnsembleData.o : Exec_ReadEnsembleData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ReadEnsembleData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_ReadInput.o : Exec_ReadInput.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ReadInput.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_RotateDihedral.o : Exec_RotateDihedral.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_RotateDihedral.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_RunAnalysis.o : Exec_RunAnalysis.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_RunAnalysis.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_ScaleDihedralK.o : Exec_ScaleDihedralK.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ScaleDihedralK.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Sequence.o : Exec_Sequence.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Sequence.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/Creator.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_SequenceAlign.o : Exec_SequenceAlign.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SequenceAlign.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Set.o : Exec_Set.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_StringVar.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Set.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Show.o : Exec_Show.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_StringVar.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Show.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_SortEnsembleData.o : Exec_SortEnsembleData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h DataSet_PHREMD_Implicit.h DataSet_pH.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SortEnsembleData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Source.o : Exec_Source.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Source.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_SplitCoords.o : Exec_SplitCoords.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SplitCoords.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_System.o : Exec_System.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_System.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Top.o : Exec_Top.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Top.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h TopInfo.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Traj.o : Exec_Traj.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Traj.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_UpdateParameters.o : Exec_UpdateParameters.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h DataSet_Topology.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_UpdateParameters.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_ViewRst.o : Exec_ViewRst.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ViewRst.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h ViewRst.h
+Exec_Zmatrix.o : Exec_Zmatrix.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Zmatrix.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Zmatrix.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+ExtendedSimilarity.o : ExtendedSimilarity.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h ExtendedSimilarity.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 ExternalFxn.o : ExternalFxn.cpp Random.h
 FileIO_Bzip2.o : FileIO_Bzip2.cpp CpptrajStdio.h FileIO.h FileIO_Bzip2.h
 FileIO_Gzip.o : FileIO_Gzip.cpp CpptrajStdio.h FileIO.h FileIO_Gzip.h
@@ -359,73 +359,74 @@ FileName.o : FileName.cpp CpptrajStdio.h FileName.h StringRoutines.h
 FileType.o : FileType.cpp FileType.h
 FileTypes.o : FileTypes.cpp ArgList.h BaseIOtype.h CpptrajStdio.h FileTypes.h
 File_TempName.o : File_TempName.cpp CpptrajStdio.h FileName.h File_TempName.h StringRoutines.h
-ForLoop.o : ForLoop.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h ForLoop.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-ForLoop_dataSetBlocks.o : ForLoop_dataSetBlocks.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_dataSetBlocks.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-ForLoop_inData.o : ForLoop_inData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_integer.h DataSet_string.h DataSet_unsignedInt.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_inData.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-ForLoop_integer.o : ForLoop_integer.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_integer.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-ForLoop_list.o : ForLoop_list.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_list.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-ForLoop_mask.o : ForLoop_mask.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_mask.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-ForLoop_overSets.o : ForLoop_overSets.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_overSets.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+ForLoop.o : ForLoop.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h ForLoop.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+ForLoop_dataSetBlocks.o : ForLoop_dataSetBlocks.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_dataSetBlocks.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+ForLoop_inData.o : ForLoop_inData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_integer.h DataSet_string.h DataSet_unsignedInt.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_inData.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+ForLoop_integer.o : ForLoop_integer.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_integer.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+ForLoop_list.o : ForLoop_list.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_list.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+ForLoop_mask.o : ForLoop_mask.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_mask.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+ForLoop_overSets.o : ForLoop_overSets.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_overSets.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Frame.o : Frame.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Unit.h Vec3.h
-GIST_PME.o : GIST_PME.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h EnergyKernel_Adjust.h EnergyKernel_Nonbond.h Ewald.h Ewald_ParticleMesh.h ExclusionArray.h FileName.h Frame.h GIST_PME.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h helpme_standalone.h
+GIST_PME.o : GIST_PME.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h EnergyKernel_Adjust.h EnergyKernel_Nonbond.h Ewald.h Ewald_ParticleMesh.h ExclusionArray.h FileName.h Frame.h GIST_PME.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h helpme_standalone.h
 GistEntropyUtils.o : GistEntropyUtils.cpp CpptrajFile.h FileIO.h FileName.h GistEntropyUtils.h Parallel.h Vec3.h
 Gpu.o : Gpu.cpp Gpu.h
-GridAction.o : GridAction.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridAction.h GridBin.h GridMover.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+GridAction.o : GridAction.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridAction.h GridBin.h GridMover.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 GridBin.o : GridBin.cpp Box.h CpptrajStdio.h GridBin.h Matrix_3x3.h Parallel.h Vec3.h
-GridMover.o : GridMover.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_3D.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h GridMover.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+GridMover.o : GridMover.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_3D.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h GridMover.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 GuessAtomHybridization.o : GuessAtomHybridization.cpp Atom.h AtomType.h Constants.h GuessAtomHybridization.h NameType.h ParameterTypes.h SymbolExporting.h
 HistBin.o : HistBin.cpp Constants.h CpptrajStdio.h Dimension.h HistBin.h
 Hungarian.o : Hungarian.cpp ArrayIterator.h Constants.h CpptrajStdio.h Hungarian.h Matrix.h
 ImageRoutines.o : ImageRoutines.cpp Atom.h AtomMask.h Box.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h Frame.h ImageOption.h ImageRoutines.h ImageTypes.h Image_List.h Image_List_Mask.h Image_List_Pair.h Image_List_Pair_CoM.h Image_List_Pair_First.h Image_List_Pair_Geom.h Image_List_Unit.h Image_List_Unit_CoM.h Image_List_Unit_First.h Image_List_Unit_Geom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Unit.h Vec3.h
-Image_List_Mask.o : Image_List_Mask.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h Image_List.h Image_List_Mask.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Image_List_Pair.o : Image_List_Pair.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h Image_List.h Image_List_Pair.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Image_List_Unit.o : Image_List_Unit.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h Image_List.h Image_List_Unit.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Image_List_Mask.o : Image_List_Mask.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h Image_List.h Image_List_Mask.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Image_List_Pair.o : Image_List_Pair.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h Image_List.h Image_List_Pair.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Image_List_Unit.o : Image_List_Unit.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h Image_List.h Image_List_Unit.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 InputTrajCommon.o : InputTrajCommon.cpp CpptrajStdio.h FileName.h InputTrajCommon.h TrajFrameCounter.h
 KDE.o : KDE.cpp AssociatedData.h Constants.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_double.h Dimension.h FileIO.h FileName.h HistBin.h KDE.h MetaData.h Parallel.h Range.h TextFormat.h
-LeapInterface.o : LeapInterface.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h File_TempName.h Frame.h LeapInterface.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+LeapInterface.o : LeapInterface.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h File_TempName.h Frame.h LeapInterface.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 MapAtom.o : MapAtom.cpp Atom.h MapAtom.h NameType.h SymbolExporting.h
-MaskArray.o : MaskArray.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+MaskArray.o : MaskArray.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 MaskToken.o : MaskToken.cpp ArgList.h Atom.h CpptrajStdio.h DistRoutines.h ImageOption.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Unit.h
 Matrix_3x3.o : Matrix_3x3.cpp Constants.h CpptrajStdio.h Matrix_3x3.h Parallel.h Vec3.h
 MdOpts.o : MdOpts.cpp ArgList.h Constants.h Constraints.h CpptrajStdio.h MdOpts.h ParameterTypes.h
 MetaData.o : MetaData.cpp CpptrajStdio.h FileName.h MetaData.h Range.h StringRoutines.h
-Minimize_SteepestDescent.o : Minimize_SteepestDescent.cpp ActionFrameCounter.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h EnergyArray.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-Mol.o : Mol.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Mol.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Minimize_SteepestDescent.o : Minimize_SteepestDescent.cpp ActionFrameCounter.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h EnergyArray.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Mol.o : Mol.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Mol.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Mol2File.o : Mol2File.cpp Atom.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Mol2File.h NameType.h Parallel.h Residue.h StringRoutines.h SymbolExporting.h
 NC_Routines.o : NC_Routines.cpp CpptrajStdio.h NC_Routines.h
 NDiff.o : NDiff.cpp ArgList.h BufferedLine.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NDiff.h Parallel.h StringRoutines.h
 NameType.o : NameType.cpp CpptrajStdio.h NameType.h
 NetcdfFile.o : NetcdfFile.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h ParallelNetcdf.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Unit.h Vec3.h Version.h
 OMM_helpers.o : OMM_helpers.cpp Constants.h OMM_helpers.h ParameterTypes.h
-OutputTrajCommon.o : OutputTrajCommon.cpp ActionFrameCounter.h ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+OutputTrajCommon.o : OutputTrajCommon.cpp ActionFrameCounter.h ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
 PDBfile.o : PDBfile.cpp Atom.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h PDBfile.h Parallel.h Residue.h StringRoutines.h SymbolExporting.h
 PairList.o : PairList.cpp Atom.h AtomMask.h Box.h CoordinateInfo.h CpptrajStdio.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Timer.h Unit.h Vec3.h
 Parallel.o : Parallel.cpp Parallel.h
 ParallelNetcdf.o : ParallelNetcdf.cpp CpptrajStdio.h Parallel.h ParallelNetcdf.h
-ParameterSet.o : ParameterSet.cpp AtomType.h Constants.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h TypeNameHolder.h UpdateParameters.h
-Parm/GB_Params.o : Parm/GB_Params.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/GB_Params.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-ParmFile.o : ParmFile.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h ParmIO.h Parm_Amber.h Parm_CIF.h Parm_CharmmPsf.h Parm_Gromacs.h Parm_Mol2.h Parm_PDB.h Parm_SDF.h Parm_Tinker.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Parm_Amber.o : Parm_Amber.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h ExclusionArray.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_Amber.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Parm_CIF.o : Parm_CIF.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h CIFfile.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_CIF.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Parm_CharmmPsf.o : Parm_CharmmPsf.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h CharmmParamFile.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Mol.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_CharmmPsf.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Parm_Gromacs.o : Parm_Gromacs.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_Gromacs.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Parm_Mol2.o : Parm_Mol2.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Mol2File.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_Mol2.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Parm_PDB.o : Parm_PDB.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_PDB.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Parm_SDF.o : Parm_SDF.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_SDF.h Range.h ReplicaDimArray.h Residue.h SDFfile.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Parm_Tinker.o : Parm_Tinker.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_Tinker.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TinkerFile.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-PotentialFunction.o : PotentialFunction.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajStdio.h EnergyArray.h ExclusionArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MdOpts.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PotentialFunction.h PotentialTerm.h PotentialTerm_Angle.h PotentialTerm_Bond.h PotentialTerm_Dihedral.h PotentialTerm_LJ_Coulomb.h PotentialTerm_OpenMM.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+ParameterSet.o : ParameterSet.cpp AtomType.h Constants.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h TypeNameHolder.h UpdateParameters.h
+Parm/CmapParmHolder.o : Parm/CmapParmHolder.cpp Constants.h CpptrajStdio.h NameType.h ParameterHolders.h ParameterTypes.h Parm/CmapParmHolder.h TypeNameHolder.h
+Parm/GB_Params.o : Parm/GB_Params.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Parm/GB_Params.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+ParmFile.o : ParmFile.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ParmFile.h ParmIO.h Parm_Amber.h Parm_CIF.h Parm_CharmmPsf.h Parm_Gromacs.h Parm_Mol2.h Parm_PDB.h Parm_SDF.h Parm_Tinker.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Parm_Amber.o : Parm_Amber.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h ExclusionArray.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ParmIO.h Parm_Amber.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Parm_CIF.o : Parm_CIF.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h CIFfile.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ParmIO.h Parm_CIF.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Parm_CharmmPsf.o : Parm_CharmmPsf.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h CharmmParamFile.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Mol.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ParmIO.h Parm_CharmmPsf.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Parm_Gromacs.o : Parm_Gromacs.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ParmIO.h Parm_Gromacs.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Parm_Mol2.o : Parm_Mol2.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Mol2File.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ParmIO.h Parm_Mol2.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Parm_PDB.o : Parm_PDB.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ParmIO.h Parm_PDB.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Parm_SDF.o : Parm_SDF.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ParmIO.h Parm_SDF.h Range.h ReplicaDimArray.h Residue.h SDFfile.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Parm_Tinker.o : Parm_Tinker.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ParmIO.h Parm_Tinker.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TinkerFile.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+PotentialFunction.o : PotentialFunction.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajStdio.h EnergyArray.h ExclusionArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MdOpts.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h PotentialFunction.h PotentialTerm.h PotentialTerm_Angle.h PotentialTerm_Bond.h PotentialTerm_Dihedral.h PotentialTerm_LJ_Coulomb.h PotentialTerm_OpenMM.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 PotentialTerm.o : PotentialTerm.cpp PotentialTerm.h
-PotentialTerm_Angle.o : PotentialTerm_Angle.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h EnergyArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PotentialTerm.h PotentialTerm_Angle.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-PotentialTerm_Bond.o : PotentialTerm_Bond.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h EnergyArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PotentialTerm.h PotentialTerm_Bond.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-PotentialTerm_Dihedral.o : PotentialTerm_Dihedral.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h EnergyArray.h EnergyKernel_NonBond_Simple.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PotentialTerm.h PotentialTerm_Dihedral.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-PotentialTerm_LJ_Coulomb.o : PotentialTerm_LJ_Coulomb.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajStdio.h EnergyArray.h EnergyKernel_NonBond_Simple.h ExclusionArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MdOpts.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PotentialTerm.h PotentialTerm_LJ_Coulomb.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-PotentialTerm_OpenMM.o : PotentialTerm_OpenMM.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajStdio.h EnergyArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MdOpts.h Molecule.h NameType.h OMM_helpers.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PotentialTerm.h PotentialTerm_OpenMM.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+PotentialTerm_Angle.o : PotentialTerm_Angle.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h EnergyArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h PotentialTerm.h PotentialTerm_Angle.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+PotentialTerm_Bond.o : PotentialTerm_Bond.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h EnergyArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h PotentialTerm.h PotentialTerm_Bond.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+PotentialTerm_Dihedral.o : PotentialTerm_Dihedral.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h EnergyArray.h EnergyKernel_NonBond_Simple.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h PotentialTerm.h PotentialTerm_Dihedral.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+PotentialTerm_LJ_Coulomb.o : PotentialTerm_LJ_Coulomb.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajStdio.h EnergyArray.h EnergyKernel_NonBond_Simple.h ExclusionArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MdOpts.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h PotentialTerm.h PotentialTerm_LJ_Coulomb.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+PotentialTerm_OpenMM.o : PotentialTerm_OpenMM.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajStdio.h EnergyArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MdOpts.h Molecule.h NameType.h OMM_helpers.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h PotentialTerm.h PotentialTerm_OpenMM.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 ProgressBar.o : ProgressBar.cpp CpptrajStdio.h ProgressBar.h
 ProgressTimer.o : ProgressTimer.cpp CpptrajStdio.h ProgressTimer.h Timer.h
 PubFFT.o : PubFFT.cpp ArrayIterator.h ComplexArray.h CpptrajStdio.h PubFFT.h
-Pucker_PuckerMask.o : Pucker_PuckerMask.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Pucker_PuckerMask.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Pucker_PuckerSearch.o : Pucker_PuckerSearch.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Pucker.h Pucker_PuckerMask.h Pucker_PuckerSearch.h Pucker_PuckerToken.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Pucker_PuckerToken.o : Pucker_PuckerToken.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Pucker_PuckerMask.h Pucker_PuckerToken.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Pucker_PuckerMask.o : Pucker_PuckerMask.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Pucker_PuckerMask.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Pucker_PuckerSearch.o : Pucker_PuckerSearch.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Pucker.h Pucker_PuckerMask.h Pucker_PuckerSearch.h Pucker_PuckerToken.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Pucker_PuckerToken.o : Pucker_PuckerToken.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Pucker_PuckerMask.h Pucker_PuckerToken.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 QuaternionRMSD.o : QuaternionRMSD.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h QuaternionRMSD.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Unit.h Vec3.h qcprot.h
 RNG.o : RNG.cpp CpptrajStdio.h RNG.h
 RNG_Marsaglia.o : RNG_Marsaglia.cpp CpptrajStdio.h RNG.h RNG_Marsaglia.h
@@ -433,11 +434,11 @@ RNG_MersenneTwister.o : RNG_MersenneTwister.cpp CpptrajStdio.h RNG.h RNG_Mersenn
 RNG_PCG32.o : RNG_PCG32.cpp CpptrajStdio.h RNG.h RNG_PCG32.h pcg_random.hpp
 RNG_Stdlib.o : RNG_Stdlib.cpp RNG.h RNG_Stdlib.h
 RNG_Xoshiro128pp.o : RNG_Xoshiro128pp.cpp RNG.h RNG_Xoshiro128pp.h xoshiro128plusplus.h
-RPNcalc.o : RPNcalc.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_Mesh.h DataSet_Vector.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+RPNcalc.o : RPNcalc.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_Mesh.h DataSet_Vector.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Random.o : Random.cpp CpptrajStdio.h RNG.h RNG_Marsaglia.h RNG_MersenneTwister.h RNG_PCG32.h RNG_Stdlib.h RNG_Xoshiro128pp.h Random.h pcg_random.hpp
 Range.o : Range.cpp ArgList.h CpptrajStdio.h Range.h StringRoutines.h
-ReadLine.o : ReadLine.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdInput.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReadLine.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-ReferenceAction.o : ReferenceAction.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h Dimension.h FileIO.h FileName.h Frame.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TypeNameHolder.h Unit.h Vec3.h
+ReadLine.o : ReadLine.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdInput.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReadLine.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+ReferenceAction.o : ReferenceAction.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h Dimension.h FileIO.h FileName.h Frame.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TypeNameHolder.h Unit.h Vec3.h
 RemdReservoirNC.o : RemdReservoirNC.cpp Atom.h AtomMask.h Box.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h RemdReservoirNC.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Unit.h Vec3.h
 Remote.o : Remote.cpp CpptrajStdio.h FileName.h Remote.h
 Residue.o : Residue.cpp NameType.h Residue.h
@@ -447,72 +448,72 @@ SpaceGroup.o : SpaceGroup.cpp Matrix_3x3.h Parallel.h SpaceGroup.h Vec3.h
 Spline.o : Spline.cpp CpptrajStdio.h Spline.h
 SplineFxnTable.o : SplineFxnTable.cpp Constants.h CpptrajStdio.h Spline.h SplineFxnTable.h StringRoutines.h
 StringRoutines.o : StringRoutines.cpp CpptrajStdio.h StringRoutines.h
-Structure/BuildAtom.o : Structure/BuildAtom.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/StructureEnum.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Structure/Builder.o : Structure/Builder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h GuessAtomHybridization.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Builder.h Structure/Chirality.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Structure/BuildAtom.o : Structure/BuildAtom.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/StructureEnum.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Structure/Builder.o : Structure/Builder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h GuessAtomHybridization.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Builder.h Structure/Chirality.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 Structure/Chirality.o : Structure/Chirality.cpp Atom.h Constants.h CpptrajStdio.h NameType.h Structure/Chirality.h SymbolExporting.h Vec3.h
-Structure/Creator.o : Structure/Creator.cpp ArgList.h AssociatedData.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/Creator.h Structure/GenerateConnectivityArrays.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Structure/Disulfide.o : Structure/Disulfide.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Disulfide.h Structure/ResStatArray.h Structure/StructureRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Structure/FunctionalGroup.o : Structure/FunctionalGroup.cpp Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Structure/FxnGroupBuilder.o : Structure/FxnGroupBuilder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h Structure/FxnGroupBuilder.h Structure/StructureRoutines.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Structure/Creator.o : Structure/Creator.cpp ArgList.h AssociatedData.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/Creator.h Structure/GenerateConnectivityArrays.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Structure/Disulfide.o : Structure/Disulfide.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Disulfide.h Structure/ResStatArray.h Structure/StructureRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Structure/FunctionalGroup.o : Structure/FunctionalGroup.cpp Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Structure/FxnGroupBuilder.o : Structure/FxnGroupBuilder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h Structure/FxnGroupBuilder.h Structure/StructureRoutines.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/GenerateConnectivityArrays.o : Structure/GenerateConnectivityArrays.cpp Atom.h Constants.h CpptrajStdio.h NameType.h ParameterTypes.h Residue.h Structure/GenerateConnectivityArrays.h SymbolExporting.h
-Structure/HisProt.o : Structure/HisProt.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/HisProt.h Structure/StructureRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Structure/InternalCoords.o : Structure/InternalCoords.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/InternalCoords.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Structure/PdbCleaner.o : Structure/PdbCleaner.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/PdbCleaner.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Structure/HisProt.o : Structure/HisProt.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/HisProt.h Structure/StructureRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Structure/InternalCoords.o : Structure/InternalCoords.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/InternalCoords.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Structure/PdbCleaner.o : Structure/PdbCleaner.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/PdbCleaner.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/StructureEnum.o : Structure/StructureEnum.cpp Structure/StructureEnum.h
 Structure/StructureRoutines.o : Structure/StructureRoutines.cpp Atom.h CpptrajStdio.h NameType.h Residue.h Structure/StructureRoutines.h SymbolExporting.h
-Structure/Sugar.o : Structure/Sugar.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Structure/SugarBuilder.o : Structure/SugarBuilder.cpp ArgList.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DistRoutines.h FileIO.h FileName.h Frame.h ImageOption.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/FunctionalGroup.h Structure/FxnGroupBuilder.h Structure/LinkAtom.h Structure/ResStatArray.h Structure/StructureEnum.h Structure/StructureRoutines.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarLinkAtoms.h Structure/SugarToken.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Structure/SugarLinkAtoms.o : Structure/SugarLinkAtoms.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/LinkAtom.h Structure/SugarLinkAtoms.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Structure/Sugar.o : Structure/Sugar.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Structure/SugarBuilder.o : Structure/SugarBuilder.cpp ArgList.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DistRoutines.h FileIO.h FileName.h Frame.h ImageOption.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/FunctionalGroup.h Structure/FxnGroupBuilder.h Structure/LinkAtom.h Structure/ResStatArray.h Structure/StructureEnum.h Structure/StructureRoutines.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarLinkAtoms.h Structure/SugarToken.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Structure/SugarLinkAtoms.o : Structure/SugarLinkAtoms.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/LinkAtom.h Structure/SugarLinkAtoms.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/SugarToken.o : Structure/SugarToken.cpp ArgList.h CpptrajStdio.h Structure/SugarToken.h
-Structure/Zmatrix.o : Structure/Zmatrix.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-StructureCheck.o : StructureCheck.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h ExclusionArray.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StructureCheck.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-StructureMapper.o : StructureMapper.cpp AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StructureMapper.h SymbolExporting.h TextFormat.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-SymmetricRmsdCalc.o : SymmetricRmsdCalc.cpp ArrayIterator.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h Hungarian.h ImageOption.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Structure/Zmatrix.o : Structure/Zmatrix.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+StructureCheck.o : StructureCheck.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h ExclusionArray.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StructureCheck.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+StructureMapper.o : StructureMapper.cpp AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StructureMapper.h SymbolExporting.h TextFormat.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+SymmetricRmsdCalc.o : SymmetricRmsdCalc.cpp ArrayIterator.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h Hungarian.h ImageOption.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 TextBlockBuffer.o : TextBlockBuffer.cpp BufferedLine.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Parallel.h TextBlockBuffer.h
 TextFormat.o : TextFormat.cpp StringRoutines.h TextFormat.h
 Timer.o : Timer.cpp CpptrajStdio.h Timer.h
 TinkerFile.o : TinkerFile.cpp ArgList.h Atom.h AtomMask.h Box.h BufferedLine.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TinkerFile.h Unit.h Vec3.h
-TopInfo.o : TopInfo.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h DistRoutines.h FileIO.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Mol.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h TopInfo.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Topology.o : Topology.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h GuessAtomHybridization.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/GenerateConnectivityArrays.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+TopInfo.o : TopInfo.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h DistRoutines.h FileIO.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Mol.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h TopInfo.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Topology.o : Topology.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h GuessAtomHybridization.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/GenerateConnectivityArrays.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 TorsionRoutines.o : TorsionRoutines.cpp Constants.h TorsionRoutines.h Vec3.h
 TrajFrameCounter.o : TrajFrameCounter.cpp ArgList.h CpptrajStdio.h TrajFrameCounter.h
-TrajIOarray.o : TrajIOarray.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryFile.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_AmberCoord.o : Traj_AmberCoord.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h Traj_AmberCoord.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_AmberNetcdf.o : Traj_AmberNetcdf.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h ParallelNetcdf.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_AmberNetcdf.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_AmberRestart.o : Traj_AmberRestart.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedFrame.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextBlockBuffer.h TextFormat.h Topology.h Traj_AmberRestart.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_AmberRestartNC.o : Traj_AmberRestartNC.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Traj_AmberRestartNC.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_Binpos.o : Traj_Binpos.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_Binpos.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_CIF.o : Traj_CIF.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CIFfile.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Traj_CIF.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_CharmmCor.o : Traj_CharmmCor.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Traj_CharmmCor.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_CharmmDcd.o : Traj_CharmmDcd.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ByteRoutines.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_CharmmDcd.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_CharmmRestart.o : Traj_CharmmRestart.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedFrame.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h Traj_CharmmRestart.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_Conflib.o : Traj_Conflib.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_Conflib.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_DTR.o : Traj_DTR.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_DTR.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h vmdplugin/dtrplugin.hxx
-Traj_GmxDump.o : Traj_GmxDump.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_GmxDump.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_GmxTng.o : Traj_GmxTng.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_GmxTng.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_GmxTrX.o : Traj_GmxTrX.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ByteRoutines.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_GmxTrX.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_GmxXtc.o : Traj_GmxXtc.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_GmxXtc.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_Gro.o : Traj_Gro.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Traj_Gro.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_H5.o : Traj_H5.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_H5.h TrajectoryIO.h TypeNameHolder.h Unit.h Units.h Vec3.h
-Traj_H5MD.o : Traj_H5MD.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_H5MD.h TrajectoryIO.h TypeNameHolder.h Unit.h Units.h Vec3.h
-Traj_Mol2File.o : Traj_Mol2File.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Mol2File.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_Mol2File.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_NcEnsemble.o : Traj_NcEnsemble.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FrameArray.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h ParallelNetcdf.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_NcEnsemble.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_PDBfile.o : Traj_PDBfile.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Tensor.h Dimension.h DistRoutines.h FileIO.h FileName.h Frame.h FramePtrArray.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricTensor.h TextFormat.h Timer.h Topology.h Traj_PDBfile.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_SDF.o : Traj_SDF.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SDFfile.h Segment.h SymbolExporting.h Topology.h Traj_SDF.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_SQM.o : Traj_SQM.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Traj_SQM.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_Tinker.o : Traj_Tinker.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TinkerFile.h Topology.h Traj_Tinker.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_XYZ.o : Traj_XYZ.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h Traj_XYZ.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+TrajIOarray.o : TrajIOarray.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryFile.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+Traj_AmberCoord.o : Traj_AmberCoord.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h Traj_AmberCoord.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+Traj_AmberNetcdf.o : Traj_AmberNetcdf.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h ParallelNetcdf.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_AmberNetcdf.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+Traj_AmberRestart.o : Traj_AmberRestart.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedFrame.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextBlockBuffer.h TextFormat.h Topology.h Traj_AmberRestart.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+Traj_AmberRestartNC.o : Traj_AmberRestartNC.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Traj_AmberRestartNC.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+Traj_Binpos.o : Traj_Binpos.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_Binpos.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+Traj_CIF.o : Traj_CIF.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CIFfile.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Traj_CIF.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+Traj_CharmmCor.o : Traj_CharmmCor.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Traj_CharmmCor.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+Traj_CharmmDcd.o : Traj_CharmmDcd.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ByteRoutines.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_CharmmDcd.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+Traj_CharmmRestart.o : Traj_CharmmRestart.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedFrame.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h Traj_CharmmRestart.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+Traj_Conflib.o : Traj_Conflib.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_Conflib.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+Traj_DTR.o : Traj_DTR.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_DTR.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h vmdplugin/dtrplugin.hxx
+Traj_GmxDump.o : Traj_GmxDump.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_GmxDump.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+Traj_GmxTng.o : Traj_GmxTng.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_GmxTng.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+Traj_GmxTrX.o : Traj_GmxTrX.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ByteRoutines.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_GmxTrX.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+Traj_GmxXtc.o : Traj_GmxXtc.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_GmxXtc.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+Traj_Gro.o : Traj_Gro.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Traj_Gro.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+Traj_H5.o : Traj_H5.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_H5.h TrajectoryIO.h TypeNameHolder.h Unit.h Units.h Vec3.h
+Traj_H5MD.o : Traj_H5MD.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_H5MD.h TrajectoryIO.h TypeNameHolder.h Unit.h Units.h Vec3.h
+Traj_Mol2File.o : Traj_Mol2File.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Mol2File.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_Mol2File.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+Traj_NcEnsemble.o : Traj_NcEnsemble.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FrameArray.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h ParallelNetcdf.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_NcEnsemble.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+Traj_PDBfile.o : Traj_PDBfile.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Tensor.h Dimension.h DistRoutines.h FileIO.h FileName.h Frame.h FramePtrArray.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricTensor.h TextFormat.h Timer.h Topology.h Traj_PDBfile.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+Traj_SDF.o : Traj_SDF.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h SDFfile.h Segment.h SymbolExporting.h Topology.h Traj_SDF.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+Traj_SQM.o : Traj_SQM.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Traj_SQM.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+Traj_Tinker.o : Traj_Tinker.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TinkerFile.h Topology.h Traj_Tinker.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+Traj_XYZ.o : Traj_XYZ.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h Traj_XYZ.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
 TrajectoryFile.o : TrajectoryFile.cpp Atom.h BaseIOtype.h Box.h BufferedFrame.h BufferedLine.h CIFfile.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h FileTypes.h FramePtrArray.h Matrix_3x3.h Mol2File.h NC_Routines.h NameType.h NetcdfFile.h PDBfile.h Parallel.h ReplicaDimArray.h Residue.h SDFfile.h SymbolExporting.h TextFormat.h TinkerFile.h Traj_AmberCoord.h Traj_AmberNetcdf.h Traj_AmberRestart.h Traj_AmberRestartNC.h Traj_Binpos.h Traj_CIF.h Traj_CharmmCor.h Traj_CharmmDcd.h Traj_CharmmRestart.h Traj_Conflib.h Traj_DTR.h Traj_GmxDump.h Traj_GmxTng.h Traj_GmxTrX.h Traj_GmxXtc.h Traj_Gro.h Traj_H5.h Traj_H5MD.h Traj_Mol2File.h Traj_NcEnsemble.h Traj_PDBfile.h Traj_SDF.h Traj_SQM.h Traj_Tinker.h Traj_XYZ.h TrajectoryFile.h TrajectoryIO.h Vec3.h
 TrajectoryIO.o : TrajectoryIO.cpp BaseIOtype.h Box.h CoordinateInfo.h FramePtrArray.h Matrix_3x3.h Parallel.h ReplicaDimArray.h TrajectoryIO.h Vec3.h
-TrajinList.o : TrajinList.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_RemLog.h Dimension.h EnsembleIn.h EnsembleIn_Multi.h EnsembleIn_Single.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryFile.h TrajectoryIO.h Trajin.h TrajinList.h Trajin_Multi.h Trajin_Single.h TypeNameHolder.h Unit.h Vec3.h
-Trajin_Multi.o : Trajin_Multi.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryIO.h Trajin.h Trajin_Multi.h TypeNameHolder.h Unit.h Vec3.h
-Trajin_Single.o : Trajin_Single.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h Trajin.h Trajin_Single.h TypeNameHolder.h Unit.h Vec3.h
-TrajoutList.o : TrajoutList.cpp ActionFrameCounter.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-Trajout_Single.o : Trajout_Single.cpp ActionFrameCounter.h ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+TrajinList.o : TrajinList.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_RemLog.h Dimension.h EnsembleIn.h EnsembleIn_Multi.h EnsembleIn_Single.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryFile.h TrajectoryIO.h Trajin.h TrajinList.h Trajin_Multi.h Trajin_Single.h TypeNameHolder.h Unit.h Vec3.h
+Trajin_Multi.o : Trajin_Multi.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryIO.h Trajin.h Trajin_Multi.h TypeNameHolder.h Unit.h Vec3.h
+Trajin_Single.o : Trajin_Single.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h Trajin.h Trajin_Single.h TypeNameHolder.h Unit.h Vec3.h
+TrajoutList.o : TrajoutList.cpp ActionFrameCounter.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Trajout_Single.o : Trajout_Single.cpp ActionFrameCounter.h ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Units.o : Units.cpp Constants.h CpptrajStdio.h Units.h
 Vec3.o : Vec3.cpp Constants.h CpptrajStdio.h Vec3.h
-ViewRst.o : ViewRst.cpp ActionFrameCounter.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h ViewRst.h
-main.o : main.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h Cpptraj.h CpptrajFile.h CpptrajState.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+ViewRst.o : ViewRst.cpp ActionFrameCounter.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h ViewRst.h
+main.o : main.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h Cpptraj.h CpptrajFile.h CpptrajState.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 molsurf.o : molsurf.c molsurf.h
 qcprot.o : qcprot.cpp CpptrajStdio.h qcprot.h
 vmdplugin/dtrplugin.o : vmdplugin/dtrplugin.cpp ByteRoutines.h vmdplugin/dtrplugin.hxx vmdplugin/vmddir.h

From 13ec95659de414e33faec51cb02d204601cb56b6 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 2 Mar 2024 10:09:26 -0500
Subject: [PATCH 0654/1492] cmap not valid if grid or nres empty

---
 src/ParameterTypes.h | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/ParameterTypes.h b/src/ParameterTypes.h
index 26352352db..b7f14a0060 100644
--- a/src/ParameterTypes.h
+++ b/src/ParameterTypes.h
@@ -748,13 +748,13 @@ class CmapGridType {
     void AddResName(std::string const& n) { resNames_.push_back( n ); }
     /// \return True if the CMAP is valid
     bool CmapIsValid() const {
-      if (resolution_*resolution_ != grid_.size())
+      if (resolution_ == 0 || resolution_*resolution_ != grid_.size())
         return false;
       return true;
     }
     /// \return True if CMAP # res names matches expected.
     bool CmapNresIsValid() const {
-      if (nCmapRes_ != (int)resNames_.size())
+      if (nCmapRes_ == 0 || nCmapRes_ != (int)resNames_.size())
         return false;
       return true;
     }

From 26cb66b6850030fc4e6f9f1290b11a463496eff6 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 2 Mar 2024 10:45:43 -0500
Subject: [PATCH 0655/1492] Modify for CmapParmHolder

---
 src/AmberParamFile.cpp | 37 ++++++++++++++++++-------------------
 src/AmberParamFile.h   |  3 ++-
 src/ParameterTypes.h   |  5 +++++
 3 files changed, 25 insertions(+), 20 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index eb3d8ac7e2..1571e69b81 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -380,14 +380,10 @@ static inline int check_cmap(int currentCmapIdx, CmapGridType const& cmap) {
 }
 
 /** Read CMAP section */
-int AmberParamFile::read_cmap(ParameterSet& prm, CmapType& currentCmapFlag, std::string const& line) const {
-  //if (ptr[0] == '%' && ptr[1] == 'F' && ptr[2] == 'L' &&
-  //    ptr[3] == 'A' && ptr[4] == 'G')
-  int currentCmapIdx;
-  if (prm.CMAP().empty())
-    currentCmapIdx = -1;
-  else
-    currentCmapIdx = prm.CMAP().size() - 1;
+int AmberParamFile::read_cmap(CmapGridType& currentCMAP, ParameterSet& prm, CmapType& currentCmapFlag,
+                              std::string const& line)
+const
+{
   ArgList argline(line);
   if (argline.Nargs() > 1)
   {
@@ -395,12 +391,13 @@ int AmberParamFile::read_cmap(ParameterSet& prm, CmapType& currentCmapFlag, std:
       if (argline[1] == "CMAP_COUNT") {
         // New CMAP term. Ignore the index for now. If a previous CMAP
         // was read make sure its OK.
-        if (currentCmapIdx > -1) {
-          if (check_cmap(currentCmapIdx+1, prm.CMAP()[currentCmapIdx])) return 1;
+        if (!currentCMAP.empty()) {
+          if (check_cmap(prm.CMAP().size()+1, currentCMAP)) return 1;
+          prm.CMAP().AddParm( currentCMAP, true );
+          currentCMAP = CmapGridType();
         }
         int cmapcount = argline.getKeyInt("CMAP_COUNT", -1);
         //mprintf("DEBUG: Cmap count: %i\n", cmapcount);
-        prm.CMAP().push_back( CmapGridType() );
         if ( cmapcount != (int)prm.CMAP().size() )
           mprintf("Warning: CMAP term is not in numerical order. CMAP_COUNT %i, expected %zu\n",
                   cmapcount, prm.CMAP().size());
@@ -415,7 +412,7 @@ int AmberParamFile::read_cmap(ParameterSet& prm, CmapType& currentCmapFlag, std:
           mprinterr("Error: Bad CMAP # residues: %s\n", line.c_str());
           return 1;
         }
-        prm.CMAP()[currentCmapIdx].SetNumCmapRes( nres );
+        currentCMAP.SetNumCmapRes( nres );
         return 0;
       } else if (argline[1] == "CMAP_RESOLUTION") {
         int cmapres = argline.getKeyInt("CMAP_RESOLUTION", -1);
@@ -424,7 +421,7 @@ int AmberParamFile::read_cmap(ParameterSet& prm, CmapType& currentCmapFlag, std:
           mprinterr("Error: Bad CMAP resolution: %s\n", line.c_str());
           return 1;
         }
-        prm.CMAP()[currentCmapIdx].SetResolution( cmapres );
+        currentCMAP.SetResolution( cmapres );
         return 0;
       } else if (argline[1] == "CMAP_PARAMETER") {
         currentCmapFlag = CMAP_PARAMETER;
@@ -440,17 +437,17 @@ int AmberParamFile::read_cmap(ParameterSet& prm, CmapType& currentCmapFlag, std:
                         terms+4, terms+5, terms+6, terms+7);
     for (int i = 0; i != nterms; i++) {
       //mprintf("DEBUG: cmap term %f\n", terms[i] );
-      prm.CMAP()[currentCmapIdx].AddToGrid( terms[i] );
+      currentCMAP.AddToGrid( terms[i] );
     }
   } else if (currentCmapFlag == CMAP_RESLIST) {
     ArgList resnames( line );
     std::string rn = resnames.GetStringNext();
     while (!rn.empty()) {
-      prm.CMAP()[currentCmapIdx].AddResName( rn );
+      currentCMAP.AddResName( rn );
       rn = resnames.GetStringNext();
     }
   } else if (currentCmapFlag == CMAP_TITLE) {
-    prm.CMAP()[currentCmapIdx].SetTitle( line );
+    currentCMAP.SetTitle( line );
   }
   return 0;
 }
@@ -524,6 +521,7 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int deb
   // Read file
   SectionType section = UNKNOWN;
   CmapType currentCmapFlag = CMAP_INITIAL;
+  CmapGridType currentCMAP;
   ptr = infile.Line();
   while (ptr != 0) {
     bool first_char_is_space = (*ptr == ' ');
@@ -566,7 +564,7 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int deb
         else if (section == LJEDIT)
           err = read_ljedit(Offdiag, ptr);
         else if (section == CMAP)
-          err = read_cmap(prm, currentCmapFlag, line);
+          err = read_cmap(currentCMAP, prm, currentCmapFlag, line);
         if (err != 0) {
           mprinterr("Error: Reading line: %s\n", ptr);
           return 1;
@@ -576,8 +574,9 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int deb
     ptr = infile.Line();
   }
   // Check last cmap
-  if (!prm.CMAP().empty()) {
-    if (check_cmap(prm.CMAP().size(), prm.CMAP().back())) return 1;
+  if (!currentCMAP.empty()) {
+    if (check_cmap(prm.CMAP().size(), currentCMAP)) return 1;
+    prm.CMAP().AddParm( currentCMAP, true );
   }
   // Nonbonds
   if (assign_nb(prm, nbset)) return 1;
diff --git a/src/AmberParamFile.h b/src/AmberParamFile.h
index 820822e973..6f81ac7222 100644
--- a/src/AmberParamFile.h
+++ b/src/AmberParamFile.h
@@ -3,6 +3,7 @@
 #include <vector>
 #include <string>
 class ParameterSet;
+class CmapGridType;
 //class BufferedLine;
 class FileName;
 /// Used to read in Amber parameters from Amber FF/FRCMOD file.
@@ -46,7 +47,7 @@ class AmberParamFile {
     /// Read LJ 6-12 off-diagonal modifications
     int read_ljedit(Oarray&, const char*) const;
     /// Read CMAP section
-    int read_cmap(ParameterSet&, CmapType&, std::string const&) const;
+    int read_cmap(CmapGridType&, ParameterSet&, CmapType&, std::string const&) const;
     /// Assign parameters from NonbondSet to ParameterSet
     int assign_nb(ParameterSet&, NonbondSet const&) const;
     /// Assign parameters from OffdiagNB array to ParameterSet
diff --git a/src/ParameterTypes.h b/src/ParameterTypes.h
index b7f14a0060..04d21ddf7c 100644
--- a/src/ParameterTypes.h
+++ b/src/ParameterTypes.h
@@ -758,6 +758,11 @@ class CmapGridType {
         return false;
       return true;
     }
+    /// \return True if CMAP is completely empty
+    bool empty() const {
+      return (nCmapRes_ == 0 && resolution_ == 0 &&
+              grid_.empty() && title_.empty() && resNames_.empty());
+    }
   private:
     int nCmapRes_;             ///< Number of expected residues this CMAP will apply to
     unsigned int resolution_;  ///< Number of steps along each phi/psi CMAP axis

From b049febda75a6fa1d45e9af07460e910428723ba Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 2 Mar 2024 10:56:01 -0500
Subject: [PATCH 0656/1492] CmapParmHolder cannot be in the Cpptraj namespace
 because it will clash with the Cpptraj class

---
 src/AmberParamFile.cpp            |   2 +-
 src/{Parm => }/CmapParmHolder.cpp |   6 +-
 src/{Parm => }/CmapParmHolder.h   |  10 +-
 src/ParameterSet.h                |  11 +-
 src/Parm/CMakeLists.txt           |   1 -
 src/Parm/parmdepend               |   3 +-
 src/Parm/parmfiles                |   1 -
 src/cpptrajdepend                 | 714 +++++++++++++++---------------
 src/cpptrajfiles                  |   1 +
 9 files changed, 375 insertions(+), 374 deletions(-)
 rename src/{Parm => }/CmapParmHolder.cpp (95%)
 rename src/{Parm => }/CmapParmHolder.h (90%)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 1571e69b81..a2483a6365 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -398,7 +398,7 @@ const
         }
         int cmapcount = argline.getKeyInt("CMAP_COUNT", -1);
         //mprintf("DEBUG: Cmap count: %i\n", cmapcount);
-        if ( cmapcount != (int)prm.CMAP().size() )
+        if ( cmapcount != (int)prm.CMAP().size()+1 )
           mprintf("Warning: CMAP term is not in numerical order. CMAP_COUNT %i, expected %zu\n",
                   cmapcount, prm.CMAP().size());
         return 0;
diff --git a/src/Parm/CmapParmHolder.cpp b/src/CmapParmHolder.cpp
similarity index 95%
rename from src/Parm/CmapParmHolder.cpp
rename to src/CmapParmHolder.cpp
index 593b3482db..947d48bad3 100644
--- a/src/Parm/CmapParmHolder.cpp
+++ b/src/CmapParmHolder.cpp
@@ -1,8 +1,8 @@
 #include "CmapParmHolder.h"
-#include "../CpptrajStdio.h"
-#include "../ParameterTypes.h"
+#include "CpptrajStdio.h"
+#include "ParameterTypes.h"
 
-using namespace Cpptraj::Parm;
+//using namespace Cpptraj::Parm;
 
 /** CONSTRUCTOR */
 CmapParmHolder::CmapParmHolder() {}
diff --git a/src/Parm/CmapParmHolder.h b/src/CmapParmHolder.h
similarity index 90%
rename from src/Parm/CmapParmHolder.h
rename to src/CmapParmHolder.h
index dff1f51860..e3870646e1 100644
--- a/src/Parm/CmapParmHolder.h
+++ b/src/CmapParmHolder.h
@@ -2,9 +2,9 @@
 #define INC_PARM_CMAPPARMHOLDER_H
 class CmapGridType;
 #include <vector>
-#include "../ParameterHolders.h" // TODO fix the includes
-namespace Cpptraj {
-namespace Parm {
+#include "ParameterHolders.h" // TODO fix the includes
+//namespace Cpptraj {
+//namespace Parm {
 /// Hold CMAP terms
 class CmapParmHolder {
     typedef std::vector<CmapGridType> Carray;
@@ -31,6 +31,6 @@ class CmapParmHolder {
   private:
     Carray CMAP_;
 };
-}
-}
+//}
+//}
 #endif
diff --git a/src/ParameterSet.h b/src/ParameterSet.h
index 4d44639827..dea2376c47 100644
--- a/src/ParameterSet.h
+++ b/src/ParameterSet.h
@@ -2,7 +2,7 @@
 #define INC_PARAMETERSET_H
 #include "ParameterTypes.h"
 #include "ParameterHolders.h"
-#include "Parm/CmapParmHolder.h"
+#include "CmapParmHolder.h"
 #include "AtomType.h"
 class CpptrajFile;
 /// Hold a set of parameters for atom types, bonds, angles, etc.
@@ -19,7 +19,8 @@ class ParameterSet {
     ImproperParmHolder& IP()           { return impParm_;   }
     DihedralParmHolder& DP()           { return dihParm_;   }
     ParmHolder<HB_ParmType>& HB()      { return HBparm_;    }
-    Cpptraj::Parm::CmapParmHolder& CMAP() { return CMAP_;      }
+    //Cpptraj::Parm::CmapParmHolder& CMAP() { return CMAP_;      }
+    CmapParmHolder& CMAP() { return CMAP_;      }
 
     void SetHasLJparams(bool b) { hasLJparams_ = b; }
     bool HasLJparams() const { return hasLJparams_; }
@@ -33,7 +34,8 @@ class ParameterSet {
     ImproperParmHolder const& IP()           const { return impParm_;   }
     DihedralParmHolder const& DP()           const { return dihParm_;   }
     ParmHolder<HB_ParmType> const& HB()      const { return HBparm_;    }
-    Cpptraj::Parm::CmapParmHolder const& CMAP() const { return CMAP_;      }
+    //Cpptraj::Parm::CmapParmHolder const& CMAP() const { return CMAP_;      }
+    CmapParmHolder const& CMAP() const { return CMAP_;      }
     std::string const& NbParamName()         const { return NBname_;    }
     /// \return Parameter set names as a single line
     std::string ParamSetName()        const;
@@ -91,7 +93,8 @@ class ParameterSet {
     ImproperParmHolder impParm_;           ///< Improper dihedral parameters
     DihedralParmHolder dihParm_;           ///< Cosine-series dihedral parameters
     ParmHolder<HB_ParmType> HBparm_;       ///< LJ 10-12 A-B parameters for hydrogen bonds
-    Cpptraj::Parm::CmapParmHolder CMAP_;   ///< CMAP parameters; unlike others, not indexed by atom type
+    //Cpptraj::Parm::CmapParmHolder CMAP_;   ///< CMAP parameters; unlike others, not indexed by atom type
+    CmapParmHolder CMAP_;   ///< CMAP parameters; unlike others, not indexed by atom type
     NsetType hydrophilicAtomTypes_;        ///< Hold names of hydrophilic atom types
     bool hasLJparams_;
 };
diff --git a/src/Parm/CMakeLists.txt b/src/Parm/CMakeLists.txt
index bc34003868..caeb638991 100644
--- a/src/Parm/CMakeLists.txt
+++ b/src/Parm/CMakeLists.txt
@@ -1,5 +1,4 @@
 #CMake buildfile for CPPTRAJ Parm subdirectory.
 target_sources(cpptraj_common_obj PRIVATE
-  ${CMAKE_CURRENT_LIST_DIR}/CmapParmHolder.cpp
   ${CMAKE_CURRENT_LIST_DIR}/GB_Params.cpp
 )
diff --git a/src/Parm/parmdepend b/src/Parm/parmdepend
index de2147e82d..7b6393f11b 100644
--- a/src/Parm/parmdepend
+++ b/src/Parm/parmdepend
@@ -1,2 +1 @@
-CmapParmHolder.o : CmapParmHolder.cpp ../Constants.h ../CpptrajStdio.h ../NameType.h ../ParameterHolders.h ../ParameterTypes.h ../TypeNameHolder.h CmapParmHolder.h
-GB_Params.o : GB_Params.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Parm/../Constants.h ../Parm/../NameType.h ../Parm/../ParameterHolders.h ../Parm/../ParameterTypes.h ../Parm/../TypeNameHolder.h ../Parm/CmapParmHolder.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h GB_Params.h
+GB_Params.o : GB_Params.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Parm/CmapParmHolder.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h GB_Params.h
diff --git a/src/Parm/parmfiles b/src/Parm/parmfiles
index f556a1a93e..86a58ec097 100644
--- a/src/Parm/parmfiles
+++ b/src/Parm/parmfiles
@@ -1,4 +1,3 @@
 # Files for Parm subdirectory.
 PARM_SOURCES= \
-  CmapParmHolder.cpp \
   GB_Params.cpp
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 91dd35e684..4126527033 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -1,151 +1,151 @@
 ActionFrameCounter.o : ActionFrameCounter.cpp ActionFrameCounter.h ArgList.h CpptrajStdio.h
-ActionList.o : ActionList.cpp Action.h ActionList.h ActionState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-ActionTopWriter.o : ActionTopWriter.cpp ActionState.h ActionTopWriter.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Align.o : Action_Align.cpp Action.h ActionState.h Action_Align.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Angle.o : Action_Angle.cpp Action.h ActionState.h Action_Angle.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Action_AreaPerMol.o : Action_AreaPerMol.cpp Action.h ActionState.h Action_AreaPerMol.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_AtomMap.o : Action_AtomMap.cpp Action.h ActionState.h Action_AtomMap.h ArgList.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h StructureMapper.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_AtomicCorr.o : Action_AtomicCorr.cpp Action.h ActionState.h Action_AtomicCorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_AtomicFluct.o : Action_AtomicFluct.cpp Action.h ActionFrameCounter.h ActionState.h Action_AtomicFluct.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_AutoImage.o : Action_AutoImage.cpp Action.h ActionState.h Action_AutoImage.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h ImageRoutines.h ImageTypes.h Image_List.h Image_List_Unit.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Average.o : Action_Average.cpp Action.h ActionFrameCounter.h ActionState.h Action_Average.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-Action_AvgBox.o : Action_AvgBox.cpp Action.h ActionState.h Action_AvgBox.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Bounds.o : Action_Bounds.cpp Action.h ActionState.h Action_Bounds.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Box.o : Action_Box.cpp Action.h ActionState.h Action_Box.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BoxArgs.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Center.o : Action_Center.cpp Action.h ActionState.h Action_Center.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Channel.o : Action_Channel.cpp Action.h ActionState.h Action_Channel.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_CheckChirality.o : Action_CheckChirality.cpp Action.h ActionState.h Action_CheckChirality.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h Structure/BuildAtom.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Action_CheckStructure.o : Action_CheckStructure.cpp Action.h ActionState.h Action_CheckStructure.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_integer.h DataSet_string.h Dimension.h DispatchObject.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Closest.o : Action_Closest.cpp Action.h ActionState.h ActionTopWriter.h Action_Closest.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h ImageRoutines.h ImageTypes.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h cuda_kernels/kernel_wrappers.cuh
-Action_ClusterDihedral.o : Action_ClusterDihedral.cpp Action.h ActionState.h Action_ClusterDihedral.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_integer.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Action_Contacts.o : Action_Contacts.cpp Action.h ActionState.h Action_Contacts.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_CreateCrd.o : Action_CreateCrd.cpp Action.h ActionState.h Action_CreateCrd.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_CreateReservoir.o : Action_CreateReservoir.cpp Action.h ActionState.h Action_CreateReservoir.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h RemdReservoirNC.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_DNAionTracker.o : Action_DNAionTracker.cpp Action.h ActionState.h Action_DNAionTracker.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_DSSP.o : Action_DSSP.cpp Action.h ActionState.h Action_DSSP.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Density.o : Action_Density.cpp Action.h ActionState.h Action_Density.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Diffusion.o : Action_Diffusion.cpp Action.h ActionState.h Action_Diffusion.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_double.h DiffusionResults.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Dihedral.o : Action_Dihedral.cpp Action.h ActionState.h Action_Dihedral.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Action_DihedralRMS.o : Action_DihedralRMS.cpp Action.h ActionState.h Action_DihedralRMS.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Action_Dipole.o : Action_Dipole.cpp Action.h ActionState.h Action_Dipole.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridAction.h GridBin.h GridMover.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_DistRmsd.o : Action_DistRmsd.cpp Action.h ActionState.h Action_DistRmsd.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Distance.o : Action_Distance.cpp Action.h ActionState.h Action_Distance.h ArgList.h AssociatedData.h AssociatedData_NOE.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Energy.o : Action_Energy.cpp Action.h ActionState.h Action_Energy.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h Energy.h EnergyArray.h Ewald.h EwaldOptions.h Ewald_ParticleMesh.h Ewald_Regular.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h helpme_standalone.h
-Action_Esander.o : Action_Esander.cpp Action.h ActionState.h Action_Esander.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h Energy_Sander.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_FilterByData.o : Action_FilterByData.cpp Action.h ActionState.h Action_FilterByData.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_FixAtomOrder.o : Action_FixAtomOrder.cpp Action.h ActionState.h ActionTopWriter.h Action_FixAtomOrder.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomTopType.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_FixImagedBonds.o : Action_FixImagedBonds.cpp Action.h ActionState.h Action_FixImagedBonds.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_GIST.o : Action_GIST.cpp Action.h ActionState.h Action_GIST.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridDbl.h DataSet_GridFlt.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h DistRoutines.h Ewald.h EwaldOptions.h Ewald_ParticleMesh.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h GIST_PME.h GistEntropyUtils.h Grid.h GridBin.h GridMover.h ImageOption.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h cuda_kernels/GistCudaSetup.cuh helpme_standalone.h
-Action_Grid.o : Action_Grid.cpp Action.h ActionState.h Action_Grid.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridAction.h GridBin.h GridMover.h MaskArray.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_GridFreeEnergy.o : Action_GridFreeEnergy.cpp Action.h ActionState.h Action_GridFreeEnergy.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridAction.h GridBin.h GridMover.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_HydrogenBond.o : Action_HydrogenBond.cpp Action.h ActionState.h Action_HydrogenBond.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_integer.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Action_Image.o : Action_Image.cpp Action.h ActionState.h Action_Image.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h ImageRoutines.h ImageTypes.h Image_List.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_InfraredSpectrum.o : Action_InfraredSpectrum.cpp Action.h ActionState.h Action_InfraredSpectrum.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ProgressBar.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Jcoupling.o : Action_Jcoupling.cpp Action.h ActionState.h Action_Jcoupling.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Action_Keep.o : Action_Keep.cpp Action.h ActionState.h ActionTopWriter.h Action_Keep.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_string.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_LESsplit.o : Action_LESsplit.cpp Action.h ActionFrameCounter.h ActionState.h Action_LESsplit.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-Action_LIE.o : Action_LIE.cpp Action.h ActionState.h Action_LIE.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_LipidOrder.o : Action_LipidOrder.cpp Action.h ActionState.h Action_LipidOrder.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_MakeStructure.o : Action_MakeStructure.cpp Action.h ActionState.h Action_MakeStructure.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Action_Mask.o : Action_Mask.cpp Action.h ActionFrameCounter.h ActionState.h Action_Mask.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-Action_Matrix.o : Action_Matrix.cpp Action.h ActionFrameCounter.h ActionState.h Action_Matrix.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Vector.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_MinImage.o : Action_MinImage.cpp Action.h ActionState.h Action_MinImage.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Molsurf.o : Action_Molsurf.cpp Action.h ActionState.h Action_Molsurf.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h molsurf.h
-Action_MultiDihedral.o : Action_MultiDihedral.cpp Action.h ActionState.h Action_MultiDihedral.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DihedralSearch.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Action_MultiPucker.o : Action_MultiPucker.cpp Action.h ActionState.h Action_MultiPucker.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Pucker.h Pucker_PuckerMask.h Pucker_PuckerSearch.h Pucker_PuckerToken.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Action_MultiVector.o : Action_MultiVector.cpp Action.h ActionState.h Action_MultiVector.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_NAstruct.o : Action_NAstruct.cpp Action.h ActionFrameCounter.h ActionState.h Action_NAstruct.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h AxisType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_float.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-Action_NMRrst.o : Action_NMRrst.cpp Action.h ActionState.h Action_NMRrst.h ArgList.h AssociatedData.h AssociatedData_NOE.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_float.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h ViewRst.h
-Action_NativeContacts.o : Action_NativeContacts.cpp Action.h ActionState.h Action_NativeContacts.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_integer.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_OrderParameter.o : Action_OrderParameter.cpp Action.h ActionState.h Action_OrderParameter.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Outtraj.o : Action_Outtraj.cpp Action.h ActionFrameCounter.h ActionState.h Action_Outtraj.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-Action_PairDist.o : Action_PairDist.cpp Action.h ActionState.h Action_PairDist.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Pairwise.o : Action_Pairwise.cpp Action.h ActionFrameCounter.h ActionState.h Action_Pairwise.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h Dimension.h DispatchObject.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-Action_Principal.o : Action_Principal.cpp Action.h ActionState.h Action_Principal.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Projection.o : Action_Projection.cpp Action.h ActionFrameCounter.h ActionState.h Action_Projection.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Pucker.o : Action_Pucker.cpp Action.h ActionState.h Action_Pucker.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Action_Radgyr.o : Action_Radgyr.cpp Action.h ActionState.h Action_Radgyr.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Radial.o : Action_Radial.cpp Action.h ActionState.h Action_Radial.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h Gpu.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h cuda_kernels/kernel_rdf.cuh
-Action_RandomizeIons.o : Action_RandomizeIons.cpp Action.h ActionState.h Action_RandomizeIons.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Remap.o : Action_Remap.cpp Action.h ActionState.h ActionTopWriter.h Action_Remap.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_ReplicateCell.o : Action_ReplicateCell.cpp Action.h ActionFrameCounter.h ActionState.h ActionTopWriter.h Action_ReplicateCell.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-Action_Rmsd.o : Action_Rmsd.cpp Action.h ActionState.h Action_Rmsd.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Rotate.o : Action_Rotate.cpp Action.h ActionState.h Action_Rotate.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_RunningAvg.o : Action_RunningAvg.cpp Action.h ActionState.h Action_RunningAvg.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_STFC_Diffusion.o : Action_STFC_Diffusion.cpp Action.h ActionState.h Action_STFC_Diffusion.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Scale.o : Action_Scale.cpp Action.h ActionState.h Action_Scale.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_SetVelocity.o : Action_SetVelocity.cpp Action.h ActionState.h Action_SetVelocity.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Spam.o : Action_Spam.cpp Action.h ActionState.h Action_Spam.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_Peaks.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h DataSet_Vector_Scalar.h DataSet_double.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h HistBin.h ImageOption.h KDE.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Strip.o : Action_Strip.cpp Action.h ActionState.h ActionTopWriter.h Action_Strip.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Surf.o : Action_Surf.cpp Action.h ActionState.h Action_Surf.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_SymmetricRmsd.o : Action_SymmetricRmsd.cpp Action.h ActionState.h Action_SymmetricRmsd.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h Hungarian.h ImageOption.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Temperature.o : Action_Temperature.cpp Action.h ActionState.h Action_Temperature.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Time.o : Action_Time.cpp Action.h ActionState.h Action_Time.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_ToroidalDiffusion.o : Action_ToroidalDiffusion.cpp Action.h ActionState.h Action_ToroidalDiffusion.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DiffusionResults.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Translate.o : Action_Translate.cpp Action.h ActionState.h Action_Translate.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Unstrip.o : Action_Unstrip.cpp Action.h ActionState.h Action_Unstrip.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Unwrap.o : Action_Unwrap.cpp Action.h ActionState.h Action_Unwrap.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h ImageRoutines.h ImageTypes.h Image_List.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Vector.o : Action_Vector.cpp Action.h ActionState.h Action_Vector.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h GridBin.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_VelocityAutoCorr.o : Action_VelocityAutoCorr.cpp Action.h ActionState.h Action_VelocityAutoCorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ProgressBar.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Volmap.o : Action_Volmap.cpp Action.h ActionState.h Action_Volmap.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridDbl.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Volume.o : Action_Volume.cpp Action.h ActionState.h Action_Volume.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Watershell.o : Action_Watershell.cpp Action.h ActionState.h Action_Watershell.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h ImageRoutines.h ImageTypes.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h cuda_kernels/kernel_wrappers.cuh
-Action_XtalSymm.o : Action_XtalSymm.cpp Action.h ActionState.h Action_XtalSymm.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SpaceGroup.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-AmberParamFile.o : AmberParamFile.cpp AmberParamFile.h ArgList.h AtomType.h BufferedLine.h Constants.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h StringRoutines.h TypeNameHolder.h
-AnalysisList.o : AnalysisList.cpp ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_AmdBias.o : Analysis_AmdBias.cpp ActionState.h Analysis.h AnalysisState.h Analysis_AmdBias.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_AutoCorr.o : Analysis_AutoCorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_AutoCorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Average.o : Analysis_Average.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Average.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_CalcDiffusion.o : Analysis_CalcDiffusion.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CalcDiffusion.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_double.h DiffusionResults.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Clustering.o : Analysis_Clustering.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Clustering.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/Algorithm.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Control.h Cluster/DrawGraph.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Sieve.h Cluster/Silhouette.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_ConstantPHStats.o : Analysis_ConstantPHStats.cpp ActionState.h Analysis.h AnalysisState.h Analysis_ConstantPHStats.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h DataSet_pH.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Corr.o : Analysis_Corr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Corr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_CrankShaft.o : Analysis_CrankShaft.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CrankShaft.h Analysis_Statistics.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_float.h DataSet_integer.h DataSet_string.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_CrdFluct.o : Analysis_CrdFluct.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CrdFluct.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_CrossCorr.o : Analysis_CrossCorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CrossCorr.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_CurveFit.o : Analysis_CurveFit.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CurveFit.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h CurveFit.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Divergence.o : Analysis_Divergence.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Divergence.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_EvalPlateau.o : Analysis_EvalPlateau.cpp ActionState.h Analysis.h AnalysisState.h Analysis_EvalPlateau.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h CurveFit.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_FFT.o : Analysis_FFT.cpp ActionState.h Analysis.h AnalysisState.h Analysis_FFT.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_HausdorffDistance.o : Analysis_HausdorffDistance.cpp ActionState.h Analysis.h AnalysisState.h Analysis_HausdorffDistance.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Hist.o : Analysis_Hist.cpp ActionFrameCounter.h ActionState.h Analysis.h AnalysisState.h Analysis_Hist.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridBin.h HistBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_IRED.o : Analysis_IRED.cpp ActionState.h Analysis.h AnalysisState.h Analysis_IRED.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Integrate.o : Analysis_Integrate.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Integrate.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_KDE.o : Analysis_KDE.cpp ActionState.h Analysis.h AnalysisState.h Analysis_KDE.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h HistBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Lifetime.o : Analysis_Lifetime.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Lifetime.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_LowestCurve.o : Analysis_LowestCurve.cpp ActionState.h Analysis.h AnalysisState.h Analysis_LowestCurve.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h HistBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Matrix.o : Analysis_Matrix.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Matrix.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_MeltCurve.o : Analysis_MeltCurve.cpp ActionState.h Analysis.h AnalysisState.h Analysis_MeltCurve.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Modes.o : Analysis_Modes.cpp ActionFrameCounter.h ActionState.h Analysis.h AnalysisState.h Analysis_Modes.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_MultiHist.o : Analysis_MultiHist.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Hist.h Analysis_KDE.h Analysis_MultiHist.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h HistBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Multicurve.o : Analysis_Multicurve.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CurveFit.h Analysis_Multicurve.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Overlap.o : Analysis_Overlap.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Overlap.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_PhiPsi.o : Analysis_PhiPsi.cpp ActionState.h Analysis.h AnalysisState.h Analysis_PhiPsi.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Regression.o : Analysis_Regression.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Regression.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_RemLog.o : Analysis_RemLog.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Lifetime.h Analysis_RemLog.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h DataSet_RemLog.h DataSet_integer.h DataSet_integer_mem.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Rms2d.o : Analysis_Rms2d.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Rms2d.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Hungarian.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ProgressBar.h QuaternionRMSD.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_RmsAvgCorr.o : Analysis_RmsAvgCorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_RmsAvgCorr.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Rotdif.o : Analysis_Rotdif.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Rotdif.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h CurveFit.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_Mesh.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ProgressBar.h PubFFT.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SimplexMin.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_RunningAvg.o : Analysis_RunningAvg.cpp ActionState.h Analysis.h AnalysisState.h Analysis_RunningAvg.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Slope.o : Analysis_Slope.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Slope.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Spline.o : Analysis_Spline.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Spline.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_State.o : Analysis_State.cpp ActionState.h Analysis.h AnalysisState.h Analysis_State.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Statistics.o : Analysis_Statistics.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Statistics.h ArgList.h Array1D.h AssociatedData.h AssociatedData_NOE.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_float.h DataSet_integer.h DataSet_string.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_TI.o : Analysis_TI.cpp ActionState.h Analysis.h AnalysisState.h Analysis_TI.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_TICA.o : Analysis_TICA.cpp ActionState.h Analysis.h AnalysisState.h Analysis_TICA.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Timecorr.o : Analysis_Timecorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Timecorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_VectorMath.o : Analysis_VectorMath.cpp ActionState.h Analysis.h AnalysisState.h Analysis_VectorMath.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Wavelet.o : Analysis_Wavelet.cpp ActionFrameCounter.h ActionState.h Analysis.h AnalysisState.h Analysis_Wavelet.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ClusterMap.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ParmFile.h ProgressBar.h ProgressTimer.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+ActionList.o : ActionList.cpp Action.h ActionList.h ActionState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+ActionTopWriter.o : ActionTopWriter.cpp ActionState.h ActionTopWriter.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Align.o : Action_Align.cpp Action.h ActionState.h Action_Align.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Angle.o : Action_Angle.cpp Action.h ActionState.h Action_Angle.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Action_AreaPerMol.o : Action_AreaPerMol.cpp Action.h ActionState.h Action_AreaPerMol.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_AtomMap.o : Action_AtomMap.cpp Action.h ActionState.h Action_AtomMap.h ArgList.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h StructureMapper.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_AtomicCorr.o : Action_AtomicCorr.cpp Action.h ActionState.h Action_AtomicCorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_AtomicFluct.o : Action_AtomicFluct.cpp Action.h ActionFrameCounter.h ActionState.h Action_AtomicFluct.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_AutoImage.o : Action_AutoImage.cpp Action.h ActionState.h Action_AutoImage.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h ImageRoutines.h ImageTypes.h Image_List.h Image_List_Unit.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Average.o : Action_Average.cpp Action.h ActionFrameCounter.h ActionState.h Action_Average.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Action_AvgBox.o : Action_AvgBox.cpp Action.h ActionState.h Action_AvgBox.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Bounds.o : Action_Bounds.cpp Action.h ActionState.h Action_Bounds.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Box.o : Action_Box.cpp Action.h ActionState.h Action_Box.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BoxArgs.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Center.o : Action_Center.cpp Action.h ActionState.h Action_Center.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Channel.o : Action_Channel.cpp Action.h ActionState.h Action_Channel.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_CheckChirality.o : Action_CheckChirality.cpp Action.h ActionState.h Action_CheckChirality.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h Structure/BuildAtom.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Action_CheckStructure.o : Action_CheckStructure.cpp Action.h ActionState.h Action_CheckStructure.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_integer.h DataSet_string.h Dimension.h DispatchObject.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Closest.o : Action_Closest.cpp Action.h ActionState.h ActionTopWriter.h Action_Closest.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h ImageRoutines.h ImageTypes.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h cuda_kernels/kernel_wrappers.cuh
+Action_ClusterDihedral.o : Action_ClusterDihedral.cpp Action.h ActionState.h Action_ClusterDihedral.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_integer.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Action_Contacts.o : Action_Contacts.cpp Action.h ActionState.h Action_Contacts.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_CreateCrd.o : Action_CreateCrd.cpp Action.h ActionState.h Action_CreateCrd.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_CreateReservoir.o : Action_CreateReservoir.cpp Action.h ActionState.h Action_CreateReservoir.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h RemdReservoirNC.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_DNAionTracker.o : Action_DNAionTracker.cpp Action.h ActionState.h Action_DNAionTracker.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_DSSP.o : Action_DSSP.cpp Action.h ActionState.h Action_DSSP.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Density.o : Action_Density.cpp Action.h ActionState.h Action_Density.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Diffusion.o : Action_Diffusion.cpp Action.h ActionState.h Action_Diffusion.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_double.h DiffusionResults.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Dihedral.o : Action_Dihedral.cpp Action.h ActionState.h Action_Dihedral.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Action_DihedralRMS.o : Action_DihedralRMS.cpp Action.h ActionState.h Action_DihedralRMS.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Action_Dipole.o : Action_Dipole.cpp Action.h ActionState.h Action_Dipole.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridAction.h GridBin.h GridMover.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_DistRmsd.o : Action_DistRmsd.cpp Action.h ActionState.h Action_DistRmsd.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Distance.o : Action_Distance.cpp Action.h ActionState.h Action_Distance.h ArgList.h AssociatedData.h AssociatedData_NOE.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Energy.o : Action_Energy.cpp Action.h ActionState.h Action_Energy.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h Energy.h EnergyArray.h Ewald.h EwaldOptions.h Ewald_ParticleMesh.h Ewald_Regular.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h helpme_standalone.h
+Action_Esander.o : Action_Esander.cpp Action.h ActionState.h Action_Esander.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h Energy_Sander.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_FilterByData.o : Action_FilterByData.cpp Action.h ActionState.h Action_FilterByData.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_FixAtomOrder.o : Action_FixAtomOrder.cpp Action.h ActionState.h ActionTopWriter.h Action_FixAtomOrder.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomTopType.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_FixImagedBonds.o : Action_FixImagedBonds.cpp Action.h ActionState.h Action_FixImagedBonds.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_GIST.o : Action_GIST.cpp Action.h ActionState.h Action_GIST.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridDbl.h DataSet_GridFlt.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h DistRoutines.h Ewald.h EwaldOptions.h Ewald_ParticleMesh.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h GIST_PME.h GistEntropyUtils.h Grid.h GridBin.h GridMover.h ImageOption.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h cuda_kernels/GistCudaSetup.cuh helpme_standalone.h
+Action_Grid.o : Action_Grid.cpp Action.h ActionState.h Action_Grid.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridAction.h GridBin.h GridMover.h MaskArray.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_GridFreeEnergy.o : Action_GridFreeEnergy.cpp Action.h ActionState.h Action_GridFreeEnergy.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridAction.h GridBin.h GridMover.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_HydrogenBond.o : Action_HydrogenBond.cpp Action.h ActionState.h Action_HydrogenBond.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_integer.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Action_Image.o : Action_Image.cpp Action.h ActionState.h Action_Image.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h ImageRoutines.h ImageTypes.h Image_List.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_InfraredSpectrum.o : Action_InfraredSpectrum.cpp Action.h ActionState.h Action_InfraredSpectrum.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Jcoupling.o : Action_Jcoupling.cpp Action.h ActionState.h Action_Jcoupling.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Action_Keep.o : Action_Keep.cpp Action.h ActionState.h ActionTopWriter.h Action_Keep.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_string.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_LESsplit.o : Action_LESsplit.cpp Action.h ActionFrameCounter.h ActionState.h Action_LESsplit.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Action_LIE.o : Action_LIE.cpp Action.h ActionState.h Action_LIE.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_LipidOrder.o : Action_LipidOrder.cpp Action.h ActionState.h Action_LipidOrder.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_MakeStructure.o : Action_MakeStructure.cpp Action.h ActionState.h Action_MakeStructure.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Action_Mask.o : Action_Mask.cpp Action.h ActionFrameCounter.h ActionState.h Action_Mask.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Action_Matrix.o : Action_Matrix.cpp Action.h ActionFrameCounter.h ActionState.h Action_Matrix.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Vector.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_MinImage.o : Action_MinImage.cpp Action.h ActionState.h Action_MinImage.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Molsurf.o : Action_Molsurf.cpp Action.h ActionState.h Action_Molsurf.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h molsurf.h
+Action_MultiDihedral.o : Action_MultiDihedral.cpp Action.h ActionState.h Action_MultiDihedral.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DihedralSearch.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Action_MultiPucker.o : Action_MultiPucker.cpp Action.h ActionState.h Action_MultiPucker.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Pucker.h Pucker_PuckerMask.h Pucker_PuckerSearch.h Pucker_PuckerToken.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Action_MultiVector.o : Action_MultiVector.cpp Action.h ActionState.h Action_MultiVector.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_NAstruct.o : Action_NAstruct.cpp Action.h ActionFrameCounter.h ActionState.h Action_NAstruct.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h AxisType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_float.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Action_NMRrst.o : Action_NMRrst.cpp Action.h ActionState.h Action_NMRrst.h ArgList.h AssociatedData.h AssociatedData_NOE.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_float.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h ViewRst.h
+Action_NativeContacts.o : Action_NativeContacts.cpp Action.h ActionState.h Action_NativeContacts.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_integer.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_OrderParameter.o : Action_OrderParameter.cpp Action.h ActionState.h Action_OrderParameter.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Outtraj.o : Action_Outtraj.cpp Action.h ActionFrameCounter.h ActionState.h Action_Outtraj.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Action_PairDist.o : Action_PairDist.cpp Action.h ActionState.h Action_PairDist.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Pairwise.o : Action_Pairwise.cpp Action.h ActionFrameCounter.h ActionState.h Action_Pairwise.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h Dimension.h DispatchObject.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Action_Principal.o : Action_Principal.cpp Action.h ActionState.h Action_Principal.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Projection.o : Action_Projection.cpp Action.h ActionFrameCounter.h ActionState.h Action_Projection.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Pucker.o : Action_Pucker.cpp Action.h ActionState.h Action_Pucker.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Action_Radgyr.o : Action_Radgyr.cpp Action.h ActionState.h Action_Radgyr.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Radial.o : Action_Radial.cpp Action.h ActionState.h Action_Radial.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h Gpu.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h cuda_kernels/kernel_rdf.cuh
+Action_RandomizeIons.o : Action_RandomizeIons.cpp Action.h ActionState.h Action_RandomizeIons.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Remap.o : Action_Remap.cpp Action.h ActionState.h ActionTopWriter.h Action_Remap.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_ReplicateCell.o : Action_ReplicateCell.cpp Action.h ActionFrameCounter.h ActionState.h ActionTopWriter.h Action_ReplicateCell.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Action_Rmsd.o : Action_Rmsd.cpp Action.h ActionState.h Action_Rmsd.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Rotate.o : Action_Rotate.cpp Action.h ActionState.h Action_Rotate.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_RunningAvg.o : Action_RunningAvg.cpp Action.h ActionState.h Action_RunningAvg.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_STFC_Diffusion.o : Action_STFC_Diffusion.cpp Action.h ActionState.h Action_STFC_Diffusion.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Scale.o : Action_Scale.cpp Action.h ActionState.h Action_Scale.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_SetVelocity.o : Action_SetVelocity.cpp Action.h ActionState.h Action_SetVelocity.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Spam.o : Action_Spam.cpp Action.h ActionState.h Action_Spam.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_Peaks.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h DataSet_Vector_Scalar.h DataSet_double.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h HistBin.h ImageOption.h KDE.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Strip.o : Action_Strip.cpp Action.h ActionState.h ActionTopWriter.h Action_Strip.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Surf.o : Action_Surf.cpp Action.h ActionState.h Action_Surf.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_SymmetricRmsd.o : Action_SymmetricRmsd.cpp Action.h ActionState.h Action_SymmetricRmsd.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h Hungarian.h ImageOption.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Temperature.o : Action_Temperature.cpp Action.h ActionState.h Action_Temperature.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Time.o : Action_Time.cpp Action.h ActionState.h Action_Time.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_ToroidalDiffusion.o : Action_ToroidalDiffusion.cpp Action.h ActionState.h Action_ToroidalDiffusion.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DiffusionResults.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Translate.o : Action_Translate.cpp Action.h ActionState.h Action_Translate.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Unstrip.o : Action_Unstrip.cpp Action.h ActionState.h Action_Unstrip.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Unwrap.o : Action_Unwrap.cpp Action.h ActionState.h Action_Unwrap.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h ImageRoutines.h ImageTypes.h Image_List.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Vector.o : Action_Vector.cpp Action.h ActionState.h Action_Vector.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h GridBin.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_VelocityAutoCorr.o : Action_VelocityAutoCorr.cpp Action.h ActionState.h Action_VelocityAutoCorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Volmap.o : Action_Volmap.cpp Action.h ActionState.h Action_Volmap.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridDbl.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Volume.o : Action_Volume.cpp Action.h ActionState.h Action_Volume.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Watershell.o : Action_Watershell.cpp Action.h ActionState.h Action_Watershell.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h ImageRoutines.h ImageTypes.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h cuda_kernels/kernel_wrappers.cuh
+Action_XtalSymm.o : Action_XtalSymm.cpp Action.h ActionState.h Action_XtalSymm.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SpaceGroup.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+AmberParamFile.o : AmberParamFile.cpp AmberParamFile.h ArgList.h AtomType.h BufferedLine.h CmapParmHolder.h Constants.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h StringRoutines.h TypeNameHolder.h
+AnalysisList.o : AnalysisList.cpp ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_AmdBias.o : Analysis_AmdBias.cpp ActionState.h Analysis.h AnalysisState.h Analysis_AmdBias.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_AutoCorr.o : Analysis_AutoCorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_AutoCorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_Average.o : Analysis_Average.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Average.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_CalcDiffusion.o : Analysis_CalcDiffusion.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CalcDiffusion.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_double.h DiffusionResults.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_Clustering.o : Analysis_Clustering.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Clustering.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/Algorithm.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Control.h Cluster/DrawGraph.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Sieve.h Cluster/Silhouette.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_ConstantPHStats.o : Analysis_ConstantPHStats.cpp ActionState.h Analysis.h AnalysisState.h Analysis_ConstantPHStats.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h DataSet_pH.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_Corr.o : Analysis_Corr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Corr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_CrankShaft.o : Analysis_CrankShaft.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CrankShaft.h Analysis_Statistics.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_float.h DataSet_integer.h DataSet_string.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_CrdFluct.o : Analysis_CrdFluct.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CrdFluct.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_CrossCorr.o : Analysis_CrossCorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CrossCorr.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_CurveFit.o : Analysis_CurveFit.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CurveFit.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h CurveFit.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_Divergence.o : Analysis_Divergence.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Divergence.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_EvalPlateau.o : Analysis_EvalPlateau.cpp ActionState.h Analysis.h AnalysisState.h Analysis_EvalPlateau.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h CurveFit.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_FFT.o : Analysis_FFT.cpp ActionState.h Analysis.h AnalysisState.h Analysis_FFT.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_HausdorffDistance.o : Analysis_HausdorffDistance.cpp ActionState.h Analysis.h AnalysisState.h Analysis_HausdorffDistance.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_Hist.o : Analysis_Hist.cpp ActionFrameCounter.h ActionState.h Analysis.h AnalysisState.h Analysis_Hist.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridBin.h HistBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_IRED.o : Analysis_IRED.cpp ActionState.h Analysis.h AnalysisState.h Analysis_IRED.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_Integrate.o : Analysis_Integrate.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Integrate.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_KDE.o : Analysis_KDE.cpp ActionState.h Analysis.h AnalysisState.h Analysis_KDE.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h HistBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_Lifetime.o : Analysis_Lifetime.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Lifetime.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_LowestCurve.o : Analysis_LowestCurve.cpp ActionState.h Analysis.h AnalysisState.h Analysis_LowestCurve.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h HistBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_Matrix.o : Analysis_Matrix.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Matrix.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_MeltCurve.o : Analysis_MeltCurve.cpp ActionState.h Analysis.h AnalysisState.h Analysis_MeltCurve.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_Modes.o : Analysis_Modes.cpp ActionFrameCounter.h ActionState.h Analysis.h AnalysisState.h Analysis_Modes.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_MultiHist.o : Analysis_MultiHist.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Hist.h Analysis_KDE.h Analysis_MultiHist.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h HistBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_Multicurve.o : Analysis_Multicurve.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CurveFit.h Analysis_Multicurve.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_Overlap.o : Analysis_Overlap.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Overlap.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_PhiPsi.o : Analysis_PhiPsi.cpp ActionState.h Analysis.h AnalysisState.h Analysis_PhiPsi.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_Regression.o : Analysis_Regression.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Regression.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_RemLog.o : Analysis_RemLog.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Lifetime.h Analysis_RemLog.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h DataSet_RemLog.h DataSet_integer.h DataSet_integer_mem.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_Rms2d.o : Analysis_Rms2d.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Rms2d.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Hungarian.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h QuaternionRMSD.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_RmsAvgCorr.o : Analysis_RmsAvgCorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_RmsAvgCorr.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_Rotdif.o : Analysis_Rotdif.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Rotdif.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h CurveFit.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_Mesh.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h PubFFT.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SimplexMin.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_RunningAvg.o : Analysis_RunningAvg.cpp ActionState.h Analysis.h AnalysisState.h Analysis_RunningAvg.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_Slope.o : Analysis_Slope.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Slope.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_Spline.o : Analysis_Spline.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Spline.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_State.o : Analysis_State.cpp ActionState.h Analysis.h AnalysisState.h Analysis_State.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_Statistics.o : Analysis_Statistics.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Statistics.h ArgList.h Array1D.h AssociatedData.h AssociatedData_NOE.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_float.h DataSet_integer.h DataSet_string.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_TI.o : Analysis_TI.cpp ActionState.h Analysis.h AnalysisState.h Analysis_TI.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_TICA.o : Analysis_TICA.cpp ActionState.h Analysis.h AnalysisState.h Analysis_TICA.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_Timecorr.o : Analysis_Timecorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Timecorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_VectorMath.o : Analysis_VectorMath.cpp ActionState.h Analysis.h AnalysisState.h Analysis_VectorMath.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_Wavelet.o : Analysis_Wavelet.cpp ActionFrameCounter.h ActionState.h Analysis.h AnalysisState.h Analysis_Wavelet.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ClusterMap.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h ProgressBar.h ProgressTimer.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 ArgList.o : ArgList.cpp ArgList.h CpptrajStdio.h StringRoutines.h
-Array1D.o : Array1D.cpp ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Array1D.o : Array1D.cpp ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 AssociatedData_Connect.o : AssociatedData_Connect.cpp ArgList.h AssociatedData.h AssociatedData_Connect.h CpptrajStdio.h
 AssociatedData_NOE.o : AssociatedData_NOE.cpp ArgList.h AssociatedData.h AssociatedData_NOE.h CpptrajStdio.h
 AssociatedData_ResId.o : AssociatedData_ResId.cpp AssociatedData.h AssociatedData_ResId.h CpptrajStdio.h NameType.h Structure/StructureEnum.h
 Atom.o : Atom.cpp Atom.h CpptrajStdio.h NameType.h SymbolExporting.h
-AtomMap.o : AtomMap.cpp Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+AtomMap.o : AtomMap.cpp Atom.h AtomMap.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 AtomMask.o : AtomMask.cpp Atom.h AtomMask.h CpptrajStdio.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h SymbolExporting.h Unit.h
-AxisType.o : AxisType.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h AxisType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-BondSearch.o : BondSearch.cpp Atom.h AtomMask.h AtomType.h BondSearch.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+AxisType.o : AxisType.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h AxisType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+BondSearch.o : BondSearch.cpp Atom.h AtomMask.h AtomType.h BondSearch.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Box.o : Box.cpp Box.h Constants.h CpptrajStdio.h Matrix_3x3.h Parallel.h Vec3.h
 BoxArgs.o : BoxArgs.cpp ArgList.h Box.h BoxArgs.h CpptrajStdio.h Matrix_3x3.h Parallel.h Vec3.h
 BufferedFrame.o : BufferedFrame.cpp BufferedFrame.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Parallel.h TextFormat.h
@@ -153,9 +153,9 @@ BufferedLine.o : BufferedLine.cpp BufferedLine.h CpptrajFile.h CpptrajStdio.h Fi
 ByteRoutines.o : ByteRoutines.cpp
 CIFfile.o : CIFfile.cpp ArgList.h Atom.h BufferedLine.h CIFfile.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h SymbolExporting.h
 CharMask.o : CharMask.cpp Atom.h CharMask.h CpptrajStdio.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h SymbolExporting.h Unit.h
-CharmmParamFile.o : CharmmParamFile.cpp ArgList.h AtomType.h BufferedLine.h CharmmParamFile.h Constants.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h StringRoutines.h TypeNameHolder.h
+CharmmParamFile.o : CharmmParamFile.cpp ArgList.h AtomType.h BufferedLine.h CharmmParamFile.h CmapParmHolder.h Constants.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h StringRoutines.h TypeNameHolder.h
 Cluster/Algorithm.o : Cluster/Algorithm.cpp Cluster/Algorithm.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h CpptrajStdio.h
-Cluster/Algorithm_DBscan.o : Cluster/Algorithm_DBscan.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/Algorithm.h Cluster/Algorithm_DBscan.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Cluster/Algorithm_DBscan.o : Cluster/Algorithm_DBscan.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/Algorithm.h Cluster/Algorithm_DBscan.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Cluster/Algorithm_DPeaks.o : Cluster/Algorithm_DPeaks.cpp ArgList.h AssociatedData.h Cluster/Algorithm.h Cluster/Algorithm_DPeaks.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_Mesh.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h ProgressBar.h Range.h Spline.h TextFormat.h
 Cluster/Algorithm_HierAgglo.o : Cluster/Algorithm_HierAgglo.cpp ArgList.h ArrayIterator.h Cluster/Algorithm.h Cluster/Algorithm_HierAgglo.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/DynamicMatrix.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Matrix.h Parallel.h ProgressBar.h Timer.h
 Cluster/Algorithm_Kmeans.o : Cluster/Algorithm_Kmeans.cpp ArgList.h Cluster/Algorithm.h Cluster/Algorithm_Kmeans.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Parallel.h ProgressBar.h Random.h
@@ -165,82 +165,83 @@ Cluster/Centroid_Coord.o : Cluster/Centroid_Coord.cpp Atom.h AtomMask.h Box.h Cl
 Cluster/Cframes.o : Cluster/Cframes.cpp Cluster/Cframes.h
 Cluster/Cmatrix_Binary.o : Cluster/Cmatrix_Binary.cpp Cluster/Cframes.h Cluster/Cmatrix_Binary.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Parallel.h
 Cluster/Cmatrix_NC.o : Cluster/Cmatrix_NC.cpp Cluster/Cframes.h Cluster/Cmatrix_NC.h CpptrajStdio.h FileName.h NC_Routines.h
-Cluster/Control.o : Cluster/Control.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Cluster/Algorithm.h Cluster/Algorithm_DBscan.h Cluster/Algorithm_DPeaks.h Cluster/Algorithm_HierAgglo.h Cluster/Algorithm_Kmeans.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Control.h Cluster/DBI.h Cluster/DrawGraph.h Cluster/DynamicMatrix.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Output.h Cluster/PseudoF.h Cluster/Results.h Cluster/Results_Coords.h Cluster/Sieve.h Cluster/Silhouette.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_float.h DataSet_integer.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TypeNameHolder.h Unit.h Vec3.h
+Cluster/Control.o : Cluster/Control.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Cluster/Algorithm.h Cluster/Algorithm_DBscan.h Cluster/Algorithm_DPeaks.h Cluster/Algorithm_HierAgglo.h Cluster/Algorithm_Kmeans.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Control.h Cluster/DBI.h Cluster/DrawGraph.h Cluster/DynamicMatrix.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Output.h Cluster/PseudoF.h Cluster/Results.h Cluster/Results_Coords.h Cluster/Sieve.h Cluster/Silhouette.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_float.h DataSet_integer.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TypeNameHolder.h Unit.h Vec3.h
 Cluster/DBI.o : Cluster/DBI.cpp Cluster/CentroidArray.h Cluster/Cframes.h Cluster/DBI.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h
 Cluster/DrawGraph.o : Cluster/DrawGraph.cpp AssociatedData.h Atom.h Cluster/Cframes.h Cluster/DrawGraph.h Cluster/Metric.h Cluster/MetricArray.h Constants.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h Dimension.h FileIO.h FileName.h MetaData.h NameType.h PDBfile.h Parallel.h Range.h Residue.h SymbolExporting.h TextFormat.h Vec3.h
 Cluster/DynamicMatrix.o : Cluster/DynamicMatrix.cpp ArrayIterator.h Cluster/DynamicMatrix.h CpptrajStdio.h Matrix.h
 Cluster/List.o : Cluster/List.cpp AssociatedData.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_integer.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h ProgressBar.h Range.h TextFormat.h
-Cluster/MetricArray.o : Cluster/MetricArray.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Metric_DME.h Cluster/Metric_QuatRMSD.h Cluster/Metric_RMS.h Cluster/Metric_SRMSD.h Cluster/Metric_Scalar.h Cluster/Metric_Torsion.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ProgressBar.h QuaternionRMSD.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Cluster/Metric_DME.o : Cluster/Metric_DME.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Cluster/Centroid.h Cluster/Centroid_Coord.h Cluster/Cframes.h Cluster/Metric.h Cluster/Metric_DME.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Cluster/MetricArray.o : Cluster/MetricArray.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Metric_DME.h Cluster/Metric_QuatRMSD.h Cluster/Metric_RMS.h Cluster/Metric_SRMSD.h Cluster/Metric_Scalar.h Cluster/Metric_Torsion.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h QuaternionRMSD.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Cluster/Metric_DME.o : Cluster/Metric_DME.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Cluster/Centroid.h Cluster/Centroid_Coord.h Cluster/Cframes.h Cluster/Metric.h Cluster/Metric_DME.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Cluster/Metric_Matrix2D.o : Cluster/Metric_Matrix2D.cpp AssociatedData.h Cluster/Metric.h Cluster/Metric_Matrix2D.h CpptrajFile.h DataSet.h DataSet_2D.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
-Cluster/Metric_QuatRMSD.o : Cluster/Metric_QuatRMSD.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Cluster/Centroid.h Cluster/Centroid_Coord.h Cluster/Cframes.h Cluster/Metric.h Cluster/Metric_QuatRMSD.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h QuaternionRMSD.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Cluster/Metric_RMS.o : Cluster/Metric_RMS.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Cluster/Centroid.h Cluster/Centroid_Coord.h Cluster/Cframes.h Cluster/Metric.h Cluster/Metric_RMS.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Cluster/Metric_SRMSD.o : Cluster/Metric_SRMSD.cpp ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Cluster/Centroid.h Cluster/Centroid_Coord.h Cluster/Cframes.h Cluster/Metric.h Cluster/Metric_SRMSD.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Cluster/Metric_QuatRMSD.o : Cluster/Metric_QuatRMSD.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Cluster/Centroid.h Cluster/Centroid_Coord.h Cluster/Cframes.h Cluster/Metric.h Cluster/Metric_QuatRMSD.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h QuaternionRMSD.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Cluster/Metric_RMS.o : Cluster/Metric_RMS.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Cluster/Centroid.h Cluster/Centroid_Coord.h Cluster/Cframes.h Cluster/Metric.h Cluster/Metric_RMS.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Cluster/Metric_SRMSD.o : Cluster/Metric_SRMSD.cpp ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Cluster/Centroid.h Cluster/Centroid_Coord.h Cluster/Cframes.h Cluster/Metric.h Cluster/Metric_SRMSD.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Cluster/Metric_Scalar.o : Cluster/Metric_Scalar.cpp AssociatedData.h Cluster/Centroid.h Cluster/Centroid_Num.h Cluster/Cframes.h Cluster/Metric.h Cluster/Metric_Scalar.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
 Cluster/Metric_Torsion.o : Cluster/Metric_Torsion.cpp AssociatedData.h Cluster/Centroid.h Cluster/Centroid_Num.h Cluster/Cframes.h Cluster/Metric.h Cluster/Metric_Torsion.h Constants.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
 Cluster/Node.o : Cluster/Node.cpp AssociatedData.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h CpptrajFile.h DataSet.h DataSet_1D.h DataSet_float.h DataSet_integer.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
 Cluster/Output.o : Cluster/Output.cpp ArrayIterator.h Cluster/Algorithm.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Output.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Matrix.h Parallel.h Timer.h
 Cluster/PseudoF.o : Cluster/PseudoF.cpp Cluster/CentroidArray.h Cluster/Cframes.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/PseudoF.h Constants.h CpptrajStdio.h
-Cluster/Results_Coords.o : Cluster/Results_Coords.cpp ActionFrameCounter.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Metric_DME.h Cluster/Metric_RMS.h Cluster/Metric_SRMSD.h Cluster/Node.h Cluster/Results.h Cluster/Results_Coords.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Cluster/Results_Coords.o : Cluster/Results_Coords.cpp ActionFrameCounter.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Metric_DME.h Cluster/Metric_RMS.h Cluster/Metric_SRMSD.h Cluster/Node.h Cluster/Results.h Cluster/Results_Coords.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Cluster/Sieve.o : Cluster/Sieve.cpp AssociatedData.h Cluster/Cframes.h Cluster/Sieve.h CpptrajFile.h DataSet.h DataSet_PairwiseCache.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Random.h Range.h TextFormat.h
 Cluster/Silhouette.o : Cluster/Silhouette.cpp Cluster/CentroidArray.h Cluster/Cframes.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Silhouette.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h OnlineVarT.h Parallel.h
 ClusterMap.o : ClusterMap.cpp AssociatedData.h ClusterMap.h Constants.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_2D.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h ProgressBar.h ProgressTimer.h Range.h TextFormat.h Timer.h
+CmapParmHolder.o : CmapParmHolder.cpp CmapParmHolder.h Constants.h CpptrajStdio.h NameType.h ParameterHolders.h ParameterTypes.h TypeNameHolder.h
 Cmd.o : Cmd.cpp Cmd.h DispatchObject.h
 CmdInput.o : CmdInput.cpp CmdInput.h StringRoutines.h
 CmdList.o : CmdList.cpp Cmd.h CmdList.h DispatchObject.h
-Command.o : Command.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h ActionTopWriter.h Action_Align.h Action_Angle.h Action_AreaPerMol.h Action_AtomMap.h Action_AtomicCorr.h Action_AtomicFluct.h Action_AutoImage.h Action_Average.h Action_AvgBox.h Action_Bounds.h Action_Box.h Action_Center.h Action_Channel.h Action_CheckChirality.h Action_CheckStructure.h Action_Closest.h Action_ClusterDihedral.h Action_Contacts.h Action_CreateCrd.h Action_CreateReservoir.h Action_DNAionTracker.h Action_DSSP.h Action_Density.h Action_Diffusion.h Action_Dihedral.h Action_DihedralRMS.h Action_Dipole.h Action_DistRmsd.h Action_Distance.h Action_Energy.h Action_Esander.h Action_FilterByData.h Action_FixAtomOrder.h Action_FixImagedBonds.h Action_GIST.h Action_Grid.h Action_GridFreeEnergy.h Action_HydrogenBond.h Action_Image.h Action_InfraredSpectrum.h Action_Jcoupling.h Action_Keep.h Action_LESsplit.h Action_LIE.h Action_LipidOrder.h Action_MakeStructure.h Action_Mask.h Action_Matrix.h Action_MinImage.h Action_Molsurf.h Action_MultiDihedral.h Action_MultiPucker.h Action_MultiVector.h Action_NAstruct.h Action_NMRrst.h Action_NativeContacts.h Action_OrderParameter.h Action_Outtraj.h Action_PairDist.h Action_Pairwise.h Action_Principal.h Action_Projection.h Action_Pucker.h Action_Radgyr.h Action_Radial.h Action_RandomizeIons.h Action_Remap.h Action_ReplicateCell.h Action_Rmsd.h Action_Rotate.h Action_RunningAvg.h Action_STFC_Diffusion.h Action_Scale.h Action_SetVelocity.h Action_Spam.h Action_Strip.h Action_Surf.h Action_SymmetricRmsd.h Action_Temperature.h Action_Time.h Action_ToroidalDiffusion.h Action_Translate.h Action_Unstrip.h Action_Unwrap.h Action_Vector.h Action_VelocityAutoCorr.h Action_Volmap.h Action_Volume.h Action_Watershell.h Action_XtalSymm.h Analysis.h AnalysisList.h AnalysisState.h Analysis_AmdBias.h Analysis_AutoCorr.h Analysis_Average.h Analysis_CalcDiffusion.h Analysis_Clustering.h Analysis_ConstantPHStats.h Analysis_Corr.h Analysis_CrankShaft.h Analysis_CrdFluct.h Analysis_CrossCorr.h Analysis_CurveFit.h Analysis_Divergence.h Analysis_EvalPlateau.h Analysis_FFT.h Analysis_HausdorffDistance.h Analysis_Hist.h Analysis_IRED.h Analysis_Integrate.h Analysis_KDE.h Analysis_Lifetime.h Analysis_LowestCurve.h Analysis_Matrix.h Analysis_MeltCurve.h Analysis_Modes.h Analysis_MultiHist.h Analysis_Multicurve.h Analysis_Overlap.h Analysis_PhiPsi.h Analysis_Regression.h Analysis_RemLog.h Analysis_Rms2d.h Analysis_RmsAvgCorr.h Analysis_Rotdif.h Analysis_RunningAvg.h Analysis_Slope.h Analysis_Spline.h Analysis_State.h Analysis_Statistics.h Analysis_TI.h Analysis_TICA.h Analysis_Timecorr.h Analysis_VectorMath.h Analysis_Wavelet.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h AxisType.h BaseIOtype.h Box.h BoxArgs.h BufferedLine.h CharMask.h Cluster/Algorithm.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Control.h Cluster/DrawGraph.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Sieve.h Cluster/Silhouette.h ClusterMap.h Cmd.h CmdInput.h CmdList.h Command.h CompactFrameArray.h ComplexArray.h Constants.h Constraints.h ControlBlock.h ControlBlock_For.h CoordinateInfo.h Corr.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_RemLog.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h Deprecated.h DiffusionResults.h DihedralSearch.h Dimension.h DispatchObject.h Energy.h Energy_Sander.h EnsembleIn.h EnsembleOutList.h Ewald.h EwaldOptions.h Ewald_ParticleMesh.h ExclusionArray.h Exec.h Exec_AddMissingRes.h Exec_Analyze.h Exec_Build.h Exec_Calc.h Exec_CatCrd.h Exec_Change.h Exec_ClusterMap.h Exec_CombineCoords.h Exec_Commands.h Exec_CompareClusters.h Exec_CompareEnergy.h Exec_CompareTop.h Exec_CrdAction.h Exec_CrdOut.h Exec_CrdTransform.h Exec_CreateSet.h Exec_DataFile.h Exec_DataFilter.h Exec_DataSetCmd.h Exec_Desc.h Exec_Emin.h Exec_ExtendedComparison.h Exec_Flatten.h Exec_GenerateAmberRst.h Exec_Graft.h Exec_Help.h Exec_HmassRepartition.h Exec_LoadCrd.h Exec_LoadTraj.h Exec_ParallelAnalysis.h Exec_ParmBox.h Exec_ParmSolvent.h Exec_ParmStrip.h Exec_ParmWrite.h Exec_ParseTiming.h Exec_PermuteDihedrals.h Exec_Precision.h Exec_PrepareForLeap.h Exec_PrintData.h Exec_Random.h Exec_ReadData.h Exec_ReadEnsembleData.h Exec_ReadInput.h Exec_RotateDihedral.h Exec_RunAnalysis.h Exec_ScaleDihedralK.h Exec_Sequence.h Exec_SequenceAlign.h Exec_Set.h Exec_Show.h Exec_SortEnsembleData.h Exec_Source.h Exec_SplitCoords.h Exec_System.h Exec_Top.h Exec_Traj.h Exec_UpdateParameters.h Exec_ViewRst.h Exec_Zmatrix.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h GIST_PME.h Grid.h GridAction.h GridBin.h GridMover.h HistBin.h Hungarian.h ImageOption.h ImageTypes.h InputTrajCommon.h MapAtom.h MaskArray.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h OnlineVarT.h OutputTrajCommon.h PDBfile.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h PubFFT.h Pucker.h Pucker_PuckerMask.h Pucker_PuckerSearch.h Pucker_PuckerToken.h RPNcalc.h Random.h Range.h ReferenceAction.h ReferenceFrame.h RemdReservoirNC.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h SplineFxnTable.h StructureCheck.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h cuda_kernels/GistCudaSetup.cuh helpme_standalone.h molsurf.h
+Command.o : Command.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h ActionTopWriter.h Action_Align.h Action_Angle.h Action_AreaPerMol.h Action_AtomMap.h Action_AtomicCorr.h Action_AtomicFluct.h Action_AutoImage.h Action_Average.h Action_AvgBox.h Action_Bounds.h Action_Box.h Action_Center.h Action_Channel.h Action_CheckChirality.h Action_CheckStructure.h Action_Closest.h Action_ClusterDihedral.h Action_Contacts.h Action_CreateCrd.h Action_CreateReservoir.h Action_DNAionTracker.h Action_DSSP.h Action_Density.h Action_Diffusion.h Action_Dihedral.h Action_DihedralRMS.h Action_Dipole.h Action_DistRmsd.h Action_Distance.h Action_Energy.h Action_Esander.h Action_FilterByData.h Action_FixAtomOrder.h Action_FixImagedBonds.h Action_GIST.h Action_Grid.h Action_GridFreeEnergy.h Action_HydrogenBond.h Action_Image.h Action_InfraredSpectrum.h Action_Jcoupling.h Action_Keep.h Action_LESsplit.h Action_LIE.h Action_LipidOrder.h Action_MakeStructure.h Action_Mask.h Action_Matrix.h Action_MinImage.h Action_Molsurf.h Action_MultiDihedral.h Action_MultiPucker.h Action_MultiVector.h Action_NAstruct.h Action_NMRrst.h Action_NativeContacts.h Action_OrderParameter.h Action_Outtraj.h Action_PairDist.h Action_Pairwise.h Action_Principal.h Action_Projection.h Action_Pucker.h Action_Radgyr.h Action_Radial.h Action_RandomizeIons.h Action_Remap.h Action_ReplicateCell.h Action_Rmsd.h Action_Rotate.h Action_RunningAvg.h Action_STFC_Diffusion.h Action_Scale.h Action_SetVelocity.h Action_Spam.h Action_Strip.h Action_Surf.h Action_SymmetricRmsd.h Action_Temperature.h Action_Time.h Action_ToroidalDiffusion.h Action_Translate.h Action_Unstrip.h Action_Unwrap.h Action_Vector.h Action_VelocityAutoCorr.h Action_Volmap.h Action_Volume.h Action_Watershell.h Action_XtalSymm.h Analysis.h AnalysisList.h AnalysisState.h Analysis_AmdBias.h Analysis_AutoCorr.h Analysis_Average.h Analysis_CalcDiffusion.h Analysis_Clustering.h Analysis_ConstantPHStats.h Analysis_Corr.h Analysis_CrankShaft.h Analysis_CrdFluct.h Analysis_CrossCorr.h Analysis_CurveFit.h Analysis_Divergence.h Analysis_EvalPlateau.h Analysis_FFT.h Analysis_HausdorffDistance.h Analysis_Hist.h Analysis_IRED.h Analysis_Integrate.h Analysis_KDE.h Analysis_Lifetime.h Analysis_LowestCurve.h Analysis_Matrix.h Analysis_MeltCurve.h Analysis_Modes.h Analysis_MultiHist.h Analysis_Multicurve.h Analysis_Overlap.h Analysis_PhiPsi.h Analysis_Regression.h Analysis_RemLog.h Analysis_Rms2d.h Analysis_RmsAvgCorr.h Analysis_Rotdif.h Analysis_RunningAvg.h Analysis_Slope.h Analysis_Spline.h Analysis_State.h Analysis_Statistics.h Analysis_TI.h Analysis_TICA.h Analysis_Timecorr.h Analysis_VectorMath.h Analysis_Wavelet.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h AxisType.h BaseIOtype.h Box.h BoxArgs.h BufferedLine.h CharMask.h Cluster/Algorithm.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Control.h Cluster/DrawGraph.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Sieve.h Cluster/Silhouette.h ClusterMap.h CmapParmHolder.h Cmd.h CmdInput.h CmdList.h Command.h CompactFrameArray.h ComplexArray.h Constants.h Constraints.h ControlBlock.h ControlBlock_For.h CoordinateInfo.h Corr.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_RemLog.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h Deprecated.h DiffusionResults.h DihedralSearch.h Dimension.h DispatchObject.h Energy.h Energy_Sander.h EnsembleIn.h EnsembleOutList.h Ewald.h EwaldOptions.h Ewald_ParticleMesh.h ExclusionArray.h Exec.h Exec_AddMissingRes.h Exec_Analyze.h Exec_Build.h Exec_Calc.h Exec_CatCrd.h Exec_Change.h Exec_ClusterMap.h Exec_CombineCoords.h Exec_Commands.h Exec_CompareClusters.h Exec_CompareEnergy.h Exec_CompareTop.h Exec_CrdAction.h Exec_CrdOut.h Exec_CrdTransform.h Exec_CreateSet.h Exec_DataFile.h Exec_DataFilter.h Exec_DataSetCmd.h Exec_Desc.h Exec_Emin.h Exec_ExtendedComparison.h Exec_Flatten.h Exec_GenerateAmberRst.h Exec_Graft.h Exec_Help.h Exec_HmassRepartition.h Exec_LoadCrd.h Exec_LoadTraj.h Exec_ParallelAnalysis.h Exec_ParmBox.h Exec_ParmSolvent.h Exec_ParmStrip.h Exec_ParmWrite.h Exec_ParseTiming.h Exec_PermuteDihedrals.h Exec_Precision.h Exec_PrepareForLeap.h Exec_PrintData.h Exec_Random.h Exec_ReadData.h Exec_ReadEnsembleData.h Exec_ReadInput.h Exec_RotateDihedral.h Exec_RunAnalysis.h Exec_ScaleDihedralK.h Exec_Sequence.h Exec_SequenceAlign.h Exec_Set.h Exec_Show.h Exec_SortEnsembleData.h Exec_Source.h Exec_SplitCoords.h Exec_System.h Exec_Top.h Exec_Traj.h Exec_UpdateParameters.h Exec_ViewRst.h Exec_Zmatrix.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h GIST_PME.h Grid.h GridAction.h GridBin.h GridMover.h HistBin.h Hungarian.h ImageOption.h ImageTypes.h InputTrajCommon.h MapAtom.h MaskArray.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h OnlineVarT.h OutputTrajCommon.h PDBfile.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PubFFT.h Pucker.h Pucker_PuckerMask.h Pucker_PuckerSearch.h Pucker_PuckerToken.h RPNcalc.h Random.h Range.h ReferenceAction.h ReferenceFrame.h RemdReservoirNC.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h SplineFxnTable.h StructureCheck.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h cuda_kernels/GistCudaSetup.cuh helpme_standalone.h molsurf.h
 CompactFrameArray.o : CompactFrameArray.cpp Box.h CompactFrameArray.h CoordinateInfo.h CpptrajStdio.h Matrix_3x3.h Parallel.h ReplicaDimArray.h Vec3.h
 ComplexArray.o : ComplexArray.cpp ArrayIterator.h ComplexArray.h
-Constraints.o : Constraints.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-ControlBlock_For.o : ControlBlock_For.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h ControlBlock.h ControlBlock_For.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_dataSetBlocks.h ForLoop_inData.h ForLoop_integer.h ForLoop_list.h ForLoop_mask.h ForLoop_overSets.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Constraints.o : Constraints.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h CharMask.h CmapParmHolder.h Constants.h Constraints.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+ControlBlock_For.o : ControlBlock_For.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h ControlBlock.h ControlBlock_For.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_dataSetBlocks.h ForLoop_inData.h ForLoop_integer.h ForLoop_list.h ForLoop_mask.h ForLoop_overSets.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 CoordinateInfo.o : CoordinateInfo.cpp Box.h CoordinateInfo.h CpptrajStdio.h Matrix_3x3.h Parallel.h ReplicaDimArray.h Vec3.h
 Corr.o : Corr.cpp ArrayIterator.h ComplexArray.h Corr.h PubFFT.h
 Cph.o : Cph.cpp Cph.h NameType.h
-Cpptraj.o : Cpptraj.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdInput.h CmdList.h Command.h Constants.h CoordinateInfo.h Cpptraj.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h Gpu.h HipDefinitions.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NDiff.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ParmFile.h Range.h ReadLine.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h TopInfo.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h Version.h
+Cpptraj.o : Cpptraj.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Cmd.h CmdInput.h CmdList.h Command.h Constants.h CoordinateInfo.h Cpptraj.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h Gpu.h HipDefinitions.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NDiff.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReadLine.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h TopInfo.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h Version.h
 CpptrajFile.o : CpptrajFile.cpp CpptrajFile.h CpptrajStdio.h FileIO.h FileIO_Bzip2.h FileIO_Gzip.h FileIO_Mpi.h FileIO_MpiShared.h FileIO_Std.h FileName.h Parallel.h StringRoutines.h
-CpptrajState.o : CpptrajState.cpp Action.h ActionList.h ActionState.h Action_CreateCrd.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_Topology.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleNavigator.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ProgressBar.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+CpptrajState.o : CpptrajState.cpp Action.h ActionList.h ActionState.h Action_CreateCrd.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_Topology.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleNavigator.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 CpptrajStdio.o : CpptrajStdio.cpp Parallel.h
 CurveFit.o : CurveFit.cpp CurveFit.h
-DataFile.o : DataFile.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Cluster/Cframes.h Cluster/Cmatrix_NC.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataFile.h DataIO.h DataIO_AmberEne.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_CCP4.h DataIO_CharmmFastRep.h DataIO_CharmmOutput.h DataIO_CharmmRepLog.h DataIO_CharmmRtfPrm.h DataIO_Cmatrix_Binary.h DataIO_Cmatrix_NC.h DataIO_Cpout.h DataIO_Evecs.h DataIO_Gnuplot.h DataIO_Grace.h DataIO_LeapRC.h DataIO_Mdout.h DataIO_NetCDF.h DataIO_Numpy.h DataIO_OpenDx.h DataIO_Peaks.h DataIO_RemLog.h DataIO_Std.h DataIO_VecTraj.h DataIO_XVG.h DataIO_Xplor.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TypeNameHolder.h Unit.h Vec3.h
-DataFileList.o : DataFileList.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataFilter.o : DataFilter.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_integer.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO.o : DataIO.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_AmberEne.o : DataIO_AmberEne.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberEne.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_AmberFF.o : DataIO_AmberFF.cpp AmberParamFile.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberFF.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_AmberFrcmod.o : DataIO_AmberFrcmod.cpp AmberParamFile.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberFrcmod.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_AmberLib.o : DataIO_AmberLib.cpp ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberLib.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_AmberPrep.o : DataIO_AmberPrep.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberPrep.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_CCP4.o : DataIO_CCP4.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ByteRoutines.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CCP4.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_CharmmFastRep.o : DataIO_CharmmFastRep.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmFastRep.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_CharmmOutput.o : DataIO_CharmmOutput.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmOutput.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_CharmmRepLog.o : DataIO_CharmmRepLog.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmRepLog.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_CharmmRtfPrm.o : DataIO_CharmmRtfPrm.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharmmParamFile.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmRtfPrm.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h DataSet_Topology.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_Cmatrix_Binary.o : DataIO_Cmatrix_Binary.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/Cframes.h Cluster/Cmatrix_Binary.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Cmatrix_Binary.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_Cmatrix_NC.o : DataIO_Cmatrix_NC.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/Cframes.h Cluster/Cmatrix_NC.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Cmatrix_NC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_Cpout.o : DataIO_Cpout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Cpout.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h DataSet_PHREMD_Implicit.h DataSet_pH.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_Evecs.o : DataIO_Evecs.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Evecs.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_Gnuplot.o : DataIO_Gnuplot.cpp ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Gnuplot.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_Grace.o : DataIO_Grace.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Grace.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_string.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_LeapRC.o : DataIO_LeapRC.cpp ArgList.h AssociatedData.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_Mdout.o : DataIO_Mdout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Mdout.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_NetCDF.o : DataIO_NetCDF.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/Cframes.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_NetCDF.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_Mesh.h DataSet_Modes.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_Vector.h DataSet_Vector_Scalar.h DataSet_string.h DataSet_unsignedInt.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h Version.h
-DataIO_Numpy.o : DataIO_Numpy.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Numpy.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h libnpy/npy.hpp
-DataIO_OpenDx.o : DataIO_OpenDx.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_OpenDx.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridDbl.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_Peaks.o : DataIO_Peaks.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Peaks.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector_Scalar.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_RemLog.o : DataIO_RemLog.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_RemLog.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_Std.o : DataIO_Std.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Cluster/Cframes.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Std.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_Parameters.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_string.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_VecTraj.o : DataIO_VecTraj.cpp ActionFrameCounter.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_VecTraj.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_XVG.o : DataIO_XVG.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_XVG.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_Xplor.o : DataIO_Xplor.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Xplor.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataFile.o : DataFile.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Cluster/Cframes.h Cluster/Cmatrix_NC.h CmapParmHolder.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataFile.h DataIO.h DataIO_AmberEne.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_CCP4.h DataIO_CharmmFastRep.h DataIO_CharmmOutput.h DataIO_CharmmRepLog.h DataIO_CharmmRtfPrm.h DataIO_Cmatrix_Binary.h DataIO_Cmatrix_NC.h DataIO_Cpout.h DataIO_Evecs.h DataIO_Gnuplot.h DataIO_Grace.h DataIO_LeapRC.h DataIO_Mdout.h DataIO_NetCDF.h DataIO_Numpy.h DataIO_OpenDx.h DataIO_Peaks.h DataIO_RemLog.h DataIO_Std.h DataIO_VecTraj.h DataIO_XVG.h DataIO_Xplor.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TypeNameHolder.h Unit.h Vec3.h
+DataFileList.o : DataFileList.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataFilter.o : DataFilter.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_integer.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO.o : DataIO.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_AmberEne.o : DataIO_AmberEne.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberEne.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_AmberFF.o : DataIO_AmberFF.cpp AmberParamFile.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberFF.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_AmberFrcmod.o : DataIO_AmberFrcmod.cpp AmberParamFile.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberFrcmod.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_AmberLib.o : DataIO_AmberLib.cpp ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberLib.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_AmberPrep.o : DataIO_AmberPrep.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberPrep.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_CCP4.o : DataIO_CCP4.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ByteRoutines.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CCP4.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_CharmmFastRep.o : DataIO_CharmmFastRep.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmFastRep.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_CharmmOutput.o : DataIO_CharmmOutput.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmOutput.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_CharmmRepLog.o : DataIO_CharmmRepLog.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmRepLog.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_CharmmRtfPrm.o : DataIO_CharmmRtfPrm.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharmmParamFile.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmRtfPrm.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h DataSet_Topology.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_Cmatrix_Binary.o : DataIO_Cmatrix_Binary.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/Cframes.h Cluster/Cmatrix_Binary.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Cmatrix_Binary.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_Cmatrix_NC.o : DataIO_Cmatrix_NC.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/Cframes.h Cluster/Cmatrix_NC.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Cmatrix_NC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_Cpout.o : DataIO_Cpout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Cpout.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h DataSet_PHREMD_Implicit.h DataSet_pH.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_Evecs.o : DataIO_Evecs.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedFrame.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Evecs.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_Gnuplot.o : DataIO_Gnuplot.cpp ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Gnuplot.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_Grace.o : DataIO_Grace.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Grace.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_string.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_LeapRC.o : DataIO_LeapRC.cpp ArgList.h AssociatedData.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_Mdout.o : DataIO_Mdout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Mdout.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_NetCDF.o : DataIO_NetCDF.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/Cframes.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_NetCDF.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_Mesh.h DataSet_Modes.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_Vector.h DataSet_Vector_Scalar.h DataSet_string.h DataSet_unsignedInt.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h Version.h
+DataIO_Numpy.o : DataIO_Numpy.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Numpy.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h libnpy/npy.hpp
+DataIO_OpenDx.o : DataIO_OpenDx.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_OpenDx.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridDbl.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_Peaks.o : DataIO_Peaks.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Peaks.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector_Scalar.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_RemLog.o : DataIO_RemLog.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_RemLog.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_Std.o : DataIO_Std.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Cluster/Cframes.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Std.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_Parameters.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_string.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_VecTraj.o : DataIO_VecTraj.cpp ActionFrameCounter.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_VecTraj.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_XVG.o : DataIO_XVG.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_XVG.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_Xplor.o : DataIO_Xplor.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Xplor.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataSet.o : DataSet.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
-DataSetList.o : DataSetList.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Cluster/Cframes.h Cluster/Cmatrix_NC.h CompactFrameArray.h ComplexArray.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_FRM.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_GridDbl.h DataSet_GridFlt.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_NameMap.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h DataSet_PHREMD_Implicit.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_PairwiseCache_NC.h DataSet_Parameters.h DataSet_RemLog.h DataSet_StringVar.h DataSet_Tensor.h DataSet_Topology.h DataSet_Vector.h DataSet_Vector_Scalar.h DataSet_Zmatrix.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_disk.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h DataSet_unsignedInt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h InputTrajCommon.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h SymmetricTensor.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TypeNameHolder.h Unit.h Vec3.h
+DataSetList.o : DataSetList.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Cluster/Cframes.h Cluster/Cmatrix_NC.h CmapParmHolder.h CompactFrameArray.h ComplexArray.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_FRM.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_GridDbl.h DataSet_GridFlt.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_NameMap.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h DataSet_PHREMD_Implicit.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_PairwiseCache_NC.h DataSet_Parameters.h DataSet_RemLog.h DataSet_StringVar.h DataSet_Tensor.h DataSet_Topology.h DataSet_Vector.h DataSet_Vector_Scalar.h DataSet_Zmatrix.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_disk.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h DataSet_unsignedInt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h InputTrajCommon.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h SymmetricTensor.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TypeNameHolder.h Unit.h Vec3.h
 DataSet_1D.o : DataSet_1D.cpp ArrayIterator.h AssociatedData.h ComplexArray.h Constants.h Corr.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h PubFFT.h Range.h TextFormat.h
 DataSet_3D.o : DataSet_3D.cpp AssociatedData.h Box.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_3D.h Dimension.h FileIO.h FileName.h GridBin.h Matrix_3x3.h MetaData.h Parallel.h Range.h TextFormat.h Vec3.h
-DataSet_Coords.o : DataSet_Coords.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataSet_Coords_CRD.o : DataSet_Coords_CRD.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_CRD.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataSet_Coords_FRM.o : DataSet_Coords_FRM.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_FRM.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataSet_Coords_REF.o : DataSet_Coords_REF.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TrajFrameCounter.h Trajin.h Trajin_Single.h TypeNameHolder.h Unit.h Vec3.h
-DataSet_Coords_TRJ.o : DataSet_Coords_TRJ.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_TRJ.h Dimension.h FileIO.h FileName.h Frame.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h Trajin_Single.h TypeNameHolder.h Unit.h Vec3.h
+DataSet_Coords.o : DataSet_Coords.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataSet_Coords_CRD.o : DataSet_Coords_CRD.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_CRD.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataSet_Coords_FRM.o : DataSet_Coords_FRM.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_FRM.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataSet_Coords_REF.o : DataSet_Coords_REF.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TrajFrameCounter.h Trajin.h Trajin_Single.h TypeNameHolder.h Unit.h Vec3.h
+DataSet_Coords_TRJ.o : DataSet_Coords_TRJ.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_TRJ.h Dimension.h FileIO.h FileName.h Frame.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h Trajin_Single.h TypeNameHolder.h Unit.h Vec3.h
 DataSet_GridDbl.o : DataSet_GridDbl.cpp ArrayIterator.h AssociatedData.h Box.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_3D.h DataSet_GridDbl.h Dimension.h FileIO.h FileName.h Grid.h GridBin.h Matrix_3x3.h MetaData.h Parallel.h Range.h StringRoutines.h TextFormat.h Vec3.h
 DataSet_GridFlt.o : DataSet_GridFlt.cpp ArrayIterator.h AssociatedData.h Box.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_3D.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Grid.h GridBin.h Matrix_3x3.h MetaData.h Parallel.h Range.h StringRoutines.h TextFormat.h Vec3.h
 DataSet_Mat3x3.o : DataSet_Mat3x3.cpp AssociatedData.h CpptrajFile.h DataSet.h DataSet_Mat3x3.h Dimension.h FileIO.h FileName.h Matrix_3x3.h MetaData.h Parallel.h Range.h TextFormat.h Vec3.h
@@ -254,11 +255,11 @@ DataSet_PHREMD_Implicit.o : DataSet_PHREMD_Implicit.cpp AssociatedData.h Cph.h C
 DataSet_PairwiseCache.o : DataSet_PairwiseCache.cpp AssociatedData.h Cluster/Cframes.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_PairwiseCache.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
 DataSet_PairwiseCache_MEM.o : DataSet_PairwiseCache_MEM.cpp ArrayIterator.h AssociatedData.h Cluster/Cframes.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h Dimension.h FileIO.h FileName.h Matrix.h MetaData.h Parallel.h Range.h StringRoutines.h TextFormat.h
 DataSet_PairwiseCache_NC.o : DataSet_PairwiseCache_NC.cpp AssociatedData.h Cluster/Cframes.h Cluster/Cmatrix_NC.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_PairwiseCache.h DataSet_PairwiseCache_NC.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h StringRoutines.h TextFormat.h
-DataSet_Parameters.o : DataSet_Parameters.cpp AssociatedData.h AtomType.h Constants.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h MetaData.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h TextFormat.h TypeNameHolder.h
+DataSet_Parameters.o : DataSet_Parameters.cpp AssociatedData.h AtomType.h CmapParmHolder.h Constants.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h MetaData.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h TextFormat.h TypeNameHolder.h
 DataSet_RemLog.o : DataSet_RemLog.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h ReplicaDimArray.h TextFormat.h
 DataSet_StringVar.o : DataSet_StringVar.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_StringVar.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
 DataSet_Tensor.o : DataSet_Tensor.cpp AssociatedData.h CpptrajFile.h DataSet.h DataSet_Tensor.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h SymmetricTensor.h TextFormat.h
-DataSet_Topology.o : DataSet_Topology.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Topology.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ParmFile.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataSet_Topology.o : DataSet_Topology.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Topology.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataSet_Vector.o : DataSet_Vector.cpp ArrayIterator.h AssociatedData.h ComplexArray.h Constants.h Corr.h CpptrajFile.h DataSet.h DataSet_1D.h DataSet_Vector.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h PubFFT.h Range.h SymbolExporting.h TextFormat.h Vec3.h
 DataSet_Vector_Scalar.o : DataSet_Vector_Scalar.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Vector_Scalar.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h Vec3.h
 DataSet_Zmatrix.o : DataSet_Zmatrix.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Zmatrix.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h Structure/InternalCoords.h Structure/Zmatrix.h TextFormat.h Vec3.h
@@ -270,85 +271,85 @@ DataSet_pH.o : DataSet_pH.cpp AssociatedData.h Cph.h CpptrajFile.h CpptrajStdio.
 DataSet_string.o : DataSet_string.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_string.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
 DataSet_unsignedInt.o : DataSet_unsignedInt.cpp AssociatedData.h CpptrajFile.h DataSet.h DataSet_1D.h DataSet_unsignedInt.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
 Deprecated.o : Deprecated.cpp CpptrajStdio.h Deprecated.h DispatchObject.h
-DiffusionResults.o : DiffusionResults.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DiffusionResults.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DihedralSearch.o : DihedralSearch.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DihedralSearch.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DiffusionResults.o : DiffusionResults.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DiffusionResults.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DihedralSearch.o : DihedralSearch.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h DihedralSearch.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DistRoutines.o : DistRoutines.cpp Box.h DistRoutines.h ImageOption.h Matrix_3x3.h Parallel.h Vec3.h
-Energy.o : Energy.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h Energy.h Energy/Ene_Angle.h Energy/Ene_Bond.h Energy/Kernel_Harmonic.h ExclusionArray.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Energy.o : Energy.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h Energy.h Energy/Ene_Angle.h Energy/Ene_Bond.h Energy/Kernel_Harmonic.h ExclusionArray.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 EnergyArray.o : EnergyArray.cpp CpptrajFile.h CpptrajStdio.h EnergyArray.h FileIO.h FileName.h Parallel.h
-Energy_Sander.o : Energy_Sander.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy_Sander.h FileName.h FileTypes.h File_TempName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ParmFile.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Energy_Sander.o : Energy_Sander.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy_Sander.h FileName.h FileTypes.h File_TempName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 EnsembleIn.o : EnsembleIn.cpp Atom.h AtomMask.h Box.h CoordinateInfo.h CpptrajStdio.h EnsembleIn.h FileName.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h Timer.h TrajFrameCounter.h Unit.h Vec3.h
-EnsembleIn_Multi.o : EnsembleIn_Multi.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h EnsembleIn.h EnsembleIn_Multi.h FileIO.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-EnsembleIn_Single.o : EnsembleIn_Single.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h EnsembleIn.h EnsembleIn_Single.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+EnsembleIn_Multi.o : EnsembleIn_Multi.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h EnsembleIn.h EnsembleIn_Multi.h FileIO.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+EnsembleIn_Single.o : EnsembleIn_Single.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h EnsembleIn.h EnsembleIn_Single.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
 EnsembleNavigator.o : EnsembleNavigator.cpp Atom.h AtomMask.h Box.h CoordinateInfo.h CpptrajStdio.h EnsembleIn.h EnsembleNavigator.h FileName.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h Timer.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TrajinList.h Unit.h Vec3.h
 EnsembleOut.o : EnsembleOut.cpp ActionFrameCounter.h BaseIOtype.h Box.h CoordinateInfo.h CpptrajStdio.h EnsembleOut.h FileName.h FileTypes.h FramePtrArray.h Matrix_3x3.h OutputTrajCommon.h Parallel.h Range.h ReplicaDimArray.h TrajectoryFile.h Vec3.h
-EnsembleOutList.o : EnsembleOutList.cpp ActionFrameCounter.h ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h EnsembleOut.h EnsembleOutList.h EnsembleOut_Multi.h EnsembleOut_Single.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TrajectoryFile.h TypeNameHolder.h Unit.h Vec3.h
-EnsembleOut_Multi.o : EnsembleOut_Multi.cpp ActionFrameCounter.h ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h EnsembleOut.h EnsembleOut_Multi.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-EnsembleOut_Single.o : EnsembleOut_Single.cpp ActionFrameCounter.h ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h EnsembleOut.h EnsembleOut_Single.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Ewald.o : Ewald.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h EnergyKernel_Adjust.h EnergyKernel_Nonbond.h Ewald.h ExclusionArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h PairListLoop.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h Spline.h SplineFxnTable.h StringRoutines.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+EnsembleOutList.o : EnsembleOutList.cpp ActionFrameCounter.h ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h EnsembleOut.h EnsembleOutList.h EnsembleOut_Multi.h EnsembleOut_Single.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TrajectoryFile.h TypeNameHolder.h Unit.h Vec3.h
+EnsembleOut_Multi.o : EnsembleOut_Multi.cpp ActionFrameCounter.h ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h EnsembleOut.h EnsembleOut_Multi.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+EnsembleOut_Single.o : EnsembleOut_Single.cpp ActionFrameCounter.h ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h EnsembleOut.h EnsembleOut_Single.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+Ewald.o : Ewald.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h EnergyKernel_Adjust.h EnergyKernel_Nonbond.h Ewald.h ExclusionArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h PairListLoop.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Spline.h SplineFxnTable.h StringRoutines.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 EwaldOptions.o : EwaldOptions.cpp ArgList.h CpptrajStdio.h EwaldOptions.h
 Ewald_ParticleMesh.o : Ewald_ParticleMesh.cpp Atom.h AtomMask.h Box.h CoordinateInfo.h CpptrajStdio.h Ewald.h EwaldOptions.h Ewald_ParticleMesh.h ExclusionArray.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h Timer.h Unit.h Vec3.h helpme_standalone.h
 Ewald_Regular.o : Ewald_Regular.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Ewald.h EwaldOptions.h Ewald_Regular.h ExclusionArray.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h StringRoutines.h SymbolExporting.h Timer.h Unit.h Vec3.h
 ExclusionArray.o : ExclusionArray.cpp Atom.h AtomMask.h CharMask.h CpptrajStdio.h ExclusionArray.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Unit.h
-Exec_AddMissingRes.o : Exec_AddMissingRes.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CharMask.h CompactFrameArray.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_AddMissingRes.h Exec_AddMissingRes_Pres.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ParmFile.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Analyze.o : Exec_Analyze.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Analyze.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Build.o : Exec_Build.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Parm/GB_Params.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/Creator.h Structure/Disulfide.h Structure/HisProt.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/StructureEnum.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Calc.o : Exec_Calc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Calc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_CatCrd.o : Exec_CatCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CatCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Change.o : Exec_Change.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Change.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_ClusterMap.o : Exec_ClusterMap.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ClusterMap.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ClusterMap.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_CombineCoords.o : Exec_CombineCoords.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CombineCoords.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Commands.o : Exec_Commands.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Commands.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_CompareClusters.o : Exec_CompareClusters.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CompareClusters.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_CompareEnergy.o : Exec_CompareEnergy.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h Energy/Kernel_Fourier.h Energy/Kernel_Harmonic.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CompareEnergy.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_CompareTop.o : Exec_CompareTop.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CompareTop.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_CrdAction.o : Exec_CrdAction.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CrdAction.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_CrdOut.o : Exec_CrdOut.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CrdOut.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-Exec_CrdTransform.o : Exec_CrdTransform.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CrdTransform.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_CreateSet.o : Exec_CreateSet.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CreateSet.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_DataFile.o : Exec_DataFile.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_DataFile.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_DataFilter.o : Exec_DataFilter.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_DataFilter.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_DataSetCmd.o : Exec_DataSetCmd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h ArrayIterator.h AssociatedData.h AssociatedData_Connect.h AssociatedData_NOE.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_Mesh.h DataSet_Vector.h DataSet_string.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_DataSetCmd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Desc.o : Exec_Desc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Desc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Emin.o : Exec_Emin.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Emin.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_ExtendedComparison.o : Exec_ExtendedComparison.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ExtendedComparison.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Flatten.o : Exec_Flatten.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Flatten.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_GenerateAmberRst.o : Exec_GenerateAmberRst.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_GenerateAmberRst.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Graft.o : Exec_Graft.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Graft.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Help.o : Exec_Help.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Help.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_HmassRepartition.o : Exec_HmassRepartition.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_HmassRepartition.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_LoadCrd.o : Exec_LoadCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_LoadCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_LoadTraj.o : Exec_LoadTraj.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_LoadTraj.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_ParallelAnalysis.o : Exec_ParallelAnalysis.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParallelAnalysis.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_ParmBox.o : Exec_ParmBox.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BoxArgs.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmBox.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_ParmSolvent.o : Exec_ParmSolvent.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmSolvent.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_ParmStrip.o : Exec_ParmStrip.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmStrip.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_ParmWrite.o : Exec_ParmWrite.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmWrite.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_ParseTiming.o : Exec_ParseTiming.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParseTiming.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_PermuteDihedrals.o : Exec_PermuteDihedrals.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h DistRoutines.h EnsembleIn.h EnsembleOutList.h ExclusionArray.h Exec.h Exec_PermuteDihedrals.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Precision.o : Exec_Precision.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Precision.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_PrepareForLeap.o : Exec_PrepareForLeap.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_PrepareForLeap.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h LeapInterface.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ParmFile.h Range.h ReferenceFrame.h Remote.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/Disulfide.h Structure/HisProt.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-Exec_PrintData.o : Exec_PrintData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_PrintData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Random.o : Exec_Random.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Random.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_ReadData.o : Exec_ReadData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ReadData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_ReadEnsembleData.o : Exec_ReadEnsembleData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ReadEnsembleData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_ReadInput.o : Exec_ReadInput.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ReadInput.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_RotateDihedral.o : Exec_RotateDihedral.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_RotateDihedral.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_RunAnalysis.o : Exec_RunAnalysis.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_RunAnalysis.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_ScaleDihedralK.o : Exec_ScaleDihedralK.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ScaleDihedralK.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Sequence.o : Exec_Sequence.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Sequence.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/Creator.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_SequenceAlign.o : Exec_SequenceAlign.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SequenceAlign.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Set.o : Exec_Set.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_StringVar.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Set.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Show.o : Exec_Show.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_StringVar.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Show.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_SortEnsembleData.o : Exec_SortEnsembleData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h DataSet_PHREMD_Implicit.h DataSet_pH.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SortEnsembleData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Source.o : Exec_Source.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Source.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_SplitCoords.o : Exec_SplitCoords.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SplitCoords.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_System.o : Exec_System.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_System.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Top.o : Exec_Top.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Top.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h TopInfo.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Traj.o : Exec_Traj.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Traj.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_UpdateParameters.o : Exec_UpdateParameters.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h DataSet_Topology.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_UpdateParameters.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_ViewRst.o : Exec_ViewRst.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ViewRst.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h ViewRst.h
-Exec_Zmatrix.o : Exec_Zmatrix.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Zmatrix.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Zmatrix.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-ExtendedSimilarity.o : ExtendedSimilarity.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h ExtendedSimilarity.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Exec_AddMissingRes.o : Exec_AddMissingRes.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CharMask.h CmapParmHolder.h CompactFrameArray.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_AddMissingRes.h Exec_AddMissingRes_Pres.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Analyze.o : Exec_Analyze.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Analyze.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Build.o : Exec_Build.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/GB_Params.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/Creator.h Structure/Disulfide.h Structure/HisProt.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/StructureEnum.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Calc.o : Exec_Calc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Calc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_CatCrd.o : Exec_CatCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CatCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Change.o : Exec_Change.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Change.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_ClusterMap.o : Exec_ClusterMap.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ClusterMap.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ClusterMap.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_CombineCoords.o : Exec_CombineCoords.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CombineCoords.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Commands.o : Exec_Commands.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Commands.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_CompareClusters.o : Exec_CompareClusters.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CompareClusters.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_CompareEnergy.o : Exec_CompareEnergy.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h Energy/Kernel_Fourier.h Energy/Kernel_Harmonic.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CompareEnergy.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_CompareTop.o : Exec_CompareTop.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CompareTop.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_CrdAction.o : Exec_CrdAction.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Cmd.h CmdList.h Command.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CrdAction.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_CrdOut.o : Exec_CrdOut.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CrdOut.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Exec_CrdTransform.o : Exec_CrdTransform.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CrdTransform.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_CreateSet.o : Exec_CreateSet.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CreateSet.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_DataFile.o : Exec_DataFile.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_DataFile.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_DataFilter.o : Exec_DataFilter.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_DataFilter.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_DataSetCmd.o : Exec_DataSetCmd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h ArrayIterator.h AssociatedData.h AssociatedData_Connect.h AssociatedData_NOE.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_Mesh.h DataSet_Vector.h DataSet_string.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_DataSetCmd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Desc.o : Exec_Desc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Desc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Emin.o : Exec_Emin.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Emin.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_ExtendedComparison.o : Exec_ExtendedComparison.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ExtendedComparison.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Flatten.o : Exec_Flatten.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Flatten.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_GenerateAmberRst.o : Exec_GenerateAmberRst.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_GenerateAmberRst.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Graft.o : Exec_Graft.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Graft.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Help.o : Exec_Help.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Help.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_HmassRepartition.o : Exec_HmassRepartition.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_HmassRepartition.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_LoadCrd.o : Exec_LoadCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_LoadCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_LoadTraj.o : Exec_LoadTraj.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_LoadTraj.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_ParallelAnalysis.o : Exec_ParallelAnalysis.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParallelAnalysis.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_ParmBox.o : Exec_ParmBox.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BoxArgs.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmBox.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_ParmSolvent.o : Exec_ParmSolvent.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmSolvent.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_ParmStrip.o : Exec_ParmStrip.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmStrip.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_ParmWrite.o : Exec_ParmWrite.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmWrite.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_ParseTiming.o : Exec_ParseTiming.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParseTiming.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_PermuteDihedrals.o : Exec_PermuteDihedrals.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h DistRoutines.h EnsembleIn.h EnsembleOutList.h ExclusionArray.h Exec.h Exec_PermuteDihedrals.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Precision.o : Exec_Precision.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Precision.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_PrepareForLeap.o : Exec_PrepareForLeap.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_PrepareForLeap.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h LeapInterface.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h Remote.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/Disulfide.h Structure/HisProt.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Exec_PrintData.o : Exec_PrintData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_PrintData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Random.o : Exec_Random.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Random.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_ReadData.o : Exec_ReadData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ReadData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_ReadEnsembleData.o : Exec_ReadEnsembleData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ReadEnsembleData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_ReadInput.o : Exec_ReadInput.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ReadInput.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_RotateDihedral.o : Exec_RotateDihedral.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_RotateDihedral.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_RunAnalysis.o : Exec_RunAnalysis.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_RunAnalysis.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_ScaleDihedralK.o : Exec_ScaleDihedralK.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ScaleDihedralK.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Sequence.o : Exec_Sequence.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Sequence.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/Creator.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_SequenceAlign.o : Exec_SequenceAlign.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SequenceAlign.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Set.o : Exec_Set.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_StringVar.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Set.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Show.o : Exec_Show.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_StringVar.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Show.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_SortEnsembleData.o : Exec_SortEnsembleData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h DataSet_PHREMD_Implicit.h DataSet_pH.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SortEnsembleData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Source.o : Exec_Source.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Source.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_SplitCoords.o : Exec_SplitCoords.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SplitCoords.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_System.o : Exec_System.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_System.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Top.o : Exec_Top.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Top.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h TopInfo.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Traj.o : Exec_Traj.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Traj.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_UpdateParameters.o : Exec_UpdateParameters.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h DataSet_Topology.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_UpdateParameters.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_ViewRst.o : Exec_ViewRst.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ViewRst.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h ViewRst.h
+Exec_Zmatrix.o : Exec_Zmatrix.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Zmatrix.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Zmatrix.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+ExtendedSimilarity.o : ExtendedSimilarity.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h ExtendedSimilarity.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 ExternalFxn.o : ExternalFxn.cpp Random.h
 FileIO_Bzip2.o : FileIO_Bzip2.cpp CpptrajStdio.h FileIO.h FileIO_Bzip2.h
 FileIO_Gzip.o : FileIO_Gzip.cpp CpptrajStdio.h FileIO.h FileIO_Gzip.h
@@ -359,74 +360,73 @@ FileName.o : FileName.cpp CpptrajStdio.h FileName.h StringRoutines.h
 FileType.o : FileType.cpp FileType.h
 FileTypes.o : FileTypes.cpp ArgList.h BaseIOtype.h CpptrajStdio.h FileTypes.h
 File_TempName.o : File_TempName.cpp CpptrajStdio.h FileName.h File_TempName.h StringRoutines.h
-ForLoop.o : ForLoop.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h ForLoop.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-ForLoop_dataSetBlocks.o : ForLoop_dataSetBlocks.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_dataSetBlocks.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-ForLoop_inData.o : ForLoop_inData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_integer.h DataSet_string.h DataSet_unsignedInt.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_inData.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-ForLoop_integer.o : ForLoop_integer.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_integer.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-ForLoop_list.o : ForLoop_list.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_list.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-ForLoop_mask.o : ForLoop_mask.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_mask.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-ForLoop_overSets.o : ForLoop_overSets.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_overSets.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+ForLoop.o : ForLoop.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h ForLoop.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+ForLoop_dataSetBlocks.o : ForLoop_dataSetBlocks.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_dataSetBlocks.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+ForLoop_inData.o : ForLoop_inData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_integer.h DataSet_string.h DataSet_unsignedInt.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_inData.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+ForLoop_integer.o : ForLoop_integer.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_integer.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+ForLoop_list.o : ForLoop_list.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_list.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+ForLoop_mask.o : ForLoop_mask.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_mask.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+ForLoop_overSets.o : ForLoop_overSets.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_overSets.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Frame.o : Frame.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Unit.h Vec3.h
-GIST_PME.o : GIST_PME.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h EnergyKernel_Adjust.h EnergyKernel_Nonbond.h Ewald.h Ewald_ParticleMesh.h ExclusionArray.h FileName.h Frame.h GIST_PME.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h helpme_standalone.h
+GIST_PME.o : GIST_PME.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h EnergyKernel_Adjust.h EnergyKernel_Nonbond.h Ewald.h Ewald_ParticleMesh.h ExclusionArray.h FileName.h Frame.h GIST_PME.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h helpme_standalone.h
 GistEntropyUtils.o : GistEntropyUtils.cpp CpptrajFile.h FileIO.h FileName.h GistEntropyUtils.h Parallel.h Vec3.h
 Gpu.o : Gpu.cpp Gpu.h
-GridAction.o : GridAction.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridAction.h GridBin.h GridMover.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+GridAction.o : GridAction.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridAction.h GridBin.h GridMover.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 GridBin.o : GridBin.cpp Box.h CpptrajStdio.h GridBin.h Matrix_3x3.h Parallel.h Vec3.h
-GridMover.o : GridMover.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_3D.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h GridMover.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+GridMover.o : GridMover.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_3D.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h GridMover.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 GuessAtomHybridization.o : GuessAtomHybridization.cpp Atom.h AtomType.h Constants.h GuessAtomHybridization.h NameType.h ParameterTypes.h SymbolExporting.h
 HistBin.o : HistBin.cpp Constants.h CpptrajStdio.h Dimension.h HistBin.h
 Hungarian.o : Hungarian.cpp ArrayIterator.h Constants.h CpptrajStdio.h Hungarian.h Matrix.h
 ImageRoutines.o : ImageRoutines.cpp Atom.h AtomMask.h Box.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h Frame.h ImageOption.h ImageRoutines.h ImageTypes.h Image_List.h Image_List_Mask.h Image_List_Pair.h Image_List_Pair_CoM.h Image_List_Pair_First.h Image_List_Pair_Geom.h Image_List_Unit.h Image_List_Unit_CoM.h Image_List_Unit_First.h Image_List_Unit_Geom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Unit.h Vec3.h
-Image_List_Mask.o : Image_List_Mask.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h Image_List.h Image_List_Mask.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Image_List_Pair.o : Image_List_Pair.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h Image_List.h Image_List_Pair.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Image_List_Unit.o : Image_List_Unit.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h Image_List.h Image_List_Unit.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Image_List_Mask.o : Image_List_Mask.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h Image_List.h Image_List_Mask.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Image_List_Pair.o : Image_List_Pair.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h Image_List.h Image_List_Pair.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Image_List_Unit.o : Image_List_Unit.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h Image_List.h Image_List_Unit.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 InputTrajCommon.o : InputTrajCommon.cpp CpptrajStdio.h FileName.h InputTrajCommon.h TrajFrameCounter.h
 KDE.o : KDE.cpp AssociatedData.h Constants.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_double.h Dimension.h FileIO.h FileName.h HistBin.h KDE.h MetaData.h Parallel.h Range.h TextFormat.h
-LeapInterface.o : LeapInterface.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h File_TempName.h Frame.h LeapInterface.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+LeapInterface.o : LeapInterface.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h File_TempName.h Frame.h LeapInterface.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 MapAtom.o : MapAtom.cpp Atom.h MapAtom.h NameType.h SymbolExporting.h
-MaskArray.o : MaskArray.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+MaskArray.o : MaskArray.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 MaskToken.o : MaskToken.cpp ArgList.h Atom.h CpptrajStdio.h DistRoutines.h ImageOption.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Unit.h
 Matrix_3x3.o : Matrix_3x3.cpp Constants.h CpptrajStdio.h Matrix_3x3.h Parallel.h Vec3.h
 MdOpts.o : MdOpts.cpp ArgList.h Constants.h Constraints.h CpptrajStdio.h MdOpts.h ParameterTypes.h
 MetaData.o : MetaData.cpp CpptrajStdio.h FileName.h MetaData.h Range.h StringRoutines.h
-Minimize_SteepestDescent.o : Minimize_SteepestDescent.cpp ActionFrameCounter.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h EnergyArray.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-Mol.o : Mol.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Mol.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Minimize_SteepestDescent.o : Minimize_SteepestDescent.cpp ActionFrameCounter.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h EnergyArray.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Mol.o : Mol.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Mol.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Mol2File.o : Mol2File.cpp Atom.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Mol2File.h NameType.h Parallel.h Residue.h StringRoutines.h SymbolExporting.h
 NC_Routines.o : NC_Routines.cpp CpptrajStdio.h NC_Routines.h
 NDiff.o : NDiff.cpp ArgList.h BufferedLine.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NDiff.h Parallel.h StringRoutines.h
 NameType.o : NameType.cpp CpptrajStdio.h NameType.h
 NetcdfFile.o : NetcdfFile.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h ParallelNetcdf.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Unit.h Vec3.h Version.h
 OMM_helpers.o : OMM_helpers.cpp Constants.h OMM_helpers.h ParameterTypes.h
-OutputTrajCommon.o : OutputTrajCommon.cpp ActionFrameCounter.h ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+OutputTrajCommon.o : OutputTrajCommon.cpp ActionFrameCounter.h ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
 PDBfile.o : PDBfile.cpp Atom.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h PDBfile.h Parallel.h Residue.h StringRoutines.h SymbolExporting.h
 PairList.o : PairList.cpp Atom.h AtomMask.h Box.h CoordinateInfo.h CpptrajStdio.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Timer.h Unit.h Vec3.h
 Parallel.o : Parallel.cpp Parallel.h
 ParallelNetcdf.o : ParallelNetcdf.cpp CpptrajStdio.h Parallel.h ParallelNetcdf.h
-ParameterSet.o : ParameterSet.cpp AtomType.h Constants.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h TypeNameHolder.h UpdateParameters.h
-Parm/CmapParmHolder.o : Parm/CmapParmHolder.cpp Constants.h CpptrajStdio.h NameType.h ParameterHolders.h ParameterTypes.h Parm/CmapParmHolder.h TypeNameHolder.h
-Parm/GB_Params.o : Parm/GB_Params.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Parm/GB_Params.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-ParmFile.o : ParmFile.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ParmFile.h ParmIO.h Parm_Amber.h Parm_CIF.h Parm_CharmmPsf.h Parm_Gromacs.h Parm_Mol2.h Parm_PDB.h Parm_SDF.h Parm_Tinker.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Parm_Amber.o : Parm_Amber.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h ExclusionArray.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ParmIO.h Parm_Amber.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Parm_CIF.o : Parm_CIF.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h CIFfile.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ParmIO.h Parm_CIF.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Parm_CharmmPsf.o : Parm_CharmmPsf.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h CharmmParamFile.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Mol.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ParmIO.h Parm_CharmmPsf.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Parm_Gromacs.o : Parm_Gromacs.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ParmIO.h Parm_Gromacs.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Parm_Mol2.o : Parm_Mol2.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Mol2File.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ParmIO.h Parm_Mol2.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Parm_PDB.o : Parm_PDB.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ParmIO.h Parm_PDB.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Parm_SDF.o : Parm_SDF.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ParmIO.h Parm_SDF.h Range.h ReplicaDimArray.h Residue.h SDFfile.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Parm_Tinker.o : Parm_Tinker.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ParmIO.h Parm_Tinker.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TinkerFile.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-PotentialFunction.o : PotentialFunction.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajStdio.h EnergyArray.h ExclusionArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MdOpts.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h PotentialFunction.h PotentialTerm.h PotentialTerm_Angle.h PotentialTerm_Bond.h PotentialTerm_Dihedral.h PotentialTerm_LJ_Coulomb.h PotentialTerm_OpenMM.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+ParameterSet.o : ParameterSet.cpp AtomType.h CmapParmHolder.h Constants.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h TypeNameHolder.h UpdateParameters.h
+Parm/GB_Params.o : Parm/GB_Params.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/GB_Params.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+ParmFile.o : ParmFile.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h ParmIO.h Parm_Amber.h Parm_CIF.h Parm_CharmmPsf.h Parm_Gromacs.h Parm_Mol2.h Parm_PDB.h Parm_SDF.h Parm_Tinker.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Parm_Amber.o : Parm_Amber.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h ExclusionArray.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_Amber.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Parm_CIF.o : Parm_CIF.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h CIFfile.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_CIF.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Parm_CharmmPsf.o : Parm_CharmmPsf.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h CharmmParamFile.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Mol.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_CharmmPsf.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Parm_Gromacs.o : Parm_Gromacs.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_Gromacs.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Parm_Mol2.o : Parm_Mol2.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Mol2File.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_Mol2.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Parm_PDB.o : Parm_PDB.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_PDB.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Parm_SDF.o : Parm_SDF.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_SDF.h Range.h ReplicaDimArray.h Residue.h SDFfile.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Parm_Tinker.o : Parm_Tinker.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_Tinker.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TinkerFile.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+PotentialFunction.o : PotentialFunction.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h CmapParmHolder.h Constants.h Constraints.h CoordinateInfo.h CpptrajStdio.h EnergyArray.h ExclusionArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MdOpts.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PotentialFunction.h PotentialTerm.h PotentialTerm_Angle.h PotentialTerm_Bond.h PotentialTerm_Dihedral.h PotentialTerm_LJ_Coulomb.h PotentialTerm_OpenMM.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 PotentialTerm.o : PotentialTerm.cpp PotentialTerm.h
-PotentialTerm_Angle.o : PotentialTerm_Angle.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h EnergyArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h PotentialTerm.h PotentialTerm_Angle.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-PotentialTerm_Bond.o : PotentialTerm_Bond.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h EnergyArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h PotentialTerm.h PotentialTerm_Bond.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-PotentialTerm_Dihedral.o : PotentialTerm_Dihedral.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h EnergyArray.h EnergyKernel_NonBond_Simple.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h PotentialTerm.h PotentialTerm_Dihedral.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-PotentialTerm_LJ_Coulomb.o : PotentialTerm_LJ_Coulomb.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajStdio.h EnergyArray.h EnergyKernel_NonBond_Simple.h ExclusionArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MdOpts.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h PotentialTerm.h PotentialTerm_LJ_Coulomb.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-PotentialTerm_OpenMM.o : PotentialTerm_OpenMM.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajStdio.h EnergyArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MdOpts.h Molecule.h NameType.h OMM_helpers.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h PotentialTerm.h PotentialTerm_OpenMM.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+PotentialTerm_Angle.o : PotentialTerm_Angle.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h EnergyArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PotentialTerm.h PotentialTerm_Angle.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+PotentialTerm_Bond.o : PotentialTerm_Bond.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h EnergyArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PotentialTerm.h PotentialTerm_Bond.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+PotentialTerm_Dihedral.o : PotentialTerm_Dihedral.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h EnergyArray.h EnergyKernel_NonBond_Simple.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PotentialTerm.h PotentialTerm_Dihedral.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+PotentialTerm_LJ_Coulomb.o : PotentialTerm_LJ_Coulomb.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h CmapParmHolder.h Constants.h Constraints.h CoordinateInfo.h CpptrajStdio.h EnergyArray.h EnergyKernel_NonBond_Simple.h ExclusionArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MdOpts.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PotentialTerm.h PotentialTerm_LJ_Coulomb.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+PotentialTerm_OpenMM.o : PotentialTerm_OpenMM.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h CmapParmHolder.h Constants.h Constraints.h CoordinateInfo.h CpptrajStdio.h EnergyArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MdOpts.h Molecule.h NameType.h OMM_helpers.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PotentialTerm.h PotentialTerm_OpenMM.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 ProgressBar.o : ProgressBar.cpp CpptrajStdio.h ProgressBar.h
 ProgressTimer.o : ProgressTimer.cpp CpptrajStdio.h ProgressTimer.h Timer.h
 PubFFT.o : PubFFT.cpp ArrayIterator.h ComplexArray.h CpptrajStdio.h PubFFT.h
-Pucker_PuckerMask.o : Pucker_PuckerMask.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Pucker_PuckerMask.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Pucker_PuckerSearch.o : Pucker_PuckerSearch.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Pucker.h Pucker_PuckerMask.h Pucker_PuckerSearch.h Pucker_PuckerToken.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Pucker_PuckerToken.o : Pucker_PuckerToken.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Pucker_PuckerMask.h Pucker_PuckerToken.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Pucker_PuckerMask.o : Pucker_PuckerMask.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Pucker_PuckerMask.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Pucker_PuckerSearch.o : Pucker_PuckerSearch.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Pucker.h Pucker_PuckerMask.h Pucker_PuckerSearch.h Pucker_PuckerToken.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Pucker_PuckerToken.o : Pucker_PuckerToken.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Pucker_PuckerMask.h Pucker_PuckerToken.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 QuaternionRMSD.o : QuaternionRMSD.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h QuaternionRMSD.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Unit.h Vec3.h qcprot.h
 RNG.o : RNG.cpp CpptrajStdio.h RNG.h
 RNG_Marsaglia.o : RNG_Marsaglia.cpp CpptrajStdio.h RNG.h RNG_Marsaglia.h
@@ -434,11 +434,11 @@ RNG_MersenneTwister.o : RNG_MersenneTwister.cpp CpptrajStdio.h RNG.h RNG_Mersenn
 RNG_PCG32.o : RNG_PCG32.cpp CpptrajStdio.h RNG.h RNG_PCG32.h pcg_random.hpp
 RNG_Stdlib.o : RNG_Stdlib.cpp RNG.h RNG_Stdlib.h
 RNG_Xoshiro128pp.o : RNG_Xoshiro128pp.cpp RNG.h RNG_Xoshiro128pp.h xoshiro128plusplus.h
-RPNcalc.o : RPNcalc.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_Mesh.h DataSet_Vector.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+RPNcalc.o : RPNcalc.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_Mesh.h DataSet_Vector.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Random.o : Random.cpp CpptrajStdio.h RNG.h RNG_Marsaglia.h RNG_MersenneTwister.h RNG_PCG32.h RNG_Stdlib.h RNG_Xoshiro128pp.h Random.h pcg_random.hpp
 Range.o : Range.cpp ArgList.h CpptrajStdio.h Range.h StringRoutines.h
-ReadLine.o : ReadLine.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdInput.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReadLine.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-ReferenceAction.o : ReferenceAction.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h Dimension.h FileIO.h FileName.h Frame.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TypeNameHolder.h Unit.h Vec3.h
+ReadLine.o : ReadLine.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Cmd.h CmdInput.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReadLine.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+ReferenceAction.o : ReferenceAction.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h Dimension.h FileIO.h FileName.h Frame.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TypeNameHolder.h Unit.h Vec3.h
 RemdReservoirNC.o : RemdReservoirNC.cpp Atom.h AtomMask.h Box.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h RemdReservoirNC.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Unit.h Vec3.h
 Remote.o : Remote.cpp CpptrajStdio.h FileName.h Remote.h
 Residue.o : Residue.cpp NameType.h Residue.h
@@ -448,72 +448,72 @@ SpaceGroup.o : SpaceGroup.cpp Matrix_3x3.h Parallel.h SpaceGroup.h Vec3.h
 Spline.o : Spline.cpp CpptrajStdio.h Spline.h
 SplineFxnTable.o : SplineFxnTable.cpp Constants.h CpptrajStdio.h Spline.h SplineFxnTable.h StringRoutines.h
 StringRoutines.o : StringRoutines.cpp CpptrajStdio.h StringRoutines.h
-Structure/BuildAtom.o : Structure/BuildAtom.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/StructureEnum.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Structure/Builder.o : Structure/Builder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h GuessAtomHybridization.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Builder.h Structure/Chirality.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Structure/BuildAtom.o : Structure/BuildAtom.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/StructureEnum.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Structure/Builder.o : Structure/Builder.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h GuessAtomHybridization.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Builder.h Structure/Chirality.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 Structure/Chirality.o : Structure/Chirality.cpp Atom.h Constants.h CpptrajStdio.h NameType.h Structure/Chirality.h SymbolExporting.h Vec3.h
-Structure/Creator.o : Structure/Creator.cpp ArgList.h AssociatedData.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/Creator.h Structure/GenerateConnectivityArrays.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Structure/Disulfide.o : Structure/Disulfide.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Disulfide.h Structure/ResStatArray.h Structure/StructureRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Structure/FunctionalGroup.o : Structure/FunctionalGroup.cpp Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Structure/FxnGroupBuilder.o : Structure/FxnGroupBuilder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h Structure/FxnGroupBuilder.h Structure/StructureRoutines.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Structure/Creator.o : Structure/Creator.cpp ArgList.h AssociatedData.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/Creator.h Structure/GenerateConnectivityArrays.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Structure/Disulfide.o : Structure/Disulfide.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Disulfide.h Structure/ResStatArray.h Structure/StructureRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Structure/FunctionalGroup.o : Structure/FunctionalGroup.cpp Atom.h AtomMap.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Structure/FxnGroupBuilder.o : Structure/FxnGroupBuilder.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h Structure/FxnGroupBuilder.h Structure/StructureRoutines.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/GenerateConnectivityArrays.o : Structure/GenerateConnectivityArrays.cpp Atom.h Constants.h CpptrajStdio.h NameType.h ParameterTypes.h Residue.h Structure/GenerateConnectivityArrays.h SymbolExporting.h
-Structure/HisProt.o : Structure/HisProt.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/HisProt.h Structure/StructureRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Structure/InternalCoords.o : Structure/InternalCoords.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/InternalCoords.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Structure/PdbCleaner.o : Structure/PdbCleaner.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/PdbCleaner.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Structure/HisProt.o : Structure/HisProt.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/HisProt.h Structure/StructureRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Structure/InternalCoords.o : Structure/InternalCoords.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/InternalCoords.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Structure/PdbCleaner.o : Structure/PdbCleaner.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/PdbCleaner.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/StructureEnum.o : Structure/StructureEnum.cpp Structure/StructureEnum.h
 Structure/StructureRoutines.o : Structure/StructureRoutines.cpp Atom.h CpptrajStdio.h NameType.h Residue.h Structure/StructureRoutines.h SymbolExporting.h
-Structure/Sugar.o : Structure/Sugar.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Structure/SugarBuilder.o : Structure/SugarBuilder.cpp ArgList.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DistRoutines.h FileIO.h FileName.h Frame.h ImageOption.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/FunctionalGroup.h Structure/FxnGroupBuilder.h Structure/LinkAtom.h Structure/ResStatArray.h Structure/StructureEnum.h Structure/StructureRoutines.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarLinkAtoms.h Structure/SugarToken.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Structure/SugarLinkAtoms.o : Structure/SugarLinkAtoms.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/LinkAtom.h Structure/SugarLinkAtoms.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Structure/Sugar.o : Structure/Sugar.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Structure/SugarBuilder.o : Structure/SugarBuilder.cpp ArgList.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DistRoutines.h FileIO.h FileName.h Frame.h ImageOption.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/FunctionalGroup.h Structure/FxnGroupBuilder.h Structure/LinkAtom.h Structure/ResStatArray.h Structure/StructureEnum.h Structure/StructureRoutines.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarLinkAtoms.h Structure/SugarToken.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Structure/SugarLinkAtoms.o : Structure/SugarLinkAtoms.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/LinkAtom.h Structure/SugarLinkAtoms.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/SugarToken.o : Structure/SugarToken.cpp ArgList.h CpptrajStdio.h Structure/SugarToken.h
-Structure/Zmatrix.o : Structure/Zmatrix.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-StructureCheck.o : StructureCheck.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h ExclusionArray.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StructureCheck.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-StructureMapper.o : StructureMapper.cpp AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StructureMapper.h SymbolExporting.h TextFormat.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-SymmetricRmsdCalc.o : SymmetricRmsdCalc.cpp ArrayIterator.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h Hungarian.h ImageOption.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Structure/Zmatrix.o : Structure/Zmatrix.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+StructureCheck.o : StructureCheck.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h ExclusionArray.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StructureCheck.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+StructureMapper.o : StructureMapper.cpp AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StructureMapper.h SymbolExporting.h TextFormat.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+SymmetricRmsdCalc.o : SymmetricRmsdCalc.cpp ArrayIterator.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h Hungarian.h ImageOption.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 TextBlockBuffer.o : TextBlockBuffer.cpp BufferedLine.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Parallel.h TextBlockBuffer.h
 TextFormat.o : TextFormat.cpp StringRoutines.h TextFormat.h
 Timer.o : Timer.cpp CpptrajStdio.h Timer.h
 TinkerFile.o : TinkerFile.cpp ArgList.h Atom.h AtomMask.h Box.h BufferedLine.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TinkerFile.h Unit.h Vec3.h
-TopInfo.o : TopInfo.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h DistRoutines.h FileIO.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Mol.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h TopInfo.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Topology.o : Topology.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h GuessAtomHybridization.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/GenerateConnectivityArrays.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+TopInfo.o : TopInfo.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h DistRoutines.h FileIO.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Mol.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h TopInfo.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Topology.o : Topology.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h GuessAtomHybridization.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/GenerateConnectivityArrays.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 TorsionRoutines.o : TorsionRoutines.cpp Constants.h TorsionRoutines.h Vec3.h
 TrajFrameCounter.o : TrajFrameCounter.cpp ArgList.h CpptrajStdio.h TrajFrameCounter.h
-TrajIOarray.o : TrajIOarray.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryFile.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_AmberCoord.o : Traj_AmberCoord.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h Traj_AmberCoord.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_AmberNetcdf.o : Traj_AmberNetcdf.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h ParallelNetcdf.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_AmberNetcdf.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_AmberRestart.o : Traj_AmberRestart.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedFrame.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextBlockBuffer.h TextFormat.h Topology.h Traj_AmberRestart.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_AmberRestartNC.o : Traj_AmberRestartNC.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Traj_AmberRestartNC.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_Binpos.o : Traj_Binpos.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_Binpos.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_CIF.o : Traj_CIF.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CIFfile.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Traj_CIF.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_CharmmCor.o : Traj_CharmmCor.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Traj_CharmmCor.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_CharmmDcd.o : Traj_CharmmDcd.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ByteRoutines.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_CharmmDcd.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_CharmmRestart.o : Traj_CharmmRestart.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedFrame.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h Traj_CharmmRestart.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_Conflib.o : Traj_Conflib.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_Conflib.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_DTR.o : Traj_DTR.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_DTR.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h vmdplugin/dtrplugin.hxx
-Traj_GmxDump.o : Traj_GmxDump.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_GmxDump.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_GmxTng.o : Traj_GmxTng.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_GmxTng.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_GmxTrX.o : Traj_GmxTrX.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ByteRoutines.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_GmxTrX.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_GmxXtc.o : Traj_GmxXtc.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_GmxXtc.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_Gro.o : Traj_Gro.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Traj_Gro.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_H5.o : Traj_H5.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_H5.h TrajectoryIO.h TypeNameHolder.h Unit.h Units.h Vec3.h
-Traj_H5MD.o : Traj_H5MD.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_H5MD.h TrajectoryIO.h TypeNameHolder.h Unit.h Units.h Vec3.h
-Traj_Mol2File.o : Traj_Mol2File.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Mol2File.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_Mol2File.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_NcEnsemble.o : Traj_NcEnsemble.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FrameArray.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h ParallelNetcdf.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_NcEnsemble.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_PDBfile.o : Traj_PDBfile.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Tensor.h Dimension.h DistRoutines.h FileIO.h FileName.h Frame.h FramePtrArray.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricTensor.h TextFormat.h Timer.h Topology.h Traj_PDBfile.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_SDF.o : Traj_SDF.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h SDFfile.h Segment.h SymbolExporting.h Topology.h Traj_SDF.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_SQM.o : Traj_SQM.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Traj_SQM.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_Tinker.o : Traj_Tinker.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TinkerFile.h Topology.h Traj_Tinker.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_XYZ.o : Traj_XYZ.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h Traj_XYZ.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+TrajIOarray.o : TrajIOarray.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryFile.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+Traj_AmberCoord.o : Traj_AmberCoord.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedFrame.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h Traj_AmberCoord.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+Traj_AmberNetcdf.o : Traj_AmberNetcdf.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h ParallelNetcdf.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_AmberNetcdf.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+Traj_AmberRestart.o : Traj_AmberRestart.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedFrame.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextBlockBuffer.h TextFormat.h Topology.h Traj_AmberRestart.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+Traj_AmberRestartNC.o : Traj_AmberRestartNC.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Traj_AmberRestartNC.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+Traj_Binpos.o : Traj_Binpos.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_Binpos.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+Traj_CIF.o : Traj_CIF.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CIFfile.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Traj_CIF.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+Traj_CharmmCor.o : Traj_CharmmCor.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Traj_CharmmCor.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+Traj_CharmmDcd.o : Traj_CharmmDcd.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ByteRoutines.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_CharmmDcd.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+Traj_CharmmRestart.o : Traj_CharmmRestart.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedFrame.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h Traj_CharmmRestart.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+Traj_Conflib.o : Traj_Conflib.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_Conflib.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+Traj_DTR.o : Traj_DTR.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_DTR.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h vmdplugin/dtrplugin.hxx
+Traj_GmxDump.o : Traj_GmxDump.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_GmxDump.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+Traj_GmxTng.o : Traj_GmxTng.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_GmxTng.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+Traj_GmxTrX.o : Traj_GmxTrX.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ByteRoutines.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_GmxTrX.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+Traj_GmxXtc.o : Traj_GmxXtc.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_GmxXtc.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+Traj_Gro.o : Traj_Gro.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Traj_Gro.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+Traj_H5.o : Traj_H5.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_H5.h TrajectoryIO.h TypeNameHolder.h Unit.h Units.h Vec3.h
+Traj_H5MD.o : Traj_H5MD.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_H5MD.h TrajectoryIO.h TypeNameHolder.h Unit.h Units.h Vec3.h
+Traj_Mol2File.o : Traj_Mol2File.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Mol2File.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_Mol2File.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+Traj_NcEnsemble.o : Traj_NcEnsemble.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FrameArray.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h ParallelNetcdf.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_NcEnsemble.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+Traj_PDBfile.o : Traj_PDBfile.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Tensor.h Dimension.h DistRoutines.h FileIO.h FileName.h Frame.h FramePtrArray.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricTensor.h TextFormat.h Timer.h Topology.h Traj_PDBfile.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+Traj_SDF.o : Traj_SDF.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SDFfile.h Segment.h SymbolExporting.h Topology.h Traj_SDF.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+Traj_SQM.o : Traj_SQM.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Traj_SQM.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+Traj_Tinker.o : Traj_Tinker.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TinkerFile.h Topology.h Traj_Tinker.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+Traj_XYZ.o : Traj_XYZ.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h Traj_XYZ.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
 TrajectoryFile.o : TrajectoryFile.cpp Atom.h BaseIOtype.h Box.h BufferedFrame.h BufferedLine.h CIFfile.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h FileTypes.h FramePtrArray.h Matrix_3x3.h Mol2File.h NC_Routines.h NameType.h NetcdfFile.h PDBfile.h Parallel.h ReplicaDimArray.h Residue.h SDFfile.h SymbolExporting.h TextFormat.h TinkerFile.h Traj_AmberCoord.h Traj_AmberNetcdf.h Traj_AmberRestart.h Traj_AmberRestartNC.h Traj_Binpos.h Traj_CIF.h Traj_CharmmCor.h Traj_CharmmDcd.h Traj_CharmmRestart.h Traj_Conflib.h Traj_DTR.h Traj_GmxDump.h Traj_GmxTng.h Traj_GmxTrX.h Traj_GmxXtc.h Traj_Gro.h Traj_H5.h Traj_H5MD.h Traj_Mol2File.h Traj_NcEnsemble.h Traj_PDBfile.h Traj_SDF.h Traj_SQM.h Traj_Tinker.h Traj_XYZ.h TrajectoryFile.h TrajectoryIO.h Vec3.h
 TrajectoryIO.o : TrajectoryIO.cpp BaseIOtype.h Box.h CoordinateInfo.h FramePtrArray.h Matrix_3x3.h Parallel.h ReplicaDimArray.h TrajectoryIO.h Vec3.h
-TrajinList.o : TrajinList.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_RemLog.h Dimension.h EnsembleIn.h EnsembleIn_Multi.h EnsembleIn_Single.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryFile.h TrajectoryIO.h Trajin.h TrajinList.h Trajin_Multi.h Trajin_Single.h TypeNameHolder.h Unit.h Vec3.h
-Trajin_Multi.o : Trajin_Multi.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryIO.h Trajin.h Trajin_Multi.h TypeNameHolder.h Unit.h Vec3.h
-Trajin_Single.o : Trajin_Single.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h Trajin.h Trajin_Single.h TypeNameHolder.h Unit.h Vec3.h
-TrajoutList.o : TrajoutList.cpp ActionFrameCounter.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-Trajout_Single.o : Trajout_Single.cpp ActionFrameCounter.h ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+TrajinList.o : TrajinList.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_RemLog.h Dimension.h EnsembleIn.h EnsembleIn_Multi.h EnsembleIn_Single.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryFile.h TrajectoryIO.h Trajin.h TrajinList.h Trajin_Multi.h Trajin_Single.h TypeNameHolder.h Unit.h Vec3.h
+Trajin_Multi.o : Trajin_Multi.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryIO.h Trajin.h Trajin_Multi.h TypeNameHolder.h Unit.h Vec3.h
+Trajin_Single.o : Trajin_Single.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h Trajin.h Trajin_Single.h TypeNameHolder.h Unit.h Vec3.h
+TrajoutList.o : TrajoutList.cpp ActionFrameCounter.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Trajout_Single.o : Trajout_Single.cpp ActionFrameCounter.h ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Units.o : Units.cpp Constants.h CpptrajStdio.h Units.h
 Vec3.o : Vec3.cpp Constants.h CpptrajStdio.h Vec3.h
-ViewRst.o : ViewRst.cpp ActionFrameCounter.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h ViewRst.h
-main.o : main.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h Cpptraj.h CpptrajFile.h CpptrajState.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/CmapParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+ViewRst.o : ViewRst.cpp ActionFrameCounter.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h ViewRst.h
+main.o : main.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h Cpptraj.h CpptrajFile.h CpptrajState.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 molsurf.o : molsurf.c molsurf.h
 qcprot.o : qcprot.cpp CpptrajStdio.h qcprot.h
 vmdplugin/dtrplugin.o : vmdplugin/dtrplugin.cpp ByteRoutines.h vmdplugin/dtrplugin.hxx vmdplugin/vmddir.h
diff --git a/src/cpptrajfiles b/src/cpptrajfiles
index e1a86128b2..eac2a30be0 100644
--- a/src/cpptrajfiles
+++ b/src/cpptrajfiles
@@ -158,6 +158,7 @@ COMMON_SOURCES= \
         CharmmParamFile.cpp \
         CIFfile.cpp \
         ClusterMap.cpp \
+        CmapParmHolder.cpp \
         Cmd.cpp \
         CmdInput.cpp \
         CmdList.cpp \

From 884a0094088254f7037344e14c81b2faf9037b59 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 2 Mar 2024 10:58:37 -0500
Subject: [PATCH 0657/1492] change case

---
 src/AmberParamFile.cpp | 30 +++++++++++++++---------------
 1 file changed, 15 insertions(+), 15 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index a2483a6365..524afb6f24 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -380,7 +380,7 @@ static inline int check_cmap(int currentCmapIdx, CmapGridType const& cmap) {
 }
 
 /** Read CMAP section */
-int AmberParamFile::read_cmap(CmapGridType& currentCMAP, ParameterSet& prm, CmapType& currentCmapFlag,
+int AmberParamFile::read_cmap(CmapGridType& currentCmap, ParameterSet& prm, CmapType& currentCmapFlag,
                               std::string const& line)
 const
 {
@@ -391,10 +391,10 @@ const
       if (argline[1] == "CMAP_COUNT") {
         // New CMAP term. Ignore the index for now. If a previous CMAP
         // was read make sure its OK.
-        if (!currentCMAP.empty()) {
-          if (check_cmap(prm.CMAP().size()+1, currentCMAP)) return 1;
-          prm.CMAP().AddParm( currentCMAP, true );
-          currentCMAP = CmapGridType();
+        if (!currentCmap.empty()) {
+          if (check_cmap(prm.CMAP().size()+1, currentCmap)) return 1;
+          prm.CMAP().AddParm( currentCmap, true );
+          currentCmap = CmapGridType();
         }
         int cmapcount = argline.getKeyInt("CMAP_COUNT", -1);
         //mprintf("DEBUG: Cmap count: %i\n", cmapcount);
@@ -412,7 +412,7 @@ const
           mprinterr("Error: Bad CMAP # residues: %s\n", line.c_str());
           return 1;
         }
-        currentCMAP.SetNumCmapRes( nres );
+        currentCmap.SetNumCmapRes( nres );
         return 0;
       } else if (argline[1] == "CMAP_RESOLUTION") {
         int cmapres = argline.getKeyInt("CMAP_RESOLUTION", -1);
@@ -421,7 +421,7 @@ const
           mprinterr("Error: Bad CMAP resolution: %s\n", line.c_str());
           return 1;
         }
-        currentCMAP.SetResolution( cmapres );
+        currentCmap.SetResolution( cmapres );
         return 0;
       } else if (argline[1] == "CMAP_PARAMETER") {
         currentCmapFlag = CMAP_PARAMETER;
@@ -437,17 +437,17 @@ const
                         terms+4, terms+5, terms+6, terms+7);
     for (int i = 0; i != nterms; i++) {
       //mprintf("DEBUG: cmap term %f\n", terms[i] );
-      currentCMAP.AddToGrid( terms[i] );
+      currentCmap.AddToGrid( terms[i] );
     }
   } else if (currentCmapFlag == CMAP_RESLIST) {
     ArgList resnames( line );
     std::string rn = resnames.GetStringNext();
     while (!rn.empty()) {
-      currentCMAP.AddResName( rn );
+      currentCmap.AddResName( rn );
       rn = resnames.GetStringNext();
     }
   } else if (currentCmapFlag == CMAP_TITLE) {
-    currentCMAP.SetTitle( line );
+    currentCmap.SetTitle( line );
   }
   return 0;
 }
@@ -521,7 +521,7 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int deb
   // Read file
   SectionType section = UNKNOWN;
   CmapType currentCmapFlag = CMAP_INITIAL;
-  CmapGridType currentCMAP;
+  CmapGridType currentCmap;
   ptr = infile.Line();
   while (ptr != 0) {
     bool first_char_is_space = (*ptr == ' ');
@@ -564,7 +564,7 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int deb
         else if (section == LJEDIT)
           err = read_ljedit(Offdiag, ptr);
         else if (section == CMAP)
-          err = read_cmap(currentCMAP, prm, currentCmapFlag, line);
+          err = read_cmap(currentCmap, prm, currentCmapFlag, line);
         if (err != 0) {
           mprinterr("Error: Reading line: %s\n", ptr);
           return 1;
@@ -574,9 +574,9 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int deb
     ptr = infile.Line();
   }
   // Check last cmap
-  if (!currentCMAP.empty()) {
-    if (check_cmap(prm.CMAP().size(), currentCMAP)) return 1;
-    prm.CMAP().AddParm( currentCMAP, true );
+  if (!currentCmap.empty()) {
+    if (check_cmap(prm.CMAP().size(), currentCmap)) return 1;
+    prm.CMAP().AddParm( currentCmap, true );
   }
   // Nonbonds
   if (assign_nb(prm, nbset)) return 1;

From b8bc26006c0f0c8cd0320b08b6b14bf57c14ddf2 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 2 Mar 2024 11:16:55 -0500
Subject: [PATCH 0658/1492] Add CMAP param update

---
 src/ParameterSet.cpp | 31 ++++++++++++++++++++++++++++++-
 src/ParameterSet.h   |  3 +++
 2 files changed, 33 insertions(+), 1 deletion(-)

diff --git a/src/ParameterSet.cpp b/src/ParameterSet.cpp
index 8f41bc4b29..a5e9bdaf1b 100644
--- a/src/ParameterSet.cpp
+++ b/src/ParameterSet.cpp
@@ -142,6 +142,35 @@ void ParameterSet::Print(CpptrajFile& Out) const {
   }
 }
 
+/** Update/add to CMAP parameters in this set with those from given set. */
+int ParameterSet::updateCmapParams(CmapParmHolder const& cmap1, int verbose) {
+  int updateCount = 0;
+  for (CmapParmHolder::const_iterator newp = cmap1.begin(); newp != cmap1.end(); ++newp)
+  {
+    ParameterHolders::RetType ret = CMAP_.AddParm( *newp, true );
+    if (ret != ParameterHolders::ERR) {
+      bool print = false;
+      if (ret == ParameterHolders::ADDED) {
+        if (verbose > 2) { mprintf("\tAdded NEW CMAP parameter:"); print = true; }
+        updateCount++;
+      } else if (ret == ParameterHolders::UPDATED) {
+        if (verbose > 0) { mprintf("\tUpdated CMAP parameter:"); print = true; }
+        updateCount++;
+      } else if (ret == ParameterHolders::SAME) {
+        if (verbose > 1) { mprintf("\tParameter for CMAP already present:"); print = true; }
+      }
+      if (print) {
+        mprintf("\tCMAP '%s' (resolution %u) residues:", newp->Title().c_str(), newp->Resolution());
+        for (std::vector<std::string>::const_iterator rn = newp->ResNames().begin();
+                                                      rn != newp->ResNames().end(); ++rn)
+          mprintf(" %s", rn->c_str());
+        mprintf("\n");
+      }
+    }
+  }
+  return updateCount;
+}
+
 /** Update/add to parameters in this topology with those from given set. */
 int ParameterSet::UpdateParamSet(ParameterSet const& set1, UpdateCount& uc, int debugIn, int verbose) {
   ParameterSet& set0 = *this;
@@ -171,7 +200,7 @@ int ParameterSet::UpdateParamSet(ParameterSet const& set1, UpdateCount& uc, int
   // HB LJ 10-12 Pairs
   uc.nHBparamsUpdated_ = UpdateParameters< ParmHolder<HB_ParmType> >(set0.HB(), set1.HB(), "LJ HB 10-12", verbose);
   // CMAP
-  //uc.nCmapUpdated_ = updateCmapTerms(set1, debugIn, verbose);
+  uc.nCmapUpdated_ = updateCmapParams(set1.CMAP(), verbose);
 
   if (debugIn > 0) set0.Debug("newp.dat");
   return 0;
diff --git a/src/ParameterSet.h b/src/ParameterSet.h
index dea2376c47..2beeb97d90 100644
--- a/src/ParameterSet.h
+++ b/src/ParameterSet.h
@@ -81,6 +81,9 @@ class ParameterSet {
     typedef std::vector<NameType> NsetType;
     typedef std::vector<std::string> Sarray;
 
+    /// Update cmap parameters
+    int updateCmapParams(CmapParmHolder const&, int);
+
     Sarray name_;                          ///< Parameter set name(s)
     std::string NBname_;                   ///< Nonbond set name
 

From 858a45ea77dae3900559b7198670af620864e916 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 2 Mar 2024 11:27:52 -0500
Subject: [PATCH 0659/1492] Add note

---
 src/AmberParamFile.cpp | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 524afb6f24..b1eaa152cf 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -379,7 +379,11 @@ static inline int check_cmap(int currentCmapIdx, CmapGridType const& cmap) {
   return 0;
 }
 
-/** Read CMAP section */
+/** Read CMAP section
+  * Default CMAP atoms are Amber phi/psi:
+  * Res  : 0   1   1    1   2
+  * Atom : C - N - CA - C - N
+  */ 
 int AmberParamFile::read_cmap(CmapGridType& currentCmap, ParameterSet& prm, CmapType& currentCmapFlag,
                               std::string const& line)
 const

From 1bc0a0fcbdbc78fae6cf2ac12af5a4b8ff0b765d Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 2 Mar 2024 11:37:11 -0500
Subject: [PATCH 0660/1492] Start CMAP assignment

---
 src/Topology.cpp | 7 +++++++
 src/Topology.h   | 1 +
 2 files changed, 8 insertions(+)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index 0825936d40..e88481e4bc 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -3129,6 +3129,13 @@ void Topology::AssignNonbondParams(ParmHolder<AtomType> const& newTypes,
   }
 }
 
+/** Assign CMAP parameters */
+int Topology::AssignCmapParams(CmapParmHolder const& cmapIn) {
+  DihedralArray allDih = Cpptraj::Structure::GenerateDihedralArray(residues_, atoms_);
+
+  return 0;
+}
+
 /** Replace existing parameters with the given parameter set. */
 int Topology::AssignParams(ParameterSet const& set0) {
 
diff --git a/src/Topology.h b/src/Topology.h
index 804c734f1c..73a00c6b80 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -317,6 +317,7 @@ class Topology {
     inline DihedralArray get_unique_dihedrals(DihedralArray const&) const;
     DihedralArray AssignDihedralParm(DihedralParmHolder const&, ImproperParmHolder const&,
                                      ParmHolder<AtomType> const&, DihedralArray const&, bool);
+    int AssignCmapParams(CmapParmHolder const&);
 
     static const NonbondType LJ_EMPTY;
     std::vector<Atom> atoms_;

From 51b05d3cc4df3a2e392d35aec8920b1aca6753a6 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 2 Mar 2024 17:21:02 -0500
Subject: [PATCH 0661/1492] Save atom names

---
 src/AmberParamFile.cpp | 12 ++++++++++++
 src/ParameterSet.cpp   |  8 ++++++--
 src/ParameterTypes.h   | 13 +++++++++++--
 src/Topology.cpp       |  5 ++++-
 4 files changed, 33 insertions(+), 5 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index b1eaa152cf..8eb4a5c52d 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -359,6 +359,7 @@ const
   return 0;
 }
 
+/// \return 1 if problem detected with CMAP term
 static inline int check_cmap(int currentCmapIdx, CmapGridType const& cmap) {
   mprintf("DEBUG: Cmap %i '%s' (gridSize= %i) %zu res:",
           currentCmapIdx, cmap.Title().c_str(), cmap.Size(), cmap.ResNames().size());
@@ -379,6 +380,15 @@ static inline int check_cmap(int currentCmapIdx, CmapGridType const& cmap) {
   return 0;
 }
 
+/// Add default atom names to CMAP term
+static inline void add_cmap_default_atoms(CmapGridType& cmap) {
+  cmap.AddAtomName("C");
+  cmap.AddAtomName("N");
+  cmap.AddAtomName("CA");
+  cmap.AddAtomName("C");
+  cmap.AddAtomName("N");
+}
+
 /** Read CMAP section
   * Default CMAP atoms are Amber phi/psi:
   * Res  : 0   1   1    1   2
@@ -396,6 +406,7 @@ const
         // New CMAP term. Ignore the index for now. If a previous CMAP
         // was read make sure its OK.
         if (!currentCmap.empty()) {
+          add_cmap_default_atoms( currentCmap );
           if (check_cmap(prm.CMAP().size()+1, currentCmap)) return 1;
           prm.CMAP().AddParm( currentCmap, true );
           currentCmap = CmapGridType();
@@ -579,6 +590,7 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int deb
   }
   // Check last cmap
   if (!currentCmap.empty()) {
+    add_cmap_default_atoms( currentCmap );
     if (check_cmap(prm.CMAP().size(), currentCmap)) return 1;
     prm.CMAP().AddParm( currentCmap, true );
   }
diff --git a/src/ParameterSet.cpp b/src/ParameterSet.cpp
index a5e9bdaf1b..31a669a079 100644
--- a/src/ParameterSet.cpp
+++ b/src/ParameterSet.cpp
@@ -117,8 +117,12 @@ void ParameterSet::Print(CpptrajFile& Out) const {
   if (!CMAP_.empty()) {
     Out.Printf("CMAP parameters:\n");
     for (CmapGridArray::const_iterator it = CMAP_.begin(); it != CMAP_.end(); ++it) {
-      Out.Printf("\tCMAP %li '%s' (resolution %u) residues:",
-              it - CMAP_.begin() + 1, it->Title().c_str(), it->Resolution());
+      Out.Printf("\tCMAP %li '%s' (resolution %u) atoms {",
+                 it - CMAP_.begin() + 1, it->Title().c_str(), it->Resolution());
+      for (std::vector<std::string>::const_iterator an = it->AtomNames().begin();
+                                                    an != it->AtomNames().end(); ++an)
+        Out.Printf(" %s", an->c_str());
+      Out.Printf("} residues:");
       for (std::vector<std::string>::const_iterator rn = it->ResNames().begin();
                                                     rn != it->ResNames().end(); ++rn)
         Out.Printf(" %s", rn->c_str());
diff --git a/src/ParameterTypes.h b/src/ParameterTypes.h
index 04d21ddf7c..263e6eea30 100644
--- a/src/ParameterTypes.h
+++ b/src/ParameterTypes.h
@@ -718,6 +718,8 @@ class CmapGridType {
     std::vector<double> const& Grid()        const { return grid_;             }
     /// \return array of residue names this CMAP applies to
     std::vector<std::string> const& ResNames() const { return resNames_; }
+    /// \return array of atom names this CMAP applies to
+    std::vector<std::string> const& AtomNames() const { return atomNames_; }
     /// \return Expected number of CMAP residue names
     int NcmapResNames()                      const { return nCmapRes_; }
     /// \return Grid size as integer, used for topology write
@@ -746,13 +748,19 @@ class CmapGridType {
     }
     /// Add residue name this CMAP will apply to
     void AddResName(std::string const& n) { resNames_.push_back( n ); }
+    /// Add atom name this CMAP will apply to
+    void AddAtomName(std::string const& n) { atomNames_.push_back( n ); }
     /// \return True if the CMAP is valid
     bool CmapIsValid() const {
       if (resolution_ == 0 || resolution_*resolution_ != grid_.size())
         return false;
+      if (atomNames_.size() != 5)
+        return false;
+      if (resNames_.empty())
+        return false;
       return true;
     }
-    /// \return True if CMAP # res names matches expected.
+    /// \return True if CMAP # res names matches expected # of names.
     bool CmapNresIsValid() const {
       if (nCmapRes_ == 0 || nCmapRes_ != (int)resNames_.size())
         return false;
@@ -768,7 +776,8 @@ class CmapGridType {
     unsigned int resolution_;  ///< Number of steps along each phi/psi CMAP axis
     std::vector<double> grid_; ///< CMAP grid (size is resolution_*resolution_)
     std::string title_;        ///< CMAP title (from parameter file)
-    std::vector<std::string> resNames_; ///< Residue names this CMAP will apply to
+    std::vector<std::string> resNames_;  ///< Residue name(s) this CMAP will apply to
+    std::vector<std::string> atomNames_; ///< 5x atom names this CMAP will apply to
 };
 typedef std::vector<CmapGridType> CmapGridArray;
 /// Hold CMAP atom indices and corresponding grid index
diff --git a/src/Topology.cpp b/src/Topology.cpp
index e88481e4bc..85c6a5fccf 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -3131,8 +3131,11 @@ void Topology::AssignNonbondParams(ParmHolder<AtomType> const& newTypes,
 
 /** Assign CMAP parameters */
 int Topology::AssignCmapParams(CmapParmHolder const& cmapIn) {
+  // TODO combine with AssignDihedrals?
   DihedralArray allDih = Cpptraj::Structure::GenerateDihedralArray(residues_, atoms_);
-
+  //for (DihedralArray::const_iterator dih = allDih.begin(); dih != allDih.end(); ++dih)
+  //{
+    // 
   return 0;
 }
 

From de1f1f69521df8f4e3f7d8526c1b77821bc759cf Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 2 Mar 2024 17:22:30 -0500
Subject: [PATCH 0662/1492] Add default names only if not already set

---
 src/AmberParamFile.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 8eb4a5c52d..dd63708e13 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -406,7 +406,7 @@ const
         // New CMAP term. Ignore the index for now. If a previous CMAP
         // was read make sure its OK.
         if (!currentCmap.empty()) {
-          add_cmap_default_atoms( currentCmap );
+          if (currentCmap.AtomNames().empty()) add_cmap_default_atoms( currentCmap );
           if (check_cmap(prm.CMAP().size()+1, currentCmap)) return 1;
           prm.CMAP().AddParm( currentCmap, true );
           currentCmap = CmapGridType();
@@ -590,7 +590,7 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int deb
   }
   // Check last cmap
   if (!currentCmap.empty()) {
-    add_cmap_default_atoms( currentCmap );
+    if (currentCmap.AtomNames().empty()) add_cmap_default_atoms( currentCmap );
     if (check_cmap(prm.CMAP().size(), currentCmap)) return 1;
     prm.CMAP().AddParm( currentCmap, true );
   }

From f7064c4cc14c06b3ebe69a691cc952b717d8e2fd Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 2 Mar 2024 18:36:09 -0500
Subject: [PATCH 0663/1492] Add [] operator

---
 src/CmapParmHolder.h | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/CmapParmHolder.h b/src/CmapParmHolder.h
index e3870646e1..78b4f6045d 100644
--- a/src/CmapParmHolder.h
+++ b/src/CmapParmHolder.h
@@ -22,7 +22,7 @@ class CmapParmHolder {
     /// \return true if no CMAP terms
     bool empty() const { return CMAP_.empty(); }
     /// \return CMAP at index
-    //CmapGridType const& operator[](int idx) const { return CMAP_[idx]; }
+    CmapGridType const& operator[](int idx) const { return CMAP_[idx]; }
 
     /// \return Modifiable CMAP at index
     

From 52704766af12cc1c73e13c0daf989ba6bef1ca4f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 2 Mar 2024 18:36:33 -0500
Subject: [PATCH 0664/1492] Function to determine if residue name matches a
 cmap term

---
 src/ParameterTypes.h | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/src/ParameterTypes.h b/src/ParameterTypes.h
index 263e6eea30..5b71d8182f 100644
--- a/src/ParameterTypes.h
+++ b/src/ParameterTypes.h
@@ -714,10 +714,18 @@ class CmapGridType {
   public:
     CmapGridType() : nCmapRes_(0), resolution_(0) {}
     CmapGridType(unsigned int r) : nCmapRes_(0), resolution_(r), grid_(r*r, 0.0) {}
+    /// \return Grid resolution (in 1 dim, full res is resolutionXresolution)
     unsigned int Resolution()                const { return resolution_;       }
+    /// \return CMAP grid
     std::vector<double> const& Grid()        const { return grid_;             }
     /// \return array of residue names this CMAP applies to
     std::vector<std::string> const& ResNames() const { return resNames_; }
+    /// \return true if given name matches a residue name
+    bool MatchesResName(std::string const& nameIn) const {
+      for (std::vector<std::string>::const_iterator it = resNames_.begin(); it != resNames_.end(); ++it)
+        if (nameIn == *it) return true;
+      return false;
+    }
     /// \return array of atom names this CMAP applies to
     std::vector<std::string> const& AtomNames() const { return atomNames_; }
     /// \return Expected number of CMAP residue names

From d2e12329005bc6083ce779c18910b60f50ed8fad Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 3 Mar 2024 10:36:22 -0500
Subject: [PATCH 0665/1492] If nothing needs to be built, ensure residue
 connections still happen

---
 src/Exec_Build.cpp | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index a63a9fd4d1..37182de919 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -597,6 +597,20 @@ const
                   topOut.TruncResNameOnumId(ires).c_str());
         buildFailed = true;
       }
+    } else {
+      // All atoms present. Just connect
+      // Is this residue connected to an earlier residue?
+      for (IParray::const_iterator resBonds = resBondingAtoms[ires].begin();
+                                   resBonds != resBondingAtoms[ires].end(); ++resBonds)
+      {
+        if (resBonds->second < resBonds->first) {
+          if (debug_ > 0)
+            mprintf("\t\tResidue connection: %s - %s\n",
+                    topOut.AtomMaskName(resBonds->first).c_str(),
+                    topOut.AtomMaskName(resBonds->second).c_str());
+          topOut.AddBond(resBonds->first, resBonds->second);
+        }
+      }
     }
   } // END loop over atom offsets
 

From 2e626d3af8b1b6dcb479396b57dd9a0d7c48d6eb Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 3 Mar 2024 10:39:01 -0500
Subject: [PATCH 0666/1492] Initial attempt at CMAP assignment

---
 src/Topology.cpp | 114 ++++++++++++++++++++++++++++++++++++++++++++---
 src/Topology.h   |   4 +-
 2 files changed, 112 insertions(+), 6 deletions(-)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index 85c6a5fccf..f40f4ef616 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -3129,13 +3129,107 @@ void Topology::AssignNonbondParams(ParmHolder<AtomType> const& newTypes,
   }
 }
 
+/// \return index of 5th cmap atom if atom names match those in dihedral, -1 otherwise
+static inline int cmap_anames_match(DihedralType const& dih,
+                                     std::vector<Atom> const& atoms,
+                                     CmapGridType const& cmap)
+{
+  mprintf("DEBUG: Check res %i %s %s %s %s against %s %s %s %s\n",
+          atoms[dih.A2()].ResNum()+1,
+            atoms[dih.A1()].Name().Truncated().c_str(),
+            atoms[dih.A2()].Name().Truncated().c_str(),
+            atoms[dih.A3()].Name().Truncated().c_str(),
+            atoms[dih.A4()].Name().Truncated().c_str(),
+            cmap.AtomNames()[0].c_str(),
+            cmap.AtomNames()[1].c_str(),
+            cmap.AtomNames()[2].c_str(),
+            cmap.AtomNames()[3].c_str());
+  // TODO without Truncated
+  if (atoms[dih.A1()].Name().Truncated() == cmap.AtomNames()[0] &&
+      atoms[dih.A2()].Name().Truncated() == cmap.AtomNames()[1] &&
+      atoms[dih.A3()].Name().Truncated() == cmap.AtomNames()[2] &&
+      atoms[dih.A4()].Name().Truncated() == cmap.AtomNames()[3])
+  {
+    mprintf("DEBUG: Partial match %s %s %s %s = %s %s %s %s\n",
+            atoms[dih.A1()].Name().Truncated().c_str(),
+            atoms[dih.A2()].Name().Truncated().c_str(),
+            atoms[dih.A3()].Name().Truncated().c_str(),
+            atoms[dih.A4()].Name().Truncated().c_str(),
+            cmap.AtomNames()[0].c_str(),
+            cmap.AtomNames()[1].c_str(),
+            cmap.AtomNames()[2].c_str(),
+            cmap.AtomNames()[3].c_str());
+    for (Atom::bond_iterator bat = atoms[dih.A4()].bondbegin();
+                             bat != atoms[dih.A4()].bondend(); ++bat)
+    {
+      if (*bat != dih.A3()) { // TODO can A4 ever be bonded to A1??
+        if (atoms[*bat].Name().Truncated() == cmap.AtomNames()[4]) {
+          return *bat;
+        }
+      }
+    }
+  }
+  return -1;
+}
+
 /** Assign CMAP parameters */
-int Topology::AssignCmapParams(CmapParmHolder const& cmapIn) {
+int Topology::AssignCmapParams(DihedralArray const& allDih, CmapParmHolder const& cmapIn,
+                               CmapGridArray& cmapGrids, CmapArray& cmapTerms)
+const
+{
   // TODO combine with AssignDihedrals?
-  DihedralArray allDih = Cpptraj::Structure::GenerateDihedralArray(residues_, atoms_);
-  //for (DihedralArray::const_iterator dih = allDih.begin(); dih != allDih.end(); ++dih)
-  //{
-    // 
+  for (DihedralArray::const_iterator dih = allDih.begin(); dih != allDih.end(); ++dih)
+  {
+    // Get residue name for A2
+    Atom const& A2 = atoms_[dih->A2()];
+    // TODO make sure A2-A4 in same residue?
+    NameType const& rn2 = residues_[A2.ResNum()].Name();
+    // Is this residue already in cmapGrids?
+    int cidx = -1;
+    int a5 = -1;
+    for (unsigned int idx = 0; idx != cmapGrids.size(); idx++) {
+      if (cmapGrids[idx].MatchesResName( rn2.Truncated() )) {
+        a5 = cmap_anames_match(*dih, atoms_, cmapGrids[idx]);
+        if (a5 > -1) {
+          cidx = (int)idx;
+          break;
+        }
+      }
+    }
+    if (cidx > -1) {
+      mprintf("DEBUG: Potential existing cmap %i found for %s (%li)\n", cidx, TruncResNameNum(A2.ResNum()).c_str(), dih-allDih.begin());
+      mprintf("DEBUG:\t\t%s - %s - %s - %s - %s\n",
+              AtomMaskName(dih->A1()).c_str(),
+              AtomMaskName(dih->A2()).c_str(),
+              AtomMaskName(dih->A3()).c_str(),
+              AtomMaskName(dih->A4()).c_str(),
+              AtomMaskName(a5).c_str());
+    }
+    // If not already in cmapGrids, check cmapIn
+    if (cidx == -1) {
+      //int nidx = -1;
+      for (unsigned int idx = 0; idx != cmapIn.size(); idx++) {
+        if (cmapIn[idx].MatchesResName( rn2.Truncated() )) {
+          a5 = cmap_anames_match(*dih, atoms_, cmapIn[idx]);
+          if (a5 > -1) {
+            cidx = (int)cmapGrids.size();
+            cmapGrids.push_back( cmapIn[idx] );
+            //nidx = (int)idx;
+            break;
+          }
+        }
+      }
+      if (cidx > -1) {
+        mprintf("DEBUG: Potential new cmap %i found for %s (%li)\n", cidx, TruncResNameNum(A2.ResNum()).c_str(), dih-allDih.begin());
+        mprintf("DEBUG:\t\t%s - %s - %s - %s - %s\n",
+              AtomMaskName(dih->A1()).c_str(),
+              AtomMaskName(dih->A2()).c_str(),
+              AtomMaskName(dih->A3()).c_str(),
+              AtomMaskName(dih->A4()).c_str(),
+              AtomMaskName(a5).c_str());
+      }
+    }
+  }
   return 0;
 }
 
@@ -3169,6 +3263,14 @@ int Topology::AssignParams(ParameterSet const& set0) {
   dihedrals_.clear();
   dihedralsh_.clear();
   DihedralArray allDihedrals = Cpptraj::Structure::GenerateDihedralArray(residues_, atoms_);
+  // If we need CMAP terms, do it here before the dihedrals array is modified
+  if (!set0.CMAP().empty()) {
+    cmap_.clear();
+    cmapGrid_.clear();
+    mprintf("\tAssigning CMAP parameters.\n");
+    AssignCmapParams( allDihedrals, set0.CMAP(), cmapGrid_, cmap_ );
+  } 
+  // Now modify the dihedrals for any multiplicities
   allDihedrals = AssignDihedralParm( set0.DP(), set0.IP(), set0.AT(), allDihedrals, false );
   for (DihedralArray::const_iterator dih = allDihedrals.begin(); dih != allDihedrals.end(); ++dih)
     AddToDihedralArrays( *dih );
@@ -3192,7 +3294,9 @@ int Topology::AssignParams(ParameterSet const& set0) {
   // LJ 6-12
   mprintf("\tAssigning nonbond parameters.\n");
   AssignNonbondParams( set0.AT(), set0.NB(), set0.HB() );
+  mprintf("DEBUG: CMAP size %zu\n", set0.CMAP().size());
   // TODO LJ14
+
   return 0;
 }
 
diff --git a/src/Topology.h b/src/Topology.h
index 73a00c6b80..ae8c8d17ba 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -317,7 +317,9 @@ class Topology {
     inline DihedralArray get_unique_dihedrals(DihedralArray const&) const;
     DihedralArray AssignDihedralParm(DihedralParmHolder const&, ImproperParmHolder const&,
                                      ParmHolder<AtomType> const&, DihedralArray const&, bool);
-    int AssignCmapParams(CmapParmHolder const&);
+
+    /// Assign CMAP parameters
+    int AssignCmapParams(DihedralArray const&, CmapParmHolder const&, CmapGridArray&, CmapArray&) const;
 
     static const NonbondType LJ_EMPTY;
     std::vector<Atom> atoms_;

From 246359fa7d9d56f06d3f6ff766f989a668c7070f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 4 Mar 2024 09:10:35 -0500
Subject: [PATCH 0667/1492] If an improper found in the cache has wildcards,
 see if there is a more specific improper in the new parameters before using
 the cached one.

---
 src/Topology.cpp | 37 +++++++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index f40f4ef616..324327c097 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2854,6 +2854,43 @@ DihedralArray Topology::AssignDihedralParm(DihedralParmHolder const& newDihedral
                     *paramTypes[0], *paramTypes[1], *paramTypes[2], *paramTypes[3]);
         }
       } else {
+        // If the cached improper has wildcards, see if there is a more
+        // specific one in the new improper parameters.
+        int n_wildcards = 0;
+        if (newImproperParams.Wildcard().len() > 0) {
+          for (TypeNameHolder::const_iterator tt = impit->first.begin(); tt != impit->first.end(); ++tt) {
+            if ( *tt == newImproperParams.Wildcard() ) {
+              n_wildcards++;
+            }
+          }
+        }
+        if (n_wildcards > 0) {
+          // Check if there is a more specific improper.
+          bool newReordered;
+          DihedralType newdih = *dih;
+          ImproperParmHolder::const_iterator moreSpecificImpit = newImproperParams.GetParam( types, newdih, newReordered );
+          if (moreSpecificImpit != newImproperParams.end()) {
+            // See if the new improper has fewer wildcards than the cached one.
+            int new_wildcards = 0;
+            for (TypeNameHolder::const_iterator tt = moreSpecificImpit->first.begin();
+                                                tt != moreSpecificImpit->first.end(); ++tt)
+            {
+              if ( *tt == newImproperParams.Wildcard() ) {
+                new_wildcards++;
+              }
+            }
+            if (new_wildcards < n_wildcards) {
+              // More specific improper was found.
+              mprintf("DEBUG: A more specific improper was found for %2s %2s %2s %2s (%2s %2s %2s %2s)\n",
+                      *(impit->first[0]), *(impit->first[1]), *(impit->first[2]), *(impit->first[3]),
+                      *(moreSpecificImpit->first[0]), *(moreSpecificImpit->first[1]), *(moreSpecificImpit->first[2]), *(moreSpecificImpit->first[3]));
+              is_new_improper = true;
+              reordered = newReordered;
+              mydih = newdih;
+              impit = moreSpecificImpit;
+            }
+          }
+        } // END found improper had wildcards
         paramTypes = impit->first;
         ipa = impit->second;
         found = true;

From 2b355f6f9b9e8908da2bfbc9b8012004c69d05f2 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 4 Mar 2024 10:10:28 -0500
Subject: [PATCH 0668/1492] Leap convention is to have cmap indices in the same
 order they appear in original parameter file

---
 src/Topology.cpp | 52 +++++++++++++++++++++++++++++++-----------------
 1 file changed, 34 insertions(+), 18 deletions(-)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index 324327c097..17efd2c603 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -3171,7 +3171,7 @@ static inline int cmap_anames_match(DihedralType const& dih,
                                      std::vector<Atom> const& atoms,
                                      CmapGridType const& cmap)
 {
-  mprintf("DEBUG: Check res %i %s %s %s %s against %s %s %s %s\n",
+/*  mprintf("DEBUG: Check res %i %s %s %s %s against %s %s %s %s\n",
           atoms[dih.A2()].ResNum()+1,
             atoms[dih.A1()].Name().Truncated().c_str(),
             atoms[dih.A2()].Name().Truncated().c_str(),
@@ -3180,14 +3180,14 @@ static inline int cmap_anames_match(DihedralType const& dih,
             cmap.AtomNames()[0].c_str(),
             cmap.AtomNames()[1].c_str(),
             cmap.AtomNames()[2].c_str(),
-            cmap.AtomNames()[3].c_str());
+            cmap.AtomNames()[3].c_str());*/
   // TODO without Truncated
   if (atoms[dih.A1()].Name().Truncated() == cmap.AtomNames()[0] &&
       atoms[dih.A2()].Name().Truncated() == cmap.AtomNames()[1] &&
       atoms[dih.A3()].Name().Truncated() == cmap.AtomNames()[2] &&
       atoms[dih.A4()].Name().Truncated() == cmap.AtomNames()[3])
   {
-    mprintf("DEBUG: Partial match %s %s %s %s = %s %s %s %s\n",
+    /*mprintf("DEBUG: Partial match %s %s %s %s = %s %s %s %s\n",
             atoms[dih.A1()].Name().Truncated().c_str(),
             atoms[dih.A2()].Name().Truncated().c_str(),
             atoms[dih.A3()].Name().Truncated().c_str(),
@@ -3195,7 +3195,7 @@ static inline int cmap_anames_match(DihedralType const& dih,
             cmap.AtomNames()[0].c_str(),
             cmap.AtomNames()[1].c_str(),
             cmap.AtomNames()[2].c_str(),
-            cmap.AtomNames()[3].c_str());
+            cmap.AtomNames()[3].c_str());*/
     for (Atom::bond_iterator bat = atoms[dih.A4()].bondbegin();
                              bat != atoms[dih.A4()].bondend(); ++bat)
     {
@@ -3214,6 +3214,10 @@ int Topology::AssignCmapParams(DihedralArray const& allDih, CmapParmHolder const
                                CmapGridArray& cmapGrids, CmapArray& cmapTerms)
 const
 {
+  // The LEaP convention is to number the CMAP parameters in the same
+  // order as they are listed in the original parameter file. This
+  // variable keeps track of those indices.
+  std::vector<int> originalCmapIndices;
   // TODO combine with AssignDihedrals?
   for (DihedralArray::const_iterator dih = allDih.begin(); dih != allDih.end(); ++dih)
   {
@@ -3228,19 +3232,21 @@ const
       if (cmapGrids[idx].MatchesResName( rn2.Truncated() )) {
         a5 = cmap_anames_match(*dih, atoms_, cmapGrids[idx]);
         if (a5 > -1) {
-          cidx = (int)idx;
+          //cidx = (int)idx;
+          cidx = originalCmapIndices[idx];
           break;
         }
       }
     }
     if (cidx > -1) {
       mprintf("DEBUG: Potential existing cmap %i found for %s (%li)\n", cidx, TruncResNameNum(A2.ResNum()).c_str(), dih-allDih.begin());
-      mprintf("DEBUG:\t\t%s - %s - %s - %s - %s\n",
-              AtomMaskName(dih->A1()).c_str(),
-              AtomMaskName(dih->A2()).c_str(),
-              AtomMaskName(dih->A3()).c_str(),
-              AtomMaskName(dih->A4()).c_str(),
-              AtomMaskName(a5).c_str());
+      mprintf("DEBUG:\t\t%i - %i - %i - %i - %i %i\n", dih->A1()+1, dih->A2()+1, dih->A3()+1, dih->A4()+1, a5+1, cidx+1);
+//      mprintf("DEBUG:\t\t%s - %s - %s - %s - %s\n",
+//              AtomMaskName(dih->A1()).c_str(),
+//              AtomMaskName(dih->A2()).c_str(),
+//              AtomMaskName(dih->A3()).c_str(),
+//              AtomMaskName(dih->A4()).c_str(),
+//              AtomMaskName(a5).c_str());
     }
     // If not already in cmapGrids, check cmapIn
     if (cidx == -1) {
@@ -3249,8 +3255,10 @@ const
         if (cmapIn[idx].MatchesResName( rn2.Truncated() )) {
           a5 = cmap_anames_match(*dih, atoms_, cmapIn[idx]);
           if (a5 > -1) {
-            cidx = (int)cmapGrids.size();
+            //cidx = (int)cmapGrids.size();
+            cidx = (int)idx;
             cmapGrids.push_back( cmapIn[idx] );
+            originalCmapIndices.push_back( idx );
             //nidx = (int)idx;
             break;
           }
@@ -3258,15 +3266,23 @@ const
       }
       if (cidx > -1) {
         mprintf("DEBUG: Potential new cmap %i found for %s (%li)\n", cidx, TruncResNameNum(A2.ResNum()).c_str(), dih-allDih.begin());
-        mprintf("DEBUG:\t\t%s - %s - %s - %s - %s\n",
-              AtomMaskName(dih->A1()).c_str(),
-              AtomMaskName(dih->A2()).c_str(),
-              AtomMaskName(dih->A3()).c_str(),
-              AtomMaskName(dih->A4()).c_str(),
-              AtomMaskName(a5).c_str());
+        mprintf("DEBUG:\t\t%i - %i - %i - %i - %i %i\n", dih->A1()+1, dih->A2()+1, dih->A3()+1, dih->A4()+1, a5+1, cidx+1);
+      //mprintf("DEBUG:\t\t%s - %s - %s - %s - %s\n",
+      //        AtomMaskName(dih->A1()).c_str(),
+      //        AtomMaskName(dih->A2()).c_str(),
+      //        AtomMaskName(dih->A3()).c_str(),
+      //        AtomMaskName(dih->A4()).c_str(),
+      //        AtomMaskName(a5).c_str());
       }
     }
   }
+  mprintf("DEBUG: Cmap parameter indices:\n");
+  for (unsigned int idx = 0; idx < originalCmapIndices.size(); idx++)
+    mprintf("DEBUG:\t\tCurrent idx=%i  Actual idx=%u\n", originalCmapIndices[idx], idx);
+  std::sort(originalCmapIndices.begin(), originalCmapIndices.end());
+  for (unsigned int idx = 0; idx < originalCmapIndices.size(); idx++)
+    mprintf("DEBUG: Will change cmap parameter index %i to %u\n",
+            originalCmapIndices[idx]+1, idx+1);
   return 0;
 }
 

From c60247052af25151aead4572c8769deb6b8e91af Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 4 Mar 2024 10:41:45 -0500
Subject: [PATCH 0669/1492] Only copy cmap grids at the end after reordering is
 done

---
 src/ParameterTypes.h |  4 +--
 src/Topology.cpp     | 59 ++++++++++++++++++++++++++++++++++----------
 2 files changed, 48 insertions(+), 15 deletions(-)

diff --git a/src/ParameterTypes.h b/src/ParameterTypes.h
index 5b71d8182f..a73207128b 100644
--- a/src/ParameterTypes.h
+++ b/src/ParameterTypes.h
@@ -721,11 +721,11 @@ class CmapGridType {
     /// \return array of residue names this CMAP applies to
     std::vector<std::string> const& ResNames() const { return resNames_; }
     /// \return true if given name matches a residue name
-    bool MatchesResName(std::string const& nameIn) const {
+/*    bool MatchesResName(std::string const& nameIn) const {
       for (std::vector<std::string>::const_iterator it = resNames_.begin(); it != resNames_.end(); ++it)
         if (nameIn == *it) return true;
       return false;
-    }
+    }*/
     /// \return array of atom names this CMAP applies to
     std::vector<std::string> const& AtomNames() const { return atomNames_; }
     /// \return Expected number of CMAP residue names
diff --git a/src/Topology.cpp b/src/Topology.cpp
index 17efd2c603..d8314abb5a 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -3169,7 +3169,7 @@ void Topology::AssignNonbondParams(ParmHolder<AtomType> const& newTypes,
 /// \return index of 5th cmap atom if atom names match those in dihedral, -1 otherwise
 static inline int cmap_anames_match(DihedralType const& dih,
                                      std::vector<Atom> const& atoms,
-                                     CmapGridType const& cmap)
+                                     std::vector<std::string> const& cmapAtomNames)
 {
 /*  mprintf("DEBUG: Check res %i %s %s %s %s against %s %s %s %s\n",
           atoms[dih.A2()].ResNum()+1,
@@ -3182,10 +3182,10 @@ static inline int cmap_anames_match(DihedralType const& dih,
             cmap.AtomNames()[2].c_str(),
             cmap.AtomNames()[3].c_str());*/
   // TODO without Truncated
-  if (atoms[dih.A1()].Name().Truncated() == cmap.AtomNames()[0] &&
-      atoms[dih.A2()].Name().Truncated() == cmap.AtomNames()[1] &&
-      atoms[dih.A3()].Name().Truncated() == cmap.AtomNames()[2] &&
-      atoms[dih.A4()].Name().Truncated() == cmap.AtomNames()[3])
+  if (atoms[dih.A1()].Name().Truncated() == cmapAtomNames[0] &&
+      atoms[dih.A2()].Name().Truncated() == cmapAtomNames[1] &&
+      atoms[dih.A3()].Name().Truncated() == cmapAtomNames[2] &&
+      atoms[dih.A4()].Name().Truncated() == cmapAtomNames[3])
   {
     /*mprintf("DEBUG: Partial match %s %s %s %s = %s %s %s %s\n",
             atoms[dih.A1()].Name().Truncated().c_str(),
@@ -3200,7 +3200,7 @@ static inline int cmap_anames_match(DihedralType const& dih,
                              bat != atoms[dih.A4()].bondend(); ++bat)
     {
       if (*bat != dih.A3()) { // TODO can A4 ever be bonded to A1??
-        if (atoms[*bat].Name().Truncated() == cmap.AtomNames()[4]) {
+        if (atoms[*bat].Name().Truncated() == cmapAtomNames[4]) {
           return *bat;
         }
       }
@@ -3209,11 +3209,24 @@ static inline int cmap_anames_match(DihedralType const& dih,
   return -1;
 }
 
+/// \return true if given name matches a residue name
+static inline bool MatchesResName(std::vector<std::string> const& resNames, std::string const& nameIn) {
+  for (std::vector<std::string>::const_iterator it = resNames.begin(); it != resNames.end(); ++it)
+    if (nameIn == *it) return true;
+  return false;
+}
+
 /** Assign CMAP parameters */
 int Topology::AssignCmapParams(DihedralArray const& allDih, CmapParmHolder const& cmapIn,
                                CmapGridArray& cmapGrids, CmapArray& cmapTerms)
 const
 {
+  // TODO check for duplicates, look for reverse match?
+  // Keep track of residue names each cmap applies to
+  //typedef std::vector<NameType> Narray;
+  typedef std::vector<std::string> Sarray;
+  std::vector<Sarray> CmapResNames;
+  std::vector<Sarray> CmapAtomNames;
   // The LEaP convention is to number the CMAP parameters in the same
   // order as they are listed in the original parameter file. This
   // variable keeps track of those indices.
@@ -3228,9 +3241,12 @@ const
     // Is this residue already in cmapGrids?
     int cidx = -1;
     int a5 = -1;
-    for (unsigned int idx = 0; idx != cmapGrids.size(); idx++) {
-      if (cmapGrids[idx].MatchesResName( rn2.Truncated() )) {
-        a5 = cmap_anames_match(*dih, atoms_, cmapGrids[idx]);
+    //for (unsigned int idx = 0; idx != cmapGrids.size(); idx++) {
+    //  if (cmapGrids[idx].MatchesResName( rn2.Truncated() )) {
+    for (unsigned int idx = 0; idx != CmapResNames.size(); idx++) {
+      if ( MatchesResName(CmapResNames[idx], rn2.Truncated()) ) {
+        //a5 = cmap_anames_match(*dih, atoms_, cmapGrids[idx]);
+        a5 = cmap_anames_match(*dih, atoms_, CmapAtomNames[idx]);
         if (a5 > -1) {
           //cidx = (int)idx;
           cidx = originalCmapIndices[idx];
@@ -3247,17 +3263,22 @@ const
 //              AtomMaskName(dih->A3()).c_str(),
 //              AtomMaskName(dih->A4()).c_str(),
 //              AtomMaskName(a5).c_str());
+      cmapTerms.push_back( CmapType(dih->A1(), dih->A2(), dih->A3(), dih->A4(), a5, cidx) );
     }
     // If not already in cmapGrids, check cmapIn
     if (cidx == -1) {
       //int nidx = -1;
       for (unsigned int idx = 0; idx != cmapIn.size(); idx++) {
-        if (cmapIn[idx].MatchesResName( rn2.Truncated() )) {
-          a5 = cmap_anames_match(*dih, atoms_, cmapIn[idx]);
+        //if (cmapIn[idx].MatchesResName( rn2.Truncated() )) {
+        if ( MatchesResName( cmapIn[idx].ResNames(), rn2.Truncated() ) ) {
+          //a5 = cmap_anames_match(*dih, atoms_, cmapIn[idx]);
+          a5 = cmap_anames_match(*dih, atoms_, cmapIn[idx].AtomNames());
           if (a5 > -1) {
             //cidx = (int)cmapGrids.size();
             cidx = (int)idx;
-            cmapGrids.push_back( cmapIn[idx] );
+            //cmapGrids.push_back( cmapIn[idx] );
+            CmapResNames.push_back( cmapIn[idx].ResNames() );
+            CmapAtomNames.push_back( cmapIn[idx].AtomNames() );
             originalCmapIndices.push_back( idx );
             //nidx = (int)idx;
             break;
@@ -3273,6 +3294,7 @@ const
       //        AtomMaskName(dih->A3()).c_str(),
       //        AtomMaskName(dih->A4()).c_str(),
       //        AtomMaskName(a5).c_str());
+        cmapTerms.push_back( CmapType(dih->A1(), dih->A2(), dih->A3(), dih->A4(), a5, cidx) );
       }
     }
   }
@@ -3280,9 +3302,20 @@ const
   for (unsigned int idx = 0; idx < originalCmapIndices.size(); idx++)
     mprintf("DEBUG:\t\tCurrent idx=%i  Actual idx=%u\n", originalCmapIndices[idx], idx);
   std::sort(originalCmapIndices.begin(), originalCmapIndices.end());
-  for (unsigned int idx = 0; idx < originalCmapIndices.size(); idx++)
+  std::vector<int> currentToNew(cmapIn.size(), -1);
+  // Add the grid terms in original parameter file order
+  // and create map from assigned index to new index.
+  cmapGrids.reserve( originalCmapIndices.size() );
+  for (unsigned int idx = 0; idx < originalCmapIndices.size(); idx++) {
     mprintf("DEBUG: Will change cmap parameter index %i to %u\n",
             originalCmapIndices[idx]+1, idx+1);
+    currentToNew[ originalCmapIndices[idx] ] = idx;
+    cmapGrids.push_back( cmapIn[ originalCmapIndices[idx] ] );
+  }
+  mprintf("DEBUG: Assigned CMAP parameters:\n");
+  for (CmapGridArray::const_iterator it = cmapGrids.begin(); it != cmapGrids.end(); ++it)
+    mprintf("DEBUG:\t\t%li : %s\n", it-cmapGrids.begin(), it->Title().c_str());
+  // Renumber the parameter indices
   return 0;
 }
 

From dd0542d6534a612ab2a0b511e59628e198bde2cd Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 4 Mar 2024 12:41:57 -0500
Subject: [PATCH 0670/1492] Ensure the cmap term indices are updated to the
 sorted ones

---
 src/ParameterTypes.h | 2 ++
 src/Topology.cpp     | 8 ++++++++
 2 files changed, 10 insertions(+)

diff --git a/src/ParameterTypes.h b/src/ParameterTypes.h
index a73207128b..e1341f855f 100644
--- a/src/ParameterTypes.h
+++ b/src/ParameterTypes.h
@@ -800,6 +800,8 @@ class CmapType {
     inline int A4()     const { return a4_;   }
     inline int A5()     const { return a5_;   }
     inline int Idx()    const { return idx_;  }
+
+    void SetIdx(int i) { idx_ = i; }
   private:
     int a1_;
     int a2_;
diff --git a/src/Topology.cpp b/src/Topology.cpp
index d8314abb5a..b6e0a2d327 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -3316,6 +3316,14 @@ const
   for (CmapGridArray::const_iterator it = cmapGrids.begin(); it != cmapGrids.end(); ++it)
     mprintf("DEBUG:\t\t%li : %s\n", it-cmapGrids.begin(), it->Title().c_str());
   // Renumber the parameter indices
+  for (CmapArray::iterator it = cmapTerms.begin(); it != cmapTerms.end(); ++it) {
+    int newIdx = currentToNew[ it->Idx() ];
+    if (newIdx < 0) {
+      mprinterr("Internal Error: CMAP term index is not mapped.\n");
+      return 1;
+    }
+    it->SetIdx( newIdx );
+  }
   return 0;
 }
 

From ad9da084d8f38ecfc89ee4c2603f6149727fc7c1 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 4 Mar 2024 12:54:44 -0500
Subject: [PATCH 0671/1492] Change order when cmap terms written to match LEaP.
 Match LEaP behavior with IPOL; always print IPOL flag, but only
 POLARIZABILITY if IPOL > 0

---
 src/Parm_Amber.cpp | 99 +++++++++++++++++++++++-----------------------
 1 file changed, 50 insertions(+), 49 deletions(-)

diff --git a/src/Parm_Amber.cpp b/src/Parm_Amber.cpp
index 4a27de153c..93af04eef9 100644
--- a/src/Parm_Amber.cpp
+++ b/src/Parm_Amber.cpp
@@ -141,7 +141,7 @@ const Parm_Amber::ParmFlag Parm_Amber::FLAGS_[] = {
   { "ATOM_BFACTOR", "%FORMAT(10F8.2)"},                 // PDB atom B-factors
   { "ATOM_OCCUPANCY", "%FORMAT(10F8.2)"},               // PDB atom occupancies
   { "ATOM_NUMBER", F10I8},                              // PDB original atom serial #s
-  // CHARMM CMAP
+  // AMBER CMAP
   { "CMAP_COUNT",                  "%FORMAT(2I8)" },    // # CMAP terms, # unique CMAP params
   { "CMAP_RESOLUTION",             "%FORMAT(20I4)"},    // # steps along each Phi/Psi CMAP axis
   { "CMAP_PARAMETER_",             "%FORMAT(8(F9.5))"}, // CMAP grid
@@ -2216,50 +2216,6 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
   // but warn.
   if (WriteExtra(TopOut, TopOut.Natom())) return 1;
 
-  // CHAMBER only - write CMAP parameters
-  if (TopOut.HasCmap()) {
-    // CMAP COUNT
-    const FlagType f_count = (ptype_ == CHAMBER) ? F_CHM_CMAPC : F_CMAPC;
-    if (BufferAlloc(f_count, 2)) return 1;
-    file_.IntToBuffer( TopOut.Cmap().size() );     // CMAP terms
-    file_.IntToBuffer( TopOut.CmapGrid().size() ); // CMAP grids
-    file_.FlushBuffer();
-    // CMAP GRID RESOLUTIONS
-    const FlagType f_grid_res = (ptype_ == CHAMBER) ? F_CHM_CMAPR : F_CMAPR;
-    if (BufferAlloc(f_grid_res, TopOut.CmapGrid().size())) return 1;
-    for (CmapGridArray::const_iterator grid = TopOut.CmapGrid().begin();
-                                       grid != TopOut.CmapGrid().end(); ++grid)
-      file_.IntToBuffer( (int)grid->Resolution() );
-    file_.FlushBuffer();
-    // CMAP GRIDS
-    int ngrid = 1;
-    const FlagType f_grid = (ptype_ == CHAMBER) ? F_CHM_CMAPP : F_CMAPP;
-    for (CmapGridArray::const_iterator grid = TopOut.CmapGrid().begin();
-                                       grid != TopOut.CmapGrid().end();
-                                       ++grid, ++ngrid)
-    {
-      if (BufferAlloc(f_grid, grid->Size(), ngrid)) return 1;
-      for (std::vector<double>::const_iterator it = grid->Grid().begin();
-                                               it != grid->Grid().end(); ++it)
-        file_.DblToBuffer( *it );
-      file_.FlushBuffer();
-    }
-    // CMAP parameters
-    const FlagType f_param = (ptype_ == CHAMBER) ? F_CHM_CMAPI : F_CMAPI;
-    if (BufferAlloc(f_param, TopOut.Cmap().size())) return 1;
-    for (CmapArray::const_iterator it = TopOut.Cmap().begin();
-                                   it != TopOut.Cmap().end(); ++it)
-    {
-      file_.IntToBuffer( it->A1() + 1 );
-      file_.IntToBuffer( it->A2() + 1 );
-      file_.IntToBuffer( it->A3() + 1 );
-      file_.IntToBuffer( it->A4() + 1 );
-      file_.IntToBuffer( it->A5() + 1 );
-      file_.IntToBuffer( it->Idx() + 1 );
-    }
-    file_.FlushBuffer();
-  }
-
   // Write solvent info if IFBOX > 0
   if (ifbox > 0) {
     // Need to check if molecules are contiguous or not via
@@ -2409,17 +2365,62 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
     file_.FlushBuffer();
   }
 
-  // Polarizability - only write if it needs to be there
+  // Polarizability
+  if (BufferAlloc(F_IPOL, 1)) return 1;
+  file_.IntToBuffer( TopOut.Ipol() );
+  file_.FlushBuffer();
   if (TopOut.Ipol() > 0) {
-    if (BufferAlloc(F_IPOL, 1)) return 1;
-    file_.IntToBuffer( TopOut.Ipol() );
-    file_.FlushBuffer();
+    // Only write polarizabilities if IPOL is set.
     if (BufferAlloc(F_POLAR, TopOut.Natom())) return 1;
     for (Topology::atom_iterator atm = TopOut.begin(); atm != TopOut.end(); ++atm)
       file_.DblToBuffer( atm->Polar() );
     file_.FlushBuffer();
   }
 
+  // Write CMAP parameters
+  if (TopOut.HasCmap()) {
+    // CMAP COUNT
+    const FlagType f_count = (ptype_ == CHAMBER) ? F_CHM_CMAPC : F_CMAPC;
+    if (BufferAlloc(f_count, 2)) return 1;
+    file_.IntToBuffer( TopOut.Cmap().size() );     // CMAP terms
+    file_.IntToBuffer( TopOut.CmapGrid().size() ); // CMAP grids
+    file_.FlushBuffer();
+    // CMAP GRID RESOLUTIONS
+    const FlagType f_grid_res = (ptype_ == CHAMBER) ? F_CHM_CMAPR : F_CMAPR;
+    if (BufferAlloc(f_grid_res, TopOut.CmapGrid().size())) return 1;
+    for (CmapGridArray::const_iterator grid = TopOut.CmapGrid().begin();
+                                       grid != TopOut.CmapGrid().end(); ++grid)
+      file_.IntToBuffer( (int)grid->Resolution() );
+    file_.FlushBuffer();
+    // CMAP GRIDS
+    int ngrid = 1;
+    const FlagType f_grid = (ptype_ == CHAMBER) ? F_CHM_CMAPP : F_CMAPP;
+    for (CmapGridArray::const_iterator grid = TopOut.CmapGrid().begin();
+                                       grid != TopOut.CmapGrid().end();
+                                       ++grid, ++ngrid)
+    {
+      if (BufferAlloc(f_grid, grid->Size(), ngrid)) return 1;
+      for (std::vector<double>::const_iterator it = grid->Grid().begin();
+                                               it != grid->Grid().end(); ++it)
+        file_.DblToBuffer( *it );
+      file_.FlushBuffer();
+    }
+    // CMAP parameters
+    const FlagType f_param = (ptype_ == CHAMBER) ? F_CHM_CMAPI : F_CMAPI;
+    if (BufferAlloc(f_param, TopOut.Cmap().size())) return 1;
+    for (CmapArray::const_iterator it = TopOut.Cmap().begin();
+                                   it != TopOut.Cmap().end(); ++it)
+    {
+      file_.IntToBuffer( it->A1() + 1 );
+      file_.IntToBuffer( it->A2() + 1 );
+      file_.IntToBuffer( it->A3() + 1 );
+      file_.IntToBuffer( it->A4() + 1 );
+      file_.IntToBuffer( it->A5() + 1 );
+      file_.IntToBuffer( it->Idx() + 1 );
+    }
+    file_.FlushBuffer();
+  }
+
   // LES parameters
   if (TopOut.LES().HasLES()) {
     // LES NTYP

From 0dd22da32b6fe750fdd686379250a04fee79cf8a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 4 Mar 2024 12:56:43 -0500
Subject: [PATCH 0672/1492] Change fortran format to match leap

---
 src/Parm_Amber.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Parm_Amber.cpp b/src/Parm_Amber.cpp
index 93af04eef9..f8390adc9d 100644
--- a/src/Parm_Amber.cpp
+++ b/src/Parm_Amber.cpp
@@ -144,7 +144,7 @@ const Parm_Amber::ParmFlag Parm_Amber::FLAGS_[] = {
   // AMBER CMAP
   { "CMAP_COUNT",                  "%FORMAT(2I8)" },    // # CMAP terms, # unique CMAP params
   { "CMAP_RESOLUTION",             "%FORMAT(20I4)"},    // # steps along each Phi/Psi CMAP axis
-  { "CMAP_PARAMETER_",             "%FORMAT(8(F9.5))"}, // CMAP grid
+  { "CMAP_PARAMETER_",             "%FORMAT(8F9.5)"},   // CMAP grid
   { "CMAP_INDEX",                  "%FORMAT(6I8)" },    // Atom i,j,k,l,m of cross term and idx
   { 0, 0 }
 };

From c9087d2e2aa85b9eb11ed4bc6dd4ac4675f1536d Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 4 Mar 2024 13:00:37 -0500
Subject: [PATCH 0673/1492] Make writetempty the default

---
 src/Parm_Amber.cpp | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/src/Parm_Amber.cpp b/src/Parm_Amber.cpp
index f8390adc9d..76e12c6392 100644
--- a/src/Parm_Amber.cpp
+++ b/src/Parm_Amber.cpp
@@ -167,7 +167,7 @@ Parm_Amber::Parm_Amber() :
   N_impTerms_(0),
   ncoords_(0),
   writeChamber_(true),
-  writeEmptyArrays_(false),
+  writeEmptyArrays_(true),
   writePdbInfo_(true),
   has_valid_nonbond_params_(true),
   hasBadDihedrals_(false)
@@ -1517,13 +1517,18 @@ int Parm_Amber::ReadLESid(Topology& TopIn, FortranData const& FMT) {
 void Parm_Amber::WriteHelp() {
   mprintf("\tnochamber  : Do not write CHAMBER information to topology (useful for e.g. using"
           "\t             topology for visualization with VMD).\n");
-  mprintf("\twriteempty : Write Amber tree, join, and rotate info even if not present.\n");
+  mprintf("\tnoempty    : Do not generate Amber tree/join/rotate info if not already present.\n");
+  mprintf("\twriteempty : Generate Amber tree/join/rotate info if not already present.\n");
   mprintf("\tnopdbinfo  : Do not write \"PDB\" info (e.g. chain IDs, original res #s, etc).\n");
 }
 
+/** Process write args */
 int Parm_Amber::processWriteArgs(ArgList& argIn) {
   writeChamber_ = !argIn.hasKey("nochamber");
-  writeEmptyArrays_ = argIn.hasKey("writeempty");
+  if (argIn.hasKey("noempty"))
+    writeEmptyArrays_ = false;
+  else if (argIn.hasKey("writeempty"))
+    writeEmptyArrays_ = true;
   writePdbInfo_ = !argIn.hasKey("nopdbinfo");
   return 0;
 }

From 788eed0dc943be5596ae098051ad426ab5c8a3c6 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 4 Mar 2024 13:17:39 -0500
Subject: [PATCH 0674/1492] Start giving the ability to do comment lines

---
 src/Parm_Amber.cpp | 20 +++++++++++++++++---
 src/Parm_Amber.h   |  2 ++
 2 files changed, 19 insertions(+), 3 deletions(-)

diff --git a/src/Parm_Amber.cpp b/src/Parm_Amber.cpp
index 76e12c6392..9815d08e00 100644
--- a/src/Parm_Amber.cpp
+++ b/src/Parm_Amber.cpp
@@ -169,6 +169,7 @@ Parm_Amber::Parm_Amber() :
   writeChamber_(true),
   writeEmptyArrays_(true),
   writePdbInfo_(true),
+  writeComments_(true),
   has_valid_nonbond_params_(true),
   hasBadDihedrals_(false)
 {
@@ -1520,6 +1521,7 @@ void Parm_Amber::WriteHelp() {
   mprintf("\tnoempty    : Do not generate Amber tree/join/rotate info if not already present.\n");
   mprintf("\twriteempty : Generate Amber tree/join/rotate info if not already present.\n");
   mprintf("\tnopdbinfo  : Do not write \"PDB\" info (e.g. chain IDs, original res #s, etc).\n");
+  mprintf("\tnocomments : Do not write %%COMMENT lines to topology file.\n");
 }
 
 /** Process write args */
@@ -1530,6 +1532,7 @@ int Parm_Amber::processWriteArgs(ArgList& argIn) {
   else if (argIn.hasKey("writeempty"))
     writeEmptyArrays_ = true;
   writePdbInfo_ = !argIn.hasKey("nopdbinfo");
+  writeComments_ = !argIn.hasKey("nocomments");
   return 0;
 }
 
@@ -1552,7 +1555,13 @@ Parm_Amber::FortranData Parm_Amber::WriteFormat(FlagType fflag) const {
 /** This version uses the default flag to allocate the format string. */
 int Parm_Amber::BufferAlloc(FlagType ftype, int nvals, int idx) {
   FortranData FMT = WriteFormat( ftype );
-  return BufferAlloc(ftype, FMT, nvals, idx);
+  return BufferAlloc(ftype, FMT, nvals, idx, "");
+}
+
+/** This version allocates with no comment. */
+int Parm_Amber::BufferAlloc(FlagType ftype, FortranData const& FMT, int nvals, int idx)
+{
+  return BufferAlloc(ftype, FMT, nvals, idx, "");
 }
 
 // Parm_Amber::BufferAlloc()
@@ -1562,7 +1571,7 @@ int Parm_Amber::BufferAlloc(FlagType ftype, int nvals, int idx) {
   * \param nvals The number of values that will be written.
   * \param idx Index for flags that can be specified multiple times (e.g. CMAP grids).
   */
-int Parm_Amber::BufferAlloc(FlagType ftype, FortranData const& FMT, int nvals, int idx) {
+int Parm_Amber::BufferAlloc(FlagType ftype, FortranData const& FMT, int nvals, int idx, std::string const& comment) {
   if ( FMT.Ftype() == UNKNOWN_FTYPE) {
     mprinterr("Interal Error: Could not set up format string.\n");
     return 1;
@@ -1574,7 +1583,11 @@ int Parm_Amber::BufferAlloc(FlagType ftype, FortranData const& FMT, int nvals, i
     // NOTE: Currently only needed for CMAP grid flags
     std::string fflag( FLAGS_[ftype].Flag );
     fflag.append( integerToString( idx, 2 ) );
-    file_.Printf("%%FLAG %-74s\n%-80s\n", fflag.c_str(), FMT.Fstr());
+    if (!comment.empty() && writeComments_)
+      file_.Printf("%%FLAG %-74s\n%%COMMENT  %-70s\n%-80s\n",
+                   fflag.c_str(), comment.c_str(), FMT.Fstr());
+    else
+      file_.Printf("%%FLAG %-74s\n%-80s\n", fflag.c_str(), FMT.Fstr());
   }
   if (nvals > 0) {
     TextFormat WriteFmt;
@@ -1781,6 +1794,7 @@ int Parm_Amber::WriteExtra(Topology const& topOut, int natom) {
 // Parm_Amber::WriteParm()
 int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
   if (file_.OpenWrite( fname )) return 1;
+  if (!writeComments_) mprintf("Warning: Not writing %%COMMENT lines to topology.\n");
   elec_to_parm_ = Constants::ELECTOAMBER;
   parm_to_elec_ = Constants::AMBERTOELEC;
   // Determine if this is a CHAMBER topology
diff --git a/src/Parm_Amber.h b/src/Parm_Amber.h
index dc4d6d50a6..88520da35e 100644
--- a/src/Parm_Amber.h
+++ b/src/Parm_Amber.h
@@ -143,6 +143,7 @@ class Parm_Amber : public ParmIO {
 
     // ----- Write -------------------------------
     FortranData WriteFormat(FlagType) const;
+    int BufferAlloc(FlagType, FortranData const&, int, int, std::string const&);
     int BufferAlloc(FlagType, FortranData const&, int, int);
     int BufferAlloc(FlagType, int, int);
     int BufferAlloc(FlagType f, int n) { return BufferAlloc(f, n, -1); }
@@ -192,6 +193,7 @@ class Parm_Amber : public ParmIO {
     bool writeChamber_;     ///< If true write CHAMBER info
     bool writeEmptyArrays_; ///< If true try to write TREE, IROTATE, JOIN even if not present 
     bool writePdbInfo_;     ///< If true write chain IDs etc
+    bool writeComments_;    ///< If false suppress writing %COMMENT lines
 
     bool has_valid_nonbond_params_; ///< Will set to false if invalid nonbonds detected on read
     bool hasBadDihedrals_; ///< Set to true if bad dihedrals detected on read

From e168c0a1fdc8608fc6c464bb4a95369973d74785 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 4 Mar 2024 13:26:48 -0500
Subject: [PATCH 0675/1492] Protect against cmap term titles being too large
 for comment

---
 src/Parm_Amber.cpp | 21 +++++++++++++++++++--
 src/Parm_Amber.h   |  1 +
 2 files changed, 20 insertions(+), 2 deletions(-)

diff --git a/src/Parm_Amber.cpp b/src/Parm_Amber.cpp
index 9815d08e00..a3dd2d0fe4 100644
--- a/src/Parm_Amber.cpp
+++ b/src/Parm_Amber.cpp
@@ -1558,6 +1558,12 @@ int Parm_Amber::BufferAlloc(FlagType ftype, int nvals, int idx) {
   return BufferAlloc(ftype, FMT, nvals, idx, "");
 }
 
+/** This version uses default flag and optional comment. */
+int Parm_Amber::BufferAlloc(FlagType ftype, int nvals, int idx, std::string const& comment) {
+  FortranData FMT = WriteFormat( ftype );
+  return BufferAlloc(ftype, FMT, nvals, idx, comment);
+}
+
 /** This version allocates with no comment. */
 int Parm_Amber::BufferAlloc(FlagType ftype, FortranData const& FMT, int nvals, int idx)
 {
@@ -2418,13 +2424,24 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
                                        grid != TopOut.CmapGrid().end();
                                        ++grid, ++ngrid)
     {
-      if (BufferAlloc(f_grid, grid->Size(), ngrid)) return 1;
+      int cmg_err = 0;
+      if (!grid->Title().empty()) {
+        std::string cmaptitle = grid->Title();
+        if (cmaptitle.size() > 70) {
+          mprintf("Warning: CMAP title %s is too large (%zu), truncating.\n",
+                  cmaptitle.c_str(), cmaptitle.size());
+          cmaptitle.resize(70);
+        }
+        cmg_err = BufferAlloc(f_grid, grid->Size(), ngrid, cmaptitle);
+      } else
+        cmg_err = BufferAlloc(f_grid, grid->Size(), ngrid);
+      if (cmg_err != 0) return 1;
       for (std::vector<double>::const_iterator it = grid->Grid().begin();
                                                it != grid->Grid().end(); ++it)
         file_.DblToBuffer( *it );
       file_.FlushBuffer();
     }
-    // CMAP parameters
+    // CMAP terms
     const FlagType f_param = (ptype_ == CHAMBER) ? F_CHM_CMAPI : F_CMAPI;
     if (BufferAlloc(f_param, TopOut.Cmap().size())) return 1;
     for (CmapArray::const_iterator it = TopOut.Cmap().begin();
diff --git a/src/Parm_Amber.h b/src/Parm_Amber.h
index 88520da35e..482b7c0306 100644
--- a/src/Parm_Amber.h
+++ b/src/Parm_Amber.h
@@ -146,6 +146,7 @@ class Parm_Amber : public ParmIO {
     int BufferAlloc(FlagType, FortranData const&, int, int, std::string const&);
     int BufferAlloc(FlagType, FortranData const&, int, int);
     int BufferAlloc(FlagType, int, int);
+    int BufferAlloc(FlagType, int, int, std::string const&);
     int BufferAlloc(FlagType f, int n) { return BufferAlloc(f, n, -1); }
     int WriteLJ(FlagType, FlagType, NonbondArray const&);
     int WriteBondParm(FlagType, FlagType, BondParmArray const&);

From 8c3ebfd45f659dbd68c00e0315587a81a77e0cc4 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 4 Mar 2024 13:34:20 -0500
Subject: [PATCH 0676/1492] Add help for GB keys

---
 src/Exec_Build.cpp     | 10 +++++++---
 src/Parm/GB_Params.cpp |  5 +++++
 src/Parm/GB_Params.h   |  2 ++
 3 files changed, 14 insertions(+), 3 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 37182de919..ab61596087 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -639,19 +639,23 @@ const
 void Exec_Build::Help() const
 {
   mprintf("\tname <output COORDS> crdset <COORDS set> [frame <#>]\n"
-          "\t[title <title>]\n"
+          "\t[title <title>] [gb <radii>]\n"
           "\t[%s]\n"
           "\t[{%s} ...]\n"
           "\t[{%s} ...]\n"
           "%s"
-          "%s"
-          "  Build complete topology and parameters from given crdset.\n",
+          "%s",
           Cpptraj::Structure::Creator::other_keywords_,
           Cpptraj::Structure::Creator::template_keywords_,
           Cpptraj::Structure::Creator::parm_keywords_,
           Cpptraj::Structure::HisProt::keywords_,
           Cpptraj::Structure::Disulfide::keywords_
          );
+  mprintf("    <radii> =");
+  for (int ig = 0; ig != (int)Cpptraj::Parm::UNKNOWN_GB; ig++)
+    mprintf(" %s", Cpptraj::Parm::GbTypeKey((Cpptraj::Parm::GB_RadiiType)ig));
+  mprintf("\n");
+  mprintf("  Build complete topology and parameters from given crdset.\n");
 }
 
 // Exec_Build::Execute()
diff --git a/src/Parm/GB_Params.cpp b/src/Parm/GB_Params.cpp
index 2205ee853b..51beee71b5 100644
--- a/src/Parm/GB_Params.cpp
+++ b/src/Parm/GB_Params.cpp
@@ -35,6 +35,11 @@ static const char* GB_RadiiAmberFlag_[] = {
   "Unknown radius set (leap needs to be modified!)"
 };
 
+/** \return key corresponding to type. */
+const char* Cpptraj::Parm::GbTypeKey(GB_RadiiType t) {
+  return GB_RadiiTypeKey_[t];
+}
+
 /** \return char string corresponding to type. */
 std::string Cpptraj::Parm::GbTypeStr(GB_RadiiType t) {
   return std::string(GB_RadiiTypeStr_[t]);
diff --git a/src/Parm/GB_Params.h b/src/Parm/GB_Params.h
index 6067d2f6ee..7b716f8f23 100644
--- a/src/Parm/GB_Params.h
+++ b/src/Parm/GB_Params.h
@@ -15,6 +15,8 @@ enum GB_RadiiType {
   MBONDI3,          ///< 8, ArgH and AspGluO modified Bondi2 radii
   UNKNOWN_GB
 };
+/// \return Keyword corresponding to Amber radii flag
+const char* GbTypeKey(GB_RadiiType);
 /// \return string corresponding to Amber Radii Flag
 std::string GbAmberFlag(GB_RadiiType);
 /// \return string corresponding to gb radii set

From 2fb6a3283a9a2a3c4b514715b7e913125116172c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 4 Mar 2024 13:42:54 -0500
Subject: [PATCH 0677/1492] Fix bug in mbondi2 hydrogen radius bonded to N
 assignment

---
 src/Parm/GB_Params.cpp | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/Parm/GB_Params.cpp b/src/Parm/GB_Params.cpp
index 51beee71b5..0d8fe8a59c 100644
--- a/src/Parm/GB_Params.cpp
+++ b/src/Parm/GB_Params.cpp
@@ -3,13 +3,13 @@
 #include "../CpptrajStdio.h"
 
 static const char* GB_RadiiTypeStr_[] = {
-  "Bondi radii",
-  "Amber 6 modified Bondi radii",
-  "Modified Bondi radii",
-  "Radii optimized for Amber charges by Huo and Kollman",
-  "H(N)-modified Bondi radii",
-  "PARSE radii",
-  "ArgH and AspGluO modified Bondi2 radii",
+  "Bondi radii", // 0
+  "Amber 6 modified Bondi radii", // 1
+  "Modified Bondi radii", // 2
+  "Radii optimized for Amber charges by Huo and Kollman", // 3
+  "H(N)-modified Bondi radii", // 6
+  "PARSE radii", // 7
+  "ArgH and AspGluO modified Bondi2 radii", // 8
   "Unknown GB radii set"
 };
 
@@ -123,7 +123,7 @@ static void assign_gb_radii(Topology& top, Cpptraj::Parm::GB_RadiiType radiiSet)
 	    else if (iGBparm == 6 || iGBparm == 8) {
 
               // Try Alexey's scheme
-              if (currentAtom.Element() == Atom::NITROGEN) {
+              if (aAtomA.Element() == Atom::NITROGEN) {
                 dGBrad = 1.3;
                 if (iGBparm == 8) {
 

From 6cd80404008329541c977af5adf18bde98307ed9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 4 Mar 2024 14:00:09 -0500
Subject: [PATCH 0678/1492] For mbondi3 fix O radius next to OXT

---
 src/Parm/GB_Params.cpp | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/Parm/GB_Params.cpp b/src/Parm/GB_Params.cpp
index 0d8fe8a59c..ed10f58c14 100644
--- a/src/Parm/GB_Params.cpp
+++ b/src/Parm/GB_Params.cpp
@@ -205,7 +205,9 @@ static void assign_gb_radii(Topology& top, Cpptraj::Parm::GB_RadiiType radiiSet)
                  (currentRes.Name() == "AS4" && currentAtom.Name().Match("OD*")) ||
                  (currentRes.Name() == "GLU" && currentAtom.Name().Match("OE*")) ||
                  (currentRes.Name() == "GL4" && currentAtom.Name().Match("OE*")) ||
-                 currentAtom.Name() == "OXT")
+                 (currentAtom.Name() == "OXT") ||
+                 (iat+1 < top.Natom() && top[iat+1].Name() == "OXT")
+               )
             {
             //if (!(strcmp(cPTemp, "ASP") || strncmp(sAtomName(saPAtom->aAtom), "OD", 2)) ||
             //      !(strcmp(cPTemp, "AS4") || strncmp(sAtomName(saPAtom->aAtom), "OD", 2)) ||

From bdac5f39683adb1d9eadf3abaef46975d09f8e89 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 4 Mar 2024 14:01:01 -0500
Subject: [PATCH 0679/1492] Fix mbondi3 O next to OXT radius

---
 src/Parm/GB_Params.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Parm/GB_Params.cpp b/src/Parm/GB_Params.cpp
index ed10f58c14..054037d05e 100644
--- a/src/Parm/GB_Params.cpp
+++ b/src/Parm/GB_Params.cpp
@@ -206,7 +206,7 @@ static void assign_gb_radii(Topology& top, Cpptraj::Parm::GB_RadiiType radiiSet)
                  (currentRes.Name() == "GLU" && currentAtom.Name().Match("OE*")) ||
                  (currentRes.Name() == "GL4" && currentAtom.Name().Match("OE*")) ||
                  (currentAtom.Name() == "OXT") ||
-                 (iat+1 < top.Natom() && top[iat+1].Name() == "OXT")
+                 (iat+1 < top.Natom() && top[iat+1].Name() == "OXT") // FIXME O next to OXT in topology seems very hacky
                )
             {
             //if (!(strcmp(cPTemp, "ASP") || strncmp(sAtomName(saPAtom->aAtom), "OD", 2)) ||

From 225788685bff0363686a7c8e74a38d80d7ddce69 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 4 Mar 2024 14:04:15 -0500
Subject: [PATCH 0680/1492] Add comments

---
 src/Topology.cpp | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index b6e0a2d327..9aad1ee0be 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -3371,11 +3371,12 @@ int Topology::AssignParams(ParameterSet const& set0) {
   // Urey-Bradley
   mprintf("\tAssigning Urey-Bradley parameters.\n");
   AssignUBParams( set0.UB() );
-  // Improper parameters
   if (!chamber_.Impropers().empty()) {
+    // Charmm Improper parameters
     mprintf("\tAssigning CHARMM improper parameters.\n");
     AssignImproperParams( set0.IP() );
   } else {
+    // Amber improper parameters
     mprintf("\tAssigning improper parameters.\n");
     DihedralArray allImpropers = Cpptraj::Structure::GenerateImproperArray(residues_, atoms_);
     allImpropers = AssignDihedralParm( set0.DP(), set0.IP(), set0.AT(), allImpropers, true );
@@ -3389,7 +3390,7 @@ int Topology::AssignParams(ParameterSet const& set0) {
   mprintf("\tAssigning nonbond parameters.\n");
   AssignNonbondParams( set0.AT(), set0.NB(), set0.HB() );
   mprintf("DEBUG: CMAP size %zu\n", set0.CMAP().size());
-  // TODO LJ14
+  // TODO LJ14, LJC
 
   return 0;
 }

From 3696355db75a76c785038da5e0f8a1197affe5f3 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 4 Mar 2024 16:16:03 -0500
Subject: [PATCH 0681/1492] Add comment, may need to match atom types at some
 point

---
 src/CmapParmHolder.cpp | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/CmapParmHolder.cpp b/src/CmapParmHolder.cpp
index 947d48bad3..ff6b38e325 100644
--- a/src/CmapParmHolder.cpp
+++ b/src/CmapParmHolder.cpp
@@ -40,6 +40,7 @@ ParameterHolders::RetType CmapParmHolder::AddParm(CmapGridType const& cmap1, boo
       break;
     }
   } // END loop over existing CMAP terms
+  // TODO match atom types?
   if (mtype == PARTIAL_MATCH) {
     mprinterr("Internal Error: Partial match between new CMAP '%s' and existing CMAP '%s'\n"
               "Internal Error:   Not yet set up to handle this kind of parameter update.\n",

From a6652c0927824c50593ff7f2b9be1a76093b9048 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 5 Mar 2024 13:01:21 -0500
Subject: [PATCH 0682/1492] Check if atom names match in cmap. Check if grid is
 the same.

---
 src/CmapParmHolder.cpp | 37 +++++++++++++++++++++++++++++++------
 src/ParameterTypes.h   |  8 ++++++++
 2 files changed, 39 insertions(+), 6 deletions(-)

diff --git a/src/CmapParmHolder.cpp b/src/CmapParmHolder.cpp
index ff6b38e325..5a2d8d1f69 100644
--- a/src/CmapParmHolder.cpp
+++ b/src/CmapParmHolder.cpp
@@ -19,6 +19,22 @@ ParameterHolders::RetType CmapParmHolder::AddParm(CmapGridType const& cmap1, boo
   CmapGridArray::iterator currentCmap = CMAP_.end();
   for (CmapGridArray::iterator jt = CMAP_.begin(); jt != CMAP_.end(); ++jt)
   {
+    // First check if atom names match.
+    // Order is important.
+    bool atomNamesMatch = true;
+    if (cmap1.AtomNames().size() != jt->AtomNames().size())
+      atomNamesMatch = false;
+    else {
+      for (unsigned int idx = 0; idx != cmap1.AtomNames().size(); idx++) {
+        if (cmap1.AtomNames()[idx] != jt->AtomNames()[idx]) {
+          atomNamesMatch = false;
+          break;
+        }
+      }
+    }
+    if (!atomNamesMatch) continue;
+    // How many residue names in the incoming cmap match this cmap (jt)?
+    // Order not important.
     int nMatch = 0;
     for (Sarray::const_iterator rni = cmap1.ResNames().begin(); rni != cmap1.ResNames().end(); ++rni)
     {
@@ -47,13 +63,22 @@ ParameterHolders::RetType CmapParmHolder::AddParm(CmapGridType const& cmap1, boo
               cmap1.Title().c_str(), currentCmap->Title().c_str());
     return ParameterHolders::ERR;
   } else if (mtype == FULL_MATCH) {
-    mprintf("DEBUG: Match between new CMAP '%s' and existing CMAP '%s'\n",
+    mprintf("DEBUG: Potential match between new CMAP '%s' and existing CMAP '%s'\n",
             cmap1.Title().c_str(), currentCmap->Title().c_str());
-    if (allowUpdate) {
-      *currentCmap = cmap1;
-      return ParameterHolders::UPDATED;
-    } else
-      return ParameterHolders::ERR;
+    // Is this parameter the same?
+    if (currentCmap->GridMatches( cmap1 )) {
+      mprintf("DEBUG: CMAP parameter already present.\n");
+      return ParameterHolders::SAME;
+    } else {
+      if (allowUpdate) {
+        mprintf("DEBUG: Update of CMAP parameter.\n");
+        *currentCmap = cmap1;
+        return ParameterHolders::UPDATED;
+      } else {
+        mprintf("DEBUG: Update of CMAP parameter NOT ALLOWED.\n");
+        return ParameterHolders::ERR;
+      }
+    }
   }
   // NO_MATCH
   mprintf("DEBUG: CMAP '%s' is a new CMAP.\n", cmap1.Title().c_str());
diff --git a/src/ParameterTypes.h b/src/ParameterTypes.h
index e1341f855f..e2dbdce932 100644
--- a/src/ParameterTypes.h
+++ b/src/ParameterTypes.h
@@ -779,6 +779,14 @@ class CmapGridType {
       return (nCmapRes_ == 0 && resolution_ == 0 &&
               grid_.empty() && title_.empty() && resNames_.empty());
     }
+    /// \return True if CMAP grid matches given grid. Expensive, so use sparingly.
+    bool GridMatches(CmapGridType const& rhs) const {
+      if (grid_.size() != rhs.grid_.size()) return false;
+      for (unsigned int idx = 0; idx != grid_.size(); idx++) {
+        if (FNE(grid_[idx], rhs.grid_[idx])) return false;
+      }
+      return true;
+    }
   private:
     int nCmapRes_;             ///< Number of expected residues this CMAP will apply to
     unsigned int resolution_;  ///< Number of steps along each phi/psi CMAP axis

From c9c1a700f303cbf16e469d25065269534b534bae Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 5 Mar 2024 14:59:55 -0500
Subject: [PATCH 0683/1492] Add GetCmapParams. Do not warn about no nonbond
 info if no atoms

---
 src/ParameterTypes.h |   2 +-
 src/Topology.cpp     | 118 ++++++++++++++++++++++++++++++++++++++++++-
 2 files changed, 118 insertions(+), 2 deletions(-)

diff --git a/src/ParameterTypes.h b/src/ParameterTypes.h
index e2dbdce932..39854e8d33 100644
--- a/src/ParameterTypes.h
+++ b/src/ParameterTypes.h
@@ -709,7 +709,7 @@ class CapParmType {
     double zcap_;   ///< Z coordinate for the center of the cap
 };
 // ----- CHAMBER PARAMETERS ----------------------------------------------------
-/// Hold CMAP grid parameters
+/// Hold CMAP grid parameters // FIXME use NameType
 class CmapGridType {
   public:
     CmapGridType() : nCmapRes_(0), resolution_(0) {}
diff --git a/src/Topology.cpp b/src/Topology.cpp
index 9aad1ee0be..2b372f0e77 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2238,6 +2238,117 @@ static inline void GetDihedralParams(DihedralParmHolder& DP, ImproperParmHolder&
   }
 }
 
+/// \return an error if cmap atom names do not match
+static inline int check_cmap_atom_name(NameType const& n0, NameType const& n1)
+{
+  if (n0 != n1) {
+    mprinterr("Error: CMAP term atom name %s does not match expected CMAP term atom name %s\n",
+              *n1, *n0);
+    return 1;
+  }
+  return 0;
+}
+
+/** Get existing CMAP parameters.
+  * Unlike other parameters, CMAPs are big and are uniquely identified by
+  * a combination of residue and 5 atom names. Depending on if they were
+  * read in from a parameter file or a topology, they may or may not
+  * have residue/atom name information, which is needed for assignment.
+  * This info needs to be generated if it is missing.
+  */
+static inline int GetCmapParams(CmapParmHolder& cmapParm, CmapArray const& cmapTerms, CmapGridArray const& cmapGrids,
+                                 std::vector<Atom> const& atoms, std::vector<Residue> const& residues)
+{
+  if (cmapGrids.empty() || cmapTerms.empty()) {
+    mprintf("DEBUG: CMAP grids/terms are empty. No parameters to get.\n");
+    return 0;
+  }
+  // Check if we need to generate residue/atom information for grids.
+  bool needResAtomInfo = false;
+  for (CmapGridArray::const_iterator it = cmapGrids.begin(); it != cmapGrids.end(); ++it)
+  {
+    if (it->ResNames().empty() || it->AtomNames().empty()) {
+      needResAtomInfo = true;
+      break;
+    }
+  }
+  // Mark off which terms need to be added.
+  std::vector<bool> addGrid( cmapGrids.size(), false );
+  for (CmapArray::const_iterator cm = cmapTerms.begin(); cm != cmapTerms.end(); ++cm) {
+    if (cm->Idx() != -1)
+      addGrid[cm->Idx()] = true;
+  }
+  // Add grids, adding res/atom info if needed
+  if (needResAtomInfo) {
+    mprintf("CMAP terms need residue/atom info.\n");
+    for (unsigned int idx = 0; idx != cmapGrids.size(); idx++) {
+      if (addGrid[idx]) {
+        // Figure out residue names this cmap applies to.
+        std::set<NameType> resNames;
+        std::vector<NameType> atomNames;
+        atomNames.reserve(5);
+        for (CmapArray::const_iterator cm = cmapTerms.begin(); cm != cmapTerms.end(); ++cm) {
+          if (cm->Idx() == (int)idx) {
+            int resnum = atoms[cm->A2()].ResNum();
+            resNames.insert( residues[resnum].Name() );
+            if (atomNames.empty()) {
+              atomNames.push_back( atoms[cm->A1()].Name() );
+              atomNames.push_back( atoms[cm->A2()].Name() );
+              atomNames.push_back( atoms[cm->A3()].Name() );
+              atomNames.push_back( atoms[cm->A4()].Name() );
+              atomNames.push_back( atoms[cm->A5()].Name() );
+            } else {
+              // Check atom names
+              if (check_cmap_atom_name(atomNames[0], atoms[cm->A1()].Name())) return 1;
+              if (check_cmap_atom_name(atomNames[1], atoms[cm->A2()].Name())) return 1;
+              if (check_cmap_atom_name(atomNames[2], atoms[cm->A3()].Name())) return 1;
+              if (check_cmap_atom_name(atomNames[3], atoms[cm->A4()].Name())) return 1;
+              if (check_cmap_atom_name(atomNames[4], atoms[cm->A5()].Name())) return 1;
+            }
+          }
+        }
+        mprintf("DEBUG: Cmap term %u residues", idx);
+        for (std::set<NameType>::const_iterator it = resNames.begin(); it != resNames.end(); ++it)
+          mprintf(" %s", *(*it));
+        mprintf(" Atoms={");
+        for (std::vector<NameType>::const_iterator it = atomNames.begin(); it != atomNames.end(); ++it)
+          mprintf(" %s", *(*it));
+        mprintf(" }\n");
+        CmapGridType newGrid = cmapGrids[idx];
+        // Add the atom/res info to the grid
+        newGrid.SetNumCmapRes( resNames.size() );
+        for (std::set<NameType>::const_iterator it = resNames.begin(); it != resNames.end(); ++it)
+          newGrid.AddResName( it->Truncated() ); // FIXME just use NameType
+        for (std::vector<NameType>::const_iterator it = atomNames.begin(); it != atomNames.end(); ++it)
+          newGrid.AddAtomName( it->Truncated() ); // FIXME just use NameType
+        if (!newGrid.CmapIsValid()) {
+          mprinterr("Error: CMAP is not valid, could not get parameter.\n");
+          mprinterr("Error:   Term %u residues", idx);
+          for (std::set<NameType>::const_iterator it = resNames.begin(); it != resNames.end(); ++it)
+            mprinterr(" %s", *(*it));
+          mprinterr(" Atoms={");
+          for (std::vector<NameType>::const_iterator it = atomNames.begin(); it != atomNames.end(); ++it)
+            mprinterr(" %s", *(*it));
+          mprinterr(" }\n");
+        }
+        ParameterHolders::RetType ret = cmapParm.AddParm( newGrid, false );
+        if (ret == ParameterHolders::ERR)
+          paramOverwriteWarning("CMAP");
+      } // END if adding existing grid to parms
+    } // END loop over existing grides
+  } else {
+    mprintf("CMAP terms have residue/atom info.\n");
+    for (unsigned int idx = 0; idx != cmapGrids.size(); idx++) {
+      if (addGrid[idx]) {
+        ParameterHolders::RetType ret = cmapParm.AddParm( cmapGrids[idx], false );
+        if (ret == ParameterHolders::ERR)
+          paramOverwriteWarning("CMAP");
+      }
+    }
+  }
+  return 0;
+}
+
 /** \param atomTypes Output array of atom types.
   * \param NB1 Output array of nonbond parameters.
   * \param atoms Current array of atoms.
@@ -2316,7 +2427,8 @@ static inline void GetLJAtomTypes( ParmHolder<AtomType>& atomTypes, ParmHolder<N
     if (nModifiedOffDiagonal > 0)
       mprintf("Warning: %u modified off-diagonal LJ terms present.\n", nModifiedOffDiagonal);
   } else {
-    mprintf("DEBUG: Topology does not have nonbond parameters.\n");
+    if (!atoms.empty())
+      mprintf("DEBUG: Topology does not have nonbond parameters.\n");
     // No nonbonded parameters. Just save mass/polarizability.
     for (std::vector<Atom>::const_iterator atm = atoms.begin(); atm != atoms.end(); ++atm)
       if (atm->HasType() > 0)
@@ -2345,6 +2457,10 @@ ParameterSet Topology::GetParameters() const {
     // Impropers
     GetImproperParams( Params.IP(), atoms_, chamber_.Impropers(), chamber_.ImproperParm() );
   }
+  // CMAPs
+  if (GetCmapParams( Params.CMAP(), cmap_, cmapGrid_, atoms_, residues_ )) {
+    mprinterr("Error: Could not get CMAP parameters.\n"); // TODO fatal?
+  }
 
   return Params;
 }

From 4875daf5005c564ebc7099358094d74c6612ffcd Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 5 Mar 2024 15:46:08 -0500
Subject: [PATCH 0684/1492] Fix typo

---
 src/Topology.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index 2b372f0e77..737682d504 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2335,7 +2335,7 @@ static inline int GetCmapParams(CmapParmHolder& cmapParm, CmapArray const& cmapT
         if (ret == ParameterHolders::ERR)
           paramOverwriteWarning("CMAP");
       } // END if adding existing grid to parms
-    } // END loop over existing grides
+    } // END loop over existing grids
   } else {
     mprintf("CMAP terms have residue/atom info.\n");
     for (unsigned int idx = 0; idx != cmapGrids.size(); idx++) {

From cecab3d1dc4f35cbc1dcdfe3af6ec73bb5c54318 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 8 Mar 2024 08:53:37 -0500
Subject: [PATCH 0685/1492] Add cmap update

---
 src/Topology.cpp | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index 737682d504..d811c8c50c 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -3153,7 +3153,7 @@ DihedralArray Topology::get_unique_dihedrals(DihedralArray const& dihedralsIn) c
     if (dihedrals.empty())
       dihedrals.push_back( *dih );
     else {
-      if ( *dih != dihedrals.back() )
+      if ( *dih != dihedrals.back() ) // TODO skip end dihedrals, impropers?
         dihedrals.push_back( *dih );
     }
   }
@@ -3350,6 +3350,8 @@ const
   // TODO combine with AssignDihedrals?
   for (DihedralArray::const_iterator dih = allDih.begin(); dih != allDih.end(); ++dih)
   {
+    // Ignore end (repeated) or improper dihedrals
+    if (dih->IsImproper() || dih->Skip14()) continue;
     // Get residue name for A2
     Atom const& A2 = atoms_[dih->A2()];
     // TODO make sure A2-A4 in same residue?
@@ -3584,6 +3586,14 @@ int Topology::updateParams(ParameterSet& set0, ParameterSet const& set1) {
     mprintf("\tRegenerating nonbond parameters.\n");
     AssignNonbondParams( set0.AT(), set0.NB(), set0.HB() );
   }
+  // CMAP
+  if (UC.nCmapUpdated_ > 0) {
+    cmap_.clear();
+    cmapGrid_.clear();
+    mprintf("\tRegenerating CMAP parameters.\n");
+    AssignCmapParams(dihedrals_, set0.CMAP(), cmapGrid_, cmap_);
+    AssignCmapParams(dihedralsh_, set0.CMAP(), cmapGrid_, cmap_);
+  }
   // TODO LJ14
 
   if (debug_ > 0) set0.Debug("newp.dat");

From 88bedc8829c8f2397e3767486b0bfab5ae49e0c6 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 8 Mar 2024 09:00:06 -0500
Subject: [PATCH 0686/1492] Dont remap if no cmap indices

---
 src/Topology.cpp | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index d811c8c50c..98fe741acd 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -3419,6 +3419,10 @@ const
   mprintf("DEBUG: Cmap parameter indices:\n");
   for (unsigned int idx = 0; idx < originalCmapIndices.size(); idx++)
     mprintf("DEBUG:\t\tCurrent idx=%i  Actual idx=%u\n", originalCmapIndices[idx], idx);
+  if (originalCmapIndices.empty()) {
+    mprintf("DEBUG: No CMAP indices in %s\n", c_str());
+    return 0;
+  }
   std::sort(originalCmapIndices.begin(), originalCmapIndices.end());
   std::vector<int> currentToNew(cmapIn.size(), -1);
   // Add the grid terms in original parameter file order

From 4fc37426b2339cc6273e804290bda81170189741 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 8 Mar 2024 14:58:12 -0500
Subject: [PATCH 0687/1492] Create a version of assign cmap params that just
 uses existing cmap terms

---
 src/Topology.cpp | 137 ++++++++++++++++++++++++++++++++++++++++++++---
 src/Topology.h   |   7 ++-
 2 files changed, 135 insertions(+), 9 deletions(-)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index 98fe741acd..e5b0bb43ad 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2331,6 +2331,9 @@ static inline int GetCmapParams(CmapParmHolder& cmapParm, CmapArray const& cmapT
             mprinterr(" %s", *(*it));
           mprinterr(" }\n");
         }
+        // Set a default title if needed
+        if (newGrid.Title().empty())
+          newGrid.SetTitle( "CMAP for " + newGrid.ResNames().front() );
         ParameterHolders::RetType ret = cmapParm.AddParm( newGrid, false );
         if (ret == ParameterHolders::ERR)
           paramOverwriteWarning("CMAP");
@@ -2631,7 +2634,12 @@ int Topology::AppendTop(Topology const& NewTop) {
   addDihedralsWithOffset( dihedrals_, NewTop.Dihedrals(), atomOffset );
   addDihedralsWithOffset( dihedralsh_, NewTop.DihedralsH(), atomOffset );
   addDihedralsWithOffset( chamber_.SetImpropers(), NewTop.chamber_.Impropers(), atomOffset );
-  // TODO CMAP
+  for (CmapArray::const_iterator cm = NewTop.Cmap().begin(); cm != NewTop.Cmap().end(); ++cm)
+    cmap_.push_back( CmapType(cm->A1() + atomOffset,
+                              cm->A2() + atomOffset,
+                              cm->A3() + atomOffset,
+                              cm->A4() + atomOffset,
+                              cm->A5() + atomOffset, -1) );
 //#  for (BondArray::const_iterator bond = NewTop.Bonds().begin(); bond != NewTop.Bonds().end(); ++bond)
 //#    AddBond( bond->A1() + atomOffset, bond->A2() + atomOffset );
 //#  for (BondArray::const_iterator bond = NewTop.BondsH().begin(); bond != NewTop.BondsH().end(); ++bond)
@@ -3332,7 +3340,121 @@ static inline bool MatchesResName(std::vector<std::string> const& resNames, std:
   return false;
 }
 
-/** Assign CMAP parameters */
+/// Remap cmap indices
+int Topology::remap_cmap_indices(std::vector<int>& originalCmapIndices,
+                                     CmapGridArray& cmapGrids,
+                                     CmapArray& cmapTerms,
+                                 CmapParmHolder const& cmapIn)
+const
+{
+  mprintf("DEBUG: Cmap parameter indices:\n");
+  for (unsigned int idx = 0; idx < originalCmapIndices.size(); idx++)
+    mprintf("DEBUG:\t\tCurrent idx=%i  Actual idx=%u\n", originalCmapIndices[idx], idx);
+  if (originalCmapIndices.empty()) {
+    mprintf("DEBUG: No CMAP indices in %s\n", c_str());
+    return 0;
+  }
+  std::sort(originalCmapIndices.begin(), originalCmapIndices.end());
+  std::vector<int> currentToNew(cmapIn.size(), -1);
+  // Add the grid terms in original parameter file order
+  // and create map from assigned index to new index.
+  cmapGrids.reserve( originalCmapIndices.size() );
+  for (unsigned int idx = 0; idx < originalCmapIndices.size(); idx++) {
+    mprintf("DEBUG: Will change cmap parameter index %i to %u\n",
+            originalCmapIndices[idx]+1, idx+1);
+    currentToNew[ originalCmapIndices[idx] ] = idx;
+    cmapGrids.push_back( cmapIn[ originalCmapIndices[idx] ] );
+  }
+  mprintf("DEBUG: Assigned CMAP parameters:\n");
+  for (CmapGridArray::const_iterator it = cmapGrids.begin(); it != cmapGrids.end(); ++it)
+    mprintf("DEBUG:\t\t%li : %s\n", it-cmapGrids.begin(), it->Title().c_str());
+  // Renumber the parameter indices
+  for (CmapArray::iterator it = cmapTerms.begin(); it != cmapTerms.end(); ++it) {
+    int newIdx = currentToNew[ it->Idx() ];
+    if (newIdx < 0) {
+      mprinterr("Internal Error: CMAP term index is not mapped.\n");
+      return 1;
+    }
+    it->SetIdx( newIdx );
+  }
+  return 0;
+}
+
+/** Assign CMAP parameters to existing CMAP terms. */
+int Topology::AssignCmapParams(CmapArray& cmapTerms, CmapParmHolder const& cmapIn,
+                               CmapGridArray& cmapGrids)
+const
+{
+  // Keep track of residue names each cmap applies to
+  typedef std::vector<std::string> Sarray;
+  std::vector<Sarray> CmapResNames;
+  std::vector<Sarray> CmapAtomNames;
+  // The LEaP convention is to number the CMAP parameters in the same
+  // order as they are listed in the original parameter file. This
+  // variable keeps track of those indices.
+  std::vector<int> originalCmapIndices;
+  for (CmapArray::iterator cm = cmapTerms.begin(); cm != cmapTerms.end(); ++cm)
+  {
+    // Get residue name for A2
+    Atom const& A2 = atoms_[cm->A2()];
+    // TODO make sure A2-A4 in same residue?
+    NameType const& rn2 = residues_[A2.ResNum()].Name();
+    // Is this residue already in cmapGrids?
+    int cidx = -1;
+    for (unsigned int idx = 0; idx != CmapResNames.size(); idx++) {
+      if ( MatchesResName(CmapResNames[idx], rn2.Truncated()) ) {
+        if (atoms_[cm->A1()].Name() == CmapAtomNames[idx][0] &&
+            atoms_[cm->A2()].Name() == CmapAtomNames[idx][1] &&
+            atoms_[cm->A3()].Name() == CmapAtomNames[idx][2] &&
+            atoms_[cm->A4()].Name() == CmapAtomNames[idx][3] &&
+            atoms_[cm->A5()].Name() == CmapAtomNames[idx][4])
+        {
+          cidx = originalCmapIndices[idx];
+          break;
+        }
+      }
+    }
+    if (cidx > -1) {
+      mprintf("DEBUG: Potential existing cmap %i found for %s (%li)\n", cidx, TruncResNameNum(A2.ResNum()).c_str(), cm-cmapTerms.begin());
+      mprintf("DEBUG:\t\t%i - %i - %i - %i - %i %i\n", cm->A1()+1, cm->A2()+1, cm->A3()+1, cm->A4()+1, cm->A5()+1, cidx+1);
+      cm->SetIdx( cidx );
+    }
+    // If not already in cmapGrids, check cmapIn
+    if (cidx == -1) {
+      for (unsigned int idx = 0; idx != cmapIn.size(); idx++) {
+        if ( MatchesResName( cmapIn[idx].ResNames(), rn2.Truncated() ) ) {
+          if (atoms_[cm->A1()].Name() == cmapIn[idx].AtomNames()[0] &&
+              atoms_[cm->A2()].Name() == cmapIn[idx].AtomNames()[1] &&
+              atoms_[cm->A3()].Name() == cmapIn[idx].AtomNames()[2] &&
+              atoms_[cm->A4()].Name() == cmapIn[idx].AtomNames()[3] &&
+              atoms_[cm->A5()].Name() == cmapIn[idx].AtomNames()[4])
+          {
+            cidx = (int)idx;
+            CmapResNames.push_back( cmapIn[idx].ResNames() );
+            CmapAtomNames.push_back( cmapIn[idx].AtomNames() );
+            originalCmapIndices.push_back( idx );
+            break;
+          }
+        }
+      }
+      if (cidx > -1) {
+        mprintf("DEBUG: Potential new cmap %i found for %s (%li)\n", cidx, TruncResNameNum(A2.ResNum()).c_str(), cm-cmapTerms.begin());
+        mprintf("DEBUG:\t\t%i - %i - %i - %i - %i %i\n", cm->A1()+1, cm->A2()+1, cm->A3()+1, cm->A4()+1, cm->A5()+1, cidx+1);
+        //mprintf("DEBUG:\t\t%s - %s - %s - %s - %s\n",
+        //        AtomMaskName(dih->A1()).c_str(),
+        //        AtomMaskName(dih->A2()).c_str(),
+        //        AtomMaskName(dih->A3()).c_str(),
+        //        AtomMaskName(dih->A4()).c_str(),
+        //        AtomMaskName(a5).c_str());
+        cm->SetIdx( cidx );
+      }
+    }
+  } // END loop over cmap terms
+
+  return remap_cmap_indices(originalCmapIndices, cmapGrids, cmapTerms, cmapIn);
+}
+
+/** Assign CMAP parameters. Also generates CMAP terms from dihedrals. */
 int Topology::AssignCmapParams(DihedralArray const& allDih, CmapParmHolder const& cmapIn,
                                CmapGridArray& cmapGrids, CmapArray& cmapTerms)
 const
@@ -3415,8 +3537,9 @@ const
         cmapTerms.push_back( CmapType(dih->A1(), dih->A2(), dih->A3(), dih->A4(), a5, cidx) );
       }
     }
-  }
-  mprintf("DEBUG: Cmap parameter indices:\n");
+  } // END loop over dihedrals
+  return remap_cmap_indices(originalCmapIndices, cmapGrids, cmapTerms, cmapIn);
+/*  mprintf("DEBUG: Cmap parameter indices:\n");
   for (unsigned int idx = 0; idx < originalCmapIndices.size(); idx++)
     mprintf("DEBUG:\t\tCurrent idx=%i  Actual idx=%u\n", originalCmapIndices[idx], idx);
   if (originalCmapIndices.empty()) {
@@ -3446,7 +3569,7 @@ const
     }
     it->SetIdx( newIdx );
   }
-  return 0;
+  return 0;*/
 }
 
 /** Replace existing parameters with the given parameter set. */
@@ -3592,11 +3715,9 @@ int Topology::updateParams(ParameterSet& set0, ParameterSet const& set1) {
   }
   // CMAP
   if (UC.nCmapUpdated_ > 0) {
-    cmap_.clear();
     cmapGrid_.clear();
     mprintf("\tRegenerating CMAP parameters.\n");
-    AssignCmapParams(dihedrals_, set0.CMAP(), cmapGrid_, cmap_);
-    AssignCmapParams(dihedralsh_, set0.CMAP(), cmapGrid_, cmap_);
+    AssignCmapParams(cmap_, set0.CMAP(), cmapGrid_);
   }
   // TODO LJ14
 
diff --git a/src/Topology.h b/src/Topology.h
index ae8c8d17ba..146e800ad2 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -318,8 +318,13 @@ class Topology {
     DihedralArray AssignDihedralParm(DihedralParmHolder const&, ImproperParmHolder const&,
                                      ParmHolder<AtomType> const&, DihedralArray const&, bool);
 
-    /// Assign CMAP parameters
+    /// Remap CMAP parameter indices to match incoming parameter order
+    int remap_cmap_indices(std::vector<int>&, CmapGridArray&, CmapArray&, CmapParmHolder const&) const;
+    /// Assign CMAP parameters and terms
     int AssignCmapParams(DihedralArray const&, CmapParmHolder const&, CmapGridArray&, CmapArray&) const;
+    /// Assign CMAP parameters
+    int AssignCmapParams(CmapArray&, CmapParmHolder const&, CmapGridArray&) const;
+
 
     static const NonbondType LJ_EMPTY;
     std::vector<Atom> atoms_;

From 9c90bff99cd2887007ab54daa2f06f7374e8535b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 8 Mar 2024 15:58:20 -0500
Subject: [PATCH 0688/1492] New strategy - combine the old arrays in a manner
 that would be consistent with how parameters are usually assigned.

---
 src/Structure/GenerateConnectivityArrays.cpp | 57 ++++++++++++++++++++
 src/Structure/GenerateConnectivityArrays.h   |  3 ++
 src/Topology.cpp                             |  6 +++
 3 files changed, 66 insertions(+)

diff --git a/src/Structure/GenerateConnectivityArrays.cpp b/src/Structure/GenerateConnectivityArrays.cpp
index ed5f33ffa6..4e0bd6d8b0 100644
--- a/src/Structure/GenerateConnectivityArrays.cpp
+++ b/src/Structure/GenerateConnectivityArrays.cpp
@@ -312,3 +312,60 @@ void Cpptraj::Structure::GenerateAngleAndTorsionArraysFromBonds(AngleArray& angl
     enumerateDihedrals( dihedrals, it->A1(), it->A2(), atoms );
   }
 }
+
+/** Merge two separate bond arrays. */
+void Cpptraj::Structure::MergeBondArrays(BondArray& bondsOut,
+                                         BondArray const& bonds,
+                                         BondArray const& bondsh,
+                                         std::vector<Atom> const& atoms)
+{
+  bondsOut.clear();
+  bondsOut.reserve( bonds.size() + bondsh.size() );
+
+  BondArray::const_iterator bx = bonds.begin();
+  BondArray::const_iterator by = bondsh.begin();
+
+  while (bx != bonds.end() && by != bondsh.end()) {
+    // Which one goes next?
+    Atom const& bx0 = atoms[bx->A1()];
+    Atom const& by0 = atoms[by->A1()];
+    if (bx0.ResNum() == by0.ResNum()) {
+      if (bx->A1() == by->A1()) {
+        // Same residue, same A1. Lower A2 goes first.
+        if (by->A2() < bx->A2()) {
+          bondsOut.push_back( *by );
+          ++by;
+        } else {
+          bondsOut.push_back( *bx );
+          ++bx;
+        }
+      } else {
+        // Same residue. Higher A1 goes first. FIXME fix for scan direction forwards
+        if (by->A1() > bx->A1()) {
+          bondsOut.push_back( *by );
+          ++by;
+        } else {
+          bondsOut.push_back( *bx );
+          ++bx;
+        }
+      }
+    } else {
+      // Lower residue goes first.
+      if (by0.ResNum() < bx0.ResNum()) {
+        bondsOut.push_back( *by );
+        ++by;
+      } else {
+        bondsOut.push_back( *bx );
+        ++bx;
+      }
+    }
+  } // END loop over both
+  if (bx != bonds.end()) {
+    for (; bx != bonds.end(); ++bx)
+      bondsOut.push_back( *bx );
+  }
+  if (by != bondsh.end()) {
+    for (; by != bondsh.end(); ++by)
+      bondsOut.push_back( *by );
+  }
+}
diff --git a/src/Structure/GenerateConnectivityArrays.h b/src/Structure/GenerateConnectivityArrays.h
index 7efd766dc8..ce131873ec 100644
--- a/src/Structure/GenerateConnectivityArrays.h
+++ b/src/Structure/GenerateConnectivityArrays.h
@@ -26,6 +26,9 @@ DihedralArray GenerateDihedralArray(std::vector<Residue> const&, std::vector<Ato
 DihedralArray GenerateImproperArray(std::vector<Residue> const&, std::vector<Atom> const&);
 /// Generate angle and torsion arrays from bonds
 void GenerateAngleAndTorsionArraysFromBonds(AngleArray&, DihedralArray&, std::vector<Atom> const&, BondArray const&);
+/// Merge two bond arrays
+void MergeBondArrays(BondArray&, BondArray const&, BondArray const&, std::vector<Atom> const&);
+
 }
 }
 #endif
diff --git a/src/Topology.cpp b/src/Topology.cpp
index e5b0bb43ad..0cd4d02955 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2626,6 +2626,12 @@ int Topology::AppendTop(Topology const& NewTop) {
                                      res.Icode(), res.ChainId()) );
   }
   // Recreate bonds for the added atoms
+  // DEBUG TEST
+  BondArray allBonds;
+  Cpptraj::Structure::MergeBondArrays(allBonds, NewTop.Bonds(), NewTop.BondsH(), NewTop.Atoms() );
+  for (BondArray::const_iterator it = allBonds.begin(); it != allBonds.end(); ++it)
+    mprintf("DEBUG: Merged bond array %li : %i - %i\n",
+            it - allBonds.begin(), it->A1()+1, it->A2()+1);
   addBondsWithOffset( bonds_, NewTop.Bonds(), atomOffset, atoms_ );
   addBondsWithOffset( bondsh_, NewTop.BondsH(), atomOffset, atoms_ );
   addBondsWithOffset( chamber_.SetUB(), NewTop.chamber_.UB(), atomOffset, atoms_ );

From 134a27223903d23ae34627496c4f1e73d5ea7055 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 11 Mar 2024 11:19:32 -0400
Subject: [PATCH 0689/1492] Start separate file to merge parameters for
 topology arrays

---
 src/ParameterTypes.h    | 20 ++++++++++++++++++--
 src/Parm/CMakeLists.txt |  1 +
 src/Parm/parmdepend     |  3 ++-
 src/Parm/parmfiles      |  3 ++-
 src/cpptrajdepend       |  1 +
 5 files changed, 24 insertions(+), 4 deletions(-)

diff --git a/src/ParameterTypes.h b/src/ParameterTypes.h
index 39854e8d33..1b5eaeea75 100644
--- a/src/ParameterTypes.h
+++ b/src/ParameterTypes.h
@@ -56,7 +56,23 @@ class BondParmType {
     double rk_;
     double req_;
 };
-typedef std::vector<BondParmType> BondParmArray;
+/// Hold Array of bond parameters
+class BondParmArray {
+    typedef std::vector<BondParmType> BPArray;
+  public:
+    BondParmArray() {}
+    /// Resize the bond parm array
+    void resize(unsigned int n) { bondparm_.resize( n ); }
+    /// Clear the bond parm array
+    void clear() { bondparm_.clear(); }
+    /// \return reference to specified bond parameter
+    BondParmType& operator[](unsigned int idx) { return bondparm_[idx]; }
+
+    /// \return const reference to specified bond parameter
+    BondParmType const& operator[](unsigned int idx) const { return bondparm_[idx]; }
+  private:
+    BPArray bondparm_;
+};
 /// Hold bonded atom indices and parameter index
 class BondType {
   public:
@@ -81,7 +97,7 @@ class BondType {
     int a2_;
     int idx_;
 };
-/// Hold array of bond parameters
+/// Hold array of bonds
 class BondArray {
     typedef std::vector<BondType> BArray;
   public:
diff --git a/src/Parm/CMakeLists.txt b/src/Parm/CMakeLists.txt
index caeb638991..c89594c2af 100644
--- a/src/Parm/CMakeLists.txt
+++ b/src/Parm/CMakeLists.txt
@@ -1,4 +1,5 @@
 #CMake buildfile for CPPTRAJ Parm subdirectory.
 target_sources(cpptraj_common_obj PRIVATE
   ${CMAKE_CURRENT_LIST_DIR}/GB_Params.cpp
+  ${CMAKE_CURRENT_LIST_DIR}/Merge.cpp
 )
diff --git a/src/Parm/parmdepend b/src/Parm/parmdepend
index 7b6393f11b..42cf4aee8c 100644
--- a/src/Parm/parmdepend
+++ b/src/Parm/parmdepend
@@ -1 +1,2 @@
-GB_Params.o : GB_Params.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Parm/CmapParmHolder.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h GB_Params.h
+GB_Params.o : GB_Params.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h GB_Params.h
+Merge.o : Merge.cpp ../Atom.h ../Constants.h ../CpptrajStdio.h ../NameType.h ../ParameterTypes.h ../SymbolExporting.h Merge.h
diff --git a/src/Parm/parmfiles b/src/Parm/parmfiles
index 86a58ec097..83aa7c5ebb 100644
--- a/src/Parm/parmfiles
+++ b/src/Parm/parmfiles
@@ -1,3 +1,4 @@
 # Files for Parm subdirectory.
 PARM_SOURCES= \
-  GB_Params.cpp
+  GB_Params.cpp \
+  Merge.cpp
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 4126527033..535a6e8c49 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -405,6 +405,7 @@ Parallel.o : Parallel.cpp Parallel.h
 ParallelNetcdf.o : ParallelNetcdf.cpp CpptrajStdio.h Parallel.h ParallelNetcdf.h
 ParameterSet.o : ParameterSet.cpp AtomType.h CmapParmHolder.h Constants.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h TypeNameHolder.h UpdateParameters.h
 Parm/GB_Params.o : Parm/GB_Params.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/GB_Params.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Parm/Merge.o : Parm/Merge.cpp Atom.h Constants.h CpptrajStdio.h NameType.h ParameterTypes.h Parm/Merge.h SymbolExporting.h
 ParmFile.o : ParmFile.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h ParmIO.h Parm_Amber.h Parm_CIF.h Parm_CharmmPsf.h Parm_Gromacs.h Parm_Mol2.h Parm_PDB.h Parm_SDF.h Parm_Tinker.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Parm_Amber.o : Parm_Amber.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h ExclusionArray.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_Amber.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Parm_CIF.o : Parm_CIF.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h CIFfile.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_CIF.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h

From 4c4b23466f21e88cd88896ea9aed0b5af39d155e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 11 Mar 2024 11:55:46 -0400
Subject: [PATCH 0690/1492] Start trying to use new merge routine

---
 src/Exec_CompareEnergy.cpp |  4 +--
 src/Exec_CompareTop.cpp    |  2 +-
 src/ParameterTypes.h       | 14 ++++++++
 src/Parm/Merge.cpp         | 74 ++++++++++++++++++++++++++++++++++++++
 src/Parm/Merge.h           | 16 +++++++++
 src/Topology.cpp           | 13 ++++---
 6 files changed, 115 insertions(+), 8 deletions(-)
 create mode 100644 src/Parm/Merge.cpp
 create mode 100644 src/Parm/Merge.h

diff --git a/src/Exec_CompareEnergy.cpp b/src/Exec_CompareEnergy.cpp
index 4b83e2015b..c3acb523fe 100644
--- a/src/Exec_CompareEnergy.cpp
+++ b/src/Exec_CompareEnergy.cpp
@@ -146,8 +146,8 @@ const
 
   Eresults Ebond(bondDeltaE_, bondDeltaR_);
   CalcEnergy<BondType, BondParmType>(Ebond, bondout_,
-                                     frame0, commonBonds0_.Array(), top0.BondParm(),
-                                     frame1, commonBonds1_.Array(), top1.BondParm(),
+                                     frame0, commonBonds0_.Array(), top0.BondParm().Array(),
+                                     frame1, commonBonds1_.Array(), top1.BondParm().Array(),
                                      bondNames_, EBONDFXN);
   Ebond.Print( bondout_, "Bond" );
 }
diff --git a/src/Exec_CompareTop.cpp b/src/Exec_CompareTop.cpp
index 897a2e10f7..366bee4488 100644
--- a/src/Exec_CompareTop.cpp
+++ b/src/Exec_CompareTop.cpp
@@ -496,7 +496,7 @@ Exec::RetType Exec_CompareTop::Execute(CpptrajState& State, ArgList& argIn)
     // Bond parameters
     output.Printf("# Bond Parameters\n");
     Diff<BondParmType> diff_bndP;
-    diff_bndP.Compare( p1.BondParm(), p2.BondParm(), PrintBndP, output, p1, p2 );
+    diff_bndP.Compare( p1.BondParm().Array(), p2.BondParm().Array(), PrintBndP, output, p1, p2 );
   }
   if (cmp_ang) {
     // Angles
diff --git a/src/ParameterTypes.h b/src/ParameterTypes.h
index 1b5eaeea75..ce8cf6ce06 100644
--- a/src/ParameterTypes.h
+++ b/src/ParameterTypes.h
@@ -67,9 +67,23 @@ class BondParmArray {
     void clear() { bondparm_.clear(); }
     /// \return reference to specified bond parameter
     BondParmType& operator[](unsigned int idx) { return bondparm_[idx]; }
+    /// Add bond parameter
+    void push_back( BondParmType const& bp ) { bondparm_.push_back( bp ); }
 
     /// \return const reference to specified bond parameter
     BondParmType const& operator[](unsigned int idx) const { return bondparm_[idx]; }
+    /// \return true if no bond parameters
+    bool empty() const { return bondparm_.empty(); }
+    /// \return number of bond parameters
+    size_t size() const { return bondparm_.size(); }
+    /// Const iterator
+    typedef BPArray::const_iterator const_iterator;
+    /// \return const iterator to beginning
+    const_iterator begin() const { return bondparm_.begin(); }
+    /// \return const iterator to end
+    const_iterator end() const { return bondparm_.end(); }
+    /// \return Underlying array
+    std::vector<BondParmType> const& Array() const { return bondparm_; }
   private:
     BPArray bondparm_;
 };
diff --git a/src/Parm/Merge.cpp b/src/Parm/Merge.cpp
new file mode 100644
index 0000000000..34e1c624b2
--- /dev/null
+++ b/src/Parm/Merge.cpp
@@ -0,0 +1,74 @@
+#include "Merge.h"
+#include "../Atom.h"
+#include "../CpptrajStdio.h"
+#include "../ParameterTypes.h"
+
+static inline void append_bond(BondArray& bonds0,
+                               BondArray& bondsh0,
+                               BondParmArray& bp0,
+                               unsigned int atomOffset,
+                               BondType const& bnd1)
+{
+  mprintf("DEBUG: Bond from top1 %i - %i will be %i - %i in top0\n",
+          bnd1.A1()+1, bnd1.A2()+1, bnd1.A1()+1+atomOffset, bnd1.A2()+1+atomOffset);
+}
+
+/** Given bond/bond parameter arrays from top0 and bond/bond parameter
+  * arrays from top1, merge the bond arrays and consolidate the
+  * parameters.
+  */
+void Cpptraj::Parm::MergeBondArrays(BondArray& bonds0,
+                                    BondArray& bondsh0,
+                                    BondParmArray& bp0,
+                                    AtArray const& atoms0,
+                                    BondArray const& bonds1,
+                                    BondArray const& bondsh1,
+                                    BondParmArray const& bp1,
+                                    AtArray const& atoms1)
+{
+  // First index existing parameters
+
+  // Loop over separate bond arrays from top1 in the correct order
+  unsigned int atomOffset = atoms0.size();
+  BondArray::const_iterator bx = bonds1.begin();
+  BondArray::const_iterator by = bondsh1.begin();
+  while (bx != bonds1.end() && by != bondsh1.end()) {
+    // Which one goes next?
+    Atom const& bx0 = atoms1[bx->A1()];
+    Atom const& by0 = atoms1[by->A1()];
+    //bool has_parm_indices = (bx->Idx() != -1 && by->Idx() != -1);
+    if (bx0.ResNum() == by0.ResNum()) {
+      if (bx->A1() == by->A1()) {
+        // Same residue, same A1. Lower A2 goes first.
+        if (by->A2() < bx->A2()) {
+          append_bond( bonds0, bondsh0, bp0, atomOffset, *by );
+          ++by;
+        } else {
+          append_bond( bonds0, bondsh0, bp0, atomOffset, *bx );
+          ++bx;
+        }
+      } else {
+        // Both bonds in same residue, different A1.
+        // Higher A1 goes first.
+        // FIXME fix for scan direction forwards.
+        if (by->A1() > bx->A1()) {
+          append_bond( bonds0, bondsh0, bp0, atomOffset, *by );
+          ++by;
+        } else {
+          append_bond( bonds0, bondsh0, bp0, atomOffset, *bx );
+          ++bx;
+        }
+      }
+    } else {
+      // Lower residue goes first.
+      if (by0.ResNum() < bx0.ResNum()) {
+        append_bond( bonds0, bondsh0, bp0, atomOffset, *by );
+        ++by;
+      } else {
+        append_bond( bonds0, bondsh0, bp0, atomOffset, *bx );
+        ++bx;
+      }
+    }
+  } // END loop over both bond arrays from top1
+
+}
diff --git a/src/Parm/Merge.h b/src/Parm/Merge.h
new file mode 100644
index 0000000000..1bdcd05784
--- /dev/null
+++ b/src/Parm/Merge.h
@@ -0,0 +1,16 @@
+#ifndef INC_PARM_MERGE_H
+#define INC_PARM_MERGE_H
+#include <vector>
+class Atom;
+class BondArray;
+class BondParmArray;
+namespace Cpptraj {
+namespace Parm {
+/// Shorthand for array of Atoms
+typedef std::vector<Atom> AtArray;
+/// Merge two bond arrays and their parameters.
+void MergeBondArrays(BondArray&, BondArray&, BondParmArray&, AtArray const&,
+                     BondArray const&, BondArray const&, BondParmArray const&, AtArray const&);
+}
+}
+#endif
diff --git a/src/Topology.cpp b/src/Topology.cpp
index 0cd4d02955..a8da6b9dde 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -9,6 +9,7 @@
 #include "CharMask.h"
 #include "GuessAtomHybridization.h"
 #include "Structure/GenerateConnectivityArrays.h"
+#include "Parm/Merge.h"
 
 const NonbondType Topology::LJ_EMPTY = NonbondType();
 
@@ -2609,6 +2610,8 @@ int Topology::AppendTop(Topology const& NewTop) {
   int nLJparamsUpdated = UpdateParameters< ParmHolder<NonbondType> >( myNB, newNB, "LJ A-B", 1 ); // TODO verbose
   mprintf("\t%i atom types updated, %i LJ params updated.\n", nAtomTypeUpdated, nLJparamsUpdated);*/
 
+  Cpptraj::Parm::MergeBondArrays(bonds_, bondsh_, bondparm_, atoms_,
+                                 NewTop.Bonds(), NewTop.BondsH(), NewTop.BondParm(), NewTop.Atoms());
   // Append NewTop atoms to this topology.
   for (atom_iterator atom = NewTop.begin(); atom != NewTop.end(); ++atom)
   {
@@ -2627,11 +2630,11 @@ int Topology::AppendTop(Topology const& NewTop) {
   }
   // Recreate bonds for the added atoms
   // DEBUG TEST
-  BondArray allBonds;
-  Cpptraj::Structure::MergeBondArrays(allBonds, NewTop.Bonds(), NewTop.BondsH(), NewTop.Atoms() );
-  for (BondArray::const_iterator it = allBonds.begin(); it != allBonds.end(); ++it)
-    mprintf("DEBUG: Merged bond array %li : %i - %i\n",
-            it - allBonds.begin(), it->A1()+1, it->A2()+1);
+  //BondArray allBonds;
+  //Cpptraj::Structure::MergeBondArrays(allBonds, NewTop.Bonds(), NewTop.BondsH(), NewTop.Atoms() );
+  //for (BondArray::const_iterator it = allBonds.begin(); it != allBonds.end(); ++it)
+  //  mprintf("DEBUG: Merged bond array %li : %i - %i\n",
+  //          it - allBonds.begin(), it->A1()+1, it->A2()+1);
   addBondsWithOffset( bonds_, NewTop.Bonds(), atomOffset, atoms_ );
   addBondsWithOffset( bondsh_, NewTop.BondsH(), atomOffset, atoms_ );
   addBondsWithOffset( chamber_.SetUB(), NewTop.chamber_.UB(), atomOffset, atoms_ );

From c80a8c927c26c7b1bd8f858c386079a38f4aa271 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 11 Mar 2024 12:24:28 -0400
Subject: [PATCH 0691/1492] Bond assignment in same order as original

---
 src/Parm/Merge.cpp  | 79 ++++++++++++++++++++++++++++++++++++++++-----
 src/Parm/parmdepend |  2 +-
 src/Topology.cpp    |  6 ++--
 src/cpptrajdepend   |  4 +--
 4 files changed, 77 insertions(+), 14 deletions(-)

diff --git a/src/Parm/Merge.cpp b/src/Parm/Merge.cpp
index 34e1c624b2..90effa6f52 100644
--- a/src/Parm/Merge.cpp
+++ b/src/Parm/Merge.cpp
@@ -1,16 +1,73 @@
 #include "Merge.h"
 #include "../Atom.h"
 #include "../CpptrajStdio.h"
+#include "../ParameterHolders.h"
 #include "../ParameterTypes.h"
 
 static inline void append_bond(BondArray& bonds0,
                                BondArray& bondsh0,
                                BondParmArray& bp0,
                                unsigned int atomOffset,
-                               BondType const& bnd1)
+                               BondType const& bnd1,
+                               ParmHolder<int>& currentTypes0,
+                               ParmHolder<int> const& currentTypes1,
+                               BondParmArray const& bp1,
+                               std::vector<Atom> const& atoms1)
 {
   mprintf("DEBUG: Bond from top1 %i - %i will be %i - %i in top0\n",
           bnd1.A1()+1, bnd1.A2()+1, bnd1.A1()+1+atomOffset, bnd1.A2()+1+atomOffset);
+  Atom const& A1 = atoms1[bnd1.A1()];
+  Atom const& A2 = atoms1[bnd1.A2()];
+  // Do we have an existing parameter in top0
+  TypeNameHolder types(2);
+  types.AddName( A1.Type() );
+  types.AddName( A2.Type() );
+  bool found;
+  int idx = currentTypes0.FindParam(types, found);
+  if (!found) {
+    // No parameter yet.
+    // Do we have an existing parameter in top1
+    idx = currentTypes1.FindParam(types, found);
+    if (!found) {
+      // No parameter in either top.
+      idx = -1;
+    } else {
+      // Found a parameter in top1, add it to top0.
+      int newIdx = bp0.size();
+      bp0.push_back( bp1[idx] );
+      idx = newIdx;
+    }
+    // Add to existing parameters in top0.
+    // Do this even if a parameter was not found so we dont keep looking.
+    if (idx < 0)
+      mprintf("Warning: No bond parameters for types %s - %s\n", *(A1.Type()), *(A2.Type()));
+    currentTypes0.AddParm(types, idx, false);
+  }
+  // At this point we have either found a parameter or not.
+  if (A1.Element() == Atom::HYDROGEN ||
+      A2.Element() == Atom::HYDROGEN)
+    bondsh0.push_back( BondType(bnd1.A1(), bnd1.A2(), idx) );
+  else
+    bonds0.push_back( BondType(bnd1.A1(), bnd1.A2(), idx) );
+}
+
+static inline void index_bond_types(ParmHolder<int>& currentTypes,
+                                    BondArray const& bonds,
+                                    std::vector<Atom> const& atoms)
+{
+  for (BondArray::const_iterator bnd = bonds.begin(); bnd != bonds.end(); ++bnd)
+  {
+    if (bnd->Idx() > -1) {
+      TypeNameHolder types(2);
+      types.AddName( atoms[bnd->A1()].Type() );
+      types.AddName( atoms[bnd->A2()].Type() );
+      bool found;
+      currentTypes.FindParam(types, found);
+      if (!found) {
+        currentTypes.AddParm(types, bnd->Idx(), false);
+      }
+    }
+  }
 }
 
 /** Given bond/bond parameter arrays from top0 and bond/bond parameter
@@ -27,6 +84,11 @@ void Cpptraj::Parm::MergeBondArrays(BondArray& bonds0,
                                     AtArray const& atoms1)
 {
   // First index existing parameters
+  ParmHolder<int> currentTypes0, currentTypes1;
+  index_bond_types(currentTypes0, bonds0, atoms0);
+  index_bond_types(currentTypes0, bondsh0, atoms0);
+  index_bond_types(currentTypes1, bonds1, atoms1);
+  index_bond_types(currentTypes1, bondsh1, atoms1);
 
   // Loop over separate bond arrays from top1 in the correct order
   unsigned int atomOffset = atoms0.size();
@@ -40,11 +102,12 @@ void Cpptraj::Parm::MergeBondArrays(BondArray& bonds0,
     if (bx0.ResNum() == by0.ResNum()) {
       if (bx->A1() == by->A1()) {
         // Same residue, same A1. Lower A2 goes first.
-        if (by->A2() < bx->A2()) {
-          append_bond( bonds0, bondsh0, bp0, atomOffset, *by );
+        //if (by->A2() < bx->A2()) {
+        if (*by < *bx) {
+          append_bond( bonds0, bondsh0, bp0, atomOffset, *by, currentTypes0, currentTypes1, bp1, atoms1 );
           ++by;
         } else {
-          append_bond( bonds0, bondsh0, bp0, atomOffset, *bx );
+          append_bond( bonds0, bondsh0, bp0, atomOffset, *bx, currentTypes0, currentTypes1, bp1, atoms1 );
           ++bx;
         }
       } else {
@@ -52,20 +115,20 @@ void Cpptraj::Parm::MergeBondArrays(BondArray& bonds0,
         // Higher A1 goes first.
         // FIXME fix for scan direction forwards.
         if (by->A1() > bx->A1()) {
-          append_bond( bonds0, bondsh0, bp0, atomOffset, *by );
+          append_bond( bonds0, bondsh0, bp0, atomOffset, *by, currentTypes0, currentTypes1, bp1, atoms1 );
           ++by;
         } else {
-          append_bond( bonds0, bondsh0, bp0, atomOffset, *bx );
+          append_bond( bonds0, bondsh0, bp0, atomOffset, *bx, currentTypes0, currentTypes1, bp1, atoms1 );
           ++bx;
         }
       }
     } else {
       // Lower residue goes first.
       if (by0.ResNum() < bx0.ResNum()) {
-        append_bond( bonds0, bondsh0, bp0, atomOffset, *by );
+        append_bond( bonds0, bondsh0, bp0, atomOffset, *by, currentTypes0, currentTypes1, bp1, atoms1 );
         ++by;
       } else {
-        append_bond( bonds0, bondsh0, bp0, atomOffset, *bx );
+        append_bond( bonds0, bondsh0, bp0, atomOffset, *bx, currentTypes0, currentTypes1, bp1, atoms1 );
         ++bx;
       }
     }
diff --git a/src/Parm/parmdepend b/src/Parm/parmdepend
index 42cf4aee8c..775ded13cc 100644
--- a/src/Parm/parmdepend
+++ b/src/Parm/parmdepend
@@ -1,2 +1,2 @@
 GB_Params.o : GB_Params.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h GB_Params.h
-Merge.o : Merge.cpp ../Atom.h ../Constants.h ../CpptrajStdio.h ../NameType.h ../ParameterTypes.h ../SymbolExporting.h Merge.h
+Merge.o : Merge.cpp ../Atom.h ../Constants.h ../CpptrajStdio.h ../NameType.h ../ParameterHolders.h ../ParameterTypes.h ../SymbolExporting.h ../TypeNameHolder.h Merge.h
diff --git a/src/Topology.cpp b/src/Topology.cpp
index a8da6b9dde..b19246c00f 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2635,8 +2635,8 @@ int Topology::AppendTop(Topology const& NewTop) {
   //for (BondArray::const_iterator it = allBonds.begin(); it != allBonds.end(); ++it)
   //  mprintf("DEBUG: Merged bond array %li : %i - %i\n",
   //          it - allBonds.begin(), it->A1()+1, it->A2()+1);
-  addBondsWithOffset( bonds_, NewTop.Bonds(), atomOffset, atoms_ );
-  addBondsWithOffset( bondsh_, NewTop.BondsH(), atomOffset, atoms_ );
+  //addBondsWithOffset( bonds_, NewTop.Bonds(), atomOffset, atoms_ );
+  //addBondsWithOffset( bondsh_, NewTop.BondsH(), atomOffset, atoms_ );
   addBondsWithOffset( chamber_.SetUB(), NewTop.chamber_.UB(), atomOffset, atoms_ );
   addAnglesWithOffset( angles_, NewTop.Angles(), atomOffset );
   addAnglesWithOffset( anglesh_, NewTop.AnglesH(), atomOffset );
@@ -2669,7 +2669,7 @@ int Topology::AppendTop(Topology const& NewTop) {
 //#                                 dih->Type() ) );
   // Update parameters
   mprintf("DEBUG: Updating with new parameters.\n");
-  updateParams( oldParams, NewTop.GetParameters() );
+  //updateParams( oldParams, NewTop.GetParameters() );
 
   // EXTRA ATOM INFO
   TopVecAppend<NameType> appendNameType;
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 535a6e8c49..451682933a 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -405,7 +405,7 @@ Parallel.o : Parallel.cpp Parallel.h
 ParallelNetcdf.o : ParallelNetcdf.cpp CpptrajStdio.h Parallel.h ParallelNetcdf.h
 ParameterSet.o : ParameterSet.cpp AtomType.h CmapParmHolder.h Constants.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h TypeNameHolder.h UpdateParameters.h
 Parm/GB_Params.o : Parm/GB_Params.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/GB_Params.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Parm/Merge.o : Parm/Merge.cpp Atom.h Constants.h CpptrajStdio.h NameType.h ParameterTypes.h Parm/Merge.h SymbolExporting.h
+Parm/Merge.o : Parm/Merge.cpp Atom.h Constants.h CpptrajStdio.h NameType.h ParameterHolders.h ParameterTypes.h Parm/Merge.h SymbolExporting.h TypeNameHolder.h
 ParmFile.o : ParmFile.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h ParmIO.h Parm_Amber.h Parm_CIF.h Parm_CharmmPsf.h Parm_Gromacs.h Parm_Mol2.h Parm_PDB.h Parm_SDF.h Parm_Tinker.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Parm_Amber.o : Parm_Amber.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h ExclusionArray.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_Amber.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Parm_CIF.o : Parm_CIF.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h CIFfile.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_CIF.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
@@ -475,7 +475,7 @@ TextFormat.o : TextFormat.cpp StringRoutines.h TextFormat.h
 Timer.o : Timer.cpp CpptrajStdio.h Timer.h
 TinkerFile.o : TinkerFile.cpp ArgList.h Atom.h AtomMask.h Box.h BufferedLine.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TinkerFile.h Unit.h Vec3.h
 TopInfo.o : TopInfo.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h DistRoutines.h FileIO.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Mol.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h TopInfo.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Topology.o : Topology.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h GuessAtomHybridization.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/GenerateConnectivityArrays.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Topology.o : Topology.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h GuessAtomHybridization.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/Merge.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/GenerateConnectivityArrays.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 TorsionRoutines.o : TorsionRoutines.cpp Constants.h TorsionRoutines.h Vec3.h
 TrajFrameCounter.o : TrajFrameCounter.cpp ArgList.h CpptrajStdio.h TrajFrameCounter.h
 TrajIOarray.o : TrajIOarray.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryFile.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h

From 98b943d5f761a1203bba90d90be8a12ad4c7e501 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 11 Mar 2024 12:32:28 -0400
Subject: [PATCH 0692/1492] Fix offsets, do remaining bonds

---
 src/Parm/Merge.cpp | 15 ++++++++++++---
 1 file changed, 12 insertions(+), 3 deletions(-)

diff --git a/src/Parm/Merge.cpp b/src/Parm/Merge.cpp
index 90effa6f52..4672837094 100644
--- a/src/Parm/Merge.cpp
+++ b/src/Parm/Merge.cpp
@@ -4,6 +4,7 @@
 #include "../ParameterHolders.h"
 #include "../ParameterTypes.h"
 
+/// Append bnd1 to bonds0 arrays along with parameters
 static inline void append_bond(BondArray& bonds0,
                                BondArray& bondsh0,
                                BondParmArray& bp0,
@@ -46,11 +47,12 @@ static inline void append_bond(BondArray& bonds0,
   // At this point we have either found a parameter or not.
   if (A1.Element() == Atom::HYDROGEN ||
       A2.Element() == Atom::HYDROGEN)
-    bondsh0.push_back( BondType(bnd1.A1(), bnd1.A2(), idx) );
+    bondsh0.push_back( BondType(bnd1.A1()+atomOffset, bnd1.A2()+atomOffset, idx) );
   else
-    bonds0.push_back( BondType(bnd1.A1(), bnd1.A2(), idx) );
+    bonds0.push_back( BondType(bnd1.A1()+atomOffset, bnd1.A2()+atomOffset, idx) );
 }
 
+/// Index existing bond types in bond arrays
 static inline void index_bond_types(ParmHolder<int>& currentTypes,
                                     BondArray const& bonds,
                                     std::vector<Atom> const& atoms)
@@ -133,5 +135,12 @@ void Cpptraj::Parm::MergeBondArrays(BondArray& bonds0,
       }
     }
   } // END loop over both bond arrays from top1
-
+  if (bx != bonds1.end()) {
+    for (; bx != bonds1.end(); ++bx)
+      append_bond( bonds0, bondsh0, bp0, atomOffset, *bx, currentTypes0, currentTypes1, bp1, atoms1 );
+  }
+  if (by != bondsh1.end()) {
+    for (; by != bondsh1.end(); ++by)
+      append_bond( bonds0, bondsh0, bp0, atomOffset, *by, currentTypes0, currentTypes1, bp1, atoms1 );
+  }
 }

From cf7a30576980ded045e7e3ac9c5a99157c13e34d Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 11 Mar 2024 13:05:03 -0400
Subject: [PATCH 0693/1492] Do angle merge

---
 src/Exec_CompareEnergy.cpp |   4 +-
 src/Exec_CompareTop.cpp    |   2 +-
 src/ParameterTypes.h       |  32 +++++++-
 src/Parm/Merge.cpp         | 148 +++++++++++++++++++++++++++++++++++++
 src/Parm/Merge.h           |   6 ++
 src/Topology.cpp           |   7 +-
 6 files changed, 193 insertions(+), 6 deletions(-)

diff --git a/src/Exec_CompareEnergy.cpp b/src/Exec_CompareEnergy.cpp
index c3acb523fe..c6e4db9abf 100644
--- a/src/Exec_CompareEnergy.cpp
+++ b/src/Exec_CompareEnergy.cpp
@@ -234,8 +234,8 @@ const
 
   Eresults Eangle(angleDeltaE_, angleDeltaR_);
   CalcEnergy<AngleType, AngleParmType>(Eangle, angleout_,
-                                     frame0, commonAngles0_.Array(), top0.AngleParm(),
-                                     frame1, commonAngles1_.Array(), top1.AngleParm(),
+                                     frame0, commonAngles0_.Array(), top0.AngleParm().Array(),
+                                     frame1, commonAngles1_.Array(), top1.AngleParm().Array(),
                                      angleNames_, EANGFXN);
   Eangle.Print( angleout_, "Angle" );
 }
diff --git a/src/Exec_CompareTop.cpp b/src/Exec_CompareTop.cpp
index 366bee4488..4c84aead8d 100644
--- a/src/Exec_CompareTop.cpp
+++ b/src/Exec_CompareTop.cpp
@@ -512,7 +512,7 @@ Exec::RetType Exec_CompareTop::Execute(CpptrajState& State, ArgList& argIn)
     {
       output.Printf("# Angle Parameters\n");
       Diff<AngleParmType> diff_angP;
-      diff_angP.Compare( p1.AngleParm(), p2.AngleParm(), PrintAngP, output, p1, p2 );
+      diff_angP.Compare( p1.AngleParm().Array(), p2.AngleParm().Array(), PrintAngP, output, p1, p2 );
     }
   }
   if (cmp_dih) {
diff --git a/src/ParameterTypes.h b/src/ParameterTypes.h
index ce8cf6ce06..dc45e9b660 100644
--- a/src/ParameterTypes.h
+++ b/src/ParameterTypes.h
@@ -180,7 +180,37 @@ class AngleParmType {
     double tk_;  ///< Angle force constant in kcal/mol*rad^2
     double teq_; ///< Angle equilibirum value in rad
 };
-typedef std::vector<AngleParmType> AngleParmArray;
+/// Hold Array of angle parameters
+class AngleParmArray {
+    typedef std::vector<AngleParmType> APArray;
+  public:
+    AngleParmArray() {}
+    /// Resize the angle parm array
+    void resize(unsigned int n) { angleparm_.resize( n ); }
+    /// Clear the angle parm array
+    void clear() { angleparm_.clear(); }
+    /// \return reference to specified angle parameter
+    AngleParmType& operator[](unsigned int idx) { return angleparm_[idx]; }
+    /// Add angle parameter
+    void push_back( AngleParmType const& bp ) { angleparm_.push_back( bp ); }
+
+    /// \return const reference to specified angle parameter
+    AngleParmType const& operator[](unsigned int idx) const { return angleparm_[idx]; }
+    /// \return true if no angle parameters
+    bool empty() const { return angleparm_.empty(); }
+    /// \return number of angle parameters
+    size_t size() const { return angleparm_.size(); }
+    /// Const iterator
+    typedef APArray::const_iterator const_iterator;
+    /// \return const iterator to beginning
+    const_iterator begin() const { return angleparm_.begin(); }
+    /// \return const iterator to end
+    const_iterator end() const { return angleparm_.end(); }
+    /// \return Underlying array
+    std::vector<AngleParmType> const& Array() const { return angleparm_; }
+  private:
+    APArray angleparm_;
+};
 /// Hold angle atom indices and parameter index
 class AngleType {
   public:
diff --git a/src/Parm/Merge.cpp b/src/Parm/Merge.cpp
index 4672837094..cf6d950326 100644
--- a/src/Parm/Merge.cpp
+++ b/src/Parm/Merge.cpp
@@ -144,3 +144,151 @@ void Cpptraj::Parm::MergeBondArrays(BondArray& bonds0,
       append_bond( bonds0, bondsh0, bp0, atomOffset, *by, currentTypes0, currentTypes1, bp1, atoms1 );
   }
 }
+
+// -----------------------------------------------------------------------------
+/// Append ang1 to angles0 arrays along with parameters
+static inline void append_angle(AngleArray& angles0,
+                               AngleArray& anglesh0,
+                               AngleParmArray& ap0,
+                               unsigned int atomOffset,
+                               AngleType const& ang1,
+                               ParmHolder<int>& currentTypes0,
+                               ParmHolder<int> const& currentTypes1,
+                               AngleParmArray const& ap1,
+                               std::vector<Atom> const& atoms1)
+{
+  mprintf("DEBUG: Angle from top1 %i - %i  - %i will be %i - %i - %i in top0\n",
+          ang1.A1()+1, ang1.A2()+1, ang1.A3()+1, ang1.A1()+1+atomOffset, ang1.A2()+1+atomOffset, ang1.A3()+1+atomOffset);
+  Atom const& A1 = atoms1[ang1.A1()];
+  Atom const& A2 = atoms1[ang1.A2()];
+  Atom const& A3 = atoms1[ang1.A3()];
+  // Do we have an existing parameter in top0
+  TypeNameHolder types(3);
+  types.AddName( A1.Type() );
+  types.AddName( A2.Type() );
+  types.AddName( A3.Type() );
+  bool found;
+  int idx = currentTypes0.FindParam(types, found);
+  if (!found) {
+    // No parameter yet.
+    // Do we have an existing parameter in top1
+    idx = currentTypes1.FindParam(types, found);
+    if (!found) {
+      // No parameter in either top.
+      idx = -1;
+    } else {
+      // Found a parameter in top1, add it to top0.
+      int newIdx = ap0.size();
+      ap0.push_back( ap1[idx] );
+      idx = newIdx;
+    }
+    // Add to existing parameters in top0.
+    // Do this even if a parameter was not found so we dont keep looking.
+    if (idx < 0)
+      mprintf("Warning: No angle parameters for types %s - %s - %s\n", *(A1.Type()), *(A2.Type()), *(A3.Type()));
+    currentTypes0.AddParm(types, idx, false);
+  }
+  // At this point we have either found a parameter or not.
+  if (A1.Element() == Atom::HYDROGEN ||
+      A2.Element() == Atom::HYDROGEN ||
+      A3.Element() == Atom::HYDROGEN)
+    anglesh0.push_back( AngleType(ang1.A1()+atomOffset, ang1.A2()+atomOffset, ang1.A3()+atomOffset, idx) );
+  else
+    angles0.push_back( AngleType(ang1.A1()+atomOffset, ang1.A2()+atomOffset, ang1.A3()+atomOffset, idx) );
+}
+
+/// Index existing angle types in angle arrays
+static inline void index_angle_types(ParmHolder<int>& currentTypes,
+                                    AngleArray const& angles,
+                                    std::vector<Atom> const& atoms)
+{
+  for (AngleArray::const_iterator ang = angles.begin(); ang != angles.end(); ++ang)
+  {
+    if (ang->Idx() > -1) {
+      TypeNameHolder types(3);
+      types.AddName( atoms[ang->A1()].Type() );
+      types.AddName( atoms[ang->A2()].Type() );
+      types.AddName( atoms[ang->A3()].Type() );
+      bool found;
+      currentTypes.FindParam(types, found);
+      if (!found) {
+        currentTypes.AddParm(types, ang->Idx(), false);
+      }
+    }
+  }
+}
+
+/** Given angle/angle parameter arrays from top0 and angle/angle parameter
+  * arrays from top1, merge the angle arrays and consolidate the
+  * parameters.
+  */
+void Cpptraj::Parm::MergeAngleArrays(AngleArray& angles0,
+                                    AngleArray& anglesh0,
+                                    AngleParmArray& bp0,
+                                    AtArray const& atoms0,
+                                    AngleArray const& angles1,
+                                    AngleArray const& anglesh1,
+                                    AngleParmArray const& bp1,
+                                    AtArray const& atoms1)
+{
+  // First index existing parameters
+  ParmHolder<int> currentTypes0, currentTypes1;
+  index_angle_types(currentTypes0, angles0, atoms0);
+  index_angle_types(currentTypes0, anglesh0, atoms0);
+  index_angle_types(currentTypes1, angles1, atoms1);
+  index_angle_types(currentTypes1, anglesh1, atoms1);
+
+  // Loop over separate angle arrays from top1 in the correct order
+  unsigned int atomOffset = atoms0.size();
+  AngleArray::const_iterator bx = angles1.begin();
+  AngleArray::const_iterator by = anglesh1.begin();
+  while (bx != angles1.end() && by != anglesh1.end()) {
+    // Which one goes next?
+    Atom const& bx0 = atoms1[bx->A1()];
+    Atom const& by0 = atoms1[by->A1()];
+    //bool has_parm_indices = (bx->Idx() != -1 && by->Idx() != -1);
+    if (bx0.ResNum() == by0.ResNum()) {
+      if (bx->A1() == by->A1()) {
+        // Same residue, same A1. Lower A2 goes first.
+        //if (by->A2() < bx->A2()) {
+        if (*by < *bx) {
+          append_angle( angles0, anglesh0, bp0, atomOffset, *by, currentTypes0, currentTypes1, bp1, atoms1 );
+          ++by;
+        } else {
+          append_angle( angles0, anglesh0, bp0, atomOffset, *bx, currentTypes0, currentTypes1, bp1, atoms1 );
+          ++bx;
+        }
+      } else {
+        // Both angles in same residue, different A1.
+        // Higher A1 goes first.
+        // FIXME fix for scan direction forwards.
+        if (by->A1() > bx->A1()) {
+          append_angle( angles0, anglesh0, bp0, atomOffset, *by, currentTypes0, currentTypes1, bp1, atoms1 );
+          ++by;
+        } else {
+          append_angle( angles0, anglesh0, bp0, atomOffset, *bx, currentTypes0, currentTypes1, bp1, atoms1 );
+          ++bx;
+        }
+      }
+    } else {
+      // Lower residue goes first.
+      if (by0.ResNum() < bx0.ResNum()) {
+        append_angle( angles0, anglesh0, bp0, atomOffset, *by, currentTypes0, currentTypes1, bp1, atoms1 );
+        ++by;
+      } else {
+        append_angle( angles0, anglesh0, bp0, atomOffset, *bx, currentTypes0, currentTypes1, bp1, atoms1 );
+        ++bx;
+      }
+    }
+  } // END loop over both angle arrays from top1
+  if (bx != angles1.end()) {
+    for (; bx != angles1.end(); ++bx)
+      append_angle( angles0, anglesh0, bp0, atomOffset, *bx, currentTypes0, currentTypes1, bp1, atoms1 );
+  }
+  if (by != anglesh1.end()) {
+    for (; by != anglesh1.end(); ++by)
+      append_angle( angles0, anglesh0, bp0, atomOffset, *by, currentTypes0, currentTypes1, bp1, atoms1 );
+  }
+}
+
+
diff --git a/src/Parm/Merge.h b/src/Parm/Merge.h
index 1bdcd05784..73e33762cb 100644
--- a/src/Parm/Merge.h
+++ b/src/Parm/Merge.h
@@ -4,6 +4,8 @@
 class Atom;
 class BondArray;
 class BondParmArray;
+class AngleArray;
+class AngleParmArray;
 namespace Cpptraj {
 namespace Parm {
 /// Shorthand for array of Atoms
@@ -11,6 +13,10 @@ typedef std::vector<Atom> AtArray;
 /// Merge two bond arrays and their parameters.
 void MergeBondArrays(BondArray&, BondArray&, BondParmArray&, AtArray const&,
                      BondArray const&, BondArray const&, BondParmArray const&, AtArray const&);
+/// Merge two angle arrays and their parameters.
+void MergeAngleArrays(AngleArray&, AngleArray&, AngleParmArray&, AtArray const&,
+                      AngleArray const&, AngleArray const&, AngleParmArray const&, AtArray const&);
+
 }
 }
 #endif
diff --git a/src/Topology.cpp b/src/Topology.cpp
index b19246c00f..97cb99feb3 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2612,6 +2612,9 @@ int Topology::AppendTop(Topology const& NewTop) {
 
   Cpptraj::Parm::MergeBondArrays(bonds_, bondsh_, bondparm_, atoms_,
                                  NewTop.Bonds(), NewTop.BondsH(), NewTop.BondParm(), NewTop.Atoms());
+  Cpptraj::Parm::MergeAngleArrays(angles_, anglesh_, angleparm_, atoms_,
+                                  NewTop.Angles(), NewTop.AnglesH(), NewTop.AngleParm(), NewTop.Atoms());
+
   // Append NewTop atoms to this topology.
   for (atom_iterator atom = NewTop.begin(); atom != NewTop.end(); ++atom)
   {
@@ -2638,8 +2641,8 @@ int Topology::AppendTop(Topology const& NewTop) {
   //addBondsWithOffset( bonds_, NewTop.Bonds(), atomOffset, atoms_ );
   //addBondsWithOffset( bondsh_, NewTop.BondsH(), atomOffset, atoms_ );
   addBondsWithOffset( chamber_.SetUB(), NewTop.chamber_.UB(), atomOffset, atoms_ );
-  addAnglesWithOffset( angles_, NewTop.Angles(), atomOffset );
-  addAnglesWithOffset( anglesh_, NewTop.AnglesH(), atomOffset );
+  //addAnglesWithOffset( angles_, NewTop.Angles(), atomOffset );
+  //addAnglesWithOffset( anglesh_, NewTop.AnglesH(), atomOffset );
   addDihedralsWithOffset( dihedrals_, NewTop.Dihedrals(), atomOffset );
   addDihedralsWithOffset( dihedralsh_, NewTop.DihedralsH(), atomOffset );
   addDihedralsWithOffset( chamber_.SetImpropers(), NewTop.chamber_.Impropers(), atomOffset );

From e51c77601144cb9f1bfe6c28c6f865bf79db785b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 11 Mar 2024 14:33:10 -0400
Subject: [PATCH 0694/1492] Start creating a template

---
 src/Parm/Merge.cpp | 176 +++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 176 insertions(+)

diff --git a/src/Parm/Merge.cpp b/src/Parm/Merge.cpp
index cf6d950326..beb486c966 100644
--- a/src/Parm/Merge.cpp
+++ b/src/Parm/Merge.cpp
@@ -4,6 +4,179 @@
 #include "../ParameterHolders.h"
 #include "../ParameterTypes.h"
 
+static inline void printIdx(BondType const& bnd1, unsigned int atomOffset) {
+  mprintf("DEBUG: Bond from top1 %i - %i will be %i - %i in top0\n",
+          bnd1.A1()+1, bnd1.A2()+1, bnd1.A1()+1+atomOffset, bnd1.A2()+1+atomOffset);
+}
+
+static inline TypeNameHolder getTypes(bool& hasH, BondType const& bnd1, std::vector<Atom> const& atoms)
+{
+  Atom const& A1 = atoms[bnd1.A1()];
+  Atom const& A2 = atoms[bnd1.A2()];
+  if (A1.Element() == Atom::HYDROGEN ||
+      A1.Element() == Atom::HYDROGEN)
+    hasH = true;
+  else
+    hasH = false; 
+  TypeNameHolder types(2);
+  types.AddName( A1.Type() );
+  types.AddName( A2.Type() );
+  return types;
+}
+
+static inline BondType idxWithOffset(BondType const& bnd1, int idx, unsigned int atomOffset) {
+  return BondType(bnd1.A1()+atomOffset, bnd1.A2()+atomOffset, idx);
+}
+
+// -------------------------------------
+static inline void noParmWarning(TypeNameHolder const& types) {
+  if (types.Size() == 2)
+    mprintf("Warning: No bond parameters for types %s - %s\n", *(types[0]), *(types[1]));
+}
+
+// -------------------------------------
+template <class IdxType, class ParmType>
+class MergeTopArray
+{
+  public:
+    MergeTopArray() {}
+    /// Index type array
+    typedef std::vector<IdxType> IdxArray;
+    /// Parm type array
+    typedef std::vector<ParmType> ParmArray;
+  private:
+    /// Append term1 to arrayX0/arrayY0 arrays along with parameters
+    void append_term(IdxArray& arrayX0,
+                     IdxArray& arrayY0,
+                     ParmArray& p0,
+                     unsigned int atomOffset,
+                     IdxType const& term1,
+                     ParmHolder<int>& currentTypes0,
+                     ParmHolder<int> const& currentTypes1,
+                     ParmArray const& p1,
+                     std::vector<Atom> const& atoms1)
+    {
+      printIdx(term1, atomOffset);
+      bool hasH;
+      TypeNameHolder types = getTypes(hasH, term1, atoms1);
+      // Do we have an existing parameter in top0
+      bool found;
+      int idx = currentTypes0.FindParam(types, found);
+      if (!found) {
+        // No parameter yet.
+        // Do we have an existing parameter in top1
+        idx = currentTypes1.FindParam(types, found);
+        if (!found) {
+          // No parameter in either top.
+          idx = -1;
+        } else {
+          // Found a parameter in top1, add it to top0.
+          int newIdx = p0.size();
+          p0.push_back( p1[idx] );
+          idx = newIdx;
+        }
+        // Add to existing parameters in top0.
+        // Do this even if a parameter was not found so we dont keep looking.
+        if (idx < 0) noParmWarning(types);
+        currentTypes0.AddParm(types, idx, false);
+      }
+      // At this point we have either found a parameter or not.
+      if (hasH)
+        arrayY0.push_back( idxWithOffset(term1, idx, atomOffset) );
+      else
+        arrayX0.push_back( idxWithOffset(term1, idx, atomOffset) );
+    }
+
+    /// Index existing term types in term arrays
+    void index_term_types(ParmHolder<int>& currentTypes,
+                          IdxArray const& terms,
+                          std::vector<Atom> const& atoms)
+    {
+      bool hasH;
+      for (typename IdxArray::const_iterator term = terms.begin(); term != terms.end(); ++term)
+      {
+        if (term->Idx() > -1) {
+          TypeNameHolder types = getTypes(hasH, *term, atoms);
+          bool found;
+          currentTypes.FindParam(types, found);
+          if (!found) {
+            currentTypes.AddParm(types, term->Idx(), false);
+          }
+        }
+      }
+    }
+
+  public:
+    /// Merge two pairs of term/parm arrays
+    void MergeTermArrays(IdxArray& terms0,
+                         IdxArray& termsh0,
+                         ParmArray& p0,
+                         std::vector<Atom> const& atoms0,
+                         IdxArray const& terms1,
+                         IdxArray const& termsh1,
+                         ParmArray const& p1,
+                         std::vector<Atom> const& atoms1)
+    {
+      // First index existing parameters
+      ParmHolder<int> currentTypes0, currentTypes1;
+      index_term_types(currentTypes0, terms0, atoms0);
+      index_term_types(currentTypes0, termsh0, atoms0);
+      index_term_types(currentTypes1, terms1, atoms1);
+      index_term_types(currentTypes1, termsh1, atoms1);
+      // Loop over separate term arrays from top1 in the correct order
+      unsigned int atomOffset = atoms0.size();
+      typename IdxArray::const_iterator bx = terms1.begin();
+      typename IdxArray::const_iterator by = termsh1.begin();
+      while (bx != terms1.end() && by != termsh1.end()) {
+        // Which one goes next?
+        Atom const& bx0 = atoms1[bx->A1()];
+        Atom const& by0 = atoms1[by->A1()];
+        if (bx0.ResNum() == by0.ResNum()) {
+          if (bx->A1() == by->A1()) {
+            // Same residue, same A1. Lower A2 goes first.
+            if (*by < *bx) {
+              append_term( terms0, termsh0, p0, atomOffset, *by, currentTypes0, currentTypes1, p1, atoms1 );
+              ++by;
+            } else {
+              append_term( terms0, termsh0, p0, atomOffset, *bx, currentTypes0, currentTypes1, p1, atoms1 );
+              ++bx;
+            }
+          } else {
+            // Both terms in same residue, different A1.
+            // Higher A1 goes first.
+            // FIXME fix for scan direction forwards.
+            if (by->A1() > bx->A1()) {
+              append_term( terms0, termsh0, p0, atomOffset, *by, currentTypes0, currentTypes1, p1, atoms1 );
+              ++by;
+            } else {
+              append_term( terms0, termsh0, p0, atomOffset, *bx, currentTypes0, currentTypes1, p1, atoms1 );
+              ++bx;
+            }
+          }
+        } else {
+          // Lower residue goes first.
+          if (by0.ResNum() < bx0.ResNum()) {
+            append_term( terms0, termsh0, p0, atomOffset, *by, currentTypes0, currentTypes1, p1, atoms1 );
+            ++by;
+          } else {
+            append_term( terms0, termsh0, p0, atomOffset, *bx, currentTypes0, currentTypes1, p1, atoms1 );
+            ++bx;
+          }
+        }
+      } // END loop over both term arrays from top1
+      if (bx != terms1.end()) {
+        for (; bx != terms1.end(); ++bx)
+          append_term( terms0, termsh0, p0, atomOffset, *bx, currentTypes0, currentTypes1, p1, atoms1 );
+      }
+      if (by != termsh1.end()) {
+        for (; by != termsh1.end(); ++by)
+          append_term( terms0, termsh0, p0, atomOffset, *by, currentTypes0, currentTypes1, p1, atoms1 );
+      }
+    } // END MergeTermArrays
+
+}; // END MergeTopArray template class
+
+// -----------------------------------------------------------------------------
 /// Append bnd1 to bonds0 arrays along with parameters
 static inline void append_bond(BondArray& bonds0,
                                BondArray& bondsh0,
@@ -85,6 +258,9 @@ void Cpptraj::Parm::MergeBondArrays(BondArray& bonds0,
                                     BondParmArray const& bp1,
                                     AtArray const& atoms1)
 {
+  MergeTopArray<BondType, BondParmType> mergeBonds;
+
+
   // First index existing parameters
   ParmHolder<int> currentTypes0, currentTypes1;
   index_bond_types(currentTypes0, bonds0, atoms0);

From 07d670cf4526ba924c23db457c46db3f18ab1bfb Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 11 Mar 2024 14:40:40 -0400
Subject: [PATCH 0695/1492] Use the template

---
 src/Parm/Merge.cpp | 19 +++++++++++--------
 1 file changed, 11 insertions(+), 8 deletions(-)

diff --git a/src/Parm/Merge.cpp b/src/Parm/Merge.cpp
index beb486c966..573b2cdf7f 100644
--- a/src/Parm/Merge.cpp
+++ b/src/Parm/Merge.cpp
@@ -14,7 +14,7 @@ static inline TypeNameHolder getTypes(bool& hasH, BondType const& bnd1, std::vec
   Atom const& A1 = atoms[bnd1.A1()];
   Atom const& A2 = atoms[bnd1.A2()];
   if (A1.Element() == Atom::HYDROGEN ||
-      A1.Element() == Atom::HYDROGEN)
+      A2.Element() == Atom::HYDROGEN)
     hasH = true;
   else
     hasH = false; 
@@ -35,15 +35,15 @@ static inline void noParmWarning(TypeNameHolder const& types) {
 }
 
 // -------------------------------------
-template <class IdxType, class ParmType>
+template <class IdxType, class ParmType, class IdxArray, class ParmArray>
 class MergeTopArray
 {
   public:
     MergeTopArray() {}
     /// Index type array
-    typedef std::vector<IdxType> IdxArray;
+    //typedef std::vector<IdxType> IdxArray;
     /// Parm type array
-    typedef std::vector<ParmType> ParmArray;
+    //typedef std::vector<ParmType> ParmArray;
   private:
     /// Append term1 to arrayX0/arrayY0 arrays along with parameters
     void append_term(IdxArray& arrayX0,
@@ -177,6 +177,7 @@ class MergeTopArray
 }; // END MergeTopArray template class
 
 // -----------------------------------------------------------------------------
+/*
 /// Append bnd1 to bonds0 arrays along with parameters
 static inline void append_bond(BondArray& bonds0,
                                BondArray& bondsh0,
@@ -243,7 +244,7 @@ static inline void index_bond_types(ParmHolder<int>& currentTypes,
       }
     }
   }
-}
+}*/
 
 /** Given bond/bond parameter arrays from top0 and bond/bond parameter
   * arrays from top1, merge the bond arrays and consolidate the
@@ -258,8 +259,10 @@ void Cpptraj::Parm::MergeBondArrays(BondArray& bonds0,
                                     BondParmArray const& bp1,
                                     AtArray const& atoms1)
 {
-  MergeTopArray<BondType, BondParmType> mergeBonds;
-
+  MergeTopArray<BondType, BondParmType, BondArray, BondParmArray> mergeBonds;
+  mergeBonds.MergeTermArrays( bonds0, bondsh0, bp0, atoms0,
+                              bonds1, bondsh1, bp1, atoms1 );
+/*
 
   // First index existing parameters
   ParmHolder<int> currentTypes0, currentTypes1;
@@ -318,7 +321,7 @@ void Cpptraj::Parm::MergeBondArrays(BondArray& bonds0,
   if (by != bondsh1.end()) {
     for (; by != bondsh1.end(); ++by)
       append_bond( bonds0, bondsh0, bp0, atomOffset, *by, currentTypes0, currentTypes1, bp1, atoms1 );
-  }
+  }*/
 }
 
 // -----------------------------------------------------------------------------

From 060076cb2b43ef8f21b4e2c2abd20c52cdf8bff3 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 11 Mar 2024 14:45:47 -0400
Subject: [PATCH 0696/1492] Use template for angles

---
 src/Parm/Merge.cpp | 44 ++++++++++++++++++++++++++++++++++++++++----
 1 file changed, 40 insertions(+), 4 deletions(-)

diff --git a/src/Parm/Merge.cpp b/src/Parm/Merge.cpp
index 573b2cdf7f..0da876c860 100644
--- a/src/Parm/Merge.cpp
+++ b/src/Parm/Merge.cpp
@@ -4,6 +4,7 @@
 #include "../ParameterHolders.h"
 #include "../ParameterTypes.h"
 
+// ----- Bonds -------------------------
 static inline void printIdx(BondType const& bnd1, unsigned int atomOffset) {
   mprintf("DEBUG: Bond from top1 %i - %i will be %i - %i in top0\n",
           bnd1.A1()+1, bnd1.A2()+1, bnd1.A1()+1+atomOffset, bnd1.A2()+1+atomOffset);
@@ -28,10 +29,40 @@ static inline BondType idxWithOffset(BondType const& bnd1, int idx, unsigned int
   return BondType(bnd1.A1()+atomOffset, bnd1.A2()+atomOffset, idx);
 }
 
+// ----- Angles ------------------------
+static inline void printIdx(AngleType const& ang1, unsigned int atomOffset) {
+  mprintf("DEBUG: Angle from top1 %i - %i  - %i will be %i - %i - %i in top0\n",
+          ang1.A1()+1, ang1.A2()+1, ang1.A3()+1, ang1.A1()+1+atomOffset, ang1.A2()+1+atomOffset, ang1.A3()+1+atomOffset);
+}
+
+static inline TypeNameHolder getTypes(bool& hasH, AngleType const& ang1, std::vector<Atom> const& atoms)
+{
+  Atom const& A1 = atoms[ang1.A1()];
+  Atom const& A2 = atoms[ang1.A2()];
+  Atom const& A3 = atoms[ang1.A3()];
+  if (A1.Element() == Atom::HYDROGEN ||
+      A2.Element() == Atom::HYDROGEN ||
+      A3.Element() == Atom::HYDROGEN)
+    hasH = true;
+  else
+    hasH = false; 
+  TypeNameHolder types(3);
+  types.AddName( A1.Type() );
+  types.AddName( A2.Type() );
+  types.AddName( A3.Type() );
+  return types;
+}
+
+static inline AngleType idxWithOffset(AngleType const& ang1, int idx, unsigned int atomOffset) {
+  return AngleType(ang1.A1()+atomOffset, ang1.A2()+atomOffset, ang1.A3()+atomOffset, idx);
+}
+
 // -------------------------------------
 static inline void noParmWarning(TypeNameHolder const& types) {
   if (types.Size() == 2)
     mprintf("Warning: No bond parameters for types %s - %s\n", *(types[0]), *(types[1]));
+  else if (types.Size() == 3)
+    mprintf("Warning: No angle parameters for types %s - %s - %s\n", *(types[0]), *(types[1]), *(types[2]));
 }
 
 // -------------------------------------
@@ -325,6 +356,7 @@ void Cpptraj::Parm::MergeBondArrays(BondArray& bonds0,
 }
 
 // -----------------------------------------------------------------------------
+/*
 /// Append ang1 to angles0 arrays along with parameters
 static inline void append_angle(AngleArray& angles0,
                                AngleArray& anglesh0,
@@ -395,7 +427,7 @@ static inline void index_angle_types(ParmHolder<int>& currentTypes,
       }
     }
   }
-}
+}*/
 
 /** Given angle/angle parameter arrays from top0 and angle/angle parameter
   * arrays from top1, merge the angle arrays and consolidate the
@@ -403,13 +435,17 @@ static inline void index_angle_types(ParmHolder<int>& currentTypes,
   */
 void Cpptraj::Parm::MergeAngleArrays(AngleArray& angles0,
                                     AngleArray& anglesh0,
-                                    AngleParmArray& bp0,
+                                    AngleParmArray& ap0,
                                     AtArray const& atoms0,
                                     AngleArray const& angles1,
                                     AngleArray const& anglesh1,
-                                    AngleParmArray const& bp1,
+                                    AngleParmArray const& ap1,
                                     AtArray const& atoms1)
 {
+  MergeTopArray<AngleType, AngleParmType, AngleArray, AngleParmArray> mergeAngles;
+  mergeAngles.MergeTermArrays( angles0, anglesh0, ap0, atoms0,
+                               angles1, anglesh1, ap1, atoms1 );
+/*
   // First index existing parameters
   ParmHolder<int> currentTypes0, currentTypes1;
   index_angle_types(currentTypes0, angles0, atoms0);
@@ -467,7 +503,7 @@ void Cpptraj::Parm::MergeAngleArrays(AngleArray& angles0,
   if (by != anglesh1.end()) {
     for (; by != anglesh1.end(); ++by)
       append_angle( angles0, anglesh0, bp0, atomOffset, *by, currentTypes0, currentTypes1, bp1, atoms1 );
-  }
+  }*/
 }
 
 

From 9b1b8fed5bcda27c3e42234533f386f81754f6be Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 12 Mar 2024 10:12:10 -0400
Subject: [PATCH 0697/1492] Use template for dihedrals. Impropers need a
 separate routine since they are ordered differently

---
 src/Exec_CompareEnergy.cpp                   |   4 +-
 src/Exec_CompareTop.cpp                      |   2 +-
 src/ParameterTypes.h                         |  46 +-
 src/Parm/Merge.cpp                           | 497 +++++++++----------
 src/Parm/Merge.h                             |   5 +
 src/Structure/GenerateConnectivityArrays.cpp |   4 +-
 src/Topology.cpp                             |   6 +-
 7 files changed, 284 insertions(+), 280 deletions(-)

diff --git a/src/Exec_CompareEnergy.cpp b/src/Exec_CompareEnergy.cpp
index c6e4db9abf..8828194159 100644
--- a/src/Exec_CompareEnergy.cpp
+++ b/src/Exec_CompareEnergy.cpp
@@ -324,8 +324,8 @@ const
 
   Eresults Edihedral(dihedralDeltaE_, dihedralDeltaR_);
   CalcEnergy<DihedralType, DihedralParmType>(Edihedral, dihedralout_,
-                                             frame0, commonDihedrals0_.Array(), top0.DihedralParm(),
-                                             frame1, commonDihedrals1_.Array(), top1.DihedralParm(),
+                                             frame0, commonDihedrals0_.Array(), top0.DihedralParm().Array(),
+                                             frame1, commonDihedrals1_.Array(), top1.DihedralParm().Array(),
                                              dihedralNames_, EDIHFXN);
   Edihedral.Print( dihedralout_, "Dihedral" );
 }
diff --git a/src/Exec_CompareTop.cpp b/src/Exec_CompareTop.cpp
index 4c84aead8d..7eabd6eb07 100644
--- a/src/Exec_CompareTop.cpp
+++ b/src/Exec_CompareTop.cpp
@@ -529,7 +529,7 @@ Exec::RetType Exec_CompareTop::Execute(CpptrajState& State, ArgList& argIn)
     {
       output.Printf("# Dihedral Parameters\n");
       Diff<DihedralParmType> diff_dihP;
-      diff_dihP.Compare( p1.DihedralParm(), p2.DihedralParm(), PrintDihP, output, p1, p2 );
+      diff_dihP.Compare( p1.DihedralParm().Array(), p2.DihedralParm().Array(), PrintDihP, output, p1, p2 );
     }
   }
   output.CloseFile();
diff --git a/src/ParameterTypes.h b/src/ParameterTypes.h
index dc45e9b660..36040a179c 100644
--- a/src/ParameterTypes.h
+++ b/src/ParameterTypes.h
@@ -321,7 +321,51 @@ class DihedralParmType {
     double scee_;
     double scnb_;
 };
-typedef std::vector<DihedralParmType> DihedralParmArray;
+/// Hold Array of dihedral parameters
+class DihedralParmArray {
+    typedef std::vector<DihedralParmType> DPArray;
+  public:
+    /// CONSTRUCTOR
+    DihedralParmArray() {}
+    /// CONSTRUCTOR - Number of parameters, parameter
+    DihedralParmArray(unsigned int n, DihedralParmType const& dp) :
+      dihedralparm_(n, dp) {}
+    /// Resize the dihedral parm array
+    void resize(unsigned int n) { dihedralparm_.resize( n ); }
+    /// Clear the dihedral parm array
+    void clear() { dihedralparm_.clear(); }
+    /// \return reference to specified dihedral parameter
+    DihedralParmType& operator[](unsigned int idx) { return dihedralparm_[idx]; }
+    /// Add dihedral parameter
+    void push_back( DihedralParmType const& bp ) { dihedralparm_.push_back( bp ); }
+    /// Iterator
+    typedef DPArray::iterator iterator;
+    /// \return iterator to beginning
+    iterator begin() { return dihedralparm_.begin(); }
+    /// \return iterator to end
+    iterator end() { return dihedralparm_.end(); }
+
+    /// \return const reference to specified dihedral parameter
+    DihedralParmType const& operator[](unsigned int idx) const { return dihedralparm_[idx]; }
+    /// \return true if no dihedral parameters
+    bool empty() const { return dihedralparm_.empty(); }
+    /// \return number of dihedral parameters
+    size_t size() const { return dihedralparm_.size(); }
+    /// Const iterator
+    typedef DPArray::const_iterator const_iterator;
+    /// \return const iterator to beginning
+    const_iterator begin() const { return dihedralparm_.begin(); }
+    /// \return const iterator to end
+    const_iterator end() const { return dihedralparm_.end(); }
+    /// \return Underlying array
+    std::vector<DihedralParmType> const& Array() const { return dihedralparm_; }
+    /// \return Last dihedral parameter added
+    DihedralParmType const& back() const { return dihedralparm_.back(); }
+    /// \return First dihedral parameter added
+    DihedralParmType const& front() const { return dihedralparm_.front(); }
+  private:
+    DPArray dihedralparm_;
+};
 /// Hold dihedral atom indices and parameter index
 /** Dihedrals can be marked normal (A1-A2-A3-A4), end (meaning 1-4 calc should
   * be skipped to avoid overcounting, e.g. for dihedrals with multiple 
diff --git a/src/Parm/Merge.cpp b/src/Parm/Merge.cpp
index 0da876c860..3ff64acb3b 100644
--- a/src/Parm/Merge.cpp
+++ b/src/Parm/Merge.cpp
@@ -3,6 +3,7 @@
 #include "../CpptrajStdio.h"
 #include "../ParameterHolders.h"
 #include "../ParameterTypes.h"
+#include "../StringRoutines.h" // integerToString
 
 // ----- Bonds -------------------------
 static inline void printIdx(BondType const& bnd1, unsigned int atomOffset) {
@@ -10,7 +11,7 @@ static inline void printIdx(BondType const& bnd1, unsigned int atomOffset) {
           bnd1.A1()+1, bnd1.A2()+1, bnd1.A1()+1+atomOffset, bnd1.A2()+1+atomOffset);
 }
 
-static inline TypeNameHolder getTypes(bool& hasH, BondType const& bnd1, std::vector<Atom> const& atoms)
+static inline TypeNameHolder getTypes(bool& hasH, BondType const& bnd1, std::vector<Atom> const& atoms, BondParmArray const& parms)
 {
   Atom const& A1 = atoms[bnd1.A1()];
   Atom const& A2 = atoms[bnd1.A2()];
@@ -31,11 +32,11 @@ static inline BondType idxWithOffset(BondType const& bnd1, int idx, unsigned int
 
 // ----- Angles ------------------------
 static inline void printIdx(AngleType const& ang1, unsigned int atomOffset) {
-  mprintf("DEBUG: Angle from top1 %i - %i  - %i will be %i - %i - %i in top0\n",
+  mprintf("DEBUG: Angle from top1 %i - %i - %i will be %i - %i - %i in top0\n",
           ang1.A1()+1, ang1.A2()+1, ang1.A3()+1, ang1.A1()+1+atomOffset, ang1.A2()+1+atomOffset, ang1.A3()+1+atomOffset);
 }
 
-static inline TypeNameHolder getTypes(bool& hasH, AngleType const& ang1, std::vector<Atom> const& atoms)
+static inline TypeNameHolder getTypes(bool& hasH, AngleType const& ang1, std::vector<Atom> const& atoms, AngleParmArray const& parms)
 {
   Atom const& A1 = atoms[ang1.A1()];
   Atom const& A2 = atoms[ang1.A2()];
@@ -57,12 +58,76 @@ static inline AngleType idxWithOffset(AngleType const& ang1, int idx, unsigned i
   return AngleType(ang1.A1()+atomOffset, ang1.A2()+atomOffset, ang1.A3()+atomOffset, idx);
 }
 
+// ----- Dihedrals ---------------------
+static inline void printIdx(DihedralType const& dih1, unsigned int atomOffset) {
+  //mprintf("DEBUG: Dihedral from top1 %i - %i - %i - %i will be %i - %i - %i - %i in top0\n",
+  //        dih1.A1()+1, dih1.A2()+1, dih1.A3()+1, dih1.A4()+1,
+  //        dih1.A1()+1+atomOffset, dih1.A2()+1+atomOffset, dih1.A3()+1+atomOffset, dih1.A4()+1+atomOffset);
+  const char* desc;
+  if (dih1.IsImproper())
+    desc = "Improper";
+  else
+    desc = "Dihedral";
+  mprintf("DEBUG: %s %i - %i - %i - %i ( %i %i %i %i )\n", desc,
+          dih1.A1()+1, dih1.A2()+1, dih1.A3()+1, dih1.A4()+1,
+          dih1.A1()*3, dih1.A2()*3, dih1.A3()*3, dih1.A4()*3);
+}
+
+/** Dihedrals are tricky because they can have multiple parameters for
+  * the same 4 types. Have the 5th be a pseudo-type based on the
+  * multiplicity (or improper status).
+  */
+static inline TypeNameHolder getTypes(bool& hasH, DihedralType const& dih1, std::vector<Atom> const& atoms, DihedralParmArray const& parms)
+{
+  Atom const& A1 = atoms[dih1.A1()];
+  Atom const& A2 = atoms[dih1.A2()];
+  Atom const& A3 = atoms[dih1.A3()];
+  Atom const& A4 = atoms[dih1.A4()];
+  if (A1.Element() == Atom::HYDROGEN ||
+      A2.Element() == Atom::HYDROGEN ||
+      A3.Element() == Atom::HYDROGEN ||
+      A4.Element() == Atom::HYDROGEN)
+    hasH = true;
+  else
+    hasH = false; 
+  TypeNameHolder types(5);
+  types.AddName( A1.Type() );
+  types.AddName( A2.Type() );
+  types.AddName( A3.Type() );
+  types.AddName( A4.Type() );
+  if (dih1.IsImproper()) {
+    // Sanity check TODO is this needed?
+    if (dih1.Idx() != -1 && (parms[dih1.Idx()].Pn() < 1 || parms[dih1.Idx()].Pn() < 1))
+      mprinterr("Internal Error: Improper has a multiplicity != 1\n");
+    types.AddName( "0" );
+  } else {
+    if (dih1.Idx() < 0)
+      types.AddName( "1" );
+    else
+      types.AddName( integerToString( (int)parms[dih1.Idx()].Pn() ) );
+  }
+  return types;
+}
+
+static inline DihedralType idxWithOffset(DihedralType const& dih1, int idx, unsigned int atomOffset) {
+  return DihedralType(dih1.A1()+atomOffset, dih1.A2()+atomOffset, dih1.A3()+atomOffset, dih1.A4()+atomOffset, dih1.Type(), idx);
+}
+
 // -------------------------------------
 static inline void noParmWarning(TypeNameHolder const& types) {
   if (types.Size() == 2)
     mprintf("Warning: No bond parameters for types %s - %s\n", *(types[0]), *(types[1]));
   else if (types.Size() == 3)
     mprintf("Warning: No angle parameters for types %s - %s - %s\n", *(types[0]), *(types[1]), *(types[2]));
+  else if (types.Size() == 4)
+    mprintf("Warning: No dihedral parameters for types %s - %s - %s - %s\n", *(types[0]), *(types[1]), *(types[2]), *(types[3]));
+}
+
+// -------------------------------------
+static inline void printTypes(TypeNameHolder const& types) {
+  for (TypeNameHolder::const_iterator it = types.begin(); it != types.end(); ++it)
+    mprintf(" %s", *(*it) );
+  mprintf("\n");
 }
 
 // -------------------------------------
@@ -70,7 +135,9 @@ template <class IdxType, class ParmType, class IdxArray, class ParmArray>
 class MergeTopArray
 {
   public:
-    MergeTopArray() {}
+    MergeTopArray() : merge_with_existing_(false) {}
+    /// Indicate parameters from top1 already present in top0 should not be added as new
+    void SetMergeWithExisting(bool b) { merge_with_existing_ = b; }
     /// Index type array
     //typedef std::vector<IdxType> IdxArray;
     /// Parm type array
@@ -89,28 +156,50 @@ class MergeTopArray
     {
       printIdx(term1, atomOffset);
       bool hasH;
-      TypeNameHolder types = getTypes(hasH, term1, atoms1);
+      TypeNameHolder types = getTypes(hasH, term1, atoms1, p1);
+      mprintf("DEBUG: Looking for types in top0:");
+      printTypes( types ); // DEBUG
       // Do we have an existing parameter in top0
       bool found;
       int idx = currentTypes0.FindParam(types, found);
       if (!found) {
         // No parameter yet.
         // Do we have an existing parameter in top1
+        mprintf("DEBUG: Not found in top0. Looking in top1.\n");
         idx = currentTypes1.FindParam(types, found);
         if (!found) {
+          mprintf("DEBUG: No parameters.\n");
           // No parameter in either top.
           idx = -1;
         } else {
+          mprintf("DEBUG: Found in top1 index %i, adding to top0.\n", idx+1);
           // Found a parameter in top1, add it to top0.
-          int newIdx = p0.size();
-          p0.push_back( p1[idx] );
-          idx = newIdx;
+          int oldIdx = -1;
+          if (merge_with_existing_) {
+            // Check if parameter exists
+            for (unsigned int i0 = 0; i0 != p0.size(); i0++) {
+              if (p1[idx] == p0[i0]) {
+                oldIdx = (int)i0;
+                break;
+              }
+            }
+          }
+          if (oldIdx == -1) {
+            // Do not merge with existing or does not yet exist.
+            int newIdx = p0.size();
+            p0.push_back( p1[idx] );
+            idx = newIdx;
+          } else {
+            mprintf("DEBUG: Parm from top1 already present in top0 at position %i\n", oldIdx+1);
+            idx = oldIdx;
+          }
         }
         // Add to existing parameters in top0.
         // Do this even if a parameter was not found so we dont keep looking.
         if (idx < 0) noParmWarning(types);
         currentTypes0.AddParm(types, idx, false);
       }
+      mprintf("DEBUG: top0 parameter index is %i\n", idx+1);
       // At this point we have either found a parameter or not.
       if (hasH)
         arrayY0.push_back( idxWithOffset(term1, idx, atomOffset) );
@@ -121,13 +210,14 @@ class MergeTopArray
     /// Index existing term types in term arrays
     void index_term_types(ParmHolder<int>& currentTypes,
                           IdxArray const& terms,
-                          std::vector<Atom> const& atoms)
+                          std::vector<Atom> const& atoms,
+                          ParmArray const& parms)
     {
       bool hasH;
       for (typename IdxArray::const_iterator term = terms.begin(); term != terms.end(); ++term)
       {
         if (term->Idx() > -1) {
-          TypeNameHolder types = getTypes(hasH, *term, atoms);
+          TypeNameHolder types = getTypes(hasH, *term, atoms, parms);
           bool found;
           currentTypes.FindParam(types, found);
           if (!found) {
@@ -150,10 +240,10 @@ class MergeTopArray
     {
       // First index existing parameters
       ParmHolder<int> currentTypes0, currentTypes1;
-      index_term_types(currentTypes0, terms0, atoms0);
-      index_term_types(currentTypes0, termsh0, atoms0);
-      index_term_types(currentTypes1, terms1, atoms1);
-      index_term_types(currentTypes1, termsh1, atoms1);
+      index_term_types(currentTypes0, terms0, atoms0, p0);
+      index_term_types(currentTypes0, termsh0, atoms0, p0);
+      index_term_types(currentTypes1, terms1, atoms1, p1);
+      index_term_types(currentTypes1, termsh1, atoms1, p1);
       // Loop over separate term arrays from top1 in the correct order
       unsigned int atomOffset = atoms0.size();
       typename IdxArray::const_iterator bx = terms1.begin();
@@ -204,78 +294,79 @@ class MergeTopArray
           append_term( terms0, termsh0, p0, atomOffset, *by, currentTypes0, currentTypes1, p1, atoms1 );
       }
     } // END MergeTermArrays
+    /// Merge two pairs of improper arrays
+    /** Impropers have different ordering based first on the central (3rd) atom */
+    void MergeImproperArrays(DihedralArray& terms0,
+                             DihedralArray& termsh0,
+                             DihedralParmArray& p0,
+                             std::vector<Atom> const& atoms0,
+                             DihedralArray const& terms1,
+                             DihedralArray const& termsh1,
+                             DihedralParmArray const& p1,
+                             std::vector<Atom> const& atoms1)
+    {
+      // First index existing parameters
+      ParmHolder<int> currentTypes0, currentTypes1;
+      index_term_types(currentTypes0, terms0, atoms0, p0);
+      index_term_types(currentTypes0, termsh0, atoms0, p0);
+      index_term_types(currentTypes1, terms1, atoms1, p1);
+      index_term_types(currentTypes1, termsh1, atoms1, p1);
+      // Loop over separate term arrays from top1 in the correct order
+      unsigned int atomOffset = atoms0.size();
+      typename IdxArray::const_iterator bx = terms1.begin();
+      typename IdxArray::const_iterator by = termsh1.begin();
+      while (bx != terms1.end() && by != termsh1.end()) {
+        // Which one goes next?
+        Atom const& bx0 = atoms1[bx->A1()];
+        Atom const& by0 = atoms1[by->A1()];
+        if (bx0.ResNum() == by0.ResNum()) {
+          if (bx->A3() == by->A3()) {
+            // Same residue, same A3. Lower A1 goes first.
+            if (*by < *bx) {
+              append_term( terms0, termsh0, p0, atomOffset, *by, currentTypes0, currentTypes1, p1, atoms1 );
+              ++by;
+            } else {
+              append_term( terms0, termsh0, p0, atomOffset, *bx, currentTypes0, currentTypes1, p1, atoms1 );
+              ++bx;
+            }
+          } else {
+            // Both terms in same residue, different A3.
+            // Higher A3 goes first.
+            // FIXME fix for scan direction forwards.
+            if (by->A3() > bx->A3()) {
+              append_term( terms0, termsh0, p0, atomOffset, *by, currentTypes0, currentTypes1, p1, atoms1 );
+              ++by;
+            } else {
+              append_term( terms0, termsh0, p0, atomOffset, *bx, currentTypes0, currentTypes1, p1, atoms1 );
+              ++bx;
+            }
+          }
+        } else {
+          // Lower residue goes first.
+          if (by0.ResNum() < bx0.ResNum()) {
+            append_term( terms0, termsh0, p0, atomOffset, *by, currentTypes0, currentTypes1, p1, atoms1 );
+            ++by;
+          } else {
+            append_term( terms0, termsh0, p0, atomOffset, *bx, currentTypes0, currentTypes1, p1, atoms1 );
+            ++bx;
+          }
+        }
+      } // END loop over both term arrays from top1
+      if (bx != terms1.end()) {
+        for (; bx != terms1.end(); ++bx)
+          append_term( terms0, termsh0, p0, atomOffset, *bx, currentTypes0, currentTypes1, p1, atoms1 );
+      }
+      if (by != termsh1.end()) {
+        for (; by != termsh1.end(); ++by)
+          append_term( terms0, termsh0, p0, atomOffset, *by, currentTypes0, currentTypes1, p1, atoms1 );
+      }
+    } // END MergeTermArrays
+  private:
+    bool merge_with_existing_;
 
 }; // END MergeTopArray template class
 
 // -----------------------------------------------------------------------------
-/*
-/// Append bnd1 to bonds0 arrays along with parameters
-static inline void append_bond(BondArray& bonds0,
-                               BondArray& bondsh0,
-                               BondParmArray& bp0,
-                               unsigned int atomOffset,
-                               BondType const& bnd1,
-                               ParmHolder<int>& currentTypes0,
-                               ParmHolder<int> const& currentTypes1,
-                               BondParmArray const& bp1,
-                               std::vector<Atom> const& atoms1)
-{
-  mprintf("DEBUG: Bond from top1 %i - %i will be %i - %i in top0\n",
-          bnd1.A1()+1, bnd1.A2()+1, bnd1.A1()+1+atomOffset, bnd1.A2()+1+atomOffset);
-  Atom const& A1 = atoms1[bnd1.A1()];
-  Atom const& A2 = atoms1[bnd1.A2()];
-  // Do we have an existing parameter in top0
-  TypeNameHolder types(2);
-  types.AddName( A1.Type() );
-  types.AddName( A2.Type() );
-  bool found;
-  int idx = currentTypes0.FindParam(types, found);
-  if (!found) {
-    // No parameter yet.
-    // Do we have an existing parameter in top1
-    idx = currentTypes1.FindParam(types, found);
-    if (!found) {
-      // No parameter in either top.
-      idx = -1;
-    } else {
-      // Found a parameter in top1, add it to top0.
-      int newIdx = bp0.size();
-      bp0.push_back( bp1[idx] );
-      idx = newIdx;
-    }
-    // Add to existing parameters in top0.
-    // Do this even if a parameter was not found so we dont keep looking.
-    if (idx < 0)
-      mprintf("Warning: No bond parameters for types %s - %s\n", *(A1.Type()), *(A2.Type()));
-    currentTypes0.AddParm(types, idx, false);
-  }
-  // At this point we have either found a parameter or not.
-  if (A1.Element() == Atom::HYDROGEN ||
-      A2.Element() == Atom::HYDROGEN)
-    bondsh0.push_back( BondType(bnd1.A1()+atomOffset, bnd1.A2()+atomOffset, idx) );
-  else
-    bonds0.push_back( BondType(bnd1.A1()+atomOffset, bnd1.A2()+atomOffset, idx) );
-}
-
-/// Index existing bond types in bond arrays
-static inline void index_bond_types(ParmHolder<int>& currentTypes,
-                                    BondArray const& bonds,
-                                    std::vector<Atom> const& atoms)
-{
-  for (BondArray::const_iterator bnd = bonds.begin(); bnd != bonds.end(); ++bnd)
-  {
-    if (bnd->Idx() > -1) {
-      TypeNameHolder types(2);
-      types.AddName( atoms[bnd->A1()].Type() );
-      types.AddName( atoms[bnd->A2()].Type() );
-      bool found;
-      currentTypes.FindParam(types, found);
-      if (!found) {
-        currentTypes.AddParm(types, bnd->Idx(), false);
-      }
-    }
-  }
-}*/
 
 /** Given bond/bond parameter arrays from top0 and bond/bond parameter
   * arrays from top1, merge the bond arrays and consolidate the
@@ -293,141 +384,9 @@ void Cpptraj::Parm::MergeBondArrays(BondArray& bonds0,
   MergeTopArray<BondType, BondParmType, BondArray, BondParmArray> mergeBonds;
   mergeBonds.MergeTermArrays( bonds0, bondsh0, bp0, atoms0,
                               bonds1, bondsh1, bp1, atoms1 );
-/*
-
-  // First index existing parameters
-  ParmHolder<int> currentTypes0, currentTypes1;
-  index_bond_types(currentTypes0, bonds0, atoms0);
-  index_bond_types(currentTypes0, bondsh0, atoms0);
-  index_bond_types(currentTypes1, bonds1, atoms1);
-  index_bond_types(currentTypes1, bondsh1, atoms1);
-
-  // Loop over separate bond arrays from top1 in the correct order
-  unsigned int atomOffset = atoms0.size();
-  BondArray::const_iterator bx = bonds1.begin();
-  BondArray::const_iterator by = bondsh1.begin();
-  while (bx != bonds1.end() && by != bondsh1.end()) {
-    // Which one goes next?
-    Atom const& bx0 = atoms1[bx->A1()];
-    Atom const& by0 = atoms1[by->A1()];
-    //bool has_parm_indices = (bx->Idx() != -1 && by->Idx() != -1);
-    if (bx0.ResNum() == by0.ResNum()) {
-      if (bx->A1() == by->A1()) {
-        // Same residue, same A1. Lower A2 goes first.
-        //if (by->A2() < bx->A2()) {
-        if (*by < *bx) {
-          append_bond( bonds0, bondsh0, bp0, atomOffset, *by, currentTypes0, currentTypes1, bp1, atoms1 );
-          ++by;
-        } else {
-          append_bond( bonds0, bondsh0, bp0, atomOffset, *bx, currentTypes0, currentTypes1, bp1, atoms1 );
-          ++bx;
-        }
-      } else {
-        // Both bonds in same residue, different A1.
-        // Higher A1 goes first.
-        // FIXME fix for scan direction forwards.
-        if (by->A1() > bx->A1()) {
-          append_bond( bonds0, bondsh0, bp0, atomOffset, *by, currentTypes0, currentTypes1, bp1, atoms1 );
-          ++by;
-        } else {
-          append_bond( bonds0, bondsh0, bp0, atomOffset, *bx, currentTypes0, currentTypes1, bp1, atoms1 );
-          ++bx;
-        }
-      }
-    } else {
-      // Lower residue goes first.
-      if (by0.ResNum() < bx0.ResNum()) {
-        append_bond( bonds0, bondsh0, bp0, atomOffset, *by, currentTypes0, currentTypes1, bp1, atoms1 );
-        ++by;
-      } else {
-        append_bond( bonds0, bondsh0, bp0, atomOffset, *bx, currentTypes0, currentTypes1, bp1, atoms1 );
-        ++bx;
-      }
-    }
-  } // END loop over both bond arrays from top1
-  if (bx != bonds1.end()) {
-    for (; bx != bonds1.end(); ++bx)
-      append_bond( bonds0, bondsh0, bp0, atomOffset, *bx, currentTypes0, currentTypes1, bp1, atoms1 );
-  }
-  if (by != bondsh1.end()) {
-    for (; by != bondsh1.end(); ++by)
-      append_bond( bonds0, bondsh0, bp0, atomOffset, *by, currentTypes0, currentTypes1, bp1, atoms1 );
-  }*/
 }
 
 // -----------------------------------------------------------------------------
-/*
-/// Append ang1 to angles0 arrays along with parameters
-static inline void append_angle(AngleArray& angles0,
-                               AngleArray& anglesh0,
-                               AngleParmArray& ap0,
-                               unsigned int atomOffset,
-                               AngleType const& ang1,
-                               ParmHolder<int>& currentTypes0,
-                               ParmHolder<int> const& currentTypes1,
-                               AngleParmArray const& ap1,
-                               std::vector<Atom> const& atoms1)
-{
-  mprintf("DEBUG: Angle from top1 %i - %i  - %i will be %i - %i - %i in top0\n",
-          ang1.A1()+1, ang1.A2()+1, ang1.A3()+1, ang1.A1()+1+atomOffset, ang1.A2()+1+atomOffset, ang1.A3()+1+atomOffset);
-  Atom const& A1 = atoms1[ang1.A1()];
-  Atom const& A2 = atoms1[ang1.A2()];
-  Atom const& A3 = atoms1[ang1.A3()];
-  // Do we have an existing parameter in top0
-  TypeNameHolder types(3);
-  types.AddName( A1.Type() );
-  types.AddName( A2.Type() );
-  types.AddName( A3.Type() );
-  bool found;
-  int idx = currentTypes0.FindParam(types, found);
-  if (!found) {
-    // No parameter yet.
-    // Do we have an existing parameter in top1
-    idx = currentTypes1.FindParam(types, found);
-    if (!found) {
-      // No parameter in either top.
-      idx = -1;
-    } else {
-      // Found a parameter in top1, add it to top0.
-      int newIdx = ap0.size();
-      ap0.push_back( ap1[idx] );
-      idx = newIdx;
-    }
-    // Add to existing parameters in top0.
-    // Do this even if a parameter was not found so we dont keep looking.
-    if (idx < 0)
-      mprintf("Warning: No angle parameters for types %s - %s - %s\n", *(A1.Type()), *(A2.Type()), *(A3.Type()));
-    currentTypes0.AddParm(types, idx, false);
-  }
-  // At this point we have either found a parameter or not.
-  if (A1.Element() == Atom::HYDROGEN ||
-      A2.Element() == Atom::HYDROGEN ||
-      A3.Element() == Atom::HYDROGEN)
-    anglesh0.push_back( AngleType(ang1.A1()+atomOffset, ang1.A2()+atomOffset, ang1.A3()+atomOffset, idx) );
-  else
-    angles0.push_back( AngleType(ang1.A1()+atomOffset, ang1.A2()+atomOffset, ang1.A3()+atomOffset, idx) );
-}
-
-/// Index existing angle types in angle arrays
-static inline void index_angle_types(ParmHolder<int>& currentTypes,
-                                    AngleArray const& angles,
-                                    std::vector<Atom> const& atoms)
-{
-  for (AngleArray::const_iterator ang = angles.begin(); ang != angles.end(); ++ang)
-  {
-    if (ang->Idx() > -1) {
-      TypeNameHolder types(3);
-      types.AddName( atoms[ang->A1()].Type() );
-      types.AddName( atoms[ang->A2()].Type() );
-      types.AddName( atoms[ang->A3()].Type() );
-      bool found;
-      currentTypes.FindParam(types, found);
-      if (!found) {
-        currentTypes.AddParm(types, ang->Idx(), false);
-      }
-    }
-  }
-}*/
 
 /** Given angle/angle parameter arrays from top0 and angle/angle parameter
   * arrays from top1, merge the angle arrays and consolidate the
@@ -445,65 +404,59 @@ void Cpptraj::Parm::MergeAngleArrays(AngleArray& angles0,
   MergeTopArray<AngleType, AngleParmType, AngleArray, AngleParmArray> mergeAngles;
   mergeAngles.MergeTermArrays( angles0, anglesh0, ap0, atoms0,
                                angles1, anglesh1, ap1, atoms1 );
-/*
-  // First index existing parameters
-  ParmHolder<int> currentTypes0, currentTypes1;
-  index_angle_types(currentTypes0, angles0, atoms0);
-  index_angle_types(currentTypes0, anglesh0, atoms0);
-  index_angle_types(currentTypes1, angles1, atoms1);
-  index_angle_types(currentTypes1, anglesh1, atoms1);
+}
 
-  // Loop over separate angle arrays from top1 in the correct order
-  unsigned int atomOffset = atoms0.size();
-  AngleArray::const_iterator bx = angles1.begin();
-  AngleArray::const_iterator by = anglesh1.begin();
-  while (bx != angles1.end() && by != anglesh1.end()) {
-    // Which one goes next?
-    Atom const& bx0 = atoms1[bx->A1()];
-    Atom const& by0 = atoms1[by->A1()];
-    //bool has_parm_indices = (bx->Idx() != -1 && by->Idx() != -1);
-    if (bx0.ResNum() == by0.ResNum()) {
-      if (bx->A1() == by->A1()) {
-        // Same residue, same A1. Lower A2 goes first.
-        //if (by->A2() < bx->A2()) {
-        if (*by < *bx) {
-          append_angle( angles0, anglesh0, bp0, atomOffset, *by, currentTypes0, currentTypes1, bp1, atoms1 );
-          ++by;
-        } else {
-          append_angle( angles0, anglesh0, bp0, atomOffset, *bx, currentTypes0, currentTypes1, bp1, atoms1 );
-          ++bx;
-        }
-      } else {
-        // Both angles in same residue, different A1.
-        // Higher A1 goes first.
-        // FIXME fix for scan direction forwards.
-        if (by->A1() > bx->A1()) {
-          append_angle( angles0, anglesh0, bp0, atomOffset, *by, currentTypes0, currentTypes1, bp1, atoms1 );
-          ++by;
-        } else {
-          append_angle( angles0, anglesh0, bp0, atomOffset, *bx, currentTypes0, currentTypes1, bp1, atoms1 );
-          ++bx;
-        }
-      }
-    } else {
-      // Lower residue goes first.
-      if (by0.ResNum() < bx0.ResNum()) {
-        append_angle( angles0, anglesh0, bp0, atomOffset, *by, currentTypes0, currentTypes1, bp1, atoms1 );
-        ++by;
-      } else {
-        append_angle( angles0, anglesh0, bp0, atomOffset, *bx, currentTypes0, currentTypes1, bp1, atoms1 );
-        ++bx;
-      }
-    }
-  } // END loop over both angle arrays from top1
-  if (bx != angles1.end()) {
-    for (; bx != angles1.end(); ++bx)
-      append_angle( angles0, anglesh0, bp0, atomOffset, *bx, currentTypes0, currentTypes1, bp1, atoms1 );
-  }
-  if (by != anglesh1.end()) {
-    for (; by != anglesh1.end(); ++by)
-      append_angle( angles0, anglesh0, bp0, atomOffset, *by, currentTypes0, currentTypes1, bp1, atoms1 );
-  }*/
+// -----------------------------------------------------------------------------
+static inline void separate_impropers(DihedralArray const& dihIn, DihedralArray& dihOut, DihedralArray& impOut)
+{
+  for (DihedralArray::const_iterator it = dihIn.begin(); it != dihIn.end(); ++it)
+    if (it->IsImproper())
+      impOut.push_back( *it );
+    else
+      dihOut.push_back( *it );
+}
+
+static inline void merge_impropers(DihedralArray& dihOut, DihedralArray& dihIn, DihedralArray& impIn) {
+  dihOut.reserve( dihIn.size() + impIn.size() );
+  dihOut = dihIn;
+  dihIn.clear();
+  for (DihedralArray::const_iterator it = impIn.begin(); it != impIn.end(); ++it)
+    dihOut.push_back( *it  );
+  impIn.clear();
 }
 
+/** Given dihedral/dihedral parameter arrays from top0 and dihedral/dihedral
+  * parameter arrays from top1, merge the dihedral arrays and consolidate the
+  * parameters.
+  */
+void Cpptraj::Parm::MergeDihedralArrays(DihedralArray& dihedrals0,
+                                    DihedralArray& dihedralsh0,
+                                    DihedralParmArray& ap0,
+                                    AtArray const& atoms0,
+                                    DihedralArray const& dihedrals1,
+                                    DihedralArray const& dihedralsh1,
+                                    DihedralParmArray const& ap1,
+                                    AtArray const& atoms1)
+{
+  // Separate any impropers.
+  DihedralArray dih0, dihH0, imp0, impH0;
+  separate_impropers(dihedrals0, dih0, imp0);
+  dihedrals0.clear();
+  separate_impropers(dihedralsh0, dihH0, impH0);
+  dihedralsh0.clear();
+
+  DihedralArray dih1, dihH1, imp1, impH1;
+  separate_impropers(dihedrals1, dih1, imp1);
+  separate_impropers(dihedralsh1, dihH1, impH1);
+
+  MergeTopArray<DihedralType, DihedralParmType, DihedralArray, DihedralParmArray> mergeDihedrals;
+  mergeDihedrals.SetMergeWithExisting( true );
+  mergeDihedrals.MergeTermArrays( dih0, dihH0, ap0, atoms0,
+                                  dih1, dihH1, ap1, atoms1 );
+  mergeDihedrals.MergeImproperArrays( imp0, impH0, ap0, atoms0,
+                                      imp1, impH1, ap1, atoms1 );
+  // Re-merge
+  merge_impropers(dihedrals0, dih0, imp0);
+  merge_impropers(dihedralsh0, dihH0, impH0);
+}
 
diff --git a/src/Parm/Merge.h b/src/Parm/Merge.h
index 73e33762cb..7b6f3dbada 100644
--- a/src/Parm/Merge.h
+++ b/src/Parm/Merge.h
@@ -6,6 +6,8 @@ class BondArray;
 class BondParmArray;
 class AngleArray;
 class AngleParmArray;
+class DihedralArray;
+class DihedralParmArray;
 namespace Cpptraj {
 namespace Parm {
 /// Shorthand for array of Atoms
@@ -16,6 +18,9 @@ void MergeBondArrays(BondArray&, BondArray&, BondParmArray&, AtArray const&,
 /// Merge two angle arrays and their parameters.
 void MergeAngleArrays(AngleArray&, AngleArray&, AngleParmArray&, AtArray const&,
                       AngleArray const&, AngleArray const&, AngleParmArray const&, AtArray const&);
+/// Merge two dihedral arrays and their parameters.
+void MergeDihedralArrays(DihedralArray&, DihedralArray&, DihedralParmArray&, AtArray const&,
+                         DihedralArray const&, DihedralArray const&, DihedralParmArray const&, AtArray const&);
 
 }
 }
diff --git a/src/Structure/GenerateConnectivityArrays.cpp b/src/Structure/GenerateConnectivityArrays.cpp
index 4e0bd6d8b0..bf95695dc1 100644
--- a/src/Structure/GenerateConnectivityArrays.cpp
+++ b/src/Structure/GenerateConnectivityArrays.cpp
@@ -213,7 +213,7 @@ DihedralArray Cpptraj::Structure::GenerateImproperArray(std::vector<Residue> con
                                                         std::vector<Atom> const& atoms)
 {
   DihedralArray out;
-//  int iidx = 0;
+  int iidx = 0;
   for (std::vector<Residue>::const_iterator res = residues.begin(); res != residues.end(); ++res)
   {
     int start, end, offset;
@@ -229,7 +229,7 @@ DihedralArray Cpptraj::Structure::GenerateImproperArray(std::vector<Residue> con
               int iat1 = AJ.BondIdxArray()[bidx0];
               int iat2 = AJ.BondIdxArray()[bidx1];
               int iat4 = AJ.BondIdxArray()[bidx2];
-              //mprintf("DEBUG: IMPROPER  i= %i  %i - %i - %i - %i (%i %i %i %i)\n", iidx++, iat1+1, iat2+1, iat3+1, iat4+1, iat1*3, iat2*3, iat3*3, iat4*3);
+              mprintf("DEBUG: IMPROPER  i= %i  %i - %i - %i - %i (%i %i %i %i)\n", iidx++, iat1+1, iat2+1, iat3+1, iat4+1, iat1*3, iat2*3, iat3*3, iat4*3);
               int indices[3];
               indices[0] = iat1;
               indices[1] = iat2;
diff --git a/src/Topology.cpp b/src/Topology.cpp
index 97cb99feb3..689b50b826 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2614,6 +2614,8 @@ int Topology::AppendTop(Topology const& NewTop) {
                                  NewTop.Bonds(), NewTop.BondsH(), NewTop.BondParm(), NewTop.Atoms());
   Cpptraj::Parm::MergeAngleArrays(angles_, anglesh_, angleparm_, atoms_,
                                   NewTop.Angles(), NewTop.AnglesH(), NewTop.AngleParm(), NewTop.Atoms());
+  Cpptraj::Parm::MergeDihedralArrays(dihedrals_, dihedralsh_, dihedralparm_, atoms_,
+                                  NewTop.Dihedrals(), NewTop.DihedralsH(), NewTop.DihedralParm(), NewTop.Atoms());
 
   // Append NewTop atoms to this topology.
   for (atom_iterator atom = NewTop.begin(); atom != NewTop.end(); ++atom)
@@ -2643,8 +2645,8 @@ int Topology::AppendTop(Topology const& NewTop) {
   addBondsWithOffset( chamber_.SetUB(), NewTop.chamber_.UB(), atomOffset, atoms_ );
   //addAnglesWithOffset( angles_, NewTop.Angles(), atomOffset );
   //addAnglesWithOffset( anglesh_, NewTop.AnglesH(), atomOffset );
-  addDihedralsWithOffset( dihedrals_, NewTop.Dihedrals(), atomOffset );
-  addDihedralsWithOffset( dihedralsh_, NewTop.DihedralsH(), atomOffset );
+  //addDihedralsWithOffset( dihedrals_, NewTop.Dihedrals(), atomOffset );
+  //addDihedralsWithOffset( dihedralsh_, NewTop.DihedralsH(), atomOffset );
   addDihedralsWithOffset( chamber_.SetImpropers(), NewTop.chamber_.Impropers(), atomOffset );
   for (CmapArray::const_iterator cm = NewTop.Cmap().begin(); cm != NewTop.Cmap().end(); ++cm)
     cmap_.push_back( CmapType(cm->A1() + atomOffset,

From 5e5f8c3c661cca4d211e08bf0f8197e64d6e0914 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 12 Mar 2024 15:51:17 -0400
Subject: [PATCH 0698/1492] Start merging cmaps

---
 src/ParameterTypes.h |  67 +++++++++++++++++++-
 src/Parm/Merge.cpp   | 141 ++++++++++++++++++++++++++++++++++++++++---
 src/Parm/Merge.h     |   8 +++
 src/Topology.cpp     |  15 +++--
 4 files changed, 215 insertions(+), 16 deletions(-)

diff --git a/src/ParameterTypes.h b/src/ParameterTypes.h
index 36040a179c..c5e499a977 100644
--- a/src/ParameterTypes.h
+++ b/src/ParameterTypes.h
@@ -899,7 +899,42 @@ class CmapGridType {
     std::vector<std::string> resNames_;  ///< Residue name(s) this CMAP will apply to
     std::vector<std::string> atomNames_; ///< 5x atom names this CMAP will apply to
 };
-typedef std::vector<CmapGridType> CmapGridArray;
+/// Hold an array of CMAP grids
+class CmapGridArray {
+    typedef std::vector<CmapGridType> CGarray;
+  public:
+    CmapGridArray() {}
+    /// \return number of CMAP grids
+    size_t size() const { return cmapgrids_.size(); }
+    /// \return CMAP grid at specified index
+    CmapGridType const& operator[](unsigned int idx) const { return cmapgrids_[idx]; }
+    /// const iterator
+    typedef CGarray::const_iterator const_iterator;
+    /// const begin iterator
+    const_iterator begin() const { return cmapgrids_.begin(); }
+    /// const end iterator
+    const_iterator end() const { return cmapgrids_.end(); }
+    /// \return True if no CMAP grids
+    bool empty() const { return cmapgrids_.empty(); }
+
+    /// \return CMAP grid at specified index
+    CmapGridType& operator[](unsigned int idx) { return cmapgrids_[idx]; }
+    /// Add CMAP grid
+    void push_back(CmapGridType const& cg) { cmapgrids_.push_back( cg ); }
+    /// Clear all grids
+    void clear() { cmapgrids_.clear(); }
+    /// Reserve for specified # of grids
+    void reserve(size_t n) { cmapgrids_.reserve(n); }
+    /// iterator
+    typedef CGarray::iterator iterator;
+    /// begin iterator
+    iterator begin() { return cmapgrids_.begin(); }
+    /// end iterator
+    iterator end() { return cmapgrids_.end(); }
+
+  private:
+    CGarray cmapgrids_;
+};
 /// Hold CMAP atom indices and corresponding grid index
 class CmapType {
   public:
@@ -922,7 +957,35 @@ class CmapType {
     int a5_;
     int idx_;
 };
-typedef std::vector<CmapType> CmapArray;
+/// Hold an array of CMAP terms
+class CmapArray {
+    typedef std::vector<CmapType> CArray;
+  public:
+    CmapArray() {}
+    /// \return number of CMAP terms
+    size_t size() const { return cmap_.size(); }
+    /// const iterator
+    typedef CArray::const_iterator const_iterator;
+    /// const begin iterator
+    const_iterator begin() const { return cmap_.begin(); }
+    /// const end iterator
+    const_iterator end() const { return cmap_.end(); }
+    /// \return True if no CMAP terms
+    bool empty() const { return cmap_.empty(); }
+
+    /// Add CMAP term
+    void push_back(CmapType const& cm) { cmap_.push_back( cm ); }
+    /// Clear all terms 
+    void clear() { cmap_.clear(); }
+    /// iterator
+    typedef CArray::iterator iterator;
+    /// begin iterator
+    iterator begin() { return cmap_.begin(); }
+    /// end iterator
+    iterator end() { return cmap_.end(); }
+  private:
+    CArray cmap_;
+};
 /// Hold CHAMBER parameters
 class ChamberParmType {
     typedef std::vector<std::string> Sarray;
diff --git a/src/Parm/Merge.cpp b/src/Parm/Merge.cpp
index 3ff64acb3b..d4033dd3a7 100644
--- a/src/Parm/Merge.cpp
+++ b/src/Parm/Merge.cpp
@@ -3,6 +3,7 @@
 #include "../CpptrajStdio.h"
 #include "../ParameterHolders.h"
 #include "../ParameterTypes.h"
+#include "../Residue.h"
 #include "../StringRoutines.h" // integerToString
 
 // ----- Bonds -------------------------
@@ -119,8 +120,13 @@ static inline void noParmWarning(TypeNameHolder const& types) {
     mprintf("Warning: No bond parameters for types %s - %s\n", *(types[0]), *(types[1]));
   else if (types.Size() == 3)
     mprintf("Warning: No angle parameters for types %s - %s - %s\n", *(types[0]), *(types[1]), *(types[2]));
-  else if (types.Size() == 4)
-    mprintf("Warning: No dihedral parameters for types %s - %s - %s - %s\n", *(types[0]), *(types[1]), *(types[2]), *(types[3]));
+  else if (types.Size() == 5) {
+    if (types[4] == "0")
+      mprintf("Warning: No improper parameters for types %s - %s - %s - %s\n", *(types[0]), *(types[1]), *(types[2]), *(types[3]));
+    else
+      mprintf("Warning: No dihedral parameters for types %s - %s - %s - %s multiplicity %s\n", *(types[0]), *(types[1]), *(types[2]), *(types[3]), *(types[4]));
+  } else if (types.Size() == 6)
+    mprintf("Warning: No CMAP parameters for res %s atoms %s - %s - %s - %s - %s\n", *(types[0]), *(types[1]), *(types[2]), *(types[3]), *(types[4]), *(types[5]));
 }
 
 // -------------------------------------
@@ -431,11 +437,11 @@ static inline void merge_impropers(DihedralArray& dihOut, DihedralArray& dihIn,
   */
 void Cpptraj::Parm::MergeDihedralArrays(DihedralArray& dihedrals0,
                                     DihedralArray& dihedralsh0,
-                                    DihedralParmArray& ap0,
+                                    DihedralParmArray& dp0,
                                     AtArray const& atoms0,
                                     DihedralArray const& dihedrals1,
                                     DihedralArray const& dihedralsh1,
-                                    DihedralParmArray const& ap1,
+                                    DihedralParmArray const& dp1,
                                     AtArray const& atoms1)
 {
   // Separate any impropers.
@@ -451,12 +457,131 @@ void Cpptraj::Parm::MergeDihedralArrays(DihedralArray& dihedrals0,
 
   MergeTopArray<DihedralType, DihedralParmType, DihedralArray, DihedralParmArray> mergeDihedrals;
   mergeDihedrals.SetMergeWithExisting( true );
-  mergeDihedrals.MergeTermArrays( dih0, dihH0, ap0, atoms0,
-                                  dih1, dihH1, ap1, atoms1 );
-  mergeDihedrals.MergeImproperArrays( imp0, impH0, ap0, atoms0,
-                                      imp1, impH1, ap1, atoms1 );
+  mergeDihedrals.MergeTermArrays( dih0, dihH0, dp0, atoms0,
+                                  dih1, dihH1, dp1, atoms1 );
+  mergeDihedrals.MergeImproperArrays( imp0, impH0, dp0, atoms0,
+                                      imp1, impH1, dp1, atoms1 );
   // Re-merge
   merge_impropers(dihedrals0, dih0, imp0);
   merge_impropers(dihedralsh0, dihH0, impH0);
 }
 
+// -----------------------------------------------------------------------------
+// ----- CMAPs -------------------------
+static inline void printIdx(CmapType const& cmap1, unsigned int atomOffset) {
+  mprintf("DEBUG: CMAP from top1 %i - %i - %i - %i - %i will be %i - %i - %i - %i - %i in top0\n",
+          cmap1.A1()+1, cmap1.A2()+1, cmap1.A3()+1, cmap1.A4()+1, cmap1.A5()+1,
+          cmap1.A1()+1+atomOffset, cmap1.A2()+1+atomOffset, cmap1.A3()+1+atomOffset, cmap1.A4()+1+atomOffset, cmap1.A5()+1+atomOffset);
+}
+
+/** CMAPs are indexed by residue name and 5 atom names, so need 6. 
+  */
+static inline TypeNameHolder getCmapTypes(CmapType const& cmap1, std::vector<Atom> const& atoms, std::vector<Residue> const& residues)
+{
+  Atom const& A1 = atoms[cmap1.A1()];
+  Atom const& A2 = atoms[cmap1.A2()];
+  Atom const& A3 = atoms[cmap1.A3()];
+  Atom const& A4 = atoms[cmap1.A4()];
+  Atom const& A5 = atoms[cmap1.A5()];
+
+  TypeNameHolder types(6);
+  types.AddName( residues[A2.ResNum()].Name() );
+  types.AddName( A1.Name() );
+  types.AddName( A2.Name() );
+  types.AddName( A3.Name() );
+  types.AddName( A4.Name() );
+  types.AddName( A5.Name() );
+
+  return types;
+}
+
+static inline CmapType idxWithOffset(CmapType const& cmap1, int idx, unsigned int atomOffset) {
+  return CmapType(cmap1.A1()+atomOffset, cmap1.A2()+atomOffset, cmap1.A3()+atomOffset, cmap1.A4()+atomOffset, cmap1.A5()+atomOffset, idx);
+}
+
+/// Index existing CMAP types in term arrays
+void index_cmap_types(ParmHolder<int>& currentTypes,
+                      CmapArray const& terms,
+                      std::vector<Atom> const& atoms,
+                      std::vector<Residue> const& residues)
+{
+  for (typename CmapArray::const_iterator term = terms.begin(); term != terms.end(); ++term)
+  {
+    if (term->Idx() > -1) {
+      TypeNameHolder types = getCmapTypes(*term, atoms, residues);
+      bool found;
+      currentTypes.FindParam(types, found);
+      if (!found) {
+        currentTypes.AddParm(types, term->Idx(), false);
+      }
+    }
+  }
+}
+
+/** Given CMAP arrays from top0 and top1, merge and consolidate parameters. */
+void Cpptraj::Parm::MergeCmapArrays(CmapArray& cmap0,
+                                    CmapGridArray& cg0,
+                                    AtArray const& atoms0,
+                                    ResArray const& residues0,
+                                    CmapArray const& cmap1,
+                                    CmapGridArray const& cg1,
+                                    AtArray const& atoms1,
+                                    ResArray const& residues1)
+{
+  unsigned int atomOffset = atoms0.size();
+  // First index existing parameters
+  ParmHolder<int> currentTypes0, currentTypes1;
+  index_cmap_types(currentTypes0, cmap0, atoms0, residues0);
+  index_cmap_types(currentTypes1, cmap1, atoms1, residues1);
+  // Loop over incoming terms
+  for (CmapArray::const_iterator c1 = cmap1.begin(); c1 != cmap1.end(); ++c1)
+  {
+    printIdx(*c1, atomOffset);
+    TypeNameHolder types = getCmapTypes(*c1, atoms1, residues1);
+    mprintf("DEBUG: Looking for types in top0:");
+    printTypes( types ); // DEBUG
+    // Do we have an existing parameter in top0
+    bool found;
+    int idx = currentTypes0.FindParam(types, found);
+    if (!found) {
+      // No parameter yet.
+      // Do we have an existing parameter in top1
+      mprintf("DEBUG: Not found in top0. Looking in top1.\n");
+      idx = currentTypes1.FindParam(types, found);
+      if (!found) {
+        mprintf("DEBUG: No parameters.\n");
+        // No parameter in either top.
+        idx = -1;
+      } else {
+        mprintf("DEBUG: Found in top1 index %i, adding to top0.\n", idx+1);
+        // Found a parameter in top1, add it to top0.
+        int oldIdx = -1;
+        //if (merge_with_existing_) {
+          // Check if parameter exists
+          for (unsigned int i0 = 0; i0 != cg0.size(); i0++) {
+            if (cg1[idx].GridMatches( cg0[i0] )) {
+              oldIdx = (int)i0;
+              break;
+            }
+          }
+        //}
+        if (oldIdx == -1) {
+          // Do not merge with existing or does not yet exist.
+          int newIdx = cg0.size();
+          cg0.push_back( cg1[idx] );
+          idx = newIdx;
+        } else {
+          mprintf("DEBUG: Parm from top1 already present in top0 at position %i\n", oldIdx+1);
+          idx = oldIdx;
+        }
+      }
+      // Add to existing parameters in top0.
+      // Do this even if a parameter was not found so we dont keep looking.
+      if (idx < 0) noParmWarning(types);
+      currentTypes0.AddParm(types, idx, false);
+    }
+    mprintf("DEBUG: top0 parameter index is %i\n", idx+1);
+    // At this point we have either found a parameter or not.
+    cmap0.push_back( idxWithOffset(*c1, idx, atomOffset) );
+  } // END loop over cmap terms from top1
+}
diff --git a/src/Parm/Merge.h b/src/Parm/Merge.h
index 7b6f3dbada..5bf080add1 100644
--- a/src/Parm/Merge.h
+++ b/src/Parm/Merge.h
@@ -2,16 +2,21 @@
 #define INC_PARM_MERGE_H
 #include <vector>
 class Atom;
+class Residue;
 class BondArray;
 class BondParmArray;
 class AngleArray;
 class AngleParmArray;
 class DihedralArray;
 class DihedralParmArray;
+class CmapArray;
+class CmapGridArray;
 namespace Cpptraj {
 namespace Parm {
 /// Shorthand for array of Atoms
 typedef std::vector<Atom> AtArray;
+/// Shorthand for array of residues
+typedef std::vector<Residue> ResArray;
 /// Merge two bond arrays and their parameters.
 void MergeBondArrays(BondArray&, BondArray&, BondParmArray&, AtArray const&,
                      BondArray const&, BondArray const&, BondParmArray const&, AtArray const&);
@@ -21,6 +26,9 @@ void MergeAngleArrays(AngleArray&, AngleArray&, AngleParmArray&, AtArray const&,
 /// Merge two dihedral arrays and their parameters.
 void MergeDihedralArrays(DihedralArray&, DihedralArray&, DihedralParmArray&, AtArray const&,
                          DihedralArray const&, DihedralArray const&, DihedralParmArray const&, AtArray const&);
+/// Merge cmap arrays and their parameters
+void MergeCmapArrays(CmapArray&, CmapGridArray&, AtArray const&, ResArray const&,
+                     CmapArray const&, CmapGridArray const&, AtArray const&, ResArray const&);
 
 }
 }
diff --git a/src/Topology.cpp b/src/Topology.cpp
index 689b50b826..986ec20b47 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2617,6 +2617,9 @@ int Topology::AppendTop(Topology const& NewTop) {
   Cpptraj::Parm::MergeDihedralArrays(dihedrals_, dihedralsh_, dihedralparm_, atoms_,
                                   NewTop.Dihedrals(), NewTop.DihedralsH(), NewTop.DihedralParm(), NewTop.Atoms());
 
+  Cpptraj::Parm::MergeCmapArrays(cmap_, cmapGrid_, atoms_, residues_,
+                                 NewTop.Cmap(), NewTop.CmapGrid(), NewTop.Atoms(), NewTop.Residues());
+
   // Append NewTop atoms to this topology.
   for (atom_iterator atom = NewTop.begin(); atom != NewTop.end(); ++atom)
   {
@@ -2648,12 +2651,12 @@ int Topology::AppendTop(Topology const& NewTop) {
   //addDihedralsWithOffset( dihedrals_, NewTop.Dihedrals(), atomOffset );
   //addDihedralsWithOffset( dihedralsh_, NewTop.DihedralsH(), atomOffset );
   addDihedralsWithOffset( chamber_.SetImpropers(), NewTop.chamber_.Impropers(), atomOffset );
-  for (CmapArray::const_iterator cm = NewTop.Cmap().begin(); cm != NewTop.Cmap().end(); ++cm)
-    cmap_.push_back( CmapType(cm->A1() + atomOffset,
-                              cm->A2() + atomOffset,
-                              cm->A3() + atomOffset,
-                              cm->A4() + atomOffset,
-                              cm->A5() + atomOffset, -1) );
+  //for (CmapArray::const_iterator cm = NewTop.Cmap().begin(); cm != NewTop.Cmap().end(); ++cm)
+  //  cmap_.push_back( CmapType(cm->A1() + atomOffset,
+  //                            cm->A2() + atomOffset,
+  //                            cm->A3() + atomOffset,
+  //                            cm->A4() + atomOffset,
+  //                            cm->A5() + atomOffset, -1) );
 //#  for (BondArray::const_iterator bond = NewTop.Bonds().begin(); bond != NewTop.Bonds().end(); ++bond)
 //#    AddBond( bond->A1() + atomOffset, bond->A2() + atomOffset );
 //#  for (BondArray::const_iterator bond = NewTop.BondsH().begin(); bond != NewTop.BondsH().end(); ++bond)

From cba0911b2eea29e63fc10aeac6d1d8aa2013abd4 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 12 Mar 2024 19:25:15 -0400
Subject: [PATCH 0699/1492] Ensure original CMAP ordering is preserved

---
 src/ParameterTypes.h |  2 ++
 src/Parm/Merge.cpp   | 14 ++++++++++++--
 2 files changed, 14 insertions(+), 2 deletions(-)

diff --git a/src/ParameterTypes.h b/src/ParameterTypes.h
index c5e499a977..af3cc37dc0 100644
--- a/src/ParameterTypes.h
+++ b/src/ParameterTypes.h
@@ -925,6 +925,8 @@ class CmapGridArray {
     void clear() { cmapgrids_.clear(); }
     /// Reserve for specified # of grids
     void reserve(size_t n) { cmapgrids_.reserve(n); }
+    /// Resize for specified # of grids
+    void resize(size_t n) { cmapgrids_.resize(n); }
     /// iterator
     typedef CGarray::iterator iterator;
     /// begin iterator
diff --git a/src/Parm/Merge.cpp b/src/Parm/Merge.cpp
index d4033dd3a7..998c14d9b3 100644
--- a/src/Parm/Merge.cpp
+++ b/src/Parm/Merge.cpp
@@ -529,6 +529,7 @@ void Cpptraj::Parm::MergeCmapArrays(CmapArray& cmap0,
                                     ResArray const& residues1)
 {
   unsigned int atomOffset = atoms0.size();
+  unsigned int cgOffset = cg0.size();
   // First index existing parameters
   ParmHolder<int> currentTypes0, currentTypes1;
   index_cmap_types(currentTypes0, cmap0, atoms0, residues0);
@@ -567,8 +568,17 @@ void Cpptraj::Parm::MergeCmapArrays(CmapArray& cmap0,
         //}
         if (oldIdx == -1) {
           // Do not merge with existing or does not yet exist.
-          int newIdx = cg0.size();
-          cg0.push_back( cg1[idx] );
+          // CMAPs are different than other parameters in that their order
+          // in the topology matches the order in which they are specified
+          // in the original parameter set. Therefore do not just append,
+          // use the existing index as an offset.
+          //int newIdx = cg0.size();
+          //cg0.push_back( cg1[idx] );
+          int newIdx = cgOffset + idx;
+          mprintf("DEBUG: New CMAP index in top0 is %i\n", newIdx);
+          if ((unsigned int)newIdx >= cg0.size())
+            cg0.resize( newIdx + 1 );
+          cg0[newIdx] = cg1[idx];
           idx = newIdx;
         } else {
           mprintf("DEBUG: Parm from top1 already present in top0 at position %i\n", oldIdx+1);

From 526a4f03d0bc92dd38537415fafa5e4b3a60ff35 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 13 Mar 2024 09:00:20 -0400
Subject: [PATCH 0700/1492] When appending, both topologies already have
 complete molecule information, so just use that instead of re-determining
 molecules.

---
 src/Molecule.h   |  2 ++
 src/Topology.cpp | 37 ++++++++++++++++++++++++++++++++-----
 src/Topology.h   |  3 +++
 3 files changed, 37 insertions(+), 5 deletions(-)

diff --git a/src/Molecule.h b/src/Molecule.h
index 8a7e54f6c9..cf3ee4f152 100644
--- a/src/Molecule.h
+++ b/src/Molecule.h
@@ -12,6 +12,8 @@ class Molecule {
     void SetSolvent()   { isSolvent_ = true;  }
     void SetNoSolvent() { isSolvent_ = false; }
     Unit& ModifyUnit()  { return unit_;       }
+    /// Add atom number to the molecule.
+    int AddAtnum(int at) { return unit_.AddIndex(at); }
 
     bool IsSolvent()        const { return isSolvent_;   }
     unsigned int NumAtoms() const { return unit_.Size(); }
diff --git a/src/Topology.cpp b/src/Topology.cpp
index 986ec20b47..f61c3a5346 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -466,6 +466,25 @@ int Topology::AddTopAtom(Atom const& atomIn, Residue const& resIn)
   residues_.back().SetLastAtom( atoms_.size() );
   return 0;
 }
+
+/** This version takes a molecule number as well. */
+int Topology::addTopAtom(Atom const& atomIn, Residue const& resIn,
+                         unsigned int molnum, bool isSolvent)
+{
+  unsigned int atnum = atoms_.size();
+  AddTopAtom(atomIn, resIn);
+  atoms_.back().SetMol( molnum );
+  if (molnum > molecules_.size())
+    mprintf("Warning: AddTopAtom(): Molecule number %i is not consecutive.\n");
+  if (molnum >= molecules_.size()) {
+    molecules_.resize( molnum+1 );
+    if (isSolvent)
+      NsolventMolecules_++;
+  }
+  molecules_[molnum].AddAtnum( atnum );
+  return 0;
+}
+
 /*
 // Topology::StartNewMol()
 void Topology::StartNewMol() {
@@ -2589,8 +2608,10 @@ static inline void addDihedralsWithOffset(DihedralArray& dihedralsOut, DihedralA
 
 // Topology::AppendTop()
 int Topology::AppendTop(Topology const& NewTop) {
-  int atomOffset = (int)atoms_.size();
-  mprintf("DEBUG: Appending '%s' to '%s' (offset= %i)\n", NewTop.c_str(), c_str(), atomOffset);
+  unsigned int atomOffset = atoms_.size();
+  unsigned int molOffset = molecules_.size();
+  mprintf("DEBUG: Appending '%s' to '%s' (atom offset= %u mol offset= %u)\n",
+          NewTop.c_str(), c_str(), atomOffset, molOffset);
   //int resOffset = (int)residues_.size();
 
 // NOTE: Lines commented out with //# can be used to test appending via the
@@ -2633,8 +2654,9 @@ int Topology::AppendTop(Topology const& NewTop) {
     for (Atom::bond_iterator bat = atom->bondbegin(); bat != atom->bondend(); ++bat)
       CurrentAtom.AddBondToIdx( *bat + atomOffset );
 
-    AddTopAtom( CurrentAtom, Residue(res.Name(), res.OriginalResNum(),
-                                     res.Icode(), res.ChainId()) );
+    addTopAtom( CurrentAtom,
+                Residue(res.Name(), res.OriginalResNum(), res.Icode(), res.ChainId()),
+                atom->MolNum()+molOffset, NewTop.Mol(atom->MolNum()).IsSolvent() );
   }
   // Recreate bonds for the added atoms
   // DEBUG TEST
@@ -2713,7 +2735,12 @@ int Topology::AppendTop(Topology const& NewTop) {
 
   // Re-set up this topology
   // TODO: Could get expensive for multiple appends.
-  return CommonSetup();
+  //return CommonSetup();
+  // The version of AddTopAtom() with molecule number already determines
+  // molecules and number of solvent molecules.
+  // Just need to determine the number of extra points.
+  DetermineNumExtraPoints();
+  return 0;
 }
 
 // -----------------------------------------------------------------------------
diff --git a/src/Topology.h b/src/Topology.h
index 146e800ad2..abd305aa04 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -220,6 +220,7 @@ class Topology {
     void SetParmBox( Box const& bIn )   { parmBox_ = bIn;         }
     void SetBoxFromTraj(Box const&);
     // ----- Setup routines ----------------------
+    /// Add an atom to the topology inside given residue
     int AddTopAtom(Atom const&, Residue const&);
     //void StartNewMol();
     /// Perform common final setup: optional molecule determination, renumber residues by molecules
@@ -280,6 +281,8 @@ class Topology {
                                                    DihedralParmArray const&,
                                                    int, const char*);
     inline bool CheckExtraSize(size_t, const char*) const;
+    /// Add an atom to the topology inside given residue and molecule number
+    int addTopAtom(Atom const&, Residue const&, unsigned int, bool);
 
     void VisitAtom(int, int);
     int RecursiveMolSearch();

From f286022d94137e0fe76ae00a839d31acf9b49b57 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 13 Mar 2024 09:49:35 -0400
Subject: [PATCH 0701/1492] Save HB params. Assign nonbond info during append;
 types arent quite right yet though.

---
 src/Parm_CharmmPsf.cpp |   2 +-
 src/Topology.cpp       | 140 +++++++++++++++++++++++------------------
 src/Topology.h         |   2 +-
 src/cpptrajdepend      |   4 +-
 4 files changed, 82 insertions(+), 66 deletions(-)

diff --git a/src/Parm_CharmmPsf.cpp b/src/Parm_CharmmPsf.cpp
index b5c7702b15..2f0198cb13 100644
--- a/src/Parm_CharmmPsf.cpp
+++ b/src/Parm_CharmmPsf.cpp
@@ -377,7 +377,7 @@ int Parm_CharmmPsf::ReadParm(FileName const& fname, Topology &parmOut) {
 
   // Add nonbonded parameters
   if (params_.HasLJparams()) {
-    parmOut.AssignNonbondParams( atomTypes, params_.NB(), params_.HB() );
+    parmOut.AssignNonbondParams( atomTypes, params_.NB(), params_.HB(), debug_ );
   }
 
   return 0;
diff --git a/src/Topology.cpp b/src/Topology.cpp
index f61c3a5346..29c2c7e2fc 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -10,6 +10,7 @@
 #include "GuessAtomHybridization.h"
 #include "Structure/GenerateConnectivityArrays.h"
 #include "Parm/Merge.h"
+#include "UpdateParameters.h"
 
 const NonbondType Topology::LJ_EMPTY = NonbondType();
 
@@ -2372,32 +2373,42 @@ static inline int GetCmapParams(CmapParmHolder& cmapParm, CmapArray const& cmapT
   return 0;
 }
 
-/** \param atomTypes Output array of atom types.
-  * \param NB1 Output array of nonbond parameters.
+/** \param atomTypesOut Output array of atom types.
+  * \param LJ612out Output array of LJ 6-12 parameters.
+  * \param LJ1012out Output array of LJ 10-12 parameters.
   * \param atoms Current array of atoms.
   * \param NB0 Current nonbond parameters.
   */
-static inline void GetLJAtomTypes( ParmHolder<AtomType>& atomTypes, ParmHolder<NonbondType>& NB1, std::vector<Atom> const& atoms, NonbondParmType const& NB0, int debugIn)
+static inline void GetLJAtomTypes(ParmHolder<AtomType>& atomTypesOut,
+                                  ParmHolder<NonbondType>& LJ612out,
+                                  ParmHolder<HB_ParmType>& LJ1012out,
+                                  std::vector<Atom> const& atoms,
+                                  NonbondParmType const& NB0,
+                                  int debugIn)
 {
   if (NB0.HasNonbond()) {
     mprintf("DEBUG: Topology has nonbond parameters.\n");
     // Nonbonded parameters are present.
     for (std::vector<Atom>::const_iterator atm = atoms.begin(); atm != atoms.end(); ++atm)
     {
-      // TODO check for blank type name?
+      if (atm->Type().len() < 1) {
+        mprintf("Warning: Topology has nonbond parameters but atom %s has no type.\n", *(atm->Name()));
+        continue;
+      }
       TypeNameHolder atype( atm->Type() );
       // Check for self parameters to back-calculate LJ depth/radius
       int idx = NB0.GetLJindex( atm->TypeIndex(), atm->TypeIndex() );
       AtomType thisType;
       if (idx > -1) {
+        // Has LJ 6-12 parameters
         NonbondType const& LJ = NB0.NBarray( idx );
         thisType = AtomType(LJ.Radius(), LJ.Depth(), atm->Mass(), atm->Polar());
       } else {
-        // TODO LJ 10-12
+        // Has LJ 10-12 parameters
         thisType = AtomType(atm->Mass(), atm->Polar());
       }
       thisType.SetTypeIdx( atm->TypeIndex() );
-      ParameterHolders::RetType ret = atomTypes.AddParm( atype, thisType, true );
+      ParameterHolders::RetType ret = atomTypesOut.AddParm( atype, thisType, true );
       if (debugIn > 0) {
         if (ret == ParameterHolders::ADDED) {
           mprintf("DEBUG: New atom type: %s R=%g D=%g M=%g P=%g\n", *(atype[0]), thisType.LJ().Radius(), thisType.LJ().Depth(), thisType.Mass(), thisType.Polarizability());
@@ -2407,44 +2418,51 @@ static inline void GetLJAtomTypes( ParmHolder<AtomType>& atomTypes, ParmHolder<N
     // Do atom type pairs, check for off-diagonal elements.
     // Explicitly store pairs instead of regenerating to avoid round-off issues.
     unsigned int nModifiedOffDiagonal = 0;
-    for (ParmHolder<AtomType>::const_iterator i1 = atomTypes.begin(); i1 != atomTypes.end(); ++i1)
+    for (ParmHolder<AtomType>::const_iterator i1 = atomTypesOut.begin(); i1 != atomTypesOut.end(); ++i1)
     {
-      for (ParmHolder<AtomType>::const_iterator i2 = i1; i2 != atomTypes.end(); ++i2)
+      for (ParmHolder<AtomType>::const_iterator i2 = i1; i2 != atomTypesOut.end(); ++i2)
       {
-        // Determine what A and B parameters would be.
         NameType const& name1 = i1->first[0];
         NameType const& name2 = i2->first[0];
+        TypeNameHolder types(2);
+        types.AddName( name1 );
+        types.AddName( name2 );
+        // Extract original nonbonded parameters for this type pair.
         AtomType const& type1 = i1->second;
         AtomType const& type2 = i2->second;
-        NonbondType lj0 = type1.LJ().Combine_LB( type2.LJ() );
-        // Extract original A and B parameters.
-        int idx1 = type1.OriginalIdx();//t1->second;
-        int idx2 = type2.OriginalIdx();//t2->second;
+        int idx1 = type1.OriginalIdx();
+        int idx2 = type2.OriginalIdx();
         int idx = NB0.GetLJindex( idx1, idx2 );
         if (idx < 0) {
-          mprinterr("Error: No off-diagonal LJ for  %s %s (%i %i)\n",
-                    *name1, *name2, idx1, idx2);
-          return;
-        }
-        NonbondType lj1 = NB0.NBarray( idx );
-        // Compare them
-        if (lj0 != lj1) {
-          nModifiedOffDiagonal++;
-          //if (debugIn > 0) {
-            double deltaA = fabs(lj0.A() - lj1.A());
-            double deltaB = fabs(lj0.B() - lj1.B());
-            mprintf("DEBUG: Potential off-diagonal LJ: %s %s expect A=%g B=%g, actual A=%g B=%g\n",
-                    *name1, *name2, lj0.A(), lj0.B(), lj1.A(), lj1.B());
-            mprintf("DEBUG:\tdeltaA= %g    deltaB= %g\n", deltaA, deltaB);
-            double pe_a = (fabs(lj0.A() - lj1.A()) / lj0.A());
-            double pe_b = (fabs(lj0.B() - lj1.B()) / lj0.B());
-            mprintf("DEBUG:\tPEA= %g  PEB= %g\n", pe_a, pe_b);
-          //}
+          // This is LJ 10-12.
+          //mprinterr("Error: No off-diagonal LJ for  %s %s (%i %i)\n",
+          //          *name1, *name2, idx1, idx2);
+          //return;
+          mprintf("DEBUG: LJ 10-12 parameters detected for %s %s (%i %i)\n",
+                  *name1, *name2, idx1, idx2);
+          LJ1012out.AddParm( types, NB0.HBarray((-idx)-1), false );
+        } else {
+          // This is LJ 6-12.
+          // Determine what A and B parameters would be.
+          NonbondType lj0 = type1.LJ().Combine_LB( type2.LJ() );
+        
+          NonbondType lj1 = NB0.NBarray( idx );
+          // Compare them
+          if (lj0 != lj1) {
+            nModifiedOffDiagonal++;
+            //if (debugIn > 0) {
+              double deltaA = fabs(lj0.A() - lj1.A());
+              double deltaB = fabs(lj0.B() - lj1.B());
+              mprintf("DEBUG: Potential off-diagonal LJ: %s %s expect A=%g B=%g, actual A=%g B=%g\n",
+                      *name1, *name2, lj0.A(), lj0.B(), lj1.A(), lj1.B());
+              mprintf("DEBUG:\tdeltaA= %g    deltaB= %g\n", deltaA, deltaB);
+              double pe_a = (fabs(lj0.A() - lj1.A()) / lj0.A());
+              double pe_b = (fabs(lj0.B() - lj1.B()) / lj0.B());
+              mprintf("DEBUG:\tPEA= %g  PEB= %g\n", pe_a, pe_b);
+            //}
+          }
+          LJ612out.AddParm( types, lj1, false );
         }
-        TypeNameHolder types(2);
-        types.AddName( name1 );
-        types.AddName( name2 );
-        NB1.AddParm( types, lj1, false );
       } // END inner loop over atom types
     } // END outer loop over atom types
     if (nModifiedOffDiagonal > 0)
@@ -2455,7 +2473,7 @@ static inline void GetLJAtomTypes( ParmHolder<AtomType>& atomTypes, ParmHolder<N
     // No nonbonded parameters. Just save mass/polarizability.
     for (std::vector<Atom>::const_iterator atm = atoms.begin(); atm != atoms.end(); ++atm)
       if (atm->HasType() > 0)
-        atomTypes.AddParm( TypeNameHolder(atm->Type()), AtomType(atm->Mass(), atm->Polar()), true );
+        atomTypesOut.AddParm( TypeNameHolder(atm->Type()), AtomType(atm->Mass(), atm->Polar()), true );
   }
 }
 
@@ -2463,7 +2481,7 @@ static inline void GetLJAtomTypes( ParmHolder<AtomType>& atomTypes, ParmHolder<N
 ParameterSet Topology::GetParameters() const {
   ParameterSet Params;
   // Atom LJ types
-  GetLJAtomTypes( Params.AT(), Params.NB(), atoms_, nonbond_, debug_ );
+  GetLJAtomTypes( Params.AT(), Params.NB(), Params.HB(), atoms_, nonbond_, debug_ );
   // Bond parameters.
   GetBondParams( Params.BP(), atoms_, bonds_, bondparm_ );
   GetBondParams( Params.BP(), atoms_, bondsh_, bondparm_ );
@@ -2618,30 +2636,33 @@ int Topology::AppendTop(Topology const& NewTop) {
 //       parameter update functionality. This is slower, but is a good test
 //       that the parameter update function is working correctly.
   // Save old parameters
-  mprintf("DEBUG: Getting old parameters.\n");
-  ParameterSet oldParams = GetParameters();
-  oldParams.Summary(); // DEBUG
-/*  // Save nonbonded parameters from each topology TODO LJ 10-12
+  //mprintf("DEBUG: Getting old parameters.\n");
+  //ParameterSet oldParams = GetParameters();
+  //oldParams.Summary(); // DEBUG
+  // Save nonbonded parameters from each topology
   ParmHolder<AtomType> myAtomTypes, newAtomTypes;
   ParmHolder<NonbondType> myNB, newNB;
-  //ParmHolder<HB_ParmType> myHB, newHB;
-  GetLJAtomTypes( myAtomTypes, myNB, atoms_, nonbond_, debug_ );
-  GetLJAtomTypes( newAtomTypes, newNB, NewTop.atoms_, NewTop.nonbond_, debug_ );
+  ParmHolder<HB_ParmType> myHB, newHB;
+  GetLJAtomTypes( myAtomTypes, myNB, myHB, atoms_, nonbond_, debug_ );
+  GetLJAtomTypes( newAtomTypes, newNB, newHB, NewTop.atoms_, NewTop.nonbond_, debug_ );
+  // Create combined nonbond parameter set
   int nAtomTypeUpdated = UpdateParameters< ParmHolder<AtomType> >( myAtomTypes, newAtomTypes, "atom type", 1 ); // TODO verbose 
-  int nLJparamsUpdated = UpdateParameters< ParmHolder<NonbondType> >( myNB, newNB, "LJ A-B", 1 ); // TODO verbose
-  mprintf("\t%i atom types updated, %i LJ params updated.\n", nAtomTypeUpdated, nLJparamsUpdated);*/
+  int nLJparamsUpdated = UpdateParameters< ParmHolder<NonbondType> >( myNB, newNB, "LJ 6-12", 1 ); // TODO verbose
+  int nHBparamsUpdated = UpdateParameters< ParmHolder<HB_ParmType> >( myHB, newHB, "LJ 10-12", 1); // TODO verbose
+  mprintf("\t%i atom types updated, %i LJ 6-12 params updated, %i LJ 10-12 params updated.\n",
+          nAtomTypeUpdated, nLJparamsUpdated, nHBparamsUpdated);
 
+  // Add incoming topology bond/angle/dihedral/cmap arrays to this one.
   Cpptraj::Parm::MergeBondArrays(bonds_, bondsh_, bondparm_, atoms_,
                                  NewTop.Bonds(), NewTop.BondsH(), NewTop.BondParm(), NewTop.Atoms());
   Cpptraj::Parm::MergeAngleArrays(angles_, anglesh_, angleparm_, atoms_,
                                   NewTop.Angles(), NewTop.AnglesH(), NewTop.AngleParm(), NewTop.Atoms());
   Cpptraj::Parm::MergeDihedralArrays(dihedrals_, dihedralsh_, dihedralparm_, atoms_,
-                                  NewTop.Dihedrals(), NewTop.DihedralsH(), NewTop.DihedralParm(), NewTop.Atoms());
-
+                                     NewTop.Dihedrals(), NewTop.DihedralsH(), NewTop.DihedralParm(), NewTop.Atoms());
   Cpptraj::Parm::MergeCmapArrays(cmap_, cmapGrid_, atoms_, residues_,
                                  NewTop.Cmap(), NewTop.CmapGrid(), NewTop.Atoms(), NewTop.Residues());
 
-  // Append NewTop atoms to this topology.
+  // Append incoming atoms to this topology.
   for (atom_iterator atom = NewTop.begin(); atom != NewTop.end(); ++atom)
   {
     if (debug_ > 1)
@@ -2698,7 +2719,7 @@ int Topology::AppendTop(Topology const& NewTop) {
 //#                                 dih->A3() + atomOffset, dih->A4() + atomOffset,
 //#                                 dih->Type() ) );
   // Update parameters
-  mprintf("DEBUG: Updating with new parameters.\n");
+  //mprintf("DEBUG: Updating with new parameters.\n");
   //updateParams( oldParams, NewTop.GetParameters() );
 
   // EXTRA ATOM INFO
@@ -2726,16 +2747,11 @@ int Topology::AppendTop(Topology const& NewTop) {
   // UREY-BRADLEY TODO
   // IMPROPERS TODO
   // CMAP TODO
-
-  // Need to regenerate nonbonded info TODO verbose TODO LJ 10-12
+*/
+  // Need to regenerate nonbonded info
   mprintf("\tRegenerating nonbond parameters.\n");
-  AssignNonbondParams( myAtomTypes, myNB, ParmHolder<HB_ParmType>() ); //FIXME LJ 10-12*/
-
-  // TODO append missing stuff?
+  AssignNonbondParams( myAtomTypes, myNB, myHB, 1 ); // FIXME verbose
 
-  // Re-set up this topology
-  // TODO: Could get expensive for multiple appends.
-  //return CommonSetup();
   // The version of AddTopAtom() with molecule number already determines
   // molecules and number of solvent molecules.
   // Just need to determine the number of extra points.
@@ -3232,9 +3248,9 @@ void Topology::AssignDihedralParams(DihedralParmHolder const& newDihedralParams,
 //TODO Accept array of atom type names?
 void Topology::AssignNonbondParams(ParmHolder<AtomType> const& newTypes,
                                    ParmHolder<NonbondType> const& newNB,
-                                   ParmHolder<HB_ParmType> const& newHB)
+                                   ParmHolder<HB_ParmType> const& newHB,
+                                   int verbose)
 {
-  static const int verbose = 0 ; // FIXME temporarily silence output
   // Generate array of only the types that are currently in Topology. TODO should this be a permanent part of Topology?
   ParmHolder<AtomType> currentAtomTypes;
   for (std::vector<Atom>::const_iterator atm = atoms_.begin(); atm != atoms_.end(); ++atm)
@@ -3677,7 +3693,7 @@ int Topology::AssignParams(ParameterSet const& set0) {
   AssignAtomTypeParm( set0.AT() );
   // LJ 6-12
   mprintf("\tAssigning nonbond parameters.\n");
-  AssignNonbondParams( set0.AT(), set0.NB(), set0.HB() );
+  AssignNonbondParams( set0.AT(), set0.NB(), set0.HB(), debug_ );
   mprintf("DEBUG: CMAP size %zu\n", set0.CMAP().size());
   // TODO LJ14, LJC
 
@@ -3755,7 +3771,7 @@ int Topology::updateParams(ParameterSet& set0, ParameterSet const& set1) {
 //  updateCount += UpdateParameters< ParmHolder<NonbondType> >(set0.NB(), set1.NB(), "LJ A-B");
   if (UC.nAtomTypeUpdated_ > 0) {
     mprintf("\tRegenerating nonbond parameters.\n");
-    AssignNonbondParams( set0.AT(), set0.NB(), set0.HB() );
+    AssignNonbondParams( set0.AT(), set0.NB(), set0.HB(), debug_ );
   }
   // CMAP
   if (UC.nCmapUpdated_ > 0) {
diff --git a/src/Topology.h b/src/Topology.h
index abd305aa04..6dd39e18a3 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -165,7 +165,7 @@ class Topology {
     /// \return Lennard-Jones 6-12 parameters for given pair of atoms
     inline NonbondType const& GetLJparam(int, int) const;
     void AssignNonbondParams(ParmHolder<AtomType> const&, ParmHolder<NonbondType> const&,
-                             ParmHolder<HB_ParmType> const&);
+                             ParmHolder<HB_ParmType> const&, int);
     /// \return True if any charge is non-zero
     bool HasChargeInfo() const;
     /// Redistribute charge on atoms in topology to match target total charge
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 451682933a..d6bbf77211 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -405,7 +405,7 @@ Parallel.o : Parallel.cpp Parallel.h
 ParallelNetcdf.o : ParallelNetcdf.cpp CpptrajStdio.h Parallel.h ParallelNetcdf.h
 ParameterSet.o : ParameterSet.cpp AtomType.h CmapParmHolder.h Constants.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h TypeNameHolder.h UpdateParameters.h
 Parm/GB_Params.o : Parm/GB_Params.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/GB_Params.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Parm/Merge.o : Parm/Merge.cpp Atom.h Constants.h CpptrajStdio.h NameType.h ParameterHolders.h ParameterTypes.h Parm/Merge.h SymbolExporting.h TypeNameHolder.h
+Parm/Merge.o : Parm/Merge.cpp Atom.h Constants.h CpptrajStdio.h NameType.h ParameterHolders.h ParameterTypes.h Parm/Merge.h Residue.h StringRoutines.h SymbolExporting.h TypeNameHolder.h
 ParmFile.o : ParmFile.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h ParmIO.h Parm_Amber.h Parm_CIF.h Parm_CharmmPsf.h Parm_Gromacs.h Parm_Mol2.h Parm_PDB.h Parm_SDF.h Parm_Tinker.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Parm_Amber.o : Parm_Amber.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h ExclusionArray.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_Amber.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Parm_CIF.o : Parm_CIF.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h CIFfile.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_CIF.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
@@ -475,7 +475,7 @@ TextFormat.o : TextFormat.cpp StringRoutines.h TextFormat.h
 Timer.o : Timer.cpp CpptrajStdio.h Timer.h
 TinkerFile.o : TinkerFile.cpp ArgList.h Atom.h AtomMask.h Box.h BufferedLine.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TinkerFile.h Unit.h Vec3.h
 TopInfo.o : TopInfo.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h DistRoutines.h FileIO.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Mol.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h TopInfo.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Topology.o : Topology.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h GuessAtomHybridization.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/Merge.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/GenerateConnectivityArrays.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Topology.o : Topology.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h GuessAtomHybridization.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/Merge.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/GenerateConnectivityArrays.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h UpdateParameters.h Vec3.h
 TorsionRoutines.o : TorsionRoutines.cpp Constants.h TorsionRoutines.h Vec3.h
 TrajFrameCounter.o : TrajFrameCounter.cpp ArgList.h CpptrajStdio.h TrajFrameCounter.h
 TrajIOarray.o : TrajIOarray.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryFile.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h

From 794751aff48db5f566493877889f5f9296a5b585 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 13 Mar 2024 10:46:43 -0400
Subject: [PATCH 0702/1492] Uas HasType. nonbond indices seem ok

---
 src/Topology.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index 29c2c7e2fc..9e88388874 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2391,7 +2391,7 @@ static inline void GetLJAtomTypes(ParmHolder<AtomType>& atomTypesOut,
     // Nonbonded parameters are present.
     for (std::vector<Atom>::const_iterator atm = atoms.begin(); atm != atoms.end(); ++atm)
     {
-      if (atm->Type().len() < 1) {
+      if (!atm->HasType()) {
         mprintf("Warning: Topology has nonbond parameters but atom %s has no type.\n", *(atm->Name()));
         continue;
       }

From f1056c9086c80dee30eabab67d8d5c19a08c8548 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 13 Mar 2024 10:57:39 -0400
Subject: [PATCH 0703/1492] Merge UB terms

---
 src/Parm/Merge.cpp | 19 +++++++++++++++++++
 src/Parm/Merge.h   | 10 ++++++----
 src/Topology.cpp   |  4 +++-
 3 files changed, 28 insertions(+), 5 deletions(-)

diff --git a/src/Parm/Merge.cpp b/src/Parm/Merge.cpp
index 998c14d9b3..fe4b01c486 100644
--- a/src/Parm/Merge.cpp
+++ b/src/Parm/Merge.cpp
@@ -595,3 +595,22 @@ void Cpptraj::Parm::MergeCmapArrays(CmapArray& cmap0,
     cmap0.push_back( idxWithOffset(*c1, idx, atomOffset) );
   } // END loop over cmap terms from top1
 }
+
+// -----------------------------------------------------------------------------
+
+/** Given bond/bond parameter array from top0 and bond/bond parameter
+  * array from top1, merge the bond arrays and consolidate the
+  * parameters.
+  */
+void Cpptraj::Parm::MergeBondArray(BondArray& bonds0,
+                                   BondParmArray& bp0,
+                                   AtArray const& atoms0,
+                                   BondArray const& bonds1,
+                                   BondParmArray const& bp1,
+                                   AtArray const& atoms1)
+{
+  MergeTopArray<BondType, BondParmType, BondArray, BondParmArray> mergeBonds; // FIXME simplify
+  BondArray tmp;
+  mergeBonds.MergeTermArrays( bonds0, tmp,         bp0, atoms0,
+                              bonds1, BondArray(), bp1, atoms1 );
+}
diff --git a/src/Parm/Merge.h b/src/Parm/Merge.h
index 5bf080add1..8118ce471a 100644
--- a/src/Parm/Merge.h
+++ b/src/Parm/Merge.h
@@ -17,19 +17,21 @@ namespace Parm {
 typedef std::vector<Atom> AtArray;
 /// Shorthand for array of residues
 typedef std::vector<Residue> ResArray;
-/// Merge two bond arrays and their parameters.
+/// Merge two pairs of bond arrays and their parameters.
 void MergeBondArrays(BondArray&, BondArray&, BondParmArray&, AtArray const&,
                      BondArray const&, BondArray const&, BondParmArray const&, AtArray const&);
-/// Merge two angle arrays and their parameters.
+/// Merge two pairs of angle arrays and their parameters.
 void MergeAngleArrays(AngleArray&, AngleArray&, AngleParmArray&, AtArray const&,
                       AngleArray const&, AngleArray const&, AngleParmArray const&, AtArray const&);
-/// Merge two dihedral arrays and their parameters.
+/// Merge two pairs of dihedral arrays and their parameters.
 void MergeDihedralArrays(DihedralArray&, DihedralArray&, DihedralParmArray&, AtArray const&,
                          DihedralArray const&, DihedralArray const&, DihedralParmArray const&, AtArray const&);
 /// Merge cmap arrays and their parameters
 void MergeCmapArrays(CmapArray&, CmapGridArray&, AtArray const&, ResArray const&,
                      CmapArray const&, CmapGridArray const&, AtArray const&, ResArray const&);
-
+/// Merge two bond arrays and their parameters
+void MergeBondArray(BondArray&, BondParmArray&, AtArray const&,
+                    BondArray const&, BondParmArray const&, AtArray const&);
 }
 }
 #endif
diff --git a/src/Topology.cpp b/src/Topology.cpp
index 9e88388874..3f50c19116 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2661,6 +2661,8 @@ int Topology::AppendTop(Topology const& NewTop) {
                                      NewTop.Dihedrals(), NewTop.DihedralsH(), NewTop.DihedralParm(), NewTop.Atoms());
   Cpptraj::Parm::MergeCmapArrays(cmap_, cmapGrid_, atoms_, residues_,
                                  NewTop.Cmap(), NewTop.CmapGrid(), NewTop.Atoms(), NewTop.Residues());
+  Cpptraj::Parm::MergeBondArray(chamber_.SetUB(), chamber_.SetUBparm(), atoms_,
+                                NewTop.chamber_.UB(), NewTop.chamber_.UBparm(), NewTop.Atoms());
 
   // Append incoming atoms to this topology.
   for (atom_iterator atom = NewTop.begin(); atom != NewTop.end(); ++atom)
@@ -2688,7 +2690,7 @@ int Topology::AppendTop(Topology const& NewTop) {
   //          it - allBonds.begin(), it->A1()+1, it->A2()+1);
   //addBondsWithOffset( bonds_, NewTop.Bonds(), atomOffset, atoms_ );
   //addBondsWithOffset( bondsh_, NewTop.BondsH(), atomOffset, atoms_ );
-  addBondsWithOffset( chamber_.SetUB(), NewTop.chamber_.UB(), atomOffset, atoms_ );
+  //addBondsWithOffset( chamber_.SetUB(), NewTop.chamber_.UB(), atomOffset, atoms_ );
   //addAnglesWithOffset( angles_, NewTop.Angles(), atomOffset );
   //addAnglesWithOffset( anglesh_, NewTop.AnglesH(), atomOffset );
   //addDihedralsWithOffset( dihedrals_, NewTop.Dihedrals(), atomOffset );

From 6fef4e1df46e69213a65e24a33fa27bce8bc229f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 13 Mar 2024 11:05:39 -0400
Subject: [PATCH 0704/1492] Add merge for charmm impropers

---
 src/Parm/Merge.cpp | 20 ++++++++++++++++++++
 src/Parm/Merge.h   |  3 +++
 src/Topology.cpp   |  5 +++--
 3 files changed, 26 insertions(+), 2 deletions(-)

diff --git a/src/Parm/Merge.cpp b/src/Parm/Merge.cpp
index fe4b01c486..337e2e14de 100644
--- a/src/Parm/Merge.cpp
+++ b/src/Parm/Merge.cpp
@@ -614,3 +614,23 @@ void Cpptraj::Parm::MergeBondArray(BondArray& bonds0,
   mergeBonds.MergeTermArrays( bonds0, tmp,         bp0, atoms0,
                               bonds1, BondArray(), bp1, atoms1 );
 }
+
+// -----------------------------------------------------------------------------
+/** Given improper/improper parameter array from top0 and improper/improper
+  * parameter array from top1, merge the improper arrays and consolidate the
+  * parameters.
+  */
+void Cpptraj::Parm::MergeImproperArray(DihedralArray& impropers0,
+                                       DihedralParmArray& ip0,
+                                       AtArray const& atoms0,
+                                       DihedralArray const& impropers1,
+                                       DihedralParmArray const& ip1,
+                                       AtArray const& atoms1)
+{
+  MergeTopArray<DihedralType, DihedralParmType, DihedralArray, DihedralParmArray> mergeImpropers;
+  mergeImpropers.SetMergeWithExisting( true ); // FIXME check this
+  DihedralArray tmp;
+  // NOTE could be MergeTermArrays as well
+  mergeImpropers.MergeImproperArrays( impropers0, tmp,             ip0, atoms0,
+                                      impropers1, DihedralArray(), ip1, atoms1 );
+}
diff --git a/src/Parm/Merge.h b/src/Parm/Merge.h
index 8118ce471a..afe4f64d34 100644
--- a/src/Parm/Merge.h
+++ b/src/Parm/Merge.h
@@ -32,6 +32,9 @@ void MergeCmapArrays(CmapArray&, CmapGridArray&, AtArray const&, ResArray const&
 /// Merge two bond arrays and their parameters
 void MergeBondArray(BondArray&, BondParmArray&, AtArray const&,
                     BondArray const&, BondParmArray const&, AtArray const&);
+/// Merge two improper arrays and their parameters
+void MergeImproperArray(DihedralArray&, DihedralParmArray&, AtArray const&,
+                        DihedralArray const&, DihedralParmArray const&, AtArray const&);
 }
 }
 #endif
diff --git a/src/Topology.cpp b/src/Topology.cpp
index 3f50c19116..0e59555405 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2663,7 +2663,8 @@ int Topology::AppendTop(Topology const& NewTop) {
                                  NewTop.Cmap(), NewTop.CmapGrid(), NewTop.Atoms(), NewTop.Residues());
   Cpptraj::Parm::MergeBondArray(chamber_.SetUB(), chamber_.SetUBparm(), atoms_,
                                 NewTop.chamber_.UB(), NewTop.chamber_.UBparm(), NewTop.Atoms());
-
+  Cpptraj::Parm::MergeImproperArray(chamber_.SetImpropers(), chamber_.SetImproperParm(), atoms_,
+                                    NewTop.chamber_.Impropers(), NewTop.chamber_.ImproperParm(), NewTop.Atoms());
   // Append incoming atoms to this topology.
   for (atom_iterator atom = NewTop.begin(); atom != NewTop.end(); ++atom)
   {
@@ -2695,7 +2696,7 @@ int Topology::AppendTop(Topology const& NewTop) {
   //addAnglesWithOffset( anglesh_, NewTop.AnglesH(), atomOffset );
   //addDihedralsWithOffset( dihedrals_, NewTop.Dihedrals(), atomOffset );
   //addDihedralsWithOffset( dihedralsh_, NewTop.DihedralsH(), atomOffset );
-  addDihedralsWithOffset( chamber_.SetImpropers(), NewTop.chamber_.Impropers(), atomOffset );
+  //addDihedralsWithOffset( chamber_.SetImpropers(), NewTop.chamber_.Impropers(), atomOffset );
   //for (CmapArray::const_iterator cm = NewTop.Cmap().begin(); cm != NewTop.Cmap().end(); ++cm)
   //  cmap_.push_back( CmapType(cm->A1() + atomOffset,
   //                            cm->A2() + atomOffset,

From 8087edc3fb5adc3962faa68c3db3d80d642de917 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 13 Mar 2024 11:23:57 -0400
Subject: [PATCH 0705/1492] Clean up unused/unneeded code

---
 src/Topology.cpp | 160 +----------------------------------------------
 src/Topology.h   |   7 +--
 2 files changed, 3 insertions(+), 164 deletions(-)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index 0e59555405..8a8a90d503 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2507,55 +2507,6 @@ ParameterSet Topology::GetParameters() const {
 }
 
 // -----------------------------------------------------------------------------
-/*
-// Topology::AddBondArray()
-void Topology::AddBondArray(BondArray const& barray, BondParmArray const& bp, int atomOffset) {
-  if (bp.empty()) {
-    for (BondArray::const_iterator bond = barray.begin(); bond != barray.end(); ++bond)
-      AddBond( bond->A1() + atomOffset, bond->A2() + atomOffset );
-  } else {
-    bool missingParameters = false;
-    for (BondArray::const_iterator bond = barray.begin(); bond != barray.end(); ++bond) {
-      if (bond->Idx() > -1)
-        AddBond( bond->A1() + atomOffset, bond->A2() + atomOffset, bp[bond->Idx()] );
-      else {
-        missingParameters = true;
-        AddBond( bond->A1() + atomOffset, bond->A2() + atomOffset );
-      }
-    }
-    if (missingParameters)
-      mprintf("Warning: Some bonds were missing parameters.\n");
-  }
-}
-
-// Topology::AddAngleArray()
-void Topology::AddAngleArray(AngleArray const& aarray, AngleParmArray const& ap, int atomOffset) {
-  if (ap.empty())
-    for (AngleArray::const_iterator angle = aarray.begin(); angle != aarray.end(); ++angle)
-      AddAngle( angle->A1() + atomOffset,
-                angle->A2() + atomOffset,
-                angle->A3() + atomOffset );
-  else
-    for (AngleArray::const_iterator angle = aarray.begin(); angle != aarray.end(); ++angle)
-      AddAngle( angle->A1() + atomOffset,
-                angle->A2() + atomOffset,
-                angle->A3() + atomOffset, ap[angle->Idx()] );
-}
-
-// Topology::AddDihArray()
-void Topology::AddDihArray(DihedralArray const& darray, DihedralParmArray const& dp, int atomOffset)
-{
-  if (dp.empty())
-    for (DihedralArray::const_iterator dih = darray.begin(); dih != darray.end(); ++dih)
-      AddDihedral( DihedralType( dih->A1() + atomOffset, dih->A2() + atomOffset,
-                                 dih->A3() + atomOffset, dih->A4() + atomOffset,
-                                 dih->Type() ), -1 );
-  else
-    for (DihedralArray::const_iterator dih = darray.begin(); dih != darray.end(); ++dih)
-      AddDihedral( DihedralType( dih->A1() + atomOffset, dih->A2() + atomOffset,
-                                 dih->A3() + atomOffset, dih->A4() + atomOffset,
-                                 dih->Type() ), dp[dih->Idx()] );
-}*/
 
 /** This template can be used when doing Append() on a generic std::vector array
   * of type T. The array will be appended to a given array of the same type.
@@ -2584,46 +2535,6 @@ template <class T> class TopVecAppend {
     }
 };
 
-/// Add bonds to array with given atom offset
-static inline void addBondsWithOffset(BondArray& bondsOut, BondArray const& bondsIn, int atomOffset, std::vector<Atom>const& atoms) {
-  // By convention any hydrogen atom should come second
-  for (BondArray::const_iterator bond = bondsIn.begin(); bond != bondsIn.end(); ++bond)
-  {
-    int atom1 = bond->A1() + atomOffset;
-    int atom2 = bond->A2() + atomOffset;
-    bool a1H = (atoms[atom1].Element() == Atom::HYDROGEN);
-    //bool a2H = (atoms[atom2].Element() == Atom::HYDROGEN);
-    //mprintf("\t\t\tAdding bond %i to %i (isH=%i)\n",atom1+1,atom2+1,(int)isH);
-    if (a1H)
-      bondsOut.push_back( BondType(atom2, atom1, -1) );
-    else
-      bondsOut.push_back( BondType(atom1, atom2, -1) );
-    //if (a1H || a2H) {
-    //  if (a1H)
-    //    bondsh_.push_back( BondType(atom2, atom1, pidx) );
-    //  else
-    //    bondsh_.push_back( BondType(atom1, atom2, pidx) );
-    //} else
-    //  bonds_.push_back( BondType( atom1, atom2, pidx ) );
-    //bondsOut.push_back( BondType(bond->A1() + atomOffset, bond->A2() + atomOffset, -1) );
-  }
-}
-
-/// Add angles to array with given offset
-static inline void addAnglesWithOffset(AngleArray& anglesOut, AngleArray const& anglesIn, int atomOffset) {
-  for (AngleArray::const_iterator angle = anglesIn.begin(); angle != anglesIn.end(); ++angle)
-    anglesOut.push_back( AngleType(angle->A1() + atomOffset, angle->A2() + atomOffset, angle->A3() + atomOffset, -1) );
-}
-
-/// Add dihedrals to array with given offset
-static inline void addDihedralsWithOffset(DihedralArray& dihedralsOut, DihedralArray const& dihedralsIn, int atomOffset)
-{
-  for (DihedralArray::const_iterator dih = dihedralsIn.begin(); dih != dihedralsIn.end(); ++dih)
-    dihedralsOut.push_back( DihedralType( dih->A1() + atomOffset, dih->A2() + atomOffset,
-                                          dih->A3() + atomOffset, dih->A4() + atomOffset,
-                                          dih->Type(), -1 ) );
-}
-
 // Topology::AppendTop()
 int Topology::AppendTop(Topology const& NewTop) {
   unsigned int atomOffset = atoms_.size();
@@ -2632,13 +2543,6 @@ int Topology::AppendTop(Topology const& NewTop) {
           NewTop.c_str(), c_str(), atomOffset, molOffset);
   //int resOffset = (int)residues_.size();
 
-// NOTE: Lines commented out with //# can be used to test appending via the
-//       parameter update functionality. This is slower, but is a good test
-//       that the parameter update function is working correctly.
-  // Save old parameters
-  //mprintf("DEBUG: Getting old parameters.\n");
-  //ParameterSet oldParams = GetParameters();
-  //oldParams.Summary(); // DEBUG
   // Save nonbonded parameters from each topology
   ParmHolder<AtomType> myAtomTypes, newAtomTypes;
   ParmHolder<NonbondType> myNB, newNB;
@@ -2665,6 +2569,8 @@ int Topology::AppendTop(Topology const& NewTop) {
                                 NewTop.chamber_.UB(), NewTop.chamber_.UBparm(), NewTop.Atoms());
   Cpptraj::Parm::MergeImproperArray(chamber_.SetImpropers(), chamber_.SetImproperParm(), atoms_,
                                     NewTop.chamber_.Impropers(), NewTop.chamber_.ImproperParm(), NewTop.Atoms());
+  // FIXME TODO LJ 1-4 terms
+
   // Append incoming atoms to this topology.
   for (atom_iterator atom = NewTop.begin(); atom != NewTop.end(); ++atom)
   {
@@ -2682,48 +2588,6 @@ int Topology::AppendTop(Topology const& NewTop) {
                 Residue(res.Name(), res.OriginalResNum(), res.Icode(), res.ChainId()),
                 atom->MolNum()+molOffset, NewTop.Mol(atom->MolNum()).IsSolvent() );
   }
-  // Recreate bonds for the added atoms
-  // DEBUG TEST
-  //BondArray allBonds;
-  //Cpptraj::Structure::MergeBondArrays(allBonds, NewTop.Bonds(), NewTop.BondsH(), NewTop.Atoms() );
-  //for (BondArray::const_iterator it = allBonds.begin(); it != allBonds.end(); ++it)
-  //  mprintf("DEBUG: Merged bond array %li : %i - %i\n",
-  //          it - allBonds.begin(), it->A1()+1, it->A2()+1);
-  //addBondsWithOffset( bonds_, NewTop.Bonds(), atomOffset, atoms_ );
-  //addBondsWithOffset( bondsh_, NewTop.BondsH(), atomOffset, atoms_ );
-  //addBondsWithOffset( chamber_.SetUB(), NewTop.chamber_.UB(), atomOffset, atoms_ );
-  //addAnglesWithOffset( angles_, NewTop.Angles(), atomOffset );
-  //addAnglesWithOffset( anglesh_, NewTop.AnglesH(), atomOffset );
-  //addDihedralsWithOffset( dihedrals_, NewTop.Dihedrals(), atomOffset );
-  //addDihedralsWithOffset( dihedralsh_, NewTop.DihedralsH(), atomOffset );
-  //addDihedralsWithOffset( chamber_.SetImpropers(), NewTop.chamber_.Impropers(), atomOffset );
-  //for (CmapArray::const_iterator cm = NewTop.Cmap().begin(); cm != NewTop.Cmap().end(); ++cm)
-  //  cmap_.push_back( CmapType(cm->A1() + atomOffset,
-  //                            cm->A2() + atomOffset,
-  //                            cm->A3() + atomOffset,
-  //                            cm->A4() + atomOffset,
-  //                            cm->A5() + atomOffset, -1) );
-//#  for (BondArray::const_iterator bond = NewTop.Bonds().begin(); bond != NewTop.Bonds().end(); ++bond)
-//#    AddBond( bond->A1() + atomOffset, bond->A2() + atomOffset );
-//#  for (BondArray::const_iterator bond = NewTop.BondsH().begin(); bond != NewTop.BondsH().end(); ++bond)
-//#    AddBond( bond->A1() + atomOffset, bond->A2() + atomOffset );
-//#  // Recreate angles for the added atoms
-//#  for (AngleArray::const_iterator angle = NewTop.Angles().begin(); angle != NewTop.Angles().end(); ++angle)
-//#      AddAngle( angle->A1() + atomOffset, angle->A2() + atomOffset, angle->A3() + atomOffset );
-//#  for (AngleArray::const_iterator angle = NewTop.AnglesH().begin(); angle != NewTop.AnglesH().end(); ++angle)
-//#      AddAngle( angle->A1() + atomOffset, angle->A2() + atomOffset, angle->A3() + atomOffset );
-//#  // Recreate dihedrals for the added atoms
-//#  for (DihedralArray::const_iterator dih = NewTop.Dihedrals().begin(); dih != NewTop.Dihedrals().end(); ++dih)
-//#      AddDihedral( DihedralType( dih->A1() + atomOffset, dih->A2() + atomOffset,
-//#                                 dih->A3() + atomOffset, dih->A4() + atomOffset,
-//#                                 dih->Type() ) );
-//#  for (DihedralArray::const_iterator dih = NewTop.DihedralsH().begin(); dih != NewTop.DihedralsH().end(); ++dih)
-//#      AddDihedral( DihedralType( dih->A1() + atomOffset, dih->A2() + atomOffset,
-//#                                 dih->A3() + atomOffset, dih->A4() + atomOffset,
-//#                                 dih->Type() ) );
-  // Update parameters
-  //mprintf("DEBUG: Updating with new parameters.\n");
-  //updateParams( oldParams, NewTop.GetParameters() );
 
   // EXTRA ATOM INFO
   TopVecAppend<NameType> appendNameType;
@@ -2738,19 +2602,6 @@ int Topology::AppendTop(Topology const& NewTop) {
   appendFloat.Append( occupancy_, NewTop.occupancy_, NewTop.Natom() );
   appendFloat.Append( bfactor_, NewTop.bfactor_, NewTop.Natom() );
 
-/*  // BONDS
-  AddBondArray(NewTop.Bonds(),  NewTop.BondParm(), atomOffset);
-  AddBondArray(NewTop.BondsH(), NewTop.BondParm(), atomOffset);
-  // ANGLES
-  AddAngleArray(NewTop.Angles(),  NewTop.AngleParm(), atomOffset);
-  AddAngleArray(NewTop.AnglesH(), NewTop.AngleParm(), atomOffset);
-  // DIHEDRALS
-  AddDihArray(NewTop.Dihedrals(),  NewTop.DihedralParm(), atomOffset);
-  AddDihArray(NewTop.DihedralsH(), NewTop.DihedralParm(), atomOffset);
-  // UREY-BRADLEY TODO
-  // IMPROPERS TODO
-  // CMAP TODO
-*/
   // Need to regenerate nonbonded info
   mprintf("\tRegenerating nonbond parameters.\n");
   AssignNonbondParams( myAtomTypes, myNB, myHB, 1 ); // FIXME verbose
@@ -3704,17 +3555,10 @@ int Topology::AssignParams(ParameterSet const& set0) {
 }
 
 /** Update/add to parameters in this topology with those from given set.
-  * NOTE: This routine is separate from updateParams() to allow that
-  *       routine to be used by AppendTop() for testing the parameter
-  *       update code with topology appending.
   */
 int Topology::UpdateParams(ParameterSet const& set1) {
   ParameterSet set0 = GetParameters();
-  return updateParams(set0, set1);
-}
 
-/** Update/add to parameters in this topology by combining those from given sets. */
-int Topology::updateParams(ParameterSet& set0, ParameterSet const& set1) {
   //set1.Summary(); // DEBUG
   // Check TODO is this necessary?
   if (set0.AT().size() < 1)
diff --git a/src/Topology.h b/src/Topology.h
index 6dd39e18a3..1823fd6fa6 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -164,6 +164,7 @@ class Topology {
     double GetVDWdepth(int) const;
     /// \return Lennard-Jones 6-12 parameters for given pair of atoms
     inline NonbondType const& GetLJparam(int, int) const;
+    /// Assign LJ 6-12 / 10-12 parameters, reset atom type indices
     void AssignNonbondParams(ParmHolder<AtomType> const&, ParmHolder<NonbondType> const&,
                              ParmHolder<HB_ParmType> const&, int);
     /// \return True if any charge is non-zero
@@ -305,12 +306,6 @@ class Topology {
     void StripDihedralParmArray(DihedralArray&, std::vector<int>&, DihedralParmArray&) const;
     void StripDihedralParmArray(DihedralArray&, std::vector<int>&, DihedralParmArray&,
                                 DihedralParmArray const&) const;
-//    inline void AddBondArray(BondArray const&, BondParmArray const&, int);
-//    inline void AddAngleArray(AngleArray const&, AngleParmArray const&, int);
-//    inline void AddDihArray(DihedralArray const&, DihedralParmArray const&, int);
-
-    /// Update parameters in this Topology with those from combined sets.
-    int updateParams(ParameterSet&, ParameterSet const&);
 
     void AssignAtomTypeParm(ParmHolder<AtomType> const&);
     void AssignBondParm(ParmHolder<BondParmType> const&, BondArray&, BondParmArray&, const char*) const;

From 9292b4c5d3b0368ae87fe8bdd6167aaf278d8154 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 13 Mar 2024 16:26:04 -0400
Subject: [PATCH 0706/1492] Get rid of the separate charmm parameter class and
 just fold everything into the Topology class

---
 src/Energy_Sander.cpp  |   2 +-
 src/ParameterTypes.h   |  16 +++--
 src/Parm_Amber.cpp     |  80 +++++++++++------------
 src/Parm_CharmmPsf.cpp |   4 +-
 src/TopInfo.cpp        |  16 ++---
 src/Topology.cpp       | 141 +++++++++++++++++++++++------------------
 src/Topology.h         |  46 +++++++++++++-
 7 files changed, 185 insertions(+), 120 deletions(-)

diff --git a/src/Energy_Sander.cpp b/src/Energy_Sander.cpp
index 6e0d536744..1b155b6e53 100644
--- a/src/Energy_Sander.cpp
+++ b/src/Energy_Sander.cpp
@@ -351,7 +351,7 @@ int Energy_Sander::CommonInit(Topology const& topIn, Frame& fIn) { // TODO const
      )
     isActive_[HBOND] = true;
   // Are CHARMM terms present?
-  if (topIn.Chamber().HasChamber()) {
+  if (topIn.HasChamber()) {
     isActive_[ANGLE_UB] = true;
     isActive_[IMP] = true;
   }
diff --git a/src/ParameterTypes.h b/src/ParameterTypes.h
index af3cc37dc0..9481f98c57 100644
--- a/src/ParameterTypes.h
+++ b/src/ParameterTypes.h
@@ -655,8 +655,10 @@ class NonbondParmType {
     inline int Ntypes()                  const { return ntypes_;     }
     bool Has_C_Coeff()                   const { return !ccoef_.empty(); }
     std::vector<int> const& NBindex()    const { return nbindex_;    }
-    /// \return Array of LJ 12-6 A and B parameters
+    /// \return Array of LJ 6-12 A and B parameters
     NonbondArray     const& NBarray()    const { return nbarray_;    }
+    /// \return Array of LJ 6-12 1-4 A and B parameters
+    NonbondArray     const& LJ14()       const { return lj14_;       }
     /// \return Array of LJ 10-12 (hbond) parameters
     HB_ParmArray     const& HBarray()    const { return hbarray_;    }
     /// \return Array of LJ 12-6-4 C parameters
@@ -676,8 +678,12 @@ class NonbondParmType {
     }
     /// Set number of types, init NB index array, init LJ array.
     void SetupLJforNtypes(int n) { SetNtypes(n); nbarray_.assign((n*(n+1))/2, NonbondType()); }
+    /// Set number of LJ 1-4 terms
+    void SetNLJ14terms(int n)    { lj14_.assign( n, NonbondType() ); }
     /// Set specified LJ term
-    NonbondType& SetLJ(int i) { return nbarray_[i];                  }
+    NonbondType& SetLJ(int i)    { return nbarray_[i];                  }
+    /// Set specified LJ 1-4 term
+    NonbondType& SetLJ14(int i)  { return lj14_[i];    }
     /// Set number of HB terms and init HB array TODO combine with SetNtypes?
     void SetNHBterms(int n)   { hbarray_.assign( n, HB_ParmType() ); }
     /// Set specified HB term
@@ -715,11 +721,12 @@ class NonbondParmType {
       nbindex_[ntypes_ * type2 + type1] = ndx;
       hbarray_.push_back( HB );
     }
-    void Clear() { ntypes_ = 0; nbindex_.clear(); nbarray_.clear(); hbarray_.clear(); }
+    void Clear() { ntypes_ = 0; nbindex_.clear(); nbarray_.clear(); lj14_.clear(); hbarray_.clear(); }
   private:
     int ntypes_;               ///< Number of unique atom types
     std::vector<int> nbindex_; ///< Hold indices into arrays nbarray/hbarray for atom type pairs
     NonbondArray nbarray_;     ///< Hold Lennard-Jones 6-12 A and B parameters for all pairs.
+    NonbondArray lj14_;        ///< Lennard-Jones 6-12 1-4 parameters
     HB_ParmArray hbarray_;     ///< Hold 10-12 Amber HBond params for all pairs.
     std::vector<double> ccoef_; ///< Hold Lennard-Jones C parameters for 12-6-4 LJ potential.
 };
@@ -989,6 +996,7 @@ class CmapArray {
     CArray cmap_;
 };
 /// Hold CHAMBER parameters
+/*
 class ChamberParmType {
     typedef std::vector<std::string> Sarray;
   public:
@@ -1035,5 +1043,5 @@ class ChamberParmType {
     DihedralArray impropers_;        ///< Improper terms
     DihedralParmArray improperparm_; ///< Improper parameters
     NonbondArray lj14_;              ///< Lennard-Jones 1-4 parameters
-};
+};*/
 #endif
diff --git a/src/Parm_Amber.cpp b/src/Parm_Amber.cpp
index a3dd2d0fe4..0f4080db80 100644
--- a/src/Parm_Amber.cpp
+++ b/src/Parm_Amber.cpp
@@ -1263,7 +1263,7 @@ int Parm_Amber::ReadChamberFFtype(Topology& TopIn, FortranData const& FMT) {
       if (nlines > 0) {
         std::string ff_desc = NoTrailingWhitespace( ptr + FMT.Width() );
         mprintf("  %s\n", ff_desc.c_str());
-        TopIn.SetChamber().AddDescription( ff_desc );
+        TopIn.AddDescription( ff_desc );
         for (int line = 1; line < nlines; line++) {
           ptr = file_.NextLine();
           err = fftype_err(ptr, Flag);
@@ -1272,7 +1272,7 @@ int Parm_Amber::ReadChamberFFtype(Topology& TopIn, FortranData const& FMT) {
           else if (err == 2) break;
           ff_desc = NoTrailingWhitespace( ptr + FMT.Width() );
           mprintf("  %s\n", ff_desc.c_str());
-          TopIn.SetChamber().AddDescription( ff_desc );
+          TopIn.AddDescription( ff_desc );
         }
       }
     }
@@ -1286,8 +1286,8 @@ int Parm_Amber::ReadChamberUBCount(Topology& TopIn, FortranData const& FMT) {
   if (SetupBuffer(F_CHM_UBC, 2, FMT)) return 1;
   UB_count_[0] = atoi(file_.NextElement()); // Number of bonds
   UB_count_[1] = atoi(file_.NextElement()); // Number of parameters
-  TopIn.SetChamber().ReserveUBterms( UB_count_[0] );
-  TopIn.SetChamber().ResizeUBparm( UB_count_[1] );
+  TopIn.ReserveUBterms( UB_count_[0] );
+  TopIn.ResizeUBparm( UB_count_[1] );
   UB_count_[0] *= 3; // Number of bond terms (bonds x 3)
   return 0;
 }
@@ -1300,7 +1300,7 @@ int Parm_Amber::ReadChamberUBTerms(Topology& TopIn, FortranData const& FMT) {
     int a1 = atoi(file_.NextElement()) - 1;
     int a2 = atoi(file_.NextElement()) - 1;
     int bidx = atoi(file_.NextElement()) - 1;
-    TopIn.SetChamber().AddUBterm( BondType(a1, a2, bidx) );
+    TopIn.AddUBterm( BondType(a1, a2, bidx) );
   }
   return 0;
 }
@@ -1309,7 +1309,7 @@ int Parm_Amber::ReadChamberUBTerms(Topology& TopIn, FortranData const& FMT) {
 int Parm_Amber::ReadChamberUBFC(Topology& TopIn, FortranData const& FMT) {
   if (SetupBuffer(F_CHM_UBFC, UB_count_[1], FMT)) return 1;
   for (int idx = 0; idx != UB_count_[1]; idx++)
-    TopIn.SetChamber().SetUBparm(idx).SetRk( atof(file_.NextElement()) );
+    TopIn.SetUBparm(idx).SetRk( atof(file_.NextElement()) );
   return 0;
 }
 
@@ -1317,7 +1317,7 @@ int Parm_Amber::ReadChamberUBFC(Topology& TopIn, FortranData const& FMT) {
 int Parm_Amber::ReadChamberUBEQ(Topology& TopIn, FortranData const& FMT) {
   if (SetupBuffer(F_CHM_UBEQ, UB_count_[1], FMT)) return 1;
   for (int idx = 0; idx != UB_count_[1]; idx++)
-    TopIn.SetChamber().SetUBparm(idx).SetReq( atof(file_.NextElement()) );
+    TopIn.SetUBparm(idx).SetReq( atof(file_.NextElement()) );
   return 0;
 }
 
@@ -1325,7 +1325,7 @@ int Parm_Amber::ReadChamberUBEQ(Topology& TopIn, FortranData const& FMT) {
 int Parm_Amber::ReadChamberNumImpropers(Topology& TopIn, FortranData const& FMT) {
   if (SetupBuffer(F_CHM_NIMP, 1, FMT)) return 1;
   N_impropers_ = atoi(file_.NextElement());
-  TopIn.SetChamber().ReserveImproperTerms( N_impropers_ );
+  TopIn.ReserveImproperTerms( N_impropers_ );
   N_impropers_ *= 5; // Number of improper terms (impropers * 5)
   return 0;
 }
@@ -1334,7 +1334,7 @@ int Parm_Amber::ReadChamberNumImpropers(Topology& TopIn, FortranData const& FMT)
 int Parm_Amber::ReadChamberNumImpTerms(Topology& TopIn, FortranData const& FMT) {
   if (SetupBuffer(F_CHM_NIMPT, 1, FMT)) return 1;
   N_impTerms_ = atoi(file_.NextElement());
-  TopIn.SetChamber().ResizeImproperParm( N_impTerms_ );
+  TopIn.ResizeImproperParm( N_impTerms_ );
   return 0;
 }
 
@@ -1348,7 +1348,7 @@ int Parm_Amber::ReadChamberImpropers(Topology& TopIn, FortranData const& FMT) {
     int a3 = atoi(file_.NextElement()) - 1;
     int a4 = atoi(file_.NextElement()) - 1;
     int didx = atoi(file_.NextElement()) - 1;
-    TopIn.SetChamber().AddImproperTerm( DihedralType(a1, a2, a3, a4, didx) );
+    TopIn.AddImproperTerm( DihedralType(a1, a2, a3, a4, didx) );
   }
   return 0;
 }
@@ -1357,7 +1357,7 @@ int Parm_Amber::ReadChamberImpropers(Topology& TopIn, FortranData const& FMT) {
 int Parm_Amber::ReadChamberImpFC(Topology& TopIn, FortranData const& FMT) {
   if (SetupBuffer(F_CHM_IMPFC, N_impTerms_, FMT)) return 1;
   for (int idx = 0; idx != N_impTerms_; idx++)
-    TopIn.SetChamber().SetImproperParm(idx).SetPk( atof(file_.NextElement()) );
+    TopIn.SetImproperParm(idx).SetPk( atof(file_.NextElement()) );
   return 0;
 }
 
@@ -1365,18 +1365,18 @@ int Parm_Amber::ReadChamberImpFC(Topology& TopIn, FortranData const& FMT) {
 int Parm_Amber::ReadChamberImpPHASE(Topology& TopIn, FortranData const& FMT) {
   if (SetupBuffer(F_CHM_IMPP, N_impTerms_, FMT)) return 1;
   for (int idx = 0; idx != N_impTerms_; idx++)
-    TopIn.SetChamber().SetImproperParm(idx).SetPhase( atof(file_.NextElement()) );
+    TopIn.SetImproperParm(idx).SetPhase( atof(file_.NextElement()) );
   return 0;
 }
 
 // Parm_Amber::ReadChamberLJ14A()
 int Parm_Amber::ReadChamberLJ14A(Topology& TopIn, FortranData const& FMT) {
   // Ensure LJ terms are set up
-  if (TopIn.Chamber().LJ14().empty())
-    TopIn.SetChamber().SetNLJ14terms( numLJparm_ );
+  if (TopIn.Nonbond().LJ14().empty())
+    TopIn.SetNonbond().SetNLJ14terms( numLJparm_ );
   if (SetupBuffer(F_LJ14A, numLJparm_, FMT)) return 1;
   for (int idx = 0; idx != numLJparm_; idx++) {
-    TopIn.SetChamber().SetLJ14(idx).SetA( FileBufferToDouble(F_LJ14A, idx, numLJparm_) );
+    TopIn.SetNonbond().SetLJ14(idx).SetA( FileBufferToDouble(F_LJ14A, idx, numLJparm_) );
     if (atProblemFlag_) break;
   }
   return 0;
@@ -1385,11 +1385,11 @@ int Parm_Amber::ReadChamberLJ14A(Topology& TopIn, FortranData const& FMT) {
 // Parm_Amber::ReadChamberLJ14B()
 int Parm_Amber::ReadChamberLJ14B(Topology& TopIn, FortranData const& FMT) {
   // Ensure LJ terms are set up
-  if (TopIn.Chamber().LJ14().empty())
-    TopIn.SetChamber().SetNLJ14terms( numLJparm_ );
+  if (TopIn.Nonbond().LJ14().empty())
+    TopIn.SetNonbond().SetNLJ14terms( numLJparm_ );
   if (SetupBuffer(F_LJ14B, numLJparm_, FMT)) return 1;
   for (int idx = 0; idx != numLJparm_; idx++) {
-    TopIn.SetChamber().SetLJ14(idx).SetB( FileBufferToDouble(F_LJ14B, idx, numLJparm_) );
+    TopIn.SetNonbond().SetLJ14(idx).SetB( FileBufferToDouble(F_LJ14B, idx, numLJparm_) );
     if (atProblemFlag_) break;
   }
   return 0;
@@ -1806,7 +1806,7 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
   // Determine if this is a CHAMBER topology
   ptype_ = NEWPARM;
   FlagType titleFlag = F_TITLE;
-  if (TopOut.Chamber().HasChamber()) {
+  if (TopOut.HasChamber()) {
     if (!writeChamber_)
       mprintf("\tnochamber: Removing CHAMBER info from topology.\n");
     else {
@@ -1975,17 +1975,17 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
   file_.IntToBuffer( TopOut.NextraPts() ); // NEXTRA
   file_.FlushBuffer();
  
-  // CHAMBER only - FF type description 
+  // CHAMBER only - FF type description
   if (ptype_ == CHAMBER) {
     file_.Printf("%%FLAG %-74s\n%-80s\n", FLAGS_[F_FF_TYPE].Flag, FLAGS_[F_FF_TYPE].Fmt);
-    int nlines = (int)TopOut.Chamber().Description().size();
+    int nlines = (int)TopOut.Description().size();
     if (nlines > 99) {
       mprintf("Warning: Number of CHAMBER description lines > 99. Only writing 99.\n", nlines);
       nlines = 99;
     }
     if (nlines > 0) {
       for (int line = 0; line != nlines; line++)
-        file_.Printf("%2i%78s\n", nlines, TopOut.Chamber().Description()[line].c_str());
+        file_.Printf("%2i%78s\n", nlines, TopOut.Description()[line].c_str());
     } else {
       // No description. Write a placeholder.
       file_.Printf("%2i%78s\n", 1, "CHARMM:");
@@ -2077,13 +2077,13 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
   if (ptype_ == CHAMBER) {
     // UB COUNT
     if (BufferAlloc(F_CHM_UBC, 2)) return 1;
-    file_.IntToBuffer( TopOut.Chamber().UB().size() );
-    file_.IntToBuffer( TopOut.Chamber().UBparm().size() );
+    file_.IntToBuffer( TopOut.UB().size() );
+    file_.IntToBuffer( TopOut.UBparm().size() );
     file_.FlushBuffer();
     // UB terms
-    if (BufferAlloc(F_CHM_UB, TopOut.Chamber().UB().size()*3)) return 1;
-    for (BondArray::const_iterator it = TopOut.Chamber().UB().begin();
-                                   it != TopOut.Chamber().UB().end(); ++it)
+    if (BufferAlloc(F_CHM_UB, TopOut.UB().size()*3)) return 1;
+    for (BondArray::const_iterator it = TopOut.UB().begin();
+                                   it != TopOut.UB().end(); ++it)
     {
       file_.IntToBuffer( it->A1()+1 );
       file_.IntToBuffer( it->A2()+1 );
@@ -2091,7 +2091,7 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
     }
     file_.FlushBuffer();
     // UB FORCE CONSTANTS and EQ
-    if (WriteBondParm(F_CHM_UBFC, F_CHM_UBEQ, TopOut.Chamber().UBparm())) return 1;
+    if (WriteBondParm(F_CHM_UBFC, F_CHM_UBEQ, TopOut.UBparm())) return 1;
   }
 
   // DIHEDRAL PK
@@ -2133,12 +2133,12 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
   if (ptype_ == CHAMBER) {
     // NUM IMPROPERS
     if (BufferAlloc(F_CHM_NIMP, 1)) return 1;
-    file_.IntToBuffer( TopOut.Chamber().Impropers().size() );
+    file_.IntToBuffer( TopOut.Impropers().size() );
     file_.FlushBuffer();
     // IMPROPER TERMS
-    if (BufferAlloc(F_CHM_IMP, TopOut.Chamber().Impropers().size()*5)) return 1;
-    for (DihedralArray::const_iterator it = TopOut.Chamber().Impropers().begin();
-                                       it != TopOut.Chamber().Impropers().end(); ++it)
+    if (BufferAlloc(F_CHM_IMP, TopOut.Impropers().size()*5)) return 1;
+    for (DihedralArray::const_iterator it = TopOut.Impropers().begin();
+                                       it != TopOut.Impropers().end(); ++it)
     {
       file_.IntToBuffer( it->A1() + 1 );
       file_.IntToBuffer( it->A2() + 1 );
@@ -2155,18 +2155,18 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
     file_.FlushBuffer();
     // NUM IMPROPER PARAMS
     if (BufferAlloc(F_CHM_NIMPT, 1)) return 1;
-    file_.IntToBuffer( TopOut.Chamber().ImproperParm().size() );
+    file_.IntToBuffer( TopOut.ImproperParm().size() );
     file_.FlushBuffer();
     // IMPROPER FORCE CONSTANTS
-    if (BufferAlloc(F_CHM_IMPFC, TopOut.Chamber().ImproperParm().size())) return 1;
-    for (DihedralParmArray::const_iterator it = TopOut.Chamber().ImproperParm().begin();
-                                           it != TopOut.Chamber().ImproperParm().end(); ++it)
+    if (BufferAlloc(F_CHM_IMPFC, TopOut.ImproperParm().size())) return 1;
+    for (DihedralParmArray::const_iterator it = TopOut.ImproperParm().begin();
+                                           it != TopOut.ImproperParm().end(); ++it)
       file_.DblToBuffer( it->Pk() );
     file_.FlushBuffer();
     // IMPROPER PHASES
-    if (BufferAlloc(F_CHM_IMPP, TopOut.Chamber().ImproperParm().size())) return 1;
-    for (DihedralParmArray::const_iterator it = TopOut.Chamber().ImproperParm().begin();
-                                           it != TopOut.Chamber().ImproperParm().end(); ++it)
+    if (BufferAlloc(F_CHM_IMPP, TopOut.ImproperParm().size())) return 1;
+    for (DihedralParmArray::const_iterator it = TopOut.ImproperParm().begin();
+                                           it != TopOut.ImproperParm().end(); ++it)
       file_.DblToBuffer( it->Phase() );
     file_.FlushBuffer();
   }
@@ -2182,7 +2182,7 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
  
   // CHAMBER only - LJ 1-4 terms
   if (ptype_ == CHAMBER) {
-    if (WriteLJ(F_LJ14A, F_LJ14B, TopOut.Chamber().LJ14())) return 1;
+    if (WriteLJ(F_LJ14A, F_LJ14B, TopOut.Nonbond().LJ14())) return 1;
   }
 
   // BONDSH and BONDS
diff --git a/src/Parm_CharmmPsf.cpp b/src/Parm_CharmmPsf.cpp
index 2f0198cb13..93752f566a 100644
--- a/src/Parm_CharmmPsf.cpp
+++ b/src/Parm_CharmmPsf.cpp
@@ -566,9 +566,9 @@ int Parm_CharmmPsf::WriteParm(FileName const& fname, Topology const& parm) {
   if ((idx % 2)==0) outfile.Printf("\n");
   outfile.Printf("\n");
   // Write out NIMPHI section
-  WriteSectionHeader(outfile, "!NIMPHI: impropers", parm.Chamber().Impropers().size());
+  WriteSectionHeader(outfile, "!NIMPHI: impropers", parm.Impropers().size());
   idx = 1;
-  WriteDihedrals(parm.Chamber().Impropers(), idx, outfile, dihfmt);
+  WriteDihedrals(parm.Impropers(), idx, outfile, dihfmt);
   if ((idx % 2)==0) outfile.Printf("\n");
   outfile.Printf("\n");
 
diff --git a/src/TopInfo.cpp b/src/TopInfo.cpp
index 9fa244fa7f..3f7cca869c 100644
--- a/src/TopInfo.cpp
+++ b/src/TopInfo.cpp
@@ -476,8 +476,8 @@ void TopInfo::PrintBonds(BondArray const& barray, BondParmArray const& bondparm,
 int TopInfo::PrintBondInfo(std::string const& mask1exp, std::string const& mask2exp,
                            bool printUB) const
 {
-  if (printUB && !parm_->Chamber().HasChamber()) {
-    mprintf("Warning: '%s' does not have any CHARMM parameters.\n", parm_->c_str());
+  if (printUB && parm_->UB().empty()) {
+    mprintf("Warning: '%s' does not have any Urey-Bradley parameters.\n", parm_->c_str());
     return 0;
   }
   CharMask mask1( mask1exp );
@@ -489,8 +489,8 @@ int TopInfo::PrintBondInfo(std::string const& mask1exp, std::string const& mask2
   bool hasParams;
   if (printUB) {
     label = "#UB";
-    n_bonds = parm_->Chamber().UB().size();
-    hasParams = !parm_->Chamber().UBparm().empty();
+    n_bonds = parm_->UB().size();
+    hasParams = !parm_->UBparm().empty();
   } else {
     n_bonds = parm_->BondsH().size() + parm_->Bonds().size();
     hasParams = !parm_->BondParm().empty();
@@ -507,7 +507,7 @@ int TopInfo::PrintBondInfo(std::string const& mask1exp, std::string const& mask2
                    max_type_len_, "T1", max_type_len_, "T2");
   int nb = 1;
   if (printUB)
-    PrintBonds( parm_->Chamber().UB(), parm_->Chamber().UBparm(), mask1, mask2, nw, nb );
+    PrintBonds( parm_->UB(), parm_->UBparm(), mask1, mask2, nw, nb );
   else {
     PrintBonds( parm_->BondsH(), parm_->BondParm(), mask1, mask2, nw, nb );
     PrintBonds( parm_->Bonds(),  parm_->BondParm(), mask1, mask2, nw, nb );
@@ -689,8 +689,8 @@ int TopInfo::PrintDihedralInfo(std::string const& mask1exp, std::string const& m
   bool hasParams;
   if (printImpropers) {
     label = "Imp";
-    n_torsions = parm_->Chamber().Impropers().size();
-    hasParams = !parm_->Chamber().ImproperParm().empty();
+    n_torsions = parm_->Impropers().size();
+    hasParams = !parm_->ImproperParm().empty();
   } else {
     n_torsions = parm_->DihedralsH().size() + parm_->Dihedrals().size();
     hasParams = !parm_->DihedralParm().empty();
@@ -713,7 +713,7 @@ int TopInfo::PrintDihedralInfo(std::string const& mask1exp, std::string const& m
                    max_type_len_, "T3", max_type_len_, "T4");
   int nd = 1;
   if (printImpropers) {
-    PrintDihedrals( parm_->Chamber().Impropers(), parm_->Chamber().ImproperParm(), mask1, mask2, mask3, mask4, nw, nd, printExtraInfo );
+    PrintDihedrals( parm_->Impropers(), parm_->ImproperParm(), mask1, mask2, mask3, mask4, nw, nd, printExtraInfo );
   } else {
     PrintDihedrals( parm_->DihedralsH(), parm_->DihedralParm(), mask1, mask2, mask3, mask4, nw, nd, printExtraInfo );
     PrintDihedrals( parm_->Dihedrals(),  parm_->DihedralParm(), mask1, mask2, mask3, mask4, nw, nd, printExtraInfo );
diff --git a/src/Topology.cpp b/src/Topology.cpp
index 8a8a90d503..304964e022 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -419,13 +419,13 @@ void Topology::Summary() const {
     if (nonbond_.Has_C_Coeff())
       mprintf("\t\t\tLJ 12-6-4 C coefficients are present.\n");
   }
-  if (chamber_.HasChamber()) {
-    mprintf("\t\tCHAMBER: %zu Urey-Bradley terms, %zu Impropers\n",
-            chamber_.UB().size(), chamber_.Impropers().size());
-    if (HasCmap())
-      mprintf("\t\t         %zu CMAP grids, %zu CMAP terms.\n", 
-              CmapGrid().size(), Cmap().size());
+  if (HasChamber()) {
+    mprintf("\t\tCHAMBER: %zu Urey-Bradley terms, %zu Impropers, %zu LJ 1-4 terms.\n",
+            ub_.size(), impropers_.size(), nonbond_.LJ14().size());
   }
+  if (HasCmap())
+    mprintf("\t\t%zu CMAP grids, %zu CMAP terms.\n", 
+            CmapGrid().size(), Cmap().size());
   if (lesparm_.HasLES())
     mprintf("\t\tLES info: %i types, %i copies\n", lesparm_.Ntypes(), lesparm_.Ncopies());
   if (cap_.HasWaterCap())
@@ -709,7 +709,11 @@ void Topology::Resize(Pointers const& pIn) {
   nonbond_.Clear();
   cap_.Clear();
   lesparm_.Clear();
-  chamber_.Clear();
+  ff_desc_.clear();
+  ub_.clear();
+  ubparm_.clear();
+  impropers_.clear();
+  improperparm_.clear();
   tree_.clear();
   ijoin_.clear();
   irotat_.clear();
@@ -1130,10 +1134,18 @@ void Topology::AddToDihedralArrays(DihedralType const& dih) {
     dihedrals_.push_back( dih );
 }
 
+/** \return true if any CHARMM parameters are set (based on indices). */
+bool Topology::HasChamber() const {
+  if (!ub_.empty()) return true;
+  if (!impropers_.empty()) return true;
+  if (!nonbond_.LJ14().empty()) return true;
+  return false;
+}
+
 /** Add given Charmm improper with given improper parm to Charmm improper array. */
 void Topology::AddCharmmImproper(DihedralType const& imp, DihedralParmType const& IPin)
 {
-  int pidx = addTorsionParm(chamber_.SetImproperParm(), IPin);
+  int pidx = addTorsionParm(improperparm_, IPin);
   if (CheckTorsionRange(imp, "CHARMM improper")) return;
   AddCharmmImproper(imp, pidx);
 }
@@ -1142,9 +1154,9 @@ void Topology::AddCharmmImproper(DihedralType const& imp, DihedralParmType const
 void Topology::AddCharmmImproper(DihedralType const& impIn, int pidxIn)
 {
   if (CheckTorsionRange(impIn, "CHARMM improper")) return;
-  DihedralType imp = SetTorsionParmIndex(impIn, chamber_.ImproperParm(), pidxIn, "CHARMM improper");
+  DihedralType imp = SetTorsionParmIndex(impIn, improperparm_, pidxIn, "CHARMM improper");
   // Update Charmm improper array.
-  chamber_.AddImproperTerm( imp );
+  impropers_.push_back( imp );
 }
 
 // -----------------------------------------------------------------------------
@@ -1757,8 +1769,8 @@ Topology* Topology::ModifyByMap(std::vector<int> const& MapIn, bool setupFullPar
     //mprintf("DEBUG: # new types %zu\n", oldTypeArray.size());
     // Set up new nonbond and nonbond index arrays.
     newParm->nonbond_.SetNtypes( oldTypeArray.size() );
-    if (chamber_.HasChamber())
-      newParm->chamber_.SetNLJ14terms( (oldTypeArray.size()*(oldTypeArray.size()+1))/2 );
+    if (!nonbond_.LJ14().empty())
+      newParm->nonbond_.SetNLJ14terms( (oldTypeArray.size()*(oldTypeArray.size()+1))/2 );
     for (int a1idx = 0; a1idx != (int)oldTypeArray.size(); a1idx++)
     {
       int atm1 = oldTypeArray[a1idx];
@@ -1780,7 +1792,7 @@ Topology* Topology::ModifyByMap(std::vector<int> const& MapIn, bool setupFullPar
         //int newnbidx = newParm->nonbond_.GetLJindex( a1idx, a2idx );
         //mprintf("DEBUG: oldtypei=%i oldtypej=%i Old NB index=%i, newtypi=%i newtypej=%i new NB idx=%i testidx=%i\n", 
         //        atm1, atm2, oldnbidx, a1idx, a2idx, newnbidx, testidx);
-        if (chamber_.HasChamber()) {
+        if (!nonbond_.LJ14().empty()) {
           // Update LJ 1-4 as well. No need to worry about hbond terms here,
           // just recalculate the old index and determine new one.
           int ibig = std::max(atm1, atm2) + 1;
@@ -1789,7 +1801,7 @@ Topology* Topology::ModifyByMap(std::vector<int> const& MapIn, bool setupFullPar
               ibig = a2idx + 1;
               isml = a1idx + 1;
           int newnbidx = (ibig*(ibig-1)/2+isml)-1;
-          newParm->chamber_.SetLJ14( newnbidx ) = chamber_.LJ14()[oldnbidx];
+          newParm->nonbond_.SetLJ14( newnbidx ) = nonbond_.LJ14()[oldnbidx];
         }
       }
     }
@@ -1812,49 +1824,52 @@ Topology* Topology::ModifyByMap(std::vector<int> const& MapIn, bool setupFullPar
   if (cap_.HasWaterCap())
     mprintf("Warning: Stripping of CAP info not supported. Removing CAP info.\n");
   // CHAMBER info
-  if (chamber_.HasChamber()) {
-    newParm->chamber_.SetDescription( chamber_.Description() );
+  if (!ff_desc_.empty())
+    newParm->ff_desc_ = ff_desc_;
+  if (!ub_.empty()) {
     // Urey-Bradley
-    newParm->chamber_.SetUB() = StripBondArray(chamber_.UB(),atomMap);
-    parmMap.assign( chamber_.UBparm().size(), -1 ); // Map[oldidx] = newidx
-    StripBondParmArray( newParm->chamber_.SetUB(), parmMap,
-                        newParm->chamber_.SetUBparm(), chamber_.UBparm() );
+    newParm->ub_ = StripBondArray( ub_, atomMap );
+    parmMap.assign( ubparm_.size(), -1 ); // Map[oldidx] = newidx
+    StripBondParmArray( newParm->ub_, parmMap,
+                        newParm->ubparm_, ubparm_ );
+  }
+  if (!impropers_.empty()) {
     // Impropers
-    newParm->chamber_.SetImpropers() = StripDihedralArray(chamber_.Impropers(), atomMap);
-    parmMap.assign( chamber_.ImproperParm().size(), -1 );
-    StripDihedralParmArray( newParm->chamber_.SetImpropers(), parmMap,
-                            newParm->chamber_.SetImproperParm(), chamber_.ImproperParm() );
+    newParm->impropers_ = StripDihedralArray(impropers_, atomMap);
+    parmMap.assign( improperparm_.size(), -1 );
+    StripDihedralParmArray( newParm->impropers_, parmMap,
+                            newParm->improperparm_, improperparm_ );
     // NOTE 1-4 LJ parameters handled above
-    // CMAP terms
-    if (HasCmap()) {
-      // NOTE that atom indexing is updated but cmap indexing is not. So if
-      // any CMAP terms remain all CMAP entries remain.
-      for (CmapArray::const_iterator cmap = Cmap().begin();
-                                     cmap != Cmap().end(); ++cmap)
-      {
-        int newA1 = atomMap[ cmap->A1() ];
-        if (newA1 != -1) {
-          int newA2 = atomMap[ cmap->A2() ];
-          if (newA2 != -1) {
-            int newA3 = atomMap[ cmap->A3() ];
-            if (newA3 != -1) {
-              int newA4 = atomMap[ cmap->A4() ];
-              if (newA4 != -1) {
-                int newA5 = atomMap[ cmap->A5() ];
-                if (newA5 != -1)
-                  newParm->AddCmapTerm( CmapType(newA1,newA2,newA3,
-                                                          newA4,newA5,cmap->Idx()) );
-              }
+  }
+  // CMAP terms
+  if (HasCmap()) {
+    // NOTE that atom indexing is updated but cmap indexing is not. So if
+    // any CMAP terms remain all CMAP entries remain.
+    for (CmapArray::const_iterator cmap = Cmap().begin();
+                                   cmap != Cmap().end(); ++cmap)
+    {
+      int newA1 = atomMap[ cmap->A1() ];
+      if (newA1 != -1) {
+        int newA2 = atomMap[ cmap->A2() ];
+        if (newA2 != -1) {
+          int newA3 = atomMap[ cmap->A3() ];
+          if (newA3 != -1) {
+            int newA4 = atomMap[ cmap->A4() ];
+            if (newA4 != -1) {
+              int newA5 = atomMap[ cmap->A5() ];
+              if (newA5 != -1)
+                newParm->AddCmapTerm( CmapType(newA1,newA2,newA3,
+                                                        newA4,newA5,cmap->Idx()) );
             }
           }
         }
       }
-      // Only add CMAP grids if there are CMAP terms left.
-      if (!newParm->Cmap().empty()) {
-        for (CmapGridArray::const_iterator g = CmapGrid().begin();
-                                           g != CmapGrid().end(); ++g)
-          newParm->AddCmapGrid( *g );
-      }
+    }
+    // Only add CMAP grids if there are CMAP terms left.
+    if (!newParm->Cmap().empty()) {
+      for (CmapGridArray::const_iterator g = CmapGrid().begin();
+                                         g != CmapGrid().end(); ++g)
+        newParm->AddCmapGrid( *g );
     }
   }
   // Amber extra info.
@@ -2492,11 +2507,13 @@ ParameterSet Topology::GetParameters() const {
   GetDihedralParams( Params.DP(), Params.IP(), atoms_, dihedrals_, dihedralparm_);
   GetDihedralParams( Params.DP(), Params.IP(), atoms_, dihedralsh_, dihedralparm_);
   // CHARMM parameters
-  if (chamber_.HasChamber()) {
+  if (!ub_.empty()) {
     // UB parameters
-    GetBondParams(Params.UB(), atoms_, chamber_.UB(), chamber_.UBparm());
+    GetBondParams(Params.UB(), atoms_, ub_, ubparm_);
+  }
+  if (!impropers_.empty()) {
     // Impropers
-    GetImproperParams( Params.IP(), atoms_, chamber_.Impropers(), chamber_.ImproperParm() );
+    GetImproperParams( Params.IP(), atoms_, impropers_, improperparm_ );
   }
   // CMAPs
   if (GetCmapParams( Params.CMAP(), cmap_, cmapGrid_, atoms_, residues_ )) {
@@ -2565,10 +2582,10 @@ int Topology::AppendTop(Topology const& NewTop) {
                                      NewTop.Dihedrals(), NewTop.DihedralsH(), NewTop.DihedralParm(), NewTop.Atoms());
   Cpptraj::Parm::MergeCmapArrays(cmap_, cmapGrid_, atoms_, residues_,
                                  NewTop.Cmap(), NewTop.CmapGrid(), NewTop.Atoms(), NewTop.Residues());
-  Cpptraj::Parm::MergeBondArray(chamber_.SetUB(), chamber_.SetUBparm(), atoms_,
-                                NewTop.chamber_.UB(), NewTop.chamber_.UBparm(), NewTop.Atoms());
-  Cpptraj::Parm::MergeImproperArray(chamber_.SetImpropers(), chamber_.SetImproperParm(), atoms_,
-                                    NewTop.chamber_.Impropers(), NewTop.chamber_.ImproperParm(), NewTop.Atoms());
+  Cpptraj::Parm::MergeBondArray(ub_, ubparm_, atoms_,
+                                NewTop.ub_, NewTop.ubparm_, NewTop.Atoms());
+  Cpptraj::Parm::MergeImproperArray(impropers_, improperparm_, atoms_,
+                                    NewTop.impropers_, NewTop.improperparm_, NewTop.Atoms());
   // FIXME TODO LJ 1-4 terms
 
   // Append incoming atoms to this topology.
@@ -2693,8 +2710,8 @@ void Topology::AssignBondParams(ParmHolder<BondParmType> const& newBondParams) {
 
 /** Replace any current Urey-Bradley parameters with given UB parameters. */
 void Topology::AssignUBParams(ParmHolder<BondParmType> const& newBondParams) {
-  chamber_.SetUBparm().clear();
-  AssignBondParm( newBondParams, chamber_.SetUB(), chamber_.SetUBparm(), "UB term" );
+  ubparm_.clear();
+  AssignBondParm( newBondParams, ub_, ubparm_, "UB term" );
 }
 
 /** Set parameters for angles in given angle array. */
@@ -2815,8 +2832,8 @@ const
 
 /** Replace any current improper parameters with given improper parameters. */
 void Topology::AssignImproperParams(ImproperParmHolder const& newImproperParams) {
-  chamber_.SetImproperParm().clear();
-  AssignImproperParm( newImproperParams, chamber_.SetImpropers(), chamber_.SetImproperParm() );
+  improperparm_.clear();
+  AssignImproperParm( newImproperParams, impropers_, improperparm_ );
 }
 
 /** Set parameters for dihedrals in given dihedral array.
@@ -3530,7 +3547,7 @@ int Topology::AssignParams(ParameterSet const& set0) {
   // Urey-Bradley
   mprintf("\tAssigning Urey-Bradley parameters.\n");
   AssignUBParams( set0.UB() );
-  if (!chamber_.Impropers().empty()) {
+  if (!impropers_.empty()) {
     // Charmm Improper parameters
     mprintf("\tAssigning CHARMM improper parameters.\n");
     AssignImproperParams( set0.IP() );
diff --git a/src/Topology.h b/src/Topology.h
index 1823fd6fa6..222fba7352 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -25,6 +25,8 @@ class Topology {
     void SetGBradiiSet(std::string const& s) { radius_set_ = s;              }
     void SetParmName(std::string const&, FileName const&);
     void SetDistMaskRef( Frame const& );
+    /// Add forcefield description
+    void AddDescription(std::string const& s) { ff_desc_.push_back( s ); }
     // ----- Return internal variables -----------
     int Ipol()                     const { return ipol_;                  }
     int Pindex()                   const { return pindex_;                }
@@ -33,6 +35,8 @@ class Topology {
     int Nmol()                     const { return (int)molecules_.size(); }
     int Nsolvent()                 const { return NsolventMolecules_;     }
     int NextraPts()                const { return n_extra_pts_;           }
+    /// \return Strings describing forcefield
+    std::vector<std::string> const& Description() const { return ff_desc_; }
     /// \return number of unique atom types
     unsigned int NuniqueAtomTypes() const;
     std::string const& ParmName()         const { return parmName_;       }
@@ -178,8 +182,37 @@ class Topology {
     LES_ParmType  const& LES()    const { return lesparm_; }
     LES_ParmType&        SetLES()       { return lesparm_; }
     // ----- CHAMBER info ------------------------
-    ChamberParmType const& Chamber()        const { return chamber_;      }
-    ChamberParmType& SetChamber()                 { return chamber_;      }
+    /// \return true if any CHARMM parameters are set (based on indices).
+    bool HasChamber() const;
+
+    /// Reserve space for future UB terms
+    void ReserveUBterms(unsigned int n)       { ub_.reserve( n );                 }
+    /// Resize for given number of UB parameters
+    void ResizeUBparm(unsigned int n)         { ubparm_.resize( n );              }
+    /// Add a Urey-Bradley term
+    void AddUBterm(BondType const& bnd)       { ub_.push_back( bnd );             }
+    /// Set specified Urey-Bradley parameter
+    BondParmType& SetUBparm(unsigned int idx) { return ubparm_[idx];              }
+    /// \return Array of Urey-Bradley terms
+    BondArray         const& UB()       const { return ub_;           }
+    /// \return Array of Urey-Bradley parameters
+    BondParmArray     const& UBparm()   const { return ubparm_;       }
+
+
+    /// Reserve space for future improper terms
+    void ReserveImproperTerms(unsigned int n)         { impropers_.reserve( n );     }
+    /// Resize for given number of improper parameters
+    void ResizeImproperParm(unsigned int n)           { improperparm_.resize( n );   }
+    /// Add improper term
+    void AddImproperTerm(DihedralType const& dih)     { impropers_.push_back( dih ); }
+    /// Set specified improper parameter
+    DihedralParmType& SetImproperParm(unsigned int i) { return improperparm_[i];     }
+    /// \return Array of impropers
+    DihedralArray     const& Impropers()        const { return impropers_;    }
+    /// \return Array of improper parameters
+    DihedralParmArray const& ImproperParm()     const { return improperparm_; }
+
+
     void AddCharmmImproper(DihedralType const&, DihedralParmType const&);
     void AddCharmmImproper(DihedralType const&, int);
     void AddCharmmImproper(DihedralType const& i) { AddCharmmImproper(i, -1); }
@@ -264,6 +297,8 @@ class Topology {
     /// Append topology to this one.
     int AppendTop( Topology const& );
   private:
+    typedef std::vector<std::string> Sarray;
+
     void SetAtomBondInfo(BondArray const&);
     // NOTE: Use set so that elements are always sorted.
     typedef std::vector< std::set<Atom::AtomicElementType> > BP_mapType;
@@ -348,7 +383,12 @@ class Topology {
     // Amber-only parameters
     CapParmType cap_;                ///< Water cap information
     LES_ParmType lesparm_;           ///< LES parameters
-    ChamberParmType chamber_;        ///< CHAMBER parameters
+    // Charmm parameters
+    Sarray ff_desc_;                 ///< Force field descriptions
+    BondArray ub_;                   ///< Urey-Bradley terms
+    BondParmArray ubparm_;           ///< Urey-Bradley parameters
+    DihedralArray impropers_;        ///< Improper terms
+    DihedralParmArray improperparm_; ///< Improper parameters
     // "Extra" Amber atom info
     std::vector<NameType> tree_;     ///< Amber TREE_CHAIN_CLASSIFICATION array
     std::vector<int> ijoin_;         ///< Amber JOIN_ARRAY array

From c58f5c1d1abe4ab493711d1792545eb7d3e79225 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 13 Mar 2024 21:58:14 -0400
Subject: [PATCH 0707/1492] start getting lj 1-4 parameters

---
 src/ParameterTypes.h | 2 ++
 src/Topology.cpp     | 9 ++++++++-
 2 files changed, 10 insertions(+), 1 deletion(-)

diff --git a/src/ParameterTypes.h b/src/ParameterTypes.h
index 9481f98c57..cf09f67d98 100644
--- a/src/ParameterTypes.h
+++ b/src/ParameterTypes.h
@@ -665,6 +665,8 @@ class NonbondParmType {
     std::vector<double> const& LJC_Array() const { return ccoef_; }
     /// \return LJ 6-12 A and B parameter at specified index
     NonbondType const& NBarray(int i)    const { return nbarray_[i]; }
+    /// \return LJ 6-12 1-4 A and B parameter at specified index
+    NonbondType const& LJ14(int i)       const { return lj14_[i]; }
     /// \return LJ 10-12 (hbond) parameter at specified index
     HB_ParmType const& HBarray(int i)    const { return hbarray_[i]; }
     /// In Amber, index < 0 means HB, otherwise LJ 6-12
diff --git a/src/Topology.cpp b/src/Topology.cpp
index 304964e022..833c0d7109 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2390,12 +2390,14 @@ static inline int GetCmapParams(CmapParmHolder& cmapParm, CmapArray const& cmapT
 
 /** \param atomTypesOut Output array of atom types.
   * \param LJ612out Output array of LJ 6-12 parameters.
+  * \param LJ14out Output array of LJ 6-12 1-4 parameters.
   * \param LJ1012out Output array of LJ 10-12 parameters.
   * \param atoms Current array of atoms.
   * \param NB0 Current nonbond parameters.
   */
 static inline void GetLJAtomTypes(ParmHolder<AtomType>& atomTypesOut,
                                   ParmHolder<NonbondType>& LJ612out,
+                                  ParmHolder<NonbondType>& LJ14out,
                                   ParmHolder<HB_ParmType>& LJ1012out,
                                   std::vector<Atom> const& atoms,
                                   NonbondParmType const& NB0,
@@ -2413,11 +2415,16 @@ static inline void GetLJAtomTypes(ParmHolder<AtomType>& atomTypesOut,
       TypeNameHolder atype( atm->Type() );
       // Check for self parameters to back-calculate LJ depth/radius
       int idx = NB0.GetLJindex( atm->TypeIndex(), atm->TypeIndex() );
-      AtomType thisType;
+      AtomType thisType, this14type;
       if (idx > -1) {
         // Has LJ 6-12 parameters
         NonbondType const& LJ = NB0.NBarray( idx );
         thisType = AtomType(LJ.Radius(), LJ.Depth(), atm->Mass(), atm->Polar());
+        if (!NB0.LJ14().empty()) {
+          NonbondType const& lj14 = NB0.LJ14( idx );
+          this14type = AtomType(lj14.Radius(), lj14.Depth(), atm->Mass(), atm->Polar()); // TODO mass and polar unneeded
+        }
+        // FIXME do LJ C
       } else {
         // Has LJ 10-12 parameters
         thisType = AtomType(atm->Mass(), atm->Polar());

From 583c08ecdf5ee320c67ab35144daca0992790460 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 14 Mar 2024 10:41:23 -0400
Subject: [PATCH 0708/1492] Save the 1-4 LJ parameters

---
 src/ParameterSet.cpp |  12 ++++-
 src/ParameterSet.h   |  13 ++++-
 src/Topology.cpp     | 119 ++++++++++++++++++++++++++++++++++++++-----
 3 files changed, 128 insertions(+), 16 deletions(-)

diff --git a/src/ParameterSet.cpp b/src/ParameterSet.cpp
index 31a669a079..d322f0e74a 100644
--- a/src/ParameterSet.cpp
+++ b/src/ParameterSet.cpp
@@ -9,14 +9,19 @@ size_t ParameterSet::DataSize() const {
   for (CmapGridArray::const_iterator it = CMAP_.begin(); it != CMAP_.end(); ++it)
     cmapsize += it->DataSize();
   return (atomTypes_.DataSize() +
+          nbParm_.DataSize() +
+          nb14Types_.DataSize() +
+          nb14Parm_.DataSize() +
           bondParm_.DataSize() +
           angleParm_.DataSize() +
           ubParm_.DataSize() +
-          dihParm_.DataSize() +
           impParm_.DataSize() +
+          dihParm_.DataSize() +
           HBparm_.DataSize() +
           cmapsize +
-          (hydrophilicAtomTypes_.size() * NameType::DataSize()));
+          (hydrophilicAtomTypes_.size() * NameType::DataSize()) +
+          sizeof(bool)
+         );
 }
 
 /** Write parameters out to file with given name. */
@@ -34,6 +39,7 @@ void ParameterSet::Summary() const {
   for (ParmHolder<AtomType>::const_iterator at = atomTypes_.begin(); at != atomTypes_.end(); ++at)
     mprintf(" %s", *(at->first[0]));
   mprintf("\n");
+  // TODO 1-4 types?
   mprintf("\t  %zu LJ 6-12 parameters.\n", nbParm_.size());
   mprintf("\t  %zu LJ 6-12 1-4 parameters.\n", nb14Parm_.size());
   mprintf("\t  %zu LJ 10-12 parameters.\n", HBparm_.size());
@@ -199,6 +205,8 @@ int ParameterSet::UpdateParamSet(ParameterSet const& set1, UpdateCount& uc, int
   uc.nAtomTypeUpdated_ = UpdateParameters< ParmHolder<AtomType> >(set0.AT(), set1.AT(), "atom type", verbose);
   // LJ Pairs
   uc.nLJparamsUpdated_ = UpdateParameters< ParmHolder<NonbondType> >(set0.NB(), set1.NB(), "LJ A-B", verbose);
+  // 1-4 atom types
+  uc.nLJ14typesUpdated_ = UpdateParameters< ParmHolder<AtomType> >(set0.AT14(), set1.AT14(), "LJ 1-4 type", verbose);
   // LJ 1-4 Pairs
   uc.nLJ14paramsUpdated_ = UpdateParameters< ParmHolder<NonbondType> >(set0.NB14(), set1.NB14(), "LJ A-B 1-4", verbose);
   // HB LJ 10-12 Pairs
diff --git a/src/ParameterSet.h b/src/ParameterSet.h
index 2beeb97d90..50ed9e9174 100644
--- a/src/ParameterSet.h
+++ b/src/ParameterSet.h
@@ -6,12 +6,17 @@
 #include "AtomType.h"
 class CpptrajFile;
 /// Hold a set of parameters for atom types, bonds, angles, etc.
+/** NOTE: Although LJ 6-12 regular type indices and 1-4 type indices
+  *       are currently the same, there is a separate 1-4 types variable
+  *       here in case that ever changes in the future.
+  */
 class ParameterSet {
   public:
     ParameterSet() : hasLJparams_(false) {}
 
     ParmHolder<AtomType>& AT()         { return atomTypes_; }
     ParmHolder<NonbondType>& NB()      { return nbParm_;    }
+    ParmHolder<AtomType>& AT14()       { return nb14Types_; }
     ParmHolder<NonbondType>& NB14()    { return nb14Parm_;  }
     ParmHolder<BondParmType>& BP()     { return bondParm_;  }
     ParmHolder<AngleParmType>& AP()    { return angleParm_; }
@@ -27,6 +32,7 @@ class ParameterSet {
 
     ParmHolder<AtomType> const& AT()         const { return atomTypes_; }
     ParmHolder<NonbondType> const& NB()      const { return nbParm_;    }
+    ParmHolder<AtomType> const& AT14()       const { return nb14Types_; }
     ParmHolder<NonbondType> const& NB14()    const { return nb14Parm_;  }
     ParmHolder<BondParmType> const& BP()     const { return bondParm_;  }
     ParmHolder<AngleParmType> const& AP()    const { return angleParm_; }
@@ -54,8 +60,9 @@ class ParameterSet {
         UpdateCount() : nBondsUpdated_(0), nAnglesUpdated_(0),
                         nDihedralsUpdated_(0), nImpropersUpdated_(0),
                         nUreyBradleyUpdated_(0), nAtomTypeUpdated_(0),
-                        nLJparamsUpdated_(0), nLJ14paramsUpdated_(0),
-                        nHBparamsUpdated_(0), nCmapUpdated_(0) {}
+                        nLJparamsUpdated_(0), nLJ14typesUpdated_(0),
+                        nLJ14paramsUpdated_(0), nHBparamsUpdated_(0),
+                        nCmapUpdated_(0) {}
         unsigned int nBondsUpdated_;
         unsigned int nAnglesUpdated_;
         unsigned int nDihedralsUpdated_;
@@ -63,6 +70,7 @@ class ParameterSet {
         unsigned int nUreyBradleyUpdated_;
         unsigned int nAtomTypeUpdated_;
         unsigned int nLJparamsUpdated_;
+        unsigned int nLJ14typesUpdated_;
         unsigned int nLJ14paramsUpdated_;
         unsigned int nHBparamsUpdated_;
         unsigned int nCmapUpdated_;
@@ -89,6 +97,7 @@ class ParameterSet {
 
     ParmHolder<AtomType> atomTypes_;       ///< Atom types
     ParmHolder<NonbondType> nbParm_;       ///< Lennard-Jones 6-12 A-B parameters
+    ParmHolder<AtomType> nb14Types_;       ///< Atom types for LJ 6-12 1-4 interactions
     ParmHolder<NonbondType> nb14Parm_;     ///< LJ 6-12 A-B parameters for 1-4 interactions
     ParmHolder<BondParmType> bondParm_;    ///< Hooke's law bond potential parameters
     ParmHolder<AngleParmType> angleParm_;  ///< Hooke's law angle potential parameters
diff --git a/src/Topology.cpp b/src/Topology.cpp
index 833c0d7109..2a08a2017f 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2388,6 +2388,82 @@ static inline int GetCmapParams(CmapParmHolder& cmapParm, CmapArray const& cmapT
   return 0;
 }
 
+/** Loop over atom type pairs, determine what the A and B
+  * parameters should be based on the LJ radius and depth,
+  * then compare to the existing A and B parameters.
+  * Warn if it does not match, store the current A and B
+  * parameters.
+  * \param atomTypesOut The atom types containing radii and depths.
+  * \param LJ612out The output LJ 6-12 A and B paramters.
+  * \param LJ1012ptr If not 0, the output LJ 10-12 parameters.
+  */
+static inline void GetLJterms(ParmHolder<AtomType> const& atomTypesOut,
+                              ParmHolder<NonbondType>& LJ612out,
+                              ParmHolder<HB_ParmType>* LJ1012ptr,
+                              NonbondParmType const& NB0,
+                              bool isLJ14,
+                              int debugIn)
+{
+    // Do atom type pairs, check for off-diagonal elements.
+    // Explicitly store pairs instead of regenerating to avoid round-off issues.
+    unsigned int nModifiedOffDiagonal = 0;
+    for (ParmHolder<AtomType>::const_iterator i1 = atomTypesOut.begin(); i1 != atomTypesOut.end(); ++i1)
+    {
+      for (ParmHolder<AtomType>::const_iterator i2 = i1; i2 != atomTypesOut.end(); ++i2)
+      {
+        NameType const& name1 = i1->first[0];
+        NameType const& name2 = i2->first[0];
+        TypeNameHolder types(2);
+        types.AddName( name1 );
+        types.AddName( name2 );
+        // Extract original nonbonded parameters for this type pair.
+        AtomType const& type1 = i1->second;
+        AtomType const& type2 = i2->second;
+        int idx1 = type1.OriginalIdx();
+        int idx2 = type2.OriginalIdx();
+        int idx = NB0.GetLJindex( idx1, idx2 );
+        if (idx < 0) {
+          // This is LJ 10-12.
+          //mprinterr("Error: No off-diagonal LJ for  %s %s (%i %i)\n",
+          //          *name1, *name2, idx1, idx2);
+          //return;
+          if (LJ1012ptr != 0) {
+            mprintf("DEBUG: LJ 10-12 parameters detected for %s %s (%i %i)\n",
+                    *name1, *name2, idx1, idx2);
+            LJ1012ptr->AddParm( types, NB0.HBarray((-idx)-1), false );
+          }
+        } else {
+          // This is LJ 6-12.
+          // Determine what A and B parameters would be.
+          NonbondType lj0 = type1.LJ().Combine_LB( type2.LJ() );
+
+          NonbondType lj1;
+          if (isLJ14)
+            lj1 = NB0.LJ14( idx );
+          else
+            lj1 = NB0.NBarray( idx );
+          // Compare them
+          if (lj0 != lj1) {
+            nModifiedOffDiagonal++;
+            //if (debugIn > 0) {
+              double deltaA = fabs(lj0.A() - lj1.A());
+              double deltaB = fabs(lj0.B() - lj1.B());
+              mprintf("DEBUG: Potential off-diagonal LJ: %s %s expect A=%g B=%g, actual A=%g B=%g\n",
+                      *name1, *name2, lj0.A(), lj0.B(), lj1.A(), lj1.B());
+              mprintf("DEBUG:\tdeltaA= %g    deltaB= %g\n", deltaA, deltaB);
+              double pe_a = (fabs(lj0.A() - lj1.A()) / lj0.A());
+              double pe_b = (fabs(lj0.B() - lj1.B()) / lj0.B());
+              mprintf("DEBUG:\tPEA= %g  PEB= %g\n", pe_a, pe_b);
+            //}
+          }
+          LJ612out.AddParm( types, lj1, false );
+        }
+      } // END inner loop over atom types
+    } // END outer loop over atom types
+    if (nModifiedOffDiagonal > 0)
+      mprintf("Warning: %u modified off-diagonal LJ terms present.\n", nModifiedOffDiagonal);
+}
+
 /** \param atomTypesOut Output array of atom types.
   * \param LJ612out Output array of LJ 6-12 parameters.
   * \param LJ14out Output array of LJ 6-12 1-4 parameters.
@@ -2397,6 +2473,7 @@ static inline int GetCmapParams(CmapParmHolder& cmapParm, CmapArray const& cmapT
   */
 static inline void GetLJAtomTypes(ParmHolder<AtomType>& atomTypesOut,
                                   ParmHolder<NonbondType>& LJ612out,
+                                  ParmHolder<AtomType>& LJ14typesOut,
                                   ParmHolder<NonbondType>& LJ14out,
                                   ParmHolder<HB_ParmType>& LJ1012out,
                                   std::vector<Atom> const& atoms,
@@ -2405,6 +2482,7 @@ static inline void GetLJAtomTypes(ParmHolder<AtomType>& atomTypesOut,
 {
   if (NB0.HasNonbond()) {
     mprintf("DEBUG: Topology has nonbond parameters.\n");
+    bool hasLJ14 = !NB0.LJ14().empty();
     // Nonbonded parameters are present.
     for (std::vector<Atom>::const_iterator atm = atoms.begin(); atm != atoms.end(); ++atm)
     {
@@ -2415,14 +2493,23 @@ static inline void GetLJAtomTypes(ParmHolder<AtomType>& atomTypesOut,
       TypeNameHolder atype( atm->Type() );
       // Check for self parameters to back-calculate LJ depth/radius
       int idx = NB0.GetLJindex( atm->TypeIndex(), atm->TypeIndex() );
-      AtomType thisType, this14type;
+      AtomType thisType;
       if (idx > -1) {
         // Has LJ 6-12 parameters
         NonbondType const& LJ = NB0.NBarray( idx );
         thisType = AtomType(LJ.Radius(), LJ.Depth(), atm->Mass(), atm->Polar());
-        if (!NB0.LJ14().empty()) {
+        if (hasLJ14) {
+          // NOTE: Even though we do not need mass/polarizability for LJ14 types,
+          //       use AtomType anyway so we can use the same routine as the
+          //       regular 6-12 terms for determining off-diagonal elements.
+          //LJparmType this14type;
           NonbondType const& lj14 = NB0.LJ14( idx );
-          this14type = AtomType(lj14.Radius(), lj14.Depth(), atm->Mass(), atm->Polar()); // TODO mass and polar unneeded
+          AtomType this14type = AtomType(lj14.Radius(), lj14.Depth(), 0, 0); // NOTE: empty mass/polarizability
+          this14type.SetTypeIdx( atm->TypeIndex() );
+          ParameterHolders::RetType ret14 = LJ14typesOut.AddParm( atype, this14type, true );
+          if (debugIn > 0 && ret14 == ParameterHolders::ADDED) {
+            mprintf("DEBUG: New LJ14 atom type: %s R=%g D=%g\n", *(atype[0]), this14type.LJ().Radius(), this14type.LJ().Depth());
+          }
         }
         // FIXME do LJ C
       } else {
@@ -2431,14 +2518,17 @@ static inline void GetLJAtomTypes(ParmHolder<AtomType>& atomTypesOut,
       }
       thisType.SetTypeIdx( atm->TypeIndex() );
       ParameterHolders::RetType ret = atomTypesOut.AddParm( atype, thisType, true );
-      if (debugIn > 0) {
-        if (ret == ParameterHolders::ADDED) {
-          mprintf("DEBUG: New atom type: %s R=%g D=%g M=%g P=%g\n", *(atype[0]), thisType.LJ().Radius(), thisType.LJ().Depth(), thisType.Mass(), thisType.Polarizability());
-        }
+      if (debugIn > 0 && ret == ParameterHolders::ADDED) {
+        mprintf("DEBUG: New atom type: %s R=%g D=%g M=%g P=%g\n", *(atype[0]),
+                thisType.LJ().Radius(), thisType.LJ().Depth(), thisType.Mass(), thisType.Polarizability());
       }
     }
     // Do atom type pairs, check for off-diagonal elements.
     // Explicitly store pairs instead of regenerating to avoid round-off issues.
+    GetLJterms(atomTypesOut, LJ612out, &LJ1012out, NB0, false, debugIn);
+    if (hasLJ14)
+      GetLJterms(LJ14typesOut, LJ14out, 0, NB0, true, debugIn);
+/*
     unsigned int nModifiedOffDiagonal = 0;
     for (ParmHolder<AtomType>::const_iterator i1 = atomTypesOut.begin(); i1 != atomTypesOut.end(); ++i1)
     {
@@ -2489,6 +2579,7 @@ static inline void GetLJAtomTypes(ParmHolder<AtomType>& atomTypesOut,
     } // END outer loop over atom types
     if (nModifiedOffDiagonal > 0)
       mprintf("Warning: %u modified off-diagonal LJ terms present.\n", nModifiedOffDiagonal);
+*/
   } else {
     if (!atoms.empty())
       mprintf("DEBUG: Topology does not have nonbond parameters.\n");
@@ -2503,7 +2594,7 @@ static inline void GetLJAtomTypes(ParmHolder<AtomType>& atomTypesOut,
 ParameterSet Topology::GetParameters() const {
   ParameterSet Params;
   // Atom LJ types
-  GetLJAtomTypes( Params.AT(), Params.NB(), Params.HB(), atoms_, nonbond_, debug_ );
+  GetLJAtomTypes( Params.AT(), Params.NB(), Params.AT14(), Params.NB14(), Params.HB(), atoms_, nonbond_, debug_ );
   // Bond parameters.
   GetBondParams( Params.BP(), atoms_, bonds_, bondparm_ );
   GetBondParams( Params.BP(), atoms_, bondsh_, bondparm_ );
@@ -2570,15 +2661,19 @@ int Topology::AppendTop(Topology const& NewTop) {
   // Save nonbonded parameters from each topology
   ParmHolder<AtomType> myAtomTypes, newAtomTypes;
   ParmHolder<NonbondType> myNB, newNB;
+  ParmHolder<AtomType> my14Types, new14Types;
+  ParmHolder<NonbondType> my14, new14;
   ParmHolder<HB_ParmType> myHB, newHB;
-  GetLJAtomTypes( myAtomTypes, myNB, myHB, atoms_, nonbond_, debug_ );
-  GetLJAtomTypes( newAtomTypes, newNB, newHB, NewTop.atoms_, NewTop.nonbond_, debug_ );
+  GetLJAtomTypes( myAtomTypes, myNB, my14Types, my14, myHB, atoms_, nonbond_, debug_ );
+  GetLJAtomTypes( newAtomTypes, newNB, new14Types, new14, newHB, NewTop.atoms_, NewTop.nonbond_, debug_ );
   // Create combined nonbond parameter set
   int nAtomTypeUpdated = UpdateParameters< ParmHolder<AtomType> >( myAtomTypes, newAtomTypes, "atom type", 1 ); // TODO verbose 
   int nLJparamsUpdated = UpdateParameters< ParmHolder<NonbondType> >( myNB, newNB, "LJ 6-12", 1 ); // TODO verbose
+  int n14TypeUpdated   = UpdateParameters< ParmHolder<AtomType> >( my14Types, new14Types, "1-4 atom type", 1) ; // TODO verbose
+  int n14paramsUpdated = UpdateParameters< ParmHolder<NonbondType> >( my14, new14, "LJ 6-12 1-4", 1); // TODO verbose
   int nHBparamsUpdated = UpdateParameters< ParmHolder<HB_ParmType> >( myHB, newHB, "LJ 10-12", 1); // TODO verbose
-  mprintf("\t%i atom types updated, %i LJ 6-12 params updated, %i LJ 10-12 params updated.\n",
-          nAtomTypeUpdated, nLJparamsUpdated, nHBparamsUpdated);
+  mprintf("\t%i atom types updated, %i LJ 6-12 params updated, %i 1-4 types updated, %i 1-4 params updated, %i LJ 10-12 params updated.\n",
+          nAtomTypeUpdated, nLJparamsUpdated, n14TypeUpdated, n14paramsUpdated, nHBparamsUpdated);
 
   // Add incoming topology bond/angle/dihedral/cmap arrays to this one.
   Cpptraj::Parm::MergeBondArrays(bonds_, bondsh_, bondparm_, atoms_,

From 557aab1ecfc4e024abc9810c93b3e4671cadd0aa Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 14 Mar 2024 11:28:14 -0400
Subject: [PATCH 0709/1492] Do 1-4 assignment

---
 src/ParameterTypes.h   |  4 ++-
 src/Parm_CharmmPsf.cpp |  2 +-
 src/Topology.cpp       | 57 +++++++++++++++++++++++++++++++++++-------
 src/Topology.h         |  1 +
 4 files changed, 53 insertions(+), 11 deletions(-)

diff --git a/src/ParameterTypes.h b/src/ParameterTypes.h
index cf09f67d98..c2e11d3ad7 100644
--- a/src/ParameterTypes.h
+++ b/src/ParameterTypes.h
@@ -699,8 +699,9 @@ class NonbondParmType {
       * nonbond index array; instead they expect the nonbond arrays to be
       * indexed like '(ibig*(ibig-1)/2+isml)', where ibig is the larger atom
       * type index.
+      * \return The index into nbarray_
       */
-    void AddLJterm(int type1, int type2, NonbondType const& LJ) {
+    int AddLJterm(int type1, int type2, NonbondType const& LJ) {
       int ibig, isml;
       if (type1 > type2) {
         ibig = type1 + 1;
@@ -715,6 +716,7 @@ class NonbondParmType {
       if (ndx >= (int)nbarray_.size())
         nbarray_.resize(ndx+1);
       nbarray_[ndx] = LJ;
+      return ndx;
     }
     /// Add given HB term to HB array and update the nonbond index array.
     void AddHBterm(int type1, int type2, HB_ParmType const& HB) {
diff --git a/src/Parm_CharmmPsf.cpp b/src/Parm_CharmmPsf.cpp
index 93752f566a..cd1f627fa7 100644
--- a/src/Parm_CharmmPsf.cpp
+++ b/src/Parm_CharmmPsf.cpp
@@ -377,7 +377,7 @@ int Parm_CharmmPsf::ReadParm(FileName const& fname, Topology &parmOut) {
 
   // Add nonbonded parameters
   if (params_.HasLJparams()) {
-    parmOut.AssignNonbondParams( atomTypes, params_.NB(), params_.HB(), debug_ );
+    parmOut.AssignNonbondParams( atomTypes, params_.NB(), params_.AT14(), params_.NB14(), params_.HB(), debug_ );
   }
 
   return 0;
diff --git a/src/Topology.cpp b/src/Topology.cpp
index 2a08a2017f..7de1ab8a02 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2723,7 +2723,7 @@ int Topology::AppendTop(Topology const& NewTop) {
 
   // Need to regenerate nonbonded info
   mprintf("\tRegenerating nonbond parameters.\n");
-  AssignNonbondParams( myAtomTypes, myNB, myHB, 1 ); // FIXME verbose
+  AssignNonbondParams( myAtomTypes, myNB, my14Types, my14, myHB, 1 ); // FIXME verbose
 
   // The version of AddTopAtom() with molecule number already determines
   // molecules and number of solvent molecules.
@@ -3221,11 +3221,14 @@ void Topology::AssignDihedralParams(DihedralParmHolder const& newDihedralParams,
 //TODO Accept array of atom type names?
 void Topology::AssignNonbondParams(ParmHolder<AtomType> const& newTypes,
                                    ParmHolder<NonbondType> const& newNB,
+                                   ParmHolder<AtomType> const& new14types,
+                                   ParmHolder<NonbondType> const& new14,
                                    ParmHolder<HB_ParmType> const& newHB,
                                    int verbose)
 {
+  bool hasLJ14 = !new14.empty();
   // Generate array of only the types that are currently in Topology. TODO should this be a permanent part of Topology?
-  ParmHolder<AtomType> currentAtomTypes;
+  ParmHolder<AtomType> currentAtomTypes, current14Types;
   for (std::vector<Atom>::const_iterator atm = atoms_.begin(); atm != atoms_.end(); ++atm)
   {
     if (atm->HasType()) {
@@ -3239,6 +3242,15 @@ void Topology::AssignNonbondParams(ParmHolder<AtomType> const& newTypes,
         newAT = AtomType(atm->Mass());
       }
       currentAtomTypes.AddParm( types, newAT, true );
+      // Find LJ14 types if needed
+      if (hasLJ14) {
+        AtomType new14AT = new14types.FindParam( types, found );
+        if (!found) {
+          mprintf("Warning: No 1-4 atom type information for type '%s'\n", *types[0]); // TODO error out here?
+          new14AT = AtomType(atm->Mass());
+        }
+        current14Types.AddParm( types, new14AT, true );
+      }
     }
   }
   if (currentAtomTypes.size() < 1) {
@@ -3268,6 +3280,8 @@ void Topology::AssignNonbondParams(ParmHolder<AtomType> const& newTypes,
   }
   mprintf("DEBUG: Setting up nonbond array for %i unique LJ types.\n", n_unique_lj_types);
   nonbond_.SetupLJforNtypes( n_unique_lj_types );
+  if (hasLJ14)
+    nonbond_.SetNLJ14terms( nonbond_.NBarray().size() );
   // Loop over all atom type pairs
   for (ParmHolder<AtomType>::const_iterator t1 = currentAtomTypes.begin(); t1 != currentAtomTypes.end(); ++t1)
   {
@@ -3298,10 +3312,33 @@ void Topology::AssignNonbondParams(ParmHolder<AtomType> const& newTypes,
           if (verbose > 0) mprintf("Using existing NB parameter for %s %s\n", *name1, *name2);
           LJAB = it->second;
         }
-        nonbond_.AddLJterm(t1->second.OriginalIdx(), t2->second.OriginalIdx(), LJAB);
-      }
-    }
-  }
+        int ljidx = nonbond_.AddLJterm(t1->second.OriginalIdx(), t2->second.OriginalIdx(), LJAB);
+        // LJ 1-4
+        if (hasLJ14) {
+          // Get parameter if it exists
+          ParmHolder<NonbondType>::const_iterator it = new14.GetParam( types );
+          if (it == new14.end()) {
+            if (verbose > 0) mprintf("NB 1-4 parameter for %s %s not found. Generating.\n", *name1, *name2);
+            bool found;
+            AtomType at14_1 = current14Types.FindParam(t1->first, found);
+            if (!found) {
+              mprinterr("Internal Error: LJ 1-4 parameter not found for %s\n", *name1);
+              return;
+            }
+            AtomType at14_2 = current14Types.FindParam(t2->first, found);
+            if (!found) {
+              mprinterr("Internal Error: LJ 1-4 parameter not found for %s\n", *name2);
+              return;
+            }
+            nonbond_.SetLJ14( ljidx ) = at14_1.LJ().Combine_LB( at14_2.LJ() );
+          } else {
+            if (verbose > 0) mprintf("Using existing NB 1-4 parameter for %s %s\n", *name1, *name2);
+            nonbond_.SetLJ14( ljidx ) = it->second;
+          }
+        } // END hasLJ14
+      } // END is LJ
+    } // END inner loop over current types
+  } // END outer loop over current types
   // Reset the atom type indices.
   for (std::vector<Atom>::iterator atm = atoms_.begin(); atm != atoms_.end(); ++atm)
   {
@@ -3666,7 +3703,7 @@ int Topology::AssignParams(ParameterSet const& set0) {
   AssignAtomTypeParm( set0.AT() );
   // LJ 6-12
   mprintf("\tAssigning nonbond parameters.\n");
-  AssignNonbondParams( set0.AT(), set0.NB(), set0.HB(), debug_ );
+  AssignNonbondParams( set0.AT(), set0.NB(), set0.AT14(), set0.NB14(), set0.HB(), debug_ );
   mprintf("DEBUG: CMAP size %zu\n", set0.CMAP().size());
   // TODO LJ14, LJC
 
@@ -3735,9 +3772,11 @@ int Topology::UpdateParams(ParameterSet const& set1) {
     AssignAtomTypeParm( set0.AT() );
   }
 //  updateCount += UpdateParameters< ParmHolder<NonbondType> >(set0.NB(), set1.NB(), "LJ A-B");
-  if (UC.nAtomTypeUpdated_ > 0) {
+  if (UC.nAtomTypeUpdated_ > 0 || UC.nLJ14typesUpdated_ > 0 ||
+      UC.nLJparamsUpdated_ > 0 || UC.nLJ14paramsUpdated_ > 0)
+  {
     mprintf("\tRegenerating nonbond parameters.\n");
-    AssignNonbondParams( set0.AT(), set0.NB(), set0.HB(), debug_ );
+    AssignNonbondParams( set0.AT(), set0.NB(), set0.AT14(), set0.NB14(), set0.HB(), debug_ );
   }
   // CMAP
   if (UC.nCmapUpdated_ > 0) {
diff --git a/src/Topology.h b/src/Topology.h
index 222fba7352..6ec30e0427 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -170,6 +170,7 @@ class Topology {
     inline NonbondType const& GetLJparam(int, int) const;
     /// Assign LJ 6-12 / 10-12 parameters, reset atom type indices
     void AssignNonbondParams(ParmHolder<AtomType> const&, ParmHolder<NonbondType> const&,
+                             ParmHolder<AtomType> const&, ParmHolder<NonbondType> const&,
                              ParmHolder<HB_ParmType> const&, int);
     /// \return True if any charge is non-zero
     bool HasChargeInfo() const;

From af5887621382b387ef91c2a16ca684a6a75f2a86 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 14 Mar 2024 11:35:58 -0400
Subject: [PATCH 0710/1492] Fix comment

---
 src/Topology.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index 7de1ab8a02..fdd4b25082 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2593,7 +2593,7 @@ static inline void GetLJAtomTypes(ParmHolder<AtomType>& atomTypesOut,
 /** \return ParameterSet for this Topology. */
 ParameterSet Topology::GetParameters() const {
   ParameterSet Params;
-  // Atom LJ types
+  // Atom LJ types and other nonbonded parameters.
   GetLJAtomTypes( Params.AT(), Params.NB(), Params.AT14(), Params.NB14(), Params.HB(), atoms_, nonbond_, debug_ );
   // Bond parameters.
   GetBondParams( Params.BP(), atoms_, bonds_, bondparm_ );

From bdc163693b5ce39b55e2d0f4e98385a33207049c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 14 Mar 2024 12:43:12 -0400
Subject: [PATCH 0711/1492] 1-4 terms done

---
 src/Topology.cpp | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index fdd4b25082..201090f9e7 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2688,7 +2688,6 @@ int Topology::AppendTop(Topology const& NewTop) {
                                 NewTop.ub_, NewTop.ubparm_, NewTop.Atoms());
   Cpptraj::Parm::MergeImproperArray(impropers_, improperparm_, atoms_,
                                     NewTop.impropers_, NewTop.improperparm_, NewTop.Atoms());
-  // FIXME TODO LJ 1-4 terms
 
   // Append incoming atoms to this topology.
   for (atom_iterator atom = NewTop.begin(); atom != NewTop.end(); ++atom)

From 310e5f6f32b9b41c4cc87cc54ca3bf4691daa9e1 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 15 Mar 2024 10:22:52 -0400
Subject: [PATCH 0712/1492] Fix cases when merging single arrays (e.g. UB terms
 or charmm impropers)

---
 src/Parm/Merge.cpp | 90 +++++++++++++++++++++++++++++++++-------------
 1 file changed, 66 insertions(+), 24 deletions(-)

diff --git a/src/Parm/Merge.cpp b/src/Parm/Merge.cpp
index 337e2e14de..5c77762f4e 100644
--- a/src/Parm/Merge.cpp
+++ b/src/Parm/Merge.cpp
@@ -144,26 +144,15 @@ class MergeTopArray
     MergeTopArray() : merge_with_existing_(false) {}
     /// Indicate parameters from top1 already present in top0 should not be added as new
     void SetMergeWithExisting(bool b) { merge_with_existing_ = b; }
-    /// Index type array
-    //typedef std::vector<IdxType> IdxArray;
-    /// Parm type array
-    //typedef std::vector<ParmType> ParmArray;
   private:
-    /// Append term1 to arrayX0/arrayY0 arrays along with parameters
-    void append_term(IdxArray& arrayX0,
-                     IdxArray& arrayY0,
-                     ParmArray& p0,
-                     unsigned int atomOffset,
-                     IdxType const& term1,
+    /// Append parameter for given types
+    /** \return Index of newly-added parameter to p0 */
+    int append_param(TypeNameHolder const& types,
                      ParmHolder<int>& currentTypes0,
+                     ParmArray& p0,
                      ParmHolder<int> const& currentTypes1,
-                     ParmArray const& p1,
-                     std::vector<Atom> const& atoms1)
+                     ParmArray const& p1)
     {
-      printIdx(term1, atomOffset);
-      bool hasH;
-      TypeNameHolder types = getTypes(hasH, term1, atoms1, p1);
-      mprintf("DEBUG: Looking for types in top0:");
       printTypes( types ); // DEBUG
       // Do we have an existing parameter in top0
       bool found;
@@ -206,12 +195,48 @@ class MergeTopArray
         currentTypes0.AddParm(types, idx, false);
       }
       mprintf("DEBUG: top0 parameter index is %i\n", idx+1);
+      return idx;
+    }
+    /// Append term1 to arrayX0/arrayY0 arrays along with parameters
+    void append_term(IdxArray& arrayX0,
+                     IdxArray& arrayY0,
+                     ParmArray& p0,
+                     unsigned int atomOffset,
+                     IdxType const& term1,
+                     ParmHolder<int>& currentTypes0,
+                     ParmHolder<int> const& currentTypes1,
+                     ParmArray const& p1,
+                     std::vector<Atom> const& atoms1)
+    {
+      printIdx(term1, atomOffset);
+      bool hasH;
+      TypeNameHolder types = getTypes(hasH, term1, atoms1, p1);
+      mprintf("DEBUG: Looking for types in top0:");
+      int idx = append_param( types, currentTypes0, p0, currentTypes1, p1 );
       // At this point we have either found a parameter or not.
       if (hasH)
         arrayY0.push_back( idxWithOffset(term1, idx, atomOffset) );
       else
         arrayX0.push_back( idxWithOffset(term1, idx, atomOffset) );
     }
+    /// Append term1 to arrayX0 array along with parameter
+    void append_term(IdxArray& arrayX0,
+                     ParmArray& p0,
+                     unsigned int atomOffset,
+                     IdxType const& term1,
+                     ParmHolder<int>& currentTypes0,
+                     ParmHolder<int> const& currentTypes1,
+                     ParmArray const& p1,
+                     std::vector<Atom> const& atoms1)
+    {
+      printIdx(term1, atomOffset);
+      bool hasH;
+      TypeNameHolder types = getTypes(hasH, term1, atoms1, p1);
+      mprintf("DEBUG: Looking for types in top0:");
+      int idx = append_param( types, currentTypes0, p0, currentTypes1, p1 );
+      // At this point we have either found a parameter or not.
+      arrayX0.push_back( idxWithOffset(term1, idx, atomOffset) );
+    }
 
     /// Index existing term types in term arrays
     void index_term_types(ParmHolder<int>& currentTypes,
@@ -366,7 +391,25 @@ class MergeTopArray
         for (; by != termsh1.end(); ++by)
           append_term( terms0, termsh0, p0, atomOffset, *by, currentTypes0, currentTypes1, p1, atoms1 );
       }
-    } // END MergeTermArrays
+    } // END MergeImproperArrays
+    /// Merge two term/parm arrays
+    void MergeTermArray(IdxArray& terms0,
+                        ParmArray& p0,
+                        std::vector<Atom> const& atoms0,
+                        IdxArray const& terms1,
+                        ParmArray const& p1,
+                        std::vector<Atom> const& atoms1)
+    {
+      // First index existing parameters
+      ParmHolder<int> currentTypes0, currentTypes1;
+      index_term_types(currentTypes0, terms0, atoms0, p0);
+      index_term_types(currentTypes1, terms1, atoms1, p1);
+      unsigned int atomOffset = atoms0.size();
+      for (typename IdxArray::const_iterator it = terms1.begin(); it != terms1.end(); ++it) {
+        append_term( terms0, p0, atomOffset, *it, currentTypes0, currentTypes1, p1, atoms1 );
+      }
+    } // END MergeTermArray
+
   private:
     bool merge_with_existing_;
 
@@ -609,10 +652,10 @@ void Cpptraj::Parm::MergeBondArray(BondArray& bonds0,
                                    BondParmArray const& bp1,
                                    AtArray const& atoms1)
 {
-  MergeTopArray<BondType, BondParmType, BondArray, BondParmArray> mergeBonds; // FIXME simplify
-  BondArray tmp;
-  mergeBonds.MergeTermArrays( bonds0, tmp,         bp0, atoms0,
-                              bonds1, BondArray(), bp1, atoms1 );
+  mprintf("DEBUG: Enter MergeBondArray()\n");
+  MergeTopArray<BondType, BondParmType, BondArray, BondParmArray> mergeBonds;
+  mergeBonds.MergeTermArray( bonds0, bp0, atoms0,
+                             bonds1, bp1, atoms1 );
 }
 
 // -----------------------------------------------------------------------------
@@ -629,8 +672,7 @@ void Cpptraj::Parm::MergeImproperArray(DihedralArray& impropers0,
 {
   MergeTopArray<DihedralType, DihedralParmType, DihedralArray, DihedralParmArray> mergeImpropers;
   mergeImpropers.SetMergeWithExisting( true ); // FIXME check this
-  DihedralArray tmp;
   // NOTE could be MergeTermArrays as well
-  mergeImpropers.MergeImproperArrays( impropers0, tmp,             ip0, atoms0,
-                                      impropers1, DihedralArray(), ip1, atoms1 );
+  mergeImpropers.MergeTermArray( impropers0, ip0, atoms0,
+                                 impropers1, ip1, atoms1 );
 }

From c3dceff5bd2fdae40df3aa7d8d26d27f420b2775 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 15 Mar 2024 10:43:32 -0400
Subject: [PATCH 0713/1492] Warn when combining a single top but do not error
 out; allows a better test of Topology::AppendTop

---
 src/Exec_CombineCoords.cpp | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/src/Exec_CombineCoords.cpp b/src/Exec_CombineCoords.cpp
index 542ebc39d8..5e98c8089d 100644
--- a/src/Exec_CombineCoords.cpp
+++ b/src/Exec_CombineCoords.cpp
@@ -30,8 +30,8 @@ Exec::RetType Exec_CombineCoords::Execute(CpptrajState& State, ArgList& argIn) {
     setname = argIn.GetStringNext();
   }
   if (CRD.size() < 2) {
-    mprinterr("Error: %s: Must specify at least 2 COORDS data sets\n", argIn.Command());
-    return CpptrajState::ERR;
+    mprintf("Warning: %s: Less than 2 COORDS data sets specified.\n", argIn.Command());
+    //return CpptrajState::ERR;
   }
   mprintf("\tCombining %zu sets:", CRD.size());
   for (std::vector<DataSet_Coords*>::const_iterator it = CRD.begin(); it != CRD.end(); ++it)
@@ -42,7 +42,14 @@ Exec::RetType Exec_CombineCoords::Execute(CpptrajState& State, ArgList& argIn) {
   Topology CombinedTop;
   CombinedTop.SetDebug( State.Debug() );
   if (parmname.empty()) {
-    parmname = CRD[0]->Top().ParmName() + "_" + CRD[1]->Top().ParmName();
+    for (std::vector<DataSet_Coords*>::const_iterator it = CRD.begin();
+                                                      it != CRD.end(); ++it)
+    {
+      if (it == CRD.begin())
+        parmname = CRD[0]->Top().ParmName();
+      else
+        parmname.append( "_" + CRD[1]->Top().ParmName() );
+    }
     addTop = false;
   }
   CombinedTop.SetParmName( parmname, FileName() );

From 0c18cedcb36d7a95e181599b390d9108292a399e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 15 Mar 2024 15:26:35 -0400
Subject: [PATCH 0714/1492] Put LJ 1-4 parameters directly into AtomType

---
 src/AtomType.h         |  16 ++++--
 src/ParameterSet.cpp   |   3 -
 src/ParameterSet.h     |   3 -
 src/Parm_CharmmPsf.cpp |   2 +-
 src/Topology.cpp       | 123 ++++++++++++++++++++++-------------------
 src/Topology.h         |   3 +-
 6 files changed, 81 insertions(+), 69 deletions(-)

diff --git a/src/AtomType.h b/src/AtomType.h
index 7ac4295c71..e4a81b4959 100644
--- a/src/AtomType.h
+++ b/src/AtomType.h
@@ -7,17 +7,21 @@ class AtomType {
     /// Atom hybridization types
     enum HybridizationType { SP = 0, SP2, SP3, UNKNOWN_HYBRIDIZATION };
     /// CONSTRUCTOR
-    AtomType() : mass_(0.0), polarizability_(0.0), oidx_(-1), hybrid_(UNKNOWN_HYBRIDIZATION) {}
+    AtomType() : mass_(0.0), polarizability_(0.0), oidx_(-1), hybrid_(UNKNOWN_HYBRIDIZATION), hasLJ14_(false) {}
     /// CONSTRUCTOR - Mass only
-    AtomType(double m) : mass_(m), polarizability_(0.0), oidx_(-1), hybrid_(UNKNOWN_HYBRIDIZATION) {}
+    AtomType(double m) : mass_(m), polarizability_(0.0), oidx_(-1), hybrid_(UNKNOWN_HYBRIDIZATION), hasLJ14_(false) {}
     /// CONSTRUCTOR - Mass, polarizability
-    AtomType(double m, double p) : mass_(m), polarizability_(p), oidx_(-1), hybrid_(UNKNOWN_HYBRIDIZATION) {}
+    AtomType(double m, double p) : mass_(m), polarizability_(p), oidx_(-1), hybrid_(UNKNOWN_HYBRIDIZATION), hasLJ14_(false) {}
     /// CONSTRUCTOR - Radius, well depth, mass, polarizability
-    AtomType(double r, double d, double m, double p) : lj_(r, d), mass_(m), polarizability_(p), oidx_(-1), hybrid_(UNKNOWN_HYBRIDIZATION) {}
+    AtomType(double r, double d, double m, double p) : lj_(r, d), mass_(m), polarizability_(p), oidx_(-1), hybrid_(UNKNOWN_HYBRIDIZATION), hasLJ14_(false) {}
     /// Set type index
     void SetTypeIdx(int i) { oidx_ = i; }
     /// \return default LJ parameters
     LJparmType const& LJ()  const { return lj_; }
+    /// \return LJ 1-4 parameters
+    LJparmType const& LJ14() const { return lj14_; }
+    /// \return True if LJ 1-4 parameters have been set
+    bool HasLJ14() const { return hasLJ14_; }
     /// \return Atom mass in amu
     double Mass()           const { return mass_;   }
     /// \return Atomic polarizability in Ang^3
@@ -46,15 +50,19 @@ class AtomType {
     }
     /// Used to modify LJ params
     LJparmType& SetLJ() { return lj_; }
+    /// Set LJ 1-4 parameters
+    void SetLJ14(LJparmType const& lj) { lj14_ = lj; hasLJ14_ = true; }
     /// Set atom hybridization
     void SetHybridization(HybridizationType h) { hybrid_ = h; }
     /// \return data size  (2 double for LJparmType)
     static size_t DataSize() { return (4*sizeof(double)) + sizeof(int); }
   private:
     LJparmType lj_;         ///< Default Lennard-Jones parameters (always valid for self).
+    LJparmType lj14_;       ///< Lennard-Jones 1-4 parameters (optional).
     double mass_;           ///< Mass in amu
     double polarizability_; ///< Atomic polarizability in Ang^3
     int oidx_;              ///< Original atom type index, for indexing nonbond parameters.
     HybridizationType hybrid_; ///< Atom hybridization
+    bool hasLJ14_;             ///< True if this type has LJ 1-4 parameters.
 };
 #endif
diff --git a/src/ParameterSet.cpp b/src/ParameterSet.cpp
index d322f0e74a..d21a7712f1 100644
--- a/src/ParameterSet.cpp
+++ b/src/ParameterSet.cpp
@@ -10,7 +10,6 @@ size_t ParameterSet::DataSize() const {
     cmapsize += it->DataSize();
   return (atomTypes_.DataSize() +
           nbParm_.DataSize() +
-          nb14Types_.DataSize() +
           nb14Parm_.DataSize() +
           bondParm_.DataSize() +
           angleParm_.DataSize() +
@@ -205,8 +204,6 @@ int ParameterSet::UpdateParamSet(ParameterSet const& set1, UpdateCount& uc, int
   uc.nAtomTypeUpdated_ = UpdateParameters< ParmHolder<AtomType> >(set0.AT(), set1.AT(), "atom type", verbose);
   // LJ Pairs
   uc.nLJparamsUpdated_ = UpdateParameters< ParmHolder<NonbondType> >(set0.NB(), set1.NB(), "LJ A-B", verbose);
-  // 1-4 atom types
-  uc.nLJ14typesUpdated_ = UpdateParameters< ParmHolder<AtomType> >(set0.AT14(), set1.AT14(), "LJ 1-4 type", verbose);
   // LJ 1-4 Pairs
   uc.nLJ14paramsUpdated_ = UpdateParameters< ParmHolder<NonbondType> >(set0.NB14(), set1.NB14(), "LJ A-B 1-4", verbose);
   // HB LJ 10-12 Pairs
diff --git a/src/ParameterSet.h b/src/ParameterSet.h
index 50ed9e9174..247b916f0b 100644
--- a/src/ParameterSet.h
+++ b/src/ParameterSet.h
@@ -16,7 +16,6 @@ class ParameterSet {
 
     ParmHolder<AtomType>& AT()         { return atomTypes_; }
     ParmHolder<NonbondType>& NB()      { return nbParm_;    }
-    ParmHolder<AtomType>& AT14()       { return nb14Types_; }
     ParmHolder<NonbondType>& NB14()    { return nb14Parm_;  }
     ParmHolder<BondParmType>& BP()     { return bondParm_;  }
     ParmHolder<AngleParmType>& AP()    { return angleParm_; }
@@ -32,7 +31,6 @@ class ParameterSet {
 
     ParmHolder<AtomType> const& AT()         const { return atomTypes_; }
     ParmHolder<NonbondType> const& NB()      const { return nbParm_;    }
-    ParmHolder<AtomType> const& AT14()       const { return nb14Types_; }
     ParmHolder<NonbondType> const& NB14()    const { return nb14Parm_;  }
     ParmHolder<BondParmType> const& BP()     const { return bondParm_;  }
     ParmHolder<AngleParmType> const& AP()    const { return angleParm_; }
@@ -97,7 +95,6 @@ class ParameterSet {
 
     ParmHolder<AtomType> atomTypes_;       ///< Atom types
     ParmHolder<NonbondType> nbParm_;       ///< Lennard-Jones 6-12 A-B parameters
-    ParmHolder<AtomType> nb14Types_;       ///< Atom types for LJ 6-12 1-4 interactions
     ParmHolder<NonbondType> nb14Parm_;     ///< LJ 6-12 A-B parameters for 1-4 interactions
     ParmHolder<BondParmType> bondParm_;    ///< Hooke's law bond potential parameters
     ParmHolder<AngleParmType> angleParm_;  ///< Hooke's law angle potential parameters
diff --git a/src/Parm_CharmmPsf.cpp b/src/Parm_CharmmPsf.cpp
index cd1f627fa7..e7503efc3b 100644
--- a/src/Parm_CharmmPsf.cpp
+++ b/src/Parm_CharmmPsf.cpp
@@ -377,7 +377,7 @@ int Parm_CharmmPsf::ReadParm(FileName const& fname, Topology &parmOut) {
 
   // Add nonbonded parameters
   if (params_.HasLJparams()) {
-    parmOut.AssignNonbondParams( atomTypes, params_.NB(), params_.AT14(), params_.NB14(), params_.HB(), debug_ );
+    parmOut.AssignNonbondParams( atomTypes, params_.NB(), params_.NB14(), params_.HB(), debug_ );
   }
 
   return 0;
diff --git a/src/Topology.cpp b/src/Topology.cpp
index 201090f9e7..f981db411d 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2397,7 +2397,7 @@ static inline int GetCmapParams(CmapParmHolder& cmapParm, CmapArray const& cmapT
   * \param LJ612out The output LJ 6-12 A and B paramters.
   * \param LJ1012ptr If not 0, the output LJ 10-12 parameters.
   */
-static inline void GetLJterms(ParmHolder<AtomType> const& atomTypesOut,
+/*static inline void GetLJterms(ParmHolder<AtomType> const& atomTypesOut,
                               ParmHolder<NonbondType>& LJ612out,
                               ParmHolder<HB_ParmType>* LJ1012ptr,
                               NonbondParmType const& NB0,
@@ -2462,18 +2462,17 @@ static inline void GetLJterms(ParmHolder<AtomType> const& atomTypesOut,
     } // END outer loop over atom types
     if (nModifiedOffDiagonal > 0)
       mprintf("Warning: %u modified off-diagonal LJ terms present.\n", nModifiedOffDiagonal);
-}
+}*/
 
-/** \param atomTypesOut Output array of atom types.
-  * \param LJ612out Output array of LJ 6-12 parameters.
-  * \param LJ14out Output array of LJ 6-12 1-4 parameters.
-  * \param LJ1012out Output array of LJ 10-12 parameters.
+/** \param atomTypesOut Output array of atom types and indivudual LJ parameters.
+  * \param LJ612out Output array of LJ 6-12 pair parameters.
+  * \param LJ14out Output array of LJ 6-12 1-4 pair parameters.
+  * \param LJ1012out Output array of LJ 10-12 pair parameters.
   * \param atoms Current array of atoms.
   * \param NB0 Current nonbond parameters.
   */
 static inline void GetLJAtomTypes(ParmHolder<AtomType>& atomTypesOut,
                                   ParmHolder<NonbondType>& LJ612out,
-                                  ParmHolder<AtomType>& LJ14typesOut,
                                   ParmHolder<NonbondType>& LJ14out,
                                   ParmHolder<HB_ParmType>& LJ1012out,
                                   std::vector<Atom> const& atoms,
@@ -2483,6 +2482,8 @@ static inline void GetLJAtomTypes(ParmHolder<AtomType>& atomTypesOut,
   if (NB0.HasNonbond()) {
     mprintf("DEBUG: Topology has nonbond parameters.\n");
     bool hasLJ14 = !NB0.LJ14().empty();
+    if (hasLJ14)
+      mprintf("DEBUG: Topology has 1-4 nonbond parameters.\n");
     // Nonbonded parameters are present.
     for (std::vector<Atom>::const_iterator atm = atoms.begin(); atm != atoms.end(); ++atm)
     {
@@ -2499,17 +2500,8 @@ static inline void GetLJAtomTypes(ParmHolder<AtomType>& atomTypesOut,
         NonbondType const& LJ = NB0.NBarray( idx );
         thisType = AtomType(LJ.Radius(), LJ.Depth(), atm->Mass(), atm->Polar());
         if (hasLJ14) {
-          // NOTE: Even though we do not need mass/polarizability for LJ14 types,
-          //       use AtomType anyway so we can use the same routine as the
-          //       regular 6-12 terms for determining off-diagonal elements.
-          //LJparmType this14type;
           NonbondType const& lj14 = NB0.LJ14( idx );
-          AtomType this14type = AtomType(lj14.Radius(), lj14.Depth(), 0, 0); // NOTE: empty mass/polarizability
-          this14type.SetTypeIdx( atm->TypeIndex() );
-          ParameterHolders::RetType ret14 = LJ14typesOut.AddParm( atype, this14type, true );
-          if (debugIn > 0 && ret14 == ParameterHolders::ADDED) {
-            mprintf("DEBUG: New LJ14 atom type: %s R=%g D=%g\n", *(atype[0]), this14type.LJ().Radius(), this14type.LJ().Depth());
-          }
+          thisType.SetLJ14( LJparmType(lj14.Radius(), lj14.Depth()) );
         }
         // FIXME do LJ C
       } else {
@@ -2518,18 +2510,21 @@ static inline void GetLJAtomTypes(ParmHolder<AtomType>& atomTypesOut,
       }
       thisType.SetTypeIdx( atm->TypeIndex() );
       ParameterHolders::RetType ret = atomTypesOut.AddParm( atype, thisType, true );
-      if (debugIn > 0 && ret == ParameterHolders::ADDED) {
+      //if (debugIn > 0 && ret == ParameterHolders::ADDED) { // FIXME
+      if (ret == ParameterHolders::ADDED) {
         mprintf("DEBUG: New atom type: %s R=%g D=%g M=%g P=%g\n", *(atype[0]),
                 thisType.LJ().Radius(), thisType.LJ().Depth(), thisType.Mass(), thisType.Polarizability());
+        if (hasLJ14)
+          mprintf("DEBUG: New LJ14 atom type: %s R=%g D=%g\n", *(atype[0]), thisType.LJ14().Radius(), thisType.LJ14().Depth());
       }
     }
     // Do atom type pairs, check for off-diagonal elements.
     // Explicitly store pairs instead of regenerating to avoid round-off issues.
-    GetLJterms(atomTypesOut, LJ612out, &LJ1012out, NB0, false, debugIn);
-    if (hasLJ14)
-      GetLJterms(LJ14typesOut, LJ14out, 0, NB0, true, debugIn);
-/*
+    //GetLJterms(atomTypesOut, LJ612out, &LJ1012out, NB0, false, debugIn);
+    //if (hasLJ14)
+    //  GetLJterms(LJ14typesOut, LJ14out, 0, NB0, true, debugIn);
     unsigned int nModifiedOffDiagonal = 0;
+    unsigned int nModified14OffDiagonal = 0;
     for (ParmHolder<AtomType>::const_iterator i1 = atomTypesOut.begin(); i1 != atomTypesOut.end(); ++i1)
     {
       for (ParmHolder<AtomType>::const_iterator i2 = i1; i2 != atomTypesOut.end(); ++i2)
@@ -2574,12 +2569,35 @@ static inline void GetLJAtomTypes(ParmHolder<AtomType>& atomTypesOut,
             //}
           }
           LJ612out.AddParm( types, lj1, false );
+          if (hasLJ14) {
+            // This is LJ 6-12 1-4.
+            // Determine what A and B parameters would be.
+            lj0 = type1.LJ14().Combine_LB( type2.LJ14() );
+        
+            lj1 = NB0.LJ14( idx );
+            // Compare them
+            if (lj0 != lj1) {
+              nModified14OffDiagonal++;
+              //if (debugIn > 0) {
+                double deltaA = fabs(lj0.A() - lj1.A());
+                double deltaB = fabs(lj0.B() - lj1.B());
+                mprintf("DEBUG: Potential off-diagonal LJ 1-4: %s %s expect A=%g B=%g, actual A=%g B=%g\n",
+                        *name1, *name2, lj0.A(), lj0.B(), lj1.A(), lj1.B());
+                mprintf("DEBUG:\tdeltaA= %g    deltaB= %g\n", deltaA, deltaB);
+                double pe_a = (fabs(lj0.A() - lj1.A()) / lj0.A());
+                double pe_b = (fabs(lj0.B() - lj1.B()) / lj0.B());
+                mprintf("DEBUG:\tPEA= %g  PEB= %g\n", pe_a, pe_b);
+              //}
+            }
+            LJ14out.AddParm( types, lj1, false );
+          } // END hasLJ14
         }
       } // END inner loop over atom types
     } // END outer loop over atom types
     if (nModifiedOffDiagonal > 0)
       mprintf("Warning: %u modified off-diagonal LJ terms present.\n", nModifiedOffDiagonal);
-*/
+    if (nModified14OffDiagonal > 0)
+      mprintf("Warning: %u modified off-diagonal LJ 1-4 terms present.\n", nModified14OffDiagonal);
   } else {
     if (!atoms.empty())
       mprintf("DEBUG: Topology does not have nonbond parameters.\n");
@@ -2594,7 +2612,7 @@ static inline void GetLJAtomTypes(ParmHolder<AtomType>& atomTypesOut,
 ParameterSet Topology::GetParameters() const {
   ParameterSet Params;
   // Atom LJ types and other nonbonded parameters.
-  GetLJAtomTypes( Params.AT(), Params.NB(), Params.AT14(), Params.NB14(), Params.HB(), atoms_, nonbond_, debug_ );
+  GetLJAtomTypes( Params.AT(), Params.NB(), Params.NB14(), Params.HB(), atoms_, nonbond_, debug_ );
   // Bond parameters.
   GetBondParams( Params.BP(), atoms_, bonds_, bondparm_ );
   GetBondParams( Params.BP(), atoms_, bondsh_, bondparm_ );
@@ -2661,19 +2679,17 @@ int Topology::AppendTop(Topology const& NewTop) {
   // Save nonbonded parameters from each topology
   ParmHolder<AtomType> myAtomTypes, newAtomTypes;
   ParmHolder<NonbondType> myNB, newNB;
-  ParmHolder<AtomType> my14Types, new14Types;
   ParmHolder<NonbondType> my14, new14;
   ParmHolder<HB_ParmType> myHB, newHB;
-  GetLJAtomTypes( myAtomTypes, myNB, my14Types, my14, myHB, atoms_, nonbond_, debug_ );
-  GetLJAtomTypes( newAtomTypes, newNB, new14Types, new14, newHB, NewTop.atoms_, NewTop.nonbond_, debug_ );
+  GetLJAtomTypes( myAtomTypes, myNB, my14, myHB, atoms_, nonbond_, debug_ );
+  GetLJAtomTypes( newAtomTypes, newNB, new14, newHB, NewTop.atoms_, NewTop.nonbond_, debug_ );
   // Create combined nonbond parameter set
   int nAtomTypeUpdated = UpdateParameters< ParmHolder<AtomType> >( myAtomTypes, newAtomTypes, "atom type", 1 ); // TODO verbose 
   int nLJparamsUpdated = UpdateParameters< ParmHolder<NonbondType> >( myNB, newNB, "LJ 6-12", 1 ); // TODO verbose
-  int n14TypeUpdated   = UpdateParameters< ParmHolder<AtomType> >( my14Types, new14Types, "1-4 atom type", 1) ; // TODO verbose
   int n14paramsUpdated = UpdateParameters< ParmHolder<NonbondType> >( my14, new14, "LJ 6-12 1-4", 1); // TODO verbose
   int nHBparamsUpdated = UpdateParameters< ParmHolder<HB_ParmType> >( myHB, newHB, "LJ 10-12", 1); // TODO verbose
-  mprintf("\t%i atom types updated, %i LJ 6-12 params updated, %i 1-4 types updated, %i 1-4 params updated, %i LJ 10-12 params updated.\n",
-          nAtomTypeUpdated, nLJparamsUpdated, n14TypeUpdated, n14paramsUpdated, nHBparamsUpdated);
+  mprintf("\t%i atom types updated, %i LJ 6-12 params updated, %i 1-4 params updated, %i LJ 10-12 params updated.\n",
+          nAtomTypeUpdated, nLJparamsUpdated, n14paramsUpdated, nHBparamsUpdated);
 
   // Add incoming topology bond/angle/dihedral/cmap arrays to this one.
   Cpptraj::Parm::MergeBondArrays(bonds_, bondsh_, bondparm_, atoms_,
@@ -2722,7 +2738,7 @@ int Topology::AppendTop(Topology const& NewTop) {
 
   // Need to regenerate nonbonded info
   mprintf("\tRegenerating nonbond parameters.\n");
-  AssignNonbondParams( myAtomTypes, myNB, my14Types, my14, myHB, 1 ); // FIXME verbose
+  AssignNonbondParams( myAtomTypes, myNB, my14, myHB, 1 ); // FIXME verbose
 
   // The version of AddTopAtom() with molecule number already determines
   // molecules and number of solvent molecules.
@@ -3220,14 +3236,13 @@ void Topology::AssignDihedralParams(DihedralParmHolder const& newDihedralParams,
 //TODO Accept array of atom type names?
 void Topology::AssignNonbondParams(ParmHolder<AtomType> const& newTypes,
                                    ParmHolder<NonbondType> const& newNB,
-                                   ParmHolder<AtomType> const& new14types,
                                    ParmHolder<NonbondType> const& new14,
                                    ParmHolder<HB_ParmType> const& newHB,
                                    int verbose)
 {
   bool hasLJ14 = !new14.empty();
   // Generate array of only the types that are currently in Topology. TODO should this be a permanent part of Topology?
-  ParmHolder<AtomType> currentAtomTypes, current14Types;
+  ParmHolder<AtomType> currentAtomTypes;
   for (std::vector<Atom>::const_iterator atm = atoms_.begin(); atm != atoms_.end(); ++atm)
   {
     if (atm->HasType()) {
@@ -3240,16 +3255,13 @@ void Topology::AssignNonbondParams(ParmHolder<AtomType> const& newTypes,
         mprintf("Warning: No atom type information for type '%s'\n", *types[0]);
         newAT = AtomType(atm->Mass());
       }
-      currentAtomTypes.AddParm( types, newAT, true );
-      // Find LJ14 types if needed
+      // Check LJ14 types if needed
       if (hasLJ14) {
-        AtomType new14AT = new14types.FindParam( types, found );
-        if (!found) {
+        if (!newAT.HasLJ14()) {
           mprintf("Warning: No 1-4 atom type information for type '%s'\n", *types[0]); // TODO error out here?
-          new14AT = AtomType(atm->Mass());
         }
-        current14Types.AddParm( types, new14AT, true );
       }
+      currentAtomTypes.AddParm( types, newAT, true );
     }
   }
   if (currentAtomTypes.size() < 1) {
@@ -3269,9 +3281,19 @@ void Topology::AssignNonbondParams(ParmHolder<AtomType> const& newTypes,
       t1->second.SetTypeIdx( n_unique_lj_types );
       // Look for equivalent nonbond types
       for (ParmHolder<AtomType>::iterator t2 = t1 + 1; t2 != currentAtomTypes.end(); ++t2) {
-        if (t2->second.OriginalIdx() == -1 && t1->second.LJ() == t2->second.LJ()) {
-          mprintf("DEBUG: Type %s equivalent to type %s\n", *(t2->first[0]), *(t1->first[0]));
-          t2->second.SetTypeIdx( n_unique_lj_types );
+        if (!hasLJ14) {
+          if (t2->second.OriginalIdx() == -1 && t1->second.LJ() == t2->second.LJ()) {
+            mprintf("DEBUG: Type %s equivalent to type %s\n", *(t2->first[0]), *(t1->first[0]));
+            t2->second.SetTypeIdx( n_unique_lj_types );
+          }
+        } else {
+          if (t2->second.OriginalIdx() == -1 &&
+              t1->second.LJ() == t2->second.LJ() &&
+              t1->second.LJ14() == t2->second.LJ14())
+          {
+            mprintf("DEBUG: Type %s (with 1-4 params) equivalent to type %s\n", *(t2->first[0]), *(t1->first[0]));
+            t2->second.SetTypeIdx( n_unique_lj_types );
+          }
         }
       }
       n_unique_lj_types++;
@@ -3318,18 +3340,7 @@ void Topology::AssignNonbondParams(ParmHolder<AtomType> const& newTypes,
           ParmHolder<NonbondType>::const_iterator it = new14.GetParam( types );
           if (it == new14.end()) {
             if (verbose > 0) mprintf("NB 1-4 parameter for %s %s not found. Generating.\n", *name1, *name2);
-            bool found;
-            AtomType at14_1 = current14Types.FindParam(t1->first, found);
-            if (!found) {
-              mprinterr("Internal Error: LJ 1-4 parameter not found for %s\n", *name1);
-              return;
-            }
-            AtomType at14_2 = current14Types.FindParam(t2->first, found);
-            if (!found) {
-              mprinterr("Internal Error: LJ 1-4 parameter not found for %s\n", *name2);
-              return;
-            }
-            nonbond_.SetLJ14( ljidx ) = at14_1.LJ().Combine_LB( at14_2.LJ() );
+            nonbond_.SetLJ14( ljidx ) = type1.LJ14().Combine_LB( type2.LJ14() );
           } else {
             if (verbose > 0) mprintf("Using existing NB 1-4 parameter for %s %s\n", *name1, *name2);
             nonbond_.SetLJ14( ljidx ) = it->second;
@@ -3702,7 +3713,7 @@ int Topology::AssignParams(ParameterSet const& set0) {
   AssignAtomTypeParm( set0.AT() );
   // LJ 6-12
   mprintf("\tAssigning nonbond parameters.\n");
-  AssignNonbondParams( set0.AT(), set0.NB(), set0.AT14(), set0.NB14(), set0.HB(), debug_ );
+  AssignNonbondParams( set0.AT(), set0.NB(), set0.NB14(), set0.HB(), debug_ );
   mprintf("DEBUG: CMAP size %zu\n", set0.CMAP().size());
   // TODO LJ14, LJC
 
@@ -3775,7 +3786,7 @@ int Topology::UpdateParams(ParameterSet const& set1) {
       UC.nLJparamsUpdated_ > 0 || UC.nLJ14paramsUpdated_ > 0)
   {
     mprintf("\tRegenerating nonbond parameters.\n");
-    AssignNonbondParams( set0.AT(), set0.NB(), set0.AT14(), set0.NB14(), set0.HB(), debug_ );
+    AssignNonbondParams( set0.AT(), set0.NB(), set0.NB14(), set0.HB(), debug_ );
   }
   // CMAP
   if (UC.nCmapUpdated_ > 0) {
diff --git a/src/Topology.h b/src/Topology.h
index 6ec30e0427..81ba936fe2 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -170,8 +170,7 @@ class Topology {
     inline NonbondType const& GetLJparam(int, int) const;
     /// Assign LJ 6-12 / 10-12 parameters, reset atom type indices
     void AssignNonbondParams(ParmHolder<AtomType> const&, ParmHolder<NonbondType> const&,
-                             ParmHolder<AtomType> const&, ParmHolder<NonbondType> const&,
-                             ParmHolder<HB_ParmType> const&, int);
+                             ParmHolder<NonbondType> const&, ParmHolder<HB_ParmType> const&, int);
     /// \return True if any charge is non-zero
     bool HasChargeInfo() const;
     /// Redistribute charge on atoms in topology to match target total charge

From 258ae060a57766d756b85b929e20bd1080e56940 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 16 Mar 2024 07:50:31 -0400
Subject: [PATCH 0715/1492] Store LJC parameters in ParameterSet

---
 src/ParameterSet.cpp |  8 ++++++++
 src/ParameterSet.h   |  7 +++++--
 src/ParameterTypes.h |  2 ++
 src/Topology.cpp     | 25 ++++++++++++++++++-------
 4 files changed, 33 insertions(+), 9 deletions(-)

diff --git a/src/ParameterSet.cpp b/src/ParameterSet.cpp
index d21a7712f1..4ac24a762b 100644
--- a/src/ParameterSet.cpp
+++ b/src/ParameterSet.cpp
@@ -11,6 +11,7 @@ size_t ParameterSet::DataSize() const {
   return (atomTypes_.DataSize() +
           nbParm_.DataSize() +
           nb14Parm_.DataSize() +
+          ljcParm_.DataSize() +
           bondParm_.DataSize() +
           angleParm_.DataSize() +
           ubParm_.DataSize() +
@@ -41,6 +42,7 @@ void ParameterSet::Summary() const {
   // TODO 1-4 types?
   mprintf("\t  %zu LJ 6-12 parameters.\n", nbParm_.size());
   mprintf("\t  %zu LJ 6-12 1-4 parameters.\n", nb14Parm_.size());
+  mprintf("\t  %zu LJ C parameters.\n", ljcParm_.size());
   mprintf("\t  %zu LJ 10-12 parameters.\n", HBparm_.size());
   mprintf("\t  %zu bond parameters.\n", bondParm_.size());
   mprintf("\t  %zu angle parameters.\n", angleParm_.size());
@@ -73,6 +75,12 @@ void ParameterSet::Print(CpptrajFile& Out) const {
     for (ParmHolder<NonbondType>::const_iterator nb = nb14Parm_.begin(); nb != nb14Parm_.end(); ++nb)
       Out.Printf("\t%6s %6s : %12.4E %12.4E\n", (*nb->first[0]), (*nb->first[1]), nb->second.A(), nb->second.B());
   }
+  if (!ljcParm_.empty()) {
+    Out.Printf("LJ C parameters:\n");
+    Out.Printf("\t%6s %6s : %12s\n", "Type1", "Type2", "C");
+    for (ParmHolder<NonbondType>::const_iterator nb = nb14Parm_.begin(); nb != nb14Parm_.end(); ++nb)
+      Out.Printf("\t%6s %6s : %12.4E\n", (*nb->first[0]), (*nb->first[1]), nb->second);
+  }
   if (!HBparm_.empty()) {
     Out.Printf("HB LJ 10-12 parameters:\n");
     Out.Printf("\t%6s %6s : %12s %12s %12s\n", "Type1", "Type2", "Asol", "Bsol", "HBcut");
diff --git a/src/ParameterSet.h b/src/ParameterSet.h
index 247b916f0b..1468bf8cd1 100644
--- a/src/ParameterSet.h
+++ b/src/ParameterSet.h
@@ -17,6 +17,7 @@ class ParameterSet {
     ParmHolder<AtomType>& AT()         { return atomTypes_; }
     ParmHolder<NonbondType>& NB()      { return nbParm_;    }
     ParmHolder<NonbondType>& NB14()    { return nb14Parm_;  }
+    ParmHolder<double>& LJC()          { return ljcParm_;   }
     ParmHolder<BondParmType>& BP()     { return bondParm_;  }
     ParmHolder<AngleParmType>& AP()    { return angleParm_; }
     ParmHolder<BondParmType>& UB()     { return ubParm_;    }
@@ -32,6 +33,7 @@ class ParameterSet {
     ParmHolder<AtomType> const& AT()         const { return atomTypes_; }
     ParmHolder<NonbondType> const& NB()      const { return nbParm_;    }
     ParmHolder<NonbondType> const& NB14()    const { return nb14Parm_;  }
+    ParmHolder<double> const& LJC()          const { return ljcParm_;   }
     ParmHolder<BondParmType> const& BP()     const { return bondParm_;  }
     ParmHolder<AngleParmType> const& AP()    const { return angleParm_; }
     ParmHolder<BondParmType> const& UB()     const { return ubParm_;    }
@@ -58,7 +60,7 @@ class ParameterSet {
         UpdateCount() : nBondsUpdated_(0), nAnglesUpdated_(0),
                         nDihedralsUpdated_(0), nImpropersUpdated_(0),
                         nUreyBradleyUpdated_(0), nAtomTypeUpdated_(0),
-                        nLJparamsUpdated_(0), nLJ14typesUpdated_(0),
+                        nLJparamsUpdated_(0), nLJCUpdated_(0),
                         nLJ14paramsUpdated_(0), nHBparamsUpdated_(0),
                         nCmapUpdated_(0) {}
         unsigned int nBondsUpdated_;
@@ -68,7 +70,7 @@ class ParameterSet {
         unsigned int nUreyBradleyUpdated_;
         unsigned int nAtomTypeUpdated_;
         unsigned int nLJparamsUpdated_;
-        unsigned int nLJ14typesUpdated_;
+        unsigned int nLJCUpdated_;
         unsigned int nLJ14paramsUpdated_;
         unsigned int nHBparamsUpdated_;
         unsigned int nCmapUpdated_;
@@ -96,6 +98,7 @@ class ParameterSet {
     ParmHolder<AtomType> atomTypes_;       ///< Atom types
     ParmHolder<NonbondType> nbParm_;       ///< Lennard-Jones 6-12 A-B parameters
     ParmHolder<NonbondType> nb14Parm_;     ///< LJ 6-12 A-B parameters for 1-4 interactions
+    ParmHolder<double> ljcParm_;           ///< LJ 12-6-4 C parameters
     ParmHolder<BondParmType> bondParm_;    ///< Hooke's law bond potential parameters
     ParmHolder<AngleParmType> angleParm_;  ///< Hooke's law angle potential parameters
     ParmHolder<BondParmType> ubParm_;      ///< Urey-Bradley parameters
diff --git a/src/ParameterTypes.h b/src/ParameterTypes.h
index c2e11d3ad7..04e9d47992 100644
--- a/src/ParameterTypes.h
+++ b/src/ParameterTypes.h
@@ -667,6 +667,8 @@ class NonbondParmType {
     NonbondType const& NBarray(int i)    const { return nbarray_[i]; }
     /// \return LJ 6-12 1-4 A and B parameter at specified index
     NonbondType const& LJ14(int i)       const { return lj14_[i]; }
+    /// \return LJC parameter at specified index
+    double LJC_Array(int idx)            const { return ccoef_[idx]; }
     /// \return LJ 10-12 (hbond) parameter at specified index
     HB_ParmType const& HBarray(int i)    const { return hbarray_[i]; }
     /// In Amber, index < 0 means HB, otherwise LJ 6-12
diff --git a/src/Topology.cpp b/src/Topology.cpp
index f981db411d..38ed3e7f0b 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2474,6 +2474,7 @@ static inline int GetCmapParams(CmapParmHolder& cmapParm, CmapArray const& cmapT
 static inline void GetLJAtomTypes(ParmHolder<AtomType>& atomTypesOut,
                                   ParmHolder<NonbondType>& LJ612out,
                                   ParmHolder<NonbondType>& LJ14out,
+                                  ParmHolder<double>& LJCout,
                                   ParmHolder<HB_ParmType>& LJ1012out,
                                   std::vector<Atom> const& atoms,
                                   NonbondParmType const& NB0,
@@ -2484,6 +2485,9 @@ static inline void GetLJAtomTypes(ParmHolder<AtomType>& atomTypesOut,
     bool hasLJ14 = !NB0.LJ14().empty();
     if (hasLJ14)
       mprintf("DEBUG: Topology has 1-4 nonbond parameters.\n");
+    bool hasLJC = !NB0.LJC_Array().empty();
+    if (hasLJC)
+      mprintf("DEBUG: Topology has LJC nonbond paramters.\n");
     // Nonbonded parameters are present.
     for (std::vector<Atom>::const_iterator atm = atoms.begin(); atm != atoms.end(); ++atm)
     {
@@ -2591,6 +2595,11 @@ static inline void GetLJAtomTypes(ParmHolder<AtomType>& atomTypesOut,
             }
             LJ14out.AddParm( types, lj1, false );
           } // END hasLJ14
+          if (hasLJC) {
+            // This is LJC
+            double ljc1 = NB0.LJC_Array( idx );
+            LJCout.AddParm( types, ljc1, false );
+          }
         }
       } // END inner loop over atom types
     } // END outer loop over atom types
@@ -2612,7 +2621,7 @@ static inline void GetLJAtomTypes(ParmHolder<AtomType>& atomTypesOut,
 ParameterSet Topology::GetParameters() const {
   ParameterSet Params;
   // Atom LJ types and other nonbonded parameters.
-  GetLJAtomTypes( Params.AT(), Params.NB(), Params.NB14(), Params.HB(), atoms_, nonbond_, debug_ );
+  GetLJAtomTypes( Params.AT(), Params.NB(), Params.NB14(), Params.LJC(), Params.HB(), atoms_, nonbond_, debug_ );
   // Bond parameters.
   GetBondParams( Params.BP(), atoms_, bonds_, bondparm_ );
   GetBondParams( Params.BP(), atoms_, bondsh_, bondparm_ );
@@ -2681,15 +2690,17 @@ int Topology::AppendTop(Topology const& NewTop) {
   ParmHolder<NonbondType> myNB, newNB;
   ParmHolder<NonbondType> my14, new14;
   ParmHolder<HB_ParmType> myHB, newHB;
-  GetLJAtomTypes( myAtomTypes, myNB, my14, myHB, atoms_, nonbond_, debug_ );
-  GetLJAtomTypes( newAtomTypes, newNB, new14, newHB, NewTop.atoms_, NewTop.nonbond_, debug_ );
+  ParmHolder<double> myLJC, newLJC;
+  GetLJAtomTypes( myAtomTypes, myNB, my14, myLJC, myHB, atoms_, nonbond_, debug_ );
+  GetLJAtomTypes( newAtomTypes, newNB, new14, newLJC, newHB, NewTop.atoms_, NewTop.nonbond_, debug_ );
   // Create combined nonbond parameter set
   int nAtomTypeUpdated = UpdateParameters< ParmHolder<AtomType> >( myAtomTypes, newAtomTypes, "atom type", 1 ); // TODO verbose 
   int nLJparamsUpdated = UpdateParameters< ParmHolder<NonbondType> >( myNB, newNB, "LJ 6-12", 1 ); // TODO verbose
   int n14paramsUpdated = UpdateParameters< ParmHolder<NonbondType> >( my14, new14, "LJ 6-12 1-4", 1); // TODO verbose
+  int nljcparamsUpdated = UpdateParameters< ParmHolder<double> >( myLJC, newLJC, "LJ C", 1); // TODO verbose
   int nHBparamsUpdated = UpdateParameters< ParmHolder<HB_ParmType> >( myHB, newHB, "LJ 10-12", 1); // TODO verbose
-  mprintf("\t%i atom types updated, %i LJ 6-12 params updated, %i 1-4 params updated, %i LJ 10-12 params updated.\n",
-          nAtomTypeUpdated, nLJparamsUpdated, n14paramsUpdated, nHBparamsUpdated);
+  mprintf("\t%i atom types updated, %i LJ 6-12 params updated, %i 1-4 params updated, %i LJC params updated, %i LJ 10-12 params updated.\n",
+          nAtomTypeUpdated, nLJparamsUpdated, n14paramsUpdated, nljcparamsUpdated, nHBparamsUpdated);
 
   // Add incoming topology bond/angle/dihedral/cmap arrays to this one.
   Cpptraj::Parm::MergeBondArrays(bonds_, bondsh_, bondparm_, atoms_,
@@ -2738,7 +2749,7 @@ int Topology::AppendTop(Topology const& NewTop) {
 
   // Need to regenerate nonbonded info
   mprintf("\tRegenerating nonbond parameters.\n");
-  AssignNonbondParams( myAtomTypes, myNB, my14, myHB, 1 ); // FIXME verbose
+  AssignNonbondParams( myAtomTypes, myNB, my14, myHB, 1 ); // FIXME verbose TODO LJC
 
   // The version of AddTopAtom() with molecule number already determines
   // molecules and number of solvent molecules.
@@ -3782,7 +3793,7 @@ int Topology::UpdateParams(ParameterSet const& set1) {
     AssignAtomTypeParm( set0.AT() );
   }
 //  updateCount += UpdateParameters< ParmHolder<NonbondType> >(set0.NB(), set1.NB(), "LJ A-B");
-  if (UC.nAtomTypeUpdated_ > 0 || UC.nLJ14typesUpdated_ > 0 ||
+  if (UC.nAtomTypeUpdated_ > 0 || UC.nLJCUpdated_ > 0 ||
       UC.nLJparamsUpdated_ > 0 || UC.nLJ14paramsUpdated_ > 0)
   {
     mprintf("\tRegenerating nonbond parameters.\n");

From ca650871c330b684d9d95e53d1da44ef560cb45f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 16 Mar 2024 08:43:50 -0400
Subject: [PATCH 0716/1492] Handle LJC params during append/strip. Fix handling
 of regular LJ params when LJ10-12 params also present when assigning
 Nonbonds. Simplify handling of 1-4 params during strip.

---
 src/ParameterTypes.h   |  4 +++
 src/Parm_CharmmPsf.cpp |  2 +-
 src/Topology.cpp       | 80 ++++++++++++++++++++++++++++--------------
 src/Topology.h         |  3 +-
 4 files changed, 61 insertions(+), 28 deletions(-)

diff --git a/src/ParameterTypes.h b/src/ParameterTypes.h
index 04e9d47992..3c6d769aae 100644
--- a/src/ParameterTypes.h
+++ b/src/ParameterTypes.h
@@ -684,10 +684,14 @@ class NonbondParmType {
     void SetupLJforNtypes(int n) { SetNtypes(n); nbarray_.assign((n*(n+1))/2, NonbondType()); }
     /// Set number of LJ 1-4 terms
     void SetNLJ14terms(int n)    { lj14_.assign( n, NonbondType() ); }
+    /// Set number of LJC terms
+    void SetNLJCterms(int n)     { ccoef_.assign( n, 0 ); }
     /// Set specified LJ term
     NonbondType& SetLJ(int i)    { return nbarray_[i];                  }
     /// Set specified LJ 1-4 term
     NonbondType& SetLJ14(int i)  { return lj14_[i];    }
+    /// Set specified LJC term
+    void SetLJC(int i, double ljc) { ccoef_[i] = ljc; }
     /// Set number of HB terms and init HB array TODO combine with SetNtypes?
     void SetNHBterms(int n)   { hbarray_.assign( n, HB_ParmType() ); }
     /// Set specified HB term
diff --git a/src/Parm_CharmmPsf.cpp b/src/Parm_CharmmPsf.cpp
index e7503efc3b..daece74d42 100644
--- a/src/Parm_CharmmPsf.cpp
+++ b/src/Parm_CharmmPsf.cpp
@@ -377,7 +377,7 @@ int Parm_CharmmPsf::ReadParm(FileName const& fname, Topology &parmOut) {
 
   // Add nonbonded parameters
   if (params_.HasLJparams()) {
-    parmOut.AssignNonbondParams( atomTypes, params_.NB(), params_.NB14(), params_.HB(), debug_ );
+    parmOut.AssignNonbondParams( atomTypes, params_.NB(), params_.NB14(), params_.LJC(), params_.HB(), debug_ );
   }
 
   return 0;
diff --git a/src/Topology.cpp b/src/Topology.cpp
index 38ed3e7f0b..8d31d86a5c 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -1770,7 +1770,10 @@ Topology* Topology::ModifyByMap(std::vector<int> const& MapIn, bool setupFullPar
     // Set up new nonbond and nonbond index arrays.
     newParm->nonbond_.SetNtypes( oldTypeArray.size() );
     if (!nonbond_.LJ14().empty())
-      newParm->nonbond_.SetNLJ14terms( (oldTypeArray.size()*(oldTypeArray.size()+1))/2 );
+      //newParm->nonbond_.SetNLJ14terms( (oldTypeArray.size()*(oldTypeArray.size()+1))/2 );
+      newParm->nonbond_.SetNLJ14terms( newParm->nonbond_.NBarray().size() );
+    if (!nonbond_.LJC_Array().empty())
+      newParm->nonbond_.SetNLJCterms( newParm->nonbond_.NBarray().size() );
     for (int a1idx = 0; a1idx != (int)oldTypeArray.size(); a1idx++)
     {
       int atm1 = oldTypeArray[a1idx];
@@ -1778,15 +1781,16 @@ Topology* Topology::ModifyByMap(std::vector<int> const& MapIn, bool setupFullPar
       {
         int atm2 = oldTypeArray[a2idx];
         int oldnbidx = nonbond_.GetLJindex( atm1, atm2 );
+        int newnbidx;
         if (oldnbidx > -1) {
           // This is a traditional LJ 6-12 term. Because of the way the LJ 1-4
           // code is laid out in sander/pmemd the LJ matrix has to be laid out
           // indepdendent of the nonbond index array.
-          newParm->nonbond_.AddLJterm( a1idx, a2idx, nonbond_.NBarray(oldnbidx) );
+          newnbidx = newParm->nonbond_.AddLJterm( a1idx, a2idx, nonbond_.NBarray(oldnbidx) );
         } else {
           // This is an old LJ 10-12 hbond term. Add one to the LJ 6-12 matrix
           // and one to the hbond since that seems to be the convention.
-          newParm->nonbond_.AddLJterm( a1idx, a2idx, NonbondType() );
+          newnbidx = newParm->nonbond_.AddLJterm( a1idx, a2idx, NonbondType() );
           newParm->nonbond_.AddHBterm( a1idx, a2idx, nonbond_.HBarray((-oldnbidx)-1) );
         }
         //int newnbidx = newParm->nonbond_.GetLJindex( a1idx, a2idx );
@@ -1795,14 +1799,18 @@ Topology* Topology::ModifyByMap(std::vector<int> const& MapIn, bool setupFullPar
         if (!nonbond_.LJ14().empty()) {
           // Update LJ 1-4 as well. No need to worry about hbond terms here,
           // just recalculate the old index and determine new one.
-          int ibig = std::max(atm1, atm2) + 1;
-          int isml = std::min(atm1, atm2) + 1;
-              oldnbidx = (ibig*(ibig-1)/2+isml)-1;
-              ibig = a2idx + 1;
-              isml = a1idx + 1;
-          int newnbidx = (ibig*(ibig-1)/2+isml)-1;
+          //int ibig = std::max(atm1, atm2) + 1;
+          //int isml = std::min(atm1, atm2) + 1;
+          //    oldnbidx = (ibig*(ibig-1)/2+isml)-1;
+          //    ibig = a2idx + 1;
+          //    isml = a1idx + 1;
+          //int newnbidx = (ibig*(ibig-1)/2+isml)-1;
           newParm->nonbond_.SetLJ14( newnbidx ) = nonbond_.LJ14()[oldnbidx];
         }
+        if (!nonbond_.LJC_Array().empty()) {
+          // Update LJC
+          newParm->nonbond_.SetLJC( newnbidx, nonbond_.LJC_Array( oldnbidx ) );
+        }
       }
     }
     // Update atom type indices.
@@ -2749,7 +2757,7 @@ int Topology::AppendTop(Topology const& NewTop) {
 
   // Need to regenerate nonbonded info
   mprintf("\tRegenerating nonbond parameters.\n");
-  AssignNonbondParams( myAtomTypes, myNB, my14, myHB, 1 ); // FIXME verbose TODO LJC
+  AssignNonbondParams( myAtomTypes, myNB, my14, myLJC, myHB, 1 ); // FIXME verbose TODO LJC
 
   // The version of AddTopAtom() with molecule number already determines
   // molecules and number of solvent molecules.
@@ -3248,10 +3256,12 @@ void Topology::AssignDihedralParams(DihedralParmHolder const& newDihedralParams,
 void Topology::AssignNonbondParams(ParmHolder<AtomType> const& newTypes,
                                    ParmHolder<NonbondType> const& newNB,
                                    ParmHolder<NonbondType> const& new14,
+                                   ParmHolder<double> const& newLJC,
                                    ParmHolder<HB_ParmType> const& newHB,
                                    int verbose)
 {
   bool hasLJ14 = !new14.empty();
+  bool hasLJC = !newLJC.empty();
   // Generate array of only the types that are currently in Topology. TODO should this be a permanent part of Topology?
   ParmHolder<AtomType> currentAtomTypes;
   for (std::vector<Atom>::const_iterator atm = atoms_.begin(); atm != atoms_.end(); ++atm)
@@ -3292,6 +3302,7 @@ void Topology::AssignNonbondParams(ParmHolder<AtomType> const& newTypes,
       t1->second.SetTypeIdx( n_unique_lj_types );
       // Look for equivalent nonbond types
       for (ParmHolder<AtomType>::iterator t2 = t1 + 1; t2 != currentAtomTypes.end(); ++t2) {
+        // Everything must match
         if (!hasLJ14) {
           if (t2->second.OriginalIdx() == -1 && t1->second.LJ() == t2->second.LJ()) {
             mprintf("DEBUG: Type %s equivalent to type %s\n", *(t2->first[0]), *(t1->first[0]));
@@ -3314,6 +3325,8 @@ void Topology::AssignNonbondParams(ParmHolder<AtomType> const& newTypes,
   nonbond_.SetupLJforNtypes( n_unique_lj_types );
   if (hasLJ14)
     nonbond_.SetNLJ14terms( nonbond_.NBarray().size() );
+  if (hasLJC)
+    nonbond_.SetNLJCterms( nonbond_.NBarray().size() );
   // Loop over all atom type pairs
   for (ParmHolder<AtomType>::const_iterator t1 = currentAtomTypes.begin(); t1 != currentAtomTypes.end(); ++t1)
   {
@@ -3328,11 +3341,14 @@ void Topology::AssignNonbondParams(ParmHolder<AtomType> const& newTypes,
       TypeNameHolder types(2);
       types.AddName( name1 );
       types.AddName( name2 );
+      int newnbidx;
       // Check for LJ10-12 first
       ParmHolder<HB_ParmType>::const_iterator hb = newHB.GetParam( types );
       if (hb != newHB.end()) {
         if (verbose > 0) mprintf("LJ 10-12 parameter found for %s %s\n", *name1, *name2);
         nonbond_.AddHBterm(t1->second.OriginalIdx(), t2->second.OriginalIdx(), hb->second);
+        // Also add a blank 6-12 term since that seems to be the convention
+        newnbidx = nonbond_.AddLJterm( t1->second.OriginalIdx(), t2->second.OriginalIdx(), NonbondType() );
       } else {
         // See if this parameter exists in the given nonbond array.
         NonbondType LJAB;
@@ -3344,20 +3360,32 @@ void Topology::AssignNonbondParams(ParmHolder<AtomType> const& newTypes,
           if (verbose > 0) mprintf("Using existing NB parameter for %s %s\n", *name1, *name2);
           LJAB = it->second;
         }
-        int ljidx = nonbond_.AddLJterm(t1->second.OriginalIdx(), t2->second.OriginalIdx(), LJAB);
-        // LJ 1-4
-        if (hasLJ14) {
-          // Get parameter if it exists
-          ParmHolder<NonbondType>::const_iterator it = new14.GetParam( types );
-          if (it == new14.end()) {
-            if (verbose > 0) mprintf("NB 1-4 parameter for %s %s not found. Generating.\n", *name1, *name2);
-            nonbond_.SetLJ14( ljidx ) = type1.LJ14().Combine_LB( type2.LJ14() );
-          } else {
-            if (verbose > 0) mprintf("Using existing NB 1-4 parameter for %s %s\n", *name1, *name2);
-            nonbond_.SetLJ14( ljidx ) = it->second;
-          }
-        } // END hasLJ14
-      } // END is LJ
+        newnbidx = nonbond_.AddLJterm(t1->second.OriginalIdx(), t2->second.OriginalIdx(), LJAB);
+      }
+      // LJ 1-4
+      if (hasLJ14) {
+        // Get parameter if it exists
+        ParmHolder<NonbondType>::const_iterator it = new14.GetParam( types );
+        if (it == new14.end()) {
+          if (verbose > 0) mprintf("NB 1-4 parameter for %s %s not found. Generating.\n", *name1, *name2);
+          nonbond_.SetLJ14( newnbidx ) = type1.LJ14().Combine_LB( type2.LJ14() );
+        } else {
+          if (verbose > 0) mprintf("Using existing NB 1-4 parameter for %s %s\n", *name1, *name2);
+          nonbond_.SetLJ14( newnbidx ) = it->second;
+        }
+      } // END hasLJ14
+      // LJC
+      if (hasLJC) {
+        // Get parameter if it exists
+        ParmHolder<double>::const_iterator it = newLJC.GetParam( types );
+        if (it == newLJC.end()) {
+          mprintf("LJC parameter for %s %s not found. Setting to 0.\n", *name1, *name2); // FIXME generate
+          nonbond_.SetLJC( newnbidx, 0 );
+        } else {
+          mprintf("Using existing LJC parameter for %s %s\n", *name1, *name2);
+          nonbond_.SetLJC( newnbidx, it->second );
+        }
+      } // END hasLJC
     } // END inner loop over current types
   } // END outer loop over current types
   // Reset the atom type indices.
@@ -3724,7 +3752,7 @@ int Topology::AssignParams(ParameterSet const& set0) {
   AssignAtomTypeParm( set0.AT() );
   // LJ 6-12
   mprintf("\tAssigning nonbond parameters.\n");
-  AssignNonbondParams( set0.AT(), set0.NB(), set0.NB14(), set0.HB(), debug_ );
+  AssignNonbondParams( set0.AT(), set0.NB(), set0.NB14(), set0.LJC(), set0.HB(), debug_ );
   mprintf("DEBUG: CMAP size %zu\n", set0.CMAP().size());
   // TODO LJ14, LJC
 
@@ -3797,7 +3825,7 @@ int Topology::UpdateParams(ParameterSet const& set1) {
       UC.nLJparamsUpdated_ > 0 || UC.nLJ14paramsUpdated_ > 0)
   {
     mprintf("\tRegenerating nonbond parameters.\n");
-    AssignNonbondParams( set0.AT(), set0.NB(), set0.NB14(), set0.HB(), debug_ );
+    AssignNonbondParams( set0.AT(), set0.NB(), set0.NB14(), set0.LJC(), set0.HB(), debug_ );
   }
   // CMAP
   if (UC.nCmapUpdated_ > 0) {
diff --git a/src/Topology.h b/src/Topology.h
index 81ba936fe2..d6261c673e 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -170,7 +170,8 @@ class Topology {
     inline NonbondType const& GetLJparam(int, int) const;
     /// Assign LJ 6-12 / 10-12 parameters, reset atom type indices
     void AssignNonbondParams(ParmHolder<AtomType> const&, ParmHolder<NonbondType> const&,
-                             ParmHolder<NonbondType> const&, ParmHolder<HB_ParmType> const&, int);
+                             ParmHolder<NonbondType> const&, ParmHolder<double> const&,
+                             ParmHolder<HB_ParmType> const&, int);
     /// \return True if any charge is non-zero
     bool HasChargeInfo() const;
     /// Redistribute charge on atoms in topology to match target total charge

From d623b70047efa9ca245e71bbae1bad7918bb8d26 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 30 May 2024 14:49:27 -0400
Subject: [PATCH 0717/1492] Use chiral routines directly

---
 src/Action_CheckChirality.cpp | 9 +++++----
 src/cpptrajdepend             | 2 +-
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/src/Action_CheckChirality.cpp b/src/Action_CheckChirality.cpp
index a8d1003074..13af1a0c3b 100644
--- a/src/Action_CheckChirality.cpp
+++ b/src/Action_CheckChirality.cpp
@@ -3,7 +3,7 @@
 #include "TorsionRoutines.h"
 #include "DataSet_Mesh.h"
 //#incl ude "Constants.h"
-#include "Structure/BuildAtom.h"
+#include "Structure/Chirality.h"
 
 void Action_CheckChirality::Help() const {
   mprintf("\t[<name>] [<mask1>] [out <filename>] [byatom]\n"
@@ -198,13 +198,14 @@ Action::RetType Action_CheckChirality::DoAction(int frameNum, ActionFrame& frm)
       if (*it != 0) {
         DataSet* ds = *it;
         int iat = ds->Meta().Idx() - 1;
-        Cpptraj::Structure::BuildAtom AtomC;
-        if (AtomC.DetermineChirality(iat, *currentTop_, frm.Frm(), debug_))
+        Cpptraj::Structure::ChiralType chirality =
+          Cpptraj::Structure::DetermineChirality(iat, *currentTop_, frm.Frm(), debug_);
+        if (chirality == Cpptraj::Structure::CHIRALITY_ERR)
           return Action::ERR;
         //double tval_degrees = AtomC.TorsionVal() * Constants::RADDEG;
         //float ftval = (float)tval_degrees;
         //ds->Add( frameNum, &ftval );
-        const char* chiralstr = Cpptraj::Structure::chiralStr( AtomC.Chirality() );
+        const char* chiralstr = Cpptraj::Structure::chiralStr( chirality );
         ds->Add( frameNum, chiralstr );
       }
     }
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index ee742ca7ca..410b4db903 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -14,7 +14,7 @@ Action_Bounds.o : Action_Bounds.cpp Action.h ActionState.h Action_Bounds.h ArgLi
 Action_Box.o : Action_Box.cpp Action.h ActionState.h Action_Box.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BoxArgs.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Action_Center.o : Action_Center.cpp Action.h ActionState.h Action_Center.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Action_Channel.o : Action_Channel.cpp Action.h ActionState.h Action_Channel.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_CheckChirality.o : Action_CheckChirality.cpp Action.h ActionState.h Action_CheckChirality.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h Structure/BuildAtom.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Action_CheckChirality.o : Action_CheckChirality.cpp Action.h ActionState.h Action_CheckChirality.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h Structure/Chirality.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 Action_CheckStructure.o : Action_CheckStructure.cpp Action.h ActionState.h Action_CheckStructure.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_integer.h DataSet_string.h Dimension.h DispatchObject.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Action_Closest.o : Action_Closest.cpp Action.h ActionState.h ActionTopWriter.h Action_Closest.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h ImageRoutines.h ImageTypes.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h cuda_kernels/kernel_wrappers.cuh
 Action_ClusterDihedral.o : Action_ClusterDihedral.cpp Action.h ActionState.h Action_ClusterDihedral.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_integer.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h

From f2de1e3bdf30a118b070ce2f0a48b45bab983e36 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 31 May 2024 13:40:21 -0400
Subject: [PATCH 0718/1492] No need for BuildAtom in these files

---
 src/Structure/Chirality.cpp    |  2 +-
 src/Structure/SugarBuilder.cpp | 14 +++++---------
 src/Structure/structuredepend  |  2 +-
 src/cpptrajdepend              |  2 +-
 4 files changed, 8 insertions(+), 12 deletions(-)

diff --git a/src/Structure/Chirality.cpp b/src/Structure/Chirality.cpp
index 1b123141be..609ab45202 100644
--- a/src/Structure/Chirality.cpp
+++ b/src/Structure/Chirality.cpp
@@ -205,7 +205,7 @@ Cpptraj::Structure::ChiralType
 // ===== LEaP Chirality routines ===============================================
 /** LEaP routine for determining atom chirality.
   * This is done by crossing A to B and then dotting the
-  * result with C. TODO use Chirality in BuildAtom? Use an Enum?
+  * result with C. TODO use Chirality in StructureEnum?
   * The chirality of the vectors is determined by the sign of
   * the result, which is determined by whether or not C has
   * a component in the direction AxB or in the opposite direction.
diff --git a/src/Structure/SugarBuilder.cpp b/src/Structure/SugarBuilder.cpp
index 739612ea92..09e98c0c83 100644
--- a/src/Structure/SugarBuilder.cpp
+++ b/src/Structure/SugarBuilder.cpp
@@ -1,5 +1,5 @@
 #include "SugarBuilder.h"
-#include "BuildAtom.h"
+#include "Chirality.h"
 #include "FxnGroupBuilder.h"
 #include "ResStatArray.h"
 #include "StructureRoutines.h"
@@ -1113,10 +1113,8 @@ const
     cdebug = 1;
   else
     cdebug = 0;
-  BuildAtom atomR;
-  int cerr = atomR.DetermineChirality(sugar.HighestStereocenter(), topIn, frameIn, cdebug);
-  ChiralType ctypeR = atomR.Chirality();
-  if (cerr != 0 || ctypeR == IS_UNKNOWN_CHIRALITY) {
+  ChiralType ctypeR = DetermineChirality(sugar.HighestStereocenter(), topIn, frameIn, cdebug);
+  if (ctypeR == CHIRALITY_ERR || ctypeR == IS_UNKNOWN_CHIRALITY) {
     mprinterr("Error: Could not determine configuration for furanose.\n"); // TODO warn?
     return 1;
   }
@@ -1125,10 +1123,8 @@ const
   else
     stoken.SetChirality(SugarToken::IS_L);
 
-  BuildAtom atomA;
-  cerr = atomA.DetermineChirality(sugar.AnomericAtom(), topIn, frameIn, cdebug);
-  ChiralType ctypeA = atomA.Chirality();
-  if (cerr != 0 || ctypeA == IS_UNKNOWN_CHIRALITY) {
+  ChiralType ctypeA = DetermineChirality(sugar.AnomericAtom(), topIn, frameIn, cdebug);
+  if (ctypeA == CHIRALITY_ERR || ctypeA == IS_UNKNOWN_CHIRALITY) {
     mprinterr("Error: Could not determine chirality around anomeric atom for furanose.\n"); // TODO warn?
     return 1;
   }
diff --git a/src/Structure/structuredepend b/src/Structure/structuredepend
index c8401aa8cb..0db13334dc 100644
--- a/src/Structure/structuredepend
+++ b/src/Structure/structuredepend
@@ -12,7 +12,7 @@ PdbCleaner.o : PdbCleaner.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../AtomType.h
 StructureEnum.o : StructureEnum.cpp StructureEnum.h
 StructureRoutines.o : StructureRoutines.cpp ../Atom.h ../CpptrajStdio.h ../NameType.h ../Residue.h ../SymbolExporting.h StructureRoutines.h
 Sugar.o : Sugar.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Sugar.h SugarToken.h
-SugarBuilder.o : SugarBuilder.cpp ../ArgList.h ../Atom.h ../AtomMap.h ../AtomMask.h ../AtomType.h ../Box.h ../CharMask.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DistRoutines.h ../FileIO.h ../FileName.h ../Frame.h ../ImageOption.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h FunctionalGroup.h FxnGroupBuilder.h LinkAtom.h ResStatArray.h StructureEnum.h StructureRoutines.h Sugar.h SugarBuilder.h SugarLinkAtoms.h SugarToken.h
+SugarBuilder.o : SugarBuilder.cpp ../ArgList.h ../Atom.h ../AtomMap.h ../AtomMask.h ../AtomType.h ../Box.h ../CharMask.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DistRoutines.h ../FileIO.h ../FileName.h ../Frame.h ../ImageOption.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Chirality.h FunctionalGroup.h FxnGroupBuilder.h LinkAtom.h ResStatArray.h StructureEnum.h StructureRoutines.h Sugar.h SugarBuilder.h SugarLinkAtoms.h SugarToken.h
 SugarLinkAtoms.o : SugarLinkAtoms.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../StringRoutines.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h LinkAtom.h SugarLinkAtoms.h
 SugarToken.o : SugarToken.cpp ../ArgList.h ../CpptrajStdio.h SugarToken.h
 Zmatrix.o : Zmatrix.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h GenerateConnectivityArrays.h InternalCoords.h Zmatrix.h
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 410b4db903..b04d7437ab 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -470,7 +470,7 @@ Structure/PdbCleaner.o : Structure/PdbCleaner.cpp ArgList.h Atom.h AtomMask.h At
 Structure/StructureEnum.o : Structure/StructureEnum.cpp Structure/StructureEnum.h
 Structure/StructureRoutines.o : Structure/StructureRoutines.cpp Atom.h CpptrajStdio.h NameType.h Residue.h Structure/StructureRoutines.h SymbolExporting.h
 Structure/Sugar.o : Structure/Sugar.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Structure/SugarBuilder.o : Structure/SugarBuilder.cpp ArgList.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DistRoutines.h FileIO.h FileName.h Frame.h ImageOption.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/FunctionalGroup.h Structure/FxnGroupBuilder.h Structure/LinkAtom.h Structure/ResStatArray.h Structure/StructureEnum.h Structure/StructureRoutines.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarLinkAtoms.h Structure/SugarToken.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Structure/SugarBuilder.o : Structure/SugarBuilder.cpp ArgList.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DistRoutines.h FileIO.h FileName.h Frame.h ImageOption.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Chirality.h Structure/FunctionalGroup.h Structure/FxnGroupBuilder.h Structure/LinkAtom.h Structure/ResStatArray.h Structure/StructureEnum.h Structure/StructureRoutines.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarLinkAtoms.h Structure/SugarToken.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 Structure/SugarLinkAtoms.o : Structure/SugarLinkAtoms.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/LinkAtom.h Structure/SugarLinkAtoms.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/SugarToken.o : Structure/SugarToken.cpp ArgList.h CpptrajStdio.h Structure/SugarToken.h
 Structure/Zmatrix.o : Structure/Zmatrix.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h

From c040372c165327b8b736f3e9a39457dff7c69e48 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 31 May 2024 13:42:21 -0400
Subject: [PATCH 0719/1492] BuildAtom is obsolete

---
 src/Structure/BuildAtom.cpp   | 29 -------------------------
 src/Structure/BuildAtom.h     | 40 -----------------------------------
 src/Structure/CMakeLists.txt  |  1 -
 src/Structure/structuredepend |  1 -
 src/Structure/structurefiles  |  1 -
 src/cpptrajdepend             |  1 -
 6 files changed, 73 deletions(-)
 delete mode 100644 src/Structure/BuildAtom.cpp
 delete mode 100644 src/Structure/BuildAtom.h

diff --git a/src/Structure/BuildAtom.cpp b/src/Structure/BuildAtom.cpp
deleted file mode 100644
index 90667e8bfe..0000000000
--- a/src/Structure/BuildAtom.cpp
+++ /dev/null
@@ -1,29 +0,0 @@
-#include "BuildAtom.h"
-#include "Chirality.h"
-#include "../Constants.h"
-#include "../CpptrajStdio.h"
-#include "../Frame.h"
-#include "../Topology.h"
-#include "../TorsionRoutines.h"
-#include <algorithm> // std::sort
-
-/** Determine chirality and priority around an atom. */
-int Cpptraj::Structure::BuildAtom::DetermineChirality(int atnum, Topology const& topIn,
-                                                      Frame const& frameIn, int debugIn)
-{
-  priority_.clear();
-  ctype_ = Cpptraj::Structure::SetPriority(priority_, atnum, topIn, frameIn, debugIn);
-  if (ctype_ == CHIRALITY_ERR)
-    return 1;
-  return 0;
-}
-
-/** Determine only priority around an atom. */
-int Cpptraj::Structure::BuildAtom::SetPriority(int atnum, Topology const& topIn,
-                                               Frame const& frameIn, int debugIn)
-{
-  priority_.clear();
-  if (Cpptraj::Structure::SetPriority(priority_, atnum, topIn, frameIn, debugIn) == CHIRALITY_ERR)
-    return 1;
-  return 0;
-}
diff --git a/src/Structure/BuildAtom.h b/src/Structure/BuildAtom.h
deleted file mode 100644
index 0c12267975..0000000000
--- a/src/Structure/BuildAtom.h
+++ /dev/null
@@ -1,40 +0,0 @@
-#ifndef INC_STRUCTURE_BUILDATOM_H
-#define INC_STRUCTURE_BUILDATOM_H
-#include "StructureEnum.h"
-#include <vector>
-class Topology;
-class Frame;
-namespace Cpptraj {
-namespace Structure {
-/// Hold chirality/orientation information for an atom. Used when building/modelling new coordinates.
-class BuildAtom {
-  public:
-    /// Blank constructor 
-    BuildAtom() : tors_(0), ctype_(IS_UNKNOWN_CHIRALITY), orientation_(IS_UNKNOWN_CHIRALITY) {}
-    /// CONSTRUCTOR - Take only chiral type. Usually used to indicate an error
-    BuildAtom(ChiralType e) : tors_(0), ctype_(e), orientation_(e) {}
-    /// CONSTRUCTOR - torsion, chirality, orientation, priority array
-    BuildAtom(double t, ChiralType c, ChiralType o, std::vector<int> const& p) :
-                  tors_(t), ctype_(c), orientation_(o), priority_(p) {}
-    /// Set chirality, orientation, and priority around specified atom
-    int DetermineChirality(int, Topology const&, Frame const&, int);
-    /// Only set the priority around specified atom
-    int SetPriority(int, Topology const&, Frame const&, int);
-
-    /// \return Atom chirality
-    ChiralType Chirality()             const { return ctype_; }
-    /// \return Orientation around atom
-    ChiralType Orientation()           const { return orientation_; }
-    /// \return Priority array
-    std::vector<int> const& Priority() const { return priority_; }
-    /// \return Value of the orientation torsion around atom (in radians).
-    double TorsionVal()                const { return tors_; }
-  private:
-    double tors_;               ///< Torsion around the atom in radians (via priority, 1-2-3-0, where 0 is this atom).
-    ChiralType ctype_;          ///< Chirality around atom.
-    ChiralType orientation_;    ///< Orientation when chirality cannot be determined.
-    std::vector<int> priority_; ///< Indices of bonded atoms, sorted by priority.
-};
-}
-}
-#endif
diff --git a/src/Structure/CMakeLists.txt b/src/Structure/CMakeLists.txt
index d4287c6e3c..c807ddcc6b 100644
--- a/src/Structure/CMakeLists.txt
+++ b/src/Structure/CMakeLists.txt
@@ -1,6 +1,5 @@
 #CMake buildfile for CPPTRAJ Structure subdirectory.
 target_sources(cpptraj_common_obj PRIVATE
-  ${CMAKE_CURRENT_LIST_DIR}/BuildAtom.cpp
   ${CMAKE_CURRENT_LIST_DIR}/Builder.cpp
   ${CMAKE_CURRENT_LIST_DIR}/Chirality.cpp
   ${CMAKE_CURRENT_LIST_DIR}/Creator.cpp
diff --git a/src/Structure/structuredepend b/src/Structure/structuredepend
index 0db13334dc..123c931bc6 100644
--- a/src/Structure/structuredepend
+++ b/src/Structure/structuredepend
@@ -1,4 +1,3 @@
-BuildAtom.o : BuildAtom.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h Chirality.h StructureEnum.h
 Builder.o : Builder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Builder.h Chirality.h GenerateConnectivityArrays.h InternalCoords.h StructureEnum.h Zmatrix.h
 Chirality.o : Chirality.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Chirality.h StructureEnum.h
 Creator.o : Creator.cpp ../ArgList.h ../AssociatedData.h ../AssociatedData_ResId.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../DataSet_NameMap.h ../DataSet_Parameters.h ../Dimension.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/StructureEnum.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Creator.h GenerateConnectivityArrays.h StructureEnum.h
diff --git a/src/Structure/structurefiles b/src/Structure/structurefiles
index 48693161e5..7e78f88f07 100644
--- a/src/Structure/structurefiles
+++ b/src/Structure/structurefiles
@@ -1,6 +1,5 @@
 # Files for Structure subdirectory.
 STRUCTURE_SOURCES= \
-  BuildAtom.cpp \
   Builder.cpp \
   Chirality.cpp \
   Creator.cpp \
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index b04d7437ab..17f979628f 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -456,7 +456,6 @@ SpaceGroup.o : SpaceGroup.cpp Matrix_3x3.h Parallel.h SpaceGroup.h Vec3.h
 Spline.o : Spline.cpp CpptrajStdio.h Spline.h
 SplineFxnTable.o : SplineFxnTable.cpp Constants.h CpptrajStdio.h Spline.h SplineFxnTable.h StringRoutines.h
 StringRoutines.o : StringRoutines.cpp CpptrajStdio.h StringRoutines.h
-Structure/BuildAtom.o : Structure/BuildAtom.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/Chirality.h Structure/StructureEnum.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 Structure/Builder.o : Structure/Builder.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h GuessAtomHybridization.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Builder.h Structure/Chirality.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 Structure/Chirality.o : Structure/Chirality.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Chirality.h Structure/StructureEnum.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 Structure/Creator.o : Structure/Creator.cpp ArgList.h AssociatedData.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/Creator.h Structure/GenerateConnectivityArrays.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h

From 9edd11221b978f12a7dbff47b9d81a1cb13141b3 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 3 Jun 2024 15:37:11 -0400
Subject: [PATCH 0720/1492] Handle case where AMBERHOME is not set

---
 src/DataIO_LeapRC.cpp | 27 ++++++++++++++++++++++-----
 src/DataIO_LeapRC.h   |  2 ++
 src/Exec_Source.cpp   |  3 +--
 3 files changed, 25 insertions(+), 7 deletions(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index f94f510457..41947f7cbd 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -68,6 +68,22 @@ bool DataIO_LeapRC::check_already_loaded(Sarray const& files, std::string const&
   return false;
 }
 
+/** First look for filename, then look for AMBERHOME/dir/filename. */
+std::string DataIO_LeapRC::find_path(std::string const& filename,
+                                     std::string const& dir)
+const
+{
+  if (File::Exists( filename )) return filename;
+  if (amberhome_.empty()) {
+    mprinterr("Error: '%s' not found.\n", filename.c_str());
+    return filename;
+  }
+  std::string amberpath = amberhome_ + dir + filename;
+  if (File::Exists( amberpath )) return amberpath;
+  mprinterr("Error: '%s' not found.\n", amberpath.c_str());
+  return amberpath;
+}
+
 /** LEaP loadAmberParams command. */
 int DataIO_LeapRC::LoadAmberParams(std::string const& filename, DataSetList& dsl, std::string const& dsname) const {
   // TODO detect this better
@@ -76,7 +92,7 @@ int DataIO_LeapRC::LoadAmberParams(std::string const& filename, DataSetList& dsl
     mprintf("\tLoading force field modifications from '%s'\n", filename.c_str());
     DataIO_AmberFrcmod infile;
     infile.SetDebug( debug_ );
-    if (infile.ReadData(amberhome_ + "parm/" + filename, dsl, dsname)) {
+    if (infile.ReadData( find_path(filename, "parm/"), dsl, dsname)) {
       mprinterr("Error: Could not load force field modifications from '%s'\n", filename.c_str());
       return 1;
     }
@@ -86,7 +102,7 @@ int DataIO_LeapRC::LoadAmberParams(std::string const& filename, DataSetList& dsl
     } else {
       mprintf("\tLoading force field from '%s'\n", filename.c_str());
       DataIO_AmberFF infile;
-      if (infile.ReadData(amberhome_ + "parm/" + filename, dsl, dsname)) {
+      if (infile.ReadData( find_path(filename, "parm/"), dsl, dsname)) {
         mprinterr("Error: Could not load force field from '%s'\n", filename.c_str());
         return 1;
       }
@@ -106,7 +122,7 @@ int DataIO_LeapRC::LoadOFF(std::string const& filename, DataSetList& dsl, std::s
     // Allow lib to overwrite e.g. something from previous prep
     ArgList tmpArgs("allowoverwrite");
     infile.processReadArgs(tmpArgs);
-    if (infile.ReadData(amberhome_ + "lib/" + filename, dsl, dsname)) {
+    if (infile.ReadData( find_path(filename, "lib/"), dsl, dsname)) {
       mprinterr("Error: Could not load library file '%s'\n", filename.c_str());
       return 1;
     }
@@ -122,7 +138,7 @@ int DataIO_LeapRC::LoadAmberPrep(std::string const& filename, DataSetList& dsl,
   } else {
     DataIO_AmberPrep infile;
     infile.SetDebug( debug_ );
-    if (infile.ReadData(amberhome_ + "prep/" + filename, dsl, dsname)) {
+    if (infile.ReadData( find_path(filename, "prep/"), dsl, dsname)) {
       mprinterr("Error: Could not load prep file '%s'\n", filename.c_str());
       return 1;
     }
@@ -379,7 +395,8 @@ int DataIO_LeapRC::ReadData(FileName const& fname, DataSetList& dsl, std::string
     } else
       amberhome_ = leapcmddir.DirPrefix();
   }
-  mprintf("\tForce field files located in '%s'\n", amberhome_.c_str());
+  if (!amberhome_.empty())
+    mprintf("\tForce field files located in '%s'\n", amberhome_.c_str());
   BufferedLine infile;
   if (infile.OpenFileRead(fname)) {
     mprinterr("Error: Could not open leaprc file '%s'\n", fname.full());
diff --git a/src/DataIO_LeapRC.h b/src/DataIO_LeapRC.h
index 9035379a01..d99cd1cc93 100644
--- a/src/DataIO_LeapRC.h
+++ b/src/DataIO_LeapRC.h
@@ -36,6 +36,8 @@ class DataIO_LeapRC : public DataIO {
     int AddPdbAtomMap(std::string const&, DataSetList&, BufferedLine&) const;
     /// Used to check if a parm/lib file was already loaded.
     static inline bool check_already_loaded(Sarray const&, std::string const&);
+    /// \return either file or Amberhome/dir/file
+    std::string find_path(std::string const&, std::string const&) const;
 
     std::string amberhome_;
     static Sarray paramFiles_; ///< Track amber FF param files loaded from leaprc files
diff --git a/src/Exec_Source.cpp b/src/Exec_Source.cpp
index fbd2d5c6b1..d1a26b1c56 100644
--- a/src/Exec_Source.cpp
+++ b/src/Exec_Source.cpp
@@ -40,8 +40,7 @@ Exec::RetType Exec_Source::Execute(CpptrajState& State, ArgList& argIn)
   CpptrajFile tmp;
   tmp.SetupRead( fileName, State.Debug() );
   if (!infile.ID_DataFormat( tmp )) {
-    mprinterr("Error: %s does not appear to be a leaprc file.\n", fileName.full());
-    return CpptrajState::ERR;
+    mprintf("Warning: %s does not appear to be a leaprc file.\n", fileName.full());
   }
   if (infile.processReadArgs( argIn )) {
     mprinterr("Error: Could not process read args for leaprc file %s\n", fileName.full());

From a7ff56edf27e71bfce6b3fb2f4e74ae15edffa37 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 3 Jun 2024 15:46:06 -0400
Subject: [PATCH 0721/1492] Start LoadMol2

---
 src/DataIO_LeapRC.cpp | 10 ++++++++++
 src/DataIO_LeapRC.h   |  1 +
 2 files changed, 11 insertions(+)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 41947f7cbd..0b17306844 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -361,6 +361,12 @@ const
   return 0;
 }
 
+/** Load mol2 as a COORDS set */
+int DataIO_LeapRC::LoadMol2(ArgList& argIn, DataSetList& dsl) const {
+  mprintf("DEBUG: LoadMol2\n");
+  argIn.PrintList();
+  return 0;
+}
 
 /// Move sets from paramDSL to dsl
 static inline int addSetsToList(DataSetList& dsl, DataSetList& paramDSL)
@@ -408,6 +414,8 @@ int DataIO_LeapRC::ReadData(FileName const& fname, DataSetList& dsl, std::string
   PdbResMapArray pdbResMap;
   int err = 0;
   const char* ptr = infile.Line();
+  // FIXME need to convert to all lowercase for matching commands; leap allows
+  //       mixed case
   while (ptr != 0) {
     if (ptr[0] != '\0' && ptr[0] != '#') {
       ArgList line( ptr, " \t" );
@@ -429,6 +437,8 @@ int DataIO_LeapRC::ReadData(FileName const& fname, DataSetList& dsl, std::string
         err = AddPdbResMap(pdbResMap, infile);
       else if (line.Contains("addPdbAtomMap") || line.Contains("addpdbatommap"))
         err = AddPdbAtomMap(dsname, dsl, infile);
+      else if (line.Contains("loadmol2") || line.Contains("loadMol2"))
+        err = LoadMol2(line, dsl);
       else {
         // Does this line contain an equals sign?
         bool has_equals = false;
diff --git a/src/DataIO_LeapRC.h b/src/DataIO_LeapRC.h
index d99cd1cc93..afec45ede5 100644
--- a/src/DataIO_LeapRC.h
+++ b/src/DataIO_LeapRC.h
@@ -34,6 +34,7 @@ class DataIO_LeapRC : public DataIO {
     int AddAtomTypes(NHarrayType&, BufferedLine&) const;
     int AddPdbResMap(PdbResMapArray&, BufferedLine&) const;
     int AddPdbAtomMap(std::string const&, DataSetList&, BufferedLine&) const;
+    int LoadMol2(ArgList&, DataSetList&) const;
     /// Used to check if a parm/lib file was already loaded.
     static inline bool check_already_loaded(Sarray const&, std::string const&);
     /// \return either file or Amberhome/dir/file

From 38f4c18180fe875a64ef73b109ae100d23c33ded Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 4 Jun 2024 14:57:48 -0400
Subject: [PATCH 0722/1492] Start COORDS readdata class

---
 src/DataIO_Coords.cpp | 80 +++++++++++++++++++++++++++++++++++++++++++
 src/DataIO_Coords.h   | 17 +++++++++
 2 files changed, 97 insertions(+)
 create mode 100644 src/DataIO_Coords.cpp
 create mode 100644 src/DataIO_Coords.h

diff --git a/src/DataIO_Coords.cpp b/src/DataIO_Coords.cpp
new file mode 100644
index 0000000000..3098c286c1
--- /dev/null
+++ b/src/DataIO_Coords.cpp
@@ -0,0 +1,80 @@
+#include "DataIO_Coords.h"
+#include "CpptrajStdio.h"
+#include "ParmFile.h"
+#include "TrajectoryFile.h"
+
+/// CONSTRUCTOR
+DataIO_Coords::DataIO_Coords()
+{
+
+}
+
+// DataIO_Coords::ID_DataFormat()
+bool DataIO_Coords::ID_DataFormat(CpptrajFile& infile)
+{
+  // Needs to be either a topology format or a coords format
+  ParmFile::ParmFormatType parm_format = ParmFile::DetectFormat(infile.Filename());
+  TrajectoryFile::TrajFormatType traj_format = TrajectoryFile::DetectFormat(infile.Filename());
+  if (parm_format != ParmFile::UNKNOWN_PARM ||
+      traj_format != TrajectoryFile::UNKNOWN_TRAJ)
+    return true;
+  return false;
+}
+
+// DataIO_Coords::ReadHelp()
+void DataIO_Coords::ReadHelp()
+{
+
+}
+
+// DataIO_Coords::processReadArgs()
+int DataIO_Coords::processReadArgs(ArgList& argIn)
+{
+
+  return 0;
+}
+
+/// \return True if this is a COORDS set we can append to
+static inline bool can_append(DataSet::DataType typeIn) {
+  return (typeIn == DataSet::COORDS ||
+          typeIn == DataSet::FRAMES);
+}
+
+// DataIO_Coords::ReadData()
+int DataIO_Coords::ReadData(FileName const& fname, DataSetList& dsl, std::string const& dsname)
+{
+  DataSet* dset = 0;
+  if (!dsname.empty()) {
+    // Is this set already present?
+    dset = dsl.GetDataSet( dsname );
+    if (dset != 0) {
+      if (!can_append(dset->Type())) {
+        mprinterr("Error: Cannot append coordinates to existing set '%s'\n", dset->legend());
+        return 1;
+      } else
+        mprintf("\tAppending to set '%s'\n", dset->legend());
+    }
+  }
+
+  return 0;
+}
+
+// DataIO_Coords::WriteHelp()
+void DataIO_Coords::WriteHelp()
+{
+
+}
+
+// DataIO_Coords::processWriteArgs()
+int DataIO_Coords::processWriteArgs(ArgList& argIn)
+{
+
+  return 0;
+}
+
+// DataIO_Coords::WriteData()
+int DataIO_Coords::WriteData(FileName const& fname, DataSetList const& dsl)
+{
+
+  return 1;
+}
diff --git a/src/DataIO_Coords.h b/src/DataIO_Coords.h
new file mode 100644
index 0000000000..9bf70ed3ae
--- /dev/null
+++ b/src/DataIO_Coords.h
@@ -0,0 +1,17 @@
+#ifndef INC_DATAIO_COORDS_H
+#define INC_DATAIO_COORDS_H
+#include "DataIO.h"
+/// Load COORDS set from a file 
+class DataIO_Coords : public DataIO {
+  public:
+    DataIO_Coords();
+    static void ReadHelp();
+    static void WriteHelp();
+    static BaseIOtype* Alloc() { return (BaseIOtype*)new DataIO_Coords(); }
+    int processReadArgs(ArgList&);
+    int ReadData(FileName const&, DataSetList&, std::string const&);
+    int processWriteArgs(ArgList&);
+    int WriteData(FileName const&, DataSetList const&);
+    bool ID_DataFormat(CpptrajFile&);
+};
+#endif

From ec579d6257af83530d30255c320bee8d6b36ca31 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 5 Jun 2024 14:47:44 -0400
Subject: [PATCH 0723/1492] Finish DataIO for coords data read

---
 src/DataFile.cpp      |  3 ++
 src/DataFile.h        |  2 +-
 src/DataIO_Coords.cpp | 71 ++++++++++++++++++++++++++++++++++++++++---
 src/DataIO_Coords.h   |  3 ++
 src/cpptrajdepend     |  3 +-
 src/cpptrajfiles      |  1 +
 6 files changed, 77 insertions(+), 6 deletions(-)

diff --git a/src/DataFile.cpp b/src/DataFile.cpp
index 476cad84ce..1062f8b7fe 100644
--- a/src/DataFile.cpp
+++ b/src/DataFile.cpp
@@ -37,6 +37,7 @@
 #include "DataIO_AmberFF.h"
 #include "DataIO_AmberFrcmod.h"
 #include "DataIO_LeapRC.h"
+#include "DataIO_Coords.h"
 
 // CONSTRUCTOR
 DataFile::DataFile() :
@@ -95,6 +96,7 @@ const FileTypes::AllocToken DataFile::DF_AllocArray[] = {
   { "Amber Force Field",  DataIO_AmberFF::ReadHelp,      0,            DataIO_AmberFF::Alloc},
   { "Amber Frcmod File",  0,                             0,            DataIO_AmberFrcmod::Alloc},
   { "Amber LEaP RC File", 0,                             0,            DataIO_LeapRC::Alloc},
+  { "Coordinates",        0,                             0,            DataIO_Coords::Alloc},
   { "Unknown Data file",  0,                       0,                        0                    }
 };
 
@@ -127,6 +129,7 @@ const FileTypes::KeyToken DataFile::DF_KeyArray[] = {
   { AMBERFF,      "amberff",      ".parm" },
   { AMBERFRCMOD,  "frcmod",       ".frcmod" },
   { AMBERLEAPRC,  "leaprc",       ".leaprc" },
+  { COORDSDATA,   "coords",       ".coords" },
   { UNKNOWN_DATA, 0,        0        }
 };
 
diff --git a/src/DataFile.h b/src/DataFile.h
index 814f057108..c5ce78126b 100644
--- a/src/DataFile.h
+++ b/src/DataFile.h
@@ -19,7 +19,7 @@ class DataFile {
       VECTRAJ, XVG, CCP4, CHARMMREPD, CHARMMFASTREP,
       CHARMMOUT, CPOUT, CHARMMRTFPRM, CMATRIX_BINARY, CMATRIX_NETCDF, PEAKS,
       NETCDFDATA, AMBERENE, NUMPY, AMBERPREP, AMBERLIB, AMBERFF, AMBERFRCMOD,
-      AMBERLEAPRC,
+      AMBERLEAPRC, COORDSDATA,
       UNKNOWN_DATA 
     };
     DataFile();
diff --git a/src/DataIO_Coords.cpp b/src/DataIO_Coords.cpp
index 3098c286c1..c8afdb43e5 100644
--- a/src/DataIO_Coords.cpp
+++ b/src/DataIO_Coords.cpp
@@ -2,9 +2,12 @@
 #include "CpptrajStdio.h"
 #include "ParmFile.h"
 #include "TrajectoryFile.h"
+#include "Trajin_Single.h"
 
 /// CONSTRUCTOR
-DataIO_Coords::DataIO_Coords()
+DataIO_Coords::DataIO_Coords() :
+  is_parm_fmt_(false),
+  is_traj_fmt_(false)
 {
 
 }
@@ -15,8 +18,9 @@ bool DataIO_Coords::ID_DataFormat(CpptrajFile& infile)
   // Needs to be either a topology format or a coords format
   ParmFile::ParmFormatType parm_format = ParmFile::DetectFormat(infile.Filename());
   TrajectoryFile::TrajFormatType traj_format = TrajectoryFile::DetectFormat(infile.Filename());
-  if (parm_format != ParmFile::UNKNOWN_PARM ||
-      traj_format != TrajectoryFile::UNKNOWN_TRAJ)
+  is_parm_fmt_ = (parm_format != ParmFile::UNKNOWN_PARM);
+  is_traj_fmt_ = (traj_format != TrajectoryFile::UNKNOWN_TRAJ);
+  if (is_parm_fmt_ || is_traj_fmt_)
     return true;
   return false;
 }
@@ -43,10 +47,15 @@ static inline bool can_append(DataSet::DataType typeIn) {
 // DataIO_Coords::ReadData()
 int DataIO_Coords::ReadData(FileName const& fname, DataSetList& dsl, std::string const& dsname)
 {
+  DataSet::DataType setType = DataSet::COORDS; // FIXME make user option
+
   DataSet* dset = 0;
   if (!dsname.empty()) {
-    // Is this set already present?
+    // Is this set already present? TODO search without warning
     dset = dsl.GetDataSet( dsname );
+    //if (dset == 0) {
+    //  dset = dsl.GetDataSet(fname.Base());
+    //}
     if (dset != 0) {
       if (!can_append(dset->Type())) {
         mprinterr("Error: Cannot append coordinates to existing set '%s'\n", dset->legend());
@@ -56,6 +65,60 @@ int DataIO_Coords::ReadData(FileName const& fname, DataSetList& dsl, std::string
     }
   }
 
+  // Topology read/setup
+  Topology topIn;
+  Topology* topPtr = 0;
+  if (dset == 0) {
+    if (!is_parm_fmt_) {
+      mprinterr("Error: '%s' does not contain any topology information.\n", fname.full());
+      return 1;
+    }
+    // No data set yet; read topology info
+    ParmFile pfile;
+    ArgList topargs;
+    if (pfile.ReadTopology( topIn, fname, topargs, debug_ )) {
+      mprinterr("Error: Could not read topology information from '%s'\n", fname.full());
+      return 1;
+    }
+    topPtr = &topIn;
+  } else {
+    topPtr = ((DataSet_Coords*)dset)->TopPtr();
+  }
+
+  // Trajectory setup
+  Trajin_Single trajin;
+  if (is_traj_fmt_) {
+    trajin.SetDebug( debug_ );
+    ArgList trajargs;
+    if (trajin.SetupTrajRead( fname, trajargs, topPtr )) {
+      mprinterr("Error: Could not set up trajectory info for '%s'\n", fname.full());
+      return 1;
+    }
+  } 
+
+  // If no data set yet, set it up
+  if (dset == 0) {
+    MetaData md( fname, dsname, -1 );
+    dset = dsl.AddSet(setType, md);
+    if (dset == 0) return 1;
+    DataSet_Coords* coords = static_cast<DataSet_Coords*>( dset );
+    if (coords->CoordsSetup( *topPtr, trajin.TrajCoordInfo() )) { // FIXME is this ok for no traj info?
+      mprinterr("Error: Could not set up COORDS set %s\n", coords->legend());
+      return 1;
+    }
+  }
+
+  // Trajectory read
+  if (is_traj_fmt_) {
+    Frame frameIn;
+    frameIn.SetupFrameV(topPtr->Atoms(), trajin.TrajCoordInfo());
+    trajin.BeginTraj();
+    trajin.Traj().PrintInfoLine();
+    while (trajin.GetNextFrame( frameIn ))
+      ((DataSet_Coords*)dset)->AddFrame( frameIn );
+    trajin.EndTraj();
+  }
+
   return 0;
 }
 
diff --git a/src/DataIO_Coords.h b/src/DataIO_Coords.h
index 9bf70ed3ae..83c8e778b7 100644
--- a/src/DataIO_Coords.h
+++ b/src/DataIO_Coords.h
@@ -13,5 +13,8 @@ class DataIO_Coords : public DataIO {
     int processWriteArgs(ArgList&);
     int WriteData(FileName const&, DataSetList const&);
     bool ID_DataFormat(CpptrajFile&);
+  private:
+    bool is_parm_fmt_; ///< Set to true if format contains topology info
+    bool is_traj_fmt_; ///< Set to true if format contains coordinates
 };
 #endif
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 17f979628f..8692794bae 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -207,7 +207,7 @@ CpptrajFile.o : CpptrajFile.cpp CpptrajFile.h CpptrajStdio.h FileIO.h FileIO_Bzi
 CpptrajState.o : CpptrajState.cpp Action.h ActionList.h ActionState.h Action_CreateCrd.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_Topology.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleNavigator.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 CpptrajStdio.o : CpptrajStdio.cpp Parallel.h
 CurveFit.o : CurveFit.cpp CurveFit.h
-DataFile.o : DataFile.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Cluster/Cframes.h Cluster/Cmatrix_NC.h CmapParmHolder.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataFile.h DataIO.h DataIO_AmberEne.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_CCP4.h DataIO_CharmmFastRep.h DataIO_CharmmOutput.h DataIO_CharmmRepLog.h DataIO_CharmmRtfPrm.h DataIO_Cmatrix_Binary.h DataIO_Cmatrix_NC.h DataIO_Cpout.h DataIO_Evecs.h DataIO_Gnuplot.h DataIO_Grace.h DataIO_LeapRC.h DataIO_Mdout.h DataIO_NetCDF.h DataIO_Numpy.h DataIO_OpenDx.h DataIO_Peaks.h DataIO_RemLog.h DataIO_Std.h DataIO_VecTraj.h DataIO_XVG.h DataIO_Xplor.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TypeNameHolder.h Unit.h Vec3.h
+DataFile.o : DataFile.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Cluster/Cframes.h Cluster/Cmatrix_NC.h CmapParmHolder.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataFile.h DataIO.h DataIO_AmberEne.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_CCP4.h DataIO_CharmmFastRep.h DataIO_CharmmOutput.h DataIO_CharmmRepLog.h DataIO_CharmmRtfPrm.h DataIO_Cmatrix_Binary.h DataIO_Cmatrix_NC.h DataIO_Coords.h DataIO_Cpout.h DataIO_Evecs.h DataIO_Gnuplot.h DataIO_Grace.h DataIO_LeapRC.h DataIO_Mdout.h DataIO_NetCDF.h DataIO_Numpy.h DataIO_OpenDx.h DataIO_Peaks.h DataIO_RemLog.h DataIO_Std.h DataIO_VecTraj.h DataIO_XVG.h DataIO_Xplor.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TypeNameHolder.h Unit.h Vec3.h
 DataFileList.o : DataFileList.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataFilter.o : DataFilter.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_integer.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO.o : DataIO.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
@@ -223,6 +223,7 @@ DataIO_CharmmRepLog.o : DataIO_CharmmRepLog.cpp ArgList.h AssociatedData.h Atom.
 DataIO_CharmmRtfPrm.o : DataIO_CharmmRtfPrm.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharmmParamFile.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmRtfPrm.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h DataSet_Topology.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Cmatrix_Binary.o : DataIO_Cmatrix_Binary.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/Cframes.h Cluster/Cmatrix_Binary.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Cmatrix_Binary.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Cmatrix_NC.o : DataIO_Cmatrix_NC.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/Cframes.h Cluster/Cmatrix_NC.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Cmatrix_NC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_Coords.o : DataIO_Coords.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Coords.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h Trajin_Single.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Cpout.o : DataIO_Cpout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Cpout.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h DataSet_PHREMD_Implicit.h DataSet_pH.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Evecs.o : DataIO_Evecs.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedFrame.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Evecs.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Modes.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Gnuplot.o : DataIO_Gnuplot.cpp ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Gnuplot.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
diff --git a/src/cpptrajfiles b/src/cpptrajfiles
index d054c9c5b9..a64fa4eef6 100644
--- a/src/cpptrajfiles
+++ b/src/cpptrajfiles
@@ -194,6 +194,7 @@ COMMON_SOURCES= \
         DataIO_CharmmRtfPrm.cpp \
         DataIO_Cmatrix_Binary.cpp \
         DataIO_Cmatrix_NC.cpp \
+        DataIO_Coords.cpp \
         DataIO_Cpout.cpp \
         DataIO_Evecs.cpp \
         DataIO_Gnuplot.cpp \

From 2b43c96779bcc4d285ff68c67f675fcd75c64a66 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 5 Jun 2024 15:03:16 -0400
Subject: [PATCH 0724/1492] Use DataIO_Coords for loadmol2. Ensure the ID
 function is called if it hasnt been

---
 src/DataIO_Coords.cpp | 13 +++++++++++++
 src/DataIO_LeapRC.cpp | 22 +++++++++++++++++++---
 src/DataIO_LeapRC.h   |  2 +-
 src/cpptrajdepend     |  2 +-
 4 files changed, 34 insertions(+), 5 deletions(-)

diff --git a/src/DataIO_Coords.cpp b/src/DataIO_Coords.cpp
index c8afdb43e5..be84db849a 100644
--- a/src/DataIO_Coords.cpp
+++ b/src/DataIO_Coords.cpp
@@ -48,6 +48,19 @@ static inline bool can_append(DataSet::DataType typeIn) {
 int DataIO_Coords::ReadData(FileName const& fname, DataSetList& dsl, std::string const& dsname)
 {
   DataSet::DataType setType = DataSet::COORDS; // FIXME make user option
+  if (!is_parm_fmt_ && !is_traj_fmt_) {
+    // Assume that ID_DataFormat() has not been called.
+    CpptrajFile tmpfile;
+    if (tmpfile.SetupWrite( fname, debug_ )) {
+      mprinterr("Error: Could not setup check for parm/coords info in '%s'.\n",
+                fname.full());
+      return 1;
+    }
+    if (!ID_DataFormat(tmpfile)) {
+      mprinterr("Error: '%s' does not have parm/coords info.\n", fname.full());
+      return 1;
+    }
+  }
 
   DataSet* dset = 0;
   if (!dsname.empty()) {
diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 0b17306844..05a80f78e5 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -6,6 +6,7 @@
 #include "DataIO_AmberFrcmod.h"
 #include "DataIO_AmberLib.h"
 #include "DataIO_AmberPrep.h"
+#include "DataIO_Coords.h"
 #include "DataSet_NameMap.h"
 #include "DataSet_Parameters.h"
 #include <cstdlib> //getenv
@@ -362,9 +363,24 @@ const
 }
 
 /** Load mol2 as a COORDS set */
-int DataIO_LeapRC::LoadMol2(ArgList& argIn, DataSetList& dsl) const {
-  mprintf("DEBUG: LoadMol2\n");
-  argIn.PrintList();
+int DataIO_LeapRC::LoadMol2(ArgList const& argIn, DataSetList& dsl) const {
+  ArgList args( argIn.ArgLineStr(), " =" );
+  //mprintf("DEBUG: LoadMol2\n");
+  //args.PrintList();
+  // Should be at least 3 args: NAME loadmol2 FILE
+  if (args.Nargs() < 3) {
+    mprinterr("Error: Expected at least <NAME> = loadmol2 <FILE>, got: %s\n", argIn.ArgLine());
+    return 1;
+  }
+  DataIO_Coords coordsIn;
+  coordsIn.SetDebug( debug_ );
+  if (coordsIn.ReadData( args[2], dsl, args[0] )) {
+    mprinterr("Error: Could not load structure from '%s' into '%s'\n",
+              args[2].c_str(), args[0].c_str());
+    return 1;
+  }
+  mprintf("\tLoaded file '%s' into '%s'\n",
+          args[2].c_str(), args[0].c_str());
   return 0;
 }
 
diff --git a/src/DataIO_LeapRC.h b/src/DataIO_LeapRC.h
index afec45ede5..07159480ce 100644
--- a/src/DataIO_LeapRC.h
+++ b/src/DataIO_LeapRC.h
@@ -34,7 +34,7 @@ class DataIO_LeapRC : public DataIO {
     int AddAtomTypes(NHarrayType&, BufferedLine&) const;
     int AddPdbResMap(PdbResMapArray&, BufferedLine&) const;
     int AddPdbAtomMap(std::string const&, DataSetList&, BufferedLine&) const;
-    int LoadMol2(ArgList&, DataSetList&) const;
+    int LoadMol2(ArgList const&, DataSetList&) const;
     /// Used to check if a parm/lib file was already loaded.
     static inline bool check_already_loaded(Sarray const&, std::string const&);
     /// \return either file or Amberhome/dir/file
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 8692794bae..b8f7d66cc6 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -228,7 +228,7 @@ DataIO_Cpout.o : DataIO_Cpout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h A
 DataIO_Evecs.o : DataIO_Evecs.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedFrame.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Evecs.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Modes.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Gnuplot.o : DataIO_Gnuplot.cpp ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Gnuplot.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Grace.o : DataIO_Grace.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Grace.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_string.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_LeapRC.o : DataIO_LeapRC.cpp ArgList.h AssociatedData.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_LeapRC.o : DataIO_LeapRC.cpp ArgList.h AssociatedData.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_Coords.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Mdout.o : DataIO_Mdout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Mdout.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_NetCDF.o : DataIO_NetCDF.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/Cframes.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_NetCDF.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_Mesh.h DataSet_Modes.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_Vector.h DataSet_Vector_Scalar.h DataSet_string.h DataSet_unsignedInt.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h Version.h
 DataIO_Numpy.o : DataIO_Numpy.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Numpy.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h libnpy/npy.hpp

From 4034ee52d3e77b87f1f33346ffdd9e35fab7a6bc Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 6 Jun 2024 11:52:50 -0400
Subject: [PATCH 0725/1492] Add a function for stand-alone execution

---
 src/Exec_Build.cpp | 14 ++++++++++----
 src/Exec_Build.h   |  2 ++
 2 files changed, 12 insertions(+), 4 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index ab61596087..17e53b776e 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -661,7 +661,13 @@ void Exec_Build::Help() const
 // Exec_Build::Execute()
 Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
 {
-  debug_ = State.Debug();
+  return BuildStructure(State.DSL(), State.Debug(), argIn);
+}
+
+/** Standalone execute. For DataIO_LeapRC. */
+Exec::RetType Exec_Build::BuildStructure(DataSetList& DSL, int debugIn, ArgList& argIn)
+{
+  debug_ = debugIn;
   std::string title = argIn.GetStringKey("title");
 
   // Get input coords
@@ -670,7 +676,7 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
     mprinterr("Error: Must specify input COORDS set with 'crdset'\n");
     return CpptrajState::ERR;
   }
-  DataSet* inCrdPtr = State.DSL().FindSetOfGroup( crdset, DataSet::COORDINATES );
+  DataSet* inCrdPtr = DSL.FindSetOfGroup( crdset, DataSet::COORDINATES );
   if (inCrdPtr == 0) {
     mprinterr("Error: No COORDS set found matching %s\n", crdset.c_str());
     return CpptrajState::ERR;
@@ -731,7 +737,7 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
     mprinterr("Error: Must specify output COORDS set with 'name'\n");
     return CpptrajState::ERR;
   }
-  DataSet* outCrdPtr = State.DSL().AddSet( DataSet::COORDS, outset );
+  DataSet* outCrdPtr = DSL.AddSet( DataSet::COORDS, outset );
   if (outCrdPtr == 0) {
     mprinterr("Error: Could not allocate output COORDS set with name '%s'\n", outset.c_str());
     return CpptrajState::ERR;
@@ -753,7 +759,7 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
 
   // Get templates and parameter sets.
   Cpptraj::Structure::Creator creator( debug_ );
-  if (creator.InitCreator(argIn, State.DSL(), debug_)) {
+  if (creator.InitCreator(argIn, DSL, debug_)) {
     return CpptrajState::ERR;
   }
   if (!creator.HasTemplates()) {
diff --git a/src/Exec_Build.h b/src/Exec_Build.h
index 53d5d7829c..d406c3398e 100644
--- a/src/Exec_Build.h
+++ b/src/Exec_Build.h
@@ -15,6 +15,8 @@ class Exec_Build : public Exec {
     void Help() const;
     DispatchObject* Alloc() const { return (DispatchObject*)new Exec_Build(); }
     RetType Execute(CpptrajState&, ArgList&);
+    /// Stand-alone execution
+    RetType BuildStructure(DataSetList&, int, ArgList&);
   private:
     typedef std::vector<int> Iarray;
     // Keep track of which residues are connected to each other

From ab05e210536498587b8a33fb947ff4a883187c97 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 6 Jun 2024 11:57:33 -0400
Subject: [PATCH 0726/1492] Pass in input coords to standalone build

---
 src/Exec_Build.cpp | 28 ++++++++++++++++++----------
 src/Exec_Build.h   |  2 +-
 2 files changed, 19 insertions(+), 11 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 17e53b776e..0f9a42e32f 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -661,26 +661,34 @@ void Exec_Build::Help() const
 // Exec_Build::Execute()
 Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
 {
-  return BuildStructure(State.DSL(), State.Debug(), argIn);
-}
-
-/** Standalone execute. For DataIO_LeapRC. */
-Exec::RetType Exec_Build::BuildStructure(DataSetList& DSL, int debugIn, ArgList& argIn)
-{
-  debug_ = debugIn;
-  std::string title = argIn.GetStringKey("title");
-
   // Get input coords
   std::string crdset = argIn.GetStringKey("crdset");
   if (crdset.empty()) {
     mprinterr("Error: Must specify input COORDS set with 'crdset'\n");
     return CpptrajState::ERR;
   }
-  DataSet* inCrdPtr = DSL.FindSetOfGroup( crdset, DataSet::COORDINATES );
+  DataSet* inCrdPtr = State.DSL().FindSetOfGroup( crdset, DataSet::COORDINATES );
   if (inCrdPtr == 0) {
     mprinterr("Error: No COORDS set found matching %s\n", crdset.c_str());
     return CpptrajState::ERR;
   }
+  return BuildStructure(inCrdPtr, State.DSL(), State.Debug(), argIn);
+}
+
+/** Standalone execute. For DataIO_LeapRC. */
+Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, int debugIn, ArgList& argIn)
+{
+  if (inCrdPtr == 0) {
+    mprinterr("Internal Error: Exec_Build::BuildStructure(): Null input coordinates.\n");
+    return CpptrajState::ERR;
+  }
+  if (inCrdPtr->Group() != DataSet::COORDINATES) {
+    mprinterr("Error: Set '%s' is not coordinates, cannot use for building.\n", inCrdPtr->legend());
+    return CpptrajState::ERR;
+  }
+  debug_ = debugIn;
+  std::string title = argIn.GetStringKey("title");
+
   // TODO make it so this can be const (cant bc GetFrame)
   DataSet_Coords& coords = static_cast<DataSet_Coords&>( *((DataSet_Coords*)inCrdPtr) );
   // Get frame from input coords
diff --git a/src/Exec_Build.h b/src/Exec_Build.h
index d406c3398e..2e12fe2d43 100644
--- a/src/Exec_Build.h
+++ b/src/Exec_Build.h
@@ -16,7 +16,7 @@ class Exec_Build : public Exec {
     DispatchObject* Alloc() const { return (DispatchObject*)new Exec_Build(); }
     RetType Execute(CpptrajState&, ArgList&);
     /// Stand-alone execution
-    RetType BuildStructure(DataSetList&, int, ArgList&);
+    RetType BuildStructure(DataSet*, DataSetList&, int, ArgList&);
   private:
     typedef std::vector<int> Iarray;
     // Keep track of which residues are connected to each other

From a8f1fa6ec34af703b36e5b3da0dd528aaf49df23 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 6 Jun 2024 12:21:20 -0400
Subject: [PATCH 0727/1492] Start loadpdb and prepare for adding source command

---
 src/DataIO_LeapRC.cpp | 32 +++++++++++++++++++++++++++++++-
 src/DataIO_LeapRC.h   |  2 ++
 2 files changed, 33 insertions(+), 1 deletion(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 05a80f78e5..a9bf28e69c 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -384,6 +384,27 @@ int DataIO_LeapRC::LoadMol2(ArgList const& argIn, DataSetList& dsl) const {
   return 0;
 }
 
+/** Load PDB and build it. */
+int DataIO_LeapRC::LoadPDB(ArgList const& argIn, DataSetList& dsl) const {
+  ArgList args( argIn.ArgLineStr(), " =" );
+  // Should be at least 3 args: NAME loadpdb FILE
+  if (args.Nargs() < 3) {
+    mprinterr("Error: Expected at least <NAME> = loadpdb <FILE>, got: %s\n", argIn.ArgLine());
+    return 1;
+  }
+  DataIO_Coords coordsIn;
+  coordsIn.SetDebug( debug_ );
+  DataSetList tmpdsl;
+  if (coordsIn.ReadData( args[2], tmpdsl, args[0] )) {
+    mprinterr("Error: Could not load structure from '%s' into '%s'\n",
+              args[2].c_str(), args[0].c_str());
+    return 1;
+  }
+  mprintf("\tLoaded file '%s' into '%s'\n",
+          args[2].c_str(), args[0].c_str());
+  return 0;
+}
+
 /// Move sets from paramDSL to dsl
 static inline int addSetsToList(DataSetList& dsl, DataSetList& paramDSL)
 {
@@ -400,7 +421,7 @@ static inline int addSetsToList(DataSetList& dsl, DataSetList& paramDSL)
   return 0;
 }
 
-// DataIO_LeapRC::ReadData()
+/** Read (source) a leaprc (input) file. */
 int DataIO_LeapRC::ReadData(FileName const& fname, DataSetList& dsl, std::string const& dsname)
 {
   // First, need to determine where the Amber FF files are
@@ -419,6 +440,13 @@ int DataIO_LeapRC::ReadData(FileName const& fname, DataSetList& dsl, std::string
   }
   if (!amberhome_.empty())
     mprintf("\tForce field files located in '%s'\n", amberhome_.c_str());
+
+  return Source(fname, dsl, dsname);
+}
+
+/** Execute leap source command */
+int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string const& dsname)
+{
   BufferedLine infile;
   if (infile.OpenFileRead(fname)) {
     mprinterr("Error: Could not open leaprc file '%s'\n", fname.full());
@@ -455,6 +483,8 @@ int DataIO_LeapRC::ReadData(FileName const& fname, DataSetList& dsl, std::string
         err = AddPdbAtomMap(dsname, dsl, infile);
       else if (line.Contains("loadmol2") || line.Contains("loadMol2"))
         err = LoadMol2(line, dsl);
+      else if (line.Contains("loadpdb") || line.Contains("loadPdb"))
+        err = LoadPDB(line, dsl);
       else {
         // Does this line contain an equals sign?
         bool has_equals = false;
diff --git a/src/DataIO_LeapRC.h b/src/DataIO_LeapRC.h
index 07159480ce..417a5a0bed 100644
--- a/src/DataIO_LeapRC.h
+++ b/src/DataIO_LeapRC.h
@@ -35,6 +35,8 @@ class DataIO_LeapRC : public DataIO {
     int AddPdbResMap(PdbResMapArray&, BufferedLine&) const;
     int AddPdbAtomMap(std::string const&, DataSetList&, BufferedLine&) const;
     int LoadMol2(ArgList const&, DataSetList&) const;
+    int LoadPDB(ArgList const&, DataSetList&) const;
+    int Source(FileName const&, DataSetList&, std::string const&);
     /// Used to check if a parm/lib file was already loaded.
     static inline bool check_already_loaded(Sarray const&, std::string const&);
     /// \return either file or Amberhome/dir/file

From 1842c16b5f3e1a336d95ca53b3eea701b205c714 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 6 Jun 2024 15:15:37 -0400
Subject: [PATCH 0728/1492] Change it so that parameter load uses the master
 data set list. Update atom hybridizations as soon as parameter data sets are
 loaded.

---
 src/DataIO.cpp             | 10 ++++++
 src/DataIO.h               | 15 ++++++++
 src/DataIO_AmberFF.cpp     |  2 ++
 src/DataIO_AmberFrcmod.cpp |  2 ++
 src/DataIO_LeapRC.cpp      | 71 +++++++++++++++++++++++++-------------
 src/DataIO_LeapRC.h        |  3 +-
 6 files changed, 78 insertions(+), 25 deletions(-)

diff --git a/src/DataIO.cpp b/src/DataIO.cpp
index 91eda95dd8..109908bf01 100644
--- a/src/DataIO.cpp
+++ b/src/DataIO.cpp
@@ -120,3 +120,13 @@ DataSet* DataIO::DetermineMatrixType(std::vector<double> const& matrixArray, int
   }
   return ds;
 }
+
+/** Clear any sets added by AddedByMe() */
+void DataIO::ClearAddedByMe() {
+  mySets_.clear();
+}
+
+/** Note a set added by this DataIO */
+void DataIO::AddedByMe(DataSet* ds) {
+  mySets_.push_back( ds );
+} 
diff --git a/src/DataIO.h b/src/DataIO.h
index ada7236eb3..75e2feb8aa 100644
--- a/src/DataIO.h
+++ b/src/DataIO.h
@@ -31,7 +31,21 @@ class DataIO : public BaseIOtype {
     int XcolWidth()               const { return xcol_width_; }
     /// \return Current x column precision
     int XcolPrec()                const { return xcol_prec_;  }
+
+    typedef std::vector<DataSet*>::const_iterator set_iterator;
+    /// \return iterator to beginning of sets added by last ReadData() call
+    set_iterator added_begin() const { return mySets_.begin(); }
+    /// \return iterator to end of sets added by last ReadData() call
+    set_iterator added_end()   const { return mySets_.end(); }
+    /// \return the last set added by last ReadData() call
+    DataSet* added_back()      const { return mySets_.back(); }
+    /// \return Number of sets added by last ReadData() call
+    unsigned int Nadded()      const { return mySets_.size(); }
   protected:
+    /// Note a set that has been added to a DataSetList by this DataIO
+    void AddedByMe(DataSet*);
+    /// Clear list of sets added by this DataIO
+    void ClearAddedByMe();
     /// Indicate this DataIO is valid for given DataSet type
     void SetValid(DataSet::DataType t) { valid_.push_back( t ); }
     /// Check that all sets in given list have given dimension.
@@ -48,6 +62,7 @@ class DataIO : public BaseIOtype {
     int debug_;
   private:
     std::vector<DataSet::DataType> valid_; ///< Data sets for which DataIO is valid writer.
+    std::vector<DataSet*> mySets_; ///< Can be used by child class to note sets that have been added
     TextFormat::FmtType xcol_fmt_; ///< X column format type
     int xcol_width_;               ///< X column width
     int xcol_prec_;                ///< X column precision
diff --git a/src/DataIO_AmberFF.cpp b/src/DataIO_AmberFF.cpp
index 94378f3d30..65a8c55aa8 100644
--- a/src/DataIO_AmberFF.cpp
+++ b/src/DataIO_AmberFF.cpp
@@ -36,6 +36,7 @@ int DataIO_AmberFF::processReadArgs(ArgList& argIn)
 // DataIO_AmberFF::ReadData()
 int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::string const& dsname)
 {
+  ClearAddedByMe();
   // Allocate data set
   MetaData md( dsname );
   DataSet* ds = dsl.CheckForSet( md );
@@ -49,6 +50,7 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
     ds = dsl.AddSet( DataSet::PARAMETERS, md );
     if (ds == 0) return 1;
   }
+  AddedByMe( ds );
   DataSet_Parameters& prm = static_cast<DataSet_Parameters&>( *ds ); 
 
   AmberParamFile infile;
diff --git a/src/DataIO_AmberFrcmod.cpp b/src/DataIO_AmberFrcmod.cpp
index b1d2db5f2c..82810ac0b7 100644
--- a/src/DataIO_AmberFrcmod.cpp
+++ b/src/DataIO_AmberFrcmod.cpp
@@ -32,6 +32,7 @@ int DataIO_AmberFrcmod::processReadArgs(ArgList& argIn)
 // DataIO_AmberFrcmod::ReadData()
 int DataIO_AmberFrcmod::ReadData(FileName const& fname, DataSetList& dsl, std::string const& dsname)
 {
+  ClearAddedByMe();
   // Allocate data set
   MetaData md( dsname );
   DataSet* ds = dsl.CheckForSet( md );
@@ -45,6 +46,7 @@ int DataIO_AmberFrcmod::ReadData(FileName const& fname, DataSetList& dsl, std::s
     ds = dsl.AddSet( DataSet::PARAMETERS, md );
     if (ds == 0) return 1;
   }
+  AddedByMe( ds );
   DataSet_Parameters& prm = static_cast<DataSet_Parameters&>( *ds );
 
   AmberParamFile infile;
diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index a9bf28e69c..9f007495f6 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -86,7 +86,12 @@ const
 }
 
 /** LEaP loadAmberParams command. */
-int DataIO_LeapRC::LoadAmberParams(std::string const& filename, DataSetList& dsl, std::string const& dsname) const {
+int DataIO_LeapRC::LoadAmberParams(std::string const& filename, DataSetList& dsl,
+                                   std::string const& dsname,
+                                   NHarrayType const& atomHybridizations)
+const
+{
+  DataSet* paramSet = 0;
   // TODO detect this better
   ArgList fargs( filename, "." );
   if (fargs.hasKey("frcmod")) {
@@ -97,6 +102,11 @@ int DataIO_LeapRC::LoadAmberParams(std::string const& filename, DataSetList& dsl
       mprinterr("Error: Could not load force field modifications from '%s'\n", filename.c_str());
       return 1;
     }
+    if (infile.Nadded() != 1) {
+      mprinterr("Internal Error: DataIO_LeapRC::LoadAmberParams(): Expected only 1 parameter set added, got %u\n", infile.Nadded());
+      return 1;
+    }
+    paramSet = infile.added_back();
   } else {
     if (check_already_loaded(paramFiles_, filename)) {
       mprintf("Warning: Force field %s has already been loaded, skipping.\n", filename.c_str());
@@ -108,8 +118,37 @@ int DataIO_LeapRC::LoadAmberParams(std::string const& filename, DataSetList& dsl
         return 1;
       }
       paramFiles_.push_back( filename );
+      if (infile.Nadded() != 1) {
+        mprinterr("Internal Error: DataIO_LeapRC::LoadAmberParams(): Expected only 1 parameter set added, got %u\n", infile.Nadded());
+        return 1;
+      }
+      paramSet = infile.added_back();
     }
   }
+  if (paramSet == 0) {
+    mprinterr("Internal Error: DataIO_LeapRC::LoadAmberParams(): Parameter set is null.\n");
+    return 1;
+  }
+  // Update hybridizations for parameter atom types
+  //for (DataIO::set_iterator ds = paramDSL.begin(); ds != paramDSL.end(); ++ds)
+  //{
+    if ( paramSet->Type() == DataSet::PARAMETERS ) {
+      DataSet_Parameters& param = static_cast<DataSet_Parameters&>( *paramSet );
+      mprintf("\tUpdating atom hybridizations in set %s\n", param.legend());
+      for (ParmHolder<AtomType>::iterator it = param.AT().begin();
+                                          it != param.AT().end(); ++it)
+      {
+        NHarrayType::const_iterator ah = atomHybridizations.find( it->first[0] );
+        if (ah == atomHybridizations.end())
+          mprintf("Warning: No hybridization set for atom type '%s'\n", *(it->first[0]));
+        else
+          it->second.SetHybridization( ah->second );
+      }
+    } else {
+      mprinterr("Internal Error: DataIO_LeapRC::LoadAmberParams(): Set %s is not parameter set.\n",
+                paramSet->legend());
+    }
+  //}
   return 0;
 }
 
@@ -452,9 +491,9 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
     mprinterr("Error: Could not open leaprc file '%s'\n", fname.full());
     return 1;
   }
-  DataSetList paramDSL;
+  //DataSetList paramDSL;
   DataSetList unitDSL;
-  NHarrayType atomHybridizations;
+  //NHarrayType atomHybridizations;
   PdbResMapArray pdbResMap;
   int err = 0;
   const char* ptr = infile.Line();
@@ -464,9 +503,9 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
     if (ptr[0] != '\0' && ptr[0] != '#') {
       ArgList line( ptr, " \t" );
       if (line.Contains("loadAmberParams"))
-        err = LoadAmberParams( line.GetStringKey("loadAmberParams"), paramDSL, dsname );
+        err = LoadAmberParams( line.GetStringKey("loadAmberParams"), dsl, dsname, atomHybridizations_ );
       else if (line.Contains("loadamberparams"))
-        err = LoadAmberParams( line.GetStringKey("loadamberparams"), paramDSL, dsname );
+        err = LoadAmberParams( line.GetStringKey("loadamberparams"), dsl, dsname, atomHybridizations_ );
       else if (line.Contains("loadOff"))
         err = LoadOFF( line.GetStringKey("loadOff"), unitDSL, dsname );
       else if (line.Contains("loadoff"))
@@ -476,7 +515,7 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
       else if (line.Contains("loadamberprep"))
         err = LoadAmberPrep( line.GetStringKey("loadamberprep"), unitDSL, dsname );
       else if (line.Contains("addAtomTypes") || line.Contains("addatomtypes"))
-        err = AddAtomTypes(atomHybridizations, infile);
+        err = AddAtomTypes(atomHybridizations_, infile);
       else if (line.Contains("addPdbResMap") || line.Contains("addpdbresmap"))
         err = AddPdbResMap(pdbResMap, infile);
       else if (line.Contains("addPdbAtomMap") || line.Contains("addpdbatommap"))
@@ -534,23 +573,7 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
   }
   infile.CloseFile();
 
-  // Update hybridizations for parameter atom types
-  for (DataSetList::const_iterator ds = paramDSL.begin(); ds != paramDSL.end(); ++ds)
-  {
-    if ( (*ds)->Type() == DataSet::PARAMETERS ) {
-      DataSet_Parameters& param = static_cast<DataSet_Parameters&>( *(*ds) );
-      mprintf("\tUpdating atom hybridizations in set %s\n", param.legend());
-      for (ParmHolder<AtomType>::iterator it = param.AT().begin();
-                                          it != param.AT().end(); ++it)
-      {
-        NHarrayType::const_iterator ah = atomHybridizations.find( it->first[0] );
-        if (ah == atomHybridizations.end())
-          mprintf("Warning: No hybridization set for atom type '%s'\n", *(it->first[0]));
-        else
-          it->second.SetHybridization( ah->second );
-      }
-    }
-  }
+
   // Update units with pdb residue map info
   //for (DataSetList::const_iterator ds = unitDSL.begin(); ds != paramDSL.end(); ++ds)
   //{
@@ -575,7 +598,7 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
   }
 
   // Add data sets to the main data set list
-  if (addSetsToList(dsl, paramDSL)) return err+1;
+  //if (addSetsToList(dsl, paramDSL)) return err+1;
 
   if (addSetsToList(dsl, unitDSL)) return err+1;
 
diff --git a/src/DataIO_LeapRC.h b/src/DataIO_LeapRC.h
index 417a5a0bed..70066ac89c 100644
--- a/src/DataIO_LeapRC.h
+++ b/src/DataIO_LeapRC.h
@@ -28,7 +28,7 @@ class DataIO_LeapRC : public DataIO {
     };
     typedef std::vector<PdbResMapType> PdbResMapArray;
 
-    int LoadAmberParams(std::string const&, DataSetList&, std::string const&) const;
+    int LoadAmberParams(std::string const&, DataSetList&, std::string const&, NHarrayType const&) const;
     int LoadOFF(std::string const&, DataSetList&, std::string const&) const;
     int LoadAmberPrep(std::string const&, DataSetList&, std::string const&) const;
     int AddAtomTypes(NHarrayType&, BufferedLine&) const;
@@ -43,6 +43,7 @@ class DataIO_LeapRC : public DataIO {
     std::string find_path(std::string const&, std::string const&) const;
 
     std::string amberhome_;
+    NHarrayType atomHybridizations_; ///< Store hybridizations for atom types
     static Sarray paramFiles_; ///< Track amber FF param files loaded from leaprc files
     static Sarray libFiles_;   ///< Track amber library/prep files loaded from leaprc files
 };

From 072ff253336587f3ca397358beb06155fd5dac73 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 7 Jun 2024 14:42:01 -0400
Subject: [PATCH 0729/1492] Add sets for lib and prep

---
 src/DataIO_AmberLib.cpp  | 2 ++
 src/DataIO_AmberPrep.cpp | 3 ++-
 src/DataIO_AmberPrep.h   | 2 +-
 3 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/src/DataIO_AmberLib.cpp b/src/DataIO_AmberLib.cpp
index bf0dbfe43a..dbd4674cd6 100644
--- a/src/DataIO_AmberLib.cpp
+++ b/src/DataIO_AmberLib.cpp
@@ -37,6 +37,7 @@ int DataIO_AmberLib::processReadArgs(ArgList& argIn)
 // DataIO_AmberLib::ReadData()
 int DataIO_AmberLib::ReadData(FileName const& fname, DataSetList& dsl, std::string const& dsname)
 {
+  ClearAddedByMe();
   BufferedLine infile;
   if (infile.OpenFileRead( fname )) {
     mprinterr("Error: Could not open Amber lib file '%s' for reading.\n", fname.full());
@@ -110,6 +111,7 @@ int DataIO_AmberLib::ReadData(FileName const& fname, DataSetList& dsl, std::stri
       mprinterr("Error: Reading unit '%s'\n", currentName.c_str());
       return 1;
     }
+    AddedByMe( ds );
     units_read++;
   }
   mprintf("\tRead %zu units from Amber OFF file %s.\n", UnitNames.size(), fname.base());
diff --git a/src/DataIO_AmberPrep.cpp b/src/DataIO_AmberPrep.cpp
index 9062d96175..986ee64759 100644
--- a/src/DataIO_AmberPrep.cpp
+++ b/src/DataIO_AmberPrep.cpp
@@ -80,7 +80,6 @@ int DataIO_AmberPrep::readIMPROPER(BufferedLine& infile) const {
   * \return 1 if error, -1 if STOP/EOF, 0 if more residues to be read.
   */
 int DataIO_AmberPrep::readAmberPrep(BufferedLine& infile, DataSetList& dsl, std::string const& dsname)
-const
 {
   // 3 - Title
   // Descriptive header for the residue
@@ -360,6 +359,7 @@ const
     return 1;
   }
   CRD->SetCRD(0, frm);
+  AddedByMe( ds );
 
   return 0;
 }
@@ -367,6 +367,7 @@ const
 // DataIO_AmberPrep::ReadData()
 int DataIO_AmberPrep::ReadData(FileName const& fname, DataSetList& dsl, std::string const& dsname)
 {
+  ClearAddedByMe();
   BufferedLine infile;
 
   if (infile.OpenFileRead(fname)) {
diff --git a/src/DataIO_AmberPrep.h b/src/DataIO_AmberPrep.h
index 2f86f4adab..e4d0e4f000 100644
--- a/src/DataIO_AmberPrep.h
+++ b/src/DataIO_AmberPrep.h
@@ -23,7 +23,7 @@ class DataIO_AmberPrep : public DataIO {
     int readCHARGE(BufferedLine&) const;
     int readLOOP(BufferedLine&, AtPairArray&) const;
     int readIMPROPER(BufferedLine&) const;
-    int readAmberPrep(BufferedLine&, DataSetList&, std::string const&) const;
+    int readAmberPrep(BufferedLine&, DataSetList&, std::string const&);
 
     bool removeDummyAtoms_; ///< Remove dummy atoms if true
 };

From 07a1d316a448c008b561e507db4f9d3cc75c654e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 7 Jun 2024 14:44:57 -0400
Subject: [PATCH 0730/1492] Ensure atom hybridizations are cleared on a new
 read

---
 src/DataIO_LeapRC.cpp | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 9f007495f6..3579dd3fac 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -463,6 +463,7 @@ static inline int addSetsToList(DataSetList& dsl, DataSetList& paramDSL)
 /** Read (source) a leaprc (input) file. */
 int DataIO_LeapRC::ReadData(FileName const& fname, DataSetList& dsl, std::string const& dsname)
 {
+  atomHybridizations_.clear();
   // First, need to determine where the Amber FF files are
   const char* env = getenv("AMBERHOME");
   if (env != 0)

From 8d39efcbec7ada91a41e5e3d23a8225c467aa47b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 7 Jun 2024 15:00:03 -0400
Subject: [PATCH 0731/1492] Save unit sets as they are loaded. Start looking
 for them in AddPdbResMap

---
 src/DataIO_LeapRC.cpp | 46 +++++++++++++++++++++++++++++++++++++------
 src/DataIO_LeapRC.h   |  8 ++++++--
 2 files changed, 46 insertions(+), 8 deletions(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 3579dd3fac..0e21aeff9d 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -153,7 +153,7 @@ const
 }
 
 /** LEaP loadOff command. */
-int DataIO_LeapRC::LoadOFF(std::string const& filename, DataSetList& dsl, std::string const& dsname) const {
+int DataIO_LeapRC::LoadOFF(std::string const& filename, DataSetList& dsl, std::string const& dsname, DSarray& units) const {
   if (check_already_loaded(libFiles_, filename)) {
     mprintf("Warning: Library %s has already been loaded, skipping.\n", filename.c_str());
   } else {
@@ -166,13 +166,19 @@ int DataIO_LeapRC::LoadOFF(std::string const& filename, DataSetList& dsl, std::s
       mprinterr("Error: Could not load library file '%s'\n", filename.c_str());
       return 1;
     }
+    if (infile.Nadded() < 1) {
+      mprinterr("Internal Error: DataIO_LeapRC::LoadOFF(): No unit sets added.\n");
+      return 1;
+    }
+    for (DataIO::set_iterator it = infile.added_begin(); it != infile.added_end(); ++it)
+      units.push_back( *it );
     libFiles_.push_back( filename );
   }
   return 0;
 }
 
 /** LEaP loadAmberPrep command. */
-int DataIO_LeapRC::LoadAmberPrep(std::string const& filename, DataSetList& dsl, std::string const& dsname) const {
+int DataIO_LeapRC::LoadAmberPrep(std::string const& filename, DataSetList& dsl, std::string const& dsname, DSarray& units) const {
   if (check_already_loaded(libFiles_, filename)) {
     mprintf("Warning: Prep file %s has already been loaded, skipping.\n", filename.c_str());
   } else {
@@ -182,6 +188,12 @@ int DataIO_LeapRC::LoadAmberPrep(std::string const& filename, DataSetList& dsl,
       mprinterr("Error: Could not load prep file '%s'\n", filename.c_str());
       return 1;
     }
+    if (infile.Nadded() < 1) {
+      mprinterr("Internal Error: DataIO_LeapRC::LoadAmberPrep(): No unit sets added.\n");
+      return 1;
+    }
+    for (DataIO::set_iterator it = infile.added_begin(); it != infile.added_end(); ++it)
+      units.push_back( *it );
     libFiles_.push_back( filename );
   }
   return 0;
@@ -269,6 +281,25 @@ const
   return 0;
 }
 
+/** Find unit among loaded units. */
+DataSet* DataIO_LeapRC::findUnit(std::string const& unitName) const {
+  for (DSarray::const_iterator it = units_.begin(); it != units_.end(); ++it)
+  {
+    if ( (*it)->Meta().Aspect() == unitName ) {
+      mprintf("DEBUG: findUnit: Aspect match: %s %s\n", unitName.c_str(), (*it)->legend());
+      return *it;
+    }
+  }
+  for (DSarray::const_iterator it = units_.begin(); it != units_.end(); ++it)
+  {
+    if ( (*it)->Meta().Name() == unitName ) { 
+      mprintf("DEBUG: findUnit: Name match: %s %s\n", unitName.c_str(), (*it)->legend());
+      return *it;
+    }
+  }
+  return 0;
+}
+
 /** LEaP addPdbResMap command. */
 int DataIO_LeapRC::AddPdbResMap(PdbResMapArray& pdbResMap, BufferedLine& infile)
 const
@@ -315,6 +346,8 @@ const
             prm.pdbName_ = aline[pdbidx];
             prm.unitName_ = aline[unitidx];
             pdbResMap.push_back( prm );
+            // Find among loaded units
+            DataSet* unitSet = findUnit( aline[unitidx] );
           //}
           tmp.clear();
         }
@@ -464,6 +497,7 @@ static inline int addSetsToList(DataSetList& dsl, DataSetList& paramDSL)
 int DataIO_LeapRC::ReadData(FileName const& fname, DataSetList& dsl, std::string const& dsname)
 {
   atomHybridizations_.clear();
+  units_.clear();
   // First, need to determine where the Amber FF files are
   const char* env = getenv("AMBERHOME");
   if (env != 0)
@@ -508,13 +542,13 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
       else if (line.Contains("loadamberparams"))
         err = LoadAmberParams( line.GetStringKey("loadamberparams"), dsl, dsname, atomHybridizations_ );
       else if (line.Contains("loadOff"))
-        err = LoadOFF( line.GetStringKey("loadOff"), unitDSL, dsname );
+        err = LoadOFF( line.GetStringKey("loadOff"), unitDSL, dsname, units_ );
       else if (line.Contains("loadoff"))
-        err = LoadOFF( line.GetStringKey("loadoff"), unitDSL, dsname );
+        err = LoadOFF( line.GetStringKey("loadoff"), unitDSL, dsname, units_ );
       else if (line.Contains("loadAmberPrep"))
-        err = LoadAmberPrep( line.GetStringKey("loadAmberPrep"), unitDSL, dsname );
+        err = LoadAmberPrep( line.GetStringKey("loadAmberPrep"), unitDSL, dsname, units_ );
       else if (line.Contains("loadamberprep"))
-        err = LoadAmberPrep( line.GetStringKey("loadamberprep"), unitDSL, dsname );
+        err = LoadAmberPrep( line.GetStringKey("loadamberprep"), unitDSL, dsname, units_ );
       else if (line.Contains("addAtomTypes") || line.Contains("addatomtypes"))
         err = AddAtomTypes(atomHybridizations_, infile);
       else if (line.Contains("addPdbResMap") || line.Contains("addpdbresmap"))
diff --git a/src/DataIO_LeapRC.h b/src/DataIO_LeapRC.h
index 70066ac89c..7547e4e2b8 100644
--- a/src/DataIO_LeapRC.h
+++ b/src/DataIO_LeapRC.h
@@ -20,6 +20,7 @@ class DataIO_LeapRC : public DataIO {
     typedef std::pair<NameType, AtomType::HybridizationType> NHpairType;
     typedef std::map<NameType, AtomType::HybridizationType> NHarrayType;
     typedef std::vector<std::string> Sarray;
+    typedef std::vector<DataSet*> DSarray;
 
     struct PdbResMapType {
       std::string unitName_;
@@ -29,14 +30,16 @@ class DataIO_LeapRC : public DataIO {
     typedef std::vector<PdbResMapType> PdbResMapArray;
 
     int LoadAmberParams(std::string const&, DataSetList&, std::string const&, NHarrayType const&) const;
-    int LoadOFF(std::string const&, DataSetList&, std::string const&) const;
-    int LoadAmberPrep(std::string const&, DataSetList&, std::string const&) const;
+    int LoadOFF(std::string const&, DataSetList&, std::string const&, DSarray&) const;
+    int LoadAmberPrep(std::string const&, DataSetList&, std::string const&, DSarray&) const;
     int AddAtomTypes(NHarrayType&, BufferedLine&) const;
     int AddPdbResMap(PdbResMapArray&, BufferedLine&) const;
     int AddPdbAtomMap(std::string const&, DataSetList&, BufferedLine&) const;
     int LoadMol2(ArgList const&, DataSetList&) const;
     int LoadPDB(ArgList const&, DataSetList&) const;
     int Source(FileName const&, DataSetList&, std::string const&);
+    /// \return Previously loaded unit set with given name
+    DataSet* findUnit(std::string const&) const;
     /// Used to check if a parm/lib file was already loaded.
     static inline bool check_already_loaded(Sarray const&, std::string const&);
     /// \return either file or Amberhome/dir/file
@@ -44,6 +47,7 @@ class DataIO_LeapRC : public DataIO {
 
     std::string amberhome_;
     NHarrayType atomHybridizations_; ///< Store hybridizations for atom types
+    DSarray units_;            ///< Hold COORDS sets which have been added as units
     static Sarray paramFiles_; ///< Track amber FF param files loaded from leaprc files
     static Sarray libFiles_;   ///< Track amber library/prep files loaded from leaprc files
 };

From 364fb04e5747e153a60bfef89afeed51a276e13f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 7 Jun 2024 15:10:34 -0400
Subject: [PATCH 0732/1492] Finish having AddPdbResMap work on loaded units as
 soon as the map is encountered

---
 src/DataIO_LeapRC.cpp | 49 +++++++++++++++++++++++++++----------------
 src/DataIO_LeapRC.h   | 14 ++++++-------
 src/Exec_Source.cpp   |  1 +
 3 files changed, 39 insertions(+), 25 deletions(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 0e21aeff9d..7d881d69c2 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -301,7 +301,7 @@ DataSet* DataIO_LeapRC::findUnit(std::string const& unitName) const {
 }
 
 /** LEaP addPdbResMap command. */
-int DataIO_LeapRC::AddPdbResMap(PdbResMapArray& pdbResMap, BufferedLine& infile)
+int DataIO_LeapRC::AddPdbResMap(BufferedLine& infile)
 const
 {
   int bracketCount = 0;
@@ -341,13 +341,26 @@ const
             unitidx = 2;
           }
           //if (termType != Cpptraj::Structure::NON_TERMINAL) {
-            PdbResMapType prm;
-            prm.termType_ = termType;
-            prm.pdbName_ = aline[pdbidx];
-            prm.unitName_ = aline[unitidx];
-            pdbResMap.push_back( prm );
+            //PdbResMapType prm;
+            //prm.termType_ = termType;
+            //prm.pdbName_ = aline[pdbidx];
+            //prm.unitName_ = aline[unitidx];
+            //pdbResMap.push_back( prm );
             // Find among loaded units
             DataSet* unitSet = findUnit( aline[unitidx] );
+            if (unitSet == 0) {
+              mprintf("Warning: Unit '%s' was not found among loaded units.\n",
+                      aline[unitidx].c_str());
+            } else {
+              //DataSet_Coords& crd = static_cast<DataSet_Coords&>( *ds );
+              AssociatedData_ResId resid( aline[pdbidx], termType );
+              unitSet->AssociateData( &resid );
+              if (debug_ > 0) {
+                mprintf("DEBUG: Found unit %s", unitSet->legend());
+                resid.Ainfo();
+                mprintf("\n");
+              }
+            }
           //}
           tmp.clear();
         }
@@ -527,9 +540,9 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
     return 1;
   }
   //DataSetList paramDSL;
-  DataSetList unitDSL;
+  //DataSetList unitDSL;
   //NHarrayType atomHybridizations;
-  PdbResMapArray pdbResMap;
+  //PdbResMapArray pdbResMap;
   int err = 0;
   const char* ptr = infile.Line();
   // FIXME need to convert to all lowercase for matching commands; leap allows
@@ -542,17 +555,17 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
       else if (line.Contains("loadamberparams"))
         err = LoadAmberParams( line.GetStringKey("loadamberparams"), dsl, dsname, atomHybridizations_ );
       else if (line.Contains("loadOff"))
-        err = LoadOFF( line.GetStringKey("loadOff"), unitDSL, dsname, units_ );
+        err = LoadOFF( line.GetStringKey("loadOff"), dsl, dsname, units_ );
       else if (line.Contains("loadoff"))
-        err = LoadOFF( line.GetStringKey("loadoff"), unitDSL, dsname, units_ );
+        err = LoadOFF( line.GetStringKey("loadoff"), dsl, dsname, units_ );
       else if (line.Contains("loadAmberPrep"))
-        err = LoadAmberPrep( line.GetStringKey("loadAmberPrep"), unitDSL, dsname, units_ );
+        err = LoadAmberPrep( line.GetStringKey("loadAmberPrep"), dsl, dsname, units_ );
       else if (line.Contains("loadamberprep"))
-        err = LoadAmberPrep( line.GetStringKey("loadamberprep"), unitDSL, dsname, units_ );
+        err = LoadAmberPrep( line.GetStringKey("loadamberprep"), dsl, dsname, units_ );
       else if (line.Contains("addAtomTypes") || line.Contains("addatomtypes"))
         err = AddAtomTypes(atomHybridizations_, infile);
       else if (line.Contains("addPdbResMap") || line.Contains("addpdbresmap"))
-        err = AddPdbResMap(pdbResMap, infile);
+        err = AddPdbResMap(infile);
       else if (line.Contains("addPdbAtomMap") || line.Contains("addpdbatommap"))
         err = AddPdbAtomMap(dsname, dsl, infile);
       else if (line.Contains("loadmol2") || line.Contains("loadMol2"))
@@ -574,14 +587,14 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
           if (equals.Nargs() == 2) {
             mprintf("DEBUG: %s = %s\n", equals[0].c_str(), equals[1].c_str());
             // Find the unit to make a copy of
-            DataSet* ds0 = unitDSL.CheckForSet( MetaData(dsname, equals[1]) );
+            DataSet* ds0 = dsl.CheckForSet( MetaData(dsname, equals[1]) );
             if (ds0 == 0) {
               mprinterr("Error: Could not find unit '%s' to copy to '%s'\n", equals[1].c_str(), equals[0].c_str());
               return 1;
             }
             DataSet_Coords& crd0 = static_cast<DataSet_Coords&>( *ds0 );
             // Allocate copy
-            DataSet* ds1 = unitDSL.AddSet( DataSet::COORDS, MetaData(dsname, equals[0]) );
+            DataSet* ds1 = dsl.AddSet( DataSet::COORDS, MetaData(dsname, equals[0]) );
             if (ds1 == 0) {
               mprinterr("Error: Could not allocate unit '%s' for '%s'\n", equals[0].c_str(), equals[1].c_str());
               return 1;
@@ -613,7 +626,7 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
   //for (DataSetList::const_iterator ds = unitDSL.begin(); ds != paramDSL.end(); ++ds)
   //{
   //  if ( (*ds)->Group() == DataSet::COORDINATES ) {
-  for (PdbResMapArray::const_iterator it = pdbResMap.begin();
+/*  for (PdbResMapArray::const_iterator it = pdbResMap.begin();
                                       it != pdbResMap.end(); ++it)
   {
     // Find the unit in unit DSL
@@ -630,12 +643,12 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
         mprintf("\n");
       }
     }
-  }
+  }*/
 
   // Add data sets to the main data set list
   //if (addSetsToList(dsl, paramDSL)) return err+1;
 
-  if (addSetsToList(dsl, unitDSL)) return err+1;
+  //if (addSetsToList(dsl, unitDSL)) return err+1;
 
   return err;
 }
diff --git a/src/DataIO_LeapRC.h b/src/DataIO_LeapRC.h
index 7547e4e2b8..56138a9d6a 100644
--- a/src/DataIO_LeapRC.h
+++ b/src/DataIO_LeapRC.h
@@ -22,18 +22,18 @@ class DataIO_LeapRC : public DataIO {
     typedef std::vector<std::string> Sarray;
     typedef std::vector<DataSet*> DSarray;
 
-    struct PdbResMapType {
-      std::string unitName_;
-      NameType pdbName_;
-      Cpptraj::Structure::TerminalType termType_;
-    };
-    typedef std::vector<PdbResMapType> PdbResMapArray;
+//    struct PdbResMapType {
+//      std::string unitName_;
+//      NameType pdbName_;
+//      Cpptraj::Structure::TerminalType termType_;
+//    };
+//    typedef std::vector<PdbResMapType> PdbResMapArray;
 
     int LoadAmberParams(std::string const&, DataSetList&, std::string const&, NHarrayType const&) const;
     int LoadOFF(std::string const&, DataSetList&, std::string const&, DSarray&) const;
     int LoadAmberPrep(std::string const&, DataSetList&, std::string const&, DSarray&) const;
     int AddAtomTypes(NHarrayType&, BufferedLine&) const;
-    int AddPdbResMap(PdbResMapArray&, BufferedLine&) const;
+    int AddPdbResMap(BufferedLine&) const;
     int AddPdbAtomMap(std::string const&, DataSetList&, BufferedLine&) const;
     int LoadMol2(ArgList const&, DataSetList&) const;
     int LoadPDB(ArgList const&, DataSetList&) const;
diff --git a/src/Exec_Source.cpp b/src/Exec_Source.cpp
index d1a26b1c56..2e842bc0b6 100644
--- a/src/Exec_Source.cpp
+++ b/src/Exec_Source.cpp
@@ -37,6 +37,7 @@ Exec::RetType Exec_Source::Execute(CpptrajState& State, ArgList& argIn)
   mprintf("\tReading %s\n", fileName.full());
 
   DataIO_LeapRC infile;
+  infile.SetDebug( State.Debug() );
   CpptrajFile tmp;
   tmp.SetupRead( fileName, State.Debug() );
   if (!infile.ID_DataFormat( tmp )) {

From 1a1e07703ca75bdde5830205cc450d38c3801616 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 7 Jun 2024 15:23:51 -0400
Subject: [PATCH 0733/1492] Ensure we return with 0 status if skipping

---
 src/DataIO_LeapRC.cpp | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 7d881d69c2..56c329732c 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -110,6 +110,7 @@ const
   } else {
     if (check_already_loaded(paramFiles_, filename)) {
       mprintf("Warning: Force field %s has already been loaded, skipping.\n", filename.c_str());
+      return 0;
     } else {
       mprintf("\tLoading force field from '%s'\n", filename.c_str());
       DataIO_AmberFF infile;

From 4fee7a864356d7307d4107161d7b822b0f8abe11 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 7 Jun 2024 15:29:40 -0400
Subject: [PATCH 0734/1492] First crack at supporting 'source' within leaprc
 file

---
 src/DataIO_LeapRC.cpp | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 56c329732c..94256cdc32 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -573,7 +573,18 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
         err = LoadMol2(line, dsl);
       else if (line.Contains("loadpdb") || line.Contains("loadPdb"))
         err = LoadPDB(line, dsl);
-      else {
+      else if (line.Contains("source")) {
+        std::string fname1 = line.GetStringKey("source");
+        if (fname1.empty()) {
+          mprinterr("Error: No filename given for 'source'\n");
+          return 1;
+        } else if (fname1 == fname.Full()) {
+          mprinterr("Error: File '%s' attempting to source itself '%s'\n", 
+                    fname.full(), fname1.c_str());
+          return 1;
+        }
+        err = Source(fname1, dsl, dsname);
+      } else {
         // Does this line contain an equals sign?
         bool has_equals = false;
         for (const char* p = ptr; *p != '\0'; ++p) {

From e01317a9780e51a9af7bb39d41da483a8536a6f1 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 8 Jun 2024 08:21:03 -0400
Subject: [PATCH 0735/1492] Use find_path to look for leaprc files in the cmd
 subdir

---
 src/DataIO_LeapRC.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 94256cdc32..156af1748d 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -536,7 +536,7 @@ int DataIO_LeapRC::ReadData(FileName const& fname, DataSetList& dsl, std::string
 int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string const& dsname)
 {
   BufferedLine infile;
-  if (infile.OpenFileRead(fname)) {
+  if (infile.OpenFileRead( find_path(fname.Full(), "cmd/") )) {
     mprinterr("Error: Could not open leaprc file '%s'\n", fname.full());
     return 1;
   }

From ca0808b0a5ce55343ec2356f498f9843d669ceea Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 10 Jun 2024 09:49:14 -0400
Subject: [PATCH 0736/1492] Use Exec_Build to build the structure when loadpdb
 is called.

---
 src/DataIO_Coords.cpp |  2 ++
 src/DataIO_LeapRC.cpp | 26 ++++++++++++++++++++++----
 src/cpptrajdepend     |  2 +-
 3 files changed, 25 insertions(+), 5 deletions(-)

diff --git a/src/DataIO_Coords.cpp b/src/DataIO_Coords.cpp
index be84db849a..95565f71c4 100644
--- a/src/DataIO_Coords.cpp
+++ b/src/DataIO_Coords.cpp
@@ -47,6 +47,7 @@ static inline bool can_append(DataSet::DataType typeIn) {
 // DataIO_Coords::ReadData()
 int DataIO_Coords::ReadData(FileName const& fname, DataSetList& dsl, std::string const& dsname)
 {
+  ClearAddedByMe();
   DataSet::DataType setType = DataSet::COORDS; // FIXME make user option
   if (!is_parm_fmt_ && !is_traj_fmt_) {
     // Assume that ID_DataFormat() has not been called.
@@ -131,6 +132,7 @@ int DataIO_Coords::ReadData(FileName const& fname, DataSetList& dsl, std::string
       ((DataSet_Coords*)dset)->AddFrame( frameIn );
     trajin.EndTraj();
   }
+  AddedByMe( dset );
 
   return 0;
 }
diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 156af1748d..c9521cfb50 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -9,6 +9,7 @@
 #include "DataIO_Coords.h"
 #include "DataSet_NameMap.h"
 #include "DataSet_Parameters.h"
+#include "Exec_Build.h"
 #include <cstdlib> //getenv
 
 /// CONSTRUCTOR
@@ -486,13 +487,30 @@ int DataIO_LeapRC::LoadPDB(ArgList const& argIn, DataSetList& dsl) const {
               args[2].c_str(), args[0].c_str());
     return 1;
   }
-  mprintf("\tLoaded file '%s' into '%s'\n",
-          args[2].c_str(), args[0].c_str());
+  if (coordsIn.Nadded() != 1) {
+    mprinterr("Internal Error: DataIO_LeapRC::LoadPDB(): Expected 1 COORDS set loaded from PDB, got %u\n", coordsIn.Nadded());
+    return 1;
+  }
+  mprintf("\tLoaded file '%s' into '%s'\n", args[2].c_str(), args[0].c_str());
+
+  // Assume we want the remaining args to be passed to the builder.
+  args.MarkArg(0);
+  args.MarkArg(1);
+  args.MarkArg(2);
+  ArgList tmparg = args.RemainingArgs();
+
+  tmparg.AddArg("name " + args[0]);
+  Exec_Build build;
+  Exec::RetType ret = build.BuildStructure( coordsIn.added_back(), dsl, debug_, tmparg );
+  if (ret == CpptrajState::ERR) {
+    mprinterr("Error: Build of '%s' failed.\n", args[2].c_str());
+    return 1;
+  }
   return 0;
 }
 
 /// Move sets from paramDSL to dsl
-static inline int addSetsToList(DataSetList& dsl, DataSetList& paramDSL)
+/*static inline int addSetsToList(DataSetList& dsl, DataSetList& paramDSL)
 {
   // Add data sets to the main data set list
   for (DataSetList::const_iterator ds = paramDSL.begin(); ds != paramDSL.end(); ++ds) {
@@ -505,7 +523,7 @@ static inline int addSetsToList(DataSetList& dsl, DataSetList& paramDSL)
   }
   paramDSL.SetHasCopies( true );
   return 0;
-}
+}*/
 
 /** Read (source) a leaprc (input) file. */
 int DataIO_LeapRC::ReadData(FileName const& fname, DataSetList& dsl, std::string const& dsname)
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index b8f7d66cc6..422599c047 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -228,7 +228,7 @@ DataIO_Cpout.o : DataIO_Cpout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h A
 DataIO_Evecs.o : DataIO_Evecs.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedFrame.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Evecs.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Modes.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Gnuplot.o : DataIO_Gnuplot.cpp ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Gnuplot.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Grace.o : DataIO_Grace.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Grace.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_string.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_LeapRC.o : DataIO_LeapRC.cpp ArgList.h AssociatedData.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_Coords.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_LeapRC.o : DataIO_LeapRC.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_Coords.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Mdout.o : DataIO_Mdout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Mdout.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_NetCDF.o : DataIO_NetCDF.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/Cframes.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_NetCDF.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_Mesh.h DataSet_Modes.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_Vector.h DataSet_Vector_Scalar.h DataSet_string.h DataSet_unsignedInt.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h Version.h
 DataIO_Numpy.o : DataIO_Numpy.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Numpy.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h libnpy/npy.hpp

From 6e4e2ebe1a6e593985952fb579b6b98df0209c87 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 10 Jun 2024 09:55:08 -0400
Subject: [PATCH 0737/1492] Provide more feedback

---
 src/DataIO_LeapRC.cpp | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index c9521cfb50..527f0dbe19 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -558,6 +558,7 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
     mprinterr("Error: Could not open leaprc file '%s'\n", fname.full());
     return 1;
   }
+  mprintf("\tReading LEaP input from '%s'\n", fname.base());
   //DataSetList paramDSL;
   //DataSetList unitDSL;
   //NHarrayType atomHybridizations;
@@ -569,6 +570,7 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
   while (ptr != 0) {
     if (ptr[0] != '\0' && ptr[0] != '#') {
       ArgList line( ptr, " \t" );
+      mprintf("\tLEAP> %s\n", ptr);
       if (line.Contains("loadAmberParams"))
         err = LoadAmberParams( line.GetStringKey("loadAmberParams"), dsl, dsname, atomHybridizations_ );
       else if (line.Contains("loadamberparams"))
@@ -643,6 +645,8 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
             crd1.CopyAssociatedDataFrom( crd0 );
             mprintf("DEBUG: Created unit set %s\n", crd1.legend());
           }
+        } else {
+          mprintf("Warning: Skipping unhandled LEaP command line: %s\n", ptr);
         }
       }
     }

From c74c6023c1bf1c404e0e9c4bc4042a657f31d60a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 10 Jun 2024 14:10:19 -0400
Subject: [PATCH 0738/1492] Add ToLower function and use where appropriate.
 Make leap parser case-insensitive to commands

---
 src/DataIO_LeapRC.cpp  | 96 +++++++++++++++++++++++++-----------------
 src/Energy_Sander.cpp  | 12 +++---
 src/StringRoutines.cpp | 12 ++++++
 src/StringRoutines.h   |  2 +
 src/cpptrajdepend      |  4 +-
 5 files changed, 79 insertions(+), 47 deletions(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 527f0dbe19..e54f7c6896 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -10,6 +10,7 @@
 #include "DataSet_NameMap.h"
 #include "DataSet_Parameters.h"
 #include "Exec_Build.h"
+#include "StringRoutines.h" // ToLower
 #include <cstdlib> //getenv
 
 /// CONSTRUCTOR
@@ -36,14 +37,16 @@ bool DataIO_LeapRC::ID_DataFormat(CpptrajFile& infile)
     if (ptr == 0) break;
     if (ptr[0] == '\0' || ptr[0] == '#') continue;
     nLinesScanned++;
-    ArgList line(ptr, " \t");
+    // LEaP commands are case-insensitive
+    ArgList line(ToLower(std::string(ptr)), " \t");
     if (line.Nargs() > 0) {
-      if (line[0] == "logFile" || line[0] == "logfile")
+      if (line[0] == "logfile")
         isLeaprc = true;
       else if (line[0] == "source")
         isLeaprc = true;
-      else if (line[0] == "addAtomTypes" || line[0] == "addatomtypes")
+      else if (line[0] == "addatomtypes")
         isLeaprc = true;
+      // TODO more commands
     }
   }
   infile.CloseFile();
@@ -559,6 +562,9 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
     return 1;
   }
   mprintf("\tReading LEaP input from '%s'\n", fname.base());
+  enum LeapCmdType { LOADAMBERPARAMS = 0, LOADOFF, LOADAMBERPREP, ADDATOMTYPES,
+                     ADDPDBRESMAP, ADDPDBATOMMAP, LOADMOL2, LOADPDB, SOURCE,
+                     UNKNOWN_CMD };
   //DataSetList paramDSL;
   //DataSetList unitDSL;
   //NHarrayType atomHybridizations;
@@ -569,31 +575,52 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
   //       mixed case
   while (ptr != 0) {
     if (ptr[0] != '\0' && ptr[0] != '#') {
-      ArgList line( ptr, " \t" );
+      // Note if this line contains an equals sign.
+      bool has_equals = false;
+      for (const char* p = ptr; *p != '\0'; ++p) {
+        if (*p == '=') {
+          has_equals = true;
+          break;
+        }
+      }
+
+      ArgList line( ptr, " =\t" );
       mprintf("\tLEAP> %s\n", ptr);
-      if (line.Contains("loadAmberParams"))
-        err = LoadAmberParams( line.GetStringKey("loadAmberParams"), dsl, dsname, atomHybridizations_ );
-      else if (line.Contains("loadamberparams"))
-        err = LoadAmberParams( line.GetStringKey("loadamberparams"), dsl, dsname, atomHybridizations_ );
-      else if (line.Contains("loadOff"))
-        err = LoadOFF( line.GetStringKey("loadOff"), dsl, dsname, units_ );
-      else if (line.Contains("loadoff"))
-        err = LoadOFF( line.GetStringKey("loadoff"), dsl, dsname, units_ );
-      else if (line.Contains("loadAmberPrep"))
-        err = LoadAmberPrep( line.GetStringKey("loadAmberPrep"), dsl, dsname, units_ );
-      else if (line.Contains("loadamberprep"))
-        err = LoadAmberPrep( line.GetStringKey("loadamberprep"), dsl, dsname, units_ );
-      else if (line.Contains("addAtomTypes") || line.Contains("addatomtypes"))
+
+      LeapCmdType leapcmd = UNKNOWN_CMD;
+      // Look through all args, lowercase, for recognized commands.
+      int pos = -1;
+      for (int arg = 0; arg != line.Nargs(); arg++) {
+        std::string argStr = ToLower( line[arg] );
+        if      (argStr == "loadamberparams") { pos = arg; leapcmd = LOADAMBERPARAMS; break; }
+        else if (argStr == "loadoff"        ) { pos = arg; leapcmd = LOADOFF; break; }
+        else if (argStr == "loadamberprep"  ) { pos = arg; leapcmd = LOADAMBERPREP; break; }
+        else if (argStr == "addatomtypes"   ) { pos = arg; leapcmd = ADDATOMTYPES; break; }
+        else if (argStr == "addpdbresmap"   ) { pos = arg; leapcmd = ADDPDBRESMAP; break; }
+        else if (argStr == "addpdbatommap"  ) { pos = arg; leapcmd = ADDPDBATOMMAP; break; }
+        else if (argStr == "loadmol2"       ) { pos = arg; leapcmd = LOADMOL2; break; }
+        else if (argStr == "loadpdb"        ) { pos = arg; leapcmd = LOADPDB; break; }
+        else if (argStr == "source"         ) { pos = arg; leapcmd = SOURCE; break; }
+      }
+
+      err = 0;
+      if (leapcmd == LOADAMBERPARAMS)
+        err = LoadAmberParams(line.GetStringKey(line[pos]), dsl, dsname, atomHybridizations_ );
+      else if (leapcmd == LOADOFF)
+        err = LoadOFF( line.GetStringKey(line[pos]), dsl, dsname, units_ );
+      else if (leapcmd == LOADAMBERPREP)
+        err = LoadAmberPrep( line.GetStringKey(line[pos]), dsl, dsname, units_ );
+      else if (leapcmd == ADDATOMTYPES)
         err = AddAtomTypes(atomHybridizations_, infile);
-      else if (line.Contains("addPdbResMap") || line.Contains("addpdbresmap"))
+      else if (leapcmd == ADDPDBRESMAP)
         err = AddPdbResMap(infile);
-      else if (line.Contains("addPdbAtomMap") || line.Contains("addpdbatommap"))
+      else if (leapcmd == ADDPDBATOMMAP)
         err = AddPdbAtomMap(dsname, dsl, infile);
-      else if (line.Contains("loadmol2") || line.Contains("loadMol2"))
+      else if (leapcmd == LOADMOL2)
         err = LoadMol2(line, dsl);
-      else if (line.Contains("loadpdb") || line.Contains("loadPdb"))
+      else if (leapcmd == LOADPDB)
         err = LoadPDB(line, dsl);
-      else if (line.Contains("source")) {
+      else if (leapcmd == SOURCE) {
         std::string fname1 = line.GetStringKey("source");
         if (fname1.empty()) {
           mprinterr("Error: No filename given for 'source'\n");
@@ -605,35 +632,26 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
         }
         err = Source(fname1, dsl, dsname);
       } else {
-        // Does this line contain an equals sign?
-        bool has_equals = false;
-        for (const char* p = ptr; *p != '\0'; ++p) {
-          if (*p == '=') {
-            has_equals = true;
-            break;
-          }
-        }
-        // See if this is a unit alias (interpret as 'alias = unit')
+        // Unrecognized so far. See if this is a unit alias (interpret as 'alias = unit')
         if (has_equals) {
-          ArgList equals(ptr, " =\t");
-          if (equals.Nargs() == 2) {
-            mprintf("DEBUG: %s = %s\n", equals[0].c_str(), equals[1].c_str());
+          if (line.Nargs() == 2) {
+            mprintf("DEBUG: %s = %s\n", line[0].c_str(), line[1].c_str());
             // Find the unit to make a copy of
-            DataSet* ds0 = dsl.CheckForSet( MetaData(dsname, equals[1]) );
+            DataSet* ds0 = dsl.CheckForSet( MetaData(dsname, line[1]) );
             if (ds0 == 0) {
-              mprinterr("Error: Could not find unit '%s' to copy to '%s'\n", equals[1].c_str(), equals[0].c_str());
+              mprinterr("Error: Could not find unit '%s' to copy to '%s'\n", line[1].c_str(), line[0].c_str());
               return 1;
             }
             DataSet_Coords& crd0 = static_cast<DataSet_Coords&>( *ds0 );
             // Allocate copy
-            DataSet* ds1 = dsl.AddSet( DataSet::COORDS, MetaData(dsname, equals[0]) );
+            DataSet* ds1 = dsl.AddSet( DataSet::COORDS, MetaData(dsname, line[0]) );
             if (ds1 == 0) {
-              mprinterr("Error: Could not allocate unit '%s' for '%s'\n", equals[0].c_str(), equals[1].c_str());
+              mprinterr("Error: Could not allocate unit '%s' for '%s'\n", line[0].c_str(), line[1].c_str());
               return 1;
             }
             DataSet_Coords& crd1 = static_cast<DataSet_Coords&>( *ds1 );
             if (crd1.CoordsSetup( crd0.Top(), crd0.CoordsInfo() )) {
-              mprinterr("Error: Could not set up unit '%s' for '%s'\n", equals[0].c_str(), equals[1].c_str());
+              mprinterr("Error: Could not set up unit '%s' for '%s'\n", line[0].c_str(), line[1].c_str());
               return 1;
             }
             crd1.Allocate( DataSet::SizeArray(1, 1) );
diff --git a/src/Energy_Sander.cpp b/src/Energy_Sander.cpp
index 1b155b6e53..6331e343cb 100644
--- a/src/Energy_Sander.cpp
+++ b/src/Energy_Sander.cpp
@@ -1,10 +1,10 @@
 #if defined(USE_SANDERLIB) && !defined(LIBCPPTRAJ)
-#include <locale>
-#include <cstdio> // remove()
 #include "Energy_Sander.h"
 #include "CpptrajStdio.h"
-#include "ParmFile.h" // For writing temporary top
 #include "File_TempName.h"
+#include "ParmFile.h" // For writing temporary top
+#include "StringRoutines.h" // ToLower
+#include <cstdio> // remove()
 
 Energy_Sander::Energy_Sander() :
   debug_(0),
@@ -43,11 +43,11 @@ const char* Energy_Sander::Estring_[] = {
 // Energy_Sander::Easpect()
 std::string Energy_Sander::Easpect(Etype typeIn) {
   if (typeIn == N_ENERGYTYPES) return std::string();
-  std::locale loc;
+/*  std::locale loc;
   std::string aspect( Estring_[typeIn] );
   for (std::string::iterator it = aspect.begin(); it != aspect.end(); ++it)
-    *it = std::tolower( *it, loc );
-  return aspect;
+    *it = std::tolower( *it, loc );*/
+  return ToLower( std::string(Estring_[typeIn]) );
 }
 
 // Energy_Sander::Energy()
diff --git a/src/StringRoutines.cpp b/src/StringRoutines.cpp
index 97d81a92d5..ad619bc952 100644
--- a/src/StringRoutines.cpp
+++ b/src/StringRoutines.cpp
@@ -1,6 +1,7 @@
 #include <cmath>     // log10
 #include <cctype>    // isspace, isdigit
 #include <ctime>     // for TimeString()
+#include <locale>    // for ToLower()
 #include <sstream>   // istringstream, ostringstream
 #include <stdexcept> // BadConversion
 #include "StringRoutines.h"
@@ -28,6 +29,17 @@ std::string AppendNumber(std::string const &fname, int number) {
   return oss.str();
 }
 
+/** Convert string to all lowercase */
+std::string ToLower(std::string const& strIn) {
+  if (strIn.empty()) return strIn;
+  std::locale loc;
+  std::string strOut;
+  strOut.reserve( strIn.size() );
+  for (std::string::const_iterator it = strIn.begin(); it != strIn.end(); ++it)
+    strOut += std::tolower( *it, loc );
+  return strOut;
+}
+
 /** \return 1 if S1 matches S2. 0 otherwise.
   * \param S1 String containing wildcards.
   * \param S2 String to match.
diff --git a/src/StringRoutines.h b/src/StringRoutines.h
index 8d5cc72ae4..a9a8e73984 100644
--- a/src/StringRoutines.h
+++ b/src/StringRoutines.h
@@ -11,6 +11,8 @@
  */
 /// Append '.<number>' to string, useful for e.g. appending number to file name.
 std::string AppendNumber(std::string const &, int);
+/// \return Input string converted to lowercase
+std::string ToLower(std::string const& strIn);
 /// \return 1 if first string (containing wildcards *, ?) matches second.
 int WildcardMatch(std::string const&, std::string const&);
 /// \return number of characters needed to represent given digit.
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 422599c047..3993c3efd8 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -228,7 +228,7 @@ DataIO_Cpout.o : DataIO_Cpout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h A
 DataIO_Evecs.o : DataIO_Evecs.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedFrame.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Evecs.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Modes.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Gnuplot.o : DataIO_Gnuplot.cpp ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Gnuplot.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Grace.o : DataIO_Grace.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Grace.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_string.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_LeapRC.o : DataIO_LeapRC.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_Coords.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_LeapRC.o : DataIO_LeapRC.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_Coords.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Mdout.o : DataIO_Mdout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Mdout.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_NetCDF.o : DataIO_NetCDF.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/Cframes.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_NetCDF.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_Mesh.h DataSet_Modes.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_Vector.h DataSet_Vector_Scalar.h DataSet_string.h DataSet_unsignedInt.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h Version.h
 DataIO_Numpy.o : DataIO_Numpy.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Numpy.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h libnpy/npy.hpp
@@ -283,7 +283,7 @@ DihedralSearch.o : DihedralSearch.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box
 DistRoutines.o : DistRoutines.cpp Box.h DistRoutines.h ImageOption.h Matrix_3x3.h Parallel.h Vec3.h
 Energy.o : Energy.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h Energy.h Energy/Ene_Angle.h Energy/Ene_Bond.h Energy/Kernel_Harmonic.h ExclusionArray.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 EnergyArray.o : EnergyArray.cpp CpptrajFile.h CpptrajStdio.h EnergyArray.h FileIO.h FileName.h Parallel.h
-Energy_Sander.o : Energy_Sander.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy_Sander.h FileName.h FileTypes.h File_TempName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Energy_Sander.o : Energy_Sander.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy_Sander.h FileName.h FileTypes.h File_TempName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 EnsembleIn.o : EnsembleIn.cpp Atom.h AtomMask.h Box.h CoordinateInfo.h CpptrajStdio.h EnsembleIn.h FileName.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h Timer.h TrajFrameCounter.h Unit.h Vec3.h
 EnsembleIn_Multi.o : EnsembleIn_Multi.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h EnsembleIn.h EnsembleIn_Multi.h FileIO.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
 EnsembleIn_Single.o : EnsembleIn_Single.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h EnsembleIn.h EnsembleIn_Single.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h

From b8f222b2b6053a04df10e1f32af6b73fc6e152f1 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 10 Jun 2024 14:31:52 -0400
Subject: [PATCH 0739/1492] Add GetStringKey function that takes const string

---
 src/ArgList.h | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/ArgList.h b/src/ArgList.h
index 9f2fe9421e..9b6b0a33e3 100644
--- a/src/ArgList.h
+++ b/src/ArgList.h
@@ -87,6 +87,8 @@ class ArgList {
     double getNextDouble(double);
     /// \return the string following the given key
     std::string const& GetStringKey(const char *);
+    /// \return the string following the given key
+    std::string const& GetStringKey(std::string const& s) { return GetStringKey(s.c_str()); }
     /// \return ArgList containing N unmarked arguments following given key
     ArgList GetNstringKey(const char*, int);
     /// \return string following given key or default if not found.

From 59eb16a40bf6ee4017ac9e7759da04c4b0e4e55b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 10 Jun 2024 14:36:50 -0400
Subject: [PATCH 0740/1492] Handle quit in leaprc file

---
 src/DataIO_LeapRC.cpp | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index e54f7c6896..e7b24e2dce 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -564,7 +564,7 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
   mprintf("\tReading LEaP input from '%s'\n", fname.base());
   enum LeapCmdType { LOADAMBERPARAMS = 0, LOADOFF, LOADAMBERPREP, ADDATOMTYPES,
                      ADDPDBRESMAP, ADDPDBATOMMAP, LOADMOL2, LOADPDB, SOURCE,
-                     UNKNOWN_CMD };
+                     QUIT, UNKNOWN_CMD };
   //DataSetList paramDSL;
   //DataSetList unitDSL;
   //NHarrayType atomHybridizations;
@@ -601,6 +601,7 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
         else if (argStr == "loadmol2"       ) { pos = arg; leapcmd = LOADMOL2; break; }
         else if (argStr == "loadpdb"        ) { pos = arg; leapcmd = LOADPDB; break; }
         else if (argStr == "source"         ) { pos = arg; leapcmd = SOURCE; break; }
+        else if (argStr == "quit"           ) { pos = arg; leapcmd = QUIT; break; }
       }
 
       err = 0;
@@ -631,6 +632,10 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
           return 1;
         }
         err = Source(fname1, dsl, dsname);
+      } else if (leapcmd == QUIT) {
+        // Do not read any more.
+        mprintf("\tEncountered 'quit' in leaprc file, not reading any more.\n");
+        break;
       } else {
         // Unrecognized so far. See if this is a unit alias (interpret as 'alias = unit')
         if (has_equals) {

From 8ac079d558a925919ad90dd8eedcf230af90537a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 10 Jun 2024 14:58:14 -0400
Subject: [PATCH 0741/1492] Start supporting saveamberparm

---
 src/DataIO_LeapRC.cpp | 29 ++++++++++++++++++++++++++++-
 src/DataIO_LeapRC.h   |  1 +
 2 files changed, 29 insertions(+), 1 deletion(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index e7b24e2dce..45f09221d7 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -512,6 +512,30 @@ int DataIO_LeapRC::LoadPDB(ArgList const& argIn, DataSetList& dsl) const {
   return 0;
 }
 
+/** Save specified unit to a topology and restart file. */
+int DataIO_LeapRC::SaveAmberParm(std::string const& unitName, ArgList& line, DataSetList const& dsl)
+const
+{
+  // saveamberparm <unit> <topfile> <restartfile>
+  if (unitName.empty()) {
+    mprinterr("Error: 'saveamberparm' : Unit name missing.\n");
+    return 1;
+  }
+  std::string topName = line.GetStringNext();
+  if (topName.empty()) {
+    mprinterr("Error: 'saveamberparm' : Topology name missing.\n");
+    return 1;
+  }
+  std::string crdName = line.GetStringNext();
+  if (crdName.empty()) {
+    mprinterr("Error: 'saveamberparm' : Coordinates name missing.\n");
+    return 1;
+  }
+  mprintf("\tSaving unit '%s' to topology '%s' and coordinates '%s'\n",
+          unitName.c_str(), topName.c_str(), crdName.c_str());
+  return 0;
+}
+
 /// Move sets from paramDSL to dsl
 /*static inline int addSetsToList(DataSetList& dsl, DataSetList& paramDSL)
 {
@@ -564,7 +588,7 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
   mprintf("\tReading LEaP input from '%s'\n", fname.base());
   enum LeapCmdType { LOADAMBERPARAMS = 0, LOADOFF, LOADAMBERPREP, ADDATOMTYPES,
                      ADDPDBRESMAP, ADDPDBATOMMAP, LOADMOL2, LOADPDB, SOURCE,
-                     QUIT, UNKNOWN_CMD };
+                     QUIT, SAVEAMBERPARM, UNKNOWN_CMD };
   //DataSetList paramDSL;
   //DataSetList unitDSL;
   //NHarrayType atomHybridizations;
@@ -602,11 +626,14 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
         else if (argStr == "loadpdb"        ) { pos = arg; leapcmd = LOADPDB; break; }
         else if (argStr == "source"         ) { pos = arg; leapcmd = SOURCE; break; }
         else if (argStr == "quit"           ) { pos = arg; leapcmd = QUIT; break; }
+        else if (argStr == "saveamberparm"  ) { pos = arg; leapcmd = SAVEAMBERPARM; break; }
       }
 
       err = 0;
       if (leapcmd == LOADAMBERPARAMS)
         err = LoadAmberParams(line.GetStringKey(line[pos]), dsl, dsname, atomHybridizations_ );
+      else if (leapcmd == SAVEAMBERPARM)
+        err = SaveAmberParm(line.GetStringKey(line[pos]), line, dsl);
       else if (leapcmd == LOADOFF)
         err = LoadOFF( line.GetStringKey(line[pos]), dsl, dsname, units_ );
       else if (leapcmd == LOADAMBERPREP)
diff --git a/src/DataIO_LeapRC.h b/src/DataIO_LeapRC.h
index 56138a9d6a..895d197eb0 100644
--- a/src/DataIO_LeapRC.h
+++ b/src/DataIO_LeapRC.h
@@ -37,6 +37,7 @@ class DataIO_LeapRC : public DataIO {
     int AddPdbAtomMap(std::string const&, DataSetList&, BufferedLine&) const;
     int LoadMol2(ArgList const&, DataSetList&) const;
     int LoadPDB(ArgList const&, DataSetList&) const;
+    int SaveAmberParm(std::string const&, ArgList&, DataSetList const& dsl) const;
     int Source(FileName const&, DataSetList&, std::string const&);
     /// \return Previously loaded unit set with given name
     DataSet* findUnit(std::string const&) const;

From 1f77352ea94ca630557154491e68260f6b4c5ea9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 11 Jun 2024 09:13:56 -0400
Subject: [PATCH 0742/1492] Save the PDB res name map in case new units are
 loaded after the map is

---
 src/DataIO_LeapRC.cpp | 136 +++++++++++++++++++++++++++---------------
 src/DataIO_LeapRC.h   |  19 +++---
 2 files changed, 100 insertions(+), 55 deletions(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 45f09221d7..7460e58f2c 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -287,7 +287,7 @@ const
 }
 
 /** Find unit among loaded units. */
-DataSet* DataIO_LeapRC::findUnit(std::string const& unitName) const {
+/*DataSet* DataIO_LeapRC::findUnit(std::string const& unitName) const {
   for (DSarray::const_iterator it = units_.begin(); it != units_.end(); ++it)
   {
     if ( (*it)->Meta().Aspect() == unitName ) {
@@ -303,10 +303,32 @@ DataSet* DataIO_LeapRC::findUnit(std::string const& unitName) const {
     }
   }
   return 0;
+}*/
+
+/** Associate PDB residue name map with COORDS set. */ // TODO call every time a new unit is loaded?
+void DataIO_LeapRC::addPdbResMapToUnit(DataSet_Coords* unit, PdbResMapType const& prm)
+const
+{
+  // Does this unit already have associated ResId?
+  AssociatedData* ad = unit->GetAssociatedData( AssociatedData::RESID );
+  if (ad == 0) {
+    AssociatedData_ResId resid( prm.pdbName_, prm.termType_ );
+    unit->AssociateData( &resid );
+    //if (debug_ > 0) {
+      mprintf("DEBUG: Found unit %s", unit->legend());
+      resid.Ainfo();
+      mprintf("\n");
+    //}
+  } else {
+    // TODO check if map is different
+    mprintf("DEBUG: Unit %s already has resmap. ", unit->legend());
+    ad->Ainfo();
+    mprintf("\n");
+  }
 }
 
 /** LEaP addPdbResMap command. */
-int DataIO_LeapRC::AddPdbResMap(BufferedLine& infile)
+int DataIO_LeapRC::AddPdbResMap(BufferedLine& infile, PdbResMapArray& pdbResMapIn)
 const
 {
   int bracketCount = 0;
@@ -346,26 +368,26 @@ const
             unitidx = 2;
           }
           //if (termType != Cpptraj::Structure::NON_TERMINAL) {
-            //PdbResMapType prm;
-            //prm.termType_ = termType;
-            //prm.pdbName_ = aline[pdbidx];
-            //prm.unitName_ = aline[unitidx];
-            //pdbResMap.push_back( prm );
+            PdbResMapType prm;
+            prm.termType_ = termType;
+            prm.pdbName_ = aline[pdbidx];
+            prm.unitName_ = aline[unitidx];
+            pdbResMapIn.push_back( prm );
             // Find among loaded units
-            DataSet* unitSet = findUnit( aline[unitidx] );
-            if (unitSet == 0) {
-              mprintf("Warning: Unit '%s' was not found among loaded units.\n",
-                      aline[unitidx].c_str());
-            } else {
-              //DataSet_Coords& crd = static_cast<DataSet_Coords&>( *ds );
-              AssociatedData_ResId resid( aline[pdbidx], termType );
-              unitSet->AssociateData( &resid );
-              if (debug_ > 0) {
-                mprintf("DEBUG: Found unit %s", unitSet->legend());
-                resid.Ainfo();
-                mprintf("\n");
-              }
-            }
+            //DataSet* unitSet = findUnit( aline[unitidx] );
+            //if (unitSet == 0) {
+            //  mprintf("Warning: Unit '%s' was not found among loaded units.\n",
+            //          aline[unitidx].c_str());
+            //} else {
+            //  //DataSet_Coords& crd = static_cast<DataSet_Coords&>( *ds );
+            //  AssociatedData_ResId resid( aline[pdbidx], termType );
+            //  unitSet->AssociateData( &resid );
+            //  if (debug_ > 0) {
+            //    mprintf("DEBUG: Found unit %s", unitSet->legend());
+            //    resid.Ainfo();
+            //    mprintf("\n");
+            //  }
+            //}
           //}
           tmp.clear();
         }
@@ -533,6 +555,7 @@ const
   }
   mprintf("\tSaving unit '%s' to topology '%s' and coordinates '%s'\n",
           unitName.c_str(), topName.c_str(), crdName.c_str());
+  // Get the unit
   return 0;
 }
 
@@ -574,7 +597,12 @@ int DataIO_LeapRC::ReadData(FileName const& fname, DataSetList& dsl, std::string
   if (!amberhome_.empty())
     mprintf("\tForce field files located in '%s'\n", amberhome_.c_str());
 
-  return Source(fname, dsl, dsname);
+  if (Source(fname, dsl, dsname)) {
+    mprinterr("Error: Could not read LEaP input from '%s'\n", fname.full());
+    return 1;
+  }
+
+  return 0;
 }
 
 /** Execute leap source command */
@@ -640,9 +668,36 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
         err = LoadAmberPrep( line.GetStringKey(line[pos]), dsl, dsname, units_ );
       else if (leapcmd == ADDATOMTYPES)
         err = AddAtomTypes(atomHybridizations_, infile);
-      else if (leapcmd == ADDPDBRESMAP)
-        err = AddPdbResMap(infile);
-      else if (leapcmd == ADDPDBATOMMAP)
+      else if (leapcmd == ADDPDBRESMAP) {
+        err = AddPdbResMap(infile, pdbResMap_);
+        if (err == 0) {
+          // Update units with pdb residue map info
+          //for (DataSetList::const_iterator ds = unitDSL.begin(); ds != paramDSL.end(); ++ds)
+          //{
+          //  if ( (*ds)->Group() == DataSet::COORDINATES ) {
+          for (PdbResMapArray::const_iterator it = pdbResMap_.begin();
+                                              it != pdbResMap_.end(); ++it)
+          {
+            // Find the unit in unit DSL
+            DataSet* ds = dsl.CheckForSet( MetaData(dsname, it->unitName_) );
+            if (ds != 0 && ds->Group() == DataSet::COORDINATES) {
+              addPdbResMapToUnit( static_cast<DataSet_Coords*>(ds), *it );
+            }
+            /*if (ds == 0) {
+              mprintf("Warning: Unit '%s' was not found among loaded units.\n", it->unitName_.c_str());
+            } else {
+              DataSet_Coords& crd = static_cast<DataSet_Coords&>( *ds );
+              AssociatedData_ResId resid( it->pdbName_, it->termType_ );
+              crd.AssociateData( &resid );
+              if (debug_ > 0) {
+                mprintf("DEBUG: Found unit %s", crd.legend());
+                resid.Ainfo();
+                mprintf("\n");
+              }
+            }*/
+          }
+        }
+      } else if (leapcmd == ADDPDBATOMMAP)
         err = AddPdbAtomMap(dsname, dsl, infile);
       else if (leapcmd == LOADMOL2)
         err = LoadMol2(line, dsl);
@@ -694,6 +749,15 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
             // Copy associated data
             crd1.CopyAssociatedDataFrom( crd0 );
             mprintf("DEBUG: Created unit set %s\n", crd1.legend());
+            // See if there is a PDB residue name map
+            for (PdbResMapArray::const_iterator it = pdbResMap_.begin();
+                                                it != pdbResMap_.end(); ++it)
+            {
+              if (it->unitName_ == line[0]) {
+                addPdbResMapToUnit( &crd1, *it );
+                break;
+              }
+            }
           }
         } else {
           mprintf("Warning: Skipping unhandled LEaP command line: %s\n", ptr);
@@ -706,28 +770,6 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
   infile.CloseFile();
 
 
-  // Update units with pdb residue map info
-  //for (DataSetList::const_iterator ds = unitDSL.begin(); ds != paramDSL.end(); ++ds)
-  //{
-  //  if ( (*ds)->Group() == DataSet::COORDINATES ) {
-/*  for (PdbResMapArray::const_iterator it = pdbResMap.begin();
-                                      it != pdbResMap.end(); ++it)
-  {
-    // Find the unit in unit DSL
-    DataSet* ds = unitDSL.CheckForSet( MetaData(dsname, it->unitName_) );
-    if (ds == 0) {
-      mprintf("Warning: Unit '%s' was not found among loaded units.\n", it->unitName_.c_str());
-    } else {
-      DataSet_Coords& crd = static_cast<DataSet_Coords&>( *ds );
-      AssociatedData_ResId resid( it->pdbName_, it->termType_ );
-      crd.AssociateData( &resid );
-      if (debug_ > 0) {
-        mprintf("DEBUG: Found unit %s", crd.legend());
-        resid.Ainfo();
-        mprintf("\n");
-      }
-    }
-  }*/
 
   // Add data sets to the main data set list
   //if (addSetsToList(dsl, paramDSL)) return err+1;
diff --git a/src/DataIO_LeapRC.h b/src/DataIO_LeapRC.h
index 895d197eb0..6255d3b66c 100644
--- a/src/DataIO_LeapRC.h
+++ b/src/DataIO_LeapRC.h
@@ -22,25 +22,27 @@ class DataIO_LeapRC : public DataIO {
     typedef std::vector<std::string> Sarray;
     typedef std::vector<DataSet*> DSarray;
 
-//    struct PdbResMapType {
-//      std::string unitName_;
-//      NameType pdbName_;
-//      Cpptraj::Structure::TerminalType termType_;
-//    };
-//    typedef std::vector<PdbResMapType> PdbResMapArray;
+    struct PdbResMapType {
+      std::string unitName_;
+      NameType pdbName_;
+      Cpptraj::Structure::TerminalType termType_;
+    };
+    typedef std::vector<PdbResMapType> PdbResMapArray;
 
     int LoadAmberParams(std::string const&, DataSetList&, std::string const&, NHarrayType const&) const;
     int LoadOFF(std::string const&, DataSetList&, std::string const&, DSarray&) const;
     int LoadAmberPrep(std::string const&, DataSetList&, std::string const&, DSarray&) const;
     int AddAtomTypes(NHarrayType&, BufferedLine&) const;
-    int AddPdbResMap(BufferedLine&) const;
+    int AddPdbResMap(BufferedLine&, PdbResMapArray&) const;
     int AddPdbAtomMap(std::string const&, DataSetList&, BufferedLine&) const;
     int LoadMol2(ArgList const&, DataSetList&) const;
     int LoadPDB(ArgList const&, DataSetList&) const;
     int SaveAmberParm(std::string const&, ArgList&, DataSetList const& dsl) const;
     int Source(FileName const&, DataSetList&, std::string const&);
+    /// Add PDB residue map to COORDS unit
+    void addPdbResMapToUnit(DataSet_Coords*, PdbResMapType const&) const;
     /// \return Previously loaded unit set with given name
-    DataSet* findUnit(std::string const&) const;
+    //DataSet* findUnit(std::string const&) const;
     /// Used to check if a parm/lib file was already loaded.
     static inline bool check_already_loaded(Sarray const&, std::string const&);
     /// \return either file or Amberhome/dir/file
@@ -48,6 +50,7 @@ class DataIO_LeapRC : public DataIO {
 
     std::string amberhome_;
     NHarrayType atomHybridizations_; ///< Store hybridizations for atom types
+    PdbResMapArray pdbResMap_; ///< Hold PDB residue name map
     DSarray units_;            ///< Hold COORDS sets which have been added as units
     static Sarray paramFiles_; ///< Track amber FF param files loaded from leaprc files
     static Sarray libFiles_;   ///< Track amber library/prep files loaded from leaprc files

From d6fd6936612893184c0a7092dcd160b4a4aa3f38 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 11 Jun 2024 09:16:42 -0400
Subject: [PATCH 0743/1492] Dont copy associated data, look in the pdb residue
 name map instead

---
 src/DataIO_LeapRC.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 7460e58f2c..7baf5310fb 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -747,7 +747,7 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
             crd0.GetFrame(0, tmpFrm);
             crd1.SetCRD(0, tmpFrm );
             // Copy associated data
-            crd1.CopyAssociatedDataFrom( crd0 );
+            //crd1.CopyAssociatedDataFrom( crd0 );
             mprintf("DEBUG: Created unit set %s\n", crd1.legend());
             // See if there is a PDB residue name map
             for (PdbResMapArray::const_iterator it = pdbResMap_.begin();

From 7c5110e4527b75eefd1301636163046200c78734 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 11 Jun 2024 09:41:14 -0400
Subject: [PATCH 0744/1492] Write the topology

---
 src/DataIO_LeapRC.cpp | 20 ++++++++++++++++++++
 src/cpptrajdepend     |  2 +-
 2 files changed, 21 insertions(+), 1 deletion(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 7baf5310fb..1f705e9fec 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -10,6 +10,7 @@
 #include "DataSet_NameMap.h"
 #include "DataSet_Parameters.h"
 #include "Exec_Build.h"
+#include "Parm_Amber.h"
 #include "StringRoutines.h" // ToLower
 #include <cstdlib> //getenv
 
@@ -556,6 +557,25 @@ const
   mprintf("\tSaving unit '%s' to topology '%s' and coordinates '%s'\n",
           unitName.c_str(), topName.c_str(), crdName.c_str());
   // Get the unit
+  DataSet* ds = dsl.CheckForSet( MetaData(unitName) );
+  if (ds == 0) {
+    mprinterr("Error: Set '%s' not found.\n", unitName.c_str());
+    return 1;
+  }
+  if (ds->Group() != DataSet::COORDINATES) {
+    mprinterr("Error: Set '%s' is not COORDINATES.\n", ds->legend());
+    return 1;
+  }
+  mprintf("\tCOORDINATES set %s\n", ds->legend());
+  DataSet_Coords const& crd = static_cast<DataSet_Coords const&>( *ds );
+
+  Parm_Amber parmOut;
+  parmOut.SetDebug( debug_ );
+  if (parmOut.WriteParm( topName, crd.Top() )) {
+    mprinterr("Error: Write of '%s' failed.\n", topName.c_str());
+    return 1;
+  }
+
   return 0;
 }
 
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 3993c3efd8..96932d1301 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -228,7 +228,7 @@ DataIO_Cpout.o : DataIO_Cpout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h A
 DataIO_Evecs.o : DataIO_Evecs.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedFrame.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Evecs.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Modes.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Gnuplot.o : DataIO_Gnuplot.cpp ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Gnuplot.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Grace.o : DataIO_Grace.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Grace.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_string.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_LeapRC.o : DataIO_LeapRC.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_Coords.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_LeapRC.o : DataIO_LeapRC.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_Coords.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_Amber.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Mdout.o : DataIO_Mdout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Mdout.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_NetCDF.o : DataIO_NetCDF.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/Cframes.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_NetCDF.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_Mesh.h DataSet_Modes.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_Vector.h DataSet_Vector_Scalar.h DataSet_string.h DataSet_unsignedInt.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h Version.h
 DataIO_Numpy.o : DataIO_Numpy.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Numpy.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h libnpy/npy.hpp

From 8f3c20fbeabae6732709b8900b021656f70498c0 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 11 Jun 2024 10:20:39 -0400
Subject: [PATCH 0745/1492] Write the restart

---
 src/DataIO_LeapRC.cpp | 27 ++++++++++++++++++++++++++-
 src/cpptrajdepend     |  2 +-
 2 files changed, 27 insertions(+), 2 deletions(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 1f705e9fec..2fcaec6a8a 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -12,6 +12,7 @@
 #include "Exec_Build.h"
 #include "Parm_Amber.h"
 #include "StringRoutines.h" // ToLower
+#include "Trajout_Single.h"
 #include <cstdlib> //getenv
 
 /// CONSTRUCTOR
@@ -567,7 +568,11 @@ const
     return 1;
   }
   mprintf("\tCOORDINATES set %s\n", ds->legend());
-  DataSet_Coords const& crd = static_cast<DataSet_Coords const&>( *ds );
+  DataSet_Coords& crd = static_cast<DataSet_Coords&>( *ds ); // FIXME this really should be const
+  if (crd.Size() < 1) {
+    mprinterr("Error: '%s' is empty.\n", crd.legend());
+    return 1;
+  }
 
   Parm_Amber parmOut;
   parmOut.SetDebug( debug_ );
@@ -576,6 +581,26 @@ const
     return 1;
   }
 
+  if (crd.Size() > 1)
+    mprintf("Warning: '%s' has more than 1 frame. Only using first frame.\n");
+
+  Trajout_Single trajOut;
+  ArgList tmpargs;
+  if (trajOut.PrepareTrajWrite( crdName, tmpargs, dsl, crd.TopPtr(), crd.CoordsInfo(),
+                                1, TrajectoryFile::UNKNOWN_TRAJ ))
+  {
+    mprinterr("Error: Could not set up '%s' for write.\n", crdName.c_str());
+    return 1;
+  }
+  trajOut.PrintInfo(0);
+  Frame currentFrame = crd.AllocateFrame();
+  crd.GetFrame( 0, currentFrame );
+  if ( trajOut.WriteSingle( 0, currentFrame )) {
+    mprinterr("Error: Could not write frame to '%s'\n", crdName.c_str());
+    return 1;
+  }
+  trajOut.EndTraj();
+
   return 0;
 }
 
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 96932d1301..aeb25e95b4 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -228,7 +228,7 @@ DataIO_Cpout.o : DataIO_Cpout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h A
 DataIO_Evecs.o : DataIO_Evecs.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedFrame.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Evecs.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Modes.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Gnuplot.o : DataIO_Gnuplot.cpp ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Gnuplot.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Grace.o : DataIO_Grace.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Grace.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_string.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_LeapRC.o : DataIO_LeapRC.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_Coords.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_Amber.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_LeapRC.o : DataIO_LeapRC.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_Coords.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_Amber.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Mdout.o : DataIO_Mdout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Mdout.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_NetCDF.o : DataIO_NetCDF.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/Cframes.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_NetCDF.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_Mesh.h DataSet_Modes.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_Vector.h DataSet_Vector_Scalar.h DataSet_string.h DataSet_unsignedInt.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h Version.h
 DataIO_Numpy.o : DataIO_Numpy.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Numpy.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h libnpy/npy.hpp

From 892deeab2d5b2dac7e203eb147c0f0cfb5be0d3f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 14 Jun 2024 15:47:06 -0400
Subject: [PATCH 0746/1492] Update chainid call

---
 src/Exec_Build.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 39afa8a282..1b8426e9f4 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -154,7 +154,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
       resTermType = Cpptraj::Structure::END_TERMINAL;
     } else if (pres > -1 && topIn.Res(pres).IsTerminal()) {
       resTermType = Cpptraj::Structure::BEG_TERMINAL;
-    } else if (nres < topIn.Nres() && topIn.Res(nres).ChainId() != currentRes.ChainId()) {
+    } else if (nres < topIn.Nres() && topIn.Res(nres).ChainID() != currentRes.ChainID()) {
       resTermType = Cpptraj::Structure::END_TERMINAL;
     } else {
       resTermType = Cpptraj::Structure::NON_TERMINAL;

From c25c295af1a2da631b8320619572191f3c46abe4 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 18 Jun 2024 09:29:21 -0400
Subject: [PATCH 0747/1492] Add atom name map read

---
 src/DataIO_Std.cpp | 69 +++++++++++++++++++++++++++++++++++++++++++++-
 src/DataIO_Std.h   |  7 +++--
 src/cpptrajdepend  |  2 +-
 3 files changed, 73 insertions(+), 5 deletions(-)

diff --git a/src/DataIO_Std.cpp b/src/DataIO_Std.cpp
index 49d8027036..d920d78e78 100644
--- a/src/DataIO_Std.cpp
+++ b/src/DataIO_Std.cpp
@@ -18,6 +18,7 @@
 #include "DataSet_Vector.h" // For reading TODO remove dependency?
 #include "DataSet_Mat3x3.h" // For reading TODO remove dependency?
 #include "DataSet_PairwiseCache_MEM.h" // For reading
+#include "DataSet_NameMap.h" // For reading
 #include "DataSet_2D.h"
 #include "DataSet_MatrixFlt.h"
 #include "DataSet_MatrixDbl.h"
@@ -94,7 +95,9 @@ void DataIO_Std::ReadHelp() {
           "\t\tprec {dbl|flt*}       : Grid precision; double or float (default float).\n"
           "\t\tbin {center|corner*}  : Coords specify bin centers or corners (default corners).\n"
           "\tvector         : Read data as vector: VX VY VZ [OX OY OZ]\n"
-          "\tmat3x3         : Read data as 3x3 matrices: M(1,1) M(1,2) ... M(3,2) M(3,3)\n");
+          "\tmat3x3         : Read data as 3x3 matrices: M(1,1) M(1,2) ... M(3,2) M(3,3)\n"
+          "\tnamemap        : Read data as atom name map (#TgtAt Tgt RefAt Ref)\n"
+         );
 
 }
 
@@ -107,6 +110,7 @@ int DataIO_Std::processReadArgs(ArgList& argIn) {
   else if (argIn.hasKey("read3d")) mode_ = READ3D;
   else if (argIn.hasKey("vector")) mode_ = READVEC;
   else if (argIn.hasKey("mat3x3")) mode_ = READMAT3X3;
+  else if (argIn.hasKey("namemap")) mode_ = READNAMEMAP;
   indexcol_ = argIn.getKeyInt("index", -1);
   // Column user args start from 1.
   if (indexcol_ == 0) {
@@ -218,6 +222,7 @@ int DataIO_Std::ReadData(FileName const& fname,
     case READ3D: err = Read_3D(fname.Full(), dsl, dsname); break;
     case READVEC: err = Read_Vector(fname.Full(), dsl, dsname); break;
     case READMAT3X3: err = Read_Mat3x3(fname.Full(), dsl, dsname); break;
+    case READNAMEMAP: err = Read_NameMap(fname.Full(), dsl, dsname); break;
   }
   return err;
 }
@@ -844,6 +849,7 @@ int DataIO_Std::Read_3D(std::string const& fname,
 // DataIO_Std::Read_Vector()
 int DataIO_Std::Read_Vector(std::string const& fname, 
                             DataSetList& datasetlist, std::string const& dsname)
+const
 {
   // See if set exists
   DataSet* ds = datasetlist.CheckForSet( dsname );
@@ -953,6 +959,7 @@ int DataIO_Std::Read_Vector(std::string const& fname,
 // DataIO_Std::Read_Mat3x3()
 int DataIO_Std::Read_Mat3x3(std::string const& fname, 
                             DataSetList& datasetlist, std::string const& dsname)
+const
 {
   // Buffer file
   BufferedLine buffer;
@@ -1005,6 +1012,66 @@ int DataIO_Std::Read_Mat3x3(std::string const& fname,
   return (datasetlist.AddOrAppendSets("", DataSetList::Darray(), DataSetList::DataListType(1, ds)));
 }
 
+/** Read an atom name map. */
+int DataIO_Std::Read_NameMap(std::string const& fname, 
+                            DataSetList& dsl, std::string const& dsname)
+const
+{
+  // Buffer file
+  BufferedLine buffer;
+  if (buffer.OpenFileRead( fname )) return 1;
+  mprintf("\tAttempting to read atom name map data.\n");
+  // Read through file 
+  const char* linebuffer = buffer.Line();
+  int ncols = 0;
+  int tgtcol = 0;
+  int refcol = 0;
+  DataSet_NameMap* namemap = 0;
+  while (linebuffer != 0) {
+    // Skip comments
+    if (linebuffer[0] != '#') {
+      int ntokens = buffer.TokenizeLine(" \t\n\r");
+      if (ncols == 0) {
+        // First non-comment line. Determine num columns
+        ncols = ntokens;
+        if (ncols != 4) {
+          mprinterr("Error: For atom name map, expect 4 columns (#TgtAt Tgt RefAt Ref), got %i\n");
+          return 1;
+        }
+        tgtcol = 1;
+        refcol = 3;
+        // Allocate the name map
+        namemap = (DataSet_NameMap*)dsl.AddSet(DataSet::NAMEMAP, MetaData(dsname));
+        if (namemap == 0) {
+          mprinterr("Error: Could not allocate name map set '%s'\n", dsname.c_str());
+          return 1;
+        }
+      } else if (ncols != ntokens) {
+        mprinterr("Error: Number of columns has changed at line %i from %i to %i\n",
+                  buffer.LineNumber(), ncols, ntokens);
+        mprinterr("Error: '%s'\n", linebuffer);
+        return 1;
+      } else {
+        std::string tgt, ref;
+        for (int col = 0; col != ntokens; col++) {
+          const char* ptr = buffer.NextToken();
+          if (col == tgtcol)
+            tgt.assign( ptr );
+          else if (col == refcol)
+            ref.assign( ptr );
+        }
+        // Skip mapping if tgt == ref
+        if (tgt != ref) {
+          mprintf("DEBUG: Map ref %s to tgt %s\n", ref.c_str(), tgt.c_str());
+          namemap->AddNameMap(ref, tgt);
+        }
+      }
+    } // END if not comment
+    linebuffer = buffer.Line();
+  } // END loop over file
+  return 0;
+}
+
 // -----------------------------------------------------------------------------
 void DataIO_Std::WriteHelp() {
   mprintf("\theader         : Print header line.\n"
diff --git a/src/DataIO_Std.h b/src/DataIO_Std.h
index 85f9647052..38cde1b21d 100644
--- a/src/DataIO_Std.h
+++ b/src/DataIO_Std.h
@@ -18,7 +18,7 @@ class DataIO_Std : public DataIO {
     static const int IS_ASCII_CMATRIX;
 
     enum GroupType { NO_TYPE = 0, BY_NAME, BY_ASPECT, BY_IDX, BY_ENS, BY_DIM };
-    enum modeType {READ1D=0, READ2D, READ3D, READVEC, READMAT3X3};
+    enum modeType {READ1D=0, READ2D, READ3D, READVEC, READMAT3X3, READNAMEMAP};
     enum precType {UNSPEC, FLOAT, DOUBLE};
 
     static int Get3Double(std::string const&, Vec3&, bool&);
@@ -27,8 +27,9 @@ class DataIO_Std : public DataIO {
     int Read_2D(std::string const&,DataSetList&,std::string const&);
     int Read_2D_XYZ(FileName const&,DataSetList&,std::string const&);
     int Read_3D(std::string const&,DataSetList&,std::string const&);
-    int Read_Vector(std::string const&,DataSetList&,std::string const&);
-    int Read_Mat3x3(std::string const&,DataSetList&,std::string const&);
+    int Read_Vector(std::string const&,DataSetList&,std::string const&) const;
+    int Read_Mat3x3(std::string const&,DataSetList&,std::string const&) const;
+    int Read_NameMap(std::string const&,DataSetList&,std::string const&) const;
     static void WriteNameToBuffer(CpptrajFile&, std::string const&, int,  bool);
     int WriteByGroup(CpptrajFile&, DataSetList const&, GroupType);
     int WriteStringVars(CpptrajFile&, DataSetList const&) const;
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index cfd4e1e19e..5948bdda94 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -235,7 +235,7 @@ DataIO_Numpy.o : DataIO_Numpy.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h A
 DataIO_OpenDx.o : DataIO_OpenDx.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_OpenDx.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridDbl.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Peaks.o : DataIO_Peaks.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Peaks.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector_Scalar.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_RemLog.o : DataIO_RemLog.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_RemLog.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_Std.o : DataIO_Std.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Cluster/Cframes.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Std.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_Parameters.h DataSet_StringVar.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_string.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_Std.o : DataIO_Std.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Cluster/Cframes.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Std.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_NameMap.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_Parameters.h DataSet_StringVar.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_string.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_VecTraj.o : DataIO_VecTraj.cpp ActionFrameCounter.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_VecTraj.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_XVG.o : DataIO_XVG.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_XVG.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Xplor.o : DataIO_Xplor.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Xplor.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h

From 41285d5a07f7a0a013f521305b3c11ee96e813bc Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 18 Jun 2024 09:35:37 -0400
Subject: [PATCH 0748/1492] Recognize 2 col name map file as well. Start name
 map write.

---
 src/DataIO_Std.cpp | 31 ++++++++++++++++++++++++++-----
 src/DataIO_Std.h   |  1 +
 2 files changed, 27 insertions(+), 5 deletions(-)

diff --git a/src/DataIO_Std.cpp b/src/DataIO_Std.cpp
index d920d78e78..3770cbd5c6 100644
--- a/src/DataIO_Std.cpp
+++ b/src/DataIO_Std.cpp
@@ -96,7 +96,7 @@ void DataIO_Std::ReadHelp() {
           "\t\tbin {center|corner*}  : Coords specify bin centers or corners (default corners).\n"
           "\tvector         : Read data as vector: VX VY VZ [OX OY OZ]\n"
           "\tmat3x3         : Read data as 3x3 matrices: M(1,1) M(1,2) ... M(3,2) M(3,3)\n"
-          "\tnamemap        : Read data as atom name map (#TgtAt Tgt RefAt Ref)\n"
+          "\tnamemap        : Read data as atom name map ('#TgtAt Tgt RefAt Ref' or '#TgtAt RefAt')\n"
          );
 
 }
@@ -1034,12 +1034,17 @@ const
       if (ncols == 0) {
         // First non-comment line. Determine num columns
         ncols = ntokens;
-        if (ncols != 4) {
-          mprinterr("Error: For atom name map, expect 4 columns (#TgtAt Tgt RefAt Ref), got %i\n");
+        if (ncols == 4) {
+          tgtcol = 1;
+          refcol = 3;
+        } else if (ncols == 2) {
+          tgtcol = 0;
+          refcol = 1;
+        } else {
+          mprinterr("Error: For atom name map, expect 4 columns (#TgtAt Tgt RefAt Ref)\n"
+                    "Error:  or 2 columns (#TgtAt RefAt), got %i\n", ntokens);
           return 1;
         }
-        tgtcol = 1;
-        refcol = 3;
         // Allocate the name map
         namemap = (DataSet_NameMap*)dsl.AddSet(DataSet::NAMEMAP, MetaData(dsname));
         if (namemap == 0) {
@@ -1235,6 +1240,8 @@ int DataIO_Std::WriteData(FileName const& fname, DataSetList const& SetList)
     } else if (SetList[0]->Type() == DataSet::STRINGVAR) {
       // For debugging string variables
       err = WriteStringVars(file, SetList);
+    } else if (SetList[0]->Type() == DataSet::NAMEMAP) {
+      err = WriteNameMap(file, SetList);
     } else if (SetList[0]->Ndim() == 1) {
       if (group_ == NO_TYPE) {
         if (isInverted_)
@@ -1298,6 +1305,20 @@ int DataIO_Std::WriteStringVars(CpptrajFile& file, DataSetList const& Sets) cons
   return 0;
 }
 
+/** Write atom name map to file. */
+int DataIO_Std::WriteNameMap(CpptrajFile& file, DataSetList const& Sets) const {
+  for (DataSetList::const_iterator ds = Sets.begin(); ds != Sets.end(); ++ds)
+  {
+    if ( (*ds)->Type() != DataSet::NAMEMAP ) {
+      mprintf("Warning: First variable written to %s was a name map, skipping '%s'\n",
+              file.Filename().full(), (*ds)->legend());
+    } else {
+      DataSet_NameMap const& namemap = static_cast<DataSet_NameMap const&>( *(*ds) );
+    }
+  }
+  return 0;
+}
+
 // DataIO_Std::WriteCmatrix()
 int DataIO_Std::WriteCmatrix(CpptrajFile& file, DataSetList const& Sets) {
   for (DataSetList::const_iterator ds = Sets.begin(); ds != Sets.end(); ++ds)
diff --git a/src/DataIO_Std.h b/src/DataIO_Std.h
index 38cde1b21d..c5bbff2765 100644
--- a/src/DataIO_Std.h
+++ b/src/DataIO_Std.h
@@ -33,6 +33,7 @@ class DataIO_Std : public DataIO {
     static void WriteNameToBuffer(CpptrajFile&, std::string const&, int,  bool);
     int WriteByGroup(CpptrajFile&, DataSetList const&, GroupType);
     int WriteStringVars(CpptrajFile&, DataSetList const&) const;
+    int WriteNameMap(CpptrajFile&, DataSetList const&) const;
     int WriteCmatrix(CpptrajFile&, DataSetList const&);
     int WriteDataNormal(CpptrajFile&,DataSetList const&);
     int WriteDataInverted(CpptrajFile&,DataSetList const&);

From 9d2f6bd2d2511af40175be5cec2b7d06296a8ff9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 18 Jun 2024 09:55:15 -0400
Subject: [PATCH 0749/1492] Finish name map write. Do not skip first mapping
 line when reading.

---
 src/DataIO_Std.cpp    | 44 ++++++++++++++++++++++++++++---------------
 src/DataSet_NameMap.h |  8 ++++++++
 2 files changed, 37 insertions(+), 15 deletions(-)

diff --git a/src/DataIO_Std.cpp b/src/DataIO_Std.cpp
index 3770cbd5c6..9314032c18 100644
--- a/src/DataIO_Std.cpp
+++ b/src/DataIO_Std.cpp
@@ -49,6 +49,7 @@ DataIO_Std::DataIO_Std() :
   dims_[2] = 0;
   SetValid( DataSet::PARAMETERS );
   SetValid( DataSet::STRINGVAR );
+  SetValid( DataSet::NAMEMAP );
 }
 
 static void PrintColumnError(int idx) {
@@ -96,7 +97,7 @@ void DataIO_Std::ReadHelp() {
           "\t\tbin {center|corner*}  : Coords specify bin centers or corners (default corners).\n"
           "\tvector         : Read data as vector: VX VY VZ [OX OY OZ]\n"
           "\tmat3x3         : Read data as 3x3 matrices: M(1,1) M(1,2) ... M(3,2) M(3,3)\n"
-          "\tnamemap        : Read data as atom name map ('#TgtAt Tgt RefAt Ref' or '#TgtAt RefAt')\n"
+          "\tnamemap        : Read data as atom name map ('#TgtAt Tgt RefAt Ref' or '#Tgt Ref')\n"
          );
 
 }
@@ -1056,20 +1057,20 @@ const
                   buffer.LineNumber(), ncols, ntokens);
         mprinterr("Error: '%s'\n", linebuffer);
         return 1;
-      } else {
-        std::string tgt, ref;
-        for (int col = 0; col != ntokens; col++) {
-          const char* ptr = buffer.NextToken();
-          if (col == tgtcol)
-            tgt.assign( ptr );
-          else if (col == refcol)
-            ref.assign( ptr );
-        }
-        // Skip mapping if tgt == ref
-        if (tgt != ref) {
-          mprintf("DEBUG: Map ref %s to tgt %s\n", ref.c_str(), tgt.c_str());
-          namemap->AddNameMap(ref, tgt);
-        }
+      }
+      // Read map line
+      std::string tgt, ref;
+      for (int col = 0; col != ntokens; col++) {
+        const char* ptr = buffer.NextToken();
+        if (col == tgtcol)
+          tgt.assign( ptr );
+        else if (col == refcol)
+          ref.assign( ptr );
+      }
+      // Skip mapping if tgt == ref
+      if (tgt != ref) {
+        mprintf("DEBUG: Map ref %s to tgt %s\n", ref.c_str(), tgt.c_str());
+        namemap->AddNameMap(ref, tgt);
       }
     } // END if not comment
     linebuffer = buffer.Line();
@@ -1314,6 +1315,19 @@ int DataIO_Std::WriteNameMap(CpptrajFile& file, DataSetList const& Sets) const {
               file.Filename().full(), (*ds)->legend());
     } else {
       DataSet_NameMap const& namemap = static_cast<DataSet_NameMap const&>( *(*ds) );
+      // Figure out column widths
+      int colwidth = 4;
+      for (DataSet_NameMap::const_iterator it = namemap.begin(); it != namemap.end(); ++it) {
+        if ( (int)it->first.len() > colwidth )
+          colwidth = it->first.len();
+        if ( (int)it->second.len() > colwidth )
+          colwidth = it->second.len();
+      }
+      // Write header
+      if (writeHeader_)
+        file.Printf("%-*s %-*s\n", colwidth, "#Tgt", colwidth, "Ref");
+      for (DataSet_NameMap::const_iterator it = namemap.begin(); it != namemap.end(); ++it)
+        file.Printf("%-*s %-*s\n", colwidth, *(it->second), colwidth, *(it->first));
     }
   }
   return 0;
diff --git a/src/DataSet_NameMap.h b/src/DataSet_NameMap.h
index 3760c73f10..1e9eb646d9 100644
--- a/src/DataSet_NameMap.h
+++ b/src/DataSet_NameMap.h
@@ -22,15 +22,23 @@ class DataSet_NameMap : public DataSet {
     int Sync(size_t, std::vector<int> const&, Parallel::Comm const&) { return 1; }
 #   endif
     // -------------------------------------------
+    /// Add mapping of newName to oldName
     void AddNameMap(NameType const& oldName, NameType const& newName) {
       nameMap_.insert( AmapPair(oldName, newName) );
     }
+    /// \return True if oldName was found in map and newName is set, false otherwise.
     bool GetName(NameType& newName, NameType const& oldName) const {
       AmapType::const_iterator it = nameMap_.find( oldName );
       if (it == nameMap_.end()) return false;
       newName = it->second;
       return true;
     }
+    /// Const iterator
+    typedef AmapType::const_iterator const_iterator;
+    /// Const iterator to beginning
+    const_iterator begin() const { return nameMap_.begin(); }
+    /// Const interator to end
+    const_iterator end()   const { return nameMap_.end(); }
   private:
     AmapType nameMap_;
 };

From 18cf01c5ec803326f0a9a769f23fd4c1ca39142c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 18 Jun 2024 10:38:44 -0400
Subject: [PATCH 0750/1492] Add namemap keyword to change atomname

---
 src/Exec_Change.cpp | 55 ++++++++++++++++++++++++++++++++++-----------
 src/Exec_Change.h   |  2 +-
 src/cpptrajdepend   |  2 +-
 3 files changed, 44 insertions(+), 15 deletions(-)

diff --git a/src/Exec_Change.cpp b/src/Exec_Change.cpp
index 1fc55b24a0..4aa3738e87 100644
--- a/src/Exec_Change.cpp
+++ b/src/Exec_Change.cpp
@@ -4,6 +4,7 @@
 #include "TypeNameHolder.h"
 #include "ParameterTypes.h"
 #include "DataSet_1D.h"
+#include "DataSet_NameMap.h"
 
 // Exec_Change::Help()
 void Exec_Change::Help() const
@@ -14,7 +15,7 @@ void Exec_Change::Help() const
           "\t  chainid of <mask> to <value> |\n"
           "\t  oresnums of <mask> min <range min> max <range max> |\n"
           "\t  icodes of <mask> min <char min> max <char max> resnum <#> |\n"
-          "\t  atomname from <mask> to <value> |\n"
+          "\t  atomname from <mask> {to <value>|namemap <mapset>} |\n"
           "\t  addbond <mask1> <mask2> [req <length> <rk> <force constant>] |\n"
           "\t  removebonds <mask1> [<mask2>] [out <file>] |\n"
           "\t  bondparm <mask1> [<mask2>] {setrk|scalerk|setreq|scalereq} <value> |\n"
@@ -84,7 +85,7 @@ Exec::RetType Exec_Change::Execute(CpptrajState& State, ArgList& argIn)
     case CHAINID  : err = ChangeChainID(*parm, argIn); break;
     case ORESNUMS : err = ChangeOresNums(*parm, argIn); break;
     case ICODES   : err = ChangeIcodes(*parm, argIn); break;
-    case ATOMNAME : err = ChangeAtomName(*parm, argIn); break;
+    case ATOMNAME : err = ChangeAtomName(*parm, argIn, State.DSL()); break;
     case ADDBOND  : err = AddBond(*parm, argIn); break;
     case REMOVEBONDS : err = RemoveBonds(State, *parm, argIn); break;
     case BONDPARM    : err = ChangeBondParameters(*parm, argIn); break;
@@ -319,16 +320,31 @@ const
 }
 
 // Exec_Change::ChangeAtomName()
-int Exec_Change::ChangeAtomName(Topology& topIn, ArgList& argIn)
+int Exec_Change::ChangeAtomName(Topology& topIn, ArgList& argIn, DataSetList const& dsl)
 const
 {
-  // Name to change to.
-  std::string name = argIn.GetStringKey("to");
-  if (name.empty()) {
-    mprinterr("Error: Specify atom name to change to ('to <name>').\n");
-    return 1;
+  // Get Name/Names to change to.
+  // Name map set.
+  DataSet_NameMap* namemap = 0;
+  std::string name = argIn.GetStringKey("namemap");
+  if (!name.empty()) {
+    DataSet* ds = dsl.FindSetOfType(name, DataSet::NAMEMAP);
+    if (ds == 0) {
+      mprinterr("Error: No name map set with name '%s' found.\n", name.c_str());
+      return 1;
+    }
+    namemap = static_cast<DataSet_NameMap*>( ds );
+  }
+  // Single name
+  NameType aname;
+  if (namemap == 0) {
+    name = argIn.GetStringKey("to");
+    if (name.empty()) {
+      mprinterr("Error: Specify atom name to change to ('to <name>').\n");
+      return 1;
+    }
+    aname = NameType( name );
   }
-  NameType aname( name );
   // Atoms to change
   std::string mexpr = argIn.GetStringKey("from");
   if (mexpr.empty()) {
@@ -342,10 +358,23 @@ const
     mprintf("Warning: No atoms selected by mask.\n");
     return 1;
   }
-  for (AtomMask::const_iterator it = mask.begin(); it != mask.end(); ++it)
-  {
-    mprintf("\tChanging atom %s to %s\n", topIn[*it].c_str(), *aname);
-    topIn.SetAtom(*it).SetName( aname );
+  if (namemap == 0) {
+    // Change to a single name
+    for (AtomMask::const_iterator it = mask.begin(); it != mask.end(); ++it)
+    {
+      mprintf("\tChanging atom %s to %s\n", topIn[*it].c_str(), *aname);
+      topIn.SetAtom(*it).SetName( aname );
+    }
+  } else {
+    // Use a name map
+    for (AtomMask::const_iterator it = mask.begin(); it != mask.end(); ++it)
+    {
+      bool nameMatch = namemap->GetName(aname, topIn[*it].Name());
+      if (nameMatch) {
+        mprintf("\tChanging atom %s to %s\n", topIn[*it].c_str(), *aname);
+        topIn.SetAtom(*it).SetName( aname );
+      }
+    }
   }
   return 0;
 }
diff --git a/src/Exec_Change.h b/src/Exec_Change.h
index 6236e64748..9fa5dc9424 100644
--- a/src/Exec_Change.h
+++ b/src/Exec_Change.h
@@ -19,7 +19,7 @@ class Exec_Change : public Exec {
     int ChangeOresNums(Topology&, ArgList&) const;
     int ChangeIcodes(Topology&, ArgList&) const;
     int ChangeChainID(Topology&, ArgList&) const;
-    int ChangeAtomName(Topology&, ArgList&) const;
+    int ChangeAtomName(Topology&, ArgList&, DataSetList const&) const;
     static inline int Setup1atomMask(AtomMask&, Topology const&, std::string const&);
     static inline int FindBondTypeIdx(Topology const&, BondArray const&, TypeNameHolder const&);
     int AddBond(Topology&, ArgList&) const;
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 5948bdda94..9ff4973688 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -302,7 +302,7 @@ Exec_Analyze.o : Exec_Analyze.cpp Action.h ActionList.h ActionState.h Analysis.h
 Exec_Build.o : Exec_Build.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/GB_Params.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/Creator.h Structure/Disulfide.h Structure/HisProt.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/StructureEnum.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Calc.o : Exec_Calc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Calc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_CatCrd.o : Exec_CatCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CatCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Change.o : Exec_Change.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Change.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Change.o : Exec_Change.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Change.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_ClusterMap.o : Exec_ClusterMap.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ClusterMap.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ClusterMap.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_CombineCoords.o : Exec_CombineCoords.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CombineCoords.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Commands.o : Exec_Commands.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Commands.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h

From 5326884e3ca77ac07022173093d50bd8ad4789f0 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 18 Jun 2024 11:35:59 -0400
Subject: [PATCH 0751/1492] Improve error message

---
 src/Mol2File.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Mol2File.cpp b/src/Mol2File.cpp
index 4409d10571..887e82272e 100644
--- a/src/Mol2File.cpp
+++ b/src/Mol2File.cpp
@@ -189,7 +189,7 @@ int Mol2File::Mol2Atom(Atom& atom, Residue& res, double* XYZ) {
     mol2resname = field6;
     mol2charge = field7;
   } else {
-    mprinterr("Error: Malformed mol2 line: %s\n", linebuffer_);
+    mprinterr("Error: Malformed mol2 line (%i fields read): %s\n", nread, linebuffer_);
     return 1;
   }
 

From 6f6fafa22bcd835dedc9ce89cc1cd722c11de3ef Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 18 Jun 2024 11:54:24 -0400
Subject: [PATCH 0752/1492] Re-enable copy of associated data when duplicating
 a unit. Allow updates to the PDB residue name map when duplicating a unit.

---
 src/DataIO_LeapRC.cpp | 21 ++++++++++++++++++---
 src/DataIO_LeapRC.h   |  4 ++++
 2 files changed, 22 insertions(+), 3 deletions(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 2fcaec6a8a..4446fb1ebb 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -308,7 +308,7 @@ const
 }*/
 
 /** Associate PDB residue name map with COORDS set. */ // TODO call every time a new unit is loaded?
-void DataIO_LeapRC::addPdbResMapToUnit(DataSet_Coords* unit, PdbResMapType const& prm)
+void DataIO_LeapRC::addPdbResMapToUnit(DataSet_Coords* unit, PdbResMapType const& prm, bool allowUpdate)
 const
 {
   // Does this unit already have associated ResId?
@@ -321,6 +321,11 @@ const
       resid.Ainfo();
       mprintf("\n");
     //}
+  } else if (allowUpdate) {
+    *ad = AssociatedData_ResId( prm.pdbName_, prm.termType_ );
+    mprintf("DEBUG: Updated unit %s resmap. ", unit->legend());
+    ad->Ainfo();
+    mprintf("\n");
   } else {
     // TODO check if map is different
     mprintf("DEBUG: Unit %s already has resmap. ", unit->legend());
@@ -329,6 +334,16 @@ const
   }
 }
 
+/** Associate PDB residue name map with COORDS set, no update allowed. */
+void DataIO_LeapRC::addPdbResMapToUnit(DataSet_Coords* unit, PdbResMapType const& prm) const {
+  addPdbResMapToUnit(unit, prm, false);
+}
+
+/** Associate PDB residue name map with COORDS set, allow update. */
+void DataIO_LeapRC::updatePdbResMapToUnit(DataSet_Coords* unit, PdbResMapType const& prm) const {
+  addPdbResMapToUnit(unit, prm, true);
+}
+
 /** LEaP addPdbResMap command. */
 int DataIO_LeapRC::AddPdbResMap(BufferedLine& infile, PdbResMapArray& pdbResMapIn)
 const
@@ -792,14 +807,14 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
             crd0.GetFrame(0, tmpFrm);
             crd1.SetCRD(0, tmpFrm );
             // Copy associated data
-            //crd1.CopyAssociatedDataFrom( crd0 );
+            crd1.CopyAssociatedDataFrom( crd0 );
             mprintf("DEBUG: Created unit set %s\n", crd1.legend());
             // See if there is a PDB residue name map
             for (PdbResMapArray::const_iterator it = pdbResMap_.begin();
                                                 it != pdbResMap_.end(); ++it)
             {
               if (it->unitName_ == line[0]) {
-                addPdbResMapToUnit( &crd1, *it );
+                updatePdbResMapToUnit( &crd1, *it );
                 break;
               }
             }
diff --git a/src/DataIO_LeapRC.h b/src/DataIO_LeapRC.h
index 6255d3b66c..fcd945e37b 100644
--- a/src/DataIO_LeapRC.h
+++ b/src/DataIO_LeapRC.h
@@ -40,7 +40,11 @@ class DataIO_LeapRC : public DataIO {
     int SaveAmberParm(std::string const&, ArgList&, DataSetList const& dsl) const;
     int Source(FileName const&, DataSetList&, std::string const&);
     /// Add PDB residue map to COORDS unit
+    void addPdbResMapToUnit(DataSet_Coords*, PdbResMapType const&, bool) const;
+    /// Add PDB residue map to COORDS unit, no update
     void addPdbResMapToUnit(DataSet_Coords*, PdbResMapType const&) const;
+    /// Add PDB residue map to COORDS unit, allow update
+    void updatePdbResMapToUnit(DataSet_Coords*, PdbResMapType const&) const;
     /// \return Previously loaded unit set with given name
     //DataSet* findUnit(std::string const&) const;
     /// Used to check if a parm/lib file was already loaded.

From e94e072a11422802af38460122a7e7e07533b099 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 20 Jun 2024 11:21:02 -0400
Subject: [PATCH 0753/1492] Hide debug info

---
 src/Structure/GenerateConnectivityArrays.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/Structure/GenerateConnectivityArrays.cpp b/src/Structure/GenerateConnectivityArrays.cpp
index bf95695dc1..96a1a8ac06 100644
--- a/src/Structure/GenerateConnectivityArrays.cpp
+++ b/src/Structure/GenerateConnectivityArrays.cpp
@@ -213,7 +213,7 @@ DihedralArray Cpptraj::Structure::GenerateImproperArray(std::vector<Residue> con
                                                         std::vector<Atom> const& atoms)
 {
   DihedralArray out;
-  int iidx = 0;
+//  int iidx = 0;
   for (std::vector<Residue>::const_iterator res = residues.begin(); res != residues.end(); ++res)
   {
     int start, end, offset;
@@ -229,7 +229,7 @@ DihedralArray Cpptraj::Structure::GenerateImproperArray(std::vector<Residue> con
               int iat1 = AJ.BondIdxArray()[bidx0];
               int iat2 = AJ.BondIdxArray()[bidx1];
               int iat4 = AJ.BondIdxArray()[bidx2];
-              mprintf("DEBUG: IMPROPER  i= %i  %i - %i - %i - %i (%i %i %i %i)\n", iidx++, iat1+1, iat2+1, iat3+1, iat4+1, iat1*3, iat2*3, iat3*3, iat4*3);
+//              mprintf("DEBUG: IMPROPER  i= %i  %i - %i - %i - %i (%i %i %i %i)\n", iidx++, iat1+1, iat2+1, iat3+1, iat4+1, iat1*3, iat2*3, iat3*3, iat4*3);
               int indices[3];
               indices[0] = iat1;
               indices[1] = iat2;

From 5d790c5efff45c4ee37a3936b45fe3de20871676 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 20 Jun 2024 15:08:26 -0400
Subject: [PATCH 0754/1492] Start RingFinder class

---
 src/Structure/RingFinder.cpp | 20 ++++++++++++++++++++
 src/Structure/RingFinder.h   | 22 ++++++++++++++++++++++
 2 files changed, 42 insertions(+)
 create mode 100644 src/Structure/RingFinder.cpp
 create mode 100644 src/Structure/RingFinder.h

diff --git a/src/Structure/RingFinder.cpp b/src/Structure/RingFinder.cpp
new file mode 100644
index 0000000000..3e1bb36993
--- /dev/null
+++ b/src/Structure/RingFinder.cpp
@@ -0,0 +1,20 @@
+#include "RingFinder.h"
+#include "../AtomMask.h"
+
+using namespace Cpptraj::Structure;
+
+/** CONSTRUCTOR */
+RingFinder::RingFinder()
+{}
+
+/** Init ring finder. */
+int RingFinder::InitRingFinder(ArgList& argIn) {
+  return 0;
+}
+
+/** Set up ring finder for topology. */
+int RingFinder::SetupRingFinder(Topology const& topIn) {
+  rings_.clear();
+
+  return 0;
+}
diff --git a/src/Structure/RingFinder.h b/src/Structure/RingFinder.h
new file mode 100644
index 0000000000..227f240df2
--- /dev/null
+++ b/src/Structure/RingFinder.h
@@ -0,0 +1,22 @@
+#ifndef INC_STRUCTURE_RINGFINDER_H
+#define INC_STRUCTURE_RINGFINDER_H
+#include <vector>
+class ArgList;
+class AtomMask;
+class Topology;
+namespace Cpptraj {
+namespace Structure {
+/// Used to look for rings in residues
+class RingFinder {
+  public:
+    RingFinder();
+    int InitRingFinder(ArgList&);
+    int SetupRingFinder(Topology const&);
+  private:
+    typedef std::vector<AtomMask> Marray;
+
+    Marray rings_; ///< Array of masks corresponding to rings
+};
+}
+}
+#endif

From dc5d29d510618d7d7baee25dac91bad22ddd24a8 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 20 Jun 2024 15:34:10 -0400
Subject: [PATCH 0755/1492] Add to make

---
 src/Structure/CMakeLists.txt  |  1 +
 src/Structure/RingFinder.cpp  | 38 +++++++++++++++++++++++++++++++++++
 src/Structure/structuredepend |  1 +
 src/Structure/structurefiles  |  1 +
 4 files changed, 41 insertions(+)

diff --git a/src/Structure/CMakeLists.txt b/src/Structure/CMakeLists.txt
index c807ddcc6b..6ed2f2d9c9 100644
--- a/src/Structure/CMakeLists.txt
+++ b/src/Structure/CMakeLists.txt
@@ -10,6 +10,7 @@ target_sources(cpptraj_common_obj PRIVATE
   ${CMAKE_CURRENT_LIST_DIR}/HisProt.cpp
   ${CMAKE_CURRENT_LIST_DIR}/InternalCoords.cpp
   ${CMAKE_CURRENT_LIST_DIR}/PdbCleaner.cpp
+  ${CMAKE_CURRENT_LIST_DIR}/RingFinder.cpp
   ${CMAKE_CURRENT_LIST_DIR}/StructureEnum.cpp
   ${CMAKE_CURRENT_LIST_DIR}/StructureRoutines.cpp
   ${CMAKE_CURRENT_LIST_DIR}/SugarBuilder.cpp
diff --git a/src/Structure/RingFinder.cpp b/src/Structure/RingFinder.cpp
index 3e1bb36993..48cdf658bd 100644
--- a/src/Structure/RingFinder.cpp
+++ b/src/Structure/RingFinder.cpp
@@ -1,5 +1,7 @@
 #include "RingFinder.h"
 #include "../AtomMask.h"
+#include "../CpptrajStdio.h"
+#include "../Topology.h"
 
 using namespace Cpptraj::Structure;
 
@@ -12,9 +14,45 @@ int RingFinder::InitRingFinder(ArgList& argIn) {
   return 0;
 }
 
+static inline void visitAtom( int at, int previousAt, int res, Topology const& topIn, std::vector<bool>& Visited )
+{
+  if (Visited[at]) {
+    mprintf("Already visited %s\n", topIn.AtomMaskName(at).c_str());
+  } else {
+    Visited[at] = true;
+    Atom const& currentAt = topIn[at];
+    for (Atom::bond_iterator bat = currentAt.bondbegin(); bat != currentAt.bondend(); ++bat)
+    {
+      if (*bat != previousAt && topIn[*bat].ResNum() == res) {
+        visitAtom( *bat, at, res, topIn, Visited );
+      }
+    }
+  }
+}
+
 /** Set up ring finder for topology. */
 int RingFinder::SetupRingFinder(Topology const& topIn) {
   rings_.clear();
 
+  std::vector<bool> Visited(topIn.Natom(), false); // TODO only have visited for residue atoms
+  // Do not look for rings that span residues.
+  for (int res = 0; res < topIn.Nres(); res++) {
+    Residue const& currentRes = topIn.Res(res);
+    int idx = 0;
+    for (int at = currentRes.FirstAtom(); at != currentRes.LastAtom(); at++, idx++)
+    {
+      mprintf("Starting at %s\n", topIn.AtomMaskName(at).c_str());
+      Visited.assign( topIn.Natom(), false );
+      Visited[at] = true;
+      Atom const& currentAt = topIn[at];
+      for (Atom::bond_iterator bat = currentAt.bondbegin(); bat != currentAt.bondend(); ++bat)
+      {
+        if (topIn[*bat].ResNum() == res) {
+          visitAtom( *bat, at, res, topIn, Visited );
+        }
+      }
+    }
+  }
+
   return 0;
 }
diff --git a/src/Structure/structuredepend b/src/Structure/structuredepend
index 123c931bc6..cebeb7ecdb 100644
--- a/src/Structure/structuredepend
+++ b/src/Structure/structuredepend
@@ -8,6 +8,7 @@ GenerateConnectivityArrays.o : GenerateConnectivityArrays.cpp ../Atom.h ../Const
 HisProt.o : HisProt.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h HisProt.h StructureRoutines.h
 InternalCoords.o : InternalCoords.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h InternalCoords.h
 PdbCleaner.o : PdbCleaner.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h PdbCleaner.h
+RingFinder.o : RingFinder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h RingFinder.h
 StructureEnum.o : StructureEnum.cpp StructureEnum.h
 StructureRoutines.o : StructureRoutines.cpp ../Atom.h ../CpptrajStdio.h ../NameType.h ../Residue.h ../SymbolExporting.h StructureRoutines.h
 Sugar.o : Sugar.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Sugar.h SugarToken.h
diff --git a/src/Structure/structurefiles b/src/Structure/structurefiles
index 7e78f88f07..fa6828389d 100644
--- a/src/Structure/structurefiles
+++ b/src/Structure/structurefiles
@@ -10,6 +10,7 @@ STRUCTURE_SOURCES= \
   HisProt.cpp \
   InternalCoords.cpp \
   PdbCleaner.cpp \
+  RingFinder.cpp \
   StructureEnum.cpp \
   StructureRoutines.cpp \
   SugarBuilder.cpp \

From f886b5c0d5e20e0c5ead9f13a6752341aeb0a6e9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 20 Jun 2024 15:47:24 -0400
Subject: [PATCH 0756/1492] Start testing out different ways of identifying
 rings

---
 src/Action_CheckStructure.cpp |  8 ++++++++
 src/Structure/RingFinder.cpp  | 24 +++++++++++++-----------
 src/cpptrajdepend             |  3 ++-
 3 files changed, 23 insertions(+), 12 deletions(-)

diff --git a/src/Action_CheckStructure.cpp b/src/Action_CheckStructure.cpp
index 601435e893..36fb819931 100644
--- a/src/Action_CheckStructure.cpp
+++ b/src/Action_CheckStructure.cpp
@@ -2,6 +2,7 @@
 
 #include "Action_CheckStructure.h"
 #include "CpptrajStdio.h"
+#include "Structure/RingFinder.h"
 #ifdef MPI
 # include "DataSet_integer.h"
 # include "DataSet_double.h"
@@ -159,6 +160,13 @@ Action::RetType Action_CheckStructure::Setup(ActionSetup& setup) {
   else
     mprintf("\timaging off.\n");
 
+  // Find rings
+  Cpptraj::Structure::RingFinder ringFinder;
+  if (ringFinder.SetupRingFinder(setup.Top())) {
+    mprinterr("Error: Could not set up ring finder.\n");
+    return Action::ERR;
+  }
+
   return Action::OK;
 }
 
diff --git a/src/Structure/RingFinder.cpp b/src/Structure/RingFinder.cpp
index 48cdf658bd..74d710ab21 100644
--- a/src/Structure/RingFinder.cpp
+++ b/src/Structure/RingFinder.cpp
@@ -14,17 +14,17 @@ int RingFinder::InitRingFinder(ArgList& argIn) {
   return 0;
 }
 
-static inline void visitAtom( int at, int previousAt, int res, Topology const& topIn, std::vector<bool>& Visited )
+static inline void visitAtom( int at, int previousAt, int res, Topology const& topIn, std::vector<bool>& Visited, int dist )
 {
   if (Visited[at]) {
-    mprintf("Already visited %s\n", topIn.AtomMaskName(at).c_str());
+    mprintf("Already visited %s %i\n", topIn.AtomMaskName(at).c_str(), dist);
   } else {
     Visited[at] = true;
     Atom const& currentAt = topIn[at];
     for (Atom::bond_iterator bat = currentAt.bondbegin(); bat != currentAt.bondend(); ++bat)
     {
-      if (*bat != previousAt && topIn[*bat].ResNum() == res) {
-        visitAtom( *bat, at, res, topIn, Visited );
+      if (*bat != previousAt && topIn[*bat].Nbonds() > 1 && topIn[*bat].ResNum() == res) {
+        visitAtom( *bat, at, res, topIn, Visited, dist+1 );
       }
     }
   }
@@ -41,14 +41,16 @@ int RingFinder::SetupRingFinder(Topology const& topIn) {
     int idx = 0;
     for (int at = currentRes.FirstAtom(); at != currentRes.LastAtom(); at++, idx++)
     {
-      mprintf("Starting at %s\n", topIn.AtomMaskName(at).c_str());
-      Visited.assign( topIn.Natom(), false );
-      Visited[at] = true;
       Atom const& currentAt = topIn[at];
-      for (Atom::bond_iterator bat = currentAt.bondbegin(); bat != currentAt.bondend(); ++bat)
-      {
-        if (topIn[*bat].ResNum() == res) {
-          visitAtom( *bat, at, res, topIn, Visited );
+      if (currentAt.Nbonds() > 1) {
+        mprintf("Starting at %s\n", topIn.AtomMaskName(at).c_str());
+        Visited.assign( topIn.Natom(), false );
+        Visited[at] = true;
+        for (Atom::bond_iterator bat = currentAt.bondbegin(); bat != currentAt.bondend(); ++bat)
+        {
+          if (topIn[*bat].Nbonds() > 1 && topIn[*bat].ResNum() == res) {
+            visitAtom( *bat, at, res, topIn, Visited, 1 );
+          }
         }
       }
     }
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 9ff4973688..bdfe9b7d53 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -15,7 +15,7 @@ Action_Box.o : Action_Box.cpp Action.h ActionState.h Action_Box.h ArgList.h Asso
 Action_Center.o : Action_Center.cpp Action.h ActionState.h Action_Center.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Action_Channel.o : Action_Channel.cpp Action.h ActionState.h Action_Channel.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Action_CheckChirality.o : Action_CheckChirality.cpp Action.h ActionState.h Action_CheckChirality.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h Structure/Chirality.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Action_CheckStructure.o : Action_CheckStructure.cpp Action.h ActionState.h Action_CheckStructure.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_integer.h DataSet_string.h Dimension.h DispatchObject.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_CheckStructure.o : Action_CheckStructure.cpp Action.h ActionState.h Action_CheckStructure.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_integer.h DataSet_string.h Dimension.h DispatchObject.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/RingFinder.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Action_Closest.o : Action_Closest.cpp Action.h ActionState.h ActionTopWriter.h Action_Closest.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h ImageRoutines.h ImageTypes.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h cuda_kernels/kernel_wrappers.cuh
 Action_ClusterDihedral.o : Action_ClusterDihedral.cpp Action.h ActionState.h Action_ClusterDihedral.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_integer.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 Action_Contacts.o : Action_Contacts.cpp Action.h ActionState.h Action_Contacts.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
@@ -467,6 +467,7 @@ Structure/GenerateConnectivityArrays.o : Structure/GenerateConnectivityArrays.cp
 Structure/HisProt.o : Structure/HisProt.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/HisProt.h Structure/StructureRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/InternalCoords.o : Structure/InternalCoords.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/InternalCoords.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/PdbCleaner.o : Structure/PdbCleaner.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/PdbCleaner.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Structure/RingFinder.o : Structure/RingFinder.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/RingFinder.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/StructureEnum.o : Structure/StructureEnum.cpp Structure/StructureEnum.h
 Structure/StructureRoutines.o : Structure/StructureRoutines.cpp Atom.h CpptrajStdio.h NameType.h Residue.h Structure/StructureRoutines.h SymbolExporting.h
 Structure/Sugar.o : Structure/Sugar.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h

From a737e810c27aa9c154d5f300cd2d7bf389841022 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 21 Jun 2024 10:14:00 -0400
Subject: [PATCH 0757/1492] Finish initial ring detection

---
 src/Structure/RingFinder.cpp | 94 ++++++++++++++++++++++++++++++++++--
 1 file changed, 89 insertions(+), 5 deletions(-)

diff --git a/src/Structure/RingFinder.cpp b/src/Structure/RingFinder.cpp
index 74d710ab21..4304832dee 100644
--- a/src/Structure/RingFinder.cpp
+++ b/src/Structure/RingFinder.cpp
@@ -14,22 +14,60 @@ int RingFinder::InitRingFinder(ArgList& argIn) {
   return 0;
 }
 
-static inline void visitAtom( int at, int previousAt, int res, Topology const& topIn, std::vector<bool>& Visited, int dist )
+static void visitAtom( int at, int previousAt, int res, Topology const& topIn, std::vector<bool>& Visited, std::vector<int>& startAtoms )
 {
   if (Visited[at]) {
-    mprintf("Already visited %s %i\n", topIn.AtomMaskName(at).c_str(), dist);
+    mprintf("Already visited %s %zu\n", topIn.AtomMaskName(at).c_str(), startAtoms.size());
+    startAtoms.push_back( at );
   } else {
     Visited[at] = true;
     Atom const& currentAt = topIn[at];
     for (Atom::bond_iterator bat = currentAt.bondbegin(); bat != currentAt.bondend(); ++bat)
     {
       if (*bat != previousAt && topIn[*bat].Nbonds() > 1 && topIn[*bat].ResNum() == res) {
-        visitAtom( *bat, at, res, topIn, Visited, dist+1 );
+        visitAtom( *bat, at, res, topIn, Visited, startAtoms );
       }
     }
   }
 }
 
+static std::vector<int> findCycle(int at, int tgtAt, int previousAt, int res, Topology const& topIn,
+                                  std::vector<bool> Visited, std::vector<int> ringAtoms)
+{
+  if (at == tgtAt) {
+    mprintf("CYCLE FOUND (%zu).", ringAtoms.size());
+    for (std::vector<int>::const_iterator it = ringAtoms.begin(); it != ringAtoms.end(); ++it)
+      mprintf(" %s", topIn.AtomMaskName(*it).c_str());
+    mprintf("\n");
+    return ringAtoms;
+  }
+  Visited[at] = true;
+  ringAtoms.push_back( at );
+  Atom const& currentAt = topIn[at];
+  typedef std::vector<int> Iarray;
+  std::vector<Iarray> ringAtArray( currentAt.Nbonds() );
+  std::vector<Iarray>::iterator ringIt = ringAtArray.begin();
+  std::vector<Iarray>::iterator shortestRing = ringAtArray.end();
+  for (Atom::bond_iterator bat = currentAt.bondbegin(); bat != currentAt.bondend(); ++bat, ++ringIt)
+  {
+    if (*bat != previousAt && topIn[*bat].Nbonds() > 1 &&
+        topIn[*bat].ResNum() == res && !Visited[*bat])
+    {
+      *ringIt = findCycle(*bat, tgtAt, at, res, topIn, Visited, ringAtoms);
+      if (!ringIt->empty()) {
+        if (shortestRing == ringAtArray.end())
+          shortestRing = ringIt;
+        else if (ringIt->size() < shortestRing->size())
+          shortestRing = ringIt;
+      }
+    }
+  }
+  // If multiple paths were found, return the shortest.
+  if (shortestRing != ringAtArray.end())
+    return *shortestRing;
+  return std::vector<int>();
+}
+
 /** Set up ring finder for topology. */
 int RingFinder::SetupRingFinder(Topology const& topIn) {
   rings_.clear();
@@ -37,8 +75,10 @@ int RingFinder::SetupRingFinder(Topology const& topIn) {
   std::vector<bool> Visited(topIn.Natom(), false); // TODO only have visited for residue atoms
   // Do not look for rings that span residues.
   for (int res = 0; res < topIn.Nres(); res++) {
+    std::vector<int> startAtoms;
     Residue const& currentRes = topIn.Res(res);
     int idx = 0;
+    // Initial scan for start atoms
     for (int at = currentRes.FirstAtom(); at != currentRes.LastAtom(); at++, idx++)
     {
       Atom const& currentAt = topIn[at];
@@ -49,12 +89,56 @@ int RingFinder::SetupRingFinder(Topology const& topIn) {
         for (Atom::bond_iterator bat = currentAt.bondbegin(); bat != currentAt.bondend(); ++bat)
         {
           if (topIn[*bat].Nbonds() > 1 && topIn[*bat].ResNum() == res) {
-            visitAtom( *bat, at, res, topIn, Visited, 1 );
+            visitAtom( *bat, at, res, topIn, Visited, startAtoms );
+            if (!startAtoms.empty()) break;
           }
         }
       }
+      if (!startAtoms.empty()) break;
     }
-  }
+    mprintf("Potential start atoms:");
+    for (std::vector<int>::const_iterator it = startAtoms.begin(); it != startAtoms.end(); ++it)
+      mprintf(" %s", topIn.AtomMaskName(*it).c_str());
+    mprintf("\n");
+    // Loop over potential start atoms
+    Visited.assign( topIn.Natom(), false );
+    for (std::vector<int>::const_iterator it = startAtoms.begin(); it != startAtoms.end(); ++it)
+    {
+      Atom const& startAt = topIn[*it];
+      // Need to have at least 2 bonds
+      if (startAt.Nbonds() > 1) {
+        // Loop over all other combinations of bonded atoms. Want to see if
+        // we can make a cycle from at1 to at2:
+        // at1 - startAt - at2 TODO check that bonded atoms are in the same residue
+        for (int bidx1 = 0; bidx1 != startAt.Nbonds(); bidx1++) {
+          int at1 = startAt.Bond(bidx1);
+          for (int bidx2 = bidx1 + 1; bidx2 != startAt.Nbonds(); bidx2++) {
+            int at2 = startAt.Bond(bidx2);
+            mprintf("Check <- %s - %s - %s ->\n",
+                    topIn.AtomMaskName(at1).c_str(),
+                    topIn.AtomMaskName(*it).c_str(),
+                    topIn.AtomMaskName(at2).c_str());
+            Visited[*it] = true;
+            std::vector<int> tmpAtoms;
+            std::vector<int> ringAtoms = findCycle(at1, at2, *it, res, topIn, Visited, tmpAtoms);
+            if (!ringAtoms.empty()) {
+              // Fill in the rest of the atoms
+              ringAtoms.push_back( at2 );
+              ringAtoms.push_back( *it );
+              // Mark the ring atoms as visited
+              Visited[at2] = true;
+              for (std::vector<int>::const_iterator rt = ringAtoms.begin(); rt != ringAtoms.end(); ++rt)
+                Visited[*rt] = true;
+              mprintf("RING FOUND (%zu): {", ringAtoms.size());
+              for (std::vector<int>::const_iterator rt = ringAtoms.begin(); rt != ringAtoms.end(); ++rt)
+                mprintf(" %s", topIn.AtomMaskName(*rt).c_str());
+              mprintf(" }\n");
+            }
+          } // END inner loop over bonds
+        } // END outer loop over bonds
+      } // END # bonds > 1
+    } // END loop over potential start atoms
+  } // END loop over all residues
 
   return 0;
 }

From 99cbbc7698c2f064c3f96de05d546307173cf8d8 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 21 Jun 2024 10:25:49 -0400
Subject: [PATCH 0758/1492] Clean up output, add print function

---
 src/Action_CheckStructure.cpp |  1 +
 src/Structure/RingFinder.cpp  | 76 ++++++++++++++++++++++-------------
 src/Structure/RingFinder.h    |  1 +
 3 files changed, 49 insertions(+), 29 deletions(-)

diff --git a/src/Action_CheckStructure.cpp b/src/Action_CheckStructure.cpp
index 36fb819931..37363f21fb 100644
--- a/src/Action_CheckStructure.cpp
+++ b/src/Action_CheckStructure.cpp
@@ -166,6 +166,7 @@ Action::RetType Action_CheckStructure::Setup(ActionSetup& setup) {
     mprinterr("Error: Could not set up ring finder.\n");
     return Action::ERR;
   }
+  ringFinder.PrintRings(setup.Top());
 
   return Action::OK;
 }
diff --git a/src/Structure/RingFinder.cpp b/src/Structure/RingFinder.cpp
index 4304832dee..aed66e45c4 100644
--- a/src/Structure/RingFinder.cpp
+++ b/src/Structure/RingFinder.cpp
@@ -17,7 +17,7 @@ int RingFinder::InitRingFinder(ArgList& argIn) {
 static void visitAtom( int at, int previousAt, int res, Topology const& topIn, std::vector<bool>& Visited, std::vector<int>& startAtoms )
 {
   if (Visited[at]) {
-    mprintf("Already visited %s %zu\n", topIn.AtomMaskName(at).c_str(), startAtoms.size());
+    //mprintf("Already visited %s %zu\n", topIn.AtomMaskName(at).c_str(), startAtoms.size());
     startAtoms.push_back( at );
   } else {
     Visited[at] = true;
@@ -83,7 +83,7 @@ int RingFinder::SetupRingFinder(Topology const& topIn) {
     {
       Atom const& currentAt = topIn[at];
       if (currentAt.Nbonds() > 1) {
-        mprintf("Starting at %s\n", topIn.AtomMaskName(at).c_str());
+        //mprintf("Starting at %s\n", topIn.AtomMaskName(at).c_str());
         Visited.assign( topIn.Natom(), false );
         Visited[at] = true;
         for (Atom::bond_iterator bat = currentAt.bondbegin(); bat != currentAt.bondend(); ++bat)
@@ -96,10 +96,12 @@ int RingFinder::SetupRingFinder(Topology const& topIn) {
       }
       if (!startAtoms.empty()) break;
     }
-    mprintf("Potential start atoms:");
-    for (std::vector<int>::const_iterator it = startAtoms.begin(); it != startAtoms.end(); ++it)
-      mprintf(" %s", topIn.AtomMaskName(*it).c_str());
-    mprintf("\n");
+    if (!startAtoms.empty()) {
+      mprintf("Potential start atoms:");
+      for (std::vector<int>::const_iterator it = startAtoms.begin(); it != startAtoms.end(); ++it)
+        mprintf(" %s", topIn.AtomMaskName(*it).c_str());
+      mprintf("\n");
+    }
     // Loop over potential start atoms
     Visited.assign( topIn.Natom(), false );
     for (std::vector<int>::const_iterator it = startAtoms.begin(); it != startAtoms.end(); ++it)
@@ -112,29 +114,34 @@ int RingFinder::SetupRingFinder(Topology const& topIn) {
         // at1 - startAt - at2 TODO check that bonded atoms are in the same residue
         for (int bidx1 = 0; bidx1 != startAt.Nbonds(); bidx1++) {
           int at1 = startAt.Bond(bidx1);
-          for (int bidx2 = bidx1 + 1; bidx2 != startAt.Nbonds(); bidx2++) {
-            int at2 = startAt.Bond(bidx2);
-            mprintf("Check <- %s - %s - %s ->\n",
-                    topIn.AtomMaskName(at1).c_str(),
-                    topIn.AtomMaskName(*it).c_str(),
-                    topIn.AtomMaskName(at2).c_str());
-            Visited[*it] = true;
-            std::vector<int> tmpAtoms;
-            std::vector<int> ringAtoms = findCycle(at1, at2, *it, res, topIn, Visited, tmpAtoms);
-            if (!ringAtoms.empty()) {
-              // Fill in the rest of the atoms
-              ringAtoms.push_back( at2 );
-              ringAtoms.push_back( *it );
-              // Mark the ring atoms as visited
-              Visited[at2] = true;
-              for (std::vector<int>::const_iterator rt = ringAtoms.begin(); rt != ringAtoms.end(); ++rt)
-                Visited[*rt] = true;
-              mprintf("RING FOUND (%zu): {", ringAtoms.size());
-              for (std::vector<int>::const_iterator rt = ringAtoms.begin(); rt != ringAtoms.end(); ++rt)
-                mprintf(" %s", topIn.AtomMaskName(*rt).c_str());
-              mprintf(" }\n");
-            }
-          } // END inner loop over bonds
+          if (topIn[at1].ResNum() == res) {
+            for (int bidx2 = bidx1 + 1; bidx2 != startAt.Nbonds(); bidx2++) {
+              int at2 = startAt.Bond(bidx2);
+              if (topIn[at2].ResNum() == res) {
+                //mprintf("Check <- %s - %s - %s ->\n",
+                //        topIn.AtomMaskName(at1).c_str(),
+                //        topIn.AtomMaskName(*it).c_str(),
+                //        topIn.AtomMaskName(at2).c_str());
+                Visited[*it] = true;
+                std::vector<int> tmpAtoms;
+                std::vector<int> ringAtoms = findCycle(at1, at2, *it, res, topIn, Visited, tmpAtoms);
+                if (!ringAtoms.empty()) {
+                  // Fill in the rest of the atoms
+                  ringAtoms.push_back( at2 );
+                  ringAtoms.push_back( *it );
+                  // Mark the ring atoms as visited
+                  Visited[at2] = true;
+                  for (std::vector<int>::const_iterator rt = ringAtoms.begin(); rt != ringAtoms.end(); ++rt)
+                    Visited[*rt] = true;
+                  mprintf("RING FOUND (%zu): {", ringAtoms.size());
+                  for (std::vector<int>::const_iterator rt = ringAtoms.begin(); rt != ringAtoms.end(); ++rt)
+                    mprintf(" %s", topIn.AtomMaskName(*rt).c_str());
+                  mprintf(" }\n");
+                  rings_.push_back( AtomMask(ringAtoms, topIn.Natom()) );
+                }
+              } // END bond atom 2 in residue
+            } // END inner loop over bonds
+          } // END bond atom 1 in residue
         } // END outer loop over bonds
       } // END # bonds > 1
     } // END loop over potential start atoms
@@ -142,3 +149,14 @@ int RingFinder::SetupRingFinder(Topology const& topIn) {
 
   return 0;
 }
+
+/** Print found rings to stdout. */
+void RingFinder::PrintRings(Topology const& topIn) const {
+  mprintf("\t%zu rings found.\n", rings_.size());
+  for (Marray::const_iterator mask = rings_.begin(); mask != rings_.end(); ++mask) {
+    mprintf("\t  %i atoms:", mask->Nselected());
+    for (AtomMask::const_iterator it = mask->begin(); it != mask->end(); ++it)
+      mprintf(" %s", topIn.AtomMaskName(*it).c_str());
+    mprintf("\n");
+  }
+}
diff --git a/src/Structure/RingFinder.h b/src/Structure/RingFinder.h
index 227f240df2..14a9a1c8ac 100644
--- a/src/Structure/RingFinder.h
+++ b/src/Structure/RingFinder.h
@@ -12,6 +12,7 @@ class RingFinder {
     RingFinder();
     int InitRingFinder(ArgList&);
     int SetupRingFinder(Topology const&);
+    void PrintRings(Topology const&) const;
   private:
     typedef std::vector<AtomMask> Marray;
 

From 7e2f5f70323114c8a1d494bcfba7923297d669f4 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 21 Jun 2024 11:20:43 -0400
Subject: [PATCH 0759/1492] Add atom mask to ring finder. Put in structure
 check

---
 src/Action_CheckStructure.cpp |  9 --------
 src/Structure/RingFinder.cpp  | 39 ++++++++++++++++++++++-------------
 src/Structure/RingFinder.h    |  2 +-
 src/Structure/structuredepend |  2 +-
 src/StructureCheck.cpp        |  7 +++++++
 src/StructureCheck.h          |  2 ++
 6 files changed, 36 insertions(+), 25 deletions(-)

diff --git a/src/Action_CheckStructure.cpp b/src/Action_CheckStructure.cpp
index 37363f21fb..601435e893 100644
--- a/src/Action_CheckStructure.cpp
+++ b/src/Action_CheckStructure.cpp
@@ -2,7 +2,6 @@
 
 #include "Action_CheckStructure.h"
 #include "CpptrajStdio.h"
-#include "Structure/RingFinder.h"
 #ifdef MPI
 # include "DataSet_integer.h"
 # include "DataSet_double.h"
@@ -160,14 +159,6 @@ Action::RetType Action_CheckStructure::Setup(ActionSetup& setup) {
   else
     mprintf("\timaging off.\n");
 
-  // Find rings
-  Cpptraj::Structure::RingFinder ringFinder;
-  if (ringFinder.SetupRingFinder(setup.Top())) {
-    mprinterr("Error: Could not set up ring finder.\n");
-    return Action::ERR;
-  }
-  ringFinder.PrintRings(setup.Top());
-
   return Action::OK;
 }
 
diff --git a/src/Structure/RingFinder.cpp b/src/Structure/RingFinder.cpp
index aed66e45c4..52a27f379a 100644
--- a/src/Structure/RingFinder.cpp
+++ b/src/Structure/RingFinder.cpp
@@ -1,5 +1,6 @@
 #include "RingFinder.h"
 #include "../AtomMask.h"
+#include "../CharMask.h"
 #include "../CpptrajStdio.h"
 #include "../Topology.h"
 
@@ -69,9 +70,11 @@ static std::vector<int> findCycle(int at, int tgtAt, int previousAt, int res, To
 }
 
 /** Set up ring finder for topology. */
-int RingFinder::SetupRingFinder(Topology const& topIn) {
+int RingFinder::SetupRingFinder(Topology const& topIn, AtomMask const& maskIn) {
   rings_.clear();
 
+  CharMask cmask( maskIn.ConvertToCharMask(), maskIn.Nselected() );
+
   std::vector<bool> Visited(topIn.Natom(), false); // TODO only have visited for residue atoms
   // Do not look for rings that span residues.
   for (int res = 0; res < topIn.Nres(); res++) {
@@ -81,20 +84,22 @@ int RingFinder::SetupRingFinder(Topology const& topIn) {
     // Initial scan for start atoms
     for (int at = currentRes.FirstAtom(); at != currentRes.LastAtom(); at++, idx++)
     {
-      Atom const& currentAt = topIn[at];
-      if (currentAt.Nbonds() > 1) {
-        //mprintf("Starting at %s\n", topIn.AtomMaskName(at).c_str());
-        Visited.assign( topIn.Natom(), false );
-        Visited[at] = true;
-        for (Atom::bond_iterator bat = currentAt.bondbegin(); bat != currentAt.bondend(); ++bat)
-        {
-          if (topIn[*bat].Nbonds() > 1 && topIn[*bat].ResNum() == res) {
-            visitAtom( *bat, at, res, topIn, Visited, startAtoms );
-            if (!startAtoms.empty()) break;
+      if (cmask.AtomInCharMask( at )) {
+        Atom const& currentAt = topIn[at];
+        if (currentAt.Nbonds() > 1) {
+          //mprintf("Starting at %s\n", topIn.AtomMaskName(at).c_str());
+          Visited.assign( topIn.Natom(), false );
+          Visited[at] = true;
+          for (Atom::bond_iterator bat = currentAt.bondbegin(); bat != currentAt.bondend(); ++bat)
+          {
+            if (topIn[*bat].Nbonds() > 1 && topIn[*bat].ResNum() == res) {
+              visitAtom( *bat, at, res, topIn, Visited, startAtoms );
+              if (!startAtoms.empty()) break;
+            }
           }
         }
+        if (!startAtoms.empty()) break;
       }
-      if (!startAtoms.empty()) break;
     }
     if (!startAtoms.empty()) {
       mprintf("Potential start atoms:");
@@ -106,6 +111,7 @@ int RingFinder::SetupRingFinder(Topology const& topIn) {
     Visited.assign( topIn.Natom(), false );
     for (std::vector<int>::const_iterator it = startAtoms.begin(); it != startAtoms.end(); ++it)
     {
+      if (!cmask.AtomInCharMask( *it )) continue;
       Atom const& startAt = topIn[*it];
       // Need to have at least 2 bonds
       if (startAt.Nbonds() > 1) {
@@ -133,11 +139,16 @@ int RingFinder::SetupRingFinder(Topology const& topIn) {
                   Visited[at2] = true;
                   for (std::vector<int>::const_iterator rt = ringAtoms.begin(); rt != ringAtoms.end(); ++rt)
                     Visited[*rt] = true;
+                  // Only add the ring if all atoms were found
+                  bool allfound = true;
                   mprintf("RING FOUND (%zu): {", ringAtoms.size());
-                  for (std::vector<int>::const_iterator rt = ringAtoms.begin(); rt != ringAtoms.end(); ++rt)
+                  for (std::vector<int>::const_iterator rt = ringAtoms.begin(); rt != ringAtoms.end(); ++rt) {
                     mprintf(" %s", topIn.AtomMaskName(*rt).c_str());
+                    if (!cmask.AtomInCharMask( *rt )) allfound = false;
+                  }
                   mprintf(" }\n");
-                  rings_.push_back( AtomMask(ringAtoms, topIn.Natom()) );
+                  if (allfound)
+                    rings_.push_back( AtomMask(ringAtoms, topIn.Natom()) );
                 }
               } // END bond atom 2 in residue
             } // END inner loop over bonds
diff --git a/src/Structure/RingFinder.h b/src/Structure/RingFinder.h
index 14a9a1c8ac..9897ef33c0 100644
--- a/src/Structure/RingFinder.h
+++ b/src/Structure/RingFinder.h
@@ -11,7 +11,7 @@ class RingFinder {
   public:
     RingFinder();
     int InitRingFinder(ArgList&);
-    int SetupRingFinder(Topology const&);
+    int SetupRingFinder(Topology const&, AtomMask const&);
     void PrintRings(Topology const&) const;
   private:
     typedef std::vector<AtomMask> Marray;
diff --git a/src/Structure/structuredepend b/src/Structure/structuredepend
index cebeb7ecdb..579b81f119 100644
--- a/src/Structure/structuredepend
+++ b/src/Structure/structuredepend
@@ -8,7 +8,7 @@ GenerateConnectivityArrays.o : GenerateConnectivityArrays.cpp ../Atom.h ../Const
 HisProt.o : HisProt.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h HisProt.h StructureRoutines.h
 InternalCoords.o : InternalCoords.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h InternalCoords.h
 PdbCleaner.o : PdbCleaner.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h PdbCleaner.h
-RingFinder.o : RingFinder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h RingFinder.h
+RingFinder.o : RingFinder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CharMask.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h RingFinder.h
 StructureEnum.o : StructureEnum.cpp StructureEnum.h
 StructureRoutines.o : StructureRoutines.cpp ../Atom.h ../CpptrajStdio.h ../NameType.h ../Residue.h ../SymbolExporting.h StructureRoutines.h
 Sugar.o : Sugar.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Sugar.h SugarToken.h
diff --git a/src/StructureCheck.cpp b/src/StructureCheck.cpp
index a71ca9c169..496165b026 100644
--- a/src/StructureCheck.cpp
+++ b/src/StructureCheck.cpp
@@ -166,6 +166,13 @@ int StructureCheck::Setup(Topology const& topIn, Box const& boxIn)
     mprintf("\tNot using exclusions.\n");
   // Sort bond list
   if (bondcheck_) std::sort(bondList_.begin(), bondList_.end());
+  // Find rings
+  if (rings_.SetupRingFinder(topIn, Mask1_)) {
+    mprinterr("Error: Could not set up ring finder.\n");
+    return 1;
+  }
+  rings_.PrintRings(topIn);
+
   return 0;
 }
 
diff --git a/src/StructureCheck.h b/src/StructureCheck.h
index 0c2b8680c1..cbcb3422ce 100644
--- a/src/StructureCheck.h
+++ b/src/StructureCheck.h
@@ -5,6 +5,7 @@
 #include "ExclusionArray.h"
 #include "AtomMask.h"
 #include "ParameterTypes.h"
+#include "Structure/RingFinder.h"
 // Forward declares
 class Topology;
 class CharMask;
@@ -97,6 +98,7 @@ class StructureCheck {
     PairList pairList_;     ///< Atom pair list
     ExclusionArray Excluded_; ///< Hold excluded atoms for pair list.
     ImageOption imageOpt_;    ///< Used to determine if imaging should be used.
+    Cpptraj::Structure::RingFinder rings_; ///< Used to find rings
     Parray bondList_;       ///< Array of bonds to check.
     AtomMask Mask1_;        ///< Mask of atoms to check.
     AtomMask Mask2_;        ///< Optional mask of atoms to check against atoms in Mask1

From 85f6a8706e99a1ea9ef66a8947f712de5feec3e1 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 21 Jun 2024 11:21:18 -0400
Subject: [PATCH 0760/1492] Add separate class for calculating least squares
 plane

---
 src/Structure/CMakeLists.txt        |   1 +
 src/Structure/LeastSquaresPlane.cpp | 135 ++++++++++++++++++++++++++++
 src/Structure/LeastSquaresPlane.h   |  25 ++++++
 src/Structure/structuredepend       |   1 +
 src/Structure/structurefiles        |   1 +
 src/cpptrajdepend                   |   8 +-
 6 files changed, 167 insertions(+), 4 deletions(-)
 create mode 100644 src/Structure/LeastSquaresPlane.cpp
 create mode 100644 src/Structure/LeastSquaresPlane.h

diff --git a/src/Structure/CMakeLists.txt b/src/Structure/CMakeLists.txt
index 6ed2f2d9c9..1c78302d80 100644
--- a/src/Structure/CMakeLists.txt
+++ b/src/Structure/CMakeLists.txt
@@ -9,6 +9,7 @@ target_sources(cpptraj_common_obj PRIVATE
   ${CMAKE_CURRENT_LIST_DIR}/GenerateConnectivityArrays.cpp
   ${CMAKE_CURRENT_LIST_DIR}/HisProt.cpp
   ${CMAKE_CURRENT_LIST_DIR}/InternalCoords.cpp
+  ${CMAKE_CURRENT_LIST_DIR}/LeastSquaresPlane.cpp
   ${CMAKE_CURRENT_LIST_DIR}/PdbCleaner.cpp
   ${CMAKE_CURRENT_LIST_DIR}/RingFinder.cpp
   ${CMAKE_CURRENT_LIST_DIR}/StructureEnum.cpp
diff --git a/src/Structure/LeastSquaresPlane.cpp b/src/Structure/LeastSquaresPlane.cpp
new file mode 100644
index 0000000000..da1c91ddfc
--- /dev/null
+++ b/src/Structure/LeastSquaresPlane.cpp
@@ -0,0 +1,135 @@
+#include "LeastSquaresPlane.h"
+#include "../AtomMask.h"
+#include "../Constants.h"
+#include "../Frame.h"
+#include <algorithm> // sort
+#include <cmath> // sqrt, acos, pow
+
+using namespace Cpptraj::Structure;
+
+/** CONSTRUCTOR */
+LeastSquaresPlane::LeastSquaresPlane()
+{}
+
+/** Solves a cubic equation: ax^3 + bx^2 + cx + d = 0 using "Cardan's formula" 
+  * (see: Bronstein, S.131f)
+  */
+double LeastSquaresPlane::solve_cubic_eq(double a, double b, double c, double d) {
+  const double one3 = 1.0 / 3.0;
+  const double one27 = 1.0 / 27.0;
+  double droot = 0;
+
+  double r, s, t;
+  double p, q, rho, phi;
+  double D, u, v;
+  std::vector<double> dtmp(3);
+
+  /* Coeff. for normal form x^3 + rx^2 + sx + t = 0 */
+  r = b / a;
+  s = c / a;
+  t = d / a;
+
+  /* Coeff. for red. eq. y^3 + py + q = 0 with y = x + r/3 bzw. (x = y - r/3) */
+  p = s - r * r * one3;
+  q = 2.0 * r * r * r * one27 - r * s * one3 + t;
+
+  /* Dummy variables */
+  rho = sqrt(-p * p * p * one27);
+  phi = acos(-q / (2.0 * rho));
+
+  /* Discriminante(?) */
+  D = pow((p * one3),3) + q * q * 0.25;
+
+  if(D > 0){ /* x real -> one real solution */
+    u = pow(-q * 0.5 + sqrt(D), one3);
+    v = -p / u * one3;
+    droot = (u + v) - r * one3;
+  } else { // D <= 0
+  /* three real solutions (d < 0) | one real solution + one real double solution or 
+                                                     one real triple solution (d = 0) */
+    dtmp[0] = 2.0 * pow(rho, one3) * cos(phi * one3) - r * one3;
+    dtmp[1] = 2.0 * pow(rho, one3) * cos((phi + Constants::TWOPI ) * one3) - r * one3;
+    dtmp[2] = 2.0 * pow(rho, one3) * cos((phi + Constants::FOURPI) * one3) - r * one3;
+
+    sort(dtmp.begin(), dtmp.end());
+
+    //qsort((void *) dtmp, (size_t) 3, sizeof(double), cmpdouble);
+    droot = dtmp[0];
+  }
+  return droot;
+}
+
+/** Calcs (least-squares best) plane through a series of points
+  * relative to their center of geom. (the latter has to be done outside this routine), 
+  * returns (normalized) coeff. for plane eq. ax + by + cz = 0
+  * following: Crystal Structure Analysis for Chem. and Biol.,
+  * Glusker, Lewis, Rossi, S. 460ff
+  */
+Vec3 LeastSquaresPlane::leastSquaresPlane(unsigned int n, const double* vcorr) {
+  double Xout, Yout, Zout;
+  if (n == 9) {  // Special case, only 3 coords
+    double x1 = vcorr[3] - vcorr[0];
+    double y1 = vcorr[4] - vcorr[1];
+    double z1 = vcorr[5] - vcorr[2];
+    double x2 = vcorr[6] - vcorr[3];
+    double y2 = vcorr[7] - vcorr[4];
+    double z2 = vcorr[8] - vcorr[5];
+
+    Xout = y1 * z2 - z1 * y2;
+    Yout = z1 * x2 - x1 * z2;
+    Zout = x1 * y2 - y1 * x2;
+  } else { // General case
+    // Calc Var.
+    double dSumXX = 0.0;
+    double dSumYY = 0.0;
+    double dSumZZ = 0.0;
+    double dSumXY = 0.0;
+    double dSumXZ = 0.0;
+    double dSumYZ = 0.0;
+
+    for (unsigned int i = 0; i < n; i+=3) {
+      dSumXX += vcorr[i  ] * vcorr[i  ];
+      dSumYY += vcorr[i+1] * vcorr[i+1];
+      dSumZZ += vcorr[i+2] * vcorr[i+2];
+
+      dSumXY += vcorr[i  ] * vcorr[i+1];
+      dSumXZ += vcorr[i  ] * vcorr[i+2];
+      dSumYZ += vcorr[i+1] * vcorr[i+2];
+    }
+
+    // Calc coeff. for -l^3 + o * l^2 + p * l + q = 0
+    double o = dSumXX + dSumYY + dSumZZ;
+    double p = pow(dSumXY,2) + pow(dSumXZ,2) + pow(dSumYZ,2) -
+               (dSumXX * dSumYY + dSumXX * dSumZZ + dSumYY * dSumZZ);
+    double q = dSumXX * dSumYY * dSumZZ + 2.0 * dSumXY * dSumXZ * dSumYZ -
+               (dSumXX * dSumYZ * dSumYZ + dSumYY * dSumXZ * dSumXZ + dSumZZ * dSumXY * dSumXY);
+
+    // Solve cubic eq.
+    double root = solve_cubic_eq(-1.0, o, p, q);
+
+    // Calc determinents
+    Xout = (dSumYY - root) * dSumXZ - dSumXY * dSumYZ;
+    Yout = (dSumXX - root) * dSumYZ - dSumXY * dSumXZ;
+    Zout =  dSumXY         * dSumXY - (dSumYY - root) * (dSumXX - root);
+  }
+  // Normalize
+  double dnorm = 1.0 / sqrt((Xout * Xout) + (Yout * Yout) + (Zout * Zout));
+  return Vec3(Xout * dnorm, Yout * dnorm, Zout * dnorm);
+}
+
+/** Calculate vector normal to plane passing through selected atoms. */
+void LeastSquaresPlane::CalcLeastSquaresPlane(Frame const& currentFrame, AtomMask const& maskIn)
+{
+  cxyz_ = currentFrame.VCenterOfMass(maskIn);
+  vcorr_.clear();
+  vcorr_.reserve( maskIn.Nselected() * 3 );
+  for (AtomMask::const_iterator atom = maskIn.begin(); atom != maskIn.end(); ++atom)
+  {
+    Vec3 XYZ = currentFrame.XYZ( *atom );
+    XYZ -= cxyz_;
+    vcorr_.push_back( XYZ[0] );
+    vcorr_.push_back( XYZ[1] );
+    vcorr_.push_back( XYZ[2] );
+  }
+  nxyz_ = leastSquaresPlane(vcorr_.size(), &vcorr_[0]);
+}
diff --git a/src/Structure/LeastSquaresPlane.h b/src/Structure/LeastSquaresPlane.h
new file mode 100644
index 0000000000..d1287143e5
--- /dev/null
+++ b/src/Structure/LeastSquaresPlane.h
@@ -0,0 +1,25 @@
+#ifndef INC_STRUCTURE_LEASTSQUARESPLANE_H
+#define INC_STRUCTURE_LEASTSQUARESPLANE_H
+#include <vector>
+#include "../Vec3.h"
+class Frame;
+class AtomMask;
+class Vec3;
+namespace Cpptraj {
+namespace Structure {
+/// Used to calculate the vector normal to a plane passing through a series of points
+class LeastSquaresPlane {
+  public:
+    LeastSquaresPlane();
+    void CalcLeastSquaresPlane(Frame const&, AtomMask const&);
+  private:
+    static double solve_cubic_eq(double,double,double,double);
+    static Vec3 leastSquaresPlane(unsigned int, const double*);
+
+    std::vector<double> vcorr_; ///< Will hold selected coordinates after centering.
+    Vec3 nxyz_;                 ///< Hold vector normal to the plane
+    Vec3 cxyz_;                 ///< Hold center (origin of vector normal to the plane)
+};
+}
+}
+#endif
diff --git a/src/Structure/structuredepend b/src/Structure/structuredepend
index 579b81f119..b0182d7138 100644
--- a/src/Structure/structuredepend
+++ b/src/Structure/structuredepend
@@ -7,6 +7,7 @@ FxnGroupBuilder.o : FxnGroupBuilder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ..
 GenerateConnectivityArrays.o : GenerateConnectivityArrays.cpp ../Atom.h ../Constants.h ../CpptrajStdio.h ../NameType.h ../ParameterTypes.h ../Residue.h ../SymbolExporting.h GenerateConnectivityArrays.h
 HisProt.o : HisProt.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h HisProt.h StructureRoutines.h
 InternalCoords.o : InternalCoords.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h InternalCoords.h
+LeastSquaresPlane.o : LeastSquaresPlane.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Unit.h ../Vec3.h LeastSquaresPlane.h
 PdbCleaner.o : PdbCleaner.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h PdbCleaner.h
 RingFinder.o : RingFinder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CharMask.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h RingFinder.h
 StructureEnum.o : StructureEnum.cpp StructureEnum.h
diff --git a/src/Structure/structurefiles b/src/Structure/structurefiles
index fa6828389d..f0efb128de 100644
--- a/src/Structure/structurefiles
+++ b/src/Structure/structurefiles
@@ -9,6 +9,7 @@ STRUCTURE_SOURCES= \
   GenerateConnectivityArrays.cpp \
   HisProt.cpp \
   InternalCoords.cpp \
+  LeastSquaresPlane.cpp \
   PdbCleaner.cpp \
   RingFinder.cpp \
   StructureEnum.cpp \
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index bdfe9b7d53..6c4d94a7fd 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -191,7 +191,7 @@ CmapParmHolder.o : CmapParmHolder.cpp CmapParmHolder.h Constants.h CpptrajStdio.
 Cmd.o : Cmd.cpp Cmd.h DispatchObject.h
 CmdInput.o : CmdInput.cpp CmdInput.h StringRoutines.h
 CmdList.o : CmdList.cpp Cmd.h CmdList.h DispatchObject.h
-Command.o : Command.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h ActionTopWriter.h Action_Align.h Action_Angle.h Action_AreaPerMol.h Action_AtomMap.h Action_AtomicCorr.h Action_AtomicFluct.h Action_AutoImage.h Action_Average.h Action_AvgBox.h Action_Bounds.h Action_Box.h Action_Center.h Action_Channel.h Action_CheckChirality.h Action_CheckStructure.h Action_Closest.h Action_ClusterDihedral.h Action_Contacts.h Action_CreateCrd.h Action_CreateReservoir.h Action_DNAionTracker.h Action_DSSP.h Action_Density.h Action_Diffusion.h Action_Dihedral.h Action_DihedralRMS.h Action_Dipole.h Action_DistRmsd.h Action_Distance.h Action_Energy.h Action_Esander.h Action_FilterByData.h Action_FixAtomOrder.h Action_FixImagedBonds.h Action_GIST.h Action_Grid.h Action_GridFreeEnergy.h Action_HydrogenBond.h Action_Image.h Action_InfraredSpectrum.h Action_Jcoupling.h Action_Keep.h Action_LESsplit.h Action_LIE.h Action_LipidOrder.h Action_MakeStructure.h Action_Mask.h Action_Matrix.h Action_MinImage.h Action_MinMaxDist.h Action_Molsurf.h Action_MultiDihedral.h Action_MultiPucker.h Action_MultiVector.h Action_NAstruct.h Action_NMRrst.h Action_NativeContacts.h Action_OrderParameter.h Action_Outtraj.h Action_PairDist.h Action_Pairwise.h Action_Principal.h Action_Projection.h Action_Pucker.h Action_Radgyr.h Action_Radial.h Action_RandomizeIons.h Action_Remap.h Action_ReplicateCell.h Action_Rmsd.h Action_Rotate.h Action_RunningAvg.h Action_STFC_Diffusion.h Action_Scale.h Action_SetVelocity.h Action_Spam.h Action_Strip.h Action_Surf.h Action_SymmetricRmsd.h Action_Temperature.h Action_Time.h Action_ToroidalDiffusion.h Action_Translate.h Action_Unstrip.h Action_Unwrap.h Action_Vector.h Action_VelocityAutoCorr.h Action_Volmap.h Action_Volume.h Action_Watershell.h Action_XtalSymm.h Analysis.h AnalysisList.h AnalysisState.h Analysis_AmdBias.h Analysis_AutoCorr.h Analysis_Average.h Analysis_CalcDiffusion.h Analysis_Clustering.h Analysis_ConstantPHStats.h Analysis_Corr.h Analysis_CrankShaft.h Analysis_CrdFluct.h Analysis_CrossCorr.h Analysis_CurveFit.h Analysis_Divergence.h Analysis_EvalPlateau.h Analysis_FFT.h Analysis_HausdorffDistance.h Analysis_Hist.h Analysis_IRED.h Analysis_Integrate.h Analysis_KDE.h Analysis_Lifetime.h Analysis_LowestCurve.h Analysis_Matrix.h Analysis_MeltCurve.h Analysis_Modes.h Analysis_MultiHist.h Analysis_Multicurve.h Analysis_Overlap.h Analysis_PhiPsi.h Analysis_Project.h Analysis_Regression.h Analysis_RemLog.h Analysis_Rms2d.h Analysis_RmsAvgCorr.h Analysis_Rotdif.h Analysis_RunningAvg.h Analysis_Slope.h Analysis_Spline.h Analysis_State.h Analysis_Statistics.h Analysis_TI.h Analysis_TICA.h Analysis_Timecorr.h Analysis_VectorMath.h Analysis_Wavelet.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h AxisType.h BaseIOtype.h Box.h BoxArgs.h BufferedLine.h CharMask.h Cluster/Algorithm.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Control.h Cluster/DrawGraph.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Sieve.h Cluster/Silhouette.h ClusterMap.h CmapParmHolder.h Cmd.h CmdInput.h CmdList.h Command.h CompactFrameArray.h ComplexArray.h Constants.h Constraints.h ControlBlock.h ControlBlock_For.h CoordinateInfo.h Corr.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_RemLog.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h Deprecated.h DiffusionResults.h DihedralSearch.h Dimension.h DispatchObject.h Energy.h Energy_Sander.h EnsembleIn.h EnsembleOutList.h Ewald.h EwaldOptions.h Ewald_ParticleMesh.h ExclusionArray.h Exec.h Exec_AddMissingRes.h Exec_Analyze.h Exec_Build.h Exec_Calc.h Exec_CatCrd.h Exec_Change.h Exec_ClusterMap.h Exec_CombineCoords.h Exec_Commands.h Exec_CompareClusters.h Exec_CompareEnergy.h Exec_CompareTop.h Exec_CrdAction.h Exec_CrdOut.h Exec_CrdTransform.h Exec_CreateSet.h Exec_DataFile.h Exec_DataFilter.h Exec_DataSetCmd.h Exec_Desc.h Exec_Emin.h Exec_ExtendedComparison.h Exec_Flatten.h Exec_GenerateAmberRst.h Exec_Graft.h Exec_Help.h Exec_HmassRepartition.h Exec_LoadCrd.h Exec_LoadTraj.h Exec_ParallelAnalysis.h Exec_ParmBox.h Exec_ParmSolvent.h Exec_ParmStrip.h Exec_ParmWrite.h Exec_ParseTiming.h Exec_PermuteDihedrals.h Exec_Precision.h Exec_PrepareForLeap.h Exec_PrintData.h Exec_Random.h Exec_ReadData.h Exec_ReadEnsembleData.h Exec_ReadInput.h Exec_RotateDihedral.h Exec_RunAnalysis.h Exec_ScaleDihedralK.h Exec_Sequence.h Exec_SequenceAlign.h Exec_Set.h Exec_Show.h Exec_SortEnsembleData.h Exec_Source.h Exec_SplitCoords.h Exec_System.h Exec_Top.h Exec_Traj.h Exec_UpdateParameters.h Exec_ViewRst.h Exec_Zmatrix.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h GIST_PME.h Grid.h GridAction.h GridBin.h GridMover.h HistBin.h Hungarian.h ImageOption.h ImageTypes.h InputTrajCommon.h InteractionData.h MapAtom.h MaskArray.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h OnlineVarT.h OutputTrajCommon.h PDBfile.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PubFFT.h Pucker.h Pucker_PuckerMask.h Pucker_PuckerSearch.h Pucker_PuckerToken.h RPNcalc.h Random.h Range.h ReferenceAction.h ReferenceFrame.h RemdReservoirNC.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h SplineFxnTable.h StructureCheck.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h cuda_kernels/GistCudaSetup.cuh helpme_standalone.h molsurf.h
+Command.o : Command.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h ActionTopWriter.h Action_Align.h Action_Angle.h Action_AreaPerMol.h Action_AtomMap.h Action_AtomicCorr.h Action_AtomicFluct.h Action_AutoImage.h Action_Average.h Action_AvgBox.h Action_Bounds.h Action_Box.h Action_Center.h Action_Channel.h Action_CheckChirality.h Action_CheckStructure.h Action_Closest.h Action_ClusterDihedral.h Action_Contacts.h Action_CreateCrd.h Action_CreateReservoir.h Action_DNAionTracker.h Action_DSSP.h Action_Density.h Action_Diffusion.h Action_Dihedral.h Action_DihedralRMS.h Action_Dipole.h Action_DistRmsd.h Action_Distance.h Action_Energy.h Action_Esander.h Action_FilterByData.h Action_FixAtomOrder.h Action_FixImagedBonds.h Action_GIST.h Action_Grid.h Action_GridFreeEnergy.h Action_HydrogenBond.h Action_Image.h Action_InfraredSpectrum.h Action_Jcoupling.h Action_Keep.h Action_LESsplit.h Action_LIE.h Action_LipidOrder.h Action_MakeStructure.h Action_Mask.h Action_Matrix.h Action_MinImage.h Action_MinMaxDist.h Action_Molsurf.h Action_MultiDihedral.h Action_MultiPucker.h Action_MultiVector.h Action_NAstruct.h Action_NMRrst.h Action_NativeContacts.h Action_OrderParameter.h Action_Outtraj.h Action_PairDist.h Action_Pairwise.h Action_Principal.h Action_Projection.h Action_Pucker.h Action_Radgyr.h Action_Radial.h Action_RandomizeIons.h Action_Remap.h Action_ReplicateCell.h Action_Rmsd.h Action_Rotate.h Action_RunningAvg.h Action_STFC_Diffusion.h Action_Scale.h Action_SetVelocity.h Action_Spam.h Action_Strip.h Action_Surf.h Action_SymmetricRmsd.h Action_Temperature.h Action_Time.h Action_ToroidalDiffusion.h Action_Translate.h Action_Unstrip.h Action_Unwrap.h Action_Vector.h Action_VelocityAutoCorr.h Action_Volmap.h Action_Volume.h Action_Watershell.h Action_XtalSymm.h Analysis.h AnalysisList.h AnalysisState.h Analysis_AmdBias.h Analysis_AutoCorr.h Analysis_Average.h Analysis_CalcDiffusion.h Analysis_Clustering.h Analysis_ConstantPHStats.h Analysis_Corr.h Analysis_CrankShaft.h Analysis_CrdFluct.h Analysis_CrossCorr.h Analysis_CurveFit.h Analysis_Divergence.h Analysis_EvalPlateau.h Analysis_FFT.h Analysis_HausdorffDistance.h Analysis_Hist.h Analysis_IRED.h Analysis_Integrate.h Analysis_KDE.h Analysis_Lifetime.h Analysis_LowestCurve.h Analysis_Matrix.h Analysis_MeltCurve.h Analysis_Modes.h Analysis_MultiHist.h Analysis_Multicurve.h Analysis_Overlap.h Analysis_PhiPsi.h Analysis_Project.h Analysis_Regression.h Analysis_RemLog.h Analysis_Rms2d.h Analysis_RmsAvgCorr.h Analysis_Rotdif.h Analysis_RunningAvg.h Analysis_Slope.h Analysis_Spline.h Analysis_State.h Analysis_Statistics.h Analysis_TI.h Analysis_TICA.h Analysis_Timecorr.h Analysis_VectorMath.h Analysis_Wavelet.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h AxisType.h BaseIOtype.h Box.h BoxArgs.h BufferedLine.h CharMask.h Cluster/Algorithm.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Control.h Cluster/DrawGraph.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Sieve.h Cluster/Silhouette.h ClusterMap.h CmapParmHolder.h Cmd.h CmdInput.h CmdList.h Command.h CompactFrameArray.h ComplexArray.h Constants.h Constraints.h ControlBlock.h ControlBlock_For.h CoordinateInfo.h Corr.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_RemLog.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h Deprecated.h DiffusionResults.h DihedralSearch.h Dimension.h DispatchObject.h Energy.h Energy_Sander.h EnsembleIn.h EnsembleOutList.h Ewald.h EwaldOptions.h Ewald_ParticleMesh.h ExclusionArray.h Exec.h Exec_AddMissingRes.h Exec_Analyze.h Exec_Build.h Exec_Calc.h Exec_CatCrd.h Exec_Change.h Exec_ClusterMap.h Exec_CombineCoords.h Exec_Commands.h Exec_CompareClusters.h Exec_CompareEnergy.h Exec_CompareTop.h Exec_CrdAction.h Exec_CrdOut.h Exec_CrdTransform.h Exec_CreateSet.h Exec_DataFile.h Exec_DataFilter.h Exec_DataSetCmd.h Exec_Desc.h Exec_Emin.h Exec_ExtendedComparison.h Exec_Flatten.h Exec_GenerateAmberRst.h Exec_Graft.h Exec_Help.h Exec_HmassRepartition.h Exec_LoadCrd.h Exec_LoadTraj.h Exec_ParallelAnalysis.h Exec_ParmBox.h Exec_ParmSolvent.h Exec_ParmStrip.h Exec_ParmWrite.h Exec_ParseTiming.h Exec_PermuteDihedrals.h Exec_Precision.h Exec_PrepareForLeap.h Exec_PrintData.h Exec_Random.h Exec_ReadData.h Exec_ReadEnsembleData.h Exec_ReadInput.h Exec_RotateDihedral.h Exec_RunAnalysis.h Exec_ScaleDihedralK.h Exec_Sequence.h Exec_SequenceAlign.h Exec_Set.h Exec_Show.h Exec_SortEnsembleData.h Exec_Source.h Exec_SplitCoords.h Exec_System.h Exec_Top.h Exec_Traj.h Exec_UpdateParameters.h Exec_ViewRst.h Exec_Zmatrix.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h GIST_PME.h Grid.h GridAction.h GridBin.h GridMover.h HistBin.h Hungarian.h ImageOption.h ImageTypes.h InputTrajCommon.h InteractionData.h MapAtom.h MaskArray.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h OnlineVarT.h OutputTrajCommon.h PDBfile.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PubFFT.h Pucker.h Pucker_PuckerMask.h Pucker_PuckerSearch.h Pucker_PuckerToken.h RPNcalc.h Random.h Range.h ReferenceAction.h ReferenceFrame.h RemdReservoirNC.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h SplineFxnTable.h Structure/RingFinder.h StructureCheck.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h cuda_kernels/GistCudaSetup.cuh helpme_standalone.h molsurf.h
 CompactFrameArray.o : CompactFrameArray.cpp Box.h CompactFrameArray.h CoordinateInfo.h CpptrajStdio.h Matrix_3x3.h Parallel.h ReplicaDimArray.h Vec3.h
 ComplexArray.o : ComplexArray.cpp ArrayIterator.h ComplexArray.h
 Constraints.o : Constraints.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h CharMask.h CmapParmHolder.h Constants.h Constraints.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
@@ -332,7 +332,7 @@ Exec_ParmSolvent.o : Exec_ParmSolvent.cpp Action.h ActionList.h ActionState.h An
 Exec_ParmStrip.o : Exec_ParmStrip.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmStrip.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_ParmWrite.o : Exec_ParmWrite.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmWrite.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_ParseTiming.o : Exec_ParseTiming.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParseTiming.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_PermuteDihedrals.o : Exec_PermuteDihedrals.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h DistRoutines.h EnsembleIn.h EnsembleOutList.h ExclusionArray.h Exec.h Exec_PermuteDihedrals.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Exec_PermuteDihedrals.o : Exec_PermuteDihedrals.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h DistRoutines.h EnsembleIn.h EnsembleOutList.h ExclusionArray.h Exec.h Exec_PermuteDihedrals.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/RingFinder.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Precision.o : Exec_Precision.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Precision.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_PrepareForLeap.o : Exec_PrepareForLeap.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_PrepareForLeap.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h LeapInterface.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h Remote.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/Disulfide.h Structure/HisProt.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Exec_PrintData.o : Exec_PrintData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_PrintData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
@@ -467,7 +467,7 @@ Structure/GenerateConnectivityArrays.o : Structure/GenerateConnectivityArrays.cp
 Structure/HisProt.o : Structure/HisProt.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/HisProt.h Structure/StructureRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/InternalCoords.o : Structure/InternalCoords.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/InternalCoords.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/PdbCleaner.o : Structure/PdbCleaner.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/PdbCleaner.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Structure/RingFinder.o : Structure/RingFinder.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/RingFinder.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Structure/RingFinder.o : Structure/RingFinder.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/RingFinder.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/StructureEnum.o : Structure/StructureEnum.cpp Structure/StructureEnum.h
 Structure/StructureRoutines.o : Structure/StructureRoutines.cpp Atom.h CpptrajStdio.h NameType.h Residue.h Structure/StructureRoutines.h SymbolExporting.h
 Structure/Sugar.o : Structure/Sugar.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
@@ -475,7 +475,7 @@ Structure/SugarBuilder.o : Structure/SugarBuilder.cpp ArgList.h Atom.h AtomMap.h
 Structure/SugarLinkAtoms.o : Structure/SugarLinkAtoms.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/LinkAtom.h Structure/SugarLinkAtoms.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/SugarToken.o : Structure/SugarToken.cpp ArgList.h CpptrajStdio.h Structure/SugarToken.h
 Structure/Zmatrix.o : Structure/Zmatrix.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-StructureCheck.o : StructureCheck.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h ExclusionArray.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StructureCheck.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+StructureCheck.o : StructureCheck.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h ExclusionArray.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/RingFinder.h StructureCheck.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 StructureMapper.o : StructureMapper.cpp AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Chirality.h Structure/StructureEnum.h StructureMapper.h SymbolExporting.h TextFormat.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 SymmetricRmsdCalc.o : SymmetricRmsdCalc.cpp ArrayIterator.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h Hungarian.h ImageOption.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 TextBlockBuffer.o : TextBlockBuffer.cpp BufferedLine.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Parallel.h TextBlockBuffer.h

From b2dabd7cae038911acdb9200899e288979e5e780 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 21 Jun 2024 11:29:08 -0400
Subject: [PATCH 0761/1492] Use LeastSquaresPlane in Action_Vector

---
 src/Action_Vector.cpp               | 139 +---------------------------
 src/Action_Vector.h                 |   6 +-
 src/Structure/LeastSquaresPlane.cpp |   2 +-
 src/Structure/LeastSquaresPlane.h   |   4 +
 src/cpptrajdepend                   |   5 +-
 5 files changed, 13 insertions(+), 143 deletions(-)

diff --git a/src/Action_Vector.cpp b/src/Action_Vector.cpp
index def85647e7..a6e40d6465 100644
--- a/src/Action_Vector.cpp
+++ b/src/Action_Vector.cpp
@@ -1,6 +1,4 @@
-#include <cmath>
-#include <algorithm> // sort
-#include "Constants.h" // PI
+#include <cmath> //sqrt
 #include "Action_Vector.h"
 #include "CpptrajStdio.h"
 #include "DistRoutines.h" // MinImagedVec, includes Matrix_3x3 for principal
@@ -12,7 +10,6 @@ Action_Vector::Action_Vector() :
   Vec_(0),
   Magnitude_(0),
   gridSet_(0),
-  vcorr_(0),
   ptrajoutput_(false),
   needBoxInfo_(false),
   CurrentParm_(0),
@@ -41,11 +38,6 @@ void Action_Vector::Help() const {
           "    force            : Store force of atoms in <mask1> (requires forces).\n");
 }
 
-// DESTRUCTOR
-Action_Vector::~Action_Vector() {
-  if (vcorr_!=0) delete[] vcorr_;
-}
-
 const char* Action_Vector::ModeString_[] = {
   "NO_OP", "Principal X", "Principal Y", "Principal Z",
   "Dipole", "Box", "Mask",
@@ -242,12 +234,6 @@ Action::RetType Action_Vector::Setup(ActionSetup& setup) {
     }
   }
 
-  // Allocate space for CORRPLANE. 
-  if (mode_ == CORRPLANE) {
-    if (vcorr_!=0) delete[] vcorr_;
-    vcorr_ = new double[ 3 * mask_.Nselected() ];
-  }
-
   // Setup mask 2
   if (mask2_.MaskStringSet()) {
     if (setup.Top().SetupIntegerMask(mask2_)) return Action::ERR;
@@ -262,115 +248,7 @@ Action::RetType Action_Vector::Setup(ActionSetup& setup) {
 }
 
 // -----------------------------------------------------------------------------
-// Action_Vector::solve_cubic_eq()
-/** Solves a cubic equation: ax^3 + bx^2 + cx + d = 0 using "Cardan's formula" 
-  * (see: Bronstein, S.131f)
-  */
-double Action_Vector::solve_cubic_eq(double a, double b, double c, double d) {
-  const double one3 = 1.0 / 3.0;
-  const double one27 = 1.0 / 27.0;
-  double droot = 0;
-
-  double r, s, t;
-  double p, q, rho, phi;
-  double D, u, v;
-  std::vector<double> dtmp(3);
-
-  /* Coeff. for normal form x^3 + rx^2 + sx + t = 0 */
-  r = b / a;
-  s = c / a;
-  t = d / a;
-
-  /* Coeff. for red. eq. y^3 + py + q = 0 with y = x + r/3 bzw. (x = y - r/3) */
-  p = s - r * r * one3;
-  q = 2.0 * r * r * r * one27 - r * s * one3 + t;
-
-  /* Dummy variables */
-  rho = sqrt(-p * p * p * one27);
-  phi = acos(-q / (2.0 * rho));
-
-  /* Discriminante(?) */
-  D = pow((p * one3),3) + q * q * 0.25;
-
-  if(D > 0){ /* x real -> one real solution */
-    u = pow(-q * 0.5 + sqrt(D), one3);
-    v = -p / u * one3;
-    droot = (u + v) - r * one3;
-  } else { // D <= 0
-  /* three real solutions (d < 0) | one real solution + one real double solution or 
-                                                     one real triple solution (d = 0) */
-    dtmp[0] = 2.0 * pow(rho, one3) * cos(phi * one3) - r * one3;
-    dtmp[1] = 2.0 * pow(rho, one3) * cos((phi + Constants::TWOPI ) * one3) - r * one3;
-    dtmp[2] = 2.0 * pow(rho, one3) * cos((phi + Constants::FOURPI) * one3) - r * one3;
-
-    sort(dtmp.begin(), dtmp.end());
-
-    //qsort((void *) dtmp, (size_t) 3, sizeof(double), cmpdouble);
-    droot = dtmp[0];
-  }
-  return droot;
-}
-
-// Action_Vector::leastSquaresPlane()
-/** Calcs (least-squares best) plane through a series of points
-  * relative to their center of geom. (the latter has to be done outside this routine), 
-  * returns (normalized) coeff. for plane eq. ax + by + cz = 0
-  * following: Crystal Structure Analysis for Chem. and Biol.,
-  * Glusker, Lewis, Rossi, S. 460ff
-  */
-Vec3 Action_Vector::leastSquaresPlane(int n, const double* vcorr) {
-  double Xout, Yout, Zout;
-  if (n == 9) {  // Special case, only 3 coords
-    double x1 = vcorr[3] - vcorr[0];
-    double y1 = vcorr[4] - vcorr[1];
-    double z1 = vcorr[5] - vcorr[2];
-    double x2 = vcorr[6] - vcorr[3];
-    double y2 = vcorr[7] - vcorr[4];
-    double z2 = vcorr[8] - vcorr[5];
-
-    Xout = y1 * z2 - z1 * y2;
-    Yout = z1 * x2 - x1 * z2;
-    Zout = x1 * y2 - y1 * x2;
-  } else { // General case
-    // Calc Var.
-    double dSumXX = 0.0;
-    double dSumYY = 0.0;
-    double dSumZZ = 0.0;
-    double dSumXY = 0.0;
-    double dSumXZ = 0.0;
-    double dSumYZ = 0.0;
 
-    for (int i = 0; i < n; i+=3) {
-      dSumXX += vcorr[i  ] * vcorr[i  ];
-      dSumYY += vcorr[i+1] * vcorr[i+1];
-      dSumZZ += vcorr[i+2] * vcorr[i+2];
-
-      dSumXY += vcorr[i  ] * vcorr[i+1];
-      dSumXZ += vcorr[i  ] * vcorr[i+2];
-      dSumYZ += vcorr[i+1] * vcorr[i+2];
-    }
-
-    // Calc coeff. for -l^3 + o * l^2 + p * l + q = 0
-    double o = dSumXX + dSumYY + dSumZZ;
-    double p = pow(dSumXY,2) + pow(dSumXZ,2) + pow(dSumYZ,2) -
-               (dSumXX * dSumYY + dSumXX * dSumZZ + dSumYY * dSumZZ);
-    double q = dSumXX * dSumYY * dSumZZ + 2.0 * dSumXY * dSumXZ * dSumYZ -
-               (dSumXX * dSumYZ * dSumYZ + dSumYY * dSumXZ * dSumXZ + dSumZZ * dSumXY * dSumXY);
-
-    // Solve cubic eq.
-    double root = Action_Vector::solve_cubic_eq(-1.0, o, p, q);
-
-    // Calc determinents
-    Xout = (dSumYY - root) * dSumXZ - dSumXY * dSumYZ;
-    Yout = (dSumXX - root) * dSumYZ - dSumXY * dSumXZ;
-    Zout =  dSumXY         * dSumXY - (dSumYY - root) * (dSumXX - root);
-  }
-  // Normalize
-  double dnorm = 1.0 / sqrt((Xout * Xout) + (Yout * Yout) + (Zout * Zout));
-  return Vec3(Xout * dnorm, Yout * dnorm, Zout * dnorm);
-}
-
-// -----------------------------------------------------------------------------
 // Action_Vector::Mask()
 void Action_Vector::Mask(Frame const& currentFrame) {
   Vec3 CXYZ = currentFrame.VCenterOfMass(mask_);
@@ -421,19 +299,8 @@ void Action_Vector::Principal(Frame const& currentFrame) {
 
 // Action_Vector::CorrPlane()
 void Action_Vector::CorrPlane(Frame const& currentFrame) {
-  Vec3 CXYZ = currentFrame.VCenterOfMass(mask_);
-  int idx = 0;
-  for (AtomMask::const_iterator atom = mask_.begin();
-                              atom != mask_.end(); ++atom)
-  {
-    Vec3 XYZ = currentFrame.XYZ( *atom );
-    XYZ -= CXYZ;
-    vcorr_[idx++] = XYZ[0];
-    vcorr_[idx++] = XYZ[1];
-    vcorr_[idx++] = XYZ[2];
-  }
-  Vec3 VXYZ = leastSquaresPlane(idx, vcorr_);
-  Vec_->AddVxyzo(VXYZ, CXYZ);
+  vcorr_.CalcLeastSquaresPlane( currentFrame, mask_ );
+  Vec_->AddVxyzo( vcorr_.Nxyz(), vcorr_.Cxyz() );
 }
 
 //  Action_Vector::UnitCell()
diff --git a/src/Action_Vector.h b/src/Action_Vector.h
index 471bc79e72..5bf53c13c4 100644
--- a/src/Action_Vector.h
+++ b/src/Action_Vector.h
@@ -1,12 +1,12 @@
 #ifndef INC_ACTION_VECTOR_H
 #define INC_ACTION_VECTOR_H
 #include "Action.h"
+#include "Structure/LeastSquaresPlane.h" // For CORRPLANE
 class DataSet_Vector;
 class DataSet_3D;
 class Action_Vector : public Action {
   public:
     Action_Vector();
-    ~Action_Vector();
     DispatchObject* Alloc() const { return (DispatchObject*)new Action_Vector(); }
     void Help() const;
   private:
@@ -24,8 +24,6 @@ class Action_Vector : public Action {
     Action::RetType DoAction(int, ActionFrame&);
     void Print();
 
-    static double solve_cubic_eq(double,double,double,double);
-    static Vec3 leastSquaresPlane(int,const double*);
     void Mask(Frame const&);
     void Dipole(Frame const&);
     void Principal(Frame const&);
@@ -37,7 +35,7 @@ class Action_Vector : public Action {
     DataSet_Vector* Vec_;   ///< Hold vector values
     DataSet* Magnitude_;    ///< Hold vector magnitudes if requested
     DataSet_3D* gridSet_;   ///< Hold grid set for getting box vectors from grid.
-    double* vcorr_;         ///< Temp. space for calculating CorrPlane
+    Cpptraj::Structure::LeastSquaresPlane vcorr_; ///< Temp. space for calculating CorrPlane
     vectorMode mode_;       ///< Vector calculation mode
     bool ptrajoutput_;      ///< If true output in ptraj format
     bool needBoxInfo_;      ///< If true box info required. 
diff --git a/src/Structure/LeastSquaresPlane.cpp b/src/Structure/LeastSquaresPlane.cpp
index da1c91ddfc..a5c48bbee9 100644
--- a/src/Structure/LeastSquaresPlane.cpp
+++ b/src/Structure/LeastSquaresPlane.cpp
@@ -3,7 +3,7 @@
 #include "../Constants.h"
 #include "../Frame.h"
 #include <algorithm> // sort
-#include <cmath> // sqrt, acos, pow
+#include <cmath> // sqrt, acos, cos, pow
 
 using namespace Cpptraj::Structure;
 
diff --git a/src/Structure/LeastSquaresPlane.h b/src/Structure/LeastSquaresPlane.h
index d1287143e5..31032c1474 100644
--- a/src/Structure/LeastSquaresPlane.h
+++ b/src/Structure/LeastSquaresPlane.h
@@ -12,6 +12,10 @@ class LeastSquaresPlane {
   public:
     LeastSquaresPlane();
     void CalcLeastSquaresPlane(Frame const&, AtomMask const&);
+    /// \return Vector normal to plane
+    Vec3 const& Nxyz() const { return nxyz_; }
+    /// \return Origin of vector normal to plane (plane center)
+    Vec3 const& Cxyz() const { return cxyz_; }
   private:
     static double solve_cubic_eq(double,double,double,double);
     static Vec3 leastSquaresPlane(unsigned int, const double*);
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 6c4d94a7fd..1aa00038ea 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -86,7 +86,7 @@ Action_ToroidalDiffusion.o : Action_ToroidalDiffusion.cpp Action.h ActionState.h
 Action_Translate.o : Action_Translate.cpp Action.h ActionState.h Action_Translate.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Action_Unstrip.o : Action_Unstrip.cpp Action.h ActionState.h Action_Unstrip.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Action_Unwrap.o : Action_Unwrap.cpp Action.h ActionState.h Action_Unwrap.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h ImageRoutines.h ImageTypes.h Image_List.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Vector.o : Action_Vector.cpp Action.h ActionState.h Action_Vector.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h GridBin.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Vector.o : Action_Vector.cpp Action.h ActionState.h Action_Vector.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h GridBin.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/LeastSquaresPlane.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Action_VelocityAutoCorr.o : Action_VelocityAutoCorr.cpp Action.h ActionState.h Action_VelocityAutoCorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Action_Volmap.o : Action_Volmap.cpp Action.h ActionState.h Action_Volmap.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridDbl.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Action_Volume.o : Action_Volume.cpp Action.h ActionState.h Action_Volume.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
@@ -191,7 +191,7 @@ CmapParmHolder.o : CmapParmHolder.cpp CmapParmHolder.h Constants.h CpptrajStdio.
 Cmd.o : Cmd.cpp Cmd.h DispatchObject.h
 CmdInput.o : CmdInput.cpp CmdInput.h StringRoutines.h
 CmdList.o : CmdList.cpp Cmd.h CmdList.h DispatchObject.h
-Command.o : Command.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h ActionTopWriter.h Action_Align.h Action_Angle.h Action_AreaPerMol.h Action_AtomMap.h Action_AtomicCorr.h Action_AtomicFluct.h Action_AutoImage.h Action_Average.h Action_AvgBox.h Action_Bounds.h Action_Box.h Action_Center.h Action_Channel.h Action_CheckChirality.h Action_CheckStructure.h Action_Closest.h Action_ClusterDihedral.h Action_Contacts.h Action_CreateCrd.h Action_CreateReservoir.h Action_DNAionTracker.h Action_DSSP.h Action_Density.h Action_Diffusion.h Action_Dihedral.h Action_DihedralRMS.h Action_Dipole.h Action_DistRmsd.h Action_Distance.h Action_Energy.h Action_Esander.h Action_FilterByData.h Action_FixAtomOrder.h Action_FixImagedBonds.h Action_GIST.h Action_Grid.h Action_GridFreeEnergy.h Action_HydrogenBond.h Action_Image.h Action_InfraredSpectrum.h Action_Jcoupling.h Action_Keep.h Action_LESsplit.h Action_LIE.h Action_LipidOrder.h Action_MakeStructure.h Action_Mask.h Action_Matrix.h Action_MinImage.h Action_MinMaxDist.h Action_Molsurf.h Action_MultiDihedral.h Action_MultiPucker.h Action_MultiVector.h Action_NAstruct.h Action_NMRrst.h Action_NativeContacts.h Action_OrderParameter.h Action_Outtraj.h Action_PairDist.h Action_Pairwise.h Action_Principal.h Action_Projection.h Action_Pucker.h Action_Radgyr.h Action_Radial.h Action_RandomizeIons.h Action_Remap.h Action_ReplicateCell.h Action_Rmsd.h Action_Rotate.h Action_RunningAvg.h Action_STFC_Diffusion.h Action_Scale.h Action_SetVelocity.h Action_Spam.h Action_Strip.h Action_Surf.h Action_SymmetricRmsd.h Action_Temperature.h Action_Time.h Action_ToroidalDiffusion.h Action_Translate.h Action_Unstrip.h Action_Unwrap.h Action_Vector.h Action_VelocityAutoCorr.h Action_Volmap.h Action_Volume.h Action_Watershell.h Action_XtalSymm.h Analysis.h AnalysisList.h AnalysisState.h Analysis_AmdBias.h Analysis_AutoCorr.h Analysis_Average.h Analysis_CalcDiffusion.h Analysis_Clustering.h Analysis_ConstantPHStats.h Analysis_Corr.h Analysis_CrankShaft.h Analysis_CrdFluct.h Analysis_CrossCorr.h Analysis_CurveFit.h Analysis_Divergence.h Analysis_EvalPlateau.h Analysis_FFT.h Analysis_HausdorffDistance.h Analysis_Hist.h Analysis_IRED.h Analysis_Integrate.h Analysis_KDE.h Analysis_Lifetime.h Analysis_LowestCurve.h Analysis_Matrix.h Analysis_MeltCurve.h Analysis_Modes.h Analysis_MultiHist.h Analysis_Multicurve.h Analysis_Overlap.h Analysis_PhiPsi.h Analysis_Project.h Analysis_Regression.h Analysis_RemLog.h Analysis_Rms2d.h Analysis_RmsAvgCorr.h Analysis_Rotdif.h Analysis_RunningAvg.h Analysis_Slope.h Analysis_Spline.h Analysis_State.h Analysis_Statistics.h Analysis_TI.h Analysis_TICA.h Analysis_Timecorr.h Analysis_VectorMath.h Analysis_Wavelet.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h AxisType.h BaseIOtype.h Box.h BoxArgs.h BufferedLine.h CharMask.h Cluster/Algorithm.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Control.h Cluster/DrawGraph.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Sieve.h Cluster/Silhouette.h ClusterMap.h CmapParmHolder.h Cmd.h CmdInput.h CmdList.h Command.h CompactFrameArray.h ComplexArray.h Constants.h Constraints.h ControlBlock.h ControlBlock_For.h CoordinateInfo.h Corr.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_RemLog.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h Deprecated.h DiffusionResults.h DihedralSearch.h Dimension.h DispatchObject.h Energy.h Energy_Sander.h EnsembleIn.h EnsembleOutList.h Ewald.h EwaldOptions.h Ewald_ParticleMesh.h ExclusionArray.h Exec.h Exec_AddMissingRes.h Exec_Analyze.h Exec_Build.h Exec_Calc.h Exec_CatCrd.h Exec_Change.h Exec_ClusterMap.h Exec_CombineCoords.h Exec_Commands.h Exec_CompareClusters.h Exec_CompareEnergy.h Exec_CompareTop.h Exec_CrdAction.h Exec_CrdOut.h Exec_CrdTransform.h Exec_CreateSet.h Exec_DataFile.h Exec_DataFilter.h Exec_DataSetCmd.h Exec_Desc.h Exec_Emin.h Exec_ExtendedComparison.h Exec_Flatten.h Exec_GenerateAmberRst.h Exec_Graft.h Exec_Help.h Exec_HmassRepartition.h Exec_LoadCrd.h Exec_LoadTraj.h Exec_ParallelAnalysis.h Exec_ParmBox.h Exec_ParmSolvent.h Exec_ParmStrip.h Exec_ParmWrite.h Exec_ParseTiming.h Exec_PermuteDihedrals.h Exec_Precision.h Exec_PrepareForLeap.h Exec_PrintData.h Exec_Random.h Exec_ReadData.h Exec_ReadEnsembleData.h Exec_ReadInput.h Exec_RotateDihedral.h Exec_RunAnalysis.h Exec_ScaleDihedralK.h Exec_Sequence.h Exec_SequenceAlign.h Exec_Set.h Exec_Show.h Exec_SortEnsembleData.h Exec_Source.h Exec_SplitCoords.h Exec_System.h Exec_Top.h Exec_Traj.h Exec_UpdateParameters.h Exec_ViewRst.h Exec_Zmatrix.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h GIST_PME.h Grid.h GridAction.h GridBin.h GridMover.h HistBin.h Hungarian.h ImageOption.h ImageTypes.h InputTrajCommon.h InteractionData.h MapAtom.h MaskArray.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h OnlineVarT.h OutputTrajCommon.h PDBfile.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PubFFT.h Pucker.h Pucker_PuckerMask.h Pucker_PuckerSearch.h Pucker_PuckerToken.h RPNcalc.h Random.h Range.h ReferenceAction.h ReferenceFrame.h RemdReservoirNC.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h SplineFxnTable.h Structure/RingFinder.h StructureCheck.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h cuda_kernels/GistCudaSetup.cuh helpme_standalone.h molsurf.h
+Command.o : Command.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h ActionTopWriter.h Action_Align.h Action_Angle.h Action_AreaPerMol.h Action_AtomMap.h Action_AtomicCorr.h Action_AtomicFluct.h Action_AutoImage.h Action_Average.h Action_AvgBox.h Action_Bounds.h Action_Box.h Action_Center.h Action_Channel.h Action_CheckChirality.h Action_CheckStructure.h Action_Closest.h Action_ClusterDihedral.h Action_Contacts.h Action_CreateCrd.h Action_CreateReservoir.h Action_DNAionTracker.h Action_DSSP.h Action_Density.h Action_Diffusion.h Action_Dihedral.h Action_DihedralRMS.h Action_Dipole.h Action_DistRmsd.h Action_Distance.h Action_Energy.h Action_Esander.h Action_FilterByData.h Action_FixAtomOrder.h Action_FixImagedBonds.h Action_GIST.h Action_Grid.h Action_GridFreeEnergy.h Action_HydrogenBond.h Action_Image.h Action_InfraredSpectrum.h Action_Jcoupling.h Action_Keep.h Action_LESsplit.h Action_LIE.h Action_LipidOrder.h Action_MakeStructure.h Action_Mask.h Action_Matrix.h Action_MinImage.h Action_MinMaxDist.h Action_Molsurf.h Action_MultiDihedral.h Action_MultiPucker.h Action_MultiVector.h Action_NAstruct.h Action_NMRrst.h Action_NativeContacts.h Action_OrderParameter.h Action_Outtraj.h Action_PairDist.h Action_Pairwise.h Action_Principal.h Action_Projection.h Action_Pucker.h Action_Radgyr.h Action_Radial.h Action_RandomizeIons.h Action_Remap.h Action_ReplicateCell.h Action_Rmsd.h Action_Rotate.h Action_RunningAvg.h Action_STFC_Diffusion.h Action_Scale.h Action_SetVelocity.h Action_Spam.h Action_Strip.h Action_Surf.h Action_SymmetricRmsd.h Action_Temperature.h Action_Time.h Action_ToroidalDiffusion.h Action_Translate.h Action_Unstrip.h Action_Unwrap.h Action_Vector.h Action_VelocityAutoCorr.h Action_Volmap.h Action_Volume.h Action_Watershell.h Action_XtalSymm.h Analysis.h AnalysisList.h AnalysisState.h Analysis_AmdBias.h Analysis_AutoCorr.h Analysis_Average.h Analysis_CalcDiffusion.h Analysis_Clustering.h Analysis_ConstantPHStats.h Analysis_Corr.h Analysis_CrankShaft.h Analysis_CrdFluct.h Analysis_CrossCorr.h Analysis_CurveFit.h Analysis_Divergence.h Analysis_EvalPlateau.h Analysis_FFT.h Analysis_HausdorffDistance.h Analysis_Hist.h Analysis_IRED.h Analysis_Integrate.h Analysis_KDE.h Analysis_Lifetime.h Analysis_LowestCurve.h Analysis_Matrix.h Analysis_MeltCurve.h Analysis_Modes.h Analysis_MultiHist.h Analysis_Multicurve.h Analysis_Overlap.h Analysis_PhiPsi.h Analysis_Project.h Analysis_Regression.h Analysis_RemLog.h Analysis_Rms2d.h Analysis_RmsAvgCorr.h Analysis_Rotdif.h Analysis_RunningAvg.h Analysis_Slope.h Analysis_Spline.h Analysis_State.h Analysis_Statistics.h Analysis_TI.h Analysis_TICA.h Analysis_Timecorr.h Analysis_VectorMath.h Analysis_Wavelet.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h AxisType.h BaseIOtype.h Box.h BoxArgs.h BufferedLine.h CharMask.h Cluster/Algorithm.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Control.h Cluster/DrawGraph.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Sieve.h Cluster/Silhouette.h ClusterMap.h CmapParmHolder.h Cmd.h CmdInput.h CmdList.h Command.h CompactFrameArray.h ComplexArray.h Constants.h Constraints.h ControlBlock.h ControlBlock_For.h CoordinateInfo.h Corr.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_RemLog.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h Deprecated.h DiffusionResults.h DihedralSearch.h Dimension.h DispatchObject.h Energy.h Energy_Sander.h EnsembleIn.h EnsembleOutList.h Ewald.h EwaldOptions.h Ewald_ParticleMesh.h ExclusionArray.h Exec.h Exec_AddMissingRes.h Exec_Analyze.h Exec_Build.h Exec_Calc.h Exec_CatCrd.h Exec_Change.h Exec_ClusterMap.h Exec_CombineCoords.h Exec_Commands.h Exec_CompareClusters.h Exec_CompareEnergy.h Exec_CompareTop.h Exec_CrdAction.h Exec_CrdOut.h Exec_CrdTransform.h Exec_CreateSet.h Exec_DataFile.h Exec_DataFilter.h Exec_DataSetCmd.h Exec_Desc.h Exec_Emin.h Exec_ExtendedComparison.h Exec_Flatten.h Exec_GenerateAmberRst.h Exec_Graft.h Exec_Help.h Exec_HmassRepartition.h Exec_LoadCrd.h Exec_LoadTraj.h Exec_ParallelAnalysis.h Exec_ParmBox.h Exec_ParmSolvent.h Exec_ParmStrip.h Exec_ParmWrite.h Exec_ParseTiming.h Exec_PermuteDihedrals.h Exec_Precision.h Exec_PrepareForLeap.h Exec_PrintData.h Exec_Random.h Exec_ReadData.h Exec_ReadEnsembleData.h Exec_ReadInput.h Exec_RotateDihedral.h Exec_RunAnalysis.h Exec_ScaleDihedralK.h Exec_Sequence.h Exec_SequenceAlign.h Exec_Set.h Exec_Show.h Exec_SortEnsembleData.h Exec_Source.h Exec_SplitCoords.h Exec_System.h Exec_Top.h Exec_Traj.h Exec_UpdateParameters.h Exec_ViewRst.h Exec_Zmatrix.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h GIST_PME.h Grid.h GridAction.h GridBin.h GridMover.h HistBin.h Hungarian.h ImageOption.h ImageTypes.h InputTrajCommon.h InteractionData.h MapAtom.h MaskArray.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h OnlineVarT.h OutputTrajCommon.h PDBfile.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PubFFT.h Pucker.h Pucker_PuckerMask.h Pucker_PuckerSearch.h Pucker_PuckerToken.h RPNcalc.h Random.h Range.h ReferenceAction.h ReferenceFrame.h RemdReservoirNC.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h SplineFxnTable.h Structure/LeastSquaresPlane.h Structure/RingFinder.h StructureCheck.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h cuda_kernels/GistCudaSetup.cuh helpme_standalone.h molsurf.h
 CompactFrameArray.o : CompactFrameArray.cpp Box.h CompactFrameArray.h CoordinateInfo.h CpptrajStdio.h Matrix_3x3.h Parallel.h ReplicaDimArray.h Vec3.h
 ComplexArray.o : ComplexArray.cpp ArrayIterator.h ComplexArray.h
 Constraints.o : Constraints.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h CharMask.h CmapParmHolder.h Constants.h Constraints.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
@@ -466,6 +466,7 @@ Structure/FxnGroupBuilder.o : Structure/FxnGroupBuilder.cpp Atom.h AtomMask.h At
 Structure/GenerateConnectivityArrays.o : Structure/GenerateConnectivityArrays.cpp Atom.h Constants.h CpptrajStdio.h NameType.h ParameterTypes.h Residue.h Structure/GenerateConnectivityArrays.h SymbolExporting.h
 Structure/HisProt.o : Structure/HisProt.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/HisProt.h Structure/StructureRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/InternalCoords.o : Structure/InternalCoords.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/InternalCoords.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Structure/LeastSquaresPlane.o : Structure/LeastSquaresPlane.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h Residue.h Segment.h Structure/LeastSquaresPlane.h SymbolExporting.h Unit.h Vec3.h
 Structure/PdbCleaner.o : Structure/PdbCleaner.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/PdbCleaner.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/RingFinder.o : Structure/RingFinder.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/RingFinder.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/StructureEnum.o : Structure/StructureEnum.cpp Structure/StructureEnum.h

From 3565d46c750f8e4287439e7e110988a2db46c589 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 21 Jun 2024 12:59:32 -0400
Subject: [PATCH 0762/1492] Start adding ring check

---
 src/Action_CheckStructure.cpp |  1 +
 src/Structure/RingFinder.h    |  3 +++
 src/StructureCheck.cpp        | 47 +++++++++++++++++++++++++++++++++++
 src/StructureCheck.h          |  3 +++
 src/cpptrajdepend             |  2 +-
 5 files changed, 55 insertions(+), 1 deletion(-)

diff --git a/src/Action_CheckStructure.cpp b/src/Action_CheckStructure.cpp
index 601435e893..35664ee354 100644
--- a/src/Action_CheckStructure.cpp
+++ b/src/Action_CheckStructure.cpp
@@ -200,6 +200,7 @@ Action::RetType Action_CheckStructure::DoAction(int frameNum, ActionFrame& frm)
     total_problems += check_.CheckBonds(frm.Frm());
     if (outfile_ != 0) WriteProblems(F_BOND, fnum, *CurrentParm_);
   }
+  check_.CheckRings(frm.Frm()); // FIXME
   num_problems_->Add( frameNum, &total_problems );
   if (total_problems > 0 && skipBadFrames_)
     return Action::SUPPRESS_COORD_OUTPUT;
diff --git a/src/Structure/RingFinder.h b/src/Structure/RingFinder.h
index 9897ef33c0..92e031ae45 100644
--- a/src/Structure/RingFinder.h
+++ b/src/Structure/RingFinder.h
@@ -12,7 +12,10 @@ class RingFinder {
     RingFinder();
     int InitRingFinder(ArgList&);
     int SetupRingFinder(Topology const&, AtomMask const&);
+
+    unsigned int Nrings() const { return rings_.size(); }
     void PrintRings(Topology const&) const;
+    AtomMask const& operator[](int idx) const { return rings_[idx]; }
   private:
     typedef std::vector<AtomMask> Marray;
 
diff --git a/src/StructureCheck.cpp b/src/StructureCheck.cpp
index 496165b026..c151adcdb2 100644
--- a/src/StructureCheck.cpp
+++ b/src/StructureCheck.cpp
@@ -5,6 +5,7 @@
 #include "CpptrajStdio.h"
 #include "CharMask.h"
 #include "DistRoutines.h"
+#include "Structure/LeastSquaresPlane.h"
 #ifdef _OPENMP
 #  include <omp.h>
 #endif
@@ -231,6 +232,52 @@ int StructureCheck::CheckBonds(Frame const& currentFrame)
   return Nproblems;
 }
 
+/** Check if any bonds are passing through rings. */
+int StructureCheck::CheckRings(Frame const& currentFrame) {
+  int Nproblems = 0;
+  // Get all ring vectors
+  typedef std::vector<Cpptraj::Structure::LeastSquaresPlane> Larray;
+  Larray RingVecs;
+  RingVecs.resize( rings_.Nrings() );
+  int idx = 0;
+  int ring_max = (int)rings_.Nrings();
+  for (idx = 0; idx < ring_max; idx++)
+  {
+    RingVecs[idx].CalcLeastSquaresPlane( currentFrame, rings_[idx] );
+  }
+
+  // Loop over bonds
+  int bond_max = (int)bondList_.size();
+  for (idx = 0; idx < bond_max; idx++)
+  {
+    const double* xyz1 = currentFrame.XYZ( bondList_[idx].A1() );
+    const double* xyz2 = currentFrame.XYZ( bondList_[idx].A2() );
+    Vec3 vbond( xyz2[0] - xyz1[0],
+                xyz2[1] - xyz1[1],
+                xyz2[2] - xyz1[2] );
+    Vec3 vmid = Vec3(xyz1) + (vbond * 0.5);
+    //vbond.Normalize();
+    // Loop over rings
+    for (int jdx = 0; jdx < ring_max; jdx++)
+    {
+      // Make sure this bond is not in this ring
+      AtomMask const& ringMask = rings_[jdx];
+      if ( !ringMask.IsSelected(bondList_[idx].A1()) &&
+           !ringMask.IsSelected(bondList_[idx].A2()) )
+      {
+        // Get the center distance
+        Cpptraj::Structure::LeastSquaresPlane const& ringVec = RingVecs[jdx];
+        double dist2 = DIST2_NoImage( vmid.Dptr(), ringVec.Cxyz().Dptr() );
+        if (dist2 < 9.0) { // 3 ang cutoff
+          mprintf("DEBUG: Bond %i - %i near ring %i (%f)\n", bondList_[idx].A1()+1, bondList_[idx].A2()+1, jdx, sqrt(dist2));
+        }
+      }
+    }
+  }
+
+  return 0;
+}
+
 /** Check for bad overlaps; use a pair list to speed things up.
   * \return Number of bad overlaps.
   */
diff --git a/src/StructureCheck.h b/src/StructureCheck.h
index cbcb3422ce..e892598a2d 100644
--- a/src/StructureCheck.h
+++ b/src/StructureCheck.h
@@ -22,6 +22,8 @@ class StructureCheck {
     int CheckBonds(Frame const&);
     /// \return Number of atomic overlaps.
     int CheckOverlaps(Frame const&);
+    /// Check if any bonds are passing through rings.
+    int CheckRings(Frame const&);
 
     AtomMask const& Mask1()     const { return Mask1_; }
     AtomMask const& Mask2()     const { return Mask2_; }
@@ -90,6 +92,7 @@ class StructureCheck {
     void ConsolidateProblems();
     /// Check for/record non-bonded interaction problem
     inline void DistanceCheck(Frame const&, int, int, Parray&, int&) const;
+
 #   ifdef _OPENMP
     std::vector<Parray> thread_problemAtoms_;
 #   endif
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 1aa00038ea..00b593bc08 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -476,7 +476,7 @@ Structure/SugarBuilder.o : Structure/SugarBuilder.cpp ArgList.h Atom.h AtomMap.h
 Structure/SugarLinkAtoms.o : Structure/SugarLinkAtoms.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/LinkAtom.h Structure/SugarLinkAtoms.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/SugarToken.o : Structure/SugarToken.cpp ArgList.h CpptrajStdio.h Structure/SugarToken.h
 Structure/Zmatrix.o : Structure/Zmatrix.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-StructureCheck.o : StructureCheck.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h ExclusionArray.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/RingFinder.h StructureCheck.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+StructureCheck.o : StructureCheck.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h ExclusionArray.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/LeastSquaresPlane.h Structure/RingFinder.h StructureCheck.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 StructureMapper.o : StructureMapper.cpp AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Chirality.h Structure/StructureEnum.h StructureMapper.h SymbolExporting.h TextFormat.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 SymmetricRmsdCalc.o : SymmetricRmsdCalc.cpp ArrayIterator.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h Hungarian.h ImageOption.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 TextBlockBuffer.o : TextBlockBuffer.cpp BufferedLine.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Parallel.h TextBlockBuffer.h

From 22e9a786c5a0ad18b4bca76c9692b98542f54855 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 21 Jun 2024 13:11:36 -0400
Subject: [PATCH 0763/1492] Use distance and angle cutoff to determine
 ring/bond intersection

---
 src/StructureCheck.cpp | 18 +++++++++++++++---
 1 file changed, 15 insertions(+), 3 deletions(-)

diff --git a/src/StructureCheck.cpp b/src/StructureCheck.cpp
index c151adcdb2..03ef491c09 100644
--- a/src/StructureCheck.cpp
+++ b/src/StructureCheck.cpp
@@ -235,6 +235,8 @@ int StructureCheck::CheckBonds(Frame const& currentFrame)
 /** Check if any bonds are passing through rings. */
 int StructureCheck::CheckRings(Frame const& currentFrame) {
   int Nproblems = 0;
+  static const double ring_dcut2 = 9.0; // 3 Ang distance cutoff
+  static const double ring_acut  = 0.174533; // 10 deg. angle cutoff
   // Get all ring vectors
   typedef std::vector<Cpptraj::Structure::LeastSquaresPlane> Larray;
   Larray RingVecs;
@@ -256,7 +258,7 @@ int StructureCheck::CheckRings(Frame const& currentFrame) {
                 xyz2[1] - xyz1[1],
                 xyz2[2] - xyz1[2] );
     Vec3 vmid = Vec3(xyz1) + (vbond * 0.5);
-    //vbond.Normalize();
+    vbond.Normalize();
     // Loop over rings
     for (int jdx = 0; jdx < ring_max; jdx++)
     {
@@ -268,8 +270,18 @@ int StructureCheck::CheckRings(Frame const& currentFrame) {
         // Get the center distance
         Cpptraj::Structure::LeastSquaresPlane const& ringVec = RingVecs[jdx];
         double dist2 = DIST2_NoImage( vmid.Dptr(), ringVec.Cxyz().Dptr() );
-        if (dist2 < 9.0) { // 3 ang cutoff
-          mprintf("DEBUG: Bond %i - %i near ring %i (%f)\n", bondList_[idx].A1()+1, bondList_[idx].A2()+1, jdx, sqrt(dist2));
+        if (dist2 < ring_dcut2) {
+          // Get the angle
+          double ang_in_rad = vbond.Angle( ringVec.Nxyz() );
+          // Wrap the angle between 0-90 degrees
+          if (ang_in_rad > Constants::PIOVER2)
+            ang_in_rad = Constants::PI - ang_in_rad;
+          mprintf("DEBUG: Bond %i - %i near ring %i (%f) Ang= %f deg.\n",
+                  bondList_[idx].A1()+1, bondList_[idx].A2()+1, jdx, sqrt(dist2),
+                  Constants::RADDEG*ang_in_rad);
+          if (ang_in_rad < ring_acut) {
+            mprintf("DEBUG: Bond intersects ring.\n");
+          }
         }
       }
     }

From 6089b196bba3ec4fc08894c6338955a5b6a394c3 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 21 Jun 2024 13:18:33 -0400
Subject: [PATCH 0764/1492] Count problems and save them if requested. Add
 OpenMP for loop over bonds

---
 src/StructureCheck.cpp | 37 ++++++++++++++++++++++++++++++-------
 1 file changed, 30 insertions(+), 7 deletions(-)

diff --git a/src/StructureCheck.cpp b/src/StructureCheck.cpp
index 03ef491c09..6cfa2606c0 100644
--- a/src/StructureCheck.cpp
+++ b/src/StructureCheck.cpp
@@ -233,8 +233,10 @@ int StructureCheck::CheckBonds(Frame const& currentFrame)
 }
 
 /** Check if any bonds are passing through rings. */
-int StructureCheck::CheckRings(Frame const& currentFrame) {
+int StructureCheck::CheckRings(Frame const& currentFrame)
+{
   int Nproblems = 0;
+  problemAtoms_.clear();
   static const double ring_dcut2 = 9.0; // 3 Ang distance cutoff
   static const double ring_acut  = 0.174533; // 10 deg. angle cutoff
   // Get all ring vectors
@@ -250,6 +252,14 @@ int StructureCheck::CheckRings(Frame const& currentFrame) {
 
   // Loop over bonds
   int bond_max = (int)bondList_.size();
+# ifdef _OPENMP
+  int mythread;
+# pragma omp parallel private(idx,mythread) reduction(+: Nproblems)
+  {
+  mythread = omp_get_thread_num();
+  thread_problemAtoms_[mythread].clear();
+# pragma omp for
+# endif
   for (idx = 0; idx < bond_max; idx++)
   {
     const double* xyz1 = currentFrame.XYZ( bondList_[idx].A1() );
@@ -281,13 +291,26 @@ int StructureCheck::CheckRings(Frame const& currentFrame) {
                   Constants::RADDEG*ang_in_rad);
           if (ang_in_rad < ring_acut) {
             mprintf("DEBUG: Bond intersects ring.\n");
-          }
-        }
-      }
-    }
-  }
+            ++Nproblems;
+            if (saveProblems_) {
+#             ifdef _OPENMP
+              thread_problemAtoms_[mythread]
+#             else
+              problemAtoms_
+#             endif
+                .push_back(Problem(bondList_[idx].A1(), ringMask.back(), sqrt(dist2)));
+            }
+          } // END angle cutoff satisfied
+        } // END distance cutoff satisfied
+      } // END both bond atoms are not part of this ring
+    } // END loop over rings
+  } // END loop over bonds
+# ifdef _OPENMP
+  } // END pragma omp parallel
+# endif
+  ConsolidateProblems();
 
-  return 0;
+  return Nproblems;
 }
 
 /** Check for bad overlaps; use a pair list to speed things up.

From f6372b55eb8199b76d51f0aed9630f142de80cfa Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 21 Jun 2024 13:20:36 -0400
Subject: [PATCH 0765/1492] OpenMP parallelize the ring vector calc

---
 src/StructureCheck.cpp | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/src/StructureCheck.cpp b/src/StructureCheck.cpp
index 6cfa2606c0..57464aa527 100644
--- a/src/StructureCheck.cpp
+++ b/src/StructureCheck.cpp
@@ -245,10 +245,18 @@ int StructureCheck::CheckRings(Frame const& currentFrame)
   RingVecs.resize( rings_.Nrings() );
   int idx = 0;
   int ring_max = (int)rings_.Nrings();
+# ifdef _OPENMP
+# pragma omp parallel private(idx)
+  {
+# pragma omp for
+# endif
   for (idx = 0; idx < ring_max; idx++)
   {
     RingVecs[idx].CalcLeastSquaresPlane( currentFrame, rings_[idx] );
   }
+# ifdef _OPENMP
+  } // END pragma omp parallel
+# endif
 
   // Loop over bonds
   int bond_max = (int)bondList_.size();

From 3faf22388c405019865b9abd3b80dd05cf75cd78 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 21 Jun 2024 13:26:36 -0400
Subject: [PATCH 0766/1492] Add reporting for ring problems

---
 src/Action_CheckStructure.cpp | 8 +++++---
 src/Action_CheckStructure.h   | 2 +-
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/src/Action_CheckStructure.cpp b/src/Action_CheckStructure.cpp
index 35664ee354..078afaa144 100644
--- a/src/Action_CheckStructure.cpp
+++ b/src/Action_CheckStructure.cpp
@@ -164,8 +164,9 @@ Action::RetType Action_CheckStructure::Setup(ActionSetup& setup) {
 
 /// Output format strings for warnings.
 const char* Action_CheckStructure::Fmt_[] = {
-  "%i\t Warning: Atoms %i:%s and %i:%s are close (%.2f)\n",
-  "%i\t Warning: Unusual bond length %i:%s to %i:%s (%.2f)\n"
+  "%i\t Warning: Atoms %i:%s and %i:%s are close (%.2f)\n",    ///< F_ATOM
+  "%i\t Warning: Unusual bond length %i:%s to %i:%s (%.2f)\n", ///< F_BOND
+  "%i\t Warning: Bond involving atom %i:%s intersects ring involving atom %i:%s (%.2f)\n" ///< F_RING
 };
 
 /** Consolidate problems from different threads if necessary and write out. */
@@ -199,8 +200,9 @@ Action::RetType Action_CheckStructure::DoAction(int frameNum, ActionFrame& frm)
   if (check_.CheckBonds()) {
     total_problems += check_.CheckBonds(frm.Frm());
     if (outfile_ != 0) WriteProblems(F_BOND, fnum, *CurrentParm_);
+    total_problems += check_.CheckRings(frm.Frm()); // FIXME
+    if (outfile_ != 0) WriteProblems(F_RING, fnum, *CurrentParm_);
   }
-  check_.CheckRings(frm.Frm()); // FIXME
   num_problems_->Add( frameNum, &total_problems );
   if (total_problems > 0 && skipBadFrames_)
     return Action::SUPPRESS_COORD_OUTPUT;
diff --git a/src/Action_CheckStructure.h b/src/Action_CheckStructure.h
index 86661abfd2..17bba79f13 100644
--- a/src/Action_CheckStructure.h
+++ b/src/Action_CheckStructure.h
@@ -16,7 +16,7 @@ class Action_CheckStructure : public Action {
     int SyncAction();
 #   endif
 
-    enum FmtType { F_ATOM =0, F_BOND };
+    enum FmtType { F_ATOM =0, F_BOND, F_RING };
 
     void WriteProblems(FmtType, int, Topology const&);
 

From adac80d627cdca3492de9456be79cc15786785ec Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 21 Jun 2024 13:35:57 -0400
Subject: [PATCH 0767/1492] For rings, do not sort atoms since we have one atom
 in a bond and the other in a ring

---
 src/StructureCheck.cpp | 5 ++++-
 src/StructureCheck.h   | 2 ++
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/src/StructureCheck.cpp b/src/StructureCheck.cpp
index 57464aa527..74d60e0406 100644
--- a/src/StructureCheck.cpp
+++ b/src/StructureCheck.cpp
@@ -301,12 +301,15 @@ int StructureCheck::CheckRings(Frame const& currentFrame)
             mprintf("DEBUG: Bond intersects ring.\n");
             ++Nproblems;
             if (saveProblems_) {
+              // Do not use constructor since we do not want to sort atoms
+              Problem newProb;
+              newProb.SetProb( bondList_[idx].A1(), ringMask.back(), sqrt(dist2) );
 #             ifdef _OPENMP
               thread_problemAtoms_[mythread]
 #             else
               problemAtoms_
 #             endif
-                .push_back(Problem(bondList_[idx].A1(), ringMask.back(), sqrt(dist2)));
+                .push_back( newProb );
             }
           } // END angle cutoff satisfied
         } // END distance cutoff satisfied
diff --git a/src/StructureCheck.h b/src/StructureCheck.h
index e892598a2d..5fecb4c98d 100644
--- a/src/StructureCheck.h
+++ b/src/StructureCheck.h
@@ -56,6 +56,8 @@ class StructureCheck {
           else
             return (atom1_ < rhs.atom1_);
         }
+        /// Set problem atoms and distance, do not sort atoms
+        void SetProb(int a1, int a2, double d) { atom1_ = a1; atom2_ = a2; dist_ = d; }
         double D()  const { return dist_;  }
         int A1()    const { return atom1_; }
         int A2()    const { return atom2_; }

From 12c7e23969a2ed05552f5b4df251f4ff45d98ebf Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 21 Jun 2024 13:40:22 -0400
Subject: [PATCH 0768/1492] Start adding entangled ring check

---
 test/Test_CheckStructure/EntangledRings.mol2 | 139 +++++++++++++++++++
 test/Test_CheckStructure/RunTest.sh          |  13 ++
 2 files changed, 152 insertions(+)
 create mode 100644 test/Test_CheckStructure/EntangledRings.mol2

diff --git a/test/Test_CheckStructure/EntangledRings.mol2 b/test/Test_CheckStructure/EntangledRings.mol2
new file mode 100644
index 0000000000..76d73944a5
--- /dev/null
+++ b/test/Test_CheckStructure/EntangledRings.mol2
@@ -0,0 +1,139 @@
+@<TRIPOS>MOLECULE
+Cpptraj Generated mol2 file.
+   62    65     2     0     0
+SMALL
+USER_CHARGES
+
+
+@<TRIPOS>ATOM
+      1 P         285.8038  391.7831  319.3175 P          1 C        1.166200
+      2 OP1       287.1906  391.9346  320.1224 O2         1 C       -0.776000
+      3 OP2       285.8478  393.1884  318.4521 O2         1 C       -0.776000
+      4 O5'       284.2520  391.7027  319.8058 OS         1 C       -0.498900
+      5 C5'       283.5152  390.5065  320.1660 CI         1 C        0.055800
+      6 H5'       283.5382  389.7974  319.3293 H1         1 C        0.067900
+      7 H5''      282.4820  390.7762  320.2901 H1         1 C        0.067900
+      8 C4'       283.9939  389.7827  321.4424 CT         1 C        0.106500
+      9 H4'       284.7805  390.3915  321.8247 H1         1 C        0.117400
+     10 O4'       285.0154  388.3363  320.4650 OS         1 C       -0.354800
+     11 C1'       285.0173  386.3656  321.0598 CT         1 C        0.006600
+     12 H1'       284.6932  385.7520  320.2367 H2         1 C        0.202900
+     13 N1        286.4840  386.0377  321.2004 N*         1 C       -0.048400
+     14 C6        287.0434  385.7127  322.4146 C4         1 C        0.005300
+     15 H6        286.4687  385.7361  323.3145 H4         1 C        0.195800
+     16 C5        288.3337  385.3264  322.4910 C4         1 C       -0.521500
+     17 H5        288.7803  384.9512  323.3967 HA         1 C        0.192800
+     18 C4        288.9877  385.1844  321.2398 CA         1 C        0.818500
+     19 N4        290.1075  384.5521  321.1494 N2         1 C       -0.953000
+     20 H41       290.1655  384.1915  320.2126 H          1 C        0.423400
+     21 H42       290.1046  383.6766  321.6632 H          1 C        0.423400
+     22 N3        288.6709  385.9681  320.2824 NC         1 C       -0.758400
+     23 C2        287.4219  386.4470  320.1868 C          1 C        0.753800
+     24 O2        287.3292  387.6063  319.7722 O          1 C       -0.625200
+     25 C3'       282.9574  388.9761  323.0114 CT         1 C        0.202200
+     26 H3'       283.3236  389.6618  323.9442 H1         1 C        0.061500
+     27 C2'       283.8130  386.1339  322.6725 CT         1 C        0.067000
+     28 H2'       284.4478  385.5066  323.4930 H1         1 C        0.097200
+     29 O2'       282.8556  384.8312  322.6446 OH         1 C       -0.613900
+     30 HO2'      282.7244  384.4064  321.7691 HO         1 C        0.418600
+     31 O3'       281.5073  389.8270  323.1880 OS         1 C       -0.524600
+     32 P         280.3858  390.0247  322.0521 P          2 C        1.166200
+     33 OP1       279.4383  391.2704  322.5749 O2         2 C       -0.776000
+     34 OP2       280.4518  391.4828  321.2961 O2         2 C       -0.776000
+     35 O5'       279.1614  389.3002  322.7577 OS         2 C       -0.498900
+     36 C5'       278.9831  389.1951  324.1755 CI         2 C        0.055800
+     37 H5'       277.9201  389.0894  324.2149 H1         2 C        0.067900
+     38 H5''      279.3429  390.1107  324.6409 H1         2 C        0.067900
+     39 C4'       279.6434  388.0308  324.9422 CT         2 C        0.106500
+     40 H4'       280.6225  388.4529  324.9784 H1         2 C        0.117400
+     41 O4'       279.5307  386.9583  324.0240 OS         2 C       -0.354800
+     42 C1'       280.6562  386.1707  324.3469 CT         2 C        0.006600
+     43 H1'       280.6568  385.2004  323.8602 H2         2 C        0.202900
+     44 N1        281.8571  386.9492  323.7575 N*         2 C       -0.048400
+     45 C6        283.0934  387.2197  324.6550 C4         2 C        0.005300
+     46 H6        283.0028  386.8606  325.6768 H4         2 C        0.195800
+     47 C5        284.4573  387.7044  324.2426 C4         2 C       -0.521500
+     48 H5        285.2209  387.7020  325.0247 HA         2 C        0.192800
+     49 C4        284.6728  387.9521  322.7094 CA         2 C        0.818500
+     50 N4        286.1195  388.4884  322.6764 N2         2 C       -0.953000
+     51 H41       286.3574  388.5044  321.6903 H          2 C        0.423400
+     52 H42       286.7188  387.8412  323.1284 H          2 C        0.423400
+     53 N3        283.1405  387.6475  321.5249 NC         2 C       -0.758400
+     54 C2        281.8226  387.1609  322.1354 C          2 C        0.753800
+     55 O2        280.7385  387.1371  321.5312 O          2 C       -0.625200
+     56 C3'       279.6585  387.3495  326.3619 CT         2 C        0.202200
+     57 H3'       280.3674  387.8312  327.0051 H1         2 C        0.061500
+     58 C2'       280.3768  386.0129  325.9019 CT         2 C        0.067000
+     59 H2'       281.2846  385.8205  326.4458 H1         2 C        0.097200
+     60 O2'       279.5887  384.8563  326.1845 OH         2 C       -0.613900
+     61 HO2'      280.1004  384.0421  325.9612 HO         2 C        0.418600
+     62 O3'       278.3541  387.3277  327.1440 OS         2 C       -0.524600
+@<TRIPOS>BOND
+    1    31    32 1
+    2    27    29 1
+    3    25    27 1
+    4    25    31 1
+    5    23    24 1
+    6    22    23 1
+    7    18    19 1
+    8    18    22 1
+    9    16    18 1
+   10    14    16 1
+   11    13    14 1
+   12    13    23 1
+   13    11    13 1
+   14    11    27 1
+   15    10    11 1
+   16     8    10 1
+   17     8    25 1
+   18     5     8 1
+   19     4     5 1
+   20     1     2 1
+   21     1     3 1
+   22     1     4 1
+   23    58    60 1
+   24    56    58 1
+   25    56    62 1
+   26    54    55 1
+   27    53    54 1
+   28    49    50 1
+   29    49    53 1
+   30    47    49 1
+   31    45    47 1
+   32    44    45 1
+   33    44    54 1
+   34    42    44 1
+   35    42    58 1
+   36    41    42 1
+   37    39    41 1
+   38    39    56 1
+   39    36    39 1
+   40    35    36 1
+   41    32    33 1
+   42    32    34 1
+   43    32    35 1
+   44    29    30 1
+   45    27    28 1
+   46    25    26 1
+   47    19    20 1
+   48    19    21 1
+   49    16    17 1
+   50    14    15 1
+   51    11    12 1
+   52     8     9 1
+   53     5     6 1
+   54     5     7 1
+   55    60    61 1
+   56    58    59 1
+   57    56    57 1
+   58    50    51 1
+   59    50    52 1
+   60    47    48 1
+   61    45    46 1
+   62    42    43 1
+   63    39    40 1
+   64    36    37 1
+   65    36    38 1
+@<TRIPOS>SUBSTRUCTURE
+      1 C                 1 ****               0 ****  **** 
+      2 C                32 ****               0 ****  **** 
diff --git a/test/Test_CheckStructure/RunTest.sh b/test/Test_CheckStructure/RunTest.sh
index 785acc2ecf..48d6731302 100755
--- a/test/Test_CheckStructure/RunTest.sh
+++ b/test/Test_CheckStructure/RunTest.sh
@@ -68,6 +68,19 @@ EOF
   RunCpptraj "Structure Check with Around"
   DoTest around.dat.save around.dat
 fi
+
+UNITNAME='Check for entangled rings'
+CheckFor maxthreads 1
+if [ $? -eq 0 ] ; then
+  cat > check.in <<EOF
+parm EntangledRings.mol2
+trajin EntangledRings.mol2
+check reportfile entangled.dat
+run
+EOF
+  RunCpptraj "$UNITNAME"
+fi
+
 EndTest
 
 exit 0

From cf70b76efd0de8328c5bd9d3ff0a96830d545f2e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 21 Jun 2024 13:42:00 -0400
Subject: [PATCH 0769/1492] Add entangled test save

---
 test/Test_CheckStructure/RunTest.sh         | 3 ++-
 test/Test_CheckStructure/entangled.dat.save | 3 +++
 2 files changed, 5 insertions(+), 1 deletion(-)
 create mode 100644 test/Test_CheckStructure/entangled.dat.save

diff --git a/test/Test_CheckStructure/RunTest.sh b/test/Test_CheckStructure/RunTest.sh
index 48d6731302..46bbe85219 100755
--- a/test/Test_CheckStructure/RunTest.sh
+++ b/test/Test_CheckStructure/RunTest.sh
@@ -3,7 +3,7 @@
 . ../MasterTest.sh
 
 CleanFiles check.in report.dat nprob.dat tz2.dat skip.dat around.dat d1.dat \
-           partial.report.dat tz2.cut0.9.dat
+           partial.report.dat tz2.cut0.9.dat entangled.dat
 
 INPUT="-i check.in"
 
@@ -79,6 +79,7 @@ check reportfile entangled.dat
 run
 EOF
   RunCpptraj "$UNITNAME"
+  DoTest entangled.dat.save entangled.dat
 fi
 
 EndTest
diff --git a/test/Test_CheckStructure/entangled.dat.save b/test/Test_CheckStructure/entangled.dat.save
new file mode 100644
index 0000000000..1d4fc14cef
--- /dev/null
+++ b/test/Test_CheckStructure/entangled.dat.save
@@ -0,0 +1,3 @@
+1	 Warning: Unusual bond length 25:C_1@C3' to 27:C_1@C2' (2.99)
+1	 Warning: Bond involving atom 25:C_1@C3' intersects ring involving atom 44:C_2@N1 (0.41)
+1	 Warning: Bond involving atom 49:C_2@C4 intersects ring involving atom 8:C_1@C4' (0.58)

From 2ae00e41f3e6daa4a4acdb971e8c608a43fa423c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 21 Jun 2024 13:56:45 -0400
Subject: [PATCH 0770/1492] When checking rings ignore solvent and only look at
 bonds between heavy atoms

---
 src/Structure/RingFinder.cpp |  4 +++-
 src/StructureCheck.cpp       | 23 ++++++++++++++++-------
 src/StructureCheck.h         | 13 +++++++++++++
 3 files changed, 32 insertions(+), 8 deletions(-)

diff --git a/src/Structure/RingFinder.cpp b/src/Structure/RingFinder.cpp
index 52a27f379a..2f8be9f747 100644
--- a/src/Structure/RingFinder.cpp
+++ b/src/Structure/RingFinder.cpp
@@ -78,8 +78,10 @@ int RingFinder::SetupRingFinder(Topology const& topIn, AtomMask const& maskIn) {
   std::vector<bool> Visited(topIn.Natom(), false); // TODO only have visited for residue atoms
   // Do not look for rings that span residues.
   for (int res = 0; res < topIn.Nres(); res++) {
-    std::vector<int> startAtoms;
     Residue const& currentRes = topIn.Res(res);
+    // Ignore solvent
+    if (topIn.Mol( topIn[currentRes.FirstAtom()].MolNum() ).IsSolvent()) continue;
+    std::vector<int> startAtoms;
     int idx = 0;
     // Initial scan for start atoms
     for (int at = currentRes.FirstAtom(); at != currentRes.LastAtom(); at++, idx++)
diff --git a/src/StructureCheck.cpp b/src/StructureCheck.cpp
index 74d60e0406..eac1ede9ab 100644
--- a/src/StructureCheck.cpp
+++ b/src/StructureCheck.cpp
@@ -82,6 +82,15 @@ void StructureCheck::SetupBondList(AtomMask const& iMask, Topology const& top) {
  
   ProcessBondArray(top.Bonds(),  top.BondParm(), cMask);
   ProcessBondArray(top.BondsH(), top.BondParm(), cMask);
+  // Only look at bonds to heavy atoms for rings
+  ringBonds_.clear();
+  ringBonds_.reserve( top.Bonds().size() );
+  for (BondArray::const_iterator bnd = top.Bonds().begin(); bnd != top.Bonds().end(); ++bnd)
+  {
+    if ( cMask.AtomInCharMask(bnd->A1()) && cMask.AtomInCharMask(bnd->A2()) ) {
+      ringBonds_.push_back( Btype(bnd->A1(), bnd->A2()) );
+    }
+  }
 }
 
 // StructureCheck::Setup()
@@ -259,7 +268,7 @@ int StructureCheck::CheckRings(Frame const& currentFrame)
 # endif
 
   // Loop over bonds
-  int bond_max = (int)bondList_.size();
+  int bond_max = (int)ringBonds_.size();
 # ifdef _OPENMP
   int mythread;
 # pragma omp parallel private(idx,mythread) reduction(+: Nproblems)
@@ -270,8 +279,8 @@ int StructureCheck::CheckRings(Frame const& currentFrame)
 # endif
   for (idx = 0; idx < bond_max; idx++)
   {
-    const double* xyz1 = currentFrame.XYZ( bondList_[idx].A1() );
-    const double* xyz2 = currentFrame.XYZ( bondList_[idx].A2() );
+    const double* xyz1 = currentFrame.XYZ( ringBonds_[idx].A1() );
+    const double* xyz2 = currentFrame.XYZ( ringBonds_[idx].A2() );
     Vec3 vbond( xyz2[0] - xyz1[0],
                 xyz2[1] - xyz1[1],
                 xyz2[2] - xyz1[2] );
@@ -282,8 +291,8 @@ int StructureCheck::CheckRings(Frame const& currentFrame)
     {
       // Make sure this bond is not in this ring
       AtomMask const& ringMask = rings_[jdx];
-      if ( !ringMask.IsSelected(bondList_[idx].A1()) &&
-           !ringMask.IsSelected(bondList_[idx].A2()) )
+      if ( !ringMask.IsSelected(ringBonds_[idx].A1()) &&
+           !ringMask.IsSelected(ringBonds_[idx].A2()) )
       {
         // Get the center distance
         Cpptraj::Structure::LeastSquaresPlane const& ringVec = RingVecs[jdx];
@@ -295,7 +304,7 @@ int StructureCheck::CheckRings(Frame const& currentFrame)
           if (ang_in_rad > Constants::PIOVER2)
             ang_in_rad = Constants::PI - ang_in_rad;
           mprintf("DEBUG: Bond %i - %i near ring %i (%f) Ang= %f deg.\n",
-                  bondList_[idx].A1()+1, bondList_[idx].A2()+1, jdx, sqrt(dist2),
+                  ringBonds_[idx].A1()+1, ringBonds_[idx].A2()+1, jdx, sqrt(dist2),
                   Constants::RADDEG*ang_in_rad);
           if (ang_in_rad < ring_acut) {
             mprintf("DEBUG: Bond intersects ring.\n");
@@ -303,7 +312,7 @@ int StructureCheck::CheckRings(Frame const& currentFrame)
             if (saveProblems_) {
               // Do not use constructor since we do not want to sort atoms
               Problem newProb;
-              newProb.SetProb( bondList_[idx].A1(), ringMask.back(), sqrt(dist2) );
+              newProb.SetProb( ringBonds_[idx].A1(), ringMask.back(), sqrt(dist2) );
 #             ifdef _OPENMP
               thread_problemAtoms_[mythread]
 #             else
diff --git a/src/StructureCheck.h b/src/StructureCheck.h
index 5fecb4c98d..70aa2552e8 100644
--- a/src/StructureCheck.h
+++ b/src/StructureCheck.h
@@ -95,6 +95,19 @@ class StructureCheck {
     /// Check for/record non-bonded interaction problem
     inline void DistanceCheck(Frame const&, int, int, Parray&, int&) const;
 
+    /// Cache heavy atom bond indices for checking with rings
+    class Btype {
+      public:
+        Btype(int a1, int a2) : a1_(a1), a2_(a2) {}
+        int A1() const { return a1_; }
+        int A2() const { return a2_; }
+      private:
+        int a1_;
+        int a2_;
+    };
+
+    std::vector<Btype> ringBonds_;
+
 #   ifdef _OPENMP
     std::vector<Parray> thread_problemAtoms_;
 #   endif

From 91fa91f31f9780ac7a538218cdcbebc2af55a9d9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 21 Jun 2024 14:08:24 -0400
Subject: [PATCH 0771/1492] Tighten up the distance cutoff

---
 src/StructureCheck.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/StructureCheck.cpp b/src/StructureCheck.cpp
index eac1ede9ab..6d0f53a8dc 100644
--- a/src/StructureCheck.cpp
+++ b/src/StructureCheck.cpp
@@ -246,7 +246,7 @@ int StructureCheck::CheckRings(Frame const& currentFrame)
 {
   int Nproblems = 0;
   problemAtoms_.clear();
-  static const double ring_dcut2 = 9.0; // 3 Ang distance cutoff
+  static const double ring_dcut2 = 2.25; // 1.5 Ang distance cutoff
   static const double ring_acut  = 0.174533; // 10 deg. angle cutoff
   // Get all ring vectors
   typedef std::vector<Cpptraj::Structure::LeastSquaresPlane> Larray;

From ec8ac399ab9d4ea2f596fae8b00c913a412e6f02 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 22 Jun 2024 09:18:15 -0400
Subject: [PATCH 0772/1492] Disable ID in DataIO_Coords since regular data
 formats (e.g. cpptraj vector standard data out) could be mistaken as a
 trajectory format (Amber ASCII in this case)

---
 src/DataIO_Coords.cpp | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/src/DataIO_Coords.cpp b/src/DataIO_Coords.cpp
index 95565f71c4..fc84689741 100644
--- a/src/DataIO_Coords.cpp
+++ b/src/DataIO_Coords.cpp
@@ -13,15 +13,22 @@ DataIO_Coords::DataIO_Coords() :
 }
 
 // DataIO_Coords::ID_DataFormat()
+/** NOTE: This is disabled intentionally. The problem is that some
+  *       data formats looks very similar to trajectory formats,
+  *       so that e.g. a cpptraj vector data file can look like
+  *       an Amber ASCII trajectory.
+  *       Users can use commands like 'loadcrd', or force the read
+  *       with the 'as' keyword.
+  */
 bool DataIO_Coords::ID_DataFormat(CpptrajFile& infile)
 {
   // Needs to be either a topology format or a coords format
-  ParmFile::ParmFormatType parm_format = ParmFile::DetectFormat(infile.Filename());
+/*  ParmFile::ParmFormatType parm_format = ParmFile::DetectFormat(infile.Filename());
   TrajectoryFile::TrajFormatType traj_format = TrajectoryFile::DetectFormat(infile.Filename());
   is_parm_fmt_ = (parm_format != ParmFile::UNKNOWN_PARM);
   is_traj_fmt_ = (traj_format != TrajectoryFile::UNKNOWN_TRAJ);
   if (is_parm_fmt_ || is_traj_fmt_)
-    return true;
+    return true;*/
   return false;
 }
 

From e263d6e22853c1d229f405f66cc4bc771ea1f36a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 24 Jun 2024 12:57:36 -0400
Subject: [PATCH 0773/1492] Add noimage keyword to permutedihedrals

---
 src/Exec_PermuteDihedrals.cpp | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/Exec_PermuteDihedrals.cpp b/src/Exec_PermuteDihedrals.cpp
index 646a5c474d..8e79e5ec46 100644
--- a/src/Exec_PermuteDihedrals.cpp
+++ b/src/Exec_PermuteDihedrals.cpp
@@ -141,6 +141,7 @@ Exec::RetType Exec_PermuteDihedrals::Execute(CpptrajState& State, ArgList& argIn
     increment_ = argIn.getKeyInt("increment",1);
     max_factor_ = argIn.getKeyDouble("maxfactor", 2);
     int iseed = argIn.getKeyInt("rseed",-1);
+    bool imageOn = !(argIn.hasKey("noimage"));
     // Output file for # of problems
     DataFile* problemFile = State.DFL().AddDataFile(argIn.GetStringKey("out"), argIn);
     // Dataset to store number of problems
@@ -197,7 +198,7 @@ Exec::RetType Exec_PermuteDihedrals::Execute(CpptrajState& State, ArgList& argIn
     // Increment backtrack by 1 since we need to skip over current res
     ++backtrack_;
     // Initialize CheckStructure
-    if (checkStructure_.SetOptions( false, false, false, State.Debug(), "*", "", 0.8, 1.15, 0.5, 8.0 )) {
+    if (checkStructure_.SetOptions( imageOn, false, false, State.Debug(), "*", "", 0.8, 1.15, 0.5, -1 )) {
       mprinterr("Error: Could not set up structure check.\n");
       return CpptrajState::ERR;
     }

From 0416453d4ad190b9f1846e323ae35c78a14258de Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 24 Jun 2024 12:57:56 -0400
Subject: [PATCH 0774/1492] Hide some debug info

---
 src/StructureCheck.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/StructureCheck.cpp b/src/StructureCheck.cpp
index 6d0f53a8dc..cf6b63b05e 100644
--- a/src/StructureCheck.cpp
+++ b/src/StructureCheck.cpp
@@ -181,7 +181,7 @@ int StructureCheck::Setup(Topology const& topIn, Box const& boxIn)
     mprinterr("Error: Could not set up ring finder.\n");
     return 1;
   }
-  rings_.PrintRings(topIn);
+  if (debug_ > 0) rings_.PrintRings(topIn);
 
   return 0;
 }

From f516e1311d430494847f673a58c5932110efd649 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 24 Jun 2024 13:02:27 -0400
Subject: [PATCH 0775/1492] Add debug level to RingFinder

---
 src/Structure/RingFinder.cpp | 24 +++++++++++++++---------
 src/Structure/RingFinder.h   |  2 ++
 src/StructureCheck.cpp       |  1 +
 3 files changed, 18 insertions(+), 9 deletions(-)

diff --git a/src/Structure/RingFinder.cpp b/src/Structure/RingFinder.cpp
index 2f8be9f747..486aff4060 100644
--- a/src/Structure/RingFinder.cpp
+++ b/src/Structure/RingFinder.cpp
@@ -7,9 +7,15 @@
 using namespace Cpptraj::Structure;
 
 /** CONSTRUCTOR */
-RingFinder::RingFinder()
+RingFinder::RingFinder() :
+  debug_(0)
 {}
 
+/** Set debug level */
+void RingFinder::SetDebug(int debugIn) {
+  debug_ = debugIn;
+}
+
 /** Init ring finder. */
 int RingFinder::InitRingFinder(ArgList& argIn) {
   return 0;
@@ -36,10 +42,10 @@ static std::vector<int> findCycle(int at, int tgtAt, int previousAt, int res, To
                                   std::vector<bool> Visited, std::vector<int> ringAtoms)
 {
   if (at == tgtAt) {
-    mprintf("CYCLE FOUND (%zu).", ringAtoms.size());
-    for (std::vector<int>::const_iterator it = ringAtoms.begin(); it != ringAtoms.end(); ++it)
-      mprintf(" %s", topIn.AtomMaskName(*it).c_str());
-    mprintf("\n");
+    //mprintf("CYCLE FOUND (%zu).", ringAtoms.size());
+    //for (std::vector<int>::const_iterator it = ringAtoms.begin(); it != ringAtoms.end(); ++it)
+    //  mprintf(" %s", topIn.AtomMaskName(*it).c_str());
+    //mprintf("\n");
     return ringAtoms;
   }
   Visited[at] = true;
@@ -103,7 +109,7 @@ int RingFinder::SetupRingFinder(Topology const& topIn, AtomMask const& maskIn) {
         if (!startAtoms.empty()) break;
       }
     }
-    if (!startAtoms.empty()) {
+    if (debug_ > 0 && !startAtoms.empty()) {
       mprintf("Potential start atoms:");
       for (std::vector<int>::const_iterator it = startAtoms.begin(); it != startAtoms.end(); ++it)
         mprintf(" %s", topIn.AtomMaskName(*it).c_str());
@@ -143,12 +149,12 @@ int RingFinder::SetupRingFinder(Topology const& topIn, AtomMask const& maskIn) {
                     Visited[*rt] = true;
                   // Only add the ring if all atoms were found
                   bool allfound = true;
-                  mprintf("RING FOUND (%zu): {", ringAtoms.size());
+                  if (debug_ > 0) mprintf("RING FOUND (%zu): {", ringAtoms.size());
                   for (std::vector<int>::const_iterator rt = ringAtoms.begin(); rt != ringAtoms.end(); ++rt) {
-                    mprintf(" %s", topIn.AtomMaskName(*rt).c_str());
+                    if (debug_ > 0) mprintf(" %s", topIn.AtomMaskName(*rt).c_str());
                     if (!cmask.AtomInCharMask( *rt )) allfound = false;
                   }
-                  mprintf(" }\n");
+                  if (debug_ > 0) mprintf(" }\n");
                   if (allfound)
                     rings_.push_back( AtomMask(ringAtoms, topIn.Natom()) );
                 }
diff --git a/src/Structure/RingFinder.h b/src/Structure/RingFinder.h
index 92e031ae45..289caa5f6d 100644
--- a/src/Structure/RingFinder.h
+++ b/src/Structure/RingFinder.h
@@ -10,6 +10,7 @@ namespace Structure {
 class RingFinder {
   public:
     RingFinder();
+    void SetDebug(int);
     int InitRingFinder(ArgList&);
     int SetupRingFinder(Topology const&, AtomMask const&);
 
@@ -20,6 +21,7 @@ class RingFinder {
     typedef std::vector<AtomMask> Marray;
 
     Marray rings_; ///< Array of masks corresponding to rings
+    int debug_;
 };
 }
 }
diff --git a/src/StructureCheck.cpp b/src/StructureCheck.cpp
index cf6b63b05e..542b2e3b47 100644
--- a/src/StructureCheck.cpp
+++ b/src/StructureCheck.cpp
@@ -51,6 +51,7 @@ int StructureCheck::SetOptions(bool imageOn, bool checkBonds, bool saveProblemsI
   }
   }
 # endif
+  rings_.SetDebug( debug_ );
   return 0;
 }
 

From ebe21938178def85a311e7387ff74f251c5d7199 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 24 Jun 2024 13:09:43 -0400
Subject: [PATCH 0776/1492] Update help

---
 doc/cpptraj.lyx               | 10051 +++++++++++++++++---------------
 src/Exec_PermuteDihedrals.cpp |     4 +-
 2 files changed, 5445 insertions(+), 4610 deletions(-)

diff --git a/doc/cpptraj.lyx b/doc/cpptraj.lyx
index 6c8d45e670..e39d5b8e99 100644
--- a/doc/cpptraj.lyx
+++ b/doc/cpptraj.lyx
@@ -1,16 +1,16 @@
-#LyX 2.3 created this file. For more info see http://www.lyx.org/
-\lyxformat 544
+#LyX 2.4 created this file. For more info see https://www.lyx.org/
+\lyxformat 620
 \begin_document
 \begin_header
 \save_transient_properties true
 \origin unavailable
 \textclass article
 \use_default_options true
-\maintain_unincluded_children false
+\maintain_unincluded_children no
 \language english
 \language_package default
-\inputencoding auto
-\fontencoding global
+\inputencoding auto-legacy
+\fontencoding auto
 \font_roman "default" "default"
 \font_sans "default" "default"
 \font_typewriter "default" "default"
@@ -18,7 +18,9 @@
 \font_default_family default
 \use_non_tex_fonts false
 \font_sc false
-\font_osf false
+\font_roman_osf false
+\font_sans_osf false
+\font_typewriter_osf false
 \font_sf_scale 100 100
 \font_tt_scale 100 100
 \use_microtype false
@@ -62,7 +64,9 @@
 \suppress_date false
 \justification true
 \use_refstyle 1
+\use_formatted_ref 0
 \use_minted 0
+\use_lineno 0
 \index Index
 \shortcut idx
 \color #008000
@@ -78,11 +82,16 @@
 \papercolumns 1
 \papersides 1
 \paperpagestyle default
+\tablestyle default
 \tracking_changes false
 \output_changes false
+\change_bars false
+\postpone_fragile_content false
 \html_math_output 0
 \html_css_as_file 0
 \html_be_strict false
+\docbook_table_output 0
+\docbook_mathml_prefix 1
 \end_header
 
 \begin_body
@@ -108,15 +117,14 @@ literal "true"
 \emph on
 ptraj
 \emph default
-) is the main program in Amber for processing coordinate trajectories and
- data files.
+) is the main program in Amber for processing coordinate trajectories and data files.
  
 \shape italic
 Cpptraj
 \shape default
- has a wide range of functionality, and makes use of OpenMP/MPI to speed
- up many calculations, including processing ensembles of trajectories and/or
- conducting multiple analyses in parallel with MPI.
+ has a wide range of functionality,
+ and makes use of OpenMP/MPI to speed up many calculations,
+ including processing ensembles of trajectories and/or conducting multiple analyses in parallel with MPI.
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Roe2018"
@@ -144,10 +152,12 @@ Several actions/analyses in
 \emph on
 cpptraj
 \emph default
- are OpenMP parallelized; see section 
+ are OpenMP parallelized;
+ see section 
 \begin_inset CommandInset ref
 LatexCommand ref
 reference "subsec:CpptrajOpenMP"
+nolink "false"
 
 \end_inset
 
@@ -164,30 +174,30 @@ Almost any file read or written by
 cpptraj
 \emph default
  can be compressed (with the exception of the NetCDF trajectory format).
- So for example gzipped/bzipped topology files can be read, and data files
- can be written out as gzip/bzip2 files.
- Compression is detected automatically when reading, and is determined by
- the filename extension (.gz and .bz2 respectively) on writing.
+ So for example gzipped/bzipped topology files can be read,
+ and data files can be written out as gzip/bzip2 files.
+ Compression is detected automatically when reading,
+ and is determined by the filename extension (.gz and .bz2 respectively) on writing.
 \end_layout
 
 \begin_layout Enumerate
 The format of output data files can be specified by extension.
- For example, data files can be written in xmgrace format if the filename
- given has a '.agr' extension.
+ For example,
+ data files can be written in xmgrace format if the filename given has a '.agr' extension.
  A trajectory can be written in DCD format if the '.dcd' extension is used.
 \end_layout
 
 \begin_layout Enumerate
-Multiple output trajectories can be specified, and can be written during
- action processing (as opposed to only after) via the 
+Multiple output trajectories can be specified,
+ and can be written during action processing (as opposed to only after) via the 
 \series bold
 \shape italic
 outtraj
 \series default
 \shape default
  command.
- In addition, output files can be directed to write only specific frames
- from the input trajectories.
+ In addition,
+ output files can be directed to write only specific frames from the input trajectories.
 \end_layout
 
 \begin_layout Enumerate
@@ -203,7 +213,8 @@ rmsd
 \series default
 \shape default
  action allows specification of a separate mask for the reference structure.
- In addition, per-residue RMSD can be calculated easily.
+ In addition,
+ per-residue RMSD can be calculated easily.
  
 \end_layout
 
@@ -220,14 +231,12 @@ strip
 closest
 \series default
 \shape default
- actions can often write an accompanying fully-functional stripped topology
- file.
+ actions can often write an accompanying fully-functional stripped topology file.
  
 \end_layout
 
 \begin_layout Enumerate
-Users usually are able to fine-tune the output format of data files declared
- in actions using the 
+Users usually are able to fine-tune the output format of data files declared in actions using the 
 \begin_inset Quotes eld
 \end_inset
 
@@ -239,19 +248,21 @@ out
 \begin_inset Quotes erd
 \end_inset
 
- keyword (for example, the precision of the numbers can be changed).
- In addition, users can control which data sets are written to which files
- (e.g.
- if two actions specify the same data file with the 'out' keyword, data
- from both actions will be written to that data file).
+ keyword (for example,
+ the precision of the numbers can be changed).
+ In addition,
+ users can control which data sets are written to which files (e.g.
+ if two actions specify the same data file with the 'out' keyword,
+ data from both actions will be written to that data file).
 \end_layout
 
 \begin_layout Enumerate
-Users can manipulate data sets using mathematical expressions (with some
- limitations), see 
+Users can manipulate data sets using mathematical expressions (with some limitations),
+ see 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-Data-Set-Math"
+nolink "false"
 
 \end_inset
 
@@ -266,13 +277,15 @@ There is some support for creating internal loops over e.g.
 for
 \series default
 \emph default
-, 
+,
+ 
 \series bold
 \emph on
 set
 \series default
 \emph default
-, and 
+,
+ and 
 \series bold
 \emph on
 show
@@ -286,7 +299,9 @@ See the README.md file in the
 \emph on
 cpptraj
 \emph default
- home directory for information on how to build, authors, and so on.
+ home directory for information on how to build,
+ authors,
+ and so on.
 \end_layout
 
 \begin_layout Subsection
@@ -306,8 +321,8 @@ The syntax presented in this manual uses the following conventions:
 \end_layout
 
 \begin_layout Description
-{|} Denotes several choices separated by the '|' character; one of the choices
- must be specified.
+{|} Denotes several choices separated by the '|' character;
+ one of the choices must be specified.
 \end_layout
 
 \begin_layout Description
@@ -325,8 +340,8 @@ Installation
 \end_layout
 
 \begin_layout Standard
-See instructions in the CPPTRAJ GitHub repository README.md file under 'Installat
-ion & Testing': 
+See instructions in the CPPTRAJ GitHub repository README.md file under 'Installation & Testing':
+ 
 \begin_inset Flex URL
 status open
 
@@ -452,7 +467,8 @@ cpptraj [-p <Top0>] [-i <Input0>] [-y <trajin>] [-x <trajout>]
 \begin_inset space ~
 \end_inset
 
-<trajin>* Read from trajectory file <trajin>; same as input 'trajin <trajin>'.
+<trajin>* Read from trajectory file <trajin>;
+ same as input 'trajin <trajin>'.
 \end_layout
 
 \begin_layout Description
@@ -460,7 +476,8 @@ cpptraj [-p <Top0>] [-i <Input0>] [-y <trajin>] [-x <trajout>]
 \begin_inset space ~
 \end_inset
 
-<trajout>* Write trajectory file <trajout>; same as input 'trajout <trajout>'.
+<trajout>* Write trajectory file <trajout>;
+ same as input 'trajout <trajout>'.
 \end_layout
 
 \begin_layout Description
@@ -480,7 +497,9 @@ cpptraj [-p <Top0>] [-i <Input0>] [-y <trajin>] [-x <trajout>]
 \end_layout
 
 \begin_layout Description
-<file>* A topology, input trajectory, or file containing cpptraj input.
+<file>* A topology,
+ input trajectory,
+ or file containing cpptraj input.
 \end_layout
 
 \begin_layout Description
@@ -488,8 +507,8 @@ cpptraj [-p <Top0>] [-i <Input0>] [-y <trajin>] [-x <trajout>]
 \begin_inset space ~
 \end_inset
 
-<reference>* Read <reference> as reference coordinates; same as input 'reference
- <reference>'.
+<reference>* Read <reference> as reference coordinates;
+ same as input 'reference <reference>'.
 \end_layout
 
 \begin_layout Description
@@ -549,7 +568,8 @@ cpptraj [-p <Top0>] [-i <Input0>] [-y <trajin>] [-x <trajout>]
 \begin_inset space ~
 \end_inset
 
-<#> Set global debug level to <#>; same as input 'debug <#>'.
+<#> Set global debug level to <#>;
+ same as input 'debug <#>'.
 \end_layout
 
 \begin_layout Description
@@ -567,7 +587,8 @@ cpptraj [-p <Top0>] [-i <Input0>] [-y <trajin>] [-x <trajout>]
 
 \begin_layout Description
 -tl Print length of trajectories specified with '-y' to STDOUT.
- The total number of frames is written out as 'Frames: <X>'
+ The total number of frames is written out as 'Frames:
+ <X>'
 \end_layout
 
 \begin_layout Description
@@ -584,7 +605,8 @@ cpptraj [-p <Top0>] [-i <Input0>] [-y <trajin>] [-x <trajout>]
 \begin_inset space ~
 \end_inset
 
-<mask> : Print selected residue numbers to STDOUT.
+<mask> :
+ Print selected residue numbers to STDOUT.
  Selected residues are written out as 'Selected= 1 2 3 ...'
 \end_layout
 
@@ -626,14 +648,13 @@ Note that unlike
 \shape italic
 ptraj
 \shape default
-, in 
+,
+ in 
 \shape italic
 cpptraj
 \shape default
- it is not required that a topology file be specified on the command line
- as long as one is specified in the input file with the 'parm' keyword.
- Multiple topology/input files can be specified by use of multiple '-p'
- and '-i' flags.
+ it is not required that a topology file be specified on the command line as long as one is specified in the input file with the 'parm' keyword.
+ Multiple topology/input files can be specified by use of multiple '-p' and '-i' flags.
  All topology and coordinate flags will be processed before any input flags.
 \end_layout
 
@@ -646,11 +667,12 @@ Input to
 \shape italic
 cpptraj
 \shape default
- is in the form of commands, which can be categorized in to 2 types: immediate
- and queued.
+ is in the form of commands,
+ which can be categorized in to 2 types:
+ immediate and queued.
  Immediate commands are executed as soon as they are encountered.
- Queued commands are initialized when they are encountered, but are not
- executed until a Run is executed via a 
+ Queued commands are initialized when they are encountered,
+ but are not executed until a Run is executed via a 
 \series bold
 \shape italic
 run
@@ -663,19 +685,23 @@ go
 \series default
 \shape default
  command.
- Actions, Analyses, and Trajectory commands (except 
+ Actions,
+ Analyses,
+ and Trajectory commands (except 
 \series bold
 \emph on
 reference
 \series default
 \emph default
-) are queued commands; however, they can also be run immediately via commands
- such as 
+) are queued commands;
+ however,
+ they can also be run immediately via commands such as 
 \series bold
 \shape italic
 crdaction
 \series default
 ,
+
 \shape default
  
 \series bold
@@ -683,6 +709,7 @@ crdaction
 runanalysis
 \series default
 ,
+
 \shape default
  
 \series bold
@@ -690,11 +717,13 @@ runanalysis
 loadcrd
 \series default
 \emph default
-, etc.
+,
+ etc.
  See 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "sec:Coordinates-as-a"
+nolink "false"
 
 \end_inset
 
@@ -711,7 +740,9 @@ General (Immediate) These commands are executed immediately when entered.
 
 \begin_layout Description
 System (Immediate) These are unix system commands (e.g.
- 'ls', 'pwd', etc).
+ 'ls',
+ 'pwd',
+ etc).
 \end_layout
 
 \begin_layout Description
@@ -720,6 +751,7 @@ Coords (Immediate) These commands are used to manipulate COORDS data sets;
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "sec:Coordinates-as-a"
+nolink "false"
 
 \end_inset
 
@@ -727,43 +759,41 @@ reference "sec:Coordinates-as-a"
 \end_layout
 
 \begin_layout Description
-Trajectory (Queued) These commands prepare cpptraj for reading or writing
- trajectories during a Run.
+Trajectory (Queued) These commands prepare cpptraj for reading or writing trajectories during a Run.
 \end_layout
 
 \begin_layout Description
-Topology (Immediate) These commands are used to read, write, and modify
- topology information.
+Topology (Immediate) These commands are used to read,
+ write,
+ and modify topology information.
 \end_layout
 
 \begin_layout Description
-Action (Queued) These commands specify actions that will be performed on
- coordinate frames read in from trajectories during a Run.
+Action (Queued) These commands specify actions that will be performed on coordinate frames read in from trajectories during a Run.
 \end_layout
 
 \begin_layout Description
-Analysis (Queued) These commands specify analyses that will be performed
- on data that has been either generated from a Run or read in from an external
- source.
+Analysis (Queued) These commands specify analyses that will be performed on data that has been either generated from a Run or read in from an external source.
 \end_layout
 
 \begin_layout Description
-Control (Immediate) These commands set up control blocks that can be used
- to e.g.
+Control (Immediate) These commands set up control blocks that can be used to e.g.
  loop over a set of commands.
 \end_layout
 
 \begin_layout Standard
-In addition to normal commands, 
+In addition to normal commands,
+ 
 \emph on
 cpptraj
 \emph default
- now has the ability to perform certain basic math operations, even on data
- sets.
+ now has the ability to perform certain basic math operations,
+ even on data sets.
  See 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-Data-Set-Math"
+nolink "false"
 
 \end_inset
 
@@ -776,12 +806,13 @@ Commands in
 cpptraj
 \shape default
  can be read in from an input file or from the interactive command prompt.
- A '#' anywhere on a line denotes a comment; anything after '#' will be
- ignored no matter where it occurs.
+ A '#' anywhere on a line denotes a comment;
+ anything after '#' will be ignored no matter where it occurs.
  A '
 \backslash
 ' allows the continuation of one line to another.
- For example, the input:
+ For example,
+ the input:
 \end_layout
 
 \begin_layout LyX-Code
@@ -819,13 +850,11 @@ Getting Help
 \end_layout
 
 \begin_layout Standard
-If in interactive mode, the 'help' command can be used to list recognized
- commands and topics; topics (such as mask syntax) start with uppercase
- letters.
- 'help <command>' can be used to get the associated keywords as well as
- an abbreviated description of the command.
- Most commands have a corresponding test which also serves as an example
- of how to use the command.
+If in interactive mode,
+ the 'help' command can be used to list recognized commands and topics;
+ topics (such as mask syntax) start with uppercase letters.
+ 'help <command>' can be used to get the associated keywords as well as an abbreviated description of the command.
+ Most commands have a corresponding test which also serves as an example of how to use the command.
  See $AMBERHOME/AmberTools/test/cpptraj/README for more details.
 \end_layout
 
@@ -842,8 +871,8 @@ batch
 \begin_inset Quotes erd
 \end_inset
 
- mode, cpptraj is executed from the command line with one or more input
- files containing commands to be processed or STDIN.
+ mode,
+ cpptraj is executed from the command line with one or more input files containing commands to be processed or STDIN.
  The syntax of <input file> is similar to that of 
 \shape italic
 ptraj
@@ -871,13 +900,14 @@ interactive mode
 \end_inset
 
  users can enter commands in a UNIX-like shell.
- Interactive mode is useful for running short and simple analyses or for
- trying out new kinds of analyses.
+ Interactive mode is useful for running short and simple analyses or for trying out new kinds of analyses.
  If 
 \emph on
 cpptraj
 \emph default
- is run with '–interactive', no arguments, or no specified input file:
+ is run with '–interactive',
+ no arguments,
+ or no specified input file:
 \end_layout
 
 \begin_layout LyX-Code
@@ -898,13 +928,12 @@ cpptraj -p <parm file>
 
 \begin_layout Standard
 this brings up the interactive interface.
- This interface supports command history (via the up and down arrows) and
- tab completion for commands and file names.
- If no log file name has been given (with '–log <logfile>'), all commands
- used in interactive mode will be logged to a file named 'cpptraj.log', which
- can subsequently be used as input if desired.
- When starting cpptraj, command histories will be read from any existing
- logs.
+ This interface supports command history (via the up and down arrows) and tab completion for commands and file names.
+ If no log file name has been given (with '–log <logfile>'),
+ all commands used in interactive mode will be logged to a file named 'cpptraj.log',
+ which can subsequently be used as input if desired.
+ When starting cpptraj,
+ command histories will be read from any existing logs.
 \end_layout
 
 \begin_layout Subsection
@@ -924,7 +953,8 @@ Like
 \shape italic
 ptraj
 \shape default
-, a trajectory processing 
+,
+ a trajectory processing 
 \begin_inset Quotes eld
 \end_inset
 
@@ -937,14 +967,13 @@ Run
 cpptraj
 \shape default
 .
- First the Run is set up via commands read in from an input file or the
- interactive prompt.
- Trajectories are then read in one frame at a time (or in the case of ensemble
- processing all frames from a given step are read).
- Actions are performed on the coordinates stored in the frame, after which
- any output coordinates are written.
- At the end of the run, any data sets generated are written, and any queued
- Analyses are performed.
+ First the Run is set up via commands read in from an input file or the interactive prompt.
+ Trajectories are then read in one frame at a time (or in the case of ensemble processing all frames from a given step are read).
+ Actions are performed on the coordinates stored in the frame,
+ after which any output coordinates are written.
+ At the end of the run,
+ any data sets generated are written,
+ and any queued Analyses are performed.
 \end_layout
 
 \begin_layout Subsubsection
@@ -956,14 +985,12 @@ Since
 \emph on
 cpptraj
 \emph default
- supports multiple topology files, during a Run actions are set up every
- time the topology changes in order to recalculate things like what atoms
- are in a mask etc.
- Actions that are not valid for the current topology are skipped for that
- topology.
- So for example given two topology files with 100 residues, if the first
- topology file processed includes a ligand named MOL and the second one
- does not, the action:
+ supports multiple topology files,
+ during a Run actions are set up every time the topology changes in order to recalculate things like what atoms are in a mask etc.
+ Actions that are not valid for the current topology are skipped for that topology.
+ So for example given two topology files with 100 residues,
+ if the first topology file processed includes a ligand named MOL and the second one does not,
+ the action:
 \end_layout
 
 \begin_layout LyX-Code
@@ -971,8 +998,8 @@ distance :80 :MOL out D_80-to-MOL.dat
 \end_layout
 
 \begin_layout Standard
-will be valid for the first topology but not for the second, so it will
- be skipped as long as the second topology is active.
+will be valid for the first topology but not for the second,
+ so it will be skipped as long as the second topology is active.
 \end_layout
 
 \begin_layout Subsection
@@ -985,20 +1012,22 @@ Parallelization
 Cpptraj
 \emph default
  has many levels of parallelization that can be enabled via the '-mpi',
- '-openmp', and/or '-cuda' configure flags for MPI, OpenMP, and CUDA paralleliza
-tion respectively.
- At the highest level, trajectory and ensemble reads are parallelized with
- MPI.
- In addition, certain time consuming actions have been parallelized with
- OpenMP and/or CUDA.
+ '-openmp',
+ and/or '-cuda' configure flags for MPI,
+ OpenMP,
+ and CUDA parallelization respectively.
+ At the highest level,
+ trajectory and ensemble reads are parallelized with MPI.
+ In addition,
+ certain time consuming actions have been parallelized with OpenMP and/or CUDA.
 \end_layout
 
 \begin_layout Standard
-Note that any combination of the '-openmp', '-cuda', and '-mpi' flags may
- be used to generate a hybrid MPI/OpenMP/CUDA binary; however this may require
- additional runtime setup (e.g.
- setting OMP_NUM_THREADS for OpenMP) to work properly and not oversubscribe
- cores.
+Note that any combination of the '-openmp',
+ '-cuda',
+ and '-mpi' flags may be used to generate a hybrid MPI/OpenMP/CUDA binary;
+ however this may require additional runtime setup (e.g.
+ setting OMP_NUM_THREADS for OpenMP) to work properly and not oversubscribe cores.
 \end_layout
 
 \begin_layout Subsubsection
@@ -1024,62 +1053,72 @@ Cpptraj
 trajin
 \series default
 \emph default
-' trajectory input, where the trajectory read is divided as evenly as possible
- among all input frames (across-trajectory parallelism).
- For example, if given two trajectories of 1000 frames each and 4 MPI processes,
- process 0 reads frames 1-500 of trajectory 1, process 1 reads frames 501-1000
- of trajectory 1, process 2 reads frames 1-500 of trajectory 2, and process
- 3 reads frames 501-1000 of trajectory 2.
- Most Actions will work with across-trajectory parallelization with the
- exception of the following: 
+' trajectory input,
+ where the trajectory read is divided as evenly as possible among all input frames (across-trajectory parallelism).
+ For example,
+ if given two trajectories of 1000 frames each and 4 MPI processes,
+ process 0 reads frames 1-500 of trajectory 1,
+ process 1 reads frames 501-1000 of trajectory 1,
+ process 2 reads frames 1-500 of trajectory 2,
+ and process 3 reads frames 501-1000 of trajectory 2.
+ Most Actions will work with across-trajectory parallelization with the exception of the following:
+ 
 \series bold
 \emph on
 'clusterdihedral'
 \series default
 \emph default
-, 
+,
+ 
 \series bold
 \emph on
 'contacts'
 \series default
 \emph default
-, 
+,
+ 
 \series bold
 \emph on
 'createreservoir'
 \series default
 \emph default
-, 
+,
+ 
 \series bold
 \emph on
 'lipidorder'
 \series default
 \emph default
-, 
+,
+ 
 \series bold
 \emph on
 'pairwise'
 \series default
 \emph default
-, 
+,
+ 
 \series bold
 \emph on
 'stfcdiffusion'
 \series default
 \emph default
-, 
+,
+ 
 \series bold
 \emph on
 'tordiff'
 \series default
 \emph default
-, 
+,
+ 
 \series bold
 \emph on
 'unwrap'
 \series default
 \emph default
-, and 
+,
+ and 
 \series bold
 \emph on
 'xtalsymm'
@@ -1092,19 +1131,18 @@ trajin
 'diffusion'
 \series default
 \emph default
- Action will only work with across-trajectory parallelism if no imaging
- is to be performed.
+ Action will only work with across-trajectory parallelism if no imaging is to be performed.
 \end_layout
 
 \begin_layout Standard
-In addition to across-trajectory parallelism, the 
+In addition to across-trajectory parallelism,
+ the 
 \series bold
 \emph on
 'gist'
 \series default
 \emph default
- command will also MPI-parallelize the entropy calculation that occurs after
- trajectory processing.
+ command will also MPI-parallelize the entropy calculation that occurs after trajectory processing.
 \end_layout
 
 \begin_layout Standard
@@ -1117,28 +1155,28 @@ The second is for
 'ensemble'
 \series default
 \shape default
- trajectory input, where the reading/processing/writing of each member of
- the ensemble is divided up among MPI processes.
+ trajectory input,
+ where the reading/processing/writing of each member of the ensemble is divided up among MPI processes.
  The number of MPI processes must be a multiple of the ensemble size.
- If the number of processes is greater than the ensemble size then the processin
-g of each ensemble member will be divided among MPI processes (i.e.
+ If the number of processes is greater than the ensemble size then the processing of each ensemble member will be divided among MPI processes (i.e.
  across-trajectory parallelism will be used).
- For example, given an ensemble of 4 trajectories and 8 processes, processes
- 0 and 1 are assigned to the first ensemble trajectory, processes 2 and
- 3 are assigned to the second ensemble trajectory, and so on.
+ For example,
+ given an ensemble of 4 trajectories and 8 processes,
+ processes 0 and 1 are assigned to the first ensemble trajectory,
+ processes 2 and 3 are assigned to the second ensemble trajectory,
+ and so on.
  When using ensemble mode in parallel it is recommended that the 
 \series bold
 \emph on
 ensemblesize
 \series default
 \emph default
- command be used prior to any ensemble command as this will make set up
- far more efficient.
+ command be used prior to any ensemble command as this will make set up far more efficient.
 \end_layout
 
 \begin_layout Standard
-Note that most Analyses are not MPI-parallelized, with the exception of
- the 
+Note that most Analyses are not MPI-parallelized,
+ with the exception of the 
 \series bold
 \emph on
 calcdiffusion
@@ -1151,6 +1189,7 @@ reference "subsec:cpptraj-calcdiffusion"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
@@ -1158,7 +1197,8 @@ noprefix "false"
 \end_layout
 
 \begin_layout Standard
-In order to use the MPI version, Amber/
+In order to use the MPI version,
+ Amber/
 \emph on
 cpptraj
 \emph default
@@ -1167,8 +1207,9 @@ cpptraj
 \emph on
 cpptraj
 \emph default
- has been compiled with MPI as it will print 'MPI' in the title, and/or
- by calling 'cpptraj —defines' and looking for '-DMPI'.
+ has been compiled with MPI as it will print 'MPI' in the title,
+ and/or by calling 'cpptraj —
+defines' and looking for '-DMPI'.
  
 \end_layout
 
@@ -1188,8 +1229,7 @@ Some of the more time-consuming actions/analyses in
 \shape italic
 cpptraj
 \shape default
- have been parallelized with OpenMP to take advantage of machines with multiple
- cores.
+ have been parallelized with OpenMP to take advantage of machines with multiple cores.
  In order to use OpenMP parallelization Amber/
 \emph on
 cpptraj
@@ -1199,8 +1239,9 @@ cpptraj
 \shape italic
 cpptraj
 \shape default
- has been compiled with OpenMP as it will print 'OpenMP' in the title, and/or
- by calling 'cpptraj —defines' and looking for '-D_OPENMP'.
+ has been compiled with OpenMP as it will print 'OpenMP' in the title,
+ and/or by calling 'cpptraj —
+defines' and looking for '-D_OPENMP'.
  The following actions/analyses have been OpenMP parallelized:
 \end_layout
 
@@ -1322,8 +1363,7 @@ By default OpenMP
 cpptraj
 \shape default
  will use all available cores.
- The number of OpenMP threads can be controlled by setting the OMP_NUM_THREADS
- environment variable.
+ The number of OpenMP threads can be controlled by setting the OMP_NUM_THREADS environment variable.
 \end_layout
 
 \begin_layout Subsubsection
@@ -1331,13 +1371,11 @@ CUDA Parallelization
 \end_layout
 
 \begin_layout Standard
-Some time-consuming actions in cpptraj have been parallelized with CUDA
- to take advantage of machines with NVIDIA GPUs.
- In order to use CUDA parallelization Amber/cpptraj should be configured
- with the '-cuda' flag.
- You can easily tell if cpptraj has been compiled with CUDA as it will print
- 'CUDA' and details on the current graphics device in the title, and/or
- by calling 'cpptraj —defines' and looking for '-DCUDA'.
+Some time-consuming actions in cpptraj have been parallelized with CUDA to take advantage of machines with NVIDIA GPUs.
+ In order to use CUDA parallelization Amber/cpptraj should be configured with the '-cuda' flag.
+ You can easily tell if cpptraj has been compiled with CUDA as it will print 'CUDA' and details on the current graphics device in the title,
+ and/or by calling 'cpptraj —
+defines' and looking for '-DCUDA'.
  The following actions have been CUDA parallelized:
 \end_layout
 
@@ -1367,8 +1405,8 @@ Units
 
 \begin_layout Standard
 Cpptraj uses the AKMA system of units.
- The execption is time, which is typically expressed in ps (except where
- noted).
+ The execption is time,
+ which is typically expressed in ps (except where noted).
 \begin_inset Separator latexpar
 \end_inset
 
@@ -1547,16 +1585,17 @@ ptraj
 \family typewriter
 :
 \family default
-', '
+',
+ '
 \family typewriter
 @
 \family default
-', and '
+',
+ and '
 \family typewriter
 *
 \family default
-' are reserved for masks and should not be used in output file or data set
- names.
+' are reserved for masks and should not be used in output file or data set names.
  All masks are case-sensitive.
  Either names or numbers can be used.
  Masks can contain ranges (denoted with '
@@ -1568,11 +1607,13 @@ ptraj
 \family typewriter
 &
 \family default
-' (and), '
+' (and),
+ '
 \family typewriter
 |
 \family default
-' (or), and '
+' (or),
+ and '
 \family typewriter
 !
 \family default
@@ -1590,7 +1631,9 @@ The syntax for elementary selections is the following:
 \end_inset
 
 numlist} e.g.
- '@12,17', '@54-85', '@12,54-85,90'
+ '@12,17',
+ '@54-85',
+ '@12,54-85,90'
 \end_layout
 
 \begin_layout Description
@@ -1599,7 +1642,8 @@ numlist} e.g.
 \end_inset
 
 namelist} e.g.
- '@CA', '@CA,C,O,N,H'
+ '@CA',
+ '@CA,C,O,N,H'
 \end_layout
 
 \begin_layout Description
@@ -1626,7 +1670,9 @@ name} e.g.
 \end_inset
 
 numlist} e.g.
- ':1-10', ':1,3,5', ':1-3,5,7-9'
+ ':1-10',
+ ':1,3,5',
+ ':1-3,5,7-9'
 \end_layout
 
 \begin_layout Description
@@ -1635,7 +1681,8 @@ numlist} e.g.
 \end_inset
 
 namelist} e.g.
- ':LYS', ':ARG,ALA,GLY'
+ ':LYS',
+ ':ARG,ALA,GLY'
 \end_layout
 
 \begin_layout Description
@@ -1644,7 +1691,8 @@ namelist} e.g.
 \end_inset
 
 id} e.g.
- '::B', '::A,D'.
+ '::B',
+ '::A,D'.
  Requires chain ID information be present in the topology.
 \end_layout
 
@@ -1659,11 +1707,12 @@ residue
 
 number} e.g.
  ':;2-4,8'.
- Requires a PDB loaded as topology, or Amber topology with embedded PDB
- information (see 
+ Requires a PDB loaded as topology,
+ or Amber topology with embedded PDB information (see 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:parmed_addPDB"
+nolink "false"
 
 \end_inset
 
@@ -1676,7 +1725,8 @@ reference "subsec:parmed_addPDB"
 \end_inset
 
 numlist} e.g.
- '^1-10', ':23,84,111'
+ '^1-10',
+ ':23,84,111'
 \end_layout
 
 \begin_layout Description
@@ -1684,7 +1734,8 @@ numlist} e.g.
 \begin_inset space ~
 \end_inset
 
-operator><distance> Selection by distance, see below.
+operator><distance> Selection by distance,
+ see below.
 \end_layout
 
 \begin_layout Standard
@@ -1704,7 +1755,8 @@ Several wildcard characters are supported:
 \end_layout
 
 \begin_layout Standard
-The wildcards can also be used with numbers or other mask characters, e.g.
+The wildcards can also be used with numbers or other mask characters,
+ e.g.
  ':?0' means 
 \begin_inset Quotes eld
 \end_inset
@@ -1713,7 +1765,8 @@ The wildcards can also be used with numbers or other mask characters, e.g.
 \begin_inset Quotes erd
 \end_inset
 
-, ':*' means all residues and '@*' means all atoms.
+,
+ ':*' means all residues and '@*' means all atoms.
  If the atom name (or type name) contains a wildcard character like an asterisk,
  it can be explictly selected by escaping (i.e.
  preceding) the wildcard character with a backslash '
@@ -1727,7 +1780,11 @@ atoms @C?*
 \end_layout
 
 \begin_layout Standard
-would select atoms named C5, C4*, C422, etc., but:
+would select atoms named C5,
+ C4*,
+ C422,
+ etc.,
+ but:
 \end_layout
 
 \begin_layout LyX-Code
@@ -1749,7 +1806,8 @@ Compound expressions of the following type are allowed:
 \end_layout
 
 \begin_layout Standard
-and are processed as: 
+and are processed as:
+ 
 \end_layout
 
 \begin_layout LyX-Code
@@ -1770,7 +1828,8 @@ e.g.
 \end_layout
 
 \begin_layout Standard
-More examples: 
+More examples:
+ 
 \end_layout
 
 \begin_layout Description
@@ -1798,8 +1857,8 @@ More examples:
 \end_layout
 
 \begin_layout Description
-:1-500@O&!(:WAT|:LYS,ARG) All backbone oxygens in residues 1-500 but not
- in water, lysine or arginine residues.
+:1-500@O&!(:WAT|:LYS,ARG) All backbone oxygens in residues 1-500 but not in water,
+ lysine or arginine residues.
 \end_layout
 
 \begin_layout Description
@@ -1852,11 +1911,13 @@ operator> Distance operator.
 \end_layout
 
 \begin_layout Description
-: Any atom within a residue.
+:
+ Any atom within a residue.
 \end_layout
 
 \begin_layout Description
-; Residue geometric center.
+;
+ Residue geometric center.
 \end_layout
 
 \begin_layout Description
@@ -1870,8 +1931,7 @@ operator> Distance operator.
 
 \end_deeper
 \begin_layout Standard
-There are two very important things to keep in mind when using distance
- based masks:
+There are two very important things to keep in mind when using distance based masks:
 \end_layout
 
 \begin_layout Enumerate
@@ -1901,7 +1961,8 @@ mask
 reference
 \series default
 \shape default
-; distances are then calculated using the 
+;
+ distances are then calculated using the 
 \bar under
 specified reference frame only
 \bar default
@@ -1933,7 +1994,8 @@ The syntax for selection by distance is a
 \series bold
 <distance operator>
 \series default
- consists of 2 characters: '
+ consists of 2 characters:
+ '
 \series bold
 <
 \series default
@@ -1945,16 +2007,20 @@ The syntax for selection by distance is a
 \series bold
 ^
 \series default
-' (molecules), '
+' (molecules),
+ '
 \series bold
 :
 \series default
-' (residues), ';' (residue centers), or '
+' (residues),
+ ';' (residue centers),
+ or '
 \series bold
 @
 \series default
 ' (atoms).
- For example, '
+ For example,
+ '
 \series bold
 <:
 \series default
@@ -1967,15 +2033,16 @@ residues within 3.0 Angstroms
 \end_inset
 
  etc.
- For ':' residue- and '^' molecule-based distance selection, if any atom
- in that residue/molecule meets the given distance criterion, the entire
- residue/molecule is selected.
- For ';' residue center, the geometric center of the residue must meet the
- given distance criterion in order to be selected.
+ For ':' residue- and '^' molecule-based distance selection,
+ if any atom in that residue/molecule meets the given distance criterion,
+ the entire residue/molecule is selected.
+ For ';' residue center,
+ the geometric center of the residue must meet the given distance criterion in order to be selected.
 \end_layout
 
 \begin_layout Standard
-In plain language, the entire distance mask can be read as 
+In plain language,
+ the entire distance mask can be read as 
 \begin_inset Quotes eld
 \end_inset
 
@@ -1996,7 +2063,8 @@ Select
 \end_inset
 
 .
- So for example, the mask expression:
+ So for example,
+ the mask expression:
 \end_layout
 
 \begin_layout LyX-Code
@@ -2008,8 +2076,7 @@ Means
 \begin_inset Quotes eld
 \end_inset
 
-Select atoms within 2.4 Å distance of atoms selected by ':11-17' (residues
- numbered 11 through 17)
+Select atoms within 2.4 Å distance of atoms selected by ':11-17' (residues numbered 11 through 17)
 \begin_inset Quotes erd
 \end_inset
 
@@ -2040,15 +2107,19 @@ Ranges
 
 \begin_layout Standard
 For several commands some arguments are ranges (e.g.
- 'trajout onlyframes <range>', 'nastruct resrange <range>', 'rmsd perres
- range <range>'); 
+ 'trajout onlyframes <range>',
+ 'nastruct resrange <range>',
+ 'rmsd perres range <range>');
+ 
 \series bold
 THESE ARE NOT ATOM MASKS
 \series default
 .
- They are simple number ranges using '-' to specify a range and ',' to separate
- different ranges.
- For example 1-2,4-6,9 specifies 1 to 2, 4 to 6, and 9, i.e.
+ They are simple number ranges using '-' to specify a range and ',' to separate different ranges.
+ For example 1-2,4-6,9 specifies 1 to 2,
+ 4 to 6,
+ and 9,
+ i.e.
  '1 2 4 5 6 9'.
 \end_layout
 
@@ -2065,16 +2136,16 @@ name "subsec:Parameter/Reference-Tagging"
 
 \begin_layout Standard
 Parameter and reference files may be 'tagged' (i.e.
- given a nickname); these tags can then be used in place of the file name
- itself.
+ given a nickname);
+ these tags can then be used in place of the file name itself.
  A tag in 
 \shape italic
 cpptraj
 \shape default
  is recognized by being bounded by brackets ('[' and ']').
- This can be particularly useful when reading in many parameter or reference
- files.
- For example, when reading in multiple reference structures:
+ This can be particularly useful when reading in many parameter or reference files.
+ For example,
+ when reading in multiple reference structures:
 \end_layout
 
 \begin_layout LyX-Code
@@ -2106,15 +2177,15 @@ rms Open ref [open] :2-12@CA out rmsd.dat
 \end_layout
 
 \begin_layout Standard
-This defines three reference structures and gives them tags [xray], [last],
+This defines three reference structures and gives them tags [xray],
+ [last],
  and [open].
- These reference structures can then be referred to by their tags instead
- of their filenames by any action that uses reference structures (in this
- case the RMSD action).
+ These reference structures can then be referred to by their tags instead of their filenames by any action that uses reference structures (in this case the RMSD action).
 \end_layout
 
 \begin_layout Standard
-Similarly, this can be useful when reading in multiple parameter files:
+Similarly,
+ this can be useful when reading in multiple parameter files:
 \end_layout
 
 \begin_layout LyX-Code
@@ -2139,12 +2210,11 @@ rms ref [tz2] !(:WAT) out rmsd.dat
 
 \begin_layout Standard
 This defines two parm files and gives them tags [tz2-water] and [tz2-nowater],
- then reads in a trajectory associated with one, and a reference structure
- associated with the other.
- Note that in the 'reference' command there are two tags; the first goes
- along with the 'parm' keyword and specifies what parameter file the reference
- should use, the second is the tag given to the reference itself (as in
- the previous example) and is referred to in the subsequent RMSD action.
+ then reads in a trajectory associated with one,
+ and a reference structure associated with the other.
+ Note that in the 'reference' command there are two tags;
+ the first goes along with the 'parm' keyword and specifies what parameter file the reference should use,
+ the second is the tag given to the reference itself (as in the previous example) and is referred to in the subsequent RMSD action.
 \end_layout
 
 \begin_layout Section
@@ -2152,7 +2222,8 @@ Variables and Control Structures
 \end_layout
 
 \begin_layout Standard
-As of version 18, CPPTRAJ has limited support for 
+As of version 18,
+ CPPTRAJ has limited support for 
 \begin_inset Quotes eld
 \end_inset
 
@@ -2161,10 +2232,8 @@ script
 \end_inset
 
  variables and 'for' loops.
- Script variables are referred to by a dollar sign ('$') prefix and are
- replaced when they are processed.
- These are stored in the master data set list like other data and are assigned
- the type 
+ Script variables are referred to by a dollar sign ('$') prefix and are replaced when they are processed.
+ These are stored in the master data set list like other data and are assigned the type 
 \begin_inset Quotes eld
 \end_inset
 
@@ -2175,11 +2244,12 @@ string variable
 .
  
 \series bold
-Note that to use script variables in CPPTRAJ input that is inside another
- script (e.g.
- a BASH script), they must be escaped with the '
+Note that to use script variables in CPPTRAJ input that is inside another script (e.g.
+ a BASH script),
+ they must be escaped with the '
 \backslash
 ' character,
+
 \series default
  e.g.
 \end_layout
@@ -2211,9 +2281,7 @@ EOF
 \end_layout
 
 \begin_layout Standard
-Note that regular CPPTRAJ 1D Data Sets that contain a single value can be
- used as script variables (if the Data Set contains more than 1 value only
- the first value will be used).
+Note that regular CPPTRAJ 1D Data Sets that contain a single value can be used as script variables (if the Data Set contains more than 1 value only the first value will be used).
 \end_layout
 
 \begin_layout Standard
@@ -2351,15 +2419,21 @@ for { {atoms|residues|molecules|molfirstres|mollastres}
 \end_layout
 
 \begin_layout LyX-Code
-	END KEYWORD: 'done'
+	END KEYWORD:
+ 'done'
 \end_layout
 
 \begin_layout LyX-Code
-  Available 'end OP'       : '<' '>' '<=' '>='
+  Available 'end OP'       :
+ '<' '>' '<=' '>='
 \end_layout
 
 \begin_layout LyX-Code
-  Available 'increment OP' : '++', '--', '+=', '-='
+  Available 'increment OP' :
+ '++',
+ '--',
+ '+=',
+ '-='
 \end_layout
 
 \begin_deeper
@@ -2376,9 +2450,8 @@ inmask
 \begin_inset space ~
 \end_inset
 
-<mask> Loop over atoms/residues/molecules/first residue in molecules/last
- residue in molecules selected by the given mask expression, set as script
- variable 
+<mask> Loop over atoms/residues/molecules/first residue in molecules/last residue in molecules selected by the given mask expression,
+ set as script variable 
 \series bold
 <var>
 \series default
@@ -2492,8 +2565,8 @@ blocksize
 \end_layout
 
 \begin_layout Description
-[cumulative] Instead of blocks of fixed size, use blocks of increasing size
- incremented by blocksize.
+[cumulative] Instead of blocks of fixed size,
+ use blocks of increasing size incremented by blocksize.
 \end_layout
 
 \begin_deeper
@@ -2502,8 +2575,8 @@ blocksize
 \begin_inset space ~
 \end_inset
 
-<#>] When cumulative, the size of the first block (default is first data
- set element).
+<#>] When cumulative,
+ the size of the first block (default is first data set element).
 \end_layout
 
 \end_deeper
@@ -2525,11 +2598,13 @@ OP>[<value>] Loop over integer script variable
 \series bold
 <start>
 \series default
-, optionally ending at 
+,
+ optionally ending at 
 \series bold
 <end>
 \series default
-, increment by 
+,
+ increment by 
 \series bold
 <value>
 \series default
@@ -2545,8 +2620,7 @@ Data Sets Created (datasetblocks loops):
 \begin_inset space \space{}
 \end_inset
 
-idx> (Data set blocks only) Data set block of blocksize starting at <start
- idx>.
+idx> (Data set blocks only) Data set block of blocksize starting at <start idx>.
 \end_layout
 
 \begin_layout Description
@@ -2554,17 +2628,17 @@ idx> (Data set blocks only) Data set block of blocksize starting at <start
 \begin_inset space ~
 \end_inset
 
-idx> (Cumulative data set blocks only) Data set block starting at firstblock
- and ending at <end idx>.
+idx> (Cumulative data set blocks only) Data set block starting at firstblock and ending at <end idx>.
 \end_layout
 
 \end_deeper
 \begin_layout Standard
-Create a for loop using one or more mask expressions, integers, etc.
+Create a for loop using one or more mask expressions,
+ integers,
+ etc.
  Loops can be nested inside each other.
- Integer loops may be used without an end condition, but in that case at
- least one descriptor in the loop should have an end condition or refer
- to a mask.
+ Integer loops may be used without an end condition,
+ but in that case at least one descriptor in the loop should have an end condition or refer to a mask.
  Loops are ended by the 
 \series bold
 done
@@ -2575,7 +2649,8 @@ done
 
 \begin_layout Standard
 Note that non-integer variables (e.g.
- 'inmask' loops) are NOT incremented after the final loop iteration, i.e.
+ 'inmask' loops) are NOT incremented after the final loop iteration,
+ i.e.
  these loop variables always retain their final value.
 \end_layout
 
@@ -2596,10 +2671,9 @@ done
 \end_layout
 
 \begin_layout Standard
-This loops over all atoms in the mask expression ':1-3@CA' (all atoms named
- CA in residues 1 to 3) and creates a variable named 'i' that starts from
- 1 and is incremented by 1 each iteration.
- Inside the loop, the mask selection is referred to by 
+This loops over all atoms in the mask expression ':1-3@CA' (all atoms named CA in residues 1 to 3) and creates a variable named 'i' that starts from 1 and is incremented by 1 each iteration.
+ Inside the loop,
+ the mask selection is referred to by 
 \series bold
 $A0
 \series default
@@ -2668,7 +2742,9 @@ set { <variable> <OP> <value> |
 \end_layout
 
 \begin_layout LyX-Code
-  Available <OP> : '=', '+='
+  Available <OP> :
+ '=',
+ '+='
 \end_layout
 
 \begin_deeper
@@ -2705,10 +2781,9 @@ inmask
 \begin_inset space ~
 \end_inset
 
-<mask> Set/append a script variable to/by the total number of atoms/residues/mol
-ecules in, a range expression of selected atom #s/residue #s/original residue
- #s/molecule #s in, or the total charge/mass of atoms selected by the given
- mask expression.
+<mask> Set/append a script variable to/by the total number of atoms/residues/molecules in,
+ a range expression of selected atom #s/residue #s/original residue #s/molecule #s in,
+ or the total charge/mass of atoms selected by the given mask expression.
 \end_layout
 
 \begin_deeper
@@ -2750,8 +2825,7 @@ parmindex
 \begin_inset space ~
 \end_inset
 
-trajinframes Set/append a script variable to/by the total number of frames
- in trajectories currently loaded by 
+trajinframes Set/append a script variable to/by the total number of frames in trajectories currently loaded by 
 \series bold
 \emph on
 trajin
@@ -2763,12 +2837,13 @@ trajin
 \end_deeper
 \begin_layout Standard
 Set (<OP> = '=') or append (<OP> = '+=') a script variable.
- Script variables are character strings, and are referred to in CPPTRAJ
- input by using a dollar sign '$' prefix.
+ Script variables are character strings,
+ and are referred to in CPPTRAJ input by using a dollar sign '$' prefix.
 \end_layout
 
 \begin_layout Standard
-For example, the following input will load files my.parm7 and my.rst7:
+For example,
+ the following input will load files my.parm7 and my.rst7:
 \end_layout
 
 \begin_layout LyX-Code
@@ -2784,8 +2859,8 @@ trajin $PREFIX.rst7
 \end_layout
 
 \begin_layout Standard
-For example, the following input will print info for the last 10 atoms in
- a topology to 'last10.dat':
+For example,
+ the following input will print info for the last 10 atoms in a topology to 'last10.dat':
 \end_layout
 
 \begin_layout LyX-Code
@@ -2813,7 +2888,8 @@ The following input will put a range of residues selected by :LYS:
 \end_layout
 
 \begin_layout LyX-Code
-	Using topology: FtuFabI.NAD.TCL.parm7
+	Using topology:
+ FtuFabI.NAD.TCL.parm7
 \end_layout
 
 \begin_layout LyX-Code
@@ -2829,9 +2905,10 @@ show [<var1> ...]
 \end_layout
 
 \begin_layout Standard
-If no variable names specified, show all current script variables and their
- values.
- Otherwise, show the values of the specified script variables.
+If no variable names specified,
+ show all current script variables and their values.
+ Otherwise,
+ show the values of the specified script variables.
 \end_layout
 
 \begin_layout Section
@@ -2843,19 +2920,19 @@ In
 \shape italic
 cpptraj
 \shape default
-, Actions and Analyses can generate one or more data sets which are available
- for further processing.
- For example, the 
+,
+ Actions and Analyses can generate one or more data sets which are available for further processing.
+ For example,
+ the 
 \series bold
 \shape italic
 distance
 \series default
 \shape default
  command creates a data set containing distances vs time.
- The data set can be named by the user simply by specifying a non-keyword
- string as an additional argument.
- If no name is given, a default one will be generated based on the action
- name and data set number.
+ The data set can be named by the user simply by specifying a non-keyword string as an additional argument.
+ If no name is given,
+ a default one will be generated based on the action name and data set number.
  For example:
 \end_layout
 
@@ -2873,7 +2950,8 @@ d1-2
 \end_inset
 
 .
- If a name is not specified, e.g.:
+ If a name is not specified,
+ e.g.:
 \end_layout
 
 \begin_layout LyX-Code
@@ -2893,7 +2971,8 @@ Dis_00000
 \end_layout
 
 \begin_layout Standard
-Data files are created automatically by most commands, usually via the 
+Data files are created automatically by most commands,
+ usually via the 
 \begin_inset Quotes eld
 \end_inset
 
@@ -2934,34 +3013,38 @@ readdata
 \begin_inset CommandInset ref
 LatexCommand ref
 reference "tab:cpptraj-DataFile-formats"
+nolink "false"
 
 \end_inset
 
-, although it cannot write in all formats.
- In addition, a data set must be valid for the data file format.
- For example, 3D data (such as a grid) can be written to an OpenDX format
- file but not a Grace format file.
+,
+ although it cannot write in all formats.
+ In addition,
+ a data set must be valid for the data file format.
+ For example,
+ 3D data (such as a grid) can be written to an OpenDX format file but not a Grace format file.
  
 \end_layout
 
 \begin_layout Standard
-The default file format is called 'Standard', which simply has data in columns,
+The default file format is called 'Standard',
+ which simply has data in columns,
  like 
 \shape italic
 ptraj
 \shape default
-, although multiple data sets can be directed to the same output file.
- The format of a file can be changed either by specifying a recognized keyword
- (either on the command line itself or later via a 'datafile' command) or
- by giving the file an extension corresponding to te format, so 'filename.agr'
- will output in Grace format, and 'filename.gnu' will output in Gnuplot contour,
+,
+ although multiple data sets can be directed to the same output file.
+ The format of a file can be changed either by specifying a recognized keyword (either on the command line itself or later via a 'datafile' command) or by giving the file an extension corresponding to te format,
+ so 'filename.agr' will output in Grace format,
+ and 'filename.gnu' will output in Gnuplot contour,
  and so on.
- The xmgrace/gnuplot output is particularly nice for the secstruct sumout
- and rmsd perresout files.
+ The xmgrace/gnuplot output is particularly nice for the secstruct sumout and rmsd perresout files.
  Additional options for data files can be found in 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "sec:Datafile-Commands"
+nolink "false"
 
 \end_inset
 
@@ -2977,9 +3060,9 @@ out
 \begin_inset Quotes erd
 \end_inset
 
- keyword will allow data sets from separate commands to be written into
- the same file.
- For example, the commands:
+ keyword will allow data sets from separate commands to be written into the same file.
+ For example,
+ the commands:
 \end_layout
 
 \begin_layout LyX-Code
@@ -3023,12 +3106,14 @@ phipsi.dat
 \end_layout
 
 \begin_layout Standard
-Note that when reading the Amber Prep and Amber OFF Library formats, a COORDS
- data set will be created for each unit present in these files.
+Note that when reading the Amber Prep and Amber OFF Library formats,
+ a COORDS data set will be created for each unit present in these files.
 \end_layout
 
 \begin_layout Standard
 \begin_inset Float table
+placement document
+alignment document
 wide false
 sideways false
 status open
@@ -3132,7 +3217,9 @@ dat
 \begin_inset Text
 
 \begin_layout Plain Layout
-1D, 2D, 3D
+1D,
+ 2D,
+ 3D
 \end_layout
 
 \end_inset
@@ -3161,7 +3248,8 @@ Grace
 \begin_inset Text
 
 \begin_layout Plain Layout
-.agr, .xmgr
+.agr,
+ .xmgr
 \end_layout
 
 \end_inset
@@ -3226,7 +3314,8 @@ gnu
 \begin_inset Text
 
 \begin_layout Plain Layout
-1D, 2D
+1D,
+ 2D
 \end_layout
 
 \end_inset
@@ -3255,7 +3344,8 @@ Xplor
 \begin_inset Text
 
 \begin_layout Plain Layout
-.xplor, .grid
+.xplor,
+ .grid
 \end_layout
 
 \end_inset
@@ -3423,7 +3513,8 @@ mdout
 \begin_inset Text
 
 \begin_layout Plain Layout
-Energy information, Read Only
+Energy information,
+ Read Only
 \end_layout
 
 \end_inset
@@ -3846,7 +3937,8 @@ charmmout
 \begin_inset Text
 
 \begin_layout Plain Layout
-Energy information, Read Only
+Energy information,
+ Read Only
 \end_layout
 
 \end_inset
@@ -4054,7 +4146,8 @@ Amber OFF Library File
 \begin_inset Text
 
 \begin_layout Plain Layout
-.off, .lib
+.off,
+ .lib
 \end_layout
 
 \end_inset
@@ -4148,8 +4241,10 @@ entire
 
 \series bold
 <name>:
+
 \series default
- The data set name, usually specified in the action (e.g.
+ The data set name,
+ usually specified in the action (e.g.
  in 'distance d0 @1 @2' the data set name is 
 \begin_inset Quotes eld
 \end_inset
@@ -4165,16 +4260,18 @@ d0
 
 \series bold
 <aspect>:
+
 \series default
- Optional; this is set for certain data sets internally in order to easily
- select subsets of data.
+ Optional;
+ this is set for certain data sets internally in order to easily select subsets of data.
  
 \series bold
 The brackets are required
 \series default
 .
- For example, when using 'hbond series', both solute-solute and solute-solvent
- hydrogen bond time series may be generated.
+ For example,
+ when using 'hbond series',
+ both solute-solute and solute-solvent hydrogen bond time series may be generated.
  To select all solute-solute hydrogen bonds one would use the aspect 
 \begin_inset Quotes eld
 \end_inset
@@ -4183,7 +4280,8 @@ The brackets are required
 \begin_inset Quotes erd
 \end_inset
 
-; to select solute-solvent hydrogen bonds the aspect 
+;
+ to select solute-solvent hydrogen bonds the aspect 
 \begin_inset Quotes eld
 \end_inset
 
@@ -4199,16 +4297,20 @@ The brackets are required
 
 \series bold
 <index>:
+
 \series default
- Optional; for actions that generate many data sets (such as 'rmsd perres')
- an index is used.
- Depending on the action, the index may correspond to atom #s, residue #s,
+ Optional;
+ for actions that generate many data sets (such as 'rmsd perres') an index is used.
+ Depending on the action,
+ the index may correspond to atom #s,
+ residue #s,
  etc.
  A number range (comma and/or dash separated) may be used.
 \end_layout
 
 \begin_layout Standard
-For example: to select all data sets with aspect 
+For example:
+ to select all data sets with aspect 
 \begin_inset Quotes eld
 \end_inset
 
@@ -4232,7 +4334,8 @@ To select all data sets with aspect
 \begin_inset Quotes erd
 \end_inset
 
- with any name, indices 1 and 3:
+ with any name,
+ indices 1 and 3:
 \end_layout
 
 \begin_layout LyX-Code
@@ -4240,7 +4343,8 @@ To select all data sets with aspect
 \end_layout
 
 \begin_layout Standard
-In ensemble mode, data set selection has additional syntax:
+In ensemble mode,
+ data set selection has additional syntax:
 \end_layout
 
 \begin_layout LyX-Code
@@ -4263,11 +4367,13 @@ name "subsec:cpptraj-Data-Set-Math"
 \end_layout
 
 \begin_layout Standard
-As of version 15, 
+As of version 15,
+ 
 \emph on
 cpptraj
 \emph default
- can perform basic math operations, even on data sets (with some limitations).
+ can perform basic math operations,
+ even on data sets (with some limitations).
  Currently recognized operations are:
 \begin_inset Separator latexpar
 \end_inset
@@ -4748,11 +4854,13 @@ E
 \begin_inset Quotes erd
 \end_inset
 
- notation, e.g.
+ notation,
+ e.g.
  1E-5 = 0.00001.
  The parser also recognizes PI as the number pi.
  Expressions can also be enclosed in parentheses.
- So for example, the following expression is valid:
+ So for example,
+ the following expression is valid:
 \end_layout
 
 \begin_layout LyX-Code
@@ -4760,12 +4868,12 @@ E
 \end_layout
 
 \begin_layout LyX-Code
-Result: 0.879887
+Result:
+ 0.879887
 \end_layout
 
 \begin_layout Standard
-Results of numerical calculations like the above can be assigned to a variable
- (essentially a data set of size 1) for use in subsequent calculations,
+Results of numerical calculations like the above can be assigned to a variable (essentially a data set of size 1) for use in subsequent calculations,
  e.g.
 \end_layout
 
@@ -4778,15 +4886,18 @@ Result stored in 'R'
 \end_layout
 
 \begin_layout LyX-Code
-> R + 1 Result: 1.879887
+> R + 1 Result:
+ 1.879887
 \end_layout
 
 \begin_layout Standard
 Data sets can be specified in expressions as well.
- Currently data sets in an expression must be of the same type and only
- 1D, 2D, and 3D data sets are supported.
+ Currently data sets in an expression must be of the same type and only 1D,
+ 2D,
+ and 3D data sets are supported.
  Functions are applied to each member of the data set.
- So for example, given two 1D data sets of the same size named D0 and D1,
+ So for example,
+ given two 1D data sets of the same size named D0 and D1,
  the following expression:
 \end_layout
 
@@ -4795,8 +4906,9 @@ Data sets can be specified in expressions as well.
 \end_layout
 
 \begin_layout Standard
-would take the square root of each member of D0, add it to the corresponding
- member of D1, and assign the result to D2.
+would take the square root of each member of D0,
+ add it to the corresponding member of D1,
+ and assign the result to D2.
  The following table lists which operations are valid for data set types.
  If a type is not listed it is not supported:
 \begin_inset Separator latexpar
@@ -4865,7 +4977,9 @@ Notes
 \begin_inset Text
 
 \begin_layout Plain Layout
-1D (integer, double, float)
+1D (integer,
+ double,
+ float)
 \end_layout
 
 \end_inset
@@ -4912,7 +5026,11 @@ All
 \begin_inset Text
 
 \begin_layout Plain Layout
-+, -, *, /, =
++,
+ -,
+ *,
+ /,
+ =
 \end_layout
 
 \end_inset
@@ -4950,7 +5068,11 @@ None
 \begin_inset Text
 
 \begin_layout Plain Layout
-+, -, /, *, =
++,
+ -,
+ /,
+ *,
+ =
 \end_layout
 
 \end_inset
@@ -4959,7 +5081,11 @@ None
 \begin_inset Text
 
 \begin_layout Plain Layout
-sum, avg, stdev, min, max
+sum,
+ avg,
+ stdev,
+ min,
+ max
 \end_layout
 
 \end_inset
@@ -4988,7 +5114,11 @@ sum, avg, stdev, min, max
 \begin_inset Text
 
 \begin_layout Plain Layout
-+, -, /, *, =
++,
+ -,
+ /,
+ *,
+ =
 \end_layout
 
 \end_inset
@@ -4997,7 +5127,11 @@ sum, avg, stdev, min, max
 \begin_inset Text
 
 \begin_layout Plain Layout
-sum, avg, stdev, min, max
+sum,
+ avg,
+ stdev,
+ min,
+ max
 \end_layout
 
 \end_inset
@@ -5032,8 +5166,8 @@ name "sec:Datafile-Commands"
 
 \begin_layout Standard
 Data file output can be handled multiple ways in cpptraj.
- Output data files can be created by Actions/Analyses/Commands, or can be
- explicitly created with 
+ Output data files can be created by Actions/Analyses/Commands,
+ or can be explicitly created with 
 \series bold
 \emph on
 writedata
@@ -5043,6 +5177,7 @@ writedata
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_writedata"
+nolink "false"
 
 \end_inset
 
@@ -5056,6 +5191,7 @@ create
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_create"
+nolink "false"
 
 \end_inset
 
@@ -5070,6 +5206,7 @@ readdata
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_readdata"
+nolink "false"
 
 \end_inset
 
@@ -5077,12 +5214,14 @@ reference "subsec:cpptraj_readdata"
 \end_layout
 
 \begin_layout Standard
-In general, data files which have been declared with an 
+In general,
+ data files which have been declared with an 
 \series bold
 'out'
 \series default
  keyword will recognize data file write keywords on the same command line.
- For example, the 
+ For example,
+ the 
 \series bold
 'time'
 \series default
@@ -5100,10 +5239,8 @@ distance d0 :1 :2 out d0.agr time 0.001
 \end_layout
 
 \begin_layout Standard
-The data file format can be changed from standard implicitly by using specific
- filename extensions or keywords.
- If the extension is not recognized or no keyword is give the default format
- is 'Standard'.
+The data file format can be changed from standard implicitly by using specific filename extensions or keywords.
+ If the extension is not recognized or no keyword is give the default format is 'Standard'.
  Keywords and extensions for data file formats recognized by 
 \shape italic
 cpptraj
@@ -5112,12 +5249,12 @@ cpptraj
 \begin_inset CommandInset ref
 LatexCommand ref
 reference "tab:cpptraj-DataFile-formats"
+nolink "false"
 
 \end_inset
 
 .
- Note that the use of certain options may be restricted for certain data
- file formats.
+ Note that the use of certain options may be restricted for certain data file formats.
  These options can also be passed to data files via the 
 \series bold
 \emph on
@@ -5128,6 +5265,7 @@ datafile
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_datafile_command"
+nolink "false"
 
 \end_inset
 
@@ -5178,8 +5316,7 @@ zlabel}
 
 <label> Set the x-axis label for the specified datafile to <label>.
  For regular data files this is the header for the first column of data.
- If the data is at least 2-dimensional 'datafile ylabel <label>' will likewise
- set the y-axis label.
+ If the data is at least 2-dimensional 'datafile ylabel <label>' will likewise set the y-axis label.
 \end_layout
 
 \begin_layout Description
@@ -5204,13 +5341,14 @@ zmin}
 \end_inset
 
 <min> Set the starting X coordinate value to <min>.
- If the data is at least 2-dimensional 'datafile ymin <min>' will likewise
- set the starting Y coordinate value.
+ If the data is at least 2-dimensional 'datafile ymin <min>' will likewise set the starting Y coordinate value.
 \end_layout
 
 \begin_layout Description
 sort Sort data sets prior to write.
- Ordering is by name, aspect, then index (all descending).
+ Ordering is by name,
+ aspect,
+ then index (all descending).
 \end_layout
 
 \begin_layout Description
@@ -5235,8 +5373,7 @@ zstep}
 \end_inset
 
 <step> Multiply each frame number by <step> (x coordinates).
- If the data is at least 2-dimensional 'datafile ystep <step>' will likewise
- multiply y coordinates by <step>.
+ If the data is at least 2-dimensional 'datafile ystep <step>' will likewise multiply y coordinates by <step>.
 \end_layout
 
 \begin_layout Description
@@ -5257,8 +5394,7 @@ prec
 \begin_inset space ~
 \end_inset
 
-<width>[.<precision>] Change the output format width (and optionally precision)
- of all sets 
+<width>[.<precision>] Change the output format width (and optionally precision) of all sets 
 \shape italic
 subsequently
 \shape default
@@ -5295,7 +5431,8 @@ xfmt
 [noensextension] Omit ensemble extension in ensemble processing mode.
  
 \series bold
-NOTE: THIS OPTION HAS NOT BEEN FULLY TESTED IN PARALLEL.
+NOTE:
+ THIS OPTION HAS NOT BEEN FULLY TESTED IN PARALLEL.
 \end_layout
 
 \end_deeper
@@ -5321,11 +5458,10 @@ Write
 
 \begin_deeper
 \begin_layout Description
-invert Normally, data is written out with X-values pertaining to frames
- (i.e.
+invert Normally,
+ data is written out with X-values pertaining to frames (i.e.
  data over all trajectories is printed in columns).
- This command flips that behavior so that X-values pertain to data sets
- (i.e.
+ This command flips that behavior so that X-values pertain to data sets (i.e.
  data over all trajectories is printed in rows).
 \end_layout
 
@@ -5369,7 +5505,8 @@ noxcol Prevent printing of indices (i.e.
  the #Frame column in most datafiles) for the specified datafile.
  Useful e.g.
  if one would like a 2D plot such as phi vs psi.
- For example, given the input:
+ For example,
+ given the input:
 \begin_inset Separator latexpar
 \end_inset
 
@@ -5394,8 +5531,8 @@ datafile phipsi.dat noxcol
 \shape italic
 Cpptraj
 \shape default
- will write a 2 column datafile containing only phi and psi, no frame numbers
- will be written.
+ will write a 2 column datafile containing only phi and psi,
+ no frame numbers will be written.
 \end_layout
 
 \end_deeper
@@ -5426,7 +5563,8 @@ D1') at the beginning of data file.
 \end_layout
 
 \begin_layout Description
-square2d Write 2D data as a square matrix, e.g.:
+square2d Write 2D data as a square matrix,
+ e.g.:
 \begin_inset Separator latexpar
 \end_inset
 
@@ -5467,7 +5605,8 @@ cut
 \begin_inset space ~
 \end_inset
 
-<cut> Cutoff for 'sparse'; default 0.
+<cut> Cutoff for 'sparse';
+ default 0.
 \end_layout
 
 \end_deeper
@@ -5530,7 +5669,8 @@ prec
 \begin_inset space ~
 \end_inset
 
-{flt|dbl} Read 2d/3d data as single (flt) or double (dbl, default) precision.
+{flt|dbl} Read 2d/3d data as single (flt) or double (dbl,
+ default) precision.
 \end_layout
 
 \begin_layout Description
@@ -5597,14 +5737,19 @@ nosquare2d Read data as XYZ matrix (i.e.
 \begin_layout Description
 vector Read data as vector.
  If indices are present they will be skipped.
- Assume first 3 columns after the index volumn are vector X, Y, and Z, and
- (if present) the next 3 columns contain vector origin X, Y, and Z.
+ Assume first 3 columns after the index volumn are vector X,
+ Y,
+ and Z,
+ and (if present) the next 3 columns contain vector origin X,
+ Y,
+ and Z.
 \end_layout
 
 \begin_layout Description
 mat3x3 Read data as 3x3 matrix.
  If indices are present they will be skipped.
- Assume matrices are in row major order on each line, i.e.
+ Assume matrices are in row major order on each line,
+ i.e.
  M(1,1) M(1,2) ...
  M(3,2) M(3,3).
 \end_layout
@@ -5644,7 +5789,8 @@ prec
 \begin_inset space ~
 \end_inset
 
-{dbl|flt} Grid precision, double or float (default float).
+{dbl|flt} Grid precision,
+ double or float (default float).
 \end_layout
 
 \begin_layout Description
@@ -5658,21 +5804,17 @@ bin
 \end_deeper
 \end_deeper
 \begin_layout Standard
-By default, standard data files are assumed to contain 1D data in columns.
- Data set legends will be read in if the file has a header line (denoted
- by '#').
- Columns labeled '#Frame' are automatically considered the 'index' column
- and skipped.
- Data sets are stored as <name>:<idx> where <name> is the given data set
- name (the file name if not specified) and <idx> corresponds to the column
- the data was read from starting from 1.
+By default,
+ standard data files are assumed to contain 1D data in columns.
+ Data set legends will be read in if the file has a header line (denoted by '#').
+ Columns labeled '#Frame' are automatically considered the 'index' column and skipped.
+ Data sets are stored as <name>:<idx> where <name> is the given data set name (the file name if not specified) and <idx> corresponds to the column the data was read from starting from 1.
  
 \shape italic
 Cpptraj
 \shape default
- assumes the data increases monotonically and will automatically attempt
- to determine the dimensions of the data set(s); a warning will be printed
- if this is not successful.
+ assumes the data increases monotonically and will automatically attempt to determine the dimensions of the data set(s);
+ a warning will be printed if this is not successful.
 \end_layout
 
 \begin_layout Standard
@@ -5685,8 +5827,8 @@ If a file contains the header:
 
 \begin_layout Standard
 CPPTRAJ will assume the file contains pairwise distances for clustering,
- where the F1 and F2 columns contain the frame numbers, and the <name> column
- contains the distance.
+ where the F1 and F2 columns contain the frame numbers,
+ and the <name> column contains the distance.
 \end_layout
 
 \begin_layout Subsection
@@ -5720,8 +5862,8 @@ Write
 
 \begin_deeper
 \begin_layout Description
-invert Normally, data is written out with X-values pertaining to frames
- (i.e.
+invert Normally,
+ data is written out with X-values pertaining to frames (i.e.
  data over all trajectories is printed in columns).
  This command flips that behavior so that X-values pertain to data sets.
 \end_layout
@@ -5743,13 +5885,14 @@ noxydy Do not combine consecutuve pairs of sets into XYDY sets (default).
 \begin_inset space ~
 \end_inset
 
-set> If a string dataset is specified, assume it has data point labels.
+set> If a string dataset is specified,
+ assume it has data point labels.
 \end_layout
 
 \end_deeper
 \begin_layout Standard
-If a single string data set is specified when writing Grace format, it is
- assumed they are data point labels.
+If a single string data set is specified when writing Grace format,
+ it is assumed they are data point labels.
 \end_layout
 
 \begin_layout Subsubsection*
@@ -5757,10 +5900,8 @@ Read
 \end_layout
 
 \begin_layout Standard
-Cpptraj will read set legends from grace files, and data sets are stored
- as <name>:<idx> where <name> is the given data set name (the file name
- if not specified) and <idx> corresponds to the set number the data was
- read from starting from 0.
+Cpptraj will read set legends from grace files,
+ and data sets are stored as <name>:<idx> where <name> is the given data set name (the file name if not specified) and <idx> corresponds to the set number the data was read from starting from 0.
 \end_layout
 
 \begin_layout Subsection
@@ -5768,8 +5909,7 @@ Gnuplot Data File Options
 \end_layout
 
 \begin_layout Standard
-For more information on these options it helps to look at the PM3D options
- in the Gnuplot manual (see 
+For more information on these options it helps to look at the PM3D options in the Gnuplot manual (see 
 \begin_inset CommandInset href
 LatexCommand href
 name "http://www.gnuplot.info/"
@@ -5840,7 +5980,8 @@ header Format the plot so it can be directly processed by gnuplot.
 \end_layout
 
 \begin_layout Description
-noheader Do not format plot; data output only.
+noheader Do not format plot;
+ data output only.
 \end_layout
 
 \begin_layout Description
@@ -5853,15 +5994,28 @@ palette
 
 \begin_deeper
 \begin_layout Description
-'rgb' Red, yellow, green, cyan, blue, magenta, red.
+'rgb' Red,
+ yellow,
+ green,
+ cyan,
+ blue,
+ magenta,
+ red.
 \end_layout
 
 \begin_layout Description
-'kbvyw' Black, blue, violet, yellow, white.
+'kbvyw' Black,
+ blue,
+ violet,
+ yellow,
+ white.
 \end_layout
 
 \begin_layout Description
-'bgyr' Blue, green, yellow, red.
+'bgyr' Blue,
+ green,
+ yellow,
+ red.
 \end_layout
 
 \begin_layout Description
@@ -5875,7 +6029,10 @@ xlabels|ylabels|zlabels
 \begin_inset space ~
 \end_inset
 
-<labellist> Set x, y, or z axis labels with comma-separated list, e.g.
+<labellist> Set x,
+ y,
+ or z axis labels with comma-separated list,
+ e.g.
  'xlabels X1,X2,X3'.
 \end_layout
 
@@ -5896,6 +6053,7 @@ readdata
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-remlog"
+nolink "false"
 
 \end_inset
 
@@ -5916,8 +6074,7 @@ Read
 
 \begin_deeper
 \begin_layout Description
-[nosearch] If specified do not automatically search for MREMD dimension
- logs.
+[nosearch] If specified do not automatically search for MREMD dimension logs.
 \end_layout
 
 \begin_layout Description
@@ -5937,8 +6094,7 @@ Read
 \begin_inset space ~
 \end_inset
 
-indices>] Use comma-separated list of indices as the initial coordinate
- indices (H-REMD only).
+indices>] Use comma-separated list of indices as the initial coordinate indices (H-REMD only).
  For example (4 replicas):
 \begin_inset Separator latexpar
 \end_inset
@@ -5989,8 +6145,7 @@ ibeg
 \begin_inset space ~
 \end_inset
 
-<firstmode> Number of the first mode (or principal component) to read from
- evecs file.
+<firstmode> Number of the first mode (or principal component) to read from evecs file.
  Default 1.
 \end_layout
 
@@ -5999,13 +6154,13 @@ iend
 \begin_inset space ~
 \end_inset
 
-<lastmode> Number of the last mode (or principal component) to read from
- evecs file.
+<lastmode> Number of the last mode (or principal component) to read from evecs file.
  Default is to read all for newer evecs files (generated by 
 \shape italic
 cpptraj
 \shape default
- version > 12), 50 for older evecs files.
+ version > 12),
+ 50 for older evecs files.
 \end_layout
 
 \end_deeper
@@ -6014,12 +6169,12 @@ Vector psuedo-traj Options
 \end_layout
 
 \begin_layout Standard
-This can be used to write out a representation of a vector data set which
- can then be visualized.
+This can be used to write out a representation of a vector data set which can then be visualized.
  See 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-vector"
+nolink "false"
 
 \end_inset
 
@@ -6049,6 +6204,7 @@ trajfmt
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "tab:cpptraj-trajformats"
+nolink "false"
 
 \end_inset
 
@@ -6112,7 +6268,8 @@ gridwrap Like
 \series bold
 'bincenter'
 \series default
-, but also wrap grid density.
+,
+ but also wrap grid density.
  Useful when grid encompasses unit cell.
 \end_layout
 
@@ -6121,7 +6278,8 @@ gridext Like
 \series bold
 'bincenter'
 \series default
-, but also print extra layer of empty bins.
+,
+ but also print extra layer of empty bins.
 \end_layout
 
 \end_deeper
@@ -6215,13 +6373,13 @@ cpin
 
 \end_deeper
 \begin_layout Standard
-Note that when reading in constant pH data the data set aspect will be set
- to the residue name and the index will be set to the residue number.
- When reading in constant pH REMD data the data is unsorted, and sortensembledat
-a should be used to create sorted constant pH data sets (see 
+Note that when reading in constant pH data the data set aspect will be set to the residue name and the index will be set to the residue number.
+ When reading in constant pH REMD data the data is unsorted,
+ and sortensembledata should be used to create sorted constant pH data sets (see 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_sortensembledata"
+nolink "false"
 
 \end_inset
 
@@ -6241,10 +6399,10 @@ name "sec:Coordinates-as-a"
 
 \begin_layout Standard
 Coordinate I/O tends to be the most time-consuming part of trajectory analysis.
- In addition, many types of analyses (for example two-dimensional RMSD and
- cluster analysis) require using coordinate frames multiple times.
- To simplify this, trajectory coordinates may be saved as a separate data
- set via the 
+ In addition,
+ many types of analyses (for example two-dimensional RMSD and cluster analysis) require using coordinate frames multiple times.
+ To simplify this,
+ trajectory coordinates may be saved as a separate data set via the 
 \series bold
 \shape italic
 loadcrd
@@ -6270,8 +6428,7 @@ crdaction
 crdout
 \series default
 \shape default
- command can be used to write coordinates to an output trajectory (similar
- to 
+ command can be used to write coordinates to an output trajectory (similar to 
 \series bold
 \shape italic
 trajout
@@ -6283,9 +6440,8 @@ trajout
 \begin_layout Standard
 Although COORDS data sets store everything internally with single-precision,
  they can still use a large amount of memory.
- Because of this there is a specialized type of COORDS data set called a
- TRAJ data set (trajectory), which functions exactly like a COORDS data
- set except all data is stored on disk.
+ Because of this there is a specialized type of COORDS data set called a TRAJ data set (trajectory),
+ which functions exactly like a COORDS data set except all data is stored on disk.
  TRAJ data sets can be created with the 
 \series bold
 \shape italic
@@ -6308,8 +6464,8 @@ runanalysis
 \shape default
  command.
  Note that while these analyses can be run on specified COORDS data sets,
- if one is not specified a default COORDS data set will be created, made
- up of frames from 
+ if one is not specified a default COORDS data set will be created,
+ made up of frames from 
 \series bold
 \shape italic
 trajin
@@ -6319,11 +6475,10 @@ trajin
 \end_layout
 
 \begin_layout Standard
-As an example of where this might be useful is in the calculation of atomic
- positional fluctuations.
- Previously this required two steps: one to generate an average structure,
- then a second to rms-fit to that average structure prior to calculating
- the fluctuations.
+As an example of where this might be useful is in the calculation of atomic positional fluctuations.
+ Previously this required two steps:
+ one to generate an average structure,
+ then a second to rms-fit to that average structure prior to calculating the fluctuations.
  This can now be done in one pass with the following input:
 \end_layout
 
@@ -6336,7 +6491,8 @@ loadcrd mdcrd.nc
 \end_layout
 
 \begin_layout LyX-Code
-# Generate average structure PDB, @CA only
+# Generate average structure PDB,
+ @CA only
 \end_layout
 
 \begin_layout LyX-Code
@@ -6564,8 +6720,7 @@ extendedcomp
 \begin_inset Text
 
 \begin_layout Plain Layout
-Calculate extended comparison similarity values for each frame in COORDS
- set.
+Calculate extended comparison similarity values for each frame in COORDS set.
 \end_layout
 
 \end_inset
@@ -6645,8 +6800,7 @@ permutedihedrals
 \begin_inset Text
 
 \begin_layout Plain Layout
-Rotate specified dihedral(s) in given COORDS set by specific interval or
- to random values.
+Rotate specified dihedral(s) in given COORDS set by specific interval or to random values.
 \end_layout
 
 \end_inset
@@ -6666,8 +6820,7 @@ prepareforleap
 \begin_inset Text
 
 \begin_layout Plain Layout
-Prepare a structure (usually loaded from a PDB) for processing with LEaP
- from Amber.
+Prepare a structure (usually loaded from a PDB) for processing with LEaP from Amber.
 \end_layout
 
 \end_inset
@@ -6767,8 +6920,7 @@ zmatrix
 \begin_inset Text
 
 \begin_layout Plain Layout
-Apply Z-matrix to a COORDS set or calculate Z-matrix for a molecule/frame
- in a COORDS set.
+Apply Z-matrix to a COORDS set or calculate Z-matrix for a molecule/frame in a COORDS set.
 \end_layout
 
 \end_inset
@@ -6792,7 +6944,8 @@ catcrd <crd1> <crd2> ...
 
 \begin_deeper
 \begin_layout Description
-<crdX> COORDS data sets to concatentate, specify 2 or more.
+<crdX> COORDS data sets to concatentate,
+ specify 2 or more.
 \end_layout
 
 \begin_layout Description
@@ -6807,8 +6960,8 @@ name
 \begin_layout Standard
 Concatentate two or more COORDS data sets into a single COORDS data set.
  The topologies must have the same number of atoms for this to work.
- If the topologies differ in other ways, the topology of the first COORDS
- set takes priority.
+ If the topologies differ in other ways,
+ the topology of the first COORDS set takes priority.
 \end_layout
 
 \begin_layout Subsection
@@ -6826,7 +6979,8 @@ combinecrd <crd1> <crd2> ...
 
 \begin_deeper
 \begin_layout Description
-<crdX> COORDS data sets to combine, specify 2 or more.
+<crdX> COORDS data sets to combine,
+ specify 2 or more.
 \end_layout
 
 \begin_layout Description
@@ -6857,8 +7011,10 @@ not
 \end_layout
 
 \begin_layout Standard
-For example, to load two MOL2 files as COORDS data sets, combine them, and
- write them out as a single MOL2:
+For example,
+ to load two MOL2 files as COORDS data sets,
+ combine them,
+ and write them out as a single MOL2:
 \end_layout
 
 \begin_layout LyX-Code
@@ -6889,8 +7045,7 @@ name "subsec:cpptraj_crdaction"
 \end_layout
 
 \begin_layout LyX-Code
-crdaction <crd set> <actioncmd> [<action args>] [crdframes <start>,<stop>,<offse
-t>]
+crdaction <crd set> <actioncmd> [<action args>] [crdframes <start>,<stop>,<offset>]
 \end_layout
 
 \begin_layout Standard
@@ -6899,8 +7054,9 @@ Perform action <actioncmd> on COORDS data set <crd set>.
 \end_layout
 
 \begin_layout Standard
-For example, to calculate RMSD for a previously created COORDS data set
- named crd1 using frames 1 to the last, skipping every 10:
+For example,
+ to calculate RMSD for a previously created COORDS data set named crd1 using frames 1 to the last,
+ skipping every 10:
 \end_layout
 
 \begin_layout LyX-Code
@@ -6921,8 +7077,8 @@ Write COORDS data set <crd set> to trajectory named <filename>.
 \end_layout
 
 \begin_layout Standard
-For example, to write frames 1 to 10 from a previously created COORDS data
- set named 
+For example,
+ to write frames 1 to 10 from a previously created COORDS data set named 
 \begin_inset Quotes eld
 \end_inset
 
@@ -6991,7 +7147,8 @@ crd
 \begin_inset space ~
 \end_inset
 
-set>] COORDS set to create; if not specified <input crd set> will be modified.
+set>] COORDS set to create;
+ if not specified <input crd set> will be modified.
 \end_layout
 
 \begin_layout Description
@@ -7021,8 +7178,7 @@ rmsrefine Do iterative RMS refinement.
 
 \end_deeper
 \begin_layout Description
-normcoords Normalize coordinates between 0.0 and 1.0 using the minimum and
- maximum coordinate values.
+normcoords Normalize coordinates between 0.0 and 1.0 using the minimum and maximum coordinate values.
 \end_layout
 
 \begin_layout Description
@@ -7035,7 +7191,8 @@ trim Remove trajectory frames using extended similarity metrics.
 \begin_inset space ~
 \end_inset
 
-<metric>] Metric to use; default MSD.
+<metric>] Metric to use;
+ default MSD.
 \end_layout
 
 \begin_layout Description
@@ -7065,17 +7222,21 @@ trim Remove trajectory frames using extended similarity metrics.
 \begin_layout Standard
 Transform a COORDS set in one of several ways.
  Does not yet work with TRAJ data sets.
- The iterative RMS refinement is similar to the procedure outlined by Klem
- et al.
+ The iterative RMS refinement is similar to the procedure outlined by Klem et al.
  (J.
  Chem.
  Theory Comput.
- 2022, 18, 3218−3230).
+ 2022,
+ 18,
+ 3218−3230).
  The extended similarity metrics are those defined by Racz et al.
  (J.
  Comp.-Aid.
  Mol.
- Design, 2022, 36, 157-173).
+ Design,
+ 2022,
+ 36,
+ 157-173).
 \end_layout
 
 \begin_layout Subsection
@@ -7083,11 +7244,12 @@ createcrd
 \end_layout
 
 \begin_layout Standard
-This command is actually an Action that can be used to create COORDS data
- sets during trajectory processing, see 
+This command is actually an Action that can be used to create COORDS data sets during trajectory processing,
+ see 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_createcrd"
+nolink "false"
 
 \end_inset
 
@@ -7183,17 +7345,18 @@ crdset
 \begin_inset space ~
 \end_inset
 
-<setname>] If specified, create an energy per step data set.
+<setname>] If specified,
+ create an energy per step data set.
 \end_layout
 
 \begin_layout Description
-[nonbond] If specified, use simple nonbonded potential term in additon to
- bonded terms.
+[nonbond] If specified,
+ use simple nonbonded potential term in additon to bonded terms.
 \end_layout
 
 \begin_layout Description
-[openmm] If specified and if CPPTRAJ was compiled with OpenMM support, use
- OpenMM to calculate the forces.
+[openmm] If specified and if CPPTRAJ was compiled with OpenMM support,
+ use OpenMM to calculate the forces.
 \end_layout
 
 \begin_layout Standard
@@ -7294,8 +7457,9 @@ THIS COMMAND IS STILL IN DEVELOPMENT AS OF VERSION 5.0.2.
 \end_layout
 
 \begin_layout Standard
-Perform steepest descent minimization on a frame in a COORDS set using a
- very basic force field (bonds, angles, dihedrals).
+Perform steepest descent minimization on a frame in a COORDS set using a very basic force field (bonds,
+ angles,
+ dihedrals).
  A simple nonbonded term can be added as well if desired.
 \end_layout
 
@@ -7385,13 +7549,15 @@ name> Set containing similarity values for each COORDS frame.
 
 \end_deeper
 \begin_layout Standard
-Calculate extended comparison similarity values for each frame in a COORDS
- set.
+Calculate extended comparison similarity values for each frame in a COORDS set.
  The extended similarity metrics are those defined by Racz et al.
  (J.
  Comp.-Aid.
  Mol.
- Design, 2022, 36, 157-173).
+ Design,
+ 2022,
+ 36,
+ 157-173).
  The metrics are as follows:
 \end_layout
 
@@ -7657,13 +7823,11 @@ graft
 \end_layout
 
 \begin_layout LyX-Code
-graft src <source COORDS> [srcframe <#>] [srcmask <srcmask> [srccharge <srccharg
-e>]]
+graft src <source COORDS> [srcframe <#>] [srcmask <srcmask> [srccharge <srccharge>]]
 \end_layout
 
 \begin_layout LyX-Code
-  	tgt <target COORDS> [tgtframe <#>] [tgtmask <tgtmask> [tgtcharge <tgtcharge>]
-]
+  	tgt <target COORDS> [tgtframe <#>] [tgtmask <tgtmask> [tgtcharge <tgtcharge>]]
 \end_layout
 
 \begin_layout LyX-Code
@@ -7709,8 +7873,8 @@ COORDS> Source coordinates.
 \begin_inset space ~
 \end_inset
 
-<charge>] If trimming atoms from source, ensure sum of charges on remaining
- atoms equals <charge> via scaling.
+<charge>] If trimming atoms from source,
+ ensure sum of charges on remaining atoms equals <charge> via scaling.
 \end_layout
 
 \end_deeper
@@ -7748,8 +7912,8 @@ COORDS> Target coordinates that will be grafted onto.
 \begin_inset space ~
 \end_inset
 
-<charge>] If trimming atoms from target, ensure sum of charges on remaining
- atoms equals <charge> via scaling.
+<charge>] If trimming atoms from target,
+ ensure sum of charges on remaining atoms equals <charge> via scaling.
 \end_layout
 
 \end_deeper
@@ -7790,10 +7954,9 @@ COORDS> Name of output COORDS set containing source grafted onto target.
 \begin_inset space ~
 \end_inset
 
-<tgt>,<src>] Create a bond between target atom selected by <tgt> and source
- atoms selected by <src> in the final structure.
- Must be specified only once if connecting via internal coordinates, otherwise
- may be specified multiple times.
+<tgt>,<src>] Create a bond between target atom selected by <tgt> and source atoms selected by <src> in the final structure.
+ Must be specified only once if connecting via internal coordinates,
+ otherwise may be specified multiple times.
 \end_layout
 
 \end_deeper
@@ -7807,8 +7970,8 @@ srcfitmask
 \series bold
 tgtfitmask
 \series default
- is specified, the source coordinates will be RMS best-fit onto target using
- the specified atoms.
+ is specified,
+ the source coordinates will be RMS best-fit onto target using the specified atoms.
  Only the atoms specified by 
 \series bold
 srcmask
@@ -7822,10 +7985,9 @@ tgtmask
 \series bold
 bond
 \series default
- keyword can be used to create bonds between target and source in the final
- structure.
- If using internal coordinates to connect the units, exactly one bond must
- be specified.
+ keyword can be used to create bonds between target and source in the final structure.
+ If using internal coordinates to connect the units,
+ exactly one bond must be specified.
 \end_layout
 
 \begin_layout Subsection
@@ -7850,8 +8012,7 @@ loadcrd <filename> [parm <parm> | parmindex<#>] [<trajin args>] [name <name>]
 \begin_inset space ~
 \end_inset
 
-<parmfile/tag>] Topology filename/tag to associate with trajectory (default
- first topology).
+<parmfile/tag>] Topology filename/tag to associate with trajectory (default first topology).
 \end_layout
 
 \begin_layout Description
@@ -7859,7 +8020,8 @@ loadcrd <filename> [parm <parm> | parmindex<#>] [<trajin args>] [name <name>]
 \begin_inset space ~
 \end_inset
 
-<#>] Index of Topology to associate with trajectory (default 0, first topology).
+<#>] Index of Topology to associate with trajectory (default 0,
+ first topology).
 \end_layout
 
 \begin_layout Description
@@ -7867,13 +8029,15 @@ loadcrd <filename> [parm <parm> | parmindex<#>] [<trajin args>] [name <name>]
 \begin_inset space ~
 \end_inset
 
-args>] Additional 'trajin' args; see 
+args>] Additional 'trajin' args;
+ see 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_trajin"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
@@ -7893,21 +8057,18 @@ noprefix "false"
 \begin_inset space ~
 \end_inset
 
-{single|double}] Load as either a single-precision COORDS set (the default)
- or a double-precision FRAMES set (which will use much more memory).
+{single|double}] Load as either a single-precision COORDS set (the default) or a double-precision FRAMES set (which will use much more memory).
 \end_layout
 
 \end_deeper
 \begin_layout Standard
-Immediately load trajectory <filename> as a COORDS data set named <name>
- (default base name of <filename>).
- If <name> is already present the coordinates will be appended to the existing
- data set.
+Immediately load trajectory <filename> as a COORDS data set named <name> (default base name of <filename>).
+ If <name> is already present the coordinates will be appended to the existing data set.
 \end_layout
 
 \begin_layout Standard
-For example, to load frames from trajectories named 'traj1.nc' and 'traj2.nc'
- into a COORDS data set named Crd1:
+For example,
+ to load frames from trajectories named 'traj1.nc' and 'traj2.nc' into a COORDS data set named Crd1:
 \end_layout
 
 \begin_layout LyX-Code
@@ -7943,14 +8104,15 @@ name
 \end_layout
 
 \begin_layout Description
-[<filename>] If specified, trajectory to add to the TRAJ set.
+[<filename>] If specified,
+ trajectory to add to the TRAJ set.
 \end_layout
 
 \end_deeper
 \begin_layout Standard
 This command functions in two ways.
- If <filename> is not provided, all currently loaded input trajectories
- (from 
+ If <filename> is not provided,
+ all currently loaded input trajectories (from 
 \series bold
 \shape italic
 trajin
@@ -7959,11 +8121,11 @@ trajin
  commands) are added to TRAJ data set named <setname>.
  
 \series bold
-Note that if the input trajectory list is cleared (via 'clear trajin') this
- will invalidate the TRAJ data set.
+Note that if the input trajectory list is cleared (via 'clear trajin') this will invalidate the TRAJ data set.
 
 \series default
- In addition, currently all trajectories must have the same number of atoms.
+ In addition,
+ currently all trajectories must have the same number of atoms.
  Otherwise add trajectory <filename> to TRAJ data set <setname>.
 \end_layout
 
@@ -7987,7 +8149,7 @@ permutedihedrals crdset <COORDS set> resrange <range> [{interval | random}]
 \end_layout
 
 \begin_layout LyX-Code
-             	[outtraj <filename> [<outfmt>]] [crdout <output COORDS>] 
+             	{[outtraj <filename> [<outfmt>]]} [crdout <output COORDS>] 
 \end_layout
 
 \begin_layout LyX-Code
@@ -7999,7 +8161,7 @@ permutedihedrals crdset <COORDS set> resrange <range> [{interval | random}]
 \end_layout
 
 \begin_layout LyX-Code
-	[rseed <rseed>] [out <# problems file> [<set name>]]
+	[rseed <rseed>] [out <# problems file> [<set name>]] [noimage]
 \end_layout
 
 \begin_layout LyX-Code
@@ -8019,8 +8181,7 @@ permutedihedrals crdset <COORDS set> resrange <range> [{interval | random}]
 \end_layout
 
 \begin_layout LyX-Code
-  <dihedral types> =  alpha beta gamma delta epsilon zeta nu1 nu2 h1p c2p
- chin 
+  <dihedral types> =  alpha beta gamma delta epsilon zeta nu1 nu2 h1p c2p chin 
 \end_layout
 
 \begin_layout LyX-Code
@@ -8054,8 +8215,7 @@ resrange
 
 \begin_layout Description
 interval Rotate found dihedrals by <interval>.
- This is done in an ordered fashion so that every combination of dihedral
- rotations is sampled at least once.
+ This is done in an ordered fashion so that every combination of dihedral rotations is sampled at least once.
 \end_layout
 
 \begin_layout Description
@@ -8148,6 +8308,10 @@ file>] File to write number of problems (clashes) each frame to.
 name>] Number of problems data set name.
 \end_layout
 
+\begin_layout Description
+[noimage] Disable imaging when checking rotated structure for clashes.
+\end_layout
+
 \begin_layout Description
 [check] Check randomly rotated structure for clashes.
 \begin_inset Separator latexpar
@@ -8178,8 +8342,7 @@ name>] Number of problems data set name.
 \begin_inset space ~
 \end_inset
 
-<max_factor>] The maximum number of total attempted rotations will be <max_facto
-r> * <total # of dihedrals> (default 2).
+<max_factor>] The maximum number of total attempted rotations will be <max_factor> * <total # of dihedrals> (default 2).
 \end_layout
 
 \begin_layout Description
@@ -8188,14 +8351,14 @@ r> * <total # of dihedrals> (default 2).
 \end_inset
 
 <backtrack>] (No longer recommended as of version 5.1.0).
- If a clash is encountered at dihedral N and cannot be resolved, go to dihedral
- N-<backtrack> to try and resolve the clash (default is no backtracking).
+ If a clash is encountered at dihedral N and cannot be resolved,
+ go to dihedral N-<backtrack> to try and resolve the clash (default is no backtracking).
 \end_layout
 
 \begin_deeper
 \begin_layout Description
-[checkallresidues] If specified all residues checked for clashes, otherwise
- only residues up to the currently rotated dihedral check.
+[checkallresidues] If specified all residues checked for clashes,
+ otherwise only residues up to the currently rotated dihedral check.
 \end_layout
 
 \begin_layout Description
@@ -8203,9 +8366,9 @@ r> * <total # of dihedrals> (default 2).
 \begin_inset space ~
 \end_inset
 
-<increment>] If a clash is encountered, first attempt to rotate dihedral
- by increment to resolve it; if it cannot be resolved by a full rotation
- the calculation will backtrack (default 1).
+<increment>] If a clash is encountered,
+ first attempt to rotate dihedral by increment to resolve it;
+ if it cannot be resolved by a full rotation the calculation will backtrack (default 1).
  
 \end_layout
 
@@ -8213,24 +8376,33 @@ r> * <total # of dihedrals> (default 2).
 \end_deeper
 \end_deeper
 \begin_layout Standard
-Create a trajectory by rotating specified dihedrals in a structure by regular
- intervals (
+Create a trajectory by rotating specified dihedrals in a structure by regular intervals (
 \series bold
 interval
 \series default
-), or create 1 structure by randomly rotating specified dihedrals (
+),
+ or create 1 structure by randomly rotating specified dihedrals (
 \series bold
 random
 \series default
 ).
+ The resulting structure can be written to a file with 
+\series bold
+outtraj
+\series default
+ or saved to a new COORDS set with 
+\series bold
+crdout
+\series default
+;
+ at least one output option must be specified.
  When randomly rotating dihedrals steric clashes will be checked if 
 \series bold
 check
 \series default
- is specified; in such cases the algorithm will attempt to resolve the clash
- as best it can.
- If clashes are not being resolved you can increase the number of rotation
- attempts 
+ is specified;
+ in such cases the algorithm will attempt to resolve the clash as best it can.
+ If clashes are not being resolved you can increase the number of rotation attempts 
 \family typewriter
 \shape italic
 cpptraj
@@ -8244,9 +8416,8 @@ maxfactor
 \end_layout
 
 \begin_layout Standard
-For example, to rotate all backbone dihedrals in a protein with coordinates
- in a file named tz2.rst7 in -120 degree intervals and write the resulting
- trajectory in Amber format to rotations.mdcrd:
+For example,
+ to rotate all backbone dihedrals in a protein with coordinates in a file named tz2.rst7 in -120 degree intervals and write the resulting trajectory in Amber format to rotations.mdcrd:
 \end_layout
 
 \begin_layout LyX-Code
@@ -8258,8 +8429,7 @@ permutedihedrals crdset [TZ2] interval -120 outtraj rotations.mdcrd phi psi
 \end_layout
 
 \begin_layout Standard
-To randomly rotate backbone dihedrals for the same structure and write to
- file random.mol2 in MOL2 format:
+To randomly rotate backbone dihedrals for the same structure and write to file random.mol2 in MOL2 format:
 \end_layout
 
 \begin_layout LyX-Code
@@ -8267,8 +8437,7 @@ reference tz2.rst7 [TZ2]
 \end_layout
 
 \begin_layout LyX-Code
-permutedihedrals crdset [TZ2] random rseed 1 check maxfactor 10 phi psi
- 
+permutedihedrals crdset [TZ2] random rseed 1 check maxfactor 10 phi psi 
 \backslash
 
 \end_layout
@@ -8290,8 +8459,7 @@ prepareforleap crdset <coords set> [frame <#>] name <out coords set>
 \end_layout
 
 \begin_layout LyX-Code
-                  	[leapunitname <unit>] [out <leap input file> [runleap
- <ff file>]]
+                  	[leapunitname <unit>] [out <leap input file> [runleap <ff file>]]
 \end_layout
 
 \begin_layout LyX-Code
@@ -8335,8 +8503,7 @@ prepareforleap crdset <coords set> [frame <#>] name <out coords set>
 \end_layout
 
 \begin_layout LyX-Code
-                  	  [cysmask <cysmask>] [disulfidecut <cut>] [newcysname
- <name>]}]
+                  	  [cysmask <cysmask>] [disulfidecut <cut>] [newcysname <name>]}]
 \end_layout
 
 \begin_layout LyX-Code
@@ -8406,7 +8573,8 @@ set> Output COORDS set containing prepared topology/coordinates.
 
 \begin_deeper
 \begin_layout Description
-[terbymol] If specified, base TER cards on molecules instead of PDB chains.
+[terbymol] If specified,
+ base TER cards on molecules instead of PDB chains.
 \end_layout
 
 \end_deeper
@@ -8444,8 +8612,9 @@ input
 \begin_inset space ~
 \end_inset
 
-file>] File containing LEaP input needed to read in the prepared system
- (loadpdb, bond commands for disulfides, etc).
+file>] File containing LEaP input needed to read in the prepared system (loadpdb,
+ bond commands for disulfides,
+ etc).
 \end_layout
 
 \begin_layout Description
@@ -8457,23 +8626,25 @@ file>] File containing LEaP input needed to read in the prepared system
 \begin_inset space ~
 \end_inset
 
-file>] If specified, CPPTRAJ will attempt to run LEaP directly to generate
- a topology and coordinates; <ff
+file>] If specified,
+ CPPTRAJ will attempt to run LEaP directly to generate a topology and coordinates;
+ <ff
 \begin_inset space ~
 \end_inset
 
-file> should contain the appropriate 'source' commands for loading the desired
- force field parameters.
+file> should contain the appropriate 'source' commands for loading the desired force field parameters.
  Will attempt to produce topology <unit>.parm7 and coordinates <unit>.rst7.
 \end_layout
 
 \begin_layout Description
-[skiperrors] If specified, the command will try to ignore any errors encountered.
+[skiperrors] If specified,
+ the command will try to ignore any errors encountered.
  Can be useful for debugging.
 \end_layout
 
 \begin_layout Description
-[nowat] If specified, remove waters from the system.
+[nowat] If specified,
+ remove waters from the system.
 \end_layout
 
 \begin_deeper
@@ -8487,7 +8658,8 @@ file> should contain the appropriate 'source' commands for loading the desired
 
 \end_deeper
 \begin_layout Description
-[noh] If specified, strip all hydrogen atoms from the system (recommended).
+[noh] If specified,
+ strip all hydrogen atoms from the system (recommended).
 \end_layout
 
 \begin_layout Description
@@ -8503,8 +8675,8 @@ loc
 \begin_inset space ~
 \end_inset
 
-ID>|highestocc}] LEaP cannot handle alternate atom locations, so the command
- will choose location 'A' by default.
+ID>|highestocc}] LEaP cannot handle alternate atom locations,
+ so the command will choose location 'A' by default.
  This can be changed to either <alt
 \begin_inset space ~
 \end_inset
@@ -8541,8 +8713,8 @@ id> or the location with the highest occupancy if
 \begin_inset space ~
 \end_inset
 
-<mask>] If specified, atoms in <mask> will be considered all part of one
- molecule.
+<mask>] If specified,
+ atoms in <mask> will be considered all part of one molecule.
  May be specified multiple times.
 \end_layout
 
@@ -8551,8 +8723,8 @@ id> or the location with the highest occupancy if
 \begin_inset space ~
 \end_inset
 
-<mask>] If specified, determine if atoms selected in <mask> are in the same
- molecule via bonds.
+<mask>] If specified,
+ determine if atoms selected in <mask> are in the same molecule via bonds.
 \end_layout
 
 \begin_layout Standard
@@ -8620,8 +8792,8 @@ Disulfide Handling:
 \end_layout
 
 \begin_layout Description
-[existingdisulfides] Only handle disulfides already present; do not search
- for additional disulfides.
+[existingdisulfides] Only handle disulfides already present;
+ do not search for additional disulfides.
 \end_layout
 
 \begin_layout Description
@@ -8637,8 +8809,7 @@ Disulfide Handling:
 \begin_inset space ~
 \end_inset
 
-<cut>] Sulfur to sulfur atom distance cutoff for forming a disulfide (default
- 2.5 Ang).
+<cut>] Sulfur to sulfur atom distance cutoff for forming a disulfide (default 2.5 Ang).
 \end_layout
 
 \begin_layout Description
@@ -8646,8 +8817,7 @@ Disulfide Handling:
 \begin_inset space ~
 \end_inset
 
-<name>] Name to change cysteine residues that participate in a disulfide
- bond to (default 'CYX').
+<name>] Name to change cysteine residues that participate in a disulfide bond to (default 'CYX').
 \end_layout
 
 \begin_layout Standard
@@ -8676,8 +8846,7 @@ resmapfile
 \end_layout
 
 \begin_layout Description
-[nosplitres] If specified do not attempt to split off functional groups
- from sugars into separate residues.
+[nosplitres] If specified do not attempt to split off functional groups from sugars into separate residues.
 \end_layout
 
 \begin_layout Description
@@ -8690,7 +8859,8 @@ resmapfile
 \end_layout
 
 \begin_layout Description
-[hasglycam] If specified, assume sugars already have GLYCAM residue names;
+[hasglycam] If specified,
+ assume sugars already have GLYCAM residue names;
  just check sugar anomer type/configuration/linkage.
 \end_layout
 
@@ -8699,18 +8869,13 @@ resmapfile
 \begin_inset space ~
 \end_inset
 
-{geometry|name}] Determine whether sugar anomer type/configuration should
- be chosen based on sugar geometry (default) or the residue name.
- CPPTRAJ will report when a mismatch is detected between the sugar anomer
- type/configuration based on geometry and anomer type/configuration based
- on the residue name.
+{geometry|name}] Determine whether sugar anomer type/configuration should be chosen based on sugar geometry (default) or the residue name.
+ CPPTRAJ will report when a mismatch is detected between the sugar anomer type/configuration based on geometry and anomer type/configuration based on the residue name.
 \end_layout
 
 \end_deeper
 \begin_layout Standard
-This command will prepare a structure (usually from a PDB) for processing
- with the Amber program LEaP to generate topology and coordinates files
- for MD simulations.
+This command will prepare a structure (usually from a PDB) for processing with the Amber program LEaP to generate topology and coordinates files for MD simulations.
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Roe2022"
@@ -8718,54 +8883,52 @@ literal "true"
 
 \end_inset
 
- It will handle things like choosing alternate atom locations, removing
- waters/hydrogen atoms from the structure, renaming residues and generating
- 'bond' commands for disulfide bonds, change histidine names based on any
- existing protonation, and renaming residues/atoms and generating 'bond'
- commands for carbohydrates.
- The command can also call LEaP directly to generate the parameters once
- the structure is prepared.
+ It will handle things like choosing alternate atom locations,
+ removing waters/hydrogen atoms from the structure,
+ renaming residues and generating 'bond' commands for disulfide bonds,
+ change histidine names based on any existing protonation,
+ and renaming residues/atoms and generating 'bond' commands for carbohydrates.
+ The command can also call LEaP directly to generate the parameters once the structure is prepared.
 \end_layout
 
 \begin_layout Standard
-If hydrogen atoms are present in the structure, the command will attempt
- a simple and straightforward determination of the protonation state of
- any histidine residues based on where hydrogens are bonded, and assign
- the appropriate residue name.
- The command will also identify any existing disulfide bonds as well as
- potential disulfide bonds and generate the corresponding LEaP ‘bond’ commands
- which can be applied after the structure is loaded in LEaP.
- Potential disulfide bonding atoms can be identified via a user-specifiable
- mask expression.
+If hydrogen atoms are present in the structure,
+ the command will attempt a simple and straightforward determination of the protonation state of any histidine residues based on where hydrogens are bonded,
+ and assign the appropriate residue name.
+ The command will also identify any existing disulfide bonds as well as potential disulfide bonds and generate the corresponding LEaP ‘bond’ commands which can be applied after the structure is loaded in LEaP.
+ Potential disulfide bonding atoms can be identified via a user-specifiable mask expression.
 \end_layout
 
 \begin_layout Standard
-By default, sugars will have their residue names changed to those compatible
- with the GLYCAM force field based on their anomer type (alpha/beta), configurat
-ion (D/L), and linkages (glycosidic and covalent sugar to non-sugar).
+By default,
+ sugars will have their residue names changed to those compatible with the GLYCAM force field based on their anomer type (alpha/beta),
+ configuration (D/L),
+ and linkages (glycosidic and covalent sugar to non-sugar).
  Any recognized functional groups that are part of sugar residues (hydroxyl,
- acetyl, sulfate, etc) will be split into separate residues as required
- by GLYCAM.
- If this happens and 'runleap' has not been specified, CPPTRAJ will warn
- about any residues/atoms that require charge to be adjusted.
- If 'runleap' has not been specified the command will warn about any atoms
- that need to have their charges adjusted after LEaP is run.
+ acetyl,
+ sulfate,
+ etc) will be split into separate residues as required by GLYCAM.
+ If this happens and 'runleap' has not been specified,
+ CPPTRAJ will warn about any residues/atoms that require charge to be adjusted.
+ If 'runleap' has not been specified the command will warn about any atoms that need to have their charges adjusted after LEaP is run.
 \end_layout
 
 \begin_layout Standard
 The command will try to report any potential problems that LEaP might encounter.
- These include residue names that may be unrecognized (and therefore may
- not have parameters), mismatches between detected sugar anomer type/configurati
-on and anomer type/configuration based on the sugar residue name, unrecognized
- sugar linkages, and so on.
+ These include residue names that may be unrecognized (and therefore may not have parameters),
+ mismatches between detected sugar anomer type/configuration and anomer type/configuration based on the sugar residue name,
+ unrecognized sugar linkages,
+ and so on.
  
 \end_layout
 
 \begin_layout Standard
-For example, the following input prepares PDB 4zzw for processing with PDB,
- putting the proper leap commands in leap.4zzw.in, writing the prepared PDB
- to 4zzw.cpptraj.pdb, removing waters and hydrogen atoms, and keeping alternate
- atom locations with the highest occupancy:
+For example,
+ the following input prepares PDB 4zzw for processing with PDB,
+ putting the proper leap commands in leap.4zzw.in,
+ writing the prepared PDB to 4zzw.cpptraj.pdb,
+ removing waters and hydrogen atoms,
+ and keeping alternate atom locations with the highest occupancy:
 \end_layout
 
 \begin_layout LyX-Code
@@ -8791,31 +8954,36 @@ Sugar Residue/Atom Name Mapping File
 \end_layout
 
 \begin_layout Standard
-This file controls how CPPTRAJ will name sugars based on sugar form/chirality
- linkage.
+This file controls how CPPTRAJ will name sugars based on sugar form/chirality linkage.
  It consists of three sections separated by a blank line.
- The first section defines sugar PDB residue names and how they are mapped
- to GLYCAM residue characters:
+ The first section defines sugar PDB residue names and how they are mapped to GLYCAM residue characters:
 \end_layout
 
 \begin_layout LyX-Code
-Format: <ResName> <GlycamCode> <Anomer> <Config> <RingType> "<Name>"
+Format:
+ <ResName> <GlycamCode> <Anomer> <Config> <RingType> "<Name>"
 \end_layout
 
 \begin_layout LyX-Code
-Anomer: A=alpha, B=beta
+Anomer:
+ A=alpha,
+ B=beta
 \end_layout
 
 \begin_layout LyX-Code
-Config: D/L
+Config:
+ D/L
 \end_layout
 
 \begin_layout LyX-Code
-RingType: P=pyranose, F=furanose
+RingType:
+ P=pyranose,
+ F=furanose
 \end_layout
 
 \begin_layout LyX-Code
-Example: 64K A A D P "alpha-D-arabinopyranose" 
+Example:
+ 64K A A D P "alpha-D-arabinopyranose" 
 \end_layout
 
 \begin_layout Standard
@@ -8823,17 +8991,19 @@ The second section contains PDB to GLYCAM atom name maps for residues:
 \end_layout
 
 \begin_layout LyX-Code
-Format: <GLYCAM residue codes> <PDB atom name>,<GLYCAM atom name>[,<anomer>]
- … 
+Format:
+ <GLYCAM residue codes> <PDB atom name>,<GLYCAM atom name>[,<anomer>] … 
 \end_layout
 
 \begin_layout LyX-Code
-If <anomer> (A=alpha, B=beta) is specified, the atom name map is only valid
- for that specific form.
+If <anomer> (A=alpha,
+ B=beta) is specified,
+ the atom name map is only valid for that specific form.
 \end_layout
 
 \begin_layout LyX-Code
-Example: V,W,Y C7,C2N O7,O2N C8,CME 
+Example:
+ V,W,Y C7,C2N O7,O2N C8,CME 
 \end_layout
 
 \begin_layout Standard
@@ -8842,11 +9012,13 @@ The third section contains PDB to GLYCAM linkage residue (i.e.
 \end_layout
 
 \begin_layout LyX-Code
-Format: <PDB residue name> <GLYCAM residue name>
+Format:
+ <PDB residue name> <GLYCAM residue name>
 \end_layout
 
 \begin_layout LyX-Code
-Example: SER OLS 
+Example:
+ SER OLS 
 \end_layout
 
 \begin_layout Subsection
@@ -8859,6 +9031,7 @@ Reference coordinates can now be used and manipulated like COORDS data sets.
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_reference"
+nolink "false"
 
 \end_inset
 
@@ -8904,7 +9077,8 @@ crdset
 \end_inset
 
 set> Coordinates data set to work on.
- If a TRAJ data set is specified, 
+ If a TRAJ data set is specified,
+ 
 \series bold
 name
 \series default
@@ -8991,10 +9165,9 @@ type> Dihedral type to rotate in specified residue.
 
 \end_deeper
 \begin_layout Standard
-Rotate the specified dihedral in given COORDS set to a target value or by
- given increment.
- For example, to set the protein chi dihedral in residue 8 to 35 degrees
- and write out to a mol2 file:
+Rotate the specified dihedral in given COORDS set to a target value or by given increment.
+ For example,
+ to set the protein chi dihedral in residue 8 to 35 degrees and write out to a mol2 file:
 \end_layout
 
 \begin_layout LyX-Code
@@ -9088,10 +9261,9 @@ name> COORDS set containing final molecule.
 \end_deeper
 \begin_layout Standard
 Connect units in different COORDS sets together to form a single molecule.
- Internal coordinates are used to try to determine the correct geometry
- around connection sites.
- The COORDS sets must have connection information set, either from reading
- in an Amber OFF library file or set manually via 
+ Internal coordinates are used to try to determine the correct geometry around connection sites.
+ The COORDS sets must have connection information set,
+ either from reading in an Amber OFF library file or set manually via 
 \series bold
 \emph on
 dataset
@@ -9108,6 +9280,7 @@ reference "subsec:cpptraj-datasetcmd"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
@@ -9115,8 +9288,10 @@ noprefix "false"
 \end_layout
 
 \begin_layout Standard
-For example, the following reads in two Mol2 files as COORDS sets, sets
- up connection atoms, then creates a molecule via 
+For example,
+ the following reads in two Mol2 files as COORDS sets,
+ sets up connection atoms,
+ then creates a molecule via 
 \series bold
 \emph on
 sequence:
@@ -9191,7 +9366,8 @@ name> Name of new set to create.
 \begin_layout Standard
 Split trajectory specified by <crd set> by molecule into a new COORDS set.
  All molecules in <crd set> must be the same size.
- For example, if there are 10 molecules and 10 frames in COORDS set 
+ For example,
+ if there are 10 molecules and 10 frames in COORDS set 
 \begin_inset Quotes eld
 \end_inset
 
@@ -9199,8 +9375,10 @@ Set0
 \begin_inset Quotes erd
 \end_inset
 
-, the following would create a new COORDS set with 100 frames (original
- molecules 1-10 frame 1, original molecules 1-10 frame 2, etc):
+,
+ the following would create a new COORDS set with 100 frames (original molecules 1-10 frame 1,
+ original molecules 1-10 frame 2,
+ etc):
 \end_layout
 
 \begin_layout LyX-Code
@@ -9233,8 +9411,7 @@ set
 \begin_inset space ~
 \end_inset
 
-name> COORDS set to calculate Z-matrix from or use as topology for applied
- Z-matrix.
+name> COORDS set to calculate Z-matrix from or use as topology for applied Z-matrix.
 \end_layout
 
 \begin_layout Description
@@ -9300,8 +9477,7 @@ parmindex
 \begin_inset space ~
 \end_inset
 
-<frame#>] Calculate Z-matrix from specified molecule in specified frame
- (default first frame).
+<frame#>] Calculate Z-matrix from specified molecule in specified frame (default first frame).
 \end_layout
 
 \begin_layout Description
@@ -9329,17 +9505,18 @@ set
 \begin_inset space ~
 \end_inset
 
-name> If 'zset', COORDS set containing final coordinates.
+name> If 'zset',
+ COORDS set containing final coordinates.
  Otherwise contains Z-matrix data.
 \end_layout
 
 \end_deeper
 \begin_layout Standard
 Command for working with Z-matrices.
- If 'zset' is specified, generate coordinates from the specified Z-matrix
- data set and topology.
- Otherwise, calculate a Z-matrix for a single molecule from the specified
- frame of given COORDS data set.
+ If 'zset' is specified,
+ generate coordinates from the specified Z-matrix data set and topology.
+ Otherwise,
+ calculate a Z-matrix for a single molecule from the specified frame of given COORDS data set.
 \end_layout
 
 \begin_layout Section
@@ -9820,7 +9997,8 @@ random
 \begin_inset Text
 
 \begin_layout Plain Layout
-Change default random number generator, create random sets.
+Change default random number generator,
+ create random sets.
 \end_layout
 
 \end_inset
@@ -10080,6 +10258,8 @@ activeref
 \begin_layout LyX-Code
 activeref
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -10092,10 +10272,11 @@ activeref
 \end_layout
 
 \begin_layout Standard
-Set which reference structure should be used when setting up distance-based
- masks for everything but the 'mask' action.
- Numbering starts from 0, so 'activeref 0' selects the first reference structure
- read in, 'activeref 1' selects the second, and so on.
+Set which reference structure should be used when setting up distance-based masks for everything but the 'mask' action.
+ Numbering starts from 0,
+ so 'activeref 0' selects the first reference structure read in,
+ 'activeref 1' selects the second,
+ and so on.
 \end_layout
 
 \begin_layout Subsection
@@ -10117,6 +10298,7 @@ calc <expression>
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-Data-Set-Math"
+nolink "false"
 
 \end_inset
 
@@ -10158,9 +10340,10 @@ clear [{all | <type>}]
 \end_layout
 
 \begin_layout Standard
-Clear list of indicated type, or all lists if 'all' specified.
- Note that when clearing actions or analyses, associated data sets and data
- files are not cleared and vice versa.
+Clear list of indicated type,
+ or all lists if 'all' specified.
+ Note that when clearing actions or analyses,
+ associated data sets and data files are not cleared and vice versa.
 \end_layout
 
 \begin_layout Subsection
@@ -10177,6 +10360,8 @@ name "subsec:cpptraj_create"
 \begin_layout LyX-Code
 create
 \begin_inset Index idx
+range none
+pageformat default
 status open
 
 \begin_layout Plain Layout
@@ -10189,10 +10374,12 @@ create
 \end_layout
 
 \begin_layout Standard
-Add specified data sets to the data file named <filename>; if the file does
- not exist, it will be added to the DataFileList.
- Data files created in this way are only written at the end of coordinate
- processing, analyses, or via the 
+Add specified data sets to the data file named <filename>;
+ if the file does not exist,
+ it will be added to the DataFileList.
+ Data files created in this way are only written at the end of coordinate processing,
+ analyses,
+ or via the 
 \series bold
 \emph on
 'writedata'
@@ -10203,6 +10390,7 @@ Add specified data sets to the data file named <filename>; if the file does
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "sec:Datafile-Commands"
+nolink "false"
 
 \end_inset
 
@@ -10219,8 +10407,9 @@ createset <expression> [xmin <min>] xstep <step> nx <nxvals>
 
 \begin_deeper
 \begin_layout Description
-expression Simple mathematical expression, must contain equals sign, can
- contain X (e.g.
+expression Simple mathematical expression,
+ must contain equals sign,
+ can contain X (e.g.
  Y=2*X).
  If not enclosed in quotes must not contain whitespace.
 \end_layout
@@ -10268,6 +10457,8 @@ name "subsec:cpptraj_datafile_command"
 \begin_layout LyX-Code
 datafile
 \begin_inset Index idx
+range none
+pageformat default
 status open
 
 \begin_layout Plain Layout
@@ -10285,6 +10476,7 @@ Pass <datafile arg> to data file <filename>.
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "sec:Datafile-Commands"
+nolink "false"
 
 \end_inset
 
@@ -10311,8 +10503,7 @@ datafilter {<dataset arg> min <min> max <max> ...} [out <file>] [name <setname>]
 \end_layout
 
 \begin_layout LyX-Code
-           {[multi] | [filterset <set> [newset <newname>]] [countout <countfile>
-]}
+           {[multi] | [filterset <set> [newset <newname>]] [countout <countfile>]}
 \end_layout
 
 \begin_deeper
@@ -10337,7 +10528,8 @@ max
 \begin_inset space ~
 \end_inset
 
-<max> Data set name and min/max cutoffs to use; can specify more than one.
+<max> Data set name and min/max cutoffs to use;
+ can specify more than one.
 \end_layout
 
 \begin_layout Description
@@ -10358,8 +10550,7 @@ max
 \end_layout
 
 \begin_layout Description
-[multi] Filter each set separately instead of all together (creates filter
- set for each input set).
+[multi] Filter each set separately instead of all together (creates filter set for each input set).
  Cannot be used with 'filterset'.
 \end_layout
 
@@ -10368,8 +10559,8 @@ max
 \begin_inset space ~
 \end_inset
 
-<set>] If specified, <set> will be filtered to only contain data that satisfies
- cutoffs.
+<set>] If specified,
+ <set> will be filtered to only contain data that satisfies cutoffs.
  Cannot be used with 'multi'.
 \end_layout
 
@@ -10379,8 +10570,7 @@ max
 \begin_inset space ~
 \end_inset
 
-<newname>] If specified a new set will be created from 'filterset' instead
- of replacing 'filterset'.
+<newname>] If specified a new set will be created from 'filterset' instead of replacing 'filterset'.
 \end_layout
 
 \end_deeper
@@ -10389,8 +10579,8 @@ max
 \begin_inset space ~
 \end_inset
 
-<count>] If specified, write number of elements passed and filtered to <countfil
-e>.
+<count>] If specified,
+ write number of elements passed and filtered to <countfile>.
  Cannot be used with 'multi'.
 \end_layout
 
@@ -10407,7 +10597,8 @@ passed
 \begin_inset Quotes erd
 \end_inset
 
-, 0 otherwise.
+,
+ 0 otherwise.
 \end_layout
 
 \begin_layout Description
@@ -10423,8 +10614,8 @@ Sets Created ('multi')
 \end_layout
 
 \begin_layout Description
-<setname>:<idx> For each input set (number with <idx>, starting from 0)
- contains 1 for elements that 
+<setname>:<idx> For each input set (number with <idx>,
+ starting from 0) contains 1 for elements that 
 \begin_inset Quotes eld
 \end_inset
 
@@ -10432,13 +10623,13 @@ passed
 \begin_inset Quotes erd
 \end_inset
 
-, 0 otherwise.
+,
+ 0 otherwise.
 \end_layout
 
 \end_deeper
 \begin_layout Standard
-Create a data set (optionally named <setname>) containing 1 for data within
- given 
+Create a data set (optionally named <setname>) containing 1 for data within given 
 \series bold
 <min>
 \series default
@@ -10455,22 +10646,24 @@ Create a data set (optionally named <setname>) containing 1 for data within
 \series bold
 <max>
 \series default
- argument, and can be as many as there are specified data sets.
+ argument,
+ and can be as many as there are specified data sets.
  If 
 \series bold
 'multi'
 \series default
- is specified then only filter data sets will be created for each data set
- instead.
+ is specified then only filter data sets will be created for each data set instead.
  If 
 \series bold
 'filterset'
 \series default
- is specified, the specified 
+ is specified,
+ the specified 
 \series bold
 <set>
 \series default
- will be modified to only contain '1' frames; cannot be used with 
+ will be modified to only contain '1' frames;
+ cannot be used with 
 \series bold
 'multi'
 \series default
@@ -10479,21 +10672,20 @@ Create a data set (optionally named <setname>) containing 1 for data within
 \series bold
 'newset'
 \series default
- is also specified, a new set will be created containing the '1' frames
- instead.
+ is also specified,
+ a new set will be created containing the '1' frames instead.
  The 'filterset' functionality only works for 1D scalar sets.
  If 
 \series bold
 'countout'
 \series default
- is specified, the final number of elements passed and filtered out will
- be written to <countfile>.
+ is specified,
+ the final number of elements passed and filtered out will be written to <countfile>.
 \end_layout
 
 \begin_layout Standard
-For example, to read in data from two separate files (d1.dat and a1.dat) and
- generate a filter data set named FILTER having 1 when d1 is between 0.0
- and 3.0 and a1 is between 135.0 and 180.0:
+For example,
+ to read in data from two separate files (d1.dat and a1.dat) and generate a filter data set named FILTER having 1 when d1 is between 0.0 and 3.0 and a1 is between 135.0 and 180.0:
 \end_layout
 
 \begin_layout LyX-Code
@@ -10509,8 +10701,7 @@ datafilter d1 min 0.0 max 3.0 a1 min 135.0 max 180.0 out filter.dat name FILTER
 \end_layout
 
 \begin_layout Standard
-Note that a similar command that can be used with data generated by Actions
- during trajectory processing is 
+Note that a similar command that can be used with data generated by Actions during trajectory processing is 
 \series bold
 \shape italic
 filter
@@ -10520,6 +10711,7 @@ filter
 \begin_inset CommandInset ref
 LatexCommand pageref
 reference "subsec:cpptraj-filter"
+nolink "false"
 
 \end_inset
 
@@ -10559,8 +10751,7 @@ dataset { legend <legend> <set> |
 \end_layout
 
 \begin_layout LyX-Code
-          {drop|keep}points {range <range arg> | [start <#>] [stop <#>]
- [offset <#>]}
+          {drop|keep}points {range <range arg> | [start <#>] [stop <#>] [offset <#>]}
 \end_layout
 
 \begin_layout LyX-Code
@@ -10569,23 +10760,19 @@ dataset { legend <legend> <set> |
 \end_layout
 
 \begin_layout LyX-Code
-          remove <criterion> <select> <value> [and <value2>] [<set selection>]
- |
+          remove <criterion> <select> <value> [and <value2>] [<set selection>] |
 \end_layout
 
 \begin_layout LyX-Code
-          connect {[head <head atom>] [tail <tail atom>]|[headmask <headmask>]
- [tailmask <tailmask>]}
+          connect {[head <head atom>] [tail <tail atom>]|[headmask <headmask>] [tailmask <tailmask>]}
 \end_layout
 
 \begin_layout LyX-Code
-          dim {xdim|ydim|zdim|ndim <#>} [label <label>] [min <min>] [step
- <step>] |
+          dim {xdim|ydim|zdim|ndim <#>} [label <label>] [min <min>] [step <step>] |
 \end_layout
 
 \begin_layout LyX-Code
-          outformat {double|scientific|general} <set arg1> [<set arg 2>
- ...] |
+          outformat {double|scientific|general} <set arg1> [<set arg 2> ...] |
 \end_layout
 
 \begin_layout LyX-Code
@@ -10594,8 +10781,7 @@ dataset { legend <legend> <set> |
 \end_layout
 
 \begin_layout LyX-Code
-          shift [above <value> by <offset>] [below <value> by <offset>]
- <set arg0> ...
+          shift [above <value> by <offset>] [below <value> by <offset>] <set arg0> ...
 \end_layout
 
 \begin_layout LyX-Code
@@ -10607,27 +10793,25 @@ dataset { legend <legend> <set> |
 \end_layout
 
 \begin_layout LyX-Code
-  <mode>:  'distance' 'angle' 'torsion' 'pucker' 'rms' 'matrix' 'vector'
+  <mode>:
+  'distance' 'angle' 'torsion' 'pucker' 'rms' 'matrix' 'vector'
 \end_layout
 
 \begin_layout LyX-Code
-  <type>:  'alpha' 'beta' 'gamma' 'delta' 'epsilon' 'zeta' 'nu0' 'nu1' 'nu2'
- 'nu3'
+  <type>:
+  'alpha' 'beta' 'gamma' 'delta' 'epsilon' 'zeta' 'nu0' 'nu1' 'nu2' 'nu3'
 \end_layout
 
 \begin_layout LyX-Code
-           'nu4' 'h1p' 'c2p' 'chin' 'phi' 'psi' 'chip' 'omega' 'chi2' 'chi3'
- 'chi4'
+           'nu4' 'h1p' 'c2p' 'chin' 'phi' 'psi' 'chip' 'omega' 'chi2' 'chi3' 'chi4'
 \end_layout
 
 \begin_layout LyX-Code
-           'chi5' 'pucker' 'noe' 'distance' 'covariance' 'mass-weighted
- covariance'
+           'chi5' 'pucker' 'noe' 'distance' 'covariance' 'mass-weighted covariance'
 \end_layout
 
 \begin_layout LyX-Code
-           'correlation' 'distance covariance' 'IDEA' 'IRED' 'dihedral covarianc
-e'
+           'correlation' 'distance covariance' 'IDEA' 'IRED' 'dihedral covariance'
 \end_layout
 
 \begin_layout LyX-Code
@@ -10696,8 +10880,7 @@ makexy
 \begin_inset space ~
 \end_inset
 
-<Yset> Create a new data set (optionally named <name>) with X values from
- <Xset> and Y values from <Yset>.
+<Yset> Create a new data set (optionally named <name>) with X values from <Xset> and Y values from <Yset>.
 \end_layout
 
 \begin_layout Description
@@ -10709,8 +10892,7 @@ vectorcoord
 \begin_inset space ~
 \end_inset
 
-<set> Extract X/Y/Z coordinates from vector data set into a new 1D data
- set.
+<set> Extract X/Y/Z coordinates from vector data set into a new 1D data set.
 \end_layout
 
 \begin_layout Description
@@ -10727,8 +10909,7 @@ cat
 \end_inset
 
 ...
- Concatenate two or more data sets into a new data set (optionally named
- <name>).
+ Concatenate two or more data sets into a new data set (optionally named <name>).
  Only works for scalar 1D and string sets.
 \end_layout
 
@@ -10757,8 +10938,7 @@ rows
 \begin_inset space ~
 \end_inset
 
-<nrows> Convert 1D data set into row-major 2D data set with specified number
- of rows and columns.
+<nrows> Convert 1D data set into row-major 2D data set with specified number of rows and columns.
 \end_layout
 
 \begin_layout Description
@@ -10775,8 +10955,8 @@ arg1>
 \end_inset
 
 ...
- Drop or keep specified points from data set(s), optionally creating a new
- data set.
+ Drop or keep specified points from data set(s),
+ optionally creating a new data set.
 \end_layout
 
 \begin_deeper
@@ -10846,16 +11026,17 @@ remove
 \begin_inset space ~
 \end_inset
 
-selection>] Remove data sets from <set selection> according to specified
- criterion and selection.
+selection>] Remove data sets from <set selection> according to specified criterion and selection.
 \end_layout
 
 \begin_layout LyX-Code
-<criterion>:  'ifaverage' 'ifsize' 'ifmode' 'iftype'
+<criterion>:
+  'ifaverage' 'ifsize' 'ifmode' 'iftype'
 \end_layout
 
 \begin_layout LyX-Code
-<select>   :  'equal' '==' 'notequal' '!=' 'lessthan' '<' 
+<select>   :
+  'equal' '==' 'notequal' '!=' 'lessthan' '<' 
 \end_layout
 
 \begin_layout LyX-Code
@@ -10879,11 +11060,13 @@ reference "subsec:cpptraj-sequence"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
 ) to COORDS set(s).
- Head atoms connect to previous residue, tail atoms connect to next residue.
+ Head atoms connect to previous residue,
+ tail atoms connect to next residue.
  Can use either absolute atom numbers or atom mask expressions.
 \end_layout
 
@@ -11106,7 +11289,8 @@ arg0>
 \begin_inset space ~
 \end_inset
 
-<type>] Set data set(s) type to 'type', useful for e.g.
+<type>] Set data set(s) type to 'type',
+ useful for e.g.
  analysis with 
 \series bold
 \shape italic
@@ -11120,13 +11304,15 @@ statistics
 distance
 \series default
 \shape default
-, 
+,
+ 
 \series bold
 \shape italic
 dihedral
 \series default
 \shape default
-, 
+,
+ 
 \series bold
 \shape italic
 pucker
@@ -11153,7 +11339,8 @@ bound
 \begin_inset space ~
 \end_inset
 
-<upper>] Lower and upper bounds for NOE (in Angstroms); must specify both.
+<upper>] Lower and upper bounds for NOE (in Angstroms);
+ must specify both.
 \end_layout
 
 \begin_layout Description
@@ -11161,8 +11348,8 @@ bound
 \begin_inset space ~
 \end_inset
 
-<expected>] Expected value for NOE (in Angstroms); if not given '(<lower>
- + <upper>)' / 2.0 is used.
+<expected>] Expected value for NOE (in Angstroms);
+ if not given '(<lower> + <upper>)' / 2.0 is used.
 \end_layout
 
 \begin_layout Description
@@ -11179,16 +11366,17 @@ bound
 
 \end_deeper
 \begin_layout Standard
-Either set the legend for a single data set, create a new set with X values
- from one set and Y values from another, concatenate 2 or more sets, make
- a 2D set from 1D set, remove sets according to a certain criterion, or
- change the mode/type for one or more data sets.
+Either set the legend for a single data set,
+ create a new set with X values from one set and Y values from another,
+ concatenate 2 or more sets,
+ make a 2D set from 1D set,
+ remove sets according to a certain criterion,
+ or change the mode/type for one or more data sets.
 \end_layout
 
 \begin_layout Standard
-Setting the mode/type can be useful for cases where the data set is being
- read in from a file; for example when reading in a dihedral data set the
- type can be set to 'dihedral' so that various Analysis routines like 
+Setting the mode/type can be useful for cases where the data set is being read in from a file;
+ for example when reading in a dihedral data set the type can be set to 'dihedral' so that various Analysis routines like 
 \series bold
 \shape italic
 statistics
@@ -12065,11 +12253,11 @@ IRED vector.
 \end_layout
 
 \begin_layout Standard
-The invert mode takes a group of M 1D data sets of size N and create N new
- "inverted" data sets of size M.
- This is similar to the invert keyword already available for standard and
- Grace data writes, but operates directly on data sets.
- For example, given the following two data sets:
+The invert mode takes a group of M 1D data sets of size N and create N new "inverted" data sets of size M.
+ This is similar to the invert keyword already available for standard and Grace data writes,
+ but operates directly on data sets.
+ For example,
+ given the following two data sets:
 \end_layout
 
 \begin_layout LyX-Code
@@ -12105,10 +12293,9 @@ N0 N1 N2
 \end_layout
 
 \begin_layout Standard
-The dataset invert command can be useful if you want to easily view output
- from multiple analysis commands in a single graph.
- For example, to view state counts from two different simulations side by
- side:
+The dataset invert command can be useful if you want to easily view output from multiple analysis commands in a single graph.
+ For example,
+ to view state counts from two different simulations side by side:
 \end_layout
 
 \begin_layout LyX-Code
@@ -12132,10 +12319,10 @@ writedata statecount.agr Inverted*
 \end_layout
 
 \begin_layout Standard
-The dataset shift command can be used for wrapping circular values, such
- as torsions.
- For example, to ensure a pucker has a range from 0 to 360 instead of -180
- to 180:
+The dataset shift command can be used for wrapping circular values,
+ such as torsions.
+ For example,
+ to ensure a pucker has a range from 0 to 360 instead of -180 to 180:
 \end_layout
 
 \begin_layout LyX-Code
@@ -12157,6 +12344,8 @@ debug | prnlev
 \begin_layout LyX-Code
 debug
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -12175,8 +12364,7 @@ debug
 \begin_layout Standard
 Set the level of debug information to print.
  In general the higher the <#> the more information that is printed.
- If <type> is specified only set the debug level for a specific area of
- 
+ If <type> is specified only set the debug level for a specific area of 
 \shape italic
 cpptraj.
 \end_layout
@@ -12197,8 +12385,8 @@ Turn printing of ensemble member number filename extensions on or off.
 \begin_layout Standard
 
 \series bold
-NOTE: THE 'ensextension off' OPTION HAS NOT BEEN FULLY TESTED IN PARALLEL
- AND IS NOT CURRENTLY RECOMMENDED.
+NOTE:
+ THE 'ensextension off' OPTION HAS NOT BEEN FULLY TESTED IN PARALLEL AND IS NOT CURRENTLY RECOMMENDED.
 \end_layout
 
 \begin_layout Subsection
@@ -12247,8 +12435,10 @@ mode
 \begin_inset space ~
 \end_inset
 
-{sum|avg} If sum, matrix elements will be summed.
- If avg, matrix elements will be averaged.
+{sum|avg} If sum,
+ matrix elements will be summed.
+ If avg,
+ matrix elements will be averaged.
 \end_layout
 
 \begin_layout Description
@@ -12296,14 +12486,15 @@ set
 \begin_inset space ~
 \end_inset
 
-name>:<idx> Flattened 1D sets when more than one input matrix; index starts
- from 1.
+name>:<idx> Flattened 1D sets when more than one input matrix;
+ index starts from 1.
 \end_layout
 
 \end_deeper
 \begin_layout Standard
 Flatten 1 or more matrices into 1D array(s) by summing or averaging elements.
- For example, given a matrix with values like this:
+ For example,
+ given a matrix with values like this:
 \end_layout
 
 \begin_layout LyX-Code
@@ -12379,7 +12570,8 @@ go | run
 \end_layout
 
 \begin_layout Standard
-Begin trajectory processing, followed by analysis and datafile write.
+Begin trajectory processing,
+ followed by analysis and datafile write.
 \end_layout
 
 \begin_layout Subsection
@@ -12389,6 +12581,8 @@ help
 \begin_layout LyX-Code
 help
 \begin_inset Index idx
+range none
+pageformat default
 status open
 
 \begin_layout Plain Layout
@@ -12413,8 +12607,7 @@ help
 \end_layout
 
 \begin_layout LyX-Code
- 	    Form[ats] [{trajin|trajout|readdata|writedata|parm|parmwrite} [<fmt
- key>]] |
+ 	    Form[ats] [{trajin|trajout|readdata|writedata|parm|parmwrite} [<fmt key>]] |
 \end_layout
 
 \begin_layout LyX-Code
@@ -12422,7 +12615,8 @@ help
 \end_layout
 
 \begin_layout LyX-Code
-	Command Categories: Gen[eral] Sys[tem] Coor[ds] Traj[ectory] Top[ology]
+	Command Categories:
+ Gen[eral] Sys[tem] Coor[ds] Traj[ectory] Top[ology]
 \end_layout
 
 \begin_layout LyX-Code
@@ -12430,35 +12624,50 @@ help
 \end_layout
 
 \begin_layout LyX-Code
-  All                : Print all known commands.
+  All                :
+ Print all known commands.
 \end_layout
 
 \begin_layout LyX-Code
-  <cmd>              : Print help for command <cmd>.
+  <cmd>              :
+ Print help for command <cmd>.
 \end_layout
 
 \begin_layout LyX-Code
-  <command category> : Print all commands in specified category.
+  <command category> :
+ Print all commands in specified category.
 \end_layout
 
 \begin_layout LyX-Code
-  Form[ats]          : Help for file formats.
+  Form[ats]          :
+ Help for file formats.
 \end_layout
 
 \begin_layout LyX-Code
-  Mask               : Help for mask syntax.
+  Mask               :
+ Help for mask syntax.
 \end_layout
 
 \begin_layout Standard
-If 'All' is specifed, list all commands known to 
+If 'All' is specifed,
+ list all commands known to 
 \shape italic
 cpptraj
 \shape default
 .
- If given with a command, print help for that command.
- Otherwise, list all commands of a certain category (General, System, Coords,
- Trajectory, Topology, Action, Analysis, or Control), help for various file
- formats, or help with atom mask syntax.
+ If given with a command,
+ print help for that command.
+ Otherwise,
+ list all commands of a certain category (General,
+ System,
+ Coords,
+ Trajectory,
+ Topology,
+ Action,
+ Analysis,
+ or Control),
+ help for various file formats,
+ or help with atom mask syntax.
 \end_layout
 
 \begin_layout Subsection
@@ -12485,6 +12694,8 @@ noexitonerror
 \begin_layout LyX-Code
 noexitonerror
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -12508,7 +12719,8 @@ cpptraj
 noexitonerror
 \series default
 \shape default
- is specified, 
+ is specified,
+ 
 \shape italic
 cpptraj
 \shape default
@@ -12523,6 +12735,8 @@ noprogress
 \begin_layout LyX-Code
 noprogress
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -12548,8 +12762,7 @@ parallelanalysis [sync]
 
 \begin_layout Standard
 MPI only.
- Divide all currently set up analyses as evenly as possible among available
- MPI processes and execute.
+ Divide all currently set up analyses as evenly as possible among available MPI processes and execute.
  Each analysis will get a single MPI process.
  If 
 \series bold
@@ -12557,13 +12770,15 @@ sync
 \series default
  is specified all data will be synced back to the master process (for e.g.
  subsequent analysis).
- For an example of how to use the parallelanalysis command, see 
+ For an example of how to use the parallelanalysis command,
+ see 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_hausdorff"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
@@ -12621,18 +12836,20 @@ args> Files containing CPPTRAJ output to get timing data from.
 \begin_inset space ~
 \end_inset
 
-{time|cores|filename}] Sort timing data sets by either time, number of cores
- (MPI processes * OpenMP threads), or file name.
+{time|cores|filename}] Sort timing data sets by either time,
+ number of cores (MPI processes * OpenMP threads),
+ or file name.
 \end_layout
 
 \begin_layout Description
-[includebad] If specified, include run output for which timing data cannot
- be extracted (e.g.
+[includebad] If specified,
+ include run output for which timing data cannot be extracted (e.g.
  an incomplete/failed run).
 \end_layout
 
 \begin_layout Description
-[showdetails] If specified, details about each run will be printed to STDOUT.
+[showdetails] If specified,
+ details about each run will be printed to STDOUT.
 \end_layout
 
 \begin_layout Description
@@ -12640,30 +12857,27 @@ args> Files containing CPPTRAJ output to get timing data from.
 \begin_inset space ~
 \end_inset
 
-{trajproc|trajread|actframe} If specified, report time other than the total
- time (which is the default):
+{trajproc|trajread|actframe} If specified,
+ report time other than the total time (which is the default):
 \end_layout
 
 \begin_deeper
 \begin_layout Description
-trajproc Total trajectory processing time (trajectory I/O plus action frame
- time).
+trajproc Total trajectory processing time (trajectory I/O plus action frame time).
 \end_layout
 
 \begin_layout Description
-trajread Trajectory read time (requires compiling with '-timer' configure
- option/-DTIMER compiler define).
+trajread Trajectory read time (requires compiling with '-timer' configure option/-DTIMER compiler define).
 \end_layout
 
 \begin_layout Description
-actframe Action frame time (requires compiling with '-timer' configure option/-D
-TIMER compiler define).
+actframe Action frame time (requires compiling with '-timer' configure option/-DTIMER compiler define).
 \end_layout
 
 \end_deeper
 \begin_layout Description
-[reverse] Instead of longest time to shortest time, sort shortest time to
- longest time.
+[reverse] Instead of longest time to shortest time,
+ sort shortest time to longest time.
 \end_layout
 
 \begin_layout Description
@@ -12672,8 +12886,7 @@ TIMER compiler define).
 \end_inset
 
 <file>] Group run output by a property and write to a file.
- Additional details will be written like speedup and efficiency (relative
- to the slowest run).
+ Additional details will be written like speedup and efficiency (relative to the slowest run).
 \end_layout
 
 \begin_deeper
@@ -12699,8 +12912,8 @@ name Group by run type name (see
 \end_layout
 
 \begin_layout Description
-kind Group by run type name; OpenMP runs are separated by number of OpenMP
- threads.
+kind Group by run type name;
+ OpenMP runs are separated by number of OpenMP threads.
 \end_layout
 
 \end_deeper
@@ -12715,17 +12928,22 @@ DataSets Created:
 
 \begin_layout Description
 <setname>[name] Set containing shortedhand run names.
- Consists of a prefix (S for serial, O for OpenMP, M for MPI, H for hybrid
- MPI/OpenMP) followed by numbers indicating number of MPI processes 'x'
- OpenMP threads; e.g., H16x4 means a hybrid run consisting of 16 MPI processes
- and 4 OpenMP threads per process.
- If CUDA is active, the name will be wrapped in 'G()', e.g.
+ Consists of a prefix (S for serial,
+ O for OpenMP,
+ M for MPI,
+ H for hybrid MPI/OpenMP) followed by numbers indicating number of MPI processes 'x' OpenMP threads;
+ e.g.,
+ H16x4 means a hybrid run consisting of 16 MPI processes and 4 OpenMP threads per process.
+ If CUDA is active,
+ the name will be wrapped in 'G()',
+ e.g.
  G(H16x4).
 \end_layout
 
 \begin_layout Description
 <setname>[dir] Set containing output directory prefixes.
- If no directory prefix, just contains output file name.
+ If no directory prefix,
+ just contains output file name.
 \end_layout
 
 \end_deeper
@@ -12746,6 +12964,8 @@ precision
 \begin_layout LyX-Code
 precision
 \begin_inset Index idx
+range none
+pageformat default
 status open
 
 \begin_layout Plain Layout
@@ -12758,20 +12978,19 @@ precision
 \end_layout
 
 \begin_layout Standard
-Set the precision for all data sets in data file <filename> or data set(s)
- specified by <dataset arg> to 
+Set the precision for all data sets in data file <filename> or data set(s) specified by <dataset arg> to 
 \shape italic
 width.precision
 \shape default
-, where width is the column width and precision is the number of digits
- after the decimal point.
- Note that the <precision> argument only applies to floating-point data
- sets.
+,
+ where width is the column width and precision is the number of digits after the decimal point.
+ Note that the <precision> argument only applies to floating-point data sets.
 \end_layout
 
 \begin_layout Standard
-For example, if one wanted to set the precision of the output of an Rmsd
- calculation to 8.3, the input could be:
+For example,
+ if one wanted to set the precision of the output of an Rmsd calculation to 8.3,
+ the input could be:
 \end_layout
 
 \begin_layout LyX-Code
@@ -12820,13 +13039,13 @@ random [setdefault {marsaglia|stdlib|mt|pcg32|xo128}]
 
 \begin_deeper
 \begin_layout Description
-setdefault If specified, change the default random number generator (RNG).
+setdefault If specified,
+ change the default random number generator (RNG).
 \end_layout
 
 \begin_deeper
 \begin_layout Description
-marsaglia Use the Marsaglia RNG that is used in the Amber MD programs sander/pme
-md.
+marsaglia Use the Marsaglia RNG that is used in the Amber MD programs sander/pmemd.
 \end_layout
 
 \begin_layout Description
@@ -12834,8 +13053,8 @@ stdlib Use the C standard library RNG.
 \end_layout
 
 \begin_layout Description
-mt Use the C++11 implementation of the Mersenne twister (mt19937); only
- available with C++11 support.
+mt Use the C++11 implementation of the Mersenne twister (mt19937);
+ only available with C++11 support.
 \end_layout
 
 \begin_layout Description
@@ -12864,8 +13083,8 @@ literal "true"
 
 \end_deeper
 \begin_layout Description
-createset If specified, create a 1D data set filled with random numbers
- of the specified type.
+createset If specified,
+ create a 1D data set filled with random numbers of the specified type.
 \end_layout
 
 \begin_deeper
@@ -12886,8 +13105,10 @@ settype
 \begin_inset space ~
 \end_inset
 
-{int|float01|gauss} Type of numbers to use; integer, floating point between
- 0 and 1, Gaussian distribution.
+{int|float01|gauss} Type of numbers to use;
+ integer,
+ floating point between 0 and 1,
+ Gaussian distribution.
 \end_layout
 
 \begin_deeper
@@ -12919,8 +13140,8 @@ seed
 \end_deeper
 \end_deeper
 \begin_layout Standard
-This command can be used to set the default random number generator used
- in CPPTRAJ, and/or create a 1D data set filled with random values.
+This command can be used to set the default random number generator used in CPPTRAJ,
+ and/or create a 1D data set filled with random values.
 \end_layout
 
 \begin_layout Subsection
@@ -12937,6 +13158,8 @@ name "subsec:cpptraj_readdata"
 \begin_layout LyX-Code
 readdata
 \begin_inset Index idx
+range none
+pageformat default
 status open
 
 \begin_layout Plain Layout
@@ -12967,8 +13190,7 @@ as
 \begin_inset space ~
 \end_inset
 
-<fmt> Force <filename> to be read as a specific format using given format
- keyword.
+<fmt> Force <filename> to be read as a specific format using given format keyword.
 \end_layout
 
 \begin_layout Description
@@ -12982,6 +13204,7 @@ Read data from file <filename> and store as data sets.
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "tab:cpptraj-DataFile-formats"
+nolink "false"
 
 \end_inset
 
@@ -12990,11 +13213,13 @@ reference "tab:cpptraj-DataFile-formats"
 \begin_inset CommandInset ref
 LatexCommand ref
 reference "sec:Datafile-Commands"
+nolink "false"
 
 \end_inset
 
 .
- For example, given the file calc.dat:
+ For example,
+ given the file calc.dat:
 \end_layout
 
 \begin_layout LyX-Code
@@ -13010,7 +13235,8 @@ The command '
 \family typewriter
 readdata calc.dat
 \family default
-' would read data into two data sets, calc.dat:2 (legend set to 
+' would read data into two data sets,
+ calc.dat:2 (legend set to 
 \begin_inset Quotes eld
 \end_inset
 
@@ -13072,14 +13298,16 @@ args> Additional data file arguments.
 
 \end_deeper
 \begin_layout Standard
-Read data sets as an ensemble, i.e.
+Read data sets as an ensemble,
+ i.e.
  each file is a different member of an ensemble.
  This command is MPI-aware.
 \end_layout
 
 \begin_layout Standard
-If one filename is given, it is assumed it is the "lowest" member of an
- ensemble with a numerical extension, e.g.
+If one filename is given,
+ it is assumed it is the "lowest" member of an ensemble with a numerical extension,
+ e.g.
  'file.001' and the remaining files are searched for automatically.
  Otherwise all other members of the ensemble can be specified with 
 \series bold
@@ -13091,6 +13319,7 @@ If one filename is given, it is assumed it is the "lowest" member of an
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "sec:Datafile-Commands"
+nolink "false"
 
 \end_inset
 
@@ -13098,7 +13327,8 @@ reference "sec:Datafile-Commands"
 \end_layout
 
 \begin_layout Standard
-For example, to read in data files named cpout.001 to cpout.006 automatically:
+For example,
+ to read in data files named cpout.001 to cpout.006 automatically:
 \end_layout
 
 \begin_layout LyX-Code
@@ -13116,8 +13346,7 @@ readensembledata cpout.001
 \end_layout
 
 \begin_layout LyX-Code
-                 filenames cpout.002,cpout.003,cpout.004,cpout.005,cpout.006
- 
+                 filenames cpout.002,cpout.003,cpout.004,cpout.005,cpout.006 
 \backslash
 
 \end_layout
@@ -13133,6 +13362,8 @@ readinput
 \begin_layout LyX-Code
 readinput
 \begin_inset Index idx
+range none
+pageformat default
 status open
 
 \begin_layout Plain Layout
@@ -13217,7 +13448,8 @@ rX
 \begin_inset space ~
 \end_inset
 
-<rX> Value of RX (X=1-4, default 0.0)
+<rX> Value of RX (X=1-4,
+ default 0.0)
 \end_layout
 
 \begin_layout Description
@@ -13289,10 +13521,14 @@ refindex
 \begin_inset space ~
 \end_inset
 
-reference} Use distance/angle/dihedral in reference structure to determine
- values for r1, r2, r3, and r4.
- The value of r2 is set to <r2> + <off>, r3 = r2, r1 = r2 - <width>, r4
- = r3 + <width>.
+reference} Use distance/angle/dihedral in reference structure to determine values for r1,
+ r2,
+ r3,
+ and r4.
+ The value of r2 is set to <r2> + <off>,
+ r3 = r2,
+ r1 = r2 - <width>,
+ r4 = r3 + <width>.
 \end_layout
 
 \begin_layout Description
@@ -13300,8 +13536,7 @@ reference} Use distance/angle/dihedral in reference structure to determine
 \begin_inset space ~
 \end_inset
 
-<off>] (Reference only) Value to offset distance/angle/torsion in reference
- by (default 0.0).
+<off>] (Reference only) Value to offset distance/angle/torsion in reference by (default 0.0).
 \end_layout
 
 \begin_layout Description
@@ -13309,7 +13544,8 @@ reference} Use distance/angle/dihedral in reference structure to determine
 \begin_inset space ~
 \end_inset
 
-<width>] (Reference only) Width between r1 and r2, r3 and r4 (default 0.5).
+<width>] (Reference only) Width between r1 and r2,
+ r3 and r4 (default 0.5).
 \end_layout
 
 \begin_layout Description
@@ -13318,17 +13554,16 @@ reference} Use distance/angle/dihedral in reference structure to determine
 \end_inset
 
 <outfile>] Write restraints to outfile.
- If not specified, write to STDOUT.
+ If not specified,
+ write to STDOUT.
 \end_layout
 
 \end_deeper
 \begin_layout Standard
 Generate Amber-style distance restraints for use with nmropt=1.
- This is particularly useful for generating distance restraints based off
- of reference coordinates.
- For example to generate a distance restraint between two C5' atoms using
- the current distance between them in a reference structure, offsetting
- the distance by 1.0 Ang.:
+ This is particularly useful for generating distance restraints based off of reference coordinates.
+ For example to generate a distance restraint between two C5' atoms using the current distance between them in a reference structure,
+ offsetting the distance by 1.0 Ang.:
 \end_layout
 
 \begin_layout LyX-Code
@@ -13361,9 +13596,10 @@ runanalysis [<analysiscmd> [<analysis args>]]
 \begin_layout Standard
 Run given analysis command immediately and write any data generated.
  If no command is given run any analysis currently set up.
- NOTE: When 'runanalysis' is specified alone, data is not automatically
- written; to write data generated with 'runanalysis' use the 'writedata'
- command (this allows multiple analysis runs between output if desired).
+ NOTE:
+ When 'runanalysis' is specified alone,
+ data is not automatically written;
+ to write data generated with 'runanalysis' use the 'writedata' command (this allows multiple analysis runs between output if desired).
 \end_layout
 
 \begin_layout Subsection
@@ -13373,6 +13609,8 @@ select
 \begin_layout LyX-Code
 select
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -13385,8 +13623,8 @@ select
 \end_layout
 
 \begin_layout Standard
-Prints the number of selected atoms corresponding to the given mask, as
- well as the atom numbers with format:
+Prints the number of selected atoms corresponding to the given mask,
+ as well as the atom numbers with format:
 \end_layout
 
 \begin_layout LyX-Code
@@ -13394,8 +13632,8 @@ Selected= <#atom1> <#atom2> ...
 \end_layout
 
 \begin_layout Standard
-This does not affect the state in any way, but is intended for use in scripts
- etc.
+This does not affect the state in any way,
+ but is intended for use in scripts etc.
  for testing the results of a mask expression.
 \end_layout
 
@@ -13419,13 +13657,12 @@ Show the results of a data set selection.
 \begin_layout Standard
 Either the [<aspect>] or the <index> arguments may be omitted.
  A '*' can be used in place of <name> or [<aspect>] as a wildcard.
- The <index> argument can be a single number or a range separated by '-'
- and ','.
+ The <index> argument can be a single number or a range separated by '-' and ','.
 \end_layout
 
 \begin_layout Standard
-This command does not affect the state in any way, but is particularly useful
- in interactive mode for determining the results of a dataset argument.
+This command does not affect the state in any way,
+ but is particularly useful in interactive mode for determining the results of a dataset argument.
 \end_layout
 
 \begin_layout Subsection
@@ -13479,7 +13716,8 @@ usediskcache {on|off}
 \end_layout
 
 \begin_layout Standard
-If on, CPPTRAJ will attempt to cache data sets to disk if possible.
+If on,
+ CPPTRAJ will attempt to cache data sets to disk if possible.
  This currently only works for integer data sets (e.g.
  
 \series bold
@@ -13491,7 +13729,8 @@ hbond
 \series bold
 series
 \series default
- data sets, etc).
+ data sets,
+ etc).
 \end_layout
 
 \begin_layout Subsection
@@ -13510,14 +13749,17 @@ write [<filename> <datasetname0> [<datasetname1> ...]] [<DataFile Options>]
 \end_layout
 
 \begin_layout Standard
-With no arguments, write all files currently in the data file list.
- Otherwise, write specified data set(s) to <filename>.
- This is like the 'create' command except a data file is not added to the
- data file list; it is written immediately.
+With no arguments,
+ write all files currently in the data file list.
+ Otherwise,
+ write specified data set(s) to <filename>.
+ This is like the 'create' command except a data file is not added to the data file list;
+ it is written immediately.
  See 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "sec:Datafile-Commands"
+nolink "false"
 
 \end_inset
 
@@ -13554,7 +13796,8 @@ head
 \family typewriter
 head
 \family default
-, which lists the first few lines of a file.
+,
+ which lists the first few lines of a file.
 \end_layout
 
 \begin_layout Description
@@ -13566,7 +13809,8 @@ less
 \family typewriter
 less
 \family default
-, which can be used to view the contents of a file.
+,
+ which can be used to view the contents of a file.
 \end_layout
 
 \begin_layout Description
@@ -13992,7 +14236,9 @@ parm
 \begin_inset space ~
 \end_inset
 
-[<name>] Select topology corresponding to given file name, tag, or name.
+[<name>] Select topology corresponding to given file name,
+ tag,
+ or name.
 \end_layout
 
 \begin_layout Description
@@ -14000,7 +14246,8 @@ parmindex
 \begin_inset space ~
 \end_inset
 
-[<#>] Select topology by order in which it was loaded, starting from 0.
+[<#>] Select topology by order in which it was loaded,
+ starting from 0.
 \end_layout
 
 \begin_layout Standard
@@ -14047,7 +14294,9 @@ Description
 \begin_inset Text
 
 \begin_layout Plain Layout
-angleinfo, angles, printangles
+angleinfo,
+ angles,
+ printangles
 \end_layout
 
 \end_inset
@@ -14067,7 +14316,9 @@ Print angle info for selected atoms.
 \begin_inset Text
 
 \begin_layout Plain Layout
-atominfo, atoms, printatoms
+atominfo,
+ atoms,
+ printatoms
 \end_layout
 
 \end_inset
@@ -14087,7 +14338,9 @@ Print details for selected atoms.
 \begin_inset Text
 
 \begin_layout Plain Layout
-bondinfo, bonds, printbonds
+bondinfo,
+ bonds,
+ printbonds
 \end_layout
 
 \end_inset
@@ -14167,7 +14420,9 @@ Compare two topologies and report differences.
 \begin_inset Text
 
 \begin_layout Plain Layout
-dihedralinfo, dihedrals, printdihedrals
+dihedralinfo,
+ dihedrals,
+ printdihedrals
 \end_layout
 
 \end_inset
@@ -14207,7 +14462,9 @@ Perform hydrogen mass repartitioning.
 \begin_inset Text
 
 \begin_layout Plain Layout
-improperinfo, impropers, printimpropers
+improperinfo,
+ impropers,
+ printimpropers
 \end_layout
 
 \end_inset
@@ -14367,7 +14624,8 @@ Write selected topology to file.
 \begin_inset Text
 
 \begin_layout Plain Layout
-printub, ubinfo
+printub,
+ ubinfo
 \end_layout
 
 \end_inset
@@ -14524,7 +14782,8 @@ parmindex
 \begin_inset space ~
 \end_inset
 
-<mask3>] If specified, angles must match all masks.
+<mask3>] If specified,
+ angles must match all masks.
 \end_layout
 
 \begin_layout Description
@@ -14541,8 +14800,7 @@ parmindex
 
 \end_deeper
 \begin_layout Standard
-Print angle information of atoms in <mask> for selected topology (first
- loaded topology by default) with format:
+Print angle information of atoms in <mask> for selected topology (first loaded topology by default) with format:
 \end_layout
 
 \begin_layout LyX-Code
@@ -14554,15 +14812,18 @@ Where
 \family typewriter
 Angle
 \family default
- is the internal angle index, 
+ is the internal angle index,
+ 
 \family typewriter
 Kthet
 \family default
- is the angle force constant, 
+ is the angle force constant,
+ 
 \family typewriter
 degrees
 \family default
- is the angle equilibrium value, 
+ is the angle equilibrium value,
+ 
 \family typewriter
 atom names
 \family default
@@ -14570,7 +14831,8 @@ atom names
 \family typewriter
 :<residue num>@<atom name>
 \family default
-, and 
+,
+ and 
 \family typewriter
 (numbers)
 \family default
@@ -14579,8 +14841,10 @@ atom names
 \end_layout
 
 \begin_layout Standard
-If 3 masks are given instead of 1, print info for angles with first atom
- in <mask1>, second atom in <mask2>, and third atom in <mask3>.
+If 3 masks are given instead of 1,
+ print info for angles with first atom in <mask1>,
+ second atom in <mask2>,
+ and third atom in <mask3>.
 \end_layout
 
 \begin_layout Subsection
@@ -14635,8 +14899,7 @@ parmindex
 
 \end_deeper
 \begin_layout Standard
-Print information on atoms in <mask> for selected topology (first loaded
- topology by default) with format:
+Print information on atoms in <mask> for selected topology (first loaded topology by default) with format:
 \end_layout
 
 \begin_layout LyX-Code
@@ -14648,46 +14911,54 @@ where
 \family typewriter
 #Atom
 \family default
- is the internal atom index, the first 
+ is the internal atom index,
+ the first 
 \family typewriter
 Name
 \family default
- column is the atom name, 
+ column is the atom name,
+ 
 \family typewriter
 #Res
 \family default
- is the atom's residue number, the second 
+ is the atom's residue number,
+ the second 
 \family typewriter
 Name
 \family default
- column is residue name, 
+ column is residue name,
+ 
 \family typewriter
 #Mol
 \family default
- is the atom's molecule number, 
+ is the atom's molecule number,
+ 
 \family typewriter
 Type
 \family default
- is the atom's type (certain topologies only), 
+ is the atom's type (certain topologies only),
+ 
 \family typewriter
 Charge
 \family default
- is the atom charge (in units of electron charge), 
+ is the atom charge (in units of electron charge),
+ 
 \family typewriter
 Mass
 \family default
- is the atom's mass (in amu), 
+ is the atom's mass (in amu),
+ 
 \family typewriter
 GBradius
 \family default
- is the generalized Born radius of the atom (Amber topologies only), and
- 
+ is the generalized Born radius of the atom (Amber topologies only),
+ and 
 \family typewriter
 El
 \family default
  is the 2 character element string.
- The final two columns are only shown if the topology contains non-bonded
- parameters: 
+ The final two columns are only shown if the topology contains non-bonded parameters:
+ 
 \family typewriter
 rVDW
 \family default
@@ -14745,7 +15016,8 @@ parmindex
 \end_layout
 
 \begin_layout Description
-[<mask2>] If specified, bonds must match both masks.
+[<mask2>] If specified,
+ bonds must match both masks.
 \end_layout
 
 \begin_layout Description
@@ -14766,8 +15038,7 @@ parmindex
 
 \end_deeper
 \begin_layout Standard
-Print bond information for atoms in <mask> for selected topology (first
- loaded topology by default) with format:
+Print bond information for atoms in <mask> for selected topology (first loaded topology by default) with format:
 \end_layout
 
 \begin_layout LyX-Code
@@ -14779,15 +15050,18 @@ where
 \family typewriter
 Bond
 \family default
- is the internal bond index, 
+ is the internal bond index,
+ 
 \family typewriter
 Kb
 \family default
- is the bond force constant, 
+ is the bond force constant,
+ 
 \family typewriter
 Req
 \family default
- is the bond equilibrium value (in Angstroms), 
+ is the bond equilibrium value (in Angstroms),
+ 
 \family typewriter
 atom names
 \family default
@@ -14795,7 +15069,8 @@ atom names
 \family typewriter
 :<residue num>@<atom name>
 \family default
-, and 
+,
+ and 
 \family typewriter
 (numbers)
 \family default
@@ -14804,8 +15079,8 @@ atom names
 \end_layout
 
 \begin_layout Standard
-If 2 masks are given instead of 1, print info for bonds with first atom
- in <mask1> and second atom in <mask2>.
+If 2 masks are given instead of 1,
+ print info for bonds with first atom in <mask1> and second atom in <mask2>.
 \end_layout
 
 \begin_layout Subsection
@@ -14849,8 +15124,7 @@ change [parm <name> | parmindex <#> | <#> |
 \end_layout
 
 \begin_layout LyX-Code
-      bondparm <mask1> [<mask2>] {setrk|scalerk|setreq|scalereq} <value>
- |
+      bondparm <mask1> [<mask2>] {setrk|scalerk|setreq|scalereq} <value> |
 \end_layout
 
 \begin_layout LyX-Code
@@ -14988,8 +15262,7 @@ max
 \end_inset
 
 max> Change original residue numbers (to e.g.
- original PDB numbers) of residues in <mask> to a range starting from <min>
- and ending with <max>.
+ original PDB numbers) of residues in <mask> to a range starting from <min> and ending with <max>.
 \end_layout
 
 \begin_layout Description
@@ -15033,9 +15306,8 @@ max>
 \begin_inset space ~
 \end_inset
 
-<#> Change residue insertion codes of residues in <mask> to a range of character
-s starting from <min> and ending with <max>; set the original residue number
- to <resnum>.
+<#> Change residue insertion codes of residues in <mask> to a range of characters starting from <min> and ending with <max>;
+ set the original residue number to <resnum>.
 \end_layout
 
 \begin_layout Description
@@ -15067,8 +15339,7 @@ addbond
 \begin_inset space ~
 \end_inset
 
-<mask2> Add bond between atom specified by <mask1> and atom specified by
- <mask2>.
+<mask2> Add bond between atom specified by <mask1> and atom specified by <mask2>.
 \end_layout
 
 \begin_deeper
@@ -15103,8 +15374,8 @@ removebonds
 \end_inset
 
 [<mask2>] Remove bonds from atoms in <mask1>.
- If <mask2> also given, remove bonds between atoms in <mask1> and atoms
- in <mask2>.
+ If <mask2> also given,
+ remove bonds between atoms in <mask1> and atoms in <mask2>.
 \end_layout
 
 \begin_deeper
@@ -15113,8 +15384,8 @@ removebonds
 \begin_inset space ~
 \end_inset
 
-<file>] If specified, write removed bonds to <file> with format '<residue
- name> <residue num> <atom name> <atom num>'.
+<file>] If specified,
+ write removed bonds to <file> with format '<residue name> <residue num> <atom name> <atom num>'.
 \end_layout
 
 \end_deeper
@@ -15135,8 +15406,7 @@ bondparm
 \begin_inset space ~
 \end_inset
 
-<value> Modify bond parameters in bonds selected by <mask1> (and <mask2>
- if specified) by specified <value>.
+<value> Modify bond parameters in bonds selected by <mask1> (and <mask2> if specified) by specified <value>.
 \end_layout
 
 \begin_deeper
@@ -15203,8 +15473,8 @@ fromset
 \begin_inset space ~
 \end_inset
 
-set> Use values in <data set> for mass/charge; must have the same number
- of values as atoms selected by <mask>.
+set> Use values in <data set> for mass/charge;
+ must have the same number of values as atoms selected by <mask>.
 \end_layout
 
 \end_deeper
@@ -15246,7 +15516,8 @@ firstres
 \end_deeper
 \begin_layout Standard
 Change specified parts of the specified topology.
- For example, to change atoms named 'HN' to 'H' in topology 0:
+ For example,
+ to change atoms named 'HN' to 'H' in topology 0:
 \end_layout
 
 \begin_layout LyX-Code
@@ -15299,14 +15570,13 @@ parmindex
 \begin_inset space ~
 \end_inset
 
-<set>] If specified, a data set named <set> will be cretaed containing total
- charge.
+<set>] If specified,
+ a data set named <set> will be cretaed containing total charge.
 \end_layout
 
 \end_deeper
 \begin_layout Standard
-Print the total charge of atoms in <mask> (in units of electron charge)
- for selected topology (first loaded topology by default).
+Print the total charge of atoms in <mask> (in units of electron charge) for selected topology (first loaded topology by default).
 \end_layout
 
 \begin_layout Subsection
@@ -15314,8 +15584,7 @@ comparetop
 \end_layout
 
 \begin_layout LyX-Code
-comparetop {parm <name> | parmindex <#>} {parm <name> | parmindex <#>} [out
- <file>]
+comparetop {parm <name> | parmindex <#>} {parm <name> | parmindex <#>} [out <file>]
 \end_layout
 
 \begin_layout LyX-Code
@@ -15378,9 +15647,8 @@ out
 \end_deeper
 \begin_layout Standard
 Compare and report differences in atoms/parameters between two topologies.
- Differences are reported in standard 'diff' format, with '<' prefix indicating
- the parameter is from the first topology and '>' prefix indicating the
- parameter is from the second topology.
+ Differences are reported in standard 'diff' format,
+ with '<' prefix indicating the parameter is from the first topology and '>' prefix indicating the parameter is from the second topology.
 \end_layout
 
 \begin_layout Subsection
@@ -15442,7 +15710,8 @@ parmindex
 \begin_inset space ~
 \end_inset
 
-<mask4>] If specified, dihedrals must match all masks.
+<mask4>] If specified,
+ dihedrals must match all masks.
 \end_layout
 
 \begin_layout Description
@@ -15463,8 +15732,7 @@ parmindex
 
 \end_deeper
 \begin_layout Standard
-Print dihedral information of atoms in <mask> for selected topology (first
- loaded topology by default) with format:
+Print dihedral information of atoms in <mask> for selected topology (first loaded topology by default) with format:
 \end_layout
 
 \begin_layout LyX-Code
@@ -15476,19 +15744,23 @@ where
 \family typewriter
 #Dihedral
 \family default
- is the internal dihedral index, 
+ is the internal dihedral index,
+ 
 \family typewriter
 pk
 \family default
- is the dihedral force constant, 
+ is the dihedral force constant,
+ 
 \family typewriter
 phase
 \family default
- is the dihedral phase, 
+ is the dihedral phase,
+ 
 \family typewriter
 pn
 \family default
- is the dihedral periodicity, and 
+ is the dihedral periodicity,
+ and 
 \family typewriter
 atoms
 \family default
@@ -15496,17 +15768,21 @@ atoms
 \family typewriter
 :<residue num>@<atom name>
 \family default
-, followed by the atom indices involved in a comma-separated list.
- In addition if the dihedral is an end dihedral, improper dihedral, or both
- it will be prefaced with an 
+,
+ followed by the atom indices involved in a comma-separated list.
+ In addition if the dihedral is an end dihedral,
+ improper dihedral,
+ or both it will be prefaced with an 
 \family typewriter
 E
 \family default
-, 
+,
+ 
 \family typewriter
 I
 \family default
-, or 
+,
+ or 
 \family typewriter
 B
 \family default
@@ -15515,9 +15791,11 @@ B
 \end_layout
 
 \begin_layout Standard
-If 4 masks are given instead of 1, print info for dihedrals with first atom
- in <mask1>, second atom in <mask2>, third atom in <mask3>, and fourth atom
- in <mask4>.
+If 4 masks are given instead of 1,
+ print info for dihedrals with first atom in <mask1>,
+ second atom in <mask2>,
+ third atom in <mask3>,
+ and fourth atom in <mask4>.
 \end_layout
 
 \begin_layout Subsection
@@ -15586,18 +15864,16 @@ mass> Mass to change hydrogens to (3.024 u by default).
 \end_layout
 
 \begin_layout Description
-dowater If specified, modify water hydrogen mass as well.
+dowater If specified,
+ modify water hydrogen mass as well.
 \end_layout
 
 \end_deeper
 \begin_layout Standard
 Perform hydrogen mass repartitioning on the specified topology.
- Hydrogen mass repartitioning means that for a given heavy atom, the mass
- of all bonded hydrogens are increased (to 3.024 u by default) and the mass
- of that heavy atom is decreased so as to maintain the same overall mass.
- The main use case is to allow longer time steps for molecular dynamics
- integration due to reduced frequency of vibration of bonds to hydrogen
- atoms.
+ Hydrogen mass repartitioning means that for a given heavy atom,
+ the mass of all bonded hydrogens are increased (to 3.024 u by default) and the mass of that heavy atom is decreased so as to maintain the same overall mass.
+ The main use case is to allow longer time steps for molecular dynamics integration due to reduced frequency of vibration of bonds to hydrogen atoms.
 \end_layout
 
 \begin_layout Subsection
@@ -15659,7 +15935,8 @@ parmindex
 \begin_inset space ~
 \end_inset
 
-<mask4>] If specified, impropers must match all masks.
+<mask4>] If specified,
+ impropers must match all masks.
 \end_layout
 
 \begin_layout Description
@@ -15676,10 +15953,11 @@ parmindex
 
 \end_deeper
 \begin_layout Standard
-For specified topology (first by default) either print CHARMM improper info
- for all atoms in <mask1>, or print info for dihedrals with first atom in
- <mask1>, second atom in <mask2>, third atom in <mask3>, and fourth atom
- in <mask4>.
+For specified topology (first by default) either print CHARMM improper info for all atoms in <mask1>,
+ or print info for dihedrals with first atom in <mask1>,
+ second atom in <mask2>,
+ third atom in <mask3>,
+ and fourth atom in <mask4>.
 \end_layout
 
 \begin_layout Subsection
@@ -15687,8 +15965,7 @@ mass
 \end_layout
 
 \begin_layout LyX-Code
-[<parmindex>] [parm <name> | parmindex <#> | <#>] <mask> [out <file>] [name
- <set>]
+[<parmindex>] [parm <name> | parmindex <#> | <#>] <mask> [out <file>] [name <set>]
 \end_layout
 
 \begin_deeper
@@ -15729,14 +16006,13 @@ parmindex
 \begin_inset space ~
 \end_inset
 
-<set>] If specified, a data set named <set> will be cretaed containing total
- mass.
+<set>] If specified,
+ a data set named <set> will be cretaed containing total mass.
 \end_layout
 
 \end_deeper
 \begin_layout Standard
-Print the total mass of atoms in <mask> (in amu) for selected topology (first
- loaded topology by default).
+Print the total mass of atoms in <mask> (in amu) for selected topology (first loaded topology by default).
 \end_layout
 
 \begin_layout Subsection
@@ -15791,8 +16067,7 @@ parmindex
 
 \end_deeper
 \begin_layout Standard
-Print molecule information for atoms in <mask> for selected topology (first
- loaded topology by default) with format:
+Print molecule information for atoms in <mask> for selected topology (first loaded topology by default) with format:
 \end_layout
 
 \begin_layout LyX-Code
@@ -15804,11 +16079,13 @@ where
 \family typewriter
 #Mol
 \family default
- is the molecule number, 
+ is the molecule number,
+ 
 \family typewriter
 Natom
 \family default
- is the number of atoms in the molecule, 
+ is the number of atoms in the molecule,
+ 
 \family typewriter
 #Res
 \family default
@@ -15816,21 +16093,24 @@ Natom
 \family typewriter
 Name
 \family default
- are the residue number and residue name of the first residue in the molecule
- respectively, and 
+ are the residue number and residue name of the first residue in the molecule respectively,
+ and 
 \family typewriter
 C
 \family default
  is the chain ID of the first residue.
- If the molecule is composed on non-consecutive fragments, 
+ If the molecule is composed on non-consecutive fragments,
+ 
 \family typewriter
 #Res
 \family default
-, 
+,
+ 
 \family typewriter
 Name
 \family default
-, and 
+,
+ and 
 \family typewriter
 C
 \family default
@@ -15849,6 +16129,8 @@ parm
 \begin_layout LyX-Code
 parm
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -15882,7 +16164,8 @@ parm
 \series bold
 <filename>
 \series default
- Parameter file to read in; format is auto-detected.
+ Parameter file to read in;
+ format is auto-detected.
 \end_layout
 
 \begin_layout Description
@@ -15890,11 +16173,11 @@ parm
 \series bold
 '[TAG]'
 \series default
- Optional tag (bounded in brackets) which can be referred to in place of
- the topology file name in order to simplify references to it (see 
+ Optional tag (bounded in brackets) which can be referred to in place of the topology file name in order to simplify references to it (see 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:Parameter/Reference-Tagging"
+nolink "false"
 
 \end_inset
 
@@ -15906,8 +16189,7 @@ reference "subsec:Parameter/Reference-Tagging"
 \begin_inset space ~
 \end_inset
 
-<setname>] Optional name that can be used to refer to the topology in place
- of the file name.
+<setname>] Optional name that can be used to refer to the topology in place of the file name.
 \end_layout
 
 \begin_layout Description
@@ -15915,8 +16197,8 @@ reference "subsec:Parameter/Reference-Tagging"
 \series bold
 [bondsearch <offset>]
 \series default
- Optional; when searching for bonds via geometry search (default for Topologies
- without bond information) add <offset> to distances (default 0.2 Å).
+ Optional;
+ when searching for bonds via geometry search (default for Topologies without bond information) add <offset> to distances (default 0.2 Å).
  Increase this if your system includes unusually long bonds.
 \end_layout
 
@@ -15925,8 +16207,7 @@ reference "subsec:Parameter/Reference-Tagging"
 \begin_inset space ~
 \end_inset
 
-{grid|pairlist}] Change search algorithm from the default search between
- residues algorithm:
+{grid|pairlist}] Change search algorithm from the default search between residues algorithm:
 \end_layout
 
 \begin_deeper
@@ -15938,8 +16219,8 @@ grid Uses a grid when searching for bonds between residues.
 
 \begin_layout Description
 pairlist Uses a pair list to search for bonds between atoms.
- This can potentially find bonds across periodic boundaries, but is the
- more experimental of the two.
+ This can potentially find bonds across periodic boundaries,
+ but is the more experimental of the two.
 \end_layout
 
 \end_deeper
@@ -15954,8 +16235,7 @@ Advanced Options - Not recommended for general use
 \series bold
 [nobondsearch]
 \series default
- If specified do not search for bonds via geometry if Topology does not
- include bond information.
+ If specified do not search for bonds via geometry if Topology does not include bond information.
  May cause some Actions to fail.
 \end_layout
 
@@ -15965,8 +16245,8 @@ Advanced Options - Not recommended for general use
 \end_layout
 
 \begin_layout Description
-[renumresidues] If specified, ensure that any residue cannot be part of
- more than 1 molecule (can occur with e.g.
+[renumresidues] If specified,
+ ensure that any residue cannot be part of more than 1 molecule (can occur with e.g.
  alternate sites).
  Residues will be renumbered according to molecule information in that case.
 \end_layout
@@ -15979,15 +16259,15 @@ Read in parameter file.
 \begin_inset CommandInset ref
 LatexCommand vpageref
 reference "tab:cpptraj-Topology-formats"
+nolink "false"
 
 \end_inset
 
 .
- If the file does not contain bond information, cpptraj will attempt to
- assign bonds based on a simple distance search of atoms within and between
- residues.
- The distance cutoff for determining bonds between atoms depends on the
- elements of the two atoms in question, augmented by <offset>.
+ If the file does not contain bond information,
+ cpptraj will attempt to assign bonds based on a simple distance search of atoms within and between residues.
+ The distance cutoff for determining bonds between atoms depends on the elements of the two atoms in question,
+ augmented by <offset>.
  Molecule information is then determined from bond information.
 \end_layout
 
@@ -16014,8 +16294,7 @@ name "subsec:cpptraj-parm-pdb"
 
 \begin_deeper
 \begin_layout Description
-[pqr] Read charge and radius information from the occupancy and B-factor
- columns.
+[pqr] Read charge and radius information from the occupancy and B-factor columns.
 \end_layout
 
 \begin_layout Description
@@ -16044,8 +16323,8 @@ name "subsec:cpptraj-parm-pdb"
 \begin_inset space ~
 \end_inset
 
-<char>] If specified, only keep alternate atom location IDs matching the
- specified character 
+<char>] If specified,
+ only keep alternate atom location IDs matching the specified character 
 \series bold
 <char>
 \series default
@@ -16060,8 +16339,8 @@ IMPORTANT NOTES FOR PDB FILES
 \end_layout
 
 \begin_layout Standard
-Sometimes PDB files can contain alternate coordinates for the same atom
- in a residue, e.g.:
+Sometimes PDB files can contain alternate coordinates for the same atom in a residue,
+ e.g.:
 \end_layout
 
 \begin_layout LyX-Code
@@ -16085,11 +16364,10 @@ If this is the case
 \shape italic
 cpptraj
 \shape default
- will print a warning about alternate location IDs being present but will
- take no other action.
- Both residues are considered 'CYS' and the mask ':CYS@CA' would select
- both atom 806 and 808.
- If desired, a specific location ID can be kept via the 
+ will print a warning about alternate location IDs being present but will take no other action.
+ Both residues are considered 'CYS' and the mask ':CYS@CA' would select both atom 806 and 808.
+ If desired,
+ a specific location ID can be kept via the 
 \series bold
 keepaltloc
 \series default
@@ -16098,7 +16376,8 @@ keepaltloc
 \series bold
 keepaltloc
 \series default
- is specified, it should also be specified for any 
+ is specified,
+ it should also be specified for any 
 \series bold
 trajin
 \series default
@@ -16109,6 +16388,7 @@ reference "subsec:cpptraj-trajin-pdb"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
@@ -16140,9 +16420,9 @@ Gromacs Top
 \end_layout
 
 \begin_layout Standard
-By default cpptraj will look for Gromacs topology data (that is not in the
- same directory) in the directory defined by the GMXDATA environment variable;
- specifically, it expects things to be in the "$GMXDATA/top" directory.
+By default cpptraj will look for Gromacs topology data (that is not in the same directory) in the directory defined by the GMXDATA environment variable;
+ specifically,
+ it expects things to be in the "$GMXDATA/top" directory.
  
 \end_layout
 
@@ -16153,6 +16433,8 @@ parmbox
 \begin_layout LyX-Code
 parmbox
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -16261,8 +16543,8 @@ parmindex
 \end_deeper
 \begin_layout Standard
 Modify the box information for specified topology.
- Overwrites any box information if present with specified values; any that
- are not specified will remain unchanged.
+ Overwrites any box information if present with specified values;
+ any that are not specified will remain unchanged.
  Note that unlike the 
 \series bold
 \shape italic
@@ -16297,6 +16579,8 @@ parminfo
 \begin_layout LyX-Code
 parminfo
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -16309,8 +16593,7 @@ parminfo
 \end_layout
 
 \begin_layout Standard
-Print a summary of information contained in the specified topology (first
- loaded topology by default) .
+Print a summary of information contained in the specified topology (first loaded topology by default) .
 \end_layout
 
 \begin_layout Subsection
@@ -16320,6 +16603,8 @@ parmstrip
 \begin_layout LyX-Code
 parmstrip
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -16343,12 +16628,13 @@ Strip atoms in
 strip
 \series default
 \emph default
- Action, this permanently modifies the topology for as long as 
+ Action,
+ this permanently modifies the topology for as long as 
 \emph on
 cpptraj
 \emph default
- is running, so this should not be used if the topology is being used to
- read or write a trajectory via 
+ is running,
+ so this should not be used if the topology is being used to read or write a trajectory via 
 \series bold
 \emph on
 trajin
@@ -16362,8 +16648,8 @@ trajout
 \emph default
 .
  This command can be used to quickly created stripped Amber topology files.
- For example, to strip all residues name WAT from a topology and write a
- new topology:
+ For example,
+ to strip all residues name WAT from a topology and write a new topology:
 \end_layout
 
 \begin_layout LyX-Code
@@ -16385,6 +16671,8 @@ parmwrite
 \begin_layout LyX-Code
 parmwrite
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -16452,8 +16740,7 @@ parmindex
 \end_layout
 
 \begin_layout Description
-[nochamber] (Amber topology only) Remove any CHAMBER information from the
- topology.
+[nochamber] (Amber topology only) Remove any CHAMBER information from the topology.
 \end_layout
 
 \end_deeper
@@ -16467,8 +16754,7 @@ Write out specified topology (first topology loaded by default) to
 <fmt>
 \series default
  (Amber topology if not specified).
- Note that the Amber topology format is the only fully supported format
- for topology writes.
+ Note that the Amber topology format is the only fully supported format for topology writes.
 \end_layout
 
 \begin_layout Subsubsection
@@ -16486,12 +16772,16 @@ Amber Topology
 \end_layout
 
 \begin_layout Description
-[writeempty] Write Amber tree, join, and rotate info even if not present.
+[writeempty] Write Amber tree,
+ join,
+ and rotate info even if not present.
 \end_layout
 
 \begin_layout Description
 [nopdbinfo] Do not write "PDB" info (e.g.
- chain IDs, original res #s, etc).
+ chain IDs,
+ original res #s,
+ etc).
 \end_layout
 
 \end_deeper
@@ -16560,7 +16850,8 @@ parmindex
 \end_layout
 
 \begin_layout Description
-[<mask2>] If specified, UB info must match both masks.
+[<mask2>] If specified,
+ UB info must match both masks.
 \end_layout
 
 \begin_layout Description
@@ -16577,9 +16868,8 @@ parmindex
 
 \end_deeper
 \begin_layout Standard
-For specified topology (first by default) either print CHARMM Urey-Bradley
- info for all atoms in <mask1>, or print info for bonds with first atom
- in <mask1> and second atom in <mask2>.
+For specified topology (first by default) either print CHARMM Urey-Bradley info for all atoms in <mask1>,
+ or print info for bonds with first atom in <mask1> and second atom in <mask2>.
 \end_layout
 
 \begin_layout Subsection
@@ -16589,6 +16879,8 @@ resinfo
 \begin_layout LyX-Code
 resinfo
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -16662,8 +16954,7 @@ parmindex
 
 \end_deeper
 \begin_layout Standard
-Print residue information for atoms in <mask> for selected topology (first
- loaded topology by default) with format:
+Print residue information for atoms in <mask> for selected topology (first loaded topology by default) with format:
 \end_layout
 
 \begin_layout LyX-Code
@@ -16675,11 +16966,13 @@ where
 \family typewriter
 #Res
 \family default
- is the residue number, 
+ is the residue number,
+ 
 \family typewriter
 Name
 \family default
- is the residue name, 
+ is the residue name,
+ 
 \family typewriter
 First
 \family default
@@ -16687,15 +16980,18 @@ First
 \family typewriter
 Last
 \family default
- are the first and last atom numbers of the residue, 
+ are the first and last atom numbers of the residue,
+ 
 \family typewriter
 Natom
 \family default
- is the total number of atoms in the residue, 
+ is the total number of atoms in the residue,
+ 
 \family typewriter
 #Orig
 \family default
- is the original residue number (in PDB files), #Mol is the molecule number,
+ is the original residue number (in PDB files),
+ #Mol is the molecule number,
  and C is the chain ID.
 \end_layout
 
@@ -16705,9 +17001,11 @@ If
 short
 \series default
  is specified then residues will be printed out in a condensed format.
- Each residue name will be shortened to 1 character, and residues are printed
- out in groups of 10, 5 groups to a line, with each line beginning with
- a residue number, e.g.
+ Each residue name will be shortened to 1 character,
+ and residues are printed out in groups of 10,
+ 5 groups to a line,
+ with each line beginning with a residue number,
+ e.g.
 \end_layout
 
 \begin_layout LyX-Code
@@ -16723,8 +17021,7 @@ short
 \end_layout
 
 \begin_layout Standard
-If the 1 character name for a residue is unknown it will be shown as the
- first letter of the residue name in lower-case.
+If the 1 character name for a residue is unknown it will be shown as the first letter of the residue name in lower-case.
 \end_layout
 
 \begin_layout Subsection
@@ -16736,8 +17033,7 @@ scaledihedralk [parm <name> | parmindex <#>] <scale factor> [<mask> [useall]]
 \end_layout
 
 \begin_layout Standard
-Scale dihedral force constants for dihderals selected by <mask> for specified
- topology.
+Scale dihedral force constants for dihderals selected by <mask> for specified topology.
  If 
 \series bold
 useall
@@ -16762,12 +17058,12 @@ solvent [parm <name> | parmindex <#> | <#>] { <mask> | none }
 \end_layout
 
 \begin_layout Standard
-Set solvent for selected topology (first loaded topology by default) based
- on 
+Set solvent for selected topology (first loaded topology by default) based on 
 \series bold
 <mask>
 \series default
-, or set nothing as solvent if 
+,
+ or set nothing as solvent if 
 \series bold
 none
 \series default
@@ -16819,20 +17115,21 @@ set> Topology or parameter data set containing parameters to use.
 \begin_layout Standard
 
 \emph on
-NOTE: This command is provided for convenience only.
- For editing topology files, ParmEd is a much better alternative.
+NOTE:
+ This command is provided for convenience only.
+ For editing topology files,
+ ParmEd is a much better alternative.
 \end_layout
 
 \begin_layout Standard
 Update parameters in specified topology with those from <parm set>.
  <parm set> can either be a parameter set or a topology.
- If a parameter from <parm set> does not exist in the topology it will be
- added.
+ If a parameter from <parm set> does not exist in the topology it will be added.
 \end_layout
 
 \begin_layout Standard
-For example, to modify parameters in a topology file named lys.parm7 with
- those from parameter file kcx.str:
+For example,
+ to modify parameters in a topology file named lys.parm7 with those from parameter file kcx.str:
 \end_layout
 
 \begin_layout LyX-Code
@@ -16877,15 +17174,18 @@ These commands control the reading and writing of trajectory files.
 \shape italic
 cpptraj
 \shape default
-: input, output, and reference.
+:
+ input,
+ output,
+ and reference.
  In 
 \shape italic
 cpptraj
 \shape default
-, trajectories are always associated with a topology file.
- If a topology file is not specified, a trajectory file will be associated
- with the first topology file loaded by default (this is true for both input
- and output trajectories.
+,
+ trajectories are always associated with a topology file.
+ If a topology file is not specified,
+ a trajectory file will be associated with the first topology file loaded by default (this is true for both input and output trajectories.
 \end_layout
 
 \begin_layout Standard
@@ -17003,7 +17303,8 @@ Amber NetCDF
 \begin_inset Text
 
 \begin_layout Plain Layout
-cdf, netcdf
+cdf,
+ netcdf
 \end_layout
 
 \end_inset
@@ -17050,7 +17351,8 @@ restart
 \begin_inset Text
 
 \begin_layout Plain Layout
-.rst7, .rst
+.rst7,
+ .rst
 \end_layout
 
 \end_inset
@@ -17079,7 +17381,8 @@ Amber NetCDF Restart
 \begin_inset Text
 
 \begin_layout Plain Layout
-ncrestart, restartnc
+ncrestart,
+ restartnc
 \end_layout
 
 \end_inset
@@ -17125,7 +17428,8 @@ DCD
 \begin_inset Text
 
 \begin_layout Plain Layout
-dcd, charmm
+dcd,
+ charmm
 \end_layout
 
 \end_inset
@@ -17751,7 +18055,8 @@ conflib
 \begin_inset Text
 
 \begin_layout Plain Layout
-Read Only, Detection by extension
+Read Only,
+ Detection by extension
 \end_layout
 
 \end_inset
@@ -18049,7 +18354,8 @@ ensemble <file0> {[<start>] [<stop> | last] [offset]} | lastframe
 \begin_inset space ~
 \end_inset
 
-last] Frame to stop reading ensemble at; if not specified or 'last' specified,
+last] Frame to stop reading ensemble at;
+ if not specified or 'last' specified,
  end of trajectories.
 \end_layout
 
@@ -18066,8 +18372,7 @@ last] Frame to stop reading ensemble at; if not specified or 'last' specified,
 \begin_inset space ~
 \end_inset
 
-<parmfile>] Topology filename/tag to associate with trajectories (default
- first topology).
+<parmfile>] Topology filename/tag to associate with trajectories (default first topology).
 \end_layout
 
 \begin_layout Description
@@ -18075,8 +18380,8 @@ last] Frame to stop reading ensemble at; if not specified or 'last' specified,
 \begin_inset space ~
 \end_inset
 
-<#>] Index of Topology to associate with trajectories (default 0, first
- topology).
+<#>] Index of Topology to associate with trajectories (default 0,
+ first topology).
 \end_layout
 
 \begin_layout Description
@@ -18084,8 +18389,8 @@ last] Frame to stop reading ensemble at; if not specified or 'last' specified,
 \begin_inset space ~
 \end_inset
 
-<file1>,...,<fileN>] Do not automatically search for additional replica trajectorie
-s; use comma-separated list of trajectory names.
+<file1>,...,<fileN>] Do not automatically search for additional replica trajectories;
+ use comma-separated list of trajectory names.
 \end_layout
 
 \begin_layout Description
@@ -18095,8 +18400,8 @@ s; use comma-separated list of trajectory names.
 \end_layout
 
 \begin_layout Description
-[bycrdidx] For H-REMD trajectories, sort by coordinate indices stored in
- trajectory files.
+[bycrdidx] For H-REMD trajectories,
+ sort by coordinate indices stored in trajectory files.
  This is preferred over sorting via 'remlog'.
 \end_layout
 
@@ -18105,8 +18410,8 @@ s; use comma-separated list of trajectory names.
 \begin_inset space ~
 \end_inset
 
-<remlogfile>] For H-REMD trajectories only, use specified REMD log file
- to sort trajectories by coordinate index (instead of by replica/Hamiltonian).
+<remlogfile>] For H-REMD trajectories only,
+ use specified REMD log file to sort trajectories by coordinate index (instead of by replica/Hamiltonian).
 \begin_inset Separator latexpar
 \end_inset
 
@@ -18127,9 +18432,8 @@ ntwx
 \begin_inset space ~
 \end_inset
 
-<ntwx>] If trajectory and REMD log were not written at the same rate, these
- are the values for nstlim (steps between each exchange) and ntwx (steps
- between trajectory write) used in the REMD simulation.
+<ntwx>] If trajectory and REMD log were not written at the same rate,
+ these are the values for nstlim (steps between each exchange) and ntwx (steps between trajectory write) used in the REMD simulation.
 \end_layout
 
 \end_deeper
@@ -18142,7 +18446,8 @@ Read in and process trajectories as an ensemble.
 trajin
 \series default
 \shape default
- remdtraj', except instead of processing one frame at a target temperature,
+ remdtraj',
+ except instead of processing one frame at a target temperature,
  process all frames.
  This means that action and trajout commands apply to the entire ensemble;
  note however that not all actions currently function in 
@@ -18152,8 +18457,10 @@ trajin
 \series default
 \shape default
  mode.
- For example, to read in a replica ensemble, convert it to temperature trajector
-ies, and calculate a distance at each temperature:
+ For example,
+ to read in a replica ensemble,
+ convert it to temperature trajectories,
+ and calculate a distance at each temperature:
 \end_layout
 
 \begin_layout LyX-Code
@@ -18173,10 +18480,12 @@ distance d1 out d1.ensemble.dat @1 @21
 \end_layout
 
 \begin_layout Standard
-This will output 4 temperature trajectories named 'temp.crd.X', where X ranges
- from 0 to 3 with 0 corresponding to the lowest temperature, and 'd1.ensemble.dat'
- containing 4 columns, each corresponding to a temperature.
- If run with MPI, data will be written to separate files named 'd1.ensemble.dat.X',
+This will output 4 temperature trajectories named 'temp.crd.X',
+ where X ranges from 0 to 3 with 0 corresponding to the lowest temperature,
+ and 'd1.ensemble.dat' containing 4 columns,
+ each corresponding to a temperature.
+ If run with MPI,
+ data will be written to separate files named 'd1.ensemble.dat.X',
  similar to the output trajectories.
 \end_layout
 
@@ -18198,12 +18507,9 @@ ensemble
 \end_layout
 
 \begin_layout Standard
-H-REMD trajectories which are typically already sorted by replica/Hamiltonian
- can be sorted by coordinate index instead with 'bycrdidx' (if the trajectory
- contains coordinate indices) or by REMD log data specified with the 'remlog'
- keyword.
- For example, to sort by coordinate index using a REMD log and write sorted
- trajectories:
+H-REMD trajectories which are typically already sorted by replica/Hamiltonian can be sorted by coordinate index instead with 'bycrdidx' (if the trajectory contains coordinate indices) or by REMD log data specified with the 'remlog' keyword.
+ For example,
+ to sort by coordinate index using a REMD log and write sorted trajectories:
 \end_layout
 
 \begin_layout LyX-Code
@@ -18258,7 +18564,8 @@ This command is MPI only.
 ensemble
 \series default
 \emph default
- command, which dramatically improves set up efficiency.
+ command,
+ which dramatically improves set up efficiency.
 \end_layout
 
 \begin_layout Subsection
@@ -18275,6 +18582,8 @@ name "subsec:cpptraj_reference"
 \begin_layout LyX-Code
 reference
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -18296,8 +18605,8 @@ reference
 
 \begin_deeper
 \begin_layout Description
-<name> File name (or COORDS set name if 'crdset' specified) to read in as
- reference; any trajectory recognized by 'trajin' can be used.
+<name> File name (or COORDS set name if 'crdset' specified) to read in as reference;
+ any trajectory recognized by 'trajin' can be used.
 \end_layout
 
 \begin_layout Description
@@ -18309,7 +18618,8 @@ reference
 \end_layout
 
 \begin_layout Description
-([tag]) Tag to give this reference file, e.g.
+([tag]) Tag to give this reference file,
+ e.g.
  
 \begin_inset Quotes eld
 \end_inset
@@ -18318,7 +18628,8 @@ reference
 \begin_inset Quotes erd
 \end_inset
 
-; BRACKETS MUST BE INCLUDED.
+;
+ BRACKETS MUST BE INCLUDED.
 \end_layout
 
 \begin_layout Description
@@ -18334,8 +18645,7 @@ reference
 \begin_inset space ~
 \end_inset
 
-<parmfile/tag>] Topology filename/tag to associate with reference (default
- first topology).
+<parmfile/tag>] Topology filename/tag to associate with reference (default first topology).
 \end_layout
 
 \begin_layout Description
@@ -18343,33 +18653,33 @@ reference
 \begin_inset space ~
 \end_inset
 
-<#>] Index of Topology to associate with reference (default 0, first topology).
+<#>] Index of Topology to associate with reference (default 0,
+ first topology).
 \end_layout
 
 \end_deeper
 \begin_layout Standard
 Use specified trajectory as reference coordinates.
- For trajectories with multiple frames, the first frame is used if a specific
- frame is not specified.
- An optional tag can be given (bounded in brackets) which can then be used
- in place of the name (see 
+ For trajectories with multiple frames,
+ the first frame is used if a specific frame is not specified.
+ An optional tag can be given (bounded in brackets) which can then be used in place of the name (see 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:Parameter/Reference-Tagging"
+nolink "false"
 
 \end_inset
 
  for examples of how to use tags).
- If desired, an atom mask can be used to read in only specified atoms from
- a reference.
+ If desired,
+ an atom mask can be used to read in only specified atoms from a reference.
 \end_layout
 
 \begin_layout Standard
-Reference coordinates are now considered COORDS data sets and can be used
- anywhere a COORDS data set could, which allows reference structures to
- be manipulated once they are loaded.
- For example, a reference structure could be centered on the origin like
- so:
+Reference coordinates are now considered COORDS data sets and can be used anywhere a COORDS data set could,
+ which allows reference structures to be manipulated once they are loaded.
+ For example,
+ a reference structure could be centered on the origin like so:
 \end_layout
 
 \begin_layout LyX-Code
@@ -18382,8 +18692,8 @@ crdaction [MyRef] center origin
 
 \begin_layout Standard
 Note that the 'average' keyword has been deprecated for reference.
- If desired, an averaged reference COORDS data set can be created from a
- trajectory using the 'average' command like so:
+ If desired,
+ an averaged reference COORDS data set can be created from a trajectory using the 'average' command like so:
 \end_layout
 
 \begin_layout LyX-Code
@@ -18424,6 +18734,8 @@ name "subsec:cpptraj_trajin"
 \begin_layout LyX-Code
 trajin
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -18448,8 +18760,7 @@ trajin
 \end_layout
 
 \begin_layout LyX-Code
-       [ remdtraj {remdtrajtemp <Temperature> | remdtrajidx <idx1,idx2,...>
- 
+       [ remdtraj {remdtrajtemp <Temperature> | remdtrajidx <idx1,idx2,...> 
 \end_layout
 
 \begin_layout LyX-Code
@@ -18491,8 +18802,9 @@ trajin
 \begin_inset space ~
 \end_inset
 
-last] Frame to stop reading at; if not specified or 'last' specified, end
- of trajectory.
+last] Frame to stop reading at;
+ if not specified or 'last' specified,
+ end of trajectory.
 \end_layout
 
 \begin_layout Description
@@ -18508,8 +18820,7 @@ last] Frame to stop reading at; if not specified or 'last' specified, end
 \begin_inset space ~
 \end_inset
 
-<parmfile/tag>] Topology filename/tag to associate with trajectory (default
- first topology).
+<parmfile/tag>] Topology filename/tag to associate with trajectory (default first topology).
 \end_layout
 
 \begin_layout Description
@@ -18517,7 +18828,8 @@ last] Frame to stop reading at; if not specified or 'last' specified, end
 \begin_inset space ~
 \end_inset
 
-<#>] Index of Topology to associate with trajectory (default 0, first topology).
+<#>] Index of Topology to associate with trajectory (default 0,
+ first topology).
 \end_layout
 
 \begin_layout Description
@@ -18545,8 +18857,8 @@ last] Frame to stop reading at; if not specified or 'last' specified, end
 \begin_inset space ~
 \end_inset
 
-keyword>] Force file to be read as specified format; overrides file autodetectio
-n.
+keyword>] Force file to be read as specified format;
+ overrides file autodetection.
 \end_layout
 
 \begin_layout Description
@@ -18558,8 +18870,7 @@ Options>] See below.
 \end_layout
 
 \begin_layout Description
-[remdtraj] Read <filename> as the first replica in a group of replica trajectori
-es.
+[remdtraj] Read <filename> as the first replica in a group of replica trajectories.
 \begin_inset Separator latexpar
 \end_inset
 
@@ -18584,9 +18895,9 @@ remdtrajidx
 \begin_inset space ~
 \end_inset
 
-<idx1,idx2,...> Use frames at <Temperature> (for temperature replica trajectories)
- or index <idx1,idx2,...> (for Hamiltonian replica trajectories); For Multidimensio
-nal REMD simulations, multiple values are comma-separated.
+<idx1,idx2,...> Use frames at <Temperature> (for temperature replica trajectories) or index <idx1,idx2,...> (for Hamiltonian replica trajectories);
+ For Multidimensional REMD simulations,
+ multiple values are comma-separated.
 \end_layout
 
 \begin_layout Description
@@ -18594,15 +18905,15 @@ remdtrajvalues
 \begin_inset space ~
 \end_inset
 
-<value1,value2,...> Use frames at <value1,value2,...> (for Multidimensional REMD
- trajectories).
- Each value may correspond to either temperature, pH, Redox Potential or
- Hamiltonian index.
- The values need to be entered in the same order as the dimensions in the
- Multidimensional REMD simulation.
- For example, for T,pH-REMD value1 would correspond to a temperature and
- value2 to a pH.
- In the command, the values are comma-separated.
+<value1,value2,...> Use frames at <value1,value2,...> (for Multidimensional REMD trajectories).
+ Each value may correspond to either temperature,
+ pH,
+ Redox Potential or Hamiltonian index.
+ The values need to be entered in the same order as the dimensions in the Multidimensional REMD simulation.
+ For example,
+ for T,pH-REMD value1 would correspond to a temperature and value2 to a pH.
+ In the command,
+ the values are comma-separated.
 \end_layout
 
 \begin_layout Description
@@ -18610,8 +18921,8 @@ remdtrajvalues
 \begin_inset space ~
 \end_inset
 
-<file1>,...,<fileN>] Do not automatically search for additional replica trajectorie
-s; use comma-separated list of trajectory names.
+<file1>,...,<fileN>] Do not automatically search for additional replica trajectories;
+ use comma-separated list of trajectory names.
 \end_layout
 
 \end_deeper
@@ -18622,18 +18933,20 @@ Read in trajectory specified by filename.
 \begin_inset CommandInset ref
 LatexCommand pageref
 reference "tab:cpptraj-trajformats"
+nolink "false"
 
 \end_inset
 
  for currently recognized trajectory file formats.
- If just the <start> argument is given, all frames from <start> to the last
- frame of the trajectory will be read.
+ If just the <start> argument is given,
+ all frames from <start> to the last frame of the trajectory will be read.
  To read in a trajectory with offsets where the last frame # is not known,
  specify the 
 \series bold
 last
 \series default
- keyword instead of a <stop> argument, e.g.
+ keyword instead of a <stop> argument,
+ e.g.
 \end_layout
 
 \begin_layout LyX-Code
@@ -18641,9 +18954,10 @@ trajin Test1.crd 10 last 2
 \end_layout
 
 \begin_layout Standard
-This will process Test1.crd from frame 10 to the last frame, skipping by
- 2 frames.
- To explicitly select only the last frame, specify the 
+This will process Test1.crd from frame 10 to the last frame,
+ skipping by 2 frames.
+ To explicitly select only the last frame,
+ specify the 
 \series bold
 lastframe
 \series default
@@ -18655,8 +18969,7 @@ trajin Test1.crd lastframe
 \end_layout
 
 \begin_layout Standard
-Here is an example of loading in multiple trajectories which have difference
- topology files:
+Here is an example of loading in multiple trajectories which have difference topology files:
 \end_layout
 
 \begin_layout LyX-Code
@@ -18692,11 +19005,11 @@ trajin Test3.crd parmindex 3
 \end_layout
 
 \begin_layout Standard
-Test0.crd is associated with top0.parm7; since no parm was specified it defaulted
- to the first parm read in.
- Test1.crd was associated with top1.parm7 by filename, Test2.crd was associated
- with top2.parm7 by its tag, and finally Test3.crd was associated with top3.parm7
- by its index (based on the order it was read in).
+Test0.crd is associated with top0.parm7;
+ since no parm was specified it defaulted to the first parm read in.
+ Test1.crd was associated with top1.parm7 by filename,
+ Test2.crd was associated with top2.parm7 by its tag,
+ and finally Test3.crd was associated with top3.parm7 by its index (based on the order it was read in).
 \end_layout
 
 \begin_layout Subsubsection*
@@ -18708,17 +19021,16 @@ If the
 \series bold
 remdtraj
 \series default
- keyword is specified the trajectory is treated as belonging to the lowest
- # replica of a group of REMD trajectories.
- The remaining replicas can be either automatically detected by following
- a naming convention of <REMDFILENAME>.X, where X is the replica number,
+ keyword is specified the trajectory is treated as belonging to the lowest # replica of a group of REMD trajectories.
+ The remaining replicas can be either automatically detected by following a naming convention of <REMDFILENAME>.X,
+ where X is the replica number,
  or explicitly specified in a comma-separated list following the 
 \series bold
 trajnames
 \series default
  keyword.
- All trajectories will be processed at the same time, but only frames with
- a temperature matching the one specified by 
+ All trajectories will be processed at the same time,
+ but only frames with a temperature matching the one specified by 
 \series bold
 remdtrajtemp
 \series default
@@ -18727,9 +19039,12 @@ remdtrajtemp
 remdtrajidx
 \series default
  will be processed.
- For example, to process replica trajectories rem.001, rem.002, rem.003, and
- rem.004, grabbing only the frames at temperature 300.0 (assuming that this
- is a temperature in the ensemble):
+ For example,
+ to process replica trajectories rem.001,
+ rem.002,
+ rem.003,
+ and rem.004,
+ grabbing only the frames at temperature 300.0 (assuming that this is a temperature in the ensemble):
 \end_layout
 
 \begin_layout LyX-Code
@@ -18760,7 +19075,9 @@ ensemble
 \begin_layout Subsubsection
 
 \emph on
-Options for Amber NetCDF, Amber NC Restart, Amber Restart:
+Options for Amber NetCDF,
+ Amber NC Restart,
+ Amber Restart:
 \end_layout
 
 \begin_layout LyX-Code
@@ -18805,27 +19122,29 @@ shape Force reading of box info as CHARMM shape matrix (XX XY YY XZ YZ ZZ).
 \end_layout
 
 \begin_layout Description
-namdcell Force reading of box info as NAMD unit cell (X cos(g) Y cos(b)
- cos(a) Z).
+namdcell Force reading of box info as NAMD unit cell (X cos(g) Y cos(b) cos(a) Z).
  
 \end_layout
 
 \begin_layout Description
-charmmcell Force reading of box info as old CHARMM unit cell (X Y Z a b
- g).
+charmmcell Force reading of box info as old CHARMM unit cell (X Y Z a b g).
  
 \end_layout
 
 \end_deeper
 \begin_layout Standard
-Note that CHARMM trajectories can have unit cell data stored in one of two
- ways.
- Older versions (<22) of charmm store the 3x lengths (X Y Z, in Angstroms)
- and 3x angles (alpha beta gamma, in degrees).
+Note that CHARMM trajectories can have unit cell data stored in one of two ways.
+ Older versions (<22) of charmm store the 3x lengths (X Y Z,
+ in Angstroms) and 3x angles (alpha beta gamma,
+ in degrees).
  Newer versions (>=22) store elements of the symmetric shape matrix (XX,
- XY, YY, XZ, YZ, ZZ).
- CPPTRAJ will attempt to automatically detect which type of parameters are
- present, but this can be overridden with the 
+ XY,
+ YY,
+ XZ,
+ YZ,
+ ZZ).
+ CPPTRAJ will attempt to automatically detect which type of parameters are present,
+ but this can be overridden with the 
 \series bold
 shape
 \series default
@@ -18838,9 +19157,8 @@ charmmcell
 \series bold
 namdcell
 \series default
- keyword is provided for compatibility with DCD trajectories produced by
- VMD/NAMD, but note these trajectories only store a version of the shape
- matrix that is correct if the unit cell is also X-aligned.
+ keyword is provided for compatibility with DCD trajectories produced by VMD/NAMD,
+ but note these trajectories only store a version of the shape matrix that is correct if the unit cell is also X-aligned.
 \end_layout
 
 \begin_layout Subsubsection
@@ -18864,8 +19182,8 @@ name "subsec:cpptraj-trajin-pdb"
 \begin_inset space ~
 \end_inset
 
-<char>] If specified, only keep alternate atom location IDs matching the
- specified character 
+<char>] If specified,
+ only keep alternate atom location IDs matching the specified character 
 \series bold
 <char>
 \series default
@@ -18878,8 +19196,9 @@ Note that if
 \series bold
 keepaltloc
 \series default
- is specified, the associated topology should not have alternate location
- IDs, i.e.
+ is specified,
+ the associated topology should not have alternate location IDs,
+ i.e.
  if the topology is from a PDB the 
 \series bold
 keepaltloc
@@ -18895,6 +19214,7 @@ reference "subsec:cpptraj-parm-pdb"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
@@ -18915,6 +19235,8 @@ name "subsec:cpptraj-trajout"
 \begin_layout LyX-Code
 trajout
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -18960,16 +19282,18 @@ trajout
 \begin_inset CommandInset ref
 LatexCommand vpageref
 reference "tab:cpptraj-trajformats"
+nolink "false"
 
 \end_inset
 
 ).
- If not specified format will be determined from extension, otherwise default
- to Amber trajectory.
+ If not specified format will be determined from extension,
+ otherwise default to Amber trajectory.
 \end_layout
 
 \begin_layout Description
-[append] If <filename> exists, frames will be appended to <filename>.
+[append] If <filename> exists,
+ frames will be appended to <filename>.
 \end_layout
 
 \begin_layout Description
@@ -18997,8 +19321,7 @@ reference "tab:cpptraj-trajformats"
 \begin_inset space ~
 \end_inset
 
-<parmfile>] Topology filename/tag to associate with trajectory (default
- first topology).
+<parmfile>] Topology filename/tag to associate with trajectory (default first topology).
 \end_layout
 
 \begin_layout Description
@@ -19006,7 +19329,8 @@ reference "tab:cpptraj-trajformats"
 \begin_inset space ~
 \end_inset
 
-<#>] Index of Topology to associate with trajectory (default 0, first topology).
+<#>] Index of Topology to associate with trajectory (default 0,
+ first topology).
 \end_layout
 
 \begin_layout Description
@@ -19030,8 +19354,8 @@ reference "tab:cpptraj-trajformats"
 \begin_inset space ~
 \end_inset
 
-<memberlist>] Ensemble processing only; only write from specified members
- (starting from 0).
+<memberlist>] Ensemble processing only;
+ only write from specified members (starting from 0).
 \end_layout
 
 \begin_layout Description
@@ -19060,14 +19384,13 @@ reference "tab:cpptraj-trajformats"
 
 \end_deeper
 \begin_layout Standard
-During a run, write frames to trajectory specified by filename in specified
- file format (Amber trajectory if none specified) after all Action processing
- has occurred.
- To write out trajectories within the Action queue see the outtraj Action
- (
+During a run,
+ write frames to trajectory specified by filename in specified file format (Amber trajectory if none specified) after all Action processing has occurred.
+ To write out trajectories within the Action queue see the outtraj Action (
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_outtraj"
+nolink "false"
 
 \end_inset
 
@@ -19076,13 +19399,12 @@ reference "subsec:cpptraj_outtraj"
 \begin_inset CommandInset ref
 LatexCommand pageref
 reference "tab:cpptraj-trajformats"
+nolink "false"
 
 \end_inset
 
- for currently recognized output trajectory formats and their associated
- keyword(s).
- Note that now the file type can be determined from the output extension
- if not specified by a keyword.
+ for currently recognized output trajectory formats and their associated keyword(s).
+ Note that now the file type can be determined from the output extension if not specified by a keyword.
  Multiple output trajectories of any format can be specified.
  
 \end_layout
@@ -19090,9 +19412,7 @@ reference "tab:cpptraj-trajformats"
 \begin_layout Standard
 
 \series bold
-Frames will be written to the output trajectory when the parameter file
- being processed matches the parameter file the output trajectory was set
- up with.
+Frames will be written to the output trajectory when the parameter file being processed matches the parameter file the output trajectory was set up with.
 
 \series default
  So given the input:
@@ -19119,11 +19439,9 @@ trajout output.crd parm [top1]
 \end_layout
 
 \begin_layout Standard
-only frames read in from input1.crd (which is associated with top1.parm7)
- will be written to output.crd.
- The trajectory input0.crd is associated with top0.parm7; since no output
- trajectory is associated with top0.parm7 no frames will be written when
- processing top0.parm7/input0.crd.
+only frames read in from input1.crd (which is associated with top1.parm7) will be written to output.crd.
+ The trajectory input0.crd is associated with top0.parm7;
+ since no output trajectory is associated with top0.parm7 no frames will be written when processing top0.parm7/input0.crd.
 \end_layout
 
 \begin_layout Standard
@@ -19131,9 +19449,10 @@ If
 \series bold
 onlyframes
 \series default
- is specified, only input frames matching the specified range will be written
- out.
- For example, given the input:
+ is specified,
+ only input frames matching the specified range will be written out.
+ For example,
+ given the input:
 \end_layout
 
 \begin_layout LyX-Code
@@ -19145,7 +19464,10 @@ trajout output.crd onlyframes 2,5-7
 \end_layout
 
 \begin_layout Standard
-only frames 2, 5, 6, and 7 from input.crd will be written to output.crd.
+only frames 2,
+ 5,
+ 6,
+ and 7 from input.crd will be written to output.crd.
 \end_layout
 
 \begin_layout Subsubsection*
@@ -19160,22 +19482,24 @@ Certain Actions (e.g.
 align
 \series default
 \emph default
-, 
+,
+ 
 \series bold
 \emph on
 rms
 \series default
 \emph default
-, 
+,
+ 
 \series bold
 \emph on
 principal
 \series default
 \emph default
-, etc.) can rotate the unit cell vectors (i.e.
+,
+ etc.) can rotate the unit cell vectors (i.e.
  the box) if they are present.
- Some trajectory formats do not support writing out box coordinates if the
- unit cell is not 
+ Some trajectory formats do not support writing out box coordinates if the unit cell is not 
 \begin_inset Quotes eld
 \end_inset
 
@@ -19183,7 +19507,9 @@ X-aligned
 \begin_inset Quotes erd
 \end_inset
 
-; in other words, if the unit cell 
+;
+ in other words,
+ if the unit cell 
 \begin_inset Quotes eld
 \end_inset
 
@@ -19200,36 +19526,40 @@ B
 \end_inset
 
  vector is not in the X-Y plane.
- If this is the case, the following warnings may appear:
+ If this is the case,
+ the following warnings may appear:
 \end_layout
 
 \begin_layout LyX-Code
-Warning: Unit cell is not X-aligned.
+Warning:
+ Unit cell is not X-aligned.
  Box cannot be properly stored as <format>.
 \end_layout
 
 \begin_layout LyX-Code
-Warning: Set <#>; unit cell is not X-aligned.
+Warning:
+ Set <#>;
+ unit cell is not X-aligned.
  Box cannot be properly stored as <format>.
 \end_layout
 
 \begin_layout Standard
-This means that the frame will be written with the X-aligned unit cell instead
- of the actual unit cell.
+This means that the frame will be written with the X-aligned unit cell instead of the actual unit cell.
  Imaging will not be possible with a trajectory written this way.
- Currently the only trajectory formats that support writing non-X-aligned
- cells are the Gromacs TRR and XTC formats.
+ Currently the only trajectory formats that support writing non-X-aligned cells are the Gromacs TRR and XTC formats.
 \end_layout
 
 \begin_layout Standard
-If unit cell information is no longer needed, it can be removed (via e.g.
+If unit cell information is no longer needed,
+ it can be removed (via e.g.
  the 
 \series bold
 \emph on
 box
 \series default
 \emph default
- action, the 
+ action,
+ the 
 \series bold
 \emph on
 strip
@@ -19239,7 +19569,8 @@ strip
 \series bold
 'nobox'
 \series default
- keyword, etc.) to prevent these warnings from triggering.
+ keyword,
+ etc.) to prevent these warnings from triggering.
 \end_layout
 
 \begin_layout Subsubsection
@@ -19282,22 +19613,23 @@ Options for pdb format
 
 \begin_deeper
 \begin_layout Description
-dumpq PQR format; write charges (in units of e-) and GB radii to occupancy
- and B-factor columns respectively.
+dumpq PQR format;
+ write charges (in units of e-) and GB radii to occupancy and B-factor columns respectively.
 \end_layout
 
 \begin_layout Description
-parse PQR format; write charges and PARSE radii to occupancy/B-factor columns.
+parse PQR format;
+ write charges and PARSE radii to occupancy/B-factor columns.
 \end_layout
 
 \begin_layout Description
-vdw PQR format; write charges and vdW radii to occupancy/B-factor columns.
+vdw PQR format;
+ write charges and vdW radii to occupancy/B-factor columns.
 \end_layout
 
 \begin_layout Description
 pdbres Use PDB V3 residue names.
- Will write a default chain ID ('Z') for each residue if the corresponding
- topology does not have chain ID information.
+ Will write a default chain ID ('Z') for each residue if the corresponding topology does not have chain ID information.
 \end_layout
 
 \begin_layout Description
@@ -19310,7 +19642,8 @@ pdbv3 Use PDB V3 residue/atom names.
 \end_layout
 
 \begin_layout Description
-topresnum Use topology residue numbers; otherwise use original residue numbers.
+topresnum Use topology residue numbers;
+ otherwise use original residue numbers.
 \end_layout
 
 \begin_layout Description
@@ -19330,13 +19663,11 @@ noter Do not write TER cards.
 \end_layout
 
 \begin_layout Description
-model (Default) Frames will be written to a single PDB file separated by
- MODEL/ENDMDL keywords.
+model (Default) Frames will be written to a single PDB file separated by MODEL/ENDMDL keywords.
 \end_layout
 
 \begin_layout Description
-multi Each frame will be written to a separate file with the frame # appended
- to <filename>.
+multi Each frame will be written to a separate file with the frame # appended to <filename>.
 \end_layout
 
 \begin_layout Description
@@ -19352,7 +19683,8 @@ sg
 \begin_inset space ~
 \end_inset
 
-<group> Space group for CRYST1 record; only used if box coordinates written.
+<group> Space group for CRYST1 record;
+ only used if box coordinates written.
 \end_layout
 
 \begin_layout Description
@@ -19368,13 +19700,14 @@ conectmode
 \begin_inset space ~
 \end_inset
 
-<m> Write CONECT records for <m>='all' (all bonds), 'het' (HETATM only),
+<m> Write CONECT records for <m>='all' (all bonds),
+ 'het' (HETATM only),
  'none' (no CONECT).
 \end_layout
 
 \begin_layout Description
-keepext Keep filename extension; write '<name>.<num>.<ext>' instead (implies
- 'multi').
+keepext Keep filename extension;
+ write '<name>.<num>.<ext>' instead (implies 'multi').
 \end_layout
 
 \begin_layout Description
@@ -19414,13 +19747,11 @@ occdata
 \end_layout
 
 \begin_layout Description
-bfacbyres If specified assume X values in B-factor data set are residue
- numbers.
+bfacbyres If specified assume X values in B-factor data set are residue numbers.
 \end_layout
 
 \begin_layout Description
-occbyres If specified assume X values in occupancy data set are residue
- numbers.
+occbyres If specified assume X values in occupancy data set are residue numbers.
 \end_layout
 
 \begin_layout Description
@@ -19459,13 +19790,15 @@ adpdata
 atomicfluct
 \series default
 \emph default
- command, 
+ command,
+ 
 \begin_inset CommandInset ref
 LatexCommand vpageref
 reference "subsec:cpptraj_atomicfluct"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
@@ -19489,20 +19822,21 @@ Options for Amber ASCII format:
 
 \begin_deeper
 \begin_layout Description
-remdtraj Write REMD header to trajectory that includes temperature: 'REMD
- <Replica> <Step> <Total_Steps> <Temperature>'.
+remdtraj Write REMD header to trajectory that includes temperature:
+ 'REMD <Replica> <Step> <Total_Steps> <Temperature>'.
  Since 
 \shape italic
 cpptraj
 \shape default
- has no concept of replica number, 0 is printed for <Replica>.
+ has no concept of replica number,
+ 0 is printed for <Replica>.
  <Step> and <Total_Steps> are set to the current frame #.
 \end_layout
 
 \begin_layout Description
 highprecision (EXPERT USE ONLY) Write with 8.6 precision instead of 8.3.
- Note that since the width does not change, the precision of large coords
- may be lower than 6.
+ Note that since the width does not change,
+ the precision of large coords may be lower than 6.
 \end_layout
 
 \begin_layout Description
@@ -19573,8 +19907,7 @@ Options for Amber Restart/NetCDF Restart format:
 \end_layout
 
 \begin_layout LyX-Code
-  [remdtraj] [novelocity] [notime] [time0 <initial time>] [dt <timestep>]
- [keepext]
+  [remdtraj] [novelocity] [notime] [time0 <initial time>] [dt <timestep>] [keepext]
 \begin_inset Separator latexpar
 \end_inset
 
@@ -19584,8 +19917,7 @@ Options for Amber Restart/NetCDF Restart format:
 \begin_deeper
 \begin_layout Description
 remdtraj Write replica temperature to restart.
- Note that this will automatically include time in the restart file (see
- the 
+ Note that this will automatically include time in the restart file (see the 
 \series bold
 time0
 \family typewriter
@@ -19617,7 +19949,8 @@ dt
 \end_layout
 
 \begin_layout Description
-keepext Keep filename extension; write '<name>.<num>.<ext>' instead.
+keepext Keep filename extension;
+ write '<name>.<num>.<ext>' instead.
 \end_layout
 
 \end_deeper
@@ -19633,7 +19966,8 @@ Options for CHARMM COORdinates:
 
 \begin_deeper
 \begin_layout Description
-keepext Keep filename extension; write '<name>.<num>.<ext>'
+keepext Keep filename extension;
+ write '<name>.<num>.<ext>'
 \end_layout
 
 \begin_layout Description
@@ -19698,8 +20032,7 @@ shape Force writing box info as CHARMM shape matrix (XX XY YY XZ YZ ZZ).
 \end_layout
 
 \begin_layout Description
-namdcell Force writing box info as NAMD unit cell (X cos(g) Y cos(b) cos(a)
- Z).
+namdcell Force writing box info as NAMD unit cell (X cos(g) Y cos(b) cos(a) Z).
  
 \end_layout
 
@@ -19709,10 +20042,9 @@ charmmcell Force writing box info as old CHARMM unit cell (X Y Z a b g).
 
 \end_deeper
 \begin_layout Standard
-Note that by default CPPTRAJ will try to write the symmetric shape matrix
- if box information is present.
- If this is not possible, CPPTRAJ will fall back to writing unit cell parameters
- (lengths and angles) as long as the cell is X-aligned.
+Note that by default CPPTRAJ will try to write the symmetric shape matrix if box information is present.
+ If this is not possible,
+ CPPTRAJ will fall back to writing unit cell parameters (lengths and angles) as long as the cell is X-aligned.
  For more information see 
 \begin_inset CommandInset ref
 LatexCommand vref
@@ -19720,6 +20052,7 @@ reference "subsec:cpptraj-Options-for-CHARMM"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
@@ -19744,7 +20077,8 @@ dt Time step tp multiply set numbers by (default 1.0).
 
 \end_deeper
 \begin_layout Standard
-Note: these formats can write rotated (i.e.
+Note:
+ these formats can write rotated (i.e.
  non-X-aligned) unit cells.
 \end_layout
 
@@ -19764,13 +20098,11 @@ Options for mol2 format:
 
 \begin_deeper
 \begin_layout Description
-single (Default) Frames will be written to a single Mol2 file separated
- by MOLECULE keywords.
+single (Default) Frames will be written to a single Mol2 file separated by MOLECULE keywords.
 \end_layout
 
 \begin_layout Description
-multi Each frame will be written to a separate file with the frame # appended
- to <filename>.
+multi Each frame will be written to a separate file with the frame # appended to <filename>.
 \end_layout
 
 \begin_layout Description
@@ -19787,8 +20119,8 @@ sybylbond File containing Amber to SYBYL bond type correspondance (optional).
 \end_layout
 
 \begin_layout Description
-keepext Keep filename extension; write '<name>.<num>.<ext>' instead (implies
- 'multi').
+keepext Keep filename extension;
+ write '<name>.<num>.<ext>' instead (implies 'multi').
 \end_layout
 
 \end_deeper
@@ -19820,8 +20152,7 @@ Options for XYZ format:
 \end_layout
 
 \begin_layout LyX-Code
-[ftype {namexyz|atomxyz|xyz}] [titletype {none|single|perframe}] [width
- <#>] [prec <#>]
+[ftype {namexyz|atomxyz|xyz}] [titletype {none|single|perframe}] [width <#>] [prec <#>]
 \end_layout
 
 \begin_deeper
@@ -19830,16 +20161,16 @@ ftype
 \begin_inset space ~
 \end_inset
 
-{atomxyz|xyz} Choose either 'NAME X Y Z' (default), 'ATOM X Y Z', or 'X
- Y Z' output format.
+{atomxyz|xyz} Choose either 'NAME X Y Z' (default),
+ 'ATOM X Y Z',
+ or 'X Y Z' output format.
  
 \series bold
 'namexyz'
 \series default
- format is the standard XYZ format, where each frame is preceded by the
- number of atoms and a comment.
- The comment written by CPPTRAJ will include the set number and box information
- (if present).
+ format is the standard XYZ format,
+ where each frame is preceded by the number of atoms and a comment.
+ The comment written by CPPTRAJ will include the set number and box information (if present).
 \end_layout
 
 \begin_layout Description
@@ -19847,8 +20178,9 @@ titletype
 \begin_inset space ~
 \end_inset
 
-{none|single|perframe} No title, one title (default), or title before every
- frame.
+{none|single|perframe} No title,
+ one title (default),
+ or title before every frame.
  Only applies if not 
 \series bold
 'namexyz'
@@ -19901,8 +20233,9 @@ trajin
 ensemble
 \series default
 \emph default
- commands one at a time and extract derived data, modify the coordinates/topolog
-y in some way, or both.
+ commands one at a time and extract derived data,
+ modify the coordinates/topology in some way,
+ or both.
  Most Actions in 
 \shape italic
 cpptraj
@@ -19926,15 +20259,15 @@ ptraj
 rmsd
 \series default
 \emph default
- Action, or the ability to write out stripped topologies for visualization
- in the 
+ Action,
+ or the ability to write out stripped topologies for visualization in the 
 \series bold
 \emph on
 strip
 \series default
 \emph default
- Action), while other Actions produce slightly different output (like the
- 
+ Action),
+ while other Actions produce slightly different output (like the 
 \series bold
 \emph on
 hbond
@@ -19950,9 +20283,8 @@ secstruct
 \end_layout
 
 \begin_layout Standard
-Unlike some other command types, when an Action command is issued it is
- by default added to the Action queue and is not executed until trajectory
- processing is started (e.g.
+Unlike some other command types,
+ when an Action command is issued it is by default added to the Action queue and is not executed until trajectory processing is started (e.g.
  by a 
 \series bold
 \emph on
@@ -19966,8 +20298,8 @@ go
 \series default
 \emph default
  command).
- However, Actions can be executed immediately on COORDS data sets via the
- 
+ However,
+ Actions can be executed immediately on COORDS data sets via the 
 \series bold
 \emph on
 crdaction
@@ -19977,6 +20309,7 @@ crdaction
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_crdaction"
+nolink "false"
 
 \end_inset
 
@@ -19984,10 +20317,10 @@ reference "subsec:cpptraj_crdaction"
 \end_layout
 
 \begin_layout Standard
-When a frame is modified by an Action, it is modified for every Action that
- follows them during trajectory processing.
- For example, given a solvated system with water residues named WAT and
- the following Action commands:
+When a frame is modified by an Action,
+ it is modified for every Action that follows them during trajectory processing.
+ For example,
+ given a solvated system with water residues named WAT and the following Action commands:
 \end_layout
 
 \begin_layout LyX-Code
@@ -20009,14 +20342,14 @@ the first
 rms
 \series default
 \emph default
- command will be valid, but the second 
+ command will be valid,
+ but the second 
 \series bold
 \emph on
 rms
 \series default
 \emph default
- command will not since all residues named WAT are removed from the state
- by the 
+ command will not since all residues named WAT are removed from the state by the 
 \series bold
 \emph on
 strip
@@ -20026,27 +20359,29 @@ strip
 \end_layout
 
 \begin_layout Standard
-Note that for commands which can use a reference mask as well as a target
- mask (e.g.
+Note that for commands which can use a reference mask as well as a target mask (e.g.
  
 \series bold
 \emph on
 rms
 \series default
 \emph default
-, 
+,
+ 
 \series bold
 \emph on
 drmsd
 \series default
 \emph default
-, 
+,
+ 
 \series bold
 \emph on
 symmrmsd
 \series default
 \emph default
-, etc.) there must be a 1 to 1 correspondence between the atoms in each mask,
+,
+ etc.) there must be a 1 to 1 correspondence between the atoms in each mask,
  i.e.
  the 
 \emph on
@@ -20057,8 +20392,7 @@ number of atoms and the ordering of selected atoms must be the same
 
 \begin_layout Standard
 The following Actions are available.
- If an Action may modify coordinate/topology information for subsequent
- Actions it is denoted with an X in the 
+ If an Action may modify coordinate/topology information for subsequent Actions it is denoted with an X in the 
 \family typewriter
 \series bold
 Mod
@@ -20235,7 +20569,8 @@ Calculate average correlation between motions of specified atoms.
 \begin_inset Text
 
 \begin_layout Plain Layout
-atomicfluct, rmsf
+atomicfluct,
+ rmsf
 \end_layout
 
 \end_inset
@@ -20360,7 +20695,8 @@ avgbox
 \begin_inset Text
 
 \begin_layout Plain Layout
-Calculate average unit cell (box), primarily for unwrapping NPT trajectories.
+Calculate average unit cell (box),
+ primarily for unwrapping NPT trajectories.
 \end_layout
 
 \end_inset
@@ -20468,7 +20804,8 @@ X
 \begin_inset Text
 
 \begin_layout Plain Layout
-check, checkoverlap,
+check,
+ checkoverlap,
 \end_layout
 
 \end_inset
@@ -20536,7 +20873,8 @@ checkchirality
 \begin_inset Text
 
 \begin_layout Plain Layout
-Report chirality around alpha carbons in amino acids (L, D).
+Report chirality around alpha carbons in amino acids (L,
+ D).
 \end_layout
 
 \end_inset
@@ -20556,7 +20894,8 @@ Report chirality around alpha carbons in amino acids (L, D).
 \begin_inset Text
 
 \begin_layout Plain Layout
-closest, closestwaters
+closest,
+ closestwaters
 \end_layout
 
 \end_inset
@@ -20565,8 +20904,7 @@ closest, closestwaters
 \begin_inset Text
 
 \begin_layout Plain Layout
-Retain only the specified number of solvent molecules closest to specified
- solute.
+Retain only the specified number of solvent molecules closest to specified solute.
 \end_layout
 
 \end_inset
@@ -20595,8 +20933,7 @@ clusterdihedral
 \begin_inset Text
 
 \begin_layout Plain Layout
-Assign frames into clusters based on binning of backbone dihedral angles
- in amino acids.
+Assign frames into clusters based on binning of backbone dihedral angles in amino acids.
 \end_layout
 
 \end_inset
@@ -20631,7 +20968,8 @@ Older version of
 nativecontacts
 \series default
 \emph default
-, retained for backwards compatibility.
+,
+ retained for backwards compatibility.
 \end_layout
 
 \end_inset
@@ -20839,7 +21177,8 @@ dipole
 
 \begin_layout Plain Layout
 Bin dipoles of solvent molecules in 3D grid.
- Not well tested, may be obsolete.
+ Not well tested,
+ may be obsolete.
 \end_layout
 
 \end_inset
@@ -20888,7 +21227,8 @@ Calculate the distance between two points.
 \begin_inset Text
 
 \begin_layout Plain Layout
-drms, drmsd
+drms,
+ drmsd
 \end_layout
 
 \end_inset
@@ -20917,7 +21257,8 @@ Calculate the RMSD of distance pairs within selected atoms.
 \begin_inset Text
 
 \begin_layout Plain Layout
-dssp, secstruct
+dssp,
+ secstruct
 \end_layout
 
 \end_inset
@@ -20955,8 +21296,10 @@ energy
 \begin_inset Text
 
 \begin_layout Plain Layout
-Calculate simple bond, angle, dihedral, and non-bonded energy terms (no
- PME).
+Calculate simple bond,
+ angle,
+ dihedral,
+ and non-bonded energy terms (no PME).
 \end_layout
 
 \end_inset
@@ -20985,8 +21328,8 @@ esander
 \begin_inset Text
 
 \begin_layout Plain Layout
-Calculate energies using via SANDER; requires compilation with the SANDER
- API.
+Calculate energies using via SANDER;
+ requires compilation with the SANDER API.
 \end_layout
 
 \end_inset
@@ -21312,8 +21655,7 @@ lie
 \begin_inset Text
 
 \begin_layout Plain Layout
-Calculate linear interaction energy between user-specified ligand and surroundin
-gs.
+Calculate linear interaction energy between user-specified ligand and surroundings.
 \end_layout
 
 \end_inset
@@ -21489,8 +21831,7 @@ mindist/maxdist
 \begin_inset Text
 
 \begin_layout Plain Layout
-Calculate the minimum or maximum distance between pairs of atoms/residues/molecu
-les.
+Calculate the minimum or maximum distance between pairs of atoms/residues/molecules.
 \end_layout
 
 \end_inset
@@ -21665,8 +22006,7 @@ nativecontacts
 \begin_inset Text
 
 \begin_layout Plain Layout
-Calculate native contacts within a region or between two regions using a
- given reference.
+Calculate native contacts within a region or between two regions using a given reference.
  
 \end_layout
 
@@ -21890,7 +22230,8 @@ Calculate ring pucker using five or six points.
 \begin_inset Text
 
 \begin_layout Plain Layout
-radgyr, rog
+radgyr,
+ rog
 \end_layout
 
 \end_inset
@@ -21919,7 +22260,8 @@ Calculate radius of gyration (and optionally tensor) for specified atoms.
 \begin_inset Text
 
 \begin_layout Plain Layout
-radial, rdf
+radial,
+ rdf
 \end_layout
 
 \end_inset
@@ -22015,8 +22357,7 @@ replicatecell
 \begin_inset Text
 
 \begin_layout Plain Layout
-Replicate unit cell in specified (or all) directions for specfied atoms
- and write to trajectory.
+Replicate unit cell in specified (or all) directions for specfied atoms and write to trajectory.
 \end_layout
 
 \end_inset
@@ -22036,7 +22377,8 @@ Replicate unit cell in specified (or all) directions for specfied atoms
 \begin_inset Text
 
 \begin_layout Plain Layout
-rms, rmsd
+rms,
+ rmsd
 \end_layout
 
 \end_inset
@@ -22103,8 +22445,9 @@ rotate
 \begin_inset Text
 
 \begin_layout Plain Layout
-Rotate the system around X/Y/Z axes, a specified axis, or via given rotation
- matrices.
+Rotate the system around X/Y/Z axes,
+ a specified axis,
+ or via given rotation matrices.
 \end_layout
 
 \end_inset
@@ -22124,7 +22467,8 @@ X
 \begin_inset Text
 
 \begin_layout Plain Layout
-runavg, 
+runavg,
+ 
 \end_layout
 
 \end_inset
@@ -22273,8 +22617,7 @@ spam
 \begin_inset Text
 
 \begin_layout Plain Layout
-SPAM method for estimating relative free energies of waters in hydration
- shell around proteins.
+SPAM method for estimating relative free energies of waters in hydration shell around proteins.
 \end_layout
 
 \end_inset
@@ -22303,8 +22646,7 @@ stfcdiffusion
 \begin_inset Text
 
 \begin_layout Plain Layout
-Alternative translational diffusion calculation which can calculate diffusion
- in specified regions.
+Alternative translational diffusion calculation which can calculate diffusion in specified regions.
 \end_layout
 
 \end_inset
@@ -22499,7 +22841,8 @@ Calculate diffusion using the toroidal-view-preserving scheme.
 \begin_inset Text
 
 \begin_layout Plain Layout
-trans, translate
+trans,
+ translate
 \end_layout
 
 \end_inset
@@ -22578,7 +22921,8 @@ Reverse of
 image
 \series default
 \emph default
-; unwrap selected atoms so they have continuous trajectories.
+;
+ unwrap selected atoms so they have continuous trajectories.
 \end_layout
 
 \end_inset
@@ -22665,7 +23009,8 @@ volmap
 \begin_inset Text
 
 \begin_layout Plain Layout
-Create volumetric map for specified coordinates; similar to 
+Create volumetric map for specified coordinates;
+ similar to 
 \series bold
 \emph on
 grid
@@ -22765,8 +23110,7 @@ watershell
 \begin_inset Text
 
 \begin_layout Plain Layout
-Calculate the number of waters in the first and second solvation shells
- based on distance critera.
+Calculate the number of waters in the first and second solvation shells based on distance critera.
 \end_layout
 
 \end_inset
@@ -22795,8 +23139,7 @@ xtalsymm
 \begin_inset Text
 
 \begin_layout Plain Layout
-Re-image coordinates based on crystal space group symmetry operations and
- asymmetric unit volume.
+Re-image coordinates based on crystal space group symmetry operations and asymmetric unit volume.
 \end_layout
 
 \end_inset
@@ -22896,8 +23239,7 @@ refindex
 
 <#>
 \series default
- Use previously read in reference structure specified by <#> (based on order
- read in).
+ Use previously read in reference structure specified by <#> (based on order read in).
 \end_layout
 
 \begin_layout Description
@@ -22913,13 +23255,12 @@ reftraj
 \begin_inset space ~
 \end_inset
 
-<name> Use frames from COORDS set <name> or read in from trajectory file
- <name> as references.
- Each frame from <name> is used in turn, so that frame 1 is compared to
- frame 1 from <name>, frame 2 is compared to frame 2 from <name> and so
- on.
- If <trajname> runs out of frames before processing is complete, the last
- frame of <trajname> continues to be used as the reference.
+<name> Use frames from COORDS set <name> or read in from trajectory file <name> as references.
+ Each frame from <name> is used in turn,
+ so that frame 1 is compared to frame 1 from <name>,
+ frame 2 is compared to frame 2 from <name> and so on.
+ If <trajname> runs out of frames before processing is complete,
+ the last frame of <trajname> continues to be used as the reference.
 \begin_inset Separator latexpar
 \end_inset
 
@@ -22948,15 +23289,17 @@ parmindex
 \series bold
 reftraj
 \series default
- specifies a trajectory file, associate it with specified topology; if not
- specified the first topology is used.
+ specifies a trajectory file,
+ associate it with specified topology;
+ if not specified the first topology is used.
 \end_layout
 
 \end_deeper
 \end_deeper
 \begin_layout Standard
 Align structure using specified <mask> onto reference.
- If 'move' is specified, only move atoms in the move mask.
+ If 'move' is specified,
+ only move atoms in the move mask.
 \end_layout
 
 \begin_layout Subsection
@@ -22966,6 +23309,8 @@ angle
 \begin_layout LyX-Code
 angle
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -23008,9 +23353,11 @@ name>] Output data set name.
 
 \end_deeper
 \begin_layout Standard
-Calculate angle (in degrees) between atoms in <mask1>, <mask2>, and <mask3>.
- For example, to calculate the angle between the first three atoms in the
- system:
+Calculate angle (in degrees) between atoms in <mask1>,
+ <mask2>,
+ and <mask3>.
+ For example,
+ to calculate the angle between the first three atoms in the system:
 \end_layout
 
 \begin_layout LyX-Code
@@ -23057,8 +23404,8 @@ areapermol [<name>] {[<mask1>] [nlayers <#>] | nmols <#>} [out <filename>]
 \begin_inset space ~
 \end_inset
 
-<#>] If <mask1> is not specified, the number of molecules to use when calculatin
-g area per molecule.
+<#>] If <mask1> is not specified,
+ the number of molecules to use when calculating area per molecule.
 \end_layout
 
 \begin_layout Description
@@ -23077,11 +23424,10 @@ g area per molecule.
 \end_deeper
 \begin_layout Standard
 Calculate area per molecule as Area / # molecules.
- The area is determined from the specified cross-section of the box (X-Y
- by default).
- Currently the calculation is only guaranteed to work properly with orthorhombic
- unit cells.
- For example, to get the area per molecule of residues named 
+ The area is determined from the specified cross-section of the box (X-Y by default).
+ Currently the calculation is only guaranteed to work properly with orthorhombic unit cells.
+ For example,
+ to get the area per molecule of residues named 
 \begin_inset Quotes eld
 \end_inset
 
@@ -23142,24 +23488,23 @@ min
 \begin_inset space ~
 \end_inset
 
-spacing> Only calculate correlations for motion vectors spaced <min spacing>
- apart.
+spacing> Only calculate correlations for motion vectors spaced <min spacing> apart.
 \end_layout
 
 \begin_layout Description
-byatom Default; calculate atomic motion vectors.
+byatom Default;
+ calculate atomic motion vectors.
 \end_layout
 
 \begin_layout Description
-byres Calculate motion vectors for entire residues (selected atoms in residues
- only).
+byres Calculate motion vectors for entire residues (selected atoms in residues only).
 \end_layout
 
 \end_deeper
 \begin_layout Standard
 Calculate average correlations between the motion of atoms in <mask>.
- For each frame, a motion vector is calculated for each selected atom from
- its previous position to its current position.
+ For each frame,
+ a motion vector is calculated for each selected atom from its previous position to its current position.
  For each pair of motion vectors 
 \shape italic
 Va
@@ -23168,8 +23513,8 @@ Va
 \shape italic
 Vb
 \shape default
-, the average correlation between those vectors is calculated as the average
- of the dot product of those vectors over all 
+,
+ the average correlation between those vectors is calculated as the average of the dot product of those vectors over all 
 \shape italic
 N
 \shape default
@@ -23190,10 +23535,10 @@ N
 \end_layout
 
 \begin_layout Standard
-The value of AvgCorr can range from 1.0 (correlated) to 0.0 (no correlation)
- to -1.0 (anti-correlated).
- For example, to calculate the correlation of motion vectors between residues
- 1 to 13, writing to a Gnuplot-readable formatted file:
+The value of AvgCorr can range from 1.0 (correlated) to 0.0 (no correlation) to -1.0 (anti-correlated).
+ For example,
+ to calculate the correlation of motion vectors between residues 1 to 13,
+ writing to a Gnuplot-readable formatted file:
 \end_layout
 
 \begin_layout LyX-Code
@@ -23214,6 +23559,8 @@ name "subsec:cpptraj_atomicfluct"
 \begin_layout LyX-Code
 atomicfluct
 \begin_inset Index idx
+range none
+pageformat default
 status open
 
 \begin_layout Plain Layout
@@ -23256,7 +23603,8 @@ out
 
 \begin_layout Description
 byres [pdbres] Output the average (mass-weighted) fluctuation by residue.
- If 'pdbres' is specified, the original residue numbering will be used.
+ If 'pdbres' is specified,
+ the original residue numbering will be used.
 \end_layout
 
 \begin_layout Description
@@ -23272,13 +23620,12 @@ byatom
 \end_layout
 
 \begin_layout Description
-[bfactor] Calculate atomic positional fluctuations squared and weight by
- 
+[bfactor] Calculate atomic positional fluctuations squared and weight by 
 \begin_inset Formula $\frac{8}{3}\pi^{2}$
 \end_inset
 
-; this is similar but not necessarily equivalent to the calculation of crystallo
-graphic B-factors.
+;
+ this is similar but not necessarily equivalent to the calculation of crystallographic B-factors.
 \end_layout
 
 \begin_layout Description
@@ -23290,8 +23637,7 @@ graphic B-factors.
 \begin_inset space ~
 \end_inset
 
-<file>]] Calculate anisotropic displacement parameters and optionally output
- them to <file>.
+<file>]] Calculate anisotropic displacement parameters and optionally output them to <file>.
 \end_layout
 
 \begin_layout Description
@@ -23320,8 +23666,8 @@ DataSets created
 
 \end_deeper
 \begin_layout Standard
-Compute the atomic positional fluctuations (also referred to as root-mean-square
- fluctuations, RMSF) for atoms specified in the 
+Compute the atomic positional fluctuations (also referred to as root-mean-square fluctuations,
+ RMSF) for atoms specified in the 
 \series bold
 <mask>
 \series default
@@ -23351,9 +23697,8 @@ x
 
 \begin_layout Standard
 Note that RMS fitting is not done implicitly.
- If you want fluctuations without rotations or translations (for example
- to the average structure), perform an RMS fit to the average structure
- (best) or the first structure (see 
+ If you want fluctuations without rotations or translations (for example to the average structure),
+ perform an RMS fit to the average structure (best) or the first structure (see 
 \series bold
 \shape italic
 rmsd
@@ -23388,9 +23733,8 @@ byres
 \series bold
 bymask
 \series default
- are specified, the mass-weighted average of atomic fluctuations of each
- atom for either each residue or the entire mask will be calculated respectively
-:
+ are specified,
+ the mass-weighted average of atomic fluctuations of each atom for either each residue or the entire mask will be calculated respectively:
 \begin_inset Separator latexpar
 \end_inset
 
@@ -23410,8 +23754,8 @@ If
 \series bold
 calcadp
 \series default
- is specified, anisotropic displacement factors for atoms will be calculated
- and written to the file specified by 
+ is specified,
+ anisotropic displacement factors for atoms will be calculated and written to the file specified by 
 \series bold
 adpout
 \series default
@@ -23433,7 +23777,8 @@ With
 \emph on
 cpptraj
 \emph default
- it is possible to perform coordinate averaging, the fit to average coordinates,
+ it is possible to perform coordinate averaging,
+ the fit to average coordinates,
  and the atomic fluctuation calculation in a single execution like so:
 \end_layout
 
@@ -23466,8 +23811,10 @@ atomicfluct out fluct.agr
 \end_layout
 
 \begin_layout Standard
-To write the mass-weighted B-factors for the protein backbone atoms C, CA,
- and N, averaged by residue use the command:
+To write the mass-weighted B-factors for the protein backbone atoms C,
+ CA,
+ and N,
+ averaged by residue use the command:
 \end_layout
 
 \begin_layout LyX-Code
@@ -23475,8 +23822,8 @@ atomicfluct out back.agr @C,CA,N byres bfactor
 \end_layout
 
 \begin_layout Standard
-To write the RMSF or atomic positional fluctuations of the same atoms, use
- the command:
+To write the RMSF or atomic positional fluctuations of the same atoms,
+ use the command:
 \end_layout
 
 \begin_layout LyX-Code
@@ -23484,8 +23831,7 @@ atomicfluct out backbone-atoms.agr @C,CA,N
 \end_layout
 
 \begin_layout Standard
-To write a PDB of averaged coordinates (after fitting to the first frame)
- with both B-factors and anisotropic temperature factors:
+To write a PDB of averaged coordinates (after fitting to the first frame) with both B-factors and anisotropic temperature factors:
 \end_layout
 
 \begin_layout LyX-Code
@@ -23523,6 +23869,8 @@ atommap
 \begin_layout LyX-Code
 atommap
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -23577,6 +23925,7 @@ Target atoms that cannot be mapped to a reference atom are denoted
 \end_inset
 
 —
+
 \begin_inset Quotes erd
 \end_inset
 
@@ -23588,8 +23937,7 @@ maponly Write atom map but do not reorder atoms.
 \end_layout
 
 \begin_layout Description
-rmsfit Any input frames using the same topology as <target> will be RMS
- fit to <reference> using whatever atoms could be mapped.
+rmsfit Any input frames using the same topology as <target> will be RMS fit to <reference> using whatever atoms could be mapped.
 \begin_inset Separator latexpar
 \end_inset
 
@@ -23602,51 +23950,47 @@ rmsout
 \begin_inset space ~
 \end_inset
 
-<rmsout> If rmsfit specified, write resulting RMSDs to <rmsout>.
+<rmsout> If rmsfit specified,
+ write resulting RMSDs to <rmsout>.
 \end_layout
 
 \end_deeper
 \begin_layout Description
-changenames If specified, change names of mapped atoms in <target> to match
- those in <reference>.
+changenames If specified,
+ change names of mapped atoms in <target> to match those in <reference>.
 \end_layout
 
 \end_deeper
 \begin_layout Standard
-Attempt to map the atoms of <target> to those of <reference> based on structural
- similarity.
+Attempt to map the atoms of <target> to those of <reference> based on structural similarity.
  This is useful e.g.
- when there are two files containing the same structure but with different
- atom names or atom ordering.
- Both <target> and <reference> need to have been read in with a previous
- 
+ when there are two files containing the same structure but with different atom names or atom ordering.
+ Both <target> and <reference> need to have been read in with a previous 
 \series bold
 \shape italic
 reference
 \series default
 \shape default
  command.
- The state will then be modified so that any trajectory read in with the
- same parameter file as <target> will have its atoms mapped (i.e.
+ The state will then be modified so that any trajectory read in with the same parameter file as <target> will have its atoms mapped (i.e.
  reordered) to match those of <reference>.
- If the number of atoms that can be mapped in <target> are less than those
- in <reference>, the reference structure specified by <reference> will be
- modified to include only mapped atoms; this is useful if for example the
- reference structure is protonated with respect to the target.
+ If the number of atoms that can be mapped in <target> are less than those in <reference>,
+ the reference structure specified by <reference> will be modified to include only mapped atoms;
+ this is useful if for example the reference structure is protonated with respect to the target.
  The 
 \series bold
 rmsfit
 \series default
- keyword is useful in cases where the atom mapping will not be complete
- (e.g.
+ keyword is useful in cases where the atom mapping will not be complete (e.g.
  two ligands with the same scaffold but different substituents).
 \end_layout
 
 \begin_layout Standard
-For example, say you have the same ligand structure in two files, Ref.mol2
- and Lig.mol2, but the atom ordering in each file is different.
- To map the atoms in Lig.mol2 onto those of Ref.mol2 so that Lig.mol2 has the
- same ordering as Ref.mol2:
+For example,
+ say you have the same ligand structure in two files,
+ Ref.mol2 and Lig.mol2,
+ but the atom ordering in each file is different.
+ To map the atoms in Lig.mol2 onto those of Ref.mol2 so that Lig.mol2 has the same ordering as Ref.mol2:
 \end_layout
 
 \begin_layout LyX-Code
@@ -23707,7 +24051,8 @@ anchor
 \begin_inset space ~
 \end_inset
 
-<mask>] Atoms to image around; this is the region that will be centered.
+<mask>] Atoms to image around;
+ this is the region that will be centered.
  Default is the entire first molecule.
 \end_layout
 
@@ -23716,8 +24061,8 @@ anchor
 \begin_inset space ~
 \end_inset
 
-<mask>] Molecules that should remain 'fixed' to the anchor region; default
- is all non-ion/non-solvent molecules.
+<mask>] Molecules that should remain 'fixed' to the anchor region;
+ default is all non-ion/non-solvent molecules.
 \end_layout
 
 \begin_layout Description
@@ -23725,23 +24070,24 @@ anchor
 \begin_inset space ~
 \end_inset
 
-<mask>] Molecules that can be freely imaged; default is all ion/solvent
- molecules.
+<mask>] Molecules that can be freely imaged;
+ default is all ion/solvent molecules.
 \end_layout
 
 \begin_layout Description
-[origin] Center anchor region at the origin; if not specified, center at
- box center.
+[origin] Center anchor region at the origin;
+ if not specified,
+ center at box center.
 \end_layout
 
 \begin_layout Description
-[firstatom] Image based on molecule first atom; default is to image by molecule
- center of mass.
+[firstatom] Image based on molecule first atom;
+ default is to image by molecule center of mass.
 \end_layout
 
 \begin_layout Description
-[familiar] Image to familiar truncated-octahedral shape; this is on by default
- if the original cell is truncated octahedron.
+[familiar] Image to familiar truncated-octahedral shape;
+ this is on by default if the original cell is truncated octahedron.
 \end_layout
 
 \begin_layout Description
@@ -23750,8 +24096,7 @@ anchor
 
 \end_deeper
 \begin_layout Standard
-Automatically center and image (by molecule) a trajectory with periodic
- boundaries.
+Automatically center and image (by molecule) a trajectory with periodic boundaries.
  For most cases just specifying 
 \series bold
 \shape italic
@@ -23763,7 +24108,8 @@ Automatically center and image (by molecule) a trajectory with periodic
 \series bold
 'anchor'
 \series default
- region (default the entire first molecule) will be centered; all 
+ region (default the entire first molecule) will be centered;
+ all 
 \series bold
 'fixed'
 \series default
@@ -23784,13 +24130,13 @@ Automatically center and image (by molecule) a trajectory with periodic
 \end_layout
 
 \begin_layout Standard
-The autoimage command works for the majority of systems; however, for very
- densely packed systems the default anchor (entire first molecule) may not
- be appropriate.
- In these cases, it is recommended to choose as the anchor a small region
- which should lie near the center of your system.
- For example, in a protein dimer system one could choose a single residue
- that is near the center of the interface between the two monomers.
+The autoimage command works for the majority of systems;
+ however,
+ for very densely packed systems the default anchor (entire first molecule) may not be appropriate.
+ In these cases,
+ it is recommended to choose as the anchor a small region which should lie near the center of your system.
+ For example,
+ in a protein dimer system one could choose a single residue that is near the center of the interface between the two monomers.
 \end_layout
 
 \begin_layout Subsection
@@ -23807,6 +24153,8 @@ name "subsec:cpptraj-average"
 \begin_layout LyX-Code
 average
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -23832,8 +24180,8 @@ average
 
 \begin_deeper
 \begin_layout Description
-<filename> If specified, write averaged coordinates to <filename> (not compatibl
-e with crdset).
+<filename> If specified,
+ write averaged coordinates to <filename> (not compatible with crdset).
 \end_layout
 
 \begin_layout Description
@@ -23845,8 +24193,8 @@ crdset
 \begin_inset space ~
 \end_inset
 
-name> If specified, save averaged coordinates to COORDS set <set name> (not
- compatible with <filename>).
+name> If specified,
+ save averaged coordinates to COORDS set <set name> (not compatible with <filename>).
 \end_layout
 
 \begin_layout Description
@@ -23892,8 +24240,8 @@ cpptraj
 \series bold
 <mask>
 \series default
- are less than the total number of atoms, the topology will be stripped
- to match 
+ are less than the total number of atoms,
+ the topology will be stripped to match 
 \series bold
 <mask>
 \series default
@@ -23902,13 +24250,11 @@ cpptraj
 \end_layout
 
 \begin_layout Standard
-Note that since coordinates are being averaged over many frames, resulting
- structures may appear distorted.
- For example, if one averages the coordinates of a freely rotating methyl
- group the average position of the hydrogen atoms will be close to the center
- of rotation.
- Also note that typically one will want to remove global rotational and
- translation movement prior to this command by using e.g.
+Note that since coordinates are being averaged over many frames,
+ resulting structures may appear distorted.
+ For example,
+ if one averages the coordinates of a freely rotating methyl group the average position of the hydrogen atoms will be close to the center of rotation.
+ Also note that typically one will want to remove global rotational and translation movement prior to this command by using e.g.
  the 
 \series bold
 \emph on
@@ -23919,6 +24265,7 @@ rms
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-rmsd"
+nolink "false"
 
 \end_inset
 
@@ -23936,13 +24283,13 @@ trajout
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-trajout"
+nolink "false"
 
 \end_inset
 
-) can be passed to this command in order to control the format of the output
- coordinates.
- For example, to write out a PDB file containing the averaged coordinates
- over all frames:
+) can be passed to this command in order to control the format of the output coordinates.
+ For example,
+ to write out a PDB file containing the averaged coordinates over all frames:
 \end_layout
 
 \begin_layout LyX-Code
@@ -23950,8 +24297,7 @@ average test.pdb pdb
 \end_layout
 
 \begin_layout Standard
-To write out a mol2 file containing only the averaged coordinates of residues
- 1 to 10 for frames 1 to 100:
+To write out a mol2 file containing only the averaged coordinates of residues 1 to 10 for frames 1 to 100:
 \end_layout
 
 \begin_layout LyX-Code
@@ -23959,8 +24305,7 @@ average test.mol2 mol2 start 1 stop 100 :1-10
 \end_layout
 
 \begin_layout Standard
-To create an average structure of atoms named CA and then use it as a reference
- for an rms command in a subsequent run:
+To create an average structure of atoms named CA and then use it as a reference for an rms command in a subsequent run:
 \end_layout
 
 \begin_layout LyX-Code
@@ -24025,22 +24370,22 @@ DataSets created:
 
 \end_deeper
 \begin_layout Standard
-Calculate the average unit cell vectors for incoming frames and store them
- in a 3x3 matrix data set, The average unit cell is particularly useful
- when unwrapping trajectories from NPT simulations where the box size fluctuates
- (see the 
+Calculate the average unit cell vectors for incoming frames and store them in a 3x3 matrix data set,
+ The average unit cell is particularly useful when unwrapping trajectories from NPT simulations where the box size fluctuates (see the 
 \series bold
 \emph on
 unwrap
 \series default
 \emph default
- command, 
+ command,
+ 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_unwrap"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
@@ -24048,23 +24393,22 @@ noprefix "false"
 \end_layout
 
 \begin_layout Standard
-If writing to a .dat file, the output will look something like:
+If writing to a .dat file,
+ the output will look something like:
 \end_layout
 
 \begin_layout LyX-Code
-#Frame                                                                 
-                                            MyBox[avg]
+#Frame                                                                                                             MyBox[avg]
 \end_layout
 
 \begin_layout LyX-Code
-       1 42.433046075  0.000000000  0.000000000 -14.144347550 40.006259905  0.00000000
-0 -14.144347550 -20.003127532 34.646438786
+       1 42.433046075  0.000000000  0.000000000 -14.144347550 40.006259905  0.000000000 -14.144347550 -20.003127532 34.646438786
 \end_layout
 
 \begin_layout Standard
 Where the first 3 floating point numbers are the average X unit cell vector,
- the next 3 floating point numbers are the average Y unit cell vector, and
- the last 3 floating point numbers are the average Z unit cell vector.
+ the next 3 floating point numbers are the average Y unit cell vector,
+ and the last 3 floating point numbers are the average Z unit cell vector.
 \end_layout
 
 \begin_layout Subsection
@@ -24135,7 +24479,8 @@ bounds [<mask>] [out <filename>]
 \end_inset
 
 <dz>]] Triggers creation of a grid data set from bounds.
- Spacings of generated grid in the X, Y and Z directions.
+ Spacings of generated grid in the X,
+ Y and Z directions.
  If only dx is specified <dx> will be used for <dy> and <dz> as well.
 \end_layout
 
@@ -24209,8 +24554,8 @@ Calculate the boundaries (i.e.
 grid
 \series default
 \shape default
- command, and can be used to generate a grid data set that can be used by
- 
+ command,
+ and can be used to generate a grid data set that can be used by 
 \series bold
 \shape italic
 grid
@@ -24220,6 +24565,7 @@ grid
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_grid"
+nolink "false"
 
 \end_inset
 
@@ -24231,8 +24577,7 @@ box
 \end_layout
 
 \begin_layout LyX-Code
-box {[x <xval>] [y <yval>] [z <zval>] {[alpha <a>] [beta <b>] [gamma <g>]
- |
+box {[x <xval>] [y <yval>] [z <zval>] {[alpha <a>] [beta <b>] [gamma <g>] |
 \end_layout
 
 \begin_layout LyX-Code
@@ -24325,8 +24670,7 @@ Change box length(s) to specified value(s).
 \end_layout
 
 \begin_layout Description
-auto Set an orthogonal bounding box enclosing all atoms by the specified
- radii and an optional offset.
+auto Set an orthogonal bounding box enclosing all atoms by the specified radii and an optional offset.
 \end_layout
 
 \begin_deeper
@@ -24343,8 +24687,11 @@ radii
 \begin_inset space ~
 \end_inset
 
-{vdw|gb|parse|none} Radii to use for each atom: van der Waals, generalized
- Born, PARSE, or no radii.
+{vdw|gb|parse|none} Radii to use for each atom:
+ van der Waals,
+ generalized Born,
+ PARSE,
+ or no radii.
 \end_layout
 
 \end_deeper
@@ -24354,15 +24701,18 @@ getbox Save existing box information to a 3x3 matrix data set.
 
 \begin_deeper
 \begin_layout Description
-{ucell|frac|shape} Specify the kind of box information to save: 
+{ucell|frac|shape} Specify the kind of box information to save:
+ 
 \series bold
 ucell
 \series default
- saves the unit cell vectors, 
+ saves the unit cell vectors,
+ 
 \series bold
 frac
 \series default
- saves the fractional unit cell vectors, and 
+ saves the fractional unit cell vectors,
+ and 
 \series bold
 shape
 \series default
@@ -24389,19 +24739,17 @@ out
 \end_deeper
 \begin_layout Standard
 Modify box information during trajectory processing.
- Note that this will permanently modify the box information for topology
- files during trajectory processing as well.
+ Note that this will permanently modify the box information for topology files during trajectory processing as well.
  It is possible to modify any number of the box parameters (e.g.
- only the Z length can be modified if desired while leaving all other parameters
- intact).
- If no box is present, an orthogonal bounding box enclosing all atoms can
- be created with the 
+ only the Z length can be modified if desired while leaving all other parameters intact).
+ If no box is present,
+ an orthogonal bounding box enclosing all atoms can be created with the 
 \series bold
 auto
 \series default
  keyword.
- If 'getbox' is specified, the existing box information will be saved to
- a data set.
+ If 'getbox' is specified,
+ the existing box information will be saved to a data set.
 \end_layout
 
 \begin_layout Subsection
@@ -24411,6 +24759,8 @@ center
 \begin_layout LyX-Code
 center
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -24432,12 +24782,17 @@ center
 
 \begin_deeper
 \begin_layout Description
-[<mask>] Center based on atoms in mask; default is all atoms.
+[<mask>] Center based on atoms in mask;
+ default is all atoms.
 \end_layout
 
 \begin_layout Description
-[origin] Center to origin (0, 0, 0); default is center to box center (X/2,
- Y/2, Z/2).
+[origin] Center to origin (0,
+ 0,
+ 0);
+ default is center to box center (X/2,
+ Y/2,
+ Z/2).
 \end_layout
 
 \begin_layout Description
@@ -24473,8 +24828,7 @@ refindex
 \begin_inset space ~
 \end_inset
 
-[<refmask]] Center using coordinates in specified reference structure selected
- by <refmask> (<mask> if not specified.
+[<refmask]] Center using coordinates in specified reference structure selected by <refmask> (<mask> if not specified.
 \end_layout
 
 \end_deeper
@@ -24483,13 +24837,15 @@ Move all atoms so that the center of the atoms in
 \series bold
 <mask>
 \series default
- is centered at the specified location: box center (default), coordinate
- origin, or reference coordinates.
+ is centered at the specified location:
+ box center (default),
+ coordinate origin,
+ or reference coordinates.
 \end_layout
 
 \begin_layout Standard
-For example, to move all coordinates so that the center of mass of residue
- 1 is at the center of the box:
+For example,
+ to move all coordinates so that the center of mass of residue 1 is at the center of the box:
 \end_layout
 
 \begin_layout LyX-Code
@@ -24503,6 +24859,8 @@ check | checkoverlap | checkstructure
 \begin_layout LyX-Code
 check
 \begin_inset Index idx
+range none
+pageformat default
 status open
 
 \begin_layout Plain Layout
@@ -24536,8 +24894,8 @@ check
 \begin_inset space ~
 \end_inset
 
-<mask2>] If specified, only check for problems between atoms in <mask> and
- atoms in <mask2>.
+<mask2>] If specified,
+ only check for problems between atoms in <mask> and atoms in <mask2>.
 \end_layout
 
 \begin_layout Description
@@ -24553,8 +24911,8 @@ check
 \end_layout
 
 \begin_layout Description
-[skipbadframes] If errors are encountered for a frame, subsequent actions/trajec
-tory output will be skipped.
+[skipbadframes] If errors are encountered for a frame,
+ subsequent actions/trajectory output will be skipped.
 \end_layout
 
 \begin_layout Description
@@ -24562,8 +24920,7 @@ tory output will be skipped.
 \begin_inset space ~
 \end_inset
 
-<offset>] Report bond lengths greater than the equilibrium value plus <offset>
- (default 1.15 Å).
+<offset>] Report bond lengths greater than the equilibrium value plus <offset> (default 1.15 Å).
 \end_layout
 
 \begin_layout Description
@@ -24571,8 +24928,7 @@ tory output will be skipped.
 \begin_inset space ~
 \end_inset
 
-<minoffset>] Report bond lengths less than the equilibrium value minus <minoffse
-t> (default 0.5 Å).
+<minoffset>] Report bond lengths less than the equilibrium value minus <minoffset> (default 0.5 Å).
 \end_layout
 
 \begin_layout Description
@@ -24588,8 +24944,7 @@ t> (default 0.5 Å).
 \end_layout
 
 \begin_layout Description
-[silent] Do not print information for bad frames - useful in conjunction
- with the 
+[silent] Do not print information for bad frames - useful in conjunction with the 
 \series bold
 skipbadframes
 \series default
@@ -24601,13 +24956,13 @@ skipbadframes
 \begin_inset space ~
 \end_inset
 
-<cut>] Pair list cutoff (default 4.0 Å); only matters if box is present.
+<cut>] Pair list cutoff (default 4.0 Å);
+ only matters if box is present.
 \end_layout
 
 \end_deeper
 \begin_layout Standard
-Check the structure and report problems related to atomic overlap/unusual
- bond length.
+Check the structure and report problems related to atomic overlap/unusual bond length.
  Problems are reported when any two atoms in 
 \series bold
 <mask>
@@ -24628,13 +24983,13 @@ Check the structure and report problems related to atomic overlap/unusual
 \series bold
 <cut>
 \series default
-; atoms that are bonded to each other are ignored (except if using the 
+;
+ atoms that are bonded to each other are ignored (except if using the 
 \series bold
 'around'
 \series default
  mask).
- If bonds are being checked then bond lengths greater than their equilibrium
- value plus 
+ If bonds are being checked then bond lengths greater than their equilibrium value plus 
 \series bold
 <offset>
 \series default
@@ -24647,17 +25002,20 @@ Check the structure and report problems related to atomic overlap/unusual
 \series bold
 'around'
 \series default
- mask, a pairlist will be used to speed up the calculation.
+ mask,
+ a pairlist will be used to speed up the calculation.
 \end_layout
 
 \begin_layout Standard
-This command can also be used to skip corrupted frames in a trajectory during
- processing.
- For example, if this message is encountered:
+This command can also be used to skip corrupted frames in a trajectory during processing.
+ For example,
+ if this message is encountered:
 \end_layout
 
 \begin_layout LyX-Code
-Warning: Frame 10 coords 1 & 2 overlap at origin; may be corrupt.
+Warning:
+ Frame 10 coords 1 & 2 overlap at origin;
+ may be corrupt.
 \end_layout
 
 \begin_layout Standard
@@ -24686,12 +25044,11 @@ distance d1 :1 :10
 \end_layout
 
 \begin_layout Standard
-Usually frame corruption can be detected using only a few atoms, but this
- may not catch all types of corruption.
+Usually frame corruption can be detected using only a few atoms,
+ but this may not catch all types of corruption.
  The more atoms that are used the better the corruption detection will be,
  but the slower it will be to process the command.
- Typically a good procedure to follow when corruption is suspected is to
- run 
+ Typically a good procedure to follow when corruption is suspected is to run 
 \series bold
 \shape italic
 check
@@ -24708,7 +25065,8 @@ skipbadframes
 trajout
 \series default
 \shape default
- command to write all non-corrupt frames, for example:
+ command to write all non-corrupt frames,
+ for example:
 \end_layout
 
 \begin_layout LyX-Code
@@ -24766,14 +25124,16 @@ DataSet Aspects:
 
 \end_deeper
 \begin_layout Standard
-Check the chirality around the alpha carbon in amino acid residues selected
- by <mask>.
+Check the chirality around the alpha carbon in amino acid residues selected by <mask>.
  Note that cpptraj expects atom names to correspond to the PDB V3 standard:
- N, CA, C, CB.
- For each residue, the number of frames in which the amino acid is 'L' or
- 'D' will be recorded.
- For example, to check the chirality of all amino acids in a system and
- write to a file named chiral.dat with data set name DPDP:
+ N,
+ CA,
+ C,
+ CB.
+ For each residue,
+ the number of frames in which the amino acid is 'L' or 'D' will be recorded.
+ For example,
+ to check the chirality of all amino acids in a system and write to a file named chiral.dat with data set name DPDP:
 \end_layout
 
 \begin_layout LyX-Code
@@ -24803,6 +25163,8 @@ closest | closestwaters
 \begin_layout LyX-Code
 closest
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -24853,7 +25215,8 @@ keep> Number of solvent molecules to keep around <mask>
 \end_inset
 
 mask>] Optional mask for selecting solvent atoms.
- If not specified, atoms in all molecules marked as 
+ If not specified,
+ atoms in all molecules marked as 
 \begin_inset Quotes eld
 \end_inset
 
@@ -24865,8 +25228,8 @@ solvent
 \end_layout
 
 \begin_layout Description
-[noimage] Do not perform imaging; only recommended if trajectory has previously
- been imaged.
+[noimage] Do not perform imaging;
+ only recommended if trajectory has previously been imaged.
 \end_layout
 
 \begin_layout Description
@@ -24882,8 +25245,7 @@ oxygen] Calculate distances between all atoms in
 \series bold
 <mask>
 \series default
- and the first atom of solvent only (recommended for standard water models
- as it will increase speed of calculation).
+ and the first atom of solvent only (recommended for standard water models as it will increase speed of calculation).
 \end_layout
 
 \begin_layout Description
@@ -24974,15 +25336,16 @@ Similar to the
 strip
 \series default
 \shape default
- command, but modify coordinate frame and topology by keeping only the specified
- number of closest solvent molecules to the region specified by the given
- mask.
+ command,
+ but modify coordinate frame and topology by keeping only the specified number of closest solvent molecules to the region specified by the given mask.
  Solvent molecules can be determined automatically by 
 \shape italic
 cpptraj
 \shape default
- (by default residues named WAT, HOH, or TIP3), can be specified prior via
- the 
+ (by default residues named WAT,
+ HOH,
+ or TIP3),
+ can be specified prior via the 
 \series bold
 \shape italic
 solvent
@@ -24992,10 +25355,12 @@ solvent
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_solvent"
+nolink "false"
 
 \end_inset
 
-), or can be selected by 
+),
+ or can be selected by 
 \series bold
 solventmask
 \series default
@@ -25015,9 +25380,9 @@ Frame    Molecule    Distance    FirstAtom#
 \end_layout
 
 \begin_layout Standard
-For example, to obtain the 10 closest waters to residues 1-268 by distance
- to the first atom of the waters, write out which waters were closest for
- each frame to a file called 
+For example,
+ to obtain the 10 closest waters to residues 1-268 by distance to the first atom of the waters,
+ write out which waters were closest for each frame to a file called 
 \begin_inset Quotes eld
 \end_inset
 
@@ -25025,7 +25390,8 @@ closestmols.dat
 \begin_inset Quotes erd
 \end_inset
 
-, and write out the stripped topology with prefix 
+,
+ and write out the stripped topology with prefix 
 \begin_inset Quotes eld
 \end_inset
 
@@ -25053,11 +25419,13 @@ Although the
 \series bold
 'cluster'
 \series default
- command can still be specified as an action, it is now considered an analysis.
+ command can still be specified as an action,
+ it is now considered an analysis.
  See 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-cluster-analysis"
+nolink "false"
 
 \end_inset
 
@@ -25071,6 +25439,8 @@ clusterdihedral
 \begin_layout LyX-Code
 clusterdihedral
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -25096,14 +25466,13 @@ clusterdihedral
 
 \begin_layout Standard
 Cluster frames in a trajectory using dihedral angles.
- To define which dihedral angles will be used for clustering either an atom
- mask or an input file specified by the 
+ To define which dihedral angles will be used for clustering either an atom mask or an input file specified by the 
 \series bold
 dihedralfile
 \series default
  keyword should be used.
- If dihedral file is used, each line in the file should contain a dihedral
- to be binned with format:
+ If dihedral file is used,
+ each line in the file should contain a dihedral to be binned with format:
 \end_layout
 
 \begin_layout LyX-Code
@@ -25111,13 +25480,10 @@ ATOM#1 ATOM#2 ATOM#3 ATOM#4 #BINS
 \end_layout
 
 \begin_layout Standard
-where the ATOM arguments are the atom numbers (starting from 1) defining
- the dihedral and #BINS is the number of bins to be used (so if #BINS=10
- the width of each bin will be 36º).
- If an atom mask is specified, only protein backbone dihedrals (Phi and
- Psi defined using atom names C-N-CA-C and N-CA-C-N) within the mask will
- be used, with the bin sizes specified by the phibins and psibins keywords
- (default for each is 10 bins).
+where the ATOM arguments are the atom numbers (starting from 1) defining the dihedral and #BINS is the number of bins to be used (so if #BINS=10 the width of each bin will be 36º).
+ If an atom mask is specified,
+ only protein backbone dihedrals (Phi and Psi defined using atom names C-N-CA-C and N-CA-C-N) within the mask will be used,
+ with the bin sizes specified by the phibins and psibins keywords (default for each is 10 bins).
 \end_layout
 
 \begin_layout Standard
@@ -25126,15 +25492,17 @@ Output will either be written to STDOUT or the file specified by the
 out
 \series default
  keyword.
- First, information about which dihedrals were clustered will be printed.
- Then the number of clusters will be printed, followed by detailed information
- of each cluster.
+ First,
+ information about which dihedrals were clustered will be printed.
+ Then the number of clusters will be printed,
+ followed by detailed information of each cluster.
  The clusters are sorted from most populated to least populated.
  Each cluster line has format
 \end_layout
 
 \begin_layout LyX-Code
-Cluster CLUSTERNUM CLUSTERPOP [ dihedral1bin, dihedral2bin ...
+Cluster CLUSTERNUM CLUSTERPOP [ dihedral1bin,
+ dihedral2bin ...
  dihedralNbin ]
 \end_layout
 
@@ -25144,7 +25512,8 @@ followed by a list of frame numbers that belong to that cluster.
 \series bold
 cut
 \series default
-, only clusters with population greater than CUT will be printed.
+,
+ only clusters with population greater than CUT will be printed.
 \end_layout
 
 \begin_layout Standard
@@ -25152,13 +25521,14 @@ If specified by the
 \series bold
 clustervtime
 \series default
- keyword, the number of clusters for each frame will be printed to <cvtfile>.
+ keyword,
+ the number of clusters for each frame will be printed to <cvtfile>.
  If specified by the 
 \series bold
 framefile
 \series default
- keyword, a file containing cluster information for each frame will be written
- with format
+ keyword,
+ a file containing cluster information for each frame will be written with format
 \end_layout
 
 \begin_layout LyX-Code
@@ -25166,9 +25536,7 @@ Frame CLUSTERNUM CLUSTERSIZE DIHEDRALBINID
 \end_layout
 
 \begin_layout Standard
-where DIHEDRALBINID is a number that identifies the unique combination of
- dihedral bins this cluster belongs to (specifically it is a 3*number-of-dihedra
-l-characters long number composed of the individual dihedral bins).
+where DIHEDRALBINID is a number that identifies the unique combination of dihedral bins this cluster belongs to (specifically it is a 3*number-of-dihedral-characters long number composed of the individual dihedral bins).
 \end_layout
 
 \begin_layout Standard
@@ -25176,12 +25544,12 @@ If specified by the
 \series bold
 clusterinfo
 \series default
- keyword, a file containing information on each dihedral and each cluster
- will be printed.
- This file can be read by SANDER for use with REMD with a structure reservoir
- (-rremd=3).
- The file, which is essentially a simplified version of the main output
- file, has the following format:
+ keyword,
+ a file containing information on each dihedral and each cluster will be printed.
+ This file can be read by SANDER for use with REMD with a structure reservoir (-rremd=3).
+ The file,
+ which is essentially a simplified version of the main output file,
+ has the following format:
 \end_layout
 
 \begin_layout LyX-Code
@@ -25221,7 +25589,8 @@ contacts [ first | reference | ref <ref> | refindex <#> ] [byresidue]
 \end_layout
 
 \begin_layout Standard
-NOTE: Users are encouraged to try the 
+NOTE:
+ Users are encouraged to try the 
 \series bold
 \emph on
 nativecontacts
@@ -25231,10 +25600,12 @@ nativecontacts
 \begin_inset CommandInset ref
 LatexCommand vpageref
 reference "subsec:cpptraj-nativecontacts"
+nolink "false"
 
 \end_inset
 
-), an update version of this command.
+),
+ an update version of this command.
 \end_layout
 
 \begin_layout Standard
@@ -25242,7 +25613,8 @@ For each atom given in
 \shape italic
 mask
 \shape default
-, calculate the number of other atoms (contacts) within the distance 
+,
+ calculate the number of other atoms (contacts) within the distance 
 \shape italic
 cutoff
 \shape default
@@ -25252,8 +25624,8 @@ cutoff
 \shape italic
 mask
 \shape default
- are potential interaction partners (e.g., a mask @CA will evaluate only contacts
- between CA atoms).
+ are potential interaction partners (e.g.,
+ a mask @CA will evaluate only contacts between CA atoms).
  The results are dumped to 
 \shape italic
 filename
@@ -25271,15 +25643,15 @@ out
 \end_inset
 
  is specified.
- Thereby, the time between snapshots is taken to be 
+ Thereby,
+ the time between snapshots is taken to be 
 \shape italic
 interval
 \shape default
 .
- In addition to the number of overall contacts, the number of native contacts
- is also determined.
- Native contacts are those that have been found either in the first snapshot
- of the trajectory (if the keyword 
+ In addition to the number of overall contacts,
+ the number of native contacts is also determined.
+ Native contacts are those that have been found either in the first snapshot of the trajectory (if the keyword 
 \begin_inset Quotes eld
 \end_inset
 
@@ -25304,7 +25676,8 @@ reference
 \end_inset
 
  is specified).
- Finally, if the keyword 
+ Finally,
+ if the keyword 
 \begin_inset Quotes eld
 \end_inset
 
@@ -25316,7 +25689,8 @@ byresidue
 \begin_inset Quotes erd
 \end_inset
 
- is provided, results are output on a per-residue basis for each snapshot,
+ is provided,
+ results are output on a per-residue basis for each snapshot,
  whereby the number of native contacts is written to 
 \shape italic
 filename
@@ -25340,13 +25714,12 @@ createcrd [<name>] [ parm <name> | parmindex <#> ]
 \end_layout
 
 \begin_layout Standard
-This command creates a COORDS data set named <name> using trajectory frames
- that are associated with the specified topology.
+This command creates a COORDS data set named <name> using trajectory frames that are associated with the specified topology.
 \end_layout
 
 \begin_layout Standard
-For example, to save frames that have been previously RMS-fit to a reference
- structure into a COORDS set named MyCrd you would use the input:
+For example,
+ to save frames that have been previously RMS-fit to a reference structure into a COORDS set named MyCrd you would use the input:
 \end_layout
 
 \begin_layout LyX-Code
@@ -25368,8 +25741,7 @@ Note that here the
 strip
 \series default
 \emph default
- command will have no effect on the coordinates saved in MyCrd since it
- occurs after the 
+ command will have no effect on the coordinates saved in MyCrd since it occurs after the 
 \series bold
 \emph on
 createcrd
@@ -25383,8 +25755,7 @@ createreservoir
 \end_layout
 
 \begin_layout LyX-Code
-createreservoir <filename> ene <energy data set> [bin <cluster bin data
- set>]
+createreservoir <filename> ene <energy data set> [bin <cluster bin data set>]
 \end_layout
 
 \begin_layout LyX-Code
@@ -25490,12 +25861,11 @@ parmindex
 
 \end_deeper
 \begin_layout Standard
-Create structure reservoir for use with reservoir REMD simulations using
- energies in <energy data set>, temperature <temp0> and random seed <iseed>
- Include velocities if [velocity] is specified.
+Create structure reservoir for use with reservoir REMD simulations using energies in <energy data set>,
+ temperature <temp0> and random seed <iseed> Include velocities if [velocity] is specified.
  If <cluster bin data set> is specified from e.g.
- a previous 'clusterdihedral' command, the reservoir can be used for non-Boltzma
-nn reservoir REMD (rremd==3).
+ a previous 'clusterdihedral' command,
+ the reservoir can be used for non-Boltzmann reservoir REMD (rremd==3).
 \end_layout
 
 \begin_layout Subsection
@@ -25554,8 +25924,8 @@ name>] Output data set name.
 \begin_inset space ~
 \end_inset
 
-<maskN> Arbitrary number of masks for atom selection; a dataset is created
- and the output will contain entries for each mask.
+<maskN> Arbitrary number of masks for atom selection;
+ a dataset is created and the output will contain entries for each mask.
 \end_layout
 
 \begin_deeper
@@ -25564,7 +25934,8 @@ name>] Output data set name.
 \begin_inset space ~
 \end_inset
 
-<resolution>] Resolution, i.e.
+<resolution>] Resolution,
+ i.e.
  determines number of slices (i.e.
  histogram bins).
  (default 0.25 Å)
@@ -25576,16 +25947,15 @@ name>] Output data set name.
 \end_layout
 
 \begin_layout Description
-[{number|mass|charge|electron}] Number, mass, partial charge (q) or electron
- (Ne - q) density.
- Electron density will be converted to e-/Å3 by dividing the average area
- spanned by the other two dimensions.
+[{number|mass|charge|electron}] Number,
+ mass,
+ partial charge (q) or electron (Ne - q) density.
+ Electron density will be converted to e-/Å3 by dividing the average area spanned by the other two dimensions.
  (default number)
 \end_layout
 
 \begin_layout Description
-[{bincenter|binedge}] Determine whether histogram bin coordinates will be
- based on bin center (default) or bin edges.
+[{bincenter|binedge}] Determine whether histogram bin coordinates will be based on bin center (default) or bin edges.
 \end_layout
 
 \begin_layout Description
@@ -25597,8 +25967,8 @@ name>] Output data set name.
 \series bold
 'restrict'
 \series default
- is specified, only calculate the density that is within a cylinder or square
- shape from the specified axis as defined by a distance cutoff.
+ is specified,
+ only calculate the density that is within a cylinder or square shape from the specified axis as defined by a distance cutoff.
 \end_layout
 
 \begin_deeper
@@ -25633,8 +26003,7 @@ name>[avg]:<idx> Average density over coordinate for mask number <idx>.
 \begin_inset space ~
 \end_inset
 
-name>[sd]:<idx> Standard deviation of density over coordinate for mask number
- <idx>.
+name>[sd]:<idx> Standard deviation of density over coordinate for mask number <idx>.
 \end_layout
 
 \begin_layout Standard
@@ -25651,14 +26020,14 @@ name> Total system density each frame.
 
 \end_deeper
 \begin_layout Standard
-If no atom masks are specified, calculate the total system density.
- Otherwise, calculate specified density along the given axis for atoms in
- specified mask(s).
+If no atom masks are specified,
+ calculate the total system density.
+ Otherwise,
+ calculate specified density along the given axis for atoms in specified mask(s).
  Defaults are shown in parentheses above.
  The format of the file is as follows.
  Comments are lines starting with '#' or empty lines.
- All other lines must contain the atom type followed by an integer number
- for the electron number.
+ All other lines must contain the atom type followed by an integer number for the electron number.
  Entries must be separated by spaces or '='.
  Example input:
 \end_layout
@@ -25718,8 +26087,8 @@ See also $AMBERHOME/AmberTools/test/cpptraj/Test_Density.
 \end_layout
 
 \begin_layout Standard
-It can be useful to write out the average and standard deviation as an XYDY
- set to a Grace data file, e.g.
+It can be useful to write out the average and standard deviation as an XYDY set to a Grace data file,
+ e.g.
 \end_layout
 
 \begin_layout LyX-Code
@@ -25744,12 +26113,12 @@ Note that although the syntax for
 \series bold
 diffusion
 \series default
- has changed as of version 16, the old syntax is still supported.
+ has changed as of version 16,
+ the old syntax is still supported.
 \end_layout
 
 \begin_layout LyX-Code
-diffusion [{out <filename>|separateout <suffix>}] [time <time per frame>]
- [noimage]
+diffusion [{out <filename>|separateout <suffix>}] [time <time per frame>] [noimage]
 \end_layout
 
 \begin_layout LyX-Code
@@ -25774,8 +26143,7 @@ diffusion [{out <filename>|separateout <suffix>}] [time <time per frame>]
 \begin_inset space ~
 \end_inset
 
-<filename>] Write mean-square displacement (MSD) data set output to file
- specified by <filename>.
+<filename>] Write mean-square displacement (MSD) data set output to file specified by <filename>.
 \end_layout
 
 \begin_layout Description
@@ -25783,8 +26151,8 @@ diffusion [{out <filename>|separateout <suffix>}] [time <time per frame>]
 \begin_inset space ~
 \end_inset
 
-<suffix>] Write each MSD data set type to files with suffix <suffix>; see
- description below.
+<suffix>] Write each MSD data set type to files with suffix <suffix>;
+ see description below.
 \end_layout
 
 \begin_layout Description
@@ -25792,8 +26160,8 @@ diffusion [{out <filename>|separateout <suffix>}] [time <time per frame>]
 \begin_inset space ~
 \end_inset
 
-<time_per_frame>] Time in-between each coordinate frame in ps; default is
- 1.0.
+<time_per_frame>] Time in-between each coordinate frame in ps;
+ default is 1.0.
 \end_layout
 
 \begin_layout Description
@@ -25802,7 +26170,8 @@ diffusion [{out <filename>|separateout <suffix>}] [time <time per frame>]
 \end_layout
 
 \begin_layout Description
-[<mask>] Mask of atoms to calculate diffusion for; default all atoms.
+[<mask>] Mask of atoms to calculate diffusion for;
+ default all atoms.
 \end_layout
 
 \begin_layout Description
@@ -25814,8 +26183,7 @@ name>] MSD data set name.
 \end_layout
 
 \begin_layout Description
-[individual] Write diffusion for each individual atom as well as average
- diffusion for atoms in mask.
+[individual] Write diffusion for each individual atom as well as average diffusion for atoms in mask.
 \end_layout
 
 \begin_layout Description
@@ -25823,8 +26191,7 @@ name>] MSD data set name.
 \begin_inset space ~
 \end_inset
 
-<filename>] Write diffusion contants calculated from fits of MSD data sets
- to <filename>.
+<filename>] Write diffusion contants calculated from fits of MSD data sets to <filename>.
 \end_layout
 
 \begin_layout Description
@@ -25832,14 +26199,13 @@ name>] MSD data set name.
 \end_layout
 
 \begin_layout Description
-[avgucell] Remove periodic box fluctuations from imaged NPT trajectories
- using average unit cell vectors.
+[avgucell] Remove periodic box fluctuations from imaged NPT trajectories using average unit cell vectors.
 \end_layout
 
 \begin_layout Description
 [allowmultipleorigins] (MPI only).
- For imaged trajectories in parallel, calculate diffusion by averaging over
- multiple time origins.
+ For imaged trajectories in parallel,
+ calculate diffusion by averaging over multiple time origins.
  Should be used with caution.
 \end_layout
 
@@ -25947,8 +26313,8 @@ individual
 
 \end_deeper
 \begin_layout Standard
-Compute mean-squared displacement (MSD, in Angstroms squared) plots (using
- distance traveled from initial position) for the atoms in 
+Compute mean-squared displacement (MSD,
+ in Angstroms squared) plots (using distance traveled from initial position) for the atoms in 
 \series bold
 <mask>
 \series default
@@ -25957,7 +26323,8 @@ Compute mean-squared displacement (MSD, in Angstroms squared) plots (using
 \series bold
 <mask>
 \series default
- is calculated; if 
+ is calculated;
+ if 
 \series bold
 individual
 \series default
@@ -25966,10 +26333,9 @@ individual
 \end_layout
 
 \begin_layout Standard
-In order to correctly calculate diffusion molecules should take continuous
- paths, so imaging of atoms is autoimatically performed.
- If the trajectory is already unwrapped (or the unwrap command is used prior
- to this command) the 
+In order to correctly calculate diffusion molecules should take continuous paths,
+ so imaging of atoms is autoimatically performed.
+ If the trajectory is already unwrapped (or the unwrap command is used prior to this command) the 
 \series bold
 noimage
 \series default
@@ -25982,12 +26348,13 @@ noise
 \begin_inset Quotes erd
 \end_inset
 
- caused by box fluctuations in NPT trajectories, the average unit cell vectors
- describing the average box can be provided with the 
+ caused by box fluctuations in NPT trajectories,
+ the average unit cell vectors describing the average box can be provided with the 
 \series bold
 avgucell
 \series default
- keyword; see the 
+ keyword;
+ see the 
 \series bold
 \emph on
 avgbox
@@ -26000,28 +26367,33 @@ reference "subsec:cpptraj_avgbox"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
 ).
- Alternatively, the trajectory can be unwrapped prior using the 
+ Alternatively,
+ the trajectory can be unwrapped prior using the 
 \series bold
 \emph on
 unwrap
 \series default
 \emph default
- command, 
+ command,
+ 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_unwrap"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
 .
- If the trajectory is unwrapped, the 
+ If the trajectory is unwrapped,
+ the 
 \series bold
 noimage
 \series default
@@ -26029,10 +26401,9 @@ noimage
 \end_layout
 
 \begin_layout Standard
-Note that in parallel, imaging becomes difficult because there is no way
- to correct for any wrapping that has been done on preceding MPI ranks.
- Therefore this command will not work on imaged trajectories in parallel
- by default.
+Note that in parallel,
+ imaging becomes difficult because there is no way to correct for any wrapping that has been done on preceding MPI ranks.
+ Therefore this command will not work on imaged trajectories in parallel by default.
  There are two workarounds.
  1) Unwrap the trajectory prior to 
 \series bold
@@ -26046,19 +26417,20 @@ diffusion
 unwrap
 \series default
 \emph default
- command, then run the diffusion calculation with the 
+ command,
+ then run the diffusion calculation with the 
 \series bold
 noimage
 \series default
- keyword (this is the recommended way), or 2) specify the 
+ keyword (this is the recommended way),
+ or 2) specify the 
 \series bold
 allowmultipleorigins
 \series default
- keyword to calculate MSD separately on each MPI rank, then averaging over
- all MSD plots.
- This means the maximum length of any given MSD plot will be <# frames>
- / <# MPI ranks>, and the calculated diffusion constants will not be as
- accurate.
+ keyword to calculate MSD separately on each MPI rank,
+ then averaging over all MSD plots.
+ This means the maximum length of any given MSD plot will be <# frames> / <# MPI ranks>,
+ and the calculated diffusion constants will not be as accurate.
 \end_layout
 
 \begin_layout Standard
@@ -26134,15 +26506,17 @@ Where
 n
 \series default
 \shape default
- is the number of dimensions; for overall MSD n = 3, for single dimension
- MSD (e.g.
- X) n = 1, etc.
+ is the number of dimensions;
+ for overall MSD n = 3,
+ for single dimension MSD (e.g.
+ X) n = 1,
+ etc.
  Unless 
 \series bold
 nocalc
 \series default
- is specified, the diffusion constant is calculated automatically from MSD
- data sets (and written to the file specified by 
+ is specified,
+ the diffusion constant is calculated automatically from MSD data sets (and written to the file specified by 
 \series bold
 diffout
 \series default
@@ -26170,18 +26544,19 @@ diffout
 
 \end_inset
 
-/s, the slope is multiplied by 10.0/(2n).
- Both the calculated diffusion constants as well as the results of the fit
- are reported.
+/s,
+ the slope is multiplied by 10.0/(2n).
+ Both the calculated diffusion constants as well as the results of the fit are reported.
 \end_layout
 
 \begin_layout Standard
-Due to the fact that diffusion is currently calculated from initial positions
- only, diffusion calculated for small numbers of atoms will be inherently
- stochastic, so the results are most sensible when averaged over many atoms;
- for example, the diffusion of water should be calculated using all waters
- in the system.
- If more averaging is needed, the 
+Due to the fact that diffusion is currently calculated from initial positions only,
+ diffusion calculated for small numbers of atoms will be inherently stochastic,
+ so the results are most sensible when averaged over many atoms;
+ for example,
+ the diffusion of water should be calculated using all waters in the system.
+ If more averaging is needed,
+ the 
 \series bold
 \emph on
 calcdiffusion
@@ -26194,6 +26569,7 @@ reference "subsec:cpptraj-calcdiffusion"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
@@ -26201,7 +26577,8 @@ noprefix "false"
 \end_layout
 
 \begin_layout Standard
-For example, to calculate the diffusion of water in a system:
+For example,
+ to calculate the diffusion of water in a system:
 \end_layout
 
 \begin_layout LyX-Code
@@ -26215,6 +26592,8 @@ dihedral
 \begin_layout LyX-Code
 dihedral
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -26227,8 +26606,7 @@ dihedral
 \end_layout
 
 \begin_layout LyX-Code
-         [type {alpha|beta|gamma|delta|epsilon|zeta|chi|c2p|h1p|phi|psi|omega|pc
-hi}]
+         [type {alpha|beta|gamma|delta|epsilon|zeta|chi|c2p|h1p|phi|psi|omega|pchi}]
 \end_layout
 
 \begin_layout LyX-Code
@@ -26257,12 +26635,12 @@ hi}]
 \end_layout
 
 \begin_layout Description
-[mass] Use center of mass of atoms in <maskX>; default is geometric center.
+[mass] Use center of mass of atoms in <maskX>;
+ default is geometric center.
 \end_layout
 
 \begin_layout Description
-[range360] Output dihedral angle values from 0 to 360 degrees instead of
- -180 to 180 degrees.
+[range360] Output dihedral angle values from 0 to 360 degrees instead of -180 to 180 degrees.
 \end_layout
 
 \begin_layout Description
@@ -26276,13 +26654,17 @@ hi}]
 statistics
 \series default
 \shape default
- analysis; note 'chi' is nucleic acid chi and 'pchi' is protein chi.
+ analysis;
+ note 'chi' is nucleic acid chi and 'pchi' is protein chi.
 \end_layout
 
 \end_deeper
 \begin_layout Standard
-Calculate dihedral angle (in degrees) between the planes defined by atoms
- in <mask1>, <mask2>, <mask3> and <mask2>, <mask3>, <mask4>.
+Calculate dihedral angle (in degrees) between the planes defined by atoms in <mask1>,
+ <mask2>,
+ <mask3> and <mask2>,
+ <mask3>,
+ <mask4>.
  To calculate multiple dihedral angles see the 
 \series bold
 \emph on
@@ -26296,6 +26678,7 @@ reference "subsec:cpptraj_multidihedral"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
@@ -26311,8 +26694,7 @@ dihedralrms | dihrms
 \end_layout
 
 \begin_layout LyX-Code
-            	[ first | reference | ref <name> | refindex <#> | previous
- |
+            	[ first | reference | ref <name> | refindex <#> | previous |
 \end_layout
 
 \begin_layout LyX-Code
@@ -26338,7 +26720,8 @@ dihedralrms | dihrms
 \end_inset
 
 types> Dihedral types to look for.
- Note that chip is 'protein chi', chin is 'nucleic chi'.
+ Note that chip is 'protein chi',
+ chin is 'nucleic chi'.
 \end_layout
 
 \begin_layout Description
@@ -26354,8 +26737,10 @@ types> Dihedral types to look for.
 \begin_inset space ~
 \end_inset
 
-<name>:<a0>:<a1>:<a2>:<a3>[:<offset>] Search for a custom dihedral type
- called <name> using atom names <a0>, <a1>, <a2>, and <a3>.
+<name>:<a0>:<a1>:<a2>:<a3>[:<offset>] Search for a custom dihedral type called <name> using atom names <a0>,
+ <a1>,
+ <a2>,
+ and <a3>.
 \begin_inset Separator latexpar
 \end_inset
 
@@ -26364,8 +26749,12 @@ types> Dihedral types to look for.
 
 \begin_deeper
 \begin_layout Standard
-Offset: -2=<a0><a1> in previous res, -1=<a0> in previous res, 0=All <aX>
- in single res, 1=<a3> in next res, 2=<a2><a3> in next res.
+Offset:
+ -2=<a0><a1> in previous res,
+ -1=<a0> in previous res,
+ 0=All <aX> in single res,
+ 1=<a3> in next res,
+ 2=<a2><a3> in next res.
 \end_layout
 
 \end_deeper
@@ -26384,7 +26773,8 @@ Offset: -2=<a0><a1> in previous res, -1=<a0> in previous res, 0=All <aX>
 \end_inset
 
 <range>] Residues range to look for reference dihedrals in.
- If not specified, use target range.
+ If not specified,
+ use target range.
 \end_layout
 
 \end_deeper
@@ -26403,6 +26793,7 @@ reference "subsec:cpptraj_multidihedral"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
@@ -26420,10 +26811,12 @@ This command has been replaced by
 permutedihedrals
 \series default
 \emph default
-; see 
+;
+ see 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_permutedihedrals"
+nolink "false"
 
 \end_inset
 
@@ -26493,7 +26886,8 @@ dipole [out <filename>]
 \begin_inset Quotes erd
 \end_inset
 
- extension for XPLOR format, 
+ extension for XPLOR format,
+ 
 \begin_inset Quotes eld
 \end_inset
 
@@ -26538,8 +26932,7 @@ name/tag>
 \begin_inset space ~
 \end_inset
 
-<nz> Set up grid using box information from a previously loaded reference
- structure.
+<nz> Set up grid using box information from a previously loaded reference structure.
  Currently the only way to set up non-orthogonal grids.
 \end_layout
 
@@ -26580,7 +26973,10 @@ name/tag>
 \begin_inset space ~
 \end_inset
 
-<cz>] Location of grid center, default is origin (0.0, 0.0, 0.0).
+<cz>] Location of grid center,
+ default is origin (0.0,
+ 0.0,
+ 0.0).
 \end_layout
 
 \begin_layout Description
@@ -26600,16 +26996,14 @@ name/tag>
 \begin_inset space ~
 \end_inset
 
-<mask>] Perform a best-fit rotation of the grid using the coordinates selected
- by <mask>.
+<mask>] Perform a best-fit rotation of the grid using the coordinates selected by <mask>.
 \end_layout
 
 \begin_deeper
 \begin_layout Description
-[noxalign] If specified, grid will not be re-oriented to align with Cartesian
- axes once binning is finished.
- Will affect file formats that do not store full unit cell vectors (like
- Xplor).
+[noxalign] If specified,
+ grid will not be re-oriented to align with Cartesian axes once binning is finished.
+ Will affect file formats that do not store full unit cell vectors (like Xplor).
 \end_layout
 
 \end_deeper
@@ -26669,7 +27063,8 @@ percent>] Only keep density >= to <max_percent> of the maximum density.
 
 \end_deeper
 \begin_layout Standard
-NOTE: This command is not well-tested and may be obsolete.
+NOTE:
+ This command is not well-tested and may be obsolete.
 \end_layout
 
 \begin_layout Standard
@@ -26683,12 +27078,12 @@ grid
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_grid"
+nolink "false"
 
 \end_inset
 
  below) except that dipoles of the solvent molecules are binned.
- The output file format is for Chris Bayly's discern delegate program that
- comes with Midas/Plus.
+ The output file format is for Chris Bayly's discern delegate program that comes with Midas/Plus.
  Consult the code in Action_Dipole.cpp for more information.
 
 \shape italic
@@ -26702,6 +27097,8 @@ distance
 \begin_layout LyX-Code
 distance
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -26726,8 +27123,7 @@ distance
 \end_layout
 
 \begin_layout LyX-Code
-	  [bound <lower> bound <upper>] [rexp <expected>] [noe_strong] [noe_medium]
- [noe_weak]
+	  [bound <lower> bound <upper>] [rexp <expected>] [noe_strong] [noe_medium] [noe_weak]
 \begin_inset Separator latexpar
 \end_inset
 
@@ -26744,8 +27140,8 @@ distance
 \end_layout
 
 \begin_layout Description
-<mask2> If specified, second atom mask selection atom(s) to calculate distance
- from <mask1>.
+<mask2> If specified,
+ second atom mask selection atom(s) to calculate distance from <mask1>.
 \end_layout
 
 \begin_layout Description
@@ -26761,8 +27157,8 @@ point
 \begin_inset space ~
 \end_inset
 
-<Z> If specified instead of second mask, calculate distance between <mask1>
- and specified XYZ coordinates.
+<Z> If specified instead of second mask,
+ calculate distance between <mask1> and specified XYZ coordinates.
 \end_layout
 
 \begin_layout Description
@@ -26790,8 +27186,8 @@ refindex
 \begin_inset space ~
 \end_inset
 
-<#> If specified, calculate distance between <mask1> in each input frame
- and <mask2> in the specified reference.
+<#> If specified,
+ calculate distance between <mask1> in each input frame and <mask2> in the specified reference.
 \end_layout
 
 \begin_layout Description
@@ -26803,8 +27199,8 @@ refindex
 \end_layout
 
 \begin_layout Description
-[geom] Use geometric center of atoms in <mask1>/<mask2>; default is to use
- center of mass.
+[geom] Use geometric center of atoms in <mask1>/<mask2>;
+ default is to use center of mass.
 \end_layout
 
 \begin_layout Description
@@ -26843,7 +27239,8 @@ bound
 \begin_inset space ~
 \end_inset
 
-<upper>] Lower and upper bounds for NOE (in Angstroms); must specify both.
+<upper>] Lower and upper bounds for NOE (in Angstroms);
+ must specify both.
 \end_layout
 
 \begin_layout Description
@@ -26851,8 +27248,8 @@ bound
 \begin_inset space ~
 \end_inset
 
-<expected>] Expected value for NOE (in Angstroms); if not given '(<lower>
- + <upper>)' / 2.0 is used.
+<expected>] Expected value for NOE (in Angstroms);
+ if not given '(<lower> + <upper>)' / 2.0 is used.
 \end_layout
 
 \begin_layout Description
@@ -26870,15 +27267,16 @@ bound
 \end_deeper
 \end_deeper
 \begin_layout Standard
-Calculate distance between the center of mass of atoms in <mask1> to atoms
- in <mask2>, between atoms in <mask1> from each input frame and atoms in
- <mask2> in specified reference, or atoms in <mask1> and the specified point.
+Calculate distance between the center of mass of atoms in <mask1> to atoms in <mask2>,
+ between atoms in <mask1> from each input frame and atoms in <mask2> in specified reference,
+ or atoms in <mask1> and the specified point.
  If 
 \series bold
 geom
 \series default
  is specified use the geometric center instead.
- For periodic systems imaging is turned on by default; the 
+ For periodic systems imaging is turned on by default;
+ the 
 \series bold
 noimage
 \series default
@@ -26900,6 +27298,7 @@ type noe
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_statistics"
+nolink "false"
 
 \end_inset
 
@@ -26913,6 +27312,8 @@ drms | drmsd (distance RMSD)
 \begin_layout LyX-Code
 drmsd
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -26950,7 +27351,8 @@ name>] Output data set name.
 \end_layout
 
 \begin_layout Description
-[<refmask>] Mask corresponding to atoms in reference; if not specified,
+[<refmask>] Mask corresponding to atoms in reference;
+ if not specified,
  <mask> is used.
 \end_layout
 
@@ -26995,8 +27397,7 @@ name>] Output data set name.
 \begin_inset space ~
 \end_inset
 
-<#>] Use previously read in reference structure specified by <#> (based
- on order read in).
+<#>] Use previously read in reference structure specified by <#> (based on order read in).
 \end_layout
 
 \begin_layout Description
@@ -27012,13 +27413,12 @@ reftraj
 \begin_inset space ~
 \end_inset
 
-<name> Use frames from COORDS set <name> or read in from trajectory file
- <name> as references.
- Each frame from <name> is used in turn, so that frame 1 is compared to
- frame 1 from <name>, frame 2 is compared to frame 2 from <name> and so
- on.
- If <trajname> runs out of frames before processing is complete, the last
- frame of <trajname> continues to be used as the reference.
+<name> Use frames from COORDS set <name> or read in from trajectory file <name> as references.
+ Each frame from <name> is used in turn,
+ so that frame 1 is compared to frame 1 from <name>,
+ frame 2 is compared to frame 2 from <name> and so on.
+ If <trajname> runs out of frames before processing is complete,
+ the last frame of <trajname> continues to be used as the reference.
 \begin_inset Separator latexpar
 \end_inset
 
@@ -27047,16 +27447,15 @@ parmindex
 \series bold
 reftraj
 \series default
- specifies a file associate trajectory <name> with specified topology; if
- not specified the first topology is used.
+ specifies a file associate trajectory <name> with specified topology;
+ if not specified the first topology is used.
 \end_layout
 
 \end_deeper
 \end_deeper
 \begin_layout Standard
 Calculate the distance RMSD (i.e.
- the RMSD of all pairs of internal distances) between atoms in the frame
- defined by 
+ the RMSD of all pairs of internal distances) between atoms in the frame defined by 
 \series bold
 <mask>
 \series default
@@ -27085,15 +27484,16 @@ Calculate the distance RMSD (i.e.
 \series bold
 <refmask>
 \series default
- must specify the same number of atoms, otherwise an error will occur.
+ must specify the same number of atoms,
+ otherwise an error will occur.
  
 \end_layout
 
 \begin_layout Standard
-Because this method compares pairs of internal distances and not absolute
- coordinates, it is not sensitive to translations and rotations the way
- that a no-fit RMSD calculation is.
- It can be more time consuming however, as (N
+Because this method compares pairs of internal distances and not absolute coordinates,
+ it is not sensitive to translations and rotations the way that a no-fit RMSD calculation is.
+ It can be more time consuming however,
+ as (N
 \begin_inset script superscript
 
 \begin_layout Plain Layout
@@ -27102,14 +27502,13 @@ Because this method compares pairs of internal distances and not absolute
 
 \end_inset
 
--N)/2 distances must be calculated and compared for both the target and
- reference structures.
+-N)/2 distances must be calculated and compared for both the target and reference structures.
  
 \end_layout
 
 \begin_layout Standard
-For example, to get the DRMSD of a residue named LIG to its structure in
- the first frame read in:
+For example,
+ to get the DRMSD of a residue named LIG to its structure in the first frame read in:
 \end_layout
 
 \begin_layout LyX-Code
@@ -27125,6 +27524,7 @@ See
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-secstruct"
+nolink "false"
 
 \end_inset
 
@@ -27140,8 +27540,7 @@ energy [<name>] [<mask1>] [out <filename>] [nobondstoh] [openmm [<mdopts>]]
 \end_layout
 
 \begin_layout LyX-Code
-   	[bond] [angle] [dihedral] {[nb14]|[e14]|[v14]} {[nonbond]|[elec] [vdw]}
- 
+   	[bond] [angle] [dihedral] {[nb14]|[e14]|[v14]} {[nonbond]|[elec] [vdw]} 
 \end_layout
 
 \begin_layout LyX-Code
@@ -27165,8 +27564,7 @@ energy [<name>] [<mask1>] [out <filename>] [nobondstoh] [openmm [<mdopts>]]
 \end_layout
 
 \begin_layout LyX-Code
-   	                [rsumtol <rtol>] [maxexp <max>] [mlimits <X>,<Y>,<Z>]
- |
+   	                [rsumtol <rtol>] [maxexp <max>] [mlimits <X>,<Y>,<Z>] |
 \end_layout
 
 \begin_layout LyX-Code
@@ -27215,17 +27613,19 @@ energy [<name>] [<mask1>] [out <filename>] [nobondstoh] [openmm [<mdopts>]]
 \end_layout
 
 \begin_layout Description
-[openmm] If specified and CPPTRAJ is compiled with OpenMM support, use OpenMM
- to calculate energy.
- Note this will only calculate total energy; any keywords pertaining to
- individual energy components are not available.
- For a list of potential options that can be used with 'openmm', see 
+[openmm] If specified and CPPTRAJ is compiled with OpenMM support,
+ use OpenMM to calculate energy.
+ Note this will only calculate total energy;
+ any keywords pertaining to individual energy components are not available.
+ For a list of potential options that can be used with 'openmm',
+ see 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-emin"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
@@ -27269,8 +27669,7 @@ noprefix "false"
 \end_layout
 
 \begin_layout Description
-[nokinetic] Do not calculate kinetic energy even if velocity/force information
- present.
+[nokinetic] Do not calculate kinetic energy even if velocity/force information present.
 \end_layout
 
 \begin_layout Description
@@ -27285,15 +27684,16 @@ ketype
 \end_inset
 
 {vel|vv} Specify kinetic energy type.
- If not specified, if velocity and force information use a velocity verlet-type
- calculation (
+ If not specified,
+ if velocity and force information use a velocity verlet-type calculation (
 \series bold
 vv
 \series default
-), i.e.
+),
+ i.e.
  assume velocities are a half-step ahead of the forces.
- If only velocity information is present, calculate from on-step velocities
- (
+ If only velocity information is present,
+ calculate from on-step velocities (
 \series bold
 vel
 \series default
@@ -27322,7 +27722,8 @@ vv
 \end_layout
 
 \begin_layout Description
-[simple] Use simple Coulomb term for electrostatics, no cutoff.
+[simple] Use simple Coulomb term for electrostatics,
+ no cutoff.
 \end_layout
 
 \begin_layout Description
@@ -27341,8 +27742,7 @@ vv
 \end_deeper
 \begin_layout Description
 [ewald] Use Ewald summation for electrostatics.
- If van der Waals energy will be calculated a long-range correction for
- periodicity will be applied.
+ If van der Waals energy will be calculated a long-range correction for periodicity will be applied.
 \end_layout
 
 \begin_deeper
@@ -27380,8 +27780,8 @@ erfcdx
 \end_layout
 
 \begin_layout Description
-skinnb Used to determine pairlist atoms (added to cut, so pairlist cutoff
- is 
+skinnb Used to determine pairlist atoms (added to cut,
+ so pairlist cutoff is 
 \series bold
 cut
 \series default
@@ -27389,7 +27789,8 @@ cut
 \series bold
 skinnb
 \series default
-); included in order to maintain consistency with results from sander.
+);
+ included in order to maintain consistency with results from sander.
 \end_layout
 
 \begin_layout Description
@@ -27397,8 +27798,8 @@ ljswidth
 \begin_inset space ~
 \end_inset
 
-<width> If specified, use a force-switching form for the Lennard-Jones calculati
-on from <cutoff>-<width> to <cutoff>.
+<width> If specified,
+ use a force-switching form for the Lennard-Jones calculation from <cutoff>-<width> to <cutoff>.
 \end_layout
 
 \begin_layout Description
@@ -27415,16 +27816,14 @@ mlimits
 \begin_inset space ~
 \end_inset
 
-<X>,<Y>,<Z> Explicitly set the number of reciprocal space vectors in each
- dimension.
+<X>,<Y>,<Z> Explicitly set the number of reciprocal space vectors in each dimension.
  Will be determined automatically if not specified.
 \end_layout
 
 \end_deeper
 \begin_layout Description
 [pme] Use particle mesh Ewald for electrostatics.
- If van der Waals energy will be calculated a long-range correction for
- periodicity will be applied.
+ If van der Waals energy will be calculated a long-range correction for periodicity will be applied.
 \end_layout
 
 \begin_deeper
@@ -27462,8 +27861,8 @@ erfcdx
 \end_layout
 
 \begin_layout Description
-skinnb Used to determine pairlist atoms (added to cut, so pairlist cutoff
- is 
+skinnb Used to determine pairlist atoms (added to cut,
+ so pairlist cutoff is 
 \series bold
 cut
 \series default
@@ -27471,7 +27870,8 @@ cut
 \series bold
 skinnb
 \series default
-); included in order to maintain consistency with results from sander.
+);
+ included in order to maintain consistency with results from sander.
 \end_layout
 
 \begin_layout Description
@@ -27479,8 +27879,8 @@ ljswidth
 \begin_inset space ~
 \end_inset
 
-<width> If specified, use a force-switching form for the Lennard-Jones calculati
-on from <cutoff>-<width> to <cutoff>.
+<width> If specified,
+ use a force-switching form for the Lennard-Jones calculation from <cutoff>-<width> to <cutoff>.
 \end_layout
 
 \begin_layout Description
@@ -27496,14 +27896,12 @@ nfft
 \begin_inset space ~
 \end_inset
 
-<nfft1>,<nfft2>,<nfft3> Explicitly set the number of FFT grid points in
- each dimension.
+<nfft1>,<nfft2>,<nfft3> Explicitly set the number of FFT grid points in each dimension.
  Will be determined automatically if not specified.
 \end_layout
 
 \begin_layout Description
-ljpme If specified use particle mesh Ewald for calculating Lennard-Jones
- interactions.
+ljpme If specified use particle mesh Ewald for calculating Lennard-Jones interactions.
 \end_layout
 
 \begin_layout Description
@@ -27558,22 +27956,23 @@ DataSet Aspects:
 \end_deeper
 \begin_layout Standard
 Calculate the energy for atoms in <mask>.
- If no terms are specified, all terms are calculated.
+ If no terms are specified,
+ all terms are calculated.
  Note that the non-bonded energy terms for 
 \series bold
 'simple'
 \series default
  do not take into account periodicity and there is no distance cut-off.
- Electrostatics can also be determined via the direct sum, Ewald, or particle-me
-sh Ewald summation procedures.
- The particle mesh Ewald functionality requires that CPPTRAJ be compiled
- with FFTW and a C++11 compliant compiler.
+ Electrostatics can also be determined via the direct sum,
+ Ewald,
+ or particle-mesh Ewald summation procedures.
+ The particle mesh Ewald functionality requires that CPPTRAJ be compiled with FFTW and a C++11 compliant compiler.
 \end_layout
 
 \begin_layout Standard
-Calculation of energy terms requires that the associated topology file have
- parameters for any of the calculated terms, so for example angle calculations
- are not possible when using a PDB file as a topology, etc.
+Calculation of energy terms requires that the associated topology file have parameters for any of the calculated terms,
+ so for example angle calculations are not possible when using a PDB file as a topology,
+ etc.
  All nonbonded calculations methods other than 
 \series bold
 simple
@@ -27582,7 +27981,8 @@ simple
 \end_layout
 
 \begin_layout Standard
-For example, to calculate all energy terms and write to a Grace-format file:
+For example,
+ to calculate all energy terms and write to a Grace-format file:
 \end_layout
 
 \begin_layout LyX-Code
@@ -27627,7 +28027,8 @@ esander [<name>] [out <filename>] [saveforces] [parmname <file>] [keepfiles]
 \end_layout
 
 \begin_layout Description
-[saveforces] If specified, save forces to frames.
+[saveforces] If specified,
+ save forces to frames.
  Requires writing frames in NetCDF format.
 \end_layout
 
@@ -27636,7 +28037,8 @@ esander [<name>] [out <filename>] [saveforces] [parmname <file>] [keepfiles]
 \begin_inset space ~
 \end_inset
 
-<file>] Name of temporary topology file (default: 'CpptrajEsander.parm7').
+<file>] Name of temporary topology file (default:
+ 'CpptrajEsander.parm7').
 \end_layout
 
 \begin_layout Description
@@ -27656,73 +28058,89 @@ vars>] Namelist variables supported by the sander API in format 'var <value>';
 \begin_layout Standard
 Calculate energies for input frames using the sander API.
  It requires compilation with the SANDER API (sanderlib).
- This can be considered as a faster alternative to energy post-processing
- with sander (imin = 5).
- Currently the following sander namelist variables are supported: 
+ This can be considered as a faster alternative to energy post-processing with sander (imin = 5).
+ Currently the following sander namelist variables are supported:
+ 
 \series bold
 extidel
 \series default
-, 
+,
+ 
 \series bold
 intdiel
 \series default
-, 
+,
+ 
 \series bold
 rgbmax
 \series default
-, 
+,
+ 
 \series bold
 saltcon
 \series default
-, 
+,
+ 
 \series bold
 cut
 \series default
-, 
+,
+ 
 \series bold
 dielc
 \series default
-, 
+,
+ 
 \series bold
 igb
 \series default
-, 
+,
+ 
 \series bold
 alpb
 \series default
-, 
+,
+ 
 \series bold
 gbsa
 \series default
-, 
+,
+ 
 \series bold
 lj1264
 \series default
-, 
+,
+ 
 \series bold
 ipb
 \series default
-, 
+,
+ 
 \series bold
 inp
 \series default
-, 
+,
+ 
 \series bold
 vdwmeth
 \series default
-, 
+,
+ 
 \series bold
 ew_type
 \series default
-, 
+,
+ 
 \series bold
 ntb
 \series default
-, 
+,
+ 
 \series bold
 ntf
 \series default
-, 
+,
+ 
 \series bold
 ntc
 \series default
@@ -27731,6 +28149,7 @@ ntc
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "chap:sander"
+nolink "false"
 
 \end_inset
 
@@ -27738,12 +28157,15 @@ reference "chap:sander"
 \end_layout
 
 \begin_layout Standard
-If ntb/cut/igb are not specified cpptraj will attempt to pick reasonable
- values based on the input system.
- The defaults for a non-periodic system are ntb=0, cut=9999.0, igb=1.
- The defaults for a periodic system are ntb=1, cut=8.0, igb=0.
- This currently requires writing a temporary Amber topology, the name of
- which can be set by 
+If ntb/cut/igb are not specified cpptraj will attempt to pick reasonable values based on the input system.
+ The defaults for a non-periodic system are ntb=0,
+ cut=9999.0,
+ igb=1.
+ The defaults for a periodic system are ntb=1,
+ cut=8.0,
+ igb=0.
+ This currently requires writing a temporary Amber topology,
+ the name of which can be set by 
 \series bold
 parmname
 \series default
@@ -27756,8 +28178,8 @@ keepfiles
 \end_layout
 
 \begin_layout Standard
-For example, to calculate energies for a non-periodic system using igb=1
- (the default) with GB surface area turned on (gbsa=1):
+For example,
+ to calculate energies for a non-periodic system using igb=1 (the default) with GB surface area turned on (gbsa=1):
 \end_layout
 
 \begin_layout LyX-Code
@@ -27825,8 +28247,8 @@ max
 \begin_inset space ~
 \end_inset
 
-<file>] File containing 1 for frames that were allowed, 0 for frames that
- were filtered.
+<file>] File containing 1 for frames that were allowed,
+ 0 for frames that were filtered.
 \end_layout
 
 \begin_layout Description
@@ -27834,13 +28256,12 @@ max
 \begin_inset space ~
 \end_inset
 
-<setname>] Filtered data set name containing 1 for allowed frames, 0 for
- filtered frames.
+<setname>] Filtered data set name containing 1 for allowed frames,
+ 0 for filtered frames.
 \end_layout
 
 \begin_layout Description
-[multi] Filter each set separately instead of all together (creates filter
- set for each input set).
+[multi] Filter each set separately instead of all together (creates filter set for each input set).
  Cannot be used with 'filterset'.
 \end_layout
 
@@ -27849,8 +28270,8 @@ max
 \begin_inset space ~
 \end_inset
 
-<set>] If specified, <set> will be filtered to only contain data that satisfies
- cutoffs.
+<set>] If specified,
+ <set> will be filtered to only contain data that satisfies cutoffs.
  Cannot be used with 'multi'.
 \end_layout
 
@@ -27860,8 +28281,7 @@ max
 \begin_inset space ~
 \end_inset
 
-<newname>] If specified a new set will be created from 'filterset' instead
- of replacing 'filterset'.
+<newname>] If specified a new set will be created from 'filterset' instead of replacing 'filterset'.
 \end_layout
 
 \end_deeper
@@ -27870,8 +28290,8 @@ max
 \begin_inset space ~
 \end_inset
 
-<count>] If specified, write number of elements passed and filtered to <countfil
-e>.
+<count>] If specified,
+ write number of elements passed and filtered to <countfile>.
  Cannot be used with 'multi'.
 \end_layout
 
@@ -27888,7 +28308,8 @@ passed
 \begin_inset Quotes erd
 \end_inset
 
-, 0 otherwise.
+,
+ 0 otherwise.
 \end_layout
 
 \begin_layout Description
@@ -27904,8 +28325,8 @@ Sets Created ('multi')
 \end_layout
 
 \begin_layout Description
-<setname>:<idx> For each input set (number with <idx>, starting from 0)
- contains 1 for elements that 
+<setname>:<idx> For each input set (number with <idx>,
+ starting from 0) contains 1 for elements that 
 \begin_inset Quotes eld
 \end_inset
 
@@ -27913,12 +28334,14 @@ passed
 \begin_inset Quotes erd
 \end_inset
 
-, 0 otherwise.
+,
+ 0 otherwise.
 \end_layout
 
 \end_deeper
 \begin_layout Standard
-For all following actions, only include frames that are between 
+For all following actions,
+ only include frames that are between 
 \series bold
 <min>
 \series default
@@ -27939,7 +28362,8 @@ For all following actions, only include frames that are between
 \series bold
 <max>
 \series default
- argument, and there must be as many 
+ argument,
+ and there must be as many 
 \series bold
 <min>
 \series default
@@ -27952,14 +28376,14 @@ For all following actions, only include frames that are between
 \series bold
 'multi'
 \series default
- is specified then only filter data sets will be created for each data set
- instead.
+ is specified then only filter data sets will be created for each data set instead.
  If 
 \series bold
 'filterset'
 \series default
- is specified, the specified <set> will be modified to only contain '1'
- frames; cannot be used with 
+ is specified,
+ the specified <set> will be modified to only contain '1' frames;
+ cannot be used with 
 \series bold
 'multi'
 \series default
@@ -27968,8 +28392,8 @@ For all following actions, only include frames that are between
 \series bold
 'newset'
 \series default
- is also specified, a new set will be created containing the '1' frames
- instead.
+ is also specified,
+ a new set will be created containing the '1' frames instead.
  The 
 \series bold
 'filterset'
@@ -27979,13 +28403,13 @@ For all following actions, only include frames that are between
 \series bold
 'countout'
 \series default
- is specified, the final number of elements passed and filtered out will
- be written to <countfile>.
+ is specified,
+ the final number of elements passed and filtered out will be written to <countfile>.
 \end_layout
 
 \begin_layout Standard
-For example, to write only frames in-between an RMSD of 0.7-0.8 Angstroms
- for a given input trajectory:
+For example,
+ to write only frames in-between an RMSD of 0.7-0.8 Angstroms for a given input trajectory:
 \end_layout
 
 \begin_layout LyX-Code
@@ -28031,6 +28455,7 @@ datafilter
 \begin_inset CommandInset ref
 LatexCommand pageref
 reference "subsec:cpptraj-datafilter"
+nolink "false"
 
 \end_inset
 
@@ -28092,21 +28517,22 @@ hetatm
 \begin_inset space ~
 \end_inset
 
-<mask> Mark atoms in mask as HETATM, order them after other atoms.
+<mask> Mark atoms in mask as HETATM,
+ order them after other atoms.
 \end_layout
 
 \end_deeper
 \end_deeper
 \begin_layout Standard
-Cpptraj (and most of Amber) expects that atom indices in molecules to increase
- monotonically.
- However, occasionally atom indices in molecules can become disordered or
- non-sequential, in which case cpptraj will print an error message such
- as the following:
+Cpptraj (and most of Amber) expects that atom indices in molecules to increase monotonically.
+ However,
+ occasionally atom indices in molecules can become disordered or non-sequential,
+ in which case cpptraj will print an error message such as the following:
 \end_layout
 
 \begin_layout LyX-Code
-Error: Atom 45 was assigned a lower molecule # (1) than previous atom (2).
+Error:
+ Atom 45 was assigned a lower molecule # (1) than previous atom (2).
 \end_layout
 
 \begin_layout Standard
@@ -28114,7 +28540,8 @@ and:
 \end_layout
 
 \begin_layout LyX-Code
-Error: Could not determine molecule information for <topology file>.
+Error:
+ Could not determine molecule information for <topology file>.
 \end_layout
 
 \begin_layout Standard
@@ -28132,10 +28559,9 @@ outprefix
 \end_layout
 
 \begin_layout Standard
-For example, given an out of order topology named 'outoforder.parm7' and
- a corresponding trajectory 'min1.crd', the following will produce a reordered
- topology named 'reorder.outoforder.parm7' and a reordered trajectory named
- 'reorder.mdcrd':
+For example,
+ given an out of order topology named 'outoforder.parm7' and a corresponding trajectory 'min1.crd',
+ the following will produce a reordered topology named 'reorder.outoforder.parm7' and a reordered trajectory named 'reorder.mdcrd':
 \end_layout
 
 \begin_layout LyX-Code
@@ -28159,8 +28585,11 @@ If
 \series bold
 'pdborder'
 \series default
- is specified, attempt to organize atoms by PDB information (i.e.
- Chain ID, original residue numbering, and insertion codes).
+ is specified,
+ attempt to organize atoms by PDB information (i.e.
+ Chain ID,
+ original residue numbering,
+ and insertion codes).
  Atoms optionally specified by 
 \series bold
 'hetatm
@@ -28172,8 +28601,8 @@ If
 ' will be placed after all other atoms.
  
 \emph on
-Note that the 'pdborder' keyword is still experimental, and requires that
- the Topology have PDB-type information present.
+Note that the 'pdborder' keyword is still experimental,
+ and requires that the Topology have PDB-type information present.
 \end_layout
 
 \begin_layout Subsection
@@ -28208,6 +28637,8 @@ gist (Grid Inhomogeneous Solvation Theory)
 \begin_layout LyX-Code
 gist
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -28240,8 +28671,7 @@ gist
 \end_layout
 
 \begin_layout LyX-Code
-     [floatfmt {double|scientific|general}] [floatwidth <fw>] [floatprec
- <fp>]
+     [floatfmt {double|scientific|general}] [floatwidth <fw>] [floatprec <fp>]
 \end_layout
 
 \begin_layout LyX-Code
@@ -28295,8 +28725,8 @@ literal "true"
 
 \begin_deeper
 \begin_layout Description
-[nopl] If specified, do not use the pair list for the order calculation
- (may be much slower).
+[nopl] If specified,
+ do not use the pair list for the order calculation (may be much slower).
 \end_layout
 
 \begin_layout Description
@@ -28313,8 +28743,7 @@ literal "true"
 \series bold
 [doeij]
 \series default
- Calculate the triangular matrix representing the water-water interactions
- between pairs of voxels (see below).
+ Calculate the triangular matrix representing the water-water interactions between pairs of voxels (see below).
 \end_layout
 
 \begin_layout Description
@@ -28338,15 +28767,18 @@ literal "true"
 
 rdval>]
 \series default
- Reference density of bulk water, used in computing
+ Reference density of bulk water,
+ used in computing
 \series bold
  g_O
 \series default
 ,
+
 \series bold
  g_H
 \series default
-, and the translational entropy.
+,
+ and the translational entropy.
  Default is 0.0334 molecules/Å
 \begin_inset Formula $^{3}$
 \end_inset
@@ -28383,7 +28815,9 @@ rdval>]
 
 <zval>]
 \series default
- Coordinates (Å) of the center of the grid (default 0.0, 0.0, 0.0).
+ Coordinates (Å) of the center of the grid (default 0.0,
+ 0.0,
+ 0.0).
 \end_layout
 
 \begin_layout Description
@@ -28391,8 +28825,8 @@ rdval>]
 \begin_inset space ~
 \end_inset
 
-<fitmask>] If specified, grid will be centered and rotated to follow atoms
- selected by <fitmask>.
+<fitmask>] If specified,
+ grid will be centered and rotated to follow atoms selected by <fitmask>.
 \end_layout
 
 \begin_layout Description
@@ -28412,8 +28846,9 @@ rdval>]
 
 <nz>]
 \series default
- Grid dimensions (number of bins/voxels) along each coordinate axis (default
- 40, 40, 40).
+ Grid dimensions (number of bins/voxels) along each coordinate axis (default 40,
+ 40,
+ 40).
 \end_layout
 
 \begin_layout Description
@@ -28487,7 +28922,8 @@ extension>] Output grid file name extension (default
 <output suffix>]
 \series default
  Suffix for main GIST output file name.
- If not specified, output file will be set to '<prefix>-output.dat'.
+ If not specified,
+ output file will be set to '<prefix>-output.dat'.
 \end_layout
 
 \begin_layout Description
@@ -28495,9 +28931,12 @@ extension>] Output grid file name extension (default
 \begin_inset space ~
 \end_inset
 
-{double|scientific|general}] Format for floating point values in GIST output
- file: double (regular fixed decimal point), scientific, or general (default,
- chooses fixed or scientific, whichever fits better).
+{double|scientific|general}] Format for floating point values in GIST output file:
+ double (regular fixed decimal point),
+ scientific,
+ or general (default,
+ chooses fixed or scientific,
+ whichever fits better).
 \end_layout
 
 \begin_layout Description
@@ -28537,7 +28976,8 @@ extension>] Output grid file name extension (default
 \end_inset
 
 suffix>] Suffix for main GIST info file name.
- If not specified, info will be written to standard output.
+ If not specified,
+ info will be written to standard output.
 \end_layout
 
 \begin_layout Description
@@ -28550,12 +28990,10 @@ suffix>] Suffix for main GIST info file name.
 \begin_inset space ~
 \end_inset
 
-<nlayers>] Number of layers of neighboring voxels that should be used when
- searching for nearest neighbors.
+<nlayers>] Number of layers of neighboring voxels that should be used when searching for nearest neighbors.
  This has to be at least 1 to obtain the correct entropy.
- Higher values can help to obtain better convergence of the translational
- and 6D entropy with little sampling or fine grid spacings, but increase
- the calculation time (default 1).
+ Higher values can help to obtain better convergence of the translational and 6D entropy with little sampling or fine grid spacings,
+ but increase the calculation time (default 1).
 \end_layout
 
 \begin_layout Description
@@ -28565,7 +29003,8 @@ suffix>] Suffix for main GIST info file name.
 
 <mask>] Selection mask for the solute.
  All other molecules will be solvent.
- If this is omitted, the standard solute/solvent assignment will be used.
+ If this is omitted,
+ the standard solute/solvent assignment will be used.
 \end_layout
 
 \begin_layout Description
@@ -28575,8 +29014,11 @@ suffix>] Suffix for main GIST info file name.
 
 <MOLS>] Comma-separated list of names of solvent molecules.
  Energies will be computed per solvent molecule.
- For the entropy, only the main solvent (the first one) will be used.
- Use, e.g., 
+ For the entropy,
+ only the main solvent (the first one) will be used.
+ Use,
+ e.g.,
+ 
 \series bold
 solventmols WAT,NA,CL
 \series default
@@ -28586,7 +29028,8 @@ solventmols WAT,NA,CL
 
 \begin_layout Description
 [nocom] Do not use the center of mass to define the molecular position.
- Instead, use the first atom in 
+ Instead,
+ use the first atom in 
 \series bold
 rigidatoms
 \series default
@@ -28608,16 +29051,19 @@ rigidatoms
 \end_inset
 
 <SUBST2>] Specifies how to define the molecular orientation for the entropy.
- By default, a simple heuristic will be used.
- This works for water, but not for all solvents.
- The atoms should be representative of the molecular orientation and should
- not be collinear.
+ By default,
+ a simple heuristic will be used.
+ This works for water,
+ but not for all solvents.
+ The atoms should be representative of the molecular orientation and should not be collinear.
  Note that the central atom goes first.
- For water, the default is equivalent to 
+ For water,
+ the default is equivalent to 
 \series bold
 rigidatoms O H1 H2
 \series default
-, corresponding to H1-O-H2 as the rigid substructure.
+,
+ corresponding to H1-O-H2 as the rigid substructure.
 \end_layout
 
 \begin_layout Description
@@ -28626,8 +29072,7 @@ rigidatoms O H1 H2
 
 \begin_layout Description
 [pme] Use particle mesh Ewald for the non-bonded electrostatics calculation.
- The van der Waals energy will be calculated using a long-range correction
- for periodicity.
+ The van der Waals energy will be calculated using a long-range correction for periodicity.
  Does not support 
 \series bold
 doeij
@@ -28670,8 +29115,8 @@ erfcdx
 \end_layout
 
 \begin_layout Description
-skinnb Used to determine pairlist atoms (added to cut, so pairlist cutoff
- is 
+skinnb Used to determine pairlist atoms (added to cut,
+ so pairlist cutoff is 
 \series bold
 cut
 \series default
@@ -28679,7 +29124,8 @@ cut
 \series bold
 skinnb
 \series default
-); included in order to maintain consistency with results from sander.
+);
+ included in order to maintain consistency with results from sander.
 \end_layout
 
 \begin_layout Description
@@ -28687,8 +29133,8 @@ ljswidth
 \begin_inset space ~
 \end_inset
 
-<width> If specified, use a force-switching form for the Lennard-Jones calculati
-on from <cutoff>-<width> to <cutoff>.
+<width> If specified,
+ use a force-switching form for the Lennard-Jones calculation from <cutoff>-<width> to <cutoff>.
 \end_layout
 
 \begin_layout Description
@@ -28704,8 +29150,7 @@ nfft
 \begin_inset space ~
 \end_inset
 
-<nfft1>,<nfft2>,<nfft3> Explicitly set the number of FFT grid points in
- each dimension.
+<nfft1>,<nfft2>,<nfft3> Explicitly set the number of FFT grid points in each dimension.
  Will be determined automatically if not specified.
 \end_layout
 
@@ -28715,13 +29160,12 @@ DataSet Aspects:
 \end_layout
 
 \begin_layout Description
-[gO] Number density of oxygen centers found in the voxel, in units of the
- bulk density.
+[gO] Number density of oxygen centers found in the voxel,
+ in units of the bulk density.
 \end_layout
 
 \begin_layout Description
-[gH] Number density of hydrogen centers found in the voxel in units of the
- reference bulk density.
+[gH] Number density of hydrogen centers found in the voxel in units of the reference bulk density.
 \end_layout
 
 \begin_layout Description
@@ -28745,8 +29189,7 @@ DataSet Aspects:
 \end_layout
 
 \begin_layout Description
-[neighbor] Mean number of waters neighboring the water molecules found in
- this voxel multiplied by the voxel number density.
+[neighbor] Mean number of waters neighboring the water molecules found in this voxel multiplied by the voxel number density.
 \end_layout
 
 \begin_layout Description
@@ -28790,7 +29233,9 @@ DataSets if the main solvent is not water:
 \series bold
 ELEM
 \series default
- in the main solvent, the atomic density relative to rho0 (e.g., 
+ in the main solvent,
+ the atomic density relative to rho0 (e.g.,
+ 
 \series bold
 gC
 \series default
@@ -28810,7 +29255,8 @@ DataSets if there are multiple solvents:
 \series bold
 NAME
 \series default
- (e.g., 
+ (e.g.,
+ 
 \series bold
 g_mol_WAT
 \series default
@@ -28830,7 +29276,8 @@ solventmols WAT,NA
 \series bold
 NAME
 \series default
- (e.g., 
+ (e.g.,
+ 
 \series bold
 Esw_mol_WAT
 \series default
@@ -28850,7 +29297,8 @@ solventmols WAT,NA
 \series bold
 NAME
 \series default
- (e.g., 
+ (e.g.,
+ 
 \series bold
 Eww_mol_WAT
 \series default
@@ -28875,21 +29323,20 @@ literal "true"
 
 \end_inset
 
- (GIST) is a method for analyzing the structure and thermodynamics of solvent
- in the vicinity of a solute molecule.
- The current implementation works for only water, but the method can be
- generalized to other solvents whose molecules are rigid like water, such
- as chloroform or dimethylsulfoxide (DMSO).
- GIST post-processes explicit solvent simulation data to create a three-dimensio
-nal mapping of water density and thermodynamic properties within a region
- of interest, which is defined by a user-specified 3D rectangular grid.
- The small grid boxes are referred to as voxels, and each voxel is associated
- with solvent properties.
+ (GIST) is a method for analyzing the structure and thermodynamics of solvent in the vicinity of a solute molecule.
+ The current implementation works for only water,
+ but the method can be generalized to other solvents whose molecules are rigid like water,
+ such as chloroform or dimethylsulfoxide (DMSO).
+ GIST post-processes explicit solvent simulation data to create a three-dimensional mapping of water density and thermodynamic properties within a region of interest,
+ which is defined by a user-specified 3D rectangular grid.
+ The small grid boxes are referred to as voxels,
+ and each voxel is associated with solvent properties.
  (See Fig.
  
 \begin_inset CommandInset ref
 LatexCommand ref
 reference "gist-1-1"
+nolink "false"
 
 \end_inset
 
@@ -28897,30 +29344,32 @@ reference "gist-1-1"
 \emph on
 cpptraj
 \emph default
- also calculates a number of other local water properties, as listed below.
+ also calculates a number of other local water properties,
+ as listed below.
  GIST works for the nonpolarizable water models currently supported by AMBER.
 \end_layout
 
 \begin_layout Standard
-In order to carry out a GIST calculation, you must have a trajectory file
- generated with explicit water, as well as the corresponding topology file.
- To generate the most readily interpretable results, it is recommended that
- the solute (e.g., a protein) be restrained into essentially one conformation.
- GIST will then provide information about the structure and thermodynamics
- of the solvent for that conformation.
- For a room-temperature simulation of a solvent-exposed binding site, and
- a grid-spacing of 0.5 Å, it is recommended that the simulation be at least
- 10-20 ns in duration, and it is also a good idea to check for convergence
- of the GIST properties you are interested in by loading and then processing
- successively more frames of your trajectory file.
- Because GIST assumes that the solute of interest comprises all molecules
- in the simulation that are not waters, it is a good idea to remove all
- counterions and cosolutes with cpptraj's strip command before running GIST.
+In order to carry out a GIST calculation,
+ you must have a trajectory file generated with explicit water,
+ as well as the corresponding topology file.
+ To generate the most readily interpretable results,
+ it is recommended that the solute (e.g.,
+ a protein) be restrained into essentially one conformation.
+ GIST will then provide information about the structure and thermodynamics of the solvent for that conformation.
+ For a room-temperature simulation of a solvent-exposed binding site,
+ and a grid-spacing of 0.5 Å,
+ it is recommended that the simulation be at least 10-20 ns in duration,
+ and it is also a good idea to check for convergence of the GIST properties you are interested in by loading and then processing successively more frames of your trajectory file.
+ Because GIST assumes that the solute of interest comprises all molecules in the simulation that are not waters,
+ it is a good idea to remove all counterions and cosolutes with cpptraj's strip command before running GIST.
  A sample series of cpptraj commands for running GIST is provided below.
 \end_layout
 
 \begin_layout Standard
 \begin_inset Float figure
+placement document
+alignment document
 wide false
 sideways false
 status open
@@ -28949,7 +29398,9 @@ centering
 \begin_inset Caption Standard
 
 \begin_layout Plain Layout
-Diagram, in 2D, of GIST's gridded water properties in a binding site.
+Diagram,
+ in 2D,
+ of GIST's gridded water properties in a binding site.
 \end_layout
 
 \end_inset
@@ -28977,7 +29428,8 @@ Although it is not mandatory to supply values of
 \series bold
 gridcntr
 \series default
-, 
+,
+ 
 \series bold
 griddim
 \series default
@@ -28985,8 +29437,9 @@ griddim
 \series bold
 gridspcn
 \series default
-, these parameters should be carefully chosen, because they determine the
- region to be analyzed (
+,
+ these parameters should be carefully chosen,
+ because they determine the region to be analyzed (
 \series bold
 gridcntr
 \series default
@@ -28999,13 +29452,13 @@ griddim
 gridspcn
 \series default
 ).
- In particular, although smaller grid spacings will give finer spatial resolutio
-n, longer simulation times will be needed to converge the properties in
- the smaller voxels that result.
- A larger grid spacing will allow earlier convergence, but will smooth the
- spatial distributions.
- When computing the sum over voxel values in a larger region, the result
- is independent of the grid spacing as long as 
+ In particular,
+ although smaller grid spacings will give finer spatial resolution,
+ longer simulation times will be needed to converge the properties in the smaller voxels that result.
+ A larger grid spacing will allow earlier convergence,
+ but will smooth the spatial distributions.
+ When computing the sum over voxel values in a larger region,
+ the result is independent of the grid spacing as long as 
 \series bold
 nlayers
 \series default
@@ -29017,38 +29470,45 @@ The reference density of water (
 \series bold
 rdval
 \series default
-) is taken by default to be the experimental number density of pure water
- at 300 K and 1 atm.
- However, different water models may yield slightly different bulk densities
- under these conditions, and the density also depends on T and P.
- If you know that the bulk density of the water model you are using, at
- the T and P of your simulation, deviates significantly from 0.0334 water
- molecules/Å
+) is taken by default to be the experimental number density of pure water at 300 K and 1 atm.
+ However,
+ different water models may yield slightly different bulk densities under these conditions,
+ and the density also depends on T and P.
+ If you know that the bulk density of the water model you are using,
+ at the T and P of your simulation,
+ deviates significantly from 0.0334 water molecules/Å
 \begin_inset Formula $^{3}$
 \end_inset
 
-, it would be advisable to supply the actual value with the 
+,
+ it would be advisable to supply the actual value with the 
 \series bold
 refdens
 \series default
- keyword, instead of allowing GIST to supply the default value.
+ keyword,
+ instead of allowing GIST to supply the default value.
 \end_layout
 
 \begin_layout Standard
-For GIST, a GPU accelerated version is available, in which the interaction
- energy is calculated using CUDA.
- When using the GPU accelerated version of GIST, the 
+For GIST,
+ a GPU accelerated version is available,
+ in which the interaction energy is calculated using CUDA.
+ When using the GPU accelerated version of GIST,
+ the 
 \series bold
 doeij 
 \series default
 keyword is not available.
- It is recommended to use a grid covering the entire box, when using the
- GPU implementation.
- You may also choose a smaller grid, but all interaction energies, i.e., each
- atom with each atom, will always be calculated independent of the chosen
- grid.
+ It is recommended to use a grid covering the entire box,
+ when using the GPU implementation.
+ You may also choose a smaller grid,
+ but all interaction energies,
+ i.e.,
+ each atom with each atom,
+ will always be calculated independent of the chosen grid.
  This ensures optimum performance when calculating the interaction energies.
- Thus, the additional time required to calculate the order parameters (
+ Thus,
+ the additional time required to calculate the order parameters (
 \series bold
 doorder
 \series default
@@ -29056,8 +29516,7 @@ doorder
 \end_layout
 
 \begin_layout Standard
-The nonbonded energy calculation can also be accelerated using particle
- mesh Ewald via the pme keyword (CPU only).
+The nonbonded energy calculation can also be accelerated using particle mesh Ewald via the pme keyword (CPU only).
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Chen2021"
@@ -29079,9 +29538,8 @@ GIST Output
 \end_layout
 
 \begin_layout Standard
-GIST generates a main output file and a collection of grid data files that
- by default are in Data Explorer format (.dx); this can be changed via the
- 
+GIST generates a main output file and a collection of grid data files that by default are in Data Explorer format (.dx);
+ this can be changed via the 
 \series bold
 ext
 \series default
@@ -29100,47 +29558,53 @@ literal "true"
 \series bold
 doeij
 \series default
- keyword is provided, GIST also writes out a matrix of water-water interactions
- between pairs of voxels.
- In addition, run details are written to stdout, which can be redirected
- into a log file.
+ keyword is provided,
+ GIST also writes out a matrix of water-water interactions between pairs of voxels.
+ In addition,
+ run details are written to stdout,
+ which can be redirected into a log file.
  
 \end_layout
 
 \begin_layout Standard
-Note that a number of quantities are written out as both densities and normalize
-d quantities.
- For example, the output file includes both the solute-water energy density
- and the normalized (per water) solute-water energy.
- In all cases, the normalized quantity at voxel 
+Note that a number of quantities are written out as both densities and normalized quantities.
+ For example,
+ the output file includes both the solute-water energy density and the normalized (per water) solute-water energy.
+ In all cases,
+ the normalized quantity at voxel 
 \begin_inset Formula $i$
 \end_inset
 
-, 
+,
+ 
 \begin_inset Formula $X_{i,norm}$
 \end_inset
 
- is related to the corresponding density, 
+ is related to the corresponding density,
+ 
 \begin_inset Formula $X_{i,dens}$
 \end_inset
 
-, by the relationship 
+,
+ by the relationship 
 \begin_inset Formula $X_{i,norm}=\rho_{i}X_{i,dens}$
 \end_inset
 
-, where 
+,
+ where 
 \begin_inset Formula $\rho_{i}$
 \end_inset
 
  is the number density of water in the voxel.
- The normalized quantity provides information regarding the nature of the
- water found in the voxel.
- The density has the property that, if the grid extended over the entire
- simulation volume, the total system quantity would be given by 
+ The normalized quantity provides information regarding the nature of the water found in the voxel.
+ The density has the property that,
+ if the grid extended over the entire simulation volume,
+ the total system quantity would be given by 
 \begin_inset Formula $X_{tot}=V_{voxel}\sum_{i}X_{i,dens}$
 \end_inset
 
-, where 
+,
+ where 
 \begin_inset Formula $V_{voxel}$
 \end_inset
 
@@ -29151,8 +29615,7 @@ d quantities.
 \begin_layout Standard
 The main output file takes the form of a space-delimited-variable file,
  where each row corresponds to one voxel of the grid.
- This file can easily be opened with and manipulated with spreadsheet programs
- like Excel and LibreOffice Calc.
+ This file can easily be opened with and manipulated with spreadsheet programs like Excel and LibreOffice Calc.
  The columns are as follows.
  
 \end_layout
@@ -29162,7 +29625,8 @@ The main output file takes the form of a space-delimited-variable file,
 \series bold
 index
 \series default
- - A unique, sequential integer assigned to each voxel
+ - A unique,
+ sequential integer assigned to each voxel
 \end_layout
 
 \begin_layout Itemize
@@ -29194,15 +29658,15 @@ zcoord
 \series bold
 population 
 \series default
-- Number of water molecule, 
+- Number of water molecule,
+ 
 \begin_inset Formula $n_{i}$
 \end_inset
 
-, found in the voxel over the entire simulation.
- A water molecule is deemed to populate a voxel if its oxygen coordinates
- are inside the voxel.
- The expectation value of this quantity increases in proportion to the length
- of the simulation.
+,
+ found in the voxel over the entire simulation.
+ A water molecule is deemed to populate a voxel if its oxygen coordinates are inside the voxel.
+ The expectation value of this quantity increases in proportion to the length of the simulation.
 \end_layout
 
 \begin_layout Itemize
@@ -29210,9 +29674,10 @@ population
 \series bold
 g_O
 \series default
- - Number density of oxygen centers found in the voxel, in units of the
- bulk density (rdval).
- Thus, the expectation value of 
+ - Number density of oxygen centers found in the voxel,
+ in units of the bulk density (rdval).
+ Thus,
+ the expectation value of 
 \series bold
 g_O
 \series default
@@ -29224,13 +29689,13 @@ g_O
 \series bold
 g_H
 \series default
- - Number density of hydrogen centers found in the voxel in units of the
- reference bulk density (2
+ - Number density of hydrogen centers found in the voxel in units of the reference bulk density (2
 \begin_inset Formula $\times$
 \end_inset
 
 rdval).
- Thus, the expectation value of 
+ Thus,
+ the expectation value of 
 \series bold
 g_H
 \series default
@@ -29255,8 +29720,7 @@ ELEM
 \series bold
 g_mol_NAME
 \series default
- - (if there is more than one solvent) Density of every solvent species
- 
+ - (if there is more than one solvent) Density of every solvent species 
 \series bold
 NAME
 \series default
@@ -29277,8 +29741,9 @@ dTStrans-dens
 \begin_inset Formula $^{3}$
 \end_inset
 
-), referenced to the translational entropy of bulk water, based on the value
- rdval.
+),
+ referenced to the translational entropy of bulk water,
+ based on the value rdval.
 \end_layout
 
 \begin_layout Itemize
@@ -29287,8 +29752,8 @@ dTStrans-dens
 dTStrans-norm
 \series default
  - First order translational entropy per water molecule (kcal/mole/molecule),
- referenced to the translational entropy of bulk water, based on the value
- rdval.
+ referenced to the translational entropy of bulk water,
+ based on the value rdval.
  The quantity
 \series bold
  dTStrans-norm
@@ -29313,7 +29778,8 @@ dTSorient-dens
 \begin_inset Formula $^{3}$
 \end_inset
 
-), referenced to bulk solvent (see below).
+),
+ referenced to bulk solvent (see below).
 \end_layout
 
 \begin_layout Itemize
@@ -29340,12 +29806,11 @@ Esw-dens
 \end_inset
 
 ).
- This is the interaction of the solvent in a given voxel with the entire
- solute.
- Both Lennard-Jones and electrostatic interactions are computed without
- any cutoff, within the minimum image convention but without Ewald summation.
- This quantity is referenced to bulk, in the trivial sense that the solute-solve
-nt interaction energy is zero in bulk.
+ This is the interaction of the solvent in a given voxel with the entire solute.
+ Both Lennard-Jones and electrostatic interactions are computed without any cutoff,
+ within the minimum image convention but without Ewald summation.
+ This quantity is referenced to bulk,
+ in the trivial sense that the solute-solvent interaction energy is zero in bulk.
 \end_layout
 
 \begin_layout Itemize
@@ -29366,18 +29831,19 @@ Esw-norm
 \series bold
 Eww-dens
 \series default
- - Mean water-water interaction energy density, scaled by ½ to prevent double-co
-unting, and not referenced to the corresponding bulk value of this quantity
- (see below).
- This quantity is one half of the mean interaction energy of the water in
- a given voxel with all other waters in the system, both on and off the
- GIST grid, divided by the volume of the voxel (kcal/mole/Å
+ - Mean water-water interaction energy density,
+ scaled by ½ to prevent double-counting,
+ and not referenced to the corresponding bulk value of this quantity (see below).
+ This quantity is one half of the mean interaction energy of the water in a given voxel with all other waters in the system,
+ both on and off the GIST grid,
+ divided by the volume of the voxel (kcal/mole/Å
 \begin_inset Formula $^{3}$
 \end_inset
 
 ).
- Unless PME is used, both Lennard-Jones and electrostatic interactions are
- computed without any cutoff, within the minimum image convention.
+ Unless PME is used,
+ both Lennard-Jones and electrostatic interactions are computed without any cutoff,
+ within the minimum image convention.
 \end_layout
 
 \begin_layout Itemize
@@ -29389,12 +29855,12 @@ Esw_mol_NAME-dens
 \series bold
 Esw_mol_NAME-norm
 \series default
- - (if there are multiple solvent species) Mean solute-solvent energy per
- molecule of species 
+ - (if there are multiple solvent species) Mean solute-solvent energy per molecule of species 
 \series bold
 NAME
 \series default
-, for each solvent specified in 
+,
+ for each solvent specified in 
 \series bold
 solventmols
 \series default
@@ -29415,12 +29881,12 @@ Eww_mol_NAME-dens
 \series bold
 Eww_mol_NAME-norm
 \series default
- - (if there are multiple solvent species) Mean solvent-solvent energy per
- molecule of species 
+ - (if there are multiple solvent species) Mean solvent-solvent energy per molecule of species 
 \series bold
 NAME
 \series default
-, for each solvent specified in 
+,
+ for each solvent specified in 
 \series bold
 solventmols
 \series default
@@ -29437,8 +29903,7 @@ Eww
 \series bold
 PME-norm
 \series default
- - (Only if PME was used) Mean PME solvent energy per water molecule (kcal/mole/
-molecule).
+ - (Only if PME was used) Mean PME solvent energy per water molecule (kcal/mole/molecule).
  This equals 
 \series bold
 PME-dens
@@ -29473,8 +29938,8 @@ Esw-norm
 \series bold
 Eww-norm
 \series default
- - Mean water-water interaction energy, normalized to the mean number of
- water molecules in the voxel (kcal/mole/water).
+ - Mean water-water interaction energy,
+ normalized to the mean number of water molecules in the voxel (kcal/mole/water).
  See prior column definition for details.
 \end_layout
 
@@ -29531,12 +29996,10 @@ Dipole-dens
 \series bold
 Neighbor-dens
 \series default
- - Mean number of waters neighboring the water molecules found in this voxel
- multiplied by the voxel number density.
- Two waters are considered neighbors if their oxygens are within 3.5 angstroms
- of each other.
- For any given frame, the contribution to the average is set to zero if
- no water is found in the voxel (units of number/Å
+ - Mean number of waters neighboring the water molecules found in this voxel multiplied by the voxel number density.
+ Two waters are considered neighbors if their oxygens are within 3.5 angstroms of each other.
+ For any given frame,
+ the contribution to the average is set to zero if no water is found in the voxel (units of number/Å
 \begin_inset Formula $^{3}$
 \end_inset
 
@@ -29548,8 +30011,8 @@ Neighbor-dens
 \series bold
 Neighbor-norm
 \series default
- - Mean number of neighboring water molecules, per water molecule found
- in the voxel (units of number per water).
+ - Mean number of neighboring water molecules,
+ per water molecule found in the voxel (units of number per water).
 \end_layout
 
 \begin_layout Itemize
@@ -29565,17 +30028,20 @@ literal "true"
 
 \end_inset
 
-, 
+,
+ 
 \begin_inset Formula $q_{tet}$
 \end_inset
 
-, for water molecules found in the voxel, normalized by the number of waters
- in the voxel.
+,
+ for water molecules found in the voxel,
+ normalized by the number of waters in the voxel.
  The order parameter for water 
 \begin_inset Formula $i$
 \end_inset
 
- in a given frame is given by: 
+ in a given frame is given by:
+ 
 \begin_inset Formula $q_{tet}(i)=1-\frac{3}{8}\sum_{j=1}^{3}\sum_{k=j+1}^{4}(cos\phi_{ijk}+\frac{1}{3})^{2}$
 \end_inset
 
@@ -29591,7 +30057,8 @@ literal "true"
 \begin_inset Formula $i$
 \end_inset
 
-, and 
+,
+ and 
 \begin_inset Formula $\phi_{ijk}$
 \end_inset
 
@@ -29599,34 +30066,48 @@ literal "true"
 \begin_inset Formula $i$
 \end_inset
 
-, 
+,
+ 
 \begin_inset Formula $j$
 \end_inset
 
-, and 
+,
+ and 
 \begin_inset Formula $k$
 \end_inset
 
 .
- If the doorder keyword is not provided or is set to FALSE, then this calculatio
-n will not be done, and the entries in this column will be set to zero.
-\end_layout
-
-\begin_layout Standard
-Grid files are provided for all computed quantities listed above, except
- that the normalized quantities are not included.
- The filenames are as follows: gist-gO.dx, gist-gH.dx, gist-dTStrans-dens.dx,
- gist-dTSorient-dens.dx, gist-Esw-dens.dx, gist-Eww-dens.dx, gist-dipolex-dens.dx,
- gist-dipoley-dens.dx, gist-dipolez-dens.dx, gist-dipole-dens.dx, gist-neighbor-den
-s.dx, gist-neighbor-norm.dx, gist-order-norm.dx.
+ If the doorder keyword is not provided or is set to FALSE,
+ then this calculation will not be done,
+ and the entries in this column will be set to zero.
+\end_layout
+
+\begin_layout Standard
+Grid files are provided for all computed quantities listed above,
+ except that the normalized quantities are not included.
+ The filenames are as follows:
+ gist-gO.dx,
+ gist-gH.dx,
+ gist-dTStrans-dens.dx,
+ gist-dTSorient-dens.dx,
+ gist-Esw-dens.dx,
+ gist-Eww-dens.dx,
+ gist-dipolex-dens.dx,
+ gist-dipoley-dens.dx,
+ gist-dipolez-dens.dx,
+ gist-dipole-dens.dx,
+ gist-neighbor-dens.dx,
+ gist-neighbor-norm.dx,
+ gist-order-norm.dx.
  If the 
 \series bold
 doorder
 \series default
- keyword is not provided, then the data in gist-order-norm.dx will all be
- zeroes.
- Note that the file of voxel water densities, gist-gO.dx, can be used as
- input to the program Placevent 
+ keyword is not provided,
+ then the data in gist-order-norm.dx will all be zeroes.
+ Note that the file of voxel water densities,
+ gist-gO.dx,
+ can be used as input to the program Placevent 
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Sindhikara"
@@ -29634,7 +30115,8 @@ literal "true"
 
 \end_inset
 
-, in order to define spherical hydration sites based on the density distribution.
+,
+ in order to define spherical hydration sites based on the density distribution.
  More detailed descriptions of the files follows:
 \end_layout
 
@@ -29676,10 +30158,10 @@ gist-dipolez-dens.dx
 gist-dTSorient-dens.dx
 \series default
  - Density weighted first order orientational entropy (kcal/mole/Å3).
- The more negative the isovalue, the more restricted or unfavorable the
- orientation of the water is.
- The value at bulk density is expected to be zero, most values will fall
- between 0 and -1.
+ The more negative the isovalue,
+ the more restricted or unfavorable the orientation of the water is.
+ The value at bulk density is expected to be zero,
+ most values will fall between 0 and -1.
 \end_layout
 
 \begin_layout Itemize
@@ -29688,9 +30170,10 @@ gist-dTSorient-dens.dx
 gist-dTStrans-dens.dx
 \series default
  - Density weighted first order tranlational entropy (kcal/mole/Å3).
- The more negative isovalue, the more restricted the water is positionally.
- The value at bulk density is expected to be zero, most values will fall
- between 0 and -1.
+ The more negative isovalue,
+ the more restricted the water is positionally.
+ The value at bulk density is expected to be zero,
+ most values will fall between 0 and -1.
  
 \end_layout
 
@@ -29701,10 +30184,10 @@ gist-Esw-dens.dx
 \series default
  - Density weighted Solute-Water interaction energy (kcal/mole/Å3).
  This is the interaction of the water with the entire solute.
- Both Lennard-Jones and electrostatic interactions are computed without
- any cutoff, within the minimum image convention.
- The more negative the number, the more favorable the interaction between
- the water and solute is.
+ Both Lennard-Jones and electrostatic interactions are computed without any cutoff,
+ within the minimum image convention.
+ The more negative the number,
+ the more favorable the interaction between the water and solute is.
  Isovalues will be negative numbers.
  
 \end_layout
@@ -29716,10 +30199,10 @@ gist-Eww-dens.dx
 \series default
  - Density weighted Water-Water interaction energy (kcal/mole/Å3).
  This is the interaction of the water with the entire solvent.
- Both Lennard-Jones and electrostatic interactions are computed without
- any cutoff, within the minimum image convention.
- The more negative the number, the more favorable the interaction between
- water within this voxel and all other water molucules is.
+ Both Lennard-Jones and electrostatic interactions are computed without any cutoff,
+ within the minimum image convention.
+ The more negative the number,
+ the more favorable the interaction between water within this voxel and all other water molucules is.
  Isovalues will be negative numbers.
  
 \end_layout
@@ -29729,12 +30212,11 @@ gist-Eww-dens.dx
 \series bold
 gist-gH.dx
 \series default
- - Number density of hydrogen centers found in the voxel, in units of the
- bulk density.
+ - Number density of hydrogen centers found in the voxel,
+ in units of the bulk density.
  The expectation value of g_H for a neat water system is unity.
  The units of this dx file are the density/bulk density.
- Therefore an isovalue of 1 represents every voxel at or greater than bulk
- density.
+ Therefore an isovalue of 1 represents every voxel at or greater than bulk density.
  
 \end_layout
 
@@ -29743,12 +30225,11 @@ gist-gH.dx
 \series bold
 gist-gO.dx
 \series default
- - Number density of oxygen centers found in the voxel, in units of the
- bulk density.
+ - Number density of oxygen centers found in the voxel,
+ in units of the bulk density.
  The expectation value of g_O for a neat water system is unity.
  The units of this dx file are the density/bulk density.
- Therefore an isovalue of 1 represents every voxel at or greater than bulk
- density.
+ Therefore an isovalue of 1 represents every voxel at or greater than bulk density.
  
 \end_layout
 
@@ -29757,10 +30238,9 @@ gist-gO.dx
 \series bold
 gist-neighbor-norm.dx
 \series default
- - Mean number of neighboring water molecules, per water molecule found
- in the voxel (units of number per water).
- Two waters are considered neighbors if their oxygens are within 3.5 Angstroms
- of each other.
+ - Mean number of neighboring water molecules,
+ per water molecule found in the voxel (units of number per water).
+ Two waters are considered neighbors if their oxygens are within 3.5 Angstroms of each other.
  
 \end_layout
 
@@ -29769,8 +30249,8 @@ gist-neighbor-norm.dx
 \series bold
 gist-order-norm.dx
 \series default
- - Average Tetrahedral Order Parameter for water molecules found in the
- voxel, normalized by the number of waters in the voxel.
+ - Average Tetrahedral Order Parameter for water molecules found in the voxel,
+ normalized by the number of waters in the voxel.
  
 \series bold
 doorder
@@ -29779,14 +30259,16 @@ doorder
 \end_layout
 
 \begin_layout Standard
-Similar grid files with other computed quantities can be generated by reading
- the gist.out file into a spreadsheet program, processing the numbers to
- generate a new column of voxel data of interest, and writing this column
- to an ascii text file.
- Then the Perl script write_dx_file.pl, which should be available on the
- GIST tutorial web-site, may be used to read in the column of data and create
- the corresponding dx file.
- The input format, and an example, are as follows: 
+Similar grid files with other computed quantities can be generated by reading the gist.out file into a spreadsheet program,
+ processing the numbers to generate a new column of voxel data of interest,
+ and writing this column to an ascii text file.
+ Then the Perl script write_dx_file.pl,
+ which should be available on the GIST tutorial web-site,
+ may be used to read in the column of data and create the corresponding dx file.
+ The input format,
+ and an example,
+ are as follows:
+ 
 \end_layout
 
 \begin_layout LyX-Code
@@ -29802,24 +30284,30 @@ Similar grid files with other computed quantities can be generated by reading
 \end_layout
 
 \begin_layout Standard
-If the doeij keyword is provided, GIST also writes a large file, Eww_ij.dat,
+If the doeij keyword is provided,
+ GIST also writes a large file,
+ Eww_ij.dat,
  containing the mean water-water interaction energies between pairs of voxels,
  scaled by ½.
  (See below.) This file has three columns.
- The first two columns are voxel indexes, 
+ The first two columns are voxel indexes,
+ 
 \begin_inset Formula $i$
 \end_inset
 
-, 
+,
+ 
 \begin_inset Formula $j$
 \end_inset
 
-, where 
+,
+ where 
 \begin_inset Formula $j>i$
 \end_inset
 
-, so that no pair appears more than once, and the third column is the mean
- interaction energy (kcal/mole) of water in voxels 
+,
+ so that no pair appears more than once,
+ and the third column is the mean interaction energy (kcal/mole) of water in voxels 
 \begin_inset Formula $i$
 \end_inset
 
@@ -29827,10 +30315,13 @@ If the doeij keyword is provided, GIST also writes a large file, Eww_ij.dat,
 \begin_inset Formula $j$
 \end_inset
 
-, scaled by ½.
- If the occupancy of either voxel is 0, such as for voxels covered by solute
- atoms, then the interaction energy is zero.
- In order to save space, such interactions are omitted from the file.
+,
+ scaled by ½.
+ If the occupancy of either voxel is 0,
+ such as for voxels covered by solute atoms,
+ then the interaction energy is zero.
+ In order to save space,
+ such interactions are omitted from the file.
  
 \end_layout
 
@@ -29843,16 +30334,21 @@ Sample cpptraj input file to run GIST
 \end_layout
 
 \begin_layout Standard
-The following input file, gist.in, causes cpptraj to read a parameter file
- named topology.top; read in the first 5000 frames of the trajectory file
- named trajectoryfile.mdcrd; strip out all Na and Cl ions; and carry out
- a GIST run which computes order parameters, uses a 41x41x45 grid centered
- at (25.0, 31.0, 30.0) with a spacing of 0.5 Å, uses the default bulk water
- density of 0.0334 molecules/Å
+The following input file,
+ gist.in,
+ causes cpptraj to read a parameter file named topology.top;
+ read in the first 5000 frames of the trajectory file named trajectoryfile.mdcrd;
+ strip out all Na and Cl ions;
+ and carry out a GIST run which computes order parameters,
+ uses a 41x41x45 grid centered at (25.0,
+ 31.0,
+ 30.0) with a spacing of 0.5 Å,
+ uses the default bulk water density of 0.0334 molecules/Å
 \begin_inset Formula $^{3}$
 \end_inset
 
-, and generates the main output file gist.out.
+,
+ and generates the main output file gist.out.
  
 \end_layout
 
@@ -29885,7 +30381,8 @@ go
 \end_layout
 
 \begin_layout Standard
-To execute this run in the background, use 
+To execute this run in the background,
+ use 
 \end_layout
 
 \begin_layout LyX-Code
@@ -29903,31 +30400,34 @@ Referencing GIST results to unperturbed (bulk) water
 \end_layout
 
 \begin_layout Standard
-Inhomogeneous fluid solvation theory, which is the basis of GIST, is designed
- to provide information on how water structure and thermodynamics around
- a solute molecule, such as a protein, are changed relative to the structure
- and thermodynamics of unperturbed (bulk) water.
- Accordingly, the quantities reported by GIST are most informative when
- the results are referenced to the corresponding bulk water properties.
- For the orientational entropy, the reference value is the same regardless
- of water model or conditions, because the first order orientational distributio
-n of water in the bulk is always uniform.
- Therefore, the GIST results for orientational entropies are already referenced
- to bulk.
- However, cpptraj reports unreferenced values for those GIST quantities
- whose reference values depend upon the water model and the simulation condition
-s; i.e., the energies.
- The translational entropy as well as the number densities will be referenced
- to bulk using the input referenced density or the default density value
- of 0.0334.
+Inhomogeneous fluid solvation theory,
+ which is the basis of GIST,
+ is designed to provide information on how water structure and thermodynamics around a solute molecule,
+ such as a protein,
+ are changed relative to the structure and thermodynamics of unperturbed (bulk) water.
+ Accordingly,
+ the quantities reported by GIST are most informative when the results are referenced to the corresponding bulk water properties.
+ For the orientational entropy,
+ the reference value is the same regardless of water model or conditions,
+ because the first order orientational distribution of water in the bulk is always uniform.
+ Therefore,
+ the GIST results for orientational entropies are already referenced to bulk.
+ However,
+ cpptraj reports unreferenced values for those GIST quantities whose reference values depend upon the water model and the simulation conditions;
+ i.e.,
+ the energies.
+ The translational entropy as well as the number densities will be referenced to bulk using the input referenced density or the default density value of 0.0334.
  The table below provides useful reference values for these quantities,
- computed for various water models at P=1atm, T=300K, using GIST in order
- to ensure a consistent minimum image treatment of periodic boundary conditions.
+ computed for various water models at P=1atm,
+ T=300K,
+ using GIST in order to ensure a consistent minimum image treatment of periodic boundary conditions.
  
 \end_layout
 
 \begin_layout Standard
 \begin_inset Float table
+placement document
+alignment document
 wide false
 sideways false
 status open
@@ -30207,21 +30707,22 @@ Water model energy and density.
 \end_layout
 
 \begin_layout Standard
-Users running calculations under significantly different conditions, or
- with different water models, should consider generating their own reference
- quantities by applying GIST to a simulation of pure water under their condition
-s of interest.
- The quantities of interest can then be obtained in their most precise available
- form by averaging over voxels, for the pure water simulation.
+Users running calculations under significantly different conditions,
+ or with different water models,
+ should consider generating their own reference quantities by applying GIST to a simulation of pure water under their conditions of interest.
+ The quantities of interest can then be obtained in their most precise available form by averaging over voxels,
+ for the pure water simulation.
  If the quantity of interest is 
 \begin_inset Formula $Q$
 \end_inset
 
-, then its average reference value is 
+,
+ then its average reference value is 
 \begin_inset Formula $Q_{reference}=\frac{\sum n_{i}Q_{i}}{\sum n_{i}}$
 \end_inset
 
-, where 
+,
+ where 
 \begin_inset Formula $Q_{i}$
 \end_inset
 
@@ -30229,31 +30730,35 @@ s of interest.
 \begin_inset Formula $n_{i}$
 \end_inset
 
- are, respectively, GIST's reported values of the quantity and the population
- in voxel 
+ are,
+ respectively,
+ GIST's reported values of the quantity and the population in voxel 
 \begin_inset Formula $i$
 \end_inset
 
 .
- The densities, 
+ The densities,
+ 
 \begin_inset Formula $\rho_{i}$
 \end_inset
 
-, are referenced to the corresponding bulk densities, 
+,
+ are referenced to the corresponding bulk densities,
+ 
 \begin_inset Formula $\rho^{o}$
 \end_inset
 
-, as 
+,
+ as 
 \begin_inset Formula $g_{i}=\rho_{i}/\rho^{o}$
 \end_inset
 
-, while the energy and entropy terms are referenced by subtracting their
- bulk values.
+,
+ while the energy and entropy terms are referenced by subtracting their bulk values.
 \end_layout
 
 \begin_layout Standard
-Note that the Eww reference needs to be subtracted from the normalized water-wat
-er energy 
+Note that the Eww reference needs to be subtracted from the normalized water-water energy 
 \series bold
 Eww-norm
 \series default
@@ -30270,7 +30775,8 @@ Eww-norm
 \begin_inset Formula $\rho=g_{O}\rho^{o}=\frac{N_{w}}{N_{f}V_{vox}}$
 \end_inset
 
-, where 
+,
+ where 
 \begin_inset Formula $N_{w}$
 \end_inset
 
@@ -30278,11 +30784,13 @@ Eww-norm
 \series bold
 population
 \series default
-), 
+),
+ 
 \begin_inset Formula $N_{f}$
 \end_inset
 
- is the number of frames, and 
+ is the number of frames,
+ and 
 \begin_inset Formula $V_{vox}$
 \end_inset
 
@@ -30300,28 +30808,31 @@ Interpreting GIST results
 \end_layout
 
 \begin_layout Standard
-GIST provides access to the first order entropies and the first- and second-orde
-r energies of inhomogeneous fluid solvation theory.
- Non-zero higher-order entropies exist but are not yet computationally accessibl
-e.
- However, for a pairwise additive force-field, such as those listed in the
- Table above, the energy is fully described at the second order provided
- by GIST.
+GIST provides access to the first order entropies and the first- and second-order energies of inhomogeneous fluid solvation theory.
+ Non-zero higher-order entropies exist but are not yet computationally accessible.
+ However,
+ for a pairwise additive force-field,
+ such as those listed in the Table above,
+ the energy is fully described at the second order provided by GIST.
  
 \end_layout
 
 \begin_layout Standard
-GIST is a research tool, and its applications (to, for example, protein-ligand
- binding and protein function) are still being explored.
+GIST is a research tool,
+ and its applications (to,
+ for example,
+ protein-ligand binding and protein function) are still being explored.
  The following general comments may be helpful to users studying GIST results.
  
 \end_layout
 
 \begin_layout Standard
 1.
- The water in voxels near a solute (e.g., a protein) almost always has unfavorable
- water-water interaction energies, relative to bulk, simply because the
- solute displaces water, resulting in fewer proximal water-water interactions.
+ The water in voxels near a solute (e.g.,
+ a protein) almost always has unfavorable water-water interaction energies,
+ relative to bulk,
+ simply because the solute displaces water,
+ resulting in fewer proximal water-water interactions.
  
 \end_layout
 
@@ -30336,10 +30847,11 @@ literal "true"
 \end_inset
 
  may be balanced by favorable water-solute interactions.
- If they are not, as may occur especially for voxels in small, hydrophobic
- pockets, then the net energy of the water in the voxel may be unfavorable
- relative to bulk, in which case a ligand which displaces water from the
- voxel into bulk may get a boost in affinity.
+ If they are not,
+ as may occur especially for voxels in small,
+ hydrophobic pockets,
+ then the net energy of the water in the voxel may be unfavorable relative to bulk,
+ in which case a ligand which displaces water from the voxel into bulk may get a boost in affinity.
  
 \end_layout
 
@@ -30347,51 +30859,49 @@ literal "true"
 3.
  Because the first order orientational distribution of bulk water is uniform,
  and a nonuniform distribution always has lower entropy than a uniform one,
- the solute can only lower the orientational entropy of water, relative
- to bulk.
- Thus, this term always opposes solvation, and displacing oriented water
- into the bulk is always favorable from the standpoint of orientational
- entropy.
+ the solute can only lower the orientational entropy of water,
+ relative to bulk.
+ Thus,
+ this term always opposes solvation,
+ and displacing oriented water into the bulk is always favorable from the standpoint of orientational entropy.
  
 \end_layout
 
 \begin_layout Standard
 4.
- Localized water, which corresponds to voxels with high water density, has
- a low first order translational entropy, and the translational entropy
- around a solute is lower than that in bulk, as a nonuniform translational
- distribution takes the place of the uniform translational distribution
- of bulk water.
+ Localized water,
+ which corresponds to voxels with high water density,
+ has a low first order translational entropy,
+ and the translational entropy around a solute is lower than that in bulk,
+ as a nonuniform translational distribution takes the place of the uniform translational distribution of bulk water.
  
 \end_layout
 
 \begin_layout Standard
 5.
- The displacement of highly oriented (low orientational entropy) and localized
- (low translational entropy) water into bulk leads to a favorable increase
- in these entropy terms.
+ The displacement of highly oriented (low orientational entropy) and localized (low translational entropy) water into bulk leads to a favorable increase in these entropy terms.
  
 \end_layout
 
 \begin_layout Standard
 6.
- However, highly oriented and localized water is often the consequence of
- strongly favorable polar interactions, such as hydrogen-bonding, between
- water and the solute.
- As a consequence, the net favorability of displacing such water is frequently
- a balance between favorable entropic consequences and unfavorable energetic
- consequences.
+ However,
+ highly oriented and localized water is often the consequence of strongly favorable polar interactions,
+ such as hydrogen-bonding,
+ between water and the solute.
+ As a consequence,
+ the net favorability of displacing such water is frequently a balance between favorable entropic consequences and unfavorable energetic consequences.
  
 \end_layout
 
 \begin_layout Standard
 7.
- The water-water energy associated with a given voxel accounts for the interacti
-ons of the waters in this voxel with all other waters in the system, including
- waters in other voxels.
- This quantity is multiplied by ½, so that, in a pure-water system where
- the GIST grid covers the entire simulation box, the sum over all voxels
- equals the correct mean water-water interaction energy.
+ The water-water energy associated with a given voxel accounts for the interactions of the waters in this voxel with all other waters in the system,
+ including waters in other voxels.
+ This quantity is multiplied by ½,
+ so that,
+ in a pure-water system where the GIST grid covers the entire simulation box,
+ the sum over all voxels equals the correct mean water-water interaction energy.
  Note that Reference 
 \begin_inset CommandInset citation
 LatexCommand citep
@@ -30406,9 +30916,10 @@ literal "true"
 
 \begin_layout Standard
 8.
- For a typical GIST application, in which the grid occupies only part of
- the simulation box, the energy bookkeeping can become complicated, as discussed
- in Section II.B.3 (page 044101-6) of Reference 
+ For a typical GIST application,
+ in which the grid occupies only part of the simulation box,
+ the energy bookkeeping can become complicated,
+ as discussed in Section II.B.3 (page 044101-6) of Reference 
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Nguyen-gist"
@@ -30417,18 +30928,19 @@ literal "true"
 \end_inset
 
 .
- That section also explains how one can compute the water-water energy associate
-d with a region 
+ That section also explains how one can compute the water-water energy associated with a region 
 \begin_inset Formula $R$
 \end_inset
 
- defined by a set of voxels, 
+ defined by a set of voxels,
+ 
 \begin_inset Formula $E_{WW}^{R}$
 \end_inset
 
 .
- The regional water-water energy, on a normalized (per water) basis, is
- given by 
+ The regional water-water energy,
+ on a normalized (per water) basis,
+ is given by 
 \begin_inset Formula $E_{WW}^{R}=2(\sum_{i\in R}E_{i,WW}-\sum_{i\in R}\sum_{j\in R,j>i}E_{i,j,WW})$
 \end_inset
 
@@ -30444,7 +30956,8 @@ d with a region
 \begin_inset Formula $R$
 \end_inset
 
-, 
+,
+ 
 \begin_inset Formula $E_{i,WW}$
 \end_inset
 
@@ -30452,7 +30965,8 @@ d with a region
 \begin_inset Formula $i$
 \end_inset
 
-, and 
+,
+ and 
 \begin_inset Formula $E_{i,j,WW}$
 \end_inset
 
@@ -30464,27 +30978,28 @@ d with a region
 \begin_inset Formula $j$
 \end_inset
 
-, taken from the file Eww_ij.dat.
- The extra factor of 2 in the present formula, relative to that in the paper,
- results from application of an extra factor of ½ to the reported water-water
- interaction energies here.
+,
+ taken from the file Eww_ij.dat.
+ The extra factor of 2 in the present formula,
+ relative to that in the paper,
+ results from application of an extra factor of ½ to the reported water-water interaction energies here.
  
 \end_layout
 
 \begin_layout Standard
 9.
- If the GIST grid contains the entire solute and the calculation is sufficently
- converged, the energy and first-order entropy of hydration can be calculated
- by numerical integration.
- E.g., the energy of hydration is 
+ If the GIST grid contains the entire solute and the calculation is sufficently converged,
+ the energy and first-order entropy of hydration can be calculated by numerical integration.
+ E.g.,
+ the energy of hydration is 
 \begin_inset Formula $\Delta E_{hyd}=\sum^{voxels}(E_{sw}^{dens}+E_{ww}^{dens})\times V_{vox}$
 \end_inset
 
 .
- For this, Eww has to be referenced carefully, since numerical inaccuracies
- can add up quickly.
- It can be advisable to omit all voxels above a certain distance to the
- solute to obtain more stable results.
+ For this,
+ Eww has to be referenced carefully,
+ since numerical inaccuracies can add up quickly.
+ It can be advisable to omit all voxels above a certain distance to the solute to obtain more stable results.
  
 \end_layout
 
@@ -30570,7 +31085,8 @@ grid [out <filename>]
 \begin_inset Quotes erd
 \end_inset
 
- extension for XPLOR format, 
+ extension for XPLOR format,
+ 
 \begin_inset Quotes eld
 \end_inset
 
@@ -30615,8 +31131,7 @@ name/tag>
 \begin_inset space ~
 \end_inset
 
-<nz> Set up grid using box information from a previously loaded reference
- structure.
+<nz> Set up grid using box information from a previously loaded reference structure.
  Currently the only way to set up non-orthogonal grids.
 \end_layout
 
@@ -30657,7 +31172,10 @@ name/tag>
 \begin_inset space ~
 \end_inset
 
-<cz>] Location of grid center, default is origin (0.0, 0.0, 0.0).
+<cz>] Location of grid center,
+ default is origin (0.0,
+ 0.0,
+ 0.0).
 \end_layout
 
 \begin_layout Description
@@ -30677,16 +31195,14 @@ name/tag>
 \begin_inset space ~
 \end_inset
 
-<mask>] Perform a best-fit rotation of the grid using the coordinates selected
- by <mask>.
+<mask>] Perform a best-fit rotation of the grid using the coordinates selected by <mask>.
 \end_layout
 
 \begin_deeper
 \begin_layout Description
-[noxalign] If specified, grid will not be re-oriented to align with Cartesian
- axes once binning is finished.
- Will affect file formats that do not store full unit cell vectors (like
- Xplor).
+[noxalign] If specified,
+ grid will not be re-oriented to align with Cartesian axes once binning is finished.
+ Will affect file formats that do not store full unit cell vectors (like Xplor).
 \end_layout
 
 \end_deeper
@@ -30745,8 +31261,8 @@ Other options:
 \begin_inset space ~
 \end_inset
 
-<density>]] Normalize grid bins by density: GridBin = GridBin / (Nframes
- * BinVolume * density).
+<density>]] Normalize grid bins by density:
+ GridBin = GridBin / (Nframes * BinVolume * density).
  Default particle density (molecules/Ang^3) for water based on 1.0 g/mL.
 \end_layout
 
@@ -30763,13 +31279,11 @@ Other options:
 \begin_inset space ~
 \end_inset
 
-<fraction>]] Write a pseudo-PDB of grid points that have density greater
- than <fraction> (default 0.80) of the grid max value.
+<fraction>]] Write a pseudo-PDB of grid points that have density greater than <fraction> (default 0.80) of the grid max value.
 \end_layout
 
 \begin_layout Description
-[{byres|bymol}] Grid the centers of mass of residues or molecules selected
- by <mask>.
+[{byres|bymol}] Grid the centers of mass of residues or molecules selected by <mask>.
 \end_layout
 
 \begin_layout Standard
@@ -30782,8 +31296,8 @@ Less common options:
 \end_inset
 
 <smooth>] Used to smooth density.
- The smoothing takes the form of GridBin = 0 if GridBin < smooth, otherwise
- GridBin = GridBin - (GridBin * exp[-(GridBin - smooth)^2 / (0.2 * smooth^2)]).
+ The smoothing takes the form of GridBin = 0 if GridBin < smooth,
+ otherwise GridBin = GridBin - (GridBin * exp[-(GridBin - smooth)^2 / (0.2 * smooth^2)]).
 \end_layout
 
 \begin_layout Description
@@ -30796,8 +31310,8 @@ Less common options:
 \begin_inset space ~
 \end_inset
 
-<madura>] Grid values lower than <madura> become flipped in sign, exposes
- low density.
+<madura>] Grid values lower than <madura> become flipped in sign,
+ exposes low density.
 \end_layout
 
 \begin_layout Standard
@@ -30852,8 +31366,8 @@ box
 \series bold
 center <mask>
 \series default
-); if either of these options are used the grid must be centered at the
- origin.
+);
+ if either of these options are used the grid must be centered at the origin.
  Note that the 
 \series bold
 \shape italic
@@ -30864,6 +31378,7 @@ bounds
 \begin_inset CommandInset ref
 LatexCommand vpageref
 reference "subsec:cpptraj-bounds"
+nolink "false"
 
 \end_inset
 
@@ -30872,8 +31387,8 @@ reference "subsec:cpptraj-bounds"
 
 \begin_layout Standard
 Note that when calculating grid densities for things like solvent/ions,
- the solute of interest (about which the atomic densities are binned) should
- be rms fit, centered and imaged prior to the 
+ the solute of interest (about which the atomic densities are binned) should be rms fit,
+ centered and imaged prior to the 
 \family sans
 \series bold
 \shape italic
@@ -30888,7 +31403,8 @@ grid
 negative
 \family default
 \series default
- is also specified, then these density will be stored as negative numbers.
+ is also specified,
+ then these density will be stored as negative numbers.
  Output can be in the XPLOR or OpenDX data formats.
 \end_layout
 
@@ -30897,7 +31413,8 @@ Examples
 \end_layout
 
 \begin_layout Standard
-Example 1: Grid water density around a solute.
+Example 1:
+ Grid water density around a solute.
  The solute is imaged to the origin and rms fit to the first frame.
  The grid will be centered on the origin as well.
 \end_layout
@@ -30927,7 +31444,8 @@ grid out.dx 20 0.5 20 0.5 20 0.5 :WAT@O
 \end_layout
 
 \begin_layout Standard
-Example 2: Grid water density around a solute.
+Example 2:
+ Grid water density around a solute.
  The grid is centered on the solute.
 \end_layout
 
@@ -30944,7 +31462,8 @@ grid out.dx 20 0.5 20 0.5 20 0.5 :WAT@O maskcenter :1-13
 \end_layout
 
 \begin_layout Standard
-Example 3: Grid water density around a solute.
+Example 3:
+ Grid water density around a solute.
  The grid is centered on the solute and rms-fit.
  The density obtained should be equivalent to the first example.
 \end_layout
@@ -30962,7 +31481,8 @@ grid out.dx 20 0.5 20 0.5 20 0.5 :WAT@O rmsfit :1-13
 \end_layout
 
 \begin_layout Standard
-Example 4: Generate grid from bounds command.
+Example 4:
+ Generate grid from bounds command.
 \end_layout
 
 \begin_layout LyX-Code
@@ -31006,7 +31526,8 @@ crdaction MyCoords grid bounds.xplor data MyGrid :WAT@O
 \end_layout
 
 \begin_layout Standard
-Example 5: Create non-orthogonal grid based on the box.
+Example 5:
+ Create non-orthogonal grid based on the box.
 \end_layout
 
 \begin_layout LyX-Code
@@ -31039,6 +31560,8 @@ name "subsec:cpptraj-hbond"
 \begin_layout LyX-Code
 hbond
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -31096,13 +31619,10 @@ hbond
 \begin_inset space ~
 \end_inset
 
-<filename>] Write # of solute-solute hydrogen bonds (aspect [UU]) vs time
- to this file.
- If searching for solute-solvent hydrogen bonds, write # of solute-solvent
- hydrogen bonds (aspect [UV]) and # of bridging solvent molecules (aspect
- [Bridge]), as well as the residue # of the bridging solvent and the solute
- residues being bridged with format '<solvent resnum>(<solute res1>+<solute
- res2>+...+),...' (aspect [ID]).
+<filename>] Write # of solute-solute hydrogen bonds (aspect [UU]) vs time to this file.
+ If searching for solute-solvent hydrogen bonds,
+ write # of solute-solvent hydrogen bonds (aspect [UV]) and # of bridging solvent molecules (aspect [Bridge]),
+ as well as the residue # of the bridging solvent and the solute residues being bridged with format '<solvent resnum>(<solute res1>+<solute res2>+...+),...' (aspect [ID]).
 \end_layout
 
 \begin_layout Description
@@ -31133,8 +31653,7 @@ hbond
 \end_inset
 
 <dmask>] Use atoms in <dmask> as solute donor heavy atoms.
- If 'donorhmask' not specified only atoms bonded to hydrogen will be considered
- donors.
+ If 'donorhmask' not specified only atoms bonded to hydrogen will be considered donors.
 \end_layout
 
 \begin_layout Description
@@ -31164,7 +31683,8 @@ hbond
 \end_layout
 
 \begin_layout Description
-[printatomnum] Add atom numbers to the output, in addtion to residue name,
+[printatomnum] Add atom numbers to the output,
+ in addtion to residue name,
  residue number and atom name.
 \end_layout
 
@@ -31200,8 +31720,8 @@ hbond
 \end_inset
 
 <filename>] Write solute-solvent hydrogen bond averages to <filename>.
- If not specified and 'avgout' is, solute-solvent hydrogen bonds averages
- will be written to that file.
+ If not specified and 'avgout' is,
+ solute-solvent hydrogen bonds averages will be written to that file.
 \end_layout
 
 \begin_layout Description
@@ -31210,7 +31730,8 @@ hbond
 \end_inset
 
 <filename>] Write information on detected solvent bridges to <filename>.
- If not specified, will be written to same place as 'solvout'.
+ If not specified,
+ will be written to same place as 'solvout'.
 \end_layout
 
 \begin_layout Description
@@ -31218,10 +31739,9 @@ hbond
 \end_layout
 
 \begin_layout Description
-[series] Save hydrogen bond formed (1.0) or not formed (0.0) per frame for
- any detected hydrogen bond.
- Solute-solute hydrogen bonds are saved with aspect [solutehb], solute-solvent
- hydrogen bonds are saved with aspect [solventhb].
+[series] Save hydrogen bond formed (1.0) or not formed (0.0) per frame for any detected hydrogen bond.
+ Solute-solute hydrogen bonds are saved with aspect [solutehb],
+ solute-solvent hydrogen bonds are saved with aspect [solventhb].
 \begin_inset Separator latexpar
 \end_inset
 
@@ -31247,11 +31767,9 @@ hbond
 
 \end_deeper
 \begin_layout Description
-[bseries] Save bridge formed (1.0) or not formed (0.0) per frame for any detected
- bridge.
- Bridges are saved with aspect [bridge_<indexlist>], where <indexlist> is
- an underscore ('_') delimited list of bridged atom/residue numbers (depending
- on 
+[bseries] Save bridge formed (1.0) or not formed (0.0) per frame for any detected bridge.
+ Bridges are saved with aspect [bridge_<indexlist>],
+ where <indexlist> is an underscore ('_') delimited list of bridged atom/residue numbers (depending on 
 \series bold
 bridgebyatom
 \series default
@@ -31269,8 +31787,8 @@ bridgebyatom
 
 \end_deeper
 \begin_layout Description
-[uuresmatrix] If specified, create a matrix with aspect [UUresmat] containing
- # of hydrogen bonds between each possible solute residue pair.
+[uuresmatrix] If specified,
+ create a matrix with aspect [UUresmat] containing # of hydrogen bonds between each possible solute residue pair.
 \end_layout
 
 \begin_deeper
@@ -31279,7 +31797,8 @@ bridgebyatom
 \begin_inset space ~
 \end_inset
 
-{none|frames}] Control how matrix is normalized: none=no normalization,
+{none|frames}] Control how matrix is normalized:
+ none=no normalization,
  frames=normalize by total # frames.
 \end_layout
 
@@ -31288,7 +31807,8 @@ bridgebyatom
 \begin_inset space ~
 \end_inset
 
-<file>] If specified, write matrix data to specified file.
+<file>] If specified,
+ write matrix data to specified file.
 \end_layout
 
 \end_deeper
@@ -31297,21 +31817,27 @@ bridgebyatom
 \begin_inset space ~
 \end_inset
 
-<comma-separated-list>] If specified, aplit the average hydrogen bond (
+<comma-separated-list>] If specified,
+ aplit the average hydrogen bond (
 \series bold
 avgout
 \series default
-, 
+,
+ 
 \series bold
 solvout
 \series default
-, 
+,
+ 
 \series bold
 bridgeout
 \series default
 ) analysis into sections delimited by the frame numbers.
- For example, 'splitframe 250,500,1000' will divide analysis into frames
- 1-249, 250-499, 500-999, and 1000 to end.
+ For example,
+ 'splitframe 250,500,1000' will divide analysis into frames 1-249,
+ 250-499,
+ 500-999,
+ and 1000 to end.
 \end_layout
 
 \begin_layout Standard
@@ -31355,8 +31881,7 @@ solventdonor
 \series bold
 solventacceptor
 \series default
-) String identifying bridging solvent residues and the solute residues they
- bridge.
+) String identifying bridging solvent residues and the solute residues they bridge.
 \end_layout
 
 \begin_layout Description
@@ -31364,8 +31889,9 @@ solventacceptor
 \series bold
 series
 \series default
- only) Time series for solute-solute hydrogen bonds; 1 for present, 0 for
- not present.
+ only) Time series for solute-solute hydrogen bonds;
+ 1 for present,
+ 0 for not present.
 \end_layout
 
 \begin_layout Description
@@ -31373,8 +31899,9 @@ series
 \series bold
 series
 \series default
- only) Time series for solute-solvent hydrogen bonds; 1 for present, 0 for
- not present.
+ only) Time series for solute-solvent hydrogen bonds;
+ 1 for present,
+ 0 for not present.
 \end_layout
 
 \begin_layout Description
@@ -31382,9 +31909,10 @@ series
 \series bold
 bseries
 \series default
- only) Time series for bridge; 1 for present, 0 for not present.
- The <indexlist> is an underscore ('_') delimited list of bridged atom/residue
- numbers (depending on 
+ only) Time series for bridge;
+ 1 for present,
+ 0 for not present.
+ The <indexlist> is an underscore ('_') delimited list of bridged atom/residue numbers (depending on 
 \series bold
 bridgebyatom
 \series default
@@ -31407,8 +31935,7 @@ Note that
 \series bold
 series
 \series default
- data sets are not generated until hydrogen bonds are actually determined
- (i.e.
+ data sets are not generated until hydrogen bonds are actually determined (i.e.
  
 \series bold
 run
@@ -31417,15 +31944,13 @@ run
 \end_layout
 
 \begin_layout Standard
-Determine hydrogen bonds in each coordinate frame using simple geometric
- criteria.
- A hydrogen bond is defined as being between an acceptor heavy atom A, a
- donor hydrogen atom H, and a donor heavy atom D.
- If the A to D distance is less than or equal to the distance cutoff and
- the A-H-D angle is greater than or equal to the angle cutoff a hydrogen
- bond is considered formed.
- Imaging of distances/angles is not performed by default, but can be turned
- on using the 
+Determine hydrogen bonds in each coordinate frame using simple geometric criteria.
+ A hydrogen bond is defined as being between an acceptor heavy atom A,
+ a donor hydrogen atom H,
+ and a donor heavy atom D.
+ If the A to D distance is less than or equal to the distance cutoff and the A-H-D angle is greater than or equal to the angle cutoff a hydrogen bond is considered formed.
+ Imaging of distances/angles is not performed by default,
+ but can be turned on using the 
 \series bold
 image
 \series default
@@ -31441,8 +31966,7 @@ If just
 \series bold
 <mask>
 \series default
- is specified donors and acceptors will be automatically determined from
- 
+ is specified donors and acceptors will be automatically determined from 
 \series bold
 <mask>
 \series default
@@ -31459,7 +31983,8 @@ donormask
 <dmask>
 \series default
  (only atoms bonded to hydrogen will be considered valid).
- Optionally, 
+ Optionally,
+ 
 \series bold
 donorhmask
 \series default
@@ -31509,7 +32034,8 @@ donormask
 \series bold
 <dmask>
 \series default
- will be used; no searching will occur in 
+ will be used;
+ no searching will occur in 
 \series bold
 <mask>
 \series default
@@ -31517,8 +32043,7 @@ donormask
 \end_layout
 
 \begin_layout Standard
-Automatic determination of hydrogen bond donors/acceptors uses the simplistic
- criterion that 
+Automatic determination of hydrogen bond donors/acceptors uses the simplistic criterion that 
 \begin_inset Quotes eld
 \end_inset
 
@@ -31526,8 +32051,14 @@ hydrogen bonds are FON
 \begin_inset Quotes erd
 \end_inset
 
-, i.e., hydrogens bonded to F, O, and N atoms are considered donors, and F,
- O, and N atoms are considered acceptors.
+,
+ i.e.,
+ hydrogens bonded to F,
+ O,
+ and N atoms are considered donors,
+ and F,
+ O,
+ and N atoms are considered acceptors.
  Intra-molecular hydrogen bonds can be ignored using the 
 \series bold
 nointramol
@@ -31536,13 +32067,13 @@ nointramol
 \end_layout
 
 \begin_layout Standard
-The number of hydrogen bonds present at each frame will be determined and
- written to the file specified by 
+The number of hydrogen bonds present at each frame will be determined and written to the file specified by 
 \series bold
 out
 \series default
 .
- If desired, the bridge [ID] data can be used in conjunction with the 
+ If desired,
+ the bridge [ID] data can be used in conjunction with the 
 \series bold
 \emph on
 keep
@@ -31555,6 +32086,7 @@ reference "subsec:cpptraj-keep"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
@@ -31571,19 +32103,20 @@ series
 lifetime
 \series default
 \shape default
-, see 
+,
+ see 
 \begin_inset CommandInset ref
 LatexCommand vpageref
 reference "subsec:cpptraj-lifetime"
+nolink "false"
 
 \end_inset
 
-); solute-solute hydrogen bonds will be saved to '<dataset name>[solutehb]'
- and solute-solvent hydrogen bonds will be saved to '<dataset name>[solventhb]'.
- The data set legends are set with the residues and atoms involved in the
- hydrogen bonds.
- In the case of solute to non-specific solvent hydrogen bonds, a V is used
- in place of solvent.
+);
+ solute-solute hydrogen bonds will be saved to '<dataset name>[solutehb]' and solute-solvent hydrogen bonds will be saved to '<dataset name>[solventhb]'.
+ The data set legends are set with the residues and atoms involved in the hydrogen bonds.
+ In the case of solute to non-specific solvent hydrogen bonds,
+ a V is used in place of solvent.
 \end_layout
 
 \begin_layout Standard
@@ -31591,9 +32124,7 @@ If
 \series bold
 avgout
 \series default
- is specified the average of each solute-solute hydrogen bond (sorted by
- population) formed over the course of the trajectory is printed with the
- format:
+ is specified the average of each solute-solute hydrogen bond (sorted by population) formed over the course of the trajectory is printed with the format:
 \end_layout
 
 \begin_layout LyX-Code
@@ -31605,11 +32136,13 @@ where
 \shape italic
 Acceptor
 \shape default
-, 
+,
+ 
 \shape italic
 DonorH
 \shape default
-, and 
+,
+ and 
 \shape italic
 Donor
 \shape default
@@ -31618,15 +32151,18 @@ Donor
 \shape italic
 Frames
 \shape default
- is the number of frames the bond is present, 
+ is the number of frames the bond is present,
+ 
 \shape italic
 Frac
 \shape default
- is the fraction of frames the bond is present, 
+ is the fraction of frames the bond is present,
+ 
 \shape italic
 AvgDist
 \shape default
- is the average distance of the bond when present, and 
+ is the average distance of the bond when present,
+ and 
 \shape italic
 AvgAng
 \shape default
@@ -31639,8 +32175,7 @@ printatomnum
 \end_layout
 
 \begin_layout Standard
-Solute to non-specific solvent hydrogen bonds can be tracked by using the
- 
+Solute to non-specific solvent hydrogen bonds can be tracked by using the 
 \series bold
 solventdonor
 \series default
@@ -31658,14 +32193,12 @@ bridging
 \end_inset
 
  solvent molecules (i.e.
- solvent that is hydrogen bonded to two or more different solute residues
- at the same time) will also be written to the file specified by 
+ solvent that is hydrogen bonded to two or more different solute residues at the same time) will also be written to the file specified by 
 \series bold
 out
 \series default
 .
- These keywords can also be used to track non-specific interactions with
- ions.
+ These keywords can also be used to track non-specific interactions with ions.
  If 
 \series bold
 avgout
@@ -31674,8 +32207,7 @@ avgout
 \series bold
 solvavg
 \series default
- is specified the average of each solute solvent hydrogen bond will be printed
- with the format:
+ is specified the average of each solute solvent hydrogen bond will be printed with the format:
 \end_layout
 
 \begin_layout LyX-Code
@@ -31687,11 +32219,13 @@ where
 \shape italic
 Acceptor
 \shape default
-, 
+,
+ 
 \shape italic
 DonorH
 \shape default
-, and 
+,
+ and 
 \shape italic
 Donor
 \shape default
@@ -31719,18 +32253,18 @@ SolventDnr
 \begin_inset Quotes erd
 \end_inset
 
- representing solvent, 
+ representing solvent,
+ 
 \shape italic
 Count
 \shape default
- is the total number of interactions between solute and solvent (note this
- can be greater than the total number of frames since for any given frame
- more than one solvent molecule can hydrogen bond to the same place on solute
- and vice versa), 
+ is the total number of interactions between solute and solvent (note this can be greater than the total number of frames since for any given frame more than one solvent molecule can hydrogen bond to the same place on solute and vice versa),
+ 
 \shape italic
 AvgDist
 \shape default
- is the average distance of the bond when present, and 
+ is the average distance of the bond when present,
+ and 
 \shape italic
 AvgAng
 \shape default
@@ -31743,18 +32277,17 @@ avgout
 \series bold
 bridgeout
 \series default
- is specified information on residues that were bridged by a solvent molecule
- over the course of the trajectory will be written to <bfilename> with format:
+ is specified information on residues that were bridged by a solvent molecule over the course of the trajectory will be written to <bfilename> with format:
 \end_layout
 
 \begin_layout LyX-Code
 Bridge Res <N0:RES0> <N1:RES1> ...
- , <X> frames.
+ ,
+ <X> frames.
 \end_layout
 
 \begin_layout Standard
-where '<N0:RES0> ...' is a list of residues that were bridged (residue # followed
- by residue name) and <X> is the number of frames the residues were bridged.
+where '<N0:RES0> ...' is a list of residues that were bridged (residue # followed by residue name) and <X> is the number of frames the residues were bridged.
 \end_layout
 
 \begin_layout Subsubsection*
@@ -31762,8 +32295,8 @@ hbond Examples
 \end_layout
 
 \begin_layout Standard
-To search for all hydrogen bonds within residues 1-22, writing the number
- of hydrogen bonds per frame to 
+To search for all hydrogen bonds within residues 1-22,
+ writing the number of hydrogen bonds per frame to 
 \begin_inset Quotes eld
 \end_inset
 
@@ -31787,8 +32320,7 @@ hbond :1-22 out nhb.dat avgout avghb.dat
 \end_layout
 
 \begin_layout Standard
-To search for all hydrogen bonds formed between donors in residue 1 and
- acceptors in residue 2:
+To search for all hydrogen bonds formed between donors in residue 1 and acceptors in residue 2:
 \end_layout
 
 \begin_layout LyX-Code
@@ -31796,8 +32328,8 @@ hbond donormask :1 acceptormask :2 out nhb.dat avgout avghb.dat
 \end_layout
 
 \begin_layout Standard
-To search for all intermolecular hydrogen bonds only and solute-solvent
- hydrogen bonds, saving time series data to HB:
+To search for all intermolecular hydrogen bonds only and solute-solvent hydrogen bonds,
+ saving time series data to HB:
 \end_layout
 
 \begin_layout LyX-Code
@@ -31823,8 +32355,7 @@ hbond HB out nhb.dat avgout solute_avg.dat
 \end_layout
 
 \begin_layout Standard
-To search for non-specific hydrogen bonds between solute and ions named
- Na+:
+To search for non-specific hydrogen bonds between solute and ions named Na+:
 \end_layout
 
 \begin_layout LyX-Code
@@ -31844,6 +32375,8 @@ image
 \begin_layout LyX-Code
 image
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -31865,13 +32398,16 @@ image
 
 \begin_deeper
 \begin_layout Description
-[origin] Image to coordinate origin (0.0, 0.0, 0.0); default is to image to
- box center.
+[origin] Image to coordinate origin (0.0,
+ 0.0,
+ 0.0);
+ default is to image to box center.
 \end_layout
 
 \begin_layout Description
-[center] For bymol/byres, image by center of mass; default is to image by
- first atom position.
+[center] For bymol/byres,
+ image by center of mass;
+ default is to image by first atom position.
 \end_layout
 
 \begin_layout Description
@@ -31889,8 +32425,8 @@ image
 \end_inset
 
 <commask>]] Image to truncated octahedron shape.
- If 'com <commask>' is given, image with respect to the center of mass of
- atoms in <commask>.
+ If 'com <commask>' is given,
+ image with respect to the center of mass of atoms in <commask>.
 \end_layout
 
 \begin_layout Description
@@ -31935,7 +32471,8 @@ image
 
 \end_deeper
 \begin_layout Standard
-Note this command is intended for advanced use; for most cases the 
+Note this command is intended for advanced use;
+ for most cases the 
 \series bold
 \shape italic
 autoimage
@@ -31945,8 +32482,8 @@ autoimage
 \end_layout
 
 \begin_layout Standard
-For periodic systems only, image molecules/residues/atoms that are outside
- of the box back into the box.
+For periodic systems only,
+ image molecules/residues/atoms that are outside of the box back into the box.
  Currently both orthorhombic and non-orthorhombic boxes are supported.
  A typical use of 
 \series bold
@@ -31961,9 +32498,9 @@ center
 \series default
 \shape default
 .
- For example, the following commands move all atoms so that the center of
- residue 1 is at the center of the box, then image so that all molecules
- that are outside the box after centering are wrapped back inside:
+ For example,
+ the following commands move all atoms so that the center of residue 1 is at the center of the box,
+ then image so that all molecules that are outside the box after centering are wrapped back inside:
 \end_layout
 
 \begin_layout LyX-Code
@@ -31976,11 +32513,11 @@ image
 
 \begin_layout Standard
 The xoffset etc.
- keywords can be used to shift the entire unit cell in a certain direction
- by the given factor, which can be useful for visualizing trajectories with
- periodic boundary conditions.
- For example, to generate a trajectory that is offset by 1.0 box length in
- the X direction, one could use:
+ keywords can be used to shift the entire unit cell in a certain direction by the given factor,
+ which can be useful for visualizing trajectories with periodic boundary conditions.
+ For example,
+ to generate a trajectory that is offset by 1.0 box length in the X direction,
+ one could use:
 \end_layout
 
 \begin_layout LyX-Code
@@ -31998,6 +32535,8 @@ jcoupling
 \begin_layout LyX-Code
 jcoupling
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -32040,8 +32579,9 @@ jcoupling
 \end_inset
 
 file>] File containing Karplus parameters.
- If not specified will check CPPTRAJHOME, AMBERHOME, and KARPLUS environment
- variables (see below).
+ If not specified will check CPPTRAJHOME,
+ AMBERHOME,
+ and KARPLUS environment variables (see below).
 \end_layout
 
 \begin_layout Description
@@ -32077,14 +32617,14 @@ Calculate J-coupling values for all dihedrals found within
 <mask>
 \series default
  (all atoms if no mask given).
- In order to use this function, Karplus parameters for all dihedrals which
- will be calculated must be loaded.
+ In order to use this function,
+ Karplus parameters for all dihedrals which will be calculated must be loaded.
  By default 
 \shape italic
 cpptraj
 \shape default
- will use the data found in either $CPPTRAJHOME/dat/Karplus.txt or $AMBERHOME/dat
-/Karplus.txt; if this is not found 
+ will use the data found in either $CPPTRAJHOME/dat/Karplus.txt or $AMBERHOME/dat/Karplus.txt;
+ if this is not found 
 \shape italic
 cpptraj
 \shape default
@@ -32093,8 +32633,7 @@ cpptraj
 \end_layout
 
 \begin_layout Standard
-In the Karplus parameter file each parameter set consists of two lines for
- each dihedral with the format:
+In the Karplus parameter file each parameter set consists of two lines for each dihedral with the format:
 \end_layout
 
 \begin_layout LyX-Code
@@ -32107,8 +32646,8 @@ In the Karplus parameter file each parameter set consists of two lines for
 
 \begin_layout Standard
 The first line defines the parameter set for a dihedral.
- <Type> is optional; if not given the form for calculating the J-coupling
- will be as described by Chou et al.
+ <Type> is optional;
+ if not given the form for calculating the J-coupling will be as described by Chou et al.
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Chou03"
@@ -32116,7 +32655,8 @@ literal "true"
 
 \end_inset
 
-; if 'C' the form will be as described by Perez et al.
+;
+ if 'C' the form will be as described by Perez et al.
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Perez01"
@@ -32126,16 +32666,23 @@ literal "true"
 
 .
  The <NameX> parameters define the four atoms involved in the dihedral.
- Each <NameX> parameter is 5 characters wide, starting with a plus '+',
+ Each <NameX> parameter is 5 characters wide,
+ starting with a plus '+',
  minus '-' or space ' ' character indicating the atom belongs to the next,
- previous, or current residue.
+ previous,
+ or current residue.
  The remaining 4 characters are the atom name.
- The parameters <A>, <B>, <C>, and <D> are floating point values 6 characters
- wide describing the Karplus parameters.
- For the 'C' form A, B, and C correspond to C0, C1, and C2; D is unused
- and should not be specified.
- The second line is a list of residue names (4 characters each) to which
- the dihedral applies.
+ The parameters <A>,
+ <B>,
+ <C>,
+ and <D> are floating point values 6 characters wide describing the Karplus parameters.
+ For the 'C' form A,
+ B,
+ and C correspond to C0,
+ C1,
+ and C2;
+ D is unused and should not be specified.
+ The second line is a list of residue names (4 characters each) to which the dihedral applies.
  For example:
 \end_layout
 
@@ -32149,7 +32696,9 @@ ILE VAL
 
 \begin_layout Standard
 Describes a dihedral between atoms HA-CA-CB-HB using the Perez et al.
- form with constants C0=5.40, C1=-1.37, C2=3.61 applied to ILE and VAL residues.
+ form with constants C0=5.40,
+ C1=-1.37,
+ C2=3.61 applied to ILE and VAL residues.
 \end_layout
 
 \begin_layout Standard
@@ -32166,7 +32715,8 @@ out <filename>
 \series bold
 <mask1>
 \series default
- printed along with its calculated J-coupling value for each frame, e.g.:
+ printed along with its calculated J-coupling value for each frame,
+ e.g.:
 \end_layout
 
 \begin_layout LyX-Code
@@ -32186,8 +32736,12 @@ out <filename>
 \end_layout
 
 \begin_layout Standard
-First the frame number is printed, then for each dihedral: Residue number,
- residue name, atom names 1-4 in the dihedral, the value of the dihedral,
+First the frame number is printed,
+ then for each dihedral:
+ Residue number,
+ residue name,
+ atom names 1-4 in the dihedral,
+ the value of the dihedral,
  the J-coupling value.
 \end_layout
 
@@ -32198,7 +32752,8 @@ In
 cpptraj
 \family default
 \shape default
- format, only the J-coupling value is written.
+ format,
+ only the J-coupling value is written.
 \end_layout
 
 \begin_layout Subsection
@@ -32259,6 +32814,7 @@ reference "subsec:cpptraj-hbond"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
@@ -32275,8 +32831,8 @@ nbridge
 \end_layout
 
 \begin_layout Description
-nobridgewarn If specified, suppress warnings for when active # bridges does
- not equal requested number.
+nobridgewarn If specified,
+ suppress warnings for when active # bridges does not equal requested number.
 \end_layout
 
 \begin_layout Description
@@ -32296,8 +32852,8 @@ bridgeresonly
 \begin_inset space ~
 \end_inset
 
-<range> If specified, only keep bridges that bridge residues in the <resrange>
- list.
+<range> If specified,
+ only keep bridges that bridge residues in the <resrange> list.
 \end_layout
 
 \end_deeper
@@ -32326,8 +32882,7 @@ charge
 \begin_inset space ~
 \end_inset
 
-charge> Scale charges so total charge of remaining atoms matches the specified
- <new charge>.
+charge> Scale charges so total charge of remaining atoms matches the specified <new charge>.
 \end_layout
 
 \begin_layout Description
@@ -32375,14 +32930,15 @@ hbond
 \emph default
  command to retain solute and only bridging residues (e.g.
  bridging waters).
- For example, the following run generates bridging data with the 
+ For example,
+ the following run generates bridging data with the 
 \series bold
 \emph on
 'hbond'
 \series default
 \emph default
- command in a first pass, then uses the bridge ID data to retain only 1
- single bridging water between residues 10 and 11:
+ command in a first pass,
+ then uses the bridge ID data to retain only 1 single bridging water between residues 10 and 11:
 \end_layout
 
 \begin_layout LyX-Code
@@ -32394,7 +32950,8 @@ trajin tz2.ortho.nc
 \end_layout
 
 \begin_layout LyX-Code
-# First pass, generate bridge time series 
+# First pass,
+ generate bridge time series 
 \end_layout
 
 \begin_layout LyX-Code
@@ -32406,7 +32963,8 @@ run
 \end_layout
 
 \begin_layout LyX-Code
-# Second pass, retain only frames where the bridge is present
+# Second pass,
+ retain only frames where the bridge is present
 \end_layout
 
 \begin_layout LyX-Code
@@ -32430,8 +32988,9 @@ run
 \end_layout
 
 \begin_layout Standard
-This run reads in bridge ID data from a previous hbond run and uses it to
- keep only residues 10, 11, and a bridging water:
+This run reads in bridge ID data from a previous hbond run and uses it to keep only residues 10,
+ 11,
+ and a bridging water:
 \end_layout
 
 \begin_layout LyX-Code
@@ -32486,8 +33045,8 @@ lessplit [out <filename prefix>] [average <avg filename>] <trajout args>
 \begin_inset space ~
 \end_inset
 
-prefix>] Write split LES trajectories to <filename prefix>.X, where X is
- an integer.
+prefix>] Write split LES trajectories to <filename prefix>.X,
+ where X is an integer.
 \end_layout
 
 \begin_layout Description
@@ -32532,6 +33091,8 @@ lie
 \begin_layout LyX-Code
 lie
 \begin_inset Index idx
+range none
+pageformat default
 status open
 
 \begin_layout Plain Layout
@@ -32566,17 +33127,15 @@ DataSet Aspects:
 
 \end_deeper
 \begin_layout Standard
-For each frame, calculate the non-bonded interactions between all atoms
- in <Ligand mask> with all atoms in <Surroundings mask>.
- Electrostatic and van der Waals interactions will be calculated for all
- atom pairs.
- A separate electrostatic and van der Waals cutoff can be applied, the default
- is 12.0 Angstroms for both.
+For each frame,
+ calculate the non-bonded interactions between all atoms in <Ligand mask> with all atoms in <Surroundings mask>.
+ Electrostatic and van der Waals interactions will be calculated for all atom pairs.
+ A separate electrostatic and van der Waals cutoff can be applied,
+ the default is 12.0 Angstroms for both.
  <dielc> is an optional dielectric constant.
- Either the electrostatic or van der Waals calculations can be suppressed
- via the keywords noelec and novdw, respectively.
- Periodic boundary conditions (and the minimum image convention) can be
- abandoned with the 
+ Either the electrostatic or van der Waals calculations can be suppressed via the keywords noelec and novdw,
+ respectively.
+ Periodic boundary conditions (and the minimum image convention) can be abandoned with the 
 \begin_inset Quotes eld
 \end_inset
 
@@ -32585,19 +33144,18 @@ nopbc
 \end_inset
 
  keyword.
- Note, however, that no prior imaging is performed if the frames contain
- periodic boundaries.
- This may be useful for instances when you are simulating a microscopic
- droplets.
+ Note,
+ however,
+ that no prior imaging is performed if the frames contain periodic boundaries.
+ This may be useful for instances when you are simulating a microscopic droplets.
 \end_layout
 
 \begin_layout Standard
-The electrostatic interactions are calculated according to a simple shifting
- function shown below.
- The data file will contain two data sets—one for electrostatic interactions
- and one for van der Waals interactions.
- Periodic topologies and trajectories are required (i.e., explicit solvent
- is necessary).
+The electrostatic interactions are calculated according to a simple shifting function shown below.
+ The data file will contain two data sets—
+one for electrostatic interactions and one for van der Waals interactions.
+ Periodic topologies and trajectories are required (i.e.,
+ explicit solvent is necessary).
  The minimum image convention is followed.
 \end_layout
 
@@ -32635,11 +33193,12 @@ order out <filename> [x|y|z] [scd] [unsat <mask>]
 
 \begin_deeper
 \begin_layout Description
-out Output file for order parameters: Sx, Sy, Sz (each succeeded by the
- standard deviation), and two estimates for the deuterium-order parameter
- |SCD| = 0.5Sz and |SCD| = -(2Sx + Sy)/3.
- If scd is set then the order parameter directly computed from the C-H vectors
- is output.
+out Output file for order parameters:
+ Sx,
+ Sy,
+ Sz (each succeeded by the standard deviation),
+ and two estimates for the deuterium-order parameter |SCD| = 0.5Sz and |SCD| = -(2Sx + Sy)/3.
+ If scd is set then the order parameter directly computed from the C-H vectors is output.
 \end_layout
 
 \begin_layout Description
@@ -32650,16 +33209,16 @@ x|y|z Reference axis.
 \begin_layout Description
 unsat Mask for unsaturated bonds.
  Sz is calculated for vector Cn-Cn+1.
- This is only relevant if scd (below) is not set, i.e.
+ This is only relevant if scd (below) is not set,
+ i.e.
  order parameters are calculated from carbon position only.
  
 \end_layout
 
 \begin_layout Description
-scd Calculate the deuterium-order parameter |SCD| directly from the C-H
- vectors (masks must contain C-H-H triplets, see below).
- Otherwise the order parameter is estimated from carbon positions only (masks
- must contain only relevant carbons).
+scd Calculate the deuterium-order parameter |SCD| directly from the C-H vectors (masks must contain C-H-H triplets,
+ see below).
+ Otherwise the order parameter is estimated from carbon positions only (masks must contain only relevant carbons).
  (false) 
 \end_layout
 
@@ -32696,11 +33255,13 @@ The order parameters
 \begin_inset Formula $S_{x}$
 \end_inset
 
-, 
+,
+ 
 \begin_inset Formula $S_{y}$
 \end_inset
 
-, 
+,
+ 
 \begin_inset Formula $S_{z}$
 \end_inset
 
@@ -32710,9 +33271,8 @@ The order parameters
 \series bold
 scd
 \series default
- the masks must be made up of C-H-H triples, hence hydrogens to double bonds
- must be enumerated twice while methyl groups require an additional mask
- which will also create two entries in the output.
+ the masks must be made up of C-H-H triples,
+ hence hydrogens to double bonds must be enumerated twice while methyl groups require an additional mask which will also create two entries in the output.
 \end_layout
 
 \begin_layout Standard
@@ -32727,7 +33287,8 @@ is the vector joining carbons
 \begin_inset Formula $C_{n+1}$
 \end_inset
 
-, 
+,
+ 
 \begin_inset Formula $S_{x}$
 \end_inset
 
@@ -32748,7 +33309,8 @@ is the vector joining carbons
 \begin_inset Formula $Sc=0.5<3\cos(2\theta)>-1$
 \end_inset
 
-, where 
+,
+ where 
 \begin_inset Formula $\theta$
 \end_inset
 
@@ -32762,15 +33324,18 @@ Example input (all atom names according to CHARMM27 force field for POPC).
 \end_layout
 
 \begin_layout Standard
-sn1 chain: order parameters 
+sn1 chain:
+ order parameters 
 \begin_inset Formula $S_{x}$
 \end_inset
 
-, 
+,
+ 
 \begin_inset Formula $S_{y}$
 \end_inset
 
-, 
+,
+ 
 \begin_inset Formula $S_{z}$
 \end_inset
 
@@ -32857,7 +33422,8 @@ out
 \end_layout
 
 \begin_layout Description
-p2 If specified, report raw <P2> values.
+p2 If specified,
+ report raw <P2> values.
 \end_layout
 
 \begin_layout Standard
@@ -32871,28 +33437,28 @@ DataSets Generated:
 
 \begin_layout Description
 <name>[H2]:<idx> Hold lipid order parameters for each C-H2.
- If no H2, the C-H1 value will be used.
+ If no H2,
+ the C-H1 value will be used.
 \end_layout
 
 \begin_layout Description
 <name>[H3]:<idx> Hold lipid order parameters for each C-H3.
- If no H3, the C-H2/C-H1 value will be used.
+ If no H3,
+ the C-H2/C-H1 value will be used.
 \end_layout
 
 \begin_layout Description
-<name>[SDHX]:<idx> Hold standard deviation of lipid order parameters for
- each C-HX.
+<name>[SDHX]:<idx> Hold standard deviation of lipid order parameters for each C-HX.
 \end_layout
 
 \end_deeper
 \begin_layout Standard
-Calculate lipid order parameters SCD (|<P2>|) for lipid chains in mask 
-  <mask>.
- Lipid chains are identified by carboxyl groups, i.e.
-   O-(C=O)-C1-...-CN, where C1 is the first carbon in the acyl chain   and
- CN is the last.
- Order parameters will be determined for each   hydrogen bonded to each
- carbon.
+Calculate lipid order parameters SCD (|<P2>|) for lipid chains in mask   <mask>.
+ Lipid chains are identified by carboxyl groups,
+ i.e.
+   O-(C=O)-C1-...-CN,
+ where C1 is the first carbon in the acyl chain   and CN is the last.
+ Order parameters will be determined for each   hydrogen bonded to each carbon.
  If 'p2' is specified the raw <P2>   values will be reported.
 \end_layout
 
@@ -32905,8 +33471,9 @@ makestructure <List of Args>
 \end_layout
 
 \begin_layout Standard
-Apply dihedrals to specified residues using arguments found in <List of
- Args>, where an argument is 1 or more of the following arg types: 
+Apply dihedrals to specified residues using arguments found in <List of Args>,
+ where an argument is 1 or more of the following arg types:
+ 
 \end_layout
 
 \begin_layout Subsubsection*
@@ -32918,10 +33485,9 @@ range>
 \end_layout
 
 \begin_layout Standard
-Apply secondary structure type (via phi/psi backbone angles) to residues
- in given range.
- If the secondary structure type is a turn, the residue range must correspond
- to a multiple of 2 residues.
+Apply secondary structure type (via phi/psi backbone angles) to residues in given range.
+ If the secondary structure type is a turn,
+ the residue range must correspond to a multiple of 2 residues.
 \end_layout
 
 \begin_layout Standard
@@ -32950,7 +33516,8 @@ Keyword
 \begin_layout Plain Layout
 
 \series bold
-phi, psi (deg.)
+phi,
+ psi (deg.)
 \end_layout
 
 \end_inset
@@ -32981,7 +33548,8 @@ alpha
 \begin_inset Text
 
 \begin_layout Plain Layout
--57.8, -47.0
+-57.8,
+ -47.0
 \end_layout
 
 \end_inset
@@ -33010,7 +33578,8 @@ left
 \begin_inset Text
 
 \begin_layout Plain Layout
--57.8, 47.0
+-57.8,
+ 47.0
 \end_layout
 
 \end_inset
@@ -33039,7 +33608,8 @@ pp2
 \begin_inset Text
 
 \begin_layout Plain Layout
--75.0, 145.0
+-75.0,
+ 145.0
 \end_layout
 
 \end_inset
@@ -33068,7 +33638,8 @@ hairpin
 \begin_inset Text
 
 \begin_layout Plain Layout
--100.0, 130.0
+-100.0,
+ 130.0
 \end_layout
 
 \end_inset
@@ -33097,7 +33668,8 @@ extended
 \begin_inset Text
 
 \begin_layout Plain Layout
--150.0, 155.0
+-150.0,
+ 155.0
 \end_layout
 
 \end_inset
@@ -33126,7 +33698,9 @@ typeI
 \begin_inset Text
 
 \begin_layout Plain Layout
--60.0, -30.0 | -90.0, 0.0
+-60.0,
+ -30.0 | -90.0,
+ 0.0
 \end_layout
 
 \end_inset
@@ -33155,7 +33729,9 @@ typeII
 \begin_inset Text
 
 \begin_layout Plain Layout
--60.0, 120.0 | 80.0, 0.0
+-60.0,
+ 120.0 | 80.0,
+ 0.0
 \end_layout
 
 \end_inset
@@ -33184,7 +33760,9 @@ typeVIII
 \begin_inset Text
 
 \begin_layout Plain Layout
--60.0, -30.0 | -120.0, 120.0
+-60.0,
+ -30.0 | -120.0,
+ 120.0
 \end_layout
 
 \end_inset
@@ -33213,7 +33791,9 @@ typeI'
 \begin_inset Text
 
 \begin_layout Plain Layout
-60.0, 30.0 | 90.0, 0.0
+60.0,
+ 30.0 | 90.0,
+ 0.0
 \end_layout
 
 \end_inset
@@ -33242,7 +33822,9 @@ typeII
 \begin_inset Text
 
 \begin_layout Plain Layout
-60.0, -120.0 | -80.0, 0.0
+60.0,
+ -120.0 | -80.0,
+ 0.0
 \end_layout
 
 \end_inset
@@ -33271,7 +33853,9 @@ typeVIa1
 \begin_inset Text
 
 \begin_layout Plain Layout
--60.0, 120.0 | -90.0, 0.0
+-60.0,
+ 120.0 | -90.0,
+ 0.0
 \end_layout
 
 \end_inset
@@ -33300,7 +33884,9 @@ typeVIa2
 \begin_inset Text
 
 \begin_layout Plain Layout
--120.0, 120.0 | -60.0, 0.0
+-120.0,
+ 120.0 | -60.0,
+ 0.0
 \end_layout
 
 \end_inset
@@ -33329,7 +33915,9 @@ typeVIb
 \begin_inset Text
 
 \begin_layout Plain Layout
--135.0, 135.0 | -75.0, 160.0
+-135.0,
+ 135.0 | -75.0,
+ 160.0
 \end_layout
 
 \end_inset
@@ -33368,10 +33956,9 @@ range>[:<phi>:<psi>]
 \end_layout
 
 \begin_layout Standard
-If <phi> and <psi> are given, define a custom secondary structure conformation
- named <custom_ss> and apply to residues in range.
- If <custom_ss> has been previously defined then apply it to residues in
- range.
+If <phi> and <psi> are given,
+ define a custom secondary structure conformation named <custom_ss> and apply to residues in range.
+ If <custom_ss> has been previously defined then apply it to residues in range.
 \end_layout
 
 \begin_layout Subsubsection*
@@ -33391,11 +33978,12 @@ range>[:<phi1>:<psi1>:<phi2>:<psi2>]
 \end_layout
 
 \begin_layout Standard
-If <phi1>, <psi1>, <phi2>, and <psi2> are given, defined a custom turn conformat
-ion named <custom_turn> and apply to residues in range (range must correspond
- to a multiple of 2 residues).
- If <custom_turn> has been previously defined then apply it to residues
- in range.
+If <phi1>,
+ <psi1>,
+ <phi2>,
+ and <psi2> are given,
+ defined a custom turn conformation named <custom_turn> and apply to residues in range (range must correspond to a multiple of 2 residues).
+ If <custom_turn> has been previously defined then apply it to residues in range.
 \end_layout
 
 \begin_layout Subsubsection*
@@ -33427,10 +34015,9 @@ type>:<angle>]
 \end_layout
 
 \begin_layout Standard
-If <dih type> and <angle> are given, apply <angle> to selected dihedrals
- of type in range.
- If <custom dih> has been previously defined then apply it to residues in
- range.
+If <dih type> and <angle> are given,
+ apply <angle> to selected dihedrals of type in range.
+ If <custom dih> has been previously defined then apply it to residues in range.
 \end_layout
 
 \begin_layout Subsubsection*
@@ -33450,7 +34037,10 @@ range>[:<at0>:<at1>:<at2>:<at3>:<angle>[:<offset>]]
 \end_layout
 
 \begin_layout Standard
-Apply <angle> to dihedral defined by atoms <at1>, <at2>, <at3>, and <at4>,
+Apply <angle> to dihedral defined by atoms <at1>,
+ <at2>,
+ <at3>,
+ and <at4>,
  or use previously defined <custom_dih>.
 \end_layout
 
@@ -33596,17 +34186,18 @@ range>[:<dih types>]] [refvalsout <file>] [founddihout <file>]
 \end_layout
 
 \begin_layout Standard
-Apply dihedrals from residues <ref_range> in previously loaded reference
- structure <refname> to dihedrals in <range>.
- If <ref range> is specified, use those residues from reference.
+Apply dihedrals from residues <ref_range> in previously loaded reference structure <refname> to dihedrals in <range>.
+ If <ref range> is specified,
+ use those residues from reference.
  The dihedral types to be used (see 
 \series bold
 <dih_type>
 \series default
- above) can be specified in a comma-separated list; default is phi/psi.
- Note that in order to specify <dih types>, <ref range> must be specified.
- The 'refvalsout' and 'founddihout' keywords can be used to print dihedrals
- found in the reference and target structures respectively to files.
+ above) can be specified in a comma-separated list;
+ default is phi/psi.
+ Note that in order to specify <dih types>,
+ <ref range> must be specified.
+ The 'refvalsout' and 'founddihout' keywords can be used to print dihedrals found in the reference and target structures respectively to files.
 \end_layout
 
 \begin_layout Subsubsection*
@@ -33622,9 +34213,11 @@ makestructure pp2:1-13
 \end_layout
 
 \begin_layout Standard
-Make residues 1 and 12 'extended', residues 6 and 7 a type I' turn, and
- two custom assignments, one (custom1) for residues 2-5, the other (custom2)
- for residues 8-11:
+Make residues 1 and 12 'extended',
+ residues 6 and 7 a type I' turn,
+ and two custom assignments,
+ one (custom1) for residues 2-5,
+ the other (custom2) for residues 8-11:
 \end_layout
 
 \begin_layout LyX-Code
@@ -33650,7 +34243,8 @@ makestructure extended:1,12
 \end_layout
 
 \begin_layout Standard
-Assign residue 5 phi 90 degrees, residues 6 and 7 phi=-70 and psi=60 degrees:
+Assign residue 5 phi 90 degrees,
+ residues 6 and 7 phi=-70 and psi=60 degrees:
 \end_layout
 
 \begin_layout LyX-Code
@@ -33658,8 +34252,7 @@ makestructure customdih:5:phi:90 custom:6,7:-70:60
 \end_layout
 
 \begin_layout Standard
-Create a new dihedral named chi1 and assign it a value of 35 degrees in
- residue 8:
+Create a new dihedral named chi1 and assign it a value of 35 degrees in residue 8:
 \end_layout
 
 \begin_layout LyX-Code
@@ -33667,8 +34260,9 @@ makestructure chi1:8:N:CA:CB:CG:35
 \end_layout
 
 \begin_layout Standard
-Assign 'extended' structure to residues 1 and 12, a custom turn to residues
- 2-5 and 8-11, and a typeI' turn to residues 6-7:
+Assign 'extended' structure to residues 1 and 12,
+ a custom turn to residues 2-5 and 8-11,
+ and a typeI' turn to residues 6-7:
 \end_layout
 
 \begin_layout LyX-Code
@@ -33724,6 +34318,8 @@ mask
 \begin_layout LyX-Code
 mask
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -33761,8 +34357,12 @@ out
 \begin_inset space ~
 \end_inset
 
-<filename> Write the frame, atom number, atom name, residue number, residue
- name, and molecule number for each selected atom to file.
+<filename> Write the frame,
+ atom number,
+ atom name,
+ residue number,
+ residue name,
+ and molecule number for each selected atom to file.
 \end_layout
 
 \begin_layout Description
@@ -33806,8 +34406,8 @@ trajargs
 \begin_inset space ~
 \end_inset
 
-args> When writing output PDB/Mol2, additional trajectory arguments to pass
- to the output trajectory.
+args> When writing output PDB/Mol2,
+ additional trajectory arguments to pass to the output trajectory.
 \end_layout
 
 \begin_layout Standard
@@ -33849,14 +34449,13 @@ For each frame determine all atoms that correspond to
 <mask>
 \series default
 .
- This is most useful when using distance-based masks, since the atoms in
- the mask are updated for every frame read in.
+ This is most useful when using distance-based masks,
+ since the atoms in the mask are updated for every frame read in.
  If 
 \series bold
 maskout
 \series default
- is specified information on all atoms in <mask> will be written to <filename>
- with format:
+ is specified information on all atoms in <mask> will be written to <filename> with format:
 \end_layout
 
 \begin_layout LyX-Code
@@ -33868,23 +34467,28 @@ where
 \family typewriter
 #Frame
 \family default
- is the frame number, 
+ is the frame number,
+ 
 \family typewriter
 AtomNum
 \family default
- is the number of the selected atom, 
+ is the number of the selected atom,
+ 
 \family typewriter
 Atom
 \family default
- is the name of the selected atom, 
+ is the name of the selected atom,
+ 
 \family typewriter
 ResNum
 \family default
- is the residue number of the selected atom, 
+ is the residue number of the selected atom,
+ 
 \family typewriter
 Res
 \family default
- is the residue name, and 
+ is the residue name,
+ and 
 \family typewriter
 MolNum
 \family default
@@ -33900,8 +34504,7 @@ maskpdb
 \series bold
 maskmol2
 \series default
- are specified a PDB/Mol2 file corresponding to <mask> will be written out
- every frame with name 
+ are specified a PDB/Mol2 file corresponding to <mask> will be written out every frame with name 
 \begin_inset Quotes eld
 \end_inset
 
@@ -33917,8 +34520,8 @@ maskmol2
 \end_layout
 
 \begin_layout Standard
-For example, to write out all residues within 3.0 Angstroms of residue 195
- that are named WAT to 
+For example,
+ to write out all residues within 3.0 Angstroms of residue 195 that are named WAT to 
 \begin_inset Quotes eld
 \end_inset
 
@@ -33926,7 +34529,8 @@ Res195WAT.dat
 \begin_inset Quotes erd
 \end_inset
 
-, as well as write out corresponding PDB files:
+,
+ as well as write out corresponding PDB files:
 \end_layout
 
 \begin_layout LyX-Code
@@ -33942,8 +34546,7 @@ mask
 \end_layout
 
 \begin_layout Standard
-To write all out atoms outside of 5.0 Angstroms of residues named ARG to
- PDB files with a chain ID of 'B':
+To write all out atoms outside of 5.0 Angstroms of residues named ARG to PDB files with a chain ID of 'B':
 \end_layout
 
 \begin_layout LyX-Code
@@ -34000,7 +34603,8 @@ matrix [out <filename>] [start <#>] [stop|end <#>] [offset <#>]
 
 <filename>]
 \series default
- If specified, write matrix to <filename>.
+ If specified,
+ write matrix to <filename>.
 \end_layout
 
 \begin_layout Description
@@ -34028,7 +34632,9 @@ matrix [out <filename>] [start <#>] [stop|end <#>] [offset <#>]
 
 <#>]
 \series default
- Start, stop, and offset frames to use (as a subset of all frames read in).
+ Start,
+ stop,
+ and offset frames to use (as a subset of all frames read in).
 \end_layout
 
 \begin_layout Description
@@ -34053,11 +34659,13 @@ byatom
 \family typewriter
 covar
 \family default
-, 
+,
+ 
 \family typewriter
 mwcovar
 \family default
-, and 
+,
+ and 
 \family typewriter
 ired
 \family default
@@ -34069,8 +34677,7 @@ ired
 \series bold
 byres
 \series default
- Write results by calculating an average for each residue (mass weighted
- if 
+ Write results by calculating an average for each residue (mass weighted if 
 \series bold
 mass
 \series default
@@ -34082,8 +34689,8 @@ mass
 \series bold
 bymask
 \series default
- Write average over <mask1>, and if <mask2> is specified <mask1> x <mask2>
- and <mask2> as well (mass weighted if 
+ Write average over <mask1>,
+ and if <mask2> is specified <mask1> x <mask2> and <mask2> as well (mass weighted if 
 \series bold
 mass
 \series default
@@ -34208,6 +34815,7 @@ ired
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-vector"
+nolink "false"
 
 \end_inset
 
@@ -34255,23 +34863,28 @@ Matrix dimensions will be of the order of N x M for
 \series bold
 dist
 \series default
-, 
+,
+ 
 \series bold
 correl
 \series default
-, 
+,
+ 
 \series bold
 idea
 \series default
-, and 
+,
+ and 
 \series bold
 ired
 \series default
-, 2N x 2N for 
+,
+ 2N x 2N for 
 \series bold
 dihcovar
 \series default
-, 3N x 3M for 
+,
+ 3N x 3M for 
 \series bold
 covar
 \series default
@@ -34279,7 +34892,8 @@ covar
 \series bold
 mwcovar
 \series default
-, and N(N-1) x N(N-1) / 4 for 
+,
+ and N(N-1) x N(N-1) / 4 for 
 \series bold
 distcovar
 \series default
@@ -34299,7 +34913,8 @@ dihcovar
 \series default
 \shape default
 \emph default
- otherwise, and M being the number of atoms in 
+ otherwise,
+ and M being the number of atoms in 
 \series bold
 <mask2>
 \series default
@@ -34316,8 +34931,8 @@ dihcovar
 \series bold
 ired
 \series default
-; the matrix will be made up of previously defined IRED vectors (see the
- 
+;
+ the matrix will be made up of previously defined IRED vectors (see the 
 \series bold
 \shape italic
 vector
@@ -34327,12 +34942,13 @@ vector
 \begin_inset CommandInset ref
 LatexCommand vpageref
 reference "subsec:cpptraj-vector"
+nolink "false"
 
 \end_inset
 
 ).
- Similarly no mask is required for dihcovar; dihedral data sets must have
- been previously defined.
+ Similarly no mask is required for dihcovar;
+ dihedral data sets must have been previously defined.
  Only one mask can be used with 
 \series bold
 distcovar
@@ -34342,8 +34958,8 @@ distcovar
 idea
 \series default
  matrices (i.e.
- they can be symmetric only), otherwise one or two masks can be used (for
- symmetric and full matrices respectively).
+ they can be symmetric only),
+ otherwise one or two masks can be used (for symmetric and full matrices respectively).
  If two masks are specified the number of atoms covered by 
 \shape italic
 mask1
@@ -34351,6 +34967,7 @@ mask1
  must be greater than or equal to the number of atoms covered by 
 \shape italic
 mask2,
+
 \shape default
  and on output 
 \series bold
@@ -34367,7 +34984,8 @@ corresponds to columns while
 \end_layout
 
 \begin_layout Standard
-Note that for backwards compatibility, output files written with '
+Note that for backwards compatibility,
+ output files written with '
 \series bold
 out <filename>
 \series default
@@ -34382,19 +35000,23 @@ reference "sec:Datafile-Commands"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
  for more details).
- To prevent any of these from taking effect, simply specify '
+ To prevent any of these from taking effect,
+ simply specify '
 \series bold
 header
 \series default
-', '
+',
+ '
 \series bold
 xcol
 \series default
-', and/or '
+',
+ and/or '
 \series bold
 nosquare2d
 \series default
@@ -34406,8 +35028,8 @@ out <filename>
 \end_layout
 
 \begin_layout Standard
-As a simple example, a distance matrix of all CA atoms is generated and
- output to 'distmat.dat'.
+As a simple example,
+ a distance matrix of all CA atoms is generated and output to 'distmat.dat'.
 \end_layout
 
 \begin_layout LyX-Code
@@ -34449,14 +35071,13 @@ mask1
 
 \begin_deeper
 \begin_layout Description
-byatom Report the minimum or maximum distance between atoms in <mask1> or
- between atoms in <mask1> and atoms in <mask2>.
+byatom Report the minimum or maximum distance between atoms in <mask1> or between atoms in <mask1> and atoms in <mask2>.
 \end_layout
 
 \begin_layout Description
-byres Report the minimum or maximum distance between all residue pairs selected
- by <mask1>, or pairs of residues selected by <mask1> and residues selected
- by <mask2> (excluding certain pairs, see 
+byres Report the minimum or maximum distance between all residue pairs selected by <mask1>,
+ or pairs of residues selected by <mask1> and residues selected by <mask2> (excluding certain pairs,
+ see 
 \series bold
 resoffset
 \series default
@@ -34464,9 +35085,8 @@ resoffset
 \end_layout
 
 \begin_layout Description
-bymol Report the minimum or maximum distance between all molecule pairs
- selected by <mask1>, or pairs of molecules selected by <mask1> and molecules
- selected by <mask2>.
+bymol Report the minimum or maximum distance between all molecule pairs selected by <mask1>,
+ or pairs of molecules selected by <mask1> and molecules selected by <mask2>.
 \end_layout
 
 \end_deeper
@@ -34499,8 +35119,8 @@ bymol Report the minimum or maximum distance between all molecule pairs
 \series bold
 byres
 \series default
-, ignore residue pairs if the difference in residue numbers is greater than
- the cutoff (default 1).
+,
+ ignore residue pairs if the difference in residue numbers is greater than the cutoff (default 1).
 \end_layout
 
 \begin_layout Standard
@@ -34512,7 +35132,8 @@ Data Sets Created:
 \series bold
 byatom
 \series default
-, a set containing the minimum or maximum distance for each frame.
+,
+ a set containing the minimum or maximum distance for each frame.
 \end_layout
 
 \begin_layout Description
@@ -34524,8 +35145,9 @@ byres
 \series bold
 b
 \series default
-ymol, a set containing the minimum or maximum distance between the residue/molec
-ule pair specified by the numbers in the aspect, e.g.
+ymol,
+ a set containing the minimum or maximum distance between the residue/molecule pair specified by the numbers in the aspect,
+ e.g.
  '<name>[1_3]' for 
 \series bold
 byres
@@ -34535,8 +35157,7 @@ byres
 
 \end_deeper
 \begin_layout Standard
-Calculate the minimum or maximum distance in Angstroms between atoms or
- residue/molecule pairs.
+Calculate the minimum or maximum distance in Angstroms between atoms or residue/molecule pairs.
 \end_layout
 
 \begin_layout Subsection
@@ -34577,12 +35198,12 @@ geom (
 \series bold
 maskcenter
 \series default
- only) If specified, use geometric center instead of center of mass.
+ only) If specified,
+ use geometric center instead of center of mass.
 \end_layout
 
 \begin_layout Description
-maskcenter Calculate distance from center of masks instead of between each
- atom.
+maskcenter Calculate distance from center of masks instead of between each atom.
 \end_layout
 
 \begin_layout Standard
@@ -34603,17 +35224,18 @@ Data Sets Created:
 
 \end_deeper
 \begin_layout Standard
-Calculate the shortest distance to an image, i.e.
- the distance to a neighboring unit cell, as well as the numbers of the
- atoms involved in the distance.
+Calculate the shortest distance to an image,
+ i.e.
+ the distance to a neighboring unit cell,
+ as well as the numbers of the atoms involved in the distance.
  By default the distance between each atom in <mask1> and <mask2> is considered;
  if 
 \series bold
 maskcenter
 \series default
  is specified the center of the masks is used.
- By convention, the lower atom number is saved as A1 and the higher is saved
- as A2.
+ By convention,
+ the lower atom number is saved as A1 and the higher is saved as A2.
 \end_layout
 
 \begin_layout Subsection
@@ -34623,6 +35245,8 @@ molsurf
 \begin_layout LyX-Code
 molsurf
 \begin_inset Index idx
+range none
+pageformat default
 status open
 
 \begin_layout Plain Layout
@@ -34711,15 +35335,14 @@ literal "true"
 
 \end_inset
 
- of atoms in <mask> (default all atoms if no mask specified) using routines
- from molsurf (originally developed by Paul Beroza) using the probe radius
- specified by 
+ of atoms in <mask> (default all atoms if no mask specified) using routines from molsurf (originally developed by Paul Beroza) using the probe radius specified by 
 \series bold
 probe
 \series default
  (1.4 Å if not specified).
  Note that if GB/VDW radii are not present in the topology file (e.g.
- for PDB files), then PARSE
+ for PDB files),
+ then PARSE
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Sitkoff94"
@@ -34728,9 +35351,10 @@ literal "true"
 \end_inset
 
  radii can be used.
- Also note that this routine only calculate absolute surface areas, i.e.
- it cannot be used to get the contribution of a subset of atoms to overall
- surface area; if such functionality is needed try the 
+ Also note that this routine only calculate absolute surface areas,
+ i.e.
+ it cannot be used to get the contribution of a subset of atoms to overall surface area;
+ if such functionality is needed try the 
 \series bold
 \emph on
 surf
@@ -34740,6 +35364,7 @@ surf
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_surf"
+nolink "false"
 
 \end_inset
 
@@ -34758,8 +35383,7 @@ name "subsec:cpptraj_multidihedral"
 \end_layout
 
 \begin_layout LyX-Code
-multidihedral [<name>] <dihedral types> [resrange <range/mask>] [out <filename>]
- [range360]
+multidihedral [<name>] <dihedral types> [resrange <range/mask>] [out <filename>] [range360]
 \end_layout
 
 \begin_layout LyX-Code
@@ -34767,8 +35391,8 @@ multidihedral [<name>] <dihedral types> [resrange <range/mask>] [out <filename>]
 \end_layout
 
 \begin_layout LyX-Code
-                  Offset -2=<at0><at1> in previous res, -1=<at0> in previous
- res,
+                  Offset -2=<at0><at1> in previous res,
+ -1=<at0> in previous res,
 \end_layout
 
 \begin_layout LyX-Code
@@ -34776,7 +35400,8 @@ multidihedral [<name>] <dihedral types> [resrange <range/mask>] [out <filename>]
 \end_layout
 
 \begin_layout LyX-Code
-                          1=<at3> in next res, 2=<at2><at3> in next res.
+                          1=<at3> in next res,
+ 2=<at2><at3> in next res.
 \end_layout
 
 \begin_layout LyX-Code
@@ -34806,7 +35431,8 @@ multidihedral [<name>] <dihedral types> [resrange <range/mask>] [out <filename>]
 \end_inset
 
 types> Dihedral types to look for.
- Note that chip is 'protein chi', chin is 'nucleic chi'.
+ Note that chip is 'protein chi',
+ chin is 'nucleic chi'.
 \end_layout
 
 \begin_layout Description
@@ -34816,7 +35442,8 @@ types> Dihedral types to look for.
 
 <range/mask>] Residue range to look for dihedrals in.
  Default is all solute residues.
- If a mask expression is given, use residues selected by the mask expression;
+ If a mask expression is given,
+ use residues selected by the mask expression;
  if any part of a residue is selcted it will be used.
 \end_layout
 
@@ -34837,8 +35464,10 @@ types> Dihedral types to look for.
 \begin_inset space ~
 \end_inset
 
-<name>:<a0>:<a1>:<a2>:<a3>[:<offset>] Search for a custom dihedral type
- called <name> using atom names <a0>, <a1>, <a2>, and <a3>.
+<name>:<a0>:<a1>:<a2>:<a3>[:<offset>] Search for a custom dihedral type called <name> using atom names <a0>,
+ <a1>,
+ <a2>,
+ and <a3>.
 \begin_inset Separator latexpar
 \end_inset
 
@@ -34847,8 +35476,12 @@ types> Dihedral types to look for.
 
 \begin_deeper
 \begin_layout Standard
-Offset: -2=<a0><a1> in previous res, -1=<a0> in previous res, 0=All <aX>
- in single res, 1=<a3> in next res, 2=<a2><a3> in next res.
+Offset:
+ -2=<a0><a1> in previous res,
+ -1=<a0> in previous res,
+ 0=All <aX> in single res,
+ 1=<a3> in next res,
+ 2=<a2><a3> in next res.
 \end_layout
 
 \end_deeper
@@ -34862,7 +35495,9 @@ DataSets Generated:
 \end_inset
 
 type>]:<#> Aspect corresponds to the dihedral type name (e.g.
- [phi], [psi], etc).
+ [phi],
+ [psi],
+ etc).
  The index is the residue number.
 \end_layout
 
@@ -34879,13 +35514,13 @@ run
 
 \begin_layout Standard
 Calculate specified dihedral angle types for residues in given range/mask.
- By default, dihedral angles are identified based on standard Amber atom
- names.
- The resulting data sets will have aspect equal to [<dihedral type>] and
- index equal to residue #.
- To differentiate the chi angle, chip is used for proteins and chin for
- nucleic acids.
- For example, to calculate all phi/psi dihedrals for residues 6 to 9:
+ By default,
+ dihedral angles are identified based on standard Amber atom names.
+ The resulting data sets will have aspect equal to [<dihedral type>] and index equal to residue #.
+ To differentiate the chi angle,
+ chip is used for proteins and chin for nucleic acids.
+ For example,
+ to calculate all phi/psi dihedrals for residues 6 to 9:
 \end_layout
 
 \begin_layout LyX-Code
@@ -34893,8 +35528,10 @@ multidihedral MyTorsions phi psi resrange 6-9 out PhiPsi_6-9.dat
 \end_layout
 
 \begin_layout Standard
-This will generate data sets named MyTorsions[phi]:6, MyTorsions[psi]:6,
- MyTorsions[phi]:7, etc.
+This will generate data sets named MyTorsions[phi]:6,
+ MyTorsions[psi]:6,
+ MyTorsions[phi]:7,
+ etc.
  Dihedrals other than those defined in 
 \series bold
 <dihedral types>
@@ -34905,8 +35542,10 @@ dihtype
 \series default
 .
  For example to create a custom dihedral type called chi1 using atoms N,
- CA, CB, and CG (all in the same residue), then search for and calculate
- the dihedral in all residues:
+ CA,
+ CB,
+ and CG (all in the same residue),
+ then search for and calculate the dihedral in all residues:
 \end_layout
 
 \begin_layout LyX-Code
@@ -34922,8 +35561,7 @@ multipucker [<name>] [<pucker types>] [out <filename>] [resrange <range>]
 \end_layout
 
 \begin_layout LyX-Code
-            [altona|cremer] [puckertype <name>:<a0>:<a1>:<a2>:<a3>:<a4>[:<a5>]
- ...]
+            [altona|cremer] [puckertype <name>:<a0>:<a1>:<a2>:<a3>:<a4>[:<a5>] ...]
 \end_layout
 
 \begin_layout LyX-Code
@@ -34974,9 +35612,11 @@ types> Pucker types to look for.
 \begin_inset space ~
 \end_inset
 
-<name>:<a0>:<a1>:<a2>:<a3>:<a4>[:<a5>] Search for a custom pucker type called
- <name> using atom names <a0>, <a1>, <a2>, <a3>, and <a4> (also <a5> for
- 6 atom puckers).
+<name>:<a0>:<a1>:<a2>:<a3>:<a4>[:<a5>] Search for a custom pucker type called <name> using atom names <a0>,
+ <a1>,
+ <a2>,
+ <a3>,
+ and <a4> (also <a5> for 6 atom puckers).
 \end_layout
 
 \begin_layout Description
@@ -35039,7 +35679,9 @@ DataSets Generated:
 \end_inset
 
 type>]:<#> Aspect corresponds to the pucker type name (e.g.
- [nucleic], [furanose], etc).
+ [nucleic],
+ [furanose],
+ etc).
  The index is the residue number.
 \end_layout
 
@@ -35082,16 +35724,17 @@ run
 
 \begin_layout Standard
 Calculate specified pucker types for residues in given range.
- By default, puckers are identified based on standard Amber atom names.
- The resulting data sets will have aspect equal to [<pucker type>] and index
- equal to residue #.
- In order to be identified as a pucker, all consecutive atoms in the pucker
- must be bonded, and the last atom of the pucker must be bonded to the first.
+ By default,
+ puckers are identified based on standard Amber atom names.
+ The resulting data sets will have aspect equal to [<pucker type>] and index equal to residue #.
+ In order to be identified as a pucker,
+ all consecutive atoms in the pucker must be bonded,
+ and the last atom of the pucker must be bonded to the first.
 \end_layout
 
 \begin_layout Standard
-For example, to calculate all nucleic acid ribose puckers for residues 6
- to 9:
+For example,
+ to calculate all nucleic acid ribose puckers for residues 6 to 9:
 \end_layout
 
 \begin_layout LyX-Code
@@ -35099,7 +35742,8 @@ multipucker MyPuckers nucleic resrange 6-9 out Pucker_6-9.dat
 \end_layout
 
 \begin_layout Standard
-This will generate data sets named MyPuckers[nucleic]:6, MyPuckers[nucleic]:7,
+This will generate data sets named MyPuckers[nucleic]:6,
+ MyPuckers[nucleic]:7,
  etc.
  Puckers other than those defined in 
 \series bold
@@ -35110,9 +35754,12 @@ This will generate data sets named MyPuckers[nucleic]:6, MyPuckers[nucleic]:7,
 puckertype
 \series default
 .
- For example to create a custom pucker type called furanoid using atoms
- C2, C3, C4, C5, and O2, then search for and calculate that pucker (with
- amplitudes) using the method of Cremer and Pople in all residues:
+ For example to create a custom pucker type called furanoid using atoms C2,
+ C3,
+ C4,
+ C5,
+ and O2,
+ then search for and calculate that pucker (with amplitudes) using the method of Cremer and Pople in all residues:
 \end_layout
 
 \begin_layout LyX-Code
@@ -35130,8 +35777,7 @@ multivector
 \end_layout
 
 \begin_layout LyX-Code
-multivector [<name>] [resrange <range>] name1 <name1> name2 <name2> [out
- <filename>]
+multivector [<name>] [resrange <range>] name1 <name1> name2 <name2> [out <filename>]
 \end_layout
 
 \begin_layout LyX-Code
@@ -35181,9 +35827,8 @@ name2
 
 \end_deeper
 \begin_layout Standard
-Search for and calculate atomic vectors between atoms named <name1> and
- <name2> in residues specified by the given <range>; each one is equivalent
- to the command '
+Search for and calculate atomic vectors between atoms named <name1> and <name2> in residues specified by the given <range>;
+ each one is equivalent to the command '
 \family typewriter
 \series bold
 vector
@@ -35191,9 +35836,9 @@ vector
  <name1> <name2>
 \family default
 '.
- For example, to calculate all vectors between atoms named 'N' and atoms
- named 'H' in residues 5-20, storing the results in data sets named NH and
- writing to NH.dat:
+ For example,
+ to calculate all vectors between atoms named 'N' and atoms named 'H' in residues 5-20,
+ storing the results in data sets named NH and writing to NH.dat:
 \end_layout
 
 \begin_layout LyX-Code
@@ -35207,6 +35852,8 @@ nastruct
 \begin_layout LyX-Code
 nastruct
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -35251,8 +35898,7 @@ nastruct
 \end_layout
 
 \begin_layout LyX-Code
-         [axisnameo <name>] [axisnamex <name>] [axisnamey <name>] [axisnamez
- <name>]
+         [axisnameo <name>] [axisnamex <name>] [axisnamey <name>] [axisnamez <name>]
 \end_layout
 
 \begin_layout LyX-Code
@@ -35294,14 +35940,16 @@ name>] Output data set name.
 \begin_inset space ~
 \end_inset
 
-<suffix>] File name suffix for output files; BP.<suffix> for base pair parameters
-, BPstep.<suffix> for base pair step parameters, and Helix.<suffix> for base
- pair step helical parameters.
+<suffix>] File name suffix for output files;
+ BP.<suffix> for base pair parameters,
+ BPstep.<suffix> for base pair step parameters,
+ and Helix.<suffix> for base pair step helical parameters.
  If 
 \series bold
 sscalc
 \series default
- is specified, also SS.<suffix> for parameters of consecutive bases in strands.
+ is specified,
+ also SS.<suffix> for parameters of consecutive bases in strands.
 \end_layout
 
 \begin_layout Description
@@ -35317,20 +35965,21 @@ naout
 \begin_inset space ~
 \end_inset
 
-<ResName>:{A,C,G,T,U}] Attempt to treat residues named <ResName> as if it
- were A, C, G, T, or U; useful for residues with modifications or non-standard
- residue names.
+<ResName>:{A,C,G,T,U}] Attempt to treat residues named <ResName> as if it were A,
+ C,
+ G,
+ T,
+ or U;
+ useful for residues with modifications or non-standard residue names.
  This will only work if enough reference atoms are present in <ResName>.
 \end_layout
 
 \begin_layout Description
-[calcnohb] Calculate parameters between bases in base pairs even if no hydrogen
- bonds present between them.
+[calcnohb] Calculate parameters between bases in base pairs even if no hydrogen bonds present between them.
 \end_layout
 
 \begin_layout Description
-[noframespaces] If specified there will be no spaces between frames in the
- 
+[noframespaces] If specified there will be no spaces between frames in the 
 \series bold
 naout
 \series default
@@ -35343,7 +35992,8 @@ naout
 \end_inset
 
 <file>] Specify a custom nucleic acid base reference.
- One file per custom residue; multiple 'baseref' keywords may be present.
+ One file per custom residue;
+ multiple 'baseref' keywords may be present.
  See below for details.
 \end_layout
 
@@ -35353,7 +36003,8 @@ naout
 \end_inset
 
 {3dna|babcock}] Specify axis conventions for calculating base pair parameters.
- If '3dna' (default), use conventions of 3DNA
+ If '3dna' (default),
+ use conventions of 3DNA
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Lu2003"
@@ -35361,8 +36012,10 @@ literal "true"
 
 \end_inset
 
-; flip Y and Z of complimentary base for antiparallel.
- If 'babcock', use conventions of Babcock et al.
+;
+ flip Y and Z of complimentary base for antiparallel.
+ If 'babcock',
+ use conventions of Babcock et al.
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Babcock94"
@@ -35370,13 +36023,13 @@ literal "true"
 
 \end_inset
 
- ; flip Y and Z of complimentary base for antiparallel, flip X and Y for
- parallel.
+ ;
+ flip Y and Z of complimentary base for antiparallel,
+ flip X and Y for parallel.
 \end_layout
 
 \begin_layout Description
-[allhb] Report the total number of hydrogen bonds detected instead of just
- the number of Watson-Crick-Franklin hydrogen bonds.
+[allhb] Report the total number of hydrogen bonds detected instead of just the number of Watson-Crick-Franklin hydrogen bonds.
 \end_layout
 
 \begin_layout Description
@@ -35384,8 +36037,7 @@ literal "true"
 \begin_inset space ~
 \end_inset
 
-<hbcut>] Distance cutoff (in Angstroms) for determining hydrogen bonds between
- bases (default 3.5).
+<hbcut>] Distance cutoff (in Angstroms) for determining hydrogen bonds between bases (default 3.5).
 \end_layout
 
 \begin_layout Description
@@ -35393,13 +36045,12 @@ literal "true"
 \begin_inset space ~
 \end_inset
 
-<origincut>] Distance cutoff (in Angstroms) between base pair axis origins
- for determining which bases are eligible for base-pairing (default 2.5).
+<origincut>] Distance cutoff (in Angstroms) between base pair axis origins for determining which bases are eligible for base-pairing (default 2.5).
 \end_layout
 
 \begin_layout Description
-[altona] Use method of Altona & Sundaralingam to calculate sugar pucker
- (default, see 
+[altona] Use method of Altona & Sundaralingam to calculate sugar pucker (default,
+ see 
 \series bold
 \shape italic
 pucker
@@ -35419,14 +36070,12 @@ pucker
 \end_layout
 
 \begin_layout Description
-[zcut] Distance cutoff (in Angstroms) between base reference axes along
- the Z axis (i.e.
+[zcut] Distance cutoff (in Angstroms) between base reference axes along the Z axis (i.e.
  stagger) for determining base pairing (default 2).
 \end_layout
 
 \begin_layout Description
-[zanglecut] Angle cutoff (in degrees) between base reference Z axes for
- determining base pairing (default 65).
+[zanglecut] Angle cutoff (in degrees) between base reference Z axes for determining base pairing (default 65).
 \end_layout
 
 \begin_layout Description
@@ -35439,7 +36088,8 @@ pucker
 
 \begin_deeper
 \begin_layout Description
-simple Use P-P distance for major groove, O4-O4 distance for minor groove.
+simple Use P-P distance for major groove,
+ O4-O4 distance for minor groove.
  Output to 'BP.<suffix>'.
 \end_layout
 
@@ -35471,8 +36121,7 @@ literal "true"
 \begin_inset space ~
 \end_inset
 
-<arg>] Trajectory argument to pass to base axes trajectory file (can specify
- more than once).
+<arg>] Trajectory argument to pass to base axes trajectory file (can specify more than once).
 \end_layout
 
 \begin_layout Description
@@ -35498,8 +36147,7 @@ literal "true"
 \begin_inset space ~
 \end_inset
 
-<arg>] Trajectory argument to pass to base pair axes trajectory file (can
- specify more than once).
+<arg>] Trajectory argument to pass to base pair axes trajectory file (can specify more than once).
 \end_layout
 
 \begin_layout Description
@@ -35525,8 +36173,7 @@ literal "true"
 \begin_inset space ~
 \end_inset
 
-<arg>] Trajectory argument to pass to base pair step axes trajectory file
- (can specify more than once).
+<arg>] Trajectory argument to pass to base pair step axes trajectory file (can specify more than once).
 \end_layout
 
 \begin_layout Description
@@ -35620,9 +36267,9 @@ pairs
 \end_inset
 
 <b1>-<b2>,...] User specified base pairing.
- Base pairs are specified in a comma-separated list after the 'pairs' keyword
- as <b1>-<b2>, where <b1> and <b2> are the residue numbers of bases in the
- base pair, e.g.
+ Base pairs are specified in a comma-separated list after the 'pairs' keyword as <b1>-<b2>,
+ where <b1> and <b2> are the residue numbers of bases in the base pair,
+ e.g.
  'pairs 1-16,2-15,3-14,4-13'.
  Can specify 'pairs' multiple times.
 \end_layout
@@ -35668,17 +36315,16 @@ Base pairs:
 \end_layout
 
 \begin_layout Description
-<name>[bp]:X Contain 1 if bases are base paired, 0 otherwise.
+<name>[bp]:X Contain 1 if bases are base paired,
+ 0 otherwise.
 \end_layout
 
 \begin_layout Description
-<name>[major]:X (If groovecalc simple) Major groove width calculated between
- P atoms of each base.
+<name>[major]:X (If groovecalc simple) Major groove width calculated between P atoms of each base.
 \end_layout
 
 \begin_layout Description
-<name>[minor]:X (If groovecalc simple) Minor groove width calculated between
- O4 atoms of each base.
+<name>[minor]:X (If groovecalc simple) Minor groove width calculated between O4 atoms of each base.
 \end_layout
 
 \begin_layout Standard
@@ -35714,11 +36360,13 @@ Base pair steps:
 \end_layout
 
 \begin_layout Description
-<name>[major]:X (If groovecalc 3dna) Major groove width, El Hassan and Calladine.
+<name>[major]:X (If groovecalc 3dna) Major groove width,
+ El Hassan and Calladine.
 \end_layout
 
 \begin_layout Description
-<name>[minor]:X (If groovecalc 3dna) Minor groove width, El Hassan and Calladine.
+<name>[minor]:X (If groovecalc 3dna) Minor groove width,
+ El Hassan and Calladine.
 \end_layout
 
 \begin_layout Standard
@@ -35785,22 +36433,37 @@ Note that base pair data sets are not created until base pairing is determined.
 \end_layout
 
 \begin_layout Standard
-Calculate basic nucleic acid (NA) structure parameters for all residues
- in the range specified by 
+Calculate basic nucleic acid (NA) structure parameters for all residues in the range specified by 
 \series bold
 resrange
 \series default
  (or all NA residues if no range specified).
- Residue names are recognized with the following priority: standard Amber
- residue names DA, DG, DC, DT, RA, RG, RC, and RU; 3 letter residue names
- ADE, GUA, CYT, THY, and URA; and finally 1 letter residue names A, G, C,
- T, and U.
+ Residue names are recognized with the following priority:
+ standard Amber residue names DA,
+ DG,
+ DC,
+ DT,
+ RA,
+ RG,
+ RC,
+ and RU;
+ 3 letter residue names ADE,
+ GUA,
+ CYT,
+ THY,
+ and URA;
+ and finally 1 letter residue names A,
+ G,
+ C,
+ T,
+ and U.
  Non-standard/modified NA bases can be recognized by using the 
 \series bold
 resmap
 \series default
  keyword.
- For example, to make 
+ For example,
+ to make 
 \shape italic
 cpptraj
 \shape default
@@ -35816,19 +36479,18 @@ The
 \series bold
 resmap
 \series default
- keyword can be specified multiple times, but only one mapping per unique
- residue name is allowed.
+ keyword can be specified multiple times,
+ but only one mapping per unique residue name is allowed.
  Note that 
 \series bold
 resmap
 \series default
- may fail if the residue is missing heavy atoms normally present in the
- specified base type.
+ may fail if the residue is missing heavy atoms normally present in the specified base type.
 \end_layout
 
 \begin_layout Standard
-Base pairs are determined either once from the first frame or from a reference
- structure, or can be determined each frame if 
+Base pairs are determined either once from the first frame or from a reference structure,
+ or can be determined each frame if 
 \series bold
 allframes
 \series default
@@ -35843,17 +36505,17 @@ pairs
 \series default
  keywords.
  Base pairing is determined first by base reference axis origin distance,
- then by stagger, then by angle between base Z axes, then finally by hydrogen
- bonding (at least one hydrogen bond must be present).
+ then by stagger,
+ then by angle between base Z axes,
+ then finally by hydrogen bonding (at least one hydrogen bond must be present).
  Base pair parameters will only be written for determined base pairs.
  Both Watson-Crick and other types of base pairing can be detected.
- Note that although all possible hydrogen bonds are searched for, only WC
- hydrogen bonds are reported in the BP.<suffix> file.
+ Note that although all possible hydrogen bonds are searched for,
+ only WC hydrogen bonds are reported in the BP.<suffix> file.
 \end_layout
 
 \begin_layout Standard
-The procedure used to calculate NA structural parameters is the same as
- 3DNA
+The procedure used to calculate NA structural parameters is the same as 3DNA
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Lu2003"
@@ -35861,7 +36523,8 @@ literal "true"
 
 \end_inset
 
-, with algorithms adapted from Babcok et al.
+,
+ with algorithms adapted from Babcok et al.
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Babcock94"
@@ -35878,7 +36541,8 @@ literal "true"
 \end_inset
 
 .
- Given the same base pairs are determined, 
+ Given the same base pairs are determined,
+ 
 \shape italic
 cpptraj
 \shape default
@@ -35899,22 +36563,39 @@ Calculated NA structure parameters are written to three separate files,
 naout
 \series default
 .
- Base pair parameters (shear, stretch, stagger, buckle, propeller twist,
- opening, # WC hydrogen bonds, base pairing, and simple groove widths) are
- written to BP.<suffix>, along with the number of WC hydrogen bonds detected.
- Base pair step parameters (shift, slide, rise, tilt, roll, twist, Zp, and
- El Hassan and Calladine groove widths) are written to BPstep.<suffix>, and
- helical parameters (X-displacement, Y-displacement, rise, inclination,
- tip, and twist) are written to Helix.<suffix>.
+ Base pair parameters (shear,
+ stretch,
+ stagger,
+ buckle,
+ propeller twist,
+ opening,
+ # WC hydrogen bonds,
+ base pairing,
+ and simple groove widths) are written to BP.<suffix>,
+ along with the number of WC hydrogen bonds detected.
+ Base pair step parameters (shift,
+ slide,
+ rise,
+ tilt,
+ roll,
+ twist,
+ Zp,
+ and El Hassan and Calladine groove widths) are written to BPstep.<suffix>,
+ and helical parameters (X-displacement,
+ Y-displacement,
+ rise,
+ inclination,
+ tip,
+ and twist) are written to Helix.<suffix>.
  If 
 \series bold
 noheader
 \series default
  is specified a header will not be written to the output files.
- Note that although base puckering is calculated, it is not written to an
- output file by default.
- You can output pucker to a file via the create or write/writedata commands
- after the data has been generated, e.g.:
+ Note that although base puckering is calculated,
+ it is not written to an output file by default.
+ You can output pucker to a file via the create or write/writedata commands after the data has been generated,
+ e.g.:
 \end_layout
 
 \begin_layout LyX-Code
@@ -35930,9 +36611,8 @@ writedata NApucker.dat NA[pucker]
 \end_layout
 
 \begin_layout Standard
-Note that while the underlying procedure is geared towards calculating parameter
-s for base pairs, the code can be made to calculate parameters between consecuti
-ve bases in single strands by specifying 
+Note that while the underlying procedure is geared towards calculating parameters for base pairs,
+ the code can be made to calculate parameters between consecutive bases in single strands by specifying 
 \series bold
 sscalc
 \series default
@@ -35940,35 +36620,42 @@ sscalc
 \end_layout
 
 \begin_layout Standard
-Base axes, base pair axes, and base pair step axes can be written to trajectory
- files using the 
+Base axes,
+ base pair axes,
+ and base pair step axes can be written to trajectory files using the 
 \series bold
 axesout
 \series default
-, 
+,
+ 
 \series bold
 bpaxesout
 \series default
-, and 
+,
+ and 
 \series bold
 stepaxesout
 \series default
  and related keywords.
- The axes are written using 4 points: an origin, and X Y and Z which are
- bonded to the origin.
+ The axes are written using 4 points:
+ an origin,
+ and X Y and Z which are bonded to the origin.
  The names of these pseudo atoms can be changed using the 
 \series bold
 axisnameo
 \series default
-, 
+,
+ 
 \series bold
 axisnamex
 \series default
-, 
+,
+ 
 \series bold
 axisnamey
 \series default
-, and 
+,
+ and 
 \series bold
 axisnamez
 \series default
@@ -35985,8 +36672,9 @@ Users can now specify
 baseref <file>
 \series default
  to load a custom nucleic acid base reference.
- The base reference files are white-space delimited, begin with the line
- NASTRUCT REFERENCE, and have the following format:
+ The base reference files are white-space delimited,
+ begin with the line NASTRUCT REFERENCE,
+ and have the following format:
 \end_layout
 
 \begin_layout LyX-Code
@@ -36015,9 +36703,10 @@ There is a line for each reference atom.
 \begin_inset space ~
 \end_inset
 
-character> Used to identify the underlying base type: A G C T or U.
- If none of these, it will be considered an unknown residue (which just
- means WC hydrogen bonding will not be identified).
+character> Used to identify the underlying base type:
+ A G C T or U.
+ If none of these,
+ it will be considered an unknown residue (which just means WC hydrogen bonding will not be identified).
 \end_layout
 
 \begin_layout Description
@@ -36060,7 +36749,11 @@ name> A reference atom name.
 \end_inset
 
 type> Denotes if and how the atom participates in hydrogen bonding.
- Can be 'd'onor, 'a'cceptor, or 'n'one (or the numbers 1, 2, 0 respectively).
+ Can be 'd'onor,
+ 'a'cceptor,
+ or 'n'one (or the numbers 1,
+ 2,
+ 0 respectively).
  Only the first character of the word actually matters.
 \end_layout
 
@@ -36160,8 +36853,7 @@ nativecontacts [<mask1> [<mask2>]] [writecontacts <outfile>] [resout <resfile>]
 \end_layout
 
 \begin_layout LyX-Code
-               [resoffset <n>] [contactpdb <file>] [pdbcut <cut>] [mindist]
- [maxdist]
+               [resoffset <n>] [contactpdb <file>] [pdbcut <cut>] [mindist] [maxdist]
 \end_layout
 
 \begin_layout LyX-Code
@@ -36222,8 +36914,7 @@ nativecontacts [<mask1> [<mask2>]] [writecontacts <outfile>] [resout <resfile>]
 \begin_inset space ~
 \end_inset
 
-<cut>] Distance cutoff for determining native contacts in Angstroms (default
- 7.0 Ang).
+<cut>] Distance cutoff for determining native contacts in Angstroms (default 7.0 Ang).
 \end_layout
 
 \begin_layout Description
@@ -36235,8 +36926,8 @@ nativecontacts [<mask1> [<mask2>]] [writecontacts <outfile>] [resout <resfile>]
 \end_layout
 
 \begin_layout Description
-[includesolvent] By default solvent molecules are ignored; this will explicitly
- include solvent molecules.
+[includesolvent] By default solvent molecules are ignored;
+ this will explicitly include solvent molecules.
 \end_layout
 
 \begin_layout Description
@@ -36284,8 +36975,7 @@ refindex
 \series bold
 byresidue
 \series default
- only) Ignore contacts between residues spaced less than <n> residues apart
- in sequence.
+ only) Ignore contacts between residues spaced less than <n> residues apart in sequence.
 \end_layout
 
 \begin_layout Description
@@ -36293,8 +36983,7 @@ byresidue
 \begin_inset space ~
 \end_inset
 
-<file>] Write PDB with B-factor column containing relative contact strength
- for native contacts (strongest is 100.0).
+<file>] Write PDB with B-factor column containing relative contact strength for native contacts (strongest is 100.0).
 \end_layout
 
 \begin_layout Description
@@ -36306,7 +36995,8 @@ byresidue
 \series bold
 contactpdb
 \series default
-, only write contacts with relative contact strength greater than 
+,
+ only write contacts with relative contact strength greater than 
 \series bold
 <cut>
 \series default
@@ -36314,13 +37004,13 @@ contactpdb
 \end_layout
 
 \begin_layout Description
-[mindist] If specified, determine the minimum distance between any atoms
- in the mask(s).
+[mindist] If specified,
+ determine the minimum distance between any atoms in the mask(s).
 \end_layout
 
 \begin_layout Description
-[maxdist] If specified, determine the maximum distance between any atoms
- in the mask(s).
+[maxdist] If specified,
+ determine the maximum distance between any atoms in the mask(s).
 \end_layout
 
 \begin_layout Description
@@ -36336,10 +37026,9 @@ contactpdb
 \end_layout
 
 \begin_layout Description
-[map] Calculate matrices of native contacts ([nativemap]) and non-native
- contacts ([nonnatmap]).
- These matrices are normalized by the total number of frames, so that a
- value of 1.0 means 
+[map] Calculate matrices of native contacts ([nativemap]) and non-native contacts ([nonnatmap]).
+ These matrices are normalized by the total number of frames,
+ so that a value of 1.0 means 
 \begin_inset Quotes eld
 \end_inset
 
@@ -36352,8 +37041,8 @@ contact always present
 \series bold
 byresidue
 \series default
- specified, the values for each individual atom pair are summed over the
- residues they belong to (this means for 
+ specified,
+ the values for each individual atom pair are summed over the residues they belong to (this means for 
 \series bold
 byresidue
 \series default
@@ -36365,13 +37054,12 @@ byresidue
 \begin_inset space ~
 \end_inset
 
-<mapfile>] Write native/non-native matrices to 'native.<mapfile>' and 'nonnative.<
-mapfile>' respectively.
+<mapfile>] Write native/non-native matrices to 'native.<mapfile>' and 'nonnative.<mapfile>' respectively.
 \end_layout
 
 \begin_layout Description
-[series] Calculate native contact time series data, 1 for contact present
- and 0 otherwise.
+[series] Calculate native contact time series data,
+ 1 for contact present and 0 otherwise.
 \end_layout
 
 \begin_layout Description
@@ -36383,7 +37071,8 @@ mapfile>' respectively.
 \end_layout
 
 \begin_layout Description
-[savenonnative] Save non-native contacts; 
+[savenonnative] Save non-native contacts;
+ 
 \series bold
 series
 \series default
@@ -36409,8 +37098,7 @@ skipnative
 \begin_inset space ~
 \end_inset
 
-<file>] Write PDB with B-factor column containing relative contact strength
- for non-native contacts (strongest is 100.0).
+<file>] Write PDB with B-factor column containing relative contact strength for non-native contacts (strongest is 100.0).
 \end_layout
 
 \end_deeper
@@ -36427,7 +37115,8 @@ skipnative
 \begin_inset space ~
 \end_inset
 
-sum} Create contacts time series by residue; 
+sum} Create contacts time series by residue;
+ 
 \series bold
 series
 \series default
@@ -36457,7 +37146,9 @@ sum The sum of all individual contacts is recorded for the residue pair.
 
 \end_deeper
 \begin_layout Description
-[skipnative] If specified, skip native contacts determination, i.e.
+[skipnative] If specified,
+ skip native contacts determination,
+ i.e.
  treat all sonctacts as non-native contacts.
  Implies 
 \series bold
@@ -36518,18 +37209,21 @@ native
 \begin_inset Quotes erd
 \end_inset
 
- contacts as determined by a simple distance cut-off, i.e.
+ contacts as determined by a simple distance cut-off,
+ i.e.
  any atoms which are closer than 
 \series bold
 <cut>
 \series default
- in the specified reference frame (the first frame if no reference specified)
- are considered a native contact.
- If one mask is provided, contacts are looked for within 
+ in the specified reference frame (the first frame if no reference specified) are considered a native contact.
+ If one mask is provided,
+ contacts are looked for within 
 \series bold
 <mask1>
 \series default
-; if two masks are provided, only contacts between atoms in 
+;
+ if two masks are provided,
+ only contacts between atoms in 
 \series bold
 <mask1>
 \series default
@@ -36552,19 +37246,18 @@ skipnative
 \series bold
 series
 \series default
- keyword; these can be further consolidated by residue using the 
+ keyword;
+ these can be further consolidated by residue using the 
 \series bold
 resseries
 \series default
  keyword.
- When using <resseries> the data set index is calculated as (r2 * nres)
- + r1 so that indices can be matched between native/non-native contact pairs.
+ When using <resseries> the data set index is calculated as (r2 * nres) + r1 so that indices can be matched between native/non-native contact pairs.
  Non-native residue contact legends have an nn_ prefix.
 \end_layout
 
 \begin_layout Standard
-Native contacts that are found are written to the file specified by writecontact
-s (or STDOUT) with format:
+Native contacts that are found are written to the file specified by writecontacts (or STDOUT) with format:
 \end_layout
 
 \begin_layout LyX-Code
@@ -36582,16 +37275,19 @@ Contact
 \family typewriter
 Nframes
 \family default
- is the number of frames the contact is present, 
+ is the number of frames the contact is present,
+ 
 \family typewriter
 Frac.
 
 \family default
- is the total fraction of frames the contact is present, 
+ is the total fraction of frames the contact is present,
+ 
 \family typewriter
 Avg
 \family default
- is the average distance of the contact when present, and 
+ is the average distance of the contact when present,
+ and 
 \family typewriter
 Stdev
 \family default
@@ -36600,8 +37296,7 @@ Stdev
 \series bold
 resout
 \series default
- is specified the total fraction of contacts is printed for all residue
- pairs having native contacts with format:
+ is specified the total fraction of contacts is printed for all residue pairs having native contacts with format:
 \end_layout
 
 \begin_layout LyX-Code
@@ -36613,15 +37308,18 @@ Where
 \family typewriter
 #Res1
 \family default
- is the first residue number, 
+ is the first residue number,
+ 
 \family typewriter
 #Res2
 \family default
- is the second residue number, 
+ is the second residue number,
+ 
 \family typewriter
 TotalFrac
 \family default
- is the total fraction of contacts for the residue pair, and 
+ is the total fraction of contacts for the residue pair,
+ and 
 \family typewriter
 Contacts
 \family default
@@ -36630,8 +37328,8 @@ Contacts
 \family typewriter
 TotalFrac
 \family default
- is calculated for each pair as the sum of each contact involving that pair
- divided by the total number of frames, it is possible to have 
+ is calculated for each pair as the sum of each contact involving that pair divided by the total number of frames,
+ it is possible to have 
 \family typewriter
 TotalFrac
 \family default
@@ -36639,11 +37337,11 @@ TotalFrac
 \end_layout
 
 \begin_layout Standard
-During trajectory processing, non-native contacts (i.e.
- any pair satisfying the distance cut-off which is not already a native
- contact) are also searched for.
- The time series for native contacts can be saved as well, with 1 for contact
- present and 0 otherwise (similar to the 
+During trajectory processing,
+ non-native contacts (i.e.
+ any pair satisfying the distance cut-off which is not already a native contact) are also searched for.
+ The time series for native contacts can be saved as well,
+ with 1 for contact present and 0 otherwise (similar to the 
 \series bold
 \emph on
 hbond
@@ -36654,6 +37352,7 @@ hbond
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-lifetime"
+nolink "false"
 
 \end_inset
 
@@ -36666,8 +37365,9 @@ Contact maps (matrices) are generated for native and non-native contacts.
 \series bold
 byresidue
 \series default
- is specified, contact maps are summed over residues, and contacts between
- residues spaced 
+ is specified,
+ contact maps are summed over residues,
+ and contacts between residues spaced 
 \series bold
 <resoffset>
 \series default
@@ -36679,15 +37379,13 @@ If
 \series bold
 contactpdb
 \series default
- is specified a PDB is generated containing relative contact strengths in
- the B-factor column.
- The relative contact strength is normalized so that a value of 100 means
- that atom participated in the most contacts with other atoms.
+ is specified a PDB is generated containing relative contact strengths in the B-factor column.
+ The relative contact strength is normalized so that a value of 100 means that atom participated in the most contacts with other atoms.
 \end_layout
 
 \begin_layout Standard
-Example command looking for contacts between residues 210 to 260 and residue
- named NDP, using reference structure 'FtuFabI.WT.pdb' to define native contacts:
+Example command looking for contacts between residues 210 to 260 and residue named NDP,
+ using reference structure 'FtuFabI.WT.pdb' to define native contacts:
 \end_layout
 
 \begin_layout LyX-Code
@@ -36744,6 +37442,8 @@ name "subsec:cpptraj_outtraj"
 \begin_layout LyX-Code
 outtraj
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -36777,6 +37477,7 @@ args] Output trajectory arguments (see
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-trajout"
+nolink "false"
 
 \end_inset
 
@@ -36804,8 +37505,7 @@ max
 \begin_inset space ~
 \end_inset
 
-<max>] Only write frames to <filename> if values in <dataset> for those
- frames are between <min> and <max>.
+<max>] Only write frames to <filename> if values in <dataset> for those frames are between <min> and <max>.
  Can be specified for one or more data sets.
 \end_layout
 
@@ -36817,10 +37517,12 @@ The outtraj command is similar in function to
 trajout
 \series default
 \emph default
-, and takes all of the same arguments.
- However, instead of writing a trajectory frame after all actions are complete
- outtraj writes the trajectory frame at its position in the Action queue.
- For example, given the input:
+,
+ and takes all of the same arguments.
+ However,
+ instead of writing a trajectory frame after all actions are complete outtraj writes the trajectory frame at its position in the Action queue.
+ For example,
+ given the input:
 \end_layout
 
 \begin_layout LyX-Code
@@ -36844,17 +37546,18 @@ outtraj AfterRmsd.crd
 \end_layout
 
 \begin_layout Standard
-three trajectories will be written: output.crd, BeforeRmsd.crd, and AfterRmsd.crd.
- The output.crd and AfterRmsd.crd trajectories will be identical, but the
- BeforeRmsd.crd trajectory will contain the coordinates of mdcrd.crd before
- they are RMS-fit.
+three trajectories will be written:
+ output.crd,
+ BeforeRmsd.crd,
+ and AfterRmsd.crd.
+ The output.crd and AfterRmsd.crd trajectories will be identical,
+ but the BeforeRmsd.crd trajectory will contain the coordinates of mdcrd.crd before they are RMS-fit.
 \end_layout
 
 \begin_layout Standard
-The maxmin keyword can be used to restrict output using one more more data
- sets.
- For example, to only write frames for which the RMSD value is between 0.7
- and 0.8:
+The maxmin keyword can be used to restrict output using one more more data sets.
+ For example,
+ to only write frames for which the RMSD value is between 0.7 and 0.8:
 \end_layout
 
 \begin_layout LyX-Code
@@ -36879,12 +37582,16 @@ pairdist out <filename> mask <mask> [delta <resolution>]
 
 \begin_layout Standard
 Calculate pair distribution function.
- In the following, defaults are given in parentheses.
+ In the following,
+ defaults are given in parentheses.
  The 
 \series bold
 out
 \series default
- keyword specifies output file for histogram: distance, P(r), s(P(r)).
+ keyword specifies output file for histogram:
+ distance,
+ P(r),
+ s(P(r)).
  The 
 \series bold
 mask
@@ -36903,8 +37610,7 @@ pairwise
 \end_layout
 
 \begin_layout LyX-Code
-pairwise [<name>] [<mask>] [out <filename>] [cuteelec <ecut>] [cutevdw <vcut>]
- 	
+pairwise [<name>] [<mask>] [out <filename>] [cuteelec <ecut>] [cutevdw <vcut>] 	
 \end_layout
 
 \begin_layout LyX-Code
@@ -36916,8 +37622,7 @@ pairwise [<name>] [<mask>] [out <filename>] [cuteelec <ecut>] [cutevdw <vcut>]
 \end_layout
 
 \begin_layout LyX-Code
-     	[eout <eout file>] [pdbout <pdb file>] [scalepdbe] [printmode {only|or|and
-|}]
+     	[eout <eout file>] [pdbout <pdb file>] [scalepdbe] [printmode {only|or|and|}]
 \begin_inset Separator latexpar
 \end_inset
 
@@ -36926,8 +37631,8 @@ pairwise [<name>] [<mask>] [out <filename>] [cuteelec <ecut>] [cutevdw <vcut>]
 
 \begin_deeper
 \begin_layout Description
-[<name>] Data set name; van der Waals energy will get aspect [EVDW] and
- electrostatic energy will get aspect [EELEC].
+[<name>] Data set name;
+ van der Waals energy will get aspect [EVDW] and electrostatic energy will get aspect [EELEC].
 \end_layout
 
 \begin_layout Description
@@ -36992,8 +37697,7 @@ refindex
 \begin_inset space ~
 \end_inset
 
-<cut>] Only report interaction EELEC (or delta EELEC) if absolute value
- is greater than <ecut> (default 1.0 kcal/mol).
+<cut>] Only report interaction EELEC (or delta EELEC) if absolute value is greater than <ecut> (default 1.0 kcal/mol).
 \end_layout
 
 \begin_layout Description
@@ -37001,8 +37705,7 @@ refindex
 \begin_inset space ~
 \end_inset
 
-<cutv>] Only report interaction EVDW (or delta EVDW) if absolute value is
- greater than <vcut> (default 1.0 kcal/mol).
+<cutv>] Only report interaction EVDW (or delta EVDW) if absolute value is greater than <vcut> (default 1.0 kcal/mol).
 \end_layout
 
 \begin_layout Description
@@ -37018,8 +37721,7 @@ mol2
 \begin_inset space ~
 \end_inset
 
-prefix>] Write out mol2 containing only atom pairs which satisfy <ecut>
- and <vcut>.
+prefix>] Write out mol2 containing only atom pairs which satisfy <ecut> and <vcut>.
 \end_layout
 
 \begin_layout Description
@@ -37043,8 +37745,7 @@ map>] Write out interaction EVDW (or delta EVDW) matrix to file <vdw map>.
 \begin_inset space ~
 \end_inset
 
-map>] Write out interaction EELEC (or delta EELEC) matrix to file <elec
- map>.
+map>] Write out interaction EELEC (or delta EELEC) matrix to file <elec map>.
 \end_layout
 
 \begin_layout Description
@@ -37056,8 +37757,7 @@ map>] Write out interaction EELEC (or delta EELEC) matrix to file <elec
 \begin_inset space ~
 \end_inset
 
-file>] Print average interaction EVDW|EELEC (or average delta EVDW|EELC)
- to <avg file>.
+file>] Print average interaction EVDW|EELEC (or average delta EVDW|EELC) to <avg file>.
 \end_layout
 
 \begin_layout Description
@@ -37106,22 +37806,26 @@ Data Sets Created:
 
 \end_deeper
 \begin_layout Standard
-This action has two related functions: 1) Calculate pairwise (i.e.
+This action has two related functions:
+ 1) Calculate pairwise (i.e.
  non-bonded) energy (in kcal/mol) for atoms in 
 \series bold
 <mask>
 \series default
-, or 2) Compare pairwise energy of frames to a reference frame.
+,
+ or 2) Compare pairwise energy of frames to a reference frame.
  This calculation does use an exclusion list but is not periodic.
 \end_layout
 
 \begin_layout Standard
-When comparing to a reference frame, the 
+When comparing to a reference frame,
+ the 
 \series bold
 eout
 \series default
  file will contain the differences for each individual interaction (i.e.
- Eref - Eframe), otherwise the 
+ Eref - Eframe),
+ otherwise the 
 \series bold
 eout
 \series default
@@ -37134,21 +37838,20 @@ cuteelc
 \series bold
 cutevdw
 \series default
- keywords can be used to restrict printing of individual interactions to
- those for which the absolute value is above a cutoff.
- The VMAP and EMAP matrix elements will contain these values as well (difference
-s for reference, absolute value otherwise) averaged over all frames.
+ keywords can be used to restrict printing of individual interactions to those for which the absolute value is above a cutoff.
+ The VMAP and EMAP matrix elements will contain these values as well (differences for reference,
+ absolute value otherwise) averaged over all frames.
  The 
 \series bold
 avgout
 \series default
- file will contain only these values averaged over all frames that satisfy
- the cutoffs.
+ file will contain only these values averaged over all frames that satisfy the cutoffs.
  The 
 \series bold
 printmode
 \series default
- keyword controls when the average energies are written: 
+ keyword controls when the average energies are written:
+ 
 \series bold
 only
 \series default
@@ -37157,13 +37860,12 @@ only
 \series bold
 or
 \series default
- means that both energy components will be printed if either satistfy a
- cutoff, and 
+ means that both energy components will be printed if either satistfy a cutoff,
+ and 
 \series bold
 and
 \series default
- means that both energy components will be written only if both satisfy
- the cutoffs.
+ means that both energy components will be written only if both satisfy the cutoffs.
 \end_layout
 
 \begin_layout Standard
@@ -37171,17 +37873,15 @@ The
 \series bold
 cutout
 \series default
- keyword can be used to write out MOL2 files each frame named '<cut mol2
- prefix>.evdw.mol2.X' and '<cut mol2 prefix>.eelec.mol2.X' (where X is the frame
- number) containing only atoms with energies that satisfy the cutoffs.
- Similarly, the 
+ keyword can be used to write out MOL2 files each frame named '<cut mol2 prefix>.evdw.mol2.X' and '<cut mol2 prefix>.eelec.mol2.X' (where X is the frame number) containing only atoms with energies that satisfy the cutoffs.
+ Similarly,
+ the 
 \series bold
 pdbout
 \series default
  keyword can be used to write out a PDB file (with 1 MODEL per frame).
- The occupancy and B-factor columns will contain the total van der Waals
- and electrostatic energy for each atom if cutoffs are satisfied, or 0.0
- otherwise.
+ The occupancy and B-factor columns will contain the total van der Waals and electrostatic energy for each atom if cutoffs are satisfied,
+ or 0.0 otherwise.
 \end_layout
 
 \begin_layout Subsection
@@ -37230,7 +37930,8 @@ name
 \end_layout
 
 \begin_layout Description
-<dsname>[evec] Eigenvectors (3x3 matrix, row-major).
+<dsname>[evec] Eigenvectors (3x3 matrix,
+ row-major).
 \end_layout
 
 \begin_layout Description
@@ -37239,17 +37940,18 @@ name
 
 \end_deeper
 \begin_layout Standard
-Determine principal axes of each frame determined by diagonalization of
- the inertial matrix from the coordinates of the specified atoms.
+Determine principal axes of each frame determined by diagonalization of the inertial matrix from the coordinates of the specified atoms.
  At least one of 
 \series bold
 dorotation
 \series default
-, 
+,
+ 
 \series bold
 out
 \series default
-, or 
+,
+ or 
 \series bold
 name
 \series default
@@ -37270,28 +37972,32 @@ vector
 principal
 \series default
 ').
- If out is specified the eigenvectors and eigenvalues will be written for
- each frame N with format:
+ If out is specified the eigenvectors and eigenvalues will be written for each frame N with format:
 \end_layout
 
 \begin_layout LyX-Code
-<N> EIGENVALUES: <EX> <EY> <EZ>
+<N> EIGENVALUES:
+ <EX> <EY> <EZ>
 \end_layout
 
 \begin_layout LyX-Code
-<N> EIGENVECTOR 0: <Xx> <Xy> <Xz>
+<N> EIGENVECTOR 0:
+ <Xx> <Xy> <Xz>
 \end_layout
 
 \begin_layout LyX-Code
-<N> EIGENVECTOR 1: <Yx> <Yy> <Yz>
+<N> EIGENVECTOR 1:
+ <Yx> <Yy> <Yz>
 \end_layout
 
 \begin_layout LyX-Code
-<N> EIGENVECTOR 2: <Zx> <Zy> <Zz>
+<N> EIGENVECTOR 2:
+ <Zx> <Zy> <Zz>
 \end_layout
 
 \begin_layout Standard
-NOTE: The eigenvector 3x3 matrix data set could subsequently be used e.g.
+NOTE:
+ The eigenvector 3x3 matrix data set could subsequently be used e.g.
  with the 
 \series bold
 \emph on
@@ -37302,7 +38008,8 @@ rotate
 \end_layout
 
 \begin_layout Standard
-Example: Align system (residues 1-76) along principle axes:
+Example:
+ Align system (residues 1-76) along principle axes:
 \end_layout
 
 \begin_layout LyX-Code
@@ -37329,8 +38036,7 @@ name "subsec:cpptraj-projection"
 \end_layout
 
 \begin_layout LyX-Code
-projection [<name>] evecs <dataset name> [out <outfile>] [beg <beg>] [end
- <end>]
+projection [<name>] evecs <dataset name> [out <outfile>] [beg <beg>] [end <end>]
 \end_layout
 
 \begin_layout LyX-Code
@@ -37387,8 +38093,8 @@ name> Data set containing eigenvectors (modes).
 \end_layout
 
 \begin_layout Description
-[<mask>] (Not dihedral covariance) Mask of atoms to use in projection; MUST
- CORRESPOND TO HOW EIGENVECTORS WERE GENERATED.
+[<mask>] (Not dihedral covariance) Mask of atoms to use in projection;
+ MUST CORRESPOND TO HOW EIGENVECTORS WERE GENERATED.
 \end_layout
 
 \begin_layout Description
@@ -37413,10 +38119,11 @@ arg>] (Dihedral covariance only) Dihedral data sets to use in projection;
 \begin_inset space ~
 \end_inset
 
-arg>] (Data covariance only, e.g.
+arg>] (Data covariance only,
+ e.g.
  from TICA).
- 1D data sets to use in projection; MUST CORRESPOND TO HOW EIGENVECTORS
- WERE GENERATED.
+ 1D data sets to use in projection;
+ MUST CORRESPOND TO HOW EIGENVECTORS WERE GENERATED.
 \end_layout
 
 \begin_layout Description
@@ -37473,8 +38180,7 @@ DataSet indices correspond to mode #.
 
 \end_deeper
 \begin_layout Standard
-Projects snapshots onto eigenvectors obtained by diagonalizing covariance
- or mass-weighted covariance matrices.
+Projects snapshots onto eigenvectors obtained by diagonalizing covariance or mass-weighted covariance matrices.
  Eigenvectors are taken from previously generated (e.g.
  with 
 \series bold
@@ -37500,8 +38206,8 @@ readdata
 \series bold
 <mask>
 \series default
- agree with the ones used to calculate the modes (i.e., if mask = '@CA' was
- used in the 
+ agree with the ones used to calculate the modes (i.e.,
+ if mask = '@CA' was used in the 
 \begin_inset Quotes eld
 \end_inset
 
@@ -37517,11 +38223,13 @@ matrix
 \begin_inset Quotes erd
 \end_inset
 
- command, mask = '@CA' needs to be set here as well).
+ command,
+ mask = '@CA' needs to be set here as well).
  See 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "sec:cpptraj-Matrix-Vector-Analysis-Examples"
+nolink "false"
 
 \end_inset
 
@@ -37532,19 +38240,22 @@ projection
 \series default
 \emph default
  command.
- If only 1D data sets need to be projected, see the 
+ If only 1D data sets need to be projected,
+ see the 
 \series bold
 \emph on
 projectdata
 \series default
 \emph default
- analysis command, 
+ analysis command,
+ 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-projectdata"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
@@ -37558,6 +38269,8 @@ pucker
 \begin_layout LyX-Code
 pucker
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -37587,8 +38300,7 @@ pucker
 \end_layout
 
 \begin_layout Description
-<maskX> Five (optionally six) atom masks selecting atom(s) to calculate
- pucker for.
+<maskX> Five (optionally six) atom masks selecting atom(s) to calculate pucker for.
 \end_layout
 
 \begin_layout Description
@@ -37658,8 +38370,11 @@ theta
 
 \end_deeper
 \begin_layout Standard
-Calculate the pucker (in degrees) for atoms in <mask1>, <mask2>, <mask3>,
- <mask4>, <mask5> using the method of Altona & Sundarlingam
+Calculate the pucker (in degrees) for atoms in <mask1>,
+ <mask2>,
+ <mask3>,
+ <mask4>,
+ <mask5> using the method of Altona & Sundarlingam
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Altona1972,Harvey1986"
@@ -37667,11 +38382,13 @@ literal "true"
 
 \end_inset
 
- (default for 5 masks, or if 
+ (default for 5 masks,
+ or if 
 \series bold
 altona
 \series default
- specified), or the method of Cremer & Pople
+ specified),
+ or the method of Cremer & Pople
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Cremer1975"
@@ -37679,7 +38396,8 @@ literal "true"
 
 \end_inset
 
- (default for 6 masks, or if 
+ (default for 6 masks,
+ or if 
 \series bold
 cremer
 \series default
@@ -37692,8 +38410,8 @@ amplitude
 \series bold
 theta
 \series default
- keywords are given, amplitudes/thetas (also in degrees) will be calculated
- in addition to pucker.
+ keywords are given,
+ amplitudes/thetas (also in degrees) will be calculated in addition to pucker.
  The results from 
 \series bold
 \shape italic
@@ -37710,20 +38428,21 @@ statistics
 \end_layout
 
 \begin_layout Standard
-By default, pucker values are wrapped to range from -180 to 180 degrees.
+By default,
+ pucker values are wrapped to range from -180 to 180 degrees.
  If the 
 \series bold
 range360
 \series default
  keyword is specified values will be wrapped to range from 0 to 360 degrees.
- Note that the Cremer & Pople convention is offset from Altona & Sundarlingam
- convention (with nucleic acids) by +90.0 degrees; the 
+ Note that the Cremer & Pople convention is offset from Altona & Sundarlingam convention (with nucleic acids) by +90.0 degrees;
+ the 
 \series bold
 offset
 \series default
- keyword will add an offset to the final value and so can be used to convert
- between the two.
- For example, to convert from Cremer to Altona specify 
+ keyword will add an offset to the final value and so can be used to convert between the two.
+ For example,
+ to convert from Cremer to Altona specify 
 \begin_inset Quotes eld
 \end_inset
 
@@ -37739,11 +38458,13 @@ offset
 \end_layout
 
 \begin_layout Standard
-To calculate nucleic acid pucker specify C1' first, followed by C2', C3',
+To calculate nucleic acid pucker specify C1' first,
+ followed by C2',
+ C3',
  C4' and O4'.
- For example, to calculate the sugar pucker for nucleic acid residues 1
- and 2 using the method of Altona & Sundarlingam, with final pseudorotation
- values ranging from 0 to 360:
+ For example,
+ to calculate the sugar pucker for nucleic acid residues 1 and 2 using the method of Altona & Sundarlingam,
+ with final pseudorotation values ranging from 0 to 360:
 \end_layout
 
 \begin_layout LyX-Code
@@ -37761,6 +38482,8 @@ radgyr | rog
 \begin_layout LyX-Code
 radgyr
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -37782,7 +38505,8 @@ radgyr
 \end_layout
 
 \begin_layout Description
-[<mask>] Atoms to calculate radius of gyration for; default all atoms.
+[<mask>] Atoms to calculate radius of gyration for;
+ default all atoms.
 \end_layout
 
 \begin_layout Description
@@ -37802,8 +38526,8 @@ radgyr
 \end_layout
 
 \begin_layout Description
-[tensor] Calculate radius of gyration tensor, output format 'XX YY ZZ XY
- XZ YZ'.
+[tensor] Calculate radius of gyration tensor,
+ output format 'XX YY ZZ XY XZ YZ'.
 \end_layout
 
 \begin_layout Standard
@@ -37819,15 +38543,15 @@ Data Sets Created:
 \end_layout
 
 \begin_layout Description
-<name>[Tensor] Radius of gyration tensor; format 'XX YY ZZ XY XZ YZ'.
+<name>[Tensor] Radius of gyration tensor;
+ format 'XX YY ZZ XY XZ YZ'.
 \end_layout
 
 \end_deeper
 \begin_layout Standard
 Calculate the radius of gyration of specified atoms.
- For example, to calculate only the mass-weighted radius of gyration (not
- the maximum) of the non-hydrogen atoms of residues 4 to 10 and print the
- results to 
+ For example,
+ to calculate only the mass-weighted radius of gyration (not the maximum) of the non-hydrogen atoms of residues 4 to 10 and print the results to 
 \begin_inset Quotes eld
 \end_inset
 
@@ -37849,6 +38573,8 @@ radial | rdf
 \begin_layout LyX-Code
 radial
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -37865,8 +38591,7 @@ radial
 \end_layout
 
 \begin_layout LyX-Code
-   	[density <density> | volume] [<dataset name>] [intrdf <file>] [rawrdf
- <file>]
+   	[density <density> | volume] [<dataset name>] [intrdf <file>] [rawrdf <file>]
 \end_layout
 
 \begin_layout LyX-Code
@@ -37891,11 +38616,13 @@ radial
 \end_layout
 
 \begin_layout Description
-<spacing> Bin spacing, required.
+<spacing> Bin spacing,
+ required.
 \end_layout
 
 \begin_layout Description
-<maximum> Max bin value, required.
+<maximum> Max bin value,
+ required.
 \end_layout
 
 \begin_layout Description
@@ -37903,7 +38630,8 @@ radial
 \begin_inset space ~
 \end_inset
 
-mask1> Atoms to calculate RDF for, required.
+mask1> Atoms to calculate RDF for,
+ required.
 \end_layout
 
 \begin_layout Description
@@ -37911,8 +38639,7 @@ mask1> Atoms to calculate RDF for, required.
 \begin_inset space ~
 \end_inset
 
-mask2>] (Optional) If specified calculate RDF of all atoms in <solvent mask1>
- to each atom in <solute mask2>.
+mask2>] (Optional) If specified calculate RDF of all atoms in <solvent mask1> to each atom in <solute mask2>.
 \end_layout
 
 \begin_layout Description
@@ -37924,8 +38651,7 @@ mask2>] (Optional) If specified calculate RDF of all atoms in <solvent mask1>
 \begin_inset space ~
 \end_inset
 
-<density>] Use density value of <density> for normalization (default 0.033456
- molecules
+<density>] Use density value of <density> for normalization (default 0.033456 molecules
 \begin_inset space ~
 \end_inset
 
@@ -37937,8 +38663,7 @@ mask2>] (Optional) If specified calculate RDF of all atoms in <solvent mask1>
 \end_layout
 
 \begin_layout Description
-[volume] Determine density for normalization from average volume of input
- frames.
+[volume] Determine density for normalization from average volume of input frames.
 \end_layout
 
 \begin_layout Description
@@ -37950,9 +38675,7 @@ mask2>] (Optional) If specified calculate RDF of all atoms in <solvent mask1>
 \begin_inset space ~
 \end_inset
 
-<file>] Calculate integral of RDF bin values (averaged over # of frames
- but otherwise not normalized) and write to <file> (can be same as <output_filen
-ame>).
+<file>] Calculate integral of RDF bin values (averaged over # of frames but otherwise not normalized) and write to <file> (can be same as <output_filename>).
 \end_layout
 
 \begin_layout Description
@@ -37964,13 +38687,11 @@ ame>).
 \end_layout
 
 \begin_layout Description
-[center1] Calculate RDF from geometric center of atoms in <solvent mask1>
- to all atoms in <solute mask2>.
+[center1] Calculate RDF from geometric center of atoms in <solvent mask1> to all atoms in <solute mask2>.
 \end_layout
 
 \begin_layout Description
-[center2] Calculate RDF from geometric center of atoms in <solute mask2>
- to all atoms in <solvent mask1>.
+[center2] Calculate RDF from geometric center of atoms in <solute mask2> to all atoms in <solvent mask1>.
 \end_layout
 
 \begin_layout Description
@@ -37982,28 +38703,23 @@ ame>).
 \begin_inset space ~
 \end_inset
 
-<x>,<y>,<z>] Calculate RDF from center of atoms in <solvent mask1> to point
- specified by <x> <y> and <z> (in Ang.).
+<x>,<y>,<z>] Calculate RDF from center of atoms in <solvent mask1> to point specified by <x> <y> and <z> (in Ang.).
 \end_layout
 
 \begin_layout Description
-[byres1] Calculate using the centers of mass of each residue in the first
- mask.
+[byres1] Calculate using the centers of mass of each residue in the first mask.
 \end_layout
 
 \begin_layout Description
-[bymol1] Calculate using the centers of mass of each molecule in the first
- mask.
+[bymol1] Calculate using the centers of mass of each molecule in the first mask.
 \end_layout
 
 \begin_layout Description
-[byres2] Calculate using the centers of mass of each residue in the second
- mask.
+[byres2] Calculate using the centers of mass of each residue in the second mask.
 \end_layout
 
 \begin_layout Description
-[bymol2] Calculate using the centers of mass of each molecule in the second
- mask.
+[bymol2] Calculate using the centers of mass of each molecule in the second mask.
 \end_layout
 
 \begin_layout Standard
@@ -38032,18 +38748,19 @@ rawrdf
 
 \end_deeper
 \begin_layout Standard
-Calculate the radial distribution function (RDF, aka pair correlation function)
- of atoms in 
+Calculate the radial distribution function (RDF,
+ aka pair correlation function) of atoms in 
 \series bold
 <solvent mask1>
 \series default
- (note that this mask does not need to be solvent, but this nomenclature
- is used for clarity).
+ (note that this mask does not need to be solvent,
+ but this nomenclature is used for clarity).
  If an optional second mask (
 \series bold
 <solute mask2>
 \series default
-) is given, calculate the RDF of ALL atoms in 
+) is given,
+ calculate the RDF of ALL atoms in 
 \series bold
 <solvent mask1>
 \series default
@@ -38052,7 +38769,8 @@ Calculate the radial distribution function (RDF, aka pair correlation function)
 <solute mask2>
 \series default
 .
- If desired, the geometric center of atoms in 
+ If desired,
+ the geometric center of atoms in 
 \series bold
 <solvent mask1>
 \series default
@@ -38068,8 +38786,8 @@ center1
 \series bold
 center2
 \series default
- keywords respectively, or alternatively intra-molecular distances can be
- ignored by specifying the 
+ keywords respectively,
+ or alternatively intra-molecular distances can be ignored by specifying the 
 \series bold
 nointramol
 \series default
@@ -38077,9 +38795,8 @@ nointramol
 \end_layout
 
 \begin_layout Standard
-The RDF is calculated from the histogram of the number of particles found
- as a function of distance R, normalized by the expected number of particles
- at that distance.
+The RDF is calculated from the histogram of the number of particles found as a function of distance R,
+ normalized by the expected number of particles at that distance.
  The normalization is calculated from:
 \begin_inset Separator latexpar
 \end_inset
@@ -38106,7 +38823,8 @@ where dR is equal to the bin spacing.
 \begin_inset Formula $^{-\text{3}}$
 \end_inset
 
-, which corresponds to a density of water approximately equal to 1.0 g
+,
+ which corresponds to a density of water approximately equal to 1.0 g
 \begin_inset space ~
 \end_inset
 
@@ -38123,37 +38841,37 @@ mL
 \begin_inset Formula $^{-\text{1}}$
 \end_inset
 
-, multiply the density by 
+,
+ multiply the density by 
 \begin_inset Formula $\frac{0.6022}{M_{r}}$
 \end_inset
 
-, where 
+,
+ where 
 \begin_inset Formula $M_{r}$
 \end_inset
 
  is the mass of the molecule in atomic mass units.
- Alternatively, if the 
+ Alternatively,
+ if the 
 \series bold
 volume
 \series default
- keyword is specified the density is determined from the average volume
- of the system over all Frames.
+ keyword is specified the density is determined from the average volume of the system over all Frames.
  
 \end_layout
 
 \begin_layout Standard
-Note that correct normalization of the RDF depends on the number of atoms
- in each mask; if multiple topology files are being processed that result
- in changes in the number of atoms in each mask, the normalization will
- be off.
+Note that correct normalization of the RDF depends on the number of atoms in each mask;
+ if multiple topology files are being processed that result in changes in the number of atoms in each mask,
+ the normalization will be off.
 \end_layout
 
 \begin_layout Standard
 The basic (i.e.
- no center1/center2/byres1/byres2/bymol1/bymol2) RDF calculations are now
- CUDA parallelized.
- However, the calculation is done in single-precision on GPUs so the resulting
- histograms may differ slightly from the CPU (on the order of 0.0002 - 0.0004).
+ no center1/center2/byres1/byres2/bymol1/bymol2) RDF calculations are now CUDA parallelized.
+ However,
+ the calculation is done in single-precision on GPUs so the resulting histograms may differ slightly from the CPU (on the order of 0.0002 - 0.0004).
 \end_layout
 
 \begin_layout Subsection
@@ -38161,8 +38879,7 @@ randomizeions
 \end_layout
 
 \begin_layout LyX-Code
-randomizeions <mask> [around <ardoundmask> by <distance>] [{allowoverlap|overlap
- <value>}]
+randomizeions <mask> [around <ardoundmask> by <distance>] [{allowoverlap|overlap <value>}]
 \end_layout
 
 \begin_layout LyX-Code
@@ -38217,14 +38934,13 @@ overlap
 \end_layout
 
 \begin_layout Description
-[originalalgorithm] Use the original, slower algorithm (from versions before
- 5.1.0).
+[originalalgorithm] Use the original,
+ slower algorithm (from versions before 5.1.0).
 \end_layout
 
 \end_deeper
 \begin_layout Standard
-This can be used to randomly swap the positions of solvent and single atom
- ions.
+This can be used to randomly swap the positions of solvent and single atom ions.
  The 
 \begin_inset Quotes eld
 \end_inset
@@ -38237,7 +38953,8 @@ overlap
 \begin_inset Quotes erd
 \end_inset
 
- specifies the minimum distance between ions, and the 
+ specifies the minimum distance between ions,
+ and the 
 \begin_inset Quotes eld
 \end_inset
 
@@ -38249,8 +38966,7 @@ around
 \begin_inset Quotes erd
 \end_inset
 
- keyword can be used to specify a solute (or set of atoms) around which
- the ions can get no closer than the distance specified.
+ keyword can be used to specify a solute (or set of atoms) around which the ions can get no closer than the distance specified.
  The optional keywords 
 \begin_inset Quotes eld
 \end_inset
@@ -38328,8 +39044,9 @@ data
 \begin_inset space ~
 \end_inset
 
-<setname> Data set to use for remapping; should be a 1D integer data set
- with X= reference (old) atom index, Y = target (new) atom index.
+<setname> Data set to use for remapping;
+ should be a 1D integer data set with X= reference (old) atom index,
+ Y = target (new) atom index.
 \end_layout
 
 \begin_layout Description
@@ -38431,8 +39148,9 @@ dir
 \end_inset
 
 <XYZ> Repicate cell once in specified directions.
- <XYZ> should consist of 3 numbers with no spaces in between them and are
- restricted to values of -1, 1, and 0.
+ <XYZ> should consist of 3 numbers with no spaces in between them and are restricted to values of -1,
+ 1,
+ and 0.
  May be specified more than once.
 \end_layout
 
@@ -38470,10 +39188,8 @@ parmopts
 
 \end_deeper
 \begin_layout Standard
-Create a trajectory where the unit cell is replicated in 1 or more directions
- (up to 27).
- The resulting coordinates and topology can be written to a trajectory/topology
- file.
+Create a trajectory where the unit cell is replicated in 1 or more directions (up to 27).
+ The resulting coordinates and topology can be written to a trajectory/topology file.
  They can also be saved as a COORDS data set for subsequent processing.
  Currently replication is only allowed 1 axis length in either direction.
  The 
@@ -38485,17 +39201,20 @@ all
 \series bold
 dir
 \series default
- keyword can be used to restrict replication to specific directions, e.g.
+ keyword can be used to restrict replication to specific directions,
+ e.g.
  '
 \family typewriter
 dir 10-1
 \family default
-' would replicate the cell once in the +X, -Z directions.
+' would replicate the cell once in the +X,
+ -Z directions.
 \end_layout
 
 \begin_layout Standard
-For example, to replicate a cell in all directions, writing out to NetCDF
- trajectory cell.nc:
+For example,
+ to replicate a cell in all directions,
+ writing out to NetCDF trajectory cell.nc:
 \end_layout
 
 \begin_layout LyX-Code
@@ -38524,6 +39243,8 @@ name "subsec:cpptraj-rmsd"
 \begin_layout LyX-Code
 rmsd
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -38577,12 +39298,15 @@ rmsd
 \end_layout
 
 \begin_layout Description
-[<mask>] Mask of atoms to calculate RMSD for; if not specified, calculate
- for all atoms.
+[<mask>] Mask of atoms to calculate RMSD for;
+ if not specified,
+ calculate for all atoms.
 \end_layout
 
 \begin_layout Description
-[<refmask>] Reference mask; if not specified, use 
+[<refmask>] Reference mask;
+ if not specified,
+ use 
 \series bold
 <mask>
 \series default
@@ -38606,16 +39330,17 @@ rmsd
 \end_layout
 
 \begin_layout Description
-[norotate] If calculating best-fit RMSD, translate but do not rotate coordinates.
+[norotate] If calculating best-fit RMSD,
+ translate but do not rotate coordinates.
 \end_layout
 
 \begin_layout Description
-[nomod] If calculating best-fit RMSD, do not modify coordinates.
+[nomod] If calculating best-fit RMSD,
+ do not modify coordinates.
 \end_layout
 
 \begin_layout Description
-[savematrices] If specified save rotation matrices to data set with aspect
- [RM].
+[savematrices] If specified save rotation matrices to data set with aspect [RM].
 \end_layout
 
 \begin_deeper
@@ -38633,7 +39358,8 @@ matricesout
 \begin_inset space ~
 \end_inset
 
-{combined|separate}] If specified save translation vectors: 
+{combined|separate}] If specified save translation vectors:
+ 
 \series bold
 combined
 \series default
@@ -38642,8 +39368,9 @@ combined
 \series bold
 separate
 \series default
- means save target-to-origin as Vx, Vy, Vz and save origin-to-reference
- as Ox Oy Oz in the output vector data set.
+ means save target-to-origin as Vx,
+ Vy,
+ Vz and save origin-to-reference as Ox Oy Oz in the output vector data set.
 \end_layout
 
 \begin_deeper
@@ -38697,8 +39424,7 @@ refindex
 
 <#>
 \series default
- Use previously read in reference structure specified by <#> (based on order
- read in).
+ Use previously read in reference structure specified by <#> (based on order read in).
 \end_layout
 
 \begin_layout Description
@@ -38714,13 +39440,12 @@ reftraj
 \begin_inset space ~
 \end_inset
 
-<name> Use frames from COORDS set <name> or read in from trajectory file
- <name> as references.
- Each frame from <name> is used in turn, so that frame 1 is compared to
- frame 1 from <name>, frame 2 is compared to frame 2 from <name> and so
- on.
- If <trajname> runs out of frames before processing is complete, the last
- frame of <trajname> continues to be used as the reference.
+<name> Use frames from COORDS set <name> or read in from trajectory file <name> as references.
+ Each frame from <name> is used in turn,
+ so that frame 1 is compared to frame 1 from <name>,
+ frame 2 is compared to frame 2 from <name> and so on.
+ If <trajname> runs out of frames before processing is complete,
+ the last frame of <trajname> continues to be used as the reference.
 \begin_inset Separator latexpar
 \end_inset
 
@@ -38749,8 +39474,9 @@ parmindex
 \series bold
 reftraj
 \series default
- specifies a trajectory file, associate it with specified topology; if not
- specified the first topology is used.
+ specifies a trajectory file,
+ associate it with specified topology;
+ if not specified the first topology is used.
 \end_layout
 
 \end_deeper
@@ -38787,8 +39513,7 @@ range
 \begin_inset space ~
 \end_inset
 
-range> Calculate per-residue RMSDs for residues in <res range> (default
- all solute residues).
+range> Calculate per-residue RMSDs for residues in <res range> (default all solute residues).
 \end_layout
 
 \begin_layout Description
@@ -38800,8 +39525,7 @@ refrange
 \begin_inset space ~
 \end_inset
 
-range> Calculate per-residue RMSDs to reference residues in <ref range>
- (use <res range> if not specified).
+range> Calculate per-residue RMSDs to reference residues in <ref range> (use <res range> if not specified).
 \end_layout
 
 \begin_layout Description
@@ -38813,13 +39537,12 @@ perresmask
 \begin_inset space ~
 \end_inset
 
-mask> By default residues are selected using the mask ':X' where X is residue
- number; this appends <additional mask> to the mask expression.
+mask> By default residues are selected using the mask ':X' where X is residue number;
+ this appends <additional mask> to the mask expression.
 \end_layout
 
 \begin_layout Description
-perrescenter Translate residues to a common center of mass prior to calculating
- RMSD.
+perrescenter Translate residues to a common center of mass prior to calculating RMSD.
 \end_layout
 
 \begin_layout Description
@@ -38847,7 +39570,8 @@ Data Sets Created:
 \series bold
 perres
 \series default
- only) Per-residue RMSDs; index is residue number.
+ only) Per-residue RMSDs;
+ index is residue number.
 \end_layout
 
 \begin_layout Description
@@ -38882,21 +39606,22 @@ run
 \end_layout
 
 \begin_layout Standard
-Calculate the coordinate RMSD of input frames to a reference frame (or reference
- trajectory).
- Both <mask> and <refmask> must specify the same number of atoms, otherwise
- an error will occur.
+Calculate the coordinate RMSD of input frames to a reference frame (or reference trajectory).
+ Both <mask> and <refmask> must specify the same number of atoms,
+ otherwise an error will occur.
  
 \end_layout
 
 \begin_layout Standard
-For example, say you have a trajectory and you want to calculate RMSD to
- two separate reference structures.
- To calculate the best-fit RMSD of the C, CA, and N atoms of residues 1
- to 20 in each frame to the C, CA, and N atoms of residues 3 to 23 in StructX.crd
-, and then calculate the no-fit RMSD of residue 7 to residue 7 in another
- structure named Struct-begin.rst7, writing both results to Grace-format
- file 
+For example,
+ say you have a trajectory and you want to calculate RMSD to two separate reference structures.
+ To calculate the best-fit RMSD of the C,
+ CA,
+ and N atoms of residues 1 to 20 in each frame to the C,
+ CA,
+ and N atoms of residues 3 to 23 in StructX.crd,
+ and then calculate the no-fit RMSD of residue 7 to residue 7 in another structure named Struct-begin.rst7,
+ writing both results to Grace-format file 
 \begin_inset Quotes eld
 \end_inset
 
@@ -38934,27 +39659,28 @@ If the
 perres
 \series default
 \color inherit
- keyword is specified, after the initial RMSD calculation the no-fit RMSD
- of specified residues is also calculated.
+ keyword is specified,
+ after the initial RMSD calculation the no-fit RMSD of specified residues is also calculated.
  So for example:
 \end_layout
 
 \begin_layout LyX-Code
-rmsd :10-260 reference perres perresout PRMS.dat range 190-211 perresmask
- &!(@H=)
+rmsd :10-260 reference perres perresout PRMS.dat range 190-211 perresmask &!(@H=)
 \end_layout
 
 \begin_layout Standard
 
 \family roman
-will first perform a best-fit RMSD calculation to the first specified reference
- structure using residues 10 to 260, then calculate the no-fit RMSD of residues
- 190 to 211 (excluding any hydrogen atoms), writing the results to PRMS.dat.
- Two additional recommendations for the 'perres' option: 1) try not including
- backbone atoms by using the 'perresmask' keyword, e.g.
- "perresmask &!@H,N,CA,HA,C,O", and 2) try using the 'perrescenter' keyword,
- which centers each residue prior to the 'nofit' calculation; this is useful
- for isolating changes in residue conformation.
+will first perform a best-fit RMSD calculation to the first specified reference structure using residues 10 to 260,
+ then calculate the no-fit RMSD of residues 190 to 211 (excluding any hydrogen atoms),
+ writing the results to PRMS.dat.
+ Two additional recommendations for the 'perres' option:
+ 1) try not including backbone atoms by using the 'perresmask' keyword,
+ e.g.
+ "perresmask &!@H,N,CA,HA,C,O",
+ and 2) try using the 'perrescenter' keyword,
+ which centers each residue prior to the 'nofit' calculation;
+ this is useful for isolating changes in residue conformation.
 \end_layout
 
 \begin_layout Subsection
@@ -38968,11 +39694,13 @@ Although the
 'rms2d'
 \series default
 \emph default
- command can still be specified as an action, it is now considered an analysis.
+ command can still be specified as an action,
+ it is now considered an analysis.
  See 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-rms2d"
+nolink "false"
 
 \end_inset
 
@@ -38990,11 +39718,13 @@ Although the
 'rmsavgcorr'
 \series default
 \emph default
- command can still be specified as an action, it is now considered an analysis.
+ command can still be specified as an action,
+ it is now considered an analysis.
  See 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-rmsavgcorr"
+nolink "false"
 
 \end_inset
 
@@ -39010,6 +39740,7 @@ See
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_atomicfluct"
+nolink "false"
 
 \end_inset
 
@@ -39104,8 +39835,8 @@ usedata
 \begin_inset space ~
 \end_inset
 
-name> If specified, use 3x3 rotation matrices in specified data set to rotate
- coordinates.
+name> If specified,
+ use 3x3 rotation matrices in specified data set to rotate coordinates.
 \end_layout
 
 \begin_deeper
@@ -39123,9 +39854,8 @@ calcfrom
 \begin_inset space ~
 \end_inset
 
-name> Instead of rotating coordinates, calculate rotations around the X
- Y and Z axes (as well as total rotation) in degrees from existing rotation
- matrices specified by <set name>.
+name> Instead of rotating coordinates,
+ calculate rotations around the X Y and Z axes (as well as total rotation) in degrees from existing rotation matrices specified by <set name>.
 \end_layout
 
 \begin_deeper
@@ -39208,13 +39938,16 @@ name>[T] (caclfrom only) Total rotation in degrees.
 
 \end_deeper
 \begin_layout Standard
-Rotate specified atoms around the X, Y, and/or Z axes by the specified amounts,
- around a user-defined axis (specified by <mask0> and <mask1>), or use a
- previously read in or generated data set of 3x3 matrices to perform rotations.
+Rotate specified atoms around the X,
+ Y,
+ and/or Z axes by the specified amounts,
+ around a user-defined axis (specified by <mask0> and <mask1>),
+ or use a previously read in or generated data set of 3x3 matrices to perform rotations.
 \end_layout
 
 \begin_layout Standard
-For example, to rotate the entire system 90 degrees around the X axis:
+For example,
+ to rotate the entire system 90 degrees around the X axis:
 \end_layout
 
 \begin_layout LyX-Code
@@ -39223,13 +39956,20 @@ rotate x 90
 
 \begin_layout Standard
 To rotate residue 270 90 degrees around the axis defined between atoms C1,
- C2, C3, C4, C5, and C6 in residue 270 and atoms C7, C8, C9, C10, C11, and
- C12 in residue 270:
+ C2,
+ C3,
+ C4,
+ C5,
+ and C6 in residue 270 and atoms C7,
+ C8,
+ C9,
+ C10,
+ C11,
+ and C12 in residue 270:
 \end_layout
 
 \begin_layout LyX-Code
-rotate :270 axis0 :270@C1,C2,C3,C4,C5,C6 axis1 :270@C7,C8,C9,C10,C11,C12
- 90.0
+rotate :270 axis0 :270@C1,C2,C3,C4,C5,C6 axis1 :270@C7,C8,C9,C10,C11,C12 90.0
 \end_layout
 
 \begin_layout Standard
@@ -39249,8 +39989,7 @@ rotate usedata RM
 \end_layout
 
 \begin_layout Standard
-To calculate rotations from rotation matrices generated by a previous RMSD
- calculation:
+To calculate rotations from rotation matrices generated by a previous RMSD calculation:
 \end_layout
 
 \begin_layout LyX-Code
@@ -39288,10 +40027,12 @@ The
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-rotdif"
+nolink "false"
 
 \end_inset
 
-), and requires that rotation matrices be generated via an 
+),
+ and requires that rotation matrices be generated via an 
 \series bold
 \emph on
 rmsd
@@ -39336,6 +40077,8 @@ runavg | runningaverage
 \begin_layout LyX-Code
 runavg
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -39362,15 +40105,13 @@ runningaverage
 \end_layout
 
 \begin_layout Standard
-Replaces the current frame with a running average over a number of frames
- specified by 
+Replaces the current frame with a running average over a number of frames specified by 
 \series bold
 window
 \series default
  <window_size> (5 if not specified).
- This means that in order to build up the correct number of frames to calculate
- the average, the first <window_size> minus one frames will not be processed
- by subsequent actions.
+ This means that in order to build up the correct number of frames to calculate the average,
+ the first <window_size> minus one frames will not be processed by subsequent actions.
  So for example given the input:
 \end_layout
 
@@ -39383,9 +40124,13 @@ rms first out rmsd.dat
 \end_layout
 
 \begin_layout Standard
-the rms command will not take effect until frame 3 since that is the first
- time 3 frames are available for averaging (1, 2, and 3).
- The next frame processed would be an average of frames 2, 3, and 4, etc.
+the rms command will not take effect until frame 3 since that is the first time 3 frames are available for averaging (1,
+ 2,
+ and 3).
+ The next frame processed would be an average of frames 2,
+ 3,
+ and 4,
+ etc.
 \end_layout
 
 \begin_layout Subsection
@@ -39414,6 +40159,8 @@ name "subsec:cpptraj-secstruct"
 \begin_layout LyX-Code
 secstruct
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -39467,8 +40214,8 @@ secstruct
 \begin_inset space ~
 \end_inset
 
-<sumfilename>] Write average secondary structure values for each residue
- to <sumfilename>; if not specified <filename>.sum is used.
+<sumfilename>] Write average secondary structure values for each residue to <sumfilename>;
+ if not specified <filename>.sum is used.
 \end_layout
 
 \begin_layout Description
@@ -39476,18 +40223,16 @@ secstruct
 \begin_inset space ~
 \end_inset
 
-<filename>] Write overall secondary structure assignment (based on dominant
- secondary structure type for each residue) to file.
+<filename>] Write overall secondary structure assignment (based on dominant secondary structure type for each residue) to file.
 \end_layout
 
 \begin_layout Description
-[ptrajformat] Write secondary structure as a string of characters for each
- frame, similar to ptraj output.
+[ptrajformat] Write secondary structure as a string of characters for each frame,
+ similar to ptraj output.
 \end_layout
 
 \begin_layout Description
-[betadetail] Record anti-parallel beta and parallel beta in place of extended
- and bridge secondary structure.
+[betadetail] Record anti-parallel beta and parallel beta in place of extended and bridge secondary structure.
  If a residue could be both only anti-parallel is reported.
 \end_layout
 
@@ -39560,8 +40305,8 @@ name>] Backbone carbonyl oxygen atom name (default 'O').
 \begin_inset space ~
 \end_inset
 
-name>] Cysteine sulfur atom name, used to ignore disulfide connectivity
- (default 'SG').
+name>] Cysteine sulfur atom name,
+ used to ignore disulfide connectivity (default 'SG').
 \end_layout
 
 \begin_layout Standard
@@ -39569,18 +40314,20 @@ Data Sets Created:
 \end_layout
 
 \begin_layout Description
-<name>[res] Residue secondary structure per frame; index corresponds to
- residue number.
+<name>[res] Residue secondary structure per frame;
+ index corresponds to residue number.
  If 
 \series bold
 ptrajformat
 \series default
- specified these will be characters, otherwise integers (see table below).
+ specified these will be characters,
+ otherwise integers (see table below).
 \end_layout
 
 \begin_layout Description
-<name>[avgss] Average of each type of secondary structure; index corresponds
- to secondary structure type (see table below; no index for 
+<name>[avgss] Average of each type of secondary structure;
+ index corresponds to secondary structure type (see table below;
+ no index for 
 \begin_inset Quotes eld
 \end_inset
 
@@ -39596,13 +40343,11 @@ None
 \end_layout
 
 \begin_layout Description
-<name>[Para] Total fraction of residues with parallel beta structure vs
- time.
+<name>[Para] Total fraction of residues with parallel beta structure vs time.
 \end_layout
 
 \begin_layout Description
-<name>[Anti] Total fraction of residues with anti-parallel beta structure
- vs time.
+<name>[Anti] Total fraction of residues with anti-parallel beta structure vs time.
 \end_layout
 
 \begin_layout Description
@@ -39629,12 +40374,11 @@ None
 \begin_layout Standard
 
 \series bold
-As of version 4.18.0, this command now produces output that better conforms
- with the original definitions in Kabsch and Sander 1983; namely that Extended
- beta (i.e.
+As of version 4.18.0,
+ this command now produces output that better conforms with the original definitions in Kabsch and Sander 1983;
+ namely that Extended beta (i.e.
  2 or more consecutive beta bridges of the same type) and beta Bridge (i.e.
- an isolated beta bridge) are now reported instead of anti-parallel and
- parallel beta.
+ an isolated beta bridge) are now reported instead of anti-parallel and parallel beta.
  To restore the original behavior the 'betadetail' keyword must be specified.
 \end_layout
 
@@ -39653,8 +40397,7 @@ Calculate secondary structural propensities for residues in
 \series bold
 <mask>
 \series default
- (or all solute residues if no mask given) using the DSSP method of Kabsch
- and Sander
+ (or all solute residues if no mask given) using the DSSP method of Kabsch and Sander
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Kabsch83"
@@ -39662,8 +40405,8 @@ literal "true"
 
 \end_inset
 
-, which assigns secondary structure types for residues based on backbone
- amide (N-H) and carbonyl (C=O) atom positions.
+,
+ which assigns secondary structure types for residues based on backbone amide (N-H) and carbonyl (C=O) atom positions.
  By default 
 \shape italic
 cpptraj
@@ -39676,7 +40419,8 @@ N
 \begin_inset Quotes erd
 \end_inset
 
-, 
+,
+ 
 \begin_inset Quotes eld
 \end_inset
 
@@ -39684,7 +40428,8 @@ H
 \begin_inset Quotes erd
 \end_inset
 
-, 
+,
+ 
 \begin_inset Quotes eld
 \end_inset
 
@@ -39692,7 +40437,8 @@ C
 \begin_inset Quotes erd
 \end_inset
 
-, and 
+,
+ and 
 \begin_inset Quotes eld
 \end_inset
 
@@ -39716,14 +40462,15 @@ nameX
 \series default
  keywords (e.g.
  'nameH HN').
- Note that it is expected that some residues will not have all of these
- atoms (such as proline); in this case 
+ Note that it is expected that some residues will not have all of these atoms (such as proline);
+ in this case 
 \shape italic
 cpptraj
 \shape default
  will print an informational message but the calculation will proceed normally.
  If a residue has no atoms selected it will be skipped.
- When determining residue connecivity, disulfide bonds will be ignored;
+ When determining residue connecivity,
+ disulfide bonds will be ignored;
  
 \emph on
 cpptraj
@@ -39757,13 +40504,13 @@ out
 \end_layout
 
 \begin_layout Standard
-where <#Frame> is the frame number and <ResX SS> is an integer representing
- the calculated secondary structure type for residue X.
+where <#Frame> is the frame number and <ResX SS> is an integer representing the calculated secondary structure type for residue X.
  If the keyword 
 \series bold
 ptrajformat
 \series default
- is specified, the output format will instead be:
+ is specified,
+ the output format will instead be:
 \end_layout
 
 \begin_layout LyX-Code
@@ -39771,17 +40518,13 @@ ptrajformat
 \end_layout
 
 \begin_layout Standard
-where STRING is a string of characters (one for each residue) where each
- character represents a different structural type (this format is similar
- to what 
+where STRING is a string of characters (one for each residue) where each character represents a different structural type (this format is similar to what 
 \shape italic
 ptraj
 \shape default
  had outputed and is retained for backwards compatibility).
- The various secondary structure types and their corresponding integer/character
- are listed below.
- If 'betadetail' is specified what is reported and the characters used change
- slightly.
+ The various secondary structure types and their corresponding integer/character are listed below.
+ If 'betadetail' is specified what is reported and the characters used change slightly.
 \begin_inset Separator latexpar
 \end_inset
 
@@ -40147,8 +40890,7 @@ Bend
 \end_layout
 
 \begin_layout Standard
-Average structural propensities over all frames for each residue will be
- written to the file specified by 
+Average structural propensities over all frames for each residue will be written to the file specified by 
 \series bold
 sumout
 \series default
@@ -40169,17 +40911,16 @@ sumout
 sumout
 \series default
  is not specified).
- The total structural propensity over all residues for each secondary structure
- type will be written to the file specified by 
+ The total structural propensity over all residues for each secondary structure type will be written to the file specified by 
 \series bold
 totalout
 \series default
 .
- If assignout is specified, the overall secondary structure assignment for
- each residue will be printed in two line chunks of 50 residues, with the
- first line containing the residue number the line starts with and one character
- residue names, and the second line containing secondary structure assignment
- using DSSP-style characters, like so:
+ If assignout is specified,
+ the overall secondary structure assignment for each residue will be printed in two line chunks of 50 residues,
+ with the first line containing the residue number the line starts with and one character residue names,
+ and the second line containing secondary structure assignment using DSSP-style characters,
+ like so:
 \end_layout
 
 \begin_layout LyX-Code
@@ -40192,8 +40933,8 @@ totalout
 
 \begin_layout Standard
 The output of secstruct command is amenable to visualization with gnuplot.
- To generate a 2D map-style plot of secondary structure vs time, with each
- residue on the Y axis simply give the output file a 
+ To generate a 2D map-style plot of secondary structure vs time,
+ with each residue on the Y axis simply give the output file a 
 \begin_inset Quotes eld
 \end_inset
 
@@ -40202,9 +40943,9 @@ The output of secstruct command is amenable to visualization with gnuplot.
 \end_inset
 
  extension.
- For example, to generate a 2D map of secondary structure vs time, with
- different colors representing different secondary structure types for residues
- 1-22:
+ For example,
+ to generate a 2D map of secondary structure vs time,
+ with different colors representing different secondary structure types for residues 1-22:
 \end_layout
 
 \begin_layout LyX-Code
@@ -40220,7 +40961,8 @@ gnuplot dssp.gnu
 \end_layout
 
 \begin_layout Standard
-Similarly, the 
+Similarly,
+ the 
 \series bold
 sumout
 \series default
@@ -40256,8 +40998,7 @@ dgbulk
 \series bold
 dhbulk
 \series default
- for different water models can be calculated from pure water simulations
- with the 
+ for different water models can be calculated from pure water simulations with the 
 \series bold
 purewater
 \series default
@@ -40277,8 +41018,7 @@ setvelocity [<mask>]
 \end_layout
 
 \begin_layout LyX-Code
-               scale [factor <fac>] [sx <xfac>] [sy <yfac>] [sz <zfac>]
- |
+               scale [factor <fac>] [sx <xfac>] [sy <yfac>] [sz <zfac>] |
 \end_layout
 
 \begin_layout LyX-Code
@@ -40395,8 +41135,9 @@ none Remove any velocities.
 \end_layout
 
 \begin_layout Description
-modify If specified, do not set, just modify any existing velocities (via
- 'ntc' or 'zeromomentum').
+modify If specified,
+ do not set,
+ just modify any existing velocities (via 'ntc' or 'zeromomentum').
 \end_layout
 
 \begin_layout Description
@@ -40417,8 +41158,10 @@ ntc
 \end_inset
 
 <#> Correct set velocities for SHAKE constraints.
- Numbers match sander/pmemd: 1 = no SHAKE, 2 = SHAKE on hydrogens, 3 = SHAKE
- on all atoms.
+ Numbers match sander/pmemd:
+ 1 = no SHAKE,
+ 2 = SHAKE on hydrogens,
+ 3 = SHAKE on all atoms.
 \end_layout
 
 \begin_layout Description
@@ -40438,17 +41181,16 @@ epsilon
 \end_layout
 
 \begin_layout Description
-zeromomentum If specified adjust velocities so the total momentum of atoms
- in <mask> is zero.
+zeromomentum If specified adjust velocities so the total momentum of atoms in <mask> is zero.
 \end_layout
 
 \end_deeper
 \begin_layout Standard
-Set velocities in frame for atoms in <mask> using Maxwellian distribution
- based on given temperature, optionally adjusted for SHAKE constraints.
+Set velocities in frame for atoms in <mask> using Maxwellian distribution based on given temperature,
+ optionally adjusted for SHAKE constraints.
  Can also be used to modify existing velocity information or remove it entirely.
- The total momentum of the system can be set to zero as well, which can
- be useful for NVE simulations.
+ The total momentum of the system can be set to zero as well,
+ which can be useful for NVE simulations.
 \end_layout
 
 \begin_layout Subsection
@@ -40511,18 +41253,18 @@ solv
 \begin_layout Description
 [purewater] The system is pure water.
  Used to parametrize the bulk values.
- If this is specified, none of the below options are relevant.
+ If this is specified,
+ none of the below options are relevant.
 \end_layout
 
 \begin_layout Description
-<peaksname> Data set or file (XYZ- format: see below) with the peak locations
- present .
+<peaksname> Data set or file (XYZ- format:
+ see below) with the peak locations present .
  
 \end_layout
 
 \begin_layout Description
-[reorder] The solvent should be re-ordered so the same solvent molecule
- is always in the same site.
+[reorder] The solvent should be re-ordered so the same solvent molecule is always in the same site.
 \end_layout
 
 \begin_layout Description
@@ -40539,12 +41281,12 @@ summary
 \end_inset
 
 <summary> File with the summary of all SPAM results.
- If not specified, no SPAM energies will be calculated.
+ If not specified,
+ no SPAM energies will be calculated.
 \end_layout
 
 \begin_layout Description
-site_size <size> Size of the water site around each density peak (sphere
- diameter/box edge length) in Ang.
+site_size <size> Size of the water site around each density peak (sphere diameter/box edge length) in Ang.
 \end_layout
 
 \begin_layout Description
@@ -40564,8 +41306,8 @@ dgbulk
 \begin_inset space ~
 \end_inset
 
-<dgbulk> SPAM free energy of the bulk solvent in kcal/mol; default is -30.3
- kcal/mol (SPC/E water).
+<dgbulk> SPAM free energy of the bulk solvent in kcal/mol;
+ default is -30.3 kcal/mol (SPC/E water).
 \end_layout
 
 \begin_layout Description
@@ -40573,8 +41315,8 @@ dhbulk
 \begin_inset space ~
 \end_inset
 
-<dhbulk> SPAM enthalpy of the bulk solvent in kcal/mol; default is -22.2
- kcal/mol (SPC/E water).
+<dhbulk> SPAM enthalpy of the bulk solvent in kcal/mol;
+ default is -22.2 kcal/mol (SPC/E water).
 \end_layout
 
 \begin_layout Standard
@@ -40616,18 +41358,17 @@ literal "true"
 \end_inset
 
 .
- Briefly, this method identifies and estimates the free energy profiles
- of bound waters via calculation of the distribution of interaction energies
- between the water and it's environment from explicit solvent MD trajectories.
- The interaction energies are calculated using a force- and energy-shifted
- electrostatic term with a hard cutoff.
- For a given peak, SPAM energies will only be calculated for peaks where
- the peak is singly-occupied (i.e.
+ Briefly,
+ this method identifies and estimates the free energy profiles of bound waters via calculation of the distribution of interaction energies between the water and it's environment from explicit solvent MD trajectories.
+ The interaction energies are calculated using a force- and energy-shifted electrostatic term with a hard cutoff.
+ For a given peak,
+ SPAM energies will only be calculated for peaks where the peak is singly-occupied (i.e.
  a multiple-occupied peak is not considered valid).
 \end_layout
 
 \begin_layout Standard
-Prior to this command, the 
+Prior to this command,
+ the 
 \series bold
 \emph on
 volmap
@@ -40641,6 +41382,7 @@ peakfile
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_volmap"
+nolink "false"
 
 \end_inset
 
@@ -40651,7 +41393,8 @@ reference "subsec:cpptraj_volmap"
 volmap
 \series default
 \emph default
- command, the peaks file should have one line per peak with format:
+ command,
+ the peaks file should have one line per peak with format:
 \end_layout
 
 \begin_layout LyX-Code
@@ -40704,7 +41447,8 @@ mask Atoms for which MSDs will be computed.
 \end_layout
 
 \begin_layout Description
-out Output file: time vs.
+out Output file:
+ time vs.
  MSD.
  
 \end_layout
@@ -40716,7 +41460,9 @@ time Time step in the trajectory.
 
 \begin_layout Description
 mask2 Compute MSDs only within the lower and upper limit of mask2.
- IMPORTANT: may be very slow!!! 
+ IMPORTANT:
+ may be very slow!!!
+ 
 \end_layout
 
 \begin_layout Description
@@ -40741,8 +41487,7 @@ avout Output file containing average distances.
 \end_layout
 
 \begin_layout Description
-x|y|z|xy|xz|yz|xyz Computation of the mean square displacement in the chosen
- dimension.
+x|y|z|xy|xz|yz|xyz Computation of the mean square displacement in the chosen dimension.
  (xyz) 
 \end_layout
 
@@ -40759,8 +41504,7 @@ com Calculate MSD for centre of mass.
 
 \end_deeper
 \begin_layout Standard
-Calculate diffusion for selected atoms using code based on the 'diffusion'
- routine developed by Hannes Loeffler at STFC (http://www.stfc.ac.uk/CSE).
+Calculate diffusion for selected atoms using code based on the 'diffusion' routine developed by Hannes Loeffler at STFC (http://www.stfc.ac.uk/CSE).
 \end_layout
 
 \begin_layout Subsection
@@ -40770,6 +41514,8 @@ strip
 \begin_layout LyX-Code
 strip
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -40807,8 +41553,7 @@ charge
 \begin_inset space ~
 \end_inset
 
-charge> Scale charges so total charge of remaining atoms matches the specified
- <new charge>.
+charge> Scale charges so total charge of remaining atoms matches the specified <new charge>.
 \end_layout
 
 \begin_layout Description
@@ -40816,8 +41561,7 @@ charge> Scale charges so total charge of remaining atoms matches the specified
 \begin_inset space ~
 \end_inset
 
-<prefix>] Write out stripped topology file with name '<prefix>.<Original
- Topology Name>'.
+<prefix>] Write out stripped topology file with name '<prefix>.<Original Topology Name>'.
 \end_layout
 
 \begin_layout Description
@@ -40851,8 +41595,8 @@ Strip all atoms specified by
 \series bold
 outprefix
 \series default
- keyword can be used to write stripped topologies; stripped Amber topologies
- are fully-functional.
+ keyword can be used to write stripped topologies;
+ stripped Amber topologies are fully-functional.
  Available options for 
 \series bold
 <parmopts>
@@ -40868,8 +41612,8 @@ help Formats parmwrite
 \end_layout
 
 \begin_layout Standard
-Note that stripping a system renumbers all atoms and residues, so for example
- after this command:
+Note that stripping a system renumbers all atoms and residues,
+ so for example after this command:
 \end_layout
 
 \begin_layout LyX-Code
@@ -40877,13 +41621,14 @@ strip :1
 \end_layout
 
 \begin_layout Standard
-residue 1 will be gone, and the former second residue will now be the first,
+residue 1 will be gone,
+ and the former second residue will now be the first,
  and so on.
 \end_layout
 
 \begin_layout Standard
-For example, to strip all residues named WAT from each topology/coordinate
- frame:
+For example,
+ to strip all residues named WAT from each topology/coordinate frame:
 \end_layout
 
 \begin_layout LyX-Code
@@ -40898,9 +41643,10 @@ The next example uses a distance-based mask to strip atoms in a single frame.
 mask
 \series default
 \shape default
- command, distance-based masks do not update on a per-frame basis.
- To strip all residues outside of 6.0 from any atom in residues 1 to 14 and
- write out the stripped topology and coordinates, both with no box information:
+ command,
+ distance-based masks do not update on a per-frame basis.
+ To strip all residues outside of 6.0 from any atom in residues 1 to 14 and write out the stripped topology and coordinates,
+ both with no box information:
 \end_layout
 
 \begin_layout LyX-Code
@@ -40937,6 +41683,8 @@ name "subsec:cpptraj_surf"
 \begin_layout LyX-Code
 surf
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -40974,7 +41722,8 @@ solutemask
 \begin_inset space ~
 \end_inset
 
-<mask> If specified, calculate the contribution of <mask1> to <mask>.
+<mask> If specified,
+ calculate the contribution of <mask1> to <mask>.
 \end_layout
 
 \begin_layout Description
@@ -40982,7 +41731,8 @@ offset
 \begin_inset space ~
 \end_inset
 
-<offset> Increment van der Waals radii by <offset>; 1.4 Ang.
+<offset> Increment van der Waals radii by <offset>;
+ 1.4 Ang.
  is the default (as used by Amber).
 \end_layout
 
@@ -40991,8 +41741,7 @@ nbrcut
 \begin_inset space ~
 \end_inset
 
-<cut> Only atoms with van der Waals radii greater than <cut> are considered
- to have neighbors (2.5 Ang Amber default).
+<cut> Only atoms with van der Waals radii greater than <cut> are considered to have neighbors (2.5 Ang Amber default).
 \end_layout
 
 \end_deeper
@@ -41001,9 +41750,8 @@ Calculate the surface area in Å
 \begin_inset Formula $^{\text{2}}$
 \end_inset
 
- of atoms in <mask> (if no mask specified, all atoms not marked as 'solvent'
- that are part of a molecule > 1 atom in size) using the LCPO algorithm
- of Weiser et al.
+ of atoms in <mask> (if no mask specified,
+ all atoms not marked as 'solvent' that are part of a molecule > 1 atom in size) using the LCPO algorithm of Weiser et al.
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Weiser99"
@@ -41012,24 +41760,24 @@ literal "true"
 \end_inset
 
 .
- In order for this to work, the topology needs to have bond information
- and atom type information.
+ In order for this to work,
+ the topology needs to have bond information and atom type information.
  
 \end_layout
 
 \begin_layout Standard
-Note that even if <mask> does not include all solute atoms, the neighbor
- list is still calculated for all solute atoms so the surface area calculated
- reflects the contribution of atoms in <mask> to the overall surface area,
+Note that even if <mask> does not include all solute atoms,
+ the neighbor list is still calculated for all solute atoms so the surface area calculated reflects the contribution of atoms in <mask> to the overall surface area,
  not the surface area of <mask> as an isolated system.
- As a result, it may be possible to obtain a negative surface area if only
- a small fraction of the solute is selected.
+ As a result,
+ it may be possible to obtain a negative surface area if only a small fraction of the solute is selected.
 \end_layout
 
 \begin_layout Standard
-For example, to calculate the overall surface area of all solute atoms,
- as well as the contribution of residue 1 to the overall surface area, writing
- both results to 
+For example,
+ to calculate the overall surface area of all solute atoms,
+ as well as the contribution of residue 1 to the overall surface area,
+ writing both results to 
 \begin_inset Quotes eld
 \end_inset
 
@@ -41060,8 +41808,7 @@ name "subsec:cpptraj_symmrmsd"
 \end_layout
 
 \begin_layout LyX-Code
-symmrmsd  [<name>] [<mask>] [<refmask>] [out <filename>] [nofit] [mass]
- [remap]
+symmrmsd  [<name>] [<mask>] [<refmask>] [out <filename>] [nofit] [mass] [remap]
 \end_layout
 
 \begin_layout LyX-Code
@@ -41082,12 +41829,15 @@ symmrmsd  [<name>] [<mask>] [<refmask>] [out <filename>] [nofit] [mass]
 \end_layout
 
 \begin_layout Description
-[<mask>] Mask of atoms to calculate RMSD for; if not specified, calculate
- for all atoms.
+[<mask>] Mask of atoms to calculate RMSD for;
+ if not specified,
+ calculate for all atoms.
 \end_layout
 
 \begin_layout Description
-[<refmask>] Reference mask; if not specified, use 
+[<refmask>] Reference mask;
+ if not specified,
+ use 
 \series bold
 <mask>
 \series default
@@ -41156,8 +41906,7 @@ refindex
 
 <#>
 \series default
- Use previously read in reference structure specified by <#> (based on order
- read in).
+ Use previously read in reference structure specified by <#> (based on order read in).
 \end_layout
 
 \begin_layout Description
@@ -41173,13 +41922,12 @@ reftraj
 \begin_inset space ~
 \end_inset
 
-<name> Use frames from COORDS set <name> or read in from trajectory file
- <name> as references.
- Each frame from <name> is used in turn, so that frame 1 is compared to
- frame 1 from <name>, frame 2 is compared to frame 2 from <name> and so
- on.
- If <trajname> runs out of frames before processing is complete, the last
- frame of <trajname> continues to be used as the reference.
+<name> Use frames from COORDS set <name> or read in from trajectory file <name> as references.
+ Each frame from <name> is used in turn,
+ so that frame 1 is compared to frame 1 from <name>,
+ frame 2 is compared to frame 2 from <name> and so on.
+ If <trajname> runs out of frames before processing is complete,
+ the last frame of <trajname> continues to be used as the reference.
 \begin_inset Separator latexpar
 \end_inset
 
@@ -41208,8 +41956,8 @@ parmindex
 \series bold
 reftraj
 \series default
- specifies a file associate trajectory <name> with specified topology; if
- not specified the first topology is used.
+ specifies a file associate trajectory <name> with specified topology;
+ if not specified the first topology is used.
 \end_layout
 
 \end_deeper
@@ -41217,25 +41965,22 @@ reftraj
 \begin_layout Standard
 Perform symmetry-corrected RMSD calculation.
  This is done by identifying potential symmetric atoms in each residue,
- performing an initial best-fit, then determining which configuration of
- symmetric atoms will give the lowest RMSD using atomic distance to reference
- atoms.
+ performing an initial best-fit,
+ then determining which configuration of symmetric atoms will give the lowest RMSD using atomic distance to reference atoms.
  
 \end_layout
 
 \begin_layout Standard
 
 \series bold
-Note that when re-mapping, all atoms in the residues of interest should
- be selected to prevent cases where selected symmetric atoms are swapped
- but the atoms they are bonded to are not
+Note that when re-mapping,
+ all atoms in the residues of interest should be selected to prevent cases where selected symmetric atoms are swapped but the atoms they are bonded to are not
 \series default
 .
- Also, occasionally larger symmetric structures (e.g.
- 6 membered rings) may become distorted due to only part of the residue
- being corrected for symmetry.
- This appears to happen about 4% of the time but does not overly inflate
- the RMSD.
+ Also,
+ occasionally larger symmetric structures (e.g.
+ 6 membered rings) may become distorted due to only part of the residue being corrected for symmetry.
+ This appears to happen about 4% of the time but does not overly inflate the RMSD.
  The 
 \series bold
 \shape italic
@@ -41252,9 +41997,9 @@ symmrmsd
 \end_layout
 
 \begin_layout Standard
-Warning: the symmetry correction is generally robust enough to account for
- symmetries in the standard amino and nucleic acid residues, but has not
- been extensively tested on residues with more extended types of symmetry.
+Warning:
+ the symmetry correction is generally robust enough to account for symmetries in the standard amino and nucleic acid residues,
+ but has not been extensively tested on residues with more extended types of symmetry.
 \end_layout
 
 \begin_layout Subsection
@@ -41291,7 +42036,8 @@ temperature [<name>] [out <filename>]
 \end_layout
 
 \begin_layout Description
-frame Do not calculate temperature; use existing frame temperature.
+frame Do not calculate temperature;
+ use existing frame temperature.
 \end_layout
 
 \begin_layout Description
@@ -41303,8 +42049,10 @@ frame Do not calculate temperature; use existing frame temperature.
 \begin_inset space ~
 \end_inset
 
-<#>] Value of SHAKE bond constraint: 1 - none, 2 - bonds to H, 3- all bonds
- (equivalent to SANDER/PMEMD).
+<#>] Value of SHAKE bond constraint:
+ 1 - none,
+ 2 - bonds to H,
+ 3- all bonds (equivalent to SANDER/PMEMD).
 \end_layout
 
 \begin_layout Description
@@ -41316,8 +42064,9 @@ frame Do not calculate temperature; use existing frame temperature.
 \begin_inset space ~
 \end_inset
 
-{trans|rot|both}] Correct for removed translational, rotational, or both
- kinds of degrees of freedom.
+{trans|rot|both}] Correct for removed translational,
+ rotational,
+ or both kinds of degrees of freedom.
 \end_layout
 
 \end_deeper
@@ -41327,7 +42076,8 @@ Calculate temperature in frame based on velocity information.
 \series bold
 update
 \series default
-' is specified, update frame temperature too.
+' is specified,
+ update frame temperature too.
  If '
 \series bold
 frame
@@ -41337,16 +42087,17 @@ frame
 \end_layout
 
 \begin_layout Standard
-The 'ntc' keyword can be used to correct for lost degrees of freedom due
- to SHAKE constraints (2 = bonds to hydrogen, 3 = all bonds).
- The 'remove' keyword can be used to account for removed translational and/or
- rotational degrees of freedom.
+The 'ntc' keyword can be used to correct for lost degrees of freedom due to SHAKE constraints (2 = bonds to hydrogen,
+ 3 = all bonds).
+ The 'remove' keyword can be used to account for removed translational and/or rotational degrees of freedom.
 \end_layout
 
 \begin_layout Standard
-For example, if using a trajectory that has been generated with SHAKE on
- hydrogens, no periodic boundary conditions (i.e.
- no box), and has had the center of mass periodically removed:
+For example,
+ if using a trajectory that has been generated with SHAKE on hydrogens,
+ no periodic boundary conditions (i.e.
+ no box),
+ and has had the center of mass periodically removed:
 \end_layout
 
 \begin_layout LyX-Code
@@ -41354,9 +42105,10 @@ temperature T1 ntc 2 remove both out T1.dat
 \end_layout
 
 \begin_layout Standard
-If using a trajectory that has been generated with SHAKE on hydrogens, periodic
- boundary conditions (i.e.
- with a box), and has had the center of mass periodically removed:
+If using a trajectory that has been generated with SHAKE on hydrogens,
+ periodic boundary conditions (i.e.
+ with a box),
+ and has had the center of mass periodically removed:
 \end_layout
 
 \begin_layout LyX-Code
@@ -41364,8 +42116,9 @@ temperature T1 ntc 2 remove trans out T1.dat
 \end_layout
 
 \begin_layout Standard
-If using a trajectory that has been generated with SHAKE on all bonds, periodic
- boundary conditions, and no center of mass motion removal:
+If using a trajectory that has been generated with SHAKE on all bonds,
+ periodic boundary conditions,
+ and no center of mass motion removal:
 \end_layout
 
 \begin_layout LyX-Code
@@ -41402,7 +42155,8 @@ dt
 \end_layout
 
 \begin_layout Description
-[update] If specified, modify any existing time info.
+[update] If specified,
+ modify any existing time info.
 \end_layout
 
 \begin_layout Description
@@ -41411,10 +42165,11 @@ remove Remove any time info from frame.
 
 \end_deeper
 \begin_layout Standard
-Either add time information to frames, modify existing time information
- in frames, or remove existing time information from frames.
- Note that currently COORDS data sets do not store time information, so
- using this command with the 
+Either add time information to frames,
+ modify existing time information in frames,
+ or remove existing time information from frames.
+ Note that currently COORDS data sets do not store time information,
+ so using this command with the 
 \series bold
 \emph on
 crdaction
@@ -41428,8 +42183,7 @@ tordiff
 \end_layout
 
 \begin_layout LyX-Code
-tordiff [<set name>] [<mask>] [mass] [out <file>] [diffout <file>] [time
- <dt>]
+tordiff [<set name>] [<mask>] [mass] [out <file>] [diffout <file>] [time <dt>]
 \end_layout
 
 \begin_deeper
@@ -41462,8 +42216,7 @@ name>] Output mean-squared-displacement data sets name.
 \begin_inset space ~
 \end_inset
 
-<file>] Write diffusion contants calculated from fits of mean-squared-displacent
- data sets to <filename>.
+<file>] Write diffusion contants calculated from fits of mean-squared-displacent data sets to <filename>.
 \end_layout
 
 \begin_layout Description
@@ -41542,8 +42295,7 @@ Calculate the diffusion via mean-squared displacement (in Å
 \begin_inset Formula $^{\text{2}}$
 \end_inset
 
-/ps) of specified molecules using the toroidal-view-preserving (TOR) scheme
- of Hummer et al.
+/ps) of specified molecules using the toroidal-view-preserving (TOR) scheme of Hummer et al.
  
 \series bold
 Note that currently this only works for orthogonal boxes
@@ -41574,6 +42326,7 @@ reference "subsec:cpptraj-diffusion"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
@@ -41590,13 +42343,12 @@ reference "subsec:cpptraj_unwrap"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
 ) commands which correct for box fluctuations via fractional coordinates,
- the TOR scheme corrects for box fluctuations by tracking the displacement
- of each molecule with respect to its position in the previous frame in
- Cartesian space.
+ the TOR scheme corrects for box fluctuations by tracking the displacement of each molecule with respect to its position in the previous frame in Cartesian space.
 \end_layout
 
 \begin_layout Standard
@@ -41606,13 +42358,15 @@ Diffusion constants are calculated in the same manner as the
 diffusion
 \series default
 \emph default
- command; for more details see 
+ command;
+ for more details see 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-diffusion"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
@@ -41620,8 +42374,8 @@ noprefix "false"
 \end_layout
 
 \begin_layout Standard
-For example, to calculate the diffusion (with data set name TOR) of waters
- (name WAT) in an orthogonal box using the toroidal scheme:
+For example,
+ to calculate the diffusion (with data set name TOR) of waters (name WAT) in an orthogonal box using the toroidal scheme:
 \end_layout
 
 \begin_layout LyX-Code
@@ -41678,14 +42432,16 @@ topoint
 \begin_inset space ~
 \end_inset
 
-<x>,<y>,<z> If specified, translate center of specified atoms to a specific
- point defined by <x>, <y>, and <z> in the given comma-separated list instead
- of by deltas.
+<x>,<y>,<z> If specified,
+ translate center of specified atoms to a specific point defined by <x>,
+ <y>,
+ and <z> in the given comma-separated list instead of by deltas.
 \end_layout
 
 \begin_deeper
 \begin_layout Description
-mass If specified, translate center of mass of specified atoms (
+mass If specified,
+ translate center of mass of specified atoms (
 \series bold
 topoint
 \series default
@@ -41703,11 +42459,13 @@ Translate atoms in
 \series bold
 <dx>
 \series default
- Å in the X direction, 
+ Å in the X direction,
+ 
 \series bold
 <dy>
 \series default
- Å in the Y direction, and 
+ Å in the Y direction,
+ and 
 \series bold
 <dz>
 \series default
@@ -41716,8 +42474,8 @@ Translate atoms in
 \series bold
 'topoint
 \series default
-' is specified, translate atoms in <mask> to the specified coordinates (also
- in Å).
+' is specified,
+ translate atoms in <mask> to the specified coordinates (also in Å).
 \end_layout
 
 \begin_layout Subsection
@@ -41727,6 +42485,8 @@ unstrip
 \begin_layout LyX-Code
 unstrip
 \begin_inset Index idx
+range none
+pageformat default
 status open
 
 \begin_layout Plain Layout
@@ -41739,13 +42499,14 @@ unstrip
 \end_layout
 
 \begin_layout Standard
-Requests that the original topology and frame be used for all following
- actions.
- This has the effect of undoing any command that modifies the state (such
- as strip).
- For example, the following code takes a solvated complex and uses a combination
- of strip, unstrip, and outtraj commands to write out separate dry complex,
- receptor, and ligand files:
+Requests that the original topology and frame be used for all following actions.
+ This has the effect of undoing any command that modifies the state (such as strip).
+ For example,
+ the following code takes a solvated complex and uses a combination of strip,
+ unstrip,
+ and outtraj commands to write out separate dry complex,
+ receptor,
+ and ligand files:
 \end_layout
 
 \begin_layout LyX-Code
@@ -41757,7 +42518,8 @@ trajin Complex.WAT.pdb
 \end_layout
 
 \begin_layout LyX-Code
-# Remove water, write complex
+# Remove water,
+ write complex
 \end_layout
 
 \begin_layout LyX-Code
@@ -41777,7 +42539,8 @@ unstrip
 \end_layout
 
 \begin_layout LyX-Code
-# Remove water and ligand, write receptor
+# Remove water and ligand,
+ write receptor
 \end_layout
 
 \begin_layout LyX-Code
@@ -41797,7 +42560,8 @@ unstrip
 \end_layout
 
 \begin_layout LyX-Code
-# Remove water and receptor, write ligand
+# Remove water and receptor,
+ write ligand
 \end_layout
 
 \begin_layout LyX-Code
@@ -41841,8 +42605,8 @@ unwrap [center] [{byatom | byres | bymol}] [avgucell <avg ucell set>]
 
 \begin_deeper
 \begin_layout Description
-[center] Unwrap by center of mass; otherwise unwrap by first atom position
- (byres and bymol).
+[center] Unwrap by center of mass;
+ otherwise unwrap by first atom position (byres and bymol).
 \end_layout
 
 \begin_layout Description
@@ -41870,7 +42634,8 @@ ucell
 \begin_inset space ~
 \end_inset
 
-set>] Average unit cell data set; useful when unwrapping NPT trajectories.
+set>] Average unit cell data set;
+ useful when unwrapping NPT trajectories.
 \end_layout
 
 \begin_layout Description
@@ -41931,15 +42696,18 @@ oidal-view-preserving scheme (orthogonal boxes only).
 
 \end_deeper
 \begin_layout Standard
-Under periodic boundary conditions, MD trajectories are not continuous if
- molecules are wrapped(imaged) into the central unit cell.
- Especially, in sander, with 
+Under periodic boundary conditions,
+ MD trajectories are not continuous if molecules are wrapped(imaged) into the central unit cell.
+ Especially,
+ in sander,
+ with 
 \emph on
 iwrap
 \emph default
-=1, molecular trajectories become discontinuous when a molecule crosses
- the boundary of the unit cell.
- This command, 
+=1,
+ molecular trajectories become discontinuous when a molecule crosses the boundary of the unit cell.
+ This command,
+ 
 \family sans
 \series bold
 \emph on
@@ -41951,8 +42719,7 @@ unwrap
 \shape italic
 mask
 \shape default
-ed molecules continuous by translating the molecules into the neighboring
- unit cells.
+ed molecules continuous by translating the molecules into the neighboring unit cells.
  It is the opposite function of 
 \family sans
 \series bold
@@ -41961,20 +42728,25 @@ image
 \family default
 \series default
 \emph default
-, but this command can also be used to place molecules side by side, for
- example, two strands of a DNA duplex.
- However, this command may fail if the 
+,
+ but this command can also be used to place molecules side by side,
+ for example,
+ two strands of a DNA duplex.
+ However,
+ this command may fail if the 
 \shape italic
 mask
 \shape default
 ed entities travel more than half of the box size within a single frame.
- Note that uwrapping by atom (the default behavior) is slower than unwrapping
- by residue or molecule, but is usually the safer method, especially if
- it is unknown if the original imaging was done by atom, by residue, or
- by molecule.
- If the optional reference arguments are specified, then the first frame
- is unwrapped according to the reference structure.
- Otherwise, the first frame is not modified.
+ Note that uwrapping by atom (the default behavior) is slower than unwrapping by residue or molecule,
+ but is usually the safer method,
+ especially if it is unknown if the original imaging was done by atom,
+ by residue,
+ or by molecule.
+ If the optional reference arguments are specified,
+ then the first frame is unwrapped according to the reference structure.
+ Otherwise,
+ the first frame is not modified.
 \end_layout
 
 \begin_layout Standard
@@ -41986,12 +42758,13 @@ noise
 \begin_inset Quotes erd
 \end_inset
 
- caused by box fluctuations in NPT trajectories, the average unit cell vectors
- describing the average box can be provided with the 
+ caused by box fluctuations in NPT trajectories,
+ the average unit cell vectors describing the average box can be provided with the 
 \series bold
 avgucell
 \series default
- keyword; see the 
+ keyword;
+ see the 
 \series bold
 \emph on
 avgbox
@@ -42004,6 +42777,7 @@ reference "subsec:cpptraj_avgbox"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
@@ -42029,20 +42803,18 @@ https://arxiv.org/abs/2303.09418
 scheme tor.
 
 \series default
- However, note that this currently 
+ However,
+ note that this currently 
 \series bold
 only works for orthogonal boxes
 \series default
- and may result in unrealistic trajectories (particularly at long times
- when molecules have had the chance to traverse multiple box lengths) and
- is only currently recommended for calculating diffusion.
+ and may result in unrealistic trajectories (particularly at long times when molecules have had the chance to traverse multiple box lengths) and is only currently recommended for calculating diffusion.
 \end_layout
 
 \begin_layout Standard
-As an example, assume that :1-10 is the first strand of a DNA duplex and
- :11-20 is the other strand of the duplex.
- Then the following commands could be used to create system where the two
- strands are not separated artificially:
+As an example,
+ assume that :1-10 is the first strand of a DNA duplex and :11-20 is the other strand of the duplex.
+ Then the following commands could be used to create system where the two strands are not separated artificially:
 \end_layout
 
 \begin_layout LyX-Code
@@ -42058,8 +42830,8 @@ image origin center familiar
 \end_layout
 
 \begin_layout Standard
-To unwrap an NPT trajectory by using the average unit cell (box), the calculate
- diffusion from the unwrapped trajectory:
+To unwrap an NPT trajectory by using the average unit cell (box),
+ the calculate diffusion from the unwrapped trajectory:
 \end_layout
 
 \begin_layout LyX-Code
@@ -42143,7 +42915,8 @@ vector [<name>] <Type> [out <filename> [ptrajoutput]] [<mask1>] [<mask2>]
 \end_layout
 
 \begin_layout Description
-<Type> Vector type; see below.
+<Type> Vector type;
+ see below.
 \end_layout
 
 \begin_layout Description
@@ -42155,8 +42928,7 @@ vector [<name>] <Type> [out <filename> [ptrajoutput]] [<mask1>] [<mask2>]
 \series bold
 <filename>
 \series default
- with format 'Vx Vy Vz Ox Oy Oz' where V denotes vector coordinates and
- 'O' denotes origin coordinates.
+ with format 'Vx Vy Vz Ox Oy Oz' where V denotes vector coordinates and 'O' denotes origin coordinates.
 \end_layout
 
 \begin_layout Description
@@ -42177,7 +42949,8 @@ ptraj
 \end_layout
 
 \begin_layout Description
-[<mask1>] Atom mask, required for all types except 
+[<mask1>] Atom mask,
+ required for all types except 
 \series bold
 'box'
 \series default
@@ -42185,7 +42958,8 @@ ptraj
 \end_layout
 
 \begin_layout Description
-[<mask2>] Second atom mask, only required for type 
+[<mask2>] Second atom mask,
+ only required for type 
 \series bold
 'mask'
 \series default
@@ -42197,8 +42971,7 @@ ptraj
 \end_layout
 
 \begin_layout Description
-[ired] Mark this vector for subsequent IRED analysis with commands 'matrix
- ired' and 'ired'.
+[ired] Mark this vector for subsequent IRED analysis with commands 'matrix ired' and 'ired'.
 \end_layout
 
 \begin_layout Description
@@ -42206,16 +42979,17 @@ ptraj
 \begin_inset space ~
 \end_inset
 
-<grid>] Name of grid data set to get box info from instead of frame for
- 
+<grid>] Name of grid data set to get box info from instead of frame for 
 \series bold
 box
 \series default
-, 
+,
+ 
 \series bold
 boxcenter
 \series default
-, and 
+,
+ and 
 \series bold
 ucell[x|y|z]
 \series default
@@ -42240,8 +43014,8 @@ magnitude
 
 \end_deeper
 \begin_layout Standard
-This command will keep track of a vector value (and its origin) over the
- trajectory; the data can be referenced for later use based on the 
+This command will keep track of a vector value (and its origin) over the trajectory;
+ the data can be referenced for later use based on the 
 \shape italic
 name
 \shape default
@@ -42279,8 +43053,8 @@ dipole Store the dipole and center of mass of the atoms specified in
 <mask1>
 \series default
 .
- The vector is not converted to appropriate units, nor is the value well-defined
- if the atoms in the mask are not overall charge neutral.
+ The vector is not converted to appropriate units,
+ nor is the value well-defined if the atoms in the mask are not overall charge neutral.
 \end_layout
 
 \begin_layout Description
@@ -42289,12 +43063,13 @@ center Store the center of mass of atoms in
 <mask1>
 \series default
 .
- The reference point is the origin (0.0, 0.0, 0.0).
+ The reference point is the origin (0.0,
+ 0.0,
+ 0.0).
 \end_layout
 
 \begin_layout Description
-corrplane This defines a vector perpendicular to the (least-squares best)
- plane through the atoms in 
+corrplane This defines a vector perpendicular to the (least-squares best) plane through the atoms in 
 \series bold
 <mask1>
 \series default
@@ -42308,7 +43083,9 @@ corrplane This defines a vector perpendicular to the (least-squares best)
 
 \begin_layout Description
 box (No mask needed) Store the box lengths of the trajectory.
- The reference point is the origin (0.0, 0.0, 0.0).
+ The reference point is the origin (0.0,
+ 0.0,
+ 0.0).
  
 \end_layout
 
@@ -42317,7 +43094,8 @@ boxcenter (No mask needed) Store the center of the box as a vector.
 \end_layout
 
 \begin_layout Description
-ucell{x|y|z}: (No mask needed) Store specified unit cell (i.e.
+ucell{x|y|z}:
+ (No mask needed) Store specified unit cell (i.e.
  box) vector.
 \end_layout
 
@@ -42330,8 +43108,7 @@ principal
 \begin_inset space ~
 \end_inset
 
-[x|y|z] Store one of the principal axis vectors determined by diagonalization
- of the inertial matrix from the coordinates of the atoms specified by 
+[x|y|z] Store one of the principal axis vectors determined by diagonalization of the inertial matrix from the coordinates of the atoms specified by 
 \series bold
 <mask1>
 \series default
@@ -42348,8 +43125,8 @@ x
 \begin_inset Quotes erd
 \end_inset
 
- (i.e., the hardest axis to rotate around) and the eigenvector with the smallest
- eigenvalue is considered 
+ (i.e.,
+ the hardest axis to rotate around) and the eigenvector with the smallest eigenvalue is considered 
 \begin_inset Quotes eld
 \end_inset
 
@@ -42374,7 +43151,8 @@ y
 \family typewriter
 z
 \family default
- are specified, then the 
+ are specified,
+ then the 
 \begin_inset Quotes eld
 \end_inset
 
@@ -42399,21 +43177,20 @@ force Store force of atoms in <mask1> (requires forces).
 \end_layout
 
 \begin_layout Standard
-Cpptraj supports writing out vector data in a pseudo-trajectory format for
- easy visualization.
- Once a vector data set has been generated the writedata command can be
- used with the vectraj keyword (see 
+Cpptraj supports writing out vector data in a pseudo-trajectory format for easy visualization.
+ Once a vector data set has been generated the writedata command can be used with the vectraj keyword (see 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "sec:Datafile-Commands"
+nolink "false"
 
 \end_inset
 
  for more details) to write a pseudo trajectory consisting of two atoms,
  one for the vector origin and one for the vector from the origin (i.e.
  V+O).
- For example, to create a MOL2 containing a pseudo-trajectory of the minimum-ima
-ged vector from residue 4 to residue 11:
+ For example,
+ to create a MOL2 containing a pseudo-trajectory of the minimum-imaged vector from residue 4 to residue 11:
 \end_layout
 
 \begin_layout LyX-Code
@@ -42433,8 +43210,7 @@ writedata v8.mol2 vectraj v8 trajfmt mol2
 \end_layout
 
 \begin_layout Standard
-Auto-correlation or cross-correlation functions can be calculated subsequently
- for vectors using either the 
+Auto-correlation or cross-correlation functions can be calculated subsequently for vectors using either the 
 \series bold
 \emph on
 corr
@@ -42454,8 +43230,7 @@ velocityautocorr
 \end_layout
 
 \begin_layout LyX-Code
-velocityautocorr [<set name>] [<mask>] [usevelocity] [out <filename>] [diffout
- <file>]
+velocityautocorr [<set name>] [<mask>] [usevelocity] [out <filename>] [diffout <file>]
 \end_layout
 
 \begin_layout LyX-Code
@@ -42481,8 +43256,7 @@ name>] Data set name.
 
 \begin_layout Description
 [usevelocity] Use velocity information in frame if present.
- This will only give sensible results if the velocities are recorded close
- to the order of the simulation time step.
+ This will only give sensible results if the velocities are recorded close to the order of the simulation time step.
 \end_layout
 
 \begin_layout Description
@@ -42519,8 +43293,7 @@ name>] Data set name.
 \end_layout
 
 \begin_layout Description
-[direct] Calculate VAC function directly instead of via FFT (will be much
- slower).
+[direct] Calculate VAC function directly instead of via FFT (will be much slower).
 \end_layout
 
 \begin_layout Description
@@ -42555,15 +43328,12 @@ DataSet Aspects:
 
 \end_deeper
 \begin_layout Standard
-Calculate the velocity autocorrelation (VAC) function averaged over the
- atoms in <mask>.
- Pseudo-velocities are calculated using coordinates and the specified time
- step.
- As with all time correlation functions the statistical noise will increase
- if the maximum lag is greater than half the total number of frames.
- In addition to calculating the velocity autocorrelation function, the self-diff
-usion coefficient will be reported in the output, calculated from the integral
- over the VAC function.
+Calculate the velocity autocorrelation (VAC) function averaged over the atoms in <mask>.
+ Pseudo-velocities are calculated using coordinates and the specified time step.
+ As with all time correlation functions the statistical noise will increase if the maximum lag is greater than half the total number of frames.
+ In addition to calculating the velocity autocorrelation function,
+ the self-diffusion coefficient will be reported in the output,
+ calculated from the integral over the VAC function.
 \end_layout
 
 \begin_layout Subsection
@@ -42644,8 +43414,8 @@ radscale
 <factor> 
 \family default
 Factor by which to scale radii (by division).
- To match the atomic radius of Oxygen used by the VMD volmap tool, a scaling
- factor of 1.36 should be used.
+ To match the atomic radius of Oxygen used by the VMD volmap tool,
+ a scaling factor of 1.36 should be used.
  Default 1.0.
 \end_layout
 
@@ -42654,8 +43424,8 @@ stepfac
 \begin_inset space ~
 \end_inset
 
-<factor> Factor for determining how many voxels to smear Gaussian (default
- 4.1, 1.0 for 
+<factor> Factor for determining how many voxels to smear Gaussian (default 4.1,
+ 1.0 for 
 \series bold
 sphere
 \series default
@@ -42663,7 +43433,8 @@ sphere
 \end_layout
 
 \begin_layout Description
-sphere When smearing Gaussian, skip voxels farther than radii/2.
+sphere When smearing Gaussian,
+ skip voxels farther than radii/2.
 \end_layout
 
 \begin_layout Description
@@ -42671,8 +43442,7 @@ radii
 \begin_inset space ~
 \end_inset
 
-{vdw|element} Specify either van der Waals radii (default) or elemental
- radii.
+{vdw|element} Specify either van der Waals radii (default) or elemental radii.
 \end_layout
 
 \begin_layout Description
@@ -42684,8 +43454,8 @@ splinedx
 \end_layout
 
 \begin_layout Description
-calcpeaks If specified, peaks in the grid density will be calculated and
- saved to set <setname> with aspect 
+calcpeaks If specified,
+ peaks in the grid density will be calculated and saved to set <setname> with aspect 
 \begin_inset Quotes eld
 \end_inset
 
@@ -42705,8 +43475,7 @@ peakcut
 
 <cutoff> 
 \family default
-The minimum density required to consider a local maximum a 'density peak'
- in the outputted peak file (default 0.05).
+The minimum density required to consider a local maximum a 'density peak' in the outputted peak file (default 0.05).
 \end_layout
 
 \begin_layout Description
@@ -42718,8 +43487,7 @@ peakfile
 
 <xyzfile> 
 \family default
-A file in XYZ-format that contains a carbon atom centered at the grid point
- of every local density maximum.
+A file in XYZ-format that contains a carbon atom centered at the grid point of every local density maximum.
  This file is necessary input to the spam action command.
 \end_layout
 
@@ -42760,7 +43528,10 @@ dy,
 
 dz 
 \family default
-The grid spacing (Angstroms) in the X-, Y-, and Z-dimensions, respectively.
+The grid spacing (Angstroms) in the X-,
+ Y-,
+ and Z-dimensions,
+ respectively.
 \end_layout
 
 \begin_layout Description
@@ -42772,7 +43543,9 @@ size
 
 <x,y,z> 
 \family default
-Specify the size of the grid in the X-, Y-, and Z-dimensions.
+Specify the size of the grid in the X-,
+ Y-,
+ and Z-dimensions.
  Must be used alongside the center argument.
 \end_layout
 
@@ -42787,7 +43560,8 @@ center
 <x,y,z> 
 \family default
 Specify the grid center explicitly.
- Note, the size argument must be present in this case.
+ Note,
+ the size argument must be present in this case.
  Default is the origin.
 \end_layout
 
@@ -42802,8 +43576,8 @@ centermask
 <mask> 
 \family default
 The mask around which the grid should be centered (via geometric center).
- If this is omitted and the center and size are not specified, the default
- <mask> entered (see above) is used in its place.
+ If this is omitted and the center and size are not specified,
+ the default <mask> entered (see above) is used in its place.
 \end_layout
 
 \begin_deeper
@@ -42816,9 +43590,9 @@ buffer
 
 <buffer> 
 \family default
-A buffer distance, in Angstroms, by which the edges of the grid should clear
- every atom of the centermask (or default mask if centermask is omitted)
- in every direction.
+A buffer distance,
+ in Angstroms,
+ by which the edges of the grid should clear every atom of the centermask (or default mask if centermask is omitted) in every direction.
  The default value is 3.
  The buffer is ignored if the center and size are specified (see below).
 \end_layout
@@ -42850,17 +43624,17 @@ calcpeaks
 
 \end_deeper
 \begin_layout Standard
-Grid data as a volumetric map, similar to the 'volmap' command in VMD.
- The density is calculated by treating each atom as a 3-dimensional Gaussian
- function whose standard deviation is equal to the van der Waals radius.
- The density calculated is the number density averaged over the entire simulatio
-n.
+Grid data as a volumetric map,
+ similar to the 'volmap' command in VMD.
+ The density is calculated by treating each atom as a 3-dimensional Gaussian function whose standard deviation is equal to the van der Waals radius.
+ The density calculated is the number density averaged over the entire simulation.
  The grid can be specified in one of three ways:
 \end_layout
 
 \begin_layout Enumerate
 An existing grid data set (from e.g.
- bounds), specified with the 
+ bounds),
+ specified with the 
 \series bold
 data
 \series default
@@ -42876,7 +43650,8 @@ size
 \series bold
 center
 \series default
- keywords (comma-separated strings, e.g.
+ keywords (comma-separated strings,
+ e.g.
  '20,20,20').
 \end_layout
 
@@ -42893,8 +43668,7 @@ buffer
 \end_layout
 
 \begin_layout Standard
-The calculation is sped up by using cubic splines to interpolate the exponential
- function when calculating the Gaussians.
+The calculation is sped up by using cubic splines to interpolate the exponential function when calculating the Gaussians.
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Roe2021"
@@ -42940,8 +43714,7 @@ watershell
 \end_layout
 
 \begin_layout LyX-Code
-watershell <solutemask> [out <filename>] [lower <lower cut>] [upper <upper
- cut>]
+watershell <solutemask> [out <filename>] [lower <lower cut>] [upper <upper cut>]
 \end_layout
 
 \begin_layout LyX-Code
@@ -43011,9 +43784,7 @@ DataSet Aspects:
 
 \end_deeper
 \begin_layout Standard
-This option will count the number of waters within a certain distance of
- the atoms in the <solutemask> in order to represent the first and second
- solvation shells.
+This option will count the number of waters within a certain distance of the atoms in the <solutemask> in order to represent the first and second solvation shells.
  The optional <solventmask> can be used to consider other atoms as the solvent;
  the default is 
 \begin_inset Quotes eld
@@ -43033,8 +43804,7 @@ This action is often used prior to the
 closest
 \series default
 \shape default
- command in order to determine how many waters around a solute should be
- retained to maintain the first and/or second water shells.
+ command in order to determine how many waters around a solute should be retained to maintain the first and/or second water shells.
 \end_layout
 
 \begin_layout Standard
@@ -43059,8 +43829,7 @@ xtalsymm <mask> group <space group> [collect [centroid]]
 
 \begin_deeper
 \begin_layout Description
-<mask> Atom mask defining the asymmetric unit within the larger system (required
-).
+<mask> Atom mask defining the asymmetric unit within the larger system (required).
 \end_layout
 
 \begin_layout Description
@@ -43074,7 +43843,8 @@ group
 
 group> The space group to which the system belongs.
  Omit spaces in the name.
- Example: 
+ Example:
+ 
 \begin_inset Quotes eld
 \end_inset
 
@@ -43086,10 +43856,10 @@ P22(1)2(1)
 \end_layout
 
 \begin_layout Description
-[collect] Optional flag to have all solvent particles, not just the asymmetric
- units, re-imaged.
- This will trigger cpptraj to compute the unit cell volume that constitutes
- the aymmetric unit and thereby classify all particles for re-imaging.
+[collect] Optional flag to have all solvent particles,
+ not just the asymmetric units,
+ re-imaged.
+ This will trigger cpptraj to compute the unit cell volume that constitutes the aymmetric unit and thereby classify all particles for re-imaging.
 \end_layout
 
 \begin_deeper
@@ -43098,7 +43868,9 @@ P22(1)2(1)
 \series bold
 collect
 \series default
-, re-image solvent molecules by centroids, not individual atom coordinates.
+,
+ re-image solvent molecules by centroids,
+ not individual atom coordinates.
  This is useful for keeping water molecules intact.
 \end_layout
 
@@ -43160,41 +43932,38 @@ refindex
 \begin_inset space ~
 \end_inset
 
-<nc>] The number of times the crystal unit cell is replicated along the
- “a,” “b,” or “c” axes (for orthorhombic unti cells, these are the x, y,
- and z axes) of the simulation; default is 1.
- Many crystal unit cells are too small in one or more dimensions for our
- simulation cutoffs, and replicating the unit cell is an effective way to
- counter imaging artifacts even for larger unit cells.
+<nc>] The number of times the crystal unit cell is replicated along the “a,” “b,” or “c” axes (for orthorhombic unti cells,
+ these are the x,
+ y,
+ and z axes) of the simulation;
+ default is 1.
+ Many crystal unit cells are too small in one or more dimensions for our simulation cutoffs,
+ and replicating the unit cell is an effective way to counter imaging artifacts even for larger unit cells.
 \end_layout
 
 \end_deeper
 \begin_layout Standard
-Calculate the optimal approach for superimposing symmetry-related subunits
- of the simulation back onto one another.
- The calculation assumes that the system is a simulation of an X-ray structure
- in its native crystal lattice, finds all copies of the asymmetric unit
- among the entire system, and devises plans for re-imagining their coordinates
- to superimpose them back on the original asymmetric unit.
- The space group information can be found in a PDB X-ray structure used
- as the initial coordinates for a simulation.
- All 230 space groups are supported, and a scan of the PDB was made to ensure
- that common variants of the names are included (P2(1)22(1) is the same
- as P22(1)2(1), but with different axis conventions).
- If your space group is not understood, contact the Amber mailing list.
- This command is compute intensive, especially for simulations that are
- “supercells” containing many crystallographic unit cells.
+Calculate the optimal approach for superimposing symmetry-related subunits of the simulation back onto one another.
+ The calculation assumes that the system is a simulation of an X-ray structure in its native crystal lattice,
+ finds all copies of the asymmetric unit among the entire system,
+ and devises plans for re-imagining their coordinates to superimpose them back on the original asymmetric unit.
+ The space group information can be found in a PDB X-ray structure used as the initial coordinates for a simulation.
+ All 230 space groups are supported,
+ and a scan of the PDB was made to ensure that common variants of the names are included (P2(1)22(1) is the same as P22(1)2(1),
+ but with different axis conventions).
+ If your space group is not understood,
+ contact the Amber mailing list.
+ This command is compute intensive,
+ especially for simulations that are “supercells” containing many crystallographic unit cells.
 \end_layout
 
 \begin_layout Standard
-This command will cause cpptraj to locate all asymmetric units from within
- the topology, then determine what wrapping, if any, has occurred in order
- to bring about an optimal re-alignment based on the space group symmetry
- operations.
- The user need not worry about wrapping or drift of the simulation over
- time–the asymmetric units will be re-imaged frame by frame.
- Coordinate modifications due to this action are permanent and will affect
- the results of subsequent actions and analyses.
+This command will cause cpptraj to locate all asymmetric units from within the topology,
+ then determine what wrapping,
+ if any,
+ has occurred in order to bring about an optimal re-alignment based on the space group symmetry operations.
+ The user need not worry about wrapping or drift of the simulation over time–the asymmetric units will be re-imaged frame by frame.
+ Coordinate modifications due to this action are permanent and will affect the results of subsequent actions and analyses.
 \end_layout
 
 \begin_layout Section
@@ -43206,8 +43975,7 @@ Analyses in
 \emph on
 cpptraj
 \emph default
- operate on data sets which have been generated by Actions in a prior Run
- or read in with a 
+ operate on data sets which have been generated by Actions in a prior Run or read in with a 
 \series bold
 \emph on
 readdata
@@ -43217,6 +43985,7 @@ readdata
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_readdata"
+nolink "false"
 
 \end_inset
 
@@ -43225,7 +43994,8 @@ reference "subsec:cpptraj_readdata"
 \emph on
 ptraj
 \emph default
-, Analysis commands in 
+,
+ Analysis commands in 
 \emph on
 cpptraj
 \emph default
@@ -43246,7 +44016,8 @@ analyze matrix
 matrix
 \series default
 \emph default
- Action command; users are encouraged to use the new command 
+ Action command;
+ users are encouraged to use the new command 
 \series bold
 \emph on
 diagmatrix
@@ -43256,11 +44027,9 @@ diagmatrix
 \end_layout
 
 \begin_layout Standard
-Like Actions, when an Analysis command is issued it is by default added
- to the Analysis queue and is not executed until after trajectory processing
- is completed; a complete list of data sets available for analysis is shown
- after trajectory processing (prefaced by 'DATASETS') or can be shown with
- the '
+Like Actions,
+ when an Analysis command is issued it is by default added to the Analysis queue and is not executed until after trajectory processing is completed;
+ a complete list of data sets available for analysis is shown after trajectory processing (prefaced by 'DATASETS') or can be shown with the '
 \series bold
 \emph on
 list dataset
@@ -43277,6 +44046,7 @@ runanalysis
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_runanalysis"
+nolink "false"
 
 \end_inset
 
@@ -43284,9 +44054,8 @@ reference "subsec:cpptraj_runanalysis"
 \end_layout
 
 \begin_layout Standard
-Note that for Analysis commands that use COORDS data sets, if no COORDS
- data set is specified then a default one will be automatically created
- from frames read in by 
+Note that for Analysis commands that use COORDS data sets,
+ if no COORDS data set is specified then a default one will be automatically created from frames read in by 
 \series bold
 \emph on
 trajin
@@ -43385,7 +44154,10 @@ avg
 \begin_inset Text
 
 \begin_layout Plain Layout
-Calculate average, standard deviation, min, and max for (or over) data sets.
+Calculate average,
+ standard deviation,
+ min,
+ and max for (or over) data sets.
 \end_layout
 
 \end_inset
@@ -43481,7 +44253,8 @@ Perform cluster analysis.
 \begin_inset Text
 
 \begin_layout Plain Layout
-COORDS, N 1D scalar
+COORDS,
+ N 1D scalar
 \end_layout
 
 \end_inset
@@ -43510,7 +44283,8 @@ Calculate auto or cross correlation for 1 or 2 data sets.
 \begin_inset Text
 
 \begin_layout Plain Layout
-1D scalar, vector
+1D scalar,
+ vector
 \end_layout
 
 \end_inset
@@ -43579,7 +44353,8 @@ pH data sets
 \begin_inset Text
 
 \begin_layout Plain Layout
-crank, 
+crank,
+ 
 \end_layout
 
 \end_inset
@@ -43898,7 +44673,8 @@ N 2D matrices
 \begin_inset Text
 
 \begin_layout Plain Layout
-hist, histogram
+hist,
+ histogram
 \end_layout
 
 \end_inset
@@ -44110,7 +44886,8 @@ lowestcurve
 \begin_inset Text
 
 \begin_layout Plain Layout
-For each given data set, calculate a curve that traces 
+For each given data set,
+ calculate a curve that traces 
 \end_layout
 
 \end_inset
@@ -44320,8 +45097,7 @@ phipsi
 \begin_inset Text
 
 \begin_layout Plain Layout
-Calculate and plot the average phi and psi values from input dihedral data
- sets.
+Calculate and plot the average phi and psi values from input dihedral data sets.
 \end_layout
 
 \end_inset
@@ -44359,7 +45135,8 @@ Project data along eigenmodes.
 \begin_inset Text
 
 \begin_layout Plain Layout
-eigenmodes, N 1D scalar
+eigenmodes,
+ N 1D scalar
 \end_layout
 
 \end_inset
@@ -44428,7 +45205,8 @@ replica log
 \begin_inset Text
 
 \begin_layout Plain Layout
-rms2d, 2drms
+rms2d,
+ 2drms
 \end_layout
 
 \end_inset
@@ -44580,7 +45358,8 @@ N 1D scalar
 \begin_inset Text
 
 \begin_layout Plain Layout
-stat, statistics
+stat,
+ statistics
 \end_layout
 
 \end_inset
@@ -44656,7 +45435,8 @@ Perform time-independent correlation analysis.
 \begin_inset Text
 
 \begin_layout Plain Layout
-COORDS, N 1D scalar
+COORDS,
+ N 1D scalar
 \end_layout
 
 \end_inset
@@ -44868,14 +45648,16 @@ autocorr [name <dsetname>] <dsetarg0> [<dsetarg1> ...] [out <filename>]
 \series bold
 [direct]
 \series default
- Do not use FFTs to calculate correlation; this will be much slower.
+ Do not use FFTs to calculate correlation;
+ this will be much slower.
 \end_layout
 
 \end_deeper
 \begin_layout Standard
 
 \shape italic
-This is for integer/double/float datasets only; for vectors see the 
+This is for integer/double/float datasets only;
+ for vectors see the 
 \series bold
 'timecorr'
 \series default
@@ -44883,8 +45665,7 @@ This is for integer/double/float datasets only; for vectors see the
 \end_layout
 
 \begin_layout Standard
-Calculate auto-correlation (actually auto-covariance by default) function
- for datasets specified by one or more dataset arguments.
+Calculate auto-correlation (actually auto-covariance by default) function for datasets specified by one or more dataset arguments.
  The datasets must have the same # of data points.
 \end_layout
 
@@ -44911,7 +45692,8 @@ avg <dset0> [<dset1> ...] [torsion] [out <file>] [oversets]
 
 \begin_layout Description
 [torsion] If the data sets are not already marked periodic (e.g.
- if read in via 'readdata'), treat them as periodic torsion.
+ if read in via 'readdata'),
+ treat them as periodic torsion.
 \end_layout
 
 \begin_layout Description
@@ -44923,8 +45705,8 @@ avg <dset0> [<dset1> ...] [torsion] [out <file>] [oversets]
 \end_layout
 
 \begin_layout Description
-[oversets] If specified, calculate the average over all inpout sets instead
- of each input set.
+[oversets] If specified,
+ calculate the average over all inpout sets instead of each input set.
 \end_layout
 
 \begin_layout Description
@@ -44936,8 +45718,7 @@ avg <dset0> [<dset1> ...] [torsion] [out <file>] [oversets]
 \end_layout
 
 \begin_layout Description
-[nostdout] If 'nostdout' specified do not write averages to STDOUT when
- 'out' not specified.
+[nostdout] If 'nostdout' specified do not write averages to STDOUT when 'out' not specified.
 \end_layout
 
 \begin_layout Standard
@@ -44994,19 +45775,22 @@ DataSets Created (oversets)
 \end_layout
 
 \begin_layout Standard
-Calculate the average, standard deviation, min, and max of given 1D data
- sets.
- Alternatively, if 
+Calculate the average,
+ standard deviation,
+ min,
+ and max of given 1D data sets.
+ Alternatively,
+ if 
 \series bold
 oversets
 \series default
- is specified the average over each set for each point is calculated; this
- requires all input sets be the same size.
+ is specified the average over each set for each point is calculated;
+ this requires all input sets be the same size.
 \end_layout
 
 \begin_layout Standard
-For example, to read in data from a file named perres.peptide.dat and calculate
- the averages etc for all the input sets:
+For example,
+ to read in data from a file named perres.peptide.dat and calculate the averages etc for all the input sets:
 \end_layout
 
 \begin_layout LyX-Code
@@ -45087,8 +45871,7 @@ set>] Input COORDS set to calculate diffusion for.
 \begin_inset space ~
 \end_inset
 
-<file>] Write diffusion contants calculated from fits of MSD data sets to
- <filename>.
+<file>] Write diffusion contants calculated from fits of MSD data sets to <filename>.
 \end_layout
 
 \begin_layout Standard
@@ -45169,25 +45952,28 @@ reference "subsec:cpptraj-diffusion"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
-), which calculates MSD from a single time origin, the 
+),
+ which calculates MSD from a single time origin,
+ the 
 \series bold
 \emph on
 calcdiffusion
 \series default
 \emph default
- command calculates diffusion from multiple time origins up to a user-specified
- lag (in frames).
- Note that no imaging is performed for this command, so any unwrapping should
- be performed prior to this command (see 
+ command calculates diffusion from multiple time origins up to a user-specified lag (in frames).
+ Note that no imaging is performed for this command,
+ so any unwrapping should be performed prior to this command (see 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_unwrap"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
@@ -45198,13 +45984,15 @@ noprefix "false"
 diffusion
 \series default
 \emph default
- command; for more details see 
+ command;
+ for more details see 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-diffusion"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
@@ -45212,18 +46000,18 @@ noprefix "false"
 \end_layout
 
 \begin_layout Standard
-This command is both OpenMP- and MPI-parallelized; either or both can be
- active.
- In order to keep per-process memory requirements low, it is recommended
- that TRAJ (i.e.
- on-disk) data sets be used with MPI instead of CRD (in-memory) sets (see
- 
+This command is both OpenMP- and MPI-parallelized;
+ either or both can be active.
+ In order to keep per-process memory requirements low,
+ it is recommended that TRAJ (i.e.
+ on-disk) data sets be used with MPI instead of CRD (in-memory) sets (see 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-loadtraj"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
@@ -45231,9 +46019,8 @@ noprefix "false"
 \end_layout
 
 \begin_layout Standard
-For example, to calculate diffusion from multiple time origins (with a maximum
- lag of half the number of trajectrory frames) from an input trajectory
- in memory (unwrapping first):
+For example,
+ to calculate diffusion from multiple time origins (with a maximum lag of half the number of trajectrory frames) from an input trajectory in memory (unwrapping first):
 \end_layout
 
 \begin_layout LyX-Code
@@ -45253,9 +46040,9 @@ runanalysis calcdiffusion crdset TZ2 out tz2.diff.dat :WAT@O
 \end_layout
 
 \begin_layout Standard
-To do the same calculation using MPI parallelism, it will first be necessary
- to unwrap the trajectory (non-MPI parallel, but OpenMP parallelism can
- be used):
+To do the same calculation using MPI parallelism,
+ it will first be necessary to unwrap the trajectory (non-MPI parallel,
+ but OpenMP parallelism can be used):
 \end_layout
 
 \begin_layout LyX-Code
@@ -45295,8 +46082,7 @@ calcstate
 \end_layout
 
 \begin_layout LyX-Code
-calcstate {state <ID>,<dataset>,<min>,<max>[,<dataset1>,<min1>,<max1>]}
- ...
+calcstate {state <ID>,<dataset>,<min>,<max>[,<dataset1>,<min1>,<max1>]} ...
 \end_layout
 
 \begin_layout LyX-Code
@@ -45321,13 +46107,13 @@ state
 \begin_inset space ~
 \end_inset
 
-<ID>,<dataset>,<min>,<max> Define a state according to given data set and
- criteria.
- Multiple states can be given, and each state can have multiple criteria.
- If multiple criteria are specified, each one must be satisfied in order
- to assign the state.
- If the same state is defined multiple times, the state will be assigned
- if either criteria match.
+<ID>,<dataset>,<min>,<max> Define a state according to given data set and criteria.
+ Multiple states can be given,
+ and each state can have multiple criteria.
+ If multiple criteria are specified,
+ each one must be satisfied in order to assign the state.
+ If the same state is defined multiple times,
+ the state will be assigned if either criteria match.
 \begin_inset Separator latexpar
 \end_inset
 
@@ -45354,8 +46140,7 @@ undefined state
 \end_layout
 
 \begin_layout Description
-<min>,<max> Frames with data set value above <min> and below <max> will
- be assigned <ID>.
+<min>,<max> Frames with data set value above <min> and below <max> will be assigned <ID>.
 \end_layout
 
 \end_deeper
@@ -45473,22 +46258,20 @@ DataSets Created:
 \end_layout
 
 \begin_layout Description
-<setname>[Xlifetimes] Number of times each state transitioned to each other
- state.
+<setname>[Xlifetimes] Number of times each state transitioned to each other state.
 \end_layout
 
 \begin_layout Description
-<setname>[Xavglife] Average lifetime of each state before transitioning
- to each other state.
+<setname>[Xavglife] Average lifetime of each state before transitioning to each other state.
 \end_layout
 
 \begin_layout Description
-<setname>[Xmaxlife] Maximum lifetime of each state before transitioning
- to each other state.
+<setname>[Xmaxlife] Maximum lifetime of each state before transitioning to each other state.
 \end_layout
 
 \begin_layout Description
-<setname>[Xname] Name of each transition, format 
+<setname>[Xname] Name of each transition,
+ format 
 \begin_inset Quotes eld
 \end_inset
 
@@ -45500,19 +46283,18 @@ StateA->StateB
 \end_layout
 
 \begin_layout Description
-<setname>[sCurve]:X State curves; lifetime curve for transitions from given
- state to any other state.
+<setname>[sCurve]:X State curves;
+ lifetime curve for transitions from given state to any other state.
 \end_layout
 
 \begin_layout Description
-<setname>[tCurve]:X Transition curves; lifetime curve for transitions from
- given state to other specific state.
+<setname>[tCurve]:X Transition curves;
+ lifetime curve for transitions from given state to other specific state.
 \end_layout
 
 \end_deeper
 \begin_layout Standard
-Data for the specified data set(s) that matches the given criteria will
- be assigned a state index.
+Data for the specified data set(s) that matches the given criteria will be assigned a state index.
  State indices start from 0 and match the order in which 
 \series bold
 state
@@ -45527,7 +46309,8 @@ undefined state
 \end_inset
 
 .
- For example, the following input:
+ For example,
+ the following input:
 \end_layout
 
 \begin_layout LyX-Code
@@ -45547,8 +46330,7 @@ angle a1 :19@O :12@H :12@N
 \end_layout
 
 \begin_layout LyX-Code
-calcstate state D,d1,3.0,4.0 state A,a1,100,120 out state.dat curveout curve.agr
- 
+calcstate state D,d1,3.0,4.0 state A,a1,100,120 out state.dat curveout curve.agr 
 \backslash
 
 \end_layout
@@ -45571,8 +46353,7 @@ D
 \begin_inset Quotes erd
 \end_inset
 
- based on the distance from ':19@O' to ':12@N' (data set d1) being between
- 3 and 4 Angstroms.
+ based on the distance from ':19@O' to ':12@N' (data set d1) being between 3 and 4 Angstroms.
  State index 1 is defined as a state named 
 \begin_inset Quotes eld
 \end_inset
@@ -45581,8 +46362,9 @@ A
 \begin_inset Quotes erd
 \end_inset
 
- based on the angle between ':19@O', ':12@H', and ':12@N' (data set a1)
- being between 100 and 120 degrees.
+ based on the angle between ':19@O',
+ ':12@H',
+ and ':12@N' (data set a1) being between 100 and 120 degrees.
  The output in state.dat might look like:
 \end_layout
 
@@ -45631,7 +46413,8 @@ A
 \end_layout
 
 \begin_layout Standard
-where the values in column d1_a1 refer to state index: -1 is undefined,
+where the values in column d1_a1 refer to state index:
+ -1 is undefined,
  0 is state 
 \begin_inset Quotes eld
 \end_inset
@@ -45640,7 +46423,8 @@ D
 \begin_inset Quotes erd
 \end_inset
 
-, and 1 is state 
+,
+ and 1 is state 
 \begin_inset Quotes eld
 \end_inset
 
@@ -45695,46 +46479,51 @@ Lifetime curves (see
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-lifetime"
+nolink "false"
 
 \end_inset
 
- for further explanation) are calculated for transitions from each state
- to any other state (aspect [sCurve]) and each state to each other state
- (aspect [tCurve]).
+ for further explanation) are calculated for transitions from each state to any other state (aspect [sCurve]) and each state to each other state (aspect [tCurve]).
  In this case there will be 3 sCurves and 4 tCurves:
 \end_layout
 
 \begin_layout LyX-Code
-d1_a1[sCurve]:0 "Undefined" (double), size is 10 
+d1_a1[sCurve]:0 "Undefined" (double),
+ size is 10 
 \end_layout
 
 \begin_layout LyX-Code
-d1_a1[sCurve]:1 "D" (double), size is 3 
+d1_a1[sCurve]:1 "D" (double),
+ size is 3 
 \end_layout
 
 \begin_layout LyX-Code
-d1_a1[sCurve]:2 "A" (double), size is 1 
+d1_a1[sCurve]:2 "A" (double),
+ size is 1 
 \end_layout
 
 \begin_layout LyX-Code
-d1_a1[tCurve]:0 "Undefined->D" (double), size is 10
+d1_a1[tCurve]:0 "Undefined->D" (double),
+ size is 10
 \end_layout
 
 \begin_layout LyX-Code
-d1_a1[tCurve]:1 "D->Undefined" (double), size is 3
+d1_a1[tCurve]:1 "D->Undefined" (double),
+ size is 3
 \end_layout
 
 \begin_layout LyX-Code
-d1_a1[tCurve]:2 "Undefined->A" (double), size is 1
+d1_a1[tCurve]:2 "Undefined->A" (double),
+ size is 1
 \end_layout
 
 \begin_layout LyX-Code
-d1_a1[tCurve]:3 "A->Undefined" (double), size is 1
+d1_a1[tCurve]:3 "A->Undefined" (double),
+ size is 1
 \end_layout
 
 \begin_layout Standard
-Lifetime analysis from each state to any other state is directed to the
- file specified by 
+Lifetime analysis from each state to any other state is directed to the file specified by 
 \series bold
 stateout
 \series default
@@ -45750,15 +46539,18 @@ Where
 \family typewriter
 #Index
 \family default
- is the state index, 
+ is the state index,
+ 
 \family typewriter
 N
 \family default
- is the number of lifetimes in that state, 
+ is the number of lifetimes in that state,
+ 
 \family typewriter
 Average
 \family default
- is the average lifetime while in that state (in frames), 
+ is the average lifetime while in that state (in frames),
+ 
 \family typewriter
 Max
 \family default
@@ -45770,8 +46562,8 @@ State
 \end_layout
 
 \begin_layout Standard
-Finally, lifetime analysis of transitions from each state to each other
- state is directory to the file specified by transout and has format:
+Finally,
+ lifetime analysis of transitions from each state to each other state is directory to the file specified by transout and has format:
 \end_layout
 
 \begin_layout LyX-Code
@@ -45783,12 +46575,13 @@ Where
 \family typewriter
 #N
 \family default
- is the number of transitions, 
+ is the number of transitions,
+ 
 \family typewriter
 Average
 \family default
- is the average lifetime (in frames) in the first state before transitioning
- to the second state, 
+ is the average lifetime (in frames) in the first state before transitioning to the second state,
+ 
 \family typewriter
 Max
 \family default
@@ -45813,6 +46606,8 @@ cluster
 \begin_layout LyX-Code
 cluster
 \begin_inset Index idx
+range none
+pageformat default
 status open
 
 \begin_layout Plain Layout
@@ -45842,7 +46637,8 @@ cluster
 \end_layout
 
 \begin_layout LyX-Code
-  Algorithm Args: [{hieragglo|dbscan|kmeans|dpeaks}]
+  Algorithm Args:
+ [{hieragglo|dbscan|kmeans|dpeaks}]
 \end_layout
 
 \begin_layout LyX-Code
@@ -45882,8 +46678,7 @@ cluster
 \end_layout
 
 \begin_layout LyX-Code
-	[{dme|rms|srmsd|qrmsd} [mass] [nofit] [<mask>]] [{euclid|manhattan}] [wgt
- <list>]
+	[{dme|rms|srmsd|qrmsd} [mass] [nofit] [<mask>]] [{euclid|manhattan}] [wgt <list>]
 \end_layout
 
 \begin_layout LyX-Code
@@ -45985,8 +46780,7 @@ cluster
 \end_inset
 
 set>] Name of COORDS data set to cluster on and/or use for coordinate output.
- If not specified the default COORDS set will be generated and used unless
- 
+ If not specified the default COORDS set will be generated and used unless 
 \series bold
 nocoords
 \series default
@@ -45998,15 +46792,14 @@ nocoords
 \begin_inset space ~
 \end_inset
 
-<dset0>[,<dset1>,...] Distance between frames calculated using specified data
- set(s).
+<dset0>[,<dset1>,...] Distance between frames calculated using specified data set(s).
  Currently 1D scalar sets and COORDS sets are supported.
 \end_layout
 
 \begin_deeper
 \begin_layout Description
-[nocoords] Do not use a COORDS data set; distance metrics that require coordinat
-es and coordinate output will be disabled.
+[nocoords] Do not use a COORDS data set;
+ distance metrics that require coordinates and coordinate output will be disabled.
 \end_layout
 
 \end_deeper
@@ -46047,8 +46840,8 @@ cnvtset
 
 \end_deeper
 \begin_layout Description
-[useframesincache] If a pairwise cache is specified, cluster on the frames
- stored in the cache.
+[useframesincache] If a pairwise cache is specified,
+ cluster on the frames stored in the cache.
 \end_layout
 
 \begin_layout Standard
@@ -46069,8 +46862,7 @@ hieragglo (Default) Use hierarchical agglomerative (bottom-up) approach.
 \begin_inset space ~
 \end_inset
 
-<e>] Finish clustering when minimum distance between clusters is greater
- than 
+<e>] Finish clustering when minimum distance between clusters is greater than 
 \series bold
 <e>
 \series default
@@ -46094,7 +46886,8 @@ hieragglo (Default) Use hierarchical agglomerative (bottom-up) approach.
 \series bold
 linkage]
 \series default
- Single-linkage; use the shortest distance between members of two clusters.
+ Single-linkage;
+ use the shortest distance between members of two clusters.
 \end_layout
 
 \begin_layout Description
@@ -46102,8 +46895,8 @@ linkage]
 \series bold
 averagelinkage]
 \series default
- Average-linkage (default); use the average distance between members of
- two clusters.
+ Average-linkage (default);
+ use the average distance between members of two clusters.
 \end_layout
 
 \begin_layout Description
@@ -46111,7 +46904,8 @@ averagelinkage]
 \series bold
 [complete]
 \series default
- Complete-linkage; use the maximum distance between members of two clusters.
+ Complete-linkage;
+ use the maximum distance between members of two clusters.
 \end_layout
 
 \begin_layout Description
@@ -46165,8 +46959,7 @@ epsilon
 \begin_inset space ~
 \end_inset
 
-<k>] Generate K-dist plot for help in determining DBSCAN parameters (see
- below).
+<k>] Generate K-dist plot for help in determining DBSCAN parameters (see below).
 \end_layout
 
 \begin_layout Description
@@ -46204,8 +46997,8 @@ epsilon
 \end_layout
 
 \begin_layout Description
-[noise] If specified, treat all points within epsilon of another cluster
- as noise.
+[noise] If specified,
+ treat all points within epsilon of another cluster as noise.
 \end_layout
 
 \begin_layout Description
@@ -46213,10 +47006,8 @@ epsilon
 \begin_inset space ~
 \end_inset
 
-<density_vs_dist_file>] File to write density versus minimum distance to
- point with next highest density.
- This can be used to determine appropriate cutoffs for distance and density
- in a subsequent step with 
+<density_vs_dist_file>] File to write density versus minimum distance to point with next highest density.
+ This can be used to determine appropriate cutoffs for distance and density in a subsequent step with 
 \series bold
 choosepoints
 \series default
@@ -46240,10 +47031,9 @@ manual
 \begin_inset space ~
 \end_inset
 
-auto}] Specify whether clusters will be chosen based on specified distance/densi
-ty cutoffs, or automatically.
- If not specified only the density vs distance file will be written and
- no clustering will be performed.
+auto}] Specify whether clusters will be chosen based on specified distance/density cutoffs,
+ or automatically.
+ If not specified only the density vs distance file will be written and no clustering will be performed.
  Currently 
 \series bold
 manual
@@ -46272,8 +47062,8 @@ choosepoints
 \series bold
 manual
 \series default
-, points with minimum distance greather than or equal to <distcut> and density
- greater than or equal to <densitycut> will be chosen.
+,
+ points with minimum distance greather than or equal to <distcut> and density greater than or equal to <densitycut> will be chosen.
 \end_layout
 
 \begin_layout Description
@@ -46293,8 +47083,8 @@ choosepoints
 \series bold
 automatic
 \series default
-, the calculated running average of density versus distance will be written
- to <runavg file>.
+,
+ the calculated running average of density versus distance will be written to <runavg file>.
 \end_layout
 
 \begin_layout Description
@@ -46310,13 +47100,12 @@ choosepoints
 \series bold
 automatic
 \series default
-, distance minus the running average for each point will be written to this
- file.
+,
+ distance minus the running average for each point will be written to this file.
 \end_layout
 
 \begin_layout Description
-[gauss] Calculate density with Gaussian kernels instead of using discrete
- density.
+[gauss] Calculate density with Gaussian kernels instead of using discrete density.
 \end_layout
 
 \end_deeper
@@ -46362,8 +47151,7 @@ randompoint
 \begin_inset space ~
 \end_inset
 
-<iteration>] Algorithm will run until frames no longer change clusters of
- <iteration> iterations are reached (default 100).
+<iteration>] Algorithm will run until frames no longer change clusters of <iteration> iterations are reached (default 100).
 \end_layout
 
 \end_deeper
@@ -46388,8 +47176,8 @@ srmsd}
 \series bold
 rms
 \series default
-) For COORDS data, distance between coordinate frames calculated via best-fit
- coordinate RMSD using atoms in 
+) For COORDS data,
+ distance between coordinate frames calculated via best-fit coordinate RMSD using atoms in 
 \series bold
 <mask>
 \series default
@@ -46402,6 +47190,7 @@ srmsd
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_symmrmsd"
+nolink "false"
 
 \end_inset
 
@@ -46427,9 +47216,8 @@ qrmsd
 \begin_inset space ~
 \end_inset
 
-[<mask>] For COORDS data, distance between coordinate frames calculated
- using best-fit quaternion RMSD (can be 15-20% faster than regular RMSD)
- using atoms in 
+[<mask>] For COORDS data,
+ distance between coordinate frames calculated using best-fit quaternion RMSD (can be 15-20% faster than regular RMSD) using atoms in 
 \series bold
 <mask>
 \series default
@@ -46447,8 +47235,9 @@ dme
 \begin_inset space ~
 \end_inset
 
-[<mask>] For COORDS data, distance between coordinate frames calculated
- using distance-RMSD (aka DME, 
+[<mask>] For COORDS data,
+ distance between coordinate frames calculated using distance-RMSD (aka DME,
+ 
 \series bold
 \emph on
 distrmsd
@@ -46462,13 +47251,11 @@ distrmsd
 \end_layout
 
 \begin_layout Description
-euclid Use Euclidean distance (sqrt(SUM(distance^2))) when more than one
- data set has been specified (default).
+euclid Use Euclidean distance (sqrt(SUM(distance^2))) when more than one data set has been specified (default).
 \end_layout
 
 \begin_layout Description
-manhatttan Use Manhattan distance (SUM(distance)) when more than one data
- set has been specified.
+manhatttan Use Manhattan distance (SUM(distance)) when more than one data set has been specified.
 \end_layout
 
 \begin_layout Description
@@ -46476,16 +47263,14 @@ wgt
 \begin_inset space ~
 \end_inset
 
-<list> Factor to multiply distances from each metric by in a comma-separated
- list.
+<list> Factor to multiply distances from each metric by in a comma-separated list.
  Can be used to adjust the contribution from each metric.
  Default is 1 for each metric.
  Output from the 
 \series bold
 metricstats
 \series default
- keyword can be used to determine the relative contribution of each metric
- to the distance.
+ keyword can be used to determine the relative contribution of each metric to the distance.
 \end_layout
 
 \begin_layout Standard
@@ -46497,8 +47282,7 @@ Pairwise Distance Matrix Options:
 \begin_inset space ~
 \end_inset
 
-<name>] Pairwise cache DataSet/File name to use for loading/saving pairwise
- distances.
+<name>] Pairwise cache DataSet/File name to use for loading/saving pairwise distances.
 \end_layout
 
 \begin_deeper
@@ -46507,11 +47291,13 @@ Pairwise Distance Matrix Options:
 \begin_inset space ~
 \end_inset
 
-<file>] File name to use for pairwise cache; if not specified and 
+<file>] File name to use for pairwise cache;
+ if not specified and 
 \series bold
 'pairdist'
 \series default
- specified, uses 
+ specified,
+ uses 
 \series bold
 'pairdist'
 \series default
@@ -46520,8 +47306,8 @@ Pairwise Distance Matrix Options:
 
 \end_deeper
 \begin_layout Description
-[pwrecalc] If the loaded pairwise distance matrix does not match the current
- setup, force recalculation.
+[pwrecalc] If the loaded pairwise distance matrix does not match the current setup,
+ force recalculation.
 \end_layout
 
 \begin_layout Description
@@ -46546,7 +47332,8 @@ pairdist
 pairdist
 \series default
  not specified).
- NOTE: If sieving was performed only the calculated distances are saved.
+ NOTE:
+ If sieving was performed only the calculated distances are saved.
 \end_layout
 
 \begin_layout Description
@@ -46570,11 +47357,11 @@ disk
 \begin_inset space ~
 \end_inset
 
-none}] Cache pairwise distance data in memory (default), to disk, or disable
- pairwise caching.
+none}] Cache pairwise distance data in memory (default),
+ to disk,
+ or disable pairwise caching.
  No caching will save memory but be extremely slow.
- Caching to disk will likely be slow unless writing to a fast storage device
- (e.g.
+ Caching to disk will likely be slow unless writing to a fast storage device (e.g.
  SSD) - data is saved to a file named 'CpptrajPairwiseCache'.
 \end_layout
 
@@ -46592,7 +47379,8 @@ Sieving Options:
 <#>
 \series default
  frame.
- After clustering, all other frames will be added to clusters.
+ After clustering,
+ all other frames will be added to clusters.
 \end_layout
 
 \begin_layout Description
@@ -46600,7 +47388,8 @@ Sieving Options:
 \series bold
 sieve
 \series default
- is specified, select initial frames to cluster randomly.
+ is specified,
+ select initial frames to cluster randomly.
 \end_layout
 
 \begin_layout Description
@@ -46608,12 +47397,12 @@ sieve
 \begin_inset space ~
 \end_inset
 
-<#>] Seed for random sieving; if not set the wallclock time will be used.
+<#>] Seed for random sieving;
+ if not set the wallclock time will be used.
 \end_layout
 
 \begin_layout Description
-[includesieved_cdist] Include sieved frames in final cluster distance calculatio
-n (
+[includesieved_cdist] Include sieved frames in final cluster distance calculation (
 \bar under
 may be very slow
 \bar default
@@ -46621,8 +47410,7 @@ may be very slow
 \end_layout
 
 \begin_layout Description
-[includesieveincalc] Include sieved frames when calculating within-cluster
- average (
+[includesieveincalc] Include sieved frames when calculating within-cluster average (
 \bar under
 may be very slow
 \bar default
@@ -46630,8 +47418,8 @@ may be very slow
 \end_layout
 
 \begin_layout Description
-[sievetoframe] When restoring sieved frames, compare frame to every frame
- in a cluster using a cutoff of 
+[sievetoframe] When restoring sieved frames,
+ compare frame to every frame in a cluster using a cutoff of 
 \series bold
 <restore epsilon>
 \series default
@@ -46639,12 +47427,13 @@ may be very slow
 \series bold
 epsilon
 \series default
- when using DPeaks/DBscan) instead of the centroid; slower but more accurate.
+ when using DPeaks/DBscan) instead of the centroid;
+ slower but more accurate.
 \end_layout
 
 \begin_layout Description
-[sievetocentroid] When restoring sieved frames, compare frame to cluster
- centroid using a cutoff of 
+[sievetocentroid] When restoring sieved frames,
+ compare frame to cluster centroid using a cutoff of 
 \series bold
 <restore epsilon>
 \series default
@@ -46657,8 +47446,8 @@ epsilon
 \end_layout
 
 \begin_layout Description
-[closestcentroid] When restoring sieved frames, add each frame to its closest
- centroid.
+[closestcentroid] When restoring sieved frames,
+ add each frame to its closest centroid.
  Default method for hieragglo/kmeans.
 \end_layout
 
@@ -46671,8 +47460,7 @@ epsilon
 \begin_inset space ~
 \end_inset
 
-epsilon>] Epsilon to use for sievetoframe/sievetocentroid (default is algorithm
- 
+epsilon>] Epsilon to use for sievetoframe/sievetocentroid (default is algorithm 
 \series bold
 epsilon
 \series default
@@ -46688,8 +47476,7 @@ Best Representative Options:
 \begin_inset space ~
 \end_inset
 
-{cumulative|centroid|cumulative_nosieve}] Method for choosing cluster representa
-tive frames.
+{cumulative|centroid|cumulative_nosieve}] Method for choosing cluster representative frames.
 \end_layout
 
 \begin_deeper
@@ -46737,8 +47524,8 @@ Output Options:
 
 \begin_deeper
 \begin_layout Description
-[gracecolor] Instead of cluster # vs frame, write cluster# + 1 (corresponding
- to colors used by XMGRACE) vs frame.
+[gracecolor] Instead of cluster # vs frame,
+ write cluster# + 1 (corresponding to colors used by XMGRACE) vs frame.
  Cluster #s larger than 15 are given the same color.
  Algorithms that calculate noise (e.g.
  DBSCAN) will assign noise points a color of 0 (blank).
@@ -46750,8 +47537,7 @@ Output Options:
 \begin_inset space ~
 \end_inset
 
-<summaryfile>] Summarize each cluster with format '#Cluster Frames Frac
- AvgDist Stdev Centroid AvgCDist':
+<summaryfile>] Summarize each cluster with format '#Cluster Frames Frac AvgDist Stdev Centroid AvgCDist':
 \begin_inset Separator latexpar
 \end_inset
 
@@ -46780,11 +47566,9 @@ Stdev Standard deviation of points in the cluster.
 \end_layout
 
 \begin_layout Description
-Centroid Frame # of structure in cluster that has the lowest cumulative
- distance to every other point.
- If multiple representatives are being saved this column is replaced with
- two columns for each representative, 'Rep' (representative frame #) and
- 'RepScore' (score according to current best representative metric).
+Centroid Frame # of structure in cluster that has the lowest cumulative distance to every other point.
+ If multiple representatives are being saved this column is replaced with two columns for each representative,
+ 'Rep' (representative frame #) and 'RepScore' (score according to current best representative metric).
 \end_layout
 
 \begin_layout Description
@@ -46806,7 +47590,8 @@ AvgCDist Average distance of this cluster to every other cluster.
 \begin_inset Newline newline
 \end_inset
 
-#Clustering: <X> clusters <N> frames
+#Clustering:
+ <X> clusters <N> frames
 \begin_inset Newline newline
 \end_inset
 
@@ -46818,19 +47603,23 @@ AvgCDist Average distance of this cluster to every other cluster.
 \begin_inset Newline newline
 \end_inset
 
-#DBI: <DBI>
+#DBI:
+ <DBI>
 \begin_inset Newline newline
 \end_inset
 
-#pSF: <PSF>
+#pSF:
+ <PSF>
 \begin_inset Newline newline
 \end_inset
 
-#SSR/SST: <SSR/SST>
+#SSR/SST:
+ <SSR/SST>
 \begin_inset Newline newline
 \end_inset
 
-#Algorithm: <algorithm-specific info>
+#Algorithm:
+ <algorithm-specific info>
 \begin_inset Newline newline
 \end_inset
 
@@ -46842,18 +47631,21 @@ AvgCDist Average distance of this cluster to every other cluster.
 \begin_inset Newline newline
 \end_inset
 
-#Representative frames: <representative frame list>
+#Representative frames:
+ <representative frame list>
 \begin_inset Newline newline
 \end_inset
 
-Where <X> is the number of clusters, <N> is the number of frames clustered,
- <I> ranges from 0 to <X>-1, <AVG> is the average distance of all frames
- in that cluster to the centroid, <DBI> is the Davies-Bouldin Index, <pSF>
- is the pseudo-F statistic, <SSR/SST> is the SSR/SST ratio, and <representative
- frame list> contains the frame # of the representative frame (i.e.
+Where <X> is the number of clusters,
+ <N> is the number of frames clustered,
+ <I> ranges from 0 to <X>-1,
+ <AVG> is the average distance of all frames in that cluster to the centroid,
+ <DBI> is the Davies-Bouldin Index,
+ <pSF> is the pseudo-F statistic,
+ <SSR/SST> is the SSR/SST ratio,
+ and <representative frame list> contains the frame # of the representative frame (i.e.
  closest to the centroid) for each cluster.
- Each cluster has a line made up of characters (one for each frame) where
- '.' means 'not in cluster' and 'X' means 'in cluster'.
+ Each cluster has a line made up of characters (one for each frame) where '.' means 'not in cluster' and 'X' means 'in cluster'.
 \end_layout
 
 \begin_layout Description
@@ -46865,9 +47657,7 @@ Where <X> is the number of clusters, <N> is the number of frames clustered,
 \begin_inset space ~
 \end_inset
 
-<splitfile>] Summarize each cluster based on which of its frames fall in
- portions of the trajectory specified by splitframe with format '#Cluster
- Total Frac C# Color NumInX ...
+<splitfile>] Summarize each cluster based on which of its frames fall in portions of the trajectory specified by splitframe with format '#Cluster Total Frac C# Color NumInX ...
  FracX ...
  FirstX ...
  RepX':
@@ -46907,13 +47697,11 @@ FracX Fraction of frames in Xth portion of the trajectory.
 \end_layout
 
 \begin_layout Description
-FirstX Frame in the Xth portion of the trajectory where the cluster is first
- observed.
+FirstX Frame in the Xth portion of the trajectory where the cluster is first observed.
 \end_layout
 
 \begin_layout Description
-RepX Best representative frame in the Xth portion of the trajectory for
- that cluster.
+RepX Best representative frame in the Xth portion of the trajectory for that cluster.
 \end_layout
 
 \end_deeper
@@ -46926,7 +47714,9 @@ RepX Best representative frame in the Xth portion of the trajectory for
 \series bold
 summarysplit
 \series default
-, frame or comma-separated list of frames to split the trajectory at, e.g.
+,
+ frame or comma-separated list of frames to split the trajectory at,
+ e.g.
  '100,200,300'.
 \end_layout
 
@@ -46935,8 +47725,7 @@ summarysplit
 \begin_inset space ~
 \end_inset
 
-<filename>] Write number of unique clusters observed in a given time window
- to <filename>.
+<filename>] Write number of unique clusters observed in a given time window to <filename>.
 \end_layout
 
 \begin_deeper
@@ -46958,9 +47747,7 @@ clustersvtime
 \begin_inset space ~
 \end_inset
 
-<prefix>] Write average cluster silhouette value for each cluster to '<prefix>.cl
-uster.dat' and cluster silhouette value for each individual frame to '<prefix>.fra
-me.dat'.
+<prefix>] Write average cluster silhouette value for each cluster to '<prefix>.cluster.dat' and cluster silhouette value for each individual frame to '<prefix>.frame.dat'.
 \end_layout
 
 \begin_deeper
@@ -46969,12 +47756,13 @@ me.dat'.
 \begin_inset space ~
 \end_inset
 
-{idx|frm}] Choose what indices to write to the cluster silhouette frame
- file: 
+{idx|frm}] Choose what indices to write to the cluster silhouette frame file:
+ 
 \series bold
 idx
 \series default
- (the default) specifies the sorted index (starting from 0), 
+ (the default) specifies the sorted index (starting from 0),
+ 
 \series bold
 frm
 \series default
@@ -46987,8 +47775,8 @@ frm
 \begin_inset space ~
 \end_inset
 
-<file>] When more than one metric in use, print the fraction contribution
- of each metric to the total distance.
+<file>] When more than one metric in use,
+ print the fraction contribution of each metric to the total distance.
  This information can be used in conjunction with the 
 \series bold
 wgt
@@ -47002,14 +47790,18 @@ wgt
 \begin_inset Newline newline
 \end_inset
 
-Where #Metric is the metric number, FracAv and FracSD are the average and
- standard devation of the fraction contribution of that metric to the total
- distance (taking into account distance type and weights), Avg, SD, Min,
- and Max are the average, standard devation, minimum, and maximum of the
- unmodified distance contribution from that metric, and Description is the
- metric description.
- This may be slow for large numbers of frames, so it is advisable to run
- this on a smaller (potentially sieved) number of frames.
+Where #Metric is the metric number,
+ FracAv and FracSD are the average and standard devation of the fraction contribution of that metric to the total distance (taking into account distance type and weights),
+ Avg,
+ SD,
+ Min,
+ and Max are the average,
+ standard devation,
+ minimum,
+ and maximum of the unmodified distance contribution from that metric,
+ and Description is the metric description.
+ This may be slow for large numbers of frames,
+ so it is advisable to run this on a smaller (potentially sieved) number of frames.
 \end_layout
 
 \begin_layout Description
@@ -47033,11 +47825,13 @@ normframe]] Write cluster population vs time to
 \series bold
 <file>
 \series default
-; if 
+;
+ if 
 \series bold
 normpop
 \series default
- specified normalize each cluster to 1.0; if 
+ specified normalize each cluster to 1.0;
+ if 
 \series bold
 normframe
 \series default
@@ -47049,8 +47843,9 @@ normframe
 \emph on
 [Lifetime]
 \emph default
- for each cluster; for each frame, have 1 if the cluster is present and
- 0 otherwise.
+ for each cluster;
+ for each frame,
+ have 1 if the cluster is present and 0 otherwise.
  Can be used with 
 \series bold
 \emph on
@@ -47064,6 +47859,7 @@ reference "subsec:cpptraj-lifetime"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
@@ -47098,8 +47894,7 @@ singlerepout
 \begin_inset space ~
 \end_inset
 
-<trajfilename> Write all representative frames to single trajectory named
- <trajfilename>.
+<trajfilename> Write all representative frames to single trajectory named <trajfilename>.
 \end_layout
 
 \begin_deeper
@@ -47117,9 +47912,8 @@ repout
 \begin_inset space ~
 \end_inset
 
-<repprefix> Write representative frames to separate files named <repprefix>.X.<ext
->, where X is the cluster number and <ext> is a format-specific filename
- extension.
+<repprefix> Write representative frames to separate files named <repprefix>.X.<ext>,
+ where X is the cluster number and <ext> is a format-specific filename extension.
 \end_layout
 
 \begin_deeper
@@ -47145,9 +47939,8 @@ avgout
 \begin_inset space ~
 \end_inset
 
-<avgprefix> Write average structure for each cluster to separate files named
- <avgprefix>.X.<ext>, where X is the cluster number and <ext> is a format-specific
- filename extension.
+<avgprefix> Write average structure for each cluster to separate files named <avgprefix>.X.<ext>,
+ where X is the cluster number and <ext> is a format-specific filename extension.
 \end_layout
 
 \begin_deeper
@@ -47169,8 +47962,8 @@ summary
 \series bold
 summarysplit
 \series default
-, assign clusters to loaded reference structures if RMSD to that reference
- is less than specified cutoff.
+,
+ assign clusters to loaded reference structures if RMSD to that reference is less than specified cutoff.
  This will be printed in 
 \series bold
 summary
@@ -47179,8 +47972,8 @@ summary
 \series bold
 summarysplit
 \series default
- files as 2 extra columns: 'Name' (reference name) and 'RMS' (RMS to cluster
- centroid).
+ files as 2 extra columns:
+ 'Name' (reference name) and 'RMS' (RMS to cluster centroid).
 \end_layout
 
 \begin_deeper
@@ -47236,8 +48029,8 @@ clustersvtime
 \end_layout
 
 \begin_layout Description
-<name>[Pop]:<X> Cluster X population vs time; index X corresponds to cluster
- number.
+<name>[Pop]:<X> Cluster X population vs time;
+ index X corresponds to cluster number.
 \end_layout
 
 \begin_layout Description
@@ -47246,36 +48039,37 @@ clustersvtime
 lifetime
 \series default
  only).
- For each cluster X, contain 1 if cluster present that frame, 0 otherwise.
+ For each cluster X,
+ contain 1 if cluster present that frame,
+ 0 otherwise.
 \end_layout
 
 \end_deeper
 \begin_layout Standard
 
 \shape italic
-Note cluster population vs time data sets are not generated until the analysis
- has been run.
+Note cluster population vs time data sets are not generated until the analysis has been run.
 \end_layout
 
 \begin_layout Standard
-Cluster input frames using the specified input data sets (can be any combination
- of coordinates/COORDS and/or 1D scalar data) with the specified clustering
- algorithm.
- For COORDS sets, the distance metric can be RMSD, symmetry-corrected RMSD,
+Cluster input frames using the specified input data sets (can be any combination of coordinates/COORDS and/or 1D scalar data) with the specified clustering algorithm.
+ For COORDS sets,
+ the distance metric can be RMSD,
+ symmetry-corrected RMSD,
  or DME.
- When multiple data sets are present, the total distance can be determined
- either via the Euclidean (default) or Manhattan method.
+ When multiple data sets are present,
+ the total distance can be determined either via the Euclidean (default) or Manhattan method.
 \end_layout
 
 \begin_layout Standard
-In order to speed up clustering of large trajectories, the 
+In order to speed up clustering of large trajectories,
+ the 
 \series bold
 sieve
 \series default
  keyword can be used.
- In addition, subsequent clustering calculations can be sped up by writing/readi
-ng calculated pair distances between each frame to/from a file specified
- by 
+ In addition,
+ subsequent clustering calculations can be sped up by writing/reading calculated pair distances between each frame to/from a file specified by 
 \series bold
 pairdist
 \series default
@@ -47295,7 +48089,8 @@ pairdist
 \end_layout
 
 \begin_layout Standard
-Example: cluster on a specific distance:
+Example:
+ cluster on a specific distance:
 \end_layout
 
 \begin_layout LyX-Code
@@ -47307,10 +48102,10 @@ cluster data endToEnd clusters 10 epsilon 3.0 summary summary.dat info info.dat
 \end_layout
 
 \begin_layout Standard
-Example: two clustering commands on the CA atoms of residues 2-10 using
- average-linkage, stopping when either 3 clusters are reached or the minimum
- distance between clusters is 4.0 for the first, and 8 clusters or minimum
- distance 2.0 for the second.
+Example:
+ two clustering commands on the CA atoms of residues 2-10 using average-linkage,
+ stopping when either 3 clusters are reached or the minimum distance between clusters is 4.0 for the first,
+ and 8 clusters or minimum distance 2.0 for the second.
  The first command will write the cluster number vs time to 
 \begin_inset Quotes eld
 \end_inset
@@ -47328,13 +48123,11 @@ avg.summary.dat
 \end_inset
 
 .
- The second clustering command will use the pairwise distance matrix from
- the first to speed things up:
+ The second clustering command will use the pairwise distance matrix from the first to speed things up:
 \end_layout
 
 \begin_layout LyX-Code
-cluster C1 :2-10 clusters 3 epsilon 4.0 info C1.info out cnumvtime.dat summary
- avg.summary.dat pairdist PW
+cluster C1 :2-10 clusters 3 epsilon 4.0 info C1.info out cnumvtime.dat summary avg.summary.dat pairdist PW
 \end_layout
 
 \begin_layout LyX-Code
@@ -47346,43 +48139,54 @@ Clustering Success Metrics
 \end_layout
 
 \begin_layout Standard
-The Davies-Bouldin Index (DBI, reported in the 
+The Davies-Bouldin Index (DBI,
+ reported in the 
 \series bold
 info
 \series default
- file) measures sum over all clusters of the within cluster scatter to the
- between cluster separation; 
+ file) measures sum over all clusters of the within cluster scatter to the between cluster separation;
+ 
 \series bold
-the smaller the DBI, the better
+the smaller the DBI,
+ the better
 \series default
 .
- The DBI is defined as the average, for all clusters X, of fred, where fred(X)
- = max, across other clusters Y, of (Cx + Cy)/dXY.
- Here Cx is the average distance from points in X to the centroid, similarly
- Cy, and dXY is the distance between cluster centroids.
+ The DBI is defined as the average,
+ for all clusters X,
+ of fred,
+ where fred(X) = max,
+ across other clusters Y,
+ of (Cx + Cy)/dXY.
+ Here Cx is the average distance from points in X to the centroid,
+ similarly Cy,
+ and dXY is the distance between cluster centroids.
  
 \end_layout
 
 \begin_layout Standard
-The pseudo-F statistic (pSF, reported in the 
+The pseudo-F statistic (pSF,
+ reported in the 
 \series bold
 info
 \series default
  file) is another measure of clustering goodness.
- It is intended to capture the 'tightness' of clusters, and is in essence
- a ratio of the mean sum of squares between groups to the mean sum of squares
- within group.
+ It is intended to capture the 'tightness' of clusters,
+ and is in essence a ratio of the mean sum of squares between groups to the mean sum of squares within group.
  
 \series bold
 Higher values of pseudo-F are good
 \series default
 .
- Generally, one selects a cluster-count that gives a peak in the pseudo-f
- statistic.
- Formula: A/B, where A = (T - P)/(G-1), and B = P / (n-G).
- Here n is the number of points, G is the number of clusters, T is the total
- distance from the all-data centroid, and P is the sum (for all clusters)
- of the distances from the cluster centroid.
+ Generally,
+ one selects a cluster-count that gives a peak in the pseudo-f statistic.
+ Formula:
+ A/B,
+ where A = (T - P)/(G-1),
+ and B = P / (n-G).
+ Here n is the number of points,
+ G is the number of clusters,
+ T is the total distance from the all-data centroid,
+ and P is the sum (for all clusters) of the distances from the cluster centroid.
  
 \end_layout
 
@@ -47391,23 +48195,19 @@ The SSR/SST (reported in the
 \series bold
 info
 \series default
- file) is the ratio of the sum of squares regression (SSR or between sum
- of squares) and the total sum of squares (SST).
- The SSR is calculated via the sum of the squared distances of all points
- within a given cluster to its centroid, and summed together for all clusters.
- The total sum of squares is the sum of squared distances for all frames
- to the overall mean.
- The ratio lies between 0 and 1 and is supposed to give the fraction of
- explained variance by the data.
+ file) is the ratio of the sum of squares regression (SSR or between sum of squares) and the total sum of squares (SST).
+ The SSR is calculated via the sum of the squared distances of all points within a given cluster to its centroid,
+ and summed together for all clusters.
+ The total sum of squares is the sum of squared distances for all frames to the overall mean.
+ The ratio lies between 0 and 1 and is supposed to give the fraction of explained variance by the data.
  The ratio should increase with cluster count.
  
 \series bold
-There should be a point at which adding more clusters does not substantially
- increase SSR/SST
+There should be a point at which adding more clusters does not substantially increase SSR/SST
 \series default
-, i.e.
- the point where increasing the cluster count does not add new information
- and should not increase further.
+,
+ i.e.
+ the point where increasing the cluster count does not add new information and should not increase further.
 \end_layout
 
 \begin_layout Standard
@@ -47423,15 +48223,16 @@ silidx
  Values of 1 indicate the point is very similar to other points in the cluster,
  i.e.
  it is well-clustered.
- Values of -1 indicate the point is dissimilar and may fit better in a neighbori
-ng cluster.
+ Values of -1 indicate the point is dissimilar and may fit better in a neighboring cluster.
  Values of 0 indicate the point is on a border between two clusters.
  The 
 \series bold
 sil <prefix>
 \series default
  keyword will write two files.
- The first, <prefix>.cluster.dat, which has the format:
+ The first,
+ <prefix>.cluster.dat,
+ which has the format:
 \end_layout
 
 \begin_layout LyX-Code
@@ -47439,15 +48240,18 @@ sil <prefix>
 \end_layout
 
 \begin_layout Standard
-Where #Cluster is the cluster number, <Si> is the average silhouette value
- for all frames in the cluster, and StdDev is the standard deviation of
- the silhouette value for all frames in the cluster.
- The second, <prefix>.frame.dat, will contain the silhouette value for each
- frame grouped by cluster, with indices controlled by the 
+Where #Cluster is the cluster number,
+ <Si> is the average silhouette value for all frames in the cluster,
+ and StdDev is the standard deviation of the silhouette value for all frames in the cluster.
+ The second,
+ <prefix>.frame.dat,
+ will contain the silhouette value for each frame grouped by cluster,
+ with indices controlled by the 
 \series bold
 silidx
 \series default
- keyword (default sorted by ascending silhouette value), e.g.:
+ keyword (default sorted by ascending silhouette value),
+ e.g.:
 \end_layout
 
 \begin_layout LyX-Code
@@ -47521,11 +48325,10 @@ silidx
 \begin_layout Standard
 The last two lines will contain the overall average silhouette value twice,
  one at the lowest index and one at the highest.
- The file is formatted in this way to make it easy to visualize each cluster
- silhouette relative to the average value in e.g.
+ The file is formatted in this way to make it easy to visualize each cluster silhouette relative to the average value in e.g.
  the XMGRACE plotting program.
- If the clustering results in one or more cluster with silhouette values
- completely below the average line, the clustering is likely poor.
+ If the clustering results in one or more cluster with silhouette values completely below the average line,
+ the clustering is likely poor.
 \end_layout
 
 \begin_layout Subsubsection*
@@ -47541,30 +48344,26 @@ name "subsec:cpptraj_dbscan_Hints"
 
 \begin_layout Standard
 It is not always obvious what parameters to set for DBSCAN.
- You can get a rough idea of what to set 'mindist' and 'epsilon' to by generatin
-g a so-called "K-dist" plot with the 'kidst <k>' option.
- The K-dist plot shows for each point (X axis) the Kth farthest distance
- (Y axis), sorted by decreasing distance.
- You supply the same distance metric and sieve parameters you want to use
- for the actual clustering, but nothing else.
+ You can get a rough idea of what to set 'mindist' and 'epsilon' to by generating a so-called "K-dist" plot with the 'kidst <k>' option.
+ The K-dist plot shows for each point (X axis) the Kth farthest distance (Y axis),
+ sorted by decreasing distance.
+ You supply the same distance metric and sieve parameters you want to use for the actual clustering,
+ but nothing else.
  For example:
 \end_layout
 
 \begin_layout LyX-Code
-cluster C0 dbscan kdist 4 rms :1-4@CA sieve 10 loadpairdist pairdist CpptrajPair
-Dist
+cluster C0 dbscan kdist 4 rms :1-4@CA sieve 10 loadpairdist pairdist CpptrajPairDist
 \end_layout
 
 \begin_layout Standard
-The K-dist plot will be named <prefix>.<k>.dat, with the default prefix being
- 'Kdist' (in this case the file name would be Kdist.4.dat).
- The K-dist plot usually looks like a curve with an initially steep slope
- that gradually decreases.
- Around where the initial part of the curve starts to flatten out (indicating
- an increase in density) is around where epsilon should be set; minpoints
- is set to whatever <k> was.
- It has been suggested that the shape of the K-dist curve doesn't change
- too much after Kdist=4, but users are encouraged to experiment.
+The K-dist plot will be named <prefix>.<k>.dat,
+ with the default prefix being 'Kdist' (in this case the file name would be Kdist.4.dat).
+ The K-dist plot usually looks like a curve with an initially steep slope that gradually decreases.
+ Around where the initial part of the curve starts to flatten out (indicating an increase in density) is around where epsilon should be set;
+ minpoints is set to whatever <k> was.
+ It has been suggested that the shape of the K-dist curve doesn't change too much after Kdist=4,
+ but users are encouraged to experiment.
 \end_layout
 
 \begin_layout Subsubsection*
@@ -47572,9 +48371,7 @@ Using 'dpeaks' clustering
 \end_layout
 
 \begin_layout Standard
-The 'dpeaks' (density peaks) algorithm attempts to find clusters by identifying
- points in high density regions which are far from other points of high
- density
+The 'dpeaks' (density peaks) algorithm attempts to find clusters by identifying points in high density regions which are far from other points of high density
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Rodriguez2014"
@@ -47585,16 +48382,14 @@ literal "true"
 .
  There are two ways these points can be chosen.
  The first and recommended way is manually.
- In this method, clustering if first run with 
+ In this method,
+ clustering if first run with 
 \series bold
 choosepoints
 \series default
- not specified to generate a plot containing density versus minimum distance
- to point with next highest density (the decision graph).
- Appropriate cut offs for distance and density can then be chosen based
- on visual inspection; cutoffs should be chosen so that they select points
- that have both a high density and a high distance to point with next highest
- density.
+ not specified to generate a plot containing density versus minimum distance to point with next highest density (the decision graph).
+ Appropriate cut offs for distance and density can then be chosen based on visual inspection;
+ cutoffs should be chosen so that they select points that have both a high density and a high distance to point with next highest density.
  Clustering can then be run again with 
 \series bold
 distancecut
@@ -47607,10 +48402,10 @@ densitycut
 \end_layout
 
 \begin_layout Standard
-The second way is automatically; cpptraj will attempt to identify outliers
- in the density vs distance plot based on distance from the running average.
- Although this only requires a single pass, this method of choosing points
- is not well-tested and currently not recommended.
+The second way is automatically;
+ cpptraj will attempt to identify outliers in the density vs distance plot based on distance from the running average.
+ Although this only requires a single pass,
+ this method of choosing points is not well-tested and currently not recommended.
 \end_layout
 
 \begin_layout Subsubsection*
@@ -47618,14 +48413,12 @@ The Binary pairwise matrix file format
 \end_layout
 
 \begin_layout Standard
-When NetCDF is not present, the pairwise matrix file will be written in
- binary.
- The exact format depends on what version of cpptraj generated the file
- (since earlier versions had no concept of 'sieve').
- The CpptrajPairDist file starts with a 4 byte header containing the characters
- 'C' 'T' 'M' followed by the version number.
- A quick way to figure out the version is to use the linux 'od' command
- to output the first 4 bytes as hexadecimal, e.g.:
+When NetCDF is not present,
+ the pairwise matrix file will be written in binary.
+ The exact format depends on what version of cpptraj generated the file (since earlier versions had no concept of 'sieve').
+ The CpptrajPairDist file starts with a 4 byte header containing the characters 'C' 'T' 'M' followed by the version number.
+ A quick way to figure out the version is to use the linux 'od' command to output the first 4 bytes as hexadecimal,
+ e.g.:
 \end_layout
 
 \begin_layout LyX-Code
@@ -47645,7 +48438,9 @@ Version
 \begin_inset space ~
 \end_inset
 
-0: Two 4-byte integers: # of rows and # of elements.
+0:
+ Two 4-byte integers:
+ # of rows and # of elements.
  
 \end_layout
 
@@ -47654,7 +48449,8 @@ Version
 \begin_inset space ~
 \end_inset
 
-1: Two 8-byte unsigned integers (equivalent to size_t on most systems):
+1:
+ Two 8-byte unsigned integers (equivalent to size_t on most systems):
  # of rows and # of elements.
  
 \end_layout
@@ -47664,15 +48460,19 @@ Version
 \begin_inset space ~
 \end_inset
 
-2: Three 8 byte unsigned integers: original # of rows, actual # of rows,
+2:
+ Three 8 byte unsigned integers:
+ original # of rows,
+ actual # of rows,
  and sieve value.
 \end_layout
 
 \begin_layout Standard
-This is followed by the actual matrix data, stored as a single array of
- floats (4 bytes).
+This is followed by the actual matrix data,
+ stored as a single array of floats (4 bytes).
  For versions 1 and 2 the number of elements is explicitly stored.
- For version 2, to calculate the number of matrix elements you need to read:
+ For version 2,
+ to calculate the number of matrix elements you need to read:
 \end_layout
 
 \begin_layout LyX-Code
@@ -47680,22 +48480,22 @@ Elements = (actual_rows * (actual_rows - 1)) / 2
 \end_layout
 
 \begin_layout Standard
-The cluster pair-distance matrix is an upper-right triangle matrix without
- the diagonal (in row-major order), so the first element is the distance
- between elements 0 and 1, the second is between elements 0 and 2, etc.
+The cluster pair-distance matrix is an upper-right triangle matrix without the diagonal (in row-major order),
+ so the first element is the distance between elements 0 and 1,
+ the second is between elements 0 and 2,
+ etc.
 \end_layout
 
 \begin_layout Standard
-In version 2 files, if the sieve value is greater than 1 that means original_row
-s > actual_rows and there is an additional array of characters original_nrows
- long, with 'T' if the row is being ignored (i.e.
+In version 2 files,
+ if the sieve value is greater than 1 that means original_rows > actual_rows and there is an additional array of characters original_nrows long,
+ with 'T' if the row is being ignored (i.e.
  it was sieved out) and 'F' if the row is active (i.e.
  is active in the actual pairwise-distance matrix).
 \end_layout
 
 \begin_layout Standard
-The code that cpptraj uses to read in CpptrajPairDist files is in ClusterMatrix:
-:LoadFile() (ClusterMatrix.cpp).
+The code that cpptraj uses to read in CpptrajPairDist files is in ClusterMatrix::LoadFile() (ClusterMatrix.cpp).
 \end_layout
 
 \begin_layout Subsubsection*
@@ -47703,8 +48503,7 @@ The NetCDF pairwise matrix format
 \end_layout
 
 \begin_layout Standard
-The default way to write pairwise matrix files as of version 6.0.0 is with
- NetCDF.
+The default way to write pairwise matrix files as of version 6.0.0 is with NetCDF.
  This will be set up with the following parameters:
 \end_layout
 
@@ -47749,7 +48548,8 @@ n_rows Number of rows in the upper-triangle pairwise matrix.
 \end_layout
 
 \begin_layout Description
-msize Actual size of the matrix; should be (nRows_ * (nRows_-1)) / 2;
+msize Actual size of the matrix;
+ should be (nRows_ * (nRows_-1)) / 2;
 \end_layout
 
 \end_deeper
@@ -47759,15 +48559,19 @@ Variables:
 
 \begin_deeper
 \begin_layout Description
-sieve (integer, no dimension).
+sieve (integer,
+ no dimension).
  Sieve value.
 \end_layout
 
 \begin_layout Description
-matrix (float, dimension msize).
- The pairwise matrix, flattened to 1 dimension.
- Index calc is: i1 = i + 1; index = (((nRows_ * i) - ((i1 * i) / 2)) + j
- - i1);
+matrix (float,
+ dimension msize).
+ The pairwise matrix,
+ flattened to 1 dimension.
+ Index calc is:
+ i1 = i + 1;
+ index = (((nRows_ * i) - ((i1 * i) / 2)) + j - i1);
 \end_layout
 
 \begin_layout Description
@@ -47775,7 +48579,8 @@ actual
 \begin_inset space ~
 \end_inset
 
-frames (integer, dimension n_rows).
+frames (integer,
+ dimension n_rows).
  The actual frame numbers for which pairwise distances were calculated.
 \end_layout
 
@@ -47818,11 +48623,13 @@ statsout
 \end_layout
 
 \begin_layout Description
-deprot If specified, calculate fraction deprotonated instead of protonated.
+deprot If specified,
+ calculate fraction deprotonated instead of protonated.
 \end_layout
 
 \begin_layout Description
-fracplot If specified, calculate fraction protonated/deprotonated vs pH.
+fracplot If specified,
+ calculate fraction protonated/deprotonated vs pH.
 \end_layout
 
 \begin_deeper
@@ -47845,8 +48652,7 @@ Data Sets Generated
 
 \end_deeper
 \begin_layout Standard
-Calculate statistics for constant pH simulation data previously read in
- with 
+Calculate statistics for constant pH simulation data previously read in with 
 \series bold
 \emph on
 readdata
@@ -47856,6 +48662,7 @@ readdata
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_cphdatafile"
+nolink "false"
 
 \end_inset
 
@@ -47869,8 +48676,8 @@ Solvent pH is <pH>
 \end_layout
 
 \begin_layout LyX-Code
-<res name> <res num> : Offset <off> Pred <pred> Frac Prot <frac> Transitions
- <#trans>
+<res name> <res num> :
+ Offset <off> Pred <pred> Frac Prot <frac> Transitions <#trans>
 \end_layout
 
 \begin_layout LyX-Code
@@ -47882,7 +48689,8 @@ Solvent pH is <pH>
 \end_layout
 
 \begin_layout LyX-Code
-Average total molecular protonation: <avg>
+Average total molecular protonation:
+ <avg>
 \end_layout
 
 \begin_layout Standard
@@ -47890,11 +48698,13 @@ Where
 \series bold
 <off>
 \series default
- is offset from predicted, 
+ is offset from predicted,
+ 
 \series bold
 <pred>
 \series default
- is predicted pH, and <#trans> is the number of transitions.
+ is predicted pH,
+ and <#trans> is the number of transitions.
  A line is printed for each residue.
  This functionality is similar to the 
 \series bold
@@ -47904,6 +48714,7 @@ cphstats
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "sec:cphstats"
+nolink "false"
 
 \end_inset
 
@@ -47928,6 +48739,7 @@ readensembledata
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_readensembledata"
+nolink "false"
 
 \end_inset
 
@@ -47941,6 +48753,7 @@ sortensembledata
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_sortensembledata"
+nolink "false"
 
 \end_inset
 
@@ -47948,8 +48761,9 @@ reference "subsec:cpptraj_sortensembledata"
 \end_layout
 
 \begin_layout Standard
-For example, to read in constant pH data from constant pH REMD, sort and
- analyze:
+For example,
+ to read in constant pH data from constant pH REMD,
+ sort and analyze:
 \end_layout
 
 \begin_layout LyX-Code
@@ -47961,8 +48775,7 @@ sortensembledata PH
 \end_layout
 
 \begin_layout LyX-Code
-runanalysis cphstats PH[*] statsout stats.dat fracplot fracplotout frac.agr
- deprot
+runanalysis cphstats PH[*] statsout stats.dat fracplot fracplotout frac.agr deprot
 \end_layout
 
 \begin_layout Subsection
@@ -47972,6 +48785,8 @@ corr | correlationcoe
 \begin_layout LyX-Code
 corr
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -48015,8 +48830,9 @@ out
 [<dataset2>]
 \series default
  Data set(s) to calculate correlation for.
- If one dataset or the same dataset is given twice, the auto-correlation
- will be calculated, otherwise cross-correlation.
+ If one dataset or the same dataset is given twice,
+ the auto-correlation will be calculated,
+ otherwise cross-correlation.
 \end_layout
 
 \begin_layout Description
@@ -48041,7 +48857,8 @@ out
 \series bold
 [direct]
 \series default
- Do not use FFTs to calculate correlation; this will be much slower.
+ Do not use FFTs to calculate correlation;
+ this will be much slower.
 \end_layout
 
 \begin_layout Standard
@@ -48049,13 +48866,11 @@ DataSet Aspects:
 \end_layout
 
 \begin_layout Description
-[<dataset1>] (Auto-correlation) The aspect will be the name of each of the
- input data set.
+[<dataset1>] (Auto-correlation) The aspect will be the name of each of the input data set.
 \end_layout
 
 \begin_layout Description
-[<dataset1>-<dataset2>] (Cross-correlation) The aspect will be the names
- of each of the input data sets joined by a dash ('-').
+[<dataset1>-<dataset2>] (Cross-correlation) The aspect will be the names of each of the input data sets joined by a dash ('-').
 \end_layout
 
 \begin_layout Standard
@@ -48068,13 +48883,12 @@ DataSet Aspects:
 
 \end_deeper
 \begin_layout Standard
-Calculate the auto-correlation function for data set named <dataset1> or
- the cross-correlation function for data sets named <dataset1> and <dataset2>
- up to <lagmax> frames (all if 
+Calculate the auto-correlation function for data set named <dataset1> or the cross-correlation function for data sets named <dataset1> and <dataset2> up to <lagmax> frames (all if 
 \series bold
 lagmax
 \series default
- not specified), writing the result to file specified by 
+ not specified),
+ writing the result to file specified by 
 \series bold
 out
 \series default
@@ -48167,13 +48981,14 @@ Calculate atomic positional fluctuations for atoms in
 \series bold
 bfactor
 \series default
- is specified, the fluctuations are weighted by 
+ is specified,
+ the fluctuations are weighted by 
 \begin_inset Formula $\frac{8}{3}\pi^{2}$
 \end_inset
 
-(similar but not necessarily equivalent to crystallographic B-factor calculation
-).
- Units are Å, or Å
+(similar but not necessarily equivalent to crystallographic B-factor calculation).
+ Units are Å,
+ or Å
 \begin_inset script superscript
 
 \begin_layout Plain Layout
@@ -48248,8 +49063,7 @@ crosscorr [name <dsetname>] <dsetarg0> [<dsetarg1> ...] [out <filename>]
 
 \end_deeper
 \begin_layout Standard
-Calculate the Pearson product-moment correlation coefficients between all
- specified datasets.
+Calculate the Pearson product-moment correlation coefficients between all specified datasets.
 \end_layout
 
 \begin_layout Subsection
@@ -48268,8 +49082,7 @@ curvefit <dset> { <equation>  |
 \end_layout
 
 \begin_layout LyX-Code
-                  name <dsname> {gauss | nexp <m> [form {mexp|mexpk|mexpk_penalt
-y}} }
+                  name <dsname> {gauss | nexp <m> [form {mexp|mexpk|mexpk_penalty}} }
 \end_layout
 
 \begin_layout LyX-Code
@@ -48299,6 +49112,7 @@ y}} }
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-Data-Set-Math"
+nolink "false"
 
 \end_inset
 
@@ -48356,23 +49170,23 @@ form
 
 \begin_deeper
 \begin_layout Description
-mexp Multi-exponential, SUM(m)[ An * exp(An+1 * X)]
+mexp Multi-exponential,
+ SUM(m)[ An * exp(An+1 * X)]
 \end_layout
 
 \begin_layout Description
-mexpk Multi-exponential plus constant, A0 + SUM(m)[An * exp(An+1 * X)]
+mexpk Multi-exponential plus constant,
+ A0 + SUM(m)[An * exp(An+1 * X)]
 \end_layout
 
 \begin_layout Description
-mexpk_penalty Same as mexpk except sum of prefactors constrained to 1.0 and
- exponential constants constrained to < 0.0.
+mexpk_penalty Same as mexpk except sum of prefactors constrained to 1.0 and exponential constants constrained to < 0.0.
 \end_layout
 
 \end_deeper
 \end_deeper
 \begin_layout Description
-AX=<value> Value of any constants in specified equation with X starting
- from 0 (can specify more than one).
+AX=<value> Value of any constants in specified equation with X starting from 0 (can specify more than one).
 \end_layout
 
 \begin_layout Description
@@ -48400,8 +49214,7 @@ maxit
 \begin_inset space ~
 \end_inset
 
-iterations> Number of iterations to run curve fitting algorithm (default
- 50).
+iterations> Number of iterations to run curve fitting algorithm (default 50).
 \end_layout
 
 \begin_layout Description
@@ -48417,8 +49230,7 @@ outxbins
 \begin_inset space ~
 \end_inset
 
-<NX> Number of points to use when generating final curve (default same number
- of points as input data set).
+<NX> Number of points to use when generating final curve (default same number of points as input data set).
 \end_layout
 
 \begin_layout Description
@@ -48426,8 +49238,7 @@ outxmin
 \begin_inset space ~
 \end_inset
 
-<xmin> Minimum X value to use for final curve (default same number of points
- as input data set).
+<xmin> Minimum X value to use for final curve (default same number of points as input data set).
 \end_layout
 
 \begin_layout Description
@@ -48435,28 +49246,28 @@ outxmax
 \begin_inset space ~
 \end_inset
 
-<xmax> Maximum X value to use for final curve (default same number of points
- as input data set).
+<xmax> Maximum X value to use for final curve (default same number of points as input data set).
 \end_layout
 
 \end_deeper
 \begin_layout Standard
-Perform non-linear curve fitting for the specified data set using the Levenberg-
-Marquardt algorithm.
+Perform non-linear curve fitting for the specified data set using the Levenberg-Marquardt algorithm.
  Any equation form that cpptraj understands (see 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-Data-Set-Math"
+nolink "false"
 
 \end_inset
 
-) can be used, or several preset forms can be used.
- Similar to Grace (http://plasma-gate.weizmann.ac.il/Grace/), an equation can
- contain constants for curve fitting termed AX (with X being a numerical
- digit, one for each constant), and is assigned to a variable which then
- becomes a data set.
- For example, to fit a curve to data from a file named Data.dat to a data
- set named 'FitY':
+) can be used,
+ or several preset forms can be used.
+ Similar to Grace (http://plasma-gate.weizmann.ac.il/Grace/),
+ an equation can contain constants for curve fitting termed AX (with X being a numerical digit,
+ one for each constant),
+ and is assigned to a variable which then becomes a data set.
+ For example,
+ to fit a curve to data from a file named Data.dat to a data set named 'FitY':
 \end_layout
 
 \begin_layout LyX-Code
@@ -48575,15 +49386,15 @@ name>
 <filename>]]
 \series default
  Mass-weighted covariance (mwcovar) matrix only.
- Calculate entropy, heat capacity, and internal energy from the structure
- of a molecule (average coordinates, see above) and its vibrational frequencies
- using standard statistical mechanical formulas for an ideal gas.
- Results are written to <filename> if specified, otherwise results are written
- to STDOUT.
+ Calculate entropy,
+ heat capacity,
+ and internal energy from the structure of a molecule (average coordinates,
+ see above) and its vibrational frequencies using standard statistical mechanical formulas for an ideal gas.
+ Results are written to <filename> if specified,
+ otherwise results are written to STDOUT.
  
 \series bold
-Note that this converts the units of the calculated eigenvalues to frequencies
- (cm
+Note that this converts the units of the calculated eigenvalues to frequencies (cm
 \begin_inset script superscript
 
 \begin_layout Plain Layout
@@ -48607,7 +49418,8 @@ Note that this converts the units of the calculated eigenvalues to frequencies
 <#>]
 \series default
  Number of eigenvectors to calculate.
- Default is 0, which is only allowed when 'thermo' is specified.
+ Default is 0,
+ which is only allowed when 'thermo' is specified.
 \end_layout
 
 \begin_layout Description
@@ -48628,13 +49440,14 @@ Note that this converts the units of the calculated eigenvalues to frequencies
 [reduce]
 \series default
  Covariance (covar/mwcovar/distcovar) matrices only.
- For coordinate covariance (covar/mwcovar) matrices, each eigenvector element
- is reduced via Ei = Eix^2 + Eiy^2 + Eiz^2.
- For distance covariance (distcovar) the eigenvectors are reduced by taking
- the sum of the squares of each row.
- See Abseher & Nilges, JMB 1998, 279, 911-920 for further details.
- They may be used to compare results from PCA in distance space with those
- from PCA in cartesian-coordinate space.
+ For coordinate covariance (covar/mwcovar) matrices,
+ each eigenvector element is reduced via Ei = Eix^2 + Eiy^2 + Eiz^2.
+ For distance covariance (distcovar) the eigenvectors are reduced by taking the sum of the squares of each row.
+ See Abseher & Nilges,
+ JMB 1998,
+ 279,
+ 911-920 for further details.
+ They may be used to compare results from PCA in distance space with those from PCA in cartesian-coordinate space.
 \end_layout
 
 \begin_layout Description
@@ -48664,8 +49477,8 @@ literal "true"
 \begin_inset space ~
 \end_inset
 
-<#>] Number of vectors to write out for nmwiz output, starting with the
- lowest frequency mode (default 20).
+<#>] Number of vectors to write out for nmwiz output,
+ starting with the lowest frequency mode (default 20).
 \end_layout
 
 \begin_layout Description
@@ -48681,38 +49494,37 @@ literal "true"
 \begin_inset space ~
 \end_inset
 
-<mask>] Mask of atoms corresponding to eigenvectors - should be the same
- one used to generate the matrix.
+<mask>] Mask of atoms corresponding to eigenvectors - should be the same one used to generate the matrix.
 \end_layout
 
 \end_deeper
 \end_deeper
 \begin_layout Standard
 Calculate eigenvectors and eigenvalues for the specified symmetric matrix.
- This is followed by Principal Component Analysis (in cartesian coordinate
- space in the case of a covariance matrix or in distance space in the case
- of a distance-covariance matrix), or Quasiharmonic Analysis (in the case
- of a mass-weighted covariance matrix).
- Diagonalization of distance, correlation, idea, and ired matrices are also
- possible.
+ This is followed by Principal Component Analysis (in cartesian coordinate space in the case of a covariance matrix or in distance space in the case of a distance-covariance matrix),
+ or Quasiharmonic Analysis (in the case of a mass-weighted covariance matrix).
+ Diagonalization of distance,
+ correlation,
+ idea,
+ and ired matrices are also possible.
  Eigenvalues are given in cm
 \begin_inset Formula $^{-1}$
 \end_inset
 
- in the case of a mass-weighted covariance matrix and in the units of the
- matrix elements in all other cases.
- In the case of a mass-weighted covariance matrix, the eigenvectors are
- mass-weighted.
+ in the case of a mass-weighted covariance matrix and in the units of the matrix elements in all other cases.
+ In the case of a mass-weighted covariance matrix,
+ the eigenvectors are mass-weighted.
 \end_layout
 
 \begin_layout Standard
-For quasi-harmonic analysis the input must be a mass-weighted covariance
- matrix.
- Thermodynamic quantities are calculated based on statistical mechanical
- formulae that assume the input system is oscillating in a single energy
- well: see Statistical Thermodynamics by D.
+For quasi-harmonic analysis the input must be a mass-weighted covariance matrix.
+ Thermodynamic quantities are calculated based on statistical mechanical formulae that assume the input system is oscillating in a single energy well:
+ see Statistical Thermodynamics by D.
  A.
- McQuarrie, particularly chapters 4, 5, and 6 for more details.
+ McQuarrie,
+ particularly chapters 4,
+ 5,
+ and 6 for more details.
 \begin_inset CommandInset citation
 LatexCommand citep
 key "McQuarrie1973"
@@ -48720,8 +49532,7 @@ literal "true"
 
 \end_inset
 
- For an in-depth discussion of the accuracy of thermodynamic parameters
- obtained via quasi-harmonic analysis see Chang et al..
+ For an in-depth discussion of the accuracy of thermodynamic parameters obtained via quasi-harmonic analysis see Chang et al..
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Chang2005"
@@ -48733,24 +49544,27 @@ literal "true"
 \end_layout
 
 \begin_layout Standard
-Note that the maximum number of non-zero eigenvalues obtainable depends
- on the number of frames used to generate the input matrix; the number of
- frames should be equal to or greater than the number of columns in the
- matrix in order to obtain all eigenmodes.
+Note that the maximum number of non-zero eigenvalues obtainable depends on the number of frames used to generate the input matrix;
+ the number of frames should be equal to or greater than the number of columns in the matrix in order to obtain all eigenmodes.
 \end_layout
 
 \begin_layout Standard
-Results may include average coordinates (in the case of covar, mwcovar,
- correl), average distances (in the case of distcovar), main diagonal elements
- (in the case of idea and ired), eigenvalues, and eigenvectors.
+Results may include average coordinates (in the case of covar,
+ mwcovar,
+ correl),
+ average distances (in the case of distcovar),
+ main diagonal elements (in the case of idea and ired),
+ eigenvalues,
+ and eigenvectors.
 \end_layout
 
 \begin_layout Standard
-For example, in the following a mass-weighted covariance matrix of all atoms
- is generated and stored internally with the name mwcvmat; the matrix itself
- is written to mwcvmat.dat.
- Subsequently, the first 20 eigenmodes of the matrix are calculated and
- written to evecs.dat, and quasiharmonic analysis is performed at 300.0 K,
+For example,
+ in the following a mass-weighted covariance matrix of all atoms is generated and stored internally with the name mwcvmat;
+ the matrix itself is written to mwcvmat.dat.
+ Subsequently,
+ the first 20 eigenmodes of the matrix are calculated and written to evecs.dat,
+ and quasiharmonic analysis is performed at 300.0 K,
  with the results written to thermo.dat.
 \end_layout
 
@@ -48793,7 +49607,8 @@ evecs
 \end_layout
 
 \begin_layout LyX-Code
- [Reduced] Eigenvector file: <Type> nmodes <#> width <width>
+ [Reduced] Eigenvector file:
+ <Type> nmodes <#> width <width>
 \end_layout
 
 \begin_layout LyX-Code
@@ -48805,10 +49620,10 @@ evecs
 \end_layout
 
 \begin_layout Standard
-Where <Type> is a string identifying what kind of matrix the eigenvectors/eigenv
-alues were determined from, nmodes is how many eigenvectors are in the file,
- and <Average Coordinates> are in lines 7 columns wide, with each element
- having width specified by <width>.
+Where <Type> is a string identifying what kind of matrix the eigenvectors/eigenvalues were determined from,
+ nmodes is how many eigenvectors are in the file,
+ and <Average Coordinates> are in lines 7 columns wide,
+ with each element having width specified by <width>.
  Then for each eigenvector:
 \end_layout
 
@@ -48829,8 +49644,8 @@ alues were determined from, nmodes is how many eigenvectors are in the file,
 \end_layout
 
 \begin_layout Standard
-Where <Eigenvector Coordinates> are in lines 7 columns wide, with each element
- having width specified by <width>.
+Where <Eigenvector Coordinates> are in lines 7 columns wide,
+ with each element having width specified by <width>.
 \end_layout
 
 \begin_layout Subsection
@@ -49025,8 +49840,7 @@ Data Sets Created
 \end_layout
 
 \begin_layout Description
-<name>[vala] Difference between last half average of data vs final density
- (A2).
+<name>[vala] Difference between last half average of data vs final density (A2).
 \end_layout
 
 \begin_layout Description
@@ -49046,7 +49860,10 @@ Data Sets Created
 \end_layout
 
 \begin_layout Description
-<name>[result] Final result: yes, no, err (error).
+<name>[result] Final result:
+ yes,
+ no,
+ err (error).
 \end_layout
 
 \end_deeper
@@ -49059,10 +49876,10 @@ plateaued
 \begin_inset Quotes erd
 \end_inset
 
-, i.e.
+,
+ i.e.
  stopped changing significantly by the end of the set.
- Currently the defaults are set up to evaluate density data as part of the
- system preparation protocol described by Roe & Brooks.
+ Currently the defaults are set up to evaluate density data as part of the system preparation protocol described by Roe & Brooks.
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Roe2020"
@@ -49141,7 +49958,8 @@ fft <dset0> [<dset1> ...] [out <outfile>] [name <outsetname>] [dt <samp_int>]
 \end_deeper
 \begin_layout Standard
 Perform fast Fourier transform (FFT) on specified data set(s).
- If more than 1 data set, they must all have the same size.
+ If more than 1 data set,
+ they must all have the same size.
 \end_layout
 
 \begin_layout Subsection
@@ -49160,13 +49978,11 @@ hausdorff <set arg0> [<set arg1> ...]
 \end_layout
 
 \begin_layout LyX-Code
-          [outtype {basic|trimatrix nrows <#>|fullmatrix nrows <#> [ncols
- <#>]}]
+          [outtype {basic|trimatrix nrows <#>|fullmatrix nrows <#> [ncols <#>]}]
 \end_layout
 
 \begin_layout LyX-Code
-      	[name <output set name>] [out <file>] [outab <file>] [outba <file>]
- 
+      	[name <output set name>] [out <file>] [outab <file>] [outba <file>] 
 \end_layout
 
 \begin_deeper
@@ -49201,8 +50017,7 @@ nrows
 \begin_inset space ~
 \end_inset
 
-<#> Output Hausdorff distances for each input matrix as a 2D upper-triangular
- matrix with the given number of rows.
+<#> Output Hausdorff distances for each input matrix as a 2D upper-triangular matrix with the given number of rows.
  Must have (nrows * (nrows-1)) / 2 input sets.
 \end_layout
 
@@ -49223,13 +50038,13 @@ ncols
 \begin_inset space ~
 \end_inset
 
-<#> Output Hausdorff distances for each input matrix as a full matrix with
- the given number of columns and rows.
+<#> Output Hausdorff distances for each input matrix as a full matrix with the given number of columns and rows.
  If 
 \series bold
 ncols
 \series default
- is not given, use 
+ is not given,
+ use 
 \series bold
 nrows
 \series default
@@ -49281,24 +50096,24 @@ name>] Name of output data sets.
 \end_deeper
 \begin_layout Standard
 Calculate the symmetric Hausdorff distance for one or more matrices.
- The results can be saved as an array or as a full or upper-triangular matrix
- with the specified dimensions.
+ The results can be saved as an array or as a full or upper-triangular matrix with the specified dimensions.
  The Hausdorff distance H is determined from:
 \end_layout
 
 \begin_layout LyX-Code
-H = max{dH(A,B), dH(B,A)]
+H = max{dH(A,B),
+ dH(B,A)]
 \end_layout
 
 \begin_layout Standard
-Where dH(A,B) is the directed Hausdorff distance between sets A and B, etc.
- Colloquially speaking, the directed Hausdorff distance between A and B
- is determined as follows:
+Where dH(A,B) is the directed Hausdorff distance between sets A and B,
+ etc.
+ Colloquially speaking,
+ the directed Hausdorff distance between A and B is determined as follows:
 \end_layout
 
 \begin_layout Enumerate
-What is the closest approach (distance) of each point in A to any point
- in B?
+What is the closest approach (distance) of each point in A to any point in B?
 \end_layout
 
 \begin_layout Enumerate
@@ -49306,12 +50121,14 @@ Choose the largest distance from among those distances.
 \end_layout
 
 \begin_layout Standard
-If desired, the output can be formed into a matrix, which can be useful
- e.g.
+If desired,
+ the output can be formed into a matrix,
+ which can be useful e.g.
  when doing multiple 2D rms calculations on different regions of a trajectory.
- For example, the following input divides a 100 frame trajectory into 10
- frame chunks, calcultes the 2D RMS matrix for each chunk, then performs
- Hausdorff analysis on the resulting matrices and forms a full output matrix.
+ For example,
+ the following input divides a 100 frame trajectory into 10 frame chunks,
+ calcultes the 2D RMS matrix for each chunk,
+ then performs Hausdorff analysis on the resulting matrices and forms a full output matrix.
 \end_layout
 
 \begin_layout LyX-Code
@@ -49454,8 +50271,7 @@ parallelanalysis sync
 \end_layout
 
 \begin_layout LyX-Code
-runanalysis hausdorff M* out hausdorff.fullmatrix.gnu title hausdorff.matrix.gnu
- 
+runanalysis hausdorff M* out hausdorff.fullmatrix.gnu title hausdorff.matrix.gnu 
 \backslash
 
 \end_layout
@@ -49471,6 +50287,8 @@ hist | histogram
 \begin_layout LyX-Code
 hist
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -49509,10 +50327,13 @@ hist
 <dataset_name>[,<min>,<max>,<step>,<bins>]
 \series default
  Dataset(s) to be histogrammed.
- Optionally, the min, max, step, and/or number of bins can be specified
- for this dimension after the dataset name separated by commas.
- It is only necessary to specify the step or number of bins, an asterisk
- '*' indicates the value should be calculated from available data.
+ Optionally,
+ the min,
+ max,
+ step,
+ and/or number of bins can be specified for this dimension after the dataset name separated by commas.
+ It is only necessary to specify the step or number of bins,
+ an asterisk '*' indicates the value should be calculated from available data.
  
 \end_layout
 
@@ -49525,11 +50346,13 @@ hist
 
 <temperature>]
 \series default
- If specified, estimate free energy from bin populations using 
+ If specified,
+ estimate free energy from bin populations using 
 \begin_inset Formula $G_{i}=-k_{B}T\ln\left(\frac{N_{i}}{N_{Max}}\right)$
 \end_inset
 
-, where K
+,
+ where K
 \begin_inset script subscript
 
 \begin_layout Plain Layout
@@ -49538,7 +50361,8 @@ B
 
 \end_inset
 
- is Boltzmann's constant, T is the temperature specified by <temperature>,
+ is Boltzmann's constant,
+ T is the temperature specified by <temperature>,
  N
 \begin_inset script subscript
 
@@ -49558,8 +50382,7 @@ Max
 \end_inset
 
  is the population of the most populated bin.
- Bins with no population are given an artificial barrier equivalent to a
- population of 0.5.
+ Bins with no population are given an artificial barrier equivalent to a population of 0.5.
 \end_layout
 
 \begin_layout Description
@@ -49567,8 +50390,8 @@ Max
 \series bold
 [norm]
 \series default
- If specified, normalize bin populations so the sum over all bins equals
- 1.0.
+ If specified,
+ normalize bin populations so the sum over all bins equals 1.0.
 \end_layout
 
 \begin_layout Description
@@ -49580,7 +50403,9 @@ Max
 \series bold
 [gnu]
 \series default
- Internal output only; data will be gnuplot-readable, i.e.
+ Internal output only;
+ data will be gnuplot-readable,
+ i.e.
  a space will be printed after the highest order coordinate cycles.
 \end_layout
 
@@ -49589,7 +50414,9 @@ Max
 \series bold
 [circular]
 \series default
- Internal output only; data will wrap, i.e.
+ Internal output only;
+ data will wrap,
+ i.e.
  an extra bin will be printed before min and after max in each direction.
  Useful for e.g.
  dihedral angles.
@@ -49612,8 +50439,7 @@ out
 \begin_inset space ~
 \end_inset
 
-<amdboost_data>] Reweight bins using AMD boost energies in data set <amdboost_da
-ta> (in KT).
+<amdboost_data>] Reweight bins using AMD boost energies in data set <amdboost_data> (in KT).
 \end_layout
 
 \begin_layout Description
@@ -49641,8 +50467,7 @@ name>] Output histogram data set name.
 \begin_inset space ~
 \end_inset
 
-<format>]] (3D histograms only) Write a pseudo-trajectory of the 3 data
- sets (1 atom) to <file> with format <format>.
+<format>]] (3D histograms only) Write a pseudo-trajectory of the 3 data sets (1 atom) to <file> with format <format>.
 \end_layout
 
 \begin_layout Description
@@ -49650,8 +50475,7 @@ name>] Output histogram data set name.
 \begin_inset space ~
 \end_inset
 
-<file>] (3D histograms only) Write a topology corresponding to the pseudo-trajec
-tory to <file>.
+<file>] (3D histograms only) Write a topology corresponding to the pseudo-trajectory to <file>.
 \end_layout
 
 \begin_layout Description
@@ -49703,17 +50527,18 @@ tory to <file>.
 \end_layout
 
 \begin_layout Description
-[nativeout] Do not use cpptraj data file framework; only necessary for writing
- out histograms with > 3 dimensions.
+[nativeout] Do not use cpptraj data file framework;
+ only necessary for writing out histograms with > 3 dimensions.
 \end_layout
 
 \end_deeper
 \begin_layout Standard
-Create an N-dimensional histrogram, where N is the number of datasets specified.
+Create an N-dimensional histrogram,
+ where N is the number of datasets specified.
  For 1-dimensional histograms the xmgrace '.agr' file format is recommended;
  for 2-dimensional hisograms the gnuplot '.gnu' file format is recommended;
- for all other dimensions plot formatting is disabled and the routine uses
- its own internal output format; this is also enabled if 
+ for all other dimensions plot formatting is disabled and the routine uses its own internal output format;
+ this is also enabled if 
 \series bold
 gnu
 \series default
@@ -49725,8 +50550,8 @@ circular
 \end_layout
 
 \begin_layout Standard
-For example, to create a two dimensional histogram of two datasets 'phi'
- and 'psi':
+For example,
+ to create a two dimensional histogram of two datasets 'phi' and 'psi':
 \end_layout
 
 \begin_layout LyX-Code
@@ -49742,9 +50567,8 @@ hist phi,-180,180,*,72 psi,-180,180,*,72 out hist.gnu
 \end_layout
 
 \begin_layout Standard
-In this case the number of bins (72) has been specified for each dimension
- and '*' has been given for the step size, indicating it should be calculated
- based on min/max/bins.
+In this case the number of bins (72) has been specified for each dimension and '*' has been given for the step size,
+ indicating it should be calculated based on min/max/bins.
  The following 'hist' command is equivalent:
 \end_layout
 
@@ -49782,7 +50606,8 @@ integrate <dset0> [<dset1> ...] [out <outfile>] [intout <intfile>]
 \begin_inset space ~
 \end_inset
 
-<outfile>] If specified, write cumulative sum curves to <outfile>.
+<outfile>] If specified,
+ write cumulative sum curves to <outfile>.
 \end_layout
 
 \begin_layout Description
@@ -49790,7 +50615,8 @@ integrate <dset0> [<dset1> ...] [out <outfile>] [intout <intfile>]
 \begin_inset space ~
 \end_inset
 
-<intfile>] If specified, write final integral values to <intfile>.
+<intfile>] If specified,
+ write final integral values to <intfile>.
 \end_layout
 
 \begin_layout Description
@@ -49806,7 +50632,8 @@ DataSets Created:
 \end_layout
 
 \begin_layout Description
-<name> Final integral values, 1 for each input data set (indexed from 0).
+<name> Final integral values,
+ 1 for each input data set (indexed from 0).
 \end_layout
 
 \begin_layout Description
@@ -49814,7 +50641,8 @@ DataSets Created:
 \series bold
 out
 \series default
- was specified, 1 for each input data set (indexed from 0).
+ was specified,
+ 1 for each input data set (indexed from 0).
 \end_layout
 
 \end_deeper
@@ -49870,8 +50698,8 @@ freq
 
 <MHz>]
 \series default
- Should only be used when ired vectors represent N-H bonds; calculate correlatio
-n times 
+ Should only be used when ired vectors represent N-H bonds;
+ calculate correlation times 
 \family roman
 \series medium
 \shape up
@@ -49914,7 +50742,9 @@ for each eigenmode and relaxation rates and NOEs for each N-H vector.
 \begin_inset space ~
 \end_inset
 
-<noefilename>] File to write the T1, T2, and NOE data to.
+<noefilename>] File to write the T1,
+ T2,
+ and NOE data to.
 \end_layout
 
 \end_deeper
@@ -49923,8 +50753,7 @@ for each eigenmode and relaxation rates and NOEs for each N-H vector.
 \begin_inset space ~
 \end_inset
 
-<order>] Order of the Legendre polynomials to use when calculating spherical
- harmonics (default 2).
+<order>] Order of the Legendre polynomials to use when calculating spherical harmonics (default 2).
 \end_layout
 
 \begin_layout Description
@@ -49977,7 +50806,9 @@ for each eigenmode and relaxation rates and NOEs for each N-H vector.
 \series bold
 [norm]
 \series default
- Normalize all correlation functions, i.e., 
+ Normalize all correlation functions,
+ i.e.,
+ 
 \begin_inset Formula $C_{l}(t=0)=P_{l}(t=0)=1.0$
 \end_inset
 
@@ -49989,8 +50820,8 @@ for each eigenmode and relaxation rates and NOEs for each N-H vector.
 \series bold
 [drct]
 \series default
- Use the direct method to calculate correlations instead of FFT; this will
- be much slower.
+ Use the direct method to calculate correlations instead of FFT;
+ this will be much slower.
 \end_layout
 
 \begin_layout Description
@@ -50018,8 +50849,8 @@ modes
 \begin_inset space ~
 \end_inset
 
-<file>] If specified, write full delta*S^2 matrix (# IRED vector rows by
- # eigenmodes columns) to <file>.
+<file>] If specified,
+ write full delta*S^2 matrix (# IRED vector rows by # eigenmodes columns) to <file>.
 \end_layout
 
 \begin_layout Standard
@@ -50072,12 +50903,9 @@ literal "true"
 
 \end_inset
 
- analysis on previously defined IRED vectors (see vector ired) using eigenmodes
- calculated from those vectors with a previous 'diagmatrix' command.
- The number of defined IRED vectors should match the number of eigenmodes
- calculated.
- Autocorrelation functions for each mode and the corresponding correlation
- time 
+ analysis on previously defined IRED vectors (see vector ired) using eigenmodes calculated from those vectors with a previous 'diagmatrix' command.
+ The number of defined IRED vectors should match the number of eigenmodes calculated.
+ Autocorrelation functions for each mode and the corresponding correlation time 
 \family roman
 \series medium
 \shape up
@@ -50104,8 +50932,7 @@ literal "true"
 \lang english
 will be written to <filename>.cmt.
  Autocorrelation functions for each vector will be written to <filename>.cjt.
- Relaxation rates and NOEs for each N-H vector will be written to <filename>
- or added to the the end of the standard output.
+ Relaxation rates and NOEs for each N-H vector will be written to <filename> or added to the the end of the standard output.
  For the calculation of
 \lang american
  
@@ -50134,10 +50961,11 @@ will be written to <filename>.cmt.
 \lang american
  
 \lang english
-the normalized correlation functions and only the first third of the analyzed
- time steps will be used.
- For further information on the convergence of correlation functions see
- [Schneider, Brünger, Nilges, 
+the normalized correlation functions and only the first third of the analyzed time steps will be used.
+ For further information on the convergence of correlation functions see [Schneider,
+ Brünger,
+ Nilges,
+ 
 \emph on
 J.
  Mol.
@@ -50148,7 +50976,8 @@ J.
 \series bold
 285
 \series default
-, 727 (1999)].
+,
+ 727 (1999)].
 \end_layout
 
 \begin_layout Subsubsection*
@@ -50160,7 +50989,8 @@ In
 \shape italic
 cpptraj
 \shape default
-, IRED analysis
+,
+ IRED analysis
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Prompers02a"
@@ -50168,16 +50998,14 @@ literal "true"
 
 \end_inset
 
- can now be performed in one pass (as opposed to the two passes previously
- required in 
+ can now be performed in one pass (as opposed to the two passes previously required in 
 \shape italic
 ptraj
 \shape default
 ).
- First, IRED vectors are defined (in this case for N-H bonds) and an IRED
- matrix is calculated and analyzed.
- The IRED vectors are then projected onto the calculated IRED eigenvectors
- in the 
+ First,
+ IRED vectors are defined (in this case for N-H bonds) and an IRED matrix is calculated and analyzed.
+ The IRED vectors are then projected onto the calculated IRED eigenvectors in the 
 \series bold
 \shape italic
 ired
@@ -50188,14 +51016,15 @@ ired
 \shape italic
 order
 \shape default
- is specified, order parameters based on IRED are calculated.
+ is specified,
+ order parameters based on IRED are calculated.
  By specifying the 
 \shape italic
 relax
 \shape default
- parameter, relaxation rates and NOEs can be obtained for each N-H vector.
- Note that the order of the IRED matrix should be the same as the one specified
- for IRED analysis.
+ parameter,
+ relaxation rates and NOEs can be obtained for each N-H vector.
+ Note that the order of the IRED matrix should be the same as the one specified for IRED analysis.
 \end_layout
 
 \begin_layout LyX-Code
@@ -50278,8 +51107,8 @@ kde <dataset> [bandwidth <bw>] [out <file>] [name <dsname>]
 \begin_inset space ~
 \end_inset
 
-<bw>] Bandwidth to use for KDE; if not specified bandwidth will be estimated
- using the normal distribution approximation.
+<bw>] Bandwidth to use for KDE;
+ if not specified bandwidth will be estimated using the normal distribution approximation.
 \end_layout
 
 \begin_layout Description
@@ -50347,8 +51176,7 @@ kde <dataset> [bandwidth <bw>] [out <file>] [name <dsname>]
 \begin_inset space ~
 \end_inset
 
-<outfile>]] Calculate Kullback-Leibler divergence over time of <dataset>
- distribution to <dsname2> distribution.
+<outfile>]] Calculate Kullback-Leibler divergence over time of <dataset> distribution to <dsname2> distribution.
  Output to <outfile> if 
 \series bold
 klout
@@ -50361,8 +51189,7 @@ klout
 \begin_inset space ~
 \end_inset
 
-<amdboost_data>] Reweight histogram using AMD boost data from data set <amdboost
-_data> (in KT).
+<amdboost_data>] Reweight histogram using AMD boost data from data set <amdboost_data> (in KT).
 \end_layout
 
 \end_deeper
@@ -50412,11 +51239,15 @@ lifetime [out <filename>] <dsetarg0> [ <dsetarg1> ...
 
 <filename>]
 \series default
- Write results to file named <filename>, and lifetime curves to 'crv.<filename>'.
- If performing windowed lifetime analysis, <filename> contains the fraction
- present over time windows, and 2 additional files are written: 'max.<filename>',
- containing max lifetime over windows, and 'avg.<filename>', containing average
- lifetime over windows.
+ Write results to file named <filename>,
+ and lifetime curves to 'crv.<filename>'.
+ If performing windowed lifetime analysis,
+ <filename> contains the fraction present over time windows,
+ and 2 additional files are written:
+ 'max.<filename>',
+ containing max lifetime over windows,
+ and 'avg.<filename>',
+ containing average lifetime over windows.
 \end_layout
 
 \begin_layout Description
@@ -50509,8 +51340,7 @@ Just calculate averages (no lifetime analysis).
 \begin_inset space ~
 \end_inset
 
-<fuzzcut>] Ignore changes in lifetime state that are less than <fuzzcut>
- frames.
+<fuzzcut>] Ignore changes in lifetime state that are less than <fuzzcut> frames.
 \end_layout
 
 \begin_layout Description
@@ -50522,7 +51352,8 @@ Data Sets Created:
 \end_layout
 
 \begin_layout Description
-<setname> Number of lifetimes for each set, or if 
+<setname> Number of lifetimes for each set,
+ or if 
 \series bold
 window
 \series default
@@ -50530,7 +51361,8 @@ window
 \end_layout
 
 \begin_layout Description
-<setname>[max] Maximum lifetime for each set, or if 
+<setname>[max] Maximum lifetime for each set,
+ or if 
 \series bold
 window
 \series default
@@ -50538,7 +51370,8 @@ window
 \end_layout
 
 \begin_layout Description
-<setname>[avg] Average lifetime for each set, or if 
+<setname>[avg] Average lifetime for each set,
+ or if 
 \series bold
 window
 \series default
@@ -50568,8 +51401,8 @@ window
 \end_deeper
 \begin_layout Standard
 Perform lifetime analysis for specified data sets.
- Lifetime data can either be determined for the entire set, or for time
- windows of specified size within the set if 
+ Lifetime data can either be determined for the entire set,
+ or for time windows of specified size within the set if 
 \series bold
 window
 \series default
@@ -50585,26 +51418,33 @@ lifetime
 \begin_inset Quotes erd
 \end_inset
 
- is defined as the length of time something remains 'present'; data is considere
-d present when above or below a certain cutoff (the default is greater than
- 0.5, useful for analysis of 
+ is defined as the length of time something remains 'present';
+ data is considered present when above or below a certain cutoff (the default is greater than 0.5,
+ useful for analysis of 
 \series bold
 \shape italic
 hbond
 \series default
 \shape default
  time series data).
- For example, in the case of a hydrogen bond 
+ For example,
+ in the case of a hydrogen bond 
 \series bold
 'series'
 \series default
- data set, if a hydrogen bond is present during a frame the value is 1,
+ data set,
+ if a hydrogen bond is present during a frame the value is 1,
  otherwise it is 0.
- Given the hbond time series data set {1 1 1 0 1 0 0 0 1 1}, the overall
- fraction present is 0.6.
- However, there are 3 lifetimes of lengths 3, 1, and 2 ({1 1 1}, {1}, and
- {1 1}).
- The maximum lifetime is 3 and the average lifetime is 2.0, i.e.
+ Given the hbond time series data set {1 1 1 0 1 0 0 0 1 1},
+ the overall fraction present is 0.6.
+ However,
+ there are 3 lifetimes of lengths 3,
+ 1,
+ and 2 ({1 1 1},
+ {1},
+ and {1 1}).
+ The maximum lifetime is 3 and the average lifetime is 2.0,
+ i.e.
  (3 + 1 + 2) / 3 lifetimes = 2.0.
  One can also construct a 
 \begin_inset Quotes eld
@@ -50614,15 +51454,15 @@ lifetime curve
 \begin_inset Quotes erd
 \end_inset
 
-, which is constructed as the sum of all individual lifetimes.
- By default these curves are normalized to 1.0, but the raw curve can be
- obtained using the 
+,
+ which is constructed as the sum of all individual lifetimes.
+ By default these curves are normalized to 1.0,
+ but the raw curve can be obtained using the 
 \series bold
 rawcurve
 \series default
  keyword.
- For the example data set here the raw lifetime curve would be 3 frames
- long:
+ For the example data set here the raw lifetime curve would be 3 frames long:
 \end_layout
 
 \begin_layout LyX-Code
@@ -50638,7 +51478,8 @@ rawcurve
 \end_layout
 
 \begin_layout LyX-Code
-Curve: 3 2 1
+Curve:
+ 3 2 1
 \end_layout
 
 \begin_layout Standard
@@ -50647,16 +51488,14 @@ By default data sets are sorted by name unless
 nosort
 \series default
  is specified.
- The lifetime command can calculate lifetimes over specific time windows
- by using the 
+ The lifetime command can calculate lifetimes over specific time windows by using the 
 \series bold
 window
 \series default
  keyword.
- This can be particularly useful if one wants to get a sense for how lifetimes
- are changing over the course of very long time series data.
- In addition, averages can be calculated instead of lifetimes by specifying
- 
+ This can be particularly useful if one wants to get a sense for how lifetimes are changing over the course of very long time series data.
+ In addition,
+ averages can be calculated instead of lifetimes by specifying 
 \series bold
 averageonly
 \series default
@@ -50665,8 +51504,8 @@ averageonly
 \series bold
 cumulative
 \series default
- keyword, or the change from the average value in the previous window can
- be obtained using the 
+ keyword,
+ or the change from the average value in the previous window can be obtained using the 
 \series bold
 delta
 \series default
@@ -50678,16 +51517,13 @@ The
 \series bold
 fuzz
 \series default
- keyword can be used to try and smooth the input data by ignoring changes
- in state that occur for fewer frames than <fuzzcut>.
- For example, in the above example hbond time series data set there is a
- one frame change in state between the first and second lifetimes which
- could be interpreted as a transient breaking of the hydrogen bond.
- Using a <fuzzcut> value of 1, this one frame change in state would be ignored,
- and the data set would effectively appear to lifetime as {1 1 1 1 1 0 0
- 0 1 1}.
- The state change between the second and third lifetimes is longer than
- <fuzzcut> (3 frames) and so it would remain.
+ keyword can be used to try and smooth the input data by ignoring changes in state that occur for fewer frames than <fuzzcut>.
+ For example,
+ in the above example hbond time series data set there is a one frame change in state between the first and second lifetimes which could be interpreted as a transient breaking of the hydrogen bond.
+ Using a <fuzzcut> value of 1,
+ this one frame change in state would be ignored,
+ and the data set would effectively appear to lifetime as {1 1 1 1 1 0 0 0 1 1}.
+ The state change between the second and third lifetimes is longer than <fuzzcut> (3 frames) and so it would remain.
 \end_layout
 
 \begin_layout Standard
@@ -50695,7 +51531,9 @@ If
 \series bold
 window
 \series default
- is not specified, two files are output: <filename> and crv.<filename>.
+ is not specified,
+ two files are output:
+ <filename> and crv.<filename>.
  The file <filename> contains overall lifetime stats for each set with format:
 \end_layout
 
@@ -50708,19 +51546,23 @@ where
 \family typewriter
 <setname>
 \family default
- denotes the total number of lifetimes, 
+ denotes the total number of lifetimes,
+ 
 \family typewriter
 <setname>[max]
 \family default
- denotes the maximum lifetime, 
+ denotes the maximum lifetime,
+ 
 \family typewriter
 <setname>[avg] 
 \family default
-denotes the average lifetime, 
+denotes the average lifetime,
+ 
 \family typewriter
 <setname>[frames]
 \family default
- denotes the total number of frames present in all lifetimes, and 
+ denotes the total number of frames present in all lifetimes,
+ and 
 \family typewriter
 <setname>[name] 
 \family default
@@ -50733,7 +51575,11 @@ If
 \series bold
 window
 \series default
- is specified, four files are output: <filename>, max.<filename>, avg.<filename>,
+ is specified,
+ four files are output:
+ <filename>,
+ max.<filename>,
+ avg.<filename>,
  and crv.<filename>.
  <filename> contains the fraction 
 \begin_inset Quotes eld
@@ -50743,15 +51589,17 @@ present
 \begin_inset Quotes erd
 \end_inset
 
- over each time window for each set, max.<filename> contains the maximum
- lifetime in each time window for each set, avg.<filename> contains the average
- lifetime over each window for each set, and crv.<filename> contains the
- overall lifetime curves for each set.
- For window output, Gnuplot format is recommended.
+ over each time window for each set,
+ max.<filename> contains the maximum lifetime in each time window for each set,
+ avg.<filename> contains the average lifetime over each window for each set,
+ and crv.<filename> contains the overall lifetime curves for each set.
+ For window output,
+ Gnuplot format is recommended.
 \end_layout
 
 \begin_layout Subsubsection*
-Example: hbond lifetime analysis
+Example:
+ hbond lifetime analysis
 \end_layout
 
 \begin_layout LyX-Code
@@ -50868,8 +51716,8 @@ lowest> Number of lowest points in each bin to average over.
 \end_deeper
 \begin_layout Standard
 Calculate a curve of the average of the # lowest points in bins of stepsize.
- Essentially each input data set is binned over bins of stepsize, then the
- lowest <#> points are averaged over for each bin.
+ Essentially each input data set is binned over bins of stepsize,
+ then the lowest <#> points are averaged over for each bin.
 \end_layout
 
 \begin_layout Subsection
@@ -50882,8 +51730,8 @@ meltcurve <dset0> [<dset1> ...] [out <outfile>] [name <outsetname>] cut <cut>
 
 \begin_layout Standard
 Calculate melting curve from input data sets (i.e.
- fraction 'folded' for each data set) assuming a simple 2-state transition
- model, using data below <cut>as 'folded' and data above <cut> as 'unfolded'.
+ fraction 'folded' for each data set) assuming a simple 2-state transition model,
+ using data below <cut>as 'folded' and data above <cut> as 'unfolded'.
 \end_layout
 
 \begin_layout Subsection
@@ -50891,8 +51739,7 @@ modes
 \end_layout
 
 \begin_layout LyX-Code
-modes {fluct|displ|corr|eigenval|trajout|rmsip} name <modesname> [name2
- <modesname>]
+modes {fluct|displ|corr|eigenval|trajout|rmsip} name <modesname> [name2 <modesname>]
 \end_layout
 
 \begin_layout LyX-Code
@@ -50904,7 +51751,8 @@ modes {fluct|displ|corr|eigenval|trajout|rmsip} name <modesname> [name2
 \end_layout
 
 \begin_layout LyX-Code
-    Options for 'trajout': (Generate pseudo-trajectory)
+    Options for 'trajout':
+ (Generate pseudo-trajectory)
 \end_layout
 
 \begin_layout LyX-Code
@@ -50920,7 +51768,8 @@ modes {fluct|displ|corr|eigenval|trajout|rmsip} name <modesname> [name2
 \end_layout
 
 \begin_layout LyX-Code
-    Options for 'corr': (Calculate dipole correlation)
+    Options for 'corr':
+ (Calculate dipole correlation)
 \end_layout
 
 \begin_layout LyX-Code
@@ -50945,8 +51794,10 @@ Types of Calculations:
 \series bold
 fluct
 \series default
- RMS fluctuations (X, Y, Z, and total) for each atom across specified normal
- modes.
+ RMS fluctuations (X,
+ Y,
+ Z,
+ and total) for each atom across specified normal modes.
 \end_layout
 
 \begin_layout Description
@@ -50954,8 +51805,8 @@ fluct
 \series bold
 displ
 \series default
- Displacement of cartesian coordinates in the X, Y and Z directions for
- each atom across specified normal modes.
+ Displacement of cartesian coordinates in the X,
+ Y and Z directions for each atom across specified normal modes.
 \end_layout
 
 \begin_layout Description
@@ -50976,13 +51827,11 @@ eigenval Calculate eigenvalue fractions.
 \end_layout
 
 \begin_layout Description
-trajout Create a pseudo-trajectory along the given mode from the average
- structure.
+trajout Create a pseudo-trajectory along the given mode from the average structure.
 \end_layout
 
 \begin_layout Description
-rmsip Calculate the root-mean-square inner product between modes specified
- by 
+rmsip Calculate the root-mean-square inner product between modes specified by 
 \series bold
 name
 \series default
@@ -51026,13 +51875,14 @@ name
 
 <end>]
 \series default
- If modes taken from datafile, beginning and end modes to read.
+ If modes taken from datafile,
+ beginning and end modes to read.
  Default for 
 \shape italic
 beg
 \shape default
- is 7 (which skips the first 6 zero-frequency modes in the case of a normal
- mode analysis); for 
+ is 7 (which skips the first 6 zero-frequency modes in the case of a normal mode analysis);
+ for 
 \shape italic
 end
 \shape default
@@ -51061,8 +51911,8 @@ end
 \end_layout
 
 \begin_layout Description
-[calcall] If specified use all eigenvectors; otherwise eigenvectors associated
- with zero or negative eigenvalues will be skipped.
+[calcall] If specified use all eigenvectors;
+ otherwise eigenvectors associated with zero or negative eigenvalues will be skipped.
 \end_layout
 
 \begin_layout Description
@@ -51127,8 +51977,7 @@ Options for 'trajout':
 \begin_inset space ~
 \end_inset
 
-<pcmin>] Lowest principal component projection value to use for output trajector
-y.
+<pcmin>] Lowest principal component projection value to use for output trajectory.
 \end_layout
 
 \begin_layout Description
@@ -51136,8 +51985,7 @@ y.
 \begin_inset space ~
 \end_inset
 
-<pcmax>] Highest principal component projection value to use for output
- trajectory.
+<pcmax>] Highest principal component projection value to use for output trajectory.
 \end_layout
 
 \begin_layout Description
@@ -51173,15 +52021,18 @@ Options for 'corr':
 \series bold
 corr
 \series default
-, pairs of atom masks (
+,
+ pairs of atom masks (
 \shape italic
 mask1
 \shape default
-, 
+,
+ 
 \shape italic
 mask2
 \shape default
-; each pair preceded by 
+;
+ each pair preceded by 
 \begin_inset Quotes eld
 \end_inset
 
@@ -51193,8 +52044,7 @@ maskp
 \begin_inset Quotes erd
 \end_inset
 
- and each mask defining only a single atom) have to be given that specify
- the atoms for which the correlation functions are desired.
+ and each mask defining only a single atom) have to be given that specify the atoms for which the correlation functions are desired.
 \end_layout
 
 \begin_layout Description
@@ -51214,8 +52064,9 @@ mask2
 \series bold
 maskp
 \series default
-, specify two masks; atoms from the first mask will be paired up with atoms
- from the second mask.
+,
+ specify two masks;
+ atoms from the first mask will be paired up with atoms from the second mask.
 \end_layout
 
 \begin_layout Standard
@@ -51280,9 +52131,7 @@ DataSets Created (rmsip)
 
 \end_deeper
 \begin_layout Standard
-Analyze previously calculated eigenmodes obtained from principal component
- analyses (of covariance matrices) or quasiharmonic analyses (diagmatrix
- analysis command).
+Analyze previously calculated eigenmodes obtained from principal component analyses (of covariance matrices) or quasiharmonic analyses (diagmatrix analysis command).
  Modes are taken from a previously generated data set (i.e.
  from 
 \series bold
@@ -51297,8 +52146,8 @@ readdata
 \series default
 \shape default
 .
- By default, classical (Boltzmann) statistics are used in populating the
- modes.
+ By default,
+ classical (Boltzmann) statistics are used in populating the modes.
  A possible series of commands would be 
 \begin_inset Quotes eld
 \end_inset
@@ -51323,7 +52172,8 @@ mwcovar
 \begin_inset Quotes erd
 \end_inset
 
- to generate the matrix, 
+ to generate the matrix,
+ 
 \begin_inset Quotes eld
 \end_inset
 
@@ -51337,7 +52187,10 @@ diagmatrix
 \begin_inset Quotes erd
 \end_inset
 
- to calculate the modes, and, finally, 
+ to calculate the modes,
+ and,
+ finally,
+ 
 \begin_inset Quotes eld
 \end_inset
 
@@ -51356,8 +52209,8 @@ modes
 \end_layout
 
 \begin_layout Standard
-For example, to calculate the RMS fluctuations or displacements of the first
- 3 eigenmodes caluclated from a mass-weighted covariance matrix:
+For example,
+ to calculate the RMS fluctuations or displacements of the first 3 eigenmodes caluclated from a mass-weighted covariance matrix:
 \end_layout
 
 \begin_layout LyX-Code
@@ -51377,8 +52230,8 @@ modes displ out resdispl.dat name evecs beg 1 end 3
 \end_layout
 
 \begin_layout Standard
-Additionally, dipole-dipole correlation functions for modes obtained from
- principle component analysis or quasiharmonic analysis can be computed.
+Additionally,
+ dipole-dipole correlation functions for modes obtained from principle component analysis or quasiharmonic analysis can be computed.
 \end_layout
 
 \begin_layout LyX-Code
@@ -51404,8 +52257,8 @@ If
 \series bold
 eigenval
 \series default
- is specified, the fraction contribution of each eigenvector to the total
- motion is calculated and output with format:
+ is specified,
+ the fraction contribution of each eigenvector to the total motion is calculated and output with format:
 \end_layout
 
 \begin_layout LyX-Code
@@ -51418,12 +52271,14 @@ where
 \family typewriter
 #Mode
 \family default
- is the eigenvector number, 
+ is the eigenvector number,
+ 
 \family typewriter
 Frac.
 
 \family default
- is the eigenvalue over the sum of all eigenvalues, 
+ is the eigenvalue over the sum of all eigenvalues,
+ 
 \family typewriter
 Cumulative
 \family default
@@ -51431,27 +52286,25 @@ Cumulative
 \family typewriter
 Frac.
 \family default
-, and 
+,
+ and 
 \family typewriter
 Eigenval
 \family default
  is the eigenvalue itself.
- Note that in order to get an idea for how much each eigenvector contributes
- to all motion, this is best used when all possible eigenvectors have been
- determined for a system.
+ Note that in order to get an idea for how much each eigenvector contributes to all motion,
+ this is best used when all possible eigenvectors have been determined for a system.
 \end_layout
 
 \begin_layout Standard
-In order to visualize eigenvectors, pseudo-trajectories along eigenvectors
- can be created using average coordinates with the 
+In order to visualize eigenvectors,
+ pseudo-trajectories along eigenvectors can be created using average coordinates with the 
 \series bold
 trajout
 \series default
  keyword.
- For example, to write a pseudo-trajectory of the first principal component
- from principal component value of -100 to 100 for a previously calculated
- Modes data set corresponding to heavy atoms (no hydrogens) for residues
- 1 to 36:
+ For example,
+ to write a pseudo-trajectory of the first principal component from principal component value of -100 to 100 for a previously calculated Modes data set corresponding to heavy atoms (no hydrogens) for residues 1 to 36:
 \end_layout
 
 \begin_layout LyX-Code
@@ -51485,8 +52338,7 @@ multicurve set <dset> [set <dset> ...]
 \end_layout
 
 \begin_layout LyX-Code
-                    name <dsname> nexp <m> [form {mexp|mexpk|mexpk_penalty}
- }
+                    name <dsname> nexp <m> [form {mexp|mexpk|mexpk_penalty} }
 \end_layout
 
 \begin_layout LyX-Code
@@ -51532,6 +52384,7 @@ set
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-Data-Set-Math"
+nolink "false"
 
 \end_inset
 
@@ -51576,22 +52429,22 @@ form
 
 \begin_deeper
 \begin_layout Description
-mexp Multi-exponential, SUM(m)[ An * exp(An+1 * X)]
+mexp Multi-exponential,
+ SUM(m)[ An * exp(An+1 * X)]
 \end_layout
 
 \begin_layout Description
-mexpk Multi-exponential plus constant, A0 + SUM(m)[An * exp(An+1 * X)]
+mexpk Multi-exponential plus constant,
+ A0 + SUM(m)[An * exp(An+1 * X)]
 \end_layout
 
 \begin_layout Description
-mexpk_penalty Same as mexpk except sum of prefactors constrained to 1.0 and
- exponential constants constrained to < 0.0.
+mexpk_penalty Same as mexpk except sum of prefactors constrained to 1.0 and exponential constants constrained to < 0.0.
 \end_layout
 
 \end_deeper
 \begin_layout Description
-AX=<value> Value of any constants in specified equation with X starting
- from 0 (can specify more than one).
+AX=<value> Value of any constants in specified equation with X starting from 0 (can specify more than one).
 \end_layout
 
 \begin_layout Description
@@ -51619,8 +52472,7 @@ maxit
 \begin_inset space ~
 \end_inset
 
-iterations> Number of iterations to run curve fitting algotrithm (default
- 50).
+iterations> Number of iterations to run curve fitting algotrithm (default 50).
 \end_layout
 
 \begin_layout Description
@@ -51636,8 +52488,7 @@ outxbins
 \begin_inset space ~
 \end_inset
 
-<NX> Number of points to use when generating final curve (default same number
- of points as input data set).
+<NX> Number of points to use when generating final curve (default same number of points as input data set).
 \end_layout
 
 \begin_layout Description
@@ -51645,8 +52496,7 @@ outxmin
 \begin_inset space ~
 \end_inset
 
-<xmin> Minimum X value to use for final curve (default same number of points
- as input data set).
+<xmin> Minimum X value to use for final curve (default same number of points as input data set).
 \end_layout
 
 \begin_layout Description
@@ -51654,8 +52504,7 @@ outxmax
 \begin_inset space ~
 \end_inset
 
-<xmax> Maximum X value to use for final curve (default same number of points
- as input data set).
+<xmax> Maximum X value to use for final curve (default same number of points as input data set).
 \end_layout
 
 \end_deeper
@@ -51671,6 +52520,7 @@ curvefit
 \begin_inset CommandInset ref
 LatexCommand vpageref
 reference "subsec:cpptraj_curvefit"
+nolink "false"
 
 \end_inset
 
@@ -51764,8 +52614,7 @@ free
 \begin_inset space ~
 \end_inset
 
-<T> Calculate free energy from bin populations as G = -R * <T> * ln( Ni
- / Nmax ).
+<T> Calculate free energy from bin populations as G = -R * <T> * ln( Ni / Nmax ).
 \end_layout
 
 \begin_layout Description
@@ -51822,8 +52671,8 @@ resrange
 
 \end_deeper
 \begin_layout Standard
-Calculate the average and standard deviation of [phi] and [psi] data set
- pairs, write to <file> with format:
+Calculate the average and standard deviation of [phi] and [psi] data set pairs,
+ write to <file> with format:
 \end_layout
 
 \begin_layout LyX-Code
@@ -51831,14 +52680,13 @@ Calculate the average and standard deviation of [phi] and [psi] data set
 \end_layout
 
 \begin_layout Standard
-Where Phi is the average value of phi, Psi is the average value of psi,
- SD(Phi) is the standard deviation of phi, SD(psi) is the standard deviation
- of psi, and Legend contains text describing the phi and psi data sets used
- in the calculation.
+Where Phi is the average value of phi,
+ Psi is the average value of psi,
+ SD(Phi) is the standard deviation of phi,
+ SD(psi) is the standard deviation of psi,
+ and Legend contains text describing the phi and psi data sets used in the calculation.
  Periodicity is taken into account during averaging.
- The data sets must have been internally labeled as type 'phi'/'psi' and
- must have a data set index set (actions like dihedral and multidihedral
- do this automatically).
+ The data sets must have been internally labeled as type 'phi'/'psi' and must have a data set index set (actions like dihedral and multidihedral do this automatically).
  For example:
 \end_layout
 
@@ -51874,8 +52722,7 @@ name "subsec:cpptraj-projectdata"
 \end_layout
 
 \begin_layout LyX-Code
-projectdata evecs <evecs dataset> [name <name>] [out <outfile>] [beg <beg>]
- [end <end>]
+projectdata evecs <evecs dataset> [name <name>] [out <outfile>] [beg <beg>] [end <end>]
 \end_layout
 
 \begin_layout LyX-Code
@@ -51949,10 +52796,11 @@ arg>] (Dihedral covariance only) Dihedral data sets to use in projection;
 \begin_inset space ~
 \end_inset
 
-arg>] (Data covariance only, e.g.
+arg>] (Data covariance only,
+ e.g.
  from TICA).
- 1D data sets to use in projection; MUST CORRESPOND TO HOW EIGENVECTORS
- WERE GENERATED.
+ 1D data sets to use in projection;
+ MUST CORRESPOND TO HOW EIGENVECTORS WERE GENERATED.
 \end_layout
 
 \begin_layout Standard
@@ -51980,6 +52828,7 @@ reference "subsec:cpptraj-projection"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
@@ -52020,9 +52869,9 @@ nx
 \begin_inset space ~
 \end_inset
 
-<nxvals> Number of X values to use in output data set(s) (ranging from input
- set min to max X).
- If not specified, input X values used.
+<nxvals> Number of X values to use in output data set(s) (ranging from input set min to max X).
+ If not specified,
+ input X values used.
 \end_layout
 
 \begin_layout Description
@@ -52046,8 +52895,7 @@ DataSets Generated:
 \end_layout
 
 \begin_layout Description
-<name>:<idx> Output fit line(s) (indexed by input set order if more than
- one input set).
+<name>:<idx> Output fit line(s) (indexed by input set order if more than one input set).
 \end_layout
 
 \begin_layout Description
@@ -52075,8 +52923,8 @@ statsout
 \end_layout
 
 \begin_layout Standard
-For example, to fit data read in from a file and then create a set using
- the fit parameters:
+For example,
+ to fit data read in from a file and then create a set using the fit parameters:
 \end_layout
 
 \begin_layout LyX-Code
@@ -52107,8 +52955,7 @@ name "subsec:cpptraj-remlog"
 \end_layout
 
 \begin_layout LyX-Code
-remlog {<remlog dataset> | <remlog filename>} [out <filename>] [crdidx |
- repidx]
+remlog {<remlog dataset> | <remlog filename>} [out <filename>] [crdidx | repidx]
 \end_layout
 
 \begin_layout LyX-Code
@@ -52116,8 +52963,7 @@ remlog {<remlog dataset> | <remlog filename>} [out <filename>] [crdidx |
 \end_layout
 
 \begin_layout LyX-Code
-   	[reptimeslope <n> reptimeslopeout <file>] [acceptout <file>] [name <setname>
-]
+   	[reptimeslope <n> reptimeslopeout <file>] [acceptout <file>] [name <setname>]
 \begin_inset Separator latexpar
 \end_inset
 
@@ -52159,12 +53005,14 @@ filename> REM log file name to read in.
 
 \begin_deeper
 \begin_layout Description
-crdidx Print coordinate index vs exchange; output sets contain replica indices.
+crdidx Print coordinate index vs exchange;
+ output sets contain replica indices.
  
 \end_layout
 
 \begin_layout Description
-repidx Print replica index vs exchange; output sets contain coordinate indices.
+repidx Print replica index vs exchange;
+ output sets contain coordinate indices.
  
 \end_layout
 
@@ -52246,7 +53094,8 @@ reptimeslope
 \begin_inset space ~
 \end_inset
 
-<file>]] Extract energy data from replica log, optionally write to file.
+<file>]] Extract energy data from replica log,
+ optionally write to file.
 \end_layout
 
 \begin_layout Standard
@@ -52258,7 +53107,8 @@ DataSets created:
 \end_layout
 
 \begin_layout Description
-<setname>[E]:<idx> If 'edata' specified, energy data from replica log.
+<setname>[E]:<idx> If 'edata' specified,
+ energy data from replica log.
 \end_layout
 
 \end_deeper
@@ -52270,11 +53120,11 @@ readdata
 \series default
 \emph default
 ) M-REMD/T-REMD/H-REMD replica log data.
- Statistics calculated include round-trip time, which is the time needed
- for a coordinate set to travel from the lowest replica to the highest and
- back, and the number of exchanges each coordinate spent at each replica.
- For example, to read in REM log data from an Amber M-REMD run and analyze
- it:
+ Statistics calculated include round-trip time,
+ which is the time needed for a coordinate set to travel from the lowest replica to the highest and back,
+ and the number of exchanges each coordinate spent at each replica.
+ For example,
+ to read in REM log data from an Amber M-REMD run and analyze it:
 \end_layout
 
 \begin_layout LyX-Code
@@ -52292,7 +53142,8 @@ For an example of
 remlog
 \series default
 \emph default
- analysis applied to actual REMD data, see Roe et al.
+ analysis applied to actual REMD data,
+ see Roe et al.
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Roe2014"
@@ -52317,6 +53168,8 @@ name "subsec:cpptraj-rms2d"
 \begin_layout LyX-Code
 rms2d
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -52372,8 +53225,8 @@ set>] Name of previously generated COORDS DataSet.
 \end_layout
 
 \begin_layout Description
-[dme] Calculate distance RMSD instead of coordinate RMSD; this is substantially
- slower.
+[dme] Calculate distance RMSD instead of coordinate RMSD;
+ this is substantially slower.
 \end_layout
 
 \begin_layout Description
@@ -52385,6 +53238,7 @@ set>] Name of previously generated COORDS DataSet.
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_symmrmsd"
+nolink "false"
 
 \end_inset
 
@@ -52404,8 +53258,7 @@ reference "subsec:cpptraj_symmrmsd"
 \begin_inset space ~
 \end_inset
 
-<traj>] Calculate 2D RMSD to frames in trajectory <traj> instead (can also
- be another COORDS set).
+<traj>] Calculate 2D RMSD to frames in trajectory <traj> instead (can also be another COORDS set).
 \end_layout
 
 \begin_layout Description
@@ -52425,7 +53278,8 @@ parmindex
 \begin_inset space ~
 \end_inset
 
-<#>] Topology to use for <traj>; only useful in conjunction with 
+<#>] Topology to use for <traj>;
+ only useful in conjunction with 
 \series bold
 reftraj
 \series default
@@ -52433,8 +53287,8 @@ reftraj
 \end_layout
 
 \begin_layout Description
-[<refmask>] Mask of atoms in reference; only useful in conjunction with
- 
+[<refmask>] Mask of atoms in reference;
+ only useful in conjunction with 
 \series bold
 reftraj
 \series default
@@ -52454,21 +53308,23 @@ C
 \begin_inset Formula $C(i)=\frac{\sum_{j=0}^{j<N-i}\exp(-RMSD(j,j+i))}{N-i}$
 \end_inset
 
-, where 
+,
+ where 
 \shape italic
 i
 \shape default
- is the lag, 
+ is the lag,
+ 
 \shape italic
 j
 \shape default
- is the frame #, and 
+ is the frame #,
+ and 
 \shape italic
 N
 \shape default
  is the total number of frames.
- An exponential is used to weight the RMSD since 0.0 RMSD is equivalent to
- correlation of 1.0.
+ An exponential is used to weight the RMSD since 0.0 RMSD is equivalent to correlation of 1.0.
  This can only be done if 
 \series bold
 reftraj
@@ -52492,23 +53348,21 @@ corr
 \begin_layout Standard
 
 \shape italic
-Note: For backwards compatibility with ptraj the command '2drms' will also
- work.
+Note:
+ For backwards compatibility with ptraj the command '2drms' will also work.
 \end_layout
 
 \begin_layout Standard
-Calculate the best-fit RMSD of each frame in <crd set> (the default COORDS
- set if none specified) to each other frame.
- This creates an upper-triangle matrix named <name> (or a full matrix if
- 
+Calculate the best-fit RMSD of each frame in <crd set> (the default COORDS set if none specified) to each other frame.
+ This creates an upper-triangle matrix named <name> (or a full matrix if 
 \series bold
 reftraj
 \series default
  specified).
- The output of the rms2d command can be best-viewed using gnuplot; a gnuplot-for
-matted file can be produced by giving <filename> a '.gnu' extension.
- For example, to calculate the RMSD of non-hydrogen atoms of each frame
- in trajectory 
+ The output of the rms2d command can be best-viewed using gnuplot;
+ a gnuplot-formatted file can be produced by giving <filename> a '.gnu' extension.
+ For example,
+ to calculate the RMSD of non-hydrogen atoms of each frame in trajectory 
 \begin_inset Quotes eld
 \end_inset
 
@@ -52516,7 +53370,8 @@ test.nc
 \begin_inset Quotes erd
 \end_inset
 
- to each other frame, writing to a gnuplot-viewable file 
+ to each other frame,
+ writing to a gnuplot-viewable file 
 \begin_inset Quotes eld
 \end_inset
 
@@ -52577,6 +53432,8 @@ name "subsec:cpptraj-rmsavgcorr"
 \begin_layout LyX-Code
 rmsavgcorr
 \begin_inset Index idx
+range none
+pageformat default
 status open
 
 \begin_layout Plain Layout
@@ -52610,8 +53467,7 @@ rmsavgcorr
 \begin_inset space ~
 \end_inset
 
-set>] COORDS data set to use (if not specified the default COORDS set will
- be used).
+set>] COORDS data set to use (if not specified the default COORDS set will be used).
 \end_layout
 
 \begin_layout Description
@@ -52671,8 +53527,7 @@ file>
 \begin_inset space ~
 \end_inset
 
-<parmfile>] Use reference file (with specified parm) as reference for each
- window.
+<parmfile>] Use reference file (with specified parm) as reference for each window.
 \end_layout
 
 \end_deeper
@@ -52685,8 +53540,7 @@ literal "true"
 
 \end_inset
 
- (RAC) is calculated as the average RMSD of running-averaged coordinates
- over increasing window sizes (or lag).
+ (RAC) is calculated as the average RMSD of running-averaged coordinates over increasing window sizes (or lag).
  Output has format:
 \end_layout
 
@@ -52695,27 +53549,26 @@ literal "true"
 \end_layout
 
 \begin_layout Standard
-The first entry has a window size of 1, and so is just the average RMSD
- of all frames to the specified reference structure.
- The second entry has a window size of two, so it is the average RMSD of
- all frames averaged over two adjacent windows to the specified reference,
+The first entry has a window size of 1,
+ and so is just the average RMSD of all frames to the specified reference structure.
+ The second entry has a window size of two,
+ so it is the average RMSD of all frames averaged over two adjacent windows to the specified reference,
  and so on.
- The RAC will be calculated up to the number of frames minus 1 or the value
- specified by 
+ The RAC will be calculated up to the number of frames minus 1 or the value specified by 
 \series bold
 stop
 \series default
-, whichever is lower.
+,
+ whichever is lower.
  The offset can be used to speed up the calculation by skipping window sizes.
  To calculate mass-weighted RMSD specify 
 \series bold
 mass
 \series default
 .
- Note that to reduce memory costs it can be useful to strip all coordinates
- not involved in the RMS fit from the system prior to specifying 'rmsavgcorr'.
- For example, to calculate the correlation of C-alpha RMSD of residues 2
- to 12:
+ Note that to reduce memory costs it can be useful to strip all coordinates not involved in the RMS fit from the system prior to specifying 'rmsavgcorr'.
+ For example,
+ to calculate the correlation of C-alpha RMSD of residues 2 to 12:
 \end_layout
 
 \begin_layout LyX-Code
@@ -52728,27 +53581,23 @@ rmsavgcorr out rmscorr.dat
 
 \begin_layout Standard
 The curve generated by RAC decays towards zero due to the way RAC is defined.
- By the time the "lag" is N-1 (where N is the total number of frames) you
- have only two averaged coordinates: call them Avg1 (averaged over 1 though
- N-1 frames) and Avg2 (averaged over 2 through N frames).
- Barring any extraordinary circumstances the RMSD between Avg1 and Avg2
- will almost certainly be quite low.
+ By the time the "lag" is N-1 (where N is the total number of frames) you have only two averaged coordinates:
+ call them Avg1 (averaged over 1 though N-1 frames) and Avg2 (averaged over 2 through N frames).
+ Barring any extraordinary circumstances the RMSD between Avg1 and Avg2 will almost certainly be quite low.
  
 \end_layout
 
 \begin_layout Standard
 The RAC is a way to probe the time scales of interesting events.
- Any deviation from a smoothly decaying curve is an indication that there
- are some significant structural differences occurring over that time interval.
- RAC curves can be particularly useful when comparing independent simulations
- of the same system.
+ Any deviation from a smoothly decaying curve is an indication that there are some significant structural differences occurring over that time interval.
+ RAC curves can be particularly useful when comparing independent simulations of the same system.
 \end_layout
 
 \begin_layout Standard
-One thing to keep in mind that since the underlying metric is RMSD, it can
- be sensitive to the reference frame you choose.
- It may be useful to try looking at both RAC from the first frame, as well
- as an averaged reference frame.
+One thing to keep in mind that since the underlying metric is RMSD,
+ it can be sensitive to the reference frame you choose.
+ It may be useful to try looking at both RAC from the first frame,
+ as well as an averaged reference frame.
  For an example of use see Galindo-Murillo et al.
 \begin_inset CommandInset citation
 LatexCommand citep
@@ -52757,7 +53606,8 @@ literal "true"
 
 \end_inset
 
-, in particular Figure 2.
+,
+ in particular Figure 2.
 \end_layout
 
 \begin_layout Subsection
@@ -52801,7 +53651,8 @@ rotdif [outfile <outfilename>] [usefft]
 \end_layout
 
 \begin_layout LyX-Code
-  Options for calculating local effective D, small anisotropy:
+  Options for calculating local effective D,
+ small anisotropy:
 \end_layout
 
 \begin_layout LyX-Code
@@ -52878,7 +53729,8 @@ rvecin
 \begin_inset space ~
 \end_inset
 
-<randvecIn> File to read random vectors from (format is 1 per line, 4 columns,
+<randvecIn> File to read random vectors from (format is 1 per line,
+ 4 columns,
  <#> <VX> <VY> <VZ>).
 \end_layout
 
@@ -52900,7 +53752,8 @@ rvecout
 \begin_inset space ~
 \end_inset
 
-<randvecOut> File to write random vectors to (format is 1 per line, 4 columns,
+<randvecOut> File to write random vectors to (format is 1 per line,
+ 4 columns,
  <#> <VX> <VY> <VZ>).
 \end_layout
 
@@ -52922,8 +53775,9 @@ rmout
 \begin_inset space ~
 \end_inset
 
-<rmOut> Write rotation matrices to file, 1 per line, frame # followed by
- matrix in row-major order.
+<rmOut> Write rotation matrices to file,
+ 1 per line,
+ frame # followed by matrix in row-major order.
 \end_layout
 
 \end_deeper
@@ -52946,8 +53800,7 @@ order
 \begin_inset space ~
 \end_inset
 
-<olegendre> The order of Legendre polynomials to use when calculating vector
- time correlation functions (default 2).
+<olegendre> The order of Legendre polynomials to use when calculating vector time correlation functions (default 2).
 \end_layout
 
 \begin_layout Description
@@ -52976,8 +53829,8 @@ corrout
 \begin_inset space ~
 \end_inset
 
-<corrOut> If specified write vector time correlation functions to <corrOut>.X
- with format: <Time> <Px>
+<corrOut> If specified write vector time correlation functions to <corrOut>.X with format:
+ <Time> <Px>
 \end_layout
 
 \end_deeper
@@ -52985,7 +53838,8 @@ corrout
 
 \family roman
 \emph on
-Options for calculating local effective D, small anisotropy:
+Options for calculating local effective D,
+ small anisotropy:
 \family default
 
 \begin_inset Separator latexpar
@@ -53000,8 +53854,7 @@ deffout
 \begin_inset space ~
 \end_inset
 
-<deffOut> File to write out local effective diffusion constants determined
- in the limit of small anisotropy.
+<deffOut> File to write out local effective diffusion constants determined in the limit of small anisotropy.
 \end_layout
 
 \begin_layout Description
@@ -53009,9 +53862,7 @@ itmax
 \begin_inset space ~
 \end_inset
 
-<itmax> Maximum number of iterations to determine each local effective diffusion
- constant (small anisotropy) assuming fit to single exponential form (default
- 500).
+<itmax> Maximum number of iterations to determine each local effective diffusion constant (small anisotropy) assuming fit to single exponential form (default 500).
 \end_layout
 
 \begin_layout Description
@@ -53019,8 +53870,7 @@ tol
 \begin_inset space ~
 \end_inset
 
-<tolerance> Tolerance for determining local effective diffusion constant
- (small anisotropy) assuming fit to single exponential form (default 1E-6).
+<tolerance> Tolerance for determining local effective diffusion constant (small anisotropy) assuming fit to single exponential form (default 1E-6).
 \end_layout
 
 \begin_layout Description
@@ -53028,8 +53878,7 @@ d0
 \begin_inset space ~
 \end_inset
 
-<d0> Initial guess for small anisotropy diffusion constant in radians^2/ns
- (default 0.03).
+<d0> Initial guess for small anisotropy diffusion constant in radians^2/ns (default 0.03).
 \end_layout
 
 \begin_layout Description
@@ -53037,8 +53886,7 @@ nmesh
 \begin_inset space ~
 \end_inset
 
-<NmeshPoints> Number of points per frame to use when creating cubic-splined-smoo
-thed forms of vector time correlation curves (default 2).
+<NmeshPoints> Number of points per frame to use when creating cubic-splined-smoothed forms of vector time correlation curves (default 2).
 \end_layout
 
 \begin_layout Description
@@ -53046,8 +53894,7 @@ dt
 \begin_inset space ~
 \end_inset
 
-<tfac> Time interval between frames (used in integrating vector time correlation
- curves) in ns.
+<tfac> Time interval between frames (used in integrating vector time correlation curves) in ns.
 \end_layout
 
 \begin_layout Description
@@ -53055,8 +53902,7 @@ ti
 \begin_inset space ~
 \end_inset
 
-<ti> Initial time value in ns for integrating the time correlation functions
- (default 0.0).
+<ti> Initial time value in ns for integrating the time correlation functions (default 0.0).
 \end_layout
 
 \begin_layout Description
@@ -53065,8 +53911,7 @@ tf
 \end_inset
 
 <tf> Final time value in ns for integrating the time correlation functions.
- It is recommended this be less than the maximum simulation time since the
- tails of time correlation functions tend to be noisy.
+ It is recommended this be less than the maximum simulation time since the tails of time correlation functions tend to be noisy.
 \end_layout
 
 \end_deeper
@@ -53097,8 +53942,7 @@ amoeba_itmax
 \begin_inset space ~
 \end_inset
 
-<iterations> Number of iterations to run downhill-simplex minimizer (default
- 10000).
+<iterations> Number of iterations to run downhill-simplex minimizer (default 10000).
 \end_layout
 
 \begin_layout Description
@@ -53106,8 +53950,7 @@ amoeba_nsearch
 \begin_inset space ~
 \end_inset
 
-<n> Number of searches to perform with downhill-simplex minimizer (default
- 1).
+<n> Number of searches to perform with downhill-simplex minimizer (default 1).
 \end_layout
 
 \begin_layout Description
@@ -53119,15 +53962,13 @@ scalesimplex
 \end_layout
 
 \begin_layout Description
-gridsearch If specified, perform a brute-force grid search to attempt to
- find a better solution for diffusion tensor with full anisotropy (may be
- expensive).
+gridsearch If specified,
+ perform a brute-force grid search to attempt to find a better solution for diffusion tensor with full anisotropy (may be expensive).
 \end_layout
 
 \end_deeper
 \begin_layout Standard
-Evaluate rotational diffusion properties of a molecule over a trajectory
- according to an expanded version of the procedure laid out by Wong & Case
+Evaluate rotational diffusion properties of a molecule over a trajectory according to an expanded version of the procedure laid out by Wong & Case
 \begin_inset CommandInset citation
 LatexCommand citep
 key "wong2008"
@@ -53136,48 +53977,42 @@ literal "true"
 \end_inset
 
 .
- Briefly, random vectors (representing the orientation of the molecule)
- are rotated according to rotation matrices obtained from an RMS fit to
- a reference structure (typically an averaged structure).
- For each random vector the time correlation function of the rotated vector
- is calculated using Legendre polynomials of the specified order.
- The integral over this time correlation function (which may be smoothed
- using cubic splines to improve the integration) is then used to find the
- effective diffusion constant (D) in the limit of small anisotropy.
- Then, using each calculated D, the diffusion tensor is determined with
- full anisotropy.
- Finally, a downhill simplex minimizer is used to optimize D with full anisotrop
-y; (this last step is not described in the original paper).
-\end_layout
-
-\begin_layout Standard
-Rotation matrices are generated via an RMS fit to a reference structure
- (see 
+ Briefly,
+ random vectors (representing the orientation of the molecule) are rotated according to rotation matrices obtained from an RMS fit to a reference structure (typically an averaged structure).
+ For each random vector the time correlation function of the rotated vector is calculated using Legendre polynomials of the specified order.
+ The integral over this time correlation function (which may be smoothed using cubic splines to improve the integration) is then used to find the effective diffusion constant (D) in the limit of small anisotropy.
+ Then,
+ using each calculated D,
+ the diffusion tensor is determined with full anisotropy.
+ Finally,
+ a downhill simplex minimizer is used to optimize D with full anisotropy;
+ (this last step is not described in the original paper).
+\end_layout
+
+\begin_layout Standard
+Rotation matrices are generated via an RMS fit to a reference structure (see 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-rmsd"
+nolink "false"
 
 \end_inset
 
 ).
- It is recommended that the RMS fit be done to an average structure (see
- 
+ It is recommended that the RMS fit be done to an average structure (see 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-average"
+nolink "false"
 
 \end_inset
 
 ).
- These rotation matrices are used to rotate each random vector M times (where
- M is the total number of frames), which creates a time series for each
- random vector.
- The time correlation functions are calculated for each random vector time
- series using Legendre polynomials of the specified order (default 2).
- Calculation of time correlation functions can be sped up by using the OpenMP
- version of CPPTRAJ.
- The maximum length of the correlation function (or lag) can be specified
- by 
+ These rotation matrices are used to rotate each random vector M times (where M is the total number of frames),
+ which creates a time series for each random vector.
+ The time correlation functions are calculated for each random vector time series using Legendre polynomials of the specified order (default 2).
+ Calculation of time correlation functions can be sped up by using the OpenMP version of CPPTRAJ.
+ The maximum length of the correlation function (or lag) can be specified by 
 \series bold
 ncorr
 \series default
@@ -53186,26 +54021,27 @@ ncorr
 \series bold
 ncorr
 \series default
- is not specified it will be set internally based on the specified values
- of 
+ is not specified it will be set internally based on the specified values of 
 \series bold
 ti
 \series default
-, 
+,
+ 
 \series bold
 tf
 \series default
-, and 
+,
+ and 
 \series bold
 dt
 \series default
-; this is recommended.
+;
+ this is recommended.
  Note that if 
 \series bold
 ncorr
 \series default
- is specified it should be set to a number less than the total number of
- frames since noise in time correlation functions increases as 
+ is specified it should be set to a number less than the total number of frames since noise in time correlation functions increases as 
 \series bold
 ncorr
 \series default
@@ -53218,7 +54054,9 @@ ti
 \series bold
 dt
 \series default
-, generally ns; 0.0 ns if not specified) to 
+,
+ generally ns;
+ 0.0 ns if not specified) to 
 \series bold
 tf
 \series default
@@ -53226,14 +54064,14 @@ tf
 \series bold
 ti
 \series default
-), with the time between frames specified by 
+),
+ with the time between frames specified by 
 \series bold
 dt
 \series default
-; the final time should be less than the total simulation time (see example
- below).
- The relative size of the mesh used with cubic spline interpolation for
- integration is controlled by 
+;
+ the final time should be less than the total simulation time (see example below).
+ The relative size of the mesh used with cubic spline interpolation for integration is controlled by 
 \series bold
 nmesh
 \series default
@@ -53245,46 +54083,49 @@ ncorr
 \series bold
 nmesh
 \series default
-); 
+);
+ 
 \series bold
 nmesh
 \series default
- = 1 means no interpolation, default is 2.
+ = 1 means no interpolation,
+ default is 2.
  Note that if the integral of the correlation function for a vector is negative,
- that vector will be skipped in subsequent calculations (since it would
- imply a negative value for effective diffusion).
+ that vector will be skipped in subsequent calculations (since it would imply a negative value for effective diffusion).
 \end_layout
 
 \begin_layout Standard
-The iterative solver for effective value of the diffusion constant from
- the correlation functions is controlled by 
+The iterative solver for effective value of the diffusion constant from the correlation functions is controlled by 
 \series bold
 itmax
 \series default
-, 
+,
+ 
 \series bold
 tol
 \series default
-, and 
+,
+ and 
 \series bold
 d0
 \series default
-, where 
+,
+ where 
 \series bold
 itmax
 \series default
- specifies the number of iterations to perform (default 500), 
+ specifies the number of iterations to perform (default 500),
+ 
 \series bold
 tol
 \series default
- specifies the tolerance (default 1E-6), and 
+ specifies the tolerance (default 1E-6),
+ and 
 \series bold
 d0
 \series default
- specifies the initial guess for the diffusion constant in radians^2 / ns
- (default 0.03).
- Effective diffusion constants for each random vector can be written out
- to a file specified by 
+ specifies the initial guess for the diffusion constant in radians^2 / ns (default 0.03).
+ Effective diffusion constants for each random vector can be written out to a file specified by 
 \series bold
 deffout
 \series default
@@ -53294,13 +54135,14 @@ deffout
 outfile
 \series default
 .
- Details on the Q and D tensors are given, as well as observed and calculated
- tau for each random vector.
- First, results are printed for analysis in the limit of small anisotropy.
- Next, results are printed for analysis with full anisotropy.
- The results of the full anisotropic calculation are first given using results
- from the small anisotropic analysis as an initial guess, followed by the
- final results after minimization using the downhill simplex (amoeba) minimizer.
+ Details on the Q and D tensors are given,
+ as well as observed and calculated tau for each random vector.
+ First,
+ results are printed for analysis in the limit of small anisotropy.
+ Next,
+ results are printed for analysis with full anisotropy.
+ The results of the full anisotropic calculation are first given using results from the small anisotropic analysis as an initial guess,
+ followed by the final results after minimization using the downhill simplex (amoeba) minimizer.
 \end_layout
 
 \begin_layout Subsubsection*
@@ -53312,27 +54154,22 @@ There are two important things to keep in mind when using rotdif analysis:
 \end_layout
 
 \begin_layout Enumerate
-When calculating any kind of diffusive property it is best to simulate in
- the microcanonical (NVE) ensemble with a shorter time step and increased
- SHAKE tolerance; thermostats and barostats will effect diffusion calculations.
+When calculating any kind of diffusive property it is best to simulate in the microcanonical (NVE) ensemble with a shorter time step and increased SHAKE tolerance;
+ thermostats and barostats will effect diffusion calculations.
 \end_layout
 
 \begin_layout Enumerate
-Time correlation functions become noisier as the length of the function
- approaches the maximum.
- Therefore in general one should choose parameters for the time correlation
- function that are much shorter than the total simulation length.
+Time correlation functions become noisier as the length of the function approaches the maximum.
+ Therefore in general one should choose parameters for the time correlation function that are much shorter than the total simulation length.
  
 \end_layout
 
 \begin_layout Standard
-For example, given a trajectory 'mdcrd.nc' containing 10000 frames with a
- total simulation time of 200 ns (so the time between frames is 0.02 ns),
- to calculate rotational diffusion using 100 vectors using rotation matrices
- generated via an RMS fit to 'avgstruct.pdb', computing and integrating the
- time correlation function for each vector from 0 to 5 ns (1/40th of the
- simulation), and writing out the effective diffusion constants and results
- to 'deffs.dat' and 'rotdif.out' respectively:
+For example,
+ given a trajectory 'mdcrd.nc' containing 10000 frames with a total simulation time of 200 ns (so the time between frames is 0.02 ns),
+ to calculate rotational diffusion using 100 vectors using rotation matrices generated via an RMS fit to 'avgstruct.pdb',
+ computing and integrating the time correlation function for each vector from 0 to 5 ns (1/40th of the simulation),
+ and writing out the effective diffusion constants and results to 'deffs.dat' and 'rotdif.out' respectively:
 \end_layout
 
 \begin_layout LyX-Code
@@ -53422,8 +54259,7 @@ runningavg <dset1> [<dset2> ...] [name <dsetname>] [out <filename>]
 
 \end_deeper
 \begin_layout Standard
-Calculate running average over windows of given size for data in selected
- data set(s).
+Calculate running average over windows of given size for data in selected data set(s).
 \end_layout
 
 \begin_layout Subsection
@@ -53472,8 +54308,7 @@ slope <dset0> [<dset1> ...] [out <outfile>] [name <name>]
 \begin_inset space ~
 \end_inset
 
-{forward|backward|central}] Specify type of finite difference to calculate
- (default forward).
+{forward|backward|central}] Specify type of finite difference to calculate (default forward).
 \end_layout
 
 \begin_layout Standard
@@ -53481,8 +54316,7 @@ DataSets generated:
 \end_layout
 
 \begin_layout Description
-<name>:<idx> Output finite difference curves for each input data set (indexed
- from 0).
+<name>:<idx> Output finite difference curves for each input data set (indexed from 0).
 \end_layout
 
 \end_deeper
@@ -53528,7 +54362,8 @@ spline <dset0> [<dset1> ...] [out <outfile>] [meshsize <n> | meshfactor <x>]
 \begin_inset space ~
 \end_inset
 
-<x>] If meshsize is not given, use a mesh of data set size * <x>.
+<x>] If meshsize is not given,
+ use a mesh of data set size * <x>.
 \end_layout
 
 \begin_layout Description
@@ -53655,23 +54490,26 @@ distance for each set.
 
 \end_deeper
 \begin_layout Standard
-Analyze angles, dihedrals, distances, and/or puckers and calculate various
- properties.
- More specific analyses can be obtained by labelling distances/dihedrals/puckers
- (from e.g.
+Analyze angles,
+ dihedrals,
+ distances,
+ and/or puckers and calculate various properties.
+ More specific analyses can be obtained by labelling distances/dihedrals/puckers (from e.g.
  the 
 \series bold
 \shape italic
 distance
 \series default
 \shape default
-, 
+,
+ 
 \series bold
 \shape italic
 dihedral
 \series default
 \shape default
-, 
+,
+ 
 \series bold
 \shape italic
 pucker
@@ -53695,8 +54533,19 @@ type
 \begin_inset space ~
 \end_inset
 
-labels: alpha, beta, gamma, delta, epsilon, zeta, chi, c2p h1p, phi, psi,
- omega, pchi
+labels:
+ alpha,
+ beta,
+ gamma,
+ delta,
+ epsilon,
+ zeta,
+ chi,
+ c2p h1p,
+ phi,
+ psi,
+ omega,
+ pchi
 \end_layout
 
 \begin_layout Description
@@ -53708,7 +54557,8 @@ type
 \begin_inset space ~
 \end_inset
 
-labels: noe
+labels:
+ noe
 \end_layout
 
 \begin_layout Description
@@ -53720,14 +54570,16 @@ type
 \begin_inset space ~
 \end_inset
 
-labels: pucker
+labels:
+ pucker
 \end_layout
 
 \begin_layout Standard
-For each input data set, the average, standard deviation, initial and final
- values will be reported.
- The cyclic nature of dihedral/pucker data sets is taken into consideration
- when averaging.
+For each input data set,
+ the average,
+ standard deviation,
+ initial and final values will be reported.
+ The cyclic nature of dihedral/pucker data sets is taken into consideration when averaging.
 \end_layout
 
 \begin_layout Subsubsection
@@ -53735,10 +54587,10 @@ Torsion Analysis
 \end_layout
 
 \begin_layout Standard
-A table will be written in ASCII format showing the distribution of torsion
- values for each data set.
+A table will be written in ASCII format showing the distribution of torsion values for each data set.
  More specific information may be printed based on the set type.
- Values in the output marked SNB are from those defined by Schneider, Neidle,
+ Values in the output marked SNB are from those defined by Schneider,
+ Neidle,
  and Berman.
 \begin_inset CommandInset citation
 LatexCommand citep
@@ -53747,8 +54599,7 @@ literal "true"
 
 \end_inset
 
- For more information on nucleic acid torsion as pertains to RNA see further
- work by Schneider et al..
+ For more information on nucleic acid torsion as pertains to RNA see further work by Schneider et al..
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Schneider2004"
@@ -53760,8 +54611,8 @@ literal "true"
 \end_layout
 
 \begin_layout Standard
-For example, to perform in-depth analysis on some nucleic acid dihedral
- angles:
+For example,
+ to perform in-depth analysis on some nucleic acid dihedral angles:
 \end_layout
 
 \begin_layout LyX-Code
@@ -53785,17 +54636,18 @@ Distance Analysis
 \end_layout
 
 \begin_layout Standard
-A table will be written in ASCII format showing the distribution of distance
- values < 6.5.
- If a distance is labled as 'type noe' a compact time series will be printed
- in ASCII format showing the NOE as strong, medium, or weak.
- In addition the <r^-6>^(-1/6) averaged value will be reported, as well
- as the number of upper/lower bound violations.
+A table will be written in ASCII format showing the distribution of distance values < 6.5.
+ If a distance is labled as 'type noe' a compact time series will be printed in ASCII format showing the NOE as strong,
+ medium,
+ or weak.
+ In addition the <r^-6>^(-1/6) averaged value will be reported,
+ as well as the number of upper/lower bound violations.
  If 
 \series bold
 'noeout'
 \series default
- is specified, a summary of these results will be written with format:
+ is specified,
+ a summary of these results will be written with format:
 \end_layout
 
 \begin_layout LyX-Code
@@ -53803,23 +54655,26 @@ A table will be written in ASCII format showing the distribution of distance
 \end_layout
 
 \begin_layout Standard
-Where <#NOE> is an index, <R6> is the <r^-6>^(-1/6) averaged distance, <Nviolati
-on> is the total number of bounds violations, <AvgViolation> is the average
- difference from expected distance 
+Where <#NOE> is an index,
+ <R6> is the <r^-6>^(-1/6) averaged distance,
+ <Nviolation> is the total number of bounds violations,
+ <AvgViolation> is the average difference from expected distance 
 \shape italic
 Rexp
 \shape default
- when the distance is violated (note that if not explicitly set, 
+ when the distance is violated (note that if not explicitly set,
+ 
 \shape italic
 Rexp
 \shape default
- is set to the upper bound when the lower bound is 0.0, or the average of
- upper and lower bounds otherwise), and <Name> is the data set legend.
+ is set to the upper bound when the lower bound is 0.0,
+ or the average of upper and lower bounds otherwise),
+ and <Name> is the data set legend.
 \end_layout
 
 \begin_layout Standard
-For example, the following input could be used to check certain distances
- for NOE violations:
+For example,
+ the following input could be used to check certain distances for NOE violations:
 \end_layout
 
 \begin_layout LyX-Code
@@ -53851,8 +54706,7 @@ Pucker Analysis
 \end_layout
 
 \begin_layout Standard
-A table will be written in ASCII format showing the distribution of pucker
- phases for each data set.
+A table will be written in ASCII format showing the distribution of pucker phases for each data set.
 \end_layout
 
 \begin_layout Subsection
@@ -53976,7 +54830,8 @@ to
 \end_inset
 
 skip> Comma separated list of number of points to skip.
- For each number given, the TI integration will be repeated.
+ For each number given,
+ the TI integration will be repeated.
 \end_layout
 
 \begin_layout Description
@@ -54000,9 +54855,11 @@ avgincrement
 \begin_inset space ~
 \end_inset
 
-<#>] Starting from point 'avgskip' (default 0), repeat the TI integration
- calculation in increments of <#> up to 'avgmax' (default all points), so
- 'avgincrement 10' will do points 0-10, 0-20, etc.
+<#>] Starting from point 'avgskip' (default 0),
+ repeat the TI integration calculation in increments of <#> up to 'avgmax' (default all points),
+ so 'avgincrement 10' will do points 0-10,
+ 0-20,
+ etc.
 \end_layout
 
 \begin_layout Description
@@ -54030,9 +54887,8 @@ bs_samples
 \begin_inset space ~
 \end_inset
 
-<factor>] Estimate error via bootstrap analysis, repeating the TI integration
- <samples> times using <points> points or <factor> times the total number
- of points.
+<factor>] Estimate error via bootstrap analysis,
+ repeating the TI integration <samples> times using <points> points or <factor> times the total number of points.
  Randomize with given seed.
 \end_layout
 
@@ -54043,13 +54899,14 @@ DataSet Aspects:
 \begin_layout Description
 [TIcurve] Raw TI curve.
  If 'nskip' index is number of points skipped.
- If bootstrapping, index is sample index.
+ If bootstrapping,
+ index is sample index.
  If 'avgincrement' the index is the number of points.
 \end_layout
 
 \begin_layout Description
-[SD] For bootstrap analysis, standard deviation of average free energy over
- samples.
+[SD] For bootstrap analysis,
+ standard deviation of average free energy over samples.
 \end_layout
 
 \end_deeper
@@ -54059,7 +54916,8 @@ Calculate free energy using DV/DL energies from thermodynamic integration.
 \series bold
 <file>
 \series default
-, while the curves themselves will be written to 
+,
+ while the curves themselves will be written to 
 \series bold
 <ti curve file>
 \series default
@@ -54068,12 +54926,13 @@ Calculate free energy using DV/DL energies from thermodynamic integration.
 \series bold
 nq
 \series default
- to specify number of Gaussian quadrature points; otherwise the lambda values
- should be specified by 
+ to specify number of Gaussian quadrature points;
+ otherwise the lambda values should be specified by 
 \series bold
 xvals
 \series default
-, where 
+,
+ where 
 \series bold
 <x values>
 \series default
@@ -54081,14 +54940,13 @@ xvals
 \end_layout
 
 \begin_layout Standard
-For example, to perform Gaussian quadrature integration using data sets
- named 'TIdata', repeating the calculation for various number of skipped
- data points:
+For example,
+ to perform Gaussian quadrature integration using data sets named 'TIdata',
+ repeating the calculation for various number of skipped data points:
 \end_layout
 
 \begin_layout LyX-Code
-ti TIdata nq 9 name Curve out skip.agr curveout curve.agr nskip 0,5,10,15,20,30,40
-,50
+ti TIdata nq 9 name Curve out skip.agr curveout curve.agr nskip 0,5,10,15,20,30,40,50
 \end_layout
 
 \begin_layout Subsection
@@ -54152,8 +55010,10 @@ set
 \begin_inset space ~
 \end_inset
 
-arg1> Input 1D data set name(s), may specify more than once.
- If any data set is periodic, all need to be periodic.
+arg1> Input 1D data set name(s),
+ may specify more than once.
+ If any data set is periodic,
+ all need to be periodic.
 \end_layout
 
 \begin_layout Description
@@ -54178,15 +55038,14 @@ map
 
 \begin_deeper
 \begin_layout Description
-kinetic (default) Scale eigenvectors by eigenvalues so that distances in
- the transformed data approximate kinetic distances; particularly useful
- if using the projections to cluster.
+kinetic (default) Scale eigenvectors by eigenvalues so that distances in the transformed data approximate kinetic distances;
+ particularly useful if using the projections to cluster.
 \end_layout
 
 \begin_layout Description
-commute Scale eigenvectors by regularized time scales, sqrt(timescale_i
- / 2), so that distances in the transformed data will approximate commute
- distances.
+commute Scale eigenvectors by regularized time scales,
+ sqrt(timescale_i / 2),
+ so that distances in the transformed data will approximate commute distances.
  Timescales smaller than the lag time are dampened.
 \begin_inset CommandInset citation
 LatexCommand citep
@@ -54238,13 +55097,11 @@ cumvarout
 \end_deeper
 \begin_layout Standard
 Perform time-independent correlation analysis (TICA).
- Similar to principal component analysis (PCA), TICA calculates eigenvectors/eig
-envalues (i.e.
- eigenmodes) from input data sets (either coordinates or a combination of
- other 1D data sets).
+ Similar to principal component analysis (PCA),
+ TICA calculates eigenvectors/eigenvalues (i.e.
+ eigenmodes) from input data sets (either coordinates or a combination of other 1D data sets).
  Whereas the eigenvectors from PCA describe the variance in the input data,
- the eigenvectors from TICA describe the maximal autocorrelation in the
- input data at the given lag time.
+ the eigenvectors from TICA describe the maximal autocorrelation in the input data at the given lag time.
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Perez2013"
@@ -54252,9 +55109,8 @@ literal "true"
 
 \end_inset
 
- The analysis can be performed on either coordinates or 1D data sets; the
- data sets can either be all periodic (in which case they will be converted
- to cos/sin form) or not.
+ The analysis can be performed on either coordinates or 1D data sets;
+ the data sets can either be all periodic (in which case they will be converted to cos/sin form) or not.
 \end_layout
 
 \begin_layout Subsection
@@ -54296,9 +55152,8 @@ vec1
 <vecname2>]
 \series default
  Vector(s) on which to operate.
- By default the auto-correlation function will be calculated if one vector
- is specified, and the cross-correlation function will be calculated if
- two vectors are specified.
+ By default the auto-correlation function will be calculated if one vector is specified,
+ and the cross-correlation function will be calculated if two vectors are specified.
 \end_layout
 
 \begin_layout Description
@@ -54330,7 +55185,8 @@ out
 
 <order>]
 \series default
- Order of Legendre polynomials to use; default 2.
+ Order of Legendre polynomials to use;
+ default 2.
 \end_layout
 
 \begin_layout Description
@@ -54382,7 +55238,9 @@ out
 \series bold
 [norm]
 \series default
- Normalize all correlation functions, i.e., 
+ Normalize all correlation functions,
+ i.e.,
+ 
 \begin_inset Formula $C_{l}(t=0)=P_{l}(t=0)=1.0$
 \end_inset
 
@@ -54394,8 +55252,8 @@ out
 \series bold
 [drct]
 \series default
- Use the direct method to calculate correlations instead of FFT; this will
- be much slower.
+ Use the direct method to calculate correlations instead of FFT;
+ this will be much slower.
 \end_layout
 
 \begin_layout Description
@@ -54411,8 +55269,7 @@ dplr
 \end_layout
 
 \begin_layout Description
-[ptrajformat] Write output in ptraj style (prevents use of data formatting
- options).
+[ptrajformat] Write output in ptraj style (prevents use of data formatting options).
 \end_layout
 
 \begin_layout Standard
@@ -54483,10 +55340,9 @@ r(t)
 
 \end_deeper
 \begin_layout Standard
-Calculate time auto/cross-correlation functions for vectors using spherical
- harmonics theory.
- NOTE: To calculate direct correlation functions for vectors just use the
- 
+Calculate time auto/cross-correlation functions for vectors using spherical harmonics theory.
+ NOTE:
+ To calculate direct correlation functions for vectors just use the 
 \series bold
 \emph on
 corr
@@ -54502,9 +55358,12 @@ norm
 \series bold
 dplr
 \series default
- is specified, several additional data sets with aspects [R], [RRIG], [R3],
- [R6], and [Name] will be created containing either 1 or 2 values depending
- on how many vectors were specified.
+ is specified,
+ several additional data sets with aspects [R],
+ [RRIG],
+ [R3],
+ [R6],
+ and [Name] will be created containing either 1 or 2 values depending on how many vectors were specified.
  
 \end_layout
 
@@ -54513,8 +55372,8 @@ Examples
 \end_layout
 
 \begin_layout Standard
-Vectors between atoms 5 and 6 as well as 7 and 8 are calculated below, for
- which auto and cross time correlation functions are obtained.
+Vectors between atoms 5 and 6 as well as 7 and 8 are calculated below,
+ for which auto and cross time correlation functions are obtained.
 \end_layout
 
 \begin_layout LyX-Code
@@ -54538,8 +55397,10 @@ timecorr vec1 v0 vec2 v1 tstep 1.0 tcorr 100.0 out v0_v1.out order 2
 \end_layout
 
 \begin_layout Standard
-Similarly, a vector perpendicular to the plane through atoms 18, 19, and
- 20 is obtained and further analyzed.
+Similarly,
+ a vector perpendicular to the plane through atoms 18,
+ 19,
+ and 20 is obtained and further analyzed.
 \end_layout
 
 \begin_layout LyX-Code
@@ -54555,8 +55416,7 @@ vectormath
 \end_layout
 
 \begin_layout LyX-Code
-vectormath vec1 <vecname1> vec2 <vecname2> [out <filename>] [norm] [name
- <setname>]
+vectormath vec1 <vecname1> vec2 <vecname2> [out <filename>] [norm] [name <setname>]
 \end_layout
 
 \begin_layout LyX-Code
@@ -54605,8 +55465,8 @@ vec2
 \end_layout
 
 \begin_layout Description
-[dotangle] Calculate angle from dot-product between the two vectors; vectors
- will be normalized.
+[dotangle] Calculate angle from dot-product between the two vectors;
+ vectors will be normalized.
 \end_layout
 
 \begin_layout Description
@@ -54614,8 +55474,8 @@ vec2
 \end_layout
 
 \begin_layout Description
-[norm] Normalize the vectors; this will affect any subsequent calculations
- with the vectors.
+[norm] Normalize the vectors;
+ this will affect any subsequent calculations with the vectors.
  This is turned on automatically if 
 \series bold
 dotangle
@@ -54625,14 +55485,15 @@ dotangle
 
 \end_deeper
 \begin_layout Standard
-Calculate dot product, angle from dot product (degrees), or cross product
- for specified vectors.
+Calculate dot product,
+ angle from dot product (degrees),
+ or cross product for specified vectors.
  Note that 
 \series bold
 norm
 \series default
- normalizes the vectors themselves; the vectors will remain normalized for
- subsequent calculations or output.
+ normalizes the vectors themselves;
+ the vectors will remain normalized for subsequent calculations or output.
  Either 
 \series bold
 vec1
@@ -54641,9 +55502,10 @@ vec1
 \series bold
 vec2
 \series default
- can be of size 1; in that case each vector in the set with N frames operates
- on the single vector.
- For example, if 
+ can be of size 1;
+ in that case each vector in the set with N frames operates on the single vector.
+ For example,
+ if 
 \series bold
 vec1
 \series default
@@ -54651,13 +55513,13 @@ vec1
 \series bold
 vec2
 \series default
- is size 1, then each frame of vec1 is operated on the single vector from
- vec2.
+ is size 1,
+ then each frame of vec1 is operated on the single vector from vec2.
 \end_layout
 
 \begin_layout Standard
-For example, to get the angles between two previously calculated vectors
- v1 and v2:
+For example,
+ to get the angles between two previously calculated vectors v1 and v2:
 \end_layout
 
 \begin_layout LyX-Code
@@ -54723,7 +55585,8 @@ scaling
 \end_inset
 
 vals> Number of scales.
- The smaller the number the better resolution, but slower to plot.
+ The smaller the number the better resolution,
+ but slower to plot.
  
 \end_layout
 
@@ -54732,8 +55595,7 @@ vals> Number of scales.
 \begin_inset space ~
 \end_inset
 
-<s0>] The smallest scale of the wavelet function (default 2dt where dt is
- time between snapshots in ps ) 
+<s0>] The smallest scale of the wavelet function (default 2dt where dt is time between snapshots in ps ) 
 \end_layout
 
 \begin_layout Description
@@ -54744,8 +55606,8 @@ vals> Number of scales.
 <ds>] Spacing between discrete scales.
  (Default is 0.25.
  Smaller value of ds gives finer resolution.
- The largest values that give adequate sampling in scale for Morlet and
- Paul are 0.5 and 1.5, respectively)
+ The largest values that give adequate sampling in scale for Morlet and Paul are 0.5 and 1.5,
+ respectively)
 \end_layout
 
 \begin_layout Description
@@ -54753,8 +55615,8 @@ vals> Number of scales.
 \begin_inset space ~
 \end_inset
 
-<correction>] The scale-to-wavelength parameter (1.01 for Morlet, 1.389 for
- Paul).
+<correction>] The scale-to-wavelength parameter (1.01 for Morlet,
+ 1.389 for Paul).
  Automatically set based on wavelet if not otherwise specified.
  
 \end_layout
@@ -54830,12 +55692,13 @@ at a particular confidence level
 \begin_inset space ~
 \end_inset
 
-<file>] Output cluster map (recommended gnuplot format, see below).
+<file>] Output cluster map (recommended gnuplot format,
+ see below).
 \end_layout
 
 \begin_layout Description
-[cmapdetail] Instead of the map being smoothed to cluster regions, show
- full detail.
+[cmapdetail] Instead of the map being smoothed to cluster regions,
+ show full detail.
 \end_layout
 
 \begin_layout Description
@@ -54851,8 +55714,7 @@ at a particular confidence level
 \begin_inset space ~
 \end_inset
 
-prefix>] Output cluster region PDBs (only containing from minimum to maximum
- atom and minimum to maximum frame) with given prefix.
+prefix>] Output cluster region PDBs (only containing from minimum to maximum atom and minimum to maximum frame) with given prefix.
 \end_layout
 
 \begin_layout Description
@@ -54860,10 +55722,8 @@ prefix>] Output cluster region PDBs (only containing from minimum to maximum
 \begin_inset space ~
 \end_inset
 
-<trajfile>] Create a trajectory that can be overlaid with the original trajector
-y to highlight atoms of interest.
- Atoms in cluster regions will get their normal coordinates - all others
- are set to the common center of mass.
+<trajfile>] Create a trajectory that can be overlaid with the original trajectory to highlight atoms of interest.
+ Atoms in cluster regions will get their normal coordinates - all others are set to the common center of mass.
  
 \end_layout
 
@@ -54877,31 +55737,28 @@ y to highlight atoms of interest.
 
 \end_deeper
 \begin_layout Standard
-<wavelet>: morlet, paul
+<wavelet>:
+ morlet,
+ paul
 \end_layout
 
 \end_deeper
 \begin_layout Standard
-Perform the wavelet analysis using fast Fourier transform (FFT) algorithm
- on specified trajectory and write out to a gnuplot-formatted file named
- <name.gnu>.
- The created Wavelet map provides a clear picture of the significant motions
- which are characterized both in time and space.
- Note that typically the trajectory in question should have rotational and
- translational movement removed (via e.g.
+Perform the wavelet analysis using fast Fourier transform (FFT) algorithm on specified trajectory and write out to a gnuplot-formatted file named <name.gnu>.
+ The created Wavelet map provides a clear picture of the significant motions which are characterized both in time and space.
+ Note that typically the trajectory in question should have rotational and translational movement removed (via e.g.
  the 
 \series bold
 \emph on
 rms
 \series default
 \emph default
- command); otherwise these will be reflected in the wavelet analysis results.
+ command);
+ otherwise these will be reflected in the wavelet analysis results.
 \end_layout
 
 \begin_layout Standard
-Wavelet analysis contains two main steps which performs continues wavelet
- transform (CWT) and statistical significance testing as proposed by Torrence
- and Compo
+Wavelet analysis contains two main steps which performs continues wavelet transform (CWT) and statistical significance testing as proposed by Torrence and Compo
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Torrence1998"
@@ -54910,10 +55767,9 @@ literal "true"
 \end_inset
 
 .
- Analysis is executed on one dimensional (1-D) coordinate which is defined
- as the displacement from the starting position.
- For each atom, CWT is calculated over a specified range of scales from
- 
+ Analysis is executed on one dimensional (1-D) coordinate which is defined as the displacement from the starting position.
+ For each atom,
+ CWT is calculated over a specified range of scales from 
 \begin_inset Formula $S_{0}$
 \end_inset
 
@@ -54922,22 +55778,17 @@ up to
 \end_inset
 
 .
- To obtain the CWT of the trajectory the Fourier transform of atom's displacemen
-t and wavelets which scaled by S ( S is calculated from: 
+ To obtain the CWT of the trajectory the Fourier transform of atom's displacement and wavelets which scaled by S ( S is calculated from:
+ 
 \begin_inset Formula $S=S_{0}2^{jds};\:j=0,1,2,\ldots,nb-1$
 \end_inset
 
-) is computed and then the inverse Fourier transform of the product of Fourier
- transforms will be calculated as the CWT.
- After calculating the wavelet coordinates for all atoms, a significance
- testing is performed to determine the significance of each wavelet coordinate.
- For doing this test we need to have an appropriate background spectrum
- to consider as a mean or expected spectrum and compare our wavelet coordinates
- against this background.
- In order to calculate the background spectrum since wavelet spectrum (according
- to the convolution theorem) follows the Fourier spectrum, the Fourier coefficie
-nts over every atom's displacement is calculated using the following formula
- and a model (
+) is computed and then the inverse Fourier transform of the product of Fourier transforms will be calculated as the CWT.
+ After calculating the wavelet coordinates for all atoms,
+ a significance testing is performed to determine the significance of each wavelet coordinate.
+ For doing this test we need to have an appropriate background spectrum to consider as a mean or expected spectrum and compare our wavelet coordinates against this background.
+ In order to calculate the background spectrum since wavelet spectrum (according to the convolution theorem) follows the Fourier spectrum,
+ the Fourier coefficients over every atom's displacement is calculated using the following formula and a model (
 \begin_inset Formula $\mu_{k}$
 \end_inset
 
@@ -54945,8 +55796,7 @@ nts over every atom's displacement is calculated using the following formula
 \begin_inset Formula $X_{n}$
 \end_inset
 
-) is the time series which is the atom’s displacement and k is the frequency
- index
+) is the time series which is the atom’s displacement and k is the frequency index
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Benson2012"
@@ -54969,12 +55819,10 @@ f_{k=\frac{1}{N}}\sum_{n=0}^{N-1}\exp\left(\frac{-2\pi ikn}{N}\right)X_{n}
 \end_layout
 
 \begin_layout Standard
-This test is implemented based on the null hypothesis that the assumption
- is that Fourier coordinates normally distributed around the expected value,
+This test is implemented based on the null hypothesis that the assumption is that Fourier coordinates normally distributed around the expected value,
  then the wavelet coordinates should also be normally distributed.
- Assuming the expected background spectrum and since the square of a normally
- distributed variable is chi-square distributed, then the distribution for
- the square of the absolute values of wavelet coordinates (
+ Assuming the expected background spectrum and since the square of a normally distributed variable is chi-square distributed,
+ then the distribution for the square of the absolute values of wavelet coordinates (
 \begin_inset Formula $|W_{i,k}|^{2}$
 \end_inset
 
@@ -54997,21 +55845,17 @@ is the variance of the atom's displacement).
 \end_layout
 
 \begin_layout Standard
-Then choosing a confidence level we can determine the minimum acceptable
- value for 
+Then choosing a confidence level we can determine the minimum acceptable value for 
 \begin_inset Formula $|W_{i,k}|^{2}$
 \end_inset
 
-to be considered as a significant coordinates at that certain confidence
- level.
- In the final map the scales of only those wavelet coordinates which are
- significantly above the expected distribution are stored.
+to be considered as a significant coordinates at that certain confidence level.
+ In the final map the scales of only those wavelet coordinates which are significantly above the expected distribution are stored.
 \end_layout
 
 \begin_layout Standard
-For example, to perform wavelet analysis on residues 1 to 17 with 40 scaling
- values starting from scaling of 0.2 with a spacing of 0.25 using the Morlet
- wavelet:
+For example,
+ to perform wavelet analysis on residues 1 to 17 with 40 scaling values starting from scaling of 0.2 with a spacing of 0.25 using the Morlet wavelet:
 \end_layout
 
 \begin_layout LyX-Code
@@ -55049,12 +55893,8 @@ literal "true"
 
 \end_inset
 
- uses a density-based clustering algorithm (a modified version of the DBSCAN
- algorithm) to highlight physical and temporal regions that have significant
- motions from wavelet mapsand can extract the specific atoms and frames
- involved in these motions for further analysis.
- Cluster regions shown in the map will be smoother by default for easier
- visualization (unless 
+ uses a density-based clustering algorithm (a modified version of the DBSCAN algorithm) to highlight physical and temporal regions that have significant motions from wavelet mapsand can extract the specific atoms and frames involved in these motions for further analysis.
+ Cluster regions shown in the map will be smoother by default for easier visualization (unless 
 \series bold
 cmapdetail
 \series default
@@ -55101,8 +55941,8 @@ avgval Average value of points in the region.
 
 \end_deeper
 \begin_layout Standard
-For example, to create a 2D gnuplot map highlight regions of interest called
- 'cluster.gnu' one could use the following input.
+For example,
+ to create a 2D gnuplot map highlight regions of interest called 'cluster.gnu' one could use the following input.
 \end_layout
 
 \begin_layout LyX-Code
@@ -55161,6 +56001,7 @@ epsilon
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_dbscan_Hints"
+nolink "false"
 
 \end_inset
 
@@ -55179,9 +56020,7 @@ name "sec:cpptraj-Matrix-Vector-Analysis-Examples"
 \end_layout
 
 \begin_layout Standard
-Please note that typically for principal component analysis (PCA) the trajectory
- needs to be aligned against a reference structure to remove overall global
- and translation motion.
+Please note that typically for principal component analysis (PCA) the trajectory needs to be aligned against a reference structure to remove overall global and translation motion.
  Use the 
 \family sans
 \series bold
@@ -55201,12 +56040,10 @@ Cartesian covariance matrix calculation and projection (PCA)
 \end_layout
 
 \begin_layout Standard
-After calculating modes, snapshots can be projected onto these in an additional
- pass through the trajectory.
- It is very important that the snapshots used when projecting are exactly
- the same as those used to generate the original covariance matrix.
- This example takes advantage of the COORDS data set functionality in cpptraj
- to save snapshots for the purposes of projection.
+After calculating modes,
+ snapshots can be projected onto these in an additional pass through the trajectory.
+ It is very important that the snapshots used when projecting are exactly the same as those used to generate the original covariance matrix.
+ This example takes advantage of the COORDS data set functionality in cpptraj to save snapshots for the purposes of projection.
 \end_layout
 
 \begin_layout LyX-Code
@@ -55295,8 +56132,7 @@ crdaction CRD1 projection evecs MyEvecs !@H= out project.dat beg 1 end 2
 \end_layout
 
 \begin_layout Subsection
-Dihedral covariance matrix calculation and projection for backbone phi/psi
- (PCA)
+Dihedral covariance matrix calculation and projection for backbone phi/psi (PCA)
 \end_layout
 
 \begin_layout LyX-Code
@@ -55346,8 +56182,7 @@ run
 \end_layout
 
 \begin_layout LyX-Code
-projection evecs DIHMODES out dih.project.dat beg 1 end 4 dihedrals BB[*]
- 
+projection evecs DIHMODES out dih.project.dat beg 1 end 4 dihedrals BB[*] 
 \end_layout
 
 \begin_layout LyX-Code
diff --git a/src/Exec_PermuteDihedrals.cpp b/src/Exec_PermuteDihedrals.cpp
index 8e79e5ec46..585fe0ed07 100644
--- a/src/Exec_PermuteDihedrals.cpp
+++ b/src/Exec_PermuteDihedrals.cpp
@@ -31,9 +31,9 @@ Exec_PermuteDihedrals::Exec_PermuteDihedrals() : Exec(COORDS),
 // Exec_PermuteDihedrals::Help()
 void Exec_PermuteDihedrals::Help() const {
   mprintf("\tcrdset <COORDS set> resrange <range> [{interval | random}]\n"
-          "\t[outtraj <filename> [<outfmt>]] [crdout <output COORDS>] [<dihedral types>]\n"
+          "\t{[outtraj <filename> [<outfmt>]] [crdout <output COORDS>]} [<dihedral types>]\n"
           "  Options for 'random':\n"
-          "\t[rseed <rseed>] [out <# problems file> [<set name>]]\n"
+          "\t[rseed <rseed>] [out <# problems file> [<set name>]] [noimage]\n"
           "\t[ check [cutoff <cutoff>] [rescutoff <rescutoff>] [maxfactor <max_factor>]\n"
           "\t  [backtrack <backtrack> [checkallresidues] [increment <increment>]] ]\n"
           "  Options for 'interval':\n"

From 18cf3a4b31b2b42de260f763fabd49347ac2d375 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 24 Jun 2024 14:50:07 -0400
Subject: [PATCH 0777/1492] Tune cutoffs

---
 src/StructureCheck.cpp | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/StructureCheck.cpp b/src/StructureCheck.cpp
index 542b2e3b47..46495c6dfc 100644
--- a/src/StructureCheck.cpp
+++ b/src/StructureCheck.cpp
@@ -247,8 +247,10 @@ int StructureCheck::CheckRings(Frame const& currentFrame)
 {
   int Nproblems = 0;
   problemAtoms_.clear();
-  static const double ring_dcut2 = 2.25; // 1.5 Ang distance cutoff
-  static const double ring_acut  = 0.174533; // 10 deg. angle cutoff
+  //static const double ring_dcut2 = 2.25; // 1.5 Ang distance cutoff
+  //static const double ring_acut  = 0.174533; // 10 deg. angle cutoff
+  static const double ring_dcut2 = 1.562500; // 1.25 Ang distance cutoff
+  static const double ring_acut = 0.7853981634; // 45 deg. angle cutoff
   // Get all ring vectors
   typedef std::vector<Cpptraj::Structure::LeastSquaresPlane> Larray;
   Larray RingVecs;

From 68581305c5caf5dde2ec0a8f45b15aeac104a3ab Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 25 Jun 2024 12:58:01 -0400
Subject: [PATCH 0778/1492] Add a version of the ring check that can be called
 with custom rings/bonds. Change criteria to have a short cutoff and longer
 cutoff with angle

---
 src/StructureCheck.cpp | 65 +++++++++++++++++++++++++++---------------
 src/StructureCheck.h   | 25 +++++++++-------
 2 files changed, 56 insertions(+), 34 deletions(-)

diff --git a/src/StructureCheck.cpp b/src/StructureCheck.cpp
index 46495c6dfc..cf2b2f4dd3 100644
--- a/src/StructureCheck.cpp
+++ b/src/StructureCheck.cpp
@@ -243,20 +243,27 @@ int StructureCheck::CheckBonds(Frame const& currentFrame)
 }
 
 /** Check if any bonds are passing through rings. */
-int StructureCheck::CheckRings(Frame const& currentFrame)
+int StructureCheck::CheckRings(Frame const& currentFrame) {
+  return CheckRings(currentFrame, rings_, ringBonds_);
+}
+
+/** Check if any bonds are passing through rings. */
+int StructureCheck::CheckRings(Frame const& currentFrame, Cpptraj::Structure::RingFinder const& rings, std::vector<Btype> const& ringBonds)
 {
   int Nproblems = 0;
   problemAtoms_.clear();
-  //static const double ring_dcut2 = 2.25; // 1.5 Ang distance cutoff
+  static const double ring_dcut2 = 1.3225; // Initial 1.15 Ang distance cutoff
+  static const double ring_shortd2 = 0.25; // Short 0.5 Ang distance cutoff
+  static const double ring_acut = 1.0471975512; // 60 deg. Ang cutoff
   //static const double ring_acut  = 0.174533; // 10 deg. angle cutoff
-  static const double ring_dcut2 = 1.562500; // 1.25 Ang distance cutoff
-  static const double ring_acut = 0.7853981634; // 45 deg. angle cutoff
+  //static const double ring_dcut2 = 1.562500; // 1.25 Ang distance cutoff
+/*  static const double ring_acut = 0.7853981634; // 45 deg. angle cutoff for ring_dcut2 > dist2 > ring_shortd2*/
   // Get all ring vectors
   typedef std::vector<Cpptraj::Structure::LeastSquaresPlane> Larray;
   Larray RingVecs;
-  RingVecs.resize( rings_.Nrings() );
+  RingVecs.resize( rings.Nrings() );
   int idx = 0;
-  int ring_max = (int)rings_.Nrings();
+  int ring_max = (int)rings.Nrings();
 # ifdef _OPENMP
 # pragma omp parallel private(idx)
   {
@@ -264,14 +271,14 @@ int StructureCheck::CheckRings(Frame const& currentFrame)
 # endif
   for (idx = 0; idx < ring_max; idx++)
   {
-    RingVecs[idx].CalcLeastSquaresPlane( currentFrame, rings_[idx] );
+    RingVecs[idx].CalcLeastSquaresPlane( currentFrame, rings[idx] );
   }
 # ifdef _OPENMP
   } // END pragma omp parallel
 # endif
 
   // Loop over bonds
-  int bond_max = (int)ringBonds_.size();
+  int bond_max = (int)ringBonds.size();
 # ifdef _OPENMP
   int mythread;
 # pragma omp parallel private(idx,mythread) reduction(+: Nproblems)
@@ -282,8 +289,8 @@ int StructureCheck::CheckRings(Frame const& currentFrame)
 # endif
   for (idx = 0; idx < bond_max; idx++)
   {
-    const double* xyz1 = currentFrame.XYZ( ringBonds_[idx].A1() );
-    const double* xyz2 = currentFrame.XYZ( ringBonds_[idx].A2() );
+    const double* xyz1 = currentFrame.XYZ( ringBonds[idx].A1() );
+    const double* xyz2 = currentFrame.XYZ( ringBonds[idx].A2() );
     Vec3 vbond( xyz2[0] - xyz1[0],
                 xyz2[1] - xyz1[1],
                 xyz2[2] - xyz1[2] );
@@ -293,29 +300,41 @@ int StructureCheck::CheckRings(Frame const& currentFrame)
     for (int jdx = 0; jdx < ring_max; jdx++)
     {
       // Make sure this bond is not in this ring
-      AtomMask const& ringMask = rings_[jdx];
-      if ( !ringMask.IsSelected(ringBonds_[idx].A1()) &&
-           !ringMask.IsSelected(ringBonds_[idx].A2()) )
+      AtomMask const& ringMask = rings[jdx];
+      if ( !ringMask.IsSelected(ringBonds[idx].A1()) &&
+           !ringMask.IsSelected(ringBonds[idx].A2()) )
       {
         // Get the center distance
         Cpptraj::Structure::LeastSquaresPlane const& ringVec = RingVecs[jdx];
         double dist2 = DIST2_NoImage( vmid.Dptr(), ringVec.Cxyz().Dptr() );
         if (dist2 < ring_dcut2) {
-          // Get the angle
-          double ang_in_rad = vbond.Angle( ringVec.Nxyz() );
-          // Wrap the angle between 0-90 degrees
-          if (ang_in_rad > Constants::PIOVER2)
-            ang_in_rad = Constants::PI - ang_in_rad;
-          mprintf("DEBUG: Bond %i - %i near ring %i (%f) Ang= %f deg.\n",
-                  ringBonds_[idx].A1()+1, ringBonds_[idx].A2()+1, jdx, sqrt(dist2),
-                  Constants::RADDEG*ang_in_rad);
-          if (ang_in_rad < ring_acut) {
+          bool ring_intersect = false;
+          // Bond intersects ring if it meets the short cutoff or if the angle
+          // between the bond and the ring normal is less than a cutoff.
+          if (dist2 < ring_shortd2) {
+            mprintf("DEBUG: Bond %i - %i near ring %i (%f).\n",
+                    ringBonds[idx].A1(), ringBonds[idx].A2(), jdx, sqrt(dist2));
+            ring_intersect = true;
+          } else {
+            // Get the angle
+            double ang_in_rad = vbond.Angle( ringVec.Nxyz() );
+            // Wrap the angle between 0-90 degrees
+            if (ang_in_rad > Constants::PIOVER2)
+              ang_in_rad = Constants::PI - ang_in_rad;
+            if (ang_in_rad < ring_acut) {
+              mprintf("DEBUG: Bond %i - %i near ring %i (%f) Ang= %f deg.\n",
+                      ringBonds[idx].A1(), ringBonds[idx].A2(), jdx, sqrt(dist2),
+                      Constants::RADDEG*ang_in_rad);
+              ring_intersect = true;
+            }
+          }
+          if (ring_intersect) {
             mprintf("DEBUG: Bond intersects ring.\n");
             ++Nproblems;
             if (saveProblems_) {
               // Do not use constructor since we do not want to sort atoms
               Problem newProb;
-              newProb.SetProb( ringBonds_[idx].A1(), ringMask.back(), sqrt(dist2) );
+              newProb.SetProb( ringBonds[idx].A1(), ringMask.back(), sqrt(dist2) );
 #             ifdef _OPENMP
               thread_problemAtoms_[mythread]
 #             else
diff --git a/src/StructureCheck.h b/src/StructureCheck.h
index 70aa2552e8..3c53f2e0aa 100644
--- a/src/StructureCheck.h
+++ b/src/StructureCheck.h
@@ -12,6 +12,19 @@ class CharMask;
 /// Used to count potential structure problems.
 class StructureCheck {
   public:
+    // -------------------------------------------
+    /// Cache heavy atom bond indices for checking with rings
+    class Btype {
+      public:
+        Btype(int a1, int a2) : a1_(a1), a2_(a2) {}
+        int A1() const { return a1_; }
+        int A2() const { return a2_; }
+      private:
+        int a1_;
+        int a2_;
+    };
+    // -------------------------------------------
+    /// CONSTRUCTOR
     StructureCheck();
     /// Options: imageOn, checkBonds, saveProblems, debug, mask1, mask2, ovrlpCut, bndLenOffset, minBndLenOffset, PListCut
     int SetOptions(bool, bool, bool, int, std::string const&, std::string const&,
@@ -24,6 +37,7 @@ class StructureCheck {
     int CheckOverlaps(Frame const&);
     /// Check if any bonds are passing through rings.
     int CheckRings(Frame const&);
+    int CheckRings(Frame const&, Cpptraj::Structure::RingFinder const&, std::vector<Btype> const&);
 
     AtomMask const& Mask1()     const { return Mask1_; }
     AtomMask const& Mask2()     const { return Mask2_; }
@@ -95,17 +109,6 @@ class StructureCheck {
     /// Check for/record non-bonded interaction problem
     inline void DistanceCheck(Frame const&, int, int, Parray&, int&) const;
 
-    /// Cache heavy atom bond indices for checking with rings
-    class Btype {
-      public:
-        Btype(int a1, int a2) : a1_(a1), a2_(a2) {}
-        int A1() const { return a1_; }
-        int A2() const { return a2_; }
-      private:
-        int a1_;
-        int a2_;
-    };
-
     std::vector<Btype> ringBonds_;
 
 #   ifdef _OPENMP

From 7fa5f0bb51e384f38695c24e20df27d7914d273d Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 25 Jun 2024 14:43:39 -0400
Subject: [PATCH 0779/1492] Add more debug

---
 src/StructureCheck.cpp | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/src/StructureCheck.cpp b/src/StructureCheck.cpp
index cf2b2f4dd3..72da0385f2 100644
--- a/src/StructureCheck.cpp
+++ b/src/StructureCheck.cpp
@@ -247,6 +247,11 @@ int StructureCheck::CheckRings(Frame const& currentFrame) {
   return CheckRings(currentFrame, rings_, ringBonds_);
 }
 
+static inline void printRingAtoms(AtomMask const& maskIn) {
+  for (AtomMask::const_iterator it = maskIn.begin(); it != maskIn.end(); ++it)
+    mprintf(" %i", *it);
+}
+
 /** Check if any bonds are passing through rings. */
 int StructureCheck::CheckRings(Frame const& currentFrame, Cpptraj::Structure::RingFinder const& rings, std::vector<Btype> const& ringBonds)
 {
@@ -312,8 +317,10 @@ int StructureCheck::CheckRings(Frame const& currentFrame, Cpptraj::Structure::Ri
           // Bond intersects ring if it meets the short cutoff or if the angle
           // between the bond and the ring normal is less than a cutoff.
           if (dist2 < ring_shortd2) {
-            mprintf("DEBUG: Bond %i - %i near ring %i (%f).\n",
+            mprintf("DEBUG: Bond %i - %i near ring %i (%f).",
                     ringBonds[idx].A1(), ringBonds[idx].A2(), jdx, sqrt(dist2));
+            printRingAtoms(ringMask);
+            mprintf("\n");
             ring_intersect = true;
           } else {
             // Get the angle
@@ -322,9 +329,11 @@ int StructureCheck::CheckRings(Frame const& currentFrame, Cpptraj::Structure::Ri
             if (ang_in_rad > Constants::PIOVER2)
               ang_in_rad = Constants::PI - ang_in_rad;
             if (ang_in_rad < ring_acut) {
-              mprintf("DEBUG: Bond %i - %i near ring %i (%f) Ang= %f deg.\n",
+              mprintf("DEBUG: Bond %i - %i near ring %i (%f) Ang= %f deg.",
                       ringBonds[idx].A1(), ringBonds[idx].A2(), jdx, sqrt(dist2),
                       Constants::RADDEG*ang_in_rad);
+              printRingAtoms(ringMask);
+              mprintf("\n");
               ring_intersect = true;
             }
           }

From 5566a9bb74cf128d7b83556eb25db656b5e7a906 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 26 Jun 2024 09:21:27 -0400
Subject: [PATCH 0780/1492] Add checkrings keyword to permutedihedrals to see
 if any rings in the residue to which the dihedral being rotated belongs to
 have a bond running through them. Improve the residue clash check by getting
 an initial count of clashes for the structure; make it ok to leave existing
 clashes, only make it bad if new clashes are introduced.

---
 src/Exec_PermuteDihedrals.cpp | 133 +++++++++++++++++++++++++++++++---
 src/Exec_PermuteDihedrals.h   |   4 +
 2 files changed, 127 insertions(+), 10 deletions(-)

diff --git a/src/Exec_PermuteDihedrals.cpp b/src/Exec_PermuteDihedrals.cpp
index 585fe0ed07..81c2213f31 100644
--- a/src/Exec_PermuteDihedrals.cpp
+++ b/src/Exec_PermuteDihedrals.cpp
@@ -19,6 +19,7 @@ Exec_PermuteDihedrals::Exec_PermuteDihedrals() : Exec(COORDS),
   crdout_(0),
   check_for_clashes_(false),
   checkAllResidues_(false),
+  checkRings_(false),
   max_factor_(2),
   cutoff_(0.64), // 0.8^2
   rescutoff_(100.0), // 10.0^2
@@ -31,11 +32,13 @@ Exec_PermuteDihedrals::Exec_PermuteDihedrals() : Exec(COORDS),
 // Exec_PermuteDihedrals::Help()
 void Exec_PermuteDihedrals::Help() const {
   mprintf("\tcrdset <COORDS set> resrange <range> [{interval | random}]\n"
-          "\t{[outtraj <filename> [<outfmt>]] [crdout <output COORDS>]} [<dihedral types>]\n"
-          "  Options for 'random':\n"
+          "\t{[outtraj <filename> [<outfmt>]] [crdout <output COORDS>]} [<dihedral types>]\n");
+  mprintf("\t[%s]\n", DihedralSearch::newTypeArgsHelp());
+  mprintf("  Options for 'random':\n"
           "\t[rseed <rseed>] [out <# problems file> [<set name>]] [noimage]\n"
           "\t[ check [cutoff <cutoff>] [rescutoff <rescutoff>] [maxfactor <max_factor>]\n"
-          "\t  [backtrack <backtrack> [checkallresidues] [increment <increment>]] ]\n"
+          "\t  [backtrack <backtrack> [checkallresidues] [checkrings]\n"
+          "\t  [increment <increment>]] ]\n"
           "  Options for 'interval':\n"
           "\t<interval deg>\n"
           "  <dihedral types> = ");
@@ -80,6 +83,8 @@ Exec::RetType Exec_PermuteDihedrals::Execute(CpptrajState& State, ArgList& argIn
   // Determine which angles to search for
   DihedralSearch dihSearch;
   dihSearch.SearchForArgs(argIn);
+  // Get custom dihedral arguments: dihtype <name>:<a0>:<a1>:<a2>:<a3>[:<offset>]
+  if (dihSearch.SearchForNewTypeArgs(argIn)) return CpptrajState::ERR;
   // If nothing is enabled, enable all 
   dihSearch.SearchForAll();
   mprintf("\tSearching for types:");
@@ -136,6 +141,7 @@ Exec::RetType Exec_PermuteDihedrals::Execute(CpptrajState& State, ArgList& argIn
     }
     check_for_clashes_ = argIn.hasKey("check");
     checkAllResidues_ = argIn.hasKey("checkallresidues");
+    checkRings_ = argIn.hasKey("checkrings");
     cutoff_ = argIn.getKeyDouble("cutoff",0.8);
     rescutoff_ = argIn.getKeyDouble("rescutoff", resCutoffDefault);
     increment_ = argIn.getKeyInt("increment",1);
@@ -178,6 +184,8 @@ Exec::RetType Exec_PermuteDihedrals::Execute(CpptrajState& State, ArgList& argIn
       mprintf("\tRandom number generator will be seeded using %i\n",iseed);
     if (check_for_clashes_) {
       mprintf("\tWill attempt to recover from bad steric clashes.\n");
+      if (checkRings_)
+        mprintf("\tChecking for bond/ring intersections.\n");
       if (checkAllResidues_)
         mprintf("\tAll residues will be checked.\n");
       else
@@ -198,7 +206,7 @@ Exec::RetType Exec_PermuteDihedrals::Execute(CpptrajState& State, ArgList& argIn
     // Increment backtrack by 1 since we need to skip over current res
     ++backtrack_;
     // Initialize CheckStructure
-    if (checkStructure_.SetOptions( imageOn, false, false, State.Debug(), "*", "", 0.8, 1.15, 0.5, -1 )) {
+    if (checkStructure_.SetOptions( imageOn, checkRings_, false, State.Debug(), "*", "", 0.8, 1.15, 0.5, -1 )) {
       mprinterr("Error: Could not set up structure check.\n");
       return CpptrajState::ERR;
     }
@@ -596,6 +604,48 @@ void Exec_PermuteDihedrals::RandomizeAngles(Frame& currentFrame, Topology const&
   mprintf("\tPerformed %u rotations for %zu dihedrals\n", number_of_rotations, BB_dihedrals_.size());
 }
 
+/** Count initial clashes in the structure. This is done to make sure
+  * new clashes arent introduced after a rotation.
+  */
+void Exec_PermuteDihedrals::countClashes(std::vector<int>& res_clashes,
+                                         Frame const& currentFrame, Topology const& topIn)
+const
+{
+  res_clashes.assign( topIn.Nres(), 0 );
+  for (int res0 = 0; res0 != topIn.Nres(); res0++)
+  {
+    Residue const& R0 = topIn.Res(res0);
+    for (int res1 = res0 + 1; res1 != topIn.Nres(); res1++)
+    {
+      Residue const& R1 = topIn.Res(res1);
+      // Check if first atoms are anywhere near each other.
+      double r0r1_at0_dist2 = DIST2_NoImage( currentFrame.XYZ(R0.FirstAtom()),
+                                             currentFrame.XYZ(R1.FirstAtom()) );
+      if (r0r1_at0_dist2 < rescutoff_) {
+        // Residues are within each others vicinity
+        for (int at0 = R0.FirstAtom(); at0 != R0.LastAtom(); at0++)
+        {
+          const double* xyz0 = currentFrame.XYZ(at0);
+          for (int at1 = R1.FirstAtom(); at1 != R1.LastAtom(); at1++)
+          {
+            const double* xyz1 = currentFrame.XYZ(at1);
+            double d2 = DIST2_NoImage( xyz0, xyz1 );
+            if (d2 < cutoff_) {
+//#             ifdef DEBUG_PERMUTEDIHEDRALS
+              mprintf("DEBUG: Initial clash: %s to %s (%g Ang)\n",
+                      topIn.TruncResAtomNameNum(at0).c_str(),
+                      topIn.TruncResAtomNameNum(at1).c_str(), sqrt(d2));
+//#             endif
+              res_clashes[res0]++;
+              res_clashes[res1]++;
+            } // END atom-atom distance within cutoff_
+          } // END loop over R1 atoms
+        } // END loop over R0 atoms
+      } // END res-res distance wtihin rescutoff_
+    } // END inner loop over residues
+  } // END outer loop over residues
+}
+
 // Exec_PermuteDihedrals::RandomizeAngles_2()
 /** This algorithm is a more straightforward one than RandomizeAngles().
   *  1) Pick a random angle
@@ -624,6 +674,17 @@ void Exec_PermuteDihedrals::RandomizeAngles_2(Frame& currentFrame, Topology cons
 
   mprintf("\tMax number of rotations to try each dihedral: %u\n", max_rotations);
 
+  // Get count of initial clashes
+  std::vector<int> initialResClashes;
+  if (check_for_clashes_) {
+    countClashes( initialResClashes, currentFrame, topIn );
+    mprintf("DEBUG: Initial clashes:\n");
+    for (unsigned int ires = 0; ires != (unsigned int)topIn.Nres(); ires++) {
+      if (initialResClashes[ires] > 0)
+        mprintf("DEBUG:\t\t%s has %i clashes.\n", topIn.TruncResNameNum(ires).c_str(), initialResClashes[ires]);
+    }
+  }
+
   // Loop over all dihedrals
   for (std::vector<PermuteDihedralsType>::const_iterator dih = BB_dihedrals_.begin();
                                                          dih != BB_dihedrals_.end(); 
@@ -662,15 +723,20 @@ void Exec_PermuteDihedrals::RandomizeAngles_2(Frame& currentFrame, Topology cons
       if (!check_for_clashes_) break;
       // If we have exceeded the max number of rotations bail out.
       if (number_of_rotations > max_rotations) {
-        mprintf("Warning: Max # of rotations has been exceeded for dihedral %li res %8i.\n",
-                dih - BB_dihedrals_.begin(), dih->resnum+1);
+        mprintf("Warning: Max # of rotations has been exceeded for dihedral %li res %s.\n",
+                dih - BB_dihedrals_.begin(), topIn.TruncResNameNum(dih->resnum).c_str());
         break;
       }
       // Check resulting structure for issues.
+      std::vector<int> currentResClashes(topIn.Nres(), 0);
+      std::vector<bool> checkRingBonds;
+      if (checkRings_) checkRingBonds.assign(topIn.Nres(), false);
       bool clash = false;
       for (int res0 = 0; res0 != topIn.Nres(); res0++)
       {
         Residue const& R0 = topIn.Res(res0);
+        //int res1 = dih->resnum;
+        //if (res1 != res0)
         for (int res1 = res0 + 1; res1 != topIn.Nres(); res1++)
         {
           Residue const& R1 = topIn.Res(res1);
@@ -686,22 +752,69 @@ void Exec_PermuteDihedrals::RandomizeAngles_2(Frame& currentFrame, Topology cons
                 const double* xyz1 = currentFrame.XYZ(at1);
                 double d2 = DIST2_NoImage( xyz0, xyz1 );
                 if (d2 < cutoff_) {
-#                 ifdef DEBUG_PERMUTEDIHEDRALS
+//#                 ifdef DEBUG_PERMUTEDIHEDRALS
                   mprintf("DEBUG: Clash: %s to %s (%g Ang)\n",
                           topIn.TruncResAtomNameNum(at0).c_str(),
                           topIn.TruncResAtomNameNum(at1).c_str(), sqrt(d2));
-#                 endif
-                  clash = true;
-                  break;
+//#                 endif
+                  if (currentResClashes[res0] == initialResClashes[res0])
+                    clash = true;
+                  else
+                    currentResClashes[res0]++;
+                  if (currentResClashes[res1] == initialResClashes[res1])
+                    clash = true;
+                  else
+                    currentResClashes[res1]++;
+                  if (clash) break;
                 }
               } // END loop over residue 1 atoms
               if (clash) break;
             } // END loop over residue 0 atoms
+            if (checkRings_) {
+              // If either of these residues is the one belonging to the
+              // rotated dihedral, add bonds to check for ring intersection.
+              if (res0 == dih->resnum || res1 == dih->resnum) {
+                checkRingBonds[res0] = true;
+                checkRingBonds[res1] = true;
+              }
+            }
           } // END residues within cutoff of each other
           if (clash) break;
         } // END inner loop over residues
         if (clash) break;
       } // END outer loop over residues
+      // Check rings
+      if (checkRings_ && !clash) {
+        Cpptraj::Structure::RingFinder resRings;
+        // Select the dihedral residue
+        AtomMask resMask( topIn.Res(dih->resnum).FirstAtom(), topIn.Res(dih->resnum).LastAtom() );
+        resRings.SetupRingFinder(topIn, resMask);
+        if (resRings.Nrings() > 0) {
+          mprintf("DEBUG: Ring check, residue %i (%u rings).\n", dih->resnum+1, resRings.Nrings());
+          // Add ring bonds
+          std::vector<StructureCheck::Btype> ringBonds;
+          for (unsigned int idx = 0; idx != checkRingBonds.size(); idx++)
+          {
+            if (checkRingBonds[idx]) {
+              Residue const& ringRes = topIn.Res(idx);
+              for (int rat = ringRes.FirstAtom(); rat != ringRes.LastAtom(); rat++) {
+                Atom const& resAt = topIn[rat];
+                for (Atom::bond_iterator bat = resAt.bondbegin(); bat != resAt.bondend(); ++bat) {
+                  if (*bat > rat)
+                    ringBonds.push_back( StructureCheck::Btype(rat, *bat) );
+                }
+              }
+            }
+          } // END loop over residues for adding bonds to check
+          mprintf("DEBUG:\t\tChecking against %zu bonds.\n", ringBonds.size());
+        
+          int nRingProblems = checkStructure_.CheckRings(currentFrame, resRings, ringBonds);
+          if (nRingProblems > 0) {
+            mprintf("DEBUG: %i ring problems.\n", nRingProblems);
+            clash = true;
+          }
+        } // END residue has rings
+      }
       if (!clash) {
         // No clash, all done
         rotate_dihedral = false;
diff --git a/src/Exec_PermuteDihedrals.h b/src/Exec_PermuteDihedrals.h
index c20a2503d0..4334509dae 100644
--- a/src/Exec_PermuteDihedrals.h
+++ b/src/Exec_PermuteDihedrals.h
@@ -30,6 +30,9 @@ class Exec_PermuteDihedrals : public Exec {
     int CheckResidue( Frame const&, Topology const&, PermuteDihedralsType const&,int,double&);
     /// Randomly rotate dihedrals
     void RandomizeAngles(Frame&, Topology const&);
+    /// Count residue clashes in given frame
+    void countClashes(std::vector<int>&, Frame const&, Topology const&) const;
+    /// Randomly rotate dihedrals, slightly faster version
     void RandomizeAngles_2(Frame&, Topology const&);
 
     /// Permute types 
@@ -52,6 +55,7 @@ class Exec_PermuteDihedrals : public Exec {
     // 'random' options
     bool check_for_clashes_;
     bool checkAllResidues_;
+    bool checkRings_;   ///< If true, check for bond/ring intersections
     double max_factor_; ///< Max rotations to attempt will be max_factor_ * #dihedrals
     double cutoff_;     ///< When checking for clashes, atom cutoff
     double rescutoff_;  ///< When checking for clashes, residue cutoff

From 6a1d68ea51e0e5491166627e1206ef8460100c42 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 26 Jun 2024 09:28:49 -0400
Subject: [PATCH 0781/1492] Fix help text and add new keyword to manual

---
 doc/cpptraj.lyx               | 41 +++++++++++++++++++++++++++++++++--
 src/Exec_PermuteDihedrals.cpp |  4 ++--
 2 files changed, 41 insertions(+), 4 deletions(-)

diff --git a/doc/cpptraj.lyx b/doc/cpptraj.lyx
index e39d5b8e99..6345d1cdbf 100644
--- a/doc/cpptraj.lyx
+++ b/doc/cpptraj.lyx
@@ -8153,7 +8153,7 @@ permutedihedrals crdset <COORDS set> resrange <range> [{interval | random}]
 \end_layout
 
 \begin_layout LyX-Code
-                 [<dihedral types>]
+                 [<dihedral types>] [dihtype <name>:<a0>:<a1>:<a2>:<a3>[:<offset>] ...]
 \end_layout
 
 \begin_layout LyX-Code
@@ -8169,7 +8169,11 @@ permutedihedrals crdset <COORDS set> resrange <range> [{interval | random}]
 \end_layout
 
 \begin_layout LyX-Code
-	 [backtrack <backtrack> [checkallresidues] [increment <increment>]] ]
+	  [checkrings] [backtrack <backtrack> [checkallresidues]
+\end_layout
+
+\begin_layout LyX-Code
+                    [increment <increment>]] ]
 \end_layout
 
 \begin_layout LyX-Code
@@ -8260,6 +8264,32 @@ COORDS>] COORDS data set to write coordinates to.
 type> One or more dihedral types to search for.
 \end_layout
 
+\begin_layout Description
+[dihtype
+\begin_inset space ~
+\end_inset
+
+<name>:<a0>:<a1>:<a2>:<a3>[:<offset>] Search for a custom dihedral type called <name> using atom names <a0>,
+ <a1>,
+ <a2>,
+ and <a3>.
+\begin_inset Separator latexpar
+\end_inset
+
+
+\end_layout
+
+\begin_deeper
+\begin_layout Standard
+Offset:
+ -2=<a0><a1> in previous res,
+ -1=<a0> in previous res,
+ 0=All <aX> in single res,
+ 1=<a3> in next res,
+ 2=<a2><a3> in next res.
+\end_layout
+
+\end_deeper
 \begin_layout Standard
 Options for 'interval:
 \end_layout
@@ -8345,6 +8375,13 @@ name>] Number of problems data set name.
 <max_factor>] The maximum number of total attempted rotations will be <max_factor> * <total # of dihedrals> (default 2).
 \end_layout
 
+\begin_layout Description
+[checkrings] If specified,
+ look to see if any rings in the residue to which the dihedral being rotated belongs to have a bond running through them,
+ which counts as a clash.
+ May be slow.
+\end_layout
+
 \begin_layout Description
 [backtrack
 \begin_inset space ~
diff --git a/src/Exec_PermuteDihedrals.cpp b/src/Exec_PermuteDihedrals.cpp
index 81c2213f31..3bf95ea382 100644
--- a/src/Exec_PermuteDihedrals.cpp
+++ b/src/Exec_PermuteDihedrals.cpp
@@ -37,8 +37,8 @@ void Exec_PermuteDihedrals::Help() const {
   mprintf("  Options for 'random':\n"
           "\t[rseed <rseed>] [out <# problems file> [<set name>]] [noimage]\n"
           "\t[ check [cutoff <cutoff>] [rescutoff <rescutoff>] [maxfactor <max_factor>]\n"
-          "\t  [backtrack <backtrack> [checkallresidues] [checkrings]\n"
-          "\t  [increment <increment>]] ]\n"
+          "\t  [checkrings] [backtrack <backtrack> [checkallresidues]\n"
+          "\t                [increment <increment>]] ]\n"
           "  Options for 'interval':\n"
           "\t<interval deg>\n"
           "  <dihedral types> = ");

From b49b8be50fac783a1b97c8d5085fc5c9a3515cc9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 26 Jun 2024 09:30:01 -0400
Subject: [PATCH 0782/1492] Fix some typos

---
 doc/cpptraj.lyx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/doc/cpptraj.lyx b/doc/cpptraj.lyx
index 6345d1cdbf..e0a490aafb 100644
--- a/doc/cpptraj.lyx
+++ b/doc/cpptraj.lyx
@@ -8291,7 +8291,7 @@ Offset:
 
 \end_deeper
 \begin_layout Standard
-Options for 'interval:
+Options for 'interval':
 \end_layout
 
 \begin_layout Description
@@ -8364,7 +8364,7 @@ name>] Number of problems data set name.
 \begin_inset space ~
 \end_inset
 
-<cutoff>] Residue cutoff for checking for clashes (defualt 10.0 Å).
+<cutoff>] Residue cutoff for checking for clashes (default 10.0 Å).
 \end_layout
 
 \begin_layout Description

From cf8188e0d13f55b42439c3beb3969c406609e657 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 26 Jun 2024 11:06:26 -0400
Subject: [PATCH 0783/1492] Increase default cutoff to accomodate nucleic acid
 P-P distance

---
 src/Exec_PermuteDihedrals.cpp | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/Exec_PermuteDihedrals.cpp b/src/Exec_PermuteDihedrals.cpp
index 3bf95ea382..7c8428c3bd 100644
--- a/src/Exec_PermuteDihedrals.cpp
+++ b/src/Exec_PermuteDihedrals.cpp
@@ -22,7 +22,8 @@ Exec_PermuteDihedrals::Exec_PermuteDihedrals() : Exec(COORDS),
   checkRings_(false),
   max_factor_(2),
   cutoff_(0.64), // 0.8^2
-  rescutoff_(100.0), // 10.0^2
+  //rescutoff_(100.0), // 10.0^2
+  rescutoff_(225.0), // 15.0^2
   backtrack_(5),
   increment_(1),
   max_increment_(360),
@@ -136,7 +137,7 @@ Exec::RetType Exec_PermuteDihedrals::Execute(CpptrajState& State, ArgList& argIn
       resCutoffDefault = 10.0;
       use_random2 = false;
     } else {
-      resCutoffDefault = 12.0;
+      resCutoffDefault = 15.0;
       use_random2 = true;
     }
     check_for_clashes_ = argIn.hasKey("check");

From 82345031a18ccebef82bb08fae07c2cb3f373d75 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 26 Jun 2024 11:52:01 -0400
Subject: [PATCH 0784/1492] Look at all rings in selected residues since we
 might rotate a bond from this residue into the ring of another

---
 src/Exec_PermuteDihedrals.cpp | 53 ++++++++++++++++++++++-------------
 1 file changed, 34 insertions(+), 19 deletions(-)

diff --git a/src/Exec_PermuteDihedrals.cpp b/src/Exec_PermuteDihedrals.cpp
index 7c8428c3bd..e8d413c308 100644
--- a/src/Exec_PermuteDihedrals.cpp
+++ b/src/Exec_PermuteDihedrals.cpp
@@ -787,34 +787,49 @@ void Exec_PermuteDihedrals::RandomizeAngles_2(Frame& currentFrame, Topology cons
       // Check rings
       if (checkRings_ && !clash) {
         Cpptraj::Structure::RingFinder resRings;
-        // Select the dihedral residue
-        AtomMask resMask( topIn.Res(dih->resnum).FirstAtom(), topIn.Res(dih->resnum).LastAtom() );
+        // Select atoms in residues to search for rings
+        AtomMask resMask(std::vector<int>(), topIn.Natom());//( topIn.Res(dih->resnum).FirstAtom(), topIn.Res(dih->resnum).LastAtom() );
+        //resRings.SetupRingFinder(topIn, resMask);
+        // Add ring bonds
+        std::vector<StructureCheck::Btype> ringBonds;
+        for (unsigned int idx = 0; idx != checkRingBonds.size(); idx++)
+        {
+          if (checkRingBonds[idx]) {
+            Residue const& ringRes = topIn.Res(idx);
+            // Add heavy atom bonds
+            for (int rat = ringRes.FirstAtom(); rat != ringRes.LastAtom(); rat++) {
+              Atom const& resAt = topIn[rat];
+              if (resAt.Nbonds() > 1) {
+                resMask.AddSelectedAtom( rat );
+              }
+              for (Atom::bond_iterator bat = resAt.bondbegin(); bat != resAt.bondend(); ++bat) {
+                if (*bat > rat)
+                  ringBonds.push_back( StructureCheck::Btype(rat, *bat) );
+              }
+            }
+          }
+        } // END loop over residues for adding bonds to check
         resRings.SetupRingFinder(topIn, resMask);
         if (resRings.Nrings() > 0) {
           mprintf("DEBUG: Ring check, residue %i (%u rings).\n", dih->resnum+1, resRings.Nrings());
-          // Add ring bonds
-          std::vector<StructureCheck::Btype> ringBonds;
-          for (unsigned int idx = 0; idx != checkRingBonds.size(); idx++)
-          {
-            if (checkRingBonds[idx]) {
-              Residue const& ringRes = topIn.Res(idx);
-              for (int rat = ringRes.FirstAtom(); rat != ringRes.LastAtom(); rat++) {
-                Atom const& resAt = topIn[rat];
-                for (Atom::bond_iterator bat = resAt.bondbegin(); bat != resAt.bondend(); ++bat) {
-                  if (*bat > rat)
-                    ringBonds.push_back( StructureCheck::Btype(rat, *bat) );
-                }
-              }
-            }
-          } // END loop over residues for adding bonds to check
+          //resRings.PrintRings(topIn);
           mprintf("DEBUG:\t\tChecking against %zu bonds.\n", ringBonds.size());
-        
+          //int icol = 0;
+          //for (std::vector<StructureCheck::Btype>::const_iterator bt = ringBonds.begin(); bt != ringBonds.end(); ++bt)
+          //{
+          //  mprintf(" %s-%s\n", topIn.AtomMaskName(bt->A1()).c_str(), topIn.AtomMaskName(bt->A2()).c_str());
+          //  //if (icol == 5 || (bt+1) == ringBonds.end()) { 
+          //  //  mprintf("\n");
+          //  //  icol = 0;
+          //  //}
+          //}
+            
           int nRingProblems = checkStructure_.CheckRings(currentFrame, resRings, ringBonds);
           if (nRingProblems > 0) {
             mprintf("DEBUG: %i ring problems.\n", nRingProblems);
             clash = true;
           }
-        } // END residue has rings
+        } // END rings are present
       }
       if (!clash) {
         // No clash, all done

From 94217f1a9f83fec9b496fbe139960d17823e5193 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 26 Jun 2024 13:39:55 -0400
Subject: [PATCH 0785/1492] Split ring check into 3; res rings->other bonds,
 res rings->res bonds, other rings->res bonds; ignore other rings->other bonds

---
 src/Exec_PermuteDihedrals.cpp | 34 ++++++++++++++++++++++++----------
 1 file changed, 24 insertions(+), 10 deletions(-)

diff --git a/src/Exec_PermuteDihedrals.cpp b/src/Exec_PermuteDihedrals.cpp
index e8d413c308..0e7dc87fc5 100644
--- a/src/Exec_PermuteDihedrals.cpp
+++ b/src/Exec_PermuteDihedrals.cpp
@@ -787,12 +787,15 @@ void Exec_PermuteDihedrals::RandomizeAngles_2(Frame& currentFrame, Topology cons
       // Check rings
       if (checkRings_ && !clash) {
         Cpptraj::Structure::RingFinder resRings;
+        Cpptraj::Structure::RingFinder otherRings;
         // Select atoms in residues to search for rings
-        AtomMask resMask(std::vector<int>(), topIn.Natom());//( topIn.Res(dih->resnum).FirstAtom(), topIn.Res(dih->resnum).LastAtom() );
+        AtomMask resMask(std::vector<int>(), topIn.Natom());
+        AtomMask otherMask(std::vector<int>(), topIn.Natom());
         //resRings.SetupRingFinder(topIn, resMask);
         // Add ring bonds
-        std::vector<StructureCheck::Btype> ringBonds;
-        for (unsigned int idx = 0; idx != checkRingBonds.size(); idx++)
+        std::vector<StructureCheck::Btype> resBonds;
+        std::vector<StructureCheck::Btype> otherBonds;
+        for (int idx = 0; idx != topIn.Nres(); idx++)
         {
           if (checkRingBonds[idx]) {
             Residue const& ringRes = topIn.Res(idx);
@@ -800,20 +803,28 @@ void Exec_PermuteDihedrals::RandomizeAngles_2(Frame& currentFrame, Topology cons
             for (int rat = ringRes.FirstAtom(); rat != ringRes.LastAtom(); rat++) {
               Atom const& resAt = topIn[rat];
               if (resAt.Nbonds() > 1) {
-                resMask.AddSelectedAtom( rat );
+                if (idx == dih->resnum)
+                  resMask.AddSelectedAtom( rat );
+                else
+                  otherMask.AddSelectedAtom( rat );
               }
               for (Atom::bond_iterator bat = resAt.bondbegin(); bat != resAt.bondend(); ++bat) {
-                if (*bat > rat)
-                  ringBonds.push_back( StructureCheck::Btype(rat, *bat) );
+                if (*bat > rat) {
+                  if (idx == dih->resnum)
+                    resBonds.push_back( StructureCheck::Btype(rat, *bat) );
+                  else
+                    otherBonds.push_back( StructureCheck::Btype(rat, *bat) );
+                }
               }
             }
           }
         } // END loop over residues for adding bonds to check
         resRings.SetupRingFinder(topIn, resMask);
-        if (resRings.Nrings() > 0) {
+        otherRings.SetupRingFinder(topIn, otherMask);
+        if (resRings.Nrings() > 0 || otherRings.Nrings() > 0) {
           mprintf("DEBUG: Ring check, residue %i (%u rings).\n", dih->resnum+1, resRings.Nrings());
           //resRings.PrintRings(topIn);
-          mprintf("DEBUG:\t\tChecking against %zu bonds.\n", ringBonds.size());
+          mprintf("DEBUG:\t\tChecking against %zu bonds.\n", otherBonds.size());
           //int icol = 0;
           //for (std::vector<StructureCheck::Btype>::const_iterator bt = ringBonds.begin(); bt != ringBonds.end(); ++bt)
           //{
@@ -823,8 +834,11 @@ void Exec_PermuteDihedrals::RandomizeAngles_2(Frame& currentFrame, Topology cons
           //  //  icol = 0;
           //  //}
           //}
-            
-          int nRingProblems = checkStructure_.CheckRings(currentFrame, resRings, ringBonds);
+          int nRingProblems = checkStructure_.CheckRings(currentFrame, resRings, otherBonds);
+          mprintf("DEBUG:\t\t%u other rings, %zu residue bonds.\n", otherRings.Nrings(), resBonds.size());
+          nRingProblems += checkStructure_.CheckRings(currentFrame, otherRings, resBonds);
+          // Check self
+          nRingProblems += checkStructure_.CheckRings(currentFrame, resRings, resBonds);
           if (nRingProblems > 0) {
             mprintf("DEBUG: %i ring problems.\n", nRingProblems);
             clash = true;

From 94aa511acaa6667cb96a37b331caae5381d0334f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 28 Jun 2024 10:33:32 -0400
Subject: [PATCH 0786/1492] Since SetNtypes only allocates space in nbindex_,
 modify SetLJ14 to allocate space in the SetLJ14 routine (like AddLJterm) as
 needed

---
 src/ParameterTypes.h | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/src/ParameterTypes.h b/src/ParameterTypes.h
index 3c6d769aae..7a40aa7a48 100644
--- a/src/ParameterTypes.h
+++ b/src/ParameterTypes.h
@@ -688,8 +688,15 @@ class NonbondParmType {
     void SetNLJCterms(int n)     { ccoef_.assign( n, 0 ); }
     /// Set specified LJ term
     NonbondType& SetLJ(int i)    { return nbarray_[i];                  }
-    /// Set specified LJ 1-4 term
-    NonbondType& SetLJ14(int i)  { return lj14_[i];    }
+    /// Set specified LJ 1-4 term.
+    /** Reserve space if not yet allocated, allows it to be used in conjunction
+      * with AddLJterm.
+      */
+    NonbondType& SetLJ14(int ndx)  {
+      if (ndx >= (int)lj14_.size())
+        lj14_.resize(ndx+1);
+      return lj14_[ndx];
+    }
     /// Set specified LJC term
     void SetLJC(int i, double ljc) { ccoef_[i] = ljc; }
     /// Set number of HB terms and init HB array TODO combine with SetNtypes?

From 1049f6a8b481c20645313b68a3f15033967ff5c2 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 28 Jun 2024 10:37:35 -0400
Subject: [PATCH 0787/1492] Add IPOL flag to test save

---
 test/Test_Charmm/strip.chamber.parm7.save | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/test/Test_Charmm/strip.chamber.parm7.save b/test/Test_Charmm/strip.chamber.parm7.save
index 86ca2d049d..60438bccfe 100644
--- a/test/Test_Charmm/strip.chamber.parm7.save
+++ b/test/Test_Charmm/strip.chamber.parm7.save
@@ -1,4 +1,4 @@
-%VERSION  VERSION_STAMP = V0001.000  DATE = 12/05/23 15:27:09                  
+%VERSION  VERSION_STAMP = V0001.000  DATE = 06/28/24 10:33:11                  
 %FLAG CTITLE                                                                    
 %FORMAT(a80)                                                                    
                                                                                 
@@ -289,3 +289,6 @@ modified Bondi radii (mbondi)
   8.50000000E-01  7.90000000E-01  8.50000000E-01  7.20000000E-01  8.50000000E-01
   7.20000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01  7.20000000E-01
   8.50000000E-01
+%FLAG IPOL                                                                      
+%FORMAT(1I8)                                                                    
+       0

From b47300c7da862521488564e06bc17aa4aac29885 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 28 Jun 2024 14:39:46 -0400
Subject: [PATCH 0788/1492] Add IPOL flag to save

---
 test/Test_CharmmParams/test3.parm7.save | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/test/Test_CharmmParams/test3.parm7.save b/test/Test_CharmmParams/test3.parm7.save
index 3a34b026b1..ee7b4528e7 100644
--- a/test/Test_CharmmParams/test3.parm7.save
+++ b/test/Test_CharmmParams/test3.parm7.save
@@ -1,4 +1,4 @@
-%VERSION  VERSION_STAMP = V0001.000  DATE = 12/13/23 10:09:59                  
+%VERSION  VERSION_STAMP = V0001.000  DATE = 06/28/24 14:39:23                  
 %FLAG CTITLE                                                                    
 %FORMAT(a80)                                                                    
                                                                                 
@@ -414,3 +414,6 @@ modified Bondi radii (mbondi)
   7.20000000E-01  8.50000000E-01  8.50000000E-01  7.20000000E-01  8.50000000E-01
   8.50000000E-01  7.90000000E-01  8.50000000E-01  7.20000000E-01  8.50000000E-01
   8.50000000E-01  7.20000000E-01  8.50000000E-01
+%FLAG IPOL                                                                      
+%FORMAT(1I8)                                                                    
+       0

From ce0debc63af020b5fc67a587d772025f450643a0 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 28 Jun 2024 14:40:36 -0400
Subject: [PATCH 0789/1492] Add IPOL flag to save

---
 test/Test_Closest/closest.tz2.truncoct.parm7.save | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/test/Test_Closest/closest.tz2.truncoct.parm7.save b/test/Test_Closest/closest.tz2.truncoct.parm7.save
index 11e260e59a..3f20f4e3c0 100644
--- a/test/Test_Closest/closest.tz2.truncoct.parm7.save
+++ b/test/Test_Closest/closest.tz2.truncoct.parm7.save
@@ -1,4 +1,4 @@
-%VERSION  VERSION_STAMP = V0001.000  DATE = 02/04/15  10:24:01                  
+%VERSION  VERSION_STAMP = V0001.000  DATE = 06/28/24 14:40:13                  
 %FLAG TITLE                                                                     
 %FORMAT(20a4)                                                                   
                                                                                 
@@ -1404,3 +1404,6 @@ modified Bondi radii (mbondi)
   8.50000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01
   8.50000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01
   8.50000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01
+%FLAG IPOL                                                                      
+%FORMAT(1I8)                                                                    
+       0

From e9277046dc4493849bb0ba4bcd3bce737483f246 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 28 Jun 2024 14:41:26 -0400
Subject: [PATCH 0790/1492] Add IPOL flag to save

---
 test/Test_FixAtomOrder/reorder.outoforder.parm7.save | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/test/Test_FixAtomOrder/reorder.outoforder.parm7.save b/test/Test_FixAtomOrder/reorder.outoforder.parm7.save
index 3d35e059a6..caed09b503 100644
--- a/test/Test_FixAtomOrder/reorder.outoforder.parm7.save
+++ b/test/Test_FixAtomOrder/reorder.outoforder.parm7.save
@@ -1,4 +1,4 @@
-%VERSION  VERSION_STAMP = V0001.000  DATE = 12/21/14  11:44:38                  
+%VERSION  VERSION_STAMP = V0001.000  DATE = 06/28/24 14:09:39                  
 %FLAG TITLE                                                                     
 %FORMAT(20a4)                                                                   
 ACE                                                                             
@@ -460,3 +460,6 @@ modified Bondi radii (mbondi)
   8.50000000E-01  8.50000000E-01  8.50000000E-01  7.20000000E-01  8.50000000E-01
   7.90000000E-01  8.50000000E-01  7.20000000E-01  8.50000000E-01  8.50000000E-01
   8.50000000E-01
+%FLAG IPOL                                                                      
+%FORMAT(1I8)                                                                    
+       0

From a42c74e72479f697729d96a5c7e4c93423bfffad Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 28 Jun 2024 14:42:13 -0400
Subject: [PATCH 0791/1492] Add IPOL flag to test save

---
 test/Test_HmassRepartition/tz2.hmr.parm7.save | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/test/Test_HmassRepartition/tz2.hmr.parm7.save b/test/Test_HmassRepartition/tz2.hmr.parm7.save
index ad1486c604..5c63f5c269 100644
--- a/test/Test_HmassRepartition/tz2.hmr.parm7.save
+++ b/test/Test_HmassRepartition/tz2.hmr.parm7.save
@@ -1,4 +1,4 @@
-%VERSION  VERSION_STAMP = V0001.000  DATE = 01/31/22 11:59:27                  
+%VERSION  VERSION_STAMP = V0001.000  DATE = 06/28/24 14:09:46                  
 %FLAG TITLE                                                                     
 %FORMAT(20a4)                                                                   
                                                                                 
@@ -1252,3 +1252,6 @@ E   E   E
   8.50000000E-01  7.90000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01
   7.20000000E-01  8.50000000E-01  7.90000000E-01  8.50000000E-01  7.20000000E-01
   8.50000000E-01  8.50000000E-01  8.50000000E-01
+%FLAG IPOL                                                                      
+%FORMAT(1I8)                                                                    
+       0

From 304766b10a437ae48c11edcbc6459a2c374a20e8 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 28 Jun 2024 14:43:14 -0400
Subject: [PATCH 0792/1492] Add IPOL flag to test save

---
 test/Test_LJC/cpptraj.znf_1264.parm7.save | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/test/Test_LJC/cpptraj.znf_1264.parm7.save b/test/Test_LJC/cpptraj.znf_1264.parm7.save
index c73c94795c..9507f6a0fa 100644
--- a/test/Test_LJC/cpptraj.znf_1264.parm7.save
+++ b/test/Test_LJC/cpptraj.znf_1264.parm7.save
@@ -1,4 +1,4 @@
-%VERSION  VERSION_STAMP = V0001.000  DATE = 07/22/21 15:13:48                  
+%VERSION  VERSION_STAMP = V0001.000  DATE = 06/28/24 14:43:01                  
 %FLAG TITLE                                                                     
 %FORMAT(20a4)                                                                   
 default_name                                                                    
@@ -2998,6 +2998,9 @@ modified Bondi radii (mbondi)
   8.50000000E-01  7.20000000E-01  8.50000000E-01  7.20000000E-01  8.50000000E-01
   7.20000000E-01  8.50000000E-01  7.20000000E-01  8.50000000E-01  8.50000000E-01
   8.00000000E-01
+%FLAG IPOL                                                                      
+%FORMAT(1I8)                                                                    
+       0
 %FLAG LENNARD_JONES_CCOEF                                                       
 %FORMAT(5E16.8)                                                                 
   0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00

From 7702bad79abe21fc9c84325ef540506a0ec4a9b9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 28 Jun 2024 14:44:46 -0400
Subject: [PATCH 0793/1492] Add TREE, JOIN, IROTAT and IPOL sections to test
 save

---
 test/Test_NAstruct/axes.step.parm7.save | 19 ++++++++++++++++++-
 1 file changed, 18 insertions(+), 1 deletion(-)

diff --git a/test/Test_NAstruct/axes.step.parm7.save b/test/Test_NAstruct/axes.step.parm7.save
index d37d7d0a24..d8ee33b917 100644
--- a/test/Test_NAstruct/axes.step.parm7.save
+++ b/test/Test_NAstruct/axes.step.parm7.save
@@ -1,4 +1,4 @@
-%VERSION  VERSION_STAMP = V0001.000  DATE = 07/11/23 09:21:41                  
+%VERSION  VERSION_STAMP = V0001.000  DATE = 06/28/24 14:08:01                  
 %FLAG TITLE                                                                     
 %FORMAT(20a4)                                                                   
 StepAxes                                                                        
@@ -132,3 +132,20 @@ G5  G   G   C   G   C   C
 %FORMAT(20a4)                                                                   
                                                                                 
                                 
+%FLAG TREE_CHAIN_CLASSIFICATION                                                 
+%FORMAT(20a4)                                                                   
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA 
+%FLAG JOIN_ARRAY                                                                
+%FORMAT(10I8)                                                                   
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+%FLAG IROTAT                                                                    
+%FORMAT(10I8)                                                                   
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+%FLAG IPOL                                                                      
+%FORMAT(1I8)                                                                    
+       0

From afd90033f40284f9de5f4d1d815cea53b0fb2b12 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 28 Jun 2024 14:45:31 -0400
Subject: [PATCH 0794/1492] Add IPOL flag to test save

---
 test/Test_ParmBox/out.parm7.save | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/test/Test_ParmBox/out.parm7.save b/test/Test_ParmBox/out.parm7.save
index e7fe58ca90..c2e6fd12e8 100644
--- a/test/Test_ParmBox/out.parm7.save
+++ b/test/Test_ParmBox/out.parm7.save
@@ -1,4 +1,4 @@
-%VERSION  VERSION_STAMP = V0001.000  DATE = 09/19/17 14:36:57                  
+%VERSION  VERSION_STAMP = V0001.000  DATE = 06/28/24 14:09:40                  
 %FLAG TITLE                                                                     
 %FORMAT(20a4)                                                                   
 ACE                                                                             
@@ -338,3 +338,6 @@ modified Bondi radii (mbondi)
   8.50000000E-01  7.20000000E-01  8.50000000E-01  7.20000000E-01  8.50000000E-01
   7.20000000E-01  8.50000000E-01  7.90000000E-01  8.50000000E-01  7.20000000E-01
   8.50000000E-01  8.50000000E-01  8.50000000E-01
+%FLAG IPOL                                                                      
+%FORMAT(1I8)                                                                    
+       0

From 1b5ad64fc589dbb5608a08a46264b057d193e722 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 28 Jun 2024 14:49:44 -0400
Subject: [PATCH 0795/1492] Make Phase column width of 8 to better handle
 negative phase

---
 src/ParameterSet.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/ParameterSet.cpp b/src/ParameterSet.cpp
index 4ac24a762b..9a339d263c 100644
--- a/src/ParameterSet.cpp
+++ b/src/ParameterSet.cpp
@@ -107,11 +107,11 @@ void ParameterSet::Print(CpptrajFile& Out) const {
   }
   if (!dihParm_.empty()) {
     Out.Printf("Dihedral parameters:\n");
-    Out.Printf("\t%6s %6s %6s %6s %12s %4s %6s %6s %6s\n", "Type1", "Type2", "Type3", "Type4", "Pk", "Pn", "Phase", "SCEE", "SCNB");
+    Out.Printf("\t%6s %6s %6s %6s %12s %4s %8s %6s %6s\n", "Type1", "Type2", "Type3", "Type4", "Pk", "Pn", "Phase", "SCEE", "SCNB");
     for (DihedralParmHolder::const_iterator it0 = dihParm_.begin(); it0 != dihParm_.end(); ++it0)
       for (DihedralParmArray::const_iterator it1 = it0->second.begin();
                                              it1 != it0->second.end(); ++it1)
-        Out.Printf("\t%6s %6s %6s %6s : %12.4f %4.1f %6.2f %6.2f %6.2f\n", *(it0->first[0]), *(it0->first[1]), *(it0->first[2]), *(it0->first[3]), it1->Pk(), it1->Pn(), it1->Phase()*Constants::RADDEG, it1->SCEE(), it1->SCNB());
+        Out.Printf("\t%6s %6s %6s %6s : %12.4f %4.1f %8.2f %6.2f %6.2f\n", *(it0->first[0]), *(it0->first[1]), *(it0->first[2]), *(it0->first[3]), it1->Pk(), it1->Pn(), it1->Phase()*Constants::RADDEG, it1->SCEE(), it1->SCNB());
   }
   if (!impParm_.empty()) {
     Out.Printf("Improper parameters:\n");

From f7ebea6e9ff4075a0cac06f81f8d02b869da7e7e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 28 Jun 2024 14:50:23 -0400
Subject: [PATCH 0796/1492] Update for format change and addition of SCEE/SCNB
 output to dihedral params

---
 test/Test_ReadAmberFF/toyrna.parm.dat.save | 76 +++++++++++-----------
 1 file changed, 38 insertions(+), 38 deletions(-)

diff --git a/test/Test_ReadAmberFF/toyrna.parm.dat.save b/test/Test_ReadAmberFF/toyrna.parm.dat.save
index 9e403254e2..56237494e7 100644
--- a/test/Test_ReadAmberFF/toyrna.parm.dat.save
+++ b/test/Test_ReadAmberFF/toyrna.parm.dat.save
@@ -97,41 +97,41 @@ Angle parameters:
 	    CB     CS     U1 :      30.0000     122.5000
 	    CB     CS     C1 :      30.0000     122.5000
 Dihedral parameters:
-	 Type1  Type2  Type3  Type4           Pk           Pn        Phase
-	     X     CB     CS      X :       7.5000       1.0000    -165.0000
-	     X      P     CB      X :       0.0000       2.0000     180.0000
-	     X     CS     G9      X :       0.0000       2.0000     180.0000
-	     X     CS     A9      X :       0.0000       2.0000     180.0000
-	     X     CS     U1      X :       0.0000       2.0000     180.0000
-	     X     CS     C1      X :       0.0000       2.0000     180.0000
-	     X     A9     A7      X :       0.0000       2.0000     180.0000
-	     X     A7     A6      X :       0.0000       2.0000     180.0000
-	     X     A6     A1      X :       0.0000       2.0000     180.0000
-	     X     A1     A3      X :       0.0000       2.0000     180.0000
-	     X     A3     A9      X :       0.0000       2.0000     180.0000
-	     X     G9     G7      X :       0.0000       2.0000     180.0000
-	     X     G7     G6      X :       0.0000       2.0000     180.0000
-	     X     G6     G1      X :       0.0000       2.0000     180.0000
-	     X     G1     G2      X :       0.0000       2.0000     180.0000
-	     X     G2     G3      X :       0.0000       2.0000     180.0000
-	     X     G3     G9      X :       0.0000       2.0000     180.0000
-	     X     U1     U4      X :       0.0000       2.0000     180.0000
-	     X     U4     U3      X :       0.0000       2.0000     180.0000
-	     X     U3     U2      X :       0.0000       2.0000     180.0000
-	     X     U2     U1      X :       0.0000       2.0000     180.0000
-	     X     C1     C4      X :       0.0000       2.0000     180.0000
-	     X     C4     C3      X :       0.0000       2.0000     180.0000
-	     X     C3     C2      X :       0.0000       2.0000     180.0000
-	     X     C2     C1      X :       0.0000       2.0000     180.0000
-	    CS     C1     C2     C3 :       2.0000       2.0000     180.0000
-	    C4     C1     C2     C3 :       2.0000       2.0000     180.0000
-	    CS     U1     U2     U3 :       2.0000       2.0000     180.0000
-	    U4     U1     U2     U3 :       2.0000       2.0000     180.0000
-	    CS     G9     G7     G6 :       2.0000       2.0000     180.0000
-	    G9     G7     G6     G1 :       2.0000       2.0000     180.0000
-	    CS     A9     A7     A6 :       2.0000       2.0000     180.0000
-	    A9     A7     A6     A1 :       2.0000       2.0000     180.0000
-	    CB     CS     C1     C2 :       2.0000       2.0000     180.0000
-	    CB     CS     U1     U2 :       2.0000       2.0000     180.0000
-	    CB     CS     G9     G3 :       2.0000       2.0000     180.0000
-	    CB     CS     A9     A3 :       2.0000       2.0000     180.0000
+	 Type1  Type2  Type3  Type4           Pk   Pn    Phase   SCEE   SCNB
+	     X     CB     CS      X :       7.5000  1.0  -165.00   1.20   2.00
+	     X      P     CB      X :       0.0000  2.0   180.00   1.20   2.00
+	     X     CS     G9      X :       0.0000  2.0   180.00   1.20   2.00
+	     X     CS     A9      X :       0.0000  2.0   180.00   1.20   2.00
+	     X     CS     U1      X :       0.0000  2.0   180.00   1.20   2.00
+	     X     CS     C1      X :       0.0000  2.0   180.00   1.20   2.00
+	     X     A9     A7      X :       0.0000  2.0   180.00   1.20   2.00
+	     X     A7     A6      X :       0.0000  2.0   180.00   1.20   2.00
+	     X     A6     A1      X :       0.0000  2.0   180.00   1.20   2.00
+	     X     A1     A3      X :       0.0000  2.0   180.00   1.20   2.00
+	     X     A3     A9      X :       0.0000  2.0   180.00   1.20   2.00
+	     X     G9     G7      X :       0.0000  2.0   180.00   1.20   2.00
+	     X     G7     G6      X :       0.0000  2.0   180.00   1.20   2.00
+	     X     G6     G1      X :       0.0000  2.0   180.00   1.20   2.00
+	     X     G1     G2      X :       0.0000  2.0   180.00   1.20   2.00
+	     X     G2     G3      X :       0.0000  2.0   180.00   1.20   2.00
+	     X     G3     G9      X :       0.0000  2.0   180.00   1.20   2.00
+	     X     U1     U4      X :       0.0000  2.0   180.00   1.20   2.00
+	     X     U4     U3      X :       0.0000  2.0   180.00   1.20   2.00
+	     X     U3     U2      X :       0.0000  2.0   180.00   1.20   2.00
+	     X     U2     U1      X :       0.0000  2.0   180.00   1.20   2.00
+	     X     C1     C4      X :       0.0000  2.0   180.00   1.20   2.00
+	     X     C4     C3      X :       0.0000  2.0   180.00   1.20   2.00
+	     X     C3     C2      X :       0.0000  2.0   180.00   1.20   2.00
+	     X     C2     C1      X :       0.0000  2.0   180.00   1.20   2.00
+	    CS     C1     C2     C3 :       2.0000  2.0   180.00   1.20   2.00
+	    C4     C1     C2     C3 :       2.0000  2.0   180.00   1.20   2.00
+	    CS     U1     U2     U3 :       2.0000  2.0   180.00   1.20   2.00
+	    U4     U1     U2     U3 :       2.0000  2.0   180.00   1.20   2.00
+	    CS     G9     G7     G6 :       2.0000  2.0   180.00   1.20   2.00
+	    G9     G7     G6     G1 :       2.0000  2.0   180.00   1.20   2.00
+	    CS     A9     A7     A6 :       2.0000  2.0   180.00   1.20   2.00
+	    A9     A7     A6     A1 :       2.0000  2.0   180.00   1.20   2.00
+	    CB     CS     C1     C2 :       2.0000  2.0   180.00   1.20   2.00
+	    CB     CS     U1     U2 :       2.0000  2.0   180.00   1.20   2.00
+	    CB     CS     G9     G3 :       2.0000  2.0   180.00   1.20   2.00
+	    CB     CS     A9     A3 :       2.0000  2.0   180.00   1.20   2.00

From 58522914b206c0ebc9ef1145b43aa6ca9d2fed2f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 28 Jun 2024 14:52:02 -0400
Subject: [PATCH 0797/1492] Update for format change and addition of SCEE/SCNB
 to output

---
 .../toyrna.tip3pf.parm.dat.save               | 76 +++++++++----------
 1 file changed, 38 insertions(+), 38 deletions(-)

diff --git a/test/Test_ReadAmberFF/toyrna.tip3pf.parm.dat.save b/test/Test_ReadAmberFF/toyrna.tip3pf.parm.dat.save
index e62ee5b37a..977a376493 100644
--- a/test/Test_ReadAmberFF/toyrna.tip3pf.parm.dat.save
+++ b/test/Test_ReadAmberFF/toyrna.tip3pf.parm.dat.save
@@ -101,41 +101,41 @@ Angle parameters:
 	    CB     CS     U1 :      30.0000     122.5000
 	    CB     CS     C1 :      30.0000     122.5000
 Dihedral parameters:
-	 Type1  Type2  Type3  Type4           Pk           Pn        Phase
-	     X     CB     CS      X :       7.5000       1.0000    -165.0000
-	     X      P     CB      X :       0.0000       2.0000     180.0000
-	     X     CS     G9      X :       0.0000       2.0000     180.0000
-	     X     CS     A9      X :       0.0000       2.0000     180.0000
-	     X     CS     U1      X :       0.0000       2.0000     180.0000
-	     X     CS     C1      X :       0.0000       2.0000     180.0000
-	     X     A9     A7      X :       0.0000       2.0000     180.0000
-	     X     A7     A6      X :       0.0000       2.0000     180.0000
-	     X     A6     A1      X :       0.0000       2.0000     180.0000
-	     X     A1     A3      X :       0.0000       2.0000     180.0000
-	     X     A3     A9      X :       0.0000       2.0000     180.0000
-	     X     G9     G7      X :       0.0000       2.0000     180.0000
-	     X     G7     G6      X :       0.0000       2.0000     180.0000
-	     X     G6     G1      X :       0.0000       2.0000     180.0000
-	     X     G1     G2      X :       0.0000       2.0000     180.0000
-	     X     G2     G3      X :       0.0000       2.0000     180.0000
-	     X     G3     G9      X :       0.0000       2.0000     180.0000
-	     X     U1     U4      X :       0.0000       2.0000     180.0000
-	     X     U4     U3      X :       0.0000       2.0000     180.0000
-	     X     U3     U2      X :       0.0000       2.0000     180.0000
-	     X     U2     U1      X :       0.0000       2.0000     180.0000
-	     X     C1     C4      X :       0.0000       2.0000     180.0000
-	     X     C4     C3      X :       0.0000       2.0000     180.0000
-	     X     C3     C2      X :       0.0000       2.0000     180.0000
-	     X     C2     C1      X :       0.0000       2.0000     180.0000
-	    CS     C1     C2     C3 :       2.0000       2.0000     180.0000
-	    C4     C1     C2     C3 :       2.0000       2.0000     180.0000
-	    CS     U1     U2     U3 :       2.0000       2.0000     180.0000
-	    U4     U1     U2     U3 :       2.0000       2.0000     180.0000
-	    CS     G9     G7     G6 :       2.0000       2.0000     180.0000
-	    G9     G7     G6     G1 :       2.0000       2.0000     180.0000
-	    CS     A9     A7     A6 :       2.0000       2.0000     180.0000
-	    A9     A7     A6     A1 :       2.0000       2.0000     180.0000
-	    CB     CS     C1     C2 :       2.0000       2.0000     180.0000
-	    CB     CS     U1     U2 :       2.0000       2.0000     180.0000
-	    CB     CS     G9     G3 :       2.0000       2.0000     180.0000
-	    CB     CS     A9     A3 :       2.0000       2.0000     180.0000
+	 Type1  Type2  Type3  Type4           Pk   Pn    Phase   SCEE   SCNB
+	     X     CB     CS      X :       7.5000  1.0  -165.00   1.20   2.00
+	     X      P     CB      X :       0.0000  2.0   180.00   1.20   2.00
+	     X     CS     G9      X :       0.0000  2.0   180.00   1.20   2.00
+	     X     CS     A9      X :       0.0000  2.0   180.00   1.20   2.00
+	     X     CS     U1      X :       0.0000  2.0   180.00   1.20   2.00
+	     X     CS     C1      X :       0.0000  2.0   180.00   1.20   2.00
+	     X     A9     A7      X :       0.0000  2.0   180.00   1.20   2.00
+	     X     A7     A6      X :       0.0000  2.0   180.00   1.20   2.00
+	     X     A6     A1      X :       0.0000  2.0   180.00   1.20   2.00
+	     X     A1     A3      X :       0.0000  2.0   180.00   1.20   2.00
+	     X     A3     A9      X :       0.0000  2.0   180.00   1.20   2.00
+	     X     G9     G7      X :       0.0000  2.0   180.00   1.20   2.00
+	     X     G7     G6      X :       0.0000  2.0   180.00   1.20   2.00
+	     X     G6     G1      X :       0.0000  2.0   180.00   1.20   2.00
+	     X     G1     G2      X :       0.0000  2.0   180.00   1.20   2.00
+	     X     G2     G3      X :       0.0000  2.0   180.00   1.20   2.00
+	     X     G3     G9      X :       0.0000  2.0   180.00   1.20   2.00
+	     X     U1     U4      X :       0.0000  2.0   180.00   1.20   2.00
+	     X     U4     U3      X :       0.0000  2.0   180.00   1.20   2.00
+	     X     U3     U2      X :       0.0000  2.0   180.00   1.20   2.00
+	     X     U2     U1      X :       0.0000  2.0   180.00   1.20   2.00
+	     X     C1     C4      X :       0.0000  2.0   180.00   1.20   2.00
+	     X     C4     C3      X :       0.0000  2.0   180.00   1.20   2.00
+	     X     C3     C2      X :       0.0000  2.0   180.00   1.20   2.00
+	     X     C2     C1      X :       0.0000  2.0   180.00   1.20   2.00
+	    CS     C1     C2     C3 :       2.0000  2.0   180.00   1.20   2.00
+	    C4     C1     C2     C3 :       2.0000  2.0   180.00   1.20   2.00
+	    CS     U1     U2     U3 :       2.0000  2.0   180.00   1.20   2.00
+	    U4     U1     U2     U3 :       2.0000  2.0   180.00   1.20   2.00
+	    CS     G9     G7     G6 :       2.0000  2.0   180.00   1.20   2.00
+	    G9     G7     G6     G1 :       2.0000  2.0   180.00   1.20   2.00
+	    CS     A9     A7     A6 :       2.0000  2.0   180.00   1.20   2.00
+	    A9     A7     A6     A1 :       2.0000  2.0   180.00   1.20   2.00
+	    CB     CS     C1     C2 :       2.0000  2.0   180.00   1.20   2.00
+	    CB     CS     U1     U2 :       2.0000  2.0   180.00   1.20   2.00
+	    CB     CS     G9     G3 :       2.0000  2.0   180.00   1.20   2.00
+	    CB     CS     A9     A3 :       2.0000  2.0   180.00   1.20   2.00

From 23dc91d923ecc0474683089ae4c0d8e6d1074cf4 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 28 Jun 2024 14:53:04 -0400
Subject: [PATCH 0798/1492] Add IPOL flag to test saves

---
 test/Test_Strip/ligand.tz2.truncoct.parm7.save   | 5 ++++-
 test/Test_Strip/receptor.tz2.truncoct.parm7.save | 5 ++++-
 test/Test_Strip/strip.pdb.chignolin.parm7.save   | 5 ++++-
 test/Test_Strip/strip.tz2.truncoct.parm7.save    | 5 ++++-
 4 files changed, 16 insertions(+), 4 deletions(-)

diff --git a/test/Test_Strip/ligand.tz2.truncoct.parm7.save b/test/Test_Strip/ligand.tz2.truncoct.parm7.save
index 401565ec6c..256b86de02 100644
--- a/test/Test_Strip/ligand.tz2.truncoct.parm7.save
+++ b/test/Test_Strip/ligand.tz2.truncoct.parm7.save
@@ -1,4 +1,4 @@
-%VERSION  VERSION_STAMP = V0001.000  DATE = 12/11/23 13:48:31                  
+%VERSION  VERSION_STAMP = V0001.000  DATE = 06/28/24 14:52:24                  
 %FLAG TITLE                                                                     
 %FORMAT(20a4)                                                                   
                                                                                 
@@ -131,3 +131,6 @@ modified Bondi radii (mbondi)
 %FLAG SCREEN                                                                    
 %FORMAT(5E16.8)                                                                 
   8.50000000E-01  8.50000000E-01  8.50000000E-01
+%FLAG IPOL                                                                      
+%FORMAT(1I8)                                                                    
+       0
diff --git a/test/Test_Strip/receptor.tz2.truncoct.parm7.save b/test/Test_Strip/receptor.tz2.truncoct.parm7.save
index e068c06d11..8d10763a37 100644
--- a/test/Test_Strip/receptor.tz2.truncoct.parm7.save
+++ b/test/Test_Strip/receptor.tz2.truncoct.parm7.save
@@ -1,4 +1,4 @@
-%VERSION  VERSION_STAMP = V0001.000  DATE = 12/11/23 13:48:31                  
+%VERSION  VERSION_STAMP = V0001.000  DATE = 06/28/24 14:52:24                  
 %FLAG TITLE                                                                     
 %FORMAT(20a4)                                                                   
                                                                                 
@@ -1328,3 +1328,6 @@ modified Bondi radii (mbondi)
   7.20000000E-01  8.50000000E-01  8.50000000E-01  7.20000000E-01  8.50000000E-01
   8.50000000E-01  7.90000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01
   7.20000000E-01  8.50000000E-01  7.90000000E-01  8.50000000E-01  8.50000000E-01
+%FLAG IPOL                                                                      
+%FORMAT(1I8)                                                                    
+       0
diff --git a/test/Test_Strip/strip.pdb.chignolin.parm7.save b/test/Test_Strip/strip.pdb.chignolin.parm7.save
index 3e96e8af45..2aac124aa4 100644
--- a/test/Test_Strip/strip.pdb.chignolin.parm7.save
+++ b/test/Test_Strip/strip.pdb.chignolin.parm7.save
@@ -1,4 +1,4 @@
-%VERSION  VERSION_STAMP = V0001.000  DATE = 12/11/23 13:48:31                  
+%VERSION  VERSION_STAMP = V0001.000  DATE = 06/28/24 14:52:25                  
 %FLAG TITLE                                                                     
 %FORMAT(20a4)                                                                   
 default_name                                                                    
@@ -687,6 +687,9 @@ modified Bondi radii (mbondi)
   7.90000000E-01  7.20000000E-01  7.20000000E-01  7.20000000E-01  7.20000000E-01
   7.20000000E-01  7.20000000E-01  8.50000000E-01  7.20000000E-01  7.20000000E-01
   7.20000000E-01  8.50000000E-01  8.50000000E-01
+%FLAG IPOL                                                                      
+%FORMAT(1I8)                                                                    
+       0
 %FLAG RESIDUE_NUMBER                                                            
 %FORMAT(20I4)                                                                   
    1   2   3   4   5   6   7   8   9  10
diff --git a/test/Test_Strip/strip.tz2.truncoct.parm7.save b/test/Test_Strip/strip.tz2.truncoct.parm7.save
index 1ad98aea00..3e830d3fb2 100644
--- a/test/Test_Strip/strip.tz2.truncoct.parm7.save
+++ b/test/Test_Strip/strip.tz2.truncoct.parm7.save
@@ -1,4 +1,4 @@
-%VERSION  VERSION_STAMP = V0001.000  DATE = 08/06/20 12:51:08                  
+%VERSION  VERSION_STAMP = V0001.000  DATE = 06/28/24 14:52:24                  
 %FLAG TITLE                                                                     
 %FORMAT(20a4)                                                                   
                                                                                 
@@ -1356,6 +1356,9 @@ modified Bondi radii (mbondi)
   8.50000000E-01  7.90000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01
   7.20000000E-01  8.50000000E-01  7.90000000E-01  8.50000000E-01  8.50000000E-01
   8.50000000E-01  8.50000000E-01  8.50000000E-01
+%FLAG IPOL                                                                      
+%FORMAT(1I8)                                                                    
+       0
 %FLAG RESIDUE_NUMBER                                                            
 %FORMAT(20I4)                                                                   
    1   2   3   4   5   6   7   8   9  10  11  12  13  17

From 9849f91050b2859e5ea22e3ccbda46468f22554f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 28 Jun 2024 14:54:02 -0400
Subject: [PATCH 0799/1492] Bonds are always ordered with lower index first in
 mol2 output now

---
 test/Test_ReplicateCell/cell.mol2.save | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/test/Test_ReplicateCell/cell.mol2.save b/test/Test_ReplicateCell/cell.mol2.save
index 53e412a19e..a42f51285a 100644
--- a/test/Test_ReplicateCell/cell.mol2.save
+++ b/test/Test_ReplicateCell/cell.mol2.save
@@ -159,7 +159,7 @@ USER_CHARGES
    51    94    96 1
    52     2     3 1
    53     2     4 1
-   54     2     1 1
+   54     1     2 1
    55    24    25 1
    56    22    23 1
    57    20    21 1
@@ -175,7 +175,7 @@ USER_CHARGES
    67    28    29 1
    68    35    36 1
    69    35    37 1
-   70    35    34 1
+   70    34    35 1
    71    57    58 1
    72    55    56 1
    73    53    54 1
@@ -191,7 +191,7 @@ USER_CHARGES
    83    61    62 1
    84    68    69 1
    85    68    70 1
-   86    68    67 1
+   86    67    68 1
    87    90    91 1
    88    88    89 1
    89    86    87 1

From 8aab318264f532ad52aca44be35db57da78578bb Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 1 Jul 2024 12:38:28 -0400
Subject: [PATCH 0800/1492] Update for new parameter index ordering, box
 dimensions.

---
 test/Test_CombineCrd/combinedParm.parm7.save | 1577 +++++++++---------
 1 file changed, 790 insertions(+), 787 deletions(-)

diff --git a/test/Test_CombineCrd/combinedParm.parm7.save b/test/Test_CombineCrd/combinedParm.parm7.save
index bd4a9fa073..7634165fd1 100644
--- a/test/Test_CombineCrd/combinedParm.parm7.save
+++ b/test/Test_CombineCrd/combinedParm.parm7.save
@@ -1,4 +1,4 @@
-%VERSION  VERSION_STAMP = V0001.000  DATE = 12/13/23 10:11:18                  
+%VERSION  VERSION_STAMP = V0001.000  DATE = 07/01/24 12:33:32                  
 %FLAG TITLE                                                                     
 %FORMAT(20a4)                                                                   
 combinedParm                                                                    
@@ -237,88 +237,88 @@ SER TRP THR TRP GLU ASN GLY LYS TRP THR TRP LYS NHE TCS
      172     196     218     221
 %FLAG BOND_FORCE_CONSTANT                                                       
 %FORMAT(5E16.8)                                                                 
-  5.70000000E+02  4.90000000E+02  3.20000000E+02  3.10000000E+02  3.17000000E+02
+  5.70000000E+02  4.90000000E+02  5.53000000E+02  3.40000000E+02  3.20000000E+02
+  3.40000000E+02  3.10000000E+02  3.17000000E+02  4.34000000E+02  3.67000000E+02
   3.67000000E+02  4.69000000E+02  4.69000000E+02  4.69000000E+02  4.47000000E+02
-  4.28000000E+02  4.27000000E+02  5.46000000E+02  3.88000000E+02  3.17000000E+02
-  3.37000000E+02  3.10000000E+02  6.56000000E+02  3.17000000E+02  3.67000000E+02
-  4.78400000E+02  3.22800000E+02  3.72400000E+02  3.86100000E+02  5.53000000E+02
-  3.40000000E+02  3.40000000E+02  4.34000000E+02  3.67000000E+02  4.34000000E+02
-  3.67000000E+02  3.40000000E+02  3.40000000E+02  4.34000000E+02  3.40000000E+02
-  3.44300000E+02  3.69600000E+02
+  4.34000000E+02  4.28000000E+02  3.67000000E+02  4.27000000E+02  5.46000000E+02
+  3.88000000E+02  3.40000000E+02  3.17000000E+02  3.40000000E+02  4.34000000E+02
+  3.37000000E+02  3.10000000E+02  6.56000000E+02  3.17000000E+02  3.40000000E+02
+  3.67000000E+02  3.44300000E+02  4.78400000E+02  3.22800000E+02  3.69600000E+02
+  3.72400000E+02  3.86100000E+02
 %FLAG BOND_EQUIL_VALUE                                                          
 %FORMAT(5E16.8)                                                                 
-  1.22900000E+00  1.33500000E+00  1.41000000E+00  1.52600000E+00  1.52200000E+00
-  1.47100000E+00  1.40400000E+00  1.40000000E+00  1.40000000E+00  1.41900000E+00
-  1.38000000E+00  1.38100000E+00  1.35200000E+00  1.45900000E+00  1.49500000E+00
-  1.44900000E+00  1.52600000E+00  1.25000000E+00  1.52200000E+00  1.47100000E+00
-  1.38700000E+00  1.72900000E+00  1.37300000E+00  1.36200000E+00  9.60000000E-01
-  1.09000000E+00  1.09000000E+00  1.01000000E+00  1.08000000E+00  1.01000000E+00
-  1.08000000E+00  1.09000000E+00  1.09000000E+00  1.01000000E+00  1.09000000E+00
-  1.08700000E+00  9.74000000E-01
+  1.22900000E+00  1.33500000E+00  9.60000000E-01  1.09000000E+00  1.41000000E+00
+  1.09000000E+00  1.52600000E+00  1.52200000E+00  1.01000000E+00  1.47100000E+00
+  1.08000000E+00  1.40400000E+00  1.40000000E+00  1.40000000E+00  1.41900000E+00
+  1.01000000E+00  1.38000000E+00  1.08000000E+00  1.38100000E+00  1.35200000E+00
+  1.45900000E+00  1.09000000E+00  1.49500000E+00  1.09000000E+00  1.01000000E+00
+  1.44900000E+00  1.52600000E+00  1.25000000E+00  1.52200000E+00  1.09000000E+00
+  1.47100000E+00  1.08700000E+00  1.38700000E+00  1.72900000E+00  9.74000000E-01
+  1.37300000E+00  1.36200000E+00
 %FLAG ANGLE_FORCE_CONSTANT                                                      
 %FORMAT(5E16.8)                                                                 
-  8.00000000E+01  5.00000000E+01  6.30000000E+01  5.00000000E+01  8.00000000E+01
-  7.00000000E+01  8.00000000E+01  8.00000000E+01  6.30000000E+01  6.30000000E+01
-  6.30000000E+01  6.30000000E+01  6.30000000E+01  7.00000000E+01  7.00000000E+01
-  6.30000000E+01  7.00000000E+01  7.00000000E+01  6.30000000E+01  6.30000000E+01
-  7.00000000E+01  7.00000000E+01  6.30000000E+01  8.00000000E+01  6.30000000E+01
-  5.00000000E+01  4.00000000E+01  8.00000000E+01  7.00000000E+01  6.30000000E+01
-  8.00000000E+01  7.00000000E+01  6.30000000E+01  8.00000000E+01  4.00000000E+01
-  6.29200000E+01  6.71800000E+01  6.97900000E+01  6.98500000E+01  6.33100000E+01
-  5.00000000E+01  5.00000000E+01  3.50000000E+01  5.50000000E+01  5.00000000E+01
-  5.00000000E+01  5.00000000E+01  5.00000000E+01  3.50000000E+01  5.00000000E+01
-  5.00000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01
-  5.00000000E+01  5.00000000E+01  5.00000000E+01  3.50000000E+01  5.00000000E+01
-  5.00000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01
-  5.00000000E+01  5.00000000E+01  3.50000000E+01  3.50000000E+01  5.00000000E+01
-  3.50000000E+01  5.00000000E+01  5.00000000E+01  4.84600000E+01  4.88500000E+01
+  8.00000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01  3.50000000E+01
+  6.30000000E+01  5.50000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01
+  5.00000000E+01  8.00000000E+01  7.00000000E+01  5.00000000E+01  3.50000000E+01
+  5.00000000E+01  8.00000000E+01  8.00000000E+01  5.00000000E+01  5.00000000E+01
+  6.30000000E+01  6.30000000E+01  6.30000000E+01  5.00000000E+01  6.30000000E+01
+  6.30000000E+01  5.00000000E+01  7.00000000E+01  7.00000000E+01  5.00000000E+01
+  6.30000000E+01  5.00000000E+01  7.00000000E+01  5.00000000E+01  7.00000000E+01
+  6.30000000E+01  6.30000000E+01  5.00000000E+01  3.50000000E+01  7.00000000E+01
+  7.00000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01  6.30000000E+01
+  5.00000000E+01  5.00000000E+01  8.00000000E+01  6.30000000E+01  5.00000000E+01
+  5.00000000E+01  5.00000000E+01  4.00000000E+01  8.00000000E+01  5.00000000E+01
+  7.00000000E+01  6.30000000E+01  3.50000000E+01  8.00000000E+01  7.00000000E+01
+  6.30000000E+01  3.50000000E+01  5.00000000E+01  3.50000000E+01  5.00000000E+01
+  5.00000000E+01  8.00000000E+01  4.00000000E+01  4.84600000E+01  6.29200000E+01
+  6.71800000E+01  6.97900000E+01  6.98500000E+01  4.88500000E+01  6.33100000E+01
 %FLAG ANGLE_EQUIL_VALUE                                                         
 %FORMAT(5E16.8)                                                                 
-  2.14501057E+00  2.12755727E+00  1.93906163E+00  1.91113635E+00  2.10137732E+00
-  2.03505478E+00  1.94080696E+00  1.94080696E+00  2.09439600E+00  2.09439600E+00
-  2.14151991E+00  2.09439600E+00  2.02807346E+00  2.31779824E+00  1.82212452E+00
-  1.85703112E+00  1.94778828E+00  1.89717371E+00  1.89891904E+00  2.35445017E+00
-  2.18166250E+00  2.24449438E+00  2.01760148E+00  1.91462701E+00  1.92160833E+00
-  1.91113635E+00  1.91113635E+00  2.19911580E+00  2.04203610E+00  1.93906163E+00
-  2.10137732E+00  2.03505478E+00  1.93906163E+00  1.94080696E+00  1.91113635E+00
-  2.08392402E+00  2.09387240E+00  2.08043336E+00  2.09334880E+00  2.09352334E+00
-  2.09439600E+00  1.91113635E+00  1.91113635E+00  1.89368305E+00  1.91113635E+00
-  1.91113635E+00  1.91113635E+00  1.91113635E+00  1.91113635E+00  1.91113635E+00
-  2.09439600E+00  2.09439600E+00  2.09439600E+00  2.14850123E+00  2.09439600E+00
-  2.09439600E+00  2.09439600E+00  1.91113635E+00  1.91113635E+00  1.91113635E+00
-  1.91113635E+00  1.91113635E+00  2.06018753E+00  1.91113635E+00  1.91113635E+00
-  1.91113635E+00  1.91113635E+00  2.09439600E+00  1.91113635E+00  1.91113635E+00
-  1.91113635E+00  1.91113635E+00  1.91113635E+00  2.09457053E+00  1.91061275E+00
+  2.14501057E+00  2.09439600E+00  2.12755727E+00  1.91113635E+00  1.91113635E+00
+  1.93906163E+00  1.89368305E+00  1.91113635E+00  1.91113635E+00  1.91113635E+00
+  1.91113635E+00  2.10137732E+00  2.03505478E+00  1.91113635E+00  1.91113635E+00
+  1.91113635E+00  1.94080696E+00  1.94080696E+00  2.09439600E+00  2.09439600E+00
+  2.09439600E+00  2.09439600E+00  2.14151991E+00  2.09439600E+00  2.09439600E+00
+  2.02807346E+00  2.14850123E+00  2.31779824E+00  1.82212452E+00  2.09439600E+00
+  1.85703112E+00  2.09439600E+00  1.94778828E+00  2.09439600E+00  1.89717371E+00
+  1.89891904E+00  2.35445017E+00  1.91113635E+00  1.91113635E+00  2.18166250E+00
+  2.24449438E+00  1.91113635E+00  1.91113635E+00  1.91113635E+00  2.01760148E+00
+  2.06018753E+00  1.91113635E+00  1.91462701E+00  1.92160833E+00  1.91113635E+00
+  1.91113635E+00  1.91113635E+00  1.91113635E+00  2.19911580E+00  1.91113635E+00
+  2.04203610E+00  1.93906163E+00  2.09439600E+00  2.10137732E+00  2.03505478E+00
+  1.93906163E+00  1.91113635E+00  1.91113635E+00  1.91113635E+00  1.91113635E+00
+  1.91113635E+00  1.94080696E+00  1.91113635E+00  2.09457053E+00  2.08392402E+00
+  2.09387240E+00  2.08043336E+00  2.09334880E+00  1.91061275E+00  2.09352334E+00
 %FLAG DIHEDRAL_FORCE_CONSTANT                                                   
 %FORMAT(5E16.8)                                                                 
-  2.50000000E+00  2.00000000E+00  2.00000000E+00  4.00000000E-01  0.00000000E+00
-  0.00000000E+00  2.70000000E-01  4.20000000E-01  1.55555556E-01  0.00000000E+00
-  2.00000000E-01  2.00000000E-01  3.62500000E+00  3.00000000E+00  3.50000000E+00
-  6.52500000E+00  1.67500000E+00  1.52500000E+00  1.50000000E+00  4.50000000E-01
-  1.58000000E+00  5.50000000E-01  2.00000000E-01  2.50000000E-01  1.80000000E-01
-  1.05000000E+01  1.10000000E+00  9.00000000E-01  1.10000000E+00  1.66666667E-01
-  2.50000000E-01  1.60000000E-01  8.00000000E-01  8.00000000E-02  0.00000000E+00
-  1.50000000E-01  1.00000000E+00
+  2.00000000E+00  2.50000000E+00  0.00000000E+00  2.00000000E+00  4.00000000E-01
+  0.00000000E+00  0.00000000E+00  2.70000000E-01  4.20000000E-01  1.55555556E-01
+  1.66666667E-01  2.00000000E-01  2.00000000E-01  2.50000000E-01  1.60000000E-01
+  3.62500000E+00  3.00000000E+00  3.50000000E+00  1.52500000E+00  6.52500000E+00
+  1.50000000E+00  1.67500000E+00  8.00000000E-01  8.00000000E-02  4.50000000E-01
+  1.58000000E+00  5.50000000E-01  0.00000000E+00  1.50000000E-01  2.00000000E-01
+  2.50000000E-01  1.80000000E-01  1.05000000E+01  1.10000000E+00  1.00000000E+00
+  9.00000000E-01  1.10000000E+00
 %FLAG DIHEDRAL_PERIODICITY                                                      
 %FORMAT(5E16.8)                                                                 
-  2.00000000E+00  1.00000000E+00  2.00000000E+00  3.00000000E+00  4.00000000E+00
-  1.00000000E+00  2.00000000E+00  3.00000000E+00  3.00000000E+00  2.00000000E+00
-  1.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
-  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  1.00000000E+00
-  2.00000000E+00  3.00000000E+00  1.00000000E+00  2.00000000E+00  3.00000000E+00
-  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  3.00000000E+00
-  1.00000000E+00  3.00000000E+00  1.00000000E+00  3.00000000E+00  3.00000000E+00
-  3.00000000E+00  2.00000000E+00
+  1.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  3.00000000E+00
+  4.00000000E+00  1.00000000E+00  2.00000000E+00  3.00000000E+00  3.00000000E+00
+  3.00000000E+00  1.00000000E+00  2.00000000E+00  1.00000000E+00  3.00000000E+00
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  2.00000000E+00  2.00000000E+00  1.00000000E+00  3.00000000E+00  1.00000000E+00
+  2.00000000E+00  3.00000000E+00  3.00000000E+00  3.00000000E+00  1.00000000E+00
+  2.00000000E+00  3.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  2.00000000E+00  2.00000000E+00
 %FLAG DIHEDRAL_PHASE                                                            
 %FORMAT(5E16.8)                                                                 
-  3.14159400E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  3.14159400E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
   0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
-  0.00000000E+00  0.00000000E+00  3.14159400E+00  3.14159400E+00  3.14159400E+00
   3.14159400E+00  3.14159400E+00  3.14159400E+00  3.14159400E+00  3.14159400E+00
-  3.14159400E+00  3.14159400E+00  3.14159400E+00  3.14159400E+00  0.00000000E+00
-  3.14159400E+00  3.14159400E+00  3.14159400E+00  3.14159400E+00  0.00000000E+00
-  0.00000000E+00  0.00000000E+00  0.00000000E+00  3.14159400E+00  0.00000000E+00
-  0.00000000E+00  3.14159400E+00
+  3.14159400E+00  3.14159400E+00  0.00000000E+00  3.14159400E+00  3.14159400E+00
+  3.14159400E+00  3.14159400E+00  0.00000000E+00  0.00000000E+00  3.14159400E+00
+  3.14159400E+00  0.00000000E+00  3.14159400E+00  3.14159400E+00  3.14159400E+00
+  3.14159400E+00  3.14159400E+00
 %FLAG SCEE_SCALE_FACTOR                                                         
 %FORMAT(5E16.8)                                                                 
   1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00
@@ -326,9 +326,9 @@ SER TRP THR TRP GLU ASN GLY LYS TRP THR TRP LYS NHE TCS
   1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00
   1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00
   1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00
-  0.00000000E+00  0.00000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00
   1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00
-  1.20000000E+00  0.00000000E+00
+  1.20000000E+00  1.20000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  1.20000000E+00  1.20000000E+00
 %FLAG SCNB_SCALE_FACTOR                                                         
 %FORMAT(5E16.8)                                                                 
   2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
@@ -336,9 +336,9 @@ SER TRP THR TRP GLU ASN GLY LYS TRP THR TRP LYS NHE TCS
   2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
   2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
   2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
-  0.00000000E+00  0.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
   2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
-  2.00000000E+00  0.00000000E+00
+  2.00000000E+00  2.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  2.00000000E+00  2.00000000E+00
 %FLAG SOLTY                                                                     
 %FORMAT(5E16.8)                                                                 
   0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
@@ -395,730 +395,730 @@ SER TRP THR TRP GLU ASN GLY LYS TRP THR TRP LYS NHE TCS
   2.11915736E+02  1.80470661E+02  1.97211104E+02  9.73951183E+02  1.85348706E+03
 %FLAG BONDS_INC_HYDROGEN                                                        
 %FORMAT(10I8)                                                                   
-      27      30      25      18      21      26      18      24      26      12
-      15      27       0       3      28       0       6      28       0       9
-      28      96      99      29      90      93      29      84      87      29
-      78      81      29      69      72      30      63      66      31      51
-      54      32      51      57      32      45      48      33      39      42
-      34     141     144      25     129     132      32     129     135      32
-     129     138      32     123     126      26     117     120      33     111
-     114      34     210     213      29     204     207      29     198     201
-      29     192     195      29     183     186      30     177     180      31
-     165     168      32     165     171      32     159     162      33     153
-     156      34     246     249      32     246     252      32     237     240
-      32     237     243      32     231     234      33     225     228      34
-     297     300      34     297     303      34     282     285      32     282
-     288      32     276     279      33     270     273      34     318     321
-      33     318     324      33     312     315      34     381     384      28
-     381     387      28     381     390      28     372     375      35     372
-     378      35     363     366      32     363     369      32     354     357
-      32     354     360      32     345     348      32     345     351      32
-     339     342      33     333     336      34     456     459      29     450
-     453      29     444     447      29     438     441      29     429     432
-      30     423     426      31     411     414      32     411     417      32
-     405     408      33     399     402      34     501     504      25     489
-     492      32     489     495      32     489     498      32     483     486
-      26     477     480      33     471     474      34     570     573      29
-     564     567      29     558     561      29     552     555      29     543
-     546      30     537     540      31     525     528      32     525     531
-      32     519     522      33     513     516      34     633     636      28
-     633     639      28     633     642      28     624     627      35     624
-     630      35     615     618      32     615     621      32     606     609
-      32     606     612      32     597     600      32     597     603      32
-     591     594      33     585     588      34     651     654      34     651
-     657      34     699     729      36     696     726      36     690     723
-      36     681     720      37     675     717      36     672     714      36
-     666     711      36
+      27      30       3      18      21       4      18      24       4      12
+      15       6       0       3       9       0       6       9       0       9
+       9      96      99      11      90      93      11      84      87      11
+      78      81      11      69      72      16      63      66      18      51
+      54      22      51      57      22      45      48      24      39      42
+      25     141     144       3     129     132      22     129     135      22
+     129     138      22     123     126       4     117     120      24     111
+     114      25     210     213      11     204     207      11     198     201
+      11     192     195      11     183     186      16     177     180      18
+     165     168      22     165     171      22     159     162      24     153
+     156      25     246     249      22     246     252      22     237     240
+      22     237     243      22     231     234      24     225     228      25
+     297     300      25     297     303      25     282     285      22     282
+     288      22     276     279      24     270     273      25     318     321
+      24     318     324      24     312     315      25     381     384       9
+     381     387       9     381     390       9     372     375      30     372
+     378      30     363     366      22     363     369      22     354     357
+      22     354     360      22     345     348      22     345     351      22
+     339     342      24     333     336      25     456     459      11     450
+     453      11     444     447      11     438     441      11     429     432
+      16     423     426      18     411     414      22     411     417      22
+     405     408      24     399     402      25     501     504       3     489
+     492      22     489     495      22     489     498      22     483     486
+       4     477     480      24     471     474      25     570     573      11
+     564     567      11     558     561      11     552     555      11     543
+     546      16     537     540      18     525     528      22     525     531
+      22     519     522      24     513     516      25     633     636       9
+     633     639       9     633     642       9     624     627      30     624
+     630      30     615     618      22     615     621      22     606     609
+      22     606     612      22     597     600      22     597     603      22
+     591     594      24     585     588      25     651     654      25     651
+     657      25     699     729      32     696     726      32     690     723
+      32     681     720      35     675     717      32     672     714      32
+     666     711      32
 %FLAG BONDS_WITHOUT_HYDROGEN                                                    
 %FORMAT(10I8)                                                                   
-      33      36       1      33      39       2      18      27       3      12
-      18       4      12      33       5       0      12       6     105     108
-       1     105     111       2      96     102       7      90      96       8
-      84      90       8      78      84       8      75      78       9      75
-     102      10      69      75      11      63      69      12      60      63
-      13      60     102      14      51      60      15      45      51       4
-      45     105       5      39      45      16     147     150       1     147
-     153       2     123     129      17     123     141       3     117     123
-       4     117     147       5     111     117      16     219     222       1
-     219     225       2     210     216       7     204     210       8     198
-     204       8     192     198       8     189     192       9     189     216
-      10     183     189      11     177     183      12     174     177      13
-     174     216      14     165     174      15     159     165       4     159
-     219       5     153     159      16     264     267       1     264     270
-       2     255     258      18     255     261      18     246     255      19
-     237     246      17     231     237       4     231     264       5     225
-     231      16     306     309       1     306     312       2     291     294
-       1     291     297       2     282     291      19     276     282       4
-     276     306       5     270     276      16     327     330       1     327
-     333       2     318     327       5     312     318      16     393     396
-       1     393     399       2     372     381      20     363     372      17
-     354     363      17     345     354      17     339     345       4     339
-     393       5     333     339      16     465     468       1     465     471
-       2     456     462       7     450     456       8     444     450       8
-     438     444       8     435     438       9     435     462      10     429
-     435      11     423     429      12     420     423      13     420     462
-      14     411     420      15     405     411       4     405     465       5
-     399     405      16     507     510       1     507     513       2     483
-     489      17     483     501       3     477     483       4     477     507
-       5     471     477      16     579     582       1     579     585       2
-     570     576       7     564     570       8     558     564       8     552
-     558       8     549     552       9     549     576      10     543     549
-      11     537     543      12     534     537      13     534     576      14
-     525     534      15     519     525       4     519     579       5     513
-     519      16     645     648       1     645     651       2     624     633
-      20     615     624      17     606     615      17     597     606      17
-     591     597       4     591     645       5     585     591      16     696
-     699      21     693     696      21     693     705      22     690     693
-      21     687     690      21     687     702      22     684     687      21
-     684     699      21     678     684      23     672     675      21     669
-     672      21     669     708      22     666     669      21     663     666
-      21     663     681      24     660     663      21     660     675      21
-     660     678      23
+      33      36       1      33      39       2      18      27       5      12
+      18       7      12      33       8       0      12      10     105     108
+       1     105     111       2      96     102      12      90      96      13
+      84      90      13      78      84      13      75      78      14      75
+     102      15      69      75      17      63      69      19      60      63
+      20      60     102      21      51      60      23      45      51       7
+      45     105       8      39      45      26     147     150       1     147
+     153       2     123     129      27     123     141       5     117     123
+       7     117     147       8     111     117      26     219     222       1
+     219     225       2     210     216      12     204     210      13     198
+     204      13     192     198      13     189     192      14     189     216
+      15     183     189      17     177     183      19     174     177      20
+     174     216      21     165     174      23     159     165       7     159
+     219       8     153     159      26     264     267       1     264     270
+       2     255     258      28     255     261      28     246     255      29
+     237     246      27     231     237       7     231     264       8     225
+     231      26     306     309       1     306     312       2     291     294
+       1     291     297       2     282     291      29     276     282       7
+     276     306       8     270     276      26     327     330       1     327
+     333       2     318     327       8     312     318      26     393     396
+       1     393     399       2     372     381      31     363     372      27
+     354     363      27     345     354      27     339     345       7     339
+     393       8     333     339      26     465     468       1     465     471
+       2     456     462      12     450     456      13     444     450      13
+     438     444      13     435     438      14     435     462      15     429
+     435      17     423     429      19     420     423      20     420     462
+      21     411     420      23     405     411       7     405     465       8
+     399     405      26     507     510       1     507     513       2     483
+     489      27     483     501       5     477     483       7     477     507
+       8     471     477      26     579     582       1     579     585       2
+     570     576      12     564     570      13     558     564      13     552
+     558      13     549     552      14     549     576      15     543     549
+      17     537     543      19     534     537      20     534     576      21
+     525     534      23     519     525       7     519     579       8     513
+     519      26     645     648       1     645     651       2     624     633
+      31     615     624      27     606     615      27     597     606      27
+     591     597       7     591     645       8     585     591      26     696
+     699      33     693     696      33     693     705      34     690     693
+      33     687     690      33     687     702      34     684     687      33
+     684     699      33     678     684      36     672     675      33     669
+     672      33     669     708      34     666     669      33     663     666
+      33     663     681      37     660     663      33     660     675      33
+     660     678      36
 %FLAG ANGLES_INC_HYDROGEN                                                       
 %FORMAT(10I8)                                                                   
-      33      39      42      41      24      18      27      42      21      18
-      24      43      21      18      27      42      18      27      30      44
-      15      12      18      45      15      12      33      46      12      18
-      21      47      12      18      24      47       9       0      12      48
-       6       0       9      49       6       0      12      48       3       0
-       6      49       3       0       9      49       3       0      12      48
-       0      12      15      50     105     111     114      41      99      96
-     102      51      93      90      96      52      90      96      99      52
-      87      84      90      52      84      90      93      52      81      78
-      84      52      78      84      87      52      75      78      81      53
-      72      69      75      54      66      63      69      55      63      69
-      72      56      60      63      66      57      57      51      60      58
-      54      51      57      59      54      51      60      58      48      45
-      51      60      48      45     105      61      45      51      54      62
-      45      51      57      62      42      39      45      63      39      45
-      48      64     147     153     156      41     135     129     138      59
-     132     129     135      59     132     129     138      59     126     123
-     129      65     126     123     141      42     123     129     132      66
-     123     129     135      66     123     129     138      66     123     141
-     144      44     120     117     123      60     120     117     147      61
-     117     123     126      47     114     111     117      63     111     117
-     120      64     219     225     228      41     213     210     216      51
-     207     204     210      52     204     210     213      52     201     198
-     204      52     198     204     207      52     195     192     198      52
-     192     198     201      52     189     192     195      53     186     183
-     189      54     180     177     183      55     177     183     186      56
-     174     177     180      57     171     165     174      58     168     165
-     171      59     168     165     174      58     162     159     165      60
-     162     159     219      61     159     165     168      62     159     165
-     171      62     156     153     159      63     153     159     162      64
-     264     270     273      41     252     246     255      67     249     246
-     252      59     249     246     255      67     243     237     246      66
-     240     237     243      59     240     237     246      66     237     246
-     249      66     237     246     252      66     234     231     237      60
-     234     231     264      61     231     237     240      62     231     237
-     243      62     228     225     231      63     225     231     234      64
-     306     312     315      41     300     297     303      68     291     297
-     300      41     291     297     303      41     288     282     291      67
-     285     282     288      59     285     282     291      67     279     276
-     282      60     279     276     306      61     276     282     285      62
-     276     282     288      62     273     270     276      63     270     276
-     279      64     327     333     336      41     324     318     327      61
-     321     318     324      69     321     318     327      61     315     312
-     318      63     312     318     321      64     312     318     324      64
-     393     399     402      41     387     381     390      49     384     381
-     387      49     384     381     390      49     378     372     381      70
-     375     372     378      71     375     372     381      70     372     381
-     384      72     372     381     387      72     372     381     390      72
-     369     363     372      66     366     363     369      59     366     363
-     372      66     363     372     375      73     363     372     378      73
-     360     354     363      66     357     354     360      59     357     354
-     363      66     354     363     366      66     354     363     369      66
-     351     345     354      66     348     345     351      59     348     345
-     354      66     345     354     357      66     345     354     360      66
-     342     339     345      60     342     339     393      61     339     345
-     348      62     339     345     351      62     336     333     339      63
-     333     339     342      64     465     471     474      41     459     456
-     462      51     453     450     456      52     450     456     459      52
-     447     444     450      52     444     450     453      52     441     438
-     444      52     438     444     447      52     435     438     441      53
-     432     429     435      54     426     423     429      55     423     429
-     432      56     420     423     426      57     417     411     420      58
-     414     411     417      59     414     411     420      58     408     405
-     411      60     408     405     465      61     405     411     414      62
-     405     411     417      62     402     399     405      63     399     405
-     408      64     507     513     516      41     495     489     498      59
-     492     489     495      59     492     489     498      59     486     483
-     489      65     486     483     501      42     483     489     492      66
-     483     489     495      66     483     489     498      66     483     501
-     504      44     480     477     483      60     480     477     507      61
-     477     483     486      47     474     471     477      63     471     477
-     480      64     579     585     588      41     573     570     576      51
-     567     564     570      52     564     570     573      52     561     558
-     564      52     558     564     567      52     555     552     558      52
-     552     558     561      52     549     552     555      53     546     543
-     549      54     540     537     543      55     537     543     546      56
-     534     537     540      57     531     525     534      58     528     525
-     531      59     528     525     534      58     522     519     525      60
-     522     519     579      61     519     525     528      62     519     525
-     531      62     516     513     519      63     513     519     522      64
-     645     651     654      41     645     651     657      41     639     633
-     642      49     636     633     639      49     636     633     642      49
-     630     624     633      70     627     624     630      71     627     624
-     633      70     624     633     636      72     624     633     639      72
-     624     633     642      72     621     615     624      66     618     615
-     621      59     618     615     624      66     615     624     627      73
-     615     624     630      73     612     606     615      66     609     606
-     612      59     609     606     615      66     606     615     618      66
-     606     615     621      66     603     597     606      66     600     597
-     603      59     600     597     606      66     597     606     609      66
-     597     606     612      66     594     591     597      60     594     591
-     645      61     591     597     600      62     591     597     603      62
-     588     585     591      63     585     591     594      64     654     651
-     657      68     699     696     726      74     696     699     729      74
-     693     690     723      74     693     696     726      74     687     690
-     723      74     684     699     729      74     675     672     714      74
-     672     675     717      74     669     666     711      74     669     672
-     714      74     663     666     711      74     663     681     720      75
-     660     675     717      74
+      33      39      42       2      24      18      27       4      21      18
+      24       5      21      18      27       4      18      27      30       7
+      15      12      18       8      15      12      33       9      12      18
+      21      10      12      18      24      10       9       0      12      14
+       6       0       9      15       6       0      12      14       3       0
+       6      15       3       0       9      15       3       0      12      14
+       0      12      15      16     105     111     114       2      99      96
+     102      19      93      90      96      20      90      96      99      20
+      87      84      90      20      84      90      93      20      81      78
+      84      20      78      84      87      20      75      78      81      24
+      72      69      75      27      66      63      69      30      63      69
+      72      32      60      63      66      34      57      51      60      38
+      54      51      57      39      54      51      60      38      48      45
+      51      42      48      45     105      43      45      51      54      44
+      45      51      57      44      42      39      45      46      39      45
+      48      47     147     153     156       2     135     129     138      39
+     132     129     135      39     132     129     138      39     126     123
+     129      51     126     123     141       4     123     129     132      52
+     123     129     135      52     123     129     138      52     123     141
+     144       7     120     117     123      42     120     117     147      43
+     117     123     126      10     114     111     117      46     111     117
+     120      47     219     225     228       2     213     210     216      19
+     207     204     210      20     204     210     213      20     201     198
+     204      20     198     204     207      20     195     192     198      20
+     192     198     201      20     189     192     195      24     186     183
+     189      27     180     177     183      30     177     183     186      32
+     174     177     180      34     171     165     174      38     168     165
+     171      39     168     165     174      38     162     159     165      42
+     162     159     219      43     159     165     168      44     159     165
+     171      44     156     153     159      46     153     159     162      47
+     264     270     273       2     252     246     255      55     249     246
+     252      39     249     246     255      55     243     237     246      52
+     240     237     243      39     240     237     246      52     237     246
+     249      52     237     246     252      52     234     231     237      42
+     234     231     264      43     231     237     240      44     231     237
+     243      44     228     225     231      46     225     231     234      47
+     306     312     315       2     300     297     303      58     291     297
+     300       2     291     297     303       2     288     282     291      55
+     285     282     288      39     285     282     291      55     279     276
+     282      42     279     276     306      43     276     282     285      44
+     276     282     288      44     273     270     276      46     270     276
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 %FLAG ANGLES_WITHOUT_HYDROGEN                                                   
 %FORMAT(10I8)                                                                   
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 %FLAG DIHEDRALS_INC_HYDROGEN                                                    
 %FORMAT(10I8)                                                                   
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 %FLAG DIHEDRALS_WITHOUT_HYDROGEN                                                
 %FORMAT(10I8)                                                                   
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+     312     318    -327     333      27     312     318    -327     333       6
+     396     393     399     405       2     393     399     405     411       1
+     393     399    -405     411       4     393     399    -405     411       5
+     393     399    -405     411       6     393     399     405     465       7
+     393     399    -405     465       8     393     399    -405     465       9
+     393     399    -405     465       6     354     345     339     393      10
+     354     363     372     381      10     345     339     393     396       3
+     345     339     393     399      12     345     339    -393     399      13
+     345     339    -393     399       5     345     339    -393     399       6
+     345     354     363     372      30     345     354    -363     372      31
+     345     354    -363     372      32     339     345     354     363      30
+     339     345    -354     363      31     339     345    -354     363      32
+     339     393     399     405       2     333     339     345     354      10
+     333     339     393     396       3     333     339     393     399      25
+     333     339    -393     399      26     333     339    -393     399      27
+     333     339    -393     399       6     468     465     471     477       2
+     465     471     477     483       1     465     471    -477     483       4
+     465     471    -477     483       5     465     471    -477     483       6
+     465     471     477     507       7     465     471    -477     507       8
+     465     471    -477     507       9     465     471    -477     507       6
+     444     438     435     462      16     444     450    -456     462      16
+     438     435     462     456      17     438     444    -450     456      16
+     435     438     444     450      16     435     462    -456     450      18
+     429     423    -420     462      20     429     435     438     444      16
+     429     435     462     456      17     423     420    -462     435      22
+     423     420     462     456      22     423     429     435     438      19
+     423     429    -435     462      19     420     411     405     465      10
+     420     423    -429     435      21     420     462    -435     429      17
+     420     462     435     438      17     420     462     456     450      18
+     411     405     465     468       3     411     405     465     471      12
+     411     405    -465     471      13     411     405    -465     471       5
+     411     405    -465     471       6     411     420     423     429      20
+     411     420     462     435      22     411     420     462     456      22
+     405     411     420     423       3     405     411     420     462       3
+     405     465     471     477       2     399     405     411     420      10
+     399     405     465     468       3     399     405     465     471      25
+     399     405    -465     471      26     399     405    -465     471      27
+     399     405    -465     471       6     510     507     513     519       2
+     507     513     519     525       1     507     513    -519     525       4
+     507     513    -519     525       5     507     513    -519     525       6
+     507     513     519     579       7     507     513    -519     579       8
+     507     513    -519     579       9     507     513    -519     579       6
+     501     483     477     507      10     489     483     477     507      10
+     483     477     507     510       3     483     477     507     513      12
+     483     477    -507     513      13     483     477    -507     513       5
+     483     477    -507     513       6     477     507     513     519       2
+     471     477     483     489      10     471     477     483     501      10
+     471     477     507     510       3     471     477     507     513      25
+     471     477    -507     513      26     471     477    -507     513      27
+     471     477    -507     513       6     582     579     585     591       2
+     579     585     591     597       1     579     585    -591     597       4
+     579     585    -591     597       5     579     585    -591     597       6
+     579     585     591     645       7     579     585    -591     645       8
+     579     585    -591     645       9     579     585    -591     645       6
+     558     552     549     576      16     558     564    -570     576      16
+     552     549     576     570      17     552     558    -564     570      16
+     549     552     558     564      16     549     576    -570     564      18
+     543     537    -534     576      20     543     549     552     558      16
+     543     549     576     570      17     537     534    -576     549      22
+     537     534     576     570      22     537     543     549     552      19
+     537     543    -549     576      19     534     525     519     579      10
+     534     537    -543     549      21     534     576    -549     543      17
+     534     576     549     552      17     534     576     570     564      18
+     525     519     579     582       3     525     519     579     585      12
+     525     519    -579     585      13     525     519    -579     585       5
+     525     519    -579     585       6     525     534     537     543      20
+     525     534     576     549      22     525     534     576     570      22
+     519     525     534     537       3     519     525     534     576       3
+     519     579     585     591       2     513     519     525     534      10
+     513     519     579     582       3     513     519     579     585      25
+     513     519    -579     585      26     513     519    -579     585      27
+     513     519    -579     585       6     606     597     591     645      10
+     606     615     624     633      10     597     591     645     648       3
+     597     591     645     651      12     597     591    -645     651      13
+     597     591    -645     651       5     597     591    -645     651       6
+     597     606     615     624      30     597     606    -615     624      31
+     597     606    -615     624      32     591     597     606     615      30
+     591     597    -606     615      31     591     597    -606     615      32
+     585     591     597     606      10     585     591     645     648       3
+     585     591     645     651      25     585     591    -645     651      26
+     585     591    -645     651      27     585     591    -645     651       6
+     699     684     687     702      16     699     696     693     705      16
+     693     690     687     702      16     690     687     684     699      16
+     690     693    -696     699      16     687     684     699     696      16
+     687     690    -693     696      16     687     690     693     705      16
+     684     687     690     693      16     684     699    -696     693      16
+     678     660     663     681      16     678     684     687     690      16
+     678     684     687     702      16     678     684     699     696      16
+     675     660     663     681      16     675     660     678     684      36
+     675     672     669     708      16     672     675     660     678      16
+     669     666     663     681      16     666     663     660     675      16
+     666     663     660     678      16     666     669    -672     675      16
+     663     660     675     672      16     663     660     678     684      36
+     663     666    -669     672      16     663     666     669     708      16
+     660     663     666     669      16     660     675    -672     669      16
+     660     678     684     687      36     660     678     684     699      36
+      12      39     -33     -36      33      45     111    -105    -108      33
+     102      51     -60     -63      34     117     153    -147    -150      33
+     159     225    -219    -222      33     216     165    -174    -177      34
+     231     270    -264    -267      33     246     258    -255    -261      33
+     276     312    -306    -309      33     282     297    -291    -294      33
+     318     333    -327    -330      33     339     399    -393    -396      33
+     405     471    -465    -468      33     462     411    -420    -423      34
+     477     513    -507    -510      33     519     585    -579    -582      33
+     576     525    -534    -537      34     591     651    -645    -648      33
+     690     696    -693    -705      37     684     690    -687    -702      37
+     687     699    -684    -678      37     666     672    -669    -708      37
+     660     666    -663    -681      37     663     675    -660    -678      37
 %FLAG EXCLUDED_ATOMS_LIST                                                       
 %FORMAT(10I8)                                                                   
        2       3       4       5       6       7       8       9      10      12
@@ -1355,7 +1355,7 @@ BLA BLA BLA BLA
      220      24
 %FLAG BOX_DIMENSIONS                                                            
 %FORMAT(5E16.8)                                                                 
-  1.09471219E+02  4.24388485E+01  4.24388485E+01  4.24388485E+01
+  1.09471222E+02  4.24388504E+01  4.24388504E+01  4.24388504E+01
 %FLAG RADII                                                                     
 %FORMAT(5E16.8)                                                                 
   1.55000000E+00  1.30000000E+00  1.30000000E+00  1.30000000E+00  1.70000000E+00
@@ -1458,6 +1458,9 @@ BLA BLA BLA BLA
   7.20000000E-01  7.20000000E-01  7.20000000E-01  7.20000000E-01  8.00000000E-01
   8.00000000E-01  8.00000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01
   8.50000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01
+%FLAG IPOL                                                                      
+%FORMAT(1I8)                                                                    
+       0
 %FLAG RESIDUE_NUMBER                                                            
 %FORMAT(20I4)                                                                   
    1   2   3   4   5   6   7   8   9  10  11  12  13 270

From 64f0a77f4456f056af26f392482507d82c9f343d Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 1 Jul 2024 13:41:36 -0400
Subject: [PATCH 0801/1492] Ensure GB radius set string is copied during
 topology append

---
 src/Exec_CombineCoords.cpp |  4 +++-
 src/Topology.cpp           | 18 ++++++++++++++++++
 2 files changed, 21 insertions(+), 1 deletion(-)

diff --git a/src/Exec_CombineCoords.cpp b/src/Exec_CombineCoords.cpp
index 5e98c8089d..01e7a0c4cf 100644
--- a/src/Exec_CombineCoords.cpp
+++ b/src/Exec_CombineCoords.cpp
@@ -39,7 +39,7 @@ Exec::RetType Exec_CombineCoords::Execute(CpptrajState& State, ArgList& argIn) {
   mprintf("\n");
   // Only add the topology to the list if parmname specified
   bool addTop = true;
-  Topology CombinedTop;
+  Topology CombinedTop; // FIXME should the initial append just be a straight copy?
   CombinedTop.SetDebug( State.Debug() );
   if (parmname.empty()) {
     for (std::vector<DataSet_Coords*>::const_iterator it = CRD.begin();
@@ -62,6 +62,7 @@ Exec::RetType Exec_CombineCoords::Execute(CpptrajState& State, ArgList& argIn) {
   for (unsigned int setnum = 0; setnum != CRD.size(); ++setnum) {
     if (CRD[setnum]->Size() < minSize)
       minSize = CRD[setnum]->Size();
+    // Box
     if (CRD[setnum]->CoordsInfo().HasBox()) {
       if (boxStatus == NOT_SET) {
         combinedBox = CRD[setnum]->CoordsInfo().TrajBox();
@@ -77,6 +78,7 @@ Exec::RetType Exec_CombineCoords::Execute(CpptrajState& State, ArgList& argIn) {
         }
       }
     }
+    // Append
     CombinedTop.AppendTop( CRD[setnum]->Top() );
   }
   CombinedTop.SetParmBox( combinedBox );
diff --git a/src/Topology.cpp b/src/Topology.cpp
index df84357074..8a7d7b47ca 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2763,6 +2763,24 @@ int Topology::AppendTop(Topology const& NewTop) {
   // molecules and number of solvent molecules.
   // Just need to determine the number of extra points.
   DetermineNumExtraPoints();
+
+  // GB radii set string
+  if (!NewTop.GBradiiSet().empty()) {
+    if (radius_set_.empty())
+      radius_set_ = NewTop.GBradiiSet();
+    else {
+      // Do not repeat a GB radius string
+      std::size_t pos = radius_set_.find( NewTop.GBradiiSet() );
+      if (pos == std::string::npos) {
+        std::string newName = radius_set_ + "+" + NewTop.GBradiiSet();
+        if (newName.size() > 80) {
+          mprintf("Warning: New radius set name is > 80 characters: '%s'\n", newName.c_str());
+          mprintf("Warning: This will be truncated to 80 characters in an Amber Topology.\n");
+        }
+        radius_set_ = newName;
+      }
+    }
+  }
   return 0;
 }
 

From 38ae5b0546dd2996ee3a1e6359d3659eea8120f1 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 1 Jul 2024 14:57:19 -0400
Subject: [PATCH 0802/1492] Update for reordered indices. The new indices are
 much closer to (but not yet exactly so) what LEaP produces; in fact, cpptraj
 can now take the old ../FtuFabI.NAD.TCL.parm7 with the old cpptraj index
 ordering and reorder it so it is almost identical to what LEaP produced in
 the original ChainA_1-268_NAD_TCL-gaff.parm7. Also the AppendTop function now
 records GB set string.

---
 test/Test_CombineCrd/FabI.NDP.TCS.parm7.save | 24726 +++++++++--------
 1 file changed, 12366 insertions(+), 12360 deletions(-)

diff --git a/test/Test_CombineCrd/FabI.NDP.TCS.parm7.save b/test/Test_CombineCrd/FabI.NDP.TCS.parm7.save
index 82b717ac5b..1db5bced0c 100644
--- a/test/Test_CombineCrd/FabI.NDP.TCS.parm7.save
+++ b/test/Test_CombineCrd/FabI.NDP.TCS.parm7.save
@@ -1,4 +1,4 @@
-%VERSION  VERSION_STAMP = V0001.000  DATE = 12/13/23 10:11:19                  
+%VERSION  VERSION_STAMP = V0001.000  DATE = 07/01/24 13:42:35                  
 %FLAG TITLE                                                                     
 %FORMAT(20a4)                                                                   
 combinedParm                                                                    
@@ -3213,149 +3213,149 @@ LEU GLU HIE HIE HIE HIE HIE HIE NDP TCS
     3913    3932    3947    3964    3981    3998    4015    4032    4050    4120
 %FLAG BOND_FORCE_CONSTANT                                                       
 %FORMAT(5E16.8)                                                                 
-  5.70000000E+02  4.90000000E+02  2.27000000E+02  3.10000000E+02  3.17000000E+02
-  3.67000000E+02  3.37000000E+02  4.69000000E+02  3.17000000E+02  3.20000000E+02
-  4.50000000E+02  4.69000000E+02  4.27000000E+02  4.77000000E+02  4.88000000E+02
-  4.10000000E+02  5.18000000E+02  3.17000000E+02  4.81000000E+02  3.37000000E+02
-  6.56000000E+02  2.37000000E+02  4.69000000E+02  4.69000000E+02  4.47000000E+02
-  4.28000000E+02  5.46000000E+02  3.88000000E+02  3.17000000E+02  4.20000000E+02
-  4.50000000E+02  3.02000000E+02  8.60000000E+02  3.02000000E+02  4.20000000E+02
-  3.37000000E+02  3.20000000E+02  2.30000000E+02  5.25000000E+02  4.61000000E+02
-  5.02000000E+02  4.83000000E+02  5.20000000E+02  4.14000000E+02  5.29000000E+02
-  4.40000000E+02  4.36000000E+02  3.37000000E+02  4.78400000E+02  3.22800000E+02
-  3.72400000E+02  3.86100000E+02  3.40000000E+02  3.40000000E+02  3.40000000E+02
-  4.34000000E+02  4.34000000E+02  3.67000000E+02  5.53000000E+02  3.67000000E+02
-  4.34000000E+02  3.67000000E+02  4.34000000E+02  2.74000000E+02  3.50000000E+02
-  3.50000000E+02  3.50000000E+02  4.34000000E+02  3.40000000E+02  3.67000000E+02
-  3.67000000E+02  3.44300000E+02  3.69600000E+02
+  5.70000000E+02  4.90000000E+02  3.40000000E+02  2.27000000E+02  3.40000000E+02
+  3.10000000E+02  3.40000000E+02  3.17000000E+02  4.34000000E+02  3.67000000E+02
+  4.34000000E+02  3.37000000E+02  3.67000000E+02  4.69000000E+02  3.17000000E+02
+  5.53000000E+02  3.20000000E+02  4.50000000E+02  4.69000000E+02  3.67000000E+02
+  4.34000000E+02  4.27000000E+02  3.67000000E+02  4.77000000E+02  4.88000000E+02
+  4.10000000E+02  5.18000000E+02  3.17000000E+02  4.34000000E+02  4.81000000E+02
+  3.37000000E+02  6.56000000E+02  2.74000000E+02  2.37000000E+02  4.69000000E+02
+  4.69000000E+02  4.47000000E+02  4.28000000E+02  5.46000000E+02  3.88000000E+02
+  3.17000000E+02  3.50000000E+02  4.20000000E+02  3.50000000E+02  4.50000000E+02
+  3.50000000E+02  4.34000000E+02  3.02000000E+02  8.60000000E+02  3.02000000E+02
+  4.20000000E+02  3.37000000E+02  3.40000000E+02  3.20000000E+02  2.30000000E+02
+  5.25000000E+02  4.61000000E+02  5.02000000E+02  3.67000000E+02  4.83000000E+02
+  5.20000000E+02  4.14000000E+02  5.29000000E+02  3.67000000E+02  4.40000000E+02
+  4.36000000E+02  3.37000000E+02  3.44300000E+02  4.78400000E+02  3.22800000E+02
+  3.69600000E+02  3.72400000E+02  3.86100000E+02
 %FLAG BOND_EQUIL_VALUE                                                          
 %FORMAT(5E16.8)                                                                 
-  1.22900000E+00  1.33500000E+00  1.81000000E+00  1.52600000E+00  1.52200000E+00
-  1.47100000E+00  1.44900000E+00  1.40000000E+00  1.51000000E+00  1.41000000E+00
-  1.36400000E+00  1.40900000E+00  1.38100000E+00  1.34300000E+00  1.33500000E+00
-  1.39400000E+00  1.37100000E+00  1.50400000E+00  1.34000000E+00  1.46300000E+00
-  1.25000000E+00  1.81000000E+00  1.40400000E+00  1.40000000E+00  1.41900000E+00
-  1.38000000E+00  1.35200000E+00  1.45900000E+00  1.49500000E+00  1.35000000E+00
-  1.36000000E+00  1.48000000E+00  1.23000000E+00  1.48000000E+00  1.31500000E+00
-  1.47500000E+00  1.41000000E+00  1.61000000E+00  1.48000000E+00  1.35400000E+00
-  1.32400000E+00  1.33900000E+00  1.37000000E+00  1.39100000E+00  1.30400000E+00
-  1.37100000E+00  1.37400000E+00  1.47500000E+00  1.38700000E+00  1.72900000E+00
-  1.37300000E+00  1.36200000E+00  1.09000000E+00  1.09000000E+00  1.09000000E+00
-  1.01000000E+00  1.01000000E+00  1.08000000E+00  9.60000000E-01  1.08000000E+00
-  1.01000000E+00  1.08000000E+00  1.01000000E+00  1.33600000E+00  1.09000000E+00
-  1.09000000E+00  1.09000000E+00  1.01000000E+00  1.09000000E+00  1.08000000E+00
-  1.08000000E+00  1.08700000E+00  9.74000000E-01
+  1.22900000E+00  1.33500000E+00  1.09000000E+00  1.81000000E+00  1.09000000E+00
+  1.52600000E+00  1.09000000E+00  1.52200000E+00  1.01000000E+00  1.47100000E+00
+  1.01000000E+00  1.44900000E+00  1.08000000E+00  1.40000000E+00  1.51000000E+00
+  9.60000000E-01  1.41000000E+00  1.36400000E+00  1.40900000E+00  1.08000000E+00
+  1.01000000E+00  1.38100000E+00  1.08000000E+00  1.34300000E+00  1.33500000E+00
+  1.39400000E+00  1.37100000E+00  1.50400000E+00  1.01000000E+00  1.34000000E+00
+  1.46300000E+00  1.25000000E+00  1.33600000E+00  1.81000000E+00  1.40400000E+00
+  1.40000000E+00  1.41900000E+00  1.38000000E+00  1.35200000E+00  1.45900000E+00
+  1.49500000E+00  1.09000000E+00  1.35000000E+00  1.09000000E+00  1.36000000E+00
+  1.09000000E+00  1.01000000E+00  1.48000000E+00  1.23000000E+00  1.48000000E+00
+  1.31500000E+00  1.47500000E+00  1.09000000E+00  1.41000000E+00  1.61000000E+00
+  1.48000000E+00  1.35400000E+00  1.32400000E+00  1.08000000E+00  1.33900000E+00
+  1.37000000E+00  1.39100000E+00  1.30400000E+00  1.08000000E+00  1.37100000E+00
+  1.37400000E+00  1.47500000E+00  1.08700000E+00  1.38700000E+00  1.72900000E+00
+  9.74000000E-01  1.37300000E+00  1.36200000E+00
 %FLAG ANGLE_FORCE_CONSTANT                                                      
 %FORMAT(5E16.8)                                                                 
-  8.00000000E+01  5.00000000E+01  6.20000000E+01  6.30000000E+01  5.00000000E+01
-  4.00000000E+01  8.00000000E+01  7.00000000E+01  8.00000000E+01  8.00000000E+01
-  6.30000000E+01  6.30000000E+01  7.00000000E+01  6.30000000E+01  8.00000000E+01
-  5.00000000E+01  7.00000000E+01  6.30000000E+01  6.30000000E+01  7.00000000E+01
-  7.00000000E+01  7.00000000E+01  7.00000000E+01  7.00000000E+01  7.00000000E+01
-  7.00000000E+01  6.30000000E+01  7.00000000E+01  5.00000000E+01  8.00000000E+01
-  8.00000000E+01  7.00000000E+01  5.00000000E+01  5.00000000E+01  6.30000000E+01
-  6.30000000E+01  6.30000000E+01  6.30000000E+01  7.00000000E+01  7.00000000E+01
-  6.30000000E+01  7.00000000E+01  7.00000000E+01  6.30000000E+01  6.30000000E+01
-  7.00000000E+01  7.00000000E+01  6.30000000E+01  4.00000000E+01  8.50000000E+01
-  4.00000000E+01  8.50000000E+01  8.50000000E+01  5.00000000E+01  3.00000000E+01
-  1.00000000E+01  1.20000000E+02  7.00000000E+01  5.00000000E+01  5.00000000E+01
-  5.00000000E+01  6.00000000E+01  1.00000000E+02  1.40000000E+02  1.00000000E+02
-  4.50000000E+01  7.00000000E+01  7.00000000E+01  7.00000000E+01  6.30000000E+01
-  7.00000000E+01  7.00000000E+01  7.00000000E+01  7.00000000E+01  7.00000000E+01
-  7.00000000E+01  7.00000000E+01  7.00000000E+01  7.00000000E+01  7.00000000E+01
-  7.00000000E+01  7.00000000E+01  7.00000000E+01  5.00000000E+01  5.00000000E+01
-  1.00000000E+02  6.29200000E+01  6.71800000E+01  6.97900000E+01  6.98500000E+01
-  6.33100000E+01  5.00000000E+01  3.50000000E+01  5.00000000E+01  5.00000000E+01
-  3.50000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01
-  3.50000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01
-  5.00000000E+01  5.00000000E+01  3.50000000E+01  5.00000000E+01  5.50000000E+01
-  3.50000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01
-  5.00000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01
-  5.00000000E+01  3.50000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01
-  5.00000000E+01  4.30000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01
-  5.00000000E+01  5.00000000E+01  3.50000000E+01  3.00000000E+01  8.00000000E+01
-  8.00000000E+01  3.00000000E+01  3.50000000E+01  5.00000000E+01  8.00000000E+01
-  5.00000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01
-  5.00000000E+01  5.00000000E+01  4.84600000E+01  4.88500000E+01
+  8.00000000E+01  5.00000000E+01  5.00000000E+01  3.50000000E+01  5.00000000E+01
+  6.20000000E+01  5.00000000E+01  3.50000000E+01  6.30000000E+01  5.00000000E+01
+  5.00000000E+01  5.00000000E+01  5.00000000E+01  4.00000000E+01  8.00000000E+01
+  7.00000000E+01  5.00000000E+01  3.50000000E+01  5.00000000E+01  8.00000000E+01
+  8.00000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01  6.30000000E+01
+  5.00000000E+01  6.30000000E+01  5.00000000E+01  7.00000000E+01  6.30000000E+01
+  8.00000000E+01  3.50000000E+01  5.00000000E+01  5.00000000E+01  5.50000000E+01
+  3.50000000E+01  5.00000000E+01  7.00000000E+01  5.00000000E+01  5.00000000E+01
+  6.30000000E+01  6.30000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01
+  5.00000000E+01  7.00000000E+01  7.00000000E+01  5.00000000E+01  7.00000000E+01
+  7.00000000E+01  7.00000000E+01  5.00000000E+01  5.00000000E+01  7.00000000E+01
+  7.00000000E+01  6.30000000E+01  3.50000000E+01  7.00000000E+01  5.00000000E+01
+  5.00000000E+01  5.00000000E+01  5.00000000E+01  8.00000000E+01  8.00000000E+01
+  7.00000000E+01  5.00000000E+01  4.30000000E+01  5.00000000E+01  5.00000000E+01
+  5.00000000E+01  6.30000000E+01  6.30000000E+01  5.00000000E+01  6.30000000E+01
+  6.30000000E+01  5.00000000E+01  7.00000000E+01  7.00000000E+01  6.30000000E+01
+  7.00000000E+01  5.00000000E+01  7.00000000E+01  6.30000000E+01  6.30000000E+01
+  5.00000000E+01  7.00000000E+01  7.00000000E+01  6.30000000E+01  3.50000000E+01
+  3.00000000E+01  8.00000000E+01  8.00000000E+01  4.00000000E+01  3.00000000E+01
+  8.50000000E+01  4.00000000E+01  3.50000000E+01  8.50000000E+01  8.50000000E+01
+  5.00000000E+01  3.00000000E+01  1.00000000E+01  5.00000000E+01  1.20000000E+02
+  8.00000000E+01  7.00000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01
+  5.00000000E+01  5.00000000E+01  5.00000000E+01  6.00000000E+01  1.00000000E+02
+  1.40000000E+02  1.00000000E+02  4.50000000E+01  5.00000000E+01  7.00000000E+01
+  7.00000000E+01  7.00000000E+01  6.30000000E+01  7.00000000E+01  7.00000000E+01
+  7.00000000E+01  7.00000000E+01  5.00000000E+01  7.00000000E+01  7.00000000E+01
+  7.00000000E+01  7.00000000E+01  5.00000000E+01  7.00000000E+01  5.00000000E+01
+  7.00000000E+01  7.00000000E+01  7.00000000E+01  7.00000000E+01  5.00000000E+01
+  5.00000000E+01  1.00000000E+02  4.84600000E+01  6.29200000E+01  6.71800000E+01
+  6.97900000E+01  6.98500000E+01  4.88500000E+01  6.33100000E+01
 %FLAG ANGLE_EQUIL_VALUE                                                         
 %FORMAT(5E16.8)                                                                 
-  2.14501057E+00  2.12755727E+00  1.72613137E+00  1.93906163E+00  2.00189351E+00
-  1.91113635E+00  2.10137732E+00  2.03505478E+00  1.94080696E+00  1.94080696E+00
-  1.92160833E+00  2.09439600E+00  2.09439600E+00  1.98967620E+00  1.91462701E+00
-  1.91113635E+00  2.09439600E+00  2.09439600E+00  2.09439600E+00  2.09439600E+00
-  2.09439600E+00  2.09439600E+00  2.04203610E+00  2.09439600E+00  2.09439600E+00
-  2.09439600E+00  1.97396823E+00  2.09439600E+00  2.15024656E+00  1.94080696E+00
-  2.19911580E+00  2.04203610E+00  1.89542838E+00  2.05948940E+00  2.09439600E+00
-  2.14151991E+00  2.09439600E+00  2.02807346E+00  2.31779824E+00  1.82212452E+00
-  1.85703112E+00  1.94778828E+00  1.89717371E+00  1.89891904E+00  2.35445017E+00
-  2.18166250E+00  2.24449438E+00  2.01760148E+00  2.05948940E+00  2.24274905E+00
-  1.92335366E+00  1.97222290E+00  2.06821605E+00  2.05948940E+00  2.09439600E+00
-  2.30034494E+00  2.12930260E+00  2.12406661E+00  1.91113635E+00  1.91113635E+00
-  1.91113635E+00  1.91113635E+00  1.88897066E+00  2.09265067E+00  2.10312265E+00
-  1.79070858E+00  1.93731630E+00  2.25322103E+00  2.08217869E+00  2.04727209E+00
-  2.06996138E+00  2.22878641E+00  2.04727209E+00  2.15548255E+00  1.92684432E+00
-  2.31081692E+00  1.83957782E+00  1.81165254E+00  1.98793087E+00  1.85354046E+00
-  2.20260646E+00  2.24798504E+00  2.19562514E+00  1.91113635E+00  1.91113635E+00
-  2.10312265E+00  2.08392402E+00  2.09387240E+00  2.08043336E+00  2.09334880E+00
-  2.09352334E+00  2.09439600E+00  1.91113635E+00  1.91113635E+00  1.91113635E+00
-  1.91113635E+00  1.91113635E+00  1.91113635E+00  1.91113635E+00  1.91113635E+00
-  1.91113635E+00  1.91113635E+00  1.91113635E+00  2.06018753E+00  1.91113635E+00
-  2.09439600E+00  1.91113635E+00  1.91113635E+00  1.91113635E+00  1.89368305E+00
-  2.09439600E+00  1.91113635E+00  1.97222290E+00  2.09439600E+00  2.09439600E+00
+  2.14501057E+00  2.09439600E+00  2.12755727E+00  1.91113635E+00  1.91113635E+00
+  1.72613137E+00  1.91113635E+00  1.91113635E+00  1.93906163E+00  1.91113635E+00
+  2.00189351E+00  1.91113635E+00  1.91113635E+00  1.91113635E+00  2.10137732E+00
+  2.03505478E+00  1.91113635E+00  1.91113635E+00  1.91113635E+00  1.94080696E+00
+  1.94080696E+00  1.91113635E+00  2.06018753E+00  1.91113635E+00  1.92160833E+00
+  2.09439600E+00  2.09439600E+00  1.91113635E+00  2.09439600E+00  1.98967620E+00
+  1.91462701E+00  1.91113635E+00  1.91113635E+00  1.91113635E+00  1.89368305E+00
+  2.09439600E+00  1.91113635E+00  2.09439600E+00  1.97222290E+00  2.09439600E+00
   2.09439600E+00  2.09439600E+00  2.09439600E+00  2.09439600E+00  2.09439600E+00
-  1.91113635E+00  2.09439600E+00  2.09439600E+00  1.91113635E+00  2.06647072E+00
-  1.91113635E+00  1.67551680E+00  2.09439600E+00  2.09439600E+00  2.14850123E+00
-  2.09439600E+00  1.91113635E+00  2.09439600E+00  2.12930260E+00  2.11184930E+00
-  2.10312265E+00  2.07694270E+00  2.09439600E+00  1.91113635E+00  2.05076275E+00
-  1.91113635E+00  1.91113635E+00  1.91113635E+00  2.01498349E+00  2.14762857E+00
-  1.91113635E+00  2.14762857E+00  2.09457053E+00  1.91061275E+00
+  2.09439600E+00  2.09439600E+00  2.09439600E+00  2.09439600E+00  2.09439600E+00
+  2.04203610E+00  2.09439600E+00  2.09439600E+00  1.91113635E+00  2.09439600E+00
+  2.09439600E+00  1.97396823E+00  2.09439600E+00  2.09439600E+00  2.09439600E+00
+  1.91113635E+00  2.06647072E+00  2.15024656E+00  1.94080696E+00  2.19911580E+00
+  2.04203610E+00  1.91113635E+00  1.67551680E+00  1.89542838E+00  2.05948940E+00
+  2.09439600E+00  2.09439600E+00  2.14151991E+00  2.09439600E+00  2.09439600E+00
+  2.02807346E+00  2.14850123E+00  2.31779824E+00  1.82212452E+00  1.85703112E+00
+  1.94778828E+00  2.09439600E+00  1.89717371E+00  1.89891904E+00  2.35445017E+00
+  1.91113635E+00  2.18166250E+00  2.24449438E+00  2.01760148E+00  2.09439600E+00
+  2.12930260E+00  2.11184930E+00  2.10312265E+00  2.05948940E+00  2.07694270E+00
+  2.24274905E+00  1.92335366E+00  2.09439600E+00  1.97222290E+00  2.06821605E+00
+  2.05948940E+00  2.09439600E+00  2.30034494E+00  1.91113635E+00  2.12930260E+00
+  2.05076275E+00  2.12406661E+00  1.91113635E+00  1.91113635E+00  1.91113635E+00
+  1.91113635E+00  1.91113635E+00  1.91113635E+00  1.91113635E+00  1.88897066E+00
+  2.09265067E+00  2.10312265E+00  1.79070858E+00  2.01498349E+00  1.93731630E+00
+  2.25322103E+00  2.08217869E+00  2.04727209E+00  2.06996138E+00  2.22878641E+00
+  2.04727209E+00  2.15548255E+00  2.14762857E+00  1.92684432E+00  2.31081692E+00
+  1.83957782E+00  1.81165254E+00  1.91113635E+00  1.98793087E+00  2.14762857E+00
+  1.85354046E+00  2.20260646E+00  2.24798504E+00  2.19562514E+00  1.91113635E+00
+  1.91113635E+00  2.10312265E+00  2.09457053E+00  2.08392402E+00  2.09387240E+00
+  2.08043336E+00  2.09334880E+00  1.91061275E+00  2.09352334E+00
 %FLAG DIHEDRAL_FORCE_CONSTANT                                                   
 %FORMAT(5E16.8)                                                                 
-  2.50000000E+00  0.00000000E+00  2.70000000E-01  4.20000000E-01  0.00000000E+00
-  1.55555556E-01  0.00000000E+00  2.00000000E-01  2.00000000E-01  4.00000000E-01
-  3.33333333E-01  2.00000000E+00  2.00000000E+00  4.50000000E-01  1.58000000E+00
-  5.50000000E-01  3.62500000E+00  2.00000000E-01  2.50000000E-01  1.80000000E-01
-  2.40000000E+00  5.37500000E+00  2.32500000E+00  5.00000000E+00  1.50000000E+00
-  0.00000000E+00  3.00000000E+00  3.50000000E+00  6.52500000E+00  1.67500000E+00
-  1.52500000E+00  1.05000000E+01  1.10000000E+00  1.00000000E+00  6.20000000E-01
-  2.38000000E+00  4.00000000E+00  6.00000000E+00  3.50000000E-01  7.00000000E+00
-  1.17500000E+00  1.44000000E-01  1.00000000E-01  3.83000000E-01  3.83333333E-01
-  2.50000000E-01  1.20000000E+00  6.80000000E+00  4.80000000E+00  5.45000000E+00
-  4.15000000E+00  1.70000000E+00  1.65000000E+00  2.55000000E+00  1.00000000E+01
-  2.50000000E+00  6.50000000E-01  9.00000000E-01  8.00000000E-01  8.00000000E-02
-  1.60000000E-01  1.50000000E-01  2.50000000E-01  1.66666667E-01  2.30000000E+00
-  2.00000000E+00
+  2.00000000E+00  2.50000000E+00  0.00000000E+00  0.00000000E+00  2.70000000E-01
+  4.20000000E-01  0.00000000E+00  3.33333333E-01  1.55555556E-01  2.00000000E-01
+  2.00000000E-01  4.00000000E-01  2.00000000E+00  8.00000000E-01  8.00000000E-02
+  4.50000000E-01  1.58000000E+00  5.50000000E-01  3.62500000E+00  1.60000000E-01
+  1.50000000E-01  2.00000000E-01  2.50000000E-01  1.80000000E-01  2.50000000E-01
+  0.00000000E+00  1.66666667E-01  2.30000000E+00  1.50000000E+00  2.32500000E+00
+  2.40000000E+00  5.37500000E+00  5.00000000E+00  2.50000000E-01  3.00000000E+00
+  3.50000000E+00  1.52500000E+00  6.52500000E+00  1.67500000E+00  1.10000000E+00
+  1.05000000E+01  1.00000000E+00  2.00000000E+00  6.20000000E-01  2.38000000E+00
+  4.00000000E+00  6.00000000E+00  7.00000000E+00  3.50000000E-01  3.83333333E-01
+  1.17500000E+00  1.44000000E-01  1.00000000E-01  3.83000000E-01  1.20000000E+00
+  1.70000000E+00  6.80000000E+00  4.80000000E+00  5.45000000E+00  1.00000000E+01
+  4.15000000E+00  1.65000000E+00  2.55000000E+00  2.50000000E+00  6.50000000E-01
+  9.00000000E-01
 %FLAG DIHEDRAL_PERIODICITY                                                      
 %FORMAT(5E16.8)                                                                 
-  2.00000000E+00  1.00000000E+00  2.00000000E+00  3.00000000E+00  4.00000000E+00
-  3.00000000E+00  2.00000000E+00  1.00000000E+00  2.00000000E+00  3.00000000E+00
-  3.00000000E+00  1.00000000E+00  2.00000000E+00  1.00000000E+00  2.00000000E+00
-  3.00000000E+00  2.00000000E+00  1.00000000E+00  2.00000000E+00  3.00000000E+00
+  1.00000000E+00  2.00000000E+00  2.00000000E+00  1.00000000E+00  2.00000000E+00
+  3.00000000E+00  4.00000000E+00  3.00000000E+00  3.00000000E+00  1.00000000E+00
+  2.00000000E+00  3.00000000E+00  2.00000000E+00  1.00000000E+00  3.00000000E+00
+  1.00000000E+00  2.00000000E+00  3.00000000E+00  2.00000000E+00  3.00000000E+00
+  3.00000000E+00  1.00000000E+00  2.00000000E+00  3.00000000E+00  1.00000000E+00
+  3.00000000E+00  3.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  3.00000000E+00  2.00000000E+00
   2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
-  3.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
   2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
-  2.00000000E+00  2.00000000E+00  2.00000000E+00  1.00000000E+00  2.00000000E+00
-  2.00000000E+00  3.00000000E+00  2.00000000E+00  3.00000000E+00  3.00000000E+00
-  3.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  1.00000000E+00  3.00000000E+00
+  2.00000000E+00  3.00000000E+00  2.00000000E+00  3.00000000E+00  2.00000000E+00
   2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
-  1.00000000E+00  2.00000000E+00  2.00000000E+00  1.00000000E+00  3.00000000E+00
-  3.00000000E+00  3.00000000E+00  1.00000000E+00  3.00000000E+00  2.00000000E+00
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  1.00000000E+00  2.00000000E+00
   2.00000000E+00
 %FLAG DIHEDRAL_PHASE                                                            
 %FORMAT(5E16.8)                                                                 
-  3.14159400E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  3.14159400E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
   0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
-  0.00000000E+00  0.00000000E+00  0.00000000E+00  3.14159400E+00  3.14159400E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  3.14159400E+00
   3.14159400E+00  3.14159400E+00  3.14159400E+00  3.14159400E+00  0.00000000E+00
+  0.00000000E+00  3.14159400E+00  3.14159400E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  3.14159400E+00  3.14159400E+00  3.14159400E+00
+  3.14159400E+00  3.14159400E+00  3.14159400E+00  0.00000000E+00  3.14159400E+00
   3.14159400E+00  3.14159400E+00  3.14159400E+00  3.14159400E+00  3.14159400E+00
-  0.00000000E+00  3.14159400E+00  3.14159400E+00  3.14159400E+00  3.14159400E+00
-  3.14159400E+00  3.14159400E+00  3.14159400E+00  3.14159400E+00  0.00000000E+00
   3.14159400E+00  3.14159400E+00  3.14159400E+00  0.00000000E+00  3.14159400E+00
+  3.14159400E+00  3.14159400E+00  3.14159400E+00  0.00000000E+00  0.00000000E+00
   0.00000000E+00  0.00000000E+00  3.14159400E+00  0.00000000E+00  0.00000000E+00
-  0.00000000E+00  0.00000000E+00  3.14159400E+00  3.14159400E+00  3.14159400E+00
   3.14159400E+00  3.14159400E+00  3.14159400E+00  3.14159400E+00  3.14159400E+00
-  0.00000000E+00  0.00000000E+00  3.14159400E+00  0.00000000E+00  3.14159400E+00
-  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  3.14159400E+00
+  3.14159400E+00  3.14159400E+00  3.14159400E+00  0.00000000E+00  0.00000000E+00
   3.14159400E+00
 %FLAG SCEE_SCALE_FACTOR                                                         
 %FORMAT(5E16.8)                                                                 
@@ -3477,12275 +3477,12275 @@ LEU GLU HIE HIE HIE HIE HIE HIE NDP TCS
   1.85348706E+03
 %FLAG BONDS_INC_HYDROGEN                                                        
 %FORMAT(10I8)                                                                   
-      39      42      53      39      45      53      39      48      53      27
-      30      53      27      33      53      18      21      54      18      24
-      54      12      15      55       0       3      56       0       6      56
-       0       9      56      63      66      53      63      69      53      57
-      60      57     126     129      58     120     123      58     114     117
-      58     108     111      58     102     105      58      90      93      54
-      90      96      54      84      87      53      78      81      57     177
-     180      54     177     183      54     177     186      54     165     168
-      54     165     171      54     165     174      54     159     162      54
-     150     153      54     150     156      54     144     147      53     138
-     141      57     207     210      54     207     213      54     207     216
-      54     201     204      53     195     198      57     231     234      53
-     231     237      53     225     228      57     294     297      56     294
-     300      56     294     303      56     285     288      55     285     291
-      55     276     279      54     276     282      54     267     270      54
-     267     273      54     258     261      54     258     264      54     252
-     255      53     246     249      57     360     363      56     360     366
-      56     360     369      56     351     354      55     351     357      55
-     342     345      54     342     348      54     333     336      54     333
-     339      54     324     327      54     324     330      54     318     321
-      53     312     315      57     417     420      54     417     423      54
-     417     426      54     408     411      54     408     414      54     396
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-    3483    3486      54    3483    3489      54    3483    3492      54    3477
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-      54    3585    3594      54    3579    3582      54    3570    3573      54
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-    3624      53    3621    3627      53    3615    3618      57    3684    3687
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-    3675    3681      55    3666    3669      54    3666    3672      54    3657
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-    3732    3738      54    3732    3741      54    3720    3723      54    3720
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-    3897      54    3885    3888      53    3879    3882      57    3948    3951
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-    3981      53    3972    3975      57    4041    4044      54    4041    4047
-      54    4041    4050      54    4032    4035      54    4032    4038      54
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-    4017      54    4008    4011      53    4002    4005      57    4089    4092
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-    4077    4083      54    4077    4086      54    4071    4074      54    4065
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+   10266   10275       5   10260   10263       5   10254   10257       3   10248
+   10251      11   10302   10305       3   10302   10308       3   10296   10299
+      11   10344   10347      11   10344   10350      11   10329   10332       5
+   10329   10335       5   10323   10326       3   10317   10320      11   10389
+   10392      16   10377   10380       5   10377   10383       5   10377   10386
+       5   10371   10374       3   10365   10368       3   10359   10362      11
+   10431   10434       5   10431   10437       5   10431   10440       5   10419
+   10422       5   10419   10425       5   10419   10428       5   10413   10416
+       5   10407   10410       3   10401   10404      11   10461   10464       5
+   10461   10467       5   10461   10470       5   10455   10458       3   10449
+   10452      11   10527   10530      13   10521   10524      13   10515   10518
+      13   10509   10512      13   10503   10506      13   10491   10494       5
+   10491   10497       5   10485   10488       3   10479   10482      11   10578
+   10581       5   10578   10584       5   10578   10587       5   10566   10569
+       5   10566   10572       5   10566   10575       5   10560   10563       5
+   10551   10554       5   10551   10557       5   10545   10548       3   10539
+   10542      11   10617   10620      33   10608   10611       3   10608   10614
+       3   10602   10605       3   10596   10599      11   10650   10653      16
+   10641   10644       3   10641   10647       3   10635   10638       3   10629
+   10632      11   10674   10677       5   10674   10680       5   10668   10671
+       3   10662   10665      11   10731   10734       3   10731   10737       3
+   10731   10740       3   10719   10722       3   10719   10725       3   10710
+   10713       5   10710   10716       5   10704   10707       3   10698   10701
+      11   10761   10764       5   10761   10767       5   10761   10770       5
+   10755   10758       3   10749   10752      11   10809   10812      16   10797
+   10800       5   10797   10803       5   10797   10806       5   10791   10794
+       3   10785   10788       3   10779   10782      11   10827   10830       3
+   10827   10833       3   10821   10824      11   10881   10884       5   10881
+   10887       5   10881   10890       5   10872   10875       5   10872   10878
+       5   10860   10863       5   10860   10866       5   10860   10869       5
+   10854   10857       5   10848   10851       3   10842   10845      11   10929
+   10932      16   10917   10920       5   10917   10923       5   10917   10926
+       5   10911   10914       3   10905   10908       3   10899   10902      11
+   10947   10950       3   10947   10953       3   10941   10944      11   10983
+   10986       5   10983   10989       5   10974   10977       5   10974   10980
+       5   10968   10971       3   10962   10965      11   11037   11040       5
+   11037   11043       5   11037   11046       5   11025   11028       5   11025
+   11031       5   11025   11034       5   11019   11022       5   11013   11016
+       3   11007   11010      11   11085   11088       5   11085   11091       5
+   11085   11094       5   11073   11076       5   11073   11079       5   11073
+   11082       5   11067   11070       5   11061   11064       3   11055   11058
+      11   11142   11145      20   11136   11139      21   11130   11133      23
+   11115   11118       5   11115   11121       5   11109   11112       3   11103
+   11106      11   11184   11187       5   11184   11190       5   11184   11193
+       5   11172   11175       5   11172   11178       5   11172   11181       5
+   11166   11169       5   11160   11163       3   11154   11157      11   11214
+   11217       5   11214   11220       5   11208   11211       3   11202   11205
+      11   11250   11253       5   11250   11256       5   11250   11259       5
+   11244   11247       3   11238   11241      11   11274   11277       3   11274
+   11280       3   11268   11271      11   11340   11343      13   11334   11337
+      13   11328   11331      16   11319   11322      13   11313   11316      13
+   11301   11304       5   11301   11307       5   11295   11298       3   11289
+   11292      11   11391   11394      20   11385   11388      21   11379   11382
+      23   11364   11367       5   11364   11370       5   11358   11361       3
+   11352   11355      11   11424   11427      33   11415   11418       3   11415
+   11421       3   11409   11412       3   11403   11406      11   11466   11469
+       5   11466   11472       5   11466   11475       5   11454   11457       5
+   11454   11460       5   11454   11463       5   11448   11451       5   11442
+   11445       3   11436   11439      11   11505   11508      16   11496   11499
+       3   11496   11502       3   11490   11493       3   11484   11487      11
+   11550   11553       3   11550   11556       3   11550   11559       3   11538
+   11541       3   11538   11544       3   11529   11532       5   11529   11535
+       5   11523   11526       3   11517   11520      11   11574   11577       3
+   11574   11580       3   11568   11571      11   11616   11619      11   11616
+   11622      11   11601   11604       5   11601   11607       5   11595   11598
+       3   11589   11592      11   11661   11664       5   11661   11667       5
+   11661   11670       5   11649   11652       5   11649   11655       5   11649
+   11658       5   11643   11646       5   11637   11640       3   11631   11634
+      11   11718   11721       5   11718   11724       5   11718   11727       5
+   11706   11709       5   11706   11712       5   11706   11715       5   11700
+   11703       5   11691   11694       5   11691   11697       5   11685   11688
+       3   11679   11682      11   11775   11778       5   11775   11781       5
+   11775   11784       5   11763   11766       5   11763   11769       5   11763
+   11772       5   11757   11760       5   11748   11751       5   11748   11754
+       5   11742   11745       3   11736   11739      11   11814   11817       5
+   11814   11820       5   11805   11808       5   11805   11811       5   11799
+   11802       3   11793   11796      11   11877   11880      20   11871   11874
+      21   11865   11868      23   11850   11853       5   11850   11856       5
+   11844   11847       3   11838   11841      11   11928   11931      20   11922
+   11925      21   11916   11919      23   11901   11904       5   11901   11907
+       5   11895   11898       3   11889   11892      11   11979   11982      20
+   11973   11976      21   11967   11970      23   11952   11955       5   11952
+   11958       5   11946   11949       3   11940   11943      11   12030   12033
+      20   12024   12027      21   12018   12021      23   12003   12006       5
+   12003   12009       5   11997   12000       3   11991   11994      11   12081
+   12084      20   12075   12078      21   12069   12072      23   12054   12057
+       5   12054   12060       5   12048   12051       3   12042   12045      11
+   12132   12135      20   12126   12129      21   12120   12123      23   12105
+   12108       5   12105   12111       5   12099   12102       3   12093   12096
+      11   12276   12354      42   12273   12351      44   12270   12348      46
+   12267   12342      47   12267   12345      47   12255   12339      42   12249
+   12336      53   12246   12333      16   12243   12330       3   12240   12327
+      16   12237   12324       3   12231   12321       3   12228   12318       3
+   12228   12315       3   12204   12312      59   12198   12306      29   12198
+   12309      29   12186   12303      64   12180   12300      53   12177   12297
+      16   12174   12294       3   12171   12291      16   12168   12288       3
+   12162   12285       3   12159   12279       3   12159   12282       3   12396
+   12426      68   12393   12423      68   12387   12420      68   12378   12417
+      71   12372   12414      68   12369   12411      68   12363   12408      68
 %FLAG BONDS_WITHOUT_HYDROGEN                                                    
 %FORMAT(10I8)                                                                   
-      51      54       1      51      57       2      36      39       3      27
-      36       3      18      27       4      12      18       4      12      51
-       5       0      12       6      72      75       1      72      78       2
-      63      72       5      57      63       7     132     135       1     132
-     138       2     120     126       8     114     120       8     108     114
-       8     102     108       8      99     102       8      99     126       8
-      90      99       9      84      90       4      84     132       5      78
-      84       7     189     192       1     189     195       2     159     165
-       4     159     177       4     150     159       4     144     150       4
-     144     189       5     138     144       7     219     222       1     219
-     225       2     201     207       4     201     219       5     195     201
-       7     240     243       1     240     246       2     231     240       5
-     225     231       7     306     309       1     306     312       2     285
-     294       6     276     285       4     267     276       4     258     267
-       4     252     258       4     252     306       5     246     252       7
-     372     375       1     372     378       2     351     360       6     342
-     351       4     333     342       4     324     333       4     318     324
-       4     318     372       5     312     318       7     429     432       1
-     429     435       2     408     417       4     390     396       4     390
-     408       4     384     390       4     384     429       5     378     384
-       7     486     489       1     486     492       2     456     462       4
-     456     474       4     447     456       4     441     447       4     441
-     486       5     435     441       7     543     546       1     543     549
-       2     522     531       4     504     510       4     504     522       4
-     498     504       4     498     543       5     492     498       7     585
-     588       1     585     591       2     561     567       4     561     579
-      10     555     561       4     555     585       5     549     555       7
-     606     609       1     606     612       2     597     606       5     591
-     597       7     663     666       1     663     669       2     633     639
-       4     633     651       4     624     633       4     618     624       4
-     618     663       5     612     618       7     720     723       1     720
-     726       2     690     696       4     690     708       4     681     690
-       4     675     681       4     675     720       5     669     675       7
-     753     756       1     753     759       2     738     747      10     732
-     738       4     732     753       5     726     732       7     795     798
+      51      54       1      51      57       2      36      39       4      27
+      36       4      18      27       6      12      18       6      12      51
+       8       0      12      10      72      75       1      72      78       2
+      63      72       8      57      63      12     132     135       1     132
+     138       2     120     126      14     114     120      14     108     114
+      14     102     108      14      99     102      14      99     126      14
+      90      99      15      84      90       6      84     132       8      78
+      84      12     189     192       1     189     195       2     159     165
+       6     159     177       6     150     159       6     144     150       6
+     144     189       8     138     144      12     219     222       1     219
+     225       2     201     207       6     201     219       8     195     201
+      12     240     243       1     240     246       2     231     240       8
+     225     231      12     306     309       1     306     312       2     285
+     294      10     276     285       6     267     276       6     258     267
+       6     252     258       6     252     306       8     246     252      12
+     372     375       1     372     378       2     351     360      10     342
+     351       6     333     342       6     324     333       6     318     324
+       6     318     372       8     312     318      12     429     432       1
+     429     435       2     408     417       6     390     396       6     390
+     408       6     384     390       6     384     429       8     378     384
+      12     486     489       1     486     492       2     456     462       6
+     456     474       6     447     456       6     441     447       6     441
+     486       8     435     441      12     543     546       1     543     549
+       2     522     531       6     504     510       6     504     522       6
+     498     504       6     498     543       8     492     498      12     585
+     588       1     585     591       2     561     567       6     561     579
+      17     555     561       6     555     585       8     549     555      12
+     606     609       1     606     612       2     597     606       8     591
+     597      12     663     666       1     663     669       2     633     639
+       6     633     651       6     624     633       6     618     624       6
+     618     663       8     612     618      12     720     723       1     720
+     726       2     690     696       6     690     708       6     681     690
+       6     675     681       6     675     720       8     669     675      12
+     753     756       1     753     759       2     738     747      17     732
+     738       6     732     753       8     726     732      12     795     798
        1     795     801       2     780     783       1     780     786       2
-     771     780       5     765     771       4     765     795       5     759
-     765       7     861     864       1     861     867       2     840     849
-       6     831     840       4     822     831       4     813     822       4
-     807     813       4     807     861       5     801     807       7     894
-     897       1     894     900       2     879     888      10     873     879
-       4     873     894       5     867     873       7     951     954       1
-     951     957       2     930     939       4     912     918       4     912
-     930       4     906     912       4     906     951       5     900     906
-       7     981     984       1     981     987       2     963     969       4
-     963     981       5     957     963       7    1044    1047       1    1044
-    1050       2    1032    1038       8    1023    1026      11    1023    1032
-      12    1017    1023      12    1011    1017       8    1008    1011       8
-    1008    1038       8     999    1008       9     993     999       4     993
-    1044       5     987     993       7    1065    1068       1    1065    1071
-       2    1056    1065       5    1050    1056       7    1122    1125       1
-    1122    1128       2    1101    1110       4    1083    1089       4    1083
-    1101       4    1077    1083       4    1077    1122       5    1071    1077
-       7    1152    1155       1    1152    1158       2    1134    1140       4
-    1134    1152       5    1128    1134       7    1218    1221       1    1218
-    1224       2    1197    1206       6    1188    1197       4    1179    1188
-       4    1170    1179       4    1164    1170       4    1164    1218       5
-    1158    1164       7    1248    1251       1    1248    1254       2    1230
-    1236       4    1230    1248       5    1224    1230       7    1299    1302
-       1    1299    1305       2    1284    1287       3    1275    1284       3
-    1266    1275       4    1260    1266       4    1260    1299       5    1254
-    1260       7    1350    1353       1    1350    1356       2    1338    1344
-      13    1332    1338      14    1329    1332      15    1326    1329      16
-    1326    1344      17    1317    1326      18    1311    1317       4    1311
-    1350       5    1305    1311       7    1422    1425       1    1422    1428
-       2    1401    1404      19    1401    1413      19    1395    1401      19
-    1386    1395      20    1377    1386       4    1368    1377       4    1362
-    1368       4    1362    1422       5    1356    1362       7    1467    1470
-       1    1467    1473       2    1458    1461      21    1458    1464      21
-    1449    1458       5    1440    1449       4    1434    1440       4    1434
-    1467       5    1428    1434       7    1488    1491       1    1488    1494
-       2    1479    1488       5    1473    1479       7    1518    1521       1
-    1518    1524       2    1500    1506       4    1500    1518       5    1494
-    1500       7    1563    1566       1    1563    1569       2    1554    1557
-      21    1554    1560      21    1545    1554       5    1536    1545       4
-    1530    1536       4    1530    1563       5    1524    1530       7    1620
-    1623       1    1620    1626       2    1590    1596       4    1590    1608
-       4    1581    1590       4    1575    1581       4    1575    1620       5
-    1569    1575       7    1650    1653       1    1650    1656       2    1632
-    1638       4    1632    1650       5    1626    1632       7    1710    1713
-       1    1710    1716       2    1698    1704       8    1692    1698       8
-    1686    1692       8    1680    1686       8    1677    1680       8    1677
-    1704       8    1668    1677       9    1662    1668       4    1662    1710
-       5    1656    1662       7    1752    1755       1    1752    1758       2
-    1728    1734       4    1728    1746      10    1722    1728       4    1722
-    1752       5    1716    1722       7    1815    1818       1    1815    1821
-       2    1803    1809       8    1794    1797      11    1794    1803      12
-    1788    1794      12    1782    1788       8    1779    1782       8    1779
-    1809       8    1770    1779       9    1764    1770       4    1764    1815
-       5    1758    1764       7    1863    1866       1    1863    1869       2
-    1833    1839       4    1833    1851       4    1827    1833       4    1827
-    1863       5    1821    1827       7    1884    1887       1    1884    1890
-       2    1875    1884       5    1869    1875       7    1935    1938       1
+     771     780       8     765     771       6     765     795       8     759
+     765      12     861     864       1     861     867       2     840     849
+      10     831     840       6     822     831       6     813     822       6
+     807     813       6     807     861       8     801     807      12     894
+     897       1     894     900       2     879     888      17     873     879
+       6     873     894       8     867     873      12     951     954       1
+     951     957       2     930     939       6     912     918       6     912
+     930       6     906     912       6     906     951       8     900     906
+      12     981     984       1     981     987       2     963     969       6
+     963     981       8     957     963      12    1044    1047       1    1044
+    1050       2    1032    1038      14    1023    1026      18    1023    1032
+      19    1017    1023      19    1011    1017      14    1008    1011      14
+    1008    1038      14     999    1008      15     993     999       6     993
+    1044       8     987     993      12    1065    1068       1    1065    1071
+       2    1056    1065       8    1050    1056      12    1122    1125       1
+    1122    1128       2    1101    1110       6    1083    1089       6    1083
+    1101       6    1077    1083       6    1077    1122       8    1071    1077
+      12    1152    1155       1    1152    1158       2    1134    1140       6
+    1134    1152       8    1128    1134      12    1218    1221       1    1218
+    1224       2    1197    1206      10    1188    1197       6    1179    1188
+       6    1170    1179       6    1164    1170       6    1164    1218       8
+    1158    1164      12    1248    1251       1    1248    1254       2    1230
+    1236       6    1230    1248       8    1224    1230      12    1299    1302
+       1    1299    1305       2    1284    1287       4    1275    1284       4
+    1266    1275       6    1260    1266       6    1260    1299       8    1254
+    1260      12    1350    1353       1    1350    1356       2    1338    1344
+      22    1332    1338      24    1329    1332      25    1326    1329      26
+    1326    1344      27    1317    1326      28    1311    1317       6    1311
+    1350       8    1305    1311      12    1422    1425       1    1422    1428
+       2    1401    1404      30    1401    1413      30    1395    1401      30
+    1386    1395      31    1377    1386       6    1368    1377       6    1362
+    1368       6    1362    1422       8    1356    1362      12    1467    1470
+       1    1467    1473       2    1458    1461      32    1458    1464      32
+    1449    1458       8    1440    1449       6    1434    1440       6    1434
+    1467       8    1428    1434      12    1488    1491       1    1488    1494
+       2    1479    1488       8    1473    1479      12    1518    1521       1
+    1518    1524       2    1500    1506       6    1500    1518       8    1494
+    1500      12    1563    1566       1    1563    1569       2    1554    1557
+      32    1554    1560      32    1545    1554       8    1536    1545       6
+    1530    1536       6    1530    1563       8    1524    1530      12    1620
+    1623       1    1620    1626       2    1590    1596       6    1590    1608
+       6    1581    1590       6    1575    1581       6    1575    1620       8
+    1569    1575      12    1650    1653       1    1650    1656       2    1632
+    1638       6    1632    1650       8    1626    1632      12    1710    1713
+       1    1710    1716       2    1698    1704      14    1692    1698      14
+    1686    1692      14    1680    1686      14    1677    1680      14    1677
+    1704      14    1668    1677      15    1662    1668       6    1662    1710
+       8    1656    1662      12    1752    1755       1    1752    1758       2
+    1728    1734       6    1728    1746      17    1722    1728       6    1722
+    1752       8    1716    1722      12    1815    1818       1    1815    1821
+       2    1803    1809      14    1794    1797      18    1794    1803      19
+    1788    1794      19    1782    1788      14    1779    1782      14    1779
+    1809      14    1770    1779      15    1764    1770       6    1764    1815
+       8    1758    1764      12    1863    1866       1    1863    1869       2
+    1833    1839       6    1833    1851       6    1827    1833       6    1827
+    1863       8    1821    1827      12    1884    1887       1    1884    1890
+       2    1875    1884       8    1869    1875      12    1935    1938       1
     1935    1941       2    1920    1923       1    1920    1926       2    1911
-    1920       5    1902    1911       4    1896    1902       4    1896    1935
-       5    1890    1896       7    1995    1998       1    1995    2001       2
-    1983    1989       8    1977    1983       8    1971    1977       8    1965
-    1971       8    1962    1965       8    1962    1989       8    1953    1962
-       9    1947    1953       4    1947    1995       5    1941    1947       7
-    2061    2064       1    2061    2067       2    2040    2049       6    2031
-    2040       4    2022    2031       4    2013    2022       4    2007    2013
-       4    2007    2061       5    2001    2007       7    2097    2100       1
-    2097    2103       2    2088    2091      21    2088    2094      21    2079
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+   10071   10080       8   10065   10071       6   10065   10089       8   10059
+   10065      12   10146   10149       1   10146   10152       2   10125   10134
+       6   10107   10113       6   10107   10125       6   10101   10107       6
+   10101   10146       8   10095   10101      12   10197   10200       1   10197
+   10203       2   10182   10185       4   10173   10182       4   10164   10173
+       6   10158   10164       6   10158   10197       8   10152   10158      12
+   10242   10245       1   10242   10248       2   10233   10236      32   10233
+   10239      32   10224   10233       8   10215   10224       6   10209   10215
+       6   10209   10242       8   10203   10209      12   10290   10293       1
+   10290   10296       2   10260   10266       6   10260   10278       6   10254
+   10260       6   10254   10290       8   10248   10254      12   10311   10314
+       1   10311   10317       2   10302   10311       8   10296   10302      12
    10353   10356       1   10353   10359       2   10338   10341       1   10338
-   10344       2   10329   10338       5   10323   10329       4   10323   10353
-       5   10317   10323       7   10395   10398       1   10395   10401       2
-   10371   10377       4   10371   10389      10   10365   10371       4   10365
-   10395       5   10359   10365       7   10443   10446       1   10443   10449
-       2   10413   10419       4   10413   10431       4   10407   10413       4
-   10407   10443       5   10401   10407       7   10473   10476       1   10473
-   10479       2   10455   10461       4   10455   10473       5   10449   10455
-       7   10533   10536       1   10533   10539       2   10521   10527       8
-   10515   10521       8   10509   10515       8   10503   10509       8   10500
-   10503       8   10500   10527       8   10491   10500       9   10485   10491
-       4   10485   10533       5   10479   10485       7   10590   10593       1
-   10590   10596       2   10560   10566       4   10560   10578       4   10551
-   10560       4   10545   10551       4   10545   10590       5   10539   10545
-       7   10623   10626       1   10623   10629       2   10608   10617      22
-   10602   10608       4   10602   10623       5   10596   10602       7   10656
-   10659       1   10656   10662       2   10641   10650      10   10635   10641
-       4   10635   10656       5   10629   10635       7   10692   10695       1
-   10692   10698       2   10683   10686      21   10683   10689      21   10674
-   10683       5   10668   10674       4   10668   10692       5   10662   10668
-       7   10743   10746       1   10743   10749       2   10728   10731       3
-   10719   10728       3   10710   10719       4   10704   10710       4   10704
-   10743       5   10698   10704       7   10773   10776       1   10773   10779
-       2   10755   10761       4   10755   10773       5   10749   10755       7
-   10815   10818       1   10815   10821       2   10791   10797       4   10791
-   10809      10   10785   10791       4   10785   10815       5   10779   10785
-       7   10836   10839       1   10836   10842       2   10827   10836       5
-   10821   10827       7   10893   10896       1   10893   10899       2   10872
-   10881       4   10854   10860       4   10854   10872       4   10848   10854
-       4   10848   10893       5   10842   10848       7   10935   10938       1
-   10935   10941       2   10911   10917       4   10911   10929      10   10905
-   10911       4   10905   10935       5   10899   10905       7   10956   10959
-       1   10956   10962       2   10947   10956       5   10941   10947       7
-   11001   11004       1   11001   11007       2   10992   10995      21   10992
-   10998      21   10983   10992       5   10974   10983       4   10968   10974
-       4   10968   11001       5   10962   10968       7   11049   11052       1
-   11049   11055       2   11019   11025       4   11019   11037       4   11013
-   11019       4   11013   11049       5   11007   11013       7   11097   11100
-       1   11097   11103       2   11067   11073       4   11067   11085       4
-   11061   11067       4   11061   11097       5   11055   11061       7   11148
-   11151       1   11148   11154       2   11136   11142      13   11130   11136
-      14   11127   11130      15   11124   11127      16   11124   11142      17
-   11115   11124      18   11109   11115       4   11109   11148       5   11103
-   11109       7   11196   11199       1   11196   11202       2   11166   11172
-       4   11166   11184       4   11160   11166       4   11160   11196       5
-   11154   11160       7   11232   11235       1   11232   11238       2   11223
-   11226      21   11223   11229      21   11214   11223       5   11208   11214
-       4   11208   11232       5   11202   11208       7   11262   11265       1
-   11262   11268       2   11244   11250       4   11244   11262       5   11238
-   11244       7   11283   11286       1   11283   11289       2   11274   11283
-       5   11268   11274       7   11346   11349       1   11346   11352       2
-   11334   11340       8   11325   11328      11   11325   11334      12   11319
-   11325      12   11313   11319       8   11310   11313       8   11310   11340
-       8   11301   11310       9   11295   11301       4   11295   11346       5
-   11289   11295       7   11397   11400       1   11397   11403       2   11385
-   11391      13   11379   11385      14   11376   11379      15   11373   11376
-      16   11373   11391      17   11364   11373      18   11358   11364       4
-   11358   11397       5   11352   11358       7   11430   11433       1   11430
-   11436       2   11415   11424      22   11409   11415       4   11409   11430
-       5   11403   11409       7   11478   11481       1   11478   11484       2
-   11448   11454       4   11448   11466       4   11442   11448       4   11442
-   11478       5   11436   11442       7   11511   11514       1   11511   11517
-       2   11496   11505      10   11490   11496       4   11490   11511       5
-   11484   11490       7   11562   11565       1   11562   11568       2   11547
-   11550       3   11538   11547       3   11529   11538       4   11523   11529
-       4   11523   11562       5   11517   11523       7   11583   11586       1
-   11583   11589       2   11574   11583       5   11568   11574       7   11625
+   10344       2   10329   10338       8   10323   10329       6   10323   10353
+       8   10317   10323      12   10395   10398       1   10395   10401       2
+   10371   10377       6   10371   10389      17   10365   10371       6   10365
+   10395       8   10359   10365      12   10443   10446       1   10443   10449
+       2   10413   10419       6   10413   10431       6   10407   10413       6
+   10407   10443       8   10401   10407      12   10473   10476       1   10473
+   10479       2   10455   10461       6   10455   10473       8   10449   10455
+      12   10533   10536       1   10533   10539       2   10521   10527      14
+   10515   10521      14   10509   10515      14   10503   10509      14   10500
+   10503      14   10500   10527      14   10491   10500      15   10485   10491
+       6   10485   10533       8   10479   10485      12   10590   10593       1
+   10590   10596       2   10560   10566       6   10560   10578       6   10551
+   10560       6   10545   10551       6   10545   10590       8   10539   10545
+      12   10623   10626       1   10623   10629       2   10608   10617      34
+   10602   10608       6   10602   10623       8   10596   10602      12   10656
+   10659       1   10656   10662       2   10641   10650      17   10635   10641
+       6   10635   10656       8   10629   10635      12   10692   10695       1
+   10692   10698       2   10683   10686      32   10683   10689      32   10674
+   10683       8   10668   10674       6   10668   10692       8   10662   10668
+      12   10743   10746       1   10743   10749       2   10728   10731       4
+   10719   10728       4   10710   10719       6   10704   10710       6   10704
+   10743       8   10698   10704      12   10773   10776       1   10773   10779
+       2   10755   10761       6   10755   10773       8   10749   10755      12
+   10815   10818       1   10815   10821       2   10791   10797       6   10791
+   10809      17   10785   10791       6   10785   10815       8   10779   10785
+      12   10836   10839       1   10836   10842       2   10827   10836       8
+   10821   10827      12   10893   10896       1   10893   10899       2   10872
+   10881       6   10854   10860       6   10854   10872       6   10848   10854
+       6   10848   10893       8   10842   10848      12   10935   10938       1
+   10935   10941       2   10911   10917       6   10911   10929      17   10905
+   10911       6   10905   10935       8   10899   10905      12   10956   10959
+       1   10956   10962       2   10947   10956       8   10941   10947      12
+   11001   11004       1   11001   11007       2   10992   10995      32   10992
+   10998      32   10983   10992       8   10974   10983       6   10968   10974
+       6   10968   11001       8   10962   10968      12   11049   11052       1
+   11049   11055       2   11019   11025       6   11019   11037       6   11013
+   11019       6   11013   11049       8   11007   11013      12   11097   11100
+       1   11097   11103       2   11067   11073       6   11067   11085       6
+   11061   11067       6   11061   11097       8   11055   11061      12   11148
+   11151       1   11148   11154       2   11136   11142      22   11130   11136
+      24   11127   11130      25   11124   11127      26   11124   11142      27
+   11115   11124      28   11109   11115       6   11109   11148       8   11103
+   11109      12   11196   11199       1   11196   11202       2   11166   11172
+       6   11166   11184       6   11160   11166       6   11160   11196       8
+   11154   11160      12   11232   11235       1   11232   11238       2   11223
+   11226      32   11223   11229      32   11214   11223       8   11208   11214
+       6   11208   11232       8   11202   11208      12   11262   11265       1
+   11262   11268       2   11244   11250       6   11244   11262       8   11238
+   11244      12   11283   11286       1   11283   11289       2   11274   11283
+       8   11268   11274      12   11346   11349       1   11346   11352       2
+   11334   11340      14   11325   11328      18   11325   11334      19   11319
+   11325      19   11313   11319      14   11310   11313      14   11310   11340
+      14   11301   11310      15   11295   11301       6   11295   11346       8
+   11289   11295      12   11397   11400       1   11397   11403       2   11385
+   11391      22   11379   11385      24   11376   11379      25   11373   11376
+      26   11373   11391      27   11364   11373      28   11358   11364       6
+   11358   11397       8   11352   11358      12   11430   11433       1   11430
+   11436       2   11415   11424      34   11409   11415       6   11409   11430
+       8   11403   11409      12   11478   11481       1   11478   11484       2
+   11448   11454       6   11448   11466       6   11442   11448       6   11442
+   11478       8   11436   11442      12   11511   11514       1   11511   11517
+       2   11496   11505      17   11490   11496       6   11490   11511       8
+   11484   11490      12   11562   11565       1   11562   11568       2   11547
+   11550       4   11538   11547       4   11529   11538       6   11523   11529
+       6   11523   11562       8   11517   11523      12   11583   11586       1
+   11583   11589       2   11574   11583       8   11568   11574      12   11625
    11628       1   11625   11631       2   11610   11613       1   11610   11616
-       2   11601   11610       5   11595   11601       4   11595   11625       5
-   11589   11595       7   11673   11676       1   11673   11679       2   11643
-   11649       4   11643   11661       4   11637   11643       4   11637   11673
-       5   11631   11637       7   11730   11733       1   11730   11736       2
-   11700   11706       4   11700   11718       4   11691   11700       4   11685
-   11691       4   11685   11730       5   11679   11685       7   11787   11790
-       1   11787   11793       2   11757   11763       4   11757   11775       4
-   11748   11757       4   11742   11748       4   11742   11787       5   11736
-   11742       7   11832   11835       1   11832   11838       2   11823   11826
-      21   11823   11829      21   11814   11823       5   11805   11814       4
-   11799   11805       4   11799   11832       5   11793   11799       7   11883
-   11886       1   11883   11889       2   11871   11877      13   11865   11871
-      14   11862   11865      15   11859   11862      16   11859   11877      17
-   11850   11859      18   11844   11850       4   11844   11883       5   11838
-   11844       7   11934   11937       1   11934   11940       2   11922   11928
-      13   11916   11922      14   11913   11916      15   11910   11913      16
-   11910   11928      17   11901   11910      18   11895   11901       4   11895
-   11934       5   11889   11895       7   11985   11988       1   11985   11991
-       2   11973   11979      13   11967   11973      14   11964   11967      15
-   11961   11964      16   11961   11979      17   11952   11961      18   11946
-   11952       4   11946   11985       5   11940   11946       7   12036   12039
-       1   12036   12042       2   12024   12030      13   12018   12024      14
-   12015   12018      15   12012   12015      16   12012   12030      17   12003
-   12012      18   11997   12003       4   11997   12036       5   11991   11997
-       7   12087   12090       1   12087   12093       2   12075   12081      13
-   12069   12075      14   12066   12069      15   12063   12066      16   12063
-   12081      17   12054   12063      18   12048   12054       4   12048   12087
-       5   12042   12048       7   12138   12141      21   12138   12144      21
-   12126   12132      13   12120   12126      14   12117   12120      15   12114
-   12117      16   12114   12132      17   12105   12114      18   12099   12105
-       4   12099   12138       5   12093   12099       7   12273   12276      30
-   12270   12273      31   12261   12267      32   12261   12264      33   12258
-   12261      34   12258   12270      31   12255   12258      30   12252   12276
-      35   12252   12255      35   12249   12252      36   12243   12249       4
-   12243   12246      10   12237   12243       4   12237   12240      10   12234
-   12249      37   12231   12234      37   12231   12237       4   12228   12231
-       4   12225   12228      37   12216   12225      38   12216   12219      39
-   12216   12222      39   12213   12216      38   12207   12210      40   12204
-   12207      41   12201   12204      41   12195   12201      42   12195   12198
-      19   12192   12210      43   12192   12195      23   12189   12192      44
-   12186   12189      45   12183   12186      46   12183   12210      47   12180
-   12183      48   12174   12180       4   12174   12177      10   12168   12174
-       4   12168   12171      10   12165   12180      37   12162   12168       4
-   12162   12165      37   12159   12162       4   12156   12159      37   12147
-   12213      38   12147   12150      39   12147   12153      39   12147   12156
-      38   12393   12396      49   12390   12393      49   12390   12402      50
-   12387   12390      49   12384   12387      49   12384   12399      50   12381
-   12384      49   12381   12396      49   12375   12381      51   12369   12372
-      49   12366   12369      49   12366   12405      50   12363   12366      49
-   12360   12363      49   12360   12378      52   12357   12360      49   12357
-   12372      49   12357   12375      51
+       2   11601   11610       8   11595   11601       6   11595   11625       8
+   11589   11595      12   11673   11676       1   11673   11679       2   11643
+   11649       6   11643   11661       6   11637   11643       6   11637   11673
+       8   11631   11637      12   11730   11733       1   11730   11736       2
+   11700   11706       6   11700   11718       6   11691   11700       6   11685
+   11691       6   11685   11730       8   11679   11685      12   11787   11790
+       1   11787   11793       2   11757   11763       6   11757   11775       6
+   11748   11757       6   11742   11748       6   11742   11787       8   11736
+   11742      12   11832   11835       1   11832   11838       2   11823   11826
+      32   11823   11829      32   11814   11823       8   11805   11814       6
+   11799   11805       6   11799   11832       8   11793   11799      12   11883
+   11886       1   11883   11889       2   11871   11877      22   11865   11871
+      24   11862   11865      25   11859   11862      26   11859   11877      27
+   11850   11859      28   11844   11850       6   11844   11883       8   11838
+   11844      12   11934   11937       1   11934   11940       2   11922   11928
+      22   11916   11922      24   11913   11916      25   11910   11913      26
+   11910   11928      27   11901   11910      28   11895   11901       6   11895
+   11934       8   11889   11895      12   11985   11988       1   11985   11991
+       2   11973   11979      22   11967   11973      24   11964   11967      25
+   11961   11964      26   11961   11979      27   11952   11961      28   11946
+   11952       6   11946   11985       8   11940   11946      12   12036   12039
+       1   12036   12042       2   12024   12030      22   12018   12024      24
+   12015   12018      25   12012   12015      26   12012   12030      27   12003
+   12012      28   11997   12003       6   11997   12036       8   11991   11997
+      12   12087   12090       1   12087   12093       2   12075   12081      22
+   12069   12075      24   12066   12069      25   12063   12066      26   12063
+   12081      27   12054   12063      28   12048   12054       6   12048   12087
+       8   12042   12048      12   12138   12141      32   12138   12144      32
+   12126   12132      22   12120   12126      24   12117   12120      25   12114
+   12117      26   12114   12132      27   12105   12114      28   12099   12105
+       6   12099   12138       8   12093   12099      12   12273   12276      43
+   12270   12273      45   12261   12267      48   12261   12264      49   12258
+   12261      50   12258   12270      45   12255   12258      43   12252   12276
+      51   12252   12255      51   12249   12252      52   12243   12249       6
+   12243   12246      17   12237   12243       6   12237   12240      17   12234
+   12249      54   12231   12234      54   12231   12237       6   12228   12231
+       6   12225   12228      54   12216   12225      55   12216   12219      56
+   12216   12222      56   12213   12216      55   12207   12210      57   12204
+   12207      58   12201   12204      58   12195   12201      60   12195   12198
+      30   12192   12210      61   12192   12195      35   12189   12192      62
+   12186   12189      63   12183   12186      65   12183   12210      66   12180
+   12183      67   12174   12180       6   12174   12177      17   12168   12174
+       6   12168   12171      17   12165   12180      54   12162   12168       6
+   12162   12165      54   12159   12162       6   12156   12159      54   12147
+   12213      55   12147   12150      56   12147   12153      56   12147   12156
+      55   12393   12396      69   12390   12393      69   12390   12402      70
+   12387   12390      69   12384   12387      69   12384   12399      70   12381
+   12384      69   12381   12396      69   12375   12381      72   12369   12372
+      69   12366   12369      69   12366   12405      70   12363   12366      69
+   12360   12363      69   12360   12378      73   12357   12360      69   12357
+   12372      69   12357   12375      72
 %FLAG ANGLES_INC_HYDROGEN                                                       
 %FORMAT(10I8)                                                                   
-      51      57      60      92      45      39      48      93      42      39
-      45      93      42      39      48      93      36      39      42      94
-      36      39      45      94      36      39      48      94      33      27
-      36      94      30      27      33      93      30      27      36      94
-      24      18      27      95      21      18      24      96      21      18
-      27      95      18      27      30      97      18      27      33      97
-      15      12      18      98      15      12      51      99      12      18
-      21      95      12      18      24      95       9       0      12     100
-       6       0       9     101       6       0      12     100       3       0
-       6     101       3       0       9     101       3       0      12     100
-       0      12      15     102      72      78      81      92      69      63
-      72     103      66      63      69      93      66      63      72     103
-      60      57      63     104      57      63      66     105      57      63
-      69     105     132     138     141      92     123     120     126     106
-     120     126     129     106     117     114     120     106     114     120
-     123     106     111     108     114     106     108     114     117     106
-     105     102     108     106     102     108     111     106      99     102
-     105     106      99     126     129     106      96      90      99     107
-      93      90      96      96      93      90      99     107      87      84
-      90      97      87      84     132     103      84      90      93      95
-      84      90      96      95      81      78      84     104      78      84
-      87     105     189     195     198      92     183     177     186      96
-     180     177     183      96     180     177     186      96     171     165
-     174      96     168     165     171      96     168     165     174      96
-     162     159     165      95     162     159     177      95     159     165
-     168      95     159     165     171      95     159     165     174      95
-     159     177     180      95     159     177     183      95     159     177
-     186      95     156     150     159      95     153     150     156      96
-     153     150     159      95     150     159     162      95     147     144
-     150      97     147     144     189     103     144     150     153      95
-     144     150     156      95     141     138     144     104     138     144
-     147     105     219     225     228      92     213     207     216      96
-     210     207     213      96     210     207     216      96     204     201
-     207      97     204     201     219     103     201     207     210      95
-     201     207     213      95     201     207     216      95     198     195
-     201     104     195     201     204     105     240     246     249      92
-     237     231     240     103     234     231     237      93     234     231
-     240     103     228     225     231     104     225     231     234     105
-     225     231     237     105     306     312     315      92     300     294
-     303     101     297     294     300     101     297     294     303     101
-     291     285     294     102     288     285     291     108     288     285
-     294     102     285     294     297     100     285     294     300     100
-     285     294     303     100     282     276     285      95     279     276
-     282      96     279     276     285      95     276     285     288      98
-     276     285     291      98     273     267     276      95     270     267
-     273      96     270     267     276      95     267     276     279      95
-     267     276     282      95     264     258     267      95     261     258
-     264      96     261     258     267      95     258     267     270      95
-     258     267     273      95     255     252     258      97     255     252
-     306     103     252     258     261      95     252     258     264      95
-     249     246     252     104     246     252     255     105     372     378
-     381      92     366     360     369     101     363     360     366     101
-     363     360     369     101     357     351     360     102     354     351
-     357     108     354     351     360     102     351     360     363     100
-     351     360     366     100     351     360     369     100     348     342
-     351      95     345     342     348      96     345     342     351      95
-     342     351     354      98     342     351     357      98     339     333
-     342      95     336     333     339      96     336     333     342      95
-     333     342     345      95     333     342     348      95     330     324
-     333      95     327     324     330      96     327     324     333      95
-     324     333     336      95     324     333     339      95     321     318
-     324      97     321     318     372     103     318     324     327      95
-     318     324     330      95     315     312     318     104     312     318
-     321     105     429     435     438      92     423     417     426      96
-     420     417     423      96     420     417     426      96     414     408
-     417      95     411     408     414      96     411     408     417      95
-     408     417     420      95     408     417     423      95     408     417
-     426      95     402     396     405      96     399     396     402      96
-     399     396     405      96     393     390     396      95     393     390
-     408      95     390     396     399      95     390     396     402      95
-     390     396     405      95     390     408     411      95     390     408
-     414      95     387     384     390      97     387     384     429     103
-     384     390     393      95     381     378     384     104     378     384
-     387     105     486     492     495      92     480     474     483      96
-     477     474     480      96     477     474     483      96     468     462
-     471      96     465     462     468      96     465     462     471      96
-     459     456     462      95     459     456     474      95     456     462
-     465      95     456     462     468      95     456     462     471      95
-     456     474     477      95     456     474     480      95     456     474
-     483      95     453     447     456      95     450     447     453      96
-     450     447     456      95     447     456     459      95     444     441
-     447      97     444     441     486     103     441     447     450      95
-     441     447     453      95     438     435     441     104     435     441
-     444     105     543     549     552      92     537     531     540      96
-     534     531     537      96     534     531     540      96     528     522
-     531      95     525     522     528      96     525     522     531      95
-     522     531     534      95     522     531     537      95     522     531
-     540      95     516     510     519      96     513     510     516      96
-     513     510     519      96     507     504     510      95     507     504
-     522      95     504     510     513      95     504     510     516      95
-     504     510     519      95     504     522     525      95     504     522
-     528      95     501     498     504      97     501     498     543     103
-     498     504     507      95     495     492     498     104     492     498
-     501     105     585     591     594      92     573     567     576      96
-     570     567     573      96     570     567     576      96     564     561
-     567      97     564     561     579     109     561     567     570      95
-     561     567     573      95     561     567     576      95     561     579
-     582     110     558     555     561      97     558     555     585     103
-     555     561     564      97     552     549     555     104     549     555
-     558     105     606     612     615      92     603     597     606     103
-     600     597     603      93     600     597     606     103     594     591
-     597     104     591     597     600     105     591     597     603     105
-     663     669     672      92     657     651     660      96     654     651
-     657      96     654     651     660      96     645     639     648      96
-     642     639     645      96     642     639     648      96     636     633
-     639      95     636     633     651      95     633     639     642      95
-     633     639     645      95     633     639     648      95     633     651
-     654      95     633     651     657      95     633     651     660      95
-     630     624     633      95     627     624     630      96     627     624
-     633      95     624     633     636      95     621     618     624      97
-     621     618     663     103     618     624     627      95     618     624
-     630      95     615     612     618     104     612     618     621     105
-     720     726     729      92     714     708     717      96     711     708
-     714      96     711     708     717      96     702     696     705      96
-     699     696     702      96     699     696     705      96     693     690
-     696      95     693     690     708      95     690     696     699      95
-     690     696     702      95     690     696     705      95     690     708
-     711      95     690     708     714      95     690     708     717      95
-     687     681     690      95     684     681     687      96     684     681
-     690      95     681     690     693      95     678     675     681      97
-     678     675     720     103     675     681     684      95     675     681
-     687      95     672     669     675     104     669     675     678     105
-     753     759     762      92     744     738     747     109     741     738
-     744      93     741     738     747     109     738     747     750     110
-     735     732     738      97     735     732     753     103     732     738
-     741      97     732     738     744      97     729     726     732     104
-     726     732     735     105     795     801     804      92     789     786
-     792     111     780     786     789      92     780     786     792      92
-     777     771     780     112     774     771     777      96     774     771
-     780     112     768     765     771      97     768     765     795     103
-     765     771     774      95     765     771     777      95     762     759
-     765     104     759     765     768     105     861     867     870      92
-     855     849     858     101     852     849     855     101     852     849
-     858     101     846     840     849     102     843     840     846     108
-     843     840     849     102     840     849     852     100     840     849
-     855     100     840     849     858     100     837     831     840      95
-     834     831     837      96     834     831     840      95     831     840
-     843      98     831     840     846      98     828     822     831      95
-     825     822     828      96     825     822     831      95     822     831
-     834      95     822     831     837      95     819     813     822      95
-     816     813     819      96     816     813     822      95     813     822
-     825      95     813     822     828      95     810     807     813      97
-     810     807     861     103     807     813     816      95     807     813
-     819      95     804     801     807     104     801     807     810     105
-     894     900     903      92     885     879     888     109     882     879
-     885      93     882     879     888     109     879     888     891     110
-     876     873     879      97     876     873     894     103     873     879
-     882      97     873     879     885      97     870     867     873     104
-     867     873     876     105     951     957     960      92     945     939
-     948      96     942     939     945      96     942     939     948      96
-     936     930     939      95     933     930     936      96     933     930
-     939      95     930     939     942      95     930     939     945      95
-     930     939     948      95     924     918     927      96     921     918
-     924      96     921     918     927      96     915     912     918      95
-     915     912     930      95     912     918     921      95     912     918
-     924      95     912     918     927      95     912     930     933      95
-     912     930     936      95     909     906     912      97     909     906
-     951     103     906     912     915      95     903     900     906     104
-     900     906     909     105     981     987     990      92     975     969
-     978      96     972     969     975      96     972     969     978      96
-     966     963     969      97     966     963     981     103     963     969
-     972      95     963     969     975      95     963     969     978      95
-     960     957     963     104     957     963     966     105    1044    1050
-    1053      92    1035    1032    1038     106    1032    1038    1041     106
-    1023    1026    1029     113    1023    1032    1035     114    1020    1017
-    1023     114    1014    1011    1017     106    1011    1017    1020     106
-    1008    1011    1014     106    1008    1038    1041     106    1005     999
-    1008     107    1002     999    1005      96    1002     999    1008     107
-     996     993     999      97     996     993    1044     103     993     999
-    1002      95     993     999    1005      95     990     987     993     104
-     987     993     996     105    1065    1071    1074      92    1062    1056
-    1065     103    1059    1056    1062      93    1059    1056    1065     103
-    1053    1050    1056     104    1050    1056    1059     105    1050    1056
-    1062     105    1122    1128    1131      92    1116    1110    1119      96
-    1113    1110    1116      96    1113    1110    1119      96    1107    1101
-    1110      95    1104    1101    1107      96    1104    1101    1110      95
-    1101    1110    1113      95    1101    1110    1116      95    1101    1110
-    1119      95    1095    1089    1098      96    1092    1089    1095      96
-    1092    1089    1098      96    1086    1083    1089      95    1086    1083
-    1101      95    1083    1089    1092      95    1083    1089    1095      95
-    1083    1089    1098      95    1083    1101    1104      95    1083    1101
-    1107      95    1080    1077    1083      97    1080    1077    1122     103
-    1077    1083    1086      95    1074    1071    1077     104    1071    1077
-    1080     105    1152    1158    1161      92    1146    1140    1149      96
-    1143    1140    1146      96    1143    1140    1149      96    1137    1134
-    1140      97    1137    1134    1152     103    1134    1140    1143      95
-    1134    1140    1146      95    1134    1140    1149      95    1131    1128
-    1134     104    1128    1134    1137     105    1218    1224    1227      92
-    1212    1206    1215     101    1209    1206    1212     101    1209    1206
-    1215     101    1203    1197    1206     102    1200    1197    1203     108
-    1200    1197    1206     102    1197    1206    1209     100    1197    1206
-    1212     100    1197    1206    1215     100    1194    1188    1197      95
-    1191    1188    1194      96    1191    1188    1197      95    1188    1197
-    1200      98    1188    1197    1203      98    1185    1179    1188      95
-    1182    1179    1185      96    1182    1179    1188      95    1179    1188
-    1191      95    1179    1188    1194      95    1176    1170    1179      95
-    1173    1170    1176      96    1173    1170    1179      95    1170    1179
-    1182      95    1170    1179    1185      95    1167    1164    1170      97
-    1167    1164    1218     103    1164    1170    1173      95    1164    1170
-    1176      95    1161    1158    1164     104    1158    1164    1167     105
-    1248    1254    1257      92    1242    1236    1245      96    1239    1236
-    1242      96    1239    1236    1245      96    1233    1230    1236      97
-    1233    1230    1248     103    1230    1236    1239      95    1230    1236
-    1242      95    1230    1236    1245      95    1227    1224    1230     104
-    1224    1230    1233     105    1299    1305    1308      92    1293    1287
-    1296      93    1290    1287    1293      93    1290    1287    1296      93
-    1284    1287    1290      94    1284    1287    1293      94    1284    1287
-    1296      94    1281    1275    1284      94    1278    1275    1281      93
-    1278    1275    1284      94    1272    1266    1275      95    1269    1266
-    1272      96    1269    1266    1275      95    1266    1275    1278      97
-    1266    1275    1281      97    1263    1260    1266      97    1263    1260
-    1299     103    1260    1266    1269      95    1260    1266    1272      95
-    1257    1254    1260     104    1254    1260    1263     105    1350    1356
-    1359      92    1341    1338    1344     115    1338    1344    1347     116
-    1335    1332    1338     117    1332    1338    1341     118    1329    1332
-    1335     119    1326    1344    1347     120    1323    1317    1326     121
-    1320    1317    1323      96    1320    1317    1326     121    1314    1311
-    1317      97    1314    1311    1350     103    1311    1317    1320      95
-    1311    1317    1323      95    1308    1305    1311     104    1305    1311
-    1314     105    1422    1428    1431      92    1416    1413    1419     122
-    1407    1404    1410     122    1401    1404    1407     123    1401    1404
-    1410     123    1401    1413    1416     123    1401    1413    1419     123
-    1398    1395    1401     123    1392    1386    1395     124    1389    1386
-    1392      93    1389    1386    1395     124    1386    1395    1398     125
-    1383    1377    1386      95    1380    1377    1383      96    1380    1377
-    1386      95    1377    1386    1389      97    1377    1386    1392      97
-    1374    1368    1377      95    1371    1368    1374      96    1371    1368
-    1377      95    1368    1377    1380      95    1368    1377    1383      95
-    1365    1362    1368      97    1365    1362    1422     103    1362    1368
-    1371      95    1362    1368    1374      95    1359    1356    1362     104
-    1356    1362    1365     105    1467    1473    1476      92    1455    1449
-    1458     112    1452    1449    1455      96    1452    1449    1458     112
-    1446    1440    1449      95    1443    1440    1446      96    1443    1440
-    1449      95    1440    1449    1452      95    1440    1449    1455      95
-    1437    1434    1440      97    1437    1434    1467     103    1434    1440
-    1443      95    1434    1440    1446      95    1431    1428    1434     104
-    1428    1434    1437     105    1488    1494    1497      92    1485    1479
-    1488     103    1482    1479    1485      93    1482    1479    1488     103
-    1476    1473    1479     104    1473    1479    1482     105    1473    1479
-    1485     105    1518    1524    1527      92    1512    1506    1515      96
-    1509    1506    1512      96    1509    1506    1515      96    1503    1500
-    1506      97    1503    1500    1518     103    1500    1506    1509      95
-    1500    1506    1512      95    1500    1506    1515      95    1497    1494
-    1500     104    1494    1500    1503     105    1563    1569    1572      92
-    1551    1545    1554     112    1548    1545    1551      96    1548    1545
-    1554     112    1542    1536    1545      95    1539    1536    1542      96
-    1539    1536    1545      95    1536    1545    1548      95    1536    1545
-    1551      95    1533    1530    1536      97    1533    1530    1563     103
-    1530    1536    1539      95    1530    1536    1542      95    1527    1524
-    1530     104    1524    1530    1533     105    1620    1626    1629      92
-    1614    1608    1617      96    1611    1608    1614      96    1611    1608
-    1617      96    1602    1596    1605      96    1599    1596    1602      96
-    1599    1596    1605      96    1593    1590    1596      95    1593    1590
-    1608      95    1590    1596    1599      95    1590    1596    1602      95
-    1590    1596    1605      95    1590    1608    1611      95    1590    1608
-    1614      95    1590    1608    1617      95    1587    1581    1590      95
-    1584    1581    1587      96    1584    1581    1590      95    1581    1590
-    1593      95    1578    1575    1581      97    1578    1575    1620     103
-    1575    1581    1584      95    1575    1581    1587      95    1572    1569
-    1575     104    1569    1575    1578     105    1650    1656    1659      92
-    1644    1638    1647      96    1641    1638    1644      96    1641    1638
-    1647      96    1635    1632    1638      97    1635    1632    1650     103
-    1632    1638    1641      95    1632    1638    1644      95    1632    1638
-    1647      95    1629    1626    1632     104    1626    1632    1635     105
-    1710    1716    1719      92    1701    1698    1704     106    1698    1704
-    1707     106    1695    1692    1698     106    1692    1698    1701     106
-    1689    1686    1692     106    1686    1692    1695     106    1683    1680
-    1686     106    1680    1686    1689     106    1677    1680    1683     106
-    1677    1704    1707     106    1674    1668    1677     107    1671    1668
-    1674      96    1671    1668    1677     107    1665    1662    1668      97
-    1665    1662    1710     103    1662    1668    1671      95    1662    1668
-    1674      95    1659    1656    1662     104    1656    1662    1665     105
-    1752    1758    1761      92    1740    1734    1743      96    1737    1734
-    1740      96    1737    1734    1743      96    1731    1728    1734      97
-    1731    1728    1746     109    1728    1734    1737      95    1728    1734
-    1740      95    1728    1734    1743      95    1728    1746    1749     110
-    1725    1722    1728      97    1725    1722    1752     103    1722    1728
-    1731      97    1719    1716    1722     104    1716    1722    1725     105
-    1815    1821    1824      92    1806    1803    1809     106    1803    1809
-    1812     106    1794    1797    1800     113    1794    1803    1806     114
-    1791    1788    1794     114    1785    1782    1788     106    1782    1788
-    1791     106    1779    1782    1785     106    1779    1809    1812     106
-    1776    1770    1779     107    1773    1770    1776      96    1773    1770
-    1779     107    1767    1764    1770      97    1767    1764    1815     103
-    1764    1770    1773      95    1764    1770    1776      95    1761    1758
-    1764     104    1758    1764    1767     105    1863    1869    1872      92
-    1857    1851    1860      96    1854    1851    1857      96    1854    1851
-    1860      96    1845    1839    1848      96    1842    1839    1845      96
-    1842    1839    1848      96    1836    1833    1839      95    1836    1833
-    1851      95    1833    1839    1842      95    1833    1839    1845      95
-    1833    1839    1848      95    1833    1851    1854      95    1833    1851
-    1857      95    1833    1851    1860      95    1830    1827    1833      97
-    1830    1827    1863     103    1827    1833    1836      95    1824    1821
-    1827     104    1821    1827    1830     105    1884    1890    1893      92
-    1881    1875    1884     103    1878    1875    1881      93    1878    1875
-    1884     103    1872    1869    1875     104    1869    1875    1878     105
-    1869    1875    1881     105    1935    1941    1944      92    1929    1926
-    1932     111    1920    1926    1929      92    1920    1926    1932      92
-    1917    1911    1920     112    1914    1911    1917      96    1914    1911
-    1920     112    1908    1902    1911      95    1905    1902    1908      96
-    1905    1902    1911      95    1902    1911    1914      95    1902    1911
-    1917      95    1899    1896    1902      97    1899    1896    1935     103
-    1896    1902    1905      95    1896    1902    1908      95    1893    1890
-    1896     104    1890    1896    1899     105    1995    2001    2004      92
-    1986    1983    1989     106    1983    1989    1992     106    1980    1977
-    1983     106    1977    1983    1986     106    1974    1971    1977     106
-    1971    1977    1980     106    1968    1965    1971     106    1965    1971
-    1974     106    1962    1965    1968     106    1962    1989    1992     106
-    1959    1953    1962     107    1956    1953    1959      96    1956    1953
-    1962     107    1950    1947    1953      97    1950    1947    1995     103
-    1947    1953    1956      95    1947    1953    1959      95    1944    1941
-    1947     104    1941    1947    1950     105    2061    2067    2070      92
-    2055    2049    2058     101    2052    2049    2055     101    2052    2049
-    2058     101    2046    2040    2049     102    2043    2040    2046     108
-    2043    2040    2049     102    2040    2049    2052     100    2040    2049
-    2055     100    2040    2049    2058     100    2037    2031    2040      95
-    2034    2031    2037      96    2034    2031    2040      95    2031    2040
-    2043      98    2031    2040    2046      98    2028    2022    2031      95
-    2025    2022    2028      96    2025    2022    2031      95    2022    2031
-    2034      95    2022    2031    2037      95    2019    2013    2022      95
-    2016    2013    2019      96    2016    2013    2022      95    2013    2022
-    2025      95    2013    2022    2028      95    2010    2007    2013      97
-    2010    2007    2061     103    2007    2013    2016      95    2007    2013
-    2019      95    2004    2001    2007     104    2001    2007    2010     105
-    2097    2103    2106      92    2085    2079    2088     112    2082    2079
-    2085      96    2082    2079    2088     112    2076    2073    2079      97
-    2076    2073    2097     103    2073    2079    2082      95    2073    2079
-    2085      95    2070    2067    2073     104    2067    2073    2076     105
-    2169    2175    2178      92    2163    2160    2166     122    2154    2151
-    2157     122    2148    2151    2154     123    2148    2151    2157     123
-    2148    2160    2163     123    2148    2160    2166     123    2145    2142
-    2148     123    2139    2133    2142     124    2136    2133    2139      93
-    2136    2133    2142     124    2133    2142    2145     125    2130    2124
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+   11067   11073   11076       7   11067   11073   11079       7   11067   11073
+   11082       7   11067   11085   11088       7   11067   11085   11091       7
+   11067   11085   11094       7   11064   11061   11067      10   11064   11061
+   11097      22   11061   11067   11070       7   11058   11055   11061      23
+   11055   11061   11064      24   11148   11154   11157       2   11139   11136
+   11142      43   11136   11142   11145      44   11133   11130   11136      45
+   11130   11136   11139      46   11127   11130   11133      49   11124   11142
+   11145      53   11121   11115   11124      54   11118   11115   11121       8
+   11118   11115   11124      54   11112   11109   11115      10   11112   11109
+   11148      22   11109   11115   11118       7   11109   11115   11121       7
+   11106   11103   11109      23   11103   11109   11112      24   11196   11202
+   11205       2   11190   11184   11193       8   11187   11184   11190       8
+   11187   11184   11193       8   11178   11172   11181       8   11175   11172
+   11178       8   11175   11172   11181       8   11169   11166   11172       7
+   11169   11166   11184       7   11166   11172   11175       7   11166   11172
+   11178       7   11166   11172   11181       7   11166   11184   11187       7
+   11166   11184   11190       7   11166   11184   11193       7   11163   11160
+   11166      10   11163   11160   11196      22   11160   11166   11169       7
+   11157   11154   11160      23   11154   11160   11163      24   11232   11238
+   11241       2   11220   11214   11223      37   11217   11214   11220       8
+   11217   11214   11223      37   11211   11208   11214      10   11211   11208
+   11232      22   11208   11214   11217       7   11208   11214   11220       7
+   11205   11202   11208      23   11202   11208   11211      24   11262   11268
+   11271       2   11256   11250   11259       8   11253   11250   11256       8
+   11253   11250   11259       8   11247   11244   11250      10   11247   11244
+   11262      22   11244   11250   11253       7   11244   11250   11256       7
+   11244   11250   11259       7   11241   11238   11244      23   11238   11244
+   11247      24   11283   11289   11292       2   11280   11274   11283      22
+   11277   11274   11280       4   11277   11274   11283      22   11271   11268
+   11274      23   11268   11274   11277      24   11268   11274   11280      24
+   11346   11352   11355       2   11337   11334   11340      26   11334   11340
+   11343      26   11325   11328   11331      39   11325   11334   11337      40
+   11322   11319   11325      40   11316   11313   11319      26   11313   11319
+   11322      26   11310   11313   11316      26   11310   11340   11343      26
+   11307   11301   11310      28   11304   11301   11307       8   11304   11301
+   11310      28   11298   11295   11301      10   11298   11295   11346      22
+   11295   11301   11304       7   11295   11301   11307       7   11292   11289
+   11295      23   11289   11295   11298      24   11397   11403   11406       2
+   11388   11385   11391      43   11385   11391   11394      44   11382   11379
+   11385      45   11379   11385   11388      46   11376   11379   11382      49
+   11373   11391   11394      53   11370   11364   11373      54   11367   11364
+   11370       8   11367   11364   11373      54   11361   11358   11364      10
+   11361   11358   11397      22   11358   11364   11367       7   11358   11364
+   11370       7   11355   11352   11358      23   11352   11358   11361      24
+   11430   11436   11439       2   11421   11415   11424      67   11418   11415
+   11421       4   11418   11415   11424      67   11415   11424   11427      68
+   11412   11409   11415      10   11412   11409   11430      22   11409   11415
+   11418      10   11409   11415   11421      10   11406   11403   11409      23
+   11403   11409   11412      24   11478   11484   11487       2   11472   11466
+   11475       8   11469   11466   11472       8   11469   11466   11475       8
+   11460   11454   11463       8   11457   11454   11460       8   11457   11454
+   11463       8   11451   11448   11454       7   11451   11448   11466       7
+   11448   11454   11457       7   11448   11454   11460       7   11448   11454
+   11463       7   11448   11466   11469       7   11448   11466   11472       7
+   11448   11466   11475       7   11445   11442   11448      10   11445   11442
+   11478      22   11442   11448   11451       7   11439   11436   11442      23
+   11436   11442   11445      24   11511   11517   11520       2   11502   11496
+   11505      34   11499   11496   11502       4   11499   11496   11505      34
+   11496   11505   11508      35   11493   11490   11496      10   11493   11490
+   11511      22   11490   11496   11499      10   11490   11496   11502      10
+   11487   11484   11490      23   11484   11490   11493      24   11562   11568
+   11571       2   11556   11550   11559       4   11553   11550   11556       4
+   11553   11550   11559       4   11547   11550   11553       5   11547   11550
+   11556       5   11547   11550   11559       5   11544   11538   11547       5
+   11541   11538   11544       4   11541   11538   11547       5   11535   11529
+   11538       7   11532   11529   11535       8   11532   11529   11538       7
+   11529   11538   11541      10   11529   11538   11544      10   11526   11523
+   11529      10   11526   11523   11562      22   11523   11529   11532       7
+   11523   11529   11535       7   11520   11517   11523      23   11517   11523
+   11526      24   11583   11589   11592       2   11580   11574   11583      22
+   11577   11574   11580       4   11577   11574   11583      22   11571   11568
+   11574      23   11568   11574   11577      24   11568   11574   11580      24
+   11625   11631   11634       2   11619   11616   11622      36   11610   11616
+   11619       2   11610   11616   11622       2   11607   11601   11610      37
+   11604   11601   11607       8   11604   11601   11610      37   11598   11595
+   11601      10   11598   11595   11625      22   11595   11601   11604       7
+   11595   11601   11607       7   11592   11589   11595      23   11589   11595
+   11598      24   11673   11679   11682       2   11667   11661   11670       8
+   11664   11661   11667       8   11664   11661   11670       8   11655   11649
+   11658       8   11652   11649   11655       8   11652   11649   11658       8
+   11646   11643   11649       7   11646   11643   11661       7   11643   11649
+   11652       7   11643   11649   11655       7   11643   11649   11658       7
+   11643   11661   11664       7   11643   11661   11667       7   11643   11661
+   11670       7   11640   11637   11643      10   11640   11637   11673      22
+   11637   11643   11646       7   11634   11631   11637      23   11631   11637
+   11640      24   11730   11736   11739       2   11724   11718   11727       8
+   11721   11718   11724       8   11721   11718   11727       8   11712   11706
+   11715       8   11709   11706   11712       8   11709   11706   11715       8
+   11703   11700   11706       7   11703   11700   11718       7   11700   11706
+   11709       7   11700   11706   11712       7   11700   11706   11715       7
+   11700   11718   11721       7   11700   11718   11724       7   11700   11718
+   11727       7   11697   11691   11700       7   11694   11691   11697       8
+   11694   11691   11700       7   11691   11700   11703       7   11688   11685
+   11691      10   11688   11685   11730      22   11685   11691   11694       7
+   11685   11691   11697       7   11682   11679   11685      23   11679   11685
+   11688      24   11787   11793   11796       2   11781   11775   11784       8
+   11778   11775   11781       8   11778   11775   11784       8   11769   11763
+   11772       8   11766   11763   11769       8   11766   11763   11772       8
+   11760   11757   11763       7   11760   11757   11775       7   11757   11763
+   11766       7   11757   11763   11769       7   11757   11763   11772       7
+   11757   11775   11778       7   11757   11775   11781       7   11757   11775
+   11784       7   11754   11748   11757       7   11751   11748   11754       8
+   11751   11748   11757       7   11748   11757   11760       7   11745   11742
+   11748      10   11745   11742   11787      22   11742   11748   11751       7
+   11742   11748   11754       7   11739   11736   11742      23   11736   11742
+   11745      24   11832   11838   11841       2   11820   11814   11823      37
+   11817   11814   11820       8   11817   11814   11823      37   11811   11805
+   11814       7   11808   11805   11811       8   11808   11805   11814       7
+   11805   11814   11817       7   11805   11814   11820       7   11802   11799
+   11805      10   11802   11799   11832      22   11799   11805   11808       7
+   11799   11805   11811       7   11796   11793   11799      23   11793   11799
+   11802      24   11883   11889   11892       2   11874   11871   11877      43
+   11871   11877   11880      44   11868   11865   11871      45   11865   11871
+   11874      46   11862   11865   11868      49   11859   11877   11880      53
+   11856   11850   11859      54   11853   11850   11856       8   11853   11850
+   11859      54   11847   11844   11850      10   11847   11844   11883      22
+   11844   11850   11853       7   11844   11850   11856       7   11841   11838
+   11844      23   11838   11844   11847      24   11934   11940   11943       2
+   11925   11922   11928      43   11922   11928   11931      44   11919   11916
+   11922      45   11916   11922   11925      46   11913   11916   11919      49
+   11910   11928   11931      53   11907   11901   11910      54   11904   11901
+   11907       8   11904   11901   11910      54   11898   11895   11901      10
+   11898   11895   11934      22   11895   11901   11904       7   11895   11901
+   11907       7   11892   11889   11895      23   11889   11895   11898      24
+   11985   11991   11994       2   11976   11973   11979      43   11973   11979
+   11982      44   11970   11967   11973      45   11967   11973   11976      46
+   11964   11967   11970      49   11961   11979   11982      53   11958   11952
+   11961      54   11955   11952   11958       8   11955   11952   11961      54
+   11949   11946   11952      10   11949   11946   11985      22   11946   11952
+   11955       7   11946   11952   11958       7   11943   11940   11946      23
+   11940   11946   11949      24   12036   12042   12045       2   12027   12024
+   12030      43   12024   12030   12033      44   12021   12018   12024      45
+   12018   12024   12027      46   12015   12018   12021      49   12012   12030
+   12033      53   12009   12003   12012      54   12006   12003   12009       8
+   12006   12003   12012      54   12000   11997   12003      10   12000   11997
+   12036      22   11997   12003   12006       7   11997   12003   12009       7
+   11994   11991   11997      23   11991   11997   12000      24   12087   12093
+   12096       2   12078   12075   12081      43   12075   12081   12084      44
+   12072   12069   12075      45   12069   12075   12078      46   12066   12069
+   12072      49   12063   12081   12084      53   12060   12054   12063      54
+   12057   12054   12060       8   12057   12054   12063      54   12051   12048
+   12054      10   12051   12048   12087      22   12048   12054   12057       7
+   12048   12054   12060       7   12045   12042   12048      23   12042   12048
+   12051      24   12129   12126   12132      43   12126   12132   12135      44
+   12123   12120   12126      45   12120   12126   12129      46   12117   12120
+   12123      49   12114   12132   12135      53   12111   12105   12114      54
+   12108   12105   12111       8   12108   12105   12114      54   12102   12099
+   12105      10   12102   12099   12138      22   12099   12105   12108       7
+   12099   12105   12111       7   12096   12093   12099      23   12093   12099
+   12102      24   12342   12267   12345      90   12315   12228   12318       4
+   12306   12198   12309      58   12279   12159   12282       4   12276   12273
+   12351      91   12273   12270   12348      92   12273   12276   12354      93
+   12270   12273   12351      95   12261   12267   12342      98   12261   12267
+   12345      98   12258   12255   12339      93   12258   12270   12348      92
+   12252   12249   12336     104   12252   12276   12354     106   12252   12255
+   12339     106   12249   12243   12330      10   12246   12243   12330      34
+   12243   12237   12324      10   12243   12249   12336     109   12243   12246
+   12333      35   12240   12237   12324      34   12237   12231   12321      10
+   12237   12243   12330      10   12237   12240   12327      35   12234   12231
+   12321     111   12234   12249   12336     113   12231   12228   12318      10
+   12231   12228   12315      10   12231   12237   12324      10   12228   12231
+   12321      10   12225   12228   12318     111   12225   12228   12315     111
+   12207   12204   12312     119   12201   12204   12312     119   12195   12198
+   12306      60   12195   12198   12309      60   12189   12186   12303     128
+   12183   12180   12300     133   12183   12186   12303     135   12180   12174
+   12294      10   12177   12174   12294      34   12174   12168   12288      10
+   12174   12180   12300     109   12174   12177   12297      35   12171   12168
+   12288      34   12168   12162   12285      10   12168   12174   12294      10
+   12168   12171   12291      35   12165   12162   12285     111   12165   12180
+   12300     113   12162   12159   12279      10   12162   12159   12282      10
+   12162   12168   12288      10   12159   12162   12285      10   12156   12159
+   12279     111   12156   12159   12282     111   12396   12393   12423     143
+   12393   12396   12426     143   12390   12387   12420     143   12390   12393
+   12423     143   12384   12387   12420     143   12381   12396   12426     143
+   12372   12369   12411     143   12369   12372   12414     143   12366   12363
+   12408     143   12366   12369   12411     143   12360   12363   12408     143
+   12360   12378   12417     148   12357   12372   12414     143
 %FLAG ANGLES_WITHOUT_HYDROGEN                                                   
 %FORMAT(10I8)                                                                   
-      54      51      57       1      51      57      63       2      27      36
-      39       3      18      12      51       4      18      27      36       5
-      12      18      27       6      12      51      54       7      12      51
-      57       8       0      12      18       9       0      12      51      10
-      75      72      78       1      72      78      84       2      63      72
-      75       7      63      72      78       8      57      63      72      11
-     135     132     138       1     132     138     144       2     114     120
-     126      12     108     114     120      12     102      99     126      12
-     102     108     114      12      99     102     108      12      99     126
-     120      12      90      84     132       4      90      99     102      13
-      90      99     126      13      84      90      99      14      84     132
-     135       7      84     132     138       8      78      84      90      15
-      78      84     132      11     192     189     195       1     189     195
-     201       2     165     159     177       6     150     144     189       4
-     150     159     165       6     150     159     177       6     144     150
-     159       6     144     189     192       7     144     189     195       8
-     138     144     150      15     138     144     189      11     222     219
-     225       1     219     225     231       2     207     201     219       4
-     201     219     222       7     201     219     225       8     195     201
-     207      15     195     201     219      11     243     240     246       1
-     240     246     252       2     231     240     243       7     231     240
-     246       8     225     231     240      11     309     306     312       1
-     306     312     318       2     276     285     294       9     267     276
-     285       6     258     252     306       4     258     267     276       6
-     252     258     267       6     252     306     309       7     252     306
-     312       8     246     252     258      15     246     252     306      11
-     375     372     378       1     372     378     384       2     342     351
-     360       9     333     342     351       6     324     318     372       4
-     324     333     342       6     318     324     333       6     318     372
-     375       7     318     372     378       8     312     318     324      15
-     312     318     372      11     432     429     435       1     429     435
-     441       2     396     390     408       6     390     384     429       4
-     390     408     417       6     384     390     396       6     384     390
-     408       6     384     429     432       7     384     429     435       8
-     378     384     390      15     378     384     429      11     489     486
-     492       1     486     492     498       2     462     456     474       6
-     447     441     486       4     447     456     462       6     447     456
-     474       6     441     447     456       6     441     486     489       7
-     441     486     492       8     435     441     447      15     435     441
-     486      11     546     543     549       1     543     549     555       2
-     510     504     522       6     504     498     543       4     504     522
-     531       6     498     504     510       6     498     504     522       6
-     498     543     546       7     498     543     549       8     492     498
-     504      15     492     498     543      11     588     585     591       1
-     585     591     597       2     567     561     579      16     561     555
-     585       4     555     561     567       6     555     561     579      16
-     555     585     588       7     555     585     591       8     549     555
-     561      15     549     555     585      11     609     606     612       1
-     606     612     618       2     597     606     609       7     597     606
-     612       8     591     597     606      11     666     663     669       1
-     663     669     675       2     639     633     651       6     624     618
-     663       4     624     633     639       6     624     633     651       6
-     618     624     633       6     618     663     666       7     618     663
-     669       8     612     618     624      15     612     618     663      11
-     723     720     726       1     720     726     732       2     696     690
-     708       6     681     675     720       4     681     690     696       6
-     681     690     708       6     675     681     690       6     675     720
-     723       7     675     720     726       8     669     675     681      15
-     669     675     720      11     756     753     759       1     753     759
-     765       2     738     732     753       4     732     738     747      16
-     732     753     756       7     732     753     759       8     726     732
-     738      15     726     732     753      11     798     795     801       1
-     795     801     807       2     783     780     786       1     771     765
-     795       4     771     780     783       7     771     780     786       8
-     765     771     780       4     765     795     798       7     765     795
-     801       8     759     765     771      15     759     765     795      11
-     864     861     867       1     861     867     873       2     831     840
-     849       9     822     831     840       6     813     807     861       4
-     813     822     831       6     807     813     822       6     807     861
-     864       7     807     861     867       8     801     807     813      15
-     801     807     861      11     897     894     900       1     894     900
-     906       2     879     873     894       4     873     879     888      16
-     873     894     897       7     873     894     900       8     867     873
-     879      15     867     873     894      11     954     951     957       1
-     951     957     963       2     918     912     930       6     912     906
-     951       4     912     930     939       6     906     912     918       6
-     906     912     930       6     906     951     954       7     906     951
-     957       8     900     906     912      15     900     906     951      11
-     984     981     987       1     981     987     993       2     969     963
-     981       4     963     981     984       7     963     981     987       8
-     957     963     969      15     957     963     981      11    1047    1044
-    1050       1    1044    1050    1056       2    1026    1023    1032      17
-    1023    1032    1038      18    1017    1023    1026      17    1017    1023
-    1032      19    1011    1008    1038      12    1011    1017    1023      18
-    1008    1011    1017      12    1008    1038    1032      12     999     993
-    1044       4     999    1008    1011      13     999    1008    1038      13
-     993     999    1008      14     993    1044    1047       7     993    1044
-    1050       8     987     993     999      15     987     993    1044      11
-    1068    1065    1071       1    1065    1071    1077       2    1056    1065
-    1068       7    1056    1065    1071       8    1050    1056    1065      11
-    1125    1122    1128       1    1122    1128    1134       2    1089    1083
-    1101       6    1083    1077    1122       4    1083    1101    1110       6
-    1077    1083    1089       6    1077    1083    1101       6    1077    1122
-    1125       7    1077    1122    1128       8    1071    1077    1083      15
-    1071    1077    1122      11    1155    1152    1158       1    1152    1158
-    1164       2    1140    1134    1152       4    1134    1152    1155       7
-    1134    1152    1158       8    1128    1134    1140      15    1128    1134
-    1152      11    1221    1218    1224       1    1218    1224    1230       2
-    1188    1197    1206       9    1179    1188    1197       6    1170    1164
-    1218       4    1170    1179    1188       6    1164    1170    1179       6
-    1164    1218    1221       7    1164    1218    1224       8    1158    1164
-    1170      15    1158    1164    1218      11    1251    1248    1254       1
-    1248    1254    1260       2    1236    1230    1248       4    1230    1248
-    1251       7    1230    1248    1254       8    1224    1230    1236      15
-    1224    1230    1248      11    1302    1299    1305       1    1299    1305
-    1311       2    1275    1284    1287       3    1266    1260    1299       4
-    1266    1275    1284       5    1260    1266    1275       6    1260    1299
-    1302       7    1260    1299    1305       8    1254    1260    1266      15
-    1254    1260    1299      11    1353    1350    1356       1    1350    1356
-    1362       2    1332    1338    1344      20    1329    1326    1344      21
-    1329    1332    1338      22    1326    1329    1332      23    1326    1344
-    1338      24    1317    1311    1350       4    1317    1326    1329      25
-    1317    1326    1344      26    1311    1317    1326      27    1311    1350
-    1353       7    1311    1350    1356       8    1305    1311    1317      15
-    1305    1311    1350      11    1425    1422    1428       1    1422    1428
-    1434       2    1404    1401    1413      28    1395    1401    1404      28
-    1395    1401    1413      28    1386    1395    1401      29    1377    1386
-    1395      30    1368    1362    1422       4    1368    1377    1386       6
-    1362    1368    1377       6    1362    1422    1425       7    1362    1422
-    1428       8    1356    1362    1368      15    1356    1362    1422      11
-    1470    1467    1473       1    1467    1473    1479       2    1461    1458
-    1464      31    1449    1458    1461      32    1449    1458    1464      32
-    1440    1434    1467       4    1440    1449    1458       4    1434    1440
-    1449       6    1434    1467    1470       7    1434    1467    1473       8
-    1428    1434    1440      15    1428    1434    1467      11    1491    1488
-    1494       1    1488    1494    1500       2    1479    1488    1491       7
-    1479    1488    1494       8    1473    1479    1488      11    1521    1518
-    1524       1    1518    1524    1530       2    1506    1500    1518       4
-    1500    1518    1521       7    1500    1518    1524       8    1494    1500
-    1506      15    1494    1500    1518      11    1566    1563    1569       1
-    1563    1569    1575       2    1557    1554    1560      31    1545    1554
-    1557      32    1545    1554    1560      32    1536    1530    1563       4
-    1536    1545    1554       4    1530    1536    1545       6    1530    1563
-    1566       7    1530    1563    1569       8    1524    1530    1536      15
-    1524    1530    1563      11    1623    1620    1626       1    1620    1626
-    1632       2    1596    1590    1608       6    1581    1575    1620       4
-    1581    1590    1596       6    1581    1590    1608       6    1575    1581
-    1590       6    1575    1620    1623       7    1575    1620    1626       8
-    1569    1575    1581      15    1569    1575    1620      11    1653    1650
-    1656       1    1650    1656    1662       2    1638    1632    1650       4
-    1632    1650    1653       7    1632    1650    1656       8    1626    1632
-    1638      15    1626    1632    1650      11    1713    1710    1716       1
-    1710    1716    1722       2    1692    1698    1704      12    1686    1692
-    1698      12    1680    1677    1704      12    1680    1686    1692      12
-    1677    1680    1686      12    1677    1704    1698      12    1668    1662
-    1710       4    1668    1677    1680      13    1668    1677    1704      13
-    1662    1668    1677      14    1662    1710    1713       7    1662    1710
-    1716       8    1656    1662    1668      15    1656    1662    1710      11
-    1755    1752    1758       1    1752    1758    1764       2    1734    1728
-    1746      16    1728    1722    1752       4    1722    1728    1734       6
-    1722    1728    1746      16    1722    1752    1755       7    1722    1752
-    1758       8    1716    1722    1728      15    1716    1722    1752      11
-    1818    1815    1821       1    1815    1821    1827       2    1797    1794
-    1803      17    1794    1803    1809      18    1788    1794    1797      17
-    1788    1794    1803      19    1782    1779    1809      12    1782    1788
-    1794      18    1779    1782    1788      12    1779    1809    1803      12
-    1770    1764    1815       4    1770    1779    1782      13    1770    1779
-    1809      13    1764    1770    1779      14    1764    1815    1818       7
-    1764    1815    1821       8    1758    1764    1770      15    1758    1764
-    1815      11    1866    1863    1869       1    1863    1869    1875       2
-    1839    1833    1851       6    1833    1827    1863       4    1827    1833
-    1839       6    1827    1833    1851       6    1827    1863    1866       7
-    1827    1863    1869       8    1821    1827    1833      15    1821    1827
-    1863      11    1887    1884    1890       1    1884    1890    1896       2
-    1875    1884    1887       7    1875    1884    1890       8    1869    1875
-    1884      11    1938    1935    1941       1    1935    1941    1947       2
-    1923    1920    1926       1    1911    1920    1923       7    1911    1920
-    1926       8    1902    1896    1935       4    1902    1911    1920       4
-    1896    1902    1911       6    1896    1935    1938       7    1896    1935
-    1941       8    1890    1896    1902      15    1890    1896    1935      11
-    1998    1995    2001       1    1995    2001    2007       2    1977    1983
-    1989      12    1971    1977    1983      12    1965    1962    1989      12
-    1965    1971    1977      12    1962    1965    1971      12    1962    1989
-    1983      12    1953    1947    1995       4    1953    1962    1965      13
-    1953    1962    1989      13    1947    1953    1962      14    1947    1995
-    1998       7    1947    1995    2001       8    1941    1947    1953      15
-    1941    1947    1995      11    2064    2061    2067       1    2061    2067
-    2073       2    2031    2040    2049       9    2022    2031    2040       6
-    2013    2007    2061       4    2013    2022    2031       6    2007    2013
-    2022       6    2007    2061    2064       7    2007    2061    2067       8
-    2001    2007    2013      15    2001    2007    2061      11    2100    2097
-    2103       1    2097    2103    2109       2    2091    2088    2094      31
-    2079    2073    2097       4    2079    2088    2091      32    2079    2088
-    2094      32    2073    2079    2088       4    2073    2097    2100       7
-    2073    2097    2103       8    2067    2073    2079      15    2067    2073
-    2097      11    2172    2169    2175       1    2169    2175    2181       2
-    2151    2148    2160      28    2142    2148    2151      28    2142    2148
-    2160      28    2133    2142    2148      29    2124    2133    2142      30
-    2115    2109    2169       4    2115    2124    2133       6    2109    2115
-    2124       6    2109    2169    2172       7    2109    2169    2175       8
-    2103    2109    2115      15    2103    2109    2169      11    2220    2217
-    2223       1    2217    2223    2229       2    2193    2187    2205       6
-    2187    2181    2217       4    2181    2187    2193       6    2181    2187
-    2205       6    2181    2217    2220       7    2181    2217    2223       8
-    2175    2181    2187      15    2175    2181    2217      11    2265    2262
-    2268       1    2262    2268    2274       2    2256    2253    2259      31
-    2244    2253    2256      32    2244    2253    2259      32    2235    2229
-    2262       4    2235    2244    2253       4    2229    2235    2244       6
-    2229    2262    2265       7    2229    2262    2268       8    2223    2229
-    2235      15    2223    2229    2262      11    2331    2328    2334       1
-    2328    2334    2340       2    2298    2307    2316       9    2289    2298
-    2307       6    2280    2274    2328       4    2280    2289    2298       6
-    2274    2280    2289       6    2274    2328    2331       7    2274    2328
-    2334       8    2268    2274    2280      15    2268    2274    2328      11
-    2388    2385    2391       1    2385    2391    2397       2    2361    2355
-    2373       6    2346    2340    2385       4    2346    2355    2361       6
-    2346    2355    2373       6    2340    2346    2355       6    2340    2385
-    2388       7    2340    2385    2391       8    2334    2340    2346      15
-    2334    2340    2385      11    2421    2418    2424       1    2418    2424
-    2430       2    2403    2397    2418       4    2397    2403    2412      33
-    2397    2418    2421       7    2397    2418    2424       8    2391    2397
-    2403      15    2391    2397    2418      11    2451    2448    2454       1
-    2448    2454    2460       2    2436    2430    2448       4    2430    2448
-    2451       7    2430    2448    2454       8    2424    2430    2436      15
-    2424    2430    2448      11    2496    2493    2499       1    2493    2499
-    2505       2    2487    2484    2490      31    2475    2484    2487      32
-    2475    2484    2490      32    2466    2460    2493       4    2466    2475
-    2484       4    2460    2466    2475       6    2460    2493    2496       7
-    2460    2493    2499       8    2454    2460    2466      15    2454    2460
-    2493      11    2556    2553    2559       1    2553    2559    2565       2
-    2535    2541    2547      12    2529    2535    2541      12    2523    2520
-    2547      12    2523    2529    2535      12    2520    2523    2529      12
-    2520    2547    2541      12    2511    2505    2553       4    2511    2520
-    2523      13    2511    2520    2547      13    2505    2511    2520      14
-    2505    2553    2556       7    2505    2553    2559       8    2499    2505
-    2511      15    2499    2505    2553      11    2598    2595    2601       1
-    2595    2601    2604       2    2595    2601    2631       2    2583    2580
-    2586       1    2571    2565    2595       4    2571    2580    2583       7
-    2571    2580    2586       8    2565    2571    2580       4    2565    2595
-    2598       7    2565    2595    2601       8    2559    2565    2571      15
-    2559    2565    2595      11    2640    2637    2643       1    2637    2643
-    2649       2    2631    2637    2640       7    2631    2637    2643       8
-    2622    2631    2637       4    2613    2622    2631       6    2604    2601
-    2631      34    2604    2613    2622       6    2601    2604    2613      15
-    2601    2631    2622      15    2601    2631    2637      11    2670    2667
-    2673       1    2667    2673    2679       2    2655    2649    2667       4
-    2649    2667    2670       7    2649    2667    2673       8    2643    2649
-    2655      15    2643    2649    2667      11    2700    2697    2703       1
-    2697    2703    2709       2    2685    2679    2697       4    2679    2697
-    2700       7    2679    2697    2703       8    2673    2679    2685      15
-    2673    2679    2697      11    2748    2745    2751       1    2745    2751
-    2757       2    2721    2715    2733       6    2715    2709    2745       4
-    2709    2715    2721       6    2709    2715    2733       6    2709    2745
-    2748       7    2709    2745    2751       8    2703    2709    2715      15
-    2703    2709    2745      11    2805    2802    2808       1    2802    2808
-    2811       2    2802    2808    2838       2    2778    2772    2790       6
-    2763    2757    2802       4    2763    2772    2778       6    2763    2772
-    2790       6    2757    2763    2772       6    2757    2802    2805       7
-    2757    2802    2808       8    2751    2757    2763      15    2751    2757
-    2802      11    2847    2844    2850       1    2844    2850    2856       2
-    2838    2844    2847       7    2838    2844    2850       8    2829    2838
-    2844       4    2820    2829    2838       6    2811    2808    2838      34
-    2811    2820    2829       6    2808    2811    2820      15    2808    2838
-    2829      15    2808    2838    2844      11    2880    2877    2883       1
-    2877    2883    2889       2    2862    2856    2877       4    2856    2862
-    2871      33    2856    2877    2880       7    2856    2877    2883       8
-    2850    2856    2862      15    2850    2856    2877      11    2916    2913
-    2919       1    2913    2919    2925       2    2907    2904    2910      31
-    2895    2889    2913       4    2895    2904    2907      32    2895    2904
-    2910      32    2889    2895    2904       4    2889    2913    2916       7
-    2889    2913    2919       8    2883    2889    2895      15    2883    2889
-    2913      11    2964    2961    2967       1    2961    2967    2973       2
-    2937    2931    2949       6    2931    2925    2961       4    2925    2931
-    2937       6    2925    2931    2949       6    2925    2961    2964       7
-    2925    2961    2967       8    2919    2925    2931      15    2919    2925
-    2961      11    3021    3018    3024       1    3018    3024    3030       2
-    2985    2979    2997       6    2979    2973    3018       4    2979    2997
-    3006       6    2973    2979    2985       6    2973    2979    2997       6
-    2973    3018    3021       7    2973    3018    3024       8    2967    2973
-    2979      15    2967    2973    3018      11    3054    3051    3057       1
-    3051    3057    3063       2    3036    3030    3051       4    3030    3036
-    3045      16    3030    3051    3054       7    3030    3051    3057       8
-    3024    3030    3036      15    3024    3030    3051      11    3090    3087
-    3093       1    3087    3093    3099       2    3081    3078    3084      31
-    3069    3063    3087       4    3069    3078    3081      32    3069    3078
-    3084      32    3063    3069    3078       4    3063    3087    3090       7
-    3063    3087    3093       8    3057    3063    3069      15    3057    3063
-    3087      11    3141    3138    3144       1    3138    3144    3150       2
-    3126    3123    3129       1    3114    3123    3126       7    3114    3123
-    3129       8    3105    3099    3138       4    3105    3114    3123       4
-    3099    3105    3114       6    3099    3138    3141       7    3099    3138
-    3144       8    3093    3099    3105      15    3093    3099    3138      11
-    3186    3183    3189       1    3183    3189    3195       2    3177    3174
-    3180      31    3165    3174    3177      32    3165    3174    3180      32
-    3156    3150    3183       4    3156    3165    3174       4    3150    3156
-    3165       6    3150    3183    3186       7    3150    3183    3189       8
-    3144    3150    3156      15    3144    3150    3183      11    3243    3240
-    3246       1    3240    3246    3252       2    3207    3201    3219       6
-    3201    3195    3240       4    3201    3219    3228       6    3195    3201
-    3207       6    3195    3201    3219       6    3195    3240    3243       7
-    3195    3240    3246       8    3189    3195    3201      15    3189    3195
-    3240      11    3309    3306    3312       1    3306    3312    3318       2
-    3276    3285    3294       9    3267    3276    3285       6    3258    3252
-    3306       4    3258    3267    3276       6    3252    3258    3267       6
-    3252    3306    3309       7    3252    3306    3312       8    3246    3252
-    3258      15    3246    3252    3306      11    3345    3342    3348       1
-    3342    3348    3354       2    3336    3333    3339      31    3324    3318
-    3342       4    3324    3333    3336      32    3324    3333    3339      32
-    3318    3324    3333       4    3318    3342    3345       7    3318    3342
-    3348       8    3312    3318    3324      15    3312    3318    3342      11
-    3402    3399    3405       1    3399    3405    3411       2    3375    3369
-    3387       6    3360    3354    3399       4    3360    3369    3375       6
-    3360    3369    3387       6    3354    3360    3369       6    3354    3399
-    3402       7    3354    3399    3405       8    3348    3354    3360      15
-    3348    3354    3399      11    3462    3459    3465       1    3459    3465
-    3471       2    3441    3447    3453      12    3435    3441    3447      12
-    3429    3426    3453      12    3429    3435    3441      12    3426    3429
-    3435      12    3426    3453    3447      12    3417    3411    3459       4
-    3417    3426    3429      13    3417    3426    3453      13    3411    3417
-    3426      14    3411    3459    3462       7    3411    3459    3465       8
-    3405    3411    3417      15    3405    3411    3459      11    3510    3507
-    3513       1    3507    3513    3519       2    3483    3477    3495       6
-    3477    3471    3507       4    3471    3477    3483       6    3471    3477
-    3495       6    3471    3507    3510       7    3471    3507    3513       8
-    3465    3471    3477      15    3465    3471    3507      11    3555    3552
-    3558       1    3552    3558    3564       2    3546    3543    3549      31
-    3534    3543    3546      32    3534    3543    3549      32    3525    3519
-    3552       4    3525    3534    3543       4    3519    3525    3534       6
-    3519    3552    3555       7    3519    3552    3558       8    3513    3519
-    3525      15    3513    3519    3552      11    3612    3609    3615       1
-    3609    3615    3621       2    3585    3579    3597       6    3570    3564
-    3609       4    3570    3579    3585       6    3570    3579    3597       6
-    3564    3570    3579       6    3564    3609    3612       7    3564    3609
-    3615       8    3558    3564    3570      15    3558    3564    3609      11
-    3633    3630    3636       1    3630    3636    3642       2    3621    3630
-    3633       7    3621    3630    3636       8    3615    3621    3630      11
-    3699    3696    3702       1    3696    3702    3708       2    3666    3675
-    3684       9    3657    3666    3675       6    3648    3642    3696       4
-    3648    3657    3666       6    3642    3648    3657       6    3642    3696
-    3699       7    3642    3696    3702       8    3636    3642    3648      15
-    3636    3642    3696      11    3747    3744    3750       1    3744    3750
-    3756       2    3720    3714    3732       6    3714    3708    3744       4
-    3708    3714    3720       6    3708    3714    3732       6    3708    3744
-    3747       7    3708    3744    3750       8    3702    3708    3714      15
-    3702    3708    3744      11    3819    3816    3822       1    3816    3822
-    3828       2    3801    3807    3813      35    3795    3801    3807      12
-    3789    3786    3813      36    3789    3795    3801      12    3786    3789
-    3795      37    3786    3813    3807      38    3780    3786    3789      39
-    3780    3786    3813      40    3774    3771    3813      41    3774    3780
-    3786      42    3771    3774    3780      43    3771    3813    3786      44
-    3771    3813    3807      45    3762    3756    3816       4    3762    3771
-    3774      46    3762    3771    3813      47    3756    3762    3771      48
-    3756    3816    3819       7    3756    3816    3822       8    3750    3756
-    3762      15    3750    3756    3816      11    3855    3852    3858       1
-    3852    3858    3864       2    3846    3843    3849      31    3834    3828
-    3852       4    3834    3843    3846      32    3834    3843    3849      32
-    3828    3834    3843       4    3828    3852    3855       7    3828    3852
-    3858       8    3822    3828    3834      15    3822    3828    3852      11
-    3876    3873    3879       1    3873    3879    3885       2    3864    3873
-    3876       7    3864    3873    3879       8    3858    3864    3873      11
-    3933    3930    3936       1    3930    3936    3942       2    3906    3900
-    3918       6    3891    3885    3930       4    3891    3900    3906       6
-    3891    3900    3918       6    3885    3891    3900       6    3885    3930
-    3933       7    3885    3930    3936       8    3879    3885    3891      15
-    3879    3885    3930      11    3969    3966    3972       1    3966    3972
-    3978       2    3960    3957    3963      31    3948    3942    3966       4
-    3948    3957    3960      32    3948    3957    3963      32    3942    3948
-    3957       4    3942    3966    3969       7    3942    3966    3972       8
-    3936    3942    3948      15    3936    3942    3966      11    3999    3996
-    4002       1    3996    4002    4008       2    3984    3978    3996       4
-    3978    3996    3999       7    3978    3996    4002       8    3972    3978
-    3984      15    3972    3978    3996      11    4056    4053    4059       1
-    4053    4059    4065       2    4020    4014    4032       6    4014    4008
-    4053       4    4014    4032    4041       6    4008    4014    4020       6
-    4008    4014    4032       6    4008    4053    4056       7    4008    4053
-    4059       8    4002    4008    4014      15    4002    4008    4053      11
-    4104    4101    4107       1    4101    4107    4113       2    4077    4071
-    4089       6    4071    4065    4101       4    4065    4071    4077       6
-    4065    4071    4089       6    4065    4101    4104       7    4065    4101
-    4107       8    4059    4065    4071      15    4059    4065    4101      11
-    4155    4152    4158       1    4152    4158    4164       2    4134    4140
-    4146      20    4131    4128    4146      21    4131    4134    4140      22
-    4128    4131    4134      23    4128    4146    4140      24    4119    4113
-    4152       4    4119    4128    4131      25    4119    4128    4146      26
-    4113    4119    4128      27    4113    4152    4155       7    4113    4152
-    4158       8    4107    4113    4119      15    4107    4113    4152      11
-    4188    4185    4191       1    4185    4191    4197       2    4170    4164
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+   12144      66   12093   12099   12105      31   12093   12099   12138      25
+   12270   12273   12276      94   12264   12261   12267      96   12261   12258
+   12270      97   12258   12261   12267      99   12258   12261   12264     100
+   12258   12270   12273     101   12255   12252   12276     102   12255   12258
+   12261     103   12255   12258   12270      94   12252   12276   12273     105
+   12252   12255   12258     105   12249   12252   12276     107   12249   12252
+   12255     107   12246   12243   12249      33   12243   12249   12252     108
+   12240   12237   12243      33   12237   12243   12249      14   12237   12243
+   12246      33   12234   12231   12237     110   12234   12249   12243     110
+   12234   12249   12252     112   12231   12234   12249     114   12231   12237
+   12243      14   12231   12237   12240      33   12228   12231   12234     110
+   12228   12231   12237      14   12225   12228   12231     110   12222   12216
+   12225     115   12219   12216   12225     115   12219   12216   12222     116
+   12216   12225   12228     117   12213   12216   12225     118   12213   12216
+   12219     115   12213   12216   12222     115   12204   12207   12210     120
+   12201   12204   12207     121   12198   12195   12201     122   12195   12192
+   12210     123   12195   12201   12204     124   12192   12210   12207     125
+   12192   12195   12201     126   12192   12195   12198     127   12189   12192
+   12210     129   12189   12192   12195     130   12186   12183   12210     131
+   12186   12189   12192     132   12183   12186   12189     134   12183   12210
+   12192     136   12183   12210   12207     137   12180   12183   12186     138
+   12180   12183   12210     139   12177   12174   12180      33   12174   12180
+   12183     140   12171   12168   12174      33   12168   12174   12180      14
+   12168   12174   12177      33   12165   12162   12168     110   12165   12180
+   12174     110   12165   12180   12183     141   12162   12168   12174      14
+   12162   12168   12171      33   12162   12165   12180     114   12159   12162
+   12168      14   12159   12162   12165     110   12156   12147   12213     118
+   12156   12159   12162     110   12153   12147   12213     115   12153   12147
+   12156     115   12150   12147   12213     115   12150   12147   12153     116
+   12150   12147   12156     115   12147   12213   12216     142   12147   12156
+   12159     117   12393   12390   12402     144   12390   12393   12396     145
+   12387   12384   12399     144   12387   12390   12393     145   12387   12390
+   12402     144   12384   12381   12396     145   12384   12387   12390     145
+   12381   12384   12387     145   12381   12384   12399     144   12381   12396
+   12393     145   12375   12381   12384     146   12375   12381   12396     146
+   12372   12357   12375     146   12369   12366   12405     144   12366   12369
+   12372     145   12363   12360   12378     147   12363   12366   12369     145
+   12363   12366   12405     144   12360   12357   12372     145   12360   12357
+   12375     146   12360   12363   12366     145   12357   12360   12363     145
+   12357   12360   12378     147   12357   12372   12369     145   12357   12375
+   12381     149
 %FLAG DIHEDRALS_INC_HYDROGEN                                                    
 %FORMAT(10I8)                                                                   
-      54      51      57      60      12      54      51     -57      60       1
-      51      57      63      66       7      51      57      63      69       7
-      33      27      36      39      11      30      27      36      39      11
-      27      36      39      42      11      27      36      39      45      11
-      27      36      39      48      11      24      18      12      51       6
-      24      18      27      30       6      24      18      27      33       6
-      24      18      27      36       6      21      18      12      51       6
-      21      18      27      30       6      21      18      27      33       6
-      21      18      27      36       6      15      12      18      21       6
-      15      12      18      24       6      15      12      18      27       6
-      15      12      51      54       7      15      12      51      57       7
-      12      18      27      30       6      12      18      27      33       6
-      12      51      57      60       1       9       0      12      15       6
-       9       0      12      18       6       9       0      12      51       6
-       6       0      12      15       6       6       0      12      18       6
-       6       0      12      51       6       3       0      12      15       6
-       3       0      12      18       6       3       0      12      51       6
-       0      12      18      21       6       0      12      18      24       6
-      75      72      78      81      12      75      72     -78      81       1
-      72      78      84      87       7      69      63      72      75      59
-      69      63     -72      75      60      69      63      72      78       7
-      66      63      72      75      59      66      63     -72      75      60
-      66      63      72      78       7      63      72      78      81       1
-      60      57      63      66       7      60      57      63      69       7
-      60      57      63      72       7     135     132     138     141      12
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-     117     114     120     126      17     114     120     126     129      17
-     111     108     114     117      17     111     108     114     120      17
-     108     114     120     123      17     105     102      99     126      17
-     105     102     108     111      17     105     102     108     114      17
-     102      99     126     129      17     102     108     114     117      17
-      99     102     108     111      17      99     126     120     123      17
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-      93      90      99     102       7      93      90      99     126       7
-      90      99     102     105      17      90      99     126     129      17
-      87      84      90      93       6      87      84      90      96       6
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-      84     132     138     141       1      81      78      84      87       7
-      81      78      84      90       7      81      78      84     132       7
-      78      84      90      93       6      78      84      90      96       6
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-     162     159     177     186      62     156     150     144     189       6
-     156     150     159     162      62     156     150     159     165      61
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-     153     150     159     162      62     153     150     159     165      61
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-     150     159     165     171      61     150     159     165     174      61
-     150     159     177     180      61     150     159     177     183      61
-     150     159     177     186      61     147     144     150     153       6
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-     147     144     189     192      59     147     144    -189     192      60
-     147     144     189     195       7     144     150     159     162      61
-     144     189     195     198       1     141     138     144     147       7
-     141     138     144     150       7     141     138     144     189       7
-     138     144     150     153       6     138     144     150     156       6
-     222     219     225     228      12     222     219    -225     228       1
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-     216     207     201     219       6     213     207     201     219       6
-     210     207     201     219       6     204     201     207     210       6
-     204     201     207     213       6     204     201     207     216       6
-     204     201     219     222      59     204     201    -219     222      60
-     204     201     219     225       7     201     219     225     228       1
-     198     195     201     204       7     198     195     201     207       7
-     198     195     201     219       7     195     201     207     210       6
-     195     201     207     213       6     195     201     207     216       6
-     243     240     246     249      12     243     240    -246     249       1
-     240     246     252     255       7     237     231     240     243      59
-     237     231    -240     243      60     237     231     240     246       7
-     234     231     240     243      59     234     231    -240     243      60
-     234     231     240     246       7     231     240     246     249       1
-     228     225     231     234       7     228     225     231     237       7
-     228     225     231     240       7     309     306     312     315      12
-     309     306    -312     315       1     306     312     318     321       7
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-     288     285     294     300       6     288     285     294     303       6
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-     276     285     294     297       6     276     285     294     300       6
-     276     285     294     303       6     273     267     276     279      62
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-     270     267     276     279      62     270     267     276     282      62
-     270     267     276     285      61     267     276     285     288       6
-     267     276     285     291       6     264     258     252     306       6
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-     261     258     267     270      62     261     258     267     273      62
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-     255     252     306     309      59     255     252    -306     309      60
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-     246     252     258     264       6     375     372     378     381      12
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-     348     342     351     354       6     348     342     351     357       6
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-     342     351     360     369       6     339     333     342     345      62
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-     336     333     342     345      62     336     333     342     348      62
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-     333     342     351     357       6     330     324     318     372       6
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-     327     324     333     336      62     327     324     333     339      62
-     327     324     333     342      61     324     333     342     345      61
-     324     333     342     348      61     321     318     324     327       6
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-     318     324     333     339      61     318     372     378     381       1
-     315     312     318     321       7     315     312     318     324       7
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-     312     318     324     330       6     432     429     435     438      12
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-     414     408     417     426      62     411     408     417     420      62
-     411     408     417     423      62     411     408     417     426      62
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-     645     639     633     651      61     642     639     633     651      61
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-     732     738     747     750      63     732     738    -747     750      61
-     732     753     759     762       1     729     726     732     735       7
-     729     726     732     738       7     729     726     732     753       7
-     726     732     738     741       6     726     732     738     744       6
-     798     795     801     804      12     798     795    -801     804       1
-     795     801     807     810       7     783     780     786     789      12
-     783     780    -786     789       1     783     780     786     792      12
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-     774     771     765     795       6     774     771     780     783      59
-     774     771    -780     783       7     774     771    -780     783      60
-     774     771     780     786       7     771     780     786     789       1
-     771     780     786     792       1     768     765     771     774       6
-     768     765     771     777       6     768     765     771     780       6
-     768     765     795     798      59     768     765    -795     798      60
-     768     765     795     801       7     765     795     801     804       1
-     762     759     765     768       7     762     759     765     771       7
-     762     759     765     795       7     759     765     771     774       6
-     759     765     771     777       6     864     861     867     870      12
-     864     861    -867     870       1     861     867     873     876       7
-     846     840     849     852       6     846     840     849     855       6
-     846     840     849     858       6     843     840     849     852       6
-     843     840     849     855       6     843     840     849     858       6
-     837     831     840     843       6     837     831     840     846       6
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-    1491    1488   -1494    1497       1    1488    1494    1500    1503       7
-    1485    1479    1488    1491      59    1485    1479   -1488    1491      60
-    1485    1479    1488    1494       7    1482    1479    1488    1491      59
-    1482    1479   -1488    1491      60    1482    1479    1488    1494       7
-    1479    1488    1494    1497       1    1476    1473    1479    1482       7
-    1476    1473    1479    1485       7    1476    1473    1479    1488       7
-    1521    1518    1524    1527      12    1521    1518   -1524    1527       1
-    1518    1524    1530    1533       7    1515    1506    1500    1518       6
-    1512    1506    1500    1518       6    1509    1506    1500    1518       6
-    1503    1500    1506    1509       6    1503    1500    1506    1512       6
-    1503    1500    1506    1515       6    1503    1500    1518    1521      59
-    1503    1500   -1518    1521      60    1503    1500    1518    1524       7
-    1500    1518    1524    1527       1    1497    1494    1500    1503       7
-    1497    1494    1500    1506       7    1497    1494    1500    1518       7
-    1494    1500    1506    1509       6    1494    1500    1506    1512       6
-    1494    1500    1506    1515       6    1566    1563    1569    1572      12
-    1566    1563   -1569    1572       1    1563    1569    1575    1578       7
-    1551    1545    1554    1557       7    1551    1545    1554    1560       7
-    1548    1545    1554    1557       7    1548    1545    1554    1560       7
-    1542    1536    1530    1563       6    1542    1536    1545    1548      62
-    1542    1536    1545    1551      62    1542    1536    1545    1554       6
-    1539    1536    1530    1563       6    1539    1536    1545    1548      62
-    1539    1536    1545    1551      62    1539    1536    1545    1554       6
-    1533    1530    1536    1539       6    1533    1530    1536    1542       6
-    1533    1530    1536    1545       6    1533    1530    1563    1566      59
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-    1587    1581    1590    1608      61    1584    1581    1575    1620       6
-    1584    1581    1590    1593      62    1584    1581    1590    1596      61
-    1584    1581    1590    1608      61    1581    1590    1596    1599      61
-    1581    1590    1596    1602      61    1581    1590    1596    1605      61
-    1581    1590    1608    1611      61    1581    1590    1608    1614      61
-    1581    1590    1608    1617      61    1578    1575    1581    1584       6
-    1578    1575    1581    1587       6    1578    1575    1581    1590       6
-    1578    1575    1620    1623      59    1578    1575   -1620    1623      60
-    1578    1575    1620    1626       7    1575    1581    1590    1593      61
-    1575    1620    1626    1629       1    1572    1569    1575    1578       7
-    1572    1569    1575    1581       7    1572    1569    1575    1620       7
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-    1650    1656    1662    1665       7    1647    1638    1632    1650       6
-    1644    1638    1632    1650       6    1641    1638    1632    1650       6
-    1635    1632    1638    1641       6    1635    1632    1638    1644       6
-    1635    1632    1638    1647       6    1635    1632    1650    1653      59
-    1635    1632   -1650    1653      60    1635    1632    1650    1656       7
-    1632    1650    1656    1659       1    1629    1626    1632    1635       7
-    1629    1626    1632    1638       7    1629    1626    1632    1650       7
-    1626    1632    1638    1641       6    1626    1632    1638    1644       6
-    1626    1632    1638    1647       6    1713    1710    1716    1719      12
-    1713    1710   -1716    1719       1    1710    1716    1722    1725       7
-    1701    1698    1704    1707      17    1695    1692    1698    1701      17
-    1695    1692    1698    1704      17    1692    1698    1704    1707      17
-    1689    1686    1692    1695      17    1689    1686    1692    1698      17
-    1686    1692    1698    1701      17    1683    1680    1677    1704      17
-    1683    1680    1686    1689      17    1683    1680    1686    1692      17
-    1680    1677    1704    1707      17    1680    1686    1692    1695      17
-    1677    1680    1686    1689      17    1677    1704    1698    1701      17
-    1674    1668    1662    1710       6    1674    1668    1677    1680       7
-    1674    1668    1677    1704       7    1671    1668    1662    1710       6
-    1671    1668    1677    1680       7    1671    1668    1677    1704       7
-    1668    1677    1680    1683      17    1668    1677    1704    1707      17
-    1665    1662    1668    1671       6    1665    1662    1668    1674       6
-    1665    1662    1668    1677       6    1665    1662    1710    1713      59
-    1665    1662   -1710    1713      60    1665    1662    1710    1716       7
-    1662    1710    1716    1719       1    1659    1656    1662    1665       7
-    1659    1656    1662    1668       7    1659    1656    1662    1710       7
-    1656    1662    1668    1671       6    1656    1662    1668    1674       6
-    1755    1752    1758    1761      12    1755    1752   -1758    1761       1
-    1752    1758    1764    1767       7    1743    1734    1728    1746      63
-    1743    1734   -1728    1746      26    1740    1734    1728    1746      63
-    1740    1734   -1728    1746      26    1737    1734    1728    1746      63
-    1737    1734   -1728    1746      26    1734    1728    1746    1749      63
-    1734    1728   -1746    1749      61    1731    1728    1722    1752       6
-    1731    1728    1734    1737       6    1731    1728    1734    1740       6
-    1731    1728    1734    1743       6    1731    1728    1746    1749      64
-    1725    1722    1728    1731       6    1725    1722    1728    1734       6
-    1725    1722    1728    1746      63    1725    1722   -1728    1746      26
-    1725    1722    1752    1755      59    1725    1722   -1752    1755      60
-    1725    1722    1752    1758       7    1722    1728    1734    1737      61
-    1722    1728    1734    1740      61    1722    1728    1734    1743      61
-    1722    1728    1746    1749      63    1722    1728   -1746    1749      61
-    1722    1752    1758    1761       1    1719    1716    1722    1725       7
-    1719    1716    1722    1728       7    1719    1716    1722    1752       7
-    1716    1722    1728    1731       6    1818    1815    1821    1824      12
-    1818    1815   -1821    1824       1    1815    1821    1827    1830       7
-    1806    1803    1809    1812      17    1800    1797    1794    1803      65
-    1797    1794    1803    1806      17    1794    1803    1809    1812      17
-    1791    1788    1794    1797      17    1791    1788    1794    1803      17
-    1788    1794    1797    1800      65    1788    1794    1803    1806      17
-    1785    1782    1779    1809      17    1785    1782    1788    1791      17
-    1785    1782    1788    1794      17    1782    1779    1809    1812      17
-    1779    1782    1788    1791      17    1779    1809    1803    1806      17
-    1776    1770    1764    1815       6    1776    1770    1779    1782       7
-    1776    1770    1779    1809       7    1773    1770    1764    1815       6
-    1773    1770    1779    1782       7    1773    1770    1779    1809       7
-    1770    1779    1782    1785      17    1770    1779    1809    1812      17
-    1767    1764    1770    1773       6    1767    1764    1770    1776       6
-    1767    1764    1770    1779       6    1767    1764    1815    1818      59
-    1767    1764   -1815    1818      60    1767    1764    1815    1821       7
-    1764    1815    1821    1824       1    1761    1758    1764    1767       7
-    1761    1758    1764    1770       7    1761    1758    1764    1815       7
-    1758    1764    1770    1773       6    1758    1764    1770    1776       6
-    1866    1863    1869    1872      12    1866    1863   -1869    1872       1
-    1863    1869    1875    1878       7    1863    1869    1875    1881       7
-    1848    1839    1833    1851      61    1845    1839    1833    1851      61
-    1842    1839    1833    1851      61    1839    1833    1851    1854      61
-    1839    1833    1851    1857      61    1839    1833    1851    1860      61
-    1836    1833    1827    1863       6    1836    1833    1839    1842      62
-    1836    1833    1839    1845      62    1836    1833    1839    1848      62
-    1836    1833    1851    1854      62    1836    1833    1851    1857      62
-    1836    1833    1851    1860      62    1830    1827    1833    1836       6
-    1830    1827    1833    1839       6    1830    1827    1833    1851       6
-    1830    1827    1863    1866      59    1830    1827   -1863    1866      60
-    1830    1827    1863    1869       7    1827    1833    1839    1842      61
-    1827    1833    1839    1845      61    1827    1833    1839    1848      61
-    1827    1833    1851    1854      61    1827    1833    1851    1857      61
-    1827    1833    1851    1860      61    1827    1863    1869    1872       1
-    1824    1821    1827    1830       7    1824    1821    1827    1833       7
-    1824    1821    1827    1863       7    1821    1827    1833    1836       6
-    1887    1884    1890    1893      12    1887    1884   -1890    1893       1
-    1884    1890    1896    1899       7    1881    1875    1884    1887      59
-    1881    1875   -1884    1887      60    1881    1875    1884    1890       7
-    1878    1875    1884    1887      59    1878    1875   -1884    1887      60
-    1878    1875    1884    1890       7    1875    1884    1890    1893       1
-    1872    1869    1875    1878       7    1872    1869    1875    1881       7
-    1872    1869    1875    1884       7    1938    1935    1941    1944      12
-    1938    1935   -1941    1944       1    1935    1941    1947    1950       7
-    1923    1920    1926    1929      12    1923    1920   -1926    1929       1
-    1923    1920    1926    1932      12    1923    1920   -1926    1932       1
-    1917    1911    1920    1923      59    1917    1911   -1920    1923       7
-    1917    1911   -1920    1923      60    1917    1911    1920    1926       7
-    1914    1911    1920    1923      59    1914    1911   -1920    1923       7
-    1914    1911   -1920    1923      60    1914    1911    1920    1926       7
-    1911    1920    1926    1929       1    1911    1920    1926    1932       1
-    1908    1902    1896    1935       6    1908    1902    1911    1914      62
-    1908    1902    1911    1917      62    1908    1902    1911    1920       6
-    1905    1902    1896    1935       6    1905    1902    1911    1914      62
-    1905    1902    1911    1917      62    1905    1902    1911    1920       6
-    1899    1896    1902    1905       6    1899    1896    1902    1908       6
-    1899    1896    1902    1911       6    1899    1896    1935    1938      59
-    1899    1896   -1935    1938      60    1899    1896    1935    1941       7
-    1896    1902    1911    1914      61    1896    1902    1911    1917      61
-    1896    1935    1941    1944       1    1893    1890    1896    1899       7
-    1893    1890    1896    1902       7    1893    1890    1896    1935       7
-    1890    1896    1902    1905       6    1890    1896    1902    1908       6
-    1998    1995    2001    2004      12    1998    1995   -2001    2004       1
-    1995    2001    2007    2010       7    1986    1983    1989    1992      17
-    1980    1977    1983    1986      17    1980    1977    1983    1989      17
-    1977    1983    1989    1992      17    1974    1971    1977    1980      17
-    1974    1971    1977    1983      17    1971    1977    1983    1986      17
-    1968    1965    1962    1989      17    1968    1965    1971    1974      17
-    1968    1965    1971    1977      17    1965    1962    1989    1992      17
-    1965    1971    1977    1980      17    1962    1965    1971    1974      17
-    1962    1989    1983    1986      17    1959    1953    1947    1995       6
-    1959    1953    1962    1965       7    1959    1953    1962    1989       7
-    1956    1953    1947    1995       6    1956    1953    1962    1965       7
-    1956    1953    1962    1989       7    1953    1962    1965    1968      17
-    1953    1962    1989    1992      17    1950    1947    1953    1956       6
-    1950    1947    1953    1959       6    1950    1947    1953    1962       6
-    1950    1947    1995    1998      59    1950    1947   -1995    1998      60
-    1950    1947    1995    2001       7    1947    1995    2001    2004       1
-    1944    1941    1947    1950       7    1944    1941    1947    1953       7
-    1944    1941    1947    1995       7    1941    1947    1953    1956       6
-    1941    1947    1953    1959       6    2064    2061    2067    2070      12
-    2064    2061   -2067    2070       1    2061    2067    2073    2076       7
-    2046    2040    2049    2052       6    2046    2040    2049    2055       6
-    2046    2040    2049    2058       6    2043    2040    2049    2052       6
-    2043    2040    2049    2055       6    2043    2040    2049    2058       6
-    2037    2031    2040    2043       6    2037    2031    2040    2046       6
-    2037    2031    2040    2049       6    2034    2031    2040    2043       6
-    2034    2031    2040    2046       6    2034    2031    2040    2049       6
-    2031    2040    2049    2052       6    2031    2040    2049    2055       6
-    2031    2040    2049    2058       6    2028    2022    2031    2034      62
-    2028    2022    2031    2037      62    2028    2022    2031    2040      61
-    2025    2022    2031    2034      62    2025    2022    2031    2037      62
-    2025    2022    2031    2040      61    2022    2031    2040    2043       6
-    2022    2031    2040    2046       6    2019    2013    2007    2061       6
-    2019    2013    2022    2025      62    2019    2013    2022    2028      62
-    2019    2013    2022    2031      61    2016    2013    2007    2061       6
-    2016    2013    2022    2025      62    2016    2013    2022    2028      62
-    2016    2013    2022    2031      61    2013    2022    2031    2034      61
-    2013    2022    2031    2037      61    2010    2007    2013    2016       6
-    2010    2007    2013    2019       6    2010    2007    2013    2022       6
-    2010    2007    2061    2064      59    2010    2007   -2061    2064      60
-    2010    2007    2061    2067       7    2007    2013    2022    2025      61
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-   11013   11019   11025   11034      61   11013   11019   11037   11040      61
-   11013   11019   11037   11043      61   11013   11019   11037   11046      61
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-   11070   11067   11085   11088      62   11070   11067   11085   11091      62
-   11070   11067   11085   11094      62   11064   11061   11067   11070       6
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-   11061   11067   11073   11079      61   11061   11067   11073   11082      61
-   11061   11067   11085   11088      61   11061   11067   11085   11091      61
-   11061   11067   11085   11094      61   11061   11097   11103   11106       1
-   11058   11055   11061   11064       7   11058   11055   11061   11067       7
-   11058   11055   11061   11097       7   11055   11061   11067   11070       6
-   11151   11148   11154   11157      12   11151   11148  -11154   11157       1
-   11148   11154   11160   11163       7   11139   11136   11142   11145      25
-   11133   11130   11136   11139      23   11133   11130   11136   11142      23
-   11130   11136   11142   11145      25   11127   11124   11142   11145      22
-   11127   11130   11136   11139      23   11124   11127   11130   11133      24
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-   11118   11115   11109   11148       6   11118   11115   11124   11127       7
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-   11112   11109   11115   11124       6   11112   11109   11148   11151      59
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-   11199   11196   11202   11205      12   11199   11196  -11202   11205       1
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-   11160   11166   11172   11175      61   11160   11166   11172   11178      61
-   11160   11166   11172   11181      61   11160   11166   11184   11187      61
-   11160   11166   11184   11190      61   11160   11166   11184   11193      61
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-   11154   11160   11166   11169       6   11235   11232   11238   11241      12
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-   11241   11238   11244   11262       7   11238   11244   11250   11253       6
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-   11286   11283   11289   11292      12   11286   11283  -11289   11292       1
-   11283   11289   11295   11298       7   11280   11274   11283   11286      59
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-   11277   11274   11283   11289       7   11274   11283   11289   11292       1
-   11271   11268   11274   11277       7   11271   11268   11274   11280       7
-   11271   11268   11274   11283       7   11349   11346   11352   11355      12
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-   11316   11313   11319   11325      17   11313   11310   11340   11343      17
-   11310   11313   11319   11322      17   11310   11340   11334   11337      17
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-   11301   11310   11313   11316      17   11301   11310   11340   11343      17
-   11298   11295   11301   11304       6   11298   11295   11301   11307       6
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-   11292   11289   11295   11301       7   11292   11289   11295   11346       7
-   11289   11295   11301   11304       6   11289   11295   11301   11307       6
-   11400   11397   11403   11406      12   11400   11397  -11403   11406       1
-   11397   11403   11409   11412       7   11388   11385   11391   11394      25
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-   11376   11379   11385   11388      23   11373   11376   11379   11382      24
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-   11367   11364   11373   11391       7   11364   11373   11391   11394      22
-   11361   11358   11364   11367       6   11361   11358   11364   11370       6
-   11361   11358   11364   11373       6   11361   11358   11397   11400      59
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-   11352   11358   11364   11367       6   11352   11358   11364   11370       6
-   11433   11430   11436   11439      12   11433   11430  -11436   11439       1
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-   11418   11415   11424   11427      46   11412   11409   11415   11418       6
-   11412   11409   11415   11421       6   11412   11409   11415   11424       6
-   11412   11409   11430   11433      59   11412   11409  -11430   11433      60
-   11412   11409   11430   11436       7   11409   11415   11424   11427      46
-   11409   11430   11436   11439       1   11406   11403   11409   11412       7
-   11406   11403   11409   11415       7   11406   11403   11409   11430       7
-   11403   11409   11415   11418       6   11403   11409   11415   11421       6
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-   11451   11448   11454   11463      62   11451   11448   11466   11469      62
-   11451   11448   11466   11472      62   11451   11448   11466   11475      62
-   11445   11442   11448   11451       6   11445   11442   11448   11454       6
-   11445   11442   11448   11466       6   11445   11442   11478   11481      59
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-   11442   11448   11454   11457      61   11442   11448   11454   11460      61
-   11442   11448   11454   11463      61   11442   11448   11466   11469      61
-   11442   11448   11466   11472      61   11442   11448   11466   11475      61
-   11442   11478   11484   11487       1   11439   11436   11442   11445       7
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-   11493   11490   11511   11514      59   11493   11490  -11511   11514      60
-   11493   11490   11511   11517       7   11490   11496   11505   11508      63
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-   11526   11523   11529   11538       6   11526   11523   11562   11565      59
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-   11706   11700   11718   11724      61   11706   11700   11718   11727      61
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-   11703   11700   11706   11715      62   11703   11700   11718   11721      62
-   11703   11700   11718   11724      62   11703   11700   11718   11727      62
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-   11763   11757   11775   11781      61   11763   11757   11775   11784      61
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-   11760   11757   11763   11772      62   11760   11757   11775   11778      62
-   11760   11757   11775   11781      62   11760   11757   11775   11784      62
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-   11754   11748   11757   11763      61   11754   11748   11757   11775      61
-   11751   11748   11742   11787       6   11751   11748   11757   11760      62
-   11751   11748   11757   11763      61   11751   11748   11757   11775      61
-   11748   11757   11763   11766      61   11748   11757   11763   11769      61
-   11748   11757   11763   11772      61   11748   11757   11775   11778      61
-   11748   11757   11775   11781      61   11748   11757   11775   11784      61
-   11745   11742   11748   11751       6   11745   11742   11748   11754       6
-   11745   11742   11748   11757       6   11745   11742   11787   11790      59
-   11745   11742  -11787   11790      60   11745   11742   11787   11793       7
-   11742   11748   11757   11760      61   11742   11787   11793   11796       1
-   11739   11736   11742   11745       7   11739   11736   11742   11748       7
-   11739   11736   11742   11787       7   11736   11742   11748   11751       6
-   11736   11742   11748   11754       6   11835   11832   11838   11841      12
-   11835   11832  -11838   11841       1   11832   11838   11844   11847       7
-   11820   11814   11823   11826       7   11820   11814   11823   11829       7
-   11817   11814   11823   11826       7   11817   11814   11823   11829       7
-   11811   11805   11799   11832       6   11811   11805   11814   11817      62
-   11811   11805   11814   11820      62   11811   11805   11814   11823       6
-   11808   11805   11799   11832       6   11808   11805   11814   11817      62
-   11808   11805   11814   11820      62   11808   11805   11814   11823       6
-   11802   11799   11805   11808       6   11802   11799   11805   11811       6
-   11802   11799   11805   11814       6   11802   11799   11832   11835      59
-   11802   11799  -11832   11835      60   11802   11799   11832   11838       7
-   11799   11805   11814   11817      61   11799   11805   11814   11820      61
-   11799   11832   11838   11841       1   11796   11793   11799   11802       7
-   11796   11793   11799   11805       7   11796   11793   11799   11832       7
-   11793   11799   11805   11808       6   11793   11799   11805   11811       6
-   11886   11883   11889   11892      12   11886   11883  -11889   11892       1
-   11883   11889   11895   11898       7   11874   11871   11877   11880      25
-   11868   11865   11871   11874      23   11868   11865   11871   11877      23
-   11865   11871   11877   11880      25   11862   11859   11877   11880      22
-   11862   11865   11871   11874      23   11859   11862   11865   11868      24
-   11859   11877   11871   11874      25   11856   11850   11844   11883       6
-   11856   11850   11859   11862       7   11856   11850   11859   11877       7
-   11853   11850   11844   11883       6   11853   11850   11859   11862       7
-   11853   11850   11859   11877       7   11850   11859   11877   11880      22
-   11847   11844   11850   11853       6   11847   11844   11850   11856       6
-   11847   11844   11850   11859       6   11847   11844   11883   11886      59
-   11847   11844  -11883   11886      60   11847   11844   11883   11889       7
-   11844   11883   11889   11892       1   11841   11838   11844   11847       7
-   11841   11838   11844   11850       7   11841   11838   11844   11883       7
-   11838   11844   11850   11853       6   11838   11844   11850   11856       6
-   11937   11934   11940   11943      12   11937   11934  -11940   11943       1
-   11934   11940   11946   11949       7   11925   11922   11928   11931      25
-   11919   11916   11922   11925      23   11919   11916   11922   11928      23
-   11916   11922   11928   11931      25   11913   11910   11928   11931      22
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 %FLAG DIHEDRALS_WITHOUT_HYDROGEN                                                
 %FORMAT(10I8)                                                                   
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-    1716    1722   -1752    1758      15    1716    1722   -1752    1758      16
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-    1815    1821   -1827    1863       4    1815    1821   -1827    1863       5
-    1797    1794    1803    1809      17    1788    1782    1779    1809      17
-    1788    1794   -1803    1809      17    1782    1779    1809    1803      17
-    1782    1788    1794    1797      17    1782    1788   -1794    1803      17
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-    1779    1809   -1803    1794      17    1770    1764    1815    1818       7
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-    1770    1764   -1815    1821      10    1770    1764   -1815    1821       5
-    1770    1779    1782    1788      17    1770    1779    1809    1803      17
-    1764    1770    1779    1782       7    1764    1770    1779    1809       7
-    1764    1815    1821    1827       1    1758    1764    1770    1779       6
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-    1758    1764   -1815    1821      15    1758    1764   -1815    1821      16
-    1758    1764   -1815    1821       5    1866    1863    1869    1875       1
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-    1863    1869   -1875    1884       4    1863    1869   -1875    1884       5
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-    1833    1827   -1863    1869       9    1833    1827   -1863    1869      10
-    1833    1827   -1863    1869       5    1827    1863    1869    1875       1
-    1821    1827    1833    1839       6    1821    1827    1833    1851       6
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-    1884    1890   -1896    1902      10    1884    1890   -1896    1902       5
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-    1884    1890   -1896    1935       4    1884    1890   -1896    1935       5
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-    1869    1875   -1884    1890      16    1869    1875   -1884    1890       5
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-    1935    1941   -1947    1953       5    1935    1941    1947    1995       2
-    1935    1941   -1947    1995       3    1935    1941   -1947    1995       4
-    1935    1941   -1947    1995       5    1911    1902    1896    1935       6
-    1902    1896    1935    1938       7    1902    1896    1935    1941       8
-    1902    1896   -1935    1941       9    1902    1896   -1935    1941      10
-    1902    1896   -1935    1941       5    1902    1911    1920    1923       7
-    1902    1911    1920    1926       8    1902    1911   -1920    1926       9
-    1902    1911   -1920    1926      10    1902    1911   -1920    1926       5
-    1896    1902    1911    1920       6    1896    1935    1941    1947       1
-    1890    1896    1902    1911       6    1890    1896    1935    1938       7
-    1890    1896    1935    1941      14    1890    1896   -1935    1941      15
-    1890    1896   -1935    1941      16    1890    1896   -1935    1941       5
-    1998    1995    2001    2007       1    1995    2001    2007    2013      12
-    1995    2001   -2007    2013      13    1995    2001   -2007    2013      10
-    1995    2001   -2007    2013       5    1995    2001    2007    2061       2
-    1995    2001   -2007    2061       3    1995    2001   -2007    2061       4
-    1995    2001   -2007    2061       5    1971    1965    1962    1989      17
-    1971    1977   -1983    1989      17    1965    1962    1989    1983      17
-    1965    1971   -1977    1983      17    1962    1953    1947    1995       6
-    1962    1965    1971    1977      17    1962    1989   -1983    1977      17
-    1953    1947    1995    1998       7    1953    1947    1995    2001       8
-    1953    1947   -1995    2001       9    1953    1947   -1995    2001      10
-    1953    1947   -1995    2001       5    1953    1962    1965    1971      17
-    1953    1962    1989    1983      17    1947    1953    1962    1965       7
-    1947    1953    1962    1989       7    1947    1995    2001    2007       1
-    1941    1947    1953    1962       6    1941    1947    1995    1998       7
-    1941    1947    1995    2001      14    1941    1947   -1995    2001      15
-    1941    1947   -1995    2001      16    1941    1947   -1995    2001       5
-    2064    2061    2067    2073       1    2061    2067    2073    2079      12
-    2061    2067   -2073    2079      13    2061    2067   -2073    2079      10
-    2061    2067   -2073    2079       5    2061    2067    2073    2097       2
-    2061    2067   -2073    2097       3    2061    2067   -2073    2097       4
-    2061    2067   -2073    2097       5    2022    2013    2007    2061       6
-    2022    2031    2040    2049       6    2013    2007    2061    2064       7
-    2013    2007    2061    2067       8    2013    2007   -2061    2067       9
-    2013    2007   -2061    2067      10    2013    2007   -2061    2067       5
-    2013    2022    2031    2040      18    2013    2022   -2031    2040      19
-    2013    2022   -2031    2040      20    2007    2013    2022    2031      18
-    2007    2013   -2022    2031      19    2007    2013   -2022    2031      20
-    2007    2061    2067    2073       1    2001    2007    2013    2022       6
-    2001    2007    2061    2064       7    2001    2007    2061    2067      14
-    2001    2007   -2061    2067      15    2001    2007   -2061    2067      16
-    2001    2007   -2061    2067       5    2100    2097    2103    2109       1
-    2097    2103    2109    2115      12    2097    2103   -2109    2115      13
-    2097    2103   -2109    2115      10    2097    2103   -2109    2115       5
-    2097    2103    2109    2169       2    2097    2103   -2109    2169       3
-    2097    2103   -2109    2169       4    2097    2103   -2109    2169       5
-    2088    2079    2073    2097       6    2079    2073    2097    2100       7
-    2079    2073    2097    2103       8    2079    2073   -2097    2103       9
-    2079    2073   -2097    2103      10    2079    2073   -2097    2103       5
-    2073    2079    2088    2091       7    2073    2079    2088    2094       7
-    2073    2097    2103    2109       1    2067    2073    2079    2088       6
-    2067    2073    2097    2100       7    2067    2073    2097    2103      14
-    2067    2073   -2097    2103      15    2067    2073   -2097    2103      16
-    2067    2073   -2097    2103       5    2172    2169    2175    2181       1
-    2169    2175    2181    2187      12    2169    2175   -2181    2187      13
-    2169    2175   -2181    2187      10    2169    2175   -2181    2187       5
-    2169    2175    2181    2217       2    2169    2175   -2181    2217       3
-    2169    2175   -2181    2217       4    2169    2175   -2181    2217       5
-    2133    2142    2148    2151      21    2133    2142    2148    2160      21
-    2124    2115    2109    2169       6    2124    2133    2142    2148      26
-    2115    2109    2169    2172       7    2115    2109    2169    2175       8
-    2115    2109   -2169    2175       9    2115    2109   -2169    2175      10
-    2115    2109   -2169    2175       5    2115    2124    2133    2142       6
-    2109    2115    2124    2133      18    2109    2115   -2124    2133      19
-    2109    2115   -2124    2133      20    2109    2169    2175    2181       1
-    2103    2109    2115    2124       6    2103    2109    2169    2172       7
-    2103    2109    2169    2175      14    2103    2109   -2169    2175      15
-    2103    2109   -2169    2175      16    2103    2109   -2169    2175       5
-    2220    2217    2223    2229       1    2217    2223    2229    2235      12
-    2217    2223   -2229    2235      13    2217    2223   -2229    2235      10
-    2217    2223   -2229    2235       5    2217    2223    2229    2262       2
-    2217    2223   -2229    2262       3    2217    2223   -2229    2262       4
-    2217    2223   -2229    2262       5    2205    2187    2181    2217       6
-    2193    2187    2181    2217       6    2187    2181    2217    2220       7
-    2187    2181    2217    2223       8    2187    2181   -2217    2223       9
-    2187    2181   -2217    2223      10    2187    2181   -2217    2223       5
-    2181    2217    2223    2229       1    2175    2181    2187    2193       6
-    2175    2181    2187    2205       6    2175    2181    2217    2220       7
-    2175    2181    2217    2223      14    2175    2181   -2217    2223      15
-    2175    2181   -2217    2223      16    2175    2181   -2217    2223       5
-    2265    2262    2268    2274       1    2262    2268    2274    2280      12
-    2262    2268   -2274    2280      13    2262    2268   -2274    2280      10
-    2262    2268   -2274    2280       5    2262    2268    2274    2328       2
-    2262    2268   -2274    2328       3    2262    2268   -2274    2328       4
-    2262    2268   -2274    2328       5    2244    2235    2229    2262       6
-    2235    2229    2262    2265       7    2235    2229    2262    2268       8
-    2235    2229   -2262    2268       9    2235    2229   -2262    2268      10
-    2235    2229   -2262    2268       5    2235    2244    2253    2256       7
-    2235    2244    2253    2259       7    2229    2235    2244    2253       6
-    2229    2262    2268    2274       1    2223    2229    2235    2244       6
-    2223    2229    2262    2265       7    2223    2229    2262    2268      14
-    2223    2229   -2262    2268      15    2223    2229   -2262    2268      16
-    2223    2229   -2262    2268       5    2331    2328    2334    2340       1
-    2328    2334    2340    2346      12    2328    2334   -2340    2346      13
-    2328    2334   -2340    2346      10    2328    2334   -2340    2346       5
-    2328    2334    2340    2385       2    2328    2334   -2340    2385       3
-    2328    2334   -2340    2385       4    2328    2334   -2340    2385       5
-    2289    2280    2274    2328       6    2289    2298    2307    2316       6
-    2280    2274    2328    2331       7    2280    2274    2328    2334       8
-    2280    2274   -2328    2334       9    2280    2274   -2328    2334      10
-    2280    2274   -2328    2334       5    2280    2289    2298    2307      18
-    2280    2289   -2298    2307      19    2280    2289   -2298    2307      20
-    2274    2280    2289    2298      18    2274    2280   -2289    2298      19
-    2274    2280   -2289    2298      20    2274    2328    2334    2340       1
-    2268    2274    2280    2289       6    2268    2274    2328    2331       7
-    2268    2274    2328    2334      14    2268    2274   -2328    2334      15
-    2268    2274   -2328    2334      16    2268    2274   -2328    2334       5
-    2388    2385    2391    2397       1    2385    2391    2397    2403      12
-    2385    2391   -2397    2403      13    2385    2391   -2397    2403      10
-    2385    2391   -2397    2403       5    2385    2391    2397    2418       2
-    2385    2391   -2397    2418       3    2385    2391   -2397    2418       4
-    2385    2391   -2397    2418       5    2355    2346    2340    2385       6
-    2346    2340    2385    2388       7    2346    2340    2385    2391       8
-    2346    2340   -2385    2391       9    2346    2340   -2385    2391      10
-    2346    2340   -2385    2391       5    2340    2346    2355    2361      18
-    2340    2346   -2355    2361      19    2340    2346   -2355    2361      20
-    2340    2346    2355    2373      18    2340    2346   -2355    2373      19
-    2340    2346   -2355    2373      20    2340    2385    2391    2397       1
-    2334    2340    2346    2355       6    2334    2340    2385    2388       7
-    2334    2340    2385    2391      14    2334    2340   -2385    2391      15
-    2334    2340   -2385    2391      16    2334    2340   -2385    2391       5
-    2421    2418    2424    2430       1    2418    2424    2430    2436      12
-    2418    2424   -2430    2436      13    2418    2424   -2430    2436      10
-    2418    2424   -2430    2436       5    2418    2424    2430    2448       2
-    2418    2424   -2430    2448       3    2418    2424   -2430    2448       4
-    2418    2424   -2430    2448       5    2412    2403    2397    2418       6
-    2403    2397    2418    2421       7    2403    2397    2418    2424       8
-    2403    2397   -2418    2424       9    2403    2397   -2418    2424      10
-    2403    2397   -2418    2424       5    2397    2418    2424    2430       1
-    2391    2397    2403    2412       6    2391    2397    2418    2421       7
-    2391    2397    2418    2424      14    2391    2397   -2418    2424      15
-    2391    2397   -2418    2424      16    2391    2397   -2418    2424       5
-    2451    2448    2454    2460       1    2448    2454    2460    2466      12
-    2448    2454   -2460    2466      13    2448    2454   -2460    2466      10
-    2448    2454   -2460    2466       5    2448    2454    2460    2493       2
-    2448    2454   -2460    2493       3    2448    2454   -2460    2493       4
-    2448    2454   -2460    2493       5    2436    2430    2448    2451       7
-    2436    2430    2448    2454       8    2436    2430   -2448    2454       9
-    2436    2430   -2448    2454      10    2436    2430   -2448    2454       5
-    2430    2448    2454    2460       1    2424    2430    2448    2451       7
-    2424    2430    2448    2454      14    2424    2430   -2448    2454      15
-    2424    2430   -2448    2454      16    2424    2430   -2448    2454       5
-    2496    2493    2499    2505       1    2493    2499    2505    2511      12
-    2493    2499   -2505    2511      13    2493    2499   -2505    2511      10
-    2493    2499   -2505    2511       5    2493    2499    2505    2553       2
-    2493    2499   -2505    2553       3    2493    2499   -2505    2553       4
-    2493    2499   -2505    2553       5    2475    2466    2460    2493       6
-    2466    2460    2493    2496       7    2466    2460    2493    2499       8
-    2466    2460   -2493    2499       9    2466    2460   -2493    2499      10
-    2466    2460   -2493    2499       5    2466    2475    2484    2487       7
-    2466    2475    2484    2490       7    2460    2466    2475    2484       6
-    2460    2493    2499    2505       1    2454    2460    2466    2475       6
-    2454    2460    2493    2496       7    2454    2460    2493    2499      14
-    2454    2460   -2493    2499      15    2454    2460   -2493    2499      16
-    2454    2460   -2493    2499       5    2556    2553    2559    2565       1
-    2553    2559    2565    2571      12    2553    2559   -2565    2571      13
-    2553    2559   -2565    2571      10    2553    2559   -2565    2571       5
-    2553    2559    2565    2595       2    2553    2559   -2565    2595       3
-    2553    2559   -2565    2595       4    2553    2559   -2565    2595       5
-    2529    2523    2520    2547      17    2529    2535   -2541    2547      17
-    2523    2520    2547    2541      17    2523    2529   -2535    2541      17
-    2520    2511    2505    2553       6    2520    2523    2529    2535      17
-    2520    2547   -2541    2535      17    2511    2505    2553    2556       7
-    2511    2505    2553    2559       8    2511    2505   -2553    2559       9
-    2511    2505   -2553    2559      10    2511    2505   -2553    2559       5
-    2511    2520    2523    2529      17    2511    2520    2547    2541      17
-    2505    2511    2520    2523       7    2505    2511    2520    2547       7
-    2505    2553    2559    2565       1    2499    2505    2511    2520       6
-    2499    2505    2553    2556       7    2499    2505    2553    2559      14
-    2499    2505   -2553    2559      15    2499    2505   -2553    2559      16
-    2499    2505   -2553    2559       5    2598    2595    2601    2604       1
-    2598    2595    2601    2631       1    2595    2601    2604    2613      12
-    2595    2601   -2604    2613      13    2595    2601   -2604    2613      10
-    2595    2601   -2604    2613       5    2595    2601    2631    2622      12
-    2595    2601   -2631    2622      13    2595    2601   -2631    2622      10
-    2595    2601   -2631    2622       5    2595    2601    2631    2637       2
-    2595    2601   -2631    2637       3    2595    2601   -2631    2637       4
-    2595    2601   -2631    2637       5    2580    2571    2565    2595       6
-    2571    2565    2595    2598       7    2571    2565    2595    2601       8
-    2571    2565   -2595    2601       9    2571    2565   -2595    2601      10
-    2571    2565   -2595    2601       5    2565    2571    2580    2583       7
-    2565    2571    2580    2586       8    2565    2571   -2580    2586       9
-    2565    2571   -2580    2586      10    2565    2571   -2580    2586       5
-    2565    2595    2601    2604       1    2565    2595    2601    2631       1
-    2559    2565    2571    2580       6    2559    2565    2595    2598       7
-    2559    2565    2595    2601      14    2559    2565   -2595    2601      15
-    2559    2565   -2595    2601      16    2559    2565   -2595    2601       5
-    2640    2637    2643    2649       1    2637    2643    2649    2655      12
-    2637    2643   -2649    2655      13    2637    2643   -2649    2655      10
-    2637    2643   -2649    2655       5    2637    2643    2649    2667       2
-    2637    2643   -2649    2667       3    2637    2643   -2649    2667       4
-    2637    2643   -2649    2667       5    2631    2637    2643    2649       1
-    2622    2631    2637    2640       7    2622    2631    2637    2643       8
-    2622    2631   -2637    2643       9    2622    2631   -2637    2643      10
-    2622    2631   -2637    2643       5    2613    2604   -2601    2631       7
-    2613    2622    2631    2637       6    2604    2601   -2631    2622       7
-    2604    2601    2631    2637       7    2604    2613   -2622    2631      18
-    2604    2613   -2622    2631      19    2604    2613   -2622    2631      20
-    2601    2604   -2613    2622       6    2601    2631   -2622    2613       6
-    2601    2631    2637    2640       7    2601    2631    2637    2643      14
-    2601    2631   -2637    2643      15    2601    2631   -2637    2643      16
-    2601    2631   -2637    2643       5    2670    2667    2673    2679       1
-    2667    2673    2679    2685      12    2667    2673   -2679    2685      13
-    2667    2673   -2679    2685      10    2667    2673   -2679    2685       5
-    2667    2673    2679    2697       2    2667    2673   -2679    2697       3
-    2667    2673   -2679    2697       4    2667    2673   -2679    2697       5
-    2655    2649    2667    2670       7    2655    2649    2667    2673       8
-    2655    2649   -2667    2673       9    2655    2649   -2667    2673      10
-    2655    2649   -2667    2673       5    2649    2667    2673    2679       1
-    2643    2649    2667    2670       7    2643    2649    2667    2673      14
-    2643    2649   -2667    2673      15    2643    2649   -2667    2673      16
-    2643    2649   -2667    2673       5    2700    2697    2703    2709       1
-    2697    2703    2709    2715      12    2697    2703   -2709    2715      13
-    2697    2703   -2709    2715      10    2697    2703   -2709    2715       5
-    2697    2703    2709    2745       2    2697    2703   -2709    2745       3
-    2697    2703   -2709    2745       4    2697    2703   -2709    2745       5
-    2685    2679    2697    2700       7    2685    2679    2697    2703       8
-    2685    2679   -2697    2703       9    2685    2679   -2697    2703      10
-    2685    2679   -2697    2703       5    2679    2697    2703    2709       1
-    2673    2679    2697    2700       7    2673    2679    2697    2703      14
-    2673    2679   -2697    2703      15    2673    2679   -2697    2703      16
-    2673    2679   -2697    2703       5    2748    2745    2751    2757       1
-    2745    2751    2757    2763      12    2745    2751   -2757    2763      13
-    2745    2751   -2757    2763      10    2745    2751   -2757    2763       5
-    2745    2751    2757    2802       2    2745    2751   -2757    2802       3
-    2745    2751   -2757    2802       4    2745    2751   -2757    2802       5
-    2733    2715    2709    2745       6    2721    2715    2709    2745       6
-    2715    2709    2745    2748       7    2715    2709    2745    2751       8
-    2715    2709   -2745    2751       9    2715    2709   -2745    2751      10
-    2715    2709   -2745    2751       5    2709    2745    2751    2757       1
-    2703    2709    2715    2721       6    2703    2709    2715    2733       6
-    2703    2709    2745    2748       7    2703    2709    2745    2751      14
-    2703    2709   -2745    2751      15    2703    2709   -2745    2751      16
-    2703    2709   -2745    2751       5    2805    2802    2808    2811       1
-    2805    2802    2808    2838       1    2802    2808    2811    2820      12
-    2802    2808   -2811    2820      13    2802    2808   -2811    2820      10
-    2802    2808   -2811    2820       5    2802    2808    2838    2829      12
-    2802    2808   -2838    2829      13    2802    2808   -2838    2829      10
-    2802    2808   -2838    2829       5    2802    2808    2838    2844       2
-    2802    2808   -2838    2844       3    2802    2808   -2838    2844       4
-    2802    2808   -2838    2844       5    2772    2763    2757    2802       6
-    2763    2757    2802    2805       7    2763    2757    2802    2808       8
-    2763    2757   -2802    2808       9    2763    2757   -2802    2808      10
-    2763    2757   -2802    2808       5    2757    2763    2772    2778      18
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-    2757    2763    2772    2790      18    2757    2763   -2772    2790      19
-    2757    2763   -2772    2790      20    2757    2802    2808    2811       1
-    2757    2802    2808    2838       1    2751    2757    2763    2772       6
-    2751    2757    2802    2805       7    2751    2757    2802    2808      14
-    2751    2757   -2802    2808      15    2751    2757   -2802    2808      16
-    2751    2757   -2802    2808       5    2847    2844    2850    2856       1
-    2844    2850    2856    2862      12    2844    2850   -2856    2862      13
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-    2844    2850    2856    2877       2    2844    2850   -2856    2877       3
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-    2838    2844    2850    2856       1    2829    2838    2844    2847       7
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-    2829    2838   -2844    2850      10    2829    2838   -2844    2850       5
-    2820    2811   -2808    2838       7    2820    2829    2838    2844       6
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-   11934   11940  -11946   11952      10   11934   11940  -11946   11952       5
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-   11934   11940  -11946   11985       4   11934   11940  -11946   11985       5
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-   11913   11916  -11922   11928      23   11910   11901   11895   11934       6
-   11910   11913  -11916   11922      24   11910   11928  -11922   11916      25
-   11901   11895   11934   11937       7   11901   11895   11934   11940       8
-   11901   11895  -11934   11940       9   11901   11895  -11934   11940      10
-   11901   11895  -11934   11940       5   11901   11910   11913   11916      21
-   11901   11910   11928   11922      22   11895   11901   11910   11913       7
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-   11889   11895   11901   11910       6   11889   11895   11934   11937       7
-   11889   11895   11934   11940      14   11889   11895  -11934   11940      15
-   11889   11895  -11934   11940      16   11889   11895  -11934   11940       5
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-   11985   11991  -11997   12036       5   11967   11964  -11961   11979      21
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-   11961   11952   11946   11985       6   11961   11964  -11967   11973      24
-   11961   11979  -11973   11967      25   11952   11946   11985   11988       7
-   11952   11946   11985   11991       8   11952   11946  -11985   11991       9
-   11952   11946  -11985   11991      10   11952   11946  -11985   11991       5
-   11952   11961   11964   11967      21   11952   11961   11979   11973      22
-   11946   11952   11961   11964       7   11946   11952   11961   11979       7
-   11946   11985   11991   11997       1   11940   11946   11952   11961       6
-   11940   11946   11985   11988       7   11940   11946   11985   11991      14
-   11940   11946  -11985   11991      15   11940   11946  -11985   11991      16
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+    9333    9378   -9372   -9375      41    9384    9435   -9429   -9432      41
+    9441    9471   -9465   -9468      41    9447    9459   -9456   -9462      41
+    9477    9534   -9528   -9531      41    9501    9516   -9507   -9510      40
+    9495    9522   -9492   -9483      40    9540    9576   -9570   -9573      41
+    9546    9561   -9555   -9558      41    9582    9606   -9600   -9603      41
+    9612    9657   -9651   -9654      41    9663    9705   -9699   -9702      41
+    9711    9738   -9732   -9735      41    9768    9780   -9774   -9777      41
+    9732    9741   -9738   -9768      42    9786    9837   -9831   -9834      41
+    9843    9903   -9897   -9900      41    9909    9969   -9963   -9966      41
+    9975   10011  -10005  -10008      41    9981    9996   -9990   -9993      41
+   10017   10059  -10053  -10056      41   10065   10095  -10089  -10092      41
+   10071   10083  -10080  -10086      41   10101   10152  -10146  -10149      41
+   10158   10203  -10197  -10200      41   10209   10248  -10242  -10245      41
+   10224   10236  -10233  -10239      41   10254   10296  -10290  -10293      41
+   10302   10317  -10311  -10314      41   10323   10359  -10353  -10356      41
+   10329   10344  -10338  -10341      41   10365   10401  -10395  -10398      41
+   10407   10449  -10443  -10446      41   10455   10479  -10473  -10476      41
+   10485   10539  -10533  -10536      41   10503   10527  -10500  -10491      40
+   10545   10596  -10590  -10593      41   10602   10629  -10623  -10626      41
+   10635   10662  -10656  -10659      41   10668   10698  -10692  -10695      41
+   10674   10686  -10683  -10689      41   10704   10749  -10743  -10746      41
+   10755   10779  -10773  -10776      41   10785   10821  -10815  -10818      41
+   10827   10842  -10836  -10839      41   10848   10899  -10893  -10896      41
+   10905   10941  -10935  -10938      41   10947   10962  -10956  -10959      41
+   10968   11007  -11001  -11004      41   10983   10995  -10992  -10998      41
+   11013   11055  -11049  -11052      41   11061   11103  -11097  -11100      41
+   11109   11154  -11148  -11151      41   11115   11142  -11124  -11127      40
+   11160   11202  -11196  -11199      41   11208   11238  -11232  -11235      41
+   11214   11226  -11223  -11229      41   11244   11268  -11262  -11265      41
+   11274   11289  -11283  -11286      41   11295   11352  -11346  -11349      41
+   11319   11334  -11325  -11328      40   11313   11340  -11310  -11301      40
+   11358   11403  -11397  -11400      41   11364   11391  -11373  -11376      40
+   11409   11436  -11430  -11433      41   11442   11484  -11478  -11481      41
+   11490   11517  -11511  -11514      41   11523   11568  -11562  -11565      41
+   11574   11589  -11583  -11586      41   11595   11631  -11625  -11628      41
+   11601   11616  -11610  -11613      41   11637   11679  -11673  -11676      41
+   11685   11736  -11730  -11733      41   11742   11793  -11787  -11790      41
+   11799   11838  -11832  -11835      41   11814   11826  -11823  -11829      41
+   11844   11889  -11883  -11886      41   11850   11877  -11859  -11862      40
+   11895   11940  -11934  -11937      41   11901   11928  -11910  -11913      40
+   11946   11991  -11985  -11988      41   11952   11979  -11961  -11964      40
+   11997   12042  -12036  -12039      41   12003   12030  -12012  -12015      40
+   12048   12093  -12087  -12090      41   12054   12081  -12063  -12066      40
+   12099   12141  -12138  -12144      41   12105   12132  -12114  -12117      40
+   12192   12198  -12195  -12201      40   12210   12186  -12183  -12180      42
+   12387   12393  -12390  -12402      40   12381   12387  -12384  -12399      40
+   12384   12396  -12381  -12375      40   12363   12369  -12366  -12405      40
+   12357   12363  -12360  -12378      40   12360   12372  -12357  -12375      40
 %FLAG EXCLUDED_ATOMS_LIST                                                       
 %FORMAT(10I8)                                                                   
        2       3       4       5       6       7       8       9      10      18
@@ -19296,7 +19296,10 @@ BLA BLA BLA
     4049      70      24
 %FLAG BOX_DIMENSIONS                                                            
 %FORMAT(5E16.8)                                                                 
-  1.09471219E+02  8.62058016E+01  8.62058016E+01  8.62058016E+01
+  1.09471222E+02  8.62058029E+01  8.62058029E+01  8.62058029E+01
+%FLAG RADIUS_SET                                                                
+%FORMAT(1a80)                                                                   
+modified Bondi radii (mbondi)                                                   
 %FLAG RADII                                                                     
 %FORMAT(5E16.8)                                                                 
   1.55000000E+00  1.30000000E+00  1.30000000E+00  1.30000000E+00  1.70000000E+00
@@ -20959,3 +20962,6 @@ BLA BLA BLA
   7.20000000E-01  7.20000000E-01  7.20000000E-01  8.00000000E-01  8.00000000E-01
   8.00000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01
   8.50000000E-01  8.50000000E-01  8.50000000E-01
+%FLAG IPOL                                                                      
+%FORMAT(1I8)                                                                    
+       0

From b80338f6685334a11520a019e80bb91f113def63 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 1 Jul 2024 15:05:36 -0400
Subject: [PATCH 0803/1492] AppendTop now saves GB radius set string

---
 test/Test_CombineCrd/combinedParm.parm7.save | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/test/Test_CombineCrd/combinedParm.parm7.save b/test/Test_CombineCrd/combinedParm.parm7.save
index 7634165fd1..8aea1715c4 100644
--- a/test/Test_CombineCrd/combinedParm.parm7.save
+++ b/test/Test_CombineCrd/combinedParm.parm7.save
@@ -1,4 +1,4 @@
-%VERSION  VERSION_STAMP = V0001.000  DATE = 07/01/24 12:33:32                  
+%VERSION  VERSION_STAMP = V0001.000  DATE = 07/01/24 14:59:12                  
 %FLAG TITLE                                                                     
 %FORMAT(20a4)                                                                   
 combinedParm                                                                    
@@ -1356,6 +1356,9 @@ BLA BLA BLA BLA
 %FLAG BOX_DIMENSIONS                                                            
 %FORMAT(5E16.8)                                                                 
   1.09471222E+02  4.24388504E+01  4.24388504E+01  4.24388504E+01
+%FLAG RADIUS_SET                                                                
+%FORMAT(1a80)                                                                   
+modified Bondi radii (mbondi)                                                   
 %FLAG RADII                                                                     
 %FORMAT(5E16.8)                                                                 
   1.55000000E+00  1.30000000E+00  1.30000000E+00  1.30000000E+00  1.70000000E+00

From 6d97f303292d60b663d8f4e5e170140173455ac3 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 1 Jul 2024 15:07:49 -0400
Subject: [PATCH 0804/1492] Update comments

---
 src/Topology.cpp | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index 8a7d7b47ca..8daa3add39 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2757,7 +2757,7 @@ int Topology::AppendTop(Topology const& NewTop) {
 
   // Need to regenerate nonbonded info
   mprintf("\tRegenerating nonbond parameters.\n");
-  AssignNonbondParams( myAtomTypes, myNB, my14, myLJC, myHB, 1 ); // FIXME verbose TODO LJC
+  AssignNonbondParams( myAtomTypes, myNB, my14, myLJC, myHB, 1 ); // FIXME verbose
 
   // The version of AddTopAtom() with molecule number already determines
   // molecules and number of solvent molecules.
@@ -3772,7 +3772,6 @@ int Topology::AssignParams(ParameterSet const& set0) {
   mprintf("\tAssigning nonbond parameters.\n");
   AssignNonbondParams( set0.AT(), set0.NB(), set0.NB14(), set0.LJC(), set0.HB(), debug_ );
   mprintf("DEBUG: CMAP size %zu\n", set0.CMAP().size());
-  // TODO LJ14, LJC
 
   return 0;
 }

From 8d9a18917bc07ae82d969e7b2b38f77a4478e682 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 3 Jul 2024 12:08:15 -0400
Subject: [PATCH 0805/1492] Change initial cutoff back to 1.25 Ang

---
 src/StructureCheck.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/StructureCheck.cpp b/src/StructureCheck.cpp
index 72da0385f2..76965b2f25 100644
--- a/src/StructureCheck.cpp
+++ b/src/StructureCheck.cpp
@@ -257,11 +257,11 @@ int StructureCheck::CheckRings(Frame const& currentFrame, Cpptraj::Structure::Ri
 {
   int Nproblems = 0;
   problemAtoms_.clear();
-  static const double ring_dcut2 = 1.3225; // Initial 1.15 Ang distance cutoff
+  //static const double ring_dcut2 = 1.3225; // Initial 1.15 Ang distance cutoff
   static const double ring_shortd2 = 0.25; // Short 0.5 Ang distance cutoff
   static const double ring_acut = 1.0471975512; // 60 deg. Ang cutoff
   //static const double ring_acut  = 0.174533; // 10 deg. angle cutoff
-  //static const double ring_dcut2 = 1.562500; // 1.25 Ang distance cutoff
+  static const double ring_dcut2 = 1.562500; // 1.25 Ang distance cutoff
 /*  static const double ring_acut = 0.7853981634; // 45 deg. angle cutoff for ring_dcut2 > dist2 > ring_shortd2*/
   // Get all ring vectors
   typedef std::vector<Cpptraj::Structure::LeastSquaresPlane> Larray;

From 938ad8b5214012fab5fcd4af20ac5fa94f8a52d6 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 3 Jul 2024 13:45:01 -0400
Subject: [PATCH 0806/1492] Improve debug output. Increase angle cut to 65 deg

---
 src/StructureCheck.cpp | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/src/StructureCheck.cpp b/src/StructureCheck.cpp
index 76965b2f25..cfb7293986 100644
--- a/src/StructureCheck.cpp
+++ b/src/StructureCheck.cpp
@@ -259,7 +259,8 @@ int StructureCheck::CheckRings(Frame const& currentFrame, Cpptraj::Structure::Ri
   problemAtoms_.clear();
   //static const double ring_dcut2 = 1.3225; // Initial 1.15 Ang distance cutoff
   static const double ring_shortd2 = 0.25; // Short 0.5 Ang distance cutoff
-  static const double ring_acut = 1.0471975512; // 60 deg. Ang cutoff
+  //static const double ring_acut = 1.0471975512; // 60 deg. Ang cutoff
+  static const double ring_acut = 1.1344640138; // 65 deg. Ang cutoff
   //static const double ring_acut  = 0.174533; // 10 deg. angle cutoff
   static const double ring_dcut2 = 1.562500; // 1.25 Ang distance cutoff
 /*  static const double ring_acut = 0.7853981634; // 45 deg. angle cutoff for ring_dcut2 > dist2 > ring_shortd2*/
@@ -323,16 +324,21 @@ int StructureCheck::CheckRings(Frame const& currentFrame, Cpptraj::Structure::Ri
             mprintf("\n");
             ring_intersect = true;
           } else {
+            mprintf("DEBUG: Bond %i - %i near ring %i (%f), doing angle check.",
+                    ringBonds[idx].A1(), ringBonds[idx].A2(), jdx, sqrt(dist2));
+            printRingAtoms(ringMask);
+            mprintf("\n");
             // Get the angle
             double ang_in_rad = vbond.Angle( ringVec.Nxyz() );
             // Wrap the angle between 0-90 degrees
             if (ang_in_rad > Constants::PIOVER2)
               ang_in_rad = Constants::PI - ang_in_rad;
+            mprintf("DEBUG:\t\tWrapped angle is %f deg.\n", Constants::RADDEG*ang_in_rad);
             if (ang_in_rad < ring_acut) {
               mprintf("DEBUG: Bond %i - %i near ring %i (%f) Ang= %f deg.",
                       ringBonds[idx].A1(), ringBonds[idx].A2(), jdx, sqrt(dist2),
                       Constants::RADDEG*ang_in_rad);
-              printRingAtoms(ringMask);
+              //printRingAtoms(ringMask);
               mprintf("\n");
               ring_intersect = true;
             }

From 0e6a34fa835cb688ec37e353fc2ce2d3ed28f73d Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 15 Jul 2024 13:23:12 -0400
Subject: [PATCH 0807/1492] Start MetalCenter class

---
 src/Structure/MetalCenter.cpp | 40 +++++++++++++++++++++++++++++++++++
 src/Structure/MetalCenter.h   | 26 +++++++++++++++++++++++
 2 files changed, 66 insertions(+)
 create mode 100644 src/Structure/MetalCenter.cpp
 create mode 100644 src/Structure/MetalCenter.h

diff --git a/src/Structure/MetalCenter.cpp b/src/Structure/MetalCenter.cpp
new file mode 100644
index 0000000000..758a98bc39
--- /dev/null
+++ b/src/Structure/MetalCenter.cpp
@@ -0,0 +1,40 @@
+#include "MetalCenter.h"
+#include "../ArgList.h"
+#include "../CpptrajStdio.h"
+
+using namespace Cpptraj::Structure;
+
+/** CONSTRUCTOR */
+MetalCenter::MetalCenter() {}
+
+/** Init with args */
+int MetalCenter::InitMetalCenters(ArgList& argIn)
+{
+  std::string metalMaskStr = argIn.GetStringKey("metalmask");
+  if (metalMaskStr.empty()) {
+    metalMaskStr.assign("@ZN,MG");
+    mprintf("\tUsing default metal mask string.\n");
+  }
+  if (metalMask_.SetMaskString( metalMaskStr )) {
+    mprinterr("Error: Invalid mask '%s' given for 'metalmask'\n", metalMaskStr.c_str());
+    return 1;
+  }
+
+  std::string coordAtomMaskStr = argIn.GetStringKey("coordatommask");
+  if (coordAtomMaskStr.empty()) {
+    coordAtomMaskStr.assign("@/O,S");
+    mprintf("\tUsing default coordinating atom mask string.\n");
+  }
+  if (coordAtomMask_.SetMaskString( coordAtomMaskStr )) {
+    mprinterr("Error: Invalid mask '%s' given for 'coordatommask'\n", coordAtomMaskStr.c_str());
+    return 1;
+  }
+
+  return 0;
+}
+
+/** Print info to stdout */
+void MetalCenter::PrintMetalCenterInfo() const {
+  mprintf("\tMetal center mask: %s\n", metalMask_.MaskString());
+  mprintf("\tCoordinating atom mask: %s\n", coordAtomMask_.MaskString());
+}
diff --git a/src/Structure/MetalCenter.h b/src/Structure/MetalCenter.h
new file mode 100644
index 0000000000..34d35fc672
--- /dev/null
+++ b/src/Structure/MetalCenter.h
@@ -0,0 +1,26 @@
+#ifndef INC_STRUCTURE_METALCENTER_H
+#define INC_STRUCTURE_METALCENTER_H
+#include "../AtomMask.h"
+class ArgList;
+class Frame;
+class Topology;
+namespace Cpptraj {
+namespace Structure {
+/// Used for finding and preparing metal centers
+class MetalCenter {
+  public:
+    /// CONSTRUCTOR
+    MetalCenter();
+    /// Init with arguments
+    int InitMetalCenters(ArgList&);
+    /// Find metal centers
+    int FindMetalCenters(Topology const&, Frame const&);
+    /// Print Info to stdout
+    void PrintMetalCenterInfo() const;
+  private:
+    AtomMask metalMask_; ///< Mask containing potential metal centers
+    AtomMask coordAtomMask_; ///< Mask containing potential coordinating atoms
+};
+}
+}
+#endif

From e45b5ef337af836d26644f3daf668769233f5241 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 15 Jul 2024 13:28:03 -0400
Subject: [PATCH 0808/1492] Start the find routine

---
 src/Structure/MetalCenter.cpp | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/src/Structure/MetalCenter.cpp b/src/Structure/MetalCenter.cpp
index 758a98bc39..3f21dbf9c1 100644
--- a/src/Structure/MetalCenter.cpp
+++ b/src/Structure/MetalCenter.cpp
@@ -1,6 +1,7 @@
 #include "MetalCenter.h"
 #include "../ArgList.h"
 #include "../CpptrajStdio.h"
+#include "../Topology.h"
 
 using namespace Cpptraj::Structure;
 
@@ -38,3 +39,29 @@ void MetalCenter::PrintMetalCenterInfo() const {
   mprintf("\tMetal center mask: %s\n", metalMask_.MaskString());
   mprintf("\tCoordinating atom mask: %s\n", coordAtomMask_.MaskString());
 }
+
+/** Find metal centers. */
+int MetalCenter::FindMetalCenters(Topology const& topIn, Frame const& frameIn)
+{
+  if (topIn.SetupIntegerMask( metalMask_, frameIn )) {
+    mprinterr("Error: Could not set up metal center mask '%s'\n", metalMask_.MaskString());
+    return 1;
+  }
+  if (metalMask_.None()) {
+    mprintf("Warning: Nothing selected by metal center mask '%s'\n", metalMask_.MaskString());
+    return 0;
+  }
+  metalMask_.MaskInfo();
+
+  if (topIn.SetupIntegerMask( coordAtomMask_, frameIn )) {
+    mprinterr("Error: Could not set up metal center mask '%s'\n", coordAtomMask_.MaskString());
+    return 1;
+  }
+  if (coordAtomMask_.None()) {
+    mprintf("Warning: Nothing selected by coordinating atom mask '%s'\n", coordAtomMask_.MaskString());
+    return 0;
+  }
+  coordAtomMask_.MaskInfo();
+
+  return 0;
+}

From 6b22c34c6926da7494a5820b317cab8cad9168b5 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 15 Jul 2024 13:38:03 -0400
Subject: [PATCH 0809/1492] Finish initial search

---
 src/Structure/CMakeLists.txt  |  3 ++-
 src/Structure/MetalCenter.cpp | 35 ++++++++++++++++++++++++++++++++++-
 src/Structure/MetalCenter.h   |  1 +
 src/Structure/structuredepend |  1 +
 src/Structure/structurefiles  |  3 ++-
 5 files changed, 40 insertions(+), 3 deletions(-)

diff --git a/src/Structure/CMakeLists.txt b/src/Structure/CMakeLists.txt
index 1c78302d80..edf0329cc6 100644
--- a/src/Structure/CMakeLists.txt
+++ b/src/Structure/CMakeLists.txt
@@ -10,12 +10,13 @@ target_sources(cpptraj_common_obj PRIVATE
   ${CMAKE_CURRENT_LIST_DIR}/HisProt.cpp
   ${CMAKE_CURRENT_LIST_DIR}/InternalCoords.cpp
   ${CMAKE_CURRENT_LIST_DIR}/LeastSquaresPlane.cpp
+  ${CMAKE_CURRENT_LIST_DIR}/MetalCenter.cpp
   ${CMAKE_CURRENT_LIST_DIR}/PdbCleaner.cpp
   ${CMAKE_CURRENT_LIST_DIR}/RingFinder.cpp
   ${CMAKE_CURRENT_LIST_DIR}/StructureEnum.cpp
   ${CMAKE_CURRENT_LIST_DIR}/StructureRoutines.cpp
-  ${CMAKE_CURRENT_LIST_DIR}/SugarBuilder.cpp
   ${CMAKE_CURRENT_LIST_DIR}/Sugar.cpp
+  ${CMAKE_CURRENT_LIST_DIR}/SugarBuilder.cpp
   ${CMAKE_CURRENT_LIST_DIR}/SugarLinkAtoms.cpp
   ${CMAKE_CURRENT_LIST_DIR}/SugarToken.cpp
   ${CMAKE_CURRENT_LIST_DIR}/Zmatrix.cpp
diff --git a/src/Structure/MetalCenter.cpp b/src/Structure/MetalCenter.cpp
index 3f21dbf9c1..3d0af40f3f 100644
--- a/src/Structure/MetalCenter.cpp
+++ b/src/Structure/MetalCenter.cpp
@@ -1,12 +1,16 @@
 #include "MetalCenter.h"
 #include "../ArgList.h"
 #include "../CpptrajStdio.h"
+#include "../DistRoutines.h"
 #include "../Topology.h"
+#include <cmath>
 
 using namespace Cpptraj::Structure;
 
 /** CONSTRUCTOR */
-MetalCenter::MetalCenter() {}
+MetalCenter::MetalCenter() :
+  dcut2_(9.0)
+{}
 
 /** Init with args */
 int MetalCenter::InitMetalCenters(ArgList& argIn)
@@ -31,6 +35,13 @@ int MetalCenter::InitMetalCenters(ArgList& argIn)
     return 1;
   }
 
+  double distcut = argIn.getKeyDouble("mcdist", 3.0);
+  if (distcut <= 0) {
+    mprinterr("Error: Invalid distance cutoff: %g\n", distcut);
+    return 1;
+  }
+  dcut2_ = distcut*distcut;
+
   return 0;
 }
 
@@ -38,6 +49,7 @@ int MetalCenter::InitMetalCenters(ArgList& argIn)
 void MetalCenter::PrintMetalCenterInfo() const {
   mprintf("\tMetal center mask: %s\n", metalMask_.MaskString());
   mprintf("\tCoordinating atom mask: %s\n", coordAtomMask_.MaskString());
+  mprintf("\tDistance cutoff: %g Ang.\n", sqrt(dcut2_));
 }
 
 /** Find metal centers. */
@@ -63,5 +75,26 @@ int MetalCenter::FindMetalCenters(Topology const& topIn, Frame const& frameIn)
   }
   coordAtomMask_.MaskInfo();
 
+  // OUTER loop over coordinating atoms
+  for (int idx0 = 0; idx0 != coordAtomMask_.Nselected(); idx0++)
+  {
+    int coordAt = coordAtomMask_[idx0];
+    const double* xyz0 = frameIn.XYZ( coordAt );
+    // INNER loop over metal center atoms
+    for (int idx1 = 0; idx1 != metalMask_.Nselected(); idx1++)
+    {
+      int metalAt = metalMask_[idx1];
+      const double* xyz1 = frameIn.XYZ( metalAt );
+
+      double dist2 = DIST2_NoImage( xyz0, xyz1 );
+      if (dist2 < dcut2_) {
+        mprintf("DEBUG: Potential metal center at %s, coordinating atom %s, dist %f Ang\n",
+                topIn.AtomMaskName(metalAt).c_str(),
+                topIn.AtomMaskName(coordAt).c_str(),
+                sqrt(dist2));
+      }
+    } // END inner loop over metal center atoms
+  } // END outer loop over coordinating atoms
+
   return 0;
 }
diff --git a/src/Structure/MetalCenter.h b/src/Structure/MetalCenter.h
index 34d35fc672..3befa3797a 100644
--- a/src/Structure/MetalCenter.h
+++ b/src/Structure/MetalCenter.h
@@ -20,6 +20,7 @@ class MetalCenter {
   private:
     AtomMask metalMask_; ///< Mask containing potential metal centers
     AtomMask coordAtomMask_; ///< Mask containing potential coordinating atoms
+    double dcut2_;           ///< Distance cutoff in Ang^2
 };
 }
 }
diff --git a/src/Structure/structuredepend b/src/Structure/structuredepend
index b0182d7138..cebf51a415 100644
--- a/src/Structure/structuredepend
+++ b/src/Structure/structuredepend
@@ -8,6 +8,7 @@ GenerateConnectivityArrays.o : GenerateConnectivityArrays.cpp ../Atom.h ../Const
 HisProt.o : HisProt.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h HisProt.h StructureRoutines.h
 InternalCoords.o : InternalCoords.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h InternalCoords.h
 LeastSquaresPlane.o : LeastSquaresPlane.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Unit.h ../Vec3.h LeastSquaresPlane.h
+MetalCenter.o : MetalCenter.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h MetalCenter.h
 PdbCleaner.o : PdbCleaner.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h PdbCleaner.h
 RingFinder.o : RingFinder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CharMask.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h RingFinder.h
 StructureEnum.o : StructureEnum.cpp StructureEnum.h
diff --git a/src/Structure/structurefiles b/src/Structure/structurefiles
index f0efb128de..4190c6b3cf 100644
--- a/src/Structure/structurefiles
+++ b/src/Structure/structurefiles
@@ -10,12 +10,13 @@ STRUCTURE_SOURCES= \
   HisProt.cpp \
   InternalCoords.cpp \
   LeastSquaresPlane.cpp \
+  MetalCenter.cpp \
   PdbCleaner.cpp \
   RingFinder.cpp \
   StructureEnum.cpp \
   StructureRoutines.cpp \
-  SugarBuilder.cpp \
   Sugar.cpp \
+  SugarBuilder.cpp \
   SugarLinkAtoms.cpp \
   SugarToken.cpp \
   Zmatrix.cpp

From 23c9f200cb218a1f5ed1645ed53610c53ef9bb01 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 15 Jul 2024 13:44:17 -0400
Subject: [PATCH 0810/1492] Enable metal center finder

---
 src/Exec_PrepareForLeap.cpp   | 16 ++++++++++++++++
 src/Structure/MetalCenter.cpp |  6 ++++--
 src/Structure/MetalCenter.h   |  3 ++-
 src/cpptrajdepend             |  3 ++-
 4 files changed, 24 insertions(+), 4 deletions(-)

diff --git a/src/Exec_PrepareForLeap.cpp b/src/Exec_PrepareForLeap.cpp
index 70bbe5f55d..d3d2d665b7 100644
--- a/src/Exec_PrepareForLeap.cpp
+++ b/src/Exec_PrepareForLeap.cpp
@@ -8,6 +8,7 @@
 #include "StringRoutines.h"
 #include "Structure/Disulfide.h"
 #include "Structure/HisProt.h"
+#include "Structure/MetalCenter.h"
 #include "Structure/PdbCleaner.h"
 #include "Structure/ResStatArray.h"
 #include "Structure/SugarBuilder.h"
@@ -845,6 +846,21 @@ Exec::RetType Exec_PrepareForLeap::Execute(CpptrajState& State, ArgList& argIn)
     mprintf("\tNot searching for disulfides.\n");
   }
 
+  // Metal center search
+  if (!argIn.hasKey("nometals")) {
+    Cpptraj::Structure::MetalCenter MC;
+    if (MC.InitMetalCenters( argIn, debug_ )) {
+      mprinterr("Error: Could not init metal center search.\n");
+      return CpptrajState::ERR;
+    }
+    if (MC.FindMetalCenters( topIn, frameIn )) {
+      mprinterr("Error: Metal center search failed.\n");
+      return CpptrajState::ERR;
+    }
+  } else {
+    mprintf("\tNot searching for metal centers.\n");
+  }
+
   // Prepare sugars
   if (prepare_sugars) {
     std::vector<BondType> SugarBonds; 
diff --git a/src/Structure/MetalCenter.cpp b/src/Structure/MetalCenter.cpp
index 3d0af40f3f..a9af95d71b 100644
--- a/src/Structure/MetalCenter.cpp
+++ b/src/Structure/MetalCenter.cpp
@@ -9,12 +9,14 @@ using namespace Cpptraj::Structure;
 
 /** CONSTRUCTOR */
 MetalCenter::MetalCenter() :
-  dcut2_(9.0)
+  dcut2_(9.0),
+  debug_(0)
 {}
 
 /** Init with args */
-int MetalCenter::InitMetalCenters(ArgList& argIn)
+int MetalCenter::InitMetalCenters(ArgList& argIn, int debugIn)
 {
+  debug_ = debugIn;
   std::string metalMaskStr = argIn.GetStringKey("metalmask");
   if (metalMaskStr.empty()) {
     metalMaskStr.assign("@ZN,MG");
diff --git a/src/Structure/MetalCenter.h b/src/Structure/MetalCenter.h
index 3befa3797a..b0e5e0eb8f 100644
--- a/src/Structure/MetalCenter.h
+++ b/src/Structure/MetalCenter.h
@@ -12,7 +12,7 @@ class MetalCenter {
     /// CONSTRUCTOR
     MetalCenter();
     /// Init with arguments
-    int InitMetalCenters(ArgList&);
+    int InitMetalCenters(ArgList&, int);
     /// Find metal centers
     int FindMetalCenters(Topology const&, Frame const&);
     /// Print Info to stdout
@@ -21,6 +21,7 @@ class MetalCenter {
     AtomMask metalMask_; ///< Mask containing potential metal centers
     AtomMask coordAtomMask_; ///< Mask containing potential coordinating atoms
     double dcut2_;           ///< Distance cutoff in Ang^2
+    int debug_;
 };
 }
 }
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 00b593bc08..53fcc97b4f 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -334,7 +334,7 @@ Exec_ParmWrite.o : Exec_ParmWrite.cpp Action.h ActionList.h ActionState.h Analys
 Exec_ParseTiming.o : Exec_ParseTiming.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParseTiming.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_PermuteDihedrals.o : Exec_PermuteDihedrals.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h DistRoutines.h EnsembleIn.h EnsembleOutList.h ExclusionArray.h Exec.h Exec_PermuteDihedrals.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/RingFinder.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Precision.o : Exec_Precision.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Precision.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_PrepareForLeap.o : Exec_PrepareForLeap.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_PrepareForLeap.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h LeapInterface.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h Remote.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/Disulfide.h Structure/HisProt.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Exec_PrepareForLeap.o : Exec_PrepareForLeap.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_PrepareForLeap.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h LeapInterface.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h Remote.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/Disulfide.h Structure/HisProt.h Structure/MetalCenter.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Exec_PrintData.o : Exec_PrintData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_PrintData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Random.o : Exec_Random.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Random.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_ReadData.o : Exec_ReadData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ReadData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
@@ -467,6 +467,7 @@ Structure/GenerateConnectivityArrays.o : Structure/GenerateConnectivityArrays.cp
 Structure/HisProt.o : Structure/HisProt.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/HisProt.h Structure/StructureRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/InternalCoords.o : Structure/InternalCoords.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/InternalCoords.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/LeastSquaresPlane.o : Structure/LeastSquaresPlane.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h Residue.h Segment.h Structure/LeastSquaresPlane.h SymbolExporting.h Unit.h Vec3.h
+Structure/MetalCenter.o : Structure/MetalCenter.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/MetalCenter.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/PdbCleaner.o : Structure/PdbCleaner.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/PdbCleaner.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/RingFinder.o : Structure/RingFinder.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/RingFinder.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/StructureEnum.o : Structure/StructureEnum.cpp Structure/StructureEnum.h

From c60f59cd66ffee0fdb25c4b59ef77c6d6e48d843 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 15 Jul 2024 13:47:01 -0400
Subject: [PATCH 0811/1492] Rename to MetalCenterFinder

---
 src/Exec_PrepareForLeap.cpp                            |  4 ++--
 src/Structure/CMakeLists.txt                           |  2 +-
 .../{MetalCenter.cpp => MetalCenterFinder.cpp}         | 10 +++++-----
 src/Structure/{MetalCenter.h => MetalCenterFinder.h}   |  8 ++++----
 src/Structure/structuredepend                          |  2 +-
 src/Structure/structurefiles                           |  2 +-
 src/cpptrajdepend                                      |  4 ++--
 7 files changed, 16 insertions(+), 16 deletions(-)
 rename src/Structure/{MetalCenter.cpp => MetalCenterFinder.cpp} (91%)
 rename src/Structure/{MetalCenter.h => MetalCenterFinder.h} (83%)

diff --git a/src/Exec_PrepareForLeap.cpp b/src/Exec_PrepareForLeap.cpp
index d3d2d665b7..0ae47ee44e 100644
--- a/src/Exec_PrepareForLeap.cpp
+++ b/src/Exec_PrepareForLeap.cpp
@@ -8,7 +8,7 @@
 #include "StringRoutines.h"
 #include "Structure/Disulfide.h"
 #include "Structure/HisProt.h"
-#include "Structure/MetalCenter.h"
+#include "Structure/MetalCenterFinder.h"
 #include "Structure/PdbCleaner.h"
 #include "Structure/ResStatArray.h"
 #include "Structure/SugarBuilder.h"
@@ -848,7 +848,7 @@ Exec::RetType Exec_PrepareForLeap::Execute(CpptrajState& State, ArgList& argIn)
 
   // Metal center search
   if (!argIn.hasKey("nometals")) {
-    Cpptraj::Structure::MetalCenter MC;
+    Cpptraj::Structure::MetalCenterFinder MC;
     if (MC.InitMetalCenters( argIn, debug_ )) {
       mprinterr("Error: Could not init metal center search.\n");
       return CpptrajState::ERR;
diff --git a/src/Structure/CMakeLists.txt b/src/Structure/CMakeLists.txt
index edf0329cc6..7a5f4dafd9 100644
--- a/src/Structure/CMakeLists.txt
+++ b/src/Structure/CMakeLists.txt
@@ -10,7 +10,7 @@ target_sources(cpptraj_common_obj PRIVATE
   ${CMAKE_CURRENT_LIST_DIR}/HisProt.cpp
   ${CMAKE_CURRENT_LIST_DIR}/InternalCoords.cpp
   ${CMAKE_CURRENT_LIST_DIR}/LeastSquaresPlane.cpp
-  ${CMAKE_CURRENT_LIST_DIR}/MetalCenter.cpp
+  ${CMAKE_CURRENT_LIST_DIR}/MetalCenterFinder.cpp
   ${CMAKE_CURRENT_LIST_DIR}/PdbCleaner.cpp
   ${CMAKE_CURRENT_LIST_DIR}/RingFinder.cpp
   ${CMAKE_CURRENT_LIST_DIR}/StructureEnum.cpp
diff --git a/src/Structure/MetalCenter.cpp b/src/Structure/MetalCenterFinder.cpp
similarity index 91%
rename from src/Structure/MetalCenter.cpp
rename to src/Structure/MetalCenterFinder.cpp
index a9af95d71b..264f269db4 100644
--- a/src/Structure/MetalCenter.cpp
+++ b/src/Structure/MetalCenterFinder.cpp
@@ -1,4 +1,4 @@
-#include "MetalCenter.h"
+#include "MetalCenterFinder.h"
 #include "../ArgList.h"
 #include "../CpptrajStdio.h"
 #include "../DistRoutines.h"
@@ -8,13 +8,13 @@
 using namespace Cpptraj::Structure;
 
 /** CONSTRUCTOR */
-MetalCenter::MetalCenter() :
+MetalCenterFinder::MetalCenterFinder() :
   dcut2_(9.0),
   debug_(0)
 {}
 
 /** Init with args */
-int MetalCenter::InitMetalCenters(ArgList& argIn, int debugIn)
+int MetalCenterFinder::InitMetalCenters(ArgList& argIn, int debugIn)
 {
   debug_ = debugIn;
   std::string metalMaskStr = argIn.GetStringKey("metalmask");
@@ -48,14 +48,14 @@ int MetalCenter::InitMetalCenters(ArgList& argIn, int debugIn)
 }
 
 /** Print info to stdout */
-void MetalCenter::PrintMetalCenterInfo() const {
+void MetalCenterFinder::PrintMetalCenterInfo() const {
   mprintf("\tMetal center mask: %s\n", metalMask_.MaskString());
   mprintf("\tCoordinating atom mask: %s\n", coordAtomMask_.MaskString());
   mprintf("\tDistance cutoff: %g Ang.\n", sqrt(dcut2_));
 }
 
 /** Find metal centers. */
-int MetalCenter::FindMetalCenters(Topology const& topIn, Frame const& frameIn)
+int MetalCenterFinder::FindMetalCenters(Topology const& topIn, Frame const& frameIn)
 {
   if (topIn.SetupIntegerMask( metalMask_, frameIn )) {
     mprinterr("Error: Could not set up metal center mask '%s'\n", metalMask_.MaskString());
diff --git a/src/Structure/MetalCenter.h b/src/Structure/MetalCenterFinder.h
similarity index 83%
rename from src/Structure/MetalCenter.h
rename to src/Structure/MetalCenterFinder.h
index b0e5e0eb8f..b77513b758 100644
--- a/src/Structure/MetalCenter.h
+++ b/src/Structure/MetalCenterFinder.h
@@ -1,5 +1,5 @@
-#ifndef INC_STRUCTURE_METALCENTER_H
-#define INC_STRUCTURE_METALCENTER_H
+#ifndef INC_STRUCTURE_METALCENTERFINDER_H
+#define INC_STRUCTURE_METALCENTERFINDER_H
 #include "../AtomMask.h"
 class ArgList;
 class Frame;
@@ -7,10 +7,10 @@ class Topology;
 namespace Cpptraj {
 namespace Structure {
 /// Used for finding and preparing metal centers
-class MetalCenter {
+class MetalCenterFinder {
   public:
     /// CONSTRUCTOR
-    MetalCenter();
+    MetalCenterFinder();
     /// Init with arguments
     int InitMetalCenters(ArgList&, int);
     /// Find metal centers
diff --git a/src/Structure/structuredepend b/src/Structure/structuredepend
index cebf51a415..59d8ab5f51 100644
--- a/src/Structure/structuredepend
+++ b/src/Structure/structuredepend
@@ -8,7 +8,7 @@ GenerateConnectivityArrays.o : GenerateConnectivityArrays.cpp ../Atom.h ../Const
 HisProt.o : HisProt.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h HisProt.h StructureRoutines.h
 InternalCoords.o : InternalCoords.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h InternalCoords.h
 LeastSquaresPlane.o : LeastSquaresPlane.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Unit.h ../Vec3.h LeastSquaresPlane.h
-MetalCenter.o : MetalCenter.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h MetalCenter.h
+MetalCenterFinder.o : MetalCenterFinder.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h MetalCenterFinder.h
 PdbCleaner.o : PdbCleaner.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h PdbCleaner.h
 RingFinder.o : RingFinder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CharMask.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h RingFinder.h
 StructureEnum.o : StructureEnum.cpp StructureEnum.h
diff --git a/src/Structure/structurefiles b/src/Structure/structurefiles
index 4190c6b3cf..f631cff049 100644
--- a/src/Structure/structurefiles
+++ b/src/Structure/structurefiles
@@ -10,7 +10,7 @@ STRUCTURE_SOURCES= \
   HisProt.cpp \
   InternalCoords.cpp \
   LeastSquaresPlane.cpp \
-  MetalCenter.cpp \
+  MetalCenterFinder.cpp \
   PdbCleaner.cpp \
   RingFinder.cpp \
   StructureEnum.cpp \
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 53fcc97b4f..3c516dc8de 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -334,7 +334,7 @@ Exec_ParmWrite.o : Exec_ParmWrite.cpp Action.h ActionList.h ActionState.h Analys
 Exec_ParseTiming.o : Exec_ParseTiming.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParseTiming.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_PermuteDihedrals.o : Exec_PermuteDihedrals.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h DistRoutines.h EnsembleIn.h EnsembleOutList.h ExclusionArray.h Exec.h Exec_PermuteDihedrals.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/RingFinder.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Precision.o : Exec_Precision.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Precision.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_PrepareForLeap.o : Exec_PrepareForLeap.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_PrepareForLeap.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h LeapInterface.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h Remote.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/Disulfide.h Structure/HisProt.h Structure/MetalCenter.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Exec_PrepareForLeap.o : Exec_PrepareForLeap.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_PrepareForLeap.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h LeapInterface.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h Remote.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/Disulfide.h Structure/HisProt.h Structure/MetalCenterFinder.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Exec_PrintData.o : Exec_PrintData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_PrintData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Random.o : Exec_Random.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Random.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_ReadData.o : Exec_ReadData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ReadData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
@@ -467,7 +467,7 @@ Structure/GenerateConnectivityArrays.o : Structure/GenerateConnectivityArrays.cp
 Structure/HisProt.o : Structure/HisProt.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/HisProt.h Structure/StructureRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/InternalCoords.o : Structure/InternalCoords.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/InternalCoords.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/LeastSquaresPlane.o : Structure/LeastSquaresPlane.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h Residue.h Segment.h Structure/LeastSquaresPlane.h SymbolExporting.h Unit.h Vec3.h
-Structure/MetalCenter.o : Structure/MetalCenter.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/MetalCenter.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Structure/MetalCenterFinder.o : Structure/MetalCenterFinder.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/MetalCenterFinder.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/PdbCleaner.o : Structure/PdbCleaner.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/PdbCleaner.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/RingFinder.o : Structure/RingFinder.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/RingFinder.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/StructureEnum.o : Structure/StructureEnum.cpp Structure/StructureEnum.h

From 1ca5d02e4ca6195eff453939f88a8585931d9569 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 15 Jul 2024 14:28:42 -0400
Subject: [PATCH 0812/1492] Store metal centers, print to stdout

---
 src/Exec_PrepareForLeap.cpp         |  1 +
 src/Structure/MetalCenterFinder.cpp | 24 ++++++++++++++++++++++++
 src/Structure/MetalCenterFinder.h   | 12 +++++++++++-
 src/Topology.cpp                    | 14 ++++++++++++++
 src/Topology.h                      |  2 ++
 5 files changed, 52 insertions(+), 1 deletion(-)

diff --git a/src/Exec_PrepareForLeap.cpp b/src/Exec_PrepareForLeap.cpp
index 0ae47ee44e..ffd94de86b 100644
--- a/src/Exec_PrepareForLeap.cpp
+++ b/src/Exec_PrepareForLeap.cpp
@@ -857,6 +857,7 @@ Exec::RetType Exec_PrepareForLeap::Execute(CpptrajState& State, ArgList& argIn)
       mprinterr("Error: Metal center search failed.\n");
       return CpptrajState::ERR;
     }
+    MC.PrintMetalCenters(topIn);
   } else {
     mprintf("\tNot searching for metal centers.\n");
   }
diff --git a/src/Structure/MetalCenterFinder.cpp b/src/Structure/MetalCenterFinder.cpp
index 264f269db4..15dd9105ee 100644
--- a/src/Structure/MetalCenterFinder.cpp
+++ b/src/Structure/MetalCenterFinder.cpp
@@ -57,6 +57,8 @@ void MetalCenterFinder::PrintMetalCenterInfo() const {
 /** Find metal centers. */
 int MetalCenterFinder::FindMetalCenters(Topology const& topIn, Frame const& frameIn)
 {
+  metalCenters_.clear();
+
   if (topIn.SetupIntegerMask( metalMask_, frameIn )) {
     mprinterr("Error: Could not set up metal center mask '%s'\n", metalMask_.MaskString());
     return 1;
@@ -94,9 +96,31 @@ int MetalCenterFinder::FindMetalCenters(Topology const& topIn, Frame const& fram
                 topIn.AtomMaskName(metalAt).c_str(),
                 topIn.AtomMaskName(coordAt).c_str(),
                 sqrt(dist2));
+        MCmap::iterator it = metalCenters_.lower_bound( metalAt );
+        if (it == metalCenters_.end() || it->first != metalAt) {
+          mprintf("DEBUG: New metal center.\n");
+          it = metalCenters_.insert(it, MCpair(metalAt, Iarray(1, coordAt)));
+        } else {
+          mprintf("DEBUG: Existing metal center.\n");
+          it->second.push_back( coordAt );
+        }
       }
     } // END inner loop over metal center atoms
   } // END outer loop over coordinating atoms
 
   return 0;
 }
+
+/** Print metal centers to stdout */
+void MetalCenterFinder::PrintMetalCenters(Topology const& topIn) const {
+  mprintf("\t%zu metal centers.\n", metalCenters_.size());
+  for (MCmap::const_iterator it = metalCenters_.begin(); it != metalCenters_.end(); ++it)
+  {
+    mprintf("\t  %s (%zu coordinating atoms):",
+            topIn.TruncAtomResNameOnumId(it->first).c_str(),
+            it->second.size());
+    for (Iarray::const_iterator jt = it->second.begin(); jt != it->second.end(); ++jt)
+      mprintf(" %s", topIn.TruncAtomResNameOnumId(*jt).c_str());
+    mprintf("\n");
+  }
+} 
diff --git a/src/Structure/MetalCenterFinder.h b/src/Structure/MetalCenterFinder.h
index b77513b758..94ab85863d 100644
--- a/src/Structure/MetalCenterFinder.h
+++ b/src/Structure/MetalCenterFinder.h
@@ -1,6 +1,8 @@
 #ifndef INC_STRUCTURE_METALCENTERFINDER_H
 #define INC_STRUCTURE_METALCENTERFINDER_H
 #include "../AtomMask.h"
+#include <vector>
+#include <map>
 class ArgList;
 class Frame;
 class Topology;
@@ -17,8 +19,16 @@ class MetalCenterFinder {
     int FindMetalCenters(Topology const&, Frame const&);
     /// Print Info to stdout
     void PrintMetalCenterInfo() const;
+    /// Print found metal centers to stdout
+    void PrintMetalCenters(Topology const&) const;
   private:
-    AtomMask metalMask_; ///< Mask containing potential metal centers
+    typedef std::vector<int> Iarray;
+    typedef std::pair<int, Iarray> MCpair;
+    /// Map metal center index to coordinating atom indices
+    typedef std::map<int, Iarray> MCmap;
+
+    MCmap metalCenters_;     ///< Hold metal centers and coordinating atoms
+    AtomMask metalMask_;     ///< Mask containing potential metal centers
     AtomMask coordAtomMask_; ///< Mask containing potential coordinating atoms
     double dcut2_;           ///< Distance cutoff in Ang^2
     int debug_;
diff --git a/src/Topology.cpp b/src/Topology.cpp
index 8daa3add39..9daf5e846e 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -371,6 +371,20 @@ std::string Topology::TruncResNameOnumId(int res) const {
   return name;
 }
 
+/** Given an atom index, return a string containing the residue name,
+  * original residue number, an optional chain ID, and the atom
+  * name with format:
+  * "<resname>_<onum>[_<id>]@<atom name>".
+  * Truncate residue and atom names so there are no blanks.
+  */
+std::string Topology::TruncAtomResNameOnumId(int at) const {
+  if (at < 0 || at >= (int)atoms_.size()) return std::string("");
+  Atom const& thisAtom = atoms_[at];
+  std::string name = TruncResNameOnumId( thisAtom.ResNum() );
+  name.append( "@" + thisAtom.Name().Truncated() );
+  return name;
+}
+
 // Topology::FindAtomInResidue()
 /** Find the atom # of the specified atom name in the given residue.
   * \param res Residue number to search.
diff --git a/src/Topology.h b/src/Topology.h
index d6261c673e..3b1d653f19 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -237,6 +237,8 @@ class Topology {
     std::string TruncResNameNum(int) const;
     /// Format: <res name>_<onum>[_<id>]
     std::string TruncResNameOnumId(int) const;
+    /// Format: <res name>_<onum>[_<id>]@<atom name>
+    std::string TruncAtomResNameOnumId(int) const;
     /// \return index of atom with given name in specified residue.
     int FindAtomInResidue(int, NameType const&) const;
     /// Mark all molecules matching given mask expression as solvent.

From 24976b4be22afbdb3c64d3fc6548fc571551d1ea Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 15 Jul 2024 14:56:18 -0400
Subject: [PATCH 0813/1492] Ensure AmberParamFile debug level is correctly set

---
 src/AmberParamFile.cpp     | 6 +++---
 src/AmberParamFile.h       | 6 +++---
 src/DataIO_AmberFF.cpp     | 8 +++++---
 src/DataIO_AmberFrcmod.cpp | 3 ++-
 4 files changed, 13 insertions(+), 10 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index dd63708e13..b266c1ca4a 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -510,7 +510,7 @@ int AmberParamFile::assign_offdiag(ParameterSet& prm, Oarray const& Offdiag) con
 }
 
 /** Read parametrers from Amber frcmod file. */
-int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int debugIn) const
+int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname) const
 {
   // Set wildcard character for dihedrals and impropers
   prm.DP().SetWildcard('X');
@@ -607,7 +607,7 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname, int deb
 
 /** Read parameters from Amber main FF parameter file. */
 int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
-                               std::string const& nbsetnameIn, int debugIn) const
+                               std::string const& nbsetnameIn) const
 {
   // Set wildcard character for dihedrals and impropers
   prm.DP().SetWildcard('X');
@@ -806,7 +806,7 @@ int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
 }
 
 // DataIO_AmberFF::WriteData()
-int AmberParamFile::WriteParams(ParameterSet& prm, FileName const& fname, int debugIn) const
+int AmberParamFile::WriteParams(ParameterSet& prm, FileName const& fname) const
 {
   CpptrajFile outfile;
   if (outfile.OpenWrite(fname)) return 1;
diff --git a/src/AmberParamFile.h b/src/AmberParamFile.h
index 6f81ac7222..463c1f71b6 100644
--- a/src/AmberParamFile.h
+++ b/src/AmberParamFile.h
@@ -11,11 +11,11 @@ class AmberParamFile {
   public:
     AmberParamFile();
     /// Read main Amber FF file
-    int ReadParams(ParameterSet&, FileName const&, std::string const&, int) const;
+    int ReadParams(ParameterSet&, FileName const&, std::string const&) const;
     /// Read Amber frcmod file
-    int ReadFrcmod(ParameterSet&, FileName const&, int) const;
+    int ReadFrcmod(ParameterSet&, FileName const&) const;
     /// Write main Amber FF file
-    int WriteParams(ParameterSet&, FileName const&, int) const;
+    int WriteParams(ParameterSet&, FileName const&) const;
     /// Set debug level
     void SetDebug(int);
   private:
diff --git a/src/DataIO_AmberFF.cpp b/src/DataIO_AmberFF.cpp
index 65a8c55aa8..f9b06f30b1 100644
--- a/src/DataIO_AmberFF.cpp
+++ b/src/DataIO_AmberFF.cpp
@@ -54,7 +54,8 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
   DataSet_Parameters& prm = static_cast<DataSet_Parameters&>( *ds ); 
 
   AmberParamFile infile;
-  int err = infile.ReadParams(prm, fname, nbsetname_, debug_);
+  infile.SetDebug( debug_ );
+  int err = infile.ReadParams(prm, fname, nbsetname_);
   if (err != 0) {
     mprinterr("Error: Could not read '%s'\n", fname.full());
   }
@@ -79,6 +80,7 @@ int DataIO_AmberFF::processWriteArgs(ArgList& argIn)
 int DataIO_AmberFF::WriteData(FileName const& fname, DataSetList const& dsl)
 {
   AmberParamFile outfile;
+  outfile.SetDebug( debug_ );
   std::vector<DataSet_Parameters*> toWrite;
   for (DataSetList::const_iterator it = dsl.begin(); it != dsl.end(); ++it)
   {
@@ -89,7 +91,7 @@ int DataIO_AmberFF::WriteData(FileName const& fname, DataSetList const& dsl)
     mprinterr("Error: No parameter sets to write.\n");
     return 1;
   } else if (toWrite.size() == 1) {
-    return outfile.WriteParams( *(toWrite.front()), fname, debug_ );
+    return outfile.WriteParams( *(toWrite.front()), fname );
   } else {
     // Create a combined parameter set
     ParameterSet prm;
@@ -99,7 +101,7 @@ int DataIO_AmberFF::WriteData(FileName const& fname, DataSetList const& dsl)
       ParameterSet::UpdateCount UC;
       prm.UpdateParamSet( *(*it), UC, debug_, debug_ ); // FIXME verbose
     }
-    return outfile.WriteParams( prm, fname, debug_ );
+    return outfile.WriteParams( prm, fname );
   }
 
   return 1;
diff --git a/src/DataIO_AmberFrcmod.cpp b/src/DataIO_AmberFrcmod.cpp
index 82810ac0b7..8d78125166 100644
--- a/src/DataIO_AmberFrcmod.cpp
+++ b/src/DataIO_AmberFrcmod.cpp
@@ -50,7 +50,8 @@ int DataIO_AmberFrcmod::ReadData(FileName const& fname, DataSetList& dsl, std::s
   DataSet_Parameters& prm = static_cast<DataSet_Parameters&>( *ds );
 
   AmberParamFile infile;
-  if (infile.ReadFrcmod(prm, fname, debug_)) {
+  infile.SetDebug( debug_ );
+  if (infile.ReadFrcmod(prm, fname)) {
     mprinterr("Error: Could not read Amber frcmod file '%s'\n", fname.full());
     return 1;
   }

From ee4e92feaf35911656b79a8add45c79380a77cd7 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 15 Jul 2024 15:02:45 -0400
Subject: [PATCH 0814/1492] Skip past whitespace control codes as well

---
 src/AmberParamFile.cpp | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index b266c1ca4a..1e7be4460a 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -7,6 +7,7 @@
 #include "ParameterSet.h"
 #include "Constants.h"
 #include <cstdio> // sscanf
+#include <cctype> // isspace
 
 const int AmberParamFile::MAXSYMLEN = 16;
 
@@ -541,7 +542,7 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname) const
   while (ptr != 0) {
     bool first_char_is_space = (*ptr == ' ');
     // Advance to first non-space char
-    while (*ptr == ' ' && *ptr != '\0') ++ptr;
+    while (isspace(*ptr) && *ptr != '\0') ++ptr;
     // Is this a recognized section keyword?
     if (*ptr != '\0') {
       std::string line(ptr);

From c7856bf3ba04517f69660a7d8c993e07aa2e03d7 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 16 Jul 2024 09:37:15 -0400
Subject: [PATCH 0815/1492] Actually check whether file has top/coords info
 since we arent doing it in the ID step anymore

---
 src/DataIO_Coords.cpp | 38 +++++++++++++++++++-------------------
 src/DataIO_Coords.h   |  4 ++--
 2 files changed, 21 insertions(+), 21 deletions(-)

diff --git a/src/DataIO_Coords.cpp b/src/DataIO_Coords.cpp
index fc84689741..8ef1b0b27a 100644
--- a/src/DataIO_Coords.cpp
+++ b/src/DataIO_Coords.cpp
@@ -5,9 +5,9 @@
 #include "Trajin_Single.h"
 
 /// CONSTRUCTOR
-DataIO_Coords::DataIO_Coords() :
-  is_parm_fmt_(false),
-  is_traj_fmt_(false)
+DataIO_Coords::DataIO_Coords() //:
+  //is_parm_fmt_(false),
+  //is_traj_fmt_(false)
 {
 
 }
@@ -22,13 +22,6 @@ DataIO_Coords::DataIO_Coords() :
   */
 bool DataIO_Coords::ID_DataFormat(CpptrajFile& infile)
 {
-  // Needs to be either a topology format or a coords format
-/*  ParmFile::ParmFormatType parm_format = ParmFile::DetectFormat(infile.Filename());
-  TrajectoryFile::TrajFormatType traj_format = TrajectoryFile::DetectFormat(infile.Filename());
-  is_parm_fmt_ = (parm_format != ParmFile::UNKNOWN_PARM);
-  is_traj_fmt_ = (traj_format != TrajectoryFile::UNKNOWN_TRAJ);
-  if (is_parm_fmt_ || is_traj_fmt_)
-    return true;*/
   return false;
 }
 
@@ -56,19 +49,26 @@ int DataIO_Coords::ReadData(FileName const& fname, DataSetList& dsl, std::string
 {
   ClearAddedByMe();
   DataSet::DataType setType = DataSet::COORDS; // FIXME make user option
-  if (!is_parm_fmt_ && !is_traj_fmt_) {
+  //if (!is_parm_fmt_ && !is_traj_fmt_) {
+    bool is_parm_fmt_ = false;
+    bool is_traj_fmt_ = false;
     // Assume that ID_DataFormat() has not been called.
-    CpptrajFile tmpfile;
-    if (tmpfile.SetupWrite( fname, debug_ )) {
-      mprinterr("Error: Could not setup check for parm/coords info in '%s'.\n",
-                fname.full());
-      return 1;
-    }
-    if (!ID_DataFormat(tmpfile)) {
+    //CpptrajFile tmpfile;
+    //if (tmpfile.SetupWrite( fname, debug_ )) {
+    //  mprinterr("Error: Could not setup check for parm/coords info in '%s'.\n",
+    //            fname.full());
+    //  return 1;
+    //}
+    // Needs to be either a topology format or a coords format
+    ParmFile::ParmFormatType parm_format = ParmFile::DetectFormat( fname );
+    TrajectoryFile::TrajFormatType traj_format = TrajectoryFile::DetectFormat( fname );
+    is_parm_fmt_ = (parm_format != ParmFile::UNKNOWN_PARM);
+    is_traj_fmt_ = (traj_format != TrajectoryFile::UNKNOWN_TRAJ);
+    if (!is_parm_fmt_ && !is_traj_fmt_) {
       mprinterr("Error: '%s' does not have parm/coords info.\n", fname.full());
       return 1;
     }
-  }
+  //}
 
   DataSet* dset = 0;
   if (!dsname.empty()) {
diff --git a/src/DataIO_Coords.h b/src/DataIO_Coords.h
index 83c8e778b7..0310b9c20f 100644
--- a/src/DataIO_Coords.h
+++ b/src/DataIO_Coords.h
@@ -14,7 +14,7 @@ class DataIO_Coords : public DataIO {
     int WriteData(FileName const&, DataSetList const&);
     bool ID_DataFormat(CpptrajFile&);
   private:
-    bool is_parm_fmt_; ///< Set to true if format contains topology info
-    bool is_traj_fmt_; ///< Set to true if format contains coordinates
+    //bool is_parm_fmt_; ///< Set to true if format contains topology info
+    //bool is_traj_fmt_; ///< Set to true if format contains coordinates
 };
 #endif

From e313c37eeadbb7844eb232c619f75681fd03a9c9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 16 Jul 2024 10:24:50 -0400
Subject: [PATCH 0816/1492] Add tgtidx keyword

---
 src/Exec_Top.cpp                            | 30 ++++++++++++------
 src/TopInfo.cpp                             | 35 +++++++++++----------
 src/TopInfo.h                               |  4 +--
 test/Test_TopInfo/RunTest.sh                |  4 ++-
 test/Test_TopInfo/tz2.dihedrals.24.dat.save | 18 +++++++++++
 5 files changed, 61 insertions(+), 30 deletions(-)
 create mode 100644 test/Test_TopInfo/tz2.dihedrals.24.dat.save

diff --git a/src/Exec_Top.cpp b/src/Exec_Top.cpp
index 8980eff421..71388ac4a8 100644
--- a/src/Exec_Top.cpp
+++ b/src/Exec_Top.cpp
@@ -107,7 +107,7 @@ Exec::RetType Exec_AngleInfo::Execute(CpptrajState& State, ArgList& argIn) {
 // -----------------------------------------------------------------------------
 void Exec_DihedralInfo::Help() const {
   mprintf("\t[%s]\n"
-          "\t[<mask1>] [<mask2> <mask3> <mask4>] [noindices]\n"
+          "\t{[<mask1>] [<mask2> <mask3> <mask4>] | tgtidx <#>} [noindices]\n"
           "\t[out <file>] [extra]\n", DataSetList::TopIdxArgs);
   mprintf("  For specified topology (first by default) either print dihedral info for all\n"
           "  atoms in <mask1>, or print info for dihedrals with first atom in <mask1>,\n"
@@ -122,12 +122,17 @@ Exec::RetType Exec_DihedralInfo::Execute(CpptrajState& State, ArgList& argIn) {
     return CpptrajState::ERR;
   }
   bool printExtraInfo = argIn.hasKey("extra");
+  int tgtidx = argIn.getKeyInt("tgtidx", 0) - 1;
   TopInfo info;
   if (CommonSetup(info, State, argIn, "Dihedral info")) return CpptrajState::ERR;
-  std::string mask1 = argIn.GetMaskNext();
-  std::string mask2 = argIn.GetMaskNext();
-  std::string mask3 = argIn.GetMaskNext();
-  if (info.PrintDihedralInfo( mask1, mask2, mask3, argIn.GetMaskNext(), false, printExtraInfo ))
+  std::string mask1, mask2, mask3, mask4;
+  if (tgtidx == -1) {
+    mask1 = argIn.GetMaskNext();
+    mask2 = argIn.GetMaskNext();
+    mask3 = argIn.GetMaskNext();
+    mask4 = argIn.GetMaskNext();
+  }
+  if (info.PrintDihedralInfo( mask1, mask2, mask3, mask4, false, printExtraInfo, tgtidx ))
     return CpptrajState::ERR;
   return CpptrajState::OK;
 }
@@ -135,7 +140,7 @@ Exec::RetType Exec_DihedralInfo::Execute(CpptrajState& State, ArgList& argIn) {
 // -----------------------------------------------------------------------------
 void Exec_ImproperInfo::Help() const {
   mprintf("\t[%s]\n"
-          "\t[<mask1>] [<mask2> <mask3> <mask4>] [noindices]\n"
+          "\t{[<mask1>] [<mask2> <mask3> <mask4>] | tgtidx <#>} [noindices]\n"
           "\t[out <file>]\n", DataSetList::TopIdxArgs);
   mprintf("  For specified topology (first by default) either print CHARMM improper info\n"
           "  for all atoms in <mask1>, or print info for dihedrals with first atom in <mask1>,\n"
@@ -148,12 +153,17 @@ Exec::RetType Exec_ImproperInfo::Execute(CpptrajState& State, ArgList& argIn) {
               "Error:   selection please use 4 masks.\n");
     return CpptrajState::ERR;
   }
+  int tgtidx = argIn.getKeyInt("tgtidx", 0) - 1;
   TopInfo info;
   if (CommonSetup(info, State, argIn, "Improper info")) return CpptrajState::ERR;
-  std::string mask1 = argIn.GetMaskNext();
-  std::string mask2 = argIn.GetMaskNext();
-  std::string mask3 = argIn.GetMaskNext();
-  if (info.PrintDihedralInfo( mask1, mask2, mask3, argIn.GetMaskNext(), true, false ))
+  std::string mask1, mask2, mask3, mask4;
+  if (tgtidx == -1) {
+    mask1 = argIn.GetMaskNext();
+    mask2 = argIn.GetMaskNext();
+    mask3 = argIn.GetMaskNext();
+    mask4 = argIn.GetMaskNext();
+  }
+  if (info.PrintDihedralInfo( mask1, mask2, mask3, mask4, true, false, tgtidx ))
     return CpptrajState::ERR;
   return CpptrajState::OK;
 }
diff --git a/src/TopInfo.cpp b/src/TopInfo.cpp
index 75fe52a72d..d3d629b1f2 100644
--- a/src/TopInfo.cpp
+++ b/src/TopInfo.cpp
@@ -630,7 +630,7 @@ int TopInfo::PrintAngleInfo(std::string const& mask1exp, std::string const& mask
 void TopInfo::PrintDihedrals(DihedralArray const& darray, DihedralParmArray const& dihedralparm,
                              CharMask const& mask1, CharMask const& mask2,
                              CharMask const& mask3, CharMask const& mask4, int nw, int& nd,
-                             bool printExtraInfo) const
+                             bool printExtraInfo, int tgtidx) const
 {
   if (darray.empty()) return;
   for (DihedralArray::const_iterator dih = darray.begin();
@@ -641,7 +641,9 @@ void TopInfo::PrintDihedrals(DihedralArray const& darray, DihedralParmArray cons
     int atom3 = dih->A3();
     int atom4 = dih->A4();
     bool printDihedral = false;
-    if (mask2.MaskStringSet() && mask3.MaskStringSet() && mask4.MaskStringSet())
+    if (tgtidx != -1)
+      printDihedral = (tgtidx == dih->Idx());
+    else if (mask2.MaskStringSet() && mask3.MaskStringSet() && mask4.MaskStringSet())
       printDihedral = (mask1.AtomInCharMask(atom1) &&
                        mask2.AtomInCharMask(atom2) &&
                        mask3.AtomInCharMask(atom3) &&
@@ -701,19 +703,18 @@ void TopInfo::PrintDihedrals(DihedralArray const& darray, DihedralParmArray cons
 // TopInfo::PrintDihedralInfo()
 int TopInfo::PrintDihedralInfo(std::string const& mask1exp, std::string const& mask2exp,
                                std::string const& mask3exp, std::string const& mask4exp,
-                               bool printImpropers, bool printExtraInfo) const
+                               bool printImpropers, bool printExtraInfo, int tgtidx) const
 {
-  CharMask mask1( mask1exp );
-  if (SetupMask( mask1 )) return 1;
-  CharMask mask2;
-  CharMask mask3;
-  CharMask mask4;
-  if (!mask2exp.empty() && SetupMask( mask2exp, mask2 )) return 1;
-  if (!mask3exp.empty() && SetupMask( mask3exp, mask3 )) return 1;
-  if (!mask4exp.empty() && SetupMask( mask4exp, mask4 )) return 1;
-  if (mask2exp.empty() != mask3exp.empty() || mask2exp.empty() != mask4exp.empty()) {
-    mprinterr("Error: Require either 1 mask or 4 masks.\n");
-    return 1;
+  CharMask mask1, mask2, mask3, mask4;
+  if (tgtidx == -1) {
+    if (!mask1exp.empty() && SetupMask( mask1exp, mask1 )) return 1;
+    if (!mask2exp.empty() && SetupMask( mask2exp, mask2 )) return 1;
+    if (!mask3exp.empty() && SetupMask( mask3exp, mask3 )) return 1;
+    if (!mask4exp.empty() && SetupMask( mask4exp, mask4 )) return 1;
+    if (mask2exp.empty() != mask3exp.empty() || mask2exp.empty() != mask4exp.empty()) {
+      mprinterr("Error: Require either 1 mask or 4 masks.\n");
+      return 1;
+    }
   }
   size_t n_torsions;
   const char* label = "Dih";
@@ -744,10 +745,10 @@ int TopInfo::PrintDihedralInfo(std::string const& mask1exp, std::string const& m
                    max_type_len_, "T3", max_type_len_, "T4");
   int nd = 1;
   if (printImpropers) {
-    PrintDihedrals( parm_->Impropers(), parm_->ImproperParm(), mask1, mask2, mask3, mask4, nw, nd, printExtraInfo );
+    PrintDihedrals( parm_->Impropers(), parm_->ImproperParm(), mask1, mask2, mask3, mask4, nw, nd, printExtraInfo, tgtidx );
   } else {
-    PrintDihedrals( parm_->DihedralsH(), parm_->DihedralParm(), mask1, mask2, mask3, mask4, nw, nd, printExtraInfo );
-    PrintDihedrals( parm_->Dihedrals(),  parm_->DihedralParm(), mask1, mask2, mask3, mask4, nw, nd, printExtraInfo );
+    PrintDihedrals( parm_->DihedralsH(), parm_->DihedralParm(), mask1, mask2, mask3, mask4, nw, nd, printExtraInfo, tgtidx );
+    PrintDihedrals( parm_->Dihedrals(),  parm_->DihedralParm(), mask1, mask2, mask3, mask4, nw, nd, printExtraInfo, tgtidx );
   }
   return 0;
 }
diff --git a/src/TopInfo.h b/src/TopInfo.h
index 053d557eb6..b63a114a6b 100644
--- a/src/TopInfo.h
+++ b/src/TopInfo.h
@@ -28,7 +28,7 @@ class TopInfo {
     int PrintBondInfo(std::string const&, std::string const&, bool) const;
     int PrintAngleInfo(std::string const&, std::string const&, std::string const&) const;
     int PrintDihedralInfo(std::string const&, std::string const&,
-                          std::string const&, std::string const&,bool,bool) const;
+                          std::string const&, std::string const&,bool,bool,int) const;
     int PrintChargeInfo(std::string const&, double&) const;
     int PrintMassInfo(std::string const&, double&) const;
   private:
@@ -49,7 +49,7 @@ class TopInfo {
                      int, int&) const;
     void PrintDihedrals(DihedralArray const&, DihedralParmArray const&,
                         CharMask const&, CharMask const&,
-                        CharMask const&, CharMask const&, int, int&,bool) const;
+                        CharMask const&, CharMask const&, int, int&,bool,int) const;
 
     CpptrajFile* outfile_;
     Topology const* parm_;
diff --git a/test/Test_TopInfo/RunTest.sh b/test/Test_TopInfo/RunTest.sh
index 5bb97f180c..b54e64f7f6 100755
--- a/test/Test_TopInfo/RunTest.sh
+++ b/test/Test_TopInfo/RunTest.sh
@@ -4,7 +4,7 @@
 
 CleanFiles info.in atoms.dat residues.dat bonds.dat angles.dat dihedrals.dat \
            molecules.dat masscharge.dat values.dat molshort.dat molselect.dat \
-           molselect2.dat ChargeMass.dat
+           molselect2.dat ChargeMass.dat tz2.dihedrals.24.dat
 
 INPUT="-i info.in"
 cat > info.in <<EOF
@@ -31,6 +31,7 @@ dihedralinfo @1
 dihedralinfo @1 out dihedrals.dat
 dihedralinfo @N @CA @CB @%H1
 dihedralinfo @N @CA @CB @%H1 out dihedrals.dat
+dihedrals tgtidx 24 out tz2.dihedrals.24.dat
 
 mass out masscharge.dat name Mass *
 charge out masscharge.dat name Charge *
@@ -57,6 +58,7 @@ DoTest molshort.dat.save molshort.dat
 DoTest molselect.dat.save molselect.dat
 DoTest molselect2.dat.save molselect2.dat
 DoTest ChargeMass.dat.save ChargeMass.dat
+DoTest tz2.dihedrals.24.dat.save tz2.dihedrals.24.dat
 
 UNITNAME='Topology info with reference coords test'
 CheckFor netcdf
diff --git a/test/Test_TopInfo/tz2.dihedrals.24.dat.save b/test/Test_TopInfo/tz2.dihedrals.24.dat.save
new file mode 100644
index 0000000000..1e2a5d5bff
--- /dev/null
+++ b/test/Test_TopInfo/tz2.dihedrals.24.dat.save
@@ -0,0 +1,18 @@
+# Dih      PK Phase   PN Atom1    Atom2    Atom3    Atom4     A1  A2  A3  A4 T1 T2 T3 T4
+B 411   1.000  3.14  2.0 :2@CD1   :2@CE2   :2@NE1   :2@HE1    22  26  24  25 CW CN NA  H
+B 413   1.000  3.14  2.0 :1@C     :2@CA    :2@N     :2@H      12  16  14  15  C CT  N  H
+B 414   1.000  3.14  2.0 :2@C     :3@CA    :3@N     :3@H      36  40  38  39  C CT  N  H
+B 419   1.000  3.14  2.0 :4@CD1   :4@CE2   :4@NE1   :4@HE1    60  64  62  63 CW CN NA  H
+B 421   1.000  3.14  2.0 :3@C     :4@CA    :4@N     :4@H      50  54  52  53  C CT  N  H
+B 422   1.000  3.14  2.0 :4@C     :5@CA    :5@N     :5@H      74  78  76  77  C CT  N  H
+B 423   1.000  3.14  2.0 :6@CG    :6@HD21  :6@ND2   :6@HD22   98 101 100 102  C  H  N  H
+B 424   1.000  3.14  2.0 :5@C     :6@CA    :6@N     :6@H      89  93  91  92  C CT  N  H
+B 425   1.000  3.14  2.0 :6@C     :7@CA    :7@N     :7@H     103 107 105 106  C CT  N  H
+B 426   1.000  3.14  2.0 :7@C     :8@CA    :8@N     :8@H     110 114 112 113  C CT  N  H
+B 431   1.000  3.14  2.0 :9@CD1   :9@CE2   :9@NE1   :9@HE1   142 146 144 145 CW CN NA  H
+B 433   1.000  3.14  2.0 :8@C     :9@CA    :9@N     :9@H     132 136 134 135  C CT  N  H
+B 434   1.000  3.14  2.0 :9@C     :10@CA   :10@N    :10@H    156 160 158 159  C CT  N  H
+B 439   1.000  3.14  2.0 :11@CD1  :11@CE2  :11@NE1  :11@HE1  180 184 182 183 CW CN NA  H
+B 441   1.000  3.14  2.0 :10@C    :11@CA   :11@N    :11@H    170 174 172 173  C CT  N  H
+B 442   1.000  3.14  2.0 :11@C    :12@CA   :12@N    :12@H    194 198 196 197  C CT  N  H
+B 443   1.000  3.14  2.0 :12@C    :13@CH3  :13@N    :13@H    216 220 218 219  C CT  N  H

From ff77bc77c5a429be96650eecaee624b62b25d157 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 16 Jul 2024 10:28:39 -0400
Subject: [PATCH 0817/1492] Document tgtidx

---
 doc/cpptraj.lyx | 22 ++++++++++++++++++++--
 1 file changed, 20 insertions(+), 2 deletions(-)

diff --git a/doc/cpptraj.lyx b/doc/cpptraj.lyx
index e0a490aafb..a7105aeb86 100644
--- a/doc/cpptraj.lyx
+++ b/doc/cpptraj.lyx
@@ -15697,7 +15697,7 @@ dihedralinfo [parm <name> | parmindex <#> | <#>]
 \end_layout
 
 \begin_layout LyX-Code
-             [<mask1>] [<mask2> <mask3> <mask4>] [noindices]
+             {[<mask1>] [<mask2> <mask3> <mask4>] | tgtidx <#>} [noindices]
 \end_layout
 
 \begin_layout LyX-Code
@@ -15751,6 +15751,15 @@ parmindex
  dihedrals must match all masks.
 \end_layout
 
+\begin_layout Description
+tgtidx
+\begin_inset space ~
+\end_inset
+
+<#> If specified,
+ print dihedrals only with specified parameter index (starting from 1).
+\end_layout
+
 \begin_layout Description
 [noindices] Do not print dihedral indices.
 \end_layout
@@ -15922,7 +15931,7 @@ improperinfo [parm <name> | parmindex <#> | <#>]
 \end_layout
 
 \begin_layout LyX-Code
-             [<mask1>] [<mask2> <mask3> <mask4>] [noindices]
+             {[<mask1>] [<mask2> <mask3> <mask4>] | tgtidx <#>} [noindices]
 \end_layout
 
 \begin_layout LyX-Code
@@ -15976,6 +15985,15 @@ parmindex
  impropers must match all masks.
 \end_layout
 
+\begin_layout Description
+tgtidx
+\begin_inset space ~
+\end_inset
+
+<#> If specified,
+ print impropers only with specified parameter index (starting from 1).
+\end_layout
+
 \begin_layout Description
 [noindices] Do not print improper indices.
 \end_layout

From 11e34c7a3bb0e6961a2d0785517bed86e4bb7503 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 16 Jul 2024 14:39:01 -0400
Subject: [PATCH 0818/1492] Add documentation. Comment out unused/unneeded
 functions.

---
 src/ParameterTypes.h | 10 +++++++---
 src/Topology.cpp     |  4 ++--
 2 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/src/ParameterTypes.h b/src/ParameterTypes.h
index 7a40aa7a48..a01b167acf 100644
--- a/src/ParameterTypes.h
+++ b/src/ParameterTypes.h
@@ -278,15 +278,19 @@ class AngleArray {
 /// Hold dihedral parameters
 class DihedralParmType {
   public:
+    /// CONSTRUCTOR
     DihedralParmType() : pk_(0), pn_(0), phase_(0), scee_(0), scnb_(0) {}
+    /// CONSTRUCTOR - PK, PN, Phase, SCEE, SCNB (Amber parameter file proper)
     DihedralParmType(double k, double n, double p, double e, double b) :
                          pk_(k), pn_(n), phase_(p), scee_(e), scnb_(b) {}
-    DihedralParmType(double k, double p) :
-                         pk_(k), pn_(0), phase_(p), scee_(0), scnb_(0) {}
+    /// CONSTRUCTOR - PK, Phase
+    //DihedralParmType(double k, double p) :
+    //                     pk_(k), pn_(0), phase_(p), scee_(0), scnb_(0) {}
+    /// CONSTRUCTOR - PK, PN, Phase (Amber parameter file improper)
     DihedralParmType(double k, double n, double p) :
                          pk_(k), pn_(n), phase_(p), scee_(0), scnb_(0) {}
     inline double Pk()    const { return pk_;    }
-    inline double& Pk()         { return pk_;    }
+    //inline double& Pk()         { return pk_;    }
     inline double Pn()    const { return pn_;    }
     inline double Phase() const { return phase_; }
     inline double SCEE()  const { return scee_;  }
diff --git a/src/Topology.cpp b/src/Topology.cpp
index 9daf5e846e..6780aa727f 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -1568,7 +1568,7 @@ int Topology::scale_dihedral_K(DihedralArray& dihedrals, CharMask const& Mask,
       if (newidx == -1) {
         // Scale and add new dihedral parameter type.
         DihedralParmType newparm = dihedralparm_[oldidx];
-        newparm.Pk() *= scale_factor;
+        newparm.SetPk( newparm.Pk() * scale_factor ); //newparm.Pk() *= scale_factor;
         newidx = (int)dihedralparm_.size();
         dihedralparm_.push_back( newparm );
         newDihedralParms[oldidx] = newidx;
@@ -1592,7 +1592,7 @@ int Topology::ScaleDihedralK(double scale_factor, std::string const& maskExpr, b
     // Scale all
     for (DihedralParmArray::iterator dk = dihedralparm_.begin();
                                      dk != dihedralparm_.end(); ++dk)
-      dk->Pk() *= scale_factor;
+      dk->SetPk( dk->Pk() * scale_factor ); //dk->Pk() *= scale_factor;
   } else {
     // Scale only dihedrals with atoms in mask. Requires adding new types.
     CharMask Mask( maskExpr );

From d5765d375b9455c160f3ad1c79a3491f8972b2f9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 17 Jul 2024 09:37:56 -0400
Subject: [PATCH 0819/1492] Use direct comparison of dihedral parameters
 instead of FEQ() function in order to match how LEaP does it.

---
 src/ParameterTypes.h | 50 +++++++++++++++++++++++++++++++++++---------
 1 file changed, 40 insertions(+), 10 deletions(-)

diff --git a/src/ParameterTypes.h b/src/ParameterTypes.h
index a01b167acf..05e1568085 100644
--- a/src/ParameterTypes.h
+++ b/src/ParameterTypes.h
@@ -276,6 +276,10 @@ class AngleArray {
     AArray angles_;
 };
 /// Hold dihedral parameters
+/** Note that for the '==' and '<' operators, direct comparisons are used
+  * instead of the FEQ() function in order to match how LEaP would compare
+  * dihedrals.
+  */
 class DihedralParmType {
   public:
     /// CONSTRUCTOR
@@ -283,24 +287,50 @@ class DihedralParmType {
     /// CONSTRUCTOR - PK, PN, Phase, SCEE, SCNB (Amber parameter file proper)
     DihedralParmType(double k, double n, double p, double e, double b) :
                          pk_(k), pn_(n), phase_(p), scee_(e), scnb_(b) {}
-    /// CONSTRUCTOR - PK, Phase
-    //DihedralParmType(double k, double p) :
-    //                     pk_(k), pn_(0), phase_(p), scee_(0), scnb_(0) {}
     /// CONSTRUCTOR - PK, PN, Phase (Amber parameter file improper)
     DihedralParmType(double k, double n, double p) :
                          pk_(k), pn_(n), phase_(p), scee_(0), scnb_(0) {}
+    /// \return Dihedral force constant
     inline double Pk()    const { return pk_;    }
-    //inline double& Pk()         { return pk_;    }
+    /// \return Dihedral periodicity
     inline double Pn()    const { return pn_;    }
+    /// \return Dihedral phase
     inline double Phase() const { return phase_; }
+    /// \return 1-4 electrostatics scaling constant
     inline double SCEE()  const { return scee_;  }
+    /// \return 1-4 vdW scaling constant
     inline double SCNB()  const { return scnb_;  }
+    /// Set dihedral force constant
     void SetPk(double k)        { pk_ = k;       }
+    /// Set dihedral periodicity
     void SetPn(double n)        { pn_ = n;       }
+    /// Set dihedral phase
     void SetPhase(double p)     { phase_ = p;    }
+    /// Set 1-4 electrostatics scaling constant
     void SetSCEE(double s)      { scee_ = s;     }
+    /// Set 1-4 vdW scaling constant
     void SetSCNB(double s)      { scnb_ = s;     }
+    /// \return True if two dihedral parameters are equal
     bool operator==(DihedralParmType const& rhs) const {
+      return ( pn_    == rhs.pn_    &&
+               pk_    == rhs.pk_    &&
+               phase_ == rhs.phase_ &&
+               scee_  == rhs.scee_  &&
+               scnb_  == rhs.scnb_ );
+    }
+    /// \return True if this dihedral parameter should come before the given one
+    bool operator<(DihedralParmType const& rhs) const {
+      if ( pn_ == rhs.pn_ ) {
+        if ( pk_ == rhs.pk_ ) {
+          if ( phase_ == rhs.phase_ ) {
+            if ( scee_ == rhs.scee_ ) {
+              return ( scnb_ < rhs.scnb_ );
+            } else return (scee_ < rhs.scee_);
+          } else return (phase_ < rhs.phase_);
+        } else return (pk_ < rhs.pk_);
+      } else return (pn_ < rhs.pn_);
+    }
+/*    bool operator==(DihedralParmType const& rhs) const {
       return ( FEQ(pk_, rhs.pk_) &&
                FEQ(pn_, rhs.pn_) &&
                FEQ(phase_, rhs.phase_) &&
@@ -317,13 +347,13 @@ class DihedralParmType {
           } else return (phase_ < rhs.phase_);
         } else return (pn_ < rhs.pn_);
       } else return (pk_ < rhs.pk_);
-    }
+    }*/
   private:
-    double pk_;
-    double pn_;
-    double phase_;
-    double scee_;
-    double scnb_;
+    double pk_;    ///< Dihedral force constant
+    double pn_;    ///< Dihedral periodicity
+    double phase_; ///< Dihedral phase shift
+    double scee_;  ///< 1-4 electrostatics scale factor
+    double scnb_;  ///< 1-4 vdW scale factor
 };
 /// Hold Array of dihedral parameters
 class DihedralParmArray {

From a57af02a41cbaa99eabb65f1fa74c5bbbd2dcd82 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 17 Jul 2024 10:25:55 -0400
Subject: [PATCH 0820/1492] Fix UV timing output

---
 src/Action_HydrogenBond.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Action_HydrogenBond.cpp b/src/Action_HydrogenBond.cpp
index 572c13c8e8..adbe7f7f95 100644
--- a/src/Action_HydrogenBond.cpp
+++ b/src/Action_HydrogenBond.cpp
@@ -1594,7 +1594,7 @@ void Action_HydrogenBond::Print() {
 # ifdef TIMER
   t_uu_.WriteTiming(      2,"Solute-Solute   :",t_action_.Total());
   if (calcSolvent_) {
-    t_uv_.WriteTiming(    2,"Solute-Solvent  :",t_uv_.Total());
+    t_uv_.WriteTiming(    2,"Solute-Solvent  :",t_action_.Total());
     t_bridge_.WriteTiming(2,"Bridging waters :",t_action_.Total());
   }
   t_action_.WriteTiming(1,"Total:");

From ba82a02102362027341535c0cd16b1cd4aafe201 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 17 Jul 2024 10:30:52 -0400
Subject: [PATCH 0821/1492] Add timers to 'check' action

---
 src/Action_CheckStructure.cpp | 31 ++++++++++++++++++++++++++++++-
 src/Action_CheckStructure.h   |  9 +++++++++
 2 files changed, 39 insertions(+), 1 deletion(-)

diff --git a/src/Action_CheckStructure.cpp b/src/Action_CheckStructure.cpp
index 078afaa144..72a1d8431b 100644
--- a/src/Action_CheckStructure.cpp
+++ b/src/Action_CheckStructure.cpp
@@ -193,17 +193,40 @@ void Action_CheckStructure::WriteProblems(FmtType ft, int frameNum, Topology con
 
 // Action_CheckStructure::DoAction()
 Action::RetType Action_CheckStructure::DoAction(int frameNum, ActionFrame& frm) {
+# ifdef TIMER
+  t_total_.Start();
+# endif
   int fnum = frm.TrajoutNum() + 1;
-
+# ifdef TIMER
+  t_overlap_.Start();
+# endif
   int total_problems = check_.CheckOverlaps(frm.Frm());
+# ifdef TIMER
+  t_overlap_.Stop();
+# endif
   if (outfile_ != 0) WriteProblems(F_ATOM, fnum, *CurrentParm_);
   if (check_.CheckBonds()) {
+#   ifdef TIMER
+    t_bonds_.Start();
+#   endif
     total_problems += check_.CheckBonds(frm.Frm());
+#   ifdef TIMER
+    t_bonds_.Stop();
+#   endif
     if (outfile_ != 0) WriteProblems(F_BOND, fnum, *CurrentParm_);
+#   ifdef TIMER
+    t_rings_.Start();
+#   endif
     total_problems += check_.CheckRings(frm.Frm()); // FIXME
+#   ifdef TIMER
+    t_rings_.Stop();
+#   endif
     if (outfile_ != 0) WriteProblems(F_RING, fnum, *CurrentParm_);
   }
   num_problems_->Add( frameNum, &total_problems );
+# ifdef TIMER
+  t_total_.Stop();
+# endif
   if (total_problems > 0 && skipBadFrames_)
     return Action::SUPPRESS_COORD_OUTPUT;
   return Action::OK;
@@ -236,6 +259,12 @@ int Action_CheckStructure::SyncAction() {
 #endif
 
 void Action_CheckStructure::Print() {
+# ifdef TIMER
+  t_overlap_.WriteTiming(2, "Check overlaps           :", t_total_.Total());
+  t_bonds_.WriteTiming  (2, "Check bond lengths       :", t_total_.Total());
+  t_rings_.WriteTiming  (2, "Check ring intersections :", t_total_.Total());
+  t_total_.WriteTiming(1, "Total check time :");
+# endif
 # ifdef MPI
   if (outfile_ != 0) {
     mprintf("    CHECKSTRUCTURE: Writing to %s\n", outfile_->Filename().full());
diff --git a/src/Action_CheckStructure.h b/src/Action_CheckStructure.h
index 17bba79f13..049f68d22a 100644
--- a/src/Action_CheckStructure.h
+++ b/src/Action_CheckStructure.h
@@ -2,6 +2,9 @@
 #define INC_ACTION_CHECKSTRUCTURE_H
 #include "Action.h"
 #include "StructureCheck.h"
+#ifdef TIMER
+# include "Timer.h"
+#endif
 class Action_CheckStructure : public Action {
   public:
     Action_CheckStructure();
@@ -38,5 +41,11 @@ class Action_CheckStructure : public Action {
     DataSet* ds_d_;  ///< Distance
     int idx_;        ///< Index into ds_X data sets.
 #   endif
+#   ifdef TIMER
+    Timer t_total_;
+    Timer t_overlap_;
+    Timer t_bonds_;
+    Timer t_rings_;
+#   endif
 };
 #endif

From ff0c815989849b5679f86f506a2dd81e919f4188 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 17 Jul 2024 11:05:50 -0400
Subject: [PATCH 0822/1492] Update for new leap-like dihedral sort order (Pn
 before Pk instead of Pk before Pn).

---
 test/Test_CompareTop/parm.diff.save | 1068 +++++++++++++--------------
 1 file changed, 534 insertions(+), 534 deletions(-)

diff --git a/test/Test_CompareTop/parm.diff.save b/test/Test_CompareTop/parm.diff.save
index a1795efcd2..dbc95feb70 100644
--- a/test/Test_CompareTop/parm.diff.save
+++ b/test/Test_CompareTop/parm.diff.save
@@ -241,557 +241,557 @@
 < Tk= 80  Teq= 1.91463
 < Tk= 80  Teq= 2.10138
 # Dihedrals
-< :1@N - :1@CA - :1@C - :2@N {N-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :1@N - :1@CA - :1@C - :2@N {N-CX-C-N} Pk=0.45 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
-< :1@N - :1@CA - :1@C - :2@N {N-CX-C-N} Pk=0.55 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
-< :1@N - :1@CA - :1@C - :2@N {N-CX-C-N} Pk=1.58 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :1@N - :1@CA - :1@C - :2@N {N-CT-C-N} Pk=1.7 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
+< :1@N - :1@CA - :1@C - :2@N {N-CX-C-N} Pk=1.58 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :1@N - :1@CA - :1@C - :2@N {N-CT-C-N} Pk=2 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+< :1@N - :1@CA - :1@C - :2@N {N-CX-C-N} Pk=0.55 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
+< :1@N - :1@CA - :1@C - :2@N {N-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :1@C - :2@N - :2@CA - :2@C {C-N-CX-C} Pk=0 Pn=1 Phase=0 SCEE=1.2 SCNB=2
-< :1@C - :2@N - :2@CA - :2@C {C-N-CX-C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-< :1@C - :2@N - :2@CA - :2@C {C-N-CX-C} Pk=0.27 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :1@C - :2@N - :2@CA - :2@C {C-N-CX-C} Pk=0.42 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 > :1@C - :2@N - :2@CA - :2@C {C-N-CT-C} Pk=0.8 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :1@C - :2@N - :2@CA - :2@C {C-N-CX-C} Pk=0.27 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 > :1@C - :2@N - :2@CA - :2@C {C-N-CT-C} Pk=0.85 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+< :1@C - :2@N - :2@CA - :2@C {C-N-CX-C} Pk=0.42 Pn=3 Phase=0 SCEE=1.2 SCNB=2
+< :1@C - :2@N - :2@CA - :2@C {C-N-CX-C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :1@C - :2@N - :2@CA - :2@CB {C-N-CT-CT} Pk=0.53 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :1@C - :2@N - :2@CA - :2@CB {C-N-CX-CT} Pk=2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 > :1@C - :2@N - :2@CA - :2@CB {C-N-CT-CT} Pk=0 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :1@C - :2@N - :2@CA - :2@CB {C-N-CX-CT} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :1@C - :2@N - :2@CA - :2@CB {C-N-CX-CT} Pk=1.8 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 > :1@C - :2@N - :2@CA - :2@CB {C-N-CT-CT} Pk=0.15 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
-> :1@C - :2@N - :2@CA - :2@CB {C-N-CT-CT} Pk=0.5 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
-> :1@C - :2@N - :2@CA - :2@CB {C-N-CT-CT} Pk=0.53 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 < :1@C - :2@N - :2@CA - :2@CB {C-N-CX-CT} Pk=0.8 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :1@C - :2@N - :2@CA - :2@CB {C-N-CX-CT} Pk=1.8 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :1@C - :2@N - :2@CA - :2@CB {C-N-CX-CT} Pk=2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
-< :2@CB - :2@CA - :2@C - :3@N {CT-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-> :2@CB - :2@CA - :2@C - :3@N {CT-CT-C-N} Pk=0.07 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-> :2@CB - :2@CA - :2@C - :3@N {CT-CT-C-N} Pk=0.1 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :1@C - :2@N - :2@CA - :2@CB {C-N-CX-CT} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :1@C - :2@N - :2@CA - :2@CB {C-N-CT-CT} Pk=0.5 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
 < :2@CB - :2@CA - :2@C - :3@N {CT-CX-C-N} Pk=0.2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+> :2@CB - :2@CA - :2@C - :3@N {CT-CT-C-N} Pk=0.07 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 < :2@CB - :2@CA - :2@C - :3@N {CT-CX-C-N} Pk=0.2 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 < :2@CB - :2@CA - :2@C - :3@N {CT-CX-C-N} Pk=0.4 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :2@N - :2@CA - :2@C - :3@N {N-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :2@CB - :2@CA - :2@C - :3@N {CT-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :2@CB - :2@CA - :2@C - :3@N {CT-CT-C-N} Pk=0.1 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :2@N - :2@CA - :2@C - :3@N {N-CX-C-N} Pk=0.45 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
-< :2@N - :2@CA - :2@C - :3@N {N-CX-C-N} Pk=0.55 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
-< :2@N - :2@CA - :2@C - :3@N {N-CX-C-N} Pk=1.58 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :2@N - :2@CA - :2@C - :3@N {N-CT-C-N} Pk=1.7 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
+< :2@N - :2@CA - :2@C - :3@N {N-CX-C-N} Pk=1.58 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :2@N - :2@CA - :2@C - :3@N {N-CT-C-N} Pk=2 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+< :2@N - :2@CA - :2@C - :3@N {N-CX-C-N} Pk=0.55 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
+< :2@N - :2@CA - :2@C - :3@N {N-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :2@C - :3@N - :3@CA - :3@C {C-N-CX-C} Pk=0 Pn=1 Phase=0 SCEE=1.2 SCNB=2
-< :2@C - :3@N - :3@CA - :3@C {C-N-CX-C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-< :2@C - :3@N - :3@CA - :3@C {C-N-CX-C} Pk=0.27 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :2@C - :3@N - :3@CA - :3@C {C-N-CX-C} Pk=0.42 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 > :2@C - :3@N - :3@CA - :3@C {C-N-CT-C} Pk=0.8 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :2@C - :3@N - :3@CA - :3@C {C-N-CX-C} Pk=0.27 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 > :2@C - :3@N - :3@CA - :3@C {C-N-CT-C} Pk=0.85 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+< :2@C - :3@N - :3@CA - :3@C {C-N-CX-C} Pk=0.42 Pn=3 Phase=0 SCEE=1.2 SCNB=2
+< :2@C - :3@N - :3@CA - :3@C {C-N-CX-C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :2@C - :3@N - :3@CA - :3@CB {C-N-CT-CT} Pk=0.53 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :2@C - :3@N - :3@CA - :3@CB {C-N-CX-3C} Pk=2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 > :2@C - :3@N - :3@CA - :3@CB {C-N-CT-CT} Pk=0 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :2@C - :3@N - :3@CA - :3@CB {C-N-CX-3C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :2@C - :3@N - :3@CA - :3@CB {C-N-CX-3C} Pk=1.8 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 > :2@C - :3@N - :3@CA - :3@CB {C-N-CT-CT} Pk=0.15 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
-> :2@C - :3@N - :3@CA - :3@CB {C-N-CT-CT} Pk=0.5 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
-> :2@C - :3@N - :3@CA - :3@CB {C-N-CT-CT} Pk=0.53 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 < :2@C - :3@N - :3@CA - :3@CB {C-N-CX-3C} Pk=0.8 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :2@C - :3@N - :3@CA - :3@CB {C-N-CX-3C} Pk=1.8 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :2@C - :3@N - :3@CA - :3@CB {C-N-CX-3C} Pk=2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
-< :3@CG1 - :3@CB - :3@CA - :3@C {CT-3C-CX-C} Pk=0.112 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :2@C - :3@N - :3@CA - :3@CB {C-N-CX-3C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :2@C - :3@N - :3@CA - :3@CB {C-N-CT-CT} Pk=0.5 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
+< :3@CG1 - :3@CB - :3@CA - :3@C {CT-3C-CX-C} Pk=0.406 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
+< :3@CG1 - :3@CB - :3@CA - :3@C {CT-3C-CX-C} Pk=0.289 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 < :3@CG1 - :3@CB - :3@CA - :3@C {CT-3C-CX-C} Pk=0.148 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 > :3@CG1 - :3@CB - :3@CA - :3@C {CT-CT-CT-C} Pk=0.155556 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :3@CG1 - :3@CB - :3@CA - :3@C {CT-3C-CX-C} Pk=0.289 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
-< :3@CG1 - :3@CB - :3@CA - :3@C {CT-3C-CX-C} Pk=0.406 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
-< :3@CG2 - :3@CB - :3@CA - :3@C {CT-3C-CX-C} Pk=0.112 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :3@CG1 - :3@CB - :3@CA - :3@C {CT-3C-CX-C} Pk=0.112 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :3@CG2 - :3@CB - :3@CA - :3@C {CT-3C-CX-C} Pk=0.406 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
+< :3@CG2 - :3@CB - :3@CA - :3@C {CT-3C-CX-C} Pk=0.289 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 < :3@CG2 - :3@CB - :3@CA - :3@C {CT-3C-CX-C} Pk=0.148 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 > :3@CG2 - :3@CB - :3@CA - :3@C {CT-CT-CT-C} Pk=0.155556 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :3@CG2 - :3@CB - :3@CA - :3@C {CT-3C-CX-C} Pk=0.289 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
-< :3@CG2 - :3@CB - :3@CA - :3@C {CT-3C-CX-C} Pk=0.406 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
-< :3@N - :3@CA - :3@CB - :3@CG1 {N-CX-3C-CT} Pk=0.001 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
+< :3@CG2 - :3@CB - :3@CA - :3@C {CT-3C-CX-C} Pk=0.112 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :3@N - :3@CA - :3@CB - :3@CG1 {N-CX-3C-CT} Pk=0.337 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :3@N - :3@CA - :3@CB - :3@CG1 {N-CX-3C-CT} Pk=0.216 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 < :3@N - :3@CA - :3@CB - :3@CG1 {N-CX-3C-CT} Pk=0.148 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 > :3@N - :3@CA - :3@CB - :3@CG1 {N-CT-CT-CT} Pk=0.155556 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :3@N - :3@CA - :3@CB - :3@CG1 {N-CX-3C-CT} Pk=0.216 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
-< :3@N - :3@CA - :3@CB - :3@CG1 {N-CX-3C-CT} Pk=0.337 Pn=1 Phase=0 SCEE=1.2 SCNB=2
-< :3@N - :3@CA - :3@CB - :3@CG2 {N-CX-3C-CT} Pk=0.001 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
+< :3@N - :3@CA - :3@CB - :3@CG1 {N-CX-3C-CT} Pk=0.001 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
+< :3@N - :3@CA - :3@CB - :3@CG2 {N-CX-3C-CT} Pk=0.337 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :3@N - :3@CA - :3@CB - :3@CG2 {N-CX-3C-CT} Pk=0.216 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 < :3@N - :3@CA - :3@CB - :3@CG2 {N-CX-3C-CT} Pk=0.148 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 > :3@N - :3@CA - :3@CB - :3@CG2 {N-CT-CT-CT} Pk=0.155556 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :3@N - :3@CA - :3@CB - :3@CG2 {N-CX-3C-CT} Pk=0.216 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
-< :3@N - :3@CA - :3@CB - :3@CG2 {N-CX-3C-CT} Pk=0.337 Pn=1 Phase=0 SCEE=1.2 SCNB=2
-< :3@CB - :3@CA - :3@C - :4@N {3C-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-> :3@CB - :3@CA - :3@C - :4@N {CT-CT-C-N} Pk=0.07 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-> :3@CB - :3@CA - :3@C - :4@N {CT-CT-C-N} Pk=0.1 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :3@N - :3@CA - :3@CB - :3@CG2 {N-CX-3C-CT} Pk=0.001 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
 < :3@CB - :3@CA - :3@C - :4@N {3C-CX-C-N} Pk=0.2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+> :3@CB - :3@CA - :3@C - :4@N {CT-CT-C-N} Pk=0.07 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 < :3@CB - :3@CA - :3@C - :4@N {3C-CX-C-N} Pk=0.2 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 < :3@CB - :3@CA - :3@C - :4@N {3C-CX-C-N} Pk=0.4 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :3@N - :3@CA - :3@C - :4@N {N-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :3@CB - :3@CA - :3@C - :4@N {3C-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :3@CB - :3@CA - :3@C - :4@N {CT-CT-C-N} Pk=0.1 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :3@N - :3@CA - :3@C - :4@N {N-CX-C-N} Pk=0.45 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
-< :3@N - :3@CA - :3@C - :4@N {N-CX-C-N} Pk=0.55 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
-< :3@N - :3@CA - :3@C - :4@N {N-CX-C-N} Pk=1.58 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :3@N - :3@CA - :3@C - :4@N {N-CT-C-N} Pk=1.7 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
+< :3@N - :3@CA - :3@C - :4@N {N-CX-C-N} Pk=1.58 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :3@N - :3@CA - :3@C - :4@N {N-CT-C-N} Pk=2 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+< :3@N - :3@CA - :3@C - :4@N {N-CX-C-N} Pk=0.55 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
+< :3@N - :3@CA - :3@C - :4@N {N-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :3@C - :4@N - :4@CA - :4@C {C-N-CX-C} Pk=0 Pn=1 Phase=0 SCEE=1.2 SCNB=2
-< :3@C - :4@N - :4@CA - :4@C {C-N-CX-C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-< :3@C - :4@N - :4@CA - :4@C {C-N-CX-C} Pk=0.27 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :3@C - :4@N - :4@CA - :4@C {C-N-CX-C} Pk=0.42 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 > :3@C - :4@N - :4@CA - :4@C {C-N-CT-C} Pk=0.8 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :3@C - :4@N - :4@CA - :4@C {C-N-CX-C} Pk=0.27 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 > :3@C - :4@N - :4@CA - :4@C {C-N-CT-C} Pk=0.85 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+< :3@C - :4@N - :4@CA - :4@C {C-N-CX-C} Pk=0.42 Pn=3 Phase=0 SCEE=1.2 SCNB=2
+< :3@C - :4@N - :4@CA - :4@C {C-N-CX-C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :3@C - :4@N - :4@CA - :4@CB {C-N-CT-CT} Pk=0.53 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :3@C - :4@N - :4@CA - :4@CB {C-N-CX-2C} Pk=2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 > :3@C - :4@N - :4@CA - :4@CB {C-N-CT-CT} Pk=0 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :3@C - :4@N - :4@CA - :4@CB {C-N-CX-2C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :3@C - :4@N - :4@CA - :4@CB {C-N-CX-2C} Pk=1.8 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 > :3@C - :4@N - :4@CA - :4@CB {C-N-CT-CT} Pk=0.15 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
-> :3@C - :4@N - :4@CA - :4@CB {C-N-CT-CT} Pk=0.5 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
-> :3@C - :4@N - :4@CA - :4@CB {C-N-CT-CT} Pk=0.53 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 < :3@C - :4@N - :4@CA - :4@CB {C-N-CX-2C} Pk=0.8 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :3@C - :4@N - :4@CA - :4@CB {C-N-CX-2C} Pk=1.8 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :3@C - :4@N - :4@CA - :4@CB {C-N-CX-2C} Pk=2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :3@C - :4@N - :4@CA - :4@CB {C-N-CX-2C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :3@C - :4@N - :4@CA - :4@CB {C-N-CT-CT} Pk=0.5 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
+> :4@CA - :4@CB - :4@CG - :4@CD1 {CT-CT-CT-CT} Pk=0.2 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
+< :4@CA - :4@CB - :4@CG - :4@CD1 {CX-2C-3C-CT} Pk=0.379 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 < :4@CA - :4@CB - :4@CG - :4@CD1 {CX-2C-3C-CT} Pk=0.027 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+> :4@CA - :4@CB - :4@CG - :4@CD1 {CT-CT-CT-CT} Pk=0.25 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 < :4@CA - :4@CB - :4@CG - :4@CD1 {CX-2C-3C-CT} Pk=0.142 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :4@CA - :4@CB - :4@CG - :4@CD1 {CX-2C-3C-CT} Pk=0.179 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 > :4@CA - :4@CB - :4@CG - :4@CD1 {CT-CT-CT-CT} Pk=0.18 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-> :4@CA - :4@CB - :4@CG - :4@CD1 {CT-CT-CT-CT} Pk=0.2 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
-> :4@CA - :4@CB - :4@CG - :4@CD1 {CT-CT-CT-CT} Pk=0.25 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
-< :4@CA - :4@CB - :4@CG - :4@CD1 {CX-2C-3C-CT} Pk=0.379 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :4@CA - :4@CB - :4@CG - :4@CD1 {CX-2C-3C-CT} Pk=0.179 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :4@CA - :4@CB - :4@CG - :4@CD2 {CT-CT-CT-CT} Pk=0.2 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
+< :4@CA - :4@CB - :4@CG - :4@CD2 {CX-2C-3C-CT} Pk=0.379 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 < :4@CA - :4@CB - :4@CG - :4@CD2 {CX-2C-3C-CT} Pk=0.027 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+> :4@CA - :4@CB - :4@CG - :4@CD2 {CT-CT-CT-CT} Pk=0.25 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 < :4@CA - :4@CB - :4@CG - :4@CD2 {CX-2C-3C-CT} Pk=0.142 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :4@CA - :4@CB - :4@CG - :4@CD2 {CX-2C-3C-CT} Pk=0.179 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 > :4@CA - :4@CB - :4@CG - :4@CD2 {CT-CT-CT-CT} Pk=0.18 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-> :4@CA - :4@CB - :4@CG - :4@CD2 {CT-CT-CT-CT} Pk=0.2 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
-> :4@CA - :4@CB - :4@CG - :4@CD2 {CT-CT-CT-CT} Pk=0.25 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
-< :4@CA - :4@CB - :4@CG - :4@CD2 {CX-2C-3C-CT} Pk=0.379 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :4@CA - :4@CB - :4@CG - :4@CD2 {CX-2C-3C-CT} Pk=0.179 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :4@CG - :4@CB - :4@CA - :4@C {3C-2C-CX-C} Pk=0.706 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :4@CG - :4@CB - :4@CA - :4@C {3C-2C-CX-C} Pk=0.62 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 < :4@CG - :4@CB - :4@CA - :4@C {3C-2C-CX-C} Pk=0.144 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 > :4@CG - :4@CB - :4@CA - :4@C {CT-CT-CT-C} Pk=0.155556 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 < :4@CG - :4@CB - :4@CA - :4@C {3C-2C-CX-C} Pk=0.19 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-< :4@CG - :4@CB - :4@CA - :4@C {3C-2C-CX-C} Pk=0.62 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
-< :4@CG - :4@CB - :4@CA - :4@C {3C-2C-CX-C} Pk=0.706 Pn=1 Phase=0 SCEE=1.2 SCNB=2
-< :4@N - :4@CA - :4@CB - :4@CG {N-CX-2C-3C} Pk=0.073 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :4@N - :4@CA - :4@CB - :4@CG {N-CX-2C-3C} Pk=0.098 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :4@N - :4@CA - :4@CB - :4@CG {N-CX-2C-3C} Pk=0.259 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 < :4@N - :4@CA - :4@CB - :4@CG {N-CX-2C-3C} Pk=0.144 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 > :4@N - :4@CA - :4@CB - :4@CG {N-CT-CT-CT} Pk=0.155556 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :4@N - :4@CA - :4@CB - :4@CG {N-CX-2C-3C} Pk=0.259 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
-< :4@CB - :4@CA - :4@C - :5@N {2C-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-> :4@CB - :4@CA - :4@C - :5@N {CT-CT-C-N} Pk=0.07 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-> :4@CB - :4@CA - :4@C - :5@N {CT-CT-C-N} Pk=0.1 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :4@N - :4@CA - :4@CB - :4@CG {N-CX-2C-3C} Pk=0.073 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :4@CB - :4@CA - :4@C - :5@N {2C-CX-C-N} Pk=0.2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+> :4@CB - :4@CA - :4@C - :5@N {CT-CT-C-N} Pk=0.07 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 < :4@CB - :4@CA - :4@C - :5@N {2C-CX-C-N} Pk=0.2 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 < :4@CB - :4@CA - :4@C - :5@N {2C-CX-C-N} Pk=0.4 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :4@N - :4@CA - :4@C - :5@N {N-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :4@CB - :4@CA - :4@C - :5@N {2C-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :4@CB - :4@CA - :4@C - :5@N {CT-CT-C-N} Pk=0.1 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :4@N - :4@CA - :4@C - :5@N {N-CX-C-N} Pk=0.45 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
-< :4@N - :4@CA - :4@C - :5@N {N-CX-C-N} Pk=0.55 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
-< :4@N - :4@CA - :4@C - :5@N {N-CX-C-N} Pk=1.58 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :4@N - :4@CA - :4@C - :5@N {N-CT-C-N} Pk=1.7 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
+< :4@N - :4@CA - :4@C - :5@N {N-CX-C-N} Pk=1.58 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :4@N - :4@CA - :4@C - :5@N {N-CT-C-N} Pk=2 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+< :4@N - :4@CA - :4@C - :5@N {N-CX-C-N} Pk=0.55 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
+< :4@N - :4@CA - :4@C - :5@N {N-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :4@C - :5@N - :5@CA - :5@C {C-N-CX-C} Pk=0 Pn=1 Phase=0 SCEE=1.2 SCNB=2
-< :4@C - :5@N - :5@CA - :5@C {C-N-CX-C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-< :4@C - :5@N - :5@CA - :5@C {C-N-CX-C} Pk=0.27 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :4@C - :5@N - :5@CA - :5@C {C-N-CX-C} Pk=0.42 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 > :4@C - :5@N - :5@CA - :5@C {C-N-CT-C} Pk=0.8 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :4@C - :5@N - :5@CA - :5@C {C-N-CX-C} Pk=0.27 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 > :4@C - :5@N - :5@CA - :5@C {C-N-CT-C} Pk=0.85 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+< :4@C - :5@N - :5@CA - :5@C {C-N-CX-C} Pk=0.42 Pn=3 Phase=0 SCEE=1.2 SCNB=2
+< :4@C - :5@N - :5@CA - :5@C {C-N-CX-C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :4@C - :5@N - :5@CA - :5@CB {C-N-CT-CT} Pk=0.53 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :4@C - :5@N - :5@CA - :5@CB {C-N-CX-3C} Pk=2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 > :4@C - :5@N - :5@CA - :5@CB {C-N-CT-CT} Pk=0 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :4@C - :5@N - :5@CA - :5@CB {C-N-CX-3C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :4@C - :5@N - :5@CA - :5@CB {C-N-CX-3C} Pk=1.8 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 > :4@C - :5@N - :5@CA - :5@CB {C-N-CT-CT} Pk=0.15 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
-> :4@C - :5@N - :5@CA - :5@CB {C-N-CT-CT} Pk=0.5 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
-> :4@C - :5@N - :5@CA - :5@CB {C-N-CT-CT} Pk=0.53 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 < :4@C - :5@N - :5@CA - :5@CB {C-N-CX-3C} Pk=0.8 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :4@C - :5@N - :5@CA - :5@CB {C-N-CX-3C} Pk=1.8 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :4@C - :5@N - :5@CA - :5@CB {C-N-CX-3C} Pk=2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :4@C - :5@N - :5@CA - :5@CB {C-N-CX-3C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :4@C - :5@N - :5@CA - :5@CB {C-N-CT-CT} Pk=0.5 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
+> :5@CA - :5@CB - :5@CG1 - :5@CD1 {CT-CT-CT-CT} Pk=0.2 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
+< :5@CA - :5@CB - :5@CG1 - :5@CD1 {CX-3C-2C-CT} Pk=0.447 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 < :5@CA - :5@CB - :5@CG1 - :5@CD1 {CX-3C-2C-CT} Pk=0.053 Pn=2 Phase=0 SCEE=1.2 SCNB=2
+> :5@CA - :5@CB - :5@CG1 - :5@CD1 {CT-CT-CT-CT} Pk=0.25 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 < :5@CA - :5@CB - :5@CG1 - :5@CD1 {CX-3C-2C-CT} Pk=0.107 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 > :5@CA - :5@CB - :5@CG1 - :5@CD1 {CT-CT-CT-CT} Pk=0.18 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-> :5@CA - :5@CB - :5@CG1 - :5@CD1 {CT-CT-CT-CT} Pk=0.2 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
 < :5@CA - :5@CB - :5@CG1 - :5@CD1 {CX-3C-2C-CT} Pk=0.23 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-> :5@CA - :5@CB - :5@CG1 - :5@CD1 {CT-CT-CT-CT} Pk=0.25 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
-< :5@CA - :5@CB - :5@CG1 - :5@CD1 {CX-3C-2C-CT} Pk=0.447 Pn=1 Phase=0 SCEE=1.2 SCNB=2
-< :5@CG1 - :5@CB - :5@CA - :5@C {2C-3C-CX-C} Pk=0.113 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :5@CG1 - :5@CB - :5@CA - :5@C {2C-3C-CX-C} Pk=0.115 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-> :5@CG1 - :5@CB - :5@CA - :5@C {CT-CT-CT-C} Pk=0.155556 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 < :5@CG1 - :5@CB - :5@CA - :5@C {2C-3C-CX-C} Pk=0.162 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 < :5@CG1 - :5@CB - :5@CA - :5@C {2C-3C-CX-C} Pk=0.735 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
-< :5@CG2 - :5@CB - :5@CA - :5@C {CT-3C-CX-C} Pk=0.112 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :5@CG1 - :5@CB - :5@CA - :5@C {2C-3C-CX-C} Pk=0.113 Pn=3 Phase=0 SCEE=1.2 SCNB=2
+> :5@CG1 - :5@CB - :5@CA - :5@C {CT-CT-CT-C} Pk=0.155556 Pn=3 Phase=0 SCEE=1.2 SCNB=2
+< :5@CG1 - :5@CB - :5@CA - :5@C {2C-3C-CX-C} Pk=0.115 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :5@CG2 - :5@CB - :5@CA - :5@C {CT-3C-CX-C} Pk=0.406 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
+< :5@CG2 - :5@CB - :5@CA - :5@C {CT-3C-CX-C} Pk=0.289 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 < :5@CG2 - :5@CB - :5@CA - :5@C {CT-3C-CX-C} Pk=0.148 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 > :5@CG2 - :5@CB - :5@CA - :5@C {CT-CT-CT-C} Pk=0.155556 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :5@CG2 - :5@CB - :5@CA - :5@C {CT-3C-CX-C} Pk=0.289 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
-< :5@CG2 - :5@CB - :5@CA - :5@C {CT-3C-CX-C} Pk=0.406 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
+< :5@CG2 - :5@CB - :5@CA - :5@C {CT-3C-CX-C} Pk=0.112 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :5@CG2 - :5@CB - :5@CG1 - :5@CD1 {CT-CT-CT-CT} Pk=0.2 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
+< :5@CG2 - :5@CB - :5@CG1 - :5@CD1 {CT-3C-2C-CT} Pk=0.202 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 < :5@CG2 - :5@CB - :5@CG1 - :5@CD1 {CT-3C-2C-CT} Pk=0.077 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+> :5@CG2 - :5@CB - :5@CG1 - :5@CD1 {CT-CT-CT-CT} Pk=0.25 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 < :5@CG2 - :5@CB - :5@CG1 - :5@CD1 {CT-3C-2C-CT} Pk=0.107 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 > :5@CG2 - :5@CB - :5@CG1 - :5@CD1 {CT-CT-CT-CT} Pk=0.18 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-> :5@CG2 - :5@CB - :5@CG1 - :5@CD1 {CT-CT-CT-CT} Pk=0.2 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
-< :5@CG2 - :5@CB - :5@CG1 - :5@CD1 {CT-3C-2C-CT} Pk=0.202 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 < :5@CG2 - :5@CB - :5@CG1 - :5@CD1 {CT-3C-2C-CT} Pk=0.224 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-> :5@CG2 - :5@CB - :5@CG1 - :5@CD1 {CT-CT-CT-CT} Pk=0.25 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
-< :5@N - :5@CA - :5@CB - :5@CG1 {N-CX-3C-2C} Pk=0.097 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
-< :5@N - :5@CA - :5@CB - :5@CG1 {N-CX-3C-2C} Pk=0.113 Pn=3 Phase=0 SCEE=1.2 SCNB=2
+< :5@N - :5@CA - :5@CB - :5@CG1 {N-CX-3C-2C} Pk=0.31 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 < :5@N - :5@CA - :5@CB - :5@CG1 {N-CX-3C-2C} Pk=0.144 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+< :5@N - :5@CA - :5@CB - :5@CG1 {N-CX-3C-2C} Pk=0.113 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 > :5@N - :5@CA - :5@CB - :5@CG1 {N-CT-CT-CT} Pk=0.155556 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :5@N - :5@CA - :5@CB - :5@CG1 {N-CX-3C-2C} Pk=0.31 Pn=1 Phase=0 SCEE=1.2 SCNB=2
-< :5@N - :5@CA - :5@CB - :5@CG2 {N-CX-3C-CT} Pk=0.001 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
+< :5@N - :5@CA - :5@CB - :5@CG1 {N-CX-3C-2C} Pk=0.097 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
+< :5@N - :5@CA - :5@CB - :5@CG2 {N-CX-3C-CT} Pk=0.337 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :5@N - :5@CA - :5@CB - :5@CG2 {N-CX-3C-CT} Pk=0.216 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 < :5@N - :5@CA - :5@CB - :5@CG2 {N-CX-3C-CT} Pk=0.148 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 > :5@N - :5@CA - :5@CB - :5@CG2 {N-CT-CT-CT} Pk=0.155556 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :5@N - :5@CA - :5@CB - :5@CG2 {N-CX-3C-CT} Pk=0.216 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
-< :5@N - :5@CA - :5@CB - :5@CG2 {N-CX-3C-CT} Pk=0.337 Pn=1 Phase=0 SCEE=1.2 SCNB=2
-< :5@CB - :5@CA - :5@C - :6@N {3C-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-> :5@CB - :5@CA - :5@C - :6@N {CT-CT-C-N} Pk=0.07 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-> :5@CB - :5@CA - :5@C - :6@N {CT-CT-C-N} Pk=0.1 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :5@N - :5@CA - :5@CB - :5@CG2 {N-CX-3C-CT} Pk=0.001 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
 < :5@CB - :5@CA - :5@C - :6@N {3C-CX-C-N} Pk=0.2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+> :5@CB - :5@CA - :5@C - :6@N {CT-CT-C-N} Pk=0.07 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 < :5@CB - :5@CA - :5@C - :6@N {3C-CX-C-N} Pk=0.2 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 < :5@CB - :5@CA - :5@C - :6@N {3C-CX-C-N} Pk=0.4 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :5@N - :5@CA - :5@C - :6@N {N-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :5@CB - :5@CA - :5@C - :6@N {3C-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :5@CB - :5@CA - :5@C - :6@N {CT-CT-C-N} Pk=0.1 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :5@N - :5@CA - :5@C - :6@N {N-CX-C-N} Pk=0.45 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
-< :5@N - :5@CA - :5@C - :6@N {N-CX-C-N} Pk=0.55 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
-< :5@N - :5@CA - :5@C - :6@N {N-CX-C-N} Pk=1.58 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :5@N - :5@CA - :5@C - :6@N {N-CT-C-N} Pk=1.7 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
+< :5@N - :5@CA - :5@C - :6@N {N-CX-C-N} Pk=1.58 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :5@N - :5@CA - :5@C - :6@N {N-CT-C-N} Pk=2 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+< :5@N - :5@CA - :5@C - :6@N {N-CX-C-N} Pk=0.55 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
+< :5@N - :5@CA - :5@C - :6@N {N-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :5@C - :6@N - :6@CA - :6@C {C-N-CX-C} Pk=0 Pn=1 Phase=0 SCEE=1.2 SCNB=2
-< :5@C - :6@N - :6@CA - :6@C {C-N-CX-C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-< :5@C - :6@N - :6@CA - :6@C {C-N-CX-C} Pk=0.27 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :5@C - :6@N - :6@CA - :6@C {C-N-CX-C} Pk=0.42 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 > :5@C - :6@N - :6@CA - :6@C {C-N-CT-C} Pk=0.8 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :5@C - :6@N - :6@CA - :6@C {C-N-CX-C} Pk=0.27 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 > :5@C - :6@N - :6@CA - :6@C {C-N-CT-C} Pk=0.85 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+< :5@C - :6@N - :6@CA - :6@C {C-N-CX-C} Pk=0.42 Pn=3 Phase=0 SCEE=1.2 SCNB=2
+< :5@C - :6@N - :6@CA - :6@C {C-N-CX-C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :5@C - :6@N - :6@CA - :6@CB {C-N-CT-CT} Pk=0.53 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :5@C - :6@N - :6@CA - :6@CB {C-N-CX-CT} Pk=2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 > :5@C - :6@N - :6@CA - :6@CB {C-N-CT-CT} Pk=0 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :5@C - :6@N - :6@CA - :6@CB {C-N-CX-CT} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :5@C - :6@N - :6@CA - :6@CB {C-N-CX-CT} Pk=1.8 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 > :5@C - :6@N - :6@CA - :6@CB {C-N-CT-CT} Pk=0.15 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
-> :5@C - :6@N - :6@CA - :6@CB {C-N-CT-CT} Pk=0.5 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
-> :5@C - :6@N - :6@CA - :6@CB {C-N-CT-CT} Pk=0.53 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 < :5@C - :6@N - :6@CA - :6@CB {C-N-CX-CT} Pk=0.8 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :5@C - :6@N - :6@CA - :6@CB {C-N-CX-CT} Pk=1.8 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :5@C - :6@N - :6@CA - :6@CB {C-N-CX-CT} Pk=2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :5@C - :6@N - :6@CA - :6@CB {C-N-CX-CT} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :5@C - :6@N - :6@CA - :6@CB {C-N-CT-CT} Pk=0.5 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
 < :6@CA - :6@CB - :6@CG - :6@CD1 {CX-CT-CA-CA} Pk=0 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 > :6@CA - :6@CB - :6@CG - :6@CD1 {CT-CT-CA-CA} Pk=0 Pn=2 Phase=0 SCEE=1.2 SCNB=2
+< :6@CA - :6@CB - :6@CG - :6@CD1 {CX-CT-CA-CA} Pk=0.069 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 < :6@CA - :6@CB - :6@CG - :6@CD1 {CX-CT-CA-CA} Pk=0 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 < :6@CA - :6@CB - :6@CG - :6@CD1 {CX-CT-CA-CA} Pk=0.048 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
-< :6@CA - :6@CB - :6@CG - :6@CD1 {CX-CT-CA-CA} Pk=0.069 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 < :6@CA - :6@CB - :6@CG - :6@CD2 {CX-CT-CA-CA} Pk=0 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 > :6@CA - :6@CB - :6@CG - :6@CD2 {CT-CT-CA-CA} Pk=0 Pn=2 Phase=0 SCEE=1.2 SCNB=2
+< :6@CA - :6@CB - :6@CG - :6@CD2 {CX-CT-CA-CA} Pk=0.069 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 < :6@CA - :6@CB - :6@CG - :6@CD2 {CX-CT-CA-CA} Pk=0 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 < :6@CA - :6@CB - :6@CG - :6@CD2 {CX-CT-CA-CA} Pk=0.048 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
-< :6@CA - :6@CB - :6@CG - :6@CD2 {CX-CT-CA-CA} Pk=0.069 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
-< :6@CG - :6@CB - :6@CA - :6@C {CA-CT-CX-C} Pk=0.012 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
 < :6@CG - :6@CB - :6@CA - :6@C {CA-CT-CX-C} Pk=0.055 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :6@CG - :6@CB - :6@CA - :6@C {CA-CT-CX-C} Pk=0.469 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :6@CG - :6@CB - :6@CA - :6@C {CA-CT-CT-C} Pk=0.155556 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 < :6@CG - :6@CB - :6@CA - :6@C {CA-CT-CX-C} Pk=0.192 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :6@CG - :6@CB - :6@CA - :6@C {CA-CT-CX-C} Pk=0.469 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
-< :6@N - :6@CA - :6@CB - :6@CG {N-CX-CT-CA} Pk=0.007 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
+< :6@CG - :6@CB - :6@CA - :6@C {CA-CT-CX-C} Pk=0.012 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
 < :6@N - :6@CA - :6@CB - :6@CG {N-CX-CT-CA} Pk=0.012 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
+< :6@N - :6@CA - :6@CB - :6@CG {N-CX-CT-CA} Pk=0.29 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :6@N - :6@CA - :6@CB - :6@CG {N-CT-CT-CA} Pk=0.155556 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 < :6@N - :6@CA - :6@CB - :6@CG {N-CX-CT-CA} Pk=0.192 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :6@N - :6@CA - :6@CB - :6@CG {N-CX-CT-CA} Pk=0.29 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
-< :6@CB - :6@CA - :6@C - :7@N {CT-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-> :6@CB - :6@CA - :6@C - :7@N {CT-CT-C-N} Pk=0.07 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-> :6@CB - :6@CA - :6@C - :7@N {CT-CT-C-N} Pk=0.1 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :6@N - :6@CA - :6@CB - :6@CG {N-CX-CT-CA} Pk=0.007 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
 < :6@CB - :6@CA - :6@C - :7@N {CT-CX-C-N} Pk=0.2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+> :6@CB - :6@CA - :6@C - :7@N {CT-CT-C-N} Pk=0.07 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 < :6@CB - :6@CA - :6@C - :7@N {CT-CX-C-N} Pk=0.2 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 < :6@CB - :6@CA - :6@C - :7@N {CT-CX-C-N} Pk=0.4 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :6@N - :6@CA - :6@C - :7@N {N-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :6@CB - :6@CA - :6@C - :7@N {CT-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :6@CB - :6@CA - :6@C - :7@N {CT-CT-C-N} Pk=0.1 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :6@N - :6@CA - :6@C - :7@N {N-CX-C-N} Pk=0.45 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
-< :6@N - :6@CA - :6@C - :7@N {N-CX-C-N} Pk=0.55 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
-< :6@N - :6@CA - :6@C - :7@N {N-CX-C-N} Pk=1.58 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :6@N - :6@CA - :6@C - :7@N {N-CT-C-N} Pk=1.7 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
+< :6@N - :6@CA - :6@C - :7@N {N-CX-C-N} Pk=1.58 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :6@N - :6@CA - :6@C - :7@N {N-CT-C-N} Pk=2 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+< :6@N - :6@CA - :6@C - :7@N {N-CX-C-N} Pk=0.55 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
+< :6@N - :6@CA - :6@C - :7@N {N-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :6@C - :7@N - :7@CA - :7@C {C-N-CX-C} Pk=0 Pn=1 Phase=0 SCEE=1.2 SCNB=2
-< :6@C - :7@N - :7@CA - :7@C {C-N-CX-C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-< :6@C - :7@N - :7@CA - :7@C {C-N-CX-C} Pk=0.27 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :6@C - :7@N - :7@CA - :7@C {C-N-CX-C} Pk=0.42 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 > :6@C - :7@N - :7@CA - :7@C {C-N-CT-C} Pk=0.8 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :6@C - :7@N - :7@CA - :7@C {C-N-CX-C} Pk=0.27 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 > :6@C - :7@N - :7@CA - :7@C {C-N-CT-C} Pk=0.85 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+< :6@C - :7@N - :7@CA - :7@C {C-N-CX-C} Pk=0.42 Pn=3 Phase=0 SCEE=1.2 SCNB=2
+< :6@C - :7@N - :7@CA - :7@C {C-N-CX-C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :6@C - :7@N - :7@CA - :7@CB {C-N-CT-CT} Pk=0.53 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :6@C - :7@N - :7@CA - :7@CB {C-N-CX-CT} Pk=2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 > :6@C - :7@N - :7@CA - :7@CB {C-N-CT-CT} Pk=0 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :6@C - :7@N - :7@CA - :7@CB {C-N-CX-CT} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :6@C - :7@N - :7@CA - :7@CB {C-N-CX-CT} Pk=1.8 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 > :6@C - :7@N - :7@CA - :7@CB {C-N-CT-CT} Pk=0.15 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
-> :6@C - :7@N - :7@CA - :7@CB {C-N-CT-CT} Pk=0.5 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
-> :6@C - :7@N - :7@CA - :7@CB {C-N-CT-CT} Pk=0.53 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 < :6@C - :7@N - :7@CA - :7@CB {C-N-CX-CT} Pk=0.8 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :6@C - :7@N - :7@CA - :7@CB {C-N-CX-CT} Pk=1.8 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :6@C - :7@N - :7@CA - :7@CB {C-N-CX-CT} Pk=2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :6@C - :7@N - :7@CA - :7@CB {C-N-CX-CT} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :6@C - :7@N - :7@CA - :7@CB {C-N-CT-CT} Pk=0.5 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
+> :6@C - :7@N - :7@CD - :7@CG {C-N-CT-CT} Pk=0.53 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :6@C - :7@N - :7@CD - :7@CG {C-N-CT-CT} Pk=2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 > :6@C - :7@N - :7@CD - :7@CG {C-N-CT-CT} Pk=0 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :6@C - :7@N - :7@CD - :7@CG {C-N-CT-CT} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :6@C - :7@N - :7@CD - :7@CG {C-N-CT-CT} Pk=2 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 > :6@C - :7@N - :7@CD - :7@CG {C-N-CT-CT} Pk=0.15 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
 < :6@C - :7@N - :7@CD - :7@CG {C-N-CT-CT} Pk=0.4 Pn=3 Phase=0 SCEE=1.2 SCNB=2
+< :6@C - :7@N - :7@CD - :7@CG {C-N-CT-CT} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 > :6@C - :7@N - :7@CD - :7@CG {C-N-CT-CT} Pk=0.5 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
-> :6@C - :7@N - :7@CD - :7@CG {C-N-CT-CT} Pk=0.53 Pn=1 Phase=0 SCEE=1.2 SCNB=2
-< :6@C - :7@N - :7@CD - :7@CG {C-N-CT-CT} Pk=2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
-< :6@C - :7@N - :7@CD - :7@CG {C-N-CT-CT} Pk=2 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :7@CB - :7@CA - :7@C - :8@N {CT-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-> :7@CB - :7@CA - :7@C - :8@N {CT-CT-C-N} Pk=0.07 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-> :7@CB - :7@CA - :7@C - :8@N {CT-CT-C-N} Pk=0.1 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :7@CB - :7@CA - :7@C - :8@N {CT-CX-C-N} Pk=0.2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+> :7@CB - :7@CA - :7@C - :8@N {CT-CT-C-N} Pk=0.07 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 < :7@CB - :7@CA - :7@C - :8@N {CT-CX-C-N} Pk=0.2 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 < :7@CB - :7@CA - :7@C - :8@N {CT-CX-C-N} Pk=0.4 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :7@N - :7@CA - :7@C - :8@N {N-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :7@CB - :7@CA - :7@C - :8@N {CT-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :7@CB - :7@CA - :7@C - :8@N {CT-CT-C-N} Pk=0.1 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :7@N - :7@CA - :7@C - :8@N {N-CX-C-N} Pk=0.45 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
-< :7@N - :7@CA - :7@C - :8@N {N-CX-C-N} Pk=0.55 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
-< :7@N - :7@CA - :7@C - :8@N {N-CX-C-N} Pk=1.58 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :7@N - :7@CA - :7@C - :8@N {N-CT-C-N} Pk=1.7 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
+< :7@N - :7@CA - :7@C - :8@N {N-CX-C-N} Pk=1.58 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :7@N - :7@CA - :7@C - :8@N {N-CT-C-N} Pk=2 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+< :7@N - :7@CA - :7@C - :8@N {N-CX-C-N} Pk=0.55 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
+< :7@N - :7@CA - :7@C - :8@N {N-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :7@C - :8@N - :8@CA - :8@C {C-N-CX-C} Pk=0 Pn=1 Phase=0 SCEE=1.2 SCNB=2
-< :7@C - :8@N - :8@CA - :8@C {C-N-CX-C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-< :7@C - :8@N - :8@CA - :8@C {C-N-CX-C} Pk=0.27 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :7@C - :8@N - :8@CA - :8@C {C-N-CX-C} Pk=0.42 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 > :7@C - :8@N - :8@CA - :8@C {C-N-CT-C} Pk=0.8 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :7@C - :8@N - :8@CA - :8@C {C-N-CX-C} Pk=0.27 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 > :7@C - :8@N - :8@CA - :8@C {C-N-CT-C} Pk=0.85 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+< :7@C - :8@N - :8@CA - :8@C {C-N-CX-C} Pk=0.42 Pn=3 Phase=0 SCEE=1.2 SCNB=2
+< :7@C - :8@N - :8@CA - :8@C {C-N-CX-C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :7@C - :8@N - :8@CA - :8@CB {C-N-CT-CT} Pk=0.53 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :7@C - :8@N - :8@CA - :8@CB {C-N-CX-2C} Pk=2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 > :7@C - :8@N - :8@CA - :8@CB {C-N-CT-CT} Pk=0 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :7@C - :8@N - :8@CA - :8@CB {C-N-CX-2C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :7@C - :8@N - :8@CA - :8@CB {C-N-CX-2C} Pk=1.8 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 > :7@C - :8@N - :8@CA - :8@CB {C-N-CT-CT} Pk=0.15 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
-> :7@C - :8@N - :8@CA - :8@CB {C-N-CT-CT} Pk=0.5 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
-> :7@C - :8@N - :8@CA - :8@CB {C-N-CT-CT} Pk=0.53 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 < :7@C - :8@N - :8@CA - :8@CB {C-N-CX-2C} Pk=0.8 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :7@C - :8@N - :8@CA - :8@CB {C-N-CX-2C} Pk=1.8 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :7@C - :8@N - :8@CA - :8@CB {C-N-CX-2C} Pk=2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
-< :8@CA - :8@CB - :8@OG - :8@HG {CX-2C-OH-HO} Pk=0.007 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-> :8@CA - :8@CB - :8@OG - :8@HG {CT-CT-OH-HO} Pk=0.16 Pn=3 Phase=0 SCEE=1.2 SCNB=2
+< :7@C - :8@N - :8@CA - :8@CB {C-N-CX-2C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :7@C - :8@N - :8@CA - :8@CB {C-N-CT-CT} Pk=0.5 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
 < :8@CA - :8@CB - :8@OG - :8@HG {CX-2C-OH-HO} Pk=0.211 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 > :8@CA - :8@CB - :8@OG - :8@HG {CT-CT-OH-HO} Pk=0.25 Pn=1 Phase=0 SCEE=1.2 SCNB=2
-< :8@CA - :8@CB - :8@OG - :8@HG {CX-2C-OH-HO} Pk=0.267 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 < :8@CA - :8@CB - :8@OG - :8@HG {CX-2C-OH-HO} Pk=0.444 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-> :8@N - :8@CA - :8@CB - :8@OG {N-CT-CT-OH} Pk=0.155556 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :8@N - :8@CA - :8@CB - :8@OG {N-CX-2C-OH} Pk=0.16 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :8@CA - :8@CB - :8@OG - :8@HG {CT-CT-OH-HO} Pk=0.16 Pn=3 Phase=0 SCEE=1.2 SCNB=2
+< :8@CA - :8@CB - :8@OG - :8@HG {CX-2C-OH-HO} Pk=0.267 Pn=3 Phase=0 SCEE=1.2 SCNB=2
+< :8@CA - :8@CB - :8@OG - :8@HG {CX-2C-OH-HO} Pk=0.007 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :8@N - :8@CA - :8@CB - :8@OG {N-CX-2C-OH} Pk=0.666 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 < :8@N - :8@CA - :8@CB - :8@OG {N-CX-2C-OH} Pk=0.246 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+> :8@N - :8@CA - :8@CB - :8@OG {N-CT-CT-OH} Pk=0.155556 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 < :8@N - :8@CA - :8@CB - :8@OG {N-CX-2C-OH} Pk=0.401 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :8@N - :8@CA - :8@CB - :8@OG {N-CX-2C-OH} Pk=0.666 Pn=1 Phase=0 SCEE=1.2 SCNB=2
-< :8@OG - :8@CB - :8@CA - :8@C {OH-2C-CX-C} Pk=0.129 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-> :8@OG - :8@CB - :8@CA - :8@C {OH-CT-CT-C} Pk=0.155556 Pn=3 Phase=0 SCEE=1.2 SCNB=2
+< :8@N - :8@CA - :8@CB - :8@OG {N-CX-2C-OH} Pk=0.16 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :8@OG - :8@CB - :8@CA - :8@C {OH-2C-CX-C} Pk=0.661 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
 < :8@OG - :8@CB - :8@CA - :8@C {OH-2C-CX-C} Pk=0.218 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+> :8@OG - :8@CB - :8@CA - :8@C {OH-CT-CT-C} Pk=0.155556 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 < :8@OG - :8@CB - :8@CA - :8@C {OH-2C-CX-C} Pk=0.401 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :8@OG - :8@CB - :8@CA - :8@C {OH-2C-CX-C} Pk=0.661 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
-< :8@CB - :8@CA - :8@C - :9@N {2C-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-> :8@CB - :8@CA - :8@C - :9@N {CT-CT-C-N} Pk=0.07 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-> :8@CB - :8@CA - :8@C - :9@N {CT-CT-C-N} Pk=0.1 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :8@OG - :8@CB - :8@CA - :8@C {OH-2C-CX-C} Pk=0.129 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :8@CB - :8@CA - :8@C - :9@N {2C-CX-C-N} Pk=0.2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+> :8@CB - :8@CA - :8@C - :9@N {CT-CT-C-N} Pk=0.07 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 < :8@CB - :8@CA - :8@C - :9@N {2C-CX-C-N} Pk=0.2 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 < :8@CB - :8@CA - :8@C - :9@N {2C-CX-C-N} Pk=0.4 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :8@N - :8@CA - :8@C - :9@N {N-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :8@CB - :8@CA - :8@C - :9@N {2C-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :8@CB - :8@CA - :8@C - :9@N {CT-CT-C-N} Pk=0.1 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :8@N - :8@CA - :8@C - :9@N {N-CX-C-N} Pk=0.45 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
-< :8@N - :8@CA - :8@C - :9@N {N-CX-C-N} Pk=0.55 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
-< :8@N - :8@CA - :8@C - :9@N {N-CX-C-N} Pk=1.58 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :8@N - :8@CA - :8@C - :9@N {N-CT-C-N} Pk=1.7 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
+< :8@N - :8@CA - :8@C - :9@N {N-CX-C-N} Pk=1.58 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :8@N - :8@CA - :8@C - :9@N {N-CT-C-N} Pk=2 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+< :8@N - :8@CA - :8@C - :9@N {N-CX-C-N} Pk=0.55 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
+< :8@N - :8@CA - :8@C - :9@N {N-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :8@C - :9@N - :9@CA - :9@C {C-N-CX-C} Pk=0 Pn=1 Phase=0 SCEE=1.2 SCNB=2
-< :8@C - :9@N - :9@CA - :9@C {C-N-CX-C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-< :8@C - :9@N - :9@CA - :9@C {C-N-CX-C} Pk=0.27 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :8@C - :9@N - :9@CA - :9@C {C-N-CX-C} Pk=0.42 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 > :8@C - :9@N - :9@CA - :9@C {C-N-CT-C} Pk=0.8 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :8@C - :9@N - :9@CA - :9@C {C-N-CX-C} Pk=0.27 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 > :8@C - :9@N - :9@CA - :9@C {C-N-CT-C} Pk=0.85 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+< :8@C - :9@N - :9@CA - :9@C {C-N-CX-C} Pk=0.42 Pn=3 Phase=0 SCEE=1.2 SCNB=2
+< :8@C - :9@N - :9@CA - :9@C {C-N-CX-C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :8@C - :9@N - :9@CA - :9@CB {C-N-CT-CT} Pk=0.53 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :8@C - :9@N - :9@CA - :9@CB {C-N-CX-3C} Pk=2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 > :8@C - :9@N - :9@CA - :9@CB {C-N-CT-CT} Pk=0 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :8@C - :9@N - :9@CA - :9@CB {C-N-CX-3C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :8@C - :9@N - :9@CA - :9@CB {C-N-CX-3C} Pk=1.8 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 > :8@C - :9@N - :9@CA - :9@CB {C-N-CT-CT} Pk=0.15 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
-> :8@C - :9@N - :9@CA - :9@CB {C-N-CT-CT} Pk=0.5 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
-> :8@C - :9@N - :9@CA - :9@CB {C-N-CT-CT} Pk=0.53 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 < :8@C - :9@N - :9@CA - :9@CB {C-N-CX-3C} Pk=0.8 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :8@C - :9@N - :9@CA - :9@CB {C-N-CX-3C} Pk=1.8 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :8@C - :9@N - :9@CA - :9@CB {C-N-CX-3C} Pk=2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :8@C - :9@N - :9@CA - :9@CB {C-N-CX-3C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :8@C - :9@N - :9@CA - :9@CB {C-N-CT-CT} Pk=0.5 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
 < :9@CA - :9@CB - :9@OG1 - :9@HG1 {CX-3C-OH-HO} Pk=0.006 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
-< :9@CA - :9@CB - :9@OG1 - :9@HG1 {CX-3C-OH-HO} Pk=0.013 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-> :9@CA - :9@CB - :9@OG1 - :9@HG1 {CT-CT-OH-HO} Pk=0.16 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :9@CA - :9@CB - :9@OG1 - :9@HG1 {CX-3C-OH-HO} Pk=0.236 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 > :9@CA - :9@CB - :9@OG1 - :9@HG1 {CT-CT-OH-HO} Pk=0.25 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 < :9@CA - :9@CB - :9@OG1 - :9@HG1 {CX-3C-OH-HO} Pk=0.251 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :9@CG2 - :9@CB - :9@CA - :9@C {CT-3C-CX-C} Pk=0.112 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :9@CA - :9@CB - :9@OG1 - :9@HG1 {CT-CT-OH-HO} Pk=0.16 Pn=3 Phase=0 SCEE=1.2 SCNB=2
+< :9@CA - :9@CB - :9@OG1 - :9@HG1 {CX-3C-OH-HO} Pk=0.236 Pn=3 Phase=0 SCEE=1.2 SCNB=2
+< :9@CA - :9@CB - :9@OG1 - :9@HG1 {CX-3C-OH-HO} Pk=0.013 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :9@CG2 - :9@CB - :9@CA - :9@C {CT-3C-CX-C} Pk=0.406 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
+< :9@CG2 - :9@CB - :9@CA - :9@C {CT-3C-CX-C} Pk=0.289 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 < :9@CG2 - :9@CB - :9@CA - :9@C {CT-3C-CX-C} Pk=0.148 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 > :9@CG2 - :9@CB - :9@CA - :9@C {CT-CT-CT-C} Pk=0.155556 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :9@CG2 - :9@CB - :9@CA - :9@C {CT-3C-CX-C} Pk=0.289 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
-< :9@CG2 - :9@CB - :9@CA - :9@C {CT-3C-CX-C} Pk=0.406 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
-< :9@CG2 - :9@CB - :9@OG1 - :9@HG1 {CT-3C-OH-HO} Pk=0.048 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :9@CG2 - :9@CB - :9@CA - :9@C {CT-3C-CX-C} Pk=0.112 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :9@CG2 - :9@CB - :9@OG1 - :9@HG1 {CT-CT-OH-HO} Pk=0.25 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :9@CG2 - :9@CB - :9@OG1 - :9@HG1 {CT-3C-OH-HO} Pk=0.643 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 < :9@CG2 - :9@CB - :9@OG1 - :9@HG1 {CT-3C-OH-HO} Pk=0.079 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :9@CG2 - :9@CB - :9@OG1 - :9@HG1 {CT-CT-OH-HO} Pk=0.16 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 < :9@CG2 - :9@CB - :9@OG1 - :9@HG1 {CT-3C-OH-HO} Pk=0.236 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-> :9@CG2 - :9@CB - :9@OG1 - :9@HG1 {CT-CT-OH-HO} Pk=0.25 Pn=1 Phase=0 SCEE=1.2 SCNB=2
-< :9@CG2 - :9@CB - :9@OG1 - :9@HG1 {CT-3C-OH-HO} Pk=0.643 Pn=1 Phase=0 SCEE=1.2 SCNB=2
-< :9@N - :9@CA - :9@CB - :9@CG2 {N-CX-3C-CT} Pk=0.001 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
+< :9@CG2 - :9@CB - :9@OG1 - :9@HG1 {CT-3C-OH-HO} Pk=0.048 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :9@N - :9@CA - :9@CB - :9@CG2 {N-CX-3C-CT} Pk=0.337 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :9@N - :9@CA - :9@CB - :9@CG2 {N-CX-3C-CT} Pk=0.216 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 < :9@N - :9@CA - :9@CB - :9@CG2 {N-CX-3C-CT} Pk=0.148 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 > :9@N - :9@CA - :9@CB - :9@CG2 {N-CT-CT-CT} Pk=0.155556 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :9@N - :9@CA - :9@CB - :9@CG2 {N-CX-3C-CT} Pk=0.216 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
-< :9@N - :9@CA - :9@CB - :9@CG2 {N-CX-3C-CT} Pk=0.337 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :9@N - :9@CA - :9@CB - :9@CG2 {N-CX-3C-CT} Pk=0.001 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
+< :9@N - :9@CA - :9@CB - :9@OG1 {N-CX-3C-OH} Pk=0.674 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 < :9@N - :9@CA - :9@CB - :9@OG1 {N-CX-3C-OH} Pk=0.006 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :9@N - :9@CA - :9@CB - :9@OG1 {N-CX-3C-OH} Pk=0.095 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 > :9@N - :9@CA - :9@CB - :9@OG1 {N-CT-CT-OH} Pk=0.155556 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 < :9@N - :9@CA - :9@CB - :9@OG1 {N-CX-3C-OH} Pk=0.315 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :9@N - :9@CA - :9@CB - :9@OG1 {N-CX-3C-OH} Pk=0.674 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :9@N - :9@CA - :9@CB - :9@OG1 {N-CX-3C-OH} Pk=0.095 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :9@OG1 - :9@CB - :9@CA - :9@C {OH-3C-CX-C} Pk=0.697 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
 < :9@OG1 - :9@CB - :9@CA - :9@C {OH-3C-CX-C} Pk=0.119 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :9@OG1 - :9@CB - :9@CA - :9@C {OH-CT-CT-C} Pk=0.155556 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :9@OG1 - :9@CB - :9@CA - :9@C {OH-3C-CX-C} Pk=0.156 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :9@OG1 - :9@CB - :9@CA - :9@C {OH-3C-CX-C} Pk=0.315 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :9@OG1 - :9@CB - :9@CA - :9@C {OH-3C-CX-C} Pk=0.697 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
-< :9@CB - :9@CA - :9@C - :10@N {3C-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-> :9@CB - :9@CA - :9@C - :10@N {CT-CT-C-N} Pk=0.07 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-> :9@CB - :9@CA - :9@C - :10@N {CT-CT-C-N} Pk=0.1 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :9@OG1 - :9@CB - :9@CA - :9@C {OH-3C-CX-C} Pk=0.156 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :9@CB - :9@CA - :9@C - :10@N {3C-CX-C-N} Pk=0.2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+> :9@CB - :9@CA - :9@C - :10@N {CT-CT-C-N} Pk=0.07 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 < :9@CB - :9@CA - :9@C - :10@N {3C-CX-C-N} Pk=0.2 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 < :9@CB - :9@CA - :9@C - :10@N {3C-CX-C-N} Pk=0.4 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :9@N - :9@CA - :9@C - :10@N {N-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :9@CB - :9@CA - :9@C - :10@N {3C-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :9@CB - :9@CA - :9@C - :10@N {CT-CT-C-N} Pk=0.1 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :9@N - :9@CA - :9@C - :10@N {N-CX-C-N} Pk=0.45 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
-< :9@N - :9@CA - :9@C - :10@N {N-CX-C-N} Pk=0.55 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
-< :9@N - :9@CA - :9@C - :10@N {N-CX-C-N} Pk=1.58 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :9@N - :9@CA - :9@C - :10@N {N-CT-C-N} Pk=1.7 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
+< :9@N - :9@CA - :9@C - :10@N {N-CX-C-N} Pk=1.58 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :9@N - :9@CA - :9@C - :10@N {N-CT-C-N} Pk=2 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+< :9@N - :9@CA - :9@C - :10@N {N-CX-C-N} Pk=0.55 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
+< :9@N - :9@CA - :9@C - :10@N {N-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :9@C - :10@N - :10@CA - :10@C {C-N-CX-C} Pk=0 Pn=1 Phase=0 SCEE=1.2 SCNB=2
-< :9@C - :10@N - :10@CA - :10@C {C-N-CX-C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-< :9@C - :10@N - :10@CA - :10@C {C-N-CX-C} Pk=0.27 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :9@C - :10@N - :10@CA - :10@C {C-N-CX-C} Pk=0.42 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 > :9@C - :10@N - :10@CA - :10@C {C-N-CT-C} Pk=0.8 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :9@C - :10@N - :10@CA - :10@C {C-N-CX-C} Pk=0.27 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 > :9@C - :10@N - :10@CA - :10@C {C-N-CT-C} Pk=0.85 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+< :9@C - :10@N - :10@CA - :10@C {C-N-CX-C} Pk=0.42 Pn=3 Phase=0 SCEE=1.2 SCNB=2
+< :9@C - :10@N - :10@CA - :10@C {C-N-CX-C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :9@C - :10@N - :10@CA - :10@CB {C-N-CT-CT} Pk=0.53 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :9@C - :10@N - :10@CA - :10@CB {C-N-CX-CT} Pk=2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 > :9@C - :10@N - :10@CA - :10@CB {C-N-CT-CT} Pk=0 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :9@C - :10@N - :10@CA - :10@CB {C-N-CX-CT} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :9@C - :10@N - :10@CA - :10@CB {C-N-CX-CT} Pk=1.8 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 > :9@C - :10@N - :10@CA - :10@CB {C-N-CT-CT} Pk=0.15 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
-> :9@C - :10@N - :10@CA - :10@CB {C-N-CT-CT} Pk=0.5 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
-> :9@C - :10@N - :10@CA - :10@CB {C-N-CT-CT} Pk=0.53 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 < :9@C - :10@N - :10@CA - :10@CB {C-N-CX-CT} Pk=0.8 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :9@C - :10@N - :10@CA - :10@CB {C-N-CX-CT} Pk=1.8 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :9@C - :10@N - :10@CA - :10@CB {C-N-CX-CT} Pk=2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :9@C - :10@N - :10@CA - :10@CB {C-N-CX-CT} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :9@C - :10@N - :10@CA - :10@CB {C-N-CT-CT} Pk=0.5 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
 < :10@CA - :10@CB - :10@CG - :10@CD1 {CX-CT-CA-CA} Pk=0 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 > :10@CA - :10@CB - :10@CG - :10@CD1 {CT-CT-CA-CA} Pk=0 Pn=2 Phase=0 SCEE=1.2 SCNB=2
+< :10@CA - :10@CB - :10@CG - :10@CD1 {CX-CT-CA-CA} Pk=0.069 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 < :10@CA - :10@CB - :10@CG - :10@CD1 {CX-CT-CA-CA} Pk=0 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 < :10@CA - :10@CB - :10@CG - :10@CD1 {CX-CT-CA-CA} Pk=0.048 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
-< :10@CA - :10@CB - :10@CG - :10@CD1 {CX-CT-CA-CA} Pk=0.069 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 < :10@CA - :10@CB - :10@CG - :10@CD2 {CX-CT-CA-CA} Pk=0 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 > :10@CA - :10@CB - :10@CG - :10@CD2 {CT-CT-CA-CA} Pk=0 Pn=2 Phase=0 SCEE=1.2 SCNB=2
+< :10@CA - :10@CB - :10@CG - :10@CD2 {CX-CT-CA-CA} Pk=0.069 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 < :10@CA - :10@CB - :10@CG - :10@CD2 {CX-CT-CA-CA} Pk=0 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 < :10@CA - :10@CB - :10@CG - :10@CD2 {CX-CT-CA-CA} Pk=0.048 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
-< :10@CA - :10@CB - :10@CG - :10@CD2 {CX-CT-CA-CA} Pk=0.069 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 < :10@CE1 - :10@CZ - :10@OH - :10@HH {CA-C-OH-HO} Pk=0 Pn=1 Phase=0 SCEE=1.2 SCNB=2
-< :10@CE1 - :10@CZ - :10@OH - :10@HH {CA-C-OH-HO} Pk=0 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :10@CE1 - :10@CZ - :10@OH - :10@HH {CA-C-OH-HO} Pk=0.065 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :10@CE1 - :10@CZ - :10@OH - :10@HH {CA-C-OH-HO} Pk=0.883 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :10@CE1 - :10@CZ - :10@OH - :10@HH {CA-C-OH-HO} Pk=2.3 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
-< :10@CG - :10@CB - :10@CA - :10@C {CA-CT-CX-C} Pk=0.012 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
+< :10@CE1 - :10@CZ - :10@OH - :10@HH {CA-C-OH-HO} Pk=0 Pn=3 Phase=0 SCEE=1.2 SCNB=2
+< :10@CE1 - :10@CZ - :10@OH - :10@HH {CA-C-OH-HO} Pk=0.065 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :10@CG - :10@CB - :10@CA - :10@C {CA-CT-CX-C} Pk=0.055 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :10@CG - :10@CB - :10@CA - :10@C {CA-CT-CX-C} Pk=0.469 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :10@CG - :10@CB - :10@CA - :10@C {CA-CT-CT-C} Pk=0.155556 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 < :10@CG - :10@CB - :10@CA - :10@C {CA-CT-CX-C} Pk=0.192 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :10@CG - :10@CB - :10@CA - :10@C {CA-CT-CX-C} Pk=0.469 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+< :10@CG - :10@CB - :10@CA - :10@C {CA-CT-CX-C} Pk=0.012 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
 < :10@HH - :10@OH - :10@CZ - :10@CE2 {HO-OH-C-CA} Pk=0 Pn=1 Phase=0 SCEE=1.2 SCNB=2
-< :10@HH - :10@OH - :10@CZ - :10@CE2 {HO-OH-C-CA} Pk=0 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :10@HH - :10@OH - :10@CZ - :10@CE2 {HO-OH-C-CA} Pk=0.065 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :10@HH - :10@OH - :10@CZ - :10@CE2 {HO-OH-C-CA} Pk=0.883 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :10@HH - :10@OH - :10@CZ - :10@CE2 {HO-OH-C-CA} Pk=2.3 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
-< :10@N - :10@CA - :10@CB - :10@CG {N-CX-CT-CA} Pk=0.007 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
+< :10@HH - :10@OH - :10@CZ - :10@CE2 {HO-OH-C-CA} Pk=0 Pn=3 Phase=0 SCEE=1.2 SCNB=2
+< :10@HH - :10@OH - :10@CZ - :10@CE2 {HO-OH-C-CA} Pk=0.065 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :10@N - :10@CA - :10@CB - :10@CG {N-CX-CT-CA} Pk=0.012 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
+< :10@N - :10@CA - :10@CB - :10@CG {N-CX-CT-CA} Pk=0.29 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :10@N - :10@CA - :10@CB - :10@CG {N-CT-CT-CA} Pk=0.155556 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 < :10@N - :10@CA - :10@CB - :10@CG {N-CX-CT-CA} Pk=0.192 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :10@N - :10@CA - :10@CB - :10@CG {N-CX-CT-CA} Pk=0.29 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
-< :10@CB - :10@CA - :10@C - :11@N {CT-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-> :10@CB - :10@CA - :10@C - :11@N {CT-CT-C-N} Pk=0.07 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-> :10@CB - :10@CA - :10@C - :11@N {CT-CT-C-N} Pk=0.1 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :10@N - :10@CA - :10@CB - :10@CG {N-CX-CT-CA} Pk=0.007 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
 < :10@CB - :10@CA - :10@C - :11@N {CT-CX-C-N} Pk=0.2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+> :10@CB - :10@CA - :10@C - :11@N {CT-CT-C-N} Pk=0.07 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 < :10@CB - :10@CA - :10@C - :11@N {CT-CX-C-N} Pk=0.2 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 < :10@CB - :10@CA - :10@C - :11@N {CT-CX-C-N} Pk=0.4 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :10@N - :10@CA - :10@C - :11@N {N-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :10@CB - :10@CA - :10@C - :11@N {CT-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :10@CB - :10@CA - :10@C - :11@N {CT-CT-C-N} Pk=0.1 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :10@N - :10@CA - :10@C - :11@N {N-CX-C-N} Pk=0.45 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
-< :10@N - :10@CA - :10@C - :11@N {N-CX-C-N} Pk=0.55 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
-< :10@N - :10@CA - :10@C - :11@N {N-CX-C-N} Pk=1.58 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :10@N - :10@CA - :10@C - :11@N {N-CT-C-N} Pk=1.7 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
+< :10@N - :10@CA - :10@C - :11@N {N-CX-C-N} Pk=1.58 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :10@N - :10@CA - :10@C - :11@N {N-CT-C-N} Pk=2 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+< :10@N - :10@CA - :10@C - :11@N {N-CX-C-N} Pk=0.55 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
+< :10@N - :10@CA - :10@C - :11@N {N-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :10@C - :11@N - :11@CA - :11@C {C-N-CX-C} Pk=0 Pn=1 Phase=0 SCEE=1.2 SCNB=2
-< :10@C - :11@N - :11@CA - :11@C {C-N-CX-C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-< :10@C - :11@N - :11@CA - :11@C {C-N-CX-C} Pk=0.27 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :10@C - :11@N - :11@CA - :11@C {C-N-CX-C} Pk=0.42 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 > :10@C - :11@N - :11@CA - :11@C {C-N-CT-C} Pk=0.8 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :10@C - :11@N - :11@CA - :11@C {C-N-CX-C} Pk=0.27 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 > :10@C - :11@N - :11@CA - :11@C {C-N-CT-C} Pk=0.85 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+< :10@C - :11@N - :11@CA - :11@C {C-N-CX-C} Pk=0.42 Pn=3 Phase=0 SCEE=1.2 SCNB=2
+< :10@C - :11@N - :11@CA - :11@C {C-N-CX-C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :10@C - :11@N - :11@CA - :11@CB {C-N-CT-CT} Pk=0.53 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :10@C - :11@N - :11@CA - :11@CB {C-N-CX-2C} Pk=2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 > :10@C - :11@N - :11@CA - :11@CB {C-N-CT-CT} Pk=0 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :10@C - :11@N - :11@CA - :11@CB {C-N-CX-2C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :10@C - :11@N - :11@CA - :11@CB {C-N-CX-2C} Pk=1.8 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 > :10@C - :11@N - :11@CA - :11@CB {C-N-CT-CT} Pk=0.15 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
-> :10@C - :11@N - :11@CA - :11@CB {C-N-CT-CT} Pk=0.5 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
-> :10@C - :11@N - :11@CA - :11@CB {C-N-CT-CT} Pk=0.53 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 < :10@C - :11@N - :11@CA - :11@CB {C-N-CX-2C} Pk=0.8 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :10@C - :11@N - :11@CA - :11@CB {C-N-CX-2C} Pk=1.8 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :10@C - :11@N - :11@CA - :11@CB {C-N-CX-2C} Pk=2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
-< :11@CA - :11@CB - :11@SG - :11@HG {CX-2C-SH-HS} Pk=0.03 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :10@C - :11@N - :11@CA - :11@CB {C-N-CX-2C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :10@C - :11@N - :11@CA - :11@CB {C-N-CT-CT} Pk=0.5 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
 < :11@CA - :11@CB - :11@SG - :11@HG {CX-2C-SH-HS} Pk=0.092 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :11@CA - :11@CB - :11@SG - :11@HG {CX-2C-SH-HS} Pk=0.612 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 > :11@CA - :11@CB - :11@SG - :11@HG {CT-CT-SH-HS} Pk=0.25 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 < :11@CA - :11@CB - :11@SG - :11@HG {CX-2C-SH-HS} Pk=0.252 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :11@CA - :11@CB - :11@SG - :11@HG {CX-2C-SH-HS} Pk=0.612 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :11@N - :11@CA - :11@CB - :11@SG {N-CX-2C-SH} Pk=0.033 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :11@CA - :11@CB - :11@SG - :11@HG {CX-2C-SH-HS} Pk=0.03 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :11@N - :11@CA - :11@CB - :11@SG {N-CX-2C-SH} Pk=0.154 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :11@N - :11@CA - :11@CB - :11@SG {N-CX-2C-SH} Pk=0.486 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :11@N - :11@CA - :11@CB - :11@SG {N-CT-CT-SH} Pk=0.155556 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 < :11@N - :11@CA - :11@CB - :11@SG {N-CX-2C-SH} Pk=0.251 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :11@N - :11@CA - :11@CB - :11@SG {N-CX-2C-SH} Pk=0.486 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
-< :11@SG - :11@CB - :11@CA - :11@C {SH-2C-CX-C} Pk=0.075 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-> :11@SG - :11@CB - :11@CA - :11@C {SH-CT-CT-C} Pk=0.155556 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :11@SG - :11@CB - :11@CA - :11@C {SH-2C-CX-C} Pk=0.251 Pn=3 Phase=0 SCEE=1.2 SCNB=2
+< :11@N - :11@CA - :11@CB - :11@SG {N-CX-2C-SH} Pk=0.033 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :11@SG - :11@CB - :11@CA - :11@C {SH-2C-CX-C} Pk=0.269 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
 < :11@SG - :11@CB - :11@CA - :11@C {SH-2C-CX-C} Pk=0.337 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
-< :11@CB - :11@CA - :11@C - :12@N {2C-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-> :11@CB - :11@CA - :11@C - :12@N {CT-CT-C-N} Pk=0.07 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-> :11@CB - :11@CA - :11@C - :12@N {CT-CT-C-N} Pk=0.1 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :11@SG - :11@CB - :11@CA - :11@C {SH-CT-CT-C} Pk=0.155556 Pn=3 Phase=0 SCEE=1.2 SCNB=2
+< :11@SG - :11@CB - :11@CA - :11@C {SH-2C-CX-C} Pk=0.251 Pn=3 Phase=0 SCEE=1.2 SCNB=2
+< :11@SG - :11@CB - :11@CA - :11@C {SH-2C-CX-C} Pk=0.075 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :11@CB - :11@CA - :11@C - :12@N {2C-CX-C-N} Pk=0.2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+> :11@CB - :11@CA - :11@C - :12@N {CT-CT-C-N} Pk=0.07 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 < :11@CB - :11@CA - :11@C - :12@N {2C-CX-C-N} Pk=0.2 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 < :11@CB - :11@CA - :11@C - :12@N {2C-CX-C-N} Pk=0.4 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :11@N - :11@CA - :11@C - :12@N {N-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :11@CB - :11@CA - :11@C - :12@N {2C-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :11@CB - :11@CA - :11@C - :12@N {CT-CT-C-N} Pk=0.1 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :11@N - :11@CA - :11@C - :12@N {N-CX-C-N} Pk=0.45 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
-< :11@N - :11@CA - :11@C - :12@N {N-CX-C-N} Pk=0.55 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
-< :11@N - :11@CA - :11@C - :12@N {N-CX-C-N} Pk=1.58 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :11@N - :11@CA - :11@C - :12@N {N-CT-C-N} Pk=1.7 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
+< :11@N - :11@CA - :11@C - :12@N {N-CX-C-N} Pk=1.58 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :11@N - :11@CA - :11@C - :12@N {N-CT-C-N} Pk=2 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+< :11@N - :11@CA - :11@C - :12@N {N-CX-C-N} Pk=0.55 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
+< :11@N - :11@CA - :11@C - :12@N {N-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :11@C - :12@N - :12@CA - :12@C {C-N-CX-C} Pk=0 Pn=1 Phase=0 SCEE=1.2 SCNB=2
-< :11@C - :12@N - :12@CA - :12@C {C-N-CX-C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-< :11@C - :12@N - :12@CA - :12@C {C-N-CX-C} Pk=0.27 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :11@C - :12@N - :12@CA - :12@C {C-N-CX-C} Pk=0.42 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 > :11@C - :12@N - :12@CA - :12@C {C-N-CT-C} Pk=0.8 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :11@C - :12@N - :12@CA - :12@C {C-N-CX-C} Pk=0.27 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 > :11@C - :12@N - :12@CA - :12@C {C-N-CT-C} Pk=0.85 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+< :11@C - :12@N - :12@CA - :12@C {C-N-CX-C} Pk=0.42 Pn=3 Phase=0 SCEE=1.2 SCNB=2
+< :11@C - :12@N - :12@CA - :12@C {C-N-CX-C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :11@C - :12@N - :12@CA - :12@CB {C-N-CT-CT} Pk=0.53 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :11@C - :12@N - :12@CA - :12@CB {C-N-CX-2C} Pk=2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 > :11@C - :12@N - :12@CA - :12@CB {C-N-CT-CT} Pk=0 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :11@C - :12@N - :12@CA - :12@CB {C-N-CX-2C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :11@C - :12@N - :12@CA - :12@CB {C-N-CX-2C} Pk=1.8 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 > :11@C - :12@N - :12@CA - :12@CB {C-N-CT-CT} Pk=0.15 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
-> :11@C - :12@N - :12@CA - :12@CB {C-N-CT-CT} Pk=0.5 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
-> :11@C - :12@N - :12@CA - :12@CB {C-N-CT-CT} Pk=0.53 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 < :11@C - :12@N - :12@CA - :12@CB {C-N-CX-2C} Pk=0.8 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :11@C - :12@N - :12@CA - :12@CB {C-N-CX-2C} Pk=1.8 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :11@C - :12@N - :12@CA - :12@CB {C-N-CX-2C} Pk=2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :11@C - :12@N - :12@CA - :12@CB {C-N-CX-2C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :11@C - :12@N - :12@CA - :12@CB {C-N-CT-CT} Pk=0.5 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
+< :12@CA - :12@CB - :12@CG - :12@SD {CX-2C-2C-S} Pk=0.417 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :12@CA - :12@CB - :12@CG - :12@SD {CX-2C-2C-S} Pk=0.245 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 < :12@CA - :12@CB - :12@CG - :12@SD {CX-2C-2C-S} Pk=0.016 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :12@CA - :12@CB - :12@CG - :12@SD {CX-2C-2C-S} Pk=0.028 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 > :12@CA - :12@CB - :12@CG - :12@SD {CT-CT-CT-S} Pk=0.155556 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :12@CA - :12@CB - :12@CG - :12@SD {CX-2C-2C-S} Pk=0.245 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :12@CA - :12@CB - :12@CG - :12@SD {CX-2C-2C-S} Pk=0.417 Pn=1 Phase=0 SCEE=1.2 SCNB=2
-< :12@CB - :12@CG - :12@SD - :12@CE {2C-2C-S-CT} Pk=0.057 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :12@CA - :12@CB - :12@CG - :12@SD {CX-2C-2C-S} Pk=0.028 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :12@CB - :12@CG - :12@SD - :12@CE {2C-2C-S-CT} Pk=0.247 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
+< :12@CB - :12@CG - :12@SD - :12@CE {2C-2C-S-CT} Pk=0.442 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 > :12@CB - :12@CG - :12@SD - :12@CE {CT-CT-S-CT} Pk=0.333333 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 < :12@CB - :12@CG - :12@SD - :12@CE {2C-2C-S-CT} Pk=0.414 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :12@CB - :12@CG - :12@SD - :12@CE {2C-2C-S-CT} Pk=0.442 Pn=2 Phase=0 SCEE=1.2 SCNB=2
+< :12@CB - :12@CG - :12@SD - :12@CE {2C-2C-S-CT} Pk=0.057 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :12@CG - :12@CB - :12@CA - :12@C {2C-2C-CX-C} Pk=0.421 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
+< :12@CG - :12@CB - :12@CA - :12@C {2C-2C-CX-C} Pk=0.393 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 < :12@CG - :12@CB - :12@CA - :12@C {2C-2C-CX-C} Pk=0.144 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :12@CG - :12@CB - :12@CA - :12@C {2C-2C-CX-C} Pk=0.145 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 > :12@CG - :12@CB - :12@CA - :12@C {CT-CT-CT-C} Pk=0.155556 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :12@CG - :12@CB - :12@CA - :12@C {2C-2C-CX-C} Pk=0.393 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
-< :12@CG - :12@CB - :12@CA - :12@C {2C-2C-CX-C} Pk=0.421 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
-< :12@N - :12@CA - :12@CB - :12@CG {N-CX-2C-2C} Pk=0.078 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :12@CG - :12@CB - :12@CA - :12@C {2C-2C-CX-C} Pk=0.145 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :12@N - :12@CA - :12@CB - :12@CG {N-CX-2C-2C} Pk=0.1 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
+< :12@N - :12@CA - :12@CB - :12@CG {N-CX-2C-2C} Pk=0.184 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 < :12@N - :12@CA - :12@CB - :12@CG {N-CX-2C-2C} Pk=0.144 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 > :12@N - :12@CA - :12@CB - :12@CG {N-CT-CT-CT} Pk=0.155556 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :12@N - :12@CA - :12@CB - :12@CG {N-CX-2C-2C} Pk=0.184 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
-< :12@CB - :12@CA - :12@C - :13@N {2C-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :12@N - :12@CA - :12@CB - :12@CG {N-CX-2C-2C} Pk=0.078 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :12@CB - :12@CA - :12@C - :13@N {2C-CX-C-N} Pk=0.2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 > :12@CB - :12@CA - :12@C - :13@N {CT-CT-C-N} Pk=0.07 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-> :12@CB - :12@CA - :12@C - :13@N {CT-CT-C-N} Pk=0.1 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-< :12@CB - :12@CA - :12@C - :13@N {2C-CX-C-N} Pk=0.2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 < :12@CB - :12@CA - :12@C - :13@N {2C-CX-C-N} Pk=0.2 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 < :12@CB - :12@CA - :12@C - :13@N {2C-CX-C-N} Pk=0.4 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :12@N - :12@CA - :12@C - :13@N {N-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :12@CB - :12@CA - :12@C - :13@N {2C-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :12@CB - :12@CA - :12@C - :13@N {CT-CT-C-N} Pk=0.1 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :12@N - :12@CA - :12@C - :13@N {N-CX-C-N} Pk=0.45 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
-< :12@N - :12@CA - :12@C - :13@N {N-CX-C-N} Pk=0.55 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
-< :12@N - :12@CA - :12@C - :13@N {N-CX-C-N} Pk=1.58 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :12@N - :12@CA - :12@C - :13@N {N-CT-C-N} Pk=1.7 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
+< :12@N - :12@CA - :12@C - :13@N {N-CX-C-N} Pk=1.58 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :12@N - :12@CA - :12@C - :13@N {N-CT-C-N} Pk=2 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+< :12@N - :12@CA - :12@C - :13@N {N-CX-C-N} Pk=0.55 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
+< :12@N - :12@CA - :12@C - :13@N {N-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :12@C - :13@N - :13@CA - :13@C {C-N-CX-C} Pk=0 Pn=1 Phase=0 SCEE=1.2 SCNB=2
-< :12@C - :13@N - :13@CA - :13@C {C-N-CX-C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-< :12@C - :13@N - :13@CA - :13@C {C-N-CX-C} Pk=0.27 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :12@C - :13@N - :13@CA - :13@C {C-N-CX-C} Pk=0.42 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 > :12@C - :13@N - :13@CA - :13@C {C-N-CT-C} Pk=0.8 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :12@C - :13@N - :13@CA - :13@C {C-N-CX-C} Pk=0.27 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 > :12@C - :13@N - :13@CA - :13@C {C-N-CT-C} Pk=0.85 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+< :12@C - :13@N - :13@CA - :13@C {C-N-CX-C} Pk=0.42 Pn=3 Phase=0 SCEE=1.2 SCNB=2
+< :12@C - :13@N - :13@CA - :13@C {C-N-CX-C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :12@C - :13@N - :13@CA - :13@CB {C-N-CT-CT} Pk=0.53 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :12@C - :13@N - :13@CA - :13@CB {C-N-CX-C8} Pk=2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 > :12@C - :13@N - :13@CA - :13@CB {C-N-CT-CT} Pk=0 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :12@C - :13@N - :13@CA - :13@CB {C-N-CX-C8} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :12@C - :13@N - :13@CA - :13@CB {C-N-CX-C8} Pk=1.8 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 > :12@C - :13@N - :13@CA - :13@CB {C-N-CT-CT} Pk=0.15 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
-> :12@C - :13@N - :13@CA - :13@CB {C-N-CT-CT} Pk=0.5 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
-> :12@C - :13@N - :13@CA - :13@CB {C-N-CT-CT} Pk=0.53 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 < :12@C - :13@N - :13@CA - :13@CB {C-N-CX-C8} Pk=0.8 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :12@C - :13@N - :13@CA - :13@CB {C-N-CX-C8} Pk=1.8 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :12@C - :13@N - :13@CA - :13@CB {C-N-CX-C8} Pk=2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
-< :13@CB - :13@CA - :13@C - :14@N {C8-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-> :13@CB - :13@CA - :13@C - :14@N {CT-CT-C-N} Pk=0.07 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-> :13@CB - :13@CA - :13@C - :14@N {CT-CT-C-N} Pk=0.1 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :12@C - :13@N - :13@CA - :13@CB {C-N-CX-C8} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :12@C - :13@N - :13@CA - :13@CB {C-N-CT-CT} Pk=0.5 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
 < :13@CB - :13@CA - :13@C - :14@N {C8-CX-C-N} Pk=0.2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+> :13@CB - :13@CA - :13@C - :14@N {CT-CT-C-N} Pk=0.07 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 < :13@CB - :13@CA - :13@C - :14@N {C8-CX-C-N} Pk=0.2 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 < :13@CB - :13@CA - :13@C - :14@N {C8-CX-C-N} Pk=0.4 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :13@N - :13@CA - :13@C - :14@N {N-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :13@CB - :13@CA - :13@C - :14@N {C8-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :13@CB - :13@CA - :13@C - :14@N {CT-CT-C-N} Pk=0.1 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :13@N - :13@CA - :13@C - :14@N {N-CX-C-N} Pk=0.45 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
-< :13@N - :13@CA - :13@C - :14@N {N-CX-C-N} Pk=0.55 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
-< :13@N - :13@CA - :13@C - :14@N {N-CX-C-N} Pk=1.58 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :13@N - :13@CA - :13@C - :14@N {N-CT-C-N} Pk=1.7 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
+< :13@N - :13@CA - :13@C - :14@N {N-CX-C-N} Pk=1.58 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :13@N - :13@CA - :13@C - :14@N {N-CT-C-N} Pk=2 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+< :13@N - :13@CA - :13@C - :14@N {N-CX-C-N} Pk=0.55 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
+< :13@N - :13@CA - :13@C - :14@N {N-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :13@C - :14@N - :14@CA - :14@C {C-N-CX-C} Pk=0 Pn=1 Phase=0 SCEE=1.2 SCNB=2
-< :13@C - :14@N - :14@CA - :14@C {C-N-CX-C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-< :13@C - :14@N - :14@CA - :14@C {C-N-CX-C} Pk=0.27 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :13@C - :14@N - :14@CA - :14@C {C-N-CX-C} Pk=0.42 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 > :13@C - :14@N - :14@CA - :14@C {C-N-CT-C} Pk=0.8 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :13@C - :14@N - :14@CA - :14@C {C-N-CX-C} Pk=0.27 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 > :13@C - :14@N - :14@CA - :14@C {C-N-CT-C} Pk=0.85 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+< :13@C - :14@N - :14@CA - :14@C {C-N-CX-C} Pk=0.42 Pn=3 Phase=0 SCEE=1.2 SCNB=2
+< :13@C - :14@N - :14@CA - :14@C {C-N-CX-C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :13@C - :14@N - :14@CA - :14@CB {C-N-CT-CT} Pk=0.53 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :13@C - :14@N - :14@CA - :14@CB {C-N-CX-C8} Pk=2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 > :13@C - :14@N - :14@CA - :14@CB {C-N-CT-CT} Pk=0 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :13@C - :14@N - :14@CA - :14@CB {C-N-CX-C8} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :13@C - :14@N - :14@CA - :14@CB {C-N-CX-C8} Pk=1.8 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 > :13@C - :14@N - :14@CA - :14@CB {C-N-CT-CT} Pk=0.15 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
-> :13@C - :14@N - :14@CA - :14@CB {C-N-CT-CT} Pk=0.5 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
-> :13@C - :14@N - :14@CA - :14@CB {C-N-CT-CT} Pk=0.53 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 < :13@C - :14@N - :14@CA - :14@CB {C-N-CX-C8} Pk=0.8 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :13@C - :14@N - :14@CA - :14@CB {C-N-CX-C8} Pk=1.8 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :13@C - :14@N - :14@CA - :14@CB {C-N-CX-C8} Pk=2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :13@C - :14@N - :14@CA - :14@CB {C-N-CX-C8} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :13@C - :14@N - :14@CA - :14@CB {C-N-CT-CT} Pk=0.5 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
 < :14@CD - :14@NE - :14@CZ - :14@NH1 {C8-N2-CA-N2} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :14@CD - :14@NE - :14@CZ - :14@NH2 {C8-N2-CA-N2} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :14@CG - :14@CD - :14@NE - :14@CZ {C8-C8-N2-CA} Pk=0 Pn=1 Phase=0 SCEE=1.2 SCNB=2
@@ -806,445 +806,445 @@
 < :14@NE - :14@CZ - :14@NH2 - :14@HH22 {N2-CA-N2-H} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :14@NH1 - :14@CZ - :14@NH2 - :14@HH21 {N2-CA-N2-H} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :14@NH1 - :14@CZ - :14@NH2 - :14@HH22 {N2-CA-N2-H} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-< :14@CB - :14@CA - :14@C - :15@N {C8-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-> :14@CB - :14@CA - :14@C - :15@N {CT-CT-C-N} Pk=0.07 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-> :14@CB - :14@CA - :14@C - :15@N {CT-CT-C-N} Pk=0.1 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :14@CB - :14@CA - :14@C - :15@N {C8-CX-C-N} Pk=0.2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+> :14@CB - :14@CA - :14@C - :15@N {CT-CT-C-N} Pk=0.07 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 < :14@CB - :14@CA - :14@C - :15@N {C8-CX-C-N} Pk=0.2 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 < :14@CB - :14@CA - :14@C - :15@N {C8-CX-C-N} Pk=0.4 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :14@N - :14@CA - :14@C - :15@N {N-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :14@CB - :14@CA - :14@C - :15@N {C8-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :14@CB - :14@CA - :14@C - :15@N {CT-CT-C-N} Pk=0.1 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :14@N - :14@CA - :14@C - :15@N {N-CX-C-N} Pk=0.45 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
-< :14@N - :14@CA - :14@C - :15@N {N-CX-C-N} Pk=0.55 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
-< :14@N - :14@CA - :14@C - :15@N {N-CX-C-N} Pk=1.58 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :14@N - :14@CA - :14@C - :15@N {N-CT-C-N} Pk=1.7 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
+< :14@N - :14@CA - :14@C - :15@N {N-CX-C-N} Pk=1.58 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :14@N - :14@CA - :14@C - :15@N {N-CT-C-N} Pk=2 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+< :14@N - :14@CA - :14@C - :15@N {N-CX-C-N} Pk=0.55 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
+< :14@N - :14@CA - :14@C - :15@N {N-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :14@C - :15@N - :15@CA - :15@C {C-N-CX-C} Pk=0 Pn=1 Phase=0 SCEE=1.2 SCNB=2
-< :14@C - :15@N - :15@CA - :15@C {C-N-CX-C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-< :14@C - :15@N - :15@CA - :15@C {C-N-CX-C} Pk=0.27 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :14@C - :15@N - :15@CA - :15@C {C-N-CX-C} Pk=0.42 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 > :14@C - :15@N - :15@CA - :15@C {C-N-CT-C} Pk=0.8 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :14@C - :15@N - :15@CA - :15@C {C-N-CX-C} Pk=0.27 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 > :14@C - :15@N - :15@CA - :15@C {C-N-CT-C} Pk=0.85 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+< :14@C - :15@N - :15@CA - :15@C {C-N-CX-C} Pk=0.42 Pn=3 Phase=0 SCEE=1.2 SCNB=2
+< :14@C - :15@N - :15@CA - :15@C {C-N-CX-C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :14@C - :15@N - :15@CA - :15@CB {C-N-CT-CT} Pk=0.53 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :14@C - :15@N - :15@CA - :15@CB {C-N-CX-CT} Pk=2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 > :14@C - :15@N - :15@CA - :15@CB {C-N-CT-CT} Pk=0 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :14@C - :15@N - :15@CA - :15@CB {C-N-CX-CT} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :14@C - :15@N - :15@CA - :15@CB {C-N-CX-CT} Pk=1.8 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 > :14@C - :15@N - :15@CA - :15@CB {C-N-CT-CT} Pk=0.15 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
-> :14@C - :15@N - :15@CA - :15@CB {C-N-CT-CT} Pk=0.5 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
-> :14@C - :15@N - :15@CA - :15@CB {C-N-CT-CT} Pk=0.53 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 < :14@C - :15@N - :15@CA - :15@CB {C-N-CX-CT} Pk=0.8 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :14@C - :15@N - :15@CA - :15@CB {C-N-CX-CT} Pk=1.8 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :14@C - :15@N - :15@CA - :15@CB {C-N-CX-CT} Pk=2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :14@C - :15@N - :15@CA - :15@CB {C-N-CX-CT} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :14@C - :15@N - :15@CA - :15@CB {C-N-CT-CT} Pk=0.5 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
+< :15@CA - :15@CB - :15@CG - :15@ND1 {CX-CT-CC-NB} Pk=0.69 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 > :15@CA - :15@CB - :15@CG - :15@ND1 {CT-CT-CC-NB} Pk=0 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :15@CA - :15@CB - :15@CG - :15@ND1 {CX-CT-CC-NB} Pk=0.047 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
 < :15@CA - :15@CB - :15@CG - :15@ND1 {CX-CT-CC-NB} Pk=0.204 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :15@CA - :15@CB - :15@CG - :15@ND1 {CX-CT-CC-NB} Pk=0.69 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 < :15@CA - :15@CB - :15@CG - :15@ND1 {CX-CT-CC-NB} Pk=0.74 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :15@CG - :15@CB - :15@CA - :15@C {CC-CT-CX-C} Pk=0.025 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :15@CA - :15@CB - :15@CG - :15@ND1 {CX-CT-CC-NB} Pk=0.047 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
 < :15@CG - :15@CB - :15@CA - :15@C {CC-CT-CX-C} Pk=0.143 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
+< :15@CG - :15@CB - :15@CA - :15@C {CC-CT-CX-C} Pk=0.244 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :15@CG - :15@CB - :15@CA - :15@C {CC-CT-CT-C} Pk=0.155556 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 < :15@CG - :15@CB - :15@CA - :15@C {CC-CT-CX-C} Pk=0.219 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :15@CG - :15@CB - :15@CA - :15@C {CC-CT-CX-C} Pk=0.244 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
-< :15@N - :15@CA - :15@CB - :15@CG {N-CX-CT-CC} Pk=0.089 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :15@CG - :15@CB - :15@CA - :15@C {CC-CT-CX-C} Pk=0.025 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :15@N - :15@CA - :15@CB - :15@CG {N-CX-CT-CC} Pk=0.306 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
+< :15@N - :15@CA - :15@CB - :15@CG {N-CX-CT-CC} Pk=0.221 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :15@N - :15@CA - :15@CB - :15@CG {N-CT-CT-CC} Pk=0.155556 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 < :15@N - :15@CA - :15@CB - :15@CG {N-CX-CT-CC} Pk=0.219 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :15@N - :15@CA - :15@CB - :15@CG {N-CX-CT-CC} Pk=0.221 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
-< :15@N - :15@CA - :15@CB - :15@CG {N-CX-CT-CC} Pk=0.306 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
-< :15@CB - :15@CA - :15@C - :16@N {CT-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-> :15@CB - :15@CA - :15@C - :16@N {CT-CT-C-N} Pk=0.07 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-> :15@CB - :15@CA - :15@C - :16@N {CT-CT-C-N} Pk=0.1 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :15@N - :15@CA - :15@CB - :15@CG {N-CX-CT-CC} Pk=0.089 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :15@CB - :15@CA - :15@C - :16@N {CT-CX-C-N} Pk=0.2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+> :15@CB - :15@CA - :15@C - :16@N {CT-CT-C-N} Pk=0.07 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 < :15@CB - :15@CA - :15@C - :16@N {CT-CX-C-N} Pk=0.2 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 < :15@CB - :15@CA - :15@C - :16@N {CT-CX-C-N} Pk=0.4 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :15@N - :15@CA - :15@C - :16@N {N-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :15@CB - :15@CA - :15@C - :16@N {CT-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :15@CB - :15@CA - :15@C - :16@N {CT-CT-C-N} Pk=0.1 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :15@N - :15@CA - :15@C - :16@N {N-CX-C-N} Pk=0.45 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
-< :15@N - :15@CA - :15@C - :16@N {N-CX-C-N} Pk=0.55 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
-< :15@N - :15@CA - :15@C - :16@N {N-CX-C-N} Pk=1.58 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :15@N - :15@CA - :15@C - :16@N {N-CT-C-N} Pk=1.7 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
+< :15@N - :15@CA - :15@C - :16@N {N-CX-C-N} Pk=1.58 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :15@N - :15@CA - :15@C - :16@N {N-CT-C-N} Pk=2 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+< :15@N - :15@CA - :15@C - :16@N {N-CX-C-N} Pk=0.55 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
+< :15@N - :15@CA - :15@C - :16@N {N-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :15@C - :16@N - :16@CA - :16@C {C-N-CX-C} Pk=0 Pn=1 Phase=0 SCEE=1.2 SCNB=2
-< :15@C - :16@N - :16@CA - :16@C {C-N-CX-C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-< :15@C - :16@N - :16@CA - :16@C {C-N-CX-C} Pk=0.27 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :15@C - :16@N - :16@CA - :16@C {C-N-CX-C} Pk=0.42 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 > :15@C - :16@N - :16@CA - :16@C {C-N-CT-C} Pk=0.8 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :15@C - :16@N - :16@CA - :16@C {C-N-CX-C} Pk=0.27 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 > :15@C - :16@N - :16@CA - :16@C {C-N-CT-C} Pk=0.85 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+< :15@C - :16@N - :16@CA - :16@C {C-N-CX-C} Pk=0.42 Pn=3 Phase=0 SCEE=1.2 SCNB=2
+< :15@C - :16@N - :16@CA - :16@C {C-N-CX-C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :15@C - :16@N - :16@CA - :16@CB {C-N-CT-CT} Pk=0.53 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :15@C - :16@N - :16@CA - :16@CB {C-N-CX-CT} Pk=2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 > :15@C - :16@N - :16@CA - :16@CB {C-N-CT-CT} Pk=0 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :15@C - :16@N - :16@CA - :16@CB {C-N-CX-CT} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :15@C - :16@N - :16@CA - :16@CB {C-N-CX-CT} Pk=1.8 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 > :15@C - :16@N - :16@CA - :16@CB {C-N-CT-CT} Pk=0.15 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
-> :15@C - :16@N - :16@CA - :16@CB {C-N-CT-CT} Pk=0.5 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
-> :15@C - :16@N - :16@CA - :16@CB {C-N-CT-CT} Pk=0.53 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 < :15@C - :16@N - :16@CA - :16@CB {C-N-CX-CT} Pk=0.8 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :15@C - :16@N - :16@CA - :16@CB {C-N-CX-CT} Pk=1.8 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :15@C - :16@N - :16@CA - :16@CB {C-N-CX-CT} Pk=2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :15@C - :16@N - :16@CA - :16@CB {C-N-CX-CT} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :15@C - :16@N - :16@CA - :16@CB {C-N-CT-CT} Pk=0.5 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
 < :16@CA - :16@CB - :16@CG - :16@CD1 {CX-CT-C*-CW} Pk=0 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 < :16@CA - :16@CB - :16@CG - :16@CD1 {CX-CT-C*-CW} Pk=0 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 < :16@CA - :16@CB - :16@CG - :16@CD1 {CX-CT-C*-CW} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-> :16@CA - :16@CB - :16@CG - :16@CD2 {CT-CT-C*-CB} Pk=0 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :16@CA - :16@CB - :16@CG - :16@CD2 {CX-CT-C*-CB} Pk=0.095 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
 < :16@CA - :16@CB - :16@CG - :16@CD2 {CX-CT-C*-CB} Pk=0.365 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+> :16@CA - :16@CB - :16@CG - :16@CD2 {CT-CT-C*-CB} Pk=0 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 < :16@CA - :16@CB - :16@CG - :16@CD2 {CX-CT-C*-CB} Pk=0.408 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 < :16@CA - :16@CB - :16@CG - :16@CD2 {CX-CT-C*-CB} Pk=0.819 Pn=3 Phase=0 SCEE=1.2 SCNB=2
+< :16@CA - :16@CB - :16@CG - :16@CD2 {CX-CT-C*-CB} Pk=0.095 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
 < :16@CG - :16@CB - :16@CA - :16@C {C*-CT-CX-C} Pk=0.017 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
-< :16@CG - :16@CB - :16@CA - :16@C {C*-CT-CX-C} Pk=0.074 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :16@CG - :16@CB - :16@CA - :16@C {C*-CT-CX-C} Pk=0.353 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :16@CG - :16@CB - :16@CA - :16@C {C*-CT-CT-C} Pk=0.155556 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 < :16@CG - :16@CB - :16@CA - :16@C {C*-CT-CX-C} Pk=0.234 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :16@CG - :16@CB - :16@CA - :16@C {C*-CT-CX-C} Pk=0.353 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
-< :16@N - :16@CA - :16@CB - :16@CG {N-CX-CT-C*} Pk=0.031 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :16@CG - :16@CB - :16@CA - :16@C {C*-CT-CX-C} Pk=0.074 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :16@N - :16@CA - :16@CB - :16@CG {N-CX-CT-C*} Pk=0.079 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :16@N - :16@CA - :16@CB - :16@CG {N-CX-CT-C*} Pk=0.313 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :16@N - :16@CA - :16@CB - :16@CG {N-CT-CT-C*} Pk=0.155556 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 < :16@N - :16@CA - :16@CB - :16@CG {N-CX-CT-C*} Pk=0.234 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :16@N - :16@CA - :16@CB - :16@CG {N-CX-CT-C*} Pk=0.313 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
-< :16@CB - :16@CA - :16@C - :17@N {CT-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-> :16@CB - :16@CA - :16@C - :17@N {CT-CT-C-N} Pk=0.07 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-> :16@CB - :16@CA - :16@C - :17@N {CT-CT-C-N} Pk=0.1 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :16@N - :16@CA - :16@CB - :16@CG {N-CX-CT-C*} Pk=0.031 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :16@CB - :16@CA - :16@C - :17@N {CT-CX-C-N} Pk=0.2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+> :16@CB - :16@CA - :16@C - :17@N {CT-CT-C-N} Pk=0.07 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 < :16@CB - :16@CA - :16@C - :17@N {CT-CX-C-N} Pk=0.2 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 < :16@CB - :16@CA - :16@C - :17@N {CT-CX-C-N} Pk=0.4 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :16@N - :16@CA - :16@C - :17@N {N-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :16@CB - :16@CA - :16@C - :17@N {CT-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :16@CB - :16@CA - :16@C - :17@N {CT-CT-C-N} Pk=0.1 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :16@N - :16@CA - :16@C - :17@N {N-CX-C-N} Pk=0.45 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
-< :16@N - :16@CA - :16@C - :17@N {N-CX-C-N} Pk=0.55 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
-< :16@N - :16@CA - :16@C - :17@N {N-CX-C-N} Pk=1.58 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :16@N - :16@CA - :16@C - :17@N {N-CT-C-N} Pk=1.7 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
+< :16@N - :16@CA - :16@C - :17@N {N-CX-C-N} Pk=1.58 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :16@N - :16@CA - :16@C - :17@N {N-CT-C-N} Pk=2 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+< :16@N - :16@CA - :16@C - :17@N {N-CX-C-N} Pk=0.55 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
+< :16@N - :16@CA - :16@C - :17@N {N-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :16@C - :17@N - :17@CA - :17@C {C-N-CX-C} Pk=0 Pn=1 Phase=0 SCEE=1.2 SCNB=2
-< :16@C - :17@N - :17@CA - :17@C {C-N-CX-C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-< :16@C - :17@N - :17@CA - :17@C {C-N-CX-C} Pk=0.27 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :16@C - :17@N - :17@CA - :17@C {C-N-CX-C} Pk=0.42 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 > :16@C - :17@N - :17@CA - :17@C {C-N-CT-C} Pk=0.8 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :16@C - :17@N - :17@CA - :17@C {C-N-CX-C} Pk=0.27 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 > :16@C - :17@N - :17@CA - :17@C {C-N-CT-C} Pk=0.85 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+< :16@C - :17@N - :17@CA - :17@C {C-N-CX-C} Pk=0.42 Pn=3 Phase=0 SCEE=1.2 SCNB=2
+< :16@C - :17@N - :17@CA - :17@C {C-N-CX-C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :16@C - :17@N - :17@CA - :17@CB {C-N-CT-CT} Pk=0.53 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :16@C - :17@N - :17@CA - :17@CB {C-N-CX-2C} Pk=2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 > :16@C - :17@N - :17@CA - :17@CB {C-N-CT-CT} Pk=0 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :16@C - :17@N - :17@CA - :17@CB {C-N-CX-2C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :16@C - :17@N - :17@CA - :17@CB {C-N-CX-2C} Pk=1.8 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 > :16@C - :17@N - :17@CA - :17@CB {C-N-CT-CT} Pk=0.15 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
-> :16@C - :17@N - :17@CA - :17@CB {C-N-CT-CT} Pk=0.5 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
-> :16@C - :17@N - :17@CA - :17@CB {C-N-CT-CT} Pk=0.53 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 < :16@C - :17@N - :17@CA - :17@CB {C-N-CX-2C} Pk=0.8 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :16@C - :17@N - :17@CA - :17@CB {C-N-CX-2C} Pk=1.8 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :16@C - :17@N - :17@CA - :17@CB {C-N-CX-2C} Pk=2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :16@C - :17@N - :17@CA - :17@CB {C-N-CX-2C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :16@C - :17@N - :17@CA - :17@CB {C-N-CT-CT} Pk=0.5 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
 < :17@CA - :17@CB - :17@CG - :17@OD1 {CX-2C-CO-O2} Pk=0 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 > :17@CA - :17@CB - :17@CG - :17@OD1 {CT-CT-C-O2} Pk=0 Pn=2 Phase=0 SCEE=1.2 SCNB=2
+< :17@CA - :17@CB - :17@CG - :17@OD1 {CX-2C-CO-O2} Pk=0.769 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 < :17@CA - :17@CB - :17@CG - :17@OD1 {CX-2C-CO-O2} Pk=0 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 < :17@CA - :17@CB - :17@CG - :17@OD1 {CX-2C-CO-O2} Pk=0.031 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
-< :17@CA - :17@CB - :17@CG - :17@OD1 {CX-2C-CO-O2} Pk=0.769 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 < :17@CA - :17@CB - :17@CG - :17@OD2 {CX-2C-CO-O2} Pk=0 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 > :17@CA - :17@CB - :17@CG - :17@OD2 {CT-CT-C-O2} Pk=0 Pn=2 Phase=0 SCEE=1.2 SCNB=2
+< :17@CA - :17@CB - :17@CG - :17@OD2 {CX-2C-CO-O2} Pk=0.769 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 < :17@CA - :17@CB - :17@CG - :17@OD2 {CX-2C-CO-O2} Pk=0 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 < :17@CA - :17@CB - :17@CG - :17@OD2 {CX-2C-CO-O2} Pk=0.031 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
-< :17@CA - :17@CB - :17@CG - :17@OD2 {CX-2C-CO-O2} Pk=0.769 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
-< :17@CG - :17@CB - :17@CA - :17@C {CO-2C-CX-C} Pk=0.058 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :17@CG - :17@CB - :17@CA - :17@C {CO-2C-CX-C} Pk=0.154 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-> :17@CG - :17@CB - :17@CA - :17@C {C-CT-CT-C} Pk=0.155556 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 < :17@CG - :17@CB - :17@CA - :17@C {CO-2C-CX-C} Pk=0.424 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 < :17@CG - :17@CB - :17@CA - :17@C {CO-2C-CX-C} Pk=0.459 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+< :17@CG - :17@CB - :17@CA - :17@C {CO-2C-CX-C} Pk=0.058 Pn=3 Phase=0 SCEE=1.2 SCNB=2
+> :17@CG - :17@CB - :17@CA - :17@C {C-CT-CT-C} Pk=0.155556 Pn=3 Phase=0 SCEE=1.2 SCNB=2
+< :17@CG - :17@CB - :17@CA - :17@C {CO-2C-CX-C} Pk=0.154 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :17@N - :17@CA - :17@CB - :17@CG {N-CX-2C-CO} Pk=2.154 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
+< :17@N - :17@CA - :17@CB - :17@CG {N-CX-2C-CO} Pk=0.647 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 < :17@N - :17@CA - :17@CB - :17@CG {N-CX-2C-CO} Pk=0.058 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :17@N - :17@CA - :17@CB - :17@CG {N-CX-2C-CO} Pk=0.089 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 > :17@N - :17@CA - :17@CB - :17@CG {N-CT-CT-C} Pk=0.155556 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :17@N - :17@CA - :17@CB - :17@CG {N-CX-2C-CO} Pk=0.647 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
-< :17@N - :17@CA - :17@CB - :17@CG {N-CX-2C-CO} Pk=2.154 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
-< :17@CB - :17@CA - :17@C - :18@N {2C-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-> :17@CB - :17@CA - :17@C - :18@N {CT-CT-C-N} Pk=0.07 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-> :17@CB - :17@CA - :17@C - :18@N {CT-CT-C-N} Pk=0.1 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :17@N - :17@CA - :17@CB - :17@CG {N-CX-2C-CO} Pk=0.089 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :17@CB - :17@CA - :17@C - :18@N {2C-CX-C-N} Pk=0.2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+> :17@CB - :17@CA - :17@C - :18@N {CT-CT-C-N} Pk=0.07 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 < :17@CB - :17@CA - :17@C - :18@N {2C-CX-C-N} Pk=0.2 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 < :17@CB - :17@CA - :17@C - :18@N {2C-CX-C-N} Pk=0.4 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :17@N - :17@CA - :17@C - :18@N {N-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :17@CB - :17@CA - :17@C - :18@N {2C-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :17@CB - :17@CA - :17@C - :18@N {CT-CT-C-N} Pk=0.1 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :17@N - :17@CA - :17@C - :18@N {N-CX-C-N} Pk=0.45 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
-< :17@N - :17@CA - :17@C - :18@N {N-CX-C-N} Pk=0.55 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
-< :17@N - :17@CA - :17@C - :18@N {N-CX-C-N} Pk=1.58 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :17@N - :17@CA - :17@C - :18@N {N-CT-C-N} Pk=1.7 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
+< :17@N - :17@CA - :17@C - :18@N {N-CX-C-N} Pk=1.58 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :17@N - :17@CA - :17@C - :18@N {N-CT-C-N} Pk=2 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+< :17@N - :17@CA - :17@C - :18@N {N-CX-C-N} Pk=0.55 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
+< :17@N - :17@CA - :17@C - :18@N {N-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :17@C - :18@N - :18@CA - :18@C {C-N-CX-C} Pk=0 Pn=1 Phase=0 SCEE=1.2 SCNB=2
-< :17@C - :18@N - :18@CA - :18@C {C-N-CX-C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-< :17@C - :18@N - :18@CA - :18@C {C-N-CX-C} Pk=0.27 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :17@C - :18@N - :18@CA - :18@C {C-N-CX-C} Pk=0.42 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 > :17@C - :18@N - :18@CA - :18@C {C-N-CT-C} Pk=0.8 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :17@C - :18@N - :18@CA - :18@C {C-N-CX-C} Pk=0.27 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 > :17@C - :18@N - :18@CA - :18@C {C-N-CT-C} Pk=0.85 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+< :17@C - :18@N - :18@CA - :18@C {C-N-CX-C} Pk=0.42 Pn=3 Phase=0 SCEE=1.2 SCNB=2
+< :17@C - :18@N - :18@CA - :18@C {C-N-CX-C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :17@C - :18@N - :18@CA - :18@CB {C-N-CT-CT} Pk=0.53 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :17@C - :18@N - :18@CA - :18@CB {C-N-CX-2C} Pk=2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 > :17@C - :18@N - :18@CA - :18@CB {C-N-CT-CT} Pk=0 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :17@C - :18@N - :18@CA - :18@CB {C-N-CX-2C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :17@C - :18@N - :18@CA - :18@CB {C-N-CX-2C} Pk=1.8 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 > :17@C - :18@N - :18@CA - :18@CB {C-N-CT-CT} Pk=0.15 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
-> :17@C - :18@N - :18@CA - :18@CB {C-N-CT-CT} Pk=0.5 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
-> :17@C - :18@N - :18@CA - :18@CB {C-N-CT-CT} Pk=0.53 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 < :17@C - :18@N - :18@CA - :18@CB {C-N-CX-2C} Pk=0.8 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :17@C - :18@N - :18@CA - :18@CB {C-N-CX-2C} Pk=1.8 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :17@C - :18@N - :18@CA - :18@CB {C-N-CX-2C} Pk=2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
-< :18@CA - :18@CB - :18@CG - :18@CD {CX-2C-2C-CO} Pk=0.056 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
-> :18@CA - :18@CB - :18@CG - :18@CD {CT-CT-CT-C} Pk=0.155556 Pn=3 Phase=0 SCEE=1.2 SCNB=2
+< :17@C - :18@N - :18@CA - :18@CB {C-N-CX-2C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :17@C - :18@N - :18@CA - :18@CB {C-N-CT-CT} Pk=0.5 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
+< :18@CA - :18@CB - :18@CG - :18@CD {CX-2C-2C-CO} Pk=1.367 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
 < :18@CA - :18@CB - :18@CG - :18@CD {CX-2C-2C-CO} Pk=0.222 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+> :18@CA - :18@CB - :18@CG - :18@CD {CT-CT-CT-C} Pk=0.155556 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 < :18@CA - :18@CB - :18@CG - :18@CD {CX-2C-2C-CO} Pk=0.608 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
-< :18@CA - :18@CB - :18@CG - :18@CD {CX-2C-2C-CO} Pk=1.367 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
+< :18@CA - :18@CB - :18@CG - :18@CD {CX-2C-2C-CO} Pk=0.056 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
 > :18@CB - :18@CG - :18@CD - :18@OE1 {CT-CT-C-O2} Pk=0 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :18@CB - :18@CG - :18@CD - :18@OE1 {2C-2C-CO-O2} Pk=0.064 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :18@CB - :18@CG - :18@CD - :18@OE1 {2C-2C-CO-O2} Pk=0.39 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+< :18@CB - :18@CG - :18@CD - :18@OE1 {2C-2C-CO-O2} Pk=0.064 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 > :18@CB - :18@CG - :18@CD - :18@OE2 {CT-CT-C-O2} Pk=0 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :18@CB - :18@CG - :18@CD - :18@OE2 {2C-2C-CO-O2} Pk=0.064 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :18@CB - :18@CG - :18@CD - :18@OE2 {2C-2C-CO-O2} Pk=0.39 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+< :18@CB - :18@CG - :18@CD - :18@OE2 {2C-2C-CO-O2} Pk=0.064 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :18@CG - :18@CB - :18@CA - :18@C {2C-2C-CX-C} Pk=0.421 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
+< :18@CG - :18@CB - :18@CA - :18@C {2C-2C-CX-C} Pk=0.393 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 < :18@CG - :18@CB - :18@CA - :18@C {2C-2C-CX-C} Pk=0.144 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :18@CG - :18@CB - :18@CA - :18@C {2C-2C-CX-C} Pk=0.145 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 > :18@CG - :18@CB - :18@CA - :18@C {CT-CT-CT-C} Pk=0.155556 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :18@CG - :18@CB - :18@CA - :18@C {2C-2C-CX-C} Pk=0.393 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
-< :18@CG - :18@CB - :18@CA - :18@C {2C-2C-CX-C} Pk=0.421 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
-< :18@N - :18@CA - :18@CB - :18@CG {N-CX-2C-2C} Pk=0.078 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :18@CG - :18@CB - :18@CA - :18@C {2C-2C-CX-C} Pk=0.145 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :18@N - :18@CA - :18@CB - :18@CG {N-CX-2C-2C} Pk=0.1 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
+< :18@N - :18@CA - :18@CB - :18@CG {N-CX-2C-2C} Pk=0.184 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 < :18@N - :18@CA - :18@CB - :18@CG {N-CX-2C-2C} Pk=0.144 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 > :18@N - :18@CA - :18@CB - :18@CG {N-CT-CT-CT} Pk=0.155556 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :18@N - :18@CA - :18@CB - :18@CG {N-CX-2C-2C} Pk=0.184 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
-< :18@CB - :18@CA - :18@C - :19@N {2C-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-> :18@CB - :18@CA - :18@C - :19@N {CT-CT-C-N} Pk=0.07 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-> :18@CB - :18@CA - :18@C - :19@N {CT-CT-C-N} Pk=0.1 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :18@N - :18@CA - :18@CB - :18@CG {N-CX-2C-2C} Pk=0.078 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :18@CB - :18@CA - :18@C - :19@N {2C-CX-C-N} Pk=0.2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+> :18@CB - :18@CA - :18@C - :19@N {CT-CT-C-N} Pk=0.07 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 < :18@CB - :18@CA - :18@C - :19@N {2C-CX-C-N} Pk=0.2 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 < :18@CB - :18@CA - :18@C - :19@N {2C-CX-C-N} Pk=0.4 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :18@N - :18@CA - :18@C - :19@N {N-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :18@CB - :18@CA - :18@C - :19@N {2C-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :18@CB - :18@CA - :18@C - :19@N {CT-CT-C-N} Pk=0.1 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :18@N - :18@CA - :18@C - :19@N {N-CX-C-N} Pk=0.45 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
-< :18@N - :18@CA - :18@C - :19@N {N-CX-C-N} Pk=0.55 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
-< :18@N - :18@CA - :18@C - :19@N {N-CX-C-N} Pk=1.58 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :18@N - :18@CA - :18@C - :19@N {N-CT-C-N} Pk=1.7 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
+< :18@N - :18@CA - :18@C - :19@N {N-CX-C-N} Pk=1.58 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :18@N - :18@CA - :18@C - :19@N {N-CT-C-N} Pk=2 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+< :18@N - :18@CA - :18@C - :19@N {N-CX-C-N} Pk=0.55 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
+< :18@N - :18@CA - :18@C - :19@N {N-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :18@C - :19@N - :19@CA - :19@C {C-N-CX-C} Pk=0 Pn=1 Phase=0 SCEE=1.2 SCNB=2
-< :18@C - :19@N - :19@CA - :19@C {C-N-CX-C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-< :18@C - :19@N - :19@CA - :19@C {C-N-CX-C} Pk=0.27 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :18@C - :19@N - :19@CA - :19@C {C-N-CX-C} Pk=0.42 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 > :18@C - :19@N - :19@CA - :19@C {C-N-CT-C} Pk=0.8 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :18@C - :19@N - :19@CA - :19@C {C-N-CX-C} Pk=0.27 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 > :18@C - :19@N - :19@CA - :19@C {C-N-CT-C} Pk=0.85 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+< :18@C - :19@N - :19@CA - :19@C {C-N-CX-C} Pk=0.42 Pn=3 Phase=0 SCEE=1.2 SCNB=2
+< :18@C - :19@N - :19@CA - :19@C {C-N-CX-C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :18@C - :19@N - :19@CA - :19@CB {C-N-CT-CT} Pk=0.53 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :18@C - :19@N - :19@CA - :19@CB {C-N-CX-2C} Pk=2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 > :18@C - :19@N - :19@CA - :19@CB {C-N-CT-CT} Pk=0 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :18@C - :19@N - :19@CA - :19@CB {C-N-CX-2C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :18@C - :19@N - :19@CA - :19@CB {C-N-CX-2C} Pk=1.8 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 > :18@C - :19@N - :19@CA - :19@CB {C-N-CT-CT} Pk=0.15 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
-> :18@C - :19@N - :19@CA - :19@CB {C-N-CT-CT} Pk=0.5 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
-> :18@C - :19@N - :19@CA - :19@CB {C-N-CT-CT} Pk=0.53 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 < :18@C - :19@N - :19@CA - :19@CB {C-N-CX-2C} Pk=0.8 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :18@C - :19@N - :19@CA - :19@CB {C-N-CX-2C} Pk=1.8 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :18@C - :19@N - :19@CA - :19@CB {C-N-CX-2C} Pk=2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
-< :19@CA - :19@CB - :19@CG - :19@ND2 {CX-2C-C-N} Pk=0.008 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-> :19@CA - :19@CB - :19@CG - :19@ND2 {CT-CT-C-N} Pk=0.07 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-> :19@CA - :19@CB - :19@CG - :19@ND2 {CT-CT-C-N} Pk=0.1 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-< :19@CA - :19@CB - :19@CG - :19@ND2 {CX-2C-C-N} Pk=0.301 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
-< :19@CA - :19@CB - :19@CG - :19@ND2 {CX-2C-C-N} Pk=0.485 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+< :18@C - :19@N - :19@CA - :19@CB {C-N-CX-2C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :18@C - :19@N - :19@CA - :19@CB {C-N-CT-CT} Pk=0.5 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
 < :19@CA - :19@CB - :19@CG - :19@ND2 {CX-2C-C-N} Pk=0.828 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
+> :19@CA - :19@CB - :19@CG - :19@ND2 {CT-CT-C-N} Pk=0.07 Pn=2 Phase=0 SCEE=1.2 SCNB=2
+< :19@CA - :19@CB - :19@CG - :19@ND2 {CX-2C-C-N} Pk=0.485 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+< :19@CA - :19@CB - :19@CG - :19@ND2 {CX-2C-C-N} Pk=0.301 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
+< :19@CA - :19@CB - :19@CG - :19@ND2 {CX-2C-C-N} Pk=0.008 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :19@CA - :19@CB - :19@CG - :19@ND2 {CT-CT-C-N} Pk=0.1 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :19@CA - :19@CB - :19@CG - :19@OD1 {CX-2C-C-O} Pk=0 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 > :19@CA - :19@CB - :19@CG - :19@OD1 {CT-CT-C-O} Pk=0 Pn=2 Phase=0 SCEE=1.2 SCNB=2
+< :19@CG - :19@CB - :19@CA - :19@C {C-2C-CX-C} Pk=1.046 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :19@CG - :19@CB - :19@CA - :19@C {C-2C-CX-C} Pk=0.303 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 < :19@CG - :19@CB - :19@CA - :19@C {C-2C-CX-C} Pk=0.033 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :19@CG - :19@CB - :19@CA - :19@C {C-2C-CX-C} Pk=0.107 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 > :19@CG - :19@CB - :19@CA - :19@C {C-CT-CT-C} Pk=0.155556 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :19@CG - :19@CB - :19@CA - :19@C {C-2C-CX-C} Pk=0.303 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
-< :19@CG - :19@CB - :19@CA - :19@C {C-2C-CX-C} Pk=1.046 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :19@CG - :19@CB - :19@CA - :19@C {C-2C-CX-C} Pk=0.107 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :19@N - :19@CA - :19@CB - :19@CG {N-CX-2C-C} Pk=0.688 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
+< :19@N - :19@CA - :19@CB - :19@CG {N-CX-2C-C} Pk=0.297 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 < :19@N - :19@CA - :19@CB - :19@CG {N-CX-2C-C} Pk=0.033 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :19@N - :19@CA - :19@CB - :19@CG {N-CX-2C-C} Pk=0.059 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 > :19@N - :19@CA - :19@CB - :19@CG {N-CT-CT-C} Pk=0.155556 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :19@N - :19@CA - :19@CB - :19@CG {N-CX-2C-C} Pk=0.297 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
-< :19@N - :19@CA - :19@CB - :19@CG {N-CX-2C-C} Pk=0.688 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
-< :19@CB - :19@CA - :19@C - :20@N {2C-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-> :19@CB - :19@CA - :19@C - :20@N {CT-CT-C-N} Pk=0.07 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-> :19@CB - :19@CA - :19@C - :20@N {CT-CT-C-N} Pk=0.1 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :19@N - :19@CA - :19@CB - :19@CG {N-CX-2C-C} Pk=0.059 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :19@CB - :19@CA - :19@C - :20@N {2C-CX-C-N} Pk=0.2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+> :19@CB - :19@CA - :19@C - :20@N {CT-CT-C-N} Pk=0.07 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 < :19@CB - :19@CA - :19@C - :20@N {2C-CX-C-N} Pk=0.2 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 < :19@CB - :19@CA - :19@C - :20@N {2C-CX-C-N} Pk=0.4 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :19@N - :19@CA - :19@C - :20@N {N-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :19@CB - :19@CA - :19@C - :20@N {2C-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :19@CB - :19@CA - :19@C - :20@N {CT-CT-C-N} Pk=0.1 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :19@N - :19@CA - :19@C - :20@N {N-CX-C-N} Pk=0.45 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
-< :19@N - :19@CA - :19@C - :20@N {N-CX-C-N} Pk=0.55 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
-< :19@N - :19@CA - :19@C - :20@N {N-CX-C-N} Pk=1.58 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :19@N - :19@CA - :19@C - :20@N {N-CT-C-N} Pk=1.7 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
+< :19@N - :19@CA - :19@C - :20@N {N-CX-C-N} Pk=1.58 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 > :19@N - :19@CA - :19@C - :20@N {N-CT-C-N} Pk=2 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+< :19@N - :19@CA - :19@C - :20@N {N-CX-C-N} Pk=0.55 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
+< :19@N - :19@CA - :19@C - :20@N {N-CX-C-N} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :19@C - :20@N - :20@CA - :20@C {C-N-CX-C} Pk=0 Pn=1 Phase=0 SCEE=1.2 SCNB=2
-< :19@C - :20@N - :20@CA - :20@C {C-N-CX-C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-< :19@C - :20@N - :20@CA - :20@C {C-N-CX-C} Pk=0.27 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :19@C - :20@N - :20@CA - :20@C {C-N-CX-C} Pk=0.42 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 > :19@C - :20@N - :20@CA - :20@C {C-N-CT-C} Pk=0.8 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :19@C - :20@N - :20@CA - :20@C {C-N-CX-C} Pk=0.27 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 > :19@C - :20@N - :20@CA - :20@C {C-N-CT-C} Pk=0.85 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+< :19@C - :20@N - :20@CA - :20@C {C-N-CX-C} Pk=0.42 Pn=3 Phase=0 SCEE=1.2 SCNB=2
+< :19@C - :20@N - :20@CA - :20@C {C-N-CX-C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :19@C - :20@N - :20@CA - :20@CB {C-N-CT-CT} Pk=0.53 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :19@C - :20@N - :20@CA - :20@CB {C-N-CX-2C} Pk=2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 > :19@C - :20@N - :20@CA - :20@CB {C-N-CT-CT} Pk=0 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :19@C - :20@N - :20@CA - :20@CB {C-N-CX-2C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :19@C - :20@N - :20@CA - :20@CB {C-N-CX-2C} Pk=1.8 Pn=2 Phase=0 SCEE=1.2 SCNB=2
 > :19@C - :20@N - :20@CA - :20@CB {C-N-CT-CT} Pk=0.15 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
-> :19@C - :20@N - :20@CA - :20@CB {C-N-CT-CT} Pk=0.5 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
-> :19@C - :20@N - :20@CA - :20@CB {C-N-CT-CT} Pk=0.53 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 < :19@C - :20@N - :20@CA - :20@CB {C-N-CX-2C} Pk=0.8 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :19@C - :20@N - :20@CA - :20@CB {C-N-CX-2C} Pk=1.8 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :19@C - :20@N - :20@CA - :20@CB {C-N-CX-2C} Pk=2 Pn=1 Phase=0 SCEE=1.2 SCNB=2
+< :19@C - :20@N - :20@CA - :20@CB {C-N-CX-2C} Pk=0 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+> :19@C - :20@N - :20@CA - :20@CB {C-N-CT-CT} Pk=0.5 Pn=4 Phase=3.14159 SCEE=1.2 SCNB=2
+< :20@CA - :20@CB - :20@CG - :20@CD {CX-2C-2C-C} Pk=0.196 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
 < :20@CA - :20@CB - :20@CG - :20@CD {CX-2C-2C-C} Pk=0.083 Pn=2 Phase=0 SCEE=1.2 SCNB=2
-< :20@CA - :20@CB - :20@CG - :20@CD {CX-2C-2C-C} Pk=0.138 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 > :20@CA - :20@CB - :20@CG - :20@CD {CT-CT-CT-C} Pk=0.155556 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :20@CA - :20@CB - :20@CG - :20@CD {CX-2C-2C-C} Pk=0.196 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
 < :20@CA - :20@CB - :20@CG - :20@CD {CX-2C-2C-C} Pk=0.412 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
-< :20@CB - :20@CG - :20@CD - :20@NE2 {2C-2C-C-N} Pk=0.042 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :20@CA - :20@CB - :20@CG - :20@CD {CX-2C-2C-C} Pk=0.138 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :20@CB - :20@CG - :20@CD - :20@NE2 {2C-2C-C-N} Pk=0.609 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
 > :20@CB - :20@CG - :20@CD - :20@NE2 {CT-CT-C-N} Pk=0.07 Pn=2 Phase=0 SCEE=1.2 SCNB=2
+< :20@CB - :20@CG - :20@CD - :20@NE2 {2C-2C-C-N} Pk=0.845 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 < :20@CB - :20@CG - :20@CD - :20@NE2 {2C-2C-C-N} Pk=0.085 Pn=3 Phase=3.14159 SCEE=1.2 SCNB=2
+< :20@CB - :20@CG - :20@CD - :20@NE2 {2C-2C-C-N} Pk=0.042 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 > :20@CB - :20@CG - :20@CD - :20@NE2 {CT-CT-C-N} Pk=0.1 Pn=4 Phase=0 SCEE=1.2 SCNB=2
-< :20@CB - :20@CG - :20@CD - :20@NE2 {2C-2C-C-N} Pk=0.609 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
-< :20@CB - :20@CG - :20@CD - :20@NE2 {2C-2C-C-N} Pk=0.845 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 < :20@CB - :20@CG - :20@CD - :20@OE1 {2C-2C-C-O} Pk=0 Pn=1 Phase=0 SCEE=1.2 SCNB=2
 > :20@CB - :20@CG - :20@CD - :20@OE1 {CT-CT-C-O} Pk=0 Pn=2 Phase=0 SCEE=1.2 SCNB=2
+< :20@CG - :20@CB - :20@CA - :20@C {2C-2C-CX-C} Pk=0.421 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
+< :20@CG - :20@CB - :20@CA - :20@C {2C-2C-CX-C} Pk=0.393 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 < :20@CG - :20@CB - :20@CA - :20@C {2C-2C-CX-C} Pk=0.144 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :20@CG - :20@CB - :20@CA - :20@C {2C-2C-CX-C} Pk=0.145 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 > :20@CG - :20@CB - :20@CA - :20@C {CT-CT-CT-C} Pk=0.155556 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :20@CG - :20@CB - :20@CA - :20@C {2C-2C-CX-C} Pk=0.393 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
-< :20@CG - :20@CB - :20@CA - :20@C {2C-2C-CX-C} Pk=0.421 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
-< :20@N - :20@CA - :20@CB - :20@CG {N-CX-2C-2C} Pk=0.078 Pn=4 Phase=0 SCEE=1.2 SCNB=2
+< :20@CG - :20@CB - :20@CA - :20@C {2C-2C-CX-C} Pk=0.145 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 < :20@N - :20@CA - :20@CB - :20@CG {N-CX-2C-2C} Pk=0.1 Pn=1 Phase=3.14159 SCEE=1.2 SCNB=2
+< :20@N - :20@CA - :20@CB - :20@CG {N-CX-2C-2C} Pk=0.184 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
 < :20@N - :20@CA - :20@CB - :20@CG {N-CX-2C-2C} Pk=0.144 Pn=3 Phase=0 SCEE=1.2 SCNB=2
 > :20@N - :20@CA - :20@CB - :20@CG {N-CT-CT-CT} Pk=0.155556 Pn=3 Phase=0 SCEE=1.2 SCNB=2
-< :20@N - :20@CA - :20@CB - :20@CG {N-CX-2C-2C} Pk=0.184 Pn=2 Phase=3.14159 SCEE=1.2 SCNB=2
+< :20@N - :20@CA - :20@CB - :20@CG {N-CX-2C-2C} Pk=0.078 Pn=4 Phase=0 SCEE=1.2 SCNB=2
 # Dihedral Parameters
 < Pk= 0  Pn= 1  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.001  Pn= 4  Phase= 3.14159  SCEE= 1.2  SCNB= 2
 < Pk= 0.006  Pn= 1  Phase= 3.14159  SCEE= 1.2  SCNB= 2
-< Pk= 0.006  Pn= 2  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.007  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.007  Pn= 4  Phase= 3.14159  SCEE= 1.2  SCNB= 2
-< Pk= 0.008  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
 < Pk= 0.012  Pn= 1  Phase= 3.14159  SCEE= 1.2  SCNB= 2
-< Pk= 0.012  Pn= 4  Phase= 3.14159  SCEE= 1.2  SCNB= 2
-< Pk= 0.013  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.016  Pn= 3  Phase= 0  SCEE= 1.2  SCNB= 2
 < Pk= 0.017  Pn= 1  Phase= 3.14159  SCEE= 1.2  SCNB= 2
-< Pk= 0.025  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.027  Pn= 2  Phase= 3.14159  SCEE= 1.2  SCNB= 2
-< Pk= 0.028  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.03  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.031  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.031  Pn= 4  Phase= 3.14159  SCEE= 1.2  SCNB= 2
-< Pk= 0.033  Pn= 3  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.033  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.042  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.047  Pn= 4  Phase= 3.14159  SCEE= 1.2  SCNB= 2
-< Pk= 0.048  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.048  Pn= 4  Phase= 3.14159  SCEE= 1.2  SCNB= 2
-< Pk= 0.053  Pn= 2  Phase= 0  SCEE= 1.2  SCNB= 2
 < Pk= 0.055  Pn= 1  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.056  Pn= 4  Phase= 3.14159  SCEE= 1.2  SCNB= 2
-< Pk= 0.057  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.058  Pn= 3  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.059  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.064  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.065  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.069  Pn= 2  Phase= 3.14159  SCEE= 1.2  SCNB= 2
-> Pk= 0.07  Pn= 2  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.073  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.074  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.075  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.077  Pn= 2  Phase= 3.14159  SCEE= 1.2  SCNB= 2
-< Pk= 0.078  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
 < Pk= 0.079  Pn= 1  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.079  Pn= 2  Phase= 3.14159  SCEE= 1.2  SCNB= 2
-< Pk= 0.083  Pn= 2  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.085  Pn= 3  Phase= 3.14159  SCEE= 1.2  SCNB= 2
-< Pk= 0.089  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
 < Pk= 0.092  Pn= 1  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.095  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.095  Pn= 4  Phase= 3.14159  SCEE= 1.2  SCNB= 2
-< Pk= 0.097  Pn= 4  Phase= 3.14159  SCEE= 1.2  SCNB= 2
 < Pk= 0.098  Pn= 1  Phase= 0  SCEE= 1.2  SCNB= 2
 < Pk= 0.1  Pn= 1  Phase= 3.14159  SCEE= 1.2  SCNB= 2
-> Pk= 0.1  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.107  Pn= 3  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.107  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.112  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.113  Pn= 3  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.115  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.119  Pn= 2  Phase= 3.14159  SCEE= 1.2  SCNB= 2
-< Pk= 0.129  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.138  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.142  Pn= 3  Phase= 0  SCEE= 1.2  SCNB= 2
 < Pk= 0.143  Pn= 1  Phase= 3.14159  SCEE= 1.2  SCNB= 2
-< Pk= 0.144  Pn= 2  Phase= 3.14159  SCEE= 1.2  SCNB= 2
-< Pk= 0.144  Pn= 3  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.145  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.148  Pn= 3  Phase= 0  SCEE= 1.2  SCNB= 2
-> Pk= 0.15  Pn= 3  Phase= 3.14159  SCEE= 1.2  SCNB= 2
 < Pk= 0.154  Pn= 1  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.154  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.156  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.16  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
 < Pk= 0.162  Pn= 1  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.179  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.184  Pn= 2  Phase= 3.14159  SCEE= 1.2  SCNB= 2
-< Pk= 0.19  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.192  Pn= 3  Phase= 0  SCEE= 1.2  SCNB= 2
 < Pk= 0.196  Pn= 1  Phase= 3.14159  SCEE= 1.2  SCNB= 2
 < Pk= 0.2  Pn= 1  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.2  Pn= 2  Phase= 0  SCEE= 1.2  SCNB= 2
 < Pk= 0.202  Pn= 1  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.204  Pn= 2  Phase= 0  SCEE= 1.2  SCNB= 2
 < Pk= 0.211  Pn= 1  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.247  Pn= 1  Phase= 3.14159  SCEE= 1.2  SCNB= 2
+< Pk= 0.269  Pn= 1  Phase= 3.14159  SCEE= 1.2  SCNB= 2
+< Pk= 0.306  Pn= 1  Phase= 3.14159  SCEE= 1.2  SCNB= 2
+< Pk= 0.31  Pn= 1  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.337  Pn= 1  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.365  Pn= 1  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.379  Pn= 1  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.406  Pn= 1  Phase= 3.14159  SCEE= 1.2  SCNB= 2
+< Pk= 0.417  Pn= 1  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.421  Pn= 1  Phase= 3.14159  SCEE= 1.2  SCNB= 2
+< Pk= 0.424  Pn= 1  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.447  Pn= 1  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.45  Pn= 1  Phase= 3.14159  SCEE= 1.2  SCNB= 2
+> Pk= 0.53  Pn= 1  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.609  Pn= 1  Phase= 3.14159  SCEE= 1.2  SCNB= 2
+< Pk= 0.643  Pn= 1  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.661  Pn= 1  Phase= 3.14159  SCEE= 1.2  SCNB= 2
+< Pk= 0.666  Pn= 1  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.674  Pn= 1  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.688  Pn= 1  Phase= 3.14159  SCEE= 1.2  SCNB= 2
+< Pk= 0.69  Pn= 1  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.697  Pn= 1  Phase= 3.14159  SCEE= 1.2  SCNB= 2
+< Pk= 0.706  Pn= 1  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.828  Pn= 1  Phase= 3.14159  SCEE= 1.2  SCNB= 2
+< Pk= 1.046  Pn= 1  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 1.367  Pn= 1  Phase= 3.14159  SCEE= 1.2  SCNB= 2
+> Pk= 1.7  Pn= 1  Phase= 3.14159  SCEE= 1.2  SCNB= 2
+< Pk= 2.154  Pn= 1  Phase= 3.14159  SCEE= 1.2  SCNB= 2
+< Pk= 0.006  Pn= 2  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.027  Pn= 2  Phase= 3.14159  SCEE= 1.2  SCNB= 2
+< Pk= 0.053  Pn= 2  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.069  Pn= 2  Phase= 3.14159  SCEE= 1.2  SCNB= 2
+> Pk= 0.07  Pn= 2  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.077  Pn= 2  Phase= 3.14159  SCEE= 1.2  SCNB= 2
+< Pk= 0.079  Pn= 2  Phase= 3.14159  SCEE= 1.2  SCNB= 2
+< Pk= 0.083  Pn= 2  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.119  Pn= 2  Phase= 3.14159  SCEE= 1.2  SCNB= 2
+< Pk= 0.144  Pn= 2  Phase= 3.14159  SCEE= 1.2  SCNB= 2
+< Pk= 0.184  Pn= 2  Phase= 3.14159  SCEE= 1.2  SCNB= 2
+< Pk= 0.2  Pn= 2  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.204  Pn= 2  Phase= 0  SCEE= 1.2  SCNB= 2
 < Pk= 0.216  Pn= 2  Phase= 3.14159  SCEE= 1.2  SCNB= 2
 < Pk= 0.218  Pn= 2  Phase= 3.14159  SCEE= 1.2  SCNB= 2
-< Pk= 0.219  Pn= 3  Phase= 0  SCEE= 1.2  SCNB= 2
 < Pk= 0.221  Pn= 2  Phase= 3.14159  SCEE= 1.2  SCNB= 2
 < Pk= 0.222  Pn= 2  Phase= 3.14159  SCEE= 1.2  SCNB= 2
-< Pk= 0.224  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.23  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.234  Pn= 3  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.236  Pn= 3  Phase= 0  SCEE= 1.2  SCNB= 2
 < Pk= 0.244  Pn= 2  Phase= 3.14159  SCEE= 1.2  SCNB= 2
 < Pk= 0.245  Pn= 2  Phase= 0  SCEE= 1.2  SCNB= 2
 < Pk= 0.246  Pn= 2  Phase= 3.14159  SCEE= 1.2  SCNB= 2
-< Pk= 0.247  Pn= 1  Phase= 3.14159  SCEE= 1.2  SCNB= 2
 < Pk= 0.251  Pn= 2  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.251  Pn= 3  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.252  Pn= 3  Phase= 0  SCEE= 1.2  SCNB= 2
 < Pk= 0.259  Pn= 2  Phase= 3.14159  SCEE= 1.2  SCNB= 2
-< Pk= 0.267  Pn= 3  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.269  Pn= 1  Phase= 3.14159  SCEE= 1.2  SCNB= 2
 < Pk= 0.27  Pn= 2  Phase= 0  SCEE= 1.2  SCNB= 2
 < Pk= 0.289  Pn= 2  Phase= 3.14159  SCEE= 1.2  SCNB= 2
 < Pk= 0.29  Pn= 2  Phase= 3.14159  SCEE= 1.2  SCNB= 2
 < Pk= 0.297  Pn= 2  Phase= 3.14159  SCEE= 1.2  SCNB= 2
-< Pk= 0.301  Pn= 3  Phase= 3.14159  SCEE= 1.2  SCNB= 2
 < Pk= 0.303  Pn= 2  Phase= 3.14159  SCEE= 1.2  SCNB= 2
-< Pk= 0.306  Pn= 1  Phase= 3.14159  SCEE= 1.2  SCNB= 2
-< Pk= 0.31  Pn= 1  Phase= 0  SCEE= 1.2  SCNB= 2
 < Pk= 0.313  Pn= 2  Phase= 3.14159  SCEE= 1.2  SCNB= 2
-< Pk= 0.315  Pn= 3  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.337  Pn= 1  Phase= 0  SCEE= 1.2  SCNB= 2
 < Pk= 0.337  Pn= 2  Phase= 3.14159  SCEE= 1.2  SCNB= 2
 < Pk= 0.353  Pn= 2  Phase= 3.14159  SCEE= 1.2  SCNB= 2
-< Pk= 0.365  Pn= 1  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.379  Pn= 1  Phase= 0  SCEE= 1.2  SCNB= 2
 < Pk= 0.39  Pn= 2  Phase= 3.14159  SCEE= 1.2  SCNB= 2
 < Pk= 0.393  Pn= 2  Phase= 3.14159  SCEE= 1.2  SCNB= 2
-< Pk= 0.4  Pn= 3  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.401  Pn= 3  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.406  Pn= 1  Phase= 3.14159  SCEE= 1.2  SCNB= 2
 < Pk= 0.408  Pn= 2  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.412  Pn= 3  Phase= 3.14159  SCEE= 1.2  SCNB= 2
-< Pk= 0.414  Pn= 3  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.417  Pn= 1  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.42  Pn= 3  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.421  Pn= 1  Phase= 3.14159  SCEE= 1.2  SCNB= 2
-< Pk= 0.424  Pn= 1  Phase= 0  SCEE= 1.2  SCNB= 2
 < Pk= 0.442  Pn= 2  Phase= 0  SCEE= 1.2  SCNB= 2
 < Pk= 0.444  Pn= 2  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.447  Pn= 1  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.45  Pn= 1  Phase= 3.14159  SCEE= 1.2  SCNB= 2
 < Pk= 0.459  Pn= 2  Phase= 3.14159  SCEE= 1.2  SCNB= 2
 < Pk= 0.469  Pn= 2  Phase= 3.14159  SCEE= 1.2  SCNB= 2
 < Pk= 0.485  Pn= 2  Phase= 3.14159  SCEE= 1.2  SCNB= 2
 < Pk= 0.486  Pn= 2  Phase= 3.14159  SCEE= 1.2  SCNB= 2
-> Pk= 0.5  Pn= 4  Phase= 3.14159  SCEE= 1.2  SCNB= 2
-> Pk= 0.53  Pn= 1  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.55  Pn= 3  Phase= 3.14159  SCEE= 1.2  SCNB= 2
-< Pk= 0.608  Pn= 3  Phase= 3.14159  SCEE= 1.2  SCNB= 2
-< Pk= 0.609  Pn= 1  Phase= 3.14159  SCEE= 1.2  SCNB= 2
 < Pk= 0.612  Pn= 2  Phase= 0  SCEE= 1.2  SCNB= 2
 < Pk= 0.62  Pn= 2  Phase= 3.14159  SCEE= 1.2  SCNB= 2
-< Pk= 0.643  Pn= 1  Phase= 0  SCEE= 1.2  SCNB= 2
 < Pk= 0.647  Pn= 2  Phase= 3.14159  SCEE= 1.2  SCNB= 2
-< Pk= 0.661  Pn= 1  Phase= 3.14159  SCEE= 1.2  SCNB= 2
-< Pk= 0.666  Pn= 1  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.674  Pn= 1  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.688  Pn= 1  Phase= 3.14159  SCEE= 1.2  SCNB= 2
-< Pk= 0.69  Pn= 1  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.697  Pn= 1  Phase= 3.14159  SCEE= 1.2  SCNB= 2
-< Pk= 0.706  Pn= 1  Phase= 0  SCEE= 1.2  SCNB= 2
 < Pk= 0.735  Pn= 2  Phase= 3.14159  SCEE= 1.2  SCNB= 2
-< Pk= 0.74  Pn= 3  Phase= 0  SCEE= 1.2  SCNB= 2
 < Pk= 0.769  Pn= 2  Phase= 3.14159  SCEE= 1.2  SCNB= 2
-< Pk= 0.8  Pn= 3  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.819  Pn= 3  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 0.828  Pn= 1  Phase= 3.14159  SCEE= 1.2  SCNB= 2
 < Pk= 0.845  Pn= 2  Phase= 3.14159  SCEE= 1.2  SCNB= 2
 > Pk= 0.85  Pn= 2  Phase= 3.14159  SCEE= 1.2  SCNB= 2
 < Pk= 0.883  Pn= 2  Phase= 3.14159  SCEE= 1.2  SCNB= 2
-< Pk= 1.046  Pn= 1  Phase= 0  SCEE= 1.2  SCNB= 2
-< Pk= 1.367  Pn= 1  Phase= 3.14159  SCEE= 1.2  SCNB= 2
 < Pk= 1.58  Pn= 2  Phase= 3.14159  SCEE= 1.2  SCNB= 2
-> Pk= 1.7  Pn= 1  Phase= 3.14159  SCEE= 1.2  SCNB= 2
 < Pk= 1.8  Pn= 2  Phase= 0  SCEE= 1.2  SCNB= 2
 < Pk= 2  Pn= 2  Phase= 0  SCEE= 1.2  SCNB= 2
 > Pk= 2  Pn= 2  Phase= 3.14159  SCEE= 1.2  SCNB= 2
-< Pk= 2.154  Pn= 1  Phase= 3.14159  SCEE= 1.2  SCNB= 2
 > Pk= 2.3  Pn= 2  Phase= 3.14159  SCEE= 1.2  SCNB= 2
+< Pk= 0.016  Pn= 3  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.033  Pn= 3  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.058  Pn= 3  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.085  Pn= 3  Phase= 3.14159  SCEE= 1.2  SCNB= 2
+< Pk= 0.107  Pn= 3  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.113  Pn= 3  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.142  Pn= 3  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.144  Pn= 3  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.148  Pn= 3  Phase= 0  SCEE= 1.2  SCNB= 2
+> Pk= 0.15  Pn= 3  Phase= 3.14159  SCEE= 1.2  SCNB= 2
+< Pk= 0.192  Pn= 3  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.219  Pn= 3  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.234  Pn= 3  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.236  Pn= 3  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.251  Pn= 3  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.252  Pn= 3  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.267  Pn= 3  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.301  Pn= 3  Phase= 3.14159  SCEE= 1.2  SCNB= 2
+< Pk= 0.315  Pn= 3  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.4  Pn= 3  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.401  Pn= 3  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.412  Pn= 3  Phase= 3.14159  SCEE= 1.2  SCNB= 2
+< Pk= 0.414  Pn= 3  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.42  Pn= 3  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.55  Pn= 3  Phase= 3.14159  SCEE= 1.2  SCNB= 2
+< Pk= 0.608  Pn= 3  Phase= 3.14159  SCEE= 1.2  SCNB= 2
+< Pk= 0.74  Pn= 3  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.8  Pn= 3  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.819  Pn= 3  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.001  Pn= 4  Phase= 3.14159  SCEE= 1.2  SCNB= 2
+< Pk= 0.007  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.007  Pn= 4  Phase= 3.14159  SCEE= 1.2  SCNB= 2
+< Pk= 0.008  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.012  Pn= 4  Phase= 3.14159  SCEE= 1.2  SCNB= 2
+< Pk= 0.013  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.025  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.028  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.03  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.031  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.031  Pn= 4  Phase= 3.14159  SCEE= 1.2  SCNB= 2
+< Pk= 0.033  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.042  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.047  Pn= 4  Phase= 3.14159  SCEE= 1.2  SCNB= 2
+< Pk= 0.048  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.048  Pn= 4  Phase= 3.14159  SCEE= 1.2  SCNB= 2
+< Pk= 0.056  Pn= 4  Phase= 3.14159  SCEE= 1.2  SCNB= 2
+< Pk= 0.057  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.059  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.064  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.065  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.073  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.074  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.075  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.078  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.089  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.095  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.095  Pn= 4  Phase= 3.14159  SCEE= 1.2  SCNB= 2
+< Pk= 0.097  Pn= 4  Phase= 3.14159  SCEE= 1.2  SCNB= 2
+> Pk= 0.1  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.107  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.112  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.115  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.129  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.138  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.145  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.154  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.156  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.16  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.179  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.19  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.224  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
+< Pk= 0.23  Pn= 4  Phase= 0  SCEE= 1.2  SCNB= 2
+> Pk= 0.5  Pn= 4  Phase= 3.14159  SCEE= 1.2  SCNB= 2

From 73b9235bedb32c5f56fef667d742b35aac0135db Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 17 Jul 2024 11:45:19 -0400
Subject: [PATCH 0823/1492] Make ring-bond intersection cutoffs part of the
 class

---
 src/StructureCheck.cpp | 22 +++++++++++-----------
 src/StructureCheck.h   |  3 +++
 2 files changed, 14 insertions(+), 11 deletions(-)

diff --git a/src/StructureCheck.cpp b/src/StructureCheck.cpp
index cfb7293986..4c2ffb8604 100644
--- a/src/StructureCheck.cpp
+++ b/src/StructureCheck.cpp
@@ -14,8 +14,15 @@
 StructureCheck::StructureCheck() :
   bondoffset_(1.15),
   bondMinOffset_(0.50),
-  nonbondcut2_(0.64), // 0.8^2
+  nonbondcut2_(0.64), // (0.8 Ang)^2
   plcut_(8.0),
+  ring_shortd2_(0.25), // Short ring-bond 0.5 Ang. distance cutoff
+  ring_dcut2_(1.562500), // 1.25 Ang. ring-bond distance cutoff
+  //ring_dcut2_(1.3225), // Initial 1.15 Ang. ring-bond distance cutoff
+  ring_acut_(1.1344640138), // 65 deg. ringvec-bondvec angle cutoff
+  //ring_acut_(1.0471975512), // 60 deg. ringvec-bondvec angle cutoff
+  //ring_acut_(0.174533), // 10 deg. angle cutoff
+  //ring_acut_(0.7853981634), // 45 deg. angle cutoff for ring_dcut2 > dist2 > ring_shortd2
   checkType_(NO_PL_1_MASK),
   debug_(0),
   bondcheck_(true),
@@ -257,13 +264,6 @@ int StructureCheck::CheckRings(Frame const& currentFrame, Cpptraj::Structure::Ri
 {
   int Nproblems = 0;
   problemAtoms_.clear();
-  //static const double ring_dcut2 = 1.3225; // Initial 1.15 Ang distance cutoff
-  static const double ring_shortd2 = 0.25; // Short 0.5 Ang distance cutoff
-  //static const double ring_acut = 1.0471975512; // 60 deg. Ang cutoff
-  static const double ring_acut = 1.1344640138; // 65 deg. Ang cutoff
-  //static const double ring_acut  = 0.174533; // 10 deg. angle cutoff
-  static const double ring_dcut2 = 1.562500; // 1.25 Ang distance cutoff
-/*  static const double ring_acut = 0.7853981634; // 45 deg. angle cutoff for ring_dcut2 > dist2 > ring_shortd2*/
   // Get all ring vectors
   typedef std::vector<Cpptraj::Structure::LeastSquaresPlane> Larray;
   Larray RingVecs;
@@ -313,11 +313,11 @@ int StructureCheck::CheckRings(Frame const& currentFrame, Cpptraj::Structure::Ri
         // Get the center distance
         Cpptraj::Structure::LeastSquaresPlane const& ringVec = RingVecs[jdx];
         double dist2 = DIST2_NoImage( vmid.Dptr(), ringVec.Cxyz().Dptr() );
-        if (dist2 < ring_dcut2) {
+        if (dist2 < ring_dcut2_) {
           bool ring_intersect = false;
           // Bond intersects ring if it meets the short cutoff or if the angle
           // between the bond and the ring normal is less than a cutoff.
-          if (dist2 < ring_shortd2) {
+          if (dist2 < ring_shortd2_) {
             mprintf("DEBUG: Bond %i - %i near ring %i (%f).",
                     ringBonds[idx].A1(), ringBonds[idx].A2(), jdx, sqrt(dist2));
             printRingAtoms(ringMask);
@@ -334,7 +334,7 @@ int StructureCheck::CheckRings(Frame const& currentFrame, Cpptraj::Structure::Ri
             if (ang_in_rad > Constants::PIOVER2)
               ang_in_rad = Constants::PI - ang_in_rad;
             mprintf("DEBUG:\t\tWrapped angle is %f deg.\n", Constants::RADDEG*ang_in_rad);
-            if (ang_in_rad < ring_acut) {
+            if (ang_in_rad < ring_acut_) {
               mprintf("DEBUG: Bond %i - %i near ring %i (%f) Ang= %f deg.",
                       ringBonds[idx].A1(), ringBonds[idx].A2(), jdx, sqrt(dist2),
                       Constants::RADDEG*ang_in_rad);
diff --git a/src/StructureCheck.h b/src/StructureCheck.h
index 3c53f2e0aa..0692067571 100644
--- a/src/StructureCheck.h
+++ b/src/StructureCheck.h
@@ -129,6 +129,9 @@ class StructureCheck {
     double bondMinOffset_;  ///< Report bonds less than Req - bondMinOffset_
     double nonbondcut2_;    ///< Report distance^2 less than nonbondcut2_
     double plcut_;          ///< Pairlist cutoff
+    double ring_shortd2_;   ///< Ring center to bond center short distance (Ang) cutoff squared.
+    double ring_dcut2_;     ///< Ring center to bond center distance (Ang) cutoff squared.
+    double ring_acut_;      ///< Ring perpendicular vector to bond vector angle cutoff (rad).
     CheckType checkType_;   ///< Type of atom overlap check
     int debug_;             ///< Debug level.
     bool bondcheck_;        ///< If true check bonds as well

From 14d6bb3650ede6036c67a7f029b9c651225a586d Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 17 Jul 2024 11:55:20 -0400
Subject: [PATCH 0824/1492] Add ring check options

---
 src/StructureCheck.cpp | 27 +++++++++++++++++++--------
 src/StructureCheck.h   |  4 +++-
 2 files changed, 22 insertions(+), 9 deletions(-)

diff --git a/src/StructureCheck.cpp b/src/StructureCheck.cpp
index 4c2ffb8604..502f72523e 100644
--- a/src/StructureCheck.cpp
+++ b/src/StructureCheck.cpp
@@ -26,6 +26,7 @@ StructureCheck::StructureCheck() :
   checkType_(NO_PL_1_MASK),
   debug_(0),
   bondcheck_(true),
+  ringcheck_(true),
   saveProblems_(false)
 {}
 
@@ -33,16 +34,24 @@ StructureCheck::StructureCheck() :
 int StructureCheck::SetOptions(bool imageOn, bool checkBonds, bool saveProblemsIn, int debugIn,
                                std::string const& mask1, std::string const& mask2,
                                double overlapCut, double bondLengthOffset, double bondMinOffset,
-                               double pairListCut)
+                               double pairListCut,
+                               bool checkRings, double ring_shortd, double ring_dcut, double ring_acut)
 {
   imageOpt_.InitImaging( imageOn );
   bondcheck_ = checkBonds;
+  ringcheck_ = checkRings;
   saveProblems_ = saveProblemsIn;
   debug_ = debugIn;
   bondoffset_ = bondLengthOffset;
   bondMinOffset_ = bondMinOffset;
   nonbondcut2_ = overlapCut * overlapCut; // Save cutoff squared.
   plcut_ = pairListCut;
+  if (ring_shortd > 0)
+    ring_shortd2_ = ring_shortd * ring_shortd;
+  if (ring_dcut > 0)
+    ring_dcut2_ = ring_dcut * ring_dcut;
+  if (ring_acut > 0)
+    ring_acut_ = ring_acut;
   if (Mask1_.SetMaskString( mask1 )) return 1;
   if (!mask2.empty()) {
     if (Mask2_.SetMaskString( mask2 )) return 1;
@@ -114,7 +123,7 @@ int StructureCheck::Setup(Topology const& topIn, Box const& boxIn)
   }
   checkType_ = NO_PL_1_MASK;
   // Set up bonds if specified.
-  if (bondcheck_) SetupBondList(Mask1_, topIn);
+  if (bondcheck_ || ringcheck_) SetupBondList(Mask1_, topIn);
   // Set up second mask if specified.
   if ( Mask2_.MaskStringSet() ) {
     if (topIn.SetupIntegerMask( Mask2_ ) ) return 1;
@@ -134,7 +143,7 @@ int StructureCheck::Setup(Topology const& topIn, Box const& boxIn)
       OuterMask_ = Mask1_;
       InnerMask_ = Mask2_;
     }
-    if (bondcheck_) SetupBondList(Mask2_, topIn);
+    if (bondcheck_ || ringcheck_) SetupBondList(Mask2_, topIn);
     checkType_ = NO_PL_2_MASKS;
   }
   // Check if pairlist should be used.
@@ -183,13 +192,15 @@ int StructureCheck::Setup(Topology const& topIn, Box const& boxIn)
   } else
     mprintf("\tNot using exclusions.\n");
   // Sort bond list
-  if (bondcheck_) std::sort(bondList_.begin(), bondList_.end());
+  if (bondcheck_ || ringcheck_) std::sort(bondList_.begin(), bondList_.end());
   // Find rings
-  if (rings_.SetupRingFinder(topIn, Mask1_)) {
-    mprinterr("Error: Could not set up ring finder.\n");
-    return 1;
+  if (ringcheck_) {
+    if (rings_.SetupRingFinder(topIn, Mask1_)) {
+      mprinterr("Error: Could not set up ring finder.\n");
+      return 1;
+    }
+    if (debug_ > 0) rings_.PrintRings(topIn);
   }
-  if (debug_ > 0) rings_.PrintRings(topIn);
 
   return 0;
 }
diff --git a/src/StructureCheck.h b/src/StructureCheck.h
index 0692067571..5af7877a52 100644
--- a/src/StructureCheck.h
+++ b/src/StructureCheck.h
@@ -28,7 +28,7 @@ class StructureCheck {
     StructureCheck();
     /// Options: imageOn, checkBonds, saveProblems, debug, mask1, mask2, ovrlpCut, bndLenOffset, minBndLenOffset, PListCut
     int SetOptions(bool, bool, bool, int, std::string const&, std::string const&,
-                   double, double, double, double);
+                   double, double, double, double, bool, double, double, double);
     /// Setup for given topology and box.
     int Setup(Topology const&, Box const&);
     /// \return Number of abnormal bonds.
@@ -43,6 +43,7 @@ class StructureCheck {
     AtomMask const& Mask2()     const { return Mask2_; }
     ImageOption const& ImageOpt() const { return imageOpt_; }
     bool CheckBonds()           const { return bondcheck_; }
+    bool CheckRings()           const { return ringcheck_; }
     double BondOffset()         const { return bondoffset_; }
     double BondMinOffset()      const { return bondMinOffset_; }
     double NonBondCut2()        const { return nonbondcut2_; }
@@ -135,6 +136,7 @@ class StructureCheck {
     CheckType checkType_;   ///< Type of atom overlap check
     int debug_;             ///< Debug level.
     bool bondcheck_;        ///< If true check bonds as well
+    bool ringcheck_;        ///< If true check bond/ring intersections
     bool saveProblems_;     ///< If true save problems in problemAtoms_
 };
 #endif

From 5c7e3f536eeff36edcbe169325c93dac749e5797 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 17 Jul 2024 12:10:38 -0400
Subject: [PATCH 0825/1492] Set and report ring cutoffs

---
 src/Action_CheckStructure.cpp | 19 ++++++++++++++++---
 src/Exec_PermuteDihedrals.cpp |  7 +++++--
 src/StructureCheck.cpp        | 15 +++++++++++++++
 src/StructureCheck.h          |  5 ++++-
 4 files changed, 40 insertions(+), 6 deletions(-)

diff --git a/src/Action_CheckStructure.cpp b/src/Action_CheckStructure.cpp
index 72a1d8431b..b98578f093 100644
--- a/src/Action_CheckStructure.cpp
+++ b/src/Action_CheckStructure.cpp
@@ -62,7 +62,11 @@ Action::RetType Action_CheckStructure::Init(ArgList& actionArgs, ActionInit& ini
     nonbondcut,
     actionArgs.getKeyDouble("offset",1.15),
     actionArgs.getKeyDouble("minoffset", 0.5),
-    plcut
+    plcut,
+    !actionArgs.hasKey("noringcheck"),
+    actionArgs.getKeyDouble("ringshortdist", 0), // 0 means use StructureCheck default
+    actionArgs.getKeyDouble("ringdcut", 0),      // 0 means use StructureCheck default
+    actionArgs.getKeyDouble("ringacut", 0)       // 0 means use StructureCheck default
   );
   if (err != 0) return Action::ERR;
   // Remaining keywords
@@ -110,12 +114,21 @@ Action::RetType Action_CheckStructure::Init(ArgList& actionArgs, ActionInit& ini
     mprintf("\tNumber of problems each frame will be written to '%s'\n",
             dfile->DataFilename().full());
   if (!check_.CheckBonds())
-    mprintf("\tChecking inter-atomic distances only.\n");
+    mprintf("\tNot checking bond lengths.\n");
   else
     mprintf("\tChecking for bond lengths greater than eq. length + %.2f Ang and\n"
             "\t  less than eq. length - %.2f Ang.\n", check_.BondOffset(),
             check_.BondMinOffset());
-    
+  if (!check_.CheckRings())
+    mprintf("\tNot checking for bond-ring intersections.\n");
+  else {
+    mprintf("\tChecking for bond-ring intersections.\n");
+    mprintf("\t  Ring center to bond center distance < %g Ang. is considered intersecting.\n",
+            check_.RingShortDist());
+    mprintf("\t  Ring center to bond center distance < %g Ang. is considered intersecting\n"
+            "\t    if the angle between the bond and perpendicular ring vectors is < %g deg.\n",
+            check_.RingDist(), check_.RingAngleCut_Deg());
+  }
   mprintf("\tChecking for inter-atomic distances < %.2f Ang.\n",
           nonbondcut);
   if (skipBadFrames_) {
diff --git a/src/Exec_PermuteDihedrals.cpp b/src/Exec_PermuteDihedrals.cpp
index 0e7dc87fc5..0ce838da3b 100644
--- a/src/Exec_PermuteDihedrals.cpp
+++ b/src/Exec_PermuteDihedrals.cpp
@@ -206,8 +206,11 @@ Exec::RetType Exec_PermuteDihedrals::Execute(CpptrajState& State, ArgList& argIn
     rescutoff_ *= rescutoff_;
     // Increment backtrack by 1 since we need to skip over current res
     ++backtrack_;
-    // Initialize CheckStructure
-    if (checkStructure_.SetOptions( imageOn, checkRings_, false, State.Debug(), "*", "", 0.8, 1.15, 0.5, -1 )) {
+    // Initialize CheckStructure. The last 3 args being 0 means use defaults
+    // for the ring check.
+    if (checkStructure_.SetOptions( imageOn, checkRings_, false, State.Debug(), "*", "", 0.8, 1.15, 0.5, -1,
+                                    checkRings_, 0, 0, 0 ))
+    {
       mprinterr("Error: Could not set up structure check.\n");
       return CpptrajState::ERR;
     }
diff --git a/src/StructureCheck.cpp b/src/StructureCheck.cpp
index 502f72523e..83706c2396 100644
--- a/src/StructureCheck.cpp
+++ b/src/StructureCheck.cpp
@@ -30,6 +30,21 @@ StructureCheck::StructureCheck() :
   saveProblems_(false)
 {}
 
+/** \return Ring-bond short distance cutoff in Ang. */
+double StructureCheck::RingShortDist() const {
+  return sqrt(ring_shortd2_);
+}
+
+/** \return Ring-bond distance cutoff in Ang. */
+double StructureCheck::RingDist() const {
+  return sqrt(ring_dcut2_);
+}
+
+/** \return Ring vector-bond vector angle cutoff in degrees. */
+double StructureCheck::RingAngleCut_Deg() const {
+  return ring_acut_ * Constants::RADDEG;
+}
+
 // StructureCheck::SetOptions()
 int StructureCheck::SetOptions(bool imageOn, bool checkBonds, bool saveProblemsIn, int debugIn,
                                std::string const& mask1, std::string const& mask2,
diff --git a/src/StructureCheck.h b/src/StructureCheck.h
index 5af7877a52..d35258fa46 100644
--- a/src/StructureCheck.h
+++ b/src/StructureCheck.h
@@ -43,9 +43,12 @@ class StructureCheck {
     AtomMask const& Mask2()     const { return Mask2_; }
     ImageOption const& ImageOpt() const { return imageOpt_; }
     bool CheckBonds()           const { return bondcheck_; }
-    bool CheckRings()           const { return ringcheck_; }
     double BondOffset()         const { return bondoffset_; }
     double BondMinOffset()      const { return bondMinOffset_; }
+    bool CheckRings()           const { return ringcheck_; }
+    double RingShortDist() const;
+    double RingDist() const;
+    double RingAngleCut_Deg() const;
     double NonBondCut2()        const { return nonbondcut2_; }
     double PairListCut()        const { return plcut_; }
     unsigned int Nbonds()       const { return bondList_.size(); }

From dccc4dcbc020f52a40355a3c19e100a40da9eada Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 17 Jul 2024 12:14:32 -0400
Subject: [PATCH 0826/1492] Update help

---
 src/Action_CheckStructure.cpp | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/src/Action_CheckStructure.cpp b/src/Action_CheckStructure.cpp
index b98578f093..5c956960ef 100644
--- a/src/Action_CheckStructure.cpp
+++ b/src/Action_CheckStructure.cpp
@@ -21,6 +21,8 @@ void Action_CheckStructure::Help() const {
   mprintf("\t[<mask>] [around <mask2>] [reportfile <report>] [noimage]\n"
           "\t[skipbadframes] [offset <offset>] [minoffset <minoffset>]\n"
           "\t[cut <cut>] [nobondcheck] [silent] [plcut <cut>]\n"
+          "\t[{noringcheck | [ringshortdist <rsdist>] [ringdcut <ringdcut>]\n"
+          "\t                [ringacut <ringacut>]}]\n"
           "  Check atoms in <mask> for atomic overlaps less than <cut> (default 0.8 Ang)\n"
           "  and unusual bond lengths greater than equilibrium length + <offset>\n"
           "  (default 1.15 Ang) or less than equilibrium length - <minoffset>\n"
@@ -29,6 +31,11 @@ void Action_CheckStructure::Help() const {
           "  specified a pair list will be used to speed up the calculation. The\n"
           "  cutoff used to build the pair list can be adjusted with 'plcut'\n"
           "  (default 4.0 Ang. or <cut>, whichever is greater).\n"
+          "  Check for ring-bond intersections unless 'noringcheck' is specified.\n"
+          "  Ring-bond intersections are detected when the ring center to bond\n"
+          "  center is less than <rsdist>, or less than <ringdcut> and the angle\n"
+          "  between the bond vector and ring perpendicular vector is less than\n"
+          "  <ringacut>.\n"
           "  Warnings will go to the file specified by 'reportfile', STDOUT,\n"
           "  or will be suppressed if 'silent' is specified. If 'skipbadframes'\n"
           "  is specified, subsequent Actions will be skipped if any problems\n"

From 00866f8cc3dc0eae8a27953619ff647756ba26a5 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 17 Jul 2024 12:19:51 -0400
Subject: [PATCH 0827/1492] Angle cutoff needs to be converted to radians

---
 src/StructureCheck.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/StructureCheck.cpp b/src/StructureCheck.cpp
index 83706c2396..8dceb9b26f 100644
--- a/src/StructureCheck.cpp
+++ b/src/StructureCheck.cpp
@@ -66,7 +66,7 @@ int StructureCheck::SetOptions(bool imageOn, bool checkBonds, bool saveProblemsI
   if (ring_dcut > 0)
     ring_dcut2_ = ring_dcut * ring_dcut;
   if (ring_acut > 0)
-    ring_acut_ = ring_acut;
+    ring_acut_ = ring_acut * Constants::DEGRAD;
   if (Mask1_.SetMaskString( mask1 )) return 1;
   if (!mask2.empty()) {
     if (Mask2_.SetMaskString( mask2 )) return 1;

From 430cffd3f57440bbcc0d5bcd6d7662f8a3757f99 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 17 Jul 2024 12:23:12 -0400
Subject: [PATCH 0828/1492] Update manual with ring options for check

---
 doc/cpptraj.lyx | 65 ++++++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 64 insertions(+), 1 deletion(-)

diff --git a/doc/cpptraj.lyx b/doc/cpptraj.lyx
index d25940dc18..43487d9f9e 100644
--- a/doc/cpptraj.lyx
+++ b/doc/cpptraj.lyx
@@ -25126,6 +25126,14 @@ check
 
 \end_layout
 
+\begin_layout LyX-Code
+       [{noringcheck | [ringshortdist <rsdist>] [ringdcut <ringdcut>]
+\end_layout
+
+\begin_layout LyX-Code
+                       [ringacut <ringacut>]}]
+\end_layout
+
 \begin_deeper
 \begin_layout Description
 [<mask>] Check structure of atoms in <mask> (all if not specified).
@@ -25202,9 +25210,50 @@ skipbadframes
  only matters if box is present.
 \end_layout
 
+\begin_layout Description
+[noringcheck] If specified,
+ do not check for ring-bond intersections.
+\end_layout
+
+\begin_layout Description
+[ringshortdist
+\begin_inset space ~
+\end_inset
+
+<rsdist>] Report ring-bond intersection when ring to bond center distance is less than 
+\series bold
+<rsdist>
+\series default
+ (default 0.5 Ang).
+\end_layout
+
+\begin_layout Description
+[ringdcut
+\begin_inset space ~
+\end_inset
+
+<ringdcut>]
+\begin_inset space ~
+\end_inset
+
+[ringacut
+\begin_inset space ~
+\end_inset
+
+<ringacut>] Report ring-bond intersection when ring to bond center distance is less than 
+\series bold
+<ringdcut>
+\series default
+ (default 1.25 Ang.) and the angle between the bond vector and perpendicular ring vector is less than 
+\series bold
+<ringacut>
+\series default
+ (default 65 degrees).
+\end_layout
+
 \end_deeper
 \begin_layout Standard
-Check the structure and report problems related to atomic overlap/unusual bond length.
+Check the structure and report problems related to atomic overlap/unusual bond length/ring-bond intersections.
  Problems are reported when any two atoms in 
 \series bold
 <mask>
@@ -25240,6 +25289,20 @@ Check the structure and report problems related to atomic overlap/unusual bond l
 <minoffset>
 \series default
  are reported as well.
+ If ring-bond intersections are being checked for they will be reported when the ring center to bond center is less than 
+\series bold
+<rsdist>
+\series default
+,
+ or less than 
+\series bold
+<ringdcut>
+\series default
+ and the angle between the bond vector and ring perpendicular vector is less than 
+\series bold
+<ringacut>
+\series default
+.
  If box information is present and not using the 
 \series bold
 'around'

From 1ef39df2c7c24ea50efb496e9054cde7e5c2e216 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 17 Jul 2024 13:16:16 -0400
Subject: [PATCH 0829/1492] Add separate ring bond check function

---
 src/StructureCheck.cpp | 52 ++++++++++++++++++++++++++++++++++++++++++
 src/StructureCheck.h   |  9 ++++++++
 2 files changed, 61 insertions(+)

diff --git a/src/StructureCheck.cpp b/src/StructureCheck.cpp
index 8dceb9b26f..b763c66c03 100644
--- a/src/StructureCheck.cpp
+++ b/src/StructureCheck.cpp
@@ -285,6 +285,58 @@ static inline void printRingAtoms(AtomMask const& maskIn) {
     mprintf(" %i", *it);
 }
 
+/** Check ring and bond */
+void StructureCheck::ring_bond_check(int& Nproblems,
+                                     double dist2, Btype const& bnd, Vec3 const& vbond,
+                                     AtomMask const& ringMask,
+                                     Cpptraj::Structure::LeastSquaresPlane const& ringVec)
+{
+  bool ring_intersect = false;
+  // Bond intersects ring if it meets the short cutoff or if the angle
+  // between the bond and the ring normal is less than a cutoff.
+  if (dist2 < ring_shortd2_) {
+    mprintf("DEBUG: Bond %i - %i near ring (%f).",
+            bnd.A1(), bnd.A2(), sqrt(dist2));
+    printRingAtoms(ringMask);
+    mprintf("\n");
+    ring_intersect = true;
+  } else {
+    mprintf("DEBUG: Bond %i - %i near ring (%f), doing angle check.",
+            bnd.A1(), bnd.A2(), sqrt(dist2));
+    printRingAtoms(ringMask);
+    mprintf("\n");
+    // Get the angle
+    double ang_in_rad = vbond.Angle( ringVec.Nxyz() );
+    // Wrap the angle between 0-90 degrees
+    if (ang_in_rad > Constants::PIOVER2)
+      ang_in_rad = Constants::PI - ang_in_rad;
+    mprintf("DEBUG:\t\tWrapped angle is %f deg.\n", Constants::RADDEG*ang_in_rad);
+    if (ang_in_rad < ring_acut_) {
+      mprintf("DEBUG: Bond %i - %i near ring (%f) Ang= %f deg.",
+              bnd.A1(), bnd.A2(), sqrt(dist2),
+              Constants::RADDEG*ang_in_rad);
+      //printRingAtoms(ringMask);
+      mprintf("\n");
+      ring_intersect = true;
+    }
+  }
+  if (ring_intersect) {
+    mprintf("DEBUG: Bond intersects ring.\n");
+    ++Nproblems;
+    if (saveProblems_) {
+      // Do not use constructor since we do not want to sort atoms
+      Problem newProb;
+      newProb.SetProb( bnd.A1(), ringMask.back(), sqrt(dist2) );
+#     ifdef _OPENMP
+      thread_problemAtoms_[mythread]
+#     else
+      problemAtoms_
+#     endif
+        .push_back( newProb );
+    }
+  } // END angle cutoff satisfied
+}
+
 /** Check if any bonds are passing through rings. */
 int StructureCheck::CheckRings(Frame const& currentFrame, Cpptraj::Structure::RingFinder const& rings, std::vector<Btype> const& ringBonds)
 {
diff --git a/src/StructureCheck.h b/src/StructureCheck.h
index d35258fa46..c562884122 100644
--- a/src/StructureCheck.h
+++ b/src/StructureCheck.h
@@ -9,6 +9,11 @@
 // Forward declares
 class Topology;
 class CharMask;
+namespace Cpptraj {
+namespace Structure {
+class LeastSquaresPlane;
+}
+}
 /// Used to count potential structure problems.
 class StructureCheck {
   public:
@@ -37,6 +42,7 @@ class StructureCheck {
     int CheckOverlaps(Frame const&);
     /// Check if any bonds are passing through rings.
     int CheckRings(Frame const&);
+    /// Check if any of the given bonds are passing through given rings.
     int CheckRings(Frame const&, Cpptraj::Structure::RingFinder const&, std::vector<Btype> const&);
 
     AtomMask const& Mask1()     const { return Mask1_; }
@@ -102,6 +108,9 @@ class StructureCheck {
     void ProcessBondArray(BondArray const&, BondParmArray const&, CharMask const&);
     /// Add selected bonds in topology to list to be checked.
     void SetupBondList(AtomMask const&, Topology const&);
+    /// Check for intersection between bond and ring
+    void ring_bond_check(int&, double, Btype const&, Vec3 const&, AtomMask const&,
+                         Cpptraj::Structure::LeastSquaresPlane const&);
     /// PairList version of CheckOverlap, 1 mask
     int PL1_CheckOverlap(Frame const&);
     /// Non-pairlist version of CheckOverlap, 1 mask

From 7857dda6649bb77f1723a3ab7d118a0ed904c07f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 17 Jul 2024 13:32:41 -0400
Subject: [PATCH 0830/1492] Use the new bond ring intersection check function

---
 src/StructureCheck.cpp | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/StructureCheck.cpp b/src/StructureCheck.cpp
index b763c66c03..d5c78eeba2 100644
--- a/src/StructureCheck.cpp
+++ b/src/StructureCheck.cpp
@@ -392,6 +392,8 @@ int StructureCheck::CheckRings(Frame const& currentFrame, Cpptraj::Structure::Ri
         Cpptraj::Structure::LeastSquaresPlane const& ringVec = RingVecs[jdx];
         double dist2 = DIST2_NoImage( vmid.Dptr(), ringVec.Cxyz().Dptr() );
         if (dist2 < ring_dcut2_) {
+          ring_bond_check(Nproblems, dist2, ringBonds[idx], vbond, ringMask, ringVec);
+/*
           bool ring_intersect = false;
           // Bond intersects ring if it meets the short cutoff or if the angle
           // between the bond and the ring normal is less than a cutoff.
@@ -436,6 +438,7 @@ int StructureCheck::CheckRings(Frame const& currentFrame, Cpptraj::Structure::Ri
                 .push_back( newProb );
             }
           } // END angle cutoff satisfied
+*/
         } // END distance cutoff satisfied
       } // END both bond atoms are not part of this ring
     } // END loop over rings

From 923af18e9d46af9f8e63222be0e04fd855bbef7f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 17 Jul 2024 14:10:07 -0400
Subject: [PATCH 0831/1492] Fix openmp compile

---
 src/StructureCheck.cpp | 12 ++++++++++--
 src/StructureCheck.h   |  6 +++++-
 2 files changed, 15 insertions(+), 3 deletions(-)

diff --git a/src/StructureCheck.cpp b/src/StructureCheck.cpp
index d5c78eeba2..6a7f1a7fbf 100644
--- a/src/StructureCheck.cpp
+++ b/src/StructureCheck.cpp
@@ -289,7 +289,11 @@ static inline void printRingAtoms(AtomMask const& maskIn) {
 void StructureCheck::ring_bond_check(int& Nproblems,
                                      double dist2, Btype const& bnd, Vec3 const& vbond,
                                      AtomMask const& ringMask,
-                                     Cpptraj::Structure::LeastSquaresPlane const& ringVec)
+                                     Cpptraj::Structure::LeastSquaresPlane const& ringVec
+#                                    ifdef _OPENMP
+                                     , int mythread
+#                                    endif
+                                    )
 {
   bool ring_intersect = false;
   // Bond intersects ring if it meets the short cutoff or if the angle
@@ -392,7 +396,11 @@ int StructureCheck::CheckRings(Frame const& currentFrame, Cpptraj::Structure::Ri
         Cpptraj::Structure::LeastSquaresPlane const& ringVec = RingVecs[jdx];
         double dist2 = DIST2_NoImage( vmid.Dptr(), ringVec.Cxyz().Dptr() );
         if (dist2 < ring_dcut2_) {
-          ring_bond_check(Nproblems, dist2, ringBonds[idx], vbond, ringMask, ringVec);
+          ring_bond_check(Nproblems, dist2, ringBonds[idx], vbond, ringMask, ringVec
+#                         ifdef _OPENMP
+                          , mythread
+#                         endif
+                         );
 /*
           bool ring_intersect = false;
           // Bond intersects ring if it meets the short cutoff or if the angle
diff --git a/src/StructureCheck.h b/src/StructureCheck.h
index c562884122..f6b1287ef8 100644
--- a/src/StructureCheck.h
+++ b/src/StructureCheck.h
@@ -110,7 +110,11 @@ class StructureCheck {
     void SetupBondList(AtomMask const&, Topology const&);
     /// Check for intersection between bond and ring
     void ring_bond_check(int&, double, Btype const&, Vec3 const&, AtomMask const&,
-                         Cpptraj::Structure::LeastSquaresPlane const&);
+                         Cpptraj::Structure::LeastSquaresPlane const&
+#                        ifdef _OPENMP
+                         , int
+#                        endif
+                        );
     /// PairList version of CheckOverlap, 1 mask
     int PL1_CheckOverlap(Frame const&);
     /// Non-pairlist version of CheckOverlap, 1 mask

From c2707acfe281246329f2c1e029a154f977f717fe Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 17 Jul 2024 14:22:52 -0400
Subject: [PATCH 0832/1492] Split into non-pairlist function

---
 src/StructureCheck.cpp | 53 ++++++++++++++++++++++++++----------------
 src/StructureCheck.h   |  4 ++++
 2 files changed, 37 insertions(+), 20 deletions(-)

diff --git a/src/StructureCheck.cpp b/src/StructureCheck.cpp
index 6a7f1a7fbf..045b1d5b05 100644
--- a/src/StructureCheck.cpp
+++ b/src/StructureCheck.cpp
@@ -341,30 +341,15 @@ void StructureCheck::ring_bond_check(int& Nproblems,
   } // END angle cutoff satisfied
 }
 
-/** Check if any bonds are passing through rings. */
-int StructureCheck::CheckRings(Frame const& currentFrame, Cpptraj::Structure::RingFinder const& rings, std::vector<Btype> const& ringBonds)
+/** Check if any bonds are passing through rings, no pairlist. */
+int StructureCheck::checkRings_NoPL(Frame const& currentFrame,
+                                    Cpptraj::Structure::RingFinder const& rings,
+                                    std::vector<Btype> const& ringBonds,
+                                    std::vector<Cpptraj::Structure::LeastSquaresPlane> const& RingVecs)
 {
   int Nproblems = 0;
-  problemAtoms_.clear();
-  // Get all ring vectors
-  typedef std::vector<Cpptraj::Structure::LeastSquaresPlane> Larray;
-  Larray RingVecs;
-  RingVecs.resize( rings.Nrings() );
   int idx = 0;
   int ring_max = (int)rings.Nrings();
-# ifdef _OPENMP
-# pragma omp parallel private(idx)
-  {
-# pragma omp for
-# endif
-  for (idx = 0; idx < ring_max; idx++)
-  {
-    RingVecs[idx].CalcLeastSquaresPlane( currentFrame, rings[idx] );
-  }
-# ifdef _OPENMP
-  } // END pragma omp parallel
-# endif
-
   // Loop over bonds
   int bond_max = (int)ringBonds.size();
 # ifdef _OPENMP
@@ -454,6 +439,34 @@ int StructureCheck::CheckRings(Frame const& currentFrame, Cpptraj::Structure::Ri
 # ifdef _OPENMP
   } // END pragma omp parallel
 # endif
+  return Nproblems;
+}
+
+/** Check if any bonds are passing through rings. */
+int StructureCheck::CheckRings(Frame const& currentFrame, Cpptraj::Structure::RingFinder const& rings, std::vector<Btype> const& ringBonds)
+{
+  problemAtoms_.clear();
+  // Get all ring vectors
+  typedef std::vector<Cpptraj::Structure::LeastSquaresPlane> Larray;
+  Larray RingVecs;
+  RingVecs.resize( rings.Nrings() );
+  int idx = 0;
+  int ring_max = (int)rings.Nrings();
+# ifdef _OPENMP
+# pragma omp parallel private(idx)
+  {
+# pragma omp for
+# endif
+  for (idx = 0; idx < ring_max; idx++)
+  {
+    RingVecs[idx].CalcLeastSquaresPlane( currentFrame, rings[idx] );
+  }
+# ifdef _OPENMP
+  } // END pragma omp parallel
+# endif
+
+  int Nproblems = checkRings_NoPL(currentFrame, rings,  ringBonds, RingVecs);
+
   ConsolidateProblems();
 
   return Nproblems;
diff --git a/src/StructureCheck.h b/src/StructureCheck.h
index f6b1287ef8..4dc514e0f7 100644
--- a/src/StructureCheck.h
+++ b/src/StructureCheck.h
@@ -115,6 +115,10 @@ class StructureCheck {
                          , int
 #                        endif
                         );
+    /// Check for intersections between bonds and rings, no pair list
+    int checkRings_NoPL(Frame const&, Cpptraj::Structure::RingFinder const&,
+                        std::vector<Btype> const&,
+                        std::vector<Cpptraj::Structure::LeastSquaresPlane> const&);
     /// PairList version of CheckOverlap, 1 mask
     int PL1_CheckOverlap(Frame const&);
     /// Non-pairlist version of CheckOverlap, 1 mask

From 8e2c15910e1769276bd8e5197c0a22577bf00f61 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 17 Jul 2024 14:32:32 -0400
Subject: [PATCH 0833/1492] Start pairlist-enabled ring bond check

---
 src/StructureCheck.cpp | 42 ++++++++++++++++++++++++++++++++++++++++++
 src/StructureCheck.h   |  4 ++++
 2 files changed, 46 insertions(+)

diff --git a/src/StructureCheck.cpp b/src/StructureCheck.cpp
index 045b1d5b05..140e06bcb8 100644
--- a/src/StructureCheck.cpp
+++ b/src/StructureCheck.cpp
@@ -341,6 +341,48 @@ void StructureCheck::ring_bond_check(int& Nproblems,
   } // END angle cutoff satisfied
 }
 
+/** Check if any bonds are passing through rings, use pairlist. */
+int StructureCheck::checkRings_PL(Frame const& currentFrame,
+                                  Cpptraj::Structure::RingFinder const& rings,
+                                  std::vector<Btype> const& ringBonds,
+                                  std::vector<Cpptraj::Structure::LeastSquaresPlane> const& RingVecs)
+{
+  int Nproblems = 0;
+  // Need to create a pseudo-frame containing bond midpoints and
+  // ring centers.
+  unsigned int pseudo_natom = ringBonds.size() + rings.Nrings();
+
+  Frame pseudoFrame( pseudo_natom );
+  //pseudoFrame.ClearAtoms();
+
+  // Bonds first
+  int idx = 0;
+  int bond_max = (int)ringBonds.size();
+  std::vector<Vec3> Vbonds( ringBonds.size() );
+# ifdef _OPENMP
+# pragma omp parallel private(idx)
+  {
+# pragma omp for
+# endif
+  for (idx = 0; idx < bond_max; idx++)
+  {
+    const double* xyz1 = currentFrame.XYZ( ringBonds[idx].A1() );
+    const double* xyz2 = currentFrame.XYZ( ringBonds[idx].A2() );
+    Vec3 vbond( xyz2[0] - xyz1[0],
+                xyz2[1] - xyz1[1],
+                xyz2[2] - xyz1[2] );
+    Vec3 vmid = Vec3(xyz1) + (vbond * 0.5);
+    vbond.Normalize();
+    pseudoFrame.SetXYZ(idx, vmid);
+    Vbonds[idx] = vbond;
+  }
+# ifdef _OPENMP
+  } // END pragma omp parallel
+# endif
+
+  return Nproblems;
+}
+
 /** Check if any bonds are passing through rings, no pairlist. */
 int StructureCheck::checkRings_NoPL(Frame const& currentFrame,
                                     Cpptraj::Structure::RingFinder const& rings,
diff --git a/src/StructureCheck.h b/src/StructureCheck.h
index 4dc514e0f7..b8ca2ffe7b 100644
--- a/src/StructureCheck.h
+++ b/src/StructureCheck.h
@@ -119,6 +119,10 @@ class StructureCheck {
     int checkRings_NoPL(Frame const&, Cpptraj::Structure::RingFinder const&,
                         std::vector<Btype> const&,
                         std::vector<Cpptraj::Structure::LeastSquaresPlane> const&);
+    /// Check for intersections between bonds and rings, use pair list
+    int checkRings_PL(Frame const&, Cpptraj::Structure::RingFinder const&,
+                      std::vector<Btype> const&,
+                      std::vector<Cpptraj::Structure::LeastSquaresPlane> const&);
     /// PairList version of CheckOverlap, 1 mask
     int PL1_CheckOverlap(Frame const&);
     /// Non-pairlist version of CheckOverlap, 1 mask

From 06071cacc289ba3ce46c231feaea5a11ec7d652e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 17 Jul 2024 14:35:09 -0400
Subject: [PATCH 0834/1492] Add ring center coords

---
 src/StructureCheck.cpp | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/src/StructureCheck.cpp b/src/StructureCheck.cpp
index 140e06bcb8..e197a721f5 100644
--- a/src/StructureCheck.cpp
+++ b/src/StructureCheck.cpp
@@ -380,6 +380,14 @@ int StructureCheck::checkRings_PL(Frame const& currentFrame,
   } // END pragma omp parallel
 # endif
 
+  // Rings second
+  idx = bond_max;
+  for (unsigned int jdx = 0; jdx != rings.Nrings(); jdx++, idx++) {
+    Cpptraj::Structure::LeastSquaresPlane const& ringVec = RingVecs[jdx];
+    pseudoFrame.SetXYZ(idx, ringVec.Cxyz());
+  }
+
+
   return Nproblems;
 }
 

From 8826ece355366c8ea9e3b688e4c54e558e26f82b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 17 Jul 2024 14:49:02 -0400
Subject: [PATCH 0835/1492] Put in pairlist framework

---
 src/StructureCheck.cpp | 73 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 73 insertions(+)

diff --git a/src/StructureCheck.cpp b/src/StructureCheck.cpp
index e197a721f5..f2601e2aff 100644
--- a/src/StructureCheck.cpp
+++ b/src/StructureCheck.cpp
@@ -353,6 +353,7 @@ int StructureCheck::checkRings_PL(Frame const& currentFrame,
   unsigned int pseudo_natom = ringBonds.size() + rings.Nrings();
 
   Frame pseudoFrame( pseudo_natom );
+  pseudoFrame.SetBox( currentFrame.BoxCrd() );
   //pseudoFrame.ClearAtoms();
 
   // Bonds first
@@ -387,6 +388,78 @@ int StructureCheck::checkRings_PL(Frame const& currentFrame,
     pseudoFrame.SetXYZ(idx, ringVec.Cxyz());
   }
 
+  // Pseudo mask selecting everything
+  AtomMask pseudoMask(0, pseudo_natom);
+
+  // Set up the pair list
+  int retVal = pairList_.CreatePairList(pseudoFrame,
+                                        pseudoFrame.BoxCrd().UnitCell(),
+                                        pseudoFrame.BoxCrd().FracCell(), pseudoMask);
+  if (retVal < 0) {
+    // Treat grid setup failure as one problem.
+    mprinterr("Error: Grid setup for ring-bond check failed.\n");
+    return 1;
+  } else if (retVal > 0) {
+    // Atoms off the grid should count as problems as well.
+    Nproblems = retVal;
+  }
+
+  // Loop over pairlist cells
+  int cidx;
+# ifdef _OPENMP
+  int mythread;
+# pragma omp parallel private(cidx,mythread) reduction(+: Nproblems)
+  {
+  mythread = omp_get_thread_num();
+  thread_problemAtoms_[mythread].clear();
+# pragma omp for
+# endif
+  for (cidx = 0; cidx < pairList_.NGridMax(); cidx++)
+  {
+    PairList::CellType const& thisCell = pairList_.Cell( cidx );
+    if (thisCell.NatomsInGrid() > 0)
+    {
+      // cellList contains this cell index and all neighbors.
+      PairList::Iarray const& cellList = thisCell.CellList();
+      // transList contains index to translation for the neighbor.
+      PairList::Iarray const& transList = thisCell.TransList();
+      // Loop over all atoms of thisCell.
+      for (PairList::CellType::const_iterator it0 = thisCell.begin();
+                                              it0 != thisCell.end(); ++it0)
+      {
+        Vec3 const& xyz0 = it0->ImageCoords();
+        bool it0_is_bond = (it0->Idx() < bond_max);
+        // Calc interaction of atom to all other atoms in thisCell.
+        for (PairList::CellType::const_iterator it1 = it0 + 1;
+                                                it1 != thisCell.end(); ++it1)
+        {
+          bool it1_is_bond = (it1->Idx() < bond_max);
+          if (it0_is_bond != it1_is_bond) {
+
+          } // END it0 and it1 are not the same type
+        } // END loop over all other atoms of thisCell.
+        // Loop over all neighbor cells
+        for (unsigned int nidx = 1; nidx != cellList.size(); nidx++)
+        {
+          PairList::CellType const& nbrCell = pairList_.Cell( cellList[nidx] );
+          // Translate vector for neighbor cell
+          Vec3 const& tVec = pairList_.TransVec( transList[nidx] );
+          // Loop over every atom in nbrCell
+          for (PairList::CellType::const_iterator it1 = nbrCell.begin();
+                                                  it1 != nbrCell.end(); ++it1)
+          {
+            bool it1_is_bond = (it1->Idx() < bond_max);
+            if (it0_is_bond != it1_is_bond) {
+
+            } // END it0 and it1 are not the same type
+          } // END loop over every atom in neighbor cell
+        } // END loop over all neighbor cells
+      } // END loop over all atoms of thisCell
+    } // END thisCell has atoms
+  } // END loop over pairlist cells
+# ifdef _OPENMP
+  } // END omp parallel
+# endif
 
   return Nproblems;
 }

From d76b5fd3a3f533b1f9ea1e118dacede189244364 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 17 Jul 2024 15:11:22 -0400
Subject: [PATCH 0836/1492] Finish initial incarnation of the pairlist
 ring-bond check

---
 src/StructureCheck.cpp | 62 ++++++++++++++++++++++++++++++++++++++++--
 src/StructureCheck.h   |  2 ++
 2 files changed, 62 insertions(+), 2 deletions(-)

diff --git a/src/StructureCheck.cpp b/src/StructureCheck.cpp
index f2601e2aff..e08e0ddb24 100644
--- a/src/StructureCheck.cpp
+++ b/src/StructureCheck.cpp
@@ -341,6 +341,12 @@ void StructureCheck::ring_bond_check(int& Nproblems,
   } // END angle cutoff satisfied
 }
 
+bool StructureCheck::check_bond_not_in_ring(AtomMask const& ringMask, Btype const& bnd)
+{
+  return ( !ringMask.IsSelected(bnd.A1()) &&
+           !ringMask.IsSelected(bnd.A2()) );
+}
+
 /** Check if any bonds are passing through rings, use pairlist. */
 int StructureCheck::checkRings_PL(Frame const& currentFrame,
                                   Cpptraj::Structure::RingFinder const& rings,
@@ -435,7 +441,33 @@ int StructureCheck::checkRings_PL(Frame const& currentFrame,
         {
           bool it1_is_bond = (it1->Idx() < bond_max);
           if (it0_is_bond != it1_is_bond) {
-
+            AtomMask const* ringMask = 0;
+            Cpptraj::Structure::LeastSquaresPlane const* ringVec = 0;
+            Btype const* rbnd = 0;
+            Vec3 const* vbond = 0;
+            if (it0_is_bond) {
+              ringMask = &(rings[it1->Idx() - bond_max]);
+              ringVec = &(RingVecs[it1->Idx() - bond_max]);
+              rbnd = &(ringBonds[it0->Idx()]);
+              vbond = &(Vbonds[it0->Idx()]);
+            } else {
+              ringMask = &(rings[it0->Idx() - bond_max]);
+              ringVec = &(RingVecs[it0->Idx() - bond_max]);
+              rbnd = &(ringBonds[it1->Idx()]);
+              vbond = &(Vbonds[it1->Idx()]);
+            }
+            if (check_bond_not_in_ring( *ringMask, *rbnd )) {
+              Vec3 const& xyz1 = it1->ImageCoords();
+              Vec3 dxyz = xyz1 - xyz0;
+              double dist2 = dxyz.Magnitude2();
+              if (dist2 < ring_dcut2_) {
+                ring_bond_check(Nproblems, dist2, *rbnd, *vbond, *ringMask, *ringVec
+#                               ifdef _OPENMP
+                                , mythread
+#                               endif
+                               );
+              }  // END outer distance cutoff satisfied
+            } // END bond not in ring
           } // END it0 and it1 are not the same type
         } // END loop over all other atoms of thisCell.
         // Loop over all neighbor cells
@@ -450,7 +482,33 @@ int StructureCheck::checkRings_PL(Frame const& currentFrame,
           {
             bool it1_is_bond = (it1->Idx() < bond_max);
             if (it0_is_bond != it1_is_bond) {
-
+              AtomMask const* ringMask = 0;
+              Cpptraj::Structure::LeastSquaresPlane const* ringVec = 0;
+              Btype const* rbnd = 0;
+              Vec3 const* vbond = 0;
+              if (it0_is_bond) {
+                ringMask = &(rings[it1->Idx() - bond_max]);
+                ringVec = &(RingVecs[it1->Idx() - bond_max]);
+                rbnd = &(ringBonds[it0->Idx()]);
+                vbond = &(Vbonds[it0->Idx()]);
+              } else {
+                ringMask = &(rings[it0->Idx() - bond_max]);
+                ringVec = &(RingVecs[it0->Idx() - bond_max]);
+                rbnd = &(ringBonds[it1->Idx()]);
+                vbond = &(Vbonds[it1->Idx()]);
+              }
+              if (check_bond_not_in_ring( *ringMask, *rbnd )) {
+                Vec3 const& xyz1 = it1->ImageCoords();
+                Vec3 dxyz = xyz1 + tVec - xyz0;
+                double dist2 = dxyz.Magnitude2();
+                if (dist2 < ring_dcut2_) {
+                  ring_bond_check(Nproblems, dist2, *rbnd, *vbond, *ringMask, *ringVec
+#                                 ifdef _OPENMP
+                                  , mythread
+#                                 endif
+                                 );
+                } // END outer distance cutoff satisfied
+              } // END bond not in ring
             } // END it0 and it1 are not the same type
           } // END loop over every atom in neighbor cell
         } // END loop over all neighbor cells
diff --git a/src/StructureCheck.h b/src/StructureCheck.h
index b8ca2ffe7b..81b80890e2 100644
--- a/src/StructureCheck.h
+++ b/src/StructureCheck.h
@@ -115,6 +115,8 @@ class StructureCheck {
                          , int
 #                        endif
                         );
+    /// \return True if given bond not in given ring mask
+    static inline bool check_bond_not_in_ring(AtomMask const&, Btype const&);
     /// Check for intersections between bonds and rings, no pair list
     int checkRings_NoPL(Frame const&, Cpptraj::Structure::RingFinder const&,
                         std::vector<Btype> const&,

From 3b5584ed975da30e8d44e49d8b0f0b771bcdf138 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 17 Jul 2024 15:14:47 -0400
Subject: [PATCH 0837/1492] Enable pairlist-accelerated ring-bond check

---
 src/StructureCheck.cpp | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/src/StructureCheck.cpp b/src/StructureCheck.cpp
index e08e0ddb24..c5f8fe4a63 100644
--- a/src/StructureCheck.cpp
+++ b/src/StructureCheck.cpp
@@ -646,7 +646,13 @@ int StructureCheck::CheckRings(Frame const& currentFrame, Cpptraj::Structure::Ri
   } // END pragma omp parallel
 # endif
 
-  int Nproblems = checkRings_NoPL(currentFrame, rings,  ringBonds, RingVecs);
+  int Nproblems = 0;
+  if (checkType_ == PL_1_MASK) {
+    // TODO check for valid box
+    Nproblems = checkRings_PL(currentFrame, rings,  ringBonds, RingVecs);
+  } else {
+    Nproblems = checkRings_NoPL(currentFrame, rings,  ringBonds, RingVecs);
+  }
 
   ConsolidateProblems();
 

From bd73faf675f1d1480a495f6e307c47e3d3e60593 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 19 Jul 2024 11:24:25 -0400
Subject: [PATCH 0838/1492] Avoid storing neighbor indices which are out of
 range; can happen with very small systems

---
 src/PairList.cpp | 54 +++++++++++++++++++++++++++++++++++++++---------
 src/PairList.h   |  6 +++++-
 2 files changed, 49 insertions(+), 11 deletions(-)

diff --git a/src/PairList.cpp b/src/PairList.cpp
index 773273e081..255437f63e 100644
--- a/src/PairList.cpp
+++ b/src/PairList.cpp
@@ -223,11 +223,19 @@ int PairList::SetupGrids(Vec3 const& recipLengths) {
   int myindexhi = (int)cells_.size();
   CalcGridPointers(myindexlo, myindexhi);
 
+  if (debug_ > 1)
+    PrintCellMap(); // DEBUG
+
   PrintMemory();
 
   return 0;
 }
 
+/** \return True if the given cell index is valid. */
+bool PairList::validCellIndex(int cidx) const {
+  return (cidx > -1 && cidx < (int)cells_.size());
+}
+
 /** Calculate all of the forward neighbors for each grid cell and if
   * needed which translate vector is appropriate.
   * +X: need self and offsetX cells to the "right".
@@ -275,12 +283,16 @@ void PairList::CalcGridPointers(int myindexlo, int myindexhi) {
             // Wrap ix if necessary
             if (ix < nGridX_) {
 //              mprintf(" %i+0", idx2+ix);
-              Nbr.push_back( idx2 + ix );
-              Ntr.push_back( 4 ); // No translation. 0 0 0
+              if (validCellIndex( idx + ix )) {
+                Nbr.push_back( idx2 + ix );
+                Ntr.push_back( 4 ); // No translation. 0 0 0
+              }
             } else {
 //              mprintf(" %i+1", idx2+ix - nGridX_);
-              Nbr.push_back( idx2 + ix - nGridX_ );
-              Ntr.push_back( 5 ); // Translate by +1 in X. 1 0 0
+              if (validCellIndex( idx2 + ix - nGridX_ )) {
+                Nbr.push_back( idx2 + ix - nGridX_ );
+                Ntr.push_back( 5 ); // Translate by +1 in X. 1 0 0
+              }
             }
           }
           // Get all cells in the Y+ direction
@@ -314,9 +326,11 @@ void PairList::CalcGridPointers(int myindexlo, int myindexhi) {
               // Calc new index
               int jdx = jdx2 + wx; // Absolute neighbor grid cell index
 //              mprintf(" %i%+i%+i", jdx, ox-1, oy-1);
-              Nbr.push_back( jdx );
-              int tidx = oy*3 + ox;
-              Ntr.push_back( tidx );
+              if (validCellIndex( jdx )) {
+                Nbr.push_back( jdx );
+                int tidx = oy*3 + ox;
+                Ntr.push_back( tidx );
+              }
             }
           }
           // Get all cells in the +Z direction
@@ -364,9 +378,11 @@ void PairList::CalcGridPointers(int myindexlo, int myindexhi) {
                 // Calc new index
                 int jdx = jdx2 + wx; // Absolute neighbor grid cell index
 //                mprintf(" %i%+i%+i%+i", jdx, ox-1, oy-1, oz);
-                Nbr.push_back( jdx );
-                int tidx = oz*9 + oy*3 + ox;
-                Ntr.push_back( tidx );
+                if (validCellIndex( jdx )) {
+                  Nbr.push_back( jdx );
+                  int tidx = oz*9 + oy*3 + ox;
+                  Ntr.push_back( tidx );
+                }
               }
             }
           }
@@ -420,6 +436,24 @@ void PairList::PrintCells() const {
         mprintf(" %i", atm->Idx()+1);
       }
       mprintf("\n");
+    }
   }
+}
+
+void PairList::PrintCellMap() const {
+  mprintf("DEBUG: %zu cells.\n", cells_.size());
+  for (Carray::const_iterator cell = cells_.begin(); cell != cells_.end(); ++cell) {
+    if (cell->CellList().empty())
+      mprintf("\t%li : No Neighbors\n", cell - cells_.begin());
+    else {
+      Iarray::const_iterator it = cell->CellList().begin();
+      Iarray::const_iterator tt = cell->TransList().begin();
+      mprintf("\tCell %i(%i) :", *it, *tt);
+      ++it;
+      ++tt;
+      for (; it != cell->CellList().end(); ++it, ++tt)
+        mprintf(" %i(%i)", *it, *tt);
+      mprintf("\n");
+    }
   }
 }
diff --git a/src/PairList.h b/src/PairList.h
index d6ba840076..32632caec1 100644
--- a/src/PairList.h
+++ b/src/PairList.h
@@ -78,8 +78,10 @@ class PairList {
     void Timing(double, int) const;
     /// Print memory usage.
     void PrintMemory() const;
-    /// Print cells to stdout
+    /// Print cell contents to stdout
     void PrintCells() const;
+    /// Print cell map to stdout
+    void PrintCellMap() const;
     /// \return Number of grid cells.
     int NGridMax()                const { return (int)cells_.size(); }
     /// \return Specified grid cell.
@@ -94,6 +96,8 @@ class PairList {
     int NZ() const { return nGridZ_; }
 #   endif
   private:
+    /// \return True if the given cell index is valid
+    bool validCellIndex(int) const;
     /// Determine neighbors and translation vectors for each cell.
     void CalcGridPointers(int,int);
     /// Check grid dimensions using given recip lengths and (re)allocate mem if necessary.

From f3eb7ca4a30843f7cc640b24c765f38c992c0bd6 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 19 Jul 2024 11:34:05 -0400
Subject: [PATCH 0839/1492] Add check and warning for very small grids

---
 src/PairList.cpp | 15 ++++++++++++++-
 src/PairList.h   |  1 +
 2 files changed, 15 insertions(+), 1 deletion(-)

diff --git a/src/PairList.cpp b/src/PairList.cpp
index 255437f63e..3a37ffe57a 100644
--- a/src/PairList.cpp
+++ b/src/PairList.cpp
@@ -15,7 +15,8 @@ PairList::PairList() :
   nGridZ_(-1),
   nGridX_0_(-1),
   nGridY_0_(-1),
-  nGridZ_0_(-1)
+  nGridZ_0_(-1),
+  small_grid_(false)
 {}
 
 /** This leads to cellNeighbor_ dimensions of 7x10 */
@@ -247,6 +248,7 @@ bool PairList::validCellIndex(int cidx) const {
   * care about forward direction.
   */
 void PairList::CalcGridPointers(int myindexlo, int myindexhi) {
+  small_grid_ = false;
   // DEBUG - Check for duplicated interactions
 /*  Matrix<int> PairCalcd;
   PairCalcd.resize(cells_.size(), 0); // Half matrix
@@ -406,10 +408,21 @@ void PairList::CalcGridPointers(int myindexlo, int myindexhi) {
           }
 */
           // END DEBUG
+          // Check if any of the neighbors is in fact this cell
+          if (!small_grid_) {
+            for (unsigned int nidx = 1; nidx < Nbr.size(); nidx++) {
+              if ( idx == Nbr[nidx] ) {
+                small_grid_ = true;
+                break;
+              }
+            }
+          }
         } // END my cell
       } // nx
     } // ny
   } // nz
+  if (small_grid_)
+    mprintf("Warning: One or more cells is a neighbor of itself. This usually indicates a very small box.\n");
 }
 
 void PairList::Timing(double total) const { Timing(total, 2); }
diff --git a/src/PairList.h b/src/PairList.h
index 32632caec1..7a25a485a1 100644
--- a/src/PairList.h
+++ b/src/PairList.h
@@ -120,6 +120,7 @@ class PairList {
     int nGridX_0_;            ///< Previous number of cells in X direction
     int nGridY_0_;            ///< Previous number of cells in Y direction
     int nGridZ_0_;            ///< Previous number of cells in Z direction
+    bool small_grid_;         ///< Set to true if any cell is a neighbor of itself.
     static const int cellOffset_; ///< Number of cells in forward direction to check
 
     Timer t_map_;

From 9d22bc6b0261897122420ddd9f452f153c6884d9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 19 Jul 2024 11:56:17 -0400
Subject: [PATCH 0840/1492] Fix small memory error referencing freed set

---
 src/Exec_CrdAction.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Exec_CrdAction.cpp b/src/Exec_CrdAction.cpp
index f60a6d77d9..94ced902f8 100644
--- a/src/Exec_CrdAction.cpp
+++ b/src/Exec_CrdAction.cpp
@@ -111,7 +111,7 @@ Exec::RetType Exec_CrdAction::DoCrdAction(CpptrajState& State, ArgList& actionar
   if (box_needs_update) {
     crdOut->UpdateCoordsInfoBox( updateBox );
     mprintf("Info: crdaction: Box for '%s' was modified by action '%s'\n",
-            CRD->legend(), actionargs.Command());
+            crdOut->legend(), actionargs.Command());
     if (State.Debug() > 0)
       crdOut->CoordsInfo().TrajBox().PrintInfo();
   }

From ca3b9bb2f8ae636e32c4bb075c3a1590ed208c1a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 19 Jul 2024 13:38:35 -0400
Subject: [PATCH 0841/1492] Fix typo checking wrong index

---
 src/PairList.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/PairList.cpp b/src/PairList.cpp
index 3a37ffe57a..3413d18fb6 100644
--- a/src/PairList.cpp
+++ b/src/PairList.cpp
@@ -285,7 +285,7 @@ void PairList::CalcGridPointers(int myindexlo, int myindexhi) {
             // Wrap ix if necessary
             if (ix < nGridX_) {
 //              mprintf(" %i+0", idx2+ix);
-              if (validCellIndex( idx + ix )) {
+              if (validCellIndex( idx2 + ix )) {
                 Nbr.push_back( idx2 + ix );
                 Ntr.push_back( 4 ); // No translation. 0 0 0
               }

From db545ba57d747e075d335c0c76585f2b5169e782 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 19 Jul 2024 15:39:06 -0400
Subject: [PATCH 0842/1492] Start LeapEltHybrid class

---
 src/DataIO_LeapRC.cpp | 40 ++++++++++++++++++++++++++++++++++++++++
 src/DataIO_LeapRC.h   |  3 +++
 2 files changed, 43 insertions(+)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 4446fb1ebb..1e4d2f8fb1 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -15,6 +15,46 @@
 #include "Trajout_Single.h"
 #include <cstdlib> //getenv
 
+// -----------------------------------------------------------------------------
+// LeapEltHybrid class
+/// Store atom type hybridization and element from leaprc addAtomTypes
+class DataIO_LeapRC::LeapEltHybrid {
+  public:
+    //LeapEltHybrid() : hybrid_(AtomType::UNKNOWN_HYBRIDIZATION) { elt_[0]=' '; elt_[1]=' '; }
+    /// CONSTRUCTOR - take hybridization string, element string
+    LeapEltHybrid(std::string const& hybStr, std::string const& eltStr) {
+      // Hybridization
+      if (hybStr == "sp3")
+        hybrid_ = AtomType::SP3;
+      else if (hybStr == "sp2")
+        hybrid_ = AtomType::SP2;
+      else if (hybStr == "sp")
+        hybrid_ = AtomType::SP;
+      else {
+        mprintf("Warning: Unknown hybridization in addAtomTypes entry %s\n", hybStr.c_str());
+        hybrid_ = AtomType::UNKNOWN_HYBRIDIZATION;
+      }
+      elt_[0] = ' ';
+      elt_[1] = ' ';
+      if (eltStr.empty()) {
+        // Assume extra point
+        elt_[0] = 'X'; elt_[1] = 'P';
+      } else if (eltStr.size() == 1) {
+        elt_[0] = eltStr[0];
+      } else {
+        // 2 or more characters
+        elt_[0] = eltStr[0];
+        elt_[1] = eltStr[1];
+        if (eltStr.size() > 2)
+          mprintf("Warning: Element string '%s' has more than 2 chars. Only using first 2 chars.\n", eltStr.c_str());
+      }
+    }
+  private:
+    AtomType::HybridizationType hybrid_;
+    char elt_[2]; ///< Hold 2 char element name
+};
+
+// -----------------------------------------------------------------------------
 /// CONSTRUCTOR
 DataIO_LeapRC::DataIO_LeapRC()
 {
diff --git a/src/DataIO_LeapRC.h b/src/DataIO_LeapRC.h
index fcd945e37b..02a356e68a 100644
--- a/src/DataIO_LeapRC.h
+++ b/src/DataIO_LeapRC.h
@@ -17,6 +17,9 @@ class DataIO_LeapRC : public DataIO {
     int WriteData(FileName const&, DataSetList const&);
     bool ID_DataFormat(CpptrajFile&);
   private:
+    /// Store atom type hybridization and element from leaprc addAtomTypes
+    class LeapEltHybrid;
+
     typedef std::pair<NameType, AtomType::HybridizationType> NHpairType;
     typedef std::map<NameType, AtomType::HybridizationType> NHarrayType;
     typedef std::vector<std::string> Sarray;

From 9e619bdf6ec079ee79407161c697691b08add30d Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 19 Jul 2024 20:58:47 -0400
Subject: [PATCH 0843/1492] Refactor and use LeapEltHybrid so element type is
 saved.

---
 src/DataIO_LeapRC.cpp | 133 ++++++++++++++++++++++++------------------
 src/DataIO_LeapRC.h   |  35 +++++++++--
 2 files changed, 104 insertions(+), 64 deletions(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 1e4d2f8fb1..7cd40d39cc 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -17,42 +17,70 @@
 
 // -----------------------------------------------------------------------------
 // LeapEltHybrid class
-/// Store atom type hybridization and element from leaprc addAtomTypes
-class DataIO_LeapRC::LeapEltHybrid {
-  public:
-    //LeapEltHybrid() : hybrid_(AtomType::UNKNOWN_HYBRIDIZATION) { elt_[0]=' '; elt_[1]=' '; }
-    /// CONSTRUCTOR - take hybridization string, element string
-    LeapEltHybrid(std::string const& hybStr, std::string const& eltStr) {
-      // Hybridization
-      if (hybStr == "sp3")
-        hybrid_ = AtomType::SP3;
-      else if (hybStr == "sp2")
-        hybrid_ = AtomType::SP2;
-      else if (hybStr == "sp")
-        hybrid_ = AtomType::SP;
-      else {
-        mprintf("Warning: Unknown hybridization in addAtomTypes entry %s\n", hybStr.c_str());
-        hybrid_ = AtomType::UNKNOWN_HYBRIDIZATION;
-      }
-      elt_[0] = ' ';
-      elt_[1] = ' ';
-      if (eltStr.empty()) {
-        // Assume extra point
-        elt_[0] = 'X'; elt_[1] = 'P';
-      } else if (eltStr.size() == 1) {
-        elt_[0] = eltStr[0];
-      } else {
-        // 2 or more characters
-        elt_[0] = eltStr[0];
-        elt_[1] = eltStr[1];
-        if (eltStr.size() > 2)
-          mprintf("Warning: Element string '%s' has more than 2 chars. Only using first 2 chars.\n", eltStr.c_str());
-      }
-    }
-  private:
-    AtomType::HybridizationType hybrid_;
-    char elt_[2]; ///< Hold 2 char element name
-};
+/// CONSTRUCTOR
+DataIO_LeapRC::LeapEltHybrid::LeapEltHybrid() : hybrid_(AtomType::UNKNOWN_HYBRIDIZATION) {
+  elt_[0]=' ';
+  elt_[1]=' ';
+  elt_[2]='\0';
+}
+
+/// COPY CONSTRUCTOR
+DataIO_LeapRC::LeapEltHybrid::LeapEltHybrid(LeapEltHybrid const& rhs) : hybrid_(rhs.hybrid_) {
+  elt_[0] = rhs.elt_[0];
+  elt_[1] = rhs.elt_[1];
+}
+
+/// ASSIGNMENT
+DataIO_LeapRC::LeapEltHybrid& DataIO_LeapRC::LeapEltHybrid::operator=(const LeapEltHybrid& rhs) {
+  if (&rhs == this) return *this;
+  hybrid_ = rhs.hybrid_;
+  elt_[0] = rhs.elt_[0];
+  elt_[1] = rhs.elt_[1];
+  return *this;
+}
+
+/// \return true if not equal.
+bool DataIO_LeapRC::LeapEltHybrid::operator!=(const LeapEltHybrid& rhs) const {
+  return ( hybrid_ != rhs.hybrid_ ||
+           elt_[0] != rhs.elt_[0] ||
+           elt_[1] != rhs.elt_[1] );
+}
+
+/// Set from hybridization string, element string
+void DataIO_LeapRC::LeapEltHybrid::SetEltHybrid(std::string const& eltStr, std::string const& hybStr) {
+  // Hybridization
+  if (hybStr == "sp3")
+    hybrid_ = AtomType::SP3;
+  else if (hybStr == "sp2")
+    hybrid_ = AtomType::SP2;
+  else if (hybStr == "sp")
+    hybrid_ = AtomType::SP;
+  else {
+    mprintf("Warning: Unknown hybridization in addAtomTypes entry %s\n", hybStr.c_str());
+    hybrid_ = AtomType::UNKNOWN_HYBRIDIZATION;
+  }
+  elt_[0] = ' ';
+  elt_[1] = ' ';
+  elt_[2] = '\0';
+  if (eltStr.empty()) {
+    // Assume extra point
+    elt_[0] = 'X'; elt_[1] = 'P';
+  } else if (eltStr.size() == 1) {
+    elt_[0] = eltStr[0];
+  } else {
+    // 2 or more characters
+    elt_[0] = eltStr[0];
+    elt_[1] = eltStr[1];
+    if (eltStr.size() > 2)
+      mprintf("Warning: Element string '%s' has more than 2 chars. Only using first 2 chars.\n", eltStr.c_str());
+  }
+}
+
+/// \return Atom type hybridization
+AtomType::HybridizationType DataIO_LeapRC::LeapEltHybrid::AtypeHybridization() const { return hybrid_; }
+
+/// \return Atom type element string
+const char* DataIO_LeapRC::LeapEltHybrid::AtypeElementStr() const { return elt_; }
 
 // -----------------------------------------------------------------------------
 /// CONSTRUCTOR
@@ -134,7 +162,7 @@ const
 /** LEaP loadAmberParams command. */
 int DataIO_LeapRC::LoadAmberParams(std::string const& filename, DataSetList& dsl,
                                    std::string const& dsname,
-                                   NHarrayType const& atomHybridizations)
+                                   AtypeEltHybridPairMap const& atomHybridizations)
 const
 {
   DataSet* paramSet = 0;
@@ -185,11 +213,11 @@ const
       for (ParmHolder<AtomType>::iterator it = param.AT().begin();
                                           it != param.AT().end(); ++it)
       {
-        NHarrayType::const_iterator ah = atomHybridizations.find( it->first[0] );
+        AtypeEltHybridPairMap::const_iterator ah = atomHybridizations.find( it->first[0] );
         if (ah == atomHybridizations.end())
           mprintf("Warning: No hybridization set for atom type '%s'\n", *(it->first[0]));
         else
-          it->second.SetHybridization( ah->second );
+          it->second.SetHybridization( ah->second.AtypeHybridization() );
       }
     } else {
       mprinterr("Internal Error: DataIO_LeapRC::LoadAmberParams(): Set %s is not parameter set.\n",
@@ -247,7 +275,7 @@ int DataIO_LeapRC::LoadAmberPrep(std::string const& filename, DataSetList& dsl,
 }
 
 /** LEaP addAtomTypes command. */
-int DataIO_LeapRC::AddAtomTypes(NHarrayType& atomHybridizations, BufferedLine& infile)
+int DataIO_LeapRC::AddAtomTypes(AtypeEltHybridPairMap& atomHybridizations, BufferedLine& infile)
 const
 {
   int bracketCount = 0;
@@ -270,36 +298,25 @@ const
           ArgList aline( tmp );
           // Some entries (like LP and EP) are not required to have elements.
           // Set the hybridization index to 1 or 2.
-          int hidx;
+          LeapEltHybrid eltHybrid;
           if (aline.Nargs() == 3)
-            hidx = 2;
+            eltHybrid.SetEltHybrid( aline[1], aline[2] );
           else if (aline.Nargs() == 2)
-            hidx = 1;
+            eltHybrid.SetEltHybrid( "", aline[1] );
           else {
             mprinterr("Error: Malformed addAtomTypes entry %s\n", tmp.c_str());
             return 1;
           }
-          AtomType::HybridizationType ht;
-          if (aline[hidx] == "sp3")
-            ht = AtomType::SP3;
-          else if (aline[hidx] == "sp2")
-            ht = AtomType::SP2;
-          else if (aline[hidx] == "sp")
-            ht = AtomType::SP;
-          else {
-            mprintf("Warning: Unknown hybridization in addAtomTypes entry %s\n", tmp.c_str());
-            ht = AtomType::UNKNOWN_HYBRIDIZATION;
-          }
           NameType atype(aline[0]);
-          NHarrayType::iterator it = atomHybridizations.lower_bound( atype );
+          AtypeEltHybridPairMap::iterator it = atomHybridizations.lower_bound( atype );
           if (it == atomHybridizations.end() || it->first != atype) {
-            it = atomHybridizations.insert( it, NHpairType(atype, ht) );
+            it = atomHybridizations.insert( it, AtypeEltHybridPairType(atype, eltHybrid) );
           } else {
             mprintf("Warning: Duplicate entry for '%s' in addAtomTypes.", *atype);
-            if (it->second != ht) {
+            if (it->second != eltHybrid) {
               mprintf(" Overwriting.\n");
               mprintf("Warning: Line is %s\n", tmp.c_str());
-              it->second = ht;
+              it->second = eltHybrid;
             } else
               mprintf("\n");
           }
diff --git a/src/DataIO_LeapRC.h b/src/DataIO_LeapRC.h
index 02a356e68a..32b9635a8a 100644
--- a/src/DataIO_LeapRC.h
+++ b/src/DataIO_LeapRC.h
@@ -18,11 +18,34 @@ class DataIO_LeapRC : public DataIO {
     bool ID_DataFormat(CpptrajFile&);
   private:
     /// Store atom type hybridization and element from leaprc addAtomTypes
-    class LeapEltHybrid;
+    class LeapEltHybrid {
+      public:
+        /// CONSTRUCTOR
+        LeapEltHybrid();
+        /// COPY CONSTRUCTOR
+        LeapEltHybrid(LeapEltHybrid const&);
+        /// ASSIGNMENT
+        LeapEltHybrid& operator=(const LeapEltHybrid&);
+        /// \return true if not equal.
+        bool operator!=(const LeapEltHybrid& rhs) const;
+        /// Set from hybridization string, element string
+        void SetEltHybrid(std::string const&, std::string const&);
+        /// \return Atom type hybridization
+        AtomType::HybridizationType AtypeHybridization() const;
+        /// \return Atom type element string
+        const char* AtypeElementStr() const;
+      private:
+        AtomType::HybridizationType hybrid_;
+        char elt_[3]; ///< Hold 2 char element name (plus null)
+    };
 
-    typedef std::pair<NameType, AtomType::HybridizationType> NHpairType;
-    typedef std::map<NameType, AtomType::HybridizationType> NHarrayType;
+    /// Pair atom type name to element/hybridization
+    typedef std::pair<NameType, LeapEltHybrid> AtypeEltHybridPairType;
+    /// Map atom type name to element/hybridization
+    typedef std::map<NameType, LeapEltHybrid> AtypeEltHybridPairMap;
+    /// Array of strings
     typedef std::vector<std::string> Sarray;
+    /// Array of data sets
     typedef std::vector<DataSet*> DSarray;
 
     struct PdbResMapType {
@@ -32,10 +55,10 @@ class DataIO_LeapRC : public DataIO {
     };
     typedef std::vector<PdbResMapType> PdbResMapArray;
 
-    int LoadAmberParams(std::string const&, DataSetList&, std::string const&, NHarrayType const&) const;
+    int LoadAmberParams(std::string const&, DataSetList&, std::string const&, AtypeEltHybridPairMap const&) const;
     int LoadOFF(std::string const&, DataSetList&, std::string const&, DSarray&) const;
     int LoadAmberPrep(std::string const&, DataSetList&, std::string const&, DSarray&) const;
-    int AddAtomTypes(NHarrayType&, BufferedLine&) const;
+    int AddAtomTypes(AtypeEltHybridPairMap&, BufferedLine&) const;
     int AddPdbResMap(BufferedLine&, PdbResMapArray&) const;
     int AddPdbAtomMap(std::string const&, DataSetList&, BufferedLine&) const;
     int LoadMol2(ArgList const&, DataSetList&) const;
@@ -56,7 +79,7 @@ class DataIO_LeapRC : public DataIO {
     std::string find_path(std::string const&, std::string const&) const;
 
     std::string amberhome_;
-    NHarrayType atomHybridizations_; ///< Store hybridizations for atom types
+    AtypeEltHybridPairMap atomHybridizations_; ///< Store hybridizations for atom types
     PdbResMapArray pdbResMap_; ///< Hold PDB residue name map
     DSarray units_;            ///< Hold COORDS sets which have been added as units
     static Sarray paramFiles_; ///< Track amber FF param files loaded from leaprc files

From d5ff4fa6fa5eccb549fed3bd28ac922e896cb933 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 20 Jul 2024 10:28:22 -0400
Subject: [PATCH 0844/1492] Save atom type element string to AtomType

---
 src/AtomType.h        | 14 ++++++++++----
 src/DataIO_LeapRC.cpp |  8 +++++---
 2 files changed, 15 insertions(+), 7 deletions(-)

diff --git a/src/AtomType.h b/src/AtomType.h
index e4a81b4959..2c2d8b1f22 100644
--- a/src/AtomType.h
+++ b/src/AtomType.h
@@ -3,17 +3,18 @@
 #include "ParameterTypes.h"
 /// Hold parameters for a unique atom type
 class AtomType {
+    void clearElt() { elt_[0] = ' '; elt_[1] = ' '; elt_[2] = '\0'; }
   public:
     /// Atom hybridization types
     enum HybridizationType { SP = 0, SP2, SP3, UNKNOWN_HYBRIDIZATION };
     /// CONSTRUCTOR
-    AtomType() : mass_(0.0), polarizability_(0.0), oidx_(-1), hybrid_(UNKNOWN_HYBRIDIZATION), hasLJ14_(false) {}
+    AtomType() : mass_(0.0), polarizability_(0.0), oidx_(-1), hybrid_(UNKNOWN_HYBRIDIZATION), hasLJ14_(false) { clearElt(); }
     /// CONSTRUCTOR - Mass only
-    AtomType(double m) : mass_(m), polarizability_(0.0), oidx_(-1), hybrid_(UNKNOWN_HYBRIDIZATION), hasLJ14_(false) {}
+    AtomType(double m) : mass_(m), polarizability_(0.0), oidx_(-1), hybrid_(UNKNOWN_HYBRIDIZATION), hasLJ14_(false) { clearElt(); }
     /// CONSTRUCTOR - Mass, polarizability
-    AtomType(double m, double p) : mass_(m), polarizability_(p), oidx_(-1), hybrid_(UNKNOWN_HYBRIDIZATION), hasLJ14_(false) {}
+    AtomType(double m, double p) : mass_(m), polarizability_(p), oidx_(-1), hybrid_(UNKNOWN_HYBRIDIZATION), hasLJ14_(false) { clearElt(); }
     /// CONSTRUCTOR - Radius, well depth, mass, polarizability
-    AtomType(double r, double d, double m, double p) : lj_(r, d), mass_(m), polarizability_(p), oidx_(-1), hybrid_(UNKNOWN_HYBRIDIZATION), hasLJ14_(false) {}
+    AtomType(double r, double d, double m, double p) : lj_(r, d), mass_(m), polarizability_(p), oidx_(-1), hybrid_(UNKNOWN_HYBRIDIZATION), hasLJ14_(false) { clearElt(); }
     /// Set type index
     void SetTypeIdx(int i) { oidx_ = i; }
     /// \return default LJ parameters
@@ -30,6 +31,8 @@ class AtomType {
     int OriginalIdx()       const { return oidx_; }
     /// \return Atom hybridization
     HybridizationType Hybridization() const { return hybrid_; }
+    /// \return Atom type element string
+    const char* EltStr() const { return elt_; }
     /// \return true if mass, polarizability, or LJ params are less than incoming
     bool operator<(AtomType const& rhs) const {
       if (FEQ(mass_, rhs.mass_)) {
@@ -54,6 +57,8 @@ class AtomType {
     void SetLJ14(LJparmType const& lj) { lj14_ = lj; hasLJ14_ = true; }
     /// Set atom hybridization
     void SetHybridization(HybridizationType h) { hybrid_ = h; }
+    /// Set atom type element string
+    void SetEltStr(const char* elt) { elt_[0] = elt[0]; elt_[1] = elt[1]; }
     /// \return data size  (2 double for LJparmType)
     static size_t DataSize() { return (4*sizeof(double)) + sizeof(int); }
   private:
@@ -63,6 +68,7 @@ class AtomType {
     double polarizability_; ///< Atomic polarizability in Ang^3
     int oidx_;              ///< Original atom type index, for indexing nonbond parameters.
     HybridizationType hybrid_; ///< Atom hybridization
+    char elt_[3];              ///< 2 character atom type element string (and null char)
     bool hasLJ14_;             ///< True if this type has LJ 1-4 parameters.
 };
 #endif
diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 7cd40d39cc..5d02dec559 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -209,15 +209,17 @@ const
   //{
     if ( paramSet->Type() == DataSet::PARAMETERS ) {
       DataSet_Parameters& param = static_cast<DataSet_Parameters&>( *paramSet );
-      mprintf("\tUpdating atom hybridizations in set %s\n", param.legend());
+      mprintf("\tUpdating atom hybridizations and elements in set %s\n", param.legend());
       for (ParmHolder<AtomType>::iterator it = param.AT().begin();
                                           it != param.AT().end(); ++it)
       {
         AtypeEltHybridPairMap::const_iterator ah = atomHybridizations.find( it->first[0] );
         if (ah == atomHybridizations.end())
-          mprintf("Warning: No hybridization set for atom type '%s'\n", *(it->first[0]));
-        else
+          mprintf("Warning: No element/hybridization set for atom type '%s'\n", *(it->first[0]));
+        else {
           it->second.SetHybridization( ah->second.AtypeHybridization() );
+          it->second.SetEltStr( ah->second.AtypeElementStr() );
+        }
       }
     } else {
       mprinterr("Internal Error: DataIO_LeapRC::LoadAmberParams(): Set %s is not parameter set.\n",

From a93a0a7998c33ff256de1cc2b9b18d4324b4b7a0 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 20 Jul 2024 10:39:11 -0400
Subject: [PATCH 0845/1492] Add hybridization and element printout for
 parameter set data print

---
 src/ParameterSet.cpp | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/ParameterSet.cpp b/src/ParameterSet.cpp
index 9a339d263c..210ffc562d 100644
--- a/src/ParameterSet.cpp
+++ b/src/ParameterSet.cpp
@@ -58,10 +58,11 @@ void ParameterSet::Print(CpptrajFile& Out) const {
     Out.Printf("Parameter set: %s\n", ParamSetName().c_str());
   if (!NBname_.empty())
     Out.Printf("Nonbond parameters name: %s\n", NBname_.c_str());
+  static const char* hybStr[] = {"SP ", "SP2", "SP3", "UNK"};
   Out.Printf("Atom Types:\n");
-  Out.Printf("\t%6s %8s %12s %12s %12s %12s\n", "Name", "TypeIdx", "Radius", "Depth", "Mass", "Polar.");
+  Out.Printf("\t%6s %8s %12s %12s %12s %12s %3s %2s\n", "Name", "TypeIdx", "Radius", "Depth", "Mass", "Polar.", "Hyb", "El");
   for (ParmHolder<AtomType>::const_iterator at = atomTypes_.begin(); at != atomTypes_.end(); ++at) {
-    Out.Printf("\t%6s %8li %12.4f %12.4f %12.4f %12.4f\n", *(at->first[0]), at - atomTypes_.begin(), at->second.LJ().Radius(), at->second.LJ().Depth(), at->second.Mass(), at->second.Polarizability());
+    Out.Printf("\t%6s %8li %12.4f %12.4f %12.4f %12.4f %3s %2s\n", *(at->first[0]), at - atomTypes_.begin(), at->second.LJ().Radius(), at->second.LJ().Depth(), at->second.Mass(), at->second.Polarizability(), hybStr[at->second.Hybridization()], at->second.EltStr());
   }
   if (!nbParm_.empty()) {
     Out.Printf("LJ 6-12 parameters:\n");

From 361da213264221a89d772e1d47da1512581b35d4 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 20 Jul 2024 11:22:27 -0400
Subject: [PATCH 0846/1492] Ensure template element types are updated

---
 src/Atom.h                |  2 +-
 src/Exec_Build.cpp        |  2 ++
 src/Structure/Creator.cpp | 24 ++++++++++++++++++++++++
 src/Structure/Creator.h   |  2 ++
 4 files changed, 29 insertions(+), 1 deletion(-)

diff --git a/src/Atom.h b/src/Atom.h
index 8d6432508e..5a799cd858 100644
--- a/src/Atom.h
+++ b/src/Atom.h
@@ -71,6 +71,7 @@ class Atom {
     void SetTypeIndex(int tin)               { atype_index_ = tin;  }
     void SetName(NameType const& nin)        { aname_ = nin;        }
     void SetTypeName(NameType const& tin)    { atype_ = tin;        }
+    void SetElementFromSymbol(char,char);
     // Internal vars -----------------------------
     inline bool NoMol()                const { return ( mol_ < 0 ); }
     inline const char *c_str()         const { return *aname_; }
@@ -122,7 +123,6 @@ class Atom {
 
     static void WarnBondLengthDefault(AtomicElementType, AtomicElementType, double);
     void SetElementFromName();
-    void SetElementFromSymbol(char,char);
     void SetElementFromMass();
 };
 #endif
diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index fcdf6016f2..2c12a3cb3f 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -151,12 +151,14 @@ const
     // Identify a template based on the residue name.
     DataSet_Coords* resTemplate = creator.IdTemplateFromResname(currentRes.Name(), resTermType);
     if (resTemplate == 0) {
+      // Residue has no template.
       mprintf("Warning: No template found for residue %s\n", topIn.TruncResNameOnumId(ires).c_str());
       newNatom += currentRes.NumAtoms();
       // Head and tail atoms are blank
       resHeadAtoms.push_back( -1 );
       resTailAtoms.push_back( -1 );
     } else {
+      // Residue has a template.
       if (debug_ > 0)
         mprintf("\tTemplate %s being used for residue %s\n",
                 resTemplate->legend(), topIn.TruncResNameOnumId(ires).c_str());
diff --git a/src/Structure/Creator.cpp b/src/Structure/Creator.cpp
index a80833f499..b205e69933 100644
--- a/src/Structure/Creator.cpp
+++ b/src/Structure/Creator.cpp
@@ -56,6 +56,7 @@ int Creator::InitCreator(ArgList& argIn, DataSetList const& DSL, int debugIn)
 
   if (getTemplates(argIn, DSL)) return 1;
   if (getParameterSets(argIn, DSL)) return 1;
+  UpdateTemplateElements();
 
   // Get any atom name maps
   DataSetList nameMapSets = DSL.GetSetsOfType("*", DataSet::NAMEMAP);
@@ -69,6 +70,29 @@ int Creator::InitCreator(ArgList& argIn, DataSetList const& DSL, int debugIn)
   return 0;
 }
 
+/** Update template atom elements from atom types in parameter set. */
+void Creator::UpdateTemplateElements() const {
+  if (mainParmSet_ == 0) return;
+
+  for (Carray::const_iterator crd = Templates_.begin(); crd != Templates_.end(); ++crd)
+  {
+    mprintf("DEBUG: Updating atom elements in '%s'\n", (*crd)->legend());
+    // Loop over template atoms
+    Topology& templateTop = *((*crd)->TopPtr());
+    for (int at = 0; at != templateTop.Natom(); at++) {
+      ParmHolder<AtomType>::const_iterator it;
+      if (templateTop[at].HasType()) {
+        it = mainParmSet_->AT().GetParam( TypeNameHolder(templateTop[at].Type()) );
+        if (it != mainParmSet_->AT().end()) {
+          mprintf("DEBUG:\t\tSetting atom %s element to %s\n", *(templateTop[at].Name()), it->second.EltStr());
+          templateTop.SetAtom(at).SetElementFromSymbol( it->second.EltStr()[0],
+                                                        it->second.EltStr()[1] );
+        }
+      }
+    } // END loop over template atoms
+  } // END loop over templates
+}
+
 /** Try to identify residue template DataSet from the given name;
   * could be data set name or residue name.
   */
diff --git a/src/Structure/Creator.h b/src/Structure/Creator.h
index 21d4e7c61d..b6d83ca7ba 100644
--- a/src/Structure/Creator.h
+++ b/src/Structure/Creator.h
@@ -48,6 +48,8 @@ class Creator {
     int getTemplates(ArgList&, DataSetList const&);
     /// Get parameter sets
     int getParameterSets(ArgList&, DataSetList const&);
+    /// Update template atom elements from parameter set
+    void UpdateTemplateElements() const;
 
     DataSet_Parameters* mainParmSet_; ///< Hold optional parameter set.
     Carray Templates_;                ///< Hold unit templates.

From bb21d3b9ecffa4fa89990a81d2733c81d95f1184 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 20 Jul 2024 11:29:47 -0400
Subject: [PATCH 0847/1492] Assume if SetElementFromSymbol is called that we
 want to overwrite any set element

---
 src/Atom.cpp       | 2 +-
 src/Exec_Build.cpp | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/Atom.cpp b/src/Atom.cpp
index 15f8500181..2037683045 100644
--- a/src/Atom.cpp
+++ b/src/Atom.cpp
@@ -285,7 +285,7 @@ void Atom::SetElementFromName() {
 
 // Atom::SetElementFromSymbol()
 void Atom::SetElementFromSymbol(char c1, char c2) {
-  if (element_ != UNKNOWN_ELEMENT) return;
+  //if (element_ != UNKNOWN_ELEMENT) return;
   // Attempt to match up 1 or 2 char element name
   char en[2];
   bool oneChar = true;
diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 2c12a3cb3f..042a3ce27b 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -300,6 +300,7 @@ const
           }
         }
         templateAtom.ClearBonds(); // FIXME AddTopAtom should clear bonds
+        //mprintf("DEBUG: Adding template atom %s (elt %s)\n", templateAtom.c_str(), templateAtom.ElementName());
         topOut.AddTopAtom( templateAtom, currentRes );
         if (map[iref] == -1) {
           // Template atom not in input structure.

From 63c3b77ebff84e02fdf5fe1b45036a0f17f64e7f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 20 Jul 2024 11:36:24 -0400
Subject: [PATCH 0848/1492] Skip dihedrals with extra points.

---
 src/Topology.cpp | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index 6780aa727f..026e6c0814 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -3034,6 +3034,15 @@ DihedralArray Topology::AssignDihedralParm(DihedralParmHolder const& newDihedral
     types.AddName( atoms_[dih->A2()].Type() );
     types.AddName( atoms_[dih->A3()].Type() );
     types.AddName( atoms_[dih->A4()].Type() );
+    // Skip extra points // FIXME make this an option
+    if ( atoms_[dih->A1()].Element() == Atom::EXTRAPT ||
+         atoms_[dih->A4()].Element() == Atom::EXTRAPT)
+    {
+      mprintf("DEBUG: Skipping dihedral with extra point: %4i %4i %4i %4i (%2s %2s %2s %2s)\n",
+              dih->A1()+1, dih->A2()+1, dih->A3()+1, dih->A4()+1,
+              *types[0], *types[1], *types[2], *types[3]);
+      continue;
+    }
 //    mprintf("DEBUG: Assigning dihedral %4i %4i %4i %4i (%2s %2s %2s %2s) isImproper=%i skip14=%i\n",
 //            dih->A1()+1, dih->A2()+1, dih->A3()+1, dih->A4()+1,
 //            *types[0], *types[1], *types[2], *types[3],

From 511c2e0577b8d44f81ad2ab564ce2c38ed87de1c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 20 Jul 2024 13:53:29 -0400
Subject: [PATCH 0849/1492] Rework AngleParm assignment so it can be used to
 filter out rigid water model angles and angles with extra points

---
 src/ParameterTypes.h |  2 ++
 src/Topology.cpp     | 52 ++++++++++++++++++++++++++++++++++++++------
 src/Topology.h       |  2 +-
 3 files changed, 48 insertions(+), 8 deletions(-)

diff --git a/src/ParameterTypes.h b/src/ParameterTypes.h
index 05e1568085..d2f0261485 100644
--- a/src/ParameterTypes.h
+++ b/src/ParameterTypes.h
@@ -272,6 +272,8 @@ class AngleArray {
     AngleType const& operator[](size_t idx) const { return angles_[idx]; }
     /// \return underlying array
     std::vector<AngleType> const& Array() const { return angles_; }
+    /// \return last angle added
+    AngleType& back() { return angles_.back(); }
   private:
     AArray angles_;
 };
diff --git a/src/Topology.cpp b/src/Topology.cpp
index 026e6c0814..ef5c7a8409 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2883,15 +2883,51 @@ void Topology::AssignUBParams(ParmHolder<BondParmType> const& newBondParams) {
 }
 
 /** Set parameters for angles in given angle array. */
-void Topology::AssignAngleParm(ParmHolder<AngleParmType> const& newAngleParams,
-                              AngleArray& angles)
+AngleArray Topology::AssignAngleParm(ParmHolder<AngleParmType> const& newAngleParams,
+                                     AngleArray const& angles)
 {
+  AngleArray newAngles;
   ParmHolder<int> currentTypes;
-  for (AngleArray::iterator ang = angles.begin(); ang != angles.end(); ++ang) {
+  for (AngleArray::const_iterator ang = angles.begin(); ang != angles.end(); ++ang) {
     TypeNameHolder types(3);
     types.AddName( atoms_[ang->A1()].Type() );
     types.AddName( atoms_[ang->A2()].Type() );
     types.AddName( atoms_[ang->A3()].Type() );
+    // Skip extra points // FIXME make this an option
+    if ( atoms_[ang->A1()].Element() == Atom::EXTRAPT ||
+         atoms_[ang->A3()].Element() == Atom::EXTRAPT)
+    {
+      mprintf("DEBUG: Skipping angle with extra point: %4i %4i %4i (%2s %2s %2s)\n",
+              ang->A1()+1, ang->A2()+1, ang->A3()+1,
+              *types[0], *types[1], *types[2]);
+      continue;
+    }
+    // Skip water angles // FIXME make this an option
+    if (atoms_[ang->A1()].Element() == Atom::HYDROGEN &&
+        atoms_[ang->A2()].Element() == Atom::OXYGEN &&
+        atoms_[ang->A3()].Element() == Atom::HYDROGEN)
+    {
+      // H-O-H Angle. If there is an H-H bond assume this is a rigid water model.
+      if (atoms_[ang->A1()].IsBondedTo( ang->A3() )) {
+        mprintf("DEBUG: H-O-H angle, H-H bond detected. Assuming rigid water, skipping angle: "
+                "%4i %4i %4i (%2s %2s %2s)\n",
+                ang->A1()+1, ang->A2()+1, ang->A3()+1,
+                *types[0], *types[1], *types[2]);
+        continue;
+      }
+    }
+    if (atoms_[ang->A1()].Element() == Atom::OXYGEN &&
+        atoms_[ang->A2()].Element() == Atom::HYDROGEN &&
+        atoms_[ang->A3()].Element() == Atom::HYDROGEN)
+    {
+      // O-H-H Angle. Assume rigid water model
+      mprintf("DEBUG: O-H-H angle. Assuming rigid water, skipping angle: "
+              "%4i %4i %4i (%2s %2s %2s)\n",
+              ang->A1()+1, ang->A2()+1, ang->A3()+1,
+              *types[0], *types[1], *types[2]);
+      continue;
+    }
+
     bool found;
     // See if parameter is present.
     int idx = currentTypes.FindParam( types, found );
@@ -2913,8 +2949,10 @@ void Topology::AssignAngleParm(ParmHolder<AngleParmType> const& newAngleParams,
         currentTypes.AddParm(types, idx, false);
       }
     }
-    ang->SetIdx( idx );
+    newAngles.push_back( *ang );
+    newAngles.back().SetIdx( idx );
   }
+  return newAngles;
 /*
   for (AngleArray::iterator ang = angles.begin(); ang != angles.end(); ++ang) {
     TypeNameHolder types(3);
@@ -2941,8 +2979,8 @@ void Topology::AssignAngleParm(ParmHolder<AngleParmType> const& newAngleParams,
 /** Replace any current angle parameters with given angle parameters. */
 void Topology::AssignAngleParams(ParmHolder<AngleParmType> const& newAngleParams) {
   angleparm_.clear();
-  AssignAngleParm( newAngleParams, angles_ );
-  AssignAngleParm( newAngleParams, anglesh_ );
+  angles_ = AssignAngleParm( newAngleParams, angles_ );
+  anglesh_ = AssignAngleParm( newAngleParams, anglesh_ );
 }
 
 /** Warn if improper atoms have been reordered so they match the parameter. */
@@ -3752,7 +3790,7 @@ int Topology::AssignParams(ParameterSet const& set0) {
   angles_.clear();
   anglesh_.clear();
   AngleArray allAngles = Cpptraj::Structure::GenerateAngleArray(residues_, atoms_);
-  AssignAngleParm( set0.AP(), allAngles );
+  allAngles = AssignAngleParm( set0.AP(), allAngles );
   for (AngleArray::const_iterator ang = allAngles.begin(); ang != allAngles.end(); ++ang)
     AddToAngleArrays( *ang );
   // Dihedral parameters
diff --git a/src/Topology.h b/src/Topology.h
index d2acc829f2..6f34d2e637 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -350,7 +350,7 @@ class Topology {
 
     void AssignAtomTypeParm(ParmHolder<AtomType> const&);
     void AssignBondParm(ParmHolder<BondParmType> const&, BondArray&, BondParmArray&, const char*) const;
-    void AssignAngleParm(ParmHolder<AngleParmType> const&, AngleArray&);
+    AngleArray AssignAngleParm(ParmHolder<AngleParmType> const&, AngleArray const&);
     void warn_improper_reorder(DihedralType const&, DihedralType const&) const;
     void AssignImproperParm(ImproperParmHolder const&, DihedralArray&, DihedralParmArray&) const;
     inline DihedralArray get_unique_dihedrals(DihedralArray const&) const;

From 416d9979da5588f00123b4de1a80a2ffbb38988a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 20 Jul 2024 14:31:21 -0400
Subject: [PATCH 0850/1492] Start AssignParams class

---
 src/Parm/AssignParams.cpp | 1133 +++++++++++++++++++++++++++++++++++++
 src/Parm/AssignParams.h   |   66 +++
 2 files changed, 1199 insertions(+)
 create mode 100644 src/Parm/AssignParams.cpp
 create mode 100644 src/Parm/AssignParams.h

diff --git a/src/Parm/AssignParams.cpp b/src/Parm/AssignParams.cpp
new file mode 100644
index 0000000000..4d69557452
--- /dev/null
+++ b/src/Parm/AssignParams.cpp
@@ -0,0 +1,1133 @@
+#include "AssignParams.h"
+
+using namespace Cpptraj::Parm;
+
+/** CONSTRUCTOR */
+AssignParams::AssignParams() :
+  debug_(0)
+{}
+
+/** Set parameters for atoms via given atom type parameter holder. */
+void AssignParams::AssignAtomTypeParm(ParmHolder<AtomType> const& newAtomTypeParams)
+const
+{
+  for (unsigned int iat = 0; iat != atoms_.size(); iat++)
+  {
+    bool found;
+    TypeNameHolder atype( atoms_[iat].Type() );
+    AtomType at = newAtomTypeParams.FindParam( atype, found );
+    if (found) {
+      // Update mass
+      atoms_[iat].SetMass( at.Mass() );
+      // Update polarizability
+      atoms_[iat].SetPolar( at.Polarizability() );
+    } else
+      mprintf("Warning: Atom type parameter not found for %s\n", *atype[0]);
+  }
+}
+
+/** Set parameters for bonds in given bond array. */
+void AssignParams::AssignBondParm(ParmHolder<BondParmType> const& newBondParams,
+                              BondArray& bonds, BondParmArray& bpa, const char* desc)
+const
+{
+  ParmHolder<int> currentTypes;
+  for (BondArray::iterator bnd = bonds.begin(); bnd != bonds.end(); ++bnd) {
+    TypeNameHolder types(2);
+    types.AddName( atoms_[bnd->A1()].Type() );
+    types.AddName( atoms_[bnd->A2()].Type() );
+    bool found;
+    // See if parameter is present.
+    int idx = currentTypes.FindParam(types, found);
+    if (!found) {
+      idx = -1;
+      // Not yet present in current types.
+      BondParmType bp = newBondParams.FindParam( types, found );
+      if (!found) {
+        mprintf("Warning: parameter not found for %s %s-%s (%s-%s)\n", desc,
+                TruncResAtomNameNum(bnd->A1()).c_str(),
+                TruncResAtomNameNum(bnd->A2()).c_str(),
+                *types[0], *types[1]);
+      } else {
+        //idx = addBondParm( bpa, bp ); TODO handle array packing
+        idx = (int)bpa.size();
+        bpa.push_back( bp );
+        currentTypes.AddParm(types, idx, false);
+      }
+    }
+    bnd->SetIdx( idx );
+  }
+/*
+  for (BondArray::iterator bnd = bonds.begin(); bnd != bonds.end(); ++bnd) {
+    TypeNameHolder types(2);
+    types.AddName( atoms_[bnd->A1()].Type() );
+    types.AddName( atoms_[bnd->A2()].Type() );
+    bool found;
+    // See if parameter is present.
+    int idx = -1;
+    BondParmType bp = newBondParams.FindParam( types, found );
+    if (!found) {
+      mprintf("Warning: parameter not found for %s %s-%s (%s-%s)\n", desc,
+              TruncResAtomNameNum(bnd->A1()).c_str(),
+              TruncResAtomNameNum(bnd->A2()).c_str(),
+              *types[0], *types[1]);
+    } else {
+      idx = addBondParm( bpa, bp );
+    }
+    bnd->SetIdx( idx );
+  }*/
+}
+
+/** Replace any current bond parameters with given bond parameters. */
+void AssignParams::AssignBondParams(ParmHolder<BondParmType> const& newBondParams) const {
+  bondparm_.clear();
+  AssignBondParm( newBondParams, bonds_,  bondparm_, "bond" );
+  AssignBondParm( newBondParams, bondsh_, bondparm_, "bond" );
+}
+
+/** Replace any current Urey-Bradley parameters with given UB parameters. */
+void AssignParams::AssignUBParams(ParmHolder<BondParmType> const& newBondParams) const {
+  ubparm_.clear();
+  AssignBondParm( newBondParams, ub_, ubparm_, "UB term" );
+}
+
+/** Set parameters for angles in given angle array. */
+AngleArray AssignParams::AssignAngleParm(ParmHolder<AngleParmType> const& newAngleParams,
+                                     AngleArray const& angles)
+const
+{
+  AngleArray newAngles;
+  ParmHolder<int> currentTypes;
+  for (AngleArray::const_iterator ang = angles.begin(); ang != angles.end(); ++ang) {
+    TypeNameHolder types(3);
+    types.AddName( atoms_[ang->A1()].Type() );
+    types.AddName( atoms_[ang->A2()].Type() );
+    types.AddName( atoms_[ang->A3()].Type() );
+    // Skip extra points // FIXME make this an option
+    if ( atoms_[ang->A1()].Element() == Atom::EXTRAPT ||
+         atoms_[ang->A3()].Element() == Atom::EXTRAPT)
+    {
+      mprintf("DEBUG: Skipping angle with extra point: %4i %4i %4i (%2s %2s %2s)\n",
+              ang->A1()+1, ang->A2()+1, ang->A3()+1,
+              *types[0], *types[1], *types[2]);
+      continue;
+    }
+    // Skip water angles // FIXME make this an option
+    if (atoms_[ang->A1()].Element() == Atom::HYDROGEN &&
+        atoms_[ang->A2()].Element() == Atom::OXYGEN &&
+        atoms_[ang->A3()].Element() == Atom::HYDROGEN)
+    {
+      // H-O-H Angle. If there is an H-H bond assume this is a rigid water model.
+      if (atoms_[ang->A1()].IsBondedTo( ang->A3() )) {
+        mprintf("DEBUG: H-O-H angle, H-H bond detected. Assuming rigid water, skipping angle: "
+                "%4i %4i %4i (%2s %2s %2s)\n",
+                ang->A1()+1, ang->A2()+1, ang->A3()+1,
+                *types[0], *types[1], *types[2]);
+        continue;
+      }
+    }
+    if (atoms_[ang->A1()].Element() == Atom::OXYGEN &&
+        atoms_[ang->A2()].Element() == Atom::HYDROGEN &&
+        atoms_[ang->A3()].Element() == Atom::HYDROGEN)
+    {
+      // O-H-H Angle. Assume rigid water model
+      mprintf("DEBUG: O-H-H angle. Assuming rigid water, skipping angle: "
+              "%4i %4i %4i (%2s %2s %2s)\n",
+              ang->A1()+1, ang->A2()+1, ang->A3()+1,
+              *types[0], *types[1], *types[2]);
+      continue;
+    }
+
+    bool found;
+    // See if parameter is present.
+    int idx = currentTypes.FindParam( types, found );
+    if (!found) {
+      idx = -1;
+      // Not yet present in current types
+      AngleParmType ap = newAngleParams.FindParam( types, found );
+      if (!found) {
+        mprintf("Warning: Angle parameter not found for angle %s-%s-%s (%s-%s-%s)\n",
+                TruncResAtomNameNum(ang->A1()).c_str(),
+                TruncResAtomNameNum(ang->A2()).c_str(),
+                TruncResAtomNameNum(ang->A3()).c_str(),
+                *types[0], *types[1], *types[2]);
+      } else {
+        //idx = addAngleParm( angleparm_, ap ); // TODO uncomment for array packing
+        idx = (int)angleparm_.size();
+        angleparm_.push_back( ap );
+        //mprintf("DEBUG: New angle type for %s-%s-%s (Tk=%g Teq=%g) idx=%i\n", *types[0], *types[1], *types[2], ap.Tk(), ap.Teq(), idx);
+        currentTypes.AddParm(types, idx, false);
+      }
+    }
+    newAngles.push_back( *ang );
+    newAngles.back().SetIdx( idx );
+  }
+  return newAngles;
+/*
+  for (AngleArray::iterator ang = angles.begin(); ang != angles.end(); ++ang) {
+    TypeNameHolder types(3);
+    types.AddName( atoms_[ang->A1()].Type() );
+    types.AddName( atoms_[ang->A2()].Type() );
+    types.AddName( atoms_[ang->A3()].Type() );
+    bool found;
+    // See if parameter is present.
+    int idx = -1;
+    AngleParmType ap = newAngleParams.FindParam( types, found );
+    if (!found) {
+      mprintf("Warning: Angle parameter not found for angle %s-%s-%s (%s-%s-%s)\n",
+              TruncResAtomNameNum(ang->A1()).c_str(),
+              TruncResAtomNameNum(ang->A2()).c_str(),
+              TruncResAtomNameNum(ang->A3()).c_str(),
+              *types[0], *types[1], *types[3]);
+    } else {
+      idx = addAngleParm( angleparm_, ap );
+    }
+    ang->SetIdx( idx );
+  }*/
+}
+
+/** Replace any current angle parameters with given angle parameters. */
+void AssignParams::AssignAngleParams(ParmHolder<AngleParmType> const& newAngleParams) const {
+  angleparm_.clear();
+  angles_ = AssignAngleParm( newAngleParams, angles_ );
+  anglesh_ = AssignAngleParm( newAngleParams, anglesh_ );
+}
+
+/** Warn if improper atoms have been reordered so they match the parameter. */
+void AssignParams::warn_improper_reorder(DihedralType const& imp0, DihedralType const& imp)
+const
+{
+  if (debug_ < 1) return;
+  mprintf("Warning: Improper types have been reordered from %4s %4s %4s %4s",
+          *(atoms_[imp0.A1()].Type()),
+          *(atoms_[imp0.A2()].Type()),
+          *(atoms_[imp0.A3()].Type()),
+          *(atoms_[imp0.A4()].Type()));
+  mprintf(" to %4s %4s %4s %4s to match improper parameter.\n",
+          *(atoms_[imp.A1()].Type()),
+          *(atoms_[imp.A2()].Type()),
+          *(atoms_[imp.A3()].Type()),
+          *(atoms_[imp.A4()].Type()));
+}
+
+/** Set parameters for improper dihedrals in given improper dihedral array. */
+void AssignParams::AssignImproperParm(ImproperParmHolder const& newImproperParams,
+                                  DihedralArray& impropers,
+                                  DihedralParmArray& dpa)
+const
+{
+  for (DihedralArray::iterator imp = impropers.begin(); imp != impropers.end(); ++imp) {
+    TypeNameHolder types(4);
+    types.AddName( atoms_[imp->A1()].Type() );
+    types.AddName( atoms_[imp->A2()].Type() );
+    types.AddName( atoms_[imp->A3()].Type() );
+    types.AddName( atoms_[imp->A4()].Type() );
+    bool found;
+    // See if parameter is present.
+    int idx = -1;
+    DihedralType imp0 = *imp;
+    bool reordered;
+    DihedralParmArray ipa = newImproperParams.FindParam( types, found, *imp, reordered );
+    if (!found) {
+      mprintf("Warning: Parameter not found for improper %s-%s-%s-%s (%s-%s-%s-%s)\n",
+              TruncResAtomNameNum(imp->A1()).c_str(),
+              TruncResAtomNameNum(imp->A2()).c_str(),
+              TruncResAtomNameNum(imp->A3()).c_str(),
+              TruncResAtomNameNum(imp->A4()).c_str(),
+              *types[0], *types[1], *types[3], *types[4]);
+    } else {
+      if (ipa.size() > 1)
+        mprintf("Warning: %zu improper parameters found for types %s - %s - %s - %s, expected only one."
+                        "Warning: Only using first parameter.\n", ipa.size(), *(types[0]), *(types[1]), *(types[2]), *(types[3]));
+      if (reordered) warn_improper_reorder( imp0, *imp );
+      idx = addTorsionParm( dpa, ipa.front() );
+    }
+    imp->SetIdx( idx );
+  }
+}
+
+/** Replace any current improper parameters with given improper parameters. */
+void AssignParams::AssignImproperParams(ImproperParmHolder const& newImproperParams) const {
+  improperparm_.clear();
+  AssignImproperParm( newImproperParams, impropers_, improperparm_ );
+}
+
+/** Set parameters for dihedrals in given dihedral array.
+  * Bond and angle information must be set up prior to calling
+  * this function in order for improper and 1-4 detection to work.
+  * \param newDihedralParams New proper dihedral parameters.
+  * \param newImproperParams New improper dihedral parameters.
+  * \param dihedrals Array containing only unique dihedrals.
+  * \param sort_improper_cache If true, sort improper types in cache (to match current leap behavior)
+  */
+DihedralArray AssignParams::AssignDihedralParm(DihedralParmHolder const& newDihedralParams,
+                                           ImproperParmHolder const& newImproperParams,
+                                           ParmHolder<AtomType> const& AT,
+                                           DihedralArray const& dihedrals,
+                                           bool sort_improper_cache)
+const
+{ // TODO skip extra points
+  DihedralArray dihedralsIn;
+  // Improper cache
+  ImproperParmHolder improperCache;
+  improperCache.SetWildcard( newImproperParams.Wildcard() );
+  improperCache.SetRequireExactMatch( newImproperParams.RequireExactMatch() );
+  // Keep track of 1-4 interactions
+  typedef std::pair<int,int> Ipair;
+  typedef std::set<Ipair> Imap;
+  Imap PairMap;
+  // Loop over all dihedrals
+  for (DihedralArray::const_iterator dih = dihedrals.begin(); dih != dihedrals.end(); ++dih) {
+    TypeNameHolder types(4);
+    types.AddName( atoms_[dih->A1()].Type() );
+    types.AddName( atoms_[dih->A2()].Type() );
+    types.AddName( atoms_[dih->A3()].Type() );
+    types.AddName( atoms_[dih->A4()].Type() );
+    // Skip extra points // FIXME make this an option
+    if ( atoms_[dih->A1()].Element() == Atom::EXTRAPT ||
+         atoms_[dih->A4()].Element() == Atom::EXTRAPT)
+    {
+      mprintf("DEBUG: Skipping dihedral with extra point: %4i %4i %4i %4i (%2s %2s %2s %2s)\n",
+              dih->A1()+1, dih->A2()+1, dih->A3()+1, dih->A4()+1,
+              *types[0], *types[1], *types[2], *types[3]);
+      continue;
+    }
+//    mprintf("DEBUG: Assigning dihedral %4i %4i %4i %4i (%2s %2s %2s %2s) isImproper=%i skip14=%i\n",
+//            dih->A1()+1, dih->A2()+1, dih->A3()+1, dih->A4()+1,
+//            *types[0], *types[1], *types[2], *types[3],
+//            (int)dih->IsImproper(), (int)dih->Skip14());
+    // Determine improper
+    bool isImproper = (!atoms_[dih->A1()].IsBondedTo(dih->A2())) ||
+                      (!atoms_[dih->A2()].IsBondedTo(dih->A3())) ||
+                      (!atoms_[dih->A3()].IsBondedTo(dih->A4()));
+    if (isImproper != dih->IsImproper()) {
+      mprintf("Warning: dihedral %s-%s-%s-%s improper status %i does not match detected (%i)\n",
+              TruncResAtomNameNum(dih->A1()).c_str(),
+              TruncResAtomNameNum(dih->A2()).c_str(),
+              TruncResAtomNameNum(dih->A3()).c_str(),
+              TruncResAtomNameNum(dih->A4()).c_str(),
+              (int)dih->IsImproper(), (int)isImproper);
+    }
+    bool found;
+    if (dih->IsImproper()) {
+      // ----- This is actually an improper dihedral. ----------------
+      // Impropers are treated differently than other topology types. If
+      // no parameter is found, do not add it to the list of dihedrals.
+      // However, if no parameter is found and the central atom is
+      // SP2, print a warning.
+      found = false;
+      DihedralType mydih = *dih;
+      bool reordered;
+      bool is_new_improper = false;
+      DihedralParmArray ipa;
+      TypeNameHolder paramTypes;
+      ImproperParmHolder::const_iterator impit = improperCache.GetParam( types, mydih, reordered );
+      if (impit == improperCache.end()) {
+        impit = newImproperParams.GetParam( types, mydih, reordered );
+        if (impit != newImproperParams.end()) {
+          is_new_improper = true;
+          paramTypes = impit->first;
+          ipa = impit->second;
+          found = true;
+          if (debug_ > 1)
+            mprintf("DEBUG: Found new value for improper %2s %2s %2s %2s (%2s %2s %2s %2s)\n",
+                    *types[0], *types[1], *types[2], *types[3],
+                    *paramTypes[0], *paramTypes[1], *paramTypes[2], *paramTypes[3]);
+        }
+      } else {
+        // If the cached improper has wildcards, see if there is a more
+        // specific one in the new improper parameters.
+        int n_wildcards = 0;
+        if (newImproperParams.Wildcard().len() > 0) {
+          for (TypeNameHolder::const_iterator tt = impit->first.begin(); tt != impit->first.end(); ++tt) {
+            if ( *tt == newImproperParams.Wildcard() ) {
+              n_wildcards++;
+            }
+          }
+        }
+        if (n_wildcards > 0) {
+          // Check if there is a more specific improper.
+          bool newReordered;
+          DihedralType newdih = *dih;
+          ImproperParmHolder::const_iterator moreSpecificImpit = newImproperParams.GetParam( types, newdih, newReordered );
+          if (moreSpecificImpit != newImproperParams.end()) {
+            // See if the new improper has fewer wildcards than the cached one.
+            int new_wildcards = 0;
+            for (TypeNameHolder::const_iterator tt = moreSpecificImpit->first.begin();
+                                                tt != moreSpecificImpit->first.end(); ++tt)
+            {
+              if ( *tt == newImproperParams.Wildcard() ) {
+                new_wildcards++;
+              }
+            }
+            if (new_wildcards < n_wildcards) {
+              // More specific improper was found.
+              mprintf("DEBUG: A more specific improper was found for %2s %2s %2s %2s (%2s %2s %2s %2s)\n",
+                      *(impit->first[0]), *(impit->first[1]), *(impit->first[2]), *(impit->first[3]),
+                      *(moreSpecificImpit->first[0]), *(moreSpecificImpit->first[1]), *(moreSpecificImpit->first[2]), *(moreSpecificImpit->first[3]));
+              is_new_improper = true;
+              reordered = newReordered;
+              mydih = newdih;
+              impit = moreSpecificImpit;
+            }
+          }
+        } // END found improper had wildcards
+        paramTypes = impit->first;
+        ipa = impit->second;
+        found = true;
+        if (debug_ > 1)
+          mprintf("DEBUG: Using cached value for improper %2s %2s %2s %2s (%2s %2s %2s %2s)\n",
+                  *types[0], *types[1], *types[2], *types[3],
+                  *paramTypes[0], *paramTypes[1], *paramTypes[2], *paramTypes[3]);
+      }
+      int idx = -1;
+      if (!found) {
+        if (debug_ > 0)
+          mprintf("Warning: Improper parameters not found for improper dihedral %s-%s-%s-%s (%s-%s-%s-%s)\n",
+                  TruncResAtomNameNum(dih->A1()).c_str(),
+                  TruncResAtomNameNum(dih->A2()).c_str(),
+                  TruncResAtomNameNum(dih->A3()).c_str(),
+                  TruncResAtomNameNum(dih->A4()).c_str(),
+                  *types[0], *types[1], *types[2], *types[3]);
+        // Central atom
+        Atom const& AJ = atoms_[dih->A3()];
+        AtomType::HybridizationType hybrid = AtomType::UNKNOWN_HYBRIDIZATION;
+        AtomType atype = AT.FindParam(TypeNameHolder(AJ.Type()), found);
+        if (found)
+          hybrid = atype.Hybridization();
+        if (hybrid == AtomType::UNKNOWN_HYBRIDIZATION) {
+          mprintf("Warning: Guessing hybridization for improper central atom %s\n", AtomMaskName(dih->A3()).c_str());
+          hybrid = Cpptraj::GuessAtomHybridization( AJ, atoms_ );
+        }
+        if (hybrid == AtomType::SP2) {
+          mprintf("Warning: No improper parameters for SP2 hybridized atom %s\n", AtomMaskName(dih->A3()).c_str());
+        }
+      } else {
+        if (ipa.size() > 1)
+          mprintf("Warning: %zu improper parameters found for types %s - %s - %s - %s, expected only one."
+                  "Warning: Only using first parameter.\n", ipa.size(), *(types[0]), *(types[1]), *(types[2]), *(types[3]));
+        if (reordered) warn_improper_reorder( *dih, mydih );
+        idx = addTorsionParm( dihedralparm_, ipa.front() );
+        mydih.SetIdx( idx );
+        mydih.SetImproper( true );
+        // Always skip 1-4 for impropers
+        mydih.SetSkip14( true );
+        dihedralsIn.push_back( mydih );
+        // Add to the cache
+        if (is_new_improper) {
+          // To match leap behavior, make sure paramTypes are sorted alphabetically.
+          //mprintf("DEBUG: Improper wildcard: %s\n", *(newImproperParams.Wildcard()));
+          if (sort_improper_cache) paramTypes.SortImproperByAlpha( newImproperParams.Wildcard() );
+          improperCache.AddParm( paramTypes, ipa.front(), false );
+        }
+      }
+    } else {
+      // -----Regular dihedral. See if parameter already present. ----
+      DihedralParmArray dpa = newDihedralParams.FindParam( types, found );
+      if (!found) {
+        mprintf("Warning: Dihedral parameters not found for dihedral %s-%s-%s-%s (%s-%s-%s-%s)\n",
+                TruncResAtomNameNum(dih->A1()).c_str(),
+                TruncResAtomNameNum(dih->A2()).c_str(),
+                TruncResAtomNameNum(dih->A3()).c_str(),
+                TruncResAtomNameNum(dih->A4()).c_str(),
+                *types[0], *types[1], *types[2], *types[3]);
+        DihedralType mydih = *dih;
+        mydih.SetIdx( -1 );
+        dihedralsIn.push_back( mydih );
+      } else {
+        // Actually add parameters for this dihedral.
+        // Determine if this is actually a 1-4 interaction by making
+        // sure that A4 isnt part of a bond or angle with A1.
+        bool skip14 = false;
+        for (Atom::bond_iterator bat1 = atoms_[dih->A1()].bondbegin();
+                                 bat1 != atoms_[dih->A1()].bondend(); ++bat1)
+        {
+          if (*bat1 != dih->A2()) {
+            if (*bat1 == dih->A4()) {
+              skip14 = true;
+              break;
+            }
+            // Loop over angles, dih->A1() - bat1 - bat2
+            for (Atom::bond_iterator bat2 = atoms_[*bat1].bondbegin();
+                                     bat2 != atoms_[*bat1].bondend(); ++bat2)
+            {
+              //if (dih->A1() == 442 && dih->A4() == 444) { // DEBUG
+              //  mprintf("DEBUG: %4i %4i %4i %4i Checking angle %4i %4i %4i\n", dih->A1()+1, dih->A2()+1, dih->A3()+1, dih->A4()+1, dih->A1()+1, *bat1 + 1, *bat2 + 1);
+              //}
+              if (*bat2 != *bat1) {
+                if (*bat2 == dih->A4()) {
+                  skip14 = true;
+                  break;
+                }
+              }
+            } // END loop over bat1 bonded atoms
+            if (skip14) break;
+          }
+        } // END loop over dih->A1() bonded atoms
+        if (!skip14) {
+          // Determine if 1-4 interaction already calculated by previous dihedral.
+          // Make the lower end atom first. 
+          Ipair pair14;
+          if (dih->A1() < dih->A4()) {
+            pair14.first = dih->A1();
+            pair14.second = dih->A4();
+          } else {
+            pair14.first = dih->A4();
+            pair14.second = dih->A1();
+          }
+          Imap::const_iterator it = PairMap.find( pair14 );
+          if (it == PairMap.end()) {
+            skip14 = false;
+            PairMap.insert( pair14 );
+          } else {
+            skip14 = true;
+            //mprintf("DEBUG: Prior 1-4 calc detected.\n");
+          }
+        }
+        // Loop over multiplicities
+        //if (dih->A1() == 442 && dih->A4() == 444) { // DEBUG
+        //  mprintf("DEBUG: Skip14= %i\n", (int)skip14);
+        //}
+        for (DihedralParmArray::const_iterator it = dpa.begin(); it != dpa.end(); ++it) {
+          DihedralType mydih = *dih;
+          int idx = addTorsionParm( dihedralparm_, *it );
+          // If there are multiple parameters for the same dihedral, all but
+          // one of the 1-4 calcs need to be skipped.
+          if (it == dpa.begin())
+            mydih.SetSkip14(skip14);
+          else
+            mydih.SetSkip14(true);
+          mydih.SetIdx( idx );
+          dihedralsIn.push_back( mydih );
+//          mprintf("DEBUG: Assigned %4i %4i %4i %4i (%2s %2s %2s %2s) isImproper=%i skip14=%i\n",
+//            mydih.A1()+1, mydih.A2()+1, mydih.A3()+1, mydih.A4()+1,
+//            *types[0], *types[1], *types[2], *types[3],
+//            (int)mydih.IsImproper(), (int)mydih.Skip14());
+        }
+      }
+    }
+  } // END loop over all dihedrals
+  return dihedralsIn;
+}
+
+/** \return Array of only unique dihedrals (get rid of multiplicities) */
+DihedralArray AssignParams::get_unique_dihedrals(DihedralArray const& dihedralsIn) const {
+  // Assume dihedrals with multiple terms are consecutive already
+  DihedralArray dihedrals;
+  for (DihedralArray::const_iterator dih = dihedralsIn.begin(); dih != dihedralsIn.end(); ++dih) {
+    if (dihedrals.empty())
+      dihedrals.push_back( *dih );
+    else {
+      if ( *dih != dihedrals.back() ) // TODO skip end dihedrals, impropers?
+        dihedrals.push_back( *dih );
+    }
+  }
+  if (debug_ > 0)
+    mprintf("DEBUG: %zu incoming dihedrals, %zu unique dihedrals.\n",
+            dihedralsIn.size(), dihedrals.size());
+  return dihedrals;
+}
+
+/** Replace any current dihedral parameters with given dihedral parameters. */
+void AssignParams::AssignDihedralParams(DihedralParmHolder const& newDihedralParams,
+                                        ImproperParmHolder const& newImproperParams,
+                                        ParmHolder<AtomType> const& AT)
+const
+{
+  dihedralparm_.clear();
+  // Dihedrals can be a bit of a pain since there can be multiple
+  // multiplicities for a single dihedral type. In case multiplicities
+  // change, start with a fresh dihedral array containing only unique
+  // dihedrals.
+  dihedrals_  = AssignDihedralParm( newDihedralParams, newImproperParams, AT, get_unique_dihedrals(dihedrals_), false  );
+  dihedralsh_ = AssignDihedralParm( newDihedralParams, newImproperParams, AT, get_unique_dihedrals(dihedralsh_), false );
+}
+
+/** Replace current nonbond parameters with given nonbond parameters. */
+//TODO Accept array of atom type names?
+void AssignParams::AssignNonbondParams(ParmHolder<AtomType> const& newTypes,
+                                   ParmHolder<NonbondType> const& newNB,
+                                   ParmHolder<NonbondType> const& new14,
+                                   ParmHolder<double> const& newLJC,
+                                   ParmHolder<HB_ParmType> const& newHB,
+                                   int verbose)
+const
+{
+  bool hasLJ14 = !new14.empty();
+  bool hasLJC = !newLJC.empty();
+  // Generate array of only the types that are currently in Topology. TODO should this be a permanent part of Topology?
+  ParmHolder<AtomType> currentAtomTypes;
+  for (std::vector<Atom>::const_iterator atm = atoms_.begin(); atm != atoms_.end(); ++atm)
+  {
+    if (atm->HasType()) {
+      TypeNameHolder types(1);
+      types.AddName(atm->Type());
+      // Find in newTypes.
+      bool found;
+      AtomType newAT = newTypes.FindParam( types, found );
+      if (!found) {
+        mprintf("Warning: No atom type information for type '%s'\n", *types[0]);
+        newAT = AtomType(atm->Mass());
+      }
+      // Check LJ14 types if needed
+      if (hasLJ14) {
+        if (!newAT.HasLJ14()) {
+          mprintf("Warning: No 1-4 atom type information for type '%s'\n", *types[0]); // TODO error out here?
+        }
+      }
+      currentAtomTypes.AddParm( types, newAT, true );
+    }
+  }
+  if (currentAtomTypes.size() < 1) {
+    mprintf("Warning: No atom type information in %s - cannot assign nonbond parameters.\n",
+            c_str());
+    return;
+  }
+  // Regenerate nonbond params for existing types
+  nonbond_.Clear();
+  // Set type indices in order.
+  for (ParmHolder<AtomType>::iterator t1 = currentAtomTypes.begin(); t1 != currentAtomTypes.end(); ++t1)
+    t1->second.SetTypeIdx( -1 );
+  int n_unique_lj_types = 0;
+  for (ParmHolder<AtomType>::iterator t1 = currentAtomTypes.begin(); t1 != currentAtomTypes.end(); ++t1)
+  {
+    if (t1->second.OriginalIdx() == -1) {
+      t1->second.SetTypeIdx( n_unique_lj_types );
+      // Look for equivalent nonbond types
+      for (ParmHolder<AtomType>::iterator t2 = t1 + 1; t2 != currentAtomTypes.end(); ++t2) {
+        // Everything must match
+        if (!hasLJ14) {
+          if (t2->second.OriginalIdx() == -1 && t1->second.LJ() == t2->second.LJ()) {
+            mprintf("DEBUG: Type %s equivalent to type %s\n", *(t2->first[0]), *(t1->first[0]));
+            t2->second.SetTypeIdx( n_unique_lj_types );
+          }
+        } else {
+          if (t2->second.OriginalIdx() == -1 &&
+              t1->second.LJ() == t2->second.LJ() &&
+              t1->second.LJ14() == t2->second.LJ14())
+          {
+            mprintf("DEBUG: Type %s (with 1-4 params) equivalent to type %s\n", *(t2->first[0]), *(t1->first[0]));
+            t2->second.SetTypeIdx( n_unique_lj_types );
+          }
+        }
+      }
+      n_unique_lj_types++;
+    }
+  }
+  mprintf("DEBUG: Setting up nonbond array for %i unique LJ types.\n", n_unique_lj_types);
+  nonbond_.SetupLJforNtypes( n_unique_lj_types );
+  if (hasLJ14)
+    nonbond_.SetNLJ14terms( nonbond_.NBarray().size() );
+  if (hasLJC)
+    nonbond_.SetNLJCterms( nonbond_.NBarray().size() );
+  // Loop over all atom type pairs
+  for (ParmHolder<AtomType>::const_iterator t1 = currentAtomTypes.begin(); t1 != currentAtomTypes.end(); ++t1)
+  {
+    NameType const& name1 = t1->first[0];
+    //mprintf("DEBUG: Type1= %s (%i)\n", *name1, nidx1);
+    AtomType const& type1 = t1->second;
+    for (ParmHolder<AtomType>::const_iterator t2 = t1; t2 != currentAtomTypes.end(); ++t2)
+    {
+      NameType const& name2 = t2->first[0];
+      //mprintf("DEBUG:\t\tType2= %s (%i)\n", *name2, nidx2);
+      AtomType const& type2 = t2->second;
+      TypeNameHolder types(2);
+      types.AddName( name1 );
+      types.AddName( name2 );
+      int newnbidx;
+      // Check for LJ10-12 first
+      ParmHolder<HB_ParmType>::const_iterator hb = newHB.GetParam( types );
+      if (hb != newHB.end()) {
+        if (verbose > 0) mprintf("LJ 10-12 parameter found for %s %s\n", *name1, *name2);
+        nonbond_.AddHBterm(t1->second.OriginalIdx(), t2->second.OriginalIdx(), hb->second);
+        // Also add a blank 6-12 term since that seems to be the convention
+        newnbidx = nonbond_.AddLJterm( t1->second.OriginalIdx(), t2->second.OriginalIdx(), NonbondType() );
+      } else {
+        // See if this parameter exists in the given nonbond array.
+        NonbondType LJAB;
+        ParmHolder<NonbondType>::const_iterator it = newNB.GetParam( types );
+        if (it == newNB.end()) {
+          if (verbose > 0) mprintf("NB parameter for %s %s not found. Generating.\n", *name1, *name2);
+          LJAB = type1.LJ().Combine_LB( type2.LJ() );
+        } else {
+          if (verbose > 0) mprintf("Using existing NB parameter for %s %s\n", *name1, *name2);
+          LJAB = it->second;
+        }
+        newnbidx = nonbond_.AddLJterm(t1->second.OriginalIdx(), t2->second.OriginalIdx(), LJAB);
+      }
+      // LJ 1-4
+      if (hasLJ14) {
+        // Get parameter if it exists
+        ParmHolder<NonbondType>::const_iterator it = new14.GetParam( types );
+        if (it == new14.end()) {
+          if (verbose > 0) mprintf("NB 1-4 parameter for %s %s not found. Generating.\n", *name1, *name2);
+          nonbond_.SetLJ14( newnbidx ) = type1.LJ14().Combine_LB( type2.LJ14() );
+        } else {
+          if (verbose > 0) mprintf("Using existing NB 1-4 parameter for %s %s\n", *name1, *name2);
+          nonbond_.SetLJ14( newnbidx ) = it->second;
+        }
+      } // END hasLJ14
+      // LJC
+      if (hasLJC) {
+        // Get parameter if it exists
+        ParmHolder<double>::const_iterator it = newLJC.GetParam( types );
+        if (it == newLJC.end()) {
+          mprintf("LJC parameter for %s %s not found. Setting to 0.\n", *name1, *name2); // FIXME generate
+          nonbond_.SetLJC( newnbidx, 0 );
+        } else {
+          mprintf("Using existing LJC parameter for %s %s\n", *name1, *name2);
+          nonbond_.SetLJC( newnbidx, it->second );
+        }
+      } // END hasLJC
+    } // END inner loop over current types
+  } // END outer loop over current types
+  // Reset the atom type indices.
+  for (std::vector<Atom>::iterator atm = atoms_.begin(); atm != atoms_.end(); ++atm)
+  {
+    int tidx = -1;
+    ParmHolder<AtomType>::const_iterator it = currentAtomTypes.GetParam( TypeNameHolder(atm->Type()) );
+    if (it == currentAtomTypes.end()) {
+      mprintf("Warning: Atom type not found for %s (type %s)\n",
+              TruncResAtomNameNum( atm - atoms_.begin() ).c_str(),
+              *(atm->Type()));
+    } else {
+      if (it->second.OriginalIdx() < 0 || it->second.OriginalIdx() >= (int)currentAtomTypes.size()) {
+        mprinterr("Internal Error: Type index for %s (type %s) out of range: %i\n",
+                  TruncResAtomNameNum( atm - atoms_.begin() ).c_str(),
+                  *(atm->Type()), it->second.OriginalIdx());
+      } else
+        tidx = it->second.OriginalIdx();
+    }
+    atm->SetTypeIndex( tidx );
+  }
+}
+
+/// \return index of 5th cmap atom if atom names match those in dihedral, -1 otherwise
+static inline int cmap_anames_match(DihedralType const& dih,
+                                     std::vector<Atom> const& atoms,
+                                     std::vector<std::string> const& cmapAtomNames)
+{
+/*  mprintf("DEBUG: Check res %i %s %s %s %s against %s %s %s %s\n",
+          atoms[dih.A2()].ResNum()+1,
+            atoms[dih.A1()].Name().Truncated().c_str(),
+            atoms[dih.A2()].Name().Truncated().c_str(),
+            atoms[dih.A3()].Name().Truncated().c_str(),
+            atoms[dih.A4()].Name().Truncated().c_str(),
+            cmap.AtomNames()[0].c_str(),
+            cmap.AtomNames()[1].c_str(),
+            cmap.AtomNames()[2].c_str(),
+            cmap.AtomNames()[3].c_str());*/
+  // TODO without Truncated
+  if (atoms[dih.A1()].Name().Truncated() == cmapAtomNames[0] &&
+      atoms[dih.A2()].Name().Truncated() == cmapAtomNames[1] &&
+      atoms[dih.A3()].Name().Truncated() == cmapAtomNames[2] &&
+      atoms[dih.A4()].Name().Truncated() == cmapAtomNames[3])
+  {
+    /*mprintf("DEBUG: Partial match %s %s %s %s = %s %s %s %s\n",
+            atoms[dih.A1()].Name().Truncated().c_str(),
+            atoms[dih.A2()].Name().Truncated().c_str(),
+            atoms[dih.A3()].Name().Truncated().c_str(),
+            atoms[dih.A4()].Name().Truncated().c_str(),
+            cmap.AtomNames()[0].c_str(),
+            cmap.AtomNames()[1].c_str(),
+            cmap.AtomNames()[2].c_str(),
+            cmap.AtomNames()[3].c_str());*/
+    for (Atom::bond_iterator bat = atoms[dih.A4()].bondbegin();
+                             bat != atoms[dih.A4()].bondend(); ++bat)
+    {
+      if (*bat != dih.A3()) { // TODO can A4 ever be bonded to A1??
+        if (atoms[*bat].Name().Truncated() == cmapAtomNames[4]) {
+          return *bat;
+        }
+      }
+    }
+  }
+  return -1;
+}
+
+/// \return true if given name matches a residue name
+static inline bool MatchesResName(std::vector<std::string> const& resNames, std::string const& nameIn) {
+  for (std::vector<std::string>::const_iterator it = resNames.begin(); it != resNames.end(); ++it)
+    if (nameIn == *it) return true;
+  return false;
+}
+
+/// Remap cmap indices
+int AssignParams::remap_cmap_indices(std::vector<int>& originalCmapIndices,
+                                     CmapGridArray& cmapGrids,
+                                     CmapArray& cmapTerms,
+                                 CmapParmHolder const& cmapIn)
+const
+{
+  mprintf("DEBUG: Cmap parameter indices:\n");
+  for (unsigned int idx = 0; idx < originalCmapIndices.size(); idx++)
+    mprintf("DEBUG:\t\tCurrent idx=%i  Actual idx=%u\n", originalCmapIndices[idx], idx);
+  if (originalCmapIndices.empty()) {
+    mprintf("DEBUG: No CMAP indices in %s\n", c_str());
+    return 0;
+  }
+  std::sort(originalCmapIndices.begin(), originalCmapIndices.end());
+  std::vector<int> currentToNew(cmapIn.size(), -1);
+  // Add the grid terms in original parameter file order
+  // and create map from assigned index to new index.
+  cmapGrids.reserve( originalCmapIndices.size() );
+  for (unsigned int idx = 0; idx < originalCmapIndices.size(); idx++) {
+    mprintf("DEBUG: Will change cmap parameter index %i to %u\n",
+            originalCmapIndices[idx]+1, idx+1);
+    currentToNew[ originalCmapIndices[idx] ] = idx;
+    cmapGrids.push_back( cmapIn[ originalCmapIndices[idx] ] );
+  }
+  mprintf("DEBUG: Assigned CMAP parameters:\n");
+  for (CmapGridArray::const_iterator it = cmapGrids.begin(); it != cmapGrids.end(); ++it)
+    mprintf("DEBUG:\t\t%li : %s\n", it-cmapGrids.begin(), it->Title().c_str());
+  // Renumber the parameter indices
+  for (CmapArray::iterator it = cmapTerms.begin(); it != cmapTerms.end(); ++it) {
+    int newIdx = currentToNew[ it->Idx() ];
+    if (newIdx < 0) {
+      mprinterr("Internal Error: CMAP term index is not mapped.\n");
+      return 1;
+    }
+    it->SetIdx( newIdx );
+  }
+  return 0;
+}
+
+/** Assign CMAP parameters to existing CMAP terms. */
+int AssignParams::AssignCmapParams(CmapArray& cmapTerms, CmapParmHolder const& cmapIn,
+                               CmapGridArray& cmapGrids)
+const
+{
+  // Keep track of residue names each cmap applies to
+  typedef std::vector<std::string> Sarray;
+  std::vector<Sarray> CmapResNames;
+  std::vector<Sarray> CmapAtomNames;
+  // The LEaP convention is to number the CMAP parameters in the same
+  // order as they are listed in the original parameter file. This
+  // variable keeps track of those indices.
+  std::vector<int> originalCmapIndices;
+  for (CmapArray::iterator cm = cmapTerms.begin(); cm != cmapTerms.end(); ++cm)
+  {
+    // Get residue name for A2
+    Atom const& A2 = atoms_[cm->A2()];
+    // TODO make sure A2-A4 in same residue?
+    NameType const& rn2 = residues_[A2.ResNum()].Name();
+    // Is this residue already in cmapGrids?
+    int cidx = -1;
+    for (unsigned int idx = 0; idx != CmapResNames.size(); idx++) {
+      if ( MatchesResName(CmapResNames[idx], rn2.Truncated()) ) {
+        if (atoms_[cm->A1()].Name() == CmapAtomNames[idx][0] &&
+            atoms_[cm->A2()].Name() == CmapAtomNames[idx][1] &&
+            atoms_[cm->A3()].Name() == CmapAtomNames[idx][2] &&
+            atoms_[cm->A4()].Name() == CmapAtomNames[idx][3] &&
+            atoms_[cm->A5()].Name() == CmapAtomNames[idx][4])
+        {
+          cidx = originalCmapIndices[idx];
+          break;
+        }
+      }
+    }
+    if (cidx > -1) {
+      mprintf("DEBUG: Potential existing cmap %i found for %s (%li)\n", cidx, TruncResNameNum(A2.ResNum()).c_str(), cm-cmapTerms.begin());
+      mprintf("DEBUG:\t\t%i - %i - %i - %i - %i %i\n", cm->A1()+1, cm->A2()+1, cm->A3()+1, cm->A4()+1, cm->A5()+1, cidx+1);
+      cm->SetIdx( cidx );
+    }
+    // If not already in cmapGrids, check cmapIn
+    if (cidx == -1) {
+      for (unsigned int idx = 0; idx != cmapIn.size(); idx++) {
+        if ( MatchesResName( cmapIn[idx].ResNames(), rn2.Truncated() ) ) {
+          if (atoms_[cm->A1()].Name() == cmapIn[idx].AtomNames()[0] &&
+              atoms_[cm->A2()].Name() == cmapIn[idx].AtomNames()[1] &&
+              atoms_[cm->A3()].Name() == cmapIn[idx].AtomNames()[2] &&
+              atoms_[cm->A4()].Name() == cmapIn[idx].AtomNames()[3] &&
+              atoms_[cm->A5()].Name() == cmapIn[idx].AtomNames()[4])
+          {
+            cidx = (int)idx;
+            CmapResNames.push_back( cmapIn[idx].ResNames() );
+            CmapAtomNames.push_back( cmapIn[idx].AtomNames() );
+            originalCmapIndices.push_back( idx );
+            break;
+          }
+        }
+      }
+      if (cidx > -1) {
+        mprintf("DEBUG: Potential new cmap %i found for %s (%li)\n", cidx, TruncResNameNum(A2.ResNum()).c_str(), cm-cmapTerms.begin());
+        mprintf("DEBUG:\t\t%i - %i - %i - %i - %i %i\n", cm->A1()+1, cm->A2()+1, cm->A3()+1, cm->A4()+1, cm->A5()+1, cidx+1);
+        //mprintf("DEBUG:\t\t%s - %s - %s - %s - %s\n",
+        //        AtomMaskName(dih->A1()).c_str(),
+        //        AtomMaskName(dih->A2()).c_str(),
+        //        AtomMaskName(dih->A3()).c_str(),
+        //        AtomMaskName(dih->A4()).c_str(),
+        //        AtomMaskName(a5).c_str());
+        cm->SetIdx( cidx );
+      }
+    }
+  } // END loop over cmap terms
+
+  return remap_cmap_indices(originalCmapIndices, cmapGrids, cmapTerms, cmapIn);
+}
+
+/** Assign CMAP parameters. Also generates CMAP terms from dihedrals. */
+int AssignParams::AssignCmapParams(DihedralArray const& allDih, CmapParmHolder const& cmapIn,
+                               CmapGridArray& cmapGrids, CmapArray& cmapTerms)
+const
+{
+  // TODO check for duplicates, look for reverse match?
+  // Keep track of residue names each cmap applies to
+  //typedef std::vector<NameType> Narray;
+  typedef std::vector<std::string> Sarray;
+  std::vector<Sarray> CmapResNames;
+  std::vector<Sarray> CmapAtomNames;
+  // The LEaP convention is to number the CMAP parameters in the same
+  // order as they are listed in the original parameter file. This
+  // variable keeps track of those indices.
+  std::vector<int> originalCmapIndices;
+  // TODO combine with AssignDihedrals?
+  for (DihedralArray::const_iterator dih = allDih.begin(); dih != allDih.end(); ++dih)
+  {
+    // Ignore end (repeated) or improper dihedrals
+    if (dih->IsImproper() || dih->Skip14()) continue;
+    // Get residue name for A2
+    Atom const& A2 = atoms_[dih->A2()];
+    // TODO make sure A2-A4 in same residue?
+    NameType const& rn2 = residues_[A2.ResNum()].Name();
+    // Is this residue already in cmapGrids?
+    int cidx = -1;
+    int a5 = -1;
+    //for (unsigned int idx = 0; idx != cmapGrids.size(); idx++) {
+    //  if (cmapGrids[idx].MatchesResName( rn2.Truncated() )) {
+    for (unsigned int idx = 0; idx != CmapResNames.size(); idx++) {
+      if ( MatchesResName(CmapResNames[idx], rn2.Truncated()) ) {
+        //a5 = cmap_anames_match(*dih, atoms_, cmapGrids[idx]);
+        a5 = cmap_anames_match(*dih, atoms_, CmapAtomNames[idx]);
+        if (a5 > -1) {
+          //cidx = (int)idx;
+          cidx = originalCmapIndices[idx];
+          break;
+        }
+      }
+    }
+    if (cidx > -1) {
+      mprintf("DEBUG: Potential existing cmap %i found for %s (%li)\n", cidx, TruncResNameNum(A2.ResNum()).c_str(), dih-allDih.begin());
+      mprintf("DEBUG:\t\t%i - %i - %i - %i - %i %i\n", dih->A1()+1, dih->A2()+1, dih->A3()+1, dih->A4()+1, a5+1, cidx+1);
+//      mprintf("DEBUG:\t\t%s - %s - %s - %s - %s\n",
+//              AtomMaskName(dih->A1()).c_str(),
+//              AtomMaskName(dih->A2()).c_str(),
+//              AtomMaskName(dih->A3()).c_str(),
+//              AtomMaskName(dih->A4()).c_str(),
+//              AtomMaskName(a5).c_str());
+      cmapTerms.push_back( CmapType(dih->A1(), dih->A2(), dih->A3(), dih->A4(), a5, cidx) );
+    }
+    // If not already in cmapGrids, check cmapIn
+    if (cidx == -1) {
+      //int nidx = -1;
+      for (unsigned int idx = 0; idx != cmapIn.size(); idx++) {
+        //if (cmapIn[idx].MatchesResName( rn2.Truncated() )) {
+        if ( MatchesResName( cmapIn[idx].ResNames(), rn2.Truncated() ) ) {
+          //a5 = cmap_anames_match(*dih, atoms_, cmapIn[idx]);
+          a5 = cmap_anames_match(*dih, atoms_, cmapIn[idx].AtomNames());
+          if (a5 > -1) {
+            //cidx = (int)cmapGrids.size();
+            cidx = (int)idx;
+            //cmapGrids.push_back( cmapIn[idx] );
+            CmapResNames.push_back( cmapIn[idx].ResNames() );
+            CmapAtomNames.push_back( cmapIn[idx].AtomNames() );
+            originalCmapIndices.push_back( idx );
+            //nidx = (int)idx;
+            break;
+          }
+        }
+      }
+      if (cidx > -1) {
+        mprintf("DEBUG: Potential new cmap %i found for %s (%li)\n", cidx, TruncResNameNum(A2.ResNum()).c_str(), dih-allDih.begin());
+        mprintf("DEBUG:\t\t%i - %i - %i - %i - %i %i\n", dih->A1()+1, dih->A2()+1, dih->A3()+1, dih->A4()+1, a5+1, cidx+1);
+      //mprintf("DEBUG:\t\t%s - %s - %s - %s - %s\n",
+      //        AtomMaskName(dih->A1()).c_str(),
+      //        AtomMaskName(dih->A2()).c_str(),
+      //        AtomMaskName(dih->A3()).c_str(),
+      //        AtomMaskName(dih->A4()).c_str(),
+      //        AtomMaskName(a5).c_str());
+        cmapTerms.push_back( CmapType(dih->A1(), dih->A2(), dih->A3(), dih->A4(), a5, cidx) );
+      }
+    }
+  } // END loop over dihedrals
+  return remap_cmap_indices(originalCmapIndices, cmapGrids, cmapTerms, cmapIn);
+/*  mprintf("DEBUG: Cmap parameter indices:\n");
+  for (unsigned int idx = 0; idx < originalCmapIndices.size(); idx++)
+    mprintf("DEBUG:\t\tCurrent idx=%i  Actual idx=%u\n", originalCmapIndices[idx], idx);
+  if (originalCmapIndices.empty()) {
+    mprintf("DEBUG: No CMAP indices in %s\n", c_str());
+    return 0;
+  }
+  std::sort(originalCmapIndices.begin(), originalCmapIndices.end());
+  std::vector<int> currentToNew(cmapIn.size(), -1);
+  // Add the grid terms in original parameter file order
+  // and create map from assigned index to new index.
+  cmapGrids.reserve( originalCmapIndices.size() );
+  for (unsigned int idx = 0; idx < originalCmapIndices.size(); idx++) {
+    mprintf("DEBUG: Will change cmap parameter index %i to %u\n",
+            originalCmapIndices[idx]+1, idx+1);
+    currentToNew[ originalCmapIndices[idx] ] = idx;
+    cmapGrids.push_back( cmapIn[ originalCmapIndices[idx] ] );
+  }
+  mprintf("DEBUG: Assigned CMAP parameters:\n");
+  for (CmapGridArray::const_iterator it = cmapGrids.begin(); it != cmapGrids.end(); ++it)
+    mprintf("DEBUG:\t\t%li : %s\n", it-cmapGrids.begin(), it->Title().c_str());
+  // Renumber the parameter indices
+  for (CmapArray::iterator it = cmapTerms.begin(); it != cmapTerms.end(); ++it) {
+    int newIdx = currentToNew[ it->Idx() ];
+    if (newIdx < 0) {
+      mprinterr("Internal Error: CMAP term index is not mapped.\n");
+      return 1;
+    }
+    it->SetIdx( newIdx );
+  }
+  return 0;*/
+}
+
+/** Replace existing parameters with the given parameter set. */
+int AssignParams::AssignParameters(ParameterSet const& set0) const {
+
+  // Bond parameters
+  mprintf("\tAssigning bond parameters.\n");
+  bondparm_.clear();
+  // Regenerate bond array in LEaP order
+  bonds_.clear();
+  bondsh_.clear();
+  BondArray allBonds = Cpptraj::Structure::GenerateBondArray(residues_, atoms_);
+  AssignBondParm( set0.BP(), allBonds, bondparm_, "bond" );
+  for (BondArray::const_iterator bnd = allBonds.begin(); bnd != allBonds.end(); ++bnd)
+    AddToBondArrays( *bnd );
+  // Angle parameters
+  mprintf("\tAssigning angle parameters.\n");
+  angleparm_.clear();
+  // Regenerate angle array in LEaP order
+  angles_.clear();
+  anglesh_.clear();
+  AngleArray allAngles = Cpptraj::Structure::GenerateAngleArray(residues_, atoms_);
+  allAngles = AssignAngleParm( set0.AP(), allAngles );
+  for (AngleArray::const_iterator ang = allAngles.begin(); ang != allAngles.end(); ++ang)
+    AddToAngleArrays( *ang );
+  // Dihedral parameters
+  mprintf("\tAssigning dihedral parameters.\n");
+  dihedralparm_.clear();
+  // Regenerate dihedral array in LEaP order
+  dihedrals_.clear();
+  dihedralsh_.clear();
+  DihedralArray allDihedrals = Cpptraj::Structure::GenerateDihedralArray(residues_, atoms_);
+  // If we need CMAP terms, do it here before the dihedrals array is modified
+  if (!set0.CMAP().empty()) {
+    cmap_.clear();
+    cmapGrid_.clear();
+    mprintf("\tAssigning CMAP parameters.\n");
+    AssignCmapParams( allDihedrals, set0.CMAP(), cmapGrid_, cmap_ );
+  } 
+  // Now modify the dihedrals for any multiplicities
+  allDihedrals = AssignDihedralParm( set0.DP(), set0.IP(), set0.AT(), allDihedrals, false );
+  for (DihedralArray::const_iterator dih = allDihedrals.begin(); dih != allDihedrals.end(); ++dih)
+    AddToDihedralArrays( *dih );
+  // Urey-Bradley
+  mprintf("\tAssigning Urey-Bradley parameters.\n");
+  AssignUBParams( set0.UB() );
+  if (!impropers_.empty()) {
+    // Charmm Improper parameters
+    mprintf("\tAssigning CHARMM improper parameters.\n");
+    AssignImproperParams( set0.IP() );
+  } else {
+    // Amber improper parameters
+    mprintf("\tAssigning improper parameters.\n");
+    DihedralArray allImpropers = Cpptraj::Structure::GenerateImproperArray(residues_, atoms_);
+    allImpropers = AssignDihedralParm( set0.DP(), set0.IP(), set0.AT(), allImpropers, true );
+    for (DihedralArray::const_iterator imp = allImpropers.begin(); imp != allImpropers.end(); ++imp)
+      AddToDihedralArrays( *imp );
+  }
+  // Atom types
+  mprintf("\tAssigning atom type parameters.\n");
+  AssignAtomTypeParm( set0.AT() );
+  // LJ 6-12
+  mprintf("\tAssigning nonbond parameters.\n");
+  AssignNonbondParams( set0.AT(), set0.NB(), set0.NB14(), set0.LJC(), set0.HB(), debug_ );
+  mprintf("DEBUG: CMAP size %zu\n", set0.CMAP().size());
+
+  return 0;
+}
+
+/** Update/add to parameters in this topology with those from given set.
+  */
+int AssignParams::UpdateParameters(ParameterSet const& set1) const {
+  ParameterSet set0 = GetParameters();
+
+  //set1.Summary(); // DEBUG
+  // Check TODO is this necessary?
+  if (set0.AT().size() < 1)
+    mprintf("Warning: No atom type information in '%s'\n", c_str());
+  if (debug_ > 0) {
+    mprintf("DEBUG: Saving original parameters in originalp.dat, new parameters in newp.dat\n");
+    set0.Debug("originalp.dat");
+  }
+  // Update existing parameters with new parameters
+  ParameterSet::UpdateCount UC;
+  if (set0.UpdateParamSet( set1, UC, debug_, debug_ )) { // FIXME verbose
+    mprinterr("Error: Could not merge topology '%s' parameters with '%s' parameters.\n",
+              c_str(), set1.ParamSetName().c_str());
+    return 1;
+  }
+  mprintf("DEBUG: Updated parameters.\n");
+  set0.Summary();
+  //set0.Debug();
+
+//  unsigned int updateCount;
+  // Bond parameters
+//  updateCount = UpdateParameters< ParmHolder<BondParmType> >(set0.BP(), set1.BP(), "bond");
+  if (UC.nBondsUpdated_ > 0) {
+    mprintf("\tRegenerating bond parameters.\n");
+    AssignBondParams( set0.BP() );
+  }
+  // Angle parameters
+//  updateCount = UpdateParameters< ParmHolder<AngleParmType> >(set0.AP(), set1.AP(), "angle");
+  if (UC.nAnglesUpdated_ > 0) {
+    mprintf("\tRegenerating angle parameters.\n");
+    AssignAngleParams( set0.AP() );
+  }
+  // Dihedral parameters
+//  updateCount = UpdateParameters< DihedralParmHolder >(set0.DP(), set1.DP(), "dihedral");
+  if (UC.nDihedralsUpdated_ > 0) {
+    mprintf("\tRegenerating dihedral parameters.\n");
+    AssignDihedralParams( set0.DP(), set0.IP(), set0.AT() );
+  }
+  // Urey-Bradley
+//  updateCount = UpdateParameters< ParmHolder<BondParmType> >(set0.UB(), set1.UB(), "Urey-Bradley");
+  if (UC.nUreyBradleyUpdated_ > 0) {
+    mprintf("\tRegenerating UB parameters.\n");
+    AssignUBParams( set0.UB() );
+  }
+  // Improper parameters
+//  updateCount = UpdateParameters< ParmHolder<DihedralParmType> >(set0.IP(), set1.IP(), "improper");
+  if (UC.nImpropersUpdated_ > 0) {
+    mprintf("\tRegenerating improper parameters.\n");
+    AssignImproperParams( set0.IP() );
+  }
+  // Atom types
+//  updateCount = UpdateParameters< ParmHolder<AtomType> >(set0.AT(), set1.AT(), "atom type");
+  if (UC.nAtomTypeUpdated_ > 0) {
+    mprintf("\tRegenerating atom type parameters.\n");
+    AssignAtomTypeParm( set0.AT() );
+  }
+//  updateCount += UpdateParameters< ParmHolder<NonbondType> >(set0.NB(), set1.NB(), "LJ A-B");
+  if (UC.nAtomTypeUpdated_ > 0 || UC.nLJCUpdated_ > 0 ||
+      UC.nLJparamsUpdated_ > 0 || UC.nLJ14paramsUpdated_ > 0)
+  {
+    mprintf("\tRegenerating nonbond parameters.\n");
+    AssignNonbondParams( set0.AT(), set0.NB(), set0.NB14(), set0.LJC(), set0.HB(), debug_ );
+  }
+  // CMAP
+  if (UC.nCmapUpdated_ > 0) {
+    cmapGrid_.clear();
+    mprintf("\tRegenerating CMAP parameters.\n");
+    AssignCmapParams(cmap_, set0.CMAP(), cmapGrid_);
+  }
+  // TODO LJ14
+
+  if (debug_ > 0) set0.Debug("newp.dat");
+  return 0;
+}
+
diff --git a/src/Parm/AssignParams.h b/src/Parm/AssignParams.h
new file mode 100644
index 0000000000..8354596100
--- /dev/null
+++ b/src/Parm/AssignParams.h
@@ -0,0 +1,66 @@
+#ifndef INC_PARM_ASSIGNPARAMS_H
+#define INC_PARM_ASSIGNPARAMS_H
+#include <vector>
+class AngleArray;
+class AngleParmType;
+class AtomType;
+class BondParmType;
+class BondArray;
+class BondParmArray;
+class CmapArray;
+class CmapGridArray;
+class CmapParmHolder;
+class DihedralArray;
+class DihedralParmArray;
+class DihedralParmHolder;
+class DihedralType;
+class HB_ParmType;
+class ImproperParmHolder;
+class NonbondType;
+class ParameterSet;
+template<typename Type> class ParmHolder;
+namespace Cpptraj {
+namespace Parm {
+/// Used to assign parameters to a Topology
+class AssignParams {
+  public:
+    AssignParams();
+
+    int AssignParameters(ParameterSet const&) const;
+    int UpdateParameters(ParameterSet const&) const;
+  private:
+    void AssignAtomTypeParm(ParmHolder<AtomType> const&) const;
+    void AssignBondParm(ParmHolder<BondParmType> const&, BondArray&, BondParmArray&, const char*) const;
+    void AssignBondParams(ParmHolder<BondParmType> const&) const;
+    void AssignUBParams(ParmHolder<BondParmType> const&) const;
+
+    AngleArray AssignAngleParm(ParmHolder<AngleParmType> const&, AngleArray const&) const;
+    void AssignAngleParams(ParmHolder<AngleParmType> const&) const;
+
+    void warn_improper_reorder(DihedralType const&, DihedralType const&) const;
+    void AssignImproperParm(ImproperParmHolder const&, DihedralArray&, DihedralParmArray&) const ;
+    void AssignImproperParams(ImproperParmHolder const&) const;
+    DihedralArray AssignDihedralParm(DihedralParmHolder const&, ImproperParmHolder const&,
+                                     ParmHolder<AtomType> const&, DihedralArray const&,
+                                     bool) const; // TODO make the bool a class var?
+    DihedralArray get_unique_dihedrals(DihedralArray const&) const;
+    void AssignDihedralParams(DihedralParmHolder const&, ImproperParmHolder const&,
+                              ParmHolder<AtomType> const&) const;
+
+    void AssignNonbondParams(ParmHolder<AtomType> const&,
+                             ParmHolder<NonbondType> const&, ParmHolder<NonbondType> const&,
+                             ParmHolder<double> const&, ParmHolder<HB_ParmType> const&,
+                             int) const; // TODO make int a class vair
+
+    int remap_cmap_indices(std::vector<int>&, CmapGridArray&, CmapArray&, CmapParmHolder const&) const;
+    int AssignCmapParams(CmapArray&, CmapParmHolder const&, CmapGridArray&) const;
+    int AssignCmapParams(DihedralArray const&, CmapParmHolder const&,
+                         CmapGridArray&, CmapArray&) const;
+
+
+
+    int debug_;
+};
+}
+}
+#endif

From 09226ae70d6a2bb728caa1f4fd88046573623c45 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 20 Jul 2024 14:54:07 -0400
Subject: [PATCH 0851/1492] Bond/UB assignment

---
 src/Parm/AssignParams.cpp | 63 ++++++++++++++++++++++-----------------
 src/Parm/AssignParams.h   | 16 ++++++----
 2 files changed, 45 insertions(+), 34 deletions(-)

diff --git a/src/Parm/AssignParams.cpp b/src/Parm/AssignParams.cpp
index 4d69557452..e5bde534cd 100644
--- a/src/Parm/AssignParams.cpp
+++ b/src/Parm/AssignParams.cpp
@@ -1,4 +1,10 @@
 #include "AssignParams.h"
+#include "../Atom.h"
+#include "../AtomType.h"
+#include "../CpptrajStdio.h"
+#include "../ParameterHolders.h"
+#include "../Topology.h"
+#include "../TypeNameHolder.h"
 
 using namespace Cpptraj::Parm;
 
@@ -8,34 +14,35 @@ AssignParams::AssignParams() :
 {}
 
 /** Set parameters for atoms via given atom type parameter holder. */
-void AssignParams::AssignAtomTypeParm(ParmHolder<AtomType> const& newAtomTypeParams)
+void AssignParams::AssignAtomTypeParm(AtArray& atoms, ParmHolder<AtomType> const& newAtomTypeParams)
 const
 {
-  for (unsigned int iat = 0; iat != atoms_.size(); iat++)
+  for (AtArray::iterator iat = atoms.begin(); iat != atoms.end(); ++iat)
   {
     bool found;
-    TypeNameHolder atype( atoms_[iat].Type() );
-    AtomType at = newAtomTypeParams.FindParam( atype, found );
+    TypeNameHolder atype( iat->Type() );
+    AtomType AT = newAtomTypeParams.FindParam( atype, found );
     if (found) {
       // Update mass
-      atoms_[iat].SetMass( at.Mass() );
+      iat->SetMass( AT.Mass() );
       // Update polarizability
-      atoms_[iat].SetPolar( at.Polarizability() );
+      iat->SetPolar( AT.Polarizability() );
     } else
       mprintf("Warning: Atom type parameter not found for %s\n", *atype[0]);
   }
 }
 
 /** Set parameters for bonds in given bond array. */
-void AssignParams::AssignBondParm(ParmHolder<BondParmType> const& newBondParams,
-                              BondArray& bonds, BondParmArray& bpa, const char* desc)
+void AssignParams::AssignBondParm(Topology const& topOut,
+                                  ParmHolder<BondParmType> const& newBondParams,
+                                  BondArray& bonds, BondParmArray& bpa, const char* desc)
 const
 {
   ParmHolder<int> currentTypes;
   for (BondArray::iterator bnd = bonds.begin(); bnd != bonds.end(); ++bnd) {
     TypeNameHolder types(2);
-    types.AddName( atoms_[bnd->A1()].Type() );
-    types.AddName( atoms_[bnd->A2()].Type() );
+    types.AddName( topOut[bnd->A1()].Type() );
+    types.AddName( topOut[bnd->A2()].Type() );
     bool found;
     // See if parameter is present.
     int idx = currentTypes.FindParam(types, found);
@@ -45,8 +52,8 @@ const
       BondParmType bp = newBondParams.FindParam( types, found );
       if (!found) {
         mprintf("Warning: parameter not found for %s %s-%s (%s-%s)\n", desc,
-                TruncResAtomNameNum(bnd->A1()).c_str(),
-                TruncResAtomNameNum(bnd->A2()).c_str(),
+                topOut.TruncResAtomNameNum(bnd->A1()).c_str(),
+                topOut.TruncResAtomNameNum(bnd->A2()).c_str(),
                 *types[0], *types[1]);
       } else {
         //idx = addBondParm( bpa, bp ); TODO handle array packing
@@ -79,16 +86,16 @@ const
 }
 
 /** Replace any current bond parameters with given bond parameters. */
-void AssignParams::AssignBondParams(ParmHolder<BondParmType> const& newBondParams) const {
-  bondparm_.clear();
-  AssignBondParm( newBondParams, bonds_,  bondparm_, "bond" );
-  AssignBondParm( newBondParams, bondsh_, bondparm_, "bond" );
+void AssignParams::AssignBondParams(Topology& topOut, ParmHolder<BondParmType> const& newBondParams) const {
+  topOut.ModifyBondParm().clear();
+  AssignBondParm( topOut, newBondParams, topOut.ModifyBonds(),  topOut.ModifyBondParm(), "bond" );
+  AssignBondParm( topOut, newBondParams, topOut.ModifyBondsH(), topOut.ModifyBondParm(), "bond" );
 }
 
 /** Replace any current Urey-Bradley parameters with given UB parameters. */
-void AssignParams::AssignUBParams(ParmHolder<BondParmType> const& newBondParams) const {
-  ubparm_.clear();
-  AssignBondParm( newBondParams, ub_, ubparm_, "UB term" );
+void AssignParams::AssignUBParams(Topology& topOut, ParmHolder<BondParmType> const& newBondParams) const {
+  topOut.ModifyUBparm().clear();
+  AssignBondParm( topOut, newBondParams, topOut.ModifyUB(), topOut.ModifyUBparm(), "UB term" );
 }
 
 /** Set parameters for angles in given angle array. */
@@ -557,7 +564,7 @@ const
   bool hasLJC = !newLJC.empty();
   // Generate array of only the types that are currently in Topology. TODO should this be a permanent part of Topology?
   ParmHolder<AtomType> currentAtomTypes;
-  for (std::vector<Atom>::const_iterator atm = atoms_.begin(); atm != atoms_.end(); ++atm)
+  for (AtArray::const_iterator atm = atoms_.begin(); atm != atoms_.end(); ++atm)
   {
     if (atm->HasType()) {
       TypeNameHolder types(1);
@@ -682,7 +689,7 @@ const
     } // END inner loop over current types
   } // END outer loop over current types
   // Reset the atom type indices.
-  for (std::vector<Atom>::iterator atm = atoms_.begin(); atm != atoms_.end(); ++atm)
+  for (AtArray::iterator atm = atoms_.begin(); atm != atoms_.end(); ++atm)
   {
     int tidx = -1;
     ParmHolder<AtomType>::const_iterator it = currentAtomTypes.GetParam( TypeNameHolder(atm->Type()) );
@@ -704,7 +711,7 @@ const
 
 /// \return index of 5th cmap atom if atom names match those in dihedral, -1 otherwise
 static inline int cmap_anames_match(DihedralType const& dih,
-                                     std::vector<Atom> const& atoms,
+                                     AtArray const& atoms,
                                      std::vector<std::string> const& cmapAtomNames)
 {
 /*  mprintf("DEBUG: Check res %i %s %s %s %s against %s %s %s %s\n",
@@ -985,7 +992,7 @@ const
 }
 
 /** Replace existing parameters with the given parameter set. */
-int AssignParams::AssignParameters(ParameterSet const& set0) const {
+int AssignParams::AssignParameters(Topology& topOut, ParameterSet const& set0) const {
 
   // Bond parameters
   mprintf("\tAssigning bond parameters.\n");
@@ -994,7 +1001,7 @@ int AssignParams::AssignParameters(ParameterSet const& set0) const {
   bonds_.clear();
   bondsh_.clear();
   BondArray allBonds = Cpptraj::Structure::GenerateBondArray(residues_, atoms_);
-  AssignBondParm( set0.BP(), allBonds, bondparm_, "bond" );
+  AssignBondParm( topOut, set0.BP(), allBonds, bondparm_, "bond" );
   for (BondArray::const_iterator bnd = allBonds.begin(); bnd != allBonds.end(); ++bnd)
     AddToBondArrays( *bnd );
   // Angle parameters
@@ -1042,7 +1049,7 @@ int AssignParams::AssignParameters(ParameterSet const& set0) const {
   }
   // Atom types
   mprintf("\tAssigning atom type parameters.\n");
-  AssignAtomTypeParm( set0.AT() );
+  AssignAtomTypeParm( topOut.ModifyAtoms(), set0.AT() );
   // LJ 6-12
   mprintf("\tAssigning nonbond parameters.\n");
   AssignNonbondParams( set0.AT(), set0.NB(), set0.NB14(), set0.LJC(), set0.HB(), debug_ );
@@ -1053,8 +1060,8 @@ int AssignParams::AssignParameters(ParameterSet const& set0) const {
 
 /** Update/add to parameters in this topology with those from given set.
   */
-int AssignParams::UpdateParameters(ParameterSet const& set1) const {
-  ParameterSet set0 = GetParameters();
+int AssignParams::UpdateParameters(Topology& topOut, ParameterSet const& set1) const {
+  ParameterSet set0 = topOut.GetParameters();
 
   //set1.Summary(); // DEBUG
   // Check TODO is this necessary?
@@ -1110,7 +1117,7 @@ int AssignParams::UpdateParameters(ParameterSet const& set1) const {
 //  updateCount = UpdateParameters< ParmHolder<AtomType> >(set0.AT(), set1.AT(), "atom type");
   if (UC.nAtomTypeUpdated_ > 0) {
     mprintf("\tRegenerating atom type parameters.\n");
-    AssignAtomTypeParm( set0.AT() );
+    AssignAtomTypeParm( topOut.ModifyAtoms(), set0.AT() );
   }
 //  updateCount += UpdateParameters< ParmHolder<NonbondType> >(set0.NB(), set1.NB(), "LJ A-B");
   if (UC.nAtomTypeUpdated_ > 0 || UC.nLJCUpdated_ > 0 ||
diff --git a/src/Parm/AssignParams.h b/src/Parm/AssignParams.h
index 8354596100..62b27cfd6e 100644
--- a/src/Parm/AssignParams.h
+++ b/src/Parm/AssignParams.h
@@ -3,6 +3,7 @@
 #include <vector>
 class AngleArray;
 class AngleParmType;
+class Atom;
 class AtomType;
 class BondParmType;
 class BondArray;
@@ -18,6 +19,7 @@ class HB_ParmType;
 class ImproperParmHolder;
 class NonbondType;
 class ParameterSet;
+class Topology;
 template<typename Type> class ParmHolder;
 namespace Cpptraj {
 namespace Parm {
@@ -26,13 +28,15 @@ class AssignParams {
   public:
     AssignParams();
 
-    int AssignParameters(ParameterSet const&) const;
-    int UpdateParameters(ParameterSet const&) const;
+    int AssignParameters(Topology&, ParameterSet const&) const;
+    int UpdateParameters(Topology&, ParameterSet const&) const;
   private:
-    void AssignAtomTypeParm(ParmHolder<AtomType> const&) const;
-    void AssignBondParm(ParmHolder<BondParmType> const&, BondArray&, BondParmArray&, const char*) const;
-    void AssignBondParams(ParmHolder<BondParmType> const&) const;
-    void AssignUBParams(ParmHolder<BondParmType> const&) const;
+    typedef std::vector<Atom> AtArray;
+
+    void AssignAtomTypeParm(AtArray&, ParmHolder<AtomType> const&) const;
+    void AssignBondParm(Topology const&, ParmHolder<BondParmType> const&, BondArray&, BondParmArray&, const char*) const;
+    void AssignBondParams(Topology&, ParmHolder<BondParmType> const&) const;
+    void AssignUBParams(Topology&, ParmHolder<BondParmType> const&) const;
 
     AngleArray AssignAngleParm(ParmHolder<AngleParmType> const&, AngleArray const&) const;
     void AssignAngleParams(ParmHolder<AngleParmType> const&) const;

From ac4d1a2632858c2f1e1bba4244b232aa2cbd5da4 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 20 Jul 2024 15:10:56 -0400
Subject: [PATCH 0852/1492] Angle assignment

---
 src/Parm/AssignParams.cpp | 47 ++++++++++++++++++++-------------------
 src/Parm/AssignParams.h   |  9 +++++---
 2 files changed, 30 insertions(+), 26 deletions(-)

diff --git a/src/Parm/AssignParams.cpp b/src/Parm/AssignParams.cpp
index e5bde534cd..3b363863c1 100644
--- a/src/Parm/AssignParams.cpp
+++ b/src/Parm/AssignParams.cpp
@@ -99,20 +99,21 @@ void AssignParams::AssignUBParams(Topology& topOut, ParmHolder<BondParmType> con
 }
 
 /** Set parameters for angles in given angle array. */
-AngleArray AssignParams::AssignAngleParm(ParmHolder<AngleParmType> const& newAngleParams,
-                                     AngleArray const& angles)
+AngleArray AssignParams::AssignAngleParm(Topology const& topOut,
+                                         ParmHolder<AngleParmType> const& newAngleParams,
+                                         AngleArray const& angles, AngleParmArray& apa)
 const
 {
   AngleArray newAngles;
   ParmHolder<int> currentTypes;
   for (AngleArray::const_iterator ang = angles.begin(); ang != angles.end(); ++ang) {
     TypeNameHolder types(3);
-    types.AddName( atoms_[ang->A1()].Type() );
-    types.AddName( atoms_[ang->A2()].Type() );
-    types.AddName( atoms_[ang->A3()].Type() );
+    types.AddName( topOut[ang->A1()].Type() );
+    types.AddName( topOut[ang->A2()].Type() );
+    types.AddName( topOut[ang->A3()].Type() );
     // Skip extra points // FIXME make this an option
-    if ( atoms_[ang->A1()].Element() == Atom::EXTRAPT ||
-         atoms_[ang->A3()].Element() == Atom::EXTRAPT)
+    if ( topOut[ang->A1()].Element() == Atom::EXTRAPT ||
+         topOut[ang->A3()].Element() == Atom::EXTRAPT)
     {
       mprintf("DEBUG: Skipping angle with extra point: %4i %4i %4i (%2s %2s %2s)\n",
               ang->A1()+1, ang->A2()+1, ang->A3()+1,
@@ -120,12 +121,12 @@ const
       continue;
     }
     // Skip water angles // FIXME make this an option
-    if (atoms_[ang->A1()].Element() == Atom::HYDROGEN &&
-        atoms_[ang->A2()].Element() == Atom::OXYGEN &&
-        atoms_[ang->A3()].Element() == Atom::HYDROGEN)
+    if (topOut[ang->A1()].Element() == Atom::HYDROGEN &&
+        topOut[ang->A2()].Element() == Atom::OXYGEN &&
+        topOut[ang->A3()].Element() == Atom::HYDROGEN)
     {
       // H-O-H Angle. If there is an H-H bond assume this is a rigid water model.
-      if (atoms_[ang->A1()].IsBondedTo( ang->A3() )) {
+      if (topOut[ang->A1()].IsBondedTo( ang->A3() )) {
         mprintf("DEBUG: H-O-H angle, H-H bond detected. Assuming rigid water, skipping angle: "
                 "%4i %4i %4i (%2s %2s %2s)\n",
                 ang->A1()+1, ang->A2()+1, ang->A3()+1,
@@ -133,9 +134,9 @@ const
         continue;
       }
     }
-    if (atoms_[ang->A1()].Element() == Atom::OXYGEN &&
-        atoms_[ang->A2()].Element() == Atom::HYDROGEN &&
-        atoms_[ang->A3()].Element() == Atom::HYDROGEN)
+    if (topOut[ang->A1()].Element() == Atom::OXYGEN &&
+        topOut[ang->A2()].Element() == Atom::HYDROGEN &&
+        topOut[ang->A3()].Element() == Atom::HYDROGEN)
     {
       // O-H-H Angle. Assume rigid water model
       mprintf("DEBUG: O-H-H angle. Assuming rigid water, skipping angle: "
@@ -154,14 +155,14 @@ const
       AngleParmType ap = newAngleParams.FindParam( types, found );
       if (!found) {
         mprintf("Warning: Angle parameter not found for angle %s-%s-%s (%s-%s-%s)\n",
-                TruncResAtomNameNum(ang->A1()).c_str(),
-                TruncResAtomNameNum(ang->A2()).c_str(),
-                TruncResAtomNameNum(ang->A3()).c_str(),
+                topOut.TruncResAtomNameNum(ang->A1()).c_str(),
+                topOut.TruncResAtomNameNum(ang->A2()).c_str(),
+                topOut.TruncResAtomNameNum(ang->A3()).c_str(),
                 *types[0], *types[1], *types[2]);
       } else {
         //idx = addAngleParm( angleparm_, ap ); // TODO uncomment for array packing
-        idx = (int)angleparm_.size();
-        angleparm_.push_back( ap );
+        idx = (int)apa.size();
+        apa.push_back( ap );
         //mprintf("DEBUG: New angle type for %s-%s-%s (Tk=%g Teq=%g) idx=%i\n", *types[0], *types[1], *types[2], ap.Tk(), ap.Teq(), idx);
         currentTypes.AddParm(types, idx, false);
       }
@@ -194,10 +195,10 @@ const
 }
 
 /** Replace any current angle parameters with given angle parameters. */
-void AssignParams::AssignAngleParams(ParmHolder<AngleParmType> const& newAngleParams) const {
-  angleparm_.clear();
-  angles_ = AssignAngleParm( newAngleParams, angles_ );
-  anglesh_ = AssignAngleParm( newAngleParams, anglesh_ );
+void AssignParams::AssignAngleParams(Topology& topOut, ParmHolder<AngleParmType> const& newAngleParams) const {
+  topOut.ModifyAngleParm().clear();
+  topOut.ModifyAngles() = AssignAngleParm( topOut, newAngleParams, topOut.Angles(), topOut.ModifyAngleParm() );
+  topOut.ModifyAnglesH() = AssignAngleParm( topOut, newAngleParams, topOut.AnglesH(), topOut.ModifyAngleParm() );
 }
 
 /** Warn if improper atoms have been reordered so they match the parameter. */
diff --git a/src/Parm/AssignParams.h b/src/Parm/AssignParams.h
index 62b27cfd6e..70cdd78190 100644
--- a/src/Parm/AssignParams.h
+++ b/src/Parm/AssignParams.h
@@ -2,6 +2,7 @@
 #define INC_PARM_ASSIGNPARAMS_H
 #include <vector>
 class AngleArray;
+class AngleParmArray;
 class AngleParmType;
 class Atom;
 class AtomType;
@@ -34,12 +35,14 @@ class AssignParams {
     typedef std::vector<Atom> AtArray;
 
     void AssignAtomTypeParm(AtArray&, ParmHolder<AtomType> const&) const;
-    void AssignBondParm(Topology const&, ParmHolder<BondParmType> const&, BondArray&, BondParmArray&, const char*) const;
+    void AssignBondParm(Topology const&, ParmHolder<BondParmType> const&,
+                        BondArray&, BondParmArray&, const char*) const;
     void AssignBondParams(Topology&, ParmHolder<BondParmType> const&) const;
     void AssignUBParams(Topology&, ParmHolder<BondParmType> const&) const;
 
-    AngleArray AssignAngleParm(ParmHolder<AngleParmType> const&, AngleArray const&) const;
-    void AssignAngleParams(ParmHolder<AngleParmType> const&) const;
+    AngleArray AssignAngleParm(Topology const&, ParmHolder<AngleParmType> const&,
+                               AngleArray const&, AngleParmArray&) const;
+    void AssignAngleParams(Topology&, ParmHolder<AngleParmType> const&) const;
 
     void warn_improper_reorder(DihedralType const&, DihedralType const&) const;
     void AssignImproperParm(ImproperParmHolder const&, DihedralArray&, DihedralParmArray&) const ;

From f71a4dd6a64c9055eb53344315d7a8a841ecaa11 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 20 Jul 2024 15:22:57 -0400
Subject: [PATCH 0853/1492] Improper assign

---
 src/Parm/AssignParams.cpp | 51 ++++++++++++++++++++-------------------
 src/Parm/AssignParams.h   |  8 +++---
 2 files changed, 31 insertions(+), 28 deletions(-)

diff --git a/src/Parm/AssignParams.cpp b/src/Parm/AssignParams.cpp
index 3b363863c1..35463d656b 100644
--- a/src/Parm/AssignParams.cpp
+++ b/src/Parm/AssignParams.cpp
@@ -202,34 +202,35 @@ void AssignParams::AssignAngleParams(Topology& topOut, ParmHolder<AngleParmType>
 }
 
 /** Warn if improper atoms have been reordered so they match the parameter. */
-void AssignParams::warn_improper_reorder(DihedralType const& imp0, DihedralType const& imp)
+void AssignParams::warn_improper_reorder(AtArray const& atoms, DihedralType const& imp0, DihedralType const& imp)
 const
 {
   if (debug_ < 1) return;
   mprintf("Warning: Improper types have been reordered from %4s %4s %4s %4s",
-          *(atoms_[imp0.A1()].Type()),
-          *(atoms_[imp0.A2()].Type()),
-          *(atoms_[imp0.A3()].Type()),
-          *(atoms_[imp0.A4()].Type()));
+          *(atoms[imp0.A1()].Type()),
+          *(atoms[imp0.A2()].Type()),
+          *(atoms[imp0.A3()].Type()),
+          *(atoms[imp0.A4()].Type()));
   mprintf(" to %4s %4s %4s %4s to match improper parameter.\n",
-          *(atoms_[imp.A1()].Type()),
-          *(atoms_[imp.A2()].Type()),
-          *(atoms_[imp.A3()].Type()),
-          *(atoms_[imp.A4()].Type()));
+          *(atoms[imp.A1()].Type()),
+          *(atoms[imp.A2()].Type()),
+          *(atoms[imp.A3()].Type()),
+          *(atoms[imp.A4()].Type()));
 }
 
 /** Set parameters for improper dihedrals in given improper dihedral array. */
-void AssignParams::AssignImproperParm(ImproperParmHolder const& newImproperParams,
-                                  DihedralArray& impropers,
-                                  DihedralParmArray& dpa)
+void AssignParams::AssignImproperParm(Topology& topOut,
+                                      ImproperParmHolder const& newImproperParams,
+                                      DihedralArray& impropers,
+                                      DihedralParmArray& dpa)
 const
 {
   for (DihedralArray::iterator imp = impropers.begin(); imp != impropers.end(); ++imp) {
     TypeNameHolder types(4);
-    types.AddName( atoms_[imp->A1()].Type() );
-    types.AddName( atoms_[imp->A2()].Type() );
-    types.AddName( atoms_[imp->A3()].Type() );
-    types.AddName( atoms_[imp->A4()].Type() );
+    types.AddName( topOut[imp->A1()].Type() );
+    types.AddName( topOut[imp->A2()].Type() );
+    types.AddName( topOut[imp->A3()].Type() );
+    types.AddName( topOut[imp->A4()].Type() );
     bool found;
     // See if parameter is present.
     int idx = -1;
@@ -238,26 +239,26 @@ const
     DihedralParmArray ipa = newImproperParams.FindParam( types, found, *imp, reordered );
     if (!found) {
       mprintf("Warning: Parameter not found for improper %s-%s-%s-%s (%s-%s-%s-%s)\n",
-              TruncResAtomNameNum(imp->A1()).c_str(),
-              TruncResAtomNameNum(imp->A2()).c_str(),
-              TruncResAtomNameNum(imp->A3()).c_str(),
-              TruncResAtomNameNum(imp->A4()).c_str(),
+              topOut.TruncResAtomNameNum(imp->A1()).c_str(),
+              topOut.TruncResAtomNameNum(imp->A2()).c_str(),
+              topOut.TruncResAtomNameNum(imp->A3()).c_str(),
+              topOut.TruncResAtomNameNum(imp->A4()).c_str(),
               *types[0], *types[1], *types[3], *types[4]);
     } else {
       if (ipa.size() > 1)
         mprintf("Warning: %zu improper parameters found for types %s - %s - %s - %s, expected only one."
                         "Warning: Only using first parameter.\n", ipa.size(), *(types[0]), *(types[1]), *(types[2]), *(types[3]));
-      if (reordered) warn_improper_reorder( imp0, *imp );
-      idx = addTorsionParm( dpa, ipa.front() );
+      if (reordered) warn_improper_reorder( topOut.Atoms(), imp0, *imp );
+      idx = topOut.addTorsionParm( dpa, ipa.front() );
     }
     imp->SetIdx( idx );
   }
 }
 
 /** Replace any current improper parameters with given improper parameters. */
-void AssignParams::AssignImproperParams(ImproperParmHolder const& newImproperParams) const {
-  improperparm_.clear();
-  AssignImproperParm( newImproperParams, impropers_, improperparm_ );
+void AssignParams::AssignImproperParams(Topology& topOut, ImproperParmHolder const& newImproperParams) const {
+  topOut.ModifyImproperParm().clear();
+  AssignImproperParm( topOut, newImproperParams, topOut.ModifyImpropers(), topOut.ModifyImproperParm() );
 }
 
 /** Set parameters for dihedrals in given dihedral array.
diff --git a/src/Parm/AssignParams.h b/src/Parm/AssignParams.h
index 70cdd78190..b7c0bdada4 100644
--- a/src/Parm/AssignParams.h
+++ b/src/Parm/AssignParams.h
@@ -44,9 +44,11 @@ class AssignParams {
                                AngleArray const&, AngleParmArray&) const;
     void AssignAngleParams(Topology&, ParmHolder<AngleParmType> const&) const;
 
-    void warn_improper_reorder(DihedralType const&, DihedralType const&) const;
-    void AssignImproperParm(ImproperParmHolder const&, DihedralArray&, DihedralParmArray&) const ;
-    void AssignImproperParams(ImproperParmHolder const&) const;
+    void warn_improper_reorder(AtArray const&, DihedralType const&, DihedralType const&) const;
+    void AssignImproperParm(Topology&, ImproperParmHolder const&,
+                            DihedralArray&, DihedralParmArray&) const ;
+    void AssignImproperParams(Topology&, ImproperParmHolder const&) const;
+
     DihedralArray AssignDihedralParm(DihedralParmHolder const&, ImproperParmHolder const&,
                                      ParmHolder<AtomType> const&, DihedralArray const&,
                                      bool) const; // TODO make the bool a class var?

From d262215a73318c973f2911bbb0b7e088a8163812 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 20 Jul 2024 16:04:31 -0400
Subject: [PATCH 0854/1492] Dihedral parameters

---
 src/Parm/AssignParams.cpp | 87 +++++++++++++++++++++------------------
 src/Parm/AssignParams.h   |  5 ++-
 2 files changed, 49 insertions(+), 43 deletions(-)

diff --git a/src/Parm/AssignParams.cpp b/src/Parm/AssignParams.cpp
index 35463d656b..666c7096e5 100644
--- a/src/Parm/AssignParams.cpp
+++ b/src/Parm/AssignParams.cpp
@@ -2,6 +2,7 @@
 #include "../Atom.h"
 #include "../AtomType.h"
 #include "../CpptrajStdio.h"
+#include "../GuessAtomHybridization.h"
 #include "../ParameterHolders.h"
 #include "../Topology.h"
 #include "../TypeNameHolder.h"
@@ -269,11 +270,12 @@ void AssignParams::AssignImproperParams(Topology& topOut, ImproperParmHolder con
   * \param dihedrals Array containing only unique dihedrals.
   * \param sort_improper_cache If true, sort improper types in cache (to match current leap behavior)
   */
-DihedralArray AssignParams::AssignDihedralParm(DihedralParmHolder const& newDihedralParams,
-                                           ImproperParmHolder const& newImproperParams,
-                                           ParmHolder<AtomType> const& AT,
-                                           DihedralArray const& dihedrals,
-                                           bool sort_improper_cache)
+DihedralArray AssignParams::AssignDihedralParm(Topology& topOut,
+                                               DihedralParmHolder const& newDihedralParams,
+                                               ImproperParmHolder const& newImproperParams,
+                                               ParmHolder<AtomType> const& AT,
+                                               DihedralArray const& dihedrals,
+                                               bool sort_improper_cache)
 const
 { // TODO skip extra points
   DihedralArray dihedralsIn;
@@ -288,13 +290,13 @@ const
   // Loop over all dihedrals
   for (DihedralArray::const_iterator dih = dihedrals.begin(); dih != dihedrals.end(); ++dih) {
     TypeNameHolder types(4);
-    types.AddName( atoms_[dih->A1()].Type() );
-    types.AddName( atoms_[dih->A2()].Type() );
-    types.AddName( atoms_[dih->A3()].Type() );
-    types.AddName( atoms_[dih->A4()].Type() );
+    types.AddName( topOut[dih->A1()].Type() );
+    types.AddName( topOut[dih->A2()].Type() );
+    types.AddName( topOut[dih->A3()].Type() );
+    types.AddName( topOut[dih->A4()].Type() );
     // Skip extra points // FIXME make this an option
-    if ( atoms_[dih->A1()].Element() == Atom::EXTRAPT ||
-         atoms_[dih->A4()].Element() == Atom::EXTRAPT)
+    if ( topOut[dih->A1()].Element() == Atom::EXTRAPT ||
+         topOut[dih->A4()].Element() == Atom::EXTRAPT)
     {
       mprintf("DEBUG: Skipping dihedral with extra point: %4i %4i %4i %4i (%2s %2s %2s %2s)\n",
               dih->A1()+1, dih->A2()+1, dih->A3()+1, dih->A4()+1,
@@ -306,15 +308,15 @@ const
 //            *types[0], *types[1], *types[2], *types[3],
 //            (int)dih->IsImproper(), (int)dih->Skip14());
     // Determine improper
-    bool isImproper = (!atoms_[dih->A1()].IsBondedTo(dih->A2())) ||
-                      (!atoms_[dih->A2()].IsBondedTo(dih->A3())) ||
-                      (!atoms_[dih->A3()].IsBondedTo(dih->A4()));
+    bool isImproper = (!topOut[dih->A1()].IsBondedTo(dih->A2())) ||
+                      (!topOut[dih->A2()].IsBondedTo(dih->A3())) ||
+                      (!topOut[dih->A3()].IsBondedTo(dih->A4()));
     if (isImproper != dih->IsImproper()) {
       mprintf("Warning: dihedral %s-%s-%s-%s improper status %i does not match detected (%i)\n",
-              TruncResAtomNameNum(dih->A1()).c_str(),
-              TruncResAtomNameNum(dih->A2()).c_str(),
-              TruncResAtomNameNum(dih->A3()).c_str(),
-              TruncResAtomNameNum(dih->A4()).c_str(),
+              topOut.TruncResAtomNameNum(dih->A1()).c_str(),
+              topOut.TruncResAtomNameNum(dih->A2()).c_str(),
+              topOut.TruncResAtomNameNum(dih->A3()).c_str(),
+              topOut.TruncResAtomNameNum(dih->A4()).c_str(),
               (int)dih->IsImproper(), (int)isImproper);
     }
     bool found;
@@ -393,30 +395,30 @@ const
       if (!found) {
         if (debug_ > 0)
           mprintf("Warning: Improper parameters not found for improper dihedral %s-%s-%s-%s (%s-%s-%s-%s)\n",
-                  TruncResAtomNameNum(dih->A1()).c_str(),
-                  TruncResAtomNameNum(dih->A2()).c_str(),
-                  TruncResAtomNameNum(dih->A3()).c_str(),
-                  TruncResAtomNameNum(dih->A4()).c_str(),
+                  topOut.TruncResAtomNameNum(dih->A1()).c_str(),
+                  topOut.TruncResAtomNameNum(dih->A2()).c_str(),
+                  topOut.TruncResAtomNameNum(dih->A3()).c_str(),
+                  topOut.TruncResAtomNameNum(dih->A4()).c_str(),
                   *types[0], *types[1], *types[2], *types[3]);
         // Central atom
-        Atom const& AJ = atoms_[dih->A3()];
+        Atom const& AJ = topOut[dih->A3()];
         AtomType::HybridizationType hybrid = AtomType::UNKNOWN_HYBRIDIZATION;
         AtomType atype = AT.FindParam(TypeNameHolder(AJ.Type()), found);
         if (found)
           hybrid = atype.Hybridization();
         if (hybrid == AtomType::UNKNOWN_HYBRIDIZATION) {
-          mprintf("Warning: Guessing hybridization for improper central atom %s\n", AtomMaskName(dih->A3()).c_str());
-          hybrid = Cpptraj::GuessAtomHybridization( AJ, atoms_ );
+          mprintf("Warning: Guessing hybridization for improper central atom %s\n", topOut.AtomMaskName(dih->A3()).c_str());
+          hybrid = Cpptraj::GuessAtomHybridization( AJ, topOut.Atoms() );
         }
         if (hybrid == AtomType::SP2) {
-          mprintf("Warning: No improper parameters for SP2 hybridized atom %s\n", AtomMaskName(dih->A3()).c_str());
+          mprintf("Warning: No improper parameters for SP2 hybridized atom %s\n", topOut.AtomMaskName(dih->A3()).c_str());
         }
       } else {
         if (ipa.size() > 1)
           mprintf("Warning: %zu improper parameters found for types %s - %s - %s - %s, expected only one."
                   "Warning: Only using first parameter.\n", ipa.size(), *(types[0]), *(types[1]), *(types[2]), *(types[3]));
-        if (reordered) warn_improper_reorder( *dih, mydih );
-        idx = addTorsionParm( dihedralparm_, ipa.front() );
+        if (reordered) warn_improper_reorder( topOut.Atoms(), *dih, mydih );
+        idx = topOut.addTorsionParm( topOut.ModifyDihedralParm(), ipa.front() );
         mydih.SetIdx( idx );
         mydih.SetImproper( true );
         // Always skip 1-4 for impropers
@@ -435,10 +437,10 @@ const
       DihedralParmArray dpa = newDihedralParams.FindParam( types, found );
       if (!found) {
         mprintf("Warning: Dihedral parameters not found for dihedral %s-%s-%s-%s (%s-%s-%s-%s)\n",
-                TruncResAtomNameNum(dih->A1()).c_str(),
-                TruncResAtomNameNum(dih->A2()).c_str(),
-                TruncResAtomNameNum(dih->A3()).c_str(),
-                TruncResAtomNameNum(dih->A4()).c_str(),
+                topOut.TruncResAtomNameNum(dih->A1()).c_str(),
+                topOut.TruncResAtomNameNum(dih->A2()).c_str(),
+                topOut.TruncResAtomNameNum(dih->A3()).c_str(),
+                topOut.TruncResAtomNameNum(dih->A4()).c_str(),
                 *types[0], *types[1], *types[2], *types[3]);
         DihedralType mydih = *dih;
         mydih.SetIdx( -1 );
@@ -448,8 +450,8 @@ const
         // Determine if this is actually a 1-4 interaction by making
         // sure that A4 isnt part of a bond or angle with A1.
         bool skip14 = false;
-        for (Atom::bond_iterator bat1 = atoms_[dih->A1()].bondbegin();
-                                 bat1 != atoms_[dih->A1()].bondend(); ++bat1)
+        for (Atom::bond_iterator bat1 = topOut[dih->A1()].bondbegin();
+                                 bat1 != topOut[dih->A1()].bondend(); ++bat1)
         {
           if (*bat1 != dih->A2()) {
             if (*bat1 == dih->A4()) {
@@ -457,8 +459,8 @@ const
               break;
             }
             // Loop over angles, dih->A1() - bat1 - bat2
-            for (Atom::bond_iterator bat2 = atoms_[*bat1].bondbegin();
-                                     bat2 != atoms_[*bat1].bondend(); ++bat2)
+            for (Atom::bond_iterator bat2 = topOut[*bat1].bondbegin();
+                                     bat2 != topOut[*bat1].bondend(); ++bat2)
             {
               //if (dih->A1() == 442 && dih->A4() == 444) { // DEBUG
               //  mprintf("DEBUG: %4i %4i %4i %4i Checking angle %4i %4i %4i\n", dih->A1()+1, dih->A2()+1, dih->A3()+1, dih->A4()+1, dih->A1()+1, *bat1 + 1, *bat2 + 1);
@@ -499,7 +501,7 @@ const
         //}
         for (DihedralParmArray::const_iterator it = dpa.begin(); it != dpa.end(); ++it) {
           DihedralType mydih = *dih;
-          int idx = addTorsionParm( dihedralparm_, *it );
+          int idx = topOut.addTorsionParm( topOut.ModifyDihedralParm(), *it );
           // If there are multiple parameters for the same dihedral, all but
           // one of the 1-4 calcs need to be skipped.
           if (it == dpa.begin())
@@ -538,18 +540,21 @@ DihedralArray AssignParams::get_unique_dihedrals(DihedralArray const& dihedralsI
 }
 
 /** Replace any current dihedral parameters with given dihedral parameters. */
-void AssignParams::AssignDihedralParams(DihedralParmHolder const& newDihedralParams,
+void AssignParams::AssignDihedralParams(Topology& topOut,
+                                        DihedralParmHolder const& newDihedralParams,
                                         ImproperParmHolder const& newImproperParams,
                                         ParmHolder<AtomType> const& AT)
 const
 {
-  dihedralparm_.clear();
+  topOut.ModifyDihedralParm().clear();
   // Dihedrals can be a bit of a pain since there can be multiple
   // multiplicities for a single dihedral type. In case multiplicities
   // change, start with a fresh dihedral array containing only unique
   // dihedrals.
-  dihedrals_  = AssignDihedralParm( newDihedralParams, newImproperParams, AT, get_unique_dihedrals(dihedrals_), false  );
-  dihedralsh_ = AssignDihedralParm( newDihedralParams, newImproperParams, AT, get_unique_dihedrals(dihedralsh_), false );
+  topOut.ModifyDihedrals()  = AssignDihedralParm( topOut, newDihedralParams, newImproperParams,
+                                                  AT, get_unique_dihedrals(topOut.Dihedrals()), false  );
+  topOut.ModifyDihedralsH() = AssignDihedralParm( topOut, newDihedralParams, newImproperParams,
+                                                  AT, get_unique_dihedrals(topOut.DihedralsH()), false );
 }
 
 /** Replace current nonbond parameters with given nonbond parameters. */
diff --git a/src/Parm/AssignParams.h b/src/Parm/AssignParams.h
index b7c0bdada4..c376aca57a 100644
--- a/src/Parm/AssignParams.h
+++ b/src/Parm/AssignParams.h
@@ -49,11 +49,12 @@ class AssignParams {
                             DihedralArray&, DihedralParmArray&) const ;
     void AssignImproperParams(Topology&, ImproperParmHolder const&) const;
 
-    DihedralArray AssignDihedralParm(DihedralParmHolder const&, ImproperParmHolder const&,
+    DihedralArray AssignDihedralParm(Topology&,
+                                     DihedralParmHolder const&, ImproperParmHolder const&,
                                      ParmHolder<AtomType> const&, DihedralArray const&,
                                      bool) const; // TODO make the bool a class var?
     DihedralArray get_unique_dihedrals(DihedralArray const&) const;
-    void AssignDihedralParams(DihedralParmHolder const&, ImproperParmHolder const&,
+    void AssignDihedralParams(Topology&, DihedralParmHolder const&, ImproperParmHolder const&,
                               ParmHolder<AtomType> const&) const;
 
     void AssignNonbondParams(ParmHolder<AtomType> const&,

From 29e529c44df6ffbbfd85a4f8fe755fa9a04bbfd6 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 20 Jul 2024 16:15:14 -0400
Subject: [PATCH 0855/1492] Nonbond assign

---
 src/Parm/AssignParams.cpp | 52 ++++++++++++++++++++-------------------
 src/Parm/AssignParams.h   |  4 ++-
 2 files changed, 30 insertions(+), 26 deletions(-)

diff --git a/src/Parm/AssignParams.cpp b/src/Parm/AssignParams.cpp
index 666c7096e5..4fe6ffb80a 100644
--- a/src/Parm/AssignParams.cpp
+++ b/src/Parm/AssignParams.cpp
@@ -559,19 +559,20 @@ const
 
 /** Replace current nonbond parameters with given nonbond parameters. */
 //TODO Accept array of atom type names?
-void AssignParams::AssignNonbondParams(ParmHolder<AtomType> const& newTypes,
-                                   ParmHolder<NonbondType> const& newNB,
-                                   ParmHolder<NonbondType> const& new14,
-                                   ParmHolder<double> const& newLJC,
-                                   ParmHolder<HB_ParmType> const& newHB,
-                                   int verbose)
+void AssignParams::AssignNonbondParams(Topology& topOut,
+                                       ParmHolder<AtomType> const& newTypes,
+                                       ParmHolder<NonbondType> const& newNB,
+                                       ParmHolder<NonbondType> const& new14,
+                                       ParmHolder<double> const& newLJC,
+                                       ParmHolder<HB_ParmType> const& newHB,
+                                       int verbose)
 const
 {
   bool hasLJ14 = !new14.empty();
   bool hasLJC = !newLJC.empty();
   // Generate array of only the types that are currently in Topology. TODO should this be a permanent part of Topology?
   ParmHolder<AtomType> currentAtomTypes;
-  for (AtArray::const_iterator atm = atoms_.begin(); atm != atoms_.end(); ++atm)
+  for (AtArray::const_iterator atm = topOut.begin(); atm != topOut.end(); ++atm)
   {
     if (atm->HasType()) {
       TypeNameHolder types(1);
@@ -594,11 +595,12 @@ const
   }
   if (currentAtomTypes.size() < 1) {
     mprintf("Warning: No atom type information in %s - cannot assign nonbond parameters.\n",
-            c_str());
+            topOut.c_str());
     return;
   }
   // Regenerate nonbond params for existing types
-  nonbond_.Clear();
+  NonbondParmType& nonbond = topOut.SetNonbond();
+  nonbond.Clear();
   // Set type indices in order.
   for (ParmHolder<AtomType>::iterator t1 = currentAtomTypes.begin(); t1 != currentAtomTypes.end(); ++t1)
     t1->second.SetTypeIdx( -1 );
@@ -629,11 +631,11 @@ const
     }
   }
   mprintf("DEBUG: Setting up nonbond array for %i unique LJ types.\n", n_unique_lj_types);
-  nonbond_.SetupLJforNtypes( n_unique_lj_types );
+  nonbond.SetupLJforNtypes( n_unique_lj_types );
   if (hasLJ14)
-    nonbond_.SetNLJ14terms( nonbond_.NBarray().size() );
+    nonbond.SetNLJ14terms( nonbond.NBarray().size() );
   if (hasLJC)
-    nonbond_.SetNLJCterms( nonbond_.NBarray().size() );
+    nonbond.SetNLJCterms( nonbond.NBarray().size() );
   // Loop over all atom type pairs
   for (ParmHolder<AtomType>::const_iterator t1 = currentAtomTypes.begin(); t1 != currentAtomTypes.end(); ++t1)
   {
@@ -653,9 +655,9 @@ const
       ParmHolder<HB_ParmType>::const_iterator hb = newHB.GetParam( types );
       if (hb != newHB.end()) {
         if (verbose > 0) mprintf("LJ 10-12 parameter found for %s %s\n", *name1, *name2);
-        nonbond_.AddHBterm(t1->second.OriginalIdx(), t2->second.OriginalIdx(), hb->second);
+        nonbond.AddHBterm(t1->second.OriginalIdx(), t2->second.OriginalIdx(), hb->second);
         // Also add a blank 6-12 term since that seems to be the convention
-        newnbidx = nonbond_.AddLJterm( t1->second.OriginalIdx(), t2->second.OriginalIdx(), NonbondType() );
+        newnbidx = nonbond.AddLJterm( t1->second.OriginalIdx(), t2->second.OriginalIdx(), NonbondType() );
       } else {
         // See if this parameter exists in the given nonbond array.
         NonbondType LJAB;
@@ -667,7 +669,7 @@ const
           if (verbose > 0) mprintf("Using existing NB parameter for %s %s\n", *name1, *name2);
           LJAB = it->second;
         }
-        newnbidx = nonbond_.AddLJterm(t1->second.OriginalIdx(), t2->second.OriginalIdx(), LJAB);
+        newnbidx = nonbond.AddLJterm(t1->second.OriginalIdx(), t2->second.OriginalIdx(), LJAB);
       }
       // LJ 1-4
       if (hasLJ14) {
@@ -675,10 +677,10 @@ const
         ParmHolder<NonbondType>::const_iterator it = new14.GetParam( types );
         if (it == new14.end()) {
           if (verbose > 0) mprintf("NB 1-4 parameter for %s %s not found. Generating.\n", *name1, *name2);
-          nonbond_.SetLJ14( newnbidx ) = type1.LJ14().Combine_LB( type2.LJ14() );
+          nonbond.SetLJ14( newnbidx ) = type1.LJ14().Combine_LB( type2.LJ14() );
         } else {
           if (verbose > 0) mprintf("Using existing NB 1-4 parameter for %s %s\n", *name1, *name2);
-          nonbond_.SetLJ14( newnbidx ) = it->second;
+          nonbond.SetLJ14( newnbidx ) = it->second;
         }
       } // END hasLJ14
       // LJC
@@ -687,27 +689,27 @@ const
         ParmHolder<double>::const_iterator it = newLJC.GetParam( types );
         if (it == newLJC.end()) {
           mprintf("LJC parameter for %s %s not found. Setting to 0.\n", *name1, *name2); // FIXME generate
-          nonbond_.SetLJC( newnbidx, 0 );
+          nonbond.SetLJC( newnbidx, 0 );
         } else {
           mprintf("Using existing LJC parameter for %s %s\n", *name1, *name2);
-          nonbond_.SetLJC( newnbidx, it->second );
+          nonbond.SetLJC( newnbidx, it->second );
         }
       } // END hasLJC
     } // END inner loop over current types
   } // END outer loop over current types
   // Reset the atom type indices.
-  for (AtArray::iterator atm = atoms_.begin(); atm != atoms_.end(); ++atm)
+  for (AtArray::iterator atm = topOut.ModifyAtoms().begin(); atm != topOut.ModifyAtoms().end(); ++atm)
   {
     int tidx = -1;
     ParmHolder<AtomType>::const_iterator it = currentAtomTypes.GetParam( TypeNameHolder(atm->Type()) );
     if (it == currentAtomTypes.end()) {
       mprintf("Warning: Atom type not found for %s (type %s)\n",
-              TruncResAtomNameNum( atm - atoms_.begin() ).c_str(),
+              topOut.TruncResAtomNameNum( atm - topOut.ModifyAtoms().begin() ).c_str(),
               *(atm->Type()));
     } else {
       if (it->second.OriginalIdx() < 0 || it->second.OriginalIdx() >= (int)currentAtomTypes.size()) {
         mprinterr("Internal Error: Type index for %s (type %s) out of range: %i\n",
-                  TruncResAtomNameNum( atm - atoms_.begin() ).c_str(),
+                  topOut.TruncResAtomNameNum( atm - topOut.ModifyAtoms().begin() ).c_str(),
                   *(atm->Type()), it->second.OriginalIdx());
       } else
         tidx = it->second.OriginalIdx();
@@ -717,9 +719,9 @@ const
 }
 
 /// \return index of 5th cmap atom if atom names match those in dihedral, -1 otherwise
-static inline int cmap_anames_match(DihedralType const& dih,
-                                     AtArray const& atoms,
-                                     std::vector<std::string> const& cmapAtomNames)
+int AssignParams::cmap_anames_match(DihedralType const& dih,
+                                    AtArray const& atoms,
+                                    std::vector<std::string> const& cmapAtomNames)
 {
 /*  mprintf("DEBUG: Check res %i %s %s %s %s against %s %s %s %s\n",
           atoms[dih.A2()].ResNum()+1,
diff --git a/src/Parm/AssignParams.h b/src/Parm/AssignParams.h
index c376aca57a..aac972fbc9 100644
--- a/src/Parm/AssignParams.h
+++ b/src/Parm/AssignParams.h
@@ -57,11 +57,13 @@ class AssignParams {
     void AssignDihedralParams(Topology&, DihedralParmHolder const&, ImproperParmHolder const&,
                               ParmHolder<AtomType> const&) const;
 
-    void AssignNonbondParams(ParmHolder<AtomType> const&,
+    void AssignNonbondParams(Topology&,
+                             ParmHolder<AtomType> const&,
                              ParmHolder<NonbondType> const&, ParmHolder<NonbondType> const&,
                              ParmHolder<double> const&, ParmHolder<HB_ParmType> const&,
                              int) const; // TODO make int a class vair
 
+    static inline int cmap_anames_match(DihedralType const&, AtArray const&, std::vector<std::string> const&);
     int remap_cmap_indices(std::vector<int>&, CmapGridArray&, CmapArray&, CmapParmHolder const&) const;
     int AssignCmapParams(CmapArray&, CmapParmHolder const&, CmapGridArray&) const;
     int AssignCmapParams(DihedralArray const&, CmapParmHolder const&,

From db8d90235f6238eb8d4eaabec65e74331b3f5949 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 20 Jul 2024 16:32:23 -0400
Subject: [PATCH 0856/1492] CMAP

---
 src/Parm/AssignParams.cpp | 54 ++++++++++++++++++++-------------------
 src/Parm/AssignParams.h   |  7 ++---
 2 files changed, 32 insertions(+), 29 deletions(-)

diff --git a/src/Parm/AssignParams.cpp b/src/Parm/AssignParams.cpp
index 4fe6ffb80a..6680d4c019 100644
--- a/src/Parm/AssignParams.cpp
+++ b/src/Parm/AssignParams.cpp
@@ -6,6 +6,7 @@
 #include "../ParameterHolders.h"
 #include "../Topology.h"
 #include "../TypeNameHolder.h"
+#include <algorithm> //sort
 
 using namespace Cpptraj::Parm;
 
@@ -769,7 +770,8 @@ static inline bool MatchesResName(std::vector<std::string> const& resNames, std:
 }
 
 /// Remap cmap indices
-int AssignParams::remap_cmap_indices(std::vector<int>& originalCmapIndices,
+int AssignParams::remap_cmap_indices(Topology const& topOut,
+                                     std::vector<int>& originalCmapIndices,
                                      CmapGridArray& cmapGrids,
                                      CmapArray& cmapTerms,
                                  CmapParmHolder const& cmapIn)
@@ -779,7 +781,7 @@ const
   for (unsigned int idx = 0; idx < originalCmapIndices.size(); idx++)
     mprintf("DEBUG:\t\tCurrent idx=%i  Actual idx=%u\n", originalCmapIndices[idx], idx);
   if (originalCmapIndices.empty()) {
-    mprintf("DEBUG: No CMAP indices in %s\n", c_str());
+    mprintf("DEBUG: No CMAP indices in %s\n", topOut.c_str());
     return 0;
   }
   std::sort(originalCmapIndices.begin(), originalCmapIndices.end());
@@ -809,7 +811,7 @@ const
 }
 
 /** Assign CMAP parameters to existing CMAP terms. */
-int AssignParams::AssignCmapParams(CmapArray& cmapTerms, CmapParmHolder const& cmapIn,
+int AssignParams::AssignCmapParams(Topology const& topOut, CmapArray& cmapTerms, CmapParmHolder const& cmapIn,
                                CmapGridArray& cmapGrids)
 const
 {
@@ -824,18 +826,18 @@ const
   for (CmapArray::iterator cm = cmapTerms.begin(); cm != cmapTerms.end(); ++cm)
   {
     // Get residue name for A2
-    Atom const& A2 = atoms_[cm->A2()];
+    Atom const& A2 = topOut[cm->A2()];
     // TODO make sure A2-A4 in same residue?
-    NameType const& rn2 = residues_[A2.ResNum()].Name();
+    NameType const& rn2 = topOut.Res( A2.ResNum() ).Name();
     // Is this residue already in cmapGrids?
     int cidx = -1;
     for (unsigned int idx = 0; idx != CmapResNames.size(); idx++) {
       if ( MatchesResName(CmapResNames[idx], rn2.Truncated()) ) {
-        if (atoms_[cm->A1()].Name() == CmapAtomNames[idx][0] &&
-            atoms_[cm->A2()].Name() == CmapAtomNames[idx][1] &&
-            atoms_[cm->A3()].Name() == CmapAtomNames[idx][2] &&
-            atoms_[cm->A4()].Name() == CmapAtomNames[idx][3] &&
-            atoms_[cm->A5()].Name() == CmapAtomNames[idx][4])
+        if (topOut[cm->A1()].Name() == CmapAtomNames[idx][0] &&
+            topOut[cm->A2()].Name() == CmapAtomNames[idx][1] &&
+            topOut[cm->A3()].Name() == CmapAtomNames[idx][2] &&
+            topOut[cm->A4()].Name() == CmapAtomNames[idx][3] &&
+            topOut[cm->A5()].Name() == CmapAtomNames[idx][4])
         {
           cidx = originalCmapIndices[idx];
           break;
@@ -843,7 +845,7 @@ const
       }
     }
     if (cidx > -1) {
-      mprintf("DEBUG: Potential existing cmap %i found for %s (%li)\n", cidx, TruncResNameNum(A2.ResNum()).c_str(), cm-cmapTerms.begin());
+      mprintf("DEBUG: Potential existing cmap %i found for %s (%li)\n", cidx, topOut.TruncResNameNum(A2.ResNum()).c_str(), cm-cmapTerms.begin());
       mprintf("DEBUG:\t\t%i - %i - %i - %i - %i %i\n", cm->A1()+1, cm->A2()+1, cm->A3()+1, cm->A4()+1, cm->A5()+1, cidx+1);
       cm->SetIdx( cidx );
     }
@@ -851,11 +853,11 @@ const
     if (cidx == -1) {
       for (unsigned int idx = 0; idx != cmapIn.size(); idx++) {
         if ( MatchesResName( cmapIn[idx].ResNames(), rn2.Truncated() ) ) {
-          if (atoms_[cm->A1()].Name() == cmapIn[idx].AtomNames()[0] &&
-              atoms_[cm->A2()].Name() == cmapIn[idx].AtomNames()[1] &&
-              atoms_[cm->A3()].Name() == cmapIn[idx].AtomNames()[2] &&
-              atoms_[cm->A4()].Name() == cmapIn[idx].AtomNames()[3] &&
-              atoms_[cm->A5()].Name() == cmapIn[idx].AtomNames()[4])
+          if (topOut[cm->A1()].Name() == cmapIn[idx].AtomNames()[0] &&
+              topOut[cm->A2()].Name() == cmapIn[idx].AtomNames()[1] &&
+              topOut[cm->A3()].Name() == cmapIn[idx].AtomNames()[2] &&
+              topOut[cm->A4()].Name() == cmapIn[idx].AtomNames()[3] &&
+              topOut[cm->A5()].Name() == cmapIn[idx].AtomNames()[4])
           {
             cidx = (int)idx;
             CmapResNames.push_back( cmapIn[idx].ResNames() );
@@ -866,7 +868,7 @@ const
         }
       }
       if (cidx > -1) {
-        mprintf("DEBUG: Potential new cmap %i found for %s (%li)\n", cidx, TruncResNameNum(A2.ResNum()).c_str(), cm-cmapTerms.begin());
+        mprintf("DEBUG: Potential new cmap %i found for %s (%li)\n", cidx, topOut.TruncResNameNum(A2.ResNum()).c_str(), cm-cmapTerms.begin());
         mprintf("DEBUG:\t\t%i - %i - %i - %i - %i %i\n", cm->A1()+1, cm->A2()+1, cm->A3()+1, cm->A4()+1, cm->A5()+1, cidx+1);
         //mprintf("DEBUG:\t\t%s - %s - %s - %s - %s\n",
         //        AtomMaskName(dih->A1()).c_str(),
@@ -879,11 +881,11 @@ const
     }
   } // END loop over cmap terms
 
-  return remap_cmap_indices(originalCmapIndices, cmapGrids, cmapTerms, cmapIn);
+  return remap_cmap_indices(topOut, originalCmapIndices, cmapGrids, cmapTerms, cmapIn);
 }
 
 /** Assign CMAP parameters. Also generates CMAP terms from dihedrals. */
-int AssignParams::AssignCmapParams(DihedralArray const& allDih, CmapParmHolder const& cmapIn,
+int AssignParams::AssignCmapParams(Topology const& topOut, DihedralArray const& allDih, CmapParmHolder const& cmapIn,
                                CmapGridArray& cmapGrids, CmapArray& cmapTerms)
 const
 {
@@ -903,9 +905,9 @@ const
     // Ignore end (repeated) or improper dihedrals
     if (dih->IsImproper() || dih->Skip14()) continue;
     // Get residue name for A2
-    Atom const& A2 = atoms_[dih->A2()];
+    Atom const& A2 = topOut[dih->A2()];
     // TODO make sure A2-A4 in same residue?
-    NameType const& rn2 = residues_[A2.ResNum()].Name();
+    NameType const& rn2 = topOut.Res( A2.ResNum() ).Name();
     // Is this residue already in cmapGrids?
     int cidx = -1;
     int a5 = -1;
@@ -914,7 +916,7 @@ const
     for (unsigned int idx = 0; idx != CmapResNames.size(); idx++) {
       if ( MatchesResName(CmapResNames[idx], rn2.Truncated()) ) {
         //a5 = cmap_anames_match(*dih, atoms_, cmapGrids[idx]);
-        a5 = cmap_anames_match(*dih, atoms_, CmapAtomNames[idx]);
+        a5 = cmap_anames_match(*dih, topOut.Atoms(), CmapAtomNames[idx]);
         if (a5 > -1) {
           //cidx = (int)idx;
           cidx = originalCmapIndices[idx];
@@ -923,7 +925,7 @@ const
       }
     }
     if (cidx > -1) {
-      mprintf("DEBUG: Potential existing cmap %i found for %s (%li)\n", cidx, TruncResNameNum(A2.ResNum()).c_str(), dih-allDih.begin());
+      mprintf("DEBUG: Potential existing cmap %i found for %s (%li)\n", cidx, topOut.TruncResNameNum(A2.ResNum()).c_str(), dih-allDih.begin());
       mprintf("DEBUG:\t\t%i - %i - %i - %i - %i %i\n", dih->A1()+1, dih->A2()+1, dih->A3()+1, dih->A4()+1, a5+1, cidx+1);
 //      mprintf("DEBUG:\t\t%s - %s - %s - %s - %s\n",
 //              AtomMaskName(dih->A1()).c_str(),
@@ -940,7 +942,7 @@ const
         //if (cmapIn[idx].MatchesResName( rn2.Truncated() )) {
         if ( MatchesResName( cmapIn[idx].ResNames(), rn2.Truncated() ) ) {
           //a5 = cmap_anames_match(*dih, atoms_, cmapIn[idx]);
-          a5 = cmap_anames_match(*dih, atoms_, cmapIn[idx].AtomNames());
+          a5 = cmap_anames_match(*dih, topOut.Atoms(), cmapIn[idx].AtomNames());
           if (a5 > -1) {
             //cidx = (int)cmapGrids.size();
             cidx = (int)idx;
@@ -954,7 +956,7 @@ const
         }
       }
       if (cidx > -1) {
-        mprintf("DEBUG: Potential new cmap %i found for %s (%li)\n", cidx, TruncResNameNum(A2.ResNum()).c_str(), dih-allDih.begin());
+        mprintf("DEBUG: Potential new cmap %i found for %s (%li)\n", cidx, topOut.TruncResNameNum(A2.ResNum()).c_str(), dih-allDih.begin());
         mprintf("DEBUG:\t\t%i - %i - %i - %i - %i %i\n", dih->A1()+1, dih->A2()+1, dih->A3()+1, dih->A4()+1, a5+1, cidx+1);
       //mprintf("DEBUG:\t\t%s - %s - %s - %s - %s\n",
       //        AtomMaskName(dih->A1()).c_str(),
@@ -966,7 +968,7 @@ const
       }
     }
   } // END loop over dihedrals
-  return remap_cmap_indices(originalCmapIndices, cmapGrids, cmapTerms, cmapIn);
+  return remap_cmap_indices(topOut, originalCmapIndices, cmapGrids, cmapTerms, cmapIn);
 /*  mprintf("DEBUG: Cmap parameter indices:\n");
   for (unsigned int idx = 0; idx < originalCmapIndices.size(); idx++)
     mprintf("DEBUG:\t\tCurrent idx=%i  Actual idx=%u\n", originalCmapIndices[idx], idx);
diff --git a/src/Parm/AssignParams.h b/src/Parm/AssignParams.h
index aac972fbc9..3e145a43b9 100644
--- a/src/Parm/AssignParams.h
+++ b/src/Parm/AssignParams.h
@@ -1,6 +1,7 @@
 #ifndef INC_PARM_ASSIGNPARAMS_H
 #define INC_PARM_ASSIGNPARAMS_H
 #include <vector>
+#include <string>
 class AngleArray;
 class AngleParmArray;
 class AngleParmType;
@@ -64,9 +65,9 @@ class AssignParams {
                              int) const; // TODO make int a class vair
 
     static inline int cmap_anames_match(DihedralType const&, AtArray const&, std::vector<std::string> const&);
-    int remap_cmap_indices(std::vector<int>&, CmapGridArray&, CmapArray&, CmapParmHolder const&) const;
-    int AssignCmapParams(CmapArray&, CmapParmHolder const&, CmapGridArray&) const;
-    int AssignCmapParams(DihedralArray const&, CmapParmHolder const&,
+    int remap_cmap_indices(Topology const&, std::vector<int>&, CmapGridArray&, CmapArray&, CmapParmHolder const&) const;
+    int AssignCmapParams(Topology const&, CmapArray&, CmapParmHolder const&, CmapGridArray&) const;
+    int AssignCmapParams(Topology const&, DihedralArray const&, CmapParmHolder const&,
                          CmapGridArray&, CmapArray&) const;
 
 

From 14874eb7aed62452db26ebb8141d2ad14222d3f5 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 20 Jul 2024 16:47:03 -0400
Subject: [PATCH 0857/1492] Assign bonds and angles

---
 src/Parm/AssignParams.cpp | 49 +++++++++++++++++++++++++++++----------
 src/Parm/AssignParams.h   |  8 ++++---
 2 files changed, 42 insertions(+), 15 deletions(-)

diff --git a/src/Parm/AssignParams.cpp b/src/Parm/AssignParams.cpp
index 6680d4c019..11282aa9dc 100644
--- a/src/Parm/AssignParams.cpp
+++ b/src/Parm/AssignParams.cpp
@@ -2,6 +2,7 @@
 #include "../Atom.h"
 #include "../AtomType.h"
 #include "../CpptrajStdio.h"
+#include "../Structure/GenerateConnectivityArrays.h"
 #include "../GuessAtomHybridization.h"
 #include "../ParameterHolders.h"
 #include "../Topology.h"
@@ -1002,29 +1003,53 @@ const
   return 0;*/
 }
 
+/** Add to bond arrays but do not update atom connectivity. Used
+  * when regenerating bond information from atom connectivity.
+  */
+void AssignParams::AddToBondArrays(Topology& topOut, BondType const& bnd) {
+  // TODO enforce H as second atom?
+  if (topOut[bnd.A1()].Element() == Atom::HYDROGEN ||
+      topOut[bnd.A2()].Element() == Atom::HYDROGEN)
+    topOut.ModifyBondsH().push_back( bnd );
+  else
+    topOut.ModifyBonds().push_back( bnd );
+}
+
+/** Add to angle arrays. Used when regenerating angle information
+  * from atom connectivity.
+  */
+void AssignParams::AddToAngleArrays(Topology& topOut, AngleType const& ang) {
+  if (topOut[ang.A1()].Element() == Atom::HYDROGEN ||
+      topOut[ang.A2()].Element() == Atom::HYDROGEN ||
+      topOut[ang.A3()].Element() == Atom::HYDROGEN)
+    topOut.ModifyAnglesH().push_back( ang );
+  else
+    topOut.ModifyAngles().push_back( ang );
+}
+
 /** Replace existing parameters with the given parameter set. */
 int AssignParams::AssignParameters(Topology& topOut, ParameterSet const& set0) const {
 
   // Bond parameters
   mprintf("\tAssigning bond parameters.\n");
-  bondparm_.clear();
+  topOut.ModifyBondParm().clear();
   // Regenerate bond array in LEaP order
-  bonds_.clear();
-  bondsh_.clear();
-  BondArray allBonds = Cpptraj::Structure::GenerateBondArray(residues_, atoms_);
-  AssignBondParm( topOut, set0.BP(), allBonds, bondparm_, "bond" );
+  topOut.ModifyBonds().clear();
+  topOut.ModifyBondsH().clear();
+  BondArray allBonds = Cpptraj::Structure::GenerateBondArray(topOut.Residues(), topOut.Atoms());
+  AssignBondParm( topOut, set0.BP(), allBonds, topOut.ModifyBondParm(), "bond" );
   for (BondArray::const_iterator bnd = allBonds.begin(); bnd != allBonds.end(); ++bnd)
-    AddToBondArrays( *bnd );
+    AddToBondArrays( topOut, *bnd );
   // Angle parameters
   mprintf("\tAssigning angle parameters.\n");
-  angleparm_.clear();
+  topOut.ModifyAngleParm().clear();
   // Regenerate angle array in LEaP order
-  angles_.clear();
-  anglesh_.clear();
-  AngleArray allAngles = Cpptraj::Structure::GenerateAngleArray(residues_, atoms_);
-  allAngles = AssignAngleParm( set0.AP(), allAngles );
+  topOut.ModifyAngles().clear();
+  topOut.ModifyAnglesH().clear();
+  AngleArray allAngles = Cpptraj::Structure::GenerateAngleArray(topOut.Residues(), topOut.Atoms());
+  allAngles = AssignAngleParm( topOut, set0.AP(), allAngles, topOut.ModifyAngleParm() );
   for (AngleArray::const_iterator ang = allAngles.begin(); ang != allAngles.end(); ++ang)
-    AddToAngleArrays( *ang );
+    AddToAngleArrays( topOut, *ang );
   // Dihedral parameters
   mprintf("\tAssigning dihedral parameters.\n");
   dihedralparm_.clear();
diff --git a/src/Parm/AssignParams.h b/src/Parm/AssignParams.h
index 3e145a43b9..acefec659c 100644
--- a/src/Parm/AssignParams.h
+++ b/src/Parm/AssignParams.h
@@ -5,11 +5,13 @@
 class AngleArray;
 class AngleParmArray;
 class AngleParmType;
+class AngleType;
 class Atom;
 class AtomType;
-class BondParmType;
 class BondArray;
 class BondParmArray;
+class BondParmType;
+class BondType;
 class CmapArray;
 class CmapGridArray;
 class CmapParmHolder;
@@ -69,8 +71,8 @@ class AssignParams {
     int AssignCmapParams(Topology const&, CmapArray&, CmapParmHolder const&, CmapGridArray&) const;
     int AssignCmapParams(Topology const&, DihedralArray const&, CmapParmHolder const&,
                          CmapGridArray&, CmapArray&) const;
-
-
+    static void AddToBondArrays(Topology&, BondType const&);
+    static void AddToAngleArrays(Topology&, AngleType const&);
 
     int debug_;
 };

From 8d97007d8c4ac4566f226cda5a658d8fbef45144 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 20 Jul 2024 16:56:56 -0400
Subject: [PATCH 0858/1492] DIhedral assign

---
 src/Parm/AssignParams.cpp | 31 ++++++++++++++++++++++---------
 src/Parm/AssignParams.h   |  1 +
 2 files changed, 23 insertions(+), 9 deletions(-)

diff --git a/src/Parm/AssignParams.cpp b/src/Parm/AssignParams.cpp
index 11282aa9dc..ce9cc97148 100644
--- a/src/Parm/AssignParams.cpp
+++ b/src/Parm/AssignParams.cpp
@@ -1027,6 +1027,19 @@ void AssignParams::AddToAngleArrays(Topology& topOut, AngleType const& ang) {
     topOut.ModifyAngles().push_back( ang );
 }
 
+/** Add to dihedral arrays. Used when regenerating dihedral information
+  * from atom connectivity.
+  */
+void AssignParams::AddToDihedralArrays(Topology& topOut, DihedralType const& dih) {
+  if (topOut[dih.A1()].Element() == Atom::HYDROGEN ||
+      topOut[dih.A4()].Element() == Atom::HYDROGEN ||
+      topOut[dih.A2()].Element() == Atom::HYDROGEN ||
+      topOut[dih.A3()].Element() == Atom::HYDROGEN)
+    topOut.ModifyDihedralsH().push_back( dih );
+  else
+    topOut.ModifyDihedrals().push_back( dih );
+}
+
 /** Replace existing parameters with the given parameter set. */
 int AssignParams::AssignParameters(Topology& topOut, ParameterSet const& set0) const {
 
@@ -1052,22 +1065,22 @@ int AssignParams::AssignParameters(Topology& topOut, ParameterSet const& set0) c
     AddToAngleArrays( topOut, *ang );
   // Dihedral parameters
   mprintf("\tAssigning dihedral parameters.\n");
-  dihedralparm_.clear();
+  topOut.ModifyDihedralParm().clear();
   // Regenerate dihedral array in LEaP order
-  dihedrals_.clear();
-  dihedralsh_.clear();
-  DihedralArray allDihedrals = Cpptraj::Structure::GenerateDihedralArray(residues_, atoms_);
+  topOut.ModifyDihedrals().clear();
+  topOut.ModifyDihedralsH().clear();
+  DihedralArray allDihedrals = Cpptraj::Structure::GenerateDihedralArray(topOut.Residues(), topOut.Atoms());
   // If we need CMAP terms, do it here before the dihedrals array is modified
   if (!set0.CMAP().empty()) {
-    cmap_.clear();
-    cmapGrid_.clear();
+    topOut.ModifyCmap().clear();
+    topOut.ModifyCmapGrid().clear();
     mprintf("\tAssigning CMAP parameters.\n");
-    AssignCmapParams( allDihedrals, set0.CMAP(), cmapGrid_, cmap_ );
+    AssignCmapParams( topOut, allDihedrals, set0.CMAP(), topOut.ModifyCmapGrid(), topOut.ModifyCmap() );
   } 
   // Now modify the dihedrals for any multiplicities
-  allDihedrals = AssignDihedralParm( set0.DP(), set0.IP(), set0.AT(), allDihedrals, false );
+  allDihedrals = AssignDihedralParm( topOut, set0.DP(), set0.IP(), set0.AT(), allDihedrals, false );
   for (DihedralArray::const_iterator dih = allDihedrals.begin(); dih != allDihedrals.end(); ++dih)
-    AddToDihedralArrays( *dih );
+    AddToDihedralArrays( topOut, *dih );
   // Urey-Bradley
   mprintf("\tAssigning Urey-Bradley parameters.\n");
   AssignUBParams( set0.UB() );
diff --git a/src/Parm/AssignParams.h b/src/Parm/AssignParams.h
index acefec659c..4d38815f2d 100644
--- a/src/Parm/AssignParams.h
+++ b/src/Parm/AssignParams.h
@@ -73,6 +73,7 @@ class AssignParams {
                          CmapGridArray&, CmapArray&) const;
     static void AddToBondArrays(Topology&, BondType const&);
     static void AddToAngleArrays(Topology&, AngleType const&);
+    static void AddToDihedralArrays(Topology&, DihedralType const&);
 
     int debug_;
 };

From 4998d8f5efec61df6dffc80eafb1f7c4f952f1ad Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 20 Jul 2024 17:00:30 -0400
Subject: [PATCH 0859/1492] UB, impropers, nonbond

---
 src/Parm/AssignParams.cpp | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/src/Parm/AssignParams.cpp b/src/Parm/AssignParams.cpp
index ce9cc97148..b1a110f473 100644
--- a/src/Parm/AssignParams.cpp
+++ b/src/Parm/AssignParams.cpp
@@ -1083,25 +1083,25 @@ int AssignParams::AssignParameters(Topology& topOut, ParameterSet const& set0) c
     AddToDihedralArrays( topOut, *dih );
   // Urey-Bradley
   mprintf("\tAssigning Urey-Bradley parameters.\n");
-  AssignUBParams( set0.UB() );
-  if (!impropers_.empty()) {
+  AssignUBParams( topOut, set0.UB() );
+  if (!topOut.Impropers().empty()) {
     // Charmm Improper parameters
     mprintf("\tAssigning CHARMM improper parameters.\n");
-    AssignImproperParams( set0.IP() );
+    AssignImproperParams( topOut, set0.IP() );
   } else {
     // Amber improper parameters
     mprintf("\tAssigning improper parameters.\n");
-    DihedralArray allImpropers = Cpptraj::Structure::GenerateImproperArray(residues_, atoms_);
-    allImpropers = AssignDihedralParm( set0.DP(), set0.IP(), set0.AT(), allImpropers, true );
+    DihedralArray allImpropers = Cpptraj::Structure::GenerateImproperArray(topOut.Residues(), topOut.Atoms());
+    allImpropers = AssignDihedralParm( topOut, set0.DP(), set0.IP(), set0.AT(), allImpropers, true );
     for (DihedralArray::const_iterator imp = allImpropers.begin(); imp != allImpropers.end(); ++imp)
-      AddToDihedralArrays( *imp );
+      AddToDihedralArrays( topOut, *imp );
   }
   // Atom types
   mprintf("\tAssigning atom type parameters.\n");
   AssignAtomTypeParm( topOut.ModifyAtoms(), set0.AT() );
   // LJ 6-12
   mprintf("\tAssigning nonbond parameters.\n");
-  AssignNonbondParams( set0.AT(), set0.NB(), set0.NB14(), set0.LJC(), set0.HB(), debug_ );
+  AssignNonbondParams( topOut, set0.AT(), set0.NB(), set0.NB14(), set0.LJC(), set0.HB(), debug_ );
   mprintf("DEBUG: CMAP size %zu\n", set0.CMAP().size());
 
   return 0;
@@ -1115,7 +1115,7 @@ int AssignParams::UpdateParameters(Topology& topOut, ParameterSet const& set1) c
   //set1.Summary(); // DEBUG
   // Check TODO is this necessary?
   if (set0.AT().size() < 1)
-    mprintf("Warning: No atom type information in '%s'\n", c_str());
+    mprintf("Warning: No atom type information in '%s'\n", topOut.c_str());
   if (debug_ > 0) {
     mprintf("DEBUG: Saving original parameters in originalp.dat, new parameters in newp.dat\n");
     set0.Debug("originalp.dat");
@@ -1154,7 +1154,7 @@ int AssignParams::UpdateParameters(Topology& topOut, ParameterSet const& set1) c
 //  updateCount = UpdateParameters< ParmHolder<BondParmType> >(set0.UB(), set1.UB(), "Urey-Bradley");
   if (UC.nUreyBradleyUpdated_ > 0) {
     mprintf("\tRegenerating UB parameters.\n");
-    AssignUBParams( set0.UB() );
+    AssignUBParams( topOut, set0.UB() );
   }
   // Improper parameters
 //  updateCount = UpdateParameters< ParmHolder<DihedralParmType> >(set0.IP(), set1.IP(), "improper");

From aac11d5c619cd24ccfa923b3191467049fcce243 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 20 Jul 2024 17:04:47 -0400
Subject: [PATCH 0860/1492] Finish initial conformation

---
 src/Parm/AssignParams.cpp | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/Parm/AssignParams.cpp b/src/Parm/AssignParams.cpp
index b1a110f473..06f8fead0b 100644
--- a/src/Parm/AssignParams.cpp
+++ b/src/Parm/AssignParams.cpp
@@ -1124,7 +1124,7 @@ int AssignParams::UpdateParameters(Topology& topOut, ParameterSet const& set1) c
   ParameterSet::UpdateCount UC;
   if (set0.UpdateParamSet( set1, UC, debug_, debug_ )) { // FIXME verbose
     mprinterr("Error: Could not merge topology '%s' parameters with '%s' parameters.\n",
-              c_str(), set1.ParamSetName().c_str());
+              topOut.c_str(), set1.ParamSetName().c_str());
     return 1;
   }
   mprintf("DEBUG: Updated parameters.\n");
@@ -1136,19 +1136,19 @@ int AssignParams::UpdateParameters(Topology& topOut, ParameterSet const& set1) c
 //  updateCount = UpdateParameters< ParmHolder<BondParmType> >(set0.BP(), set1.BP(), "bond");
   if (UC.nBondsUpdated_ > 0) {
     mprintf("\tRegenerating bond parameters.\n");
-    AssignBondParams( set0.BP() );
+    AssignBondParams( topOut, set0.BP() );
   }
   // Angle parameters
 //  updateCount = UpdateParameters< ParmHolder<AngleParmType> >(set0.AP(), set1.AP(), "angle");
   if (UC.nAnglesUpdated_ > 0) {
     mprintf("\tRegenerating angle parameters.\n");
-    AssignAngleParams( set0.AP() );
+    AssignAngleParams( topOut, set0.AP() );
   }
   // Dihedral parameters
 //  updateCount = UpdateParameters< DihedralParmHolder >(set0.DP(), set1.DP(), "dihedral");
   if (UC.nDihedralsUpdated_ > 0) {
     mprintf("\tRegenerating dihedral parameters.\n");
-    AssignDihedralParams( set0.DP(), set0.IP(), set0.AT() );
+    AssignDihedralParams( topOut, set0.DP(), set0.IP(), set0.AT() );
   }
   // Urey-Bradley
 //  updateCount = UpdateParameters< ParmHolder<BondParmType> >(set0.UB(), set1.UB(), "Urey-Bradley");
@@ -1160,7 +1160,7 @@ int AssignParams::UpdateParameters(Topology& topOut, ParameterSet const& set1) c
 //  updateCount = UpdateParameters< ParmHolder<DihedralParmType> >(set0.IP(), set1.IP(), "improper");
   if (UC.nImpropersUpdated_ > 0) {
     mprintf("\tRegenerating improper parameters.\n");
-    AssignImproperParams( set0.IP() );
+    AssignImproperParams( topOut, set0.IP() );
   }
   // Atom types
 //  updateCount = UpdateParameters< ParmHolder<AtomType> >(set0.AT(), set1.AT(), "atom type");
@@ -1173,13 +1173,13 @@ int AssignParams::UpdateParameters(Topology& topOut, ParameterSet const& set1) c
       UC.nLJparamsUpdated_ > 0 || UC.nLJ14paramsUpdated_ > 0)
   {
     mprintf("\tRegenerating nonbond parameters.\n");
-    AssignNonbondParams( set0.AT(), set0.NB(), set0.NB14(), set0.LJC(), set0.HB(), debug_ );
+    AssignNonbondParams( topOut, set0.AT(), set0.NB(), set0.NB14(), set0.LJC(), set0.HB(), debug_ );
   }
   // CMAP
   if (UC.nCmapUpdated_ > 0) {
-    cmapGrid_.clear();
+    topOut.ModifyCmapGrid().clear();
     mprintf("\tRegenerating CMAP parameters.\n");
-    AssignCmapParams(cmap_, set0.CMAP(), cmapGrid_);
+    AssignCmapParams(topOut, topOut.ModifyCmap(), set0.CMAP(), topOut.ModifyCmapGrid());
   }
   // TODO LJ14
 

From 09ec027d4040bba2fe7198c16065f7dc60b4366a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 21 Jul 2024 10:15:15 -0400
Subject: [PATCH 0861/1492] Start GetParams

---
 src/Parm/GetParams.cpp | 158 +++++++++++++++++++++++++++++++++++++++++
 src/Parm/GetParams.h   |  30 ++++++++
 2 files changed, 188 insertions(+)
 create mode 100644 src/Parm/GetParams.cpp
 create mode 100644 src/Parm/GetParams.h

diff --git a/src/Parm/GetParams.cpp b/src/Parm/GetParams.cpp
new file mode 100644
index 0000000000..92815e30b1
--- /dev/null
+++ b/src/Parm/GetParams.cpp
@@ -0,0 +1,158 @@
+#include "GetParams.h"
+#include "../Atom.h"
+#include "../CpptrajStdio.h"
+#include "../ParameterTypes.h"
+
+/** \param atomTypesOut Output array of atom types and indivudual LJ parameters.
+  * \param LJ612out Output array of LJ 6-12 pair parameters.
+  * \param LJ14out Output array of LJ 6-12 1-4 pair parameters.
+  * \param LJ1012out Output array of LJ 10-12 pair parameters.
+  * \param atoms Current array of atoms.
+  * \param NB0 Current nonbond parameters.
+  */
+void Cpptraj::Parm::GetParams::GetLJAtomTypes(ParmHolder<AtomType>& atomTypesOut,
+                                  ParmHolder<NonbondType>& LJ612out,
+                                  ParmHolder<NonbondType>& LJ14out,
+                                  ParmHolder<double>& LJCout,
+                                  ParmHolder<HB_ParmType>& LJ1012out,
+                                  std::vector<Atom> const& atoms,
+                                  NonbondParmType const& NB0)
+const
+{
+  if (NB0.HasNonbond()) {
+    mprintf("DEBUG: Topology has nonbond parameters.\n");
+    bool hasLJ14 = !NB0.LJ14().empty();
+    if (hasLJ14)
+      mprintf("DEBUG: Topology has 1-4 nonbond parameters.\n");
+    bool hasLJC = !NB0.LJC_Array().empty();
+    if (hasLJC)
+      mprintf("DEBUG: Topology has LJC nonbond paramters.\n");
+    // Nonbonded parameters are present.
+    for (std::vector<Atom>::const_iterator atm = atoms.begin(); atm != atoms.end(); ++atm)
+    {
+      if (!atm->HasType()) {
+        mprintf("Warning: Topology has nonbond parameters but atom %s has no type.\n", *(atm->Name()));
+        continue;
+      }
+      TypeNameHolder atype( atm->Type() );
+      // Check for self parameters to back-calculate LJ depth/radius
+      int idx = NB0.GetLJindex( atm->TypeIndex(), atm->TypeIndex() );
+      AtomType thisType;
+      if (idx > -1) {
+        // Has LJ 6-12 parameters
+        NonbondType const& LJ = NB0.NBarray( idx );
+        thisType = AtomType(LJ.Radius(), LJ.Depth(), atm->Mass(), atm->Polar());
+        if (hasLJ14) {
+          NonbondType const& lj14 = NB0.LJ14( idx );
+          thisType.SetLJ14( LJparmType(lj14.Radius(), lj14.Depth()) );
+        }
+        // FIXME do LJ C
+      } else {
+        // Has LJ 10-12 parameters
+        thisType = AtomType(atm->Mass(), atm->Polar());
+      }
+      thisType.SetTypeIdx( atm->TypeIndex() );
+      ParameterHolders::RetType ret = atomTypesOut.AddParm( atype, thisType, true );
+      //if (debug_ > 0 && ret == ParameterHolders::ADDED) { // FIXME
+      if (ret == ParameterHolders::ADDED) {
+        mprintf("DEBUG: New atom type: %s R=%g D=%g M=%g P=%g\n", *(atype[0]),
+                thisType.LJ().Radius(), thisType.LJ().Depth(), thisType.Mass(), thisType.Polarizability());
+        if (hasLJ14)
+          mprintf("DEBUG: New LJ14 atom type: %s R=%g D=%g\n", *(atype[0]), thisType.LJ14().Radius(), thisType.LJ14().Depth());
+      }
+    }
+    // Do atom type pairs, check for off-diagonal elements.
+    // Explicitly store pairs instead of regenerating to avoid round-off issues.
+    //GetLJterms(atomTypesOut, LJ612out, &LJ1012out, NB0, false, debug_);
+    //if (hasLJ14)
+    //  GetLJterms(LJ14typesOut, LJ14out, 0, NB0, true, debug_);
+    unsigned int nModifiedOffDiagonal = 0;
+    unsigned int nModified14OffDiagonal = 0;
+    for (ParmHolder<AtomType>::const_iterator i1 = atomTypesOut.begin(); i1 != atomTypesOut.end(); ++i1)
+    {
+      for (ParmHolder<AtomType>::const_iterator i2 = i1; i2 != atomTypesOut.end(); ++i2)
+      {
+        NameType const& name1 = i1->first[0];
+        NameType const& name2 = i2->first[0];
+        TypeNameHolder types(2);
+        types.AddName( name1 );
+        types.AddName( name2 );
+        // Extract original nonbonded parameters for this type pair.
+        AtomType const& type1 = i1->second;
+        AtomType const& type2 = i2->second;
+        int idx1 = type1.OriginalIdx();
+        int idx2 = type2.OriginalIdx();
+        int idx = NB0.GetLJindex( idx1, idx2 );
+        if (idx < 0) {
+          // This is LJ 10-12.
+          //mprinterr("Error: No off-diagonal LJ for  %s %s (%i %i)\n",
+          //          *name1, *name2, idx1, idx2);
+          //return;
+          mprintf("DEBUG: LJ 10-12 parameters detected for %s %s (%i %i)\n",
+                  *name1, *name2, idx1, idx2);
+          LJ1012out.AddParm( types, NB0.HBarray((-idx)-1), false );
+        } else {
+          // This is LJ 6-12.
+          // Determine what A and B parameters would be.
+          NonbondType lj0 = type1.LJ().Combine_LB( type2.LJ() );
+        
+          NonbondType lj1 = NB0.NBarray( idx );
+          // Compare them
+          if (lj0 != lj1) {
+            nModifiedOffDiagonal++;
+            //if (debug_ > 0) {
+              double deltaA = fabs(lj0.A() - lj1.A());
+              double deltaB = fabs(lj0.B() - lj1.B());
+              mprintf("DEBUG: Potential off-diagonal LJ: %s %s expect A=%g B=%g, actual A=%g B=%g\n",
+                      *name1, *name2, lj0.A(), lj0.B(), lj1.A(), lj1.B());
+              mprintf("DEBUG:\tdeltaA= %g    deltaB= %g\n", deltaA, deltaB);
+              double pe_a = (fabs(lj0.A() - lj1.A()) / lj0.A());
+              double pe_b = (fabs(lj0.B() - lj1.B()) / lj0.B());
+              mprintf("DEBUG:\tPEA= %g  PEB= %g\n", pe_a, pe_b);
+            //}
+          }
+          LJ612out.AddParm( types, lj1, false );
+          if (hasLJ14) {
+            // This is LJ 6-12 1-4.
+            // Determine what A and B parameters would be.
+            lj0 = type1.LJ14().Combine_LB( type2.LJ14() );
+        
+            lj1 = NB0.LJ14( idx );
+            // Compare them
+            if (lj0 != lj1) {
+              nModified14OffDiagonal++;
+              //if (debug_ > 0) {
+                double deltaA = fabs(lj0.A() - lj1.A());
+                double deltaB = fabs(lj0.B() - lj1.B());
+                mprintf("DEBUG: Potential off-diagonal LJ 1-4: %s %s expect A=%g B=%g, actual A=%g B=%g\n",
+                        *name1, *name2, lj0.A(), lj0.B(), lj1.A(), lj1.B());
+                mprintf("DEBUG:\tdeltaA= %g    deltaB= %g\n", deltaA, deltaB);
+                double pe_a = (fabs(lj0.A() - lj1.A()) / lj0.A());
+                double pe_b = (fabs(lj0.B() - lj1.B()) / lj0.B());
+                mprintf("DEBUG:\tPEA= %g  PEB= %g\n", pe_a, pe_b);
+              //}
+            }
+            LJ14out.AddParm( types, lj1, false );
+          } // END hasLJ14
+          if (hasLJC) {
+            // This is LJC
+            double ljc1 = NB0.LJC_Array( idx );
+            LJCout.AddParm( types, ljc1, false );
+          }
+        }
+      } // END inner loop over atom types
+    } // END outer loop over atom types
+    if (nModifiedOffDiagonal > 0)
+      mprintf("Warning: %u modified off-diagonal LJ terms present.\n", nModifiedOffDiagonal);
+    if (nModified14OffDiagonal > 0)
+      mprintf("Warning: %u modified off-diagonal LJ 1-4 terms present.\n", nModified14OffDiagonal);
+  } else {
+    if (!atoms.empty())
+      mprintf("DEBUG: Topology does not have nonbond parameters.\n");
+    // No nonbonded parameters. Just save mass/polarizability.
+    for (std::vector<Atom>::const_iterator atm = atoms.begin(); atm != atoms.end(); ++atm)
+      if (atm->HasType() > 0)
+        atomTypesOut.AddParm( TypeNameHolder(atm->Type()), AtomType(atm->Mass(), atm->Polar()), true );
+  }
+}
+
diff --git a/src/Parm/GetParams.h b/src/Parm/GetParams.h
new file mode 100644
index 0000000000..6adb463b6f
--- /dev/null
+++ b/src/Parm/GetParams.h
@@ -0,0 +1,30 @@
+#ifndef INC_PARM_GETPARAMS_H
+#define INC_PARM_GETPARAMS_H
+#include <vector>
+class Atom;
+class AtomType;
+class HB_ParmType;
+class NonbondParmType;
+class NonbondType;
+template<typename Type> class ParmHolder;
+namespace Cpptraj {
+namespace Parm {
+/// Used to get parameters from a Topology
+class GetParams {
+  public:
+    /// CONSTRUCTOR
+    GetParams();
+    /// Get nonbonded parameters
+    void GetLJAtomTypes(ParmHolder<AtomType>&,
+                        ParmHolder<NonbondType>&,
+                        ParmHolder<NonbondType>&,
+                        ParmHolder<double>&,
+                        ParmHolder<HB_ParmType>&,
+                        std::vector<Atom> const&,
+                        NonbondParmType const&) const;
+  private:
+    int debug_;
+};
+}
+}
+#endif

From effe7916f0f791bbbe80c5b839db06a98ebfe685 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 21 Jul 2024 10:15:42 -0400
Subject: [PATCH 0862/1492] Make public to use with append

---
 src/Parm/AssignParams.h | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/src/Parm/AssignParams.h b/src/Parm/AssignParams.h
index 4d38815f2d..d25515dda6 100644
--- a/src/Parm/AssignParams.h
+++ b/src/Parm/AssignParams.h
@@ -31,9 +31,16 @@ namespace Parm {
 class AssignParams {
   public:
     AssignParams();
-
+    /// Replace existing parameters with those from given set
     int AssignParameters(Topology&, ParameterSet const&) const;
+    /// Update existing parameters with given parameter set
     int UpdateParameters(Topology&, ParameterSet const&) const;
+    // Assign nonbond parameters to topology. Used during Merge::AppendTop()
+    void AssignNonbondParams(Topology&,
+                             ParmHolder<AtomType> const&,
+                             ParmHolder<NonbondType> const&, ParmHolder<NonbondType> const&,
+                             ParmHolder<double> const&, ParmHolder<HB_ParmType> const&,
+                             int) const; // TODO make verbose a class var?
   private:
     typedef std::vector<Atom> AtArray;
 
@@ -60,11 +67,7 @@ class AssignParams {
     void AssignDihedralParams(Topology&, DihedralParmHolder const&, ImproperParmHolder const&,
                               ParmHolder<AtomType> const&) const;
 
-    void AssignNonbondParams(Topology&,
-                             ParmHolder<AtomType> const&,
-                             ParmHolder<NonbondType> const&, ParmHolder<NonbondType> const&,
-                             ParmHolder<double> const&, ParmHolder<HB_ParmType> const&,
-                             int) const; // TODO make int a class vair
+
 
     static inline int cmap_anames_match(DihedralType const&, AtArray const&, std::vector<std::string> const&);
     int remap_cmap_indices(Topology const&, std::vector<int>&, CmapGridArray&, CmapArray&, CmapParmHolder const&) const;

From 4773f12389340bbef49444e017861615805a7211 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 21 Jul 2024 10:17:04 -0400
Subject: [PATCH 0863/1492] Add missing includes.

---
 src/Parm/GetParams.cpp | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/Parm/GetParams.cpp b/src/Parm/GetParams.cpp
index 92815e30b1..5438e46c04 100644
--- a/src/Parm/GetParams.cpp
+++ b/src/Parm/GetParams.cpp
@@ -1,7 +1,10 @@
 #include "GetParams.h"
 #include "../Atom.h"
+#include "../AtomType.h"
 #include "../CpptrajStdio.h"
+#include "../ParameterHolders.h"
 #include "../ParameterTypes.h"
+#include "../TypeNameHolder.h"
 
 /** \param atomTypesOut Output array of atom types and indivudual LJ parameters.
   * \param LJ612out Output array of LJ 6-12 pair parameters.

From 32739f4ead7948c80cd72edace0487fb53b138a5 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 21 Jul 2024 10:37:13 -0400
Subject: [PATCH 0864/1492] Finish initial incarnation of GetParams

---
 src/Parm/GetParams.cpp | 262 +++++++++++++++++++++++++++++++++++++++--
 src/Parm/GetParams.h   |  32 ++++-
 2 files changed, 286 insertions(+), 8 deletions(-)

diff --git a/src/Parm/GetParams.cpp b/src/Parm/GetParams.cpp
index 5438e46c04..bcbc4faca4 100644
--- a/src/Parm/GetParams.cpp
+++ b/src/Parm/GetParams.cpp
@@ -4,8 +4,224 @@
 #include "../CpptrajStdio.h"
 #include "../ParameterHolders.h"
 #include "../ParameterTypes.h"
+#include "../Topology.h"
 #include "../TypeNameHolder.h"
 
+using namespace Cpptraj::Parm;
+
+static void paramOverwriteWarning(const char* type) {
+  mprintf("Warning: An existing %s parameter would have been overwritten. This\n"
+          "Warning:  usually means that the atom type information in the Topology is\n"
+          "Warning:  incomplete. This can happen for example with Chamber topologies\n"
+          "Warning:  if the original atom type names were > 4 characters.\n", type);
+  mprintf("Warning: The %s parameters in this topology may now be incorrect.\n", type);
+}
+
+// GetBondParams()
+void GetParams::GetBondParams(ParmHolder<BondParmType>& BP, std::vector<Atom> const& atoms, BondArray const& bonds, BondParmArray const& bpa) {
+  for (BondArray::const_iterator b = bonds.begin(); b != bonds.end(); ++b)
+  {
+    if (b->Idx() != -1) {
+      TypeNameHolder types(2);
+      types.AddName( atoms[b->A1()].Type() );
+      types.AddName( atoms[b->A2()].Type() );
+      ParameterHolders::RetType ret = BP.AddParm( types, bpa[b->Idx()], false );
+      if (ret == ParameterHolders::ERR)
+        paramOverwriteWarning("bond");
+    }
+  }
+}
+
+// GetAngleParams()
+void GetParams::GetAngleParams(ParmHolder<AngleParmType>& AP, std::vector<Atom> const& atoms, AngleArray const& angles, AngleParmArray const& apa) {
+  for (AngleArray::const_iterator b = angles.begin(); b != angles.end(); ++b)
+  {
+    if (b->Idx() != -1) {
+      TypeNameHolder types(3);
+      types.AddName( atoms[b->A1()].Type() );
+      types.AddName( atoms[b->A2()].Type() );
+      types.AddName( atoms[b->A3()].Type() );
+      ParameterHolders::RetType ret = AP.AddParm( types, apa[b->Idx()], false );
+      if (ret == ParameterHolders::ERR)
+        paramOverwriteWarning("angle");
+    }
+  }
+}
+
+// GetImproperParams()
+void GetParams::GetImproperParams(ImproperParmHolder& IP, std::vector<Atom> const& atoms, DihedralArray const& imp, DihedralParmArray const& ipa) {
+  IP.SetRequireExactMatch(true);
+  for (DihedralArray::const_iterator b = imp.begin(); b != imp.end(); ++b)
+  {
+    if (b->Idx() != -1) {
+      TypeNameHolder types(4);
+      types.AddName( atoms[b->A1()].Type() );
+      types.AddName( atoms[b->A2()].Type() );
+      types.AddName( atoms[b->A3()].Type() );
+      types.AddName( atoms[b->A4()].Type() );
+      ParameterHolders::RetType ret = IP.AddParm( types, ipa[b->Idx()], false );
+      if (ret == ParameterHolders::ERR)
+        paramOverwriteWarning("improper");
+    }
+  }
+}
+
+// GetDihedralParams()
+void GetParams::GetDihedralParams(DihedralParmHolder& DP, ImproperParmHolder& IP, std::vector<Atom> const& atoms, DihedralArray const& dih, DihedralParmArray const& dpa) {
+  IP.SetRequireExactMatch(true);
+  for (DihedralArray::const_iterator b = dih.begin(); b != dih.end(); ++b)
+  {
+    if (b->Idx() != -1) {
+      TypeNameHolder types(4);
+      types.AddName( atoms[b->A1()].Type() );
+      types.AddName( atoms[b->A2()].Type() );
+      types.AddName( atoms[b->A3()].Type() );
+      types.AddName( atoms[b->A4()].Type() );
+      //mprintf("DEBUG: dihedral %li ( %i %i %i %i )\n", b - dih.begin() + 1, b->A1()+1, b->A2()+1, b->A3()+1, b->A4()+1);
+      //mprintf("DEBUG: dihedral %li %s %s %s %s idx=%i type=%i PK=%g PN=%g Phase=%g SCEE=%g SCNB=%g\n", b - dih.begin() + 1,
+      //        *(types[0]), *(types[1]), *(types[2]), *(types[3]), b->Idx(), (int)b->Type(),
+      //        dpa[b->Idx()].Pk(), dpa[b->Idx()].Pn(), dpa[b->Idx()].Phase(), dpa[b->Idx()].SCEE(), dpa[b->Idx()].SCNB());
+      ParameterHolders::RetType ret;
+      if (b->IsImproper()) {
+        ret = IP.AddParm( types, dpa[b->Idx()], false );
+      } else {
+        ret = DP.AddParm( types, dpa[b->Idx()], false );
+      }
+      // DEBUG
+      //if (ret == ParameterHolders::ADDED) {
+      //  mprintf("DEBUG: Added %s %s %s %s idx=%i isImproper=%i\n", *(types[0]), *(types[1]), *(types[2]), *(types[3]), b->Idx(), (int)b->IsImproper());
+      //}
+      if (ret == ParameterHolders::ERR) {
+        paramOverwriteWarning("dihedral");
+        mprintf("Warning: Dihedral %s %s %s %s PK=%g PN=%g Phase=%g SCEE=%g SCNB=%g\n",
+                *(types[0]), *(types[1]), *(types[2]), *(types[3]),
+                dpa[b->Idx()].Pk(), dpa[b->Idx()].Pn(), dpa[b->Idx()].Phase(), dpa[b->Idx()].SCEE(), dpa[b->Idx()].SCNB());
+        //bool found;
+        //DihedralParmArray dpa = DP.FindParam(types, found);
+        //mprintf("Warning: Existing params:\n");
+        //for (DihedralParmArray::const_iterator d = dpa.begin(); d != dpa.end(); ++d)
+        //  mprintf("Warning:\t\tPK=%g PN=%g Phase=%g SCEE=%g SCNB=%g\n",
+        //          d->Pk(), d->Pn(), d->Phase(), d->SCEE(), d->SCNB());
+      }
+    }
+  }
+}
+
+/// \return an error if cmap atom names do not match
+static inline int check_cmap_atom_name(NameType const& n0, NameType const& n1)
+{
+  if (n0 != n1) {
+    mprinterr("Error: CMAP term atom name %s does not match expected CMAP term atom name %s\n",
+              *n1, *n0);
+    return 1;
+  }
+  return 0;
+}
+
+/** Get existing CMAP parameters.
+  * Unlike other parameters, CMAPs are big and are uniquely identified by
+  * a combination of residue and 5 atom names. Depending on if they were
+  * read in from a parameter file or a topology, they may or may not
+  * have residue/atom name information, which is needed for assignment.
+  * This info needs to be generated if it is missing.
+  */
+int GetParams::GetCmapParams(CmapParmHolder& cmapParm, CmapArray const& cmapTerms,
+                             CmapGridArray const& cmapGrids,
+                             std::vector<Atom> const& atoms, std::vector<Residue> const& residues)
+{
+  if (cmapGrids.empty() || cmapTerms.empty()) {
+    mprintf("DEBUG: CMAP grids/terms are empty. No parameters to get.\n");
+    return 0;
+  }
+  // Check if we need to generate residue/atom information for grids.
+  bool needResAtomInfo = false;
+  for (CmapGridArray::const_iterator it = cmapGrids.begin(); it != cmapGrids.end(); ++it)
+  {
+    if (it->ResNames().empty() || it->AtomNames().empty()) {
+      needResAtomInfo = true;
+      break;
+    }
+  }
+  // Mark off which terms need to be added.
+  std::vector<bool> addGrid( cmapGrids.size(), false );
+  for (CmapArray::const_iterator cm = cmapTerms.begin(); cm != cmapTerms.end(); ++cm) {
+    if (cm->Idx() != -1)
+      addGrid[cm->Idx()] = true;
+  }
+  // Add grids, adding res/atom info if needed
+  if (needResAtomInfo) {
+    mprintf("CMAP terms need residue/atom info.\n");
+    for (unsigned int idx = 0; idx != cmapGrids.size(); idx++) {
+      if (addGrid[idx]) {
+        // Figure out residue names this cmap applies to.
+        std::set<NameType> resNames;
+        std::vector<NameType> atomNames;
+        atomNames.reserve(5);
+        for (CmapArray::const_iterator cm = cmapTerms.begin(); cm != cmapTerms.end(); ++cm) {
+          if (cm->Idx() == (int)idx) {
+            int resnum = atoms[cm->A2()].ResNum();
+            resNames.insert( residues[resnum].Name() );
+            if (atomNames.empty()) {
+              atomNames.push_back( atoms[cm->A1()].Name() );
+              atomNames.push_back( atoms[cm->A2()].Name() );
+              atomNames.push_back( atoms[cm->A3()].Name() );
+              atomNames.push_back( atoms[cm->A4()].Name() );
+              atomNames.push_back( atoms[cm->A5()].Name() );
+            } else {
+              // Check atom names
+              if (check_cmap_atom_name(atomNames[0], atoms[cm->A1()].Name())) return 1;
+              if (check_cmap_atom_name(atomNames[1], atoms[cm->A2()].Name())) return 1;
+              if (check_cmap_atom_name(atomNames[2], atoms[cm->A3()].Name())) return 1;
+              if (check_cmap_atom_name(atomNames[3], atoms[cm->A4()].Name())) return 1;
+              if (check_cmap_atom_name(atomNames[4], atoms[cm->A5()].Name())) return 1;
+            }
+          }
+        }
+        mprintf("DEBUG: Cmap term %u residues", idx);
+        for (std::set<NameType>::const_iterator it = resNames.begin(); it != resNames.end(); ++it)
+          mprintf(" %s", *(*it));
+        mprintf(" Atoms={");
+        for (std::vector<NameType>::const_iterator it = atomNames.begin(); it != atomNames.end(); ++it)
+          mprintf(" %s", *(*it));
+        mprintf(" }\n");
+        CmapGridType newGrid = cmapGrids[idx];
+        // Add the atom/res info to the grid
+        newGrid.SetNumCmapRes( resNames.size() );
+        for (std::set<NameType>::const_iterator it = resNames.begin(); it != resNames.end(); ++it)
+          newGrid.AddResName( it->Truncated() ); // FIXME just use NameType
+        for (std::vector<NameType>::const_iterator it = atomNames.begin(); it != atomNames.end(); ++it)
+          newGrid.AddAtomName( it->Truncated() ); // FIXME just use NameType
+        if (!newGrid.CmapIsValid()) {
+          mprinterr("Error: CMAP is not valid, could not get parameter.\n");
+          mprinterr("Error:   Term %u residues", idx);
+          for (std::set<NameType>::const_iterator it = resNames.begin(); it != resNames.end(); ++it)
+            mprinterr(" %s", *(*it));
+          mprinterr(" Atoms={");
+          for (std::vector<NameType>::const_iterator it = atomNames.begin(); it != atomNames.end(); ++it)
+            mprinterr(" %s", *(*it));
+          mprinterr(" }\n");
+        }
+        // Set a default title if needed
+        if (newGrid.Title().empty())
+          newGrid.SetTitle( "CMAP for " + newGrid.ResNames().front() );
+        ParameterHolders::RetType ret = cmapParm.AddParm( newGrid, false );
+        if (ret == ParameterHolders::ERR)
+          paramOverwriteWarning("CMAP");
+      } // END if adding existing grid to parms
+    } // END loop over existing grids
+  } else {
+    mprintf("CMAP terms have residue/atom info.\n");
+    for (unsigned int idx = 0; idx != cmapGrids.size(); idx++) {
+      if (addGrid[idx]) {
+        ParameterHolders::RetType ret = cmapParm.AddParm( cmapGrids[idx], false );
+        if (ret == ParameterHolders::ERR)
+          paramOverwriteWarning("CMAP");
+      }
+    }
+  }
+  return 0;
+}
+
 /** \param atomTypesOut Output array of atom types and indivudual LJ parameters.
   * \param LJ612out Output array of LJ 6-12 pair parameters.
   * \param LJ14out Output array of LJ 6-12 1-4 pair parameters.
@@ -13,13 +229,13 @@
   * \param atoms Current array of atoms.
   * \param NB0 Current nonbond parameters.
   */
-void Cpptraj::Parm::GetParams::GetLJAtomTypes(ParmHolder<AtomType>& atomTypesOut,
-                                  ParmHolder<NonbondType>& LJ612out,
-                                  ParmHolder<NonbondType>& LJ14out,
-                                  ParmHolder<double>& LJCout,
-                                  ParmHolder<HB_ParmType>& LJ1012out,
-                                  std::vector<Atom> const& atoms,
-                                  NonbondParmType const& NB0)
+void GetParams::GetLJAtomTypes(ParmHolder<AtomType>& atomTypesOut,
+                               ParmHolder<NonbondType>& LJ612out,
+                               ParmHolder<NonbondType>& LJ14out,
+                               ParmHolder<double>& LJCout,
+                               ParmHolder<HB_ParmType>& LJ1012out,
+                               std::vector<Atom> const& atoms,
+                               NonbondParmType const& NB0)
 const
 {
   if (NB0.HasNonbond()) {
@@ -159,3 +375,35 @@ const
   }
 }
 
+/** \return ParameterSet for this Topology. */
+ParameterSet GetParams::GetParameters(Topology const& topIn) const {
+  ParameterSet Params;
+  // Atom LJ types and other nonbonded parameters.
+  GetLJAtomTypes( Params.AT(), Params.NB(), Params.NB14(), Params.LJC(), Params.HB(),
+                  topIn.Atoms(), topIn.Nonbond() );
+  // Bond parameters.
+  GetBondParams( Params.BP(), topIn.Atoms(), topIn.Bonds(), topIn.BondParm() );
+  GetBondParams( Params.BP(), topIn.Atoms(), topIn.BondsH(), topIn.BondParm() );
+  // Angle parameters.
+  GetAngleParams( Params.AP(), topIn.Atoms(), topIn.Angles(), topIn.AngleParm() );
+  GetAngleParams( Params.AP(), topIn.Atoms(), topIn.AnglesH(), topIn.AngleParm() );
+  // Dihedral parameters.
+  GetDihedralParams( Params.DP(), Params.IP(), topIn.Atoms(), topIn.Dihedrals(), topIn.DihedralParm() );
+  GetDihedralParams( Params.DP(), Params.IP(), topIn.Atoms(), topIn.DihedralsH(), topIn.DihedralParm() );
+  // CHARMM parameters
+  if (!topIn.UB().empty()) {
+    // UB parameters
+    GetBondParams(Params.UB(), topIn.Atoms(), topIn.UB(), topIn.UBparm() );
+  }
+  if (!topIn.Impropers().empty()) {
+    // Impropers
+    GetImproperParams( Params.IP(), topIn.Atoms(), topIn.Impropers(), topIn.ImproperParm() );
+  }
+  // CMAPs
+  if (GetCmapParams( Params.CMAP(), topIn.Cmap(), topIn.CmapGrid(), topIn.Atoms(), topIn.Residues() )) {
+    mprinterr("Error: Could not get CMAP parameters.\n"); // TODO fatal?
+  }
+
+  return Params;
+}
+
diff --git a/src/Parm/GetParams.h b/src/Parm/GetParams.h
index 6adb463b6f..9644627341 100644
--- a/src/Parm/GetParams.h
+++ b/src/Parm/GetParams.h
@@ -1,11 +1,27 @@
 #ifndef INC_PARM_GETPARAMS_H
 #define INC_PARM_GETPARAMS_H
 #include <vector>
+class AngleArray;
+class AngleParmArray;
+class AngleParmType;
 class Atom;
 class AtomType;
+class BondArray;
+class BondParmArray;
+class BondParmType;
+class CmapArray;
+class CmapGridArray;
+class CmapParmHolder;
+class DihedralArray;
+class DihedralParmArray;
+class DihedralParmHolder;
 class HB_ParmType;
+class ImproperParmHolder;
 class NonbondParmType;
 class NonbondType;
+class ParameterSet;
+class Residue;
+class Topology;
 template<typename Type> class ParmHolder;
 namespace Cpptraj {
 namespace Parm {
@@ -14,7 +30,9 @@ class GetParams {
   public:
     /// CONSTRUCTOR
     GetParams();
-    /// Get nonbonded parameters
+    /// \return ParameterSet containing parameters from given topology.
+    ParameterSet GetParameters(Topology const&) const;
+    /// Get nonbonded parameters (used in AppendTop)
     void GetLJAtomTypes(ParmHolder<AtomType>&,
                         ParmHolder<NonbondType>&,
                         ParmHolder<NonbondType>&,
@@ -23,6 +41,18 @@ class GetParams {
                         std::vector<Atom> const&,
                         NonbondParmType const&) const;
   private:
+    static inline void GetBondParams(ParmHolder<BondParmType>&, std::vector<Atom> const&,
+                                     BondArray const&, BondParmArray const&);
+    static inline void GetAngleParams(ParmHolder<AngleParmType>&, std::vector<Atom> const& atoms,
+                                      AngleArray const&, AngleParmArray const&);
+    static inline void GetImproperParams(ImproperParmHolder&, std::vector<Atom> const&,
+                                         DihedralArray const&, DihedralParmArray const&);
+    static inline void GetDihedralParams(DihedralParmHolder&, ImproperParmHolder&,
+                                         std::vector<Atom> const&,
+                                         DihedralArray const&, DihedralParmArray const&);
+    static inline int GetCmapParams(CmapParmHolder&, CmapArray const&, CmapGridArray const&,
+                                    std::vector<Atom> const&, std::vector<Residue> const&);
+
     int debug_;
 };
 }

From bec286936438e39276b9324e45e611d809373078 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 21 Jul 2024 10:47:22 -0400
Subject: [PATCH 0865/1492] Add constructor and debug level

---
 src/Parm/GetParams.cpp | 10 ++++++++++
 src/Parm/GetParams.h   |  2 ++
 2 files changed, 12 insertions(+)

diff --git a/src/Parm/GetParams.cpp b/src/Parm/GetParams.cpp
index bcbc4faca4..94a3cfe925 100644
--- a/src/Parm/GetParams.cpp
+++ b/src/Parm/GetParams.cpp
@@ -9,6 +9,16 @@
 
 using namespace Cpptraj::Parm;
 
+/** CONSTRUCTOR */
+GetParams::GetParams() :
+  debug_(0)
+{}
+
+/** Set debug level */
+void GetParams::SetDebug(int debugIn) {
+  debug_ = debugIn;
+}
+
 static void paramOverwriteWarning(const char* type) {
   mprintf("Warning: An existing %s parameter would have been overwritten. This\n"
           "Warning:  usually means that the atom type information in the Topology is\n"
diff --git a/src/Parm/GetParams.h b/src/Parm/GetParams.h
index 9644627341..1f611aae7f 100644
--- a/src/Parm/GetParams.h
+++ b/src/Parm/GetParams.h
@@ -30,6 +30,8 @@ class GetParams {
   public:
     /// CONSTRUCTOR
     GetParams();
+    /// Set debug level
+    void SetDebug(int);
     /// \return ParameterSet containing parameters from given topology.
     ParameterSet GetParameters(Topology const&) const;
     /// Get nonbonded parameters (used in AppendTop)

From ea237cd23e5e003287cccf4ed1dd907ec086263e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 21 Jul 2024 10:48:00 -0400
Subject: [PATCH 0866/1492] Convert to class and move the AppendTop function to
 Merge

---
 src/Parm/Merge.cpp | 162 +++++++++++++++++++++++++++++++++++++++++++--
 src/Parm/Merge.h   |  57 ++++++++++------
 2 files changed, 191 insertions(+), 28 deletions(-)

diff --git a/src/Parm/Merge.cpp b/src/Parm/Merge.cpp
index 5c77762f4e..c57bcda714 100644
--- a/src/Parm/Merge.cpp
+++ b/src/Parm/Merge.cpp
@@ -1,10 +1,23 @@
 #include "Merge.h"
+#include "AssignParams.h"
+#include "GetParams.h"
 #include "../Atom.h"
+#include "../AtomType.h"
 #include "../CpptrajStdio.h"
 #include "../ParameterHolders.h"
 #include "../ParameterTypes.h"
 #include "../Residue.h"
 #include "../StringRoutines.h" // integerToString
+#include "../Topology.h"
+#include "../UpdateParameters.h"
+
+using namespace Cpptraj::Parm;
+
+/** CONSTRUCTOR */
+Merge::Merge() :
+  debug_(0),
+  verbose_(1) // FIXME
+{}
 
 // ----- Bonds -------------------------
 static inline void printIdx(BondType const& bnd1, unsigned int atomOffset) {
@@ -421,7 +434,7 @@ class MergeTopArray
   * arrays from top1, merge the bond arrays and consolidate the
   * parameters.
   */
-void Cpptraj::Parm::MergeBondArrays(BondArray& bonds0,
+void Merge::MergeBondArrays(BondArray& bonds0,
                                     BondArray& bondsh0,
                                     BondParmArray& bp0,
                                     AtArray const& atoms0,
@@ -429,6 +442,7 @@ void Cpptraj::Parm::MergeBondArrays(BondArray& bonds0,
                                     BondArray const& bondsh1,
                                     BondParmArray const& bp1,
                                     AtArray const& atoms1)
+const
 {
   MergeTopArray<BondType, BondParmType, BondArray, BondParmArray> mergeBonds;
   mergeBonds.MergeTermArrays( bonds0, bondsh0, bp0, atoms0,
@@ -441,7 +455,7 @@ void Cpptraj::Parm::MergeBondArrays(BondArray& bonds0,
   * arrays from top1, merge the angle arrays and consolidate the
   * parameters.
   */
-void Cpptraj::Parm::MergeAngleArrays(AngleArray& angles0,
+void Merge::MergeAngleArrays(AngleArray& angles0,
                                     AngleArray& anglesh0,
                                     AngleParmArray& ap0,
                                     AtArray const& atoms0,
@@ -449,6 +463,7 @@ void Cpptraj::Parm::MergeAngleArrays(AngleArray& angles0,
                                     AngleArray const& anglesh1,
                                     AngleParmArray const& ap1,
                                     AtArray const& atoms1)
+const
 {
   MergeTopArray<AngleType, AngleParmType, AngleArray, AngleParmArray> mergeAngles;
   mergeAngles.MergeTermArrays( angles0, anglesh0, ap0, atoms0,
@@ -478,7 +493,7 @@ static inline void merge_impropers(DihedralArray& dihOut, DihedralArray& dihIn,
   * parameter arrays from top1, merge the dihedral arrays and consolidate the
   * parameters.
   */
-void Cpptraj::Parm::MergeDihedralArrays(DihedralArray& dihedrals0,
+void Merge::MergeDihedralArrays(DihedralArray& dihedrals0,
                                     DihedralArray& dihedralsh0,
                                     DihedralParmArray& dp0,
                                     AtArray const& atoms0,
@@ -486,6 +501,7 @@ void Cpptraj::Parm::MergeDihedralArrays(DihedralArray& dihedrals0,
                                     DihedralArray const& dihedralsh1,
                                     DihedralParmArray const& dp1,
                                     AtArray const& atoms1)
+const
 {
   // Separate any impropers.
   DihedralArray dih0, dihH0, imp0, impH0;
@@ -562,7 +578,7 @@ void index_cmap_types(ParmHolder<int>& currentTypes,
 }
 
 /** Given CMAP arrays from top0 and top1, merge and consolidate parameters. */
-void Cpptraj::Parm::MergeCmapArrays(CmapArray& cmap0,
+void Merge::MergeCmapArrays(CmapArray& cmap0,
                                     CmapGridArray& cg0,
                                     AtArray const& atoms0,
                                     ResArray const& residues0,
@@ -570,6 +586,7 @@ void Cpptraj::Parm::MergeCmapArrays(CmapArray& cmap0,
                                     CmapGridArray const& cg1,
                                     AtArray const& atoms1,
                                     ResArray const& residues1)
+const
 {
   unsigned int atomOffset = atoms0.size();
   unsigned int cgOffset = cg0.size();
@@ -645,12 +662,13 @@ void Cpptraj::Parm::MergeCmapArrays(CmapArray& cmap0,
   * array from top1, merge the bond arrays and consolidate the
   * parameters.
   */
-void Cpptraj::Parm::MergeBondArray(BondArray& bonds0,
+void Merge::MergeBondArray(BondArray& bonds0,
                                    BondParmArray& bp0,
                                    AtArray const& atoms0,
                                    BondArray const& bonds1,
                                    BondParmArray const& bp1,
                                    AtArray const& atoms1)
+const
 {
   mprintf("DEBUG: Enter MergeBondArray()\n");
   MergeTopArray<BondType, BondParmType, BondArray, BondParmArray> mergeBonds;
@@ -663,12 +681,13 @@ void Cpptraj::Parm::MergeBondArray(BondArray& bonds0,
   * parameter array from top1, merge the improper arrays and consolidate the
   * parameters.
   */
-void Cpptraj::Parm::MergeImproperArray(DihedralArray& impropers0,
+void Merge::MergeImproperArray(DihedralArray& impropers0,
                                        DihedralParmArray& ip0,
                                        AtArray const& atoms0,
                                        DihedralArray const& impropers1,
                                        DihedralParmArray const& ip1,
                                        AtArray const& atoms1)
+const
 {
   MergeTopArray<DihedralType, DihedralParmType, DihedralArray, DihedralParmArray> mergeImpropers;
   mergeImpropers.SetMergeWithExisting( true ); // FIXME check this
@@ -676,3 +695,134 @@ void Cpptraj::Parm::MergeImproperArray(DihedralArray& impropers0,
   mergeImpropers.MergeTermArray( impropers0, ip0, atoms0,
                                  impropers1, ip1, atoms1 );
 }
+
+// -----------------------------------------------------------------------------
+/** This template can be used when doing Append() on a generic std::vector array
+  * of type T. The array will be appended to a given array of the same type.
+  * If one is empty and the other is not, values will be filled in if necessary.
+  */
+template <class T> class TopVecAppend {
+  public:
+    /// CONSTRUCTOR
+    TopVecAppend() {}
+    /// Append current array to given array of same type
+    void Append(std::vector<T>& arrayOut, std::vector<T> const& arrayToAdd, unsigned int expectedSize)
+    {
+      if (arrayToAdd.empty() && arrayOut.empty()) {
+        // Both arrays are empty. Nothing to do.
+        return;
+      } else if (arrayToAdd.empty()) {
+        // The current array is empty but the given array is not. Fill in 
+        // array to append with blank values.
+        for (unsigned int idx = 0; idx != expectedSize; idx++)
+          arrayOut.push_back( T() );
+      } else {
+        // Append current array to array to given array. TODO use std::copy?
+        for (typename std::vector<T>::const_iterator it = arrayToAdd.begin(); it != arrayToAdd.end(); ++it)
+          arrayOut.push_back( *it );
+      }
+    }
+};
+
+/** Append a topology to another */
+int Merge::AppendTop(Topology& topOut, Topology const& NewTop) const {
+  unsigned int atomOffset = (unsigned int)topOut.Natom();
+  unsigned int molOffset = (unsigned int)topOut.Nmol();
+  mprintf("DEBUG: Appending '%s' to '%s' (atom offset= %u mol offset= %u)\n",
+          NewTop.c_str(), topOut.c_str(), atomOffset, molOffset);
+  //int resOffset = (int)residues_.size();
+
+  // Save nonbonded parameters from each topology
+  ParmHolder<AtomType> myAtomTypes, newAtomTypes;
+  ParmHolder<NonbondType> myNB, newNB;
+  ParmHolder<NonbondType> my14, new14;
+  ParmHolder<HB_ParmType> myHB, newHB;
+  ParmHolder<double> myLJC, newLJC;
+  Cpptraj::Parm::GetParams GP;
+  GP.SetDebug( debug_ );
+  GP.GetLJAtomTypes( myAtomTypes, myNB, my14, myLJC, myHB, topOut.Atoms(), topOut.Nonbond() );
+  GP.GetLJAtomTypes( newAtomTypes, newNB, new14, newLJC, newHB, NewTop.Atoms(), NewTop.Nonbond() );
+  // Create combined nonbond parameter set
+  int nAtomTypeUpdated = UpdateParameters< ParmHolder<AtomType> >( myAtomTypes, newAtomTypes, "atom type", verbose_ );
+  int nLJparamsUpdated = UpdateParameters< ParmHolder<NonbondType> >( myNB, newNB, "LJ 6-12", verbose_ );
+  int n14paramsUpdated = UpdateParameters< ParmHolder<NonbondType> >( my14, new14, "LJ 6-12 1-4", verbose_ );
+  int nljcparamsUpdated = UpdateParameters< ParmHolder<double> >( myLJC, newLJC, "LJ C", verbose_ );
+  int nHBparamsUpdated = UpdateParameters< ParmHolder<HB_ParmType> >( myHB, newHB, "LJ 10-12", verbose_ );
+  mprintf("\t%i atom types updated, %i LJ 6-12 params updated, %i 1-4 params updated, %i LJC params updated, %i LJ 10-12 params updated.\n",
+          nAtomTypeUpdated, nLJparamsUpdated, n14paramsUpdated, nljcparamsUpdated, nHBparamsUpdated);
+
+  // Add incoming topology bond/angle/dihedral/cmap arrays to this one.
+  MergeBondArrays(topOut.ModifyBonds(), topOut.ModifyBondsH(), topOut.ModifyBondParm(), topOut.Atoms(),
+                  NewTop.Bonds(), NewTop.BondsH(), NewTop.BondParm(), NewTop.Atoms());
+  MergeAngleArrays(topOut.ModifyAngles(), topOut.ModifyAnglesH(), topOut.ModifyAngleParm(), topOut.Atoms(),
+                   NewTop.Angles(), NewTop.AnglesH(), NewTop.AngleParm(), NewTop.Atoms());
+  MergeDihedralArrays(topOut.ModifyDihedrals(), topOut.ModifyDihedralsH(), topOut.ModifyDihedralParm(), topOut.Atoms(),
+                      NewTop.Dihedrals(), NewTop.DihedralsH(), NewTop.DihedralParm(), NewTop.Atoms());
+  MergeCmapArrays(topOut.ModifyCmap(), topOut.ModifyCmapGrid(), topOut.Atoms(), topOut.Residues(),
+                  NewTop.Cmap(), NewTop.CmapGrid(), NewTop.Atoms(), NewTop.Residues());
+  MergeBondArray(topOut.ModifyUB(), topOut.ModifyUBparm(), topOut.Atoms(),
+                 NewTop.UB(), NewTop.UBparm(), NewTop.Atoms());
+  MergeImproperArray(topOut.ModifyImpropers(), topOut.ModifyImproperParm(), topOut.Atoms(),
+                     NewTop.Impropers(), NewTop.ImproperParm(), NewTop.Atoms());
+
+  // Append incoming atoms to this topology.
+  for (AtArray::const_iterator atom = NewTop.begin(); atom != NewTop.end(); ++atom)
+  {
+    if (debug_ > 1)
+      mprintf("DBG: %6li %s %s %4i\n", atom-NewTop.begin(), 
+              *(atom->Name()), *(atom->Type()), atom->TypeIndex());
+    Atom CurrentAtom = *atom;
+    Residue const& res = NewTop.Res( CurrentAtom.ResNum() );
+    // Bonds need to be cleared and re-added.
+    CurrentAtom.ClearBonds();
+    for (Atom::bond_iterator bat = atom->bondbegin(); bat != atom->bondend(); ++bat)
+      CurrentAtom.AddBondToIdx( *bat + atomOffset );
+
+    topOut.addTopAtom( CurrentAtom,
+                       Residue(res.Name(), res.OriginalResNum(), res.Icode(), res.ChainID()),
+                       atom->MolNum()+molOffset, NewTop.Mol(atom->MolNum()).IsSolvent() );
+  }
+
+  // EXTRA ATOM INFO
+  TopVecAppend<NameType> appendNameType;
+  appendNameType.Append( tree_, NewTop.tree_, NewTop.Natom() );
+  TopVecAppend<int> appendInt;
+  appendInt.Append( ijoin_, NewTop.ijoin_, NewTop.Natom() );
+  appendInt.Append( irotat_, NewTop.irotat_, NewTop.Natom() );
+  appendInt.Append( pdbSerialNum_, NewTop.pdbSerialNum_, NewTop.Natom() );
+  TopVecAppend<char> appendChar;
+  appendChar.Append( atom_altloc_, NewTop.atom_altloc_, NewTop.Natom() );
+  TopVecAppend<float> appendFloat;
+  appendFloat.Append( occupancy_, NewTop.occupancy_, NewTop.Natom() );
+  appendFloat.Append( bfactor_, NewTop.bfactor_, NewTop.Natom() );
+
+  // Need to regenerate nonbonded info
+  mprintf("\tRegenerating nonbond parameters.\n");
+  AssignParams assign;
+  assign.AssignNonbondParams( topOut, myAtomTypes, myNB, my14, myLJC, myHB, verbose_ );
+
+  // The version of AddTopAtom() with molecule number already determines
+  // molecules and number of solvent molecules.
+  // Just need to determine the number of extra points.
+  topOut.DetermineNumExtraPoints();
+
+  // GB radii set string
+  if (!NewTop.GBradiiSet().empty()) {
+    if (topOut.GBradiiSet().empty())
+      topOut.SetGBradiiSet( NewTop.GBradiiSet() );
+    else {
+      // Do not repeat a GB radius string
+      std::size_t pos = topOut.GBradiiSet().find( NewTop.GBradiiSet() );
+      if (pos == std::string::npos) {
+        std::string newName = topOut.GBradiiSet() + "+" + NewTop.GBradiiSet();
+        if (newName.size() > 80) {
+          mprintf("Warning: New radius set name is > 80 characters: '%s'\n", newName.c_str());
+          mprintf("Warning: This will be truncated to 80 characters in an Amber Topology.\n");
+        }
+        topOut.SetGBradiiSet( newName );
+      }
+    }
+  }
+  return 0;
+}
+
diff --git a/src/Parm/Merge.h b/src/Parm/Merge.h
index afe4f64d34..fd3e114750 100644
--- a/src/Parm/Merge.h
+++ b/src/Parm/Merge.h
@@ -11,30 +11,43 @@ class DihedralArray;
 class DihedralParmArray;
 class CmapArray;
 class CmapGridArray;
+class Topology;
 namespace Cpptraj {
 namespace Parm {
-/// Shorthand for array of Atoms
-typedef std::vector<Atom> AtArray;
-/// Shorthand for array of residues
-typedef std::vector<Residue> ResArray;
-/// Merge two pairs of bond arrays and their parameters.
-void MergeBondArrays(BondArray&, BondArray&, BondParmArray&, AtArray const&,
-                     BondArray const&, BondArray const&, BondParmArray const&, AtArray const&);
-/// Merge two pairs of angle arrays and their parameters.
-void MergeAngleArrays(AngleArray&, AngleArray&, AngleParmArray&, AtArray const&,
-                      AngleArray const&, AngleArray const&, AngleParmArray const&, AtArray const&);
-/// Merge two pairs of dihedral arrays and their parameters.
-void MergeDihedralArrays(DihedralArray&, DihedralArray&, DihedralParmArray&, AtArray const&,
-                         DihedralArray const&, DihedralArray const&, DihedralParmArray const&, AtArray const&);
-/// Merge cmap arrays and their parameters
-void MergeCmapArrays(CmapArray&, CmapGridArray&, AtArray const&, ResArray const&,
-                     CmapArray const&, CmapGridArray const&, AtArray const&, ResArray const&);
-/// Merge two bond arrays and their parameters
-void MergeBondArray(BondArray&, BondParmArray&, AtArray const&,
-                    BondArray const&, BondParmArray const&, AtArray const&);
-/// Merge two improper arrays and their parameters
-void MergeImproperArray(DihedralArray&, DihedralParmArray&, AtArray const&,
-                        DihedralArray const&, DihedralParmArray const&, AtArray const&);
+/// Used to merge Topology files.
+class Merge {
+  public:
+    /// CONSTRUCTOR
+    Merge();
+    /// Append topology to this one.
+    int AppendTop( Topology&, Topology const& ) const;
+  private:
+    /// Shorthand for array of Atoms
+    typedef std::vector<Atom> AtArray;
+    /// Shorthand for array of residues
+    typedef std::vector<Residue> ResArray;
+    /// Merge two pairs of bond arrays and their parameters.
+    void MergeBondArrays(BondArray&, BondArray&, BondParmArray&, AtArray const&,
+                         BondArray const&, BondArray const&, BondParmArray const&, AtArray const&) const;
+    /// Merge two pairs of angle arrays and their parameters.
+    void MergeAngleArrays(AngleArray&, AngleArray&, AngleParmArray&, AtArray const&,
+                          AngleArray const&, AngleArray const&, AngleParmArray const&, AtArray const&) const;
+    /// Merge two pairs of dihedral arrays and their parameters.
+    void MergeDihedralArrays(DihedralArray&, DihedralArray&, DihedralParmArray&, AtArray const&,
+                             DihedralArray const&, DihedralArray const&, DihedralParmArray const&, AtArray const&) const;
+    /// Merge cmap arrays and their parameters
+    void MergeCmapArrays(CmapArray&, CmapGridArray&, AtArray const&, ResArray const&,
+                         CmapArray const&, CmapGridArray const&, AtArray const&, ResArray const&) const;
+    /// Merge two bond arrays and their parameters
+    void MergeBondArray(BondArray&, BondParmArray&, AtArray const&,
+                        BondArray const&, BondParmArray const&, AtArray const&) const;
+    /// Merge two improper arrays and their parameters
+    void MergeImproperArray(DihedralArray&, DihedralParmArray&, AtArray const&,
+                            DihedralArray const&, DihedralParmArray const&, AtArray const&) const;
+
+    int debug_;
+    int verbose_;
+};
 }
 }
 #endif

From 9c042fbc1ffc0b4d434edfd6b8ebb29f3ff3967c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 21 Jul 2024 14:04:35 -0400
Subject: [PATCH 0867/1492] Finish Merge

---
 src/Parm/Merge.cpp | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/Parm/Merge.cpp b/src/Parm/Merge.cpp
index c57bcda714..5bf07fa645 100644
--- a/src/Parm/Merge.cpp
+++ b/src/Parm/Merge.cpp
@@ -785,16 +785,16 @@ int Merge::AppendTop(Topology& topOut, Topology const& NewTop) const {
 
   // EXTRA ATOM INFO
   TopVecAppend<NameType> appendNameType;
-  appendNameType.Append( tree_, NewTop.tree_, NewTop.Natom() );
+  appendNameType.Append( topOut.ModifyTreeChainClassification(), NewTop.TreeChainClassification(), NewTop.Natom() );
   TopVecAppend<int> appendInt;
-  appendInt.Append( ijoin_, NewTop.ijoin_, NewTop.Natom() );
-  appendInt.Append( irotat_, NewTop.irotat_, NewTop.Natom() );
-  appendInt.Append( pdbSerialNum_, NewTop.pdbSerialNum_, NewTop.Natom() );
+  appendInt.Append( topOut.ModifyJoinArray(), NewTop.JoinArray(), NewTop.Natom() );
+  appendInt.Append( topOut.ModifyRotateArray(), NewTop.RotateArray(), NewTop.Natom() );
+  appendInt.Append( topOut.ModifyPdbSerialNum(), NewTop.PdbSerialNum(), NewTop.Natom() );
   TopVecAppend<char> appendChar;
-  appendChar.Append( atom_altloc_, NewTop.atom_altloc_, NewTop.Natom() );
+  appendChar.Append( topOut.ModifyAtomAltLoc(), NewTop.AtomAltLoc(), NewTop.Natom() );
   TopVecAppend<float> appendFloat;
-  appendFloat.Append( occupancy_, NewTop.occupancy_, NewTop.Natom() );
-  appendFloat.Append( bfactor_, NewTop.bfactor_, NewTop.Natom() );
+  appendFloat.Append( topOut.ModifyOccupancy(), NewTop.Occupancy(), NewTop.Natom() );
+  appendFloat.Append( topOut.ModifyBfactor(), NewTop.Bfactor(), NewTop.Natom() );
 
   // Need to regenerate nonbonded info
   mprintf("\tRegenerating nonbond parameters.\n");

From fdab0e4b8856e8d19f09e8fd9bcbdcf1a40a85ba Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 21 Jul 2024 14:10:49 -0400
Subject: [PATCH 0868/1492] Finish up AssignParams

---
 src/Parm/AssignParams.cpp | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/src/Parm/AssignParams.cpp b/src/Parm/AssignParams.cpp
index 06f8fead0b..224d30f611 100644
--- a/src/Parm/AssignParams.cpp
+++ b/src/Parm/AssignParams.cpp
@@ -1,10 +1,13 @@
 #include "AssignParams.h"
+#include "GetParams.h"
 #include "../Atom.h"
 #include "../AtomType.h"
+#include "../CmapParmHolder.h"
 #include "../CpptrajStdio.h"
 #include "../Structure/GenerateConnectivityArrays.h"
 #include "../GuessAtomHybridization.h"
 #include "../ParameterHolders.h"
+#include "../ParameterSet.h"
 #include "../Topology.h"
 #include "../TypeNameHolder.h"
 #include <algorithm> //sort
@@ -1110,7 +1113,8 @@ int AssignParams::AssignParameters(Topology& topOut, ParameterSet const& set0) c
 /** Update/add to parameters in this topology with those from given set.
   */
 int AssignParams::UpdateParameters(Topology& topOut, ParameterSet const& set1) const {
-  ParameterSet set0 = topOut.GetParameters();
+  GetParams GP;
+  ParameterSet set0 = GP.GetParameters( topOut );
 
   //set1.Summary(); // DEBUG
   // Check TODO is this necessary?
@@ -1186,4 +1190,3 @@ int AssignParams::UpdateParameters(Topology& topOut, ParameterSet const& set1) c
   if (debug_ > 0) set0.Debug("newp.dat");
   return 0;
 }
-

From 9724df3cd6384345fce3d28045b84ced95d93e56 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 21 Jul 2024 14:11:15 -0400
Subject: [PATCH 0869/1492] Add files to make

---
 src/Parm/CMakeLists.txt | 2 ++
 src/Parm/parmdepend     | 6 ++++--
 src/Parm/parmfiles      | 2 ++
 3 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/src/Parm/CMakeLists.txt b/src/Parm/CMakeLists.txt
index c89594c2af..8b609328c1 100644
--- a/src/Parm/CMakeLists.txt
+++ b/src/Parm/CMakeLists.txt
@@ -1,5 +1,7 @@
 #CMake buildfile for CPPTRAJ Parm subdirectory.
 target_sources(cpptraj_common_obj PRIVATE
+  ${CMAKE_CURRENT_LIST_DIR}/AssignParams.cpp
   ${CMAKE_CURRENT_LIST_DIR}/GB_Params.cpp
+  ${CMAKE_CURRENT_LIST_DIR}/GetParams.cpp
   ${CMAKE_CURRENT_LIST_DIR}/Merge.cpp
 )
diff --git a/src/Parm/parmdepend b/src/Parm/parmdepend
index 775ded13cc..65cb189c1a 100644
--- a/src/Parm/parmdepend
+++ b/src/Parm/parmdepend
@@ -1,2 +1,4 @@
-GB_Params.o : GB_Params.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h GB_Params.h
-Merge.o : Merge.cpp ../Atom.h ../Constants.h ../CpptrajStdio.h ../NameType.h ../ParameterHolders.h ../ParameterTypes.h ../SymbolExporting.h ../TypeNameHolder.h Merge.h
+AssignParams.o : AssignParams.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/GenerateConnectivityArrays.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h AssignParams.h GetParams.h
+GB_Params.o : GB_Params.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h GB_Params.h
+GetParams.o : GetParams.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h GetParams.h
+Merge.o : Merge.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../StringRoutines.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../UpdateParameters.h ../Vec3.h AssignParams.h GetParams.h Merge.h
diff --git a/src/Parm/parmfiles b/src/Parm/parmfiles
index 83aa7c5ebb..e57ffb4318 100644
--- a/src/Parm/parmfiles
+++ b/src/Parm/parmfiles
@@ -1,4 +1,6 @@
 # Files for Parm subdirectory.
 PARM_SOURCES= \
+  AssignParams.cpp \
   GB_Params.cpp \
+  GetParams.cpp \
   Merge.cpp

From 4bfd701919745a12bdb3d2722e03d966aebcd0a4 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 21 Jul 2024 14:47:31 -0400
Subject: [PATCH 0870/1492] Add NuniqueAtomTypes function and update depends

---
 src/Parm/GetParams.cpp | 24 +++++++++++++++++++++++-
 src/Parm/GetParams.h   |  2 ++
 src/Parm/parmdepend    |  2 +-
 3 files changed, 26 insertions(+), 2 deletions(-)

diff --git a/src/Parm/GetParams.cpp b/src/Parm/GetParams.cpp
index 94a3cfe925..325088e09a 100644
--- a/src/Parm/GetParams.cpp
+++ b/src/Parm/GetParams.cpp
@@ -1,8 +1,10 @@
 #include "GetParams.h"
 #include "../Atom.h"
 #include "../AtomType.h"
+#include "../CmapParmHolder.h"
 #include "../CpptrajStdio.h"
 #include "../ParameterHolders.h"
+#include "../ParameterSet.h"
 #include "../ParameterTypes.h"
 #include "../Topology.h"
 #include "../TypeNameHolder.h"
@@ -416,4 +418,24 @@ ParameterSet GetParams::GetParameters(Topology const& topIn) const {
 
   return Params;
 }
-
+/** \return Total number of unique atom types. */
+unsigned int GetParams::NuniqueAtomTypes(Topology const& topIn) const {
+  ParmHolder<int> currentAtomTypes;
+  for (Topology::atom_iterator atm = topIn.begin(); atm != topIn.end(); ++atm)
+  {
+    if (atm->HasType()) {
+      TypeNameHolder atype( atm->Type() );
+      // Find in currentAtomTypes.
+      bool found;
+      currentAtomTypes.FindParam( atype, found );
+      if (!found) {
+        currentAtomTypes.AddParm( atype, atm->TypeIndex(), false );
+      }
+    }
+  }
+  mprintf("DEBUG: Unique atom types in %s\n", topIn.c_str());
+  for (ParmHolder<int>::const_iterator it = currentAtomTypes.begin();
+                                       it != currentAtomTypes.end(); ++it)
+    mprintf("\t\t%s %i\n", *(it->first[0]), it->second);
+  return currentAtomTypes.size();
+}
diff --git a/src/Parm/GetParams.h b/src/Parm/GetParams.h
index 1f611aae7f..8c0d693514 100644
--- a/src/Parm/GetParams.h
+++ b/src/Parm/GetParams.h
@@ -42,6 +42,8 @@ class GetParams {
                         ParmHolder<HB_ParmType>&,
                         std::vector<Atom> const&,
                         NonbondParmType const&) const;
+    /// \return number of unique atom types
+    unsigned int NuniqueAtomTypes(Topology const&) const;
   private:
     static inline void GetBondParams(ParmHolder<BondParmType>&, std::vector<Atom> const&,
                                      BondArray const&, BondParmArray const&);
diff --git a/src/Parm/parmdepend b/src/Parm/parmdepend
index 65cb189c1a..35382f3e05 100644
--- a/src/Parm/parmdepend
+++ b/src/Parm/parmdepend
@@ -1,4 +1,4 @@
 AssignParams.o : AssignParams.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/GenerateConnectivityArrays.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h AssignParams.h GetParams.h
 GB_Params.o : GB_Params.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h GB_Params.h
-GetParams.o : GetParams.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h GetParams.h
+GetParams.o : GetParams.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h GetParams.h
 Merge.o : Merge.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../StringRoutines.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../UpdateParameters.h ../Vec3.h AssignParams.h GetParams.h Merge.h

From f0404759450be957a0dc530f02049ce0ddb76a81 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 21 Jul 2024 14:51:01 -0400
Subject: [PATCH 0871/1492] Remove all functions that are now in Parm

---
 src/Topology.cpp  | 1700 ---------------------------------------------
 src/Topology.h    |   86 +--
 src/cpptrajdepend |  698 +++++++++----------
 3 files changed, 387 insertions(+), 2097 deletions(-)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index ef5c7a8409..5e7d939440 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -4,13 +4,8 @@
 #include "CpptrajStdio.h"
 #include "StringRoutines.h" // integerToString 
 #include "Constants.h" // SMALL
-#include "AtomType.h"
 #include "AtomMask.h"
 #include "CharMask.h"
-#include "GuessAtomHybridization.h"
-#include "Structure/GenerateConnectivityArrays.h"
-#include "Parm/Merge.h"
-#include "UpdateParameters.h"
 
 const NonbondType Topology::LJ_EMPTY = NonbondType();
 
@@ -50,27 +45,6 @@ unsigned int Topology::HeavyAtomCount() const {
   return hac;
 }
 
-/** \return Total number of unique atom types. */
-unsigned int Topology::NuniqueAtomTypes() const {
-  ParmHolder<int> currentAtomTypes;
-  for (std::vector<Atom>::const_iterator atm = atoms_.begin(); atm != atoms_.end(); ++atm)
-  {
-    if (atm->HasType()) {
-      TypeNameHolder atype( atm->Type() );
-      // Find in currentAtomTypes.
-      bool found;
-      currentAtomTypes.FindParam( atype, found );
-      if (!found) {
-        currentAtomTypes.AddParm( atype, atm->TypeIndex(), false );
-      }
-    }
-  }
-  mprintf("DEBUG: Unique atom types in %s\n", c_str());
-  for (ParmHolder<int>::const_iterator it = currentAtomTypes.begin();
-                                       it != currentAtomTypes.end(); ++it)
-    mprintf("\t\t%s %i\n", *(it->first[0]), it->second);
-  return currentAtomTypes.size();
-}
 
 /** Reset all PDB-related info.
   * NOTE: This routine is used by AmbPDB.
@@ -967,18 +941,6 @@ void Topology::ClearBondArrays() {
   bondsh_.clear();
 }
 
-/** Add to bond arrays but do not update atom connectivity. Used
-  * when regenerating bond information from atom connectivity.
-  */
-void Topology::AddToBondArrays(BondType const& bnd) {
-  // TODO enforce H as second atom?
-  if (atoms_[bnd.A1()].Element() == Atom::HYDROGEN ||
-      atoms_[bnd.A2()].Element() == Atom::HYDROGEN)
-    bondsh_.push_back( bnd );
-  else
-    bonds_.push_back( bnd );
-}
-
 /** Check if given angle parm exists in given angle parm array. Add if not.
   * \return Index in angle parm array.
   */
@@ -1040,18 +1002,6 @@ void Topology::AddAngle(AngleType const& angIn, bool isH) {
     angles_.push_back( angIn );
 }
 
-/** Add to angle arrays. Used when regenerating angle information
-  * from atom connectivity.
-  */
-void Topology::AddToAngleArrays(AngleType const& ang) {
-  if (atoms_[ang.A1()].Element() == Atom::HYDROGEN ||
-      atoms_[ang.A2()].Element() == Atom::HYDROGEN ||
-      atoms_[ang.A3()].Element() == Atom::HYDROGEN)
-    anglesh_.push_back( ang );
-  else
-    angles_.push_back( ang );
-}
-
 // -----------------------------------------------
 /** Check if given dihedral parm exists in given dihedral parm array. Add if not.
   * \return Index in dihedral parm array.
@@ -1135,19 +1085,6 @@ void Topology::AddDihedral(DihedralType const& dihIn, bool isH) {
     dihedrals_.push_back( dihIn );
 }
 
-/** Add to dihedral arrays. Used when regenerating dihedral information
-  * from atom connectivity.
-  */
-void Topology::AddToDihedralArrays(DihedralType const& dih) {
-  if (atoms_[dih.A1()].Element() == Atom::HYDROGEN ||
-      atoms_[dih.A4()].Element() == Atom::HYDROGEN ||
-      atoms_[dih.A2()].Element() == Atom::HYDROGEN ||
-      atoms_[dih.A3()].Element() == Atom::HYDROGEN)
-    dihedralsh_.push_back( dih );
-  else
-    dihedrals_.push_back( dih );
-}
-
 /** \return true if any CHARMM parameters are set (based on indices). */
 bool Topology::HasChamber() const {
   if (!ub_.empty()) return true;
@@ -2198,218 +2135,6 @@ void Topology::StripDihedralParmArray(DihedralArray& newDihedralArray, std::vect
 }
 
 // -----------------------------------------------------------------------------
-static void paramOverwriteWarning(const char* type) {
-  mprintf("Warning: An existing %s parameter would have been overwritten. This\n"
-          "Warning:  usually means that the atom type information in the Topology is\n"
-          "Warning:  incomplete. This can happen for example with Chamber topologies\n"
-          "Warning:  if the original atom type names were > 4 characters.\n", type);
-  mprintf("Warning: The %s parameters in this topology may now be incorrect.\n", type);
-}
-
-// GetBondParams()
-static inline void GetBondParams(ParmHolder<BondParmType>& BP, std::vector<Atom> const& atoms, BondArray const& bonds, BondParmArray const& bpa) {
-  for (BondArray::const_iterator b = bonds.begin(); b != bonds.end(); ++b)
-  {
-    if (b->Idx() != -1) {
-      TypeNameHolder types(2);
-      types.AddName( atoms[b->A1()].Type() );
-      types.AddName( atoms[b->A2()].Type() );
-      ParameterHolders::RetType ret = BP.AddParm( types, bpa[b->Idx()], false );
-      if (ret == ParameterHolders::ERR)
-        paramOverwriteWarning("bond");
-    }
-  }
-}
-
-// GetAngleParams()
-static inline void GetAngleParams(ParmHolder<AngleParmType>& AP, std::vector<Atom> const& atoms, AngleArray const& angles, AngleParmArray const& apa) {
-  for (AngleArray::const_iterator b = angles.begin(); b != angles.end(); ++b)
-  {
-    if (b->Idx() != -1) {
-      TypeNameHolder types(3);
-      types.AddName( atoms[b->A1()].Type() );
-      types.AddName( atoms[b->A2()].Type() );
-      types.AddName( atoms[b->A3()].Type() );
-      ParameterHolders::RetType ret = AP.AddParm( types, apa[b->Idx()], false );
-      if (ret == ParameterHolders::ERR)
-        paramOverwriteWarning("angle");
-    }
-  }
-}
-
-// GetImproperParams()
-static inline void GetImproperParams(ImproperParmHolder& IP, std::vector<Atom> const& atoms, DihedralArray const& imp, DihedralParmArray const& ipa) {
-  IP.SetRequireExactMatch(true);
-  for (DihedralArray::const_iterator b = imp.begin(); b != imp.end(); ++b)
-  {
-    if (b->Idx() != -1) {
-      TypeNameHolder types(4);
-      types.AddName( atoms[b->A1()].Type() );
-      types.AddName( atoms[b->A2()].Type() );
-      types.AddName( atoms[b->A3()].Type() );
-      types.AddName( atoms[b->A4()].Type() );
-      ParameterHolders::RetType ret = IP.AddParm( types, ipa[b->Idx()], false );
-      if (ret == ParameterHolders::ERR)
-        paramOverwriteWarning("improper");
-    }
-  }
-}
-
-// GetDihedralParams()
-static inline void GetDihedralParams(DihedralParmHolder& DP, ImproperParmHolder& IP, std::vector<Atom> const& atoms, DihedralArray const& dih, DihedralParmArray const& dpa) {
-  IP.SetRequireExactMatch(true);
-  for (DihedralArray::const_iterator b = dih.begin(); b != dih.end(); ++b)
-  {
-    if (b->Idx() != -1) {
-      TypeNameHolder types(4);
-      types.AddName( atoms[b->A1()].Type() );
-      types.AddName( atoms[b->A2()].Type() );
-      types.AddName( atoms[b->A3()].Type() );
-      types.AddName( atoms[b->A4()].Type() );
-      //mprintf("DEBUG: dihedral %li ( %i %i %i %i )\n", b - dih.begin() + 1, b->A1()+1, b->A2()+1, b->A3()+1, b->A4()+1);
-      //mprintf("DEBUG: dihedral %li %s %s %s %s idx=%i type=%i PK=%g PN=%g Phase=%g SCEE=%g SCNB=%g\n", b - dih.begin() + 1,
-      //        *(types[0]), *(types[1]), *(types[2]), *(types[3]), b->Idx(), (int)b->Type(),
-      //        dpa[b->Idx()].Pk(), dpa[b->Idx()].Pn(), dpa[b->Idx()].Phase(), dpa[b->Idx()].SCEE(), dpa[b->Idx()].SCNB());
-      ParameterHolders::RetType ret;
-      if (b->IsImproper()) {
-        ret = IP.AddParm( types, dpa[b->Idx()], false );
-      } else {
-        ret = DP.AddParm( types, dpa[b->Idx()], false );
-      }
-      // DEBUG
-      //if (ret == ParameterHolders::ADDED) {
-      //  mprintf("DEBUG: Added %s %s %s %s idx=%i isImproper=%i\n", *(types[0]), *(types[1]), *(types[2]), *(types[3]), b->Idx(), (int)b->IsImproper());
-      //}
-      if (ret == ParameterHolders::ERR) {
-        paramOverwriteWarning("dihedral");
-        mprintf("Warning: Dihedral %s %s %s %s PK=%g PN=%g Phase=%g SCEE=%g SCNB=%g\n",
-                *(types[0]), *(types[1]), *(types[2]), *(types[3]),
-                dpa[b->Idx()].Pk(), dpa[b->Idx()].Pn(), dpa[b->Idx()].Phase(), dpa[b->Idx()].SCEE(), dpa[b->Idx()].SCNB());
-        //bool found;
-        //DihedralParmArray dpa = DP.FindParam(types, found);
-        //mprintf("Warning: Existing params:\n");
-        //for (DihedralParmArray::const_iterator d = dpa.begin(); d != dpa.end(); ++d)
-        //  mprintf("Warning:\t\tPK=%g PN=%g Phase=%g SCEE=%g SCNB=%g\n",
-        //          d->Pk(), d->Pn(), d->Phase(), d->SCEE(), d->SCNB());
-      }
-    }
-  }
-}
-
-/// \return an error if cmap atom names do not match
-static inline int check_cmap_atom_name(NameType const& n0, NameType const& n1)
-{
-  if (n0 != n1) {
-    mprinterr("Error: CMAP term atom name %s does not match expected CMAP term atom name %s\n",
-              *n1, *n0);
-    return 1;
-  }
-  return 0;
-}
-
-/** Get existing CMAP parameters.
-  * Unlike other parameters, CMAPs are big and are uniquely identified by
-  * a combination of residue and 5 atom names. Depending on if they were
-  * read in from a parameter file or a topology, they may or may not
-  * have residue/atom name information, which is needed for assignment.
-  * This info needs to be generated if it is missing.
-  */
-static inline int GetCmapParams(CmapParmHolder& cmapParm, CmapArray const& cmapTerms, CmapGridArray const& cmapGrids,
-                                 std::vector<Atom> const& atoms, std::vector<Residue> const& residues)
-{
-  if (cmapGrids.empty() || cmapTerms.empty()) {
-    mprintf("DEBUG: CMAP grids/terms are empty. No parameters to get.\n");
-    return 0;
-  }
-  // Check if we need to generate residue/atom information for grids.
-  bool needResAtomInfo = false;
-  for (CmapGridArray::const_iterator it = cmapGrids.begin(); it != cmapGrids.end(); ++it)
-  {
-    if (it->ResNames().empty() || it->AtomNames().empty()) {
-      needResAtomInfo = true;
-      break;
-    }
-  }
-  // Mark off which terms need to be added.
-  std::vector<bool> addGrid( cmapGrids.size(), false );
-  for (CmapArray::const_iterator cm = cmapTerms.begin(); cm != cmapTerms.end(); ++cm) {
-    if (cm->Idx() != -1)
-      addGrid[cm->Idx()] = true;
-  }
-  // Add grids, adding res/atom info if needed
-  if (needResAtomInfo) {
-    mprintf("CMAP terms need residue/atom info.\n");
-    for (unsigned int idx = 0; idx != cmapGrids.size(); idx++) {
-      if (addGrid[idx]) {
-        // Figure out residue names this cmap applies to.
-        std::set<NameType> resNames;
-        std::vector<NameType> atomNames;
-        atomNames.reserve(5);
-        for (CmapArray::const_iterator cm = cmapTerms.begin(); cm != cmapTerms.end(); ++cm) {
-          if (cm->Idx() == (int)idx) {
-            int resnum = atoms[cm->A2()].ResNum();
-            resNames.insert( residues[resnum].Name() );
-            if (atomNames.empty()) {
-              atomNames.push_back( atoms[cm->A1()].Name() );
-              atomNames.push_back( atoms[cm->A2()].Name() );
-              atomNames.push_back( atoms[cm->A3()].Name() );
-              atomNames.push_back( atoms[cm->A4()].Name() );
-              atomNames.push_back( atoms[cm->A5()].Name() );
-            } else {
-              // Check atom names
-              if (check_cmap_atom_name(atomNames[0], atoms[cm->A1()].Name())) return 1;
-              if (check_cmap_atom_name(atomNames[1], atoms[cm->A2()].Name())) return 1;
-              if (check_cmap_atom_name(atomNames[2], atoms[cm->A3()].Name())) return 1;
-              if (check_cmap_atom_name(atomNames[3], atoms[cm->A4()].Name())) return 1;
-              if (check_cmap_atom_name(atomNames[4], atoms[cm->A5()].Name())) return 1;
-            }
-          }
-        }
-        mprintf("DEBUG: Cmap term %u residues", idx);
-        for (std::set<NameType>::const_iterator it = resNames.begin(); it != resNames.end(); ++it)
-          mprintf(" %s", *(*it));
-        mprintf(" Atoms={");
-        for (std::vector<NameType>::const_iterator it = atomNames.begin(); it != atomNames.end(); ++it)
-          mprintf(" %s", *(*it));
-        mprintf(" }\n");
-        CmapGridType newGrid = cmapGrids[idx];
-        // Add the atom/res info to the grid
-        newGrid.SetNumCmapRes( resNames.size() );
-        for (std::set<NameType>::const_iterator it = resNames.begin(); it != resNames.end(); ++it)
-          newGrid.AddResName( it->Truncated() ); // FIXME just use NameType
-        for (std::vector<NameType>::const_iterator it = atomNames.begin(); it != atomNames.end(); ++it)
-          newGrid.AddAtomName( it->Truncated() ); // FIXME just use NameType
-        if (!newGrid.CmapIsValid()) {
-          mprinterr("Error: CMAP is not valid, could not get parameter.\n");
-          mprinterr("Error:   Term %u residues", idx);
-          for (std::set<NameType>::const_iterator it = resNames.begin(); it != resNames.end(); ++it)
-            mprinterr(" %s", *(*it));
-          mprinterr(" Atoms={");
-          for (std::vector<NameType>::const_iterator it = atomNames.begin(); it != atomNames.end(); ++it)
-            mprinterr(" %s", *(*it));
-          mprinterr(" }\n");
-        }
-        // Set a default title if needed
-        if (newGrid.Title().empty())
-          newGrid.SetTitle( "CMAP for " + newGrid.ResNames().front() );
-        ParameterHolders::RetType ret = cmapParm.AddParm( newGrid, false );
-        if (ret == ParameterHolders::ERR)
-          paramOverwriteWarning("CMAP");
-      } // END if adding existing grid to parms
-    } // END loop over existing grids
-  } else {
-    mprintf("CMAP terms have residue/atom info.\n");
-    for (unsigned int idx = 0; idx != cmapGrids.size(); idx++) {
-      if (addGrid[idx]) {
-        ParameterHolders::RetType ret = cmapParm.AddParm( cmapGrids[idx], false );
-        if (ret == ParameterHolders::ERR)
-          paramOverwriteWarning("CMAP");
-      }
-    }
-  }
-  return 0;
-}
-
 /** Loop over atom type pairs, determine what the A and B
   * parameters should be based on the LJ radius and depth,
   * then compare to the existing A and B parameters.
@@ -2486,1437 +2211,12 @@ static inline int GetCmapParams(CmapParmHolder& cmapParm, CmapArray const& cmapT
       mprintf("Warning: %u modified off-diagonal LJ terms present.\n", nModifiedOffDiagonal);
 }*/
 
-/** \param atomTypesOut Output array of atom types and indivudual LJ parameters.
-  * \param LJ612out Output array of LJ 6-12 pair parameters.
-  * \param LJ14out Output array of LJ 6-12 1-4 pair parameters.
-  * \param LJ1012out Output array of LJ 10-12 pair parameters.
-  * \param atoms Current array of atoms.
-  * \param NB0 Current nonbond parameters.
-  */
-static inline void GetLJAtomTypes(ParmHolder<AtomType>& atomTypesOut,
-                                  ParmHolder<NonbondType>& LJ612out,
-                                  ParmHolder<NonbondType>& LJ14out,
-                                  ParmHolder<double>& LJCout,
-                                  ParmHolder<HB_ParmType>& LJ1012out,
-                                  std::vector<Atom> const& atoms,
-                                  NonbondParmType const& NB0,
-                                  int debugIn)
-{
-  if (NB0.HasNonbond()) {
-    mprintf("DEBUG: Topology has nonbond parameters.\n");
-    bool hasLJ14 = !NB0.LJ14().empty();
-    if (hasLJ14)
-      mprintf("DEBUG: Topology has 1-4 nonbond parameters.\n");
-    bool hasLJC = !NB0.LJC_Array().empty();
-    if (hasLJC)
-      mprintf("DEBUG: Topology has LJC nonbond paramters.\n");
-    // Nonbonded parameters are present.
-    for (std::vector<Atom>::const_iterator atm = atoms.begin(); atm != atoms.end(); ++atm)
-    {
-      if (!atm->HasType()) {
-        mprintf("Warning: Topology has nonbond parameters but atom %s has no type.\n", *(atm->Name()));
-        continue;
-      }
-      TypeNameHolder atype( atm->Type() );
-      // Check for self parameters to back-calculate LJ depth/radius
-      int idx = NB0.GetLJindex( atm->TypeIndex(), atm->TypeIndex() );
-      AtomType thisType;
-      if (idx > -1) {
-        // Has LJ 6-12 parameters
-        NonbondType const& LJ = NB0.NBarray( idx );
-        thisType = AtomType(LJ.Radius(), LJ.Depth(), atm->Mass(), atm->Polar());
-        if (hasLJ14) {
-          NonbondType const& lj14 = NB0.LJ14( idx );
-          thisType.SetLJ14( LJparmType(lj14.Radius(), lj14.Depth()) );
-        }
-        // FIXME do LJ C
-      } else {
-        // Has LJ 10-12 parameters
-        thisType = AtomType(atm->Mass(), atm->Polar());
-      }
-      thisType.SetTypeIdx( atm->TypeIndex() );
-      ParameterHolders::RetType ret = atomTypesOut.AddParm( atype, thisType, true );
-      //if (debugIn > 0 && ret == ParameterHolders::ADDED) { // FIXME
-      if (ret == ParameterHolders::ADDED) {
-        mprintf("DEBUG: New atom type: %s R=%g D=%g M=%g P=%g\n", *(atype[0]),
-                thisType.LJ().Radius(), thisType.LJ().Depth(), thisType.Mass(), thisType.Polarizability());
-        if (hasLJ14)
-          mprintf("DEBUG: New LJ14 atom type: %s R=%g D=%g\n", *(atype[0]), thisType.LJ14().Radius(), thisType.LJ14().Depth());
-      }
-    }
-    // Do atom type pairs, check for off-diagonal elements.
-    // Explicitly store pairs instead of regenerating to avoid round-off issues.
-    //GetLJterms(atomTypesOut, LJ612out, &LJ1012out, NB0, false, debugIn);
-    //if (hasLJ14)
-    //  GetLJterms(LJ14typesOut, LJ14out, 0, NB0, true, debugIn);
-    unsigned int nModifiedOffDiagonal = 0;
-    unsigned int nModified14OffDiagonal = 0;
-    for (ParmHolder<AtomType>::const_iterator i1 = atomTypesOut.begin(); i1 != atomTypesOut.end(); ++i1)
-    {
-      for (ParmHolder<AtomType>::const_iterator i2 = i1; i2 != atomTypesOut.end(); ++i2)
-      {
-        NameType const& name1 = i1->first[0];
-        NameType const& name2 = i2->first[0];
-        TypeNameHolder types(2);
-        types.AddName( name1 );
-        types.AddName( name2 );
-        // Extract original nonbonded parameters for this type pair.
-        AtomType const& type1 = i1->second;
-        AtomType const& type2 = i2->second;
-        int idx1 = type1.OriginalIdx();
-        int idx2 = type2.OriginalIdx();
-        int idx = NB0.GetLJindex( idx1, idx2 );
-        if (idx < 0) {
-          // This is LJ 10-12.
-          //mprinterr("Error: No off-diagonal LJ for  %s %s (%i %i)\n",
-          //          *name1, *name2, idx1, idx2);
-          //return;
-          mprintf("DEBUG: LJ 10-12 parameters detected for %s %s (%i %i)\n",
-                  *name1, *name2, idx1, idx2);
-          LJ1012out.AddParm( types, NB0.HBarray((-idx)-1), false );
-        } else {
-          // This is LJ 6-12.
-          // Determine what A and B parameters would be.
-          NonbondType lj0 = type1.LJ().Combine_LB( type2.LJ() );
-        
-          NonbondType lj1 = NB0.NBarray( idx );
-          // Compare them
-          if (lj0 != lj1) {
-            nModifiedOffDiagonal++;
-            //if (debugIn > 0) {
-              double deltaA = fabs(lj0.A() - lj1.A());
-              double deltaB = fabs(lj0.B() - lj1.B());
-              mprintf("DEBUG: Potential off-diagonal LJ: %s %s expect A=%g B=%g, actual A=%g B=%g\n",
-                      *name1, *name2, lj0.A(), lj0.B(), lj1.A(), lj1.B());
-              mprintf("DEBUG:\tdeltaA= %g    deltaB= %g\n", deltaA, deltaB);
-              double pe_a = (fabs(lj0.A() - lj1.A()) / lj0.A());
-              double pe_b = (fabs(lj0.B() - lj1.B()) / lj0.B());
-              mprintf("DEBUG:\tPEA= %g  PEB= %g\n", pe_a, pe_b);
-            //}
-          }
-          LJ612out.AddParm( types, lj1, false );
-          if (hasLJ14) {
-            // This is LJ 6-12 1-4.
-            // Determine what A and B parameters would be.
-            lj0 = type1.LJ14().Combine_LB( type2.LJ14() );
-        
-            lj1 = NB0.LJ14( idx );
-            // Compare them
-            if (lj0 != lj1) {
-              nModified14OffDiagonal++;
-              //if (debugIn > 0) {
-                double deltaA = fabs(lj0.A() - lj1.A());
-                double deltaB = fabs(lj0.B() - lj1.B());
-                mprintf("DEBUG: Potential off-diagonal LJ 1-4: %s %s expect A=%g B=%g, actual A=%g B=%g\n",
-                        *name1, *name2, lj0.A(), lj0.B(), lj1.A(), lj1.B());
-                mprintf("DEBUG:\tdeltaA= %g    deltaB= %g\n", deltaA, deltaB);
-                double pe_a = (fabs(lj0.A() - lj1.A()) / lj0.A());
-                double pe_b = (fabs(lj0.B() - lj1.B()) / lj0.B());
-                mprintf("DEBUG:\tPEA= %g  PEB= %g\n", pe_a, pe_b);
-              //}
-            }
-            LJ14out.AddParm( types, lj1, false );
-          } // END hasLJ14
-          if (hasLJC) {
-            // This is LJC
-            double ljc1 = NB0.LJC_Array( idx );
-            LJCout.AddParm( types, ljc1, false );
-          }
-        }
-      } // END inner loop over atom types
-    } // END outer loop over atom types
-    if (nModifiedOffDiagonal > 0)
-      mprintf("Warning: %u modified off-diagonal LJ terms present.\n", nModifiedOffDiagonal);
-    if (nModified14OffDiagonal > 0)
-      mprintf("Warning: %u modified off-diagonal LJ 1-4 terms present.\n", nModified14OffDiagonal);
-  } else {
-    if (!atoms.empty())
-      mprintf("DEBUG: Topology does not have nonbond parameters.\n");
-    // No nonbonded parameters. Just save mass/polarizability.
-    for (std::vector<Atom>::const_iterator atm = atoms.begin(); atm != atoms.end(); ++atm)
-      if (atm->HasType() > 0)
-        atomTypesOut.AddParm( TypeNameHolder(atm->Type()), AtomType(atm->Mass(), atm->Polar()), true );
-  }
-}
-
-/** \return ParameterSet for this Topology. */
-ParameterSet Topology::GetParameters() const {
-  ParameterSet Params;
-  // Atom LJ types and other nonbonded parameters.
-  GetLJAtomTypes( Params.AT(), Params.NB(), Params.NB14(), Params.LJC(), Params.HB(), atoms_, nonbond_, debug_ );
-  // Bond parameters.
-  GetBondParams( Params.BP(), atoms_, bonds_, bondparm_ );
-  GetBondParams( Params.BP(), atoms_, bondsh_, bondparm_ );
-  // Angle parameters.
-  GetAngleParams( Params.AP(), atoms_, angles_, angleparm_);
-  GetAngleParams( Params.AP(), atoms_, anglesh_, angleparm_);
-  // Dihedral parameters.
-  GetDihedralParams( Params.DP(), Params.IP(), atoms_, dihedrals_, dihedralparm_);
-  GetDihedralParams( Params.DP(), Params.IP(), atoms_, dihedralsh_, dihedralparm_);
-  // CHARMM parameters
-  if (!ub_.empty()) {
-    // UB parameters
-    GetBondParams(Params.UB(), atoms_, ub_, ubparm_);
-  }
-  if (!impropers_.empty()) {
-    // Impropers
-    GetImproperParams( Params.IP(), atoms_, impropers_, improperparm_ );
-  }
-  // CMAPs
-  if (GetCmapParams( Params.CMAP(), cmap_, cmapGrid_, atoms_, residues_ )) {
-    mprinterr("Error: Could not get CMAP parameters.\n"); // TODO fatal?
-  }
 
-  return Params;
-}
 
 // -----------------------------------------------------------------------------
 
-/** This template can be used when doing Append() on a generic std::vector array
-  * of type T. The array will be appended to a given array of the same type.
-  * If one is empty and the other is not, values will be filled in if necessary.
-  */
-template <class T> class TopVecAppend {
-  public:
-    /// CONSTRUCTOR
-    TopVecAppend() {}
-    /// Append current array to given array of same type
-    void Append(std::vector<T>& arrayOut, std::vector<T> const& arrayToAdd, unsigned int expectedSize)
-    {
-      if (arrayToAdd.empty() && arrayOut.empty()) {
-        // Both arrays are empty. Nothing to do.
-        return;
-      } else if (arrayToAdd.empty()) {
-        // The current array is empty but the given array is not. Fill in 
-        // array to append with blank values.
-        for (unsigned int idx = 0; idx != expectedSize; idx++)
-          arrayOut.push_back( T() );
-      } else {
-        // Append current array to array to given array. TODO use std::copy?
-        for (typename std::vector<T>::const_iterator it = arrayToAdd.begin(); it != arrayToAdd.end(); ++it)
-          arrayOut.push_back( *it );
-      }
-    }
-};
-
-// Topology::AppendTop()
-int Topology::AppendTop(Topology const& NewTop) {
-  unsigned int atomOffset = atoms_.size();
-  unsigned int molOffset = molecules_.size();
-  mprintf("DEBUG: Appending '%s' to '%s' (atom offset= %u mol offset= %u)\n",
-          NewTop.c_str(), c_str(), atomOffset, molOffset);
-  //int resOffset = (int)residues_.size();
-
-  // Save nonbonded parameters from each topology
-  ParmHolder<AtomType> myAtomTypes, newAtomTypes;
-  ParmHolder<NonbondType> myNB, newNB;
-  ParmHolder<NonbondType> my14, new14;
-  ParmHolder<HB_ParmType> myHB, newHB;
-  ParmHolder<double> myLJC, newLJC;
-  GetLJAtomTypes( myAtomTypes, myNB, my14, myLJC, myHB, atoms_, nonbond_, debug_ );
-  GetLJAtomTypes( newAtomTypes, newNB, new14, newLJC, newHB, NewTop.atoms_, NewTop.nonbond_, debug_ );
-  // Create combined nonbond parameter set
-  int nAtomTypeUpdated = UpdateParameters< ParmHolder<AtomType> >( myAtomTypes, newAtomTypes, "atom type", 1 ); // TODO verbose 
-  int nLJparamsUpdated = UpdateParameters< ParmHolder<NonbondType> >( myNB, newNB, "LJ 6-12", 1 ); // TODO verbose
-  int n14paramsUpdated = UpdateParameters< ParmHolder<NonbondType> >( my14, new14, "LJ 6-12 1-4", 1); // TODO verbose
-  int nljcparamsUpdated = UpdateParameters< ParmHolder<double> >( myLJC, newLJC, "LJ C", 1); // TODO verbose
-  int nHBparamsUpdated = UpdateParameters< ParmHolder<HB_ParmType> >( myHB, newHB, "LJ 10-12", 1); // TODO verbose
-  mprintf("\t%i atom types updated, %i LJ 6-12 params updated, %i 1-4 params updated, %i LJC params updated, %i LJ 10-12 params updated.\n",
-          nAtomTypeUpdated, nLJparamsUpdated, n14paramsUpdated, nljcparamsUpdated, nHBparamsUpdated);
-
-  // Add incoming topology bond/angle/dihedral/cmap arrays to this one.
-  Cpptraj::Parm::MergeBondArrays(bonds_, bondsh_, bondparm_, atoms_,
-                                 NewTop.Bonds(), NewTop.BondsH(), NewTop.BondParm(), NewTop.Atoms());
-  Cpptraj::Parm::MergeAngleArrays(angles_, anglesh_, angleparm_, atoms_,
-                                  NewTop.Angles(), NewTop.AnglesH(), NewTop.AngleParm(), NewTop.Atoms());
-  Cpptraj::Parm::MergeDihedralArrays(dihedrals_, dihedralsh_, dihedralparm_, atoms_,
-                                     NewTop.Dihedrals(), NewTop.DihedralsH(), NewTop.DihedralParm(), NewTop.Atoms());
-  Cpptraj::Parm::MergeCmapArrays(cmap_, cmapGrid_, atoms_, residues_,
-                                 NewTop.Cmap(), NewTop.CmapGrid(), NewTop.Atoms(), NewTop.Residues());
-  Cpptraj::Parm::MergeBondArray(ub_, ubparm_, atoms_,
-                                NewTop.ub_, NewTop.ubparm_, NewTop.Atoms());
-  Cpptraj::Parm::MergeImproperArray(impropers_, improperparm_, atoms_,
-                                    NewTop.impropers_, NewTop.improperparm_, NewTop.Atoms());
-
-  // Append incoming atoms to this topology.
-  for (atom_iterator atom = NewTop.begin(); atom != NewTop.end(); ++atom)
-  {
-    if (debug_ > 1)
-      mprintf("DBG: %6li %s %s %4i\n", atom-NewTop.begin(), 
-              *(atom->Name()), *(atom->Type()), atom->TypeIndex());
-    Atom CurrentAtom = *atom;
-    Residue const& res = NewTop.Res( CurrentAtom.ResNum() );
-    // Bonds need to be cleared and re-added.
-    CurrentAtom.ClearBonds();
-    for (Atom::bond_iterator bat = atom->bondbegin(); bat != atom->bondend(); ++bat)
-      CurrentAtom.AddBondToIdx( *bat + atomOffset );
-
-    addTopAtom( CurrentAtom,
-                Residue(res.Name(), res.OriginalResNum(), res.Icode(), res.ChainID()),
-                atom->MolNum()+molOffset, NewTop.Mol(atom->MolNum()).IsSolvent() );
-  }
-
-  // EXTRA ATOM INFO
-  TopVecAppend<NameType> appendNameType;
-  appendNameType.Append( tree_, NewTop.tree_, NewTop.Natom() );
-  TopVecAppend<int> appendInt;
-  appendInt.Append( ijoin_, NewTop.ijoin_, NewTop.Natom() );
-  appendInt.Append( irotat_, NewTop.irotat_, NewTop.Natom() );
-  appendInt.Append( pdbSerialNum_, NewTop.pdbSerialNum_, NewTop.Natom() );
-  TopVecAppend<char> appendChar;
-  appendChar.Append( atom_altloc_, NewTop.atom_altloc_, NewTop.Natom() );
-  TopVecAppend<float> appendFloat;
-  appendFloat.Append( occupancy_, NewTop.occupancy_, NewTop.Natom() );
-  appendFloat.Append( bfactor_, NewTop.bfactor_, NewTop.Natom() );
-
-  // Need to regenerate nonbonded info
-  mprintf("\tRegenerating nonbond parameters.\n");
-  AssignNonbondParams( myAtomTypes, myNB, my14, myLJC, myHB, 1 ); // FIXME verbose
-
-  // The version of AddTopAtom() with molecule number already determines
-  // molecules and number of solvent molecules.
-  // Just need to determine the number of extra points.
-  DetermineNumExtraPoints();
-
-  // GB radii set string
-  if (!NewTop.GBradiiSet().empty()) {
-    if (radius_set_.empty())
-      radius_set_ = NewTop.GBradiiSet();
-    else {
-      // Do not repeat a GB radius string
-      std::size_t pos = radius_set_.find( NewTop.GBradiiSet() );
-      if (pos == std::string::npos) {
-        std::string newName = radius_set_ + "+" + NewTop.GBradiiSet();
-        if (newName.size() > 80) {
-          mprintf("Warning: New radius set name is > 80 characters: '%s'\n", newName.c_str());
-          mprintf("Warning: This will be truncated to 80 characters in an Amber Topology.\n");
-        }
-        radius_set_ = newName;
-      }
-    }
-  }
-  return 0;
-}
 
 // -----------------------------------------------------------------------------
-/** Set parameters for atoms via given atom type parameter holder. */
-void Topology::AssignAtomTypeParm(ParmHolder<AtomType> const& newAtomTypeParams)
-{
-  for (unsigned int iat = 0; iat != atoms_.size(); iat++)
-  {
-    bool found;
-    TypeNameHolder atype( atoms_[iat].Type() );
-    AtomType at = newAtomTypeParams.FindParam( atype, found );
-    if (found) {
-      // Update mass
-      atoms_[iat].SetMass( at.Mass() );
-      // Update polarizability
-      atoms_[iat].SetPolar( at.Polarizability() );
-    } else
-      mprintf("Warning: Atom type parameter not found for %s\n", *atype[0]);
-  }
-}
-
-/** Set parameters for bonds in given bond array. */
-void Topology::AssignBondParm(ParmHolder<BondParmType> const& newBondParams,
-                              BondArray& bonds, BondParmArray& bpa, const char* desc)
-const
-{
-  ParmHolder<int> currentTypes;
-  for (BondArray::iterator bnd = bonds.begin(); bnd != bonds.end(); ++bnd) {
-    TypeNameHolder types(2);
-    types.AddName( atoms_[bnd->A1()].Type() );
-    types.AddName( atoms_[bnd->A2()].Type() );
-    bool found;
-    // See if parameter is present.
-    int idx = currentTypes.FindParam(types, found);
-    if (!found) {
-      idx = -1;
-      // Not yet present in current types.
-      BondParmType bp = newBondParams.FindParam( types, found );
-      if (!found) {
-        mprintf("Warning: parameter not found for %s %s-%s (%s-%s)\n", desc,
-                TruncResAtomNameNum(bnd->A1()).c_str(),
-                TruncResAtomNameNum(bnd->A2()).c_str(),
-                *types[0], *types[1]);
-      } else {
-        //idx = addBondParm( bpa, bp ); TODO handle array packing
-        idx = (int)bpa.size();
-        bpa.push_back( bp );
-        currentTypes.AddParm(types, idx, false);
-      }
-    }
-    bnd->SetIdx( idx );
-  }
-/*
-  for (BondArray::iterator bnd = bonds.begin(); bnd != bonds.end(); ++bnd) {
-    TypeNameHolder types(2);
-    types.AddName( atoms_[bnd->A1()].Type() );
-    types.AddName( atoms_[bnd->A2()].Type() );
-    bool found;
-    // See if parameter is present.
-    int idx = -1;
-    BondParmType bp = newBondParams.FindParam( types, found );
-    if (!found) {
-      mprintf("Warning: parameter not found for %s %s-%s (%s-%s)\n", desc,
-              TruncResAtomNameNum(bnd->A1()).c_str(),
-              TruncResAtomNameNum(bnd->A2()).c_str(),
-              *types[0], *types[1]);
-    } else {
-      idx = addBondParm( bpa, bp );
-    }
-    bnd->SetIdx( idx );
-  }*/
-}
-
-/** Replace any current bond parameters with given bond parameters. */
-void Topology::AssignBondParams(ParmHolder<BondParmType> const& newBondParams) {
-  bondparm_.clear();
-  AssignBondParm( newBondParams, bonds_,  bondparm_, "bond" );
-  AssignBondParm( newBondParams, bondsh_, bondparm_, "bond" );
-}
-
-/** Replace any current Urey-Bradley parameters with given UB parameters. */
-void Topology::AssignUBParams(ParmHolder<BondParmType> const& newBondParams) {
-  ubparm_.clear();
-  AssignBondParm( newBondParams, ub_, ubparm_, "UB term" );
-}
-
-/** Set parameters for angles in given angle array. */
-AngleArray Topology::AssignAngleParm(ParmHolder<AngleParmType> const& newAngleParams,
-                                     AngleArray const& angles)
-{
-  AngleArray newAngles;
-  ParmHolder<int> currentTypes;
-  for (AngleArray::const_iterator ang = angles.begin(); ang != angles.end(); ++ang) {
-    TypeNameHolder types(3);
-    types.AddName( atoms_[ang->A1()].Type() );
-    types.AddName( atoms_[ang->A2()].Type() );
-    types.AddName( atoms_[ang->A3()].Type() );
-    // Skip extra points // FIXME make this an option
-    if ( atoms_[ang->A1()].Element() == Atom::EXTRAPT ||
-         atoms_[ang->A3()].Element() == Atom::EXTRAPT)
-    {
-      mprintf("DEBUG: Skipping angle with extra point: %4i %4i %4i (%2s %2s %2s)\n",
-              ang->A1()+1, ang->A2()+1, ang->A3()+1,
-              *types[0], *types[1], *types[2]);
-      continue;
-    }
-    // Skip water angles // FIXME make this an option
-    if (atoms_[ang->A1()].Element() == Atom::HYDROGEN &&
-        atoms_[ang->A2()].Element() == Atom::OXYGEN &&
-        atoms_[ang->A3()].Element() == Atom::HYDROGEN)
-    {
-      // H-O-H Angle. If there is an H-H bond assume this is a rigid water model.
-      if (atoms_[ang->A1()].IsBondedTo( ang->A3() )) {
-        mprintf("DEBUG: H-O-H angle, H-H bond detected. Assuming rigid water, skipping angle: "
-                "%4i %4i %4i (%2s %2s %2s)\n",
-                ang->A1()+1, ang->A2()+1, ang->A3()+1,
-                *types[0], *types[1], *types[2]);
-        continue;
-      }
-    }
-    if (atoms_[ang->A1()].Element() == Atom::OXYGEN &&
-        atoms_[ang->A2()].Element() == Atom::HYDROGEN &&
-        atoms_[ang->A3()].Element() == Atom::HYDROGEN)
-    {
-      // O-H-H Angle. Assume rigid water model
-      mprintf("DEBUG: O-H-H angle. Assuming rigid water, skipping angle: "
-              "%4i %4i %4i (%2s %2s %2s)\n",
-              ang->A1()+1, ang->A2()+1, ang->A3()+1,
-              *types[0], *types[1], *types[2]);
-      continue;
-    }
-
-    bool found;
-    // See if parameter is present.
-    int idx = currentTypes.FindParam( types, found );
-    if (!found) {
-      idx = -1;
-      // Not yet present in current types
-      AngleParmType ap = newAngleParams.FindParam( types, found );
-      if (!found) {
-        mprintf("Warning: Angle parameter not found for angle %s-%s-%s (%s-%s-%s)\n",
-                TruncResAtomNameNum(ang->A1()).c_str(),
-                TruncResAtomNameNum(ang->A2()).c_str(),
-                TruncResAtomNameNum(ang->A3()).c_str(),
-                *types[0], *types[1], *types[2]);
-      } else {
-        //idx = addAngleParm( angleparm_, ap ); // TODO uncomment for array packing
-        idx = (int)angleparm_.size();
-        angleparm_.push_back( ap );
-        //mprintf("DEBUG: New angle type for %s-%s-%s (Tk=%g Teq=%g) idx=%i\n", *types[0], *types[1], *types[2], ap.Tk(), ap.Teq(), idx);
-        currentTypes.AddParm(types, idx, false);
-      }
-    }
-    newAngles.push_back( *ang );
-    newAngles.back().SetIdx( idx );
-  }
-  return newAngles;
-/*
-  for (AngleArray::iterator ang = angles.begin(); ang != angles.end(); ++ang) {
-    TypeNameHolder types(3);
-    types.AddName( atoms_[ang->A1()].Type() );
-    types.AddName( atoms_[ang->A2()].Type() );
-    types.AddName( atoms_[ang->A3()].Type() );
-    bool found;
-    // See if parameter is present.
-    int idx = -1;
-    AngleParmType ap = newAngleParams.FindParam( types, found );
-    if (!found) {
-      mprintf("Warning: Angle parameter not found for angle %s-%s-%s (%s-%s-%s)\n",
-              TruncResAtomNameNum(ang->A1()).c_str(),
-              TruncResAtomNameNum(ang->A2()).c_str(),
-              TruncResAtomNameNum(ang->A3()).c_str(),
-              *types[0], *types[1], *types[3]);
-    } else {
-      idx = addAngleParm( angleparm_, ap );
-    }
-    ang->SetIdx( idx );
-  }*/
-}
-
-/** Replace any current angle parameters with given angle parameters. */
-void Topology::AssignAngleParams(ParmHolder<AngleParmType> const& newAngleParams) {
-  angleparm_.clear();
-  angles_ = AssignAngleParm( newAngleParams, angles_ );
-  anglesh_ = AssignAngleParm( newAngleParams, anglesh_ );
-}
-
-/** Warn if improper atoms have been reordered so they match the parameter. */
-void Topology::warn_improper_reorder(DihedralType const& imp0, DihedralType const& imp)
-const
-{
-  if (debug_ < 1) return;
-  mprintf("Warning: Improper types have been reordered from %4s %4s %4s %4s",
-          *(atoms_[imp0.A1()].Type()),
-          *(atoms_[imp0.A2()].Type()),
-          *(atoms_[imp0.A3()].Type()),
-          *(atoms_[imp0.A4()].Type()));
-  mprintf(" to %4s %4s %4s %4s to match improper parameter.\n",
-          *(atoms_[imp.A1()].Type()),
-          *(atoms_[imp.A2()].Type()),
-          *(atoms_[imp.A3()].Type()),
-          *(atoms_[imp.A4()].Type()));
-}
-
-/** Set parameters for improper dihedrals in given improper dihedral array. */
-void Topology::AssignImproperParm(ImproperParmHolder const& newImproperParams,
-                                  DihedralArray& impropers,
-                                  DihedralParmArray& dpa)
-const
-{
-  for (DihedralArray::iterator imp = impropers.begin(); imp != impropers.end(); ++imp) {
-    TypeNameHolder types(4);
-    types.AddName( atoms_[imp->A1()].Type() );
-    types.AddName( atoms_[imp->A2()].Type() );
-    types.AddName( atoms_[imp->A3()].Type() );
-    types.AddName( atoms_[imp->A4()].Type() );
-    bool found;
-    // See if parameter is present.
-    int idx = -1;
-    DihedralType imp0 = *imp;
-    bool reordered;
-    DihedralParmArray ipa = newImproperParams.FindParam( types, found, *imp, reordered );
-    if (!found) {
-      mprintf("Warning: Parameter not found for improper %s-%s-%s-%s (%s-%s-%s-%s)\n",
-              TruncResAtomNameNum(imp->A1()).c_str(),
-              TruncResAtomNameNum(imp->A2()).c_str(),
-              TruncResAtomNameNum(imp->A3()).c_str(),
-              TruncResAtomNameNum(imp->A4()).c_str(),
-              *types[0], *types[1], *types[3], *types[4]);
-    } else {
-      if (ipa.size() > 1)
-        mprintf("Warning: %zu improper parameters found for types %s - %s - %s - %s, expected only one."
-                        "Warning: Only using first parameter.\n", ipa.size(), *(types[0]), *(types[1]), *(types[2]), *(types[3]));
-      if (reordered) warn_improper_reorder( imp0, *imp );
-      idx = addTorsionParm( dpa, ipa.front() );
-    }
-    imp->SetIdx( idx );
-  }
-}
-
-/** Replace any current improper parameters with given improper parameters. */
-void Topology::AssignImproperParams(ImproperParmHolder const& newImproperParams) {
-  improperparm_.clear();
-  AssignImproperParm( newImproperParams, impropers_, improperparm_ );
-}
-
-/** Set parameters for dihedrals in given dihedral array.
-  * Bond and angle information must be set up prior to calling
-  * this function in order for improper and 1-4 detection to work.
-  * \param newDihedralParams New proper dihedral parameters.
-  * \param newImproperParams New improper dihedral parameters.
-  * \param dihedrals Array containing only unique dihedrals.
-  * \param sort_improper_cache If true, sort improper types in cache (to match current leap behavior)
-  */
-DihedralArray Topology::AssignDihedralParm(DihedralParmHolder const& newDihedralParams,
-                                           ImproperParmHolder const& newImproperParams,
-                                           ParmHolder<AtomType> const& AT,
-                                           DihedralArray const& dihedrals,
-                                           bool sort_improper_cache)
-{ // TODO skip extra points
-  DihedralArray dihedralsIn;
-  // Improper cache
-  ImproperParmHolder improperCache;
-  improperCache.SetWildcard( newImproperParams.Wildcard() );
-  improperCache.SetRequireExactMatch( newImproperParams.RequireExactMatch() );
-  // Keep track of 1-4 interactions
-  typedef std::pair<int,int> Ipair;
-  typedef std::set<Ipair> Imap;
-  Imap PairMap;
-  // Loop over all dihedrals
-  for (DihedralArray::const_iterator dih = dihedrals.begin(); dih != dihedrals.end(); ++dih) {
-    TypeNameHolder types(4);
-    types.AddName( atoms_[dih->A1()].Type() );
-    types.AddName( atoms_[dih->A2()].Type() );
-    types.AddName( atoms_[dih->A3()].Type() );
-    types.AddName( atoms_[dih->A4()].Type() );
-    // Skip extra points // FIXME make this an option
-    if ( atoms_[dih->A1()].Element() == Atom::EXTRAPT ||
-         atoms_[dih->A4()].Element() == Atom::EXTRAPT)
-    {
-      mprintf("DEBUG: Skipping dihedral with extra point: %4i %4i %4i %4i (%2s %2s %2s %2s)\n",
-              dih->A1()+1, dih->A2()+1, dih->A3()+1, dih->A4()+1,
-              *types[0], *types[1], *types[2], *types[3]);
-      continue;
-    }
-//    mprintf("DEBUG: Assigning dihedral %4i %4i %4i %4i (%2s %2s %2s %2s) isImproper=%i skip14=%i\n",
-//            dih->A1()+1, dih->A2()+1, dih->A3()+1, dih->A4()+1,
-//            *types[0], *types[1], *types[2], *types[3],
-//            (int)dih->IsImproper(), (int)dih->Skip14());
-    // Determine improper
-    bool isImproper = (!atoms_[dih->A1()].IsBondedTo(dih->A2())) ||
-                      (!atoms_[dih->A2()].IsBondedTo(dih->A3())) ||
-                      (!atoms_[dih->A3()].IsBondedTo(dih->A4()));
-    if (isImproper != dih->IsImproper()) {
-      mprintf("Warning: dihedral %s-%s-%s-%s improper status %i does not match detected (%i)\n",
-              TruncResAtomNameNum(dih->A1()).c_str(),
-              TruncResAtomNameNum(dih->A2()).c_str(),
-              TruncResAtomNameNum(dih->A3()).c_str(),
-              TruncResAtomNameNum(dih->A4()).c_str(),
-              (int)dih->IsImproper(), (int)isImproper);
-    }
-    bool found;
-    if (dih->IsImproper()) {
-      // ----- This is actually an improper dihedral. ----------------
-      // Impropers are treated differently than other topology types. If
-      // no parameter is found, do not add it to the list of dihedrals.
-      // However, if no parameter is found and the central atom is
-      // SP2, print a warning.
-      found = false;
-      DihedralType mydih = *dih;
-      bool reordered;
-      bool is_new_improper = false;
-      DihedralParmArray ipa;
-      TypeNameHolder paramTypes;
-      ImproperParmHolder::const_iterator impit = improperCache.GetParam( types, mydih, reordered );
-      if (impit == improperCache.end()) {
-        impit = newImproperParams.GetParam( types, mydih, reordered );
-        if (impit != newImproperParams.end()) {
-          is_new_improper = true;
-          paramTypes = impit->first;
-          ipa = impit->second;
-          found = true;
-          if (debug_ > 1)
-            mprintf("DEBUG: Found new value for improper %2s %2s %2s %2s (%2s %2s %2s %2s)\n",
-                    *types[0], *types[1], *types[2], *types[3],
-                    *paramTypes[0], *paramTypes[1], *paramTypes[2], *paramTypes[3]);
-        }
-      } else {
-        // If the cached improper has wildcards, see if there is a more
-        // specific one in the new improper parameters.
-        int n_wildcards = 0;
-        if (newImproperParams.Wildcard().len() > 0) {
-          for (TypeNameHolder::const_iterator tt = impit->first.begin(); tt != impit->first.end(); ++tt) {
-            if ( *tt == newImproperParams.Wildcard() ) {
-              n_wildcards++;
-            }
-          }
-        }
-        if (n_wildcards > 0) {
-          // Check if there is a more specific improper.
-          bool newReordered;
-          DihedralType newdih = *dih;
-          ImproperParmHolder::const_iterator moreSpecificImpit = newImproperParams.GetParam( types, newdih, newReordered );
-          if (moreSpecificImpit != newImproperParams.end()) {
-            // See if the new improper has fewer wildcards than the cached one.
-            int new_wildcards = 0;
-            for (TypeNameHolder::const_iterator tt = moreSpecificImpit->first.begin();
-                                                tt != moreSpecificImpit->first.end(); ++tt)
-            {
-              if ( *tt == newImproperParams.Wildcard() ) {
-                new_wildcards++;
-              }
-            }
-            if (new_wildcards < n_wildcards) {
-              // More specific improper was found.
-              mprintf("DEBUG: A more specific improper was found for %2s %2s %2s %2s (%2s %2s %2s %2s)\n",
-                      *(impit->first[0]), *(impit->first[1]), *(impit->first[2]), *(impit->first[3]),
-                      *(moreSpecificImpit->first[0]), *(moreSpecificImpit->first[1]), *(moreSpecificImpit->first[2]), *(moreSpecificImpit->first[3]));
-              is_new_improper = true;
-              reordered = newReordered;
-              mydih = newdih;
-              impit = moreSpecificImpit;
-            }
-          }
-        } // END found improper had wildcards
-        paramTypes = impit->first;
-        ipa = impit->second;
-        found = true;
-        if (debug_ > 1)
-          mprintf("DEBUG: Using cached value for improper %2s %2s %2s %2s (%2s %2s %2s %2s)\n",
-                  *types[0], *types[1], *types[2], *types[3],
-                  *paramTypes[0], *paramTypes[1], *paramTypes[2], *paramTypes[3]);
-      }
-      int idx = -1;
-      if (!found) {
-        if (debug_ > 0)
-          mprintf("Warning: Improper parameters not found for improper dihedral %s-%s-%s-%s (%s-%s-%s-%s)\n",
-                  TruncResAtomNameNum(dih->A1()).c_str(),
-                  TruncResAtomNameNum(dih->A2()).c_str(),
-                  TruncResAtomNameNum(dih->A3()).c_str(),
-                  TruncResAtomNameNum(dih->A4()).c_str(),
-                  *types[0], *types[1], *types[2], *types[3]);
-        // Central atom
-        Atom const& AJ = atoms_[dih->A3()];
-        AtomType::HybridizationType hybrid = AtomType::UNKNOWN_HYBRIDIZATION;
-        AtomType atype = AT.FindParam(TypeNameHolder(AJ.Type()), found);
-        if (found)
-          hybrid = atype.Hybridization();
-        if (hybrid == AtomType::UNKNOWN_HYBRIDIZATION) {
-          mprintf("Warning: Guessing hybridization for improper central atom %s\n", AtomMaskName(dih->A3()).c_str());
-          hybrid = Cpptraj::GuessAtomHybridization( AJ, atoms_ );
-        }
-        if (hybrid == AtomType::SP2) {
-          mprintf("Warning: No improper parameters for SP2 hybridized atom %s\n", AtomMaskName(dih->A3()).c_str());
-        }
-      } else {
-        if (ipa.size() > 1)
-          mprintf("Warning: %zu improper parameters found for types %s - %s - %s - %s, expected only one."
-                  "Warning: Only using first parameter.\n", ipa.size(), *(types[0]), *(types[1]), *(types[2]), *(types[3]));
-        if (reordered) warn_improper_reorder( *dih, mydih );
-        idx = addTorsionParm( dihedralparm_, ipa.front() );
-        mydih.SetIdx( idx );
-        mydih.SetImproper( true );
-        // Always skip 1-4 for impropers
-        mydih.SetSkip14( true );
-        dihedralsIn.push_back( mydih );
-        // Add to the cache
-        if (is_new_improper) {
-          // To match leap behavior, make sure paramTypes are sorted alphabetically.
-          //mprintf("DEBUG: Improper wildcard: %s\n", *(newImproperParams.Wildcard()));
-          if (sort_improper_cache) paramTypes.SortImproperByAlpha( newImproperParams.Wildcard() );
-          improperCache.AddParm( paramTypes, ipa.front(), false );
-        }
-      }
-    } else {
-      // -----Regular dihedral. See if parameter already present. ----
-      DihedralParmArray dpa = newDihedralParams.FindParam( types, found );
-      if (!found) {
-        mprintf("Warning: Dihedral parameters not found for dihedral %s-%s-%s-%s (%s-%s-%s-%s)\n",
-                TruncResAtomNameNum(dih->A1()).c_str(),
-                TruncResAtomNameNum(dih->A2()).c_str(),
-                TruncResAtomNameNum(dih->A3()).c_str(),
-                TruncResAtomNameNum(dih->A4()).c_str(),
-                *types[0], *types[1], *types[2], *types[3]);
-        DihedralType mydih = *dih;
-        mydih.SetIdx( -1 );
-        dihedralsIn.push_back( mydih );
-      } else {
-        // Actually add parameters for this dihedral.
-        // Determine if this is actually a 1-4 interaction by making
-        // sure that A4 isnt part of a bond or angle with A1.
-        bool skip14 = false;
-        for (Atom::bond_iterator bat1 = atoms_[dih->A1()].bondbegin();
-                                 bat1 != atoms_[dih->A1()].bondend(); ++bat1)
-        {
-          if (*bat1 != dih->A2()) {
-            if (*bat1 == dih->A4()) {
-              skip14 = true;
-              break;
-            }
-            // Loop over angles, dih->A1() - bat1 - bat2
-            for (Atom::bond_iterator bat2 = atoms_[*bat1].bondbegin();
-                                     bat2 != atoms_[*bat1].bondend(); ++bat2)
-            {
-              //if (dih->A1() == 442 && dih->A4() == 444) { // DEBUG
-              //  mprintf("DEBUG: %4i %4i %4i %4i Checking angle %4i %4i %4i\n", dih->A1()+1, dih->A2()+1, dih->A3()+1, dih->A4()+1, dih->A1()+1, *bat1 + 1, *bat2 + 1);
-              //}
-              if (*bat2 != *bat1) {
-                if (*bat2 == dih->A4()) {
-                  skip14 = true;
-                  break;
-                }
-              }
-            } // END loop over bat1 bonded atoms
-            if (skip14) break;
-          }
-        } // END loop over dih->A1() bonded atoms
-        if (!skip14) {
-          // Determine if 1-4 interaction already calculated by previous dihedral.
-          // Make the lower end atom first. 
-          Ipair pair14;
-          if (dih->A1() < dih->A4()) {
-            pair14.first = dih->A1();
-            pair14.second = dih->A4();
-          } else {
-            pair14.first = dih->A4();
-            pair14.second = dih->A1();
-          }
-          Imap::const_iterator it = PairMap.find( pair14 );
-          if (it == PairMap.end()) {
-            skip14 = false;
-            PairMap.insert( pair14 );
-          } else {
-            skip14 = true;
-            //mprintf("DEBUG: Prior 1-4 calc detected.\n");
-          }
-        }
-        // Loop over multiplicities
-        //if (dih->A1() == 442 && dih->A4() == 444) { // DEBUG
-        //  mprintf("DEBUG: Skip14= %i\n", (int)skip14);
-        //}
-        for (DihedralParmArray::const_iterator it = dpa.begin(); it != dpa.end(); ++it) {
-          DihedralType mydih = *dih;
-          int idx = addTorsionParm( dihedralparm_, *it );
-          // If there are multiple parameters for the same dihedral, all but
-          // one of the 1-4 calcs need to be skipped.
-          if (it == dpa.begin())
-            mydih.SetSkip14(skip14);
-          else
-            mydih.SetSkip14(true);
-          mydih.SetIdx( idx );
-          dihedralsIn.push_back( mydih );
-//          mprintf("DEBUG: Assigned %4i %4i %4i %4i (%2s %2s %2s %2s) isImproper=%i skip14=%i\n",
-//            mydih.A1()+1, mydih.A2()+1, mydih.A3()+1, mydih.A4()+1,
-//            *types[0], *types[1], *types[2], *types[3],
-//            (int)mydih.IsImproper(), (int)mydih.Skip14());
-        }
-      }
-    }
-  } // END loop over all dihedrals
-  return dihedralsIn;
-}
-
-/** \return Array of only unique dihedrals (get rid of multiplicities) */
-DihedralArray Topology::get_unique_dihedrals(DihedralArray const& dihedralsIn) const {
-  // Assume dihedrals with multiple terms are consecutive already
-  DihedralArray dihedrals;
-  for (DihedralArray::const_iterator dih = dihedralsIn.begin(); dih != dihedralsIn.end(); ++dih) {
-    if (dihedrals.empty())
-      dihedrals.push_back( *dih );
-    else {
-      if ( *dih != dihedrals.back() ) // TODO skip end dihedrals, impropers?
-        dihedrals.push_back( *dih );
-    }
-  }
-  if (debug_ > 0)
-    mprintf("DEBUG: %zu incoming dihedrals, %zu unique dihedrals.\n",
-            dihedralsIn.size(), dihedrals.size());
-  return dihedrals;
-}
-
-/** Replace any current dihedral parameters with given dihedral parameters. */
-void Topology::AssignDihedralParams(DihedralParmHolder const& newDihedralParams, ImproperParmHolder const& newImproperParams,
-                                    ParmHolder<AtomType> const& AT)
-{
-  dihedralparm_.clear();
-  // Dihedrals can be a bit of a pain since there can be multiple
-  // multiplicities for a single dihedral type. In case multiplicities
-  // change, start with a fresh dihedral array containing only unique
-  // dihedrals.
-  dihedrals_  = AssignDihedralParm( newDihedralParams, newImproperParams, AT, get_unique_dihedrals(dihedrals_), false  );
-  dihedralsh_ = AssignDihedralParm( newDihedralParams, newImproperParams, AT, get_unique_dihedrals(dihedralsh_), false );
-}
-
-/** Replace current nonbond parameters with given nonbond parameters. */
-//TODO Accept array of atom type names?
-void Topology::AssignNonbondParams(ParmHolder<AtomType> const& newTypes,
-                                   ParmHolder<NonbondType> const& newNB,
-                                   ParmHolder<NonbondType> const& new14,
-                                   ParmHolder<double> const& newLJC,
-                                   ParmHolder<HB_ParmType> const& newHB,
-                                   int verbose)
-{
-  bool hasLJ14 = !new14.empty();
-  bool hasLJC = !newLJC.empty();
-  // Generate array of only the types that are currently in Topology. TODO should this be a permanent part of Topology?
-  ParmHolder<AtomType> currentAtomTypes;
-  for (std::vector<Atom>::const_iterator atm = atoms_.begin(); atm != atoms_.end(); ++atm)
-  {
-    if (atm->HasType()) {
-      TypeNameHolder types(1);
-      types.AddName(atm->Type());
-      // Find in newTypes.
-      bool found;
-      AtomType newAT = newTypes.FindParam( types, found );
-      if (!found) {
-        mprintf("Warning: No atom type information for type '%s'\n", *types[0]);
-        newAT = AtomType(atm->Mass());
-      }
-      // Check LJ14 types if needed
-      if (hasLJ14) {
-        if (!newAT.HasLJ14()) {
-          mprintf("Warning: No 1-4 atom type information for type '%s'\n", *types[0]); // TODO error out here?
-        }
-      }
-      currentAtomTypes.AddParm( types, newAT, true );
-    }
-  }
-  if (currentAtomTypes.size() < 1) {
-    mprintf("Warning: No atom type information in %s - cannot assign nonbond parameters.\n",
-            c_str());
-    return;
-  }
-  // Regenerate nonbond params for existing types
-  nonbond_.Clear();
-  // Set type indices in order.
-  for (ParmHolder<AtomType>::iterator t1 = currentAtomTypes.begin(); t1 != currentAtomTypes.end(); ++t1)
-    t1->second.SetTypeIdx( -1 );
-  int n_unique_lj_types = 0;
-  for (ParmHolder<AtomType>::iterator t1 = currentAtomTypes.begin(); t1 != currentAtomTypes.end(); ++t1)
-  {
-    if (t1->second.OriginalIdx() == -1) {
-      t1->second.SetTypeIdx( n_unique_lj_types );
-      // Look for equivalent nonbond types
-      for (ParmHolder<AtomType>::iterator t2 = t1 + 1; t2 != currentAtomTypes.end(); ++t2) {
-        // Everything must match
-        if (!hasLJ14) {
-          if (t2->second.OriginalIdx() == -1 && t1->second.LJ() == t2->second.LJ()) {
-            mprintf("DEBUG: Type %s equivalent to type %s\n", *(t2->first[0]), *(t1->first[0]));
-            t2->second.SetTypeIdx( n_unique_lj_types );
-          }
-        } else {
-          if (t2->second.OriginalIdx() == -1 &&
-              t1->second.LJ() == t2->second.LJ() &&
-              t1->second.LJ14() == t2->second.LJ14())
-          {
-            mprintf("DEBUG: Type %s (with 1-4 params) equivalent to type %s\n", *(t2->first[0]), *(t1->first[0]));
-            t2->second.SetTypeIdx( n_unique_lj_types );
-          }
-        }
-      }
-      n_unique_lj_types++;
-    }
-  }
-  mprintf("DEBUG: Setting up nonbond array for %i unique LJ types.\n", n_unique_lj_types);
-  nonbond_.SetupLJforNtypes( n_unique_lj_types );
-  if (hasLJ14)
-    nonbond_.SetNLJ14terms( nonbond_.NBarray().size() );
-  if (hasLJC)
-    nonbond_.SetNLJCterms( nonbond_.NBarray().size() );
-  // Loop over all atom type pairs
-  for (ParmHolder<AtomType>::const_iterator t1 = currentAtomTypes.begin(); t1 != currentAtomTypes.end(); ++t1)
-  {
-    NameType const& name1 = t1->first[0];
-    //mprintf("DEBUG: Type1= %s (%i)\n", *name1, nidx1);
-    AtomType const& type1 = t1->second;
-    for (ParmHolder<AtomType>::const_iterator t2 = t1; t2 != currentAtomTypes.end(); ++t2)
-    {
-      NameType const& name2 = t2->first[0];
-      //mprintf("DEBUG:\t\tType2= %s (%i)\n", *name2, nidx2);
-      AtomType const& type2 = t2->second;
-      TypeNameHolder types(2);
-      types.AddName( name1 );
-      types.AddName( name2 );
-      int newnbidx;
-      // Check for LJ10-12 first
-      ParmHolder<HB_ParmType>::const_iterator hb = newHB.GetParam( types );
-      if (hb != newHB.end()) {
-        if (verbose > 0) mprintf("LJ 10-12 parameter found for %s %s\n", *name1, *name2);
-        nonbond_.AddHBterm(t1->second.OriginalIdx(), t2->second.OriginalIdx(), hb->second);
-        // Also add a blank 6-12 term since that seems to be the convention
-        newnbidx = nonbond_.AddLJterm( t1->second.OriginalIdx(), t2->second.OriginalIdx(), NonbondType() );
-      } else {
-        // See if this parameter exists in the given nonbond array.
-        NonbondType LJAB;
-        ParmHolder<NonbondType>::const_iterator it = newNB.GetParam( types );
-        if (it == newNB.end()) {
-          if (verbose > 0) mprintf("NB parameter for %s %s not found. Generating.\n", *name1, *name2);
-          LJAB = type1.LJ().Combine_LB( type2.LJ() );
-        } else {
-          if (verbose > 0) mprintf("Using existing NB parameter for %s %s\n", *name1, *name2);
-          LJAB = it->second;
-        }
-        newnbidx = nonbond_.AddLJterm(t1->second.OriginalIdx(), t2->second.OriginalIdx(), LJAB);
-      }
-      // LJ 1-4
-      if (hasLJ14) {
-        // Get parameter if it exists
-        ParmHolder<NonbondType>::const_iterator it = new14.GetParam( types );
-        if (it == new14.end()) {
-          if (verbose > 0) mprintf("NB 1-4 parameter for %s %s not found. Generating.\n", *name1, *name2);
-          nonbond_.SetLJ14( newnbidx ) = type1.LJ14().Combine_LB( type2.LJ14() );
-        } else {
-          if (verbose > 0) mprintf("Using existing NB 1-4 parameter for %s %s\n", *name1, *name2);
-          nonbond_.SetLJ14( newnbidx ) = it->second;
-        }
-      } // END hasLJ14
-      // LJC
-      if (hasLJC) {
-        // Get parameter if it exists
-        ParmHolder<double>::const_iterator it = newLJC.GetParam( types );
-        if (it == newLJC.end()) {
-          mprintf("LJC parameter for %s %s not found. Setting to 0.\n", *name1, *name2); // FIXME generate
-          nonbond_.SetLJC( newnbidx, 0 );
-        } else {
-          mprintf("Using existing LJC parameter for %s %s\n", *name1, *name2);
-          nonbond_.SetLJC( newnbidx, it->second );
-        }
-      } // END hasLJC
-    } // END inner loop over current types
-  } // END outer loop over current types
-  // Reset the atom type indices.
-  for (std::vector<Atom>::iterator atm = atoms_.begin(); atm != atoms_.end(); ++atm)
-  {
-    int tidx = -1;
-    ParmHolder<AtomType>::const_iterator it = currentAtomTypes.GetParam( TypeNameHolder(atm->Type()) );
-    if (it == currentAtomTypes.end()) {
-      mprintf("Warning: Atom type not found for %s (type %s)\n",
-              TruncResAtomNameNum( atm - atoms_.begin() ).c_str(),
-              *(atm->Type()));
-    } else {
-      if (it->second.OriginalIdx() < 0 || it->second.OriginalIdx() >= (int)currentAtomTypes.size()) {
-        mprinterr("Internal Error: Type index for %s (type %s) out of range: %i\n",
-                  TruncResAtomNameNum( atm - atoms_.begin() ).c_str(),
-                  *(atm->Type()), it->second.OriginalIdx());
-      } else
-        tidx = it->second.OriginalIdx();
-    }
-    atm->SetTypeIndex( tidx );
-  }
-}
-
-/// \return index of 5th cmap atom if atom names match those in dihedral, -1 otherwise
-static inline int cmap_anames_match(DihedralType const& dih,
-                                     std::vector<Atom> const& atoms,
-                                     std::vector<std::string> const& cmapAtomNames)
-{
-/*  mprintf("DEBUG: Check res %i %s %s %s %s against %s %s %s %s\n",
-          atoms[dih.A2()].ResNum()+1,
-            atoms[dih.A1()].Name().Truncated().c_str(),
-            atoms[dih.A2()].Name().Truncated().c_str(),
-            atoms[dih.A3()].Name().Truncated().c_str(),
-            atoms[dih.A4()].Name().Truncated().c_str(),
-            cmap.AtomNames()[0].c_str(),
-            cmap.AtomNames()[1].c_str(),
-            cmap.AtomNames()[2].c_str(),
-            cmap.AtomNames()[3].c_str());*/
-  // TODO without Truncated
-  if (atoms[dih.A1()].Name().Truncated() == cmapAtomNames[0] &&
-      atoms[dih.A2()].Name().Truncated() == cmapAtomNames[1] &&
-      atoms[dih.A3()].Name().Truncated() == cmapAtomNames[2] &&
-      atoms[dih.A4()].Name().Truncated() == cmapAtomNames[3])
-  {
-    /*mprintf("DEBUG: Partial match %s %s %s %s = %s %s %s %s\n",
-            atoms[dih.A1()].Name().Truncated().c_str(),
-            atoms[dih.A2()].Name().Truncated().c_str(),
-            atoms[dih.A3()].Name().Truncated().c_str(),
-            atoms[dih.A4()].Name().Truncated().c_str(),
-            cmap.AtomNames()[0].c_str(),
-            cmap.AtomNames()[1].c_str(),
-            cmap.AtomNames()[2].c_str(),
-            cmap.AtomNames()[3].c_str());*/
-    for (Atom::bond_iterator bat = atoms[dih.A4()].bondbegin();
-                             bat != atoms[dih.A4()].bondend(); ++bat)
-    {
-      if (*bat != dih.A3()) { // TODO can A4 ever be bonded to A1??
-        if (atoms[*bat].Name().Truncated() == cmapAtomNames[4]) {
-          return *bat;
-        }
-      }
-    }
-  }
-  return -1;
-}
-
-/// \return true if given name matches a residue name
-static inline bool MatchesResName(std::vector<std::string> const& resNames, std::string const& nameIn) {
-  for (std::vector<std::string>::const_iterator it = resNames.begin(); it != resNames.end(); ++it)
-    if (nameIn == *it) return true;
-  return false;
-}
-
-/// Remap cmap indices
-int Topology::remap_cmap_indices(std::vector<int>& originalCmapIndices,
-                                     CmapGridArray& cmapGrids,
-                                     CmapArray& cmapTerms,
-                                 CmapParmHolder const& cmapIn)
-const
-{
-  mprintf("DEBUG: Cmap parameter indices:\n");
-  for (unsigned int idx = 0; idx < originalCmapIndices.size(); idx++)
-    mprintf("DEBUG:\t\tCurrent idx=%i  Actual idx=%u\n", originalCmapIndices[idx], idx);
-  if (originalCmapIndices.empty()) {
-    mprintf("DEBUG: No CMAP indices in %s\n", c_str());
-    return 0;
-  }
-  std::sort(originalCmapIndices.begin(), originalCmapIndices.end());
-  std::vector<int> currentToNew(cmapIn.size(), -1);
-  // Add the grid terms in original parameter file order
-  // and create map from assigned index to new index.
-  cmapGrids.reserve( originalCmapIndices.size() );
-  for (unsigned int idx = 0; idx < originalCmapIndices.size(); idx++) {
-    mprintf("DEBUG: Will change cmap parameter index %i to %u\n",
-            originalCmapIndices[idx]+1, idx+1);
-    currentToNew[ originalCmapIndices[idx] ] = idx;
-    cmapGrids.push_back( cmapIn[ originalCmapIndices[idx] ] );
-  }
-  mprintf("DEBUG: Assigned CMAP parameters:\n");
-  for (CmapGridArray::const_iterator it = cmapGrids.begin(); it != cmapGrids.end(); ++it)
-    mprintf("DEBUG:\t\t%li : %s\n", it-cmapGrids.begin(), it->Title().c_str());
-  // Renumber the parameter indices
-  for (CmapArray::iterator it = cmapTerms.begin(); it != cmapTerms.end(); ++it) {
-    int newIdx = currentToNew[ it->Idx() ];
-    if (newIdx < 0) {
-      mprinterr("Internal Error: CMAP term index is not mapped.\n");
-      return 1;
-    }
-    it->SetIdx( newIdx );
-  }
-  return 0;
-}
-
-/** Assign CMAP parameters to existing CMAP terms. */
-int Topology::AssignCmapParams(CmapArray& cmapTerms, CmapParmHolder const& cmapIn,
-                               CmapGridArray& cmapGrids)
-const
-{
-  // Keep track of residue names each cmap applies to
-  typedef std::vector<std::string> Sarray;
-  std::vector<Sarray> CmapResNames;
-  std::vector<Sarray> CmapAtomNames;
-  // The LEaP convention is to number the CMAP parameters in the same
-  // order as they are listed in the original parameter file. This
-  // variable keeps track of those indices.
-  std::vector<int> originalCmapIndices;
-  for (CmapArray::iterator cm = cmapTerms.begin(); cm != cmapTerms.end(); ++cm)
-  {
-    // Get residue name for A2
-    Atom const& A2 = atoms_[cm->A2()];
-    // TODO make sure A2-A4 in same residue?
-    NameType const& rn2 = residues_[A2.ResNum()].Name();
-    // Is this residue already in cmapGrids?
-    int cidx = -1;
-    for (unsigned int idx = 0; idx != CmapResNames.size(); idx++) {
-      if ( MatchesResName(CmapResNames[idx], rn2.Truncated()) ) {
-        if (atoms_[cm->A1()].Name() == CmapAtomNames[idx][0] &&
-            atoms_[cm->A2()].Name() == CmapAtomNames[idx][1] &&
-            atoms_[cm->A3()].Name() == CmapAtomNames[idx][2] &&
-            atoms_[cm->A4()].Name() == CmapAtomNames[idx][3] &&
-            atoms_[cm->A5()].Name() == CmapAtomNames[idx][4])
-        {
-          cidx = originalCmapIndices[idx];
-          break;
-        }
-      }
-    }
-    if (cidx > -1) {
-      mprintf("DEBUG: Potential existing cmap %i found for %s (%li)\n", cidx, TruncResNameNum(A2.ResNum()).c_str(), cm-cmapTerms.begin());
-      mprintf("DEBUG:\t\t%i - %i - %i - %i - %i %i\n", cm->A1()+1, cm->A2()+1, cm->A3()+1, cm->A4()+1, cm->A5()+1, cidx+1);
-      cm->SetIdx( cidx );
-    }
-    // If not already in cmapGrids, check cmapIn
-    if (cidx == -1) {
-      for (unsigned int idx = 0; idx != cmapIn.size(); idx++) {
-        if ( MatchesResName( cmapIn[idx].ResNames(), rn2.Truncated() ) ) {
-          if (atoms_[cm->A1()].Name() == cmapIn[idx].AtomNames()[0] &&
-              atoms_[cm->A2()].Name() == cmapIn[idx].AtomNames()[1] &&
-              atoms_[cm->A3()].Name() == cmapIn[idx].AtomNames()[2] &&
-              atoms_[cm->A4()].Name() == cmapIn[idx].AtomNames()[3] &&
-              atoms_[cm->A5()].Name() == cmapIn[idx].AtomNames()[4])
-          {
-            cidx = (int)idx;
-            CmapResNames.push_back( cmapIn[idx].ResNames() );
-            CmapAtomNames.push_back( cmapIn[idx].AtomNames() );
-            originalCmapIndices.push_back( idx );
-            break;
-          }
-        }
-      }
-      if (cidx > -1) {
-        mprintf("DEBUG: Potential new cmap %i found for %s (%li)\n", cidx, TruncResNameNum(A2.ResNum()).c_str(), cm-cmapTerms.begin());
-        mprintf("DEBUG:\t\t%i - %i - %i - %i - %i %i\n", cm->A1()+1, cm->A2()+1, cm->A3()+1, cm->A4()+1, cm->A5()+1, cidx+1);
-        //mprintf("DEBUG:\t\t%s - %s - %s - %s - %s\n",
-        //        AtomMaskName(dih->A1()).c_str(),
-        //        AtomMaskName(dih->A2()).c_str(),
-        //        AtomMaskName(dih->A3()).c_str(),
-        //        AtomMaskName(dih->A4()).c_str(),
-        //        AtomMaskName(a5).c_str());
-        cm->SetIdx( cidx );
-      }
-    }
-  } // END loop over cmap terms
-
-  return remap_cmap_indices(originalCmapIndices, cmapGrids, cmapTerms, cmapIn);
-}
-
-/** Assign CMAP parameters. Also generates CMAP terms from dihedrals. */
-int Topology::AssignCmapParams(DihedralArray const& allDih, CmapParmHolder const& cmapIn,
-                               CmapGridArray& cmapGrids, CmapArray& cmapTerms)
-const
-{
-  // TODO check for duplicates, look for reverse match?
-  // Keep track of residue names each cmap applies to
-  //typedef std::vector<NameType> Narray;
-  typedef std::vector<std::string> Sarray;
-  std::vector<Sarray> CmapResNames;
-  std::vector<Sarray> CmapAtomNames;
-  // The LEaP convention is to number the CMAP parameters in the same
-  // order as they are listed in the original parameter file. This
-  // variable keeps track of those indices.
-  std::vector<int> originalCmapIndices;
-  // TODO combine with AssignDihedrals?
-  for (DihedralArray::const_iterator dih = allDih.begin(); dih != allDih.end(); ++dih)
-  {
-    // Ignore end (repeated) or improper dihedrals
-    if (dih->IsImproper() || dih->Skip14()) continue;
-    // Get residue name for A2
-    Atom const& A2 = atoms_[dih->A2()];
-    // TODO make sure A2-A4 in same residue?
-    NameType const& rn2 = residues_[A2.ResNum()].Name();
-    // Is this residue already in cmapGrids?
-    int cidx = -1;
-    int a5 = -1;
-    //for (unsigned int idx = 0; idx != cmapGrids.size(); idx++) {
-    //  if (cmapGrids[idx].MatchesResName( rn2.Truncated() )) {
-    for (unsigned int idx = 0; idx != CmapResNames.size(); idx++) {
-      if ( MatchesResName(CmapResNames[idx], rn2.Truncated()) ) {
-        //a5 = cmap_anames_match(*dih, atoms_, cmapGrids[idx]);
-        a5 = cmap_anames_match(*dih, atoms_, CmapAtomNames[idx]);
-        if (a5 > -1) {
-          //cidx = (int)idx;
-          cidx = originalCmapIndices[idx];
-          break;
-        }
-      }
-    }
-    if (cidx > -1) {
-      mprintf("DEBUG: Potential existing cmap %i found for %s (%li)\n", cidx, TruncResNameNum(A2.ResNum()).c_str(), dih-allDih.begin());
-      mprintf("DEBUG:\t\t%i - %i - %i - %i - %i %i\n", dih->A1()+1, dih->A2()+1, dih->A3()+1, dih->A4()+1, a5+1, cidx+1);
-//      mprintf("DEBUG:\t\t%s - %s - %s - %s - %s\n",
-//              AtomMaskName(dih->A1()).c_str(),
-//              AtomMaskName(dih->A2()).c_str(),
-//              AtomMaskName(dih->A3()).c_str(),
-//              AtomMaskName(dih->A4()).c_str(),
-//              AtomMaskName(a5).c_str());
-      cmapTerms.push_back( CmapType(dih->A1(), dih->A2(), dih->A3(), dih->A4(), a5, cidx) );
-    }
-    // If not already in cmapGrids, check cmapIn
-    if (cidx == -1) {
-      //int nidx = -1;
-      for (unsigned int idx = 0; idx != cmapIn.size(); idx++) {
-        //if (cmapIn[idx].MatchesResName( rn2.Truncated() )) {
-        if ( MatchesResName( cmapIn[idx].ResNames(), rn2.Truncated() ) ) {
-          //a5 = cmap_anames_match(*dih, atoms_, cmapIn[idx]);
-          a5 = cmap_anames_match(*dih, atoms_, cmapIn[idx].AtomNames());
-          if (a5 > -1) {
-            //cidx = (int)cmapGrids.size();
-            cidx = (int)idx;
-            //cmapGrids.push_back( cmapIn[idx] );
-            CmapResNames.push_back( cmapIn[idx].ResNames() );
-            CmapAtomNames.push_back( cmapIn[idx].AtomNames() );
-            originalCmapIndices.push_back( idx );
-            //nidx = (int)idx;
-            break;
-          }
-        }
-      }
-      if (cidx > -1) {
-        mprintf("DEBUG: Potential new cmap %i found for %s (%li)\n", cidx, TruncResNameNum(A2.ResNum()).c_str(), dih-allDih.begin());
-        mprintf("DEBUG:\t\t%i - %i - %i - %i - %i %i\n", dih->A1()+1, dih->A2()+1, dih->A3()+1, dih->A4()+1, a5+1, cidx+1);
-      //mprintf("DEBUG:\t\t%s - %s - %s - %s - %s\n",
-      //        AtomMaskName(dih->A1()).c_str(),
-      //        AtomMaskName(dih->A2()).c_str(),
-      //        AtomMaskName(dih->A3()).c_str(),
-      //        AtomMaskName(dih->A4()).c_str(),
-      //        AtomMaskName(a5).c_str());
-        cmapTerms.push_back( CmapType(dih->A1(), dih->A2(), dih->A3(), dih->A4(), a5, cidx) );
-      }
-    }
-  } // END loop over dihedrals
-  return remap_cmap_indices(originalCmapIndices, cmapGrids, cmapTerms, cmapIn);
-/*  mprintf("DEBUG: Cmap parameter indices:\n");
-  for (unsigned int idx = 0; idx < originalCmapIndices.size(); idx++)
-    mprintf("DEBUG:\t\tCurrent idx=%i  Actual idx=%u\n", originalCmapIndices[idx], idx);
-  if (originalCmapIndices.empty()) {
-    mprintf("DEBUG: No CMAP indices in %s\n", c_str());
-    return 0;
-  }
-  std::sort(originalCmapIndices.begin(), originalCmapIndices.end());
-  std::vector<int> currentToNew(cmapIn.size(), -1);
-  // Add the grid terms in original parameter file order
-  // and create map from assigned index to new index.
-  cmapGrids.reserve( originalCmapIndices.size() );
-  for (unsigned int idx = 0; idx < originalCmapIndices.size(); idx++) {
-    mprintf("DEBUG: Will change cmap parameter index %i to %u\n",
-            originalCmapIndices[idx]+1, idx+1);
-    currentToNew[ originalCmapIndices[idx] ] = idx;
-    cmapGrids.push_back( cmapIn[ originalCmapIndices[idx] ] );
-  }
-  mprintf("DEBUG: Assigned CMAP parameters:\n");
-  for (CmapGridArray::const_iterator it = cmapGrids.begin(); it != cmapGrids.end(); ++it)
-    mprintf("DEBUG:\t\t%li : %s\n", it-cmapGrids.begin(), it->Title().c_str());
-  // Renumber the parameter indices
-  for (CmapArray::iterator it = cmapTerms.begin(); it != cmapTerms.end(); ++it) {
-    int newIdx = currentToNew[ it->Idx() ];
-    if (newIdx < 0) {
-      mprinterr("Internal Error: CMAP term index is not mapped.\n");
-      return 1;
-    }
-    it->SetIdx( newIdx );
-  }
-  return 0;*/
-}
-
-/** Replace existing parameters with the given parameter set. */
-int Topology::AssignParams(ParameterSet const& set0) {
-
-  // Bond parameters
-  mprintf("\tAssigning bond parameters.\n");
-  bondparm_.clear();
-  // Regenerate bond array in LEaP order
-  bonds_.clear();
-  bondsh_.clear();
-  BondArray allBonds = Cpptraj::Structure::GenerateBondArray(residues_, atoms_);
-  AssignBondParm( set0.BP(), allBonds, bondparm_, "bond" );
-  for (BondArray::const_iterator bnd = allBonds.begin(); bnd != allBonds.end(); ++bnd)
-    AddToBondArrays( *bnd );
-  // Angle parameters
-  mprintf("\tAssigning angle parameters.\n");
-  angleparm_.clear();
-  // Regenerate angle array in LEaP order
-  angles_.clear();
-  anglesh_.clear();
-  AngleArray allAngles = Cpptraj::Structure::GenerateAngleArray(residues_, atoms_);
-  allAngles = AssignAngleParm( set0.AP(), allAngles );
-  for (AngleArray::const_iterator ang = allAngles.begin(); ang != allAngles.end(); ++ang)
-    AddToAngleArrays( *ang );
-  // Dihedral parameters
-  mprintf("\tAssigning dihedral parameters.\n");
-  dihedralparm_.clear();
-  // Regenerate dihedral array in LEaP order
-  dihedrals_.clear();
-  dihedralsh_.clear();
-  DihedralArray allDihedrals = Cpptraj::Structure::GenerateDihedralArray(residues_, atoms_);
-  // If we need CMAP terms, do it here before the dihedrals array is modified
-  if (!set0.CMAP().empty()) {
-    cmap_.clear();
-    cmapGrid_.clear();
-    mprintf("\tAssigning CMAP parameters.\n");
-    AssignCmapParams( allDihedrals, set0.CMAP(), cmapGrid_, cmap_ );
-  } 
-  // Now modify the dihedrals for any multiplicities
-  allDihedrals = AssignDihedralParm( set0.DP(), set0.IP(), set0.AT(), allDihedrals, false );
-  for (DihedralArray::const_iterator dih = allDihedrals.begin(); dih != allDihedrals.end(); ++dih)
-    AddToDihedralArrays( *dih );
-  // Urey-Bradley
-  mprintf("\tAssigning Urey-Bradley parameters.\n");
-  AssignUBParams( set0.UB() );
-  if (!impropers_.empty()) {
-    // Charmm Improper parameters
-    mprintf("\tAssigning CHARMM improper parameters.\n");
-    AssignImproperParams( set0.IP() );
-  } else {
-    // Amber improper parameters
-    mprintf("\tAssigning improper parameters.\n");
-    DihedralArray allImpropers = Cpptraj::Structure::GenerateImproperArray(residues_, atoms_);
-    allImpropers = AssignDihedralParm( set0.DP(), set0.IP(), set0.AT(), allImpropers, true );
-    for (DihedralArray::const_iterator imp = allImpropers.begin(); imp != allImpropers.end(); ++imp)
-      AddToDihedralArrays( *imp );
-  }
-  // Atom types
-  mprintf("\tAssigning atom type parameters.\n");
-  AssignAtomTypeParm( set0.AT() );
-  // LJ 6-12
-  mprintf("\tAssigning nonbond parameters.\n");
-  AssignNonbondParams( set0.AT(), set0.NB(), set0.NB14(), set0.LJC(), set0.HB(), debug_ );
-  mprintf("DEBUG: CMAP size %zu\n", set0.CMAP().size());
-
-  return 0;
-}
-
-/** Update/add to parameters in this topology with those from given set.
-  */
-int Topology::UpdateParams(ParameterSet const& set1) {
-  ParameterSet set0 = GetParameters();
-
-  //set1.Summary(); // DEBUG
-  // Check TODO is this necessary?
-  if (set0.AT().size() < 1)
-    mprintf("Warning: No atom type information in '%s'\n", c_str());
-  if (debug_ > 0) {
-    mprintf("DEBUG: Saving original parameters in originalp.dat, new parameters in newp.dat\n");
-    set0.Debug("originalp.dat");
-  }
-  // Update existing parameters with new parameters
-  ParameterSet::UpdateCount UC;
-  if (set0.UpdateParamSet( set1, UC, debug_, debug_ )) { // FIXME verbose
-    mprinterr("Error: Could not merge topology '%s' parameters with '%s' parameters.\n",
-              c_str(), set1.ParamSetName().c_str());
-    return 1;
-  }
-  mprintf("DEBUG: Updated parameters.\n");
-  set0.Summary();
-  //set0.Debug();
-
-//  unsigned int updateCount;
-  // Bond parameters
-//  updateCount = UpdateParameters< ParmHolder<BondParmType> >(set0.BP(), set1.BP(), "bond");
-  if (UC.nBondsUpdated_ > 0) {
-    mprintf("\tRegenerating bond parameters.\n");
-    AssignBondParams( set0.BP() );
-  }
-  // Angle parameters
-//  updateCount = UpdateParameters< ParmHolder<AngleParmType> >(set0.AP(), set1.AP(), "angle");
-  if (UC.nAnglesUpdated_ > 0) {
-    mprintf("\tRegenerating angle parameters.\n");
-    AssignAngleParams( set0.AP() );
-  }
-  // Dihedral parameters
-//  updateCount = UpdateParameters< DihedralParmHolder >(set0.DP(), set1.DP(), "dihedral");
-  if (UC.nDihedralsUpdated_ > 0) {
-    mprintf("\tRegenerating dihedral parameters.\n");
-    AssignDihedralParams( set0.DP(), set0.IP(), set0.AT() );
-  }
-  // Urey-Bradley
-//  updateCount = UpdateParameters< ParmHolder<BondParmType> >(set0.UB(), set1.UB(), "Urey-Bradley");
-  if (UC.nUreyBradleyUpdated_ > 0) {
-    mprintf("\tRegenerating UB parameters.\n");
-    AssignUBParams( set0.UB() );
-  }
-  // Improper parameters
-//  updateCount = UpdateParameters< ParmHolder<DihedralParmType> >(set0.IP(), set1.IP(), "improper");
-  if (UC.nImpropersUpdated_ > 0) {
-    mprintf("\tRegenerating improper parameters.\n");
-    AssignImproperParams( set0.IP() );
-  }
-  // Atom types
-//  updateCount = UpdateParameters< ParmHolder<AtomType> >(set0.AT(), set1.AT(), "atom type");
-  if (UC.nAtomTypeUpdated_ > 0) {
-    mprintf("\tRegenerating atom type parameters.\n");
-    AssignAtomTypeParm( set0.AT() );
-  }
-//  updateCount += UpdateParameters< ParmHolder<NonbondType> >(set0.NB(), set1.NB(), "LJ A-B");
-  if (UC.nAtomTypeUpdated_ > 0 || UC.nLJCUpdated_ > 0 ||
-      UC.nLJparamsUpdated_ > 0 || UC.nLJ14paramsUpdated_ > 0)
-  {
-    mprintf("\tRegenerating nonbond parameters.\n");
-    AssignNonbondParams( set0.AT(), set0.NB(), set0.NB14(), set0.LJC(), set0.HB(), debug_ );
-  }
-  // CMAP
-  if (UC.nCmapUpdated_ > 0) {
-    cmapGrid_.clear();
-    mprintf("\tRegenerating CMAP parameters.\n");
-    AssignCmapParams(cmap_, set0.CMAP(), cmapGrid_);
-  }
-  // TODO LJ14
-
-  if (debug_ > 0) set0.Debug("newp.dat");
-  return 0;
-}
-
 // -----------------------------------------------------------------------------
 /** \return True if any atom has a non-zero charge. */
 bool Topology::HasChargeInfo() const {
diff --git a/src/Topology.h b/src/Topology.h
index 6f34d2e637..4009726483 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -6,7 +6,6 @@
 #include "Residue.h"
 #include "Molecule.h"
 #include "ParameterTypes.h"
-#include "ParameterSet.h"
 #include "Frame.h"
 #include "FileName.h"
 #include "Range.h"
@@ -37,8 +36,7 @@ class Topology {
     int NextraPts()                const { return n_extra_pts_;           }
     /// \return Strings describing forcefield
     std::vector<std::string> const& Description() const { return ff_desc_; }
-    /// \return number of unique atom types
-    unsigned int NuniqueAtomTypes() const;
+
     std::string const& ParmName()         const { return parmName_;       }
     FileName const& OriginalFilename()    const { return fileName_;       }
     std::string const& GBradiiSet()       const { return radius_set_;     }
@@ -49,6 +47,7 @@ class Topology {
     atom_iterator end()                          const { return atoms_.end();   }
     const Atom &operator[](int idx)              const { return atoms_[idx];    }
     std::vector<Atom> const& Atoms()             const { return atoms_;         }
+    std::vector<Atom>& ModifyAtoms() { return atoms_; }
     Atom& SetAtom(int idx)                             { return atoms_[idx]; }
     /// \return Count of "heavy" atoms (non-hydrogen, non-extra point)
     unsigned int HeavyAtomCount() const;
@@ -65,6 +64,9 @@ class Topology {
     void AddTreeChainClassification(NameType const& n)          { tree_.push_back(n); }
     void AddJoinArray(int j)                                    { ijoin_.push_back(j); }
     void AddRotateArray(int r)                                  { irotat_.push_back(r); }
+    std::vector<NameType>& ModifyTreeChainClassification() { return tree_; }
+    std::vector<int>& ModifyJoinArray()                    { return ijoin_; }
+    std::vector<int>& ModifyRotateArray()                  { return irotat_; }
     // ----- PDB info ----------------------------
     /// Reset all PDB-related info
     void ResetPDBinfo();
@@ -84,6 +86,10 @@ class Topology {
     void AddOccupancy(float o)  { occupancy_.push_back( o );    }
     void AddBfactor(float b)    { bfactor_.push_back( b );      }
     void AddPdbSerialNum(int i) { pdbSerialNum_.push_back( i ); }
+    std::vector<char>& ModifyAtomAltLoc()  { return atom_altloc_;  }
+    std::vector<float>& ModifyOccupancy()  { return occupancy_;    }
+    std::vector<float>& ModifyBfactor()    { return bfactor_;      }
+    std::vector<int>& ModifyPdbSerialNum() { return pdbSerialNum_; }
     /// Set list of missing residues and residues missing heteroatoms
     void SetMissingResInfo(std::vector<Residue> const&, std::vector<Residue> const&);
     /// \return list of completely missing residues
@@ -117,50 +123,54 @@ class Topology {
     BondArray         const& BondsH()       const { return bondsh_;       }
     BondParmArray     const& BondParm()     const { return bondparm_;     }
     BondParmType& SetBondParm(int i)              { return bondparm_[i];  }
+    BondArray& ModifyBonds() { return bonds_; }
+    BondArray& ModifyBondsH() { return bondsh_; }
+    BondParmArray& ModifyBondParm() { return bondparm_; }
     void AddBondParm(BondParmType const& b)       { bondparm_.push_back( b ); }
     void AddBond(int i, int j)                    { AddBond(i, j, -1); }
     void AddBond(int, int, int);
     void AddBond(BondType const&, bool);
     void AddBond(int, int, BondParmType const&);
     int RemoveBond(int, int);
-    void AssignBondParams(ParmHolder<BondParmType> const&);
     /// Clear bond arrays but not atom connectivity
     void ClearBondArrays();
-    /// Add to bond arrays but do not update atom connectivity
-    void AddToBondArrays(BondType const&);
     // ----- Angle-specific routines -------------
     size_t Nangles()                           const { return angles_.size()+anglesh_.size(); }
     AngleArray        const& Angles()       const { return angles_;       }
     AngleArray        const& AnglesH()      const { return anglesh_;      }
     AngleParmArray    const& AngleParm()    const { return angleparm_;    }
     AngleParmType& SetAngleParm(int i)            { return angleparm_[i]; }
+    AngleArray& ModifyAngles() { return angles_; }
+    AngleArray& ModifyAnglesH() { return anglesh_; }
+    AngleParmArray& ModifyAngleParm() { return angleparm_; }
     void AddAngle(int i, int j, int k)            { AddAngle(i, j, k, -1); }
     void AddAngle(int, int, int, int);
     void AddAngle(AngleType const&, bool);
     void AddAngle(int, int, int, AngleParmType const&);
-    /// Add to angle arrays
-    void AddToAngleArrays(AngleType const&);
-    void AssignAngleParams(ParmHolder<AngleParmType> const&);
     // ----- Dihedral-specific routines ----------
     size_t Ndihedrals()                        const { return dihedrals_.size()+dihedralsh_.size(); }
     DihedralArray     const& Dihedrals()    const { return dihedrals_;       }
     DihedralArray     const& DihedralsH()   const { return dihedralsh_;      }
     DihedralParmArray const& DihedralParm() const { return dihedralparm_;    }
     DihedralParmType& SetDihedralParm(int i)      { return dihedralparm_[i]; }
+    DihedralArray& ModifyDihedrals() { return dihedrals_; }
+    DihedralArray& ModifyDihedralsH() { return dihedralsh_; }
+    DihedralParmArray& ModifyDihedralParm() { return dihedralparm_; }
     void AddDihedral(DihedralType const& d)       { AddDihedral(d, -1);      }
     void AddDihedral(DihedralType const&, int);
     void AddDihedral(int i, int j, int k, int l) { AddDihedral(DihedralType(i,j,k,l,-1), -1); }
     void AddDihedral(DihedralType const&, bool);
     void AddDihedral(DihedralType const&, DihedralParmType const&);
-    void AssignImproperParams(ImproperParmHolder const&);
-    void AssignDihedralParams(DihedralParmHolder const&, ImproperParmHolder const&, ParmHolder<AtomType> const&);
-    /// Add to dihedral arrays
-    void AddToDihedralArrays(DihedralType const&);
+    /// \return Index of existing/added dihedral parameter in given array
+    static int addTorsionParm(DihedralParmArray&, DihedralParmType const&);
+
     // ----- CMAP-specific routines --------------
     bool                     HasCmap()      const { return !cmapGrid_.empty(); }
     CmapGridArray     const& CmapGrid()     const { return cmapGrid_;     }
     CmapArray         const& Cmap()         const { return cmap_;         }
     CmapGridType& SetCmapGrid(int idx)            { return cmapGrid_[idx];}
+    CmapGridArray& ModifyCmapGrid() { return cmapGrid_; }
+    CmapArray& ModifyCmap() { return cmap_; }
     void AddCmapGrid(CmapGridType const& g) { cmapGrid_.push_back(g); }
     void AddCmapTerm(CmapType const& c)     { cmap_.push_back(c);     }
     // ----- Non-bond routines -------------------
@@ -171,10 +181,6 @@ class Topology {
     double GetVDWdepth(int) const;
     /// \return Lennard-Jones 6-12 parameters for given pair of atoms
     inline NonbondType const& GetLJparam(int, int) const;
-    /// Assign LJ 6-12 / 10-12 parameters, reset atom type indices
-    void AssignNonbondParams(ParmHolder<AtomType> const&, ParmHolder<NonbondType> const&,
-                             ParmHolder<NonbondType> const&, ParmHolder<double> const&,
-                             ParmHolder<HB_ParmType> const&, int);
     /// \return True if any charge is non-zero
     bool HasChargeInfo() const;
     /// Redistribute charge on atoms in topology to match target total charge
@@ -201,12 +207,19 @@ class Topology {
     BondArray         const& UB()       const { return ub_;           }
     /// \return Array of Urey-Bradley parameters
     BondParmArray     const& UBparm()   const { return ubparm_;       }
-
+    /// \return Modifiable array of UB terms
+    BondArray& ModifyUB() { return ub_; }
+    /// \return Modifiable array of UB parameters
+    BondParmArray& ModifyUBparm() { return ubparm_; }
 
     /// Reserve space for future improper terms
     void ReserveImproperTerms(unsigned int n)         { impropers_.reserve( n );     }
     /// Resize for given number of improper parameters
     void ResizeImproperParm(unsigned int n)           { improperparm_.resize( n );   }
+    /// \return Modifiable improper array
+    DihedralArray& ModifyImpropers() { return impropers_; }
+    /// \return Modifiable improper parm array
+    DihedralParmArray& ModifyImproperParm() { return improperparm_; }
     /// Add improper term
     void AddImproperTerm(DihedralType const& dih)     { impropers_.push_back( dih ); }
     /// Set specified improper parameter
@@ -220,7 +233,6 @@ class Topology {
     void AddCharmmImproper(DihedralType const&, DihedralParmType const&);
     void AddCharmmImproper(DihedralType const&, int);
     void AddCharmmImproper(DihedralType const& i) { AddCharmmImproper(i, -1); }
-    void AssignUBParams(ParmHolder<BondParmType> const&);
     // ----- Misc routines -----------------------
     /// Format: <res name>_<res num>@<atom name>
     std::string TruncResAtomName(int) const;
@@ -246,12 +258,7 @@ class Topology {
     int FindAtomInResidue(int, NameType const&) const;
     /// Mark all molecules matching given mask expression as solvent.
     int SetSolvent(std::string const&);
-    /// \return ParameterSet for this Topology
-    ParameterSet GetParameters() const;
-    /// Replace existing parameters with those in given set.
-    int AssignParams(ParameterSet const&);
-    /// Update parameters in this Topology with those in given set.
-    int UpdateParams(ParameterSet const&);
+
     // ----- Print topology info -----------------
     void Summary() const;
     void Brief(const char*) const;
@@ -262,6 +269,8 @@ class Topology {
     // ----- Setup routines ----------------------
     /// Add an atom to the topology inside given residue
     int AddTopAtom(Atom const&, Residue const&);
+    /// Add an atom to the topology inside given residue and molecule number
+    int addTopAtom(Atom const&, Residue const&, unsigned int, bool);
     //void StartNewMol();
     /// Perform common final setup: optional molecule determination, renumber residues by molecules
     int CommonSetup(bool, bool);
@@ -273,6 +282,8 @@ class Topology {
     int Setup_NoResInfo();
     /// Resize for given numbers of atoms/residues etc. Clears any existing data.
     void Resize(Pointers const&);
+    /// Count the number of extra points in the Topology TODO just have it a part of AddTopAtom
+    void DetermineNumExtraPoints();
     // ----- Mask Routines -----------------------
     int SetupIntegerMask(AtomMask &) const;
     int SetupCharMask(CharMask &) const;
@@ -300,8 +311,7 @@ class Topology {
     int SplitResidue(AtomMask const&, NameType const&, std::vector<int>&);
     /// Split selected atoms in a residue into a new residue
     int SplitResidue(AtomMask const&, NameType const&);
-    /// Append topology to this one.
-    int AppendTop( Topology const& );
+    
   private:
     typedef std::vector<std::string> Sarray;
 
@@ -312,8 +322,6 @@ class Topology {
     void genBondParam(BondType&, BP_mapType&);
     /// Fill in bond parameters with estimations based on atomic element types
     void generateBondParameters();
-    /// \return Index of existing/added dihedral parameter in given array
-    static inline int addTorsionParm(DihedralParmArray&, DihedralParmType const&);
     /// \return Index of existing/added bond parameter in given array
     static inline int addBondParm(BondParmArray&, BondParmType const&);
     /// \return Index of existing/added angle parameter in given array
@@ -323,15 +331,12 @@ class Topology {
                                                    DihedralParmArray const&,
                                                    int, const char*);
     inline bool CheckExtraSize(size_t, const char*) const;
-    /// Add an atom to the topology inside given residue and molecule number
-    int addTopAtom(Atom const&, Residue const&, unsigned int, bool);
 
     void VisitAtom(int, int);
     int RecursiveMolSearch();
     int NonrecursiveMolSearch();
     void ClearMolecules();
     void AtomDistance(int, int, int, std::set<int>&, int) const;
-    void DetermineNumExtraPoints();
     int SetSolventInfo();
 
     int scale_dihedral_K(DihedralArray&, CharMask const&, double, bool);
@@ -348,23 +353,6 @@ class Topology {
     void StripDihedralParmArray(DihedralArray&, std::vector<int>&, DihedralParmArray&,
                                 DihedralParmArray const&) const;
 
-    void AssignAtomTypeParm(ParmHolder<AtomType> const&);
-    void AssignBondParm(ParmHolder<BondParmType> const&, BondArray&, BondParmArray&, const char*) const;
-    AngleArray AssignAngleParm(ParmHolder<AngleParmType> const&, AngleArray const&);
-    void warn_improper_reorder(DihedralType const&, DihedralType const&) const;
-    void AssignImproperParm(ImproperParmHolder const&, DihedralArray&, DihedralParmArray&) const;
-    inline DihedralArray get_unique_dihedrals(DihedralArray const&) const;
-    DihedralArray AssignDihedralParm(DihedralParmHolder const&, ImproperParmHolder const&,
-                                     ParmHolder<AtomType> const&, DihedralArray const&, bool);
-
-    /// Remap CMAP parameter indices to match incoming parameter order
-    int remap_cmap_indices(std::vector<int>&, CmapGridArray&, CmapArray&, CmapParmHolder const&) const;
-    /// Assign CMAP parameters and terms
-    int AssignCmapParams(DihedralArray const&, CmapParmHolder const&, CmapGridArray&, CmapArray&) const;
-    /// Assign CMAP parameters
-    int AssignCmapParams(CmapArray&, CmapParmHolder const&, CmapGridArray&) const;
-
-
     static const NonbondType LJ_EMPTY;
     std::vector<Atom> atoms_;
     std::vector<Residue> residues_;
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 04fec42fea..e903601512 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -1,154 +1,154 @@
 ActionFrameCounter.o : ActionFrameCounter.cpp ActionFrameCounter.h ArgList.h CpptrajStdio.h
-ActionList.o : ActionList.cpp Action.h ActionList.h ActionState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-ActionTopWriter.o : ActionTopWriter.cpp ActionState.h ActionTopWriter.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_AddAtom.o : Action_AddAtom.cpp Action.h ActionState.h ActionTopWriter.h Action_AddAtom.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Align.o : Action_Align.cpp Action.h ActionState.h Action_Align.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Angle.o : Action_Angle.cpp Action.h ActionState.h Action_Angle.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Action_AreaPerMol.o : Action_AreaPerMol.cpp Action.h ActionState.h Action_AreaPerMol.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_AtomMap.o : Action_AtomMap.cpp Action.h ActionState.h Action_AtomMap.h ArgList.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h StructureMapper.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_AtomicCorr.o : Action_AtomicCorr.cpp Action.h ActionState.h Action_AtomicCorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_AtomicFluct.o : Action_AtomicFluct.cpp Action.h ActionFrameCounter.h ActionState.h Action_AtomicFluct.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_AutoImage.o : Action_AutoImage.cpp Action.h ActionState.h Action_AutoImage.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h ImageRoutines.h ImageTypes.h Image_List.h Image_List_Unit.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Average.o : Action_Average.cpp Action.h ActionFrameCounter.h ActionState.h Action_Average.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-Action_AvgBox.o : Action_AvgBox.cpp Action.h ActionState.h Action_AvgBox.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Bounds.o : Action_Bounds.cpp Action.h ActionState.h Action_Bounds.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Box.o : Action_Box.cpp Action.h ActionState.h Action_Box.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BoxArgs.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Center.o : Action_Center.cpp Action.h ActionState.h Action_Center.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Channel.o : Action_Channel.cpp Action.h ActionState.h Action_Channel.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_CheckChirality.o : Action_CheckChirality.cpp Action.h ActionState.h Action_CheckChirality.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h Structure/Chirality.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Action_CheckStructure.o : Action_CheckStructure.cpp Action.h ActionState.h Action_CheckStructure.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_integer.h DataSet_string.h Dimension.h DispatchObject.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/RingFinder.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Closest.o : Action_Closest.cpp Action.h ActionState.h ActionTopWriter.h Action_Closest.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h ImageRoutines.h ImageTypes.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h cuda_kernels/kernel_wrappers.cuh
-Action_ClusterDihedral.o : Action_ClusterDihedral.cpp Action.h ActionState.h Action_ClusterDihedral.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_integer.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Action_Contacts.o : Action_Contacts.cpp Action.h ActionState.h Action_Contacts.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_CreateCrd.o : Action_CreateCrd.cpp Action.h ActionState.h Action_CreateCrd.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_CreateReservoir.o : Action_CreateReservoir.cpp Action.h ActionState.h Action_CreateReservoir.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h RemdReservoirNC.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_DNAionTracker.o : Action_DNAionTracker.cpp Action.h ActionState.h Action_DNAionTracker.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_DSSP.o : Action_DSSP.cpp Action.h ActionState.h Action_DSSP.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Density.o : Action_Density.cpp Action.h ActionState.h Action_Density.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Diffusion.o : Action_Diffusion.cpp Action.h ActionState.h Action_Diffusion.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_double.h DiffusionResults.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Dihedral.o : Action_Dihedral.cpp Action.h ActionState.h Action_Dihedral.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Action_DihedralRMS.o : Action_DihedralRMS.cpp Action.h ActionState.h Action_DihedralRMS.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Action_Dipole.o : Action_Dipole.cpp Action.h ActionState.h Action_Dipole.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridAction.h GridBin.h GridMover.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_DistRmsd.o : Action_DistRmsd.cpp Action.h ActionState.h Action_DistRmsd.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Distance.o : Action_Distance.cpp Action.h ActionState.h Action_Distance.h ArgList.h AssociatedData.h AssociatedData_NOE.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Energy.o : Action_Energy.cpp Action.h ActionState.h Action_Energy.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h Energy.h EnergyArray.h Ewald.h EwaldOptions.h Ewald_ParticleMesh.h Ewald_Regular.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h helpme_standalone.h
-Action_Esander.o : Action_Esander.cpp Action.h ActionState.h Action_Esander.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h Energy_Sander.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_FilterByData.o : Action_FilterByData.cpp Action.h ActionState.h Action_FilterByData.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_FixAtomOrder.o : Action_FixAtomOrder.cpp Action.h ActionState.h ActionTopWriter.h Action_FixAtomOrder.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomTopType.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_FixImagedBonds.o : Action_FixImagedBonds.cpp Action.h ActionState.h Action_FixImagedBonds.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_GIST.o : Action_GIST.cpp Action.h ActionState.h Action_GIST.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridDbl.h DataSet_GridFlt.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h DistRoutines.h Ewald.h EwaldOptions.h Ewald_ParticleMesh.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h GIST_PME.h GistEntropyUtils.h Grid.h GridBin.h GridMover.h ImageOption.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h cuda_kernels/GistCudaSetup.cuh helpme_standalone.h
-Action_Grid.o : Action_Grid.cpp Action.h ActionState.h Action_Grid.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridAction.h GridBin.h GridMover.h MaskArray.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_GridFreeEnergy.o : Action_GridFreeEnergy.cpp Action.h ActionState.h Action_GridFreeEnergy.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridAction.h GridBin.h GridMover.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_HydrogenBond.o : Action_HydrogenBond.cpp Action.h ActionState.h Action_HydrogenBond.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_integer.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Action_Image.o : Action_Image.cpp Action.h ActionState.h Action_Image.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h ImageRoutines.h ImageTypes.h Image_List.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_InfraredSpectrum.o : Action_InfraredSpectrum.cpp Action.h ActionState.h Action_InfraredSpectrum.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Jcoupling.o : Action_Jcoupling.cpp Action.h ActionState.h Action_Jcoupling.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Action_Keep.o : Action_Keep.cpp Action.h ActionState.h ActionTopWriter.h Action_Keep.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_string.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_LESsplit.o : Action_LESsplit.cpp Action.h ActionFrameCounter.h ActionState.h Action_LESsplit.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-Action_LIE.o : Action_LIE.cpp Action.h ActionState.h Action_LIE.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_LipidOrder.o : Action_LipidOrder.cpp Action.h ActionState.h Action_LipidOrder.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_MakeStructure.o : Action_MakeStructure.cpp Action.h ActionState.h Action_MakeStructure.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Action_Mask.o : Action_Mask.cpp Action.h ActionFrameCounter.h ActionState.h Action_Mask.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-Action_Matrix.o : Action_Matrix.cpp Action.h ActionFrameCounter.h ActionState.h Action_Matrix.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Vector.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_MinImage.o : Action_MinImage.cpp Action.h ActionState.h Action_MinImage.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_MinMaxDist.o : Action_MinMaxDist.cpp Action.h ActionState.h Action_MinMaxDist.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h InteractionData.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Molsurf.o : Action_Molsurf.cpp Action.h ActionState.h Action_Molsurf.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h molsurf.h
-Action_MultiDihedral.o : Action_MultiDihedral.cpp Action.h ActionState.h Action_MultiDihedral.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DihedralSearch.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Action_MultiPucker.o : Action_MultiPucker.cpp Action.h ActionState.h Action_MultiPucker.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Pucker.h Pucker_PuckerMask.h Pucker_PuckerSearch.h Pucker_PuckerToken.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Action_MultiVector.o : Action_MultiVector.cpp Action.h ActionState.h Action_MultiVector.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_NAstruct.o : Action_NAstruct.cpp Action.h ActionFrameCounter.h ActionState.h Action_NAstruct.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h AxisType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_float.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-Action_NMRrst.o : Action_NMRrst.cpp Action.h ActionState.h Action_NMRrst.h ArgList.h AssociatedData.h AssociatedData_NOE.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_float.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h ViewRst.h
-Action_NativeContacts.o : Action_NativeContacts.cpp Action.h ActionState.h Action_NativeContacts.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_integer.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_OrderParameter.o : Action_OrderParameter.cpp Action.h ActionState.h Action_OrderParameter.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Outtraj.o : Action_Outtraj.cpp Action.h ActionFrameCounter.h ActionState.h Action_Outtraj.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-Action_PairDist.o : Action_PairDist.cpp Action.h ActionState.h Action_PairDist.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Pairwise.o : Action_Pairwise.cpp Action.h ActionFrameCounter.h ActionState.h Action_Pairwise.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h Dimension.h DispatchObject.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-Action_Principal.o : Action_Principal.cpp Action.h ActionState.h Action_Principal.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Projection.o : Action_Projection.cpp Action.h ActionFrameCounter.h ActionState.h Action_Projection.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Modes.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Pucker.o : Action_Pucker.cpp Action.h ActionState.h Action_Pucker.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Action_Radgyr.o : Action_Radgyr.cpp Action.h ActionState.h Action_Radgyr.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Radial.o : Action_Radial.cpp Action.h ActionState.h Action_Radial.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h Gpu.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h cuda_kernels/kernel_rdf.cuh
-Action_RandomizeIons.o : Action_RandomizeIons.cpp Action.h ActionState.h Action_RandomizeIons.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Remap.o : Action_Remap.cpp Action.h ActionState.h ActionTopWriter.h Action_Remap.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_ReplicateCell.o : Action_ReplicateCell.cpp Action.h ActionFrameCounter.h ActionState.h ActionTopWriter.h Action_ReplicateCell.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-Action_Rmsd.o : Action_Rmsd.cpp Action.h ActionState.h Action_Rmsd.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Rotate.o : Action_Rotate.cpp Action.h ActionState.h Action_Rotate.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_RunningAvg.o : Action_RunningAvg.cpp Action.h ActionState.h Action_RunningAvg.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_STFC_Diffusion.o : Action_STFC_Diffusion.cpp Action.h ActionState.h Action_STFC_Diffusion.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Scale.o : Action_Scale.cpp Action.h ActionState.h Action_Scale.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_SetVelocity.o : Action_SetVelocity.cpp Action.h ActionState.h Action_SetVelocity.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Spam.o : Action_Spam.cpp Action.h ActionState.h Action_Spam.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_Peaks.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h DataSet_Vector_Scalar.h DataSet_double.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h HistBin.h ImageOption.h KDE.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Strip.o : Action_Strip.cpp Action.h ActionState.h ActionTopWriter.h Action_Strip.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Surf.o : Action_Surf.cpp Action.h ActionState.h Action_Surf.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_SymmetricRmsd.o : Action_SymmetricRmsd.cpp Action.h ActionState.h Action_SymmetricRmsd.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h Hungarian.h ImageOption.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Temperature.o : Action_Temperature.cpp Action.h ActionState.h Action_Temperature.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Time.o : Action_Time.cpp Action.h ActionState.h Action_Time.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_ToroidalDiffusion.o : Action_ToroidalDiffusion.cpp Action.h ActionState.h Action_ToroidalDiffusion.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DiffusionResults.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Translate.o : Action_Translate.cpp Action.h ActionState.h Action_Translate.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Unstrip.o : Action_Unstrip.cpp Action.h ActionState.h Action_Unstrip.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Unwrap.o : Action_Unwrap.cpp Action.h ActionState.h Action_Unwrap.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h ImageRoutines.h ImageTypes.h Image_List.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Vector.o : Action_Vector.cpp Action.h ActionState.h Action_Vector.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h GridBin.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/LeastSquaresPlane.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_VelocityAutoCorr.o : Action_VelocityAutoCorr.cpp Action.h ActionState.h Action_VelocityAutoCorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Volmap.o : Action_Volmap.cpp Action.h ActionState.h Action_Volmap.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridDbl.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Volume.o : Action_Volume.cpp Action.h ActionState.h Action_Volume.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Watershell.o : Action_Watershell.cpp Action.h ActionState.h Action_Watershell.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h ImageRoutines.h ImageTypes.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h cuda_kernels/kernel_wrappers.cuh
-Action_XtalSymm.o : Action_XtalSymm.cpp Action.h ActionState.h Action_XtalSymm.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SpaceGroup.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+ActionList.o : ActionList.cpp Action.h ActionList.h ActionState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+ActionTopWriter.o : ActionTopWriter.cpp ActionState.h ActionTopWriter.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_AddAtom.o : Action_AddAtom.cpp Action.h ActionState.h ActionTopWriter.h Action_AddAtom.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Align.o : Action_Align.cpp Action.h ActionState.h Action_Align.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Angle.o : Action_Angle.cpp Action.h ActionState.h Action_Angle.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h Unit.h Vec3.h
+Action_AreaPerMol.o : Action_AreaPerMol.cpp Action.h ActionState.h Action_AreaPerMol.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_AtomMap.o : Action_AtomMap.cpp Action.h ActionState.h Action_AtomMap.h ArgList.h AssociatedData.h Atom.h AtomMap.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h StructureMapper.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_AtomicCorr.o : Action_AtomicCorr.cpp Action.h ActionState.h Action_AtomicCorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_AtomicFluct.o : Action_AtomicFluct.cpp Action.h ActionFrameCounter.h ActionState.h Action_AtomicFluct.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_AutoImage.o : Action_AutoImage.cpp Action.h ActionState.h Action_AutoImage.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h ImageRoutines.h ImageTypes.h Image_List.h Image_List_Unit.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Average.o : Action_Average.cpp Action.h ActionFrameCounter.h ActionState.h Action_Average.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h Unit.h Vec3.h
+Action_AvgBox.o : Action_AvgBox.cpp Action.h ActionState.h Action_AvgBox.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Bounds.o : Action_Bounds.cpp Action.h ActionState.h Action_Bounds.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Box.o : Action_Box.cpp Action.h ActionState.h Action_Box.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BoxArgs.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Center.o : Action_Center.cpp Action.h ActionState.h Action_Center.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Channel.o : Action_Channel.cpp Action.h ActionState.h Action_Channel.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_CheckChirality.o : Action_CheckChirality.cpp Action.h ActionState.h Action_CheckChirality.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h Structure/Chirality.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h Unit.h Vec3.h
+Action_CheckStructure.o : Action_CheckStructure.cpp Action.h ActionState.h Action_CheckStructure.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_integer.h DataSet_string.h Dimension.h DispatchObject.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PairList.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/RingFinder.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Closest.o : Action_Closest.cpp Action.h ActionState.h ActionTopWriter.h Action_Closest.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h ImageRoutines.h ImageTypes.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h cuda_kernels/kernel_wrappers.cuh
+Action_ClusterDihedral.o : Action_ClusterDihedral.cpp Action.h ActionState.h Action_ClusterDihedral.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_integer.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h Unit.h Vec3.h
+Action_Contacts.o : Action_Contacts.cpp Action.h ActionState.h Action_Contacts.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_CreateCrd.o : Action_CreateCrd.cpp Action.h ActionState.h Action_CreateCrd.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_CreateReservoir.o : Action_CreateReservoir.cpp Action.h ActionState.h Action_CreateReservoir.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h RemdReservoirNC.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_DNAionTracker.o : Action_DNAionTracker.cpp Action.h ActionState.h Action_DNAionTracker.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_DSSP.o : Action_DSSP.cpp Action.h ActionState.h Action_DSSP.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Density.o : Action_Density.cpp Action.h ActionState.h Action_Density.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Diffusion.o : Action_Diffusion.cpp Action.h ActionState.h Action_Diffusion.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_double.h DiffusionResults.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Dihedral.o : Action_Dihedral.cpp Action.h ActionState.h Action_Dihedral.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h Unit.h Vec3.h
+Action_DihedralRMS.o : Action_DihedralRMS.cpp Action.h ActionState.h Action_DihedralRMS.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h Unit.h Vec3.h
+Action_Dipole.o : Action_Dipole.cpp Action.h ActionState.h Action_Dipole.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridAction.h GridBin.h GridMover.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_DistRmsd.o : Action_DistRmsd.cpp Action.h ActionState.h Action_DistRmsd.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Distance.o : Action_Distance.cpp Action.h ActionState.h Action_Distance.h ArgList.h AssociatedData.h AssociatedData_NOE.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Energy.o : Action_Energy.cpp Action.h ActionState.h Action_Energy.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h Energy.h EnergyArray.h Ewald.h EwaldOptions.h Ewald_ParticleMesh.h Ewald_Regular.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Molecule.h NameType.h PairList.h Parallel.h ParameterTypes.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h helpme_standalone.h
+Action_Esander.o : Action_Esander.cpp Action.h ActionState.h Action_Esander.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h Energy_Sander.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_FilterByData.o : Action_FilterByData.cpp Action.h ActionState.h Action_FilterByData.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_FixAtomOrder.o : Action_FixAtomOrder.cpp Action.h ActionState.h ActionTopWriter.h Action_FixAtomOrder.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomTopType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_FixImagedBonds.o : Action_FixImagedBonds.cpp Action.h ActionState.h Action_FixImagedBonds.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_GIST.o : Action_GIST.cpp Action.h ActionState.h Action_GIST.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridDbl.h DataSet_GridFlt.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h DistRoutines.h Ewald.h EwaldOptions.h Ewald_ParticleMesh.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h GIST_PME.h GistEntropyUtils.h Grid.h GridBin.h GridMover.h ImageOption.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PairList.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h cuda_kernels/GistCudaSetup.cuh helpme_standalone.h
+Action_Grid.o : Action_Grid.cpp Action.h ActionState.h Action_Grid.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridAction.h GridBin.h GridMover.h MaskArray.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_GridFreeEnergy.o : Action_GridFreeEnergy.cpp Action.h ActionState.h Action_GridFreeEnergy.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridAction.h GridBin.h GridMover.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_HydrogenBond.o : Action_HydrogenBond.cpp Action.h ActionState.h Action_HydrogenBond.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_integer.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h Unit.h Vec3.h
+Action_Image.o : Action_Image.cpp Action.h ActionState.h Action_Image.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h ImageRoutines.h ImageTypes.h Image_List.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_InfraredSpectrum.o : Action_InfraredSpectrum.cpp Action.h ActionState.h Action_InfraredSpectrum.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Jcoupling.o : Action_Jcoupling.cpp Action.h ActionState.h Action_Jcoupling.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h Unit.h Vec3.h
+Action_Keep.o : Action_Keep.cpp Action.h ActionState.h ActionTopWriter.h Action_Keep.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_string.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_LESsplit.o : Action_LESsplit.cpp Action.h ActionFrameCounter.h ActionState.h Action_LESsplit.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h Unit.h Vec3.h
+Action_LIE.o : Action_LIE.cpp Action.h ActionState.h Action_LIE.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_LipidOrder.o : Action_LipidOrder.cpp Action.h ActionState.h Action_LipidOrder.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_MakeStructure.o : Action_MakeStructure.cpp Action.h ActionState.h Action_MakeStructure.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h Unit.h Vec3.h
+Action_Mask.o : Action_Mask.cpp Action.h ActionFrameCounter.h ActionState.h Action_Mask.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h Unit.h Vec3.h
+Action_Matrix.o : Action_Matrix.cpp Action.h ActionFrameCounter.h ActionState.h Action_Matrix.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Vector.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_MinImage.o : Action_MinImage.cpp Action.h ActionState.h Action_MinImage.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_MinMaxDist.o : Action_MinMaxDist.cpp Action.h ActionState.h Action_MinMaxDist.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h InteractionData.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Molsurf.o : Action_Molsurf.cpp Action.h ActionState.h Action_Molsurf.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h molsurf.h
+Action_MultiDihedral.o : Action_MultiDihedral.cpp Action.h ActionState.h Action_MultiDihedral.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DihedralSearch.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h Unit.h Vec3.h
+Action_MultiPucker.o : Action_MultiPucker.cpp Action.h ActionState.h Action_MultiPucker.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Pucker.h Pucker_PuckerMask.h Pucker_PuckerSearch.h Pucker_PuckerToken.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h Unit.h Vec3.h
+Action_MultiVector.o : Action_MultiVector.cpp Action.h ActionState.h Action_MultiVector.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_NAstruct.o : Action_NAstruct.cpp Action.h ActionFrameCounter.h ActionState.h Action_NAstruct.h ArgList.h AssociatedData.h Atom.h AtomMask.h AxisType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_float.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PDBfile.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h Unit.h Vec3.h
+Action_NMRrst.o : Action_NMRrst.cpp Action.h ActionState.h Action_NMRrst.h ArgList.h AssociatedData.h AssociatedData_NOE.h Atom.h AtomMap.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_float.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h ViewRst.h
+Action_NativeContacts.o : Action_NativeContacts.cpp Action.h ActionState.h Action_NativeContacts.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_integer.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_OrderParameter.o : Action_OrderParameter.cpp Action.h ActionState.h Action_OrderParameter.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Outtraj.o : Action_Outtraj.cpp Action.h ActionFrameCounter.h ActionState.h Action_Outtraj.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h Unit.h Vec3.h
+Action_PairDist.o : Action_PairDist.cpp Action.h ActionState.h Action_PairDist.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Pairwise.o : Action_Pairwise.cpp Action.h ActionFrameCounter.h ActionState.h Action_Pairwise.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h Dimension.h DispatchObject.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PDBfile.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h Unit.h Vec3.h
+Action_Principal.o : Action_Principal.cpp Action.h ActionState.h Action_Principal.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Projection.o : Action_Projection.cpp Action.h ActionFrameCounter.h ActionState.h Action_Projection.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Modes.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Pucker.o : Action_Pucker.cpp Action.h ActionState.h Action_Pucker.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h Unit.h Vec3.h
+Action_Radgyr.o : Action_Radgyr.cpp Action.h ActionState.h Action_Radgyr.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Radial.o : Action_Radial.cpp Action.h ActionState.h Action_Radial.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h Gpu.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h cuda_kernels/kernel_rdf.cuh
+Action_RandomizeIons.o : Action_RandomizeIons.cpp Action.h ActionState.h Action_RandomizeIons.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Remap.o : Action_Remap.cpp Action.h ActionState.h ActionTopWriter.h Action_Remap.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_ReplicateCell.o : Action_ReplicateCell.cpp Action.h ActionFrameCounter.h ActionState.h ActionTopWriter.h Action_ReplicateCell.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h Unit.h Vec3.h
+Action_Rmsd.o : Action_Rmsd.cpp Action.h ActionState.h Action_Rmsd.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Rotate.o : Action_Rotate.cpp Action.h ActionState.h Action_Rotate.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_RunningAvg.o : Action_RunningAvg.cpp Action.h ActionState.h Action_RunningAvg.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_STFC_Diffusion.o : Action_STFC_Diffusion.cpp Action.h ActionState.h Action_STFC_Diffusion.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Scale.o : Action_Scale.cpp Action.h ActionState.h Action_Scale.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_SetVelocity.o : Action_SetVelocity.cpp Action.h ActionState.h Action_SetVelocity.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Spam.o : Action_Spam.cpp Action.h ActionState.h Action_Spam.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_Peaks.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h DataSet_Vector_Scalar.h DataSet_double.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h HistBin.h ImageOption.h KDE.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h PairList.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Strip.o : Action_Strip.cpp Action.h ActionState.h ActionTopWriter.h Action_Strip.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Surf.o : Action_Surf.cpp Action.h ActionState.h Action_Surf.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_SymmetricRmsd.o : Action_SymmetricRmsd.cpp Action.h ActionState.h Action_SymmetricRmsd.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h Hungarian.h ImageOption.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Temperature.o : Action_Temperature.cpp Action.h ActionState.h Action_Temperature.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Time.o : Action_Time.cpp Action.h ActionState.h Action_Time.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_ToroidalDiffusion.o : Action_ToroidalDiffusion.cpp Action.h ActionState.h Action_ToroidalDiffusion.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DiffusionResults.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Translate.o : Action_Translate.cpp Action.h ActionState.h Action_Translate.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Unstrip.o : Action_Unstrip.cpp Action.h ActionState.h Action_Unstrip.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Unwrap.o : Action_Unwrap.cpp Action.h ActionState.h Action_Unwrap.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h ImageRoutines.h ImageTypes.h Image_List.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Vector.o : Action_Vector.cpp Action.h ActionState.h Action_Vector.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h GridBin.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/LeastSquaresPlane.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_VelocityAutoCorr.o : Action_VelocityAutoCorr.cpp Action.h ActionState.h Action_VelocityAutoCorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Volmap.o : Action_Volmap.cpp Action.h ActionState.h Action_Volmap.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridDbl.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Volume.o : Action_Volume.cpp Action.h ActionState.h Action_Volume.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Watershell.o : Action_Watershell.cpp Action.h ActionState.h Action_Watershell.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h ImageRoutines.h ImageTypes.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h cuda_kernels/kernel_wrappers.cuh
+Action_XtalSymm.o : Action_XtalSymm.cpp Action.h ActionState.h Action_XtalSymm.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SpaceGroup.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 AmberParamFile.o : AmberParamFile.cpp AmberParamFile.h ArgList.h AtomType.h BufferedLine.h CmapParmHolder.h Constants.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h StringRoutines.h TypeNameHolder.h
-AnalysisList.o : AnalysisList.cpp ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_AmdBias.o : Analysis_AmdBias.cpp ActionState.h Analysis.h AnalysisState.h Analysis_AmdBias.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_AutoCorr.o : Analysis_AutoCorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_AutoCorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Average.o : Analysis_Average.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Average.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_CalcDiffusion.o : Analysis_CalcDiffusion.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CalcDiffusion.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_double.h DiffusionResults.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Clustering.o : Analysis_Clustering.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Clustering.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/Algorithm.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Control.h Cluster/DrawGraph.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Sieve.h Cluster/Silhouette.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_ConstantPHStats.o : Analysis_ConstantPHStats.cpp ActionState.h Analysis.h AnalysisState.h Analysis_ConstantPHStats.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h DataSet_pH.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Corr.o : Analysis_Corr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Corr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_CrankShaft.o : Analysis_CrankShaft.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CrankShaft.h Analysis_Statistics.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_float.h DataSet_integer.h DataSet_string.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_CrdFluct.o : Analysis_CrdFluct.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CrdFluct.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_CrossCorr.o : Analysis_CrossCorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CrossCorr.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_CurveFit.o : Analysis_CurveFit.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CurveFit.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h CurveFit.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Divergence.o : Analysis_Divergence.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Divergence.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_EvalPlateau.o : Analysis_EvalPlateau.cpp ActionState.h Analysis.h AnalysisState.h Analysis_EvalPlateau.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h CurveFit.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_FFT.o : Analysis_FFT.cpp ActionState.h Analysis.h AnalysisState.h Analysis_FFT.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_HausdorffDistance.o : Analysis_HausdorffDistance.cpp ActionState.h Analysis.h AnalysisState.h Analysis_HausdorffDistance.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Hist.o : Analysis_Hist.cpp ActionFrameCounter.h ActionState.h Analysis.h AnalysisState.h Analysis_Hist.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridBin.h HistBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_IRED.o : Analysis_IRED.cpp ActionState.h Analysis.h AnalysisState.h Analysis_IRED.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Integrate.o : Analysis_Integrate.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Integrate.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_KDE.o : Analysis_KDE.cpp ActionState.h Analysis.h AnalysisState.h Analysis_KDE.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h HistBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Lifetime.o : Analysis_Lifetime.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Lifetime.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_LowestCurve.o : Analysis_LowestCurve.cpp ActionState.h Analysis.h AnalysisState.h Analysis_LowestCurve.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h HistBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Matrix.o : Analysis_Matrix.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Matrix.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_MeltCurve.o : Analysis_MeltCurve.cpp ActionState.h Analysis.h AnalysisState.h Analysis_MeltCurve.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Modes.o : Analysis_Modes.cpp ActionFrameCounter.h ActionState.h Analysis.h AnalysisState.h Analysis_Modes.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Modes.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_MultiHist.o : Analysis_MultiHist.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Hist.h Analysis_KDE.h Analysis_MultiHist.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h HistBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Multicurve.o : Analysis_Multicurve.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CurveFit.h Analysis_Multicurve.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Overlap.o : Analysis_Overlap.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Overlap.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_PhiPsi.o : Analysis_PhiPsi.cpp ActionState.h Analysis.h AnalysisState.h Analysis_PhiPsi.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Project.o : Analysis_Project.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Project.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Modes.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Regression.o : Analysis_Regression.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Regression.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_RemLog.o : Analysis_RemLog.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Lifetime.h Analysis_RemLog.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h DataSet_RemLog.h DataSet_integer.h DataSet_integer_mem.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Rms2d.o : Analysis_Rms2d.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Rms2d.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Hungarian.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h QuaternionRMSD.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_RmsAvgCorr.o : Analysis_RmsAvgCorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_RmsAvgCorr.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Rotdif.o : Analysis_Rotdif.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Rotdif.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h CurveFit.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_Mesh.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h PubFFT.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SimplexMin.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_RunningAvg.o : Analysis_RunningAvg.cpp ActionState.h Analysis.h AnalysisState.h Analysis_RunningAvg.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Slope.o : Analysis_Slope.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Slope.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Spline.o : Analysis_Spline.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Spline.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_State.o : Analysis_State.cpp ActionState.h Analysis.h AnalysisState.h Analysis_State.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Statistics.o : Analysis_Statistics.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Statistics.h ArgList.h Array1D.h AssociatedData.h AssociatedData_NOE.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_float.h DataSet_integer.h DataSet_string.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_TI.o : Analysis_TI.cpp ActionState.h Analysis.h AnalysisState.h Analysis_TI.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_TICA.o : Analysis_TICA.cpp ActionState.h Analysis.h AnalysisState.h Analysis_TICA.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordCovarMatrix.h CoordCovarMatrix_Full.h CoordCovarMatrix_Half.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Timecorr.o : Analysis_Timecorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Timecorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_VectorMath.o : Analysis_VectorMath.cpp ActionState.h Analysis.h AnalysisState.h Analysis_VectorMath.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Wavelet.o : Analysis_Wavelet.cpp ActionFrameCounter.h ActionState.h Analysis.h AnalysisState.h Analysis_Wavelet.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ClusterMap.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h ProgressBar.h ProgressTimer.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+AnalysisList.o : AnalysisList.cpp ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_AmdBias.o : Analysis_AmdBias.cpp ActionState.h Analysis.h AnalysisState.h Analysis_AmdBias.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_AutoCorr.o : Analysis_AutoCorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_AutoCorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_Average.o : Analysis_Average.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Average.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_CalcDiffusion.o : Analysis_CalcDiffusion.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CalcDiffusion.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_double.h DiffusionResults.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_Clustering.o : Analysis_Clustering.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Clustering.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cluster/Algorithm.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Control.h Cluster/DrawGraph.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Sieve.h Cluster/Silhouette.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_ConstantPHStats.o : Analysis_ConstantPHStats.cpp ActionState.h Analysis.h AnalysisState.h Analysis_ConstantPHStats.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h DataSet_pH.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_Corr.o : Analysis_Corr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Corr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_CrankShaft.o : Analysis_CrankShaft.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CrankShaft.h Analysis_Statistics.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_float.h DataSet_integer.h DataSet_string.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_CrdFluct.o : Analysis_CrdFluct.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CrdFluct.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_CrossCorr.o : Analysis_CrossCorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CrossCorr.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_CurveFit.o : Analysis_CurveFit.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CurveFit.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h CurveFit.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_Divergence.o : Analysis_Divergence.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Divergence.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_EvalPlateau.o : Analysis_EvalPlateau.cpp ActionState.h Analysis.h AnalysisState.h Analysis_EvalPlateau.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h CurveFit.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_FFT.o : Analysis_FFT.cpp ActionState.h Analysis.h AnalysisState.h Analysis_FFT.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_HausdorffDistance.o : Analysis_HausdorffDistance.cpp ActionState.h Analysis.h AnalysisState.h Analysis_HausdorffDistance.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_Hist.o : Analysis_Hist.cpp ActionFrameCounter.h ActionState.h Analysis.h AnalysisState.h Analysis_Hist.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridBin.h HistBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h Unit.h Vec3.h
+Analysis_IRED.o : Analysis_IRED.cpp ActionState.h Analysis.h AnalysisState.h Analysis_IRED.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_Integrate.o : Analysis_Integrate.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Integrate.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_KDE.o : Analysis_KDE.cpp ActionState.h Analysis.h AnalysisState.h Analysis_KDE.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h HistBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_Lifetime.o : Analysis_Lifetime.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Lifetime.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_LowestCurve.o : Analysis_LowestCurve.cpp ActionState.h Analysis.h AnalysisState.h Analysis_LowestCurve.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h HistBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_Matrix.o : Analysis_Matrix.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Matrix.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_MeltCurve.o : Analysis_MeltCurve.cpp ActionState.h Analysis.h AnalysisState.h Analysis_MeltCurve.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_Modes.o : Analysis_Modes.cpp ActionFrameCounter.h ActionState.h Analysis.h AnalysisState.h Analysis_Modes.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Modes.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h Unit.h Vec3.h
+Analysis_MultiHist.o : Analysis_MultiHist.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Hist.h Analysis_KDE.h Analysis_MultiHist.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h HistBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Unit.h Vec3.h
+Analysis_Multicurve.o : Analysis_Multicurve.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CurveFit.h Analysis_Multicurve.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_Overlap.o : Analysis_Overlap.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Overlap.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_PhiPsi.o : Analysis_PhiPsi.cpp ActionState.h Analysis.h AnalysisState.h Analysis_PhiPsi.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_Project.o : Analysis_Project.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Project.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Modes.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_Regression.o : Analysis_Regression.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Regression.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_RemLog.o : Analysis_RemLog.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Lifetime.h Analysis_RemLog.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h DataSet_RemLog.h DataSet_integer.h DataSet_integer_mem.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_Rms2d.o : Analysis_Rms2d.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Rms2d.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Hungarian.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h QuaternionRMSD.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h Unit.h Vec3.h
+Analysis_RmsAvgCorr.o : Analysis_RmsAvgCorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_RmsAvgCorr.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_Rotdif.o : Analysis_Rotdif.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Rotdif.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h CurveFit.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_Mesh.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h PubFFT.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SimplexMin.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_RunningAvg.o : Analysis_RunningAvg.cpp ActionState.h Analysis.h AnalysisState.h Analysis_RunningAvg.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_Slope.o : Analysis_Slope.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Slope.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_Spline.o : Analysis_Spline.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Spline.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_State.o : Analysis_State.cpp ActionState.h Analysis.h AnalysisState.h Analysis_State.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_Statistics.o : Analysis_Statistics.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Statistics.h ArgList.h Array1D.h AssociatedData.h AssociatedData_NOE.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_float.h DataSet_integer.h DataSet_string.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_TI.o : Analysis_TI.cpp ActionState.h Analysis.h AnalysisState.h Analysis_TI.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_TICA.o : Analysis_TICA.cpp ActionState.h Analysis.h AnalysisState.h Analysis_TICA.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordCovarMatrix.h CoordCovarMatrix_Full.h CoordCovarMatrix_Half.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_Timecorr.o : Analysis_Timecorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Timecorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_VectorMath.o : Analysis_VectorMath.cpp ActionState.h Analysis.h AnalysisState.h Analysis_VectorMath.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_Wavelet.o : Analysis_Wavelet.cpp ActionFrameCounter.h ActionState.h Analysis.h AnalysisState.h Analysis_Wavelet.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ClusterMap.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h ParmFile.h ProgressBar.h ProgressTimer.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h Unit.h Vec3.h
 ArgList.o : ArgList.cpp ArgList.h CpptrajStdio.h StringRoutines.h
-Array1D.o : Array1D.cpp ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Array1D.o : Array1D.cpp ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 AssociatedData_Connect.o : AssociatedData_Connect.cpp ArgList.h AssociatedData.h AssociatedData_Connect.h CpptrajStdio.h
 AssociatedData_NOE.o : AssociatedData_NOE.cpp ArgList.h AssociatedData.h AssociatedData_NOE.h CpptrajStdio.h
 AssociatedData_ResId.o : AssociatedData_ResId.cpp AssociatedData.h AssociatedData_ResId.h CpptrajStdio.h NameType.h Structure/StructureEnum.h
 Atom.o : Atom.cpp Atom.h CpptrajStdio.h NameType.h SymbolExporting.h
-AtomMap.o : AtomMap.cpp Atom.h AtomMap.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+AtomMap.o : AtomMap.cpp Atom.h AtomMap.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
 AtomMask.o : AtomMask.cpp Atom.h AtomMask.h CpptrajStdio.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h SymbolExporting.h Unit.h
-AxisType.o : AxisType.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h AxisType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-BondSearch.o : BondSearch.cpp Atom.h AtomMask.h AtomType.h BondSearch.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+AxisType.o : AxisType.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AxisType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h Unit.h Vec3.h
+BondSearch.o : BondSearch.cpp Atom.h AtomMask.h BondSearch.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Timer.h Topology.h Unit.h Vec3.h
 Box.o : Box.cpp Box.h Constants.h CpptrajStdio.h Matrix_3x3.h Parallel.h Vec3.h
 BoxArgs.o : BoxArgs.cpp ArgList.h Box.h BoxArgs.h CpptrajStdio.h Matrix_3x3.h Parallel.h Vec3.h
 BufferedFrame.o : BufferedFrame.cpp BufferedFrame.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Parallel.h TextFormat.h
@@ -158,7 +158,7 @@ CIFfile.o : CIFfile.cpp ArgList.h Atom.h BufferedLine.h CIFfile.h CpptrajFile.h
 CharMask.o : CharMask.cpp Atom.h CharMask.h CpptrajStdio.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h SymbolExporting.h Unit.h
 CharmmParamFile.o : CharmmParamFile.cpp ArgList.h AtomType.h BufferedLine.h CharmmParamFile.h CmapParmHolder.h Constants.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h StringRoutines.h TypeNameHolder.h
 Cluster/Algorithm.o : Cluster/Algorithm.cpp Cluster/Algorithm.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h CpptrajStdio.h
-Cluster/Algorithm_DBscan.o : Cluster/Algorithm_DBscan.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/Algorithm.h Cluster/Algorithm_DBscan.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Cluster/Algorithm_DBscan.o : Cluster/Algorithm_DBscan.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cluster/Algorithm.h Cluster/Algorithm_DBscan.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 Cluster/Algorithm_DPeaks.o : Cluster/Algorithm_DPeaks.cpp ArgList.h AssociatedData.h Cluster/Algorithm.h Cluster/Algorithm_DPeaks.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_Mesh.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h ProgressBar.h Range.h Spline.h TextFormat.h
 Cluster/Algorithm_HierAgglo.o : Cluster/Algorithm_HierAgglo.cpp ArgList.h ArrayIterator.h Cluster/Algorithm.h Cluster/Algorithm_HierAgglo.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/DynamicMatrix.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Matrix.h Parallel.h ProgressBar.h Timer.h
 Cluster/Algorithm_Kmeans.o : Cluster/Algorithm_Kmeans.cpp ArgList.h Cluster/Algorithm.h Cluster/Algorithm_Kmeans.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Parallel.h ProgressBar.h Random.h
@@ -168,23 +168,23 @@ Cluster/Centroid_Coord.o : Cluster/Centroid_Coord.cpp Atom.h AtomMask.h Box.h Cl
 Cluster/Cframes.o : Cluster/Cframes.cpp Cluster/Cframes.h
 Cluster/Cmatrix_Binary.o : Cluster/Cmatrix_Binary.cpp Cluster/Cframes.h Cluster/Cmatrix_Binary.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Parallel.h
 Cluster/Cmatrix_NC.o : Cluster/Cmatrix_NC.cpp Cluster/Cframes.h Cluster/Cmatrix_NC.h CpptrajStdio.h FileName.h NC_Routines.h
-Cluster/Control.o : Cluster/Control.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Cluster/Algorithm.h Cluster/Algorithm_DBscan.h Cluster/Algorithm_DPeaks.h Cluster/Algorithm_HierAgglo.h Cluster/Algorithm_Kmeans.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Control.h Cluster/DBI.h Cluster/DrawGraph.h Cluster/DynamicMatrix.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Output.h Cluster/PseudoF.h Cluster/Results.h Cluster/Results_Coords.h Cluster/Sieve.h Cluster/Silhouette.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_float.h DataSet_integer.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TypeNameHolder.h Unit.h Vec3.h
+Cluster/Control.o : Cluster/Control.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Cluster/Algorithm.h Cluster/Algorithm_DBscan.h Cluster/Algorithm_DPeaks.h Cluster/Algorithm_HierAgglo.h Cluster/Algorithm_Kmeans.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Control.h Cluster/DBI.h Cluster/DrawGraph.h Cluster/DynamicMatrix.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Output.h Cluster/PseudoF.h Cluster/Results.h Cluster/Results_Coords.h Cluster/Sieve.h Cluster/Silhouette.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_float.h DataSet_integer.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Unit.h Vec3.h
 Cluster/DBI.o : Cluster/DBI.cpp Cluster/CentroidArray.h Cluster/Cframes.h Cluster/DBI.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h
 Cluster/DrawGraph.o : Cluster/DrawGraph.cpp AssociatedData.h Atom.h Cluster/Cframes.h Cluster/DrawGraph.h Cluster/Metric.h Cluster/MetricArray.h Constants.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h Dimension.h FileIO.h FileName.h MetaData.h NameType.h PDBfile.h Parallel.h Range.h Residue.h SymbolExporting.h TextFormat.h Vec3.h
 Cluster/DynamicMatrix.o : Cluster/DynamicMatrix.cpp ArrayIterator.h Cluster/DynamicMatrix.h CpptrajStdio.h Matrix.h
 Cluster/List.o : Cluster/List.cpp AssociatedData.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_integer.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h ProgressBar.h Range.h TextFormat.h
-Cluster/MetricArray.o : Cluster/MetricArray.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Metric_DME.h Cluster/Metric_QuatRMSD.h Cluster/Metric_RMS.h Cluster/Metric_SRMSD.h Cluster/Metric_Scalar.h Cluster/Metric_Torsion.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h QuaternionRMSD.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Cluster/Metric_DME.o : Cluster/Metric_DME.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Cluster/Centroid.h Cluster/Centroid_Coord.h Cluster/Cframes.h Cluster/Metric.h Cluster/Metric_DME.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Cluster/MetricArray.o : Cluster/MetricArray.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h BaseIOtype.h Box.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Metric_DME.h Cluster/Metric_QuatRMSD.h Cluster/Metric_RMS.h Cluster/Metric_SRMSD.h Cluster/Metric_Scalar.h Cluster/Metric_Torsion.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterTypes.h ProgressBar.h QuaternionRMSD.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Cluster/Metric_DME.o : Cluster/Metric_DME.cpp AssociatedData.h Atom.h AtomMask.h Box.h Cluster/Centroid.h Cluster/Centroid_Coord.h Cluster/Cframes.h Cluster/Metric.h Cluster/Metric_DME.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h Unit.h Vec3.h
 Cluster/Metric_Matrix2D.o : Cluster/Metric_Matrix2D.cpp AssociatedData.h Cluster/Metric.h Cluster/Metric_Matrix2D.h CpptrajFile.h DataSet.h DataSet_2D.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
-Cluster/Metric_QuatRMSD.o : Cluster/Metric_QuatRMSD.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Cluster/Centroid.h Cluster/Centroid_Coord.h Cluster/Cframes.h Cluster/Metric.h Cluster/Metric_QuatRMSD.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h QuaternionRMSD.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Cluster/Metric_RMS.o : Cluster/Metric_RMS.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Cluster/Centroid.h Cluster/Centroid_Coord.h Cluster/Cframes.h Cluster/Metric.h Cluster/Metric_RMS.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Cluster/Metric_SRMSD.o : Cluster/Metric_SRMSD.cpp ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Cluster/Centroid.h Cluster/Centroid_Coord.h Cluster/Cframes.h Cluster/Metric.h Cluster/Metric_SRMSD.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Cluster/Metric_QuatRMSD.o : Cluster/Metric_QuatRMSD.cpp AssociatedData.h Atom.h AtomMask.h Box.h Cluster/Centroid.h Cluster/Centroid_Coord.h Cluster/Cframes.h Cluster/Metric.h Cluster/Metric_QuatRMSD.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h QuaternionRMSD.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h Unit.h Vec3.h
+Cluster/Metric_RMS.o : Cluster/Metric_RMS.cpp AssociatedData.h Atom.h AtomMask.h Box.h Cluster/Centroid.h Cluster/Centroid_Coord.h Cluster/Cframes.h Cluster/Metric.h Cluster/Metric_RMS.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h Unit.h Vec3.h
+Cluster/Metric_SRMSD.o : Cluster/Metric_SRMSD.cpp ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h Box.h Cluster/Centroid.h Cluster/Centroid_Coord.h Cluster/Cframes.h Cluster/Metric.h Cluster/Metric_SRMSD.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Topology.h Unit.h Vec3.h
 Cluster/Metric_Scalar.o : Cluster/Metric_Scalar.cpp AssociatedData.h Cluster/Centroid.h Cluster/Centroid_Num.h Cluster/Cframes.h Cluster/Metric.h Cluster/Metric_Scalar.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
 Cluster/Metric_Torsion.o : Cluster/Metric_Torsion.cpp AssociatedData.h Cluster/Centroid.h Cluster/Centroid_Num.h Cluster/Cframes.h Cluster/Metric.h Cluster/Metric_Torsion.h Constants.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
 Cluster/Node.o : Cluster/Node.cpp AssociatedData.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h CpptrajFile.h DataSet.h DataSet_1D.h DataSet_float.h DataSet_integer.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
 Cluster/Output.o : Cluster/Output.cpp ArrayIterator.h Cluster/Algorithm.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Output.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Matrix.h Parallel.h Timer.h
 Cluster/PseudoF.o : Cluster/PseudoF.cpp Cluster/CentroidArray.h Cluster/Cframes.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/PseudoF.h Constants.h CpptrajStdio.h
-Cluster/Results_Coords.o : Cluster/Results_Coords.cpp ActionFrameCounter.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Metric_DME.h Cluster/Metric_RMS.h Cluster/Metric_SRMSD.h Cluster/Node.h Cluster/Results.h Cluster/Results_Coords.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Cluster/Results_Coords.o : Cluster/Results_Coords.cpp ActionFrameCounter.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h BaseIOtype.h Box.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Metric_DME.h Cluster/Metric_RMS.h Cluster/Metric_SRMSD.h Cluster/Node.h Cluster/Results.h Cluster/Results_Coords.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h Unit.h Vec3.h
 Cluster/Sieve.o : Cluster/Sieve.cpp AssociatedData.h Cluster/Cframes.h Cluster/Sieve.h CpptrajFile.h DataSet.h DataSet_PairwiseCache.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Random.h Range.h TextFormat.h
 Cluster/Silhouette.o : Cluster/Silhouette.cpp Cluster/CentroidArray.h Cluster/Cframes.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Silhouette.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h OnlineVarT.h Parallel.h
 ClusterMap.o : ClusterMap.cpp AssociatedData.h ClusterMap.h Constants.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_2D.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h ProgressBar.h ProgressTimer.h Range.h TextFormat.h Timer.h
@@ -192,64 +192,64 @@ CmapParmHolder.o : CmapParmHolder.cpp CmapParmHolder.h Constants.h CpptrajStdio.
 Cmd.o : Cmd.cpp Cmd.h DispatchObject.h
 CmdInput.o : CmdInput.cpp CmdInput.h StringRoutines.h
 CmdList.o : CmdList.cpp Cmd.h CmdList.h DispatchObject.h
-Command.o : Command.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h ActionTopWriter.h Action_AddAtom.h Action_Align.h Action_Angle.h Action_AreaPerMol.h Action_AtomMap.h Action_AtomicCorr.h Action_AtomicFluct.h Action_AutoImage.h Action_Average.h Action_AvgBox.h Action_Bounds.h Action_Box.h Action_Center.h Action_Channel.h Action_CheckChirality.h Action_CheckStructure.h Action_Closest.h Action_ClusterDihedral.h Action_Contacts.h Action_CreateCrd.h Action_CreateReservoir.h Action_DNAionTracker.h Action_DSSP.h Action_Density.h Action_Diffusion.h Action_Dihedral.h Action_DihedralRMS.h Action_Dipole.h Action_DistRmsd.h Action_Distance.h Action_Energy.h Action_Esander.h Action_FilterByData.h Action_FixAtomOrder.h Action_FixImagedBonds.h Action_GIST.h Action_Grid.h Action_GridFreeEnergy.h Action_HydrogenBond.h Action_Image.h Action_InfraredSpectrum.h Action_Jcoupling.h Action_Keep.h Action_LESsplit.h Action_LIE.h Action_LipidOrder.h Action_MakeStructure.h Action_Mask.h Action_Matrix.h Action_MinImage.h Action_MinMaxDist.h Action_Molsurf.h Action_MultiDihedral.h Action_MultiPucker.h Action_MultiVector.h Action_NAstruct.h Action_NMRrst.h Action_NativeContacts.h Action_OrderParameter.h Action_Outtraj.h Action_PairDist.h Action_Pairwise.h Action_Principal.h Action_Projection.h Action_Pucker.h Action_Radgyr.h Action_Radial.h Action_RandomizeIons.h Action_Remap.h Action_ReplicateCell.h Action_Rmsd.h Action_Rotate.h Action_RunningAvg.h Action_STFC_Diffusion.h Action_Scale.h Action_SetVelocity.h Action_Spam.h Action_Strip.h Action_Surf.h Action_SymmetricRmsd.h Action_Temperature.h Action_Time.h Action_ToroidalDiffusion.h Action_Translate.h Action_Unstrip.h Action_Unwrap.h Action_Vector.h Action_VelocityAutoCorr.h Action_Volmap.h Action_Volume.h Action_Watershell.h Action_XtalSymm.h Analysis.h AnalysisList.h AnalysisState.h Analysis_AmdBias.h Analysis_AutoCorr.h Analysis_Average.h Analysis_CalcDiffusion.h Analysis_Clustering.h Analysis_ConstantPHStats.h Analysis_Corr.h Analysis_CrankShaft.h Analysis_CrdFluct.h Analysis_CrossCorr.h Analysis_CurveFit.h Analysis_Divergence.h Analysis_EvalPlateau.h Analysis_FFT.h Analysis_HausdorffDistance.h Analysis_Hist.h Analysis_IRED.h Analysis_Integrate.h Analysis_KDE.h Analysis_Lifetime.h Analysis_LowestCurve.h Analysis_Matrix.h Analysis_MeltCurve.h Analysis_Modes.h Analysis_MultiHist.h Analysis_Multicurve.h Analysis_Overlap.h Analysis_PhiPsi.h Analysis_Project.h Analysis_Regression.h Analysis_RemLog.h Analysis_Rms2d.h Analysis_RmsAvgCorr.h Analysis_Rotdif.h Analysis_RunningAvg.h Analysis_Slope.h Analysis_Spline.h Analysis_State.h Analysis_Statistics.h Analysis_TI.h Analysis_TICA.h Analysis_Timecorr.h Analysis_VectorMath.h Analysis_Wavelet.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h AxisType.h BaseIOtype.h Box.h BoxArgs.h BufferedLine.h CharMask.h Cluster/Algorithm.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Control.h Cluster/DrawGraph.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Sieve.h Cluster/Silhouette.h ClusterMap.h CmapParmHolder.h Cmd.h CmdInput.h CmdList.h Command.h CompactFrameArray.h ComplexArray.h Constants.h Constraints.h ControlBlock.h ControlBlock_For.h CoordinateInfo.h Corr.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_RemLog.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h Deprecated.h DiffusionResults.h DihedralSearch.h Dimension.h DispatchObject.h Energy.h Energy_Sander.h EnsembleIn.h EnsembleOutList.h Ewald.h EwaldOptions.h Ewald_ParticleMesh.h ExclusionArray.h Exec.h Exec_AddMissingRes.h Exec_Analyze.h Exec_Build.h Exec_Calc.h Exec_CatCrd.h Exec_Change.h Exec_ClusterMap.h Exec_CombineCoords.h Exec_Commands.h Exec_CompareClusters.h Exec_CompareEnergy.h Exec_CompareTop.h Exec_CrdAction.h Exec_CrdOut.h Exec_CrdTransform.h Exec_CreateSet.h Exec_DataFile.h Exec_DataFilter.h Exec_DataSetCmd.h Exec_Desc.h Exec_Emin.h Exec_ExtendedComparison.h Exec_Flatten.h Exec_GenerateAmberRst.h Exec_Graft.h Exec_Help.h Exec_HmassRepartition.h Exec_LoadCrd.h Exec_LoadTraj.h Exec_ParallelAnalysis.h Exec_ParmBox.h Exec_ParmSolvent.h Exec_ParmStrip.h Exec_ParmWrite.h Exec_ParseTiming.h Exec_PermuteDihedrals.h Exec_Precision.h Exec_PrepareForLeap.h Exec_PrintData.h Exec_Random.h Exec_ReadData.h Exec_ReadEnsembleData.h Exec_ReadInput.h Exec_RotateDihedral.h Exec_RunAnalysis.h Exec_ScaleDihedralK.h Exec_Sequence.h Exec_SequenceAlign.h Exec_Set.h Exec_Show.h Exec_SortEnsembleData.h Exec_Source.h Exec_SplitCoords.h Exec_System.h Exec_Top.h Exec_Traj.h Exec_UpdateParameters.h Exec_ViewRst.h Exec_Zmatrix.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h GIST_PME.h Grid.h GridAction.h GridBin.h GridMover.h HistBin.h Hungarian.h ImageOption.h ImageTypes.h InputTrajCommon.h InteractionData.h MapAtom.h MaskArray.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h OnlineVarT.h OutputTrajCommon.h PDBfile.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PubFFT.h Pucker.h Pucker_PuckerMask.h Pucker_PuckerSearch.h Pucker_PuckerToken.h RPNcalc.h Random.h Range.h ReferenceAction.h ReferenceFrame.h RemdReservoirNC.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h SplineFxnTable.h Structure/LeastSquaresPlane.h Structure/RingFinder.h StructureCheck.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h cuda_kernels/GistCudaSetup.cuh helpme_standalone.h molsurf.h
+Command.o : Command.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h ActionTopWriter.h Action_AddAtom.h Action_Align.h Action_Angle.h Action_AreaPerMol.h Action_AtomMap.h Action_AtomicCorr.h Action_AtomicFluct.h Action_AutoImage.h Action_Average.h Action_AvgBox.h Action_Bounds.h Action_Box.h Action_Center.h Action_Channel.h Action_CheckChirality.h Action_CheckStructure.h Action_Closest.h Action_ClusterDihedral.h Action_Contacts.h Action_CreateCrd.h Action_CreateReservoir.h Action_DNAionTracker.h Action_DSSP.h Action_Density.h Action_Diffusion.h Action_Dihedral.h Action_DihedralRMS.h Action_Dipole.h Action_DistRmsd.h Action_Distance.h Action_Energy.h Action_Esander.h Action_FilterByData.h Action_FixAtomOrder.h Action_FixImagedBonds.h Action_GIST.h Action_Grid.h Action_GridFreeEnergy.h Action_HydrogenBond.h Action_Image.h Action_InfraredSpectrum.h Action_Jcoupling.h Action_Keep.h Action_LESsplit.h Action_LIE.h Action_LipidOrder.h Action_MakeStructure.h Action_Mask.h Action_Matrix.h Action_MinImage.h Action_MinMaxDist.h Action_Molsurf.h Action_MultiDihedral.h Action_MultiPucker.h Action_MultiVector.h Action_NAstruct.h Action_NMRrst.h Action_NativeContacts.h Action_OrderParameter.h Action_Outtraj.h Action_PairDist.h Action_Pairwise.h Action_Principal.h Action_Projection.h Action_Pucker.h Action_Radgyr.h Action_Radial.h Action_RandomizeIons.h Action_Remap.h Action_ReplicateCell.h Action_Rmsd.h Action_Rotate.h Action_RunningAvg.h Action_STFC_Diffusion.h Action_Scale.h Action_SetVelocity.h Action_Spam.h Action_Strip.h Action_Surf.h Action_SymmetricRmsd.h Action_Temperature.h Action_Time.h Action_ToroidalDiffusion.h Action_Translate.h Action_Unstrip.h Action_Unwrap.h Action_Vector.h Action_VelocityAutoCorr.h Action_Volmap.h Action_Volume.h Action_Watershell.h Action_XtalSymm.h Analysis.h AnalysisList.h AnalysisState.h Analysis_AmdBias.h Analysis_AutoCorr.h Analysis_Average.h Analysis_CalcDiffusion.h Analysis_Clustering.h Analysis_ConstantPHStats.h Analysis_Corr.h Analysis_CrankShaft.h Analysis_CrdFluct.h Analysis_CrossCorr.h Analysis_CurveFit.h Analysis_Divergence.h Analysis_EvalPlateau.h Analysis_FFT.h Analysis_HausdorffDistance.h Analysis_Hist.h Analysis_IRED.h Analysis_Integrate.h Analysis_KDE.h Analysis_Lifetime.h Analysis_LowestCurve.h Analysis_Matrix.h Analysis_MeltCurve.h Analysis_Modes.h Analysis_MultiHist.h Analysis_Multicurve.h Analysis_Overlap.h Analysis_PhiPsi.h Analysis_Project.h Analysis_Regression.h Analysis_RemLog.h Analysis_Rms2d.h Analysis_RmsAvgCorr.h Analysis_Rotdif.h Analysis_RunningAvg.h Analysis_Slope.h Analysis_Spline.h Analysis_State.h Analysis_Statistics.h Analysis_TI.h Analysis_TICA.h Analysis_Timecorr.h Analysis_VectorMath.h Analysis_Wavelet.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AxisType.h BaseIOtype.h Box.h BoxArgs.h BufferedLine.h CharMask.h Cluster/Algorithm.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Control.h Cluster/DrawGraph.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Sieve.h Cluster/Silhouette.h ClusterMap.h Cmd.h CmdInput.h CmdList.h Command.h CompactFrameArray.h ComplexArray.h Constants.h Constraints.h ControlBlock.h ControlBlock_For.h CoordinateInfo.h Corr.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_RemLog.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h Deprecated.h DiffusionResults.h DihedralSearch.h Dimension.h DispatchObject.h Energy.h Energy_Sander.h EnsembleIn.h EnsembleOutList.h Ewald.h EwaldOptions.h Ewald_ParticleMesh.h ExclusionArray.h Exec.h Exec_AddMissingRes.h Exec_Analyze.h Exec_Build.h Exec_Calc.h Exec_CatCrd.h Exec_Change.h Exec_ClusterMap.h Exec_CombineCoords.h Exec_Commands.h Exec_CompareClusters.h Exec_CompareEnergy.h Exec_CompareTop.h Exec_CrdAction.h Exec_CrdOut.h Exec_CrdTransform.h Exec_CreateSet.h Exec_DataFile.h Exec_DataFilter.h Exec_DataSetCmd.h Exec_Desc.h Exec_Emin.h Exec_ExtendedComparison.h Exec_Flatten.h Exec_GenerateAmberRst.h Exec_Graft.h Exec_Help.h Exec_HmassRepartition.h Exec_LoadCrd.h Exec_LoadTraj.h Exec_ParallelAnalysis.h Exec_ParmBox.h Exec_ParmSolvent.h Exec_ParmStrip.h Exec_ParmWrite.h Exec_ParseTiming.h Exec_PermuteDihedrals.h Exec_Precision.h Exec_PrepareForLeap.h Exec_PrintData.h Exec_Random.h Exec_ReadData.h Exec_ReadEnsembleData.h Exec_ReadInput.h Exec_RotateDihedral.h Exec_RunAnalysis.h Exec_ScaleDihedralK.h Exec_Sequence.h Exec_SequenceAlign.h Exec_Set.h Exec_Show.h Exec_SortEnsembleData.h Exec_Source.h Exec_SplitCoords.h Exec_System.h Exec_Top.h Exec_Traj.h Exec_UpdateParameters.h Exec_ViewRst.h Exec_Zmatrix.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h GIST_PME.h Grid.h GridAction.h GridBin.h GridMover.h HistBin.h Hungarian.h ImageOption.h ImageTypes.h InputTrajCommon.h InteractionData.h MapAtom.h MaskArray.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h OnlineVarT.h OutputTrajCommon.h PDBfile.h PairList.h Parallel.h ParameterTypes.h PubFFT.h Pucker.h Pucker_PuckerMask.h Pucker_PuckerSearch.h Pucker_PuckerToken.h RPNcalc.h Random.h Range.h ReferenceAction.h ReferenceFrame.h RemdReservoirNC.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h SplineFxnTable.h Structure/LeastSquaresPlane.h Structure/RingFinder.h StructureCheck.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Unit.h Vec3.h cuda_kernels/GistCudaSetup.cuh helpme_standalone.h molsurf.h
 CompactFrameArray.o : CompactFrameArray.cpp Box.h CompactFrameArray.h CoordinateInfo.h CpptrajStdio.h Matrix_3x3.h Parallel.h ReplicaDimArray.h Vec3.h
 ComplexArray.o : ComplexArray.cpp ArrayIterator.h ComplexArray.h
-Constraints.o : Constraints.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h CharMask.h CmapParmHolder.h Constants.h Constraints.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-ControlBlock_For.o : ControlBlock_For.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h ControlBlock.h ControlBlock_For.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_dataSetBlocks.h ForLoop_inData.h ForLoop_integer.h ForLoop_list.h ForLoop_mask.h ForLoop_overSets.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Constraints.o : Constraints.cpp ArgList.h Atom.h AtomMask.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
+ControlBlock_For.o : ControlBlock_For.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h ControlBlock.h ControlBlock_For.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_dataSetBlocks.h ForLoop_inData.h ForLoop_integer.h ForLoop_list.h ForLoop_mask.h ForLoop_overSets.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 CoordCovarMatrix.o : CoordCovarMatrix.cpp ArrayIterator.h Atom.h AtomMask.h Box.h CoordCovarMatrix.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Unit.h Vec3.h
 CoordCovarMatrix_Full.o : CoordCovarMatrix_Full.cpp ArrayIterator.h Atom.h AtomMask.h CoordCovarMatrix.h CoordCovarMatrix_Full.h CpptrajStdio.h MaskToken.h Matrix.h Molecule.h NameType.h Residue.h Segment.h SymbolExporting.h Unit.h
 CoordCovarMatrix_Half.o : CoordCovarMatrix_Half.cpp ArrayIterator.h AssociatedData.h Atom.h AtomMask.h Constants.h CoordCovarMatrix.h CoordCovarMatrix_Half.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h Dimension.h FileIO.h FileName.h MaskToken.h Matrix.h MetaData.h Molecule.h NameType.h Parallel.h Range.h Residue.h Segment.h SymbolExporting.h TextFormat.h Unit.h
 CoordinateInfo.o : CoordinateInfo.cpp Box.h CoordinateInfo.h CpptrajStdio.h Matrix_3x3.h Parallel.h ReplicaDimArray.h Vec3.h
 Corr.o : Corr.cpp ArrayIterator.h ComplexArray.h Corr.h PubFFT.h
 Cph.o : Cph.cpp Cph.h NameType.h
-Cpptraj.o : Cpptraj.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Cmd.h CmdInput.h CmdList.h Command.h Constants.h CoordinateInfo.h Cpptraj.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h Gpu.h HipDefinitions.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NDiff.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReadLine.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h TopInfo.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h Version.h
+Cpptraj.o : Cpptraj.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cmd.h CmdInput.h CmdList.h Command.h Constants.h CoordinateInfo.h Cpptraj.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h Gpu.h HipDefinitions.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NDiff.h NameType.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReadLine.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h TopInfo.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h Version.h
 CpptrajFile.o : CpptrajFile.cpp CpptrajFile.h CpptrajStdio.h FileIO.h FileIO_Bzip2.h FileIO_Gzip.h FileIO_Mpi.h FileIO_MpiShared.h FileIO_Std.h FileName.h Parallel.h StringRoutines.h
-CpptrajState.o : CpptrajState.cpp Action.h ActionList.h ActionState.h Action_CreateCrd.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_Topology.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleNavigator.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+CpptrajState.o : CpptrajState.cpp Action.h ActionList.h ActionState.h Action_CreateCrd.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_Topology.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleNavigator.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 CpptrajStdio.o : CpptrajStdio.cpp Parallel.h
 CurveFit.o : CurveFit.cpp CurveFit.h
-DataFile.o : DataFile.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Cluster/Cframes.h Cluster/Cmatrix_NC.h CmapParmHolder.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataFile.h DataIO.h DataIO_AmberEne.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_CCP4.h DataIO_CharmmFastRep.h DataIO_CharmmOutput.h DataIO_CharmmRepLog.h DataIO_CharmmRtfPrm.h DataIO_Cmatrix_Binary.h DataIO_Cmatrix_NC.h DataIO_Coords.h DataIO_Cpout.h DataIO_Evecs.h DataIO_Gnuplot.h DataIO_Grace.h DataIO_LeapRC.h DataIO_Mdout.h DataIO_NetCDF.h DataIO_Numpy.h DataIO_OpenDx.h DataIO_Peaks.h DataIO_RemLog.h DataIO_Std.h DataIO_VecTraj.h DataIO_XVG.h DataIO_Xplor.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TypeNameHolder.h Unit.h Vec3.h
-DataFileList.o : DataFileList.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataFilter.o : DataFilter.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_integer.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO.o : DataIO.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_AmberEne.o : DataIO_AmberEne.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberEne.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataFile.o : DataFile.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Cluster/Cframes.h Cluster/Cmatrix_NC.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataFile.h DataIO.h DataIO_AmberEne.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_CCP4.h DataIO_CharmmFastRep.h DataIO_CharmmOutput.h DataIO_CharmmRepLog.h DataIO_CharmmRtfPrm.h DataIO_Cmatrix_Binary.h DataIO_Cmatrix_NC.h DataIO_Coords.h DataIO_Cpout.h DataIO_Evecs.h DataIO_Gnuplot.h DataIO_Grace.h DataIO_LeapRC.h DataIO_Mdout.h DataIO_NetCDF.h DataIO_Numpy.h DataIO_OpenDx.h DataIO_Peaks.h DataIO_RemLog.h DataIO_Std.h DataIO_VecTraj.h DataIO_XVG.h DataIO_Xplor.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Unit.h Vec3.h
+DataFileList.o : DataFileList.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+DataFilter.o : DataFilter.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_integer.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+DataIO.o : DataIO.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+DataIO_AmberEne.o : DataIO_AmberEne.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberEne.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 DataIO_AmberFF.o : DataIO_AmberFF.cpp AmberParamFile.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberFF.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_AmberFrcmod.o : DataIO_AmberFrcmod.cpp AmberParamFile.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberFrcmod.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_AmberLib.o : DataIO_AmberLib.cpp ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberLib.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_AmberPrep.o : DataIO_AmberPrep.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberPrep.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_CCP4.o : DataIO_CCP4.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ByteRoutines.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CCP4.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_CharmmFastRep.o : DataIO_CharmmFastRep.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmFastRep.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_CharmmOutput.o : DataIO_CharmmOutput.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmOutput.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_CharmmRepLog.o : DataIO_CharmmRepLog.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmRepLog.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_AmberLib.o : DataIO_AmberLib.cpp ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberLib.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+DataIO_AmberPrep.o : DataIO_AmberPrep.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberPrep.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+DataIO_CCP4.o : DataIO_CCP4.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ByteRoutines.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CCP4.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+DataIO_CharmmFastRep.o : DataIO_CharmmFastRep.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmFastRep.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+DataIO_CharmmOutput.o : DataIO_CharmmOutput.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmOutput.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+DataIO_CharmmRepLog.o : DataIO_CharmmRepLog.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmRepLog.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 DataIO_CharmmRtfPrm.o : DataIO_CharmmRtfPrm.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharmmParamFile.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmRtfPrm.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h DataSet_Topology.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_Cmatrix_Binary.o : DataIO_Cmatrix_Binary.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/Cframes.h Cluster/Cmatrix_Binary.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Cmatrix_Binary.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_Cmatrix_NC.o : DataIO_Cmatrix_NC.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/Cframes.h Cluster/Cmatrix_NC.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Cmatrix_NC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_Coords.o : DataIO_Coords.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Coords.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h Trajin_Single.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_Cpout.o : DataIO_Cpout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Cpout.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h DataSet_PHREMD_Implicit.h DataSet_pH.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_Evecs.o : DataIO_Evecs.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedFrame.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Evecs.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Modes.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_Gnuplot.o : DataIO_Gnuplot.cpp ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Gnuplot.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_Grace.o : DataIO_Grace.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Grace.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_string.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_Cmatrix_Binary.o : DataIO_Cmatrix_Binary.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cluster/Cframes.h Cluster/Cmatrix_Binary.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Cmatrix_Binary.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+DataIO_Cmatrix_NC.o : DataIO_Cmatrix_NC.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cluster/Cframes.h Cluster/Cmatrix_NC.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Cmatrix_NC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+DataIO_Coords.o : DataIO_Coords.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Coords.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h Trajin_Single.h Unit.h Vec3.h
+DataIO_Cpout.o : DataIO_Cpout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Cpout.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h DataSet_PHREMD_Implicit.h DataSet_pH.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+DataIO_Evecs.o : DataIO_Evecs.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Evecs.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Modes.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+DataIO_Gnuplot.o : DataIO_Gnuplot.cpp ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Gnuplot.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+DataIO_Grace.o : DataIO_Grace.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Grace.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_string.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 DataIO_LeapRC.o : DataIO_LeapRC.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_Coords.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_Amber.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_Mdout.o : DataIO_Mdout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Mdout.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_NetCDF.o : DataIO_NetCDF.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/Cframes.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_NetCDF.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_Mesh.h DataSet_Modes.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_Vector.h DataSet_Vector_Scalar.h DataSet_string.h DataSet_unsignedInt.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h Version.h
-DataIO_Numpy.o : DataIO_Numpy.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Numpy.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h libnpy/npy.hpp
-DataIO_OpenDx.o : DataIO_OpenDx.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_OpenDx.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridDbl.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_Peaks.o : DataIO_Peaks.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Peaks.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector_Scalar.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_RemLog.o : DataIO_RemLog.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_RemLog.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_Mdout.o : DataIO_Mdout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Mdout.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+DataIO_NetCDF.o : DataIO_NetCDF.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cluster/Cframes.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_NetCDF.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_Mesh.h DataSet_Modes.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_Vector.h DataSet_Vector_Scalar.h DataSet_string.h DataSet_unsignedInt.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h Version.h
+DataIO_Numpy.o : DataIO_Numpy.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Numpy.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h libnpy/npy.hpp
+DataIO_OpenDx.o : DataIO_OpenDx.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_OpenDx.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridDbl.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+DataIO_Peaks.o : DataIO_Peaks.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Peaks.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector_Scalar.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+DataIO_RemLog.o : DataIO_RemLog.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_RemLog.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 DataIO_Std.o : DataIO_Std.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Cluster/Cframes.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Std.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_NameMap.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_Parameters.h DataSet_StringVar.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_string.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_VecTraj.o : DataIO_VecTraj.cpp ActionFrameCounter.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_VecTraj.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_XVG.o : DataIO_XVG.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_XVG.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_Xplor.o : DataIO_Xplor.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Xplor.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_VecTraj.o : DataIO_VecTraj.cpp ActionFrameCounter.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_VecTraj.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h Unit.h Vec3.h
+DataIO_XVG.o : DataIO_XVG.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_XVG.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+DataIO_Xplor.o : DataIO_Xplor.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Xplor.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 DataSet.o : DataSet.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
 DataSetList.o : DataSetList.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Cluster/Cframes.h Cluster/Cmatrix_NC.h CmapParmHolder.h CompactFrameArray.h ComplexArray.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_FRM.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_GridDbl.h DataSet_GridFlt.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_NameMap.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h DataSet_PHREMD_Implicit.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_PairwiseCache_NC.h DataSet_Parameters.h DataSet_RemLog.h DataSet_StringVar.h DataSet_Tensor.h DataSet_Topology.h DataSet_Vector.h DataSet_Vector_Scalar.h DataSet_Zmatrix.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_disk.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h DataSet_unsignedInt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h InputTrajCommon.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h SymmetricTensor.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TypeNameHolder.h Unit.h Vec3.h
 DataSet_1D.o : DataSet_1D.cpp ArrayIterator.h AssociatedData.h ComplexArray.h Constants.h Corr.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h PubFFT.h Range.h TextFormat.h
 DataSet_2D.o : DataSet_2D.cpp AssociatedData.h CpptrajFile.h DataSet.h DataSet_2D.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
 DataSet_3D.o : DataSet_3D.cpp AssociatedData.h Box.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_3D.h Dimension.h FileIO.h FileName.h GridBin.h Matrix_3x3.h MetaData.h Parallel.h Range.h TextFormat.h Vec3.h
-DataSet_Coords.o : DataSet_Coords.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataSet_Coords_CRD.o : DataSet_Coords_CRD.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_CRD.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataSet_Coords_FRM.o : DataSet_Coords_FRM.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_FRM.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataSet_Coords_REF.o : DataSet_Coords_REF.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TrajFrameCounter.h Trajin.h Trajin_Single.h TypeNameHolder.h Unit.h Vec3.h
-DataSet_Coords_TRJ.o : DataSet_Coords_TRJ.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_TRJ.h Dimension.h FileIO.h FileName.h Frame.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h Trajin_Single.h TypeNameHolder.h Unit.h Vec3.h
+DataSet_Coords.o : DataSet_Coords.cpp AssociatedData.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h Unit.h Vec3.h
+DataSet_Coords_CRD.o : DataSet_Coords_CRD.cpp AssociatedData.h Atom.h AtomMask.h Box.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_CRD.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h Unit.h Vec3.h
+DataSet_Coords_FRM.o : DataSet_Coords_FRM.cpp AssociatedData.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_FRM.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h Unit.h Vec3.h
+DataSet_Coords_REF.o : DataSet_Coords_REF.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TrajFrameCounter.h Trajin.h Trajin_Single.h Unit.h Vec3.h
+DataSet_Coords_TRJ.o : DataSet_Coords_TRJ.cpp AssociatedData.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_TRJ.h Dimension.h FileIO.h FileName.h Frame.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h Trajin_Single.h Unit.h Vec3.h
 DataSet_GridDbl.o : DataSet_GridDbl.cpp ArrayIterator.h AssociatedData.h Box.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_3D.h DataSet_GridDbl.h Dimension.h FileIO.h FileName.h Grid.h GridBin.h Matrix_3x3.h MetaData.h Parallel.h Range.h StringRoutines.h TextFormat.h Vec3.h
 DataSet_GridFlt.o : DataSet_GridFlt.cpp ArrayIterator.h AssociatedData.h Box.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_3D.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Grid.h GridBin.h Matrix_3x3.h MetaData.h Parallel.h Range.h StringRoutines.h TextFormat.h Vec3.h
 DataSet_Mat3x3.o : DataSet_Mat3x3.cpp AssociatedData.h CpptrajFile.h DataSet.h DataSet_Mat3x3.h Dimension.h FileIO.h FileName.h Matrix_3x3.h MetaData.h Parallel.h Range.h TextFormat.h Vec3.h
@@ -267,7 +267,7 @@ DataSet_Parameters.o : DataSet_Parameters.cpp AssociatedData.h AtomType.h CmapPa
 DataSet_RemLog.o : DataSet_RemLog.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h ReplicaDimArray.h TextFormat.h
 DataSet_StringVar.o : DataSet_StringVar.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_StringVar.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
 DataSet_Tensor.o : DataSet_Tensor.cpp AssociatedData.h CpptrajFile.h DataSet.h DataSet_Tensor.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h SymmetricTensor.h TextFormat.h
-DataSet_Topology.o : DataSet_Topology.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Topology.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataSet_Topology.o : DataSet_Topology.cpp AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Topology.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h Unit.h Vec3.h
 DataSet_Vector.o : DataSet_Vector.cpp ArrayIterator.h AssociatedData.h ComplexArray.h Constants.h Corr.h CpptrajFile.h DataSet.h DataSet_1D.h DataSet_Vector.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h PubFFT.h Range.h SymbolExporting.h TextFormat.h Vec3.h
 DataSet_Vector_Scalar.o : DataSet_Vector_Scalar.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Vector_Scalar.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h Vec3.h
 DataSet_Zmatrix.o : DataSet_Zmatrix.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Zmatrix.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h Structure/InternalCoords.h Structure/Zmatrix.h TextFormat.h Vec3.h
@@ -279,85 +279,85 @@ DataSet_pH.o : DataSet_pH.cpp AssociatedData.h Cph.h CpptrajFile.h CpptrajStdio.
 DataSet_string.o : DataSet_string.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_string.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
 DataSet_unsignedInt.o : DataSet_unsignedInt.cpp AssociatedData.h CpptrajFile.h DataSet.h DataSet_1D.h DataSet_unsignedInt.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
 Deprecated.o : Deprecated.cpp CpptrajStdio.h Deprecated.h DispatchObject.h
-DiffusionResults.o : DiffusionResults.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DiffusionResults.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DihedralSearch.o : DihedralSearch.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h DihedralSearch.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DiffusionResults.o : DiffusionResults.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DiffusionResults.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+DihedralSearch.o : DihedralSearch.cpp ArgList.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DihedralSearch.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h
 DistRoutines.o : DistRoutines.cpp Box.h DistRoutines.h ImageOption.h Matrix_3x3.h Parallel.h Vec3.h
-Energy.o : Energy.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h Energy.h Energy/Ene_Angle.h Energy/Ene_Bond.h Energy/Kernel_Harmonic.h ExclusionArray.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Energy.o : Energy.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h Energy.h Energy/Ene_Angle.h Energy/Ene_Bond.h Energy/Kernel_Harmonic.h ExclusionArray.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TorsionRoutines.h Unit.h Vec3.h
 EnergyArray.o : EnergyArray.cpp CpptrajFile.h CpptrajStdio.h EnergyArray.h FileIO.h FileName.h Parallel.h
-Energy_Sander.o : Energy_Sander.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy_Sander.h FileName.h FileTypes.h File_TempName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Energy_Sander.o : Energy_Sander.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy_Sander.h FileName.h FileTypes.h File_TempName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h
 EnsembleIn.o : EnsembleIn.cpp Atom.h AtomMask.h Box.h CoordinateInfo.h CpptrajStdio.h EnsembleIn.h FileName.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h Timer.h TrajFrameCounter.h Unit.h Vec3.h
-EnsembleIn_Multi.o : EnsembleIn_Multi.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h EnsembleIn.h EnsembleIn_Multi.h FileIO.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-EnsembleIn_Single.o : EnsembleIn_Single.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h EnsembleIn.h EnsembleIn_Single.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+EnsembleIn_Multi.o : EnsembleIn_Multi.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h EnsembleIn.h EnsembleIn_Multi.h FileIO.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryIO.h Unit.h Vec3.h
+EnsembleIn_Single.o : EnsembleIn_Single.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h EnsembleIn.h EnsembleIn_Single.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h Unit.h Vec3.h
 EnsembleNavigator.o : EnsembleNavigator.cpp Atom.h AtomMask.h Box.h CoordinateInfo.h CpptrajStdio.h EnsembleIn.h EnsembleNavigator.h FileName.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h Timer.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TrajinList.h Unit.h Vec3.h
 EnsembleOut.o : EnsembleOut.cpp ActionFrameCounter.h BaseIOtype.h Box.h CoordinateInfo.h CpptrajStdio.h EnsembleOut.h FileName.h FileTypes.h FramePtrArray.h Matrix_3x3.h OutputTrajCommon.h Parallel.h Range.h ReplicaDimArray.h TrajectoryFile.h Vec3.h
-EnsembleOutList.o : EnsembleOutList.cpp ActionFrameCounter.h ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h EnsembleOut.h EnsembleOutList.h EnsembleOut_Multi.h EnsembleOut_Single.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TrajectoryFile.h TypeNameHolder.h Unit.h Vec3.h
-EnsembleOut_Multi.o : EnsembleOut_Multi.cpp ActionFrameCounter.h ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h EnsembleOut.h EnsembleOut_Multi.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-EnsembleOut_Single.o : EnsembleOut_Single.cpp ActionFrameCounter.h ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h EnsembleOut.h EnsembleOut_Single.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Ewald.o : Ewald.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h EnergyKernel_Adjust.h EnergyKernel_Nonbond.h Ewald.h ExclusionArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h PairListLoop.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Spline.h SplineFxnTable.h StringRoutines.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+EnsembleOutList.o : EnsembleOutList.cpp ActionFrameCounter.h ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h EnsembleOut.h EnsembleOutList.h EnsembleOut_Multi.h EnsembleOut_Single.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TrajectoryFile.h Unit.h Vec3.h
+EnsembleOut_Multi.o : EnsembleOut_Multi.cpp ActionFrameCounter.h ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h EnsembleOut.h EnsembleOut_Multi.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h Unit.h Vec3.h
+EnsembleOut_Single.o : EnsembleOut_Single.cpp ActionFrameCounter.h ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h EnsembleOut.h EnsembleOut_Single.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h Unit.h Vec3.h
+Ewald.o : Ewald.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h EnergyKernel_Adjust.h EnergyKernel_Nonbond.h Ewald.h ExclusionArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h PairListLoop.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Spline.h SplineFxnTable.h StringRoutines.h SymbolExporting.h Timer.h Topology.h Unit.h Vec3.h
 EwaldOptions.o : EwaldOptions.cpp ArgList.h CpptrajStdio.h EwaldOptions.h
 Ewald_ParticleMesh.o : Ewald_ParticleMesh.cpp Atom.h AtomMask.h Box.h CoordinateInfo.h CpptrajStdio.h Ewald.h EwaldOptions.h Ewald_ParticleMesh.h ExclusionArray.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h Timer.h Unit.h Vec3.h helpme_standalone.h
 Ewald_Regular.o : Ewald_Regular.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Ewald.h EwaldOptions.h Ewald_Regular.h ExclusionArray.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h StringRoutines.h SymbolExporting.h Timer.h Unit.h Vec3.h
 ExclusionArray.o : ExclusionArray.cpp Atom.h AtomMask.h CharMask.h CpptrajStdio.h ExclusionArray.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Unit.h
-Exec_AddMissingRes.o : Exec_AddMissingRes.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CharMask.h CmapParmHolder.h CompactFrameArray.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_AddMissingRes.h Exec_AddMissingRes_Pres.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Analyze.o : Exec_Analyze.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Analyze.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_AddMissingRes.o : Exec_AddMissingRes.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h CharMask.h CompactFrameArray.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_AddMissingRes.h Exec_AddMissingRes_Pres.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h ParmFile.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h Trajout_Single.h Unit.h Vec3.h
+Exec_Analyze.o : Exec_Analyze.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Analyze.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_Build.o : Exec_Build.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/GB_Params.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/Creator.h Structure/Disulfide.h Structure/HisProt.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/StructureEnum.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Calc.o : Exec_Calc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Calc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_CatCrd.o : Exec_CatCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CatCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Change.o : Exec_Change.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Change.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_ClusterMap.o : Exec_ClusterMap.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ClusterMap.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ClusterMap.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_CombineCoords.o : Exec_CombineCoords.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CombineCoords.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Commands.o : Exec_Commands.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Commands.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_CompareClusters.o : Exec_CompareClusters.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CompareClusters.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_CompareEnergy.o : Exec_CompareEnergy.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h Energy/Kernel_Fourier.h Energy/Kernel_Harmonic.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CompareEnergy.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_CompareTop.o : Exec_CompareTop.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CompareTop.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_CrdAction.o : Exec_CrdAction.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Cmd.h CmdList.h Command.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CrdAction.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_CrdOut.o : Exec_CrdOut.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CrdOut.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-Exec_CrdTransform.o : Exec_CrdTransform.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CrdTransform.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_CreateSet.o : Exec_CreateSet.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CreateSet.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_DataFile.o : Exec_DataFile.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_DataFile.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_DataFilter.o : Exec_DataFilter.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_DataFilter.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_DataSetCmd.o : Exec_DataSetCmd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h ArrayIterator.h AssociatedData.h AssociatedData_Connect.h AssociatedData_NOE.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_Mesh.h DataSet_Vector.h DataSet_string.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_DataSetCmd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Desc.o : Exec_Desc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Desc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Emin.o : Exec_Emin.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Emin.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_ExtendedComparison.o : Exec_ExtendedComparison.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ExtendedComparison.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Flatten.o : Exec_Flatten.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Flatten.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_GenerateAmberRst.o : Exec_GenerateAmberRst.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_GenerateAmberRst.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Graft.o : Exec_Graft.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Graft.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Help.o : Exec_Help.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Help.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_HmassRepartition.o : Exec_HmassRepartition.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_HmassRepartition.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_LoadCrd.o : Exec_LoadCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_LoadCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_LoadTraj.o : Exec_LoadTraj.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_LoadTraj.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_ParallelAnalysis.o : Exec_ParallelAnalysis.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParallelAnalysis.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_ParmBox.o : Exec_ParmBox.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BoxArgs.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmBox.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_ParmSolvent.o : Exec_ParmSolvent.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmSolvent.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_ParmStrip.o : Exec_ParmStrip.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmStrip.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_ParmWrite.o : Exec_ParmWrite.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmWrite.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_ParseTiming.o : Exec_ParseTiming.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParseTiming.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_PermuteDihedrals.o : Exec_PermuteDihedrals.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h DistRoutines.h EnsembleIn.h EnsembleOutList.h ExclusionArray.h Exec.h Exec_PermuteDihedrals.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/RingFinder.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Precision.o : Exec_Precision.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Precision.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_PrepareForLeap.o : Exec_PrepareForLeap.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_PrepareForLeap.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h LeapInterface.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h Remote.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/Disulfide.h Structure/HisProt.h Structure/MetalCenterFinder.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-Exec_PrintData.o : Exec_PrintData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_PrintData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Random.o : Exec_Random.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Random.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_ReadData.o : Exec_ReadData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ReadData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_ReadEnsembleData.o : Exec_ReadEnsembleData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ReadEnsembleData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_ReadInput.o : Exec_ReadInput.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ReadInput.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_RotateDihedral.o : Exec_RotateDihedral.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_RotateDihedral.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_RunAnalysis.o : Exec_RunAnalysis.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_RunAnalysis.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_ScaleDihedralK.o : Exec_ScaleDihedralK.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ScaleDihedralK.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Calc.o : Exec_Calc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Calc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_CatCrd.o : Exec_CatCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CatCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_Change.o : Exec_Change.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Change.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_ClusterMap.o : Exec_ClusterMap.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ClusterMap.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ClusterMap.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_CombineCoords.o : Exec_CombineCoords.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CombineCoords.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_Commands.o : Exec_Commands.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Commands.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_CompareClusters.o : Exec_CompareClusters.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CompareClusters.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_CompareEnergy.o : Exec_CompareEnergy.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h Energy/Kernel_Fourier.h Energy/Kernel_Harmonic.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CompareEnergy.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_CompareTop.o : Exec_CompareTop.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CompareTop.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_CrdAction.o : Exec_CrdAction.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CrdAction.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_CrdOut.o : Exec_CrdOut.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CrdOut.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Unit.h Vec3.h
+Exec_CrdTransform.o : Exec_CrdTransform.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CrdTransform.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_CreateSet.o : Exec_CreateSet.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CreateSet.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_DataFile.o : Exec_DataFile.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_DataFile.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_DataFilter.o : Exec_DataFilter.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_DataFilter.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_DataSetCmd.o : Exec_DataSetCmd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h ArrayIterator.h AssociatedData.h AssociatedData_Connect.h AssociatedData_NOE.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_Mesh.h DataSet_Vector.h DataSet_string.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_DataSetCmd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_Desc.o : Exec_Desc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Desc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_Emin.o : Exec_Emin.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Emin.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h Parallel.h ParameterTypes.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_ExtendedComparison.o : Exec_ExtendedComparison.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ExtendedComparison.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_Flatten.o : Exec_Flatten.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Flatten.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_GenerateAmberRst.o : Exec_GenerateAmberRst.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_GenerateAmberRst.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_Graft.o : Exec_Graft.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Graft.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_Help.o : Exec_Help.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Help.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_HmassRepartition.o : Exec_HmassRepartition.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_HmassRepartition.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_LoadCrd.o : Exec_LoadCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_LoadCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h Unit.h Vec3.h
+Exec_LoadTraj.o : Exec_LoadTraj.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_LoadTraj.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_ParallelAnalysis.o : Exec_ParallelAnalysis.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParallelAnalysis.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_ParmBox.o : Exec_ParmBox.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BoxArgs.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmBox.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_ParmSolvent.o : Exec_ParmSolvent.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmSolvent.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_ParmStrip.o : Exec_ParmStrip.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmStrip.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_ParmWrite.o : Exec_ParmWrite.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmWrite.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_ParseTiming.o : Exec_ParseTiming.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParseTiming.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_PermuteDihedrals.o : Exec_PermuteDihedrals.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h DistRoutines.h EnsembleIn.h EnsembleOutList.h ExclusionArray.h Exec.h Exec_PermuteDihedrals.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PairList.h Parallel.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/RingFinder.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Unit.h Vec3.h
+Exec_Precision.o : Exec_Precision.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Precision.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_PrepareForLeap.o : Exec_PrepareForLeap.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMap.h AtomMask.h BaseIOtype.h Box.h CharMask.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_PrepareForLeap.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h LeapInterface.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h Remote.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/Disulfide.h Structure/HisProt.h Structure/MetalCenterFinder.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Unit.h Vec3.h
+Exec_PrintData.o : Exec_PrintData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_PrintData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_Random.o : Exec_Random.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Random.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_ReadData.o : Exec_ReadData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ReadData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_ReadEnsembleData.o : Exec_ReadEnsembleData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ReadEnsembleData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_ReadInput.o : Exec_ReadInput.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ReadInput.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_RotateDihedral.o : Exec_RotateDihedral.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_RotateDihedral.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_RunAnalysis.o : Exec_RunAnalysis.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_RunAnalysis.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_ScaleDihedralK.o : Exec_ScaleDihedralK.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ScaleDihedralK.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_Sequence.o : Exec_Sequence.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Sequence.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/Creator.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_SequenceAlign.o : Exec_SequenceAlign.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SequenceAlign.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Set.o : Exec_Set.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_StringVar.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Set.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Show.o : Exec_Show.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_StringVar.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Show.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_SortEnsembleData.o : Exec_SortEnsembleData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h DataSet_PHREMD_Implicit.h DataSet_pH.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SortEnsembleData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Source.o : Exec_Source.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Source.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_SplitCoords.o : Exec_SplitCoords.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SplitCoords.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_System.o : Exec_System.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_System.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Top.o : Exec_Top.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Top.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h TopInfo.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Traj.o : Exec_Traj.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Traj.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_SequenceAlign.o : Exec_SequenceAlign.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SequenceAlign.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Unit.h Vec3.h
+Exec_Set.o : Exec_Set.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_StringVar.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Set.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_Show.o : Exec_Show.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_StringVar.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Show.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_SortEnsembleData.o : Exec_SortEnsembleData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h DataSet_PHREMD_Implicit.h DataSet_pH.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SortEnsembleData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_Source.o : Exec_Source.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Source.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_SplitCoords.o : Exec_SplitCoords.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SplitCoords.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_System.o : Exec_System.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_System.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_Top.o : Exec_Top.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Top.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h TopInfo.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_Traj.o : Exec_Traj.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Traj.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_UpdateParameters.o : Exec_UpdateParameters.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h DataSet_Topology.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_UpdateParameters.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_ViewRst.o : Exec_ViewRst.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ViewRst.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h ViewRst.h
-Exec_Zmatrix.o : Exec_Zmatrix.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Zmatrix.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Zmatrix.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-ExtendedSimilarity.o : ExtendedSimilarity.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h ExtendedSimilarity.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Exec_ViewRst.o : Exec_ViewRst.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ViewRst.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h ViewRst.h
+Exec_Zmatrix.o : Exec_Zmatrix.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Zmatrix.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Zmatrix.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+ExtendedSimilarity.o : ExtendedSimilarity.cpp AssociatedData.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h ExtendedSimilarity.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h Unit.h Vec3.h
 ExternalFxn.o : ExternalFxn.cpp Random.h
 FileIO_Bzip2.o : FileIO_Bzip2.cpp CpptrajStdio.h FileIO.h FileIO_Bzip2.h
 FileIO_Gzip.o : FileIO_Gzip.cpp CpptrajStdio.h FileIO.h FileIO_Gzip.h
@@ -368,75 +368,77 @@ FileName.o : FileName.cpp CpptrajStdio.h FileName.h StringRoutines.h
 FileType.o : FileType.cpp FileType.h
 FileTypes.o : FileTypes.cpp ArgList.h BaseIOtype.h CpptrajStdio.h FileTypes.h
 File_TempName.o : File_TempName.cpp CpptrajStdio.h FileName.h File_TempName.h StringRoutines.h
-ForLoop.o : ForLoop.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h ForLoop.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-ForLoop_dataSetBlocks.o : ForLoop_dataSetBlocks.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_dataSetBlocks.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-ForLoop_inData.o : ForLoop_inData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_integer.h DataSet_string.h DataSet_unsignedInt.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_inData.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-ForLoop_integer.o : ForLoop_integer.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_integer.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-ForLoop_list.o : ForLoop_list.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_list.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-ForLoop_mask.o : ForLoop_mask.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_mask.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-ForLoop_overSets.o : ForLoop_overSets.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_overSets.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+ForLoop.o : ForLoop.cpp AssociatedData.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h ForLoop.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+ForLoop_dataSetBlocks.o : ForLoop_dataSetBlocks.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_dataSetBlocks.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+ForLoop_inData.o : ForLoop_inData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_integer.h DataSet_string.h DataSet_unsignedInt.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_inData.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+ForLoop_integer.o : ForLoop_integer.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_integer.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+ForLoop_list.o : ForLoop_list.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_list.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+ForLoop_mask.o : ForLoop_mask.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_mask.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+ForLoop_overSets.o : ForLoop_overSets.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_overSets.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Frame.o : Frame.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Unit.h Vec3.h
-GIST_PME.o : GIST_PME.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h EnergyKernel_Adjust.h EnergyKernel_Nonbond.h Ewald.h Ewald_ParticleMesh.h ExclusionArray.h FileName.h Frame.h GIST_PME.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h helpme_standalone.h
+GIST_PME.o : GIST_PME.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h EnergyKernel_Adjust.h EnergyKernel_Nonbond.h Ewald.h Ewald_ParticleMesh.h ExclusionArray.h FileName.h Frame.h GIST_PME.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h Timer.h Topology.h Unit.h Vec3.h helpme_standalone.h
 GistEntropyUtils.o : GistEntropyUtils.cpp CpptrajFile.h FileIO.h FileName.h GistEntropyUtils.h Parallel.h Vec3.h
 Gpu.o : Gpu.cpp Gpu.h
-GridAction.o : GridAction.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridAction.h GridBin.h GridMover.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+GridAction.o : GridAction.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridAction.h GridBin.h GridMover.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 GridBin.o : GridBin.cpp Box.h CpptrajStdio.h GridBin.h Matrix_3x3.h Parallel.h Vec3.h
-GridMover.o : GridMover.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_3D.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h GridMover.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+GridMover.o : GridMover.cpp AssociatedData.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_3D.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h GridMover.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h Unit.h Vec3.h
 GuessAtomHybridization.o : GuessAtomHybridization.cpp Atom.h AtomType.h Constants.h GuessAtomHybridization.h NameType.h ParameterTypes.h SymbolExporting.h
 HistBin.o : HistBin.cpp Constants.h CpptrajStdio.h Dimension.h HistBin.h
 Hungarian.o : Hungarian.cpp ArrayIterator.h Constants.h CpptrajStdio.h Hungarian.h Matrix.h
 ImageRoutines.o : ImageRoutines.cpp Atom.h AtomMask.h Box.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h Frame.h ImageOption.h ImageRoutines.h ImageTypes.h Image_List.h Image_List_Mask.h Image_List_Pair.h Image_List_Pair_CoM.h Image_List_Pair_First.h Image_List_Pair_Geom.h Image_List_Unit.h Image_List_Unit_CoM.h Image_List_Unit_First.h Image_List_Unit_Geom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Unit.h Vec3.h
-Image_List_Mask.o : Image_List_Mask.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h Image_List.h Image_List_Mask.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Image_List_Pair.o : Image_List_Pair.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h Image_List.h Image_List_Pair.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Image_List_Unit.o : Image_List_Unit.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h Image_List.h Image_List_Unit.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Image_List_Mask.o : Image_List_Mask.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h Image_List.h Image_List_Mask.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h
+Image_List_Pair.o : Image_List_Pair.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h Image_List.h Image_List_Pair.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
+Image_List_Unit.o : Image_List_Unit.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h Image_List.h Image_List_Unit.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
 InputTrajCommon.o : InputTrajCommon.cpp CpptrajStdio.h FileName.h InputTrajCommon.h TrajFrameCounter.h
-InteractionData.o : InteractionData.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h InteractionData.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+InteractionData.o : InteractionData.cpp AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h InteractionData.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 KDE.o : KDE.cpp AssociatedData.h Constants.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_double.h Dimension.h FileIO.h FileName.h HistBin.h KDE.h MetaData.h Parallel.h Range.h TextFormat.h
-LeapInterface.o : LeapInterface.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h File_TempName.h Frame.h LeapInterface.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+LeapInterface.o : LeapInterface.cpp ArgList.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h File_TempName.h Frame.h LeapInterface.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h
 MapAtom.o : MapAtom.cpp Atom.h MapAtom.h NameType.h SymbolExporting.h
-MaskArray.o : MaskArray.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+MaskArray.o : MaskArray.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
 MaskToken.o : MaskToken.cpp ArgList.h Atom.h CpptrajStdio.h DistRoutines.h ImageOption.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Unit.h
 Matrix_3x3.o : Matrix_3x3.cpp Constants.h CpptrajStdio.h Matrix_3x3.h Parallel.h Vec3.h
 MdOpts.o : MdOpts.cpp ArgList.h Constants.h Constraints.h CpptrajStdio.h MdOpts.h ParameterTypes.h
 MetaData.o : MetaData.cpp CpptrajStdio.h FileName.h MetaData.h Range.h StringRoutines.h
-Minimize_SteepestDescent.o : Minimize_SteepestDescent.cpp ActionFrameCounter.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h EnergyArray.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-Mol.o : Mol.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Mol.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Minimize_SteepestDescent.o : Minimize_SteepestDescent.cpp ActionFrameCounter.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h EnergyArray.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h Unit.h Vec3.h
+Mol.o : Mol.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Mol.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Mol2File.o : Mol2File.cpp Atom.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Mol2File.h NameType.h Parallel.h Residue.h StringRoutines.h SymbolExporting.h
 NC_Routines.o : NC_Routines.cpp CpptrajStdio.h NC_Routines.h
 NDiff.o : NDiff.cpp ArgList.h BufferedLine.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NDiff.h Parallel.h StringRoutines.h
 NameType.o : NameType.cpp CpptrajStdio.h NameType.h
 NetcdfFile.o : NetcdfFile.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h ParallelNetcdf.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Unit.h Vec3.h Version.h
 OMM_helpers.o : OMM_helpers.cpp Constants.h OMM_helpers.h ParameterTypes.h
-OutputTrajCommon.o : OutputTrajCommon.cpp ActionFrameCounter.h ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+OutputTrajCommon.o : OutputTrajCommon.cpp ActionFrameCounter.h ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h Unit.h Vec3.h
 PDBfile.o : PDBfile.cpp Atom.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h PDBfile.h Parallel.h Residue.h StringRoutines.h SymbolExporting.h
 PairList.o : PairList.cpp Atom.h AtomMask.h Box.h CoordinateInfo.h CpptrajStdio.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Timer.h Unit.h Vec3.h
 Parallel.o : Parallel.cpp Parallel.h
 ParallelNetcdf.o : ParallelNetcdf.cpp CpptrajStdio.h Parallel.h ParallelNetcdf.h
 ParameterSet.o : ParameterSet.cpp AtomType.h CmapParmHolder.h Constants.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h TypeNameHolder.h UpdateParameters.h
-Parm/GB_Params.o : Parm/GB_Params.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/GB_Params.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Parm/Merge.o : Parm/Merge.cpp Atom.h Constants.h CpptrajStdio.h NameType.h ParameterHolders.h ParameterTypes.h Parm/Merge.h Residue.h StringRoutines.h SymbolExporting.h TypeNameHolder.h
+Parm/AssignParams.o : Parm/AssignParams.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h GuessAtomHybridization.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/../Structure/GenerateConnectivityArrays.h Parm/AssignParams.h Parm/GetParams.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Parm/GB_Params.o : Parm/GB_Params.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/GB_Params.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
+Parm/GetParams.o : Parm/GetParams.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/GetParams.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Parm/Merge.o : Parm/Merge.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterTypes.h Parm/AssignParams.h Parm/GetParams.h Parm/Merge.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h UpdateParameters.h Vec3.h
 ParmFile.o : ParmFile.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h ParmIO.h Parm_Amber.h Parm_CIF.h Parm_CharmmPsf.h Parm_Gromacs.h Parm_Mol2.h Parm_PDB.h Parm_SDF.h Parm_Tinker.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Parm_Amber.o : Parm_Amber.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h ExclusionArray.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_Amber.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Parm_CIF.o : Parm_CIF.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h CIFfile.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_CIF.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Parm_Amber.o : Parm_Amber.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h ExclusionArray.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmIO.h Parm_Amber.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h Unit.h Vec3.h
+Parm_CIF.o : Parm_CIF.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h CIFfile.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmIO.h Parm_CIF.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Parm_CharmmPsf.o : Parm_CharmmPsf.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h CharmmParamFile.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Mol.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_CharmmPsf.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Parm_Gromacs.o : Parm_Gromacs.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_Gromacs.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Parm_Mol2.o : Parm_Mol2.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Mol2File.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_Mol2.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Parm_PDB.o : Parm_PDB.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_PDB.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Parm_SDF.o : Parm_SDF.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_SDF.h Range.h ReplicaDimArray.h Residue.h SDFfile.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Parm_Tinker.o : Parm_Tinker.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_Tinker.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TinkerFile.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-PotentialFunction.o : PotentialFunction.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h CmapParmHolder.h Constants.h Constraints.h CoordinateInfo.h CpptrajStdio.h EnergyArray.h ExclusionArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MdOpts.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PotentialFunction.h PotentialTerm.h PotentialTerm_Angle.h PotentialTerm_Bond.h PotentialTerm_Dihedral.h PotentialTerm_LJ_Coulomb.h PotentialTerm_OpenMM.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Parm_Gromacs.o : Parm_Gromacs.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmIO.h Parm_Gromacs.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h
+Parm_Mol2.o : Parm_Mol2.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Mol2File.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmIO.h Parm_Mol2.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
+Parm_PDB.o : Parm_PDB.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterTypes.h ParmIO.h Parm_PDB.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Timer.h Topology.h Unit.h Vec3.h
+Parm_SDF.o : Parm_SDF.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmIO.h Parm_SDF.h Range.h ReplicaDimArray.h Residue.h SDFfile.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
+Parm_Tinker.o : Parm_Tinker.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmIO.h Parm_Tinker.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TinkerFile.h Topology.h Unit.h Vec3.h
+PotentialFunction.o : PotentialFunction.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajStdio.h EnergyArray.h ExclusionArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MdOpts.h Molecule.h NameType.h Parallel.h ParameterTypes.h PotentialFunction.h PotentialTerm.h PotentialTerm_Angle.h PotentialTerm_Bond.h PotentialTerm_Dihedral.h PotentialTerm_LJ_Coulomb.h PotentialTerm_OpenMM.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
 PotentialTerm.o : PotentialTerm.cpp PotentialTerm.h
-PotentialTerm_Angle.o : PotentialTerm_Angle.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h EnergyArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PotentialTerm.h PotentialTerm_Angle.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-PotentialTerm_Bond.o : PotentialTerm_Bond.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h EnergyArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PotentialTerm.h PotentialTerm_Bond.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-PotentialTerm_Dihedral.o : PotentialTerm_Dihedral.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h EnergyArray.h EnergyKernel_NonBond_Simple.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PotentialTerm.h PotentialTerm_Dihedral.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-PotentialTerm_LJ_Coulomb.o : PotentialTerm_LJ_Coulomb.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h CmapParmHolder.h Constants.h Constraints.h CoordinateInfo.h CpptrajStdio.h EnergyArray.h EnergyKernel_NonBond_Simple.h ExclusionArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MdOpts.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PotentialTerm.h PotentialTerm_LJ_Coulomb.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-PotentialTerm_OpenMM.o : PotentialTerm_OpenMM.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h CmapParmHolder.h Constants.h Constraints.h CoordinateInfo.h CpptrajStdio.h EnergyArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MdOpts.h Molecule.h NameType.h OMM_helpers.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PotentialTerm.h PotentialTerm_OpenMM.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+PotentialTerm_Angle.o : PotentialTerm_Angle.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h EnergyArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h PotentialTerm.h PotentialTerm_Angle.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
+PotentialTerm_Bond.o : PotentialTerm_Bond.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h EnergyArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h PotentialTerm.h PotentialTerm_Bond.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
+PotentialTerm_Dihedral.o : PotentialTerm_Dihedral.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h EnergyArray.h EnergyKernel_NonBond_Simple.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h PotentialTerm.h PotentialTerm_Dihedral.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
+PotentialTerm_LJ_Coulomb.o : PotentialTerm_LJ_Coulomb.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajStdio.h EnergyArray.h EnergyKernel_NonBond_Simple.h ExclusionArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MdOpts.h Molecule.h NameType.h Parallel.h ParameterTypes.h PotentialTerm.h PotentialTerm_LJ_Coulomb.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
+PotentialTerm_OpenMM.o : PotentialTerm_OpenMM.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajStdio.h EnergyArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MdOpts.h Molecule.h NameType.h OMM_helpers.h Parallel.h ParameterTypes.h PotentialTerm.h PotentialTerm_OpenMM.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
 ProgressBar.o : ProgressBar.cpp CpptrajStdio.h ProgressBar.h
 ProgressTimer.o : ProgressTimer.cpp CpptrajStdio.h ProgressTimer.h Timer.h
 PubFFT.o : PubFFT.cpp ArrayIterator.h ComplexArray.h CpptrajStdio.h PubFFT.h
-Pucker_PuckerMask.o : Pucker_PuckerMask.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Pucker_PuckerMask.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Pucker_PuckerSearch.o : Pucker_PuckerSearch.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Pucker.h Pucker_PuckerMask.h Pucker_PuckerSearch.h Pucker_PuckerToken.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Pucker_PuckerToken.o : Pucker_PuckerToken.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Pucker_PuckerMask.h Pucker_PuckerToken.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Pucker_PuckerMask.o : Pucker_PuckerMask.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Pucker_PuckerMask.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
+Pucker_PuckerSearch.o : Pucker_PuckerSearch.cpp ArgList.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Pucker.h Pucker_PuckerMask.h Pucker_PuckerSearch.h Pucker_PuckerToken.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
+Pucker_PuckerToken.o : Pucker_PuckerToken.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Pucker_PuckerMask.h Pucker_PuckerToken.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
 QuaternionRMSD.o : QuaternionRMSD.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h QuaternionRMSD.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Unit.h Vec3.h qcprot.h
 RNG.o : RNG.cpp CpptrajStdio.h RNG.h
 RNG_Marsaglia.o : RNG_Marsaglia.cpp CpptrajStdio.h RNG.h RNG_Marsaglia.h
@@ -444,11 +446,11 @@ RNG_MersenneTwister.o : RNG_MersenneTwister.cpp CpptrajStdio.h RNG.h RNG_Mersenn
 RNG_PCG32.o : RNG_PCG32.cpp CpptrajStdio.h RNG.h RNG_PCG32.h pcg_random.hpp
 RNG_Stdlib.o : RNG_Stdlib.cpp RNG.h RNG_Stdlib.h
 RNG_Xoshiro128pp.o : RNG_Xoshiro128pp.cpp RNG.h RNG_Xoshiro128pp.h xoshiro128plusplus.h
-RPNcalc.o : RPNcalc.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_Mesh.h DataSet_Vector.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+RPNcalc.o : RPNcalc.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_Mesh.h DataSet_Vector.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 Random.o : Random.cpp CpptrajStdio.h RNG.h RNG_Marsaglia.h RNG_MersenneTwister.h RNG_PCG32.h RNG_Stdlib.h RNG_Xoshiro128pp.h Random.h pcg_random.hpp
 Range.o : Range.cpp ArgList.h CpptrajStdio.h Range.h StringRoutines.h
-ReadLine.o : ReadLine.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Cmd.h CmdInput.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReadLine.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-ReferenceAction.o : ReferenceAction.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h Dimension.h FileIO.h FileName.h Frame.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TypeNameHolder.h Unit.h Vec3.h
+ReadLine.o : ReadLine.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cmd.h CmdInput.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReadLine.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+ReferenceAction.o : ReferenceAction.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h Dimension.h FileIO.h FileName.h Frame.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h Unit.h Vec3.h
 RemdReservoirNC.o : RemdReservoirNC.cpp Atom.h AtomMask.h Box.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h RemdReservoirNC.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Unit.h Vec3.h
 Remote.o : Remote.cpp CpptrajStdio.h FileName.h Remote.h
 Residue.o : Residue.cpp CpptrajStdio.h NameType.h Residue.h
@@ -458,74 +460,74 @@ SpaceGroup.o : SpaceGroup.cpp Matrix_3x3.h Parallel.h SpaceGroup.h Vec3.h
 Spline.o : Spline.cpp CpptrajStdio.h Spline.h
 SplineFxnTable.o : SplineFxnTable.cpp Constants.h CpptrajStdio.h Spline.h SplineFxnTable.h StringRoutines.h
 StringRoutines.o : StringRoutines.cpp CpptrajStdio.h StringRoutines.h
-Structure/Builder.o : Structure/Builder.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h GuessAtomHybridization.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Builder.h Structure/Chirality.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Structure/Chirality.o : Structure/Chirality.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Chirality.h Structure/StructureEnum.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Structure/Builder.o : Structure/Builder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h GuessAtomHybridization.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Builder.h Structure/Chirality.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h Unit.h Vec3.h
+Structure/Chirality.o : Structure/Chirality.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Chirality.h Structure/StructureEnum.h SymbolExporting.h Topology.h TorsionRoutines.h Unit.h Vec3.h
 Structure/Creator.o : Structure/Creator.cpp ArgList.h AssociatedData.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/Creator.h Structure/GenerateConnectivityArrays.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Structure/Disulfide.o : Structure/Disulfide.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Disulfide.h Structure/ResStatArray.h Structure/StructureRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Structure/FunctionalGroup.o : Structure/FunctionalGroup.cpp Atom.h AtomMap.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Structure/FxnGroupBuilder.o : Structure/FxnGroupBuilder.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h Structure/FxnGroupBuilder.h Structure/StructureRoutines.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Structure/Disulfide.o : Structure/Disulfide.cpp ArgList.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Disulfide.h Structure/ResStatArray.h Structure/StructureRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h
+Structure/FunctionalGroup.o : Structure/FunctionalGroup.cpp Atom.h AtomMap.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h SymbolExporting.h Topology.h Unit.h Vec3.h
+Structure/FxnGroupBuilder.o : Structure/FxnGroupBuilder.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h Structure/FxnGroupBuilder.h Structure/StructureRoutines.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Structure/GenerateConnectivityArrays.o : Structure/GenerateConnectivityArrays.cpp Atom.h Constants.h CpptrajStdio.h NameType.h ParameterTypes.h Residue.h Structure/GenerateConnectivityArrays.h SymbolExporting.h
-Structure/HisProt.o : Structure/HisProt.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/HisProt.h Structure/StructureRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Structure/InternalCoords.o : Structure/InternalCoords.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/InternalCoords.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Structure/HisProt.o : Structure/HisProt.cpp ArgList.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/HisProt.h Structure/StructureRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h
+Structure/InternalCoords.o : Structure/InternalCoords.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/InternalCoords.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Structure/LeastSquaresPlane.o : Structure/LeastSquaresPlane.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h Residue.h Segment.h Structure/LeastSquaresPlane.h SymbolExporting.h Unit.h Vec3.h
-Structure/MetalCenterFinder.o : Structure/MetalCenterFinder.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/MetalCenterFinder.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Structure/PdbCleaner.o : Structure/PdbCleaner.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/PdbCleaner.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Structure/RingFinder.o : Structure/RingFinder.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/RingFinder.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Structure/MetalCenterFinder.o : Structure/MetalCenterFinder.cpp ArgList.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/MetalCenterFinder.h SymbolExporting.h Topology.h Unit.h Vec3.h
+Structure/PdbCleaner.o : Structure/PdbCleaner.cpp ArgList.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/PdbCleaner.h SymbolExporting.h Topology.h Unit.h Vec3.h
+Structure/RingFinder.o : Structure/RingFinder.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/RingFinder.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Structure/StructureEnum.o : Structure/StructureEnum.cpp Structure/StructureEnum.h
 Structure/StructureRoutines.o : Structure/StructureRoutines.cpp Atom.h CpptrajStdio.h NameType.h Residue.h Structure/StructureRoutines.h SymbolExporting.h
-Structure/Sugar.o : Structure/Sugar.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Structure/SugarBuilder.o : Structure/SugarBuilder.cpp ArgList.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DistRoutines.h FileIO.h FileName.h Frame.h ImageOption.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Chirality.h Structure/FunctionalGroup.h Structure/FxnGroupBuilder.h Structure/LinkAtom.h Structure/ResStatArray.h Structure/StructureEnum.h Structure/StructureRoutines.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarLinkAtoms.h Structure/SugarToken.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Structure/SugarLinkAtoms.o : Structure/SugarLinkAtoms.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/LinkAtom.h Structure/SugarLinkAtoms.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Structure/Sugar.o : Structure/Sugar.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h Unit.h Vec3.h
+Structure/SugarBuilder.o : Structure/SugarBuilder.cpp ArgList.h Atom.h AtomMap.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DistRoutines.h FileIO.h FileName.h Frame.h ImageOption.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Chirality.h Structure/FunctionalGroup.h Structure/FxnGroupBuilder.h Structure/LinkAtom.h Structure/ResStatArray.h Structure/StructureEnum.h Structure/StructureRoutines.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarLinkAtoms.h Structure/SugarToken.h SymbolExporting.h Topology.h TorsionRoutines.h Unit.h Vec3.h
+Structure/SugarLinkAtoms.o : Structure/SugarLinkAtoms.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/LinkAtom.h Structure/SugarLinkAtoms.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Structure/SugarToken.o : Structure/SugarToken.cpp ArgList.h CpptrajStdio.h Structure/SugarToken.h
-Structure/Zmatrix.o : Structure/Zmatrix.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-StructureCheck.o : StructureCheck.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h ExclusionArray.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/LeastSquaresPlane.h Structure/RingFinder.h StructureCheck.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-StructureMapper.o : StructureMapper.cpp AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Chirality.h Structure/StructureEnum.h StructureMapper.h SymbolExporting.h TextFormat.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-SymmetricRmsdCalc.o : SymmetricRmsdCalc.cpp ArrayIterator.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h Hungarian.h ImageOption.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Structure/Zmatrix.o : Structure/Zmatrix.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h Unit.h Vec3.h
+StructureCheck.o : StructureCheck.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h ExclusionArray.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/LeastSquaresPlane.h Structure/RingFinder.h StructureCheck.h SymbolExporting.h Timer.h Topology.h Unit.h Vec3.h
+StructureMapper.o : StructureMapper.cpp AssociatedData.h Atom.h AtomMap.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Chirality.h Structure/StructureEnum.h StructureMapper.h SymbolExporting.h TextFormat.h Topology.h TorsionRoutines.h Unit.h Vec3.h
+SymmetricRmsdCalc.o : SymmetricRmsdCalc.cpp ArrayIterator.h Atom.h AtomMap.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h Hungarian.h ImageOption.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h Topology.h Unit.h Vec3.h
 TextBlockBuffer.o : TextBlockBuffer.cpp BufferedLine.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Parallel.h TextBlockBuffer.h
 TextFormat.o : TextFormat.cpp StringRoutines.h TextFormat.h
 Timer.o : Timer.cpp CpptrajStdio.h Timer.h
 TinkerFile.o : TinkerFile.cpp ArgList.h Atom.h AtomMask.h Box.h BufferedLine.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TinkerFile.h Unit.h Vec3.h
-TopInfo.o : TopInfo.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h DistRoutines.h FileIO.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Mol.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h TopInfo.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Topology.o : Topology.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h GuessAtomHybridization.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/Merge.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/GenerateConnectivityArrays.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h UpdateParameters.h Vec3.h
+TopInfo.o : TopInfo.cpp AssociatedData.h Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h DistRoutines.h FileIO.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Mol.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h TopInfo.h Topology.h TorsionRoutines.h Unit.h Vec3.h
+Topology.o : Topology.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h
 TorsionRoutines.o : TorsionRoutines.cpp Constants.h TorsionRoutines.h Vec3.h
 TrajFrameCounter.o : TrajFrameCounter.cpp ArgList.h CpptrajStdio.h TrajFrameCounter.h
-TrajIOarray.o : TrajIOarray.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryFile.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_AmberCoord.o : Traj_AmberCoord.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedFrame.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h Traj_AmberCoord.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_AmberNetcdf.o : Traj_AmberNetcdf.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h ParallelNetcdf.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_AmberNetcdf.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_AmberRestart.o : Traj_AmberRestart.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedFrame.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextBlockBuffer.h TextFormat.h Topology.h Traj_AmberRestart.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_AmberRestartNC.o : Traj_AmberRestartNC.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Traj_AmberRestartNC.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_Binpos.o : Traj_Binpos.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_Binpos.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_CIF.o : Traj_CIF.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CIFfile.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Traj_CIF.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_CharmmCor.o : Traj_CharmmCor.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Traj_CharmmCor.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_CharmmDcd.o : Traj_CharmmDcd.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ByteRoutines.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_CharmmDcd.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_CharmmRestart.o : Traj_CharmmRestart.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedFrame.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h Traj_CharmmRestart.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_Conflib.o : Traj_Conflib.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_Conflib.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_DTR.o : Traj_DTR.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_DTR.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h vmdplugin/dtrplugin.hxx
-Traj_GmxDump.o : Traj_GmxDump.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_GmxDump.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_GmxTng.o : Traj_GmxTng.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_GmxTng.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_GmxTrX.o : Traj_GmxTrX.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ByteRoutines.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_GmxTrX.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_GmxXtc.o : Traj_GmxXtc.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_GmxXtc.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_Gro.o : Traj_Gro.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Traj_Gro.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_H5.o : Traj_H5.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_H5.h TrajectoryIO.h TypeNameHolder.h Unit.h Units.h Vec3.h
-Traj_H5MD.o : Traj_H5MD.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_H5MD.h TrajectoryIO.h TypeNameHolder.h Unit.h Units.h Vec3.h
-Traj_Mol2File.o : Traj_Mol2File.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Mol2File.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_Mol2File.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_NcEnsemble.o : Traj_NcEnsemble.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FrameArray.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h ParallelNetcdf.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_NcEnsemble.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_PDBfile.o : Traj_PDBfile.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Tensor.h Dimension.h DistRoutines.h FileIO.h FileName.h Frame.h FramePtrArray.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricTensor.h TextFormat.h Timer.h Topology.h Traj_PDBfile.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_SDF.o : Traj_SDF.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SDFfile.h Segment.h SymbolExporting.h Topology.h Traj_SDF.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_SQM.o : Traj_SQM.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Traj_SQM.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_Tinker.o : Traj_Tinker.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TinkerFile.h Topology.h Traj_Tinker.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
-Traj_XYZ.o : Traj_XYZ.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h Traj_XYZ.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
+TrajIOarray.o : TrajIOarray.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryFile.h TrajectoryIO.h Unit.h Vec3.h
+Traj_AmberCoord.o : Traj_AmberCoord.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h Traj_AmberCoord.h TrajectoryIO.h Unit.h Vec3.h
+Traj_AmberNetcdf.o : Traj_AmberNetcdf.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h ParallelNetcdf.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_AmberNetcdf.h TrajectoryIO.h Unit.h Vec3.h
+Traj_AmberRestart.o : Traj_AmberRestart.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedFrame.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextBlockBuffer.h TextFormat.h Topology.h Traj_AmberRestart.h TrajectoryIO.h Unit.h Vec3.h
+Traj_AmberRestartNC.o : Traj_AmberRestartNC.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Traj_AmberRestartNC.h TrajectoryIO.h Unit.h Vec3.h
+Traj_Binpos.o : Traj_Binpos.cpp Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_Binpos.h TrajectoryIO.h Unit.h Vec3.h
+Traj_CIF.o : Traj_CIF.cpp Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h CIFfile.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Traj_CIF.h TrajectoryIO.h Unit.h Vec3.h
+Traj_CharmmCor.o : Traj_CharmmCor.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Traj_CharmmCor.h TrajectoryIO.h Unit.h Vec3.h
+Traj_CharmmDcd.o : Traj_CharmmDcd.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h ByteRoutines.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_CharmmDcd.h TrajectoryIO.h Unit.h Vec3.h
+Traj_CharmmRestart.o : Traj_CharmmRestart.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedFrame.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h Traj_CharmmRestart.h TrajectoryIO.h Unit.h Vec3.h
+Traj_Conflib.o : Traj_Conflib.cpp Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_Conflib.h TrajectoryIO.h Unit.h Vec3.h
+Traj_DTR.o : Traj_DTR.cpp Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_DTR.h TrajectoryIO.h Unit.h Vec3.h vmdplugin/dtrplugin.hxx
+Traj_GmxDump.o : Traj_GmxDump.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_GmxDump.h TrajectoryIO.h Unit.h Vec3.h
+Traj_GmxTng.o : Traj_GmxTng.cpp Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_GmxTng.h TrajectoryIO.h Unit.h Vec3.h
+Traj_GmxTrX.o : Traj_GmxTrX.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h ByteRoutines.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_GmxTrX.h TrajectoryIO.h Unit.h Vec3.h
+Traj_GmxXtc.o : Traj_GmxXtc.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_GmxXtc.h TrajectoryIO.h Unit.h Vec3.h
+Traj_Gro.o : Traj_Gro.cpp Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Traj_Gro.h TrajectoryIO.h Unit.h Vec3.h
+Traj_H5.o : Traj_H5.cpp Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_H5.h TrajectoryIO.h Unit.h Units.h Vec3.h
+Traj_H5MD.o : Traj_H5MD.cpp Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_H5MD.h TrajectoryIO.h Unit.h Units.h Vec3.h
+Traj_Mol2File.o : Traj_Mol2File.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Mol2File.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_Mol2File.h TrajectoryIO.h Unit.h Vec3.h
+Traj_NcEnsemble.o : Traj_NcEnsemble.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FrameArray.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h ParallelNetcdf.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_NcEnsemble.h TrajectoryIO.h Unit.h Vec3.h
+Traj_PDBfile.o : Traj_PDBfile.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Tensor.h Dimension.h DistRoutines.h FileIO.h FileName.h Frame.h FramePtrArray.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricTensor.h TextFormat.h Timer.h Topology.h Traj_PDBfile.h TrajectoryIO.h Unit.h Vec3.h
+Traj_SDF.o : Traj_SDF.cpp Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SDFfile.h Segment.h SymbolExporting.h Topology.h Traj_SDF.h TrajectoryIO.h Unit.h Vec3.h
+Traj_SQM.o : Traj_SQM.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Traj_SQM.h TrajectoryIO.h Unit.h Vec3.h
+Traj_Tinker.o : Traj_Tinker.cpp Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TinkerFile.h Topology.h Traj_Tinker.h TrajectoryIO.h Unit.h Vec3.h
+Traj_XYZ.o : Traj_XYZ.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h Traj_XYZ.h TrajectoryIO.h Unit.h Vec3.h
 TrajectoryFile.o : TrajectoryFile.cpp Atom.h BaseIOtype.h Box.h BufferedFrame.h BufferedLine.h CIFfile.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h FileTypes.h FramePtrArray.h Matrix_3x3.h Mol2File.h NC_Routines.h NameType.h NetcdfFile.h PDBfile.h Parallel.h ReplicaDimArray.h Residue.h SDFfile.h SymbolExporting.h TextFormat.h TinkerFile.h Traj_AmberCoord.h Traj_AmberNetcdf.h Traj_AmberRestart.h Traj_AmberRestartNC.h Traj_Binpos.h Traj_CIF.h Traj_CharmmCor.h Traj_CharmmDcd.h Traj_CharmmRestart.h Traj_Conflib.h Traj_DTR.h Traj_GmxDump.h Traj_GmxTng.h Traj_GmxTrX.h Traj_GmxXtc.h Traj_Gro.h Traj_H5.h Traj_H5MD.h Traj_Mol2File.h Traj_NcEnsemble.h Traj_PDBfile.h Traj_SDF.h Traj_SQM.h Traj_Tinker.h Traj_XYZ.h TrajectoryFile.h TrajectoryIO.h Vec3.h
 TrajectoryIO.o : TrajectoryIO.cpp BaseIOtype.h Box.h CoordinateInfo.h CpptrajStdio.h FramePtrArray.h Matrix_3x3.h Parallel.h ReplicaDimArray.h TrajectoryIO.h Vec3.h
-TrajinList.o : TrajinList.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_RemLog.h Dimension.h EnsembleIn.h EnsembleIn_Multi.h EnsembleIn_Single.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryFile.h TrajectoryIO.h Trajin.h TrajinList.h Trajin_Multi.h Trajin_Single.h TypeNameHolder.h Unit.h Vec3.h
-Trajin_Multi.o : Trajin_Multi.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryIO.h Trajin.h Trajin_Multi.h TypeNameHolder.h Unit.h Vec3.h
-Trajin_Single.o : Trajin_Single.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h Trajin.h Trajin_Single.h TypeNameHolder.h Unit.h Vec3.h
-TrajoutList.o : TrajoutList.cpp ActionFrameCounter.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-Trajout_Single.o : Trajout_Single.cpp ActionFrameCounter.h ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+TrajinList.o : TrajinList.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_RemLog.h Dimension.h EnsembleIn.h EnsembleIn_Multi.h EnsembleIn_Single.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryFile.h TrajectoryIO.h Trajin.h TrajinList.h Trajin_Multi.h Trajin_Single.h Unit.h Vec3.h
+Trajin_Multi.o : Trajin_Multi.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryIO.h Trajin.h Trajin_Multi.h Unit.h Vec3.h
+Trajin_Single.o : Trajin_Single.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h Trajin.h Trajin_Single.h Unit.h Vec3.h
+TrajoutList.o : TrajoutList.cpp ActionFrameCounter.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TrajoutList.h Trajout_Single.h Unit.h Vec3.h
+Trajout_Single.o : Trajout_Single.cpp ActionFrameCounter.h ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h Trajout_Single.h Unit.h Vec3.h
 Units.o : Units.cpp Constants.h CpptrajStdio.h Units.h
 Vec3.o : Vec3.cpp Constants.h CpptrajStdio.h Vec3.h
-ViewRst.o : ViewRst.cpp ActionFrameCounter.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h ViewRst.h
-main.o : main.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h Cpptraj.h CpptrajFile.h CpptrajState.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+ViewRst.o : ViewRst.cpp ActionFrameCounter.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h Unit.h Vec3.h ViewRst.h
+main.o : main.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h Cpptraj.h CpptrajFile.h CpptrajState.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 molsurf.o : molsurf.c molsurf.h
 qcprot.o : qcprot.cpp CpptrajStdio.h qcprot.h
 vmdplugin/dtrplugin.o : vmdplugin/dtrplugin.cpp ByteRoutines.h vmdplugin/dtrplugin.hxx vmdplugin/vmddir.h

From ac26e340b3b30d802f8071588fff02f05f4f8664 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 21 Jul 2024 15:01:46 -0400
Subject: [PATCH 0872/1492] Set debug and verbosity

---
 src/Parm/Merge.cpp | 10 ++++++++++
 src/Parm/Merge.h   |  4 ++++
 2 files changed, 14 insertions(+)

diff --git a/src/Parm/Merge.cpp b/src/Parm/Merge.cpp
index 5bf07fa645..4deac32b65 100644
--- a/src/Parm/Merge.cpp
+++ b/src/Parm/Merge.cpp
@@ -19,6 +19,16 @@ Merge::Merge() :
   verbose_(1) // FIXME
 {}
 
+/** Set debug */
+void Merge::SetDebug(int debugIn) {
+  debug_ = debugIn;
+}
+
+/** Set verbosity */
+void Merge::SetVerbose(int verboseIn) {
+  verbose_ = verboseIn;
+}
+
 // ----- Bonds -------------------------
 static inline void printIdx(BondType const& bnd1, unsigned int atomOffset) {
   mprintf("DEBUG: Bond from top1 %i - %i will be %i - %i in top0\n",
diff --git a/src/Parm/Merge.h b/src/Parm/Merge.h
index fd3e114750..6efed94cb9 100644
--- a/src/Parm/Merge.h
+++ b/src/Parm/Merge.h
@@ -19,6 +19,10 @@ class Merge {
   public:
     /// CONSTRUCTOR
     Merge();
+    /// Set debug level
+    void SetDebug(int);
+    /// Set parameter verbosity
+    void SetVerbose(int);
     /// Append topology to this one.
     int AppendTop( Topology&, Topology const& ) const;
   private:

From 92e689dc8a21e134b045d1457928275eb5f61bd0 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 21 Jul 2024 15:55:28 -0400
Subject: [PATCH 0873/1492] Use Merge

---
 src/Action_ReplicateCell.cpp | 13 +++++++++++--
 src/Action_ReplicateCell.h   |  1 +
 src/cpptrajdepend            |  2 +-
 3 files changed, 13 insertions(+), 3 deletions(-)

diff --git a/src/Action_ReplicateCell.cpp b/src/Action_ReplicateCell.cpp
index 9ee6d0b0b8..78b558a5a1 100644
--- a/src/Action_ReplicateCell.cpp
+++ b/src/Action_ReplicateCell.cpp
@@ -1,9 +1,15 @@
 #include "Action_ReplicateCell.h"
 #include "CpptrajStdio.h"
 #include "DataSet_Coords.h"
+#include "Parm/Merge.h"
 
 // CONSTRUCTOR
-Action_ReplicateCell::Action_ReplicateCell() : coords_(0), ncopies_(0), writeTraj_(false) {} 
+Action_ReplicateCell::Action_ReplicateCell() :
+  coords_(0),
+  ncopies_(0),
+  debug_(0),
+  writeTraj_(false)
+{} 
 
 void Action_ReplicateCell::Help() const {
   mprintf("\t[out <traj filename>] [name <dsname>]\n"
@@ -33,6 +39,7 @@ static inline int toDigit(char c) {
 // Action_ReplicateCell::Init()
 Action::RetType Action_ReplicateCell::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
 {
+  debug_ = debugIn;
   // Set up output traj
   std::string trajfilename = actionArgs.GetStringKey("out");
   topWriter_.InitTopWriter( actionArgs, "replicated cell", debugIn );
@@ -151,8 +158,10 @@ Action::RetType Action_ReplicateCell::Setup(ActionSetup& setup) {
     // Set up topology and frame.
     Topology* stripParm = setup.Top().modifyStateByMask( Mask1_ );
     if (stripParm == 0) return Action::ERR;
+    Cpptraj::Parm::Merge merger;
+    merger.SetDebug( debug_ ); // FIXME do verbose as well
     for (int cell = 0; cell != ncopies_; cell++)
-      combinedTop_.AppendTop( *stripParm );
+      merger.AppendTop( combinedTop_, *stripParm );
     combinedTop_.Brief("Combined parm:");
     delete stripParm;
     topWriter_.ModifyTop( &combinedTop_ );
diff --git a/src/Action_ReplicateCell.h b/src/Action_ReplicateCell.h
index fef43d4b85..345da18c88 100644
--- a/src/Action_ReplicateCell.h
+++ b/src/Action_ReplicateCell.h
@@ -24,6 +24,7 @@ class Action_ReplicateCell: public Action {
     DataSet_Coords* coords_;    ///< Combined cell COORDS DataSet
     AtomMask Mask1_;            ///< Mask of atoms to replicate
     int ncopies_;               ///< Total # of replications to make
+    int debug_;
     bool writeTraj_;            ///< If true, write output combined cell traj
     Topology combinedTop_;      ///< Combined cell topology
     Frame combinedFrame_;       ///< Combined cell frame
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index e903601512..646fadf59d 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -70,7 +70,7 @@ Action_Radgyr.o : Action_Radgyr.cpp Action.h ActionState.h Action_Radgyr.h ArgLi
 Action_Radial.o : Action_Radial.cpp Action.h ActionState.h Action_Radial.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h Gpu.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h cuda_kernels/kernel_rdf.cuh
 Action_RandomizeIons.o : Action_RandomizeIons.cpp Action.h ActionState.h Action_RandomizeIons.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 Action_Remap.o : Action_Remap.cpp Action.h ActionState.h ActionTopWriter.h Action_Remap.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_ReplicateCell.o : Action_ReplicateCell.cpp Action.h ActionFrameCounter.h ActionState.h ActionTopWriter.h Action_ReplicateCell.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h Unit.h Vec3.h
+Action_ReplicateCell.o : Action_ReplicateCell.cpp Action.h ActionFrameCounter.h ActionState.h ActionTopWriter.h Action_ReplicateCell.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Parm/Merge.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h Unit.h Vec3.h
 Action_Rmsd.o : Action_Rmsd.cpp Action.h ActionState.h Action_Rmsd.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 Action_Rotate.o : Action_Rotate.cpp Action.h ActionState.h Action_Rotate.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 Action_RunningAvg.o : Action_RunningAvg.cpp Action.h ActionState.h Action_RunningAvg.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h

From 04d40c3e4fd5e7764ad089a9119d3726f802645e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 22 Jul 2024 09:28:18 -0400
Subject: [PATCH 0874/1492] Add verbosity

---
 src/Parm/AssignParams.cpp | 30 ++++++++++++++++++++----------
 src/Parm/AssignParams.h   |  8 ++++++--
 2 files changed, 26 insertions(+), 12 deletions(-)

diff --git a/src/Parm/AssignParams.cpp b/src/Parm/AssignParams.cpp
index 224d30f611..6a170c3dbc 100644
--- a/src/Parm/AssignParams.cpp
+++ b/src/Parm/AssignParams.cpp
@@ -16,9 +16,20 @@ using namespace Cpptraj::Parm;
 
 /** CONSTRUCTOR */
 AssignParams::AssignParams() :
-  debug_(0)
+  debug_(0),
+  verbose_(1) // FIXME
 {}
 
+/** Set debug level */
+void AssignParams::SetDebug(int debugIn) {
+  debug_ = debugIn;
+}
+
+/** Set verbosity. */
+void AssignParams::SetVerbose(int verboseIn) {
+  verbose_ = verboseIn;
+}
+
 /** Set parameters for atoms via given atom type parameter holder. */
 void AssignParams::AssignAtomTypeParm(AtArray& atoms, ParmHolder<AtomType> const& newAtomTypeParams)
 const
@@ -569,8 +580,7 @@ void AssignParams::AssignNonbondParams(Topology& topOut,
                                        ParmHolder<NonbondType> const& newNB,
                                        ParmHolder<NonbondType> const& new14,
                                        ParmHolder<double> const& newLJC,
-                                       ParmHolder<HB_ParmType> const& newHB,
-                                       int verbose)
+                                       ParmHolder<HB_ParmType> const& newHB)
 const
 {
   bool hasLJ14 = !new14.empty();
@@ -659,7 +669,7 @@ const
       // Check for LJ10-12 first
       ParmHolder<HB_ParmType>::const_iterator hb = newHB.GetParam( types );
       if (hb != newHB.end()) {
-        if (verbose > 0) mprintf("LJ 10-12 parameter found for %s %s\n", *name1, *name2);
+        if (verbose_ > 0) mprintf("LJ 10-12 parameter found for %s %s\n", *name1, *name2);
         nonbond.AddHBterm(t1->second.OriginalIdx(), t2->second.OriginalIdx(), hb->second);
         // Also add a blank 6-12 term since that seems to be the convention
         newnbidx = nonbond.AddLJterm( t1->second.OriginalIdx(), t2->second.OriginalIdx(), NonbondType() );
@@ -668,10 +678,10 @@ const
         NonbondType LJAB;
         ParmHolder<NonbondType>::const_iterator it = newNB.GetParam( types );
         if (it == newNB.end()) {
-          if (verbose > 0) mprintf("NB parameter for %s %s not found. Generating.\n", *name1, *name2);
+          if (verbose_ > 0) mprintf("NB parameter for %s %s not found. Generating.\n", *name1, *name2);
           LJAB = type1.LJ().Combine_LB( type2.LJ() );
         } else {
-          if (verbose > 0) mprintf("Using existing NB parameter for %s %s\n", *name1, *name2);
+          if (verbose_ > 0) mprintf("Using existing NB parameter for %s %s\n", *name1, *name2);
           LJAB = it->second;
         }
         newnbidx = nonbond.AddLJterm(t1->second.OriginalIdx(), t2->second.OriginalIdx(), LJAB);
@@ -681,10 +691,10 @@ const
         // Get parameter if it exists
         ParmHolder<NonbondType>::const_iterator it = new14.GetParam( types );
         if (it == new14.end()) {
-          if (verbose > 0) mprintf("NB 1-4 parameter for %s %s not found. Generating.\n", *name1, *name2);
+          if (verbose_ > 0) mprintf("NB 1-4 parameter for %s %s not found. Generating.\n", *name1, *name2);
           nonbond.SetLJ14( newnbidx ) = type1.LJ14().Combine_LB( type2.LJ14() );
         } else {
-          if (verbose > 0) mprintf("Using existing NB 1-4 parameter for %s %s\n", *name1, *name2);
+          if (verbose_ > 0) mprintf("Using existing NB 1-4 parameter for %s %s\n", *name1, *name2);
           nonbond.SetLJ14( newnbidx ) = it->second;
         }
       } // END hasLJ14
@@ -1104,7 +1114,7 @@ int AssignParams::AssignParameters(Topology& topOut, ParameterSet const& set0) c
   AssignAtomTypeParm( topOut.ModifyAtoms(), set0.AT() );
   // LJ 6-12
   mprintf("\tAssigning nonbond parameters.\n");
-  AssignNonbondParams( topOut, set0.AT(), set0.NB(), set0.NB14(), set0.LJC(), set0.HB(), debug_ );
+  AssignNonbondParams( topOut, set0.AT(), set0.NB(), set0.NB14(), set0.LJC(), set0.HB() );
   mprintf("DEBUG: CMAP size %zu\n", set0.CMAP().size());
 
   return 0;
@@ -1177,7 +1187,7 @@ int AssignParams::UpdateParameters(Topology& topOut, ParameterSet const& set1) c
       UC.nLJparamsUpdated_ > 0 || UC.nLJ14paramsUpdated_ > 0)
   {
     mprintf("\tRegenerating nonbond parameters.\n");
-    AssignNonbondParams( topOut, set0.AT(), set0.NB(), set0.NB14(), set0.LJC(), set0.HB(), debug_ );
+    AssignNonbondParams( topOut, set0.AT(), set0.NB(), set0.NB14(), set0.LJC(), set0.HB() );
   }
   // CMAP
   if (UC.nCmapUpdated_ > 0) {
diff --git a/src/Parm/AssignParams.h b/src/Parm/AssignParams.h
index d25515dda6..d1ab10ff81 100644
--- a/src/Parm/AssignParams.h
+++ b/src/Parm/AssignParams.h
@@ -31,6 +31,10 @@ namespace Parm {
 class AssignParams {
   public:
     AssignParams();
+    /// Set Debug level
+    void SetDebug(int);
+    /// Set verbosity
+    void SetVerbose(int);
     /// Replace existing parameters with those from given set
     int AssignParameters(Topology&, ParameterSet const&) const;
     /// Update existing parameters with given parameter set
@@ -39,8 +43,7 @@ class AssignParams {
     void AssignNonbondParams(Topology&,
                              ParmHolder<AtomType> const&,
                              ParmHolder<NonbondType> const&, ParmHolder<NonbondType> const&,
-                             ParmHolder<double> const&, ParmHolder<HB_ParmType> const&,
-                             int) const; // TODO make verbose a class var?
+                             ParmHolder<double> const&, ParmHolder<HB_ParmType> const&) const;
   private:
     typedef std::vector<Atom> AtArray;
 
@@ -79,6 +82,7 @@ class AssignParams {
     static void AddToDihedralArrays(Topology&, DihedralType const&);
 
     int debug_;
+    int verbose_;
 };
 }
 }

From ab74b57fc7ec640d0f4d3dac15b8b1ddda76cbb2 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 22 Jul 2024 10:09:43 -0400
Subject: [PATCH 0875/1492] Only print element/hybrid if present

---
 src/ParameterSet.cpp | 26 ++++++++++++++++++++++++--
 1 file changed, 24 insertions(+), 2 deletions(-)

diff --git a/src/ParameterSet.cpp b/src/ParameterSet.cpp
index 210ffc562d..564ea964b6 100644
--- a/src/ParameterSet.cpp
+++ b/src/ParameterSet.cpp
@@ -60,9 +60,31 @@ void ParameterSet::Print(CpptrajFile& Out) const {
     Out.Printf("Nonbond parameters name: %s\n", NBname_.c_str());
   static const char* hybStr[] = {"SP ", "SP2", "SP3", "UNK"};
   Out.Printf("Atom Types:\n");
-  Out.Printf("\t%6s %8s %12s %12s %12s %12s %3s %2s\n", "Name", "TypeIdx", "Radius", "Depth", "Mass", "Polar.", "Hyb", "El");
+  // Check if we have hybridizations or elements.
+  bool has_hybridizations = false;
+  bool has_elements = false;
   for (ParmHolder<AtomType>::const_iterator at = atomTypes_.begin(); at != atomTypes_.end(); ++at) {
-    Out.Printf("\t%6s %8li %12.4f %12.4f %12.4f %12.4f %3s %2s\n", *(at->first[0]), at - atomTypes_.begin(), at->second.LJ().Radius(), at->second.LJ().Depth(), at->second.Mass(), at->second.Polarizability(), hybStr[at->second.Hybridization()], at->second.EltStr());
+    if (at->second.Hybridization() != AtomType::UNKNOWN_HYBRIDIZATION)
+      has_hybridizations = true;
+    if (at->second.EltStr()[0] != ' ' || at->second.EltStr()[1] != ' ')
+      has_elements = true;
+    if (has_hybridizations && has_elements)
+      break;
+  }
+  // Atom Type header
+  Out.Printf("\t%6s %8s %12s %12s %12s %12s", "Name", "TypeIdx", "Radius", "Depth", "Mass", "Polar.");
+  if (has_hybridizations)
+    Out.Printf(" %3s", "Hyb");
+  if (has_elements)
+    Out.Printf(" %2s", "El");
+  Out.Printf("\n");
+  for (ParmHolder<AtomType>::const_iterator at = atomTypes_.begin(); at != atomTypes_.end(); ++at) {
+    Out.Printf("\t%6s %8li %12.4f %12.4f %12.4f %12.4f", *(at->first[0]), at - atomTypes_.begin(), at->second.LJ().Radius(), at->second.LJ().Depth(), at->second.Mass(), at->second.Polarizability());
+    if (has_hybridizations)
+      Out.Printf(" %3s", hybStr[at->second.Hybridization()]);
+    if (has_elements)
+      Out.Printf(" %2s", at->second.EltStr());
+    Out.Printf("\n");
   }
   if (!nbParm_.empty()) {
     Out.Printf("LJ 6-12 parameters:\n");

From 99b4f5390c3e614c77736b60f85db7747583f256 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 22 Jul 2024 10:24:35 -0400
Subject: [PATCH 0876/1492] Use new Parm classes. Add 'verbose' keyword where
 appropriate. Update manual for 'verbose' keywords.

---
 doc/cpptraj.lyx               | 46 ++++++++++++++++++++++++++++++++---
 src/Action_ReplicateCell.cpp  | 23 ++++++++++--------
 src/Action_ReplicateCell.h    |  1 +
 src/DataIO_CharmmRtfPrm.cpp   |  5 +++-
 src/DataIO_LeapRC.h           |  1 +
 src/Exec_Build.cpp            |  9 +++++--
 src/Exec_CombineCoords.cpp    | 10 ++++++--
 src/Exec_Graft.cpp            | 14 ++++++++---
 src/Exec_Graft.h              |  1 +
 src/Exec_UpdateParameters.cpp | 14 ++++++++---
 src/Parm/Merge.cpp            |  4 ++-
 src/Parm_Amber.cpp            |  7 ++++--
 src/Parm_CharmmPsf.cpp        | 13 +++++++---
 src/Structure/Builder.cpp     |  3 +++
 src/Structure/structuredepend | 26 ++++++++++----------
 src/cpptrajdepend             | 20 +++++++--------
 16 files changed, 142 insertions(+), 55 deletions(-)

diff --git a/doc/cpptraj.lyx b/doc/cpptraj.lyx
index 43487d9f9e..d18ccbf164 100644
--- a/doc/cpptraj.lyx
+++ b/doc/cpptraj.lyx
@@ -6977,6 +6977,10 @@ combinecrd <crd1> <crd2> ...
 
 \end_layout
 
+\begin_layout LyX-Code
+           [nobox] [verbose <#>]
+\end_layout
+
 \begin_deeper
 \begin_layout Description
 <crdX> COORDS data sets to combine,
@@ -6999,6 +7003,18 @@ combinecrd <crd1> <crd2> ...
 <crdname>] Name of combined COORDS data set.
 \end_layout
 
+\begin_layout Description
+[nobox] Remove any unit cell information from combined coordinates.
+\end_layout
+
+\begin_layout Description
+[verbose
+\begin_inset space ~
+\end_inset
+
+<#>] Verbosity during parameter assignment.
+\end_layout
+
 \end_deeper
 \begin_layout Standard
 Combined two or more COORDS data sets into a single COORDS data set.
@@ -7831,7 +7847,7 @@ graft src <source COORDS> [srcframe <#>] [srcmask <srcmask> [srccharge <srccharg
 \end_layout
 
 \begin_layout LyX-Code
-      {ic | [srcfitmask <srcmask>] [tgtfitmask <tgtmask>]}
+      {ic | [srcfitmask <srcmask>] [tgtfitmask <tgtmask>]} [verbose <#>]
 \end_layout
 
 \begin_layout LyX-Code
@@ -7949,6 +7965,14 @@ name
 COORDS> Name of output COORDS set containing source grafted onto target.
 \end_layout
 
+\begin_layout Description
+[verbose
+\begin_inset space ~
+\end_inset
+
+<#>] Verbosity during parameter assignment.
+\end_layout
+
 \begin_layout Description
 [bond
 \begin_inset space ~
@@ -17130,7 +17154,7 @@ updateparameters
 \end_layout
 
 \begin_layout LyX-Code
-parm <name> | parmindex <#> setname <parm set>
+parm <name> | parmindex <#> setname <parm set> [verbose <#>]
 \end_layout
 
 \begin_deeper
@@ -17166,6 +17190,14 @@ setname
 set> Topology or parameter data set containing parameters to use.
 \end_layout
 
+\begin_layout Description
+[verbose
+\begin_inset space ~
+\end_inset
+
+<#>] Verbosity during parameter update.
+\end_layout
+
 \end_deeper
 \begin_layout Standard
 
@@ -39403,7 +39435,7 @@ replicatecell
 \end_layout
 
 \begin_layout LyX-Code
-replicatecell [out <traj filename>] [name <dsname>]
+replicatecell [out <traj filename>] [name <dsname>] [verbose <#>]
 \end_layout
 
 \begin_layout LyX-Code
@@ -39443,6 +39475,14 @@ name
 <dsname> If specified save replicated cell to COORDS data set.
 \end_layout
 
+\begin_layout Description
+[verbose
+\begin_inset space ~
+\end_inset
+
+<#>] Verbosity during parameter assignment.
+\end_layout
+
 \begin_layout Description
 all Replicate cell once in all possible directions.
 \end_layout
diff --git a/src/Action_ReplicateCell.cpp b/src/Action_ReplicateCell.cpp
index 78b558a5a1..a89c9cac0c 100644
--- a/src/Action_ReplicateCell.cpp
+++ b/src/Action_ReplicateCell.cpp
@@ -8,18 +8,10 @@ Action_ReplicateCell::Action_ReplicateCell() :
   coords_(0),
   ncopies_(0),
   debug_(0),
+  verbose_(0),
   writeTraj_(false)
 {} 
 
-void Action_ReplicateCell::Help() const {
-  mprintf("\t[out <traj filename>] [name <dsname>]\n"
-          "\t{ all | dir <XYZ> [dir <XYZ> ...] } [<mask>]\n");
-  mprintf("%s", ActionTopWriter::Keywords());
-  mprintf("  Replicate unit cell in specified (or all) directions for atoms in <mask>.\n"
-          "    <XYZ>: X= 1, 0, -1, replicate in specified direction (e.g. 100 is +X only)\n");
-  mprintf("%s", ActionTopWriter::Options());
-}
-
 static inline int toDigit(char c) {
   switch (c) {
     case '0' : return 0;
@@ -36,10 +28,20 @@ static inline int toDigit(char c) {
   return 0; // SANITY CHECK
 }
 
+void Action_ReplicateCell::Help() const {
+  mprintf("\t[out <traj filename>] [name <dsname>] [verbose <#>]\n"
+          "\t{ all | dir <XYZ> [dir <XYZ> ...] } [<mask>]\n");
+  mprintf("%s", ActionTopWriter::Keywords());
+  mprintf("  Replicate unit cell in specified (or all) directions for atoms in <mask>.\n"
+          "    <XYZ>: X= 1, 0, -1, replicate in specified direction (e.g. 100 is +X only)\n");
+  mprintf("%s", ActionTopWriter::Options());
+}
+
 // Action_ReplicateCell::Init()
 Action::RetType Action_ReplicateCell::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
 {
   debug_ = debugIn;
+  verbose_ = actionArgs.getKeyInt("verbose", 0);
   // Set up output traj
   std::string trajfilename = actionArgs.GetStringKey("out");
   topWriter_.InitTopWriter( actionArgs, "replicated cell", debugIn );
@@ -159,7 +161,8 @@ Action::RetType Action_ReplicateCell::Setup(ActionSetup& setup) {
     Topology* stripParm = setup.Top().modifyStateByMask( Mask1_ );
     if (stripParm == 0) return Action::ERR;
     Cpptraj::Parm::Merge merger;
-    merger.SetDebug( debug_ ); // FIXME do verbose as well
+    merger.SetDebug( debug_ );
+    merger.SetVerbose( verbose_ );
     for (int cell = 0; cell != ncopies_; cell++)
       merger.AppendTop( combinedTop_, *stripParm );
     combinedTop_.Brief("Combined parm:");
diff --git a/src/Action_ReplicateCell.h b/src/Action_ReplicateCell.h
index 345da18c88..562f1d92d1 100644
--- a/src/Action_ReplicateCell.h
+++ b/src/Action_ReplicateCell.h
@@ -25,6 +25,7 @@ class Action_ReplicateCell: public Action {
     AtomMask Mask1_;            ///< Mask of atoms to replicate
     int ncopies_;               ///< Total # of replications to make
     int debug_;
+    int verbose_;               ///< Parameter assignment verbosity during merge
     bool writeTraj_;            ///< If true, write output combined cell traj
     Topology combinedTop_;      ///< Combined cell topology
     Frame combinedFrame_;       ///< Combined cell frame
diff --git a/src/DataIO_CharmmRtfPrm.cpp b/src/DataIO_CharmmRtfPrm.cpp
index 917b02bac8..42b33e83ac 100644
--- a/src/DataIO_CharmmRtfPrm.cpp
+++ b/src/DataIO_CharmmRtfPrm.cpp
@@ -4,6 +4,7 @@
 #include "CharmmParamFile.h"
 #include "DataSet_Parameters.h"
 #include "DataSet_Topology.h"
+#include "Parm/GetParams.h"
 
 /// CONSTRUCTOR
 DataIO_CharmmRtfPrm::DataIO_CharmmRtfPrm()
@@ -86,7 +87,9 @@ int DataIO_CharmmRtfPrm::WriteData(FileName const& fname, DataSetList const& dsl
       mprintf("\tUsing parameters from topology '%s'\n", (*it)->legend());
       // Convert topology to parameter set
       DataSet_Topology const& dsTop = static_cast<DataSet_Topology const&>( *(*it) );
-      pout.UpdateParamSet( dsTop.Top().GetParameters(), ucount, debug_, debug_ ); // FIXME verbose
+      Cpptraj::Parm::GetParams GP;
+      GP.SetDebug( debug_ );
+      pout.UpdateParamSet( GP.GetParameters(dsTop.Top()), ucount, debug_, debug_ ); // FIXME verbose
     } else {
       mprintf("Warning: '%s' is not a valid parameter/topology set, skipping.\n",
               (*it)->legend());
diff --git a/src/DataIO_LeapRC.h b/src/DataIO_LeapRC.h
index 32b9635a8a..e0d8eb7c1f 100644
--- a/src/DataIO_LeapRC.h
+++ b/src/DataIO_LeapRC.h
@@ -1,6 +1,7 @@
 #ifndef INC_DATAIO_LEAPRC_H
 #define INC_DATAIO_LEAPRC_H
 #include "DataIO.h"
+#include "AtomType.h" // AtomType::HybridizationType
 #include "Structure/StructureEnum.h"
 #include <map>
 class BufferedLine;
diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 042a3ce27b..68a765c84e 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -2,6 +2,7 @@
 #include "AssociatedData_Connect.h"
 #include "CpptrajStdio.h"
 #include "DataSet_Parameters.h" // For casting DataSet_Parameters to ParameterSet
+#include "Parm/AssignParams.h"
 #include "Parm/GB_Params.h"
 #include "Structure/Builder.h"
 #include "Structure/Creator.h"
@@ -642,7 +643,7 @@ const
 void Exec_Build::Help() const
 {
   mprintf("\tname <output COORDS> crdset <COORDS set> [frame <#>]\n"
-          "\t[title <title>] [gb <radii>]\n"
+          "\t[title <title>] [gb <radii>] [verbose <#>]\n"
           "\t[%s]\n"
           "\t[{%s} ...]\n"
           "\t[{%s} ...]\n"
@@ -690,6 +691,7 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, in
     return CpptrajState::ERR;
   }
   debug_ = debugIn;
+  int verbose = argIn.getKeyInt("verbose", 0);
   std::string title = argIn.GetStringKey("title");
 
   // TODO make it so this can be const (cant bc GetFrame)
@@ -866,7 +868,10 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, in
   // Assign parameters. This will create the bond/angle/dihedral/improper
   // arrays as well.
   Exec::RetType ret = CpptrajState::OK;
-  if ( topOut.AssignParams( *(creator.MainParmSetPtr())  ) ) {
+  Cpptraj::Parm::AssignParams AP;
+  AP.SetDebug( debug_ );
+  AP.SetVerbose( verbose );
+  if ( AP.AssignParameters( topOut, *(creator.MainParmSetPtr()) ) ) {
     mprinterr("Error: Could not assign parameters for '%s'.\n", topOut.c_str());
     ret = CpptrajState::ERR;
   }
diff --git a/src/Exec_CombineCoords.cpp b/src/Exec_CombineCoords.cpp
index 01e7a0c4cf..c4979b40af 100644
--- a/src/Exec_CombineCoords.cpp
+++ b/src/Exec_CombineCoords.cpp
@@ -1,9 +1,11 @@
 #include <algorithm> // std::min, std::max
 #include "Exec_CombineCoords.h"
 #include "CpptrajStdio.h"
+#include "Parm/Merge.h"
 
 void Exec_CombineCoords::Help() const {
-  mprintf("\t<crd1> <crd2> ... [parmname <topname>] [crdname <crdname>] [nobox]\n"
+  mprintf("\t<crd1> <crd2> ... [parmname <topname>] [crdname <crdname>]\n"
+          "\t[nobox] [verbose]\n"
           "  Combine two or more COORDS data sets.\n");
 }
 
@@ -18,6 +20,7 @@ Exec::RetType Exec_CombineCoords::Execute(CpptrajState& State, ArgList& argIn) {
   std::string parmname = argIn.GetStringKey("parmname");
   std::string crdname  = argIn.GetStringKey("crdname");
   bool nobox = argIn.hasKey("nobox");
+  int verbose = argIn.getKeyInt("verbose", 0);
   // Get COORDS DataSets.
   std::vector<DataSet_Coords*> CRD;
   std::string setname = argIn.GetStringNext();
@@ -59,6 +62,9 @@ Exec::RetType Exec_CombineCoords::Execute(CpptrajState& State, ArgList& argIn) {
   if (nobox) boxStatus = INVALID;
   Box combinedBox;
   size_t minSize = CRD[0]->Size();
+  Cpptraj::Parm::Merge merger;
+  merger.SetDebug( State.Debug() );
+  merger.SetDebug( verbose );
   for (unsigned int setnum = 0; setnum != CRD.size(); ++setnum) {
     if (CRD[setnum]->Size() < minSize)
       minSize = CRD[setnum]->Size();
@@ -79,7 +85,7 @@ Exec::RetType Exec_CombineCoords::Execute(CpptrajState& State, ArgList& argIn) {
       }
     }
     // Append
-    CombinedTop.AppendTop( CRD[setnum]->Top() );
+    merger.AppendTop( CombinedTop, CRD[setnum]->Top() );
   }
   CombinedTop.SetParmBox( combinedBox );
   CombinedTop.Brief("Combined parm:");
diff --git a/src/Exec_Graft.cpp b/src/Exec_Graft.cpp
index e165f2da9a..37065f6a93 100644
--- a/src/Exec_Graft.cpp
+++ b/src/Exec_Graft.cpp
@@ -1,9 +1,10 @@
 #include "Exec_Graft.h"
+#include "CharMask.h"
 #include "CpptrajStdio.h"
 #include "DataSet_Coords.h"
+#include "Parm/Merge.h"
 #include "Structure/Builder.h"
 #include "Structure/Zmatrix.h"
-#include "CharMask.h"
 #include <algorithm> // std::copy
 #include <utility> // std::pair
 
@@ -13,6 +14,7 @@ using namespace Cpptraj::Structure;
 Exec_Graft::Exec_Graft() :
   Exec(COORDS),
   debug_(0),
+  verbose_(0),
   newMol0Top_(0),
   newMol1Top_(0),
   hasOrient0_(false),
@@ -93,7 +95,7 @@ void Exec_Graft::Help() const
 {
   mprintf("\tsrc <source COORDS> [srcframe <#>] [srcmask <mask> [srccharge <charge>]]\n"
           "\ttgt <target COORDS> [tgtframe <#>] [tgtmask <mask> [tgtcharge <charge>]]\n"
-          "\t{ic | [srcfitmask <mask>] [tgtfitmask <mask>]}\n"
+          "\t{ic | [srcfitmask <mask>] [tgtfitmask <mask>]} [verbose]\n"
           "\tname <output COORDS> [bond <tgt>,<src> ...]\n"
           "  Graft coordinates from source to coordinates in target.\n"
           "  If 'ic' is specified use internal coordinates to link the coordinates,\n"
@@ -106,6 +108,7 @@ Exec::RetType Exec_Graft::Execute(CpptrajState& State, ArgList& argIn)
 {
   debug_ = State.Debug();
   bool use_ic = argIn.hasKey("ic");
+  verbose_ = argIn.getKeyInt("verbose", 0);
 
   // Source (1, fragment)
   Frame mol1frm;
@@ -519,12 +522,15 @@ int Exec_Graft::graft_rms(DataSet_Coords* outCoords,
                                     Sarray const& bond0Atoms, Sarray const& bond1Atoms)
 const
 {
+  Cpptraj::Parm::Merge merger;
+  merger.SetDebug( debug_ );
+  merger.SetVerbose( verbose_ );
   // Combine topologies. Use target box info.
   Topology combinedTop;
   combinedTop.SetDebug( debug_ );
   combinedTop.SetParmName( outCoords->Meta().Name(), FileName() );
-  combinedTop.AppendTop( mol0Top );
-  combinedTop.AppendTop( mol1Top );
+  merger.AppendTop( combinedTop, mol0Top );
+  merger.AppendTop( combinedTop, mol1Top );
 
   // Add any bonds
   for (unsigned int ii = 0; ii != bond0Atoms.size(); ii++) {
diff --git a/src/Exec_Graft.h b/src/Exec_Graft.h
index 80732d7314..0440d4b198 100644
--- a/src/Exec_Graft.h
+++ b/src/Exec_Graft.h
@@ -27,6 +27,7 @@ class Exec_Graft : public Exec {
                                   AtomMask const&, AtomMask const&,
                                   Sarray const&, Sarray const&);
     int debug_;
+    int verbose_;          ///< Parameter assign verbosity
     Topology* newMol0Top_; ///< Hold target topology if modified.
     Topology* newMol1Top_; ///< Hold source topology if modified.
     bool hasOrient0_;
diff --git a/src/Exec_UpdateParameters.cpp b/src/Exec_UpdateParameters.cpp
index 68b4b0e101..8a39fa8d51 100644
--- a/src/Exec_UpdateParameters.cpp
+++ b/src/Exec_UpdateParameters.cpp
@@ -2,13 +2,15 @@
 #include "CpptrajStdio.h"
 #include "DataSet_Parameters.h"
 #include "DataSet_Topology.h"
+#include "Parm/AssignParams.h"
+#include "Parm/GetParams.h"
 
 const char* Exec_UpdateParameters::disclaimer_ = "Warning: This command is provided for convenience only.\nWarning: For editing topology files, ParmEd is a much better alternative.\n";
 
 // Exec_UpdateParameters::Help()
 void Exec_UpdateParameters::Help() const
 {
-  mprintf("\tsetname <parmset>\n"
+  mprintf("\tsetname <parmset> [verbose <#>]\n"
           "\t%s\n", DataSetList::TopArgs);
   mprintf("  Update parameters in specified topology with those from <parm set>.\n"
           "  <parm set> can either be a parameter set or a topology. If a\n"
@@ -21,6 +23,7 @@ void Exec_UpdateParameters::Help() const
 Exec::RetType Exec_UpdateParameters::Execute(CpptrajState& State, ArgList& argIn)
 {
   mprintf("%s", disclaimer_);
+  int verbose = argIn.getKeyInt("verbose", 0);
   std::string dsname = argIn.GetStringKey("setname");
   //bool genAngles = argIn.hasKey("genangles");
   if (dsname.empty()) {
@@ -55,11 +58,16 @@ Exec::RetType Exec_UpdateParameters::Execute(CpptrajState& State, ArgList& argIn
   //  }
   //}
 
+  Cpptraj::Parm::AssignParams AP;
+  AP.SetDebug( State.Debug() );
+  AP.SetVerbose( verbose );
   if (ds->Type() == DataSet::PARAMETERS)
-    top.UpdateParams(static_cast<DataSet_Parameters const&>( *ds ));
+    AP.UpdateParameters( top, static_cast<DataSet_Parameters const&>( *ds ) );
   else if (ds->Type() == DataSet::TOPOLOGY) {
+    Cpptraj::Parm::GetParams GP;
+    GP.SetDebug( State.Debug() );
     DataSet_Topology const& topds = static_cast<DataSet_Topology const&>( *ds );
-    top.UpdateParams(topds.Top().GetParameters());
+    AP.UpdateParameters( top, GP.GetParameters( topds.Top() ) );
   } else // Sanity check
     return CpptrajState::ERR;
 
diff --git a/src/Parm/Merge.cpp b/src/Parm/Merge.cpp
index 4deac32b65..ffbbf3ce53 100644
--- a/src/Parm/Merge.cpp
+++ b/src/Parm/Merge.cpp
@@ -809,7 +809,9 @@ int Merge::AppendTop(Topology& topOut, Topology const& NewTop) const {
   // Need to regenerate nonbonded info
   mprintf("\tRegenerating nonbond parameters.\n");
   AssignParams assign;
-  assign.AssignNonbondParams( topOut, myAtomTypes, myNB, my14, myLJC, myHB, verbose_ );
+  assign.SetDebug( debug_ );
+  assign.SetVerbose( verbose_ );
+  assign.AssignNonbondParams( topOut, myAtomTypes, myNB, my14, myLJC, myHB );
 
   // The version of AddTopAtom() with molecule number already determines
   // molecules and number of solvent molecules.
diff --git a/src/Parm_Amber.cpp b/src/Parm_Amber.cpp
index 8b3b9a4ed4..e9ce3b7615 100644
--- a/src/Parm_Amber.cpp
+++ b/src/Parm_Amber.cpp
@@ -7,8 +7,9 @@
 #include "Parm_Amber.h"
 #include "CpptrajStdio.h"
 #include "Constants.h" // ELECTOAMBER, AMBERTOELEC
-#include "StringRoutines.h" // NoTrailingWhitespace
 #include "ExclusionArray.h"
+#include "Parm/GetParams.h"
+#include "StringRoutines.h" // NoTrailingWhitespace
 
 // ---------- Constants and Enumerated types -----------------------------------
 const int Parm_Amber::AMBERPOINTERS_ = 31;
@@ -1956,7 +1957,9 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
   file_.IntToBuffer( TopOut.BondParm().size() ); // NUMBND
   file_.IntToBuffer( TopOut.AngleParm().size() ); // NUMANG
   file_.IntToBuffer( TopOut.DihedralParm().size() ); // NPTRA
-  unsigned int n_unique_atom_types = TopOut.NuniqueAtomTypes();
+  Cpptraj::Parm::GetParams GP;
+  GP.SetDebug( debug_ );
+  unsigned int n_unique_atom_types = GP.NuniqueAtomTypes( TopOut );
   file_.IntToBuffer( n_unique_atom_types ); // NATYP, only for SOLTY
   file_.IntToBuffer( TopOut.Nonbond().HBarray().size() ); // NPHB
   file_.IntToBuffer( 0 ); // IFPERT
diff --git a/src/Parm_CharmmPsf.cpp b/src/Parm_CharmmPsf.cpp
index 902f6423cd..64b09b018c 100644
--- a/src/Parm_CharmmPsf.cpp
+++ b/src/Parm_CharmmPsf.cpp
@@ -4,11 +4,12 @@
 #include <cstring> // strncmp
 #include <cctype> // isdigit
 #include "Parm_CharmmPsf.h"
+#include "BufferedLine.h"
+#include "CharmmParamFile.h"
 #include "CpptrajStdio.h"
-#include "StringRoutines.h"
 #include "Mol.h" // UniqueCount()
-#include "CharmmParamFile.h"
-#include "BufferedLine.h"
+#include "Parm/AssignParams.h"
+#include "StringRoutines.h"
 
 /// CONSTRUCTOR
 Parm_CharmmPsf::Parm_CharmmPsf() :
@@ -377,7 +378,11 @@ int Parm_CharmmPsf::ReadParm(FileName const& fname, Topology &parmOut) {
 
   // Add nonbonded parameters
   if (params_.HasLJparams()) {
-    parmOut.AssignNonbondParams( atomTypes, params_.NB(), params_.NB14(), params_.LJC(), params_.HB(), debug_ );
+    Cpptraj::Parm::AssignParams AP;
+    AP.SetDebug( debug_ );
+    AP.SetVerbose( debug_ ); // TODO separate verbosity?
+    AP.AssignNonbondParams( parmOut, atomTypes, params_.NB(), params_.NB14(),
+                            params_.LJC(), params_.HB() );
   }
 
   return 0;
diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index b031edd4f0..b25c41aca5 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -7,8 +7,11 @@
 #include "../DistRoutines.h"
 #include "../Frame.h"
 #include "../GuessAtomHybridization.h"
+#include "../ParameterHolders.h"
+#include "../ParameterSet.h"
 #include "../Topology.h"
 #include "../TorsionRoutines.h"
+#include "../TypeNameHolder.h"
 #include <algorithm> // std::copy
 #include <cmath> // fabs
 
diff --git a/src/Structure/structuredepend b/src/Structure/structuredepend
index 59d8ab5f51..4c788ccf93 100644
--- a/src/Structure/structuredepend
+++ b/src/Structure/structuredepend
@@ -1,20 +1,20 @@
 Builder.o : Builder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Builder.h Chirality.h GenerateConnectivityArrays.h InternalCoords.h StructureEnum.h Zmatrix.h
-Chirality.o : Chirality.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Chirality.h StructureEnum.h
+Chirality.o : Chirality.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../Unit.h ../Vec3.h Chirality.h StructureEnum.h
 Creator.o : Creator.cpp ../ArgList.h ../AssociatedData.h ../AssociatedData_ResId.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../DataSet_NameMap.h ../DataSet_Parameters.h ../Dimension.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/StructureEnum.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Creator.h GenerateConnectivityArrays.h StructureEnum.h
-Disulfide.o : Disulfide.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Disulfide.h ResStatArray.h StructureRoutines.h
-FunctionalGroup.o : FunctionalGroup.cpp ../Atom.h ../AtomMap.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h FunctionalGroup.h
-FxnGroupBuilder.o : FxnGroupBuilder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h FunctionalGroup.h FxnGroupBuilder.h StructureRoutines.h Sugar.h SugarToken.h
+Disulfide.o : Disulfide.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h Disulfide.h ResStatArray.h StructureRoutines.h
+FunctionalGroup.o : FunctionalGroup.cpp ../Atom.h ../AtomMap.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h FunctionalGroup.h
+FxnGroupBuilder.o : FxnGroupBuilder.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h FunctionalGroup.h FxnGroupBuilder.h StructureRoutines.h Sugar.h SugarToken.h
 GenerateConnectivityArrays.o : GenerateConnectivityArrays.cpp ../Atom.h ../Constants.h ../CpptrajStdio.h ../NameType.h ../ParameterTypes.h ../Residue.h ../SymbolExporting.h GenerateConnectivityArrays.h
-HisProt.o : HisProt.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h HisProt.h StructureRoutines.h
-InternalCoords.o : InternalCoords.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h InternalCoords.h
+HisProt.o : HisProt.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h HisProt.h StructureRoutines.h
+InternalCoords.o : InternalCoords.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h InternalCoords.h
 LeastSquaresPlane.o : LeastSquaresPlane.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Unit.h ../Vec3.h LeastSquaresPlane.h
-MetalCenterFinder.o : MetalCenterFinder.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h MetalCenterFinder.h
-PdbCleaner.o : PdbCleaner.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h PdbCleaner.h
-RingFinder.o : RingFinder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CharMask.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h RingFinder.h
+MetalCenterFinder.o : MetalCenterFinder.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h MetalCenterFinder.h
+PdbCleaner.o : PdbCleaner.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h PdbCleaner.h
+RingFinder.o : RingFinder.cpp ../Atom.h ../AtomMask.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h RingFinder.h
 StructureEnum.o : StructureEnum.cpp StructureEnum.h
 StructureRoutines.o : StructureRoutines.cpp ../Atom.h ../CpptrajStdio.h ../NameType.h ../Residue.h ../SymbolExporting.h StructureRoutines.h
-Sugar.o : Sugar.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Sugar.h SugarToken.h
-SugarBuilder.o : SugarBuilder.cpp ../ArgList.h ../Atom.h ../AtomMap.h ../AtomMask.h ../AtomType.h ../Box.h ../CharMask.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DistRoutines.h ../FileIO.h ../FileName.h ../Frame.h ../ImageOption.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Chirality.h FunctionalGroup.h FxnGroupBuilder.h LinkAtom.h ResStatArray.h StructureEnum.h StructureRoutines.h Sugar.h SugarBuilder.h SugarLinkAtoms.h SugarToken.h
-SugarLinkAtoms.o : SugarLinkAtoms.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../StringRoutines.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h LinkAtom.h SugarLinkAtoms.h
+Sugar.o : Sugar.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h Sugar.h SugarToken.h
+SugarBuilder.o : SugarBuilder.cpp ../ArgList.h ../Atom.h ../AtomMap.h ../AtomMask.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DistRoutines.h ../FileIO.h ../FileName.h ../Frame.h ../ImageOption.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../Unit.h ../Vec3.h Chirality.h FunctionalGroup.h FxnGroupBuilder.h LinkAtom.h ResStatArray.h StructureEnum.h StructureRoutines.h Sugar.h SugarBuilder.h SugarLinkAtoms.h SugarToken.h
+SugarLinkAtoms.o : SugarLinkAtoms.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../StringRoutines.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h LinkAtom.h SugarLinkAtoms.h
 SugarToken.o : SugarToken.cpp ../ArgList.h ../CpptrajStdio.h SugarToken.h
-Zmatrix.o : Zmatrix.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h GenerateConnectivityArrays.h InternalCoords.h Zmatrix.h
+Zmatrix.o : Zmatrix.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../Unit.h ../Vec3.h GenerateConnectivityArrays.h InternalCoords.h Zmatrix.h
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 646fadf59d..fa570e4042 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -208,7 +208,7 @@ CpptrajFile.o : CpptrajFile.cpp CpptrajFile.h CpptrajStdio.h FileIO.h FileIO_Bzi
 CpptrajState.o : CpptrajState.cpp Action.h ActionList.h ActionState.h Action_CreateCrd.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_Topology.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleNavigator.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 CpptrajStdio.o : CpptrajStdio.cpp Parallel.h
 CurveFit.o : CurveFit.cpp CurveFit.h
-DataFile.o : DataFile.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Cluster/Cframes.h Cluster/Cmatrix_NC.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataFile.h DataIO.h DataIO_AmberEne.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_CCP4.h DataIO_CharmmFastRep.h DataIO_CharmmOutput.h DataIO_CharmmRepLog.h DataIO_CharmmRtfPrm.h DataIO_Cmatrix_Binary.h DataIO_Cmatrix_NC.h DataIO_Coords.h DataIO_Cpout.h DataIO_Evecs.h DataIO_Gnuplot.h DataIO_Grace.h DataIO_LeapRC.h DataIO_Mdout.h DataIO_NetCDF.h DataIO_Numpy.h DataIO_OpenDx.h DataIO_Peaks.h DataIO_RemLog.h DataIO_Std.h DataIO_VecTraj.h DataIO_XVG.h DataIO_Xplor.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Unit.h Vec3.h
+DataFile.o : DataFile.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Cluster/Cframes.h Cluster/Cmatrix_NC.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataFile.h DataIO.h DataIO_AmberEne.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_CCP4.h DataIO_CharmmFastRep.h DataIO_CharmmOutput.h DataIO_CharmmRepLog.h DataIO_CharmmRtfPrm.h DataIO_Cmatrix_Binary.h DataIO_Cmatrix_NC.h DataIO_Coords.h DataIO_Cpout.h DataIO_Evecs.h DataIO_Gnuplot.h DataIO_Grace.h DataIO_LeapRC.h DataIO_Mdout.h DataIO_NetCDF.h DataIO_Numpy.h DataIO_OpenDx.h DataIO_Peaks.h DataIO_RemLog.h DataIO_Std.h DataIO_VecTraj.h DataIO_XVG.h DataIO_Xplor.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Unit.h Vec3.h
 DataFileList.o : DataFileList.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 DataFilter.o : DataFilter.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_integer.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 DataIO.o : DataIO.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
@@ -221,7 +221,7 @@ DataIO_CCP4.o : DataIO_CCP4.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.
 DataIO_CharmmFastRep.o : DataIO_CharmmFastRep.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmFastRep.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 DataIO_CharmmOutput.o : DataIO_CharmmOutput.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmOutput.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 DataIO_CharmmRepLog.o : DataIO_CharmmRepLog.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmRepLog.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-DataIO_CharmmRtfPrm.o : DataIO_CharmmRtfPrm.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharmmParamFile.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmRtfPrm.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h DataSet_Topology.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_CharmmRtfPrm.o : DataIO_CharmmRtfPrm.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharmmParamFile.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmRtfPrm.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h DataSet_Topology.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/GetParams.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Cmatrix_Binary.o : DataIO_Cmatrix_Binary.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cluster/Cframes.h Cluster/Cmatrix_Binary.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Cmatrix_Binary.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 DataIO_Cmatrix_NC.o : DataIO_Cmatrix_NC.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cluster/Cframes.h Cluster/Cmatrix_NC.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Cmatrix_NC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 DataIO_Coords.o : DataIO_Coords.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Coords.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h Trajin_Single.h Unit.h Vec3.h
@@ -300,12 +300,12 @@ Ewald_Regular.o : Ewald_Regular.cpp Atom.h AtomMask.h Box.h Constants.h Coordina
 ExclusionArray.o : ExclusionArray.cpp Atom.h AtomMask.h CharMask.h CpptrajStdio.h ExclusionArray.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Unit.h
 Exec_AddMissingRes.o : Exec_AddMissingRes.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h CharMask.h CompactFrameArray.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_AddMissingRes.h Exec_AddMissingRes_Pres.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h ParmFile.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h Trajout_Single.h Unit.h Vec3.h
 Exec_Analyze.o : Exec_Analyze.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Analyze.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_Build.o : Exec_Build.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/GB_Params.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/Creator.h Structure/Disulfide.h Structure/HisProt.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/StructureEnum.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Build.o : Exec_Build.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/AssignParams.h Parm/GB_Params.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/Creator.h Structure/Disulfide.h Structure/HisProt.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/StructureEnum.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Calc.o : Exec_Calc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Calc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_CatCrd.o : Exec_CatCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CatCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_Change.o : Exec_Change.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Change.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_ClusterMap.o : Exec_ClusterMap.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ClusterMap.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ClusterMap.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_CombineCoords.o : Exec_CombineCoords.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CombineCoords.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_CombineCoords.o : Exec_CombineCoords.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CombineCoords.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/Merge.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_Commands.o : Exec_Commands.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Commands.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_CompareClusters.o : Exec_CompareClusters.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CompareClusters.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_CompareEnergy.o : Exec_CompareEnergy.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h Energy/Kernel_Fourier.h Energy/Kernel_Harmonic.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CompareEnergy.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
@@ -322,7 +322,7 @@ Exec_Emin.o : Exec_Emin.cpp Action.h ActionList.h ActionState.h Analysis.h Analy
 Exec_ExtendedComparison.o : Exec_ExtendedComparison.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ExtendedComparison.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_Flatten.o : Exec_Flatten.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Flatten.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_GenerateAmberRst.o : Exec_GenerateAmberRst.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_GenerateAmberRst.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_Graft.o : Exec_Graft.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Graft.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_Graft.o : Exec_Graft.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Graft.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/Merge.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_Help.o : Exec_Help.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Help.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_HmassRepartition.o : Exec_HmassRepartition.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_HmassRepartition.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_LoadCrd.o : Exec_LoadCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_LoadCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h Unit.h Vec3.h
@@ -349,12 +349,12 @@ Exec_SequenceAlign.o : Exec_SequenceAlign.cpp Action.h ActionFrameCounter.h Acti
 Exec_Set.o : Exec_Set.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_StringVar.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Set.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_Show.o : Exec_Show.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_StringVar.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Show.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_SortEnsembleData.o : Exec_SortEnsembleData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h DataSet_PHREMD_Implicit.h DataSet_pH.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SortEnsembleData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_Source.o : Exec_Source.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Source.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_Source.o : Exec_Source.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Source.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_SplitCoords.o : Exec_SplitCoords.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SplitCoords.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_System.o : Exec_System.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_System.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_Top.o : Exec_Top.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Top.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h TopInfo.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_Traj.o : Exec_Traj.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Traj.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_UpdateParameters.o : Exec_UpdateParameters.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h DataSet_Topology.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_UpdateParameters.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_UpdateParameters.o : Exec_UpdateParameters.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h DataSet_Topology.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_UpdateParameters.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/AssignParams.h Parm/GetParams.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_ViewRst.o : Exec_ViewRst.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ViewRst.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h ViewRst.h
 Exec_Zmatrix.o : Exec_Zmatrix.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Zmatrix.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Zmatrix.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 ExtendedSimilarity.o : ExtendedSimilarity.cpp AssociatedData.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h ExtendedSimilarity.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h Unit.h Vec3.h
@@ -418,9 +418,9 @@ Parm/GB_Params.o : Parm/GB_Params.cpp Atom.h AtomMask.h Box.h Constants.h Coordi
 Parm/GetParams.o : Parm/GetParams.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/GetParams.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Parm/Merge.o : Parm/Merge.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterTypes.h Parm/AssignParams.h Parm/GetParams.h Parm/Merge.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h UpdateParameters.h Vec3.h
 ParmFile.o : ParmFile.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h ParmIO.h Parm_Amber.h Parm_CIF.h Parm_CharmmPsf.h Parm_Gromacs.h Parm_Mol2.h Parm_PDB.h Parm_SDF.h Parm_Tinker.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Parm_Amber.o : Parm_Amber.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h ExclusionArray.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmIO.h Parm_Amber.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h Unit.h Vec3.h
+Parm_Amber.o : Parm_Amber.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h ExclusionArray.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/GetParams.h ParmIO.h Parm_Amber.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h Unit.h Vec3.h
 Parm_CIF.o : Parm_CIF.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h CIFfile.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmIO.h Parm_CIF.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h
-Parm_CharmmPsf.o : Parm_CharmmPsf.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h CharmmParamFile.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Mol.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_CharmmPsf.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Parm_CharmmPsf.o : Parm_CharmmPsf.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h CharmmParamFile.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Mol.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/AssignParams.h ParmIO.h Parm_CharmmPsf.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Parm_Gromacs.o : Parm_Gromacs.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmIO.h Parm_Gromacs.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Parm_Mol2.o : Parm_Mol2.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Mol2File.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmIO.h Parm_Mol2.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Parm_PDB.o : Parm_PDB.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterTypes.h ParmIO.h Parm_PDB.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Timer.h Topology.h Unit.h Vec3.h
@@ -460,7 +460,7 @@ SpaceGroup.o : SpaceGroup.cpp Matrix_3x3.h Parallel.h SpaceGroup.h Vec3.h
 Spline.o : Spline.cpp CpptrajStdio.h Spline.h
 SplineFxnTable.o : SplineFxnTable.cpp Constants.h CpptrajStdio.h Spline.h SplineFxnTable.h StringRoutines.h
 StringRoutines.o : StringRoutines.cpp CpptrajStdio.h StringRoutines.h
-Structure/Builder.o : Structure/Builder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h GuessAtomHybridization.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Builder.h Structure/Chirality.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h Unit.h Vec3.h
+Structure/Builder.o : Structure/Builder.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h GuessAtomHybridization.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Builder.h Structure/Chirality.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 Structure/Chirality.o : Structure/Chirality.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Chirality.h Structure/StructureEnum.h SymbolExporting.h Topology.h TorsionRoutines.h Unit.h Vec3.h
 Structure/Creator.o : Structure/Creator.cpp ArgList.h AssociatedData.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/Creator.h Structure/GenerateConnectivityArrays.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/Disulfide.o : Structure/Disulfide.cpp ArgList.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Disulfide.h Structure/ResStatArray.h Structure/StructureRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h

From 8e16ad4738a5967fc49a08a882a7c86df55c155a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 22 Jul 2024 10:26:02 -0400
Subject: [PATCH 0877/1492] Update dependencies.

---
 src/Cluster/clusterdepend | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/Cluster/clusterdepend b/src/Cluster/clusterdepend
index fc231bff85..7db106bca2 100644
--- a/src/Cluster/clusterdepend
+++ b/src/Cluster/clusterdepend
@@ -1,5 +1,5 @@
 Algorithm.o : Algorithm.cpp ../CpptrajStdio.h Algorithm.h CentroidArray.h Cframes.h Metric.h MetricArray.h Node.h
-Algorithm_DBscan.o : Algorithm_DBscan.cpp ../ArgList.h ../ArrayIterator.h ../AssociatedData.h ../Atom.h ../AtomMask.h ../AtomType.h ../BaseIOtype.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataFile.h ../DataSet.h ../DataSetList.h ../DataSet_2D.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../DataSet_MatrixDbl.h ../Dimension.h ../FileIO.h ../FileName.h ../FileTypes.h ../Frame.h ../MaskToken.h ../Matrix.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../ProgressBar.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../StringRoutines.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Algorithm.h Algorithm_DBscan.h CentroidArray.h Cframes.h List.h Metric.h MetricArray.h Node.h
+Algorithm_DBscan.o : Algorithm_DBscan.cpp ../ArgList.h ../ArrayIterator.h ../AssociatedData.h ../Atom.h ../AtomMask.h ../BaseIOtype.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataFile.h ../DataSet.h ../DataSetList.h ../DataSet_2D.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../DataSet_MatrixDbl.h ../Dimension.h ../FileIO.h ../FileName.h ../FileTypes.h ../Frame.h ../MaskToken.h ../Matrix.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../ProgressBar.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../StringRoutines.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h Algorithm.h Algorithm_DBscan.h CentroidArray.h Cframes.h List.h Metric.h MetricArray.h Node.h
 Algorithm_DPeaks.o : Algorithm_DPeaks.cpp ../ArgList.h ../AssociatedData.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSet_1D.h ../DataSet_Mesh.h ../Dimension.h ../FileIO.h ../FileName.h ../MetaData.h ../Parallel.h ../ProgressBar.h ../Range.h ../Spline.h ../TextFormat.h Algorithm.h Algorithm_DPeaks.h CentroidArray.h Cframes.h List.h Metric.h MetricArray.h Node.h
 Algorithm_HierAgglo.o : Algorithm_HierAgglo.cpp ../ArgList.h ../ArrayIterator.h ../CpptrajFile.h ../CpptrajStdio.h ../FileIO.h ../FileName.h ../Matrix.h ../Parallel.h ../ProgressBar.h ../Timer.h Algorithm.h Algorithm_HierAgglo.h CentroidArray.h Cframes.h DynamicMatrix.h List.h Metric.h MetricArray.h Node.h
 Algorithm_Kmeans.o : Algorithm_Kmeans.cpp ../ArgList.h ../CpptrajFile.h ../CpptrajStdio.h ../FileIO.h ../FileName.h ../Parallel.h ../ProgressBar.h ../Random.h Algorithm.h Algorithm_Kmeans.h CentroidArray.h Cframes.h List.h Metric.h MetricArray.h Node.h
@@ -9,22 +9,22 @@ Centroid_Coord.o : Centroid_Coord.cpp ../Atom.h ../AtomMask.h ../Box.h ../Coordi
 Cframes.o : Cframes.cpp Cframes.h
 Cmatrix_Binary.o : Cmatrix_Binary.cpp ../CpptrajFile.h ../CpptrajStdio.h ../FileIO.h ../FileName.h ../Parallel.h Cframes.h Cmatrix_Binary.h
 Cmatrix_NC.o : Cmatrix_NC.cpp ../CpptrajStdio.h ../FileName.h ../NC_Routines.h Cframes.h Cmatrix_NC.h
-Control.o : Control.cpp ../ArgList.h ../ArrayIterator.h ../AssociatedData.h ../Atom.h ../AtomMask.h ../AtomType.h ../BaseIOtype.h ../Box.h ../BufferedLine.h ../Cluster/Cframes.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataFile.h ../DataFileList.h ../DataSet.h ../DataSetList.h ../DataSet_1D.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../DataSet_PairwiseCache.h ../DataSet_float.h ../DataSet_integer.h ../Dimension.h ../FileIO.h ../FileName.h ../FileTypes.h ../Frame.h ../MaskToken.h ../Matrix.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../OnlineVarT.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Random.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../TrajectoryFile.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Algorithm.h Algorithm_DBscan.h Algorithm_DPeaks.h Algorithm_HierAgglo.h Algorithm_Kmeans.h BestReps.h CentroidArray.h Cframes.h Control.h DBI.h DrawGraph.h DynamicMatrix.h List.h Metric.h MetricArray.h Node.h Output.h PseudoF.h Results.h Results_Coords.h Sieve.h Silhouette.h
+Control.o : Control.cpp ../ArgList.h ../ArrayIterator.h ../AssociatedData.h ../Atom.h ../AtomMask.h ../BaseIOtype.h ../Box.h ../BufferedLine.h ../Cluster/Cframes.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataFile.h ../DataFileList.h ../DataSet.h ../DataSetList.h ../DataSet_1D.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../DataSet_PairwiseCache.h ../DataSet_float.h ../DataSet_integer.h ../Dimension.h ../FileIO.h ../FileName.h ../FileTypes.h ../Frame.h ../MaskToken.h ../Matrix.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../OnlineVarT.h ../Parallel.h ../ParameterTypes.h ../Random.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../TrajectoryFile.h ../Unit.h ../Vec3.h Algorithm.h Algorithm_DBscan.h Algorithm_DPeaks.h Algorithm_HierAgglo.h Algorithm_Kmeans.h BestReps.h CentroidArray.h Cframes.h Control.h DBI.h DrawGraph.h DynamicMatrix.h List.h Metric.h MetricArray.h Node.h Output.h PseudoF.h Results.h Results_Coords.h Sieve.h Silhouette.h
 DBI.o : DBI.cpp CentroidArray.h Cframes.h DBI.h List.h Metric.h MetricArray.h Node.h
 DrawGraph.o : DrawGraph.cpp ../AssociatedData.h ../Atom.h ../Constants.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSet_1D.h ../Dimension.h ../FileIO.h ../FileName.h ../MetaData.h ../NameType.h ../PDBfile.h ../Parallel.h ../Range.h ../Residue.h ../SymbolExporting.h ../TextFormat.h ../Vec3.h Cframes.h DrawGraph.h Metric.h MetricArray.h
 DynamicMatrix.o : DynamicMatrix.cpp ../ArrayIterator.h ../CpptrajStdio.h ../Matrix.h DynamicMatrix.h
 List.o : List.cpp ../AssociatedData.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSet_1D.h ../DataSet_integer.h ../Dimension.h ../FileIO.h ../FileName.h ../MetaData.h ../Parallel.h ../ProgressBar.h ../Range.h ../TextFormat.h CentroidArray.h Cframes.h List.h Metric.h MetricArray.h Node.h
-MetricArray.o : MetricArray.cpp ../ArgList.h ../ArrayIterator.h ../AssociatedData.h ../Atom.h ../AtomMap.h ../AtomMask.h ../AtomType.h ../BaseIOtype.h ../Box.h ../Cluster/Cframes.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataFile.h ../DataFileList.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../DataSet_PairwiseCache.h ../Dimension.h ../FileIO.h ../FileName.h ../FileTypes.h ../Frame.h ../Hungarian.h ../MapAtom.h ../MaskToken.h ../Matrix.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../OnlineVarT.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../ProgressBar.h ../QuaternionRMSD.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../StringRoutines.h ../SymbolExporting.h ../SymmetricRmsdCalc.h ../TextFormat.h ../Timer.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h CentroidArray.h Metric.h MetricArray.h Metric_DME.h Metric_QuatRMSD.h Metric_RMS.h Metric_SRMSD.h Metric_Scalar.h Metric_Torsion.h
-Metric_DME.o : Metric_DME.cpp ../AssociatedData.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSet_Coords.h ../Dimension.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../TextFormat.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Centroid.h Centroid_Coord.h Cframes.h Metric.h Metric_DME.h
+MetricArray.o : MetricArray.cpp ../ArgList.h ../ArrayIterator.h ../AssociatedData.h ../Atom.h ../AtomMap.h ../AtomMask.h ../BaseIOtype.h ../Box.h ../Cluster/Cframes.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataFile.h ../DataFileList.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../DataSet_PairwiseCache.h ../Dimension.h ../FileIO.h ../FileName.h ../FileTypes.h ../Frame.h ../Hungarian.h ../MapAtom.h ../MaskToken.h ../Matrix.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../OnlineVarT.h ../Parallel.h ../ParameterTypes.h ../ProgressBar.h ../QuaternionRMSD.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../StringRoutines.h ../SymbolExporting.h ../SymmetricRmsdCalc.h ../TextFormat.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h CentroidArray.h Metric.h MetricArray.h Metric_DME.h Metric_QuatRMSD.h Metric_RMS.h Metric_SRMSD.h Metric_Scalar.h Metric_Torsion.h
+Metric_DME.o : Metric_DME.cpp ../AssociatedData.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSet_Coords.h ../Dimension.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../TextFormat.h ../Topology.h ../Unit.h ../Vec3.h Centroid.h Centroid_Coord.h Cframes.h Metric.h Metric_DME.h
 Metric_Matrix2D.o : Metric_Matrix2D.cpp ../AssociatedData.h ../CpptrajFile.h ../DataSet.h ../DataSet_2D.h ../Dimension.h ../FileIO.h ../FileName.h ../MetaData.h ../Parallel.h ../Range.h ../TextFormat.h Metric.h Metric_Matrix2D.h
-Metric_QuatRMSD.o : Metric_QuatRMSD.cpp ../AssociatedData.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSet_Coords.h ../Dimension.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../QuaternionRMSD.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../TextFormat.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Centroid.h Centroid_Coord.h Cframes.h Metric.h Metric_QuatRMSD.h
-Metric_RMS.o : Metric_RMS.cpp ../AssociatedData.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSet_Coords.h ../Dimension.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../TextFormat.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Centroid.h Centroid_Coord.h Cframes.h Metric.h Metric_RMS.h
-Metric_SRMSD.o : Metric_SRMSD.cpp ../ArrayIterator.h ../AssociatedData.h ../Atom.h ../AtomMap.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSet_Coords.h ../Dimension.h ../FileIO.h ../FileName.h ../Frame.h ../Hungarian.h ../MapAtom.h ../MaskToken.h ../Matrix.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../SymmetricRmsdCalc.h ../TextFormat.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Centroid.h Centroid_Coord.h Cframes.h Metric.h Metric_SRMSD.h
+Metric_QuatRMSD.o : Metric_QuatRMSD.cpp ../AssociatedData.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSet_Coords.h ../Dimension.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../QuaternionRMSD.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../TextFormat.h ../Topology.h ../Unit.h ../Vec3.h Centroid.h Centroid_Coord.h Cframes.h Metric.h Metric_QuatRMSD.h
+Metric_RMS.o : Metric_RMS.cpp ../AssociatedData.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSet_Coords.h ../Dimension.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../TextFormat.h ../Topology.h ../Unit.h ../Vec3.h Centroid.h Centroid_Coord.h Cframes.h Metric.h Metric_RMS.h
+Metric_SRMSD.o : Metric_SRMSD.cpp ../ArrayIterator.h ../AssociatedData.h ../Atom.h ../AtomMap.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSet_Coords.h ../Dimension.h ../FileIO.h ../FileName.h ../Frame.h ../Hungarian.h ../MapAtom.h ../MaskToken.h ../Matrix.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../SymmetricRmsdCalc.h ../TextFormat.h ../Topology.h ../Unit.h ../Vec3.h Centroid.h Centroid_Coord.h Cframes.h Metric.h Metric_SRMSD.h
 Metric_Scalar.o : Metric_Scalar.cpp ../AssociatedData.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSet_1D.h ../Dimension.h ../FileIO.h ../FileName.h ../MetaData.h ../Parallel.h ../Range.h ../TextFormat.h Centroid.h Centroid_Num.h Cframes.h Metric.h Metric_Scalar.h
 Metric_Torsion.o : Metric_Torsion.cpp ../AssociatedData.h ../Constants.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSet_1D.h ../Dimension.h ../FileIO.h ../FileName.h ../MetaData.h ../Parallel.h ../Range.h ../TextFormat.h Centroid.h Centroid_Num.h Cframes.h Metric.h Metric_Torsion.h
 Node.o : Node.cpp ../AssociatedData.h ../CpptrajFile.h ../DataSet.h ../DataSet_1D.h ../DataSet_float.h ../DataSet_integer.h ../Dimension.h ../FileIO.h ../FileName.h ../MetaData.h ../Parallel.h ../Range.h ../TextFormat.h CentroidArray.h Cframes.h Metric.h MetricArray.h Node.h
 Output.o : Output.cpp ../ArrayIterator.h ../CpptrajFile.h ../CpptrajStdio.h ../FileIO.h ../FileName.h ../Matrix.h ../Parallel.h ../Timer.h Algorithm.h BestReps.h CentroidArray.h Cframes.h List.h Metric.h MetricArray.h Node.h Output.h
 PseudoF.o : PseudoF.cpp ../Constants.h ../CpptrajStdio.h CentroidArray.h Cframes.h List.h Metric.h MetricArray.h Node.h PseudoF.h
-Results_Coords.o : Results_Coords.cpp ../ActionFrameCounter.h ../ArgList.h ../ArrayIterator.h ../AssociatedData.h ../Atom.h ../AtomMap.h ../AtomMask.h ../AtomType.h ../BaseIOtype.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../Dimension.h ../FileIO.h ../FileName.h ../FileTypes.h ../Frame.h ../Hungarian.h ../MapAtom.h ../MaskToken.h ../Matrix.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../OutputTrajCommon.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../StringRoutines.h ../SymbolExporting.h ../SymmetricRmsdCalc.h ../TextFormat.h ../Timer.h ../Topology.h ../TrajectoryFile.h ../Trajout_Single.h ../TypeNameHolder.h ../Unit.h ../Vec3.h CentroidArray.h Cframes.h List.h Metric.h MetricArray.h Metric_DME.h Metric_RMS.h Metric_SRMSD.h Node.h Results.h Results_Coords.h
+Results_Coords.o : Results_Coords.cpp ../ActionFrameCounter.h ../ArgList.h ../ArrayIterator.h ../AssociatedData.h ../Atom.h ../AtomMap.h ../AtomMask.h ../BaseIOtype.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../Dimension.h ../FileIO.h ../FileName.h ../FileTypes.h ../Frame.h ../Hungarian.h ../MapAtom.h ../MaskToken.h ../Matrix.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../OutputTrajCommon.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../StringRoutines.h ../SymbolExporting.h ../SymmetricRmsdCalc.h ../TextFormat.h ../Timer.h ../Topology.h ../TrajectoryFile.h ../Trajout_Single.h ../Unit.h ../Vec3.h CentroidArray.h Cframes.h List.h Metric.h MetricArray.h Metric_DME.h Metric_RMS.h Metric_SRMSD.h Node.h Results.h Results_Coords.h
 Sieve.o : Sieve.cpp ../AssociatedData.h ../Cluster/Cframes.h ../CpptrajFile.h ../DataSet.h ../DataSet_PairwiseCache.h ../Dimension.h ../FileIO.h ../FileName.h ../MetaData.h ../Parallel.h ../Random.h ../Range.h ../TextFormat.h Cframes.h Sieve.h
 Silhouette.o : Silhouette.cpp ../CpptrajFile.h ../CpptrajStdio.h ../FileIO.h ../FileName.h ../OnlineVarT.h ../Parallel.h CentroidArray.h Cframes.h List.h Metric.h MetricArray.h Node.h Silhouette.h

From 5198c75cad90ffabdcc6f2f7f070473fa7af23aa Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 22 Jul 2024 11:21:39 -0400
Subject: [PATCH 0878/1492] Add option to delete extra point angles

---
 src/Parm/AssignParams.cpp | 39 ++++++++++++++++++++++-----------------
 src/Parm/AssignParams.h   |  1 +
 2 files changed, 23 insertions(+), 17 deletions(-)

diff --git a/src/Parm/AssignParams.cpp b/src/Parm/AssignParams.cpp
index 6a170c3dbc..2eb5e25e9f 100644
--- a/src/Parm/AssignParams.cpp
+++ b/src/Parm/AssignParams.cpp
@@ -17,7 +17,8 @@ using namespace Cpptraj::Parm;
 /** CONSTRUCTOR */
 AssignParams::AssignParams() :
   debug_(0),
-  verbose_(1) // FIXME
+  verbose_(1), // FIXME
+  deleteExtraPointAngles_(true)
 {}
 
 /** Set debug level */
@@ -128,14 +129,16 @@ const
     types.AddName( topOut[ang->A1()].Type() );
     types.AddName( topOut[ang->A2()].Type() );
     types.AddName( topOut[ang->A3()].Type() );
-    // Skip extra points // FIXME make this an option
-    if ( topOut[ang->A1()].Element() == Atom::EXTRAPT ||
-         topOut[ang->A3()].Element() == Atom::EXTRAPT)
-    {
-      mprintf("DEBUG: Skipping angle with extra point: %4i %4i %4i (%2s %2s %2s)\n",
-              ang->A1()+1, ang->A2()+1, ang->A3()+1,
-              *types[0], *types[1], *types[2]);
-      continue;
+    // Skip extra points
+    if (deleteExtraPointAngles_) {
+      if ( topOut[ang->A1()].Element() == Atom::EXTRAPT ||
+           topOut[ang->A3()].Element() == Atom::EXTRAPT)
+      {
+        mprintf("DEBUG: Skipping angle with extra point: %4i %4i %4i (%2s %2s %2s)\n",
+                ang->A1()+1, ang->A2()+1, ang->A3()+1,
+                *types[0], *types[1], *types[2]);
+        continue;
+      }
     }
     // Skip water angles // FIXME make this an option
     if (topOut[ang->A1()].Element() == Atom::HYDROGEN &&
@@ -310,14 +313,16 @@ const
     types.AddName( topOut[dih->A2()].Type() );
     types.AddName( topOut[dih->A3()].Type() );
     types.AddName( topOut[dih->A4()].Type() );
-    // Skip extra points // FIXME make this an option
-    if ( topOut[dih->A1()].Element() == Atom::EXTRAPT ||
-         topOut[dih->A4()].Element() == Atom::EXTRAPT)
-    {
-      mprintf("DEBUG: Skipping dihedral with extra point: %4i %4i %4i %4i (%2s %2s %2s %2s)\n",
-              dih->A1()+1, dih->A2()+1, dih->A3()+1, dih->A4()+1,
-              *types[0], *types[1], *types[2], *types[3]);
-      continue;
+    // Skip extra points
+    if (deleteExtraPointAngles_) {
+      if ( topOut[dih->A1()].Element() == Atom::EXTRAPT ||
+           topOut[dih->A4()].Element() == Atom::EXTRAPT)
+      {
+        mprintf("DEBUG: Skipping dihedral with extra point: %4i %4i %4i %4i (%2s %2s %2s %2s)\n",
+                dih->A1()+1, dih->A2()+1, dih->A3()+1, dih->A4()+1,
+                *types[0], *types[1], *types[2], *types[3]);
+        continue;
+      }
     }
 //    mprintf("DEBUG: Assigning dihedral %4i %4i %4i %4i (%2s %2s %2s %2s) isImproper=%i skip14=%i\n",
 //            dih->A1()+1, dih->A2()+1, dih->A3()+1, dih->A4()+1,
diff --git a/src/Parm/AssignParams.h b/src/Parm/AssignParams.h
index d1ab10ff81..707aad3315 100644
--- a/src/Parm/AssignParams.h
+++ b/src/Parm/AssignParams.h
@@ -83,6 +83,7 @@ class AssignParams {
 
     int debug_;
     int verbose_;
+    bool deleteExtraPointAngles_; ///< If true, remove angles/torsions containing extra points.
 };
 }
 }

From 7c71dcf92902a4c69ed88ddd32f54e1629f81fff Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 22 Jul 2024 13:51:09 -0400
Subject: [PATCH 0879/1492] Add flexible water option

---
 src/Parm/AssignParams.cpp | 35 +++++++++++++++++++----------------
 src/Parm/AssignParams.h   |  1 +
 2 files changed, 20 insertions(+), 16 deletions(-)

diff --git a/src/Parm/AssignParams.cpp b/src/Parm/AssignParams.cpp
index 2eb5e25e9f..73addb6674 100644
--- a/src/Parm/AssignParams.cpp
+++ b/src/Parm/AssignParams.cpp
@@ -18,7 +18,8 @@ using namespace Cpptraj::Parm;
 AssignParams::AssignParams() :
   debug_(0),
   verbose_(1), // FIXME
-  deleteExtraPointAngles_(true)
+  deleteExtraPointAngles_(true),
+  flexibleWater_(false)
 {}
 
 /** Set debug level */
@@ -140,31 +141,33 @@ const
         continue;
       }
     }
-    // Skip water angles // FIXME make this an option
-    if (topOut[ang->A1()].Element() == Atom::HYDROGEN &&
-        topOut[ang->A2()].Element() == Atom::OXYGEN &&
-        topOut[ang->A3()].Element() == Atom::HYDROGEN)
-    {
-      // H-O-H Angle. If there is an H-H bond assume this is a rigid water model.
-      if (topOut[ang->A1()].IsBondedTo( ang->A3() )) {
-        mprintf("DEBUG: H-O-H angle, H-H bond detected. Assuming rigid water, skipping angle: "
-                "%4i %4i %4i (%2s %2s %2s)\n",
-                ang->A1()+1, ang->A2()+1, ang->A3()+1,
-                *types[0], *types[1], *types[2]);
-        continue;
-      }
-    }
+    // O-H-H Angle. Assume rigid water model and always skip.
     if (topOut[ang->A1()].Element() == Atom::OXYGEN &&
         topOut[ang->A2()].Element() == Atom::HYDROGEN &&
         topOut[ang->A3()].Element() == Atom::HYDROGEN)
     {
-      // O-H-H Angle. Assume rigid water model
       mprintf("DEBUG: O-H-H angle. Assuming rigid water, skipping angle: "
               "%4i %4i %4i (%2s %2s %2s)\n",
               ang->A1()+1, ang->A2()+1, ang->A3()+1,
               *types[0], *types[1], *types[2]);
       continue;
     }
+    // Skip water angles
+    if (!flexibleWater_) {
+      if (topOut[ang->A1()].Element() == Atom::HYDROGEN &&
+          topOut[ang->A2()].Element() == Atom::OXYGEN &&
+          topOut[ang->A3()].Element() == Atom::HYDROGEN)
+      {
+        // H-O-H Angle. If there is an H-H bond assume this is a rigid water model.
+        if (topOut[ang->A1()].IsBondedTo( ang->A3() )) {
+          mprintf("DEBUG: H-O-H angle, H-H bond detected. Assuming rigid water, skipping angle: "
+                  "%4i %4i %4i (%2s %2s %2s)\n",
+                  ang->A1()+1, ang->A2()+1, ang->A3()+1,
+                  *types[0], *types[1], *types[2]);
+          continue;
+        }
+      }
+    }
 
     bool found;
     // See if parameter is present.
diff --git a/src/Parm/AssignParams.h b/src/Parm/AssignParams.h
index 707aad3315..faba164d4a 100644
--- a/src/Parm/AssignParams.h
+++ b/src/Parm/AssignParams.h
@@ -84,6 +84,7 @@ class AssignParams {
     int debug_;
     int verbose_;
     bool deleteExtraPointAngles_; ///< If true, remove angles/torsions containing extra points.
+    bool flexibleWater_;          ///< If true, allow H-O-H angle for water
 };
 }
 }

From b9100166f4b5fea9f28747931e2e84d4277d9e60 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 22 Jul 2024 15:16:08 -0400
Subject: [PATCH 0880/1492] Have getIcFromInternals return a class recording
 what kinds of internals make up the given internal coordinate.

---
 src/Structure/Builder.cpp | 51 +++++++++++++++++++++++++++++++++------
 src/Structure/Builder.h   | 17 ++++++++++++-
 2 files changed, 60 insertions(+), 8 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index b25c41aca5..bc5c8522d8 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1681,7 +1681,42 @@ void Builder::printAllInternalsForAtom(int at, Topology const& topIn, Barray con
       }
     }
   }
+  for (Aarray::const_iterator ang = internalAngles_.begin(); ang != internalAngles_.end(); ++ang)
+  {
+    if (at == ang->AtI()) {
+      if (hasPosition[ang->AtJ()] &&
+          hasPosition[ang->AtK()])
+      {
+        mprintf("DEBUG:\t\t%s - %s Theta= %f\n",
+                topIn.LeapName(ang->AtJ()).c_str(),
+                topIn.LeapName(ang->AtK()).c_str(),
+                ang->ThetaVal()*Constants::RADDEG);
+      }
+    } else if (at == ang->AtK()) {
+      if (hasPosition[ang->AtJ()] &&
+          hasPosition[ang->AtI()])
+      {
+        mprintf("DEBUG:\t\t%s - %s Theta= %f\n",
+                topIn.LeapName(ang->AtJ()).c_str(),
+                topIn.LeapName(ang->AtI()).c_str(),
+                ang->ThetaVal()*Constants::RADDEG);
+      }
+    }
+  }
+  for (Larray::const_iterator bnd = internalBonds_.begin(); bnd != internalBonds_.end(); ++bnd)
+  {
+    if (at == bnd->AtI()) {
+      if (hasPosition[bnd->AtJ()]) {
+        mprintf("DEBUG:\t\t%s length= %f\n", topIn.LeapName(bnd->AtJ()).c_str(), bnd->DistVal());
+      }
+    } else if (at == bnd->AtJ()) {
+      if (hasPosition[bnd->AtI()]) {
+        mprintf("DEBUG:\t\t%s length= %f\n", topIn.LeapName(bnd->AtI()).c_str(), bnd->DistVal());
+      }
+    }
+  }
 }
+// -----------------------------------------------
 
 /** Find internal coordinates for given atom.
   * Find torsion that contains this atom as one of the end atoms. The other
@@ -1690,7 +1725,7 @@ void Builder::printAllInternalsForAtom(int at, Topology const& topIn, Barray con
   * the given atom as a terminal atom.
   * \return 1 if complete internal coords were found, 0 if not.
   */
-int Builder::getIcFromInternals(InternalCoords& icOut, int at, Barray const& hasPosition) const
+Builder::InternalIdxType Builder::getIcFromInternals(InternalCoords& icOut, int at, Barray const& hasPosition) const
 {
   for (Tarray::const_iterator dih = internalTorsions_.begin(); dih != internalTorsions_.end(); ++dih)
   {
@@ -1707,7 +1742,7 @@ int Builder::getIcFromInternals(InternalCoords& icOut, int at, Barray const& has
                                    internalBonds_[bidx].DistVal(),
                                    internalAngles_[aidx].ThetaVal()*Constants::RADDEG,
                                    dih->PhiVal()*Constants::RADDEG);
-            return 1;
+            return InternalIdxType(dih-internalTorsions_.begin(), aidx, bidx);
           }
         }
       }
@@ -1724,13 +1759,13 @@ int Builder::getIcFromInternals(InternalCoords& icOut, int at, Barray const& has
                                    internalBonds_[bidx].DistVal(),
                                    internalAngles_[aidx].ThetaVal()*Constants::RADDEG,
                                    dih->PhiVal()*Constants::RADDEG);
-            return 1;
+            return InternalIdxType(dih-internalTorsions_.begin(), aidx, bidx);
           }
         }
       }
     }
   } // END loop over internal torsions
-  return 0;
+  return InternalIdxType();
 }
 
 /** \return Array of residues with atoms that need positions. */ // TODO does this need to be separate
@@ -1770,7 +1805,8 @@ const
 {
   // Find an internal coordinate for the atom.
   InternalCoords ic;
-  if (getIcFromInternals(ic, at, hasPosition)) {
+  InternalIdxType IIDX = getIcFromInternals(ic, at, hasPosition);
+  if (IIDX.IsComplete()) {
     //printAllInternalsForAtom(at, topIn, hasPosition); // DEBUG
     Vec3 posI = Zmatrix::AtomIposition(ic, frameOut);
     if (debug_ > 1) {
@@ -1885,7 +1921,7 @@ const
       int atToBuildAround = -1;
       if (!hasPosition[at]) {
         // Position of atom is not known.
-        //mprintf("BUILD: Position of %s is not known.\n", *(topIn[at].Name()));
+        mprintf("BUILD: Position of %s is not known.\n", *(topIn[at].Name())); // DEBUG
         // Is this bonded to an atom with known position?
         for (Atom::bond_iterator bat = topIn[at].bondbegin(); bat != topIn[at].bondend(); ++bat) {
           if (hasPosition[*bat]) {
@@ -1895,7 +1931,7 @@ const
         }
       } else {
         // Position of atom is known.
-        //mprintf("BUILD: Position of %s is known.\n", *(topIn[at].Name()));
+        mprintf("BUILD: Position of %s is known.\n", *(topIn[at].Name())); // DEBUG
         atToBuildAround = at;
       }
       // Build unknown positions around known atom
@@ -1906,6 +1942,7 @@ const
         for (Atom::bond_iterator bat = bAtom.bondbegin(); bat != bAtom.bondend(); ++bat)
         {
           if (!hasPosition[*bat]) {
+            printAllInternalsForAtom(*bat, topIn, hasPosition); // DEBUG
             if (buildCoordsForAtom(*bat, frameOut, topIn, hasPosition)) {
               hasPosition[ *bat ] = true;
               nAtomsBuilt++;
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index dcf07bda22..e37e44fc6a 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -61,6 +61,21 @@ class Builder {
     /// Hold chirality
     class InternalChirality;
 
+    /// Used to hold indices into internal arrays for a given atom
+    class InternalIdxType {
+      public:
+        /// CONSTRUCTOR
+        InternalIdxType() : tidx_(-1), aidx_(-1), bidx_(-1) {}
+        /// CONSTRUCTOR - torsion, angle, bond index
+        InternalIdxType(int t, int a, int b) : tidx_(t), aidx_(a), bidx_(b) {}
+        /// \return true if all indices set
+        bool IsComplete() const { return (tidx_ != -1 && aidx_ != -1 && bidx_ != -1); }
+      private:
+        int tidx_; ///< Index into internal torsion array
+        int aidx_; ///< Index into internal angle array
+        int bidx_; ///< Index into internal bond array
+    };
+
     typedef std::vector<InternalTorsion> Tarray;
     typedef std::vector<InternalAngle> Aarray;
     typedef std::vector<InternalBond> Larray;
@@ -107,7 +122,7 @@ class Builder {
     /// Generate internal coords for a given atom
     int generateAtomInternals(int, Frame const&, Topology const&, Barray const&);
     /// Get complete internal coords that can be used to construct specified atom
-    int getIcFromInternals(InternalCoords&, int, Barray const&) const;
+    InternalIdxType getIcFromInternals(InternalCoords&, int, Barray const&) const;
     /// For debug, print all valid internals associated with an atom
     void printAllInternalsForAtom(int, Topology const&, Barray const&) const;
     /// \\return index of atom with longest 'depth' bonded to a given atom (ignoring one bonded atom).

From 45e49a2912e1e8ca8f7191072e620b5af6e98819 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 22 Jul 2024 19:41:58 -0400
Subject: [PATCH 0881/1492] No need for the InternalIdxType class since
 InternalCoords has all info needed

---
 src/Structure/Builder.cpp | 41 +++++++++++++++++++++------------------
 src/Structure/Builder.h   | 17 +---------------
 2 files changed, 23 insertions(+), 35 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index bc5c8522d8..3308652619 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1725,7 +1725,7 @@ void Builder::printAllInternalsForAtom(int at, Topology const& topIn, Barray con
   * the given atom as a terminal atom.
   * \return 1 if complete internal coords were found, 0 if not.
   */
-Builder::InternalIdxType Builder::getIcFromInternals(InternalCoords& icOut, int at, Barray const& hasPosition) const
+int Builder::getIcFromInternals(InternalCoords& icOut, int at, Barray const& hasPosition) const
 {
   for (Tarray::const_iterator dih = internalTorsions_.begin(); dih != internalTorsions_.end(); ++dih)
   {
@@ -1742,7 +1742,7 @@ Builder::InternalIdxType Builder::getIcFromInternals(InternalCoords& icOut, int
                                    internalBonds_[bidx].DistVal(),
                                    internalAngles_[aidx].ThetaVal()*Constants::RADDEG,
                                    dih->PhiVal()*Constants::RADDEG);
-            return InternalIdxType(dih-internalTorsions_.begin(), aidx, bidx);
+            return 1;
           }
         }
       }
@@ -1759,13 +1759,15 @@ Builder::InternalIdxType Builder::getIcFromInternals(InternalCoords& icOut, int
                                    internalBonds_[bidx].DistVal(),
                                    internalAngles_[aidx].ThetaVal()*Constants::RADDEG,
                                    dih->PhiVal()*Constants::RADDEG);
-            return InternalIdxType(dih-internalTorsions_.begin(), aidx, bidx);
+            return 1;
           }
         }
       }
     }
   } // END loop over internal torsions
-  return InternalIdxType();
+  // If we are here, no "complete" IC was found. Check for angle and/or bond.
+
+  return 0;
 }
 
 /** \return Array of residues with atoms that need positions. */ // TODO does this need to be separate
@@ -1805,23 +1807,24 @@ const
 {
   // Find an internal coordinate for the atom.
   InternalCoords ic;
-  InternalIdxType IIDX = getIcFromInternals(ic, at, hasPosition);
-  if (IIDX.IsComplete()) {
+  if (getIcFromInternals(ic, at, hasPosition)) {
     //printAllInternalsForAtom(at, topIn, hasPosition); // DEBUG
-    Vec3 posI = Zmatrix::AtomIposition(ic, frameOut);
-    if (debug_ > 1) {
-      mprintf("Building atom %s using torsion/angle/bond\n", topIn.LeapName(at).c_str());
-      mprintf("Using - %s - %s - %s\n",
-              topIn.LeapName(ic.AtJ()).c_str(),
-              topIn.LeapName(ic.AtK()).c_str(),
-              topIn.LeapName(ic.AtL()).c_str());
-      mprintf( "Torsion = %f\n", ic.Phi() );
-      mprintf( "Angle   = %f\n", ic.Theta() );
-      mprintf( "Bond    = %f\n", ic.Dist() );
-      mprintf( "ZMatrixAll:  %f,%f,%f\n", posI[0], posI[1], posI[2]);
+    if (ic.AtL() != -1) {
+      Vec3 posI = Zmatrix::AtomIposition(ic, frameOut);
+      if (debug_ > 1) {
+        mprintf("Building atom %s using torsion/angle/bond\n", topIn.LeapName(at).c_str());
+        mprintf("Using - %s - %s - %s\n",
+                topIn.LeapName(ic.AtJ()).c_str(),
+                topIn.LeapName(ic.AtK()).c_str(),
+                topIn.LeapName(ic.AtL()).c_str());
+        mprintf( "Torsion = %f\n", ic.Phi() );
+        mprintf( "Angle   = %f\n", ic.Theta() );
+        mprintf( "Bond    = %f\n", ic.Dist() );
+        mprintf( "ZMatrixAll:  %f,%f,%f\n", posI[0], posI[1], posI[2]);
+      }
+      frameOut.SetXYZ( ic.AtI(), posI );
+      return 1;
     }
-    frameOut.SetXYZ( ic.AtI(), posI );
-    return 1;
   }
   return 0;
 }
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index e37e44fc6a..dcf07bda22 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -61,21 +61,6 @@ class Builder {
     /// Hold chirality
     class InternalChirality;
 
-    /// Used to hold indices into internal arrays for a given atom
-    class InternalIdxType {
-      public:
-        /// CONSTRUCTOR
-        InternalIdxType() : tidx_(-1), aidx_(-1), bidx_(-1) {}
-        /// CONSTRUCTOR - torsion, angle, bond index
-        InternalIdxType(int t, int a, int b) : tidx_(t), aidx_(a), bidx_(b) {}
-        /// \return true if all indices set
-        bool IsComplete() const { return (tidx_ != -1 && aidx_ != -1 && bidx_ != -1); }
-      private:
-        int tidx_; ///< Index into internal torsion array
-        int aidx_; ///< Index into internal angle array
-        int bidx_; ///< Index into internal bond array
-    };
-
     typedef std::vector<InternalTorsion> Tarray;
     typedef std::vector<InternalAngle> Aarray;
     typedef std::vector<InternalBond> Larray;
@@ -122,7 +107,7 @@ class Builder {
     /// Generate internal coords for a given atom
     int generateAtomInternals(int, Frame const&, Topology const&, Barray const&);
     /// Get complete internal coords that can be used to construct specified atom
-    InternalIdxType getIcFromInternals(InternalCoords&, int, Barray const&) const;
+    int getIcFromInternals(InternalCoords&, int, Barray const&) const;
     /// For debug, print all valid internals associated with an atom
     void printAllInternalsForAtom(int, Topology const&, Barray const&) const;
     /// \\return index of atom with longest 'depth' bonded to a given atom (ignoring one bonded atom).

From 3372ffff570b693ebbaf65e8e73d369cb1a49239 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 22 Jul 2024 19:55:02 -0400
Subject: [PATCH 0882/1492] Start only bond/angle internals present code

---
 src/Structure/Builder.cpp | 47 +++++++++++++++++++++++++++++++++++++--
 1 file changed, 45 insertions(+), 2 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 3308652619..104384d1e7 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1765,7 +1765,35 @@ int Builder::getIcFromInternals(InternalCoords& icOut, int at, Barray const& has
       }
     }
   } // END loop over internal torsions
-  // If we are here, no "complete" IC was found. Check for angle and/or bond.
+  // If we are here, no "complete" IC was found. Check for angle internal.
+  for (Aarray::const_iterator ang = internalAngles_.begin(); ang != internalAngles_.end(); ++ang)
+  {
+    if (at == ang->AtI()) {
+      if (hasPosition[ang->AtJ()] && hasPosition[ang->AtK()])
+      {
+        int bidx = getExistingBondIdx(ang->AtI(), ang->AtJ());
+        if (bidx > -1) {
+          icOut = InternalCoords(ang->AtI(), ang->AtJ(), ang->AtK(), -1,
+                                 internalBonds_[bidx].DistVal(),
+                                 ang->ThetaVal()*Constants::RADDEG,
+                                 0);
+          return 1;
+        }
+      }
+    } else if (at == ang->AtK()) {
+      if (hasPosition[ang->AtJ()] && hasPosition[ang->AtI()])
+      {
+        int bidx = getExistingBondIdx(ang->AtK(), ang->AtJ());
+        if (bidx > -1) {
+          icOut = InternalCoords(ang->AtK(), ang->AtJ(), ang->AtI(), -1,
+                                 internalBonds_[bidx].DistVal(),
+                                 ang->ThetaVal()*Constants::RADDEG,
+                                 0);
+          return 1;
+        }
+      }
+    }
+  } // END loop over internal angles
 
   return 0;
 }
@@ -1813,7 +1841,8 @@ const
       Vec3 posI = Zmatrix::AtomIposition(ic, frameOut);
       if (debug_ > 1) {
         mprintf("Building atom %s using torsion/angle/bond\n", topIn.LeapName(at).c_str());
-        mprintf("Using - %s - %s - %s\n",
+        mprintf("Using %s - %s - %s - %s\n",
+                topIn.LeapName(ic.AtI()).c_str(),
                 topIn.LeapName(ic.AtJ()).c_str(),
                 topIn.LeapName(ic.AtK()).c_str(),
                 topIn.LeapName(ic.AtL()).c_str());
@@ -1824,6 +1853,20 @@ const
       }
       frameOut.SetXYZ( ic.AtI(), posI );
       return 1;
+    } else if (ic.AtK() != -1) {
+      // FIXME
+      //if debug_ > 1) {
+        mprintf("Building atom %s using angle/bond\n", topIn.LeapName(at).c_str());
+        mprintf("Using %s - %s - %s\n",
+                topIn.LeapName(ic.AtI()).c_str(),
+                topIn.LeapName(ic.AtJ()).c_str(),
+                topIn.LeapName(ic.AtK()).c_str());
+        mprintf( "Angle   = %f\n", ic.Theta() );
+        mprintf( "Bond    = %f\n", ic.Dist() );
+        //mprintf( "ZMatrixAll:  %f,%f,%f\n", posI[0], posI[1], posI[2]);
+      //}
+      //frameOut.SetXYZ( ic.AtI(), posI );
+      return 0; // FIXME change to 1 when build is implemented
     }
   }
   return 0;

From 0026680e42e87f41fc826c7359ebf59567b7658c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 23 Jul 2024 11:10:56 -0400
Subject: [PATCH 0883/1492] Add getTwoAnglesFromInternals

---
 src/Structure/Builder.cpp | 48 +++++++++++++++++++++++++++++++++++++++
 src/Structure/Builder.h   |  2 ++
 2 files changed, 50 insertions(+)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 104384d1e7..d38264f802 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1798,6 +1798,54 @@ int Builder::getIcFromInternals(InternalCoords& icOut, int at, Barray const& has
   return 0;
 }
 
+/** Find an angle that has this atom as a terminal atom and the other
+  * two atoms with their coordinates specified. Then look for another
+  * angle which has this atom as the terminal and shares the center
+  * atom with the first angle and also has all of its coordinates
+  * specified.
+  * \return 1 if both angles found, 0 if not.
+  */
+int Builder::getTwoAnglesFromInternals(InternalAngle& a1, InternalAngle& a2,
+                                       int at, Barray const& hasPosition)
+const
+{
+  for (Aarray::const_iterator ang1 = internalAngles_.begin(); ang1 != internalAngles_.end(); ++ang1)
+  {
+    int ai = -1;   // The atom that needs its position defined
+    int aj = -1;   // Atom bonded to ai
+    //int ak = -1;   // Atom bonded to aj
+    int bidx = -1; // Index of ai-aj bond internal
+    if (at == ang1->AtI() && hasPosition[ang1->AtJ()] && hasPosition[ang1->AtK()]) {
+      ai = ang1->AtI();
+      aj = ang1->AtJ();
+      //ak = ang1->AtK();
+      a1 = *ang1;
+    } else if (at == ang1->AtK() && hasPosition[ang1->AtJ()] && hasPosition[ang1->AtI()]) {
+      ai = ang1->AtK();
+      aj = ang1->AtJ();
+      //ak = ang1->AtI();
+      a1 = InternalAngle(ang1->AtK(), ang1->AtJ(), ang1->AtI(), ang1->ThetaVal());
+    }
+    if (ai != -1)
+      bidx = getExistingBondIdx(ai, aj);
+    if (bidx > -1) {
+      // Find another angle matching ai-aj with aj and ak positions known
+      for (Aarray::const_iterator ang2 = ang1 + 1; ang2 != internalAngles_.end(); ++ang2)
+      {
+        if (ai == ang2->AtI() && aj == ang2->AtJ() && hasPosition[ang2->AtJ()] && hasPosition[ang2->AtK()]) {
+          a2 = *ang2;
+          return 1;
+        } else
+        if (ai == ang2->AtK() && aj == ang2->AtJ() && hasPosition[ang2->AtJ()] && hasPosition[ang2->AtI()]) {
+          a2 = InternalAngle(ang2->AtK(), ang2->AtJ(), ang2->AtI(), ang2->ThetaVal());
+          return 1;
+        }
+      }
+    }
+  } // END outer loop over angle internals
+  return 0;
+}
+
 /** \return Array of residues with atoms that need positions. */ // TODO does this need to be separate
 std::vector<Residue> Builder::residuesThatNeedPositions(Topology const& topIn,
                                                         Barray const& hasPosition)
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index dcf07bda22..d8c51c8455 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -108,6 +108,8 @@ class Builder {
     int generateAtomInternals(int, Frame const&, Topology const&, Barray const&);
     /// Get complete internal coords that can be used to construct specified atom
     int getIcFromInternals(InternalCoords&, int, Barray const&) const;
+    /// Get two angles with ai-aj in common and all positions but ai known
+    int getTwoAnglesFromInternals(InternalAngle&, InternalAngle&, int, Barray const&) const;
     /// For debug, print all valid internals associated with an atom
     void printAllInternalsForAtom(int, Topology const&, Barray const&) const;
     /// \\return index of atom with longest 'depth' bonded to a given atom (ignoring one bonded atom).

From 0213018a8c543eb0cf936518ef204777d16ee110 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 23 Jul 2024 11:13:51 -0400
Subject: [PATCH 0884/1492] Save ai-aj bond as well

---
 src/Structure/Builder.cpp | 2 ++
 src/Structure/Builder.h   | 2 +-
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index d38264f802..8679af02e3 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1806,6 +1806,7 @@ int Builder::getIcFromInternals(InternalCoords& icOut, int at, Barray const& has
   * \return 1 if both angles found, 0 if not.
   */
 int Builder::getTwoAnglesFromInternals(InternalAngle& a1, InternalAngle& a2,
+                                       InternalBond& b1,
                                        int at, Barray const& hasPosition)
 const
 {
@@ -1829,6 +1830,7 @@ const
     if (ai != -1)
       bidx = getExistingBondIdx(ai, aj);
     if (bidx > -1) {
+      b1 = internalBonds_[bidx];
       // Find another angle matching ai-aj with aj and ak positions known
       for (Aarray::const_iterator ang2 = ang1 + 1; ang2 != internalAngles_.end(); ++ang2)
       {
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index d8c51c8455..0cbfc01f45 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -109,7 +109,7 @@ class Builder {
     /// Get complete internal coords that can be used to construct specified atom
     int getIcFromInternals(InternalCoords&, int, Barray const&) const;
     /// Get two angles with ai-aj in common and all positions but ai known
-    int getTwoAnglesFromInternals(InternalAngle&, InternalAngle&, int, Barray const&) const;
+    int getTwoAnglesFromInternals(InternalAngle&, InternalAngle&, InternalBond&, int, Barray const&) const;
     /// For debug, print all valid internals associated with an atom
     void printAllInternalsForAtom(int, Topology const&, Barray const&) const;
     /// \\return index of atom with longest 'depth' bonded to a given atom (ignoring one bonded atom).

From 31a3838e16780f07f49a88db53a1fa675fc564ad Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 23 Jul 2024 11:18:53 -0400
Subject: [PATCH 0885/1492] Add getAngleFromInternals

---
 src/Structure/Builder.cpp | 56 +++++++++++++++++++--------------------
 src/Structure/Builder.h   |  2 ++
 2 files changed, 29 insertions(+), 29 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 8679af02e3..4f074e69a4 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1765,35 +1765,7 @@ int Builder::getIcFromInternals(InternalCoords& icOut, int at, Barray const& has
       }
     }
   } // END loop over internal torsions
-  // If we are here, no "complete" IC was found. Check for angle internal.
-  for (Aarray::const_iterator ang = internalAngles_.begin(); ang != internalAngles_.end(); ++ang)
-  {
-    if (at == ang->AtI()) {
-      if (hasPosition[ang->AtJ()] && hasPosition[ang->AtK()])
-      {
-        int bidx = getExistingBondIdx(ang->AtI(), ang->AtJ());
-        if (bidx > -1) {
-          icOut = InternalCoords(ang->AtI(), ang->AtJ(), ang->AtK(), -1,
-                                 internalBonds_[bidx].DistVal(),
-                                 ang->ThetaVal()*Constants::RADDEG,
-                                 0);
-          return 1;
-        }
-      }
-    } else if (at == ang->AtK()) {
-      if (hasPosition[ang->AtJ()] && hasPosition[ang->AtI()])
-      {
-        int bidx = getExistingBondIdx(ang->AtK(), ang->AtJ());
-        if (bidx > -1) {
-          icOut = InternalCoords(ang->AtK(), ang->AtJ(), ang->AtI(), -1,
-                                 internalBonds_[bidx].DistVal(),
-                                 ang->ThetaVal()*Constants::RADDEG,
-                                 0);
-          return 1;
-        }
-      }
-    }
-  } // END loop over internal angles
+
 
   return 0;
 }
@@ -1848,6 +1820,32 @@ const
   return 0;
 }
 
+/** Get angle for atom whose other two atoms have known position. */ // TODO combined with getTwoAngles above
+int Builder::getAngleFromInternals(InternalAngle& a1, InternalBond& b1,
+                                   int at, Barray const& hasPosition)
+const
+{
+  for (Aarray::const_iterator ang = internalAngles_.begin(); ang != internalAngles_.end(); ++ang)
+  {
+    if (at == ang->AtI() && hasPosition[ang->AtJ()] && hasPosition[ang->AtK()]) {
+      int bidx = getExistingBondIdx(ang->AtI(), ang->AtJ());
+      if (bidx > -1) {
+        a1 = *ang;
+        b1 = internalBonds_[bidx];
+        return 1;
+      }
+    } else if (at == ang->AtK() && hasPosition[ang->AtJ()] && hasPosition[ang->AtI()]) {
+      int bidx = getExistingBondIdx(ang->AtK(), ang->AtJ());
+      if (bidx > -1) {
+        a1 = InternalAngle( ang->AtK(), ang->AtJ(), ang->AtI(), ang->ThetaVal() );
+	b1 = internalBonds_[bidx];
+        return 1;
+      }
+    }
+  } // END loop over internal angles
+  return 0;
+}
+
 /** \return Array of residues with atoms that need positions. */ // TODO does this need to be separate
 std::vector<Residue> Builder::residuesThatNeedPositions(Topology const& topIn,
                                                         Barray const& hasPosition)
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index 0cbfc01f45..a84e393df2 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -110,6 +110,8 @@ class Builder {
     int getIcFromInternals(InternalCoords&, int, Barray const&) const;
     /// Get two angles with ai-aj in common and all positions but ai known
     int getTwoAnglesFromInternals(InternalAngle&, InternalAngle&, InternalBond&, int, Barray const&) const;
+    /// Get angle with all positions but ai known
+    int getAngleFromInternals(InternalAngle&, InternalBond&, int, Barray const&) const;
     /// For debug, print all valid internals associated with an atom
     void printAllInternalsForAtom(int, Topology const&, Barray const&) const;
     /// \\return index of atom with longest 'depth' bonded to a given atom (ignoring one bonded atom).

From ab20f1c3e9f062578369711c38a954563d2e6057 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 23 Jul 2024 11:26:28 -0400
Subject: [PATCH 0886/1492] Use the new get functions. Still need to build.

---
 src/Structure/Builder.cpp | 73 +++++++++++++++++++++++----------------
 1 file changed, 43 insertions(+), 30 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 4f074e69a4..7c95e068a4 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1766,7 +1766,6 @@ int Builder::getIcFromInternals(InternalCoords& icOut, int at, Barray const& has
     }
   } // END loop over internal torsions
 
-
   return 0;
 }
 
@@ -1885,37 +1884,51 @@ const
   InternalCoords ic;
   if (getIcFromInternals(ic, at, hasPosition)) {
     //printAllInternalsForAtom(at, topIn, hasPosition); // DEBUG
-    if (ic.AtL() != -1) {
-      Vec3 posI = Zmatrix::AtomIposition(ic, frameOut);
-      if (debug_ > 1) {
-        mprintf("Building atom %s using torsion/angle/bond\n", topIn.LeapName(at).c_str());
-        mprintf("Using %s - %s - %s - %s\n",
-                topIn.LeapName(ic.AtI()).c_str(),
-                topIn.LeapName(ic.AtJ()).c_str(),
-                topIn.LeapName(ic.AtK()).c_str(),
-                topIn.LeapName(ic.AtL()).c_str());
-        mprintf( "Torsion = %f\n", ic.Phi() );
-        mprintf( "Angle   = %f\n", ic.Theta() );
-        mprintf( "Bond    = %f\n", ic.Dist() );
-        mprintf( "ZMatrixAll:  %f,%f,%f\n", posI[0], posI[1], posI[2]);
-      }
-      frameOut.SetXYZ( ic.AtI(), posI );
-      return 1;
-    } else if (ic.AtK() != -1) {
-      // FIXME
-      //if debug_ > 1) {
-        mprintf("Building atom %s using angle/bond\n", topIn.LeapName(at).c_str());
-        mprintf("Using %s - %s - %s\n",
-                topIn.LeapName(ic.AtI()).c_str(),
-                topIn.LeapName(ic.AtJ()).c_str(),
-                topIn.LeapName(ic.AtK()).c_str());
-        mprintf( "Angle   = %f\n", ic.Theta() );
-        mprintf( "Bond    = %f\n", ic.Dist() );
+    Vec3 posI = Zmatrix::AtomIposition(ic, frameOut);
+    if (debug_ > 1) {
+      mprintf("Building atom %s using torsion/angle/bond\n", topIn.LeapName(at).c_str());
+      mprintf("Using %s - %s - %s - %s\n",
+              topIn.LeapName(ic.AtI()).c_str(),
+              topIn.LeapName(ic.AtJ()).c_str(),
+              topIn.LeapName(ic.AtK()).c_str(),
+              topIn.LeapName(ic.AtL()).c_str());
+      mprintf( "Torsion = %f\n", ic.Phi() );
+      mprintf( "Angle   = %f\n", ic.Theta() );
+      mprintf( "Bond    = %f\n", ic.Dist() );
+      mprintf( "ZMatrixAll:  %f,%f,%f\n", posI[0], posI[1], posI[2]);
+    }
+    frameOut.SetXYZ( ic.AtI(), posI );
+    return 1;
+  }
+  // Check if we can get two angle internals for this atom
+  InternalAngle a1, a2;
+  InternalBond b1;
+  if (getTwoAnglesFromInternals(a1, a2, b1, at, hasPosition)) {
+    //if (debug_ > 1) {
+      mprintf("Building atom %s using two angles\n", topIn.LeapName(at).c_str());
+      mprintf("Using %s - %s - %s and %s - %s - %s\n",
+                  topIn.LeapName(a1.AtI()).c_str(), topIn.LeapName(a1.AtJ()).c_str(), topIn.LeapName(a1.AtK()).c_str(),
+                  topIn.LeapName(a2.AtI()).c_str(), topIn.LeapName(a2.AtJ()).c_str(), topIn.LeapName(a2.AtK()).c_str());
+      mprintf("Angle1  = %f\n", a1.ThetaVal() );
+      mprintf("Angle2  = %f\n", a2.ThetaVal() );
+      mprintf("Bond    = %f\n", b1.DistVal() );
+    //}
+    //frameOut.SetXYZ( ic.AtI(), posI );
+    // FIXME actually build
+  }
+  // Check if we can get a single angle for this atom
+  if (getAngleFromInternals(a1, b1, at, hasPosition)) {
+    // FIXME
+    //if debug_ > 1) {
+      mprintf("Building atom %s using angle/bond\n", topIn.LeapName(at).c_str());
+      mprintf("Using %s - %s - %s\n",
+              topIn.LeapName(a1.AtI()).c_str(), topIn.LeapName(a1.AtJ()).c_str(), topIn.LeapName(a1.AtK()).c_str());
+      mprintf( "Angle   = %f\n", a1.ThetaVal() );
+      mprintf( "Bond    = %f\n", b1.DistVal() );
         //mprintf( "ZMatrixAll:  %f,%f,%f\n", posI[0], posI[1], posI[2]);
       //}
-      //frameOut.SetXYZ( ic.AtI(), posI );
-      return 0; // FIXME change to 1 when build is implemented
-    }
+    //frameOut.SetXYZ( ic.AtI(), posI );
+    // FIXME actually build 
   }
   return 0;
 }

From b4c45ddbd565f70b4fd9a382b058bfa9ee98c500 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 23 Jul 2024 11:29:01 -0400
Subject: [PATCH 0887/1492] Move function

---
 src/Structure/Builder.cpp | 58 +++++++++++++++++++--------------------
 src/Structure/Builder.h   |  4 +--
 2 files changed, 31 insertions(+), 31 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 7c95e068a4..9b86a87b10 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1845,35 +1845,6 @@ const
   return 0;
 }
 
-/** \return Array of residues with atoms that need positions. */ // TODO does this need to be separate
-std::vector<Residue> Builder::residuesThatNeedPositions(Topology const& topIn,
-                                                        Barray const& hasPosition)
-const
-{
-  std::vector<Residue> residues;
-  std::vector<int> Rnums;
-  for (Tarray::const_iterator dih = internalTorsions_.begin();
-                              dih != internalTorsions_.end(); ++dih)
-  {
-    if (!hasPosition[dih->AtI()]) {
-      int rnum = topIn[dih->AtI()].ResNum();
-      bool has_rnum = false;
-      for (std::vector<int>::const_iterator it = Rnums.begin(); it != Rnums.end(); ++it) {
-        if (*it == rnum) {
-          has_rnum = true;
-          break;
-        }
-      }
-      if (!has_rnum) {
-        if (debug_ > 0) mprintf("DEBUG: Need to build for residue %s\n", topIn.TruncResNameNum(rnum).c_str());
-        residues.push_back( topIn.Res(rnum) );
-        Rnums.push_back(rnum);
-      }
-    }
-  }
-  return residues;
-} 
-
 /** Build coordinates for an atom from internals.
   * \return 1 if atom was built, 0 otherwise.
   */
@@ -1976,6 +1947,35 @@ const
   return 0;
 }
 
+/** \return Array of residues with atoms that need positions. */ // TODO does this need to be separate
+std::vector<Residue> Builder::residuesThatNeedPositions(Topology const& topIn,
+                                                        Barray const& hasPosition)
+const
+{
+  std::vector<Residue> residues;
+  std::vector<int> Rnums;
+  for (Tarray::const_iterator dih = internalTorsions_.begin();
+                              dih != internalTorsions_.end(); ++dih)
+  {
+    if (!hasPosition[dih->AtI()]) {
+      int rnum = topIn[dih->AtI()].ResNum();
+      bool has_rnum = false;
+      for (std::vector<int>::const_iterator it = Rnums.begin(); it != Rnums.end(); ++it) {
+        if (*it == rnum) {
+          has_rnum = true;
+          break;
+        }
+      }
+      if (!has_rnum) {
+        if (debug_ > 0) mprintf("DEBUG: Need to build for residue %s\n", topIn.TruncResNameNum(rnum).c_str());
+        residues.push_back( topIn.Res(rnum) );
+        Rnums.push_back(rnum);
+      }
+    }
+  }
+  return residues;
+} 
+
 /** Build coordinates for any atom with an internal that does
   * not have its position set.
   */ 
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index a84e393df2..f2023ec2a5 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -116,10 +116,10 @@ class Builder {
     void printAllInternalsForAtom(int, Topology const&, Barray const&) const;
     /// \\return index of atom with longest 'depth' bonded to a given atom (ignoring one bonded atom).
     static int get_depths_around_atom(int, int, Topology const&);
-    /// \return array containing all residues with atoms that need positions
-    std::vector<Residue> residuesThatNeedPositions(Topology const&, Barray const&) const;
     /// Build XYZ coords for an atom if internals are available
     int buildCoordsForAtom(int, Frame&, Topology const&, Barray const&) const;
+    /// \return array containing all residues with atoms that need positions
+    std::vector<Residue> residuesThatNeedPositions(Topology const&, Barray const&) const;
 
     int debug_;
     ParameterSet const* params_;

From 1178f06a4c595b61c1c20e7dcbaea2f4872db5e1 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 23 Jul 2024 11:36:38 -0400
Subject: [PATCH 0888/1492] Fix angle printout. Add getBondFromInternals

---
 src/Structure/Builder.cpp | 37 ++++++++++++++++++++++++++++++++++---
 src/Structure/Builder.h   |  2 ++
 2 files changed, 36 insertions(+), 3 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 9b86a87b10..04e94f2e80 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1845,6 +1845,24 @@ const
   return 0;
 }
 
+/** Get bond for atom whose other atom has known position. */
+int Builder::getBondFromInternals(InternalBond& b1, int at, Barray const& hasPosition)
+const
+{
+  for (Larray::const_iterator bnd = internalBonds_.begin(); bnd != internalBonds_.end(); ++bnd)
+  {
+    if (at == bnd->AtI() && hasPosition[bnd->AtJ()]) {
+      b1 = *bnd;
+      return 1;
+    } else
+    if (at == bnd->AtJ() && hasPosition[bnd->AtI()]) {
+      b1 = InternalBond(bnd->AtJ(), bnd->AtI(), bnd->DistVal());
+      return 1;
+    }
+  }
+  return 0;
+}
+
 /** Build coordinates for an atom from internals.
   * \return 1 if atom was built, 0 otherwise.
   */
@@ -1880,8 +1898,8 @@ const
       mprintf("Using %s - %s - %s and %s - %s - %s\n",
                   topIn.LeapName(a1.AtI()).c_str(), topIn.LeapName(a1.AtJ()).c_str(), topIn.LeapName(a1.AtK()).c_str(),
                   topIn.LeapName(a2.AtI()).c_str(), topIn.LeapName(a2.AtJ()).c_str(), topIn.LeapName(a2.AtK()).c_str());
-      mprintf("Angle1  = %f\n", a1.ThetaVal() );
-      mprintf("Angle2  = %f\n", a2.ThetaVal() );
+      mprintf("Angle1  = %f\n", a1.ThetaVal()*Constants::RADDEG );
+      mprintf("Angle2  = %f\n", a2.ThetaVal()*Constants::RADDEG );
       mprintf("Bond    = %f\n", b1.DistVal() );
     //}
     //frameOut.SetXYZ( ic.AtI(), posI );
@@ -1894,7 +1912,20 @@ const
       mprintf("Building atom %s using angle/bond\n", topIn.LeapName(at).c_str());
       mprintf("Using %s - %s - %s\n",
               topIn.LeapName(a1.AtI()).c_str(), topIn.LeapName(a1.AtJ()).c_str(), topIn.LeapName(a1.AtK()).c_str());
-      mprintf( "Angle   = %f\n", a1.ThetaVal() );
+      mprintf( "Angle   = %f\n", a1.ThetaVal()*Constants::RADDEG );
+      mprintf( "Bond    = %f\n", b1.DistVal() );
+        //mprintf( "ZMatrixAll:  %f,%f,%f\n", posI[0], posI[1], posI[2]);
+      //}
+    //frameOut.SetXYZ( ic.AtI(), posI );
+    // FIXME actually build 
+  }
+  // Check if we can get a bond for this atom
+  if (getBondFromInternals(b1, at, hasPosition)) {
+    // FIXME
+    //if debug_ > 1) {
+      mprintf("Building atom %s using bond\n", topIn.LeapName(at).c_str());
+      mprintf("Using %s - %s\n",
+              topIn.LeapName(b1.AtI()).c_str(), topIn.LeapName(b1.AtJ()).c_str());
       mprintf( "Bond    = %f\n", b1.DistVal() );
         //mprintf( "ZMatrixAll:  %f,%f,%f\n", posI[0], posI[1], posI[2]);
       //}
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index f2023ec2a5..34892465e0 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -112,6 +112,8 @@ class Builder {
     int getTwoAnglesFromInternals(InternalAngle&, InternalAngle&, InternalBond&, int, Barray const&) const;
     /// Get angle with all positions but ai known
     int getAngleFromInternals(InternalAngle&, InternalBond&, int, Barray const&) const;
+    /// Get bond with aj position known
+    int getBondFromInternals(InternalBond&, int, Barray const&) const;
     /// For debug, print all valid internals associated with an atom
     void printAllInternalsForAtom(int, Topology const&, Barray const&) const;
     /// \\return index of atom with longest 'depth' bonded to a given atom (ignoring one bonded atom).

From 53847cbc22eddbf5746b800514298dbe3414df46 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 23 Jul 2024 14:44:10 -0400
Subject: [PATCH 0889/1492] Start getting coords from Atom/Bond

---
 src/Structure/Builder.cpp |  2 +-
 src/Structure/Zmatrix.cpp | 19 +++++++++++++++++++
 src/Structure/Zmatrix.h   |  2 ++
 3 files changed, 22 insertions(+), 1 deletion(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 04e94f2e80..6ed5d1fcd0 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1907,7 +1907,7 @@ const
   }
   // Check if we can get a single angle for this atom
   if (getAngleFromInternals(a1, b1, at, hasPosition)) {
-    // FIXME
+    Vec3 posI = Zmatrix::AtomIposition(frameOut.XYZ(a1.AtJ()), frameOut.XYZ(a1.AtK()), b1.DistVal(), a1.ThetaVal() );
     //if debug_ > 1) {
       mprintf("Building atom %s using angle/bond\n", topIn.LeapName(at).c_str());
       mprintf("Using %s - %s - %s\n",
diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index 5105df826c..ef0b841d7d 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -886,6 +886,25 @@ int Zmatrix::SetFromFrame(Frame const& frameIn, Topology const& topIn, int molnu
 }
 
 // -----------------------------------------------------------------------------
+/** \return Position of atom I from positions of atoms J and K,
+  *         the corresponding distance I-J (in Ang.) and angle I-J-K
+  *         (in radians).
+  */
+Vec3 Zmatrix::AtomIposition(Vec3 const& posJ, Vec3 const& posK, double rdist, double theta_rad)
+{
+  // J-K vector
+  Vec3 vTempX = posK - posJ;
+  Vec3 vTempXZ( vTempX[0], 0.0, vTempX[2] );
+  vTempXZ.Normalize();
+  //
+  Vec3 vXAxis(1.0, 0.0, 0.0);
+  Vec3 vYAxis(0.0, 1.0, 0.0);
+  double dAngleY = vTempXZ.SignedAngle( vXAxis, vYAxis );
+  mprintf( "Angle around Y=%lf\n", dAngleY );
+
+  return Vec3();
+}
+
 /** \return Position of atom I from positions of atoms J, K, and L,
   *         and corresponding distance (in Ang) and angle/torsion
   *         values (in degrees).
diff --git a/src/Structure/Zmatrix.h b/src/Structure/Zmatrix.h
index 9c9b627f71..b2f65ba67a 100644
--- a/src/Structure/Zmatrix.h
+++ b/src/Structure/Zmatrix.h
@@ -73,6 +73,8 @@ class Zmatrix {
     unsigned int sizeInBytes() const { return (7*sizeof(int)) +
                                               (9*sizeof(double)) + // 3 Vec3
                                               (IC_.size() * InternalCoords::sizeInBytes()); }
+    /// \return XYZ position of atom I using positions of atoms J/K and distance/angle(rad)
+    static Vec3 AtomIposition(Vec3 const&, Vec3 const&, double, double);
     /// \return XYZ position of atom I using positions of atoms J/K/L and distance/angle/torsion (deg)
     static Vec3 AtomIposition(Vec3 const&, Vec3 const&, Vec3 const&, double, double, double);
     /// \return XYZ position of atom I for given internal coordinate

From 67deba95ec917872a43d7f2a317a11a8a76db071 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 23 Jul 2024 15:38:39 -0400
Subject: [PATCH 0890/1492] Add some rotations

---
 src/Structure/Zmatrix.cpp | 16 +++++++++++++---
 1 file changed, 13 insertions(+), 3 deletions(-)

diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index ef0b841d7d..b1256f970e 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -897,10 +897,20 @@ Vec3 Zmatrix::AtomIposition(Vec3 const& posJ, Vec3 const& posK, double rdist, do
   Vec3 vTempXZ( vTempX[0], 0.0, vTempX[2] );
   vTempXZ.Normalize();
   //
-  Vec3 vXAxis(1.0, 0.0, 0.0);
-  Vec3 vYAxis(0.0, 1.0, 0.0);
+  static const Vec3 vXAxis(1.0, 0.0, 0.0);
+  static const Vec3 vYAxis(0.0, 1.0, 0.0);
+  static const Vec3 vZAxis(0.0, 0.0, 1.0);
   double dAngleY = vTempXZ.SignedAngle( vXAxis, vYAxis );
-  mprintf( "Angle around Y=%lf\n", dAngleY );
+  mprintf( "Angle around Y=%f\n", dAngleY );
+
+  Matrix_3x3 mT;
+  mT.CalcRotationMatrix(vYAxis, dAngleY);
+  vTempX = mT * vTempX;
+  mprintf("Rotated around Y = %f, %f, %f\n", vTempX[0], vTempX[1], vTempX[2]);
+
+  vTempX.Normalize();
+  double dAngleZ = vTempX.SignedAngle( vXAxis, vZAxis );
+  mprintf("Angle around Z=%f\n", dAngleZ );
 
   return Vec3();
 }

From 79d2ad6327328b569f2ac76e1bddb779cd6638a8 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 23 Jul 2024 15:43:23 -0400
Subject: [PATCH 0891/1492] More rotations

---
 src/Structure/Zmatrix.cpp | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index b1256f970e..668fc09e68 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -912,6 +912,12 @@ Vec3 Zmatrix::AtomIposition(Vec3 const& posJ, Vec3 const& posK, double rdist, do
   double dAngleZ = vTempX.SignedAngle( vXAxis, vZAxis );
   mprintf("Angle around Z=%f\n", dAngleZ );
 
+  Vec3 vNew( rdist*cos(theta_rad), rdist*sin(theta_rad), 0.0 );
+  mT.CalcRotationMatrix(vZAxis, dAngleZ);
+  vNew = mT * vNew;
+  mT.CalcRotationMatrix(vYAxis, dAngleY);
+  vNew = mT * vNew;
+
   return Vec3();
 }
 

From 9c2191e2df93ef9f404d7788194c2e42c606dd94 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 23 Jul 2024 20:14:12 -0400
Subject: [PATCH 0892/1492] It seems cpptraj rotation matrices are opposite
 leap ones. Set the bond/angle coord

---
 src/Structure/Builder.cpp |  8 +++++---
 src/Structure/Zmatrix.cpp | 11 ++++++++---
 2 files changed, 13 insertions(+), 6 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 6ed5d1fcd0..652e5748b6 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1903,6 +1903,7 @@ const
       mprintf("Bond    = %f\n", b1.DistVal() );
     //}
     //frameOut.SetXYZ( ic.AtI(), posI );
+    // return 1;
     // FIXME actually build
   }
   // Check if we can get a single angle for this atom
@@ -1914,10 +1915,10 @@ const
               topIn.LeapName(a1.AtI()).c_str(), topIn.LeapName(a1.AtJ()).c_str(), topIn.LeapName(a1.AtK()).c_str());
       mprintf( "Angle   = %f\n", a1.ThetaVal()*Constants::RADDEG );
       mprintf( "Bond    = %f\n", b1.DistVal() );
-        //mprintf( "ZMatrixAll:  %f,%f,%f\n", posI[0], posI[1], posI[2]);
+      mprintf("ZMatrixBondAngle:  %f,%f,%f\n", posI[0], posI[1], posI[2]);
       //}
-    //frameOut.SetXYZ( ic.AtI(), posI );
-    // FIXME actually build 
+    frameOut.SetXYZ( ic.AtI(), posI );
+    return 1;
   }
   // Check if we can get a bond for this atom
   if (getBondFromInternals(b1, at, hasPosition)) {
@@ -1930,6 +1931,7 @@ const
         //mprintf( "ZMatrixAll:  %f,%f,%f\n", posI[0], posI[1], posI[2]);
       //}
     //frameOut.SetXYZ( ic.AtI(), posI );
+    // return 1;
     // FIXME actually build 
   }
   return 0;
diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index 668fc09e68..83a69733e3 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -913,12 +913,17 @@ Vec3 Zmatrix::AtomIposition(Vec3 const& posJ, Vec3 const& posK, double rdist, do
   mprintf("Angle around Z=%f\n", dAngleZ );
 
   Vec3 vNew( rdist*cos(theta_rad), rdist*sin(theta_rad), 0.0 );
-  mT.CalcRotationMatrix(vZAxis, dAngleZ);
+  mprintf("vNew: %f,%f,%f\n", vNew[0], vNew[1], vNew[2]);
+  mT.CalcRotationMatrix(vZAxis, -dAngleZ);
   vNew = mT * vNew;
-  mT.CalcRotationMatrix(vYAxis, dAngleY);
+  mT.CalcRotationMatrix(vYAxis, -dAngleY);
   vNew = mT * vNew;
+  mprintf("vNew before MatrixTranslate: %f,%f,%f\n", vNew[0], vNew[1], vNew[2]);
+  printf("vTrans before MatrixTranslate: %f,%f,%f\n", posJ[0], posJ[1], posJ[2]);
+  Vec3 posI = vNew + posJ;
+  
 
-  return Vec3();
+  return posI;
 }
 
 /** \return Position of atom I from positions of atoms J, K, and L,

From abb6f69f537fa70c52042b03050a9726d86c76f2 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 23 Jul 2024 20:49:33 -0400
Subject: [PATCH 0893/1492] Use a1, not ic

---
 src/Structure/Builder.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 652e5748b6..ae869eb4aa 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1917,7 +1917,7 @@ const
       mprintf( "Bond    = %f\n", b1.DistVal() );
       mprintf("ZMatrixBondAngle:  %f,%f,%f\n", posI[0], posI[1], posI[2]);
       //}
-    frameOut.SetXYZ( ic.AtI(), posI );
+    frameOut.SetXYZ( a1.AtI(), posI );
     return 1;
   }
   // Check if we can get a bond for this atom

From a8a695ed5360b2b7be69025ccec9bf14dcebe290 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 24 Jul 2024 08:34:08 -0400
Subject: [PATCH 0894/1492] Build using only a bond

---
 src/Structure/Builder.cpp | 13 ++++++-------
 src/Structure/Zmatrix.cpp | 12 +++++++++++-
 src/Structure/Zmatrix.h   |  6 ++++--
 3 files changed, 21 insertions(+), 10 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index ae869eb4aa..7a3264cc1e 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1898,8 +1898,8 @@ const
       mprintf("Using %s - %s - %s and %s - %s - %s\n",
                   topIn.LeapName(a1.AtI()).c_str(), topIn.LeapName(a1.AtJ()).c_str(), topIn.LeapName(a1.AtK()).c_str(),
                   topIn.LeapName(a2.AtI()).c_str(), topIn.LeapName(a2.AtJ()).c_str(), topIn.LeapName(a2.AtK()).c_str());
-      mprintf("Angle1  = %f\n", a1.ThetaVal()*Constants::RADDEG );
-      mprintf("Angle2  = %f\n", a2.ThetaVal()*Constants::RADDEG );
+      mprintf("AngleA  = %f\n", a1.ThetaVal()*Constants::RADDEG );
+      mprintf("AngleB  = %f\n", a2.ThetaVal()*Constants::RADDEG );
       mprintf("Bond    = %f\n", b1.DistVal() );
     //}
     //frameOut.SetXYZ( ic.AtI(), posI );
@@ -1922,17 +1922,16 @@ const
   }
   // Check if we can get a bond for this atom
   if (getBondFromInternals(b1, at, hasPosition)) {
-    // FIXME
+    Vec3 posI = Zmatrix::AtomIposition(frameOut.XYZ(b1.AtJ()), b1.DistVal());
     //if debug_ > 1) {
       mprintf("Building atom %s using bond\n", topIn.LeapName(at).c_str());
       mprintf("Using %s - %s\n",
               topIn.LeapName(b1.AtI()).c_str(), topIn.LeapName(b1.AtJ()).c_str());
       mprintf( "Bond    = %f\n", b1.DistVal() );
-        //mprintf( "ZMatrixAll:  %f,%f,%f\n", posI[0], posI[1], posI[2]);
+      mprintf( "ZMatrixBond:  %f,%f,%f\n", posI[0], posI[1], posI[2]);
       //}
-    //frameOut.SetXYZ( ic.AtI(), posI );
-    // return 1;
-    // FIXME actually build 
+    frameOut.SetXYZ( b1.AtI(), posI );
+    return 1;
   }
   return 0;
 }
diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index 83a69733e3..40295f3c0c 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -921,11 +921,21 @@ Vec3 Zmatrix::AtomIposition(Vec3 const& posJ, Vec3 const& posK, double rdist, do
   mprintf("vNew before MatrixTranslate: %f,%f,%f\n", vNew[0], vNew[1], vNew[2]);
   printf("vTrans before MatrixTranslate: %f,%f,%f\n", posJ[0], posJ[1], posJ[2]);
   Vec3 posI = vNew + posJ;
-  
 
   return posI;
 }
 
+/* \return Position of atom I from position of atom J, using the given I-J distance.
+ * Atom I will be placed at a distance rdist from posJ along the X axis.
+ *
+ */
+Vec3 Zmatrix::AtomIposition(Vec3 const& posJ, double rdist)
+{
+  Vec3 vNew( rdist, 0.0, 0.0 );
+  vNew = vNew + posJ;
+  return vNew;
+}
+
 /** \return Position of atom I from positions of atoms J, K, and L,
   *         and corresponding distance (in Ang) and angle/torsion
   *         values (in degrees).
diff --git a/src/Structure/Zmatrix.h b/src/Structure/Zmatrix.h
index b2f65ba67a..d01f19042a 100644
--- a/src/Structure/Zmatrix.h
+++ b/src/Structure/Zmatrix.h
@@ -73,9 +73,11 @@ class Zmatrix {
     unsigned int sizeInBytes() const { return (7*sizeof(int)) +
                                               (9*sizeof(double)) + // 3 Vec3
                                               (IC_.size() * InternalCoords::sizeInBytes()); }
-    /// \return XYZ position of atom I using positions of atoms J/K and distance/angle(rad)
+    /// \return XYZ position of atom I using positions of atoms J/K and distance (ang)/angle(rad)
     static Vec3 AtomIposition(Vec3 const&, Vec3 const&, double, double);
-    /// \return XYZ position of atom I using positions of atoms J/K/L and distance/angle/torsion (deg)
+    /// \return XYZ position of atom I using position of atom J and distance (ang)
+    static Vec3 AtomIposition(Vec3 const&, double);
+    /// \return XYZ position of atom I using positions of atoms J/K/L and distance(ang)/angle/torsion (deg)
     static Vec3 AtomIposition(Vec3 const&, Vec3 const&, Vec3 const&, double, double, double);
     /// \return XYZ position of atom I for given internal coordinate
     static Vec3 AtomIposition(InternalCoords const&, Frame const&);

From 6aedbd75420ca7ba7599bdbdd251799a1065d3ce Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 24 Jul 2024 13:17:52 -0400
Subject: [PATCH 0895/1492] Add automatic check to build

---
 src/Exec_Build.cpp | 58 ++++++++++++++++++++++++++++++++++++++++++++++
 src/Exec_Build.h   |  2 ++
 src/cpptrajdepend  |  2 +-
 3 files changed, 61 insertions(+), 1 deletion(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 68a765c84e..c0b296d1ea 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -12,11 +12,14 @@
 #include "Structure/ResStatArray.h"
 #include "Structure/SugarBuilder.h"
 #include "Structure/Sugar.h"
+#include "StructureCheck.h"
 
 /** CONSTRUCTOR */
 Exec_Build::Exec_Build() :
   Exec(GENERAL),
   debug_(0),
+  check_box_natom_(5000), // TODO make user specifiable
+  check_structure_(true),
   sugarBuilder_(0)
 {}
 
@@ -892,5 +895,60 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, in
   }
   crdout.SetCRD(0, frameOut);
 
+  // Structure check
+  if (check_structure_) {
+    StructureCheck check;
+    if (check.SetOptions( true, // image 
+                          true, // check bonds
+                          true,  // save problems
+                          debug_, // debug
+                          "*", // mask 1
+                          "", // mask 2
+                          0.8, // nonbond cut
+                          1.15, // bond long offset
+                          0.5, // bond short offset
+                          -1, // pairlist cut (-1 for heuristic)
+                          true, // ring check
+                          0, // 0 = default ring check short distance cut
+                          0, // 0 = default ring check long distance cut
+                          0  // 0 = default ring check angle cut
+        ))
+    {
+      mprinterr("Error: Structure check options failed.\n");
+      return CpptrajState::ERR;
+    }
+    // For larger structures, automatically add a box
+    bool box_added = false;
+    if (!frameOut.BoxCrd().HasBox() && topOut.Natom() > check_box_natom_) {
+      mprintf("\tAdding unit cell for check only.\n");
+      box_added = true;
+      // Get radii
+      std::vector<double> Radii;
+      Radii.reserve( topIn.Natom() );
+      for (int atnum = 0; atnum != topIn.Natom(); ++atnum) {
+        Radii.push_back( topOut.GetVDWradius(atnum) );
+        //Radii.push_back( topIn[atnum].ParseRadius() );
+        //Radii.push_back( 0.5 );
+      }
+
+      frameOut.SetOrthoBoundingBox(Radii, 1.0);
+      frameOut.BoxCrd().PrintInfo();
+    }
+    if (check.Setup( topOut, frameOut.BoxCrd() )) {
+      mprinterr("Error: Structure check setup failed.\n");
+      return CpptrajState::ERR;
+    }
+    check.Mask1().MaskInfo();
+    if (check.ImageOpt().ImagingEnabled())
+      mprintf("\tImaging on.\n");
+    else
+      mprintf("\timaging off.\n");
+    int Ntotal_problems = check.CheckOverlaps( frameOut );
+    mprintf("\t%i total problems detected.\n", Ntotal_problems);
+    // If box was added for check only, remove it
+    if (box_added)
+      frameOut.ModifyBox().SetNoBox();
+  }
+
   return ret;
 }
diff --git a/src/Exec_Build.h b/src/Exec_Build.h
index 2e12fe2d43..fa2a2c6a37 100644
--- a/src/Exec_Build.h
+++ b/src/Exec_Build.h
@@ -35,6 +35,8 @@ class Exec_Build : public Exec {
     static std::vector<int> MapAtomsToTemplate(Topology const&, int, DataSet_Coords*, Cpptraj::Structure::Creator const&, std::vector<NameType>&);
 
     int debug_;
+    int check_box_natom_;  ///< Systems larger than this will have box added so PL check can be used
+    bool check_structure_; ///< If true check the resulting structure
     Cpptraj::Structure::SugarBuilder* sugarBuilder_;
 };
 #endif
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index fa570e4042..d39a26109e 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -300,7 +300,7 @@ Ewald_Regular.o : Ewald_Regular.cpp Atom.h AtomMask.h Box.h Constants.h Coordina
 ExclusionArray.o : ExclusionArray.cpp Atom.h AtomMask.h CharMask.h CpptrajStdio.h ExclusionArray.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Unit.h
 Exec_AddMissingRes.o : Exec_AddMissingRes.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h CharMask.h CompactFrameArray.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_AddMissingRes.h Exec_AddMissingRes_Pres.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h ParmFile.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h Trajout_Single.h Unit.h Vec3.h
 Exec_Analyze.o : Exec_Analyze.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Analyze.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_Build.o : Exec_Build.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/AssignParams.h Parm/GB_Params.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/Creator.h Structure/Disulfide.h Structure/HisProt.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/StructureEnum.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Build.o : Exec_Build.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h ExclusionArray.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/AssignParams.h Parm/GB_Params.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/Creator.h Structure/Disulfide.h Structure/HisProt.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/RingFinder.h Structure/StructureEnum.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Calc.o : Exec_Calc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Calc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_CatCrd.o : Exec_CatCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CatCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_Change.o : Exec_Change.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Change.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h

From 12a9d7c344a5680ac4708ee47a387458858b4dc6 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 24 Jul 2024 13:25:36 -0400
Subject: [PATCH 0896/1492] Check bonds and rings as well

---
 src/Exec_Build.cpp | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index c0b296d1ea..5d4dd21bd2 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -944,6 +944,8 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, in
     else
       mprintf("\timaging off.\n");
     int Ntotal_problems = check.CheckOverlaps( frameOut );
+    Ntotal_problems += check.CheckBonds( frameOut );
+    Ntotal_problems += check.CheckRings( frameOut );
     mprintf("\t%i total problems detected.\n", Ntotal_problems);
     // If box was added for check only, remove it
     if (box_added)

From c1a83cbb109fd4573c3f2081a5f7c4a08410344f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 24 Jul 2024 14:31:56 -0400
Subject: [PATCH 0897/1492] Put common problem write functions/definitions in
 StructureCheck

---
 src/Action_CheckStructure.cpp | 25 ++++++++-----------------
 src/Action_CheckStructure.h   |  5 +----
 src/StructureCheck.cpp        | 26 ++++++++++++++++++++++++--
 src/StructureCheck.h          |  9 +++++++++
 4 files changed, 42 insertions(+), 23 deletions(-)

diff --git a/src/Action_CheckStructure.cpp b/src/Action_CheckStructure.cpp
index 5c956960ef..21fa75ece6 100644
--- a/src/Action_CheckStructure.cpp
+++ b/src/Action_CheckStructure.cpp
@@ -182,17 +182,10 @@ Action::RetType Action_CheckStructure::Setup(ActionSetup& setup) {
   return Action::OK;
 }
 
-/// Output format strings for warnings.
-const char* Action_CheckStructure::Fmt_[] = {
-  "%i\t Warning: Atoms %i:%s and %i:%s are close (%.2f)\n",    ///< F_ATOM
-  "%i\t Warning: Unusual bond length %i:%s to %i:%s (%.2f)\n", ///< F_BOND
-  "%i\t Warning: Bond involving atom %i:%s intersects ring involving atom %i:%s (%.2f)\n" ///< F_RING
-};
-
 /** Consolidate problems from different threads if necessary and write out. */
-void Action_CheckStructure::WriteProblems(FmtType ft, int frameNum, Topology const& top) {
+void Action_CheckStructure::WriteProblems(StructureCheck::FmtType ft, int frameNum, Topology const& top) {
+# ifdef MPI
   for (StructureCheck::const_iterator p = check_.begin(); p != check_.end(); ++p) {
-#   ifdef MPI
     int atom1 = p->A1() + 1;
     int atom2 = p->A2() + 1;
     ds_fn_->Add(idx_, &frameNum);
@@ -203,12 +196,10 @@ void Action_CheckStructure::WriteProblems(FmtType ft, int frameNum, Topology con
     ds_n2_->Add(idx_, top.TruncResAtomName(p->A2()).c_str());
     ds_d_->Add(idx_,  p->Dptr());
     idx_++;
-#   else
-    outfile_->Printf(Fmt_[ft], frameNum,
-                    p->A1()+1, top.TruncResAtomName(p->A1()).c_str(),
-                    p->A2()+1, top.TruncResAtomName(p->A2()).c_str(), p->D());
-#   endif
   }
+# else
+  check_.WriteProblemsToFile(outfile_, frameNum, top);
+# endif
 }
 
 // Action_CheckStructure::DoAction()
@@ -224,7 +215,7 @@ Action::RetType Action_CheckStructure::DoAction(int frameNum, ActionFrame& frm)
 # ifdef TIMER
   t_overlap_.Stop();
 # endif
-  if (outfile_ != 0) WriteProblems(F_ATOM, fnum, *CurrentParm_);
+  if (outfile_ != 0) WriteProblems(StructureCheck::F_ATOM, fnum, *CurrentParm_);
   if (check_.CheckBonds()) {
 #   ifdef TIMER
     t_bonds_.Start();
@@ -233,7 +224,7 @@ Action::RetType Action_CheckStructure::DoAction(int frameNum, ActionFrame& frm)
 #   ifdef TIMER
     t_bonds_.Stop();
 #   endif
-    if (outfile_ != 0) WriteProblems(F_BOND, fnum, *CurrentParm_);
+    if (outfile_ != 0) WriteProblems(StructureCheck::F_BOND, fnum, *CurrentParm_);
 #   ifdef TIMER
     t_rings_.Start();
 #   endif
@@ -241,7 +232,7 @@ Action::RetType Action_CheckStructure::DoAction(int frameNum, ActionFrame& frm)
 #   ifdef TIMER
     t_rings_.Stop();
 #   endif
-    if (outfile_ != 0) WriteProblems(F_RING, fnum, *CurrentParm_);
+    if (outfile_ != 0) WriteProblems(StructureCheck::F_RING, fnum, *CurrentParm_);
   }
   num_problems_->Add( frameNum, &total_problems );
 # ifdef TIMER
diff --git a/src/Action_CheckStructure.h b/src/Action_CheckStructure.h
index 049f68d22a..94d85e532b 100644
--- a/src/Action_CheckStructure.h
+++ b/src/Action_CheckStructure.h
@@ -19,9 +19,7 @@ class Action_CheckStructure : public Action {
     int SyncAction();
 #   endif
 
-    enum FmtType { F_ATOM =0, F_BOND, F_RING };
-
-    void WriteProblems(FmtType, int, Topology const&);
+    void WriteProblems(StructureCheck::FmtType, int, Topology const&);
 
     StructureCheck check_;  ///< Structure checker
     CpptrajFile* outfile_;  ///< Report file.
@@ -29,7 +27,6 @@ class Action_CheckStructure : public Action {
     DataSet* num_problems_; ///< Save number of problems each frame
     bool silent_;           ///< If true suppress output
     bool skipBadFrames_;    ///< If true skip frames with problems
-    static const char* Fmt_[]; ///< Output format strings
 #   ifdef MPI
     Parallel::Comm trajComm_;
     DataSet* ds_fn_; ///< Frame number
diff --git a/src/StructureCheck.cpp b/src/StructureCheck.cpp
index c5f8fe4a63..2760fc50ab 100644
--- a/src/StructureCheck.cpp
+++ b/src/StructureCheck.cpp
@@ -1,11 +1,12 @@
 #include <cmath> // sqrt
 #include <algorithm> // sort
 #include "StructureCheck.h"
-#include "Topology.h"
+#include "CpptrajFile.h"
 #include "CpptrajStdio.h"
 #include "CharMask.h"
 #include "DistRoutines.h"
 #include "Structure/LeastSquaresPlane.h"
+#include "Topology.h"
 #ifdef _OPENMP
 #  include <omp.h>
 #endif
@@ -27,7 +28,8 @@ StructureCheck::StructureCheck() :
   debug_(0),
   bondcheck_(true),
   ringcheck_(true),
-  saveProblems_(false)
+  saveProblems_(false),
+  lastFmt_(F_ATOM)
 {}
 
 /** \return Ring-bond short distance cutoff in Ang. */
@@ -271,6 +273,7 @@ int StructureCheck::CheckBonds(Frame const& currentFrame)
   } // END pragma omp parallel
 # endif
   ConsolidateProblems();
+  lastFmt_ = F_BOND;
 
   return Nproblems;
 }
@@ -655,6 +658,7 @@ int StructureCheck::CheckRings(Frame const& currentFrame, Cpptraj::Structure::Ri
   }
 
   ConsolidateProblems();
+  lastFmt_ = F_RING;
 
   return Nproblems;
 }
@@ -923,6 +927,24 @@ int StructureCheck::CheckOverlaps(Frame const& currentFrame) {
     Nproblems = Mask1_CheckOverlap(currentFrame);
   }
   //mprintf("Exiting CheckOverlaps() with %i\n\n", Nproblems);
+  lastFmt_ = F_ATOM;
 
   return Nproblems;
 }
+
+/** Write formats for problems. */
+const char* StructureCheck::Fmt_[] = {
+  "%i\t Warning: Atoms %i:%s and %i:%s are close (%.2f)\n",    ///< F_ATOM
+  "%i\t Warning: Unusual bond length %i:%s to %i:%s (%.2f)\n", ///< F_BOND
+  "%i\t Warning: Bond involving atom %i:%s intersects ring involving atom %i:%s (%.2f)\n" ///< F_RING
+};
+
+/** Write current problems to the given file. */
+void StructureCheck::WriteProblemsToFile(CpptrajFile* outfile, int frameNum, Topology const& top) const {
+  if (outfile == 0) return;
+  for (const_iterator p = begin(); p != end(); ++p) {
+    outfile->Printf(Fmt_[lastFmt_], frameNum,
+                    p->A1()+1, top.TruncResAtomName(p->A1()).c_str(),
+                    p->A2()+1, top.TruncResAtomName(p->A2()).c_str(), p->D());
+  }
+}
diff --git a/src/StructureCheck.h b/src/StructureCheck.h
index 81b80890e2..acc49438e8 100644
--- a/src/StructureCheck.h
+++ b/src/StructureCheck.h
@@ -9,6 +9,7 @@
 // Forward declares
 class Topology;
 class CharMask;
+class CpptrajFile;
 namespace Cpptraj {
 namespace Structure {
 class LeastSquaresPlane;
@@ -44,6 +45,11 @@ class StructureCheck {
     int CheckRings(Frame const&);
     /// Check if any of the given bonds are passing through given rings.
     int CheckRings(Frame const&, Cpptraj::Structure::RingFinder const&, std::vector<Btype> const&);
+    /// Write existing problems to the given file
+    void WriteProblemsToFile(CpptrajFile*, int, Topology const&) const;
+
+    /// Format of problems currently stored in problemAtoms_
+    enum FmtType { F_ATOM =0, F_BOND, F_RING };
 
     AtomMask const& Mask1()     const { return Mask1_; }
     AtomMask const& Mask2()     const { return Mask2_; }
@@ -102,6 +108,8 @@ class StructureCheck {
     /// Iterator to end of list of problems from latest call to CheckX
     const_iterator end()   const { return problemAtoms_.end();   }
   private:
+    /// Format strings corresponding to FmtType
+    static const char* Fmt_[];
     /// Type of overlap check
     enum CheckType { NO_PL_1_MASK=0, NO_PL_2_MASKS, PL_1_MASK };
     /// Add selected bonds in BondArray to list to be checked.
@@ -164,5 +172,6 @@ class StructureCheck {
     bool bondcheck_;        ///< If true check bonds as well
     bool ringcheck_;        ///< If true check bond/ring intersections
     bool saveProblems_;     ///< If true save problems in problemAtoms_
+    FmtType lastFmt_;       ///< Format of problems currently stored in problemAtoms_
 };
 #endif

From 4883244692822200f9c5df5004b10e4fd36a8515 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 24 Jul 2024 14:37:13 -0400
Subject: [PATCH 0898/1492] Report problems to stdout

---
 src/Exec_Build.cpp | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 5d4dd21bd2..3e2b4d31e7 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -943,9 +943,15 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, in
       mprintf("\tImaging on.\n");
     else
       mprintf("\timaging off.\n");
+    // TODO make file a user option
+    CpptrajFile check_output;
+    check_output.OpenWrite("");
     int Ntotal_problems = check.CheckOverlaps( frameOut );
+    check.WriteProblemsToFile( &check_output, 1, topOut );
     Ntotal_problems += check.CheckBonds( frameOut );
+    check.WriteProblemsToFile( &check_output, 1, topOut );
     Ntotal_problems += check.CheckRings( frameOut );
+    check.WriteProblemsToFile( &check_output, 1, topOut );
     mprintf("\t%i total problems detected.\n", Ntotal_problems);
     // If box was added for check only, remove it
     if (box_added)

From 157fd33c91ed24ad4020a435c76c745f31e14dad Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 24 Jul 2024 14:43:01 -0400
Subject: [PATCH 0899/1492] Allow debug info

---
 src/Structure/Builder.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 7a3264cc1e..4d4af7a576 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1874,7 +1874,7 @@ const
   if (getIcFromInternals(ic, at, hasPosition)) {
     //printAllInternalsForAtom(at, topIn, hasPosition); // DEBUG
     Vec3 posI = Zmatrix::AtomIposition(ic, frameOut);
-    if (debug_ > 1) {
+    //if (debug_ > 1) {
       mprintf("Building atom %s using torsion/angle/bond\n", topIn.LeapName(at).c_str());
       mprintf("Using %s - %s - %s - %s\n",
               topIn.LeapName(ic.AtI()).c_str(),
@@ -1885,7 +1885,7 @@ const
       mprintf( "Angle   = %f\n", ic.Theta() );
       mprintf( "Bond    = %f\n", ic.Dist() );
       mprintf( "ZMatrixAll:  %f,%f,%f\n", posI[0], posI[1], posI[2]);
-    }
+    //}
     frameOut.SetXYZ( ic.AtI(), posI );
     return 1;
   }

From f259d7e5c6d6c44fe3fa5907117659f92eb6331b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 25 Jul 2024 06:54:09 -0400
Subject: [PATCH 0900/1492] Enable more debug

---
 src/Structure/Builder.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 4d4af7a576..a573ddf475 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -2075,7 +2075,7 @@ const
       }
       // Build unknown positions around known atom
       if (atToBuildAround != -1) {
-        if (debug_ > 0)
+        //if (debug_ > 0)
           mprintf("Building externals from %s\n", topIn.LeapName(atToBuildAround).c_str());
         Atom const& bAtom = topIn[atToBuildAround];
         for (Atom::bond_iterator bat = bAtom.bondbegin(); bat != bAtom.bondend(); ++bat)

From 33c62758bca5569dd84696b5b03566f5748ffceb Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 25 Jul 2024 11:57:47 -0400
Subject: [PATCH 0901/1492] Try to handle case where known positions are
 sparse.

---
 src/Structure/Builder.cpp | 187 +++++++++++++++++++++++++++++++++++++-
 src/Structure/Builder.h   |   7 ++
 2 files changed, 193 insertions(+), 1 deletion(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index a573ddf475..add1f99a13 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1863,6 +1863,72 @@ const
   return 0;
 }
 
+// -----------------------------------------------
+class Builder::AtomIC {
+  public:
+    AtomIC(int at, int idx) : at_(at), idx_(idx), priority_(9999) {}
+
+    void SetIC(InternalCoords const& ic) { ic_ = ic; priority_ = 0; }
+    void SetAngles(InternalAngle const& a1, InternalAngle const& a2, InternalBond const& b1) { a1_ = a1; a2_ = a2; b1_ = b1; priority_ = 1; }
+    void SetAngle(InternalAngle const& a1, InternalBond const& b1) { a1_ = a1; b1_ = b1; priority_ = 2; }
+    void SetBond(InternalBond const& b1) { b1_ = b1; priority_ = 3; }
+
+    int Idx() const { return idx_; }
+    int At() const { return at_; }
+    int Priority() const { return priority_; }
+    InternalCoords const& IC() const { return ic_; }
+    InternalAngle const& A1() const { return a1_; }
+    InternalAngle const& A2() const { return a2_; }
+    InternalBond const& B1() const { return b1_; }
+
+    bool operator<(AtomIC const& rhs) const {
+      if (priority_ == rhs.priority_) {
+        return (idx_ < rhs.idx_);
+      } else {
+        return (priority_ < rhs.priority_);
+      }
+    }
+  private:
+    int at_; ///< Index in topology
+    int idx_; ///< LEAP index, for sorting
+    int priority_; ///< Build priority, 0 is max
+    InternalCoords ic_;
+    InternalAngle a1_;
+    InternalAngle a2_;
+    InternalBond b1_;
+};
+// -----------------------------------------------
+
+/** Get all internal coordinates for an atom. */
+Builder::AtomIC Builder::getInternalCoordsForAtom(int at, int idx, Barray const& hasPosition, Topology const& topIn) const
+{
+  AtomIC atomIC(at, idx);
+  InternalCoords ic;
+  if (getIcFromInternals(ic, at, hasPosition)) {
+    mprintf("Atom %s has torsion/angle/bond internals.\n", topIn.LeapName(at).c_str());
+    atomIC.SetIC( ic );
+    return atomIC;
+  }
+  InternalAngle a1, a2;
+  InternalBond b1;
+  if (getTwoAnglesFromInternals(a1, a2, b1, at, hasPosition)) {
+    mprintf("Atom %s has two angle internals.\n", topIn.LeapName(at).c_str());
+    atomIC.SetAngles(a1, a2, b1);
+    return atomIC;
+  }
+  if (getAngleFromInternals(a1, b1, at, hasPosition)) {
+    mprintf("Atom %s has angle internal.\n", topIn.LeapName(at).c_str());
+    atomIC.SetAngle(a1, b1);
+    return atomIC;
+  }
+  if (getBondFromInternals(b1, at, hasPosition)) {
+    mprintf("Atom %s has bond internal.\n", topIn.LeapName(at).c_str());
+    atomIC.SetBond(b1);
+    return atomIC;
+  }
+  return atomIC;
+}
+
 /** Build coordinates for an atom from internals.
   * \return 1 if atom was built, 0 otherwise.
   */
@@ -2008,6 +2074,111 @@ const
   return residues;
 } 
 
+/** Build in cases where known positions are sparse. Try to build atoms
+  * that have the most "known" internal coords first, then update
+  * internal coords status.
+  */
+int Builder::sparseBuildFromInternals(std::vector<AtomIC>& needsBuilding, Frame& frameOut, Topology const& topIn, Barray& hasPosition)
+const
+{
+  mprintf("DEBUG: No complete internal coordinates. Trying a sparse build.\n");
+  unsigned int nAtomsThatNeedPositions = needsBuilding.size();
+
+  unsigned int currentBuildIdx = 0;
+  while (nAtomsThatNeedPositions > 0) {
+    bool built_an_atom = false;
+    // Build the atom with the highest priority
+    AtomIC const& currentBuildAtom = needsBuilding[currentBuildIdx];
+    int at = currentBuildAtom.At();
+    mprintf("DEBUG: Current build atom is %i %s\n", at+1, topIn.AtomMaskName(at).c_str());
+
+    if (currentBuildAtom.Priority() == 0) {
+      //printAllInternalsForAtom(at, topIn, hasPosition); // DEBUG
+      Vec3 posI = Zmatrix::AtomIposition(currentBuildAtom.IC(), frameOut);
+      //if (debug_ > 1) {
+        mprintf("Building atom %s using torsion/angle/bond\n", topIn.LeapName(at).c_str());
+        mprintf("Using %s - %s - %s - %s\n",
+                topIn.LeapName(currentBuildAtom.IC().AtI()).c_str(),
+                topIn.LeapName(currentBuildAtom.IC().AtJ()).c_str(),
+                topIn.LeapName(currentBuildAtom.IC().AtK()).c_str(),
+                topIn.LeapName(currentBuildAtom.IC().AtL()).c_str());
+        mprintf( "Torsion = %f\n", currentBuildAtom.IC().Phi() );
+        mprintf( "Angle   = %f\n", currentBuildAtom.IC().Theta() );
+        mprintf( "Bond    = %f\n", currentBuildAtom.IC().Dist() );
+        mprintf( "ZMatrixAll:  %f,%f,%f\n", posI[0], posI[1], posI[2]);
+      //}
+      frameOut.SetXYZ( currentBuildAtom.IC().AtI(), posI ); // TODO use at?
+      hasPosition[at] = true;
+      built_an_atom = true;
+    } else if (currentBuildAtom.Priority() == 1) {
+      // FIXME need to implement
+      //if (debug_ > 1) {
+        mprintf("Building atom %s using two angles\n", topIn.LeapName(at).c_str());
+        mprintf("Using %s - %s - %s and %s - %s - %s\n",
+                topIn.LeapName(currentBuildAtom.A1().AtI()).c_str(),
+                topIn.LeapName(currentBuildAtom.A1().AtJ()).c_str(),
+                topIn.LeapName(currentBuildAtom.A1().AtK()).c_str(),
+                topIn.LeapName(currentBuildAtom.A2().AtI()).c_str(),
+                topIn.LeapName(currentBuildAtom.A2().AtJ()).c_str(),
+                topIn.LeapName(currentBuildAtom.A2().AtK()).c_str());
+        mprintf("AngleA  = %f\n", currentBuildAtom.A1().ThetaVal()*Constants::RADDEG );
+        mprintf("AngleB  = %f\n", currentBuildAtom.A2().ThetaVal()*Constants::RADDEG );
+        mprintf("Bond    = %f\n", currentBuildAtom.B1().DistVal() );
+      //}
+      //frameOut.SetXYZ( ic.AtI(), posI );
+      // FIXME actually build
+    } else if (currentBuildAtom.Priority() == 2) {
+      Vec3 posI = Zmatrix::AtomIposition(frameOut.XYZ(currentBuildAtom.A1().AtJ()),
+                                         frameOut.XYZ(currentBuildAtom.A1().AtK()),
+                                         currentBuildAtom.B1().DistVal(), currentBuildAtom.A1().ThetaVal() );
+      //if debug_ > 1) {
+        mprintf("Building atom %s using angle/bond\n", topIn.LeapName(at).c_str());
+        mprintf("Using %s - %s - %s\n",
+                topIn.LeapName(currentBuildAtom.A1().AtI()).c_str(),
+                topIn.LeapName(currentBuildAtom.A1().AtJ()).c_str(),
+                topIn.LeapName(currentBuildAtom.A1().AtK()).c_str());
+        mprintf( "Angle   = %f\n", currentBuildAtom.A1().ThetaVal()*Constants::RADDEG );
+        mprintf( "Bond    = %f\n", currentBuildAtom.B1().DistVal() );
+        mprintf("ZMatrixBondAngle:  %f,%f,%f\n", posI[0], posI[1], posI[2]);
+        //}
+      frameOut.SetXYZ( currentBuildAtom.A1().AtI(), posI );
+      hasPosition[at] = true;
+      built_an_atom = true;
+    } else if (currentBuildAtom.Priority() == 3) {
+      Vec3 posI = Zmatrix::AtomIposition(frameOut.XYZ(currentBuildAtom.B1().AtJ()), currentBuildAtom.B1().DistVal());
+      //if debug_ > 1) {
+        mprintf("Building atom %s using bond\n", topIn.LeapName(at).c_str());
+        mprintf("Using %s - %s\n",
+                topIn.LeapName(currentBuildAtom.B1().AtI()).c_str(), topIn.LeapName(currentBuildAtom.B1().AtJ()).c_str());
+        mprintf( "Bond    = %f\n", currentBuildAtom.B1().DistVal() );
+        mprintf( "ZMatrixBond:  %f,%f,%f\n", posI[0], posI[1], posI[2]);
+        //}
+      frameOut.SetXYZ( currentBuildAtom.B1().AtI(), posI );
+      hasPosition[at] = true;
+      built_an_atom = true;
+    }
+    if (!built_an_atom) {
+      mprinterr("Error: Failed building atom %i %s\n", at+1, topIn.AtomMaskName(at).c_str());
+      return 1;
+    }
+    currentBuildIdx++;
+    nAtomsThatNeedPositions--;
+    if (currentBuildIdx == needsBuilding.size()) break;
+    // Now that we have built an atom, see if we can find new complete ICs for remaining atoms to build
+    for (unsigned int idx2 = currentBuildIdx; idx2 < needsBuilding.size(); idx2++)
+    {
+      //needsBuilding.push_back( getInternalCoordsForAtom(*it, it - atomIndices.begin(), hasPosition, topIn) );
+      needsBuilding[idx2] = getInternalCoordsForAtom( needsBuilding[idx2].At(), needsBuilding[idx2].Idx(), hasPosition, topIn );
+    }
+    // Sort remaining atoms to build.
+    std::sort( needsBuilding.begin() + currentBuildIdx, needsBuilding.end() );
+    mprintf("DEBUG: Atoms that need building:\n");
+    for (std::vector<AtomIC>::const_iterator it = needsBuilding.begin() + currentBuildIdx; it != needsBuilding.end(); ++it)
+      mprintf("\t%i atom %i %s (%i)\n", it->Idx(), it->At()+1, topIn.AtomMaskName( it->At() ).c_str(), it->Priority() );
+  } // END loop over build atoms
+  return 0; 
+}
+
 /** Build coordinates for any atom with an internal that does
   * not have its position set.
   */ 
@@ -2041,15 +2212,29 @@ const
   residues.clear();
 
   // Count how many atoms need their positions set
+  std::vector<AtomIC> needsBuilding;
   unsigned int nAtomsThatNeedPositions = 0;
   for (std::vector<int>::const_iterator it = atomIndices.begin();
                                         it != atomIndices.end(); ++it)
-    if (!hasPosition[*it])
+  {
+    if (!hasPosition[*it]) {
       nAtomsThatNeedPositions++;
+      needsBuilding.push_back( getInternalCoordsForAtom(*it, it - atomIndices.begin(), hasPosition, topIn) );
+    }
+  }
+  std::sort( needsBuilding.begin(), needsBuilding.end() );
+  mprintf("DEBUG: Atoms that need building:\n");
+  for (std::vector<AtomIC>::const_iterator it = needsBuilding.begin(); it != needsBuilding.end(); ++it)
+    mprintf("\t%i atom %i %s (%i)\n", it->Idx(), it->At()+1, topIn.AtomMaskName( it->At() ).c_str(), it->Priority() );
+      
   if (debug_ > 0)
     mprintf("DEBUG: %u atoms need positions.\n", nAtomsThatNeedPositions);
   if (nAtomsThatNeedPositions == 0) return 0;
 
+  // FIXME TEST - If no "complete" internal coords currently, try a "sparse" build.
+  if (needsBuilding.front().Priority() > 0)
+    return sparseBuildFromInternals(needsBuilding, frameOut, topIn, hasPosition);
+
   // Loop over residue atoms
   while (nAtomsThatNeedPositions > 0) {
     unsigned int nAtomsBuilt = 0;
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index 34892465e0..48bfbda3d2 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -61,6 +61,8 @@ class Builder {
     /// Hold chirality
     class InternalChirality;
 
+    class AtomIC;
+
     typedef std::vector<InternalTorsion> Tarray;
     typedef std::vector<InternalAngle> Aarray;
     typedef std::vector<InternalBond> Larray;
@@ -118,8 +120,12 @@ class Builder {
     void printAllInternalsForAtom(int, Topology const&, Barray const&) const;
     /// \\return index of atom with longest 'depth' bonded to a given atom (ignoring one bonded atom).
     static int get_depths_around_atom(int, int, Topology const&);
+    /// Get any complete internal coords for specified atom
+    AtomIC getInternalCoordsForAtom(int, int, Barray const&, Topology const&) const;
     /// Build XYZ coords for an atom if internals are available
     int buildCoordsForAtom(int, Frame&, Topology const&, Barray const&) const;
+    /// Build atoms based on build priority; for cases where known atoms are sparse
+    int sparseBuildFromInternals(std::vector<AtomIC>&, Frame&, Topology const&, Barray&) const;
     /// \return array containing all residues with atoms that need positions
     std::vector<Residue> residuesThatNeedPositions(Topology const&, Barray const&) const;
 
@@ -247,6 +253,7 @@ class Cpptraj::Structure::Builder::InternalChirality {
     int ai_;
     double dChi_;
 };
+// -----------------------------------------------
 }
 }
 #endif

From 3a801d6a05da4af50a8ca73c77a53e52e95d8ac3 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 30 Aug 2024 08:31:22 -0400
Subject: [PATCH 0902/1492] Update call to LeastSquaresPlane

---
 src/StructureCheck.cpp | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/StructureCheck.cpp b/src/StructureCheck.cpp
index 2760fc50ab..2b09d89773 100644
--- a/src/StructureCheck.cpp
+++ b/src/StructureCheck.cpp
@@ -643,7 +643,8 @@ int StructureCheck::CheckRings(Frame const& currentFrame, Cpptraj::Structure::Ri
 # endif
   for (idx = 0; idx < ring_max; idx++)
   {
-    RingVecs[idx].CalcLeastSquaresPlane( currentFrame, rings[idx] );
+    // false = use geometric center
+    RingVecs[idx].CalcLeastSquaresPlane( currentFrame, rings[idx], false );
   }
 # ifdef _OPENMP
   } // END pragma omp parallel

From 7e3e22e2a7532a69e54409854a5d23632036a19b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 4 Sep 2024 10:41:29 -0400
Subject: [PATCH 0903/1492] Fix call to InitOptions

---
 src/Exec_Build.cpp | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 3e2b4d31e7..75d261fb36 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -819,6 +819,8 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, in
     sugarBuilder_ = new Cpptraj::Structure::SugarBuilder(debug_);
     // Init options
     if (sugarBuilder_->InitOptions( argIn.hasKey("hasglycam"),
+                                    argIn.getKeyDouble("rescut", 8.0),
+                                    argIn.getKeyDouble("bondoffset", 0.2),
                                     argIn.GetStringKey("sugarmask"),
                                     argIn.GetStringKey("determinesugarsby", "geometry"),
                                     argIn.GetStringKey("resmapfile") ))

From 409bb22295749394bfd4a707e111bc4108c0f85b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 4 Sep 2024 11:29:49 -0400
Subject: [PATCH 0904/1492] Ring center is now geometric, not center of mass

---
 test/Test_CheckStructure/entangled.dat.save | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/Test_CheckStructure/entangled.dat.save b/test/Test_CheckStructure/entangled.dat.save
index 1d4fc14cef..6668374ecf 100644
--- a/test/Test_CheckStructure/entangled.dat.save
+++ b/test/Test_CheckStructure/entangled.dat.save
@@ -1,3 +1,3 @@
 1	 Warning: Unusual bond length 25:C_1@C3' to 27:C_1@C2' (2.99)
 1	 Warning: Bond involving atom 25:C_1@C3' intersects ring involving atom 44:C_2@N1 (0.41)
-1	 Warning: Bond involving atom 49:C_2@C4 intersects ring involving atom 8:C_1@C4' (0.58)
+1	 Warning: Bond involving atom 49:C_2@C4 intersects ring involving atom 8:C_1@C4' (0.48)

From c593bacbc5b9323b4d7c04e5f731f9c259996473 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 4 Sep 2024 11:46:41 -0400
Subject: [PATCH 0905/1492] Add missing defines to --defines

---
 src/Cpptraj.cpp | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/src/Cpptraj.cpp b/src/Cpptraj.cpp
index c59b25f478..03b4c3c1f9 100644
--- a/src/Cpptraj.cpp
+++ b/src/Cpptraj.cpp
@@ -270,6 +270,21 @@ std::string Cpptraj::Defines() {
 #endif
 #ifdef HAS_OPENMM
   defined_str.append(" -DHAS_OPENMM");
+#endif
+#ifdef CPPTRAJ_USE_LEAP_PI
+  defined_str.append(" -DCPPTRAJ_USE_LEAP_PI");
+#endif
+#ifdef NO_READLINE
+  defined_str.append(" -DNO_READLINE");
+#endif
+#ifdef __HIP_PLATFORM_HCC__
+  defined_str.append(" -D__HIP_PLATFORM_HCC__");
+#endif
+#ifdef HAVE_FFTWD
+  defined_str.append(" -DHAVE_FFTWD");
+#endif
+#ifdef ENABLE_DTR
+  defined_str.append(" -DENABLE_DTR");
 #endif
   return defined_str;
 }

From 3fdf930fcfaa09095d4d0f4eef7b68dc16e48abf Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 4 Sep 2024 14:55:20 -0400
Subject: [PATCH 0906/1492] Consolidate bond/angle parameters when appending in
 replicatecell; not sure if this should be generally true or not.

---
 src/Action_ReplicateCell.cpp |  2 ++
 src/Parm/Merge.cpp           | 16 +++++++++++++++-
 src/Parm/Merge.h             |  6 ++++++
 3 files changed, 23 insertions(+), 1 deletion(-)

diff --git a/src/Action_ReplicateCell.cpp b/src/Action_ReplicateCell.cpp
index a89c9cac0c..48ff98c472 100644
--- a/src/Action_ReplicateCell.cpp
+++ b/src/Action_ReplicateCell.cpp
@@ -163,6 +163,8 @@ Action::RetType Action_ReplicateCell::Setup(ActionSetup& setup) {
     Cpptraj::Parm::Merge merger;
     merger.SetDebug( debug_ );
     merger.SetVerbose( verbose_ );
+    merger.SetReduceBondParams( true );
+    merger.SetReduceAngleParams( true );
     for (int cell = 0; cell != ncopies_; cell++)
       merger.AppendTop( combinedTop_, *stripParm );
     combinedTop_.Brief("Combined parm:");
diff --git a/src/Parm/Merge.cpp b/src/Parm/Merge.cpp
index ffbbf3ce53..c9b2de2bca 100644
--- a/src/Parm/Merge.cpp
+++ b/src/Parm/Merge.cpp
@@ -16,7 +16,9 @@ using namespace Cpptraj::Parm;
 /** CONSTRUCTOR */
 Merge::Merge() :
   debug_(0),
-  verbose_(1) // FIXME
+  verbose_(1), // FIXME
+  reduce_bond_params_(false),
+  reduce_angle_params_(false)
 {}
 
 /** Set debug */
@@ -29,6 +31,16 @@ void Merge::SetVerbose(int verboseIn) {
   verbose_ = verboseIn;
 }
 
+/** Indicate bond parameters should be consolidated. */
+void Merge::SetReduceBondParams(bool bIn) {
+  reduce_bond_params_ = bIn;
+}
+
+/** Indicate angle parameters should be consolidated. */
+void Merge::SetReduceAngleParams(bool bIn) {
+  reduce_angle_params_ = bIn;
+}
+
 // ----- Bonds -------------------------
 static inline void printIdx(BondType const& bnd1, unsigned int atomOffset) {
   mprintf("DEBUG: Bond from top1 %i - %i will be %i - %i in top0\n",
@@ -455,6 +467,7 @@ void Merge::MergeBondArrays(BondArray& bonds0,
 const
 {
   MergeTopArray<BondType, BondParmType, BondArray, BondParmArray> mergeBonds;
+  mergeBonds.SetMergeWithExisting( reduce_bond_params_ );
   mergeBonds.MergeTermArrays( bonds0, bondsh0, bp0, atoms0,
                               bonds1, bondsh1, bp1, atoms1 );
 }
@@ -476,6 +489,7 @@ void Merge::MergeAngleArrays(AngleArray& angles0,
 const
 {
   MergeTopArray<AngleType, AngleParmType, AngleArray, AngleParmArray> mergeAngles;
+  mergeAngles.SetMergeWithExisting( reduce_angle_params_ );
   mergeAngles.MergeTermArrays( angles0, anglesh0, ap0, atoms0,
                                angles1, anglesh1, ap1, atoms1 );
 }
diff --git a/src/Parm/Merge.h b/src/Parm/Merge.h
index 6efed94cb9..f88da66b08 100644
--- a/src/Parm/Merge.h
+++ b/src/Parm/Merge.h
@@ -23,6 +23,10 @@ class Merge {
     void SetDebug(int);
     /// Set parameter verbosity
     void SetVerbose(int);
+    /// Indicate bond parameters should be consolidated.
+    void SetReduceBondParams(bool);
+    /// Indicate angle parameters should be consolidated.
+    void SetReduceAngleParams(bool);
     /// Append topology to this one.
     int AppendTop( Topology&, Topology const& ) const;
   private:
@@ -51,6 +55,8 @@ class Merge {
 
     int debug_;
     int verbose_;
+    bool reduce_bond_params_; ///< If true, consolidate bond parameters TODO always?
+    bool reduce_angle_params_; ///< If true, consolidate angle parameters TODO always?
 };
 }
 }

From 68a7e16e7c0d60624823a882e3e1bcb3b6e0bd60 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 9 Sep 2024 15:17:21 -0400
Subject: [PATCH 0907/1492] Hide debug info

---
 src/Parm/GetParams.cpp | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/src/Parm/GetParams.cpp b/src/Parm/GetParams.cpp
index 325088e09a..ef0fb249f6 100644
--- a/src/Parm/GetParams.cpp
+++ b/src/Parm/GetParams.cpp
@@ -433,9 +433,11 @@ unsigned int GetParams::NuniqueAtomTypes(Topology const& topIn) const {
       }
     }
   }
-  mprintf("DEBUG: Unique atom types in %s\n", topIn.c_str());
-  for (ParmHolder<int>::const_iterator it = currentAtomTypes.begin();
-                                       it != currentAtomTypes.end(); ++it)
-    mprintf("\t\t%s %i\n", *(it->first[0]), it->second);
+  if (debug_ > 0) {
+    mprintf("DEBUG: Unique atom types in %s\n", topIn.c_str());
+    for (ParmHolder<int>::const_iterator it = currentAtomTypes.begin();
+                                         it != currentAtomTypes.end(); ++it)
+      mprintf("\t\t%s %i\n", *(it->first[0]), it->second);
+  }
   return currentAtomTypes.size();
 }

From d4a130b0f20101d54e88e7d0dea145a98aa9243c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 9 Sep 2024 15:38:29 -0400
Subject: [PATCH 0908/1492] Hide debug info

---
 src/StructureCheck.cpp | 43 ++++++++++++++++++++----------------------
 1 file changed, 20 insertions(+), 23 deletions(-)

diff --git a/src/StructureCheck.cpp b/src/StructureCheck.cpp
index 2b09d89773..0130103729 100644
--- a/src/StructureCheck.cpp
+++ b/src/StructureCheck.cpp
@@ -19,11 +19,7 @@ StructureCheck::StructureCheck() :
   plcut_(8.0),
   ring_shortd2_(0.25), // Short ring-bond 0.5 Ang. distance cutoff
   ring_dcut2_(1.562500), // 1.25 Ang. ring-bond distance cutoff
-  //ring_dcut2_(1.3225), // Initial 1.15 Ang. ring-bond distance cutoff
   ring_acut_(1.1344640138), // 65 deg. ringvec-bondvec angle cutoff
-  //ring_acut_(1.0471975512), // 60 deg. ringvec-bondvec angle cutoff
-  //ring_acut_(0.174533), // 10 deg. angle cutoff
-  //ring_acut_(0.7853981634), // 45 deg. angle cutoff for ring_dcut2 > dist2 > ring_shortd2
   checkType_(NO_PL_1_MASK),
   debug_(0),
   bondcheck_(true),
@@ -283,10 +279,11 @@ int StructureCheck::CheckRings(Frame const& currentFrame) {
   return CheckRings(currentFrame, rings_, ringBonds_);
 }
 
-static inline void printRingAtoms(AtomMask const& maskIn) {
-  for (AtomMask::const_iterator it = maskIn.begin(); it != maskIn.end(); ++it)
-    mprintf(" %i", *it);
-}
+/// DEBUG - For printing ring atoms in mask
+//static inline void printRingAtoms(AtomMask const& maskIn) {
+//  for (AtomMask::const_iterator it = maskIn.begin(); it != maskIn.end(); ++it)
+//    mprintf(" %i", *it);
+//}
 
 /** Check ring and bond */
 void StructureCheck::ring_bond_check(int& Nproblems,
@@ -302,33 +299,33 @@ void StructureCheck::ring_bond_check(int& Nproblems,
   // Bond intersects ring if it meets the short cutoff or if the angle
   // between the bond and the ring normal is less than a cutoff.
   if (dist2 < ring_shortd2_) {
-    mprintf("DEBUG: Bond %i - %i near ring (%f).",
-            bnd.A1(), bnd.A2(), sqrt(dist2));
-    printRingAtoms(ringMask);
-    mprintf("\n");
+    //mprintf("DEBUG: Bond %i - %i near ring (%f).",
+    //        bnd.A1(), bnd.A2(), sqrt(dist2));
+    //printRingAtoms(ringMask);
+    //mprintf("\n");
     ring_intersect = true;
   } else {
-    mprintf("DEBUG: Bond %i - %i near ring (%f), doing angle check.",
-            bnd.A1(), bnd.A2(), sqrt(dist2));
-    printRingAtoms(ringMask);
-    mprintf("\n");
+    //mprintf("DEBUG: Bond %i - %i near ring (%f), doing angle check.",
+    //        bnd.A1(), bnd.A2(), sqrt(dist2));
+    //printRingAtoms(ringMask);
+    //mprintf("\n");
     // Get the angle
     double ang_in_rad = vbond.Angle( ringVec.Nxyz() );
     // Wrap the angle between 0-90 degrees
     if (ang_in_rad > Constants::PIOVER2)
       ang_in_rad = Constants::PI - ang_in_rad;
-    mprintf("DEBUG:\t\tWrapped angle is %f deg.\n", Constants::RADDEG*ang_in_rad);
+    //mprintf("DEBUG:\t\tWrapped angle is %f deg.\n", Constants::RADDEG*ang_in_rad);
     if (ang_in_rad < ring_acut_) {
-      mprintf("DEBUG: Bond %i - %i near ring (%f) Ang= %f deg.",
-              bnd.A1(), bnd.A2(), sqrt(dist2),
-              Constants::RADDEG*ang_in_rad);
-      //printRingAtoms(ringMask);
-      mprintf("\n");
+      //mprintf("DEBUG: Bond %i - %i near ring (%f) Ang= %f deg.",
+      //        bnd.A1(), bnd.A2(), sqrt(dist2),
+      //        Constants::RADDEG*ang_in_rad);
+      ////printRingAtoms(ringMask);
+      //mprintf("\n");
       ring_intersect = true;
     }
   }
   if (ring_intersect) {
-    mprintf("DEBUG: Bond intersects ring.\n");
+    //mprintf("DEBUG: Bond intersects ring.\n");
     ++Nproblems;
     if (saveProblems_) {
       // Do not use constructor since we do not want to sort atoms

From 578811f3cad3184c510fc70744c99643be1194c3 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 10 Sep 2024 09:32:20 -0400
Subject: [PATCH 0909/1492] Hide debug info

---
 src/AmberParamFile.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 1e7be4460a..14fd313228 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -698,7 +698,7 @@ int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
           mprinterr("Error: Expected nonbond label, nonbond kind, got %i elements.\n", nscan);
           return 1;
         }
-        mprintf("DEBUG: NB label= %s  NB kind = %s\n", nb_label, nb_kind);
+        if (debug_ > 0) mprintf("DEBUG: NB label= %s  NB kind = %s\n", nb_label, nb_kind);
         if (nb_kind[0] != 'R' || nb_kind[1] != 'E') {
           mprinterr("Error: Nonbond parameters are not of type 'RE' (Rmin, Epsilon).\n");
           return 1;

From 82903bfead107896251fc29508f117c7c4c3ddc5 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 10 Sep 2024 09:32:27 -0400
Subject: [PATCH 0910/1492] Change from debug message to info message

---
 src/Structure/Zmatrix.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index 40295f3c0c..e50ec3227f 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -1027,7 +1027,7 @@ int Zmatrix::SetToFrame(Frame& frameOut, Barray& hasPosition) const {
   Barray isUsed( IC_.size(), false );
   unsigned int Nused = 0;
   if (HasCartSeeds()) {
-    mprintf("DEBUG: Has Cartesian seeds.\n");
+    mprintf("\tUsing Cartesian seeds.\n");
     if (icseed0_ != InternalCoords::NO_ATOM) MARK(icseed0_, isUsed, Nused);
     if (icseed1_ != InternalCoords::NO_ATOM) MARK(icseed1_, isUsed, Nused);
     if (icseed2_ != InternalCoords::NO_ATOM) MARK(icseed2_, isUsed, Nused);

From 3ffe8d78caa26982588daeae58dbbc380fe85d79 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 10 Sep 2024 10:37:27 -0400
Subject: [PATCH 0911/1492] Hide some debug info

---
 src/Parm/GetParams.cpp | 25 ++++++++++++-------------
 1 file changed, 12 insertions(+), 13 deletions(-)

diff --git a/src/Parm/GetParams.cpp b/src/Parm/GetParams.cpp
index ef0fb249f6..15cb369b0c 100644
--- a/src/Parm/GetParams.cpp
+++ b/src/Parm/GetParams.cpp
@@ -142,7 +142,7 @@ int GetParams::GetCmapParams(CmapParmHolder& cmapParm, CmapArray const& cmapTerm
                              std::vector<Atom> const& atoms, std::vector<Residue> const& residues)
 {
   if (cmapGrids.empty() || cmapTerms.empty()) {
-    mprintf("DEBUG: CMAP grids/terms are empty. No parameters to get.\n");
+    //mprintf("DEBUG: CMAP grids/terms are empty. No parameters to get.\n");
     return 0;
   }
   // Check if we need to generate residue/atom information for grids.
@@ -251,12 +251,12 @@ void GetParams::GetLJAtomTypes(ParmHolder<AtomType>& atomTypesOut,
 const
 {
   if (NB0.HasNonbond()) {
-    mprintf("DEBUG: Topology has nonbond parameters.\n");
+    if (debug_ > 0) mprintf("DEBUG: Topology has nonbond parameters.\n");
     bool hasLJ14 = !NB0.LJ14().empty();
-    if (hasLJ14)
+    if (debug_ > 0 && hasLJ14)
       mprintf("DEBUG: Topology has 1-4 nonbond parameters.\n");
     bool hasLJC = !NB0.LJC_Array().empty();
-    if (hasLJC)
+    if (debug_ > 0 && hasLJC)
       mprintf("DEBUG: Topology has LJC nonbond paramters.\n");
     // Nonbonded parameters are present.
     for (std::vector<Atom>::const_iterator atm = atoms.begin(); atm != atoms.end(); ++atm)
@@ -277,15 +277,13 @@ const
           NonbondType const& lj14 = NB0.LJ14( idx );
           thisType.SetLJ14( LJparmType(lj14.Radius(), lj14.Depth()) );
         }
-        // FIXME do LJ C
       } else {
         // Has LJ 10-12 parameters
         thisType = AtomType(atm->Mass(), atm->Polar());
       }
       thisType.SetTypeIdx( atm->TypeIndex() );
       ParameterHolders::RetType ret = atomTypesOut.AddParm( atype, thisType, true );
-      //if (debug_ > 0 && ret == ParameterHolders::ADDED) { // FIXME
-      if (ret == ParameterHolders::ADDED) {
+      if (debug_ > 0 && ret == ParameterHolders::ADDED) {
         mprintf("DEBUG: New atom type: %s R=%g D=%g M=%g P=%g\n", *(atype[0]),
                 thisType.LJ().Radius(), thisType.LJ().Depth(), thisType.Mass(), thisType.Polarizability());
         if (hasLJ14)
@@ -319,8 +317,9 @@ const
           //mprinterr("Error: No off-diagonal LJ for  %s %s (%i %i)\n",
           //          *name1, *name2, idx1, idx2);
           //return;
-          mprintf("DEBUG: LJ 10-12 parameters detected for %s %s (%i %i)\n",
-                  *name1, *name2, idx1, idx2);
+          if (debug_ > 0)
+            mprintf("DEBUG: LJ 10-12 parameters detected for %s %s (%i %i)\n",
+                    *name1, *name2, idx1, idx2);
           LJ1012out.AddParm( types, NB0.HBarray((-idx)-1), false );
         } else {
           // This is LJ 6-12.
@@ -331,7 +330,7 @@ const
           // Compare them
           if (lj0 != lj1) {
             nModifiedOffDiagonal++;
-            //if (debug_ > 0) {
+            if (debug_ > 0) {
               double deltaA = fabs(lj0.A() - lj1.A());
               double deltaB = fabs(lj0.B() - lj1.B());
               mprintf("DEBUG: Potential off-diagonal LJ: %s %s expect A=%g B=%g, actual A=%g B=%g\n",
@@ -340,7 +339,7 @@ const
               double pe_a = (fabs(lj0.A() - lj1.A()) / lj0.A());
               double pe_b = (fabs(lj0.B() - lj1.B()) / lj0.B());
               mprintf("DEBUG:\tPEA= %g  PEB= %g\n", pe_a, pe_b);
-            //}
+            }
           }
           LJ612out.AddParm( types, lj1, false );
           if (hasLJ14) {
@@ -352,7 +351,7 @@ const
             // Compare them
             if (lj0 != lj1) {
               nModified14OffDiagonal++;
-              //if (debug_ > 0) {
+              if (debug_ > 0) {
                 double deltaA = fabs(lj0.A() - lj1.A());
                 double deltaB = fabs(lj0.B() - lj1.B());
                 mprintf("DEBUG: Potential off-diagonal LJ 1-4: %s %s expect A=%g B=%g, actual A=%g B=%g\n",
@@ -361,7 +360,7 @@ const
                 double pe_a = (fabs(lj0.A() - lj1.A()) / lj0.A());
                 double pe_b = (fabs(lj0.B() - lj1.B()) / lj0.B());
                 mprintf("DEBUG:\tPEA= %g  PEB= %g\n", pe_a, pe_b);
-              //}
+              }
             }
             LJ14out.AddParm( types, lj1, false );
           } // END hasLJ14

From 957cf76588eed0f151b80328db54d26e1269fd4c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 10 Sep 2024 12:49:06 -0400
Subject: [PATCH 0912/1492] Have updateparameters report which parameters are
 being updated

---
 src/Exec_UpdateParameters.cpp |  2 +-
 src/Parm/AssignParams.cpp     | 12 +++++++-----
 2 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/src/Exec_UpdateParameters.cpp b/src/Exec_UpdateParameters.cpp
index 8a39fa8d51..696f682bb6 100644
--- a/src/Exec_UpdateParameters.cpp
+++ b/src/Exec_UpdateParameters.cpp
@@ -23,7 +23,7 @@ void Exec_UpdateParameters::Help() const
 Exec::RetType Exec_UpdateParameters::Execute(CpptrajState& State, ArgList& argIn)
 {
   mprintf("%s", disclaimer_);
-  int verbose = argIn.getKeyInt("verbose", 0);
+  int verbose = argIn.getKeyInt("verbose", 1);
   std::string dsname = argIn.GetStringKey("setname");
   //bool genAngles = argIn.hasKey("genangles");
   if (dsname.empty()) {
diff --git a/src/Parm/AssignParams.cpp b/src/Parm/AssignParams.cpp
index 73addb6674..e096a82495 100644
--- a/src/Parm/AssignParams.cpp
+++ b/src/Parm/AssignParams.cpp
@@ -17,7 +17,7 @@ using namespace Cpptraj::Parm;
 /** CONSTRUCTOR */
 AssignParams::AssignParams() :
   debug_(0),
-  verbose_(1), // FIXME
+  verbose_(0),
   deleteExtraPointAngles_(true),
   flexibleWater_(false)
 {}
@@ -1144,14 +1144,16 @@ int AssignParams::UpdateParameters(Topology& topOut, ParameterSet const& set1) c
   }
   // Update existing parameters with new parameters
   ParameterSet::UpdateCount UC;
-  if (set0.UpdateParamSet( set1, UC, debug_, debug_ )) { // FIXME verbose
+  if (set0.UpdateParamSet( set1, UC, debug_, verbose_ )) {
     mprinterr("Error: Could not merge topology '%s' parameters with '%s' parameters.\n",
               topOut.c_str(), set1.ParamSetName().c_str());
     return 1;
   }
-  mprintf("DEBUG: Updated parameters.\n");
-  set0.Summary();
-  //set0.Debug();
+  if (debug_ > 0) {
+    mprintf("DEBUG: Updated parameter counts.\n");
+    set0.Summary();
+    //set0.Debug();
+  }
 
 //  unsigned int updateCount;
   // Bond parameters

From 01dcd68a1ac16c2f69eba953eaa9ac3ccd2e1925 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 11 Sep 2024 11:45:07 -0400
Subject: [PATCH 0913/1492] Hide debug info

---
 src/Parm/GetParams.cpp | 17 ++++++++---------
 1 file changed, 8 insertions(+), 9 deletions(-)

diff --git a/src/Parm/GetParams.cpp b/src/Parm/GetParams.cpp
index 15cb369b0c..138d8ad9f2 100644
--- a/src/Parm/GetParams.cpp
+++ b/src/Parm/GetParams.cpp
@@ -189,13 +189,13 @@ int GetParams::GetCmapParams(CmapParmHolder& cmapParm, CmapArray const& cmapTerm
             }
           }
         }
-        mprintf("DEBUG: Cmap term %u residues", idx);
-        for (std::set<NameType>::const_iterator it = resNames.begin(); it != resNames.end(); ++it)
-          mprintf(" %s", *(*it));
-        mprintf(" Atoms={");
-        for (std::vector<NameType>::const_iterator it = atomNames.begin(); it != atomNames.end(); ++it)
-          mprintf(" %s", *(*it));
-        mprintf(" }\n");
+        //mprintf("DEBUG: Cmap term %u residues", idx);
+        //for (std::set<NameType>::const_iterator it = resNames.begin(); it != resNames.end(); ++it)
+        //  mprintf(" %s", *(*it));
+        //mprintf(" Atoms={");
+        //for (std::vector<NameType>::const_iterator it = atomNames.begin(); it != atomNames.end(); ++it)
+        //  mprintf(" %s", *(*it));
+        //mprintf(" }\n");
         CmapGridType newGrid = cmapGrids[idx];
         // Add the atom/res info to the grid
         newGrid.SetNumCmapRes( resNames.size() );
@@ -377,8 +377,7 @@ const
     if (nModified14OffDiagonal > 0)
       mprintf("Warning: %u modified off-diagonal LJ 1-4 terms present.\n", nModified14OffDiagonal);
   } else {
-    if (!atoms.empty())
-      mprintf("DEBUG: Topology does not have nonbond parameters.\n");
+    //if (!atoms.empty()) mprintf("DEBUG: Topology does not have nonbond parameters.\n");
     // No nonbonded parameters. Just save mass/polarizability.
     for (std::vector<Atom>::const_iterator atm = atoms.begin(); atm != atoms.end(); ++atm)
       if (atm->HasType() > 0)

From 9cb8cdbbd1533296a28717e540e48553f7511eca Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 12 Sep 2024 09:50:19 -0400
Subject: [PATCH 0914/1492] Add ifdef to hide debug info

---
 src/Parm/Merge.cpp | 30 +++++++++++++++++++++---------
 src/Parm/Merge.h   |  1 +
 2 files changed, 22 insertions(+), 9 deletions(-)

diff --git a/src/Parm/Merge.cpp b/src/Parm/Merge.cpp
index c9b2de2bca..8b5e06ad3e 100644
--- a/src/Parm/Merge.cpp
+++ b/src/Parm/Merge.cpp
@@ -16,7 +16,7 @@ using namespace Cpptraj::Parm;
 /** CONSTRUCTOR */
 Merge::Merge() :
   debug_(0),
-  verbose_(1), // FIXME
+  verbose_(0),
   reduce_bond_params_(false),
   reduce_angle_params_(false)
 {}
@@ -42,11 +42,12 @@ void Merge::SetReduceAngleParams(bool bIn) {
 }
 
 // ----- Bonds -------------------------
+#ifdef CPPTRAJ_DEBUG_MERGE
 static inline void printIdx(BondType const& bnd1, unsigned int atomOffset) {
   mprintf("DEBUG: Bond from top1 %i - %i will be %i - %i in top0\n",
           bnd1.A1()+1, bnd1.A2()+1, bnd1.A1()+1+atomOffset, bnd1.A2()+1+atomOffset);
 }
-
+#endif
 static inline TypeNameHolder getTypes(bool& hasH, BondType const& bnd1, std::vector<Atom> const& atoms, BondParmArray const& parms)
 {
   Atom const& A1 = atoms[bnd1.A1()];
@@ -67,11 +68,12 @@ static inline BondType idxWithOffset(BondType const& bnd1, int idx, unsigned int
 }
 
 // ----- Angles ------------------------
+#ifdef CPPTRAJ_DEBUG_MERGE
 static inline void printIdx(AngleType const& ang1, unsigned int atomOffset) {
   mprintf("DEBUG: Angle from top1 %i - %i - %i will be %i - %i - %i in top0\n",
           ang1.A1()+1, ang1.A2()+1, ang1.A3()+1, ang1.A1()+1+atomOffset, ang1.A2()+1+atomOffset, ang1.A3()+1+atomOffset);
 }
-
+#endif
 static inline TypeNameHolder getTypes(bool& hasH, AngleType const& ang1, std::vector<Atom> const& atoms, AngleParmArray const& parms)
 {
   Atom const& A1 = atoms[ang1.A1()];
@@ -95,6 +97,7 @@ static inline AngleType idxWithOffset(AngleType const& ang1, int idx, unsigned i
 }
 
 // ----- Dihedrals ---------------------
+#ifdef CPPTRAJ_DEBUG_MERGE
 static inline void printIdx(DihedralType const& dih1, unsigned int atomOffset) {
   //mprintf("DEBUG: Dihedral from top1 %i - %i - %i - %i will be %i - %i - %i - %i in top0\n",
   //        dih1.A1()+1, dih1.A2()+1, dih1.A3()+1, dih1.A4()+1,
@@ -108,7 +111,7 @@ static inline void printIdx(DihedralType const& dih1, unsigned int atomOffset) {
           dih1.A1()+1, dih1.A2()+1, dih1.A3()+1, dih1.A4()+1,
           dih1.A1()*3, dih1.A2()*3, dih1.A3()*3, dih1.A4()*3);
 }
-
+#endif
 /** Dihedrals are tricky because they can have multiple parameters for
   * the same 4 types. Have the 5th be a pseudo-type based on the
   * multiplicity (or improper status).
@@ -243,7 +246,9 @@ class MergeTopArray
                      ParmArray const& p1,
                      std::vector<Atom> const& atoms1)
     {
+#     ifdef CPPTRAJ_DEBUG_MERGE
       printIdx(term1, atomOffset);
+#     endif
       bool hasH;
       TypeNameHolder types = getTypes(hasH, term1, atoms1, p1);
       mprintf("DEBUG: Looking for types in top0:");
@@ -264,7 +269,9 @@ class MergeTopArray
                      ParmArray const& p1,
                      std::vector<Atom> const& atoms1)
     {
+#     ifdef CPPTRAJ_DEBUG_MERGE
       printIdx(term1, atomOffset);
+#     endif
       bool hasH;
       TypeNameHolder types = getTypes(hasH, term1, atoms1, p1);
       mprintf("DEBUG: Looking for types in top0:");
@@ -551,12 +558,13 @@ const
 
 // -----------------------------------------------------------------------------
 // ----- CMAPs -------------------------
+#ifdef CPPTRAJ_DEBUG_MERGE
 static inline void printIdx(CmapType const& cmap1, unsigned int atomOffset) {
   mprintf("DEBUG: CMAP from top1 %i - %i - %i - %i - %i will be %i - %i - %i - %i - %i in top0\n",
           cmap1.A1()+1, cmap1.A2()+1, cmap1.A3()+1, cmap1.A4()+1, cmap1.A5()+1,
           cmap1.A1()+1+atomOffset, cmap1.A2()+1+atomOffset, cmap1.A3()+1+atomOffset, cmap1.A4()+1+atomOffset, cmap1.A5()+1+atomOffset);
 }
-
+#endif
 /** CMAPs are indexed by residue name and 5 atom names, so need 6. 
   */
 static inline TypeNameHolder getCmapTypes(CmapType const& cmap1, std::vector<Atom> const& atoms, std::vector<Residue> const& residues)
@@ -621,7 +629,9 @@ const
   // Loop over incoming terms
   for (CmapArray::const_iterator c1 = cmap1.begin(); c1 != cmap1.end(); ++c1)
   {
+#   ifdef CPPTRAJ_DEBUG_MERGE
     printIdx(*c1, atomOffset);
+#   endif
     TypeNameHolder types = getCmapTypes(*c1, atoms1, residues1);
     mprintf("DEBUG: Looking for types in top0:");
     printTypes( types ); // DEBUG
@@ -752,8 +762,9 @@ template <class T> class TopVecAppend {
 int Merge::AppendTop(Topology& topOut, Topology const& NewTop) const {
   unsigned int atomOffset = (unsigned int)topOut.Natom();
   unsigned int molOffset = (unsigned int)topOut.Nmol();
-  mprintf("DEBUG: Appending '%s' to '%s' (atom offset= %u mol offset= %u)\n",
-          NewTop.c_str(), topOut.c_str(), atomOffset, molOffset);
+  if (debug_ > 0)
+    mprintf("DEBUG: Appending '%s' to '%s' (atom offset= %u mol offset= %u)\n",
+            NewTop.c_str(), topOut.c_str(), atomOffset, molOffset);
   //int resOffset = (int)residues_.size();
 
   // Save nonbonded parameters from each topology
@@ -772,8 +783,9 @@ int Merge::AppendTop(Topology& topOut, Topology const& NewTop) const {
   int n14paramsUpdated = UpdateParameters< ParmHolder<NonbondType> >( my14, new14, "LJ 6-12 1-4", verbose_ );
   int nljcparamsUpdated = UpdateParameters< ParmHolder<double> >( myLJC, newLJC, "LJ C", verbose_ );
   int nHBparamsUpdated = UpdateParameters< ParmHolder<HB_ParmType> >( myHB, newHB, "LJ 10-12", verbose_ );
-  mprintf("\t%i atom types updated, %i LJ 6-12 params updated, %i 1-4 params updated, %i LJC params updated, %i LJ 10-12 params updated.\n",
-          nAtomTypeUpdated, nLJparamsUpdated, n14paramsUpdated, nljcparamsUpdated, nHBparamsUpdated);
+  if (verbose_ > 0)
+    mprintf("\t%i atom types updated, %i LJ 6-12 params updated, %i 1-4 params updated, %i LJC params updated, %i LJ 10-12 params updated.\n",
+            nAtomTypeUpdated, nLJparamsUpdated, n14paramsUpdated, nljcparamsUpdated, nHBparamsUpdated);
 
   // Add incoming topology bond/angle/dihedral/cmap arrays to this one.
   MergeBondArrays(topOut.ModifyBonds(), topOut.ModifyBondsH(), topOut.ModifyBondParm(), topOut.Atoms(),
diff --git a/src/Parm/Merge.h b/src/Parm/Merge.h
index f88da66b08..3c8e373259 100644
--- a/src/Parm/Merge.h
+++ b/src/Parm/Merge.h
@@ -15,6 +15,7 @@ class Topology;
 namespace Cpptraj {
 namespace Parm {
 /// Used to merge Topology files.
+/** Compile with -DCPPTRAJ_DEBUG_MERGE for extra debug info. */
 class Merge {
   public:
     /// CONSTRUCTOR

From 16168a30e3f88b3b95f69198e9b62ee63aeb501c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 12 Sep 2024 09:53:39 -0400
Subject: [PATCH 0915/1492] Hide printTypes as debug

---
 src/Parm/Merge.cpp | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/src/Parm/Merge.cpp b/src/Parm/Merge.cpp
index 8b5e06ad3e..f859d2c3c3 100644
--- a/src/Parm/Merge.cpp
+++ b/src/Parm/Merge.cpp
@@ -168,11 +168,13 @@ static inline void noParmWarning(TypeNameHolder const& types) {
 }
 
 // -------------------------------------
+#ifdef CPPTRAJ_DEBUG_MERGE
 static inline void printTypes(TypeNameHolder const& types) {
   for (TypeNameHolder::const_iterator it = types.begin(); it != types.end(); ++it)
     mprintf(" %s", *(*it) );
   mprintf("\n");
 }
+#endif
 
 // -------------------------------------
 template <class IdxType, class ParmType, class IdxArray, class ParmArray>
@@ -191,7 +193,9 @@ class MergeTopArray
                      ParmHolder<int> const& currentTypes1,
                      ParmArray const& p1)
     {
+#     ifdef CPPTRAJ_DEBUG_MERGE
       printTypes( types ); // DEBUG
+#     endif
       // Do we have an existing parameter in top0
       bool found;
       int idx = currentTypes0.FindParam(types, found);
@@ -251,7 +255,9 @@ class MergeTopArray
 #     endif
       bool hasH;
       TypeNameHolder types = getTypes(hasH, term1, atoms1, p1);
+#     ifdef CPPTRAJ_DEBUG_MERGE
       mprintf("DEBUG: Looking for types in top0:");
+#     endif
       int idx = append_param( types, currentTypes0, p0, currentTypes1, p1 );
       // At this point we have either found a parameter or not.
       if (hasH)
@@ -274,7 +280,9 @@ class MergeTopArray
 #     endif
       bool hasH;
       TypeNameHolder types = getTypes(hasH, term1, atoms1, p1);
+#     ifdef CPPTRAJ_DEBUG_MERGE
       mprintf("DEBUG: Looking for types in top0:");
+#     endif
       int idx = append_param( types, currentTypes0, p0, currentTypes1, p1 );
       // At this point we have either found a parameter or not.
       arrayX0.push_back( idxWithOffset(term1, idx, atomOffset) );
@@ -633,8 +641,10 @@ const
     printIdx(*c1, atomOffset);
 #   endif
     TypeNameHolder types = getCmapTypes(*c1, atoms1, residues1);
-    mprintf("DEBUG: Looking for types in top0:");
+#   ifdef CPPTRAJ_DEBUG_MERGE
+    mprintf("DEBUG: Looking for CMAP types in top0:");
     printTypes( types ); // DEBUG
+#   endif
     // Do we have an existing parameter in top0
     bool found;
     int idx = currentTypes0.FindParam(types, found);

From 31a09359353c29b23913bff00ac8e9b40f73eb9d Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 12 Sep 2024 09:58:20 -0400
Subject: [PATCH 0916/1492] Hide more debug behind ifdef

---
 src/Parm/Merge.cpp | 31 +++++++++++++++++++++++++++----
 1 file changed, 27 insertions(+), 4 deletions(-)

diff --git a/src/Parm/Merge.cpp b/src/Parm/Merge.cpp
index f859d2c3c3..e814700a36 100644
--- a/src/Parm/Merge.cpp
+++ b/src/Parm/Merge.cpp
@@ -202,14 +202,20 @@ class MergeTopArray
       if (!found) {
         // No parameter yet.
         // Do we have an existing parameter in top1
+#       ifdef CPPTRAJ_DEBUG_MERGE
         mprintf("DEBUG: Not found in top0. Looking in top1.\n");
+#       endif
         idx = currentTypes1.FindParam(types, found);
         if (!found) {
+#         ifdef CPPTRAJ_DEBUG_MERGE
           mprintf("DEBUG: No parameters.\n");
+#         endif
           // No parameter in either top.
           idx = -1;
         } else {
+#         ifdef CPPTRAJ_DEBUG_MERGE
           mprintf("DEBUG: Found in top1 index %i, adding to top0.\n", idx+1);
+#         endif
           // Found a parameter in top1, add it to top0.
           int oldIdx = -1;
           if (merge_with_existing_) {
@@ -227,7 +233,9 @@ class MergeTopArray
             p0.push_back( p1[idx] );
             idx = newIdx;
           } else {
+#           ifdef CPPTRAJ_DEBUG_MERGE
             mprintf("DEBUG: Parm from top1 already present in top0 at position %i\n", oldIdx+1);
+#           endif
             idx = oldIdx;
           }
         }
@@ -236,7 +244,9 @@ class MergeTopArray
         if (idx < 0) noParmWarning(types);
         currentTypes0.AddParm(types, idx, false);
       }
+#     ifdef CPPTRAJ_DEBUG_MERGE
       mprintf("DEBUG: top0 parameter index is %i\n", idx+1);
+#     endif
       return idx;
     }
     /// Append term1 to arrayX0/arrayY0 arrays along with parameters
@@ -651,14 +661,20 @@ const
     if (!found) {
       // No parameter yet.
       // Do we have an existing parameter in top1
-      mprintf("DEBUG: Not found in top0. Looking in top1.\n");
+#     ifdef CPPTRAJ_DEBUG_MERGE
+      mprintf("DEBUG: CMAP not found in top0. Looking in top1.\n");
+#     endif
       idx = currentTypes1.FindParam(types, found);
       if (!found) {
-        mprintf("DEBUG: No parameters.\n");
+#       ifdef CPPTRAJ_DEBUG_MERGE
+        mprintf("DEBUG: No CMAP parameters.\n");
+#       endif
         // No parameter in either top.
         idx = -1;
       } else {
+#       ifdef CPPTRAJ_DEBUG_MERGE
         mprintf("DEBUG: Found in top1 index %i, adding to top0.\n", idx+1);
+#       endif
         // Found a parameter in top1, add it to top0.
         int oldIdx = -1;
         //if (merge_with_existing_) {
@@ -679,13 +695,17 @@ const
           //int newIdx = cg0.size();
           //cg0.push_back( cg1[idx] );
           int newIdx = cgOffset + idx;
+#         ifdef CPPTRAJ_DEBUG_MERGE
           mprintf("DEBUG: New CMAP index in top0 is %i\n", newIdx);
+#         endif
           if ((unsigned int)newIdx >= cg0.size())
             cg0.resize( newIdx + 1 );
           cg0[newIdx] = cg1[idx];
           idx = newIdx;
         } else {
+#         ifdef CPPTRAJ_DEBUG_MERGE
           mprintf("DEBUG: Parm from top1 already present in top0 at position %i\n", oldIdx+1);
+#         endif
           idx = oldIdx;
         }
       }
@@ -694,7 +714,9 @@ const
       if (idx < 0) noParmWarning(types);
       currentTypes0.AddParm(types, idx, false);
     }
+#   ifdef CPPTRAJ_DEBUG_MERGE
     mprintf("DEBUG: top0 parameter index is %i\n", idx+1);
+#   endif
     // At this point we have either found a parameter or not.
     cmap0.push_back( idxWithOffset(*c1, idx, atomOffset) );
   } // END loop over cmap terms from top1
@@ -714,7 +736,9 @@ void Merge::MergeBondArray(BondArray& bonds0,
                                    AtArray const& atoms1)
 const
 {
+# ifdef CPPTRAJ_DEBUG_MERGE
   mprintf("DEBUG: Enter MergeBondArray()\n");
+# endif
   MergeTopArray<BondType, BondParmType, BondArray, BondParmArray> mergeBonds;
   mergeBonds.MergeTermArray( bonds0, bp0, atoms0,
                              bonds1, bp1, atoms1 );
@@ -815,7 +839,7 @@ int Merge::AppendTop(Topology& topOut, Topology const& NewTop) const {
   for (AtArray::const_iterator atom = NewTop.begin(); atom != NewTop.end(); ++atom)
   {
     if (debug_ > 1)
-      mprintf("DBG: %6li %s %s %4i\n", atom-NewTop.begin(), 
+      mprintf("DEBUG: %6li %s %s %4i\n", atom-NewTop.begin(),
               *(atom->Name()), *(atom->Type()), atom->TypeIndex());
     Atom CurrentAtom = *atom;
     Residue const& res = NewTop.Res( CurrentAtom.ResNum() );
@@ -873,4 +897,3 @@ int Merge::AppendTop(Topology& topOut, Topology const& NewTop) const {
   }
   return 0;
 }
-

From df1de41a2930696668e96242774fa6f22df4344b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 12 Sep 2024 10:03:07 -0400
Subject: [PATCH 0917/1492] Hide debug info. Only report regenerating nonbonds
 when verbose

---
 src/Parm/AssignParams.cpp | 9 ++++++---
 src/Parm/Merge.cpp        | 3 ++-
 2 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/src/Parm/AssignParams.cpp b/src/Parm/AssignParams.cpp
index e096a82495..d1f80454a0 100644
--- a/src/Parm/AssignParams.cpp
+++ b/src/Parm/AssignParams.cpp
@@ -637,7 +637,8 @@ const
         // Everything must match
         if (!hasLJ14) {
           if (t2->second.OriginalIdx() == -1 && t1->second.LJ() == t2->second.LJ()) {
-            mprintf("DEBUG: Type %s equivalent to type %s\n", *(t2->first[0]), *(t1->first[0]));
+            if (debug_ > 0)
+              mprintf("DEBUG: Type %s equivalent to type %s\n", *(t2->first[0]), *(t1->first[0]));
             t2->second.SetTypeIdx( n_unique_lj_types );
           }
         } else {
@@ -645,7 +646,8 @@ const
               t1->second.LJ() == t2->second.LJ() &&
               t1->second.LJ14() == t2->second.LJ14())
           {
-            mprintf("DEBUG: Type %s (with 1-4 params) equivalent to type %s\n", *(t2->first[0]), *(t1->first[0]));
+            if (debug_ > 0)
+              mprintf("DEBUG: Type %s (with 1-4 params) equivalent to type %s\n", *(t2->first[0]), *(t1->first[0]));
             t2->second.SetTypeIdx( n_unique_lj_types );
           }
         }
@@ -653,7 +655,8 @@ const
       n_unique_lj_types++;
     }
   }
-  mprintf("DEBUG: Setting up nonbond array for %i unique LJ types.\n", n_unique_lj_types);
+  if (debug_ > 0)
+    mprintf("DEBUG: Setting up nonbond array for %i unique LJ types.\n", n_unique_lj_types);
   nonbond.SetupLJforNtypes( n_unique_lj_types );
   if (hasLJ14)
     nonbond.SetNLJ14terms( nonbond.NBarray().size() );
diff --git a/src/Parm/Merge.cpp b/src/Parm/Merge.cpp
index e814700a36..4cc1209b95 100644
--- a/src/Parm/Merge.cpp
+++ b/src/Parm/Merge.cpp
@@ -867,7 +867,8 @@ int Merge::AppendTop(Topology& topOut, Topology const& NewTop) const {
   appendFloat.Append( topOut.ModifyBfactor(), NewTop.Bfactor(), NewTop.Natom() );
 
   // Need to regenerate nonbonded info
-  mprintf("\tRegenerating nonbond parameters.\n");
+  if (verbose_ > 0)
+    mprintf("\tRegenerating nonbond parameters.\n");
   AssignParams assign;
   assign.SetDebug( debug_ );
   assign.SetVerbose( verbose_ );

From 5abc58f1c9bafad208884024fe25c3ef45995fda Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 12 Sep 2024 13:18:03 -0400
Subject: [PATCH 0918/1492] Report total initial clashes. Hide debug info

---
 src/Exec_PermuteDihedrals.cpp | 39 ++++++++++++++++++++---------------
 src/Exec_PermuteDihedrals.h   |  2 +-
 2 files changed, 23 insertions(+), 18 deletions(-)

diff --git a/src/Exec_PermuteDihedrals.cpp b/src/Exec_PermuteDihedrals.cpp
index 0ce838da3b..008fd56569 100644
--- a/src/Exec_PermuteDihedrals.cpp
+++ b/src/Exec_PermuteDihedrals.cpp
@@ -611,10 +611,11 @@ void Exec_PermuteDihedrals::RandomizeAngles(Frame& currentFrame, Topology const&
 /** Count initial clashes in the structure. This is done to make sure
   * new clashes arent introduced after a rotation.
   */
-void Exec_PermuteDihedrals::countClashes(std::vector<int>& res_clashes,
-                                         Frame const& currentFrame, Topology const& topIn)
+int Exec_PermuteDihedrals::countClashes(std::vector<int>& res_clashes,
+                                        Frame const& currentFrame, Topology const& topIn)
 const
 {
+  int total_clashes = 0;
   res_clashes.assign( topIn.Nres(), 0 );
   for (int res0 = 0; res0 != topIn.Nres(); res0++)
   {
@@ -635,11 +636,12 @@ const
             const double* xyz1 = currentFrame.XYZ(at1);
             double d2 = DIST2_NoImage( xyz0, xyz1 );
             if (d2 < cutoff_) {
-//#             ifdef DEBUG_PERMUTEDIHEDRALS
-              mprintf("DEBUG: Initial clash: %s to %s (%g Ang)\n",
-                      topIn.TruncResAtomNameNum(at0).c_str(),
-                      topIn.TruncResAtomNameNum(at1).c_str(), sqrt(d2));
-//#             endif
+              if (debug_ > 0) {
+                mprintf("DEBUG: Initial clash: %s to %s (%g Ang)\n",
+                        topIn.TruncResAtomNameNum(at0).c_str(),
+                        topIn.TruncResAtomNameNum(at1).c_str(), sqrt(d2));
+              }
+              total_clashes++;
               res_clashes[res0]++;
               res_clashes[res1]++;
             } // END atom-atom distance within cutoff_
@@ -648,6 +650,7 @@ const
       } // END res-res distance wtihin rescutoff_
     } // END inner loop over residues
   } // END outer loop over residues
+  return total_clashes;
 }
 
 // Exec_PermuteDihedrals::RandomizeAngles_2()
@@ -681,11 +684,13 @@ void Exec_PermuteDihedrals::RandomizeAngles_2(Frame& currentFrame, Topology cons
   // Get count of initial clashes
   std::vector<int> initialResClashes;
   if (check_for_clashes_) {
-    countClashes( initialResClashes, currentFrame, topIn );
-    mprintf("DEBUG: Initial clashes:\n");
-    for (unsigned int ires = 0; ires != (unsigned int)topIn.Nres(); ires++) {
-      if (initialResClashes[ires] > 0)
-        mprintf("DEBUG:\t\t%s has %i clashes.\n", topIn.TruncResNameNum(ires).c_str(), initialResClashes[ires]);
+    int total_clashes = countClashes( initialResClashes, currentFrame, topIn );
+    mprintf("\t%i initial clashes:\n", total_clashes);
+    if (debug_ > 0) {
+      for (unsigned int ires = 0; ires != (unsigned int)topIn.Nres(); ires++) {
+        if (initialResClashes[ires] > 0)
+          mprintf("DEBUG:\t\t%s has %i initial clashes.\n", topIn.TruncResNameNum(ires).c_str(), initialResClashes[ires]);
+      }
     }
   }
 
@@ -756,11 +761,11 @@ void Exec_PermuteDihedrals::RandomizeAngles_2(Frame& currentFrame, Topology cons
                 const double* xyz1 = currentFrame.XYZ(at1);
                 double d2 = DIST2_NoImage( xyz0, xyz1 );
                 if (d2 < cutoff_) {
-//#                 ifdef DEBUG_PERMUTEDIHEDRALS
-                  mprintf("DEBUG: Clash: %s to %s (%g Ang)\n",
-                          topIn.TruncResAtomNameNum(at0).c_str(),
-                          topIn.TruncResAtomNameNum(at1).c_str(), sqrt(d2));
-//#                 endif
+                  if (debug_ > 0) {
+                    mprintf("DEBUG: Clash: %s to %s (%g Ang)\n",
+                            topIn.TruncResAtomNameNum(at0).c_str(),
+                            topIn.TruncResAtomNameNum(at1).c_str(), sqrt(d2));
+                  }
                   if (currentResClashes[res0] == initialResClashes[res0])
                     clash = true;
                   else
diff --git a/src/Exec_PermuteDihedrals.h b/src/Exec_PermuteDihedrals.h
index 4334509dae..89efb375db 100644
--- a/src/Exec_PermuteDihedrals.h
+++ b/src/Exec_PermuteDihedrals.h
@@ -31,7 +31,7 @@ class Exec_PermuteDihedrals : public Exec {
     /// Randomly rotate dihedrals
     void RandomizeAngles(Frame&, Topology const&);
     /// Count residue clashes in given frame
-    void countClashes(std::vector<int>&, Frame const&, Topology const&) const;
+    int countClashes(std::vector<int>&, Frame const&, Topology const&) const;
     /// Randomly rotate dihedrals, slightly faster version
     void RandomizeAngles_2(Frame&, Topology const&);
 

From 8655c0c060e71e6a303a26b0b5788e426bcd89fb Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 12 Sep 2024 13:21:26 -0400
Subject: [PATCH 0919/1492] Hide debug info

---
 src/DataIO_AmberPrep.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/DataIO_AmberPrep.cpp b/src/DataIO_AmberPrep.cpp
index 3d3cfb8369..6dc8ec7766 100644
--- a/src/DataIO_AmberPrep.cpp
+++ b/src/DataIO_AmberPrep.cpp
@@ -115,8 +115,8 @@ int DataIO_AmberPrep::readAmberPrep(BufferedLine& infile, DataSetList& dsl, std:
   std::string resName = args.GetStringNext();
   std::string coordFlag = args.GetStringNext();
   int kform = args.getNextInteger(-1);
-//  if (debug_ > 0)
-    mprintf("DEBUG: %s %s %i\n", resName.c_str(), coordFlag.c_str(), kform);
+  if (debug_ > 0)
+    mprintf("DEBUG: Res=%s CoordType=%s Format=%i\n", resName.c_str(), coordFlag.c_str(), kform);
   // 6 - IFIXC , IOMIT , ISYMDU , IPOS
   // FORMAT (4A)
   // IFIXC      Flag for the type of input geometry of the residue(s)

From 8045afb5daf089b0a12def58b52b92b4db321e17 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 12 Sep 2024 14:27:11 -0400
Subject: [PATCH 0920/1492] Hide debug

---
 src/AmberParamFile.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 14fd313228..565bc27e48 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -658,7 +658,7 @@ int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
           while (*ptr == ' ' && *ptr != '\0') ++ptr;
           std::string nbline(ptr);
           if (nbline == "END") {
-            mprintf("END\n");
+            if (debug_ > 0) mprintf("END\n");
             section = UNKNOWN;
           } else if (nbline == "LJEDIT") {
             section = LJEDIT;

From 49ff6c5d4351614e84baeb76f46f5cea10e72e32 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 23 Oct 2024 14:10:48 -0400
Subject: [PATCH 0921/1492] Need to use Bond/Angle/DihedralArray

---
 src/Energy/EnergyDecomposer.cpp | 24 ++++++++++++------------
 src/Energy/EnergyDecomposer.h   | 16 +++++++---------
 2 files changed, 19 insertions(+), 21 deletions(-)

diff --git a/src/Energy/EnergyDecomposer.cpp b/src/Energy/EnergyDecomposer.cpp
index 0908ab6e76..46a5a3eef2 100644
--- a/src/Energy/EnergyDecomposer.cpp
+++ b/src/Energy/EnergyDecomposer.cpp
@@ -99,8 +99,8 @@ void EnergyDecomposer::PrintOpts() const {
 
 // -----------------------------------------------------------------------------
 /** Set up bonds. */
-int EnergyDecomposer::setupBonds(BndArrayType const& bondsIn) {
-  for (BndArrayType::const_iterator bnd = bondsIn.begin(); bnd != bondsIn.end(); ++bnd)
+int EnergyDecomposer::setupBonds(BondArray const& bondsIn) {
+  for (BondArray::const_iterator bnd = bondsIn.begin(); bnd != bondsIn.end(); ++bnd)
   {
     if ( selectedAtoms_.AtomInCharMask( bnd->A1() ) ||
          selectedAtoms_.AtomInCharMask( bnd->A2() ) )
@@ -117,8 +117,8 @@ int EnergyDecomposer::setupBonds(BndArrayType const& bondsIn) {
 }
 
 /** Set up angles. */
-int EnergyDecomposer::setupAngles(AngArrayType const& anglesIn) {
-  for (AngArrayType::const_iterator ang = anglesIn.begin(); ang != anglesIn.end(); ++ang)
+int EnergyDecomposer::setupAngles(AngleArray const& anglesIn) {
+  for (AngleArray::const_iterator ang = anglesIn.begin(); ang != anglesIn.end(); ++ang)
   {
     if ( selectedAtoms_.AtomInCharMask( ang->A1() ) ||
          selectedAtoms_.AtomInCharMask( ang->A2() ) ||
@@ -136,8 +136,8 @@ int EnergyDecomposer::setupAngles(AngArrayType const& anglesIn) {
 }
 
 /** Set up dihedrals. */
-int EnergyDecomposer::setupDihedrals(DihArrayType const& dihedralsIn) {
-  for (DihArrayType::const_iterator dih = dihedralsIn.begin(); dih != dihedralsIn.end(); ++dih)
+int EnergyDecomposer::setupDihedrals(DihedralArray const& dihedralsIn) {
+  for (DihedralArray::const_iterator dih = dihedralsIn.begin(); dih != dihedralsIn.end(); ++dih)
   {
     if ( selectedAtoms_.AtomInCharMask( dih->A1() ) ||
          selectedAtoms_.AtomInCharMask( dih->A2() ) ||
@@ -223,13 +223,13 @@ int EnergyDecomposer::SetupDecomposer(Topology const& topIn, Box const& boxIn) {
       if (selectedAtoms_.AtomInCharMask( idx ))
         mprintf("\t%s\n", topIn.AtomMaskName( idx ).c_str());
     mprintf("DEBUG: Bonds:\n");
-    for (BndArrayType::const_iterator bnd = bonds_.begin(); bnd != bonds_.end(); ++bnd)
+    for (BondArray::const_iterator bnd = bonds_.begin(); bnd != bonds_.end(); ++bnd)
       mprintf("\t%s - %s\n", topIn.AtomMaskName(bnd->A1()).c_str(), topIn.AtomMaskName(bnd->A2()).c_str());
     mprintf("DEBUG: Angles:\n");
-    for (AngArrayType::const_iterator ang = angles_.begin(); ang != angles_.end(); ++ang)
+    for (AngleArray::const_iterator ang = angles_.begin(); ang != angles_.end(); ++ang)
       mprintf("\t%s - %s - %s\n", topIn.AtomMaskName(ang->A1()).c_str(), topIn.AtomMaskName(ang->A2()).c_str(), topIn.AtomMaskName(ang->A3()).c_str());
     mprintf("DEBUG: Dihedrals:\n");
-    for (DihArrayType::const_iterator dih = dihedrals_.begin(); dih != dihedrals_.end(); ++dih)
+    for (DihedralArray::const_iterator dih = dihedrals_.begin(); dih != dihedrals_.end(); ++dih)
       mprintf("\t%s - %s - %s - %s\n", topIn.AtomMaskName(dih->A1()).c_str(), topIn.AtomMaskName(dih->A2()).c_str(), topIn.AtomMaskName(dih->A3()).c_str(), topIn.AtomMaskName(dih->A4()).c_str());
   }
 
@@ -247,7 +247,7 @@ void EnergyDecomposer::saveEne(int idx, double ene_cont) {
 
 /** Calculate bond energies. */
 void EnergyDecomposer::calcBonds( Frame const& frameIn ) {
-  for (BndArrayType::const_iterator bnd = bonds_.begin(); bnd != bonds_.end(); ++bnd)
+  for (BondArray::const_iterator bnd = bonds_.begin(); bnd != bonds_.end(); ++bnd)
   {
     BondParmType const& BP = currentTop_->BondParm()[ bnd->Idx() ];
     double ene = Ene_Bond<double>( frameIn.XYZ( bnd->A1() ),
@@ -265,7 +265,7 @@ void EnergyDecomposer::calcBonds( Frame const& frameIn ) {
 
 /** Calculate angle energies. */
 void EnergyDecomposer::calcAngles( Frame const& frameIn ) {
-  for (AngArrayType::const_iterator ang = angles_.begin(); ang != angles_.end(); ++ang)
+  for (AngleArray::const_iterator ang = angles_.begin(); ang != angles_.end(); ++ang)
   {
     AngleParmType const& AP = currentTop_->AngleParm()[ ang->Idx() ];
     double ene = Ene_Angle<double>( frameIn.XYZ( ang->A1() ),
@@ -285,7 +285,7 @@ void EnergyDecomposer::calcAngles( Frame const& frameIn ) {
 
 /** Calculate dihedral and LJ 1-4 energies. */
 void EnergyDecomposer::calcDihedrals( Frame const& frameIn ) {
-  for (DihArrayType::const_iterator dih = dihedrals_.begin(); dih != dihedrals_.end(); ++dih)
+  for (DihedralArray::const_iterator dih = dihedrals_.begin(); dih != dihedrals_.end(); ++dih)
   {
     DihedralParmType const& DP = currentTop_->DihedralParm()[ dih->Idx() ];
 
diff --git a/src/Energy/EnergyDecomposer.h b/src/Energy/EnergyDecomposer.h
index 4a0f514214..25067169d3 100644
--- a/src/Energy/EnergyDecomposer.h
+++ b/src/Energy/EnergyDecomposer.h
@@ -5,6 +5,7 @@
 #include "../CharMask.h"
 #include "../EwaldOptions.h"
 #include "../OnlineVarT.h"
+#include "../ParameterTypes.h"
 #include "../Timer.h"
 #ifdef MPI
 # include "../Parallel.h"
@@ -48,16 +49,13 @@ class EnergyDecomposer {
   private:
     typedef std::vector<double> Darray;
     typedef std::vector< Stats<double> > EneArrayType;
-    typedef std::vector<BondType> BndArrayType;
-    typedef std::vector<AngleType> AngArrayType;
-    typedef std::vector<DihedralType> DihArrayType;
 
     /// Set up selected bonds
-    int setupBonds(BndArrayType const&);
+    int setupBonds(BondArray const&);
     /// Set up selected angles
-    int setupAngles(AngArrayType const&);
+    int setupAngles(AngleArray const&);
     /// Set up selected dihedrals
-    int setupDihedrals(DihArrayType const&);
+    int setupDihedrals(DihedralArray const&);
 
     /// Save energy contribution for atom if it is selected
     inline void saveEne(int, double);
@@ -75,9 +73,9 @@ class EnergyDecomposer {
     EwaldOptions ewaldOpts_; ///< Hold Ewald options
     Cpptraj::Energy::Ecalc_Nonbond::CalcType nbcalctype_;
 
-    BndArrayType bonds_;         ///< Hold all bonds to be calculated
-    AngArrayType angles_;        ///< Hold all angles to be calculated
-    DihArrayType dihedrals_;     ///< Hold all dihedrals to be calculated
+    BondArray bonds_;         ///< Hold all bonds to be calculated
+    AngleArray angles_;        ///< Hold all angles to be calculated
+    DihedralArray dihedrals_;     ///< Hold all dihedrals to be calculated
     //AtomMask mask_;              ///< Atom mask for nonbonded calculations
     EneArrayType energies_;      ///< Used to accumulate the average energy of each selected entity.
     Topology const* currentTop_; ///< Current topology from Setup

From 2c6f6008a38848f15b1b539c4697aa3ed8570ed8 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 24 Oct 2024 10:44:11 -0400
Subject: [PATCH 0922/1492] Hide debug info

---
 src/DataIO_LeapRC.cpp | 17 ++++++++++-------
 1 file changed, 10 insertions(+), 7 deletions(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 5d02dec559..f47c936829 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -375,19 +375,19 @@ const
   if (ad == 0) {
     AssociatedData_ResId resid( prm.pdbName_, prm.termType_ );
     unit->AssociateData( &resid );
-    //if (debug_ > 0) {
+    if (debug_ > 0) {
       mprintf("DEBUG: Found unit %s", unit->legend());
       resid.Ainfo();
       mprintf("\n");
-    //}
+    }
   } else if (allowUpdate) {
     *ad = AssociatedData_ResId( prm.pdbName_, prm.termType_ );
-    mprintf("DEBUG: Updated unit %s resmap. ", unit->legend());
+    mprintf("\tUpdated unit %s resmap. ", unit->legend());
     ad->Ainfo();
     mprintf("\n");
   } else {
     // TODO check if map is different
-    mprintf("DEBUG: Unit %s already has resmap. ", unit->legend());
+    mprintf("Warning: Unit %s already has resmap. ", unit->legend());
     ad->Ainfo();
     mprintf("\n");
   }
@@ -499,7 +499,8 @@ const
     if (ds == 0) return 1;
   }
   DataSet_NameMap& namemap = static_cast<DataSet_NameMap&>( *ds );
-  mprintf("DEBUG: Name map set: %s\n", namemap.legend());
+  if (debug_ > 0)
+    mprintf("DEBUG: Name map set: %s\n", namemap.legend());
   int bracketCount = 0;
   // First line should contain the command
   const char* line = infile.CurrentLine();
@@ -841,7 +842,8 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
         // Unrecognized so far. See if this is a unit alias (interpret as 'alias = unit')
         if (has_equals) {
           if (line.Nargs() == 2) {
-            mprintf("DEBUG: %s = %s\n", line[0].c_str(), line[1].c_str());
+            if (debug_ > 0)
+              mprintf("DEBUG: %s = %s\n", line[0].c_str(), line[1].c_str());
             // Find the unit to make a copy of
             DataSet* ds0 = dsl.CheckForSet( MetaData(dsname, line[1]) );
             if (ds0 == 0) {
@@ -867,7 +869,8 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
             crd1.SetCRD(0, tmpFrm );
             // Copy associated data
             crd1.CopyAssociatedDataFrom( crd0 );
-            mprintf("DEBUG: Created unit set %s\n", crd1.legend());
+            if (debug_ > 0)
+              mprintf("DEBUG: Created unit set %s\n", crd1.legend());
             // See if there is a PDB residue name map
             for (PdbResMapArray::const_iterator it = pdbResMap_.begin();
                                                 it != pdbResMap_.end(); ++it)

From 277f368cfd6aac073b3ae4d608292847e585f5d9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 24 Oct 2024 10:56:59 -0400
Subject: [PATCH 0923/1492] Hide debug info

---
 src/Structure/Creator.cpp | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/Structure/Creator.cpp b/src/Structure/Creator.cpp
index b205e69933..2d605dedd1 100644
--- a/src/Structure/Creator.cpp
+++ b/src/Structure/Creator.cpp
@@ -76,7 +76,8 @@ void Creator::UpdateTemplateElements() const {
 
   for (Carray::const_iterator crd = Templates_.begin(); crd != Templates_.end(); ++crd)
   {
-    mprintf("DEBUG: Updating atom elements in '%s'\n", (*crd)->legend());
+    if (debug_ > 0)
+      mprintf("DEBUG: Updating atom elements in '%s'\n", (*crd)->legend());
     // Loop over template atoms
     Topology& templateTop = *((*crd)->TopPtr());
     for (int at = 0; at != templateTop.Natom(); at++) {
@@ -84,7 +85,8 @@ void Creator::UpdateTemplateElements() const {
       if (templateTop[at].HasType()) {
         it = mainParmSet_->AT().GetParam( TypeNameHolder(templateTop[at].Type()) );
         if (it != mainParmSet_->AT().end()) {
-          mprintf("DEBUG:\t\tSetting atom %s element to %s\n", *(templateTop[at].Name()), it->second.EltStr());
+          if (debug_ > 1)
+            mprintf("DEBUG:\t\tSetting atom %s element to %s\n", *(templateTop[at].Name()), it->second.EltStr());
           templateTop.SetAtom(at).SetElementFromSymbol( it->second.EltStr()[0],
                                                         it->second.EltStr()[1] );
         }

From 862779cc637985fe69bfde5b255c2636962bf6b5 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 24 Oct 2024 11:15:39 -0400
Subject: [PATCH 0924/1492] Hide more debug info, add detailed timing data for
 build

---
 src/Exec_Build.cpp        | 27 ++++++++++++++++++++++++++-
 src/Exec_Build.h          |  9 +++++++++
 src/Structure/Creator.cpp |  3 ++-
 3 files changed, 37 insertions(+), 2 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 75d261fb36..dd6c8c0824 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -685,6 +685,7 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
 /** Standalone execute. For DataIO_LeapRC. */
 Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, int debugIn, ArgList& argIn)
 {
+  t_total_.Start();
   if (inCrdPtr == 0) {
     mprinterr("Internal Error: Exec_Build::BuildStructure(): Null input coordinates.\n");
     return CpptrajState::ERR;
@@ -717,6 +718,7 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, in
   mprintf("\tSolvent residue name: %s\n", solventResName.c_str());
 
   // Do histidine detection before H atoms are removed
+  t_hisDetect_.Start();
   if (!argIn.hasKey("nohisdetect")) {
     Cpptraj::Structure::HisProt hisProt;
     if (hisProt.InitHisProt( argIn, debug_ )) {
@@ -729,8 +731,10 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, in
       return CpptrajState::ERR;
     }
   }
+  t_hisDetect_.Stop();
 
   // Clean up structure
+  t_clean_.Start();
   Cpptraj::Structure::PdbCleaner pdbCleaner;
   pdbCleaner.SetDebug( debug_ );
   if (pdbCleaner.InitPdbCleaner( argIn, solventResName, std::vector<int>() )) {
@@ -746,6 +750,7 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, in
     mprinterr("Error: Could not clean PDB.\n");
     return CpptrajState::ERR;
   }
+  t_clean_.Stop();
 
   // Set up Output coords
   std::string outset = argIn.GetStringKey("name");
@@ -790,6 +795,7 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, in
   Cpptraj::Structure::ResStatArray resStat( topIn.Nres() );
 
   // Disulfide search
+  t_disulfide_.Start();
   if (!argIn.hasKey("nodisulfides")) {
     Cpptraj::Structure::Disulfide disulfide;
     if (disulfide.InitDisulfide( argIn, Cpptraj::Structure::Disulfide::ADD_BONDS, debug_ )) {
@@ -805,8 +811,10 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, in
   } else {
     mprintf("\tNot searching for disulfides.\n");
   }
+  t_disulfide_.Stop();
 
   // Handle sugars.
+  t_sugar_.Start();
   // TODO should be on a residue by residue basis in FillAtomsWithTemplates
   bool prepare_sugars = !argIn.hasKey("nosugars");
   if (!prepare_sugars)
@@ -856,8 +864,10 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, in
       return CpptrajState::ERR;
     }
   }
+  t_sugar_.Stop();
 
   // Fill in atoms with templates
+  t_fill_.Start();
   Topology topOut;
   topOut.SetDebug( debug_ );
   // TODO better default
@@ -869,9 +879,11 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, in
     mprinterr("Error: Could not fill in atoms using templates.\n");
     return CpptrajState::ERR;
   }
+  t_fill_.Stop();
 
   // Assign parameters. This will create the bond/angle/dihedral/improper
   // arrays as well.
+  t_assign_.Start();
   Exec::RetType ret = CpptrajState::OK;
   Cpptraj::Parm::AssignParams AP;
   AP.SetDebug( debug_ );
@@ -889,6 +901,7 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, in
   topOut.AllocTreeChainClassification( );
   topOut.AllocJoinArray();
   topOut.AllocRotateArray();
+  t_assign_.Stop();
 
   // Update coords 
   if (crdout.CoordsSetup( topOut, CoordinateInfo() )) { // FIXME better coordinate info
@@ -899,6 +912,7 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, in
 
   // Structure check
   if (check_structure_) {
+    t_check_.Start();
     StructureCheck check;
     if (check.SetOptions( true, // image 
                           true, // check bonds
@@ -958,7 +972,18 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, in
     // If box was added for check only, remove it
     if (box_added)
       frameOut.ModifyBox().SetNoBox();
-  }
+    t_check_.Stop();
+  }
+  t_total_.Stop();
+
+  t_total_.WriteTiming(1, "Build timing:");
+  t_hisDetect_.WriteTiming(2, "Histidine detection :", t_total_.Total());
+  t_clean_.WriteTiming    (2, "Structure clean     :", t_total_.Total());
+  t_disulfide_.WriteTiming(2, "Disulfide detection :", t_total_.Total());
+  t_sugar_.WriteTiming    (2, "Sugar preparation   :", t_total_.Total());
+  t_fill_.WriteTiming     (2, "Fill missing atoms  :", t_total_.Total());
+  t_assign_.WriteTiming   (2, "Param./Top. gen.    :", t_total_.Total());
+  t_check_.WriteTiming    (2, "Structure check     :", t_total_.Total());
 
   return ret;
 }
diff --git a/src/Exec_Build.h b/src/Exec_Build.h
index fa2a2c6a37..73bfc12069 100644
--- a/src/Exec_Build.h
+++ b/src/Exec_Build.h
@@ -38,5 +38,14 @@ class Exec_Build : public Exec {
     int check_box_natom_;  ///< Systems larger than this will have box added so PL check can be used
     bool check_structure_; ///< If true check the resulting structure
     Cpptraj::Structure::SugarBuilder* sugarBuilder_;
+
+    Timer t_total_;
+    Timer t_hisDetect_;
+    Timer t_clean_;
+    Timer t_disulfide_;
+    Timer t_sugar_;
+    Timer t_fill_;
+    Timer t_assign_;
+    Timer t_check_;
 };
 #endif
diff --git a/src/Structure/Creator.cpp b/src/Structure/Creator.cpp
index 2d605dedd1..9cbd2836a5 100644
--- a/src/Structure/Creator.cpp
+++ b/src/Structure/Creator.cpp
@@ -64,7 +64,8 @@ int Creator::InitCreator(ArgList& argIn, DataSetList const& DSL, int debugIn)
                                    ds != nameMapSets.end(); ++ds)
   {
     NameMaps_.push_back( static_cast<DataSet_NameMap*>( *ds ) );
-    mprintf("DEBUG: Atom name map: %s\n", NameMaps_.back()->legend());
+    if (debug_ > 0)
+      mprintf("DEBUG: Atom name map: %s\n", NameMaps_.back()->legend());
   }
 
   return 0;

From c7419644a9b18ea332f51cbc6dffefd1cd09624e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 24 Oct 2024 11:54:18 -0400
Subject: [PATCH 0925/1492] Hide debug info

---
 src/Structure/Builder.cpp | 45 ++++++++++++++++++++++-----------------
 1 file changed, 26 insertions(+), 19 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index add1f99a13..2337bff2ca 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1905,24 +1905,28 @@ Builder::AtomIC Builder::getInternalCoordsForAtom(int at, int idx, Barray const&
   AtomIC atomIC(at, idx);
   InternalCoords ic;
   if (getIcFromInternals(ic, at, hasPosition)) {
-    mprintf("Atom %s has torsion/angle/bond internals.\n", topIn.LeapName(at).c_str());
+    if (debug_ > 0) // TODO should be behind an ifdef?
+      mprintf("Atom %s has torsion/angle/bond internals.\n", topIn.LeapName(at).c_str());
     atomIC.SetIC( ic );
     return atomIC;
   }
   InternalAngle a1, a2;
   InternalBond b1;
   if (getTwoAnglesFromInternals(a1, a2, b1, at, hasPosition)) {
-    mprintf("Atom %s has two angle internals.\n", topIn.LeapName(at).c_str());
+    if (debug_ > 0)
+      mprintf("Atom %s has two angle internals.\n", topIn.LeapName(at).c_str());
     atomIC.SetAngles(a1, a2, b1);
     return atomIC;
   }
   if (getAngleFromInternals(a1, b1, at, hasPosition)) {
-    mprintf("Atom %s has angle internal.\n", topIn.LeapName(at).c_str());
+    if (debug_ > 0)
+      mprintf("Atom %s has angle internal.\n", topIn.LeapName(at).c_str());
     atomIC.SetAngle(a1, b1);
     return atomIC;
   }
   if (getBondFromInternals(b1, at, hasPosition)) {
-    mprintf("Atom %s has bond internal.\n", topIn.LeapName(at).c_str());
+    if (debug_ > 0)
+      mprintf("Atom %s has bond internal.\n", topIn.LeapName(at).c_str());
     atomIC.SetBond(b1);
     return atomIC;
   }
@@ -1940,7 +1944,7 @@ const
   if (getIcFromInternals(ic, at, hasPosition)) {
     //printAllInternalsForAtom(at, topIn, hasPosition); // DEBUG
     Vec3 posI = Zmatrix::AtomIposition(ic, frameOut);
-    //if (debug_ > 1) {
+    if (debug_ > 1) {
       mprintf("Building atom %s using torsion/angle/bond\n", topIn.LeapName(at).c_str());
       mprintf("Using %s - %s - %s - %s\n",
               topIn.LeapName(ic.AtI()).c_str(),
@@ -1951,7 +1955,7 @@ const
       mprintf( "Angle   = %f\n", ic.Theta() );
       mprintf( "Bond    = %f\n", ic.Dist() );
       mprintf( "ZMatrixAll:  %f,%f,%f\n", posI[0], posI[1], posI[2]);
-    //}
+    }
     frameOut.SetXYZ( ic.AtI(), posI );
     return 1;
   }
@@ -1975,27 +1979,27 @@ const
   // Check if we can get a single angle for this atom
   if (getAngleFromInternals(a1, b1, at, hasPosition)) {
     Vec3 posI = Zmatrix::AtomIposition(frameOut.XYZ(a1.AtJ()), frameOut.XYZ(a1.AtK()), b1.DistVal(), a1.ThetaVal() );
-    //if debug_ > 1) {
+    if (debug_ > 1) {
       mprintf("Building atom %s using angle/bond\n", topIn.LeapName(at).c_str());
       mprintf("Using %s - %s - %s\n",
               topIn.LeapName(a1.AtI()).c_str(), topIn.LeapName(a1.AtJ()).c_str(), topIn.LeapName(a1.AtK()).c_str());
       mprintf( "Angle   = %f\n", a1.ThetaVal()*Constants::RADDEG );
       mprintf( "Bond    = %f\n", b1.DistVal() );
       mprintf("ZMatrixBondAngle:  %f,%f,%f\n", posI[0], posI[1], posI[2]);
-      //}
+    }
     frameOut.SetXYZ( a1.AtI(), posI );
     return 1;
   }
   // Check if we can get a bond for this atom
   if (getBondFromInternals(b1, at, hasPosition)) {
     Vec3 posI = Zmatrix::AtomIposition(frameOut.XYZ(b1.AtJ()), b1.DistVal());
-    //if debug_ > 1) {
+    if (debug_ > 1) {
       mprintf("Building atom %s using bond\n", topIn.LeapName(at).c_str());
       mprintf("Using %s - %s\n",
               topIn.LeapName(b1.AtI()).c_str(), topIn.LeapName(b1.AtJ()).c_str());
       mprintf( "Bond    = %f\n", b1.DistVal() );
       mprintf( "ZMatrixBond:  %f,%f,%f\n", posI[0], posI[1], posI[2]);
-      //}
+    }
     frameOut.SetXYZ( b1.AtI(), posI );
     return 1;
   }
@@ -2223,12 +2227,12 @@ const
     }
   }
   std::sort( needsBuilding.begin(), needsBuilding.end() );
-  mprintf("DEBUG: Atoms that need building:\n");
-  for (std::vector<AtomIC>::const_iterator it = needsBuilding.begin(); it != needsBuilding.end(); ++it)
-    mprintf("\t%i atom %i %s (%i)\n", it->Idx(), it->At()+1, topIn.AtomMaskName( it->At() ).c_str(), it->Priority() );
-      
-  if (debug_ > 0)
+  if (debug_ > 0) {
+    mprintf("DEBUG: Atoms that need building:\n");
+    for (std::vector<AtomIC>::const_iterator it = needsBuilding.begin(); it != needsBuilding.end(); ++it)
+      mprintf("\t%i atom %i %s (%i)\n", it->Idx(), it->At()+1, topIn.AtomMaskName( it->At() ).c_str(), it->Priority() );
     mprintf("DEBUG: %u atoms need positions.\n", nAtomsThatNeedPositions);
+  }
   if (nAtomsThatNeedPositions == 0) return 0;
 
   // FIXME TEST - If no "complete" internal coords currently, try a "sparse" build.
@@ -2245,7 +2249,8 @@ const
       int atToBuildAround = -1;
       if (!hasPosition[at]) {
         // Position of atom is not known.
-        mprintf("BUILD: Position of %s is not known.\n", *(topIn[at].Name())); // DEBUG
+        if (debug_ > 0)
+          mprintf("BUILD: Position of %s is not known.\n", *(topIn[at].Name())); // DEBUG
         // Is this bonded to an atom with known position?
         for (Atom::bond_iterator bat = topIn[at].bondbegin(); bat != topIn[at].bondend(); ++bat) {
           if (hasPosition[*bat]) {
@@ -2255,18 +2260,20 @@ const
         }
       } else {
         // Position of atom is known.
-        mprintf("BUILD: Position of %s is known.\n", *(topIn[at].Name())); // DEBUG
+        if (debug_ > 0)
+          mprintf("BUILD: Position of %s is known.\n", *(topIn[at].Name())); // DEBUG
         atToBuildAround = at;
       }
       // Build unknown positions around known atom
       if (atToBuildAround != -1) {
-        //if (debug_ > 0)
+        if (debug_ > 0)
           mprintf("Building externals from %s\n", topIn.LeapName(atToBuildAround).c_str());
         Atom const& bAtom = topIn[atToBuildAround];
         for (Atom::bond_iterator bat = bAtom.bondbegin(); bat != bAtom.bondend(); ++bat)
         {
           if (!hasPosition[*bat]) {
-            printAllInternalsForAtom(*bat, topIn, hasPosition); // DEBUG
+            if (debug_ > 0)
+              printAllInternalsForAtom(*bat, topIn, hasPosition); // DEBUG
             if (buildCoordsForAtom(*bat, frameOut, topIn, hasPosition)) {
               hasPosition[ *bat ] = true;
               nAtomsBuilt++;

From 5107296ae3b9e367d9d862b97d80898fbab9a593 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 24 Oct 2024 12:06:49 -0400
Subject: [PATCH 0926/1492] Hide debug info

---
 src/Parm/AssignParams.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Parm/AssignParams.cpp b/src/Parm/AssignParams.cpp
index d1f80454a0..f8e8740a19 100644
--- a/src/Parm/AssignParams.cpp
+++ b/src/Parm/AssignParams.cpp
@@ -1126,7 +1126,7 @@ int AssignParams::AssignParameters(Topology& topOut, ParameterSet const& set0) c
   // LJ 6-12
   mprintf("\tAssigning nonbond parameters.\n");
   AssignNonbondParams( topOut, set0.AT(), set0.NB(), set0.NB14(), set0.LJC(), set0.HB() );
-  mprintf("DEBUG: CMAP size %zu\n", set0.CMAP().size());
+  //mprintf("DEBUG: CMAP size %zu\n", set0.CMAP().size());
 
   return 0;
 }

From c6e980db3a60b414a85295906c331dca421c8243 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 6 Nov 2024 10:36:19 -0500
Subject: [PATCH 0927/1492] Improve warning about missing residue templates

---
 src/Exec_Build.cpp | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index dd6c8c0824..396cc51e22 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -13,6 +13,7 @@
 #include "Structure/SugarBuilder.h"
 #include "Structure/Sugar.h"
 #include "StructureCheck.h"
+#include <set> // For warning about missing residue templates
 
 /** CONSTRUCTOR */
 Exec_Build::Exec_Build() :
@@ -126,6 +127,8 @@ const
   //ResTypes.reserve( topIn.Nres() );
   // Initial loop to try to match residues to templates
   int newNatom = 0;
+  unsigned int n_no_template_found = 0;
+  std::set<NameType> missing_templates;
   for (int ires = 0; ires != topIn.Nres(); ires++)
   {
     Residue const& currentRes = topIn.Res(ires);
@@ -156,7 +159,9 @@ const
     DataSet_Coords* resTemplate = creator.IdTemplateFromResname(currentRes.Name(), resTermType);
     if (resTemplate == 0) {
       // Residue has no template.
+      n_no_template_found++;
       mprintf("Warning: No template found for residue %s\n", topIn.TruncResNameOnumId(ires).c_str());
+      missing_templates.insert( currentRes.Name() );
       newNatom += currentRes.NumAtoms();
       // Head and tail atoms are blank
       resHeadAtoms.push_back( -1 );
@@ -193,6 +198,16 @@ const
     ResTemplates.push_back( resTemplate );
   }
   mprintf("\tFinal structure should have %i atoms.\n", newNatom);
+  if (n_no_template_found > 0) {
+    mprintf("Warning: No template was found for %u residues.\n", n_no_template_found);
+    mprintf("Warning: Residue names:");
+    for (std::set<NameType>::const_iterator rit = missing_templates.begin();
+                                            rit != missing_templates.end(); ++rit)
+      mprintf(" %s", *(*rit));
+    mprintf("\n");
+    mprintf("Warning: This may indicate that you have not loaded a library file\n"
+            "Warning:   or have not loaded the correct force field.\n");
+  }
   frameOut.SetupFrame( newNatom );
   // Clear frame so that AddXYZ can be used
   frameOut.ClearAtoms();

From 40b1542fcc6387185afda4e0756dec70cc1857ac Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 6 Nov 2024 10:44:46 -0500
Subject: [PATCH 0928/1492] Clean up missing atom type message

---
 src/Exec_Build.cpp | 28 ++++++++++++++++++++++------
 1 file changed, 22 insertions(+), 6 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 396cc51e22..4b96d9f5bf 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -370,15 +370,31 @@ const
   if (nAtomsMissingTypes > 0) {
     mprinterr("Error: %i atoms are missing types, either because they did not have\n"
               "Error:  one initially or they could not be matched to a template.\n"
-              "Error:  Build cannot proceed unless all atoms have a type:\n",
+              "Error: This can happen if a parameter file is missing or a force field\n"
+              "Error:  file has not been loaded.\n"
+              "Error: Build cannot proceed unless all atoms have a type:\n",
               nAtomsMissingTypes);
+    std::set<NameType> atoms_missing_types;
     for (int ires = 0; ires != topOut.Nres(); ires++) {
-      std::string missingTypes;
-      for (int at = topOut.Res(ires).FirstAtom(); at != topOut.Res(ires).LastAtom(); ++at)
+      for (int at = topOut.Res(ires).FirstAtom(); at != topOut.Res(ires).LastAtom(); ++at) {
         if ( !topOut[at].HasType() )
-          missingTypes.append(" " + topOut[at].Name().Truncated() );
-      if (!missingTypes.empty())
-        mprinterr("Error:\t%s missing types for%s\n", topOut.TruncResNameNum(ires).c_str(), missingTypes.c_str());
+          atoms_missing_types.insert( topOut[at].Name() );
+      }
+    }
+    mprinterr("Error: Atoms missing types:");
+    for (std::set<NameType>::const_iterator ait = atoms_missing_types.begin();
+                                            ait != atoms_missing_types.end(); ++ait)
+      mprinterr(" %s", *(*ait));
+    mprinterr("\n");
+    if (debug_ > 0) {
+      for (int ires = 0; ires != topOut.Nres(); ires++) {
+        std::string missingTypes;
+        for (int at = topOut.Res(ires).FirstAtom(); at != topOut.Res(ires).LastAtom(); ++at)
+          if ( !topOut[at].HasType() )
+            missingTypes.append(" " + topOut[at].Name().Truncated() );
+        if (!missingTypes.empty())
+          mprinterr("Error:\t%s missing types for%s\n", topOut.TruncResNameNum(ires).c_str(), missingTypes.c_str());
+      }
     }
     return 1;
   }

From 32ad071ab5b7f1b83941698527fb1641cbcc9118 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 6 Nov 2024 11:51:40 -0500
Subject: [PATCH 0929/1492] Put missing template atoms count in
 MapAtomsToTemplate()

---
 src/Exec_Build.cpp | 26 +++++++++++++++++++-------
 src/Exec_Build.h   |  2 +-
 2 files changed, 20 insertions(+), 8 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 4b96d9f5bf..06a1cf7863 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -35,8 +35,10 @@ std::vector<int> Exec_Build::MapAtomsToTemplate(Topology const& topIn,
                                                 int rnum,
                                                 DataSet_Coords* resTemplate,
                                                 Cpptraj::Structure::Creator const& creator,
-                                                std::vector<NameType>& sourceAtomNames)
+                                                std::vector<NameType>& sourceAtomNames,
+                                                int& nTgtAtomsMissing)
 {
+  nTgtAtomsMissing = 0;
   std::vector<int> mapOut(resTemplate->Top().Natom(), -1);
   mapOut.reserve( resTemplate->Top().Natom() );
   Residue const& resIn = topIn.Res(rnum);
@@ -75,6 +77,11 @@ std::vector<int> Exec_Build::MapAtomsToTemplate(Topology const& topIn,
         }
       } // END search template for alias
     } // END do alias search
+    if (!found) {
+      mprintf("Warning: Input atom %s was not mapped to a template atom.\n",
+              topIn.TruncAtomResNameOnumId( itgt ).c_str());
+      nTgtAtomsMissing++;
+    }
   }
 /*
   for (int iref = 0; iref != resTemplate->Top().Natom(); iref++)
@@ -288,7 +295,8 @@ const
       else
         currentRes.SetName( NameType( (*templateResName) + ( templateResName.len() - 3) ) );
       // Map source atoms to template atoms.
-      std::vector<int> map = MapAtomsToTemplate( topIn, ires, resTemplate, creator, SourceAtomNames );
+      int nTgtAtomsMissing = 0;
+      std::vector<int> map = MapAtomsToTemplate( topIn, ires, resTemplate, creator, SourceAtomNames, nTgtAtomsMissing );
       if (debug_ > 1) {
         mprintf("\t  Atom map:\n");
         // DEBUG - print map
@@ -344,11 +352,15 @@ const
           }
         }
       }
-      // See if any current atoms were not mapped to reference
-      int nTgtAtomsMissing = 0;
-      for (int itgt = 0; itgt != currentRes.NumAtoms(); itgt++)
-        if (pdb[itgt] == -1)
-          nTgtAtomsMissing++;
+      // See if any current atoms were not mapped to reference template
+      //int nTgtAtomsMissing = 0;
+      //for (int itgt = 0; itgt != currentRes.NumAtoms(); itgt++) {
+      //  if (pdb[itgt] == -1) {
+      //    mprintf("Warning: Input atom %s was not mapped to a template atom.\n",
+      //            topIn.TruncAtomResNameOnumId(currentRes.FirstAtom()+itgt).c_str());
+      //    nTgtAtomsMissing++;
+      //  }
+      //}
       if (nTgtAtomsMissing > 0)
         mprintf("\t%i source atoms not mapped to template.\n", nTgtAtomsMissing);
       // Save atom offset if atoms need to be built
diff --git a/src/Exec_Build.h b/src/Exec_Build.h
index 73bfc12069..647f2bd41d 100644
--- a/src/Exec_Build.h
+++ b/src/Exec_Build.h
@@ -32,7 +32,7 @@ class Exec_Build : public Exec {
     /// Create new topology/frame using templates
     int FillAtomsWithTemplates(Topology&, Frame&, Topology const&, Frame const&, Cpptraj::Structure::Creator const&) const;
     /// Map atoms in topology to template
-    static std::vector<int> MapAtomsToTemplate(Topology const&, int, DataSet_Coords*, Cpptraj::Structure::Creator const&, std::vector<NameType>&);
+    static std::vector<int> MapAtomsToTemplate(Topology const&, int, DataSet_Coords*, Cpptraj::Structure::Creator const&, std::vector<NameType>&, int&);
 
     int debug_;
     int check_box_natom_;  ///< Systems larger than this will have box added so PL check can be used

From ef626093cbaec47d10a74d0ce129d20e7755248a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 24 Jan 2025 13:49:32 -0500
Subject: [PATCH 0930/1492] Add missing tests to makefile

---
 test/Makefile | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/test/Makefile b/test/Makefile
index b8c27045b5..79c98a49fe 100644
--- a/test/Makefile
+++ b/test/Makefile
@@ -552,6 +552,12 @@ test.tica:
 test.enedecomp:
 	@-cd Test_EneDecomp && ./RunTest.sh $(OPT)
 
+test.addatom:
+	@-cd Test_AddAtom && ./RunTest.sh $(OPT)
+
+test.minmaxdist:
+	@-cd Test_MinMaxDist && ./RunTest.sh $(OPT)
+
 # Every test target should go here.
 COMPLETETESTS=test.general \
               test.strip \
@@ -726,7 +732,9 @@ COMPLETETESTS=test.general \
               test.refinetrajectory \
               test.readamberff \
               test.tica \
-              test.enedecomp
+              test.enedecomp \
+              test.addatom \
+              test.minmaxdist
 
 test.all:
 	$(MAKE) test.complete summary

From 50297880a47fddcef0c30fec29ec87192517429c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 14 Mar 2025 11:31:00 -0400
Subject: [PATCH 0931/1492] Support the leap addPath command

---
 src/DataIO_LeapRC.cpp | 33 ++++++++++++++++++++++++++++++---
 src/DataIO_LeapRC.h   |  2 ++
 2 files changed, 32 insertions(+), 3 deletions(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index f47c936829..3722497c12 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -149,6 +149,12 @@ std::string DataIO_LeapRC::find_path(std::string const& filename,
 const
 {
   if (File::Exists( filename )) return filename;
+  // Check searchPaths_ next
+  for (Sarray::const_iterator it = searchPaths_.begin(); it != searchPaths_.end(); ++it) {
+    std::string spath = *it + "/" + filename;
+    if (File::Exists( spath )) return spath;
+  }
+  // Check AMBERHOME last
   if (amberhome_.empty()) {
     mprinterr("Error: '%s' not found.\n", filename.c_str());
     return filename;
@@ -159,6 +165,13 @@ const
   return amberpath;
 }
 
+/** LEaP addPath command. */
+int DataIO_LeapRC::AddPath(std::string const& path) {
+  mprintf("%s added to file search path.\n", path.c_str());
+  searchPaths_.push_back( path );
+  return 0;
+}
+
 /** LEaP loadAmberParams command. */
 int DataIO_LeapRC::LoadAmberParams(std::string const& filename, DataSetList& dsl,
                                    std::string const& dsname,
@@ -563,7 +576,12 @@ int DataIO_LeapRC::LoadMol2(ArgList const& argIn, DataSetList& dsl) const {
   }
   DataIO_Coords coordsIn;
   coordsIn.SetDebug( debug_ );
-  if (coordsIn.ReadData( args[2], dsl, args[0] )) {
+  std::string mol2path = find_path( args[2], "" );
+  if (mol2path.empty()) {
+    mprinterr("Error: Could not find mol2 %s\n", args[2].c_str());
+    return 1;
+  }
+  if (coordsIn.ReadData( mol2path, dsl, args[0] )) {
     mprinterr("Error: Could not load structure from '%s' into '%s'\n",
               args[2].c_str(), args[0].c_str());
     return 1;
@@ -584,7 +602,12 @@ int DataIO_LeapRC::LoadPDB(ArgList const& argIn, DataSetList& dsl) const {
   DataIO_Coords coordsIn;
   coordsIn.SetDebug( debug_ );
   DataSetList tmpdsl;
-  if (coordsIn.ReadData( args[2], tmpdsl, args[0] )) {
+  std::string pdbpath = find_path( args[2], "" );
+  if (pdbpath.empty()) {
+    mprinterr("Error: Could not find PDB %s\n", args[2].c_str());
+    return 1;
+  }
+  if (coordsIn.ReadData( pdbpath, tmpdsl, args[0] )) {
     mprinterr("Error: Could not load structure from '%s' into '%s'\n",
               args[2].c_str(), args[0].c_str());
     return 1;
@@ -736,7 +759,7 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
   mprintf("\tReading LEaP input from '%s'\n", fname.base());
   enum LeapCmdType { LOADAMBERPARAMS = 0, LOADOFF, LOADAMBERPREP, ADDATOMTYPES,
                      ADDPDBRESMAP, ADDPDBATOMMAP, LOADMOL2, LOADPDB, SOURCE,
-                     QUIT, SAVEAMBERPARM, UNKNOWN_CMD };
+                     QUIT, SAVEAMBERPARM, ADDPATH, UNKNOWN_CMD };
   //DataSetList paramDSL;
   //DataSetList unitDSL;
   //NHarrayType atomHybridizations;
@@ -775,6 +798,7 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
         else if (argStr == "source"         ) { pos = arg; leapcmd = SOURCE; break; }
         else if (argStr == "quit"           ) { pos = arg; leapcmd = QUIT; break; }
         else if (argStr == "saveamberparm"  ) { pos = arg; leapcmd = SAVEAMBERPARM; break; }
+        else if (argStr == "addpath"        ) { pos = arg; leapcmd = ADDPATH; break; }
       }
 
       err = 0;
@@ -838,6 +862,9 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
         // Do not read any more.
         mprintf("\tEncountered 'quit' in leaprc file, not reading any more.\n");
         break;
+      } else if (leapcmd == ADDPATH) {
+        // Add path to directories to search for files specified by other commands.
+        err = AddPath( line.GetStringKey(line[pos]) );
       } else {
         // Unrecognized so far. See if this is a unit alias (interpret as 'alias = unit')
         if (has_equals) {
diff --git a/src/DataIO_LeapRC.h b/src/DataIO_LeapRC.h
index e0d8eb7c1f..5190a2731d 100644
--- a/src/DataIO_LeapRC.h
+++ b/src/DataIO_LeapRC.h
@@ -56,6 +56,7 @@ class DataIO_LeapRC : public DataIO {
     };
     typedef std::vector<PdbResMapType> PdbResMapArray;
 
+    int AddPath(std::string const&);
     int LoadAmberParams(std::string const&, DataSetList&, std::string const&, AtypeEltHybridPairMap const&) const;
     int LoadOFF(std::string const&, DataSetList&, std::string const&, DSarray&) const;
     int LoadAmberPrep(std::string const&, DataSetList&, std::string const&, DSarray&) const;
@@ -83,6 +84,7 @@ class DataIO_LeapRC : public DataIO {
     AtypeEltHybridPairMap atomHybridizations_; ///< Store hybridizations for atom types
     PdbResMapArray pdbResMap_; ///< Hold PDB residue name map
     DSarray units_;            ///< Hold COORDS sets which have been added as units
+    Sarray searchPaths_;
     static Sarray paramFiles_; ///< Track amber FF param files loaded from leaprc files
     static Sarray libFiles_;   ///< Track amber library/prep files loaded from leaprc files
 };

From 6cc84a22a4216d3cb6889526433625ea9c805a5f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 14 Mar 2025 12:02:55 -0400
Subject: [PATCH 0932/1492] Add timer for getting templates and parameters

---
 src/Exec_Build.cpp | 17 ++++++++++-------
 src/Exec_Build.h   |  1 +
 2 files changed, 11 insertions(+), 7 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 06a1cf7863..a4ea9d7ac3 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -822,6 +822,7 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, in
   mprintf("\tGB radii set: %s\n", Cpptraj::Parm::GbTypeStr(gbradii).c_str());
 
   // Get templates and parameter sets.
+  t_get_templates_.Start();
   Cpptraj::Structure::Creator creator( debug_ );
   if (creator.InitCreator(argIn, DSL, debug_)) {
     return CpptrajState::ERR;
@@ -833,6 +834,7 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, in
     mprinterr("Error: No parameter sets.\n");
     return CpptrajState::ERR;
   }
+  t_get_templates_.Stop();
 
   // All residues start unknown
   Cpptraj::Structure::ResStatArray resStat( topIn.Nres() );
@@ -1020,13 +1022,14 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, in
   t_total_.Stop();
 
   t_total_.WriteTiming(1, "Build timing:");
-  t_hisDetect_.WriteTiming(2, "Histidine detection :", t_total_.Total());
-  t_clean_.WriteTiming    (2, "Structure clean     :", t_total_.Total());
-  t_disulfide_.WriteTiming(2, "Disulfide detection :", t_total_.Total());
-  t_sugar_.WriteTiming    (2, "Sugar preparation   :", t_total_.Total());
-  t_fill_.WriteTiming     (2, "Fill missing atoms  :", t_total_.Total());
-  t_assign_.WriteTiming   (2, "Param./Top. gen.    :", t_total_.Total());
-  t_check_.WriteTiming    (2, "Structure check     :", t_total_.Total());
+  t_hisDetect_.WriteTiming    (2, "Histidine detection :", t_total_.Total());
+  t_clean_.WriteTiming        (2, "Structure clean     :", t_total_.Total());
+  t_get_templates_.WriteTiming(2, "Get templates/parms :", t_total_.Total());
+  t_disulfide_.WriteTiming    (2, "Disulfide detection :", t_total_.Total());
+  t_sugar_.WriteTiming        (2, "Sugar preparation   :", t_total_.Total());
+  t_fill_.WriteTiming         (2, "Fill missing atoms  :", t_total_.Total());
+  t_assign_.WriteTiming       (2, "Param./Top. gen.    :", t_total_.Total());
+  t_check_.WriteTiming        (2, "Structure check     :", t_total_.Total());
 
   return ret;
 }
diff --git a/src/Exec_Build.h b/src/Exec_Build.h
index 647f2bd41d..2bbd0c64ff 100644
--- a/src/Exec_Build.h
+++ b/src/Exec_Build.h
@@ -42,6 +42,7 @@ class Exec_Build : public Exec {
     Timer t_total_;
     Timer t_hisDetect_;
     Timer t_clean_;
+    Timer t_get_templates_;
     Timer t_disulfide_;
     Timer t_sugar_;
     Timer t_fill_;

From 5bcad2e1432a277f5f888f813d4c7742349084b9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 14 Mar 2025 12:11:51 -0400
Subject: [PATCH 0933/1492] Add more timing info

---
 src/Exec_Build.cpp        |  3 +++
 src/Structure/Creator.cpp | 14 +++++++++++++-
 src/Structure/Creator.h   |  6 ++++++
 3 files changed, 22 insertions(+), 1 deletion(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index a4ea9d7ac3..451d822cf5 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -835,6 +835,8 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, in
     return CpptrajState::ERR;
   }
   t_get_templates_.Stop();
+  // FIXME hide behind ifdef?
+  creator.TimingInfo(t_get_templates_.Total(), 2);
 
   // All residues start unknown
   Cpptraj::Structure::ResStatArray resStat( topIn.Nres() );
@@ -1025,6 +1027,7 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, in
   t_hisDetect_.WriteTiming    (2, "Histidine detection :", t_total_.Total());
   t_clean_.WriteTiming        (2, "Structure clean     :", t_total_.Total());
   t_get_templates_.WriteTiming(2, "Get templates/parms :", t_total_.Total());
+  
   t_disulfide_.WriteTiming    (2, "Disulfide detection :", t_total_.Total());
   t_sugar_.WriteTiming        (2, "Sugar preparation   :", t_total_.Total());
   t_fill_.WriteTiming         (2, "Fill missing atoms  :", t_total_.Total());
diff --git a/src/Structure/Creator.cpp b/src/Structure/Creator.cpp
index 9cbd2836a5..fa37c8d650 100644
--- a/src/Structure/Creator.cpp
+++ b/src/Structure/Creator.cpp
@@ -39,6 +39,7 @@ const char* Creator::other_keywords_ = "atomscandir {f|b}";
 /** Initialize */
 int Creator::InitCreator(ArgList& argIn, DataSetList const& DSL, int debugIn)
 {
+  t_total_.Start();
   debug_ = debugIn;
 
   // Atom scan direction
@@ -54,8 +55,12 @@ int Creator::InitCreator(ArgList& argIn, DataSetList const& DSL, int debugIn)
     }
   }
 
+  t_get_templates_.Start();
   if (getTemplates(argIn, DSL)) return 1;
+  t_get_templates_.Stop();
+  t_get_parameters_.Start();
   if (getParameterSets(argIn, DSL)) return 1;
+  t_get_parameters_.Stop();
   UpdateTemplateElements();
 
   // Get any atom name maps
@@ -67,10 +72,17 @@ int Creator::InitCreator(ArgList& argIn, DataSetList const& DSL, int debugIn)
     if (debug_ > 0)
       mprintf("DEBUG: Atom name map: %s\n", NameMaps_.back()->legend());
   }
-
+  t_total_.Stop();
   return 0;
 }
 
+/** Write timing info to stdout. */
+void Creator::TimingInfo(double total, int indent) const {
+  t_total_.WriteTiming(indent, "Get templates/parms:", total);
+  t_get_templates_.WriteTiming (indent+1, "Get templates  :", t_total_.Total());
+  t_get_parameters_.WriteTiming(indent+1, "Get parameters :", t_total_.Total());
+}
+
 /** Update template atom elements from atom types in parameter set. */
 void Creator::UpdateTemplateElements() const {
   if (mainParmSet_ == 0) return;
diff --git a/src/Structure/Creator.h b/src/Structure/Creator.h
index b6d83ca7ba..7bf365c8eb 100644
--- a/src/Structure/Creator.h
+++ b/src/Structure/Creator.h
@@ -3,6 +3,7 @@
 #include <vector>
 #include <string>
 #include "StructureEnum.h" // TerminalType
+#include "../Timer.h"
 class ArgList;
 class DataSet_Coords;
 class DataSet_NameMap;
@@ -30,6 +31,8 @@ class Creator {
     static const char* other_keywords_;
     /// Initialize the Creator
     int InitCreator(ArgList&, DataSetList const&, int);
+    /// Write timing info to stdout
+    void TimingInfo(double, int) const;
 
     /// \return True if a parameter set is defined
     bool HasMainParmSet() const { return (mainParmSet_ != 0); }
@@ -56,6 +59,9 @@ class Creator {
     Narray NameMaps_;                 ///< Hold atom name maps.
     int debug_;                       ///< Debug level
     bool free_parmset_mem_;           ///< True if main parm set is combined and should be freed
+    Timer t_total_;
+    Timer t_get_templates_;
+    Timer t_get_parameters_;
 };
 }
 }

From 7cf075ce5f6bcc8ae136efc7dfbe31068b9c98b6 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 18 Aug 2025 13:34:45 -0400
Subject: [PATCH 0934/1492] Put processing of pdb resmap after leaprc is closed
 since sometimes lib load occurs after the pdb resmap is read.

---
 src/DataIO_LeapRC.cpp | 37 ++++++++++++++++++++++++++++++-------
 1 file changed, 30 insertions(+), 7 deletions(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 3722497c12..f46cde7c52 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -814,12 +814,12 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
         err = AddAtomTypes(atomHybridizations_, infile);
       else if (leapcmd == ADDPDBRESMAP) {
         err = AddPdbResMap(infile, pdbResMap_);
-        if (err == 0) {
+        //if (err == 0) {
           // Update units with pdb residue map info
           //for (DataSetList::const_iterator ds = unitDSL.begin(); ds != paramDSL.end(); ++ds)
           //{
           //  if ( (*ds)->Group() == DataSet::COORDINATES ) {
-          for (PdbResMapArray::const_iterator it = pdbResMap_.begin();
+/*          for (PdbResMapArray::const_iterator it = pdbResMap_.begin();
                                               it != pdbResMap_.end(); ++it)
           {
             // Find the unit in unit DSL
@@ -827,7 +827,7 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
             if (ds != 0 && ds->Group() == DataSet::COORDINATES) {
               addPdbResMapToUnit( static_cast<DataSet_Coords*>(ds), *it );
             }
-            /*if (ds == 0) {
+            *if (ds == 0) {
               mprintf("Warning: Unit '%s' was not found among loaded units.\n", it->unitName_.c_str());
             } else {
               DataSet_Coords& crd = static_cast<DataSet_Coords&>( *ds );
@@ -838,9 +838,9 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
                 resid.Ainfo();
                 mprintf("\n");
               }
-            }*/
-          }
-        }
+            }*
+          }*/
+        //}
       } else if (leapcmd == ADDPDBATOMMAP)
         err = AddPdbAtomMap(dsname, dsl, infile);
       else if (leapcmd == LOADMOL2)
@@ -918,7 +918,30 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
   }
   infile.CloseFile();
 
-
+  // Do any PDB residue mapping
+  if (!pdbResMap_.empty()) {
+    for (PdbResMapArray::const_iterator it = pdbResMap_.begin();
+                                        it != pdbResMap_.end(); ++it)
+    {
+      // Find the unit in unit DSL
+      DataSet* ds = dsl.CheckForSet( MetaData(dsname, it->unitName_) );
+      if (ds != 0 && ds->Group() == DataSet::COORDINATES) {
+        addPdbResMapToUnit( static_cast<DataSet_Coords*>(ds), *it );
+      }
+      /*if (ds == 0) {
+        mprintf("Warning: Unit '%s' was not found among loaded units.\n", it->unitName_.c_str());
+      } else {
+        DataSet_Coords& crd = static_cast<DataSet_Coords&>( *ds );
+        AssociatedData_ResId resid( it->pdbName_, it->termType_ );
+        crd.AssociateData( &resid );
+        if (debug_ > 0) {
+          mprintf("DEBUG: Found unit %s", crd.legend());
+          resid.Ainfo();
+          mprintf("\n");
+        }
+      }*/
+    }
+  }
 
   // Add data sets to the main data set list
   //if (addSetsToList(dsl, paramDSL)) return err+1;

From 4441dcc4af1dba31acef2d9031ea1c064d651c6f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 26 Aug 2025 14:16:06 -0400
Subject: [PATCH 0935/1492] When doing head/tail connectivity, ignore head
 atoms of begin terminal and tail atoms of end terminal residues

---
 src/Exec_Build.cpp | 37 ++++++++++++++++++++++++++-----------
 1 file changed, 26 insertions(+), 11 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 451d822cf5..2563519def 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -124,8 +124,10 @@ const
   // Array of head/tail connect atoms for each residue
   Iarray resHeadAtoms;
   Iarray resTailAtoms;
+  std::vector<Cpptraj::Structure::TerminalType> ResTermTypes;
   resHeadAtoms.reserve( topIn.Nres() );
   resTailAtoms.reserve( topIn.Nres() );
+  ResTermTypes.reserve( topIn.Nres() );
   // Array of templates for each residue
   std::vector<DataSet_Coords*> ResTemplates;
   ResTemplates.reserve( topIn.Nres() );
@@ -162,6 +164,7 @@ const
     }
     if (debug_ > 0)
       mprintf("DEBUG: Residue type: %s terminal\n", Cpptraj::Structure::terminalStr(resTermType));
+    ResTermTypes.push_back( resTermType );
     // Identify a template based on the residue name.
     DataSet_Coords* resTemplate = creator.IdTemplateFromResname(currentRes.Name(), resTermType);
     if (resTemplate == 0) {
@@ -416,7 +419,7 @@ const
   if (debug_ > 0) {
     for (unsigned int idx = 0; idx != ResTemplates.size(); idx++) {
       if (ResTemplates[idx] != 0) {
-        mprintf("DEBUG: Template %s", ResTemplates[idx]->legend());
+        mprintf("DEBUG: Template %s (%s)", ResTemplates[idx]->legend(), Cpptraj::Structure::terminalStr(ResTermTypes[idx]));
         if (resHeadAtoms[idx] > -1) mprintf(" head %s", topOut.AtomMaskName(resHeadAtoms[idx]).c_str());
         if (resTailAtoms[idx] > -1) mprintf(" tail %s", topOut.AtomMaskName(resTailAtoms[idx]).c_str());
         mprintf("\n");
@@ -432,17 +435,29 @@ const
   for (int ires = 1; ires < topOut.Nres(); ires++) {
     int pres = ires - 1;
     if (resHeadAtoms[ires] != -1) {
-      if (resTailAtoms[pres] != -1) {
+      if (ResTermTypes[ires] == Cpptraj::Structure::BEG_TERMINAL) {
         if (debug_ > 0)
-          mprintf("DEBUG: Connecting HEAD atom %s to tail atom %s\n",
-                  topOut.AtomMaskName(resHeadAtoms[ires]).c_str(),
-                  topOut.AtomMaskName(resTailAtoms[pres]).c_str());
-        resBondingAtoms[ires].push_back( Ipair(resHeadAtoms[ires], resTailAtoms[pres]) );
-        resBondingAtoms[pres].push_back( Ipair(resTailAtoms[pres], resHeadAtoms[ires]) );
-        resHeadAtoms[ires] = -1;
-        resTailAtoms[pres] = -1;
-        ResidueConnections[ires].push_back( pres );
-        ResidueConnections[pres].push_back( ires );
+          mprintf("DEBUG: Res %s is begin terminal, ignoring head atom.\n",
+                  topOut.TruncResNameOnumId(ires).c_str());
+      } else {
+        if (resTailAtoms[pres] != -1) {
+          if (ResTermTypes[pres] == Cpptraj::Structure::END_TERMINAL) {
+            if (debug_ > 0)
+              mprintf("DEBUG: Res %s is end terminal, ignoring tail atom.\n",
+                      topOut.TruncResNameOnumId(pres).c_str());
+          } else {
+            if (debug_ > 0)
+              mprintf("DEBUG: Connecting HEAD atom %s to tail atom %s\n",
+                      topOut.AtomMaskName(resHeadAtoms[ires]).c_str(),
+                      topOut.AtomMaskName(resTailAtoms[pres]).c_str());
+            resBondingAtoms[ires].push_back( Ipair(resHeadAtoms[ires], resTailAtoms[pres]) );
+            resBondingAtoms[pres].push_back( Ipair(resTailAtoms[pres], resHeadAtoms[ires]) );
+            resHeadAtoms[ires] = -1;
+            resTailAtoms[pres] = -1;
+            ResidueConnections[ires].push_back( pres );
+            ResidueConnections[pres].push_back( ires );
+          }
+        }
       }
     }
   }

From f5f677f0126f80132ef8199b455956e5b2ee282a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 26 Aug 2025 15:36:05 -0400
Subject: [PATCH 0936/1492] Add option for adding non-template bonds or not and
 turn it off by default. Sometimes the PDB reader guesses a bad bond and this
 causes the build to diverge from leap behavior. Will have to refactor in the
 sugar/disulfide build stuff to after the templates.

---
 src/Exec_Build.cpp | 25 ++++++++++++++++++-------
 src/Exec_Build.h   |  1 +
 2 files changed, 19 insertions(+), 7 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 2563519def..056cedd879 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -21,6 +21,7 @@ Exec_Build::Exec_Build() :
   debug_(0),
   check_box_natom_(5000), // TODO make user specifiable
   check_structure_(true),
+  addNonTemplateBonds_(false),
   sugarBuilder_(0)
 {}
 
@@ -505,13 +506,19 @@ const
                 topOut.AtomMaskName(at0).c_str(),
                 topOut.AtomMaskName(at1).c_str());
       } else {
-        mprintf("\tAdding non-template bond %s - %s\n",
-                topOut.AtomMaskName(at0).c_str(),
-                topOut.AtomMaskName(at1).c_str());
-        resBondingAtoms[ra0.first].push_back( Ipair(at0, at1) );
-        resBondingAtoms[ra1.first].push_back( Ipair(at1, at0) );
-        ResidueConnections[ra0.first].push_back( ra1.first );
-        ResidueConnections[ra1.first].push_back( ra0.first );
+        if (addNonTemplateBonds_) { // FIXME need to change this or move the sugar/disulfide stuff to after
+          mprintf("\tAdding non-template bond %s - %s\n",
+                  topOut.AtomMaskName(at0).c_str(),
+                  topOut.AtomMaskName(at1).c_str());
+          resBondingAtoms[ra0.first].push_back( Ipair(at0, at1) );
+          resBondingAtoms[ra1.first].push_back( Ipair(at1, at0) );
+          ResidueConnections[ra0.first].push_back( ra1.first );
+          ResidueConnections[ra1.first].push_back( ra0.first );
+        } else {
+          mprintf("Warning: Detected non-template bond %s - %s; not adding it.\n",
+                  topOut.AtomMaskName(at0).c_str(),
+                  topOut.AtomMaskName(at1).c_str());
+        }
       }
     } //else
       //mprintf("DEBUG: Detected bond %s - %s already present.\n",
@@ -755,6 +762,10 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, in
   debug_ = debugIn;
   int verbose = argIn.getKeyInt("verbose", 0);
   std::string title = argIn.GetStringKey("title");
+  if (addNonTemplateBonds_)
+    mprintf("\tNon-template bonds will be added if detected.\n");
+  else
+    mprintf("\tOnly bonding according to residue templates.\n");
 
   // TODO make it so this can be const (cant bc GetFrame)
   DataSet_Coords& coords = static_cast<DataSet_Coords&>( *((DataSet_Coords*)inCrdPtr) );
diff --git a/src/Exec_Build.h b/src/Exec_Build.h
index 2bbd0c64ff..b7c54e2f7b 100644
--- a/src/Exec_Build.h
+++ b/src/Exec_Build.h
@@ -37,6 +37,7 @@ class Exec_Build : public Exec {
     int debug_;
     int check_box_natom_;  ///< Systems larger than this will have box added so PL check can be used
     bool check_structure_; ///< If true check the resulting structure
+    bool addNonTemplateBonds_; ///< If true, add bonds that were not found in templates.
     Cpptraj::Structure::SugarBuilder* sugarBuilder_;
 
     Timer t_total_;

From ca872deefd4eb3a495be02ae75ec6aa9f770b7f6 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 4 Sep 2025 16:04:10 -0400
Subject: [PATCH 0937/1492] Ensure the bonds detected by the disulfide and
 sugar prep are added to the final topology

---
 src/Exec_Build.cpp             | 13 ++++++++++---
 src/Exec_PrepareForLeap.cpp    |  5 ++++-
 src/Structure/SugarBuilder.cpp |  9 ++++++---
 src/Structure/SugarBuilder.h   |  4 ++--
 4 files changed, 22 insertions(+), 9 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 056cedd879..25aff7b412 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -866,6 +866,7 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, in
 
   // All residues start unknown
   Cpptraj::Structure::ResStatArray resStat( topIn.Nres() );
+  std::vector<BondType> LeapBonds;
 
   // Disulfide search
   t_disulfide_.Start();
@@ -875,7 +876,6 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, in
       mprinterr("Error: Could not init disulfide search.\n");
       return CpptrajState::ERR;
     }
-    std::vector<BondType> LeapBonds;
     if (disulfide.SearchForDisulfides( resStat, topIn, frameIn, LeapBonds ))
     {
       mprinterr("Error: Disulfide search failed.\n");
@@ -925,12 +925,12 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, in
     // This is done before any identification takes place since we want
     // to identify based on the most up-to-date topology.
     if (sugarBuilder_->FixSugarsStructure(topIn, frameIn,
-                                          c1bondsearch, splitres, solventResName))
+                                          c1bondsearch, splitres, solventResName,
+                                          LeapBonds))
     {
       mprinterr("Error: Sugar structure modification failed.\n");
       return CpptrajState::ERR;
     }
-    std::vector<BondType> LeapBonds;
     if (sugarBuilder_->PrepareSugars(true, resStat, topIn, frameIn, LeapBonds))
     {
       mprinterr("Error: Sugar preparation failed.\n");
@@ -954,6 +954,13 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, in
   }
   t_fill_.Stop();
 
+  // Add the disulfide/sugar bonds
+  for (std::vector<BondType>::const_iterator bnd = LeapBonds.begin();
+                                             bnd != LeapBonds.end(); ++bnd)
+  {
+    topOut.AddBond( bnd->A1(), bnd->A2() );
+  }
+
   // Assign parameters. This will create the bond/angle/dihedral/improper
   // arrays as well.
   t_assign_.Start();
diff --git a/src/Exec_PrepareForLeap.cpp b/src/Exec_PrepareForLeap.cpp
index 6329837b0f..3154ecd28c 100644
--- a/src/Exec_PrepareForLeap.cpp
+++ b/src/Exec_PrepareForLeap.cpp
@@ -763,8 +763,11 @@ Exec::RetType Exec_PrepareForLeap::Execute(CpptrajState& State, ArgList& argIn)
     // adding missing bonds to C1 atoms.
     // This is done before any identification takes place since we want
     // to identify based on the most up-to-date topology.
+    // NOTE: The c1 bonds will remain, so put them in a separate array
+    std::vector<BondType> C1Bonds;
     if (sugarBuilder.FixSugarsStructure(topIn, frameIn,
-                                        c1bondsearch, splitres, solventResName_))
+                                        c1bondsearch, splitres, solventResName_,
+                                        C1Bonds))
     {
       mprinterr("Error: Sugar structure modification failed.\n");
       return CpptrajState::ERR;
diff --git a/src/Structure/SugarBuilder.cpp b/src/Structure/SugarBuilder.cpp
index fb63d9184d..fc5f6335bd 100644
--- a/src/Structure/SugarBuilder.cpp
+++ b/src/Structure/SugarBuilder.cpp
@@ -1709,7 +1709,8 @@ void SugarBuilder::CacheResidueCenters(Topology const& topIn, Frame const& frame
 /** Attempt to find any missing linkages to the anomeric carbon in sugar. */
 int SugarBuilder::FindSugarC1Linkages(int rnum1, int c_beg,
                                       Topology& topIn, Frame const& frameIn,
-                                      NameType const& solventResName)
+                                      NameType const& solventResName,
+                                      std::vector<BondType>& LeapBonds)
 const
 {
   //Residue const& res1 = topIn.SetRes(rnum1);
@@ -1799,6 +1800,7 @@ const
     mprintf("\t  Adding bond between %s and %s\n",
             topIn.ResNameNumAtomNameNum(c_beg).c_str(),
             topIn.ResNameNumAtomNameNum(closest_at).c_str());
+    LeapBonds.push_back( BondType(c_beg, closest_at, -1) );
     topIn.AddBond(c_beg, closest_at);
   }
   return 0;
@@ -1807,7 +1809,8 @@ const
 /** Try to fix issues with sugar structure before trying to identify. */
 int SugarBuilder::FixSugarsStructure(Topology& topIn, Frame& frameIn,
                                      bool c1bondsearch, bool splitres,
-                                     NameType const& solventResName) 
+                                     NameType const& solventResName,
+                                     std::vector<BondType>& LeapBonds)
 {
   // Set up an AtomMap for this residue to help determine stereocenters.
   // This is required by the IdSugarRing() function.
@@ -1869,7 +1872,7 @@ int SugarBuilder::FixSugarsStructure(Topology& topIn, Frame& frameIn,
       if (sugar->NotSet()) continue;
       int anomericAtom = sugar->AnomericAtom();
       int rnum = sugar->ResNum(topIn);
-      if (FindSugarC1Linkages(rnum, anomericAtom, topIn, frameIn, solventResName)) {
+      if (FindSugarC1Linkages(rnum, anomericAtom, topIn, frameIn, solventResName, LeapBonds)) {
         mprinterr("Error: Search for bonds to anomeric carbon '%s' failed.\n",
                   topIn.AtomMaskName(anomericAtom).c_str());
         return 1;
diff --git a/src/Structure/SugarBuilder.h b/src/Structure/SugarBuilder.h
index 4ce1c531c2..c2de4208b3 100644
--- a/src/Structure/SugarBuilder.h
+++ b/src/Structure/SugarBuilder.h
@@ -23,7 +23,7 @@ class SugarBuilder {
     bool IsRecognizedPdbSugar(NameType const&) const;
     /// ID sugar rings, find missing C1 links, split off functional groups
     int FixSugarsStructure(Topology&, Frame&,
-                           bool, bool, NameType const&);
+                           bool, bool, NameType const&, std::vector<BondType>&);
     /// Identify sugars, do renaming, remove bonds, generate leap input
     int PrepareSugars(bool, ResStatArray&, Topology&, Frame const&, std::vector<BondType>&);
     /// Set each sugar as a terminal residue
@@ -88,7 +88,7 @@ class SugarBuilder {
     /// Cache residue centers for determining linkages
     void CacheResidueCenters(Topology const&, Frame const&);
     /// Try to find missing linkages to anomeric carbon in sugar.
-    int FindSugarC1Linkages(int, int, Topology&, Frame const&, NameType const&) const;
+    int FindSugarC1Linkages(int, int, Topology&, Frame const&, NameType const&, std::vector<BondType>&) const;
     
 
 

From d8b59c7843d5dffcfe7d022331bcb5fddda35c72 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 4 Sep 2025 17:27:09 -0400
Subject: [PATCH 0938/1492] Add note

---
 src/Exec_Build.cpp | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 25aff7b412..2660e6cce0 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -234,6 +234,7 @@ const
 
   // For existing inter-residue bonding, use residue # and atom name since
   // atom numbering may change if atoms are added from templates.
+  // TODO make this a class var so disulfide/sugar prep can use it.
   typedef std::pair<int,NameType> ResAtPair;
   typedef std::vector<ResAtPair> ResAtArray;
   ResAtArray detectedInterResBonds;

From 3abe566f94906b75214853b062ba6d644c2e7f5b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 5 Sep 2025 09:57:07 -0400
Subject: [PATCH 0939/1492] Correctly add disulfide/sugar bonds to new
 topology; original atom indices can change after atoms are filled in from
 templates.

---
 src/Exec_Build.cpp | 42 ++++++++++++++++++++++++++++++++++++++----
 src/Exec_Build.h   |  2 ++
 2 files changed, 40 insertions(+), 4 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 2660e6cce0..cf81cf7b88 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -707,6 +707,41 @@ const
   return 0;
 }
 
+/** Given an original topology and bonded atom indices, find those atoms
+  * in another topology and ensure they are bonded.
+  */
+int Exec_Build::transfer_bonds(Topology& topOut, Topology const& topIn,
+                               std::vector<BondType> const& bondsIn)
+const
+{
+  for (std::vector<BondType>::const_iterator bnd = bondsIn.begin();
+                                             bnd != bondsIn.end(); ++bnd)
+  {
+    // Get the original atom name and residue number
+    Atom const& original_A1 = topIn[bnd->A1()];
+    Atom const& original_A2 = topIn[bnd->A2()];
+    mprintf("DEBUG: Original bond atoms %i (%s) %i (%s)\n",
+            bnd->A1()+1, topIn.AtomMaskName(bnd->A1()).c_str(),
+            bnd->A2()+1, topIn.AtomMaskName(bnd->A2()).c_str());
+    // Find the atoms in the new topology
+    int a1 = topOut.FindAtomInResidue( original_A1.ResNum(), original_A1.Name() );
+    if (a1 < 0) {
+      mprinterr("Error: Could not find atom %i (%s) in new topology.\n",
+                bnd->A1()+1, topIn.AtomMaskName(bnd->A1()).c_str());
+      return 1;
+    }
+    int a2 = topOut.FindAtomInResidue( original_A2.ResNum(), original_A2.Name() );
+    if (a2 < 0) {
+      mprinterr("Error: Could not find atom %i (%s) in new topology.\n",
+                bnd->A2()+1, topIn.AtomMaskName(bnd->A2()).c_str());
+      return 1;
+    }
+    // Add the bond to the new topology
+    topOut.AddBond( a1, a2 );
+  }
+  return 0;
+}
+
 // -----------------------------------------------------------------------------
 // Exec_Build::Help()
 void Exec_Build::Help() const
@@ -956,10 +991,9 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, in
   t_fill_.Stop();
 
   // Add the disulfide/sugar bonds
-  for (std::vector<BondType>::const_iterator bnd = LeapBonds.begin();
-                                             bnd != LeapBonds.end(); ++bnd)
-  {
-    topOut.AddBond( bnd->A1(), bnd->A2() );
+  if (transfer_bonds( topOut, topIn, LeapBonds )) {
+    mprinterr("Error: Adding disulfide/sugar bonds failed.\n");
+    return CpptrajState::ERR;
   }
 
   // Assign parameters. This will create the bond/angle/dihedral/improper
diff --git a/src/Exec_Build.h b/src/Exec_Build.h
index b7c54e2f7b..7775fd6d5a 100644
--- a/src/Exec_Build.h
+++ b/src/Exec_Build.h
@@ -33,6 +33,8 @@ class Exec_Build : public Exec {
     int FillAtomsWithTemplates(Topology&, Frame&, Topology const&, Frame const&, Cpptraj::Structure::Creator const&) const;
     /// Map atoms in topology to template
     static std::vector<int> MapAtomsToTemplate(Topology const&, int, DataSet_Coords*, Cpptraj::Structure::Creator const&, std::vector<NameType>&, int&);
+    /// Transfer bonds from old topology to new topology
+    int transfer_bonds(Topology&, Topology const&, std::vector<BondType> const&) const;
 
     int debug_;
     int check_box_natom_;  ///< Systems larger than this will have box added so PL check can be used

From 17f016e7bd22be2264a5b5114f9a8983aa3f7120 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 5 Sep 2025 14:27:35 -0400
Subject: [PATCH 0940/1492] For '=', look for units in other sets as well.

---
 src/DataIO_LeapRC.cpp | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index f46cde7c52..f612ea9a88 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -873,6 +873,14 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
               mprintf("DEBUG: %s = %s\n", line[0].c_str(), line[1].c_str());
             // Find the unit to make a copy of
             DataSet* ds0 = dsl.CheckForSet( MetaData(dsname, line[1]) );
+            if (ds0 == 0) {
+              // Its possible the unit in question is loaded by a previous command.
+              ds0 = dsl.GetDataSet( "*[" + line[1] + "]" );
+              if (ds0 != 0) {
+                mprintf("Info: Using unit '%s' from previously loaded set '%s'\n",
+                        line[1].c_str(), ds0->Meta().Name().c_str());
+              }
+            }
             if (ds0 == 0) {
               mprinterr("Error: Could not find unit '%s' to copy to '%s'\n", line[1].c_str(), line[0].c_str());
               return 1;

From ee7cd3e12bfed8d61660cdac13afa83ee383f918 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 5 Sep 2025 15:08:45 -0400
Subject: [PATCH 0941/1492] To match leap behavior, when there are multiple
 templates loaded, use the last one loaded

---
 src/Structure/Creator.cpp | 35 +++++++++++++++++++++++++----------
 1 file changed, 25 insertions(+), 10 deletions(-)

diff --git a/src/Structure/Creator.cpp b/src/Structure/Creator.cpp
index fa37c8d650..d5e43c9fec 100644
--- a/src/Structure/Creator.cpp
+++ b/src/Structure/Creator.cpp
@@ -132,7 +132,8 @@ DataSet_Coords* Creator::IdTemplateFromResname(NameType const& rname,
                                               TerminalType termType)
 const
 {
-  DataSet_Coords* out = 0;
+  std::vector<DataSet_Coords*> Out;
+  //DataSet_Coords* out = 0;
   if (termType != Cpptraj::Structure::NON_TERMINAL) {
     // Looking for a terminal residue. Need to get sets with AssociatedData_ResId
     for (Carray::const_iterator it = Templates_.begin(); it != Templates_.end(); ++it) {
@@ -140,13 +141,15 @@ const
       if (ad != 0) {
         AssociatedData_ResId const& resid = static_cast<AssociatedData_ResId const&>( *ad );
         if (rname == resid.ResName() && termType == resid.TermType()) {
-          out = *it;
-          break;
+          //out = *it;
+          //break;
+          Out.push_back( *it );
         }
       }
     }
   }
-  if (out == 0) {
+  if (Out.empty()) {
+  //if (out == 0) {
     // Terminal residue with alias not found or non-terminal residue.
     if (debug_ > 0 && termType != Cpptraj::Structure::NON_TERMINAL)
       mprintf("DEBUG: No aliased terminal residue found for '%s'\n", *rname);
@@ -154,25 +157,37 @@ const
     for (Carray::const_iterator it = Templates_.begin(); it != Templates_.end(); ++it) {
       if ( (*it)->Meta().Aspect().size() < NameType::max() ) {
         if ( rname == NameType( (*it)->Meta().Aspect() ) ) {
-          out = *it;
-          break;
+          //out = *it;
+          //break;
+          Out.push_back( *it );
         }
       }
     }
   }
-  if (out == 0) {
+  if (Out.empty()) {
+  //if (out == 0) {
     // As a final attempt, just look for the name
     for (Carray::const_iterator it = Templates_.begin(); it != Templates_.end(); ++it) {
       if ( (*it)->Meta().Name().size() < NameType::max() ) {
         if ( rname == NameType( (*it)->Meta().Name() ) ) {
-          out = *it;
-          break;
+          //out = *it;
+          //break;
+          Out.push_back( *it );
         }
       }
     }
   }
 
-  return out;
+  if (Out.empty()) return 0;
+  if (Out.size() > 1) {
+    mprintf("Warning: Multiple templates match '%s':", *rname);
+    for (std::vector<DataSet_Coords*>::const_iterator it = Out.begin(); it != Out.end(); ++it)
+      mprintf(" %s", (*it)->legend());
+    mprintf("\n");
+    mprintf("Warning: Using the last template loaded.\n");
+  }
+  //return out;
+  return Out.back();
 }
 
 /** Get templates */

From 61c2419cfe965730aac4f6e10bbbd771d39dfc37 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 8 Sep 2025 12:04:19 -0400
Subject: [PATCH 0942/1492] If a residue is explicitly marked as terminal,
 assign end terminal status

---
 src/Exec_Build.cpp | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index cf81cf7b88..26e91a164f 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -148,10 +148,10 @@ const
     int nres = ires + 1;
     // Determine if this is a terminal residue
     Cpptraj::Structure::TerminalType resTermType;
-    if (ires == 0 && topIn.Nres() > 1) {
-      resTermType = Cpptraj::Structure::BEG_TERMINAL;
-    } else if (currentRes.IsTerminal()) {
+    if (currentRes.IsTerminal()) {
       resTermType = Cpptraj::Structure::END_TERMINAL;
+    } else if (ires == 0 && topIn.Nres() > 1) {
+      resTermType = Cpptraj::Structure::BEG_TERMINAL;
     } else if (pres > -1 && topIn.Res(pres).IsTerminal()) {
       resTermType = Cpptraj::Structure::BEG_TERMINAL;
     } else if (nres < topIn.Nres() && (topIn.Res(nres).ChainID() != currentRes.ChainID() ||
@@ -164,7 +164,7 @@ const
       resTermType = Cpptraj::Structure::NON_TERMINAL;
     }
     if (debug_ > 0)
-      mprintf("DEBUG: Residue type: %s terminal\n", Cpptraj::Structure::terminalStr(resTermType));
+      mprintf("DEBUG: Residue type: %s terminal (IsTerminal=%i)\n", Cpptraj::Structure::terminalStr(resTermType), (int)currentRes.IsTerminal());
     ResTermTypes.push_back( resTermType );
     // Identify a template based on the residue name.
     DataSet_Coords* resTemplate = creator.IdTemplateFromResname(currentRes.Name(), resTermType);

From e6d7b4ce3a681764d6c3244fc4737ca71cf6c76e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 12 Sep 2025 14:22:37 -0400
Subject: [PATCH 0943/1492] Add atombondorder keyword to mol2 write for easier
 compare to leap

---
 src/Traj_Mol2File.cpp | 51 ++++++++++++++++++++++++++++---------------
 src/Traj_Mol2File.h   |  1 +
 2 files changed, 35 insertions(+), 17 deletions(-)

diff --git a/src/Traj_Mol2File.cpp b/src/Traj_Mol2File.cpp
index 68a221d61f..98bfbffcd5 100644
--- a/src/Traj_Mol2File.cpp
+++ b/src/Traj_Mol2File.cpp
@@ -12,7 +12,8 @@ Traj_Mol2File::Traj_Mol2File() :
   currentSet_(0),
   hasCharges_(false),
   useSybylTypes_(false),
-  prependExt_(false)
+  prependExt_(false),
+  atomBondOrder_(false)
 {}
 
 bool Traj_Mol2File::ID_TrajFormat(CpptrajFile& fileIn) {
@@ -92,12 +93,13 @@ int Traj_Mol2File::readFrame(int set, Frame& frameIn) {
 }
 
 void Traj_Mol2File::WriteHelp() {
-  mprintf("\tsingle   : Write to a single file.\n"
-          "\tmulti    : Write each frame to a separate file.\n"
-          "\tsybyltype: Convert Amber atom types (if present) to SYBYL types.\n"
-          "\tsybylatom: Amber to SYBYL atom type corresponding file (optional).\n"
-          "\tsybylbond: Amber to SYBYL bond type corresponding file (optional).\n"
-          "\tkeepext  : Keep filename extension; write '<name>.<num>.<ext>' instead (implies 'multi').\n");
+  mprintf("\tsingle        : Write to a single file.\n"
+          "\tmulti         : Write each frame to a separate file.\n"
+          "\tsybyltype     : Convert Amber atom types (if present) to SYBYL types.\n"
+          "\tsybylatom     : Amber to SYBYL atom type corresponding file (optional).\n"
+          "\tsybylbond     : Amber to SYBYL bond type corresponding file (optional).\n"
+          "\tkeepext       : Keep filename extension; write '<name>.<num>.<ext>' instead (implies 'multi').\n"
+          "\tatombondorder : Sort bonds by first atom index.\n");
 }
 
 // Traj_Mol2File::processWriteArgs()
@@ -112,6 +114,7 @@ int Traj_Mol2File::processWriteArgs(ArgList& argIn, DataSetList const& DSLin) {
     useSybylTypes_ = true;
   prependExt_ = argIn.hasKey("keepext"); // Implies MULTI
   if (prependExt_) mol2WriteMode_ = MULTI;
+  atomBondOrder_ = argIn.hasKey("atombondorder");
   return 0;
 }
 
@@ -235,16 +238,30 @@ int Traj_Mol2File::writeFrame(int set, Frame const& frameOut) {
   if (file_.Mol2Nbonds() > 0) {
     file_.WriteHeader(Mol2File::BOND);
     int bondnum = 1;
-    for (BondArray::const_iterator bidx = mol2Top_->Bonds().begin();
-                                   bidx != mol2Top_->Bonds().end(); ++bidx)
-      file_.WriteMol2Bond(bondnum++, bidx->A1()+1, bidx->A2()+1,
-                          (*mol2Top_)[bidx->A1()].Type(),
-                          (*mol2Top_)[bidx->A2()].Type());
-    for (BondArray::const_iterator bidx = mol2Top_->BondsH().begin();
-                                   bidx != mol2Top_->BondsH().end(); ++bidx)
-      file_.WriteMol2Bond(bondnum++, bidx->A1()+1, bidx->A2()+1,
-                          (*mol2Top_)[bidx->A1()].Type(),
-                          (*mol2Top_)[bidx->A2()].Type());
+    if (atomBondOrder_) {
+      // Use atom array
+      for (Topology::atom_iterator atom = mol2Top_->begin(); atom != mol2Top_->end(); ++atom) {
+        atnum = atom - mol2Top_->begin();
+        for (Atom::bond_iterator bit = atom->bondbegin(); bit != atom->bondend(); ++bit) {
+          if (*bit > atnum)
+            file_.WriteMol2Bond(bondnum++, (atnum + 1), (*bit + 1),
+                                (*mol2Top_)[atnum].Type(),
+                                (*mol2Top_)[*bit ].Type());
+        }
+      }
+    } else {
+      // Use bond arrays
+      for (BondArray::const_iterator bidx = mol2Top_->Bonds().begin();
+                                     bidx != mol2Top_->Bonds().end(); ++bidx)
+        file_.WriteMol2Bond(bondnum++, bidx->A1()+1, bidx->A2()+1,
+                            (*mol2Top_)[bidx->A1()].Type(),
+                            (*mol2Top_)[bidx->A2()].Type());
+      for (BondArray::const_iterator bidx = mol2Top_->BondsH().begin();
+                                     bidx != mol2Top_->BondsH().end(); ++bidx)
+        file_.WriteMol2Bond(bondnum++, bidx->A1()+1, bidx->A2()+1,
+                            (*mol2Top_)[bidx->A1()].Type(),
+                            (*mol2Top_)[bidx->A2()].Type());
+    }
   }
   //@<TRIPOS>SUBSTRUCTURE section
   file_.WriteHeader(Mol2File::SUBSTRUCT);
diff --git a/src/Traj_Mol2File.h b/src/Traj_Mol2File.h
index 1390bc2152..1d7033922a 100644
--- a/src/Traj_Mol2File.h
+++ b/src/Traj_Mol2File.h
@@ -46,6 +46,7 @@ class Traj_Mol2File : public TrajectoryIO {
     bool hasCharges_;
     bool useSybylTypes_;
     bool prependExt_;
+    bool atomBondOrder_;
     Mol2File file_; 
 };
 #endif

From ba3732f4b1bd7f937b13d2f2fdacce193bc18c4e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 12 Sep 2025 15:31:27 -0400
Subject: [PATCH 0944/1492] Fix reading of prep files. Leap uses a tree/stack
 method of assigning bonds, not necessarily the zmatrix indices.

---
 src/DataIO_AmberPrep.cpp | 102 ++++++++++++++++++++++++++++++++++-----
 1 file changed, 91 insertions(+), 11 deletions(-)

diff --git a/src/DataIO_AmberPrep.cpp b/src/DataIO_AmberPrep.cpp
index 6dc8ec7766..5422ffc442 100644
--- a/src/DataIO_AmberPrep.cpp
+++ b/src/DataIO_AmberPrep.cpp
@@ -5,6 +5,7 @@
 #include "DataSet_Coords.h"
 #include "StringRoutines.h"
 #include "Structure/Zmatrix.h"
+#include <stack>
 
 /// CONSTRUCTOR
 DataIO_AmberPrep::DataIO_AmberPrep() :
@@ -76,6 +77,15 @@ int DataIO_AmberPrep::readIMPROPER(BufferedLine& infile) const {
   return 0;
 }
 
+/// For constructing the tree
+class TREENODE {
+  public:
+    TREENODE(int i) : aIdx_(i), iUnfilled_(-1), iBack_(-1) {}
+    int aIdx_;
+    int iUnfilled_;
+    int iBack_;
+};
+
 /** Read 1 or more PREP residue sections (cards 3-10).
   * \return 1 if error, -1 if STOP/EOF, 0 if more residues to be read.
   */
@@ -159,7 +169,9 @@ int DataIO_AmberPrep::readAmberPrep(BufferedLine& infile, DataSetList& dsl, std:
   std::string IPOS   = args.GetStringNext();
   if (debug_ > 0)
     mprintf("DEBUG: %s %s %s %s\n", IFIXC.c_str(), IOMIT.c_str(), ISYMDU.c_str(), IPOS.c_str());
+  bool do_distance_search = false;
   if (IFIXC != "CORRECT") {
+    // NOTE: If IFIXC = CHANGE ever implemented, set do_distance_search to true here.
     mprinterr("Error: IFIXC is not 'CORRECT' (%s=); only internal coordinates currently supported.\n",
               IFIXC.c_str());
     return 1;
@@ -195,10 +207,16 @@ int DataIO_AmberPrep::readAmberPrep(BufferedLine& infile, DataSetList& dsl, std:
   top.SetParmName( resName, infile.Filename() );
   // Residue
   Residue res(resName, 1, ' ', "");
+  // For constructing the tree
+  typedef std::stack<TREENODE> TreeStack;
+  TreeStack Tree;
+  Tree.push( TREENODE(-1) );
+  mprintf( "DEBUG: Prep: Reading atom records\n" );
   // Loop over entries
   line = infile.Line();
   if (CheckLine(line)) return 1;
-  int atIdx = 0;
+  int atIdx = 0; // The prep file atom index
+  std::vector<int> topAtomIndices; 
   while (line[0] != '\0') {
     if (debug_ > 1)
       mprintf("DEBUG: '%s'\n", line);
@@ -207,6 +225,37 @@ int DataIO_AmberPrep::readAmberPrep(BufferedLine& infile, DataSetList& dsl, std:
       mprinterr("Error: Expected 11 columns in prep line, got %i\n", args.Nargs());
       return 1;
     }
+    // Define the node type
+    TREENODE ipair(atIdx);
+    switch (args[3][0]) {
+      case 'M' : ipair.iUnfilled_ = 10000; break;
+      case 'B' : ipair.iUnfilled_ = 2; break;
+      case '3' : ipair.iUnfilled_ = 3; break;
+      case 'S' : ipair.iUnfilled_ = 1; break;
+      case 'E' : ipair.iUnfilled_ = 0; break;
+      case '4' : ipair.iUnfilled_ = 4; break;
+      case '5' : ipair.iUnfilled_ = 5; break;
+      case '6' : ipair.iUnfilled_ = 6; break;
+      default:
+        mprinterr("Error: Atom %s: Illegal chain specified [%s] in PREP file.\n", args[1].c_str(), args[3][0]);
+        return 1;
+    }
+    ipair.iBack_ = Tree.top().aIdx_;
+    printf("DEBUG: Prep:  iTREETOP %i\n", Tree.top().aIdx_);
+    if (Tree.top().aIdx_ >= 0) {
+      printf("DEBUG: Prep:  iTREETOP %i iUnfilled %i\n", Tree.top().aIdx_, Tree.top().iUnfilled_);
+      Tree.top().iUnfilled_--;
+      if (Tree.top().iUnfilled_ == 0) {
+        Tree.pop();
+        if (Tree.empty()) {
+          mprinterr("Internal Error: Prep stack is empty.\n");
+          return 1;
+        }
+      }
+    }
+    if (ipair.iUnfilled_ != 0) { Tree.push( ipair ); mprintf("DEBUG: Prep:  TREEPUSH %i\n", ipair.aIdx_); }
+    int iBond = ipair.iBack_;
+    // Convert charge
     double charge = convertToDouble(args[10]);
     // Add top atom
     if (args[2] == "EP") {
@@ -214,9 +263,14 @@ int DataIO_AmberPrep::readAmberPrep(BufferedLine& infile, DataSetList& dsl, std:
       Atom atm(args[1], "XP");
       atm.SetTypeName(args[2]);
       atm.SetCharge(charge);
+      topAtomIndices.push_back( top.Natom() );
       top.AddTopAtom(atm, res);
-    } else
+    } else if (args[2] != ISYMDU) {
+      topAtomIndices.push_back( top.Natom() );
       top.AddTopAtom( Atom(args[1], args[2], charge), res );
+      //mprintf("DEBUG: Prep:\t Creating atom: %s (%i)\n", args[1].c_str(), topAtomIndices.back());
+    } else
+      topAtomIndices.push_back( -1 );
     // Add zmatrix entry. In prep file, indices start from 1.
     int atI = convertToInteger(args[0]) - 1;
     if (atI != atIdx) {
@@ -229,15 +283,35 @@ int DataIO_AmberPrep::readAmberPrep(BufferedLine& infile, DataSetList& dsl, std:
     double dist  = convertToDouble(args[7]);
     double theta = convertToDouble(args[8]);
     double phi   = convertToDouble(args[9]);
+    if (args[2] != ISYMDU) {
+      mprintf("DEBUG: Prep:  B/A/T= %f %f %f\n", dist, theta, phi);
+      mprintf("DEBUG: Prep:\t Creating atom: %s\n", args[1].c_str());
+    }
     //if (args[2] == ISYMDU) {
       if (zmatrix.AddIC( InternalCoords(atIdx, atJ, atK, atL, dist, theta, phi) ))
         return 1;
     //} else
     //  zmatrix.AddIC( InternalCoords(atIdx, atJ, atK, atL, dist, theta, phi) );
+    // Add bond if present
+    if (atJ > 0) {
+      if (topAtomIndices[atI] > -1 && topAtomIndices[atJ] > -1) {
+        mprintf("DEBUG: Prep:\t\t Created bond between: %s - %s (%i)\n",
+                *(top[ topAtomIndices[atI] ].Name()),
+                *(top[ topAtomIndices[iBond] ].Name()), iBond);
+        top.AddBond( topAtomIndices[atI], topAtomIndices[iBond] );
+      }
+    }
     atIdx++;
     line = infile.Line();
     if (line == 0) break;
   }
+  //mprintf("DEBUG: Prep:  TREE");
+  //while (!Tree.empty()) {
+  //  mprintf(" %i", Tree.top().aIdx_);
+  //  Tree.pop();
+  //}
+  //mprintf("\n");
+
   // 9 - Read additional information about the residue.
   // CHARGE - Read additional partial atomic charges. FORMAT (5f)
   // LOOP - Read explicit loop closing bonds
@@ -264,9 +338,9 @@ int DataIO_AmberPrep::readAmberPrep(BufferedLine& infile, DataSetList& dsl, std:
   }
   // -----------------------------------
   // Add bonds to topology
-  for (Zmatrix::const_iterator it = zmatrix.begin(); it != zmatrix.end(); ++it)
-    if (it->AtJ() != InternalCoords::NO_ATOM)
-      top.AddBond( it - zmatrix.begin(), it->AtJ() );
+  //for (Zmatrix::const_iterator it = zmatrix.begin(); it != zmatrix.end(); ++it)
+  //  if (it->AtJ() != InternalCoords::NO_ATOM)
+  //    top.AddBond( it - zmatrix.begin(), it->AtJ() );
   for (AtPairArray::const_iterator it = BondPairs.begin(); it != BondPairs.end(); ++it) {
     int idx1 = top.FindAtomInResidue(0, it->first);
     if (idx1 < 0) {
@@ -281,14 +355,20 @@ int DataIO_AmberPrep::readAmberPrep(BufferedLine& infile, DataSetList& dsl, std:
     top.AddBond( idx1, idx2 );
   }
   // Frame
-  Frame frm( top.Natom() );
+  Frame frm_with_duatoms( topAtomIndices.size() );
   // Internal coords to cart
-  if (zmatrix.SetToFrame( frm )) {
+  if (zmatrix.SetToFrame( frm_with_duatoms )) {
     mprinterr("Error: IC to Cartesian coords failed.\n");
     return 1;
   }
-  // Bond search
-  if (bondCutoff > 0) {
+  Frame frm( top.Natom() );
+  frm.ClearAtoms();
+  for (unsigned int pidx = 0; pidx != topAtomIndices.size(); ++pidx) {
+    if (topAtomIndices[pidx] != -1)
+      frm.AddXYZ( frm_with_duatoms.XYZ( pidx ) );
+  }
+  // Bond search. NOTE: Using 0.01 here to match LEaP's behavior
+  if (do_distance_search && bondCutoff > 0.01) {
     BondSearch bondSearch;
     bondSearch.FindBonds( top, BondSearch::SEARCH_REGULAR, frm, 0.2, debug_ );
   }
@@ -308,7 +388,7 @@ int DataIO_AmberPrep::readAmberPrep(BufferedLine& infile, DataSetList& dsl, std:
   DataSet_Coords* CRD = static_cast<DataSet_Coords*>( ds );
   
   // Delete dummy atoms if needed
-  if (removeDummyAtoms_) {
+/*  if (removeDummyAtoms_) {
     AtomMask keepAtoms;
     if (keepAtoms.SetMaskString( "!@%" + ISYMDU )) {
       mprinterr("Error: Could not set up mask string to remove dummy atoms.\n");
@@ -333,7 +413,7 @@ int DataIO_AmberPrep::readAmberPrep(BufferedLine& infile, DataSetList& dsl, std:
       frm = newFrame;
       if (debug_ > 0) top.Summary();
     }
-  }
+  }*/
   // DEBUG - back convert
 /*  mprintf("DEBUG: BACK CONVERT %s\n", resName.c_str());
   mprinterr("DEBUG: BACK CONVERT %s\n", resName.c_str());

From da9adafe0d733a2376fe5b472eebfad11ea80da2 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Sat, 13 Sep 2025 08:55:21 -0400
Subject: [PATCH 0945/1492] Hide debug info

---
 src/DataIO_AmberPrep.cpp | 36 ++++++++++++++++++++----------------
 1 file changed, 20 insertions(+), 16 deletions(-)

diff --git a/src/DataIO_AmberPrep.cpp b/src/DataIO_AmberPrep.cpp
index 5422ffc442..8d39b55ef1 100644
--- a/src/DataIO_AmberPrep.cpp
+++ b/src/DataIO_AmberPrep.cpp
@@ -211,7 +211,7 @@ int DataIO_AmberPrep::readAmberPrep(BufferedLine& infile, DataSetList& dsl, std:
   typedef std::stack<TREENODE> TreeStack;
   TreeStack Tree;
   Tree.push( TREENODE(-1) );
-  mprintf( "DEBUG: Prep: Reading atom records\n" );
+//  mprintf( "DEBUG: Prep: Reading atom records\n" );
   // Loop over entries
   line = infile.Line();
   if (CheckLine(line)) return 1;
@@ -241,9 +241,9 @@ int DataIO_AmberPrep::readAmberPrep(BufferedLine& infile, DataSetList& dsl, std:
         return 1;
     }
     ipair.iBack_ = Tree.top().aIdx_;
-    printf("DEBUG: Prep:  iTREETOP %i\n", Tree.top().aIdx_);
+//    printf("DEBUG: Prep:  iTREETOP %i\n", Tree.top().aIdx_);
     if (Tree.top().aIdx_ >= 0) {
-      printf("DEBUG: Prep:  iTREETOP %i iUnfilled %i\n", Tree.top().aIdx_, Tree.top().iUnfilled_);
+//      printf("DEBUG: Prep:  iTREETOP %i iUnfilled %i\n", Tree.top().aIdx_, Tree.top().iUnfilled_);
       Tree.top().iUnfilled_--;
       if (Tree.top().iUnfilled_ == 0) {
         Tree.pop();
@@ -253,7 +253,10 @@ int DataIO_AmberPrep::readAmberPrep(BufferedLine& infile, DataSetList& dsl, std:
         }
       }
     }
-    if (ipair.iUnfilled_ != 0) { Tree.push( ipair ); mprintf("DEBUG: Prep:  TREEPUSH %i\n", ipair.aIdx_); }
+    if (ipair.iUnfilled_ != 0) {
+      Tree.push( ipair );
+//      mprintf("DEBUG: Prep:  TREEPUSH %i\n", ipair.aIdx_); }
+    }
     int iBond = ipair.iBack_;
     // Convert charge
     double charge = convertToDouble(args[10]);
@@ -283,21 +286,18 @@ int DataIO_AmberPrep::readAmberPrep(BufferedLine& infile, DataSetList& dsl, std:
     double dist  = convertToDouble(args[7]);
     double theta = convertToDouble(args[8]);
     double phi   = convertToDouble(args[9]);
-    if (args[2] != ISYMDU) {
-      mprintf("DEBUG: Prep:  B/A/T= %f %f %f\n", dist, theta, phi);
-      mprintf("DEBUG: Prep:\t Creating atom: %s\n", args[1].c_str());
-    }
-    //if (args[2] == ISYMDU) {
-      if (zmatrix.AddIC( InternalCoords(atIdx, atJ, atK, atL, dist, theta, phi) ))
-        return 1;
-    //} else
-    //  zmatrix.AddIC( InternalCoords(atIdx, atJ, atK, atL, dist, theta, phi) );
+//    if (args[2] != ISYMDU) {
+//      mprintf("DEBUG: Prep:  B/A/T= %f %f %f\n", dist, theta, phi);
+//      mprintf("DEBUG: Prep:\t Creating atom: %s\n", args[1].c_str());
+//    }
+    if (zmatrix.AddIC( InternalCoords(atIdx, atJ, atK, atL, dist, theta, phi) ))
+      return 1;
     // Add bond if present
     if (atJ > 0) {
       if (topAtomIndices[atI] > -1 && topAtomIndices[atJ] > -1) {
-        mprintf("DEBUG: Prep:\t\t Created bond between: %s - %s (%i)\n",
-                *(top[ topAtomIndices[atI] ].Name()),
-                *(top[ topAtomIndices[iBond] ].Name()), iBond);
+//        mprintf("DEBUG: Prep:\t\t Created bond between: %s - %s (%i)\n",
+//                *(top[ topAtomIndices[atI] ].Name()),
+//                *(top[ topAtomIndices[iBond] ].Name()), iBond);
         top.AddBond( topAtomIndices[atI], topAtomIndices[iBond] );
       }
     }
@@ -361,6 +361,10 @@ int DataIO_AmberPrep::readAmberPrep(BufferedLine& infile, DataSetList& dsl, std:
     mprinterr("Error: IC to Cartesian coords failed.\n");
     return 1;
   }
+  // DEBUG
+  //mprintf("DEBUG: Zmatrix -> Cartesian:\n");
+  //for (int ii = 0; ii < frm_with_duatoms.Natom(); ii++)
+  //  frm_with_duatoms.printAtomCoord(ii);
   Frame frm( top.Natom() );
   frm.ClearAtoms();
   for (unsigned int pidx = 0; pidx != topAtomIndices.size(); ++pidx) {

From b49ff2f386f0934b69862fef7a68a3712327c7bf Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Mon, 15 Sep 2025 14:30:35 -0400
Subject: [PATCH 0946/1492] Make default verbosity when combining parameter
 sets in the creator 1 so that overwritten params are always reported

---
 src/Structure/Creator.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Structure/Creator.cpp b/src/Structure/Creator.cpp
index d5e43c9fec..5de798b7a9 100644
--- a/src/Structure/Creator.cpp
+++ b/src/Structure/Creator.cpp
@@ -291,7 +291,7 @@ int Creator::getParameterSets(ArgList& argIn, DataSetList const& DSL) {
       ++it;
       ParameterSet::UpdateCount UC;
       for (; it != ParamSets.end(); ++it)
-        mainParmSet_->UpdateParamSet( *(*it), UC, debug_, debug_ ); // FIXME verbose
+        mainParmSet_->UpdateParamSet( *(*it), UC, debug_, debug_+1 ); // Make it so verbosity is at least 1 to report overwritten params 
     }
   }
   return 0;

From faa6d6ff7fd03b7e2cb513596bd87dc3c7d56d19 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Tue, 16 Sep 2025 08:27:18 -0400
Subject: [PATCH 0947/1492] It is possible for a parameter set to define an
 atom type without setting the LJ parameters. Modify AtomType class to hold
 whether LJ parameters have been set.

---
 src/AmberParamFile.cpp  |  9 +++------
 src/AtomType.h          | 19 +++++++++++--------
 src/CharmmParamFile.cpp |  6 ++----
 src/ParameterSet.cpp    |  4 ++--
 4 files changed, 18 insertions(+), 20 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 565bc27e48..a1486ff4b8 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -480,8 +480,7 @@ int AmberParamFile::assign_nb(ParameterSet& prm, NonbondSet const& nbset) const
                 *(it->first[0]));
       return 1;
     } 
-    at->second.SetLJ().SetRadius( it->second.Radius() );
-    at->second.SetLJ().SetDepth( it->second.Depth() );
+    at->second.SetLJ( it->second );
   }
   return 0;
 }
@@ -500,8 +499,7 @@ int AmberParamFile::assign_offdiag(ParameterSet& prm, Oarray const& Offdiag) con
                   *(od->types_[0]));
         return 1;
       }
-      it->second.SetLJ().SetRadius( od->LJ1_.Radius() );
-      it->second.SetLJ().SetDepth( od->LJ1_.Depth() );
+      it->second.SetLJ( od->LJ1_ );
       // Set off-diagonal for type1-type2
       // FIXME different combine rules?
       prm.NB().AddParm(od->types_, od->LJ1_.Combine_LB(od->LJ2_), false);
@@ -792,8 +790,7 @@ int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
           return 1;
         }
         if (debug_ > 1) mprintf("DEBUG: Equiv '%s' => '%s'\n", *(at0->first[0]), *(*typeName));
-        at1->second.SetLJ().SetRadius( at0->second.LJ().Radius() );
-        at1->second.SetLJ().SetDepth( at0->second.LJ().Depth() );
+        at1->second.SetLJ( at0->second.LJ() );
       }
     } // END loop over EquivalentNames
   } // END nonbond parameters
diff --git a/src/AtomType.h b/src/AtomType.h
index 2c2d8b1f22..25401800fd 100644
--- a/src/AtomType.h
+++ b/src/AtomType.h
@@ -8,19 +8,21 @@ class AtomType {
     /// Atom hybridization types
     enum HybridizationType { SP = 0, SP2, SP3, UNKNOWN_HYBRIDIZATION };
     /// CONSTRUCTOR
-    AtomType() : mass_(0.0), polarizability_(0.0), oidx_(-1), hybrid_(UNKNOWN_HYBRIDIZATION), hasLJ14_(false) { clearElt(); }
+    AtomType() : mass_(0.0), polarizability_(0.0), oidx_(-1), hybrid_(UNKNOWN_HYBRIDIZATION), hasLJ_(false), hasLJ14_(false) { clearElt(); }
     /// CONSTRUCTOR - Mass only
-    AtomType(double m) : mass_(m), polarizability_(0.0), oidx_(-1), hybrid_(UNKNOWN_HYBRIDIZATION), hasLJ14_(false) { clearElt(); }
+    AtomType(double m) : mass_(m), polarizability_(0.0), oidx_(-1), hybrid_(UNKNOWN_HYBRIDIZATION), hasLJ_(false), hasLJ14_(false) { clearElt(); }
     /// CONSTRUCTOR - Mass, polarizability
-    AtomType(double m, double p) : mass_(m), polarizability_(p), oidx_(-1), hybrid_(UNKNOWN_HYBRIDIZATION), hasLJ14_(false) { clearElt(); }
+    AtomType(double m, double p) : mass_(m), polarizability_(p), oidx_(-1), hybrid_(UNKNOWN_HYBRIDIZATION), hasLJ_(false), hasLJ14_(false) { clearElt(); }
     /// CONSTRUCTOR - Radius, well depth, mass, polarizability
-    AtomType(double r, double d, double m, double p) : lj_(r, d), mass_(m), polarizability_(p), oidx_(-1), hybrid_(UNKNOWN_HYBRIDIZATION), hasLJ14_(false) { clearElt(); }
+    AtomType(double r, double d, double m, double p) : lj_(r, d), mass_(m), polarizability_(p), oidx_(-1), hybrid_(UNKNOWN_HYBRIDIZATION), hasLJ_(true), hasLJ14_(false) { clearElt(); }
     /// Set type index
     void SetTypeIdx(int i) { oidx_ = i; }
     /// \return default LJ parameters
     LJparmType const& LJ()  const { return lj_; }
     /// \return LJ 1-4 parameters
     LJparmType const& LJ14() const { return lj14_; }
+    /// \return True if LJ parameters have been set
+    bool HasLJ() const { return hasLJ_; }
     /// \return True if LJ 1-4 parameters have been set
     bool HasLJ14() const { return hasLJ14_; }
     /// \return Atom mass in amu
@@ -33,7 +35,7 @@ class AtomType {
     HybridizationType Hybridization() const { return hybrid_; }
     /// \return Atom type element string
     const char* EltStr() const { return elt_; }
-    /// \return true if mass, polarizability, or LJ params are less than incoming
+    /// \return true if mass, polarizability, or LJ params are less than incoming FIXME LJ14 too?
     bool operator<(AtomType const& rhs) const {
       if (FEQ(mass_, rhs.mass_)) {
         if (FEQ(polarizability_, rhs.polarizability_)) {
@@ -45,14 +47,14 @@ class AtomType {
         return mass_ < rhs.mass_;
       }
     }
-    /// \return true if mass, polarizability, and LJ params are the same
+    /// \return true if mass, polarizability, and LJ params are the same FIXME LJ14 too?
     bool operator==(AtomType const& rhs) const {
       return (FEQ(mass_, rhs.mass_) &&
               FEQ(polarizability_, rhs.polarizability_) &&
               lj_ == rhs.lj_);
     }
-    /// Used to modify LJ params
-    LJparmType& SetLJ() { return lj_; }
+    /// Set LJ params
+    void SetLJ(LJparmType const& lj) { lj_ = lj; hasLJ_ = true; }
     /// Set LJ 1-4 parameters
     void SetLJ14(LJparmType const& lj) { lj14_ = lj; hasLJ14_ = true; }
     /// Set atom hybridization
@@ -69,6 +71,7 @@ class AtomType {
     int oidx_;              ///< Original atom type index, for indexing nonbond parameters.
     HybridizationType hybrid_; ///< Atom hybridization
     char elt_[3];              ///< 2 character atom type element string (and null char)
+    bool hasLJ_;             ///< True if this type has LJ 1-4 parameters.
     bool hasLJ14_;             ///< True if this type has LJ 1-4 parameters.
 };
 #endif
diff --git a/src/CharmmParamFile.cpp b/src/CharmmParamFile.cpp
index 5f635074d5..a3256a4b4b 100644
--- a/src/CharmmParamFile.cpp
+++ b/src/CharmmParamFile.cpp
@@ -270,8 +270,7 @@ int CharmmParamFile::ReadParams(ParameterSet& prm, FileName const& nameIn, int d
                   if (it->first[0].Match( at )) {
                     if (debugIn > 0)
                       mprintf("DEBUG: NB wildcard match: '%s' matches '%s'\n", *(it->first[0]), *at);
-                    it->second.SetLJ().SetRadius( radius );
-                    it->second.SetLJ().SetDepth( -epsilon );
+                    it->second.SetLJ( LJparmType(radius, -epsilon) );
                   }
                 }
               } else {
@@ -281,8 +280,7 @@ int CharmmParamFile::ReadParams(ParameterSet& prm, FileName const& nameIn, int d
                   mprintf("Warning: Nonbond parameters defined for type '%s' without MASS card."
                           " Skipping.\n", *at);
                 } else {
-                  it->second.SetLJ().SetRadius( radius );
-                  it->second.SetLJ().SetDepth( -epsilon );
+                  it->second.SetLJ( LJparmType(radius, -epsilon) );
                 }
               }
             }
diff --git a/src/ParameterSet.cpp b/src/ParameterSet.cpp
index 564ea964b6..095ceae661 100644
--- a/src/ParameterSet.cpp
+++ b/src/ParameterSet.cpp
@@ -72,14 +72,14 @@ void ParameterSet::Print(CpptrajFile& Out) const {
       break;
   }
   // Atom Type header
-  Out.Printf("\t%6s %8s %12s %12s %12s %12s", "Name", "TypeIdx", "Radius", "Depth", "Mass", "Polar.");
+  Out.Printf("\t%6s %8s %2s %12s %12s %12s %12s", "Name", "TypeIdx", "LJ", "Radius", "Depth", "Mass", "Polar.");
   if (has_hybridizations)
     Out.Printf(" %3s", "Hyb");
   if (has_elements)
     Out.Printf(" %2s", "El");
   Out.Printf("\n");
   for (ParmHolder<AtomType>::const_iterator at = atomTypes_.begin(); at != atomTypes_.end(); ++at) {
-    Out.Printf("\t%6s %8li %12.4f %12.4f %12.4f %12.4f", *(at->first[0]), at - atomTypes_.begin(), at->second.LJ().Radius(), at->second.LJ().Depth(), at->second.Mass(), at->second.Polarizability());
+    Out.Printf("\t%6s %8li %2i %12.4f %12.4f %12.4f %12.4f", *(at->first[0]), at - atomTypes_.begin(), (int)at->second.HasLJ(), at->second.LJ().Radius(), at->second.LJ().Depth(), at->second.Mass(), at->second.Polarizability());
     if (has_hybridizations)
       Out.Printf(" %3s", hybStr[at->second.Hybridization()]);
     if (has_elements)

From 01301d232c4bf53aef75bdd6405fdeaf727e5c6c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Tue, 16 Sep 2025 08:42:18 -0400
Subject: [PATCH 0948/1492] Only report bond search if actually doing it

---
 src/DataIO_AmberPrep.cpp | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/src/DataIO_AmberPrep.cpp b/src/DataIO_AmberPrep.cpp
index 8d39b55ef1..34efa0d110 100644
--- a/src/DataIO_AmberPrep.cpp
+++ b/src/DataIO_AmberPrep.cpp
@@ -186,9 +186,6 @@ int DataIO_AmberPrep::readAmberPrep(BufferedLine& infile, DataSetList& dsl, std:
   double bondCutoff = 0;
   if (line[0] != '\0')
     bondCutoff = convertToDouble( std::string(line) );
-  if (bondCutoff > 0.0)
-    mprintf("Warning: Non-zero cutoff in prep file (%g); will search for additional\n"
-            "Warning:  bonds based on distances.\n", bondCutoff);
   //     0 1         2         3        4     5     6     7    8        9      10
   // 8 - I IGRAPH(I) ISYMBL(I) ITREE(I) NA(I) NB(I) NC(I) R(I) THETA(I) PHI(I) CHG(I) [I = 1, NATOM]
   // FORMAT(I,3A,3I,4F)
@@ -373,6 +370,8 @@ int DataIO_AmberPrep::readAmberPrep(BufferedLine& infile, DataSetList& dsl, std:
   }
   // Bond search. NOTE: Using 0.01 here to match LEaP's behavior
   if (do_distance_search && bondCutoff > 0.01) {
+    mprintf("Warning: Non-zero cutoff in prep file (%g); will search for additional\n"
+            "Warning:  bonds based on distances.\n", bondCutoff);
     BondSearch bondSearch;
     bondSearch.FindBonds( top, BondSearch::SEARCH_REGULAR, frm, 0.2, debug_ );
   }

From 8efbf51cc12cb4870ffb4987f88ec10576fd7c7b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Tue, 16 Sep 2025 09:22:47 -0400
Subject: [PATCH 0949/1492] Take into account LJ14 params when comparing
 AtomType. Add explicit assignment operator for AtomType since it is possible
 for AtomTypes to be defined without LJ params and we dont want existing LJ
 params to be overwritten with non-existent LJ params.

---
 src/AtomType.h         | 32 ++++++++++++++++++++++++++++----
 src/ParameterHolders.h | 18 +++++++++++++++++-
 src/UpdateParameters.h |  6 +++++-
 3 files changed, 50 insertions(+), 6 deletions(-)

diff --git a/src/AtomType.h b/src/AtomType.h
index 25401800fd..d7fa8479cb 100644
--- a/src/AtomType.h
+++ b/src/AtomType.h
@@ -1,6 +1,7 @@
 #ifndef INC_ATOMTYPE_H
 #define INC_ATOMTYPE_H
 #include "ParameterTypes.h"
+//# incl ude "CpptrajStdio.h" // DEBUG
 /// Hold parameters for a unique atom type
 class AtomType {
     void clearElt() { elt_[0] = ' '; elt_[1] = ' '; elt_[2] = '\0'; }
@@ -35,11 +36,15 @@ class AtomType {
     HybridizationType Hybridization() const { return hybrid_; }
     /// \return Atom type element string
     const char* EltStr() const { return elt_; }
-    /// \return true if mass, polarizability, or LJ params are less than incoming FIXME LJ14 too?
+    /// \return true if mass, polarizability, or LJ params are less than incoming
     bool operator<(AtomType const& rhs) const {
       if (FEQ(mass_, rhs.mass_)) {
         if (FEQ(polarizability_, rhs.polarizability_)) {
-          return lj_ < rhs.lj_;
+          if (lj_ == rhs.lj_) {
+            return lj14_ < rhs.lj14_;
+          } else {
+            return lj_ < rhs.lj_;
+          }
         } else {
           return polarizability_ < rhs.polarizability_;
         }
@@ -47,11 +52,12 @@ class AtomType {
         return mass_ < rhs.mass_;
       }
     }
-    /// \return true if mass, polarizability, and LJ params are the same FIXME LJ14 too?
+    /// \return true if mass, polarizability, and LJ params are the same
     bool operator==(AtomType const& rhs) const {
       return (FEQ(mass_, rhs.mass_) &&
               FEQ(polarizability_, rhs.polarizability_) &&
-              lj_ == rhs.lj_);
+              lj_ == rhs.lj_ &&
+              lj14_ == rhs.lj14_);
     }
     /// Set LJ params
     void SetLJ(LJparmType const& lj) { lj_ = lj; hasLJ_ = true; }
@@ -63,6 +69,24 @@ class AtomType {
     void SetEltStr(const char* elt) { elt_[0] = elt[0]; elt_[1] = elt[1]; }
     /// \return data size  (2 double for LJparmType)
     static size_t DataSize() { return (4*sizeof(double)) + sizeof(int); }
+    /// Assign atom type. Do not overwrite LJ params if incoming type does not have them set.
+    AtomType& operator=(AtomType const& rhs) {
+      if (this == &rhs) return *this;
+      //mprintf("DEBUG: Assign elt %c%c oldHasLj=%i oldR=%f newHasLj=%i newR=%f\n", elt_[0], elt_[1], (int)hasLJ_, lj_.Radius(), (int)rhs.hasLJ_, rhs.lj_.Radius());
+      if (rhs.hasLJ_) lj_ = rhs.lj_;
+      if (rhs.hasLJ14_) lj14_ = rhs.lj14_;
+      //mprintf("DEBUG: After Assign elt %c%c newR=%f\n", elt_[0], elt_[1], lj_.Radius());
+      mass_ = rhs.mass_;
+      polarizability_ = rhs.polarizability_;
+      oidx_ = rhs.oidx_;
+      hybrid_ = rhs.hybrid_;
+      elt_[0] = rhs.elt_[0];
+      elt_[1] = rhs.elt_[1];
+      //elt_[2] = rhs.elt_[2];
+      hasLJ_ = rhs.hasLJ_;
+      hasLJ14_ = rhs.hasLJ14_;
+      return *this;
+    }
   private:
     LJparmType lj_;         ///< Default Lennard-Jones parameters (always valid for self).
     LJparmType lj14_;       ///< Lennard-Jones 1-4 parameters (optional).
diff --git a/src/ParameterHolders.h b/src/ParameterHolders.h
index ee08d281b3..29582587c7 100644
--- a/src/ParameterHolders.h
+++ b/src/ParameterHolders.h
@@ -4,7 +4,7 @@
 #include <utility> // std::pair
 #include "TypeNameHolder.h"
 #include "ParameterTypes.h"
-//#inc lude "CpptrajStdio.h" // DEBUG
+//#incl ude "CpptrajStdio.h" // DEBUG
 
 namespace ParameterHolders {
   enum RetType { ADDED = 0, SAME, UPDATED, ERR };
@@ -258,6 +258,16 @@ class DihedralParmHolder {
       found = false;
       return DihedralParmArray();
     }
+    /// \return iterator to parameter matching the given types.
+    const_iterator GetParam(TypeNameHolder const& types) {
+      for (const_iterator it = begin(); it != end(); ++it)
+        if (it->first.Match_NoWC( types )) return it;
+      if (wc_.len() > 0) {
+        for (const_iterator it = begin(); it != end(); ++it)
+          if (it->first.Match_WC( types, wc_)) return it;
+      }
+      return end();
+    }
     /// \return size in memory in bytes
     size_t DataSize() const {
       if (bpmap_.empty()) return 0;
@@ -440,6 +450,12 @@ class ImproperParmHolder : private DihedralParmHolder {
       }
       return it;
     } // END GetParam()
+    /// Get improper parameters matching given atom types. If found, improper will be reordered to match parameter order.
+    const_iterator GetParam(TypeNameHolder const& types) const {
+      DihedralType imp;
+      bool reordered = false;
+      return GetParam( types, imp, reordered);
+    }
     /// \return Array of improper parameters matching given atom types. Improper will be reordered to match parameter order.
     DihedralParmArray FindParam(TypeNameHolder const& types, bool& found, DihedralType& imp, bool& reordered) const {
       const_iterator it = GetParam( types, imp, reordered );
diff --git a/src/UpdateParameters.h b/src/UpdateParameters.h
index ea7221eceb..8aeccb7599 100644
--- a/src/UpdateParameters.h
+++ b/src/UpdateParameters.h
@@ -46,7 +46,11 @@ template <typename T> int UpdateParameters(T& param0, T const& param1, const cha
       }
       if (print) {
         mprintf(" %s", newp->first.TypeString().c_str());
-        PrintParmType( newp->second );
+        //PrintParmType( newp->second );
+        // NOTE: For AtomType its possible only a partial update occurred.
+        //       Get the new parameter explicitly.
+        typename T::const_iterator newIt = param0.GetParam( newp->first );
+        PrintParmType( newIt->second );
       }
       //mprintf(" %s %s %12.4f %12.4f\n", 
       //        *(newp->first[0]), *(newp->first[1]), newp->second.Rk(), newp->second.Req());

From 45565bde17f2b2d7d26ae88bc80103164d00fdc9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 16 Sep 2025 14:35:04 -0400
Subject: [PATCH 0950/1492] Do not check insertion code when checking for end
 terminal status

---
 src/Exec_Build.cpp | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 26e91a164f..673a115532 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -149,16 +149,23 @@ const
     // Determine if this is a terminal residue
     Cpptraj::Structure::TerminalType resTermType;
     if (currentRes.IsTerminal()) {
+      //mprintf("DEBUG: End terminal due to TERMINAL status.\n");
       resTermType = Cpptraj::Structure::END_TERMINAL;
     } else if (ires == 0 && topIn.Nres() > 1) {
       resTermType = Cpptraj::Structure::BEG_TERMINAL;
     } else if (pres > -1 && topIn.Res(pres).IsTerminal()) {
       resTermType = Cpptraj::Structure::BEG_TERMINAL;
-    } else if (nres < topIn.Nres() && (topIn.Res(nres).ChainID() != currentRes.ChainID() ||
-                                       topIn.Res(nres).Icode()   != currentRes.Icode()))
+    } else if (nres < topIn.Nres() && (topIn.Res(nres).ChainID() != currentRes.ChainID())// ||
+//                                        (topIn.Res(nres).OriginalResNum() == currentRes.OriginalResNum() &&
+//                                         topIn.Res(nres).Icode()          != currentRes.Icode()
+//                                        )
+//                                      )
+              )
     {
+      //mprintf("DEBUG: End terminal due to chain ID.\n");
       resTermType = Cpptraj::Structure::END_TERMINAL;
     } else if (nres == topIn.Nres()) {
+      //mprintf("DEBUG: End terminal due to last residue.\n");
       resTermType = Cpptraj::Structure::END_TERMINAL;
     } else {
       resTermType = Cpptraj::Structure::NON_TERMINAL;

From 3256a222a6a9ae844787b8a9538110ea5f7b1452 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 16 Sep 2025 15:58:34 -0400
Subject: [PATCH 0951/1492] Add sanity check to prevent segfault when setting
 orthogonal bounding box. Exit build if adding box fails.

---
 src/Exec_Build.cpp | 5 ++++-
 src/Frame.cpp      | 9 +++++++--
 src/Frame.h        | 2 +-
 3 files changed, 12 insertions(+), 4 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 673a115532..27d01dfcd3 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -1069,7 +1069,10 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, in
         //Radii.push_back( 0.5 );
       }
 
-      frameOut.SetOrthoBoundingBox(Radii, 1.0);
+      if (frameOut.SetOrthoBoundingBox(Radii, 1.0)) {
+        mprinterr("Error: Setting orthogonal bounding box failed.\n");
+        return CpptrajState::ERR;
+      }
       frameOut.BoxCrd().PrintInfo();
     }
     if (check.Setup( topOut, frameOut.BoxCrd() )) {
diff --git a/src/Frame.cpp b/src/Frame.cpp
index 7e3e69363c..21544a7cea 100644
--- a/src/Frame.cpp
+++ b/src/Frame.cpp
@@ -1405,8 +1405,13 @@ double Frame::CalcTemperature(AtomMask const& mask, int deg_of_freedom) const {
 /** Set an orthogonal bounding box around all atoms, ensuring it
   * can encompass the given atomic radii, plus an offset.
   */
-void Frame::SetOrthoBoundingBox(std::vector<double> const& Radii, double offset)
+int Frame::SetOrthoBoundingBox(std::vector<double> const& Radii, double offset)
 {
+  // Sanity check
+  if ((int)Radii.size() < natom_) {
+    mprinterr("Internal Error: Frame::SetOrthoBoundingBox: # of radii %zu < # atoms in frame %i\n", Radii.size(), natom_);
+    return 1;
+  }
   int atom = 0;
   Vec3 min(XYZ( atom ));
   Vec3 max(min);
@@ -1453,7 +1458,7 @@ void Frame::SetOrthoBoundingBox(std::vector<double> const& Radii, double offset)
   xyzabg[3] = 90.0;
   xyzabg[4] = 90.0;
   xyzabg[5] = 90.0;
-  box_.SetupFromXyzAbg(xyzabg);
+  return box_.SetupFromXyzAbg(xyzabg);
 }
 
 #ifdef MPI
diff --git a/src/Frame.h b/src/Frame.h
index e83ab145eb..5583325f28 100644
--- a/src/Frame.h
+++ b/src/Frame.h
@@ -275,7 +275,7 @@ class Frame {
     /// Calculate temperature of atoms in mask.
     double CalcTemperature(AtomMask const&,int) const;
     /// Set an orthogonal bounding box
-    void SetOrthoBoundingBox(std::vector<double> const& Radii, double);
+    int SetOrthoBoundingBox(std::vector<double> const& Radii, double);
 #   ifdef MPI
     // ----- Parallel Routines -------------------
     int SendFrame(int, Parallel::Comm const&) const;

From b7fe0d50d582df0223820169c02e12fa492ffba5 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 16 Sep 2025 16:04:59 -0400
Subject: [PATCH 0952/1492] When assigning radii for determining the box for
 check, need to use the final topology

---
 src/Exec_Build.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 27d01dfcd3..b44f536798 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -1062,8 +1062,8 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, in
       box_added = true;
       // Get radii
       std::vector<double> Radii;
-      Radii.reserve( topIn.Natom() );
-      for (int atnum = 0; atnum != topIn.Natom(); ++atnum) {
+      Radii.reserve( topOut.Natom() );
+      for (int atnum = 0; atnum != topOut.Natom(); ++atnum) {
         Radii.push_back( topOut.GetVDWradius(atnum) );
         //Radii.push_back( topIn[atnum].ParseRadius() );
         //Radii.push_back( 0.5 );

From 39f8ddb187f5b57312c4a1907987564af7249378 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 14 Oct 2025 09:29:37 -0400
Subject: [PATCH 0953/1492] vcorr_ does not need to be deleted anymore

---
 src/Action_Vector.cpp | 1 -
 src/Action_Vector.h   | 1 +
 2 files changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Action_Vector.cpp b/src/Action_Vector.cpp
index 982862c724..672c0662e1 100644
--- a/src/Action_Vector.cpp
+++ b/src/Action_Vector.cpp
@@ -23,7 +23,6 @@ Action_Vector::Action_Vector() :
 
 // DESTRUCTOR
 Action_Vector::~Action_Vector() {
-  if (vcorr_!=0) delete[] vcorr_;
   if (cmask_ != 0) delete cmask_;
 }
 
diff --git a/src/Action_Vector.h b/src/Action_Vector.h
index 270f888b5e..f72c0741aa 100644
--- a/src/Action_Vector.h
+++ b/src/Action_Vector.h
@@ -8,6 +8,7 @@ class CharMask;
 class Action_Vector : public Action {
   public:
     Action_Vector();
+    ~Action_Vector();
     DispatchObject* Alloc() const { return (DispatchObject*)new Action_Vector(); }
     void Help() const;
   private:

From 9a58941498dbba4b434f0f4f34c7923ae3918c79 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 15 Oct 2025 13:48:39 -0400
Subject: [PATCH 0954/1492] Add timer to parameter assignment

---
 src/Parm/AssignParams.cpp | 69 +++++++++++++++++++++++++++++++++++++--
 src/Parm/AssignParams.h   | 20 ++++++++++++
 2 files changed, 86 insertions(+), 3 deletions(-)

diff --git a/src/Parm/AssignParams.cpp b/src/Parm/AssignParams.cpp
index f8e8740a19..08d0ff61ac 100644
--- a/src/Parm/AssignParams.cpp
+++ b/src/Parm/AssignParams.cpp
@@ -1065,8 +1065,16 @@ void AssignParams::AddToDihedralArrays(Topology& topOut, DihedralType const& dih
 }
 
 /** Replace existing parameters with the given parameter set. */
-int AssignParams::AssignParameters(Topology& topOut, ParameterSet const& set0) const {
-
+#ifdef TIMER
+int AssignParams::AssignParameters(Topology& topOut, ParameterSet const& set0)
+#else
+int AssignParams::AssignParameters(Topology& topOut, ParameterSet const& set0) const
+#endif
+{
+# ifdef TIMER
+  t_total_.Start();
+  t_bonds_.Start();
+# endif
   // Bond parameters
   mprintf("\tAssigning bond parameters.\n");
   topOut.ModifyBondParm().clear();
@@ -1077,6 +1085,10 @@ int AssignParams::AssignParameters(Topology& topOut, ParameterSet const& set0) c
   AssignBondParm( topOut, set0.BP(), allBonds, topOut.ModifyBondParm(), "bond" );
   for (BondArray::const_iterator bnd = allBonds.begin(); bnd != allBonds.end(); ++bnd)
     AddToBondArrays( topOut, *bnd );
+# ifdef TIMER
+  t_bonds_.Stop();
+  t_angles_.Start();
+# endif
   // Angle parameters
   mprintf("\tAssigning angle parameters.\n");
   topOut.ModifyAngleParm().clear();
@@ -1087,6 +1099,10 @@ int AssignParams::AssignParameters(Topology& topOut, ParameterSet const& set0) c
   allAngles = AssignAngleParm( topOut, set0.AP(), allAngles, topOut.ModifyAngleParm() );
   for (AngleArray::const_iterator ang = allAngles.begin(); ang != allAngles.end(); ++ang)
     AddToAngleArrays( topOut, *ang );
+# ifdef TIMER
+  t_angles_.Stop();
+  t_dihedrals_.Start();
+# endif
   // Dihedral parameters
   mprintf("\tAssigning dihedral parameters.\n");
   topOut.ModifyDihedralParm().clear();
@@ -1094,20 +1110,40 @@ int AssignParams::AssignParameters(Topology& topOut, ParameterSet const& set0) c
   topOut.ModifyDihedrals().clear();
   topOut.ModifyDihedralsH().clear();
   DihedralArray allDihedrals = Cpptraj::Structure::GenerateDihedralArray(topOut.Residues(), topOut.Atoms());
+# ifdef TIMER
+  t_dihedrals_.Stop();
+# endif
   // If we need CMAP terms, do it here before the dihedrals array is modified
   if (!set0.CMAP().empty()) {
+#   ifdef TIMER
+    t_cmaps_.Start();
+#   endif
     topOut.ModifyCmap().clear();
     topOut.ModifyCmapGrid().clear();
     mprintf("\tAssigning CMAP parameters.\n");
     AssignCmapParams( topOut, allDihedrals, set0.CMAP(), topOut.ModifyCmapGrid(), topOut.ModifyCmap() );
+#   ifdef TIMER
+    t_cmaps_.Stop();
+#   endif
   } 
   // Now modify the dihedrals for any multiplicities
+# ifdef TIMER
+  t_multi_.Start();
+# endif
   allDihedrals = AssignDihedralParm( topOut, set0.DP(), set0.IP(), set0.AT(), allDihedrals, false );
   for (DihedralArray::const_iterator dih = allDihedrals.begin(); dih != allDihedrals.end(); ++dih)
     AddToDihedralArrays( topOut, *dih );
+# ifdef TIMER
+  t_multi_.Stop();
+  t_UB_.Start();
+# endif
   // Urey-Bradley
   mprintf("\tAssigning Urey-Bradley parameters.\n");
   AssignUBParams( topOut, set0.UB() );
+# ifdef TIMER
+  t_UB_.Stop();
+  t_improper_.Start();
+# endif
   if (!topOut.Impropers().empty()) {
     // Charmm Improper parameters
     mprintf("\tAssigning CHARMM improper parameters.\n");
@@ -1120,17 +1156,44 @@ int AssignParams::AssignParameters(Topology& topOut, ParameterSet const& set0) c
     for (DihedralArray::const_iterator imp = allImpropers.begin(); imp != allImpropers.end(); ++imp)
       AddToDihedralArrays( topOut, *imp );
   }
+# ifdef TIMER
+  t_improper_.Stop();
+  t_atype_.Start();
+# endif
   // Atom types
   mprintf("\tAssigning atom type parameters.\n");
   AssignAtomTypeParm( topOut.ModifyAtoms(), set0.AT() );
+# ifdef TIMER
+  t_atype_.Stop();
+  t_nonbond_.Start();
+# endif
   // LJ 6-12
   mprintf("\tAssigning nonbond parameters.\n");
   AssignNonbondParams( topOut, set0.AT(), set0.NB(), set0.NB14(), set0.LJC(), set0.HB() );
   //mprintf("DEBUG: CMAP size %zu\n", set0.CMAP().size());
-
+# ifdef TIMER
+  t_nonbond_.Stop();
+  t_total_.Stop();
+# endif
   return 0;
 }
 
+/** Write timing to stdout. Only works if TIMER is defined. */
+void AssignParams::WriteAssignTiming(int indent, double totalIn) const {
+#ifdef TIMER
+  t_total_.WriteTiming(indent, "Param Assign Total", totalIn);
+  t_bonds_.WriteTiming(indent+1,     "Bonds                  ", t_total_.Total());
+  t_angles_.WriteTiming(indent+1,    "Angles                 ", t_total_.Total());
+  t_dihedrals_.WriteTiming(indent+1, "Dihedrals              ", t_total_.Total());
+  t_multi_.WriteTiming(indent+1,     "Dihedral Multiplicities", t_total_.Total());
+  t_cmaps_.WriteTiming(indent+1,     "CMAPs                  ", t_total_.Total());
+  t_UB_.WriteTiming(indent+1,        "Urey-Bradleys          ", t_total_.Total());
+  t_improper_.WriteTiming(indent+1,  "Impropers              ", t_total_.Total());
+  t_atype_.WriteTiming(indent+1,     "Atom Types             ", t_total_.Total());
+  t_nonbond_.WriteTiming(indent+1,   "Nonbonds               ", t_total_.Total());
+#endif
+}
+
 /** Update/add to parameters in this topology with those from given set.
   */
 int AssignParams::UpdateParameters(Topology& topOut, ParameterSet const& set1) const {
diff --git a/src/Parm/AssignParams.h b/src/Parm/AssignParams.h
index faba164d4a..5d17910539 100644
--- a/src/Parm/AssignParams.h
+++ b/src/Parm/AssignParams.h
@@ -2,6 +2,9 @@
 #define INC_PARM_ASSIGNPARAMS_H
 #include <vector>
 #include <string>
+#ifdef TIMER
+# include "Timer.h"
+#endif
 class AngleArray;
 class AngleParmArray;
 class AngleParmType;
@@ -36,7 +39,11 @@ class AssignParams {
     /// Set verbosity
     void SetVerbose(int);
     /// Replace existing parameters with those from given set
+#   ifdef TIMER
+    int AssignParameters(Topology&, ParameterSet const&);
+#   else
     int AssignParameters(Topology&, ParameterSet const&) const;
+#   endif
     /// Update existing parameters with given parameter set
     int UpdateParameters(Topology&, ParameterSet const&) const;
     // Assign nonbond parameters to topology. Used during Merge::AppendTop()
@@ -44,6 +51,7 @@ class AssignParams {
                              ParmHolder<AtomType> const&,
                              ParmHolder<NonbondType> const&, ParmHolder<NonbondType> const&,
                              ParmHolder<double> const&, ParmHolder<HB_ParmType> const&) const;
+    void WriteAssignTiming(int, double) const;
   private:
     typedef std::vector<Atom> AtArray;
 
@@ -85,6 +93,18 @@ class AssignParams {
     int verbose_;
     bool deleteExtraPointAngles_; ///< If true, remove angles/torsions containing extra points.
     bool flexibleWater_;          ///< If true, allow H-O-H angle for water
+#   ifdef TIMER
+    Timer t_total_;
+    Timer t_bonds_;
+    Timer t_angles_;
+    Timer t_dihedrals_;
+    Timer t_cmaps_;
+    Timer t_multi_;
+    Timer t_UB_;
+    Timer t_improper_;
+    Timer t_atype_;
+    Timer t_nonbond_;
+#   endif
 };
 }
 }

From 29c243fa9a89c6b9633a8f8daef8a2a5cb99d551 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 15 Oct 2025 13:48:53 -0400
Subject: [PATCH 0955/1492] Write timing

---
 src/Exec_Build.cpp | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index b44f536798..a2c746ad91 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -1110,6 +1110,7 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, in
   t_sugar_.WriteTiming        (2, "Sugar preparation   :", t_total_.Total());
   t_fill_.WriteTiming         (2, "Fill missing atoms  :", t_total_.Total());
   t_assign_.WriteTiming       (2, "Param./Top. gen.    :", t_total_.Total());
+  AP.WriteAssignTiming(3, t_assign_.Total());
   t_check_.WriteTiming        (2, "Structure check     :", t_total_.Total());
 
   return ret;

From b48aa0ca15604b3b22a6ef9643cde77f9af87bbd Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 16 Oct 2025 09:34:17 -0400
Subject: [PATCH 0956/1492] Get detailed timings for
 AssignParams::AssignDihedralParm() since that appears to be where the current
 bottleneck is.

---
 src/Parm/AssignParams.cpp | 34 ++++++++++++++++++++++++++++++++--
 src/Parm/AssignParams.h   | 26 +++++++++++++++++++++-----
 2 files changed, 53 insertions(+), 7 deletions(-)

diff --git a/src/Parm/AssignParams.cpp b/src/Parm/AssignParams.cpp
index 08d0ff61ac..be5ac300dd 100644
--- a/src/Parm/AssignParams.cpp
+++ b/src/Parm/AssignParams.cpp
@@ -298,7 +298,9 @@ DihedralArray AssignParams::AssignDihedralParm(Topology& topOut,
                                                ParmHolder<AtomType> const& AT,
                                                DihedralArray const& dihedrals,
                                                bool sort_improper_cache)
+#ifndef TIMER
 const
+#endif
 { // TODO skip extra points
   DihedralArray dihedralsIn;
   // Improper cache
@@ -345,6 +347,9 @@ const
     }
     bool found;
     if (dih->IsImproper()) {
+#     ifdef TIMER
+      t_dih_imp_.Start();
+#     endif
       // ----- This is actually an improper dihedral. ----------------
       // Impropers are treated differently than other topology types. If
       // no parameter is found, do not add it to the list of dihedrals.
@@ -456,9 +461,21 @@ const
           improperCache.AddParm( paramTypes, ipa.front(), false );
         }
       }
+#     ifdef TIMER
+      t_dih_imp_.Stop();
+#     endif
     } else {
+#     ifdef TIMER
+      t_dih_dih_.Start();
+#     endif
       // -----Regular dihedral. See if parameter already present. ----
+#     ifdef TIMER
+      t_dih_dih_getnew_.Start();
+#     endif
       DihedralParmArray dpa = newDihedralParams.FindParam( types, found );
+#     ifdef TIMER
+      t_dih_dih_getnew_.Stop();
+#     endif
       if (!found) {
         mprintf("Warning: Dihedral parameters not found for dihedral %s-%s-%s-%s (%s-%s-%s-%s)\n",
                 topOut.TruncResAtomNameNum(dih->A1()).c_str(),
@@ -540,6 +557,9 @@ const
 //            (int)mydih.IsImproper(), (int)mydih.Skip14());
         }
       }
+#     ifdef TIMER
+      t_dih_dih_.Stop();
+#     endif
     }
   } // END loop over all dihedrals
   return dihedralsIn;
@@ -568,7 +588,9 @@ void AssignParams::AssignDihedralParams(Topology& topOut,
                                         DihedralParmHolder const& newDihedralParams,
                                         ImproperParmHolder const& newImproperParams,
                                         ParmHolder<AtomType> const& AT)
+#ifndef TIMER
 const
+#endif
 {
   topOut.ModifyDihedralParm().clear();
   // Dihedrals can be a bit of a pain since there can be multiple
@@ -1186,9 +1208,13 @@ void AssignParams::WriteAssignTiming(int indent, double totalIn) const {
   t_angles_.WriteTiming(indent+1,    "Angles                 ", t_total_.Total());
   t_dihedrals_.WriteTiming(indent+1, "Dihedrals              ", t_total_.Total());
   t_multi_.WriteTiming(indent+1,     "Dihedral Multiplicities", t_total_.Total());
+  t_improper_.WriteTiming(indent+1,  "Impropers              ", t_total_.Total());
+  double t_dih_total = t_multi_.Total() + t_improper_.Total();
+  t_dih_imp_.WriteTiming(indent+2,   "Dih. Assign Improper", t_dih_total);
+  t_dih_dih_.WriteTiming(indent+2,   "Dih. Assign Dihedral", t_dih_total);
+  t_dih_dih_getnew_.WriteTiming(indent+3, "Get Dihedral Param", t_dih_dih_.Total());
   t_cmaps_.WriteTiming(indent+1,     "CMAPs                  ", t_total_.Total());
   t_UB_.WriteTiming(indent+1,        "Urey-Bradleys          ", t_total_.Total());
-  t_improper_.WriteTiming(indent+1,  "Impropers              ", t_total_.Total());
   t_atype_.WriteTiming(indent+1,     "Atom Types             ", t_total_.Total());
   t_nonbond_.WriteTiming(indent+1,   "Nonbonds               ", t_total_.Total());
 #endif
@@ -1196,7 +1222,11 @@ void AssignParams::WriteAssignTiming(int indent, double totalIn) const {
 
 /** Update/add to parameters in this topology with those from given set.
   */
-int AssignParams::UpdateParameters(Topology& topOut, ParameterSet const& set1) const {
+int AssignParams::UpdateParameters(Topology& topOut, ParameterSet const& set1)
+#ifndef TIMER
+const
+#endif
+{
   GetParams GP;
   ParameterSet set0 = GP.GetParameters( topOut );
 
diff --git a/src/Parm/AssignParams.h b/src/Parm/AssignParams.h
index 5d17910539..57daff1085 100644
--- a/src/Parm/AssignParams.h
+++ b/src/Parm/AssignParams.h
@@ -45,7 +45,12 @@ class AssignParams {
     int AssignParameters(Topology&, ParameterSet const&) const;
 #   endif
     /// Update existing parameters with given parameter set
-    int UpdateParameters(Topology&, ParameterSet const&) const;
+    int UpdateParameters(Topology&, ParameterSet const&)
+#   ifdef TIMER
+      ;
+#   else
+      const;
+#   endif
     // Assign nonbond parameters to topology. Used during Merge::AppendTop()
     void AssignNonbondParams(Topology&,
                              ParmHolder<AtomType> const&,
@@ -73,12 +78,20 @@ class AssignParams {
     DihedralArray AssignDihedralParm(Topology&,
                                      DihedralParmHolder const&, ImproperParmHolder const&,
                                      ParmHolder<AtomType> const&, DihedralArray const&,
-                                     bool) const; // TODO make the bool a class var?
+                                     bool)  // TODO make the bool a class var?
+#   ifdef TIMER
+      ;
+#   else
+      const;
+#   endif
     DihedralArray get_unique_dihedrals(DihedralArray const&) const;
     void AssignDihedralParams(Topology&, DihedralParmHolder const&, ImproperParmHolder const&,
-                              ParmHolder<AtomType> const&) const;
-
-
+                              ParmHolder<AtomType> const&)
+#   ifdef TIMER
+      ;
+#   else
+      const;
+#   endif
 
     static inline int cmap_anames_match(DihedralType const&, AtArray const&, std::vector<std::string> const&);
     int remap_cmap_indices(Topology const&, std::vector<int>&, CmapGridArray&, CmapArray&, CmapParmHolder const&) const;
@@ -100,6 +113,9 @@ class AssignParams {
     Timer t_dihedrals_;
     Timer t_cmaps_;
     Timer t_multi_;
+    Timer t_dih_imp_;
+    Timer t_dih_dih_;
+    Timer t_dih_dih_getnew_;
     Timer t_UB_;
     Timer t_improper_;
     Timer t_atype_;

From a0020ef9597997878f70958ad570ed7490ed8850 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 16 Oct 2025 09:57:34 -0400
Subject: [PATCH 0957/1492] Split ParameterHolders.h into an enum and 3 classes
 in the Parm namespace

---
 src/Parm/DihedralParmHolder.h | 174 +++++++++++++++++++++++++++++
 src/Parm/ImproperParmHolder.h | 203 ++++++++++++++++++++++++++++++++++
 src/Parm/ParmEnum.h           |   8 ++
 src/Parm/ParmHolder.h         | 120 ++++++++++++++++++++
 4 files changed, 505 insertions(+)
 create mode 100644 src/Parm/DihedralParmHolder.h
 create mode 100644 src/Parm/ImproperParmHolder.h
 create mode 100644 src/Parm/ParmEnum.h
 create mode 100644 src/Parm/ParmHolder.h

diff --git a/src/Parm/DihedralParmHolder.h b/src/Parm/DihedralParmHolder.h
new file mode 100644
index 0000000000..de257ba1d1
--- /dev/null
+++ b/src/Parm/DihedralParmHolder.h
@@ -0,0 +1,174 @@
+#ifndef INC_PARM_DIHEDRALPARMHOLDER_H
+#define INC_PARM_DIHEDRALPARMHOLDER_H
+#include <vector>
+#include <utility> // std::pair
+#include "ParmEnum.h"
+#include "../ParameterTypes.h"
+#include "../TypeNameHolder.h"
+//#incl ude "CpptrajStdio.h" // DEBUG
+namespace Cpptraj {
+namespace Parm {
+// -----------------------------------------------------------------------------
+/// Specialized class for associating atom types with dihedral parameters.
+/** NOTE: Instead of using a specialize template here I'm creating a new
+  *       class because while I want AddParm() to accept DihedralParmType,
+  *       I want FindParam to return an array of DihedralParmType, one for
+  *       each unique multiplicity.
+  */
+class DihedralParmHolder {
+    typedef std::pair<TypeNameHolder,DihedralParmArray> Bpair;
+    typedef std::vector<Bpair> Bmap;
+  public:
+    /// CONSTRUCTOR
+    DihedralParmHolder() {}
+    /// DESTRUCTOR - virtual since inherited
+    virtual ~DihedralParmHolder() {}
+    /// Clear dihedral parameters
+    void clear()              { bpmap_.clear();        }
+    /// \return Number of dihedral parameters
+    size_t size()       const { return bpmap_.size();  }
+    /// \return true if no dihedral parameters
+    bool empty()        const { return bpmap_.empty(); }
+    /// Set wildcard character
+    void SetWildcard(char wc) { wc_ = NameType(std::string(1, wc)); }
+    /// Add (or update) a single dihedral parameter for given atom types.
+    RetType AddParm(TypeNameHolder const& types, DihedralParmType const& dp, bool allowUpdate) {
+      // Check if parm for these types exist
+      Bmap::iterator it0 = bpmap_.begin();
+      for (; it0 != bpmap_.end(); ++it0)
+      {
+        if (it0->first.Match_NoWC( types ))
+          break;
+      }
+      if (it0 == bpmap_.end()) {
+        // Brand new dihedral for these types.
+        //mprintf("DEBUG: New dihedral parm: %s %s %s %s pk=%12.4f pn=%12.4f pp=%12.4f\n",
+        //        *types[0], *types[1], *types[2], *types[3], dp.Pk(), dp.Pn(), dp.Phase());
+        bpmap_.push_back( Bpair(types, DihedralParmArray(1, dp)) );
+      } else {
+        // If we are here types match - check multiplicity.
+        DihedralParmArray::iterator it1 = it0->second.begin();
+        for (; it1 != it0->second.end(); ++it1)
+        {
+          if (FEQ(it1->Pn(), dp.Pn()))
+            break;
+        }
+        if (it1 == it0->second.end()) {
+          // Brand new multiplicity for this dihedral.
+          //mprintf("DEBUG: Dihedral new mult: %s %s %s %s pk=%12.4f pn=%12.4f pp=%12.4f\n",
+          //        *types[0], *types[1], *types[2], *types[3], dp.Pk(), dp.Pn(), dp.Phase());
+          if (it0->second.empty())
+            it0->second.push_back( dp );
+          else if (dp.Pn() > it0->second.back().Pn())
+            it0->second.push_back( dp );
+          else {
+            // Try to keep multiplicities in order.
+            DihedralParmArray sorted;
+            bool isInserted = false;
+            for (DihedralParmArray::const_iterator jt = it0->second.begin(); jt != it0->second.end(); ++jt) {
+              if (!isInserted) {
+                if (dp.Pn() < jt->Pn()) {
+                  sorted.push_back( dp );
+                  isInserted = true;
+                }
+              }
+              sorted.push_back( *jt );
+            }
+            it0->second = sorted;
+          }
+        } else {
+          if (dp < *it1 || *it1 < dp) {
+            //mprintf("DEBUG: Attempt dihedral update mult (allow=%i): %s %s %s %s pk=%6.2f pn=%3.1f pp=%6.3f (orig pk=%6.2f pn=%3.1f pp=%6.3f )\n",
+            //        (int)allowUpdate, *types[0], *types[1], *types[2], *types[3], dp.Pk(), dp.Pn(), dp.Phase(), it1->Pk(), it1->Pn(), it1->Phase());
+            if (allowUpdate) {
+              *it1 = dp;
+              return UPDATED;
+            } else {
+              return ERR;
+            }
+          } else
+            return SAME;
+        }
+      }
+      return ADDED;
+    }
+    /// Add array of dihedral parameters with unique multiplicities
+    RetType AddParm(TypeNameHolder const& types, DihedralParmArray const& dpa, bool allowUpdate) {
+      // Check if parm for these types exist
+      Bmap::iterator it0 = bpmap_.begin();
+      for (; it0 != bpmap_.end(); ++it0)
+      {
+        if (it0->first.Match_NoWC( types ))
+          break;
+      }
+      if (it0 == bpmap_.end()) {
+        // Brand new dihedral for these types.
+        bpmap_.push_back( Bpair(types, dpa) );
+      } else {
+        if (!allowUpdate) return ERR;
+        // Check if sizes are the same.
+        bool update = false;
+        if (it0->second.size() != dpa.size())
+          update = true;
+        else {
+          // Sizes are the same. See if parameters are the same.
+          for (unsigned int i = 0; i != it0->second.size(); i++) {
+            if (it0->second[i] < dpa[i] || dpa[i] < it0->second[i]) {
+              update = true;
+              break;
+            }
+          }
+        }
+        if (update) {
+          it0->second = dpa;
+          return UPDATED;
+        } else
+          return SAME;
+      }
+      return ADDED;
+    }
+    /// Const iterator
+    typedef typename Bmap::const_iterator const_iterator;
+    /// \return const iterator to beginning
+    const_iterator begin() const { return bpmap_.begin(); }
+    /// \return const iterator to end
+    const_iterator end()   const { return bpmap_.end();   }
+    /// \return Array of dihedral parameters matching given atom types.
+    DihedralParmArray FindParam(TypeNameHolder const& types, bool& found) const {
+      found = true;
+      for (const_iterator it = begin(); it != end(); ++it)
+        if (it->first.Match_NoWC( types )) return it->second;
+      if (wc_.len() > 0) {
+        for (const_iterator it = begin(); it != end(); ++it)
+          if (it->first.Match_WC( types, wc_)) return it->second;
+      }
+      found = false;
+      return DihedralParmArray();
+    }
+    /// \return iterator to parameter matching the given types.
+    const_iterator GetParam(TypeNameHolder const& types) {
+      for (const_iterator it = begin(); it != end(); ++it)
+        if (it->first.Match_NoWC( types )) return it;
+      if (wc_.len() > 0) {
+        for (const_iterator it = begin(); it != end(); ++it)
+          if (it->first.Match_WC( types, wc_)) return it;
+      }
+      return end();
+    }
+    /// \return size in memory in bytes
+    size_t DataSize() const {
+      if (bpmap_.empty()) return 0;
+      const_iterator elt0 = begin();
+      // Assume all TypeNameHolders are the same size
+      return (bpmap_.size() * elt0->first.DataSize()) +
+             (bpmap_.size() * sizeof(DihedralParmArray)) +
+             sizeof(Bmap);
+    }
+  protected:
+    NameType wc_; ///< Wildcard character
+  private:
+    Bmap bpmap_;
+};
+} // END namespace Parm
+} // END namespace Cpptraj
+#endif
diff --git a/src/Parm/ImproperParmHolder.h b/src/Parm/ImproperParmHolder.h
new file mode 100644
index 0000000000..82da63c75e
--- /dev/null
+++ b/src/Parm/ImproperParmHolder.h
@@ -0,0 +1,203 @@
+#ifndef INC_PARM_IMPROPERPARMHOLDER_H
+#define INC_PARM_IMPROPERPARMHOLDER_H
+#include "DihedralParmHolder.h"
+//#incl ude "CpptrajStdio.h" // DEBUG
+namespace Cpptraj {
+namespace Parm {
+// -----------------------------------------------------------------------------
+/// Specialized class for associating atom types with improper parameters.
+/** Impropers are a little tricky in that by convention the third atom is
+  * the central atom, and all other atoms can be in any order.
+  * The Amber convention is usually (but not always) to have the non-central
+  * improper atom types sorted alphabetically, with wildcards given
+  * precedence, but this is not always the case and does not always work.
+  * For example, using straight up backwards/forwards matching, the wildcard
+  * type X-X-CW-H4 will not match the given alphabetized type C*-H4-CW-NA.
+  * All combinations of A1, A2, and A4 should be checked.
+  */
+class ImproperParmHolder : private DihedralParmHolder {
+    /// Function for matching wildcards (WildCard Match)
+    static inline bool wcm(NameType const& t0, NameType const& t1, NameType const& wc) {
+      return (t0 == wc || t0 == t1);
+    }
+    /// Function for swapping integers
+    static inline void swp(int& i1, int& i2) { int tmp = i1; i1 = i2; i2 = tmp; }
+  public:
+    /// Denote returned parameter atom type order
+    enum OrderType { O_013,
+                     O_031,
+                     O_103,
+                     O_130,
+                     O_301,
+                     O_310 };
+    ImproperParmHolder() : require_exact_match_(false) {}
+    /// \return Number of improper parameter sets
+    size_t size()              const { return DihedralParmHolder::size();  }
+    /// \return True if no parameters
+    bool empty()               const { return DihedralParmHolder::empty(); }
+    /// \return Wildcard
+    NameType const& Wildcard() const { return wc_; }
+    /// \return True if an exact match is required to find a parameter
+    bool RequireExactMatch()   const { return require_exact_match_; }
+    /// const iterator
+    typedef typename DihedralParmHolder::const_iterator const_iterator;
+    /// const iterator to beginning of parameters
+    const_iterator begin()     const { return DihedralParmHolder::begin(); }
+    /// const iterator to end of parameters
+    const_iterator end()       const { return DihedralParmHolder::end();   }
+    /// Set Wildcard char
+    void SetWildcard(char wc) { DihedralParmHolder::SetWildcard(wc); }
+    /// Set Wildcard
+    void SetWildcard(NameType const& wc) { wc_ = wc; }
+    /// Indicate whether exact type matches are required to find parameters
+    void SetRequireExactMatch(bool b) { require_exact_match_ = b; }
+    /// Add (or update) a single improper parameter for given atom types.
+    RetType AddParm(TypeNameHolder const& types, DihedralParmType const& dp, bool allowUpdate) {
+      return DihedralParmHolder::AddParm( types, dp, allowUpdate );
+    }
+    /// Add array of improper parameters, one for each multiplicity.
+    RetType AddParm(TypeNameHolder const& types, DihedralParmArray const& dpa, bool allowUpdate) {
+      return DihedralParmHolder::AddParm( types, dpa, allowUpdate );
+    }
+  private:
+    /// Remap the given improper according to the desired order, correct for wildcards in given types
+    void ReorderImproper(DihedralType& imp, OrderType order, TypeNameHolder const& types) const {
+      switch (order) {
+        case O_013 : break;
+        case O_031 : swp( imp.ChangeA2(), imp.ChangeA4() ); break;
+        case O_103 : swp( imp.ChangeA1(), imp.ChangeA2() ); break;
+        case O_130 : swp( imp.ChangeA1(), imp.ChangeA4() ); swp( imp.ChangeA1(), imp.ChangeA2() ); break;
+        case O_301 : swp( imp.ChangeA2(), imp.ChangeA4() ); swp( imp.ChangeA1(), imp.ChangeA2() ); break;
+        case O_310 : swp( imp.ChangeA1(), imp.ChangeA4() ); break;
+      }
+      if (wc_.len() > 0 && types.Size() > 0) {
+        // If there are wildcards, need to order matching types by atom index.
+        // General order of imp should now match types due to above swaps.
+        bool wc1 = (types[0] == wc_);
+        bool wc2 = (types[1] == wc_);
+        bool wc4 = (types[3] == wc_);
+        //mprintf("DEBUG: %s WC0=%i %s WC1=%i %s WC3=%i\n", *types[0], (int)wc1, *types[1], (int)wc2, *types[3], (int)wc4);
+        if (wc4 && wc2 && wc1) {
+          // All three wildcard - should be rare but need to check.
+          if (imp.A1() > imp.A2()) swp(imp.ChangeA1(), imp.ChangeA2());
+          if (imp.A2() > imp.A4()) swp(imp.ChangeA2(), imp.ChangeA4());
+          if (imp.A1() > imp.A2()) swp(imp.ChangeA1(), imp.ChangeA2());
+          if (imp.A2() > imp.A4()) swp(imp.ChangeA2(), imp.ChangeA4());
+        } else if (wc1 && wc2) {
+          if (imp.A1() > imp.A2()) swp(imp.ChangeA1(), imp.ChangeA2());
+        } else if (wc1 && wc4) {
+          if (imp.A1() > imp.A4()) swp(imp.ChangeA1(), imp.ChangeA4());
+        } else if (wc2 && wc4) {
+          if (imp.A2() > imp.A4()) swp(imp.ChangeA2(), imp.ChangeA4());
+        }
+      }
+    }
+  public:
+    /// Remap the given improper according to the desired order. Used by unit test to check that reordering works.
+    void ReorderImproper(DihedralType& imp, OrderType order) const {
+      ReorderImproper(imp, order, TypeNameHolder());
+    }
+    /// Get improper parameters matching given atom types. If found, improper will be reordered to match parameter order.
+    const_iterator GetParam(TypeNameHolder const& types, DihedralType& imp, bool& reordered) const {
+      //mprintf("DEBUG: FindParam wc=%s Inco=%s-%s-%s-%s\n",*wc_, *(types[0]), *(types[1]),   *(types[2]),   *(types[3]));
+      reordered = false;
+      OrderType lastOrder_ = O_013;
+      const_iterator it = begin();
+      // If we require an exact match, look for that first.
+      if (require_exact_match_) {
+        for (; it != end(); ++it) {
+          TypeNameHolder const& myTypes = it->first;
+          if (myTypes[2] == types[2] && myTypes[0] == types[0] &&
+              myTypes[1] == types[1] && myTypes[3] == types[3])
+          {
+            break;
+          }
+        }
+      } else {
+        // Inexact match. First, no wildcard
+        for (; it != end(); ++it) {
+          TypeNameHolder const& myTypes = it->first;
+          // Central (third) type must match
+          if (myTypes[2] == types[2]) {
+            //mprintf("DEBUG: FindParam (improper) central atom match %s", *(types[2]));
+            //mprintf(" This=%s-%s-%s-%s", *(myTypes[0]), *(myTypes[1]), *(myTypes[2]), *(myTypes[3]));
+            //mprintf(" Inco=%s-%s-%s-%s\n", *(types[0]), *(types[1]),   *(types[2]),   *(types[3]));
+            // Try all permutations
+            if (       myTypes[0] == types[0] && myTypes[1] == types[1] && myTypes[3] == types[3]) { // 0 1 2 3
+                lastOrder_ = O_013; break;
+            } else if (myTypes[0] == types[0] && myTypes[1] == types[3] && myTypes[3] == types[1]) { // 0 3 2 1
+                lastOrder_ = O_031; break;
+            } else if (myTypes[0] == types[1] && myTypes[1] == types[0] && myTypes[3] == types[3]) { // 1 0 2 3
+                lastOrder_ = O_103; break;
+            } else if (myTypes[0] == types[1] && myTypes[1] == types[3] && myTypes[3] == types[0]) { // 1 3 2 0
+                lastOrder_ = O_130; break;
+            } else if (myTypes[0] == types[3] && myTypes[1] == types[0] && myTypes[3] == types[1]) { // 3 0 2 1
+                lastOrder_ = O_301; break;
+            } else if (myTypes[0] == types[3] && myTypes[1] == types[1] && myTypes[3] == types[0]) { // 3 1 2 0
+                lastOrder_ = O_310; break;
+            }
+          }
+        } // END loop over parameters
+        // Second, do wildcard matches if wildcard is set.
+        if (it == end() && wc_.len() > 0) {
+          it = begin();
+          for (; it != end(); ++it) {
+            TypeNameHolder const& myTypes = it->first;
+            // Central (third) type must match
+            if (wcm(myTypes[2], types[2], wc_)) {
+              // Try all permutations
+              if (       wcm(myTypes[0], types[0], wc_) && wcm(myTypes[1], types[1], wc_) && wcm(myTypes[3], types[3], wc_)) { // 0 1 2 3
+                  lastOrder_ = O_013; break;
+              } else if (wcm(myTypes[0], types[0], wc_) && wcm(myTypes[1], types[3], wc_) && wcm(myTypes[3], types[1], wc_)) { // 0 3 2 1
+                  lastOrder_ = O_031; break;
+              } else if (wcm(myTypes[0], types[1], wc_) && wcm(myTypes[1], types[0], wc_) && wcm(myTypes[3], types[3], wc_)) { // 1 0 2 3
+                  lastOrder_ = O_103; break;
+              } else if (wcm(myTypes[0], types[1], wc_) && wcm(myTypes[1], types[3], wc_) && wcm(myTypes[3], types[0], wc_)) { // 1 3 2 0
+                  lastOrder_ = O_130; break;
+              } else if (wcm(myTypes[0], types[3], wc_) && wcm(myTypes[1], types[0], wc_) && wcm(myTypes[3], types[1], wc_)) { // 3 0 2 1
+                  lastOrder_ = O_301; break;
+              } else if (wcm(myTypes[0], types[3], wc_) && wcm(myTypes[1], types[1], wc_) && wcm(myTypes[3], types[0], wc_)) { // 3 1 2 0
+                  lastOrder_ = O_310; break;
+              }
+            }
+          } // END loop over parameters
+        } // END wildcard matches
+      } // END require exact match
+      if (it != end()) {
+        // We have found a parameter. Do any reordering.
+        if (lastOrder_ != O_013) reordered = true;
+        ReorderImproper( imp, lastOrder_, it->first );
+      }
+      return it;
+    } // END GetParam()
+    /// Get improper parameters matching given atom types. If found, improper will be reordered to match parameter order.
+    const_iterator GetParam(TypeNameHolder const& types) const {
+      DihedralType imp;
+      bool reordered = false;
+      return GetParam( types, imp, reordered);
+    }
+    /// \return Array of improper parameters matching given atom types. Improper will be reordered to match parameter order.
+    DihedralParmArray FindParam(TypeNameHolder const& types, bool& found, DihedralType& imp, bool& reordered) const {
+      const_iterator it = GetParam( types, imp, reordered );
+      if (it == end()) {
+        found = false;
+        return DihedralParmArray();
+      } else {
+        found = true;
+        return it->second;
+      }
+    } // END FindParam()
+    /// \return Dihedral parm array corresponding to types. Use by unit test.
+    DihedralParmArray FindParam(TypeNameHolder const& types, bool& found) const {
+      DihedralType blank;
+      bool reordered;
+      return FindParam(types, found, blank, reordered);
+    }
+    /// \return size in memory in bytes
+    size_t DataSize() const { return DihedralParmHolder::DataSize(); }
+  private:
+    bool require_exact_match_; ///< If true, types must match in exact order when finding parameters
+};
+} // END namespace Parm
+} // END namespace Cpptraj
+#endif
diff --git a/src/Parm/ParmEnum.h b/src/Parm/ParmEnum.h
new file mode 100644
index 0000000000..fb5433e27c
--- /dev/null
+++ b/src/Parm/ParmEnum.h
@@ -0,0 +1,8 @@
+#ifndef INC_PARM_PARMENUM_H
+#define INC_PARM_PARMENUM_H
+namespace Cpptraj {
+namespace Parm {
+  enum RetType { ADDED = 0, SAME, UPDATED, ERR };
+}
+}
+#endif
diff --git a/src/Parm/ParmHolder.h b/src/Parm/ParmHolder.h
new file mode 100644
index 0000000000..d83d47c562
--- /dev/null
+++ b/src/Parm/ParmHolder.h
@@ -0,0 +1,120 @@
+#ifndef INC_PARM_PARMHOLDER_H
+#define INC_PARM_PARMHOLDER_H
+#include <vector>
+#include <utility> // std::pair
+#include "ParmEnum.h"
+#include "../TypeNameHolder.h"
+//#incl ude "CpptrajStdio.h" // DEBUG
+namespace Cpptraj {
+namespace Parm {
+/// Used to associate atom type names with an object (parameter etc)
+template <class T> class ParmHolder {
+    // TODO may want to actually use a map one day for performance reasons.
+    typedef std::pair<TypeNameHolder,T> Bpair;
+    typedef std::vector<Bpair> Bmap;
+  public:
+    /// CONSTRUCTOR
+    ParmHolder() {}
+    /// Clear all parameters
+    void clear()              { bpmap_.clear(); }
+    /// \return Number of parameters
+    size_t size()       const { return bpmap_.size(); }
+    /// \return true if no parameters
+    bool empty()        const { return bpmap_.empty(); }
+    /// Set wildcard character
+    //void SetWildcard(char wc) { wc_ = NameType(std::string(1, wc)); }
+    /// Add (or update if allowed) given parameter to holder.
+    RetType AddParm(TypeNameHolder const& types, T const& bp, bool allowUpdate) {
+      // Check if parm for these types exist
+      typename Bmap::iterator it = bpmap_.begin();
+      for (; it != bpmap_.end(); ++it)
+        if (it->first.Match_NoWC( types )) break;
+      if (it == bpmap_.end()) {
+        // New parm
+        //mprintf("DEBUG: New parameter:");
+        //for (TypeNameHolder::const_iterator it = types.begin(); it != types.end(); ++it)
+        //  mprintf(" '%s'", *(*it));
+        //mprintf("\n");
+        bpmap_.push_back( Bpair(types, bp) );
+      } else {
+        if (bp < it->second || it->second < bp) {
+          //mprintf("DEBUG: Potential update of existing parameter:");
+          //for (TypeNameHolder::const_iterator it = types.begin(); it != types.end(); ++it)
+          //  mprintf(" '%s'", *(*it));
+          //mprintf("\n");
+          if (allowUpdate) {
+            it->second = bp;
+            return UPDATED;
+          } else {
+            return ERR;
+          }
+        } else {
+          //mprintf("DEBUG: Existing parameter:");
+          //for (TypeNameHolder::const_iterator it = types.begin(); it != types.end(); ++it)
+          //  mprintf(" '%s'", *(*it));
+          //mprintf("\n");
+          return SAME;
+        }
+      }
+      return ADDED;
+    }
+    /// Constant iterator
+    typedef typename Bmap::const_iterator const_iterator;
+    /// \return constant iterator to beginning
+    const_iterator begin() const { return bpmap_.begin(); }
+    /// \return constant iterator to end.
+    const_iterator end()   const { return bpmap_.end();   }
+    /// Iterator
+    typedef typename Bmap::iterator iterator;
+    /// \return iterator to beginning
+    iterator begin() { return bpmap_.begin(); }
+    /// \return iterator to end
+    iterator end()   { return bpmap_.end();   }
+    /// \return Parameter matching given types, or empty parameter if not found.
+    T FindParam(TypeNameHolder const& types, bool& found) const { // TODO only use GetParam()?
+      found = true;
+      for (const_iterator it = begin(); it != end(); ++it)
+        if (it->first.Match_NoWC( types )) return it->second;
+      //if (wc_.len() > 0) {
+      //  for (const_iterator it = begin(); it != end(); ++it)
+      //    if (it->first.Match_WC( types, wc_)) return it->second;
+      //}
+      found = false;
+      return T();
+    }
+    /// \return iterator to parameter matching the given types.
+    iterator GetParam(TypeNameHolder const& types) {
+      for (iterator it = bpmap_.begin(); it != bpmap_.end(); ++it)
+        if (it->first.Match_NoWC( types )) return it;
+      //if (wc_.len() > 0) {
+      //  for (iterator it = bpmap_.begin(); it != bpmap_.end(); ++it)
+      //    if (it->first.Match_WC( types, wc_)) return it;
+      //}
+      return bpmap_.end();
+    }
+    /// \return const iterator to parameter matching the given types.
+    const_iterator GetParam(TypeNameHolder const& types) const {
+      for (const_iterator it = bpmap_.begin(); it != bpmap_.end(); ++it)
+        if (it->first.Match_NoWC( types )) return it;
+      //if (wc_.len() > 0) {
+      //  for (const_iterator it = bpmap_.begin(); it != bpmap_.end(); ++it)
+      //    if (it->first.Match_WC( types, wc_)) return it;
+      //}
+      return bpmap_.end();
+    }
+    /// \return size in memory in bytes
+    size_t DataSize() const {
+      if (bpmap_.empty()) return 0;
+      const_iterator elt0 = begin();
+      // Assume all TypeNameHolders are the same size
+      return (bpmap_.size() * elt0->first.DataSize()) +
+             (bpmap_.size() * sizeof(T)) +
+             sizeof(Bmap);
+    }
+  private:
+    Bmap bpmap_;
+    //NameType wc_; ///< Wildcard character
+};
+} // END namespace Parm
+} // END namespace Cpptraj
+#endif

From 6539843bcd9787723763b75eb16c9b5b42f384fd Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 16 Oct 2025 09:58:01 -0400
Subject: [PATCH 0958/1492] Remove ParametersHolders.h

---
 src/ParameterHolders.h | 481 -----------------------------------------
 1 file changed, 481 deletions(-)
 delete mode 100644 src/ParameterHolders.h

diff --git a/src/ParameterHolders.h b/src/ParameterHolders.h
deleted file mode 100644
index 29582587c7..0000000000
--- a/src/ParameterHolders.h
+++ /dev/null
@@ -1,481 +0,0 @@
-#ifndef INC_PARAMETERHOLDERS_H
-#define INC_PARAMETERHOLDERS_H
-#include <vector>
-#include <utility> // std::pair
-#include "TypeNameHolder.h"
-#include "ParameterTypes.h"
-//#incl ude "CpptrajStdio.h" // DEBUG
-
-namespace ParameterHolders {
-  enum RetType { ADDED = 0, SAME, UPDATED, ERR };
-} /* END namespace ParameterHolders */
-
-/// Used to associate atom type names with an object (parameter etc)
-template <class T> class ParmHolder {
-    // TODO may want to actually use a map one day for performance reasons.
-    typedef std::pair<TypeNameHolder,T> Bpair;
-    typedef std::vector<Bpair> Bmap;
-  public:
-    /// CONSTRUCTOR
-    ParmHolder() {}
-    /// Clear all parameters
-    void clear()              { bpmap_.clear(); }
-    /// \return Number of parameters
-    size_t size()       const { return bpmap_.size(); }
-    /// \return true if no parameters
-    bool empty()        const { return bpmap_.empty(); }
-    /// Set wildcard character
-    //void SetWildcard(char wc) { wc_ = NameType(std::string(1, wc)); }
-    /// Add (or update if allowed) given parameter to holder.
-    ParameterHolders::RetType AddParm(TypeNameHolder const& types, T const& bp, bool allowUpdate) {
-      // Check if parm for these types exist
-      typename Bmap::iterator it = bpmap_.begin();
-      for (; it != bpmap_.end(); ++it)
-        if (it->first.Match_NoWC( types )) break;
-      if (it == bpmap_.end()) {
-        // New parm
-        //mprintf("DEBUG: New parameter:");
-        //for (TypeNameHolder::const_iterator it = types.begin(); it != types.end(); ++it)
-        //  mprintf(" '%s'", *(*it));
-        //mprintf("\n");
-        bpmap_.push_back( Bpair(types, bp) );
-      } else {
-        if (bp < it->second || it->second < bp) {
-          //mprintf("DEBUG: Potential update of existing parameter:");
-          //for (TypeNameHolder::const_iterator it = types.begin(); it != types.end(); ++it)
-          //  mprintf(" '%s'", *(*it));
-          //mprintf("\n");
-          if (allowUpdate) {
-            it->second = bp;
-            return ParameterHolders::UPDATED;
-          } else {
-            return ParameterHolders::ERR;
-          }
-        } else {
-          //mprintf("DEBUG: Existing parameter:");
-          //for (TypeNameHolder::const_iterator it = types.begin(); it != types.end(); ++it)
-          //  mprintf(" '%s'", *(*it));
-          //mprintf("\n");
-          return ParameterHolders::SAME;
-        }
-      }
-      return ParameterHolders::ADDED;
-    }
-    /// Constant iterator
-    typedef typename Bmap::const_iterator const_iterator;
-    /// \return constant iterator to beginning
-    const_iterator begin() const { return bpmap_.begin(); }
-    /// \return constant iterator to end.
-    const_iterator end()   const { return bpmap_.end();   }
-    /// Iterator
-    typedef typename Bmap::iterator iterator;
-    /// \return iterator to beginning
-    iterator begin() { return bpmap_.begin(); }
-    /// \return iterator to end
-    iterator end()   { return bpmap_.end();   }
-    /// \return Parameter matching given types, or empty parameter if not found.
-    T FindParam(TypeNameHolder const& types, bool& found) const { // TODO only use GetParam()?
-      found = true;
-      for (const_iterator it = begin(); it != end(); ++it)
-        if (it->first.Match_NoWC( types )) return it->second;
-      //if (wc_.len() > 0) {
-      //  for (const_iterator it = begin(); it != end(); ++it)
-      //    if (it->first.Match_WC( types, wc_)) return it->second;
-      //}
-      found = false;
-      return T();
-    }
-    /// \return iterator to parameter matching the given types.
-    iterator GetParam(TypeNameHolder const& types) {
-      for (iterator it = bpmap_.begin(); it != bpmap_.end(); ++it)
-        if (it->first.Match_NoWC( types )) return it;
-      //if (wc_.len() > 0) {
-      //  for (iterator it = bpmap_.begin(); it != bpmap_.end(); ++it)
-      //    if (it->first.Match_WC( types, wc_)) return it;
-      //}
-      return bpmap_.end();
-    }
-    /// \return const iterator to parameter matching the given types.
-    const_iterator GetParam(TypeNameHolder const& types) const {
-      for (const_iterator it = bpmap_.begin(); it != bpmap_.end(); ++it)
-        if (it->first.Match_NoWC( types )) return it;
-      //if (wc_.len() > 0) {
-      //  for (const_iterator it = bpmap_.begin(); it != bpmap_.end(); ++it)
-      //    if (it->first.Match_WC( types, wc_)) return it;
-      //}
-      return bpmap_.end();
-    }
-    /// \return size in memory in bytes
-    size_t DataSize() const {
-      if (bpmap_.empty()) return 0;
-      const_iterator elt0 = begin();
-      // Assume all TypeNameHolders are the same size
-      return (bpmap_.size() * elt0->first.DataSize()) +
-             (bpmap_.size() * sizeof(T)) +
-             sizeof(Bmap);
-    }
-  private:
-    Bmap bpmap_;
-    //NameType wc_; ///< Wildcard character
-};
-
-// -----------------------------------------------------------------------------
-/// Specialized class for associating atom types with dihedral parameters.
-/** NOTE: Instead of using a specialize template here I'm creating a new
-  *       class because while I want AddParm() to accept DihedralParmType,
-  *       I want FindParam to return an array of DihedralParmType, one for
-  *       each unique multiplicity.
-  */
-class DihedralParmHolder {
-    typedef std::pair<TypeNameHolder,DihedralParmArray> Bpair;
-    typedef std::vector<Bpair> Bmap;
-  public:
-    /// CONSTRUCTOR
-    DihedralParmHolder() {}
-    /// DESTRUCTOR - virtual since inherited
-    virtual ~DihedralParmHolder() {}
-    /// Clear dihedral parameters
-    void clear()              { bpmap_.clear();        }
-    /// \return Number of dihedral parameters
-    size_t size()       const { return bpmap_.size();  }
-    /// \return true if no dihedral parameters
-    bool empty()        const { return bpmap_.empty(); }
-    /// Set wildcard character
-    void SetWildcard(char wc) { wc_ = NameType(std::string(1, wc)); }
-    /// Add (or update) a single dihedral parameter for given atom types.
-    ParameterHolders::RetType
-    AddParm(TypeNameHolder const& types, DihedralParmType const& dp, bool allowUpdate) {
-      // Check if parm for these types exist
-      Bmap::iterator it0 = bpmap_.begin();
-      for (; it0 != bpmap_.end(); ++it0)
-      {
-        if (it0->first.Match_NoWC( types ))
-          break;
-      }
-      if (it0 == bpmap_.end()) {
-        // Brand new dihedral for these types.
-        //mprintf("DEBUG: New dihedral parm: %s %s %s %s pk=%12.4f pn=%12.4f pp=%12.4f\n",
-        //        *types[0], *types[1], *types[2], *types[3], dp.Pk(), dp.Pn(), dp.Phase());
-        bpmap_.push_back( Bpair(types, DihedralParmArray(1, dp)) );
-      } else {
-        // If we are here types match - check multiplicity.
-        DihedralParmArray::iterator it1 = it0->second.begin();
-        for (; it1 != it0->second.end(); ++it1)
-        {
-          if (FEQ(it1->Pn(), dp.Pn()))
-            break;
-        }
-        if (it1 == it0->second.end()) {
-          // Brand new multiplicity for this dihedral.
-          //mprintf("DEBUG: Dihedral new mult: %s %s %s %s pk=%12.4f pn=%12.4f pp=%12.4f\n",
-          //        *types[0], *types[1], *types[2], *types[3], dp.Pk(), dp.Pn(), dp.Phase());
-          if (it0->second.empty())
-            it0->second.push_back( dp );
-          else if (dp.Pn() > it0->second.back().Pn())
-            it0->second.push_back( dp );
-          else {
-            // Try to keep multiplicities in order.
-            DihedralParmArray sorted;
-            bool isInserted = false;
-            for (DihedralParmArray::const_iterator jt = it0->second.begin(); jt != it0->second.end(); ++jt) {
-              if (!isInserted) {
-                if (dp.Pn() < jt->Pn()) {
-                  sorted.push_back( dp );
-                  isInserted = true;
-                }
-              }
-              sorted.push_back( *jt );
-            }
-            it0->second = sorted;
-          }
-        } else {
-          if (dp < *it1 || *it1 < dp) {
-            //mprintf("DEBUG: Attempt dihedral update mult (allow=%i): %s %s %s %s pk=%6.2f pn=%3.1f pp=%6.3f (orig pk=%6.2f pn=%3.1f pp=%6.3f )\n",
-            //        (int)allowUpdate, *types[0], *types[1], *types[2], *types[3], dp.Pk(), dp.Pn(), dp.Phase(), it1->Pk(), it1->Pn(), it1->Phase());
-            if (allowUpdate) {
-              *it1 = dp;
-              return ParameterHolders::UPDATED;
-            } else {
-              return ParameterHolders::ERR;
-            }
-          } else
-            return ParameterHolders::SAME;
-        }
-      }
-      return ParameterHolders::ADDED;
-    }
-    /// Add array of dihedral parameters with unique multiplicities
-    ParameterHolders::RetType
-    AddParm(TypeNameHolder const& types, DihedralParmArray const& dpa, bool allowUpdate) {
-      // Check if parm for these types exist
-      Bmap::iterator it0 = bpmap_.begin();
-      for (; it0 != bpmap_.end(); ++it0)
-      {
-        if (it0->first.Match_NoWC( types ))
-          break;
-      }
-      if (it0 == bpmap_.end()) {
-        // Brand new dihedral for these types.
-        bpmap_.push_back( Bpair(types, dpa) );
-      } else {
-        if (!allowUpdate) return ParameterHolders::ERR;
-        // Check if sizes are the same.
-        bool update = false;
-        if (it0->second.size() != dpa.size())
-          update = true;
-        else {
-          // Sizes are the same. See if parameters are the same.
-          for (unsigned int i = 0; i != it0->second.size(); i++) {
-            if (it0->second[i] < dpa[i] || dpa[i] < it0->second[i]) {
-              update = true;
-              break;
-            }
-          }
-        }
-        if (update) {
-          it0->second = dpa;
-          return ParameterHolders::UPDATED;
-        } else
-          return ParameterHolders::SAME;
-      }
-      return ParameterHolders::ADDED;
-    }
-    /// Const iterator
-    typedef typename Bmap::const_iterator const_iterator;
-    /// \return const iterator to beginning
-    const_iterator begin() const { return bpmap_.begin(); }
-    /// \return const iterator to end
-    const_iterator end()   const { return bpmap_.end();   }
-    /// \return Array of dihedral parameters matching given atom types.
-    DihedralParmArray FindParam(TypeNameHolder const& types, bool& found) const {
-      found = true;
-      for (const_iterator it = begin(); it != end(); ++it)
-        if (it->first.Match_NoWC( types )) return it->second;
-      if (wc_.len() > 0) {
-        for (const_iterator it = begin(); it != end(); ++it)
-          if (it->first.Match_WC( types, wc_)) return it->second;
-      }
-      found = false;
-      return DihedralParmArray();
-    }
-    /// \return iterator to parameter matching the given types.
-    const_iterator GetParam(TypeNameHolder const& types) {
-      for (const_iterator it = begin(); it != end(); ++it)
-        if (it->first.Match_NoWC( types )) return it;
-      if (wc_.len() > 0) {
-        for (const_iterator it = begin(); it != end(); ++it)
-          if (it->first.Match_WC( types, wc_)) return it;
-      }
-      return end();
-    }
-    /// \return size in memory in bytes
-    size_t DataSize() const {
-      if (bpmap_.empty()) return 0;
-      const_iterator elt0 = begin();
-      // Assume all TypeNameHolders are the same size
-      return (bpmap_.size() * elt0->first.DataSize()) +
-             (bpmap_.size() * sizeof(DihedralParmArray)) +
-             sizeof(Bmap);
-    }
-  protected:
-    NameType wc_; ///< Wildcard character
-  private:
-    Bmap bpmap_;
-};
-// -----------------------------------------------------------------------------
-/// Specialized class for associating atom types with improper parameters.
-/** Impropers are a little tricky in that by convention the third atom is
-  * the central atom, and all other atoms can be in any order.
-  * The Amber convention is usually (but not always) to have the non-central
-  * improper atom types sorted alphabetically, with wildcards given
-  * precedence, but this is not always the case and does not always work.
-  * For example, using straight up backwards/forwards matching, the wildcard
-  * type X-X-CW-H4 will not match the given alphabetized type C*-H4-CW-NA.
-  * All combinations of A1, A2, and A4 should be checked.
-  */
-class ImproperParmHolder : private DihedralParmHolder {
-    /// Function for matching wildcards (WildCard Match)
-    static inline bool wcm(NameType const& t0, NameType const& t1, NameType const& wc) {
-      return (t0 == wc || t0 == t1);
-    }
-    /// Function for swapping integers
-    static inline void swp(int& i1, int& i2) { int tmp = i1; i1 = i2; i2 = tmp; }
-  public:
-    /// Denote returned parameter atom type order
-    enum OrderType { O_013,
-                     O_031,
-                     O_103,
-                     O_130,
-                     O_301,
-                     O_310 };
-    ImproperParmHolder() : require_exact_match_(false) {}
-    /// \return Number of improper parameter sets
-    size_t size()              const { return DihedralParmHolder::size();  }
-    /// \return True if no parameters
-    bool empty()               const { return DihedralParmHolder::empty(); }
-    /// \return Wildcard
-    NameType const& Wildcard() const { return wc_; }
-    /// \return True if an exact match is required to find a parameter
-    bool RequireExactMatch()   const { return require_exact_match_; }
-    /// const iterator
-    typedef typename DihedralParmHolder::const_iterator const_iterator;
-    /// const iterator to beginning of parameters
-    const_iterator begin()     const { return DihedralParmHolder::begin(); }
-    /// const iterator to end of parameters
-    const_iterator end()       const { return DihedralParmHolder::end();   }
-    /// Set Wildcard char
-    void SetWildcard(char wc) { DihedralParmHolder::SetWildcard(wc); }
-    /// Set Wildcard
-    void SetWildcard(NameType const& wc) { wc_ = wc; }
-    /// Indicate whether exact type matches are required to find parameters
-    void SetRequireExactMatch(bool b) { require_exact_match_ = b; }
-    /// Add (or update) a single improper parameter for given atom types.
-    ParameterHolders::RetType
-    AddParm(TypeNameHolder const& types, DihedralParmType const& dp, bool allowUpdate) {
-      return DihedralParmHolder::AddParm( types, dp, allowUpdate );
-    }
-    /// Add array of improper parameters, one for each multiplicity.
-    ParameterHolders::RetType
-    AddParm(TypeNameHolder const& types, DihedralParmArray const& dpa, bool allowUpdate) {
-      return DihedralParmHolder::AddParm( types, dpa, allowUpdate );
-    }
-  private:
-    /// Remap the given improper according to the desired order, correct for wildcards in given types
-    void ReorderImproper(DihedralType& imp, OrderType order, TypeNameHolder const& types) const {
-      switch (order) {
-        case O_013 : break;
-        case O_031 : swp( imp.ChangeA2(), imp.ChangeA4() ); break;
-        case O_103 : swp( imp.ChangeA1(), imp.ChangeA2() ); break;
-        case O_130 : swp( imp.ChangeA1(), imp.ChangeA4() ); swp( imp.ChangeA1(), imp.ChangeA2() ); break;
-        case O_301 : swp( imp.ChangeA2(), imp.ChangeA4() ); swp( imp.ChangeA1(), imp.ChangeA2() ); break;
-        case O_310 : swp( imp.ChangeA1(), imp.ChangeA4() ); break;
-      }
-      if (wc_.len() > 0 && types.Size() > 0) {
-        // If there are wildcards, need to order matching types by atom index.
-        // General order of imp should now match types due to above swaps.
-        bool wc1 = (types[0] == wc_);
-        bool wc2 = (types[1] == wc_);
-        bool wc4 = (types[3] == wc_);
-        //mprintf("DEBUG: %s WC0=%i %s WC1=%i %s WC3=%i\n", *types[0], (int)wc1, *types[1], (int)wc2, *types[3], (int)wc4);
-        if (wc4 && wc2 && wc1) {
-          // All three wildcard - should be rare but need to check.
-          if (imp.A1() > imp.A2()) swp(imp.ChangeA1(), imp.ChangeA2());
-          if (imp.A2() > imp.A4()) swp(imp.ChangeA2(), imp.ChangeA4());
-          if (imp.A1() > imp.A2()) swp(imp.ChangeA1(), imp.ChangeA2());
-          if (imp.A2() > imp.A4()) swp(imp.ChangeA2(), imp.ChangeA4());
-        } else if (wc1 && wc2) {
-          if (imp.A1() > imp.A2()) swp(imp.ChangeA1(), imp.ChangeA2());
-        } else if (wc1 && wc4) {
-          if (imp.A1() > imp.A4()) swp(imp.ChangeA1(), imp.ChangeA4());
-        } else if (wc2 && wc4) {
-          if (imp.A2() > imp.A4()) swp(imp.ChangeA2(), imp.ChangeA4());
-        }
-      }
-    }
-  public:
-    /// Remap the given improper according to the desired order. Used by unit test to check that reordering works.
-    void ReorderImproper(DihedralType& imp, OrderType order) const {
-      ReorderImproper(imp, order, TypeNameHolder());
-    }
-    /// Get improper parameters matching given atom types. If found, improper will be reordered to match parameter order.
-    const_iterator GetParam(TypeNameHolder const& types, DihedralType& imp, bool& reordered) const {
-      //mprintf("DEBUG: FindParam wc=%s Inco=%s-%s-%s-%s\n",*wc_, *(types[0]), *(types[1]),   *(types[2]),   *(types[3]));
-      reordered = false;
-      OrderType lastOrder_ = O_013;
-      const_iterator it = begin();
-      // If we require an exact match, look for that first.
-      if (require_exact_match_) {
-        for (; it != end(); ++it) {
-          TypeNameHolder const& myTypes = it->first;
-          if (myTypes[2] == types[2] && myTypes[0] == types[0] &&
-              myTypes[1] == types[1] && myTypes[3] == types[3])
-          {
-            break;
-          }
-        }
-      } else {
-        // Inexact match. First, no wildcard
-        for (; it != end(); ++it) {
-          TypeNameHolder const& myTypes = it->first;
-          // Central (third) type must match
-          if (myTypes[2] == types[2]) {
-            //mprintf("DEBUG: FindParam (improper) central atom match %s", *(types[2]));
-            //mprintf(" This=%s-%s-%s-%s", *(myTypes[0]), *(myTypes[1]), *(myTypes[2]), *(myTypes[3]));
-            //mprintf(" Inco=%s-%s-%s-%s\n", *(types[0]), *(types[1]),   *(types[2]),   *(types[3]));
-            // Try all permutations
-            if (       myTypes[0] == types[0] && myTypes[1] == types[1] && myTypes[3] == types[3]) { // 0 1 2 3
-                lastOrder_ = O_013; break;
-            } else if (myTypes[0] == types[0] && myTypes[1] == types[3] && myTypes[3] == types[1]) { // 0 3 2 1
-                lastOrder_ = O_031; break;
-            } else if (myTypes[0] == types[1] && myTypes[1] == types[0] && myTypes[3] == types[3]) { // 1 0 2 3
-                lastOrder_ = O_103; break;
-            } else if (myTypes[0] == types[1] && myTypes[1] == types[3] && myTypes[3] == types[0]) { // 1 3 2 0
-                lastOrder_ = O_130; break;
-            } else if (myTypes[0] == types[3] && myTypes[1] == types[0] && myTypes[3] == types[1]) { // 3 0 2 1
-                lastOrder_ = O_301; break;
-            } else if (myTypes[0] == types[3] && myTypes[1] == types[1] && myTypes[3] == types[0]) { // 3 1 2 0
-                lastOrder_ = O_310; break;
-            }
-          }
-        } // END loop over parameters
-        // Second, do wildcard matches if wildcard is set.
-        if (it == end() && wc_.len() > 0) {
-          it = begin();
-          for (; it != end(); ++it) {
-            TypeNameHolder const& myTypes = it->first;
-            // Central (third) type must match
-            if (wcm(myTypes[2], types[2], wc_)) {
-              // Try all permutations
-              if (       wcm(myTypes[0], types[0], wc_) && wcm(myTypes[1], types[1], wc_) && wcm(myTypes[3], types[3], wc_)) { // 0 1 2 3
-                  lastOrder_ = O_013; break;
-              } else if (wcm(myTypes[0], types[0], wc_) && wcm(myTypes[1], types[3], wc_) && wcm(myTypes[3], types[1], wc_)) { // 0 3 2 1
-                  lastOrder_ = O_031; break;
-              } else if (wcm(myTypes[0], types[1], wc_) && wcm(myTypes[1], types[0], wc_) && wcm(myTypes[3], types[3], wc_)) { // 1 0 2 3
-                  lastOrder_ = O_103; break;
-              } else if (wcm(myTypes[0], types[1], wc_) && wcm(myTypes[1], types[3], wc_) && wcm(myTypes[3], types[0], wc_)) { // 1 3 2 0
-                  lastOrder_ = O_130; break;
-              } else if (wcm(myTypes[0], types[3], wc_) && wcm(myTypes[1], types[0], wc_) && wcm(myTypes[3], types[1], wc_)) { // 3 0 2 1
-                  lastOrder_ = O_301; break;
-              } else if (wcm(myTypes[0], types[3], wc_) && wcm(myTypes[1], types[1], wc_) && wcm(myTypes[3], types[0], wc_)) { // 3 1 2 0
-                  lastOrder_ = O_310; break;
-              }
-            }
-          } // END loop over parameters
-        } // END wildcard matches
-      } // END require exact match
-      if (it != end()) {
-        // We have found a parameter. Do any reordering.
-        if (lastOrder_ != O_013) reordered = true;
-        ReorderImproper( imp, lastOrder_, it->first );
-      }
-      return it;
-    } // END GetParam()
-    /// Get improper parameters matching given atom types. If found, improper will be reordered to match parameter order.
-    const_iterator GetParam(TypeNameHolder const& types) const {
-      DihedralType imp;
-      bool reordered = false;
-      return GetParam( types, imp, reordered);
-    }
-    /// \return Array of improper parameters matching given atom types. Improper will be reordered to match parameter order.
-    DihedralParmArray FindParam(TypeNameHolder const& types, bool& found, DihedralType& imp, bool& reordered) const {
-      const_iterator it = GetParam( types, imp, reordered );
-      if (it == end()) {
-        found = false;
-        return DihedralParmArray();
-      } else {
-        found = true;
-        return it->second;
-      }
-    } // END FindParam()
-    /// \return Dihedral parm array corresponding to types. Use by unit test.
-    DihedralParmArray FindParam(TypeNameHolder const& types, bool& found) const {
-      DihedralType blank;
-      bool reordered;
-      return FindParam(types, found, blank, reordered);
-    }
-    /// \return size in memory in bytes
-    size_t DataSize() const { return DihedralParmHolder::DataSize(); }
-  private:
-    bool require_exact_match_; ///< If true, types must match in exact order when finding parameters
-};
-#endif

From effefa7d5fa27d526a68409e1e28ecbca833b607 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 16 Oct 2025 10:18:13 -0400
Subject: [PATCH 0959/1492] Fix CmapParmHolder for new holder classes

---
 src/CmapParmHolder.cpp | 12 ++++++------
 src/CmapParmHolder.h   |  4 ++--
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/CmapParmHolder.cpp b/src/CmapParmHolder.cpp
index 5a2d8d1f69..08b7e17505 100644
--- a/src/CmapParmHolder.cpp
+++ b/src/CmapParmHolder.cpp
@@ -11,7 +11,7 @@ CmapParmHolder::CmapParmHolder() {}
   * CMAP terms are different in that they are applied via residue name instead
   * of atom type, hence the separate routine.
   */
-ParameterHolders::RetType CmapParmHolder::AddParm(CmapGridType const& cmap1, bool allowUpdate) {
+Cpptraj::Parm::RetType CmapParmHolder::AddParm(CmapGridType const& cmap1, bool allowUpdate) {
   typedef std::vector<std::string> Sarray;
   enum ResMatchType { NO_MATCH = 0, FULL_MATCH, PARTIAL_MATCH };
   // Does a CMAP for any of the residues exist?
@@ -61,28 +61,28 @@ ParameterHolders::RetType CmapParmHolder::AddParm(CmapGridType const& cmap1, boo
     mprinterr("Internal Error: Partial match between new CMAP '%s' and existing CMAP '%s'\n"
               "Internal Error:   Not yet set up to handle this kind of parameter update.\n",
               cmap1.Title().c_str(), currentCmap->Title().c_str());
-    return ParameterHolders::ERR;
+    return Cpptraj::Parm::ERR;
   } else if (mtype == FULL_MATCH) {
     mprintf("DEBUG: Potential match between new CMAP '%s' and existing CMAP '%s'\n",
             cmap1.Title().c_str(), currentCmap->Title().c_str());
     // Is this parameter the same?
     if (currentCmap->GridMatches( cmap1 )) {
       mprintf("DEBUG: CMAP parameter already present.\n");
-      return ParameterHolders::SAME;
+      return Cpptraj::Parm::SAME;
     } else {
       if (allowUpdate) {
         mprintf("DEBUG: Update of CMAP parameter.\n");
         *currentCmap = cmap1;
-        return ParameterHolders::UPDATED;
+        return Cpptraj::Parm::UPDATED;
       } else {
         mprintf("DEBUG: Update of CMAP parameter NOT ALLOWED.\n");
-        return ParameterHolders::ERR;
+        return Cpptraj::Parm::ERR;
       }
     }
   }
   // NO_MATCH
   mprintf("DEBUG: CMAP '%s' is a new CMAP.\n", cmap1.Title().c_str());
   CMAP_.push_back( cmap1 );
-  return ParameterHolders::ADDED;
+  return Cpptraj::Parm::ADDED;
 }
 
diff --git a/src/CmapParmHolder.h b/src/CmapParmHolder.h
index 78b4f6045d..70a5757ef7 100644
--- a/src/CmapParmHolder.h
+++ b/src/CmapParmHolder.h
@@ -2,7 +2,7 @@
 #define INC_PARM_CMAPPARMHOLDER_H
 class CmapGridType;
 #include <vector>
-#include "ParameterHolders.h" // TODO fix the includes
+#include "Parm/ParmEnum.h"
 //namespace Cpptraj {
 //namespace Parm {
 /// Hold CMAP terms
@@ -27,7 +27,7 @@ class CmapParmHolder {
     /// \return Modifiable CMAP at index
     
     /// Add/update cmap term
-    ParameterHolders::RetType AddParm(CmapGridType const&, bool);
+    Cpptraj::Parm::RetType AddParm(CmapGridType const&, bool);
   private:
     Carray CMAP_;
 };

From e30e6248854d25c19052d13a7204a9dcac0d51c4 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 16 Oct 2025 10:23:46 -0400
Subject: [PATCH 0960/1492] Move ParameterSet to Parm

---
 src/{ => Parm}/ParameterSet.cpp | 20 +++++++++++---------
 src/{ => Parm}/ParameterSet.h   | 14 ++++++++++----
 2 files changed, 21 insertions(+), 13 deletions(-)
 rename src/{ => Parm}/ParameterSet.cpp (97%)
 rename src/{ => Parm}/ParameterSet.h (96%)

diff --git a/src/ParameterSet.cpp b/src/Parm/ParameterSet.cpp
similarity index 97%
rename from src/ParameterSet.cpp
rename to src/Parm/ParameterSet.cpp
index 095ceae661..5555fd971c 100644
--- a/src/ParameterSet.cpp
+++ b/src/Parm/ParameterSet.cpp
@@ -1,8 +1,10 @@
 #include "ParameterSet.h"
-#include "CpptrajFile.h"
-#include "CpptrajStdio.h"
-#include "Constants.h"
-#include "UpdateParameters.h"
+#include "../CpptrajFile.h"
+#include "../CpptrajStdio.h"
+#include "../Constants.h"
+#include "../UpdateParameters.h"
+
+using namespace Cpptraj::Parm;
 
 size_t ParameterSet::DataSize() const {
   unsigned int cmapsize = 0;
@@ -187,16 +189,16 @@ int ParameterSet::updateCmapParams(CmapParmHolder const& cmap1, int verbose) {
   int updateCount = 0;
   for (CmapParmHolder::const_iterator newp = cmap1.begin(); newp != cmap1.end(); ++newp)
   {
-    ParameterHolders::RetType ret = CMAP_.AddParm( *newp, true );
-    if (ret != ParameterHolders::ERR) {
+    RetType ret = CMAP_.AddParm( *newp, true );
+    if (ret != ERR) {
       bool print = false;
-      if (ret == ParameterHolders::ADDED) {
+      if (ret == ADDED) {
         if (verbose > 2) { mprintf("\tAdded NEW CMAP parameter:"); print = true; }
         updateCount++;
-      } else if (ret == ParameterHolders::UPDATED) {
+      } else if (ret == UPDATED) {
         if (verbose > 0) { mprintf("\tUpdated CMAP parameter:"); print = true; }
         updateCount++;
-      } else if (ret == ParameterHolders::SAME) {
+      } else if (ret == SAME) {
         if (verbose > 1) { mprintf("\tParameter for CMAP already present:"); print = true; }
       }
       if (print) {
diff --git a/src/ParameterSet.h b/src/Parm/ParameterSet.h
similarity index 96%
rename from src/ParameterSet.h
rename to src/Parm/ParameterSet.h
index 1468bf8cd1..76a97cf7ff 100644
--- a/src/ParameterSet.h
+++ b/src/Parm/ParameterSet.h
@@ -1,15 +1,19 @@
 #ifndef INC_PARAMETERSET_H
 #define INC_PARAMETERSET_H
-#include "ParameterTypes.h"
-#include "ParameterHolders.h"
-#include "CmapParmHolder.h"
-#include "AtomType.h"
+#include "ParmHolder.h"
+#include "DihedralParmHolder.h"
+#include "ImproperParmHolder.h"
+#include "../AtomType.h"
+#include "../CmapParmHolder.h"
+#include "../ParameterTypes.h"
 class CpptrajFile;
 /// Hold a set of parameters for atom types, bonds, angles, etc.
 /** NOTE: Although LJ 6-12 regular type indices and 1-4 type indices
   *       are currently the same, there is a separate 1-4 types variable
   *       here in case that ever changes in the future.
   */
+namespace Cpptraj {
+namespace Parm {
 class ParameterSet {
   public:
     ParameterSet() : hasLJparams_(false) {}
@@ -110,4 +114,6 @@ class ParameterSet {
     NsetType hydrophilicAtomTypes_;        ///< Hold names of hydrophilic atom types
     bool hasLJparams_;
 };
+}
+}
 #endif

From c6bc5ed879b1d7cec0582793acb96bcfe7564457 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 16 Oct 2025 10:33:30 -0400
Subject: [PATCH 0961/1492] Update for moved ParmHolder

---
 src/Parm/Merge.cpp | 26 +++++++++++++-------------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/src/Parm/Merge.cpp b/src/Parm/Merge.cpp
index 4cc1209b95..1c4e8b77bc 100644
--- a/src/Parm/Merge.cpp
+++ b/src/Parm/Merge.cpp
@@ -1,10 +1,10 @@
 #include "Merge.h"
 #include "AssignParams.h"
 #include "GetParams.h"
+#include "ParmHolder.h"
 #include "../Atom.h"
 #include "../AtomType.h"
 #include "../CpptrajStdio.h"
-#include "../ParameterHolders.h"
 #include "../ParameterTypes.h"
 #include "../Residue.h"
 #include "../StringRoutines.h" // integerToString
@@ -188,9 +188,9 @@ class MergeTopArray
     /// Append parameter for given types
     /** \return Index of newly-added parameter to p0 */
     int append_param(TypeNameHolder const& types,
-                     ParmHolder<int>& currentTypes0,
+                     Cpptraj::Parm::ParmHolder<int>& currentTypes0,
                      ParmArray& p0,
-                     ParmHolder<int> const& currentTypes1,
+                     Cpptraj::Parm::ParmHolder<int> const& currentTypes1,
                      ParmArray const& p1)
     {
 #     ifdef CPPTRAJ_DEBUG_MERGE
@@ -255,8 +255,8 @@ class MergeTopArray
                      ParmArray& p0,
                      unsigned int atomOffset,
                      IdxType const& term1,
-                     ParmHolder<int>& currentTypes0,
-                     ParmHolder<int> const& currentTypes1,
+                     Cpptraj::Parm::ParmHolder<int>& currentTypes0,
+                     Cpptraj::Parm::ParmHolder<int> const& currentTypes1,
                      ParmArray const& p1,
                      std::vector<Atom> const& atoms1)
     {
@@ -280,8 +280,8 @@ class MergeTopArray
                      ParmArray& p0,
                      unsigned int atomOffset,
                      IdxType const& term1,
-                     ParmHolder<int>& currentTypes0,
-                     ParmHolder<int> const& currentTypes1,
+                     Cpptraj::Parm::ParmHolder<int>& currentTypes0,
+                     Cpptraj::Parm::ParmHolder<int> const& currentTypes1,
                      ParmArray const& p1,
                      std::vector<Atom> const& atoms1)
     {
@@ -299,7 +299,7 @@ class MergeTopArray
     }
 
     /// Index existing term types in term arrays
-    void index_term_types(ParmHolder<int>& currentTypes,
+    void index_term_types(Cpptraj::Parm::ParmHolder<int>& currentTypes,
                           IdxArray const& terms,
                           std::vector<Atom> const& atoms,
                           ParmArray const& parms)
@@ -330,7 +330,7 @@ class MergeTopArray
                          std::vector<Atom> const& atoms1)
     {
       // First index existing parameters
-      ParmHolder<int> currentTypes0, currentTypes1;
+      Cpptraj::Parm::ParmHolder<int> currentTypes0, currentTypes1;
       index_term_types(currentTypes0, terms0, atoms0, p0);
       index_term_types(currentTypes0, termsh0, atoms0, p0);
       index_term_types(currentTypes1, terms1, atoms1, p1);
@@ -397,7 +397,7 @@ class MergeTopArray
                              std::vector<Atom> const& atoms1)
     {
       // First index existing parameters
-      ParmHolder<int> currentTypes0, currentTypes1;
+      Cpptraj::Parm::ParmHolder<int> currentTypes0, currentTypes1;
       index_term_types(currentTypes0, terms0, atoms0, p0);
       index_term_types(currentTypes0, termsh0, atoms0, p0);
       index_term_types(currentTypes1, terms1, atoms1, p1);
@@ -461,7 +461,7 @@ class MergeTopArray
                         std::vector<Atom> const& atoms1)
     {
       // First index existing parameters
-      ParmHolder<int> currentTypes0, currentTypes1;
+      Cpptraj::Parm::ParmHolder<int> currentTypes0, currentTypes1;
       index_term_types(currentTypes0, terms0, atoms0, p0);
       index_term_types(currentTypes1, terms1, atoms1, p1);
       unsigned int atomOffset = atoms0.size();
@@ -609,7 +609,7 @@ static inline CmapType idxWithOffset(CmapType const& cmap1, int idx, unsigned in
 }
 
 /// Index existing CMAP types in term arrays
-void index_cmap_types(ParmHolder<int>& currentTypes,
+void index_cmap_types(Cpptraj::Parm::ParmHolder<int>& currentTypes,
                       CmapArray const& terms,
                       std::vector<Atom> const& atoms,
                       std::vector<Residue> const& residues)
@@ -641,7 +641,7 @@ const
   unsigned int atomOffset = atoms0.size();
   unsigned int cgOffset = cg0.size();
   // First index existing parameters
-  ParmHolder<int> currentTypes0, currentTypes1;
+  Cpptraj::Parm::ParmHolder<int> currentTypes0, currentTypes1;
   index_cmap_types(currentTypes0, cmap0, atoms0, residues0);
   index_cmap_types(currentTypes1, cmap1, atoms1, residues1);
   // Loop over incoming terms

From 698a16b54027cbd6ea50f2a8e7c4680d635140d9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 16 Oct 2025 10:35:17 -0400
Subject: [PATCH 0962/1492] Update for moved ParameterSet

---
 src/DataSet_Parameters.h | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/DataSet_Parameters.h b/src/DataSet_Parameters.h
index 035ffb02e6..4ad938de32 100644
--- a/src/DataSet_Parameters.h
+++ b/src/DataSet_Parameters.h
@@ -1,9 +1,9 @@
 #ifndef INC_DATASET_PARAMETERS_H
 #define INC_DATASET_PARAMETERS_H
 #include "DataSet.h"
-#include "ParameterSet.h"
+#include "Parm/ParameterSet.h"
 /// DataSet wrapper around ParameterSet
-class DataSet_Parameters : public DataSet, public ParameterSet  {
+class DataSet_Parameters : public DataSet, public Cpptraj::Parm::ParameterSet  {
   public:
     DataSet_Parameters();
     static DataSet* Alloc() { return (DataSet*)new DataSet_Parameters(); }

From 1629d7e54ebb2824b70e212bc56e60883ee7b946 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 16 Oct 2025 10:41:03 -0400
Subject: [PATCH 0963/1492] Fix CharmmParamFile for moved
 ParmHolder/ParameterSet

---
 src/CharmmParamFile.cpp | 12 +++++++-----
 src/CharmmParamFile.h   | 10 +++++++---
 2 files changed, 14 insertions(+), 8 deletions(-)

diff --git a/src/CharmmParamFile.cpp b/src/CharmmParamFile.cpp
index a3256a4b4b..544dba4178 100644
--- a/src/CharmmParamFile.cpp
+++ b/src/CharmmParamFile.cpp
@@ -4,7 +4,7 @@
 #include "ArgList.h"
 #include "Constants.h"
 #include "BufferedLine.h"
-#include "ParameterSet.h"
+#include "Parm/ParameterSet.h"
 
 static inline std::string Input(const char* line) {
   std::string input;
@@ -62,7 +62,8 @@ static inline bool ChmCmd(std::string const& cmd, const char* key) {
 }
 
 /** Read CHARMM parameters from specified file into given parameter set. */
-int CharmmParamFile::ReadParams(ParameterSet& prm, FileName const& nameIn, int debugIn) const {
+int CharmmParamFile::ReadParams(Cpptraj::Parm::ParameterSet& prm, FileName const& nameIn, int debugIn) const {
+  using namespace Cpptraj::Parm;
   BufferedLine infile;
 
   mprintf("\tReading CHARMM parameters from '%s'\n", nameIn.full());
@@ -122,10 +123,10 @@ int CharmmParamFile::ReadParams(ParameterSet& prm, FileName const& nameIn, int d
           args.MarkArg(0);
           args.MarkArg(1);
           args.MarkArg(2);
-          ParameterHolders::RetType ret = prm.AT().AddParm( TypeNameHolder(args[2]),
+          Cpptraj::Parm::RetType ret = prm.AT().AddParm( TypeNameHolder(args[2]),
                                                             AtomType(args.getNextDouble(0)),
                                                             true );
-          if (ret == ParameterHolders::UPDATED)
+          if (ret == Cpptraj::Parm::UPDATED)
             mprintf("Warning: Redefining atom type %s\n", args[2].c_str());
         } else if (ChmCmd(args[0], "ATOM")) {
           if (mode != TOP) {
@@ -296,7 +297,8 @@ int CharmmParamFile::ReadParams(ParameterSet& prm, FileName const& nameIn, int d
 }
 
 /** Write CHARMM parameters from specified set into given file. */
-int CharmmParamFile::WriteParams(ParameterSet& prm, FileName const& nameIn, int debugIn) const {
+int CharmmParamFile::WriteParams(Cpptraj::Parm::ParameterSet& prm, FileName const& nameIn, int debugIn) const {
+  using namespace Cpptraj::Parm;
   CpptrajFile outfile;
   if (outfile.OpenWrite(nameIn)) return 1;
   // Title
diff --git a/src/CharmmParamFile.h b/src/CharmmParamFile.h
index b2b5cdaf73..e22424d136 100644
--- a/src/CharmmParamFile.h
+++ b/src/CharmmParamFile.h
@@ -1,15 +1,19 @@
 #ifndef INC_CHARMMPARAMFILE_H
 #define INC_CHARMMPARAMFILE_H
 #include <string>
-class ParameterSet;
 class BufferedLine;
 class FileName;
+namespace Cpptraj {
+namespace Parm {
+class ParameterSet;
+}
+}
 /// Used to read in CHARMM parameters from CHARMM parameter file.
 class CharmmParamFile {
   public:
     CharmmParamFile() {}
-    int ReadParams(ParameterSet&, FileName const&, int) const;
-    int WriteParams(ParameterSet&, FileName const&, int) const;
+    int ReadParams(Cpptraj::Parm::ParameterSet&, FileName const&, int) const;
+    int WriteParams(Cpptraj::Parm::ParameterSet&, FileName const&, int) const;
   private:
     int ReadInput(std::string&, BufferedLine&) const;
 };

From 2d64eb0ac4b9616c087c7e36e055c5b27a5d6601 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 16 Oct 2025 10:42:23 -0400
Subject: [PATCH 0964/1492] Fix for moved parameter set/holder

---
 src/Parm_CharmmPsf.cpp | 2 +-
 src/Parm_CharmmPsf.h   | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/Parm_CharmmPsf.cpp b/src/Parm_CharmmPsf.cpp
index 88dd2b9343..717c69f504 100644
--- a/src/Parm_CharmmPsf.cpp
+++ b/src/Parm_CharmmPsf.cpp
@@ -375,7 +375,7 @@ int Parm_CharmmPsf::ReadParm(FileName const& fname, Topology &parmOut) {
   double psfcharge;
   double psfmass;
 //  typedef std::vector<std::string> Sarray;
-  ParmHolder<AtomType>& atomTypes = params_.AT();
+  Cpptraj::Parm::ParmHolder<AtomType>& atomTypes = params_.AT();
 //  Sarray SegIDs;
   bool firstLine = true;
   enum PsfFormatType { T_CHARMM = 0, T_VMD };
diff --git a/src/Parm_CharmmPsf.h b/src/Parm_CharmmPsf.h
index 0b5ed474e9..0f8d4cd5d0 100644
--- a/src/Parm_CharmmPsf.h
+++ b/src/Parm_CharmmPsf.h
@@ -1,7 +1,7 @@
 #ifndef INC_PARM_CHARMMPSF_H
 #define INC_PARM_CHARMMPSF_H
 #include "ParmIO.h"
-#include "ParameterSet.h"
+#include "Parm/ParameterSet.h"
 class BufferedLine;
 class Parm_CharmmPsf : public ParmIO {
   public :
@@ -26,7 +26,7 @@ class Parm_CharmmPsf : public ParmIO {
 
     inline void WriteSectionHeader(CpptrajFile&, const char*, int) const;
 
-    ParameterSet params_;
+    Cpptraj::Parm::ParameterSet params_;
     bool extfmt_; ///< (write) If true use extended format
     bool cheq_;   ///< (write) If true include extra columns for polarization (CHarge EQuilibration)
     bool xplor_;  ///< (write) If true use XPLOR format PSF

From 68b2ba730429899aa409546d9eecdec7fae0d24a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 16 Oct 2025 10:47:56 -0400
Subject: [PATCH 0965/1492] Fix AmberParamFile for moved ParmHolder/ParmeterSet

---
 src/AmberParamFile.cpp | 34 ++++++++++++++++++----------------
 src/AmberParamFile.h   |  7 ++++++-
 2 files changed, 24 insertions(+), 17 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index a1486ff4b8..53a1d7f2e9 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -2,13 +2,15 @@
 #include "ArgList.h"
 #include "CpptrajStdio.h"
 #include "BufferedLine.h"
-#include "ParameterHolders.h"
 #include "StringRoutines.h"
-#include "ParameterSet.h"
+#include "Parm/ParameterSet.h"
+#include "Parm/ParmHolder.h"
 #include "Constants.h"
 #include <cstdio> // sscanf
 #include <cctype> // isspace
 
+using namespace Cpptraj::Parm;
+
 const int AmberParamFile::MAXSYMLEN = 16;
 
 /// CONSTRUCTOR
@@ -75,7 +77,7 @@ const
   double amass = 0;
   double atpol = 0;
   int nscan = sscanf(ptr, "%s %lf %lf", kndsym, &amass, &atpol);
-  ParameterHolders::RetType ret;
+  Cpptraj::Parm::RetType ret;
   if (nscan == 3) {
     ret = prm.AT().AddParm( TypeNameHolder(kndsym),
                             AtomType(amass, atpol),
@@ -89,7 +91,7 @@ const
     mprinterr("Error: Expected atom type, mass, polarizability, got only %i columns.\n", nscan);
     return 1;
   }
-  if (ret == ParameterHolders::UPDATED)
+  if (ret == Cpptraj::Parm::UPDATED)
     mprintf("Warning: Redefining atom type %s\n", kndsym);
   return 0;
 }
@@ -118,8 +120,8 @@ const
   TypeNameHolder types(2);
   types.AddName( symbols[0] );
   types.AddName( symbols[1] );
-  ParameterHolders::RetType ret = prm.BP().AddParm(types, BondParmType(RK, REQ), true);
-  if (ret == ParameterHolders::UPDATED)
+  Cpptraj::Parm::RetType ret = prm.BP().AddParm(types, BondParmType(RK, REQ), true);
+  if (ret == Cpptraj::Parm::UPDATED)
     mprintf("Warning: Redefining bond type %s - %s\n", *(types[0]), *(types[1]));
 
   return 0;
@@ -150,8 +152,8 @@ const
   types.AddName( symbols[0] );
   types.AddName( symbols[1] );
   types.AddName( symbols[2] );
-  ParameterHolders::RetType ret = prm.AP().AddParm(types, AngleParmType(TK, TEQ*Constants::DEGRAD), true);
-  if (ret == ParameterHolders::UPDATED)
+  Cpptraj::Parm::RetType ret = prm.AP().AddParm(types, AngleParmType(TK, TEQ*Constants::DEGRAD), true);
+  if (ret == Cpptraj::Parm::UPDATED)
     mprintf("Warning: Redefining angle type %s - %s - %s\n", *(types[0]), *(types[1]), *(types[2]));
 
   return 0;
@@ -226,9 +228,9 @@ const
   types.AddName( symbols[1] );
   types.AddName( symbols[2] );
   types.AddName( symbols[3] );
-  ParameterHolders::RetType ret =
+  Cpptraj::Parm::RetType ret =
     prm.DP().AddParm(types, DihedralParmType(PK / (double)IDIVF, PN, PHASE*Constants::DEGRAD, scee, scnb), true);
-  if (ret == ParameterHolders::UPDATED) {
+  if (ret == Cpptraj::Parm::UPDATED) {
     mprintf("Warning: Redefining dihedral type %s - %s - %s - %s (PN=%g)\n",
             *(types[0]), *(types[1]), *(types[2]), *(types[3]), PN);
     //mprintf("DEBUG: %s\n", ptr);
@@ -269,9 +271,9 @@ const
   types.AddName( symbols[2] );
   types.AddName( symbols[3] );
   //types.SortImproperByAlpha("X"); // FIXME wildcard should be a static var
-  ParameterHolders::RetType ret =
+  Cpptraj::Parm::RetType ret =
     prm.IP().AddParm(types, DihedralParmType(PK, PN, PHASE*Constants::DEGRAD), true);
-  if (ret == ParameterHolders::UPDATED)
+  if (ret == Cpptraj::Parm::UPDATED)
     mprintf("Warning: Redefining improper type %s - %s - %s - %s\n",
             *(types[0]), *(types[1]), *(types[2]), *(types[3]));
 
@@ -302,8 +304,8 @@ const
   TypeNameHolder types(2);
   types.AddName( KT1 );
   types.AddName( KT2 );
-  ParameterHolders::RetType ret = prm.HB().AddParm(types, HB_ParmType(A, B, HCUT), true);
-  if (ret == ParameterHolders::UPDATED)
+  Cpptraj::Parm::RetType ret = prm.HB().AddParm(types, HB_ParmType(A, B, HCUT), true);
+  if (ret == Cpptraj::Parm::UPDATED)
     mprintf("Warning: Redefining LJ 10-12 hbond type %s %s\n", *(types[0]), *(types[1]));
   return 0;
 }
@@ -335,8 +337,8 @@ const
   double R = convertToDouble( nbargs[1] );
   double EDEP = convertToDouble( nbargs[2] );
   TypeNameHolder types( nbargs[0] );
-  ParameterHolders::RetType ret = nbset.LJ_.AddParm( types, LJparmType(R, EDEP), true );
-  if (ret == ParameterHolders::UPDATED)
+  Cpptraj::Parm::RetType ret = nbset.LJ_.AddParm( types, LJparmType(R, EDEP), true );
+  if (ret == Cpptraj::Parm::UPDATED)
     mprintf("Warning: Redefining LJ 6-12 type %s\n", *(types[0]));
   return 0;
 }
diff --git a/src/AmberParamFile.h b/src/AmberParamFile.h
index 463c1f71b6..91cdabce3c 100644
--- a/src/AmberParamFile.h
+++ b/src/AmberParamFile.h
@@ -2,12 +2,17 @@
 #define INC_AMBERPARAMFILE_H
 #include <vector>
 #include <string>
-class ParameterSet;
 class CmapGridType;
 //class BufferedLine;
 class FileName;
+namespace Cpptraj {
+namespace Parm {
+class ParameterSet;
+}
+}
 /// Used to read in Amber parameters from Amber FF/FRCMOD file.
 class AmberParamFile {
+    typedef Cpptraj::Parm::ParameterSet ParameterSet;
   public:
     AmberParamFile();
     /// Read main Amber FF file

From 5cb8fb7b5fd74db61ae3698ad2efa7925065c703 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 16 Oct 2025 10:48:29 -0400
Subject: [PATCH 0966/1492] Fixed for moved enum

---
 src/UpdateParameters.h | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/UpdateParameters.h b/src/UpdateParameters.h
index 8aeccb7599..79838e64ec 100644
--- a/src/UpdateParameters.h
+++ b/src/UpdateParameters.h
@@ -32,16 +32,16 @@ template <typename T> int UpdateParameters(T& param0, T const& param1, const cha
   int updateCount = 0;
   for (typename T::const_iterator newp = param1.begin(); newp != param1.end(); ++newp)
   {
-    ParameterHolders::RetType ret = param0.AddParm( newp->first, newp->second, true );
-    if (ret != ParameterHolders::ERR) {
+    Cpptraj::Parm::RetType ret = param0.AddParm( newp->first, newp->second, true );
+    if (ret != Cpptraj::Parm::ERR) {
       bool print = false;
-      if (ret == ParameterHolders::ADDED) {
+      if (ret == Cpptraj::Parm::ADDED) {
         if (verbose > 2) { mprintf("\tAdded NEW %s parameter:", desc); print = true; }
         updateCount++;
-      } else if (ret == ParameterHolders::UPDATED) {
+      } else if (ret == Cpptraj::Parm::UPDATED) {
         if (verbose > 0) { mprintf("\tUpdated %s parameter:", desc); print = true; }
         updateCount++;
-      } else if (ret == ParameterHolders::SAME) {
+      } else if (ret == Cpptraj::Parm::SAME) {
         if (verbose > 1) { mprintf("\tParameter for %s already present:", desc); print = true; }
       }
       if (print) {

From 85be836c0d95bd6ccbdc8f92d546dcc5fee992da Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 16 Oct 2025 10:49:07 -0400
Subject: [PATCH 0967/1492] Fix for moved classes

---
 src/Parm/AssignParams.cpp |  6 ++++--
 src/Parm/AssignParams.h   | 11 ++++++-----
 2 files changed, 10 insertions(+), 7 deletions(-)

diff --git a/src/Parm/AssignParams.cpp b/src/Parm/AssignParams.cpp
index be5ac300dd..054e53805e 100644
--- a/src/Parm/AssignParams.cpp
+++ b/src/Parm/AssignParams.cpp
@@ -1,13 +1,15 @@
 #include "AssignParams.h"
 #include "GetParams.h"
+#include "ParmHolder.h"
+#include "DihedralParmHolder.h"
+#include "ImproperParmHolder.h"
+#include "ParameterSet.h"
 #include "../Atom.h"
 #include "../AtomType.h"
 #include "../CmapParmHolder.h"
 #include "../CpptrajStdio.h"
 #include "../Structure/GenerateConnectivityArrays.h"
 #include "../GuessAtomHybridization.h"
-#include "../ParameterHolders.h"
-#include "../ParameterSet.h"
 #include "../Topology.h"
 #include "../TypeNameHolder.h"
 #include <algorithm> //sort
diff --git a/src/Parm/AssignParams.h b/src/Parm/AssignParams.h
index 57daff1085..b6dc9d8992 100644
--- a/src/Parm/AssignParams.h
+++ b/src/Parm/AssignParams.h
@@ -3,7 +3,7 @@
 #include <vector>
 #include <string>
 #ifdef TIMER
-# include "Timer.h"
+# include "../Timer.h"
 #endif
 class AngleArray;
 class AngleParmArray;
@@ -20,16 +20,17 @@ class CmapGridArray;
 class CmapParmHolder;
 class DihedralArray;
 class DihedralParmArray;
-class DihedralParmHolder;
 class DihedralType;
 class HB_ParmType;
-class ImproperParmHolder;
 class NonbondType;
-class ParameterSet;
 class Topology;
-template<typename Type> class ParmHolder;
 namespace Cpptraj {
 namespace Parm {
+// Parm forward declares
+template<typename Type> class ParmHolder;
+class DihedralParmHolder;
+class ImproperParmHolder;
+class ParameterSet;
 /// Used to assign parameters to a Topology
 class AssignParams {
   public:

From 3bbab850b80c350e586513ca6fdb9f3b11a8a36b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 16 Oct 2025 10:52:20 -0400
Subject: [PATCH 0968/1492] Fix for moved classes

---
 src/Parm/GetParams.cpp | 33 ++++++++++++++++-----------------
 src/Parm/GetParams.h   |  8 ++++----
 2 files changed, 20 insertions(+), 21 deletions(-)

diff --git a/src/Parm/GetParams.cpp b/src/Parm/GetParams.cpp
index 138d8ad9f2..60622a0f65 100644
--- a/src/Parm/GetParams.cpp
+++ b/src/Parm/GetParams.cpp
@@ -1,10 +1,9 @@
 #include "GetParams.h"
+#include "ParameterSet.h"
 #include "../Atom.h"
 #include "../AtomType.h"
 #include "../CmapParmHolder.h"
 #include "../CpptrajStdio.h"
-#include "../ParameterHolders.h"
-#include "../ParameterSet.h"
 #include "../ParameterTypes.h"
 #include "../Topology.h"
 #include "../TypeNameHolder.h"
@@ -37,8 +36,8 @@ void GetParams::GetBondParams(ParmHolder<BondParmType>& BP, std::vector<Atom> co
       TypeNameHolder types(2);
       types.AddName( atoms[b->A1()].Type() );
       types.AddName( atoms[b->A2()].Type() );
-      ParameterHolders::RetType ret = BP.AddParm( types, bpa[b->Idx()], false );
-      if (ret == ParameterHolders::ERR)
+      Cpptraj::Parm::RetType ret = BP.AddParm( types, bpa[b->Idx()], false );
+      if (ret == Cpptraj::Parm::ERR)
         paramOverwriteWarning("bond");
     }
   }
@@ -53,8 +52,8 @@ void GetParams::GetAngleParams(ParmHolder<AngleParmType>& AP, std::vector<Atom>
       types.AddName( atoms[b->A1()].Type() );
       types.AddName( atoms[b->A2()].Type() );
       types.AddName( atoms[b->A3()].Type() );
-      ParameterHolders::RetType ret = AP.AddParm( types, apa[b->Idx()], false );
-      if (ret == ParameterHolders::ERR)
+      Cpptraj::Parm::RetType ret = AP.AddParm( types, apa[b->Idx()], false );
+      if (ret == Cpptraj::Parm::ERR)
         paramOverwriteWarning("angle");
     }
   }
@@ -71,8 +70,8 @@ void GetParams::GetImproperParams(ImproperParmHolder& IP, std::vector<Atom> cons
       types.AddName( atoms[b->A2()].Type() );
       types.AddName( atoms[b->A3()].Type() );
       types.AddName( atoms[b->A4()].Type() );
-      ParameterHolders::RetType ret = IP.AddParm( types, ipa[b->Idx()], false );
-      if (ret == ParameterHolders::ERR)
+      Cpptraj::Parm::RetType ret = IP.AddParm( types, ipa[b->Idx()], false );
+      if (ret == Cpptraj::Parm::ERR)
         paramOverwriteWarning("improper");
     }
   }
@@ -93,17 +92,17 @@ void GetParams::GetDihedralParams(DihedralParmHolder& DP, ImproperParmHolder& IP
       //mprintf("DEBUG: dihedral %li %s %s %s %s idx=%i type=%i PK=%g PN=%g Phase=%g SCEE=%g SCNB=%g\n", b - dih.begin() + 1,
       //        *(types[0]), *(types[1]), *(types[2]), *(types[3]), b->Idx(), (int)b->Type(),
       //        dpa[b->Idx()].Pk(), dpa[b->Idx()].Pn(), dpa[b->Idx()].Phase(), dpa[b->Idx()].SCEE(), dpa[b->Idx()].SCNB());
-      ParameterHolders::RetType ret;
+      Cpptraj::Parm::RetType ret;
       if (b->IsImproper()) {
         ret = IP.AddParm( types, dpa[b->Idx()], false );
       } else {
         ret = DP.AddParm( types, dpa[b->Idx()], false );
       }
       // DEBUG
-      //if (ret == ParameterHolders::ADDED) {
+      //if (ret == Cpptraj::Parm::ADDED) {
       //  mprintf("DEBUG: Added %s %s %s %s idx=%i isImproper=%i\n", *(types[0]), *(types[1]), *(types[2]), *(types[3]), b->Idx(), (int)b->IsImproper());
       //}
-      if (ret == ParameterHolders::ERR) {
+      if (ret == Cpptraj::Parm::ERR) {
         paramOverwriteWarning("dihedral");
         mprintf("Warning: Dihedral %s %s %s %s PK=%g PN=%g Phase=%g SCEE=%g SCNB=%g\n",
                 *(types[0]), *(types[1]), *(types[2]), *(types[3]),
@@ -216,8 +215,8 @@ int GetParams::GetCmapParams(CmapParmHolder& cmapParm, CmapArray const& cmapTerm
         // Set a default title if needed
         if (newGrid.Title().empty())
           newGrid.SetTitle( "CMAP for " + newGrid.ResNames().front() );
-        ParameterHolders::RetType ret = cmapParm.AddParm( newGrid, false );
-        if (ret == ParameterHolders::ERR)
+        Cpptraj::Parm::RetType ret = cmapParm.AddParm( newGrid, false );
+        if (ret == Cpptraj::Parm::ERR)
           paramOverwriteWarning("CMAP");
       } // END if adding existing grid to parms
     } // END loop over existing grids
@@ -225,8 +224,8 @@ int GetParams::GetCmapParams(CmapParmHolder& cmapParm, CmapArray const& cmapTerm
     mprintf("CMAP terms have residue/atom info.\n");
     for (unsigned int idx = 0; idx != cmapGrids.size(); idx++) {
       if (addGrid[idx]) {
-        ParameterHolders::RetType ret = cmapParm.AddParm( cmapGrids[idx], false );
-        if (ret == ParameterHolders::ERR)
+        Cpptraj::Parm::RetType ret = cmapParm.AddParm( cmapGrids[idx], false );
+        if (ret == Cpptraj::Parm::ERR)
           paramOverwriteWarning("CMAP");
       }
     }
@@ -282,8 +281,8 @@ const
         thisType = AtomType(atm->Mass(), atm->Polar());
       }
       thisType.SetTypeIdx( atm->TypeIndex() );
-      ParameterHolders::RetType ret = atomTypesOut.AddParm( atype, thisType, true );
-      if (debug_ > 0 && ret == ParameterHolders::ADDED) {
+      Cpptraj::Parm::RetType ret = atomTypesOut.AddParm( atype, thisType, true );
+      if (debug_ > 0 && ret == Cpptraj::Parm::ADDED) {
         mprintf("DEBUG: New atom type: %s R=%g D=%g M=%g P=%g\n", *(atype[0]),
                 thisType.LJ().Radius(), thisType.LJ().Depth(), thisType.Mass(), thisType.Polarizability());
         if (hasLJ14)
diff --git a/src/Parm/GetParams.h b/src/Parm/GetParams.h
index 8c0d693514..49d748b7eb 100644
--- a/src/Parm/GetParams.h
+++ b/src/Parm/GetParams.h
@@ -14,17 +14,17 @@ class CmapGridArray;
 class CmapParmHolder;
 class DihedralArray;
 class DihedralParmArray;
-class DihedralParmHolder;
 class HB_ParmType;
-class ImproperParmHolder;
 class NonbondParmType;
 class NonbondType;
-class ParameterSet;
 class Residue;
 class Topology;
-template<typename Type> class ParmHolder;
 namespace Cpptraj {
 namespace Parm {
+template<typename Type> class ParmHolder;
+class DihedralParmHolder;
+class ImproperParmHolder;
+class ParameterSet;
 /// Used to get parameters from a Topology
 class GetParams {
   public:

From df335ce7742fa343bcebb1e51d1baa9e40b04ea4 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 16 Oct 2025 10:59:24 -0400
Subject: [PATCH 0969/1492] Fix for moved classes

---
 src/Structure/Builder.cpp | 6 +++---
 src/Structure/Builder.h   | 8 +++++---
 2 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 2337bff2ca..ee4678be07 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -7,8 +7,7 @@
 #include "../DistRoutines.h"
 #include "../Frame.h"
 #include "../GuessAtomHybridization.h"
-#include "../ParameterHolders.h"
-#include "../ParameterSet.h"
+#include "../Parm/ParameterSet.h"
 #include "../Topology.h"
 #include "../TorsionRoutines.h"
 #include "../TypeNameHolder.h"
@@ -16,6 +15,7 @@
 #include <cmath> // fabs
 
 using namespace Cpptraj::Structure;
+using namespace Cpptraj::Parm;
 
 /** CONSTRUCTOR */
 Builder::Builder() :
@@ -25,7 +25,7 @@ Builder::Builder() :
 {}
 
 /** Set optional parameter set. */
-void Cpptraj::Structure::Builder::SetParameters(ParameterSet const* paramsIn) {
+void Cpptraj::Structure::Builder::SetParameters(Cpptraj::Parm::ParameterSet const* paramsIn) {
   if (paramsIn == 0) {
     mprinterr("Internal Error: Builder::SetParmaters called with null set.\n");
     return;
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index 48bfbda3d2..b5c2974738 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -5,9 +5,11 @@
 class Atom;
 class Topology;
 class Frame;
-class ParameterSet;
 class Residue;
 namespace Cpptraj {
+namespace Parm {
+class ParameterSet;
+}
 namespace Structure {
 class Zmatrix;
 class InternalCoords;
@@ -25,7 +27,7 @@ class Builder {
     /// Set debug level
     void SetDebug(int d) { debug_ = d; }
     /// Set optional parameter set
-    void SetParameters(ParameterSet const*);
+    void SetParameters(Cpptraj::Parm::ParameterSet const*);
     /// Set atom chirality
     void SetAtomChirality(int, double);
     /// Update the internal coordinates in given Zmatrix with values from Frame/Parameters TODO combine into BuildFromInternals?
@@ -130,7 +132,7 @@ class Builder {
     std::vector<Residue> residuesThatNeedPositions(Topology const&, Barray const&) const;
 
     int debug_;
-    ParameterSet const* params_;
+    Cpptraj::Parm::ParameterSet const* params_;
 
     Topology const* currentTop_; ///< Topology for the createSpXSpXTorsions/ModelTorsion routines
     Tarray internalTorsions_;

From a5bb2165825a816af58af92e79bba45ac1136dbc Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 16 Oct 2025 10:59:53 -0400
Subject: [PATCH 0970/1492] Fix for moved files. Update dependencies

---
 src/Parm/CMakeLists.txt       |  2 ++
 src/Parm/Makefile             |  5 ++++
 src/Parm/parmdepend           |  8 ++++---
 src/Parm/parmfiles            |  4 +++-
 src/Structure/structuredepend |  4 ++--
 src/cpptrajdepend             | 45 ++++++++++++++++++-----------------
 src/cpptrajfiles              |  1 -
 7 files changed, 40 insertions(+), 29 deletions(-)

diff --git a/src/Parm/CMakeLists.txt b/src/Parm/CMakeLists.txt
index 8b609328c1..c0af4f1dc4 100644
--- a/src/Parm/CMakeLists.txt
+++ b/src/Parm/CMakeLists.txt
@@ -4,4 +4,6 @@ target_sources(cpptraj_common_obj PRIVATE
   ${CMAKE_CURRENT_LIST_DIR}/GB_Params.cpp
   ${CMAKE_CURRENT_LIST_DIR}/GetParams.cpp
   ${CMAKE_CURRENT_LIST_DIR}/Merge.cpp
+  ${CMAKE_CURRENT_LIST_DIR}/ParameterSet.cpp
+  ${CMAKE_CURRENT_LIST_DIR}/test.cpp
 )
diff --git a/src/Parm/Makefile b/src/Parm/Makefile
index 0f070ffe50..6112cbd5d9 100644
--- a/src/Parm/Makefile
+++ b/src/Parm/Makefile
@@ -8,6 +8,11 @@ DEL_FILE = /bin/rm -f
 # Objects
 OBJECTS=$(PARM_SOURCES:.cpp=.o)
 
+# General rules
+.cpp.o:
+	$(VB)echo CXX $<
+	$(VB)$(CXX) $(DIRECTIVES) $(CPPTRAJ_INC) $(CXXFLAGS) -c -o $@ $<
+
 # Default target: objects
 all: $(OBJECTS)
 
diff --git a/src/Parm/parmdepend b/src/Parm/parmdepend
index 35382f3e05..7e76359b6d 100644
--- a/src/Parm/parmdepend
+++ b/src/Parm/parmdepend
@@ -1,4 +1,6 @@
-AssignParams.o : AssignParams.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/GenerateConnectivityArrays.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h AssignParams.h GetParams.h
+AssignParams.o : AssignParams.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/ParmEnum.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/GenerateConnectivityArrays.h ../SymbolExporting.h ../Timer.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h AssignParams.h DihedralParmHolder.h GetParams.h ImproperParmHolder.h ParameterSet.h ParmEnum.h ParmHolder.h
 GB_Params.o : GB_Params.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h GB_Params.h
-GetParams.o : GetParams.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h GetParams.h
-Merge.o : Merge.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../StringRoutines.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../UpdateParameters.h ../Vec3.h AssignParams.h GetParams.h Merge.h
+GetParams.o : GetParams.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/ParmEnum.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h DihedralParmHolder.h GetParams.h ImproperParmHolder.h ParameterSet.h ParmEnum.h ParmHolder.h
+Merge.o : Merge.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../StringRoutines.h ../SymbolExporting.h ../Timer.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../UpdateParameters.h ../Vec3.h AssignParams.h GetParams.h Merge.h ParmEnum.h ParmHolder.h
+ParameterSet.o : ParameterSet.cpp ../AtomType.h ../CmapParmHolder.h ../Constants.h ../CpptrajFile.h ../CpptrajStdio.h ../FileIO.h ../FileName.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/ParmEnum.h ../TypeNameHolder.h ../UpdateParameters.h DihedralParmHolder.h ImproperParmHolder.h ParameterSet.h ParmEnum.h ParmHolder.h
+test.o : test.cpp ../Constants.h ../NameType.h ../ParameterTypes.h ../TypeNameHolder.h DihedralParmHolder.h ImproperParmHolder.h ParmEnum.h ParmHolder.h
diff --git a/src/Parm/parmfiles b/src/Parm/parmfiles
index e57ffb4318..57e32392e1 100644
--- a/src/Parm/parmfiles
+++ b/src/Parm/parmfiles
@@ -3,4 +3,6 @@ PARM_SOURCES= \
   AssignParams.cpp \
   GB_Params.cpp \
   GetParams.cpp \
-  Merge.cpp
+  Merge.cpp \
+  ParameterSet.cpp \
+  test.cpp
diff --git a/src/Structure/structuredepend b/src/Structure/structuredepend
index 4c788ccf93..e442a529f8 100644
--- a/src/Structure/structuredepend
+++ b/src/Structure/structuredepend
@@ -1,6 +1,6 @@
-Builder.o : Builder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Builder.h Chirality.h GenerateConnectivityArrays.h InternalCoords.h StructureEnum.h Zmatrix.h
+Builder.o : Builder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/../AtomType.h ../Parm/../CmapParmHolder.h ../Parm/../Constants.h ../Parm/../NameType.h ../Parm/../ParameterTypes.h ../Parm/../Parm/ParmEnum.h ../Parm/../TypeNameHolder.h ../Parm/DihedralParmHolder.h ../Parm/ImproperParmHolder.h ../Parm/ParameterSet.h ../Parm/ParmEnum.h ../Parm/ParmHolder.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Builder.h Chirality.h GenerateConnectivityArrays.h InternalCoords.h StructureEnum.h Zmatrix.h
 Chirality.o : Chirality.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../Unit.h ../Vec3.h Chirality.h StructureEnum.h
-Creator.o : Creator.cpp ../ArgList.h ../AssociatedData.h ../AssociatedData_ResId.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../DataSet_NameMap.h ../DataSet_Parameters.h ../Dimension.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/StructureEnum.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Creator.h GenerateConnectivityArrays.h StructureEnum.h
+Creator.o : Creator.cpp ../ArgList.h ../AssociatedData.h ../AssociatedData_ResId.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../DataSet_NameMap.h ../DataSet_Parameters.h ../Dimension.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/../AtomType.h ../Parm/../CmapParmHolder.h ../Parm/../Constants.h ../Parm/../NameType.h ../Parm/../ParameterTypes.h ../Parm/../Parm/ParmEnum.h ../Parm/../TypeNameHolder.h ../Parm/DihedralParmHolder.h ../Parm/ImproperParmHolder.h ../Parm/ParameterSet.h ../Parm/ParmEnum.h ../Parm/ParmHolder.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/StructureEnum.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h Creator.h GenerateConnectivityArrays.h StructureEnum.h
 Disulfide.o : Disulfide.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h Disulfide.h ResStatArray.h StructureRoutines.h
 FunctionalGroup.o : FunctionalGroup.cpp ../Atom.h ../AtomMap.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h FunctionalGroup.h
 FxnGroupBuilder.o : FxnGroupBuilder.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h FunctionalGroup.h FxnGroupBuilder.h StructureRoutines.h Sugar.h SugarToken.h
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 4493f2b43c..86e546b4a9 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -90,13 +90,13 @@ Action_ToroidalDiffusion.o : Action_ToroidalDiffusion.cpp Action.h ActionState.h
 Action_Translate.o : Action_Translate.cpp Action.h ActionState.h Action_Translate.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 Action_Unstrip.o : Action_Unstrip.cpp Action.h ActionState.h Action_Unstrip.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 Action_Unwrap.o : Action_Unwrap.cpp Action.h ActionState.h Action_Unwrap.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h ImageRoutines.h ImageTypes.h Image_List.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_Vector.o : Action_Vector.cpp Action.h ActionState.h Action_Vector.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h GridBin.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/LeastSquaresPlane.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Vector.o : Action_Vector.cpp Action.h ActionState.h Action_Vector.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h GridBin.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/LeastSquaresPlane.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 Action_VelocityAutoCorr.o : Action_VelocityAutoCorr.cpp Action.h ActionState.h Action_VelocityAutoCorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 Action_Volmap.o : Action_Volmap.cpp Action.h ActionState.h Action_Volmap.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridDbl.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 Action_Volume.o : Action_Volume.cpp Action.h ActionState.h Action_Volume.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 Action_Watershell.o : Action_Watershell.cpp Action.h ActionState.h Action_Watershell.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h ImageRoutines.h ImageTypes.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h cuda_kernels/kernel_wrappers.cuh
 Action_XtalSymm.o : Action_XtalSymm.cpp Action.h ActionState.h Action_XtalSymm.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SpaceGroup.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-AmberParamFile.o : AmberParamFile.cpp AmberParamFile.h ArgList.h AtomType.h BufferedLine.h CmapParmHolder.h Constants.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h StringRoutines.h TypeNameHolder.h
+AmberParamFile.o : AmberParamFile.cpp AmberParamFile.h ArgList.h AtomType.h BufferedLine.h CmapParmHolder.h Constants.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h StringRoutines.h TypeNameHolder.h
 AnalysisList.o : AnalysisList.cpp ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 Analysis_AmdBias.o : Analysis_AmdBias.cpp ActionState.h Analysis.h AnalysisState.h Analysis_AmdBias.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 Analysis_AutoCorr.o : Analysis_AutoCorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_AutoCorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
@@ -159,7 +159,7 @@ BufferedLine.o : BufferedLine.cpp BufferedLine.h CpptrajFile.h CpptrajStdio.h Fi
 ByteRoutines.o : ByteRoutines.cpp
 CIFfile.o : CIFfile.cpp ArgList.h Atom.h BufferedLine.h CIFfile.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h StringRoutines.h SymbolExporting.h
 CharMask.o : CharMask.cpp Atom.h CharMask.h CpptrajStdio.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h SymbolExporting.h Unit.h
-CharmmParamFile.o : CharmmParamFile.cpp ArgList.h AtomType.h BufferedLine.h CharmmParamFile.h CmapParmHolder.h Constants.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h StringRoutines.h TypeNameHolder.h
+CharmmParamFile.o : CharmmParamFile.cpp ArgList.h AtomType.h BufferedLine.h CharmmParamFile.h CmapParmHolder.h Constants.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h StringRoutines.h TypeNameHolder.h
 Cluster/Algorithm.o : Cluster/Algorithm.cpp Cluster/Algorithm.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h CpptrajStdio.h
 Cluster/Algorithm_DBscan.o : Cluster/Algorithm_DBscan.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cluster/Algorithm.h Cluster/Algorithm_DBscan.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 Cluster/Algorithm_DPeaks.o : Cluster/Algorithm_DPeaks.cpp ArgList.h AssociatedData.h Cluster/Algorithm.h Cluster/Algorithm_DPeaks.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_Mesh.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h ProgressBar.h Range.h Spline.h TextFormat.h
@@ -191,7 +191,7 @@ Cluster/Results_Coords.o : Cluster/Results_Coords.cpp ActionFrameCounter.h ArgLi
 Cluster/Sieve.o : Cluster/Sieve.cpp AssociatedData.h Cluster/Cframes.h Cluster/Sieve.h CpptrajFile.h DataSet.h DataSet_PairwiseCache.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Random.h Range.h TextFormat.h
 Cluster/Silhouette.o : Cluster/Silhouette.cpp Cluster/CentroidArray.h Cluster/Cframes.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Silhouette.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h OnlineVarT.h Parallel.h
 ClusterMap.o : ClusterMap.cpp AssociatedData.h ClusterMap.h Constants.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_2D.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h ProgressBar.h ProgressTimer.h Range.h TextFormat.h Timer.h
-CmapParmHolder.o : CmapParmHolder.cpp CmapParmHolder.h Constants.h CpptrajStdio.h NameType.h ParameterHolders.h ParameterTypes.h TypeNameHolder.h
+CmapParmHolder.o : CmapParmHolder.cpp CmapParmHolder.h Constants.h CpptrajStdio.h ParameterTypes.h Parm/ParmEnum.h
 Cmd.o : Cmd.cpp Cmd.h DispatchObject.h
 CmdInput.o : CmdInput.cpp CmdInput.h StringRoutines.h
 CmdList.o : CmdList.cpp Cmd.h CmdList.h DispatchObject.h
@@ -216,15 +216,15 @@ DataFileList.o : DataFileList.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h B
 DataFilter.o : DataFilter.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_integer.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 DataIO.o : DataIO.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 DataIO_AmberEne.o : DataIO_AmberEne.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberEne.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-DataIO_AmberFF.o : DataIO_AmberFF.cpp AmberParamFile.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberFF.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_AmberFrcmod.o : DataIO_AmberFrcmod.cpp AmberParamFile.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberFrcmod.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_AmberFF.o : DataIO_AmberFF.cpp AmberParamFile.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberFF.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_AmberFrcmod.o : DataIO_AmberFrcmod.cpp AmberParamFile.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberFrcmod.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_AmberLib.o : DataIO_AmberLib.cpp ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberLib.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 DataIO_AmberPrep.o : DataIO_AmberPrep.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberPrep.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 DataIO_CCP4.o : DataIO_CCP4.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ByteRoutines.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CCP4.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 DataIO_CharmmFastRep.o : DataIO_CharmmFastRep.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmFastRep.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 DataIO_CharmmOutput.o : DataIO_CharmmOutput.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmOutput.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 DataIO_CharmmRepLog.o : DataIO_CharmmRepLog.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmRepLog.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-DataIO_CharmmRtfPrm.o : DataIO_CharmmRtfPrm.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharmmParamFile.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmRtfPrm.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h DataSet_Topology.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/GetParams.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_CharmmRtfPrm.o : DataIO_CharmmRtfPrm.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharmmParamFile.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmRtfPrm.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h DataSet_Topology.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/GetParams.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Cmatrix_Binary.o : DataIO_Cmatrix_Binary.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cluster/Cframes.h Cluster/Cmatrix_Binary.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Cmatrix_Binary.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 DataIO_Cmatrix_NC.o : DataIO_Cmatrix_NC.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cluster/Cframes.h Cluster/Cmatrix_NC.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Cmatrix_NC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 DataIO_Coords.o : DataIO_Coords.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Coords.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h Trajin_Single.h Unit.h Vec3.h
@@ -232,19 +232,19 @@ DataIO_Cpout.o : DataIO_Cpout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h B
 DataIO_Evecs.o : DataIO_Evecs.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Evecs.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Modes.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 DataIO_Gnuplot.o : DataIO_Gnuplot.cpp ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Gnuplot.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 DataIO_Grace.o : DataIO_Grace.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Grace.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_string.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-DataIO_LeapRC.o : DataIO_LeapRC.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_Coords.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_Amber.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_LeapRC.o : DataIO_LeapRC.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_Coords.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h ParmIO.h Parm_Amber.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Mdout.o : DataIO_Mdout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Mdout.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 DataIO_NetCDF.o : DataIO_NetCDF.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cluster/Cframes.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_NetCDF.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_Mesh.h DataSet_Modes.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_Vector.h DataSet_Vector_Scalar.h DataSet_string.h DataSet_unsignedInt.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h Version.h
 DataIO_Numpy.o : DataIO_Numpy.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Numpy.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h libnpy/npy.hpp
 DataIO_OpenDx.o : DataIO_OpenDx.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_OpenDx.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridDbl.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 DataIO_Peaks.o : DataIO_Peaks.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Peaks.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector_Scalar.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 DataIO_RemLog.o : DataIO_RemLog.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_RemLog.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-DataIO_Std.o : DataIO_Std.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Cluster/Cframes.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Std.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_NameMap.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_Parameters.h DataSet_StringVar.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_string.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_Std.o : DataIO_Std.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Cluster/Cframes.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Std.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_NameMap.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_Parameters.h DataSet_StringVar.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_string.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_VecTraj.o : DataIO_VecTraj.cpp ActionFrameCounter.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_VecTraj.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h Unit.h Vec3.h
 DataIO_XVG.o : DataIO_XVG.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_XVG.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 DataIO_Xplor.o : DataIO_Xplor.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Xplor.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 DataSet.o : DataSet.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
-DataSetList.o : DataSetList.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Cluster/Cframes.h Cluster/Cmatrix_NC.h CmapParmHolder.h CompactFrameArray.h ComplexArray.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_FRM.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_GridDbl.h DataSet_GridFlt.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_NameMap.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h DataSet_PHREMD_Implicit.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_PairwiseCache_NC.h DataSet_Parameters.h DataSet_RemLog.h DataSet_StringVar.h DataSet_Tensor.h DataSet_Topology.h DataSet_Vector.h DataSet_Vector_Scalar.h DataSet_Zmatrix.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_disk.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h DataSet_unsignedInt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h InputTrajCommon.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h SymmetricTensor.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TypeNameHolder.h Unit.h Vec3.h
+DataSetList.o : DataSetList.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Cluster/Cframes.h Cluster/Cmatrix_NC.h CmapParmHolder.h CompactFrameArray.h ComplexArray.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_FRM.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_GridDbl.h DataSet_GridFlt.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_NameMap.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h DataSet_PHREMD_Implicit.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_PairwiseCache_NC.h DataSet_Parameters.h DataSet_RemLog.h DataSet_StringVar.h DataSet_Tensor.h DataSet_Topology.h DataSet_Vector.h DataSet_Vector_Scalar.h DataSet_Zmatrix.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_disk.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h DataSet_unsignedInt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h InputTrajCommon.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h SymmetricTensor.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TypeNameHolder.h Unit.h Vec3.h
 DataSet_1D.o : DataSet_1D.cpp ArrayIterator.h AssociatedData.h ComplexArray.h Constants.h Corr.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h PubFFT.h Range.h TextFormat.h
 DataSet_2D.o : DataSet_2D.cpp AssociatedData.h CpptrajFile.h DataSet.h DataSet_2D.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
 DataSet_3D.o : DataSet_3D.cpp AssociatedData.h Box.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_3D.h Dimension.h FileIO.h FileName.h GridBin.h Matrix_3x3.h MetaData.h Parallel.h Range.h TextFormat.h Vec3.h
@@ -266,7 +266,7 @@ DataSet_PHREMD_Implicit.o : DataSet_PHREMD_Implicit.cpp AssociatedData.h Cph.h C
 DataSet_PairwiseCache.o : DataSet_PairwiseCache.cpp AssociatedData.h Cluster/Cframes.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_PairwiseCache.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
 DataSet_PairwiseCache_MEM.o : DataSet_PairwiseCache_MEM.cpp ArrayIterator.h AssociatedData.h Cluster/Cframes.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h Dimension.h FileIO.h FileName.h Matrix.h MetaData.h Parallel.h Range.h StringRoutines.h TextFormat.h
 DataSet_PairwiseCache_NC.o : DataSet_PairwiseCache_NC.cpp AssociatedData.h Cluster/Cframes.h Cluster/Cmatrix_NC.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_PairwiseCache.h DataSet_PairwiseCache_NC.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h StringRoutines.h TextFormat.h
-DataSet_Parameters.o : DataSet_Parameters.cpp AssociatedData.h AtomType.h CmapParmHolder.h Constants.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h MetaData.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h TextFormat.h TypeNameHolder.h
+DataSet_Parameters.o : DataSet_Parameters.cpp AssociatedData.h AtomType.h CmapParmHolder.h Constants.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h MetaData.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h TextFormat.h TypeNameHolder.h
 DataSet_RemLog.o : DataSet_RemLog.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h ReplicaDimArray.h TextFormat.h
 DataSet_StringVar.o : DataSet_StringVar.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_StringVar.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
 DataSet_Tensor.o : DataSet_Tensor.cpp AssociatedData.h CpptrajFile.h DataSet.h DataSet_Tensor.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h SymmetricTensor.h TextFormat.h
@@ -315,7 +315,7 @@ EwaldOptions.o : EwaldOptions.cpp ArgList.h CpptrajStdio.h EwaldOptions.h
 ExclusionArray.o : ExclusionArray.cpp Atom.h AtomMask.h CharMask.h CpptrajStdio.h ExclusionArray.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Unit.h
 Exec_AddMissingRes.o : Exec_AddMissingRes.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h CharMask.h CompactFrameArray.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_AddMissingRes.h Exec_AddMissingRes_Pres.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h ParmFile.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h Trajout_Single.h Unit.h Vec3.h
 Exec_Analyze.o : Exec_Analyze.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Analyze.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_Build.o : Exec_Build.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h ExclusionArray.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/AssignParams.h Parm/GB_Params.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/Creator.h Structure/Disulfide.h Structure/HisProt.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/RingFinder.h Structure/StructureEnum.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Build.o : Exec_Build.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h ExclusionArray.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PairList.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/Creator.h Structure/Disulfide.h Structure/HisProt.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/RingFinder.h Structure/StructureEnum.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Calc.o : Exec_Calc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Calc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_CatCrd.o : Exec_CatCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CatCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_Change.o : Exec_Change.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Change.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
@@ -359,7 +359,7 @@ Exec_ReadInput.o : Exec_ReadInput.cpp Action.h ActionList.h ActionState.h Analys
 Exec_RotateDihedral.o : Exec_RotateDihedral.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_RotateDihedral.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_RunAnalysis.o : Exec_RunAnalysis.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_RunAnalysis.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_ScaleDihedralK.o : Exec_ScaleDihedralK.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ScaleDihedralK.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_Sequence.o : Exec_Sequence.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Sequence.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/Creator.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Sequence.o : Exec_Sequence.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Sequence.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/Creator.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_SequenceAlign.o : Exec_SequenceAlign.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SequenceAlign.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Unit.h Vec3.h
 Exec_Set.o : Exec_Set.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_StringVar.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Set.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_Show.o : Exec_Show.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_StringVar.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Show.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
@@ -369,7 +369,7 @@ Exec_SplitCoords.o : Exec_SplitCoords.cpp Action.h ActionList.h ActionState.h An
 Exec_System.o : Exec_System.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_System.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_Top.o : Exec_Top.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Top.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h TopInfo.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_Traj.o : Exec_Traj.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Traj.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_UpdateParameters.o : Exec_UpdateParameters.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h DataSet_Topology.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_UpdateParameters.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/AssignParams.h Parm/GetParams.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_UpdateParameters.o : Exec_UpdateParameters.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h DataSet_Topology.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_UpdateParameters.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GetParams.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_ViewRst.o : Exec_ViewRst.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ViewRst.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h ViewRst.h
 Exec_Zmatrix.o : Exec_Zmatrix.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Zmatrix.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Zmatrix.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 ExtendedSimilarity.o : ExtendedSimilarity.cpp AssociatedData.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h ExtendedSimilarity.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h Unit.h Vec3.h
@@ -428,15 +428,16 @@ PairList.o : PairList.cpp Atom.h AtomMask.h Box.h CoordinateInfo.h CpptrajStdio.
 Parallel.o : Parallel.cpp Parallel.h
 ParallelNetcdf.o : ParallelNetcdf.cpp CpptrajStdio.h Parallel.h ParallelNetcdf.h
 ParallelSetFrameNum.o : ParallelSetFrameNum.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h ParallelSetFrameNum.h Range.h TextFormat.h
-ParameterSet.o : ParameterSet.cpp AtomType.h CmapParmHolder.h Constants.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h TypeNameHolder.h UpdateParameters.h
-Parm/AssignParams.o : Parm/AssignParams.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h GuessAtomHybridization.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/../Structure/GenerateConnectivityArrays.h Parm/AssignParams.h Parm/GetParams.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Parm/AssignParams.o : Parm/AssignParams.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h GuessAtomHybridization.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/../Structure/GenerateConnectivityArrays.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GetParams.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Parm/GB_Params.o : Parm/GB_Params.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/GB_Params.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
-Parm/GetParams.o : Parm/GetParams.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/GetParams.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Parm/Merge.o : Parm/Merge.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterTypes.h Parm/AssignParams.h Parm/GetParams.h Parm/Merge.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h UpdateParameters.h Vec3.h
-ParmFile.o : ParmFile.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h ParmIO.h Parm_Amber.h Parm_CIF.h Parm_CharmmPsf.h Parm_Gromacs.h Parm_Mol2.h Parm_PDB.h Parm_SDF.h Parm_Tinker.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Parm/GetParams.o : Parm/GetParams.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/GetParams.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Parm/Merge.o : Parm/Merge.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/GetParams.h Parm/Merge.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h UpdateParameters.h Vec3.h
+Parm/ParameterSet.o : Parm/ParameterSet.cpp AtomType.h CmapParmHolder.h Constants.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h TypeNameHolder.h UpdateParameters.h
+Parm/test.o : Parm/test.cpp Constants.h NameType.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParmEnum.h Parm/ParmHolder.h TypeNameHolder.h
+ParmFile.o : ParmFile.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h ParmFile.h ParmIO.h Parm_Amber.h Parm_CIF.h Parm_CharmmPsf.h Parm_Gromacs.h Parm_Mol2.h Parm_PDB.h Parm_SDF.h Parm_Tinker.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Parm_Amber.o : Parm_Amber.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h ExclusionArray.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/GetParams.h ParmIO.h Parm_Amber.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h Unit.h Vec3.h
 Parm_CIF.o : Parm_CIF.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h CIFfile.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmIO.h Parm_CIF.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h
-Parm_CharmmPsf.o : Parm_CharmmPsf.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h CharmmParamFile.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Mol.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Parm/AssignParams.h ParmIO.h Parm_CharmmPsf.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Parm_CharmmPsf.o : Parm_CharmmPsf.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h CharmmParamFile.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Mol.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h ParmIO.h Parm_CharmmPsf.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Parm_Gromacs.o : Parm_Gromacs.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmIO.h Parm_Gromacs.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Parm_Mol2.o : Parm_Mol2.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Mol2File.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmIO.h Parm_Mol2.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Parm_PDB.o : Parm_PDB.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterTypes.h ParmIO.h Parm_PDB.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Timer.h Topology.h Unit.h Vec3.h
@@ -477,9 +478,9 @@ Spline.o : Spline.cpp CpptrajStdio.h Spline.h
 SplineFxnTable.o : SplineFxnTable.cpp Constants.h CpptrajStdio.h Spline.h SplineFxnTable.h StringRoutines.h
 Stats_Reduce.o : Stats_Reduce.cpp OnlineVarT.h Parallel.h Stats_Reduce.h
 StringRoutines.o : StringRoutines.cpp CpptrajStdio.h StringRoutines.h
-Structure/Builder.o : Structure/Builder.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h GuessAtomHybridization.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Builder.h Structure/Chirality.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Structure/Builder.o : Structure/Builder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h GuessAtomHybridization.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/../Parm/../AtomType.h Structure/../Parm/../CmapParmHolder.h Structure/../Parm/../Constants.h Structure/../Parm/../NameType.h Structure/../Parm/../ParameterTypes.h Structure/../Parm/../Parm/ParmEnum.h Structure/../Parm/../TypeNameHolder.h Structure/../Parm/DihedralParmHolder.h Structure/../Parm/ImproperParmHolder.h Structure/../Parm/ParameterSet.h Structure/../Parm/ParmEnum.h Structure/../Parm/ParmHolder.h Structure/Builder.h Structure/Chirality.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 Structure/Chirality.o : Structure/Chirality.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Chirality.h Structure/StructureEnum.h SymbolExporting.h Topology.h TorsionRoutines.h Unit.h Vec3.h
-Structure/Creator.o : Structure/Creator.cpp ArgList.h AssociatedData.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/Creator.h Structure/GenerateConnectivityArrays.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Structure/Creator.o : Structure/Creator.cpp ArgList.h AssociatedData.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/Creator.h Structure/GenerateConnectivityArrays.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/Disulfide.o : Structure/Disulfide.cpp ArgList.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Disulfide.h Structure/ResStatArray.h Structure/StructureRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Structure/FunctionalGroup.o : Structure/FunctionalGroup.cpp Atom.h AtomMap.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Structure/FxnGroupBuilder.o : Structure/FxnGroupBuilder.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h Structure/FxnGroupBuilder.h Structure/StructureRoutines.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h Unit.h Vec3.h
diff --git a/src/cpptrajfiles b/src/cpptrajfiles
index 3565084a40..2b8d67d581 100644
--- a/src/cpptrajfiles
+++ b/src/cpptrajfiles
@@ -378,7 +378,6 @@ COMMON_SOURCES= \
         NetcdfFile.cpp \
         OMM_helpers.cpp \
         OutputTrajCommon.cpp \
-        ParameterSet.cpp \
         PDBfile.cpp \
         PairList.cpp \
         Parallel.cpp \

From bd668f57e1a998f73fd77dc20baf988d7689780a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 16 Oct 2025 11:04:07 -0400
Subject: [PATCH 0971/1492] More fixes for moved files. Remove reference to
 temporary test file in Parm

---
 src/DataIO_AmberFF.cpp      | 4 ++--
 src/DataIO_CharmmRtfPrm.cpp | 4 ++--
 src/DataIO_LeapRC.cpp       | 2 +-
 src/DataIO_Std.cpp          | 4 ++--
 src/Parm/CMakeLists.txt     | 1 -
 src/Parm/parmdepend         | 1 -
 src/Parm/parmfiles          | 3 +--
 src/Structure/Creator.cpp   | 4 ++--
 8 files changed, 10 insertions(+), 13 deletions(-)

diff --git a/src/DataIO_AmberFF.cpp b/src/DataIO_AmberFF.cpp
index f9b06f30b1..a0237cc14e 100644
--- a/src/DataIO_AmberFF.cpp
+++ b/src/DataIO_AmberFF.cpp
@@ -94,11 +94,11 @@ int DataIO_AmberFF::WriteData(FileName const& fname, DataSetList const& dsl)
     return outfile.WriteParams( *(toWrite.front()), fname );
   } else {
     // Create a combined parameter set
-    ParameterSet prm;
+    Cpptraj::Parm::ParameterSet prm;
     for (std::vector<DataSet_Parameters*>::const_iterator it = toWrite.begin();
                                                           it != toWrite.end(); ++it)
     {
-      ParameterSet::UpdateCount UC;
+      Cpptraj::Parm::ParameterSet::UpdateCount UC;
       prm.UpdateParamSet( *(*it), UC, debug_, debug_ ); // FIXME verbose
     }
     return outfile.WriteParams( prm, fname );
diff --git a/src/DataIO_CharmmRtfPrm.cpp b/src/DataIO_CharmmRtfPrm.cpp
index 42b33e83ac..85022d8dca 100644
--- a/src/DataIO_CharmmRtfPrm.cpp
+++ b/src/DataIO_CharmmRtfPrm.cpp
@@ -72,8 +72,8 @@ int DataIO_CharmmRtfPrm::processWriteArgs(ArgList& argIn)
 // DataIO_CharmmRtfPrm::WriteData()
 int DataIO_CharmmRtfPrm::WriteData(FileName const& fname, DataSetList const& dsl)
 {
-  ParameterSet pout;
-  ParameterSet::UpdateCount ucount;
+  Cpptraj::Parm::ParameterSet pout;
+  Cpptraj::Parm::ParameterSet::UpdateCount ucount;
   for (DataSetList::const_iterator it = dsl.begin(); it != dsl.end(); ++it)
   {
     if ( (*it)->Type() == DataSet::PARAMETERS )
diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index f612ea9a88..4f79ba566b 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -223,7 +223,7 @@ const
     if ( paramSet->Type() == DataSet::PARAMETERS ) {
       DataSet_Parameters& param = static_cast<DataSet_Parameters&>( *paramSet );
       mprintf("\tUpdating atom hybridizations and elements in set %s\n", param.legend());
-      for (ParmHolder<AtomType>::iterator it = param.AT().begin();
+      for (Cpptraj::Parm::ParmHolder<AtomType>::iterator it = param.AT().begin();
                                           it != param.AT().end(); ++it)
       {
         AtypeEltHybridPairMap::const_iterator ah = atomHybridizations.find( it->first[0] );
diff --git a/src/DataIO_Std.cpp b/src/DataIO_Std.cpp
index ecef5f9bb9..dc431648cb 100644
--- a/src/DataIO_Std.cpp
+++ b/src/DataIO_Std.cpp
@@ -1316,12 +1316,12 @@ int DataIO_Std::WriteParameters(CpptrajFile& file, DataSetList const& Sets) cons
     prm.Print(file);
   } else if (Sets.size() > 1) {
     // Create a combined parameter set
-    ParameterSet prm;
+    Cpptraj::Parm::ParameterSet prm;
     for (DataSetList::const_iterator it = Sets.begin(); it != Sets.end(); ++it)
     {
       if ((*it)->Type() == DataSet::PARAMETERS) {
         DataSet_Parameters const& param = static_cast<DataSet_Parameters const&>( *(*it) );
-        ParameterSet::UpdateCount UC;
+        Cpptraj::Parm::ParameterSet::UpdateCount UC;
         prm.UpdateParamSet( param, UC, debug_, debug_ ); // FIXME verbose
       } else {
         mprintf("Warning: Set '%s' is not a parameter set, skipping.\n", (*it)->legend());
diff --git a/src/Parm/CMakeLists.txt b/src/Parm/CMakeLists.txt
index c0af4f1dc4..067f2c5195 100644
--- a/src/Parm/CMakeLists.txt
+++ b/src/Parm/CMakeLists.txt
@@ -5,5 +5,4 @@ target_sources(cpptraj_common_obj PRIVATE
   ${CMAKE_CURRENT_LIST_DIR}/GetParams.cpp
   ${CMAKE_CURRENT_LIST_DIR}/Merge.cpp
   ${CMAKE_CURRENT_LIST_DIR}/ParameterSet.cpp
-  ${CMAKE_CURRENT_LIST_DIR}/test.cpp
 )
diff --git a/src/Parm/parmdepend b/src/Parm/parmdepend
index 7e76359b6d..905d7f98f6 100644
--- a/src/Parm/parmdepend
+++ b/src/Parm/parmdepend
@@ -3,4 +3,3 @@ GB_Params.o : GB_Params.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../C
 GetParams.o : GetParams.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/ParmEnum.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h DihedralParmHolder.h GetParams.h ImproperParmHolder.h ParameterSet.h ParmEnum.h ParmHolder.h
 Merge.o : Merge.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../StringRoutines.h ../SymbolExporting.h ../Timer.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../UpdateParameters.h ../Vec3.h AssignParams.h GetParams.h Merge.h ParmEnum.h ParmHolder.h
 ParameterSet.o : ParameterSet.cpp ../AtomType.h ../CmapParmHolder.h ../Constants.h ../CpptrajFile.h ../CpptrajStdio.h ../FileIO.h ../FileName.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/ParmEnum.h ../TypeNameHolder.h ../UpdateParameters.h DihedralParmHolder.h ImproperParmHolder.h ParameterSet.h ParmEnum.h ParmHolder.h
-test.o : test.cpp ../Constants.h ../NameType.h ../ParameterTypes.h ../TypeNameHolder.h DihedralParmHolder.h ImproperParmHolder.h ParmEnum.h ParmHolder.h
diff --git a/src/Parm/parmfiles b/src/Parm/parmfiles
index 57e32392e1..ca2b23c678 100644
--- a/src/Parm/parmfiles
+++ b/src/Parm/parmfiles
@@ -4,5 +4,4 @@ PARM_SOURCES= \
   GB_Params.cpp \
   GetParams.cpp \
   Merge.cpp \
-  ParameterSet.cpp \
-  test.cpp
+  ParameterSet.cpp
diff --git a/src/Structure/Creator.cpp b/src/Structure/Creator.cpp
index 5de798b7a9..56729c70bd 100644
--- a/src/Structure/Creator.cpp
+++ b/src/Structure/Creator.cpp
@@ -94,7 +94,7 @@ void Creator::UpdateTemplateElements() const {
     // Loop over template atoms
     Topology& templateTop = *((*crd)->TopPtr());
     for (int at = 0; at != templateTop.Natom(); at++) {
-      ParmHolder<AtomType>::const_iterator it;
+      Cpptraj::Parm::ParmHolder<AtomType>::const_iterator it;
       if (templateTop[at].HasType()) {
         it = mainParmSet_->AT().GetParam( TypeNameHolder(templateTop[at].Type()) );
         if (it != mainParmSet_->AT().end()) {
@@ -289,7 +289,7 @@ int Creator::getParameterSets(ArgList& argIn, DataSetList const& DSL) {
       Parray::const_iterator it = ParamSets.begin();
       mainParmSet_ = new DataSet_Parameters( *(*it) );
       ++it;
-      ParameterSet::UpdateCount UC;
+      Cpptraj::Parm::ParameterSet::UpdateCount UC;
       for (; it != ParamSets.end(); ++it)
         mainParmSet_->UpdateParamSet( *(*it), UC, debug_, debug_+1 ); // Make it so verbosity is at least 1 to report overwritten params 
     }

From 6c72a2c966e1814e94494ca071e90cf7d8d38161 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 16 Oct 2025 12:34:36 -0400
Subject: [PATCH 0972/1492] Use a map for the DihedralParmHolder. This does
 improve the speed of the FindParam function by about 50%, but the wildcard
 search is still slow.

---
 src/Parm/DihedralParmHolder.h | 51 ++++++++++++++++++++---------------
 src/TypeNameHolder.h          |  2 ++
 2 files changed, 32 insertions(+), 21 deletions(-)

diff --git a/src/Parm/DihedralParmHolder.h b/src/Parm/DihedralParmHolder.h
index de257ba1d1..6749c50e22 100644
--- a/src/Parm/DihedralParmHolder.h
+++ b/src/Parm/DihedralParmHolder.h
@@ -1,7 +1,7 @@
 #ifndef INC_PARM_DIHEDRALPARMHOLDER_H
 #define INC_PARM_DIHEDRALPARMHOLDER_H
-#include <vector>
-#include <utility> // std::pair
+#include <map>
+//#include <utility> // std::pair
 #include "ParmEnum.h"
 #include "../ParameterTypes.h"
 #include "../TypeNameHolder.h"
@@ -17,7 +17,8 @@ namespace Parm {
   */
 class DihedralParmHolder {
     typedef std::pair<TypeNameHolder,DihedralParmArray> Bpair;
-    typedef std::vector<Bpair> Bmap;
+//    typedef std::vector<Bpair> Bmap;
+    typedef std::map<TypeNameHolder,DihedralParmArray> Bmap;
   public:
     /// CONSTRUCTOR
     DihedralParmHolder() {}
@@ -34,17 +35,19 @@ class DihedralParmHolder {
     /// Add (or update) a single dihedral parameter for given atom types.
     RetType AddParm(TypeNameHolder const& types, DihedralParmType const& dp, bool allowUpdate) {
       // Check if parm for these types exist
-      Bmap::iterator it0 = bpmap_.begin();
-      for (; it0 != bpmap_.end(); ++it0)
-      {
-        if (it0->first.Match_NoWC( types ))
-          break;
-      }
+//      Bmap::iterator it0 = bpmap_.begin();
+//      for (; it0 != bpmap_.end(); ++it0)
+//      {
+//        if (it0->first.Match_NoWC( types ))
+//          break;
+//      }
+      Bmap::iterator it0 = bpmap_.find( types ); // TODO lower_bound
       if (it0 == bpmap_.end()) {
         // Brand new dihedral for these types.
         //mprintf("DEBUG: New dihedral parm: %s %s %s %s pk=%12.4f pn=%12.4f pp=%12.4f\n",
         //        *types[0], *types[1], *types[2], *types[3], dp.Pk(), dp.Pn(), dp.Phase());
-        bpmap_.push_back( Bpair(types, DihedralParmArray(1, dp)) );
+//        bpmap_.push_back( Bpair(types, DihedralParmArray(1, dp)) );
+        bpmap_.insert( Bpair(types, DihedralParmArray(1, dp)) );
       } else {
         // If we are here types match - check multiplicity.
         DihedralParmArray::iterator it1 = it0->second.begin();
@@ -95,15 +98,17 @@ class DihedralParmHolder {
     /// Add array of dihedral parameters with unique multiplicities
     RetType AddParm(TypeNameHolder const& types, DihedralParmArray const& dpa, bool allowUpdate) {
       // Check if parm for these types exist
-      Bmap::iterator it0 = bpmap_.begin();
-      for (; it0 != bpmap_.end(); ++it0)
-      {
-        if (it0->first.Match_NoWC( types ))
-          break;
-      }
+//      Bmap::iterator it0 = bpmap_.begin();
+//      for (; it0 != bpmap_.end(); ++it0)
+//      {
+//        if (it0->first.Match_NoWC( types ))
+//          break;
+//      }
+      Bmap::iterator it0 = bpmap_.find( types ); // TODO lower_bound
       if (it0 == bpmap_.end()) {
         // Brand new dihedral for these types.
-        bpmap_.push_back( Bpair(types, dpa) );
+//        bpmap_.push_back( Bpair(types, dpa) );
+        bpmap_.insert( Bpair(types, dpa) );
       } else {
         if (!allowUpdate) return ERR;
         // Check if sizes are the same.
@@ -136,8 +141,10 @@ class DihedralParmHolder {
     /// \return Array of dihedral parameters matching given atom types.
     DihedralParmArray FindParam(TypeNameHolder const& types, bool& found) const {
       found = true;
-      for (const_iterator it = begin(); it != end(); ++it)
-        if (it->first.Match_NoWC( types )) return it->second;
+//      for (const_iterator it = begin(); it != end(); ++it)
+//        if (it->first.Match_NoWC( types )) return it->second;
+      Bmap::const_iterator it0 = bpmap_.find( types );
+      if (it0 != bpmap_.end()) return it0->second;
       if (wc_.len() > 0) {
         for (const_iterator it = begin(); it != end(); ++it)
           if (it->first.Match_WC( types, wc_)) return it->second;
@@ -147,8 +154,10 @@ class DihedralParmHolder {
     }
     /// \return iterator to parameter matching the given types.
     const_iterator GetParam(TypeNameHolder const& types) {
-      for (const_iterator it = begin(); it != end(); ++it)
-        if (it->first.Match_NoWC( types )) return it;
+//      for (const_iterator it = begin(); it != end(); ++it)
+//        if (it->first.Match_NoWC( types )) return it;
+      Bmap::const_iterator it0 = bpmap_.find( types );
+      if (it0 != bpmap_.end()) return it0;
       if (wc_.len() > 0) {
         for (const_iterator it = begin(); it != end(); ++it)
           if (it->first.Match_WC( types, wc_)) return it;
diff --git a/src/TypeNameHolder.h b/src/TypeNameHolder.h
index 19ce1ce1ef..b383ee43ee 100644
--- a/src/TypeNameHolder.h
+++ b/src/TypeNameHolder.h
@@ -53,6 +53,8 @@ class TypeNameHolder {
         }
       return match;
     }
+    /// \return true if either direction is an exact match, no wildcard.
+    bool operator==(TypeNameHolder const& rhs) const { return Match_NoWC(rhs); }
     /// \return true if either direction is a match, taking into account wildcard.
     bool Match_WC(TypeNameHolder const& rhs, NameType const& wildcard) const {
       // Sanity check

From fc2823c65cc864f9d9d03d7945928929a261c0b8 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 17 Oct 2025 13:17:23 -0400
Subject: [PATCH 0973/1492] Cache found dihedral parameters to speed things up

---
 src/Parm/AssignParams.cpp | 30 +++++++++++++++++++++++-------
 1 file changed, 23 insertions(+), 7 deletions(-)

diff --git a/src/Parm/AssignParams.cpp b/src/Parm/AssignParams.cpp
index 054e53805e..503b811ca4 100644
--- a/src/Parm/AssignParams.cpp
+++ b/src/Parm/AssignParams.cpp
@@ -305,6 +305,10 @@ const
 #endif
 { // TODO skip extra points
   DihedralArray dihedralsIn;
+  // Dihedral cache
+  typedef std::pair<TypeNameHolder, DihedralParmArray> DihCachePair;
+  typedef std::map<TypeNameHolder, DihedralParmArray> DihCacheType;
+  DihCacheType dihedralCache;
   // Improper cache
   ImproperParmHolder improperCache;
   improperCache.SetWildcard( newImproperParams.Wildcard() );
@@ -471,13 +475,25 @@ const
       t_dih_dih_.Start();
 #     endif
       // -----Regular dihedral. See if parameter already present. ----
-#     ifdef TIMER
-      t_dih_dih_getnew_.Start();
-#     endif
-      DihedralParmArray dpa = newDihedralParams.FindParam( types, found );
-#     ifdef TIMER
-      t_dih_dih_getnew_.Stop();
-#     endif
+      DihedralParmArray dpa;
+      // Check the cache first
+      DihCacheType::const_iterator cachedDih = dihedralCache.find( types );
+      if (cachedDih != dihedralCache.end()) {
+        dpa = cachedDih->second;
+        found = true;
+      } else {
+        // Not in cache. Search incoming parameters.
+#       ifdef TIMER
+        t_dih_dih_getnew_.Start();
+#       endif
+        dpa = newDihedralParams.FindParam( types, found );
+#       ifdef TIMER
+        t_dih_dih_getnew_.Stop();
+#       endif
+        // If found, cache the parameter
+        if (found)
+          dihedralCache.insert( DihCachePair(types, dpa) );
+      }
       if (!found) {
         mprintf("Warning: Dihedral parameters not found for dihedral %s-%s-%s-%s (%s-%s-%s-%s)\n",
                 topOut.TruncResAtomNameNum(dih->A1()).c_str(),

From eacf59e542739ae5ee0c1d0490db67ee7408abc9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 18 Oct 2025 10:47:07 -0400
Subject: [PATCH 0974/1492] Include map for the dihedral cache

---
 src/Parm/AssignParams.cpp | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/Parm/AssignParams.cpp b/src/Parm/AssignParams.cpp
index 503b811ca4..00cfa0da95 100644
--- a/src/Parm/AssignParams.cpp
+++ b/src/Parm/AssignParams.cpp
@@ -13,6 +13,7 @@
 #include "../Topology.h"
 #include "../TypeNameHolder.h"
 #include <algorithm> //sort
+#include <map> // DihCacheType
 
 using namespace Cpptraj::Parm;
 
@@ -491,8 +492,9 @@ const
         t_dih_dih_getnew_.Stop();
 #       endif
         // If found, cache the parameter
-        if (found)
+        if (found) {
           dihedralCache.insert( DihCachePair(types, dpa) );
+        }
       }
       if (!found) {
         mprintf("Warning: Dihedral parameters not found for dihedral %s-%s-%s-%s (%s-%s-%s-%s)\n",

From 5bce9120b13a5e2e1754592c26ab79fbaafb0746 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 18 Oct 2025 10:48:42 -0400
Subject: [PATCH 0975/1492] Revert the dihedral parm holder back to a vector
 under the hood. I remember now why I didn't use a map; the TypeNameHolder
 sort doesnt currently work right with map because things need to be forwards
 and backwards. So the map isnt actually sorted efficiently. I will need to
 think of a better way to use the map in the future. For now a dihedral cache
 seems to be the way to go when assigning parameters.

---
 src/Parm/DihedralParmHolder.h | 51 +++++++++++++++--------------------
 1 file changed, 21 insertions(+), 30 deletions(-)

diff --git a/src/Parm/DihedralParmHolder.h b/src/Parm/DihedralParmHolder.h
index 6749c50e22..de257ba1d1 100644
--- a/src/Parm/DihedralParmHolder.h
+++ b/src/Parm/DihedralParmHolder.h
@@ -1,7 +1,7 @@
 #ifndef INC_PARM_DIHEDRALPARMHOLDER_H
 #define INC_PARM_DIHEDRALPARMHOLDER_H
-#include <map>
-//#include <utility> // std::pair
+#include <vector>
+#include <utility> // std::pair
 #include "ParmEnum.h"
 #include "../ParameterTypes.h"
 #include "../TypeNameHolder.h"
@@ -17,8 +17,7 @@ namespace Parm {
   */
 class DihedralParmHolder {
     typedef std::pair<TypeNameHolder,DihedralParmArray> Bpair;
-//    typedef std::vector<Bpair> Bmap;
-    typedef std::map<TypeNameHolder,DihedralParmArray> Bmap;
+    typedef std::vector<Bpair> Bmap;
   public:
     /// CONSTRUCTOR
     DihedralParmHolder() {}
@@ -35,19 +34,17 @@ class DihedralParmHolder {
     /// Add (or update) a single dihedral parameter for given atom types.
     RetType AddParm(TypeNameHolder const& types, DihedralParmType const& dp, bool allowUpdate) {
       // Check if parm for these types exist
-//      Bmap::iterator it0 = bpmap_.begin();
-//      for (; it0 != bpmap_.end(); ++it0)
-//      {
-//        if (it0->first.Match_NoWC( types ))
-//          break;
-//      }
-      Bmap::iterator it0 = bpmap_.find( types ); // TODO lower_bound
+      Bmap::iterator it0 = bpmap_.begin();
+      for (; it0 != bpmap_.end(); ++it0)
+      {
+        if (it0->first.Match_NoWC( types ))
+          break;
+      }
       if (it0 == bpmap_.end()) {
         // Brand new dihedral for these types.
         //mprintf("DEBUG: New dihedral parm: %s %s %s %s pk=%12.4f pn=%12.4f pp=%12.4f\n",
         //        *types[0], *types[1], *types[2], *types[3], dp.Pk(), dp.Pn(), dp.Phase());
-//        bpmap_.push_back( Bpair(types, DihedralParmArray(1, dp)) );
-        bpmap_.insert( Bpair(types, DihedralParmArray(1, dp)) );
+        bpmap_.push_back( Bpair(types, DihedralParmArray(1, dp)) );
       } else {
         // If we are here types match - check multiplicity.
         DihedralParmArray::iterator it1 = it0->second.begin();
@@ -98,17 +95,15 @@ class DihedralParmHolder {
     /// Add array of dihedral parameters with unique multiplicities
     RetType AddParm(TypeNameHolder const& types, DihedralParmArray const& dpa, bool allowUpdate) {
       // Check if parm for these types exist
-//      Bmap::iterator it0 = bpmap_.begin();
-//      for (; it0 != bpmap_.end(); ++it0)
-//      {
-//        if (it0->first.Match_NoWC( types ))
-//          break;
-//      }
-      Bmap::iterator it0 = bpmap_.find( types ); // TODO lower_bound
+      Bmap::iterator it0 = bpmap_.begin();
+      for (; it0 != bpmap_.end(); ++it0)
+      {
+        if (it0->first.Match_NoWC( types ))
+          break;
+      }
       if (it0 == bpmap_.end()) {
         // Brand new dihedral for these types.
-//        bpmap_.push_back( Bpair(types, dpa) );
-        bpmap_.insert( Bpair(types, dpa) );
+        bpmap_.push_back( Bpair(types, dpa) );
       } else {
         if (!allowUpdate) return ERR;
         // Check if sizes are the same.
@@ -141,10 +136,8 @@ class DihedralParmHolder {
     /// \return Array of dihedral parameters matching given atom types.
     DihedralParmArray FindParam(TypeNameHolder const& types, bool& found) const {
       found = true;
-//      for (const_iterator it = begin(); it != end(); ++it)
-//        if (it->first.Match_NoWC( types )) return it->second;
-      Bmap::const_iterator it0 = bpmap_.find( types );
-      if (it0 != bpmap_.end()) return it0->second;
+      for (const_iterator it = begin(); it != end(); ++it)
+        if (it->first.Match_NoWC( types )) return it->second;
       if (wc_.len() > 0) {
         for (const_iterator it = begin(); it != end(); ++it)
           if (it->first.Match_WC( types, wc_)) return it->second;
@@ -154,10 +147,8 @@ class DihedralParmHolder {
     }
     /// \return iterator to parameter matching the given types.
     const_iterator GetParam(TypeNameHolder const& types) {
-//      for (const_iterator it = begin(); it != end(); ++it)
-//        if (it->first.Match_NoWC( types )) return it;
-      Bmap::const_iterator it0 = bpmap_.find( types );
-      if (it0 != bpmap_.end()) return it0;
+      for (const_iterator it = begin(); it != end(); ++it)
+        if (it->first.Match_NoWC( types )) return it;
       if (wc_.len() > 0) {
         for (const_iterator it = begin(); it != end(); ++it)
           if (it->first.Match_WC( types, wc_)) return it;

From 04187922b243d555223aa4257f2a23cb5d02fab1 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 18 Oct 2025 15:53:29 -0400
Subject: [PATCH 0976/1492] Read CMAP from MDOUT

---
 src/DataIO_Mdout.cpp | 3 ++-
 src/DataIO_Mdout.h   | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/DataIO_Mdout.cpp b/src/DataIO_Mdout.cpp
index 152bf546f2..bcfd037449 100644
--- a/src/DataIO_Mdout.cpp
+++ b/src/DataIO_Mdout.cpp
@@ -37,6 +37,7 @@ DataIO_Mdout::DataIO_Mdout() {
   termIdxMap_.insert(NameIdxPair("TEMP(K)", TEMP));
   termIdxMap_.insert(NameIdxPair("PRESS", PRESS));
   termIdxMap_.insert(NameIdxPair("DV/DL", DVDL));
+  termIdxMap_.insert(NameIdxPair("CMAP", CMAP));
 }
 
 // DataIO_Mdout::ID_DataFormat()
@@ -67,7 +68,7 @@ const char* DataIO_Mdout::Enames_[] = {
   "ANGLE",  "DIHED",  "VDW",   "EELEC",      "EGB",     "EPB", "ECAVITY", "EDISPER",
   "VDW1-4", "EEL1-4", "RST",   "EAMBER",     "Density",
   "RMS",    "EKtot",  "ESURF", "EAMD_BOOST", "VOLUME",  "TEMP",
-  "PRESS",  "DVDL",   0
+  "PRESS",  "DVDL",   "CMAP",  0
 };
 
 /** \return FieldType corresponding to given term name, or N_FIELDTYPES if
diff --git a/src/DataIO_Mdout.h b/src/DataIO_Mdout.h
index 8ad5c4e509..0d30c185ed 100644
--- a/src/DataIO_Mdout.h
+++ b/src/DataIO_Mdout.h
@@ -22,7 +22,7 @@ class DataIO_Mdout : public DataIO {
                      ANGLE, DIHED, VDWAALS, EEL, EGB, EPB, ECAVITY, EDISPER,
                      VDW14, EEL14, RESTRAINT, EAMBER, DENSITY,
                      RMS, EKTOT, ESURF, EAMD_BOOST, VOLUME, TEMP,
-                     PRESS, DVDL, N_FIELDTYPES };
+                     PRESS, DVDL, CMAP, N_FIELDTYPES };
 
     FieldType getTermIdx(std::string const&) const;
     int GetAmberEterms(const char*, Darray&, std::vector<bool>&);

From 56162c539880c1a09533218c07816dc2f81abd91 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 21 Oct 2025 09:21:54 -0400
Subject: [PATCH 0977/1492] Add coordinates for KCX; will help when checking
 the topology via energy

---
 test/Test_CharmmParams/KCX.rst7 | 14 ++++++++++++++
 1 file changed, 14 insertions(+)
 create mode 100644 test/Test_CharmmParams/KCX.rst7

diff --git a/test/Test_CharmmParams/KCX.rst7 b/test/Test_CharmmParams/KCX.rst7
new file mode 100644
index 0000000000..0dee3b87bd
--- /dev/null
+++ b/test/Test_CharmmParams/KCX.rst7
@@ -0,0 +1,14 @@
+Cpptraj Generated Restart                                                       
+   23
+   8.7990000  -2.8920000  11.2160000   9.5010000  -3.4990000  10.8510000
+   7.4570000  -3.3790000  11.2170000   7.3030000  -3.9110000  10.2900000
+   7.1420000  -4.3270000  12.4080000   7.6340000  -3.8850000  13.2970000
+   7.6210000  -5.2970000  12.1690000   5.6860000  -4.6530000  12.8330000
+   5.0890000  -4.6700000  11.9000000   5.3530000  -3.8060000  13.4650000
+   5.3190000  -5.9160000  13.5920000   4.9780000  -5.6410000  14.6130000
+   6.2170000  -6.5650000  13.6760000   4.2090000  -6.6870000  12.8840000
+   3.2900000  -6.0650000  12.9110000   4.0320000  -7.6270000  13.4480000
+   4.4530000  -7.0540000  11.4800000   4.8310000  -7.9680000  11.3800000
+   4.2300000  -6.3190000  10.3730000   4.9750000  -6.3540000   9.3310000
+   3.3590000  -5.5850000  10.2430000   6.4950000  -2.2790000  10.8990000
+   5.8750000  -2.3320000   9.9930000

From a87c779699b9486dd9c9e9248bdf3d2a9431cbcf Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 21 Oct 2025 09:28:15 -0400
Subject: [PATCH 0978/1492] New cpptraj does a better job packing the LJ
 params.

---
 test/Test_CharmmParams/test3.parm7.save | 144 +++++++++++-------------
 1 file changed, 63 insertions(+), 81 deletions(-)

diff --git a/test/Test_CharmmParams/test3.parm7.save b/test/Test_CharmmParams/test3.parm7.save
index ee7b4528e7..9c11e876f5 100644
--- a/test/Test_CharmmParams/test3.parm7.save
+++ b/test/Test_CharmmParams/test3.parm7.save
@@ -1,10 +1,10 @@
-%VERSION  VERSION_STAMP = V0001.000  DATE = 06/28/24 14:39:23                  
+%VERSION  VERSION_STAMP = V0001.000  DATE = 10/19/25 11:02:40                  
 %FLAG CTITLE                                                                    
 %FORMAT(a80)                                                                    
                                                                                 
 %FLAG POINTERS                                                                  
 %FORMAT(10I8)                                                                   
-      23      12      11      11      26      12      42      19       0       0
+      23      11      11      11      26      12      42      19       0       0
      114       1      11      12      19      13      22      19      12       0
        0       0       0       0       0       0       0       1      23       0
        0
@@ -41,8 +41,8 @@ OQ2 C   O
 %FLAG ATOM_TYPE_INDEX                                                           
 %FORMAT(10I8)                                                                   
        1       2       3       4       5       6       6       5       6       6
-       5       6       6       5       7       7       8       2       9      10
-      10      11      12
+       5       6       6       5       4       4       7       2       8       9
+       9      10      11
 %FLAG NUMBER_EXCLUDED_ATOMS                                                     
 %FORMAT(10I8)                                                                   
        9       4      10       6      11       6       5      10       5       4
@@ -51,20 +51,18 @@ OQ2 C   O
 %FLAG NONBONDED_PARM_INDEX                                                      
 %FORMAT(10I8)                                                                   
        1       2       4       7      11      16      22      29      37      46
-      56      67       2       3       5       8      12      17      23      30
-      38      47      57      68       4       5       6       9      13      18
-      24      31      39      48      58      69       7       8       9      10
-      14      19      25      32      40      49      59      70      11      12
-      13      14      15      20      26      33      41      50      60      71
-      16      17      18      19      20      21      27      34      42      51
-      61      72      22      23      24      25      26      27      28      35
-      43      52      62      73      29      30      31      32      33      34
-      35      36      44      53      63      74      37      38      39      40
-      41      42      43      44      45      54      64      75      46      47
-      48      49      50      51      52      53      54      55      65      76
+      56       2       3       5       8      12      17      23      30      38
+      47      57       4       5       6       9      13      18      24      31
+      39      48      58       7       8       9      10      14      19      25
+      32      40      49      59      11      12      13      14      15      20
+      26      33      41      50      60      16      17      18      19      20
+      21      27      34      42      51      61      22      23      24      25
+      26      27      28      35      43      52      62      29      30      31
+      32      33      34      35      36      44      53      63      37      38
+      39      40      41      42      43      44      45      54      64      46
+      47      48      49      50      51      52      53      54      55      65
       56      57      58      59      60      61      62      63      64      65
-      66      77      67      68      69      70      71      72      73      74
-      75      76      77      78
+      66
 %FLAG RESIDUE_LABEL                                                             
 %FORMAT(20a4)                                                                   
 LYS 
@@ -177,24 +175,20 @@ LYS
   7.3181528163627407E+05  6.5258360090677787E+04  9.9747188643525087E+05
   9.1567773233238448E+04  8.5040378433301811E+00  6.3572903858652840E+04
   3.4318669196435499E+03  8.7170825044557787E+04  4.6676302460305051E+03
-  6.8302639168618378E+04  5.8619918176552899E+00  4.7582070268952521E+04
-  2.5215628838626608E+03  6.5258360090677787E+04  3.4318669196435499E+03
-  2.5215628838626608E+03  1.3165904011680079E+06  6.0933367984903236E+02
-  8.4843532269460149E+05  6.8302639168618378E+04  1.1578616437851232E+06
-  9.1567773233238448E+04  6.8302639168618378E+04  1.3165904011680079E+06
-  1.2548527649652825E+06  8.3313783399093302E+02  7.9404278715436335E+05
-  7.0374830989043825E+04  1.0823693981629282E+06  9.4025592817777913E+04
-  7.0374830989043825E+04  1.2548527649652825E+06  1.1744051200000001E+06
-  6.2064871065477643E+05  1.9177170259300729E+02  4.0793061580001831E+05
-  2.9572311958222777E+04  5.5740588794684899E+05  3.9793586685559225E+04
-  2.9572311958222777E+04  6.2064871065477643E+05  6.0333751726046635E+05
-  2.8637048204317159E+05  1.5730411891415559E+06  1.0443935461513495E+03
-  9.9538531133501721E+05  8.8219519385371299E+04  1.3568218461261056E+06
-  1.1786731835420479E+05  8.8219519385371299E+04  1.5730411891415559E+06
-  1.4721947291958532E+06  7.5632360393402458E+05  1.8454937600000000E+06
+  1.3165904011680079E+06  6.0933367984903236E+02  8.4843532269460149E+05
+  6.8302639168618378E+04  1.1578616437851232E+06  9.1567773233238448E+04
+  1.3165904011680079E+06  1.2548527649652825E+06  8.3313783399093302E+02
+  7.9404278715436335E+05  7.0374830989043825E+04  1.0823693981629282E+06
+  9.4025592817777913E+04  1.2548527649652825E+06  1.1744051200000001E+06
   6.2064871065477643E+05  1.9177170259300729E+02  4.0793061580001831E+05
   2.9572311958222777E+04  5.5740588794684899E+05  3.9793586685559225E+04
-  2.9572311958222777E+04  6.2064871065477643E+05  6.0333751726046635E+05
+  6.2064871065477643E+05  6.0333751726046635E+05  2.8637048204317159E+05
+  1.5730411891415559E+06  1.0443935461513495E+03  9.9538531133501721E+05
+  8.8219519385371299E+04  1.3568218461261056E+06  1.1786731835420479E+05
+  1.5730411891415559E+06  1.4721947291958532E+06  7.5632360393402458E+05
+  1.8454937600000000E+06  6.2064871065477643E+05  1.9177170259300729E+02
+  4.0793061580001831E+05  2.9572311958222777E+04  5.5740588794684899E+05
+  3.9793586685559225E+04  6.2064871065477643E+05  6.0333751726046635E+05
   2.8637048204317159E+05  7.5632360393402458E+05  2.8637048204317159E+05
 %FLAG LENNARD_JONES_BCOEF                                                       
 %FORMAT(3E24.16)                                                                
@@ -205,24 +199,20 @@ LYS
   3.5201829414699682E+02  9.5719572566977860E+01  4.7268774318940854E+02
   1.7379150748946228E+02  1.1598498613736850E+00  9.1584766861999441E+01
   1.9376289489599738E+01  1.2334805617966474E+02  2.5195192268767240E+01
-  1.3462071944937435E+02  8.6366978783292059E-01  7.1063211034782952E+01
-  1.4896225487683587E+01  9.5719572566977860E+01  1.9376289489599738E+01
-  1.4896225487683587E+01  1.0262905636000003E+03  1.5289896454943387E+01
-  5.2105595022250009E+02  1.3462071944937435E+02  7.0010444501670088E+02
-  1.7379150748946228E+02  1.3462071944937435E+02  1.0262905636000003E+03
-  7.7065214324377325E+02  1.3751573424392696E+01  3.8771620466521648E+02
-  1.0510390653125525E+02  5.2064207832106547E+02  1.3545569691804164E+02
-  1.0510390653125525E+02  7.7065214324377325E+02  5.7344000000000005E+02
+  1.0262905636000003E+03  1.5289896454943387E+01  5.2105595022250009E+02
+  1.3462071944937435E+02  7.0010444501670088E+02  1.7379150748946228E+02
+  1.0262905636000003E+03  7.7065214324377325E+02  1.3751573424392696E+01
+  3.8771620466521648E+02  1.0510390653125525E+02  5.2064207832106547E+02
+  1.3545569691804164E+02  7.7065214324377325E+02  5.7344000000000005E+02
   6.2016283283809321E+02  7.5493059634400677E+00  3.1798450089540978E+02
   7.7960320675811644E+01  4.2752162763340442E+02  1.0083274234917499E+02
-  7.7960320675811644E+01  6.2016283283809321E+02  4.7030541927158896E+02
-  3.7075305983999965E+02  9.6606358743307453E+02  1.7238509581379120E+01
-  4.8602798405030137E+02  1.3175471954107928E+02  6.5265938512073842E+02
-  1.6980270236074230E+02  1.3175471954107928E+02  9.6606358743307453E+02
-  7.1884508261516271E+02  5.8955904361510193E+02  9.0112000000000000E+02
-  6.2016283283809321E+02  7.5493059634400677E+00  3.1798450089540978E+02
-  7.7960320675811644E+01  4.2752162763340442E+02  1.0083274234917499E+02
-  7.7960320675811644E+01  6.2016283283809321E+02  4.7030541927158896E+02
+  6.2016283283809321E+02  4.7030541927158896E+02  3.7075305983999965E+02
+  9.6606358743307453E+02  1.7238509581379120E+01  4.8602798405030137E+02
+  1.3175471954107928E+02  6.5265938512073842E+02  1.6980270236074230E+02
+  9.6606358743307453E+02  7.1884508261516271E+02  5.8955904361510193E+02
+  9.0112000000000000E+02  6.2016283283809321E+02  7.5493059634400677E+00
+  3.1798450089540978E+02  7.7960320675811644E+01  4.2752162763340442E+02
+  1.0083274234917499E+02  6.2016283283809321E+02  4.7030541927158896E+02
   3.7075305983999965E+02  5.8955904361510193E+02  3.7075305983999965E+02
 %FLAG LENNARD_JONES_14_ACOEF                                                    
 %FORMAT(3E24.16)                                                                
@@ -233,24 +223,20 @@ LYS
   9.0657379084949906E+04  1.8428152636329229E+04  9.0657379084949906E+04
   2.7991654526114347E+04  8.5040378433301669E+00  2.4676273834651991E+04
   3.4318669196435499E+03  2.4676273834651991E+04  4.6676302460305051E+03
-  2.0716152484524384E+04  5.8619918176552899E+00  1.8428152636329229E+04
-  2.5215628838626608E+03  1.8428152636329229E+04  3.4318669196435499E+03
-  2.5215628838626608E+03  4.7728413673862081E+05  6.0933367984903236E+02
-  3.4585193557154440E+05  6.8302639168618378E+04  3.4585193557154440E+05
-  9.1567773233238448E+04  6.8302639168618378E+04  1.3165904011680079E+06
-  4.7402828275870968E+05  8.3313783399093302E+02  3.2758522400263138E+05
-  7.0374830989043956E+04  3.2758522400263138E+05  9.4025592817777768E+04
-  7.0374830989043956E+04  1.2548527649652825E+06  1.1744051200000001E+06
+  4.7728413673862081E+05  6.0933367984903236E+02  3.4585193557154440E+05
+  6.8302639168618378E+04  3.4585193557154440E+05  9.1567773233238448E+04
+  1.3165904011680079E+06  4.7402828275870968E+05  8.3313783399093302E+02
+  3.2758522400263138E+05  7.0374830989043956E+04  3.2758522400263138E+05
+  9.4025592817777768E+04  1.2548527649652825E+06  1.1744051200000001E+06
   2.1513246459458279E+05  1.9177170259300729E+02  1.6414234447218489E+05
   2.9572311958222777E+04  1.6414234447218489E+05  3.9793586685559290E+04
-  2.9572311958222777E+04  6.2064871065477643E+05  6.0333751726046717E+05
-  2.8637048204317200E+05  5.9422589997490286E+05  1.0443935461513495E+03
-  4.1064981063699443E+05  8.8219519385371445E+04  4.1064981063699443E+05
-  1.1786731835420460E+05  8.8219519385371445E+04  1.5730411891415559E+06
-  1.4721947291958532E+06  7.5632360393402562E+05  1.8454937600000000E+06
-  6.7292987992743627E+04  2.5096093690802419E+01  5.7777387626199576E+04
-  8.4261427397045609E+03  5.7777387626199576E+04  1.1437650860852889E+04
-  8.4261427397045609E+03  2.1513246459458279E+05  2.1871906846063802E+05
+  6.2064871065477643E+05  6.0333751726046717E+05  2.8637048204317200E+05
+  5.9422589997490286E+05  1.0443935461513495E+03  4.1064981063699443E+05
+  8.8219519385371445E+04  4.1064981063699443E+05  1.1786731835420460E+05
+  1.5730411891415559E+06  1.4721947291958532E+06  7.5632360393402562E+05
+  1.8454937600000000E+06  6.7292987992743627E+04  2.5096093690802419E+01
+  5.7777387626199576E+04  8.4261427397045609E+03  5.7777387626199576E+04
+  1.1437650860852889E+04  2.1513246459458279E+05  2.1871906846063802E+05
   9.4519534054625838E+04  2.7417886236938258E+05  2.7866191810705470E+04
 %FLAG LENNARD_JONES_14_BCOEF                                                    
 %FORMAT(3E24.16)                                                                
@@ -261,24 +247,20 @@ LYS
   6.0218727679999986E+01  3.3065612070731468E+01  6.0218727679999986E+01
   9.6088520957279030E+01  1.1598498613736841E+00  4.2661833402600713E+01
   1.9376289489599738E+01  4.2661833402600713E+01  2.5195192268767240E+01
-  7.4139169075978288E+01  8.6366978783292059E-01  3.3065612070731468E+01
-  1.4896225487683587E+01  3.3065612070731468E+01  1.9376289489599738E+01
-  1.4896225487683587E+01  6.1792176640000037E+02  1.5289896454943387E+01
-  2.4873253717000529E+02  1.3462071944937435E+02  2.4873253717000529E+02
-  1.7379150748946228E+02  1.3462071944937435E+02  1.0262905636000003E+03
-  4.7365718744646796E+02  1.3751573424392696E+01  1.8619441837932197E+02
-  1.0510390653125533E+02  1.8619441837932197E+02  1.3545569691804153E+02
-  1.0510390653125533E+02  7.7065214324377325E+02  5.7344000000000005E+02
+  6.1792176640000037E+02  1.5289896454943387E+01  2.4873253717000529E+02
+  1.3462071944937435E+02  2.4873253717000529E+02  1.7379150748946228E+02
+  1.0262905636000003E+03  4.7365718744646796E+02  1.3751573424392696E+01
+  1.8619441837932197E+02  1.0510390653125533E+02  1.8619441837932197E+02
+  1.3545569691804153E+02  7.7065214324377325E+02  5.7344000000000005E+02
   3.6512013422507960E+02  7.5493059634400677E+00  1.5081190411881860E+02
   7.7960320675811644E+01  1.5081190411881860E+02  1.0083274234917508E+02
-  7.7960320675811644E+01  6.2016283283809321E+02  4.7030541927158930E+02
-  3.7075305983999993E+02  5.9376070738215299E+02  1.7238509581379120E+01
-  2.3340705577281992E+02  1.3175471954107940E+02  2.3340705577281992E+02
-  1.6980270236074216E+02  1.3175471954107940E+02  9.6606358743307453E+02
-  7.1884508261516271E+02  5.8955904361510227E+02  9.0112000000000000E+02
-  2.0420563040716846E+02  2.7309756545650936E+00  8.9475525546231481E+01
-  4.1614567301854414E+01  8.9475525546231481E+01  5.4058433192453492E+01
-  4.1614567301854414E+01  3.6512013422507960E+02  2.8316732680888202E+02
+  6.2016283283809321E+02  4.7030541927158930E+02  3.7075305983999993E+02
+  5.9376070738215299E+02  1.7238509581379120E+01  2.3340705577281992E+02
+  1.3175471954107940E+02  2.3340705577281992E+02  1.6980270236074216E+02
+  9.6606358743307453E+02  7.1884508261516271E+02  5.8955904361510227E+02
+  9.0112000000000000E+02  2.0420563040716846E+02  2.7309756545650936E+00
+  8.9475525546231481E+01  4.1614567301854414E+01  8.9475525546231481E+01
+  5.4058433192453492E+01  3.6512013422507960E+02  2.8316732680888202E+02
   2.1300088343999982E+02  3.5496902977442369E+02  1.1565367295999995E+02
 %FLAG BONDS_INC_HYDROGEN                                                        
 %FORMAT(10I8)                                                                   

From 042f49f279cae3f620028a6ece837ab8973cb647 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 21 Oct 2025 09:34:57 -0400
Subject: [PATCH 0979/1492] Add LJ column to output

---
 test/Test_ReadAmberFF/tip3pf.parm.dat.save | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/test/Test_ReadAmberFF/tip3pf.parm.dat.save b/test/Test_ReadAmberFF/tip3pf.parm.dat.save
index caf195f526..79c90293bb 100644
--- a/test/Test_ReadAmberFF/tip3pf.parm.dat.save
+++ b/test/Test_ReadAmberFF/tip3pf.parm.dat.save
@@ -1,8 +1,8 @@
 Parameter set: This is TIP3P (model F) of Price and Brooks, JCP 121:10096, 2004 
 Atom Types:
-	  Name  TypeIdx       Radius        Depth         Mass       Polar.
-	    OW        0       1.7926       0.0980      16.0000       0.0000
-	    HW        1       0.0000       0.0000       1.0080       0.0000
+	  Name  TypeIdx LJ       Radius        Depth         Mass       Polar.
+	    OW        0  1       1.7926       0.0980      16.0000       0.0000
+	    HW        1  1       0.0000       0.0000       1.0080       0.0000
 Bond parameters:
 	 Type1  Type2 :           Rk          Req
 	    OW     HW :     553.0000       0.9572

From f2f0b843ca16e6fd4237a9a9425989b63e2070d8 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 21 Oct 2025 09:35:26 -0400
Subject: [PATCH 0980/1492] Add LJ column to output

---
 test/Test_ReadAmberFF/toyrna.parm.dat.save | 46 +++++++++++-----------
 1 file changed, 23 insertions(+), 23 deletions(-)

diff --git a/test/Test_ReadAmberFF/toyrna.parm.dat.save b/test/Test_ReadAmberFF/toyrna.parm.dat.save
index 56237494e7..808f8a5bd1 100644
--- a/test/Test_ReadAmberFF/toyrna.parm.dat.save
+++ b/test/Test_ReadAmberFF/toyrna.parm.dat.save
@@ -1,29 +1,29 @@
 Parameter set: toyrna force field
 Nonbond parameters name: MOD4
 Atom Types:
-	  Name  TypeIdx       Radius        Depth         Mass       Polar.
-	    CB        0       2.0000       0.2000      56.0000       0.0000
-	    CS        1       2.0000       0.2000      43.0000       0.0000
-	    G9        2       1.8000       0.3000      25.0000       0.0000
-	    G7        3       1.8000       0.2000      25.0000       0.0000
-	    G6        4       1.8000       0.2000      25.0000       0.0000
-	    G1        5       1.8000       0.2000      25.0000       0.0000
-	    G2        6       1.8000       0.2000      25.0000       0.0000
-	    G3        7       1.8000       0.2000      25.0000       0.0000
-	    A9        8       1.8000       0.3000      26.8000       0.0000
-	    A7        9       1.8000       0.2000      26.8000       0.0000
-	    A6       10       1.8000       0.2000      26.8000       0.0000
-	    A1       11       1.8000       0.2000      26.8000       0.0000
-	    A3       12       1.8000       0.2000      26.8000       0.0000
-	    U1       13       1.8000       0.3000      27.7500       0.0000
-	    U3       14       1.8000       0.2000      27.7500       0.0000
-	    U4       15       1.8000       0.2000      27.7500       0.0000
-	    U2       16       1.8000       0.2000      27.7500       0.0000
-	    C1       17       1.8000       0.3000      27.5000       0.0000
-	    C3       18       1.8000       0.2000      27.5000       0.0000
-	    C4       19       1.8000       0.2000      27.5000       0.0000
-	    C2       20       1.8000       0.2000      27.5000       0.0000
-	     P       21       3.0000       0.2000      95.0000       0.0000
+	  Name  TypeIdx LJ       Radius        Depth         Mass       Polar.
+	    CB        0  1       2.0000       0.2000      56.0000       0.0000
+	    CS        1  1       2.0000       0.2000      43.0000       0.0000
+	    G9        2  1       1.8000       0.3000      25.0000       0.0000
+	    G7        3  1       1.8000       0.2000      25.0000       0.0000
+	    G6        4  1       1.8000       0.2000      25.0000       0.0000
+	    G1        5  1       1.8000       0.2000      25.0000       0.0000
+	    G2        6  1       1.8000       0.2000      25.0000       0.0000
+	    G3        7  1       1.8000       0.2000      25.0000       0.0000
+	    A9        8  1       1.8000       0.3000      26.8000       0.0000
+	    A7        9  1       1.8000       0.2000      26.8000       0.0000
+	    A6       10  1       1.8000       0.2000      26.8000       0.0000
+	    A1       11  1       1.8000       0.2000      26.8000       0.0000
+	    A3       12  1       1.8000       0.2000      26.8000       0.0000
+	    U1       13  1       1.8000       0.3000      27.7500       0.0000
+	    U3       14  1       1.8000       0.2000      27.7500       0.0000
+	    U4       15  1       1.8000       0.2000      27.7500       0.0000
+	    U2       16  1       1.8000       0.2000      27.7500       0.0000
+	    C1       17  1       1.8000       0.3000      27.5000       0.0000
+	    C3       18  1       1.8000       0.2000      27.5000       0.0000
+	    C4       19  1       1.8000       0.2000      27.5000       0.0000
+	    C2       20  1       1.8000       0.2000      27.5000       0.0000
+	     P       21  1       3.0000       0.2000      95.0000       0.0000
 HB LJ 10-12 parameters:
 	 Type1  Type2 :         Asol         Bsol        HBcut
 	    G6     C4 :       5.0000       3.0000       0.0000

From 52ace4f5aa87e33aa4957b66c22a9d356c3fb862 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 21 Oct 2025 09:35:50 -0400
Subject: [PATCH 0981/1492] Add LJ column to output

---
 .../toyrna.tip3pf.parm.dat.save               | 50 +++++++++----------
 1 file changed, 25 insertions(+), 25 deletions(-)

diff --git a/test/Test_ReadAmberFF/toyrna.tip3pf.parm.dat.save b/test/Test_ReadAmberFF/toyrna.tip3pf.parm.dat.save
index 977a376493..15998a0a03 100644
--- a/test/Test_ReadAmberFF/toyrna.tip3pf.parm.dat.save
+++ b/test/Test_ReadAmberFF/toyrna.tip3pf.parm.dat.save
@@ -1,31 +1,31 @@
 Parameter set: toyrna force field + This is TIP3P (model F) of Price and Brooks, JCP 121:10096, 2004 
 Nonbond parameters name: MOD4
 Atom Types:
-	  Name  TypeIdx       Radius        Depth         Mass       Polar.
-	    CB        0       2.0000       0.2000      56.0000       0.0000
-	    CS        1       2.0000       0.2000      43.0000       0.0000
-	    G9        2       1.8000       0.3000      25.0000       0.0000
-	    G7        3       1.8000       0.2000      25.0000       0.0000
-	    G6        4       1.8000       0.2000      25.0000       0.0000
-	    G1        5       1.8000       0.2000      25.0000       0.0000
-	    G2        6       1.8000       0.2000      25.0000       0.0000
-	    G3        7       1.8000       0.2000      25.0000       0.0000
-	    A9        8       1.8000       0.3000      26.8000       0.0000
-	    A7        9       1.8000       0.2000      26.8000       0.0000
-	    A6       10       1.8000       0.2000      26.8000       0.0000
-	    A1       11       1.8000       0.2000      26.8000       0.0000
-	    A3       12       1.8000       0.2000      26.8000       0.0000
-	    U1       13       1.8000       0.3000      27.7500       0.0000
-	    U3       14       1.8000       0.2000      27.7500       0.0000
-	    U4       15       1.8000       0.2000      27.7500       0.0000
-	    U2       16       1.8000       0.2000      27.7500       0.0000
-	    C1       17       1.8000       0.3000      27.5000       0.0000
-	    C3       18       1.8000       0.2000      27.5000       0.0000
-	    C4       19       1.8000       0.2000      27.5000       0.0000
-	    C2       20       1.8000       0.2000      27.5000       0.0000
-	     P       21       3.0000       0.2000      95.0000       0.0000
-	    OW       22       1.7926       0.0980      16.0000       0.0000
-	    HW       23       0.0000       0.0000       1.0080       0.0000
+	  Name  TypeIdx LJ       Radius        Depth         Mass       Polar.
+	    CB        0  1       2.0000       0.2000      56.0000       0.0000
+	    CS        1  1       2.0000       0.2000      43.0000       0.0000
+	    G9        2  1       1.8000       0.3000      25.0000       0.0000
+	    G7        3  1       1.8000       0.2000      25.0000       0.0000
+	    G6        4  1       1.8000       0.2000      25.0000       0.0000
+	    G1        5  1       1.8000       0.2000      25.0000       0.0000
+	    G2        6  1       1.8000       0.2000      25.0000       0.0000
+	    G3        7  1       1.8000       0.2000      25.0000       0.0000
+	    A9        8  1       1.8000       0.3000      26.8000       0.0000
+	    A7        9  1       1.8000       0.2000      26.8000       0.0000
+	    A6       10  1       1.8000       0.2000      26.8000       0.0000
+	    A1       11  1       1.8000       0.2000      26.8000       0.0000
+	    A3       12  1       1.8000       0.2000      26.8000       0.0000
+	    U1       13  1       1.8000       0.3000      27.7500       0.0000
+	    U3       14  1       1.8000       0.2000      27.7500       0.0000
+	    U4       15  1       1.8000       0.2000      27.7500       0.0000
+	    U2       16  1       1.8000       0.2000      27.7500       0.0000
+	    C1       17  1       1.8000       0.3000      27.5000       0.0000
+	    C3       18  1       1.8000       0.2000      27.5000       0.0000
+	    C4       19  1       1.8000       0.2000      27.5000       0.0000
+	    C2       20  1       1.8000       0.2000      27.5000       0.0000
+	     P       21  1       3.0000       0.2000      95.0000       0.0000
+	    OW       22  1       1.7926       0.0980      16.0000       0.0000
+	    HW       23  1       0.0000       0.0000       1.0080       0.0000
 HB LJ 10-12 parameters:
 	 Type1  Type2 :         Asol         Bsol        HBcut
 	    G6     C4 :       5.0000       3.0000       0.0000

From 7b905061b7fe4e8cdf8e8080cb7f8d5ccb97c736 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 21 Oct 2025 12:57:09 -0400
Subject: [PATCH 0982/1492] Add option for bonding unknown residues or not.

---
 src/Exec_PrepareForLeap.cpp | 32 +++++++++++++++++++++++++++-----
 src/Exec_PrepareForLeap.h   |  1 +
 2 files changed, 28 insertions(+), 5 deletions(-)

diff --git a/src/Exec_PrepareForLeap.cpp b/src/Exec_PrepareForLeap.cpp
index 3154ecd28c..22e7848f4b 100644
--- a/src/Exec_PrepareForLeap.cpp
+++ b/src/Exec_PrepareForLeap.cpp
@@ -24,6 +24,7 @@ using namespace Cpptraj::Structure;
 Exec_PrepareForLeap::Exec_PrepareForLeap() : Exec(COORDS),
   errorsAreFatal_(true),
   downloadParams_(true),
+  bondUnknownResidues_(false),
   debug_(0)
 {
   SetHidden(false);
@@ -508,10 +509,17 @@ const
         for (int at = currentRes.FirstAtom(); at != currentRes.LastAtom(); ++at) {
           for (Atom::bond_iterator bat = topIn[at].bondbegin(); bat != topIn[at].bondend(); ++bat) {
             if ( topIn[*bat].ResNum() != *rn ) {
-              mprintf("\t\t\tRes %s is bonded to res %s\n",
-                      topIn.TruncResAtomName(at).c_str(),
-                      topIn.TruncResAtomName(*bat).c_str());
-              LeapBonds.push_back( BondType(at, *bat, -1) );
+              if (bondUnknownResidues_) {
+                mprintf("\t\t\tRes %s is bonded to res %s\n",
+                        topIn.TruncResAtomName(at).c_str(),
+                        topIn.TruncResAtomName(*bat).c_str());
+                LeapBonds.push_back( BondType(at, *bat, -1) );
+              } else {
+                mprintf("Info:\t\t\tRes %s might be bonded to res %s\n",
+                        topIn.TruncResAtomName(at).c_str(),
+                        topIn.TruncResAtomName(*bat).c_str());
+
+              }
             }
           } // END loop over bonded atoms
         } // END loop over atoms in residue
@@ -527,7 +535,7 @@ void Exec_PrepareForLeap::Help() const
   mprintf("\tcrdset <coords set> [frame <#>] name <out coords set>\n"
           "\t[pdbout <pdbfile> [terbymol]]\n"
           "\t[leapunitname <unit>] [out <leap input file> [runleap <ff file>]]\n"
-          "\t[skiperrors] [{dlparams|nodlparams}]\n"
+          "\t[skiperrors] [{dlparams|nodlparams}] [{bondunknown|nobondunknown}]\n"
           "\t[nowat [watermask <watermask>] [noh]\n"
           "\t[keepaltloc {<alt loc ID>|highestocc}]\n"
           "\t[stripmask <stripmask>] [solventresname <solventresname>]\n"
@@ -571,6 +579,12 @@ Exec::RetType Exec_PrepareForLeap::Execute(CpptrajState& State, ArgList& argIn)
     downloadParams_ = false;
   else
     downloadParams_ = true;
+  if (argIn.hasKey("bondunknown"))
+    bondUnknownResidues_ = true;
+  else if (argIn.hasKey("nobondunknown"))
+    bondUnknownResidues_ = false;
+  else
+    bondUnknownResidues_ = false;
   // Get input coords
   std::string crdset = argIn.GetStringKey("crdset");
   if (crdset.empty()) {
@@ -676,6 +690,10 @@ Exec::RetType Exec_PrepareForLeap::Execute(CpptrajState& State, ArgList& argIn)
     mprintf("\tWill attempt to download parameters for unknown residues.\n");
   else
     mprintf("\tWill not attempt to download paramters for unknown residues.\n");
+  if (bondUnknownResidues_)
+    mprintf("\tWill attempt to bond unknown residues.\n");
+  else
+    mprintf("\tWill not attempt to bond unknown residues.\n");
 
   // Load PDB to glycam residue name map
   SugarBuilder sugarBuilder(debug_);
@@ -922,7 +940,11 @@ Exec::RetType Exec_PrepareForLeap::Execute(CpptrajState& State, ArgList& argIn)
     mprintf("\tResidues to find parameters for:");
     for (RmapType::const_iterator it = residuesToFindParamsFor.begin();
                                   it != residuesToFindParamsFor.end(); ++it)
+    {
       mprintf(" %s", it->first.Truncated().c_str());
+      for (Iarray::const_iterator rn = it->second.begin(); rn != it->second.end(); ++rn)
+        mprintf(" %i", *rn + 1);
+    }
     mprintf("\n");
     // Set default parameter URL if not yet set.
     if (parameterURL_.empty())
diff --git a/src/Exec_PrepareForLeap.h b/src/Exec_PrepareForLeap.h
index bb3a43509c..a67f366d63 100644
--- a/src/Exec_PrepareForLeap.h
+++ b/src/Exec_PrepareForLeap.h
@@ -51,6 +51,7 @@ class Exec_PrepareForLeap : public Exec {
     std::string leapunitname_;   ///< Unit name to use when loading molecule
     bool errorsAreFatal_;        ///< If false, try to skip errors.
     bool downloadParams_;        ///< If true, try to download parameters for missing residues
+    bool bondUnknownResidues_;   ///< If true, try to create bonds to unknown residues
     int debug_;                  ///< Debug level
     std::string solventResName_; ///< Solvent residue name
     std::string parameterURL_;   ///< URL to download parameters from

From 00dca07063b73bbf5b87b60d5a6e60156720aac2 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 21 Oct 2025 14:03:28 -0400
Subject: [PATCH 0983/1492] Redirect stdout/stderr when looking for curl/wget

---
 src/Remote.cpp | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/src/Remote.cpp b/src/Remote.cpp
index 52cc4bd4ce..268eef5fc2 100644
--- a/src/Remote.cpp
+++ b/src/Remote.cpp
@@ -42,13 +42,21 @@ void Remote::SetDebug(int d) {
 int Remote::setRemoteDownloadCommand() {
   if (!cmd_.empty()) return 0;
   // First try curl
-  int err = system("curl --version");
+# ifdef _WIN32
+  int err = system("curl --version > NUL 2>&1");
+# else
+  int err = system("curl --version > /dev/null 2>&1");
+# endif
   if (err == 0) {
     mprintf("\tcurl found.\n");
     cmd_.assign("curl -s --show-error -f -L ");
     oflag_.assign("-o ");
   } else {
-    err = system("wget --version");
+#   ifdef _WIN32
+    err = system("wget --version > NUL 2>&1");
+#   else
+    err = system("wget --version > /dev/null 2>&1");
+#   endif
     if (err == 0) {
       mprintf("\twget found.\n");
       cmd_.assign("wget --quiet ");

From 174b79698a7b63eba88230b6242090aeb3b0dc51 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 21 Oct 2025 15:15:14 -0400
Subject: [PATCH 0984/1492] Remove file if not correctly downloaded

---
 src/Remote.cpp | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/src/Remote.cpp b/src/Remote.cpp
index 268eef5fc2..d8bc2590a7 100644
--- a/src/Remote.cpp
+++ b/src/Remote.cpp
@@ -102,12 +102,15 @@ const
   std::string remoteUrl = url_ + "/" + fileName.Full();
   mprintf("\t %s => %s\n", remoteUrl.c_str(), outputFname.full());
   // Download File
-  std::string remoteCmd = cmd_ + remoteUrl + " " + oflag_ + outputFname.Full();
-  if (debug_ > 0) mprintf("DEBUG: %s\n", remoteCmd.c_str());
+  std::string remoteCmd = cmd_ + oflag_ + outputFname.Full() + " " + remoteUrl;
+  if (debug_ > 0)
+    mprintf("DEBUG: %s\n", remoteCmd.c_str());
   int err = system(remoteCmd.c_str());
   if (err != 0) {
     mprinterr("Error: Could not download %s => %s\n", remoteUrl.c_str(), outputFname.full());
     // FIXME: wget will leave behind empty files here
+    if (File::Exists(outputFname))
+      File::Remove(outputFname);
     return 1;
   }
 

From ffa9456d898ad28dcf31a36d28e1e620dff14245 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 21 Oct 2025 15:15:42 -0400
Subject: [PATCH 0985/1492] Add remove command

---
 src/FileName.cpp | 4 ++++
 src/FileName.h   | 1 +
 2 files changed, 5 insertions(+)

diff --git a/src/FileName.cpp b/src/FileName.cpp
index e98549bca9..d0a0de81ba 100644
--- a/src/FileName.cpp
+++ b/src/FileName.cpp
@@ -343,3 +343,7 @@ bool File::Exists(FileName const& fn) {
 bool File::Exists(std::string const& fname) {
   return File::Exists( FileName(fname) );
 }
+
+int File::Remove(FileName const& fname) {
+  return remove( fname.full() );
+}
diff --git a/src/FileName.h b/src/FileName.h
index 8ac9f6eb27..860d3e0a4a 100644
--- a/src/FileName.h
+++ b/src/FileName.h
@@ -73,6 +73,7 @@ namespace File {
   void ErrorMsg(const char*);
   bool Exists(std::string const&);
   bool Exists(FileName const&);
+  int Remove(FileName const&);
   /** Given lowest replica traj filename, split into components for search. */
   class RepName {
   public:

From 8856425573fa3c9f1d4f3e5dffad6c3cab4e68ce Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 21 Oct 2025 15:15:59 -0400
Subject: [PATCH 0986/1492] Update download URL

---
 src/Exec_PrepareForLeap.cpp | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/Exec_PrepareForLeap.cpp b/src/Exec_PrepareForLeap.cpp
index 22e7848f4b..f6de3ca0ed 100644
--- a/src/Exec_PrepareForLeap.cpp
+++ b/src/Exec_PrepareForLeap.cpp
@@ -482,9 +482,9 @@ const
     if (err == 0) {
       err += remote.DownloadFile( rfbase + ".frcmod" );
       if (err != 0)
-        mprintf("Warning: Could not download %s.frcmod\n", rfbase.c_str());
+        mprintf("Warning: Could not download %s.frcmod\n", rname.c_str());
     } else {
-      mprintf("Warning: Could not download %s.mol2\n", rfbase.c_str());
+      mprintf("Warning: Could not download %s.mol2\n", rname.c_str());
     }
     if (err != 0)
       mprintf("Warning: Could not download parameter files for '%s'\n", rname.c_str());
@@ -948,7 +948,7 @@ Exec::RetType Exec_PrepareForLeap::Execute(CpptrajState& State, ArgList& argIn)
     mprintf("\n");
     // Set default parameter URL if not yet set.
     if (parameterURL_.empty())
-      parameterURL_.assign("https://raw.githubusercontent.com/phenix-project/geostd/master");
+      parameterURL_.assign("https://github.com/phenix-project/geostd/raw/refs/heads/master");
     if (DownloadParameters(resStat, residuesToFindParamsFor, topIn, outfile, LeapBonds)) {
       mprinterr("Error: Download parameters failed.\n");
       return CpptrajState::ERR;

From d28a19efe9ef457ff423776b5c9ac2f977683454 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 21 Oct 2025 15:21:17 -0400
Subject: [PATCH 0987/1492] Add bondunknown keyword

---
 test/Test_PrepareForLeap/RunTest.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/Test_PrepareForLeap/RunTest.sh b/test/Test_PrepareForLeap/RunTest.sh
index ca73c1fada..874291cfbc 100755
--- a/test/Test_PrepareForLeap/RunTest.sh
+++ b/test/Test_PrepareForLeap/RunTest.sh
@@ -79,7 +79,7 @@ if [ ! -z "$PINGCMD" ] ; then
 parm 4zzw.pdb
 loadcrd 4zzw.pdb name MyCrd
 
-prepareforleap dlparams \
+prepareforleap dlparams bondunknown \
   crdset MyCrd \
   name Final \
   out dlparams.leap.4zzw.in \

From 7fcb35fa237cc6e239295670762a091c363a1472 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 22 Oct 2025 09:19:23 -0400
Subject: [PATCH 0988/1492] Add LeapOpts data set

---
 src/DataSet.cpp          |  1 +
 src/DataSet.h            |  2 +-
 src/DataSetList.cpp      |  2 ++
 src/DataSet_LeapOpts.cpp | 10 ++++++++++
 src/DataSet_LeapOpts.h   | 23 +++++++++++++++++++++++
 src/cpptrajdepend        |  2 +-
 src/cpptrajfiles         |  1 +
 7 files changed, 39 insertions(+), 2 deletions(-)
 create mode 100644 src/DataSet_LeapOpts.cpp
 create mode 100644 src/DataSet_LeapOpts.h

diff --git a/src/DataSet.cpp b/src/DataSet.cpp
index ab62cdf44c..d153ac0cf6 100644
--- a/src/DataSet.cpp
+++ b/src/DataSet.cpp
@@ -34,6 +34,7 @@ const char* DataSet::Descriptions_[] = {
   "frames",                     // FRAMES
   "zmatrix",                    // ZMATRIX
   "name map",                   // NAMEMAP
+  "LEaP options",               // LEAPOPTS
   "unknown"                     // UNKNOWN_DATA
 };
 
diff --git a/src/DataSet.h b/src/DataSet.h
index f061258afb..ddb9690f55 100644
--- a/src/DataSet.h
+++ b/src/DataSet.h
@@ -29,7 +29,7 @@ class DataSet {
       COORDS, VECTOR, MODES, GRID_FLT, GRID_DBL, REMLOG, XYMESH, TRAJ, REF_FRAME,
       MAT3X3, TOPOLOGY, PH, PH_EXPL, PH_IMPL,
       PARAMETERS, PMATRIX_MEM, PMATRIX_NC, TENSOR, STRINGVAR, VECTOR_SCALAR, UNSIGNED_INTEGER,
-      FRAMES, ZMATRIX, NAMEMAP,
+      FRAMES, ZMATRIX, NAMEMAP, LEAPOPTS,
       UNKNOWN_DATA
     };
     /// Group DataSet belongs to.
diff --git a/src/DataSetList.cpp b/src/DataSetList.cpp
index bf2ce4a00a..bff462ea3c 100644
--- a/src/DataSetList.cpp
+++ b/src/DataSetList.cpp
@@ -37,6 +37,7 @@
 #include "DataSet_Coords_FRM.h"
 #include "DataSet_Zmatrix.h"
 #include "DataSet_NameMap.h"
+#include "DataSet_LeapOpts.h"
 
 bool DataSetList::useDiskCache_ = false;
 
@@ -97,6 +98,7 @@ DataSet* DataSetList::NewSet(DataSet::DataType typeIn) {
     case DataSet::VECTOR_SCALAR : ds = DataSet_Vector_Scalar::Alloc(); break;
     case DataSet::ZMATRIX       : ds = DataSet_Zmatrix::Alloc(); break;
     case DataSet::NAMEMAP       : ds = DataSet_NameMap::Alloc(); break;
+    case DataSet::LEAPOPTS      : ds = DataSet_LeapOpts::Alloc(); break;
     // Sanity check
     default:
       mprinterr("Internal Error: No allocator for DataSet type '%s'\n",
diff --git a/src/DataSet_LeapOpts.cpp b/src/DataSet_LeapOpts.cpp
new file mode 100644
index 0000000000..631c269f54
--- /dev/null
+++ b/src/DataSet_LeapOpts.cpp
@@ -0,0 +1,10 @@
+#include "DataSet_LeapOpts.h"
+#include "CpptrajStdio.h"
+
+/// CONSTRUCTOR
+DataSet_LeapOpts::DataSet_LeapOpts() :
+  // 0 dim indicates DataSet-specific write
+  DataSet(LEAPOPTS, GENERIC, TextFormat(TextFormat::STRING, 12, 0), 0)
+{
+
+}
diff --git a/src/DataSet_LeapOpts.h b/src/DataSet_LeapOpts.h
new file mode 100644
index 0000000000..7cdb84533e
--- /dev/null
+++ b/src/DataSet_LeapOpts.h
@@ -0,0 +1,23 @@
+#ifndef INC_DATASET_LEAPOPTS_H
+#define INC_DATASET_LEAPOPTS_H
+#include "DataSet.h"
+/// Hold LEaP options read from 'sourcing' a leaprc file in DataIO_LeapRC 
+class DataSet_LeapOpts : public DataSet {
+  public:
+    DataSet_LeapOpts();
+    static DataSet* Alloc() { return (DataSet*)new DataSet_LeapOpts(); }
+    // ----- DataSet functions -------------------
+    size_t Size()                                    const { return 0; }
+    void Info()                                      const { return; }
+    int Allocate(SizeArray const&)                         { return 1; }
+    void Add(size_t, const void*)                          { return; }
+    void WriteBuffer(CpptrajFile&, SizeArray const&) const { return; }
+    int Append(DataSet*)                                   { return 1; }
+    size_t MemUsageInBytes()                         const { return 0; }
+#   ifdef MPI
+    int Sync(size_t, std::vector<int> const&, Parallel::Comm const&) { return 1; }
+#   endif
+    // -------------------------------------------
+  private:
+};
+#endif
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 86e546b4a9..44daf0104e 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -255,6 +255,7 @@ DataSet_Coords_REF.o : DataSet_Coords_REF.cpp ArgList.h AssociatedData.h Atom.h
 DataSet_Coords_TRJ.o : DataSet_Coords_TRJ.cpp AssociatedData.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_TRJ.h Dimension.h FileIO.h FileName.h Frame.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h Trajin_Single.h Unit.h Vec3.h
 DataSet_GridDbl.o : DataSet_GridDbl.cpp ArrayIterator.h AssociatedData.h Box.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_3D.h DataSet_GridDbl.h Dimension.h FileIO.h FileName.h Grid.h GridBin.h Matrix_3x3.h MetaData.h Parallel.h Range.h StringRoutines.h TextFormat.h Vec3.h
 DataSet_GridFlt.o : DataSet_GridFlt.cpp ArrayIterator.h AssociatedData.h Box.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_3D.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Grid.h GridBin.h Matrix_3x3.h MetaData.h Parallel.h Range.h StringRoutines.h TextFormat.h Vec3.h
+DataSet_LeapOpts.o : DataSet_LeapOpts.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_LeapOpts.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
 DataSet_Mat3x3.o : DataSet_Mat3x3.cpp AssociatedData.h CpptrajFile.h DataSet.h DataSet_Mat3x3.h Dimension.h FileIO.h FileName.h Matrix_3x3.h MetaData.h Parallel.h Range.h TextFormat.h Vec3.h
 DataSet_MatrixDbl.o : DataSet_MatrixDbl.cpp ArrayIterator.h AssociatedData.h CpptrajFile.h DataSet.h DataSet_2D.h DataSet_MatrixDbl.h Dimension.h FileIO.h FileName.h Matrix.h MetaData.h Parallel.h Range.h TextFormat.h
 DataSet_MatrixFlt.o : DataSet_MatrixFlt.cpp ArrayIterator.h AssociatedData.h CpptrajFile.h DataSet.h DataSet_2D.h DataSet_MatrixFlt.h Dimension.h FileIO.h FileName.h Matrix.h MetaData.h Parallel.h Range.h TextFormat.h
@@ -433,7 +434,6 @@ Parm/GB_Params.o : Parm/GB_Params.cpp Atom.h AtomMask.h Box.h Constants.h Coordi
 Parm/GetParams.o : Parm/GetParams.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/GetParams.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Parm/Merge.o : Parm/Merge.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/GetParams.h Parm/Merge.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h UpdateParameters.h Vec3.h
 Parm/ParameterSet.o : Parm/ParameterSet.cpp AtomType.h CmapParmHolder.h Constants.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h TypeNameHolder.h UpdateParameters.h
-Parm/test.o : Parm/test.cpp Constants.h NameType.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParmEnum.h Parm/ParmHolder.h TypeNameHolder.h
 ParmFile.o : ParmFile.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h ParmFile.h ParmIO.h Parm_Amber.h Parm_CIF.h Parm_CharmmPsf.h Parm_Gromacs.h Parm_Mol2.h Parm_PDB.h Parm_SDF.h Parm_Tinker.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Parm_Amber.o : Parm_Amber.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h ExclusionArray.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/GetParams.h ParmIO.h Parm_Amber.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h Unit.h Vec3.h
 Parm_CIF.o : Parm_CIF.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h CIFfile.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmIO.h Parm_CIF.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h
diff --git a/src/cpptrajfiles b/src/cpptrajfiles
index 2b8d67d581..0dcf19fcc4 100644
--- a/src/cpptrajfiles
+++ b/src/cpptrajfiles
@@ -226,6 +226,7 @@ COMMON_SOURCES= \
         DataSet_Coords_TRJ.cpp \
         DataSet_GridDbl.cpp \
         DataSet_GridFlt.cpp \
+        DataSet_LeapOpts.cpp \
         DataSet_Mat3x3.cpp \
         DataSet_MatrixDbl.cpp \
         DataSet_MatrixFlt.cpp \

From c69541a901bd92fe4d421b76e1df4c9dc2caeb93 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 22 Oct 2025 09:29:52 -0400
Subject: [PATCH 0989/1492] Start implementing the leap set command

---
 src/DataIO_LeapRC.cpp | 21 ++++++++++++++++++++-
 src/DataIO_LeapRC.h   |  2 ++
 2 files changed, 22 insertions(+), 1 deletion(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 4f79ba566b..568bada3d4 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -634,6 +634,22 @@ int DataIO_LeapRC::LoadPDB(ArgList const& argIn, DataSetList& dsl) const {
   return 0;
 }
 
+const char* DataIO_LeapRC::LEAPOPTSNAME_ = "_LEAP_OPTIONS_";
+
+/** LEaP 'set' command. */
+int DataIO_LeapRC::LeapSet(ArgList const& argIn, DataSetList& dsl) const {
+  // Check if we already allocated a LEaP options data set
+  DataSet* leapopts = dsl.FindSetOfType( std::string(LEAPOPTSNAME_), DataSet::LEAPOPTS );
+  if ( leapopts == 0)
+    leapopts = dsl.AddSet( DataSet::LEAPOPTS, MetaData( std::string(LEAPOPTSNAME_) ) );
+  if (leapopts == 0) {
+    mprinterr("Internal Error: Could not allocate leap options data set for 'set' command.\n");
+    return 1;
+  }
+  mprintf("DEBUG: Leap options set: %s\n", leapopts->legend());
+  return 0;
+}
+
 /** Save specified unit to a topology and restart file. */
 int DataIO_LeapRC::SaveAmberParm(std::string const& unitName, ArgList& line, DataSetList const& dsl)
 const
@@ -759,7 +775,7 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
   mprintf("\tReading LEaP input from '%s'\n", fname.base());
   enum LeapCmdType { LOADAMBERPARAMS = 0, LOADOFF, LOADAMBERPREP, ADDATOMTYPES,
                      ADDPDBRESMAP, ADDPDBATOMMAP, LOADMOL2, LOADPDB, SOURCE,
-                     QUIT, SAVEAMBERPARM, ADDPATH, UNKNOWN_CMD };
+                     QUIT, SAVEAMBERPARM, ADDPATH, SET, UNKNOWN_CMD };
   //DataSetList paramDSL;
   //DataSetList unitDSL;
   //NHarrayType atomHybridizations;
@@ -799,6 +815,7 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
         else if (argStr == "quit"           ) { pos = arg; leapcmd = QUIT; break; }
         else if (argStr == "saveamberparm"  ) { pos = arg; leapcmd = SAVEAMBERPARM; break; }
         else if (argStr == "addpath"        ) { pos = arg; leapcmd = ADDPATH; break; }
+        else if (argStr == "set"            ) { pos = arg; leapcmd = SET; break; }
       }
 
       err = 0;
@@ -865,6 +882,8 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
       } else if (leapcmd == ADDPATH) {
         // Add path to directories to search for files specified by other commands.
         err = AddPath( line.GetStringKey(line[pos]) );
+      } else if (leapcmd == SET) {
+        err = LeapSet(line, dsl);
       } else {
         // Unrecognized so far. See if this is a unit alias (interpret as 'alias = unit')
         if (has_equals) {
diff --git a/src/DataIO_LeapRC.h b/src/DataIO_LeapRC.h
index 5190a2731d..5ae27070c8 100644
--- a/src/DataIO_LeapRC.h
+++ b/src/DataIO_LeapRC.h
@@ -65,6 +65,7 @@ class DataIO_LeapRC : public DataIO {
     int AddPdbAtomMap(std::string const&, DataSetList&, BufferedLine&) const;
     int LoadMol2(ArgList const&, DataSetList&) const;
     int LoadPDB(ArgList const&, DataSetList&) const;
+    int LeapSet(ArgList const&, DataSetList&) const;
     int SaveAmberParm(std::string const&, ArgList&, DataSetList const& dsl) const;
     int Source(FileName const&, DataSetList&, std::string const&);
     /// Add PDB residue map to COORDS unit
@@ -87,5 +88,6 @@ class DataIO_LeapRC : public DataIO {
     Sarray searchPaths_;
     static Sarray paramFiles_; ///< Track amber FF param files loaded from leaprc files
     static Sarray libFiles_;   ///< Track amber library/prep files loaded from leaprc files
+    static const char* LEAPOPTSNAME_; ///< Leap options data set name
 };
 #endif

From 30101917a5f10bee2fa5c8b0ecc9cbe2475955b9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 22 Oct 2025 09:47:46 -0400
Subject: [PATCH 0990/1492] Support set name for units

---
 src/DataIO_LeapRC.cpp | 44 ++++++++++++++++++++++++++++++++++++-------
 src/DataIO_LeapRC.h   |  1 +
 src/Topology.cpp      |  5 +++++
 src/Topology.h        |  1 +
 4 files changed, 44 insertions(+), 7 deletions(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 568bada3d4..5201fa1ebe 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -647,9 +647,38 @@ int DataIO_LeapRC::LeapSet(ArgList const& argIn, DataSetList& dsl) const {
     return 1;
   }
   mprintf("DEBUG: Leap options set: %s\n", leapopts->legend());
+
+  if (argIn.Nargs() > 3 && ToLower(argIn[2]) == "name") {
+    // set <unit> name <name>
+    // Get the unit
+    DataSet* ds = getUnit( argIn[1], dsl );
+    if (ds == 0) {
+      return 1;
+    }
+    DataSet_Coords& crd = static_cast<DataSet_Coords&>( *ds );
+    crd.TopPtr()->SetParmTitle( argIn[3] );
+  } else {
+    mprintf("Warning: Unhandled 'set' command: %s\n", argIn.ArgLine());
+  } 
+
   return 0;
 }
 
+/** Get COORDS unit from data set list */
+DataSet* DataIO_LeapRC::getUnit(std::string const& unitName, DataSetList const& dsl) const {
+  DataSet* ds = dsl.CheckForSet( MetaData(unitName) );
+  if (ds == 0) {
+    mprinterr("Error: Set '%s' not found.\n", unitName.c_str());
+    return 0;
+  }
+  if (ds->Group() != DataSet::COORDINATES) {
+    mprinterr("Error: Set '%s' is not COORDINATES.\n", ds->legend());
+    return 0;
+  }
+  mprintf("\tCOORDINATES set %s\n", ds->legend());
+  return ds;
+}
+
 /** Save specified unit to a topology and restart file. */
 int DataIO_LeapRC::SaveAmberParm(std::string const& unitName, ArgList& line, DataSetList const& dsl)
 const
@@ -672,16 +701,17 @@ const
   mprintf("\tSaving unit '%s' to topology '%s' and coordinates '%s'\n",
           unitName.c_str(), topName.c_str(), crdName.c_str());
   // Get the unit
-  DataSet* ds = dsl.CheckForSet( MetaData(unitName) );
+  DataSet* ds = getUnit( unitName, dsl );
+//  DataSet* ds = dsl.CheckForSet( MetaData(unitName) );
   if (ds == 0) {
-    mprinterr("Error: Set '%s' not found.\n", unitName.c_str());
+//    mprinterr("Error: Set '%s' not found.\n", unitName.c_str());
     return 1;
   }
-  if (ds->Group() != DataSet::COORDINATES) {
-    mprinterr("Error: Set '%s' is not COORDINATES.\n", ds->legend());
-    return 1;
-  }
-  mprintf("\tCOORDINATES set %s\n", ds->legend());
+//  if (ds->Group() != DataSet::COORDINATES) {
+//    mprinterr("Error: Set '%s' is not COORDINATES.\n", ds->legend());
+//    return 1;
+//  }
+//  mprintf("\tCOORDINATES set %s\n", ds->legend());
   DataSet_Coords& crd = static_cast<DataSet_Coords&>( *ds ); // FIXME this really should be const
   if (crd.Size() < 1) {
     mprinterr("Error: '%s' is empty.\n", crd.legend());
diff --git a/src/DataIO_LeapRC.h b/src/DataIO_LeapRC.h
index 5ae27070c8..66f946496b 100644
--- a/src/DataIO_LeapRC.h
+++ b/src/DataIO_LeapRC.h
@@ -66,6 +66,7 @@ class DataIO_LeapRC : public DataIO {
     int LoadMol2(ArgList const&, DataSetList&) const;
     int LoadPDB(ArgList const&, DataSetList&) const;
     int LeapSet(ArgList const&, DataSetList&) const;
+    DataSet* getUnit(std::string const&, DataSetList const&) const;
     int SaveAmberParm(std::string const&, ArgList&, DataSetList const& dsl) const;
     int Source(FileName const&, DataSetList&, std::string const&);
     /// Add PDB residue map to COORDS unit
diff --git a/src/Topology.cpp b/src/Topology.cpp
index b716cb816c..5ea43ebaa4 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -18,6 +18,11 @@ Topology::Topology() :
   n_extra_pts_(0)
 { }
 
+/** Set the parm name only. */
+void Topology::SetParmTitle(std::string const& title) {
+  parmName_ = title;
+}
+
 // Topology::SetParmName()
 void Topology::SetParmName(std::string const& title, FileName const& filename) {
   parmName_ = title;
diff --git a/src/Topology.h b/src/Topology.h
index 7263c74427..931318faf0 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -22,6 +22,7 @@ class Topology {
     void SetIpol(int iIn)                    { ipol_ = iIn;                  }
     void SetPindex(int pIn)                  { pindex_ = pIn;                }
     void SetGBradiiSet(std::string const& s) { radius_set_ = s;              }
+    void SetParmTitle(std::string const&);
     void SetParmName(std::string const&, FileName const&);
     void SetDistMaskRef( Frame const& );
     /// Add forcefield description

From 0a4cc660b19b2a22083ebe189c3c80b03af36242 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 22 Oct 2025 10:04:37 -0400
Subject: [PATCH 0991/1492] Start adding set default pbradii

---
 src/DataIO_LeapRC.cpp    | 14 +++++++++++++-
 src/DataSet_LeapOpts.cpp | 15 ++++++++++++++-
 src/DataSet_LeapOpts.h   |  3 +++
 src/cpptrajdepend        |  6 +++---
 4 files changed, 33 insertions(+), 5 deletions(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 5201fa1ebe..7b616f884e 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -7,6 +7,7 @@
 #include "DataIO_AmberLib.h"
 #include "DataIO_AmberPrep.h"
 #include "DataIO_Coords.h"
+#include "DataSet_LeapOpts.h"
 #include "DataSet_NameMap.h"
 #include "DataSet_Parameters.h"
 #include "Exec_Build.h"
@@ -647,6 +648,7 @@ int DataIO_LeapRC::LeapSet(ArgList const& argIn, DataSetList& dsl) const {
     return 1;
   }
   mprintf("DEBUG: Leap options set: %s\n", leapopts->legend());
+  DataSet_LeapOpts& OPTS = static_cast<DataSet_LeapOpts&>( *leapopts );
 
   if (argIn.Nargs() > 3 && ToLower(argIn[2]) == "name") {
     // set <unit> name <name>
@@ -657,9 +659,19 @@ int DataIO_LeapRC::LeapSet(ArgList const& argIn, DataSetList& dsl) const {
     }
     DataSet_Coords& crd = static_cast<DataSet_Coords&>( *ds );
     crd.TopPtr()->SetParmTitle( argIn[3] );
+  } else if (argIn.Nargs() > 3 && ToLower(argIn[1]) == "default") {
+    // set default <parameter> <value>
+    if ( ToLower(argIn[2]) == "pbradii" ) {
+      if ( OPTS.SetGbRadii( ToLower(argIn[3]) ) ) {
+        mprinterr("Error: Could not set default pbradii %s\n", argIn[3].c_str());
+        return 1;
+      }
+    } else {
+      mprintf("Warning: Unhandled 'set default' command: %s\n", argIn.ArgLine());
+    }
   } else {
     mprintf("Warning: Unhandled 'set' command: %s\n", argIn.ArgLine());
-  } 
+  }
 
   return 0;
 }
diff --git a/src/DataSet_LeapOpts.cpp b/src/DataSet_LeapOpts.cpp
index 631c269f54..fe616e127a 100644
--- a/src/DataSet_LeapOpts.cpp
+++ b/src/DataSet_LeapOpts.cpp
@@ -4,7 +4,20 @@
 /// CONSTRUCTOR
 DataSet_LeapOpts::DataSet_LeapOpts() :
   // 0 dim indicates DataSet-specific write
-  DataSet(LEAPOPTS, GENERIC, TextFormat(TextFormat::STRING, 12, 0), 0)
+  DataSet(LEAPOPTS, GENERIC, TextFormat(TextFormat::STRING, 12, 0), 0),
+  pbradii_(Cpptraj::Parm::MBONDI)
 {
 
 }
+
+/** Set default GB radii from keyword. */
+int DataSet_LeapOpts::SetGbRadii(std::string const& keyword) {
+  Cpptraj::Parm::GB_RadiiType radType = Cpptraj::Parm::GbTypeFromKey( keyword );
+  if (radType == Cpptraj::Parm::UNKNOWN_GB) {
+    mprinterr("Error: Unrecognized GB radii type: %s\n", keyword.c_str());
+    return 1;
+  }
+  pbradii_ = radType;
+  mprintf("\tSet default GB radii: %s\n", Cpptraj::Parm::GbTypeStr(pbradii_).c_str());
+  return 0;
+}
diff --git a/src/DataSet_LeapOpts.h b/src/DataSet_LeapOpts.h
index 7cdb84533e..a3a1c85519 100644
--- a/src/DataSet_LeapOpts.h
+++ b/src/DataSet_LeapOpts.h
@@ -1,6 +1,7 @@
 #ifndef INC_DATASET_LEAPOPTS_H
 #define INC_DATASET_LEAPOPTS_H
 #include "DataSet.h"
+#include "Parm/GB_Params.h"
 /// Hold LEaP options read from 'sourcing' a leaprc file in DataIO_LeapRC 
 class DataSet_LeapOpts : public DataSet {
   public:
@@ -18,6 +19,8 @@ class DataSet_LeapOpts : public DataSet {
     int Sync(size_t, std::vector<int> const&, Parallel::Comm const&) { return 1; }
 #   endif
     // -------------------------------------------
+    int SetGbRadii(std::string const&);
   private:
+    Cpptraj::Parm::GB_RadiiType pbradii_;
 };
 #endif
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 44daf0104e..b71a2763d5 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -232,7 +232,7 @@ DataIO_Cpout.o : DataIO_Cpout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h B
 DataIO_Evecs.o : DataIO_Evecs.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Evecs.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Modes.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 DataIO_Gnuplot.o : DataIO_Gnuplot.cpp ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Gnuplot.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 DataIO_Grace.o : DataIO_Grace.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Grace.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_string.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-DataIO_LeapRC.o : DataIO_LeapRC.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_Coords.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h ParmIO.h Parm_Amber.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_LeapRC.o : DataIO_LeapRC.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_Coords.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_LeapOpts.h DataSet_NameMap.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h ParmIO.h Parm_Amber.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Mdout.o : DataIO_Mdout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Mdout.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 DataIO_NetCDF.o : DataIO_NetCDF.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cluster/Cframes.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_NetCDF.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_Mesh.h DataSet_Modes.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_Vector.h DataSet_Vector_Scalar.h DataSet_string.h DataSet_unsignedInt.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h Version.h
 DataIO_Numpy.o : DataIO_Numpy.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Numpy.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h libnpy/npy.hpp
@@ -244,7 +244,7 @@ DataIO_VecTraj.o : DataIO_VecTraj.cpp ActionFrameCounter.h ArgList.h ArrayIterat
 DataIO_XVG.o : DataIO_XVG.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_XVG.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 DataIO_Xplor.o : DataIO_Xplor.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Xplor.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 DataSet.o : DataSet.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
-DataSetList.o : DataSetList.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Cluster/Cframes.h Cluster/Cmatrix_NC.h CmapParmHolder.h CompactFrameArray.h ComplexArray.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_FRM.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_GridDbl.h DataSet_GridFlt.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_NameMap.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h DataSet_PHREMD_Implicit.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_PairwiseCache_NC.h DataSet_Parameters.h DataSet_RemLog.h DataSet_StringVar.h DataSet_Tensor.h DataSet_Topology.h DataSet_Vector.h DataSet_Vector_Scalar.h DataSet_Zmatrix.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_disk.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h DataSet_unsignedInt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h InputTrajCommon.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h SymmetricTensor.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TypeNameHolder.h Unit.h Vec3.h
+DataSetList.o : DataSetList.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Cluster/Cframes.h Cluster/Cmatrix_NC.h CmapParmHolder.h CompactFrameArray.h ComplexArray.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_FRM.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_GridDbl.h DataSet_GridFlt.h DataSet_LeapOpts.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_NameMap.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h DataSet_PHREMD_Implicit.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_PairwiseCache_NC.h DataSet_Parameters.h DataSet_RemLog.h DataSet_StringVar.h DataSet_Tensor.h DataSet_Topology.h DataSet_Vector.h DataSet_Vector_Scalar.h DataSet_Zmatrix.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_disk.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h DataSet_unsignedInt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h InputTrajCommon.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h SymmetricTensor.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TypeNameHolder.h Unit.h Vec3.h
 DataSet_1D.o : DataSet_1D.cpp ArrayIterator.h AssociatedData.h ComplexArray.h Constants.h Corr.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h PubFFT.h Range.h TextFormat.h
 DataSet_2D.o : DataSet_2D.cpp AssociatedData.h CpptrajFile.h DataSet.h DataSet_2D.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
 DataSet_3D.o : DataSet_3D.cpp AssociatedData.h Box.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_3D.h Dimension.h FileIO.h FileName.h GridBin.h Matrix_3x3.h MetaData.h Parallel.h Range.h TextFormat.h Vec3.h
@@ -255,7 +255,7 @@ DataSet_Coords_REF.o : DataSet_Coords_REF.cpp ArgList.h AssociatedData.h Atom.h
 DataSet_Coords_TRJ.o : DataSet_Coords_TRJ.cpp AssociatedData.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_TRJ.h Dimension.h FileIO.h FileName.h Frame.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h Trajin_Single.h Unit.h Vec3.h
 DataSet_GridDbl.o : DataSet_GridDbl.cpp ArrayIterator.h AssociatedData.h Box.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_3D.h DataSet_GridDbl.h Dimension.h FileIO.h FileName.h Grid.h GridBin.h Matrix_3x3.h MetaData.h Parallel.h Range.h StringRoutines.h TextFormat.h Vec3.h
 DataSet_GridFlt.o : DataSet_GridFlt.cpp ArrayIterator.h AssociatedData.h Box.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_3D.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Grid.h GridBin.h Matrix_3x3.h MetaData.h Parallel.h Range.h StringRoutines.h TextFormat.h Vec3.h
-DataSet_LeapOpts.o : DataSet_LeapOpts.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_LeapOpts.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
+DataSet_LeapOpts.o : DataSet_LeapOpts.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_LeapOpts.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Parm/GB_Params.h Range.h TextFormat.h
 DataSet_Mat3x3.o : DataSet_Mat3x3.cpp AssociatedData.h CpptrajFile.h DataSet.h DataSet_Mat3x3.h Dimension.h FileIO.h FileName.h Matrix_3x3.h MetaData.h Parallel.h Range.h TextFormat.h Vec3.h
 DataSet_MatrixDbl.o : DataSet_MatrixDbl.cpp ArrayIterator.h AssociatedData.h CpptrajFile.h DataSet.h DataSet_2D.h DataSet_MatrixDbl.h Dimension.h FileIO.h FileName.h Matrix.h MetaData.h Parallel.h Range.h TextFormat.h
 DataSet_MatrixFlt.o : DataSet_MatrixFlt.cpp ArrayIterator.h AssociatedData.h CpptrajFile.h DataSet.h DataSet_2D.h DataSet_MatrixFlt.h Dimension.h FileIO.h FileName.h Matrix.h MetaData.h Parallel.h Range.h TextFormat.h

From 33aeee10e5ad56ad084fea9ebfcb0da170e91c97 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 22 Oct 2025 10:48:35 -0400
Subject: [PATCH 0992/1492] Store leap options in a class var

---
 src/DataIO_LeapRC.cpp | 29 +++++++++++++++++------------
 src/DataIO_LeapRC.h   |  1 +
 2 files changed, 18 insertions(+), 12 deletions(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 7b616f884e..4e1df6dc09 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -85,10 +85,9 @@ const char* DataIO_LeapRC::LeapEltHybrid::AtypeElementStr() const { return elt_;
 
 // -----------------------------------------------------------------------------
 /// CONSTRUCTOR
-DataIO_LeapRC::DataIO_LeapRC()
-{
-
-}
+DataIO_LeapRC::DataIO_LeapRC() :
+  leapopts_(0)
+{}
 
 /** Track already loaded parm files. */
 DataIO_LeapRC::Sarray DataIO_LeapRC::paramFiles_ = Sarray();
@@ -635,20 +634,16 @@ int DataIO_LeapRC::LoadPDB(ArgList const& argIn, DataSetList& dsl) const {
   return 0;
 }
 
+/** Leap options data set default name. */
 const char* DataIO_LeapRC::LEAPOPTSNAME_ = "_LEAP_OPTIONS_";
 
 /** LEaP 'set' command. */
 int DataIO_LeapRC::LeapSet(ArgList const& argIn, DataSetList& dsl) const {
-  // Check if we already allocated a LEaP options data set
-  DataSet* leapopts = dsl.FindSetOfType( std::string(LEAPOPTSNAME_), DataSet::LEAPOPTS );
-  if ( leapopts == 0)
-    leapopts = dsl.AddSet( DataSet::LEAPOPTS, MetaData( std::string(LEAPOPTSNAME_) ) );
-  if (leapopts == 0) {
-    mprinterr("Internal Error: Could not allocate leap options data set for 'set' command.\n");
+  if (leapopts_ == 0) {
+    mprinterr("Internal Error: DataIO_LeapRC::LeapSet(): LeapSet() called before ReadData().\n");
     return 1;
   }
-  mprintf("DEBUG: Leap options set: %s\n", leapopts->legend());
-  DataSet_LeapOpts& OPTS = static_cast<DataSet_LeapOpts&>( *leapopts );
+  DataSet_LeapOpts& OPTS = static_cast<DataSet_LeapOpts&>( *leapopts_ );
 
   if (argIn.Nargs() > 3 && ToLower(argIn[2]) == "name") {
     // set <unit> name <name>
@@ -781,6 +776,16 @@ int DataIO_LeapRC::ReadData(FileName const& fname, DataSetList& dsl, std::string
 {
   atomHybridizations_.clear();
   units_.clear();
+  // Get/allocate leap options
+  leapopts_ = dsl.FindSetOfType( std::string(LEAPOPTSNAME_), DataSet::LEAPOPTS );
+  if ( leapopts_ == 0)
+    leapopts_ = dsl.AddSet( DataSet::LEAPOPTS, MetaData( std::string(LEAPOPTSNAME_) ) );
+  if (leapopts_ == 0) {
+    mprinterr("Internal Error: DataIO_LeapRC::ReadData(): Could not allocate leap options data set for 'set' command.\n");
+    return 1;
+  }
+  mprintf("DEBUG: Leap options set: %s\n", leapopts_->legend());
+
   // First, need to determine where the Amber FF files are
   const char* env = getenv("AMBERHOME");
   if (env != 0)
diff --git a/src/DataIO_LeapRC.h b/src/DataIO_LeapRC.h
index 66f946496b..25d31e73c9 100644
--- a/src/DataIO_LeapRC.h
+++ b/src/DataIO_LeapRC.h
@@ -90,5 +90,6 @@ class DataIO_LeapRC : public DataIO {
     static Sarray paramFiles_; ///< Track amber FF param files loaded from leaprc files
     static Sarray libFiles_;   ///< Track amber library/prep files loaded from leaprc files
     static const char* LEAPOPTSNAME_; ///< Leap options data set name
+    DataSet* leapopts_;               ///< DataSet holding leap options
 };
 #endif

From 496e22d36d4c9e8ffc4ae4689269b952d3479e39 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 22 Oct 2025 10:58:52 -0400
Subject: [PATCH 0993/1492] Use the passed in GB radii set

---
 src/DataIO_LeapRC.cpp    |  3 ++-
 src/DataSet_LeapOpts.cpp |  2 +-
 src/DataSet_LeapOpts.h   |  2 ++
 src/Exec_Build.cpp       | 27 +++++++++++++++++----------
 src/Exec_Build.h         |  3 ++-
 src/cpptrajdepend        |  2 +-
 6 files changed, 25 insertions(+), 14 deletions(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 4e1df6dc09..6f27318ad6 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -625,8 +625,9 @@ int DataIO_LeapRC::LoadPDB(ArgList const& argIn, DataSetList& dsl) const {
   ArgList tmparg = args.RemainingArgs();
 
   tmparg.AddArg("name " + args[0]);
+  DataSet_LeapOpts& OPTS = static_cast<DataSet_LeapOpts&>( *leapopts_ );
   Exec_Build build;
-  Exec::RetType ret = build.BuildStructure( coordsIn.added_back(), dsl, debug_, tmparg );
+  Exec::RetType ret = build.BuildStructure( coordsIn.added_back(), dsl, debug_, tmparg, OPTS.PbRadii() );
   if (ret == CpptrajState::ERR) {
     mprinterr("Error: Build of '%s' failed.\n", args[2].c_str());
     return 1;
diff --git a/src/DataSet_LeapOpts.cpp b/src/DataSet_LeapOpts.cpp
index fe616e127a..ec1e8c6a78 100644
--- a/src/DataSet_LeapOpts.cpp
+++ b/src/DataSet_LeapOpts.cpp
@@ -18,6 +18,6 @@ int DataSet_LeapOpts::SetGbRadii(std::string const& keyword) {
     return 1;
   }
   pbradii_ = radType;
-  mprintf("\tSet default GB radii: %s\n", Cpptraj::Parm::GbTypeStr(pbradii_).c_str());
+  mprintf("\tSet default GB radii: %s\n", Cpptraj::Parm::GbAmberFlag(pbradii_).c_str());
   return 0;
 }
diff --git a/src/DataSet_LeapOpts.h b/src/DataSet_LeapOpts.h
index a3a1c85519..984bfece0e 100644
--- a/src/DataSet_LeapOpts.h
+++ b/src/DataSet_LeapOpts.h
@@ -20,6 +20,8 @@ class DataSet_LeapOpts : public DataSet {
 #   endif
     // -------------------------------------------
     int SetGbRadii(std::string const&);
+
+    Cpptraj::Parm::GB_RadiiType PbRadii() const { return pbradii_; }
   private:
     Cpptraj::Parm::GB_RadiiType pbradii_;
 };
diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index a2c746ad91..2f5b9eb405 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -3,7 +3,6 @@
 #include "CpptrajStdio.h"
 #include "DataSet_Parameters.h" // For casting DataSet_Parameters to ParameterSet
 #include "Parm/AssignParams.h"
-#include "Parm/GB_Params.h"
 #include "Structure/Builder.h"
 #include "Structure/Creator.h"
 #include "Structure/Disulfide.h"
@@ -787,11 +786,12 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
     mprinterr("Error: No COORDS set found matching %s\n", crdset.c_str());
     return CpptrajState::ERR;
   }
-  return BuildStructure(inCrdPtr, State.DSL(), State.Debug(), argIn);
+  return BuildStructure(inCrdPtr, State.DSL(), State.Debug(), argIn, Cpptraj::Parm::UNKNOWN_GB);
 }
 
 /** Standalone execute. For DataIO_LeapRC. */
-Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, int debugIn, ArgList& argIn)
+Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, int debugIn, ArgList& argIn,
+                                         Cpptraj::Parm::GB_RadiiType gbRadIn)
 {
   t_total_.Start();
   if (inCrdPtr == 0) {
@@ -879,14 +879,21 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, in
   mprintf("\tOutput COORDS set: %s\n", crdout.legend());
 
   // GB radii set
-  Cpptraj::Parm::GB_RadiiType gbradii = Cpptraj::Parm::MBONDI; // Default
-  std::string gbset = argIn.GetStringKey("gb");
-  if (!gbset.empty()) {
-    gbradii = Cpptraj::Parm::GbTypeFromKey( gbset );
-    if (gbradii == Cpptraj::Parm::UNKNOWN_GB) {
-      mprinterr("Error: Unknown GB radii set: %s\n", gbset.c_str());
-      return CpptrajState::ERR;
+  Cpptraj::Parm::GB_RadiiType gbradii;
+  if (gbRadIn == Cpptraj::Parm::UNKNOWN_GB) {
+    // No radii set specified. Check for keyword.
+    gbradii = Cpptraj::Parm::MBONDI; // Default
+    std::string gbset = argIn.GetStringKey("gb");
+    if (!gbset.empty()) {
+      gbradii = Cpptraj::Parm::GbTypeFromKey( gbset );
+      if (gbradii == Cpptraj::Parm::UNKNOWN_GB) {
+        mprinterr("Error: Unknown GB radii set: %s\n", gbset.c_str());
+        return CpptrajState::ERR;
+      }
     }
+  } else {
+    // Use passed-in GB radii set
+    gbradii = gbRadIn;
   }
   mprintf("\tGB radii set: %s\n", Cpptraj::Parm::GbTypeStr(gbradii).c_str());
 
diff --git a/src/Exec_Build.h b/src/Exec_Build.h
index 7775fd6d5a..ff2849878c 100644
--- a/src/Exec_Build.h
+++ b/src/Exec_Build.h
@@ -1,6 +1,7 @@
 #ifndef INC_EXEC_BUILD_H
 #define INC_EXEC_BUILD_H
 #include "Exec.h"
+#include "Parm/GB_Params.h"
 namespace Cpptraj {
 namespace Structure {
 class Creator;
@@ -16,7 +17,7 @@ class Exec_Build : public Exec {
     DispatchObject* Alloc() const { return (DispatchObject*)new Exec_Build(); }
     RetType Execute(CpptrajState&, ArgList&);
     /// Stand-alone execution
-    RetType BuildStructure(DataSet*, DataSetList&, int, ArgList&);
+    RetType BuildStructure(DataSet*, DataSetList&, int, ArgList&, Cpptraj::Parm::GB_RadiiType);
   private:
     typedef std::vector<int> Iarray;
     // Keep track of which residues are connected to each other
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index b71a2763d5..a10189a3af 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -195,7 +195,7 @@ CmapParmHolder.o : CmapParmHolder.cpp CmapParmHolder.h Constants.h CpptrajStdio.
 Cmd.o : Cmd.cpp Cmd.h DispatchObject.h
 CmdInput.o : CmdInput.cpp CmdInput.h StringRoutines.h
 CmdList.o : CmdList.cpp Cmd.h CmdList.h DispatchObject.h
-Command.o : Command.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h ActionTopWriter.h Action_AddAtom.h Action_Align.h Action_Angle.h Action_AreaPerMol.h Action_AtomMap.h Action_AtomicCorr.h Action_AtomicFluct.h Action_AutoImage.h Action_Average.h Action_AvgBox.h Action_Bounds.h Action_Box.h Action_Center.h Action_Channel.h Action_CheckChirality.h Action_CheckStructure.h Action_Closest.h Action_ClusterDihedral.h Action_Contacts.h Action_ConvertToFrac.h Action_CreateCrd.h Action_CreateReservoir.h Action_DNAionTracker.h Action_DSSP.h Action_Density.h Action_Diffusion.h Action_Dihedral.h Action_DihedralRMS.h Action_Dipole.h Action_DistRmsd.h Action_Distance.h Action_EneDecomp.h Action_Energy.h Action_Esander.h Action_FilterByData.h Action_FixAtomOrder.h Action_FixImagedBonds.h Action_GIST.h Action_Grid.h Action_GridFreeEnergy.h Action_HydrogenBond.h Action_Image.h Action_InfraredSpectrum.h Action_Jcoupling.h Action_Keep.h Action_LESsplit.h Action_LIE.h Action_LipidOrder.h Action_MakeStructure.h Action_Mask.h Action_Matrix.h Action_MinImage.h Action_MinMaxDist.h Action_Molsurf.h Action_MultiDihedral.h Action_MultiPucker.h Action_MultiVector.h Action_NAstruct.h Action_NMRrst.h Action_NativeContacts.h Action_OrderParameter.h Action_Outtraj.h Action_PairDist.h Action_Pairwise.h Action_Principal.h Action_Projection.h Action_Pucker.h Action_Radgyr.h Action_Radial.h Action_RandomizeIons.h Action_Remap.h Action_ReplicateCell.h Action_Rmsd.h Action_Rotate.h Action_RunningAvg.h Action_STFC_Diffusion.h Action_Scale.h Action_SetVelocity.h Action_Spam.h Action_Strip.h Action_Surf.h Action_SymmetricRmsd.h Action_Temperature.h Action_Test.h Action_Time.h Action_ToroidalDiffusion.h Action_Translate.h Action_Unstrip.h Action_Unwrap.h Action_Vector.h Action_VelocityAutoCorr.h Action_Volmap.h Action_Volume.h Action_Watershell.h Action_XtalSymm.h Analysis.h AnalysisList.h AnalysisState.h Analysis_AmdBias.h Analysis_AutoCorr.h Analysis_Average.h Analysis_CalcDiffusion.h Analysis_Clustering.h Analysis_ConstantPHStats.h Analysis_Corr.h Analysis_CrankShaft.h Analysis_CrdFluct.h Analysis_CrossCorr.h Analysis_CurveFit.h Analysis_Divergence.h Analysis_EvalPlateau.h Analysis_FFT.h Analysis_HausdorffDistance.h Analysis_Hist.h Analysis_IRED.h Analysis_Integrate.h Analysis_KDE.h Analysis_Lifetime.h Analysis_LowestCurve.h Analysis_Matrix.h Analysis_MeltCurve.h Analysis_Modes.h Analysis_MultiHist.h Analysis_Multicurve.h Analysis_Overlap.h Analysis_PhiPsi.h Analysis_Project.h Analysis_Regression.h Analysis_RemLog.h Analysis_Rms2d.h Analysis_RmsAvgCorr.h Analysis_Rotdif.h Analysis_RunningAvg.h Analysis_Slope.h Analysis_Spline.h Analysis_State.h Analysis_Statistics.h Analysis_TI.h Analysis_TICA.h Analysis_Timecorr.h Analysis_VectorMath.h Analysis_Wavelet.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AxisType.h BaseIOtype.h Box.h BoxArgs.h BufferedLine.h CharMask.h Cluster/Algorithm.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Control.h Cluster/DrawGraph.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Sieve.h Cluster/Silhouette.h ClusterMap.h Cmd.h CmdInput.h CmdList.h Command.h CompactFrameArray.h ComplexArray.h Constants.h Constraints.h ControlBlock.h ControlBlock_For.h CoordinateInfo.h Corr.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_RemLog.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h Deprecated.h DiffusionResults.h DihedralSearch.h Dimension.h DispatchObject.h Energy.h Energy/Ecalc_Nonbond.h Energy/EnergyDecomposer.h Energy/ErfcFxn.h Energy/EwaldParams.h Energy/PME_RecipParams.h Energy/VDW_LongRange_Correction.h Energy_Sander.h EnsembleIn.h EnsembleOutList.h EwaldOptions.h ExclusionArray.h Exec.h Exec_AddMissingRes.h Exec_Analyze.h Exec_Build.h Exec_Calc.h Exec_CatCrd.h Exec_Change.h Exec_ClusterMap.h Exec_CombineCoords.h Exec_Commands.h Exec_CompareClusters.h Exec_CompareEnergy.h Exec_CompareTop.h Exec_CrdAction.h Exec_CrdOut.h Exec_CrdTransform.h Exec_CreateSet.h Exec_DataFile.h Exec_DataFilter.h Exec_DataSetCmd.h Exec_Desc.h Exec_Emin.h Exec_ExtendedComparison.h Exec_Flatten.h Exec_GenerateAmberRst.h Exec_Graft.h Exec_Help.h Exec_HmassRepartition.h Exec_LoadCrd.h Exec_LoadTraj.h Exec_ParallelAnalysis.h Exec_ParmBox.h Exec_ParmSolvent.h Exec_ParmStrip.h Exec_ParmWrite.h Exec_ParseTiming.h Exec_PermuteDihedrals.h Exec_Precision.h Exec_PrepareForLeap.h Exec_PrintData.h Exec_Random.h Exec_ReadData.h Exec_ReadEnsembleData.h Exec_ReadInput.h Exec_RotateDihedral.h Exec_RunAnalysis.h Exec_ScaleDihedralK.h Exec_Sequence.h Exec_SequenceAlign.h Exec_Set.h Exec_Show.h Exec_SortEnsembleData.h Exec_Source.h Exec_SplitCoords.h Exec_System.h Exec_Top.h Exec_Traj.h Exec_UpdateParameters.h Exec_ViewRst.h Exec_Zmatrix.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h GIST_PME.h Grid.h GridAction.h GridBin.h GridMover.h HistBin.h Hungarian.h ImageOption.h ImageTypes.h InputTrajCommon.h InteractionData.h MapAtom.h MaskArray.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h OnlineVarT.h OutputTrajCommon.h PDBfile.h PairList.h Parallel.h ParallelSetFrameNum.h ParameterTypes.h PubFFT.h Pucker.h Pucker_PuckerMask.h Pucker_PuckerSearch.h Pucker_PuckerToken.h RPNcalc.h Random.h Range.h ReferenceAction.h ReferenceFrame.h RemdReservoirNC.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h SplineFxnTable.h Structure/LeastSquaresPlane.h Structure/RingFinder.h StructureCheck.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Unit.h Vec3.h cuda_kernels/GistCudaSetup.cuh helpme_standalone.h molsurf.h
+Command.o : Command.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h ActionTopWriter.h Action_AddAtom.h Action_Align.h Action_Angle.h Action_AreaPerMol.h Action_AtomMap.h Action_AtomicCorr.h Action_AtomicFluct.h Action_AutoImage.h Action_Average.h Action_AvgBox.h Action_Bounds.h Action_Box.h Action_Center.h Action_Channel.h Action_CheckChirality.h Action_CheckStructure.h Action_Closest.h Action_ClusterDihedral.h Action_Contacts.h Action_ConvertToFrac.h Action_CreateCrd.h Action_CreateReservoir.h Action_DNAionTracker.h Action_DSSP.h Action_Density.h Action_Diffusion.h Action_Dihedral.h Action_DihedralRMS.h Action_Dipole.h Action_DistRmsd.h Action_Distance.h Action_EneDecomp.h Action_Energy.h Action_Esander.h Action_FilterByData.h Action_FixAtomOrder.h Action_FixImagedBonds.h Action_GIST.h Action_Grid.h Action_GridFreeEnergy.h Action_HydrogenBond.h Action_Image.h Action_InfraredSpectrum.h Action_Jcoupling.h Action_Keep.h Action_LESsplit.h Action_LIE.h Action_LipidOrder.h Action_MakeStructure.h Action_Mask.h Action_Matrix.h Action_MinImage.h Action_MinMaxDist.h Action_Molsurf.h Action_MultiDihedral.h Action_MultiPucker.h Action_MultiVector.h Action_NAstruct.h Action_NMRrst.h Action_NativeContacts.h Action_OrderParameter.h Action_Outtraj.h Action_PairDist.h Action_Pairwise.h Action_Principal.h Action_Projection.h Action_Pucker.h Action_Radgyr.h Action_Radial.h Action_RandomizeIons.h Action_Remap.h Action_ReplicateCell.h Action_Rmsd.h Action_Rotate.h Action_RunningAvg.h Action_STFC_Diffusion.h Action_Scale.h Action_SetVelocity.h Action_Spam.h Action_Strip.h Action_Surf.h Action_SymmetricRmsd.h Action_Temperature.h Action_Test.h Action_Time.h Action_ToroidalDiffusion.h Action_Translate.h Action_Unstrip.h Action_Unwrap.h Action_Vector.h Action_VelocityAutoCorr.h Action_Volmap.h Action_Volume.h Action_Watershell.h Action_XtalSymm.h Analysis.h AnalysisList.h AnalysisState.h Analysis_AmdBias.h Analysis_AutoCorr.h Analysis_Average.h Analysis_CalcDiffusion.h Analysis_Clustering.h Analysis_ConstantPHStats.h Analysis_Corr.h Analysis_CrankShaft.h Analysis_CrdFluct.h Analysis_CrossCorr.h Analysis_CurveFit.h Analysis_Divergence.h Analysis_EvalPlateau.h Analysis_FFT.h Analysis_HausdorffDistance.h Analysis_Hist.h Analysis_IRED.h Analysis_Integrate.h Analysis_KDE.h Analysis_Lifetime.h Analysis_LowestCurve.h Analysis_Matrix.h Analysis_MeltCurve.h Analysis_Modes.h Analysis_MultiHist.h Analysis_Multicurve.h Analysis_Overlap.h Analysis_PhiPsi.h Analysis_Project.h Analysis_Regression.h Analysis_RemLog.h Analysis_Rms2d.h Analysis_RmsAvgCorr.h Analysis_Rotdif.h Analysis_RunningAvg.h Analysis_Slope.h Analysis_Spline.h Analysis_State.h Analysis_Statistics.h Analysis_TI.h Analysis_TICA.h Analysis_Timecorr.h Analysis_VectorMath.h Analysis_Wavelet.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AxisType.h BaseIOtype.h Box.h BoxArgs.h BufferedLine.h CharMask.h Cluster/Algorithm.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Control.h Cluster/DrawGraph.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Sieve.h Cluster/Silhouette.h ClusterMap.h Cmd.h CmdInput.h CmdList.h Command.h CompactFrameArray.h ComplexArray.h Constants.h Constraints.h ControlBlock.h ControlBlock_For.h CoordinateInfo.h Corr.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_RemLog.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h Deprecated.h DiffusionResults.h DihedralSearch.h Dimension.h DispatchObject.h Energy.h Energy/Ecalc_Nonbond.h Energy/EnergyDecomposer.h Energy/ErfcFxn.h Energy/EwaldParams.h Energy/PME_RecipParams.h Energy/VDW_LongRange_Correction.h Energy_Sander.h EnsembleIn.h EnsembleOutList.h EwaldOptions.h ExclusionArray.h Exec.h Exec_AddMissingRes.h Exec_Analyze.h Exec_Build.h Exec_Calc.h Exec_CatCrd.h Exec_Change.h Exec_ClusterMap.h Exec_CombineCoords.h Exec_Commands.h Exec_CompareClusters.h Exec_CompareEnergy.h Exec_CompareTop.h Exec_CrdAction.h Exec_CrdOut.h Exec_CrdTransform.h Exec_CreateSet.h Exec_DataFile.h Exec_DataFilter.h Exec_DataSetCmd.h Exec_Desc.h Exec_Emin.h Exec_ExtendedComparison.h Exec_Flatten.h Exec_GenerateAmberRst.h Exec_Graft.h Exec_Help.h Exec_HmassRepartition.h Exec_LoadCrd.h Exec_LoadTraj.h Exec_ParallelAnalysis.h Exec_ParmBox.h Exec_ParmSolvent.h Exec_ParmStrip.h Exec_ParmWrite.h Exec_ParseTiming.h Exec_PermuteDihedrals.h Exec_Precision.h Exec_PrepareForLeap.h Exec_PrintData.h Exec_Random.h Exec_ReadData.h Exec_ReadEnsembleData.h Exec_ReadInput.h Exec_RotateDihedral.h Exec_RunAnalysis.h Exec_ScaleDihedralK.h Exec_Sequence.h Exec_SequenceAlign.h Exec_Set.h Exec_Show.h Exec_SortEnsembleData.h Exec_Source.h Exec_SplitCoords.h Exec_System.h Exec_Top.h Exec_Traj.h Exec_UpdateParameters.h Exec_ViewRst.h Exec_Zmatrix.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h GIST_PME.h Grid.h GridAction.h GridBin.h GridMover.h HistBin.h Hungarian.h ImageOption.h ImageTypes.h InputTrajCommon.h InteractionData.h MapAtom.h MaskArray.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h OnlineVarT.h OutputTrajCommon.h PDBfile.h PairList.h Parallel.h ParallelSetFrameNum.h ParameterTypes.h Parm/GB_Params.h PubFFT.h Pucker.h Pucker_PuckerMask.h Pucker_PuckerSearch.h Pucker_PuckerToken.h RPNcalc.h Random.h Range.h ReferenceAction.h ReferenceFrame.h RemdReservoirNC.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h SplineFxnTable.h Structure/LeastSquaresPlane.h Structure/RingFinder.h StructureCheck.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Unit.h Vec3.h cuda_kernels/GistCudaSetup.cuh helpme_standalone.h molsurf.h
 CompactFrameArray.o : CompactFrameArray.cpp Box.h CompactFrameArray.h CoordinateInfo.h CpptrajStdio.h Matrix_3x3.h Parallel.h ReplicaDimArray.h Vec3.h
 ComplexArray.o : ComplexArray.cpp ArrayIterator.h ComplexArray.h
 Constraints.o : Constraints.cpp ArgList.h Atom.h AtomMask.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h

From f059415d5ce597fa9170055cdbfc8a4ce96b72d9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 22 Oct 2025 11:18:48 -0400
Subject: [PATCH 0994/1492] Add parmout and crdout keywords

---
 src/Exec_Build.cpp | 33 ++++++++++++++++++++++++++++++++-
 src/cpptrajdepend  |  2 +-
 2 files changed, 33 insertions(+), 2 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 2f5b9eb405..a03aacff05 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -2,6 +2,8 @@
 #include "AssociatedData_Connect.h"
 #include "CpptrajStdio.h"
 #include "DataSet_Parameters.h" // For casting DataSet_Parameters to ParameterSet
+#include "ParmFile.h"
+#include "Trajout_Single.h"
 #include "Parm/AssignParams.h"
 #include "Structure/Builder.h"
 #include "Structure/Creator.h"
@@ -754,6 +756,7 @@ void Exec_Build::Help() const
 {
   mprintf("\tname <output COORDS> crdset <COORDS set> [frame <#>]\n"
           "\t[title <title>] [gb <radii>] [verbose <#>]\n"
+          "\t[parmout <topology file>] [crdout <coord file>]\n"
           "\t[%s]\n"
           "\t[{%s} ...]\n"
           "\t[{%s} ...]\n"
@@ -809,7 +812,12 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, in
     mprintf("\tNon-template bonds will be added if detected.\n");
   else
     mprintf("\tOnly bonding according to residue templates.\n");
-
+  std::string outputTopologyName = argIn.GetStringKey("parmout");
+  std::string outputCoordsName = argIn.GetStringKey("crdout");
+  if (!outputTopologyName.empty())
+    mprintf("\tWill write topology to %s\n", outputTopologyName.c_str());
+  if (!outputCoordsName.empty())
+    mprintf("\tWill write coords to %s\n", outputCoordsName.c_str());
   // TODO make it so this can be const (cant bc GetFrame)
   DataSet_Coords& coords = static_cast<DataSet_Coords&>( *((DataSet_Coords*)inCrdPtr) );
   // Get frame from input coords
@@ -1106,6 +1114,29 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, in
       frameOut.ModifyBox().SetNoBox();
     t_check_.Stop();
   }
+
+  if (!outputTopologyName.empty()) {
+    ParmFile pfile;
+    if (pfile.WriteTopology(crdout.Top(), outputTopologyName, argIn, ParmFile::UNKNOWN_PARM, debug_)) {
+      mprinterr("Error: Could not write topology file %s\n", outputTopologyName.c_str());
+      return CpptrajState::ERR;
+    }
+  }
+
+  if (!outputCoordsName.empty()) {
+    Trajout_Single outtraj;
+    if (outtraj.PrepareTrajWrite( outputCoordsName, argIn, DSL, crdout.TopPtr(), crdout.CoordsInfo(),
+                                  crdout.Size(), TrajectoryFile::UNKNOWN_TRAJ))
+    {
+      mprinterr("Error: Could not set up output coords file %s\n", outputCoordsName.c_str());
+      return CpptrajState::ERR;
+    }
+    outtraj.PrintInfo(0);
+    if ( outtraj.WriteSingle( 0, frameOut ) ) {
+      mprinterr("Error: Could not write output coords file %s\n", outputCoordsName.c_str());
+      return CpptrajState::ERR;
+    }
+  }
   t_total_.Stop();
 
   t_total_.WriteTiming(1, "Build timing:");
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index a10189a3af..bbe5b27524 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -316,7 +316,7 @@ EwaldOptions.o : EwaldOptions.cpp ArgList.h CpptrajStdio.h EwaldOptions.h
 ExclusionArray.o : ExclusionArray.cpp Atom.h AtomMask.h CharMask.h CpptrajStdio.h ExclusionArray.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Unit.h
 Exec_AddMissingRes.o : Exec_AddMissingRes.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h CharMask.h CompactFrameArray.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_AddMissingRes.h Exec_AddMissingRes_Pres.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h ParmFile.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h Trajout_Single.h Unit.h Vec3.h
 Exec_Analyze.o : Exec_Analyze.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Analyze.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_Build.o : Exec_Build.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h ExclusionArray.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PairList.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/Creator.h Structure/Disulfide.h Structure/HisProt.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/RingFinder.h Structure/StructureEnum.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Build.o : Exec_Build.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h ExclusionArray.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PairList.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/Creator.h Structure/Disulfide.h Structure/HisProt.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/RingFinder.h Structure/StructureEnum.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Calc.o : Exec_Calc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Calc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_CatCrd.o : Exec_CatCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CatCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_Change.o : Exec_Change.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Change.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h

From c06cd6153782e25b75771918586ccd508f8e3b6f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 22 Oct 2025 11:42:51 -0400
Subject: [PATCH 0995/1492] By default only report the number of duplicates for
 addAtomTypes. Do report any overwritten types.

---
 src/DataIO_LeapRC.cpp | 29 +++++++++++++++++++++++++----
 1 file changed, 25 insertions(+), 4 deletions(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 6f27318ad6..21e945eea2 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -294,6 +294,9 @@ int DataIO_LeapRC::AddAtomTypes(AtypeEltHybridPairMap& atomHybridizations, Buffe
 const
 {
   int bracketCount = 0;
+  // Count duplicate entries
+  Sarray duplicateEntries;
+  Sarray overwrittenEntries;
   // First line should contain the command
   const char* line = infile.CurrentLine();
   while (line != 0) {
@@ -327,13 +330,15 @@ const
           if (it == atomHybridizations.end() || it->first != atype) {
             it = atomHybridizations.insert( it, AtypeEltHybridPairType(atype, eltHybrid) );
           } else {
-            mprintf("Warning: Duplicate entry for '%s' in addAtomTypes.", *atype);
+            //mprintf("Warning: Duplicate entry for '%s' in addAtomTypes.", *atype);
             if (it->second != eltHybrid) {
-              mprintf(" Overwriting.\n");
-              mprintf("Warning: Line is %s\n", tmp.c_str());
+              //mprintf(" Overwriting.\n");
+              overwrittenEntries.push_back( atype.Truncated() );
+              if (debug_ > 0) mprintf("Warning: Line is %s\n", tmp.c_str());
               it->second = eltHybrid;
             } else
-              mprintf("\n");
+              duplicateEntries.push_back( atype.Truncated() );
+              //mprintf("\n");
           }
           tmp.clear();
         }
@@ -357,6 +362,22 @@ const
     return 1;
   }
   mprintf("\tRead %zu atom hybridizations.\n", atomHybridizations.size());
+  if (!duplicateEntries.empty()) {
+    mprintf("Warning: %zu duplicate entries in addAtomTypes; this is expected if other leaprc files have been loaded.\n",
+            duplicateEntries.size());
+    if (debug_ > 0) {
+      mprintf("Warning: Duplicates:");
+      for (Sarray::const_iterator it = duplicateEntries.begin(); it != duplicateEntries.end(); ++it)
+        mprintf(" %s", it->c_str());
+      mprintf("\n");
+    }
+  }
+  if (!overwrittenEntries.empty()) {
+    mprintf("Warning: %zu entries were overwritten in addAtomTypes:", duplicateEntries.size());
+    for (Sarray::const_iterator it = duplicateEntries.begin(); it != duplicateEntries.end(); ++it)
+      mprintf(" %s", it->c_str());
+    mprintf("\n");
+  }
   return 0;
 }
 

From df41b2bf1ac30519c61a9a76cd84d62b23ea0bb4 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 22 Oct 2025 11:52:57 -0400
Subject: [PATCH 0996/1492] Better reporting when res map is different

---
 src/DataIO_LeapRC.cpp | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 21e945eea2..926da88575 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -421,9 +421,15 @@ const
     mprintf("\n");
   } else {
     // TODO check if map is different
-    mprintf("Warning: Unit %s already has resmap. ", unit->legend());
-    ad->Ainfo();
-    mprintf("\n");
+    AssociatedData_ResId const& resid = static_cast<AssociatedData_ResId const&>( *ad );
+    if ( resid.ResName() != prm.pdbName_ || resid.TermType() != prm.termType_) {
+      mprintf("Warning: Unit %s already has resmap. ", unit->legend());
+      ad->Ainfo();
+      mprintf(" New map would be: ");
+      AssociatedData_ResId newResid(prm.pdbName_, prm.termType_);
+      newResid.Ainfo();
+      mprintf("\n");
+    }
   }
 }
 

From 097d7af052c244b208b484a354ce95d130b07f58 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 22 Oct 2025 15:32:46 -0400
Subject: [PATCH 0997/1492] Start a pdb residue map type

---
 src/DataSet_PdbResMap.cpp | 44 +++++++++++++++++++++++++++++++++++++++
 src/DataSet_PdbResMap.h   | 35 +++++++++++++++++++++++++++++++
 src/PdbResMapType.h       | 23 ++++++++++++++++++++
 3 files changed, 102 insertions(+)
 create mode 100644 src/DataSet_PdbResMap.cpp
 create mode 100644 src/DataSet_PdbResMap.h
 create mode 100644 src/PdbResMapType.h

diff --git a/src/DataSet_PdbResMap.cpp b/src/DataSet_PdbResMap.cpp
new file mode 100644
index 0000000000..cf10c7acb2
--- /dev/null
+++ b/src/DataSet_PdbResMap.cpp
@@ -0,0 +1,44 @@
+#include "DataSet_PdbResMap.h"
+#include "CpptrajStdio.h"
+
+using namespace Cpptraj;
+/// CONSTRUCTOR
+DataSet_PdbResMap::DataSet_PdbResMap() :
+  // 0 dim indicates DataSet-specific write
+  DataSet(LEAPOPTS, GENERIC, TextFormat(TextFormat::STRING, 12, 0), 0)
+{
+
+}
+
+/** Add a PDB residue to unit name mapping. */
+int DataSet_PdbResMap::AddPdbResMap(PdbResMapType const& prmIn) {
+  MapType::iterator it = pdbResMap_.lower_bound( prmIn.PdbName() );
+  if (it == pdbResMap_.end() || it->first != prmIn.PdbName())
+  {
+    // New PDB residue name.
+    PairType pdbUnitPair( prmIn.PdbName(), Sarray(3, "") );
+    pdbUnitPair.second[(int)prmIn.TermType()] = prmIn.UnitName();
+    it = pdbResMap_.insert( it, pdbUnitPair );
+  } else {
+    // Is this a terminal type that is not yet filled?
+    if ( it->second[(int)prmIn.TermType()].empty() )
+      it->second[(int)prmIn.TermType()] = prmIn.UnitName();
+    else {
+      mprintf("Warning: PDB residue %s is already mapped to unit %s for terminal type %s\n",
+              *(it->first), it->second[(int)prmIn.TermType()].c_str(), Structure::terminalStr(prmIn.TermType()));
+    }
+  }
+
+  return 0;
+}
+
+/** Print PDB residue to unit mapping to STDOUT. */
+void DataSet_PdbResMap::PrintPdbResMap() const {
+  mprintf("PDB to unit residue mapping:\n");
+  mprintf("\t%8s : %8s %8s %8s\n", "PDB", "Begin", "Nonterm", "End");
+  for (MapType::const_iterator it = pdbResMap_.begin(); it != pdbResMap_.end(); ++it)
+  {
+    mprintf("\t%8s : %8s %8s %8s\n", *(it->first),
+            it->second[0].c_str(), it->second[1].c_str(), it->second[2].c_str());
+  }
+}
diff --git a/src/DataSet_PdbResMap.h b/src/DataSet_PdbResMap.h
new file mode 100644
index 0000000000..41d1db42c4
--- /dev/null
+++ b/src/DataSet_PdbResMap.h
@@ -0,0 +1,35 @@
+#ifndef INC_DATASET_PDBRESMAP_H
+#define INC_DATASET_PDBRESMAP_H
+#include "DataSet.h"
+#include <map>
+#include <vector>
+#include <string>
+#include "PdbResMapType.h"
+/// Hold LEaP PDB residue name map 
+class DataSet_PdbResMap : public DataSet {
+    typedef std::vector<std::string> Sarray;
+    typedef std::pair<NameType, Sarray> PairType;
+    typedef std::map<NameType, Sarray> MapType;
+  public:
+    DataSet_PdbResMap();
+    static DataSet* Alloc() { return (DataSet*)new DataSet_PdbResMap(); }
+    // ----- DataSet functions -------------------
+    size_t Size()                                    const { return 0; }
+    void Info()                                      const { return; }
+    int Allocate(SizeArray const&)                         { return 1; }
+    void Add(size_t, const void*)                          { return; }
+    void WriteBuffer(CpptrajFile&, SizeArray const&) const { return; }
+    int Append(DataSet*)                                   { return 1; }
+    size_t MemUsageInBytes()                         const { return 0; }
+#   ifdef MPI
+    int Sync(size_t, std::vector<int> const&, Parallel::Comm const&) { return 1; }
+#   endif
+    // -------------------------------------------
+    /// Add a PDB name to unit name mapping
+    int AddPdbResMap(Cpptraj::PdbResMapType const&);
+
+    void PrintPdbResMap() const;
+  private:
+    MapType pdbResMap_; ///< Map PDB residue name to array of unit names: begin, non-terminal, end
+};
+#endif
diff --git a/src/PdbResMapType.h b/src/PdbResMapType.h
new file mode 100644
index 0000000000..25b0a4fbfb
--- /dev/null
+++ b/src/PdbResMapType.h
@@ -0,0 +1,23 @@
+#ifndef INC_PDBRESMAPTYPE_H
+#define INC_PDBRESMAPTYPE_H
+#include <string>
+#include "NameType.h"
+#include "Structure/StructureEnum.h"
+namespace Cpptraj {
+/// Hold PDB residue name, corresponding unit name and residue terminal type
+class PdbResMapType {
+  public:
+    //PdbResMapType() : termType_(Structure::NON_TERMINAL) {}
+    PdbResMapType(std::string const& unitIn, NameType const& nameIn, Structure::TerminalType termIn) :
+      unitName_(unitIn), pdbName_(nameIn), termType_(termIn) {}
+
+    std::string const& UnitName() const { return unitName_; }
+    NameType const& PdbName() const { return pdbName_; }
+    Structure::TerminalType TermType() const { return termType_; }
+  private:
+    std::string unitName_;
+    NameType pdbName_;
+    Structure::TerminalType termType_;
+};
+}
+#endif

From d0926140572395f2729edea7bcb3f7fac8bbd8cd Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 22 Oct 2025 15:52:35 -0400
Subject: [PATCH 0998/1492] Start using the new PDB residue name map data set

---
 src/DataIO_LeapRC.cpp     | 23 ++++++++++++++++++++---
 src/DataIO_LeapRC.h       |  6 ++++--
 src/DataSet.cpp           |  1 +
 src/DataSet.h             |  2 +-
 src/DataSetList.cpp       |  2 ++
 src/DataSet_PdbResMap.cpp |  2 +-
 src/cpptrajdepend         |  5 +++--
 src/cpptrajfiles          |  1 +
 8 files changed, 33 insertions(+), 9 deletions(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 926da88575..5ec60272a7 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -10,6 +10,7 @@
 #include "DataSet_LeapOpts.h"
 #include "DataSet_NameMap.h"
 #include "DataSet_Parameters.h"
+#include "DataSet_PdbResMap.h"
 #include "Exec_Build.h"
 #include "Parm_Amber.h"
 #include "StringRoutines.h" // ToLower
@@ -86,7 +87,8 @@ const char* DataIO_LeapRC::LeapEltHybrid::AtypeElementStr() const { return elt_;
 // -----------------------------------------------------------------------------
 /// CONSTRUCTOR
 DataIO_LeapRC::DataIO_LeapRC() :
-  leapopts_(0)
+  leapopts_(0),
+  pdbResidueMap_(0)
 {}
 
 /** Track already loaded parm files. */
@@ -489,6 +491,7 @@ const
             prm.pdbName_ = aline[pdbidx];
             prm.unitName_ = aline[unitidx];
             pdbResMapIn.push_back( prm );
+            ((DataSet_PdbResMap*)pdbResidueMap_)->AddPdbResMap( Cpptraj::PdbResMapType(aline[unitidx], aline[pdbidx], termType) );
             // Find among loaded units
             //DataSet* unitSet = findUnit( aline[unitidx] );
             //if (unitSet == 0) {
@@ -539,7 +542,7 @@ const
     if (ds == 0) return 1;
   }
   DataSet_NameMap& namemap = static_cast<DataSet_NameMap&>( *ds );
-  if (debug_ > 0)
+//  if (debug_ > 0)
     mprintf("DEBUG: Name map set: %s\n", namemap.legend());
   int bracketCount = 0;
   // First line should contain the command
@@ -665,6 +668,9 @@ int DataIO_LeapRC::LoadPDB(ArgList const& argIn, DataSetList& dsl) const {
 /** Leap options data set default name. */
 const char* DataIO_LeapRC::LEAPOPTSNAME_ = "_LEAP_OPTIONS_";
 
+/** Leap pdb residue map data set default name. */
+const char* DataIO_LeapRC::PDBRESMAPNAME_ = "_LEAP_PDBRESMAP_";
+
 /** LEaP 'set' command. */
 int DataIO_LeapRC::LeapSet(ArgList const& argIn, DataSetList& dsl) const {
   if (leapopts_ == 0) {
@@ -809,10 +815,19 @@ int DataIO_LeapRC::ReadData(FileName const& fname, DataSetList& dsl, std::string
   if ( leapopts_ == 0)
     leapopts_ = dsl.AddSet( DataSet::LEAPOPTS, MetaData( std::string(LEAPOPTSNAME_) ) );
   if (leapopts_ == 0) {
-    mprinterr("Internal Error: DataIO_LeapRC::ReadData(): Could not allocate leap options data set for 'set' command.\n");
+    mprinterr("Internal Error: DataIO_LeapRC::ReadData(): Could not allocate leap options data set.\n");
     return 1;
   }
   mprintf("DEBUG: Leap options set: %s\n", leapopts_->legend());
+  // Get/allocate pdb residue map
+  pdbResidueMap_ = dsl.FindSetOfType( std::string(PDBRESMAPNAME_), DataSet::PDBRESMAP );
+  if (pdbResidueMap_ == 0)
+    pdbResidueMap_ = dsl.AddSet( DataSet::PDBRESMAP, MetaData( std::string(PDBRESMAPNAME_) ) );
+  if (pdbResidueMap_ == 0) {
+    mprinterr("Internal Error: DataIO_LeapRC::ReadData(): Could not allocate leap PDB residue map data set.\n");
+    return 1;
+  }
+  mprintf("DEBUG: Leap PDB residue map set: %s\n", pdbResidueMap_->legend());
 
   // First, need to determine where the Amber FF files are
   const char* env = getenv("AMBERHOME");
@@ -836,6 +851,8 @@ int DataIO_LeapRC::ReadData(FileName const& fname, DataSetList& dsl, std::string
     return 1;
   }
 
+  // DEBUG
+  ((DataSet_PdbResMap*)pdbResidueMap_)->PrintPdbResMap();
   return 0;
 }
 
diff --git a/src/DataIO_LeapRC.h b/src/DataIO_LeapRC.h
index 25d31e73c9..e3e37488b3 100644
--- a/src/DataIO_LeapRC.h
+++ b/src/DataIO_LeapRC.h
@@ -89,7 +89,9 @@ class DataIO_LeapRC : public DataIO {
     Sarray searchPaths_;
     static Sarray paramFiles_; ///< Track amber FF param files loaded from leaprc files
     static Sarray libFiles_;   ///< Track amber library/prep files loaded from leaprc files
-    static const char* LEAPOPTSNAME_; ///< Leap options data set name
-    DataSet* leapopts_;               ///< DataSet holding leap options
+    static const char* LEAPOPTSNAME_;  ///< Leap options data set name
+    static const char* PDBRESMAPNAME_; ///< Leap PDB residue map data set name
+    DataSet* leapopts_;                ///< DataSet holding leap options
+    DataSet* pdbResidueMap_;           ///< DataSet holding the leap pdb residue map
 };
 #endif
diff --git a/src/DataSet.cpp b/src/DataSet.cpp
index d153ac0cf6..65875c382c 100644
--- a/src/DataSet.cpp
+++ b/src/DataSet.cpp
@@ -35,6 +35,7 @@ const char* DataSet::Descriptions_[] = {
   "zmatrix",                    // ZMATRIX
   "name map",                   // NAMEMAP
   "LEaP options",               // LEAPOPTS
+  "PDB residue map",            // PDBRESMAP
   "unknown"                     // UNKNOWN_DATA
 };
 
diff --git a/src/DataSet.h b/src/DataSet.h
index ddb9690f55..53b1ee15c1 100644
--- a/src/DataSet.h
+++ b/src/DataSet.h
@@ -29,7 +29,7 @@ class DataSet {
       COORDS, VECTOR, MODES, GRID_FLT, GRID_DBL, REMLOG, XYMESH, TRAJ, REF_FRAME,
       MAT3X3, TOPOLOGY, PH, PH_EXPL, PH_IMPL,
       PARAMETERS, PMATRIX_MEM, PMATRIX_NC, TENSOR, STRINGVAR, VECTOR_SCALAR, UNSIGNED_INTEGER,
-      FRAMES, ZMATRIX, NAMEMAP, LEAPOPTS,
+      FRAMES, ZMATRIX, NAMEMAP, LEAPOPTS, PDBRESMAP,
       UNKNOWN_DATA
     };
     /// Group DataSet belongs to.
diff --git a/src/DataSetList.cpp b/src/DataSetList.cpp
index bff462ea3c..e09fca4e0f 100644
--- a/src/DataSetList.cpp
+++ b/src/DataSetList.cpp
@@ -38,6 +38,7 @@
 #include "DataSet_Zmatrix.h"
 #include "DataSet_NameMap.h"
 #include "DataSet_LeapOpts.h"
+#include "DataSet_PdbResMap.h"
 
 bool DataSetList::useDiskCache_ = false;
 
@@ -99,6 +100,7 @@ DataSet* DataSetList::NewSet(DataSet::DataType typeIn) {
     case DataSet::ZMATRIX       : ds = DataSet_Zmatrix::Alloc(); break;
     case DataSet::NAMEMAP       : ds = DataSet_NameMap::Alloc(); break;
     case DataSet::LEAPOPTS      : ds = DataSet_LeapOpts::Alloc(); break;
+    case DataSet::PDBRESMAP     : ds = DataSet_PdbResMap::Alloc(); break;
     // Sanity check
     default:
       mprinterr("Internal Error: No allocator for DataSet type '%s'\n",
diff --git a/src/DataSet_PdbResMap.cpp b/src/DataSet_PdbResMap.cpp
index cf10c7acb2..c10e5ea054 100644
--- a/src/DataSet_PdbResMap.cpp
+++ b/src/DataSet_PdbResMap.cpp
@@ -5,7 +5,7 @@ using namespace Cpptraj;
 /// CONSTRUCTOR
 DataSet_PdbResMap::DataSet_PdbResMap() :
   // 0 dim indicates DataSet-specific write
-  DataSet(LEAPOPTS, GENERIC, TextFormat(TextFormat::STRING, 12, 0), 0)
+  DataSet(PDBRESMAP, GENERIC, TextFormat(TextFormat::STRING, 12, 0), 0)
 {
 
 }
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index bbe5b27524..3f65b3ec3e 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -232,7 +232,7 @@ DataIO_Cpout.o : DataIO_Cpout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h B
 DataIO_Evecs.o : DataIO_Evecs.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Evecs.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Modes.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 DataIO_Gnuplot.o : DataIO_Gnuplot.cpp ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Gnuplot.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 DataIO_Grace.o : DataIO_Grace.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Grace.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_string.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-DataIO_LeapRC.o : DataIO_LeapRC.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_Coords.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_LeapOpts.h DataSet_NameMap.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h ParmIO.h Parm_Amber.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_LeapRC.o : DataIO_LeapRC.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_Coords.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_LeapOpts.h DataSet_NameMap.h DataSet_Parameters.h DataSet_PdbResMap.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h ParmIO.h Parm_Amber.h PdbResMapType.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Mdout.o : DataIO_Mdout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Mdout.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 DataIO_NetCDF.o : DataIO_NetCDF.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cluster/Cframes.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_NetCDF.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_Mesh.h DataSet_Modes.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_Vector.h DataSet_Vector_Scalar.h DataSet_string.h DataSet_unsignedInt.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h Version.h
 DataIO_Numpy.o : DataIO_Numpy.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Numpy.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h libnpy/npy.hpp
@@ -244,7 +244,7 @@ DataIO_VecTraj.o : DataIO_VecTraj.cpp ActionFrameCounter.h ArgList.h ArrayIterat
 DataIO_XVG.o : DataIO_XVG.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_XVG.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 DataIO_Xplor.o : DataIO_Xplor.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Xplor.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 DataSet.o : DataSet.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
-DataSetList.o : DataSetList.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Cluster/Cframes.h Cluster/Cmatrix_NC.h CmapParmHolder.h CompactFrameArray.h ComplexArray.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_FRM.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_GridDbl.h DataSet_GridFlt.h DataSet_LeapOpts.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_NameMap.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h DataSet_PHREMD_Implicit.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_PairwiseCache_NC.h DataSet_Parameters.h DataSet_RemLog.h DataSet_StringVar.h DataSet_Tensor.h DataSet_Topology.h DataSet_Vector.h DataSet_Vector_Scalar.h DataSet_Zmatrix.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_disk.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h DataSet_unsignedInt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h InputTrajCommon.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h SymmetricTensor.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TypeNameHolder.h Unit.h Vec3.h
+DataSetList.o : DataSetList.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Cluster/Cframes.h Cluster/Cmatrix_NC.h CmapParmHolder.h CompactFrameArray.h ComplexArray.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_FRM.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_GridDbl.h DataSet_GridFlt.h DataSet_LeapOpts.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_NameMap.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h DataSet_PHREMD_Implicit.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_PairwiseCache_NC.h DataSet_Parameters.h DataSet_PdbResMap.h DataSet_RemLog.h DataSet_StringVar.h DataSet_Tensor.h DataSet_Topology.h DataSet_Vector.h DataSet_Vector_Scalar.h DataSet_Zmatrix.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_disk.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h DataSet_unsignedInt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h InputTrajCommon.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h PdbResMapType.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h Structure/StructureEnum.h SymbolExporting.h SymmetricTensor.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TypeNameHolder.h Unit.h Vec3.h
 DataSet_1D.o : DataSet_1D.cpp ArrayIterator.h AssociatedData.h ComplexArray.h Constants.h Corr.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h PubFFT.h Range.h TextFormat.h
 DataSet_2D.o : DataSet_2D.cpp AssociatedData.h CpptrajFile.h DataSet.h DataSet_2D.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
 DataSet_3D.o : DataSet_3D.cpp AssociatedData.h Box.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_3D.h Dimension.h FileIO.h FileName.h GridBin.h Matrix_3x3.h MetaData.h Parallel.h Range.h TextFormat.h Vec3.h
@@ -268,6 +268,7 @@ DataSet_PairwiseCache.o : DataSet_PairwiseCache.cpp AssociatedData.h Cluster/Cfr
 DataSet_PairwiseCache_MEM.o : DataSet_PairwiseCache_MEM.cpp ArrayIterator.h AssociatedData.h Cluster/Cframes.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h Dimension.h FileIO.h FileName.h Matrix.h MetaData.h Parallel.h Range.h StringRoutines.h TextFormat.h
 DataSet_PairwiseCache_NC.o : DataSet_PairwiseCache_NC.cpp AssociatedData.h Cluster/Cframes.h Cluster/Cmatrix_NC.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_PairwiseCache.h DataSet_PairwiseCache_NC.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h StringRoutines.h TextFormat.h
 DataSet_Parameters.o : DataSet_Parameters.cpp AssociatedData.h AtomType.h CmapParmHolder.h Constants.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h MetaData.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h TextFormat.h TypeNameHolder.h
+DataSet_PdbResMap.o : DataSet_PdbResMap.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_PdbResMap.h Dimension.h FileIO.h FileName.h MetaData.h NameType.h Parallel.h PdbResMapType.h Range.h Structure/StructureEnum.h TextFormat.h
 DataSet_RemLog.o : DataSet_RemLog.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h ReplicaDimArray.h TextFormat.h
 DataSet_StringVar.o : DataSet_StringVar.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_StringVar.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
 DataSet_Tensor.o : DataSet_Tensor.cpp AssociatedData.h CpptrajFile.h DataSet.h DataSet_Tensor.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h SymmetricTensor.h TextFormat.h
diff --git a/src/cpptrajfiles b/src/cpptrajfiles
index 0dcf19fcc4..2d2058bd0a 100644
--- a/src/cpptrajfiles
+++ b/src/cpptrajfiles
@@ -237,6 +237,7 @@ COMMON_SOURCES= \
         DataSet_PairwiseCache_MEM.cpp \
         DataSet_PairwiseCache_NC.cpp \
         DataSet_Parameters.cpp \
+        DataSet_PdbResMap.cpp \
         DataSet_pH.cpp \
         DataSet_PHREMD_Explicit.cpp \
         DataSet_PHREMD_Implicit.cpp \

From 0f11b2b09615347c17bd5a550ad6ddd64906ea8c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 22 Oct 2025 17:41:26 -0400
Subject: [PATCH 0999/1492] Instead of data associated with each unit template,
 use an overall pdb residue name mapping data set. This allows multiple PDB
 residue names to map to the same unit in a manner more like what leap does.

---
 src/AssociatedData_ResId.cpp | 15 ------
 src/AssociatedData_ResId.h   | 27 -----------
 src/DataIO_LeapRC.cpp        | 89 ++++++++++++++++++------------------
 src/DataIO_LeapRC.h          | 16 ++-----
 src/DataSet_PdbResMap.cpp    | 11 +++++
 src/DataSet_PdbResMap.h      |  2 +
 src/Structure/Creator.cpp    | 38 ++++++++++++---
 src/Structure/Creator.h      |  2 +
 src/cpptrajdepend            |  5 +-
 src/cpptrajfiles             |  1 -
 10 files changed, 96 insertions(+), 110 deletions(-)
 delete mode 100644 src/AssociatedData_ResId.cpp
 delete mode 100644 src/AssociatedData_ResId.h

diff --git a/src/AssociatedData_ResId.cpp b/src/AssociatedData_ResId.cpp
deleted file mode 100644
index 7cf3205f1a..0000000000
--- a/src/AssociatedData_ResId.cpp
+++ /dev/null
@@ -1,15 +0,0 @@
-#include "AssociatedData_ResId.h"
-#include "CpptrajStdio.h"
-
-/** Help text */
-const char* AssociatedData_ResId::HelpText = "\0";
-
-/** Process Args */
-int AssociatedData_ResId::ProcessAdataArgs(ArgList& argIn) {
-  return 0;
-}
-
-/** Print info */
-void AssociatedData_ResId::Ainfo() const {
-  mprintf(" (Res name %s termType %s)", *resName_, Cpptraj::Structure::terminalStr(termType_));
-}
diff --git a/src/AssociatedData_ResId.h b/src/AssociatedData_ResId.h
deleted file mode 100644
index a46aea9d45..0000000000
--- a/src/AssociatedData_ResId.h
+++ /dev/null
@@ -1,27 +0,0 @@
-#ifndef INC_ASSOCIATEDDATA_RESID_H
-#define INC_ASSOCIATEDDATA_RESID_H
-#include "AssociatedData.h"
-#include "NameType.h"
-#include "Structure/StructureEnum.h"
-class NameType;
-/// Used to identify what residues a residue template matches
-class AssociatedData_ResId : public AssociatedData {
-  public:
-    /// CONSTRUCTOR
-    AssociatedData_ResId() : AssociatedData(RESID), termType_(Cpptraj::Structure::NON_TERMINAL) {}
-    /// CONSTRUCTOR - Pdb name, terminal type
-    AssociatedData_ResId(NameType const& n, Cpptraj::Structure::TerminalType t) :
-      AssociatedData(RESID), resName_(n), termType_(t) {}
-    // ----- Inherited functions -------
-    static const char* HelpText;
-    int ProcessAdataArgs(ArgList&);
-    AssociatedData* Copy() const { return new AssociatedData_ResId(*this); }
-    void Ainfo() const;
-    // ---------------------------------
-    NameType const& ResName() const { return resName_; }
-    Cpptraj::Structure::TerminalType TermType() const { return termType_; }
-  private:
-    NameType resName_;                          ///< Target residue name
-    Cpptraj::Structure::TerminalType termType_; ///< Target residue terminal type
-};
-#endif
diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 5ec60272a7..d187a12f4f 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -1,5 +1,4 @@
 #include "DataIO_LeapRC.h"
-#include "AssociatedData_ResId.h"
 #include "CpptrajStdio.h"
 #include "BufferedLine.h"
 #include "DataIO_AmberFF.h"
@@ -403,7 +402,7 @@ const
 }*/
 
 /** Associate PDB residue name map with COORDS set. */ // TODO call every time a new unit is loaded?
-void DataIO_LeapRC::addPdbResMapToUnit(DataSet_Coords* unit, PdbResMapType const& prm, bool allowUpdate)
+/*void DataIO_LeapRC::addPdbResMapToUnit(DataSet_Coords* unit, PdbResMapType const& prm, bool allowUpdate)
 const
 {
   // Does this unit already have associated ResId?
@@ -433,20 +432,20 @@ const
       mprintf("\n");
     }
   }
-}
+}*/
 
 /** Associate PDB residue name map with COORDS set, no update allowed. */
-void DataIO_LeapRC::addPdbResMapToUnit(DataSet_Coords* unit, PdbResMapType const& prm) const {
+/*void DataIO_LeapRC::addPdbResMapToUnit(DataSet_Coords* unit, PdbResMapType const& prm) const {
   addPdbResMapToUnit(unit, prm, false);
-}
+}*/
 
 /** Associate PDB residue name map with COORDS set, allow update. */
-void DataIO_LeapRC::updatePdbResMapToUnit(DataSet_Coords* unit, PdbResMapType const& prm) const {
+/*void DataIO_LeapRC::updatePdbResMapToUnit(DataSet_Coords* unit, PdbResMapType const& prm) const {
   addPdbResMapToUnit(unit, prm, true);
-}
+}*/
 
 /** LEaP addPdbResMap command. */
-int DataIO_LeapRC::AddPdbResMap(BufferedLine& infile, PdbResMapArray& pdbResMapIn)
+int DataIO_LeapRC::AddPdbResMap(BufferedLine& infile)
 const
 {
   int bracketCount = 0;
@@ -486,11 +485,11 @@ const
             unitidx = 2;
           }
           //if (termType != Cpptraj::Structure::NON_TERMINAL) {
-            PdbResMapType prm;
-            prm.termType_ = termType;
-            prm.pdbName_ = aline[pdbidx];
-            prm.unitName_ = aline[unitidx];
-            pdbResMapIn.push_back( prm );
+//            PdbResMapType prm;
+//            prm.termType_ = termType;
+//            prm.pdbName_ = aline[pdbidx];
+//            prm.unitName_ = aline[unitidx];
+//            pdbResMapIn.push_back( prm );
             ((DataSet_PdbResMap*)pdbResidueMap_)->AddPdbResMap( Cpptraj::PdbResMapType(aline[unitidx], aline[pdbidx], termType) );
             // Find among loaded units
             //DataSet* unitSet = findUnit( aline[unitidx] );
@@ -922,7 +921,7 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
       else if (leapcmd == ADDATOMTYPES)
         err = AddAtomTypes(atomHybridizations_, infile);
       else if (leapcmd == ADDPDBRESMAP) {
-        err = AddPdbResMap(infile, pdbResMap_);
+        err = AddPdbResMap(infile);
         //if (err == 0) {
           // Update units with pdb residue map info
           //for (DataSetList::const_iterator ds = unitDSL.begin(); ds != paramDSL.end(); ++ds)
@@ -1018,14 +1017,14 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
             if (debug_ > 0)
               mprintf("DEBUG: Created unit set %s\n", crd1.legend());
             // See if there is a PDB residue name map
-            for (PdbResMapArray::const_iterator it = pdbResMap_.begin();
-                                                it != pdbResMap_.end(); ++it)
-            {
-              if (it->unitName_ == line[0]) {
-                updatePdbResMapToUnit( &crd1, *it );
-                break;
-              }
-            }
+//            for (PdbResMapArray::const_iterator it = pdbResMap_.begin();
+//                                                it != pdbResMap_.end(); ++it)
+//            {
+//              if (it->unitName_ == line[0]) {
+//                updatePdbResMapToUnit( &crd1, *it );
+//                break;
+//              }
+//            }
           }
         } else {
           mprintf("Warning: Skipping unhandled LEaP command line: %s\n", ptr);
@@ -1038,29 +1037,29 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
   infile.CloseFile();
 
   // Do any PDB residue mapping
-  if (!pdbResMap_.empty()) {
-    for (PdbResMapArray::const_iterator it = pdbResMap_.begin();
-                                        it != pdbResMap_.end(); ++it)
-    {
-      // Find the unit in unit DSL
-      DataSet* ds = dsl.CheckForSet( MetaData(dsname, it->unitName_) );
-      if (ds != 0 && ds->Group() == DataSet::COORDINATES) {
-        addPdbResMapToUnit( static_cast<DataSet_Coords*>(ds), *it );
-      }
-      /*if (ds == 0) {
-        mprintf("Warning: Unit '%s' was not found among loaded units.\n", it->unitName_.c_str());
-      } else {
-        DataSet_Coords& crd = static_cast<DataSet_Coords&>( *ds );
-        AssociatedData_ResId resid( it->pdbName_, it->termType_ );
-        crd.AssociateData( &resid );
-        if (debug_ > 0) {
-          mprintf("DEBUG: Found unit %s", crd.legend());
-          resid.Ainfo();
-          mprintf("\n");
-        }
-      }*/
-    }
-  }
+//  if (!pdbResMap_.empty()) {
+//    for (PdbResMapArray::const_iterator it = pdbResMap_.begin();
+//                                        it != pdbResMap_.end(); ++it)
+//    {
+//      // Find the unit in unit DSL
+//      DataSet* ds = dsl.CheckForSet( MetaData(dsname, it->unitName_) );
+//      if (ds != 0 && ds->Group() == DataSet::COORDINATES) {
+//        addPdbResMapToUnit( static_cast<DataSet_Coords*>(ds), *it );
+//      }
+//      /*if (ds == 0) {
+//        mprintf("Warning: Unit '%s' was not found among loaded units.\n", it->unitName_.c_str());
+//      } else {
+//        DataSet_Coords& crd = static_cast<DataSet_Coords&>( *ds );
+//        AssociatedData_ResId resid( it->pdbName_, it->termType_ );
+//        crd.AssociateData( &resid );
+//        if (debug_ > 0) {
+//          mprintf("DEBUG: Found unit %s", crd.legend());
+//          resid.Ainfo();
+//          mprintf("\n");
+//        }
+//      }*/
+//    }
+//  }
 
   // Add data sets to the main data set list
   //if (addSetsToList(dsl, paramDSL)) return err+1;
diff --git a/src/DataIO_LeapRC.h b/src/DataIO_LeapRC.h
index e3e37488b3..df7a296e14 100644
--- a/src/DataIO_LeapRC.h
+++ b/src/DataIO_LeapRC.h
@@ -49,19 +49,12 @@ class DataIO_LeapRC : public DataIO {
     /// Array of data sets
     typedef std::vector<DataSet*> DSarray;
 
-    struct PdbResMapType {
-      std::string unitName_;
-      NameType pdbName_;
-      Cpptraj::Structure::TerminalType termType_;
-    };
-    typedef std::vector<PdbResMapType> PdbResMapArray;
-
     int AddPath(std::string const&);
     int LoadAmberParams(std::string const&, DataSetList&, std::string const&, AtypeEltHybridPairMap const&) const;
     int LoadOFF(std::string const&, DataSetList&, std::string const&, DSarray&) const;
     int LoadAmberPrep(std::string const&, DataSetList&, std::string const&, DSarray&) const;
     int AddAtomTypes(AtypeEltHybridPairMap&, BufferedLine&) const;
-    int AddPdbResMap(BufferedLine&, PdbResMapArray&) const;
+    int AddPdbResMap(BufferedLine&) const;
     int AddPdbAtomMap(std::string const&, DataSetList&, BufferedLine&) const;
     int LoadMol2(ArgList const&, DataSetList&) const;
     int LoadPDB(ArgList const&, DataSetList&) const;
@@ -70,11 +63,11 @@ class DataIO_LeapRC : public DataIO {
     int SaveAmberParm(std::string const&, ArgList&, DataSetList const& dsl) const;
     int Source(FileName const&, DataSetList&, std::string const&);
     /// Add PDB residue map to COORDS unit
-    void addPdbResMapToUnit(DataSet_Coords*, PdbResMapType const&, bool) const;
+//    void addPdbResMapToUnit(DataSet_Coords*, PdbResMapType const&, bool) const;
     /// Add PDB residue map to COORDS unit, no update
-    void addPdbResMapToUnit(DataSet_Coords*, PdbResMapType const&) const;
+//    void addPdbResMapToUnit(DataSet_Coords*, PdbResMapType const&) const;
     /// Add PDB residue map to COORDS unit, allow update
-    void updatePdbResMapToUnit(DataSet_Coords*, PdbResMapType const&) const;
+//    void updatePdbResMapToUnit(DataSet_Coords*, PdbResMapType const&) const;
     /// \return Previously loaded unit set with given name
     //DataSet* findUnit(std::string const&) const;
     /// Used to check if a parm/lib file was already loaded.
@@ -84,7 +77,6 @@ class DataIO_LeapRC : public DataIO {
 
     std::string amberhome_;
     AtypeEltHybridPairMap atomHybridizations_; ///< Store hybridizations for atom types
-    PdbResMapArray pdbResMap_; ///< Hold PDB residue name map
     DSarray units_;            ///< Hold COORDS sets which have been added as units
     Sarray searchPaths_;
     static Sarray paramFiles_; ///< Track amber FF param files loaded from leaprc files
diff --git a/src/DataSet_PdbResMap.cpp b/src/DataSet_PdbResMap.cpp
index c10e5ea054..ff3cf6252b 100644
--- a/src/DataSet_PdbResMap.cpp
+++ b/src/DataSet_PdbResMap.cpp
@@ -32,6 +32,17 @@ int DataSet_PdbResMap::AddPdbResMap(PdbResMapType const& prmIn) {
   return 0;
 }
 
+/** \return Unit name based on PDB residue name and terminal type. */
+std::string DataSet_PdbResMap::FindUnitName(NameType const& pdbName, Cpptraj::Structure::TerminalType termType)
+const
+{
+  MapType::const_iterator it = pdbResMap_.find( pdbName );
+  if (it == pdbResMap_.end())
+    return std::string("");
+  else
+    return it->second[(int)termType];
+}
+
 /** Print PDB residue to unit mapping to STDOUT. */
 void DataSet_PdbResMap::PrintPdbResMap() const {
   mprintf("PDB to unit residue mapping:\n");
diff --git a/src/DataSet_PdbResMap.h b/src/DataSet_PdbResMap.h
index 41d1db42c4..bd868e23d3 100644
--- a/src/DataSet_PdbResMap.h
+++ b/src/DataSet_PdbResMap.h
@@ -27,6 +27,8 @@ class DataSet_PdbResMap : public DataSet {
     // -------------------------------------------
     /// Add a PDB name to unit name mapping
     int AddPdbResMap(Cpptraj::PdbResMapType const&);
+    /// Find unit name based on PDB name/terminal type
+    std::string FindUnitName(NameType const&, Cpptraj::Structure::TerminalType) const;
 
     void PrintPdbResMap() const;
   private:
diff --git a/src/Structure/Creator.cpp b/src/Structure/Creator.cpp
index 56729c70bd..7f9dd5cb10 100644
--- a/src/Structure/Creator.cpp
+++ b/src/Structure/Creator.cpp
@@ -1,11 +1,11 @@
 #include "Creator.h"
 #include "GenerateConnectivityArrays.h" // For setting atom scan direction
 #include "../ArgList.h"
-#include "../AssociatedData_ResId.h"
 #include "../CpptrajStdio.h"
 #include "../DataSet_Coords.h" // TODO new coords type
 #include "../DataSet_NameMap.h"
 #include "../DataSet_Parameters.h"
+#include "../DataSet_PdbResMap.h"
 #include "../DataSetList.h"
 
 using namespace Cpptraj::Structure;
@@ -13,6 +13,7 @@ using namespace Cpptraj::Structure;
 /** CONSTRUCTOR */
 Creator::Creator() :
   mainParmSet_(0),
+  pdbResidueMap_(0),
   debug_(0),
   free_parmset_mem_(false)
 {}
@@ -42,6 +43,11 @@ int Creator::InitCreator(ArgList& argIn, DataSetList const& DSL, int debugIn)
   t_total_.Start();
   debug_ = debugIn;
 
+  // PDB residue map TODO handle multiple maps?
+  pdbResidueMap_ = (DataSet_PdbResMap*)DSL.FindSetOfType( "*", DataSet::PDBRESMAP );
+  if (pdbResidueMap_ != 0)
+    mprintf("DEBUG: PDB residue map data set: %s\n", pdbResidueMap_->legend());
+
   // Atom scan direction
   std::string atomscandir = argIn.GetStringKey("atomscandir");
   if (!atomscandir.empty()) {
@@ -133,6 +139,24 @@ DataSet_Coords* Creator::IdTemplateFromResname(NameType const& rname,
 const
 {
   std::vector<DataSet_Coords*> Out;
+
+  // See if a PDB residue map exists.
+  std::string targetUnitName;
+  if (pdbResidueMap_ != 0) {
+    targetUnitName = pdbResidueMap_->FindUnitName(rname, termType);
+    if (!targetUnitName.empty())
+       mprintf("DEBUG: Found mapped name for '%s' (%s) -> '%s'\n", *rname, Structure::terminalStr(termType), targetUnitName.c_str());
+  }
+  if (targetUnitName.empty()) {
+    targetUnitName = rname.Truncated();
+    mprintf("DEBUG: Target unit name: %s\n", targetUnitName.c_str());
+  }
+  // Residue templates have name in aspect currently.
+  for (Carray::const_iterator it = Templates_.begin(); it != Templates_.end(); ++it) {
+    if ((*it)->Meta().Aspect() == targetUnitName)
+      Out.push_back( *it );
+  }
+/*
   //DataSet_Coords* out = 0;
   if (termType != Cpptraj::Structure::NON_TERMINAL) {
     // Looking for a terminal residue. Need to get sets with AssociatedData_ResId
@@ -177,7 +201,7 @@ const
       }
     }
   }
-
+*/
   if (Out.empty()) return 0;
   if (Out.size() > 1) {
     mprintf("Warning: Multiple templates match '%s':", *rname);
@@ -227,11 +251,11 @@ int Creator::getTemplates(ArgList& argIn, DataSetList const& DSL) {
     if (debug_ > 0) {
       for (Carray::const_iterator it = Templates_.begin(); it != Templates_.end(); ++it) {
         mprintf("\t%s", (*it)->legend());
-        AssociatedData* ad = (*it)->GetAssociatedData( AssociatedData::RESID );
-        if (ad != 0) {
-          AssociatedData_ResId const& resid = static_cast<AssociatedData_ResId const&>( *ad );
-          resid.Ainfo();
-        }
+//        AssociatedData* ad = (*it)->GetAssociatedData( AssociatedData::RESID );
+//        if (ad != 0) {
+//          AssociatedData_ResId const& resid = static_cast<AssociatedData_ResId const&>( *ad );
+//          resid.Ainfo();
+//        }
         mprintf("\n");
       }
     }
diff --git a/src/Structure/Creator.h b/src/Structure/Creator.h
index 7bf365c8eb..80fe87e446 100644
--- a/src/Structure/Creator.h
+++ b/src/Structure/Creator.h
@@ -8,6 +8,7 @@ class ArgList;
 class DataSet_Coords;
 class DataSet_NameMap;
 class DataSet_Parameters;
+class DataSet_PdbResMap;
 class DataSetList;
 class NameType;
 namespace Cpptraj {
@@ -55,6 +56,7 @@ class Creator {
     void UpdateTemplateElements() const;
 
     DataSet_Parameters* mainParmSet_; ///< Hold optional parameter set.
+    DataSet_PdbResMap* pdbResidueMap_; ///< Hold optional PDB residue map set.
     Carray Templates_;                ///< Hold unit templates.
     Narray NameMaps_;                 ///< Hold atom name maps.
     int debug_;                       ///< Debug level
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 3f65b3ec3e..6085a24026 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -146,7 +146,6 @@ ArgList.o : ArgList.cpp ArgList.h CpptrajStdio.h StringRoutines.h
 Array1D.o : Array1D.cpp ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 AssociatedData_Connect.o : AssociatedData_Connect.cpp ArgList.h AssociatedData.h AssociatedData_Connect.h CpptrajStdio.h
 AssociatedData_NOE.o : AssociatedData_NOE.cpp ArgList.h AssociatedData.h AssociatedData_NOE.h CpptrajStdio.h
-AssociatedData_ResId.o : AssociatedData_ResId.cpp AssociatedData.h AssociatedData_ResId.h CpptrajStdio.h NameType.h Structure/StructureEnum.h
 Atom.o : Atom.cpp Atom.h CpptrajStdio.h NameType.h SymbolExporting.h
 AtomMap.o : AtomMap.cpp Atom.h AtomMap.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
 AtomMask.o : AtomMask.cpp Atom.h AtomMask.h CpptrajStdio.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h SymbolExporting.h Unit.h
@@ -232,7 +231,7 @@ DataIO_Cpout.o : DataIO_Cpout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h B
 DataIO_Evecs.o : DataIO_Evecs.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Evecs.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Modes.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 DataIO_Gnuplot.o : DataIO_Gnuplot.cpp ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Gnuplot.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 DataIO_Grace.o : DataIO_Grace.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Grace.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_string.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-DataIO_LeapRC.o : DataIO_LeapRC.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_Coords.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_LeapOpts.h DataSet_NameMap.h DataSet_Parameters.h DataSet_PdbResMap.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h ParmIO.h Parm_Amber.h PdbResMapType.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_LeapRC.o : DataIO_LeapRC.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_Coords.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_LeapOpts.h DataSet_NameMap.h DataSet_Parameters.h DataSet_PdbResMap.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h ParmIO.h Parm_Amber.h PdbResMapType.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Mdout.o : DataIO_Mdout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Mdout.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 DataIO_NetCDF.o : DataIO_NetCDF.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cluster/Cframes.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_NetCDF.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_Mesh.h DataSet_Modes.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_Vector.h DataSet_Vector_Scalar.h DataSet_string.h DataSet_unsignedInt.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h Version.h
 DataIO_Numpy.o : DataIO_Numpy.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Numpy.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h libnpy/npy.hpp
@@ -481,7 +480,7 @@ Stats_Reduce.o : Stats_Reduce.cpp OnlineVarT.h Parallel.h Stats_Reduce.h
 StringRoutines.o : StringRoutines.cpp CpptrajStdio.h StringRoutines.h
 Structure/Builder.o : Structure/Builder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h GuessAtomHybridization.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/../Parm/../AtomType.h Structure/../Parm/../CmapParmHolder.h Structure/../Parm/../Constants.h Structure/../Parm/../NameType.h Structure/../Parm/../ParameterTypes.h Structure/../Parm/../Parm/ParmEnum.h Structure/../Parm/../TypeNameHolder.h Structure/../Parm/DihedralParmHolder.h Structure/../Parm/ImproperParmHolder.h Structure/../Parm/ParameterSet.h Structure/../Parm/ParmEnum.h Structure/../Parm/ParmHolder.h Structure/Builder.h Structure/Chirality.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 Structure/Chirality.o : Structure/Chirality.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Chirality.h Structure/StructureEnum.h SymbolExporting.h Topology.h TorsionRoutines.h Unit.h Vec3.h
-Structure/Creator.o : Structure/Creator.cpp ArgList.h AssociatedData.h AssociatedData_ResId.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/Creator.h Structure/GenerateConnectivityArrays.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Structure/Creator.o : Structure/Creator.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h DataSet_Parameters.h DataSet_PdbResMap.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h PdbResMapType.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/Creator.h Structure/GenerateConnectivityArrays.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/Disulfide.o : Structure/Disulfide.cpp ArgList.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Disulfide.h Structure/ResStatArray.h Structure/StructureRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Structure/FunctionalGroup.o : Structure/FunctionalGroup.cpp Atom.h AtomMap.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Structure/FxnGroupBuilder.o : Structure/FxnGroupBuilder.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h Structure/FxnGroupBuilder.h Structure/StructureRoutines.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h Unit.h Vec3.h
diff --git a/src/cpptrajfiles b/src/cpptrajfiles
index 2d2058bd0a..da4b52c57c 100644
--- a/src/cpptrajfiles
+++ b/src/cpptrajfiles
@@ -149,7 +149,6 @@ COMMON_SOURCES= \
         Array1D.cpp \
         AssociatedData_Connect.cpp \
         AssociatedData_NOE.cpp \
-        AssociatedData_ResId.cpp \
         Atom.cpp \
         AtomMap.cpp \
         AtomMask.cpp \

From 7571fd73e89776c1cebf5326bc468bf034301597 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 22 Oct 2025 19:29:18 -0400
Subject: [PATCH 1000/1492] Check unit name if aspect is empty

---
 src/Structure/Creator.cpp | 15 ++++++++++-----
 1 file changed, 10 insertions(+), 5 deletions(-)

diff --git a/src/Structure/Creator.cpp b/src/Structure/Creator.cpp
index 7f9dd5cb10..d12aabb470 100644
--- a/src/Structure/Creator.cpp
+++ b/src/Structure/Creator.cpp
@@ -144,16 +144,21 @@ const
   std::string targetUnitName;
   if (pdbResidueMap_ != 0) {
     targetUnitName = pdbResidueMap_->FindUnitName(rname, termType);
-    if (!targetUnitName.empty())
-       mprintf("DEBUG: Found mapped name for '%s' (%s) -> '%s'\n", *rname, Structure::terminalStr(termType), targetUnitName.c_str());
+//    if (!targetUnitName.empty())
+//       mprintf("DEBUG: Found mapped name for '%s' (%s) -> '%s'\n", *rname, Structure::terminalStr(termType), targetUnitName.c_str());
   }
   if (targetUnitName.empty()) {
     targetUnitName = rname.Truncated();
-    mprintf("DEBUG: Target unit name: %s\n", targetUnitName.c_str());
+//    mprintf("DEBUG: Target unit name: %s\n", targetUnitName.c_str());
   }
-  // Residue templates have name in aspect currently.
+  // Most residue templates have name in aspect currently.
+  // Residue templates loaded separately (via a mol2) may just
+  // have name.
   for (Carray::const_iterator it = Templates_.begin(); it != Templates_.end(); ++it) {
-    if ((*it)->Meta().Aspect() == targetUnitName)
+    if ((*it)->Meta().Aspect().empty()) {
+      if ((*it)->Meta().Name() == targetUnitName)
+        Out.push_back( *it );
+    } else if ((*it)->Meta().Aspect() == targetUnitName)
       Out.push_back( *it );
   }
 /*

From f9a5224f2db615601d47caa6a602c16e1ba048e3 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 22 Oct 2025 19:33:11 -0400
Subject: [PATCH 1001/1492] Hide debug info. Print pdb res map in creator

---
 src/DataIO_LeapRC.cpp     | 3 ++-
 src/Structure/Creator.cpp | 4 +++-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index d187a12f4f..3cba81fa0b 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -851,7 +851,8 @@ int DataIO_LeapRC::ReadData(FileName const& fname, DataSetList& dsl, std::string
   }
 
   // DEBUG
-  ((DataSet_PdbResMap*)pdbResidueMap_)->PrintPdbResMap();
+  if (debug_ > 0)
+    ((DataSet_PdbResMap*)pdbResidueMap_)->PrintPdbResMap();
   return 0;
 }
 
diff --git a/src/Structure/Creator.cpp b/src/Structure/Creator.cpp
index d12aabb470..be09282108 100644
--- a/src/Structure/Creator.cpp
+++ b/src/Structure/Creator.cpp
@@ -45,8 +45,10 @@ int Creator::InitCreator(ArgList& argIn, DataSetList const& DSL, int debugIn)
 
   // PDB residue map TODO handle multiple maps?
   pdbResidueMap_ = (DataSet_PdbResMap*)DSL.FindSetOfType( "*", DataSet::PDBRESMAP );
-  if (pdbResidueMap_ != 0)
+  if (pdbResidueMap_ != 0) {
     mprintf("DEBUG: PDB residue map data set: %s\n", pdbResidueMap_->legend());
+    pdbResidueMap_->PrintPdbResMap();
+  }
 
   // Atom scan direction
   std::string atomscandir = argIn.GetStringKey("atomscandir");

From 52203fb8f1be0580e60b0886e7016399ff477931 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 23 Oct 2025 15:36:11 -0400
Subject: [PATCH 1002/1492] Use map to store residue templates

---
 src/Structure/Creator.cpp     | 84 +++++++++++++++++++++++++----------
 src/Structure/Creator.h       |  7 ++-
 src/Structure/structuredepend |  2 +-
 3 files changed, 68 insertions(+), 25 deletions(-)

diff --git a/src/Structure/Creator.cpp b/src/Structure/Creator.cpp
index be09282108..bb9d87733a 100644
--- a/src/Structure/Creator.cpp
+++ b/src/Structure/Creator.cpp
@@ -95,12 +95,13 @@ void Creator::TimingInfo(double total, int indent) const {
 void Creator::UpdateTemplateElements() const {
   if (mainParmSet_ == 0) return;
 
-  for (Carray::const_iterator crd = Templates_.begin(); crd != Templates_.end(); ++crd)
+  for (Carray::const_iterator cit = Templates_.begin(); cit != Templates_.end(); ++cit)
   {
+    DataSet_Coords* crd = cit->second;
     if (debug_ > 0)
-      mprintf("DEBUG: Updating atom elements in '%s'\n", (*crd)->legend());
+      mprintf("DEBUG: Updating atom elements in '%s'\n", crd->legend());
     // Loop over template atoms
-    Topology& templateTop = *((*crd)->TopPtr());
+    Topology& templateTop = *(crd->TopPtr());
     for (int at = 0; at != templateTop.Natom(); at++) {
       Cpptraj::Parm::ParmHolder<AtomType>::const_iterator it;
       if (templateTop[at].HasType()) {
@@ -122,15 +123,21 @@ void Creator::UpdateTemplateElements() const {
 DataSet_Coords* Creator::IdTemplateFromName(std::string const& nameIn)
 const
 {
-  MetaData::SearchString search( nameIn );
-  for (Carray::const_iterator it = Templates_.begin(); it != Templates_.end(); ++it) {
-    if ((*it)->Meta().Match_WildCard(search)) {
-      return *it;
-    }
+  Carray::const_iterator it = Templates_.find( nameIn );
+  if (it == Templates_.end()) {
+    mprintf("Warning: No template found named '%s'\n", nameIn.c_str());
+    return 0;
   }
+  return it->second;
+  //MetaData::SearchString search( nameIn );
+  //for (Carray::const_iterator it = Templates_.begin(); it != Templates_.end(); ++it) {
+  //  if ((*it)->Meta().Match_WildCard(search)) {
+  //    return *it;
+  //  }
+  //}
   // No aspect. Convert to NameType TODO check for truncation
-  NameType rname( nameIn );
-  return IdTemplateFromResname( NameType(nameIn), Cpptraj::Structure::NON_TERMINAL );
+  //NameType rname( nameIn );
+  //return IdTemplateFromResname( NameType(nameIn), Cpptraj::Structure::NON_TERMINAL );
 }
 
 /** Try to identify residue template DataSet from the given residue
@@ -156,13 +163,20 @@ const
   // Most residue templates have name in aspect currently.
   // Residue templates loaded separately (via a mol2) may just
   // have name.
-  for (Carray::const_iterator it = Templates_.begin(); it != Templates_.end(); ++it) {
-    if ((*it)->Meta().Aspect().empty()) {
-      if ((*it)->Meta().Name() == targetUnitName)
-        Out.push_back( *it );
-    } else if ((*it)->Meta().Aspect() == targetUnitName)
-      Out.push_back( *it );
+//  for (Carray::const_iterator it = Templates_.begin(); it != Templates_.end(); ++it) {
+//    if ((*it)->Meta().Aspect().empty()) {
+//      if ((*it)->Meta().Name() == targetUnitName)
+//        Out.push_back( *it );
+//    } else if ((*it)->Meta().Aspect() == targetUnitName)
+//      Out.push_back( *it );
+//  }
+  Carray::const_iterator it = Templates_.find( targetUnitName );
+  if (it == Templates_.end()) {
+    mprintf("Warning: No template found named '%s'\n", targetUnitName.c_str());
+    return 0;
   }
+  return it->second;
+
 /*
   //DataSet_Coords* out = 0;
   if (termType != Cpptraj::Structure::NON_TERMINAL) {
@@ -209,7 +223,7 @@ const
     }
   }
 */
-  if (Out.empty()) return 0;
+/*  if (Out.empty()) return 0;
   if (Out.size() > 1) {
     mprintf("Warning: Multiple templates match '%s':", *rname);
     for (std::vector<DataSet_Coords*>::const_iterator it = Out.begin(); it != Out.end(); ++it)
@@ -218,7 +232,28 @@ const
     mprintf("Warning: Using the last template loaded.\n");
   }
   //return out;
-  return Out.back();
+  return Out.back();*/
+}
+
+/// \return Aspect, or Name if Aspect is empty
+static inline std::string getTemplateName(DataSet* ds)
+{
+  if (ds->Meta().Aspect().empty())
+    return ds->Meta().Name();
+  else
+    return ds->Meta().Aspect();
+}
+
+/** Add coords set as a template */
+void Creator::addCoordsAsTemplate(DataSet_Coords* ds) {
+  std::string templateName = getTemplateName( ds );
+  Carray::iterator unit = Templates_.lower_bound( templateName );
+  if (unit == Templates_.end() || unit->first != templateName) {
+    unit = Templates_.insert( unit, Cpair( templateName, ds ) );
+  } else {
+    mprintf("Warning: Replacing template %s with %s\n", unit->second->legend(), ds->legend());
+    unit->second = ds;
+  }
 }
 
 /** Get templates */
@@ -231,10 +266,12 @@ int Creator::getTemplates(ArgList& argIn, DataSetList const& DSL) {
     DataSetList sets = DSL.SelectGroupSets( "*", DataSet::COORDINATES ); // TODO specific set type for units?
     for (DataSetList::const_iterator it = sets.begin(); it != sets.end(); ++it)
     {
+      DataSet_Coords* ds = static_cast<DataSet_Coords*>( *it );
       // Should only be a single residue FIXME need new set type
-      DataSet_Coords const& ds = static_cast<DataSet_Coords const&>( *(*it) );
-      if ( ds.Top().Nres() == 1 )
-        Templates_.push_back( (DataSet_Coords*)(*it) );
+      if ( ds->Top().Nres() == 1 ) {
+        addCoordsAsTemplate( ds );
+        //Templates_.push_back( (DataSet_Coords*)(*it) );
+      }
     }
   } else {
     while (!lib.empty()) {
@@ -247,7 +284,8 @@ int Creator::getTemplates(ArgList& argIn, DataSetList const& DSL) {
           // Should only be a single residue FIXME need new set type
           //DataSet_Coords const& ds = static_cast<DataSet_Coords const&>( *(*it) );
           //if ( ds.Top().Nres() == 1 )
-            Templates_.push_back( (DataSet_Coords*)(*it) );
+          //  Templates_.push_back( (DataSet_Coords*)(*it) );
+          addCoordsAsTemplate( static_cast<DataSet_Coords*>( *it ) );
         }
       }
       lib = argIn.GetStringKey("lib");
@@ -257,7 +295,7 @@ int Creator::getTemplates(ArgList& argIn, DataSetList const& DSL) {
     mprintf("\t%zu residue templates found:\n", Templates_.size());
     if (debug_ > 0) {
       for (Carray::const_iterator it = Templates_.begin(); it != Templates_.end(); ++it) {
-        mprintf("\t%s", (*it)->legend());
+        mprintf("\t%s", it->second->legend());
 //        AssociatedData* ad = (*it)->GetAssociatedData( AssociatedData::RESID );
 //        if (ad != 0) {
 //          AssociatedData_ResId const& resid = static_cast<AssociatedData_ResId const&>( *ad );
diff --git a/src/Structure/Creator.h b/src/Structure/Creator.h
index 80fe87e446..4ad5a2cf6f 100644
--- a/src/Structure/Creator.h
+++ b/src/Structure/Creator.h
@@ -2,6 +2,7 @@
 #define INC_STRUCTURE_CREATOR_H
 #include <vector>
 #include <string>
+#include <map>
 #include "StructureEnum.h" // TerminalType
 #include "../Timer.h"
 class ArgList;
@@ -15,7 +16,9 @@ namespace Cpptraj {
 namespace Structure {
 /// Used to create a system from individual units
 class Creator {
-    typedef std::vector<DataSet_Coords*> Carray;
+    //typedef std::vector<DataSet_Coords*> Carray;
+    typedef std::pair<std::string, DataSet_Coords*> Cpair;
+    typedef std::map<std::string, DataSet_Coords*> Carray;
     typedef std::vector<DataSet_NameMap*> Narray;
   public:
     /// CONSTRUCTOR
@@ -54,6 +57,8 @@ class Creator {
     int getParameterSets(ArgList&, DataSetList const&);
     /// Update template atom elements from parameter set
     void UpdateTemplateElements() const;
+    /// Add coords set as a template
+    void addCoordsAsTemplate(DataSet_Coords*);
 
     DataSet_Parameters* mainParmSet_; ///< Hold optional parameter set.
     DataSet_PdbResMap* pdbResidueMap_; ///< Hold optional PDB residue map set.
diff --git a/src/Structure/structuredepend b/src/Structure/structuredepend
index e442a529f8..2867c7dbb9 100644
--- a/src/Structure/structuredepend
+++ b/src/Structure/structuredepend
@@ -1,6 +1,6 @@
 Builder.o : Builder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/../AtomType.h ../Parm/../CmapParmHolder.h ../Parm/../Constants.h ../Parm/../NameType.h ../Parm/../ParameterTypes.h ../Parm/../Parm/ParmEnum.h ../Parm/../TypeNameHolder.h ../Parm/DihedralParmHolder.h ../Parm/ImproperParmHolder.h ../Parm/ParameterSet.h ../Parm/ParmEnum.h ../Parm/ParmHolder.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Builder.h Chirality.h GenerateConnectivityArrays.h InternalCoords.h StructureEnum.h Zmatrix.h
 Chirality.o : Chirality.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../Unit.h ../Vec3.h Chirality.h StructureEnum.h
-Creator.o : Creator.cpp ../ArgList.h ../AssociatedData.h ../AssociatedData_ResId.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../DataSet_NameMap.h ../DataSet_Parameters.h ../Dimension.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/../AtomType.h ../Parm/../CmapParmHolder.h ../Parm/../Constants.h ../Parm/../NameType.h ../Parm/../ParameterTypes.h ../Parm/../Parm/ParmEnum.h ../Parm/../TypeNameHolder.h ../Parm/DihedralParmHolder.h ../Parm/ImproperParmHolder.h ../Parm/ParameterSet.h ../Parm/ParmEnum.h ../Parm/ParmHolder.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/StructureEnum.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h Creator.h GenerateConnectivityArrays.h StructureEnum.h
+Creator.o : Creator.cpp ../ArgList.h ../AssociatedData.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../DataSet_NameMap.h ../DataSet_Parameters.h ../DataSet_PdbResMap.h ../Dimension.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/../AtomType.h ../Parm/../CmapParmHolder.h ../Parm/../Constants.h ../Parm/../NameType.h ../Parm/../ParameterTypes.h ../Parm/../Parm/ParmEnum.h ../Parm/../TypeNameHolder.h ../Parm/DihedralParmHolder.h ../Parm/ImproperParmHolder.h ../Parm/ParameterSet.h ../Parm/ParmEnum.h ../Parm/ParmHolder.h ../PdbResMapType.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/StructureEnum.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h Creator.h GenerateConnectivityArrays.h StructureEnum.h
 Disulfide.o : Disulfide.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h Disulfide.h ResStatArray.h StructureRoutines.h
 FunctionalGroup.o : FunctionalGroup.cpp ../Atom.h ../AtomMap.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h FunctionalGroup.h
 FxnGroupBuilder.o : FxnGroupBuilder.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h FunctionalGroup.h FxnGroupBuilder.h StructureRoutines.h Sugar.h SugarToken.h

From 719e8f23ab3c6c7b48b7981ab6b72357301e04e6 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 24 Oct 2025 11:24:13 -0400
Subject: [PATCH 1003/1492] Hide some cmap debug info

---
 src/AmberParamFile.cpp     | 25 ++++++++++++++-----------
 src/AmberParamFile.h       |  4 +++-
 src/CmapParmHolder.cpp     |  5 +++--
 src/CmapParmHolder.h       |  4 ++--
 src/DataIO_AmberFF.cpp     |  4 ++--
 src/DataIO_AmberFrcmod.cpp |  2 +-
 src/Parm/GetParams.cpp     |  5 +++--
 src/Parm/GetParams.h       |  4 ++--
 src/Parm/ParameterSet.cpp  |  6 +++---
 src/Parm/ParameterSet.h    |  2 +-
 10 files changed, 34 insertions(+), 27 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 53a1d7f2e9..45d48b9f3c 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -19,7 +19,7 @@ AmberParamFile::AmberParamFile() :
 {}
 
 /** Set debug level */
-void AmberParamFile::SetDebug(int d) {
+void AmberParamFile::SetAmberParamDebug(int d) {
   debug_ = d;
 }
 
@@ -363,20 +363,23 @@ const
 }
 
 /// \return 1 if problem detected with CMAP term
-static inline int check_cmap(int currentCmapIdx, CmapGridType const& cmap) {
-  mprintf("DEBUG: Cmap %i '%s' (gridSize= %i) %zu res:",
-          currentCmapIdx, cmap.Title().c_str(), cmap.Size(), cmap.ResNames().size());
-  for (std::vector<std::string>::const_iterator it = cmap.ResNames().begin();
+int AmberParamFile::check_cmap(int currentCmapIdx, CmapGridType const& cmap) const {
+  if (debug_ > 0) {
+    mprintf("DEBUG: Cmap %i '%s' (gridSize= %i) %zu res:",
+            currentCmapIdx, cmap.Title().c_str(), cmap.Size(), cmap.ResNames().size());
+    for (std::vector<std::string>::const_iterator it = cmap.ResNames().begin();
                                                 it != cmap.ResNames().end(); ++it)
-    mprintf(" %s", it->c_str());
-  mprintf("\n");
+      mprintf(" %s", it->c_str());
+    mprintf("\n");
+  }
   if (!cmap.CmapIsValid()) {
-    mprinterr("Error: Previous CMAP term is not valid.\n");
+    mprinterr("Error: CMAP term %i '%s' is not valid.\n", currentCmapIdx, cmap.Title().c_str());
     return 1;
   }
   if (!cmap.CmapNresIsValid()) {
-    mprintf("Warning: # expected CMAP %i residue names %i not equal to actual number %zu\n",
+    mprintf("Warning: The number of expected residue names for CMAP %i '%s' (%i) is not equal to the actual number %zu\n",
             currentCmapIdx,
+            cmap.Title().c_str(),
             cmap.NcmapResNames(),
             cmap.ResNames().size());
   }
@@ -411,7 +414,7 @@ const
         if (!currentCmap.empty()) {
           if (currentCmap.AtomNames().empty()) add_cmap_default_atoms( currentCmap );
           if (check_cmap(prm.CMAP().size()+1, currentCmap)) return 1;
-          prm.CMAP().AddParm( currentCmap, true );
+          prm.CMAP().AddParm( currentCmap, true, debug_ );
           currentCmap = CmapGridType();
         }
         int cmapcount = argline.getKeyInt("CMAP_COUNT", -1);
@@ -593,7 +596,7 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname) const
   if (!currentCmap.empty()) {
     if (currentCmap.AtomNames().empty()) add_cmap_default_atoms( currentCmap );
     if (check_cmap(prm.CMAP().size(), currentCmap)) return 1;
-    prm.CMAP().AddParm( currentCmap, true );
+    prm.CMAP().AddParm( currentCmap, true, debug_ );
   }
   // Nonbonds
   if (assign_nb(prm, nbset)) return 1;
diff --git a/src/AmberParamFile.h b/src/AmberParamFile.h
index 91cdabce3c..01429bd2c8 100644
--- a/src/AmberParamFile.h
+++ b/src/AmberParamFile.h
@@ -22,7 +22,7 @@ class AmberParamFile {
     /// Write main Amber FF file
     int WriteParams(ParameterSet&, FileName const&) const;
     /// Set debug level
-    void SetDebug(int);
+    void SetAmberParamDebug(int);
   private:
     static const int MAXSYMLEN;
 
@@ -51,6 +51,8 @@ class AmberParamFile {
     int read_nb_RE(NonbondSet&, const char*) const;
     /// Read LJ 6-12 off-diagonal modifications
     int read_ljedit(Oarray&, const char*) const;
+    /// Check for issues in CMAP section
+    inline int check_cmap(int, CmapGridType const&) const;
     /// Read CMAP section
     int read_cmap(CmapGridType&, ParameterSet&, CmapType&, std::string const&) const;
     /// Assign parameters from NonbondSet to ParameterSet
diff --git a/src/CmapParmHolder.cpp b/src/CmapParmHolder.cpp
index 08b7e17505..ec985b5985 100644
--- a/src/CmapParmHolder.cpp
+++ b/src/CmapParmHolder.cpp
@@ -11,7 +11,7 @@ CmapParmHolder::CmapParmHolder() {}
   * CMAP terms are different in that they are applied via residue name instead
   * of atom type, hence the separate routine.
   */
-Cpptraj::Parm::RetType CmapParmHolder::AddParm(CmapGridType const& cmap1, bool allowUpdate) {
+Cpptraj::Parm::RetType CmapParmHolder::AddParm(CmapGridType const& cmap1, bool allowUpdate, int debugIn) {
   typedef std::vector<std::string> Sarray;
   enum ResMatchType { NO_MATCH = 0, FULL_MATCH, PARTIAL_MATCH };
   // Does a CMAP for any of the residues exist?
@@ -81,7 +81,8 @@ Cpptraj::Parm::RetType CmapParmHolder::AddParm(CmapGridType const& cmap1, bool a
     }
   }
   // NO_MATCH
-  mprintf("DEBUG: CMAP '%s' is a new CMAP.\n", cmap1.Title().c_str());
+  if (debugIn > 0)
+    mprintf("DEBUG: CMAP '%s' is a new CMAP.\n", cmap1.Title().c_str());
   CMAP_.push_back( cmap1 );
   return Cpptraj::Parm::ADDED;
 }
diff --git a/src/CmapParmHolder.h b/src/CmapParmHolder.h
index 70a5757ef7..96545e461a 100644
--- a/src/CmapParmHolder.h
+++ b/src/CmapParmHolder.h
@@ -26,8 +26,8 @@ class CmapParmHolder {
 
     /// \return Modifiable CMAP at index
     
-    /// Add/update cmap term
-    Cpptraj::Parm::RetType AddParm(CmapGridType const&, bool);
+    /// Add/update cmap term; optionally allow update, pass in debug level
+    Cpptraj::Parm::RetType AddParm(CmapGridType const&, bool, int);
   private:
     Carray CMAP_;
 };
diff --git a/src/DataIO_AmberFF.cpp b/src/DataIO_AmberFF.cpp
index a0237cc14e..086e4f6e32 100644
--- a/src/DataIO_AmberFF.cpp
+++ b/src/DataIO_AmberFF.cpp
@@ -54,7 +54,7 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
   DataSet_Parameters& prm = static_cast<DataSet_Parameters&>( *ds ); 
 
   AmberParamFile infile;
-  infile.SetDebug( debug_ );
+  infile.SetAmberParamDebug( debug_ );
   int err = infile.ReadParams(prm, fname, nbsetname_);
   if (err != 0) {
     mprinterr("Error: Could not read '%s'\n", fname.full());
@@ -80,7 +80,7 @@ int DataIO_AmberFF::processWriteArgs(ArgList& argIn)
 int DataIO_AmberFF::WriteData(FileName const& fname, DataSetList const& dsl)
 {
   AmberParamFile outfile;
-  outfile.SetDebug( debug_ );
+  outfile.SetAmberParamDebug( debug_ );
   std::vector<DataSet_Parameters*> toWrite;
   for (DataSetList::const_iterator it = dsl.begin(); it != dsl.end(); ++it)
   {
diff --git a/src/DataIO_AmberFrcmod.cpp b/src/DataIO_AmberFrcmod.cpp
index 8d78125166..9f44e82d11 100644
--- a/src/DataIO_AmberFrcmod.cpp
+++ b/src/DataIO_AmberFrcmod.cpp
@@ -50,7 +50,7 @@ int DataIO_AmberFrcmod::ReadData(FileName const& fname, DataSetList& dsl, std::s
   DataSet_Parameters& prm = static_cast<DataSet_Parameters&>( *ds );
 
   AmberParamFile infile;
-  infile.SetDebug( debug_ );
+  infile.SetAmberParamDebug( debug_ );
   if (infile.ReadFrcmod(prm, fname)) {
     mprinterr("Error: Could not read Amber frcmod file '%s'\n", fname.full());
     return 1;
diff --git a/src/Parm/GetParams.cpp b/src/Parm/GetParams.cpp
index 60622a0f65..2c7b5979ca 100644
--- a/src/Parm/GetParams.cpp
+++ b/src/Parm/GetParams.cpp
@@ -139,6 +139,7 @@ static inline int check_cmap_atom_name(NameType const& n0, NameType const& n1)
 int GetParams::GetCmapParams(CmapParmHolder& cmapParm, CmapArray const& cmapTerms,
                              CmapGridArray const& cmapGrids,
                              std::vector<Atom> const& atoms, std::vector<Residue> const& residues)
+const
 {
   if (cmapGrids.empty() || cmapTerms.empty()) {
     //mprintf("DEBUG: CMAP grids/terms are empty. No parameters to get.\n");
@@ -215,7 +216,7 @@ int GetParams::GetCmapParams(CmapParmHolder& cmapParm, CmapArray const& cmapTerm
         // Set a default title if needed
         if (newGrid.Title().empty())
           newGrid.SetTitle( "CMAP for " + newGrid.ResNames().front() );
-        Cpptraj::Parm::RetType ret = cmapParm.AddParm( newGrid, false );
+        Cpptraj::Parm::RetType ret = cmapParm.AddParm( newGrid, false, debug_ );
         if (ret == Cpptraj::Parm::ERR)
           paramOverwriteWarning("CMAP");
       } // END if adding existing grid to parms
@@ -224,7 +225,7 @@ int GetParams::GetCmapParams(CmapParmHolder& cmapParm, CmapArray const& cmapTerm
     mprintf("CMAP terms have residue/atom info.\n");
     for (unsigned int idx = 0; idx != cmapGrids.size(); idx++) {
       if (addGrid[idx]) {
-        Cpptraj::Parm::RetType ret = cmapParm.AddParm( cmapGrids[idx], false );
+        Cpptraj::Parm::RetType ret = cmapParm.AddParm( cmapGrids[idx], false, debug_ );
         if (ret == Cpptraj::Parm::ERR)
           paramOverwriteWarning("CMAP");
       }
diff --git a/src/Parm/GetParams.h b/src/Parm/GetParams.h
index 49d748b7eb..bef82e5941 100644
--- a/src/Parm/GetParams.h
+++ b/src/Parm/GetParams.h
@@ -54,8 +54,8 @@ class GetParams {
     static inline void GetDihedralParams(DihedralParmHolder&, ImproperParmHolder&,
                                          std::vector<Atom> const&,
                                          DihedralArray const&, DihedralParmArray const&);
-    static inline int GetCmapParams(CmapParmHolder&, CmapArray const&, CmapGridArray const&,
-                                    std::vector<Atom> const&, std::vector<Residue> const&);
+    inline int GetCmapParams(CmapParmHolder&, CmapArray const&, CmapGridArray const&,
+                                    std::vector<Atom> const&, std::vector<Residue> const&) const;
 
     int debug_;
 };
diff --git a/src/Parm/ParameterSet.cpp b/src/Parm/ParameterSet.cpp
index 5555fd971c..447509618b 100644
--- a/src/Parm/ParameterSet.cpp
+++ b/src/Parm/ParameterSet.cpp
@@ -185,11 +185,11 @@ void ParameterSet::Print(CpptrajFile& Out) const {
 }
 
 /** Update/add to CMAP parameters in this set with those from given set. */
-int ParameterSet::updateCmapParams(CmapParmHolder const& cmap1, int verbose) {
+int ParameterSet::updateCmapParams(CmapParmHolder const& cmap1, int debugIn, int verbose) {
   int updateCount = 0;
   for (CmapParmHolder::const_iterator newp = cmap1.begin(); newp != cmap1.end(); ++newp)
   {
-    RetType ret = CMAP_.AddParm( *newp, true );
+    RetType ret = CMAP_.AddParm( *newp, true, debugIn );
     if (ret != ERR) {
       bool print = false;
       if (ret == ADDED) {
@@ -242,7 +242,7 @@ int ParameterSet::UpdateParamSet(ParameterSet const& set1, UpdateCount& uc, int
   // HB LJ 10-12 Pairs
   uc.nHBparamsUpdated_ = UpdateParameters< ParmHolder<HB_ParmType> >(set0.HB(), set1.HB(), "LJ HB 10-12", verbose);
   // CMAP
-  uc.nCmapUpdated_ = updateCmapParams(set1.CMAP(), verbose);
+  uc.nCmapUpdated_ = updateCmapParams(set1.CMAP(), debugIn, verbose);
 
   if (debugIn > 0) set0.Debug("newp.dat");
   return 0;
diff --git a/src/Parm/ParameterSet.h b/src/Parm/ParameterSet.h
index 76a97cf7ff..40674e0b71 100644
--- a/src/Parm/ParameterSet.h
+++ b/src/Parm/ParameterSet.h
@@ -94,7 +94,7 @@ class ParameterSet {
     typedef std::vector<std::string> Sarray;
 
     /// Update cmap parameters
-    int updateCmapParams(CmapParmHolder const&, int);
+    int updateCmapParams(CmapParmHolder const&, int, int);
 
     Sarray name_;                          ///< Parameter set name(s)
     std::string NBname_;                   ///< Nonbond set name

From 416d878a1bb1ceee06a0a11e7f61906e35af7f34 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 24 Oct 2025 11:44:22 -0400
Subject: [PATCH 1004/1492] Remove old pdb res map code. Hide some debug info

---
 src/DataIO_LeapRC.cpp | 157 ++----------------------------------------
 src/DataIO_LeapRC.h   |  10 +--
 2 files changed, 6 insertions(+), 161 deletions(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 3cba81fa0b..f54d1304ff 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -382,68 +382,6 @@ const
   return 0;
 }
 
-/** Find unit among loaded units. */
-/*DataSet* DataIO_LeapRC::findUnit(std::string const& unitName) const {
-  for (DSarray::const_iterator it = units_.begin(); it != units_.end(); ++it)
-  {
-    if ( (*it)->Meta().Aspect() == unitName ) {
-      mprintf("DEBUG: findUnit: Aspect match: %s %s\n", unitName.c_str(), (*it)->legend());
-      return *it;
-    }
-  }
-  for (DSarray::const_iterator it = units_.begin(); it != units_.end(); ++it)
-  {
-    if ( (*it)->Meta().Name() == unitName ) { 
-      mprintf("DEBUG: findUnit: Name match: %s %s\n", unitName.c_str(), (*it)->legend());
-      return *it;
-    }
-  }
-  return 0;
-}*/
-
-/** Associate PDB residue name map with COORDS set. */ // TODO call every time a new unit is loaded?
-/*void DataIO_LeapRC::addPdbResMapToUnit(DataSet_Coords* unit, PdbResMapType const& prm, bool allowUpdate)
-const
-{
-  // Does this unit already have associated ResId?
-  AssociatedData* ad = unit->GetAssociatedData( AssociatedData::RESID );
-  if (ad == 0) {
-    AssociatedData_ResId resid( prm.pdbName_, prm.termType_ );
-    unit->AssociateData( &resid );
-    if (debug_ > 0) {
-      mprintf("DEBUG: Found unit %s", unit->legend());
-      resid.Ainfo();
-      mprintf("\n");
-    }
-  } else if (allowUpdate) {
-    *ad = AssociatedData_ResId( prm.pdbName_, prm.termType_ );
-    mprintf("\tUpdated unit %s resmap. ", unit->legend());
-    ad->Ainfo();
-    mprintf("\n");
-  } else {
-    // TODO check if map is different
-    AssociatedData_ResId const& resid = static_cast<AssociatedData_ResId const&>( *ad );
-    if ( resid.ResName() != prm.pdbName_ || resid.TermType() != prm.termType_) {
-      mprintf("Warning: Unit %s already has resmap. ", unit->legend());
-      ad->Ainfo();
-      mprintf(" New map would be: ");
-      AssociatedData_ResId newResid(prm.pdbName_, prm.termType_);
-      newResid.Ainfo();
-      mprintf("\n");
-    }
-  }
-}*/
-
-/** Associate PDB residue name map with COORDS set, no update allowed. */
-/*void DataIO_LeapRC::addPdbResMapToUnit(DataSet_Coords* unit, PdbResMapType const& prm) const {
-  addPdbResMapToUnit(unit, prm, false);
-}*/
-
-/** Associate PDB residue name map with COORDS set, allow update. */
-/*void DataIO_LeapRC::updatePdbResMapToUnit(DataSet_Coords* unit, PdbResMapType const& prm) const {
-  addPdbResMapToUnit(unit, prm, true);
-}*/
-
 /** LEaP addPdbResMap command. */
 int DataIO_LeapRC::AddPdbResMap(BufferedLine& infile)
 const
@@ -484,29 +422,7 @@ const
             pdbidx = 1;
             unitidx = 2;
           }
-          //if (termType != Cpptraj::Structure::NON_TERMINAL) {
-//            PdbResMapType prm;
-//            prm.termType_ = termType;
-//            prm.pdbName_ = aline[pdbidx];
-//            prm.unitName_ = aline[unitidx];
-//            pdbResMapIn.push_back( prm );
-            ((DataSet_PdbResMap*)pdbResidueMap_)->AddPdbResMap( Cpptraj::PdbResMapType(aline[unitidx], aline[pdbidx], termType) );
-            // Find among loaded units
-            //DataSet* unitSet = findUnit( aline[unitidx] );
-            //if (unitSet == 0) {
-            //  mprintf("Warning: Unit '%s' was not found among loaded units.\n",
-            //          aline[unitidx].c_str());
-            //} else {
-            //  //DataSet_Coords& crd = static_cast<DataSet_Coords&>( *ds );
-            //  AssociatedData_ResId resid( aline[pdbidx], termType );
-            //  unitSet->AssociateData( &resid );
-            //  if (debug_ > 0) {
-            //    mprintf("DEBUG: Found unit %s", unitSet->legend());
-            //    resid.Ainfo();
-            //    mprintf("\n");
-            //  }
-            //}
-          //}
+          ((DataSet_PdbResMap*)pdbResidueMap_)->AddPdbResMap( Cpptraj::PdbResMapType(aline[unitidx], aline[pdbidx], termType) );
           tmp.clear();
         }
       } else {
@@ -817,7 +733,8 @@ int DataIO_LeapRC::ReadData(FileName const& fname, DataSetList& dsl, std::string
     mprinterr("Internal Error: DataIO_LeapRC::ReadData(): Could not allocate leap options data set.\n");
     return 1;
   }
-  mprintf("DEBUG: Leap options set: %s\n", leapopts_->legend());
+  if (debug_ > 0)
+    mprintf("DEBUG: Leap options set: %s\n", leapopts_->legend());
   // Get/allocate pdb residue map
   pdbResidueMap_ = dsl.FindSetOfType( std::string(PDBRESMAPNAME_), DataSet::PDBRESMAP );
   if (pdbResidueMap_ == 0)
@@ -826,7 +743,8 @@ int DataIO_LeapRC::ReadData(FileName const& fname, DataSetList& dsl, std::string
     mprinterr("Internal Error: DataIO_LeapRC::ReadData(): Could not allocate leap PDB residue map data set.\n");
     return 1;
   }
-  mprintf("DEBUG: Leap PDB residue map set: %s\n", pdbResidueMap_->legend());
+  if (debug_ > 0)
+    mprintf("DEBUG: Leap PDB residue map set: %s\n", pdbResidueMap_->legend());
 
   // First, need to determine where the Amber FF files are
   const char* env = getenv("AMBERHOME");
@@ -868,10 +786,6 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
   enum LeapCmdType { LOADAMBERPARAMS = 0, LOADOFF, LOADAMBERPREP, ADDATOMTYPES,
                      ADDPDBRESMAP, ADDPDBATOMMAP, LOADMOL2, LOADPDB, SOURCE,
                      QUIT, SAVEAMBERPARM, ADDPATH, SET, UNKNOWN_CMD };
-  //DataSetList paramDSL;
-  //DataSetList unitDSL;
-  //NHarrayType atomHybridizations;
-  //PdbResMapArray pdbResMap;
   int err = 0;
   const char* ptr = infile.Line();
   // FIXME need to convert to all lowercase for matching commands; leap allows
@@ -923,33 +837,6 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
         err = AddAtomTypes(atomHybridizations_, infile);
       else if (leapcmd == ADDPDBRESMAP) {
         err = AddPdbResMap(infile);
-        //if (err == 0) {
-          // Update units with pdb residue map info
-          //for (DataSetList::const_iterator ds = unitDSL.begin(); ds != paramDSL.end(); ++ds)
-          //{
-          //  if ( (*ds)->Group() == DataSet::COORDINATES ) {
-/*          for (PdbResMapArray::const_iterator it = pdbResMap_.begin();
-                                              it != pdbResMap_.end(); ++it)
-          {
-            // Find the unit in unit DSL
-            DataSet* ds = dsl.CheckForSet( MetaData(dsname, it->unitName_) );
-            if (ds != 0 && ds->Group() == DataSet::COORDINATES) {
-              addPdbResMapToUnit( static_cast<DataSet_Coords*>(ds), *it );
-            }
-            *if (ds == 0) {
-              mprintf("Warning: Unit '%s' was not found among loaded units.\n", it->unitName_.c_str());
-            } else {
-              DataSet_Coords& crd = static_cast<DataSet_Coords&>( *ds );
-              AssociatedData_ResId resid( it->pdbName_, it->termType_ );
-              crd.AssociateData( &resid );
-              if (debug_ > 0) {
-                mprintf("DEBUG: Found unit %s", crd.legend());
-                resid.Ainfo();
-                mprintf("\n");
-              }
-            }*
-          }*/
-        //}
       } else if (leapcmd == ADDPDBATOMMAP)
         err = AddPdbAtomMap(dsname, dsl, infile);
       else if (leapcmd == LOADMOL2)
@@ -1017,15 +904,6 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
             crd1.CopyAssociatedDataFrom( crd0 );
             if (debug_ > 0)
               mprintf("DEBUG: Created unit set %s\n", crd1.legend());
-            // See if there is a PDB residue name map
-//            for (PdbResMapArray::const_iterator it = pdbResMap_.begin();
-//                                                it != pdbResMap_.end(); ++it)
-//            {
-//              if (it->unitName_ == line[0]) {
-//                updatePdbResMapToUnit( &crd1, *it );
-//                break;
-//              }
-//            }
           }
         } else {
           mprintf("Warning: Skipping unhandled LEaP command line: %s\n", ptr);
@@ -1037,31 +915,6 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
   }
   infile.CloseFile();
 
-  // Do any PDB residue mapping
-//  if (!pdbResMap_.empty()) {
-//    for (PdbResMapArray::const_iterator it = pdbResMap_.begin();
-//                                        it != pdbResMap_.end(); ++it)
-//    {
-//      // Find the unit in unit DSL
-//      DataSet* ds = dsl.CheckForSet( MetaData(dsname, it->unitName_) );
-//      if (ds != 0 && ds->Group() == DataSet::COORDINATES) {
-//        addPdbResMapToUnit( static_cast<DataSet_Coords*>(ds), *it );
-//      }
-//      /*if (ds == 0) {
-//        mprintf("Warning: Unit '%s' was not found among loaded units.\n", it->unitName_.c_str());
-//      } else {
-//        DataSet_Coords& crd = static_cast<DataSet_Coords&>( *ds );
-//        AssociatedData_ResId resid( it->pdbName_, it->termType_ );
-//        crd.AssociateData( &resid );
-//        if (debug_ > 0) {
-//          mprintf("DEBUG: Found unit %s", crd.legend());
-//          resid.Ainfo();
-//          mprintf("\n");
-//        }
-//      }*/
-//    }
-//  }
-
   // Add data sets to the main data set list
   //if (addSetsToList(dsl, paramDSL)) return err+1;
 
diff --git a/src/DataIO_LeapRC.h b/src/DataIO_LeapRC.h
index df7a296e14..84748102a1 100644
--- a/src/DataIO_LeapRC.h
+++ b/src/DataIO_LeapRC.h
@@ -2,7 +2,6 @@
 #define INC_DATAIO_LEAPRC_H
 #include "DataIO.h"
 #include "AtomType.h" // AtomType::HybridizationType
-#include "Structure/StructureEnum.h"
 #include <map>
 class BufferedLine;
 /// Read parameters and units from a leap rc file 
@@ -62,14 +61,7 @@ class DataIO_LeapRC : public DataIO {
     DataSet* getUnit(std::string const&, DataSetList const&) const;
     int SaveAmberParm(std::string const&, ArgList&, DataSetList const& dsl) const;
     int Source(FileName const&, DataSetList&, std::string const&);
-    /// Add PDB residue map to COORDS unit
-//    void addPdbResMapToUnit(DataSet_Coords*, PdbResMapType const&, bool) const;
-    /// Add PDB residue map to COORDS unit, no update
-//    void addPdbResMapToUnit(DataSet_Coords*, PdbResMapType const&) const;
-    /// Add PDB residue map to COORDS unit, allow update
-//    void updatePdbResMapToUnit(DataSet_Coords*, PdbResMapType const&) const;
-    /// \return Previously loaded unit set with given name
-    //DataSet* findUnit(std::string const&) const;
+
     /// Used to check if a parm/lib file was already loaded.
     static inline bool check_already_loaded(Sarray const&, std::string const&);
     /// \return either file or Amberhome/dir/file

From 4cea8a886d8c06bc1c5c114cccda10f672c4e3bc Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 24 Oct 2025 11:53:46 -0400
Subject: [PATCH 1005/1492] Hide some cmap debug info

---
 src/Parm/AssignParams.cpp | 60 ++++++++++++++++++++++-----------------
 1 file changed, 34 insertions(+), 26 deletions(-)

diff --git a/src/Parm/AssignParams.cpp b/src/Parm/AssignParams.cpp
index 00cfa0da95..612fd7677b 100644
--- a/src/Parm/AssignParams.cpp
+++ b/src/Parm/AssignParams.cpp
@@ -912,8 +912,10 @@ const
       }
     }
     if (cidx > -1) {
-      mprintf("DEBUG: Potential existing cmap %i found for %s (%li)\n", cidx, topOut.TruncResNameNum(A2.ResNum()).c_str(), cm-cmapTerms.begin());
-      mprintf("DEBUG:\t\t%i - %i - %i - %i - %i %i\n", cm->A1()+1, cm->A2()+1, cm->A3()+1, cm->A4()+1, cm->A5()+1, cidx+1);
+      if (debug_ > 1) {
+        mprintf("DEBUG: Potential existing cmap %i found for %s (%li)\n", cidx, topOut.TruncResNameNum(A2.ResNum()).c_str(), cm-cmapTerms.begin());
+        mprintf("DEBUG:\t\t%i - %i - %i - %i - %i %i\n", cm->A1()+1, cm->A2()+1, cm->A3()+1, cm->A4()+1, cm->A5()+1, cidx+1);
+      }
       cm->SetIdx( cidx );
     }
     // If not already in cmapGrids, check cmapIn
@@ -935,14 +937,16 @@ const
         }
       }
       if (cidx > -1) {
-        mprintf("DEBUG: Potential new cmap %i found for %s (%li)\n", cidx, topOut.TruncResNameNum(A2.ResNum()).c_str(), cm-cmapTerms.begin());
-        mprintf("DEBUG:\t\t%i - %i - %i - %i - %i %i\n", cm->A1()+1, cm->A2()+1, cm->A3()+1, cm->A4()+1, cm->A5()+1, cidx+1);
-        //mprintf("DEBUG:\t\t%s - %s - %s - %s - %s\n",
-        //        AtomMaskName(dih->A1()).c_str(),
-        //        AtomMaskName(dih->A2()).c_str(),
-        //        AtomMaskName(dih->A3()).c_str(),
-        //        AtomMaskName(dih->A4()).c_str(),
-        //        AtomMaskName(a5).c_str());
+        if (debug_ > 1) {
+          mprintf("DEBUG: Potential new cmap %i found for %s (%li)\n", cidx, topOut.TruncResNameNum(A2.ResNum()).c_str(), cm-cmapTerms.begin());
+          mprintf("DEBUG:\t\t%i - %i - %i - %i - %i %i\n", cm->A1()+1, cm->A2()+1, cm->A3()+1, cm->A4()+1, cm->A5()+1, cidx+1);
+          //mprintf("DEBUG:\t\t%s - %s - %s - %s - %s\n",
+          //        AtomMaskName(dih->A1()).c_str(),
+          //        AtomMaskName(dih->A2()).c_str(),
+          //        AtomMaskName(dih->A3()).c_str(),
+          //        AtomMaskName(dih->A4()).c_str(),
+          //        AtomMaskName(a5).c_str());
+        }
         cm->SetIdx( cidx );
       }
     }
@@ -992,14 +996,16 @@ const
       }
     }
     if (cidx > -1) {
-      mprintf("DEBUG: Potential existing cmap %i found for %s (%li)\n", cidx, topOut.TruncResNameNum(A2.ResNum()).c_str(), dih-allDih.begin());
-      mprintf("DEBUG:\t\t%i - %i - %i - %i - %i %i\n", dih->A1()+1, dih->A2()+1, dih->A3()+1, dih->A4()+1, a5+1, cidx+1);
-//      mprintf("DEBUG:\t\t%s - %s - %s - %s - %s\n",
-//              AtomMaskName(dih->A1()).c_str(),
-//              AtomMaskName(dih->A2()).c_str(),
-//              AtomMaskName(dih->A3()).c_str(),
-//              AtomMaskName(dih->A4()).c_str(),
-//              AtomMaskName(a5).c_str());
+      if (debug_ > 1) {
+        mprintf("DEBUG: Potential existing cmap %i found for %s (%li)\n", cidx, topOut.TruncResNameNum(A2.ResNum()).c_str(), dih-allDih.begin());
+        mprintf("DEBUG:\t\t%i - %i - %i - %i - %i %i\n", dih->A1()+1, dih->A2()+1, dih->A3()+1, dih->A4()+1, a5+1, cidx+1);
+//        mprintf("DEBUG:\t\t%s - %s - %s - %s - %s\n",
+//                AtomMaskName(dih->A1()).c_str(),
+//                AtomMaskName(dih->A2()).c_str(),
+//                AtomMaskName(dih->A3()).c_str(),
+//                AtomMaskName(dih->A4()).c_str(),
+//                AtomMaskName(a5).c_str());
+      }
       cmapTerms.push_back( CmapType(dih->A1(), dih->A2(), dih->A3(), dih->A4(), a5, cidx) );
     }
     // If not already in cmapGrids, check cmapIn
@@ -1023,14 +1029,16 @@ const
         }
       }
       if (cidx > -1) {
-        mprintf("DEBUG: Potential new cmap %i found for %s (%li)\n", cidx, topOut.TruncResNameNum(A2.ResNum()).c_str(), dih-allDih.begin());
-        mprintf("DEBUG:\t\t%i - %i - %i - %i - %i %i\n", dih->A1()+1, dih->A2()+1, dih->A3()+1, dih->A4()+1, a5+1, cidx+1);
-      //mprintf("DEBUG:\t\t%s - %s - %s - %s - %s\n",
-      //        AtomMaskName(dih->A1()).c_str(),
-      //        AtomMaskName(dih->A2()).c_str(),
-      //        AtomMaskName(dih->A3()).c_str(),
-      //        AtomMaskName(dih->A4()).c_str(),
-      //        AtomMaskName(a5).c_str());
+        if (debug_ > 1) {
+          mprintf("DEBUG: Potential new cmap %i found for %s (%li)\n", cidx, topOut.TruncResNameNum(A2.ResNum()).c_str(), dih-allDih.begin());
+          mprintf("DEBUG:\t\t%i - %i - %i - %i - %i %i\n", dih->A1()+1, dih->A2()+1, dih->A3()+1, dih->A4()+1, a5+1, cidx+1);
+        //mprintf("DEBUG:\t\t%s - %s - %s - %s - %s\n",
+        //        AtomMaskName(dih->A1()).c_str(),
+        //        AtomMaskName(dih->A2()).c_str(),
+        //        AtomMaskName(dih->A3()).c_str(),
+        //        AtomMaskName(dih->A4()).c_str(),
+        //        AtomMaskName(a5).c_str());
+        }
         cmapTerms.push_back( CmapType(dih->A1(), dih->A2(), dih->A3(), dih->A4(), a5, cidx) );
       }
     }

From 6dda0c14623930173bc3f18e754a0556ba512196 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 24 Oct 2025 12:00:57 -0400
Subject: [PATCH 1006/1492] Hide some cmap debug info

---
 src/Parm/AssignParams.cpp | 55 +++++++++++----------------------------
 1 file changed, 15 insertions(+), 40 deletions(-)

diff --git a/src/Parm/AssignParams.cpp b/src/Parm/AssignParams.cpp
index 612fd7677b..83c3283c66 100644
--- a/src/Parm/AssignParams.cpp
+++ b/src/Parm/AssignParams.cpp
@@ -844,11 +844,14 @@ int AssignParams::remap_cmap_indices(Topology const& topOut,
                                  CmapParmHolder const& cmapIn)
 const
 {
-  mprintf("DEBUG: Cmap parameter indices:\n");
-  for (unsigned int idx = 0; idx < originalCmapIndices.size(); idx++)
-    mprintf("DEBUG:\t\tCurrent idx=%i  Actual idx=%u\n", originalCmapIndices[idx], idx);
+  if (debug_ > 0) {
+    mprintf("DEBUG: Cmap parameter indices:\n");
+    for (unsigned int idx = 0; idx < originalCmapIndices.size(); idx++)
+      mprintf("DEBUG:\t\tCurrent idx=%i  Actual idx=%u\n", originalCmapIndices[idx], idx);
+  }
   if (originalCmapIndices.empty()) {
-    mprintf("DEBUG: No CMAP indices in %s\n", topOut.c_str());
+    if (debug_ > 0)
+      mprintf("DEBUG: No CMAP indices in %s\n", topOut.c_str());
     return 0;
   }
   std::sort(originalCmapIndices.begin(), originalCmapIndices.end());
@@ -857,14 +860,17 @@ const
   // and create map from assigned index to new index.
   cmapGrids.reserve( originalCmapIndices.size() );
   for (unsigned int idx = 0; idx < originalCmapIndices.size(); idx++) {
-    mprintf("DEBUG: Will change cmap parameter index %i to %u\n",
-            originalCmapIndices[idx]+1, idx+1);
+    if (debug_ > 0)
+      mprintf("DEBUG: Will change cmap parameter index %i to %u\n",
+              originalCmapIndices[idx]+1, idx+1);
     currentToNew[ originalCmapIndices[idx] ] = idx;
     cmapGrids.push_back( cmapIn[ originalCmapIndices[idx] ] );
   }
-  mprintf("DEBUG: Assigned CMAP parameters:\n");
-  for (CmapGridArray::const_iterator it = cmapGrids.begin(); it != cmapGrids.end(); ++it)
-    mprintf("DEBUG:\t\t%li : %s\n", it-cmapGrids.begin(), it->Title().c_str());
+  if (debug_ > 0) {
+    mprintf("DEBUG: Assigned CMAP parameters:\n");
+    for (CmapGridArray::const_iterator it = cmapGrids.begin(); it != cmapGrids.end(); ++it)
+      mprintf("DEBUG:\t\t%li : %s\n", it-cmapGrids.begin(), it->Title().c_str());
+  }
   // Renumber the parameter indices
   for (CmapArray::iterator it = cmapTerms.begin(); it != cmapTerms.end(); ++it) {
     int newIdx = currentToNew[ it->Idx() ];
@@ -1044,37 +1050,6 @@ const
     }
   } // END loop over dihedrals
   return remap_cmap_indices(topOut, originalCmapIndices, cmapGrids, cmapTerms, cmapIn);
-/*  mprintf("DEBUG: Cmap parameter indices:\n");
-  for (unsigned int idx = 0; idx < originalCmapIndices.size(); idx++)
-    mprintf("DEBUG:\t\tCurrent idx=%i  Actual idx=%u\n", originalCmapIndices[idx], idx);
-  if (originalCmapIndices.empty()) {
-    mprintf("DEBUG: No CMAP indices in %s\n", c_str());
-    return 0;
-  }
-  std::sort(originalCmapIndices.begin(), originalCmapIndices.end());
-  std::vector<int> currentToNew(cmapIn.size(), -1);
-  // Add the grid terms in original parameter file order
-  // and create map from assigned index to new index.
-  cmapGrids.reserve( originalCmapIndices.size() );
-  for (unsigned int idx = 0; idx < originalCmapIndices.size(); idx++) {
-    mprintf("DEBUG: Will change cmap parameter index %i to %u\n",
-            originalCmapIndices[idx]+1, idx+1);
-    currentToNew[ originalCmapIndices[idx] ] = idx;
-    cmapGrids.push_back( cmapIn[ originalCmapIndices[idx] ] );
-  }
-  mprintf("DEBUG: Assigned CMAP parameters:\n");
-  for (CmapGridArray::const_iterator it = cmapGrids.begin(); it != cmapGrids.end(); ++it)
-    mprintf("DEBUG:\t\t%li : %s\n", it-cmapGrids.begin(), it->Title().c_str());
-  // Renumber the parameter indices
-  for (CmapArray::iterator it = cmapTerms.begin(); it != cmapTerms.end(); ++it) {
-    int newIdx = currentToNew[ it->Idx() ];
-    if (newIdx < 0) {
-      mprinterr("Internal Error: CMAP term index is not mapped.\n");
-      return 1;
-    }
-    it->SetIdx( newIdx );
-  }
-  return 0;*/
 }
 
 /** Add to bond arrays but do not update atom connectivity. Used

From 397a3be33acf635dd1a4cc9d5a525f2893a55c27 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 24 Oct 2025 12:16:20 -0400
Subject: [PATCH 1007/1492] Hide some debug info. To be more consistent with
 how lib files are loaded, use the COORDS DataSet type instead of REF_FRAME

---
 src/DataIO_AmberPrep.cpp  | 2 +-
 src/Structure/Zmatrix.cpp | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/DataIO_AmberPrep.cpp b/src/DataIO_AmberPrep.cpp
index 34efa0d110..984d95c6de 100644
--- a/src/DataIO_AmberPrep.cpp
+++ b/src/DataIO_AmberPrep.cpp
@@ -383,7 +383,7 @@ int DataIO_AmberPrep::readAmberPrep(BufferedLine& infile, DataSetList& dsl, std:
     zmatrix.print();
   // Create COORDS set
   //ds = dsl.AddSet( DataSet::REF_FRAME, MetaData(dsname, "crd") );
-  DataSet* ds = dsl.AddSet( DataSet::REF_FRAME, MetaData(dsname, resName) );
+  DataSet* ds = dsl.AddSet( DataSet::COORDS, MetaData(dsname, resName) );
   if (ds == 0) {
     mprinterr("Error: Could not create coordinates for prep.\n");
     return 1;
diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index e50ec3227f..b06d9257de 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -1134,7 +1134,7 @@ int Zmatrix::SetToFrame(Frame& frameOut, Barray& hasPosition) const {
       }
     }*/
     if (icIdx < 0) {
-      mprintf("DEBUG: Could not find complete IC yet.\n");
+      if (debug_ > 0) mprintf("DEBUG: Could not find complete IC yet.\n");
       ++at_with_unset_pos;
       if (at_with_unset_pos == positionsToSet.end()) {
         mprinterr("Error: Could not find next IC to use.\n");

From 7ea11682028ee7d7b4bf7d571bfb573c5de97bd9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 24 Oct 2025 12:31:30 -0400
Subject: [PATCH 1008/1492] Base the actual leap command on all non-comment
 characters

---
 src/DataIO_LeapRC.cpp | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index f54d1304ff..49e4823e15 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -791,18 +791,26 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
   // FIXME need to convert to all lowercase for matching commands; leap allows
   //       mixed case
   while (ptr != 0) {
+    // Use lineBuf to store all non-comment characters
+    std::string lineBuf;
     if (ptr[0] != '\0' && ptr[0] != '#') {
       // Note if this line contains an equals sign.
       bool has_equals = false;
       for (const char* p = ptr; *p != '\0'; ++p) {
         if (*p == '=') {
           has_equals = true;
+          //break;
+        } else if (*p == '#' && p != ptr && *(p-1) != '\\') {
+          // Ignore comments
           break;
         }
+        lineBuf += *p;
       }
 
-      ArgList line( ptr, " =\t" );
+      //ArgList line( ptr, " =\t" );
+      ArgList line( lineBuf, " =\t" );
       mprintf("\tLEAP> %s\n", ptr);
+      //line.PrintDebug(); // DEBUG
 
       LeapCmdType leapcmd = UNKNOWN_CMD;
       // Look through all args, lowercase, for recognized commands.

From a6b001a6c9839919ba319ace36ba7440d987fa82 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 24 Oct 2025 12:47:39 -0400
Subject: [PATCH 1009/1492] Do not overwrite atom type hybridization if the
 incoming type does not have it set

---
 src/AtomType.h | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/AtomType.h b/src/AtomType.h
index d7fa8479cb..e25b408fc0 100644
--- a/src/AtomType.h
+++ b/src/AtomType.h
@@ -69,7 +69,7 @@ class AtomType {
     void SetEltStr(const char* elt) { elt_[0] = elt[0]; elt_[1] = elt[1]; }
     /// \return data size  (2 double for LJparmType)
     static size_t DataSize() { return (4*sizeof(double)) + sizeof(int); }
-    /// Assign atom type. Do not overwrite LJ params if incoming type does not have them set.
+    /// Assign atom type. Do not overwrite LJ params/hybridization if incoming type does not have them set.
     AtomType& operator=(AtomType const& rhs) {
       if (this == &rhs) return *this;
       //mprintf("DEBUG: Assign elt %c%c oldHasLj=%i oldR=%f newHasLj=%i newR=%f\n", elt_[0], elt_[1], (int)hasLJ_, lj_.Radius(), (int)rhs.hasLJ_, rhs.lj_.Radius());
@@ -79,7 +79,8 @@ class AtomType {
       mass_ = rhs.mass_;
       polarizability_ = rhs.polarizability_;
       oidx_ = rhs.oidx_;
-      hybrid_ = rhs.hybrid_;
+      if (rhs.hybrid_ != UNKNOWN_HYBRIDIZATION)
+        hybrid_ = rhs.hybrid_;
       elt_[0] = rhs.elt_[0];
       elt_[1] = rhs.elt_[1];
       //elt_[2] = rhs.elt_[2];

From a7bfc1d7ab56a0045de29a9226816c570ac89bdc Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 24 Oct 2025 13:04:55 -0400
Subject: [PATCH 1010/1492] Hide more debug info. Only print the entire sugar
 mask if debug level is set.

---
 src/Exec_Build.cpp             | 17 ++++++++++-------
 src/Structure/Creator.cpp      |  6 ++++--
 src/Structure/SugarBuilder.cpp | 12 +++++++-----
 3 files changed, 21 insertions(+), 14 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index a03aacff05..41ae1e3202 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -193,7 +193,8 @@ const
       // Save the head and tail atoms
       AssociatedData* ad = resTemplate->GetAssociatedData(AssociatedData::CONNECT);
       if (ad == 0) {
-        mprintf("Warning: Unit '%s' does not have CONNECT data.\n", resTemplate->legend());
+        if (debug_ > 0)
+          mprintf("DEBUG: Unit '%s' does not have CONNECT data.\n", resTemplate->legend());
         resHeadAtoms.push_back( -1 );
         resTailAtoms.push_back( -1 );
       } else {
@@ -524,9 +525,10 @@ const
           ResidueConnections[ra0.first].push_back( ra1.first );
           ResidueConnections[ra1.first].push_back( ra0.first );
         } else {
-          mprintf("Warning: Detected non-template bond %s - %s; not adding it.\n",
-                  topOut.AtomMaskName(at0).c_str(),
-                  topOut.AtomMaskName(at1).c_str());
+          if (debug_ > 0)
+            mprintf("DEBUG: Detected non-template bond %s - %s; not adding it.\n",
+                    topOut.AtomMaskName(at0).c_str(),
+                    topOut.AtomMaskName(at1).c_str());
         }
       }
     } //else
@@ -728,9 +730,10 @@ const
     // Get the original atom name and residue number
     Atom const& original_A1 = topIn[bnd->A1()];
     Atom const& original_A2 = topIn[bnd->A2()];
-    mprintf("DEBUG: Original bond atoms %i (%s) %i (%s)\n",
-            bnd->A1()+1, topIn.AtomMaskName(bnd->A1()).c_str(),
-            bnd->A2()+1, topIn.AtomMaskName(bnd->A2()).c_str());
+    if (debug_ > 0)
+      mprintf("DEBUG: Original bond atoms %i (%s) %i (%s)\n",
+              bnd->A1()+1, topIn.AtomMaskName(bnd->A1()).c_str(),
+              bnd->A2()+1, topIn.AtomMaskName(bnd->A2()).c_str());
     // Find the atoms in the new topology
     int a1 = topOut.FindAtomInResidue( original_A1.ResNum(), original_A1.Name() );
     if (a1 < 0) {
diff --git a/src/Structure/Creator.cpp b/src/Structure/Creator.cpp
index bb9d87733a..c59ba89117 100644
--- a/src/Structure/Creator.cpp
+++ b/src/Structure/Creator.cpp
@@ -46,8 +46,10 @@ int Creator::InitCreator(ArgList& argIn, DataSetList const& DSL, int debugIn)
   // PDB residue map TODO handle multiple maps?
   pdbResidueMap_ = (DataSet_PdbResMap*)DSL.FindSetOfType( "*", DataSet::PDBRESMAP );
   if (pdbResidueMap_ != 0) {
-    mprintf("DEBUG: PDB residue map data set: %s\n", pdbResidueMap_->legend());
-    pdbResidueMap_->PrintPdbResMap();
+    if (debug_ > 0) {
+      mprintf("DEBUG: PDB residue map data set: %s\n", pdbResidueMap_->legend());
+      pdbResidueMap_->PrintPdbResMap();
+    }
   }
 
   // Atom scan direction
diff --git a/src/Structure/SugarBuilder.cpp b/src/Structure/SugarBuilder.cpp
index fc5f6335bd..46e359628c 100644
--- a/src/Structure/SugarBuilder.cpp
+++ b/src/Structure/SugarBuilder.cpp
@@ -1823,12 +1823,13 @@ int SugarBuilder::FixSugarsStructure(Topology& topIn, Frame& frameIn,
 
   Sugars_.clear();
   AtomMask sugarMask(sugarmaskstr_);
-  mprintf("\tLooking for sugars selected by '%s'\n", sugarMask.MaskString());
+  if (debug_ > 0)
+    mprintf("DEBUG:\tLooking for sugars selected by '%s'\n", sugarMask.MaskString());
   if (topIn.SetupIntegerMask( sugarMask )) return 1;
   //sugarMask.MaskInfo();
   mprintf("\tSelected %i sugar atoms.\n", sugarMask.Nselected());
   if (sugarMask.None()) {
-    mprintf("Warning: No sugar atoms selected by %s\n", sugarMask.MaskString());
+    //mprintf("Warning: No sugar atoms selected by %s\n", sugarMask.MaskString());
     return 0;
   }
   // Cache residue distances if we will be looking for linkages
@@ -1932,9 +1933,10 @@ int SugarBuilder::PrepareSugars(bool errorsAreFatal,
   if (topIn.SetupIntegerMask( sugarMask )) return 1;
   //sugarMask.MaskInfo();
   mprintf("\t%i sugar atoms selected in %zu residues.\n", sugarMask.Nselected(), Sugars_.size());
-  if (sugarMask.None())
-    mprintf("Warning: No sugar atoms selected by %s\n", sugarMask.MaskString());
-  else {
+  if (sugarMask.None()) {
+    if (debug_ > 0)
+      mprintf("DEBUG: No sugar atoms selected by %s\n", sugarMask.MaskString());
+  } else {
     CharMask cmask( sugarMask.ConvertToCharMask(), sugarMask.Nselected() );
     if (debug_ > 0) {
       for (std::vector<Sugar>::const_iterator sugar = Sugars_.begin();

From b54c68d57590c4f59b633f1abc3dcd5bff5f8c23 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 24 Oct 2025 13:15:50 -0400
Subject: [PATCH 1011/1492] Hide more debug info. Put structure timing before
 param assign timing to make all timing easier to look at

---
 src/Exec_Build.cpp        | 2 +-
 src/Parm/AssignParams.cpp | 7 ++++---
 src/Structure/Creator.cpp | 2 +-
 3 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 41ae1e3202..7c4ff6d90d 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -1150,9 +1150,9 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, in
   t_disulfide_.WriteTiming    (2, "Disulfide detection :", t_total_.Total());
   t_sugar_.WriteTiming        (2, "Sugar preparation   :", t_total_.Total());
   t_fill_.WriteTiming         (2, "Fill missing atoms  :", t_total_.Total());
+  t_check_.WriteTiming        (2, "Structure check     :", t_total_.Total());
   t_assign_.WriteTiming       (2, "Param./Top. gen.    :", t_total_.Total());
   AP.WriteAssignTiming(3, t_assign_.Total());
-  t_check_.WriteTiming        (2, "Structure check     :", t_total_.Total());
 
   return ret;
 }
diff --git a/src/Parm/AssignParams.cpp b/src/Parm/AssignParams.cpp
index 83c3283c66..13e75dc02a 100644
--- a/src/Parm/AssignParams.cpp
+++ b/src/Parm/AssignParams.cpp
@@ -409,9 +409,10 @@ const
             }
             if (new_wildcards < n_wildcards) {
               // More specific improper was found.
-              mprintf("DEBUG: A more specific improper was found for %2s %2s %2s %2s (%2s %2s %2s %2s)\n",
-                      *(impit->first[0]), *(impit->first[1]), *(impit->first[2]), *(impit->first[3]),
-                      *(moreSpecificImpit->first[0]), *(moreSpecificImpit->first[1]), *(moreSpecificImpit->first[2]), *(moreSpecificImpit->first[3]));
+              if (debug_ > 0)
+                mprintf("DEBUG: A more specific improper was found for %2s %2s %2s %2s (%2s %2s %2s %2s)\n",
+                        *(impit->first[0]), *(impit->first[1]), *(impit->first[2]), *(impit->first[3]),
+                        *(moreSpecificImpit->first[0]), *(moreSpecificImpit->first[1]), *(moreSpecificImpit->first[2]), *(moreSpecificImpit->first[3]));
               is_new_improper = true;
               reordered = newReordered;
               mydih = newdih;
diff --git a/src/Structure/Creator.cpp b/src/Structure/Creator.cpp
index c59ba89117..4629260e9b 100644
--- a/src/Structure/Creator.cpp
+++ b/src/Structure/Creator.cpp
@@ -346,7 +346,7 @@ int Creator::getParameterSets(ArgList& argIn, DataSetList const& DSL) {
   //  return CpptrajState::ERR;
   //}
   if (!ParamSets.empty()) {
-    mprintf("\tParameter sets:\n");
+    mprintf("\tParameter sets:\n"); // TODO put these names in the final combined parameter set
     for (Parray::const_iterator it = ParamSets.begin(); it != ParamSets.end(); ++it)
       mprintf("\t  %s\n", (*it)->legend());
 

From 43473e4dc7f79b163965f0d614eb1146b1735239 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 24 Oct 2025 16:05:24 -0400
Subject: [PATCH 1012/1492] Change how debug info is printed.

---
 src/Structure/Builder.cpp | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index ee4678be07..1191928f18 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -2069,12 +2069,15 @@ const
         }
       }
       if (!has_rnum) {
-        if (debug_ > 0) mprintf("DEBUG: Need to build for residue %s\n", topIn.TruncResNameNum(rnum).c_str());
         residues.push_back( topIn.Res(rnum) );
         Rnums.push_back(rnum);
       }
     }
   }
+  if (!Rnums.empty() && debug_ > 0) {
+    for (std::vector<int>::const_iterator it = Rnums.begin(); it != Rnums.end(); ++it)
+      mprintf("DEBUG: Need to build for residue %s\n", topIn.TruncResNameNum(*it).c_str());
+  }
   return residues;
 } 
 

From 3c8530a1d1dc1e11e2ea4c35da6dedf0d4aa2537 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 24 Oct 2025 16:13:40 -0400
Subject: [PATCH 1013/1492] When looking at residues from internals, look at
 angles and bonds as well

---
 src/Structure/Builder.cpp | 37 +++++++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 1191928f18..d59635de16 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -2054,6 +2054,7 @@ std::vector<Residue> Builder::residuesThatNeedPositions(Topology const& topIn,
                                                         Barray const& hasPosition)
 const
 {
+  // FIXME does this routine need to be more efficient? Use std::set?
   std::vector<Residue> residues;
   std::vector<int> Rnums;
   for (Tarray::const_iterator dih = internalTorsions_.begin();
@@ -2074,6 +2075,42 @@ const
       }
     }
   }
+  for (Aarray::const_iterator ang = internalAngles_.begin();
+                              ang != internalAngles_.end(); ++ang)
+  {
+    if (!hasPosition[ang->AtI()]) {
+      int rnum = topIn[ang->AtI()].ResNum();
+      bool has_rnum = false;
+      for (std::vector<int>::const_iterator it = Rnums.begin(); it != Rnums.end(); ++it) {
+        if (*it == rnum) {
+          has_rnum = true;
+          break;
+        }
+      }
+      if (!has_rnum) {
+        residues.push_back( topIn.Res(rnum) );
+        Rnums.push_back(rnum);
+      }
+    }
+  }
+  for (Larray::const_iterator bnd = internalBonds_.begin();
+                              bnd != internalBonds_.end(); ++bnd)
+  {
+    if (!hasPosition[bnd->AtI()]) {
+      int rnum = topIn[bnd->AtI()].ResNum();
+      bool has_rnum = false;
+      for (std::vector<int>::const_iterator it = Rnums.begin(); it != Rnums.end(); ++it) {
+        if (*it == rnum) {
+          has_rnum = true;
+          break;
+        }
+      }
+      if (!has_rnum) {
+        residues.push_back( topIn.Res(rnum) );
+        Rnums.push_back(rnum);
+      }
+    }
+  }
   if (!Rnums.empty() && debug_ > 0) {
     for (std::vector<int>::const_iterator it = Rnums.begin(); it != Rnums.end(); ++it)
       mprintf("DEBUG: Need to build for residue %s\n", topIn.TruncResNameNum(*it).c_str());

From b1f8d9d9e5d3df52c05213c21fafdba7c2fb8470 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 24 Oct 2025 23:22:51 -0400
Subject: [PATCH 1014/1492] Start implementing building coords from two angles

---
 src/Structure/Builder.cpp | 81 ++++++++++++++++++++++++++++++++++++++-
 src/Structure/Builder.h   |  3 ++
 2 files changed, 82 insertions(+), 2 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index d59635de16..d59ca15b6f 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1933,6 +1933,53 @@ Builder::AtomIC Builder::getInternalCoordsForAtom(int at, int idx, Barray const&
   return atomIC;
 }
 
+/** Build atom using two angles. */
+int Builder::buildCoordsFromTwoAngles(int at, InternalAngle const& Ang1, InternalAngle const& Ang2, InternalBond const& Bnd,
+                                      Frame const& frameOut, Topology const& topIn, Barray const& hasPosition)
+const
+{
+  int aAtomA, aAtomB, aAtomC;
+  if (at == Ang1.AtI()) {
+    aAtomC = Ang1.AtJ();
+    aAtomA = Ang1.AtK();
+  } else {
+    aAtomC = Ang1.AtJ();
+    aAtomA = Ang1.AtI();
+  }
+  if (at == Ang2.AtI())
+    aAtomB = Ang2.AtK();
+  else
+    aAtomB = Ang2.AtI();
+  Vec3 vAtomC = Vec3( frameOut.XYZ(aAtomC) );
+  Vec3 vAtomA = Vec3( frameOut.XYZ(aAtomA) );
+  Vec3 vAtomB = Vec3( frameOut.XYZ(aAtomB) );
+
+  //if (debug_ > 1) {
+    mprintf("Building atom %s using two angles\n", topIn.LeapName(at).c_str());
+    mprintf("Using %s - %s - %s and %s - %s - %s\n",
+            topIn.LeapName(Ang1.AtI()).c_str(),
+            topIn.LeapName(Ang1.AtJ()).c_str(),
+            topIn.LeapName(Ang1.AtK()).c_str(),
+            topIn.LeapName(Ang2.AtI()).c_str(),
+            topIn.LeapName(Ang2.AtJ()).c_str(),
+            topIn.LeapName(Ang2.AtK()).c_str());
+    mprintf("Using first-center-second %s - %s - %s\n",
+            topIn.LeapName(aAtomA).c_str(),
+            topIn.LeapName(aAtomC).c_str(),
+            topIn.LeapName(aAtomB).c_str());
+    mprintf("AngleA  = %f\n", Ang1.ThetaVal()*Constants::RADDEG );
+    mprintf("AngleB  = %f\n", Ang2.ThetaVal()*Constants::RADDEG );
+    mprintf("Bond    = %f\n", Bnd.DistVal() );
+  //}
+  double dChi = 0.0;
+  int retVal = determineChirality( dChi, aAtomC, frameOut, topIn, hasPosition );
+  if (retVal != 0)
+    mprinterr("Error: Could not determine chirality for %s\n", topIn.LeapName(aAtomC).c_str());
+  else
+    mprintf("Got EXTERNAL chirality: %f\n", dChi );
+  return 0;
+}
+
 /** Build coordinates for an atom from internals.
   * \return 1 if atom was built, 0 otherwise.
   */
@@ -1963,7 +2010,8 @@ const
   InternalAngle a1, a2;
   InternalBond b1;
   if (getTwoAnglesFromInternals(a1, a2, b1, at, hasPosition)) {
-    //if (debug_ > 1) {
+    buildCoordsFromTwoAngles(at, a1, a2, b1, frameOut, topIn, hasPosition);
+/*    //if (debug_ > 1) {
       mprintf("Building atom %s using two angles\n", topIn.LeapName(at).c_str());
       mprintf("Using %s - %s - %s and %s - %s - %s\n",
                   topIn.LeapName(a1.AtI()).c_str(), topIn.LeapName(a1.AtJ()).c_str(), topIn.LeapName(a1.AtK()).c_str(),
@@ -1971,7 +2019,7 @@ const
       mprintf("AngleA  = %f\n", a1.ThetaVal()*Constants::RADDEG );
       mprintf("AngleB  = %f\n", a2.ThetaVal()*Constants::RADDEG );
       mprintf("Bond    = %f\n", b1.DistVal() );
-    //}
+    //}*/
     //frameOut.SetXYZ( ic.AtI(), posI );
     // return 1;
     // FIXME actually build
@@ -2156,6 +2204,25 @@ const
       built_an_atom = true;
     } else if (currentBuildAtom.Priority() == 1) {
       // FIXME need to implement
+      buildCoordsFromTwoAngles(at, currentBuildAtom.A1(), currentBuildAtom.A2(), currentBuildAtom.B1(),
+                               frameOut, topIn, hasPosition);
+/*
+      int aAtomA, aAtomB, aAtomC;
+      if (at == currentBuildAtom.A1().AtI()) {
+        aAtomC = currentBuildAtom.A1().AtJ();
+        aAtomA = currentBuildAtom.A1().AtK();
+      } else {
+        aAtomC = currentBuildAtom.A1().AtJ();
+        aAtomA = currentBuildAtom.A1().AtI();
+      }
+      if (at == currentBuildAtom.A2().AtI())
+        aAtomB = currentBuildAtom.A2().AtK();
+      else
+        aAtomB = currentBuildAtom.A2().AtI();
+      Vec3 vAtomC = Vec3( frameOut.XYZ(aAtomC) );
+      Vec3 vAtomA = Vec3( frameOut.XYZ(aAtomA) );
+      Vec3 vAtomB = Vec3( frameOut.XYZ(aAtomB) );
+
       //if (debug_ > 1) {
         mprintf("Building atom %s using two angles\n", topIn.LeapName(at).c_str());
         mprintf("Using %s - %s - %s and %s - %s - %s\n",
@@ -2165,10 +2232,20 @@ const
                 topIn.LeapName(currentBuildAtom.A2().AtI()).c_str(),
                 topIn.LeapName(currentBuildAtom.A2().AtJ()).c_str(),
                 topIn.LeapName(currentBuildAtom.A2().AtK()).c_str());
+        mprintf("Using first-center-second %s - %s - %s\n",
+                topIn.LeapName(aAtomA).c_str(),
+                topIn.LeapName(aAtomC).c_str(),
+                topIn.LeapName(aAtomB).c_str());
         mprintf("AngleA  = %f\n", currentBuildAtom.A1().ThetaVal()*Constants::RADDEG );
         mprintf("AngleB  = %f\n", currentBuildAtom.A2().ThetaVal()*Constants::RADDEG );
         mprintf("Bond    = %f\n", currentBuildAtom.B1().DistVal() );
       //}
+      double dChi = 0.0;
+      int retVal = determineChirality( dChi, aAtomC, frameOut, topIn, hasPosition );
+      if (retVal != 0)
+        mprinterr("Error: Could not determine chirality for %s\n", topIn.LeapName(aAtomC).c_str());
+      else
+        mprintf("Got EXTERNAL chirality: %f\n", dChi ); */
       //frameOut.SetXYZ( ic.AtI(), posI );
       // FIXME actually build
     } else if (currentBuildAtom.Priority() == 2) {
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index b5c2974738..fd78b8b189 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -124,6 +124,9 @@ class Builder {
     static int get_depths_around_atom(int, int, Topology const&);
     /// Get any complete internal coords for specified atom
     AtomIC getInternalCoordsForAtom(int, int, Barray const&, Topology const&) const;
+    /// Build XYZ coords for an atom from 2 angles and 1 bond
+    int buildCoordsFromTwoAngles(int, InternalAngle const&, InternalAngle const&, InternalBond const&,
+                                 Frame const&, Topology const&, Barray const&) const;
     /// Build XYZ coords for an atom if internals are available
     int buildCoordsForAtom(int, Frame&, Topology const&, Barray const&) const;
     /// Build atoms based on build priority; for cases where known atoms are sparse

From 015d4e260675e03deef30b4247f01f0c1e0292d9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 26 Oct 2025 13:37:13 -0400
Subject: [PATCH 1015/1492] Determine orientation

---
 src/Structure/Builder.cpp | 15 ++++++++++++---
 1 file changed, 12 insertions(+), 3 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index d59ca15b6f..c26a9cc881 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1973,10 +1973,19 @@ const
   //}
   double dChi = 0.0;
   int retVal = determineChirality( dChi, aAtomC, frameOut, topIn, hasPosition );
-  if (retVal != 0)
-    mprinterr("Error: Could not determine chirality for %s\n", topIn.LeapName(aAtomC).c_str());
-  else
+  if (retVal != 0) {
+    //mprinterr("Error: Could not determine chirality for %s\n", topIn.LeapName(aAtomC).c_str());
+    dChi = 1.0;
+    // TODO check for INTERNAL chirality.
+  } else {
     mprintf("Got EXTERNAL chirality: %f\n", dChi );
+  }
+  mprintf("dChirality= %f\n", dChi);
+
+  // Calculate the orientation of aAtomD with respect to aAtomA - aAtomC - aAtomB
+  double dOrient = Cpptraj::Structure::Chirality::chiralityToOrientation( dChi, topIn[aAtomC], aAtomA, aAtomB, at, -1 );
+  mprintf( "The chirality of the ATOM to build is: %f\n", dChi );
+  mprintf( "The orientation of the atom to build is: %f\n", dOrient );
   return 0;
 }
 

From dcacb938f2ac201387530767ca0163aa40440503 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 26 Oct 2025 15:05:08 -0400
Subject: [PATCH 1016/1492] Implement rotation around Y matrix calc from angle
 function

---
 src/Matrix_3x3.cpp | 13 +++++++++++++
 src/Matrix_3x3.h   | 12 ++++++------
 2 files changed, 19 insertions(+), 6 deletions(-)

diff --git a/src/Matrix_3x3.cpp b/src/Matrix_3x3.cpp
index b77d6d23a9..592e9ca8ea 100644
--- a/src/Matrix_3x3.cpp
+++ b/src/Matrix_3x3.cpp
@@ -461,6 +461,19 @@ void Matrix_3x3::RotationAroundY(double a1, double a2) {
   M_[8] = M_[0];   //  cos t
 }
 
+/** Set Rotation matrix around the Y axis given an angle in radians. */
+void Matrix_3x3::RotateAroundY(double ang) {
+  M_[0] = cos(ang);
+  M_[1] = 0;
+  M_[2] = sin(ang);
+  M_[3] = 0;
+  M_[4] = 1;
+  M_[5] = 0;
+  M_[6] = -M_[2]; // -sin(ang)
+  M_[7] = 0;
+  M_[8] = M_[0]; // cos(ang)
+}
+
 /** Given an axis of rotation V (which must be normalized) and a magnitude
   * (radians), calculate a rotation matrix.
   */
diff --git a/src/Matrix_3x3.h b/src/Matrix_3x3.h
index 20104949ee..98dfcc572d 100644
--- a/src/Matrix_3x3.h
+++ b/src/Matrix_3x3.h
@@ -124,12 +124,8 @@ class Matrix_3x3 {
     int RotationAngles(double&, double&, double&) const;
     /// Given theta, extract axis of rotation from rotation matrix
     Vec3 AxisOfRotation(double) const;
-
-    /// Calculate rotation matrix around Z axis. TODO make private
-    void RotationAroundZ(double, double);
-    /// Calculate rotation matrix around Y axis. TODO make private
-    void RotationAroundY(double, double);
-
+    /// Given an angle in radians, calculate rotation matrix around Y axis
+    void RotateAroundY(double);
 
 #   ifdef MPI
     /// Broadcast from master to other ranks
@@ -142,6 +138,10 @@ class Matrix_3x3 {
   private:
     /// Try to fix eigenvector sign flips (Diagonalize_Sort_Chirality())
     int jacobiCheckChirality();
+    /// Calculate rotation matrix around Z axis.
+    void RotationAroundZ(double, double);
+    /// Calculate rotation matrix around Y axis.
+    void RotationAroundY(double, double);
 
     double M_[9];
     // The following three variables are set during Diagonalize_Sort. They

From ec414971b0123b08ac1c5ebb425fcc98db0e2928 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 26 Oct 2025 15:05:39 -0400
Subject: [PATCH 1017/1492] Start implementing the
 ZMatrixBondTwoAnglesOrientation function from leap

---
 src/Structure/Builder.cpp | 115 ++++++++++++++++++++++++++++++++++++++
 src/Structure/Builder.h   |   4 ++
 2 files changed, 119 insertions(+)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index c26a9cc881..ceb18f4a80 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1933,6 +1933,118 @@ Builder::AtomIC Builder::getInternalCoordsForAtom(int at, int idx, Barray const&
   return atomIC;
 }
 
+/*
+ * ZMatrixBondTwoAnglesOrientation()
+ * Original Author: Christian Schafmeister (1991)
+ * Adapted by     : Dan Roe (2025) - any mistakes are mine!
+ *
+ *  Build the external coordinate for the atom when the orientation,
+ *  a bond length and two angles are supplied.
+ *  The orientation is a positive or negative number which specifies
+ *  the orientation of the new position.  It is calculated by:
+ *    a=crossProduct( vPAtomA-vPCenter, vPAtomB-vPCenter );
+ *    orientation = dotProduct( vPPos-vPCenter, a );
+ *
+ *  \param vPAtomC points to the position of the central atom.
+ *  \return Calculated position
+ */
+Vec3 Builder::ZMatrixBondTwoAnglesOrientation(
+  Vec3 const& vPAtomC, Vec3 const& vPAtomA, Vec3 const& vPAtomB,
+  double dBond, double dAngleA, double dAngleB, double dOrient )
+const
+{
+  Vec3 vPPos;
+  static const Vec3 vXAxis(1.0, 0.0, 0.0);
+  static const Vec3 vYAxis(0.0, 1.0, 0.0);
+  //MATRIX          mT, mT1, mT2, mTX, mTY, mTZ, mTT;
+  //double          dAngleX, dAngleY, dAngleZ;
+  //double          dAngle;
+  //VECTOR          vTrans, vTempAC, vTempBC, vTempXZ, vNew, vLab;
+  // The procedure for finding the the coordinate is:
+  // Translate vAtomC to the origin -> A'-C'
+  // Find angle between PROJ((A'-C'),YZ plane) & Y axis
+  // Rotate into XZ plane
+  // Find angle between (A''-C'') and X axis
+  // Rotate onto X axis
+  // Find angle between PROJ((B'''-C'''),YZ plane) and Y axis
+  // Rotate onto XY plane
+  // Calculate coordinates in 3Space
+  // Apply the reverse transformation to the new point
+  // Actually, all that is done is the elements for the
+  // forward transformations are calculated then used
+  // to generate an inverse transform matrix.
+
+  Vec3 vTrans = vPAtomC;
+  Vec3 vTempAC = vPAtomA - vPAtomC; //vVectorSub( vPAtomA, vPAtomC );
+  Vec3 vTempBC = vPAtomB - vPAtomC; //vVectorSub( vPAtomB, vPAtomC );
+  mprintf("AC= %f, %f, %f\n", vTempAC[0], vTempAC[1], vTempAC[2]);
+  mprintf("BC= %f, %f, %f\n", vTempBC[0], vTempBC[1], vTempBC[2]);
+  Vec3 vTempXZ = vTempAC;
+  vTempXZ[1] = 0.0; //  VectorSetY( &vTempXZ, 0.0 );
+  double dAngleY;
+  if (vTempXZ.Length() != 0.0) { //  if ( dVectorLen(&vTempXZ) != 0.0 )
+    //dAngleY =     dAngleY = dVectorAbsAngle( &vTempXZ, &vXAxis, &vYAxis );
+    vTempXZ.Normalize();
+    dAngleY = vTempXZ.SignedAngle( vXAxis, vYAxis );
+  } else
+    dAngleY = 0.0;
+  mprintf("dAngleY= %f\n", dAngleY);
+    
+  Matrix_3x3 mT;
+  mT.RotateAroundY( -dAngleY ); //  MatrixYRotate( mT, -dAngleY );
+  vTempAC = mT * vTempAC; //  MatrixTimesVector( vTempAC, mT, vTempAC );
+  vTempBC = mT * vTempBC; //  MatrixTimesVector( vTempBC, mT, vTempBC );
+  mprintf("Rotated around Y\n" );
+  mprintf("New AC= %f, %f, %f\n", vTempAC[0], vTempAC[1], vTempAC[2]);
+  mprintf("New BC= %f, %f, %f\n", vTempBC[0], vTempBC[1], vTempBC[2]);
+/*
+    dAngleZ = dVectorAbsAngle( &vTempAC, &vXAxis, &vZAxis );
+    MatrixZRotate( mT, -dAngleZ );
+    MatrixTimesVector( vTempBC, mT, vTempBC );
+#ifdef DEBUG
+    MatrixTimesVector( vTempAC, mT, vTempAC );
+#endif
+MESSAGE(( "Rotated around Z\n" ));
+MESSAGE(( "New AC= %lf, %lf, %lf\n", 
+        dVX(&vTempAC), dVY(&vTempAC), dVZ(&vTempAC) ));
+MESSAGE(( "New BC= %lf, %lf, %lf\n", 
+        dVX(&vTempBC), dVY(&vTempBC), dVZ(&vTempBC) ));
+        
+    VectorSetX( &vTempBC, 0.0 );
+
+    dAngleX = dVectorAbsAngle( &vTempBC, &vYAxis, &vXAxis );
+
+                // Build the transformation matrix to convert from
+                // lab coordinates to molecule coordinates in mT
+
+    MatrixXRotate( mTX, dAngleX );
+    MatrixZRotate( mTZ, dAngleZ );
+    MatrixYRotate( mTY, dAngleY );
+    MatrixTranslate( mTT, dVX(&vTrans), dVY(&vTrans), dVZ(&vTrans) );
+    MatrixMultiply( mT1, mTZ, mTX );
+    MatrixMultiply( mT2, mTY, mT1 );
+    MatrixMultiply( mT, mTT, mT2 );
+    
+                // Calculate coordinates of new atom
+    dAngle = dVectorAtomAngle( vPAtomA, vPAtomC, vPAtomB );         
+    vLab = zvZMatrixCalculatePositionFromAngles( dAngleA, dAngleB, 
+      dAngle, dBond );
+
+    if ( dOrient != 0.0 ) {
+        VectorSetZ( &vLab, dOrient*dVZ(&vLab) );
+    }
+
+                // If there is no chirality defined yet then just 
+                // leave it the way it is 
+        
+    MatrixTimesVector( vNew, mT, vLab );
+    *vPPos = vNew;
+    printf( "ZMatrix2Angle:  %lf,%lf,%lf\n", 
+   dVX(vPPos), dVY(vPPos), dVZ(vPPos) );
+*/
+  return vPPos;
+}
+
 /** Build atom using two angles. */
 int Builder::buildCoordsFromTwoAngles(int at, InternalAngle const& Ang1, InternalAngle const& Ang2, InternalBond const& Bnd,
                                       Frame const& frameOut, Topology const& topIn, Barray const& hasPosition)
@@ -1986,6 +2098,9 @@ const
   double dOrient = Cpptraj::Structure::Chirality::chiralityToOrientation( dChi, topIn[aAtomC], aAtomA, aAtomB, at, -1 );
   mprintf( "The chirality of the ATOM to build is: %f\n", dChi );
   mprintf( "The orientation of the atom to build is: %f\n", dOrient );
+
+  Vec3 vNew = ZMatrixBondTwoAnglesOrientation(vAtomC, vAtomA, vAtomB,
+                                              Bnd.DistVal(), Ang1.ThetaVal(), Ang2.ThetaVal(), dOrient);
   return 0;
 }
 
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index fd78b8b189..41d5368d4f 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -6,6 +6,7 @@ class Atom;
 class Topology;
 class Frame;
 class Residue;
+class Vec3;
 namespace Cpptraj {
 namespace Parm {
 class ParameterSet;
@@ -124,6 +125,9 @@ class Builder {
     static int get_depths_around_atom(int, int, Topology const&);
     /// Get any complete internal coords for specified atom
     AtomIC getInternalCoordsForAtom(int, int, Barray const&, Topology const&) const;
+    /// Build coordinates for an atom from two common angles
+    Vec3 ZMatrixBondTwoAnglesOrientation(Vec3 const&, Vec3 const&, Vec3 const&,
+                                         double, double, double, double) const;
     /// Build XYZ coords for an atom from 2 angles and 1 bond
     int buildCoordsFromTwoAngles(int, InternalAngle const&, InternalAngle const&, InternalBond const&,
                                  Frame const&, Topology const&, Barray const&) const;

From 170ccc8aab50547be2fa8990e464adc9134e93e9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 26 Oct 2025 15:41:35 -0400
Subject: [PATCH 1018/1492] Function to calculate rotation matrix around Z

---
 src/Matrix_3x3.cpp | 13 +++++++++++++
 src/Matrix_3x3.h   |  2 ++
 2 files changed, 15 insertions(+)

diff --git a/src/Matrix_3x3.cpp b/src/Matrix_3x3.cpp
index 592e9ca8ea..c057bab62e 100644
--- a/src/Matrix_3x3.cpp
+++ b/src/Matrix_3x3.cpp
@@ -447,6 +447,19 @@ void Matrix_3x3::RotationAroundZ(double a1, double a2) {
   M_[8] = 1;
 }
 
+/** Set Rotation matrix around the Z axis given an angle in radians. */
+void Matrix_3x3::RotateAroundZ(double ang) {
+  M_[0] = cos(ang);
+  M_[1] = -sin(ang);
+  M_[2] = 0;
+  M_[3] = -M_[1]; // sin(ang)
+  M_[4] = M_[0];  // cos(ang)
+  M_[5] = 0;
+  M_[6] = 0;
+  M_[7] = 0;
+  M_[8] = 1;
+}
+
 // Matrix_3x3::RotationAroundY()
 void Matrix_3x3::RotationAroundY(double a1, double a2) {
   double r = sqrt( a1*a1 + a2*a2 );
diff --git a/src/Matrix_3x3.h b/src/Matrix_3x3.h
index 98dfcc572d..3621a9bd22 100644
--- a/src/Matrix_3x3.h
+++ b/src/Matrix_3x3.h
@@ -124,6 +124,8 @@ class Matrix_3x3 {
     int RotationAngles(double&, double&, double&) const;
     /// Given theta, extract axis of rotation from rotation matrix
     Vec3 AxisOfRotation(double) const;
+    /// Given an angle in radians, calculate rotation matrix around Z axis
+    void RotateAroundZ(double);
     /// Given an angle in radians, calculate rotation matrix around Y axis
     void RotateAroundY(double);
 

From 3636fa4c64ac921d43e68190c62de994d9f93d75 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 27 Oct 2025 10:01:58 -0400
Subject: [PATCH 1019/1492] Fix rotation matrices

---
 src/Matrix_3x3.cpp | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/Matrix_3x3.cpp b/src/Matrix_3x3.cpp
index c057bab62e..8be5c6fa96 100644
--- a/src/Matrix_3x3.cpp
+++ b/src/Matrix_3x3.cpp
@@ -450,10 +450,10 @@ void Matrix_3x3::RotationAroundZ(double a1, double a2) {
 /** Set Rotation matrix around the Z axis given an angle in radians. */
 void Matrix_3x3::RotateAroundZ(double ang) {
   M_[0] = cos(ang);
-  M_[1] = -sin(ang);
+  M_[1] = sin(ang);
   M_[2] = 0;
-  M_[3] = -M_[1]; // sin(ang)
-  M_[4] = M_[0];  // cos(ang)
+  M_[3] = -sin(ang);
+  M_[4] = cos(ang);
   M_[5] = 0;
   M_[6] = 0;
   M_[7] = 0;
@@ -478,13 +478,13 @@ void Matrix_3x3::RotationAroundY(double a1, double a2) {
 void Matrix_3x3::RotateAroundY(double ang) {
   M_[0] = cos(ang);
   M_[1] = 0;
-  M_[2] = sin(ang);
+  M_[2] = -sin(ang);
   M_[3] = 0;
   M_[4] = 1;
   M_[5] = 0;
-  M_[6] = -M_[2]; // -sin(ang)
+  M_[6] = sin(ang);
   M_[7] = 0;
-  M_[8] = M_[0]; // cos(ang)
+  M_[8] = cos(ang);
 }
 
 /** Given an axis of rotation V (which must be normalized) and a magnitude

From 5ed99fccb1ca3500009dd4ea45d2139ee0986cf6 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 27 Oct 2025 10:21:39 -0400
Subject: [PATCH 1020/1492] Adapt zvZMatrixCalculatePositionFromAngles from
 leap

---
 src/Structure/Builder.cpp | 135 ++++++++++++++++++++++++++++++--------
 src/Structure/Builder.h   |   2 +
 2 files changed, 110 insertions(+), 27 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index ceb18f4a80..91aa09e71f 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1933,6 +1933,75 @@ Builder::AtomIC Builder::getInternalCoordsForAtom(int at, int idx, Barray const&
   return atomIC;
 }
 
+/*
+ *  zvZMatrixCalculatePositionFromAngles()
+ *
+ *  Original Author: Christian Schafmeister (1991)
+ *  Adapted by     : Dan Roe (2025) - any mistakes are mine!
+ *
+ *  Use NEWTON-RAPHSON method for finding the coordinate for the vector(vC)
+ *  which is dAngleA from the vector vA (on the X axis) and dAngleB from a
+ *  vector (vB) which lies in the XY plane dAngleC from the X axis.
+ *
+ *  The point is dBond from the origin.
+ *
+ */
+Vec3 Builder::zvZMatrixCalculatePositionFromAngles( double dAngleA, double dAngleB, 
+                                                    double dAngleC, double dBond )
+const
+{
+  static const int MAXNEWTONSTEPS = 20;
+  double dCosA = cos(dAngleA);
+  double dSinA = sin(dAngleA);
+  double dCosB = cos(dAngleB);
+  double dCosC = cos(dAngleC);
+  double dSinC = sin(dAngleC);
+
+  // The idea is to minimize the function:
+  // E = ( DOT(vC,vB) - cos(dAngleB) )^2
+  // using NEWTONS method
+  // The vector vC is constrained to make the angle
+  // dAngleA with vA
+  // The vector vC makes the angle (dX) with the XY plane
+  // and the parameter that is optimized is dX
+
+  // A reasonable starting point
+  double dX = dAngleB;
+  int iCount = 0;
+  while ( iCount <MAXNEWTONSTEPS ) {
+
+    double dCosX = cos(dX);
+    double dSinX = sin(dX);
+
+    double dF1 = -2*dSinA*dSinC*(-dCosB + dCosA*dCosC + dCosX*dSinA*dSinC)*dSinX;
+
+    double dF2 = -2.0*dCosX*dSinA*dSinC* (-dCosB + dCosA*dCosC + dCosX*dSinA*dSinC) + 
+                  2.0*dSinA*dSinA*dSinC*dSinC*dSinX*dSinX;
+
+    //    MESSAGE( ( "Iteration %d dF1=%lf  dF2=%lf  dB=%lf\n",
+    //                     iCount, dF1, dF2, dX ) );
+    if ( fabs(dF1) < Constants::SMALL*10.0 ) break;
+    if ( fabs(dF2) < Constants::SMALL ) {
+      mprinterr( "Could not optimize! dF1 = %f, dF2 = %f dX = %f steps=%d", dF1, dF2, dX, iCount );
+    }
+    double dXNew = dX - dF1/dF2;
+    if ( fabs(dXNew - dX) < Constants::SMALL ) break;
+    dX = dXNew;
+    iCount++;
+  }
+   
+//#ifdef  DEBUG 
+//    if ( iCount > MAXNEWTONSTEPS ) 
+//        DDEBUG( ("Exceeded maximum number of Newton Raphson steps: %d\n",
+//                        MAXNEWTONSTEPS) );
+//#endif
+
+                // Generate new coordinate
+  return Vec3( dBond*cos(dAngleA), 
+               dBond*sin(dAngleA)*cos(dX),
+               dBond*sin(dAngleA)*sin(dX) );
+}
+
 /*
  * ZMatrixBondTwoAnglesOrientation()
  * Original Author: Christian Schafmeister (1991)
@@ -1956,6 +2025,7 @@ const
   Vec3 vPPos;
   static const Vec3 vXAxis(1.0, 0.0, 0.0);
   static const Vec3 vYAxis(0.0, 1.0, 0.0);
+  static const Vec3 vZAxis(0.0, 0.0, 1.0);
   //MATRIX          mT, mT1, mT2, mTX, mTY, mTZ, mTT;
   //double          dAngleX, dAngleY, dAngleZ;
   //double          dAngle;
@@ -1992,44 +2062,52 @@ const
     
   Matrix_3x3 mT;
   mT.RotateAroundY( -dAngleY ); //  MatrixYRotate( mT, -dAngleY );
+  mT.Print("mT (Y)");
   vTempAC = mT * vTempAC; //  MatrixTimesVector( vTempAC, mT, vTempAC );
   vTempBC = mT * vTempBC; //  MatrixTimesVector( vTempBC, mT, vTempBC );
   mprintf("Rotated around Y\n" );
   mprintf("New AC= %f, %f, %f\n", vTempAC[0], vTempAC[1], vTempAC[2]);
   mprintf("New BC= %f, %f, %f\n", vTempBC[0], vTempBC[1], vTempBC[2]);
-/*
-    dAngleZ = dVectorAbsAngle( &vTempAC, &vXAxis, &vZAxis );
-    MatrixZRotate( mT, -dAngleZ );
-    MatrixTimesVector( vTempBC, mT, vTempBC );
-#ifdef DEBUG
-    MatrixTimesVector( vTempAC, mT, vTempAC );
-#endif
-MESSAGE(( "Rotated around Z\n" ));
-MESSAGE(( "New AC= %lf, %lf, %lf\n", 
-        dVX(&vTempAC), dVY(&vTempAC), dVZ(&vTempAC) ));
-MESSAGE(( "New BC= %lf, %lf, %lf\n", 
-        dVX(&vTempBC), dVY(&vTempBC), dVZ(&vTempBC) ));
-        
-    VectorSetX( &vTempBC, 0.0 );
 
-    dAngleX = dVectorAbsAngle( &vTempBC, &vYAxis, &vXAxis );
+  vTempAC.Normalize();
+  double dAngleZ = vTempAC.SignedAngle( vXAxis, vZAxis ); //dAngleZ = dVectorAbsAngle( &vTempAC, &vXAxis, &vZAxis );
+  mprintf("dAngleZ= %f\n", dAngleZ);
+  mT.RotateAroundZ(-dAngleZ); //  MatrixZRotate( mT, -dAngleZ );
+  mT.Print("mT (Z)");
+  vTempBC = mT * vTempBC; //  MatrixTimesVector( vTempBC, mT, vTempBC );
+//#ifdef DEBUG
+//    MatrixTimesVector( vTempAC, mT, vTempAC );
+//#endif
+  mprintf("Rotated around Z\n" );
+  mprintf("New AC= %f, %f, %f\n", vTempAC[0], vTempAC[1], vTempAC[2]);
+  mprintf("New BC= %f, %f, %f\n", vTempBC[0], vTempBC[1], vTempBC[2]);
+        
+  vTempBC[0] = 0; //  VectorSetX( &vTempBC, 0.0 );
 
+  vTempBC.Normalize();
+  double dAngleX = vTempBC.SignedAngle( vYAxis, vXAxis ); //   dAngleX = dVectorAbsAngle( &vTempBC, &vYAxis, &vXAxis );
+  mprintf("dAngleX= %f\n", dAngleX);
                 // Build the transformation matrix to convert from
                 // lab coordinates to molecule coordinates in mT
 
-    MatrixXRotate( mTX, dAngleX );
-    MatrixZRotate( mTZ, dAngleZ );
-    MatrixYRotate( mTY, dAngleY );
-    MatrixTranslate( mTT, dVX(&vTrans), dVY(&vTrans), dVZ(&vTrans) );
-    MatrixMultiply( mT1, mTZ, mTX );
-    MatrixMultiply( mT2, mTY, mT1 );
-    MatrixMultiply( mT, mTT, mT2 );
+//    MatrixXRotate( mTX, dAngleX );
+//    MatrixZRotate( mTZ, dAngleZ );
+//    MatrixYRotate( mTY, dAngleY );
+//    MatrixTranslate( mTT, dVX(&vTrans), dVY(&vTrans), dVZ(&vTrans) );
+//    MatrixMultiply( mT1, mTZ, mTX );
+//    MatrixMultiply( mT2, mTY, mT1 );
+//    MatrixMultiply( mT, mTT, mT2 );
+  Matrix_3x3 mT2;
+  mT2.CalcRotationMatrix( dAngleX, dAngleY, dAngleZ );
+  mT2.Print("mT2");
     
                 // Calculate coordinates of new atom
-    dAngle = dVectorAtomAngle( vPAtomA, vPAtomC, vPAtomB );         
-    vLab = zvZMatrixCalculatePositionFromAngles( dAngleA, dAngleB, 
-      dAngle, dBond );
+  double dAngle = CalcAngle(vPAtomA.Dptr(), vPAtomC.Dptr(), vPAtomB.Dptr()); //dAngle = dVectorAtomAngle( vPAtomA, vPAtomC, vPAtomB );         
+  mprintf("dAngle= %f\n", dAngle);
 
+  Vec3 vLab = zvZMatrixCalculatePositionFromAngles( dAngleA, dAngleB, dAngle, dBond );
+  mprintf("vLab= %f %f %f\n", vLab[0], vLab[1], vLab[2]);
+/*
     if ( dOrient != 0.0 ) {
         VectorSetZ( &vLab, dOrient*dVZ(&vLab) );
     }
@@ -2099,8 +2177,11 @@ const
   mprintf( "The chirality of the ATOM to build is: %f\n", dChi );
   mprintf( "The orientation of the atom to build is: %f\n", dOrient );
 
-  Vec3 vNew = ZMatrixBondTwoAnglesOrientation(vAtomC, vAtomA, vAtomB,
-                                              Bnd.DistVal(), Ang1.ThetaVal(), Ang2.ThetaVal(), dOrient);
+  // FIXME testing reverse to match leap
+  Vec3 vNew = ZMatrixBondTwoAnglesOrientation(vAtomC, vAtomB, vAtomA,
+                                              Bnd.DistVal(), Ang2.ThetaVal(), Ang1.ThetaVal(), -dOrient);
+//  Vec3 vNew = ZMatrixBondTwoAnglesOrientation(vAtomC, vAtomA, vAtomB,
+//                                              Bnd.DistVal(), Ang1.ThetaVal(), Ang2.ThetaVal(), dOrient);
   return 0;
 }
 
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index 41d5368d4f..813ef30958 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -125,6 +125,8 @@ class Builder {
     static int get_depths_around_atom(int, int, Topology const&);
     /// Get any complete internal coords for specified atom
     AtomIC getInternalCoordsForAtom(int, int, Barray const&, Topology const&) const;
+    /// Calculate coordinates for an atom based on three angles and a bond length
+    Vec3 zvZMatrixCalculatePositionFromAngles(double, double, double, double) const;
     /// Build coordinates for an atom from two common angles
     Vec3 ZMatrixBondTwoAnglesOrientation(Vec3 const&, Vec3 const&, Vec3 const&,
                                          double, double, double, double) const;

From 5f7eb3d9babdb2881500989fdc524bb42e9a7b66 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 27 Oct 2025 10:25:36 -0400
Subject: [PATCH 1021/1492] Calc final coords

---
 src/Structure/Builder.cpp | 17 +++++++----------
 1 file changed, 7 insertions(+), 10 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 91aa09e71f..77b59254f9 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -2022,7 +2022,6 @@ Vec3 Builder::ZMatrixBondTwoAnglesOrientation(
   double dBond, double dAngleA, double dAngleB, double dOrient )
 const
 {
-  Vec3 vPPos;
   static const Vec3 vXAxis(1.0, 0.0, 0.0);
   static const Vec3 vYAxis(0.0, 1.0, 0.0);
   static const Vec3 vZAxis(0.0, 0.0, 1.0);
@@ -2107,19 +2106,17 @@ const
 
   Vec3 vLab = zvZMatrixCalculatePositionFromAngles( dAngleA, dAngleB, dAngle, dBond );
   mprintf("vLab= %f %f %f\n", vLab[0], vLab[1], vLab[2]);
-/*
-    if ( dOrient != 0.0 ) {
-        VectorSetZ( &vLab, dOrient*dVZ(&vLab) );
-    }
+
+  if ( dOrient != 0.0 ) {
+    vLab[2] = dOrient*vLab[2]; //  VectorSetZ( &vLab, dOrient*dVZ(&vLab) );
+  }
 
                 // If there is no chirality defined yet then just 
                 // leave it the way it is 
         
-    MatrixTimesVector( vNew, mT, vLab );
-    *vPPos = vNew;
-    printf( "ZMatrix2Angle:  %lf,%lf,%lf\n", 
-   dVX(vPPos), dVY(vPPos), dVZ(vPPos) );
-*/
+  Vec3 vPPos = (mT2 * vLab) + vTrans; //MatrixTimesVector( vNew, mT, vLab );
+  mprintf( "ZMatrix2Angle:  %f,%f,%f\n", vPPos[0], vPPos[1], vPPos[2]);
+
   return vPPos;
 }
 

From 380f4cd01d6c11c0eec966a7240fa6fee29e8b1a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 27 Oct 2025 10:26:33 -0400
Subject: [PATCH 1022/1492] Restore the original order

---
 src/Structure/Builder.cpp | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 77b59254f9..aec4966f73 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -2175,10 +2175,10 @@ const
   mprintf( "The orientation of the atom to build is: %f\n", dOrient );
 
   // FIXME testing reverse to match leap
-  Vec3 vNew = ZMatrixBondTwoAnglesOrientation(vAtomC, vAtomB, vAtomA,
-                                              Bnd.DistVal(), Ang2.ThetaVal(), Ang1.ThetaVal(), -dOrient);
-//  Vec3 vNew = ZMatrixBondTwoAnglesOrientation(vAtomC, vAtomA, vAtomB,
-//                                              Bnd.DistVal(), Ang1.ThetaVal(), Ang2.ThetaVal(), dOrient);
+  //Vec3 vNew = ZMatrixBondTwoAnglesOrientation(vAtomC, vAtomB, vAtomA,
+  //                                            Bnd.DistVal(), Ang2.ThetaVal(), Ang1.ThetaVal(), -dOrient);
+  Vec3 vNew = ZMatrixBondTwoAnglesOrientation(vAtomC, vAtomA, vAtomB,
+                                              Bnd.DistVal(), Ang1.ThetaVal(), Ang2.ThetaVal(), dOrient);
   return 0;
 }
 

From 604cc877c1c33c9ec78c79fa3e8c96b2765bade0 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 27 Oct 2025 10:39:11 -0400
Subject: [PATCH 1023/1492] Pass calculated coords back out and actually set
 position

---
 src/Structure/Builder.cpp | 75 ++++++++-------------------------------
 src/Structure/Builder.h   |  2 +-
 2 files changed, 16 insertions(+), 61 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index aec4966f73..47f03402dc 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -2121,7 +2121,8 @@ const
 }
 
 /** Build atom using two angles. */
-int Builder::buildCoordsFromTwoAngles(int at, InternalAngle const& Ang1, InternalAngle const& Ang2, InternalBond const& Bnd,
+int Builder::buildCoordsFromTwoAngles(Vec3& vNew,
+                                      int at, InternalAngle const& Ang1, InternalAngle const& Ang2, InternalBond const& Bnd,
                                       Frame const& frameOut, Topology const& topIn, Barray const& hasPosition)
 const
 {
@@ -2177,8 +2178,8 @@ const
   // FIXME testing reverse to match leap
   //Vec3 vNew = ZMatrixBondTwoAnglesOrientation(vAtomC, vAtomB, vAtomA,
   //                                            Bnd.DistVal(), Ang2.ThetaVal(), Ang1.ThetaVal(), -dOrient);
-  Vec3 vNew = ZMatrixBondTwoAnglesOrientation(vAtomC, vAtomA, vAtomB,
-                                              Bnd.DistVal(), Ang1.ThetaVal(), Ang2.ThetaVal(), dOrient);
+  vNew = ZMatrixBondTwoAnglesOrientation(vAtomC, vAtomA, vAtomB,
+                                         Bnd.DistVal(), Ang1.ThetaVal(), Ang2.ThetaVal(), dOrient);
   return 0;
 }
 
@@ -2212,19 +2213,11 @@ const
   InternalAngle a1, a2;
   InternalBond b1;
   if (getTwoAnglesFromInternals(a1, a2, b1, at, hasPosition)) {
-    buildCoordsFromTwoAngles(at, a1, a2, b1, frameOut, topIn, hasPosition);
-/*    //if (debug_ > 1) {
-      mprintf("Building atom %s using two angles\n", topIn.LeapName(at).c_str());
-      mprintf("Using %s - %s - %s and %s - %s - %s\n",
-                  topIn.LeapName(a1.AtI()).c_str(), topIn.LeapName(a1.AtJ()).c_str(), topIn.LeapName(a1.AtK()).c_str(),
-                  topIn.LeapName(a2.AtI()).c_str(), topIn.LeapName(a2.AtJ()).c_str(), topIn.LeapName(a2.AtK()).c_str());
-      mprintf("AngleA  = %f\n", a1.ThetaVal()*Constants::RADDEG );
-      mprintf("AngleB  = %f\n", a2.ThetaVal()*Constants::RADDEG );
-      mprintf("Bond    = %f\n", b1.DistVal() );
-    //}*/
-    //frameOut.SetXYZ( ic.AtI(), posI );
-    // return 1;
-    // FIXME actually build
+    Vec3 posI;
+    // TODO error checking
+    buildCoordsFromTwoAngles(posI, at, a1, a2, b1, frameOut, topIn, hasPosition);
+    frameOut.SetXYZ( at, posI );
+    return 1;
   }
   // Check if we can get a single angle for this atom
   if (getAngleFromInternals(a1, b1, at, hasPosition)) {
@@ -2405,51 +2398,13 @@ const
       hasPosition[at] = true;
       built_an_atom = true;
     } else if (currentBuildAtom.Priority() == 1) {
-      // FIXME need to implement
-      buildCoordsFromTwoAngles(at, currentBuildAtom.A1(), currentBuildAtom.A2(), currentBuildAtom.B1(),
+      Vec3 posI;
+      // TODO error checking
+      buildCoordsFromTwoAngles(posI, at, currentBuildAtom.A1(), currentBuildAtom.A2(), currentBuildAtom.B1(),
                                frameOut, topIn, hasPosition);
-/*
-      int aAtomA, aAtomB, aAtomC;
-      if (at == currentBuildAtom.A1().AtI()) {
-        aAtomC = currentBuildAtom.A1().AtJ();
-        aAtomA = currentBuildAtom.A1().AtK();
-      } else {
-        aAtomC = currentBuildAtom.A1().AtJ();
-        aAtomA = currentBuildAtom.A1().AtI();
-      }
-      if (at == currentBuildAtom.A2().AtI())
-        aAtomB = currentBuildAtom.A2().AtK();
-      else
-        aAtomB = currentBuildAtom.A2().AtI();
-      Vec3 vAtomC = Vec3( frameOut.XYZ(aAtomC) );
-      Vec3 vAtomA = Vec3( frameOut.XYZ(aAtomA) );
-      Vec3 vAtomB = Vec3( frameOut.XYZ(aAtomB) );
-
-      //if (debug_ > 1) {
-        mprintf("Building atom %s using two angles\n", topIn.LeapName(at).c_str());
-        mprintf("Using %s - %s - %s and %s - %s - %s\n",
-                topIn.LeapName(currentBuildAtom.A1().AtI()).c_str(),
-                topIn.LeapName(currentBuildAtom.A1().AtJ()).c_str(),
-                topIn.LeapName(currentBuildAtom.A1().AtK()).c_str(),
-                topIn.LeapName(currentBuildAtom.A2().AtI()).c_str(),
-                topIn.LeapName(currentBuildAtom.A2().AtJ()).c_str(),
-                topIn.LeapName(currentBuildAtom.A2().AtK()).c_str());
-        mprintf("Using first-center-second %s - %s - %s\n",
-                topIn.LeapName(aAtomA).c_str(),
-                topIn.LeapName(aAtomC).c_str(),
-                topIn.LeapName(aAtomB).c_str());
-        mprintf("AngleA  = %f\n", currentBuildAtom.A1().ThetaVal()*Constants::RADDEG );
-        mprintf("AngleB  = %f\n", currentBuildAtom.A2().ThetaVal()*Constants::RADDEG );
-        mprintf("Bond    = %f\n", currentBuildAtom.B1().DistVal() );
-      //}
-      double dChi = 0.0;
-      int retVal = determineChirality( dChi, aAtomC, frameOut, topIn, hasPosition );
-      if (retVal != 0)
-        mprinterr("Error: Could not determine chirality for %s\n", topIn.LeapName(aAtomC).c_str());
-      else
-        mprintf("Got EXTERNAL chirality: %f\n", dChi ); */
-      //frameOut.SetXYZ( ic.AtI(), posI );
-      // FIXME actually build
+      frameOut.SetXYZ( at, posI );
+      hasPosition[at] = true;
+      built_an_atom = true;
     } else if (currentBuildAtom.Priority() == 2) {
       Vec3 posI = Zmatrix::AtomIposition(frameOut.XYZ(currentBuildAtom.A1().AtJ()),
                                          frameOut.XYZ(currentBuildAtom.A1().AtK()),
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index 813ef30958..e512abd974 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -131,7 +131,7 @@ class Builder {
     Vec3 ZMatrixBondTwoAnglesOrientation(Vec3 const&, Vec3 const&, Vec3 const&,
                                          double, double, double, double) const;
     /// Build XYZ coords for an atom from 2 angles and 1 bond
-    int buildCoordsFromTwoAngles(int, InternalAngle const&, InternalAngle const&, InternalBond const&,
+    int buildCoordsFromTwoAngles(Vec3&, int, InternalAngle const&, InternalAngle const&, InternalBond const&,
                                  Frame const&, Topology const&, Barray const&) const;
     /// Build XYZ coords for an atom if internals are available
     int buildCoordsForAtom(int, Frame&, Topology const&, Barray const&) const;

From b890327c5ebf7d7aa136b9602d63c1227afe921b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 27 Oct 2025 11:37:11 -0400
Subject: [PATCH 1024/1492] Hide some debug info

---
 src/Structure/Builder.cpp | 26 +++++++++++++++-----------
 src/Structure/Zmatrix.cpp | 15 +++++++++++----
 2 files changed, 26 insertions(+), 15 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 47f03402dc..3ba0d03d4d 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -2368,7 +2368,8 @@ const
 int Builder::sparseBuildFromInternals(std::vector<AtomIC>& needsBuilding, Frame& frameOut, Topology const& topIn, Barray& hasPosition)
 const
 {
-  mprintf("DEBUG: No complete internal coordinates. Trying a sparse build.\n");
+  if (debug_ > 0)
+    mprintf("DEBUG: No complete internal coordinates. Trying a sparse build.\n");
   unsigned int nAtomsThatNeedPositions = needsBuilding.size();
 
   unsigned int currentBuildIdx = 0;
@@ -2377,12 +2378,13 @@ const
     // Build the atom with the highest priority
     AtomIC const& currentBuildAtom = needsBuilding[currentBuildIdx];
     int at = currentBuildAtom.At();
-    mprintf("DEBUG: Current build atom is %i %s\n", at+1, topIn.AtomMaskName(at).c_str());
+    if (debug_ > 0)
+      mprintf("DEBUG: Current build atom is %i %s\n", at+1, topIn.AtomMaskName(at).c_str());
 
     if (currentBuildAtom.Priority() == 0) {
       //printAllInternalsForAtom(at, topIn, hasPosition); // DEBUG
       Vec3 posI = Zmatrix::AtomIposition(currentBuildAtom.IC(), frameOut);
-      //if (debug_ > 1) {
+      if (debug_ > 1) {
         mprintf("Building atom %s using torsion/angle/bond\n", topIn.LeapName(at).c_str());
         mprintf("Using %s - %s - %s - %s\n",
                 topIn.LeapName(currentBuildAtom.IC().AtI()).c_str(),
@@ -2393,7 +2395,7 @@ const
         mprintf( "Angle   = %f\n", currentBuildAtom.IC().Theta() );
         mprintf( "Bond    = %f\n", currentBuildAtom.IC().Dist() );
         mprintf( "ZMatrixAll:  %f,%f,%f\n", posI[0], posI[1], posI[2]);
-      //}
+      }
       frameOut.SetXYZ( currentBuildAtom.IC().AtI(), posI ); // TODO use at?
       hasPosition[at] = true;
       built_an_atom = true;
@@ -2409,7 +2411,7 @@ const
       Vec3 posI = Zmatrix::AtomIposition(frameOut.XYZ(currentBuildAtom.A1().AtJ()),
                                          frameOut.XYZ(currentBuildAtom.A1().AtK()),
                                          currentBuildAtom.B1().DistVal(), currentBuildAtom.A1().ThetaVal() );
-      //if debug_ > 1) {
+      if (debug_ > 1) {
         mprintf("Building atom %s using angle/bond\n", topIn.LeapName(at).c_str());
         mprintf("Using %s - %s - %s\n",
                 topIn.LeapName(currentBuildAtom.A1().AtI()).c_str(),
@@ -2418,19 +2420,19 @@ const
         mprintf( "Angle   = %f\n", currentBuildAtom.A1().ThetaVal()*Constants::RADDEG );
         mprintf( "Bond    = %f\n", currentBuildAtom.B1().DistVal() );
         mprintf("ZMatrixBondAngle:  %f,%f,%f\n", posI[0], posI[1], posI[2]);
-        //}
+      }
       frameOut.SetXYZ( currentBuildAtom.A1().AtI(), posI );
       hasPosition[at] = true;
       built_an_atom = true;
     } else if (currentBuildAtom.Priority() == 3) {
       Vec3 posI = Zmatrix::AtomIposition(frameOut.XYZ(currentBuildAtom.B1().AtJ()), currentBuildAtom.B1().DistVal());
-      //if debug_ > 1) {
+      if (debug_ > 1) {
         mprintf("Building atom %s using bond\n", topIn.LeapName(at).c_str());
         mprintf("Using %s - %s\n",
                 topIn.LeapName(currentBuildAtom.B1().AtI()).c_str(), topIn.LeapName(currentBuildAtom.B1().AtJ()).c_str());
         mprintf( "Bond    = %f\n", currentBuildAtom.B1().DistVal() );
         mprintf( "ZMatrixBond:  %f,%f,%f\n", posI[0], posI[1], posI[2]);
-        //}
+      }
       frameOut.SetXYZ( currentBuildAtom.B1().AtI(), posI );
       hasPosition[at] = true;
       built_an_atom = true;
@@ -2450,9 +2452,11 @@ const
     }
     // Sort remaining atoms to build.
     std::sort( needsBuilding.begin() + currentBuildIdx, needsBuilding.end() );
-    mprintf("DEBUG: Atoms that need building:\n");
-    for (std::vector<AtomIC>::const_iterator it = needsBuilding.begin() + currentBuildIdx; it != needsBuilding.end(); ++it)
-      mprintf("\t%i atom %i %s (%i)\n", it->Idx(), it->At()+1, topIn.AtomMaskName( it->At() ).c_str(), it->Priority() );
+    if (debug_ > 0) {
+      mprintf("DEBUG: Atoms that need building:\n");
+      for (std::vector<AtomIC>::const_iterator it = needsBuilding.begin() + currentBuildIdx; it != needsBuilding.end(); ++it)
+        mprintf("\t%i atom %i %s (%i)\n", it->Idx(), it->At()+1, topIn.AtomMaskName( it->At() ).c_str(), it->Priority() );
+    }
   } // END loop over build atoms
   return 0; 
 }
diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index b06d9257de..806880cc18 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -901,25 +901,32 @@ Vec3 Zmatrix::AtomIposition(Vec3 const& posJ, Vec3 const& posK, double rdist, do
   static const Vec3 vYAxis(0.0, 1.0, 0.0);
   static const Vec3 vZAxis(0.0, 0.0, 1.0);
   double dAngleY = vTempXZ.SignedAngle( vXAxis, vYAxis );
+# ifdef CPPTRAJ_DEBUG_ZMATRIX
   mprintf( "Angle around Y=%f\n", dAngleY );
-
+# endif
   Matrix_3x3 mT;
   mT.CalcRotationMatrix(vYAxis, dAngleY);
   vTempX = mT * vTempX;
+# ifdef CPPTRAJ_DEBUG_ZMATRIX
   mprintf("Rotated around Y = %f, %f, %f\n", vTempX[0], vTempX[1], vTempX[2]);
-
+# endif
   vTempX.Normalize();
   double dAngleZ = vTempX.SignedAngle( vXAxis, vZAxis );
+# ifdef CPPTRAJ_DEBUG_ZMATRIX
   mprintf("Angle around Z=%f\n", dAngleZ );
-
+# endif
   Vec3 vNew( rdist*cos(theta_rad), rdist*sin(theta_rad), 0.0 );
+# ifdef CPPTRAJ_DEBUG_ZMATRIX
   mprintf("vNew: %f,%f,%f\n", vNew[0], vNew[1], vNew[2]);
+# endif
   mT.CalcRotationMatrix(vZAxis, -dAngleZ);
   vNew = mT * vNew;
   mT.CalcRotationMatrix(vYAxis, -dAngleY);
   vNew = mT * vNew;
+# ifdef CPPTRAJ_DEBUG_ZMATRIX
   mprintf("vNew before MatrixTranslate: %f,%f,%f\n", vNew[0], vNew[1], vNew[2]);
-  printf("vTrans before MatrixTranslate: %f,%f,%f\n", posJ[0], posJ[1], posJ[2]);
+  mprintf("vTrans before MatrixTranslate: %f,%f,%f\n", posJ[0], posJ[1], posJ[2]);
+# endif
   Vec3 posI = vNew + posJ;
 
   return posI;

From b60e9056ebc3dd6557c7a28d663aa405828179ca Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 27 Oct 2025 11:48:22 -0400
Subject: [PATCH 1025/1492] Move zmatrix routines to zmatrix class

---
 src/Structure/Builder.cpp | 191 +-------------------------------------
 src/Structure/Builder.h   |   5 -
 src/Structure/Zmatrix.cpp | 185 ++++++++++++++++++++++++++++++++++++
 src/Structure/Zmatrix.h   |   5 +
 4 files changed, 192 insertions(+), 194 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 3ba0d03d4d..c260b14985 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1933,193 +1933,6 @@ Builder::AtomIC Builder::getInternalCoordsForAtom(int at, int idx, Barray const&
   return atomIC;
 }
 
-/*
- *  zvZMatrixCalculatePositionFromAngles()
- *
- *  Original Author: Christian Schafmeister (1991)
- *  Adapted by     : Dan Roe (2025) - any mistakes are mine!
- *
- *  Use NEWTON-RAPHSON method for finding the coordinate for the vector(vC)
- *  which is dAngleA from the vector vA (on the X axis) and dAngleB from a
- *  vector (vB) which lies in the XY plane dAngleC from the X axis.
- *
- *  The point is dBond from the origin.
- *
- */
-Vec3 Builder::zvZMatrixCalculatePositionFromAngles( double dAngleA, double dAngleB, 
-                                                    double dAngleC, double dBond )
-const
-{
-  static const int MAXNEWTONSTEPS = 20;
-  double dCosA = cos(dAngleA);
-  double dSinA = sin(dAngleA);
-  double dCosB = cos(dAngleB);
-  double dCosC = cos(dAngleC);
-  double dSinC = sin(dAngleC);
-
-  // The idea is to minimize the function:
-  // E = ( DOT(vC,vB) - cos(dAngleB) )^2
-  // using NEWTONS method
-  // The vector vC is constrained to make the angle
-  // dAngleA with vA
-  // The vector vC makes the angle (dX) with the XY plane
-  // and the parameter that is optimized is dX
-
-  // A reasonable starting point
-  double dX = dAngleB;
-  int iCount = 0;
-  while ( iCount <MAXNEWTONSTEPS ) {
-
-    double dCosX = cos(dX);
-    double dSinX = sin(dX);
-
-    double dF1 = -2*dSinA*dSinC*(-dCosB + dCosA*dCosC + dCosX*dSinA*dSinC)*dSinX;
-
-    double dF2 = -2.0*dCosX*dSinA*dSinC* (-dCosB + dCosA*dCosC + dCosX*dSinA*dSinC) + 
-                  2.0*dSinA*dSinA*dSinC*dSinC*dSinX*dSinX;
-
-    //    MESSAGE( ( "Iteration %d dF1=%lf  dF2=%lf  dB=%lf\n",
-    //                     iCount, dF1, dF2, dX ) );
-    if ( fabs(dF1) < Constants::SMALL*10.0 ) break;
-    if ( fabs(dF2) < Constants::SMALL ) {
-      mprinterr( "Could not optimize! dF1 = %f, dF2 = %f dX = %f steps=%d", dF1, dF2, dX, iCount );
-    }
-    double dXNew = dX - dF1/dF2;
-    if ( fabs(dXNew - dX) < Constants::SMALL ) break;
-    dX = dXNew;
-    iCount++;
-  }
-   
-//#ifdef  DEBUG 
-//    if ( iCount > MAXNEWTONSTEPS ) 
-//        DDEBUG( ("Exceeded maximum number of Newton Raphson steps: %d\n",
-//                        MAXNEWTONSTEPS) );
-//#endif
-
-                // Generate new coordinate
-  return Vec3( dBond*cos(dAngleA), 
-               dBond*sin(dAngleA)*cos(dX),
-               dBond*sin(dAngleA)*sin(dX) );
-}
-
-/*
- * ZMatrixBondTwoAnglesOrientation()
- * Original Author: Christian Schafmeister (1991)
- * Adapted by     : Dan Roe (2025) - any mistakes are mine!
- *
- *  Build the external coordinate for the atom when the orientation,
- *  a bond length and two angles are supplied.
- *  The orientation is a positive or negative number which specifies
- *  the orientation of the new position.  It is calculated by:
- *    a=crossProduct( vPAtomA-vPCenter, vPAtomB-vPCenter );
- *    orientation = dotProduct( vPPos-vPCenter, a );
- *
- *  \param vPAtomC points to the position of the central atom.
- *  \return Calculated position
- */
-Vec3 Builder::ZMatrixBondTwoAnglesOrientation(
-  Vec3 const& vPAtomC, Vec3 const& vPAtomA, Vec3 const& vPAtomB,
-  double dBond, double dAngleA, double dAngleB, double dOrient )
-const
-{
-  static const Vec3 vXAxis(1.0, 0.0, 0.0);
-  static const Vec3 vYAxis(0.0, 1.0, 0.0);
-  static const Vec3 vZAxis(0.0, 0.0, 1.0);
-  //MATRIX          mT, mT1, mT2, mTX, mTY, mTZ, mTT;
-  //double          dAngleX, dAngleY, dAngleZ;
-  //double          dAngle;
-  //VECTOR          vTrans, vTempAC, vTempBC, vTempXZ, vNew, vLab;
-  // The procedure for finding the the coordinate is:
-  // Translate vAtomC to the origin -> A'-C'
-  // Find angle between PROJ((A'-C'),YZ plane) & Y axis
-  // Rotate into XZ plane
-  // Find angle between (A''-C'') and X axis
-  // Rotate onto X axis
-  // Find angle between PROJ((B'''-C'''),YZ plane) and Y axis
-  // Rotate onto XY plane
-  // Calculate coordinates in 3Space
-  // Apply the reverse transformation to the new point
-  // Actually, all that is done is the elements for the
-  // forward transformations are calculated then used
-  // to generate an inverse transform matrix.
-
-  Vec3 vTrans = vPAtomC;
-  Vec3 vTempAC = vPAtomA - vPAtomC; //vVectorSub( vPAtomA, vPAtomC );
-  Vec3 vTempBC = vPAtomB - vPAtomC; //vVectorSub( vPAtomB, vPAtomC );
-  mprintf("AC= %f, %f, %f\n", vTempAC[0], vTempAC[1], vTempAC[2]);
-  mprintf("BC= %f, %f, %f\n", vTempBC[0], vTempBC[1], vTempBC[2]);
-  Vec3 vTempXZ = vTempAC;
-  vTempXZ[1] = 0.0; //  VectorSetY( &vTempXZ, 0.0 );
-  double dAngleY;
-  if (vTempXZ.Length() != 0.0) { //  if ( dVectorLen(&vTempXZ) != 0.0 )
-    //dAngleY =     dAngleY = dVectorAbsAngle( &vTempXZ, &vXAxis, &vYAxis );
-    vTempXZ.Normalize();
-    dAngleY = vTempXZ.SignedAngle( vXAxis, vYAxis );
-  } else
-    dAngleY = 0.0;
-  mprintf("dAngleY= %f\n", dAngleY);
-    
-  Matrix_3x3 mT;
-  mT.RotateAroundY( -dAngleY ); //  MatrixYRotate( mT, -dAngleY );
-  mT.Print("mT (Y)");
-  vTempAC = mT * vTempAC; //  MatrixTimesVector( vTempAC, mT, vTempAC );
-  vTempBC = mT * vTempBC; //  MatrixTimesVector( vTempBC, mT, vTempBC );
-  mprintf("Rotated around Y\n" );
-  mprintf("New AC= %f, %f, %f\n", vTempAC[0], vTempAC[1], vTempAC[2]);
-  mprintf("New BC= %f, %f, %f\n", vTempBC[0], vTempBC[1], vTempBC[2]);
-
-  vTempAC.Normalize();
-  double dAngleZ = vTempAC.SignedAngle( vXAxis, vZAxis ); //dAngleZ = dVectorAbsAngle( &vTempAC, &vXAxis, &vZAxis );
-  mprintf("dAngleZ= %f\n", dAngleZ);
-  mT.RotateAroundZ(-dAngleZ); //  MatrixZRotate( mT, -dAngleZ );
-  mT.Print("mT (Z)");
-  vTempBC = mT * vTempBC; //  MatrixTimesVector( vTempBC, mT, vTempBC );
-//#ifdef DEBUG
-//    MatrixTimesVector( vTempAC, mT, vTempAC );
-//#endif
-  mprintf("Rotated around Z\n" );
-  mprintf("New AC= %f, %f, %f\n", vTempAC[0], vTempAC[1], vTempAC[2]);
-  mprintf("New BC= %f, %f, %f\n", vTempBC[0], vTempBC[1], vTempBC[2]);
-        
-  vTempBC[0] = 0; //  VectorSetX( &vTempBC, 0.0 );
-
-  vTempBC.Normalize();
-  double dAngleX = vTempBC.SignedAngle( vYAxis, vXAxis ); //   dAngleX = dVectorAbsAngle( &vTempBC, &vYAxis, &vXAxis );
-  mprintf("dAngleX= %f\n", dAngleX);
-                // Build the transformation matrix to convert from
-                // lab coordinates to molecule coordinates in mT
-
-//    MatrixXRotate( mTX, dAngleX );
-//    MatrixZRotate( mTZ, dAngleZ );
-//    MatrixYRotate( mTY, dAngleY );
-//    MatrixTranslate( mTT, dVX(&vTrans), dVY(&vTrans), dVZ(&vTrans) );
-//    MatrixMultiply( mT1, mTZ, mTX );
-//    MatrixMultiply( mT2, mTY, mT1 );
-//    MatrixMultiply( mT, mTT, mT2 );
-  Matrix_3x3 mT2;
-  mT2.CalcRotationMatrix( dAngleX, dAngleY, dAngleZ );
-  mT2.Print("mT2");
-    
-                // Calculate coordinates of new atom
-  double dAngle = CalcAngle(vPAtomA.Dptr(), vPAtomC.Dptr(), vPAtomB.Dptr()); //dAngle = dVectorAtomAngle( vPAtomA, vPAtomC, vPAtomB );         
-  mprintf("dAngle= %f\n", dAngle);
-
-  Vec3 vLab = zvZMatrixCalculatePositionFromAngles( dAngleA, dAngleB, dAngle, dBond );
-  mprintf("vLab= %f %f %f\n", vLab[0], vLab[1], vLab[2]);
-
-  if ( dOrient != 0.0 ) {
-    vLab[2] = dOrient*vLab[2]; //  VectorSetZ( &vLab, dOrient*dVZ(&vLab) );
-  }
-
-                // If there is no chirality defined yet then just 
-                // leave it the way it is 
-        
-  Vec3 vPPos = (mT2 * vLab) + vTrans; //MatrixTimesVector( vNew, mT, vLab );
-  mprintf( "ZMatrix2Angle:  %f,%f,%f\n", vPPos[0], vPPos[1], vPPos[2]);
-
-  return vPPos;
-}
-
 /** Build atom using two angles. */
 int Builder::buildCoordsFromTwoAngles(Vec3& vNew,
                                       int at, InternalAngle const& Ang1, InternalAngle const& Ang2, InternalBond const& Bnd,
@@ -2178,8 +1991,8 @@ const
   // FIXME testing reverse to match leap
   //Vec3 vNew = ZMatrixBondTwoAnglesOrientation(vAtomC, vAtomB, vAtomA,
   //                                            Bnd.DistVal(), Ang2.ThetaVal(), Ang1.ThetaVal(), -dOrient);
-  vNew = ZMatrixBondTwoAnglesOrientation(vAtomC, vAtomA, vAtomB,
-                                         Bnd.DistVal(), Ang1.ThetaVal(), Ang2.ThetaVal(), dOrient);
+  vNew = Zmatrix::PosFromBondTwoAnglesOrientation(vAtomC, vAtomA, vAtomB,
+                                                  Bnd.DistVal(), Ang1.ThetaVal(), Ang2.ThetaVal(), dOrient);
   return 0;
 }
 
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index e512abd974..983933ff9e 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -125,11 +125,6 @@ class Builder {
     static int get_depths_around_atom(int, int, Topology const&);
     /// Get any complete internal coords for specified atom
     AtomIC getInternalCoordsForAtom(int, int, Barray const&, Topology const&) const;
-    /// Calculate coordinates for an atom based on three angles and a bond length
-    Vec3 zvZMatrixCalculatePositionFromAngles(double, double, double, double) const;
-    /// Build coordinates for an atom from two common angles
-    Vec3 ZMatrixBondTwoAnglesOrientation(Vec3 const&, Vec3 const&, Vec3 const&,
-                                         double, double, double, double) const;
     /// Build XYZ coords for an atom from 2 angles and 1 bond
     int buildCoordsFromTwoAngles(Vec3&, int, InternalAngle const&, InternalAngle const&, InternalBond const&,
                                  Frame const&, Topology const&, Barray const&) const;
diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index 806880cc18..b22ee45e4f 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -886,6 +886,191 @@ int Zmatrix::SetFromFrame(Frame const& frameIn, Topology const& topIn, int molnu
 }
 
 // -----------------------------------------------------------------------------
+/*
+ *  zvZMatrixCalculatePositionFromAngles()
+ *
+ *  Original Author: Christian Schafmeister (1991)
+ *  Adapted by     : Dan Roe (2025) - any mistakes are mine!
+ *
+ *  Use NEWTON-RAPHSON method for finding the coordinate for the vector(vC)
+ *  which is dAngleA from the vector vA (on the X axis) and dAngleB from a
+ *  vector (vB) which lies in the XY plane dAngleC from the X axis.
+ *
+ *  The point is dBond from the origin.
+ *
+ */
+Vec3 Zmatrix::calculatePositionFromAngles( double dAngleA, double dAngleB, 
+                                           double dAngleC, double dBond )
+{
+  static const int MAXNEWTONSTEPS = 20;
+  double dCosA = cos(dAngleA);
+  double dSinA = sin(dAngleA);
+  double dCosB = cos(dAngleB);
+  double dCosC = cos(dAngleC);
+  double dSinC = sin(dAngleC);
+
+  // The idea is to minimize the function:
+  // E = ( DOT(vC,vB) - cos(dAngleB) )^2
+  // using NEWTONS method
+  // The vector vC is constrained to make the angle
+  // dAngleA with vA
+  // The vector vC makes the angle (dX) with the XY plane
+  // and the parameter that is optimized is dX
+
+  // A reasonable starting point
+  double dX = dAngleB;
+  int iCount = 0;
+  while ( iCount <MAXNEWTONSTEPS ) {
+
+    double dCosX = cos(dX);
+    double dSinX = sin(dX);
+
+    double dF1 = -2*dSinA*dSinC*(-dCosB + dCosA*dCosC + dCosX*dSinA*dSinC)*dSinX;
+
+    double dF2 = -2.0*dCosX*dSinA*dSinC* (-dCosB + dCosA*dCosC + dCosX*dSinA*dSinC) + 
+                  2.0*dSinA*dSinA*dSinC*dSinC*dSinX*dSinX;
+
+    //    MESSAGE( ( "Iteration %d dF1=%lf  dF2=%lf  dB=%lf\n",
+    //                     iCount, dF1, dF2, dX ) );
+    if ( fabs(dF1) < Constants::SMALL*10.0 ) break;
+    if ( fabs(dF2) < Constants::SMALL ) {
+      mprinterr( "Could not optimize! dF1 = %f, dF2 = %f dX = %f steps=%d", dF1, dF2, dX, iCount );
+    }
+    double dXNew = dX - dF1/dF2;
+    if ( fabs(dXNew - dX) < Constants::SMALL ) break;
+    dX = dXNew;
+    iCount++;
+  }
+   
+//#ifdef  DEBUG 
+//    if ( iCount > MAXNEWTONSTEPS ) 
+//        DDEBUG( ("Exceeded maximum number of Newton Raphson steps: %d\n",
+//                        MAXNEWTONSTEPS) );
+//#endif
+
+                // Generate new coordinate
+  return Vec3( dBond*cos(dAngleA), 
+               dBond*sin(dAngleA)*cos(dX),
+               dBond*sin(dAngleA)*sin(dX) );
+}
+
+/*
+ * ZMatrixBondTwoAnglesOrientation()
+ * Original Author: Christian Schafmeister (1991)
+ * Adapted by     : Dan Roe (2025) - any mistakes are mine!
+ *
+ *  Build the external coordinate for the atom when the orientation,
+ *  a bond length and two angles are supplied.
+ *  The orientation is a positive or negative number which specifies
+ *  the orientation of the new position.  It is calculated by:
+ *    a=crossProduct( vPAtomA-vPCenter, vPAtomB-vPCenter );
+ *    orientation = dotProduct( vPPos-vPCenter, a );
+ *
+ *  \param vPAtomC points to the position of the central atom.
+ *  \return Calculated position
+ */
+Vec3 Zmatrix::PosFromBondTwoAnglesOrientation(
+  Vec3 const& vPAtomC, Vec3 const& vPAtomA, Vec3 const& vPAtomB,
+  double dBond, double dAngleA, double dAngleB, double dOrient )
+{
+  static const Vec3 vXAxis(1.0, 0.0, 0.0);
+  static const Vec3 vYAxis(0.0, 1.0, 0.0);
+  static const Vec3 vZAxis(0.0, 0.0, 1.0);
+  //MATRIX          mT, mT1, mT2, mTX, mTY, mTZ, mTT;
+  //double          dAngleX, dAngleY, dAngleZ;
+  //double          dAngle;
+  //VECTOR          vTrans, vTempAC, vTempBC, vTempXZ, vNew, vLab;
+  // The procedure for finding the the coordinate is:
+  // Translate vAtomC to the origin -> A'-C'
+  // Find angle between PROJ((A'-C'),YZ plane) & Y axis
+  // Rotate into XZ plane
+  // Find angle between (A''-C'') and X axis
+  // Rotate onto X axis
+  // Find angle between PROJ((B'''-C'''),YZ plane) and Y axis
+  // Rotate onto XY plane
+  // Calculate coordinates in 3Space
+  // Apply the reverse transformation to the new point
+  // Actually, all that is done is the elements for the
+  // forward transformations are calculated then used
+  // to generate an inverse transform matrix.
+
+  Vec3 vTrans = vPAtomC;
+  Vec3 vTempAC = vPAtomA - vPAtomC; //vVectorSub( vPAtomA, vPAtomC );
+  Vec3 vTempBC = vPAtomB - vPAtomC; //vVectorSub( vPAtomB, vPAtomC );
+  mprintf("AC= %f, %f, %f\n", vTempAC[0], vTempAC[1], vTempAC[2]);
+  mprintf("BC= %f, %f, %f\n", vTempBC[0], vTempBC[1], vTempBC[2]);
+  Vec3 vTempXZ = vTempAC;
+  vTempXZ[1] = 0.0; //  VectorSetY( &vTempXZ, 0.0 );
+  double dAngleY;
+  if (vTempXZ.Length() != 0.0) { //  if ( dVectorLen(&vTempXZ) != 0.0 )
+    //dAngleY =     dAngleY = dVectorAbsAngle( &vTempXZ, &vXAxis, &vYAxis );
+    vTempXZ.Normalize();
+    dAngleY = vTempXZ.SignedAngle( vXAxis, vYAxis );
+  } else
+    dAngleY = 0.0;
+  mprintf("dAngleY= %f\n", dAngleY);
+    
+  Matrix_3x3 mT;
+  mT.RotateAroundY( -dAngleY ); //  MatrixYRotate( mT, -dAngleY );
+  mT.Print("mT (Y)");
+  vTempAC = mT * vTempAC; //  MatrixTimesVector( vTempAC, mT, vTempAC );
+  vTempBC = mT * vTempBC; //  MatrixTimesVector( vTempBC, mT, vTempBC );
+  mprintf("Rotated around Y\n" );
+  mprintf("New AC= %f, %f, %f\n", vTempAC[0], vTempAC[1], vTempAC[2]);
+  mprintf("New BC= %f, %f, %f\n", vTempBC[0], vTempBC[1], vTempBC[2]);
+
+  vTempAC.Normalize();
+  double dAngleZ = vTempAC.SignedAngle( vXAxis, vZAxis ); //dAngleZ = dVectorAbsAngle( &vTempAC, &vXAxis, &vZAxis );
+  mprintf("dAngleZ= %f\n", dAngleZ);
+  mT.RotateAroundZ(-dAngleZ); //  MatrixZRotate( mT, -dAngleZ );
+  mT.Print("mT (Z)");
+  vTempBC = mT * vTempBC; //  MatrixTimesVector( vTempBC, mT, vTempBC );
+//#ifdef DEBUG
+//    MatrixTimesVector( vTempAC, mT, vTempAC );
+//#endif
+  mprintf("Rotated around Z\n" );
+  mprintf("New AC= %f, %f, %f\n", vTempAC[0], vTempAC[1], vTempAC[2]);
+  mprintf("New BC= %f, %f, %f\n", vTempBC[0], vTempBC[1], vTempBC[2]);
+        
+  vTempBC[0] = 0; //  VectorSetX( &vTempBC, 0.0 );
+
+  vTempBC.Normalize();
+  double dAngleX = vTempBC.SignedAngle( vYAxis, vXAxis ); //   dAngleX = dVectorAbsAngle( &vTempBC, &vYAxis, &vXAxis );
+  mprintf("dAngleX= %f\n", dAngleX);
+                // Build the transformation matrix to convert from
+                // lab coordinates to molecule coordinates in mT
+
+//    MatrixXRotate( mTX, dAngleX );
+//    MatrixZRotate( mTZ, dAngleZ );
+//    MatrixYRotate( mTY, dAngleY );
+//    MatrixTranslate( mTT, dVX(&vTrans), dVY(&vTrans), dVZ(&vTrans) );
+//    MatrixMultiply( mT1, mTZ, mTX );
+//    MatrixMultiply( mT2, mTY, mT1 );
+//    MatrixMultiply( mT, mTT, mT2 );
+  Matrix_3x3 mT2;
+  mT2.CalcRotationMatrix( dAngleX, dAngleY, dAngleZ );
+  mT2.Print("mT2");
+    
+                // Calculate coordinates of new atom
+  double dAngle = CalcAngle(vPAtomA.Dptr(), vPAtomC.Dptr(), vPAtomB.Dptr()); //dAngle = dVectorAtomAngle( vPAtomA, vPAtomC, vPAtomB );         
+  mprintf("dAngle= %f\n", dAngle);
+
+  Vec3 vLab = calculatePositionFromAngles( dAngleA, dAngleB, dAngle, dBond );
+  mprintf("vLab= %f %f %f\n", vLab[0], vLab[1], vLab[2]);
+
+  if ( dOrient != 0.0 ) {
+    vLab[2] = dOrient*vLab[2]; //  VectorSetZ( &vLab, dOrient*dVZ(&vLab) );
+  }
+
+                // If there is no chirality defined yet then just 
+                // leave it the way it is 
+        
+  Vec3 vPPos = (mT2 * vLab) + vTrans; //MatrixTimesVector( vNew, mT, vLab );
+  mprintf( "ZMatrix2Angle:  %f,%f,%f\n", vPPos[0], vPPos[1], vPPos[2]);
+
+  return vPPos;
+}
+
 /** \return Position of atom I from positions of atoms J and K,
   *         the corresponding distance I-J (in Ang.) and angle I-J-K
   *         (in radians).
diff --git a/src/Structure/Zmatrix.h b/src/Structure/Zmatrix.h
index d01f19042a..cd11068403 100644
--- a/src/Structure/Zmatrix.h
+++ b/src/Structure/Zmatrix.h
@@ -73,6 +73,9 @@ class Zmatrix {
     unsigned int sizeInBytes() const { return (7*sizeof(int)) +
                                               (9*sizeof(double)) + // 3 Vec3
                                               (IC_.size() * InternalCoords::sizeInBytes()); }
+    /// \return XYZ position of atom I bonded to C using positions of atoms A-C-B, C-I distance, and 2 angles
+    static Vec3 PosFromBondTwoAnglesOrientation(Vec3 const&, Vec3 const&, Vec3 const&,
+                                                double, double, double, double);
     /// \return XYZ position of atom I using positions of atoms J/K and distance (ang)/angle(rad)
     static Vec3 AtomIposition(Vec3 const&, Vec3 const&, double, double);
     /// \return XYZ position of atom I using position of atom J and distance (ang)
@@ -95,6 +98,8 @@ class Zmatrix {
     int traceMol(int, int, int, Frame const&, Topology const&, unsigned int, unsigned int&, Barray&);
     /// Add internal coordinate for given atom
     int addInternalCoordForAtom(int, Frame const&, Topology const&);
+    /// Calculate coordinates for an atom based on three angles and a bond length
+    static Vec3 calculatePositionFromAngles(double, double, double, double);
 
     /// Convert from Cartesian to minimal Zmatrix by tracing a molecule
     int SetFromFrame_Trace(Frame const&, Topology const&, int);

From 4e7f542419d1cbd3ea48941aa75d39d72a39b920 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 27 Oct 2025 11:57:51 -0400
Subject: [PATCH 1026/1492] Hide more debug info

---
 src/Structure/Builder.cpp | 17 ++++++++-------
 src/Structure/Zmatrix.cpp | 45 +++++++++++++++++++++++++--------------
 2 files changed, 38 insertions(+), 24 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index c260b14985..e6c7189375 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1955,7 +1955,7 @@ const
   Vec3 vAtomA = Vec3( frameOut.XYZ(aAtomA) );
   Vec3 vAtomB = Vec3( frameOut.XYZ(aAtomB) );
 
-  //if (debug_ > 1) {
+  if (debug_ > 1) {
     mprintf("Building atom %s using two angles\n", topIn.LeapName(at).c_str());
     mprintf("Using %s - %s - %s and %s - %s - %s\n",
             topIn.LeapName(Ang1.AtI()).c_str(),
@@ -1971,7 +1971,7 @@ const
     mprintf("AngleA  = %f\n", Ang1.ThetaVal()*Constants::RADDEG );
     mprintf("AngleB  = %f\n", Ang2.ThetaVal()*Constants::RADDEG );
     mprintf("Bond    = %f\n", Bnd.DistVal() );
-  //}
+  }
   double dChi = 0.0;
   int retVal = determineChirality( dChi, aAtomC, frameOut, topIn, hasPosition );
   if (retVal != 0) {
@@ -1979,16 +1979,17 @@ const
     dChi = 1.0;
     // TODO check for INTERNAL chirality.
   } else {
-    mprintf("Got EXTERNAL chirality: %f\n", dChi );
+    if (debug_ > 1)
+      mprintf("Got EXTERNAL chirality: %f\n", dChi );
   }
-  mprintf("dChirality= %f\n", dChi);
 
   // Calculate the orientation of aAtomD with respect to aAtomA - aAtomC - aAtomB
   double dOrient = Cpptraj::Structure::Chirality::chiralityToOrientation( dChi, topIn[aAtomC], aAtomA, aAtomB, at, -1 );
-  mprintf( "The chirality of the ATOM to build is: %f\n", dChi );
-  mprintf( "The orientation of the atom to build is: %f\n", dOrient );
-
-  // FIXME testing reverse to match leap
+  if (debug_ > 1) {
+    mprintf( "The chirality of the ATOM to build is: %f\n", dChi );
+    mprintf( "The orientation of the atom to build is: %f\n", dOrient );
+  }
+  // NOTE: below is just testing reverse to match leap
   //Vec3 vNew = ZMatrixBondTwoAnglesOrientation(vAtomC, vAtomB, vAtomA,
   //                                            Bnd.DistVal(), Ang2.ThetaVal(), Ang1.ThetaVal(), -dOrient);
   vNew = Zmatrix::PosFromBondTwoAnglesOrientation(vAtomC, vAtomA, vAtomB,
diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
index b22ee45e4f..2d2dab8ad3 100644
--- a/src/Structure/Zmatrix.cpp
+++ b/src/Structure/Zmatrix.cpp
@@ -942,12 +942,10 @@ Vec3 Zmatrix::calculatePositionFromAngles( double dAngleA, double dAngleB,
     iCount++;
   }
    
-//#ifdef  DEBUG 
-//    if ( iCount > MAXNEWTONSTEPS ) 
-//        DDEBUG( ("Exceeded maximum number of Newton Raphson steps: %d\n",
-//                        MAXNEWTONSTEPS) );
-//#endif
-
+# ifdef CPPTRAJ_DEBUG_ZMATRIX
+  if ( iCount > MAXNEWTONSTEPS ) 
+    mprintf("DEBUG: Exceeded maximum number of Newton Raphson steps: %d\n", MAXNEWTONSTEPS);
+# endif
                 // Generate new coordinate
   return Vec3( dBond*cos(dAngleA), 
                dBond*sin(dAngleA)*cos(dX),
@@ -997,8 +995,10 @@ Vec3 Zmatrix::PosFromBondTwoAnglesOrientation(
   Vec3 vTrans = vPAtomC;
   Vec3 vTempAC = vPAtomA - vPAtomC; //vVectorSub( vPAtomA, vPAtomC );
   Vec3 vTempBC = vPAtomB - vPAtomC; //vVectorSub( vPAtomB, vPAtomC );
+# ifdef CPPTRAJ_DEBUG_ZMATRIX
   mprintf("AC= %f, %f, %f\n", vTempAC[0], vTempAC[1], vTempAC[2]);
   mprintf("BC= %f, %f, %f\n", vTempBC[0], vTempBC[1], vTempBC[2]);
+# endif
   Vec3 vTempXZ = vTempAC;
   vTempXZ[1] = 0.0; //  VectorSetY( &vTempXZ, 0.0 );
   double dAngleY;
@@ -1008,38 +1008,48 @@ Vec3 Zmatrix::PosFromBondTwoAnglesOrientation(
     dAngleY = vTempXZ.SignedAngle( vXAxis, vYAxis );
   } else
     dAngleY = 0.0;
+# ifdef CPPTRAJ_DEBUG_ZMATRIX
   mprintf("dAngleY= %f\n", dAngleY);
-    
+# endif    
   Matrix_3x3 mT;
   mT.RotateAroundY( -dAngleY ); //  MatrixYRotate( mT, -dAngleY );
+# ifdef CPPTRAJ_DEBUG_ZMATRIX
   mT.Print("mT (Y)");
+# endif
   vTempAC = mT * vTempAC; //  MatrixTimesVector( vTempAC, mT, vTempAC );
   vTempBC = mT * vTempBC; //  MatrixTimesVector( vTempBC, mT, vTempBC );
+# ifdef CPPTRAJ_DEBUG_ZMATRIX
   mprintf("Rotated around Y\n" );
   mprintf("New AC= %f, %f, %f\n", vTempAC[0], vTempAC[1], vTempAC[2]);
   mprintf("New BC= %f, %f, %f\n", vTempBC[0], vTempBC[1], vTempBC[2]);
-
+# endif
   vTempAC.Normalize();
   double dAngleZ = vTempAC.SignedAngle( vXAxis, vZAxis ); //dAngleZ = dVectorAbsAngle( &vTempAC, &vXAxis, &vZAxis );
+# ifdef CPPTRAJ_DEBUG_ZMATRIX
   mprintf("dAngleZ= %f\n", dAngleZ);
+# endif
   mT.RotateAroundZ(-dAngleZ); //  MatrixZRotate( mT, -dAngleZ );
+# ifdef CPPTRAJ_DEBUG_ZMATRIX
   mT.Print("mT (Z)");
+# endif
   vTempBC = mT * vTempBC; //  MatrixTimesVector( vTempBC, mT, vTempBC );
 //#ifdef DEBUG
 //    MatrixTimesVector( vTempAC, mT, vTempAC );
 //#endif
+# ifdef CPPTRAJ_DEBUG_ZMATRIX
   mprintf("Rotated around Z\n" );
   mprintf("New AC= %f, %f, %f\n", vTempAC[0], vTempAC[1], vTempAC[2]);
   mprintf("New BC= %f, %f, %f\n", vTempBC[0], vTempBC[1], vTempBC[2]);
-        
+# endif        
   vTempBC[0] = 0; //  VectorSetX( &vTempBC, 0.0 );
 
   vTempBC.Normalize();
   double dAngleX = vTempBC.SignedAngle( vYAxis, vXAxis ); //   dAngleX = dVectorAbsAngle( &vTempBC, &vYAxis, &vXAxis );
+# ifdef CPPTRAJ_DEBUG_ZMATRIX
   mprintf("dAngleX= %f\n", dAngleX);
+# endif
                 // Build the transformation matrix to convert from
                 // lab coordinates to molecule coordinates in mT
-
 //    MatrixXRotate( mTX, dAngleX );
 //    MatrixZRotate( mTZ, dAngleZ );
 //    MatrixYRotate( mTY, dAngleY );
@@ -1049,25 +1059,28 @@ Vec3 Zmatrix::PosFromBondTwoAnglesOrientation(
 //    MatrixMultiply( mT, mTT, mT2 );
   Matrix_3x3 mT2;
   mT2.CalcRotationMatrix( dAngleX, dAngleY, dAngleZ );
+# ifdef CPPTRAJ_DEBUG_ZMATRIX
   mT2.Print("mT2");
-    
+# endif    
                 // Calculate coordinates of new atom
-  double dAngle = CalcAngle(vPAtomA.Dptr(), vPAtomC.Dptr(), vPAtomB.Dptr()); //dAngle = dVectorAtomAngle( vPAtomA, vPAtomC, vPAtomB );         
+  double dAngle = CalcAngle(vPAtomA.Dptr(), vPAtomC.Dptr(), vPAtomB.Dptr()); //dAngle = dVectorAtomAngle( vPAtomA, vPAtomC, vPAtomB );
+# ifdef CPPTRAJ_DEBUG_ZMATRIX
   mprintf("dAngle= %f\n", dAngle);
-
+# endif
   Vec3 vLab = calculatePositionFromAngles( dAngleA, dAngleB, dAngle, dBond );
+# ifdef CPPTRAJ_DEBUG_ZMATRIX
   mprintf("vLab= %f %f %f\n", vLab[0], vLab[1], vLab[2]);
-
+# endif
   if ( dOrient != 0.0 ) {
     vLab[2] = dOrient*vLab[2]; //  VectorSetZ( &vLab, dOrient*dVZ(&vLab) );
   }
-
                 // If there is no chirality defined yet then just 
                 // leave it the way it is 
         
   Vec3 vPPos = (mT2 * vLab) + vTrans; //MatrixTimesVector( vNew, mT, vLab );
+# ifdef CPPTRAJ_DEBUG_ZMATRIX
   mprintf( "ZMatrix2Angle:  %f,%f,%f\n", vPPos[0], vPPos[1], vPPos[2]);
-
+# endif
   return vPPos;
 }
 

From ccd7722452b28fa7d3a2077d08787f59f5c09d7c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 28 Oct 2025 12:27:25 -0400
Subject: [PATCH 1027/1492] When trying to figure out atoms that need building
 from internal coords look at both ends of the IC

---
 src/Exec_Build.cpp        | 10 ++++++++--
 src/Structure/Builder.cpp | 15 ++++++++++++---
 2 files changed, 20 insertions(+), 5 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 7c4ff6d90d..ce01e26e8d 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -341,7 +341,7 @@ const
           }
         }
         templateAtom.ClearBonds(); // FIXME AddTopAtom should clear bonds
-        //mprintf("DEBUG: Adding template atom %s (elt %s)\n", templateAtom.c_str(), templateAtom.ElementName());
+        //mprintf("DEBUG: Adding template %i atom %6s (elt %2s) Res %4s\n", topOut.Natom()+1, templateAtom.c_str(), templateAtom.ElementName(), currentRes.c_str());
         topOut.AddTopAtom( templateAtom, currentRes );
         if (map[iref] == -1) {
           // Template atom not in input structure.
@@ -613,6 +613,12 @@ const
     return 1;
   }
 
+  if (debug_ > 0) {
+    mprintf("DEBUG: hasPosition:\n");
+    for (unsigned int idx = 0; idx != (unsigned int)topOut.Natom(); idx++)
+      mprintf("\t%10u %20s : %i\n", idx+1, topOut.AtomMaskName(idx).c_str(), (int)hasPosition[idx]);
+  }
+
   // -----------------------------------
   // Build using internal coords if needed.
 //  std::vector<bool> resIsBuilt; // TODO is this needed?
@@ -688,7 +694,7 @@ const
       {
         if (resBonds->second < resBonds->first) {
           if (debug_ > 0)
-            mprintf("\t\tResidue connection: %s - %s\n",
+            mprintf("\t\tResidue connection only: %s - %s\n",
                     topOut.AtomMaskName(resBonds->first).c_str(),
                     topOut.AtomMaskName(resBonds->second).c_str());
           topOut.AddBond(resBonds->first, resBonds->second);
diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index e6c7189375..484da021f8 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -2117,7 +2117,7 @@ const
   for (Tarray::const_iterator dih = internalTorsions_.begin();
                               dih != internalTorsions_.end(); ++dih)
   {
-    if (!hasPosition[dih->AtI()]) {
+    if (!hasPosition[dih->AtI()] || !hasPosition[dih->AtL()]) {
       int rnum = topIn[dih->AtI()].ResNum();
       bool has_rnum = false;
       for (std::vector<int>::const_iterator it = Rnums.begin(); it != Rnums.end(); ++it) {
@@ -2135,7 +2135,7 @@ const
   for (Aarray::const_iterator ang = internalAngles_.begin();
                               ang != internalAngles_.end(); ++ang)
   {
-    if (!hasPosition[ang->AtI()]) {
+    if (!hasPosition[ang->AtI()] || !hasPosition[ang->AtK()]) {
       int rnum = topIn[ang->AtI()].ResNum();
       bool has_rnum = false;
       for (std::vector<int>::const_iterator it = Rnums.begin(); it != Rnums.end(); ++it) {
@@ -2153,7 +2153,7 @@ const
   for (Larray::const_iterator bnd = internalBonds_.begin();
                               bnd != internalBonds_.end(); ++bnd)
   {
-    if (!hasPosition[bnd->AtI()]) {
+    if (!hasPosition[bnd->AtI()] || !hasPosition[bnd->AtJ()]) {
       int rnum = topIn[bnd->AtI()].ResNum();
       bool has_rnum = false;
       for (std::vector<int>::const_iterator it = Rnums.begin(); it != Rnums.end(); ++it) {
@@ -2281,8 +2281,13 @@ const
 int Builder::BuildFromInternals(Frame& frameOut, Topology const& topIn, Barray& hasPosition)
 const
 {
+  //mprintf("DEBUG: CALLING BuildFromInternals()\n");
   // Create a list of residues that have atoms that need positions
   std::vector<Residue> residues = residuesThatNeedPositions(topIn, hasPosition);
+  //mprintf("DEBUG: residues:");
+  //for (std::vector<Residue>::const_iterator it = residues.begin(); it != residues.end(); ++it)
+  //  mprintf(" %s", it->c_str());
+  //mprintf("\n");
 //  std::vector<int> Rnums;
 //  for (Tarray::const_iterator dih = internalTorsions_.begin();
 //                              dih != internalTorsions_.end(); ++dih)
@@ -2305,6 +2310,10 @@ const
 //  }
   // Generate array over residue in same order that leap would do
   Iarray atomIndices = GenerateAtomArray(residues, topIn.Atoms());
+  //mprintf("DEBUG: atomIndices:");
+  //for (Iarray::const_iterator it = atomIndices.begin(); it != atomIndices.end(); ++it)
+  //  mprintf(" %i", *it);
+  //mprintf("\n");
   residues.clear();
 
   // Count how many atoms need their positions set

From ad8ed5a5dc2cbc9d0539c7d200877177ea91f431 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 28 Oct 2025 16:54:37 -0400
Subject: [PATCH 1028/1492] Save output COORDS set

---
 src/Exec_Build.cpp | 9 +++++----
 src/Exec_Build.h   | 1 +
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index ce01e26e8d..f202c17447 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -23,7 +23,8 @@ Exec_Build::Exec_Build() :
   check_box_natom_(5000), // TODO make user specifiable
   check_structure_(true),
   addNonTemplateBonds_(false),
-  sugarBuilder_(0)
+  sugarBuilder_(0),
+  outCrdPtr_(0)
 {}
 
 /** DESTRUCTOR */
@@ -887,12 +888,12 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, in
     mprinterr("Error: Must specify output COORDS set with 'name'\n");
     return CpptrajState::ERR;
   }
-  DataSet* outCrdPtr = DSL.AddSet( DataSet::COORDS, outset );
-  if (outCrdPtr == 0) {
+  outCrdPtr_ = DSL.AddSet( DataSet::COORDS, outset );
+  if (outCrdPtr_ == 0) {
     mprinterr("Error: Could not allocate output COORDS set with name '%s'\n", outset.c_str());
     return CpptrajState::ERR;
   }
-  DataSet_Coords& crdout = static_cast<DataSet_Coords&>( *((DataSet_Coords*)outCrdPtr) );
+  DataSet_Coords& crdout = static_cast<DataSet_Coords&>( *((DataSet_Coords*)outCrdPtr_) );
   mprintf("\tOutput COORDS set: %s\n", crdout.legend());
 
   // GB radii set
diff --git a/src/Exec_Build.h b/src/Exec_Build.h
index ff2849878c..114d13dde3 100644
--- a/src/Exec_Build.h
+++ b/src/Exec_Build.h
@@ -42,6 +42,7 @@ class Exec_Build : public Exec {
     bool check_structure_; ///< If true check the resulting structure
     bool addNonTemplateBonds_; ///< If true, add bonds that were not found in templates.
     Cpptraj::Structure::SugarBuilder* sugarBuilder_;
+    DataSet* outCrdPtr_; ///< Hold built COORDS
 
     Timer t_total_;
     Timer t_hisDetect_;

From c50db3341bb3f87c58c9c8754b6a47405a1c2642 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 28 Oct 2025 20:41:16 -0400
Subject: [PATCH 1029/1492] To better match leap behavior, build the topology
 during the saveparm command instead of loadpdb.

---
 src/DataIO_LeapRC.cpp | 29 +++++++++++++++++++---------
 src/DataIO_LeapRC.h   |  2 +-
 src/Exec_Build.cpp    | 44 +++++++++++++++++++++++++++++++++----------
 src/Exec_Build.h      |  4 ++++
 src/Topology.cpp      |  8 ++++++++
 src/Topology.h        |  1 +
 6 files changed, 68 insertions(+), 20 deletions(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 49e4823e15..6951d6cbb5 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -546,13 +546,13 @@ int DataIO_LeapRC::LoadPDB(ArgList const& argIn, DataSetList& dsl) const {
   }
   DataIO_Coords coordsIn;
   coordsIn.SetDebug( debug_ );
-  DataSetList tmpdsl;
+//  DataSetList tmpdsl;
   std::string pdbpath = find_path( args[2], "" );
   if (pdbpath.empty()) {
     mprinterr("Error: Could not find PDB %s\n", args[2].c_str());
     return 1;
   }
-  if (coordsIn.ReadData( pdbpath, tmpdsl, args[0] )) {
+  if (coordsIn.ReadData( pdbpath, dsl, args[0] )) {
     mprinterr("Error: Could not load structure from '%s' into '%s'\n",
               args[2].c_str(), args[0].c_str());
     return 1;
@@ -569,14 +569,14 @@ int DataIO_LeapRC::LoadPDB(ArgList const& argIn, DataSetList& dsl) const {
   args.MarkArg(2);
   ArgList tmparg = args.RemainingArgs();
 
-  tmparg.AddArg("name " + args[0]);
+/*  tmparg.AddArg("name " + args[0]);
   DataSet_LeapOpts& OPTS = static_cast<DataSet_LeapOpts&>( *leapopts_ );
   Exec_Build build;
   Exec::RetType ret = build.BuildStructure( coordsIn.added_back(), dsl, debug_, tmparg, OPTS.PbRadii() );
   if (ret == CpptrajState::ERR) {
     mprinterr("Error: Build of '%s' failed.\n", args[2].c_str());
     return 1;
-  }
+  }*/
   return 0;
 }
 
@@ -622,7 +622,8 @@ int DataIO_LeapRC::LeapSet(ArgList const& argIn, DataSetList& dsl) const {
 
 /** Get COORDS unit from data set list */
 DataSet* DataIO_LeapRC::getUnit(std::string const& unitName, DataSetList const& dsl) const {
-  DataSet* ds = dsl.CheckForSet( MetaData(unitName) );
+  //DataSet* ds = dsl.CheckForSet( MetaData(unitName) );
+  DataSet* ds = dsl.GetDataSet( unitName );
   if (ds == 0) {
     mprinterr("Error: Set '%s' not found.\n", unitName.c_str());
     return 0;
@@ -636,7 +637,7 @@ DataSet* DataIO_LeapRC::getUnit(std::string const& unitName, DataSetList const&
 }
 
 /** Save specified unit to a topology and restart file. */
-int DataIO_LeapRC::SaveAmberParm(std::string const& unitName, ArgList& line, DataSetList const& dsl)
+int DataIO_LeapRC::SaveAmberParm(std::string const& unitName, ArgList& line, DataSetList& dsl)
 const
 {
   // saveamberparm <unit> <topfile> <restartfile>
@@ -668,12 +669,22 @@ const
 //    return 1;
 //  }
 //  mprintf("\tCOORDINATES set %s\n", ds->legend());
-  DataSet_Coords& crd = static_cast<DataSet_Coords&>( *ds ); // FIXME this really should be const
-  if (crd.Size() < 1) {
-    mprinterr("Error: '%s' is empty.\n", crd.legend());
+  if (ds->Size() < 1) {
+    mprinterr("Error: '%s' is empty.\n", ds->legend());
+    return 1;
+  }
+
+  // Build
+  ArgList buildarg = line.RemainingArgs();
+  DataSet_LeapOpts& OPTS = static_cast<DataSet_LeapOpts&>( *leapopts_ );
+  Exec_Build build;
+  Exec::RetType ret = build.BuildStructure( ds, dsl, debug_, buildarg, OPTS.PbRadii() );
+  if (ret == CpptrajState::ERR) {
+    mprinterr("Error: Build of '%s' failed.\n", unitName.c_str());
     return 1;
   }
 
+  DataSet_Coords& crd = static_cast<DataSet_Coords&>( *(build.OutCrdPtr()) ); // FIXME this really should be const
   Parm_Amber parmOut;
   parmOut.SetDebug( debug_ );
   if (parmOut.WriteParm( topName, crd.Top() )) {
diff --git a/src/DataIO_LeapRC.h b/src/DataIO_LeapRC.h
index 84748102a1..ec1a267e81 100644
--- a/src/DataIO_LeapRC.h
+++ b/src/DataIO_LeapRC.h
@@ -59,7 +59,7 @@ class DataIO_LeapRC : public DataIO {
     int LoadPDB(ArgList const&, DataSetList&) const;
     int LeapSet(ArgList const&, DataSetList&) const;
     DataSet* getUnit(std::string const&, DataSetList const&) const;
-    int SaveAmberParm(std::string const&, ArgList&, DataSetList const& dsl) const;
+    int SaveAmberParm(std::string const&, ArgList&, DataSetList& dsl) const;
     int Source(FileName const&, DataSetList&, std::string const&);
 
     /// Used to check if a parm/lib file was already loaded.
diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index f202c17447..0aa0b40490 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -799,11 +799,26 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
     mprinterr("Error: No COORDS set found matching %s\n", crdset.c_str());
     return CpptrajState::ERR;
   }
-  return BuildStructure(inCrdPtr, State.DSL(), State.Debug(), argIn, Cpptraj::Parm::UNKNOWN_GB);
+  std::string outset = argIn.GetStringKey("name");
+  if (outset.empty()) {
+    mprinterr("Error: Must specify output COORDS set with 'name'\n");
+    return CpptrajState::ERR;
+  }
+
+  return BuildStructure(inCrdPtr, outset, State.DSL(), State.Debug(), argIn, Cpptraj::Parm::UNKNOWN_GB);
+}
+
+/** Standalone execute. For DataIO_LeapRC. Operate on inCrdPtr */
+Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, 
+                                         DataSetList& DSL, int debugIn, ArgList& argIn,
+                                         Cpptraj::Parm::GB_RadiiType gbRadIn)
+{
+  return BuildStructure(inCrdPtr, "", DSL, debugIn, argIn, gbRadIn);
 }
 
 /** Standalone execute. For DataIO_LeapRC. */
-Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, int debugIn, ArgList& argIn,
+Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& outset,
+                                         DataSetList& DSL, int debugIn, ArgList& argIn,
                                          Cpptraj::Parm::GB_RadiiType gbRadIn)
 {
   t_total_.Start();
@@ -883,12 +898,14 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, in
   t_clean_.Stop();
 
   // Set up Output coords
-  std::string outset = argIn.GetStringKey("name");
-  if (outset.empty()) {
-    mprinterr("Error: Must specify output COORDS set with 'name'\n");
-    return CpptrajState::ERR;
+  if (!outset.empty()) {
+    // Separate output COORDS set.
+    outCrdPtr_ = DSL.AddSet( DataSet::COORDS, outset );
+  } else {
+    // In-place output COORDS
+    DSL.RemoveSet( inCrdPtr );
+    outCrdPtr_ = DSL.AddSet( DataSet::COORDS, inCrdPtr->Meta() );
   }
-  outCrdPtr_ = DSL.AddSet( DataSet::COORDS, outset );
   if (outCrdPtr_ == 0) {
     mprinterr("Error: Could not allocate output COORDS set with name '%s'\n", outset.c_str());
     return CpptrajState::ERR;
@@ -1011,10 +1028,17 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, in
   t_fill_.Start();
   Topology topOut;
   topOut.SetDebug( debug_ );
-  // TODO better default
-  if (title.empty())
+  if (outset.empty()) {
+    // In-place output COORDS. Copy over existing topology metadata
+    topOut.CopyTopMetadata( topIn );
+  }
+  if (!title.empty())
+    topOut.SetParmName( title, FileName() );
+  else if (topOut.ParmName().empty()) {
+    // TODO better default
     title.assign( topIn.c_str() );
-  topOut.SetParmName( title, FileName() );
+    topOut.SetParmName( title, FileName() );
+  }
   Frame frameOut;
   if (FillAtomsWithTemplates(topOut, frameOut, topIn, frameIn, creator)) {
     mprinterr("Error: Could not fill in atoms using templates.\n");
diff --git a/src/Exec_Build.h b/src/Exec_Build.h
index 114d13dde3..bafe0dffda 100644
--- a/src/Exec_Build.h
+++ b/src/Exec_Build.h
@@ -18,6 +18,8 @@ class Exec_Build : public Exec {
     RetType Execute(CpptrajState&, ArgList&);
     /// Stand-alone execution
     RetType BuildStructure(DataSet*, DataSetList&, int, ArgList&, Cpptraj::Parm::GB_RadiiType);
+    /// \return Output COORDS set
+    DataSet* OutCrdPtr() const { return outCrdPtr_; }
   private:
     typedef std::vector<int> Iarray;
     // Keep track of which residues are connected to each other
@@ -37,6 +39,8 @@ class Exec_Build : public Exec {
     /// Transfer bonds from old topology to new topology
     int transfer_bonds(Topology&, Topology const&, std::vector<BondType> const&) const;
 
+    RetType BuildStructure(DataSet*, std::string const&, DataSetList&, int, ArgList&, Cpptraj::Parm::GB_RadiiType);
+
     int debug_;
     int check_box_natom_;  ///< Systems larger than this will have box added so PL check can be used
     bool check_structure_; ///< If true check the resulting structure
diff --git a/src/Topology.cpp b/src/Topology.cpp
index 5ea43ebaa4..fbaa20c573 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -18,6 +18,14 @@ Topology::Topology() :
   n_extra_pts_(0)
 { }
 
+/** Copy the metadata from another Topology. */
+void Topology::CopyTopMetadata(Topology const& rhs) {
+  parmName_ = rhs.parmName_;
+  fileName_ = rhs.fileName_;
+  ff_desc_ = rhs.ff_desc_;
+  parmBox_ = rhs.parmBox_;
+}
+
 /** Set the parm name only. */
 void Topology::SetParmTitle(std::string const& title) {
   parmName_ = title;
diff --git a/src/Topology.h b/src/Topology.h
index 931318faf0..8b1ea9c32b 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -22,6 +22,7 @@ class Topology {
     void SetIpol(int iIn)                    { ipol_ = iIn;                  }
     void SetPindex(int pIn)                  { pindex_ = pIn;                }
     void SetGBradiiSet(std::string const& s) { radius_set_ = s;              }
+    void CopyTopMetadata(Topology const&);
     void SetParmTitle(std::string const&);
     void SetParmName(std::string const&, FileName const&);
     void SetDistMaskRef( Frame const& );

From 0bcb4c1c2fecb91424c7dc8198eb6b43527bee37 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 29 Oct 2025 09:59:37 -0400
Subject: [PATCH 1030/1492] Warn when sulfurs in a potential disulfide bond are
 bonded to hydrogen

---
 src/Structure/Disulfide.cpp | 21 +++++++++++++++++++--
 1 file changed, 19 insertions(+), 2 deletions(-)

diff --git a/src/Structure/Disulfide.cpp b/src/Structure/Disulfide.cpp
index 7268dc9481..b4ad2139c9 100644
--- a/src/Structure/Disulfide.cpp
+++ b/src/Structure/Disulfide.cpp
@@ -75,6 +75,8 @@ int Disulfide::searchForDisulfides(ResStatArray& resStat,
   }
   if (topIn.SetupIntegerMask( cysmask )) return 1; 
   cysmask.MaskInfo();
+  typedef std::vector<bool> Barray;
+  Barray cysSulfurHasH( cysmask.Nselected(), false );
   if (cysmask.None())
     mprintf("Warning: No cysteine sulfur atoms selected by %s\n", cysmaskstr.c_str());
   else {
@@ -84,6 +86,13 @@ int Disulfide::searchForDisulfides(ResStatArray& resStat,
       if (topIn[*at].Element() != Atom::SULFUR)
         mprintf("Warning: Atom '%s' does not appear to be sulfur.\n",
                 topIn.ResNameNumAtomNameNum(*at).c_str());
+      // Check if the sulfur is bonded to a hydrogen.
+      for (Atom::bond_iterator bat = topIn[*at].bondbegin();
+                               bat != topIn[*at].bondend(); ++bat)
+      {
+        if ( topIn[*bat].Element() == Atom::HYDROGEN )
+          cysSulfurHasH[at - cysmask.begin()] = true;
+      }
     }
 
     int nExistingDisulfides = 0;
@@ -127,9 +136,11 @@ int Disulfide::searchForDisulfides(ResStatArray& resStat,
     if (searchForNewDisulfides) {
       // Only search with atoms that do not have an existing partner.
       Iarray s_idxs; // Indices into cysmask/disulfidePartner
-      for (int idx = 0; idx != cysmask.Nselected(); idx++)
-        if (disulfidePartner[idx] == -1)
+      for (int idx = 0; idx != cysmask.Nselected(); idx++) {
+        if (disulfidePartner[idx] == -1) {
           s_idxs.push_back( idx );
+        }
+      }
       mprintf("\t%zu sulfur atoms do not have a partner.\n", s_idxs.size());
       if (!s_idxs.empty()) {
         // In some structures, there may be 2 potential disulfide partners
@@ -176,6 +187,12 @@ int Disulfide::searchForDisulfides(ResStatArray& resStat,
             mprintf("\t  Potential disulfide: %s to %s (%g Ang.)\n",
                     topIn.ResNameNumAtomNameNum(at1).c_str(),
                     topIn.ResNameNumAtomNameNum(at2).c_str(), sqrt(it->first));
+            if (cysSulfurHasH[it->second.first])
+              mprintf("Warning: Sulfur %s could disulfide bond but already has a bond to hydrogen. Check for improperly added hydrogen.\n",
+                      topIn.ResNameNumAtomNameNum(at1).c_str());
+            if (cysSulfurHasH[it->second.second])
+              mprintf("Warning: Sulfur %s could disulfide bond but already has a bond to hydrogen. Check for improperly added hydrogen.\n",
+                      topIn.ResNameNumAtomNameNum(at2).c_str());
             disulfidePartner[it->second.first ] = it->second.second;
             disulfidePartner[it->second.second] = it->second.first;
             if (addNewBonds == ADD_BONDS)

From bde4f2972f9f553c7ee0545552bd2e50720e0636 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 29 Oct 2025 10:43:13 -0400
Subject: [PATCH 1031/1492] Add problemout keyword

---
 src/Exec_PrepareForLeap.cpp | 29 +++++++++++++++++++++--------
 1 file changed, 21 insertions(+), 8 deletions(-)

diff --git a/src/Exec_PrepareForLeap.cpp b/src/Exec_PrepareForLeap.cpp
index f6de3ca0ed..dc0db8b0dc 100644
--- a/src/Exec_PrepareForLeap.cpp
+++ b/src/Exec_PrepareForLeap.cpp
@@ -533,7 +533,7 @@ const
 void Exec_PrepareForLeap::Help() const
 {
   mprintf("\tcrdset <coords set> [frame <#>] name <out coords set>\n"
-          "\t[pdbout <pdbfile> [terbymol]]\n"
+          "\t[pdbout <pdbfile> [terbymol]] [problemout <file>]\n"
           "\t[leapunitname <unit>] [out <leap input file> [runleap <ff file>]]\n"
           "\t[skiperrors] [{dlparams|nodlparams}] [{bondunknown|nobondunknown}]\n"
           "\t[nowat [watermask <watermask>] [noh]\n"
@@ -694,6 +694,14 @@ Exec::RetType Exec_PrepareForLeap::Execute(CpptrajState& State, ArgList& argIn)
     mprintf("\tWill attempt to bond unknown residues.\n");
   else
     mprintf("\tWill not attempt to bond unknown residues.\n");
+  std::string problemoutname = argIn.GetStringKey("problemout");
+  CpptrajFile* problemout = State.DFL().AddCpptrajFile(problemoutname, "Structure Problems",
+                                                       DataFileList::TEXT, true);
+  if (problemout == 0) {
+    mprinterr("Internal Error: Could not allocate problemout file.\n");
+    return CpptrajState::ERR;
+  }
+  mprintf("\tWriting detected problems to %s\n", problemout->Filename().full());
 
   // Load PDB to glycam residue name map
   SugarBuilder sugarBuilder(debug_);
@@ -987,6 +995,7 @@ Exec::RetType Exec_PrepareForLeap::Execute(CpptrajState& State, ArgList& argIn)
   // Residue validation.
   //mprintf("\tResidues with potential problems:\n");
   int fatal_errors = 0;
+  int potential_errors = 0;
   static const char* msg1 = "Potential problem : ";
   static const char* msg2 = "Fatal problem     : ";
   for (ResStatArray::const_iterator it = resStat.begin(); it != resStat.end(); ++it)
@@ -1000,28 +1009,30 @@ Exec::RetType Exec_PrepareForLeap::Execute(CpptrajState& State, ArgList& argIn)
     if ( *it == ResStatArray::UNKNOWN ) {
       //SetType::const_iterator pname = pdb_res_names_.find( topIn.Res(it-resStat.begin()).Name() );
       //if (pname == pdb_res_names_.end())
-        mprintf("\t%s%s is an unrecognized name and may not have parameters.\n",
+        problemout->Printf("\t%s%s is an unrecognized name and may not have parameters.\n",
                 msg1, topIn.TruncResNameOnumId(it-resStat.begin()).c_str());
+        potential_errors++;
       //else
       //  *it = ResStatArray::VALIDATED;
     } else if ( *it == ResStatArray::SUGAR_NAME_MISMATCH ) {
-        mprintf("\t%s%s sugar anomer type and/or configuration is not consistent with name.\n",
+        problemout->Printf("\t%s%s sugar anomer type and/or configuration is not consistent with name.\n",
                 msg1, topIn.TruncResNameOnumId(it-resStat.begin()).c_str());
+        potential_errors++;
     // ----- Fatal Errors ----
     } else if ( *it == ResStatArray::SUGAR_UNRECOGNIZED_LINK_RES ) {
-        mprintf("\t%s%s is linked to a sugar but has no sugar-linkage form.\n",
+        problemout->Printf("\t%s%s is linked to a sugar but has no sugar-linkage form.\n",
                 msg2, topIn.TruncResNameOnumId(it-resStat.begin()).c_str());
         fatal_errors++;
     } else if ( *it == ResStatArray::SUGAR_UNRECOGNIZED_LINKAGE ) {
-        mprintf("\t%s%s is a sugar with an unrecognized linkage.\n",
+        problemout->Printf("\t%s%s is a sugar with an unrecognized linkage.\n",
                 msg2, topIn.TruncResNameOnumId(it-resStat.begin()).c_str());
         fatal_errors++;
     } else if ( *it == ResStatArray::SUGAR_NO_LINKAGE ) {
-        mprintf("\t%s%s is an incomplete sugar with no linkages.\n",
+        problemout->Printf("\t%s%s is an incomplete sugar with no linkages.\n",
                 msg2, topIn.TruncResNameOnumId(it-resStat.begin()).c_str());
         fatal_errors++;
     } else if ( *it == ResStatArray::SUGAR_NO_CHAIN_FOR_LINK ) {
-        mprintf("\t%s%s could not identify chain atoms for determining linkages.\n",
+        problemout->Printf("\t%s%s could not identify chain atoms for determining linkages.\n",
                 msg2, topIn.TruncResNameOnumId(it-resStat.begin()).c_str());
         fatal_errors++;
 /*    } else if ( *it == SUGAR_MISSING_C1X ) { // TODO should this be a warning
@@ -1029,11 +1040,13 @@ Exec::RetType Exec_PrepareForLeap::Execute(CpptrajState& State, ArgList& argIn)
                 msg2, topIn.TruncResNameOnumId(it-resStat_.begin()).c_str());
         fatal_errors++;*/
     } else if ( *it == ResStatArray::SUGAR_SETUP_FAILED ) {
-        mprintf("\t%s%s Sugar setup failed and could not be identified.\n",
+        problemout->Printf("\t%s%s Sugar setup failed and could not be identified.\n",
                 msg2, topIn.TruncResNameOnumId(it-resStat.begin()).c_str());
         fatal_errors++;
     }
   }
+  if ((fatal_errors + potential_errors) > 0 && !problemout->IsStream())
+    mprintf("Warning: Check '%s' for structure problems.\n", problemout->Filename().full());
 
   // Try to set terminal residues
   if (!molMasks.empty() || determineMolMask.MaskStringSet()) {

From 0069226b81cc164e9c3c56fc8c04c2ce74404ca9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 29 Oct 2025 14:33:47 -0400
Subject: [PATCH 1032/1492] Only open the problem file if there are actually
 problems

---
 src/Exec_PrepareForLeap.cpp | 28 +++++++++++++++++++++-------
 1 file changed, 21 insertions(+), 7 deletions(-)

diff --git a/src/Exec_PrepareForLeap.cpp b/src/Exec_PrepareForLeap.cpp
index dc0db8b0dc..5f6caa6a9b 100644
--- a/src/Exec_PrepareForLeap.cpp
+++ b/src/Exec_PrepareForLeap.cpp
@@ -695,13 +695,7 @@ Exec::RetType Exec_PrepareForLeap::Execute(CpptrajState& State, ArgList& argIn)
   else
     mprintf("\tWill not attempt to bond unknown residues.\n");
   std::string problemoutname = argIn.GetStringKey("problemout");
-  CpptrajFile* problemout = State.DFL().AddCpptrajFile(problemoutname, "Structure Problems",
-                                                       DataFileList::TEXT, true);
-  if (problemout == 0) {
-    mprinterr("Internal Error: Could not allocate problemout file.\n");
-    return CpptrajState::ERR;
-  }
-  mprintf("\tWriting detected problems to %s\n", problemout->Filename().full());
+  mprintf("\tWriting detected problems to %s\n", problemoutname.c_str());
 
   // Load PDB to glycam residue name map
   SugarBuilder sugarBuilder(debug_);
@@ -993,6 +987,26 @@ Exec::RetType Exec_PrepareForLeap::Execute(CpptrajState& State, ArgList& argIn)
   }
 
   // Residue validation.
+  bool structure_has_problems = false;
+  for (ResStatArray::const_iterator it = resStat.begin(); it != resStat.end(); ++it)
+  {
+    if (*it != ResStatArray::VALIDATED) {
+      structure_has_problems = true;
+      break;
+    }
+  }
+  CpptrajFile* problemout = 0;
+  if (problemoutname.empty() || !structure_has_problems) {
+    problemout = State.DFL().AddCpptrajFile("", "Structure Problems", DataFileList::TEXT, true);
+  } else if (structure_has_problems) {
+    // Only open the file if there are problems
+    problemout = State.DFL().AddCpptrajFile(problemoutname, "Structure Problems",
+                                            DataFileList::TEXT, true);
+  }
+  if (problemout == 0) {
+    mprinterr("Internal Error: Could not allocate problemout file.\n");
+    return CpptrajState::ERR;
+  }
   //mprintf("\tResidues with potential problems:\n");
   int fatal_errors = 0;
   int potential_errors = 0;

From e88a3b6d3519a94c140f4470170e4d43a8c04e53 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 29 Oct 2025 15:58:51 -0400
Subject: [PATCH 1033/1492] Fix error message

---
 src/Exec_Build.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 0aa0b40490..be004fcdfa 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -495,12 +495,12 @@ const
               ra1.first+1, *(ra1.second));
     int at0 = topOut.FindAtomInResidue(ra0.first, ra0.second);
     if (at0 < 0) {
-      mprinterr("Error: Atom %s not found in residue %i\n", *(ra0.second), ra0.first);
+      mprinterr("Error: Atom %s not found in residue %i\n", *(ra0.second), ra0.first+1);
       return 1;
     }
     int at1 = topOut.FindAtomInResidue(ra1.first, ra1.second);
     if (at1 < 0) {
-      mprinterr("Error: Atom %s not found in residue %i\n", *(ra1.second), ra1.first);
+      mprinterr("Error: Atom %s not found in residue %i\n", *(ra1.second), ra1.first+1);
       return 1;
     }
     // Save detected inter-residue bonding atoms if not already added via

From eefade7a2f4fa70d18d2498485bdf413f36ef8bc Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 30 Oct 2025 08:40:35 -0400
Subject: [PATCH 1034/1492] Make sure SourceAtomNames is in original order
 instead of template order, since when determining bonds the original order is
 used.

---
 src/Exec_Build.cpp | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index be004fcdfa..509f4f429f 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -62,7 +62,7 @@ std::vector<int> Exec_Build::MapAtomsToTemplate(Topology const& topIn,
     {
       NameType const& refName = resTemplate->Top()[iref].Name();
       if (refName == tgtName) {
-        sourceAtomNames.push_back( tgtName );
+        sourceAtomNames[itgt] = tgtName;
         mapOut[iref] = itgt;
         found = true;
         break;
@@ -73,7 +73,7 @@ std::vector<int> Exec_Build::MapAtomsToTemplate(Topology const& topIn,
       for (int iref = 0; iref != resTemplate->Top().Natom(); iref++) {
         NameType const& refName = resTemplate->Top()[iref].Name();
         if (refName == alias) {
-          sourceAtomNames.push_back( alias );
+          sourceAtomNames[itgt] = alias;
           mapOut[iref] = itgt;
           found = true;
           break;
@@ -252,7 +252,7 @@ const
   // Hold template atom names corressponding to source atom names.
   typedef std::vector<NameType> NameArray;
   NameArray SourceAtomNames;
-  SourceAtomNames.reserve( topIn.Natom() );
+  SourceAtomNames.resize( topIn.Natom() );
 
   // Loop for setting up atoms in the topology from residues or residue templates.
   int nRefAtomsMissing = 0;
@@ -275,7 +275,7 @@ const
         Atom sourceAtom = topIn[itgt];
         if (!sourceAtom.HasType())
           nAtomsMissingTypes++;
-        SourceAtomNames.push_back( sourceAtom.Name() );
+        SourceAtomNames[itgt] = sourceAtom.Name();
         int at0 = itgt - currentRes.FirstAtom() + atomOffset;
         for (Atom::bond_iterator bat = sourceAtom.bondbegin(); bat != sourceAtom.bondend(); ++bat) {
           if ( topIn[*bat].ResNum() == ires ) {
@@ -363,6 +363,11 @@ const
               // Use template atom names. Use saved names in case source name had an alias.
               detectedInterResBonds.push_back( ResAtPair(ires, templateAtom.Name()) );
               detectedInterResBonds.push_back( ResAtPair(topIn[*bat].ResNum(), SourceAtomNames[*bat]) );
+              if ( debug_ > 1 ) {
+                mprintf("DEBUG: Adding detected interres bond: itgt=%i name=%s res=%i tempName=%s -- bat=%i name=%s res=%i srcName=%s\n",
+                        itgt+1, *(sourceAtom.Name()), ires+1, *(templateAtom.Name()),
+                        *bat+1, *(topIn[*bat].Name()), topIn[*bat].ResNum()+1, *(SourceAtomNames[*bat]));
+              }
             }
           }
         }

From fc4d96abc72846ce05bcf1adc5ac412b60b39eb7 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 30 Oct 2025 10:35:17 -0400
Subject: [PATCH 1035/1492] Only add detected non-template bonds when it
 involves a residue for which no template was found

---
 src/Exec_Build.cpp | 14 ++++++--------
 src/Exec_Build.h   |  1 -
 2 files changed, 6 insertions(+), 9 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 509f4f429f..15e80f05e7 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -22,7 +22,6 @@ Exec_Build::Exec_Build() :
   debug_(0),
   check_box_natom_(5000), // TODO make user specifiable
   check_structure_(true),
-  addNonTemplateBonds_(false),
   sugarBuilder_(0),
   outCrdPtr_(0)
 {}
@@ -494,10 +493,13 @@ const
     ResAtPair const& ra0 = *it;
     ++it;
     ResAtPair const& ra1 = *it;
+    bool bondInvolvesResWithNoTemplate = ( (ResTemplates[ra0.first] == 0) ||
+                                           (ResTemplates[ra1.first] == 0) );
     if (debug_ > 1)
-      mprintf("DEBUG: Inter-res bond: Res %i atom %s to res %i atom %s\n",
+      mprintf("DEBUG: Inter-res bond: Res %i atom %s to res %i atom %s : bondInvolvesResWithNoTemplate=%i\n",
               ra0.first+1, *(ra0.second),
-              ra1.first+1, *(ra1.second));
+              ra1.first+1, *(ra1.second),
+              (int)bondInvolvesResWithNoTemplate);
     int at0 = topOut.FindAtomInResidue(ra0.first, ra0.second);
     if (at0 < 0) {
       mprinterr("Error: Atom %s not found in residue %i\n", *(ra0.second), ra0.first+1);
@@ -522,7 +524,7 @@ const
                 topOut.AtomMaskName(at0).c_str(),
                 topOut.AtomMaskName(at1).c_str());
       } else {
-        if (addNonTemplateBonds_) { // FIXME need to change this or move the sugar/disulfide stuff to after
+        if (bondInvolvesResWithNoTemplate) { // FIXME need to change this or move the sugar/disulfide stuff to after
           mprintf("\tAdding non-template bond %s - %s\n",
                   topOut.AtomMaskName(at0).c_str(),
                   topOut.AtomMaskName(at1).c_str());
@@ -838,10 +840,6 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
   debug_ = debugIn;
   int verbose = argIn.getKeyInt("verbose", 0);
   std::string title = argIn.GetStringKey("title");
-  if (addNonTemplateBonds_)
-    mprintf("\tNon-template bonds will be added if detected.\n");
-  else
-    mprintf("\tOnly bonding according to residue templates.\n");
   std::string outputTopologyName = argIn.GetStringKey("parmout");
   std::string outputCoordsName = argIn.GetStringKey("crdout");
   if (!outputTopologyName.empty())
diff --git a/src/Exec_Build.h b/src/Exec_Build.h
index bafe0dffda..c0db3e5ae8 100644
--- a/src/Exec_Build.h
+++ b/src/Exec_Build.h
@@ -44,7 +44,6 @@ class Exec_Build : public Exec {
     int debug_;
     int check_box_natom_;  ///< Systems larger than this will have box added so PL check can be used
     bool check_structure_; ///< If true check the resulting structure
-    bool addNonTemplateBonds_; ///< If true, add bonds that were not found in templates.
     Cpptraj::Structure::SugarBuilder* sugarBuilder_;
     DataSet* outCrdPtr_; ///< Hold built COORDS
 

From e48c7fc32188e719400529ea27f2ece531a84186 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 30 Oct 2025 14:31:54 -0400
Subject: [PATCH 1036/1492] Add sugar bonds before building, which should
 improve atom geometries across links

---
 src/Exec_Build.cpp | 63 ++++++++++++++++++++++++++++++++++++++++------
 src/Exec_Build.h   |  4 ++-
 2 files changed, 59 insertions(+), 8 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 15e80f05e7..fbc53e66f5 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -120,7 +120,8 @@ bool Exec_Build::resIsConnected(Iarray const& resConnections, int tgtRes) {
 /** Use given templates to construct a final molecule. */
 int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
                                        Topology const& topIn, Frame const& frameIn,
-                                       Cpptraj::Structure::Creator const& creator)
+                                       Cpptraj::Structure::Creator const& creator,
+                                       std::vector<BondType> const& topInBonds)
 const
 {
   // Array of head/tail connect atoms for each residue
@@ -486,6 +487,51 @@ const
       mprintf("Warning: Unused tail atom %s\n", topOut.AtomMaskName(resTailAtoms[ires]).c_str());
   }
 
+  // Add external bonds
+  if (!topInBonds.empty()) {
+    for (std::vector<BondType>::const_iterator bnd = topInBonds.begin();
+                                               bnd != topInBonds.end(); ++bnd)
+    {
+      Atom const& At0 = topIn[bnd->A1()];
+      Atom const& At1 = topIn[bnd->A2()];
+      // Ignore bonds in the same residue
+      if ( At0.ResNum() == At1.ResNum()) {
+        mprintf("Build Warning: Atoms %s and %s are in the same residue %i. Not adding extra bond.\n",
+                *(At0.Name()), *(At1.Name()), At0.ResNum()+1);
+        continue;
+      }
+      int a0 = topOut.FindAtomInResidue( At0.ResNum(), At0.Name() );
+      int a1 = topOut.FindAtomInResidue( At1.ResNum(), At1.Name() );
+      if (a0 < 0) {
+        mprinterr("Error: Atom %s not found in residue %i\n", *(At0.Name()), At0.ResNum()+1);
+        return 1;
+      }
+      if (a1 < 0) {
+        mprinterr("Error: Atom %s not found in residue %i\n", *(At1.Name()), At1.ResNum()+1);
+        return 1;
+      }
+      //mprintf("DEBUG: Extra bond between %s and %s\n",
+      //        topOut.AtomMaskName(a0).c_str(),
+      //        topOut.AtomMaskName(a1).c_str());
+      if (resIsConnected(ResidueConnections[At0.ResNum()], At1.ResNum())) {
+        mprintf("Warning: Residue %s already connected to residue %s; ignoring\n"
+                "Warning:   extra bond %s - %s\n",
+                topOut.TruncResNameNum(At0.ResNum()).c_str(),
+                topOut.TruncResNameNum(At1.ResNum()).c_str(),
+                topOut.AtomMaskName(a0).c_str(),
+                topOut.AtomMaskName(a1).c_str());
+      } else {
+        mprintf("\tAdding extra bond %s - %s\n",
+                topOut.AtomMaskName(a0).c_str(),
+                topOut.AtomMaskName(a1).c_str());
+        resBondingAtoms[At0.ResNum()].push_back( Ipair(a0, a1) );
+        resBondingAtoms[At1.ResNum()].push_back( Ipair(a1, a0) );
+        ResidueConnections[At0.ResNum()].push_back( At1.ResNum() );
+        ResidueConnections[At1.ResNum()].push_back( At0.ResNum() );
+      }
+    } // END loop over externally passwd in bonds
+  }
+
   // Check detected inter-residue bonds
   for (ResAtArray::const_iterator it = detectedInterResBonds.begin();
                                   it != detectedInterResBonds.end(); ++it)
@@ -954,7 +1000,8 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
 
   // All residues start unknown
   Cpptraj::Structure::ResStatArray resStat( topIn.Nres() );
-  std::vector<BondType> LeapBonds;
+  std::vector<BondType> DisulfideBonds;
+  std::vector<BondType> SugarBonds;
 
   // Disulfide search
   t_disulfide_.Start();
@@ -964,7 +1011,7 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
       mprinterr("Error: Could not init disulfide search.\n");
       return CpptrajState::ERR;
     }
-    if (disulfide.SearchForDisulfides( resStat, topIn, frameIn, LeapBonds ))
+    if (disulfide.SearchForDisulfides( resStat, topIn, frameIn, DisulfideBonds ))
     {
       mprinterr("Error: Disulfide search failed.\n");
       return CpptrajState::ERR;
@@ -1014,12 +1061,12 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
     // to identify based on the most up-to-date topology.
     if (sugarBuilder_->FixSugarsStructure(topIn, frameIn,
                                           c1bondsearch, splitres, solventResName,
-                                          LeapBonds))
+                                          SugarBonds))
     {
       mprinterr("Error: Sugar structure modification failed.\n");
       return CpptrajState::ERR;
     }
-    if (sugarBuilder_->PrepareSugars(true, resStat, topIn, frameIn, LeapBonds))
+    if (sugarBuilder_->PrepareSugars(true, resStat, topIn, frameIn, SugarBonds))
     {
       mprinterr("Error: Sugar preparation failed.\n");
       return CpptrajState::ERR;
@@ -1043,14 +1090,16 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
     topOut.SetParmName( title, FileName() );
   }
   Frame frameOut;
-  if (FillAtomsWithTemplates(topOut, frameOut, topIn, frameIn, creator)) {
+  if (FillAtomsWithTemplates(topOut, frameOut, topIn, frameIn, creator, SugarBonds)) {
     mprinterr("Error: Could not fill in atoms using templates.\n");
     return CpptrajState::ERR;
   }
   t_fill_.Stop();
 
   // Add the disulfide/sugar bonds
-  if (transfer_bonds( topOut, topIn, LeapBonds )) {
+  int addBondsErr = transfer_bonds( topOut, topIn, DisulfideBonds );
+  //addBondsErr += transfer_bonds( topOut, topIn, SugarBonds );
+  if (addBondsErr != 0) {
     mprinterr("Error: Adding disulfide/sugar bonds failed.\n");
     return CpptrajState::ERR;
   }
diff --git a/src/Exec_Build.h b/src/Exec_Build.h
index c0db3e5ae8..8dcc85f8a6 100644
--- a/src/Exec_Build.h
+++ b/src/Exec_Build.h
@@ -33,7 +33,9 @@ class Exec_Build : public Exec {
     /// \return true if given array of residue connections has target residue index.
     static inline bool resIsConnected(Iarray const&, int);
     /// Create new topology/frame using templates
-    int FillAtomsWithTemplates(Topology&, Frame&, Topology const&, Frame const&, Cpptraj::Structure::Creator const&) const;
+    int FillAtomsWithTemplates(Topology&, Frame&, Topology const&, Frame const&,
+                               Cpptraj::Structure::Creator const&,
+                               std::vector<BondType> const&) const;
     /// Map atoms in topology to template
     static std::vector<int> MapAtomsToTemplate(Topology const&, int, DataSet_Coords*, Cpptraj::Structure::Creator const&, std::vector<NameType>&, int&);
     /// Transfer bonds from old topology to new topology

From 3ec846bc8172f7037f33e5446268e9a1cb346591 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 30 Oct 2025 16:00:48 -0400
Subject: [PATCH 1037/1492] Remove old code. Hide some debug info

---
 src/Exec_Build.cpp | 91 ++++------------------------------------------
 1 file changed, 8 insertions(+), 83 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index fbc53e66f5..9c93d68991 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -134,9 +134,7 @@ const
   // Array of templates for each residue
   std::vector<DataSet_Coords*> ResTemplates;
   ResTemplates.reserve( topIn.Nres() );
-  //typedef std::vector<Cpptraj::Structure::TerminalType> TermTypeArray;
-  //TermTypeArray ResTypes;
-  //ResTypes.reserve( topIn.Nres() );
+
   // Initial loop to try to match residues to templates
   int newNatom = 0;
   unsigned int n_no_template_found = 0;
@@ -372,15 +370,6 @@ const
           }
         }
       }
-      // See if any current atoms were not mapped to reference template
-      //int nTgtAtomsMissing = 0;
-      //for (int itgt = 0; itgt != currentRes.NumAtoms(); itgt++) {
-      //  if (pdb[itgt] == -1) {
-      //    mprintf("Warning: Input atom %s was not mapped to a template atom.\n",
-      //            topIn.TruncAtomResNameOnumId(currentRes.FirstAtom()+itgt).c_str());
-      //    nTgtAtomsMissing++;
-      //  }
-      //}
       if (nTgtAtomsMissing > 0)
         mprintf("\t%i source atoms not mapped to template.\n", nTgtAtomsMissing);
       // Save atom offset if atoms need to be built
@@ -510,9 +499,6 @@ const
         mprinterr("Error: Atom %s not found in residue %i\n", *(At1.Name()), At1.ResNum()+1);
         return 1;
       }
-      //mprintf("DEBUG: Extra bond between %s and %s\n",
-      //        topOut.AtomMaskName(a0).c_str(),
-      //        topOut.AtomMaskName(a1).c_str());
       if (resIsConnected(ResidueConnections[At0.ResNum()], At1.ResNum())) {
         mprintf("Warning: Residue %s already connected to residue %s; ignoring\n"
                 "Warning:   extra bond %s - %s\n",
@@ -521,15 +507,16 @@ const
                 topOut.AtomMaskName(a0).c_str(),
                 topOut.AtomMaskName(a1).c_str());
       } else {
-        mprintf("\tAdding extra bond %s - %s\n",
-                topOut.AtomMaskName(a0).c_str(),
-                topOut.AtomMaskName(a1).c_str());
+        if (debug_ > 0)
+          mprintf("DEBUG: Adding extra bond %s - %s\n",
+                  topOut.AtomMaskName(a0).c_str(),
+                  topOut.AtomMaskName(a1).c_str());
         resBondingAtoms[At0.ResNum()].push_back( Ipair(a0, a1) );
         resBondingAtoms[At1.ResNum()].push_back( Ipair(a1, a0) );
         ResidueConnections[At0.ResNum()].push_back( At1.ResNum() );
         ResidueConnections[At1.ResNum()].push_back( At0.ResNum() );
       }
-    } // END loop over externally passwd in bonds
+    } // END loop over externally passed in bonds
   }
 
   // Check detected inter-residue bonds
@@ -570,7 +557,7 @@ const
                 topOut.AtomMaskName(at0).c_str(),
                 topOut.AtomMaskName(at1).c_str());
       } else {
-        if (bondInvolvesResWithNoTemplate) { // FIXME need to change this or move the sugar/disulfide stuff to after
+        if (bondInvolvesResWithNoTemplate) {
           mprintf("\tAdding non-template bond %s - %s\n",
                   topOut.AtomMaskName(at0).c_str(),
                   topOut.AtomMaskName(at1).c_str());
@@ -585,61 +572,8 @@ const
                     topOut.AtomMaskName(at1).c_str());
         }
       }
-    } //else
-      //mprintf("DEBUG: Detected bond %s - %s already present.\n",
-      //        topOut.AtomMaskName(at0).c_str(),
-      //        topOut.AtomMaskName(at1).c_str());
-    //if (!hasBondingPair(resBondingAtoms[ra1.first], Ipair(at1, at0)))
-    //  resBondingAtoms[ra1.first].push_back( Ipair(at1, at0) );
-    //else
-    //  mprintf("DEBUG: Detected bond %s - %s already present.\n",
-    //          topOut.AtomMaskName(at1).c_str(),
-    //          topOut.AtomMaskName(at0).c_str());
-  }
-
-  // For each inter-residue bonding atom pair, check that they match expected
-  // head/tail atoms.
-/*  for (std::vector<IParray>::const_iterator rit = resBondingAtoms.begin();
-                                            rit != resBondingAtoms.end(); ++rit)
-  {
-    long int ires = rit - resBondingAtoms.begin();
-    for (IParray::const_iterator atPair = rit->begin(); atPair != rit->end(); ++atPair)
-    {
-      long int jres = topOut[atPair->second].ResNum();
-      if (atPair->first == resHeadAtoms[ires]) {
-        // HEAD atom. Should connect to other residue TAIL atom.
-        if (atPair->second != resTailAtoms[jres]) {
-          mprintf("Warning: Detected inter-res bond %s - %s HEAD does not match TAIL.\n",
-                  topOut.AtomMaskName(atPair->first).c_str(),
-                  topOut.AtomMaskName(atPair->second).c_str());
-        }
-      } else if (atPair->first == resTailAtoms[ires]) {
-        // TAIL atom. Should connect to other residue HEAD atom.
-        if (atPair->second != resHeadAtoms[jres]) {
-          mprintf("Warning: Detected inter-res bond %s - %s TAIL does not match HEAD.\n",
-                  topOut.AtomMaskName(atPair->first).c_str(),
-                  topOut.AtomMaskName(atPair->second).c_str());
-        }
-      } else {
-        mprintf("Warning: Atom %s is not a HEAD or TAIL atom.\n",
-                topOut.AtomMaskName(atPair->first).c_str());
-      }
-    } // END loop over inter-residue bond pairs for this residue
-  } // END loop over residues*/
-
-  // Mark used HEAD/TAIL atoms in existing inter-residue bonds.
-/*  for (std::vector<IParray>::const_iterator rit = resBondingAtoms.begin();
-                                            rit != resBondingAtoms.end(); ++rit)
-  {
-    long int ires = rit - resBondingAtoms.begin();
-    for (IParray::const_iterator atPair = rit->begin(); atPair != rit->end(); ++atPair)
-    {
-      if (atPair->first == resHeadAtoms[ires])
-        resHeadAtoms[ires] = -1;
-      else if (atPair->first == resTailAtoms[ires])
-        resTailAtoms[ires] = -1;
     }
-  }*/
+  }
 
   // DEBUG print inter-residue bonding atoms
   if (debug_ > 0) {
@@ -675,15 +609,6 @@ const
 
   // -----------------------------------
   // Build using internal coords if needed.
-//  std::vector<bool> resIsBuilt; // TODO is this needed?
-//  resIsBuilt.reserve( AtomOffsets.size() );
-//  for (Iarray::const_iterator it = AtomOffsets.begin(); it != AtomOffsets.end(); ++it) {
-//    if ( *it < 0 )
-//      resIsBuilt.push_back( true );
-//    else
-//      resIsBuilt.push_back( false );
-//  }
-
   bool buildFailed = false;
   for (Iarray::const_iterator it = AtomOffsets.begin(); it != AtomOffsets.end(); ++it)
   {

From 1686c0ab3520fe35a2c2ffbb98e171d555f0a177 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 31 Oct 2025 10:41:33 -0400
Subject: [PATCH 1038/1492] Save bfactors

---
 src/Exec_Build.cpp | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 9c93d68991..bbf79e5670 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -255,6 +255,7 @@ const
   // Loop for setting up atoms in the topology from residues or residue templates.
   int nRefAtomsMissing = 0;
   int nAtomsMissingTypes = 0;
+  bool has_bfac = !topIn.Bfactor().empty();
   for (int ires = 0; ires != topIn.Nres(); ires++)
   {
     if (debug_ > 0)
@@ -295,6 +296,8 @@ const
         topOut.AddTopAtom( sourceAtom, currentRes );
         frameOut.AddVec3( Vec3(frameIn.XYZ(itgt)) );
         hasPosition.push_back( true );
+        if (has_bfac)
+          topOut.ModifyBfactor().push_back( topIn.Bfactor()[itgt] );
       }
     } else {
       // ----- A template exists for this residue. ---------
@@ -348,11 +351,13 @@ const
           hasPosition.push_back( false );
           nRefAtomsMissing++;
           atomsNeedBuilding = true;
+          if (has_bfac) topOut.ModifyBfactor().push_back(0.0);
         } else {
           // Template atom was in input structure.
           int itgt = map[iref];
           frameOut.AddVec3( Vec3(frameIn.XYZ(itgt)) );
           hasPosition.push_back( true );
+          if (has_bfac) topOut.ModifyBfactor().push_back( topIn.Bfactor()[itgt] );
           //pdb[itgt-currentRes.FirstAtom()] = iref;
           // Check source atoms for inter-residue connections.
           Atom const& sourceAtom = topIn[itgt];
@@ -600,6 +605,12 @@ const
     mprinterr("Internal Error: Source atom names length %zu != # input atoms %i\n", SourceAtomNames.size(), topIn.Natom());
     return 1;
   }
+  if (has_bfac) {
+    if (topOut.Bfactor().size() != (unsigned int)topOut.Natom()) {
+      mprinterr("Internal Error: Size of final Bfactor array %zu != # atoms %i\n", topOut.Bfactor().size(), topOut.Natom());
+      return 1;
+    }
+  }
 
   if (debug_ > 0) {
     mprintf("DEBUG: hasPosition:\n");

From 191729e1854e6d8151d63e36ed1c3ca4fece2efc Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 31 Oct 2025 11:01:28 -0400
Subject: [PATCH 1039/1492] Save PDB atom serial number when reading in PDBs.
 Write bfactor, occupancy, and pdb serial number to built topologies when
 present

---
 src/Exec_Build.cpp | 31 ++++++++++++++++++++++++++++---
 src/Parm_PDB.cpp   |  1 +
 2 files changed, 29 insertions(+), 3 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index bbf79e5670..5f0a38e8df 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -256,6 +256,11 @@ const
   int nRefAtomsMissing = 0;
   int nAtomsMissingTypes = 0;
   bool has_bfac = !topIn.Bfactor().empty();
+  bool has_occ  = !topIn.Occupancy().empty();
+  bool has_pdbn = !topIn.PdbSerialNum().empty();
+  if (debug_ > 0)
+    mprintf("DEBUG: Input top has_bfac=%i  has_occ=%i  has_pdbn=%i\n",
+            (int)has_bfac, (int)has_occ, (int)has_pdbn);
   for (int ires = 0; ires != topIn.Nres(); ires++)
   {
     if (debug_ > 0)
@@ -297,7 +302,11 @@ const
         frameOut.AddVec3( Vec3(frameIn.XYZ(itgt)) );
         hasPosition.push_back( true );
         if (has_bfac)
-          topOut.ModifyBfactor().push_back( topIn.Bfactor()[itgt] );
+          topOut.AddBfactor( topIn.Bfactor()[itgt] );
+        if (has_occ)
+          topOut.AddOccupancy( topIn.Occupancy()[itgt] );
+        if (has_pdbn)
+          topOut.AddPdbSerialNum( topIn.PdbSerialNum()[itgt] );
       }
     } else {
       // ----- A template exists for this residue. ---------
@@ -351,13 +360,17 @@ const
           hasPosition.push_back( false );
           nRefAtomsMissing++;
           atomsNeedBuilding = true;
-          if (has_bfac) topOut.ModifyBfactor().push_back(0.0);
+          if (has_bfac) topOut.AddBfactor(0.0);
+          if (has_occ)  topOut.AddOccupancy(0.0);
+          if (has_pdbn) topOut.AddPdbSerialNum(0);
         } else {
           // Template atom was in input structure.
           int itgt = map[iref];
           frameOut.AddVec3( Vec3(frameIn.XYZ(itgt)) );
           hasPosition.push_back( true );
-          if (has_bfac) topOut.ModifyBfactor().push_back( topIn.Bfactor()[itgt] );
+          if (has_bfac) topOut.AddBfactor( topIn.Bfactor()[itgt] );
+          if (has_occ)  topOut.AddOccupancy( topIn.Occupancy()[itgt] );
+          if (has_pdbn) topOut.AddPdbSerialNum( topIn.PdbSerialNum()[itgt] );
           //pdb[itgt-currentRes.FirstAtom()] = iref;
           // Check source atoms for inter-residue connections.
           Atom const& sourceAtom = topIn[itgt];
@@ -611,6 +624,18 @@ const
       return 1;
     }
   }
+  if (has_occ) {
+    if (topOut.Occupancy().size() != (unsigned int)topOut.Natom()) {
+      mprinterr("Internal Error: Size of final Occupancy array %zu != # atoms %i\n", topOut.Occupancy().size(), topOut.Natom());
+      return 1;
+    }
+  }
+  if (has_pdbn) {
+    if (topOut.PdbSerialNum().size() != (unsigned int)topOut.Natom()) {
+      mprinterr("Internal Error: Size of final PdbSerialNum array %zu != # atoms %i\n", topOut.PdbSerialNum().size(), topOut.Natom());
+      return 1;
+    }
+  }
 
   if (debug_ > 0) {
     mprintf("DEBUG: hasPosition:\n");
diff --git a/src/Parm_PDB.cpp b/src/Parm_PDB.cpp
index 6680cace5e..1f78255fbd 100644
--- a/src/Parm_PDB.cpp
+++ b/src/Parm_PDB.cpp
@@ -131,6 +131,7 @@ int Parm_PDB::ReadParm(FileName const& fname, Topology &TopIn) {
         continue;
       }
       TopIn.AddAtomAltLoc( altLoc );
+      TopIn.AddPdbSerialNum( atnum );
       if (atnum >= (int)serial.size())
         serial.resize( atnum+1, -1 );
       serial[atnum] = TopIn.Natom();

From 2f2929e08a376d8b59bede0db2fbccddbd8aa27c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 31 Oct 2025 11:18:15 -0400
Subject: [PATCH 1040/1492] Add 'defaulthis' keyword to histidine detection to
 allow another default histidine name to be chosen

---
 src/Structure/HisProt.cpp | 24 ++++++++++++++++--------
 src/Structure/HisProt.h   |  4 +++-
 2 files changed, 19 insertions(+), 9 deletions(-)

diff --git a/src/Structure/HisProt.cpp b/src/Structure/HisProt.cpp
index a97ec8447c..68d2e4d726 100644
--- a/src/Structure/HisProt.cpp
+++ b/src/Structure/HisProt.cpp
@@ -19,7 +19,7 @@ static inline void warn_length(std::string const& nameIn) {
 const char* HisProt::keywords_ =
   "\t[{nohisdetect |\n"
   "\t  [nd1 <nd1>] [ne2 <ne2] [hisname <his>] [hiename <hie>]\n"
-  "\t  [hidname <hid>] [hipname <hip]}]\n";
+  "\t  [hidname <hid>] [hipname <hip]} [defaulthis <default>]]\n";
 
 /** Initialize from args. Get atom/residue names. */
 int HisProt::InitHisProt(ArgList& argIn, int debugIn) {
@@ -29,12 +29,15 @@ int HisProt::InitHisProt(ArgList& argIn, int debugIn) {
   hiename_ = argIn.GetStringKey("hiename", "HIE");
   hidname_ = argIn.GetStringKey("hidname", "HID");
   hipname_ = argIn.GetStringKey("hipname", "HIP");
+  default_ = argIn.GetStringKey("defaulthis");
   warn_length(nd1name_);
   warn_length(ne2name_);
   warn_length(hisname_);
   warn_length(hiename_);
   warn_length(hidname_);
   warn_length(hipname_);
+  if (!default_.empty())
+    warn_length(default_);
   return 0;
 }
 
@@ -47,12 +50,14 @@ void HisProt::HisProtInfo() const {
   mprintf("\t\tEpsilon-protonated residue name : %s\n", hiename_.c_str());
   mprintf("\t\tDelta-protonated residue name   : %s\n", hidname_.c_str());
   mprintf("\t\tDoubly-protonated residue name  : %s\n", hipname_.c_str());
+  if (!default_.empty())
+     mprintf("\t\tDefault residue name            : %s\n", default_.c_str());
 }
 
 /** Determine histidine protonation from hydrogens. */
 int HisProt::DetermineHisProt(Topology& topIn) const {
   return determineHisProt(topIn, nd1name_, ne2name_, hisname_,
-                          hiename_, hiename_, hipname_);
+                          hiename_, hiename_, hipname_, default_);
 }
 
 /** Try to determine histidine protonation from existing hydrogens.
@@ -64,6 +69,7 @@ int HisProt::DetermineHisProt(Topology& topIn) const {
   * \param HieName Name for epsilon-protonated His.
   * \param HidName Name for delta-protonated His.
   * \param HipName Name for doubly-protonated His.
+  * \param defaultName optional residue name for default if nothing else detected
   */
 int HisProt::determineHisProt( Topology& topIn,
                                            NameType const& ND1,
@@ -71,7 +77,8 @@ int HisProt::determineHisProt( Topology& topIn,
                                            NameType const& HisName,
                                            NameType const& HieName,
                                            NameType const& HidName,
-                                           NameType const& HipName )
+                                           NameType const& HipName,
+                                           std::string const& defaultName )
 {
   typedef std::vector<int> Iarray;
   mprintf("\tAttempting to determine histidine form from any existing H atoms.\n");
@@ -147,12 +154,13 @@ int HisProt::determineHisProt( Topology& topIn,
       mprintf("\t\t%s => %s\n", topIn.TruncResNameOnumId(*rnum).c_str(), *HieName);
       ChangeResName( topIn.SetRes(*rnum), HieName );
       nchanged++;
+    } else if (!defaultName.empty()) {
+      // Default
+      NameType defName(defaultName);
+      mprintf("\tUsing default name '%s' for %s\n", *defName, topIn.TruncResNameOnumId(*rnum).c_str());
+      ChangeResName( topIn.SetRes(*rnum), defName );
+      nchanged++;
     }
-    //else {
-    //  // Default to epsilon
-    //  mprintf("\tUsing default name '%s' for %s\n", *HieName, topIn.TruncResNameOnumId(*rnum).c_str());
-    //  HisResNames.push_back( HieName );
-    //}
   }
   if (nchanged == 0) 
     mprintf("\tNo histidine names were changed.\n");
diff --git a/src/Structure/HisProt.h b/src/Structure/HisProt.h
index 023790933b..30a609c84e 100644
--- a/src/Structure/HisProt.h
+++ b/src/Structure/HisProt.h
@@ -30,7 +30,8 @@ class HisProt {
     static int determineHisProt(Topology&,
                                 NameType const&, NameType const&,
                                 NameType const&, NameType const&,
-                                NameType const&, NameType const&);
+                                NameType const&, NameType const&,
+                                std::string const&);
 
     std::string nd1name_; ///< Delta nitrogen atom name
     std::string ne2name_; ///< Epsilon nitrogen atom name
@@ -38,6 +39,7 @@ class HisProt {
     std::string hiename_; ///< Epsilon-protonated residue name
     std::string hidname_; ///< Delta-protonated residue name
     std::string hipname_; ///< Doubly-protonated residue name
+    std::string default_; ///< Default name if nothing detected
 };
 }
 }

From 758009600fe97995ec6e84e6e1e9a4393fb60c28 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 4 Nov 2025 09:21:32 -0500
Subject: [PATCH 1041/1492] Have sequence assign params if they are available

---
 src/Exec_Build.cpp     |   5 +-
 src/Exec_Sequence.cpp  | 114 ++++++++++++++++++-----------------------
 src/Parm/GB_Params.cpp |   8 +++
 src/Parm/GB_Params.h   |   2 +
 src/cpptrajdepend      |   6 +--
 5 files changed, 65 insertions(+), 70 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 5f0a38e8df..f630a66bec 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -792,10 +792,7 @@ void Exec_Build::Help() const
           Cpptraj::Structure::HisProt::keywords_,
           Cpptraj::Structure::Disulfide::keywords_
          );
-  mprintf("    <radii> =");
-  for (int ig = 0; ig != (int)Cpptraj::Parm::UNKNOWN_GB; ig++)
-    mprintf(" %s", Cpptraj::Parm::GbTypeKey((Cpptraj::Parm::GB_RadiiType)ig));
-  mprintf("\n");
+  Cpptraj::Parm::PrintGbRadiiKeywords();
   mprintf("  Build complete topology and parameters from given crdset.\n");
 }
 
diff --git a/src/Exec_Sequence.cpp b/src/Exec_Sequence.cpp
index 955d7baca9..2b9a51f4fc 100644
--- a/src/Exec_Sequence.cpp
+++ b/src/Exec_Sequence.cpp
@@ -2,6 +2,8 @@
 #include "AssociatedData_Connect.h"
 #include "CpptrajStdio.h"
 #include "DataSet_Parameters.h" // For casting DataSet_Parameters to ParameterSet
+#include "Parm/AssignParams.h"
+#include "Parm/GB_Params.h"
 #include "Structure/Builder.h"
 #include "Structure/Creator.h"
 
@@ -12,6 +14,7 @@ int Exec_Sequence::generate_sequence(DataSet_Coords* OUT,
                                      Cpptraj::Structure::Creator const& creator)
 const
 {
+  std::string title;
   // First, get all units in order.
   typedef std::vector<DataSet_Coords*> Uarray;
   Uarray Units;
@@ -35,6 +38,9 @@ const
       mprintf("Warning: Unit '%s' has more than 1 frame. Only using first frame.\n", unit->legend());
     }
     Units.push_back( unit );
+    // Use the first unit name as title to match leap behavior
+    if (title.empty())
+      title = *it;
     total_natom += unit->Top().Natom();
   } // END loop over sequence
   mprintf("\tFound %zu units.\n", Units.size());
@@ -47,7 +53,7 @@ const
 
   Topology topOut;
   topOut.SetDebug( debug_ );
-  topOut.SetParmName( OUT->Meta().Name(), FileName() );
+  topOut.SetParmName( title, FileName() );
   Frame frameOut;
   mprintf("\tFinal structure should have %i atoms.\n", total_natom);
   frameOut.SetupFrame( total_natom );
@@ -213,50 +219,6 @@ const
   OUT->AddFrame( frameOut );
 
   if (buildFailed) return 1;
-/*
-  Topology combinedTop;
-  combinedTop.SetDebug( debug_ );
-  combinedTop.AppendTop( Units.front()->Top() );
-  //combinedTop.SetParmBox( Units // TODO
-  combinedTop.Brief("Sequence topology:");
-
-  Frame CombinedFrame = Units.front()->AllocateFrame();
-  Units.front()->GetFrame(0, CombinedFrame);
-
-  using namespace Cpptraj::Structure;
-  Builder builder;
-  builder.SetDebug( debug_ );
-  for (unsigned int idx = 1; idx < Units.size(); idx++) {
-    mprintf("\tConnect %s atom %i to %s atom %i\n",
-            Units[idx-1]->legend(), connectAt1[idx-1]+1,
-            Units[idx]->legend(),   connectAt0[idx]  +1);
-    Frame mol1frm = Units[idx]->AllocateFrame();
-    Units[idx]->GetFrame(0, mol1frm);
-    int bondat0 = connectAt1[idx-1];
-    int bondat1 = connectAt0[idx];
-    if (bondat0 < 0 || bondat1 < 0) {
-      mprinterr("Error: Invalid connect atom(s) between %s atom %i to %s atom %i\n",
-                Units[idx-1]->legend(), bondat0+1, Units[idx]->legend(), bondat1+1);
-      return 1;
-    }
-    if (builder.Combine( combinedTop, CombinedFrame, Units[idx]->Top(), mol1frm,
-                         connectAt1[idx-1], connectAt0[idx] )) {
-      mprinterr("Error: Sequence combine between units %u %s and %u %s failed.\n",
-                idx, Units[idx-1]->legend(), idx+1, Units[idx]->legend());
-      return 1;
-    }
-  }
-
-  // Generate angles and dihedrals
-  //if (combinedTop.Nbonds() > 0) {
-  //  if (Cpptraj::Structure::GenerateBondAngleTorsionArrays(combinedTop)) {
-  //    mprinterr("Error: Angle generation failed.\n");
-  //    return 1;
-  //  }
-  //}
-
-  OUT->CoordsSetup(combinedTop, CombinedFrame.CoordsInfo());
-  OUT->AddFrame( CombinedFrame );*/
 
   return 0;
 }
@@ -265,13 +227,16 @@ const
 void Exec_Sequence::Help() const
 {
   mprintf("\tname <output set name> <unit0> <unit1> ...\n"
+          "\t[gb <radii>] [verbose <#>]\n" 
           "\t[%s]\n"
           "\t[{%s} ...]\n"
-          "\t[{%s} ...]\n"
-          "  Create a molecule from a sequence of units.\n",
+          "\t[{%s} ...]\n",
           Cpptraj::Structure::Creator::other_keywords_,
           Cpptraj::Structure::Creator::template_keywords_,
           Cpptraj::Structure::Creator::parm_keywords_);
+  Cpptraj::Parm::PrintGbRadiiKeywords();
+  mprintf("  Create a molecule from a sequence of units.\n"
+          "  If parameter sets are loaded, parameters will be assigned to <output set name>.\n");
 }
 
 
@@ -281,18 +246,23 @@ Exec::RetType Exec_Sequence::Execute(CpptrajState& State, ArgList& argIn)
   debug_ = State.Debug();
 
   // Args
+  int verbose = argIn.getKeyInt("verbose", 0);
+  // GB radii set.
+  Cpptraj::Parm::GB_RadiiType gbradii = Cpptraj::Parm::MBONDI; // Default
+  std::string gbset = argIn.GetStringKey("gb");
+  if (!gbset.empty()) {
+    gbradii = Cpptraj::Parm::GbTypeFromKey( gbset );
+    if (gbradii == Cpptraj::Parm::UNKNOWN_GB) {
+      mprinterr("Error: Unknown GB radii set: %s\n", gbset.c_str());
+      return CpptrajState::ERR;
+    }
+  }
+  // Creator args
   Cpptraj::Structure::Creator creator(debug_);
   if (creator.InitCreator(argIn, State.DSL(), debug_)) {
     return CpptrajState::ERR;
   }
-
-/*
-  Sarray LibSetNames;
-  std::string libsetname = argIn.GetStringKey("libset");
-  while (!libsetname.empty()) {
-    LibSetNames.push_back( libsetname );
-    libsetname = argIn.GetStringKey("libset");
-  } */
+  // Output COORDS set name
   std::string dsname = argIn.GetStringKey("name");
   if (dsname.empty()) {
     mprinterr("Error: No output set name specified with 'name'\n");
@@ -303,7 +273,6 @@ Exec::RetType Exec_Sequence::Execute(CpptrajState& State, ArgList& argIn)
     mprinterr("Error: Could not create output COORDS set named '%s'\n", dsname.c_str());
     return CpptrajState::ERR;
   }
-
   // Get the actual sequence from remaining args.
   Sarray main_sequence;
   ArgList remaining = argIn.RemainingArgs();
@@ -318,12 +287,6 @@ Exec::RetType Exec_Sequence::Execute(CpptrajState& State, ArgList& argIn)
   }
 
   // Info
-/*  if (!LibSetNames.empty()) {
-    mprintf("\tLibrary set names:");
-    for (Sarray::const_iterator it = LibSetNames.begin(); it != LibSetNames.end(); ++it)
-      mprintf(" %s", it->c_str());
-    mprintf("\n");
-  }*/
   mprintf("\tMain sequence:");
   for (Sarray::const_iterator it = main_sequence.begin(); it != main_sequence.end(); ++it)
     mprintf(" %s", it->c_str());
@@ -336,5 +299,30 @@ Exec::RetType Exec_Sequence::Execute(CpptrajState& State, ArgList& argIn)
     return CpptrajState::ERR;
   }
 
-  return CpptrajState::OK;
+  // Assign parameters if needed
+  Exec::RetType ret = CpptrajState::OK;
+  if (creator.HasMainParmSet()) {
+    Topology& topOut = static_cast<Topology&>( *(OUT->TopPtr()) );
+    mprintf("\tAssigning parameters.\n");
+    //t_assign_.Start();
+    Cpptraj::Parm::AssignParams AP;
+    AP.SetDebug( debug_ );
+    AP.SetVerbose( verbose );
+    if ( AP.AssignParameters( topOut, *(creator.MainParmSetPtr()) ) ) {
+      mprinterr("Error: Could not assign parameters for '%s'.\n", topOut.c_str());
+      ret = CpptrajState::ERR;
+    }
+    // Assign GB parameters
+    if (Cpptraj::Parm::Assign_GB_Radii( topOut, gbradii )) {
+      mprinterr("Error: Could not assign GB parameters for '%s'\n", topOut.c_str());
+      ret = CpptrajState::ERR;
+    }
+    // Create empty arrays for the TREE, JOIN, and IROTAT arrays
+    topOut.AllocTreeChainClassification( );
+    topOut.AllocJoinArray();
+    topOut.AllocRotateArray();
+    //t_assign_.Stop();
+  }
+
+  return ret; 
 }
diff --git a/src/Parm/GB_Params.cpp b/src/Parm/GB_Params.cpp
index 054037d05e..854abf1b59 100644
--- a/src/Parm/GB_Params.cpp
+++ b/src/Parm/GB_Params.cpp
@@ -60,6 +60,14 @@ Cpptraj::Parm::GB_RadiiType Cpptraj::Parm::GbTypeFromKey(std::string const& key)
   return UNKNOWN_GB;
 }
 
+/** Print all recognized GB radii keywords to stdout */
+void Cpptraj::Parm::PrintGbRadiiKeywords() {
+  mprintf("    <radii> =");
+  for (int ig = 0; ig != (int)UNKNOWN_GB; ig++)
+    mprintf(" %s", GbTypeKey((GB_RadiiType)ig));
+  mprintf("\n");
+}
+
 /// These are the numeric iGBparm values used in LEaP
 static const int GB_RadiiTypeIGB_[] = {
   0, // bondi
diff --git a/src/Parm/GB_Params.h b/src/Parm/GB_Params.h
index 7b716f8f23..3e32c41af2 100644
--- a/src/Parm/GB_Params.h
+++ b/src/Parm/GB_Params.h
@@ -23,6 +23,8 @@ std::string GbAmberFlag(GB_RadiiType);
 std::string GbTypeStr(GB_RadiiType);
 /// \return GB radii type corresponding to string
 GB_RadiiType GbTypeFromKey(std::string const&);
+/// Print GB radii keywords to stdout
+void PrintGbRadiiKeywords();
 /// Assign GB radii
 int Assign_GB_Radii(Topology&, GB_RadiiType);
 }
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 6085a24026..e48c7fc24f 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -210,7 +210,7 @@ CpptrajFile.o : CpptrajFile.cpp CpptrajFile.h CpptrajStdio.h FileIO.h FileIO_Bzi
 CpptrajState.o : CpptrajState.cpp Action.h ActionList.h ActionState.h Action_CreateCrd.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_Topology.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleNavigator.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 CpptrajStdio.o : CpptrajStdio.cpp Parallel.h
 CurveFit.o : CurveFit.cpp CurveFit.h
-DataFile.o : DataFile.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Cluster/Cframes.h Cluster/Cmatrix_NC.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataFile.h DataIO.h DataIO_AmberEne.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_CCP4.h DataIO_CharmmFastRep.h DataIO_CharmmOutput.h DataIO_CharmmRepLog.h DataIO_CharmmRtfPrm.h DataIO_Cmatrix_Binary.h DataIO_Cmatrix_NC.h DataIO_Coords.h DataIO_Cpout.h DataIO_Evecs.h DataIO_Gnuplot.h DataIO_Grace.h DataIO_LeapRC.h DataIO_Mdout.h DataIO_NetCDF.h DataIO_Numpy.h DataIO_OpenDx.h DataIO_Peaks.h DataIO_RemLog.h DataIO_Std.h DataIO_VecTraj.h DataIO_XVG.h DataIO_Xplor.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Unit.h Vec3.h
+DataFile.o : DataFile.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Cluster/Cframes.h Cluster/Cmatrix_NC.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataFile.h DataIO.h DataIO_AmberEne.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_CCP4.h DataIO_CharmmFastRep.h DataIO_CharmmOutput.h DataIO_CharmmRepLog.h DataIO_CharmmRtfPrm.h DataIO_Cmatrix_Binary.h DataIO_Cmatrix_NC.h DataIO_Coords.h DataIO_Cpout.h DataIO_Evecs.h DataIO_Gnuplot.h DataIO_Grace.h DataIO_LeapRC.h DataIO_Mdout.h DataIO_NetCDF.h DataIO_Numpy.h DataIO_OpenDx.h DataIO_Peaks.h DataIO_RemLog.h DataIO_Std.h DataIO_VecTraj.h DataIO_XVG.h DataIO_Xplor.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Unit.h Vec3.h
 DataFileList.o : DataFileList.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 DataFilter.o : DataFilter.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_integer.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 DataIO.o : DataIO.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
@@ -360,12 +360,12 @@ Exec_ReadInput.o : Exec_ReadInput.cpp Action.h ActionList.h ActionState.h Analys
 Exec_RotateDihedral.o : Exec_RotateDihedral.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_RotateDihedral.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_RunAnalysis.o : Exec_RunAnalysis.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_RunAnalysis.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_ScaleDihedralK.o : Exec_ScaleDihedralK.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ScaleDihedralK.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_Sequence.o : Exec_Sequence.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Sequence.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/Creator.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Sequence.o : Exec_Sequence.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Sequence.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/Creator.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_SequenceAlign.o : Exec_SequenceAlign.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SequenceAlign.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Unit.h Vec3.h
 Exec_Set.o : Exec_Set.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_StringVar.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Set.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_Show.o : Exec_Show.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_StringVar.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Show.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_SortEnsembleData.o : Exec_SortEnsembleData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h DataSet_PHREMD_Implicit.h DataSet_pH.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SortEnsembleData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_Source.o : Exec_Source.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Source.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_Source.o : Exec_Source.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Source.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_SplitCoords.o : Exec_SplitCoords.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SplitCoords.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_System.o : Exec_System.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_System.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_Top.o : Exec_Top.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Top.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h TopInfo.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h

From a87c7a7b8bd6d855681bc6cb7772459298f55b41 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 4 Nov 2025 10:15:51 -0500
Subject: [PATCH 1042/1492] Full data set name no longer valid for unit names

---
 test/Test_Sequence/RunTest.sh | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/test/Test_Sequence/RunTest.sh b/test/Test_Sequence/RunTest.sh
index 3b75d54222..35a23430ff 100755
--- a/test/Test_Sequence/RunTest.sh
+++ b/test/Test_Sequence/RunTest.sh
@@ -14,8 +14,8 @@ Basic() {
 readdata ../Test_ReadOFF/aminocn15ipq_10.0.lib name A15
 readdata cph_nucleic_caps.lib name CAPS
 list
-sequence CAPS[MOC] A15[CNALA] name Mol
-crdout Mol Mol.mol2
+#sequence CAPS[MOC] A15[CNALA] name Mol
+#crdout Mol Mol.mol2
 
 sequence MOC CNALA name Mol2
 crdout Mol2 Mol2.mol2
@@ -24,7 +24,7 @@ crdout CAPS[MOC] MOC.mol2
 crdout A15[CNALA] CNALA.mol2
 EOF
   RunCpptraj "$TESTNAME, library files"
-  DoTest Mol.mol2.save Mol.mol2
+#  DoTest Mol.mol2.save Mol.mol2
   DoTest Mol.mol2.save Mol2.mol2
 
   # NOTE: Depends on mol2 generation of previous test

From 2f2b3d69ab417b70b9a81119dda366221b9e1012 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 4 Nov 2025 10:31:18 -0500
Subject: [PATCH 1043/1492] Hide some debug info

---
 src/Exec_Graft.cpp        | 35 ++++++++++++++++++-----------
 src/Exec_Sequence.cpp     | 13 ++++++-----
 src/Structure/Builder.cpp | 47 ++++++++++++++++++++++-----------------
 src/Structure/Builder.h   |  2 +-
 4 files changed, 57 insertions(+), 40 deletions(-)

diff --git a/src/Exec_Graft.cpp b/src/Exec_Graft.cpp
index 37065f6a93..1ec88cf5f6 100644
--- a/src/Exec_Graft.cpp
+++ b/src/Exec_Graft.cpp
@@ -320,14 +320,16 @@ int Exec_Graft::get_original_orientations(Topology const& mol0Top, Frame const&
   int vanish0idx = -1;
   for (Atom::bond_iterator bat = At0.bondbegin(); bat != At0.bondend(); ++bat) {
     if (!cmask0.AtomInCharMask( *bat )) { // TODO check multiple disappearing atoms
-      mprintf("DEBUG: Atom0 %s will vanish.\n", mol0Top.AtomMaskName(*bat).c_str());
+      if (debug_ > 0)
+        mprintf("DEBUG: Atom0 %s will vanish.\n", mol0Top.AtomMaskName(*bat).c_str());
       if (vanish0idx == -1) vanish0idx = *bat;
     }
   }
   if (vanish0idx != -1) {
     hasOrient0_ = true;
     chi0_    = Builder::DetermineChiralityAroundAtom(bondat0, mol0frm, mol0Top);
-    mprintf("DEBUG: Chirality around %s is %f\n", mol0Top.LeapName(bondat0).c_str(), chi0_);
+    if (debug_ > 0)
+      mprintf("DEBUG: Chirality around %s is %f\n", mol0Top.LeapName(bondat0).c_str(), chi0_);
 //    orient0_ = Builder::CalculateOrientationAroundAtom(bondat0, vanish0idx, mol0frm, mol0Top);
   }
 
@@ -337,14 +339,16 @@ int Exec_Graft::get_original_orientations(Topology const& mol0Top, Frame const&
   int vanish1idx = -1;
   for (Atom::bond_iterator bat = At1.bondbegin(); bat != At1.bondend(); ++bat) {
     if (!cmask1.AtomInCharMask( *bat )) { // TODO check multiple disappearing atoms
-      mprintf("DEBUG: Atom1 %s will vanish.\n", mol1Top.AtomMaskName(*bat).c_str());
+      if (debug_ > 0)
+        mprintf("DEBUG: Atom1 %s will vanish.\n", mol1Top.AtomMaskName(*bat).c_str());
       if (vanish1idx == -1) vanish1idx = *bat;
     }
   }
   if (vanish1idx != -1) {
     hasOrient1_ = true;
     chi1_    = Builder::DetermineChiralityAroundAtom(bondat1, mol1frm, mol1Top);
-    mprintf("DEBUG: Chirality around %s is %f\n", mol1Top.LeapName(bondat1).c_str(), chi1_);
+    if (debug_ > 0)
+      mprintf("DEBUG: Chirality around %s is %f\n", mol1Top.LeapName(bondat1).c_str(), chi1_);
 //    orient1_ = Builder::CalculateOrientationAroundAtom(bondat1, vanish1idx, mol1frm, mol1Top);
   }
 
@@ -379,12 +383,14 @@ const
     return 1;
   }
 
-  for (int at = 0; at != mol0Top.Natom(); at++)
-    mprintf("\t%6i %s %s\n", at+1, mol0Top.AtomMaskName(at).c_str(), *(mol0Top.Res(mol0Top[at].ResNum()).Name()));
-  mprintf("BOND ATOM 0 %i\n", bondat0+1);
-  for (int at = 0; at != mol1Top.Natom(); at++)
-    mprintf("\t%6i %s %s\n", at+1, mol1Top.AtomMaskName(at).c_str(), *(mol1Top.Res(mol1Top[at].ResNum()).Name()));
-  mprintf("BOND ATOM 1 %i\n", bondat1+1);
+  if (debug_ > 0) {
+    for (int at = 0; at != mol0Top.Natom(); at++)
+      mprintf("\t%6i %s %s\n", at+1, mol0Top.AtomMaskName(at).c_str(), *(mol0Top.Res(mol0Top[at].ResNum()).Name()));
+    mprintf("BOND ATOM 0 %i\n", bondat0+1);
+    for (int at = 0; at != mol1Top.Natom(); at++)
+      mprintf("\t%6i %s %s\n", at+1, mol1Top.AtomMaskName(at).c_str(), *(mol1Top.Res(mol1Top[at].ResNum()).Name()));
+    mprintf("BOND ATOM 1 %i\n", bondat1+1);
+  }
 
   // Combine topologies.
   Topology topOut;
@@ -409,7 +415,8 @@ const
     // Save the intra-residue bonds.
     for (Atom::bond_iterator bat = sourceAtom.bondbegin(); bat != sourceAtom.bondend(); ++bat) {
       if (*bat > at) {
-        mprintf("Will add bond between %i and %i\n", at+1, *bat+1);
+        if (debug_ > 1)
+          mprintf("Will add bond between %i and %i\n", at+1, *bat+1);
         intraResBonds.push_back( Ipair(at, *bat) );
       }
     }
@@ -421,7 +428,8 @@ const
   // Add mol1 atoms
   int atomOffset = mol0Top.Natom();
   int resOffset = topOut.Nres();
-  mprintf("DEBUG: Atom offset is %i\n", atomOffset);
+  if (debug_ > 0)
+    mprintf("DEBUG: Atom offset is %i\n", atomOffset);
   for (int itgt = 0; itgt < mol1Top.Natom(); itgt++) {
     Atom sourceAtom = mol1Top[itgt];
     Residue currentRes = mol1Top.Res(sourceAtom.ResNum());
@@ -431,7 +439,8 @@ const
     for (Atom::bond_iterator bat = sourceAtom.bondbegin(); bat != sourceAtom.bondend(); ++bat) {
       int at1 = *bat + atomOffset;
       if (at1 > at0) {
-        mprintf("Will add bond between %i and %i (original %i and %i)\n", at0+1, at1+1, itgt+1, *bat + 1);
+        if (debug_ > 1)
+          mprintf("Will add bond between %i and %i (original %i and %i)\n", at0+1, at1+1, itgt+1, *bat + 1);
         intraResBonds.push_back( Ipair(at0, at1) );
       }
     }
diff --git a/src/Exec_Sequence.cpp b/src/Exec_Sequence.cpp
index 2b9a51f4fc..f3394a6ae4 100644
--- a/src/Exec_Sequence.cpp
+++ b/src/Exec_Sequence.cpp
@@ -174,14 +174,15 @@ const
         return 1;
       }
       structureBuilder.UpdateIndicesWithOffset( *it );
-
-      mprintf("DEBUG: ***** BUILD unit %li %s *****\n", ires + 1,
-              topOut.TruncResNameOnumId(ires).c_str());
+      if (debug_ > 0)
+        mprintf("DEBUG: ***** BUILD unit %li %s *****\n", ires + 1,
+                topOut.TruncResNameOnumId(ires).c_str());
 
       // Connect unit
-      mprintf("DEBUG: Linking atoms %s and %s\n",
-              topOut.AtomMaskName(interResBonds[ires].first).c_str(),
-              topOut.AtomMaskName(interResBonds[ires].second).c_str());
+      if (debug_ > 0)
+        mprintf("DEBUG: Linking atoms %s and %s\n",
+                topOut.AtomMaskName(interResBonds[ires].first).c_str(),
+                topOut.AtomMaskName(interResBonds[ires].second).c_str());
       topOut.AddBond( interResBonds[ires].first, interResBonds[ires].second );
       // Generate internals around the link
       if (structureBuilder.GenerateInternalsAroundLink(interResBonds[ires].first, interResBonds[ires].second,
diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 484da021f8..16a497240b 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -116,11 +116,12 @@ static int atom_depth(int& depth,
 }
 
 /** \return Index of atom with longest 'depth' around an atom, ignoring one bonded atom. */
-int Builder::get_depths_around_atom(int at0, int at1, Topology const& topIn) {
+int Builder::get_depths_around_atom(int at0, int at1, Topology const& topIn) const {
   int largest_depth = 0;
   int largest_depth_idx = -1;
   Atom const& Atm0 = topIn[at0];
-  mprintf("DEBUG: Depths around %s\n", topIn.AtomMaskName(at0).c_str());
+  if (debug_ > 0)
+    mprintf("DEBUG: Depths around %s\n", topIn.AtomMaskName(at0).c_str());
   for (Atom::bond_iterator bat = Atm0.bondbegin(); bat != Atm0.bondend(); ++bat)
   {
     if (*bat != at1) {
@@ -130,7 +131,8 @@ int Builder::get_depths_around_atom(int at0, int at1, Topology const& topIn) {
       // Get depth from here
       int currentDepth = 0;
       int depth = atom_depth(currentDepth, *bat, topIn, visited, 10);
-      mprintf("DEBUG:\t\t%s = %i\n", topIn.AtomMaskName(*bat).c_str(), depth);
+      if (debug_ > 0)
+        mprintf("DEBUG:\t\t%s = %i\n", topIn.AtomMaskName(*bat).c_str(), depth);
       if (depth > largest_depth) {
         largest_depth = depth;
         largest_depth_idx = *bat;
@@ -146,11 +148,12 @@ int Builder::AdjustIcAroundLink(int at0, int at1, Frame const& frameIn, Topology
   int atA = get_depths_around_atom(at0, at1, topIn);
   int atD = get_depths_around_atom(at1, at0, topIn);
   if (atA < 0 || atD < 0) return 0;
-  mprintf("DEBUG: Highest depth torsion is %s - %s - %s - %s\n",
-          topIn.AtomMaskName(atA).c_str(),
-          topIn.AtomMaskName(at0).c_str(),
-          topIn.AtomMaskName(at1).c_str(),
-          topIn.AtomMaskName(atD).c_str());
+  if (debug_ > 0)
+    mprintf("DEBUG: Highest depth torsion is %s - %s - %s - %s\n",
+            topIn.AtomMaskName(atA).c_str(),
+            topIn.AtomMaskName(at0).c_str(),
+            topIn.AtomMaskName(at1).c_str(),
+            topIn.AtomMaskName(atD).c_str());
   // Get that torsion
   int tidx = getExistingTorsionIdx(atA, at0, at1, atD);
   if (tidx < 0) {
@@ -165,25 +168,29 @@ int Builder::AdjustIcAroundLink(int at0, int at1, Frame const& frameIn, Topology
   double dTorsion = 180.0 * Constants::DEGRAD;
   double dInternalValue = internalTorsions_[tidx].PhiVal();
   double tDiff = (dTorsion - dInternalValue);
-  mprintf("\tdTorsion= %f  dInternalValue= %f  tDiff= %f\n",
-          dTorsion*Constants::RADDEG, dInternalValue*Constants::RADDEG, tDiff*Constants::RADDEG);
+  if (debug_ > 0)
+    mprintf("\tdTorsion= %f  dInternalValue= %f  tDiff= %f\n",
+            dTorsion*Constants::RADDEG, dInternalValue*Constants::RADDEG, tDiff*Constants::RADDEG);
   if (fabs(tDiff) > Constants::SMALL) {
     // Find all ICs that share atoms 1 and 2 (J and K)
     Iarray iTorsions = getExistingTorsionIdxs(at0, at1);
-    mprintf("Twisting torsions centered on %s - %s by %f degrees\n",
-            topIn.LeapName(at0).c_str(),
-            topIn.LeapName(at1).c_str(),
-            tDiff*Constants::RADDEG);
+    if (debug_ > 0)
+      mprintf("Twisting torsions centered on %s - %s by %f degrees\n",
+              topIn.LeapName(at0).c_str(),
+              topIn.LeapName(at1).c_str(),
+              tDiff*Constants::RADDEG);
     for (Iarray::const_iterator idx = iTorsions.begin(); idx != iTorsions.end(); ++idx)
     {
       InternalTorsion& dih = internalTorsions_[*idx];
       double dNew = dih.PhiVal() + tDiff;
-      mprintf("Twisting torsion for atoms: %s-%s-%s-%s\n",
-              *(topIn[dih.AtI()].Name()),
-              *(topIn[dih.AtJ()].Name()),
-              *(topIn[dih.AtK()].Name()),
-              *(topIn[dih.AtL()].Name()));
-      mprintf("------- From %f to %f\n", dih.PhiVal()*Constants::RADDEG, dNew*Constants::RADDEG);
+      if (debug_ > 1) {
+        mprintf("Twisting torsion for atoms: %s-%s-%s-%s\n",
+                *(topIn[dih.AtI()].Name()),
+                *(topIn[dih.AtJ()].Name()),
+                *(topIn[dih.AtK()].Name()),
+                *(topIn[dih.AtL()].Name()));
+        mprintf("------- From %f to %f\n", dih.PhiVal()*Constants::RADDEG, dNew*Constants::RADDEG);
+      }
       dih.SetPhiVal( dNew );
     }
   }
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index 983933ff9e..a8d257457b 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -122,7 +122,7 @@ class Builder {
     /// For debug, print all valid internals associated with an atom
     void printAllInternalsForAtom(int, Topology const&, Barray const&) const;
     /// \\return index of atom with longest 'depth' bonded to a given atom (ignoring one bonded atom).
-    static int get_depths_around_atom(int, int, Topology const&);
+    int get_depths_around_atom(int, int, Topology const&) const;
     /// Get any complete internal coords for specified atom
     AtomIC getInternalCoordsForAtom(int, int, Barray const&, Topology const&) const;
     /// Build XYZ coords for an atom from 2 angles and 1 bond

From 9d1621671b2fff0f338ef342dfd9bcaffee5d94b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 4 Nov 2025 10:36:13 -0500
Subject: [PATCH 1044/1492] Hide more debug info

---
 src/Exec_PrepareForLeap.cpp         | 5 +++--
 src/Structure/MetalCenterFinder.cpp | 8 +++++---
 2 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/src/Exec_PrepareForLeap.cpp b/src/Exec_PrepareForLeap.cpp
index 5f6caa6a9b..4e9719f948 100644
--- a/src/Exec_PrepareForLeap.cpp
+++ b/src/Exec_PrepareForLeap.cpp
@@ -464,7 +464,7 @@ int Exec_PrepareForLeap::DownloadParameters(ResStatArray& resStat, RmapType cons
 const
 {
   Cpptraj::Remote remote( parameterURL_ );
-  remote.SetDebug(1); // FIXME
+  remote.SetDebug(debug_);
   for (RmapType::const_iterator it = resNames.begin(); it != resNames.end(); ++it)
   {
     std::string rname = it->first.Truncated();
@@ -476,7 +476,8 @@ const
     // of the first letter of the residue.
     char lcase = tolower( rname[0] );
     std::string rfbase = std::string(1, lcase) + "/" + rname;
-    mprintf("DEBUG: Base name: %s\n", rfbase.c_str());
+    if (debug_ > 0)
+      mprintf("DEBUG: Base name: %s\n", rfbase.c_str());
     int err = 0;
     err += remote.DownloadFile( rfbase + ".mol2" );
     if (err == 0) {
diff --git a/src/Structure/MetalCenterFinder.cpp b/src/Structure/MetalCenterFinder.cpp
index 15dd9105ee..a4c9f0e3c5 100644
--- a/src/Structure/MetalCenterFinder.cpp
+++ b/src/Structure/MetalCenterFinder.cpp
@@ -92,16 +92,18 @@ int MetalCenterFinder::FindMetalCenters(Topology const& topIn, Frame const& fram
 
       double dist2 = DIST2_NoImage( xyz0, xyz1 );
       if (dist2 < dcut2_) {
-        mprintf("DEBUG: Potential metal center at %s, coordinating atom %s, dist %f Ang\n",
+        mprintf("\tPotential metal center at %s, coordinating atom %s, dist %f Ang\n",
                 topIn.AtomMaskName(metalAt).c_str(),
                 topIn.AtomMaskName(coordAt).c_str(),
                 sqrt(dist2));
         MCmap::iterator it = metalCenters_.lower_bound( metalAt );
         if (it == metalCenters_.end() || it->first != metalAt) {
-          mprintf("DEBUG: New metal center.\n");
+          if (debug_ > 0)
+            mprintf("DEBUG: New metal center.\n");
           it = metalCenters_.insert(it, MCpair(metalAt, Iarray(1, coordAt)));
         } else {
-          mprintf("DEBUG: Existing metal center.\n");
+          if (debug_ > 0)
+            mprintf("DEBUG: Existing metal center.\n");
           it->second.push_back( coordAt );
         }
       }

From 1a76c60d78e6fd1273959188bb19731c3ce0c628 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 5 Nov 2025 09:12:22 -0500
Subject: [PATCH 1045/1492] Fix memory leak in diagmatrix

---
 src/DataSet_Modes.cpp | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/DataSet_Modes.cpp b/src/DataSet_Modes.cpp
index 5cfafe9efd..034f2d2001 100644
--- a/src/DataSet_Modes.cpp
+++ b/src/DataSet_Modes.cpp
@@ -341,8 +341,7 @@ int DataSet_Modes::CalcEigen(DataSet_2D const& mIn, int n_to_calc) {
     // for matrices/vectors used by the Lanczos iteration.
     int ipntr[11];
     std::fill( ipntr, ipntr + 11, 0 );
-    // Create copy of matrix since it will be modified 
-    double* mat = mIn.MatrixArray();
+    // Copy of matrix mat was created above since it will be modified by dsaupd_
     // LOOP
     bool loop = false;
     do {

From 4c3fe9ab0635ef5f9c2cbb6a3b35cc9838dcb37e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 5 Nov 2025 09:36:58 -0500
Subject: [PATCH 1046/1492] Fix incorrect var assignment which was causing an
 uninitialized variable message in valgrind

---
 src/StructureMapper.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/StructureMapper.cpp b/src/StructureMapper.cpp
index a03553a470..921558db44 100644
--- a/src/StructureMapper.cpp
+++ b/src/StructureMapper.cpp
@@ -616,7 +616,7 @@ int StructureMapper::mapChiral(AtomMap& Ref, AtomMap& Tgt) {
       if (dR[1] < 0)
         ref_1 = -1;
       else
-        tgt_1 = 1;
+        ref_1 = 1;
       if (dT[0] < 0)
         tgt_0 = -1;
       else

From 0bc69f28ef71b58795aa65ce602db7435037cee6 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 6 Nov 2025 08:35:36 -0500
Subject: [PATCH 1047/1492] Add comment partition

---
 src/Topology.cpp | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index fbaa20c573..62fd6a60a7 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2044,6 +2044,7 @@ int Topology::SplitResidue(AtomMask const& maskIn, NameType const& newName)
   return SplitResidue(maskIn, newName, atomMap);
 }
 
+// -----------------------------------------------------------------------------
 /** \return BondArray with bonds for which both atoms are still present.
   * \param atomMap format Map[oldAtom]=newAtom
   */

From 2fae1ad7e825950d910074b35f4799f643388144 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 6 Nov 2025 08:53:40 -0500
Subject: [PATCH 1048/1492] Alphabetize the includes

---
 src/Topology.cpp | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index 62fd6a60a7..3d7928bf23 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -1,11 +1,11 @@
 #include <algorithm> // find, copy, fill
 #include <stack> // For large system molecule search
 #include "Topology.h"
-#include "CpptrajStdio.h"
-#include "StringRoutines.h" // integerToString 
-#include "Constants.h" // SMALL
 #include "AtomMask.h"
 #include "CharMask.h"
+#include "Constants.h" // SMALL
+#include "CpptrajStdio.h"
+#include "StringRoutines.h" // integerToString 
 
 const NonbondType Topology::LJ_EMPTY = NonbondType();
 

From 5131cd8b18f92617b333a9b92030bdaf955aa4a3 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 6 Nov 2025 09:58:51 -0500
Subject: [PATCH 1049/1492] Put AppendTop back in Topology for pytraj

---
 src/Action_ReplicateCell.cpp |  10 +-
 src/Energy/energydepend      |  10 +-
 src/Exec_CombineCoords.cpp   |   9 +-
 src/Exec_Graft.cpp           |  10 +-
 src/Parm/AssignParams.h      |   2 +-
 src/Parm/Merge.cpp           | 190 ++---------------------------------
 src/Parm/Merge.h             |  64 ++++++------
 src/Parm/parmdepend          |   2 +-
 src/Topology.cpp             | 124 ++++++++++++++++++++++-
 src/Topology.h               |   4 +
 src/cpptrajdepend            |  10 +-
 11 files changed, 189 insertions(+), 246 deletions(-)

diff --git a/src/Action_ReplicateCell.cpp b/src/Action_ReplicateCell.cpp
index 48ff98c472..b40663fbb1 100644
--- a/src/Action_ReplicateCell.cpp
+++ b/src/Action_ReplicateCell.cpp
@@ -1,7 +1,6 @@
 #include "Action_ReplicateCell.h"
 #include "CpptrajStdio.h"
 #include "DataSet_Coords.h"
-#include "Parm/Merge.h"
 
 // CONSTRUCTOR
 Action_ReplicateCell::Action_ReplicateCell() :
@@ -160,13 +159,10 @@ Action::RetType Action_ReplicateCell::Setup(ActionSetup& setup) {
     // Set up topology and frame.
     Topology* stripParm = setup.Top().modifyStateByMask( Mask1_ );
     if (stripParm == 0) return Action::ERR;
-    Cpptraj::Parm::Merge merger;
-    merger.SetDebug( debug_ );
-    merger.SetVerbose( verbose_ );
-    merger.SetReduceBondParams( true );
-    merger.SetReduceAngleParams( true );
+    combinedTop_.SetDebug( debug_ );
+    // Merge topologies, reduce bond and angle params
     for (int cell = 0; cell != ncopies_; cell++)
-      merger.AppendTop( combinedTop_, *stripParm );
+      combinedTop_.AppendTop( *stripParm, verbose_, true, true );
     combinedTop_.Brief("Combined parm:");
     delete stripParm;
     topWriter_.ModifyTop( &combinedTop_ );
diff --git a/src/Energy/energydepend b/src/Energy/energydepend
index c6fb564234..55290b47e4 100644
--- a/src/Energy/energydepend
+++ b/src/Energy/energydepend
@@ -1,14 +1,14 @@
-Ecalc_Nonbond.o : Ecalc_Nonbond.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../Energy/../Constants.h ../Energy/../ParameterTypes.h ../Energy/../SplineFxnTable.h ../Energy/Ene_LJPME_6_12.h ../Energy/Ene_LJ_6_12.h ../Energy/ErfcFxn.h ../Energy/EwaldParams.h ../Energy/EwaldParams_LJPME.h ../Energy/Kernel_EwaldAdjust.h ../Energy/Kernel_LJPME_Adjust.h ../EwaldOptions.h ../ExclusionArray.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../PairList.h ../PairListEngine_Ewald_Decomp_LJLR.h ../PairListEngine_Ewald_Decomp_LJPME.h ../PairListEngine_Ewald_LJLR.h ../PairListEngine_Ewald_LJPME.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Timer.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h ../helpme_standalone.h Ecalc_Nonbond.h Ene_Decomp_Nonbond.h Ene_LJ_6_12.h Ene_Nonbond.h EwaldCalc.h EwaldCalc_Decomp.h EwaldCalc_Decomp_LJPME.h EwaldCalc_Decomp_PME.h EwaldCalc_LJPME.h EwaldCalc_PME.h EwaldCalc_Regular.h Ewald_Recip.h PME_Recip.h PME_RecipParams.h VDW_LongRange_Correction.h
-EnergyDecomposer.o : EnergyDecomposer.cpp ../ArgList.h ../AssociatedData.h ../Atom.h ../AtomMask.h ../AtomType.h ../BaseIOtype.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataFile.h ../DataFileList.h ../DataSet.h ../DataSetList.h ../DataSet_1D.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../DataSet_Mesh.h ../Dimension.h ../DistRoutines.h ../EwaldOptions.h ../ExclusionArray.h ../FileIO.h ../FileName.h ../FileTypes.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../OnlineVarT.h ../PairList.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Spline.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Ecalc_Nonbond.h Ene_Angle.h Ene_Bond.h Ene_LJ_6_12.h EnergyDecomposer.h Kernel_Fourier.h Kernel_Harmonic.h
+Ecalc_Nonbond.o : Ecalc_Nonbond.cpp ../Atom.h ../AtomMask.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../Energy/../Constants.h ../Energy/../ParameterTypes.h ../Energy/../SplineFxnTable.h ../Energy/Ene_LJPME_6_12.h ../Energy/Ene_LJ_6_12.h ../Energy/ErfcFxn.h ../Energy/EwaldParams.h ../Energy/EwaldParams_LJPME.h ../Energy/Kernel_EwaldAdjust.h ../Energy/Kernel_LJPME_Adjust.h ../EwaldOptions.h ../ExclusionArray.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../PairList.h ../PairListEngine_Ewald_Decomp_LJLR.h ../PairListEngine_Ewald_Decomp_LJPME.h ../PairListEngine_Ewald_LJLR.h ../PairListEngine_Ewald_LJPME.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h ../helpme_standalone.h Ecalc_Nonbond.h Ene_Decomp_Nonbond.h Ene_LJ_6_12.h Ene_Nonbond.h EwaldCalc.h EwaldCalc_Decomp.h EwaldCalc_Decomp_LJPME.h EwaldCalc_Decomp_PME.h EwaldCalc_LJPME.h EwaldCalc_PME.h EwaldCalc_Regular.h Ewald_Recip.h PME_Recip.h PME_RecipParams.h VDW_LongRange_Correction.h
+EnergyDecomposer.o : EnergyDecomposer.cpp ../ArgList.h ../AssociatedData.h ../Atom.h ../AtomMask.h ../BaseIOtype.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataFile.h ../DataFileList.h ../DataSet.h ../DataSetList.h ../DataSet_1D.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../DataSet_Mesh.h ../Dimension.h ../DistRoutines.h ../EwaldOptions.h ../ExclusionArray.h ../FileIO.h ../FileName.h ../FileTypes.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../OnlineVarT.h ../PairList.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Spline.h ../Stats_Reduce.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../TorsionRoutines.h ../Unit.h ../Vec3.h Ecalc_Nonbond.h Ene_Angle.h Ene_Bond.h Ene_LJ_6_12.h EnergyDecomposer.h Kernel_Fourier.h Kernel_Harmonic.h
 ErfcFxn.o : ErfcFxn.cpp ../CpptrajStdio.h ../SplineFxnTable.h ErfcFxn.h
 EwaldCalc_Decomp_LJPME.o : EwaldCalc_Decomp_LJPME.cpp ../Atom.h ../AtomMask.h ../Box.h ../CoordinateInfo.h ../CpptrajStdio.h ../Energy/../Constants.h ../Energy/../ParameterTypes.h ../Energy/../SplineFxnTable.h ../Energy/Ene_LJPME_6_12.h ../Energy/ErfcFxn.h ../Energy/EwaldParams.h ../Energy/EwaldParams_LJPME.h ../Energy/Kernel_EwaldAdjust.h ../Energy/Kernel_LJPME_Adjust.h ../EwaldOptions.h ../ExclusionArray.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../PairList.h ../PairListEngine_Ewald_Decomp_LJPME.h ../PairListTemplate.h ../Parallel.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Timer.h ../Unit.h ../Vec3.h ../helpme_standalone.h EwaldCalc.h EwaldCalc_Decomp.h EwaldCalc_Decomp_LJPME.h PME_Recip.h PME_RecipParams.h
 EwaldCalc_Decomp_PME.o : EwaldCalc_Decomp_PME.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../Energy/../Constants.h ../Energy/../ParameterTypes.h ../Energy/../SplineFxnTable.h ../Energy/Ene_LJ_6_12.h ../Energy/ErfcFxn.h ../Energy/EwaldParams.h ../Energy/Kernel_EwaldAdjust.h ../EwaldOptions.h ../ExclusionArray.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../PairList.h ../PairListEngine_Ewald_Decomp_LJLR.h ../PairListTemplate.h ../Parallel.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Timer.h ../Unit.h ../Vec3.h ../helpme_standalone.h EwaldCalc.h EwaldCalc_Decomp.h EwaldCalc_Decomp_PME.h PME_Recip.h PME_RecipParams.h VDW_LongRange_Correction.h
 EwaldCalc_LJPME.o : EwaldCalc_LJPME.cpp ../Atom.h ../AtomMask.h ../Box.h ../CoordinateInfo.h ../CpptrajStdio.h ../Energy/../Constants.h ../Energy/../ParameterTypes.h ../Energy/../SplineFxnTable.h ../Energy/Ene_LJPME_6_12.h ../Energy/ErfcFxn.h ../Energy/EwaldParams.h ../Energy/EwaldParams_LJPME.h ../Energy/Kernel_EwaldAdjust.h ../Energy/Kernel_LJPME_Adjust.h ../EwaldOptions.h ../ExclusionArray.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../PairList.h ../PairListEngine_Ewald_LJPME.h ../PairListTemplate.h ../Parallel.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Timer.h ../Unit.h ../Vec3.h ../helpme_standalone.h EwaldCalc.h EwaldCalc_LJPME.h PME_Recip.h PME_RecipParams.h
 EwaldCalc_PME.o : EwaldCalc_PME.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../Energy/../Constants.h ../Energy/../ParameterTypes.h ../Energy/../SplineFxnTable.h ../Energy/Ene_LJ_6_12.h ../Energy/ErfcFxn.h ../Energy/EwaldParams.h ../Energy/Kernel_EwaldAdjust.h ../EwaldOptions.h ../ExclusionArray.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../PairList.h ../PairListEngine_Ewald_LJLR.h ../PairListTemplate.h ../Parallel.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Timer.h ../Unit.h ../Vec3.h ../helpme_standalone.h EwaldCalc.h EwaldCalc_PME.h PME_Recip.h PME_RecipParams.h VDW_LongRange_Correction.h
 EwaldCalc_Regular.o : EwaldCalc_Regular.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../Energy/../Constants.h ../Energy/../ParameterTypes.h ../Energy/../SplineFxnTable.h ../Energy/Ene_LJ_6_12.h ../Energy/ErfcFxn.h ../Energy/EwaldParams.h ../Energy/Kernel_EwaldAdjust.h ../EwaldOptions.h ../ExclusionArray.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../PairList.h ../PairListEngine_Ewald_LJLR.h ../PairListTemplate.h ../Parallel.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Timer.h ../Unit.h ../Vec3.h EwaldCalc.h EwaldCalc_Regular.h Ewald_Recip.h VDW_LongRange_Correction.h
-EwaldParams.o : EwaldParams.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../EwaldOptions.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SplineFxnTable.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h ErfcFxn.h EwaldParams.h
-EwaldParams_LJPME.o : EwaldParams_LJPME.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../EwaldOptions.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SplineFxnTable.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h ErfcFxn.h EwaldParams.h EwaldParams_LJPME.h
+EwaldParams.o : EwaldParams.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../EwaldOptions.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SplineFxnTable.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h ErfcFxn.h EwaldParams.h
+EwaldParams_LJPME.o : EwaldParams_LJPME.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../EwaldOptions.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SplineFxnTable.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h ErfcFxn.h EwaldParams.h EwaldParams_LJPME.h
 Ewald_Recip.o : Ewald_Recip.cpp ../Box.h ../Constants.h ../CpptrajStdio.h ../EwaldOptions.h ../Matrix_3x3.h ../Parallel.h ../ParameterTypes.h ../SplineFxnTable.h ../StringRoutines.h ../Timer.h ../Vec3.h ErfcFxn.h EwaldParams.h Ewald_Recip.h
 PME_Recip.o : PME_Recip.cpp ../Box.h ../CpptrajStdio.h ../Matrix_3x3.h ../Parallel.h ../Timer.h ../Vec3.h ../helpme_standalone.h PME_Recip.h PME_RecipParams.h
 PME_RecipParams.o : PME_RecipParams.cpp ../Box.h ../CpptrajStdio.h ../EwaldOptions.h ../Matrix_3x3.h ../Parallel.h ../Vec3.h PME_RecipParams.h
-VDW_LongRange_Correction.o : VDW_LongRange_Correction.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h VDW_LongRange_Correction.h
+VDW_LongRange_Correction.o : VDW_LongRange_Correction.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h VDW_LongRange_Correction.h
diff --git a/src/Exec_CombineCoords.cpp b/src/Exec_CombineCoords.cpp
index c4979b40af..65df7f1e7c 100644
--- a/src/Exec_CombineCoords.cpp
+++ b/src/Exec_CombineCoords.cpp
@@ -1,7 +1,6 @@
 #include <algorithm> // std::min, std::max
 #include "Exec_CombineCoords.h"
 #include "CpptrajStdio.h"
-#include "Parm/Merge.h"
 
 void Exec_CombineCoords::Help() const {
   mprintf("\t<crd1> <crd2> ... [parmname <topname>] [crdname <crdname>]\n"
@@ -62,9 +61,7 @@ Exec::RetType Exec_CombineCoords::Execute(CpptrajState& State, ArgList& argIn) {
   if (nobox) boxStatus = INVALID;
   Box combinedBox;
   size_t minSize = CRD[0]->Size();
-  Cpptraj::Parm::Merge merger;
-  merger.SetDebug( State.Debug() );
-  merger.SetDebug( verbose );
+  CombinedTop.SetDebug( State.Debug() );
   for (unsigned int setnum = 0; setnum != CRD.size(); ++setnum) {
     if (CRD[setnum]->Size() < minSize)
       minSize = CRD[setnum]->Size();
@@ -84,8 +81,8 @@ Exec::RetType Exec_CombineCoords::Execute(CpptrajState& State, ArgList& argIn) {
         }
       }
     }
-    // Append
-    merger.AppendTop( CombinedTop, CRD[setnum]->Top() );
+    // Append. Do not reduce bond/angle params TODO should they be reduced?
+    CombinedTop.AppendTop( CRD[setnum]->Top(), verbose, false, false );
   }
   CombinedTop.SetParmBox( combinedBox );
   CombinedTop.Brief("Combined parm:");
diff --git a/src/Exec_Graft.cpp b/src/Exec_Graft.cpp
index 1ec88cf5f6..23521c06b2 100644
--- a/src/Exec_Graft.cpp
+++ b/src/Exec_Graft.cpp
@@ -2,7 +2,6 @@
 #include "CharMask.h"
 #include "CpptrajStdio.h"
 #include "DataSet_Coords.h"
-#include "Parm/Merge.h"
 #include "Structure/Builder.h"
 #include "Structure/Zmatrix.h"
 #include <algorithm> // std::copy
@@ -531,15 +530,12 @@ int Exec_Graft::graft_rms(DataSet_Coords* outCoords,
                                     Sarray const& bond0Atoms, Sarray const& bond1Atoms)
 const
 {
-  Cpptraj::Parm::Merge merger;
-  merger.SetDebug( debug_ );
-  merger.SetVerbose( verbose_ );
-  // Combine topologies. Use target box info.
+  // Combine topologies. Use target box info. Do not merge bond/angle params TODO should they be reduced?
   Topology combinedTop;
   combinedTop.SetDebug( debug_ );
   combinedTop.SetParmName( outCoords->Meta().Name(), FileName() );
-  merger.AppendTop( combinedTop, mol0Top );
-  merger.AppendTop( combinedTop, mol1Top );
+  combinedTop.AppendTop( mol0Top, verbose_, false, false );
+  combinedTop.AppendTop( mol1Top, verbose_, false, false );
 
   // Add any bonds
   for (unsigned int ii = 0; ii != bond0Atoms.size(); ii++) {
diff --git a/src/Parm/AssignParams.h b/src/Parm/AssignParams.h
index b6dc9d8992..8269720a57 100644
--- a/src/Parm/AssignParams.h
+++ b/src/Parm/AssignParams.h
@@ -52,7 +52,7 @@ class AssignParams {
 #   else
       const;
 #   endif
-    // Assign nonbond parameters to topology. Used during Merge::AppendTop()
+    // Assign nonbond parameters to topology. Used during Topology::AppendTop()
     void AssignNonbondParams(Topology&,
                              ParmHolder<AtomType> const&,
                              ParmHolder<NonbondType> const&, ParmHolder<NonbondType> const&,
diff --git a/src/Parm/Merge.cpp b/src/Parm/Merge.cpp
index 1c4e8b77bc..70b49ac209 100644
--- a/src/Parm/Merge.cpp
+++ b/src/Parm/Merge.cpp
@@ -1,46 +1,13 @@
 #include "Merge.h"
-#include "AssignParams.h"
-#include "GetParams.h"
 #include "ParmHolder.h"
 #include "../Atom.h"
-#include "../AtomType.h"
 #include "../CpptrajStdio.h"
 #include "../ParameterTypes.h"
 #include "../Residue.h"
 #include "../StringRoutines.h" // integerToString
-#include "../Topology.h"
-#include "../UpdateParameters.h"
 
 using namespace Cpptraj::Parm;
 
-/** CONSTRUCTOR */
-Merge::Merge() :
-  debug_(0),
-  verbose_(0),
-  reduce_bond_params_(false),
-  reduce_angle_params_(false)
-{}
-
-/** Set debug */
-void Merge::SetDebug(int debugIn) {
-  debug_ = debugIn;
-}
-
-/** Set verbosity */
-void Merge::SetVerbose(int verboseIn) {
-  verbose_ = verboseIn;
-}
-
-/** Indicate bond parameters should be consolidated. */
-void Merge::SetReduceBondParams(bool bIn) {
-  reduce_bond_params_ = bIn;
-}
-
-/** Indicate angle parameters should be consolidated. */
-void Merge::SetReduceAngleParams(bool bIn) {
-  reduce_angle_params_ = bIn;
-}
-
 // ----- Bonds -------------------------
 #ifdef CPPTRAJ_DEBUG_MERGE
 static inline void printIdx(BondType const& bnd1, unsigned int atomOffset) {
@@ -481,7 +448,7 @@ class MergeTopArray
   * arrays from top1, merge the bond arrays and consolidate the
   * parameters.
   */
-void Merge::MergeBondArrays(BondArray& bonds0,
+void Cpptraj::Parm::MergeBondArrays(bool reduce_bond_params, BondArray& bonds0,
                                     BondArray& bondsh0,
                                     BondParmArray& bp0,
                                     AtArray const& atoms0,
@@ -489,10 +456,9 @@ void Merge::MergeBondArrays(BondArray& bonds0,
                                     BondArray const& bondsh1,
                                     BondParmArray const& bp1,
                                     AtArray const& atoms1)
-const
 {
   MergeTopArray<BondType, BondParmType, BondArray, BondParmArray> mergeBonds;
-  mergeBonds.SetMergeWithExisting( reduce_bond_params_ );
+  mergeBonds.SetMergeWithExisting( reduce_bond_params );
   mergeBonds.MergeTermArrays( bonds0, bondsh0, bp0, atoms0,
                               bonds1, bondsh1, bp1, atoms1 );
 }
@@ -503,7 +469,7 @@ const
   * arrays from top1, merge the angle arrays and consolidate the
   * parameters.
   */
-void Merge::MergeAngleArrays(AngleArray& angles0,
+void Cpptraj::Parm::MergeAngleArrays(bool reduce_angle_params, AngleArray& angles0,
                                     AngleArray& anglesh0,
                                     AngleParmArray& ap0,
                                     AtArray const& atoms0,
@@ -511,10 +477,9 @@ void Merge::MergeAngleArrays(AngleArray& angles0,
                                     AngleArray const& anglesh1,
                                     AngleParmArray const& ap1,
                                     AtArray const& atoms1)
-const
 {
   MergeTopArray<AngleType, AngleParmType, AngleArray, AngleParmArray> mergeAngles;
-  mergeAngles.SetMergeWithExisting( reduce_angle_params_ );
+  mergeAngles.SetMergeWithExisting( reduce_angle_params );
   mergeAngles.MergeTermArrays( angles0, anglesh0, ap0, atoms0,
                                angles1, anglesh1, ap1, atoms1 );
 }
@@ -542,7 +507,7 @@ static inline void merge_impropers(DihedralArray& dihOut, DihedralArray& dihIn,
   * parameter arrays from top1, merge the dihedral arrays and consolidate the
   * parameters.
   */
-void Merge::MergeDihedralArrays(DihedralArray& dihedrals0,
+void Cpptraj::Parm::MergeDihedralArrays(DihedralArray& dihedrals0,
                                     DihedralArray& dihedralsh0,
                                     DihedralParmArray& dp0,
                                     AtArray const& atoms0,
@@ -550,7 +515,6 @@ void Merge::MergeDihedralArrays(DihedralArray& dihedrals0,
                                     DihedralArray const& dihedralsh1,
                                     DihedralParmArray const& dp1,
                                     AtArray const& atoms1)
-const
 {
   // Separate any impropers.
   DihedralArray dih0, dihH0, imp0, impH0;
@@ -628,7 +592,7 @@ void index_cmap_types(Cpptraj::Parm::ParmHolder<int>& currentTypes,
 }
 
 /** Given CMAP arrays from top0 and top1, merge and consolidate parameters. */
-void Merge::MergeCmapArrays(CmapArray& cmap0,
+void Cpptraj::Parm::MergeCmapArrays(CmapArray& cmap0,
                                     CmapGridArray& cg0,
                                     AtArray const& atoms0,
                                     ResArray const& residues0,
@@ -636,7 +600,6 @@ void Merge::MergeCmapArrays(CmapArray& cmap0,
                                     CmapGridArray const& cg1,
                                     AtArray const& atoms1,
                                     ResArray const& residues1)
-const
 {
   unsigned int atomOffset = atoms0.size();
   unsigned int cgOffset = cg0.size();
@@ -728,13 +691,12 @@ const
   * array from top1, merge the bond arrays and consolidate the
   * parameters.
   */
-void Merge::MergeBondArray(BondArray& bonds0,
+void Cpptraj::Parm::MergeBondArray(BondArray& bonds0,
                                    BondParmArray& bp0,
                                    AtArray const& atoms0,
                                    BondArray const& bonds1,
                                    BondParmArray const& bp1,
                                    AtArray const& atoms1)
-const
 {
 # ifdef CPPTRAJ_DEBUG_MERGE
   mprintf("DEBUG: Enter MergeBondArray()\n");
@@ -749,13 +711,12 @@ const
   * parameter array from top1, merge the improper arrays and consolidate the
   * parameters.
   */
-void Merge::MergeImproperArray(DihedralArray& impropers0,
+void Cpptraj::Parm::MergeImproperArray(DihedralArray& impropers0,
                                        DihedralParmArray& ip0,
                                        AtArray const& atoms0,
                                        DihedralArray const& impropers1,
                                        DihedralParmArray const& ip1,
                                        AtArray const& atoms1)
-const
 {
   MergeTopArray<DihedralType, DihedralParmType, DihedralArray, DihedralParmArray> mergeImpropers;
   mergeImpropers.SetMergeWithExisting( true ); // FIXME check this
@@ -763,138 +724,3 @@ const
   mergeImpropers.MergeTermArray( impropers0, ip0, atoms0,
                                  impropers1, ip1, atoms1 );
 }
-
-// -----------------------------------------------------------------------------
-/** This template can be used when doing Append() on a generic std::vector array
-  * of type T. The array will be appended to a given array of the same type.
-  * If one is empty and the other is not, values will be filled in if necessary.
-  */
-template <class T> class TopVecAppend {
-  public:
-    /// CONSTRUCTOR
-    TopVecAppend() {}
-    /// Append current array to given array of same type
-    void Append(std::vector<T>& arrayOut, std::vector<T> const& arrayToAdd, unsigned int expectedSize)
-    {
-      if (arrayToAdd.empty() && arrayOut.empty()) {
-        // Both arrays are empty. Nothing to do.
-        return;
-      } else if (arrayToAdd.empty()) {
-        // The current array is empty but the given array is not. Fill in 
-        // array to append with blank values.
-        for (unsigned int idx = 0; idx != expectedSize; idx++)
-          arrayOut.push_back( T() );
-      } else {
-        // Append current array to array to given array. TODO use std::copy?
-        for (typename std::vector<T>::const_iterator it = arrayToAdd.begin(); it != arrayToAdd.end(); ++it)
-          arrayOut.push_back( *it );
-      }
-    }
-};
-
-/** Append a topology to another */
-int Merge::AppendTop(Topology& topOut, Topology const& NewTop) const {
-  unsigned int atomOffset = (unsigned int)topOut.Natom();
-  unsigned int molOffset = (unsigned int)topOut.Nmol();
-  if (debug_ > 0)
-    mprintf("DEBUG: Appending '%s' to '%s' (atom offset= %u mol offset= %u)\n",
-            NewTop.c_str(), topOut.c_str(), atomOffset, molOffset);
-  //int resOffset = (int)residues_.size();
-
-  // Save nonbonded parameters from each topology
-  ParmHolder<AtomType> myAtomTypes, newAtomTypes;
-  ParmHolder<NonbondType> myNB, newNB;
-  ParmHolder<NonbondType> my14, new14;
-  ParmHolder<HB_ParmType> myHB, newHB;
-  ParmHolder<double> myLJC, newLJC;
-  Cpptraj::Parm::GetParams GP;
-  GP.SetDebug( debug_ );
-  GP.GetLJAtomTypes( myAtomTypes, myNB, my14, myLJC, myHB, topOut.Atoms(), topOut.Nonbond() );
-  GP.GetLJAtomTypes( newAtomTypes, newNB, new14, newLJC, newHB, NewTop.Atoms(), NewTop.Nonbond() );
-  // Create combined nonbond parameter set
-  int nAtomTypeUpdated = UpdateParameters< ParmHolder<AtomType> >( myAtomTypes, newAtomTypes, "atom type", verbose_ );
-  int nLJparamsUpdated = UpdateParameters< ParmHolder<NonbondType> >( myNB, newNB, "LJ 6-12", verbose_ );
-  int n14paramsUpdated = UpdateParameters< ParmHolder<NonbondType> >( my14, new14, "LJ 6-12 1-4", verbose_ );
-  int nljcparamsUpdated = UpdateParameters< ParmHolder<double> >( myLJC, newLJC, "LJ C", verbose_ );
-  int nHBparamsUpdated = UpdateParameters< ParmHolder<HB_ParmType> >( myHB, newHB, "LJ 10-12", verbose_ );
-  if (verbose_ > 0)
-    mprintf("\t%i atom types updated, %i LJ 6-12 params updated, %i 1-4 params updated, %i LJC params updated, %i LJ 10-12 params updated.\n",
-            nAtomTypeUpdated, nLJparamsUpdated, n14paramsUpdated, nljcparamsUpdated, nHBparamsUpdated);
-
-  // Add incoming topology bond/angle/dihedral/cmap arrays to this one.
-  MergeBondArrays(topOut.ModifyBonds(), topOut.ModifyBondsH(), topOut.ModifyBondParm(), topOut.Atoms(),
-                  NewTop.Bonds(), NewTop.BondsH(), NewTop.BondParm(), NewTop.Atoms());
-  MergeAngleArrays(topOut.ModifyAngles(), topOut.ModifyAnglesH(), topOut.ModifyAngleParm(), topOut.Atoms(),
-                   NewTop.Angles(), NewTop.AnglesH(), NewTop.AngleParm(), NewTop.Atoms());
-  MergeDihedralArrays(topOut.ModifyDihedrals(), topOut.ModifyDihedralsH(), topOut.ModifyDihedralParm(), topOut.Atoms(),
-                      NewTop.Dihedrals(), NewTop.DihedralsH(), NewTop.DihedralParm(), NewTop.Atoms());
-  MergeCmapArrays(topOut.ModifyCmap(), topOut.ModifyCmapGrid(), topOut.Atoms(), topOut.Residues(),
-                  NewTop.Cmap(), NewTop.CmapGrid(), NewTop.Atoms(), NewTop.Residues());
-  MergeBondArray(topOut.ModifyUB(), topOut.ModifyUBparm(), topOut.Atoms(),
-                 NewTop.UB(), NewTop.UBparm(), NewTop.Atoms());
-  MergeImproperArray(topOut.ModifyImpropers(), topOut.ModifyImproperParm(), topOut.Atoms(),
-                     NewTop.Impropers(), NewTop.ImproperParm(), NewTop.Atoms());
-
-  // Append incoming atoms to this topology.
-  for (AtArray::const_iterator atom = NewTop.begin(); atom != NewTop.end(); ++atom)
-  {
-    if (debug_ > 1)
-      mprintf("DEBUG: %6li %s %s %4i\n", atom-NewTop.begin(),
-              *(atom->Name()), *(atom->Type()), atom->TypeIndex());
-    Atom CurrentAtom = *atom;
-    Residue const& res = NewTop.Res( CurrentAtom.ResNum() );
-    // Bonds need to be cleared and re-added.
-    CurrentAtom.ClearBonds();
-    for (Atom::bond_iterator bat = atom->bondbegin(); bat != atom->bondend(); ++bat)
-      CurrentAtom.AddBondToIdx( *bat + atomOffset );
-
-    topOut.addTopAtom( CurrentAtom,
-                       Residue(res.Name(), res.OriginalResNum(), res.Icode(), res.ChainID()),
-                       atom->MolNum()+molOffset, NewTop.Mol(atom->MolNum()).IsSolvent() );
-  }
-
-  // EXTRA ATOM INFO
-  TopVecAppend<NameType> appendNameType;
-  appendNameType.Append( topOut.ModifyTreeChainClassification(), NewTop.TreeChainClassification(), NewTop.Natom() );
-  TopVecAppend<int> appendInt;
-  appendInt.Append( topOut.ModifyJoinArray(), NewTop.JoinArray(), NewTop.Natom() );
-  appendInt.Append( topOut.ModifyRotateArray(), NewTop.RotateArray(), NewTop.Natom() );
-  appendInt.Append( topOut.ModifyPdbSerialNum(), NewTop.PdbSerialNum(), NewTop.Natom() );
-  TopVecAppend<char> appendChar;
-  appendChar.Append( topOut.ModifyAtomAltLoc(), NewTop.AtomAltLoc(), NewTop.Natom() );
-  TopVecAppend<float> appendFloat;
-  appendFloat.Append( topOut.ModifyOccupancy(), NewTop.Occupancy(), NewTop.Natom() );
-  appendFloat.Append( topOut.ModifyBfactor(), NewTop.Bfactor(), NewTop.Natom() );
-
-  // Need to regenerate nonbonded info
-  if (verbose_ > 0)
-    mprintf("\tRegenerating nonbond parameters.\n");
-  AssignParams assign;
-  assign.SetDebug( debug_ );
-  assign.SetVerbose( verbose_ );
-  assign.AssignNonbondParams( topOut, myAtomTypes, myNB, my14, myLJC, myHB );
-
-  // The version of AddTopAtom() with molecule number already determines
-  // molecules and number of solvent molecules.
-  // Just need to determine the number of extra points.
-  topOut.DetermineNumExtraPoints();
-
-  // GB radii set string
-  if (!NewTop.GBradiiSet().empty()) {
-    if (topOut.GBradiiSet().empty())
-      topOut.SetGBradiiSet( NewTop.GBradiiSet() );
-    else {
-      // Do not repeat a GB radius string
-      std::size_t pos = topOut.GBradiiSet().find( NewTop.GBradiiSet() );
-      if (pos == std::string::npos) {
-        std::string newName = topOut.GBradiiSet() + "+" + NewTop.GBradiiSet();
-        if (newName.size() > 80) {
-          mprintf("Warning: New radius set name is > 80 characters: '%s'\n", newName.c_str());
-          mprintf("Warning: This will be truncated to 80 characters in an Amber Topology.\n");
-        }
-        topOut.SetGBradiiSet( newName );
-      }
-    }
-  }
-  return 0;
-}
diff --git a/src/Parm/Merge.h b/src/Parm/Merge.h
index 3c8e373259..2677dbe82a 100644
--- a/src/Parm/Merge.h
+++ b/src/Parm/Merge.h
@@ -11,53 +11,59 @@ class DihedralArray;
 class DihedralParmArray;
 class CmapArray;
 class CmapGridArray;
-class Topology;
 namespace Cpptraj {
 namespace Parm {
-/// Used to merge Topology files.
+/// Routines used to merge Topology files.
 /** Compile with -DCPPTRAJ_DEBUG_MERGE for extra debug info. */
-class Merge {
-  public:
-    /// CONSTRUCTOR
-    Merge();
-    /// Set debug level
-    void SetDebug(int);
-    /// Set parameter verbosity
-    void SetVerbose(int);
-    /// Indicate bond parameters should be consolidated.
-    void SetReduceBondParams(bool);
-    /// Indicate angle parameters should be consolidated.
-    void SetReduceAngleParams(bool);
-    /// Append topology to this one.
-    int AppendTop( Topology&, Topology const& ) const;
-  private:
     /// Shorthand for array of Atoms
     typedef std::vector<Atom> AtArray;
     /// Shorthand for array of residues
     typedef std::vector<Residue> ResArray;
     /// Merge two pairs of bond arrays and their parameters.
-    void MergeBondArrays(BondArray&, BondArray&, BondParmArray&, AtArray const&,
-                         BondArray const&, BondArray const&, BondParmArray const&, AtArray const&) const;
+    void MergeBondArrays(bool, BondArray&, BondArray&, BondParmArray&, AtArray const&,
+                         BondArray const&, BondArray const&, BondParmArray const&, AtArray const&);
     /// Merge two pairs of angle arrays and their parameters.
-    void MergeAngleArrays(AngleArray&, AngleArray&, AngleParmArray&, AtArray const&,
-                          AngleArray const&, AngleArray const&, AngleParmArray const&, AtArray const&) const;
+    void MergeAngleArrays(bool, AngleArray&, AngleArray&, AngleParmArray&, AtArray const&,
+                          AngleArray const&, AngleArray const&, AngleParmArray const&, AtArray const&);
     /// Merge two pairs of dihedral arrays and their parameters.
     void MergeDihedralArrays(DihedralArray&, DihedralArray&, DihedralParmArray&, AtArray const&,
-                             DihedralArray const&, DihedralArray const&, DihedralParmArray const&, AtArray const&) const;
+                             DihedralArray const&, DihedralArray const&, DihedralParmArray const&, AtArray const&);
     /// Merge cmap arrays and their parameters
     void MergeCmapArrays(CmapArray&, CmapGridArray&, AtArray const&, ResArray const&,
-                         CmapArray const&, CmapGridArray const&, AtArray const&, ResArray const&) const;
+                         CmapArray const&, CmapGridArray const&, AtArray const&, ResArray const&);
     /// Merge two bond arrays and their parameters
     void MergeBondArray(BondArray&, BondParmArray&, AtArray const&,
-                        BondArray const&, BondParmArray const&, AtArray const&) const;
+                        BondArray const&, BondParmArray const&, AtArray const&);
     /// Merge two improper arrays and their parameters
     void MergeImproperArray(DihedralArray&, DihedralParmArray&, AtArray const&,
-                            DihedralArray const&, DihedralParmArray const&, AtArray const&) const;
+                            DihedralArray const&, DihedralParmArray const&, AtArray const&);
 
-    int debug_;
-    int verbose_;
-    bool reduce_bond_params_; ///< If true, consolidate bond parameters TODO always?
-    bool reduce_angle_params_; ///< If true, consolidate angle parameters TODO always?
+// -----------------------------------------------------------------------------
+/** This template can be used when doing Append() on a generic std::vector array
+  * of type T. The array will be appended to a given array of the same type.
+  * If one is empty and the other is not, values will be filled in if necessary.
+  */
+template <class T> class TopVecAppend {
+  public:
+    /// CONSTRUCTOR
+    TopVecAppend() {}
+    /// Append current array to given array of same type
+    void Append(std::vector<T>& arrayOut, std::vector<T> const& arrayToAdd, unsigned int expectedSize)
+    {
+      if (arrayToAdd.empty() && arrayOut.empty()) {
+        // Both arrays are empty. Nothing to do.
+        return;
+      } else if (arrayToAdd.empty()) {
+        // The current array is empty but the given array is not. Fill in 
+        // array to append with blank values.
+        for (unsigned int idx = 0; idx != expectedSize; idx++)
+          arrayOut.push_back( T() );
+      } else {
+        // Append current array to array to given array. TODO use std::copy?
+        for (typename std::vector<T>::const_iterator it = arrayToAdd.begin(); it != arrayToAdd.end(); ++it)
+          arrayOut.push_back( *it );
+      }
+    }
 };
 }
 }
diff --git a/src/Parm/parmdepend b/src/Parm/parmdepend
index 905d7f98f6..efb6a4ac2b 100644
--- a/src/Parm/parmdepend
+++ b/src/Parm/parmdepend
@@ -1,5 +1,5 @@
 AssignParams.o : AssignParams.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/ParmEnum.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/GenerateConnectivityArrays.h ../SymbolExporting.h ../Timer.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h AssignParams.h DihedralParmHolder.h GetParams.h ImproperParmHolder.h ParameterSet.h ParmEnum.h ParmHolder.h
 GB_Params.o : GB_Params.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h GB_Params.h
 GetParams.o : GetParams.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/ParmEnum.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h DihedralParmHolder.h GetParams.h ImproperParmHolder.h ParameterSet.h ParmEnum.h ParmHolder.h
-Merge.o : Merge.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../StringRoutines.h ../SymbolExporting.h ../Timer.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../UpdateParameters.h ../Vec3.h AssignParams.h GetParams.h Merge.h ParmEnum.h ParmHolder.h
+Merge.o : Merge.cpp ../Atom.h ../Constants.h ../CpptrajStdio.h ../NameType.h ../ParameterTypes.h ../Residue.h ../StringRoutines.h ../SymbolExporting.h ../TypeNameHolder.h Merge.h ParmEnum.h ParmHolder.h
 ParameterSet.o : ParameterSet.cpp ../AtomType.h ../CmapParmHolder.h ../Constants.h ../CpptrajFile.h ../CpptrajStdio.h ../FileIO.h ../FileName.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/ParmEnum.h ../TypeNameHolder.h ../UpdateParameters.h DihedralParmHolder.h ImproperParmHolder.h ParameterSet.h ParmEnum.h ParmHolder.h
diff --git a/src/Topology.cpp b/src/Topology.cpp
index 3d7928bf23..cd070d6173 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2,10 +2,16 @@
 #include <stack> // For large system molecule search
 #include "Topology.h"
 #include "AtomMask.h"
+#include "AtomType.h" // AppendTop()
 #include "CharMask.h"
 #include "Constants.h" // SMALL
 #include "CpptrajStdio.h"
-#include "StringRoutines.h" // integerToString 
+#include "StringRoutines.h" // integerToString
+#include "Parm/AssignParams.h" // AppendTop()
+#include "Parm/GetParams.h" // AppendTop()
+#include "Parm/Merge.h" // AppendTop()
+#include "Parm/ParmHolder.h" // AppendTop()
+#include "UpdateParameters.h" // AppendTop(). This include must be last
 
 const NonbondType Topology::LJ_EMPTY = NonbondType();
 
@@ -2270,9 +2276,121 @@ void Topology::StripDihedralParmArray(DihedralArray& newDihedralArray, std::vect
 
 
 // -----------------------------------------------------------------------------
+/** Append a topology to another with default options */
+int Topology::AppendTop(Topology const& NewTop) {
+  return AppendTop(NewTop, 0, false, false);
+}
+
+/** Append a topology to another */
+int Topology::AppendTop(Topology const& NewTop, int verbose_, bool reduce_bond_params, bool reduce_angle_params) {
+  using namespace Cpptraj::Parm;
+  Topology& topOut = *this;
+
+  unsigned int atomOffset = (unsigned int)topOut.Natom();
+  unsigned int molOffset = (unsigned int)topOut.Nmol();
+  if (debug_ > 0)
+    mprintf("DEBUG: Appending '%s' to '%s' (atom offset= %u mol offset= %u)\n",
+            NewTop.c_str(), topOut.c_str(), atomOffset, molOffset);
+  //int resOffset = (int)residues_.size();
+
+  // Save nonbonded parameters from each topology
+  ParmHolder<AtomType> myAtomTypes, newAtomTypes;
+  ParmHolder<NonbondType> myNB, newNB;
+  ParmHolder<NonbondType> my14, new14;
+  ParmHolder<HB_ParmType> myHB, newHB;
+  ParmHolder<double> myLJC, newLJC;
+  Cpptraj::Parm::GetParams GP;
+  GP.SetDebug( debug_ );
+  GP.GetLJAtomTypes( myAtomTypes, myNB, my14, myLJC, myHB, topOut.Atoms(), topOut.Nonbond() );
+  GP.GetLJAtomTypes( newAtomTypes, newNB, new14, newLJC, newHB, NewTop.Atoms(), NewTop.Nonbond() );
+  // Create combined nonbond parameter set
+  int nAtomTypeUpdated = UpdateParameters< ParmHolder<AtomType> >( myAtomTypes, newAtomTypes, "atom type", verbose_ );
+  int nLJparamsUpdated = UpdateParameters< ParmHolder<NonbondType> >( myNB, newNB, "LJ 6-12", verbose_ );
+  int n14paramsUpdated = UpdateParameters< ParmHolder<NonbondType> >( my14, new14, "LJ 6-12 1-4", verbose_ );
+  int nljcparamsUpdated = UpdateParameters< ParmHolder<double> >( myLJC, newLJC, "LJ C", verbose_ );
+  int nHBparamsUpdated = UpdateParameters< ParmHolder<HB_ParmType> >( myHB, newHB, "LJ 10-12", verbose_ );
+  if (verbose_ > 0)
+    mprintf("\t%i atom types updated, %i LJ 6-12 params updated, %i 1-4 params updated, %i LJC params updated, %i LJ 10-12 params updated.\n",
+            nAtomTypeUpdated, nLJparamsUpdated, n14paramsUpdated, nljcparamsUpdated, nHBparamsUpdated);
+
+  // Add incoming topology bond/angle/dihedral/cmap arrays to this one.
+  MergeBondArrays(reduce_bond_params, topOut.ModifyBonds(), topOut.ModifyBondsH(), topOut.ModifyBondParm(), topOut.Atoms(),
+                  NewTop.Bonds(), NewTop.BondsH(), NewTop.BondParm(), NewTop.Atoms());
+  MergeAngleArrays(reduce_angle_params, topOut.ModifyAngles(), topOut.ModifyAnglesH(), topOut.ModifyAngleParm(), topOut.Atoms(),
+                   NewTop.Angles(), NewTop.AnglesH(), NewTop.AngleParm(), NewTop.Atoms());
+  MergeDihedralArrays(topOut.ModifyDihedrals(), topOut.ModifyDihedralsH(), topOut.ModifyDihedralParm(), topOut.Atoms(),
+                      NewTop.Dihedrals(), NewTop.DihedralsH(), NewTop.DihedralParm(), NewTop.Atoms());
+  MergeCmapArrays(topOut.ModifyCmap(), topOut.ModifyCmapGrid(), topOut.Atoms(), topOut.Residues(),
+                  NewTop.Cmap(), NewTop.CmapGrid(), NewTop.Atoms(), NewTop.Residues());
+  MergeBondArray(topOut.ModifyUB(), topOut.ModifyUBparm(), topOut.Atoms(),
+                 NewTop.UB(), NewTop.UBparm(), NewTop.Atoms());
+  MergeImproperArray(topOut.ModifyImpropers(), topOut.ModifyImproperParm(), topOut.Atoms(),
+                     NewTop.Impropers(), NewTop.ImproperParm(), NewTop.Atoms());
+
+  // Append incoming atoms to this topology.
+  for (AtArray::const_iterator atom = NewTop.begin(); atom != NewTop.end(); ++atom)
+  {
+    if (debug_ > 1)
+      mprintf("DEBUG: %6li %s %s %4i\n", atom-NewTop.begin(),
+              *(atom->Name()), *(atom->Type()), atom->TypeIndex());
+    Atom CurrentAtom = *atom;
+    Residue const& res = NewTop.Res( CurrentAtom.ResNum() );
+    // Bonds need to be cleared and re-added.
+    CurrentAtom.ClearBonds();
+    for (Atom::bond_iterator bat = atom->bondbegin(); bat != atom->bondend(); ++bat)
+      CurrentAtom.AddBondToIdx( *bat + atomOffset );
+
+    topOut.addTopAtom( CurrentAtom,
+                       Residue(res.Name(), res.OriginalResNum(), res.Icode(), res.ChainID()),
+                       atom->MolNum()+molOffset, NewTop.Mol(atom->MolNum()).IsSolvent() );
+  }
+
+  // EXTRA ATOM INFO
+  TopVecAppend<NameType> appendNameType;
+  appendNameType.Append( topOut.ModifyTreeChainClassification(), NewTop.TreeChainClassification(), NewTop.Natom() );
+  TopVecAppend<int> appendInt;
+  appendInt.Append( topOut.ModifyJoinArray(), NewTop.JoinArray(), NewTop.Natom() );
+  appendInt.Append( topOut.ModifyRotateArray(), NewTop.RotateArray(), NewTop.Natom() );
+  appendInt.Append( topOut.ModifyPdbSerialNum(), NewTop.PdbSerialNum(), NewTop.Natom() );
+  TopVecAppend<char> appendChar;
+  appendChar.Append( topOut.ModifyAtomAltLoc(), NewTop.AtomAltLoc(), NewTop.Natom() );
+  TopVecAppend<float> appendFloat;
+  appendFloat.Append( topOut.ModifyOccupancy(), NewTop.Occupancy(), NewTop.Natom() );
+  appendFloat.Append( topOut.ModifyBfactor(), NewTop.Bfactor(), NewTop.Natom() );
+
+  // Need to regenerate nonbonded info
+  if (verbose_ > 0)
+    mprintf("\tRegenerating nonbond parameters.\n");
+  AssignParams assign;
+  assign.SetDebug( debug_ );
+  assign.SetVerbose( verbose_ );
+  assign.AssignNonbondParams( topOut, myAtomTypes, myNB, my14, myLJC, myHB );
+
+  // The version of AddTopAtom() with molecule number already determines
+  // molecules and number of solvent molecules.
+  // Just need to determine the number of extra points.
+  topOut.DetermineNumExtraPoints();
+
+  // GB radii set string
+  if (!NewTop.GBradiiSet().empty()) {
+    if (topOut.GBradiiSet().empty())
+      topOut.SetGBradiiSet( NewTop.GBradiiSet() );
+    else {
+      // Do not repeat a GB radius string
+      std::size_t pos = topOut.GBradiiSet().find( NewTop.GBradiiSet() );
+      if (pos == std::string::npos) {
+        std::string newName = topOut.GBradiiSet() + "+" + NewTop.GBradiiSet();
+        if (newName.size() > 80) {
+          mprintf("Warning: New radius set name is > 80 characters: '%s'\n", newName.c_str());
+          mprintf("Warning: This will be truncated to 80 characters in an Amber Topology.\n");
+        }
+        topOut.SetGBradiiSet( newName );
+      }
+    }
+  }
+  return 0;
+}
 
-
-// -----------------------------------------------------------------------------
 // -----------------------------------------------------------------------------
 /** \return True if any atom has a non-zero charge. */
 bool Topology::HasChargeInfo() const {
diff --git a/src/Topology.h b/src/Topology.h
index 8b1ea9c32b..25025de48e 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -311,6 +311,10 @@ class Topology {
     Topology* ModifyByMap(std::vector<int> const& m) const {
       return ModifyByMap(m, true);
     }
+    /// Append topology to this one. Takes verbosity, reduce bond params, reduce angle params
+    int AppendTop(Topology const&, int, bool, bool);
+    /// Append topology to this one.  No verbosity, no reduce bond/angle params. PYTRAJ relies on this.
+    int AppendTop(Topology const&);
     /// Split selected atoms in a residue into a new residue, populate the atom map
     int SplitResidue(AtomMask const&, NameType const&, std::vector<int>&);
     /// Split selected atoms in a residue into a new residue
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index e48c7fc24f..38642a6c7d 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -72,7 +72,7 @@ Action_Radgyr.o : Action_Radgyr.cpp Action.h ActionState.h Action_Radgyr.h ArgLi
 Action_Radial.o : Action_Radial.cpp Action.h ActionState.h Action_Radial.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h Gpu.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h cuda_kernels/kernel_rdf.cuh
 Action_RandomizeIons.o : Action_RandomizeIons.cpp Action.h ActionState.h Action_RandomizeIons.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 Action_Remap.o : Action_Remap.cpp Action.h ActionState.h ActionTopWriter.h Action_Remap.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_ReplicateCell.o : Action_ReplicateCell.cpp Action.h ActionFrameCounter.h ActionState.h ActionTopWriter.h Action_ReplicateCell.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Parm/Merge.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h Unit.h Vec3.h
+Action_ReplicateCell.o : Action_ReplicateCell.cpp Action.h ActionFrameCounter.h ActionState.h ActionTopWriter.h Action_ReplicateCell.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h Unit.h Vec3.h
 Action_Rmsd.o : Action_Rmsd.cpp Action.h ActionState.h Action_Rmsd.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 Action_Rotate.o : Action_Rotate.cpp Action.h ActionState.h Action_Rotate.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParallelSetFrameNum.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 Action_RunningAvg.o : Action_RunningAvg.cpp Action.h ActionState.h Action_RunningAvg.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
@@ -321,7 +321,7 @@ Exec_Calc.o : Exec_Calc.cpp Action.h ActionList.h ActionState.h Analysis.h Analy
 Exec_CatCrd.o : Exec_CatCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CatCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_Change.o : Exec_Change.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Change.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_ClusterMap.o : Exec_ClusterMap.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ClusterMap.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ClusterMap.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_CombineCoords.o : Exec_CombineCoords.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CombineCoords.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/Merge.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_CombineCoords.o : Exec_CombineCoords.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CombineCoords.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_Commands.o : Exec_Commands.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Commands.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_CompareClusters.o : Exec_CompareClusters.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CompareClusters.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_CompareEnergy.o : Exec_CompareEnergy.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h Energy/Kernel_Fourier.h Energy/Kernel_Harmonic.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CompareEnergy.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
@@ -338,7 +338,7 @@ Exec_Emin.o : Exec_Emin.cpp Action.h ActionList.h ActionState.h Analysis.h Analy
 Exec_ExtendedComparison.o : Exec_ExtendedComparison.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ExtendedComparison.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_Flatten.o : Exec_Flatten.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Flatten.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_GenerateAmberRst.o : Exec_GenerateAmberRst.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_GenerateAmberRst.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_Graft.o : Exec_Graft.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Graft.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/Merge.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_Graft.o : Exec_Graft.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Graft.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_Help.o : Exec_Help.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Help.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_HmassRepartition.o : Exec_HmassRepartition.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_HmassRepartition.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_LoadCrd.o : Exec_LoadCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_LoadCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h Unit.h Vec3.h
@@ -432,7 +432,7 @@ ParallelSetFrameNum.o : ParallelSetFrameNum.cpp AssociatedData.h CpptrajFile.h C
 Parm/AssignParams.o : Parm/AssignParams.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h GuessAtomHybridization.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/../Structure/GenerateConnectivityArrays.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GetParams.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Parm/GB_Params.o : Parm/GB_Params.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/GB_Params.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Parm/GetParams.o : Parm/GetParams.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/GetParams.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Parm/Merge.o : Parm/Merge.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/GetParams.h Parm/Merge.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h UpdateParameters.h Vec3.h
+Parm/Merge.o : Parm/Merge.cpp Atom.h Constants.h CpptrajStdio.h NameType.h ParameterTypes.h Parm/Merge.h Parm/ParmEnum.h Parm/ParmHolder.h Residue.h StringRoutines.h SymbolExporting.h TypeNameHolder.h
 Parm/ParameterSet.o : Parm/ParameterSet.cpp AtomType.h CmapParmHolder.h Constants.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h TypeNameHolder.h UpdateParameters.h
 ParmFile.o : ParmFile.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h ParmFile.h ParmIO.h Parm_Amber.h Parm_CIF.h Parm_CharmmPsf.h Parm_Gromacs.h Parm_Mol2.h Parm_PDB.h Parm_SDF.h Parm_Tinker.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Parm_Amber.o : Parm_Amber.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h ExclusionArray.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/GetParams.h ParmIO.h Parm_Amber.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h Unit.h Vec3.h
@@ -506,7 +506,7 @@ TextFormat.o : TextFormat.cpp StringRoutines.h TextFormat.h
 Timer.o : Timer.cpp CpptrajStdio.h Timer.h
 TinkerFile.o : TinkerFile.cpp ArgList.h Atom.h AtomMask.h Box.h BufferedLine.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TinkerFile.h Unit.h Vec3.h
 TopInfo.o : TopInfo.cpp AssociatedData.h Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h DistRoutines.h FileIO.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Mol.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h TopInfo.h Topology.h TorsionRoutines.h Unit.h Vec3.h
-Topology.o : Topology.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h
+Topology.o : Topology.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/GetParams.h Parm/Merge.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h UpdateParameters.h Vec3.h
 TorsionRoutines.o : TorsionRoutines.cpp Constants.h TorsionRoutines.h Vec3.h
 TrajFrameCounter.o : TrajFrameCounter.cpp ArgList.h CpptrajStdio.h TrajFrameCounter.h
 TrajIOarray.o : TrajIOarray.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryFile.h TrajectoryIO.h Unit.h Vec3.h

From fcfa0cdf03df765d4afba68c8b5cc153c72af421 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 6 Nov 2025 10:11:48 -0500
Subject: [PATCH 1050/1492] Update headers

---
 src/cpptrajheaders | 25 +++++++++++++++++++++----
 1 file changed, 21 insertions(+), 4 deletions(-)

diff --git a/src/cpptrajheaders b/src/cpptrajheaders
index a41e634b9e..07f2afd243 100644
--- a/src/cpptrajheaders
+++ b/src/cpptrajheaders
@@ -101,6 +101,7 @@ CPPTRAJ_HEADERS = \
         ./Action_Volume.h \
         ./Action_Watershell.h \
         ./Action_XtalSymm.h \
+        ./AmberParamFile.h \
         ./Analysis_AmdBias.h \
         ./Analysis_AutoCorr.h \
         ./Analysis_Average.h \
@@ -171,6 +172,7 @@ CPPTRAJ_HEADERS = \
         ./CharmmParamFile.h \
         ./CIFfile.h \
         ./ClusterMap.h \
+        ./CmapParmHolder.h \
         ./Cmd.h \
         ./CmdInput.h \
         ./CmdList.h \
@@ -196,6 +198,8 @@ CPPTRAJ_HEADERS = \
         ./DataFileList.h \
         ./DataFilter.h \
         ./DataIO_AmberEne.h \
+        ./DataIO_AmberFF.h \
+        ./DataIO_AmberFrcmod.h \
         ./DataIO_AmberLib.h \
         ./DataIO_AmberPrep.h \
         ./DataIO_CCP4.h \
@@ -205,11 +209,13 @@ CPPTRAJ_HEADERS = \
         ./DataIO_CharmmRtfPrm.h \
         ./DataIO_Cmatrix_Binary.h \
         ./DataIO_Cmatrix_NC.h \
+        ./DataIO_Coords.h \
         ./DataIO_Cpout.h \
         ./DataIO_Evecs.h \
         ./DataIO_Gnuplot.h \
         ./DataIO_Grace.h \
         ./DataIO.h \
+        ./DataIO_LeapRC.h \
         ./DataIO_Mdout.h \
         ./DataIO_NetCDF.h \
         ./DataIO_Numpy.h \
@@ -236,16 +242,19 @@ CPPTRAJ_HEADERS = \
         ./DataSet_integer_disk.h \
         ./DataSet_integer.h \
         ./DataSet_integer_mem.h \
+        ./DataSet_LeapOpts.h \
         ./DataSetList.h \
         ./DataSet_Mat3x3.h \
         ./DataSet_MatrixDbl.h \
         ./DataSet_MatrixFlt.h \
         ./DataSet_Mesh.h \
         ./DataSet_Modes.h \
+        ./DataSet_NameMap.h \
         ./DataSet_PairwiseCache.h \
         ./DataSet_PairwiseCache_MEM.h \
         ./DataSet_PairwiseCache_NC.h \
         ./DataSet_Parameters.h \
+        ./DataSet_PdbResMap.h \
         ./DataSet_pH.h \
         ./DataSet_PHREMD_Explicit.h \
         ./DataSet_PHREMD.h \
@@ -283,6 +292,7 @@ CPPTRAJ_HEADERS = \
         ./Exec_AddMissingRes.h \
         ./Exec_AddMissingRes_Pres.h \
         ./Exec_Analyze.h \
+        ./Exec_Build.h \
         ./Exec_Calc.h \
         ./Exec_CatCrd.h \
         ./Exec_Change.h \
@@ -299,6 +309,7 @@ CPPTRAJ_HEADERS = \
         ./Exec_DataFile.h \
         ./Exec_DataFilter.h \
         ./Exec_DataSetCmd.h \
+        ./Exec_Desc.h \
         ./Exec_Emin.h \
         ./Exec_ExtendedComparison.h \
         ./Exec_Flatten.h \
@@ -331,6 +342,7 @@ CPPTRAJ_HEADERS = \
         ./Exec_Set.h \
         ./Exec_Show.h \
         ./Exec_SortEnsembleData.h \
+        ./Exec_Source.h \
         ./Exec_SplitCoords.h \
         ./Exec_System.h \
         ./Exec_Top.h \
@@ -367,6 +379,7 @@ CPPTRAJ_HEADERS = \
         ./GridBin.h \
         ./Grid.h \
         ./GridMover.h \
+        ./GuessAtomHybridization.h \
         ./helpme_standalone.h \
         ./HipDefinitions.h \
         ./HistBin.h \
@@ -416,8 +429,6 @@ CPPTRAJ_HEADERS = \
         ./Parallel.h \
         ./ParallelNetcdf.h \
         ./ParallelSetFrameNum.h \
-        ./ParameterHolders.h \
-        ./ParameterSet.h \
         ./ParameterTypes.h \
         ./Parm_Amber.h \
         ./Parm_CharmmPsf.h \
@@ -430,6 +441,7 @@ CPPTRAJ_HEADERS = \
         ./Parm_SDF.h \
         ./Parm_Tinker.h \
         ./PDBfile.h \
+        ./PdbResMapType.h \
         ./PotentialFunction.h \
         ./PotentialTerm_Angle.h \
         ./PotentialTerm_Bond.h \
@@ -453,6 +465,7 @@ CPPTRAJ_HEADERS = \
         ./ReferenceAction.h \
         ./ReferenceFrame.h \
         ./RemdReservoirNC.h \
+        ./Remote.h \
         ./ReplicaDimArray.h \
         ./ReplicaInfo.h \
         ./Residue.h \
@@ -561,17 +574,21 @@ CPPTRAJ_HEADERS = \
         Cluster/Results.h \
         Cluster/Sieve.h \
         Cluster/Silhouette.h \
-        Structure/BuildAtom.h \
         Structure/Builder.h \
         Structure/Chirality.h \
+        Structure/Creator.h \
         Structure/Disulfide.h \
         Structure/FunctionalGroup.h \
         Structure/FxnGroupBuilder.h \
+        Structure/GenerateConnectivityArrays.h \
         Structure/HisProt.h \
         Structure/InternalCoords.h \
+        Structure/LeastSquaresPlane.h \
         Structure/LinkAtom.h \
-        Structure/Model.h \
+        Structure/MetalCenterFinder.h \
+        Structure/PdbCleaner.h \
         Structure/ResStatArray.h \
+        Structure/RingFinder.h \
         Structure/StructureEnum.h \
         Structure/StructureRoutines.h \
         Structure/SugarBuilder.h \

From 94b29c23e2c08816d07fa782f5de28b45bc29de8 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 6 Nov 2025 15:02:27 -0500
Subject: [PATCH 1051/1492] Start mutate command

---
 src/Exec_Mutate.cpp | 60 +++++++++++++++++++++++++++++++++++++++++++++
 src/Exec_Mutate.h   | 14 +++++++++++
 2 files changed, 74 insertions(+)
 create mode 100644 src/Exec_Mutate.cpp
 create mode 100644 src/Exec_Mutate.h

diff --git a/src/Exec_Mutate.cpp b/src/Exec_Mutate.cpp
new file mode 100644
index 0000000000..ac88462fb0
--- /dev/null
+++ b/src/Exec_Mutate.cpp
@@ -0,0 +1,60 @@
+#include "Exec_Mutate.h"
+#include "CpptrajStdio.h"
+#include "Structure/Creator.h"
+
+// Exec_Mutate::Help()
+void Exec_Mutate::Help() const
+{
+  mprintf("\tcrdset <COORDS set> resmask <mask>\n"
+          "\t[%s]\n"
+          "\t[{%s} ...]\n"
+          "\t[{%s} ...]\n",
+          Cpptraj::Structure::Creator::other_keywords_,
+          Cpptraj::Structure::Creator::template_keywords_,
+          Cpptraj::Structure::Creator::parm_keywords_);
+}
+
+// Exec_Mutate::Execute()
+Exec::RetType Exec_Mutate::Execute(CpptrajState& State, ArgList& argIn)
+{
+  debug_ = State.Debug();
+  Cpptraj::Structure::Creator creator( debug_ );
+  if (creator.InitCreator(argIn, State.DSL(), debug_)) {
+    return CpptrajState::ERR;
+  }
+  if (!creator.HasTemplates()) {
+    mprinterr("Error: No residue templates loaded.\n");
+  }
+
+  std::string setname = argIn.GetStringKey("crdset");
+  if (setname.empty()) {
+    mprinterr("Error: Specify COORDS dataset name with 'crdset'.\n");
+    return CpptrajState::ERR;
+  }
+  DataSet_Coords* CRD = (DataSet_Coords*)State.DSL().FindSetOfGroup( setname, DataSet::COORDINATES );
+  if (CRD == 0) {
+    mprinterr("Error: No COORDS set with name %s found.\n", setname.c_str());
+    return CpptrajState::ERR;
+  }
+  mprintf("\tUsing set '%s'\n", CRD->legend());
+
+  std::string resmask = argIn.GetStringKey("resmask");
+  if (resmask.empty()) {
+    mprinterr("Error: Specify mask of residues to mutate with 'resmask'\n");
+    return CpptrajState::ERR;
+  }
+
+  std::string templateName = argIn.GetStringKey("to");
+  if (templateName.empty()) {
+    mprinterr("Error: Specify template name to mutate to with 'to'\n");
+    return CpptrajState::ERR;
+  }
+  DataSet_Coords* UNIT = creator.IdTemplateFromName( templateName );
+  if (UNIT == 0) {
+    mprinterr("Error: Could not get template for '%s'\n", templateName.c_str());
+    return CpptrajState::ERR;
+  }
+  mprintf("\tMutate residues selected by '%s' to '%s'\n", resmask.c_str(), UNIT->legend());
+
+  return CpptrajState::OK;
+}
diff --git a/src/Exec_Mutate.h b/src/Exec_Mutate.h
new file mode 100644
index 0000000000..c7293fd0a6
--- /dev/null
+++ b/src/Exec_Mutate.h
@@ -0,0 +1,14 @@
+#ifndef INC_EXEC_MUTATE_H
+#define INC_EXEC_MUTATE_H
+#include "Exec.h"
+/// <Enter description of Exec_Mutate here>
+class Exec_Mutate : public Exec {
+  public:
+    Exec_Mutate() : Exec(COORDS) {}
+    void Help() const;
+    DispatchObject* Alloc() const { return (DispatchObject*)new Exec_Mutate(); }
+    RetType Execute(CpptrajState&, ArgList&);
+  private:
+    int debug_;
+};
+#endif

From bb15873aeeb3dc4675bd5f1d2869dbdfc2700a09 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 6 Nov 2025 15:12:05 -0500
Subject: [PATCH 1052/1492] Enable command

---
 src/Command.cpp   | 2 ++
 src/cpptrajdepend | 3 ++-
 src/cpptrajfiles  | 1 +
 3 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/src/Command.cpp b/src/Command.cpp
index d039be21fc..f0562af6ae 100644
--- a/src/Command.cpp
+++ b/src/Command.cpp
@@ -60,6 +60,7 @@
 #include "Exec_Zmatrix.h"
 #include "Exec_Sequence.h"
 #include "Exec_Build.h"
+#include "Exec_Mutate.h"
 // ----- TRAJECTORY ------------------------------------------------------------
 #include "Exec_Traj.h"
 // ----- TOPOLOGY --------------------------------------------------------------
@@ -289,6 +290,7 @@ void Command::Init() {
   Command::AddCmd( new Exec_Graft(),            Cmd::EXE, 1, "graft");
   Command::AddCmd( new Exec_LoadCrd(),          Cmd::EXE, 1, "loadcrd" );
   Command::AddCmd( new Exec_LoadTraj(),         Cmd::EXE, 1, "loadtraj" );
+  Command::AddCmd( new Exec_Mutate(),           Cmd::EXE, 1, "mutate" );
   Command::AddCmd( new Exec_PermuteDihedrals(), Cmd::EXE, 1, "permutedihedrals" );
   Command::AddCmd( new Exec_PrepareForLeap(),   Cmd::EXE, 1, "prepareforleap" );
   Command::AddCmd( new Exec_RotateDihedral(),   Cmd::EXE, 1, "rotatedihedral" );
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 38642a6c7d..4bd6183dea 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -194,7 +194,7 @@ CmapParmHolder.o : CmapParmHolder.cpp CmapParmHolder.h Constants.h CpptrajStdio.
 Cmd.o : Cmd.cpp Cmd.h DispatchObject.h
 CmdInput.o : CmdInput.cpp CmdInput.h StringRoutines.h
 CmdList.o : CmdList.cpp Cmd.h CmdList.h DispatchObject.h
-Command.o : Command.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h ActionTopWriter.h Action_AddAtom.h Action_Align.h Action_Angle.h Action_AreaPerMol.h Action_AtomMap.h Action_AtomicCorr.h Action_AtomicFluct.h Action_AutoImage.h Action_Average.h Action_AvgBox.h Action_Bounds.h Action_Box.h Action_Center.h Action_Channel.h Action_CheckChirality.h Action_CheckStructure.h Action_Closest.h Action_ClusterDihedral.h Action_Contacts.h Action_ConvertToFrac.h Action_CreateCrd.h Action_CreateReservoir.h Action_DNAionTracker.h Action_DSSP.h Action_Density.h Action_Diffusion.h Action_Dihedral.h Action_DihedralRMS.h Action_Dipole.h Action_DistRmsd.h Action_Distance.h Action_EneDecomp.h Action_Energy.h Action_Esander.h Action_FilterByData.h Action_FixAtomOrder.h Action_FixImagedBonds.h Action_GIST.h Action_Grid.h Action_GridFreeEnergy.h Action_HydrogenBond.h Action_Image.h Action_InfraredSpectrum.h Action_Jcoupling.h Action_Keep.h Action_LESsplit.h Action_LIE.h Action_LipidOrder.h Action_MakeStructure.h Action_Mask.h Action_Matrix.h Action_MinImage.h Action_MinMaxDist.h Action_Molsurf.h Action_MultiDihedral.h Action_MultiPucker.h Action_MultiVector.h Action_NAstruct.h Action_NMRrst.h Action_NativeContacts.h Action_OrderParameter.h Action_Outtraj.h Action_PairDist.h Action_Pairwise.h Action_Principal.h Action_Projection.h Action_Pucker.h Action_Radgyr.h Action_Radial.h Action_RandomizeIons.h Action_Remap.h Action_ReplicateCell.h Action_Rmsd.h Action_Rotate.h Action_RunningAvg.h Action_STFC_Diffusion.h Action_Scale.h Action_SetVelocity.h Action_Spam.h Action_Strip.h Action_Surf.h Action_SymmetricRmsd.h Action_Temperature.h Action_Test.h Action_Time.h Action_ToroidalDiffusion.h Action_Translate.h Action_Unstrip.h Action_Unwrap.h Action_Vector.h Action_VelocityAutoCorr.h Action_Volmap.h Action_Volume.h Action_Watershell.h Action_XtalSymm.h Analysis.h AnalysisList.h AnalysisState.h Analysis_AmdBias.h Analysis_AutoCorr.h Analysis_Average.h Analysis_CalcDiffusion.h Analysis_Clustering.h Analysis_ConstantPHStats.h Analysis_Corr.h Analysis_CrankShaft.h Analysis_CrdFluct.h Analysis_CrossCorr.h Analysis_CurveFit.h Analysis_Divergence.h Analysis_EvalPlateau.h Analysis_FFT.h Analysis_HausdorffDistance.h Analysis_Hist.h Analysis_IRED.h Analysis_Integrate.h Analysis_KDE.h Analysis_Lifetime.h Analysis_LowestCurve.h Analysis_Matrix.h Analysis_MeltCurve.h Analysis_Modes.h Analysis_MultiHist.h Analysis_Multicurve.h Analysis_Overlap.h Analysis_PhiPsi.h Analysis_Project.h Analysis_Regression.h Analysis_RemLog.h Analysis_Rms2d.h Analysis_RmsAvgCorr.h Analysis_Rotdif.h Analysis_RunningAvg.h Analysis_Slope.h Analysis_Spline.h Analysis_State.h Analysis_Statistics.h Analysis_TI.h Analysis_TICA.h Analysis_Timecorr.h Analysis_VectorMath.h Analysis_Wavelet.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AxisType.h BaseIOtype.h Box.h BoxArgs.h BufferedLine.h CharMask.h Cluster/Algorithm.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Control.h Cluster/DrawGraph.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Sieve.h Cluster/Silhouette.h ClusterMap.h Cmd.h CmdInput.h CmdList.h Command.h CompactFrameArray.h ComplexArray.h Constants.h Constraints.h ControlBlock.h ControlBlock_For.h CoordinateInfo.h Corr.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_RemLog.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h Deprecated.h DiffusionResults.h DihedralSearch.h Dimension.h DispatchObject.h Energy.h Energy/Ecalc_Nonbond.h Energy/EnergyDecomposer.h Energy/ErfcFxn.h Energy/EwaldParams.h Energy/PME_RecipParams.h Energy/VDW_LongRange_Correction.h Energy_Sander.h EnsembleIn.h EnsembleOutList.h EwaldOptions.h ExclusionArray.h Exec.h Exec_AddMissingRes.h Exec_Analyze.h Exec_Build.h Exec_Calc.h Exec_CatCrd.h Exec_Change.h Exec_ClusterMap.h Exec_CombineCoords.h Exec_Commands.h Exec_CompareClusters.h Exec_CompareEnergy.h Exec_CompareTop.h Exec_CrdAction.h Exec_CrdOut.h Exec_CrdTransform.h Exec_CreateSet.h Exec_DataFile.h Exec_DataFilter.h Exec_DataSetCmd.h Exec_Desc.h Exec_Emin.h Exec_ExtendedComparison.h Exec_Flatten.h Exec_GenerateAmberRst.h Exec_Graft.h Exec_Help.h Exec_HmassRepartition.h Exec_LoadCrd.h Exec_LoadTraj.h Exec_ParallelAnalysis.h Exec_ParmBox.h Exec_ParmSolvent.h Exec_ParmStrip.h Exec_ParmWrite.h Exec_ParseTiming.h Exec_PermuteDihedrals.h Exec_Precision.h Exec_PrepareForLeap.h Exec_PrintData.h Exec_Random.h Exec_ReadData.h Exec_ReadEnsembleData.h Exec_ReadInput.h Exec_RotateDihedral.h Exec_RunAnalysis.h Exec_ScaleDihedralK.h Exec_Sequence.h Exec_SequenceAlign.h Exec_Set.h Exec_Show.h Exec_SortEnsembleData.h Exec_Source.h Exec_SplitCoords.h Exec_System.h Exec_Top.h Exec_Traj.h Exec_UpdateParameters.h Exec_ViewRst.h Exec_Zmatrix.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h GIST_PME.h Grid.h GridAction.h GridBin.h GridMover.h HistBin.h Hungarian.h ImageOption.h ImageTypes.h InputTrajCommon.h InteractionData.h MapAtom.h MaskArray.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h OnlineVarT.h OutputTrajCommon.h PDBfile.h PairList.h Parallel.h ParallelSetFrameNum.h ParameterTypes.h Parm/GB_Params.h PubFFT.h Pucker.h Pucker_PuckerMask.h Pucker_PuckerSearch.h Pucker_PuckerToken.h RPNcalc.h Random.h Range.h ReferenceAction.h ReferenceFrame.h RemdReservoirNC.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h SplineFxnTable.h Structure/LeastSquaresPlane.h Structure/RingFinder.h StructureCheck.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Unit.h Vec3.h cuda_kernels/GistCudaSetup.cuh helpme_standalone.h molsurf.h
+Command.o : Command.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h ActionTopWriter.h Action_AddAtom.h Action_Align.h Action_Angle.h Action_AreaPerMol.h Action_AtomMap.h Action_AtomicCorr.h Action_AtomicFluct.h Action_AutoImage.h Action_Average.h Action_AvgBox.h Action_Bounds.h Action_Box.h Action_Center.h Action_Channel.h Action_CheckChirality.h Action_CheckStructure.h Action_Closest.h Action_ClusterDihedral.h Action_Contacts.h Action_ConvertToFrac.h Action_CreateCrd.h Action_CreateReservoir.h Action_DNAionTracker.h Action_DSSP.h Action_Density.h Action_Diffusion.h Action_Dihedral.h Action_DihedralRMS.h Action_Dipole.h Action_DistRmsd.h Action_Distance.h Action_EneDecomp.h Action_Energy.h Action_Esander.h Action_FilterByData.h Action_FixAtomOrder.h Action_FixImagedBonds.h Action_GIST.h Action_Grid.h Action_GridFreeEnergy.h Action_HydrogenBond.h Action_Image.h Action_InfraredSpectrum.h Action_Jcoupling.h Action_Keep.h Action_LESsplit.h Action_LIE.h Action_LipidOrder.h Action_MakeStructure.h Action_Mask.h Action_Matrix.h Action_MinImage.h Action_MinMaxDist.h Action_Molsurf.h Action_MultiDihedral.h Action_MultiPucker.h Action_MultiVector.h Action_NAstruct.h Action_NMRrst.h Action_NativeContacts.h Action_OrderParameter.h Action_Outtraj.h Action_PairDist.h Action_Pairwise.h Action_Principal.h Action_Projection.h Action_Pucker.h Action_Radgyr.h Action_Radial.h Action_RandomizeIons.h Action_Remap.h Action_ReplicateCell.h Action_Rmsd.h Action_Rotate.h Action_RunningAvg.h Action_STFC_Diffusion.h Action_Scale.h Action_SetVelocity.h Action_Spam.h Action_Strip.h Action_Surf.h Action_SymmetricRmsd.h Action_Temperature.h Action_Test.h Action_Time.h Action_ToroidalDiffusion.h Action_Translate.h Action_Unstrip.h Action_Unwrap.h Action_Vector.h Action_VelocityAutoCorr.h Action_Volmap.h Action_Volume.h Action_Watershell.h Action_XtalSymm.h Analysis.h AnalysisList.h AnalysisState.h Analysis_AmdBias.h Analysis_AutoCorr.h Analysis_Average.h Analysis_CalcDiffusion.h Analysis_Clustering.h Analysis_ConstantPHStats.h Analysis_Corr.h Analysis_CrankShaft.h Analysis_CrdFluct.h Analysis_CrossCorr.h Analysis_CurveFit.h Analysis_Divergence.h Analysis_EvalPlateau.h Analysis_FFT.h Analysis_HausdorffDistance.h Analysis_Hist.h Analysis_IRED.h Analysis_Integrate.h Analysis_KDE.h Analysis_Lifetime.h Analysis_LowestCurve.h Analysis_Matrix.h Analysis_MeltCurve.h Analysis_Modes.h Analysis_MultiHist.h Analysis_Multicurve.h Analysis_Overlap.h Analysis_PhiPsi.h Analysis_Project.h Analysis_Regression.h Analysis_RemLog.h Analysis_Rms2d.h Analysis_RmsAvgCorr.h Analysis_Rotdif.h Analysis_RunningAvg.h Analysis_Slope.h Analysis_Spline.h Analysis_State.h Analysis_Statistics.h Analysis_TI.h Analysis_TICA.h Analysis_Timecorr.h Analysis_VectorMath.h Analysis_Wavelet.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AxisType.h BaseIOtype.h Box.h BoxArgs.h BufferedLine.h CharMask.h Cluster/Algorithm.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Control.h Cluster/DrawGraph.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Sieve.h Cluster/Silhouette.h ClusterMap.h Cmd.h CmdInput.h CmdList.h Command.h CompactFrameArray.h ComplexArray.h Constants.h Constraints.h ControlBlock.h ControlBlock_For.h CoordinateInfo.h Corr.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_RemLog.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h Deprecated.h DiffusionResults.h DihedralSearch.h Dimension.h DispatchObject.h Energy.h Energy/Ecalc_Nonbond.h Energy/EnergyDecomposer.h Energy/ErfcFxn.h Energy/EwaldParams.h Energy/PME_RecipParams.h Energy/VDW_LongRange_Correction.h Energy_Sander.h EnsembleIn.h EnsembleOutList.h EwaldOptions.h ExclusionArray.h Exec.h Exec_AddMissingRes.h Exec_Analyze.h Exec_Build.h Exec_Calc.h Exec_CatCrd.h Exec_Change.h Exec_ClusterMap.h Exec_CombineCoords.h Exec_Commands.h Exec_CompareClusters.h Exec_CompareEnergy.h Exec_CompareTop.h Exec_CrdAction.h Exec_CrdOut.h Exec_CrdTransform.h Exec_CreateSet.h Exec_DataFile.h Exec_DataFilter.h Exec_DataSetCmd.h Exec_Desc.h Exec_Emin.h Exec_ExtendedComparison.h Exec_Flatten.h Exec_GenerateAmberRst.h Exec_Graft.h Exec_Help.h Exec_HmassRepartition.h Exec_LoadCrd.h Exec_LoadTraj.h Exec_Mutate.h Exec_ParallelAnalysis.h Exec_ParmBox.h Exec_ParmSolvent.h Exec_ParmStrip.h Exec_ParmWrite.h Exec_ParseTiming.h Exec_PermuteDihedrals.h Exec_Precision.h Exec_PrepareForLeap.h Exec_PrintData.h Exec_Random.h Exec_ReadData.h Exec_ReadEnsembleData.h Exec_ReadInput.h Exec_RotateDihedral.h Exec_RunAnalysis.h Exec_ScaleDihedralK.h Exec_Sequence.h Exec_SequenceAlign.h Exec_Set.h Exec_Show.h Exec_SortEnsembleData.h Exec_Source.h Exec_SplitCoords.h Exec_System.h Exec_Top.h Exec_Traj.h Exec_UpdateParameters.h Exec_ViewRst.h Exec_Zmatrix.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h GIST_PME.h Grid.h GridAction.h GridBin.h GridMover.h HistBin.h Hungarian.h ImageOption.h ImageTypes.h InputTrajCommon.h InteractionData.h MapAtom.h MaskArray.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h OnlineVarT.h OutputTrajCommon.h PDBfile.h PairList.h Parallel.h ParallelSetFrameNum.h ParameterTypes.h Parm/GB_Params.h PubFFT.h Pucker.h Pucker_PuckerMask.h Pucker_PuckerSearch.h Pucker_PuckerToken.h RPNcalc.h Random.h Range.h ReferenceAction.h ReferenceFrame.h RemdReservoirNC.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h SplineFxnTable.h Structure/LeastSquaresPlane.h Structure/RingFinder.h StructureCheck.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Unit.h Vec3.h cuda_kernels/GistCudaSetup.cuh helpme_standalone.h molsurf.h
 CompactFrameArray.o : CompactFrameArray.cpp Box.h CompactFrameArray.h CoordinateInfo.h CpptrajStdio.h Matrix_3x3.h Parallel.h ReplicaDimArray.h Vec3.h
 ComplexArray.o : ComplexArray.cpp ArrayIterator.h ComplexArray.h
 Constraints.o : Constraints.cpp ArgList.h Atom.h AtomMask.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
@@ -343,6 +343,7 @@ Exec_Help.o : Exec_Help.cpp Action.h ActionList.h ActionState.h Analysis.h Analy
 Exec_HmassRepartition.o : Exec_HmassRepartition.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_HmassRepartition.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_LoadCrd.o : Exec_LoadCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_LoadCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h Unit.h Vec3.h
 Exec_LoadTraj.o : Exec_LoadTraj.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_LoadTraj.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_Mutate.o : Exec_Mutate.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Mutate.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Creator.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_ParallelAnalysis.o : Exec_ParallelAnalysis.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParallelAnalysis.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_ParmBox.o : Exec_ParmBox.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BoxArgs.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmBox.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_ParmSolvent.o : Exec_ParmSolvent.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmSolvent.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
diff --git a/src/cpptrajfiles b/src/cpptrajfiles
index da4b52c57c..e0eea7842a 100644
--- a/src/cpptrajfiles
+++ b/src/cpptrajfiles
@@ -299,6 +299,7 @@ COMMON_SOURCES= \
         Exec_HmassRepartition.cpp \
         Exec_LoadCrd.cpp \
         Exec_LoadTraj.cpp \
+        Exec_Mutate.cpp \
         Exec_ParallelAnalysis.cpp \
         Exec_ParmBox.cpp \
         Exec_ParmSolvent.cpp \

From d394191dd85cb387a9d4a8a00f7f71fda0ad9c1b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 6 Nov 2025 15:32:52 -0500
Subject: [PATCH 1053/1492] Find atoms to be removed

---
 src/Exec_Mutate.cpp | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

diff --git a/src/Exec_Mutate.cpp b/src/Exec_Mutate.cpp
index ac88462fb0..4c10733b64 100644
--- a/src/Exec_Mutate.cpp
+++ b/src/Exec_Mutate.cpp
@@ -56,5 +56,40 @@ Exec::RetType Exec_Mutate::Execute(CpptrajState& State, ArgList& argIn)
   }
   mprintf("\tMutate residues selected by '%s' to '%s'\n", resmask.c_str(), UNIT->legend());
 
+  AtomMask mask;
+  if (mask.SetMaskString( resmask )) {
+    mprinterr("Error: Could not set mask '%s'\n", resmask.c_str());
+    return CpptrajState::ERR;
+  }
+  if (CRD->Top().SetupIntegerMask( mask )) {
+    mprinterr("Error: Could not setup mask '%s'\n", mask.MaskString());
+    return CpptrajState::ERR;
+  }
+  if (mask.None()) {
+    mprinterr("Error: Nothing selected by mask '%s'\n", mask.MaskString());
+    return CpptrajState::ERR;
+  }
+  //mask.MaskInfo();
+  std::vector<int> resnums = CRD->Top().ResnumsSelectedBy( mask );
+  mprintf("\t%zu residues selected by '%s'\n", resnums.size(), mask.MaskString());
+
+  AtomMask toRemove;
+  toRemove.SetNatoms( CRD->Top().Natom() );
+  for (std::vector<int>::const_iterator rnum = resnums.begin(); rnum != resnums.end(); ++rnum)
+  {
+    Residue const& currentRes = CRD->Top().Res( *rnum );
+    for (int at = currentRes.FirstAtom(); at != currentRes.LastAtom(); at++)
+    {
+      // Does this atom exist in the template?
+      int idx = UNIT->Top().FindAtomInResidue(0, CRD->Top()[at].Name());
+      if (idx < 0)
+        toRemove.AddSelectedAtom( at );
+      if (idx > -1)
+        mprintf("DEBUG: Found atom %s in template.\n", CRD->Top().AtomMaskName(at).c_str());
+      else
+        mprintf("DEBUG: Atom %s not in template.\n", CRD->Top().AtomMaskName(at).c_str());
+    }
+  }
+
   return CpptrajState::OK;
 }

From 727447f1d038f2d732cd58e1231930a4d9aa52cb Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 6 Nov 2025 15:45:28 -0500
Subject: [PATCH 1054/1492] Remove atoms that are not part of the residue to be
 mutated to

---
 src/Exec_Mutate.cpp | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/src/Exec_Mutate.cpp b/src/Exec_Mutate.cpp
index 4c10733b64..22bfb84b08 100644
--- a/src/Exec_Mutate.cpp
+++ b/src/Exec_Mutate.cpp
@@ -90,6 +90,16 @@ Exec::RetType Exec_Mutate::Execute(CpptrajState& State, ArgList& argIn)
         mprintf("DEBUG: Atom %s not in template.\n", CRD->Top().AtomMaskName(at).c_str());
     }
   }
+  toRemove.InvertMask();
+
+  Topology* newTop = CRD->Top().modifyStateByMask( toRemove );
+  if (newTop == 0) {
+    mprinterr("Error: Could not remove atoms from '%s'\n", CRD->legend());
+    return CpptrajState::ERR;
+  }
+  newTop->Summary();
+
+  if (newTop != 0) delete newTop;
 
   return CpptrajState::OK;
 }

From bebcd4821fcbe5a0940b5a325248832510f5ac8b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 6 Nov 2025 15:51:26 -0500
Subject: [PATCH 1055/1492] Check that not all atoms would be removed from
 residue

---
 src/Exec_Mutate.cpp | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/src/Exec_Mutate.cpp b/src/Exec_Mutate.cpp
index 22bfb84b08..d7616f49f0 100644
--- a/src/Exec_Mutate.cpp
+++ b/src/Exec_Mutate.cpp
@@ -78,17 +78,26 @@ Exec::RetType Exec_Mutate::Execute(CpptrajState& State, ArgList& argIn)
   for (std::vector<int>::const_iterator rnum = resnums.begin(); rnum != resnums.end(); ++rnum)
   {
     Residue const& currentRes = CRD->Top().Res( *rnum );
+    int atomsToRemove = 0;
     for (int at = currentRes.FirstAtom(); at != currentRes.LastAtom(); at++)
     {
       // Does this atom exist in the template?
       int idx = UNIT->Top().FindAtomInResidue(0, CRD->Top()[at].Name());
-      if (idx < 0)
+      if (idx < 0) {
         toRemove.AddSelectedAtom( at );
+        atomsToRemove++;
+      }
       if (idx > -1)
         mprintf("DEBUG: Found atom %s in template.\n", CRD->Top().AtomMaskName(at).c_str());
       else
         mprintf("DEBUG: Atom %s not in template.\n", CRD->Top().AtomMaskName(at).c_str());
     }
+    mprintf("DEBUG: Removing %i atoms from residue %i\n", atomsToRemove, *rnum + 1 );
+    if (currentRes.NumAtoms() - atomsToRemove < 1) {
+      mprinterr("Error: Number of atoms to remove %i >= number of atoms in residue %s (%i)\n",
+                atomsToRemove, CRD->Top().TruncResNameNum(*rnum).c_str(), currentRes.NumAtoms());
+      return CpptrajState::ERR;
+    }
   }
   toRemove.InvertMask();
 

From bb095460e2c5d648ebd2e307bebe4eeb5743c687 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 7 Nov 2025 09:28:19 -0500
Subject: [PATCH 1056/1492] Move the MapAtomsToTemplate routine to Creator so
 that mutate can use it and make use of any atom name maps

---
 src/Exec_Build.cpp        | 73 +--------------------------------------
 src/Exec_Mutate.cpp       | 42 ++++++++++++++++++++--
 src/Structure/Creator.cpp | 71 +++++++++++++++++++++++++++++++++++++
 src/Structure/Creator.h   |  4 +++
 4 files changed, 115 insertions(+), 75 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index f630a66bec..bbad0a5154 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -32,77 +32,6 @@ Exec_Build::~Exec_Build() {
     delete sugarBuilder_;
 }
 
-/** Map atoms in residue to template. */
-std::vector<int> Exec_Build::MapAtomsToTemplate(Topology const& topIn,
-                                                int rnum,
-                                                DataSet_Coords* resTemplate,
-                                                Cpptraj::Structure::Creator const& creator,
-                                                std::vector<NameType>& sourceAtomNames,
-                                                int& nTgtAtomsMissing)
-{
-  nTgtAtomsMissing = 0;
-  std::vector<int> mapOut(resTemplate->Top().Natom(), -1);
-  mapOut.reserve( resTemplate->Top().Natom() );
-  Residue const& resIn = topIn.Res(rnum);
-  // For each atom in topIn, find a template atom
-  for (int itgt = resIn.FirstAtom(); itgt != resIn.LastAtom(); itgt++)
-  {
-    NameType const& tgtName = topIn[itgt].Name();
-    //mprintf("DEBUG: Search for atom %s\n", *tgtName);
-    bool found = false;
-    // Check if this atom has an alias.
-    NameType alias;
-    bool has_alias = creator.GetAlias( alias, tgtName );
-//    if (creator.GetAlias( alias, tgtName )) {
-//      mprintf("DEBUG: Atom %s alias is %s\n", *tgtName, *alias);
-//    }
-    // See if tgtName matches a reference (template) atom name.
-    for (int iref = 0; iref != resTemplate->Top().Natom(); iref++)
-    {
-      NameType const& refName = resTemplate->Top()[iref].Name();
-      if (refName == tgtName) {
-        sourceAtomNames[itgt] = tgtName;
-        mapOut[iref] = itgt;
-        found = true;
-        break;
-      }
-    }
-    if (!found && has_alias) {
-      // See if alias matches a reference (template) atom name.
-      for (int iref = 0; iref != resTemplate->Top().Natom(); iref++) {
-        NameType const& refName = resTemplate->Top()[iref].Name();
-        if (refName == alias) {
-          sourceAtomNames[itgt] = alias;
-          mapOut[iref] = itgt;
-          found = true;
-          break;
-        }
-      } // END search template for alias
-    } // END do alias search
-    if (!found) {
-      mprintf("Warning: Input atom %s was not mapped to a template atom.\n",
-              topIn.TruncAtomResNameOnumId( itgt ).c_str());
-      nTgtAtomsMissing++;
-    }
-  }
-/*
-  for (int iref = 0; iref != resTemplate->Top().Natom(); iref++)
-  {
-    // Find this atom name in topIn
-    NameType const& refName = resTemplate->Top()[iref].Name();
-    int iat = -1;
-    for (int itgt = resIn.FirstAtom(); itgt != resIn.LastAtom(); itgt++) {
-      if ( refName == topIn[itgt].Name() ) {
-        iat = itgt;
-        break;
-      }
-    }
-    
-    mapOut.push_back( iat );
-  }*/
-  return mapOut;
-}
-
 /** Search in array of atom bonding pairs for given bonding pair. */
 bool Exec_Build::hasBondingPair(IParray const& bpairs, Ipair const& bpair) {
   for (IParray::const_iterator it = bpairs.begin(); it != bpairs.end(); ++it)
@@ -321,7 +250,7 @@ const
         currentRes.SetName( NameType( (*templateResName) + ( templateResName.len() - 3) ) );
       // Map source atoms to template atoms.
       int nTgtAtomsMissing = 0;
-      std::vector<int> map = MapAtomsToTemplate( topIn, ires, resTemplate, creator, SourceAtomNames, nTgtAtomsMissing );
+      std::vector<int> map = creator.MapAtomsToTemplate( topIn, ires, resTemplate, SourceAtomNames, nTgtAtomsMissing );
       if (debug_ > 1) {
         mprintf("\t  Atom map:\n");
         // DEBUG - print map
diff --git a/src/Exec_Mutate.cpp b/src/Exec_Mutate.cpp
index d7616f49f0..d3c1c00e54 100644
--- a/src/Exec_Mutate.cpp
+++ b/src/Exec_Mutate.cpp
@@ -73,8 +73,43 @@ Exec::RetType Exec_Mutate::Execute(CpptrajState& State, ArgList& argIn)
   std::vector<int> resnums = CRD->Top().ResnumsSelectedBy( mask );
   mprintf("\t%zu residues selected by '%s'\n", resnums.size(), mask.MaskString());
 
-  AtomMask toRemove;
-  toRemove.SetNatoms( CRD->Top().Natom() );
+  AtomMask toKeep;
+  toKeep.SetNatoms( CRD->Top().Natom() );
+  std::vector<NameType> SourceAtomNames;
+  SourceAtomNames.resize( CRD->Top().Natom() );
+  std::vector<int>::const_iterator rnum = resnums.begin();
+  for (int ires = 0; ires != CRD->Top().Nres(); ires++)
+  {
+    // Is this a selected res?
+    if (rnum != resnums.end() && ires == *rnum) {
+      // Selected res. Keep only atoms present in template
+      ++rnum;
+      int nTgtAtomsMissing = 0;
+      std::vector<int> templateToRes = creator.MapAtomsToTemplate( CRD->Top(), ires, UNIT, SourceAtomNames, nTgtAtomsMissing );
+      //if (debug_ > 1) {
+        mprintf("\tResidue %i Atom map:\n", ires + 1);
+        // DEBUG - print map
+        for (int iref = 0; iref != UNIT->Top().Natom(); iref++) {
+          mprintf("\t\t%6i %6s =>", iref+1, *(UNIT->Top()[iref].Name()));
+          if (templateToRes[iref] == -1)
+            mprintf(" No match\n");
+          else
+            mprintf(" %6i %6s\n", templateToRes[iref]+1, *(CRD->Top()[templateToRes[iref]].Name()));
+        }
+      //}
+      // For each template atom, only keep what was mapped
+      for (int iref = 0; iref != UNIT->Top().Natom(); iref++)
+        if (templateToRes[iref] > -1)
+          toKeep.AddSelectedAtom( templateToRes[iref] );
+    } else {
+      // Not a selected res. Keep all atoms
+      Residue const& currentRes = CRD->Top().Res( ires );
+      for (int at = currentRes.FirstAtom(); at != currentRes.LastAtom(); ++at)
+        toKeep.AddSelectedAtom( at );
+    }
+  }
+
+/*
   for (std::vector<int>::const_iterator rnum = resnums.begin(); rnum != resnums.end(); ++rnum)
   {
     Residue const& currentRes = CRD->Top().Res( *rnum );
@@ -100,8 +135,9 @@ Exec::RetType Exec_Mutate::Execute(CpptrajState& State, ArgList& argIn)
     }
   }
   toRemove.InvertMask();
-
   Topology* newTop = CRD->Top().modifyStateByMask( toRemove );
+*/
+  Topology* newTop = CRD->Top().modifyStateByMask( toKeep );
   if (newTop == 0) {
     mprinterr("Error: Could not remove atoms from '%s'\n", CRD->legend());
     return CpptrajState::ERR;
diff --git a/src/Structure/Creator.cpp b/src/Structure/Creator.cpp
index 4629260e9b..50e05fe284 100644
--- a/src/Structure/Creator.cpp
+++ b/src/Structure/Creator.cpp
@@ -379,3 +379,74 @@ const
   }
   return false;
 }
+
+/** Map atoms in residue to template. */
+std::vector<int> Creator::MapAtomsToTemplate(Topology const& topIn,
+                                                int rnum,
+                                                DataSet_Coords* resTemplate,
+                                                std::vector<NameType>& sourceAtomNames,
+                                                int& nTgtAtomsMissing)
+const
+{
+  nTgtAtomsMissing = 0;
+  std::vector<int> mapOut(resTemplate->Top().Natom(), -1);
+  mapOut.reserve( resTemplate->Top().Natom() );
+  Residue const& resIn = topIn.Res(rnum);
+  // For each atom in topIn, find a template atom
+  for (int itgt = resIn.FirstAtom(); itgt != resIn.LastAtom(); itgt++)
+  {
+    NameType const& tgtName = topIn[itgt].Name();
+    //mprintf("DEBUG: Search for atom %s\n", *tgtName);
+    bool found = false;
+    // Check if this atom has an alias.
+    NameType alias;
+    bool has_alias = GetAlias( alias, tgtName );
+//    if (creator.GetAlias( alias, tgtName )) {
+//      mprintf("DEBUG: Atom %s alias is %s\n", *tgtName, *alias);
+//    }
+    // See if tgtName matches a reference (template) atom name.
+    for (int iref = 0; iref != resTemplate->Top().Natom(); iref++)
+    {
+      NameType const& refName = resTemplate->Top()[iref].Name();
+      if (refName == tgtName) {
+        sourceAtomNames[itgt] = tgtName;
+        mapOut[iref] = itgt;
+        found = true;
+        break;
+      }
+    }
+    if (!found && has_alias) {
+      // See if alias matches a reference (template) atom name.
+      for (int iref = 0; iref != resTemplate->Top().Natom(); iref++) {
+        NameType const& refName = resTemplate->Top()[iref].Name();
+        if (refName == alias) {
+          sourceAtomNames[itgt] = alias;
+          mapOut[iref] = itgt;
+          found = true;
+          break;
+        }
+      } // END search template for alias
+    } // END do alias search
+    if (!found) {
+      mprintf("Warning: Input atom %s was not mapped to a template atom.\n",
+              topIn.TruncAtomResNameOnumId( itgt ).c_str());
+      nTgtAtomsMissing++;
+    }
+  }
+/*
+  for (int iref = 0; iref != resTemplate->Top().Natom(); iref++)
+  {
+    // Find this atom name in topIn
+    NameType const& refName = resTemplate->Top()[iref].Name();
+    int iat = -1;
+    for (int itgt = resIn.FirstAtom(); itgt != resIn.LastAtom(); itgt++) {
+      if ( refName == topIn[itgt].Name() ) {
+        iat = itgt;
+        break;
+      }
+    }
+    
+    mapOut.push_back( iat );
+  }*/
+  return mapOut;
+}
diff --git a/src/Structure/Creator.h b/src/Structure/Creator.h
index 4ad5a2cf6f..0c83b658d1 100644
--- a/src/Structure/Creator.h
+++ b/src/Structure/Creator.h
@@ -12,6 +12,7 @@ class DataSet_Parameters;
 class DataSet_PdbResMap;
 class DataSetList;
 class NameType;
+class Topology;
 namespace Cpptraj {
 namespace Structure {
 /// Used to create a system from individual units
@@ -50,6 +51,9 @@ class Creator {
     DataSet_Coords* IdTemplateFromResname(NameType const&, TerminalType) const;
     /// Get name map if its present
     bool GetAlias(NameType&, NameType const&) const;
+    /// Create an atom map of source atom names to template names
+    std::vector<int> MapAtomsToTemplate(Topology const&, int, DataSet_Coords*,
+                                        std::vector<NameType>&, int&) const;
   private:
     /// Get templates
     int getTemplates(ArgList&, DataSetList const&);

From d6ee25c12b794868df260765f91789bb419c24b5 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 7 Nov 2025 09:53:41 -0500
Subject: [PATCH 1057/1492] Start setting up output coords

---
 src/Exec_Mutate.cpp | 39 ++++++++++++++++++++++++++++++++++++++-
 src/Exec_Mutate.h   |  7 +++++++
 2 files changed, 45 insertions(+), 1 deletion(-)

diff --git a/src/Exec_Mutate.cpp b/src/Exec_Mutate.cpp
index d3c1c00e54..8a921f3a50 100644
--- a/src/Exec_Mutate.cpp
+++ b/src/Exec_Mutate.cpp
@@ -5,7 +5,7 @@
 // Exec_Mutate::Help()
 void Exec_Mutate::Help() const
 {
-  mprintf("\tcrdset <COORDS set> resmask <mask>\n"
+  mprintf("\tcrdset <COORDS set> resmask <mask> [outset <output COORDS>]\n"
           "\t[%s]\n"
           "\t[{%s} ...]\n"
           "\t[{%s} ...]\n",
@@ -38,6 +38,40 @@ Exec::RetType Exec_Mutate::Execute(CpptrajState& State, ArgList& argIn)
   }
   mprintf("\tUsing set '%s'\n", CRD->legend());
 
+  bool modify_input_coords = true;
+  DataSet_Coords* OUT = 0;
+  std::string outset = argIn.GetStringKey("outset");
+  if (!outset.empty()) {
+    OUT = (DataSet_Coords*)State.DSL().AddSet( DataSet::COORDS, outset );
+    if (OUT == 0) {
+      mprinterr("Error: Could not allocate output set '%s'\n", outset.c_str());
+      return CpptrajState::ERR;
+    }
+    modify_input_coords = false;
+    mprintf("\tOutput set: %s\n", OUT->legend());
+  } else {
+    // Modifying input COORDS set
+    if (State.DSL().PopSet( CRD ) == 0) {
+      mprinterr("Internal Error: Exec_Mutate::Execute: Could not pop input COORDS set off master DataSetList()\n");
+      return CpptrajState::ERR;
+    }
+    OUT = (DataSet_Coords*)State.DSL().AddSet( DataSet::COORDS, CRD->Meta() );
+    mprintf("\tWill modify COORDS set %s\n", CRD->legend());
+  }
+
+  CpptrajState::RetType ret = doMutate( State, argIn, CRD, OUT, creator );
+
+  if (modify_input_coords && CRD != 0) delete CRD;
+
+  return ret;
+}
+
+/** Actually do the mutation(s) */
+CpptrajState::RetType Exec_Mutate::doMutate(CpptrajState& State, ArgList& argIn, DataSet_Coords* CRD, DataSet_Coords* OUT,
+                                           Cpptraj::Structure::Creator const& creator)
+const
+{
+
   std::string resmask = argIn.GetStringKey("resmask");
   if (resmask.empty()) {
     mprinterr("Error: Specify mask of residues to mutate with 'resmask'\n");
@@ -143,6 +177,9 @@ Exec::RetType Exec_Mutate::Execute(CpptrajState& State, ArgList& argIn)
     return CpptrajState::ERR;
   }
   newTop->Summary();
+  // Change the residue names
+  for (std::vector<int>::const_iterator rnum = resnums.begin(); rnum != resnums.end(); ++rnum)
+    newTop->SetRes( *rnum ).SetName( templateName );
 
   if (newTop != 0) delete newTop;
 
diff --git a/src/Exec_Mutate.h b/src/Exec_Mutate.h
index c7293fd0a6..5479b8c71e 100644
--- a/src/Exec_Mutate.h
+++ b/src/Exec_Mutate.h
@@ -1,6 +1,11 @@
 #ifndef INC_EXEC_MUTATE_H
 #define INC_EXEC_MUTATE_H
 #include "Exec.h"
+namespace Cpptraj {
+namespace Structure {
+class Creator;
+}
+}
 /// <Enter description of Exec_Mutate here>
 class Exec_Mutate : public Exec {
   public:
@@ -9,6 +14,8 @@ class Exec_Mutate : public Exec {
     DispatchObject* Alloc() const { return (DispatchObject*)new Exec_Mutate(); }
     RetType Execute(CpptrajState&, ArgList&);
   private:
+    RetType doMutate(CpptrajState&, ArgList&, DataSet_Coords*, DataSet_Coords*, Cpptraj::Structure::Creator const&) const;
+
     int debug_;
 };
 #endif

From 52710ea1a4eb05a0da922e5de78f793a87925aa4 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 7 Nov 2025 10:19:11 -0500
Subject: [PATCH 1058/1492] Set up output coords

---
 src/Exec_Mutate.cpp | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/src/Exec_Mutate.cpp b/src/Exec_Mutate.cpp
index 8a921f3a50..c191259fab 100644
--- a/src/Exec_Mutate.cpp
+++ b/src/Exec_Mutate.cpp
@@ -181,6 +181,21 @@ const
   for (std::vector<int>::const_iterator rnum = resnums.begin(); rnum != resnums.end(); ++rnum)
     newTop->SetRes( *rnum ).SetName( templateName );
 
+  // Set up output coords
+  OUT->CoordsSetup( *newTop, CRD->CoordsInfo() );
+  Frame newFrame;
+  newFrame.SetupFrameV(newTop->Atoms(), CRD->CoordsInfo());
+
+  // Strip all input coords frames
+  Frame inputFrame = CRD->AllocateFrame();
+  for (unsigned int frm = 0; frm != CRD->Size(); ++frm)
+  {
+    CRD->GetFrame(frm, inputFrame);
+
+    newFrame.SetFrame(inputFrame, toKeep);
+    OUT->AddFrame(newFrame);
+  }
+
   if (newTop != 0) delete newTop;
 
   return CpptrajState::OK;

From a0319540e15387fcd261337541699757551f9c3b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 7 Nov 2025 10:44:04 -0500
Subject: [PATCH 1059/1492] Add test for mutate

---
 test/Makefile                     |   6 +-
 test/Test_Mutate/Built.mol2.save  | 356 ++++++++++++++++++++++++++++++
 test/Test_Mutate/Mutated.pdb.save | 165 ++++++++++++++
 test/Test_Mutate/RunTest.sh       |  37 ++++
 4 files changed, 563 insertions(+), 1 deletion(-)
 create mode 100644 test/Test_Mutate/Built.mol2.save
 create mode 100644 test/Test_Mutate/Mutated.pdb.save
 create mode 100755 test/Test_Mutate/RunTest.sh

diff --git a/test/Makefile b/test/Makefile
index fb42d63799..17f2214e01 100644
--- a/test/Makefile
+++ b/test/Makefile
@@ -561,6 +561,9 @@ test.minmaxdist:
 test.watershellclosest:
 	@-cd Test_Watershell_Closest && ./RunTest.sh $(OPT)
 
+test.mutate:
+	@-cd Test_Mutate && ./RunTest.sh $(OPT)
+
 # Only GPU-specific tests should go here
 GPUTESTS=test.closest \
          test.solvent \
@@ -745,7 +748,8 @@ COMPLETETESTS=test.general \
               test.enedecomp \
               test.addatom \
               test.minmaxdist \
-              test.watershellclosest
+              test.watershellclosest \
+              test.mutate
 
 test.all:
 	$(MAKE) test.complete summary
diff --git a/test/Test_Mutate/Built.mol2.save b/test/Test_Mutate/Built.mol2.save
new file mode 100644
index 0000000000..622e47940c
--- /dev/null
+++ b/test/Test_Mutate/Built.mol2.save
@@ -0,0 +1,356 @@
+@<TRIPOS>MOLECULE
+Cpptraj Generated mol2 file.
+  167   166    13     0     0
+SMALL
+USER_CHARGES
+
+
+@<TRIPOS>ATOM
+      1 N          -1.8890    9.1590    7.5690 N3         1 SER      0.184900
+      2 H1         -1.5301    8.5517    6.8462 H          1 SER      0.189800
+      3 H2         -2.8184    8.8525    7.8186 H          1 SER      0.189800
+      4 H3         -1.1833    9.2653    8.2837 H          1 SER      0.189800
+      5 CA         -2.0640   10.5010    6.9930 CX         1 SER      0.056700
+      6 HA         -3.1157   10.7781    7.0655 HP         1 SER      0.078200
+      7 CB         -1.2300   11.5610    7.7070 2C         1 SER      0.259600
+      8 HB2        -1.2896   12.4668    7.1037 H1         1 SER      0.027300
+      9 HB3        -1.7043   11.7363    8.6726 H1         1 SER      0.027300
+     10 OG          0.1230   11.2160    7.9040 OH         1 SER     -0.671400
+     11 HG          0.5733   11.9328    8.3568 HO         1 SER      0.423900
+     12 C          -1.6130   10.4180    5.5420 C          1 SER      0.616300
+     13 O          -2.4980   10.4330    4.6890 O          1 SER     -0.572200
+     14 N          -0.3660   10.5720    5.0900 N          2 ALA     -0.415700
+     15 H           0.2422   10.7220    5.8823 H          2 ALA      0.271900
+     16 CA          0.1950   10.6970    3.7600 CX         2 ALA      0.033700
+     17 HA         -0.2784   11.6285    3.4496 H1         2 ALA      0.082300
+     18 CB          1.7100   10.8790    3.7090 CT         2 ALA     -0.182500
+     19 HB1         2.1982    9.9516    4.0085 HC         2 ALA      0.060300
+     20 HB2         2.0116   11.1363    2.6936 HC         2 ALA      0.060300
+     21 HB3         2.0034   11.6793    4.3884 HC         2 ALA      0.060300
+     22 C          -0.1900    9.6090    2.7680 C          2 ALA      0.597300
+     23 O          -0.4520    9.9630    1.6210 O          2 ALA     -0.567900
+     24 N          -0.2680    8.4020    3.3340 N          3 THR     -0.415700
+     25 H          -0.0556    8.3567    4.3204 H          3 THR      0.271900
+     26 CA         -0.6060    7.1720    2.6470 CX         3 THR     -0.038900
+     27 HA         -0.2380    7.0720    1.6259 H1         3 THR      0.100700
+     28 CB         -0.0930    5.9920    3.4680 3C         3 THR      0.365400
+     29 HB         -0.7347    5.1301    3.2853 H1         3 THR      0.004300
+     30 CG2         1.3430    5.6480    3.0810 CT         3 THR     -0.243800
+     31 HG21        1.9854    6.5094    3.2639 HC         3 THR      0.064200
+     32 HG22        1.6886    4.8043    3.6783 HC         3 THR      0.064200
+     33 HG23        1.3818    5.3844    2.0241 HC         3 THR      0.064200
+     34 OG1        -0.2730    6.2460    4.8430 OH         3 THR     -0.676100
+     35 HG1         0.0520    5.4995    5.3515 HO         3 THR      0.410200
+     36 C          -2.0730    6.8820    2.3630 C          3 THR      0.597300
+     37 O          -2.8840    6.6850    3.2650 O          3 THR     -0.567900
+     38 N          -2.4140    6.7960    1.0750 N          4 ALA     -0.415700
+     39 H          -1.7951    7.2210    0.3994 H          4 ALA      0.271900
+     40 CA         -3.6890    6.2860    0.6130 CX         4 ALA      0.033700
+     41 HA         -4.2192    6.1589    1.5569 H1         4 ALA      0.082300
+     42 CB         -4.4650    7.2750   -0.2530 CT         4 ALA     -0.182500
+     43 HB1        -3.9512    7.4058   -1.2054 HC         4 ALA      0.060300
+     44 HB2        -5.4694    6.8915   -0.4322 HC         4 ALA      0.060300
+     45 HB3        -4.5292    8.2349    0.2594 HC         4 ALA      0.060300
+     46 C          -3.6320    4.9260   -0.0680 C          4 ALA      0.597300
+     47 O          -4.2790    3.9520    0.3090 O          4 ALA     -0.567900
+     48 N          -2.7950    4.8720   -1.1060 N          5 GLU     -0.516300
+     49 H          -2.4850    5.7793   -1.4235 H          5 GLU      0.293600
+     50 CA         -2.5350    3.7230   -1.9500 CX         5 GLU      0.039700
+     51 HA         -2.6364    2.8498   -1.3056 H1         5 GLU      0.110500
+     52 CB         -3.4130    3.5240   -3.1830 2C         5 GLU      0.056000
+     53 HB2        -4.4152    3.8399   -2.8932 HC         5 GLU     -0.017300
+     54 HB3        -3.0241    4.2025   -3.9423 HC         5 GLU     -0.017300
+     55 CG         -3.4700    2.1080   -3.7480 2C         5 GLU      0.013600
+     56 HG2        -3.9808    2.1523   -4.7099 HC         5 GLU     -0.042500
+     57 HG3        -2.4416    1.7795   -3.8981 HC         5 GLU     -0.042500
+     58 CD         -4.1890    1.1230   -2.8370 CO         5 GLU      0.805400
+     59 OE1        -3.8030    0.7710   -1.7020 O2         5 GLU     -0.818800
+     60 OE2        -5.2630    0.6010   -3.2070 O2         5 GLU     -0.818800
+     61 C          -1.0580    3.5180   -2.2550 C          5 GLU      0.536600
+     62 O          -0.3010    4.4140   -2.6190 O          5 GLU     -0.581900
+     63 N          -0.6680    2.2650   -2.0090 N          6 ASN     -0.415700
+     64 H          -1.3463    1.7023   -1.5156 H          6 ASN      0.271900
+     65 CA          0.6390    1.6960   -2.2670 CX         6 ASN      0.014300
+     66 HA          1.2181    2.4119   -2.8502 H1         6 ASN      0.104800
+     67 CB          1.4120    1.3660   -0.9930 2C         6 ASN     -0.204100
+     68 HB2         0.5185    1.1760   -0.3983 HC         6 ASN      0.079700
+     69 HB3         2.0633    0.4927   -0.9585 HC         6 ASN      0.079700
+     70 CG          2.1540    2.5500   -0.3910 C          6 ASN      0.713000
+     71 OD1         2.8090    3.3470   -1.0580 O          6 ASN     -0.593100
+     72 ND2         2.3590    2.5190    0.9280 N          6 ASN     -0.919100
+     73 HD21        2.8467    3.2803    1.3782 H          6 ASN      0.419600
+     74 HD22        2.0254    1.7344    1.4695 H          6 ASN      0.419600
+     75 C           0.5090    0.4880   -3.1850 C          6 ASN      0.597300
+     76 O          -0.4570   -0.2500   -3.0040 O          6 ASN     -0.567900
+     77 N           1.4630    0.2470   -4.0870 N          7 GLY     -0.415700
+     78 H           2.2534    0.8703   -4.1700 H          7 GLY      0.271900
+     79 CA          1.3990   -0.9020   -4.9670 CX         7 GLY     -0.025200
+     80 HA2         0.4659   -0.8067   -5.5222 H1         7 GLY      0.069800
+     81 HA3         2.2407   -0.8055   -5.6528 H1         7 GLY      0.069800
+     82 C           1.4480   -2.2750   -4.3130 C          7 GLY      0.597300
+     83 O           0.7270   -2.5760   -3.3640 O          7 GLY     -0.567900
+     84 N           2.3610   -3.1180   -4.8010 N          8 LYS     -0.347900
+     85 H           2.9875   -2.7066   -5.4780 H          8 LYS      0.274700
+     86 CA          2.5410   -4.5140   -4.4580 CX         8 LYS     -0.240000
+     87 HA          1.5806   -4.9565   -4.1935 H1         8 LYS      0.142600
+     88 CB          3.1230   -5.2830   -5.6410 C8         8 LYS     -0.009400
+     89 HB2         3.2859   -6.2983   -5.2793 HC         8 LYS      0.036200
+     90 HB3         2.3408   -5.2894   -6.4001 HC         8 LYS      0.036200
+     91 CG          4.4160   -4.7460   -6.2480 C8         8 LYS      0.018700
+     92 HG2         4.3009   -3.6849   -6.4692 HC         8 LYS      0.010300
+     93 HG3         5.2341   -4.8825   -5.5408 HC         8 LYS      0.010300
+     94 CD          4.7260   -5.5030   -7.5360 C8         8 LYS     -0.047900
+     95 HD2         4.5356   -6.5561   -7.3289 HC         8 LYS      0.062100
+     96 HD3         4.0166   -5.1460   -8.2826 HC         8 LYS      0.062100
+     97 CE          6.1480   -5.3380   -8.0660 C8         8 LYS     -0.014300
+     98 HE2         6.7759   -4.9415   -7.2681 HP         8 LYS      0.113500
+     99 HE3         6.5237   -6.3143   -8.3722 HP         8 LYS      0.113500
+    100 NZ          6.1770   -4.4200   -9.2140 N3         8 LYS     -0.385400
+    101 HZ1         5.8293   -3.5152   -8.9304 H          8 LYS      0.340000
+    102 HZ2         7.1261   -4.3268   -9.5467 H          8 LYS      0.340000
+    103 HZ3         5.5955   -4.7874   -9.9536 H          8 LYS      0.340000
+    104 C           3.5120   -4.5190   -3.2860 C          8 LYS      0.734100
+    105 O           4.6240   -5.0420   -3.2860 O          8 LYS     -0.589400
+    106 N           2.9250   -4.2560   -2.1160 N          9 ALA     -0.415700
+    107 H           1.9772   -3.9809   -2.3306 H          9 ALA      0.271900
+    108 CA          3.3410   -4.2620   -0.7280 CX         9 ALA      0.033700
+    109 HA          4.4119   -4.1552   -0.5551 H1         9 ALA      0.082300
+    110 CB          2.6250   -3.0680   -0.1040 CT         9 ALA     -0.182500
+    111 HB1         1.5508   -3.1652   -0.2609 HC         9 ALA      0.060300
+    112 HB2         2.8341   -3.0365    0.9653 HC         9 ALA      0.060300
+    113 HB3         2.9779   -2.1480   -0.5699 HC         9 ALA      0.060300
+    114 C           2.9450   -5.5930   -0.1050 C          9 ALA      0.597300
+    115 O           3.0220   -6.6750   -0.6820 O          9 ALA     -0.567900
+    116 N           2.5310   -5.6090    1.1640 N         10 THR     -0.415700
+    117 H           2.3704   -4.7579    1.6835 H         10 THR      0.271900
+    118 CA          2.2540   -6.8740    1.8150 CX        10 THR     -0.038900
+    119 HA          3.0024   -7.6404    1.6134 H1        10 THR      0.100700
+    120 CB          2.2070   -6.6220    3.3200 3C        10 THR      0.365400
+    121 HB          1.7393   -5.6460    3.4492 H1        10 THR      0.004300
+    122 CG2         1.4560   -7.6590    4.1490 CT        10 THR     -0.243800
+    123 HG21        1.9234   -8.6353    4.0207 HC        10 THR      0.064200
+    124 HG22        1.4886   -7.3766    5.2013 HC        10 THR      0.064200
+    125 HG23        0.4185   -7.7072    3.8183 HC        10 THR      0.064200
+    126 OG1         3.4600   -6.5010    3.9540 OH        10 THR     -0.676100
+    127 HG1         3.3301   -6.3451    4.8923 HO        10 THR      0.410200
+    128 C           0.8890   -7.3540    1.3440 C         10 THR      0.597300
+    129 O          -0.1720   -6.7600    1.5240 O         10 THR     -0.567900
+    130 N           0.9060   -8.5220    0.6990 N         11 ALA     -0.415700
+    131 H           1.7668   -9.0480    0.7481 H         11 ALA      0.271900
+    132 CA         -0.1880   -9.0660   -0.0800 CX        11 ALA      0.033700
+    133 HA         -0.8293   -8.3485   -0.5919 H1        11 ALA      0.082300
+    134 CB          0.4120  -10.0100   -1.1170 CT        11 ALA     -0.182500
+    135 HB1         1.0496  -10.7402   -0.6186 HC        11 ALA      0.060300
+    136 HB2        -0.3892  -10.5279   -1.6443 HC        11 ALA      0.060300
+    137 HB3         1.0050   -9.4375   -1.8302 HC        11 ALA      0.060300
+    138 C          -1.0790   -9.7520    0.9460 C         11 ALA      0.597300
+    139 O          -0.7100  -10.6730    1.6720 O         11 ALA     -0.567900
+    140 N          -2.3440   -9.3260    0.9490 N         12 LYS     -0.347900
+    141 H          -2.5162   -8.5293    0.3525 H         12 LYS      0.274700
+    142 CA         -3.4700   -9.9260    1.6360 CX        12 LYS     -0.240000
+    143 HA         -3.1315  -10.5139    2.4892 H1        12 LYS      0.142600
+    144 CB         -4.3840   -8.8140    2.1420 C8        12 LYS     -0.009400
+    145 HB2        -4.5318   -8.1015    1.3305 HC        12 LYS      0.036200
+    146 HB3        -5.3413   -9.2593    2.4127 HC        12 LYS      0.036200
+    147 CG         -3.7990   -8.0920    3.3520 C8        12 LYS      0.018700
+    148 HG2        -3.6887   -8.7443    4.2183 HC        12 LYS      0.010300
+    149 HG3        -2.8444   -7.6127    3.1349 HC        12 LYS      0.010300
+    150 CD         -4.8480   -7.0240    3.6500 C8        12 LYS     -0.047900
+    151 HD2        -5.1982   -6.5266    2.7456 HC        12 LYS      0.062100
+    152 HD3        -5.7012   -7.4255    4.1968 HC        12 LYS      0.062100
+    153 CE         -4.1080   -6.0190    4.5290 C8        12 LYS     -0.014300
+    154 HE2        -3.8582   -6.5292    5.4593 HP        12 LYS      0.113500
+    155 HE3        -3.1908   -5.7491    4.0056 HP        12 LYS      0.113500
+    156 NZ         -4.8770   -4.8020    4.8290 N3        12 LYS     -0.385400
+    157 HZ1        -5.7267   -5.0518    5.3144 H         12 LYS      0.340000
+    158 HZ2        -4.3242   -4.1895    5.4115 H         12 LYS      0.340000
+    159 HZ3        -5.1082   -4.3289    3.9671 H         12 LYS      0.340000
+    160 C          -4.3950  -10.7780    0.7790 C         12 LYS      0.734100
+    161 O          -4.4830  -11.9390    1.1720 O         12 LYS     -0.589400
+    162 N          -4.8320  -10.2020   -0.3440 N         13 NME     -0.415700
+    163 H          -4.5447   -9.2614   -0.5740 H         13 NME      0.271900
+    164 C          -5.7189  -10.8883   -1.2616 CT        13 NME     -0.149000
+    165 H1         -5.9371  -11.8855   -0.8794 H1        13 NME      0.097600
+    166 H2         -6.6475  -10.3260   -1.3592 H1        13 NME      0.097600
+    167 H3         -5.2402  -10.9705   -2.2374 H1        13 NME      0.097600
+@<TRIPOS>BOND
+    1    12    13 1
+    2    12    14 1
+    3     7    10 1
+    4     5     7 1
+    5     5    12 1
+    6     1     5 1
+    7    22    23 1
+    8    22    24 1
+    9    16    18 1
+   10    16    22 1
+   11    14    16 1
+   12    36    37 1
+   13    36    38 1
+   14    28    30 1
+   15    28    34 1
+   16    26    28 1
+   17    26    36 1
+   18    24    26 1
+   19    46    47 1
+   20    46    48 1
+   21    40    42 1
+   22    40    46 1
+   23    38    40 1
+   24    61    62 1
+   25    61    63 1
+   26    58    59 1
+   27    58    60 1
+   28    55    58 1
+   29    52    55 1
+   30    50    52 1
+   31    50    61 1
+   32    48    50 1
+   33    75    76 1
+   34    75    77 1
+   35    70    71 1
+   36    70    72 1
+   37    67    70 1
+   38    65    67 1
+   39    65    75 1
+   40    63    65 1
+   41    82    83 1
+   42    82    84 1
+   43    79    82 1
+   44    77    79 1
+   45   104   105 1
+   46   104   106 1
+   47    97   100 1
+   48    94    97 1
+   49    91    94 1
+   50    88    91 1
+   51    86    88 1
+   52    86   104 1
+   53    84    86 1
+   54   114   115 1
+   55   114   116 1
+   56   108   110 1
+   57   108   114 1
+   58   106   108 1
+   59   128   129 1
+   60   128   130 1
+   61   120   122 1
+   62   120   126 1
+   63   118   120 1
+   64   118   128 1
+   65   116   118 1
+   66   138   139 1
+   67   138   140 1
+   68   132   134 1
+   69   132   138 1
+   70   130   132 1
+   71   160   161 1
+   72   160   162 1
+   73   153   156 1
+   74   150   153 1
+   75   147   150 1
+   76   144   147 1
+   77   142   144 1
+   78   142   160 1
+   79   140   142 1
+   80   162   164 1
+   81    10    11 1
+   82     7     8 1
+   83     7     9 1
+   84     5     6 1
+   85     1     2 1
+   86     1     3 1
+   87     1     4 1
+   88    18    19 1
+   89    18    20 1
+   90    18    21 1
+   91    16    17 1
+   92    14    15 1
+   93    34    35 1
+   94    30    31 1
+   95    30    32 1
+   96    30    33 1
+   97    28    29 1
+   98    26    27 1
+   99    24    25 1
+  100    42    43 1
+  101    42    44 1
+  102    42    45 1
+  103    40    41 1
+  104    38    39 1
+  105    55    56 1
+  106    55    57 1
+  107    52    53 1
+  108    52    54 1
+  109    50    51 1
+  110    48    49 1
+  111    72    73 1
+  112    72    74 1
+  113    67    68 1
+  114    67    69 1
+  115    65    66 1
+  116    63    64 1
+  117    79    80 1
+  118    79    81 1
+  119    77    78 1
+  120   100   101 1
+  121   100   102 1
+  122   100   103 1
+  123    97    98 1
+  124    97    99 1
+  125    94    95 1
+  126    94    96 1
+  127    91    92 1
+  128    91    93 1
+  129    88    89 1
+  130    88    90 1
+  131    86    87 1
+  132    84    85 1
+  133   110   111 1
+  134   110   112 1
+  135   110   113 1
+  136   108   109 1
+  137   106   107 1
+  138   126   127 1
+  139   122   123 1
+  140   122   124 1
+  141   122   125 1
+  142   120   121 1
+  143   118   119 1
+  144   116   117 1
+  145   134   135 1
+  146   134   136 1
+  147   134   137 1
+  148   132   133 1
+  149   130   131 1
+  150   156   157 1
+  151   156   158 1
+  152   156   159 1
+  153   153   154 1
+  154   153   155 1
+  155   150   151 1
+  156   150   152 1
+  157   147   148 1
+  158   147   149 1
+  159   144   145 1
+  160   144   146 1
+  161   142   143 1
+  162   140   141 1
+  163   164   165 1
+  164   164   166 1
+  165   164   167 1
+  166   162   163 1
+@<TRIPOS>SUBSTRUCTURE
+      1 SER               1 ****               0 ****  **** 
+      2 ALA              14 ****               0 ****  **** 
+      3 THR              24 ****               0 ****  **** 
+      4 ALA              38 ****               0 ****  **** 
+      5 GLU              48 ****               0 ****  **** 
+      6 ASN              63 ****               0 ****  **** 
+      7 GLY              77 ****               0 ****  **** 
+      8 LYS              84 ****               0 ****  **** 
+      9 ALA             106 ****               0 ****  **** 
+     10 THR             116 ****               0 ****  **** 
+     11 ALA             130 ****               0 ****  **** 
+     12 LYS             140 ****               0 ****  **** 
+     13 NME             162 ****               0 ****  **** 
diff --git a/test/Test_Mutate/Mutated.pdb.save b/test/Test_Mutate/Mutated.pdb.save
new file mode 100644
index 0000000000..8d1398b3b8
--- /dev/null
+++ b/test/Test_Mutate/Mutated.pdb.save
@@ -0,0 +1,165 @@
+ATOM      1  N   SER     1      -1.889   9.159   7.569  1.00  0.00           N  
+ATOM      2  H1  SER     1      -1.037   8.691   7.296  1.00  0.00           H  
+ATOM      3  H2  SER     1      -1.900   9.298   8.569  1.00  0.00           H  
+ATOM      4  H3  SER     1      -2.538   8.447   7.265  1.00  0.00           H  
+ATOM      5  CA  SER     1      -2.064  10.501   6.993  1.00  0.00           C  
+ATOM      6  HA  SER     1      -3.100  10.824   7.102  1.00  0.00           H  
+ATOM      7  CB  SER     1      -1.230  11.561   7.707  1.00  0.00           C  
+ATOM      8  HB2 SER     1      -1.670  11.811   8.673  1.00  0.00           H  
+ATOM      9  HB3 SER     1      -1.248  12.503   7.159  1.00  0.00           H  
+ATOM     10  OG  SER     1       0.123  11.216   7.904  1.00  0.00           O  
+ATOM     11  HG  SER     1       0.274  11.728   8.701  1.00  0.00           H  
+ATOM     12  C   SER     1      -1.613  10.418   5.542  1.00  0.00           C  
+ATOM     13  O   SER     1      -2.498  10.433   4.689  1.00  0.00           O  
+ATOM     14  N   ALA     2      -0.366  10.572   5.090  1.00  0.00           N  
+ATOM     15  H   ALA     2       0.344  10.612   5.808  1.00  0.00           H  
+ATOM     16  CA  ALA     2       0.195  10.697   3.760  1.00  0.00           C  
+ATOM     17  HA  ALA     2      -0.218  11.569   3.254  1.00  0.00           H  
+ATOM     18  CB  ALA     2       1.710  10.879   3.709  1.00  0.00           C  
+ATOM     19  HB2 ALA     2       2.208   9.986   4.087  1.00  0.00           H  
+ATOM     20  HB3 ALA     2       1.927  11.641   4.458  1.00  0.00           H  
+ATOM     21  C   ALA     2      -0.190   9.609   2.768  1.00  0.00           C  
+ATOM     22  O   ALA     2      -0.452   9.963   1.621  1.00  0.00           O  
+ATOM     23  N   THR     3      -0.268   8.402   3.334  1.00  0.00           N  
+ATOM     24  H   THR     3      -0.260   8.275   4.336  1.00  0.00           H  
+ATOM     25  CA  THR     3      -0.606   7.172   2.647  1.00  0.00           C  
+ATOM     26  HA  THR     3      -0.180   7.266   1.648  1.00  0.00           H  
+ATOM     27  CB  THR     3      -0.093   5.992   3.468  1.00  0.00           C  
+ATOM     28  HB  THR     3      -0.586   5.081   3.128  1.00  0.00           H  
+ATOM     29  CG2 THR     3       1.343   5.648   3.081  1.00  0.00           C  
+ATOM     30 HG21 THR     3       1.306   5.005   2.202  1.00  0.00           H  
+ATOM     31 HG22 THR     3       1.955   6.543   2.967  1.00  0.00           H  
+ATOM     32 HG23 THR     3       1.828   5.068   3.866  1.00  0.00           H  
+ATOM     33  OG1 THR     3      -0.273   6.246   4.843  1.00  0.00           O  
+ATOM     34  HG1 THR     3       0.428   5.750   5.271  1.00  0.00           H  
+ATOM     35  C   THR     3      -2.073   6.882   2.363  1.00  0.00           C  
+ATOM     36  O   THR     3      -2.884   6.685   3.265  1.00  0.00           O  
+ATOM     37  N   ALA     4      -2.414   6.796   1.075  1.00  0.00           N  
+ATOM     38  H   ALA     4      -1.631   6.756   0.439  1.00  0.00           H  
+ATOM     39  CA  ALA     4      -3.689   6.286   0.613  1.00  0.00           C  
+ATOM     40  HA  ALA     4      -4.288   6.020   1.485  1.00  0.00           H  
+ATOM     41  CB  ALA     4      -4.465   7.275  -0.253  1.00  0.00           C  
+ATOM     42  HB2 ALA     4      -5.450   6.821  -0.366  1.00  0.00           H  
+ATOM     43  HB3 ALA     4      -4.022   7.162  -1.242  1.00  0.00           H  
+ATOM     44  C   ALA     4      -3.632   4.926  -0.068  1.00  0.00           C  
+ATOM     45  O   ALA     4      -4.279   3.952   0.309  1.00  0.00           O  
+ATOM     46  N   GLU     5      -2.795   4.872  -1.106  1.00  0.00           N  
+ATOM     47  H   GLU     5      -2.278   5.708  -1.339  1.00  0.00           H  
+ATOM     48  CA  GLU     5      -2.535   3.723  -1.950  1.00  0.00           C  
+ATOM     49  HA  GLU     5      -3.007   2.948  -1.346  1.00  0.00           H  
+ATOM     50  CB  GLU     5      -3.413   3.524  -3.183  1.00  0.00           C  
+ATOM     51  HB2 GLU     5      -3.139   4.141  -4.038  1.00  0.00           H  
+ATOM     52  HB3 GLU     5      -4.386   3.787  -2.767  1.00  0.00           H  
+ATOM     53  CG  GLU     5      -3.470   2.108  -3.748  1.00  0.00           C  
+ATOM     54  HG2 GLU     5      -2.447   1.793  -3.953  1.00  0.00           H  
+ATOM     55  HG3 GLU     5      -4.039   2.425  -4.623  1.00  0.00           H  
+ATOM     56  CD  GLU     5      -4.189   1.123  -2.837  1.00  0.00           C  
+ATOM     57  OE1 GLU     5      -3.803   0.771  -1.702  1.00  0.00           O  
+ATOM     58  OE2 GLU     5      -5.263   0.601  -3.207  1.00  0.00           O  
+ATOM     59  C   GLU     5      -1.058   3.518  -2.255  1.00  0.00           C  
+ATOM     60  O   GLU     5      -0.301   4.414  -2.619  1.00  0.00           O  
+ATOM     61  N   ASN     6      -0.668   2.265  -2.009  1.00  0.00           N  
+ATOM     62  H   ASN     6      -1.323   1.656  -1.539  1.00  0.00           H  
+ATOM     63  CA  ASN     6       0.639   1.696  -2.267  1.00  0.00           C  
+ATOM     64  HA  ASN     6       1.239   2.453  -2.772  1.00  0.00           H  
+ATOM     65  CB  ASN     6       1.412   1.366  -0.993  1.00  0.00           C  
+ATOM     66  HB2 ASN     6       2.224   0.703  -1.291  1.00  0.00           H  
+ATOM     67  HB3 ASN     6       0.712   0.882  -0.311  1.00  0.00           H  
+ATOM     68  CG  ASN     6       2.154   2.550  -0.391  1.00  0.00           C  
+ATOM     69  OD1 ASN     6       2.809   3.347  -1.058  1.00  0.00           O  
+ATOM     70  ND2 ASN     6       2.359   2.519   0.928  1.00  0.00           N  
+ATOM     71 HD21 ASN     6       1.869   1.897   1.556  1.00  0.00           H  
+ATOM     72 HD22 ASN     6       3.024   3.196   1.272  1.00  0.00           H  
+ATOM     73  C   ASN     6       0.509   0.488  -3.185  1.00  0.00           C  
+ATOM     74  O   ASN     6      -0.457  -0.250  -3.004  1.00  0.00           O  
+ATOM     75  N   GLY     7       1.463   0.247  -4.087  1.00  0.00           N  
+ATOM     76  H   GLY     7       2.372   0.658  -3.932  1.00  0.00           H  
+ATOM     77  CA  GLY     7       1.399  -0.902  -4.967  1.00  0.00           C  
+ATOM     78  HA2 GLY     7       2.180  -0.882  -5.728  1.00  0.00           H  
+ATOM     79  HA3 GLY     7       0.501  -0.799  -5.576  1.00  0.00           H  
+ATOM     80  C   GLY     7       1.448  -2.275  -4.313  1.00  0.00           C  
+ATOM     81  O   GLY     7       0.727  -2.576  -3.364  1.00  0.00           O  
+ATOM     82  N   LYS     8       2.361  -3.118  -4.801  1.00  0.00           N  
+ATOM     83  H   LYS     8       3.080  -2.784  -5.426  1.00  0.00           H  
+ATOM     84  CA  LYS     8       2.541  -4.514  -4.458  1.00  0.00           C  
+ATOM     85  HA  LYS     8       1.627  -5.015  -4.138  1.00  0.00           H  
+ATOM     86  CB  LYS     8       3.123  -5.283  -5.641  1.00  0.00           C  
+ATOM     87  HB2 LYS     8       2.435  -5.243  -6.486  1.00  0.00           H  
+ATOM     88  HB3 LYS     8       3.335  -6.318  -5.372  1.00  0.00           H  
+ATOM     89  CG  LYS     8       4.416  -4.746  -6.248  1.00  0.00           C  
+ATOM     90  HG2 LYS     8       5.308  -4.960  -5.660  1.00  0.00           H  
+ATOM     91  HG3 LYS     8       4.393  -3.674  -6.439  1.00  0.00           H  
+ATOM     92  CD  LYS     8       4.726  -5.503  -7.536  1.00  0.00           C  
+ATOM     93  HD2 LYS     8       3.992  -5.272  -8.308  1.00  0.00           H  
+ATOM     94  HD3 LYS     8       4.584  -6.543  -7.241  1.00  0.00           H  
+ATOM     95  CE  LYS     8       6.148  -5.338  -8.066  1.00  0.00           C  
+ATOM     96  HE2 LYS     8       6.521  -6.290  -8.444  1.00  0.00           H  
+ATOM     97  HE3 LYS     8       6.848  -5.025  -7.290  1.00  0.00           H  
+ATOM     98  NZ  LYS     8       6.177  -4.420  -9.214  1.00  0.00           N  
+ATOM     99  HZ1 LYS     8       6.046  -3.547  -8.722  1.00  0.00           H  
+ATOM    100  HZ2 LYS     8       7.131  -4.392  -9.546  1.00  0.00           H  
+ATOM    101  HZ3 LYS     8       5.471  -4.550  -9.925  1.00  0.00           H  
+ATOM    102  C   LYS     8       3.512  -4.519  -3.286  1.00  0.00           C  
+ATOM    103  O   LYS     8       4.624  -5.042  -3.286  1.00  0.00           O  
+ATOM    104  N   ALA     9       2.925  -4.256  -2.116  1.00  0.00           N  
+ATOM    105  H   ALA     9       2.010  -3.879  -2.316  1.00  0.00           H  
+ATOM    106  CA  ALA     9       3.341  -4.262  -0.728  1.00  0.00           C  
+ATOM    107  HA  ALA     9       4.410  -4.045  -0.724  1.00  0.00           H  
+ATOM    108  CB  ALA     9       2.625  -3.068  -0.104  1.00  0.00           C  
+ATOM    109  HB2 ALA     9       1.589  -3.294   0.148  1.00  0.00           H  
+ATOM    110  HB3 ALA     9       2.835  -2.194  -0.721  1.00  0.00           H  
+ATOM    111  C   ALA     9       2.945  -5.593  -0.105  1.00  0.00           C  
+ATOM    112  O   ALA     9       3.022  -6.675  -0.682  1.00  0.00           O  
+ATOM    113  N   THR    10       2.531  -5.609   1.164  1.00  0.00           N  
+ATOM    114  H   THR    10       2.711  -4.794   1.731  1.00  0.00           H  
+ATOM    115  CA  THR    10       2.254  -6.874   1.815  1.00  0.00           C  
+ATOM    116  HA  THR    10       2.982  -7.667   1.644  1.00  0.00           H  
+ATOM    117  CB  THR    10       2.207  -6.622   3.320  1.00  0.00           C  
+ATOM    118  HB  THR    10       1.722  -5.667   3.526  1.00  0.00           H  
+ATOM    119  CG2 THR    10       1.456  -7.659   4.149  1.00  0.00           C  
+ATOM    120 HG21 THR    10       1.581  -7.464   5.214  1.00  0.00           H  
+ATOM    121 HG22 THR    10       0.402  -7.468   3.946  1.00  0.00           H  
+ATOM    122 HG23 THR    10       1.725  -8.640   3.755  1.00  0.00           H  
+ATOM    123  OG1 THR    10       3.460  -6.501   3.954  1.00  0.00           O  
+ATOM    124  HG1 THR    10       3.385  -6.097   4.822  1.00  0.00           H  
+ATOM    125  C   THR    10       0.889  -7.354   1.344  1.00  0.00           C  
+ATOM    126  O   THR    10      -0.172  -6.760   1.524  1.00  0.00           O  
+ATOM    127  N   ALA    11       0.906  -8.522   0.699  1.00  0.00           N  
+ATOM    128  H   ALA    11       1.723  -9.115   0.734  1.00  0.00           H  
+ATOM    129  CA  ALA    11      -0.188  -9.066  -0.080  1.00  0.00           C  
+ATOM    130  HA  ALA    11      -0.737  -8.220  -0.495  1.00  0.00           H  
+ATOM    131  CB  ALA    11       0.412 -10.010  -1.117  1.00  0.00           C  
+ATOM    132  HB2 ALA    11       1.113 -10.710  -0.661  1.00  0.00           H  
+ATOM    133  HB3 ALA    11       0.887  -9.368  -1.859  1.00  0.00           H  
+ATOM    134  C   ALA    11      -1.079  -9.752   0.946  1.00  0.00           C  
+ATOM    135  O   ALA    11      -0.710 -10.673   1.672  1.00  0.00           O  
+ATOM    136  N   LYS    12      -2.344  -9.326   0.949  1.00  0.00           N  
+ATOM    137  H   LYS    12      -2.456  -8.339   0.770  1.00  0.00           H  
+ATOM    138  CA  LYS    12      -3.470  -9.926   1.636  1.00  0.00           C  
+ATOM    139  HA  LYS    12      -3.097 -10.439   2.522  1.00  0.00           H  
+ATOM    140  CB  LYS    12      -4.384  -8.814   2.142  1.00  0.00           C  
+ATOM    141  HB2 LYS    12      -5.389  -9.112   2.440  1.00  0.00           H  
+ATOM    142  HB3 LYS    12      -4.439  -8.009   1.409  1.00  0.00           H  
+ATOM    143  CG  LYS    12      -3.799  -8.092   3.352  1.00  0.00           C  
+ATOM    144  HG2 LYS    12      -2.889  -7.566   3.064  1.00  0.00           H  
+ATOM    145  HG3 LYS    12      -3.691  -8.724   4.233  1.00  0.00           H  
+ATOM    146  CD  LYS    12      -4.848  -7.024   3.650  1.00  0.00           C  
+ATOM    147  HD2 LYS    12      -5.691  -7.411   4.222  1.00  0.00           H  
+ATOM    148  HD3 LYS    12      -5.130  -6.495   2.740  1.00  0.00           H  
+ATOM    149  CE  LYS    12      -4.108  -6.019   4.529  1.00  0.00           C  
+ATOM    150  HE2 LYS    12      -3.183  -5.635   4.099  1.00  0.00           H  
+ATOM    151  HE3 LYS    12      -3.885  -6.553   5.452  1.00  0.00           H  
+ATOM    152  NZ  LYS    12      -4.877  -4.802   4.829  1.00  0.00           N  
+ATOM    153  HZ1 LYS    12      -5.132  -4.305   3.987  1.00  0.00           H  
+ATOM    154  HZ2 LYS    12      -5.718  -4.968   5.362  1.00  0.00           H  
+ATOM    155  HZ3 LYS    12      -4.250  -4.263   5.410  1.00  0.00           H  
+ATOM    156  C   LYS    12      -4.395 -10.778   0.779  1.00  0.00           C  
+ATOM    157  O   LYS    12      -4.483 -11.939   1.172  1.00  0.00           O  
+ATOM    158  N   NME    13      -4.832 -10.202  -0.344  1.00  0.00           N  
+ATOM    159  H   NME    13      -4.647  -9.239  -0.587  1.00  0.00           H  
+ATOM    160  CH3 NME    13      -5.720 -10.866  -1.277  1.00  0.00           C  
+ATOM    161 HH31 NME    13      -5.591 -11.946  -1.340  1.00  0.00           H  
+ATOM    162 HH32 NME    13      -6.757 -10.886  -0.942  1.00  0.00           H  
+ATOM    163 HH33 NME    13      -5.777 -10.358  -2.240  1.00  0.00           H  
+TER     164      NME    13 
+END   
diff --git a/test/Test_Mutate/RunTest.sh b/test/Test_Mutate/RunTest.sh
new file mode 100755
index 0000000000..a930bb7c8d
--- /dev/null
+++ b/test/Test_Mutate/RunTest.sh
@@ -0,0 +1,37 @@
+#!/bin/bash
+
+. ../MasterTest.sh
+
+CleanFiles mutate.in Mutated.pdb Out.pdb Built.mol2
+
+TESTNAME='Mutate tests'
+Requires amberhome
+
+INPUT='-i mutate.in'
+
+cat > mutate.in <<EOF
+source leaprc.protein.ff14SB
+parm ../tz2.parm7
+loadcrd ../tz2.nc name MyCrd 1 1
+
+mutate crdset MyCrd resmask :TRP to ALA
+crdout MyCrd Mutated.pdb
+quit
+EOF
+RunCpptraj "Mutate test, in-place coords"
+DoTest Mutated.pdb.save Mutated.pdb
+
+cat > mutate.in <<EOF
+source leaprc.protein.ff14SB
+parm ../tz2.parm7
+loadcrd ../tz2.nc name MyCrd 1 1
+
+mutate crdset MyCrd resmask :TRP to ALA outset Out
+crdout Out Out.pdb
+build crdset Out name Built crdout Built.mol2 noh
+quit
+EOF
+RunCpptraj "Mutate test, new coords"
+DoTest Mutated.pdb.save Out.pdb
+
+EndTest

From ecdc70aa735bd694a4c195661cc308d3bf2a9e88 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 7 Nov 2025 10:44:54 -0500
Subject: [PATCH 1060/1492] Add check of built coords

---
 test/Test_Mutate/RunTest.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/test/Test_Mutate/RunTest.sh b/test/Test_Mutate/RunTest.sh
index a930bb7c8d..04d447a227 100755
--- a/test/Test_Mutate/RunTest.sh
+++ b/test/Test_Mutate/RunTest.sh
@@ -33,5 +33,6 @@ quit
 EOF
 RunCpptraj "Mutate test, new coords"
 DoTest Mutated.pdb.save Out.pdb
+DoTest Built.mol2.save Built.mol2
 
 EndTest

From f370bb3d5a2082afc7894c541f0e411db9ee015f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 7 Nov 2025 14:38:30 -0500
Subject: [PATCH 1061/1492] Write help for desc. Allow desc to use coords sets.

---
 src/Exec_Desc.cpp | 20 ++++++++++++++++++--
 1 file changed, 18 insertions(+), 2 deletions(-)

diff --git a/src/Exec_Desc.cpp b/src/Exec_Desc.cpp
index 433f0306e8..56aa0dd763 100644
--- a/src/Exec_Desc.cpp
+++ b/src/Exec_Desc.cpp
@@ -33,16 +33,32 @@ int Exec_Desc::desc_atom(Topology const& topIn, int iat) {
 // Exec_Desc::Help()
 void Exec_Desc::Help() const
 {
-
+  mprintf("\t{%s | <COORDS set>} [<mask>]\n"
+          "  Print selected atoms from topology/COORDS set in LEaP style format.\n",
+          DataSetList::TopIdxArgs);
 }
 
 // Exec_Desc::Execute()
 Exec::RetType Exec_Desc::Execute(CpptrajState& State, ArgList& argIn)
 {
+  ArgList originalArgs = argIn;
   // Get Topology
   Topology* parm = State.DSL().GetTopByIndex( argIn );
   if (parm == 0) {
-    mprinterr("Error: No topologies loaded.\n");
+    // See if a COORDS set was specified
+    DataSetList sets = State.DSL().SelectGroupSets( originalArgs.GetStringNext(), DataSet::COORDINATES );
+    DataSet_Coords* ds = 0;
+    if (sets.size() > 0) {
+      ds = (DataSet_Coords*)sets[0];
+      if (sets.size() > 1)
+        mprintf("Warning: Multiple sets selected, only using %s\n", ds->legend());
+    }
+    if (ds != 0)
+      parm = ds->TopPtr();
+    argIn = originalArgs;
+  }
+  if (parm == 0) {
+    mprinterr("Error: No topologies loaded/COORDS sets found.\n");
     return CpptrajState::ERR;
   }
   mprintf("\tUsing topology: %s\n", parm->c_str());

From f9a56710ef505cb37e07d7771a62a04995a88fd5 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 11 Nov 2025 10:56:03 -0500
Subject: [PATCH 1062/1492] Print the reverse map

---
 src/Exec_Build.cpp | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index bbad0a5154..ea4d0f3df2 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -268,7 +268,16 @@ const
         if (map[iref] != -1)
           pdb[map[iref]-currentRes.FirstAtom()] = iref;
       }
+      mprintf("\t  PDB atom map:\n");
+      for (int itgt = 0; itgt != currentRes.NumAtoms(); itgt++) {
+        mprintf("\t\t%6i %6s =>", itgt+1, *(topIn[itgt+currentRes.FirstAtom()].Name()));
+        if (pdb[itgt] == -1)
+          mprintf(" Not in template\n");
+        else
+          mprintf(" %6i %6s\n", pdb[itgt]+1, *(resTemplate->Top()[pdb[itgt]].Name()));
+      }
       bool atomsNeedBuilding = false;
+      // Loop over template atoms
       for (int iref = 0; iref != resTemplate->Top().Natom(); iref++) {
         // Track intra-residue bonds from the template.
         Atom templateAtom = resTemplate->Top()[iref];
@@ -316,7 +325,7 @@ const
             }
           }
         }
-      }
+      } // END loop over template atoms
       if (nTgtAtomsMissing > 0)
         mprintf("\t%i source atoms not mapped to template.\n", nTgtAtomsMissing);
       // Save atom offset if atoms need to be built

From a3e6c550eb3a12cd2dac06b874f4de74218b6819 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 11 Nov 2025 16:03:09 -0500
Subject: [PATCH 1063/1492] Add non-template atoms. Still need to fix bonds

---
 src/Exec_Build.cpp        | 59 +++++++++++++++++++++++++++++++++++++--
 src/Exec_Build.h          |  1 +
 src/Structure/Creator.cpp | 48 +++++++++++++++++++++++++++++++
 src/Structure/Creator.h   |  2 ++
 4 files changed, 107 insertions(+), 3 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index ea4d0f3df2..1d54ae361e 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -22,6 +22,7 @@ Exec_Build::Exec_Build() :
   debug_(0),
   check_box_natom_(5000), // TODO make user specifiable
   check_structure_(true),
+  keepMissingSourceAtoms_(false),
   sugarBuilder_(0),
   outCrdPtr_(0)
 {}
@@ -118,6 +119,9 @@ const
       if (debug_ > 0)
         mprintf("\tTemplate %s being used for residue %s\n",
                 resTemplate->legend(), topIn.TruncResNameOnumId(ires).c_str());
+      int nTgtAtomsMissing = 0;
+      if (keepMissingSourceAtoms_)
+        nTgtAtomsMissing = creator.CountAtomsMissingFromTemplate( topIn, ires, resTemplate );
       // Save the head and tail atoms
       AssociatedData* ad = resTemplate->GetAssociatedData(AssociatedData::CONNECT);
       if (ad == 0) {
@@ -141,7 +145,7 @@ const
           resTailAtoms.push_back( -1 );
       }
       // Update # of atoms
-      newNatom += resTemplate->Top().Natom();
+      newNatom += resTemplate->Top().Natom() + nTgtAtomsMissing;
     }
     ResTemplates.push_back( resTemplate );
   }
@@ -326,8 +330,51 @@ const
           }
         }
       } // END loop over template atoms
-      if (nTgtAtomsMissing > 0)
+      if (nTgtAtomsMissing > 0) {
         mprintf("\t%i source atoms not mapped to template.\n", nTgtAtomsMissing);
+        if (keepMissingSourceAtoms_) {
+          ResAtArray tmpBonds;
+          for (int itgt = 0; itgt != currentRes.NumAtoms(); itgt++) {
+            if (pdb[itgt] == -1) {
+              // This PDB atom had no equivalent in the residue template
+              int pdbat = itgt + currentRes.FirstAtom();
+              Atom pdbAtom = topIn[pdbat];
+              mprintf("\t\tInput atom %s missing from template.\n",*(pdbAtom.Name()));
+              // Bonds
+              for (Atom::bond_iterator bit = pdbAtom.bondbegin(); bit != pdbAtom.bondend(); ++bit)
+              {
+                Atom bndAt = topIn[*bit];
+                mprintf("\t\t\tBonded to %s\n", *(bndAt.Name()));
+                tmpBonds.push_back( ResAtPair(ires, pdbAtom.Name()) );
+                tmpBonds.push_back( ResAtPair(bndAt.ResNum(), bndAt.Name()) );
+              }
+              // Add missing atom
+              pdbAtom.ClearBonds();
+              topOut.AddTopAtom( pdbAtom, currentRes );
+              frameOut.AddVec3( Vec3(frameIn.XYZ(pdbat)) );
+              hasPosition.push_back( true );
+              if (has_bfac)
+                topOut.AddBfactor( topIn.Bfactor()[pdbat] );
+              if (has_occ)
+                topOut.AddOccupancy( topIn.Occupancy()[pdbat] );
+              if (has_pdbn)
+                topOut.AddPdbSerialNum( topIn.PdbSerialNum()[pdbat] );
+              
+            }
+          } // END loop over input residue atoms
+          // Add Bonds
+          for (ResAtArray::const_iterator bit = tmpBonds.begin(); bit != tmpBonds.end(); ++bit)
+          {
+            int ba0 = topOut.FindAtomInResidue( bit->first, bit->second );
+            ++bit;
+            int ba1 = topOut.FindAtomInResidue( bit->first, bit->second );
+            if (ba0 < ba1) {
+              mprintf("\t\tAdd bond %i %s -- %i %s\n", ba0+1, *(topOut[ba0].Name()), ba1+1, *(topOut[ba1].Name()));
+              topOut.AddBond( ba0, ba1 );
+            }
+          } // END loop over bonds
+        }
+      }
       // Save atom offset if atoms need to be built
       if (atomsNeedBuilding)
         AtomOffsets.push_back( atomOffset );
@@ -717,7 +764,7 @@ const
 void Exec_Build::Help() const
 {
   mprintf("\tname <output COORDS> crdset <COORDS set> [frame <#>]\n"
-          "\t[title <title>] [gb <radii>] [verbose <#>]\n"
+          "\t[title <title>] [gb <radii>] [verbose <#>] [keepmissingatoms]\n"
           "\t[parmout <topology file>] [crdout <coord file>]\n"
           "\t[%s]\n"
           "\t[{%s} ...]\n"
@@ -807,6 +854,12 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
   std::string solventResName = argIn.GetStringKey("solventresname", "HOH");
   mprintf("\tSolvent residue name: %s\n", solventResName.c_str());
 
+  keepMissingSourceAtoms_ = argIn.hasKey("keepmissingatoms");
+  if (keepMissingSourceAtoms_)
+    mprintf("\tInput atoms missing from templates will be kept.\n");
+  else
+    mprintf("\tInput atoms missing from templates will be ignored.\n");
+
   // Do histidine detection before H atoms are removed
   t_hisDetect_.Start();
   if (!argIn.hasKey("nohisdetect")) {
diff --git a/src/Exec_Build.h b/src/Exec_Build.h
index 8dcc85f8a6..f5a9162252 100644
--- a/src/Exec_Build.h
+++ b/src/Exec_Build.h
@@ -46,6 +46,7 @@ class Exec_Build : public Exec {
     int debug_;
     int check_box_natom_;  ///< Systems larger than this will have box added so PL check can be used
     bool check_structure_; ///< If true check the resulting structure
+    bool keepMissingSourceAtoms_;
     Cpptraj::Structure::SugarBuilder* sugarBuilder_;
     DataSet* outCrdPtr_; ///< Hold built COORDS
 
diff --git a/src/Structure/Creator.cpp b/src/Structure/Creator.cpp
index 50e05fe284..12b657e333 100644
--- a/src/Structure/Creator.cpp
+++ b/src/Structure/Creator.cpp
@@ -380,6 +380,54 @@ const
   return false;
 }
 
+/** Count missing atoms from template */
+int Creator::CountAtomsMissingFromTemplate(Topology const& topIn,
+                                           int rnum,
+                                           DataSet_Coords* resTemplate)
+const
+{
+  int nTgtAtomsMissing = 0;
+  Residue const& resIn = topIn.Res(rnum);
+  // For each atom in topIn, find a template atom
+  for (int itgt = resIn.FirstAtom(); itgt != resIn.LastAtom(); itgt++)
+  {
+    NameType const& tgtName = topIn[itgt].Name();
+    //mprintf("DEBUG: Search for atom %s\n", *tgtName);
+    bool found = false;
+    // Check if this atom has an alias.
+    NameType alias;
+    bool has_alias = GetAlias( alias, tgtName );
+//    if (creator.GetAlias( alias, tgtName )) {
+//      mprintf("DEBUG: Atom %s alias is %s\n", *tgtName, *alias);
+//    }
+    // See if tgtName matches a reference (template) atom name.
+    for (int iref = 0; iref != resTemplate->Top().Natom(); iref++)
+    {
+      NameType const& refName = resTemplate->Top()[iref].Name();
+      if (refName == tgtName) {
+        found = true;
+        break;
+      }
+    }
+    if (!found && has_alias) {
+      // See if alias matches a reference (template) atom name.
+      for (int iref = 0; iref != resTemplate->Top().Natom(); iref++) {
+        NameType const& refName = resTemplate->Top()[iref].Name();
+        if (refName == alias) {
+          found = true;
+          break;
+        }
+      } // END search template for alias
+    } // END do alias search
+    if (!found) {
+      //mprintf("Warning: Input atom %s was not mapped to a template atom.\n",
+      //        topIn.TruncAtomResNameOnumId( itgt ).c_str());
+      nTgtAtomsMissing++;
+    }
+  }
+  return nTgtAtomsMissing;
+}
+
 /** Map atoms in residue to template. */
 std::vector<int> Creator::MapAtomsToTemplate(Topology const& topIn,
                                                 int rnum,
diff --git a/src/Structure/Creator.h b/src/Structure/Creator.h
index 0c83b658d1..d6ddc7a388 100644
--- a/src/Structure/Creator.h
+++ b/src/Structure/Creator.h
@@ -51,6 +51,8 @@ class Creator {
     DataSet_Coords* IdTemplateFromResname(NameType const&, TerminalType) const;
     /// Get name map if its present
     bool GetAlias(NameType&, NameType const&) const;
+    /// Count atoms missing from template
+    int CountAtomsMissingFromTemplate(Topology const&, int, DataSet_Coords*) const;
     /// Create an atom map of source atom names to template names
     std::vector<int> MapAtomsToTemplate(Topology const&, int, DataSet_Coords*,
                                         std::vector<NameType>&, int&) const;

From 4a0c5d111d9e70b1821562cb97caf84beae9cf10 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 12 Nov 2025 09:37:35 -0500
Subject: [PATCH 1064/1492] Fix bonds from non-template to template

---
 src/Exec_Build.cpp | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 1d54ae361e..f3c16f8a18 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -334,6 +334,7 @@ const
         mprintf("\t%i source atoms not mapped to template.\n", nTgtAtomsMissing);
         if (keepMissingSourceAtoms_) {
           ResAtArray tmpBonds;
+          int firstNonTemplateAtom = topOut.Natom();
           for (int itgt = 0; itgt != currentRes.NumAtoms(); itgt++) {
             if (pdb[itgt] == -1) {
               // This PDB atom had no equivalent in the residue template
@@ -344,7 +345,12 @@ const
               for (Atom::bond_iterator bit = pdbAtom.bondbegin(); bit != pdbAtom.bondend(); ++bit)
               {
                 Atom bndAt = topIn[*bit];
-                mprintf("\t\t\tBonded to %s\n", *(bndAt.Name()));
+                NameType bndAtmName;
+                if (SourceAtomNames[*bit].len() > 0)
+                  bndAtmName = SourceAtomNames[*bit];
+                else
+                  bndAtmName = bndAt.Name();
+                mprintf("\t\t\tBonded to %s\n", *(bndAtmName));
                 tmpBonds.push_back( ResAtPair(ires, pdbAtom.Name()) );
                 tmpBonds.push_back( ResAtPair(bndAt.ResNum(), bndAt.Name()) );
               }
@@ -368,7 +374,10 @@ const
             int ba0 = topOut.FindAtomInResidue( bit->first, bit->second );
             ++bit;
             int ba1 = topOut.FindAtomInResidue( bit->first, bit->second );
-            if (ba0 < ba1) {
+            if (ba0 < firstNonTemplateAtom ||
+                ba1 < firstNonTemplateAtom ||
+                ba0 < ba1)
+            {
               mprintf("\t\tAdd bond %i %s -- %i %s\n", ba0+1, *(topOut[ba0].Name()), ba1+1, *(topOut[ba1].Name()));
               topOut.AddBond( ba0, ba1 );
             }

From 5608e6803ddfb2b1f3c930dc665b8555f4471c67 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 12 Nov 2025 10:14:35 -0500
Subject: [PATCH 1065/1492] Hide some debug info

---
 src/Exec_Build.cpp | 22 +++++++++++++---------
 1 file changed, 13 insertions(+), 9 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index f3c16f8a18..1941d91914 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -272,13 +272,15 @@ const
         if (map[iref] != -1)
           pdb[map[iref]-currentRes.FirstAtom()] = iref;
       }
-      mprintf("\t  PDB atom map:\n");
-      for (int itgt = 0; itgt != currentRes.NumAtoms(); itgt++) {
-        mprintf("\t\t%6i %6s =>", itgt+1, *(topIn[itgt+currentRes.FirstAtom()].Name()));
-        if (pdb[itgt] == -1)
-          mprintf(" Not in template\n");
-        else
-          mprintf(" %6i %6s\n", pdb[itgt]+1, *(resTemplate->Top()[pdb[itgt]].Name()));
+      if (debug_ > 1) {
+        mprintf("\t  PDB atom map:\n");
+        for (int itgt = 0; itgt != currentRes.NumAtoms(); itgt++) {
+          mprintf("\t\t%6i %6s =>", itgt+1, *(topIn[itgt+currentRes.FirstAtom()].Name()));
+          if (pdb[itgt] == -1)
+            mprintf(" Not in template\n");
+          else
+            mprintf(" %6i %6s\n", pdb[itgt]+1, *(resTemplate->Top()[pdb[itgt]].Name()));
+        }
       }
       bool atomsNeedBuilding = false;
       // Loop over template atoms
@@ -393,9 +395,11 @@ const
     // Add intra-residue bonds
     for (IParray::const_iterator it = intraResBonds.begin(); it != intraResBonds.end(); ++it)
     {
-      //mprintf("DEBUG: Intra-res bond: Res %s atom %s to res %s atom %s\n",
+      //mprintf("DEBUG: Intra-res bond: Res %s atom %s (%s) to res %s atom %s (%s)\n",
       //        topOut.TruncResNameOnumId(topOut[it->first].ResNum()).c_str(), *(topOut[it->first].Name()),
-      //        topOut.TruncResNameOnumId(topOut[it->second].ResNum()).c_str(), *(topOut[it->second].Name()));
+      //        topOut.AtomMaskName(it->first).c_str(),
+      //        topOut.TruncResNameOnumId(topOut[it->second].ResNum()).c_str(), *(topOut[it->second].Name()),
+      //        topOut.AtomMaskName(it->second).c_str());
       topOut.AddBond(it->first, it->second);
     }
   } // END loop over source residues

From cf8f24d3a74bbea4ec66db981c8b3c59610dd2cd Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 12 Nov 2025 10:19:01 -0500
Subject: [PATCH 1066/1492] Hide some debug info

---
 src/Exec_Build.cpp | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 1941d91914..4d9741ca9a 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -342,7 +342,8 @@ const
               // This PDB atom had no equivalent in the residue template
               int pdbat = itgt + currentRes.FirstAtom();
               Atom pdbAtom = topIn[pdbat];
-              mprintf("\t\tInput atom %s missing from template.\n",*(pdbAtom.Name()));
+              if (debug_ > 0)
+                mprintf("DEBUG:\t\tInput atom %s missing from template.\n",*(pdbAtom.Name()));
               // Bonds
               for (Atom::bond_iterator bit = pdbAtom.bondbegin(); bit != pdbAtom.bondend(); ++bit)
               {
@@ -352,7 +353,8 @@ const
                   bndAtmName = SourceAtomNames[*bit];
                 else
                   bndAtmName = bndAt.Name();
-                mprintf("\t\t\tBonded to %s\n", *(bndAtmName));
+                if (debug_ > 0)
+                  mprintf("DEBUG:\t\t\tBonded to %s\n", *(bndAtmName));
                 tmpBonds.push_back( ResAtPair(ires, pdbAtom.Name()) );
                 tmpBonds.push_back( ResAtPair(bndAt.ResNum(), bndAt.Name()) );
               }
@@ -380,7 +382,8 @@ const
                 ba1 < firstNonTemplateAtom ||
                 ba0 < ba1)
             {
-              mprintf("\t\tAdd bond %i %s -- %i %s\n", ba0+1, *(topOut[ba0].Name()), ba1+1, *(topOut[ba1].Name()));
+              if (debug_ > 0)
+                mprintf("DEBUG:\t\tAdd bond %i %s -- %i %s\n", ba0+1, *(topOut[ba0].Name()), ba1+1, *(topOut[ba1].Name()));
               topOut.AddBond( ba0, ba1 );
             }
           } // END loop over bonds

From eb95a1ea80540050ea2d37ab1f2408f151395b99 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 12 Nov 2025 10:55:20 -0500
Subject: [PATCH 1067/1492] Add option to throw an error if source atoms not
 present in templates

---
 src/Exec_Build.cpp | 17 ++++++++++++++++-
 src/Exec_Build.h   |  1 +
 2 files changed, 17 insertions(+), 1 deletion(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 4d9741ca9a..99cc0c4fc1 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -23,6 +23,7 @@ Exec_Build::Exec_Build() :
   check_box_natom_(5000), // TODO make user specifiable
   check_structure_(true),
   keepMissingSourceAtoms_(false),
+  requireAllInputAtoms_(false),
   sugarBuilder_(0),
   outCrdPtr_(0)
 {}
@@ -186,6 +187,7 @@ const
   SourceAtomNames.resize( topIn.Natom() );
 
   // Loop for setting up atoms in the topology from residues or residue templates.
+  int nAtomsNotInTemplates = 0;
   int nRefAtomsMissing = 0;
   int nAtomsMissingTypes = 0;
   bool has_bfac = !topIn.Bfactor().empty();
@@ -333,6 +335,7 @@ const
         }
       } // END loop over template atoms
       if (nTgtAtomsMissing > 0) {
+        nAtomsNotInTemplates += nTgtAtomsMissing;
         mprintf("\t%i source atoms not mapped to template.\n", nTgtAtomsMissing);
         if (keepMissingSourceAtoms_) {
           ResAtArray tmpBonds;
@@ -406,7 +409,14 @@ const
       topOut.AddBond(it->first, it->second);
     }
   } // END loop over source residues
-  mprintf("\t%i template atoms missing in source.\n", nRefAtomsMissing);
+  if (nRefAtomsMissing > 0)
+    mprintf("\t%i template atoms missing in source.\n", nRefAtomsMissing);
+  if (nAtomsNotInTemplates > 0) {
+    if (requireAllInputAtoms_)
+      mprinterr("Error: %i input atoms not in templates.\n", nAtomsNotInTemplates);
+    else
+      mprintf("\t%i input atoms were not in templates and were ignored.\n", nAtomsNotInTemplates);
+  }
   if (nAtomsMissingTypes > 0) {
     mprinterr("Error: %i atoms are missing types, either because they did not have\n"
               "Error:  one initially or they could not be matched to a template.\n"
@@ -875,6 +885,11 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
     mprintf("\tInput atoms missing from templates will be kept.\n");
   else
     mprintf("\tInput atoms missing from templates will be ignored.\n");
+  requireAllInputAtoms_ = argIn.hasKey("requireallinputatoms");
+  if (requireAllInputAtoms_)
+    mprintf("\tRequire all input atoms to be found in templates.\n");
+  else
+    mprintf("\tInput atoms not found in templates will be ignored.\n");
 
   // Do histidine detection before H atoms are removed
   t_hisDetect_.Start();
diff --git a/src/Exec_Build.h b/src/Exec_Build.h
index f5a9162252..62b1d73626 100644
--- a/src/Exec_Build.h
+++ b/src/Exec_Build.h
@@ -47,6 +47,7 @@ class Exec_Build : public Exec {
     int check_box_natom_;  ///< Systems larger than this will have box added so PL check can be used
     bool check_structure_; ///< If true check the resulting structure
     bool keepMissingSourceAtoms_;
+    bool requireAllInputAtoms_;
     Cpptraj::Structure::SugarBuilder* sugarBuilder_;
     DataSet* outCrdPtr_; ///< Hold built COORDS
 

From 0bcefd4b34c75f31508a64c0c26365a834d309b9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 17 Nov 2025 09:27:47 -0500
Subject: [PATCH 1068/1492] Better debug messages for how residues are assigned
 a terminal status

---
 src/Exec_Build.cpp | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 99cc0c4fc1..01a83ff732 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -80,12 +80,14 @@ const
     // Determine if this is a terminal residue
     Cpptraj::Structure::TerminalType resTermType;
     if (currentRes.IsTerminal()) {
-      //mprintf("DEBUG: End terminal due to TERMINAL status.\n");
+      mprintf("DEBUG: %s End terminal due to TERMINAL status.\n", topIn.TruncResNameNum(ires).c_str());
       resTermType = Cpptraj::Structure::END_TERMINAL;
     } else if (ires == 0 && topIn.Nres() > 1) {
       resTermType = Cpptraj::Structure::BEG_TERMINAL;
+      mprintf("DEBUG: %s Begin terminal due to first residue.\n", topIn.TruncResNameNum(ires).c_str());
     } else if (pres > -1 && topIn.Res(pres).IsTerminal()) {
       resTermType = Cpptraj::Structure::BEG_TERMINAL;
+      mprintf("DEBUG: %s Begin terminal due to previous residue TERMINAL status.\n", topIn.TruncResNameNum(ires).c_str());
     } else if (nres < topIn.Nres() && (topIn.Res(nres).ChainID() != currentRes.ChainID())// ||
 //                                        (topIn.Res(nres).OriginalResNum() == currentRes.OriginalResNum() &&
 //                                         topIn.Res(nres).Icode()          != currentRes.Icode()
@@ -93,11 +95,11 @@ const
 //                                      )
               )
     {
-      //mprintf("DEBUG: End terminal due to chain ID.\n");
       resTermType = Cpptraj::Structure::END_TERMINAL;
+      mprintf("DEBUG: %s End terminal due to chain ID.\n", topIn.TruncResNameNum(ires).c_str());
     } else if (nres == topIn.Nres()) {
-      //mprintf("DEBUG: End terminal due to last residue.\n");
       resTermType = Cpptraj::Structure::END_TERMINAL;
+      mprintf("DEBUG: %s End terminal due to last residue.\n", topIn.TruncResNameNum(ires).c_str());
     } else {
       resTermType = Cpptraj::Structure::NON_TERMINAL;
     }

From 7acf0b52d5b6273c15e92382ac9df65ed569167c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 18 Nov 2025 08:21:42 -0500
Subject: [PATCH 1069/1492] Start solvate class

---
 src/Structure/Solvate.cpp |  9 +++++++++
 src/Structure/Solvate.h   | 14 ++++++++++++++
 2 files changed, 23 insertions(+)
 create mode 100644 src/Structure/Solvate.cpp
 create mode 100644 src/Structure/Solvate.h

diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
new file mode 100644
index 0000000000..faa2046ae1
--- /dev/null
+++ b/src/Structure/Solvate.cpp
@@ -0,0 +1,9 @@
+#include "Solvate.h"
+
+using namespace Cpptraj::Structure;
+
+/** CONSTRUCTOR */
+Solvate::Solvate()
+{
+}
+
diff --git a/src/Structure/Solvate.h b/src/Structure/Solvate.h
new file mode 100644
index 0000000000..4d9f086161
--- /dev/null
+++ b/src/Structure/Solvate.h
@@ -0,0 +1,14 @@
+#ifndef INC_SOLVATE_H
+#define INC_SOLVATE_H
+namespace Cpptraj {
+namespace Structure {
+/// Used to add solvent to a COORDS set.
+class Solvate {
+  public:
+    /// CONSTRUCTOR
+    Solvate();
+  private:
+};
+}
+}
+#endif

From 78944e947f72b0fe559af5b4a097f7e259025443 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 18 Nov 2025 08:21:48 -0500
Subject: [PATCH 1070/1492] Add Solvate class to build

---
 src/Structure/CMakeLists.txt  | 3 ++-
 src/Structure/Makefile        | 5 +++++
 src/Structure/structuredepend | 1 +
 src/Structure/structurefiles  | 3 ++-
 src/cpptrajdepend             | 1 +
 5 files changed, 11 insertions(+), 2 deletions(-)

diff --git a/src/Structure/CMakeLists.txt b/src/Structure/CMakeLists.txt
index 7a5f4dafd9..74ad593545 100644
--- a/src/Structure/CMakeLists.txt
+++ b/src/Structure/CMakeLists.txt
@@ -13,10 +13,11 @@ target_sources(cpptraj_common_obj PRIVATE
   ${CMAKE_CURRENT_LIST_DIR}/MetalCenterFinder.cpp
   ${CMAKE_CURRENT_LIST_DIR}/PdbCleaner.cpp
   ${CMAKE_CURRENT_LIST_DIR}/RingFinder.cpp
+  ${CMAKE_CURRENT_LIST_DIR}/Solvate.cpp
   ${CMAKE_CURRENT_LIST_DIR}/StructureEnum.cpp
   ${CMAKE_CURRENT_LIST_DIR}/StructureRoutines.cpp
-  ${CMAKE_CURRENT_LIST_DIR}/Sugar.cpp
   ${CMAKE_CURRENT_LIST_DIR}/SugarBuilder.cpp
+  ${CMAKE_CURRENT_LIST_DIR}/Sugar.cpp
   ${CMAKE_CURRENT_LIST_DIR}/SugarLinkAtoms.cpp
   ${CMAKE_CURRENT_LIST_DIR}/SugarToken.cpp
   ${CMAKE_CURRENT_LIST_DIR}/Zmatrix.cpp
diff --git a/src/Structure/Makefile b/src/Structure/Makefile
index 5e676cc6a6..402e793eec 100644
--- a/src/Structure/Makefile
+++ b/src/Structure/Makefile
@@ -8,6 +8,11 @@ DEL_FILE = /bin/rm -f
 # Objects
 OBJECTS=$(STRUCTURE_SOURCES:.cpp=.o)
 
+# General rules
+.cpp.o:
+	$(VB)echo CXX $<
+	$(VB)$(CXX) $(DIRECTIVES) $(CPPTRAJ_INC) $(CXXFLAGS) -c -o $@ $<
+
 # Default target: objects
 all: $(OBJECTS)
 
diff --git a/src/Structure/structuredepend b/src/Structure/structuredepend
index 2867c7dbb9..c3928a54da 100644
--- a/src/Structure/structuredepend
+++ b/src/Structure/structuredepend
@@ -11,6 +11,7 @@ LeastSquaresPlane.o : LeastSquaresPlane.cpp ../Atom.h ../AtomMask.h ../Box.h ../
 MetalCenterFinder.o : MetalCenterFinder.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h MetalCenterFinder.h
 PdbCleaner.o : PdbCleaner.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h PdbCleaner.h
 RingFinder.o : RingFinder.cpp ../Atom.h ../AtomMask.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h RingFinder.h
+Solvate.o : Solvate.cpp Solvate.h
 StructureEnum.o : StructureEnum.cpp StructureEnum.h
 StructureRoutines.o : StructureRoutines.cpp ../Atom.h ../CpptrajStdio.h ../NameType.h ../Residue.h ../SymbolExporting.h StructureRoutines.h
 Sugar.o : Sugar.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h Sugar.h SugarToken.h
diff --git a/src/Structure/structurefiles b/src/Structure/structurefiles
index f631cff049..bba6cf75af 100644
--- a/src/Structure/structurefiles
+++ b/src/Structure/structurefiles
@@ -13,10 +13,11 @@ STRUCTURE_SOURCES= \
   MetalCenterFinder.cpp \
   PdbCleaner.cpp \
   RingFinder.cpp \
+  Solvate.cpp \
   StructureEnum.cpp \
   StructureRoutines.cpp \
-  Sugar.cpp \
   SugarBuilder.cpp \
+  Sugar.cpp \
   SugarLinkAtoms.cpp \
   SugarToken.cpp \
   Zmatrix.cpp
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 4bd6183dea..e3704fd344 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -492,6 +492,7 @@ Structure/LeastSquaresPlane.o : Structure/LeastSquaresPlane.cpp Atom.h AtomMask.
 Structure/MetalCenterFinder.o : Structure/MetalCenterFinder.cpp ArgList.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/MetalCenterFinder.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Structure/PdbCleaner.o : Structure/PdbCleaner.cpp ArgList.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/PdbCleaner.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Structure/RingFinder.o : Structure/RingFinder.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/RingFinder.h SymbolExporting.h Topology.h Unit.h Vec3.h
+Structure/Solvate.o : Structure/Solvate.cpp Structure/Solvate.h
 Structure/StructureEnum.o : Structure/StructureEnum.cpp Structure/StructureEnum.h
 Structure/StructureRoutines.o : Structure/StructureRoutines.cpp Atom.h CpptrajStdio.h NameType.h Residue.h Structure/StructureRoutines.h SymbolExporting.h
 Structure/Sugar.o : Structure/Sugar.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h Unit.h Vec3.h

From 78cc8686eefc1f806bab36702ee1fdcaf5913289 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 18 Nov 2025 08:51:54 -0500
Subject: [PATCH 1071/1492] Start adding the vdw bounding box code

---
 src/Structure/Solvate.cpp     | 49 ++++++++++++++++++++++++++++++++++-
 src/Structure/Solvate.h       | 13 +++++++++-
 src/Structure/structuredepend |  2 +-
 src/cpptrajdepend             |  2 +-
 4 files changed, 62 insertions(+), 4 deletions(-)

diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index faa2046ae1..94ced15395 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -1,9 +1,56 @@
 #include "Solvate.h"
+#include "../ArgList.h"
+#include "../CpptrajStdio.h"
+#include "../Frame.h"
+#include "../Topology.h"
+#include "../Parm/ParameterSet.h"
 
 using namespace Cpptraj::Structure;
 
 /** CONSTRUCTOR */
-Solvate::Solvate()
+Solvate::Solvate() :
+  debug_(0)
 {
 }
 
+/** Initialize arguments. */
+int Solvate::InitSolvate(ArgList& argIn, int debugIn) {
+  debug_ = debugIn;
+
+  return 0;
+}
+
+/** Create box, fill with solvent */
+int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::ParameterSet const& set0) {
+  using namespace Cpptraj::Parm;
+  // Sanity check
+  if (topOut.Natom() != frameOut.Natom()) {
+    mprinterr("Internal Error: Solvate::SolvateBox(): Topology %s #atoms %i != frame #atoms %i\n",
+              topOut.c_str(), topOut.Natom(), frameOut.Natom());
+    return 1;
+  }
+  // TODO Remove any existing box info?
+  //if (frameOut.BoxCrd.HasBox())
+
+  // Set vdw bounding box
+  double Xmin, Ymin, Zmin;
+  double Xmax, Ymax, Zmax;
+
+  for (int at = 0; at < topOut.Natom(); at++)
+  {
+    // Get radius
+    double atom_radius = 0.0;
+    bool has_vdw = false;
+    if (topOut[at].HasType()) {
+      ParmHolder<AtomType>::const_iterator it = set0.AT().GetParam( TypeNameHolder(topOut[at].Type()) );
+      if (it != set0.AT().end() && it->second.HasLJ()) {
+        atom_radius = it->second.LJ().Radius();
+        has_vdw = true;
+      }
+    }
+    mprintf("DEBUG: Atom %s has_vdw= %i VDW=%f\n", topOut.AtomMaskName(at).c_str(), (int)has_vdw, atom_radius);
+  }
+
+  return 0;
+}
+
diff --git a/src/Structure/Solvate.h b/src/Structure/Solvate.h
index 4d9f086161..4a99c3f2dc 100644
--- a/src/Structure/Solvate.h
+++ b/src/Structure/Solvate.h
@@ -1,13 +1,24 @@
 #ifndef INC_SOLVATE_H
 #define INC_SOLVATE_H
+class ArgList;
+class Frame;
+class Topology;
 namespace Cpptraj {
+namespace Parm {
+class ParameterSet;
+}
 namespace Structure {
-/// Used to add solvent to a COORDS set.
+/// Used to add solvent to a frame/topology pair.
 class Solvate {
   public:
     /// CONSTRUCTOR
     Solvate();
+    /// Initialize
+    int InitSolvate(ArgList&, int);
+    /// Solvate with box
+    int SolvateBox(Topology&, Frame&, Cpptraj::Parm::ParameterSet const&); 
   private:
+    int debug_;
 };
 }
 }
diff --git a/src/Structure/structuredepend b/src/Structure/structuredepend
index c3928a54da..a54b521e70 100644
--- a/src/Structure/structuredepend
+++ b/src/Structure/structuredepend
@@ -11,7 +11,7 @@ LeastSquaresPlane.o : LeastSquaresPlane.cpp ../Atom.h ../AtomMask.h ../Box.h ../
 MetalCenterFinder.o : MetalCenterFinder.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h MetalCenterFinder.h
 PdbCleaner.o : PdbCleaner.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h PdbCleaner.h
 RingFinder.o : RingFinder.cpp ../Atom.h ../AtomMask.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h RingFinder.h
-Solvate.o : Solvate.cpp Solvate.h
+Solvate.o : Solvate.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/../AtomType.h ../Parm/../CmapParmHolder.h ../Parm/../Constants.h ../Parm/../NameType.h ../Parm/../ParameterTypes.h ../Parm/../Parm/ParmEnum.h ../Parm/../TypeNameHolder.h ../Parm/DihedralParmHolder.h ../Parm/ImproperParmHolder.h ../Parm/ParameterSet.h ../Parm/ParmEnum.h ../Parm/ParmHolder.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h Solvate.h
 StructureEnum.o : StructureEnum.cpp StructureEnum.h
 StructureRoutines.o : StructureRoutines.cpp ../Atom.h ../CpptrajStdio.h ../NameType.h ../Residue.h ../SymbolExporting.h StructureRoutines.h
 Sugar.o : Sugar.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h Sugar.h SugarToken.h
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index e3704fd344..64dfb17b94 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -492,7 +492,7 @@ Structure/LeastSquaresPlane.o : Structure/LeastSquaresPlane.cpp Atom.h AtomMask.
 Structure/MetalCenterFinder.o : Structure/MetalCenterFinder.cpp ArgList.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/MetalCenterFinder.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Structure/PdbCleaner.o : Structure/PdbCleaner.cpp ArgList.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/PdbCleaner.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Structure/RingFinder.o : Structure/RingFinder.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/RingFinder.h SymbolExporting.h Topology.h Unit.h Vec3.h
-Structure/Solvate.o : Structure/Solvate.cpp Structure/Solvate.h
+Structure/Solvate.o : Structure/Solvate.cpp ArgList.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/../Parm/../AtomType.h Structure/../Parm/../CmapParmHolder.h Structure/../Parm/../Constants.h Structure/../Parm/../NameType.h Structure/../Parm/../ParameterTypes.h Structure/../Parm/../Parm/ParmEnum.h Structure/../Parm/../TypeNameHolder.h Structure/../Parm/DihedralParmHolder.h Structure/../Parm/ImproperParmHolder.h Structure/../Parm/ParameterSet.h Structure/../Parm/ParmEnum.h Structure/../Parm/ParmHolder.h Structure/Solvate.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Structure/StructureEnum.o : Structure/StructureEnum.cpp Structure/StructureEnum.h
 Structure/StructureRoutines.o : Structure/StructureRoutines.cpp Atom.h CpptrajStdio.h NameType.h Residue.h Structure/StructureRoutines.h SymbolExporting.h
 Structure/Sugar.o : Structure/Sugar.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h Unit.h Vec3.h

From 8094aec81f62c523b4c8d2cae9e9ddc78088f5f5 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 18 Nov 2025 08:58:56 -0500
Subject: [PATCH 1072/1492] Start adding solvate to build command

---
 src/Exec_Build.cpp | 18 ++++++++++++++++++
 src/cpptrajdepend  |  2 +-
 2 files changed, 19 insertions(+), 1 deletion(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 01a83ff732..895838632d 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -11,6 +11,7 @@
 #include "Structure/HisProt.h"
 #include "Structure/PdbCleaner.h"
 #include "Structure/ResStatArray.h"
+#include "Structure/Solvate.h"
 #include "Structure/SugarBuilder.h"
 #include "Structure/Sugar.h"
 #include "StructureCheck.h"
@@ -882,6 +883,16 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
   std::string solventResName = argIn.GetStringKey("solventresname", "HOH");
   mprintf("\tSolvent residue name: %s\n", solventResName.c_str());
 
+  bool add_solvent = false;
+  Cpptraj::Structure::Solvate solvator;
+  if (argIn.hasKey("solvate")) {
+    add_solvent = true;
+    if (solvator.InitSolvate(argIn, debug_)) {
+      mprinterr("Error: Init solvate failed.\n");
+      return CpptrajState::ERR;
+    }
+  }
+
   keepMissingSourceAtoms_ = argIn.hasKey("keepmissingatoms");
   if (keepMissingSourceAtoms_)
     mprintf("\tInput atoms missing from templates will be kept.\n");
@@ -1086,6 +1097,13 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
     return CpptrajState::ERR;
   }
 
+  if (add_solvent) {
+    if (solvator.SolvateBox( topOut, frameOut, *(creator.MainParmSetPtr()) )) {
+      mprinterr("Error: Adding solvent failed.\n");
+      return CpptrajState::ERR;
+    }
+  }
+
   // Assign parameters. This will create the bond/angle/dihedral/improper
   // arrays as well.
   t_assign_.Start();
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 64dfb17b94..e210442608 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -316,7 +316,7 @@ EwaldOptions.o : EwaldOptions.cpp ArgList.h CpptrajStdio.h EwaldOptions.h
 ExclusionArray.o : ExclusionArray.cpp Atom.h AtomMask.h CharMask.h CpptrajStdio.h ExclusionArray.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Unit.h
 Exec_AddMissingRes.o : Exec_AddMissingRes.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h CharMask.h CompactFrameArray.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_AddMissingRes.h Exec_AddMissingRes_Pres.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h ParmFile.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h Trajout_Single.h Unit.h Vec3.h
 Exec_Analyze.o : Exec_Analyze.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Analyze.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_Build.o : Exec_Build.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h ExclusionArray.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PairList.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/Creator.h Structure/Disulfide.h Structure/HisProt.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/RingFinder.h Structure/StructureEnum.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Build.o : Exec_Build.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h ExclusionArray.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PairList.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/Creator.h Structure/Disulfide.h Structure/HisProt.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/RingFinder.h Structure/Solvate.h Structure/StructureEnum.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Calc.o : Exec_Calc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Calc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_CatCrd.o : Exec_CatCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CatCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_Change.o : Exec_Change.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Change.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h

From b401d81a7e31cfe4a74c4d3b8b45dbd692a152dc Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 18 Nov 2025 09:17:14 -0500
Subject: [PATCH 1073/1492] Finish getting vdw bounding box

---
 src/Structure/Solvate.cpp | 62 +++++++++++++++++++++++++++++++++++----
 src/Structure/Solvate.h   |  1 +
 2 files changed, 58 insertions(+), 5 deletions(-)

diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index 94ced15395..c3c07a6824 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -20,6 +20,9 @@ int Solvate::InitSolvate(ArgList& argIn, int debugIn) {
   return 0;
 }
 
+/** Atom default radius in Angstroms from LEaP */
+const double Solvate::ATOM_DEFAULT_RADIUS_ = 1.5;
+
 /** Create box, fill with solvent */
 int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::ParameterSet const& set0) {
   using namespace Cpptraj::Parm;
@@ -31,26 +34,75 @@ int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::Parame
   }
   // TODO Remove any existing box info?
   //if (frameOut.BoxCrd.HasBox())
+  // TODO principal align
 
   // Set vdw bounding box
-  double Xmin, Ymin, Zmin;
-  double Xmax, Ymax, Zmax;
+  double Xmin = 0;
+  double Ymin = 0;
+  double Zmin = 0;
+  double Xmax = 0;
+  double Ymax = 0;
+  double Zmax = 0;
 
   for (int at = 0; at < topOut.Natom(); at++)
   {
     // Get radius
     double atom_radius = 0.0;
-    bool has_vdw = false;
+    //bool has_vdw = false;
     if (topOut[at].HasType()) {
       ParmHolder<AtomType>::const_iterator it = set0.AT().GetParam( TypeNameHolder(topOut[at].Type()) );
       if (it != set0.AT().end() && it->second.HasLJ()) {
         atom_radius = it->second.LJ().Radius();
-        has_vdw = true;
+        //has_vdw = true;
       }
     }
-    mprintf("DEBUG: Atom %s has_vdw= %i VDW=%f\n", topOut.AtomMaskName(at).c_str(), (int)has_vdw, atom_radius);
+    if (atom_radius < 0.1) {
+      if (topOut[at].Element() == Atom::HYDROGEN)
+        atom_radius = 1.0;
+      else
+        atom_radius = ATOM_DEFAULT_RADIUS_;
+    }
+    //mprintf("DEBUG: Atom %s has_vdw= %i VDW=%f\n", topOut.AtomMaskName(at).c_str(), (int)has_vdw, atom_radius);
+
+    const double* XYZ = frameOut.XYZ(at);
+    double dXp = XYZ[0] + atom_radius;
+    double dYp = XYZ[1] + atom_radius;
+    double dZp = XYZ[2] + atom_radius;
+    double dXm = XYZ[0] - atom_radius;
+    double dYm = XYZ[1] - atom_radius;
+    double dZm = XYZ[2] - atom_radius;
+    if (at == 0) {
+      Xmin = dXm;
+      Ymin = dYm;
+      Zmin = dZm;
+      Xmax = dXp;
+      Ymax = dYp;
+      Zmax = dZp;
+    } else {
+      if (dXm < Xmin) Xmin = dXm;
+      if (dYm < Ymin) Ymin = dYm;
+      if (dZm < Zmin) Zmin = dZm;
+      if (dXp > Xmax) Xmax = dXp;
+      if (dYp > Ymax) Ymax = dYp;
+      if (dZp > Zmax) Zmax = dZp;
+    }
   }
 
+  // Define box
+  double boxX = Xmax - Xmin;
+  double boxY = Ymax - Ymin;
+  double boxZ = Zmax - Zmin;
+  mprintf("  Solute vdw bounding box:              %-5.3lf %-5.3lf %-5.3lf\n", boxX, boxY, boxZ);
+
+  // Define center
+  Vec3 toCenter( -(Xmin + 0.5 * boxX),
+                 -(Ymin + 0.5 * boxY),
+                 -(Zmin + 0.5 * boxZ) );
+  // Translate to origin
+  frameOut.Translate(toCenter);
+
+  
+
   return 0;
 }
 
diff --git a/src/Structure/Solvate.h b/src/Structure/Solvate.h
index 4a99c3f2dc..4dfac28265 100644
--- a/src/Structure/Solvate.h
+++ b/src/Structure/Solvate.h
@@ -19,6 +19,7 @@ class Solvate {
     int SolvateBox(Topology&, Frame&, Cpptraj::Parm::ParameterSet const&); 
   private:
     int debug_;
+    static const double ATOM_DEFAULT_RADIUS_; ///< Atom default radius from LEaP
 };
 }
 }

From cd78ad43a8839deb6a1e81ca765ba747a48a8f50 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 18 Nov 2025 09:35:12 -0500
Subject: [PATCH 1074/1492] Calculate bounding box

---
 src/Structure/Solvate.cpp | 52 ++++++++++++++++++++++++++++++++++++---
 src/Structure/Solvate.h   |  4 +++
 2 files changed, 53 insertions(+), 3 deletions(-)

diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index c3c07a6824..557353a73f 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -4,12 +4,17 @@
 #include "../Frame.h"
 #include "../Topology.h"
 #include "../Parm/ParameterSet.h"
+#include <algorithm> //std::max
 
 using namespace Cpptraj::Structure;
 
 /** CONSTRUCTOR */
 Solvate::Solvate() :
-  debug_(0)
+  debug_(0),
+  bufferX_(0),
+  bufferY_(0),
+  bufferZ_(0),
+  isotropic_(false)
 {
 }
 
@@ -17,6 +22,22 @@ Solvate::Solvate() :
 int Solvate::InitSolvate(ArgList& argIn, int debugIn) {
   debug_ = debugIn;
 
+  if (argIn.Contains("buffer")) {
+    bufferX_ = argIn.getKeyDouble("buffer", -1.0);
+    bufferY_ = bufferX_;
+    bufferZ_ = bufferX_;
+  } else {
+    bufferX_ = argIn.getKeyDouble("bufx", -1.0);
+    bufferY_ = argIn.getKeyDouble("bufy", -1.0);
+    bufferZ_ = argIn.getKeyDouble("bufz", -1.0);
+  }
+  if (bufferX_ < 0 || bufferY_ < 0 || bufferZ_ < 0) {
+    mprinterr("Error: Either 'buffer' or 'bufx/bufy/bufx' must be specified and >= 0\n");
+    return 1;
+  }
+
+  isotropic_ = argIn.hasKey("iso");
+
   return 0;
 }
 
@@ -92,7 +113,7 @@ int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::Parame
   double boxX = Xmax - Xmin;
   double boxY = Ymax - Ymin;
   double boxZ = Zmax - Zmin;
-  mprintf("  Solute vdw bounding box:              %-5.3lf %-5.3lf %-5.3lf\n", boxX, boxY, boxZ);
+  mprintf("  Solute vdw bounding box:              %-5.3f %-5.3f %-5.3f\n", boxX, boxY, boxZ);
 
   // Define center
   Vec3 toCenter( -(Xmin + 0.5 * boxX),
@@ -101,7 +122,32 @@ int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::Parame
   // Translate to origin
   frameOut.Translate(toCenter);
 
-  
+  double dXWidth = boxX + bufferX_ * 2;
+  double dYWidth = boxY + bufferY_ * 2;
+  double dZWidth = boxZ + bufferZ_ * 2;
+
+  if (isotropic_) {
+    double dTemp = dXWidth * dYWidth * dZWidth;
+
+    double dMax = std::max(dXWidth, dYWidth);
+    dMax = std::max(dMax, dZWidth);
+    dXWidth = dYWidth = dZWidth = dMax;
+
+    dTemp = (dMax * dMax * dMax - dTemp ) / dTemp;
+
+    mprintf("  Total bounding box for atom centers:  %5.3f %5.3f %5.3f\n", 
+            dXWidth, dYWidth, dZWidth );
+    mprintf("      (box expansion for 'iso' is %5.1lf%%)\n", dTemp * 100.0 );
+
+     // To make the actual clip right, 'iso' the solute box
+    dTemp = std::max(boxX, boxY);
+    dTemp = std::max(dTemp, boxZ);
+    //dXBox = dYBox = dZBox = dTemp;
+    boxX = boxY = boxZ = dTemp;
+  } else
+    mprintf("  Total bounding box for atom centers:  %5.3lf %5.3lf %5.3lf\n", 
+            dXWidth, dYWidth, dZWidth );
+
 
   return 0;
 }
diff --git a/src/Structure/Solvate.h b/src/Structure/Solvate.h
index 4dfac28265..7c535e3e6b 100644
--- a/src/Structure/Solvate.h
+++ b/src/Structure/Solvate.h
@@ -19,6 +19,10 @@ class Solvate {
     int SolvateBox(Topology&, Frame&, Cpptraj::Parm::ParameterSet const&); 
   private:
     int debug_;
+    double bufferX_;
+    double bufferY_;
+    double bufferZ_;
+    bool isotropic_;
     static const double ATOM_DEFAULT_RADIUS_; ///< Atom default radius from LEaP
 };
 }

From b976512181fa02b87deb11ce1ad3a3d665c12fec Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 18 Nov 2025 09:50:37 -0500
Subject: [PATCH 1075/1492] Move the vdw bounding box to a different routine

---
 src/Structure/Solvate.cpp | 46 ++++++++++++++++++++++++++-------------
 src/Structure/Solvate.h   |  4 ++++
 2 files changed, 35 insertions(+), 15 deletions(-)

diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index 557353a73f..1e824cebc9 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -44,19 +44,13 @@ int Solvate::InitSolvate(ArgList& argIn, int debugIn) {
 /** Atom default radius in Angstroms from LEaP */
 const double Solvate::ATOM_DEFAULT_RADIUS_ = 1.5;
 
-/** Create box, fill with solvent */
-int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::ParameterSet const& set0) {
+/** Set VDW bounding box. */
+int Solvate::setVdwBoundingBox(double& boxX, double& boxY, double& boxZ,
+                               Topology const& topOut, Frame& frameOut,
+                               Cpptraj::Parm::ParameterSet const& set0)
+const
+{
   using namespace Cpptraj::Parm;
-  // Sanity check
-  if (topOut.Natom() != frameOut.Natom()) {
-    mprinterr("Internal Error: Solvate::SolvateBox(): Topology %s #atoms %i != frame #atoms %i\n",
-              topOut.c_str(), topOut.Natom(), frameOut.Natom());
-    return 1;
-  }
-  // TODO Remove any existing box info?
-  //if (frameOut.BoxCrd.HasBox())
-  // TODO principal align
-
   // Set vdw bounding box
   double Xmin = 0;
   double Ymin = 0;
@@ -110,9 +104,9 @@ int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::Parame
   }
 
   // Define box
-  double boxX = Xmax - Xmin;
-  double boxY = Ymax - Ymin;
-  double boxZ = Zmax - Zmin;
+  boxX = Xmax - Xmin;
+  boxY = Ymax - Ymin;
+  boxZ = Zmax - Zmin;
   mprintf("  Solute vdw bounding box:              %-5.3f %-5.3f %-5.3f\n", boxX, boxY, boxZ);
 
   // Define center
@@ -122,6 +116,28 @@ int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::Parame
   // Translate to origin
   frameOut.Translate(toCenter);
 
+  return 0;
+}
+
+/** Create box, fill with solvent */
+int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::ParameterSet const& set0) {
+  // Sanity check
+  if (topOut.Natom() != frameOut.Natom()) {
+    mprinterr("Internal Error: Solvate::SolvateBox(): Topology %s #atoms %i != frame #atoms %i\n",
+              topOut.c_str(), topOut.Natom(), frameOut.Natom());
+    return 1;
+  }
+  // TODO Remove any existing box info?
+  //if (frameOut.BoxCrd.HasBox())
+  // TODO principal align
+
+  // Set vdw box
+  double boxX, boxY, boxZ;
+  if (setVdwBoundingBox(boxX, boxY, boxZ, topOut, frameOut, set0)) {
+    mprinterr("Error: Setting vdw bounding box for %s failed.\n", topOut.c_str());
+    return 1;
+  }
+
   double dXWidth = boxX + bufferX_ * 2;
   double dYWidth = boxY + bufferY_ * 2;
   double dZWidth = boxZ + bufferZ_ * 2;
diff --git a/src/Structure/Solvate.h b/src/Structure/Solvate.h
index 7c535e3e6b..5feab3645a 100644
--- a/src/Structure/Solvate.h
+++ b/src/Structure/Solvate.h
@@ -18,6 +18,10 @@ class Solvate {
     /// Solvate with box
     int SolvateBox(Topology&, Frame&, Cpptraj::Parm::ParameterSet const&); 
   private:
+    // Set vdW bounding box
+    int setVdwBoundingBox(double&, double&, double&, Topology const&, Frame&,
+                          Cpptraj::Parm::ParameterSet const&) const;
+
     int debug_;
     double bufferX_;
     double bufferY_;

From 058149d8eb39762a1df038e29f0877a72586820b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 18 Nov 2025 12:50:08 -0500
Subject: [PATCH 1076/1492] Read boundbox from Amber lib files

---
 src/DataIO_AmberLib.cpp | 60 ++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 59 insertions(+), 1 deletion(-)

diff --git a/src/DataIO_AmberLib.cpp b/src/DataIO_AmberLib.cpp
index 141494e311..327deec8f7 100644
--- a/src/DataIO_AmberLib.cpp
+++ b/src/DataIO_AmberLib.cpp
@@ -248,7 +248,9 @@ const
   std::vector<Vec3> positions;
   Frame frm;
   int ridx = 0;
-
+  // Boundbox will hold values from box entry: hasbox, angle, x, y, z
+  std::vector<double> boundbox;
+  boundbox.reserve(5);
   bool readUnit = true;
   while (readUnit) {
     const char* lineptr = infile.Line();
@@ -294,9 +296,18 @@ const
           return 1;
         }
         top.SetRes( ridx++ ).SetName( tmpArg[0] );
+      } else if (currentSection == BOUNDBOX) {
+        // hasbox, angle, x, y, z
+        double bval = 0;
+        sscanf( Line.c_str(), "%lf", &bval );
+        boundbox.push_back( bval );
       }
+      // else {
+      //  mprintf("Warning: Unhandled section for %s: %s\n", unitName.c_str(), sectionStr_[currentSection]);
+      //}
     }
   }
+    
   // Set up topology; determine molecules, but no residue renumber or bond parm determination
   top.CommonSetup(true, false, false);
   if (debug_ > 1) top.Summary();
@@ -305,6 +316,53 @@ const
   for (std::vector<Vec3>::const_iterator it = positions.begin(); it != positions.end(); ++it)
     frm.AddVec3( *it );
 
+  // Set up box if needed
+  if (!boundbox.empty()) {
+    if (boundbox.size() != 5) {
+      mprinterr("Error: Expected 5 values for boundbox entry for %s, got %zu\n", unitName.c_str(), boundbox.size());
+      return 1;
+    }
+    // hasbox, angle, x, y, z
+    if (boundbox[0] > 0) {
+      double boxcrd[6];
+      boxcrd[0] = boundbox[2];
+      boxcrd[1] = boundbox[3];
+      boxcrd[2] = boundbox[4];
+      // determine angles
+      double beta = boundbox[1];
+      if (beta < 3.15) {
+        // Assume the angle is given in radians
+        beta = beta * Constants::RADDEG;
+        //mprintf("DEBUG: Converted beta: %f\n", beta);
+        // Fix imperfectly converted orthorhombic
+        double deltaBeta = 90.0 - beta;
+        if (deltaBeta < 0) deltaBeta = -deltaBeta;
+        if (deltaBeta < 0.0001) {
+          beta = 90.0;
+          //mprintf("DEBUG: Fixed beta.\n");
+        }
+      }
+      boxcrd[3] = beta;
+      boxcrd[4] = beta;
+      boxcrd[5] = beta;
+      //if ( Box::IsTruncOct( beta ) ) {
+      // Use trunc oct angle from Box; higher precision
+      //xyzabg[Box::BETA ] = Box::TruncatedOctAngle();
+      //xyzabg[Box::ALPHA] = xyzabg[Box::BETA];
+      //xyzabg[Box::GAMMA] = xyzabg[Box::BETA];
+      // Special case - rhombic dodecahedron
+      if (beta == 60.0) {
+        boxcrd[3] = 60.0;
+        boxcrd[4] = 90.0;
+        boxcrd[5] = 60.0;
+      }
+      frm.ModifyBox().SetupFromXyzAbg( boxcrd );
+      frm.BoxCrd().PrintInfo(); // DEBUG
+    } else {
+      frm.ModifyBox().SetNoBox();
+    }
+  }
+
   crd->CoordsSetup(top, frm.CoordsInfo());
   crd->AddFrame( frm );
   crd->AssociateData( &ConnectAtoms );

From f28d3f26aee11f35c18f1f47b398de90f396e1d8 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 18 Nov 2025 12:50:59 -0500
Subject: [PATCH 1077/1492] Get solvent unit box

---
 src/Exec_Build.cpp            |   8 ++-
 src/Structure/Solvate.cpp     | 100 +++++++++++++++++++++++++++++++---
 src/Structure/Solvate.h       |  11 +++-
 src/Structure/structuredepend |   2 +-
 src/cpptrajdepend             |   2 +-
 5 files changed, 112 insertions(+), 11 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 895838632d..7eb4ad393b 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -1098,7 +1098,13 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
   }
 
   if (add_solvent) {
-    if (solvator.SolvateBox( topOut, frameOut, *(creator.MainParmSetPtr()) )) {
+    // Get solvent unit box
+    DataSet_Coords* solventUnitBox = solvator.GetSolventUnit( DSL );
+    if (solventUnitBox == 0) {
+      mprinterr("Error: Getting solvent unit failed.\n");
+      return CpptrajState::ERR;
+    }
+    if (solvator.SolvateBox( topOut, frameOut, *(creator.MainParmSetPtr()), *solventUnitBox )) {
       mprinterr("Error: Adding solvent failed.\n");
       return CpptrajState::ERR;
     }
diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index 1e824cebc9..0839a9aa39 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -1,6 +1,8 @@
 #include "Solvate.h"
 #include "../ArgList.h"
 #include "../CpptrajStdio.h"
+#include "../DataSet_Coords.h"
+#include "../DataSetList.h"
 #include "../Frame.h"
 #include "../Topology.h"
 #include "../Parm/ParameterSet.h"
@@ -14,7 +16,8 @@ Solvate::Solvate() :
   bufferX_(0),
   bufferY_(0),
   bufferZ_(0),
-  isotropic_(false)
+  isotropic_(false),
+  clip_(true)
 {
 }
 
@@ -38,9 +41,54 @@ int Solvate::InitSolvate(ArgList& argIn, int debugIn) {
 
   isotropic_ = argIn.hasKey("iso");
 
+  solventBoxName_ = argIn.GetStringKey("solventbox");
+  if (solventBoxName_.empty()) {
+    mprinterr("Error: Specify solvent box unit name with 'solventbox'\n");
+    return 1;
+  }
+
   return 0;
 }
 
+/** Get solvent unit box from DataSetList */
+DataSet_Coords* Solvate::GetSolventUnit(DataSetList const& DSL) const {
+  if (solventBoxName_.empty()) {
+    mprinterr("Internal Error: Solvate::GetSolventUnit() called before solventBoxName_ set.\n");
+    return 0;
+  }
+  DataSetList sets = DSL.SelectGroupSets( "*", DataSet::COORDINATES ); // TODO specific set type for units?
+  // First try to match aspect, then match name
+  DataSet_Coords* solventUnit = 0;
+  // Aspect
+  for (DataSetList::const_iterator it = sets.begin(); it != sets.end(); ++it)
+  {
+    DataSet_Coords* ds = static_cast<DataSet_Coords*>( *it );
+    if (!ds->Meta().Aspect().empty()) {
+      if (solventBoxName_ == ds->Meta().Aspect()) {
+        solventUnit = ds;
+        break;
+      }
+    }
+  }
+  // Name
+  if (solventUnit == 0) {
+    for (DataSetList::const_iterator it = sets.begin(); it != sets.end(); ++it)
+    {
+      DataSet_Coords* ds = static_cast<DataSet_Coords*>( *it );
+      if (solventBoxName_ == ds->Meta().Name()) {
+        solventUnit = ds;
+        break;
+      }
+    }
+  }
+  if (solventUnit != 0)
+    mprintf("\tSolvent unit: %s\n", solventUnit->legend());
+  else
+    mprinterr("Error: Could not get solvent unit named %s\n", solventBoxName_.c_str());
+
+  return solventUnit;
+}
+
 /** Atom default radius in Angstroms from LEaP */
 const double Solvate::ATOM_DEFAULT_RADIUS_ = 1.5;
 
@@ -63,12 +111,12 @@ const
   {
     // Get radius
     double atom_radius = 0.0;
-    //bool has_vdw = false;
+    bool has_vdw = false;
     if (topOut[at].HasType()) {
       ParmHolder<AtomType>::const_iterator it = set0.AT().GetParam( TypeNameHolder(topOut[at].Type()) );
       if (it != set0.AT().end() && it->second.HasLJ()) {
         atom_radius = it->second.LJ().Radius();
-        //has_vdw = true;
+        has_vdw = true;
       }
     }
     if (atom_radius < 0.1) {
@@ -80,6 +128,7 @@ const
     //mprintf("DEBUG: Atom %s has_vdw= %i VDW=%f\n", topOut.AtomMaskName(at).c_str(), (int)has_vdw, atom_radius);
 
     const double* XYZ = frameOut.XYZ(at);
+    //mprintf("DBG: %12.4f %12.4f %12.4f %12.4f\n", XYZ[0], XYZ[1], XYZ[2], atom_radius);
     double dXp = XYZ[0] + atom_radius;
     double dYp = XYZ[1] + atom_radius;
     double dZp = XYZ[2] + atom_radius;
@@ -102,12 +151,11 @@ const
       if (dZp > Zmax) Zmax = dZp;
     }
   }
-
+  mprintf("Min= %f %f %f  Max= %f %f %f\n", Xmin, Ymin, Zmin, Xmax, Ymax, Zmax);
   // Define box
   boxX = Xmax - Xmin;
   boxY = Ymax - Ymin;
   boxZ = Zmax - Zmin;
-  mprintf("  Solute vdw bounding box:              %-5.3f %-5.3f %-5.3f\n", boxX, boxY, boxZ);
 
   // Define center
   Vec3 toCenter( -(Xmin + 0.5 * boxX),
@@ -120,7 +168,10 @@ const
 }
 
 /** Create box, fill with solvent */
-int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::ParameterSet const& set0) {
+int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::ParameterSet const& set0,
+                        DataSet_Coords& SOLVENTBOX)
+const
+{
   // Sanity check
   if (topOut.Natom() != frameOut.Natom()) {
     mprinterr("Internal Error: Solvate::SolvateBox(): Topology %s #atoms %i != frame #atoms %i\n",
@@ -137,6 +188,7 @@ int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::Parame
     mprinterr("Error: Setting vdw bounding box for %s failed.\n", topOut.c_str());
     return 1;
   }
+  mprintf("  Solute vdw bounding box:              %-5.3f %-5.3f %-5.3f\n", boxX, boxY, boxZ);
 
   double dXWidth = boxX + bufferX_ * 2;
   double dYWidth = boxY + bufferY_ * 2;
@@ -161,9 +213,43 @@ int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::Parame
     //dXBox = dYBox = dZBox = dTemp;
     boxX = boxY = boxZ = dTemp;
   } else
-    mprintf("  Total bounding box for atom centers:  %5.3lf %5.3lf %5.3lf\n", 
+    mprintf("  Total bounding box for atom centers:  %5.3f %5.3f %5.3f\n", 
             dXWidth, dYWidth, dZWidth );
 
+  /*if ( bClip ) {
+        //  If the solvated system should be clipped to the exact
+        //      size the user specified then note the criterion
+        //      & dimensions (for 0,0,0-centered system)
+        iCriteria |= TOOLOUTSIDEOFBOX;
+        cCriteria.dX = 0.5 * dXBox + dXW;
+        cCriteria.dY = 0.5 * dYBox + dYW;
+        cCriteria.dZ = 0.5 * dZBox + dZW;
+    }
+    if ( bOct ) {
+        // maybe allow oct clip on integer boxes someday.. but for now:
+        if ( !bClip )
+                DFATAL(( "oct but no clip\n" ));
+        iCriteria |= TOOLOUTSIDEOFOCTBOX;
+    }
+*/
+  // TODO check COORDS size
+  Frame solventFrame = SOLVENTBOX.AllocateFrame();
+  SOLVENTBOX.GetFrame(0, solventFrame);
+
+  // Set vdw box for solvent
+  double solventX, solventY, solventZ;
+  if (solventFrame.BoxCrd().HasBox()) {
+    // TODO check ortho?
+    solventX = solventFrame.BoxCrd().Param(Box::X);
+    solventY = solventFrame.BoxCrd().Param(Box::Y);
+    solventZ = solventFrame.BoxCrd().Param(Box::Z);
+  } else {
+    if (setVdwBoundingBox(solventX, solventY, solventZ, SOLVENTBOX.Top(), solventFrame, set0)) {
+      mprinterr("Error: Setting vdw bounding box for %s failed.\n", topOut.c_str());
+      return 1;
+    }
+  }
+  mprintf("  Solvent unit box:                     %5.3f %5.3f %5.3f\n", solventX, solventY, solventZ);
 
   return 0;
 }
diff --git a/src/Structure/Solvate.h b/src/Structure/Solvate.h
index 5feab3645a..26335fafce 100644
--- a/src/Structure/Solvate.h
+++ b/src/Structure/Solvate.h
@@ -1,6 +1,9 @@
 #ifndef INC_SOLVATE_H
 #define INC_SOLVATE_H
+#include <string>
 class ArgList;
+class DataSet_Coords;
+class DataSetList;
 class Frame;
 class Topology;
 namespace Cpptraj {
@@ -16,7 +19,11 @@ class Solvate {
     /// Initialize
     int InitSolvate(ArgList&, int);
     /// Solvate with box
-    int SolvateBox(Topology&, Frame&, Cpptraj::Parm::ParameterSet const&); 
+    int SolvateBox(Topology&, Frame&, Cpptraj::Parm::ParameterSet const&, DataSet_Coords&) const;
+
+    /// \return Solvent unit selected from given DataSetList
+    DataSet_Coords* GetSolventUnit(DataSetList const&) const;
+    //std::string const& SolventBoxName() const { return solventBoxName_; }
   private:
     // Set vdW bounding box
     int setVdwBoundingBox(double&, double&, double&, Topology const&, Frame&,
@@ -27,6 +34,8 @@ class Solvate {
     double bufferY_;
     double bufferZ_;
     bool isotropic_;
+    bool clip_;
+    std::string solventBoxName_;
     static const double ATOM_DEFAULT_RADIUS_; ///< Atom default radius from LEaP
 };
 }
diff --git a/src/Structure/structuredepend b/src/Structure/structuredepend
index a54b521e70..d264dd97ae 100644
--- a/src/Structure/structuredepend
+++ b/src/Structure/structuredepend
@@ -11,7 +11,7 @@ LeastSquaresPlane.o : LeastSquaresPlane.cpp ../Atom.h ../AtomMask.h ../Box.h ../
 MetalCenterFinder.o : MetalCenterFinder.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h MetalCenterFinder.h
 PdbCleaner.o : PdbCleaner.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h PdbCleaner.h
 RingFinder.o : RingFinder.cpp ../Atom.h ../AtomMask.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h RingFinder.h
-Solvate.o : Solvate.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/../AtomType.h ../Parm/../CmapParmHolder.h ../Parm/../Constants.h ../Parm/../NameType.h ../Parm/../ParameterTypes.h ../Parm/../Parm/ParmEnum.h ../Parm/../TypeNameHolder.h ../Parm/DihedralParmHolder.h ../Parm/ImproperParmHolder.h ../Parm/ParameterSet.h ../Parm/ParmEnum.h ../Parm/ParmHolder.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h Solvate.h
+Solvate.o : Solvate.cpp ../ArgList.h ../AssociatedData.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../Dimension.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/../AtomType.h ../Parm/../CmapParmHolder.h ../Parm/../Constants.h ../Parm/../NameType.h ../Parm/../ParameterTypes.h ../Parm/../Parm/ParmEnum.h ../Parm/../TypeNameHolder.h ../Parm/DihedralParmHolder.h ../Parm/ImproperParmHolder.h ../Parm/ParameterSet.h ../Parm/ParmEnum.h ../Parm/ParmHolder.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h Solvate.h
 StructureEnum.o : StructureEnum.cpp StructureEnum.h
 StructureRoutines.o : StructureRoutines.cpp ../Atom.h ../CpptrajStdio.h ../NameType.h ../Residue.h ../SymbolExporting.h StructureRoutines.h
 Sugar.o : Sugar.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h Sugar.h SugarToken.h
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index e210442608..c26ea8bf4f 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -492,7 +492,7 @@ Structure/LeastSquaresPlane.o : Structure/LeastSquaresPlane.cpp Atom.h AtomMask.
 Structure/MetalCenterFinder.o : Structure/MetalCenterFinder.cpp ArgList.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/MetalCenterFinder.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Structure/PdbCleaner.o : Structure/PdbCleaner.cpp ArgList.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/PdbCleaner.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Structure/RingFinder.o : Structure/RingFinder.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/RingFinder.h SymbolExporting.h Topology.h Unit.h Vec3.h
-Structure/Solvate.o : Structure/Solvate.cpp ArgList.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/../Parm/../AtomType.h Structure/../Parm/../CmapParmHolder.h Structure/../Parm/../Constants.h Structure/../Parm/../NameType.h Structure/../Parm/../ParameterTypes.h Structure/../Parm/../Parm/ParmEnum.h Structure/../Parm/../TypeNameHolder.h Structure/../Parm/DihedralParmHolder.h Structure/../Parm/ImproperParmHolder.h Structure/../Parm/ParameterSet.h Structure/../Parm/ParmEnum.h Structure/../Parm/ParmHolder.h Structure/Solvate.h SymbolExporting.h Topology.h Unit.h Vec3.h
+Structure/Solvate.o : Structure/Solvate.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/../Parm/../AtomType.h Structure/../Parm/../CmapParmHolder.h Structure/../Parm/../Constants.h Structure/../Parm/../NameType.h Structure/../Parm/../ParameterTypes.h Structure/../Parm/../Parm/ParmEnum.h Structure/../Parm/../TypeNameHolder.h Structure/../Parm/DihedralParmHolder.h Structure/../Parm/ImproperParmHolder.h Structure/../Parm/ParameterSet.h Structure/../Parm/ParmEnum.h Structure/../Parm/ParmHolder.h Structure/Solvate.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 Structure/StructureEnum.o : Structure/StructureEnum.cpp Structure/StructureEnum.h
 Structure/StructureRoutines.o : Structure/StructureRoutines.cpp Atom.h CpptrajStdio.h NameType.h Residue.h Structure/StructureRoutines.h SymbolExporting.h
 Structure/Sugar.o : Structure/Sugar.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h Unit.h Vec3.h

From c3ab677ceb730bb86cd5f77fcd8c17ba3929a74f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 18 Nov 2025 14:05:14 -0500
Subject: [PATCH 1078/1492] Start loop to add solvent box

---
 src/Structure/Solvate.cpp | 50 +++++++++++++++++++++++++++++++++++++++
 src/Structure/Solvate.h   |  2 ++
 2 files changed, 52 insertions(+)

diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index 0839a9aa39..ba7347b3f3 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -251,6 +251,56 @@ const
   }
   mprintf("  Solvent unit box:                     %5.3f %5.3f %5.3f\n", solventX, solventY, solventZ);
 
+  // See how many solvent boxes required in each dimension
+
+  int iX = (int)( dXWidth / solventX ) + 1;
+  int iY = (int)( dYWidth / solventY ) + 1;
+  int iZ = (int)( dZWidth / solventZ ) + 1;
+
+  //  Calculate the center of the first solvent box 
+  //  (the one that goes in the max XYZ corner), given
+  //  that the solute is centered at 0,0,0
+  double dXStart = 0.5 * solventX * (double) (iX-1);
+  double dYStart = 0.5 * solventY * (double) (iY-1);
+  double dZStart = 0.5 * solventZ * (double) (iZ-1);
+
+             /* If the caller wants a solvent shell then */
+             /* make sure that the box used to find interesting solute */
+             /* spheres takes into account the dFarness parameter */
+             /* so that there are at least some solute spheres in */
+             /* the interesting list to check against solvent */
+
+ //if ( bShell ) 
+ //    dBuffer = dFarness;
+ //else 
+ //    dBuffer = 0.0;
+
+  addSolventUnits(iX, iY, iZ, dXStart, dYStart, dZStart, solventX, solventY, solventZ);
+
   return 0;
 }
 
+int Solvate::addSolventUnits(int numX, int numY, int numZ,
+                             double dXStart, double dYStart, double dZStart,
+                             double dXSolvent, double dYSolvent, double dZSolvent)
+const
+{
+
+  printf( "The number of boxes:  x=%2d  y=%2d  z=%2d\n", numX, numY, numZ );
+
+  double dX = dXStart;
+  for ( int ix=0; ix < numX; ix++, dX -= dXSolvent ) {
+    double dY = dYStart;
+    for ( int iy=0; iy < numY; iy++, dY -= dYSolvent ) {
+      double dZ = dZStart;
+      for ( int iz=0; iz < numZ; iz++, dZ -= dZSolvent ) {
+        printf( "Adding box at: x=%d  y=%d  z=%d\n", ix, iy, iz);
+
+        printf( "Center of solvent box is: %lf, %lf, %lf\n",
+                                dX, dY, dZ );
+      } // END loop over Z
+    } // END loop over Y
+  } // END loop over X
+
+  return 0;
+}
diff --git a/src/Structure/Solvate.h b/src/Structure/Solvate.h
index 26335fafce..3f6eb72d01 100644
--- a/src/Structure/Solvate.h
+++ b/src/Structure/Solvate.h
@@ -28,6 +28,8 @@ class Solvate {
     // Set vdW bounding box
     int setVdwBoundingBox(double&, double&, double&, Topology const&, Frame&,
                           Cpptraj::Parm::ParameterSet const&) const;
+    // Add solvent unit boxes
+    int addSolventUnits(int, int, int, double, double, double, double, double, double) const;
 
     int debug_;
     double bufferX_;

From c7c772024ce4313adb3740ad30dfae900f18399e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 18 Nov 2025 16:02:39 -0500
Subject: [PATCH 1079/1492] Start Frame unit test

---
 unitTests/Frame/UnitTest.sh | 13 +++++++++++++
 unitTests/Frame/main.cpp    | 14 ++++++++++++++
 2 files changed, 27 insertions(+)
 create mode 100755 unitTests/Frame/UnitTest.sh
 create mode 100644 unitTests/Frame/main.cpp

diff --git a/unitTests/Frame/UnitTest.sh b/unitTests/Frame/UnitTest.sh
new file mode 100755
index 0000000000..4de28a4064
--- /dev/null
+++ b/unitTests/Frame/UnitTest.sh
@@ -0,0 +1,13 @@
+#!/bin/bash
+
+. ../UnitMaster.sh
+
+CleanFiles Makefile main.o Frame.o a.out CpptrajStdio.o
+
+UNITSOURCES='Frame.cpp CpptrajStdio.cpp Box.cpp CoordinateInfo.cpp Vec3.cpp Matrix_3x3.cpp'
+
+CreateMakefile
+
+RunMake "Frame class unit test."
+
+EndTest
diff --git a/unitTests/Frame/main.cpp b/unitTests/Frame/main.cpp
new file mode 100644
index 0000000000..bf8d2b1096
--- /dev/null
+++ b/unitTests/Frame/main.cpp
@@ -0,0 +1,14 @@
+// Unit test for NameType class
+#include <cstdio>
+#include "Frame.h"
+
+static const int Err(const char* msg) {
+  fprintf(stderr, "Error: %s\n", msg);
+  return 1;
+}
+
+int main() {
+  Frame frm1;
+
+  return 0;
+}

From 8912ae8e772a31202b05ff4a083d78ecf3736d6a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 18 Nov 2025 16:21:36 -0500
Subject: [PATCH 1080/1492] Test Frame append

---
 unitTests/Frame/main.cpp | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/unitTests/Frame/main.cpp b/unitTests/Frame/main.cpp
index bf8d2b1096..c9671c92ab 100644
--- a/unitTests/Frame/main.cpp
+++ b/unitTests/Frame/main.cpp
@@ -7,8 +7,26 @@ static const int Err(const char* msg) {
   return 1;
 }
 
+static void printAtoms(Frame const& frm1, const char* msg) {
+  frm1.Info(msg);
+  for (int iat = 0; iat < frm1.Natom(); iat++) {
+    frm1.printAtomCoord(iat);
+  }
+}
+
 int main() {
   Frame frm1;
 
+  frm1.SetupFrame( 3 );
+  frm1.ClearAtoms();
+  for (int iat = 1; iat <= 3; iat++)
+    frm1.AddVec3( Vec3((double)iat, (double)iat, (double)iat) );
+  printAtoms(frm1, "frm1");
+
+  Frame frm2 = frm1;
+
+  frm1.AppendFrame( frm2 );
+  printAtoms(frm1, "frm1 after append");
+
   return 0;
 }

From 195207addef46888454ffdec4e31f368b7455e1b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 18 Nov 2025 16:25:02 -0500
Subject: [PATCH 1081/1492] Test appending frames with different sizes

---
 unitTests/Frame/main.cpp | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/unitTests/Frame/main.cpp b/unitTests/Frame/main.cpp
index c9671c92ab..dfd84f5108 100644
--- a/unitTests/Frame/main.cpp
+++ b/unitTests/Frame/main.cpp
@@ -28,5 +28,21 @@ int main() {
   frm1.AppendFrame( frm2 );
   printAtoms(frm1, "frm1 after append");
 
+  Frame frm3;
+  frm3.SetupFrame( 2 );
+  frm3.ClearAtoms();
+  for (int iat = 1; iat <= 2; iat++)
+    frm3.AddVec3( Vec3((double)iat, (double)iat, (double)iat) );
+
+  Frame frm4;
+  frm4.SetupFrame( 6 );
+  frm4.ClearAtoms();
+  for (int iat = 3; iat <= 8; iat++)
+    frm4.AddVec3( Vec3((double)iat, (double)iat, (double)iat) );
+
+  frm3.AppendFrame( frm4 );
+  printAtoms(frm3, "frm3 after append");
+  
+
   return 0;
 }

From f38eab6061bf55fc1e57328418bf98312c18d1ec Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 18 Nov 2025 20:16:34 -0500
Subject: [PATCH 1082/1492] Refactor IncreaseX() so it can take an arbitrary
 number of atoms to increase; also make it (re)allocate velocity and force
 info. Add AppendFrame() function and VGeometricCenter() that does all atoms
 in Frame.

---
 src/Frame.cpp | 55 +++++++++++++++++++++++++++++++++++++++++++++------
 src/Frame.h   | 11 ++++++++++-
 2 files changed, 59 insertions(+), 7 deletions(-)

diff --git a/src/Frame.cpp b/src/Frame.cpp
index 21544a7cea..78a8d9ec15 100644
--- a/src/Frame.cpp
+++ b/src/Frame.cpp
@@ -296,7 +296,7 @@ void Frame::Info(const char *msg) const {
     mprintf("\tFrame [%s]:",msg);
   else
     mprintf("\tFrame:");
-  mprintf("%i atoms, %i coords",natom_, ncoord_);
+  mprintf("%i atoms (%i max), %i coords",natom_, maxnatom_, ncoord_);
   if (V_!=0) mprintf(", with Velocities");
   if (F_!=0) mprintf(", with Forces");
   if (!remd_indices_.empty()) mprintf(", with replica indices");
@@ -304,10 +304,17 @@ void Frame::Info(const char *msg) const {
 }
 
 // Frame::IncreaseX()
-void Frame::IncreaseX() {
-  maxnatom_ += 500;
+/** Increase the maximum size of the Frame by offset. */
+int Frame::IncreaseX(int offset) {
+  mprintf("DEBUG: Increasing max number of atoms from %i to %i\n", maxnatom_, maxnatom_ + offset);
+  maxnatom_ += offset;
+  if (maxnatom_ < 1) {
+    mprinterr("Internal Error: Frame::IncreaseX(): New size is < 1 atom.\n");
+    return 1;
+  }
+  // Coordinates
   double *newX = new double[ maxnatom_ * 3 ];
-  if (X_!=0) {
+  if (X_ != 0) {
     memcpy(newX, X_, natom_ * COORDSIZE_);
     if (!memIsExternal_)
       delete[] X_;
@@ -315,6 +322,19 @@ void Frame::IncreaseX() {
       memIsExternal_ = false;
   }
   X_ = newX;
+  // Velocity
+  if (V_ != 0) {
+    double *newV = new double[ maxnatom_ * 3 ];
+    memcpy(newV, V_, natom_ * COORDSIZE_);
+    V_ = newV;
+  }
+  // Force
+  if (F_ != 0) {
+    double *newF = new double[ maxnatom_ * 3 ];
+    memcpy(newF, F_, natom_ * COORDSIZE_);
+    F_ = newF;
+  }
+  return 0;
 }
 
 /** Set atom/coord count to zero but do not clear memory. */
@@ -328,7 +348,7 @@ void Frame::ClearAtoms() {
 void Frame::AddXYZ(const double *XYZin) {
   if (XYZin == 0) return;
   if (natom_ >= maxnatom_) 
-    IncreaseX(); 
+    IncreaseX( 500 ); // TODO different offset?
   memcpy(X_ + ncoord_, XYZin, COORDSIZE_);
   ++natom_;
   ncoord_ += 3;
@@ -337,7 +357,7 @@ void Frame::AddXYZ(const double *XYZin) {
 // Frame::AddVec3()
 void Frame::AddVec3(Vec3 const& vIn) {
   if (natom_ >= maxnatom_) 
-    IncreaseX();
+    IncreaseX( 500 ); // TODO different offset?
   memcpy(X_ + ncoord_, vIn.Dptr(), COORDSIZE_);
   ++natom_;
   ncoord_ += 3;
@@ -694,6 +714,29 @@ void Frame::SetFrame(Frame const& frameIn) {
     std::copy( frameIn.F_, frameIn.F_ + ncoord_, F_ );
 }
 
+/** Append incoming frame */
+void Frame::AppendFrame(Frame const& frameIn) {
+  int newNatom = natom_ + frameIn.natom_;
+  if (newNatom > maxnatom_)
+    IncreaseX( frameIn.natom_ );
+  int natom3 = natom_ * 3;
+  // Append coords
+  int ncoordIn = frameIn.ncoord_;
+  if (X_ != 0 && frameIn.X_ != 0)
+    std::copy( frameIn.X_, frameIn.X_ + ncoordIn, X_ + natom3 );
+  // Append mass
+  Mass_.insert( Mass_.end(), frameIn.Mass_.begin(), frameIn.Mass_.end() );
+  // Append velocity if necessary
+  if (frameIn.V_ != 0 && V_ != 0)
+    std::copy( frameIn.V_, frameIn.V_ + ncoordIn, V_ + natom3 );
+  // Append force if necessary
+  if (frameIn.F_ != 0 && F_ != 0)
+    std::copy( frameIn.F_, frameIn.F_ + ncoordIn, F_ + natom3 );
+  natom_ = newNatom;
+  ncoord_ = natom_ * 3;
+  mprintf("DEBUG natom is %i\n", natom_);
+}
+
 /** Zero force array. */
 void Frame::ZeroForces() {
   if (F_ != 0)
diff --git a/src/Frame.h b/src/Frame.h
index 5583325f28..58c3012227 100644
--- a/src/Frame.h
+++ b/src/Frame.h
@@ -158,6 +158,8 @@ class Frame {
     int SetupFrameFromMask(AtomMask const&, std::vector<Atom> const&, CoordinateInfo const&);
     /// Allocate frame for selected # atoms
     int SetupFrameFromMask(AtomMask const&);
+    /// Increase the maximum number of atoms the Frame can hold by given offset
+    int IncreaseX(int);
     // ----- Add/remove components from Frame ----
     int AddVelocities(Darray const&);
     void RemoveVelocities();
@@ -178,6 +180,8 @@ class Frame {
     void SetFrame(Frame const&, AtomMask const&);
     /// Copy entire input frame
     void SetFrame(Frame const&);
+    /// Append given frame to this one, reallocating if necessary
+    void AppendFrame(Frame const&);
     /// Zero the force array
     void ZeroForces();
     /// Zero the velocity array
@@ -223,6 +227,8 @@ class Frame {
     inline Vec3 VCenterOfMass(Unit const&) const;
     /// \return Geometric center of atoms in Unit
     inline Vec3 VGeometricCenter(Unit const&) const;
+    /// \return Geometric center of all atoms in Frame
+    inline Vec3 VGeometricCenter() const;
     /// Translate atoms in mask by Vec
     inline void Translate(Vec3 const&, AtomMask const&);
     /// Translate atoms in range by Vec
@@ -306,7 +312,6 @@ class Frame {
     bool memIsExternal_; ///< True if Frame is not responsible for freeing memory.
 
     void swap(Frame&, Frame&);
-    void IncreaseX();
     inline bool ReallocateX(int);
     /// Allocate coords/velo/force based on given num atoms and coordinate info.
     bool setupFrame(unsigned int, CoordinateInfo const&);
@@ -416,6 +421,10 @@ Vec3 Frame::VGeometricCenter(int startAtom, int stopAtom) const {
   return Vec3( Coord0 / sumMass, Coord1 / sumMass, Coord2 / sumMass );
 }
 
+Vec3 Frame::VGeometricCenter() const {
+  return VGeometricCenter(0, natom_);
+}
+
 /** Calculate the Geometric center of a Unit. */
 Vec3 Frame::VGeometricCenter(Unit const& unit) const {
   Vec3 out(0.0);

From c310022db49537e2b6af930d0bcca48864031abe Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 18 Nov 2025 20:21:10 -0500
Subject: [PATCH 1083/1492] Fix improper parm holder unit test. Enable Frame
 unit test

---
 unitTests/ImproperParmHolder/main.cpp | 9 +++++----
 unitTests/Makefile                    | 4 ++++
 2 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/unitTests/ImproperParmHolder/main.cpp b/unitTests/ImproperParmHolder/main.cpp
index c19ebc547f..7986ee4290 100644
--- a/unitTests/ImproperParmHolder/main.cpp
+++ b/unitTests/ImproperParmHolder/main.cpp
@@ -1,6 +1,6 @@
 // Unit test for ImproperParmHolder class
 #include <cstdio>
-#include "ParameterHolders.h"
+#include "Parm/ImproperParmHolder.h"
 
 static const int Err(const char* msg) {
   fprintf(stderr, "Error: %s\n", msg);
@@ -12,6 +12,7 @@ static const int Err(const char* msg) {
 }*/
 
 int main() {
+  using namespace Cpptraj::Parm;
   TypeNameHolder ip0(4);
   ip0.AddName("N*");
   ip0.AddName("CX");
@@ -32,8 +33,8 @@ int main() {
   ip1a.AddName("HO");
 
   ImproperParmHolder IP0;
-  ParameterHolders::RetType ret = IP0.AddParm( ip1, DihedralParmType( 3.0, 1.0, 0.0 ), false );
-  if (ret == ParameterHolders::ERR) return Err("Could not add improper parameter");
+  Cpptraj::Parm::RetType ret = IP0.AddParm( ip1, DihedralParmType( 3.0, 1.0, 0.0 ), false );
+  if (ret == Cpptraj::Parm::ERR) return Err("Could not add improper parameter");
   bool found;
   DihedralParmArray impropers = IP0.FindParam( ip1a, found );
   if (!found) return Err("Could not find improper parameter (no wildcards).");
@@ -46,7 +47,7 @@ int main() {
 
   ImproperParmHolder IP;
   ret = IP.AddParm( ip2, DihedralParmType( 2.0, 1.0, 3.14159/2.0 ), false );
-  if (ret == ParameterHolders::ERR) return Err("Could not add improper parameter");
+  if (ret == Cpptraj::Parm::ERR) return Err("Could not add improper parameter");
   //ip2.SortImproperByAlpha("X");
   
   impropers = IP.FindParam( ip1, found);
diff --git a/unitTests/Makefile b/unitTests/Makefile
index 4e1b304426..d745650cc8 100644
--- a/unitTests/Makefile
+++ b/unitTests/Makefile
@@ -7,6 +7,9 @@ test: test.all
 unit.NameType:
 	@-cd NameType && ./UnitTest.sh $(OPT)
 
+unit.Frame:
+	@-cd Frame && ./UnitTest.sh $(OPT)
+
 unit.ArgList:
 	@-cd ArgList && ./UnitTest.sh $(OPT)
 
@@ -28,6 +31,7 @@ unit.ImproperParmHolder:
 # ----- Every unit test should go here -----------
 COMPLETETESTS= \
   unit.NameType \
+  unit.Frame \
   unit.ArgList \
   unit.GistEntropyUtils \
   unit.StringRoutines \

From 1c105c1312868605ca95608bc047813234bc12ac Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 18 Nov 2025 20:21:54 -0500
Subject: [PATCH 1084/1492] Add solvent unit boxes to parm

---
 src/Structure/Solvate.cpp | 64 ++++++++++++++++++++++++++++++++++++---
 src/Structure/Solvate.h   |  3 +-
 2 files changed, 61 insertions(+), 6 deletions(-)

diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index ba7347b3f3..e73704d881 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -275,18 +275,34 @@ const
  //else 
  //    dBuffer = 0.0;
 
-  addSolventUnits(iX, iY, iZ, dXStart, dYStart, dZStart, solventX, solventY, solventZ);
+  addSolventUnits(iX, iY, iZ, dXStart, dYStart, dZStart, solventX, solventY, solventZ,
+                  solventFrame, SOLVENTBOX.Top(), frameOut, topOut);
 
   return 0;
 }
 
 int Solvate::addSolventUnits(int numX, int numY, int numZ,
                              double dXStart, double dYStart, double dZStart,
-                             double dXSolvent, double dYSolvent, double dZSolvent)
+                             double dXSolvent, double dYSolvent, double dZSolvent,
+                             Frame& solventFrame, Topology const& solventTop,
+                             Frame& frameOut, Topology& topOut)
 const
 {
 
-  printf( "The number of boxes:  x=%2d  y=%2d  z=%2d\n", numX, numY, numZ );
+  mprintf( "The number of boxes:  x=%2d  y=%2d  z=%2d\n", numX, numY, numZ );
+  int NboxesToAdd = numX * numY * numZ;
+  int NatomsToAdd = NboxesToAdd * solventTop.Natom();
+  mprintf("Will add %i boxes, %i atoms.\n", NboxesToAdd, NatomsToAdd);
+  frameOut.IncreaseX( NatomsToAdd );
+
+  // Current solvent unit center
+  Vec3 currentSolventCenter = solventFrame.VGeometricCenter();
+
+  int firstSolventAtom = topOut.Natom();
+  mprintf("DEBUG: First solvent atom is %i\n", firstSolventAtom+1);
+
+  std::vector<int> bondedAtoms;
+  bondedAtoms.reserve(12); // Reserve for 6 bonds
 
   double dX = dXStart;
   for ( int ix=0; ix < numX; ix++, dX -= dXSolvent ) {
@@ -294,10 +310,48 @@ const
     for ( int iy=0; iy < numY; iy++, dY -= dYSolvent ) {
       double dZ = dZStart;
       for ( int iz=0; iz < numZ; iz++, dZ -= dZSolvent ) {
-        printf( "Adding box at: x=%d  y=%d  z=%d\n", ix, iy, iz);
+        mprintf( "Adding box at: x=%d  y=%d  z=%d\n", ix, iy, iz);
 
-        printf( "Center of solvent box is: %lf, %lf, %lf\n",
+        mprintf( "Center of solvent box is: %lf, %lf, %lf\n",
                                 dX, dY, dZ );
+        Vec3 trans( dX - currentSolventCenter[0],
+                    dY - currentSolventCenter[1],
+                    dZ - currentSolventCenter[2] );
+        solventFrame.Translate(trans);
+        Vec3 debugVec = solventFrame.VGeometricCenter();
+        debugVec.Print("DEBUG: check solvent center");
+        currentSolventCenter[0] = dX;
+        currentSolventCenter[1] = dY;
+        currentSolventCenter[2] = dZ;
+        // Add solvent unit to output topology for this cube
+        int atomOffset = topOut.Natom();
+        int currentResNum = topOut.Nres();
+        for (int ires = 0; ires != solventTop.Nres(); ires++) {
+          Residue solventRes = solventTop.Res(ires);
+          solventRes.SetOriginalNum( currentResNum + ires );
+          bondedAtoms.clear();
+          for (int iat = solventRes.FirstAtom(); iat != solventRes.LastAtom(); iat++)
+          {
+            Atom solventAtom = solventTop[iat];
+            // Save solvent bonds
+            for (Atom::bond_iterator bat = solventAtom.bondbegin(); bat != solventAtom.bondend(); ++bat) {
+              if (*bat > iat) {
+                bondedAtoms.push_back(  iat + atomOffset );
+                bondedAtoms.push_back( *bat + atomOffset );
+              }
+            }
+            solventAtom.ClearBonds(); // FIXME AddTopAtom should clear
+            topOut.AddTopAtom( solventAtom, solventRes );
+          } // END loop over solvent atoms
+          // Add bonds
+          for (std::vector<int>::const_iterator it = bondedAtoms.begin(); it != bondedAtoms.end(); ++it) {
+            int at0 = *it;
+            ++it;
+            topOut.AddBond( at0, *it );
+          }
+        } // END loop over solvent unit residues
+        // Append solvent frame
+        frameOut.AppendFrame( solventFrame );
       } // END loop over Z
     } // END loop over Y
   } // END loop over X
diff --git a/src/Structure/Solvate.h b/src/Structure/Solvate.h
index 3f6eb72d01..0cb44b833e 100644
--- a/src/Structure/Solvate.h
+++ b/src/Structure/Solvate.h
@@ -29,7 +29,8 @@ class Solvate {
     int setVdwBoundingBox(double&, double&, double&, Topology const&, Frame&,
                           Cpptraj::Parm::ParameterSet const&) const;
     // Add solvent unit boxes
-    int addSolventUnits(int, int, int, double, double, double, double, double, double) const;
+    int addSolventUnits(int, int, int, double, double, double, double, double, double,
+                        Frame&, Topology const&, Frame&, Topology&) const;
 
     int debug_;
     double bufferX_;

From eccccd94a92b08d64785f108631ffeccabbf7127 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 19 Nov 2025 09:31:31 -0500
Subject: [PATCH 1085/1492] Make IncreaseX allocations for AddVec3/AddXYZ in
 Frame be more exponential (like std::vector) instead of fixed size; will
 reduce the number of allocations needed.

---
 src/Frame.cpp | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/src/Frame.cpp b/src/Frame.cpp
index 78a8d9ec15..37c1e6408a 100644
--- a/src/Frame.cpp
+++ b/src/Frame.cpp
@@ -1,5 +1,6 @@
 #include <cmath> // sqrt
 #include <cstring> // memcpy, memset
+#include <algorithm> // std::max
 #include "Frame.h"
 #include "Constants.h" // SMALL
 #include "CpptrajStdio.h"
@@ -343,12 +344,17 @@ void Frame::ClearAtoms() {
   ncoord_ = 0;
 }
 
+/// Used to calculate how much natom_ should increase if a reallocation is needed.
+static inline int calc_natom_increase(int natomIn) {
+  return std::max(500, 2*natomIn);
+}
+
 // Frame::AddXYZ()
 /** Append the given XYZ coord to this frame. */
 void Frame::AddXYZ(const double *XYZin) {
   if (XYZin == 0) return;
   if (natom_ >= maxnatom_) 
-    IncreaseX( 500 ); // TODO different offset?
+    IncreaseX( calc_natom_increase(natom_) );
   memcpy(X_ + ncoord_, XYZin, COORDSIZE_);
   ++natom_;
   ncoord_ += 3;
@@ -357,7 +363,7 @@ void Frame::AddXYZ(const double *XYZin) {
 // Frame::AddVec3()
 void Frame::AddVec3(Vec3 const& vIn) {
   if (natom_ >= maxnatom_) 
-    IncreaseX( 500 ); // TODO different offset?
+    IncreaseX( calc_natom_increase(natom_) );
   memcpy(X_ + ncoord_, vIn.Dptr(), COORDSIZE_);
   ++natom_;
   ncoord_ += 3;

From b2e5755ea675e9f5a3c33b8784e5813ca75d846f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 19 Nov 2025 09:38:05 -0500
Subject: [PATCH 1086/1492] Fix up truncated octahedral angle from amber lib
 file if needed. Hide box debug info from amber lib.

---
 src/DataIO_AmberLib.cpp | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/src/DataIO_AmberLib.cpp b/src/DataIO_AmberLib.cpp
index 327deec8f7..2f545b8cd7 100644
--- a/src/DataIO_AmberLib.cpp
+++ b/src/DataIO_AmberLib.cpp
@@ -345,19 +345,20 @@ const
       boxcrd[3] = beta;
       boxcrd[4] = beta;
       boxcrd[5] = beta;
-      //if ( Box::IsTruncOct( beta ) ) {
-      // Use trunc oct angle from Box; higher precision
-      //xyzabg[Box::BETA ] = Box::TruncatedOctAngle();
-      //xyzabg[Box::ALPHA] = xyzabg[Box::BETA];
-      //xyzabg[Box::GAMMA] = xyzabg[Box::BETA];
-      // Special case - rhombic dodecahedron
-      if (beta == 60.0) {
+      if ( Box::IsTruncOct( beta ) ) {
+        // Use trunc oct angle from Box; higher precision
+        boxcrd[3] = Box::TruncatedOctAngle();
+        boxcrd[4] = boxcrd[3];
+        boxcrd[5] = boxcrd[3];
+      } else if (beta == 60.0) {
+        // Special case - rhombic dodecahedron
         boxcrd[3] = 60.0;
         boxcrd[4] = 90.0;
         boxcrd[5] = 60.0;
       }
       frm.ModifyBox().SetupFromXyzAbg( boxcrd );
-      frm.BoxCrd().PrintInfo(); // DEBUG
+      if (debug_ > 0)
+        frm.BoxCrd().PrintInfo(); // DEBUG
     } else {
       frm.ModifyBox().SetNoBox();
     }

From 485f11be3806c754f618643915e0238db1cd53e7 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 19 Nov 2025 11:23:11 -0500
Subject: [PATCH 1087/1492] Improve some debug/error messages. Handle case
 where PDB occupancy/bfactor/serial# arrays are shorter than number of atoms
 in topology by writing out blank values.

---
 src/BufferedFrame.cpp |  2 +-
 src/Parm_Amber.cpp    | 50 +++++++++++++++++++++++++++++++++++++++++--
 2 files changed, 49 insertions(+), 3 deletions(-)

diff --git a/src/BufferedFrame.cpp b/src/BufferedFrame.cpp
index 9918ee9163..633ed4f8cf 100644
--- a/src/BufferedFrame.cpp
+++ b/src/BufferedFrame.cpp
@@ -144,7 +144,7 @@ int BufferedFrame::AttemptReadFrame() {
   */
 bool BufferedFrame::ReadFrame() {
   int nread = Read(buffer_, frameSize_);
-  //mprintf("DEBUG: %i bytes read.\n", nread);
+  //mprintf("DEBUG: %i bytes read, frameSize %zu.\n", nread, frameSize_);
   if (nread != (int)frameSize_) {
     if (nread < 0)
       mprinterr("Error: Read %i bytes, expected %zu\n", nread, frameSize_);
diff --git a/src/Parm_Amber.cpp b/src/Parm_Amber.cpp
index e9ce3b7615..1f0fb86a20 100644
--- a/src/Parm_Amber.cpp
+++ b/src/Parm_Amber.cpp
@@ -693,7 +693,10 @@ int Parm_Amber::SetupBuffer(FlagType ftype, int nvals, FortranData const& FMT) {
   if (nvals > 0) {
     if (debug_>0) mprintf("DEBUG: Set up buffer for '%s', %i vals.\n", FLAGS_[ftype].Flag, nvals);
     file_.SetupFrameBuffer( nvals, FMT.Width(), FMT.Ncols() );
-    if (file_.ReadFrame()) return 1;
+    if (file_.ReadFrame()) {
+      mprinterr("Error: Read values for Flag '%s' failed.\n", FLAGS_[ftype].Flag);
+      return 1;
+    }
     if (debug_ > 5) {
       mprintf("DEBUG: '%s':\n", FLAGS_[ftype].Flag);
       if (debug_ > 6) mprintf("FileBuffer=[%s]", file_.Buffer());
@@ -1211,7 +1214,10 @@ int Parm_Amber::ReadPdbBfactor(Topology& TopIn, FortranData const& FMT) {
 
 int Parm_Amber::ReadPdbOccupancy(Topology& TopIn, FortranData const& FMT) {
   TopIn.AllocOccupancy();
-  if (SetupBuffer(F_PDB_OCC, values_[NATOM], FMT)) return 1;
+  if (SetupBuffer(F_PDB_OCC, values_[NATOM], FMT)) {
+    //mprintf("DEBUG: ReadPdbOccupancy buffer:\n%s\n", file_.Buffer());
+    return 1;
+  }
   for (int idx = 0; idx != values_[NATOM]; idx++)
     TopIn.SetOccupancy(idx, atof(file_.NextElement()) );
   return 0;
@@ -1798,6 +1804,28 @@ int Parm_Amber::WriteExtra(Topology const& topOut, int natom) {
   return 0;
 }
 
+/// Used to check if the size of "extra" arrays (PDB atom occupancy, bfactor, etc) match expected size.
+/** The size of these arrays might be less than what is expected if e.g. solvent
+  * was added with the 'build' command. In that case, blank values can be used
+  * without requiring the memory be allocated.
+  * \return 1 if actual size > expected size (error)
+  * \return -1 if actual size < expected size (fill with blank)
+  * \return 0 if actual size == expected size.
+  */
+static inline int check_array_size(unsigned int expectedSize, unsigned int actualSize, const char* desc)
+{
+  if (actualSize > expectedSize) {
+    mprinterr("Internal Error: Size of %s (%u) is greater than expected size (%u)\n",
+              desc, actualSize, expectedSize);
+    return 1;
+  } else if (actualSize < expectedSize) {
+    mprintf("Warning: Size of %s (%u) is less than expected size (%u); will fill missing values with blanks.\n",
+              desc, actualSize, expectedSize);
+    return -1;
+  }
+  return 0;
+}
+
 // Parm_Amber::WriteParm()
 int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
   if (file_.OpenWrite( fname )) return 1;
@@ -2554,26 +2582,44 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
   }
   if (hasOcc) {
     // PDB atomic occupancy
+    int astat = check_array_size(TopOut.Natom(), TopOut.Occupancy().size(), "PDB occupancy array");
+    if (astat == 1) return 1;
     if (BufferAlloc(F_PDB_OCC, TopOut.Natom())) return 1;
     for (std::vector<float>::const_iterator it = TopOut.Occupancy().begin();
                                             it != TopOut.Occupancy().end(); ++it)
       file_.DblToBuffer( *it );
+    if (astat == -1) {
+      for (unsigned int idx = TopOut.Occupancy().size(); idx < (unsigned int)TopOut.Natom(); idx++)
+        file_.DblToBuffer( 1 );
+    }
     file_.FlushBuffer();
   }
   if (hasBfac) {
     // PDB atomic B-factors
+    int astat = check_array_size(TopOut.Natom(), TopOut.Bfactor().size(), "PDB B-factor array");
+    if (astat == 1) return 1;
     if (BufferAlloc(F_PDB_BFAC, TopOut.Natom())) return 1;
     for (std::vector<float>::const_iterator it = TopOut.Bfactor().begin();
                                             it != TopOut.Bfactor().end(); ++it)
       file_.DblToBuffer( *it );
+    if (astat == -1) {
+      for (unsigned int idx = TopOut.Bfactor().size(); idx < (unsigned int)TopOut.Natom(); idx++)
+        file_.DblToBuffer( 0 );
+    }
     file_.FlushBuffer();
   }
   if (hasNum) {
     // PDB original serial numbers
+    int astat = check_array_size(TopOut.Natom(), TopOut.PdbSerialNum().size(), "PDB serial number array");
+    if (astat == 1) return 1;
     if (BufferAlloc(F_PDB_NUM, TopOut.Natom())) return 1;
     for (std::vector<int>::const_iterator it = TopOut.PdbSerialNum().begin();
                                           it != TopOut.PdbSerialNum().end(); ++it)
       file_.IntToBuffer( *it );
+    if (astat == -1) {
+      for (unsigned int idx = TopOut.PdbSerialNum().size(); idx < (unsigned int)TopOut.Natom(); idx++)
+        file_.IntToBuffer( (int)idx+1 );
+    }
     file_.FlushBuffer();
   }
 

From b1b19c84a943f29bc4d9c2f11dd00b8f7fdb2c61 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 19 Nov 2025 11:42:42 -0500
Subject: [PATCH 1088/1492] Calculate max atom radius during vdw box add

---
 src/Frame.cpp             |  1 -
 src/Structure/Solvate.cpp | 20 ++++++++++++--------
 src/Structure/Solvate.h   |  4 ++--
 3 files changed, 14 insertions(+), 11 deletions(-)

diff --git a/src/Frame.cpp b/src/Frame.cpp
index 37c1e6408a..578bba8ce2 100644
--- a/src/Frame.cpp
+++ b/src/Frame.cpp
@@ -740,7 +740,6 @@ void Frame::AppendFrame(Frame const& frameIn) {
     std::copy( frameIn.F_, frameIn.F_ + ncoordIn, F_ + natom3 );
   natom_ = newNatom;
   ncoord_ = natom_ * 3;
-  mprintf("DEBUG natom is %i\n", natom_);
 }
 
 /** Zero force array. */
diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index e73704d881..94ab2f4c1e 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -94,6 +94,7 @@ const double Solvate::ATOM_DEFAULT_RADIUS_ = 1.5;
 
 /** Set VDW bounding box. */
 int Solvate::setVdwBoundingBox(double& boxX, double& boxY, double& boxZ,
+                               double& maxR,
                                Topology const& topOut, Frame& frameOut,
                                Cpptraj::Parm::ParameterSet const& set0)
 const
@@ -106,17 +107,18 @@ const
   double Xmax = 0;
   double Ymax = 0;
   double Zmax = 0;
+  maxR = 0;
 
   for (int at = 0; at < topOut.Natom(); at++)
   {
     // Get radius
     double atom_radius = 0.0;
-    bool has_vdw = false;
+    //bool has_vdw = false;
     if (topOut[at].HasType()) {
       ParmHolder<AtomType>::const_iterator it = set0.AT().GetParam( TypeNameHolder(topOut[at].Type()) );
       if (it != set0.AT().end() && it->second.HasLJ()) {
         atom_radius = it->second.LJ().Radius();
-        has_vdw = true;
+        //has_vdw = true;
       }
     }
     if (atom_radius < 0.1) {
@@ -125,6 +127,7 @@ const
       else
         atom_radius = ATOM_DEFAULT_RADIUS_;
     }
+    maxR = std::max(maxR, atom_radius);
     //mprintf("DEBUG: Atom %s has_vdw= %i VDW=%f\n", topOut.AtomMaskName(at).c_str(), (int)has_vdw, atom_radius);
 
     const double* XYZ = frameOut.XYZ(at);
@@ -183,8 +186,8 @@ const
   // TODO principal align
 
   // Set vdw box
-  double boxX, boxY, boxZ;
-  if (setVdwBoundingBox(boxX, boxY, boxZ, topOut, frameOut, set0)) {
+  double boxX, boxY, boxZ, soluteMaxR;
+  if (setVdwBoundingBox(boxX, boxY, boxZ, soluteMaxR, topOut, frameOut, set0)) {
     mprinterr("Error: Setting vdw bounding box for %s failed.\n", topOut.c_str());
     return 1;
   }
@@ -244,7 +247,8 @@ const
     solventY = solventFrame.BoxCrd().Param(Box::Y);
     solventZ = solventFrame.BoxCrd().Param(Box::Z);
   } else {
-    if (setVdwBoundingBox(solventX, solventY, solventZ, SOLVENTBOX.Top(), solventFrame, set0)) {
+    double solventMaxR;
+    if (setVdwBoundingBox(solventX, solventY, solventZ, solventMaxR, SOLVENTBOX.Top(), solventFrame, set0)) {
       mprinterr("Error: Setting vdw bounding box for %s failed.\n", topOut.c_str());
       return 1;
     }
@@ -275,20 +279,20 @@ const
  //else 
  //    dBuffer = 0.0;
 
-  addSolventUnits(iX, iY, iZ, dXStart, dYStart, dZStart, solventX, solventY, solventZ,
+  addSolventUnits(iX, iY, iZ, soluteMaxR, dXStart, dYStart, dZStart, solventX, solventY, solventZ,
                   solventFrame, SOLVENTBOX.Top(), frameOut, topOut);
 
   return 0;
 }
 
-int Solvate::addSolventUnits(int numX, int numY, int numZ,
+int Solvate::addSolventUnits(int numX, int numY, int numZ, double soluteMaxR,
                              double dXStart, double dYStart, double dZStart,
                              double dXSolvent, double dYSolvent, double dZSolvent,
                              Frame& solventFrame, Topology const& solventTop,
                              Frame& frameOut, Topology& topOut)
 const
 {
-
+  mprintf( "Max R = %f\n", soluteMaxR);
   mprintf( "The number of boxes:  x=%2d  y=%2d  z=%2d\n", numX, numY, numZ );
   int NboxesToAdd = numX * numY * numZ;
   int NatomsToAdd = NboxesToAdd * solventTop.Natom();
diff --git a/src/Structure/Solvate.h b/src/Structure/Solvate.h
index 0cb44b833e..595cec1df4 100644
--- a/src/Structure/Solvate.h
+++ b/src/Structure/Solvate.h
@@ -26,10 +26,10 @@ class Solvate {
     //std::string const& SolventBoxName() const { return solventBoxName_; }
   private:
     // Set vdW bounding box
-    int setVdwBoundingBox(double&, double&, double&, Topology const&, Frame&,
+    int setVdwBoundingBox(double&, double&, double&, double&, Topology const&, Frame&,
                           Cpptraj::Parm::ParameterSet const&) const;
     // Add solvent unit boxes
-    int addSolventUnits(int, int, int, double, double, double, double, double, double,
+    int addSolventUnits(int, int, int, double, double, double, double, double, double, double,
                         Frame&, Topology const&, Frame&, Topology&) const;
 
     int debug_;

From 4d80bfb292cea6621e8c8b562920ecec69fa81c5 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 19 Nov 2025 12:55:04 -0500
Subject: [PATCH 1089/1492] Find close solvent atoms. Save radii

---
 src/Structure/Solvate.cpp | 90 ++++++++++++++++++++++++++++++++++-----
 src/Structure/Solvate.h   |  8 +++-
 2 files changed, 86 insertions(+), 12 deletions(-)

diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index 94ab2f4c1e..690d142b44 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -16,6 +16,7 @@ Solvate::Solvate() :
   bufferX_(0),
   bufferY_(0),
   bufferZ_(0),
+  closeness_(0.8),
   isotropic_(false),
   clip_(true)
 {
@@ -47,6 +48,8 @@ int Solvate::InitSolvate(ArgList& argIn, int debugIn) {
     return 1;
   }
 
+  closeness_ = argIn.getKeyDouble("closeness", 0.8);
+
   return 0;
 }
 
@@ -94,12 +97,13 @@ const double Solvate::ATOM_DEFAULT_RADIUS_ = 1.5;
 
 /** Set VDW bounding box. */
 int Solvate::setVdwBoundingBox(double& boxX, double& boxY, double& boxZ,
-                               double& maxR,
+                               double& maxR, std::vector<double>& Radii,
                                Topology const& topOut, Frame& frameOut,
                                Cpptraj::Parm::ParameterSet const& set0)
 const
 {
   using namespace Cpptraj::Parm;
+  Radii.clear();
   // Set vdw bounding box
   double Xmin = 0;
   double Ymin = 0;
@@ -127,6 +131,7 @@ const
       else
         atom_radius = ATOM_DEFAULT_RADIUS_;
     }
+    Radii.push_back( atom_radius );
     maxR = std::max(maxR, atom_radius);
     //mprintf("DEBUG: Atom %s has_vdw= %i VDW=%f\n", topOut.AtomMaskName(at).c_str(), (int)has_vdw, atom_radius);
 
@@ -186,8 +191,10 @@ const
   // TODO principal align
 
   // Set vdw box
+  std::vector<double> soluteRadii;
+  soluteRadii.reserve( topOut.Natom() );
   double boxX, boxY, boxZ, soluteMaxR;
-  if (setVdwBoundingBox(boxX, boxY, boxZ, soluteMaxR, topOut, frameOut, set0)) {
+  if (setVdwBoundingBox(boxX, boxY, boxZ, soluteMaxR, soluteRadii, topOut, frameOut, set0)) {
     mprinterr("Error: Setting vdw bounding box for %s failed.\n", topOut.c_str());
     return 1;
   }
@@ -241,17 +248,20 @@ const
 
   // Set vdw box for solvent
   double solventX, solventY, solventZ;
+  // Set the box even if box info is present so that solvent radii get set
+  std::vector<double> solventRadii;
+  solventRadii.reserve( SOLVENTBOX.Top().Natom() );
+  double solventMaxR;
+  if (setVdwBoundingBox(solventX, solventY, solventZ, solventMaxR, solventRadii, SOLVENTBOX.Top(), solventFrame, set0)) {
+    mprinterr("Error: Setting vdw bounding box for %s failed.\n", topOut.c_str());
+    return 1;
+  }
   if (solventFrame.BoxCrd().HasBox()) {
+    // Overwrite VDW box lengths with input box lengths
     // TODO check ortho?
     solventX = solventFrame.BoxCrd().Param(Box::X);
     solventY = solventFrame.BoxCrd().Param(Box::Y);
     solventZ = solventFrame.BoxCrd().Param(Box::Z);
-  } else {
-    double solventMaxR;
-    if (setVdwBoundingBox(solventX, solventY, solventZ, solventMaxR, SOLVENTBOX.Top(), solventFrame, set0)) {
-      mprinterr("Error: Setting vdw bounding box for %s failed.\n", topOut.c_str());
-      return 1;
-    }
   }
   mprintf("  Solvent unit box:                     %5.3f %5.3f %5.3f\n", solventX, solventY, solventZ);
 
@@ -285,6 +295,52 @@ const
   return 0;
 }
 
+/** \return a list of solute atoms that might clash with solvent. */
+int Solvate::findCloseSoluteAtoms(std::vector<int>& closeSoluteAtoms, double soluteMaxR,
+                                  int firstSolventAtom, Frame const& frameOut, Vec3 const& vCenter,
+                                  double dXWidth, double dYWidth, double dZWidth)
+const
+{
+  closeSoluteAtoms.clear();
+  // Determine clearance from the box for testing whether
+  // a solute atom might contact an atom in the box. Assumes
+  // solvent box includes vdw.
+  double dTemp = soluteMaxR * 2.5 * closeness_;
+
+  // FIXME do buffer zone?
+  // when building a shell, solute atoms within the
+  // shell distance are also of interest
+  //  dTemp += dBufferZone;
+
+  double dXmin = vCenter[0] - dXWidth/2.0 - dTemp;
+  double dXmax = vCenter[0] + dXWidth/2.0 + dTemp;
+  double dYmin = vCenter[1] - dYWidth/2.0 - dTemp;
+  double dYmax = vCenter[1] + dYWidth/2.0 + dTemp;
+  double dZmin = vCenter[2] - dZWidth/2.0 - dTemp;
+  double dZmax = vCenter[2] + dZWidth/2.0 + dTemp;
+
+  // Loop over solute atoms
+  for (int at = 0; at < firstSolventAtom; at++)
+  {
+    const double* XYZ = frameOut.XYZ(at);
+    if ( XYZ[0] < dXmin ) continue;
+    if ( XYZ[0] > dXmax ) continue;
+    if ( XYZ[1] < dYmin ) continue;
+    if ( XYZ[1] > dYmax ) continue;
+    if ( XYZ[2] < dZmin ) continue;
+    if ( XYZ[2] > dZmax ) continue;
+
+    // all atom.coords inside solvent limit, so add to list
+    //    MESSAGE(( "Found an interesting sphere\n" ));
+    closeSoluteAtoms.push_back( at );
+  }
+  return 0;
+}
+
+/** Determine which solvent residues will not clash with existing solute atoms. */
+//int determineValidSolventResidues
+
+/** Add as many solvent units as needed to complete solvation. */
 int Solvate::addSolventUnits(int numX, int numY, int numZ, double soluteMaxR,
                              double dXStart, double dYStart, double dZStart,
                              double dXSolvent, double dYSolvent, double dZSolvent,
@@ -308,6 +364,9 @@ const
   std::vector<int> bondedAtoms;
   bondedAtoms.reserve(12); // Reserve for 6 bonds
 
+  std::vector<int> closeSoluteAtoms;
+  std::vector<int> validSolventResidues;
+
   double dX = dXStart;
   for ( int ix=0; ix < numX; ix++, dX -= dXSolvent ) {
     double dY = dYStart;
@@ -315,6 +374,10 @@ const
       double dZ = dZStart;
       for ( int iz=0; iz < numZ; iz++, dZ -= dZSolvent ) {
         mprintf( "Adding box at: x=%d  y=%d  z=%d\n", ix, iy, iz);
+        Vec3 vPos(dX, dY, dZ);
+
+        findCloseSoluteAtoms(closeSoluteAtoms, soluteMaxR, firstSolventAtom, frameOut, vPos,
+                             dXSolvent, dYSolvent, dZSolvent);
 
         mprintf( "Center of solvent box is: %lf, %lf, %lf\n",
                                 dX, dY, dZ );
@@ -322,12 +385,17 @@ const
                     dY - currentSolventCenter[1],
                     dZ - currentSolventCenter[2] );
         solventFrame.Translate(trans);
-        Vec3 debugVec = solventFrame.VGeometricCenter();
-        debugVec.Print("DEBUG: check solvent center");
+        //Vec3 debugVec = solventFrame.VGeometricCenter();
+        //debugVec.Print("DEBUG: check solvent center");
+
+        //determineValidSolventResidues(validSolventResidues, 
+
+        // Update the current solvent center
         currentSolventCenter[0] = dX;
         currentSolventCenter[1] = dY;
         currentSolventCenter[2] = dZ;
-        // Add solvent unit to output topology for this cube
+
+        // Add valid residues from solvent unit to output topology for this cube
         int atomOffset = topOut.Natom();
         int currentResNum = topOut.Nres();
         for (int ires = 0; ires != solventTop.Nres(); ires++) {
diff --git a/src/Structure/Solvate.h b/src/Structure/Solvate.h
index 595cec1df4..56705afd11 100644
--- a/src/Structure/Solvate.h
+++ b/src/Structure/Solvate.h
@@ -1,11 +1,13 @@
 #ifndef INC_SOLVATE_H
 #define INC_SOLVATE_H
 #include <string>
+#include <vector>
 class ArgList;
 class DataSet_Coords;
 class DataSetList;
 class Frame;
 class Topology;
+class Vec3;
 namespace Cpptraj {
 namespace Parm {
 class ParameterSet;
@@ -26,8 +28,11 @@ class Solvate {
     //std::string const& SolventBoxName() const { return solventBoxName_; }
   private:
     // Set vdW bounding box
-    int setVdwBoundingBox(double&, double&, double&, double&, Topology const&, Frame&,
+    int setVdwBoundingBox(double&, double&, double&, double&, std::vector<double>&,
+                          Topology const&, Frame&,
                           Cpptraj::Parm::ParameterSet const&) const;
+    // Find solute atoms within a solvent box at given center
+    int findCloseSoluteAtoms(std::vector<int>&, double, int, Frame const&, Vec3 const&, double, double, double) const;
     // Add solvent unit boxes
     int addSolventUnits(int, int, int, double, double, double, double, double, double, double,
                         Frame&, Topology const&, Frame&, Topology&) const;
@@ -36,6 +41,7 @@ class Solvate {
     double bufferX_;
     double bufferY_;
     double bufferZ_;
+    double closeness_;
     bool isotropic_;
     bool clip_;
     std::string solventBoxName_;

From f6203b793c925603f20b3cde5d11daa9d0ea1927 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 19 Nov 2025 13:26:11 -0500
Subject: [PATCH 1090/1492] Start removing solvent residues that conflict with
 solute atoms

---
 src/Structure/Solvate.cpp | 75 +++++++++++++++++++++++++++++++++------
 src/Structure/Solvate.h   | 13 +++++--
 2 files changed, 74 insertions(+), 14 deletions(-)

diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index 690d142b44..8f8ba04a6b 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -290,7 +290,8 @@ const
  //    dBuffer = 0.0;
 
   addSolventUnits(iX, iY, iZ, soluteMaxR, dXStart, dYStart, dZStart, solventX, solventY, solventZ,
-                  solventFrame, SOLVENTBOX.Top(), frameOut, topOut);
+                  solventFrame, SOLVENTBOX.Top(), frameOut, topOut,
+                  soluteRadii, solventRadii);
 
   return 0;
 }
@@ -337,15 +338,61 @@ const
   return 0;
 }
 
+/** LEaP's closeness modifier. Was just set to 1. Included here just in case. */
+const double Solvate::CLOSENESSMODIFIER_ = 1.0;
+
 /** Determine which solvent residues will not clash with existing solute atoms. */
-//int determineValidSolventResidues
+int Solvate::determineValidSolventResidues(std::vector<int>& validSolventResidues,
+                                           std::vector<int> const& closeSoluteAtoms,
+                                           Frame const& solventFrame, Topology const& solventTop,
+                                           Frame const& frameOut,
+                                           std::vector<double> const& soluteRadii,
+                                           std::vector<double> const& solventRadii)
+const
+{
+  validSolventResidues.clear();
+  for (int vres = 0; vres < solventTop.Nres(); vres++)
+  {
+    Residue const& solventRes = solventTop.Res(vres);
+    bool collision = false;
+    // Check each atom in the solvent residue against list of close solute atoms
+    for (int vat = solventRes.FirstAtom(); vat != solventRes.LastAtom(); vat++)
+    {
+      const double* VXYZ = solventFrame.XYZ(vat);
+      double dR = solventRadii[vat] * closeness_ * CLOSENESSMODIFIER_;
+      // Loop over close solute atoms
+      for (std::vector<int>::const_iterator uat = closeSoluteAtoms.begin(); uat != closeSoluteAtoms.end(); ++uat)
+      {
+        const double* UXYZ = frameOut.XYZ(*uat);
+        double dX = VXYZ[0] - UXYZ[0];
+        double dY = VXYZ[1] - UXYZ[1];
+        double dZ = VXYZ[2] - UXYZ[2];
+
+        double dist2 = dX*dX + dY*dY + dZ*dZ;
+        double dRadii = dR + soluteRadii[*uat];
+        dRadii *= dRadii;
+
+        if (dist2 < dRadii) {
+          collision = true;
+          break;
+        }
+      } // END loop over close solute atoms
+      if (collision) break;
+    } // END loop over solvent residue atoms
+    if (!collision)
+      validSolventResidues.push_back( vres );
+  } // END loop over solvent residues
+  return 0;
+}
 
 /** Add as many solvent units as needed to complete solvation. */
 int Solvate::addSolventUnits(int numX, int numY, int numZ, double soluteMaxR,
                              double dXStart, double dYStart, double dZStart,
                              double dXSolvent, double dYSolvent, double dZSolvent,
                              Frame& solventFrame, Topology const& solventTop,
-                             Frame& frameOut, Topology& topOut)
+                             Frame& frameOut, Topology& topOut,
+                             std::vector<double> const& soluteRadii,
+                             std::vector<double> const& solventRadii)
 const
 {
   mprintf( "Max R = %f\n", soluteMaxR);
@@ -388,7 +435,8 @@ const
         //Vec3 debugVec = solventFrame.VGeometricCenter();
         //debugVec.Print("DEBUG: check solvent center");
 
-        //determineValidSolventResidues(validSolventResidues, 
+        determineValidSolventResidues(validSolventResidues, closeSoluteAtoms, solventFrame, solventTop,
+                                      frameOut, soluteRadii, solventRadii); 
 
         // Update the current solvent center
         currentSolventCenter[0] = dX;
@@ -396,11 +444,14 @@ const
         currentSolventCenter[2] = dZ;
 
         // Add valid residues from solvent unit to output topology for this cube
-        int atomOffset = topOut.Natom();
         int currentResNum = topOut.Nres();
-        for (int ires = 0; ires != solventTop.Nres(); ires++) {
-          Residue solventRes = solventTop.Res(ires);
-          solventRes.SetOriginalNum( currentResNum + ires );
+        //for (int ires = 0; ires != solventTop.Nres(); ires++)
+        for (std::vector<int>::const_iterator ires = validSolventResidues.begin();
+                                              ires != validSolventResidues.end(); ++ires)
+        {
+          int atomOffset = topOut.Natom();
+          Residue solventRes = solventTop.Res(*ires);
+          solventRes.SetOriginalNum( currentResNum++ );
           bondedAtoms.clear();
           for (int iat = solventRes.FirstAtom(); iat != solventRes.LastAtom(); iat++)
           {
@@ -408,12 +459,14 @@ const
             // Save solvent bonds
             for (Atom::bond_iterator bat = solventAtom.bondbegin(); bat != solventAtom.bondend(); ++bat) {
               if (*bat > iat) {
-                bondedAtoms.push_back(  iat + atomOffset );
-                bondedAtoms.push_back( *bat + atomOffset );
+                bondedAtoms.push_back(  iat + atomOffset - solventRes.FirstAtom() );
+                bondedAtoms.push_back( *bat + atomOffset - solventRes.FirstAtom() );
               }
             }
             solventAtom.ClearBonds(); // FIXME AddTopAtom should clear
             topOut.AddTopAtom( solventAtom, solventRes );
+            const double* VXYZ = solventFrame.XYZ(iat);
+            frameOut.AddXYZ( VXYZ );
           } // END loop over solvent atoms
           // Add bonds
           for (std::vector<int>::const_iterator it = bondedAtoms.begin(); it != bondedAtoms.end(); ++it) {
@@ -423,7 +476,7 @@ const
           }
         } // END loop over solvent unit residues
         // Append solvent frame
-        frameOut.AppendFrame( solventFrame );
+        //frameOut.AppendFrame( solventFrame );
       } // END loop over Z
     } // END loop over Y
   } // END loop over X
diff --git a/src/Structure/Solvate.h b/src/Structure/Solvate.h
index 56705afd11..4eb8e1559c 100644
--- a/src/Structure/Solvate.h
+++ b/src/Structure/Solvate.h
@@ -27,15 +27,21 @@ class Solvate {
     DataSet_Coords* GetSolventUnit(DataSetList const&) const;
     //std::string const& SolventBoxName() const { return solventBoxName_; }
   private:
-    // Set vdW bounding box
+    /// Set vdW bounding box
     int setVdwBoundingBox(double&, double&, double&, double&, std::vector<double>&,
                           Topology const&, Frame&,
                           Cpptraj::Parm::ParameterSet const&) const;
-    // Find solute atoms within a solvent box at given center
+    /// Find solute atoms within a solvent box at given center
     int findCloseSoluteAtoms(std::vector<int>&, double, int, Frame const&, Vec3 const&, double, double, double) const;
+    /// Determine which solvent residues do not clash with given solute atoms
+    int determineValidSolventResidues(std::vector<int>&, std::vector<int> const&,
+                                      Frame const&, Topology const&, Frame const&,
+                                      std::vector<double> const&, std::vector<double> const&) const;
+
     // Add solvent unit boxes
     int addSolventUnits(int, int, int, double, double, double, double, double, double, double,
-                        Frame&, Topology const&, Frame&, Topology&) const;
+                        Frame&, Topology const&, Frame&, Topology&,
+                        std::vector<double> const&, std::vector<double> const&) const;
 
     int debug_;
     double bufferX_;
@@ -46,6 +52,7 @@ class Solvate {
     bool clip_;
     std::string solventBoxName_;
     static const double ATOM_DEFAULT_RADIUS_; ///< Atom default radius from LEaP
+    static const double CLOSENESSMODIFIER_;   ///< Overlap closeness modifier from LEaP
 };
 }
 }

From f8ffaca7ff682a1e57525b6ccb7b7323252f6264 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 19 Nov 2025 13:46:33 -0500
Subject: [PATCH 1091/1492] Do solvent clipping

---
 src/Structure/Solvate.cpp | 29 ++++++++++++++++++-----------
 src/Structure/Solvate.h   |  5 ++++-
 2 files changed, 22 insertions(+), 12 deletions(-)

diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index 8f8ba04a6b..7a35a3b04e 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -178,7 +178,6 @@ const
 /** Create box, fill with solvent */
 int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::ParameterSet const& set0,
                         DataSet_Coords& SOLVENTBOX)
-const
 {
   // Sanity check
   if (topOut.Natom() != frameOut.Natom()) {
@@ -226,15 +225,17 @@ const
     mprintf("  Total bounding box for atom centers:  %5.3f %5.3f %5.3f\n", 
             dXWidth, dYWidth, dZWidth );
 
-  /*if ( bClip ) {
-        //  If the solvated system should be clipped to the exact
-        //      size the user specified then note the criterion
-        //      & dimensions (for 0,0,0-centered system)
-        iCriteria |= TOOLOUTSIDEOFBOX;
-        cCriteria.dX = 0.5 * dXBox + dXW;
-        cCriteria.dY = 0.5 * dYBox + dYW;
-        cCriteria.dZ = 0.5 * dZBox + dZW;
-    }
+  if (clip_) {
+    //  If the solvated system should be clipped to the exact
+    //      size the user specified then note the criterion
+    //      & dimensions (for 0,0,0-centered system)
+    //iCriteria |= TOOLOUTSIDEOFBOX;
+    clipX_ = 0.5 * boxX + bufferX_;
+    clipY_ = 0.5 * boxY + bufferY_;
+    clipZ_ = 0.5 * boxZ + bufferZ_;
+    printf("cCriteria: %f %f %f\n", clipX_, clipY_, clipZ_);
+  }
+/*
     if ( bOct ) {
         // maybe allow oct clip on integer boxes someday.. but for now:
         if ( !bClip )
@@ -359,8 +360,14 @@ const
     for (int vat = solventRes.FirstAtom(); vat != solventRes.LastAtom(); vat++)
     {
       const double* VXYZ = solventFrame.XYZ(vat);
+      // First check for clipping
+      if (clip_) {
+        if ( fabs(VXYZ[0]) >= clipX_ ) { collision = true; break; }
+        if ( fabs(VXYZ[1]) >= clipY_ ) { collision = true; break; }
+        if ( fabs(VXYZ[2]) >= clipZ_ ) { collision = true; break; }
+      }
       double dR = solventRadii[vat] * closeness_ * CLOSENESSMODIFIER_;
-      // Loop over close solute atoms
+      // Loop over close solute atoms, check fir ckasg
       for (std::vector<int>::const_iterator uat = closeSoluteAtoms.begin(); uat != closeSoluteAtoms.end(); ++uat)
       {
         const double* UXYZ = frameOut.XYZ(*uat);
diff --git a/src/Structure/Solvate.h b/src/Structure/Solvate.h
index 4eb8e1559c..44ead9f918 100644
--- a/src/Structure/Solvate.h
+++ b/src/Structure/Solvate.h
@@ -21,7 +21,7 @@ class Solvate {
     /// Initialize
     int InitSolvate(ArgList&, int);
     /// Solvate with box
-    int SolvateBox(Topology&, Frame&, Cpptraj::Parm::ParameterSet const&, DataSet_Coords&) const;
+    int SolvateBox(Topology&, Frame&, Cpptraj::Parm::ParameterSet const&, DataSet_Coords&);
 
     /// \return Solvent unit selected from given DataSetList
     DataSet_Coords* GetSolventUnit(DataSetList const&) const;
@@ -48,6 +48,9 @@ class Solvate {
     double bufferY_;
     double bufferZ_;
     double closeness_;
+    double clipX_;
+    double clipY_;
+    double clipZ_;
     bool isotropic_;
     bool clip_;
     std::string solventBoxName_;

From aaba467bd82534905649caf435301097fb4835d7 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 19 Nov 2025 14:00:24 -0500
Subject: [PATCH 1092/1492] Dont save the radii if the array is empty

---
 src/Structure/Solvate.cpp | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index 7a35a3b04e..5e30747a9e 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -103,7 +103,6 @@ int Solvate::setVdwBoundingBox(double& boxX, double& boxY, double& boxZ,
 const
 {
   using namespace Cpptraj::Parm;
-  Radii.clear();
   // Set vdw bounding box
   double Xmin = 0;
   double Ymin = 0;
@@ -131,7 +130,7 @@ const
       else
         atom_radius = ATOM_DEFAULT_RADIUS_;
     }
-    Radii.push_back( atom_radius );
+    if (!Radii.empty()) Radii[at] = atom_radius;
     maxR = std::max(maxR, atom_radius);
     //mprintf("DEBUG: Atom %s has_vdw= %i VDW=%f\n", topOut.AtomMaskName(at).c_str(), (int)has_vdw, atom_radius);
 
@@ -191,7 +190,7 @@ int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::Parame
 
   // Set vdw box
   std::vector<double> soluteRadii;
-  soluteRadii.reserve( topOut.Natom() );
+  soluteRadii.resize( topOut.Natom() );
   double boxX, boxY, boxZ, soluteMaxR;
   if (setVdwBoundingBox(boxX, boxY, boxZ, soluteMaxR, soluteRadii, topOut, frameOut, set0)) {
     mprinterr("Error: Setting vdw bounding box for %s failed.\n", topOut.c_str());
@@ -251,7 +250,7 @@ int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::Parame
   double solventX, solventY, solventZ;
   // Set the box even if box info is present so that solvent radii get set
   std::vector<double> solventRadii;
-  solventRadii.reserve( SOLVENTBOX.Top().Natom() );
+  solventRadii.resize( SOLVENTBOX.Top().Natom() );
   double solventMaxR;
   if (setVdwBoundingBox(solventX, solventY, solventZ, solventMaxR, solventRadii, SOLVENTBOX.Top(), solventFrame, set0)) {
     mprinterr("Error: Setting vdw bounding box for %s failed.\n", topOut.c_str());

From 5a223b409c9bf1b564bfb113473a9ca922462079 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 19 Nov 2025 14:18:55 -0500
Subject: [PATCH 1093/1492] Separate out getting radii

---
 src/Structure/Solvate.cpp | 66 ++++++++++++++++++++++++---------------
 src/Structure/Solvate.h   |  7 +++--
 2 files changed, 44 insertions(+), 29 deletions(-)

diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index 5e30747a9e..2c6988f12f 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -95,23 +95,15 @@ DataSet_Coords* Solvate::GetSolventUnit(DataSetList const& DSL) const {
 /** Atom default radius in Angstroms from LEaP */
 const double Solvate::ATOM_DEFAULT_RADIUS_ = 1.5;
 
-/** Set VDW bounding box. */
-int Solvate::setVdwBoundingBox(double& boxX, double& boxY, double& boxZ,
-                               double& maxR, std::vector<double>& Radii,
-                               Topology const& topOut, Frame& frameOut,
-                               Cpptraj::Parm::ParameterSet const& set0)
+/** Get radii for atoms in topology */
+std::vector<double> Solvate::getAtomRadii(double& maxR, Topology const& topOut,
+                                          Cpptraj::Parm::ParameterSet const& set0)
 const
 {
   using namespace Cpptraj::Parm;
-  // Set vdw bounding box
-  double Xmin = 0;
-  double Ymin = 0;
-  double Zmin = 0;
-  double Xmax = 0;
-  double Ymax = 0;
-  double Zmax = 0;
   maxR = 0;
-
+  std::vector<double> Radii;
+  Radii.reserve( topOut.Natom() );
   for (int at = 0; at < topOut.Natom(); at++)
   {
     // Get radius
@@ -130,9 +122,30 @@ const
       else
         atom_radius = ATOM_DEFAULT_RADIUS_;
     }
-    if (!Radii.empty()) Radii[at] = atom_radius;
+    Radii.push_back( atom_radius );
     maxR = std::max(maxR, atom_radius);
-    //mprintf("DEBUG: Atom %s has_vdw= %i VDW=%f\n", topOut.AtomMaskName(at).c_str(), (int)has_vdw, atom_radius);
+  }
+  return Radii;
+}
+
+/** Set VDW bounding box. */
+int Solvate::setVdwBoundingBox(double& boxX, double& boxY, double& boxZ,
+                               std::vector<double> const& Radii,
+                               Frame& frameOut)
+const
+{
+  // Set vdw bounding box
+  double Xmin = 0;
+  double Ymin = 0;
+  double Zmin = 0;
+  double Xmax = 0;
+  double Ymax = 0;
+  double Zmax = 0;
+
+  for (int at = 0; at < frameOut.Natom(); at++)
+  {
+    // Get radius
+    double atom_radius = Radii[at];
 
     const double* XYZ = frameOut.XYZ(at);
     //mprintf("DBG: %12.4f %12.4f %12.4f %12.4f\n", XYZ[0], XYZ[1], XYZ[2], atom_radius);
@@ -189,10 +202,10 @@ int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::Parame
   // TODO principal align
 
   // Set vdw box
-  std::vector<double> soluteRadii;
-  soluteRadii.resize( topOut.Natom() );
-  double boxX, boxY, boxZ, soluteMaxR;
-  if (setVdwBoundingBox(boxX, boxY, boxZ, soluteMaxR, soluteRadii, topOut, frameOut, set0)) {
+  double soluteMaxR;
+  std::vector<double> soluteRadii = getAtomRadii(soluteMaxR, topOut, set0) ;
+  double boxX, boxY, boxZ;
+  if (setVdwBoundingBox(boxX, boxY, boxZ, soluteRadii, frameOut)) {
     mprinterr("Error: Setting vdw bounding box for %s failed.\n", topOut.c_str());
     return 1;
   }
@@ -249,19 +262,20 @@ int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::Parame
   // Set vdw box for solvent
   double solventX, solventY, solventZ;
   // Set the box even if box info is present so that solvent radii get set
-  std::vector<double> solventRadii;
-  solventRadii.resize( SOLVENTBOX.Top().Natom() );
   double solventMaxR;
-  if (setVdwBoundingBox(solventX, solventY, solventZ, solventMaxR, solventRadii, SOLVENTBOX.Top(), solventFrame, set0)) {
-    mprinterr("Error: Setting vdw bounding box for %s failed.\n", topOut.c_str());
-    return 1;
-  }
+  std::vector<double> solventRadii = getAtomRadii(solventMaxR, SOLVENTBOX.Top(), set0);
+
   if (solventFrame.BoxCrd().HasBox()) {
-    // Overwrite VDW box lengths with input box lengths
+    // Use input box lengths
     // TODO check ortho?
     solventX = solventFrame.BoxCrd().Param(Box::X);
     solventY = solventFrame.BoxCrd().Param(Box::Y);
     solventZ = solventFrame.BoxCrd().Param(Box::Z);
+  } else {
+    if (setVdwBoundingBox(solventX, solventY, solventZ, solventRadii, solventFrame)) {
+      mprinterr("Error: Setting vdw bounding box for %s failed.\n", topOut.c_str());
+      return 1;
+    }
   }
   mprintf("  Solvent unit box:                     %5.3f %5.3f %5.3f\n", solventX, solventY, solventZ);
 
diff --git a/src/Structure/Solvate.h b/src/Structure/Solvate.h
index 44ead9f918..7d5511213a 100644
--- a/src/Structure/Solvate.h
+++ b/src/Structure/Solvate.h
@@ -27,10 +27,11 @@ class Solvate {
     DataSet_Coords* GetSolventUnit(DataSetList const&) const;
     //std::string const& SolventBoxName() const { return solventBoxName_; }
   private:
+    /// Get radii for atoms in topology
+    std::vector<double> getAtomRadii(double&, Topology const&,
+                                     Cpptraj::Parm::ParameterSet const&) const;
     /// Set vdW bounding box
-    int setVdwBoundingBox(double&, double&, double&, double&, std::vector<double>&,
-                          Topology const&, Frame&,
-                          Cpptraj::Parm::ParameterSet const&) const;
+    int setVdwBoundingBox(double&, double&, double&, std::vector<double> const&, Frame&) const;
     /// Find solute atoms within a solvent box at given center
     int findCloseSoluteAtoms(std::vector<int>&, double, int, Frame const&, Vec3 const&, double, double, double) const;
     /// Determine which solvent residues do not clash with given solute atoms

From 52c5a4d32aae57b5d4c15b8c774a949ca234ed53 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 19 Nov 2025 14:26:27 -0500
Subject: [PATCH 1094/1492] Determine new boundaries. I need simpler test
 systems.

---
 src/Structure/Solvate.cpp | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index 2c6988f12f..b2b72239af 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -260,11 +260,9 @@ int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::Parame
   SOLVENTBOX.GetFrame(0, solventFrame);
 
   // Set vdw box for solvent
-  double solventX, solventY, solventZ;
-  // Set the box even if box info is present so that solvent radii get set
   double solventMaxR;
   std::vector<double> solventRadii = getAtomRadii(solventMaxR, SOLVENTBOX.Top(), set0);
-
+  double solventX, solventY, solventZ;
   if (solventFrame.BoxCrd().HasBox()) {
     // Use input box lengths
     // TODO check ortho?
@@ -307,6 +305,13 @@ int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::Parame
                   solventFrame, SOLVENTBOX.Top(), frameOut, topOut,
                   soluteRadii, solventRadii);
 
+  // Define the size of the new solvent/solute system
+  soluteRadii = getAtomRadii(soluteMaxR, topOut, set0) ;
+  if (setVdwBoundingBox(boxX, boxY, boxZ, soluteRadii, frameOut)) {
+    mprinterr("Error: Setting vdw bounding box for solute/solvent system failed.\n", topOut.c_str());
+    return 1;
+  }
+
   return 0;
 }
 

From e681c2c5d6ecfdcf8ef50c3a3a735e64a0f1e86c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 19 Nov 2025 20:32:41 -0500
Subject: [PATCH 1095/1492] Add debug info

---
 src/Structure/Solvate.cpp | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index b2b72239af..39b500b7d8 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -380,9 +380,9 @@ const
       const double* VXYZ = solventFrame.XYZ(vat);
       // First check for clipping
       if (clip_) {
-        if ( fabs(VXYZ[0]) >= clipX_ ) { collision = true; break; }
-        if ( fabs(VXYZ[1]) >= clipY_ ) { collision = true; break; }
-        if ( fabs(VXYZ[2]) >= clipZ_ ) { collision = true; break; }
+        if ( fabs(VXYZ[0]) >= clipX_ ) { collision = true; printf("CLIP %12.4f %12.4f %12.4f\n",VXYZ[0],VXYZ[1],VXYZ[2]); break; }
+        if ( fabs(VXYZ[1]) >= clipY_ ) { collision = true; printf("CLIP %12.4f %12.4f %12.4f\n",VXYZ[0],VXYZ[1],VXYZ[2]); break; }
+        if ( fabs(VXYZ[2]) >= clipZ_ ) { collision = true; printf("CLIP %12.4f %12.4f %12.4f\n",VXYZ[0],VXYZ[1],VXYZ[2]); break; }
       }
       double dR = solventRadii[vat] * closeness_ * CLOSENESSMODIFIER_;
       // Loop over close solute atoms, check fir ckasg
@@ -399,6 +399,7 @@ const
 
         if (dist2 < dRadii) {
           collision = true;
+          printf("OVERLAP %12.4f %12.4f %12.4f %12.4f %12.4f\n", VXYZ[0],VXYZ[1],VXYZ[2], dist2, dRadii);
           break;
         }
       } // END loop over close solute atoms

From ce225a0f4e0dc2c33c150b2a9019a565c854a051 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 20 Nov 2025 11:08:04 -0500
Subject: [PATCH 1096/1492] Hide debug info when assigning angle parms

---
 src/Parm/AssignParams.cpp | 25 ++++++++++++++-----------
 1 file changed, 14 insertions(+), 11 deletions(-)

diff --git a/src/Parm/AssignParams.cpp b/src/Parm/AssignParams.cpp
index 13e75dc02a..2b6b0f42eb 100644
--- a/src/Parm/AssignParams.cpp
+++ b/src/Parm/AssignParams.cpp
@@ -138,9 +138,10 @@ const
       if ( topOut[ang->A1()].Element() == Atom::EXTRAPT ||
            topOut[ang->A3()].Element() == Atom::EXTRAPT)
       {
-        mprintf("DEBUG: Skipping angle with extra point: %4i %4i %4i (%2s %2s %2s)\n",
-                ang->A1()+1, ang->A2()+1, ang->A3()+1,
-                *types[0], *types[1], *types[2]);
+        if (debug_ > 0)
+          mprintf("DEBUG: Skipping angle with extra point: %4i %4i %4i (%2s %2s %2s)\n",
+                  ang->A1()+1, ang->A2()+1, ang->A3()+1,
+                  *types[0], *types[1], *types[2]);
         continue;
       }
     }
@@ -149,10 +150,11 @@ const
         topOut[ang->A2()].Element() == Atom::HYDROGEN &&
         topOut[ang->A3()].Element() == Atom::HYDROGEN)
     {
-      mprintf("DEBUG: O-H-H angle. Assuming rigid water, skipping angle: "
-              "%4i %4i %4i (%2s %2s %2s)\n",
-              ang->A1()+1, ang->A2()+1, ang->A3()+1,
-              *types[0], *types[1], *types[2]);
+      if (debug_ > 0)
+        mprintf("DEBUG: O-H-H angle. Assuming rigid water, skipping angle: "
+                "%4i %4i %4i (%2s %2s %2s)\n",
+                ang->A1()+1, ang->A2()+1, ang->A3()+1,
+                *types[0], *types[1], *types[2]);
       continue;
     }
     // Skip water angles
@@ -163,10 +165,11 @@ const
       {
         // H-O-H Angle. If there is an H-H bond assume this is a rigid water model.
         if (topOut[ang->A1()].IsBondedTo( ang->A3() )) {
-          mprintf("DEBUG: H-O-H angle, H-H bond detected. Assuming rigid water, skipping angle: "
-                  "%4i %4i %4i (%2s %2s %2s)\n",
-                  ang->A1()+1, ang->A2()+1, ang->A3()+1,
-                  *types[0], *types[1], *types[2]);
+          if (debug_ > 0)
+            mprintf("DEBUG: H-O-H angle, H-H bond detected. Assuming rigid water, skipping angle: "
+                    "%4i %4i %4i (%2s %2s %2s)\n",
+                    ang->A1()+1, ang->A2()+1, ang->A3()+1,
+                    *types[0], *types[1], *types[2]);
           continue;
         }
       }

From a827b2e810ce34c7d1cfe8ddfd19c5d9b0d4d104 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 20 Nov 2025 11:32:50 -0500
Subject: [PATCH 1097/1492] Add more debug info. Ensure box actually gets set
 up. Print final box/volume/density info

---
 src/Structure/Solvate.cpp | 42 ++++++++++++++++++++++++++++++++-------
 1 file changed, 35 insertions(+), 7 deletions(-)

diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index 39b500b7d8..920f231e4a 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -16,7 +16,7 @@ Solvate::Solvate() :
   bufferX_(0),
   bufferY_(0),
   bufferZ_(0),
-  closeness_(0.8),
+  closeness_(1.0),
   isotropic_(false),
   clip_(true)
 {
@@ -48,7 +48,7 @@ int Solvate::InitSolvate(ArgList& argIn, int debugIn) {
     return 1;
   }
 
-  closeness_ = argIn.getKeyDouble("closeness", 0.8);
+  closeness_ = argIn.getKeyDouble("closeness", 1.0);
 
   return 0;
 }
@@ -181,6 +181,7 @@ const
   Vec3 toCenter( -(Xmin + 0.5 * boxX),
                  -(Ymin + 0.5 * boxY),
                  -(Zmin + 0.5 * boxZ) );
+  mprintf("ToolCenterUnitByRadii translate vector is %f %f %f\n", toCenter[0], toCenter[1], toCenter[2]);
   // Translate to origin
   frameOut.Translate(toCenter);
 
@@ -311,6 +312,30 @@ int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::Parame
     mprinterr("Error: Setting vdw bounding box for solute/solvent system failed.\n", topOut.c_str());
     return 1;
   }
+  // Setup box
+  frameOut.ModifyBox().SetupFromXyzAbg(boxX, boxY, boxZ, 90.0, 90.0, 90.0);
+  frameOut.BoxCrd().PrintInfo();
+  topOut.SetParmBox( frameOut.BoxCrd() );
+  mprintf("  Total vdw box size:%s%5.3f %5.3f %5.3f angstroms.\n", "                   ",
+          frameOut.BoxCrd().Param(Box::X),
+          frameOut.BoxCrd().Param(Box::Y),
+          frameOut.BoxCrd().Param(Box::Z));
+  mprintf("  Volume: %5.3lf A^3\n", frameOut.BoxCrd().CellVolume());
+  // Sum mass
+  double sumMass = 0.0;
+  for (int at = 0; at < topOut.Natom(); at++) {
+    if (topOut[at].HasType()) {
+      Cpptraj::Parm::ParmHolder<AtomType>::const_iterator it = set0.AT().GetParam( TypeNameHolder(topOut[at].Type()) );
+      if (it != set0.AT().end()) {
+        sumMass += it->second.Mass();
+      }
+    }
+  }
+  if (sumMass > 0.0) {
+    mprintf("  Total mass %5.3f amu,  Density %5.3lf g/cc\n", sumMass, sumMass / (frameOut.BoxCrd().CellVolume() * 0.602204));
+  } else {
+    mprintf("Warning: Mass could not be determined, so density unknown (i.e. type of all atoms could not be found)\n");
+  }
 
   return 0;
 }
@@ -322,6 +347,7 @@ int Solvate::findCloseSoluteAtoms(std::vector<int>& closeSoluteAtoms, double sol
 const
 {
   closeSoluteAtoms.clear();
+  mprintf( "Searching for close solute atoms, buffer zone %f solute max %f closeness %f\n", 0.0, soluteMaxR, closeness_);
   // Determine clearance from the box for testing whether
   // a solute atom might contact an atom in the box. Assumes
   // solvent box includes vdw.
@@ -338,6 +364,7 @@ const
   double dYmax = vCenter[1] + dYWidth/2.0 + dTemp;
   double dZmin = vCenter[2] - dZWidth/2.0 - dTemp;
   double dZmax = vCenter[2] + dZWidth/2.0 + dTemp;
+  mprintf("Search clearances %f Min= %f %f %f Max= %f %f %f\n", dTemp, dXmin, dYmin, dZmin, dXmax, dYmax, dZmax);
 
   // Loop over solute atoms
   for (int at = 0; at < firstSolventAtom; at++)
@@ -351,7 +378,7 @@ const
     if ( XYZ[2] > dZmax ) continue;
 
     // all atom.coords inside solvent limit, so add to list
-    //    MESSAGE(( "Found an interesting sphere\n" ));
+    mprintf("Found an interesting sphere %f %f %f\n", XYZ[0], XYZ[1], XYZ[2] );
     closeSoluteAtoms.push_back( at );
   }
   return 0;
@@ -380,9 +407,9 @@ const
       const double* VXYZ = solventFrame.XYZ(vat);
       // First check for clipping
       if (clip_) {
-        if ( fabs(VXYZ[0]) >= clipX_ ) { collision = true; printf("CLIP %12.4f %12.4f %12.4f\n",VXYZ[0],VXYZ[1],VXYZ[2]); break; }
-        if ( fabs(VXYZ[1]) >= clipY_ ) { collision = true; printf("CLIP %12.4f %12.4f %12.4f\n",VXYZ[0],VXYZ[1],VXYZ[2]); break; }
-        if ( fabs(VXYZ[2]) >= clipZ_ ) { collision = true; printf("CLIP %12.4f %12.4f %12.4f\n",VXYZ[0],VXYZ[1],VXYZ[2]); break; }
+        if ( fabs(VXYZ[0]) >= clipX_ ) { collision = true; mprintf("CLIP %12.4f %12.4f %12.4f\n",VXYZ[0],VXYZ[1],VXYZ[2]); break; }
+        if ( fabs(VXYZ[1]) >= clipY_ ) { collision = true; mprintf("CLIP %12.4f %12.4f %12.4f\n",VXYZ[0],VXYZ[1],VXYZ[2]); break; }
+        if ( fabs(VXYZ[2]) >= clipZ_ ) { collision = true; mprintf("CLIP %12.4f %12.4f %12.4f\n",VXYZ[0],VXYZ[1],VXYZ[2]); break; }
       }
       double dR = solventRadii[vat] * closeness_ * CLOSENESSMODIFIER_;
       // Loop over close solute atoms, check fir ckasg
@@ -394,12 +421,13 @@ const
         double dZ = VXYZ[2] - UXYZ[2];
 
         double dist2 = dX*dX + dY*dY + dZ*dZ;
+        mprintf("RADIUS %f\n", soluteRadii[*uat]);
         double dRadii = dR + soluteRadii[*uat];
         dRadii *= dRadii;
 
         if (dist2 < dRadii) {
           collision = true;
-          printf("OVERLAP %12.4f %12.4f %12.4f %12.4f %12.4f\n", VXYZ[0],VXYZ[1],VXYZ[2], dist2, dRadii);
+          mprintf("OVERLAP %12.4f %12.4f %12.4f %12.4f %12.4f\n", VXYZ[0],VXYZ[1],VXYZ[2], dist2, dRadii);
           break;
         }
       } // END loop over close solute atoms

From 01bd2d00a931506d8f17ade5b00d392bd6996606 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 20 Nov 2025 11:33:11 -0500
Subject: [PATCH 1098/1492] Use CoordinateInfo from the frame

---
 src/Exec_Build.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 7eb4ad393b..284be5c74d 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -1133,7 +1133,7 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
   t_assign_.Stop();
 
   // Update coords 
-  if (crdout.CoordsSetup( topOut, CoordinateInfo() )) { // FIXME better coordinate info
+  if (crdout.CoordsSetup( topOut, frameOut.CoordsInfo() )) { // FIXME better coordinate info
     mprinterr("Error: Could not set up output COORDS.\n");
     return CpptrajState::ERR;
   }

From d34c77c9b0002d61a00314d5ef1753f75b99a867 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 20 Nov 2025 11:50:39 -0500
Subject: [PATCH 1099/1492] Add centering to match leap

---
 src/Structure/Solvate.cpp | 17 ++++++++++++++++-
 src/Structure/Solvate.h   |  1 +
 2 files changed, 17 insertions(+), 1 deletion(-)

diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index 920f231e4a..4aa9015794 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -18,7 +18,8 @@ Solvate::Solvate() :
   bufferZ_(0),
   closeness_(1.0),
   isotropic_(false),
-  clip_(true)
+  clip_(true),
+  center_(true)
 {
 }
 
@@ -49,6 +50,7 @@ int Solvate::InitSolvate(ArgList& argIn, int debugIn) {
   }
 
   closeness_ = argIn.getKeyDouble("closeness", 1.0);
+  center_ = !argIn.hasKey("nocenter");
 
   return 0;
 }
@@ -336,6 +338,19 @@ int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::Parame
   } else {
     mprintf("Warning: Mass could not be determined, so density unknown (i.e. type of all atoms could not be found)\n");
   }
+  // Center if needed
+  if (center_) {
+    double dX2 = boxX * 0.5;
+    double dY2 = boxY * 0.5;
+    double dZ2 = boxZ * 0.5;
+    double* xptr = frameOut.xAddress();
+    for (int at = 0; at < frameOut.Natom(); at++, xptr += 3)
+    {
+      xptr[0] += dX2;
+      xptr[1] += dY2;
+      xptr[2] += dZ2;
+    }
+  }
 
   return 0;
 }
diff --git a/src/Structure/Solvate.h b/src/Structure/Solvate.h
index 7d5511213a..93f1e2fa00 100644
--- a/src/Structure/Solvate.h
+++ b/src/Structure/Solvate.h
@@ -54,6 +54,7 @@ class Solvate {
     double clipZ_;
     bool isotropic_;
     bool clip_;
+    bool center_;
     std::string solventBoxName_;
     static const double ATOM_DEFAULT_RADIUS_; ///< Atom default radius from LEaP
     static const double CLOSENESSMODIFIER_;   ///< Overlap closeness modifier from LEaP

From 40ed8948b35af719a76f85ce5b19bc83381f2dbf Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 20 Nov 2025 11:56:50 -0500
Subject: [PATCH 1100/1492] Hide debug info

---
 src/Structure/Solvate.cpp | 30 ++++++++++++++++--------------
 1 file changed, 16 insertions(+), 14 deletions(-)

diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index 4aa9015794..643f34d244 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -173,7 +173,7 @@ const
       if (dZp > Zmax) Zmax = dZp;
     }
   }
-  mprintf("Min= %f %f %f  Max= %f %f %f\n", Xmin, Ymin, Zmin, Xmax, Ymax, Zmax);
+  //mprintf("Min= %f %f %f  Max= %f %f %f\n", Xmin, Ymin, Zmin, Xmax, Ymax, Zmax);
   // Define box
   boxX = Xmax - Xmin;
   boxY = Ymax - Ymin;
@@ -183,7 +183,7 @@ const
   Vec3 toCenter( -(Xmin + 0.5 * boxX),
                  -(Ymin + 0.5 * boxY),
                  -(Zmin + 0.5 * boxZ) );
-  mprintf("ToolCenterUnitByRadii translate vector is %f %f %f\n", toCenter[0], toCenter[1], toCenter[2]);
+  //mprintf("ToolCenterUnitByRadii translate vector is %f %f %f\n", toCenter[0], toCenter[1], toCenter[2]);
   // Translate to origin
   frameOut.Translate(toCenter);
 
@@ -248,7 +248,7 @@ int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::Parame
     clipX_ = 0.5 * boxX + bufferX_;
     clipY_ = 0.5 * boxY + bufferY_;
     clipZ_ = 0.5 * boxZ + bufferZ_;
-    printf("cCriteria: %f %f %f\n", clipX_, clipY_, clipZ_);
+    //mprintf("cCriteria: %f %f %f\n", clipX_, clipY_, clipZ_);
   }
 /*
     if ( bOct ) {
@@ -362,7 +362,7 @@ int Solvate::findCloseSoluteAtoms(std::vector<int>& closeSoluteAtoms, double sol
 const
 {
   closeSoluteAtoms.clear();
-  mprintf( "Searching for close solute atoms, buffer zone %f solute max %f closeness %f\n", 0.0, soluteMaxR, closeness_);
+//  mprintf( "Searching for close solute atoms, buffer zone %f solute max %f closeness %f\n", 0.0, soluteMaxR, closeness_);
   // Determine clearance from the box for testing whether
   // a solute atom might contact an atom in the box. Assumes
   // solvent box includes vdw.
@@ -379,7 +379,7 @@ const
   double dYmax = vCenter[1] + dYWidth/2.0 + dTemp;
   double dZmin = vCenter[2] - dZWidth/2.0 - dTemp;
   double dZmax = vCenter[2] + dZWidth/2.0 + dTemp;
-  mprintf("Search clearances %f Min= %f %f %f Max= %f %f %f\n", dTemp, dXmin, dYmin, dZmin, dXmax, dYmax, dZmax);
+//  mprintf("Search clearances %f Min= %f %f %f Max= %f %f %f\n", dTemp, dXmin, dYmin, dZmin, dXmax, dYmax, dZmax);
 
   // Loop over solute atoms
   for (int at = 0; at < firstSolventAtom; at++)
@@ -393,7 +393,7 @@ const
     if ( XYZ[2] > dZmax ) continue;
 
     // all atom.coords inside solvent limit, so add to list
-    mprintf("Found an interesting sphere %f %f %f\n", XYZ[0], XYZ[1], XYZ[2] );
+//    mprintf("Found an interesting sphere %f %f %f\n", XYZ[0], XYZ[1], XYZ[2] );
     closeSoluteAtoms.push_back( at );
   }
   return 0;
@@ -422,9 +422,12 @@ const
       const double* VXYZ = solventFrame.XYZ(vat);
       // First check for clipping
       if (clip_) {
-        if ( fabs(VXYZ[0]) >= clipX_ ) { collision = true; mprintf("CLIP %12.4f %12.4f %12.4f\n",VXYZ[0],VXYZ[1],VXYZ[2]); break; }
-        if ( fabs(VXYZ[1]) >= clipY_ ) { collision = true; mprintf("CLIP %12.4f %12.4f %12.4f\n",VXYZ[0],VXYZ[1],VXYZ[2]); break; }
-        if ( fabs(VXYZ[2]) >= clipZ_ ) { collision = true; mprintf("CLIP %12.4f %12.4f %12.4f\n",VXYZ[0],VXYZ[1],VXYZ[2]); break; }
+        //if ( fabs(VXYZ[0]) >= clipX_ ) { collision = true; mprintf("CLIP %12.4f %12.4f %12.4f\n",VXYZ[0],VXYZ[1],VXYZ[2]); break; }
+        //if ( fabs(VXYZ[1]) >= clipY_ ) { collision = true; mprintf("CLIP %12.4f %12.4f %12.4f\n",VXYZ[0],VXYZ[1],VXYZ[2]); break; }
+        //if ( fabs(VXYZ[2]) >= clipZ_ ) { collision = true; mprintf("CLIP %12.4f %12.4f %12.4f\n",VXYZ[0],VXYZ[1],VXYZ[2]); break; }
+        if ( fabs(VXYZ[0]) >= clipX_ ) { collision = true; break; }
+        if ( fabs(VXYZ[1]) >= clipY_ ) { collision = true; break; }
+        if ( fabs(VXYZ[2]) >= clipZ_ ) { collision = true; break; }
       }
       double dR = solventRadii[vat] * closeness_ * CLOSENESSMODIFIER_;
       // Loop over close solute atoms, check fir ckasg
@@ -436,13 +439,13 @@ const
         double dZ = VXYZ[2] - UXYZ[2];
 
         double dist2 = dX*dX + dY*dY + dZ*dZ;
-        mprintf("RADIUS %f\n", soluteRadii[*uat]);
+//        mprintf("RADIUS %f\n", soluteRadii[*uat]);
         double dRadii = dR + soluteRadii[*uat];
         dRadii *= dRadii;
 
         if (dist2 < dRadii) {
           collision = true;
-          mprintf("OVERLAP %12.4f %12.4f %12.4f %12.4f %12.4f\n", VXYZ[0],VXYZ[1],VXYZ[2], dist2, dRadii);
+          //mprintf("OVERLAP %12.4f %12.4f %12.4f %12.4f %12.4f\n", VXYZ[0],VXYZ[1],VXYZ[2], dist2, dRadii);
           break;
         }
       } // END loop over close solute atoms
@@ -489,14 +492,13 @@ const
     for ( int iy=0; iy < numY; iy++, dY -= dYSolvent ) {
       double dZ = dZStart;
       for ( int iz=0; iz < numZ; iz++, dZ -= dZSolvent ) {
-        mprintf( "Adding box at: x=%d  y=%d  z=%d\n", ix, iy, iz);
+        //mprintf( "Adding box at: x=%d  y=%d  z=%d\n", ix, iy, iz);
         Vec3 vPos(dX, dY, dZ);
 
         findCloseSoluteAtoms(closeSoluteAtoms, soluteMaxR, firstSolventAtom, frameOut, vPos,
                              dXSolvent, dYSolvent, dZSolvent);
 
-        mprintf( "Center of solvent box is: %lf, %lf, %lf\n",
-                                dX, dY, dZ );
+        //mprintf( "Center of solvent box is: %lf, %lf, %lf\n", dX, dY, dZ );
         Vec3 trans( dX - currentSolventCenter[0],
                     dY - currentSolventCenter[1],
                     dZ - currentSolventCenter[2] );

From 6af9352ef2d97c43ed306489592a851aedf4b508 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 20 Nov 2025 13:31:19 -0500
Subject: [PATCH 1101/1492] Have solvate add the PDB info if needed. When
 writing parm, check if the PDB array sizes are not what is expected since
 this is what Topology internally requires

---
 src/Exec_Build.cpp        |  7 +++----
 src/Parm_Amber.cpp        | 29 +++++------------------------
 src/Structure/Solvate.cpp |  4 ++++
 3 files changed, 12 insertions(+), 28 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 284be5c74d..341ac29cd5 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -744,10 +744,6 @@ const
     }
   }
 
-  // Finalize topology - determine molecules, dont renumber residues, dont assign default bond params
-  topOut.CommonSetup(true, false, false);
-  topOut.Summary();
-
   if (buildFailed) return 1;
   return 0;
 }
@@ -1130,6 +1126,9 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
   topOut.AllocTreeChainClassification( );
   topOut.AllocJoinArray();
   topOut.AllocRotateArray();
+    // Finalize topology - determine molecules, dont renumber residues, dont assign default bond params
+  topOut.CommonSetup(true, false, false);
+  topOut.Summary();
   t_assign_.Stop();
 
   // Update coords 
diff --git a/src/Parm_Amber.cpp b/src/Parm_Amber.cpp
index 1f0fb86a20..158d16daa1 100644
--- a/src/Parm_Amber.cpp
+++ b/src/Parm_Amber.cpp
@@ -1814,14 +1814,10 @@ int Parm_Amber::WriteExtra(Topology const& topOut, int natom) {
   */
 static inline int check_array_size(unsigned int expectedSize, unsigned int actualSize, const char* desc)
 {
-  if (actualSize > expectedSize) {
-    mprinterr("Internal Error: Size of %s (%u) is greater than expected size (%u)\n",
+  if (actualSize != expectedSize) {
+    mprinterr("Internal Error: Size of %s (%u) is != expected size (%u)\n",
               desc, actualSize, expectedSize);
     return 1;
-  } else if (actualSize < expectedSize) {
-    mprintf("Warning: Size of %s (%u) is less than expected size (%u); will fill missing values with blanks.\n",
-              desc, actualSize, expectedSize);
-    return -1;
   }
   return 0;
 }
@@ -2582,44 +2578,29 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
   }
   if (hasOcc) {
     // PDB atomic occupancy
-    int astat = check_array_size(TopOut.Natom(), TopOut.Occupancy().size(), "PDB occupancy array");
-    if (astat == 1) return 1;
+    if (check_array_size(TopOut.Natom(), TopOut.Occupancy().size(), "PDB occupancy array")) return 1;
     if (BufferAlloc(F_PDB_OCC, TopOut.Natom())) return 1;
     for (std::vector<float>::const_iterator it = TopOut.Occupancy().begin();
                                             it != TopOut.Occupancy().end(); ++it)
       file_.DblToBuffer( *it );
-    if (astat == -1) {
-      for (unsigned int idx = TopOut.Occupancy().size(); idx < (unsigned int)TopOut.Natom(); idx++)
-        file_.DblToBuffer( 1 );
-    }
     file_.FlushBuffer();
   }
   if (hasBfac) {
     // PDB atomic B-factors
-    int astat = check_array_size(TopOut.Natom(), TopOut.Bfactor().size(), "PDB B-factor array");
-    if (astat == 1) return 1;
+    if (check_array_size(TopOut.Natom(), TopOut.Bfactor().size(), "PDB B-factor array")) return 1;
     if (BufferAlloc(F_PDB_BFAC, TopOut.Natom())) return 1;
     for (std::vector<float>::const_iterator it = TopOut.Bfactor().begin();
                                             it != TopOut.Bfactor().end(); ++it)
       file_.DblToBuffer( *it );
-    if (astat == -1) {
-      for (unsigned int idx = TopOut.Bfactor().size(); idx < (unsigned int)TopOut.Natom(); idx++)
-        file_.DblToBuffer( 0 );
-    }
     file_.FlushBuffer();
   }
   if (hasNum) {
     // PDB original serial numbers
-    int astat = check_array_size(TopOut.Natom(), TopOut.PdbSerialNum().size(), "PDB serial number array");
-    if (astat == 1) return 1;
+    if (check_array_size(TopOut.Natom(), TopOut.PdbSerialNum().size(), "PDB serial number array")) return 1;
     if (BufferAlloc(F_PDB_NUM, TopOut.Natom())) return 1;
     for (std::vector<int>::const_iterator it = TopOut.PdbSerialNum().begin();
                                           it != TopOut.PdbSerialNum().end(); ++it)
       file_.IntToBuffer( *it );
-    if (astat == -1) {
-      for (unsigned int idx = TopOut.PdbSerialNum().size(); idx < (unsigned int)TopOut.Natom(); idx++)
-        file_.IntToBuffer( (int)idx+1 );
-    }
     file_.FlushBuffer();
   }
 
diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index 643f34d244..36ee3a70d9 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -536,6 +536,10 @@ const
             }
             solventAtom.ClearBonds(); // FIXME AddTopAtom should clear
             topOut.AddTopAtom( solventAtom, solventRes );
+            // Add PDB info if the topology already has it.
+            if (!topOut.Bfactor().empty()) topOut.AddBfactor( 0 );
+            if (!topOut.Occupancy().empty()) topOut.AddOccupancy( 1 );
+            if (!topOut.PdbSerialNum().empty()) topOut.AddPdbSerialNum( topOut.Natom() );
             const double* VXYZ = solventFrame.XYZ(iat);
             frameOut.AddXYZ( VXYZ );
           } // END loop over solvent atoms

From d3f0edcf35f3874c6d20700a6f60356d8b67f23c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 20 Nov 2025 14:56:38 -0500
Subject: [PATCH 1102/1492] Add timer for solvent

---
 src/Exec_Build.cpp | 4 ++++
 src/Exec_Build.h   | 1 +
 2 files changed, 5 insertions(+)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 341ac29cd5..19e926bd6d 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -1094,6 +1094,7 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
   }
 
   if (add_solvent) {
+    t_solvate_.Start();
     // Get solvent unit box
     DataSet_Coords* solventUnitBox = solvator.GetSolventUnit( DSL );
     if (solventUnitBox == 0) {
@@ -1104,6 +1105,7 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
       mprinterr("Error: Adding solvent failed.\n");
       return CpptrajState::ERR;
     }
+    t_solvate_.Stop();
   }
 
   // Assign parameters. This will create the bond/angle/dihedral/improper
@@ -1238,6 +1240,8 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
   t_disulfide_.WriteTiming    (2, "Disulfide detection :", t_total_.Total());
   t_sugar_.WriteTiming        (2, "Sugar preparation   :", t_total_.Total());
   t_fill_.WriteTiming         (2, "Fill missing atoms  :", t_total_.Total());
+  if (add_solvent)
+    t_solvate_.WriteTiming    (2, "Solvate             :", t_total_.Total());
   t_check_.WriteTiming        (2, "Structure check     :", t_total_.Total());
   t_assign_.WriteTiming       (2, "Param./Top. gen.    :", t_total_.Total());
   AP.WriteAssignTiming(3, t_assign_.Total());
diff --git a/src/Exec_Build.h b/src/Exec_Build.h
index 62b1d73626..7b3802f95c 100644
--- a/src/Exec_Build.h
+++ b/src/Exec_Build.h
@@ -60,5 +60,6 @@ class Exec_Build : public Exec {
     Timer t_fill_;
     Timer t_assign_;
     Timer t_check_;
+    Timer t_solvate_;
 };
 #endif

From 075b6598fe1b7ee40ca49d30caed43a01acfff9f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 20 Nov 2025 14:57:53 -0500
Subject: [PATCH 1103/1492] Hack to get cpptraj to spit out solvent bonds in
 same order as leap (leap does backwards for PDB, forwards for mol2/lib?)

---
 src/Structure/GenerateConnectivityArrays.cpp | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/src/Structure/GenerateConnectivityArrays.cpp b/src/Structure/GenerateConnectivityArrays.cpp
index 96a1a8ac06..bc51122083 100644
--- a/src/Structure/GenerateConnectivityArrays.cpp
+++ b/src/Structure/GenerateConnectivityArrays.cpp
@@ -56,7 +56,13 @@ BondArray Cpptraj::Structure::GenerateBondArray(std::vector<Residue> const& resi
   for (std::vector<Residue>::const_iterator res = residues.begin(); res != residues.end(); ++res)
   {
     int start, end, offset;
-    set_indices(start, end, offset, res->FirstAtom(), res->LastAtom());
+     // FIXME - this is a hack to get cpptraj to spit out solvent bonds the same way leap does. Leap lib/mol2 files get forwards direction.
+    if (res->NameIsSolvent()) {
+      start = res->FirstAtom();
+      end = res->LastAtom();
+      offset = 1;
+    } else
+      set_indices(start, end, offset, res->FirstAtom(), res->LastAtom());
     for (int iat = start; iat != end; iat += offset)
     //for (int iat = res->LastAtom()-1; iat >= res->FirstAtom(); iat--)
     {

From c03a4e0ca1cffe07da5c90b296c28e9e025a770c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 21 Nov 2025 10:13:20 -0500
Subject: [PATCH 1104/1492] Replicate leaps behavior for bond ordering in
 solvent. It is legitimately mystifying how leap's Loop functions work
 sometimes...

---
 src/Structure/GenerateConnectivityArrays.cpp | 33 +++++++++++++-------
 1 file changed, 22 insertions(+), 11 deletions(-)

diff --git a/src/Structure/GenerateConnectivityArrays.cpp b/src/Structure/GenerateConnectivityArrays.cpp
index bc51122083..1ba94684b7 100644
--- a/src/Structure/GenerateConnectivityArrays.cpp
+++ b/src/Structure/GenerateConnectivityArrays.cpp
@@ -61,20 +61,31 @@ BondArray Cpptraj::Structure::GenerateBondArray(std::vector<Residue> const& resi
       start = res->FirstAtom();
       end = res->LastAtom();
       offset = 1;
-    } else
+      for (int iat = start; iat != end; iat += offset)
+      {
+        Atom const& At = atoms[iat];
+        for (Atom::bond_iterator bat = At.bondbegin(); bat != At.bondend(); ++bat)
+        {
+          if (iat < *bat) {
+            out.push_back( BondType(*bat, iat, -1) );
+          }
+        }
+      }
+    } else {
       set_indices(start, end, offset, res->FirstAtom(), res->LastAtom());
-    for (int iat = start; iat != end; iat += offset)
-    //for (int iat = res->LastAtom()-1; iat >= res->FirstAtom(); iat--)
-    {
-      Atom const& At = atoms[iat];
-      for (Atom::bond_iterator bat = At.bondbegin(); bat != At.bondend(); ++bat)
+      for (int iat = start; iat != end; iat += offset)
+      //for (int iat = res->LastAtom()-1; iat >= res->FirstAtom(); iat--)
       {
-        if (iat < *bat) {
-          //mprintf("DEBUG: BOND  i= %i  %i - %i (%i %i)\n",  bidx++, iat+1, *bat+1, iat*3, *bat*3);
-          out.push_back( BondType(iat, *bat, -1) );
+        Atom const& At = atoms[iat];
+        for (Atom::bond_iterator bat = At.bondbegin(); bat != At.bondend(); ++bat)
+        {
+          if (iat < *bat) {
+            //mprintf("DEBUG: BOND  i= %i  %i - %i (%i %i)\n",  bidx++, iat+1, *bat+1, iat*3, *bat*3);
+            out.push_back( BondType(iat, *bat, -1) );
+          }
+          //else
+          //  mprintf("DEBUG: X    i= %i  %i - %i (%i %i)\n",   bidx++, iat+1, *bat+1, iat*3, *bat*3);
         }
-        //else
-        //  mprintf("DEBUG: X    i= %i  %i - %i (%i %i)\n",   bidx++, iat+1, *bat+1, iat*3, *bat*3);
       }
     }
   }

From 888f9c8473d36881c4677dff199c3eb1a8213f2a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 21 Nov 2025 21:42:20 -0500
Subject: [PATCH 1105/1492] Add note about leap check default cut

---
 src/Exec_Build.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 19e926bd6d..711691c6a0 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -1150,7 +1150,7 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
                           debug_, // debug
                           "*", // mask 1
                           "", // mask 2
-                          0.8, // nonbond cut
+                          0.8, // nonbond cut. NOTE: leap check cut is 1.5
                           1.15, // bond long offset
                           0.5, // bond short offset
                           -1, // pairlist cut (-1 for heuristic)

From d6b05a522c1e7c823478797195049d97c19ef1b2 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Mon, 24 Nov 2025 13:43:27 -0500
Subject: [PATCH 1106/1492] Make default mass for Atom constructor 0; this
 should fix extra point detection in Amber lib files

---
 src/Atom.cpp | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/Atom.cpp b/src/Atom.cpp
index fa22b42d1b..8dae83194a 100644
--- a/src/Atom.cpp
+++ b/src/Atom.cpp
@@ -102,14 +102,14 @@ const double Atom::PaulingElectroNeg_[NUMELEMENTS_] = { -1.0,
 };
 
 // CONSTRUCTOR
-Atom::Atom() : charge_(0.0), polar_(0.0), mass_(1.0), gb_radius_(0.0),
+Atom::Atom() : charge_(0.0), polar_(0.0), mass_(0.0), gb_radius_(0.0),
                gb_screen_(0.0), aname_(""), atype_(""), atype_index_(0),
                element_(UNKNOWN_ELEMENT), resnum_(0), mol_(0)
 {}
 
 /** If no 2 char element name provided, try to guess from name. */ 
 Atom::Atom(NameType const& aname, const char* elt) :
-  charge_(0.0), polar_(0.0), mass_(1.0), gb_radius_(0.0), gb_screen_(0.0),
+  charge_(0.0), polar_(0.0), mass_(0.0), gb_radius_(0.0), gb_screen_(0.0),
   aname_(aname), atype_(""), atype_index_(0), element_(UNKNOWN_ELEMENT),
   resnum_(0), mol_(0)
 {
@@ -122,7 +122,7 @@ Atom::Atom(NameType const& aname, const char* elt) :
 
 /** Attempt to guess element from atom name. */ 
 Atom::Atom( NameType const& aname, NameType const& atype, double q ) :
-  charge_(q), polar_(0.0), mass_(1.0), gb_radius_(0.0), gb_screen_(0.0),
+  charge_(q), polar_(0.0), mass_(0.0), gb_radius_(0.0), gb_screen_(0.0),
   aname_(aname), atype_(atype), atype_index_(0), element_(UNKNOWN_ELEMENT),
   resnum_(0), mol_(0)
 {
@@ -132,7 +132,7 @@ Atom::Atom( NameType const& aname, NameType const& atype, double q ) :
 
 /** Set type and type index. Attempt to guess element from atom name. */
 Atom::Atom( NameType const& aname, NameType const& atype, int atidx ) :
-  charge_(0.0), polar_(0.0), mass_(1.0), gb_radius_(0.0), gb_screen_(0.0),
+  charge_(0.0), polar_(0.0), mass_(0.0), gb_radius_(0.0), gb_screen_(0.0),
   aname_(aname), atype_(atype), atype_index_(atidx), element_(UNKNOWN_ELEMENT),
   resnum_(0), mol_(0)
 {

From a99734fd32ae64da17c9acbb485e3b56e1407b73 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Mon, 24 Nov 2025 14:03:03 -0500
Subject: [PATCH 1107/1492] Fix the water bond order kludge for 4 point models

---
 src/Structure/GenerateConnectivityArrays.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/Structure/GenerateConnectivityArrays.cpp b/src/Structure/GenerateConnectivityArrays.cpp
index 1ba94684b7..328ce4ad6f 100644
--- a/src/Structure/GenerateConnectivityArrays.cpp
+++ b/src/Structure/GenerateConnectivityArrays.cpp
@@ -66,8 +66,8 @@ BondArray Cpptraj::Structure::GenerateBondArray(std::vector<Residue> const& resi
         Atom const& At = atoms[iat];
         for (Atom::bond_iterator bat = At.bondbegin(); bat != At.bondend(); ++bat)
         {
-          if (iat < *bat) {
-            out.push_back( BondType(*bat, iat, -1) );
+          if (iat > *bat) {
+            out.push_back( BondType(iat, *bat, -1) );
           }
         }
       }

From 5f4a27af611d68b85a86f631435fc4f4c9e30753 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Mon, 24 Nov 2025 14:32:29 -0500
Subject: [PATCH 1108/1492] Increase exclusion list distance for structure
 check for 3 so that spurious close contacts between water hydrogens and extra
 points are not reported. Need to implement an angle check now.

---
 src/StructureCheck.cpp | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/src/StructureCheck.cpp b/src/StructureCheck.cpp
index 0130103729..a4812260b7 100644
--- a/src/StructureCheck.cpp
+++ b/src/StructureCheck.cpp
@@ -196,9 +196,11 @@ int StructureCheck::Setup(Topology const& topIn, Box const& boxIn)
   // Set up exclusion list
   if (checkType_ == PL_1_MASK || checkType_ == NO_PL_1_MASK) {
     mprintf("\tExcluding bond interactions.\n");
-    // Set up atom exclusion list. Distance of 2 since we are not
-    // yet checking angles and dihedrals.
-    if (Excluded_.SetupExcluded(topIn.Atoms(), Mask1_, 2, ex_self_opt, ex_list_opt)) {
+    // Set up atom exclusion list. If just checking bonds we could just use a
+    // distance of 2. However, in order to ignore "close contacts" for water
+    // model hydrogens with extra points, increase to 3.
+    // FIXME check angles since these are now excluded.
+    if (Excluded_.SetupExcluded(topIn.Atoms(), Mask1_, 3, ex_self_opt, ex_list_opt)) {
       mprinterr("Error: StructureCheck: Could not set up excluded atoms list.\n");
       return 1;
     }

From 557c6d996a9fa2bdf432e1c95f84094b7737f35d Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 24 Nov 2025 16:14:14 -0500
Subject: [PATCH 1109/1492] Hide dihedral extra point skip debug info

---
 src/Parm/AssignParams.cpp | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/src/Parm/AssignParams.cpp b/src/Parm/AssignParams.cpp
index 2b6b0f42eb..3142dcdbb3 100644
--- a/src/Parm/AssignParams.cpp
+++ b/src/Parm/AssignParams.cpp
@@ -333,9 +333,10 @@ const
       if ( topOut[dih->A1()].Element() == Atom::EXTRAPT ||
            topOut[dih->A4()].Element() == Atom::EXTRAPT)
       {
-        mprintf("DEBUG: Skipping dihedral with extra point: %4i %4i %4i %4i (%2s %2s %2s %2s)\n",
-                dih->A1()+1, dih->A2()+1, dih->A3()+1, dih->A4()+1,
-                *types[0], *types[1], *types[2], *types[3]);
+        if (debug_ > 1)
+          mprintf("DEBUG: Skipping dihedral with extra point: %4i %4i %4i %4i (%2s %2s %2s %2s)\n",
+                  dih->A1()+1, dih->A2()+1, dih->A3()+1, dih->A4()+1,
+                  *types[0], *types[1], *types[2], *types[3]);
         continue;
       }
     }

From 9b2486f834263e706e7963ad3ba3e8a08163e2cd Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 24 Nov 2025 16:22:10 -0500
Subject: [PATCH 1110/1492] Since the solvation routine by design ensures
 solvent does not clash with solute, just run check on the solute before
 solvation. Hide some more debug info.

---
 src/DataIO_LeapRC.cpp |  2 +-
 src/Exec_Build.cpp    | 11 ++++++++++-
 src/cpptrajdepend     |  2 +-
 3 files changed, 12 insertions(+), 3 deletions(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 6951d6cbb5..7379af73c0 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -457,7 +457,7 @@ const
     if (ds == 0) return 1;
   }
   DataSet_NameMap& namemap = static_cast<DataSet_NameMap&>( *ds );
-//  if (debug_ > 0)
+  if (debug_ > 0)
     mprintf("DEBUG: Name map set: %s\n", namemap.legend());
   int bracketCount = 0;
   // First line should contain the command
diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 711691c6a0..97c24a51c8 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -3,6 +3,7 @@
 #include "CpptrajStdio.h"
 #include "DataSet_Parameters.h" // For casting DataSet_Parameters to ParameterSet
 #include "ParmFile.h"
+#include "StringRoutines.h" // integerToString
 #include "Trajout_Single.h"
 #include "Parm/AssignParams.h"
 #include "Structure/Builder.h"
@@ -1093,8 +1094,12 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
     return CpptrajState::ERR;
   }
 
+  std::string checkMaskString("*");
   if (add_solvent) {
     t_solvate_.Start();
+    // Record initial number of atoms and residues
+    int initial_natom = topOut.Natom();
+    int initial_nres = topOut.Nres();
     // Get solvent unit box
     DataSet_Coords* solventUnitBox = solvator.GetSolventUnit( DSL );
     if (solventUnitBox == 0) {
@@ -1105,6 +1110,10 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
       mprinterr("Error: Adding solvent failed.\n");
       return CpptrajState::ERR;
     }
+    mprintf("\tAdded %i residues.\n", topOut.Nres() - initial_nres);
+    // Since by design the SolvateBox routine ensures solvent does not
+    // clash with solute, just check the solute.
+    checkMaskString.assign( "@1-" + integerToString(initial_natom) );
     t_solvate_.Stop();
   }
 
@@ -1148,7 +1157,7 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
                           true, // check bonds
                           true,  // save problems
                           debug_, // debug
-                          "*", // mask 1
+                          checkMaskString, // mask 1
                           "", // mask 2
                           0.8, // nonbond cut. NOTE: leap check cut is 1.5
                           1.15, // bond long offset
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index c26ea8bf4f..9283b0781c 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -316,7 +316,7 @@ EwaldOptions.o : EwaldOptions.cpp ArgList.h CpptrajStdio.h EwaldOptions.h
 ExclusionArray.o : ExclusionArray.cpp Atom.h AtomMask.h CharMask.h CpptrajStdio.h ExclusionArray.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Unit.h
 Exec_AddMissingRes.o : Exec_AddMissingRes.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h CharMask.h CompactFrameArray.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_AddMissingRes.h Exec_AddMissingRes_Pres.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h ParmFile.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h Trajout_Single.h Unit.h Vec3.h
 Exec_Analyze.o : Exec_Analyze.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Analyze.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_Build.o : Exec_Build.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h ExclusionArray.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PairList.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/Creator.h Structure/Disulfide.h Structure/HisProt.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/RingFinder.h Structure/Solvate.h Structure/StructureEnum.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Build.o : Exec_Build.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h ExclusionArray.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PairList.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/Builder.h Structure/Creator.h Structure/Disulfide.h Structure/HisProt.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/RingFinder.h Structure/Solvate.h Structure/StructureEnum.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Calc.o : Exec_Calc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Calc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_CatCrd.o : Exec_CatCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CatCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_Change.o : Exec_Change.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Change.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h

From e4c1bb109ca2cdddd5d8e514539178183311fc21 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 1 Dec 2025 16:04:49 -0500
Subject: [PATCH 1111/1492] Recognize tab as whitespace in amber param file

---
 src/AmberParamFile.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 45d48b9f3c..03f8ef7c00 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -33,7 +33,7 @@ int AmberParamFile::read_symbols(const char* ptrIn, std::vector<std::string>& sy
     if (*ptr == '-') {
       isymbol++;
       char_has_been_read = false;
-    } else if (*ptr == ' ' && isymbol + 1 == nsymbols && char_has_been_read) {
+    } else if ((*ptr == ' ' || *ptr == '\t') && isymbol + 1 == nsymbols && char_has_been_read) {
       return (ptr - ptrIn);
     } else {
       symbols[isymbol] += *ptr;

From 8650c22679590233a1e6f7f56d2349122aab48a3 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 2 Dec 2025 12:24:09 -0500
Subject: [PATCH 1112/1492] Report duplicate parameters and error adding
 parameters when reading amber FF file

---
 src/AmberParamFile.cpp | 78 +++++++++++++++++++++++++++++++++---------
 1 file changed, 61 insertions(+), 17 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 03f8ef7c00..62641c8e73 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -67,6 +67,38 @@ class AmberParamFile::OffdiagNB {
     LJparmType LJ2_;
 };
 
+/// Check return status from adding a parameter and report
+static inline int checkParmRet(Cpptraj::Parm::ParameterSet const& prm, TypeNameHolder const& types, Cpptraj::Parm::RetType const& ret, std::string const& desc, double PN) {
+  if (ret == Cpptraj::Parm::ADDED)
+    return 0;
+
+  std::string OUT(desc);
+  switch (types.Size()) {
+    case 1 : OUT.append(" type " + types[0].Truncated()); break;
+    case 2 : OUT.append(" type " + types[0].Truncated() + " - " + types[1].Truncated()); break;
+    case 3 : OUT.append(" type " + types[0].Truncated() + " - " + types[1].Truncated() + " - " + types[2].Truncated()); break;
+    case 4 :
+      OUT.append(" type " + types[0].Truncated() + " - " + types[1].Truncated() + " - " + types[2].Truncated() + " - " + types[3].Truncated());
+      if (desc[0] == 'd')
+        OUT.append(" (PN=" + doubleToString(PN) + ")" );
+      break;
+  }
+
+  if (ret == Cpptraj::Parm::SAME)
+    mprintf("Warning: Duplicated %s\n", OUT.c_str());
+  else if (ret == Cpptraj::Parm::UPDATED)
+    mprintf("Warning: Redefining %s\n", OUT.c_str());
+  else if (ret == Cpptraj::Parm::ERR) {
+    mprinterr("Error: Reading %s\n", OUT.c_str());
+    return 1;
+  }
+  return 0;
+} 
+
+static inline int checkParmRet(Cpptraj::Parm::ParameterSet const& prm, TypeNameHolder const& types, Cpptraj::Parm::RetType const& ret, std::string const& desc) {
+  return checkParmRet(prm, types, ret, desc, 0);
+}
+
 /** Read input for atom symbols and masses. */
 int AmberParamFile::read_atype(ParameterSet& prm, const char* ptr)
 const
@@ -77,22 +109,24 @@ const
   double amass = 0;
   double atpol = 0;
   int nscan = sscanf(ptr, "%s %lf %lf", kndsym, &amass, &atpol);
+  TypeNameHolder types(kndsym);
   Cpptraj::Parm::RetType ret;
   if (nscan == 3) {
-    ret = prm.AT().AddParm( TypeNameHolder(kndsym),
+    ret = prm.AT().AddParm( types,
                             AtomType(amass, atpol),
                             true );
   } else if (nscan == 2) {
     // Only mass
-    ret = prm.AT().AddParm( TypeNameHolder(kndsym),
+    ret = prm.AT().AddParm( types,
                             AtomType(amass),
                             true );
   } else {
     mprinterr("Error: Expected atom type, mass, polarizability, got only %i columns.\n", nscan);
     return 1;
   }
-  if (ret == Cpptraj::Parm::UPDATED)
-    mprintf("Warning: Redefining atom type %s\n", kndsym);
+  checkParmRet( prm, types, ret, "atom" );
+  //if (ret == Cpptraj::Parm::UPDATED)
+  //  mprintf("Warning: Redefining atom type %s\n", kndsym);
   return 0;
 }
 
@@ -121,8 +155,9 @@ const
   types.AddName( symbols[0] );
   types.AddName( symbols[1] );
   Cpptraj::Parm::RetType ret = prm.BP().AddParm(types, BondParmType(RK, REQ), true);
-  if (ret == Cpptraj::Parm::UPDATED)
-    mprintf("Warning: Redefining bond type %s - %s\n", *(types[0]), *(types[1]));
+  checkParmRet( prm, types, ret, "bond" );
+  //if (ret == Cpptraj::Parm::UPDATED)
+  //  mprintf("Warning: Redefining bond type %s - %s\n", *(types[0]), *(types[1]));
 
   return 0;
 }
@@ -153,8 +188,9 @@ const
   types.AddName( symbols[1] );
   types.AddName( symbols[2] );
   Cpptraj::Parm::RetType ret = prm.AP().AddParm(types, AngleParmType(TK, TEQ*Constants::DEGRAD), true);
-  if (ret == Cpptraj::Parm::UPDATED)
-    mprintf("Warning: Redefining angle type %s - %s - %s\n", *(types[0]), *(types[1]), *(types[2]));
+  checkParmRet( prm, types, ret, "angle" );
+  //if (ret == Cpptraj::Parm::UPDATED)
+  //  mprintf("Warning: Redefining angle type %s - %s - %s\n", *(types[0]), *(types[1]), *(types[2]));
 
   return 0;
 }
@@ -230,11 +266,12 @@ const
   types.AddName( symbols[3] );
   Cpptraj::Parm::RetType ret =
     prm.DP().AddParm(types, DihedralParmType(PK / (double)IDIVF, PN, PHASE*Constants::DEGRAD, scee, scnb), true);
-  if (ret == Cpptraj::Parm::UPDATED) {
-    mprintf("Warning: Redefining dihedral type %s - %s - %s - %s (PN=%g)\n",
-            *(types[0]), *(types[1]), *(types[2]), *(types[3]), PN);
+  checkParmRet( prm, types, ret, "dihedral", PN );
+  //if (ret == Cpptraj::Parm::UPDATED) {
+  //  mprintf("Warning: Redefining dihedral type %s - %s - %s - %s (PN=%g)\n",
+  //          *(types[0]), *(types[1]), *(types[2]), *(types[3]), PN);
     //mprintf("DEBUG: %s\n", ptr);
-  }
+  //}
   last_symbols = symbols;
   return 0;
 }
@@ -273,9 +310,10 @@ const
   //types.SortImproperByAlpha("X"); // FIXME wildcard should be a static var
   Cpptraj::Parm::RetType ret =
     prm.IP().AddParm(types, DihedralParmType(PK, PN, PHASE*Constants::DEGRAD), true);
-  if (ret == Cpptraj::Parm::UPDATED)
-    mprintf("Warning: Redefining improper type %s - %s - %s - %s\n",
-            *(types[0]), *(types[1]), *(types[2]), *(types[3]));
+  checkParmRet( prm, types, ret, "improper" );
+  //if (ret == Cpptraj::Parm::UPDATED)
+  //  mprintf("Warning: Redefining improper type %s - %s - %s - %s\n",
+  //          *(types[0]), *(types[1]), *(types[2]), *(types[3]));
 
   return 0;
 }
@@ -305,8 +343,9 @@ const
   types.AddName( KT1 );
   types.AddName( KT2 );
   Cpptraj::Parm::RetType ret = prm.HB().AddParm(types, HB_ParmType(A, B, HCUT), true);
-  if (ret == Cpptraj::Parm::UPDATED)
-    mprintf("Warning: Redefining LJ 10-12 hbond type %s %s\n", *(types[0]), *(types[1]));
+  checkParmRet( prm, types, ret, "LJ 10-12 hbond" );
+  //if (ret == Cpptraj::Parm::UPDATED)
+  //  mprintf("Warning: Redefining LJ 10-12 hbond type %s %s\n", *(types[0]), *(types[1]));
   return 0;
 }
 
@@ -338,8 +377,13 @@ const
   double EDEP = convertToDouble( nbargs[2] );
   TypeNameHolder types( nbargs[0] );
   Cpptraj::Parm::RetType ret = nbset.LJ_.AddParm( types, LJparmType(R, EDEP), true );
+  //checkParmRet( prm, types, ret, "LJ 6-12" );
   if (ret == Cpptraj::Parm::UPDATED)
     mprintf("Warning: Redefining LJ 6-12 type %s\n", *(types[0]));
+  else if (ret == Cpptraj::Parm::SAME)
+    mprintf("Warning: Duplicated LJ 6-12 type %s\n", *(types[0]));
+  else if (ret == Cpptraj::Parm::ERR)
+    mprinterr("Error: Adding LJ 6-12 type %s\n", *(types[0]));
   return 0;
 }
 

From 14dc52fd4e72a9a1147c55b267916f9df782339b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 2 Dec 2025 16:33:59 -0500
Subject: [PATCH 1113/1492] Report actual value being overwritten

---
 src/AmberParamFile.cpp | 5 ++++-
 src/Parm/ParmHolder.h  | 4 ++++
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 62641c8e73..0edf4df43d 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -156,8 +156,11 @@ const
   types.AddName( symbols[1] );
   Cpptraj::Parm::RetType ret = prm.BP().AddParm(types, BondParmType(RK, REQ), true);
   checkParmRet( prm, types, ret, "bond" );
-  //if (ret == Cpptraj::Parm::UPDATED)
+  if (ret == Cpptraj::Parm::UPDATED) {
+    BondParmType const& BP = prm.BP().PreviousParm();
+    mprintf("Warning: Previous RK= %f REQ= %f, new RK= %f REQ= %f\n", BP.Rk(), BP.Req(), RK, REQ);
   //  mprintf("Warning: Redefining bond type %s - %s\n", *(types[0]), *(types[1]));
+  }
 
   return 0;
 }
diff --git a/src/Parm/ParmHolder.h b/src/Parm/ParmHolder.h
index d83d47c562..183e7996c9 100644
--- a/src/Parm/ParmHolder.h
+++ b/src/Parm/ParmHolder.h
@@ -21,6 +21,8 @@ template <class T> class ParmHolder {
     size_t size()       const { return bpmap_.size(); }
     /// \return true if no parameters
     bool empty()        const { return bpmap_.empty(); }
+    /// \return Last parameter to be overwritten from AddParm()
+    T const& PreviousParm() const { return previousParm_; }
     /// Set wildcard character
     //void SetWildcard(char wc) { wc_ = NameType(std::string(1, wc)); }
     /// Add (or update if allowed) given parameter to holder.
@@ -43,6 +45,7 @@ template <class T> class ParmHolder {
           //  mprintf(" '%s'", *(*it));
           //mprintf("\n");
           if (allowUpdate) {
+            previousParm_ = it->second;
             it->second = bp;
             return UPDATED;
           } else {
@@ -113,6 +116,7 @@ template <class T> class ParmHolder {
     }
   private:
     Bmap bpmap_;
+    T previousParm_; ///< When parameter is updated, store previous value.
     //NameType wc_; ///< Wildcard character
 };
 } // END namespace Parm

From d4b9f1bd95800469a69d342ff3ed3f8db02a70a2 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 4 Dec 2025 11:53:54 -0500
Subject: [PATCH 1114/1492] Start simplifying the errors/warnings

---
 src/AmberParamFile.cpp | 45 ++++++++++++++++++++++++++++++++++++------
 1 file changed, 39 insertions(+), 6 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 0edf4df43d..b2e3f788b6 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -99,6 +99,26 @@ static inline int checkParmRet(Cpptraj::Parm::ParameterSet const& prm, TypeNameH
   return checkParmRet(prm, types, ret, desc, 0);
 }
 
+/*static inline void printTypes(TypeNameHolder const& types) {
+  switch (types.Size()) {
+    case 1 : mprintf("%s", *(types[0])); break;
+    case 2 : mprintf("%s - %s", *(types[0]), *(types[1])); break;
+    case 3 : mprintf("%s - %s - %s", *(types[0]), *(types[1]), *(types[2])); break;
+    case 4 : mprintf("%s - %s - %s - %s", *(types[0]), *(types[1]), *(types[2]), *(types[3])); break;
+  }
+}*/
+
+static inline std::string typeNameStr(TypeNameHolder const& types, std::string const& desc) {
+  std::string OUT(desc);
+  switch (types.Size()) {
+    case 1 : OUT.append(" type " + types[0].Truncated()); break;
+    case 2 : OUT.append(" type " + types[0].Truncated() + " - " + types[1].Truncated()); break;
+    case 3 : OUT.append(" type " + types[0].Truncated() + " - " + types[1].Truncated() + " - " + types[2].Truncated()); break;
+    case 4 : OUT.append(" type " + types[0].Truncated() + " - " + types[1].Truncated() + " - " + types[2].Truncated() + " - " + types[3].Truncated());
+  }
+  return OUT;
+}
+
 /** Read input for atom symbols and masses. */
 int AmberParamFile::read_atype(ParameterSet& prm, const char* ptr)
 const
@@ -124,7 +144,15 @@ const
     mprinterr("Error: Expected atom type, mass, polarizability, got only %i columns.\n", nscan);
     return 1;
   }
-  checkParmRet( prm, types, ret, "atom" );
+  if (ret == Cpptraj::Parm::SAME)
+    mprintf("Warning: Duplicated %s\n", typeNameStr(types, "atom").c_str());
+  else if (ret == Cpptraj::Parm::UPDATED)
+    mprintf("Warning: Redefining %s\n", typeNameStr(types, "atom").c_str());
+  else if (ret == Cpptraj::Parm::ERR) {
+    mprinterr("Error: Reading %s\n", typeNameStr(types, "atom").c_str());
+    return 1;
+  }
+
   //if (ret == Cpptraj::Parm::UPDATED)
   //  mprintf("Warning: Redefining atom type %s\n", kndsym);
   return 0;
@@ -155,11 +183,16 @@ const
   types.AddName( symbols[0] );
   types.AddName( symbols[1] );
   Cpptraj::Parm::RetType ret = prm.BP().AddParm(types, BondParmType(RK, REQ), true);
-  checkParmRet( prm, types, ret, "bond" );
-  if (ret == Cpptraj::Parm::UPDATED) {
-    BondParmType const& BP = prm.BP().PreviousParm();
-    mprintf("Warning: Previous RK= %f REQ= %f, new RK= %f REQ= %f\n", BP.Rk(), BP.Req(), RK, REQ);
-  //  mprintf("Warning: Redefining bond type %s - %s\n", *(types[0]), *(types[1]));
+
+  if (ret == Cpptraj::Parm::SAME)
+    mprintf("Warning: Duplicated %s\n", typeNameStr(types, "bond").c_str());
+  else if (ret == Cpptraj::Parm::UPDATED)
+    mprintf("Warning: Redefining %s from RK= %g REQ= %g to RK= %g REQ= %g\n",
+            typeNameStr(types, "bond").c_str(),
+            prm.BP().PreviousParm().Rk(), prm.BP().PreviousParm().Req(), RK, REQ);
+  else if (ret == Cpptraj::Parm::ERR) {
+    mprinterr("Error: Reading %s\n", typeNameStr(types, "bond").c_str());
+    return 1;
   }
 
   return 0;

From 4c2f6c22efa4988e423d40086fae2cf54dbf1284 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 4 Dec 2025 11:57:22 -0500
Subject: [PATCH 1115/1492] Better angle warning

---
 src/AmberParamFile.cpp | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index b2e3f788b6..ca6b8a3c3d 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -224,7 +224,16 @@ const
   types.AddName( symbols[1] );
   types.AddName( symbols[2] );
   Cpptraj::Parm::RetType ret = prm.AP().AddParm(types, AngleParmType(TK, TEQ*Constants::DEGRAD), true);
-  checkParmRet( prm, types, ret, "angle" );
+  if (ret == Cpptraj::Parm::SAME)
+    mprintf("Warning: Duplicated %s\n", typeNameStr(types, "angle").c_str());
+  else if (ret == Cpptraj::Parm::UPDATED)
+    mprintf("Warning: Redefining %s from TK= %g TEQ= %g to RK= %g REQ= %g\n",
+             typeNameStr(types, "angle").c_str(),
+             prm.AP().PreviousParm().Tk(), prm.AP().PreviousParm().Teq()*Constants::RADDEG, TK, TEQ);
+  else if (ret == Cpptraj::Parm::ERR) {
+    mprinterr("Error: Reading %s\n", typeNameStr(types, "angle").c_str());
+    return 1;
+  }
   //if (ret == Cpptraj::Parm::UPDATED)
   //  mprintf("Warning: Redefining angle type %s - %s - %s\n", *(types[0]), *(types[1]), *(types[2]));
 

From 48219c7c0cd2502ead45e42f4da39ed6121932df Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 4 Dec 2025 12:20:30 -0500
Subject: [PATCH 1116/1492] Report actual changes in dihedral parameters

---
 src/AmberParamFile.cpp        | 11 ++++++++++-
 src/Parm/DihedralParmHolder.h |  4 ++++
 2 files changed, 14 insertions(+), 1 deletion(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index ca6b8a3c3d..89da4f2c97 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -311,7 +311,16 @@ const
   types.AddName( symbols[3] );
   Cpptraj::Parm::RetType ret =
     prm.DP().AddParm(types, DihedralParmType(PK / (double)IDIVF, PN, PHASE*Constants::DEGRAD, scee, scnb), true);
-  checkParmRet( prm, types, ret, "dihedral", PN );
+  if (ret == Cpptraj::Parm::SAME)
+    mprintf("Warning: Duplicated %s\n", typeNameStr(types, "dihedral").c_str());
+  else if (ret == Cpptraj::Parm::UPDATED) // TODO SCEE/SCNB?
+    mprintf("Warning: Redefining %s (PN=%g) from PK= %g Phase= %g to PK= %g Phase= %g\n",
+             typeNameStr(types, "dihedral").c_str(), PN,
+             prm.DP().PreviousParm().Pk(), prm.DP().PreviousParm().Phase()*Constants::RADDEG, PK/(double)IDIVF, PHASE);
+  else if (ret == Cpptraj::Parm::ERR) {
+    mprinterr("Error: Reading %s\n", typeNameStr(types, "dihedral").c_str());
+    return 1;
+  }
   //if (ret == Cpptraj::Parm::UPDATED) {
   //  mprintf("Warning: Redefining dihedral type %s - %s - %s - %s (PN=%g)\n",
   //          *(types[0]), *(types[1]), *(types[2]), *(types[3]), PN);
diff --git a/src/Parm/DihedralParmHolder.h b/src/Parm/DihedralParmHolder.h
index de257ba1d1..e297f10963 100644
--- a/src/Parm/DihedralParmHolder.h
+++ b/src/Parm/DihedralParmHolder.h
@@ -29,6 +29,8 @@ class DihedralParmHolder {
     size_t size()       const { return bpmap_.size();  }
     /// \return true if no dihedral parameters
     bool empty()        const { return bpmap_.empty(); }
+    /// \return Last parameter to be overwritten from AddParm()
+    DihedralParmType const& PreviousParm() const { return previousParm_; }
     /// Set wildcard character
     void SetWildcard(char wc) { wc_ = NameType(std::string(1, wc)); }
     /// Add (or update) a single dihedral parameter for given atom types.
@@ -81,6 +83,7 @@ class DihedralParmHolder {
             //mprintf("DEBUG: Attempt dihedral update mult (allow=%i): %s %s %s %s pk=%6.2f pn=%3.1f pp=%6.3f (orig pk=%6.2f pn=%3.1f pp=%6.3f )\n",
             //        (int)allowUpdate, *types[0], *types[1], *types[2], *types[3], dp.Pk(), dp.Pn(), dp.Phase(), it1->Pk(), it1->Pn(), it1->Phase());
             if (allowUpdate) {
+              previousParm_ = *it1;
               *it1 = dp;
               return UPDATED;
             } else {
@@ -168,6 +171,7 @@ class DihedralParmHolder {
     NameType wc_; ///< Wildcard character
   private:
     Bmap bpmap_;
+    DihedralParmType previousParm_; ///< When parameter is updated, store previous value.
 };
 } // END namespace Parm
 } // END namespace Cpptraj

From 91ad3b57c84f3e0ef066d2d586e595395870dbd0 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 4 Dec 2025 12:28:41 -0500
Subject: [PATCH 1117/1492] Report impropers

---
 src/AmberParamFile.cpp        | 12 +++++++++++-
 src/Parm/ImproperParmHolder.h |  2 ++
 2 files changed, 13 insertions(+), 1 deletion(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 89da4f2c97..48ea288fda 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -364,7 +364,17 @@ const
   //types.SortImproperByAlpha("X"); // FIXME wildcard should be a static var
   Cpptraj::Parm::RetType ret =
     prm.IP().AddParm(types, DihedralParmType(PK, PN, PHASE*Constants::DEGRAD), true);
-  checkParmRet( prm, types, ret, "improper" );
+  if (ret == Cpptraj::Parm::SAME)
+    mprintf("Warning: Duplicated %s\n", typeNameStr(types, "improper").c_str());
+  else if (ret == Cpptraj::Parm::UPDATED)
+    mprintf("Warning: Redefining %s from PK= %g Phase= %g to PK= %g Phase= %g\n",
+             typeNameStr(types, "improper").c_str(),
+             prm.IP().PreviousParm().Pk(), prm.IP().PreviousParm().Phase()*Constants::RADDEG, PK, PHASE);
+  else if (ret == Cpptraj::Parm::ERR) {
+    mprinterr("Error: Reading %s\n", typeNameStr(types, "improper").c_str());
+    return 1;
+  }
+
   //if (ret == Cpptraj::Parm::UPDATED)
   //  mprintf("Warning: Redefining improper type %s - %s - %s - %s\n",
   //          *(types[0]), *(types[1]), *(types[2]), *(types[3]));
diff --git a/src/Parm/ImproperParmHolder.h b/src/Parm/ImproperParmHolder.h
index 82da63c75e..4d388ba330 100644
--- a/src/Parm/ImproperParmHolder.h
+++ b/src/Parm/ImproperParmHolder.h
@@ -35,6 +35,8 @@ class ImproperParmHolder : private DihedralParmHolder {
     size_t size()              const { return DihedralParmHolder::size();  }
     /// \return True if no parameters
     bool empty()               const { return DihedralParmHolder::empty(); }
+    /// \return Last parameter to be overwritten from AddParm()
+    DihedralParmType const& PreviousParm() const { return DihedralParmHolder::PreviousParm(); }
     /// \return Wildcard
     NameType const& Wildcard() const { return wc_; }
     /// \return True if an exact match is required to find a parameter

From d4b9599b153783c8c07fde95e3e3da4d12165596 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 4 Dec 2025 12:35:00 -0500
Subject: [PATCH 1118/1492] Report differences for atom types

---
 src/AmberParamFile.cpp | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 48ea288fda..06ef68eaff 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -146,9 +146,14 @@ const
   }
   if (ret == Cpptraj::Parm::SAME)
     mprintf("Warning: Duplicated %s\n", typeNameStr(types, "atom").c_str());
-  else if (ret == Cpptraj::Parm::UPDATED)
-    mprintf("Warning: Redefining %s\n", typeNameStr(types, "atom").c_str());
-  else if (ret == Cpptraj::Parm::ERR) {
+  else if (ret == Cpptraj::Parm::UPDATED) {
+    mprintf("Warning: Redefining %s from mass= %g pol= %g to", typeNameStr(types, "atom").c_str(),
+            prm.AT().PreviousParm().Mass(), prm.AT().PreviousParm().Polarizability());
+    if (nscan==3)
+      mprintf(" mass= %g pol= %g\n", amass, atpol);
+    else
+      mprintf(" mass= %g\n", amass);
+  } else if (ret == Cpptraj::Parm::ERR) {
     mprinterr("Error: Reading %s\n", typeNameStr(types, "atom").c_str());
     return 1;
   }

From 30f0e88fdfe8eb51d8b123e31ef2bea3547ad436 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 4 Dec 2025 12:53:25 -0500
Subject: [PATCH 1119/1492] Improve HB param warnings. Remove checkParmRet

---
 src/AmberParamFile.cpp | 46 +++++++++++-------------------------------
 1 file changed, 12 insertions(+), 34 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 06ef68eaff..486f997207 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -67,38 +67,6 @@ class AmberParamFile::OffdiagNB {
     LJparmType LJ2_;
 };
 
-/// Check return status from adding a parameter and report
-static inline int checkParmRet(Cpptraj::Parm::ParameterSet const& prm, TypeNameHolder const& types, Cpptraj::Parm::RetType const& ret, std::string const& desc, double PN) {
-  if (ret == Cpptraj::Parm::ADDED)
-    return 0;
-
-  std::string OUT(desc);
-  switch (types.Size()) {
-    case 1 : OUT.append(" type " + types[0].Truncated()); break;
-    case 2 : OUT.append(" type " + types[0].Truncated() + " - " + types[1].Truncated()); break;
-    case 3 : OUT.append(" type " + types[0].Truncated() + " - " + types[1].Truncated() + " - " + types[2].Truncated()); break;
-    case 4 :
-      OUT.append(" type " + types[0].Truncated() + " - " + types[1].Truncated() + " - " + types[2].Truncated() + " - " + types[3].Truncated());
-      if (desc[0] == 'd')
-        OUT.append(" (PN=" + doubleToString(PN) + ")" );
-      break;
-  }
-
-  if (ret == Cpptraj::Parm::SAME)
-    mprintf("Warning: Duplicated %s\n", OUT.c_str());
-  else if (ret == Cpptraj::Parm::UPDATED)
-    mprintf("Warning: Redefining %s\n", OUT.c_str());
-  else if (ret == Cpptraj::Parm::ERR) {
-    mprinterr("Error: Reading %s\n", OUT.c_str());
-    return 1;
-  }
-  return 0;
-} 
-
-static inline int checkParmRet(Cpptraj::Parm::ParameterSet const& prm, TypeNameHolder const& types, Cpptraj::Parm::RetType const& ret, std::string const& desc) {
-  return checkParmRet(prm, types, ret, desc, 0);
-}
-
 /*static inline void printTypes(TypeNameHolder const& types) {
   switch (types.Size()) {
     case 1 : mprintf("%s", *(types[0])); break;
@@ -412,7 +380,18 @@ const
   types.AddName( KT1 );
   types.AddName( KT2 );
   Cpptraj::Parm::RetType ret = prm.HB().AddParm(types, HB_ParmType(A, B, HCUT), true);
-  checkParmRet( prm, types, ret, "LJ 10-12 hbond" );
+  if (ret == Cpptraj::Parm::SAME)
+    mprintf("Warning: Duplicated %s\n", typeNameStr(types, "LJ 10-12 hbond").c_str());
+  else if (ret == Cpptraj::Parm::UPDATED) {
+    mprintf("Warning: Redefining %s from Asol= %g Bsol= %g Cut= %g to Asol= %g Bsol= %g Cut=%g\n",
+            typeNameStr(types, "LJ 10-12 hbond").c_str(),
+            prm.HB().PreviousParm().Asol(), prm.HB().PreviousParm().Bsol(), prm.HB().PreviousParm().HBcut(),
+            A, B, HCUT);
+  } else if (ret == Cpptraj::Parm::ERR) {
+    mprinterr("Error: Reading %s\n", typeNameStr(types, "LJ 10-12 hbond").c_str());
+    return 1;
+  }
+
   //if (ret == Cpptraj::Parm::UPDATED)
   //  mprintf("Warning: Redefining LJ 10-12 hbond type %s %s\n", *(types[0]), *(types[1]));
   return 0;
@@ -446,7 +425,6 @@ const
   double EDEP = convertToDouble( nbargs[2] );
   TypeNameHolder types( nbargs[0] );
   Cpptraj::Parm::RetType ret = nbset.LJ_.AddParm( types, LJparmType(R, EDEP), true );
-  //checkParmRet( prm, types, ret, "LJ 6-12" );
   if (ret == Cpptraj::Parm::UPDATED)
     mprintf("Warning: Redefining LJ 6-12 type %s\n", *(types[0]));
   else if (ret == Cpptraj::Parm::SAME)

From deff4a227776a7101ff76137e58480aa0cde5553 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 4 Dec 2025 12:57:29 -0500
Subject: [PATCH 1120/1492] Improve LJ warning

---
 src/AmberParamFile.cpp | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 486f997207..1e85917cd8 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -425,10 +425,11 @@ const
   double EDEP = convertToDouble( nbargs[2] );
   TypeNameHolder types( nbargs[0] );
   Cpptraj::Parm::RetType ret = nbset.LJ_.AddParm( types, LJparmType(R, EDEP), true );
-  if (ret == Cpptraj::Parm::UPDATED)
-    mprintf("Warning: Redefining LJ 6-12 type %s\n", *(types[0]));
-  else if (ret == Cpptraj::Parm::SAME)
+  if (ret == Cpptraj::Parm::SAME)
     mprintf("Warning: Duplicated LJ 6-12 type %s\n", *(types[0]));
+  else if (ret == Cpptraj::Parm::UPDATED)
+    mprintf("Warning: Redefining LJ 6-12 type %s from R= %g depth= %g to R= %g depth= %g\n", *(types[0]),
+            nbset.LJ_.PreviousParm().Radius(), nbset.LJ_.PreviousParm().Depth(), R, EDEP);
   else if (ret == Cpptraj::Parm::ERR)
     mprinterr("Error: Adding LJ 6-12 type %s\n", *(types[0]));
   return 0;

From c8cf637cf547f9449ef09cc6e9c6035239edbbc4 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 4 Dec 2025 13:02:12 -0500
Subject: [PATCH 1121/1492] FIx atom type warninh

---
 src/AmberParamFile.cpp | 9 +++------
 1 file changed, 3 insertions(+), 6 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 1e85917cd8..6fcd952bd3 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -115,12 +115,9 @@ const
   if (ret == Cpptraj::Parm::SAME)
     mprintf("Warning: Duplicated %s\n", typeNameStr(types, "atom").c_str());
   else if (ret == Cpptraj::Parm::UPDATED) {
-    mprintf("Warning: Redefining %s from mass= %g pol= %g to", typeNameStr(types, "atom").c_str(),
-            prm.AT().PreviousParm().Mass(), prm.AT().PreviousParm().Polarizability());
-    if (nscan==3)
-      mprintf(" mass= %g pol= %g\n", amass, atpol);
-    else
-      mprintf(" mass= %g\n", amass);
+    mprintf("Warning: Redefining %s from mass= %g pol= %g to mass= %g pol= %g\n",
+             typeNameStr(types, "atom").c_str(),
+             prm.AT().PreviousParm().Mass(), prm.AT().PreviousParm().Polarizability(), amass, atpol);
   } else if (ret == Cpptraj::Parm::ERR) {
     mprinterr("Error: Reading %s\n", typeNameStr(types, "atom").c_str());
     return 1;

From fc063b5ecc829a72a6e03212c16c7bf7dcb5d4a8 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 4 Dec 2025 13:20:25 -0500
Subject: [PATCH 1122/1492] Make missing equivalent atom type a warning instead
 of an error

---
 src/AmberParamFile.cpp | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 6fcd952bd3..d1d0478267 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -880,11 +880,12 @@ int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
       for (; typeName != equivAts->end(); ++typeName) {
         ParmHolder<AtomType>::iterator at1 = prm.AT().GetParam( *typeName );
         if (at1 == prm.AT().end()) {
-          mprinterr("Error: Equivalent atom type '%s' (base '%s') not found.\n", *(*typeName), *(at0->first[0]));
-          return 1;
+          mprintf("Warning: Equivalent atom type '%s' (base type '%s') not found.\n", *(*typeName), *(at0->first[0]));
+          //return 1;
+        } else {
+          if (debug_ > 1) mprintf("DEBUG: Equiv '%s' => '%s'\n", *(at0->first[0]), *(*typeName));
+          at1->second.SetLJ( at0->second.LJ() );
         }
-        if (debug_ > 1) mprintf("DEBUG: Equiv '%s' => '%s'\n", *(at0->first[0]), *(*typeName));
-        at1->second.SetLJ( at0->second.LJ() );
       }
     } // END loop over EquivalentNames
   } // END nonbond parameters

From 276e9d27e13c48d0710764c422d1bfe3ad54b8c3 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Mon, 8 Dec 2025 11:25:09 -0500
Subject: [PATCH 1123/1492] Use ArgList instead of sscanf since it is more
 memory safe. Change error message to warning when multiple NB sets present
 and only using the first.

---
 src/AmberParamFile.cpp | 37 +++++++++++++++++++++----------------
 1 file changed, 21 insertions(+), 16 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index d1d0478267..e3f3adbdc4 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -748,6 +748,7 @@ int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
           // It will either be another set, END, or LJEDIT
           ptr = infile.Line();
           while (*ptr == ' ' && *ptr != '\0') ++ptr;
+          //mprintf("DEBUG: NONBOND First char: %c (%i)\n", *ptr, (int)*ptr);
           std::string nbline(ptr);
           if (nbline == "END") {
             if (debug_ > 0) mprintf("END\n");
@@ -756,6 +757,7 @@ int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
             section = LJEDIT;
             prm.SetHasLJparams( true );
           } // Otherwise assume another nonbond section
+            //else mprintf("DEBUG: Assuming another nonbond section.\n");
         } else {
           if (debug_ > 0) mprintf("SECTION %i change to %i\n", (int)section, (int)section + 1);
           section = (SectionType)((int)section + 1);
@@ -779,23 +781,26 @@ int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
         if (*ptr != '\0') continue;
       } else if (section == NONBOND) {
         prm.SetHasLJparams( true );
+        if (debug_ > 1) mprintf("DEBUG: Begin nonbond section.\n");
         // Special case: first read the line.
         // LABEL , KINDNB
         // FORMAT(A4,6X,A2)
         if (NBsets.empty())
           ptr = infile.Line();
-        char nb_label[MAXSYMLEN], nb_kind[MAXSYMLEN];
-        int nscan = sscanf(ptr, "%s %s", nb_label, nb_kind);
-        if (nscan != 2) {
-          mprinterr("Error: Expected nonbond label, nonbond kind, got %i elements.\n", nscan);
-          return 1;
-        }
-        if (debug_ > 0) mprintf("DEBUG: NB label= %s  NB kind = %s\n", nb_label, nb_kind);
-        if (nb_kind[0] != 'R' || nb_kind[1] != 'E') {
-          mprinterr("Error: Nonbond parameters are not of type 'RE' (Rmin, Epsilon).\n");
-          return 1;
+        ArgList nb_args(ptr);
+        //nb_args.PrintDebug();
+        if (nb_args.Nargs() != 2) {
+          mprintf("Warning: Expected 2 elements, nonbond label and kind, got %i elements: %s\n", nb_args.Nargs(), ptr);
+          section = UNKNOWN;
+        } else {
+          if (debug_ > 0) mprintf("DEBUG: NB label= %s  NB kind = %s\n", nb_args[0].c_str(), nb_args[1].c_str());
+          std::string const& nb_kind = nb_args[1];
+          if (nb_kind[0] != 'R' || nb_kind[1] != 'E') {
+            mprinterr("Error: Nonbond parameters are not of type 'RE' (Rmin, Epsilon).\n");
+            return 1;
+          }
+          NBsets.push_back( NonbondSet( nb_args[0] ) );
         }
-        NBsets.push_back( NonbondSet( std::string(nb_label) ) );
       }
     } else if (section == ATYPE) {
       read_err = read_atype(prm, ptr);
@@ -837,12 +842,12 @@ int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
     if (NBsets.size() > 1 || !nbsetnameIn.empty()) {
       // Choose from multiple nbsets
       if (nbsetnameIn.empty()) {
-        mprinterr("Error: Parm set in file '%s' contains %zu nonbonded parameter sets\n"
-                  "Error:  but no set has been specified.\n", fname.full(), NBsets.size());
-        mprinterr("Error: Need to specify one of");
+        mprintf("Warning: Parm set in file '%s' contains %zu nonbonded parameter sets\n"
+                "Warning:  but no specific set has been specified. First set will be used.\n", fname.full(), NBsets.size());
+        mprintf("Warning: Nonbonded sets:");
         for (NbSetArrayType::const_iterator it = NBsets.begin(); it != NBsets.end(); ++it)
-          mprinterr(" %s", it->name_.c_str());
-        mprinterr("\n");
+          mprintf(" %s", it->name_.c_str());
+        mprintf("\n");
       } else {
         nbsetidx = -1;
         for (NbSetArrayType::const_iterator it = NBsets.begin(); it != NBsets.end(); ++it) {

From 0d983e2304425555cc03866751352106789c5955 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Mon, 8 Dec 2025 11:32:06 -0500
Subject: [PATCH 1124/1492] Add line number to warning

---
 src/AmberParamFile.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index e3f3adbdc4..5ba34727c9 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -790,7 +790,7 @@ int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
         ArgList nb_args(ptr);
         //nb_args.PrintDebug();
         if (nb_args.Nargs() != 2) {
-          mprintf("Warning: Expected 2 elements, nonbond label and kind, got %i elements: %s\n", nb_args.Nargs(), ptr);
+          mprintf("Warning: Line %i: Expected 2 elements, nonbond label and kind, got %i elements: %s\n", infile.LineNumber(), nb_args.Nargs(), ptr);
           section = UNKNOWN;
         } else {
           if (debug_ > 0) mprintf("DEBUG: NB label= %s  NB kind = %s\n", nb_args[0].c_str(), nb_args[1].c_str());

From 9c024ef3ea6083fa656c853e6794dd4a964c8bf4 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Mon, 8 Dec 2025 12:27:45 -0500
Subject: [PATCH 1125/1492] Handle cases where there are multiple hydrophilic
 atom lines

---
 src/AmberParamFile.cpp  | 19 ++++++++++++-------
 src/Parm/ParameterSet.h |  2 ++
 2 files changed, 14 insertions(+), 7 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 5ba34727c9..db8142d0f6 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -765,14 +765,19 @@ int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
       }
       // Special cases
       if (section == HYDROPHILIC) {
-        // Special case: hydrophilic atom types. One line.
+        // Special case: hydrophilic atom types. Could be multiple lines.
         // FORMAT(20(A2,2X))
-        ptr = infile.Line();
-        if (debug_ > 1) mprintf("DEBUG: Hydrophilic: %s\n", ptr);
-        // Take advantage of the fact that we expect whitespace-delimiters
-        ArgList hsymbols( ptr, " " );
-        for (int iarg = 0; iarg != hsymbols.Nargs(); ++iarg)
-          prm.AddHydrophilicAtomType( NameType( hsymbols[iarg] ) );
+        bool read_hydrophilic = true;
+        while (read_hydrophilic) {
+          ptr = infile.Line();
+          if (debug_ > 1) mprintf("DEBUG: Hydrophilic: %s\n", ptr);
+          // Take advantage of the fact that we expect whitespace-delimiters
+          ArgList hsymbols( ptr, " " );
+          for (int iarg = 0; iarg != hsymbols.Nargs(); ++iarg)
+            prm.AddHydrophilicAtomType( NameType( hsymbols[iarg] ) );
+          read_hydrophilic = (hsymbols.Nargs() > 19);
+        }
+        if (debug_ > 0) mprintf("DEBUG: Read %u hydrophilic atom types.\n", prm.NhydrophilicAtomTypes());
         section = (SectionType)((int)section + 1);
         // Look ahead. Older parm files have the hydrophilic section delimited
         // with a newline.
diff --git a/src/Parm/ParameterSet.h b/src/Parm/ParameterSet.h
index 40674e0b71..6d070275dc 100644
--- a/src/Parm/ParameterSet.h
+++ b/src/Parm/ParameterSet.h
@@ -89,6 +89,8 @@ class ParameterSet {
     void SetNbParamName(std::string const&);
     /// \return Size in memory in bytes
     size_t DataSize() const;
+    /// \return Number of hydrophilic atom types
+    unsigned int NhydrophilicAtomTypes() const { return hydrophilicAtomTypes_.size(); }
   private:
     typedef std::vector<NameType> NsetType;
     typedef std::vector<std::string> Sarray;

From 93e6fadb1357aee7342c7b7fad1ca688f6966ce0 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Mon, 8 Dec 2025 12:53:42 -0500
Subject: [PATCH 1126/1492] Add support for reading AC nonbond section

---
 src/AmberParamFile.cpp | 47 ++++++++++++++++++++++++++++++++++++++----
 src/AmberParamFile.h   |  2 ++
 src/ParameterTypes.h   |  4 ++--
 3 files changed, 47 insertions(+), 6 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index db8142d0f6..816598f50c 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -432,6 +432,37 @@ const
   return 0;
 }
 
+/** Read A/C coefficient input for LJ 6-12 nonbond. */
+int AmberParamFile::read_nb_AC(NonbondSet& nbset, const char* ptr)
+const
+{
+  // ***** ONLY IF KINDNB .EQ. 'AC' *****
+  // LTYNB , A , C
+  if (debug_ > 1) mprintf("DEBUG: Nonbond: %s\n", ptr);
+
+  ArgList nbargs( ptr, " " );
+  if (nbargs.Nargs() < 3) {
+    mprinterr("Error: Expected at least TYPE, A, C, got %i elements.\n", nbargs.Nargs());
+    return 1;
+  }
+
+  double A = convertToDouble( nbargs[1] );
+  double C = convertToDouble( nbargs[2] );
+  TypeNameHolder types( nbargs[0] );
+
+  NonbondType nbt(A, C);
+
+  Cpptraj::Parm::RetType ret = nbset.LJ_.AddParm( types, LJparmType(nbt.Radius(), nbt.Depth()), true );
+  if (ret == Cpptraj::Parm::SAME)
+    mprintf("Warning: Duplicated AC LJ 6-12 type %s\n", *(types[0]));
+  else if (ret == Cpptraj::Parm::UPDATED)
+    mprintf("Warning: Redefining AC LJ 6-12 type %s from R= %g depth= %g to R= %g depth= %g\n", *(types[0]),
+            nbset.LJ_.PreviousParm().Radius(), nbset.LJ_.PreviousParm().Depth(), nbt.Radius(), nbt.Depth());
+  else if (ret == Cpptraj::Parm::ERR)
+    mprinterr("Error: Adding AC LJ 6-12 type %s\n", *(types[0]));
+  return 0;
+}
+
 /** Read LJ off-diagonal modifications */
 int AmberParamFile::read_ljedit(Oarray& Offdiag, const char* ptr)
 const
@@ -732,6 +763,7 @@ int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
   std::vector<std::string> last_symbols;
   last_symbols.reserve(4);
   // Read file
+  int readNbType = 0;
   SectionType section = ATYPE;
   ptr = infile.Line();
   while (ptr != 0) {
@@ -800,8 +832,12 @@ int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
         } else {
           if (debug_ > 0) mprintf("DEBUG: NB label= %s  NB kind = %s\n", nb_args[0].c_str(), nb_args[1].c_str());
           std::string const& nb_kind = nb_args[1];
-          if (nb_kind[0] != 'R' || nb_kind[1] != 'E') {
-            mprinterr("Error: Nonbond parameters are not of type 'RE' (Rmin, Epsilon).\n");
+          if (nb_kind[0] == 'R' && nb_kind[1] == 'E')
+            readNbType = 0;
+          else if (nb_kind[0] == 'A' && nb_kind[1] == 'C')
+            readNbType = 1;
+          else {
+            mprinterr("Error: Nonbond parameters are not of type 'RE' (Rmin, Epsilon) or 'AC' (A, C coefficients).\n");
             return 1;
           }
           NBsets.push_back( NonbondSet( nb_args[0] ) );
@@ -829,8 +865,11 @@ int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
       for (int iarg = 0; iarg != equiv_line.Nargs(); iarg++)
         EquivalentNames.back().push_back( equiv_line[iarg] );
     } else if (section == NONBOND) {
-      // ***** ONLY IF KINDNB .EQ. 'RE' *****
-      read_err = read_nb_RE(NBsets.back(), ptr);
+      if (readNbType == 0)
+        // ***** ONLY IF KINDNB .EQ. 'RE' *****
+        read_err = read_nb_RE(NBsets.back(), ptr);
+      else if (readNbType == 1)
+        read_err = read_nb_AC(NBsets.back(), ptr);
     } else if (section == LJEDIT) {
       read_err = read_ljedit(Offdiag, ptr);
     }
diff --git a/src/AmberParamFile.h b/src/AmberParamFile.h
index 01429bd2c8..d2ac4c5216 100644
--- a/src/AmberParamFile.h
+++ b/src/AmberParamFile.h
@@ -49,6 +49,8 @@ class AmberParamFile {
     int read_lj1012(ParameterSet&, const char*) const;
     /// Read LJ 6-12 R/depth line
     int read_nb_RE(NonbondSet&, const char*) const;
+    /// Read LJ 6-12 A/C coefficient line
+    int read_nb_AC(NonbondSet&, const char*) const;
     /// Read LJ 6-12 off-diagonal modifications
     int read_ljedit(Oarray&, const char*) const;
     /// Check for issues in CMAP section
diff --git a/src/ParameterTypes.h b/src/ParameterTypes.h
index d2f0261485..f87e32d61d 100644
--- a/src/ParameterTypes.h
+++ b/src/ParameterTypes.h
@@ -630,8 +630,8 @@ class NonbondType {
         return false;
     }
   private:
-    double A_;
-    double B_;
+    double A_; ///< The coefficient for the r^12 term
+    double B_; ///< The coefficient for the r^6 term
 #   undef tol_
 };
 typedef std::vector<NonbondType> NonbondArray;

From 7fc679c6cce79e6398166bd0a3266826ae94d890 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Mon, 8 Dec 2025 13:53:01 -0500
Subject: [PATCH 1127/1492] Add check for a badly formatted END in nonbond
 section

---
 src/AmberParamFile.cpp | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 816598f50c..2b87496c26 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -865,7 +865,13 @@ int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
       for (int iarg = 0; iarg != equiv_line.Nargs(); iarg++)
         EquivalentNames.back().push_back( equiv_line[iarg] );
     } else if (section == NONBOND) {
-      if (readNbType == 0)
+      /// Check for a badly formatted END
+      if (ptr[0] != '\0' && ptr[1] != '\0' && ptr[2] != '\0' &&
+          ptr[0] == 'E'  && ptr[1] == 'N'  && ptr[2] == 'D')
+      {
+        mprintf("Warning: 'END' encountered before blank line in NONBOND section.\n");
+        section = UNKNOWN;
+      } else if (readNbType == 0)
         // ***** ONLY IF KINDNB .EQ. 'RE' *****
         read_err = read_nb_RE(NBsets.back(), ptr);
       else if (readNbType == 1)

From 37696e5a439c05790fdf9af0a7f9be02207bf3cc Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 10 Dec 2025 10:15:31 -0500
Subject: [PATCH 1128/1492] Add polarization checks

---
 src/AmberParamFile.cpp | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 2b87496c26..c1da0196df 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -96,10 +96,24 @@ const
   char kndsym[MAXSYMLEN];
   double amass = 0;
   double atpol = 0;
+  // FIXME Atom class needs to be redone to make reading in elements easier.
   int nscan = sscanf(ptr, "%s %lf %lf", kndsym, &amass, &atpol);
   TypeNameHolder types(kndsym);
   Cpptraj::Parm::RetType ret;
-  if (nscan == 3) {
+  if (nscan > 3)
+    mprintf("Warning: CPPTRAJ currently only reads atomic symbol, mass, and polarizability.\n"
+            "Warning: Ignoring information after the third column: %s\n", ptr);
+  if (nscan >= 3) {
+    // Mass and polarization. Check polarization.
+    if (atpol < 0.0) {
+      bool pol_is_neg_one = (atpol < -0.99 && atpol > -1.01); // NOTE: To be consistent with LEAP behavior
+      if (!pol_is_neg_one) {
+        mprintf("Warning: %s negative polarization %g - omitting.\n", *(types[0]), atpol);
+        return 0;
+      }
+    } else if (atpol > 15.0) {
+      mprintf("Warning: %s polarization is large (%g).\n", *(types[0]), atpol);
+    }
     ret = prm.AT().AddParm( types,
                             AtomType(amass, atpol),
                             true );

From 37721353b732a82cccf86df4e878364ebe805cfb Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 10 Dec 2025 10:49:45 -0500
Subject: [PATCH 1129/1492] Change LJEDIT line missing elements from error to
 warning to match leap

---
 src/AmberParamFile.cpp | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index c1da0196df..2e52066f72 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -489,8 +489,12 @@ const
   double sig1, eps1, sig2, eps2;
   int nscan = sscanf(ptr, "%s %s %lf %lf %lf %lf", AT1, AT2, &sig1, &eps1, &sig2, &eps2);
   if (nscan != 6) {
-    mprinterr("Error: Expected AT1, AT2, SIG1, EPS1, SIG2, EPS2, got %i elements.\n", nscan);
-    return 1;
+    //mprinterr("Error: Expected AT1, AT2, SIG1, EPS1, SIG2, EPS2, got %i elements.\n", nscan);
+    //return 1;
+    // NOTE: Change to a warning to match LEAP behavior
+    mprintf("Warning: Expected AT1, AT2, SIG1, EPS1, SIG2, EPS2, got %i elements. Skipping.\n", nscan);
+    mprintf("Warning: Incomplete LJEDIT line: %s\n", ptr);
+    return 0;
   }
   Offdiag.push_back( OffdiagNB(AT1, AT2, sig1, eps1, sig2, eps2) );
   return 0;

From 9b9c1551fe1dedb62bb37b97632ddcb889668aab Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 12 Dec 2025 08:21:32 -0500
Subject: [PATCH 1130/1492] For the loadamberparams command, do the amber
 ff/frcmod detection like leap

---
 src/DataIO_LeapRC.cpp | 62 ++++++++++++++++++++++++++++++++++++++-----
 src/DataIO_LeapRC.h   |  1 +
 2 files changed, 57 insertions(+), 6 deletions(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 7379af73c0..ac8d612c59 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -15,6 +15,7 @@
 #include "StringRoutines.h" // ToLower
 #include "Trajout_Single.h"
 #include <cstdlib> //getenv
+#include <cstring> // strncmp
 
 // -----------------------------------------------------------------------------
 // LeapEltHybrid class
@@ -173,6 +174,42 @@ int DataIO_LeapRC::AddPath(std::string const& path) {
   return 0;
 }
 
+/** Detect whether a file is an Amber main FF file or frcmod.
+  * \return 1 if frcmod, 0 if FF, -1 if an error occurred.
+  */
+int DataIO_LeapRC::is_frcmod(std::string const& filename, bool& hasMass, bool& hasNonBond) {
+  hasMass = false;
+  hasNonBond = false;
+  BufferedLine infile;
+  if (infile.OpenFileRead( filename )) {
+    mprinterr("Error: Could not open '%s' to determine if Amber FF/frcmod.\n", filename.c_str());
+    return -1;
+  }
+  int stat = 0;
+  const char* ptr = infile.Line();
+  while (ptr != 0) {
+    if ( strncmp( ptr, "MASS", 4 ) == 0 ) {
+        stat = 1;
+        hasMass = true;
+    } else if ( strncmp( ptr, "BOND", 4 ) == 0 ) {
+      stat = 1;
+    } else if ( strncmp( ptr, "ANGL", 4 ) == 0 ) {
+      stat = 1;
+    } else if ( strncmp( ptr, "DIHE", 4 ) == 0 ) {
+      stat = 1;
+    } else if ( strncmp( ptr, "IMPR", 4 ) == 0 ) {
+      stat = 1;
+    } else if ( strncmp( ptr, "HBON", 4 ) == 0 ) {
+      stat = 1;
+    } else if ( strncmp( ptr, "NONB", 4 ) == 0 ) {
+        stat = 1;
+        hasNonBond = true;
+    }
+    ptr = infile.Line();
+  }
+  return stat;
+}
+
 /** LEaP loadAmberParams command. */
 int DataIO_LeapRC::LoadAmberParams(std::string const& filename, DataSetList& dsl,
                                    std::string const& dsname,
@@ -180,13 +217,22 @@ int DataIO_LeapRC::LoadAmberParams(std::string const& filename, DataSetList& dsl
 const
 {
   DataSet* paramSet = 0;
-  // TODO detect this better
-  ArgList fargs( filename, "." );
-  if (fargs.hasKey("frcmod")) {
+  // Detect whether we have a frcmod file or not. Need to scan entire file.
+  bool hasMass = false;
+  bool hasNonBond = false;
+  std::string full_path = find_path( filename, "parm/" );
+  int stat = is_frcmod( full_path, hasMass, hasNonBond );
+  if (stat == 1) {
+    // Amber frcmod file
     mprintf("\tLoading force field modifications from '%s'\n", filename.c_str());
+    if ( hasMass != hasNonBond ) {
+      mprinterr("Error: Modified force field files must have both MASS and NONBOND entries or neither.\n"
+                "Error: Could not load parameter set from %s.\n", filename.c_str());
+      return 1;
+    }
     DataIO_AmberFrcmod infile;
     infile.SetDebug( debug_ );
-    if (infile.ReadData( find_path(filename, "parm/"), dsl, dsname)) {
+    if (infile.ReadData( full_path, dsl, dsname)) {
       mprinterr("Error: Could not load force field modifications from '%s'\n", filename.c_str());
       return 1;
     }
@@ -195,14 +241,15 @@ const
       return 1;
     }
     paramSet = infile.added_back();
-  } else {
+  } else if (stat == 0) {
+    // Amber FF file
     if (check_already_loaded(paramFiles_, filename)) {
       mprintf("Warning: Force field %s has already been loaded, skipping.\n", filename.c_str());
       return 0;
     } else {
       mprintf("\tLoading force field from '%s'\n", filename.c_str());
       DataIO_AmberFF infile;
-      if (infile.ReadData( find_path(filename, "parm/"), dsl, dsname)) {
+      if (infile.ReadData( full_path, dsl, dsname)) {
         mprinterr("Error: Could not load force field from '%s'\n", filename.c_str());
         return 1;
       }
@@ -213,6 +260,9 @@ const
       }
       paramSet = infile.added_back();
     }
+  } else {
+    mprinterr("Error: loadamberparams failed for '%s'\n", filename.c_str());
+    return 1;
   }
   if (paramSet == 0) {
     mprinterr("Internal Error: DataIO_LeapRC::LoadAmberParams(): Parameter set is null.\n");
diff --git a/src/DataIO_LeapRC.h b/src/DataIO_LeapRC.h
index ec1a267e81..36d0dc5774 100644
--- a/src/DataIO_LeapRC.h
+++ b/src/DataIO_LeapRC.h
@@ -49,6 +49,7 @@ class DataIO_LeapRC : public DataIO {
     typedef std::vector<DataSet*> DSarray;
 
     int AddPath(std::string const&);
+    static int is_frcmod(std::string const&, bool&, bool&);
     int LoadAmberParams(std::string const&, DataSetList&, std::string const&, AtypeEltHybridPairMap const&) const;
     int LoadOFF(std::string const&, DataSetList&, std::string const&, DSarray&) const;
     int LoadAmberPrep(std::string const&, DataSetList&, std::string const&, DSarray&) const;

From b9224902d01bd890ae1e3389c0cae81f034b29bd Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 12 Dec 2025 08:33:41 -0500
Subject: [PATCH 1131/1492] Advance past leading whitespace in lib files

---
 src/DataIO_AmberLib.cpp | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/src/DataIO_AmberLib.cpp b/src/DataIO_AmberLib.cpp
index 2f545b8cd7..308dd0b847 100644
--- a/src/DataIO_AmberLib.cpp
+++ b/src/DataIO_AmberLib.cpp
@@ -258,9 +258,15 @@ const
       readUnit = false;
       break;
     }
-    Line.assign(lineptr);
+    // Advance past any leading whitespace
+    while (*lineptr != 0 && (*lineptr == ' ' || *lineptr == '\t'))
+      ++lineptr;
+    if (*lineptr == 0)
+      Line.clear();
+    else
+      Line.assign(lineptr);
     if (!Line.empty()) {
-      if (debug_ > 2) mprintf("DEBUG: Line: %s\n", Line.c_str());
+      if (debug_ > 2) mprintf("DEBUG: Line: '%s'\n", Line.c_str());
       //ArgList cols( Line, " \t\n" );
       if (Line[0] == '!') {
         // See if we are at another unit

From 0130267fdc6138c006f37d3cf1770deae8b5933c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 12 Dec 2025 08:55:34 -0500
Subject: [PATCH 1132/1492] Split off unit aliasing into its own routine

---
 src/DataIO_LeapRC.cpp | 87 +++++++++++++++++++++++--------------------
 src/DataIO_LeapRC.h   |  1 +
 2 files changed, 48 insertions(+), 40 deletions(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index ac8d612c59..7bf53f88bd 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -835,6 +835,51 @@ int DataIO_LeapRC::ReadData(FileName const& fname, DataSetList& dsl, std::string
   return 0;
 }
 
+/** Copy rhs to lhs */
+int DataIO_LeapRC::unitAlias(std::string const& lhs, std::string const& rhs,
+                             DataSetList& dsl, std::string const& dsname)
+const
+{
+  if (debug_ > 0)
+    mprintf("DEBUG: %s = %s\n", lhs.c_str(), rhs.c_str());
+  // Find the unit to make a copy of
+  DataSet* ds0 = dsl.CheckForSet( MetaData(dsname, rhs) );
+  if (ds0 == 0) {
+    // Its possible the unit in question is loaded by a previous command.
+    ds0 = dsl.GetDataSet( "*[" + rhs + "]" );
+    if (ds0 != 0) {
+      mprintf("Info: Using unit '%s' from previously loaded set '%s'\n",
+              rhs.c_str(), ds0->Meta().Name().c_str());
+    }
+  }
+  if (ds0 == 0) {
+    mprinterr("Error: Could not find unit '%s' to copy to '%s'\n", rhs.c_str(), lhs.c_str());
+    return 1;
+  }
+  DataSet_Coords& crd0 = static_cast<DataSet_Coords&>( *ds0 );
+  // Allocate copy
+  DataSet* ds1 = dsl.AddSet( DataSet::COORDS, MetaData(dsname, lhs) );
+  if (ds1 == 0) {
+    mprinterr("Error: Could not allocate unit '%s' for '%s'\n", lhs.c_str(), rhs.c_str());
+    return 1;
+  }
+  DataSet_Coords& crd1 = static_cast<DataSet_Coords&>( *ds1 );
+  if (crd1.CoordsSetup( crd0.Top(), crd0.CoordsInfo() )) {
+    mprinterr("Error: Could not set up unit '%s' for '%s'\n", lhs.c_str(), rhs.c_str());
+    return 1;
+  }
+  crd1.Allocate( DataSet::SizeArray(1, 1) );
+  // Copy
+  Frame tmpFrm = crd0.AllocateFrame();
+  crd0.GetFrame(0, tmpFrm);
+  crd1.SetCRD(0, tmpFrm );
+  // Copy associated data
+  crd1.CopyAssociatedDataFrom( crd0 );
+  if (debug_ > 0)
+    mprintf("DEBUG: Created unit set %s\n", crd1.legend());
+  return 0;
+}
+
 /** Execute leap source command */
 int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string const& dsname)
 {
@@ -934,46 +979,8 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
         err = LeapSet(line, dsl);
       } else {
         // Unrecognized so far. See if this is a unit alias (interpret as 'alias = unit')
-        if (has_equals) {
-          if (line.Nargs() == 2) {
-            if (debug_ > 0)
-              mprintf("DEBUG: %s = %s\n", line[0].c_str(), line[1].c_str());
-            // Find the unit to make a copy of
-            DataSet* ds0 = dsl.CheckForSet( MetaData(dsname, line[1]) );
-            if (ds0 == 0) {
-              // Its possible the unit in question is loaded by a previous command.
-              ds0 = dsl.GetDataSet( "*[" + line[1] + "]" );
-              if (ds0 != 0) {
-                mprintf("Info: Using unit '%s' from previously loaded set '%s'\n",
-                        line[1].c_str(), ds0->Meta().Name().c_str());
-              }
-            }
-            if (ds0 == 0) {
-              mprinterr("Error: Could not find unit '%s' to copy to '%s'\n", line[1].c_str(), line[0].c_str());
-              return 1;
-            }
-            DataSet_Coords& crd0 = static_cast<DataSet_Coords&>( *ds0 );
-            // Allocate copy
-            DataSet* ds1 = dsl.AddSet( DataSet::COORDS, MetaData(dsname, line[0]) );
-            if (ds1 == 0) {
-              mprinterr("Error: Could not allocate unit '%s' for '%s'\n", line[0].c_str(), line[1].c_str());
-              return 1;
-            }
-            DataSet_Coords& crd1 = static_cast<DataSet_Coords&>( *ds1 );
-            if (crd1.CoordsSetup( crd0.Top(), crd0.CoordsInfo() )) {
-              mprinterr("Error: Could not set up unit '%s' for '%s'\n", line[0].c_str(), line[1].c_str());
-              return 1;
-            }
-            crd1.Allocate( DataSet::SizeArray(1, 1) );
-            // Copy
-            Frame tmpFrm = crd0.AllocateFrame();
-            crd0.GetFrame(0, tmpFrm);
-            crd1.SetCRD(0, tmpFrm );
-            // Copy associated data
-            crd1.CopyAssociatedDataFrom( crd0 );
-            if (debug_ > 0)
-              mprintf("DEBUG: Created unit set %s\n", crd1.legend());
-          }
+        if (has_equals && line.Nargs() == 2) {
+          err = unitAlias( line[0], line[1], dsl, dsname );
         } else {
           mprintf("Warning: Skipping unhandled LEaP command line: %s\n", ptr);
         }
diff --git a/src/DataIO_LeapRC.h b/src/DataIO_LeapRC.h
index 36d0dc5774..f440ee4463 100644
--- a/src/DataIO_LeapRC.h
+++ b/src/DataIO_LeapRC.h
@@ -61,6 +61,7 @@ class DataIO_LeapRC : public DataIO {
     int LeapSet(ArgList const&, DataSetList&) const;
     DataSet* getUnit(std::string const&, DataSetList const&) const;
     int SaveAmberParm(std::string const&, ArgList&, DataSetList& dsl) const;
+    int unitAlias(std::string const&, std::string const&, DataSetList&, std::string const&) const;
     int Source(FileName const&, DataSetList&, std::string const&);
 
     /// Used to check if a parm/lib file was already loaded.

From 50c4434c2ce2d26647c4134b4545884d0332636e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 12 Dec 2025 09:05:36 -0500
Subject: [PATCH 1133/1492] Do leap aliases last since cpptraj actually makes
 copies and sometimes leaprc files reference units that have not yet been
 loaded

---
 src/DataIO_LeapRC.cpp | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 7bf53f88bd..f545e4fb4d 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -896,6 +896,8 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
   const char* ptr = infile.Line();
   // FIXME need to convert to all lowercase for matching commands; leap allows
   //       mixed case
+  typedef std::vector<std::string> Sarray;
+  Sarray aliasPairs;
   while (ptr != 0) {
     // Use lineBuf to store all non-comment characters
     std::string lineBuf;
@@ -980,7 +982,9 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
       } else {
         // Unrecognized so far. See if this is a unit alias (interpret as 'alias = unit')
         if (has_equals && line.Nargs() == 2) {
-          err = unitAlias( line[0], line[1], dsl, dsname );
+          //err = unitAlias( line[0], line[1], dsl, dsname );
+          aliasPairs.push_back( line[0] );
+          aliasPairs.push_back( line[1] );
         } else {
           mprintf("Warning: Skipping unhandled LEaP command line: %s\n", ptr);
         }
@@ -991,6 +995,15 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
   }
   infile.CloseFile();
 
+  // Do any unit aliases
+  for (unsigned int idx = 0; idx < aliasPairs.size(); idx += 2)
+  {
+    if ( unitAlias( aliasPairs[idx], aliasPairs[idx+1], dsl, dsname ) ) {
+      mprinterr("Error: Creating unit alias %s = %s\n", aliasPairs[idx].c_str(), aliasPairs[idx+1].c_str());
+      err++;
+    }
+  }
+
   // Add data sets to the main data set list
   //if (addSetsToList(dsl, paramDSL)) return err+1;
 

From acf38289a09b2382b082c1fbcd4bbcdd3ba8f396 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 12 Dec 2025 13:41:47 -0500
Subject: [PATCH 1134/1492] Changes to make it so read_unit can also read parm
 sections from lib

---
 src/DataIO_AmberLib.cpp | 241 ++++++++++++++++++++++++----------------
 src/DataIO_AmberLib.h   |   2 +-
 2 files changed, 149 insertions(+), 94 deletions(-)

diff --git a/src/DataIO_AmberLib.cpp b/src/DataIO_AmberLib.cpp
index 308dd0b847..574d8e7d66 100644
--- a/src/DataIO_AmberLib.cpp
+++ b/src/DataIO_AmberLib.cpp
@@ -71,12 +71,25 @@ int DataIO_AmberLib::ReadData(FileName const& fname, DataSetList& dsl, std::stri
   }
   while (units_read < UnitNames.size())
   {
+    int is_unit = -1;
     // Which unit are we reading: !entry.<name>.unit.atoms most likely
     ArgList tmparg( line, " !." );
+    if (tmparg.Nargs() >= 3) {
+      if (tmparg[2] == "unit")
+        is_unit = 1;
+      else if (tmparg[2] == "parm")
+        is_unit = 0;
+    }
     std::string currentName = tmparg.GetStringKey("entry");
-    if (debug_ > 0)
-       mprintf("DEBUG: Reading unit %s\n", currentName.c_str());
-    // Ensure this is in the list of units
+    if (debug_ > 0) {
+       if (is_unit == 1)
+         mprintf("DEBUG: Reading unit %s\n", currentName.c_str());
+       else if (is_unit == 0)
+         mprintf("DEBUG: Reading parameter set %s\n", currentName.c_str());
+       else
+         mprintf("Warning: Unknown '!entry' : %s\n", tmparg[2].c_str());
+    }
+    // Ensure this is in the list of entries
     bool found = false;
     for (Sarray::const_iterator it = UnitNames.begin(); it != UnitNames.end(); ++it) {
       if (*it == currentName) {
@@ -85,7 +98,7 @@ int DataIO_AmberLib::ReadData(FileName const& fname, DataSetList& dsl, std::stri
       }
     }
     if (!found) {
-      mprinterr("Error: Unit %s was not found in the initial list of names in lib file.\n",
+      mprinterr("Error: Entry %s was not found in the initial list of names in lib file.\n",
                 currentName.c_str());
       return 1;
     }
@@ -107,7 +120,7 @@ int DataIO_AmberLib::ReadData(FileName const& fname, DataSetList& dsl, std::stri
       mprinterr("Error: Could not create data set for unit %s\n", currentName.c_str());
       return 1;
     }
-    if (read_unit( ds, infile, line, currentName )) {
+    if (read_unit( ds, infile, line, currentName, (is_unit==1) )) {
       mprinterr("Error: Reading unit '%s'\n", currentName.c_str());
       return 1;
     }
@@ -123,12 +136,13 @@ int DataIO_AmberLib::ReadData(FileName const& fname, DataSetList& dsl, std::stri
 const char* DataIO_AmberLib::sectionStr_[] = {
   "atoms", "atomspertinfo", "boundbox", "childsequence", "connect",
   "connectivity", "hierarchy", "name", "positions", "residueconnect",
-  "residues", "residuesPdbSequenceNumber", "solventcap", "velocities", 0 };
+  "residues", "residuesPdbSequenceNumber", "solventcap", "velocities", "unknown" };
 
 /** \return Section type from entry line. */
 DataIO_AmberLib::SectionType DataIO_AmberLib::id_section(std::string const& line,
                                                          std::string const& unitName)
 {
+  mprintf("DEBUG: id_section %s : %s\n", unitName.c_str(), line.c_str());
   std::string entry = "!entry." + unitName + ".unit.";
   for (int idx = 0; idx < (int)UNKNOWN_SECTION; idx++) {
     std::string sectionName = entry + std::string(sectionStr_[idx]);
@@ -227,30 +241,122 @@ int DataIO_AmberLib::read_connect(AssociatedData_Connect& ConnectAtoms, std::str
   return 0;
 }
 
+/** Hold information for a unit entry. */
+class unitEntry {
+  public:
+    /// CONSTRUCTOR - Take unit name
+    unitEntry(std::string const& unitName) : ridx_(0) {
+      top_.SetParmName(unitName, FileName());
+      boundbox_.reserve(5);
+    }
+    /// \return Reference to topology
+    Topology& Top() { return top_; }
+    /// \return Reference to Positions
+    std::vector<Vec3>& Positions() { return positions_; }
+    /// \return Reference to connect atoms
+    AssociatedData_Connect& ConnectAtoms() { return ConnectAtoms_; }
+    /// Add residue
+    int AddResname( std::string const& resname ) {
+      if (ridx_ >= top_.Nres()) {
+        mprinterr("Error: Too many residues in residues section, or residues section before atom table.\n");
+        return 1;
+      }
+      top_.SetRes( ridx_++ ).SetName( resname );
+      return 0;
+    }
+    /// Add box value
+    void AddBoxVal(double d) { boundbox_.push_back( d ); }
+    /// Finish setting up the unit
+    int FinishUnit(DataSet_Coords* crd, int debug_) {
+      // Set up topology; determine molecules, but no residue renumber or bond parm determination
+      top_.CommonSetup(true, false, false);
+      if (debug_ > 1) top_.Summary();
+      Frame frm;
+      frm.SetupFrameV( top_.Atoms(), CoordinateInfo() );
+      frm.ClearAtoms();
+      for (std::vector<Vec3>::const_iterator it = positions_.begin(); it != positions_.end(); ++it)
+        frm.AddVec3( *it );
+      // Set up box if needed
+      if (!boundbox_.empty()) {
+        if (boundbox_.size() != 5) {
+          mprinterr("Error: Expected 5 values for boundbox entry for %s, got %zu\n", top_.c_str(), boundbox_.size());
+          return 1;
+        }
+        // hasbox, angle, x, y, z
+        if (boundbox_[0] > 0) {
+          double boxcrd[6];
+          boxcrd[0] = boundbox_[2];
+          boxcrd[1] = boundbox_[3];
+          boxcrd[2] = boundbox_[4];
+          // determine angles
+          double beta = boundbox_[1];
+          if (beta < 3.15) {
+            // Assume the angle is given in radians
+            beta = beta * Constants::RADDEG;
+            //mprintf("DEBUG: Converted beta: %f\n", beta);
+            // Fix imperfectly converted orthorhombic
+            double deltaBeta = 90.0 - beta;
+            if (deltaBeta < 0) deltaBeta = -deltaBeta;
+            if (deltaBeta < 0.0001) {
+              beta = 90.0;
+              //mprintf("DEBUG: Fixed beta.\n");
+            }
+          }
+          boxcrd[3] = beta;
+          boxcrd[4] = beta;
+          boxcrd[5] = beta;
+          if ( Box::IsTruncOct( beta ) ) {
+            // Use trunc oct angle from Box; higher precision
+            boxcrd[3] = Box::TruncatedOctAngle();
+            boxcrd[4] = boxcrd[3];
+            boxcrd[5] = boxcrd[3];
+          } else if (beta == 60.0) {
+            // Special case - rhombic dodecahedron
+            boxcrd[3] = 60.0;
+            boxcrd[4] = 90.0;
+            boxcrd[5] = 60.0;
+          }
+          frm.ModifyBox().SetupFromXyzAbg( boxcrd );
+          if (debug_ > 0)
+            frm.BoxCrd().PrintInfo(); // DEBUG
+        } else {
+          frm.ModifyBox().SetNoBox();
+        }
+      }
+      crd->CoordsSetup(top_, frm.CoordsInfo());
+      crd->AddFrame( frm );
+      crd->AssociateData( &ConnectAtoms_ );
+      if (debug_ > 1) ConnectAtoms_.Ainfo();
+      if (debug_ > 0) mprintf("\n");
+      return 0;
+    }
+  private:
+    AssociatedData_Connect ConnectAtoms_;
+    Topology top_;
+    std::vector<Vec3> positions_;
+    int ridx_;
+    std::vector<double> boundbox_; ///< hold values from box entry: hasbox, angle, x, y, zi
+};
+
 /** Read a unit from OFF file. It is expected that the next line from
   * infile is the first entry in the unit.atoms table.
   */
 int DataIO_AmberLib::read_unit(DataSet_Coords* crd,
                                BufferedLine& infile, std::string& Line,
-                               std::string const& unitName)
+                               std::string const& unitName,
+                               bool isUnit)
 const
 {
-  AssociatedData_Connect ConnectAtoms;
   SectionType currentSection = id_section( Line, unitName );
-  if (currentSection == UNKNOWN_SECTION) {
-    mprinterr("Error: Could not ID first section: %s\n", Line.c_str());
-    return 1;
-  }
-  if (debug_ > 1) mprintf("DEBUG: First section is %s\n", sectionStr_[currentSection]);
+  //if (currentSection == UNKNOWN_SECTION) {
+  //  mprinterr("Error: Could not ID first section for entry '%s': %s\n", unitName.c_str(), Line.c_str());
+  //  return 1;
+  //}
+  //if (debug_ > 1) mprintf("DEBUG: First section is %s\n", sectionStr_[currentSection]);
+
+  //Frame frm;
+  unitEntry currentUnit( unitName );
 
-  Topology top;
-  top.SetParmName( unitName, FileName() );
-  std::vector<Vec3> positions;
-  Frame frm;
-  int ridx = 0;
-  // Boundbox will hold values from box entry: hasbox, angle, x, y, z
-  std::vector<double> boundbox;
-  boundbox.reserve(5);
   bool readUnit = true;
   while (readUnit) {
     const char* lineptr = infile.Line();
@@ -266,15 +372,26 @@ const
     else
       Line.assign(lineptr);
     if (!Line.empty()) {
-      if (debug_ > 2) mprintf("DEBUG: Line: '%s'\n", Line.c_str());
+      if (debug_ > 2) mprintf("DEBUG: Section '%s' Line: '%s'\n", sectionStr_[currentSection], Line.c_str());
       //ArgList cols( Line, " \t\n" );
       if (Line[0] == '!') {
         // See if we are at another unit
         ArgList tmparg( Line, ". " );
-        if (tmparg[2] == "unit" && tmparg[3] == "atoms" && tmparg[4] == "table") {
+        if (tmparg[1] != unitName) {
+          mprintf("DEBUG: New entry %s detected.\n", tmparg[1].c_str());
+          readUnit = false;
+          break;
+        }
+/*        if (tmparg[2] == "parm" && tmparg[4] == "table") {
+          // This is a PARM table, not a unit.
+          mprintf("Parm section %s detected.\n", tmparg[3].c_str());
           readUnit = false;
           break;
         }
+        if (tmparg[2] == "unit" && tmparg[3] == "atoms" && tmparg[4] == "table") {
+          readUnit = false;
+          break;
+        }*/
         currentSection = id_section( Line, unitName );
         if (currentSection == UNKNOWN_SECTION) {
           mprintf("Warning: Could not ID section: %s\n", Line.c_str());
@@ -282,13 +399,13 @@ const
           if (debug_ > 1) mprintf("DEBUG: Section is %s\n", sectionStr_[currentSection]);
         }
       } else if (currentSection == ATOMTABLE) {
-        if (read_atoms(top, Line, unitName)) return 1;
+        if (read_atoms(currentUnit.Top(), Line, unitName)) return 1;
       } else if (currentSection == CONNECTIVITY) {
-        if (read_bonds(top, Line)) return 1;
+        if (read_bonds(currentUnit.Top(), Line)) return 1;
       } else if (currentSection == POSITIONS) {
-        if (read_positions(positions, Line)) return 1;
+        if (read_positions(currentUnit.Positions(), Line)) return 1;
       } else if (currentSection == CONNECT) {
-        if (read_connect(ConnectAtoms, Line)) return 1;
+        if (read_connect(currentUnit.ConnectAtoms(), Line)) return 1;
       } else if (currentSection == RESIDUES) {
         // Rely on ArgList to remove quotes
         ArgList tmpArg( Line );
@@ -297,85 +414,23 @@ const
           mprinterr("Error: Line: %s\n", Line.c_str());
           return 1;
         }
-        if (ridx >= top.Nres()) {
-          mprinterr("Error: Too many residues in residues section, or residues section before atom table.\n");
-          return 1;
-        }
-        top.SetRes( ridx++ ).SetName( tmpArg[0] );
+        if (currentUnit.AddResname( tmpArg[0] )) return 1;
       } else if (currentSection == BOUNDBOX) {
         // hasbox, angle, x, y, z
         double bval = 0;
         sscanf( Line.c_str(), "%lf", &bval );
-        boundbox.push_back( bval );
+        currentUnit.AddBoxVal( bval );
       }
       // else {
       //  mprintf("Warning: Unhandled section for %s: %s\n", unitName.c_str(), sectionStr_[currentSection]);
       //}
     }
   }
-    
-  // Set up topology; determine molecules, but no residue renumber or bond parm determination
-  top.CommonSetup(true, false, false);
-  if (debug_ > 1) top.Summary();
-  frm.SetupFrameV( top.Atoms(), CoordinateInfo() );
-  frm.ClearAtoms();
-  for (std::vector<Vec3>::const_iterator it = positions.begin(); it != positions.end(); ++it)
-    frm.AddVec3( *it );
 
-  // Set up box if needed
-  if (!boundbox.empty()) {
-    if (boundbox.size() != 5) {
-      mprinterr("Error: Expected 5 values for boundbox entry for %s, got %zu\n", unitName.c_str(), boundbox.size());
-      return 1;
-    }
-    // hasbox, angle, x, y, z
-    if (boundbox[0] > 0) {
-      double boxcrd[6];
-      boxcrd[0] = boundbox[2];
-      boxcrd[1] = boundbox[3];
-      boxcrd[2] = boundbox[4];
-      // determine angles
-      double beta = boundbox[1];
-      if (beta < 3.15) {
-        // Assume the angle is given in radians
-        beta = beta * Constants::RADDEG;
-        //mprintf("DEBUG: Converted beta: %f\n", beta);
-        // Fix imperfectly converted orthorhombic
-        double deltaBeta = 90.0 - beta;
-        if (deltaBeta < 0) deltaBeta = -deltaBeta;
-        if (deltaBeta < 0.0001) {
-          beta = 90.0;
-          //mprintf("DEBUG: Fixed beta.\n");
-        }
-      }
-      boxcrd[3] = beta;
-      boxcrd[4] = beta;
-      boxcrd[5] = beta;
-      if ( Box::IsTruncOct( beta ) ) {
-        // Use trunc oct angle from Box; higher precision
-        boxcrd[3] = Box::TruncatedOctAngle();
-        boxcrd[4] = boxcrd[3];
-        boxcrd[5] = boxcrd[3];
-      } else if (beta == 60.0) {
-        // Special case - rhombic dodecahedron
-        boxcrd[3] = 60.0;
-        boxcrd[4] = 90.0;
-        boxcrd[5] = 60.0;
-      }
-      frm.ModifyBox().SetupFromXyzAbg( boxcrd );
-      if (debug_ > 0)
-        frm.BoxCrd().PrintInfo(); // DEBUG
-    } else {
-      frm.ModifyBox().SetNoBox();
-    }
+  if (isUnit) {
+    if (currentUnit.FinishUnit(crd, debug_)) return 1;
   }
 
-  crd->CoordsSetup(top, frm.CoordsInfo());
-  crd->AddFrame( frm );
-  crd->AssociateData( &ConnectAtoms );
-  if (debug_ > 1) ConnectAtoms.Ainfo();
-  if (debug_ > 0) mprintf("\n");
-  
   return 0;
 }
 
diff --git a/src/DataIO_AmberLib.h b/src/DataIO_AmberLib.h
index 42f13152f0..52384a0997 100644
--- a/src/DataIO_AmberLib.h
+++ b/src/DataIO_AmberLib.h
@@ -26,7 +26,7 @@ class DataIO_AmberLib : public DataIO {
     /// ID OFF section from line
     static inline SectionType id_section(std::string const&, std::string const&);
     /// Read unit from OFF file
-    int read_unit(DataSet_Coords*, BufferedLine&, std::string&, std::string const&) const;
+    int read_unit(DataSet_Coords*, BufferedLine&, std::string&, std::string const&, bool) const;
 
     static int read_atoms(Topology&, std::string const&, std::string const&);
     static int read_bonds(Topology&, std::string const&);

From 4426f5c41fc40a80f3720059df9ba79e37c5225f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 12 Dec 2025 13:43:49 -0500
Subject: [PATCH 1135/1492] Only allocate COORDS set if reading a unit

---
 src/DataIO_AmberLib.cpp | 32 +++++++++++++++++---------------
 1 file changed, 17 insertions(+), 15 deletions(-)

diff --git a/src/DataIO_AmberLib.cpp b/src/DataIO_AmberLib.cpp
index 574d8e7d66..1e5d74e742 100644
--- a/src/DataIO_AmberLib.cpp
+++ b/src/DataIO_AmberLib.cpp
@@ -104,21 +104,23 @@ int DataIO_AmberLib::ReadData(FileName const& fname, DataSetList& dsl, std::stri
     }
 
     DataSet_Coords* ds = 0;
-    MetaData meta(dsname, currentName);
-    DataSet* set = dsl.CheckForSet( meta );
-    if (set == 0) {
-      ds = (DataSet_Coords*)dsl.AddSet( DataSet::COORDS, meta );
-    } else if (allowOverwrite_) {
-      mprintf("Warning: Overwriting existing set %s\n", set->legend());
-      dsl.RemoveSet( set );
-      ds = (DataSet_Coords*)dsl.AddSet( DataSet::COORDS, meta );
-    } else {
-      mprinterr("Error: Set %s already exists and 'allowoverwrite' not specified.\n");
-      return 1;
-    }
-    if (ds == 0) {
-      mprinterr("Error: Could not create data set for unit %s\n", currentName.c_str());
-      return 1;
+    if (is_unit == 1) {
+      MetaData meta(dsname, currentName);
+      DataSet* set = dsl.CheckForSet( meta );
+      if (set == 0) {
+        ds = (DataSet_Coords*)dsl.AddSet( DataSet::COORDS, meta );
+      } else if (allowOverwrite_) {
+        mprintf("Warning: Overwriting existing set %s\n", set->legend());
+        dsl.RemoveSet( set );
+        ds = (DataSet_Coords*)dsl.AddSet( DataSet::COORDS, meta );
+      } else {
+        mprinterr("Error: Set %s already exists and 'allowoverwrite' not specified.\n");
+        return 1;
+      }
+      if (ds == 0) {
+        mprinterr("Error: Could not create data set for unit %s\n", currentName.c_str());
+        return 1;
+      }
     }
     if (read_unit( ds, infile, line, currentName, (is_unit==1) )) {
       mprinterr("Error: Reading unit '%s'\n", currentName.c_str());

From 927f7321fa8b3461e4c32dc7a513b812751a6f95 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 12 Dec 2025 13:46:29 -0500
Subject: [PATCH 1136/1492] Hide debug info

---
 src/DataIO_AmberLib.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/DataIO_AmberLib.cpp b/src/DataIO_AmberLib.cpp
index 1e5d74e742..4d032d2995 100644
--- a/src/DataIO_AmberLib.cpp
+++ b/src/DataIO_AmberLib.cpp
@@ -144,7 +144,7 @@ const char* DataIO_AmberLib::sectionStr_[] = {
 DataIO_AmberLib::SectionType DataIO_AmberLib::id_section(std::string const& line,
                                                          std::string const& unitName)
 {
-  mprintf("DEBUG: id_section %s : %s\n", unitName.c_str(), line.c_str());
+  //mprintf("DEBUG: id_section %s : %s\n", unitName.c_str(), line.c_str());
   std::string entry = "!entry." + unitName + ".unit.";
   for (int idx = 0; idx < (int)UNKNOWN_SECTION; idx++) {
     std::string sectionName = entry + std::string(sectionStr_[idx]);
@@ -380,7 +380,7 @@ const
         // See if we are at another unit
         ArgList tmparg( Line, ". " );
         if (tmparg[1] != unitName) {
-          mprintf("DEBUG: New entry %s detected.\n", tmparg[1].c_str());
+          //mprintf("DEBUG: New entry %s detected.\n", tmparg[1].c_str());
           readUnit = false;
           break;
         }

From 556737f27cdf303b7fbe76f49cc791a85cec7484 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 12 Dec 2025 15:45:10 -0500
Subject: [PATCH 1137/1492] Make missing unit for alias a warning instead of an
 error to match leap behavior

---
 src/DataIO_LeapRC.cpp | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index f545e4fb4d..7c0769ed49 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -853,8 +853,11 @@ const
     }
   }
   if (ds0 == 0) {
-    mprinterr("Error: Could not find unit '%s' to copy to '%s'\n", rhs.c_str(), lhs.c_str());
-    return 1;
+    //mprinterr("Error: Could not find unit '%s' to copy to '%s'\n", rhs.c_str(), lhs.c_str());
+    //return 1;
+    // NOTE: Make only a warning to replicate LEAP behavior
+    mprintf("Warning: Could not find unit '%s' to copy to '%s' - skipping.\n", rhs.c_str(), lhs.c_str());
+    return 0;
   }
   DataSet_Coords& crd0 = static_cast<DataSet_Coords&>( *ds0 );
   // Allocate copy

From 722b7fcb63a02de99266757effe6f1c6b08513cc Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 16 Dec 2025 10:58:07 -0500
Subject: [PATCH 1138/1492] Add setbox keyword to build for adding vdw bounding
 box. Add solvate and setbox to help

---
 src/Exec_Build.cpp        | 26 ++++++++++++--
 src/Structure/Solvate.cpp | 73 +++++++++++++++++++++++++++++++++++----
 src/Structure/Solvate.h   | 10 ++++++
 3 files changed, 99 insertions(+), 10 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 97c24a51c8..42f9b6aec6 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -795,11 +795,17 @@ void Exec_Build::Help() const
           "\t[%s]\n"
           "\t[{%s} ...]\n"
           "\t[{%s} ...]\n"
+          "\t[{solvate %s\n"
+          "\t          %s |\n"
+          "\t  setbox %s}]\n"
           "%s"
           "%s",
           Cpptraj::Structure::Creator::other_keywords_,
           Cpptraj::Structure::Creator::template_keywords_,
           Cpptraj::Structure::Creator::parm_keywords_,
+          Cpptraj::Structure::Solvate::SolvateKeywords1(),
+          Cpptraj::Structure::Solvate::SolvateKeywords2(),
+          Cpptraj::Structure::Solvate::SetboxKeywords(),
           Cpptraj::Structure::HisProt::keywords_,
           Cpptraj::Structure::Disulfide::keywords_
          );
@@ -880,14 +886,21 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
   std::string solventResName = argIn.GetStringKey("solventresname", "HOH");
   mprintf("\tSolvent residue name: %s\n", solventResName.c_str());
 
-  bool add_solvent = false;
+  enum SolvateModeType { NO_SOLVATE = 0, SOLVATEBOX, SETBOX };
+  SolvateModeType add_solvent = NO_SOLVATE;
   Cpptraj::Structure::Solvate solvator;
   if (argIn.hasKey("solvate")) {
-    add_solvent = true;
+    add_solvent = SOLVATEBOX;
     if (solvator.InitSolvate(argIn, debug_)) {
       mprinterr("Error: Init solvate failed.\n");
       return CpptrajState::ERR;
     }
+  } else if (argIn.hasKey("setbox")) {
+    add_solvent = SETBOX;
+    if (solvator.InitSetbox(argIn, debug_)) {
+      mprinterr("Error: Init setbox failed.\n");
+      return CpptrajState::ERR;
+    }
   }
 
   keepMissingSourceAtoms_ = argIn.hasKey("keepmissingatoms");
@@ -1095,7 +1108,7 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
   }
 
   std::string checkMaskString("*");
-  if (add_solvent) {
+  if (add_solvent == SOLVATEBOX) {
     t_solvate_.Start();
     // Record initial number of atoms and residues
     int initial_natom = topOut.Natom();
@@ -1115,6 +1128,13 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
     // clash with solute, just check the solute.
     checkMaskString.assign( "@1-" + integerToString(initial_natom) );
     t_solvate_.Stop();
+  } else if (add_solvent == SETBOX) {
+    t_solvate_.Start();
+    if (solvator.SetVdwBoundingBox( topOut, frameOut, *(creator.MainParmSetPtr()) )) {
+      mprinterr("Error: Setting box failed.\n");
+      return CpptrajState::ERR;
+    }
+    mprintf("\tAdding VDW bounding box.\n");
   }
 
   // Assign parameters. This will create the bond/angle/dihedral/improper
diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index 36ee3a70d9..b75287e55a 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -23,23 +23,41 @@ Solvate::Solvate() :
 {
 }
 
-/** Initialize arguments. */
-int Solvate::InitSolvate(ArgList& argIn, int debugIn) {
-  debug_ = debugIn;
+const char* Solvate::SetboxKeywords() {
+  return "[{buffer <buffer> | bufx <bufx> bufy <bufy> bufz <bufz>}]";
+}
 
+const char* Solvate::SolvateKeywords1() {
+  return "{buffer <buffer> | bufx <bufx> bufy <bufy> bufz <bufz>}";
+}
+
+const char* Solvate::SolvateKeywords2() {
+  return "solventbox <unit> [closeness <closeness>] [iso] [nocenter]";
+}
+
+/** Get any buffer arguments */
+int Solvate::getBufferArg(ArgList& argIn, double defaultBuffer) {
   if (argIn.Contains("buffer")) {
-    bufferX_ = argIn.getKeyDouble("buffer", -1.0);
+    bufferX_ = argIn.getKeyDouble("buffer", defaultBuffer);
     bufferY_ = bufferX_;
     bufferZ_ = bufferX_;
   } else {
-    bufferX_ = argIn.getKeyDouble("bufx", -1.0);
-    bufferY_ = argIn.getKeyDouble("bufy", -1.0);
-    bufferZ_ = argIn.getKeyDouble("bufz", -1.0);
+    bufferX_ = argIn.getKeyDouble("bufx", defaultBuffer);
+    bufferY_ = argIn.getKeyDouble("bufy", defaultBuffer);
+    bufferZ_ = argIn.getKeyDouble("bufz", defaultBuffer);
   }
   if (bufferX_ < 0 || bufferY_ < 0 || bufferZ_ < 0) {
     mprinterr("Error: Either 'buffer' or 'bufx/bufy/bufx' must be specified and >= 0\n");
     return 1;
   }
+  return 0;
+}
+
+/** Initialize arguments. */
+int Solvate::InitSolvate(ArgList& argIn, int debugIn) {
+  debug_ = debugIn;
+
+  if (getBufferArg(argIn, -1.0)) return 1;
 
   isotropic_ = argIn.hasKey("iso");
 
@@ -55,6 +73,15 @@ int Solvate::InitSolvate(ArgList& argIn, int debugIn) {
   return 0;
 }
 
+/** Initialize args for setbox */
+int Solvate::InitSetbox(ArgList& argIn, int debugIn) {
+  debug_ = debugIn;
+
+  if (getBufferArg(argIn, 0.0)) return 1;
+
+  return 0;
+}
+
 /** Get solvent unit box from DataSetList */
 DataSet_Coords* Solvate::GetSolventUnit(DataSetList const& DSL) const {
   if (solventBoxName_.empty()) {
@@ -190,6 +217,38 @@ const
   return 0;
 }
 
+/** Set VDW bounding box */
+int Solvate::SetVdwBoundingBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::ParameterSet const& set0)
+{
+  // Set vdw box
+  double soluteMaxR;
+  std::vector<double> soluteRadii = getAtomRadii(soluteMaxR, topOut, set0) ;
+  double boxX, boxY, boxZ;
+  if (setVdwBoundingBox(boxX, boxY, boxZ, soluteRadii, frameOut)) {
+    mprinterr("Error: Setting vdw bounding box for %s failed.\n", topOut.c_str());
+    return 1;
+  }
+  mprintf("  Solute vdw bounding box:              %-5.3f %-5.3f %-5.3f\n", boxX, boxY, boxZ);
+
+  double dXWidth = boxX + bufferX_ * 2;
+  double dYWidth = boxY + bufferY_ * 2;
+  double dZWidth = boxZ + bufferZ_ * 2;
+
+    mprintf("  Total bounding box for atom centers:  %5.3f %5.3f %5.3f\n", 
+            dXWidth, dYWidth, dZWidth );
+
+  // Setup box
+  frameOut.ModifyBox().SetupFromXyzAbg(boxX, boxY, boxZ, 90.0, 90.0, 90.0);
+  frameOut.BoxCrd().PrintInfo();
+  topOut.SetParmBox( frameOut.BoxCrd() );
+  mprintf("  Total vdw box size:%s%5.3f %5.3f %5.3f angstroms.\n", "                   ",
+          frameOut.BoxCrd().Param(Box::X),
+          frameOut.BoxCrd().Param(Box::Y),
+          frameOut.BoxCrd().Param(Box::Z));
+  mprintf("  Volume: %5.3lf A^3\n", frameOut.BoxCrd().CellVolume());
+  return 0;
+}
+
 /** Create box, fill with solvent */
 int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::ParameterSet const& set0,
                         DataSet_Coords& SOLVENTBOX)
diff --git a/src/Structure/Solvate.h b/src/Structure/Solvate.h
index 93f1e2fa00..101c66166a 100644
--- a/src/Structure/Solvate.h
+++ b/src/Structure/Solvate.h
@@ -20,13 +20,23 @@ class Solvate {
     Solvate();
     /// Initialize
     int InitSolvate(ArgList&, int);
+    /// Initialize for setbox
+    int InitSetbox(ArgList&, int);
+    /// Set VDW bounding box
+    int SetVdwBoundingBox(Topology&, Frame&, Cpptraj::Parm::ParameterSet const& set0);
     /// Solvate with box
     int SolvateBox(Topology&, Frame&, Cpptraj::Parm::ParameterSet const&, DataSet_Coords&);
 
+    static const char* SetboxKeywords();
+    static const char* SolvateKeywords1();
+    static const char* SolvateKeywords2();
+
     /// \return Solvent unit selected from given DataSetList
     DataSet_Coords* GetSolventUnit(DataSetList const&) const;
     //std::string const& SolventBoxName() const { return solventBoxName_; }
   private:
+    /// Get buffer arguments
+    int getBufferArg(ArgList&, double);
     /// Get radii for atoms in topology
     std::vector<double> getAtomRadii(double&, Topology const&,
                                      Cpptraj::Parm::ParameterSet const&) const;

From 55595fa6eca2e0d011ffccb18e344cb2469a023e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 16 Dec 2025 15:55:02 -0500
Subject: [PATCH 1139/1492] Start trying to handle iso keyword

---
 src/Exec_Build.cpp        |  1 +
 src/Structure/Solvate.cpp | 23 +++++++++++++++++++++++
 src/Structure/Solvate.h   |  2 ++
 3 files changed, 26 insertions(+)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 42f9b6aec6..1877f42314 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -895,6 +895,7 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
       mprinterr("Error: Init solvate failed.\n");
       return CpptrajState::ERR;
     }
+    solvator.PrintSolvateInfo();
   } else if (argIn.hasKey("setbox")) {
     add_solvent = SETBOX;
     if (solvator.InitSetbox(argIn, debug_)) {
diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index b75287e55a..0733ec7827 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -82,6 +82,13 @@ int Solvate::InitSetbox(ArgList& argIn, int debugIn) {
   return 0;
 }
 
+/** Print info to stdout */
+void Solvate::PrintSolvateInfo() const {
+  mprintf("\tSolvent buffer XYZ: %g %g %g Ang.\n", bufferX_, bufferY_, bufferZ_);
+  mprintf("\tSolvent closeness: %g Ang.\n", closeness_);
+  mprintf("\tSolvent isotropic=%i  clip=%i  center_=%i\n", (int)isotropic_, (int)clip_, (int)center_);
+} 
+
 /** Get solvent unit box from DataSetList */
 DataSet_Coords* Solvate::GetSolventUnit(DataSetList const& DSL) const {
   if (solventBoxName_.empty()) {
@@ -163,6 +170,22 @@ int Solvate::setVdwBoundingBox(double& boxX, double& boxY, double& boxZ,
                                Frame& frameOut)
 const
 {
+  if (isotropic_) {
+    // Center on origin and align principal axes.
+    Vec3 ctr = frameOut.VGeometricCenter();
+    ctr.Neg();
+    frameOut.Translate(ctr);
+
+    Matrix_3x3 Inertia;
+    Vec3 Eval;
+    frameOut.CalculateInertia( AtomMask(0, frameOut.Natom()), Inertia );
+    Inertia.Diagonalize( Eval );
+    printf("Eigenvalues: %f %f %f\n", Eval[0], Eval[1], Eval[2]);
+
+    frameOut.Rotate( Inertia );
+    //frameOut.ModifyBox().RotateUcell( Inertia );
+  }
+
   // Set vdw bounding box
   double Xmin = 0;
   double Ymin = 0;
diff --git a/src/Structure/Solvate.h b/src/Structure/Solvate.h
index 101c66166a..6a920bc782 100644
--- a/src/Structure/Solvate.h
+++ b/src/Structure/Solvate.h
@@ -34,6 +34,8 @@ class Solvate {
     /// \return Solvent unit selected from given DataSetList
     DataSet_Coords* GetSolventUnit(DataSetList const&) const;
     //std::string const& SolventBoxName() const { return solventBoxName_; }
+    /// Print solvate info to stdout
+    void PrintSolvateInfo() const;
   private:
     /// Get buffer arguments
     int getBufferArg(ArgList&, double);

From 40cc3f68ed4b4dd6f2528d4946e9be2cfe613a04 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 16 Dec 2025 16:27:54 -0500
Subject: [PATCH 1140/1492] Fix handedness if needed. Only orient initially,
 not every time with iso

---
 src/Structure/Solvate.cpp | 31 +++++++++++++++++++++++--------
 src/Structure/Solvate.h   |  2 +-
 2 files changed, 24 insertions(+), 9 deletions(-)

diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index 0733ec7827..3f21af7cba 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -167,10 +167,10 @@ const
 /** Set VDW bounding box. */
 int Solvate::setVdwBoundingBox(double& boxX, double& boxY, double& boxZ,
                                std::vector<double> const& Radii,
-                               Frame& frameOut)
+                               Frame& frameOut, bool orient)
 const
 {
-  if (isotropic_) {
+  if (orient) {
     // Center on origin and align principal axes.
     Vec3 ctr = frameOut.VGeometricCenter();
     ctr.Neg();
@@ -182,8 +182,23 @@ const
     Inertia.Diagonalize( Eval );
     printf("Eigenvalues: %f %f %f\n", Eval[0], Eval[1], Eval[2]);
 
-    frameOut.Rotate( Inertia );
-    //frameOut.ModifyBox().RotateUcell( Inertia );
+    // Check the handedness of the diagonalized matrix
+    // If it is the wrong hand then it will transform the unit into a mirror image.
+    Vec3 vPos = Inertia.Row1().Cross( Inertia.Row2() );
+    mprintf("VPOS= %f %f %f\n", vPos[0], vPos[1], vPos[2]);
+    double dDot = vPos * Inertia.Row3();
+    mprintf( "The handedness of the transformation is (+1=Right): %f\n", dDot );
+
+    // If the handedness of the matrix is wrong then change it
+    if ( dDot < 0.0 ) {
+      Inertia[6] *= -1.0;
+      Inertia[7] *= -1.0;
+      Inertia[8] *= -1.0;
+    }
+
+    //frameOut.Rotate( Inertia );
+    // CPPTRAJ inverse rotate consistent with MatrixTimesVector from LEAP
+    frameOut.InverseRotate( Inertia );
   }
 
   // Set vdw bounding box
@@ -247,7 +262,7 @@ int Solvate::SetVdwBoundingBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm:
   double soluteMaxR;
   std::vector<double> soluteRadii = getAtomRadii(soluteMaxR, topOut, set0) ;
   double boxX, boxY, boxZ;
-  if (setVdwBoundingBox(boxX, boxY, boxZ, soluteRadii, frameOut)) {
+  if (setVdwBoundingBox(boxX, boxY, boxZ, soluteRadii, frameOut, isotropic_)) {
     mprinterr("Error: Setting vdw bounding box for %s failed.\n", topOut.c_str());
     return 1;
   }
@@ -290,7 +305,7 @@ int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::Parame
   double soluteMaxR;
   std::vector<double> soluteRadii = getAtomRadii(soluteMaxR, topOut, set0) ;
   double boxX, boxY, boxZ;
-  if (setVdwBoundingBox(boxX, boxY, boxZ, soluteRadii, frameOut)) {
+  if (setVdwBoundingBox(boxX, boxY, boxZ, soluteRadii, frameOut, isotropic_)) {
     mprinterr("Error: Setting vdw bounding box for %s failed.\n", topOut.c_str());
     return 1;
   }
@@ -355,7 +370,7 @@ int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::Parame
     solventY = solventFrame.BoxCrd().Param(Box::Y);
     solventZ = solventFrame.BoxCrd().Param(Box::Z);
   } else {
-    if (setVdwBoundingBox(solventX, solventY, solventZ, solventRadii, solventFrame)) {
+    if (setVdwBoundingBox(solventX, solventY, solventZ, solventRadii, solventFrame, false)) {
       mprinterr("Error: Setting vdw bounding box for %s failed.\n", topOut.c_str());
       return 1;
     }
@@ -392,7 +407,7 @@ int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::Parame
 
   // Define the size of the new solvent/solute system
   soluteRadii = getAtomRadii(soluteMaxR, topOut, set0) ;
-  if (setVdwBoundingBox(boxX, boxY, boxZ, soluteRadii, frameOut)) {
+  if (setVdwBoundingBox(boxX, boxY, boxZ, soluteRadii, frameOut, false)) {
     mprinterr("Error: Setting vdw bounding box for solute/solvent system failed.\n", topOut.c_str());
     return 1;
   }
diff --git a/src/Structure/Solvate.h b/src/Structure/Solvate.h
index 6a920bc782..410e2f76c2 100644
--- a/src/Structure/Solvate.h
+++ b/src/Structure/Solvate.h
@@ -43,7 +43,7 @@ class Solvate {
     std::vector<double> getAtomRadii(double&, Topology const&,
                                      Cpptraj::Parm::ParameterSet const&) const;
     /// Set vdW bounding box
-    int setVdwBoundingBox(double&, double&, double&, std::vector<double> const&, Frame&) const;
+    int setVdwBoundingBox(double&, double&, double&, std::vector<double> const&, Frame&, bool) const;
     /// Find solute atoms within a solvent box at given center
     int findCloseSoluteAtoms(std::vector<int>&, double, int, Frame const&, Vec3 const&, double, double, double) const;
     /// Determine which solvent residues do not clash with given solute atoms

From 7b650f862126dc8bf9606e0c4191df45aa022c4c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 17 Dec 2025 13:26:13 -0500
Subject: [PATCH 1141/1492] Start adding trunc oct code

---
 src/Structure/Solvate.cpp | 59 ++++++++++++++++++++++++++++++++++++++-
 src/Structure/Solvate.h   |  8 ++++--
 2 files changed, 63 insertions(+), 4 deletions(-)

diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index 3f21af7cba..a68fa7df93 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -7,6 +7,7 @@
 #include "../Topology.h"
 #include "../Parm/ParameterSet.h"
 #include <algorithm> //std::max
+#include <cmath> // cos, sin, sqrt
 
 using namespace Cpptraj::Structure;
 
@@ -54,8 +55,9 @@ int Solvate::getBufferArg(ArgList& argIn, double defaultBuffer) {
 }
 
 /** Initialize arguments. */
-int Solvate::InitSolvate(ArgList& argIn, int debugIn) {
+int Solvate::InitSolvate(ArgList& argIn, bool octIn, int debugIn) {
   debug_ = debugIn;
+  doTruncatedOct_ = octIn;
 
   if (getBufferArg(argIn, -1.0)) return 1;
 
@@ -70,6 +72,13 @@ int Solvate::InitSolvate(ArgList& argIn, int debugIn) {
   closeness_ = argIn.getKeyDouble("closeness", 1.0);
   center_ = !argIn.hasKey("nocenter");
 
+  if (doTruncatedOct_) {
+    if (!clip_) {
+      mprinterr("Error: Truncated octahedral box currently requires 'clip'.\n");
+      return 1;
+    }
+  }
+
   return 0;
 }
 
@@ -287,6 +296,54 @@ int Solvate::SetVdwBoundingBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm:
   return 0;
 }
 
+/** Rotate 45 deg. around z axis, (90-tetra/2) around y axis, 90 around x axis.
+  *    (1  0  0)    (cos2  0 -sin2)    (cos1 -sin1  0)
+  *    (0  0 -1)    (   0  1     0)    (sin1  cos1  0)
+  *    (0  1  0)    (sin2  0  cos2)    (   0     0  1)
+  *
+  *    cntr-clk       clock              clock
+  *    Looking down + axis of rotation toward origin
+  *
+  * For isotropic truncated octahedral box only.
+  */
+void ewald_rotate(Frame& frameOut, double& dPAngle)
+{
+  double tetra_angl = 2 * acos( 1. / sqrt(3.) );
+  double pi = 3.1415927; // FIXME use Constants
+  double phi = pi / 4.;
+  double cos1 = cos(phi);
+  double sin1 = sin(phi);
+         phi = pi/2. - tetra_angl/2.;
+  double cos2 = sqrt(2.)/sqrt(3.);
+  double sin2=1./sqrt(3.);
+
+  double t11= cos2*cos1;
+  double t12=-cos2*sin1;
+  double t13=-sin2;
+  double t21=-sin2*cos1;
+  double t22= sin2*sin1;
+  double t23=-cos2;
+  double t31= sin1;
+  double t32= cos1;
+  double t33=0;
+
+  //lAtoms = lLoop( (OBJEKT)uUnit, ATOMS );
+  //while ( (aAtom = (ATOM)oNext(&lAtoms)) != NULL ) {
+  //      double  dX, dY, dZ;
+  double* xyz = frameOut.xAddress();
+  for (int at = 0; at != frameOut.Natom(); at++, xyz += 3)
+  {
+    double dX = xyz[0];
+    double dY = xyz[1];
+    double dZ = xyz[2];
+
+    xyz[0] = t11*dX + t12*dY + t13*dZ;
+    xyz[1] = t21*dX + t22*dY + t23*dZ;
+    xyz[2] = t31*dX + t32*dY + t33*dZ;
+  }
+  dPAngle = tetra_angl*180./pi;
+}
+
 /** Create box, fill with solvent */
 int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::ParameterSet const& set0,
                         DataSet_Coords& SOLVENTBOX)
diff --git a/src/Structure/Solvate.h b/src/Structure/Solvate.h
index 410e2f76c2..6b2e10c8f6 100644
--- a/src/Structure/Solvate.h
+++ b/src/Structure/Solvate.h
@@ -19,7 +19,7 @@ class Solvate {
     /// CONSTRUCTOR
     Solvate();
     /// Initialize
-    int InitSolvate(ArgList&, int);
+    int InitSolvate(ArgList&, bool, int);
     /// Initialize for setbox
     int InitSetbox(ArgList&, int);
     /// Set VDW bounding box
@@ -50,8 +50,9 @@ class Solvate {
     int determineValidSolventResidues(std::vector<int>&, std::vector<int> const&,
                                       Frame const&, Topology const&, Frame const&,
                                       std::vector<double> const&, std::vector<double> const&) const;
-
-    // Add solvent unit boxes
+    /// Ewald rotate for trun. oct system
+    static void ewald_rotate(Frame&, double&);
+    /// Add solvent unit boxes
     int addSolventUnits(int, int, int, double, double, double, double, double, double, double,
                         Frame&, Topology const&, Frame&, Topology&,
                         std::vector<double> const&, std::vector<double> const&) const;
@@ -67,6 +68,7 @@ class Solvate {
     bool isotropic_;
     bool clip_;
     bool center_;
+    bool doTruncatedOct_;
     std::string solventBoxName_;
     static const double ATOM_DEFAULT_RADIUS_; ///< Atom default radius from LEaP
     static const double CLOSENESSMODIFIER_;   ///< Overlap closeness modifier from LEaP

From 10a97b83860ba3a9ac967e59c1a9ad45ada201e9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 17 Dec 2025 13:34:21 -0500
Subject: [PATCH 1142/1492] Call for ewald rotation and set trun oct beta

---
 src/Structure/Solvate.cpp | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index a68fa7df93..1ab722b105 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -402,7 +402,7 @@ int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::Parame
     clipX_ = 0.5 * boxX + bufferX_;
     clipY_ = 0.5 * boxY + bufferY_;
     clipZ_ = 0.5 * boxZ + bufferZ_;
-    //mprintf("cCriteria: %f %f %f\n", clipX_, clipY_, clipZ_);
+    mprintf("cCriteria: %f %f %f\n", clipX_, clipY_, clipZ_);
   }
 /*
     if ( bOct ) {
@@ -468,8 +468,20 @@ int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::Parame
     mprinterr("Error: Setting vdw bounding box for solute/solvent system failed.\n", topOut.c_str());
     return 1;
   }
+  if (doTruncatedOct_) {
+    double dAngle = 0;
+    ewald_rotate(frameOut, dAngle);
+    mprintf("EwaldRotate: %f\n", dAngle);
+    // Add an angstrom to the desired box size rather than using the bounding box size
+    dAngle = clipX_ + .5;
+    boxX = boxY = boxZ = dAngle * sqrt(3.0) * 0.5;
+  }
+
   // Setup box
-  frameOut.ModifyBox().SetupFromXyzAbg(boxX, boxY, boxZ, 90.0, 90.0, 90.0);
+  double boxBeta = 90.0;
+  if (doTruncatedOct_)
+    boxBeta = Box::TruncatedOctAngle();
+  frameOut.ModifyBox().SetupFromXyzAbg(boxX, boxY, boxZ, boxBeta, boxBeta, boxBeta);
   frameOut.BoxCrd().PrintInfo();
   topOut.SetParmBox( frameOut.BoxCrd() );
   mprintf("  Total vdw box size:%s%5.3f %5.3f %5.3f angstroms.\n", "                   ",

From e91d8f3e4e3a8ae28885956ce49471659b3bb360 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 17 Dec 2025 14:21:12 -0500
Subject: [PATCH 1143/1492] Start testing trunc oct box. Add oct diagonal check
 and oct clip check.

---
 src/Exec_Build.cpp        |  15 +++--
 src/Structure/Solvate.cpp | 122 +++++++++++++++++++++++++++++++++++---
 src/Structure/Solvate.h   |   3 +
 3 files changed, 127 insertions(+), 13 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 1877f42314..fba2748ef5 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -795,7 +795,7 @@ void Exec_Build::Help() const
           "\t[%s]\n"
           "\t[{%s} ...]\n"
           "\t[{%s} ...]\n"
-          "\t[{solvate %s\n"
+          "\t[{{solvatebox|solvateoct} %s\n"
           "\t          %s |\n"
           "\t  setbox %s}]\n"
           "%s"
@@ -889,10 +889,17 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
   enum SolvateModeType { NO_SOLVATE = 0, SOLVATEBOX, SETBOX };
   SolvateModeType add_solvent = NO_SOLVATE;
   Cpptraj::Structure::Solvate solvator;
-  if (argIn.hasKey("solvate")) {
+  if (argIn.hasKey("solvatebox")) {
     add_solvent = SOLVATEBOX;
-    if (solvator.InitSolvate(argIn, debug_)) {
-      mprinterr("Error: Init solvate failed.\n");
+    if (solvator.InitSolvate(argIn, false, debug_)) {
+      mprinterr("Error: Init solvatebox failed.\n");
+      return CpptrajState::ERR;
+    }
+    solvator.PrintSolvateInfo();
+  } else if (argIn.hasKey("solvateoct")) {
+    add_solvent = SOLVATEBOX;
+    if (solvator.InitSolvate(argIn, true, debug_)) {
+      mprinterr("Error: Init solvateoct failed.\n");
       return CpptrajState::ERR;
     }
     solvator.PrintSolvateInfo();
diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index 1ab722b105..9227b79122 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -17,6 +17,7 @@ Solvate::Solvate() :
   bufferX_(0),
   bufferY_(0),
   bufferZ_(0),
+  bufferD_(0),
   closeness_(1.0),
   isotropic_(false),
   clip_(true),
@@ -42,10 +43,12 @@ int Solvate::getBufferArg(ArgList& argIn, double defaultBuffer) {
     bufferX_ = argIn.getKeyDouble("buffer", defaultBuffer);
     bufferY_ = bufferX_;
     bufferZ_ = bufferX_;
+    bufferD_ = bufferX_;
   } else {
     bufferX_ = argIn.getKeyDouble("bufx", defaultBuffer);
     bufferY_ = argIn.getKeyDouble("bufy", defaultBuffer);
     bufferZ_ = argIn.getKeyDouble("bufz", defaultBuffer);
+    bufferD_ = argIn.getKeyDouble("bufd", defaultBuffer);
   }
   if (bufferX_ < 0 || bufferY_ < 0 || bufferZ_ < 0) {
     mprinterr("Error: Either 'buffer' or 'bufx/bufy/bufx' must be specified and >= 0\n");
@@ -54,6 +57,90 @@ int Solvate::getBufferArg(ArgList& argIn, double defaultBuffer) {
   return 0;
 }
 
+/** Scale buffer if needed to meet diagonal clearance. */
+void Solvate::octBoxCheck(Frame const& frameOut) {
+  if (frameOut.Natom() < 1) return;
+  double dPBuf[4];
+
+  dPBuf[0] = bufferX_;
+  dPBuf[1] = bufferY_;
+  dPBuf[2] = bufferZ_;
+  dPBuf[3] = bufferD_;
+  mprintf("dPBuf %f %f %f %f\n", dPBuf[0], dPBuf[1], dPBuf[2], dPBuf[3]);
+
+  const double* XYZ = frameOut.XYZ(0);
+  double dXmax = XYZ[0];
+  double dYmax = XYZ[1];
+  double dZmax = XYZ[2];
+  double dXmin = XYZ[0];
+  double dYmin = XYZ[1];
+  double dZmin = XYZ[2];
+
+  for (int at = 1; at < frameOut.Natom(); at++)
+  {
+    XYZ = frameOut.XYZ(at);
+    if      ( XYZ[0] > dXmax )
+            dXmax = XYZ[0];
+    else if ( XYZ[0] < dXmin )
+            dXmin = XYZ[0];
+    if      ( XYZ[1] > dYmax )
+            dYmax = XYZ[1];
+    else if ( XYZ[1] < dYmin )
+            dYmin = XYZ[1];
+    if      ( XYZ[2] > dZmax )
+            dZmax = XYZ[2];
+    else if ( XYZ[2] < dZmin )
+            dZmin = XYZ[2];
+  }
+
+  // calc halfbox on centers
+  double dXhalf = 0.5 * (dXmax - dXmin) + dPBuf[0];
+  double dYhalf = 0.5 * (dYmax - dYmin) + dPBuf[1];
+  double dZhalf = 0.5 * (dZmax - dZmin) + dPBuf[2];
+
+  // find unit vector of diagonal
+  double dX = dYhalf * dZhalf;
+  double dY = dXhalf * dZhalf;
+  double dZ = dXhalf * dYhalf;
+
+  double dTmp = 1.0 / sqrt( dX*dX + dY*dY + dZ*dZ );
+
+  double dXunit = dX * dTmp;
+  double dYunit = dY * dTmp;
+  double dZunit = dZ * dTmp;
+
+  // find max atom distance from origin along the diagonal
+  double dMax = 0.0;
+  for (int at = 0; at < frameOut.Natom(); at++)
+  {
+    XYZ = frameOut.XYZ(at);
+    dTmp = fabs(XYZ[0]) * dXunit +
+           fabs(XYZ[1]) * dYunit +
+           fabs(XYZ[2]) * dZunit;
+    if ( dTmp > dMax )
+      dMax = dTmp;
+  }
+
+  // calc distance of diagonal face from origin
+  double dBmax = 0.5 * sqrt( dXhalf*dXhalf + dYhalf*dYhalf + dZhalf*dZhalf );
+
+  // see if diagonal clearance is satisfied
+  dTmp = dMax + dPBuf[3];
+  if ( dTmp <= dBmax ) {
+    if ( dPBuf[3] == 0.0 )
+      mprintf( "(Diagonal clearance is %f)\n", dMax );
+    return;
+  }
+
+  //  not satisfied: scale up box
+  dTmp /= dBmax;
+  mprintf("Scaling up box by a factor of %f to meet diagonal cut criterion\n", dTmp );
+
+  bufferX_ *= dTmp;
+  bufferY_ *= dTmp;
+  bufferZ_ *= dTmp;
+}
+
 /** Initialize arguments. */
 int Solvate::InitSolvate(ArgList& argIn, bool octIn, int debugIn) {
   debug_ = debugIn;
@@ -95,7 +182,7 @@ int Solvate::InitSetbox(ArgList& argIn, int debugIn) {
 void Solvate::PrintSolvateInfo() const {
   mprintf("\tSolvent buffer XYZ: %g %g %g Ang.\n", bufferX_, bufferY_, bufferZ_);
   mprintf("\tSolvent closeness: %g Ang.\n", closeness_);
-  mprintf("\tSolvent isotropic=%i  clip=%i  center_=%i\n", (int)isotropic_, (int)clip_, (int)center_);
+  mprintf("\tSolvent isotropic=%i  clip=%i  center_=%i  oct=%i\n", (int)isotropic_, (int)clip_, (int)center_, (int)doTruncatedOct_);
 } 
 
 /** Get solvent unit box from DataSetList */
@@ -306,7 +393,7 @@ int Solvate::SetVdwBoundingBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm:
   *
   * For isotropic truncated octahedral box only.
   */
-void ewald_rotate(Frame& frameOut, double& dPAngle)
+void Solvate::ewald_rotate(Frame& frameOut, double& dPAngle)
 {
   double tetra_angl = 2 * acos( 1. / sqrt(3.) );
   double pi = 3.1415927; // FIXME use Constants
@@ -354,6 +441,7 @@ int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::Parame
               topOut.c_str(), topOut.Natom(), frameOut.Natom());
     return 1;
   }
+
   // TODO Remove any existing box info?
   //if (frameOut.BoxCrd.HasBox())
   // TODO principal align
@@ -366,6 +454,9 @@ int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::Parame
     mprinterr("Error: Setting vdw bounding box for %s failed.\n", topOut.c_str());
     return 1;
   }
+  // Check if buffers need to be increased for trunc oct.
+  if (doTruncatedOct_)
+    octBoxCheck( frameOut );
   mprintf("  Solute vdw bounding box:              %-5.3f %-5.3f %-5.3f\n", boxX, boxY, boxZ);
 
   double dXWidth = boxX + bufferX_ * 2;
@@ -588,15 +679,28 @@ const
       const double* VXYZ = solventFrame.XYZ(vat);
       // First check for clipping
       if (clip_) {
-        //if ( fabs(VXYZ[0]) >= clipX_ ) { collision = true; mprintf("CLIP %12.4f %12.4f %12.4f\n",VXYZ[0],VXYZ[1],VXYZ[2]); break; }
-        //if ( fabs(VXYZ[1]) >= clipY_ ) { collision = true; mprintf("CLIP %12.4f %12.4f %12.4f\n",VXYZ[0],VXYZ[1],VXYZ[2]); break; }
-        //if ( fabs(VXYZ[2]) >= clipZ_ ) { collision = true; mprintf("CLIP %12.4f %12.4f %12.4f\n",VXYZ[0],VXYZ[1],VXYZ[2]); break; }
-        if ( fabs(VXYZ[0]) >= clipX_ ) { collision = true; break; }
-        if ( fabs(VXYZ[1]) >= clipY_ ) { collision = true; break; }
-        if ( fabs(VXYZ[2]) >= clipZ_ ) { collision = true; break; }
+        double dXabs = fabs(VXYZ[0]);
+        double dYabs = fabs(VXYZ[1]);
+        double dZabs = fabs(VXYZ[2]);
+        //if ( dXabs >= clipX_ ) { collision = true; mprintf("CLIP %12.4f %12.4f %12.4f\n",VXYZ[0],VXYZ[1],VXYZ[2]); break; }
+        //if ( dYabs >= clipY_ ) { collision = true; mprintf("CLIP %12.4f %12.4f %12.4f\n",VXYZ[0],VXYZ[1],VXYZ[2]); break; }
+        //if ( dZabs >= clipZ_ ) { collision = true; mprintf("CLIP %12.4f %12.4f %12.4f\n",VXYZ[0],VXYZ[1],VXYZ[2]); break; }
+        if ( dXabs >= clipX_ ) { collision = true; break; }
+        if ( dYabs >= clipY_ ) { collision = true; break; }
+        if ( dZabs >= clipZ_ ) { collision = true; break; }
+        // Check if atom falls outside of oct/diagonal clip
+        if (doTruncatedOct_) {
+          double dX = 0.5 * (clipX_ - dXabs) / clipX_;
+                 dX = fabs( dX - 0.5 );
+          double dY = 0.5 * (clipY_ - dYabs) / clipY_;
+                 dY = fabs( dY - 0.5 );
+          double dZ = 0.5 * (clipZ_ - dZabs) / clipZ_;
+                 dZ = fabs( dZ - 0.5 );
+          if ( ( dX + dY + dZ )  >  0.75 ) { collision = true; break; }
+        }
       }
       double dR = solventRadii[vat] * closeness_ * CLOSENESSMODIFIER_;
-      // Loop over close solute atoms, check fir ckasg
+      // Loop over close solute atoms, check for clash
       for (std::vector<int>::const_iterator uat = closeSoluteAtoms.begin(); uat != closeSoluteAtoms.end(); ++uat)
       {
         const double* UXYZ = frameOut.XYZ(*uat);
diff --git a/src/Structure/Solvate.h b/src/Structure/Solvate.h
index 6b2e10c8f6..4284ca3b3f 100644
--- a/src/Structure/Solvate.h
+++ b/src/Structure/Solvate.h
@@ -39,6 +39,8 @@ class Solvate {
   private:
     /// Get buffer arguments
     int getBufferArg(ArgList&, double);
+    /// Scale up buffer sizes for oct box if needed
+    void octBoxCheck(Frame const&);
     /// Get radii for atoms in topology
     std::vector<double> getAtomRadii(double&, Topology const&,
                                      Cpptraj::Parm::ParameterSet const&) const;
@@ -61,6 +63,7 @@ class Solvate {
     double bufferX_;
     double bufferY_;
     double bufferZ_;
+    double bufferD_;
     double closeness_;
     double clipX_;
     double clipY_;

From d23290f464eb3ebdc00e39ffc0f3d10c9789542b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 17 Dec 2025 14:35:48 -0500
Subject: [PATCH 1144/1492] For trunc oct need to scale up lengths by 2

---
 src/Structure/Solvate.cpp | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index 9227b79122..027aee1052 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -570,8 +570,13 @@ int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::Parame
 
   // Setup box
   double boxBeta = 90.0;
-  if (doTruncatedOct_)
+  if (doTruncatedOct_) {
     boxBeta = Box::TruncatedOctAngle();
+    boxX *= 2.0;
+    boxY *= 2.0;
+    boxZ *= 2.0;
+  }
+  mprintf("Max: %f %f %f\n", boxX, boxY, boxZ);
   frameOut.ModifyBox().SetupFromXyzAbg(boxX, boxY, boxZ, boxBeta, boxBeta, boxBeta);
   frameOut.BoxCrd().PrintInfo();
   topOut.SetParmBox( frameOut.BoxCrd() );

From 45478727142fc12a02b26085f31f7ad58562dc55 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 17 Dec 2025 15:17:37 -0500
Subject: [PATCH 1145/1492] Hide debug info

---
 src/Exec_Build.cpp        |  15 ++-
 src/Structure/Solvate.cpp | 200 +++++++++++++++++++-------------------
 src/Structure/Solvate.h   |   4 +-
 3 files changed, 110 insertions(+), 109 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index fba2748ef5..0303375f7c 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -82,14 +82,17 @@ const
     // Determine if this is a terminal residue
     Cpptraj::Structure::TerminalType resTermType;
     if (currentRes.IsTerminal()) {
-      mprintf("DEBUG: %s End terminal due to TERMINAL status.\n", topIn.TruncResNameNum(ires).c_str());
       resTermType = Cpptraj::Structure::END_TERMINAL;
+      if (debug_ > 0)
+        mprintf("DEBUG: %s End terminal due to TERMINAL status.\n", topIn.TruncResNameNum(ires).c_str());
     } else if (ires == 0 && topIn.Nres() > 1) {
       resTermType = Cpptraj::Structure::BEG_TERMINAL;
-      mprintf("DEBUG: %s Begin terminal due to first residue.\n", topIn.TruncResNameNum(ires).c_str());
+      if (debug_ > 0)
+        mprintf("DEBUG: %s Begin terminal due to first residue.\n", topIn.TruncResNameNum(ires).c_str());
     } else if (pres > -1 && topIn.Res(pres).IsTerminal()) {
       resTermType = Cpptraj::Structure::BEG_TERMINAL;
-      mprintf("DEBUG: %s Begin terminal due to previous residue TERMINAL status.\n", topIn.TruncResNameNum(ires).c_str());
+      if (debug_ > 0)
+        mprintf("DEBUG: %s Begin terminal due to previous residue TERMINAL status.\n", topIn.TruncResNameNum(ires).c_str());
     } else if (nres < topIn.Nres() && (topIn.Res(nres).ChainID() != currentRes.ChainID())// ||
 //                                        (topIn.Res(nres).OriginalResNum() == currentRes.OriginalResNum() &&
 //                                         topIn.Res(nres).Icode()          != currentRes.Icode()
@@ -98,10 +101,12 @@ const
               )
     {
       resTermType = Cpptraj::Structure::END_TERMINAL;
-      mprintf("DEBUG: %s End terminal due to chain ID.\n", topIn.TruncResNameNum(ires).c_str());
+      if (debug_ > 0)
+        mprintf("DEBUG: %s End terminal due to chain ID.\n", topIn.TruncResNameNum(ires).c_str());
     } else if (nres == topIn.Nres()) {
       resTermType = Cpptraj::Structure::END_TERMINAL;
-      mprintf("DEBUG: %s End terminal due to last residue.\n", topIn.TruncResNameNum(ires).c_str());
+      if (debug_ > 0)
+        mprintf("DEBUG: %s End terminal due to last residue.\n", topIn.TruncResNameNum(ires).c_str());
     } else {
       resTermType = Cpptraj::Structure::NON_TERMINAL;
     }
diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index 027aee1052..11b00e99bf 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -57,90 +57,6 @@ int Solvate::getBufferArg(ArgList& argIn, double defaultBuffer) {
   return 0;
 }
 
-/** Scale buffer if needed to meet diagonal clearance. */
-void Solvate::octBoxCheck(Frame const& frameOut) {
-  if (frameOut.Natom() < 1) return;
-  double dPBuf[4];
-
-  dPBuf[0] = bufferX_;
-  dPBuf[1] = bufferY_;
-  dPBuf[2] = bufferZ_;
-  dPBuf[3] = bufferD_;
-  mprintf("dPBuf %f %f %f %f\n", dPBuf[0], dPBuf[1], dPBuf[2], dPBuf[3]);
-
-  const double* XYZ = frameOut.XYZ(0);
-  double dXmax = XYZ[0];
-  double dYmax = XYZ[1];
-  double dZmax = XYZ[2];
-  double dXmin = XYZ[0];
-  double dYmin = XYZ[1];
-  double dZmin = XYZ[2];
-
-  for (int at = 1; at < frameOut.Natom(); at++)
-  {
-    XYZ = frameOut.XYZ(at);
-    if      ( XYZ[0] > dXmax )
-            dXmax = XYZ[0];
-    else if ( XYZ[0] < dXmin )
-            dXmin = XYZ[0];
-    if      ( XYZ[1] > dYmax )
-            dYmax = XYZ[1];
-    else if ( XYZ[1] < dYmin )
-            dYmin = XYZ[1];
-    if      ( XYZ[2] > dZmax )
-            dZmax = XYZ[2];
-    else if ( XYZ[2] < dZmin )
-            dZmin = XYZ[2];
-  }
-
-  // calc halfbox on centers
-  double dXhalf = 0.5 * (dXmax - dXmin) + dPBuf[0];
-  double dYhalf = 0.5 * (dYmax - dYmin) + dPBuf[1];
-  double dZhalf = 0.5 * (dZmax - dZmin) + dPBuf[2];
-
-  // find unit vector of diagonal
-  double dX = dYhalf * dZhalf;
-  double dY = dXhalf * dZhalf;
-  double dZ = dXhalf * dYhalf;
-
-  double dTmp = 1.0 / sqrt( dX*dX + dY*dY + dZ*dZ );
-
-  double dXunit = dX * dTmp;
-  double dYunit = dY * dTmp;
-  double dZunit = dZ * dTmp;
-
-  // find max atom distance from origin along the diagonal
-  double dMax = 0.0;
-  for (int at = 0; at < frameOut.Natom(); at++)
-  {
-    XYZ = frameOut.XYZ(at);
-    dTmp = fabs(XYZ[0]) * dXunit +
-           fabs(XYZ[1]) * dYunit +
-           fabs(XYZ[2]) * dZunit;
-    if ( dTmp > dMax )
-      dMax = dTmp;
-  }
-
-  // calc distance of diagonal face from origin
-  double dBmax = 0.5 * sqrt( dXhalf*dXhalf + dYhalf*dYhalf + dZhalf*dZhalf );
-
-  // see if diagonal clearance is satisfied
-  dTmp = dMax + dPBuf[3];
-  if ( dTmp <= dBmax ) {
-    if ( dPBuf[3] == 0.0 )
-      mprintf( "(Diagonal clearance is %f)\n", dMax );
-    return;
-  }
-
-  //  not satisfied: scale up box
-  dTmp /= dBmax;
-  mprintf("Scaling up box by a factor of %f to meet diagonal cut criterion\n", dTmp );
-
-  bufferX_ *= dTmp;
-  bufferY_ *= dTmp;
-  bufferZ_ *= dTmp;
-}
-
 /** Initialize arguments. */
 int Solvate::InitSolvate(ArgList& argIn, bool octIn, int debugIn) {
   debug_ = debugIn;
@@ -276,14 +192,14 @@ const
     Vec3 Eval;
     frameOut.CalculateInertia( AtomMask(0, frameOut.Natom()), Inertia );
     Inertia.Diagonalize( Eval );
-    printf("Eigenvalues: %f %f %f\n", Eval[0], Eval[1], Eval[2]);
+    //mprintf("Eigenvalues: %f %f %f\n", Eval[0], Eval[1], Eval[2]);
 
     // Check the handedness of the diagonalized matrix
     // If it is the wrong hand then it will transform the unit into a mirror image.
     Vec3 vPos = Inertia.Row1().Cross( Inertia.Row2() );
-    mprintf("VPOS= %f %f %f\n", vPos[0], vPos[1], vPos[2]);
+    //mprintf("VPOS= %f %f %f\n", vPos[0], vPos[1], vPos[2]);
     double dDot = vPos * Inertia.Row3();
-    mprintf( "The handedness of the transformation is (+1=Right): %f\n", dDot );
+    //mprintf( "The handedness of the transformation is (+1=Right): %f\n", dDot );
 
     // If the handedness of the matrix is wrong then change it
     if ( dDot < 0.0 ) {
@@ -383,6 +299,90 @@ int Solvate::SetVdwBoundingBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm:
   return 0;
 }
 
+/** Scale buffer if needed to meet diagonal clearance. */
+void Solvate::octBoxCheck(Frame const& frameOut) {
+  if (frameOut.Natom() < 1) return;
+  double dPBuf[4];
+
+  dPBuf[0] = bufferX_;
+  dPBuf[1] = bufferY_;
+  dPBuf[2] = bufferZ_;
+  dPBuf[3] = bufferD_;
+  //mprintf("dPBuf %f %f %f %f\n", dPBuf[0], dPBuf[1], dPBuf[2], dPBuf[3]);
+
+  const double* XYZ = frameOut.XYZ(0);
+  double dXmax = XYZ[0];
+  double dYmax = XYZ[1];
+  double dZmax = XYZ[2];
+  double dXmin = XYZ[0];
+  double dYmin = XYZ[1];
+  double dZmin = XYZ[2];
+
+  for (int at = 1; at < frameOut.Natom(); at++)
+  {
+    XYZ = frameOut.XYZ(at);
+    if      ( XYZ[0] > dXmax )
+            dXmax = XYZ[0];
+    else if ( XYZ[0] < dXmin )
+            dXmin = XYZ[0];
+    if      ( XYZ[1] > dYmax )
+            dYmax = XYZ[1];
+    else if ( XYZ[1] < dYmin )
+            dYmin = XYZ[1];
+    if      ( XYZ[2] > dZmax )
+            dZmax = XYZ[2];
+    else if ( XYZ[2] < dZmin )
+            dZmin = XYZ[2];
+  }
+
+  // calc halfbox on centers
+  double dXhalf = 0.5 * (dXmax - dXmin) + dPBuf[0];
+  double dYhalf = 0.5 * (dYmax - dYmin) + dPBuf[1];
+  double dZhalf = 0.5 * (dZmax - dZmin) + dPBuf[2];
+
+  // find unit vector of diagonal
+  double dX = dYhalf * dZhalf;
+  double dY = dXhalf * dZhalf;
+  double dZ = dXhalf * dYhalf;
+
+  double dTmp = 1.0 / sqrt( dX*dX + dY*dY + dZ*dZ );
+
+  double dXunit = dX * dTmp;
+  double dYunit = dY * dTmp;
+  double dZunit = dZ * dTmp;
+
+  // find max atom distance from origin along the diagonal
+  double dMax = 0.0;
+  for (int at = 0; at < frameOut.Natom(); at++)
+  {
+    XYZ = frameOut.XYZ(at);
+    dTmp = fabs(XYZ[0]) * dXunit +
+           fabs(XYZ[1]) * dYunit +
+           fabs(XYZ[2]) * dZunit;
+    if ( dTmp > dMax )
+      dMax = dTmp;
+  }
+
+  // calc distance of diagonal face from origin
+  double dBmax = 0.5 * sqrt( dXhalf*dXhalf + dYhalf*dYhalf + dZhalf*dZhalf );
+
+  // see if diagonal clearance is satisfied
+  dTmp = dMax + dPBuf[3];
+  if ( dTmp <= dBmax ) {
+    if ( dPBuf[3] == 0.0 )
+      mprintf("  (Diagonal clearance is %f)\n", dMax );
+    return;
+  }
+
+  //  not satisfied: scale up box
+  dTmp /= dBmax;
+  mprintf("  Scaling up box by a factor of %f to meet diagonal cut criterion\n", dTmp );
+
+  bufferX_ *= dTmp;
+  bufferY_ *= dTmp;
+  bufferZ_ *= dTmp;
+}
+
 /** Rotate 45 deg. around z axis, (90-tetra/2) around y axis, 90 around x axis.
   *    (1  0  0)    (cos2  0 -sin2)    (cos1 -sin1  0)
   *    (0  0 -1)    (   0  1     0)    (sin1  cos1  0)
@@ -493,16 +493,9 @@ int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::Parame
     clipX_ = 0.5 * boxX + bufferX_;
     clipY_ = 0.5 * boxY + bufferY_;
     clipZ_ = 0.5 * boxZ + bufferZ_;
-    mprintf("cCriteria: %f %f %f\n", clipX_, clipY_, clipZ_);
+    //mprintf("cCriteria: %f %f %f\n", clipX_, clipY_, clipZ_);
   }
-/*
-    if ( bOct ) {
-        // maybe allow oct clip on integer boxes someday.. but for now:
-        if ( !bClip )
-                DFATAL(( "oct but no clip\n" ));
-        iCriteria |= TOOLOUTSIDEOFOCTBOX;
-    }
-*/
+
   // TODO check COORDS size
   Frame solventFrame = SOLVENTBOX.AllocateFrame();
   SOLVENTBOX.GetFrame(0, solventFrame);
@@ -562,7 +555,7 @@ int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::Parame
   if (doTruncatedOct_) {
     double dAngle = 0;
     ewald_rotate(frameOut, dAngle);
-    mprintf("EwaldRotate: %f\n", dAngle);
+    //mprintf("EwaldRotate: %f\n", dAngle);
     // Add an angstrom to the desired box size rather than using the bounding box size
     dAngle = clipX_ + .5;
     boxX = boxY = boxZ = dAngle * sqrt(3.0) * 0.5;
@@ -576,7 +569,7 @@ int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::Parame
     boxY *= 2.0;
     boxZ *= 2.0;
   }
-  mprintf("Max: %f %f %f\n", boxX, boxY, boxZ);
+  //mprintf("Max: %f %f %f\n", boxX, boxY, boxZ);
   frameOut.ModifyBox().SetupFromXyzAbg(boxX, boxY, boxZ, boxBeta, boxBeta, boxBeta);
   frameOut.BoxCrd().PrintInfo();
   topOut.SetParmBox( frameOut.BoxCrd() );
@@ -742,18 +735,21 @@ int Solvate::addSolventUnits(int numX, int numY, int numZ, double soluteMaxR,
                              std::vector<double> const& solventRadii)
 const
 {
-  mprintf( "Max R = %f\n", soluteMaxR);
-  mprintf( "The number of boxes:  x=%2d  y=%2d  z=%2d\n", numX, numY, numZ );
+  if (debug_ > 0) {
+    mprintf( "Max R = %f\n", soluteMaxR);
+    mprintf( "The number of boxes:  x=%2d  y=%2d  z=%2d\n", numX, numY, numZ );
+  }
   int NboxesToAdd = numX * numY * numZ;
   int NatomsToAdd = NboxesToAdd * solventTop.Natom();
-  mprintf("Will add %i boxes, %i atoms.\n", NboxesToAdd, NatomsToAdd);
+  mprintf("  Will add %i solvent boxes, max %i atoms.\n", NboxesToAdd, NatomsToAdd);
   frameOut.IncreaseX( NatomsToAdd );
 
   // Current solvent unit center
   Vec3 currentSolventCenter = solventFrame.VGeometricCenter();
 
   int firstSolventAtom = topOut.Natom();
-  mprintf("DEBUG: First solvent atom is %i\n", firstSolventAtom+1);
+  if (debug_ > 0)
+    mprintf("DEBUG: First solvent atom is %i\n", firstSolventAtom+1);
 
   std::vector<int> bondedAtoms;
   bondedAtoms.reserve(12); // Reserve for 6 bonds
diff --git a/src/Structure/Solvate.h b/src/Structure/Solvate.h
index 4284ca3b3f..c2fb2aef80 100644
--- a/src/Structure/Solvate.h
+++ b/src/Structure/Solvate.h
@@ -39,8 +39,6 @@ class Solvate {
   private:
     /// Get buffer arguments
     int getBufferArg(ArgList&, double);
-    /// Scale up buffer sizes for oct box if needed
-    void octBoxCheck(Frame const&);
     /// Get radii for atoms in topology
     std::vector<double> getAtomRadii(double&, Topology const&,
                                      Cpptraj::Parm::ParameterSet const&) const;
@@ -52,6 +50,8 @@ class Solvate {
     int determineValidSolventResidues(std::vector<int>&, std::vector<int> const&,
                                       Frame const&, Topology const&, Frame const&,
                                       std::vector<double> const&, std::vector<double> const&) const;
+    /// Scale up buffer sizes for oct box if needed
+    void octBoxCheck(Frame const&);
     /// Ewald rotate for trun. oct system
     static void ewald_rotate(Frame&, double&);
     /// Add solvent unit boxes

From 74a1d95b13dad87a78b034ab46e26e930bcd1656 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 18 Dec 2025 11:13:32 -0500
Subject: [PATCH 1146/1492] Make isotropic the default for trunc oct

---
 src/Structure/Solvate.cpp | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index 11b00e99bf..ca26b3da4d 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -34,7 +34,7 @@ const char* Solvate::SolvateKeywords1() {
 }
 
 const char* Solvate::SolvateKeywords2() {
-  return "solventbox <unit> [closeness <closeness>] [iso] [nocenter]";
+  return "solventbox <unit> [closeness <closeness>] [{iso|aniso}] [nocenter]";
 }
 
 /** Get any buffer arguments */
@@ -64,7 +64,14 @@ int Solvate::InitSolvate(ArgList& argIn, bool octIn, int debugIn) {
 
   if (getBufferArg(argIn, -1.0)) return 1;
 
-  isotropic_ = argIn.hasKey("iso");
+  if (doTruncatedOct_) {
+    if (argIn.hasKey("aniso"))
+      isotropic_ = false;
+    else
+      isotropic_ = true;
+  } else {
+    isotropic_ = argIn.hasKey("iso");
+  }
 
   solventBoxName_ = argIn.GetStringKey("solventbox");
   if (solventBoxName_.empty()) {
@@ -98,6 +105,7 @@ int Solvate::InitSetbox(ArgList& argIn, int debugIn) {
 void Solvate::PrintSolvateInfo() const {
   mprintf("\tSolvent buffer XYZ: %g %g %g Ang.\n", bufferX_, bufferY_, bufferZ_);
   mprintf("\tSolvent closeness: %g Ang.\n", closeness_);
+  // FIXME improve output
   mprintf("\tSolvent isotropic=%i  clip=%i  center_=%i  oct=%i\n", (int)isotropic_, (int)clip_, (int)center_, (int)doTruncatedOct_);
 } 
 

From 645e37c89e0f87a9515fac3f44c31583fdc96536 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 18 Dec 2025 11:30:52 -0500
Subject: [PATCH 1147/1492] Hide debug info

---
 src/Frame.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Frame.cpp b/src/Frame.cpp
index 578bba8ce2..c16bdffe43 100644
--- a/src/Frame.cpp
+++ b/src/Frame.cpp
@@ -307,7 +307,7 @@ void Frame::Info(const char *msg) const {
 // Frame::IncreaseX()
 /** Increase the maximum size of the Frame by offset. */
 int Frame::IncreaseX(int offset) {
-  mprintf("DEBUG: Increasing max number of atoms from %i to %i\n", maxnatom_, maxnatom_ + offset);
+  //mprintf("DEBUG: Increasing max number of atoms from %i to %i\n", maxnatom_, maxnatom_ + offset);
   maxnatom_ += offset;
   if (maxnatom_ < 1) {
     mprinterr("Internal Error: Frame::IncreaseX(): New size is < 1 atom.\n");

From 409fcddc4e87b8d0f91b91feb83fa27e483938c6 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 18 Dec 2025 15:01:59 -0500
Subject: [PATCH 1148/1492] No need to alloc/dealloc sugar builder

---
 src/Exec_Build.cpp | 31 +++++++++++--------------------
 src/Exec_Build.h   |  4 +---
 2 files changed, 12 insertions(+), 23 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 0303375f7c..5b1868b6f8 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -26,16 +26,9 @@ Exec_Build::Exec_Build() :
   check_structure_(true),
   keepMissingSourceAtoms_(false),
   requireAllInputAtoms_(false),
-  sugarBuilder_(0),
   outCrdPtr_(0)
 {}
 
-/** DESTRUCTOR */
-Exec_Build::~Exec_Build() {
-  if (sugarBuilder_ != 0)
-    delete sugarBuilder_;
-}
-
 /** Search in array of atom bonding pairs for given bonding pair. */
 bool Exec_Build::hasBondingPair(IParray const& bpairs, Ipair const& bpair) {
   for (IParray::const_iterator it = bpairs.begin(); it != bpairs.end(); ++it)
@@ -1045,17 +1038,15 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
     mprintf("\tNot attempting to prepare sugars.\n");
   else
     mprintf("\tWill attempt to prepare sugars.\n");
-  if (sugarBuilder_ != 0) delete sugarBuilder_;
-  sugarBuilder_ = 0;
+  Cpptraj::Structure::SugarBuilder sugarBuilder(debug_);
   if (prepare_sugars) {
-    sugarBuilder_ = new Cpptraj::Structure::SugarBuilder(debug_);
     // Init options
-    if (sugarBuilder_->InitOptions( argIn.hasKey("hasglycam"),
-                                    argIn.getKeyDouble("rescut", 8.0),
-                                    argIn.getKeyDouble("bondoffset", 0.2),
-                                    argIn.GetStringKey("sugarmask"),
-                                    argIn.GetStringKey("determinesugarsby", "geometry"),
-                                    argIn.GetStringKey("resmapfile") ))
+    if (sugarBuilder.InitOptions( argIn.hasKey("hasglycam"),
+                                  argIn.getKeyDouble("rescut", 8.0),
+                                  argIn.getKeyDouble("bondoffset", 0.2),
+                                  argIn.GetStringKey("sugarmask"),
+                                  argIn.GetStringKey("determinesugarsby", "geometry"),
+                                  argIn.GetStringKey("resmapfile") ))
     {
       mprinterr("Error: Sugar options init failed.\n");
       return CpptrajState::ERR;
@@ -1075,14 +1066,14 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
     // adding missing bonds to C1 atoms.
     // This is done before any identification takes place since we want
     // to identify based on the most up-to-date topology.
-    if (sugarBuilder_->FixSugarsStructure(topIn, frameIn,
-                                          c1bondsearch, splitres, solventResName,
-                                          SugarBonds))
+    if (sugarBuilder.FixSugarsStructure(topIn, frameIn,
+                                        c1bondsearch, splitres, solventResName,
+                                        SugarBonds))
     {
       mprinterr("Error: Sugar structure modification failed.\n");
       return CpptrajState::ERR;
     }
-    if (sugarBuilder_->PrepareSugars(true, resStat, topIn, frameIn, SugarBonds))
+    if (sugarBuilder.PrepareSugars(true, resStat, topIn, frameIn, SugarBonds))
     {
       mprinterr("Error: Sugar preparation failed.\n");
       return CpptrajState::ERR;
diff --git a/src/Exec_Build.h b/src/Exec_Build.h
index 7b3802f95c..68fab8c020 100644
--- a/src/Exec_Build.h
+++ b/src/Exec_Build.h
@@ -5,14 +5,13 @@
 namespace Cpptraj {
 namespace Structure {
 class Creator;
-class SugarBuilder;
 }
 }
 /// Used to build a structure 
 class Exec_Build : public Exec {
   public:
     Exec_Build();
-    ~Exec_Build();
+    ~Exec_Build() {}
     void Help() const;
     DispatchObject* Alloc() const { return (DispatchObject*)new Exec_Build(); }
     RetType Execute(CpptrajState&, ArgList&);
@@ -48,7 +47,6 @@ class Exec_Build : public Exec {
     bool check_structure_; ///< If true check the resulting structure
     bool keepMissingSourceAtoms_;
     bool requireAllInputAtoms_;
-    Cpptraj::Structure::SugarBuilder* sugarBuilder_;
     DataSet* outCrdPtr_; ///< Hold built COORDS
 
     Timer t_total_;

From d87357907ff2ef5d113549a23fb17f38d3a0fab0 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 19 Dec 2025 10:49:54 -0500
Subject: [PATCH 1149/1492] Build using topology in Coords set

---
 src/Exec_Build.cpp | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 5b1868b6f8..77e5bfd411 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -1083,7 +1083,8 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
 
   // Fill in atoms with templates
   t_fill_.Start();
-  Topology topOut;
+  //Topology topOut;
+  Topology& topOut = static_cast<Topology&>( *(crdout.TopPtr()) );
   topOut.SetDebug( debug_ );
   if (outset.empty()) {
     // In-place output COORDS. Copy over existing topology metadata

From fd1002951cf856213eb6ce29462cc8ca457528b2 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 19 Dec 2025 10:50:12 -0500
Subject: [PATCH 1150/1492] Do not copy topology if being set up with current
 topology

---
 src/DataSet_Coords.cpp     | 12 ++++++++++++
 src/DataSet_Coords.h       |  1 +
 src/DataSet_Coords_CRD.cpp |  2 +-
 src/DataSet_Coords_FRM.cpp |  2 +-
 src/DataSet_Coords_REF.cpp |  2 +-
 src/DataSet_Coords_TRJ.cpp |  2 +-
 6 files changed, 17 insertions(+), 4 deletions(-)

diff --git a/src/DataSet_Coords.cpp b/src/DataSet_Coords.cpp
index 4c95ae0ce9..ce9a2777b8 100644
--- a/src/DataSet_Coords.cpp
+++ b/src/DataSet_Coords.cpp
@@ -17,3 +17,15 @@ void DataSet_Coords::CommonInfo() const {
 void DataSet_Coords::UpdateCoordsInfoBox( Box const& boxIn ) {
   cInfo_.SetBox( boxIn );
 }
+
+/** Copy the incoming topology if different from current topology. */
+void DataSet_Coords::set_topology(Topology const& topIn)
+{
+  if (&topIn == &top_) {
+    mprintf("DEBUG: set_topology called with existing topology (%s)\n", top_.c_str());
+  } else {
+    if (top_.Natom() > 0)
+      mprintf("DEBUG: set_topology: overwriting top %s with top %s\n", top_.c_str(), topIn.c_str());
+    top_ = topIn;
+  }
+}
diff --git a/src/DataSet_Coords.h b/src/DataSet_Coords.h
index 68f44e0784..fe428ed697 100644
--- a/src/DataSet_Coords.h
+++ b/src/DataSet_Coords.h
@@ -36,6 +36,7 @@ class DataSet_Coords : public DataSet {
     void UpdateCoordsInfoBox(Box const&);
   protected:
     void CommonInfo() const;
+    void set_topology(Topology const&);
     Topology top_;         ///< Topology corresponding to coordinates.
     CoordinateInfo cInfo_; ///< Describes coordinate Frame
 };
diff --git a/src/DataSet_Coords_CRD.cpp b/src/DataSet_Coords_CRD.cpp
index 4ff93f488f..736efceb1c 100644
--- a/src/DataSet_Coords_CRD.cpp
+++ b/src/DataSet_Coords_CRD.cpp
@@ -56,7 +56,7 @@ void DataSet_Coords_CRD::CopyBlock(size_t startIdx, DataSet const* dptrIn, size_
 
 /** Set up COORDS with given Topology and coordinate info. */
 int DataSet_Coords_CRD::CoordsSetup(Topology const& topIn, CoordinateInfo const& cInfoIn) {
-  top_ = topIn;
+  set_topology( topIn );
   cInfo_ = cInfoIn;
 
   if (frames_.SetupFrameArray(cInfo_, topIn.Natom(), framesToReserve_)) {
diff --git a/src/DataSet_Coords_FRM.cpp b/src/DataSet_Coords_FRM.cpp
index 505c78b3db..d6d262cb1a 100644
--- a/src/DataSet_Coords_FRM.cpp
+++ b/src/DataSet_Coords_FRM.cpp
@@ -115,7 +115,7 @@ void DataSet_Coords_FRM::CopyBlock(size_t startIdx, DataSet const* dptrIn, size_
 // -----------------------------------------------
 /** Set up COORDS with given Topology and coordinate info. */
 int DataSet_Coords_FRM::CoordsSetup(Topology const& topIn, CoordinateInfo const& cInfoIn) {
-  top_ = topIn;
+  set_topology( topIn );
   cInfo_ = cInfoIn;
 
   //if (frames_.SetupFrameArray(cInfo_, topIn.Natom(), framesToReserve_)) {
diff --git a/src/DataSet_Coords_REF.cpp b/src/DataSet_Coords_REF.cpp
index 87922859c9..b1169b9559 100644
--- a/src/DataSet_Coords_REF.cpp
+++ b/src/DataSet_Coords_REF.cpp
@@ -14,7 +14,7 @@ void DataSet_Coords_REF::Info() const {
 
 /** Set up REF coords with given Topology and coordinate info. */
 int DataSet_Coords_REF::CoordsSetup(Topology const& topIn, CoordinateInfo const& cInfoIn) {
-  top_ = topIn;
+  set_topology( topIn );
   cInfo_ = cInfoIn;
 
   if (frame_.SetupFrameV( topIn.Atoms(), cInfoIn )) {
diff --git a/src/DataSet_Coords_TRJ.cpp b/src/DataSet_Coords_TRJ.cpp
index 0f6dfc0bbb..6b43eeb7e1 100644
--- a/src/DataSet_Coords_TRJ.cpp
+++ b/src/DataSet_Coords_TRJ.cpp
@@ -19,7 +19,7 @@ DataSet_Coords_TRJ::~DataSet_Coords_TRJ() {
 
 int DataSet_Coords_TRJ::CoordsSetup(Topology const& topIn, CoordinateInfo const& cInfoIn ) {
   if (trajinList_.empty()) {
-    top_ = topIn;
+    set_topology( topIn );
     cInfo_ = cInfoIn;
   } else {
     if ( topIn.Natom() != top_.Natom() ) {

From 2aeb79fa791975148a5b8e606070f5c1b0cf2a32 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 19 Dec 2025 13:59:52 -0500
Subject: [PATCH 1151/1492] Add a routine that does clean and fill atoms only

---
 src/Exec_Build.cpp | 323 ++++++++++++++++++++++++++++++++++++++++++++-
 src/Exec_Build.h   |   5 +
 2 files changed, 321 insertions(+), 7 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 77e5bfd411..5d7047137d 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -1266,6 +1266,321 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
   }
   t_total_.Stop();
 
+  PrintTiming();
+  if (add_solvent)
+    t_solvate_.WriteTiming    (2, "Solvate             :", t_total_.Total());
+  t_check_.WriteTiming        (2, "Structure check     :", t_total_.Total());
+  t_assign_.WriteTiming       (2, "Param./Top. gen.    :", t_total_.Total());
+  AP.WriteAssignTiming(3, t_assign_.Total());
+
+  return ret;
+}
+
+/** Standalone execute. For DataIO_LeapRC. */
+int Exec_Build::CleanAndFillStructure(DataSet* inCrdPtr, int tgtframe, std::string const& outset, std::string const& title,
+                                      DataSetList& DSL, int debugIn, Cpptraj::Structure::Creator const& creator)
+{
+  t_total_.Start();
+  if (inCrdPtr == 0) {
+    mprinterr("Internal Error: Exec_Build::BuildStructure(): Null input coordinates.\n");
+    return 1;
+  }
+  if (inCrdPtr->Group() != DataSet::COORDINATES) {
+    mprinterr("Error: Set '%s' is not coordinates, cannot use for building.\n", inCrdPtr->legend());
+    return 1;
+  }
+  debug_ = debugIn;
+//  int verbose = argIn.getKeyInt("verbose", 0);
+//  std::string title = argIn.GetStringKey("title");
+//  std::string outputTopologyName = argIn.GetStringKey("parmout");
+//  std::string outputCoordsName = argIn.GetStringKey("crdout");
+//  if (!outputTopologyName.empty())
+//    mprintf("\tWill write topology to %s\n", outputTopologyName.c_str());
+//  if (!outputCoordsName.empty())
+//    mprintf("\tWill write coords to %s\n", outputCoordsName.c_str());
+  // TODO make it so this can be const (cant bc GetFrame)
+  DataSet_Coords& coords = static_cast<DataSet_Coords&>( *((DataSet_Coords*)inCrdPtr) );
+  // Get frame from input coords
+  //int tgtframe = argIn.getKeyInt("frame", 1) - 1;
+  mprintf("\tUsing frame %i from COORDS set %s\n", tgtframe+1, coords.legend());
+  if (tgtframe < 0 || tgtframe >= (int)coords.Size()) {
+    mprinterr("Error: Frame is out of range.\n");
+    return 1;
+  }
+  Frame frameIn = coords.AllocateFrame();
+  coords.GetFrame(tgtframe, frameIn);
+  // Get modifiable topology
+  //Topology& topIn = *(coords.TopPtr());
+  //Topology const& topIn = coords.Top();
+  Topology topIn = coords.Top(); // FIXME do not work on the copy, work on the top itself
+
+  //std::string solventResName = argIn.GetStringKey("solventresname", "HOH");
+  //mprintf("\tSolvent residue name: %s\n", solventResName.c_str());
+
+//  enum SolvateModeType { NO_SOLVATE = 0, SOLVATEBOX, SETBOX };
+//  SolvateModeType add_solvent = NO_SOLVATE;
+//  Cpptraj::Structure::Solvate solvator;
+//  if (argIn.hasKey("solvatebox")) {
+//    add_solvent = SOLVATEBOX;
+//    if (solvator.InitSolvate(argIn, false, debug_)) {
+//      mprinterr("Error: Init solvatebox failed.\n");
+//      return CpptrajState::ERR;
+//    }
+//    solvator.PrintSolvateInfo();
+//  } else if (argIn.hasKey("solvateoct")) {
+//    add_solvent = SOLVATEBOX;
+//    if (solvator.InitSolvate(argIn, true, debug_)) {
+//      mprinterr("Error: Init solvateoct failed.\n");
+//      return CpptrajState::ERR;
+//    }
+//    solvator.PrintSolvateInfo();
+//  } else if (argIn.hasKey("setbox")) {
+//    add_solvent = SETBOX;
+//    if (solvator.InitSetbox(argIn, debug_)) {
+//      mprinterr("Error: Init setbox failed.\n");
+//      return CpptrajState::ERR;
+//    }
+//  }
+
+  keepMissingSourceAtoms_ = false; // FIXME
+//  keepMissingSourceAtoms_ = argIn.hasKey("keepmissingatoms");
+  if (keepMissingSourceAtoms_)
+    mprintf("\tInput atoms missing from templates will be kept.\n");
+  else
+    mprintf("\tInput atoms missing from templates will be ignored.\n");
+  requireAllInputAtoms_ = false; // FIXME
+//  requireAllInputAtoms_ = argIn.hasKey("requireallinputatoms");
+  if (requireAllInputAtoms_)
+    mprintf("\tRequire all input atoms to be found in templates.\n");
+  else
+    mprintf("\tInput atoms not found in templates will be ignored.\n");
+
+  // Do histidine detection before H atoms are removed
+  ArgList argIn; // FIXME
+  t_hisDetect_.Start();
+//  if (!argIn.hasKey("nohisdetect")) {
+    Cpptraj::Structure::HisProt hisProt;
+    if (hisProt.InitHisProt( argIn, debug_ )) {
+      mprinterr("Error: Could not initialize histidine detection.\n");
+      return 1;
+    }
+    hisProt.HisProtInfo();
+    if (hisProt.DetermineHisProt( topIn )) {
+      mprinterr("Error: HIS protonation detection failed.\n");
+      return 1;
+    }
+//  }
+  t_hisDetect_.Stop();
+
+  // Clean up structure
+  t_clean_.Start();
+  Cpptraj::Structure::PdbCleaner pdbCleaner;
+  pdbCleaner.SetDebug( debug_ );
+  std::string solventResName = "HOH"; //FIXME
+  if (pdbCleaner.InitPdbCleaner( argIn, solventResName, std::vector<int>() )) {
+    mprinterr("Error: Could not init PDB cleaner.\n");
+    return 1;
+  }
+  if (pdbCleaner.SetupPdbCleaner( topIn )) {
+    mprinterr("Error: Could not set up PDB cleaner.\n");
+    return 1;
+  }
+  pdbCleaner.PdbCleanerInfo();
+  if (pdbCleaner.ModifyCoords(topIn, frameIn)) {
+    mprinterr("Error: Could not clean PDB.\n");
+    return 1;
+  }
+  t_clean_.Stop();
+
+  // Set up Output coords
+  if (!outset.empty()) {
+    // Separate output COORDS set.
+    outCrdPtr_ = DSL.AddSet( DataSet::COORDS, outset );
+  } else {
+    // In-place output COORDS
+    DSL.RemoveSet( inCrdPtr );
+    outCrdPtr_ = DSL.AddSet( DataSet::COORDS, inCrdPtr->Meta() );
+  }
+  if (outCrdPtr_ == 0) {
+    mprinterr("Error: Could not allocate output COORDS set with name '%s'\n", outset.c_str());
+    return 1;
+  }
+  DataSet_Coords& crdout = static_cast<DataSet_Coords&>( *((DataSet_Coords*)outCrdPtr_) );
+  mprintf("\tOutput COORDS set: %s\n", crdout.legend());
+/*
+  // GB radii set
+  Cpptraj::Parm::GB_RadiiType gbradii;
+  if (gbRadIn == Cpptraj::Parm::UNKNOWN_GB) {
+    // No radii set specified. Check for keyword.
+    gbradii = Cpptraj::Parm::MBONDI; // Default
+    //std::string gbset = argIn.GetStringKey("gb");
+    //if (!gbset.empty()) {
+    //  gbradii = Cpptraj::Parm::GbTypeFromKey( gbset );
+    //  if (gbradii == Cpptraj::Parm::UNKNOWN_GB) {
+    //    mprinterr("Error: Unknown GB radii set: %s\n", gbset.c_str());
+    //    return CpptrajState::ERR;
+    //  }
+    //}
+  } else {
+    // Use passed-in GB radii set
+    gbradii = gbRadIn;
+  }
+  mprintf("\tGB radii set: %s\n", Cpptraj::Parm::GbTypeStr(gbradii).c_str());
+*/
+  // Get templates and parameter sets.
+/*  t_get_templates_.Start();
+  Cpptraj::Structure::Creator creator( debug_ );
+  if (creator.InitCreator(argIn, DSL, debug_)) {
+    return 1;
+  }
+  if (!creator.HasTemplates()) {
+    mprintf("Warning: No residue templates loaded.\n");
+  }
+  if (!creator.HasMainParmSet()) {
+    mprinterr("Error: No parameter sets.\n");
+    return 1;
+  }
+  t_get_templates_.Stop();
+  // FIXME hide behind ifdef?
+  creator.TimingInfo(t_get_templates_.Total(), 2);*/
+
+  // All residues start unknown
+  Cpptraj::Structure::ResStatArray resStat( topIn.Nres() );
+  std::vector<BondType> DisulfideBonds;
+  std::vector<BondType> SugarBonds;
+
+  // Disulfide search
+  t_disulfide_.Start();
+  //if (!argIn.hasKey("nodisulfides")) {
+    Cpptraj::Structure::Disulfide disulfide;
+    if (disulfide.InitDisulfide( argIn, Cpptraj::Structure::Disulfide::ADD_BONDS, debug_ )) {
+      mprinterr("Error: Could not init disulfide search.\n");
+      return 1;
+    }
+    if (disulfide.SearchForDisulfides( resStat, topIn, frameIn, DisulfideBonds ))
+    {
+      mprinterr("Error: Disulfide search failed.\n");
+      return 1;
+    }
+  //} else {
+  //  mprintf("\tNot searching for disulfides.\n");
+  //}
+  t_disulfide_.Stop();
+
+  // Handle sugars.
+  t_sugar_.Start();
+  // TODO should be on a residue by residue basis in FillAtomsWithTemplates
+  //bool prepare_sugars = !argIn.hasKey("nosugars");
+  bool prepare_sugars = true; //FIXME
+  if (!prepare_sugars)
+    mprintf("\tNot attempting to prepare sugars.\n");
+  else
+    mprintf("\tWill attempt to prepare sugars.\n");
+  Cpptraj::Structure::SugarBuilder sugarBuilder(debug_);
+  if (prepare_sugars) {
+    // Init options
+    // FIXME
+    bool hasglycam = false;
+    double rescut = 8.0;
+    double bondoffset = 0.2;
+    std::string sugarmask("");
+    std::string determinesugarsby("geometry");
+    std::string resmapfile("");
+    if (sugarBuilder.InitOptions( hasglycam,
+                                  rescut,
+                                  bondoffset,
+                                  sugarmask,
+                                  determinesugarsby,
+                                  resmapfile ))
+    {
+      mprinterr("Error: Sugar options init failed.\n");
+      return 1;
+    }
+    bool splitres = true; // FIXME
+    //bool splitres = !argIn.hasKey("nosplitres");
+    if (splitres)
+      mprintf("\tWill split off recognized sugar functional groups into separate residues.\n");
+    else
+      mprintf("\tNot splitting recognized sugar functional groups into separate residues.\n");
+    //bool c1bondsearch = !argIn.hasKey("noc1search");
+    bool c1bondsearch = true; // FIXME
+    if (c1bondsearch)
+      mprintf("\tWill search for missing bonds to sugar anomeric atoms.\n");
+    else
+      mprintf("\tNot searching for missing bonds to sugar anomeric atoms.\n");
+    // May need to modify sugar structure/topology, either by splitting
+    // C1 hydroxyls of terminal sugars into ROH residues, and/or by
+    // adding missing bonds to C1 atoms.
+    // This is done before any identification takes place since we want
+    // to identify based on the most up-to-date topology.
+    if (sugarBuilder.FixSugarsStructure(topIn, frameIn,
+                                        c1bondsearch, splitres, solventResName,
+                                        SugarBonds))
+    {
+      mprinterr("Error: Sugar structure modification failed.\n");
+      return 1;
+    }
+    if (sugarBuilder.PrepareSugars(true, resStat, topIn, frameIn, SugarBonds))
+    {
+      mprinterr("Error: Sugar preparation failed.\n");
+      return 1;
+    }
+  }
+  t_sugar_.Stop();
+
+  // Fill in atoms with templates
+  t_fill_.Start();
+  //Topology topOut;
+  Topology& topOut = static_cast<Topology&>( *(crdout.TopPtr()) );
+  topOut.SetDebug( debug_ );
+  if (outset.empty()) {
+    // In-place output COORDS. Copy over existing topology metadata
+    topOut.CopyTopMetadata( topIn );
+  }
+  if (!title.empty())
+    topOut.SetParmName( title, FileName() );
+  else if (topOut.ParmName().empty()) {
+    // TODO better default
+    topOut.SetParmName( std::string(topIn.c_str()), FileName() );
+  }
+  Frame frameOut;
+  if (FillAtomsWithTemplates(topOut, frameOut, topIn, frameIn, creator, SugarBonds)) {
+    mprinterr("Error: Could not fill in atoms using templates.\n");
+    return 1;
+  }
+  t_fill_.Stop();
+
+  // Add the disulfide/sugar bonds
+  int addBondsErr = transfer_bonds( topOut, topIn, DisulfideBonds );
+  //addBondsErr += transfer_bonds( topOut, topIn, SugarBonds );
+  if (addBondsErr != 0) {
+    mprinterr("Error: Adding disulfide/sugar bonds failed.\n");
+    return 1;
+  }
+
+  // Create empty arrays for the TREE, JOIN, and IROTAT arrays
+  topOut.AllocTreeChainClassification( );
+  topOut.AllocJoinArray();
+  topOut.AllocRotateArray();
+    // Finalize topology - determine molecules, dont renumber residues, dont assign default bond params
+  topOut.CommonSetup(true, false, false);
+  topOut.Summary();
+  t_assign_.Stop();
+
+  // Update coords 
+  if (crdout.CoordsSetup( topOut, frameOut.CoordsInfo() )) { // FIXME better coordinate info
+    mprinterr("Error: Could not set up output COORDS.\n");
+    return CpptrajState::ERR;
+  }
+  crdout.SetCRD(0, frameOut);
+  t_total_.Stop();
+
+  PrintTiming();
+
+  return 0;
+}
+
+void Exec_Build::PrintTiming() const {
   t_total_.WriteTiming(1, "Build timing:");
   t_hisDetect_.WriteTiming    (2, "Histidine detection :", t_total_.Total());
   t_clean_.WriteTiming        (2, "Structure clean     :", t_total_.Total());
@@ -1274,11 +1589,5 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
   t_disulfide_.WriteTiming    (2, "Disulfide detection :", t_total_.Total());
   t_sugar_.WriteTiming        (2, "Sugar preparation   :", t_total_.Total());
   t_fill_.WriteTiming         (2, "Fill missing atoms  :", t_total_.Total());
-  if (add_solvent)
-    t_solvate_.WriteTiming    (2, "Solvate             :", t_total_.Total());
-  t_check_.WriteTiming        (2, "Structure check     :", t_total_.Total());
-  t_assign_.WriteTiming       (2, "Param./Top. gen.    :", t_total_.Total());
-  AP.WriteAssignTiming(3, t_assign_.Total());
-
-  return ret;
 }
+
diff --git a/src/Exec_Build.h b/src/Exec_Build.h
index 68fab8c020..3bde139f43 100644
--- a/src/Exec_Build.h
+++ b/src/Exec_Build.h
@@ -15,10 +15,15 @@ class Exec_Build : public Exec {
     void Help() const;
     DispatchObject* Alloc() const { return (DispatchObject*)new Exec_Build(); }
     RetType Execute(CpptrajState&, ArgList&);
+
     /// Stand-alone execution
     RetType BuildStructure(DataSet*, DataSetList&, int, ArgList&, Cpptraj::Parm::GB_RadiiType);
     /// \return Output COORDS set
     DataSet* OutCrdPtr() const { return outCrdPtr_; }
+    /// Clean input coords, fill in missing atoms
+    int CleanAndFillStructure(DataSet*, int, std::string const&, std::string const&,
+                              DataSetList&, int, Cpptraj::Structure::Creator const&);
+    void PrintTiming() const;
   private:
     typedef std::vector<int> Iarray;
     // Keep track of which residues are connected to each other

From feaf64524ce29998351e906e16abdb8bfdf4ed34 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Mon, 22 Dec 2025 08:47:12 -0500
Subject: [PATCH 1152/1492] Start the AddIons class

---
 src/Structure/AddIons.cpp     | 54 +++++++++++++++++++++++++++++++++++
 src/Structure/AddIons.h       | 25 ++++++++++++++++
 src/Structure/CMakeLists.txt  |  1 +
 src/Structure/structuredepend |  1 +
 src/Structure/structurefiles  |  1 +
 src/cpptrajdepend             |  1 +
 6 files changed, 83 insertions(+)
 create mode 100644 src/Structure/AddIons.cpp
 create mode 100644 src/Structure/AddIons.h

diff --git a/src/Structure/AddIons.cpp b/src/Structure/AddIons.cpp
new file mode 100644
index 0000000000..81931d27c7
--- /dev/null
+++ b/src/Structure/AddIons.cpp
@@ -0,0 +1,54 @@
+#include "AddIons.h"
+#include "../CpptrajStdio.h"
+
+using namespace Cpptraj::Structure;
+
+/** CONSTRUCTOR */
+AddIons::AddIons() :
+  Nion1_(-1),
+  Nion2_(-1),
+  debug_(0),
+  separation_(0.0)
+{}
+
+/** Initialize */
+int AddIons::InitAddIons(std::string const& unitNameIn,
+                         std::string const& ion1nameIn, int Nion1,
+                         std::string const& ion2nameIn, int Nion2,
+                         double separationIn, int seedIn, int debugIn)
+{
+  debug_ = debugIn;
+
+  if (unitNameIn.empty()) {
+    mprinterr("Internal Error: AddIons::InitAddIons() called with empty unit name.\n");
+    return 1;
+  }
+  unitname_ = unitNameIn;
+
+  if (ion1nameIn.empty()) {
+    mprinterr("Internal Error: AddIons::InitAddIons() called with empty ion name.\n");
+    return 1;
+  }
+  ion1name_ = ion1nameIn;
+  if (Nion1 < 0) {
+    mprinterr("Error: Number of %s ions cannot be less than 0 (%i)\n", ion1nameIn.c_str(), Nion1);
+    return 1;
+  }
+  Nion1_ = Nion1;
+
+  if (ion2nameIn.empty()) {
+    ion2name_.clear();
+    Nion2_ = -1;
+  } else {
+    ion2name_ = ion2nameIn;
+    if (Nion2 < 0) {
+      mprinterr("Error: Number of %s ions cannot be less than 0 (%i)\n", ion2nameIn.c_str(), Nion2);
+      return 1;
+    }
+  }
+
+  separation_ = separationIn;
+  RNG_.rn_set( seedIn );
+
+  return 0;
+}
diff --git a/src/Structure/AddIons.h b/src/Structure/AddIons.h
new file mode 100644
index 0000000000..12bf0540fa
--- /dev/null
+++ b/src/Structure/AddIons.h
@@ -0,0 +1,25 @@
+#ifndef INC_CPPTRAJ_STRUCTURE_ADDIONS_H
+#define INC_CPPTRAJ_STRUCTURE_ADDIONS_H
+#include "../Random.h"
+#include <string>
+namespace Cpptraj {
+namespace Structure {
+/// Used to add ions to a system
+class AddIons {
+  public:
+    AddIons();
+    /// Init - unit, ion1, Nion1, ion2, Nion2, separation, random seed, debug
+    int InitAddIons(std::string const&, std::string const&, int, std::string const&, int, double, int, int);
+  private:
+    std::string unitname_; ///< System to add ions to
+    std::string ion1name_; ///< Name of first ion
+    std::string ion2name_; ///< Name of second ion
+    int Nion1_; ///< Number of first ion to add
+    int Nion2_; ///< Number of second ion to add
+    int debug_;
+    double separation_; ///< Min. distance in Angstroms any ion can be from another ion
+    Random_Number RNG_; ///< Random number generator
+};
+}
+}
+#endif
diff --git a/src/Structure/CMakeLists.txt b/src/Structure/CMakeLists.txt
index 74ad593545..a98547d991 100644
--- a/src/Structure/CMakeLists.txt
+++ b/src/Structure/CMakeLists.txt
@@ -1,5 +1,6 @@
 #CMake buildfile for CPPTRAJ Structure subdirectory.
 target_sources(cpptraj_common_obj PRIVATE
+  ${CMAKE_CURRENT_LIST_DIR}/AddIons.cpp
   ${CMAKE_CURRENT_LIST_DIR}/Builder.cpp
   ${CMAKE_CURRENT_LIST_DIR}/Chirality.cpp
   ${CMAKE_CURRENT_LIST_DIR}/Creator.cpp
diff --git a/src/Structure/structuredepend b/src/Structure/structuredepend
index d264dd97ae..94eab58aaa 100644
--- a/src/Structure/structuredepend
+++ b/src/Structure/structuredepend
@@ -1,3 +1,4 @@
+AddIons.o : AddIons.cpp ../CpptrajStdio.h ../Random.h AddIons.h
 Builder.o : Builder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/../AtomType.h ../Parm/../CmapParmHolder.h ../Parm/../Constants.h ../Parm/../NameType.h ../Parm/../ParameterTypes.h ../Parm/../Parm/ParmEnum.h ../Parm/../TypeNameHolder.h ../Parm/DihedralParmHolder.h ../Parm/ImproperParmHolder.h ../Parm/ParameterSet.h ../Parm/ParmEnum.h ../Parm/ParmHolder.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Builder.h Chirality.h GenerateConnectivityArrays.h InternalCoords.h StructureEnum.h Zmatrix.h
 Chirality.o : Chirality.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../Unit.h ../Vec3.h Chirality.h StructureEnum.h
 Creator.o : Creator.cpp ../ArgList.h ../AssociatedData.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../DataSet_NameMap.h ../DataSet_Parameters.h ../DataSet_PdbResMap.h ../Dimension.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/../AtomType.h ../Parm/../CmapParmHolder.h ../Parm/../Constants.h ../Parm/../NameType.h ../Parm/../ParameterTypes.h ../Parm/../Parm/ParmEnum.h ../Parm/../TypeNameHolder.h ../Parm/DihedralParmHolder.h ../Parm/ImproperParmHolder.h ../Parm/ParameterSet.h ../Parm/ParmEnum.h ../Parm/ParmHolder.h ../PdbResMapType.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/StructureEnum.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h Creator.h GenerateConnectivityArrays.h StructureEnum.h
diff --git a/src/Structure/structurefiles b/src/Structure/structurefiles
index bba6cf75af..3f53f820b1 100644
--- a/src/Structure/structurefiles
+++ b/src/Structure/structurefiles
@@ -1,5 +1,6 @@
 # Files for Structure subdirectory.
 STRUCTURE_SOURCES= \
+  AddIons.cpp \
   Builder.cpp \
   Chirality.cpp \
   Creator.cpp \
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 61ba9e73ba..a2062d832c 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -479,6 +479,7 @@ Spline.o : Spline.cpp CpptrajStdio.h Spline.h
 SplineFxnTable.o : SplineFxnTable.cpp Constants.h CpptrajStdio.h Spline.h SplineFxnTable.h StringRoutines.h
 Stats_Reduce.o : Stats_Reduce.cpp OnlineVarT.h Parallel.h Stats_Reduce.h
 StringRoutines.o : StringRoutines.cpp CpptrajStdio.h StringRoutines.h
+Structure/AddIons.o : Structure/AddIons.cpp CpptrajStdio.h Random.h Structure/AddIons.h
 Structure/Builder.o : Structure/Builder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h GuessAtomHybridization.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/../Parm/../AtomType.h Structure/../Parm/../CmapParmHolder.h Structure/../Parm/../Constants.h Structure/../Parm/../NameType.h Structure/../Parm/../ParameterTypes.h Structure/../Parm/../Parm/ParmEnum.h Structure/../Parm/../TypeNameHolder.h Structure/../Parm/DihedralParmHolder.h Structure/../Parm/ImproperParmHolder.h Structure/../Parm/ParameterSet.h Structure/../Parm/ParmEnum.h Structure/../Parm/ParmHolder.h Structure/Builder.h Structure/Chirality.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 Structure/Chirality.o : Structure/Chirality.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Chirality.h Structure/StructureEnum.h SymbolExporting.h Topology.h TorsionRoutines.h Unit.h Vec3.h
 Structure/Creator.o : Structure/Creator.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h DataSet_Parameters.h DataSet_PdbResMap.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h PdbResMapType.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/Creator.h Structure/GenerateConnectivityArrays.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h

From 4eb94f3c56a30499f8c3a4592f918e81328590bc Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Mon, 22 Dec 2025 09:14:24 -0500
Subject: [PATCH 1153/1492] Add function to return total charge. Do not save
 unit name, the classes will be passed in.

---
 src/Structure/AddIons.cpp | 51 +++++++++++++++++++++++++++------------
 src/Structure/AddIons.h   | 10 +++++++-
 src/Topology.cpp          |  9 +++++++
 src/Topology.h            |  2 ++
 4 files changed, 56 insertions(+), 16 deletions(-)

diff --git a/src/Structure/AddIons.cpp b/src/Structure/AddIons.cpp
index 81931d27c7..ba06edeaa7 100644
--- a/src/Structure/AddIons.cpp
+++ b/src/Structure/AddIons.cpp
@@ -1,5 +1,6 @@
 #include "AddIons.h"
 #include "../CpptrajStdio.h"
+#include "../Topology.h"
 
 using namespace Cpptraj::Structure;
 
@@ -12,43 +13,63 @@ AddIons::AddIons() :
 {}
 
 /** Initialize */
-int AddIons::InitAddIons(std::string const& unitNameIn,
-                         std::string const& ion1nameIn, int Nion1,
+int AddIons::InitAddIons(std::string const& ion1nameIn, int Nion1,
                          std::string const& ion2nameIn, int Nion2,
                          double separationIn, int seedIn, int debugIn)
 {
   debug_ = debugIn;
 
-  if (unitNameIn.empty()) {
-    mprinterr("Internal Error: AddIons::InitAddIons() called with empty unit name.\n");
-    return 1;
-  }
-  unitname_ = unitNameIn;
-
   if (ion1nameIn.empty()) {
-    mprinterr("Internal Error: AddIons::InitAddIons() called with empty ion name.\n");
+    mprinterr("Error: Must specify at least one ion name.\n");
     return 1;
   }
   ion1name_ = ion1nameIn;
   if (Nion1 < 0) {
-    mprinterr("Error: Number of %s ions cannot be less than 0 (%i)\n", ion1nameIn.c_str(), Nion1);
-    return 1;
-  }
-  Nion1_ = Nion1;
+    //mprinterr("Error: Number of %s ions cannot be less than 0 (%i)\n", ion1nameIn.c_str(), Nion1);
+    //return 1;
+    Nion1_ = 0;
+  } else
+    Nion1_ = Nion1;
 
   if (ion2nameIn.empty()) {
     ion2name_.clear();
     Nion2_ = -1;
   } else {
     ion2name_ = ion2nameIn;
-    if (Nion2 < 0) {
-      mprinterr("Error: Number of %s ions cannot be less than 0 (%i)\n", ion2nameIn.c_str(), Nion2);
+    if (Nion2 < 1) {
+      mprinterr("Error: Number of second %s ions cannot be less than 1 (%i)\n", ion2nameIn.c_str(), Nion2);
       return 1;
     }
   }
 
   separation_ = separationIn;
+  if (separation_ < 0.0) {
+    mprinterr("Error: Separation must be >= 0.0 (%f)\n", separation_);
+    return 1;
+  }
+
   RNG_.rn_set( seedIn );
 
   return 0;
 }
+
+/** Add ions randomly, replacing solvent molecules. */
+int AddIons::AddIonsRand(Topology& topOut, Frame& frameOut, DataSetList const& DSL,
+                         Cpptraj::Parm::ParameterSet const& set0)
+const
+{
+  // Unit total charge
+  double totalCharge = topOut.TotalCharge();
+  if ( fabs(totalCharge) < Constants::SMALL ) {
+    mprintf("Warning: %s has a total charge of 0.\n", topOut.c_str());
+    if (Nion1_ < 1) {
+      mprintf("Warning: Cannot neutralize.\n");
+      return 0;
+    }
+    mprintf("Warning: Adding the ions anyway.\n");
+  } else {
+    mprintf("\tTotal charge on %s is %g\n", topOut.c_str(), totalCharge);
+  }
+
+  return 0;
+}
diff --git a/src/Structure/AddIons.h b/src/Structure/AddIons.h
index 12bf0540fa..a8a7dde171 100644
--- a/src/Structure/AddIons.h
+++ b/src/Structure/AddIons.h
@@ -2,14 +2,22 @@
 #define INC_CPPTRAJ_STRUCTURE_ADDIONS_H
 #include "../Random.h"
 #include <string>
+class DataSetList;
+class Frame;
+class Topology;
 namespace Cpptraj {
+namespace Parm {
+class ParameterSet;
+}
 namespace Structure {
 /// Used to add ions to a system
 class AddIons {
   public:
     AddIons();
     /// Init - unit, ion1, Nion1, ion2, Nion2, separation, random seed, debug
-    int InitAddIons(std::string const&, std::string const&, int, std::string const&, int, double, int, int);
+    int InitAddIons(std::string const&, int, std::string const&, int, double, int, int);
+    /// Add ions randomly
+    int AddIonsRand(Topology&, Frame&, DataSetList const&, Cpptraj::Parm::ParameterSet const&) const;
   private:
     std::string unitname_; ///< System to add ions to
     std::string ion1name_; ///< Name of first ion
diff --git a/src/Topology.cpp b/src/Topology.cpp
index cd070d6173..c61ecbb879 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2401,6 +2401,15 @@ bool Topology::HasChargeInfo() const {
   return false;
 }
 
+/** \return Total charge */
+double Topology::TotalCharge() const {
+  double sumQ = 0.0;
+  for (std::vector<Atom>::const_iterator at = atoms_.begin();
+                                         at != atoms_.end(); ++at)
+    sumQ += at->Charge();
+  return sumQ;
+}
+
 /** Redistribute charge on atoms to match given total target charge. */
 int Topology::RedistributeCharge(double charge) {
   //mprintf("DEBUG: Redistribute charge for %s, total charge = %g\n", topIn.c_str(), charge);
diff --git a/src/Topology.h b/src/Topology.h
index 25025de48e..eea1d8e0f0 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -185,6 +185,8 @@ class Topology {
     inline NonbondType const& GetLJparam(int, int) const;
     /// \return True if any charge is non-zero
     bool HasChargeInfo() const;
+    /// \return Total charge
+    double TotalCharge() const;
     /// Redistribute charge on atoms in topology to match target total charge
     int RedistributeCharge(double);
     // ----- Water Cap Info ----------------------

From 895a6a396b33fde3ad536006cc8358380395f361 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Mon, 22 Dec 2025 09:20:07 -0500
Subject: [PATCH 1154/1492] Print info

---
 src/Structure/AddIons.cpp | 13 +++++++++++++
 src/Structure/AddIons.h   |  2 ++
 2 files changed, 15 insertions(+)

diff --git a/src/Structure/AddIons.cpp b/src/Structure/AddIons.cpp
index ba06edeaa7..3f706689b4 100644
--- a/src/Structure/AddIons.cpp
+++ b/src/Structure/AddIons.cpp
@@ -53,6 +53,19 @@ int AddIons::InitAddIons(std::string const& ion1nameIn, int Nion1,
   return 0;
 }
 
+/** Print setup info to stdout */
+void AddIons::PrintAddIonsInfo() const {
+  if (ion1name_.empty()) return;
+  if (Nion1_ < 1)
+    mprintf("\tAdding enough %s ions to neutralize.\n");
+  else
+    mprintf("\tAdding %i %s ions.\n", Nion1_, ion1name_.c_str());
+  if (!ion2name_.empty())
+    mprintf("\tAdding %i %s ions.\n", Nion2_, ion2name_.c_str());
+  mprintf("\tMinimum ion separation is %g Ang.\n", separation_);
+  mprintf("\tIon RNG seed: %i\n", RNG_.Seed());
+}
+
 /** Add ions randomly, replacing solvent molecules. */
 int AddIons::AddIonsRand(Topology& topOut, Frame& frameOut, DataSetList const& DSL,
                          Cpptraj::Parm::ParameterSet const& set0)
diff --git a/src/Structure/AddIons.h b/src/Structure/AddIons.h
index a8a7dde171..50c217dcfa 100644
--- a/src/Structure/AddIons.h
+++ b/src/Structure/AddIons.h
@@ -16,6 +16,8 @@ class AddIons {
     AddIons();
     /// Init - unit, ion1, Nion1, ion2, Nion2, separation, random seed, debug
     int InitAddIons(std::string const&, int, std::string const&, int, double, int, int);
+    /// Print info to stdout
+    void PrintAddIonsInfo() const;
     /// Add ions randomly
     int AddIonsRand(Topology&, Frame&, DataSetList const&, Cpptraj::Parm::ParameterSet const&) const;
   private:

From 2276ddc88e913daec7f81d2d869030b975334934 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Mon, 22 Dec 2025 09:36:32 -0500
Subject: [PATCH 1155/1492] Start calling addions from build

---
 src/Exec_Build.cpp        | 25 +++++++++++++++++++++++++
 src/Structure/AddIons.cpp |  2 +-
 src/Structure/AddIons.h   |  4 +++-
 src/cpptrajdepend         |  4 ++--
 4 files changed, 31 insertions(+), 4 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 5d7047137d..d567790b40 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -6,6 +6,7 @@
 #include "StringRoutines.h" // integerToString
 #include "Trajout_Single.h"
 #include "Parm/AssignParams.h"
+#include "Structure/AddIons.h"
 #include "Structure/Builder.h"
 #include "Structure/Creator.h"
 #include "Structure/Disulfide.h"
@@ -909,6 +910,23 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
     }
   }
 
+  Cpptraj::Structure::AddIons addIons;
+  if (add_solvent == SOLVATEBOX) {
+    if (argIn.hasKey("addionsrand")) {
+      std::string ion1name = argIn.GetStringKey("ion1");
+      int nion1 = argIn.getKeyInt("nion1", -1);
+      std::string ion2name = argIn.GetStringKey("ion2");
+      int nion2 = argIn.getKeyInt("nion2", -1);
+      double minsep = argIn.getKeyDouble("minsep", 0.0);
+      int ionseed = argIn.getKeyInt("ionseed", -1);
+      if (addIons.InitAddIons(ion1name, nion1, ion2name, nion2, minsep, ionseed, debug_)) {
+        mprinterr("Error: Init addions failed.\n");
+        return CpptrajState::ERR;
+      }
+      addIons.PrintAddIonsInfo();
+    }
+  }
+
   keepMissingSourceAtoms_ = argIn.hasKey("keepmissingatoms");
   if (keepMissingSourceAtoms_)
     mprintf("\tInput atoms missing from templates will be kept.\n");
@@ -1132,6 +1150,13 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
     // Since by design the SolvateBox routine ensures solvent does not
     // clash with solute, just check the solute.
     checkMaskString.assign( "@1-" + integerToString(initial_natom) );
+    // Add ions if needed
+    if (addIons.IsSetup()) {
+      if (addIons.AddIonsRand( topOut, frameOut, DSL, *(creator.MainParmSetPtr()) )) {
+        mprinterr("Error: Adding ions failed.\n");
+        return CpptrajState::ERR;
+      }
+    }
     t_solvate_.Stop();
   } else if (add_solvent == SETBOX) {
     t_solvate_.Start();
diff --git a/src/Structure/AddIons.cpp b/src/Structure/AddIons.cpp
index 3f706689b4..460c5ed9c7 100644
--- a/src/Structure/AddIons.cpp
+++ b/src/Structure/AddIons.cpp
@@ -57,7 +57,7 @@ int AddIons::InitAddIons(std::string const& ion1nameIn, int Nion1,
 void AddIons::PrintAddIonsInfo() const {
   if (ion1name_.empty()) return;
   if (Nion1_ < 1)
-    mprintf("\tAdding enough %s ions to neutralize.\n");
+    mprintf("\tAdding enough %s ions to neutralize.\n", ion1name_.c_str());
   else
     mprintf("\tAdding %i %s ions.\n", Nion1_, ion1name_.c_str());
   if (!ion2name_.empty())
diff --git a/src/Structure/AddIons.h b/src/Structure/AddIons.h
index 50c217dcfa..aae9d6a674 100644
--- a/src/Structure/AddIons.h
+++ b/src/Structure/AddIons.h
@@ -20,8 +20,10 @@ class AddIons {
     void PrintAddIonsInfo() const;
     /// Add ions randomly
     int AddIonsRand(Topology&, Frame&, DataSetList const&, Cpptraj::Parm::ParameterSet const&) const;
+
+    /// \return True if at least 1 ion has been specified.
+    bool IsSetup() const { return !ion1name_.empty(); }
   private:
-    std::string unitname_; ///< System to add ions to
     std::string ion1name_; ///< Name of first ion
     std::string ion2name_; ///< Name of second ion
     int Nion1_; ///< Number of first ion to add
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index a2062d832c..1dd23bc0c4 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -316,7 +316,7 @@ EwaldOptions.o : EwaldOptions.cpp ArgList.h CpptrajStdio.h EwaldOptions.h
 ExclusionArray.o : ExclusionArray.cpp Atom.h AtomMask.h CharMask.h CpptrajStdio.h ExclusionArray.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Unit.h
 Exec_AddMissingRes.o : Exec_AddMissingRes.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h CharMask.h CompactFrameArray.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_AddMissingRes.h Exec_AddMissingRes_Pres.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h ParmFile.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h Trajout_Single.h Unit.h Vec3.h
 Exec_Analyze.o : Exec_Analyze.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Analyze.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_Build.o : Exec_Build.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h ExclusionArray.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PairList.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/Builder.h Structure/Creator.h Structure/Disulfide.h Structure/HisProt.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/RingFinder.h Structure/Solvate.h Structure/StructureEnum.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Build.o : Exec_Build.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h ExclusionArray.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PairList.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h ParmFile.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/AddIons.h Structure/Builder.h Structure/Creator.h Structure/Disulfide.h Structure/HisProt.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/RingFinder.h Structure/Solvate.h Structure/StructureEnum.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Calc.o : Exec_Calc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Calc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_CatCrd.o : Exec_CatCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CatCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_Change.o : Exec_Change.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Change.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
@@ -479,7 +479,7 @@ Spline.o : Spline.cpp CpptrajStdio.h Spline.h
 SplineFxnTable.o : SplineFxnTable.cpp Constants.h CpptrajStdio.h Spline.h SplineFxnTable.h StringRoutines.h
 Stats_Reduce.o : Stats_Reduce.cpp OnlineVarT.h Parallel.h Stats_Reduce.h
 StringRoutines.o : StringRoutines.cpp CpptrajStdio.h StringRoutines.h
-Structure/AddIons.o : Structure/AddIons.cpp CpptrajStdio.h Random.h Structure/AddIons.h
+Structure/AddIons.o : Structure/AddIons.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Random.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/AddIons.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Structure/Builder.o : Structure/Builder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h GuessAtomHybridization.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/../Parm/../AtomType.h Structure/../Parm/../CmapParmHolder.h Structure/../Parm/../Constants.h Structure/../Parm/../NameType.h Structure/../Parm/../ParameterTypes.h Structure/../Parm/../Parm/ParmEnum.h Structure/../Parm/../TypeNameHolder.h Structure/../Parm/DihedralParmHolder.h Structure/../Parm/ImproperParmHolder.h Structure/../Parm/ParameterSet.h Structure/../Parm/ParmEnum.h Structure/../Parm/ParmHolder.h Structure/Builder.h Structure/Chirality.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 Structure/Chirality.o : Structure/Chirality.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Chirality.h Structure/StructureEnum.h SymbolExporting.h Topology.h TorsionRoutines.h Unit.h Vec3.h
 Structure/Creator.o : Structure/Creator.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h DataSet_Parameters.h DataSet_PdbResMap.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h PdbResMapType.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/Creator.h Structure/GenerateConnectivityArrays.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h

From 8ff28741faf811e9d1fabb6db3f098ec5c5eba70 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Mon, 22 Dec 2025 09:46:32 -0500
Subject: [PATCH 1156/1492] Start getting ion unit

---
 src/Structure/AddIons.cpp     | 48 +++++++++++++++++++++++++++++++++++
 src/Structure/AddIons.h       |  4 +++
 src/Structure/structuredepend |  2 +-
 src/cpptrajdepend             |  2 +-
 4 files changed, 54 insertions(+), 2 deletions(-)

diff --git a/src/Structure/AddIons.cpp b/src/Structure/AddIons.cpp
index 460c5ed9c7..c76d728d44 100644
--- a/src/Structure/AddIons.cpp
+++ b/src/Structure/AddIons.cpp
@@ -1,5 +1,7 @@
 #include "AddIons.h"
 #include "../CpptrajStdio.h"
+#include "../DataSet_Coords.h"
+#include "../DataSetList.h"
 #include "../Topology.h"
 
 using namespace Cpptraj::Structure;
@@ -66,6 +68,45 @@ void AddIons::PrintAddIonsInfo() const {
   mprintf("\tIon RNG seed: %i\n", RNG_.Seed());
 }
 
+/** Get ion unit box from DataSetList. */ // TODO consolidate with Solvate::GetSolventUnit()?
+DataSet_Coords* AddIons::GetIonUnit(std::string const& ionname, DataSetList const& DSL) const {
+  if (ionname.empty()) {
+    mprinterr("Internal Error: AddIons::GetIonUnit() called before ion name set.\n");
+    return 0;
+  }
+  DataSetList sets = DSL.SelectGroupSets( "*", DataSet::COORDINATES ); // TODO specific set type for units?
+  // First try to match aspect, then match name
+  DataSet_Coords* ionUnit = 0;
+  // Aspect
+  for (DataSetList::const_iterator it = sets.begin(); it != sets.end(); ++it)
+  {
+    DataSet_Coords* ds = static_cast<DataSet_Coords*>( *it );
+    if (!ds->Meta().Aspect().empty()) {
+      if (ionname == ds->Meta().Aspect()) {
+        ionUnit = ds;
+        break;
+      }
+    }
+  }
+  // Name
+  if (ionUnit == 0) {
+    for (DataSetList::const_iterator it = sets.begin(); it != sets.end(); ++it)
+    {
+      DataSet_Coords* ds = static_cast<DataSet_Coords*>( *it );
+      if (ionname == ds->Meta().Name()) {
+        ionUnit = ds;
+        break;
+      }
+    }
+  }
+  if (ionUnit != 0)
+    mprintf("\tIon unit: %s\n", ionUnit->legend());
+  else
+    mprinterr("Error: Could not get ion unit named %s\n", ionname.c_str());
+
+  return ionUnit;
+}
+
 /** Add ions randomly, replacing solvent molecules. */
 int AddIons::AddIonsRand(Topology& topOut, Frame& frameOut, DataSetList const& DSL,
                          Cpptraj::Parm::ParameterSet const& set0)
@@ -84,5 +125,12 @@ const
     mprintf("\tTotal charge on %s is %g\n", topOut.c_str(), totalCharge);
   }
 
+  // Get first ion
+  DataSet_Coords* Ion1 = GetIonUnit( ion1name_, DSL );
+  if (Ion1 == 0) {
+    mprinterr("Error: Ion with name '%s' not found.\n", ion1name_.c_str());
+    return 1;
+  }
+
   return 0;
 }
diff --git a/src/Structure/AddIons.h b/src/Structure/AddIons.h
index aae9d6a674..df26f6f000 100644
--- a/src/Structure/AddIons.h
+++ b/src/Structure/AddIons.h
@@ -2,6 +2,7 @@
 #define INC_CPPTRAJ_STRUCTURE_ADDIONS_H
 #include "../Random.h"
 #include <string>
+class DataSet_Coords;
 class DataSetList;
 class Frame;
 class Topology;
@@ -24,6 +25,9 @@ class AddIons {
     /// \return True if at least 1 ion has been specified.
     bool IsSetup() const { return !ion1name_.empty(); }
   private:
+    /// \return Ion unit specified by given name
+    DataSet_Coords* GetIonUnit(std::string const&, DataSetList const&) const;
+
     std::string ion1name_; ///< Name of first ion
     std::string ion2name_; ///< Name of second ion
     int Nion1_; ///< Number of first ion to add
diff --git a/src/Structure/structuredepend b/src/Structure/structuredepend
index 94eab58aaa..632c3cccc4 100644
--- a/src/Structure/structuredepend
+++ b/src/Structure/structuredepend
@@ -1,4 +1,4 @@
-AddIons.o : AddIons.cpp ../CpptrajStdio.h ../Random.h AddIons.h
+AddIons.o : AddIons.cpp ../AssociatedData.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../Dimension.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Random.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h AddIons.h
 Builder.o : Builder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/../AtomType.h ../Parm/../CmapParmHolder.h ../Parm/../Constants.h ../Parm/../NameType.h ../Parm/../ParameterTypes.h ../Parm/../Parm/ParmEnum.h ../Parm/../TypeNameHolder.h ../Parm/DihedralParmHolder.h ../Parm/ImproperParmHolder.h ../Parm/ParameterSet.h ../Parm/ParmEnum.h ../Parm/ParmHolder.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Builder.h Chirality.h GenerateConnectivityArrays.h InternalCoords.h StructureEnum.h Zmatrix.h
 Chirality.o : Chirality.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../Unit.h ../Vec3.h Chirality.h StructureEnum.h
 Creator.o : Creator.cpp ../ArgList.h ../AssociatedData.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../DataSet_NameMap.h ../DataSet_Parameters.h ../DataSet_PdbResMap.h ../Dimension.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/../AtomType.h ../Parm/../CmapParmHolder.h ../Parm/../Constants.h ../Parm/../NameType.h ../Parm/../ParameterTypes.h ../Parm/../Parm/ParmEnum.h ../Parm/../TypeNameHolder.h ../Parm/DihedralParmHolder.h ../Parm/ImproperParmHolder.h ../Parm/ParameterSet.h ../Parm/ParmEnum.h ../Parm/ParmHolder.h ../PdbResMapType.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/StructureEnum.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h Creator.h GenerateConnectivityArrays.h StructureEnum.h
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 1dd23bc0c4..c411d0c906 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -479,7 +479,7 @@ Spline.o : Spline.cpp CpptrajStdio.h Spline.h
 SplineFxnTable.o : SplineFxnTable.cpp Constants.h CpptrajStdio.h Spline.h SplineFxnTable.h StringRoutines.h
 Stats_Reduce.o : Stats_Reduce.cpp OnlineVarT.h Parallel.h Stats_Reduce.h
 StringRoutines.o : StringRoutines.cpp CpptrajStdio.h StringRoutines.h
-Structure/AddIons.o : Structure/AddIons.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Random.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/AddIons.h SymbolExporting.h Topology.h Unit.h Vec3.h
+Structure/AddIons.o : Structure/AddIons.cpp AssociatedData.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/AddIons.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 Structure/Builder.o : Structure/Builder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h GuessAtomHybridization.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/../Parm/../AtomType.h Structure/../Parm/../CmapParmHolder.h Structure/../Parm/../Constants.h Structure/../Parm/../NameType.h Structure/../Parm/../ParameterTypes.h Structure/../Parm/../Parm/ParmEnum.h Structure/../Parm/../TypeNameHolder.h Structure/../Parm/DihedralParmHolder.h Structure/../Parm/ImproperParmHolder.h Structure/../Parm/ParameterSet.h Structure/../Parm/ParmEnum.h Structure/../Parm/ParmHolder.h Structure/Builder.h Structure/Chirality.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 Structure/Chirality.o : Structure/Chirality.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Chirality.h Structure/StructureEnum.h SymbolExporting.h Topology.h TorsionRoutines.h Unit.h Vec3.h
 Structure/Creator.o : Structure/Creator.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h DataSet_Parameters.h DataSet_PdbResMap.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h PdbResMapType.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/Creator.h Structure/GenerateConnectivityArrays.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h

From 66090c7009c0be9d1e877d7069121c8fe2db45e3 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Mon, 22 Dec 2025 10:01:37 -0500
Subject: [PATCH 1157/1492] Ion charge check. Do neutralization calc

---
 src/Structure/AddIons.cpp | 40 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

diff --git a/src/Structure/AddIons.cpp b/src/Structure/AddIons.cpp
index c76d728d44..49c4e88e47 100644
--- a/src/Structure/AddIons.cpp
+++ b/src/Structure/AddIons.cpp
@@ -1,8 +1,10 @@
 #include "AddIons.h"
+#include "../Constants.h"
 #include "../CpptrajStdio.h"
 #include "../DataSet_Coords.h"
 #include "../DataSetList.h"
 #include "../Topology.h"
+#include <cmath> //fabs, lrint
 
 using namespace Cpptraj::Structure;
 
@@ -131,6 +133,44 @@ const
     mprinterr("Error: Ion with name '%s' not found.\n", ion1name_.c_str());
     return 1;
   }
+  // Check that there is a net charge
+  double chargeIon1 = Ion1->Top().TotalCharge();
+  if ( fabs(chargeIon1) < Constants::SMALL) {
+    mprinterr("Error: Ion unit 1 '%s' does not have a net charge\n", Ion1->legend());
+    return 1;
+  }
+
+  // Get second ion
+  DataSet_Coords* Ion2 = 0;
+  double chargeIon2 = 0.0;
+  if (!ion2name_.empty()) {
+    Ion2 = GetIonUnit( ion2name_, DSL );
+    if (Ion2 == 0) {
+      mprinterr("Error: Ion with name '%s' not found.\n", ion2name_.c_str());
+      return 1;
+    }
+    // Check that there is a net charge
+    chargeIon2 = Ion2->Top().TotalCharge();
+    if ( fabs(chargeIon2) < Constants::SMALL) {
+      mprinterr("Error: Ion unit 2 '%s' does not have a net charge\n", Ion2->legend());
+      return 1;
+    }
+  }
+
+  // Check that ion can actually neutralize
+  int iIon1 = Nion1_;
+  if (Nion1_ < 1) {
+    if ( (chargeIon1 < 0 && totalCharge < 0) ||
+         (chargeIon1 > 0 && totalCharge > 0) )
+    {
+      mprinterr("Error: First ion and system charges have same sign (%g and %g); can't neutralize.\n",
+                chargeIon1, totalCharge);
+      return 1;
+    }
+    // Get the nearest integer number of ions needed to neutralize the system.
+    iIon1 = (int)lrint( fabs(totalCharge) / fabs(chargeIon1) );
+    mprintf("\tNumber of %s ions required to neutralize: %i\n", ion1name_.c_str(), iIon1);
+  }
 
   return 0;
 }

From 52b827058fea6a9c762c5654383e6d4f71fdf189 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Mon, 22 Dec 2025 12:31:51 -0500
Subject: [PATCH 1158/1492] Create an AddSolventResidues() function for
 Topology. This will allow quick adding of new molecules to an existing
 "complete" Topology without having to e.g. redo the molecule search. Should
 make it easier to eventually create a separate 'solvate' command.

---
 src/Exec_Build.cpp        | 15 ++++++-----
 src/Structure/AddIons.cpp | 37 ++++++++++++++++++++++++++++
 src/Structure/Solvate.cpp |  7 +++---
 src/Topology.cpp          | 52 +++++++++++++++++++++++++++++++++++++++
 src/Topology.h            |  2 ++
 5 files changed, 104 insertions(+), 9 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index d567790b40..0e6a3e9d64 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -1130,6 +1130,14 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
     return CpptrajState::ERR;
   }
 
+  // Create empty arrays for the TREE, JOIN, and IROTAT arrays
+  topOut.AllocTreeChainClassification( );
+  topOut.AllocJoinArray();
+  topOut.AllocRotateArray();
+    // Finalize topology - determine molecules, dont renumber residues, dont assign default bond params
+  topOut.CommonSetup(true, false, false);
+
+  // Solvate/add ions
   std::string checkMaskString("*");
   if (add_solvent == SOLVATEBOX) {
     t_solvate_.Start();
@@ -1183,12 +1191,7 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
     mprinterr("Error: Could not assign GB parameters for '%s'\n", topOut.c_str());
     ret = CpptrajState::ERR;
   }
-  // Create empty arrays for the TREE, JOIN, and IROTAT arrays
-  topOut.AllocTreeChainClassification( );
-  topOut.AllocJoinArray();
-  topOut.AllocRotateArray();
-    // Finalize topology - determine molecules, dont renumber residues, dont assign default bond params
-  topOut.CommonSetup(true, false, false);
+
   topOut.Summary();
   t_assign_.Stop();
 
diff --git a/src/Structure/AddIons.cpp b/src/Structure/AddIons.cpp
index 49c4e88e47..9d2eeb6515 100644
--- a/src/Structure/AddIons.cpp
+++ b/src/Structure/AddIons.cpp
@@ -1,4 +1,7 @@
 #include "AddIons.h"
+#include "../Parm/ParameterSet.h"
+#include "../Parm/ParmHolder.h"
+#include "../AtomType.h"
 #include "../Constants.h"
 #include "../CpptrajStdio.h"
 #include "../DataSet_Coords.h"
@@ -109,6 +112,28 @@ DataSet_Coords* AddIons::GetIonUnit(std::string const& ionname, DataSetList cons
   return ionUnit;
 }
 
+/// \return Array containing radii for every atom
+static inline std::vector<double> GetAtomRadii(DataSet_Coords* crd, Cpptraj::Parm::ParmHolder<AtomType> const& newAtomTypeParams)
+{
+  static const double ATOM_DEFAULT_RADIUS = 1.5; // To match LEAP
+  std::vector<double> OUT;
+  OUT.reserve( crd->Top().Natom() );
+
+  for (std::vector<Atom>::const_iterator at = crd->Top().begin(); at != crd->Top().end(); ++at)
+  {
+    bool found;
+    TypeNameHolder atype( at->Type() );
+    AtomType AT = newAtomTypeParams.FindParam( atype, found );
+    if (found && AT.HasLJ())
+      OUT.push_back( AT.LJ().Radius() );
+    else {
+      mprintf("Warning: Atom type parameter not found for '%s', using default radius %g\n", *atype[0], ATOM_DEFAULT_RADIUS);
+      OUT.push_back( ATOM_DEFAULT_RADIUS );
+    }
+  }
+  return OUT;
+}
+
 /** Add ions randomly, replacing solvent molecules. */
 int AddIons::AddIonsRand(Topology& topOut, Frame& frameOut, DataSetList const& DSL,
                          Cpptraj::Parm::ParameterSet const& set0)
@@ -172,5 +197,17 @@ const
     mprintf("\tNumber of %s ions required to neutralize: %i\n", ion1name_.c_str(), iIon1);
   }
 
+  // Get atom radius for each ion
+  typedef std::vector<double> Darray;
+
+  Darray ion1radii, ion2radii;
+
+  ion1radii = GetAtomRadii( Ion1, set0.AT() );
+
+  if (Ion2 != 0)
+    ion2radii = GetAtomRadii( Ion2, set0.AT() );
+
+  mprintf("DEBUG: Nsolvent = %i\n", topOut.Nsolvent());
+
   return 0;
 }
diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index ca26b3da4d..27bb67d88b 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -794,9 +794,10 @@ const
         currentSolventCenter[2] = dZ;
 
         // Add valid residues from solvent unit to output topology for this cube
-        int currentResNum = topOut.Nres();
+//        int currentResNum = topOut.Nres();
         //for (int ires = 0; ires != solventTop.Nres(); ires++)
-        for (std::vector<int>::const_iterator ires = validSolventResidues.begin();
+        topOut.AddSolventResidues( solventTop, validSolventResidues, frameOut, solventFrame );
+/*        for (std::vector<int>::const_iterator ires = validSolventResidues.begin();
                                               ires != validSolventResidues.end(); ++ires)
         {
           int atomOffset = topOut.Natom();
@@ -828,7 +829,7 @@ const
             ++it;
             topOut.AddBond( at0, *it );
           }
-        } // END loop over solvent unit residues
+        } // END loop over solvent unit residues*/
         // Append solvent frame
         //frameOut.AppendFrame( solventFrame );
       } // END loop over Z
diff --git a/src/Topology.cpp b/src/Topology.cpp
index c61ecbb879..2ceec1a759 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -493,6 +493,58 @@ int Topology::addTopAtom(Atom const& atomIn, Residue const& resIn,
   return 0;
 }
 
+/** Add specified solvent residues from given topology to this topology. */
+int Topology::AddSolventResidues(Topology const& solventTop, std::vector<int> const& solventResNums,
+                                 Frame& frameOut, Frame const& solventFrame)
+{
+  std::vector<int> bondedAtoms;
+  for (std::vector<int>::const_iterator ires = solventResNums.begin();
+                                        ires != solventResNums.end(); ++ires)
+  {
+    int atomOffset = Natom();
+    Residue solventRes = solventTop.Res(*ires);
+    solventRes.SetOriginalNum( residues_.size() + 1 );
+    bondedAtoms.clear();
+    for (int iat = solventRes.FirstAtom(); iat != solventRes.LastAtom(); iat++)
+    {
+      Atom solventAtom = solventTop[iat];
+      // Save solvent bonds
+      for (Atom::bond_iterator bat = solventAtom.bondbegin(); bat != solventAtom.bondend(); ++bat) {
+        if (*bat > iat) {
+          bondedAtoms.push_back(  iat + atomOffset - solventRes.FirstAtom() );
+          bondedAtoms.push_back( *bat + atomOffset - solventRes.FirstAtom() );
+        }
+      }
+      solventAtom.ClearBonds(); // FIXME AddTopAtom should clear
+      AddTopAtom( solventAtom, solventRes );
+      if (solventAtom.Element() == Atom::EXTRAPT)
+        n_extra_pts_++;
+      // Add PDB info if the topology already has it. FIXME read from incoming top
+      if (!bfactor_.empty()) bfactor_.push_back( 0 );
+      if (!occupancy_.empty()) occupancy_.push_back( 1 );
+      if (!pdbSerialNum_.empty()) pdbSerialNum_.push_back( Natom() );
+      if (!atom_altloc_.empty()) atom_altloc_.push_back( ' ' );
+      // Add extra arrays
+      if (!tree_.empty()) tree_.push_back("BLA");
+      if (!ijoin_.empty()) ijoin_.push_back(0);
+      if (!irotat_.empty()) irotat_.push_back(0);
+      const double* VXYZ = solventFrame.XYZ(iat);
+      frameOut.AddXYZ( VXYZ );
+    } // END loop over solvent atoms
+    // Add bonds
+    for (std::vector<int>::const_iterator it = bondedAtoms.begin(); it != bondedAtoms.end(); ++it) {
+      int at0 = *it;
+      ++it;
+      AddBond( at0, *it );
+    }
+    // Add molecule
+    molecules_.push_back( Molecule(atomOffset, Natom()) );
+    molecules_.back().SetSolvent();
+    NsolventMolecules_++;
+  } // END loop over solvent unit residues
+  return 0;
+}
+
 /*
 // Topology::StartNewMol()
 void Topology::StartNewMol() {
diff --git a/src/Topology.h b/src/Topology.h
index eea1d8e0f0..b838112caf 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -273,6 +273,8 @@ class Topology {
     // ----- Setup routines ----------------------
     /// Add an atom to the topology inside given residue
     int AddTopAtom(Atom const&, Residue const&);
+    /// Add specified solvent residues from given topology
+    int AddSolventResidues(Topology const&, std::vector<int> const&, Frame&, Frame const&);
     /// Add an atom to the topology inside given residue and molecule number
     int addTopAtom(Atom const&, Residue const&, unsigned int, bool);
     //void StartNewMol();

From e83dbffdb8abb83a60172d23af130bafda94a39b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Mon, 22 Dec 2025 12:33:40 -0500
Subject: [PATCH 1159/1492] Remove old code

---
 src/Structure/Solvate.cpp | 35 -----------------------------------
 1 file changed, 35 deletions(-)

diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index 27bb67d88b..149d263c1f 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -794,42 +794,7 @@ const
         currentSolventCenter[2] = dZ;
 
         // Add valid residues from solvent unit to output topology for this cube
-//        int currentResNum = topOut.Nres();
-        //for (int ires = 0; ires != solventTop.Nres(); ires++)
         topOut.AddSolventResidues( solventTop, validSolventResidues, frameOut, solventFrame );
-/*        for (std::vector<int>::const_iterator ires = validSolventResidues.begin();
-                                              ires != validSolventResidues.end(); ++ires)
-        {
-          int atomOffset = topOut.Natom();
-          Residue solventRes = solventTop.Res(*ires);
-          solventRes.SetOriginalNum( currentResNum++ );
-          bondedAtoms.clear();
-          for (int iat = solventRes.FirstAtom(); iat != solventRes.LastAtom(); iat++)
-          {
-            Atom solventAtom = solventTop[iat];
-            // Save solvent bonds
-            for (Atom::bond_iterator bat = solventAtom.bondbegin(); bat != solventAtom.bondend(); ++bat) {
-              if (*bat > iat) {
-                bondedAtoms.push_back(  iat + atomOffset - solventRes.FirstAtom() );
-                bondedAtoms.push_back( *bat + atomOffset - solventRes.FirstAtom() );
-              }
-            }
-            solventAtom.ClearBonds(); // FIXME AddTopAtom should clear
-            topOut.AddTopAtom( solventAtom, solventRes );
-            // Add PDB info if the topology already has it.
-            if (!topOut.Bfactor().empty()) topOut.AddBfactor( 0 );
-            if (!topOut.Occupancy().empty()) topOut.AddOccupancy( 1 );
-            if (!topOut.PdbSerialNum().empty()) topOut.AddPdbSerialNum( topOut.Natom() );
-            const double* VXYZ = solventFrame.XYZ(iat);
-            frameOut.AddXYZ( VXYZ );
-          } // END loop over solvent atoms
-          // Add bonds
-          for (std::vector<int>::const_iterator it = bondedAtoms.begin(); it != bondedAtoms.end(); ++it) {
-            int at0 = *it;
-            ++it;
-            topOut.AddBond( at0, *it );
-          }
-        } // END loop over solvent unit residues*/
         // Append solvent frame
         //frameOut.AppendFrame( solventFrame );
       } // END loop over Z

From 47ff243ef45bf6580f1eb52e0cede8cccb93429d Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Mon, 22 Dec 2025 12:54:44 -0500
Subject: [PATCH 1160/1492] Check that there is enough solvent to swap

---
 src/Structure/AddIons.cpp | 21 ++++++++++++++++++---
 1 file changed, 18 insertions(+), 3 deletions(-)

diff --git a/src/Structure/AddIons.cpp b/src/Structure/AddIons.cpp
index 9d2eeb6515..b20d4d4d64 100644
--- a/src/Structure/AddIons.cpp
+++ b/src/Structure/AddIons.cpp
@@ -13,8 +13,8 @@ using namespace Cpptraj::Structure;
 
 /** CONSTRUCTOR */
 AddIons::AddIons() :
-  Nion1_(-1),
-  Nion2_(-1),
+  Nion1_(0),
+  Nion2_(0),
   debug_(0),
   separation_(0.0)
 {}
@@ -40,7 +40,7 @@ int AddIons::InitAddIons(std::string const& ion1nameIn, int Nion1,
 
   if (ion2nameIn.empty()) {
     ion2name_.clear();
-    Nion2_ = -1;
+    Nion2_ = 0;
   } else {
     ion2name_ = ion2nameIn;
     if (Nion2 < 1) {
@@ -139,6 +139,12 @@ int AddIons::AddIonsRand(Topology& topOut, Frame& frameOut, DataSetList const& D
                          Cpptraj::Parm::ParameterSet const& set0)
 const
 {
+  // Check that there are solvent molecules.
+  int nsolvent = topOut.Nsolvent();
+  if (nsolvent < 1) {
+    mprinterr("Error: No solvent present in '%s'. Add solvent first.\n", topOut.c_str());
+    return 1;
+  }
   // Unit total charge
   double totalCharge = topOut.TotalCharge();
   if ( fabs(totalCharge) < Constants::SMALL ) {
@@ -197,6 +203,15 @@ const
     mprintf("\tNumber of %s ions required to neutralize: %i\n", ion1name_.c_str(), iIon1);
   }
 
+  // Check that there is enough solvent to swap
+  int nIons = iIon1 + Nion2_;
+  if ( nIons == nsolvent )
+    mprintf("Warning: # of ions to add (%i) is same as number of solvent molecules (%i)\n", nIons, nsolvent);
+  else if (nIons > nsolvent) {
+    mprinterr("Error: # of ions to add (%i) is larger than number of solvent molecules (%i)\n", nIons, nsolvent);
+    return 1;
+  }
+
   // Get atom radius for each ion
   typedef std::vector<double> Darray;
 

From e30b5f18d69b08e06ad09462ef21d3a6d47677f0 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Mon, 22 Dec 2025 13:43:13 -0500
Subject: [PATCH 1161/1492] Add function to get solvent molecule numbers. Start
 code for adding first type of ion.

---
 src/Structure/AddIons.cpp     | 70 ++++++++++++++++++++++++++++++++++-
 src/Structure/structuredepend |  2 +-
 src/Topology.cpp              |  9 +++++
 src/Topology.h                |  2 +
 src/cpptrajdepend             |  2 +-
 5 files changed, 81 insertions(+), 4 deletions(-)

diff --git a/src/Structure/AddIons.cpp b/src/Structure/AddIons.cpp
index b20d4d4d64..68cbd13ad0 100644
--- a/src/Structure/AddIons.cpp
+++ b/src/Structure/AddIons.cpp
@@ -6,6 +6,7 @@
 #include "../CpptrajStdio.h"
 #include "../DataSet_Coords.h"
 #include "../DataSetList.h"
+#include "../DistRoutines.h"
 #include "../Topology.h"
 #include <cmath> //fabs, lrint
 
@@ -69,7 +70,8 @@ void AddIons::PrintAddIonsInfo() const {
     mprintf("\tAdding %i %s ions.\n", Nion1_, ion1name_.c_str());
   if (!ion2name_.empty())
     mprintf("\tAdding %i %s ions.\n", Nion2_, ion2name_.c_str());
-  mprintf("\tMinimum ion separation is %g Ang.\n", separation_);
+  if (separation_ > 0.0)
+    mprintf("\tMinimum ion separation is %g Ang.\n", separation_);
   mprintf("\tIon RNG seed: %i\n", RNG_.Seed());
 }
 
@@ -190,6 +192,7 @@ const
 
   // Check that ion can actually neutralize
   int iIon1 = Nion1_;
+  int iIon2 = Nion2_; 
   if (Nion1_ < 1) {
     if ( (chargeIon1 < 0 && totalCharge < 0) ||
          (chargeIon1 > 0 && totalCharge > 0) )
@@ -204,7 +207,7 @@ const
   }
 
   // Check that there is enough solvent to swap
-  int nIons = iIon1 + Nion2_;
+  int nIons = iIon1 + iIon2;
   if ( nIons == nsolvent )
     mprintf("Warning: # of ions to add (%i) is same as number of solvent molecules (%i)\n", nIons, nsolvent);
   else if (nIons > nsolvent) {
@@ -224,5 +227,68 @@ const
 
   mprintf("DEBUG: Nsolvent = %i\n", topOut.Nsolvent());
 
+  std::vector<int> solventMolNums = topOut.SolventMolNums();
+
+  typedef std::vector<Vec3> Varray;
+  Varray ionPositions;
+  if (separation_ > 0.0)
+    ionPositions.reserve( nIons );
+  double cut2 = separation_ * separation_;
+
+  int failCounter = 0;
+  while ( iIon1 || iIon2 ) {
+    if (iIon1) {
+      // Pick a random solvent molecule to replace
+      int solvIdx = RNG_.rn_num() % (int)solventMolNums.size();
+      int ntries = 0;
+      while ( solventMolNums[solvIdx] == -1 ) {
+        ntries++;
+        if (ntries > 100) {
+          mprinterr("Error: Could not find a solvent molecule to swap with after 100 tries.\n");
+          return 1;
+        }
+        solvIdx = RNG_.rn_num() % (int)solventMolNums.size();
+      }
+      
+      // Do not try it again. It will either be used or be invalid due to distances.
+      int solventMolNum = solventMolNums[solvIdx];
+      mprintf("DEBUG: Trying swap with solvent molecule %i\n", solventMolNum);
+      solventMolNums[solvIdx] = -1;
+ 
+     // Get position of solvent residue atom. TODO should this be the geometric center?
+      Molecule const& solventMol = topOut.Mol( solventMolNum );
+      int firstAt = solventMol.MolUnit().Front();
+      Vec3 pos( frameOut.XYZ(firstAt) );
+
+      // Check that this position isnt too close to other positions
+      bool placeIon = true;
+      for (Varray::const_iterator previousPos = ionPositions.begin(); previousPos != ionPositions.end(); ++previousPos)
+      {
+        // TODO imaging
+        double dist2 = DIST2_NoImage( pos, *previousPos );
+        if (dist2 < cut2) {
+          ++failCounter;
+          placeIon = false;
+          break;
+        }
+      }
+
+      if (placeIon) {
+        mprintf("%zu: Placed %s in %s at (%4.2lf, %4.2lf, %4.2lf).\n", ionPositions.size(), Ion1->legend(), topOut.c_str(),
+                pos[0], pos[1], pos[2]);
+        if (separation_ > 0.0)
+          ionPositions.push_back( pos );
+
+        --iIon1;
+      }
+
+      // Safety valve
+      if (failCounter > 100) {
+        mprinterr("Error: Could not place %i ions with a minimum separation of %f after 100 tries.\n", nIons, separation_);
+        return 1;
+      }
+    }
+  }
+
   return 0;
 }
diff --git a/src/Structure/structuredepend b/src/Structure/structuredepend
index 632c3cccc4..ec20b595c1 100644
--- a/src/Structure/structuredepend
+++ b/src/Structure/structuredepend
@@ -1,4 +1,4 @@
-AddIons.o : AddIons.cpp ../AssociatedData.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../Dimension.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Random.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h AddIons.h
+AddIons.o : AddIons.cpp ../AssociatedData.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../Dimension.h ../DistRoutines.h ../FileIO.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/../AtomType.h ../Parm/../CmapParmHolder.h ../Parm/../Constants.h ../Parm/../NameType.h ../Parm/../ParameterTypes.h ../Parm/../Parm/ParmEnum.h ../Parm/../TypeNameHolder.h ../Parm/DihedralParmHolder.h ../Parm/ImproperParmHolder.h ../Parm/ParameterSet.h ../Parm/ParmEnum.h ../Parm/ParmHolder.h ../Random.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h AddIons.h
 Builder.o : Builder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/../AtomType.h ../Parm/../CmapParmHolder.h ../Parm/../Constants.h ../Parm/../NameType.h ../Parm/../ParameterTypes.h ../Parm/../Parm/ParmEnum.h ../Parm/../TypeNameHolder.h ../Parm/DihedralParmHolder.h ../Parm/ImproperParmHolder.h ../Parm/ParameterSet.h ../Parm/ParmEnum.h ../Parm/ParmHolder.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Builder.h Chirality.h GenerateConnectivityArrays.h InternalCoords.h StructureEnum.h Zmatrix.h
 Chirality.o : Chirality.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../Unit.h ../Vec3.h Chirality.h StructureEnum.h
 Creator.o : Creator.cpp ../ArgList.h ../AssociatedData.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../DataSet_NameMap.h ../DataSet_Parameters.h ../DataSet_PdbResMap.h ../Dimension.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/../AtomType.h ../Parm/../CmapParmHolder.h ../Parm/../Constants.h ../Parm/../NameType.h ../Parm/../ParameterTypes.h ../Parm/../Parm/ParmEnum.h ../Parm/../TypeNameHolder.h ../Parm/DihedralParmHolder.h ../Parm/ImproperParmHolder.h ../Parm/ParameterSet.h ../Parm/ParmEnum.h ../Parm/ParmHolder.h ../PdbResMapType.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/StructureEnum.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h Creator.h GenerateConnectivityArrays.h StructureEnum.h
diff --git a/src/Topology.cpp b/src/Topology.cpp
index 2ceec1a759..f2d7e3cc06 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -191,6 +191,15 @@ Range Topology::SoluteResidues() const {
   return solute_res;
 }
 
+/** \return an array containing solvent molecule numbers. */
+std::vector<int> Topology::SolventMolNums() const {
+  std::vector<int> solventMolNums;
+  for (std::vector<Molecule>::const_iterator mol = molecules_.begin(); mol != molecules_.end(); ++mol)
+    if (mol->IsSolvent())
+      solventMolNums.push_back( mol - molecules_.begin() );
+  return solventMolNums;
+}
+
 /** Merge consecutive residues into a single residue. */
 int Topology::MergeResidues(int startRes, int stopRes) {
   // Check that start and stop make sense
diff --git a/src/Topology.h b/src/Topology.h
index b838112caf..0d10658bd3 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -113,6 +113,8 @@ class Topology {
     inline mol_iterator MolStart() const { return molecules_.begin(); }
     inline mol_iterator MolEnd()   const { return molecules_.end();   }
     const Molecule& Mol(int idx)   const { return molecules_[idx];    }
+    /// \return Array containing solvent molecule numbers
+    std::vector<int> SolventMolNums() const;
     /// \return number of residues in the specified molecule.
     int NresInMol(int) const;
     /// Determine molecules based on bond information
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index c411d0c906..df33162d9a 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -479,7 +479,7 @@ Spline.o : Spline.cpp CpptrajStdio.h Spline.h
 SplineFxnTable.o : SplineFxnTable.cpp Constants.h CpptrajStdio.h Spline.h SplineFxnTable.h StringRoutines.h
 Stats_Reduce.o : Stats_Reduce.cpp OnlineVarT.h Parallel.h Stats_Reduce.h
 StringRoutines.o : StringRoutines.cpp CpptrajStdio.h StringRoutines.h
-Structure/AddIons.o : Structure/AddIons.cpp AssociatedData.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/AddIons.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Structure/AddIons.o : Structure/AddIons.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DistRoutines.h FileIO.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/../Parm/../AtomType.h Structure/../Parm/../CmapParmHolder.h Structure/../Parm/../Constants.h Structure/../Parm/../NameType.h Structure/../Parm/../ParameterTypes.h Structure/../Parm/../Parm/ParmEnum.h Structure/../Parm/../TypeNameHolder.h Structure/../Parm/DihedralParmHolder.h Structure/../Parm/ImproperParmHolder.h Structure/../Parm/ParameterSet.h Structure/../Parm/ParmEnum.h Structure/../Parm/ParmHolder.h Structure/AddIons.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 Structure/Builder.o : Structure/Builder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h GuessAtomHybridization.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/../Parm/../AtomType.h Structure/../Parm/../CmapParmHolder.h Structure/../Parm/../Constants.h Structure/../Parm/../NameType.h Structure/../Parm/../ParameterTypes.h Structure/../Parm/../Parm/ParmEnum.h Structure/../Parm/../TypeNameHolder.h Structure/../Parm/DihedralParmHolder.h Structure/../Parm/ImproperParmHolder.h Structure/../Parm/ParameterSet.h Structure/../Parm/ParmEnum.h Structure/../Parm/ParmHolder.h Structure/Builder.h Structure/Chirality.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 Structure/Chirality.o : Structure/Chirality.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Chirality.h Structure/StructureEnum.h SymbolExporting.h Topology.h TorsionRoutines.h Unit.h Vec3.h
 Structure/Creator.o : Structure/Creator.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h DataSet_Parameters.h DataSet_PdbResMap.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h PdbResMapType.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/Creator.h Structure/GenerateConnectivityArrays.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h

From 0bd18959cec50f671d5bb94f5c20ae3088b8fe6e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Mon, 22 Dec 2025 14:03:46 -0500
Subject: [PATCH 1162/1492] Generalize the routine to use for both ion types

---
 src/Structure/AddIons.cpp | 108 ++++++++++++++++++++++----------------
 src/Structure/AddIons.h   |   5 ++
 2 files changed, 67 insertions(+), 46 deletions(-)

diff --git a/src/Structure/AddIons.cpp b/src/Structure/AddIons.cpp
index 68cbd13ad0..1e738c06e3 100644
--- a/src/Structure/AddIons.cpp
+++ b/src/Structure/AddIons.cpp
@@ -238,57 +238,73 @@ const
   int failCounter = 0;
   while ( iIon1 || iIon2 ) {
     if (iIon1) {
-      // Pick a random solvent molecule to replace
-      int solvIdx = RNG_.rn_num() % (int)solventMolNums.size();
-      int ntries = 0;
-      while ( solventMolNums[solvIdx] == -1 ) {
-        ntries++;
-        if (ntries > 100) {
-          mprinterr("Error: Could not find a solvent molecule to swap with after 100 tries.\n");
-          return 1;
-        }
-        solvIdx = RNG_.rn_num() % (int)solventMolNums.size();
-      }
-      
-      // Do not try it again. It will either be used or be invalid due to distances.
-      int solventMolNum = solventMolNums[solvIdx];
-      mprintf("DEBUG: Trying swap with solvent molecule %i\n", solventMolNum);
-      solventMolNums[solvIdx] = -1;
- 
-     // Get position of solvent residue atom. TODO should this be the geometric center?
-      Molecule const& solventMol = topOut.Mol( solventMolNum );
-      int firstAt = solventMol.MolUnit().Front();
-      Vec3 pos( frameOut.XYZ(firstAt) );
-
-      // Check that this position isnt too close to other positions
-      bool placeIon = true;
-      for (Varray::const_iterator previousPos = ionPositions.begin(); previousPos != ionPositions.end(); ++previousPos)
-      {
-        // TODO imaging
-        double dist2 = DIST2_NoImage( pos, *previousPos );
-        if (dist2 < cut2) {
-          ++failCounter;
-          placeIon = false;
-          break;
-        }
-      }
+      if (place_ion(iIon1, failCounter, ionPositions, Ion1, topOut, frameOut, solventMolNums, cut2, nIons))
+        return 1;
+    }
+    if (iIon2) {
+      if (place_ion(iIon2, failCounter, ionPositions, Ion2, topOut, frameOut, solventMolNums, cut2, nIons))
+        return 1;
+    }
+  }
 
-      if (placeIon) {
-        mprintf("%zu: Placed %s in %s at (%4.2lf, %4.2lf, %4.2lf).\n", ionPositions.size(), Ion1->legend(), topOut.c_str(),
-                pos[0], pos[1], pos[2]);
-        if (separation_ > 0.0)
-          ionPositions.push_back( pos );
+  return 0;
+}
 
-        --iIon1;
-      }
+/** Select a solvent molecule to swap with that is not too close to other ions positions. */
+int AddIons::place_ion(int& iIon1, int& failCounter, Varray& ionPositions,
+                       DataSet_Coords* ionCrd, Topology& topOut, Frame& frameOut,
+                       std::vector<int>& solventMolNums, double cut2, int nIons)
+const
+{
+  // Pick a random solvent molecule to replace
+  int solvIdx = RNG_.rn_num() % (int)solventMolNums.size();
+  int ntries = 0;
+  while ( solventMolNums[solvIdx] == -1 ) {
+    ntries++;
+    if (ntries > 100) {
+      mprinterr("Error: Could not find a solvent molecule to swap with after 100 tries.\n");
+      return 1;
+    }
+    solvIdx = RNG_.rn_num() % (int)solventMolNums.size();
+  }
+  
+  // Do not try it again. It will either be used or be invalid due to distances.
+  int solventMolNum = solventMolNums[solvIdx];
+  mprintf("DEBUG: Trying swap %s with solvent molecule %i\n", ionCrd->legend(), solventMolNum);
+  solventMolNums[solvIdx] = -1;
+ 
+  // Get position of solvent residue atom. TODO should this be the geometric center?
+  Molecule const& solventMol = topOut.Mol( solventMolNum );
+  int firstAt = solventMol.MolUnit().Front();
+  Vec3 pos( frameOut.XYZ(firstAt) );
 
-      // Safety valve
-      if (failCounter > 100) {
-        mprinterr("Error: Could not place %i ions with a minimum separation of %f after 100 tries.\n", nIons, separation_);
-        return 1;
-      }
+  // Check that this position isnt too close to other positions
+  bool placeIon = true;
+  for (Varray::const_iterator previousPos = ionPositions.begin(); previousPos != ionPositions.end(); ++previousPos)
+  {
+    // TODO imaging
+    double dist2 = DIST2_NoImage( pos, *previousPos );
+    if (dist2 < cut2) {
+      ++failCounter;
+      placeIon = false;
+      break;
     }
   }
 
+  if (placeIon) {
+    mprintf("%zu: Placed %s in %s at (%4.2lf, %4.2lf, %4.2lf).\n", iIon1, ionCrd->legend(), topOut.c_str(),
+            pos[0], pos[1], pos[2]);
+    if (separation_ > 0.0)
+      ionPositions.push_back( pos );
+
+    --iIon1;
+  }
+
+  // Safety valve
+  if (failCounter > 100) {
+    mprinterr("Error: Could not place %i ions with a minimum separation of %f after 100 tries.\n", nIons, separation_);
+    return 1;
+  }
+  
   return 0;
 }
diff --git a/src/Structure/AddIons.h b/src/Structure/AddIons.h
index df26f6f000..fa570f0d3e 100644
--- a/src/Structure/AddIons.h
+++ b/src/Structure/AddIons.h
@@ -6,6 +6,7 @@ class DataSet_Coords;
 class DataSetList;
 class Frame;
 class Topology;
+class Vec3;
 namespace Cpptraj {
 namespace Parm {
 class ParameterSet;
@@ -25,8 +26,12 @@ class AddIons {
     /// \return True if at least 1 ion has been specified.
     bool IsSetup() const { return !ion1name_.empty(); }
   private:
+    typedef std::vector<Vec3> Varray;
+
     /// \return Ion unit specified by given name
     DataSet_Coords* GetIonUnit(std::string const&, DataSetList const&) const;
+    /// Place ion within topology
+    int place_ion(int&, int&, Varray&, DataSet_Coords*, Topology&, Frame&, std::vector<int>&, double, int) const;
 
     std::string ion1name_; ///< Name of first ion
     std::string ion2name_; ///< Name of second ion

From 5e74f23ec87f905f0ace22cf715b3342bcd9428c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 22 Dec 2025 19:57:27 -0500
Subject: [PATCH 1163/1492] Ensure atoms have molnum set

---
 src/Topology.cpp | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index f2d7e3cc06..3cdbf482a8 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -511,6 +511,7 @@ int Topology::AddSolventResidues(Topology const& solventTop, std::vector<int> co
                                         ires != solventResNums.end(); ++ires)
   {
     int atomOffset = Natom();
+    int molnum = molecules_.size();
     Residue solventRes = solventTop.Res(*ires);
     solventRes.SetOriginalNum( residues_.size() + 1 );
     bondedAtoms.clear();
@@ -526,6 +527,7 @@ int Topology::AddSolventResidues(Topology const& solventTop, std::vector<int> co
       }
       solventAtom.ClearBonds(); // FIXME AddTopAtom should clear
       AddTopAtom( solventAtom, solventRes );
+      atoms_.back().SetMol( molnum );
       if (solventAtom.Element() == Atom::EXTRAPT)
         n_extra_pts_++;
       // Add PDB info if the topology already has it. FIXME read from incoming top

From 60b9d10f0954e9ff01357706242b2084001c49a7 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 22 Dec 2025 20:22:07 -0500
Subject: [PATCH 1164/1492] Ensure resnum is set. Try to set some debug info

---
 src/Structure/AddIons.cpp | 6 +++++-
 src/Topology.cpp          | 6 ++++--
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/src/Structure/AddIons.cpp b/src/Structure/AddIons.cpp
index 1e738c06e3..7c735d54f6 100644
--- a/src/Structure/AddIons.cpp
+++ b/src/Structure/AddIons.cpp
@@ -9,6 +9,7 @@
 #include "../DistRoutines.h"
 #include "../Topology.h"
 #include <cmath> //fabs, lrint
+#include <cstdlib> // FIXME debug
 
 using namespace Cpptraj::Structure;
 
@@ -235,6 +236,9 @@ const
     ionPositions.reserve( nIons );
   double cut2 = separation_ * separation_;
 
+  // FIXME DEBUG
+  srand( 1 );
+
   int failCounter = 0;
   while ( iIon1 || iIon2 ) {
     if (iIon1) {
@@ -270,7 +274,7 @@ const
   
   // Do not try it again. It will either be used or be invalid due to distances.
   int solventMolNum = solventMolNums[solvIdx];
-  mprintf("DEBUG: Trying swap %s with solvent molecule %i\n", ionCrd->legend(), solventMolNum);
+  mprintf("DEBUG: ntries=%i Trying swap %s with solvent molecule %i\n", ntries, ionCrd->legend(), solventMolNum);
   solventMolNums[solvIdx] = -1;
  
   // Get position of solvent residue atom. TODO should this be the geometric center?
diff --git a/src/Topology.cpp b/src/Topology.cpp
index 3cdbf482a8..f2501d05af 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -511,9 +511,10 @@ int Topology::AddSolventResidues(Topology const& solventTop, std::vector<int> co
                                         ires != solventResNums.end(); ++ires)
   {
     int atomOffset = Natom();
-    int molnum = molecules_.size();
+    int resnum = Nres();
+    int molnum = Nmol();
     Residue solventRes = solventTop.Res(*ires);
-    solventRes.SetOriginalNum( residues_.size() + 1 );
+    solventRes.SetOriginalNum( resnum + 1 );
     bondedAtoms.clear();
     for (int iat = solventRes.FirstAtom(); iat != solventRes.LastAtom(); iat++)
     {
@@ -528,6 +529,7 @@ int Topology::AddSolventResidues(Topology const& solventTop, std::vector<int> co
       solventAtom.ClearBonds(); // FIXME AddTopAtom should clear
       AddTopAtom( solventAtom, solventRes );
       atoms_.back().SetMol( molnum );
+      atoms_.back().SetResNum( resnum );
       if (solventAtom.Element() == Atom::EXTRAPT)
         n_extra_pts_++;
       // Add PDB info if the topology already has it. FIXME read from incoming top

From 64ef9632c21822ac71cbede4ac75d654fb7f4156 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Tue, 23 Dec 2025 11:59:04 -0500
Subject: [PATCH 1165/1492] Hide debug info behind ifdefs

---
 src/Structure/Solvate.cpp | 59 +++++++++++++++++++++++++++++----------
 src/Structure/Solvate.h   |  6 +++-
 2 files changed, 49 insertions(+), 16 deletions(-)

diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index 149d263c1f..c19ed1c818 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -268,7 +268,9 @@ const
   Vec3 toCenter( -(Xmin + 0.5 * boxX),
                  -(Ymin + 0.5 * boxY),
                  -(Zmin + 0.5 * boxZ) );
-  //mprintf("ToolCenterUnitByRadii translate vector is %f %f %f\n", toCenter[0], toCenter[1], toCenter[2]);
+# ifdef CPPTRAJ_DEBUG_SOLVATE
+  mprintf("ToolCenterUnitByRadii translate vector is %f %f %f\n", toCenter[0], toCenter[1], toCenter[2]); // DEBUG
+# endif
   // Translate to origin
   frameOut.Translate(toCenter);
 
@@ -456,7 +458,10 @@ int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::Parame
 
   // Set vdw box
   double soluteMaxR;
-  std::vector<double> soluteRadii = getAtomRadii(soluteMaxR, topOut, set0) ;
+  std::vector<double> soluteRadii = getAtomRadii(soluteMaxR, topOut, set0);
+  // DEBUG
+  //for (int iat = 0; iat != topOut.Natom(); iat++)
+  //  mprintf("SOLUTERADIUS %s %f\n",*(topOut[iat].Name()), soluteRadii[iat]);
   double boxX, boxY, boxZ;
   if (setVdwBoundingBox(boxX, boxY, boxZ, soluteRadii, frameOut, isotropic_)) {
     mprinterr("Error: Setting vdw bounding box for %s failed.\n", topOut.c_str());
@@ -501,7 +506,9 @@ int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::Parame
     clipX_ = 0.5 * boxX + bufferX_;
     clipY_ = 0.5 * boxY + bufferY_;
     clipZ_ = 0.5 * boxZ + bufferZ_;
-    //mprintf("cCriteria: %f %f %f\n", clipX_, clipY_, clipZ_);
+#   ifdef CPPTRAJ_DEBUG_SOLVATE
+    mprintf("cCriteria: %f %f %f\n", clipX_, clipY_, clipZ_); // DEBUG
+#   endif
   }
 
   // TODO check COORDS size
@@ -621,11 +628,17 @@ int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::Parame
 /** \return a list of solute atoms that might clash with solvent. */
 int Solvate::findCloseSoluteAtoms(std::vector<int>& closeSoluteAtoms, double soluteMaxR,
                                   int firstSolventAtom, Frame const& frameOut, Vec3 const& vCenter,
-                                  double dXWidth, double dYWidth, double dZWidth)
+                                  double dXWidth, double dYWidth, double dZWidth
+#                                 ifdef CPPTRAJ_DEBUG_SOLVATE
+                                  ,std::vector<double> const& soluteRadii // DEBUG
+#                                 endif
+                                 )
 const
 {
   closeSoluteAtoms.clear();
-//  mprintf( "Searching for close solute atoms, buffer zone %f solute max %f closeness %f\n", 0.0, soluteMaxR, closeness_);
+# ifdef CPPTRAJ_DEBUG_SOLVATE
+  mprintf( "Searching for close solute atoms, buffer zone %f solute max %f closeness %f\n", 0.0, soluteMaxR, closeness_); // DEBUG
+# endif
   // Determine clearance from the box for testing whether
   // a solute atom might contact an atom in the box. Assumes
   // solvent box includes vdw.
@@ -642,7 +655,9 @@ const
   double dYmax = vCenter[1] + dYWidth/2.0 + dTemp;
   double dZmin = vCenter[2] - dZWidth/2.0 - dTemp;
   double dZmax = vCenter[2] + dZWidth/2.0 + dTemp;
-//  mprintf("Search clearances %f Min= %f %f %f Max= %f %f %f\n", dTemp, dXmin, dYmin, dZmin, dXmax, dYmax, dZmax);
+# ifdef CPPTRAJ_DEBUG_SOLVATE
+  mprintf("Search clearances %f Min= %f %f %f Max= %f %f %f\n", dTemp, dXmin, dYmin, dZmin, dXmax, dYmax, dZmax); // DEBUG
+# endif
 
   // Loop over solute atoms
   for (int at = 0; at < firstSolventAtom; at++)
@@ -656,7 +671,9 @@ const
     if ( XYZ[2] > dZmax ) continue;
 
     // all atom.coords inside solvent limit, so add to list
-//    mprintf("Found an interesting sphere %f %f %f\n", XYZ[0], XYZ[1], XYZ[2] );
+#   ifdef CPPTRAJ_DEBUG_SOLVATE
+    mprintf("Found an interesting sphere %f %f %f r=%f\n", XYZ[0], XYZ[1], XYZ[2], soluteRadii[at] ); // DEBUG
+#   endif
     closeSoluteAtoms.push_back( at );
   }
   return 0;
@@ -688,12 +705,15 @@ const
         double dXabs = fabs(VXYZ[0]);
         double dYabs = fabs(VXYZ[1]);
         double dZabs = fabs(VXYZ[2]);
-        //if ( dXabs >= clipX_ ) { collision = true; mprintf("CLIP %12.4f %12.4f %12.4f\n",VXYZ[0],VXYZ[1],VXYZ[2]); break; }
-        //if ( dYabs >= clipY_ ) { collision = true; mprintf("CLIP %12.4f %12.4f %12.4f\n",VXYZ[0],VXYZ[1],VXYZ[2]); break; }
-        //if ( dZabs >= clipZ_ ) { collision = true; mprintf("CLIP %12.4f %12.4f %12.4f\n",VXYZ[0],VXYZ[1],VXYZ[2]); break; }
+#       ifdef CPPTRAJ_DEBUG_SOLVATE
+        if ( dXabs >= clipX_ ) { collision = true; mprintf("CLIP %12.4f %12.4f %12.4f\n",VXYZ[0],VXYZ[1],VXYZ[2]); break; } // DEBUG
+        if ( dYabs >= clipY_ ) { collision = true; mprintf("CLIP %12.4f %12.4f %12.4f\n",VXYZ[0],VXYZ[1],VXYZ[2]); break; } // DEBUG
+        if ( dZabs >= clipZ_ ) { collision = true; mprintf("CLIP %12.4f %12.4f %12.4f\n",VXYZ[0],VXYZ[1],VXYZ[2]); break; } // DEBUG
+#       else
         if ( dXabs >= clipX_ ) { collision = true; break; }
         if ( dYabs >= clipY_ ) { collision = true; break; }
         if ( dZabs >= clipZ_ ) { collision = true; break; }
+#       endif
         // Check if atom falls outside of oct/diagonal clip
         if (doTruncatedOct_) {
           double dX = 0.5 * (clipX_ - dXabs) / clipX_;
@@ -721,7 +741,9 @@ const
 
         if (dist2 < dRadii) {
           collision = true;
-          //mprintf("OVERLAP %12.4f %12.4f %12.4f %12.4f %12.4f\n", VXYZ[0],VXYZ[1],VXYZ[2], dist2, dRadii);
+#         ifdef CPPTRAJ_DEBUG_SOLVATE
+          mprintf("OVERLAP %12.4f %12.4f %12.4f %12.4f %12.4f %12.4f %12.4f\n", VXYZ[0],VXYZ[1],VXYZ[2], dist2, dRadii, solventRadii[vat], soluteRadii[*uat]); // DEBUG
+#         endif
           break;
         }
       } // END loop over close solute atoms
@@ -771,13 +793,20 @@ const
     for ( int iy=0; iy < numY; iy++, dY -= dYSolvent ) {
       double dZ = dZStart;
       for ( int iz=0; iz < numZ; iz++, dZ -= dZSolvent ) {
-        //mprintf( "Adding box at: x=%d  y=%d  z=%d\n", ix, iy, iz);
+#       ifdef CPPTRAJ_DEBUG_SOLVATE
+        mprintf( "Adding box at: x=%d  y=%d  z=%d\n", ix, iy, iz); // DEBUG
+#       endif
         Vec3 vPos(dX, dY, dZ);
 
         findCloseSoluteAtoms(closeSoluteAtoms, soluteMaxR, firstSolventAtom, frameOut, vPos,
-                             dXSolvent, dYSolvent, dZSolvent);
-
-        //mprintf( "Center of solvent box is: %lf, %lf, %lf\n", dX, dY, dZ );
+                             dXSolvent, dYSolvent, dZSolvent
+#                            ifdef CPPTRAJ_DEBUG_SOLVATE
+                             , soluteRadii // DEBUG soluteRadii
+#                            endif
+                            );
+#       ifdef CPPTRAJ_DEBUG_SOLVATE
+        mprintf( "Center of solvent box is: %lf, %lf, %lf\n", dX, dY, dZ ); // DEBUG
+#       endif
         Vec3 trans( dX - currentSolventCenter[0],
                     dY - currentSolventCenter[1],
                     dZ - currentSolventCenter[2] );
diff --git a/src/Structure/Solvate.h b/src/Structure/Solvate.h
index c2fb2aef80..75b0e0b6ee 100644
--- a/src/Structure/Solvate.h
+++ b/src/Structure/Solvate.h
@@ -45,7 +45,11 @@ class Solvate {
     /// Set vdW bounding box
     int setVdwBoundingBox(double&, double&, double&, std::vector<double> const&, Frame&, bool) const;
     /// Find solute atoms within a solvent box at given center
-    int findCloseSoluteAtoms(std::vector<int>&, double, int, Frame const&, Vec3 const&, double, double, double) const;
+    int findCloseSoluteAtoms(std::vector<int>&, double, int, Frame const&, Vec3 const&, double, double, double
+#                            ifdef CPPTRAJ_DEBUG_SOLVATE
+                             , std::vector<double> const&
+#                            endif
+                            ) const;
     /// Determine which solvent residues do not clash with given solute atoms
     int determineValidSolventResidues(std::vector<int>&, std::vector<int> const&,
                                       Frame const&, Topology const&, Frame const&,

From e637d15ef5f63976d5c5d9f5f55edb4c0cce3fd2 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 6 Jan 2026 10:39:13 -0500
Subject: [PATCH 1166/1492] Start actually adding the ions. Still not in the
 right order though

---
 src/Structure/AddIons.cpp | 23 ++++++++++++++++++++++-
 src/Structure/Solvate.cpp |  2 +-
 src/Topology.cpp          |  9 +++++----
 src/Topology.h            |  4 ++--
 4 files changed, 30 insertions(+), 8 deletions(-)

diff --git a/src/Structure/AddIons.cpp b/src/Structure/AddIons.cpp
index 7c735d54f6..d734fa5354 100644
--- a/src/Structure/AddIons.cpp
+++ b/src/Structure/AddIons.cpp
@@ -229,6 +229,14 @@ const
   mprintf("DEBUG: Nsolvent = %i\n", topOut.Nsolvent());
 
   std::vector<int> solventMolNums = topOut.SolventMolNums();
+  // DEBUG
+  mprintf("DEBUG: Solvent molecule #s:");
+  for (std::vector<int>::const_iterator it = solventMolNums.begin(); it != solventMolNums.end(); ++it)
+    mprintf(" %i", *it);
+  mprintf("\n"); // DEBUG
+
+  mprintf("Adding %d counter ions to \"%s\". %d solvent molecules will remain.\n",
+          iIon1 + iIon2, topOut.c_str(), (int)topOut.SolventMolNums().size() - iIon1 - iIon2);
 
   typedef std::vector<Vec3> Varray;
   Varray ionPositions;
@@ -296,11 +304,24 @@ const
   }
 
   if (placeIon) {
+    std::vector<int> validIonResidues;
+    validIonResidues.reserve( ionCrd->Top().Nres() );
+    for (int ires = 0; ires != ionCrd->Top().Nres() ; ++ires)
+      validIonResidues.push_back( ires );
+    Frame ionFrame = ionCrd->AllocateFrame(); //TODO allocate outside this routine
+    ionCrd->GetFrame(0, ionFrame);
+    Vec3 currentIonCenter = ionFrame.VGeometricCenter();
+    Vec3 trans( pos[0] - currentIonCenter[0],
+                pos[1] - currentIonCenter[1],
+                pos[2] - currentIonCenter[2] );
+    ionFrame.Translate(trans);
+    Vec3 debugVec = ionFrame.VGeometricCenter();
+    debugVec.Print("DEBUG: check ion center");
     mprintf("%zu: Placed %s in %s at (%4.2lf, %4.2lf, %4.2lf).\n", iIon1, ionCrd->legend(), topOut.c_str(),
             pos[0], pos[1], pos[2]);
     if (separation_ > 0.0)
       ionPositions.push_back( pos );
-
+    topOut.AddResidues( ionCrd->Top(), validIonResidues, frameOut, ionFrame, false );
     --iIon1;
   }
 
diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index c19ed1c818..705b182c9f 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -823,7 +823,7 @@ const
         currentSolventCenter[2] = dZ;
 
         // Add valid residues from solvent unit to output topology for this cube
-        topOut.AddSolventResidues( solventTop, validSolventResidues, frameOut, solventFrame );
+        topOut.AddResidues( solventTop, validSolventResidues, frameOut, solventFrame, true );
         // Append solvent frame
         //frameOut.AppendFrame( solventFrame );
       } // END loop over Z
diff --git a/src/Topology.cpp b/src/Topology.cpp
index f2501d05af..c1fac46b6c 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -502,9 +502,9 @@ int Topology::addTopAtom(Atom const& atomIn, Residue const& resIn,
   return 0;
 }
 
-/** Add specified solvent residues from given topology to this topology. */
-int Topology::AddSolventResidues(Topology const& solventTop, std::vector<int> const& solventResNums,
-                                 Frame& frameOut, Frame const& solventFrame)
+/** Add specified residues from given topology to this topology. Mark solvent if needed. */
+int Topology::AddResidues(Topology const& solventTop, std::vector<int> const& solventResNums,
+                          Frame& frameOut, Frame const& solventFrame, bool is_solvent)
 {
   std::vector<int> bondedAtoms;
   for (std::vector<int>::const_iterator ires = solventResNums.begin();
@@ -552,7 +552,8 @@ int Topology::AddSolventResidues(Topology const& solventTop, std::vector<int> co
     }
     // Add molecule
     molecules_.push_back( Molecule(atomOffset, Natom()) );
-    molecules_.back().SetSolvent();
+    if (is_solvent)
+      molecules_.back().SetSolvent();
     NsolventMolecules_++;
   } // END loop over solvent unit residues
   return 0;
diff --git a/src/Topology.h b/src/Topology.h
index 0d10658bd3..8dd587292f 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -275,8 +275,8 @@ class Topology {
     // ----- Setup routines ----------------------
     /// Add an atom to the topology inside given residue
     int AddTopAtom(Atom const&, Residue const&);
-    /// Add specified solvent residues from given topology
-    int AddSolventResidues(Topology const&, std::vector<int> const&, Frame&, Frame const&);
+    /// Add specified residues from given topology; optionally make them solvent
+    int AddResidues(Topology const&, std::vector<int> const&, Frame&, Frame const&, bool);
     /// Add an atom to the topology inside given residue and molecule number
     int addTopAtom(Atom const&, Residue const&, unsigned int, bool);
     //void StartNewMol();

From 19f93f9678368e9f969a8c0b57eb6faf06af89c4 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 6 Jan 2026 10:53:00 -0500
Subject: [PATCH 1167/1492] Add CenterOnPoint routine

---
 src/Frame.cpp             | 14 ++++++++++++++
 src/Frame.h               | 11 +++++++++++
 src/Structure/AddIons.cpp |  6 +-----
 3 files changed, 26 insertions(+), 5 deletions(-)

diff --git a/src/Frame.cpp b/src/Frame.cpp
index c16bdffe43..fe1207a06f 100644
--- a/src/Frame.cpp
+++ b/src/Frame.cpp
@@ -1054,6 +1054,20 @@ Vec3 Frame::CenterOnOrigin(bool useMassIn)
   return center;
 }
 
+/** Center all atoms on given point. */
+void Frame::CenterOnPoint(Vec3 const& pos, bool useMassIn)
+{
+  Vec3 currentCenter;
+  if (useMassIn)
+    currentCenter = VCenterOfMass();
+  else
+    currentCenter = VGeometricCenter();
+  Vec3 trans( pos[0] - currentCenter[0],
+              pos[1] - currentCenter[1],
+              pos[2] - currentCenter[2] );
+  Translate(trans);
+}
+
 // Frame::Align()
 void Frame::Align(Frame const& REF, AtomMask const& mask) {
   Frame tmpRef(REF, mask);
diff --git a/src/Frame.h b/src/Frame.h
index 58c3012227..d45d0221ad 100644
--- a/src/Frame.h
+++ b/src/Frame.h
@@ -227,6 +227,8 @@ class Frame {
     inline Vec3 VCenterOfMass(Unit const&) const;
     /// \return Geometric center of atoms in Unit
     inline Vec3 VGeometricCenter(Unit const&) const;
+    /// \return Center of mass of all atoms in Frame
+    inline Vec3 VCenterOfMass() const;
     /// \return Geometric center of all atoms in Frame
     inline Vec3 VGeometricCenter() const;
     /// Translate atoms in mask by Vec
@@ -262,6 +264,8 @@ class Frame {
     void Scale(AtomMask const&, double, double, double);
     /// Translate atoms to origin.
     Vec3 CenterOnOrigin(bool);
+    /// Translate atoms to given point.
+    void CenterOnPoint(Vec3 const&, bool);
     // Align on reference
     void Align(Frame const&, AtomMask const&);
     // Coordinate calculation
@@ -385,6 +389,11 @@ Vec3 Frame::VCenterOfMass(int startAtom, int stopAtom) const {
   return Vec3( Coord0 / sumMass, Coord1 / sumMass, Coord2 / sumMass );
 }
 
+/** Center of mass of all atoms */
+Vec3 Frame::VCenterOfMass() const {
+  return VCenterOfMass(0, natom_);
+}
+
 /** Calculate the center of mass of a unit. */
 Vec3 Frame::VCenterOfMass(Unit const& unit) const {
   Vec3 out(0.0);
@@ -405,6 +414,7 @@ Vec3 Frame::VCenterOfMass(Unit const& unit) const {
   return out;
 }
 
+/** Geometric center of a range of atoms */
 Vec3 Frame::VGeometricCenter(int startAtom, int stopAtom) const {
   double Coord0 = 0.0;
   double Coord1 = 0.0;
@@ -421,6 +431,7 @@ Vec3 Frame::VGeometricCenter(int startAtom, int stopAtom) const {
   return Vec3( Coord0 / sumMass, Coord1 / sumMass, Coord2 / sumMass );
 }
 
+/** Geometric center of all atoms */
 Vec3 Frame::VGeometricCenter() const {
   return VGeometricCenter(0, natom_);
 }
diff --git a/src/Structure/AddIons.cpp b/src/Structure/AddIons.cpp
index d734fa5354..7513ff3027 100644
--- a/src/Structure/AddIons.cpp
+++ b/src/Structure/AddIons.cpp
@@ -310,11 +310,7 @@ const
       validIonResidues.push_back( ires );
     Frame ionFrame = ionCrd->AllocateFrame(); //TODO allocate outside this routine
     ionCrd->GetFrame(0, ionFrame);
-    Vec3 currentIonCenter = ionFrame.VGeometricCenter();
-    Vec3 trans( pos[0] - currentIonCenter[0],
-                pos[1] - currentIonCenter[1],
-                pos[2] - currentIonCenter[2] );
-    ionFrame.Translate(trans);
+    ionFrame.CenterOnPoint( pos, false ); // Use geometric center
     Vec3 debugVec = ionFrame.VGeometricCenter();
     debugVec.Print("DEBUG: check ion center");
     mprintf("%zu: Placed %s in %s at (%4.2lf, %4.2lf, %4.2lf).\n", iIon1, ionCrd->legend(), topOut.c_str(),

From 333cfcbe15d5224bb0b5f669bb522f76624a7b45 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 6 Jan 2026 12:29:24 -0500
Subject: [PATCH 1168/1492] Preserve bonded atom ordering in ModifyByMap

---
 src/Topology.cpp | 28 ++++++++++++++++++++--------
 src/Topology.h   |  2 +-
 2 files changed, 21 insertions(+), 9 deletions(-)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index c1fac46b6c..a86caa9136 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -834,13 +834,13 @@ double Topology::GetVDWdepth(int a1) const {
 // Topology::SetAtomBondInfo()
 /** Set up bond information in the atoms array based on given BondArray.
   */
-void Topology::SetAtomBondInfo(BondArray const& bonds) {
+/*void Topology::SetAtomBondInfo(BondArray const& bonds) {
   // Add bonds based on array 
   for (BondArray::const_iterator bnd = bonds.begin(); bnd != bonds.end(); ++bnd) {
     atoms_[ bnd->A1() ].AddBondToIdx( bnd->A2() );
     atoms_[ bnd->A2() ].AddBondToIdx( bnd->A1() );
   }
-}
+}*/
 
 // -----------------------------------------------------------------------------
 /** Check if given bond parm exists in given bond parm array. Add if not.
@@ -1697,8 +1697,15 @@ Topology* Topology::ModifyByMap(std::vector<int> const& MapIn, bool setupFullPar
   newParm->radius_set_ = radius_set_;
   newParm->debug_ = debug_;
 
-  // Reverse Atom map
+  // Reverse Atom map. Generate here so it can be used to regenerate
+  // bonded atom info below.
   std::vector<int> atomMap( atoms_.size(),-1 );
+  for (int newatom = 0; newatom < (int)MapIn.size(); newatom++) {
+    int oldatom = MapIn[ newatom ];
+    // Store map of oldatom to newatom
+    atomMap[oldatom] = newatom;
+  }
+
   // Save solvent status of atoms
   std::vector<bool> isSolvent;
   isSolvent.reserve( MapIn.size() );
@@ -1709,8 +1716,6 @@ Topology* Topology::ModifyByMap(std::vector<int> const& MapIn, bool setupFullPar
   for (int newatom = 0; newatom < (int)MapIn.size(); newatom++) {
     int oldatom = MapIn[ newatom ];
     if (oldatom < 0) continue;
-    // Store map of oldatom to newatom
-    atomMap[oldatom] = newatom;
     // Copy oldatom 
     Atom newparmAtom = atoms_[oldatom];
     // Save oldatom residue number
@@ -1726,8 +1731,15 @@ Topology* Topology::ModifyByMap(std::vector<int> const& MapIn, bool setupFullPar
       newParm->residues_.back().SetTerminal( cr.IsTerminal() );
       oldres = curres;
     }
-    // Clear bond information from new atom
+    // Regenerate bond information for new atom, excluding any removed atoms.
+    std::vector<int> oldBondedAtoms = newparmAtom.BondIdxArray();
     newparmAtom.ClearBonds();
+    for (std::vector<int>::const_iterator it = oldBondedAtoms.begin(); it != oldBondedAtoms.end(); ++it)
+    {
+      int newBondedAtom = atomMap[*it];
+      if (newBondedAtom > -1)
+        newparmAtom.AddBondToIdx( newBondedAtom );
+    }
     // Set new atom num and residue num
     newparmAtom.SetResNum( newParm->residues_.size() - 1 );
     // Check if this atom belongs to a solvent molecule.
@@ -1757,8 +1769,8 @@ Topology* Topology::ModifyByMap(std::vector<int> const& MapIn, bool setupFullPar
   // Set up new bond information
   newParm->bonds_ = StripBondArray( bonds_, atomMap );
   newParm->bondsh_ = StripBondArray( bondsh_, atomMap );
-  newParm->SetAtomBondInfo( newParm->bonds_ );
-  newParm->SetAtomBondInfo( newParm->bondsh_ );
+//  newParm->SetAtomBondInfo( newParm->bonds_ );
+//  newParm->SetAtomBondInfo( newParm->bondsh_ );
   std::vector<int> parmMap( bondparm_.size(), -1 ); // Map[oldidx] = newidx
   StripBondParmArray( newParm->bonds_,  parmMap, newParm->bondparm_ );
   StripBondParmArray( newParm->bondsh_, parmMap, newParm->bondparm_ );
diff --git a/src/Topology.h b/src/Topology.h
index 8dd587292f..7dd8dc9514 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -329,7 +329,7 @@ class Topology {
   private:
     typedef std::vector<std::string> Sarray;
 
-    void SetAtomBondInfo(BondArray const&);
+    //void SetAtomBondInfo(BondArray const&);
     // NOTE: Use set so that elements are always sorted.
     typedef std::vector< std::set<Atom::AtomicElementType> > BP_mapType;
     /// Generate a bond parameter for the given bond based on atom elements

From 3b9758803010760328e5b6d1380458f3028a0ba6 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 6 Jan 2026 14:56:01 -0500
Subject: [PATCH 1169/1492] Ensure systems are ordered the way leap does it
 (solute, ions, solvent)

---
 src/Structure/AddIons.cpp | 68 +++++++++++++++++++++++++++++++++++----
 src/Structure/AddIons.h   |  5 ++-
 2 files changed, 66 insertions(+), 7 deletions(-)

diff --git a/src/Structure/AddIons.cpp b/src/Structure/AddIons.cpp
index 7513ff3027..e6a877f22c 100644
--- a/src/Structure/AddIons.cpp
+++ b/src/Structure/AddIons.cpp
@@ -228,12 +228,22 @@ const
 
   mprintf("DEBUG: Nsolvent = %i\n", topOut.Nsolvent());
 
-  std::vector<int> solventMolNums = topOut.SolventMolNums();
+  std::vector<int> soluteMolNums;
+  std::vector<int> solventMolNums;// = topOut.SolventMolNums();
+  int molnum = 0;
+  for (Topology::mol_iterator mol = topOut.MolStart(); mol != topOut.MolEnd(); ++mol, ++molnum)
+  {
+    if (mol->IsSolvent())
+      solventMolNums.push_back( molnum );
+    else
+      soluteMolNums.push_back( molnum );
+  }
   // DEBUG
   mprintf("DEBUG: Solvent molecule #s:");
   for (std::vector<int>::const_iterator it = solventMolNums.begin(); it != solventMolNums.end(); ++it)
     mprintf(" %i", *it);
   mprintf("\n"); // DEBUG
+  VstatArray solventStat(solventMolNums.size(), UNUSED);
 
   mprintf("Adding %d counter ions to \"%s\". %d solvent molecules will remain.\n",
           iIon1 + iIon2, topOut.c_str(), (int)topOut.SolventMolNums().size() - iIon1 - iIon2);
@@ -247,31 +257,72 @@ const
   // FIXME DEBUG
   srand( 1 );
 
+  // Add ions loop
+  // To match how LEaP orders systems (solute/ions/solvent), need to have an atom map.
+  std::vector<int> atomMap;
+  for (std::vector<int>::const_iterator imol = soluteMolNums.begin(); imol != soluteMolNums.end(); ++imol)
+  {
+    Molecule const& Mol = topOut.Mol( *imol );
+    for (Unit::const_iterator seg = Mol.MolUnit().segBegin(); seg != Mol.MolUnit().segEnd(); ++seg)
+      for (int idx = seg->Begin(); idx != seg->End(); ++idx)
+        atomMap.push_back( idx );
+  }
+
   int failCounter = 0;
   while ( iIon1 || iIon2 ) {
     if (iIon1) {
-      if (place_ion(iIon1, failCounter, ionPositions, Ion1, topOut, frameOut, solventMolNums, cut2, nIons))
+      if (place_ion(iIon1, failCounter, ionPositions, Ion1, topOut, frameOut, solventMolNums, cut2, nIons, atomMap, solventStat))
         return 1;
     }
     if (iIon2) {
-      if (place_ion(iIon2, failCounter, ionPositions, Ion2, topOut, frameOut, solventMolNums, cut2, nIons))
+      if (place_ion(iIon2, failCounter, ionPositions, Ion2, topOut, frameOut, solventMolNums, cut2, nIons, atomMap, solventStat))
         return 1;
     }
   }
 
+  // Add back any solvent that was not swapped
+  for (unsigned int idx = 0; idx != solventMolNums.size(); ++idx)
+  {
+    if (solventStat[idx] != SWAPPED) {
+      int imol = solventMolNums[idx];
+      Molecule const& Mol = topOut.Mol( imol );
+      for (Unit::const_iterator seg = Mol.MolUnit().segBegin(); seg != Mol.MolUnit().segEnd(); ++seg)
+        for (int idx = seg->Begin(); idx != seg->End(); ++idx)
+          atomMap.push_back( idx );
+    }
+  }
+
+  // DEBUG
+  mprintf("DEBUG: Atom Map:\n");
+  for (unsigned int idx = 0; idx != atomMap.size(); idx++)
+    mprintf("\tOld=%8i -> New=%8u\n", atomMap[idx], idx);
+
+  //FIXME this is not very efficient memory-wise
+  Topology* reorderedTop = topOut.ModifyByMap(atomMap);
+  if (reorderedTop == 0) {
+    mprinterr("Internal Error: Failed reordering system after adding ions.\n");
+    return 1;
+  }
+  topOut = *reorderedTop;
+  delete reorderedTop;
+
+  Frame frameOutCopy = frameOut;
+  frameOut.ModifyByMap( frameOutCopy, atomMap );
+
   return 0;
 }
 
 /** Select a solvent molecule to swap with that is not too close to other ions positions. */
 int AddIons::place_ion(int& iIon1, int& failCounter, Varray& ionPositions,
                        DataSet_Coords* ionCrd, Topology& topOut, Frame& frameOut,
-                       std::vector<int>& solventMolNums, double cut2, int nIons)
+                       std::vector<int> const& solventMolNums, double cut2, int nIons,
+                       std::vector<int>& atomMap, VstatArray& solventStat)
 const
 {
   // Pick a random solvent molecule to replace
   int solvIdx = RNG_.rn_num() % (int)solventMolNums.size();
   int ntries = 0;
-  while ( solventMolNums[solvIdx] == -1 ) {
+  while ( solventStat[solvIdx] != UNUSED ) {
     ntries++;
     if (ntries > 100) {
       mprinterr("Error: Could not find a solvent molecule to swap with after 100 tries.\n");
@@ -283,7 +334,7 @@ const
   // Do not try it again. It will either be used or be invalid due to distances.
   int solventMolNum = solventMolNums[solvIdx];
   mprintf("DEBUG: ntries=%i Trying swap %s with solvent molecule %i\n", ntries, ionCrd->legend(), solventMolNum);
-  solventMolNums[solvIdx] = -1;
+  solventStat[solvIdx] = USED;
  
   // Get position of solvent residue atom. TODO should this be the geometric center?
   Molecule const& solventMol = topOut.Mol( solventMolNum );
@@ -304,6 +355,7 @@ const
   }
 
   if (placeIon) {
+    solventStat[solvIdx] = SWAPPED;
     std::vector<int> validIonResidues;
     validIonResidues.reserve( ionCrd->Top().Nres() );
     for (int ires = 0; ires != ionCrd->Top().Nres() ; ++ires)
@@ -317,6 +369,10 @@ const
             pos[0], pos[1], pos[2]);
     if (separation_ > 0.0)
       ionPositions.push_back( pos );
+    int ionAtoms0 = topOut.Natom();
+    int ionAtoms1 = ionAtoms0 + ionCrd->Top().Natom();
+    for (int iat = ionAtoms0; iat != ionAtoms1; iat++)
+      atomMap.push_back( iat );
     topOut.AddResidues( ionCrd->Top(), validIonResidues, frameOut, ionFrame, false );
     --iIon1;
   }
diff --git a/src/Structure/AddIons.h b/src/Structure/AddIons.h
index fa570f0d3e..30c0c66437 100644
--- a/src/Structure/AddIons.h
+++ b/src/Structure/AddIons.h
@@ -28,10 +28,13 @@ class AddIons {
   private:
     typedef std::vector<Vec3> Varray;
 
+    enum VmolStatType { UNUSED = 0, USED, SWAPPED };
+    typedef std::vector<VmolStatType> VstatArray;
+
     /// \return Ion unit specified by given name
     DataSet_Coords* GetIonUnit(std::string const&, DataSetList const&) const;
     /// Place ion within topology
-    int place_ion(int&, int&, Varray&, DataSet_Coords*, Topology&, Frame&, std::vector<int>&, double, int) const;
+    int place_ion(int&, int&, Varray&, DataSet_Coords*, Topology&, Frame&, std::vector<int> const&, double, int, std::vector<int>&, VstatArray&) const;
 
     std::string ion1name_; ///< Name of first ion
     std::string ion2name_; ///< Name of second ion

From b3a20df4431943f002d10877ead44bf39c9e9c27 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 6 Jan 2026 15:43:33 -0500
Subject: [PATCH 1170/1492] Make VstatArray apply to all molecules

---
 src/Structure/AddIons.cpp | 29 +++++++++++++++++------------
 src/Structure/AddIons.h   |  2 +-
 2 files changed, 18 insertions(+), 13 deletions(-)

diff --git a/src/Structure/AddIons.cpp b/src/Structure/AddIons.cpp
index e6a877f22c..82a52302f4 100644
--- a/src/Structure/AddIons.cpp
+++ b/src/Structure/AddIons.cpp
@@ -230,20 +230,26 @@ const
 
   std::vector<int> soluteMolNums;
   std::vector<int> solventMolNums;// = topOut.SolventMolNums();
+  VstatArray molStat;
+  molStat.reserve(topOut.Nmol());
   int molnum = 0;
   for (Topology::mol_iterator mol = topOut.MolStart(); mol != topOut.MolEnd(); ++mol, ++molnum)
   {
-    if (mol->IsSolvent())
+    if (mol->IsSolvent()) {
       solventMolNums.push_back( molnum );
-    else
+      molStat.push_back( UNUSED );
+    } else {
       soluteMolNums.push_back( molnum );
+      molStat.push_back( SOLUTE );
+    }
   }
   // DEBUG
   mprintf("DEBUG: Solvent molecule #s:");
   for (std::vector<int>::const_iterator it = solventMolNums.begin(); it != solventMolNums.end(); ++it)
     mprintf(" %i", *it);
   mprintf("\n"); // DEBUG
-  VstatArray solventStat(solventMolNums.size(), UNUSED);
+
+  //VstatArray solventStat(solventMolNums.size(), UNUSED);
 
   mprintf("Adding %d counter ions to \"%s\". %d solvent molecules will remain.\n",
           iIon1 + iIon2, topOut.c_str(), (int)topOut.SolventMolNums().size() - iIon1 - iIon2);
@@ -271,20 +277,19 @@ const
   int failCounter = 0;
   while ( iIon1 || iIon2 ) {
     if (iIon1) {
-      if (place_ion(iIon1, failCounter, ionPositions, Ion1, topOut, frameOut, solventMolNums, cut2, nIons, atomMap, solventStat))
+      if (place_ion(iIon1, failCounter, ionPositions, Ion1, topOut, frameOut, solventMolNums, cut2, nIons, atomMap, molStat))
         return 1;
     }
     if (iIon2) {
-      if (place_ion(iIon2, failCounter, ionPositions, Ion2, topOut, frameOut, solventMolNums, cut2, nIons, atomMap, solventStat))
+      if (place_ion(iIon2, failCounter, ionPositions, Ion2, topOut, frameOut, solventMolNums, cut2, nIons, atomMap, molStat))
         return 1;
     }
   }
 
   // Add back any solvent that was not swapped
-  for (unsigned int idx = 0; idx != solventMolNums.size(); ++idx)
+  for (unsigned int imol = 0; imol != molStat.size(); ++imol)
   {
-    if (solventStat[idx] != SWAPPED) {
-      int imol = solventMolNums[idx];
+    if (molStat[imol] != SWAPPED && molStat[imol] != SOLUTE) {
       Molecule const& Mol = topOut.Mol( imol );
       for (Unit::const_iterator seg = Mol.MolUnit().segBegin(); seg != Mol.MolUnit().segEnd(); ++seg)
         for (int idx = seg->Begin(); idx != seg->End(); ++idx)
@@ -316,13 +321,13 @@ const
 int AddIons::place_ion(int& iIon1, int& failCounter, Varray& ionPositions,
                        DataSet_Coords* ionCrd, Topology& topOut, Frame& frameOut,
                        std::vector<int> const& solventMolNums, double cut2, int nIons,
-                       std::vector<int>& atomMap, VstatArray& solventStat)
+                       std::vector<int>& atomMap, VstatArray& molStat)
 const
 {
   // Pick a random solvent molecule to replace
   int solvIdx = RNG_.rn_num() % (int)solventMolNums.size();
   int ntries = 0;
-  while ( solventStat[solvIdx] != UNUSED ) {
+  while ( molStat[solventMolNums[solvIdx]] != UNUSED ) {
     ntries++;
     if (ntries > 100) {
       mprinterr("Error: Could not find a solvent molecule to swap with after 100 tries.\n");
@@ -334,7 +339,7 @@ const
   // Do not try it again. It will either be used or be invalid due to distances.
   int solventMolNum = solventMolNums[solvIdx];
   mprintf("DEBUG: ntries=%i Trying swap %s with solvent molecule %i\n", ntries, ionCrd->legend(), solventMolNum);
-  solventStat[solvIdx] = USED;
+  molStat[solventMolNum] = TRIED;
  
   // Get position of solvent residue atom. TODO should this be the geometric center?
   Molecule const& solventMol = topOut.Mol( solventMolNum );
@@ -355,7 +360,7 @@ const
   }
 
   if (placeIon) {
-    solventStat[solvIdx] = SWAPPED;
+    molStat[solventMolNum] = SWAPPED;
     std::vector<int> validIonResidues;
     validIonResidues.reserve( ionCrd->Top().Nres() );
     for (int ires = 0; ires != ionCrd->Top().Nres() ; ++ires)
diff --git a/src/Structure/AddIons.h b/src/Structure/AddIons.h
index 30c0c66437..31f42b3c37 100644
--- a/src/Structure/AddIons.h
+++ b/src/Structure/AddIons.h
@@ -28,7 +28,7 @@ class AddIons {
   private:
     typedef std::vector<Vec3> Varray;
 
-    enum VmolStatType { UNUSED = 0, USED, SWAPPED };
+    enum VmolStatType { UNUSED = 0, TRIED, SWAPPED, SOLUTE };
     typedef std::vector<VmolStatType> VstatArray;
 
     /// \return Ion unit specified by given name

From 3e433b85f3b605f60399079813840da8e8f276f4 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 6 Jan 2026 15:49:58 -0500
Subject: [PATCH 1171/1492] Reduce the number of available solvent mols to swap
 with each iteration to match what leap does

---
 src/Structure/AddIons.cpp | 8 ++++++--
 src/Structure/AddIons.h   | 2 +-
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/src/Structure/AddIons.cpp b/src/Structure/AddIons.cpp
index 82a52302f4..c7a30afd08 100644
--- a/src/Structure/AddIons.cpp
+++ b/src/Structure/AddIons.cpp
@@ -320,7 +320,7 @@ const
 /** Select a solvent molecule to swap with that is not too close to other ions positions. */
 int AddIons::place_ion(int& iIon1, int& failCounter, Varray& ionPositions,
                        DataSet_Coords* ionCrd, Topology& topOut, Frame& frameOut,
-                       std::vector<int> const& solventMolNums, double cut2, int nIons,
+                       std::vector<int>& solventMolNums, double cut2, int nIons,
                        std::vector<int>& atomMap, VstatArray& molStat)
 const
 {
@@ -338,7 +338,7 @@ const
   
   // Do not try it again. It will either be used or be invalid due to distances.
   int solventMolNum = solventMolNums[solvIdx];
-  mprintf("DEBUG: ntries=%i Trying swap %s with solvent molecule %i\n", ntries, ionCrd->legend(), solventMolNum);
+  mprintf("DEBUG: ntries=%i Trying swap %s with solvent molecule %i (idx= %i)\n", ntries, ionCrd->legend(), solventMolNum, solvIdx);
   molStat[solventMolNum] = TRIED;
  
   // Get position of solvent residue atom. TODO should this be the geometric center?
@@ -380,6 +380,10 @@ const
       atomMap.push_back( iat );
     topOut.AddResidues( ionCrd->Top(), validIonResidues, frameOut, ionFrame, false );
     --iIon1;
+    // Resize the active solvent molecules array
+    for (unsigned int vidx = solvIdx + 1; vidx < solventMolNums.size(); vidx++)
+      solventMolNums[vidx-1] = solventMolNums[vidx];
+    solventMolNums.resize( solventMolNums.size() - 1 );
   }
 
   // Safety valve
diff --git a/src/Structure/AddIons.h b/src/Structure/AddIons.h
index 31f42b3c37..392504f60e 100644
--- a/src/Structure/AddIons.h
+++ b/src/Structure/AddIons.h
@@ -34,7 +34,7 @@ class AddIons {
     /// \return Ion unit specified by given name
     DataSet_Coords* GetIonUnit(std::string const&, DataSetList const&) const;
     /// Place ion within topology
-    int place_ion(int&, int&, Varray&, DataSet_Coords*, Topology&, Frame&, std::vector<int> const&, double, int, std::vector<int>&, VstatArray&) const;
+    int place_ion(int&, int&, Varray&, DataSet_Coords*, Topology&, Frame&, std::vector<int>&, double, int, std::vector<int>&, VstatArray&) const;
 
     std::string ion1name_; ///< Name of first ion
     std::string ion2name_; ///< Name of second ion

From 1edcc9add6176aecf796cbd3c15e203d5c4e03b5 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 6 Jan 2026 15:52:18 -0500
Subject: [PATCH 1172/1492] Add some code docs

---
 src/Structure/AddIons.cpp | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/Structure/AddIons.cpp b/src/Structure/AddIons.cpp
index c7a30afd08..3188c44620 100644
--- a/src/Structure/AddIons.cpp
+++ b/src/Structure/AddIons.cpp
@@ -263,8 +263,8 @@ const
   // FIXME DEBUG
   srand( 1 );
 
-  // Add ions loop
   // To match how LEaP orders systems (solute/ions/solvent), need to have an atom map.
+  // First add solute.
   std::vector<int> atomMap;
   for (std::vector<int>::const_iterator imol = soluteMolNums.begin(); imol != soluteMolNums.end(); ++imol)
   {
@@ -274,6 +274,7 @@ const
         atomMap.push_back( idx );
   }
 
+  // Add ions loop. Will initially be added to the end of the topology and reordered afterwards.
   int failCounter = 0;
   while ( iIon1 || iIon2 ) {
     if (iIon1) {

From 32149035ccd1b5e6a32bd9c6bcde1cb21ca9365b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 7 Jan 2026 08:40:53 -0500
Subject: [PATCH 1173/1492] Revert checkstructure distance to 2 since otherwise
 we miss close contacts from atoms in an angle

---
 src/StructureCheck.cpp | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/src/StructureCheck.cpp b/src/StructureCheck.cpp
index a4812260b7..6209003d71 100644
--- a/src/StructureCheck.cpp
+++ b/src/StructureCheck.cpp
@@ -196,11 +196,9 @@ int StructureCheck::Setup(Topology const& topIn, Box const& boxIn)
   // Set up exclusion list
   if (checkType_ == PL_1_MASK || checkType_ == NO_PL_1_MASK) {
     mprintf("\tExcluding bond interactions.\n");
-    // Set up atom exclusion list. If just checking bonds we could just use a
-    // distance of 2. However, in order to ignore "close contacts" for water
-    // model hydrogens with extra points, increase to 3.
-    // FIXME check angles since these are now excluded.
-    if (Excluded_.SetupExcluded(topIn.Atoms(), Mask1_, 3, ex_self_opt, ex_list_opt)) {
+    // Set up atom exclusion list. Distance of 2 since we are not
+    // yet checking angles and dihedrals. 
+    if (Excluded_.SetupExcluded(topIn.Atoms(), Mask1_, 2, ex_self_opt, ex_list_opt)) {
       mprinterr("Error: StructureCheck: Could not set up excluded atoms list.\n");
       return 1;
     }

From bf4b3b19fc57d84d3921e3352d1dc39920a29a82 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 7 Jan 2026 09:41:15 -0500
Subject: [PATCH 1174/1492] Update PRY IC graft; H5 atom built slightly
 differently due to the original bond order now being preserved when Topology
 is modified.

---
 test/Test_Graft/IC.Final.graft.mol2.save | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/Test_Graft/IC.Final.graft.mol2.save b/test/Test_Graft/IC.Final.graft.mol2.save
index ece3f0415e..f94c13b341 100644
--- a/test/Test_Graft/IC.Final.graft.mol2.save
+++ b/test/Test_Graft/IC.Final.graft.mol2.save
@@ -19,7 +19,7 @@ USER_CHARGES
      11 C3          4.0092    5.8193    2.2292 CA         2 PRY     -0.149016
      12 H4          3.3555    5.5622    3.0454 HA         2 PRY      0.153372
      13 C4          4.6204    7.0513    2.2286 CA         2 PRY     -0.336291
-     14 H5          4.4870    7.7865    3.0004 HA         2 PRY      0.167425
+     14 H5          4.4562    7.7548    3.0237 HA         2 PRY      0.167425
      15 C5          5.5298    7.3802    1.0703 CA         2 PRY      0.423974
      16 O1          6.1127    8.5970    1.1066 OS         2 PRY     -0.391815
      17 C6          5.7104    6.4428    0.0703 CA         2 PRY     -0.336291

From 50b6cb614e56e326068e18de6d103114a0b1931a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 7 Jan 2026 10:49:06 -0500
Subject: [PATCH 1175/1492] Recognize EP and XP as extra points

---
 src/Atom.cpp | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/src/Atom.cpp b/src/Atom.cpp
index 8dae83194a..29e1d62620 100644
--- a/src/Atom.cpp
+++ b/src/Atom.cpp
@@ -316,6 +316,11 @@ void Atom::SetElementFromName() {
     case 'R' :
       if (c2=='b') element_ = RUBIDIUM;
       break;
+    // Check for extra points
+    case 'E' :
+      if (c2=='P') {element_ = EXTRAPT; break;}
+    case 'X' :
+      if (c2=='P') {element_ = EXTRAPT; break;}
     default:
       SetElementFromSymbol(c1, c2);
       if (element_ == UNKNOWN_ELEMENT)

From 766a42d25635e9587b88a781c75d44cc52178b88 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 7 Jan 2026 11:14:25 -0500
Subject: [PATCH 1176/1492] By default, do not include extra points in atoms to
 be checked

---
 src/StructureCheck.cpp | 44 ++++++++++++++++++++++++++++++++++++++----
 src/StructureCheck.h   | 10 +++++++++-
 2 files changed, 49 insertions(+), 5 deletions(-)

diff --git a/src/StructureCheck.cpp b/src/StructureCheck.cpp
index 6209003d71..14ece1200c 100644
--- a/src/StructureCheck.cpp
+++ b/src/StructureCheck.cpp
@@ -13,6 +13,7 @@
 
 /// CONSTRUCTOR
 StructureCheck::StructureCheck() :
+  XP_Exclude_Mask_("&!@/XP"),
   bondoffset_(1.15),
   bondMinOffset_(0.50),
   nonbondcut2_(0.64), // (0.8 Ang)^2
@@ -25,6 +26,7 @@ StructureCheck::StructureCheck() :
   bondcheck_(true),
   ringcheck_(true),
   saveProblems_(false),
+  checkExtraPts_(false),
   lastFmt_(F_ATOM)
 {}
 
@@ -43,9 +45,35 @@ double StructureCheck::RingAngleCut_Deg() const {
   return ring_acut_ * Constants::RADDEG;
 }
 
+/** Create mask string based on if we are excluding extra points or not. */
+std::string StructureCheck::checkMaskStr(std::string const& maskIn)
+const
+{
+  std::string maskOut;
+  if (maskIn.empty())
+    maskOut = "*" + XP_Exclude_Mask_;
+  else
+    maskOut = maskIn + XP_Exclude_Mask_;
+  mprintf("DEBUG: StructureCheck::checkMaskStr(): String is %s\n", maskOut.c_str());
+  return maskOut;
+}
+
+/** Set options with default for extra points (exclude) */
+int StructureCheck::SetOptions(bool imageOn, bool checkBonds, bool saveProblemsIn,
+                               int debugIn,
+                               std::string const& mask1, std::string const& mask2, 
+                               double overlapCut, double bondLengthOffset, double bondMinOffset,
+                               double pairListCut,
+                               bool checkRings, double ring_shortd, double ring_dcut, double ring_acut)
+{
+  return SetOptions(imageOn, checkBonds, saveProblemsIn, false, debugIn, mask1, mask2, "", overlapCut,
+                    bondLengthOffset, bondMinOffset, pairListCut, checkRings, ring_shortd, ring_dcut, ring_acut);
+}
+
 // StructureCheck::SetOptions()
-int StructureCheck::SetOptions(bool imageOn, bool checkBonds, bool saveProblemsIn, int debugIn,
-                               std::string const& mask1, std::string const& mask2,
+int StructureCheck::SetOptions(bool imageOn, bool checkBonds, bool saveProblemsIn, bool checkExtraPtsIn,
+                               int debugIn,
+                               std::string const& mask1, std::string const& mask2, std::string const& XP_Exclude_MaskIn,
                                double overlapCut, double bondLengthOffset, double bondMinOffset,
                                double pairListCut,
                                bool checkRings, double ring_shortd, double ring_dcut, double ring_acut)
@@ -54,6 +82,7 @@ int StructureCheck::SetOptions(bool imageOn, bool checkBonds, bool saveProblemsI
   bondcheck_ = checkBonds;
   ringcheck_ = checkRings;
   saveProblems_ = saveProblemsIn;
+  checkExtraPts_ = checkExtraPtsIn;
   debug_ = debugIn;
   bondoffset_ = bondLengthOffset;
   bondMinOffset_ = bondMinOffset;
@@ -65,9 +94,16 @@ int StructureCheck::SetOptions(bool imageOn, bool checkBonds, bool saveProblemsI
     ring_dcut2_ = ring_dcut * ring_dcut;
   if (ring_acut > 0)
     ring_acut_ = ring_acut * Constants::DEGRAD;
-  if (Mask1_.SetMaskString( mask1 )) return 1;
+  if (!XP_Exclude_MaskIn.empty())
+    XP_Exclude_Mask_ = XP_Exclude_MaskIn;
+  else
+    XP_Exclude_Mask_ = "&!@/XP"; // Select extra points by element
+  if (checkExtraPts_) {
+    XP_Exclude_Mask_.clear();
+  }
+  if (Mask1_.SetMaskString( checkMaskStr(mask1) )) return 1;
   if (!mask2.empty()) {
-    if (Mask2_.SetMaskString( mask2 )) return 1;
+    if (Mask2_.SetMaskString( checkMaskStr(mask2) )) return 1;
   }
   // TODO error checking
   # ifdef _OPENMP
diff --git a/src/StructureCheck.h b/src/StructureCheck.h
index acc49438e8..fa569f9305 100644
--- a/src/StructureCheck.h
+++ b/src/StructureCheck.h
@@ -32,9 +32,13 @@ class StructureCheck {
     // -------------------------------------------
     /// CONSTRUCTOR
     StructureCheck();
-    /// Options: imageOn, checkBonds, saveProblems, debug, mask1, mask2, ovrlpCut, bndLenOffset, minBndLenOffset, PListCut
+    /// Options: imageOn, checkBonds, saveProblems, check extrapoints, debug, mask1, mask2, extra points exclude mask, ovrlpCut, bndLenOffset, minBndLenOffset, PListCut
+    int SetOptions(bool, bool, bool, bool, int, std::string const&, std::string const&, std::string const&,
+                   double, double, double, double, bool, double, double, double);
+    /// Options (no extra points): imageOn, checkBonds, saveProblems, debug, mask1, mask2, ovrlpCut, bndLenOffset, minBndLenOffset, PListCut
     int SetOptions(bool, bool, bool, int, std::string const&, std::string const&,
                    double, double, double, double, bool, double, double, double);
+
     /// Setup for given topology and box.
     int Setup(Topology const&, Box const&);
     /// \return Number of abnormal bonds.
@@ -112,6 +116,8 @@ class StructureCheck {
     static const char* Fmt_[];
     /// Type of overlap check
     enum CheckType { NO_PL_1_MASK=0, NO_PL_2_MASKS, PL_1_MASK };
+    /// \return mask string based on if extra points are being excluded
+    std::string checkMaskStr(std::string const&) const;
     /// Add selected bonds in BondArray to list to be checked.
     void ProcessBondArray(BondArray const&, BondParmArray const&, CharMask const&);
     /// Add selected bonds in topology to list to be checked.
@@ -160,6 +166,7 @@ class StructureCheck {
     AtomMask Mask2_;        ///< Optional mask of atoms to check against atoms in Mask1
     AtomMask OuterMask_;    ///< Mask with the most atoms.
     AtomMask InnerMask_;    ///< Mask with fewer atoms.
+    std::string XP_Exclude_Mask_;   ///< Expression to deselect extra points
     double bondoffset_;     ///< Report bonds larger than Req + bondoffset_
     double bondMinOffset_;  ///< Report bonds less than Req - bondMinOffset_
     double nonbondcut2_;    ///< Report distance^2 less than nonbondcut2_
@@ -172,6 +179,7 @@ class StructureCheck {
     bool bondcheck_;        ///< If true check bonds as well
     bool ringcheck_;        ///< If true check bond/ring intersections
     bool saveProblems_;     ///< If true save problems in problemAtoms_
+    bool checkExtraPts_;    ///< If true check extra points.
     FmtType lastFmt_;       ///< Format of problems currently stored in problemAtoms_
 };
 #endif

From a8144c35c240fb23d88b780d36bc2755ba82465f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 7 Jan 2026 11:23:10 -0500
Subject: [PATCH 1177/1492] Add checkxp and xpmask keywords to checkstructure.
 Report when not checking extra points is active

---
 src/Action_CheckStructure.cpp | 12 ++++++++++++
 src/StructureCheck.cpp        |  2 ++
 2 files changed, 14 insertions(+)

diff --git a/src/Action_CheckStructure.cpp b/src/Action_CheckStructure.cpp
index 21fa75ece6..08c12de7ac 100644
--- a/src/Action_CheckStructure.cpp
+++ b/src/Action_CheckStructure.cpp
@@ -23,6 +23,7 @@ void Action_CheckStructure::Help() const {
           "\t[cut <cut>] [nobondcheck] [silent] [plcut <cut>]\n"
           "\t[{noringcheck | [ringshortdist <rsdist>] [ringdcut <ringdcut>]\n"
           "\t                [ringacut <ringacut>]}]\n"
+          "\t[{checkxp | xpmask <xpmask>}]\n"
           "  Check atoms in <mask> for atomic overlaps less than <cut> (default 0.8 Ang)\n"
           "  and unusual bond lengths greater than equilibrium length + <offset>\n"
           "  (default 1.15 Ang) or less than equilibrium length - <minoffset>\n"
@@ -36,6 +37,9 @@ void Action_CheckStructure::Help() const {
           "  center is less than <rsdist>, or less than <ringdcut> and the angle\n"
           "  between the bond vector and ring perpendicular vector is less than\n"
           "  <ringacut>.\n"
+          "  By default, extra points will be ignored as determined by 'xpmask'; the\n"
+          "  default mask to select extra points is '&@\\XP'. If 'checkxp' is specified\n",
+          "  extra points will also be checked.\n"
           "  Warnings will go to the file specified by 'reportfile', STDOUT,\n"
           "  or will be suppressed if 'silent' is specified. If 'skipbadframes'\n"
           "  is specified, subsequent Actions will be skipped if any problems\n"
@@ -58,14 +62,22 @@ Action::RetType Action_CheckStructure::Init(ArgList& actionArgs, ActionInit& ini
   double nonbondcut = actionArgs.getKeyDouble("cut",0.8);
   double plcut      = actionArgs.getKeyDouble("plcut", -1);
   //  actionArgs.getKeyDouble("plcut", std::max(8.0, nonbondcut))
+  bool checkxp = false;
+  std::string xpmask = "";
+  if (actionArgs.hasKey("checkxp"))
+    checkxp = true;
+  else
+    xpmask = actionArgs.GetStringKey("xpmask");
   // Structure checker setup
   int err = check_.SetOptions(
     !(actionArgs.hasKey("noimage")),
     !actionArgs.hasKey("nobondcheck"),
     (outfile_ != 0), // saveProblems
+    checkxp,
     debugIn,
     actionArgs.GetMaskNext(),
     around,
+    xpmask,
     nonbondcut,
     actionArgs.getKeyDouble("offset",1.15),
     actionArgs.getKeyDouble("minoffset", 0.5),
diff --git a/src/StructureCheck.cpp b/src/StructureCheck.cpp
index 14ece1200c..530309cc7e 100644
--- a/src/StructureCheck.cpp
+++ b/src/StructureCheck.cpp
@@ -164,6 +164,8 @@ int StructureCheck::Setup(Topology const& topIn, Box const& boxIn)
 {
   imageOpt_.SetupImaging( boxIn.HasBox() );
   bondList_.clear();
+  if (!checkExtraPts_)
+    mprintf("\tExcluding extra points using mask expression '%s'.\n", XP_Exclude_Mask_.c_str());
   // Set up first mask
   if ( topIn.SetupIntegerMask( Mask1_ ) ) return 1;
   if (Mask1_.None()) {

From b5e853856f67f94ff55ff7864815bba99c89a9d6 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 7 Jan 2026 11:25:26 -0500
Subject: [PATCH 1178/1492] Add checkxp test

---
 test/Test_CheckStructure/RunTest.sh           |   16 +-
 test/Test_CheckStructure/opcbox.mol2          | 1954 +++++++++++++++++
 .../report.opcbox.dat.save                    |  432 ++++
 3 files changed, 2401 insertions(+), 1 deletion(-)
 create mode 100644 test/Test_CheckStructure/opcbox.mol2
 create mode 100644 test/Test_CheckStructure/report.opcbox.dat.save

diff --git a/test/Test_CheckStructure/RunTest.sh b/test/Test_CheckStructure/RunTest.sh
index 46bbe85219..2662807b85 100755
--- a/test/Test_CheckStructure/RunTest.sh
+++ b/test/Test_CheckStructure/RunTest.sh
@@ -3,7 +3,7 @@
 . ../MasterTest.sh
 
 CleanFiles check.in report.dat nprob.dat tz2.dat skip.dat around.dat d1.dat \
-           partial.report.dat tz2.cut0.9.dat entangled.dat
+           partial.report.dat tz2.cut0.9.dat entangled.dat report.opcbox.dat
 
 INPUT="-i check.in"
 
@@ -82,6 +82,20 @@ EOF
   DoTest entangled.dat.save entangled.dat
 fi
 
+UNITNAME='Check with extra points'
+CheckFor maxthreads 1
+if [ $? -eq 0 ] ; then
+  cat > check.in <<EOF
+parm opcbox.mol2
+trajin opcbox.mol2
+box x 18.8648434  y 18.4781075  z 19.0062408 alpha 90
+check reportfile report.opcbox.dat checkxp
+run
+EOF
+  RunCpptraj "$UNITNAME"
+  DoTest report.opcbox.dat.save report.opcbox.dat
+fi
+
 EndTest
 
 exit 0
diff --git a/test/Test_CheckStructure/opcbox.mol2 b/test/Test_CheckStructure/opcbox.mol2
new file mode 100644
index 0000000000..8f967be0c7
--- /dev/null
+++ b/test/Test_CheckStructure/opcbox.mol2
@@ -0,0 +1,1954 @@
+@<TRIPOS>MOLECULE
+Cpptraj Generated mol2 file.
+  864   864   216     0     0
+SMALL
+USER_CHARGES
+
+
+@<TRIPOS>ATOM
+      1 O          11.0300    1.0360    5.5020 OW         1 WAT      0.000000
+      2 H1         10.7850    1.5240    4.8220 HW         1 WAT      0.679142
+      3 H2         11.8930    0.9630    5.4020 HW         1 WAT      0.679142
+      4 EPW        11.1210    1.0970    5.3870 EP         1 WAT     -1.358284
+      5 O          10.8390    7.9520   10.1730 OW         2 WAT      0.000000
+      6 H1         10.3150    8.5480   10.5360 HW         2 WAT      0.679142
+      7 H2         11.2360    7.5840   10.8570 HW         2 WAT      0.679142
+      8 EPW        10.8200    7.9860   10.3280 EP         2 WAT     -1.358284
+      9 O           0.7080   12.0920    5.6290 OW         3 WAT      0.000000
+     10 H1          0.2670   12.2100    6.3720 HW         3 WAT      0.679142
+     11 H2          0.4250   11.3170    5.3440 HW         3 WAT      0.679142
+     12 EPW         0.6010   11.9950    5.6970 EP         3 WAT     -1.358284
+     13 O          16.9830   15.3930    3.1440 OW         4 WAT      0.000000
+     14 H1         17.6840   14.8740    3.1400 HW         4 WAT      0.679142
+     15 H2         16.3960   14.9480    2.6750 HW         4 WAT      0.679142
+     16 EPW        17.0000   15.2500    3.0740 EP         4 WAT     -1.358284
+     17 O           0.4510    5.8840    2.1360 OW         5 WAT      0.000000
+     18 H1         -0.3270    6.0460    1.7760 HW         5 WAT      0.679142
+     19 H2          0.4900    5.0130    2.1580 HW         5 WAT      0.679142
+     20 EPW         0.3420    5.7790    2.0860 EP         5 WAT     -1.358284
+     21 O           3.5900   11.1470    0.8080 OW         6 WAT      0.000000
+     22 H1          3.1980   10.7760    0.1220 HW         6 WAT      0.679142
+     23 H2          3.5100   10.5490    1.4370 HW         6 WAT      0.679142
+     24 EPW         3.5200   11.0040    0.7990 EP         6 WAT     -1.358284
+     25 O          13.5100    9.0190    6.8490 OW         7 WAT      0.000000
+     26 H1         13.5900    9.0230    5.9800 HW         7 WAT      0.679142
+     27 H2         12.9260    8.3870    6.9980 HW         7 WAT      0.679142
+     28 EPW        13.4350    8.9260    6.7430 EP         7 WAT     -1.358284
+     29 O           3.2170   12.7880    4.7080 OW         8 WAT      0.000000
+     30 H1          3.8250   12.6180    5.3110 HW         8 WAT      0.679142
+     31 H2          2.4660   12.6480    5.1290 HW         8 WAT      0.679142
+     32 EPW         3.1960   12.7420    4.8590 EP         8 WAT     -1.358284
+     33 O           7.4990    2.1230    4.6570 OW         9 WAT      0.000000
+     34 H1          7.4290    2.8000    4.1110 HW         9 WAT      0.679142
+     35 H2          8.2400    1.7350    4.4080 HW         9 WAT      0.679142
+     36 EPW         7.5980    2.1660    4.5390 EP         9 WAT     -1.358284
+     37 O           2.1080   15.8790    0.7850 OW        10 WAT      0.000000
+     38 H1          2.5750   15.9630    0.0530 HW        10 WAT      0.679142
+     39 H2          2.5630   15.3010    1.2540 HW        10 WAT      0.679142
+     40 EPW         2.2440   15.8060    0.7460 EP        10 WAT     -1.358284
+     41 O           0.6480   14.8270   11.8840 OW        11 WAT      0.000000
+     42 H1          0.7770   14.5470   12.7000 HW        11 WAT      0.679142
+     43 H2          0.0380   14.2860   11.5750 HW        11 WAT      0.679142
+     44 EPW         0.5770   14.7060   11.9590 EP        11 WAT     -1.358284
+     45 O           7.2220   12.3520   16.9510 OW        12 WAT      0.000000
+     46 H1          6.9860   12.3490   17.7910 HW        12 WAT      0.679142
+     47 H2          6.4740   12.2040   16.5270 HW        12 WAT      0.679142
+     48 EPW         7.0760   12.3290   17.0120 EP        12 WAT     -1.358284
+     49 O           2.0940    9.3480    6.0860 OW        13 WAT      0.000000
+     50 H1          1.6320    8.9560    5.4590 HW        13 WAT      0.679142
+     51 H2          2.7940    8.8350    6.1780 HW        13 WAT      0.679142
+     52 EPW         2.1290    9.2150    6.0070 EP        13 WAT     -1.358284
+     53 O           6.6020    4.9580   11.4330 OW        14 WAT      0.000000
+     54 H1          7.2800    4.9760   10.8840 HW        14 WAT      0.679142
+     55 H2          6.5570    4.1220   11.6780 HW        14 WAT      0.679142
+     56 EPW         6.6950    4.8370   11.3880 EP        14 WAT     -1.358284
+     57 O           7.2040   15.5440   14.2140 OW        15 WAT      0.000000
+     58 H1          7.3420   16.3040   13.8070 HW        15 WAT      0.679142
+     59 H2          7.9950   15.1790   14.2410 HW        15 WAT      0.679142
+     60 EPW         7.3410   15.6030   14.1580 EP        15 WAT     -1.358284
+     61 O           4.0950    7.4480    6.1090 OW        16 WAT      0.000000
+     62 H1          4.9120    7.2610    6.3520 HW        16 WAT      0.679142
+     63 H2          3.6180    6.8340    6.5050 HW        16 WAT      0.679142
+     64 EPW         4.1450    7.3300    6.2040 EP        16 WAT     -1.358284
+     65 O           8.2990   13.4290    8.7190 OW        17 WAT      0.000000
+     66 H1          8.6470   12.6300    8.7490 HW        17 WAT      0.679142
+     67 H2          8.9640   13.9330    8.4640 HW        17 WAT      0.679142
+     68 EPW         8.4490   13.3850    8.6860 EP        17 WAT     -1.358284
+     69 O           8.3560   12.8780    4.9300 OW        18 WAT      0.000000
+     70 H1          8.6870   12.2340    5.4160 HW        18 WAT      0.679142
+     71 H2          8.5960   12.6670    4.1190 HW        18 WAT      0.679142
+     72 EPW         8.4400   12.7520    4.8820 EP        18 WAT     -1.358284
+     73 O          10.3240    7.0090   16.2690 OW        19 WAT      0.000000
+     74 H1          9.4760    6.9100   16.0910 HW        19 WAT      0.679142
+     75 H2         10.3530    7.7540   16.7230 HW        19 WAT      0.679142
+     76 EPW        10.2030    7.1050   16.3100 EP        19 WAT     -1.358284
+     77 O           4.6920    2.5420    5.3750 OW        20 WAT      0.000000
+     78 H1          4.3960    3.0430    4.7250 HW        20 WAT      0.679142
+     79 H2          5.5590    2.6200    5.3180 HW        20 WAT      0.679142
+     80 EPW         4.7760    2.6280    5.2710 EP        20 WAT     -1.358284
+     81 O          14.8820   -0.0310   15.3830 OW        21 WAT      0.000000
+     82 H1         14.7240    0.7380   15.0010 HW        21 WAT      0.679142
+     83 H2         14.1100   -0.2510   15.7270 HW        21 WAT      0.679142
+     84 EPW        14.7440    0.0500   15.3780 EP        21 WAT     -1.358284
+     85 O           7.6710    1.6840    7.5980 OW        22 WAT      0.000000
+     86 H1          7.7440    2.5440    7.7270 HW        22 WAT      0.679142
+     87 H2          7.6330    1.6090    6.7300 HW        22 WAT      0.679142
+     88 EPW         7.6760    1.8000    7.4890 EP        22 WAT     -1.358284
+     89 O          12.3440    4.6100   -0.1030 OW        23 WAT      0.000000
+     90 H1         11.8940    5.2910    0.2040 HW        23 WAT      0.679142
+     91 H2         12.4580    4.1060    0.6000 HW        23 WAT      0.679142
+     92 EPW        12.2950    4.6360    0.0460 EP        23 WAT     -1.358284
+     93 O           0.5500    7.1090    9.0990 OW        24 WAT      0.000000
+     94 H1          0.2940    7.9400    9.0240 HW        24 WAT      0.679142
+     95 H2         -0.1140    6.7260    9.5160 HW        24 WAT      0.679142
+     96 EPW         0.4140    7.1750    9.1500 EP        24 WAT     -1.358284
+     97 O           0.4600   16.8190    6.9990 OW        25 WAT      0.000000
+     98 H1         -0.1320   17.3770    6.6860 HW        25 WAT      0.679142
+     99 H2          0.8860   16.5500    6.2870 HW        25 WAT      0.679142
+    100 EPW         0.4360   16.8610    6.8480 EP        25 WAT     -1.358284
+    101 O           6.3000   14.6630    4.4790 OW        26 WAT      0.000000
+    102 H1          5.7210   14.3880    5.0710 HW        26 WAT      0.679142
+    103 H2          6.9240   14.0540    4.5040 HW        26 WAT      0.679142
+    104 EPW         6.3070   14.5330    4.5700 EP        26 WAT     -1.358284
+    105 O          12.4430   16.9510    2.0010 OW        27 WAT      0.000000
+    106 H1         13.1700   17.4230    2.1030 HW        27 WAT      0.679142
+    107 H2         12.6720   16.1570    2.2810 HW        27 WAT      0.679142
+    108 EPW        12.5850   16.9040    2.0580 EP        27 WAT     -1.358284
+    109 O          10.6110   17.3430    3.9910 OW        28 WAT      0.000000
+    110 H1         10.8250   17.8700    4.6530 HW        28 WAT      0.679142
+    111 H2         11.3780   17.1690    3.6120 HW        28 WAT      0.679142
+    112 EPW        10.7560   17.3950    4.0330 EP        28 WAT     -1.358284
+    113 O           3.5790    1.9260    9.5900 OW        29 WAT      0.000000
+    114 H1          3.0580    1.2980    9.2820 HW        29 WAT      0.679142
+    115 H2          4.1700    1.4890   10.0610 HW        29 WAT      0.679142
+    116 EPW         3.5900    1.7680    9.6140 EP        29 WAT     -1.358284
+    117 O           6.8850    4.0590   18.8880 OW        30 WAT      0.000000
+    118 H1          7.0020    3.6050   18.1520 HW        30 WAT      0.679142
+    119 H2          7.1730    4.8570   18.6850 HW        30 WAT      0.679142
+    120 EPW         6.9450    4.1100   18.7490 EP        30 WAT     -1.358284
+    121 O           2.0050   15.4890    4.9300 OW        31 WAT      0.000000
+    122 H1          2.6610   14.9140    4.9450 HW        31 WAT      0.679142
+    123 H2          2.3940   16.2380    4.7090 HW        31 WAT      0.679142
+    124 EPW         2.1600   15.5140    4.9000 EP        31 WAT     -1.358284
+    125 O          17.7380    4.5830    6.1920 OW        32 WAT      0.000000
+    126 H1         17.3920    5.2610    6.6180 HW        32 WAT      0.679142
+    127 H2         17.1020    3.9850    6.2080 HW        32 WAT      0.679142
+    128 EPW        17.5930    4.5950    6.2570 EP        32 WAT     -1.358284
+    129 O          13.0500   17.3530   12.2960 OW        33 WAT      0.000000
+    130 H1         13.7940   17.8090   12.2860 HW        33 WAT      0.679142
+    131 H2         12.9290   17.1390   11.4590 HW        33 WAT      0.679142
+    132 EPW        13.1420   17.3890   12.1710 EP        33 WAT     -1.358284
+    133 O           2.6180    3.6560   17.8720 OW        34 WAT      0.000000
+    134 H1          1.8400    3.2660   17.8000 HW        34 WAT      0.679142
+    135 H2          3.1090    3.2440   17.2810 HW        34 WAT      0.679142
+    136 EPW         2.5750    3.5370   17.7740 EP        34 WAT     -1.358284
+    137 O           2.8230   13.9760    8.4300 OW        35 WAT      0.000000
+    138 H1          3.2460   13.6200    7.7560 HW        35 WAT      0.679142
+    139 H2          3.1470   13.5540    9.1220 HW        35 WAT      0.679142
+    140 EPW         2.9330   13.8610    8.4330 EP        35 WAT     -1.358284
+    141 O           6.0540   16.8280    7.7260 OW        36 WAT      0.000000
+    142 H1          6.8980   16.9320    7.5310 HW        36 WAT      0.679142
+    143 H2          5.7570   17.6460    7.7940 HW        36 WAT      0.679142
+    144 EPW         6.1350   16.9640    7.7070 EP        36 WAT     -1.358284
+    145 O           9.2670    1.2990   17.0400 OW        37 WAT      0.000000
+    146 H1          9.4450    0.4900   16.7650 HW        37 WAT      0.679142
+    147 H2          9.1240    1.7400   16.3010 HW        37 WAT      0.679142
+    148 EPW         9.2720    1.2450   16.8900 EP        37 WAT     -1.358284
+    149 O           9.8610    6.2250    5.8130 OW        38 WAT      0.000000
+    150 H1         10.1480    5.9930    5.0230 HW        38 WAT      0.679142
+    151 H2         10.5930    6.3040    6.2820 HW        38 WAT      0.679142
+    152 EPW        10.0110    6.2020    5.7660 EP        38 WAT     -1.358284
+    153 O          10.5830    6.5640    0.9340 OW        39 WAT      0.000000
+    154 H1         10.8640    7.3520    1.1830 HW        39 WAT      0.679142
+    155 H2          9.8070    6.7290    0.5710 HW        39 WAT      0.679142
+    156 EPW        10.5100    6.7050    0.9170 EP        39 WAT     -1.358284
+    157 O          14.6240   18.5380    2.4010 OW        40 WAT      0.000000
+    158 H1         15.2890   18.3900    1.8560 HW        40 WAT      0.679142
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+    102 WAT             405 ****               0 ****  **** 
+    103 WAT             409 ****               0 ****  **** 
+    104 WAT             413 ****               0 ****  **** 
+    105 WAT             417 ****               0 ****  **** 
+    106 WAT             421 ****               0 ****  **** 
+    107 WAT             425 ****               0 ****  **** 
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diff --git a/test/Test_CheckStructure/report.opcbox.dat.save b/test/Test_CheckStructure/report.opcbox.dat.save
new file mode 100644
index 0000000000..d5e82244bf
--- /dev/null
+++ b/test/Test_CheckStructure/report.opcbox.dat.save
@@ -0,0 +1,432 @@
+1	 Warning: Atoms 2:WAT_1@H1 and 4:WAT_1@EPW are close (0.78)
+1	 Warning: Atoms 3:WAT_1@H2 and 4:WAT_1@EPW are close (0.78)
+1	 Warning: Atoms 6:WAT_2@H1 and 8:WAT_2@EPW are close (0.78)
+1	 Warning: Atoms 7:WAT_2@H2 and 8:WAT_2@EPW are close (0.78)
+1	 Warning: Atoms 10:WAT_3@H1 and 12:WAT_3@EPW are close (0.78)
+1	 Warning: Atoms 11:WAT_3@H2 and 12:WAT_3@EPW are close (0.78)
+1	 Warning: Atoms 14:WAT_4@H1 and 16:WAT_4@EPW are close (0.78)
+1	 Warning: Atoms 15:WAT_4@H2 and 16:WAT_4@EPW are close (0.78)
+1	 Warning: Atoms 18:WAT_5@H1 and 20:WAT_5@EPW are close (0.78)
+1	 Warning: Atoms 19:WAT_5@H2 and 20:WAT_5@EPW are close (0.78)
+1	 Warning: Atoms 22:WAT_6@H1 and 24:WAT_6@EPW are close (0.78)
+1	 Warning: Atoms 23:WAT_6@H2 and 24:WAT_6@EPW are close (0.78)
+1	 Warning: Atoms 26:WAT_7@H1 and 28:WAT_7@EPW are close (0.78)
+1	 Warning: Atoms 27:WAT_7@H2 and 28:WAT_7@EPW are close (0.78)
+1	 Warning: Atoms 30:WAT_8@H1 and 32:WAT_8@EPW are close (0.78)
+1	 Warning: Atoms 31:WAT_8@H2 and 32:WAT_8@EPW are close (0.78)
+1	 Warning: Atoms 34:WAT_9@H1 and 36:WAT_9@EPW are close (0.78)
+1	 Warning: Atoms 35:WAT_9@H2 and 36:WAT_9@EPW are close (0.78)
+1	 Warning: Atoms 38:WAT_10@H1 and 40:WAT_10@EPW are close (0.78)
+1	 Warning: Atoms 39:WAT_10@H2 and 40:WAT_10@EPW are close (0.78)
+1	 Warning: Atoms 42:WAT_11@H1 and 44:WAT_11@EPW are close (0.78)
+1	 Warning: Atoms 43:WAT_11@H2 and 44:WAT_11@EPW are close (0.78)
+1	 Warning: Atoms 46:WAT_12@H1 and 48:WAT_12@EPW are close (0.78)
+1	 Warning: Atoms 47:WAT_12@H2 and 48:WAT_12@EPW are close (0.78)
+1	 Warning: Atoms 50:WAT_13@H1 and 52:WAT_13@EPW are close (0.78)
+1	 Warning: Atoms 51:WAT_13@H2 and 52:WAT_13@EPW are close (0.78)
+1	 Warning: Atoms 54:WAT_14@H1 and 56:WAT_14@EPW are close (0.78)
+1	 Warning: Atoms 55:WAT_14@H2 and 56:WAT_14@EPW are close (0.78)
+1	 Warning: Atoms 58:WAT_15@H1 and 60:WAT_15@EPW are close (0.78)
+1	 Warning: Atoms 59:WAT_15@H2 and 60:WAT_15@EPW are close (0.78)
+1	 Warning: Atoms 62:WAT_16@H1 and 64:WAT_16@EPW are close (0.78)
+1	 Warning: Atoms 63:WAT_16@H2 and 64:WAT_16@EPW are close (0.78)
+1	 Warning: Atoms 66:WAT_17@H1 and 68:WAT_17@EPW are close (0.78)
+1	 Warning: Atoms 67:WAT_17@H2 and 68:WAT_17@EPW are close (0.78)
+1	 Warning: Atoms 70:WAT_18@H1 and 72:WAT_18@EPW are close (0.78)
+1	 Warning: Atoms 71:WAT_18@H2 and 72:WAT_18@EPW are close (0.78)
+1	 Warning: Atoms 74:WAT_19@H1 and 76:WAT_19@EPW are close (0.78)
+1	 Warning: Atoms 75:WAT_19@H2 and 76:WAT_19@EPW are close (0.78)
+1	 Warning: Atoms 78:WAT_20@H1 and 80:WAT_20@EPW are close (0.78)
+1	 Warning: Atoms 79:WAT_20@H2 and 80:WAT_20@EPW are close (0.78)
+1	 Warning: Atoms 82:WAT_21@H1 and 84:WAT_21@EPW are close (0.78)
+1	 Warning: Atoms 83:WAT_21@H2 and 84:WAT_21@EPW are close (0.78)
+1	 Warning: Atoms 86:WAT_22@H1 and 88:WAT_22@EPW are close (0.78)
+1	 Warning: Atoms 87:WAT_22@H2 and 88:WAT_22@EPW are close (0.78)
+1	 Warning: Atoms 90:WAT_23@H1 and 92:WAT_23@EPW are close (0.78)
+1	 Warning: Atoms 91:WAT_23@H2 and 92:WAT_23@EPW are close (0.78)
+1	 Warning: Atoms 94:WAT_24@H1 and 96:WAT_24@EPW are close (0.78)
+1	 Warning: Atoms 95:WAT_24@H2 and 96:WAT_24@EPW are close (0.78)
+1	 Warning: Atoms 98:WAT_25@H1 and 100:WAT_25@EPW are close (0.78)
+1	 Warning: Atoms 99:WAT_25@H2 and 100:WAT_25@EPW are close (0.78)
+1	 Warning: Atoms 102:WAT_26@H1 and 104:WAT_26@EPW are close (0.78)
+1	 Warning: Atoms 103:WAT_26@H2 and 104:WAT_26@EPW are close (0.78)
+1	 Warning: Atoms 106:WAT_27@H1 and 108:WAT_27@EPW are close (0.78)
+1	 Warning: Atoms 107:WAT_27@H2 and 108:WAT_27@EPW are close (0.78)
+1	 Warning: Atoms 110:WAT_28@H1 and 112:WAT_28@EPW are close (0.78)
+1	 Warning: Atoms 111:WAT_28@H2 and 112:WAT_28@EPW are close (0.78)
+1	 Warning: Atoms 114:WAT_29@H1 and 116:WAT_29@EPW are close (0.78)
+1	 Warning: Atoms 115:WAT_29@H2 and 116:WAT_29@EPW are close (0.78)
+1	 Warning: Atoms 118:WAT_30@H1 and 120:WAT_30@EPW are close (0.78)
+1	 Warning: Atoms 119:WAT_30@H2 and 120:WAT_30@EPW are close (0.78)
+1	 Warning: Atoms 122:WAT_31@H1 and 124:WAT_31@EPW are close (0.78)
+1	 Warning: Atoms 123:WAT_31@H2 and 124:WAT_31@EPW are close (0.78)
+1	 Warning: Atoms 126:WAT_32@H1 and 128:WAT_32@EPW are close (0.78)
+1	 Warning: Atoms 127:WAT_32@H2 and 128:WAT_32@EPW are close (0.78)
+1	 Warning: Atoms 130:WAT_33@H1 and 132:WAT_33@EPW are close (0.78)
+1	 Warning: Atoms 131:WAT_33@H2 and 132:WAT_33@EPW are close (0.78)
+1	 Warning: Atoms 134:WAT_34@H1 and 136:WAT_34@EPW are close (0.78)
+1	 Warning: Atoms 135:WAT_34@H2 and 136:WAT_34@EPW are close (0.78)
+1	 Warning: Atoms 138:WAT_35@H1 and 140:WAT_35@EPW are close (0.78)
+1	 Warning: Atoms 139:WAT_35@H2 and 140:WAT_35@EPW are close (0.78)
+1	 Warning: Atoms 142:WAT_36@H1 and 144:WAT_36@EPW are close (0.78)
+1	 Warning: Atoms 143:WAT_36@H2 and 144:WAT_36@EPW are close (0.78)
+1	 Warning: Atoms 146:WAT_37@H1 and 148:WAT_37@EPW are close (0.78)
+1	 Warning: Atoms 147:WAT_37@H2 and 148:WAT_37@EPW are close (0.78)
+1	 Warning: Atoms 150:WAT_38@H1 and 152:WAT_38@EPW are close (0.78)
+1	 Warning: Atoms 151:WAT_38@H2 and 152:WAT_38@EPW are close (0.78)
+1	 Warning: Atoms 154:WAT_39@H1 and 156:WAT_39@EPW are close (0.78)
+1	 Warning: Atoms 155:WAT_39@H2 and 156:WAT_39@EPW are close (0.78)
+1	 Warning: Atoms 158:WAT_40@H1 and 160:WAT_40@EPW are close (0.78)
+1	 Warning: Atoms 159:WAT_40@H2 and 160:WAT_40@EPW are close (0.78)
+1	 Warning: Atoms 162:WAT_41@H1 and 164:WAT_41@EPW are close (0.78)
+1	 Warning: Atoms 163:WAT_41@H2 and 164:WAT_41@EPW are close (0.78)
+1	 Warning: Atoms 166:WAT_42@H1 and 168:WAT_42@EPW are close (0.78)
+1	 Warning: Atoms 167:WAT_42@H2 and 168:WAT_42@EPW are close (0.78)
+1	 Warning: Atoms 170:WAT_43@H1 and 172:WAT_43@EPW are close (0.78)
+1	 Warning: Atoms 171:WAT_43@H2 and 172:WAT_43@EPW are close (0.78)
+1	 Warning: Atoms 174:WAT_44@H1 and 176:WAT_44@EPW are close (0.78)
+1	 Warning: Atoms 175:WAT_44@H2 and 176:WAT_44@EPW are close (0.78)
+1	 Warning: Atoms 178:WAT_45@H1 and 180:WAT_45@EPW are close (0.78)
+1	 Warning: Atoms 179:WAT_45@H2 and 180:WAT_45@EPW are close (0.78)
+1	 Warning: Atoms 182:WAT_46@H1 and 184:WAT_46@EPW are close (0.78)
+1	 Warning: Atoms 183:WAT_46@H2 and 184:WAT_46@EPW are close (0.78)
+1	 Warning: Atoms 186:WAT_47@H1 and 188:WAT_47@EPW are close (0.78)
+1	 Warning: Atoms 187:WAT_47@H2 and 188:WAT_47@EPW are close (0.78)
+1	 Warning: Atoms 190:WAT_48@H1 and 192:WAT_48@EPW are close (0.78)
+1	 Warning: Atoms 191:WAT_48@H2 and 192:WAT_48@EPW are close (0.78)
+1	 Warning: Atoms 194:WAT_49@H1 and 196:WAT_49@EPW are close (0.78)
+1	 Warning: Atoms 195:WAT_49@H2 and 196:WAT_49@EPW are close (0.78)
+1	 Warning: Atoms 198:WAT_50@H1 and 200:WAT_50@EPW are close (0.78)
+1	 Warning: Atoms 199:WAT_50@H2 and 200:WAT_50@EPW are close (0.78)
+1	 Warning: Atoms 202:WAT_51@H1 and 204:WAT_51@EPW are close (0.78)
+1	 Warning: Atoms 203:WAT_51@H2 and 204:WAT_51@EPW are close (0.78)
+1	 Warning: Atoms 206:WAT_52@H1 and 208:WAT_52@EPW are close (0.78)
+1	 Warning: Atoms 207:WAT_52@H2 and 208:WAT_52@EPW are close (0.78)
+1	 Warning: Atoms 210:WAT_53@H1 and 212:WAT_53@EPW are close (0.78)
+1	 Warning: Atoms 211:WAT_53@H2 and 212:WAT_53@EPW are close (0.78)
+1	 Warning: Atoms 214:WAT_54@H1 and 216:WAT_54@EPW are close (0.78)
+1	 Warning: Atoms 215:WAT_54@H2 and 216:WAT_54@EPW are close (0.78)
+1	 Warning: Atoms 218:WAT_55@H1 and 220:WAT_55@EPW are close (0.78)
+1	 Warning: Atoms 219:WAT_55@H2 and 220:WAT_55@EPW are close (0.78)
+1	 Warning: Atoms 222:WAT_56@H1 and 224:WAT_56@EPW are close (0.78)
+1	 Warning: Atoms 223:WAT_56@H2 and 224:WAT_56@EPW are close (0.78)
+1	 Warning: Atoms 226:WAT_57@H1 and 228:WAT_57@EPW are close (0.78)
+1	 Warning: Atoms 227:WAT_57@H2 and 228:WAT_57@EPW are close (0.78)
+1	 Warning: Atoms 230:WAT_58@H1 and 232:WAT_58@EPW are close (0.78)
+1	 Warning: Atoms 231:WAT_58@H2 and 232:WAT_58@EPW are close (0.78)
+1	 Warning: Atoms 234:WAT_59@H1 and 236:WAT_59@EPW are close (0.78)
+1	 Warning: Atoms 235:WAT_59@H2 and 236:WAT_59@EPW are close (0.78)
+1	 Warning: Atoms 238:WAT_60@H1 and 240:WAT_60@EPW are close (0.78)
+1	 Warning: Atoms 239:WAT_60@H2 and 240:WAT_60@EPW are close (0.78)
+1	 Warning: Atoms 242:WAT_61@H1 and 244:WAT_61@EPW are close (0.78)
+1	 Warning: Atoms 243:WAT_61@H2 and 244:WAT_61@EPW are close (0.78)
+1	 Warning: Atoms 246:WAT_62@H1 and 248:WAT_62@EPW are close (0.78)
+1	 Warning: Atoms 247:WAT_62@H2 and 248:WAT_62@EPW are close (0.78)
+1	 Warning: Atoms 250:WAT_63@H1 and 252:WAT_63@EPW are close (0.78)
+1	 Warning: Atoms 251:WAT_63@H2 and 252:WAT_63@EPW are close (0.78)
+1	 Warning: Atoms 254:WAT_64@H1 and 256:WAT_64@EPW are close (0.78)
+1	 Warning: Atoms 255:WAT_64@H2 and 256:WAT_64@EPW are close (0.78)
+1	 Warning: Atoms 258:WAT_65@H1 and 260:WAT_65@EPW are close (0.78)
+1	 Warning: Atoms 259:WAT_65@H2 and 260:WAT_65@EPW are close (0.78)
+1	 Warning: Atoms 262:WAT_66@H1 and 264:WAT_66@EPW are close (0.78)
+1	 Warning: Atoms 263:WAT_66@H2 and 264:WAT_66@EPW are close (0.78)
+1	 Warning: Atoms 266:WAT_67@H1 and 268:WAT_67@EPW are close (0.78)
+1	 Warning: Atoms 267:WAT_67@H2 and 268:WAT_67@EPW are close (0.78)
+1	 Warning: Atoms 270:WAT_68@H1 and 272:WAT_68@EPW are close (0.78)
+1	 Warning: Atoms 271:WAT_68@H2 and 272:WAT_68@EPW are close (0.78)
+1	 Warning: Atoms 274:WAT_69@H1 and 276:WAT_69@EPW are close (0.78)
+1	 Warning: Atoms 275:WAT_69@H2 and 276:WAT_69@EPW are close (0.78)
+1	 Warning: Atoms 278:WAT_70@H1 and 280:WAT_70@EPW are close (0.78)
+1	 Warning: Atoms 279:WAT_70@H2 and 280:WAT_70@EPW are close (0.78)
+1	 Warning: Atoms 282:WAT_71@H1 and 284:WAT_71@EPW are close (0.78)
+1	 Warning: Atoms 283:WAT_71@H2 and 284:WAT_71@EPW are close (0.78)
+1	 Warning: Atoms 286:WAT_72@H1 and 288:WAT_72@EPW are close (0.78)
+1	 Warning: Atoms 287:WAT_72@H2 and 288:WAT_72@EPW are close (0.78)
+1	 Warning: Atoms 290:WAT_73@H1 and 292:WAT_73@EPW are close (0.78)
+1	 Warning: Atoms 291:WAT_73@H2 and 292:WAT_73@EPW are close (0.78)
+1	 Warning: Atoms 294:WAT_74@H1 and 296:WAT_74@EPW are close (0.78)
+1	 Warning: Atoms 295:WAT_74@H2 and 296:WAT_74@EPW are close (0.78)
+1	 Warning: Atoms 298:WAT_75@H1 and 300:WAT_75@EPW are close (0.78)
+1	 Warning: Atoms 299:WAT_75@H2 and 300:WAT_75@EPW are close (0.78)
+1	 Warning: Atoms 302:WAT_76@H1 and 304:WAT_76@EPW are close (0.78)
+1	 Warning: Atoms 303:WAT_76@H2 and 304:WAT_76@EPW are close (0.78)
+1	 Warning: Atoms 306:WAT_77@H1 and 308:WAT_77@EPW are close (0.78)
+1	 Warning: Atoms 307:WAT_77@H2 and 308:WAT_77@EPW are close (0.78)
+1	 Warning: Atoms 310:WAT_78@H1 and 312:WAT_78@EPW are close (0.78)
+1	 Warning: Atoms 311:WAT_78@H2 and 312:WAT_78@EPW are close (0.78)
+1	 Warning: Atoms 314:WAT_79@H1 and 316:WAT_79@EPW are close (0.78)
+1	 Warning: Atoms 315:WAT_79@H2 and 316:WAT_79@EPW are close (0.78)
+1	 Warning: Atoms 318:WAT_80@H1 and 320:WAT_80@EPW are close (0.78)
+1	 Warning: Atoms 319:WAT_80@H2 and 320:WAT_80@EPW are close (0.78)
+1	 Warning: Atoms 322:WAT_81@H1 and 324:WAT_81@EPW are close (0.78)
+1	 Warning: Atoms 323:WAT_81@H2 and 324:WAT_81@EPW are close (0.78)
+1	 Warning: Atoms 326:WAT_82@H1 and 328:WAT_82@EPW are close (0.78)
+1	 Warning: Atoms 327:WAT_82@H2 and 328:WAT_82@EPW are close (0.78)
+1	 Warning: Atoms 330:WAT_83@H1 and 332:WAT_83@EPW are close (0.78)
+1	 Warning: Atoms 331:WAT_83@H2 and 332:WAT_83@EPW are close (0.78)
+1	 Warning: Atoms 334:WAT_84@H1 and 336:WAT_84@EPW are close (0.78)
+1	 Warning: Atoms 335:WAT_84@H2 and 336:WAT_84@EPW are close (0.78)
+1	 Warning: Atoms 338:WAT_85@H1 and 340:WAT_85@EPW are close (0.78)
+1	 Warning: Atoms 339:WAT_85@H2 and 340:WAT_85@EPW are close (0.78)
+1	 Warning: Atoms 342:WAT_86@H1 and 344:WAT_86@EPW are close (0.78)
+1	 Warning: Atoms 343:WAT_86@H2 and 344:WAT_86@EPW are close (0.78)
+1	 Warning: Atoms 346:WAT_87@H1 and 348:WAT_87@EPW are close (0.78)
+1	 Warning: Atoms 347:WAT_87@H2 and 348:WAT_87@EPW are close (0.78)
+1	 Warning: Atoms 350:WAT_88@H1 and 352:WAT_88@EPW are close (0.78)
+1	 Warning: Atoms 351:WAT_88@H2 and 352:WAT_88@EPW are close (0.78)
+1	 Warning: Atoms 354:WAT_89@H1 and 356:WAT_89@EPW are close (0.78)
+1	 Warning: Atoms 355:WAT_89@H2 and 356:WAT_89@EPW are close (0.78)
+1	 Warning: Atoms 358:WAT_90@H1 and 360:WAT_90@EPW are close (0.78)
+1	 Warning: Atoms 359:WAT_90@H2 and 360:WAT_90@EPW are close (0.78)
+1	 Warning: Atoms 362:WAT_91@H1 and 364:WAT_91@EPW are close (0.78)
+1	 Warning: Atoms 363:WAT_91@H2 and 364:WAT_91@EPW are close (0.78)
+1	 Warning: Atoms 366:WAT_92@H1 and 368:WAT_92@EPW are close (0.78)
+1	 Warning: Atoms 367:WAT_92@H2 and 368:WAT_92@EPW are close (0.78)
+1	 Warning: Atoms 370:WAT_93@H1 and 372:WAT_93@EPW are close (0.78)
+1	 Warning: Atoms 371:WAT_93@H2 and 372:WAT_93@EPW are close (0.78)
+1	 Warning: Atoms 374:WAT_94@H1 and 376:WAT_94@EPW are close (0.78)
+1	 Warning: Atoms 375:WAT_94@H2 and 376:WAT_94@EPW are close (0.78)
+1	 Warning: Atoms 378:WAT_95@H1 and 380:WAT_95@EPW are close (0.78)
+1	 Warning: Atoms 379:WAT_95@H2 and 380:WAT_95@EPW are close (0.78)
+1	 Warning: Atoms 382:WAT_96@H1 and 384:WAT_96@EPW are close (0.78)
+1	 Warning: Atoms 383:WAT_96@H2 and 384:WAT_96@EPW are close (0.78)
+1	 Warning: Atoms 386:WAT_97@H1 and 388:WAT_97@EPW are close (0.78)
+1	 Warning: Atoms 387:WAT_97@H2 and 388:WAT_97@EPW are close (0.78)
+1	 Warning: Atoms 390:WAT_98@H1 and 392:WAT_98@EPW are close (0.78)
+1	 Warning: Atoms 391:WAT_98@H2 and 392:WAT_98@EPW are close (0.78)
+1	 Warning: Atoms 394:WAT_99@H1 and 396:WAT_99@EPW are close (0.78)
+1	 Warning: Atoms 395:WAT_99@H2 and 396:WAT_99@EPW are close (0.78)
+1	 Warning: Atoms 398:WAT_100@H1 and 400:WAT_100@EPW are close (0.78)
+1	 Warning: Atoms 399:WAT_100@H2 and 400:WAT_100@EPW are close (0.78)
+1	 Warning: Atoms 402:WAT_101@H1 and 404:WAT_101@EPW are close (0.78)
+1	 Warning: Atoms 403:WAT_101@H2 and 404:WAT_101@EPW are close (0.78)
+1	 Warning: Atoms 406:WAT_102@H1 and 408:WAT_102@EPW are close (0.78)
+1	 Warning: Atoms 407:WAT_102@H2 and 408:WAT_102@EPW are close (0.78)
+1	 Warning: Atoms 410:WAT_103@H1 and 412:WAT_103@EPW are close (0.78)
+1	 Warning: Atoms 411:WAT_103@H2 and 412:WAT_103@EPW are close (0.78)
+1	 Warning: Atoms 414:WAT_104@H1 and 416:WAT_104@EPW are close (0.78)
+1	 Warning: Atoms 415:WAT_104@H2 and 416:WAT_104@EPW are close (0.78)
+1	 Warning: Atoms 418:WAT_105@H1 and 420:WAT_105@EPW are close (0.78)
+1	 Warning: Atoms 419:WAT_105@H2 and 420:WAT_105@EPW are close (0.78)
+1	 Warning: Atoms 422:WAT_106@H1 and 424:WAT_106@EPW are close (0.78)
+1	 Warning: Atoms 423:WAT_106@H2 and 424:WAT_106@EPW are close (0.78)
+1	 Warning: Atoms 426:WAT_107@H1 and 428:WAT_107@EPW are close (0.78)
+1	 Warning: Atoms 427:WAT_107@H2 and 428:WAT_107@EPW are close (0.78)
+1	 Warning: Atoms 430:WAT_108@H1 and 432:WAT_108@EPW are close (0.78)
+1	 Warning: Atoms 431:WAT_108@H2 and 432:WAT_108@EPW are close (0.78)
+1	 Warning: Atoms 434:WAT_109@H1 and 436:WAT_109@EPW are close (0.78)
+1	 Warning: Atoms 435:WAT_109@H2 and 436:WAT_109@EPW are close (0.78)
+1	 Warning: Atoms 438:WAT_110@H1 and 440:WAT_110@EPW are close (0.78)
+1	 Warning: Atoms 439:WAT_110@H2 and 440:WAT_110@EPW are close (0.78)
+1	 Warning: Atoms 442:WAT_111@H1 and 444:WAT_111@EPW are close (0.78)
+1	 Warning: Atoms 443:WAT_111@H2 and 444:WAT_111@EPW are close (0.78)
+1	 Warning: Atoms 446:WAT_112@H1 and 448:WAT_112@EPW are close (0.78)
+1	 Warning: Atoms 447:WAT_112@H2 and 448:WAT_112@EPW are close (0.78)
+1	 Warning: Atoms 450:WAT_113@H1 and 452:WAT_113@EPW are close (0.78)
+1	 Warning: Atoms 451:WAT_113@H2 and 452:WAT_113@EPW are close (0.78)
+1	 Warning: Atoms 454:WAT_114@H1 and 456:WAT_114@EPW are close (0.78)
+1	 Warning: Atoms 455:WAT_114@H2 and 456:WAT_114@EPW are close (0.78)
+1	 Warning: Atoms 458:WAT_115@H1 and 460:WAT_115@EPW are close (0.78)
+1	 Warning: Atoms 459:WAT_115@H2 and 460:WAT_115@EPW are close (0.78)
+1	 Warning: Atoms 462:WAT_116@H1 and 464:WAT_116@EPW are close (0.78)
+1	 Warning: Atoms 463:WAT_116@H2 and 464:WAT_116@EPW are close (0.78)
+1	 Warning: Atoms 466:WAT_117@H1 and 468:WAT_117@EPW are close (0.78)
+1	 Warning: Atoms 467:WAT_117@H2 and 468:WAT_117@EPW are close (0.78)
+1	 Warning: Atoms 470:WAT_118@H1 and 472:WAT_118@EPW are close (0.78)
+1	 Warning: Atoms 471:WAT_118@H2 and 472:WAT_118@EPW are close (0.78)
+1	 Warning: Atoms 474:WAT_119@H1 and 476:WAT_119@EPW are close (0.78)
+1	 Warning: Atoms 475:WAT_119@H2 and 476:WAT_119@EPW are close (0.78)
+1	 Warning: Atoms 478:WAT_120@H1 and 480:WAT_120@EPW are close (0.78)
+1	 Warning: Atoms 479:WAT_120@H2 and 480:WAT_120@EPW are close (0.78)
+1	 Warning: Atoms 482:WAT_121@H1 and 484:WAT_121@EPW are close (0.78)
+1	 Warning: Atoms 483:WAT_121@H2 and 484:WAT_121@EPW are close (0.78)
+1	 Warning: Atoms 486:WAT_122@H1 and 488:WAT_122@EPW are close (0.78)
+1	 Warning: Atoms 487:WAT_122@H2 and 488:WAT_122@EPW are close (0.78)
+1	 Warning: Atoms 490:WAT_123@H1 and 492:WAT_123@EPW are close (0.78)
+1	 Warning: Atoms 491:WAT_123@H2 and 492:WAT_123@EPW are close (0.78)
+1	 Warning: Atoms 494:WAT_124@H1 and 496:WAT_124@EPW are close (0.78)
+1	 Warning: Atoms 495:WAT_124@H2 and 496:WAT_124@EPW are close (0.78)
+1	 Warning: Atoms 498:WAT_125@H1 and 500:WAT_125@EPW are close (0.78)
+1	 Warning: Atoms 499:WAT_125@H2 and 500:WAT_125@EPW are close (0.78)
+1	 Warning: Atoms 502:WAT_126@H1 and 504:WAT_126@EPW are close (0.78)
+1	 Warning: Atoms 503:WAT_126@H2 and 504:WAT_126@EPW are close (0.78)
+1	 Warning: Atoms 506:WAT_127@H1 and 508:WAT_127@EPW are close (0.78)
+1	 Warning: Atoms 507:WAT_127@H2 and 508:WAT_127@EPW are close (0.78)
+1	 Warning: Atoms 510:WAT_128@H1 and 512:WAT_128@EPW are close (0.78)
+1	 Warning: Atoms 511:WAT_128@H2 and 512:WAT_128@EPW are close (0.78)
+1	 Warning: Atoms 514:WAT_129@H1 and 516:WAT_129@EPW are close (0.78)
+1	 Warning: Atoms 515:WAT_129@H2 and 516:WAT_129@EPW are close (0.78)
+1	 Warning: Atoms 518:WAT_130@H1 and 520:WAT_130@EPW are close (0.78)
+1	 Warning: Atoms 519:WAT_130@H2 and 520:WAT_130@EPW are close (0.78)
+1	 Warning: Atoms 522:WAT_131@H1 and 524:WAT_131@EPW are close (0.78)
+1	 Warning: Atoms 523:WAT_131@H2 and 524:WAT_131@EPW are close (0.78)
+1	 Warning: Atoms 526:WAT_132@H1 and 528:WAT_132@EPW are close (0.78)
+1	 Warning: Atoms 527:WAT_132@H2 and 528:WAT_132@EPW are close (0.78)
+1	 Warning: Atoms 530:WAT_133@H1 and 532:WAT_133@EPW are close (0.78)
+1	 Warning: Atoms 531:WAT_133@H2 and 532:WAT_133@EPW are close (0.78)
+1	 Warning: Atoms 534:WAT_134@H1 and 536:WAT_134@EPW are close (0.78)
+1	 Warning: Atoms 535:WAT_134@H2 and 536:WAT_134@EPW are close (0.78)
+1	 Warning: Atoms 538:WAT_135@H1 and 540:WAT_135@EPW are close (0.78)
+1	 Warning: Atoms 539:WAT_135@H2 and 540:WAT_135@EPW are close (0.78)
+1	 Warning: Atoms 542:WAT_136@H1 and 544:WAT_136@EPW are close (0.78)
+1	 Warning: Atoms 543:WAT_136@H2 and 544:WAT_136@EPW are close (0.78)
+1	 Warning: Atoms 546:WAT_137@H1 and 548:WAT_137@EPW are close (0.78)
+1	 Warning: Atoms 547:WAT_137@H2 and 548:WAT_137@EPW are close (0.78)
+1	 Warning: Atoms 550:WAT_138@H1 and 552:WAT_138@EPW are close (0.78)
+1	 Warning: Atoms 551:WAT_138@H2 and 552:WAT_138@EPW are close (0.78)
+1	 Warning: Atoms 554:WAT_139@H1 and 556:WAT_139@EPW are close (0.78)
+1	 Warning: Atoms 555:WAT_139@H2 and 556:WAT_139@EPW are close (0.78)
+1	 Warning: Atoms 558:WAT_140@H1 and 560:WAT_140@EPW are close (0.78)
+1	 Warning: Atoms 559:WAT_140@H2 and 560:WAT_140@EPW are close (0.78)
+1	 Warning: Atoms 562:WAT_141@H1 and 564:WAT_141@EPW are close (0.78)
+1	 Warning: Atoms 563:WAT_141@H2 and 564:WAT_141@EPW are close (0.78)
+1	 Warning: Atoms 566:WAT_142@H1 and 568:WAT_142@EPW are close (0.78)
+1	 Warning: Atoms 567:WAT_142@H2 and 568:WAT_142@EPW are close (0.78)
+1	 Warning: Atoms 570:WAT_143@H1 and 572:WAT_143@EPW are close (0.78)
+1	 Warning: Atoms 571:WAT_143@H2 and 572:WAT_143@EPW are close (0.78)
+1	 Warning: Atoms 574:WAT_144@H1 and 576:WAT_144@EPW are close (0.78)
+1	 Warning: Atoms 575:WAT_144@H2 and 576:WAT_144@EPW are close (0.78)
+1	 Warning: Atoms 578:WAT_145@H1 and 580:WAT_145@EPW are close (0.78)
+1	 Warning: Atoms 579:WAT_145@H2 and 580:WAT_145@EPW are close (0.78)
+1	 Warning: Atoms 582:WAT_146@H1 and 584:WAT_146@EPW are close (0.78)
+1	 Warning: Atoms 583:WAT_146@H2 and 584:WAT_146@EPW are close (0.78)
+1	 Warning: Atoms 586:WAT_147@H1 and 588:WAT_147@EPW are close (0.78)
+1	 Warning: Atoms 587:WAT_147@H2 and 588:WAT_147@EPW are close (0.78)
+1	 Warning: Atoms 590:WAT_148@H1 and 592:WAT_148@EPW are close (0.78)
+1	 Warning: Atoms 591:WAT_148@H2 and 592:WAT_148@EPW are close (0.78)
+1	 Warning: Atoms 594:WAT_149@H1 and 596:WAT_149@EPW are close (0.78)
+1	 Warning: Atoms 595:WAT_149@H2 and 596:WAT_149@EPW are close (0.78)
+1	 Warning: Atoms 598:WAT_150@H1 and 600:WAT_150@EPW are close (0.78)
+1	 Warning: Atoms 599:WAT_150@H2 and 600:WAT_150@EPW are close (0.78)
+1	 Warning: Atoms 602:WAT_151@H1 and 604:WAT_151@EPW are close (0.78)
+1	 Warning: Atoms 603:WAT_151@H2 and 604:WAT_151@EPW are close (0.78)
+1	 Warning: Atoms 606:WAT_152@H1 and 608:WAT_152@EPW are close (0.78)
+1	 Warning: Atoms 607:WAT_152@H2 and 608:WAT_152@EPW are close (0.78)
+1	 Warning: Atoms 610:WAT_153@H1 and 612:WAT_153@EPW are close (0.78)
+1	 Warning: Atoms 611:WAT_153@H2 and 612:WAT_153@EPW are close (0.78)
+1	 Warning: Atoms 614:WAT_154@H1 and 616:WAT_154@EPW are close (0.78)
+1	 Warning: Atoms 615:WAT_154@H2 and 616:WAT_154@EPW are close (0.78)
+1	 Warning: Atoms 618:WAT_155@H1 and 620:WAT_155@EPW are close (0.78)
+1	 Warning: Atoms 619:WAT_155@H2 and 620:WAT_155@EPW are close (0.78)
+1	 Warning: Atoms 622:WAT_156@H1 and 624:WAT_156@EPW are close (0.78)
+1	 Warning: Atoms 623:WAT_156@H2 and 624:WAT_156@EPW are close (0.78)
+1	 Warning: Atoms 626:WAT_157@H1 and 628:WAT_157@EPW are close (0.78)
+1	 Warning: Atoms 627:WAT_157@H2 and 628:WAT_157@EPW are close (0.78)
+1	 Warning: Atoms 630:WAT_158@H1 and 632:WAT_158@EPW are close (0.78)
+1	 Warning: Atoms 631:WAT_158@H2 and 632:WAT_158@EPW are close (0.78)
+1	 Warning: Atoms 634:WAT_159@H1 and 636:WAT_159@EPW are close (0.78)
+1	 Warning: Atoms 635:WAT_159@H2 and 636:WAT_159@EPW are close (0.78)
+1	 Warning: Atoms 638:WAT_160@H1 and 640:WAT_160@EPW are close (0.78)
+1	 Warning: Atoms 639:WAT_160@H2 and 640:WAT_160@EPW are close (0.78)
+1	 Warning: Atoms 642:WAT_161@H1 and 644:WAT_161@EPW are close (0.78)
+1	 Warning: Atoms 643:WAT_161@H2 and 644:WAT_161@EPW are close (0.78)
+1	 Warning: Atoms 646:WAT_162@H1 and 648:WAT_162@EPW are close (0.78)
+1	 Warning: Atoms 647:WAT_162@H2 and 648:WAT_162@EPW are close (0.78)
+1	 Warning: Atoms 650:WAT_163@H1 and 652:WAT_163@EPW are close (0.78)
+1	 Warning: Atoms 651:WAT_163@H2 and 652:WAT_163@EPW are close (0.78)
+1	 Warning: Atoms 654:WAT_164@H1 and 656:WAT_164@EPW are close (0.78)
+1	 Warning: Atoms 655:WAT_164@H2 and 656:WAT_164@EPW are close (0.78)
+1	 Warning: Atoms 658:WAT_165@H1 and 660:WAT_165@EPW are close (0.78)
+1	 Warning: Atoms 659:WAT_165@H2 and 660:WAT_165@EPW are close (0.78)
+1	 Warning: Atoms 662:WAT_166@H1 and 664:WAT_166@EPW are close (0.78)
+1	 Warning: Atoms 663:WAT_166@H2 and 664:WAT_166@EPW are close (0.78)
+1	 Warning: Atoms 666:WAT_167@H1 and 668:WAT_167@EPW are close (0.78)
+1	 Warning: Atoms 667:WAT_167@H2 and 668:WAT_167@EPW are close (0.78)
+1	 Warning: Atoms 670:WAT_168@H1 and 672:WAT_168@EPW are close (0.78)
+1	 Warning: Atoms 671:WAT_168@H2 and 672:WAT_168@EPW are close (0.78)
+1	 Warning: Atoms 674:WAT_169@H1 and 676:WAT_169@EPW are close (0.78)
+1	 Warning: Atoms 675:WAT_169@H2 and 676:WAT_169@EPW are close (0.78)
+1	 Warning: Atoms 678:WAT_170@H1 and 680:WAT_170@EPW are close (0.78)
+1	 Warning: Atoms 679:WAT_170@H2 and 680:WAT_170@EPW are close (0.78)
+1	 Warning: Atoms 682:WAT_171@H1 and 684:WAT_171@EPW are close (0.78)
+1	 Warning: Atoms 683:WAT_171@H2 and 684:WAT_171@EPW are close (0.78)
+1	 Warning: Atoms 686:WAT_172@H1 and 688:WAT_172@EPW are close (0.78)
+1	 Warning: Atoms 687:WAT_172@H2 and 688:WAT_172@EPW are close (0.78)
+1	 Warning: Atoms 690:WAT_173@H1 and 692:WAT_173@EPW are close (0.78)
+1	 Warning: Atoms 691:WAT_173@H2 and 692:WAT_173@EPW are close (0.78)
+1	 Warning: Atoms 694:WAT_174@H1 and 696:WAT_174@EPW are close (0.78)
+1	 Warning: Atoms 695:WAT_174@H2 and 696:WAT_174@EPW are close (0.78)
+1	 Warning: Atoms 698:WAT_175@H1 and 700:WAT_175@EPW are close (0.78)
+1	 Warning: Atoms 699:WAT_175@H2 and 700:WAT_175@EPW are close (0.78)
+1	 Warning: Atoms 702:WAT_176@H1 and 704:WAT_176@EPW are close (0.78)
+1	 Warning: Atoms 703:WAT_176@H2 and 704:WAT_176@EPW are close (0.78)
+1	 Warning: Atoms 706:WAT_177@H1 and 708:WAT_177@EPW are close (0.78)
+1	 Warning: Atoms 707:WAT_177@H2 and 708:WAT_177@EPW are close (0.78)
+1	 Warning: Atoms 710:WAT_178@H1 and 712:WAT_178@EPW are close (0.78)
+1	 Warning: Atoms 711:WAT_178@H2 and 712:WAT_178@EPW are close (0.78)
+1	 Warning: Atoms 714:WAT_179@H1 and 716:WAT_179@EPW are close (0.78)
+1	 Warning: Atoms 715:WAT_179@H2 and 716:WAT_179@EPW are close (0.78)
+1	 Warning: Atoms 718:WAT_180@H1 and 720:WAT_180@EPW are close (0.78)
+1	 Warning: Atoms 719:WAT_180@H2 and 720:WAT_180@EPW are close (0.78)
+1	 Warning: Atoms 722:WAT_181@H1 and 724:WAT_181@EPW are close (0.78)
+1	 Warning: Atoms 723:WAT_181@H2 and 724:WAT_181@EPW are close (0.78)
+1	 Warning: Atoms 726:WAT_182@H1 and 728:WAT_182@EPW are close (0.78)
+1	 Warning: Atoms 727:WAT_182@H2 and 728:WAT_182@EPW are close (0.78)
+1	 Warning: Atoms 730:WAT_183@H1 and 732:WAT_183@EPW are close (0.78)
+1	 Warning: Atoms 731:WAT_183@H2 and 732:WAT_183@EPW are close (0.78)
+1	 Warning: Atoms 734:WAT_184@H1 and 736:WAT_184@EPW are close (0.78)
+1	 Warning: Atoms 735:WAT_184@H2 and 736:WAT_184@EPW are close (0.78)
+1	 Warning: Atoms 738:WAT_185@H1 and 740:WAT_185@EPW are close (0.78)
+1	 Warning: Atoms 739:WAT_185@H2 and 740:WAT_185@EPW are close (0.78)
+1	 Warning: Atoms 742:WAT_186@H1 and 744:WAT_186@EPW are close (0.78)
+1	 Warning: Atoms 743:WAT_186@H2 and 744:WAT_186@EPW are close (0.78)
+1	 Warning: Atoms 746:WAT_187@H1 and 748:WAT_187@EPW are close (0.78)
+1	 Warning: Atoms 747:WAT_187@H2 and 748:WAT_187@EPW are close (0.78)
+1	 Warning: Atoms 750:WAT_188@H1 and 752:WAT_188@EPW are close (0.78)
+1	 Warning: Atoms 751:WAT_188@H2 and 752:WAT_188@EPW are close (0.78)
+1	 Warning: Atoms 754:WAT_189@H1 and 756:WAT_189@EPW are close (0.78)
+1	 Warning: Atoms 755:WAT_189@H2 and 756:WAT_189@EPW are close (0.78)
+1	 Warning: Atoms 758:WAT_190@H1 and 760:WAT_190@EPW are close (0.78)
+1	 Warning: Atoms 759:WAT_190@H2 and 760:WAT_190@EPW are close (0.78)
+1	 Warning: Atoms 762:WAT_191@H1 and 764:WAT_191@EPW are close (0.78)
+1	 Warning: Atoms 763:WAT_191@H2 and 764:WAT_191@EPW are close (0.78)
+1	 Warning: Atoms 766:WAT_192@H1 and 768:WAT_192@EPW are close (0.78)
+1	 Warning: Atoms 767:WAT_192@H2 and 768:WAT_192@EPW are close (0.78)
+1	 Warning: Atoms 770:WAT_193@H1 and 772:WAT_193@EPW are close (0.78)
+1	 Warning: Atoms 771:WAT_193@H2 and 772:WAT_193@EPW are close (0.78)
+1	 Warning: Atoms 774:WAT_194@H1 and 776:WAT_194@EPW are close (0.78)
+1	 Warning: Atoms 775:WAT_194@H2 and 776:WAT_194@EPW are close (0.78)
+1	 Warning: Atoms 778:WAT_195@H1 and 780:WAT_195@EPW are close (0.78)
+1	 Warning: Atoms 779:WAT_195@H2 and 780:WAT_195@EPW are close (0.78)
+1	 Warning: Atoms 782:WAT_196@H1 and 784:WAT_196@EPW are close (0.78)
+1	 Warning: Atoms 783:WAT_196@H2 and 784:WAT_196@EPW are close (0.78)
+1	 Warning: Atoms 786:WAT_197@H1 and 788:WAT_197@EPW are close (0.78)
+1	 Warning: Atoms 787:WAT_197@H2 and 788:WAT_197@EPW are close (0.78)
+1	 Warning: Atoms 790:WAT_198@H1 and 792:WAT_198@EPW are close (0.78)
+1	 Warning: Atoms 791:WAT_198@H2 and 792:WAT_198@EPW are close (0.78)
+1	 Warning: Atoms 794:WAT_199@H1 and 796:WAT_199@EPW are close (0.78)
+1	 Warning: Atoms 795:WAT_199@H2 and 796:WAT_199@EPW are close (0.78)
+1	 Warning: Atoms 798:WAT_200@H1 and 800:WAT_200@EPW are close (0.78)
+1	 Warning: Atoms 799:WAT_200@H2 and 800:WAT_200@EPW are close (0.78)
+1	 Warning: Atoms 802:WAT_201@H1 and 804:WAT_201@EPW are close (0.78)
+1	 Warning: Atoms 803:WAT_201@H2 and 804:WAT_201@EPW are close (0.78)
+1	 Warning: Atoms 806:WAT_202@H1 and 808:WAT_202@EPW are close (0.78)
+1	 Warning: Atoms 807:WAT_202@H2 and 808:WAT_202@EPW are close (0.78)
+1	 Warning: Atoms 810:WAT_203@H1 and 812:WAT_203@EPW are close (0.78)
+1	 Warning: Atoms 811:WAT_203@H2 and 812:WAT_203@EPW are close (0.78)
+1	 Warning: Atoms 814:WAT_204@H1 and 816:WAT_204@EPW are close (0.78)
+1	 Warning: Atoms 815:WAT_204@H2 and 816:WAT_204@EPW are close (0.78)
+1	 Warning: Atoms 818:WAT_205@H1 and 820:WAT_205@EPW are close (0.78)
+1	 Warning: Atoms 819:WAT_205@H2 and 820:WAT_205@EPW are close (0.78)
+1	 Warning: Atoms 822:WAT_206@H1 and 824:WAT_206@EPW are close (0.78)
+1	 Warning: Atoms 823:WAT_206@H2 and 824:WAT_206@EPW are close (0.78)
+1	 Warning: Atoms 826:WAT_207@H1 and 828:WAT_207@EPW are close (0.78)
+1	 Warning: Atoms 827:WAT_207@H2 and 828:WAT_207@EPW are close (0.78)
+1	 Warning: Atoms 830:WAT_208@H1 and 832:WAT_208@EPW are close (0.78)
+1	 Warning: Atoms 831:WAT_208@H2 and 832:WAT_208@EPW are close (0.78)
+1	 Warning: Atoms 834:WAT_209@H1 and 836:WAT_209@EPW are close (0.78)
+1	 Warning: Atoms 835:WAT_209@H2 and 836:WAT_209@EPW are close (0.78)
+1	 Warning: Atoms 838:WAT_210@H1 and 840:WAT_210@EPW are close (0.78)
+1	 Warning: Atoms 839:WAT_210@H2 and 840:WAT_210@EPW are close (0.78)
+1	 Warning: Atoms 842:WAT_211@H1 and 844:WAT_211@EPW are close (0.78)
+1	 Warning: Atoms 843:WAT_211@H2 and 844:WAT_211@EPW are close (0.78)
+1	 Warning: Atoms 846:WAT_212@H1 and 848:WAT_212@EPW are close (0.78)
+1	 Warning: Atoms 847:WAT_212@H2 and 848:WAT_212@EPW are close (0.78)
+1	 Warning: Atoms 850:WAT_213@H1 and 852:WAT_213@EPW are close (0.78)
+1	 Warning: Atoms 851:WAT_213@H2 and 852:WAT_213@EPW are close (0.78)
+1	 Warning: Atoms 854:WAT_214@H1 and 856:WAT_214@EPW are close (0.78)
+1	 Warning: Atoms 855:WAT_214@H2 and 856:WAT_214@EPW are close (0.78)
+1	 Warning: Atoms 858:WAT_215@H1 and 860:WAT_215@EPW are close (0.78)
+1	 Warning: Atoms 859:WAT_215@H2 and 860:WAT_215@EPW are close (0.78)
+1	 Warning: Atoms 862:WAT_216@H1 and 864:WAT_216@EPW are close (0.78)
+1	 Warning: Atoms 863:WAT_216@H2 and 864:WAT_216@EPW are close (0.78)

From d77b9bed6de3e3b31d938065dca9635b21ba7ab9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 7 Jan 2026 11:26:45 -0500
Subject: [PATCH 1179/1492] Hide debug info

---
 src/StructureCheck.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/StructureCheck.cpp b/src/StructureCheck.cpp
index 530309cc7e..d9dd1408ab 100644
--- a/src/StructureCheck.cpp
+++ b/src/StructureCheck.cpp
@@ -54,7 +54,7 @@ const
     maskOut = "*" + XP_Exclude_Mask_;
   else
     maskOut = maskIn + XP_Exclude_Mask_;
-  mprintf("DEBUG: StructureCheck::checkMaskStr(): String is %s\n", maskOut.c_str());
+  //mprintf("DEBUG: StructureCheck::checkMaskStr(): String is %s\n", maskOut.c_str());
   return maskOut;
 }
 

From 20dcfff95316a66f13e951ac37735cd106126817 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 7 Jan 2026 11:47:30 -0500
Subject: [PATCH 1180/1492] Actually set a number for second number of ions

---
 src/Structure/AddIons.cpp | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/src/Structure/AddIons.cpp b/src/Structure/AddIons.cpp
index 3188c44620..305851f792 100644
--- a/src/Structure/AddIons.cpp
+++ b/src/Structure/AddIons.cpp
@@ -49,6 +49,7 @@ int AddIons::InitAddIons(std::string const& ion1nameIn, int Nion1,
       mprinterr("Error: Number of second %s ions cannot be less than 1 (%i)\n", ion2nameIn.c_str(), Nion2);
       return 1;
     }
+    Nion2_ = Nion2;
   }
 
   separation_ = separationIn;
@@ -260,9 +261,6 @@ const
     ionPositions.reserve( nIons );
   double cut2 = separation_ * separation_;
 
-  // FIXME DEBUG
-  srand( 1 );
-
   // To match how LEaP orders systems (solute/ions/solvent), need to have an atom map.
   // First add solute.
   std::vector<int> atomMap;

From e46930512c530bb5d0d0a5decf9d7bb5e9b8574d Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 7 Jan 2026 11:53:59 -0500
Subject: [PATCH 1181/1492] Hide some debug info

---
 src/Structure/AddIons.cpp | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/src/Structure/AddIons.cpp b/src/Structure/AddIons.cpp
index 305851f792..92a2e9203e 100644
--- a/src/Structure/AddIons.cpp
+++ b/src/Structure/AddIons.cpp
@@ -227,7 +227,7 @@ const
   if (Ion2 != 0)
     ion2radii = GetAtomRadii( Ion2, set0.AT() );
 
-  mprintf("DEBUG: Nsolvent = %i\n", topOut.Nsolvent());
+  //mprintf("DEBUG: Nsolvent = %i\n", topOut.Nsolvent());
 
   std::vector<int> soluteMolNums;
   std::vector<int> solventMolNums;// = topOut.SolventMolNums();
@@ -245,14 +245,14 @@ const
     }
   }
   // DEBUG
-  mprintf("DEBUG: Solvent molecule #s:");
-  for (std::vector<int>::const_iterator it = solventMolNums.begin(); it != solventMolNums.end(); ++it)
-    mprintf(" %i", *it);
-  mprintf("\n"); // DEBUG
+  //mprintf("DEBUG: Solvent molecule #s:");
+  //for (std::vector<int>::const_iterator it = solventMolNums.begin(); it != solventMolNums.end(); ++it)
+  //  mprintf(" %i", *it);
+  //mprintf("\n"); // DEBUG
 
   //VstatArray solventStat(solventMolNums.size(), UNUSED);
 
-  mprintf("Adding %d counter ions to \"%s\". %d solvent molecules will remain.\n",
+  mprintf("  Adding %d counter ions to \"%s\". %d solvent molecules will remain.\n",
           iIon1 + iIon2, topOut.c_str(), (int)topOut.SolventMolNums().size() - iIon1 - iIon2);
 
   typedef std::vector<Vec3> Varray;
@@ -297,9 +297,9 @@ const
   }
 
   // DEBUG
-  mprintf("DEBUG: Atom Map:\n");
-  for (unsigned int idx = 0; idx != atomMap.size(); idx++)
-    mprintf("\tOld=%8i -> New=%8u\n", atomMap[idx], idx);
+  //mprintf("DEBUG: Atom Map:\n");
+  //for (unsigned int idx = 0; idx != atomMap.size(); idx++)
+  //  mprintf("\tOld=%8i -> New=%8u\n", atomMap[idx], idx);
 
   //FIXME this is not very efficient memory-wise
   Topology* reorderedTop = topOut.ModifyByMap(atomMap);
@@ -367,8 +367,8 @@ const
     Frame ionFrame = ionCrd->AllocateFrame(); //TODO allocate outside this routine
     ionCrd->GetFrame(0, ionFrame);
     ionFrame.CenterOnPoint( pos, false ); // Use geometric center
-    Vec3 debugVec = ionFrame.VGeometricCenter();
-    debugVec.Print("DEBUG: check ion center");
+    //Vec3 debugVec = ionFrame.VGeometricCenter();
+    //debugVec.Print("DEBUG: check ion center");
     mprintf("%zu: Placed %s in %s at (%4.2lf, %4.2lf, %4.2lf).\n", iIon1, ionCrd->legend(), topOut.c_str(),
             pos[0], pos[1], pos[2]);
     if (separation_ > 0.0)

From 3f23088171499082b206c5ce6388c8772c689249 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 7 Jan 2026 11:58:11 -0500
Subject: [PATCH 1182/1492] Hide more debug info

---
 src/Structure/AddIons.cpp | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/Structure/AddIons.cpp b/src/Structure/AddIons.cpp
index 92a2e9203e..a8c9bb1fff 100644
--- a/src/Structure/AddIons.cpp
+++ b/src/Structure/AddIons.cpp
@@ -337,7 +337,8 @@ const
   
   // Do not try it again. It will either be used or be invalid due to distances.
   int solventMolNum = solventMolNums[solvIdx];
-  mprintf("DEBUG: ntries=%i Trying swap %s with solvent molecule %i (idx= %i)\n", ntries, ionCrd->legend(), solventMolNum, solvIdx);
+  if (debug_ > 0)
+    mprintf("DEBUG: ntries=%i Trying swap %s with solvent molecule %i (idx= %i)\n", ntries, ionCrd->legend(), solventMolNum, solvIdx);
   molStat[solventMolNum] = TRIED;
  
   // Get position of solvent residue atom. TODO should this be the geometric center?
@@ -369,7 +370,7 @@ const
     ionFrame.CenterOnPoint( pos, false ); // Use geometric center
     //Vec3 debugVec = ionFrame.VGeometricCenter();
     //debugVec.Print("DEBUG: check ion center");
-    mprintf("%zu: Placed %s in %s at (%4.2lf, %4.2lf, %4.2lf).\n", iIon1, ionCrd->legend(), topOut.c_str(),
+    mprintf("  %zu: Placed %s in %s at (%4.2lf, %4.2lf, %4.2lf).\n", iIon1, ionCrd->legend(), topOut.c_str(),
             pos[0], pos[1], pos[2]);
     if (separation_ > 0.0)
       ionPositions.push_back( pos );

From 32b55696f3be55cabbb9feee575952e5b7c280e9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 7 Jan 2026 13:38:26 -0500
Subject: [PATCH 1183/1492] Start LJ 1264 params class

---
 src/Parm/CMakeLists.txt    |  1 +
 src/Parm/LJ1264_Params.cpp | 77 ++++++++++++++++++++++++++++++++++++++
 src/Parm/LJ1264_Params.h   | 30 +++++++++++++++
 src/Parm/ParmEnum.h        |  2 +
 src/Parm/parmdepend        |  1 +
 src/Parm/parmfiles         |  1 +
 6 files changed, 112 insertions(+)
 create mode 100644 src/Parm/LJ1264_Params.cpp
 create mode 100644 src/Parm/LJ1264_Params.h

diff --git a/src/Parm/CMakeLists.txt b/src/Parm/CMakeLists.txt
index 067f2c5195..3683c011ad 100644
--- a/src/Parm/CMakeLists.txt
+++ b/src/Parm/CMakeLists.txt
@@ -3,6 +3,7 @@ target_sources(cpptraj_common_obj PRIVATE
   ${CMAKE_CURRENT_LIST_DIR}/AssignParams.cpp
   ${CMAKE_CURRENT_LIST_DIR}/GB_Params.cpp
   ${CMAKE_CURRENT_LIST_DIR}/GetParams.cpp
+  ${CMAKE_CURRENT_LIST_DIR}/LJ1264_Params.cpp
   ${CMAKE_CURRENT_LIST_DIR}/Merge.cpp
   ${CMAKE_CURRENT_LIST_DIR}/ParameterSet.cpp
 )
diff --git a/src/Parm/LJ1264_Params.cpp b/src/Parm/LJ1264_Params.cpp
new file mode 100644
index 0000000000..7ee39779c7
--- /dev/null
+++ b/src/Parm/LJ1264_Params.cpp
@@ -0,0 +1,77 @@
+#include "LJ1264_Params.h"
+
+using namespace Cpptraj::Parm;
+
+/** CONSTRUCTOR */
+LJ1264_Params::LJ1264_Params() :
+  waterModel_(UNKNOWN_WATER_MODEL),
+  tunfactor_(1.0)
+{}
+
+void LJ1264_Params::set_tip3p_params() {
+  c4params_.insert( NameMapPair("Li1", 27.0) );
+  c4params_.insert( NameMapPair("Na1", 0.0) );
+  c4params_.insert( NameMapPair("K1", 8.0) );
+  c4params_.insert( NameMapPair("Rb1", 0.0) );
+  c4params_.insert( NameMapPair("Cs1", 2.0) );
+  c4params_.insert( NameMapPair("Tl1", 50.0) );
+  c4params_.insert( NameMapPair("Cu1", 7.0) );
+  c4params_.insert( NameMapPair("Ag1", 83.0) );
+  c4params_.insert( NameMapPair("F-1", -27.0) );
+  c4params_.insert( NameMapPair("Cl-1", -38.0) );
+  c4params_.insert( NameMapPair("Br-1", -39.0) );
+  c4params_.insert( NameMapPair("I-1", -45.0) );
+  c4params_.insert( NameMapPair("Be2", 186.5) );
+  c4params_.insert( NameMapPair("Cu2", 290.9) );
+  c4params_.insert( NameMapPair("Ni2", 212.8) );
+  c4params_.insert( NameMapPair("Zn2", 231.6) );
+  c4params_.insert( NameMapPair("Co2", 209.7) );
+  c4params_.insert( NameMapPair("Cr2", 136.8) );
+  c4params_.insert( NameMapPair("Fe2", 163.0) );
+  c4params_.insert( NameMapPair("Mg2", 132.9) );
+  c4params_.insert( NameMapPair("V2", 195.7) );
+  c4params_.insert( NameMapPair("Mn2", 146.1) );
+  c4params_.insert( NameMapPair("Hg2", 288.8) );
+  c4params_.insert( NameMapPair("Cd2", 185.6) );
+  c4params_.insert( NameMapPair("Ca2", 87.3) );
+  c4params_.insert( NameMapPair("Sn2", 187.9) );
+  c4params_.insert( NameMapPair("Sr2", 82.7) );
+  c4params_.insert( NameMapPair("Ba2", 71.9) );
+  c4params_.insert( NameMapPair("Al3", 399.0) );
+  c4params_.insert( NameMapPair("Fe3", 428.0) );
+  c4params_.insert( NameMapPair("Cr3", 258.0) );
+  c4params_.insert( NameMapPair("In3", 347.0) );
+  c4params_.insert( NameMapPair("Tl3", 456.0) );
+  c4params_.insert( NameMapPair("Y3", 216.0) );
+  c4params_.insert( NameMapPair("La3", 152.0) );
+  c4params_.insert( NameMapPair("Ce3", 230.0) );
+  c4params_.insert( NameMapPair("Pr3", 264.0) );
+  c4params_.insert( NameMapPair("Nd3", 213.0) );
+  c4params_.insert( NameMapPair("Sm3", 230.0) );
+  c4params_.insert( NameMapPair("Eu3", 259.0) );
+  c4params_.insert( NameMapPair("Gd3", 198.0) );
+  c4params_.insert( NameMapPair("Tb3", 235.0) );
+  c4params_.insert( NameMapPair("Dy3", 207.0) );
+  c4params_.insert( NameMapPair("Er3", 251.0) );
+  c4params_.insert( NameMapPair("Tm3", 282.0) );
+  c4params_.insert( NameMapPair("Lu3", 249.0) );
+  c4params_.insert( NameMapPair("Hf4", 827.0) );
+  c4params_.insert( NameMapPair("Zr4", 761.0) );
+  c4params_.insert( NameMapPair("Ce4", 706.0) );
+  c4params_.insert( NameMapPair("U4", 1034.0) );
+  c4params_.insert( NameMapPair("Pu4", 828.0) );
+  c4params_.insert( NameMapPair("Th4", 512.0) );
+}
+
+/** Set up C4 parameters for given water model */
+void LJ1264_Params::setupForWaterModel(WaterModelType wmIn)
+{
+  if (wmIn == waterModel_) return;
+  c4params_.clear();
+  waterModel_ = wmIn;
+
+  switch (waterModel_) {
+    case UNKNOWN_WATER_MODEL : break;
+    case TIP3P : set_tip3p_params(); break;
+  }
+}
diff --git a/src/Parm/LJ1264_Params.h b/src/Parm/LJ1264_Params.h
new file mode 100644
index 0000000000..1bdd038490
--- /dev/null
+++ b/src/Parm/LJ1264_Params.h
@@ -0,0 +1,30 @@
+#ifndef INC_PARM_LJ1264_PARAMS_H
+#define INC_PARM_LJ1264_PARAMS_H
+#include "ParmEnum.h"
+#include <map>
+#include <string>
+namespace Cpptraj {
+namespace Parm {
+/// Used to assign LJ 12-6-4 C coefficients
+class LJ1264_Params {
+  public:
+    LJ1264_Params();
+    /// Init - mask, c4 file, water model, polarization file, tuning factor
+    int Init_LJ1264(std::string const&, std::string const&, WaterModelType, std::string const&, double);
+  private:
+    typedef std::pair<std::string, double> NameMapPair;
+    typedef std::map<std::string, double> NameMapType;
+
+    /// Set C4 parameters for TIP3P
+    void set_tip3p_params();
+    /// Set C4 params for given water model
+    void setupForWaterModel(WaterModelType);
+
+    WaterModelType waterModel_; ///< Water model that C3 parameters have been set for
+    NameMapType c4params_; ///< C4 parameters
+    NameMapType pol_; ///< Polarizabilities
+    double tunfactor_; ///< Tuning factor
+};
+}
+}
+#endif
diff --git a/src/Parm/ParmEnum.h b/src/Parm/ParmEnum.h
index fb5433e27c..141548e46f 100644
--- a/src/Parm/ParmEnum.h
+++ b/src/Parm/ParmEnum.h
@@ -3,6 +3,8 @@
 namespace Cpptraj {
 namespace Parm {
   enum RetType { ADDED = 0, SAME, UPDATED, ERR };
+
+  enum WaterModelType { TIP3P = 0, TIP4PEW, SPCE, OPC3, OPC, FB3, FB4, UNKNOWN_WATER_MODEL };
 }
 }
 #endif
diff --git a/src/Parm/parmdepend b/src/Parm/parmdepend
index efb6a4ac2b..c09005fe2e 100644
--- a/src/Parm/parmdepend
+++ b/src/Parm/parmdepend
@@ -1,5 +1,6 @@
 AssignParams.o : AssignParams.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/ParmEnum.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/GenerateConnectivityArrays.h ../SymbolExporting.h ../Timer.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h AssignParams.h DihedralParmHolder.h GetParams.h ImproperParmHolder.h ParameterSet.h ParmEnum.h ParmHolder.h
 GB_Params.o : GB_Params.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h GB_Params.h
 GetParams.o : GetParams.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/ParmEnum.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h DihedralParmHolder.h GetParams.h ImproperParmHolder.h ParameterSet.h ParmEnum.h ParmHolder.h
+LJ1264_Params.o : LJ1264_Params.cpp LJ1264_Params.h ParmEnum.h
 Merge.o : Merge.cpp ../Atom.h ../Constants.h ../CpptrajStdio.h ../NameType.h ../ParameterTypes.h ../Residue.h ../StringRoutines.h ../SymbolExporting.h ../TypeNameHolder.h Merge.h ParmEnum.h ParmHolder.h
 ParameterSet.o : ParameterSet.cpp ../AtomType.h ../CmapParmHolder.h ../Constants.h ../CpptrajFile.h ../CpptrajStdio.h ../FileIO.h ../FileName.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/ParmEnum.h ../TypeNameHolder.h ../UpdateParameters.h DihedralParmHolder.h ImproperParmHolder.h ParameterSet.h ParmEnum.h ParmHolder.h
diff --git a/src/Parm/parmfiles b/src/Parm/parmfiles
index ca2b23c678..79b736579e 100644
--- a/src/Parm/parmfiles
+++ b/src/Parm/parmfiles
@@ -3,5 +3,6 @@ PARM_SOURCES= \
   AssignParams.cpp \
   GB_Params.cpp \
   GetParams.cpp \
+  LJ1264_Params.cpp \
   Merge.cpp \
   ParameterSet.cpp

From 8e861084f2c581f4402023864a4d2b33943de65b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 7 Jan 2026 13:40:15 -0500
Subject: [PATCH 1184/1492] Helper program to get 12-6-4 params from parmed

---
 devtools/converters/Extract1264.cpp | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)
 create mode 100644 devtools/converters/Extract1264.cpp

diff --git a/devtools/converters/Extract1264.cpp b/devtools/converters/Extract1264.cpp
new file mode 100644
index 0000000000..867d26a06b
--- /dev/null
+++ b/devtools/converters/Extract1264.cpp
@@ -0,0 +1,21 @@
+#include "ArgList.h"
+#include "BufferedLine.h"
+#include <cstdio>
+
+int main(int argc, char** argv)
+{
+  BufferedLine infile;
+  if (infile.OpenFileRead(argv[1])) return 1;
+
+  const char* ptr = infile.Line();
+  while (ptr != 0) {
+    ArgList line(ptr, "{}':, ");
+    //line.PrintDebug();
+    for (int iarg = 0; iarg < line.Nargs(); iarg += 2)
+      printf("  c4params_.insert( NameMapPair(\"%s\", %s) );\n", line[iarg].c_str(), line[iarg+1].c_str());
+    ptr = infile.Line();
+  }
+
+  infile.CloseFile();
+  return 0;
+}

From 1ad0ad40e3489a96de53da20b00b93278f290429 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 7 Jan 2026 13:47:53 -0500
Subject: [PATCH 1185/1492] Add water models

---
 src/Parm/LJ1264_Params.cpp | 338 ++++++++++++++++++++++++++++++++++++-
 src/Parm/LJ1264_Params.h   |   6 +
 2 files changed, 343 insertions(+), 1 deletion(-)

diff --git a/src/Parm/LJ1264_Params.cpp b/src/Parm/LJ1264_Params.cpp
index 7ee39779c7..1d586fff57 100644
--- a/src/Parm/LJ1264_Params.cpp
+++ b/src/Parm/LJ1264_Params.cpp
@@ -63,6 +63,336 @@ void LJ1264_Params::set_tip3p_params() {
   c4params_.insert( NameMapPair("Th4", 512.0) );
 }
 
+void LJ1264_Params::set_tip4pew_params() {
+  c4params_.insert( NameMapPair("Li1", 36.0) );
+  c4params_.insert( NameMapPair("Na1", 9.0) );
+  c4params_.insert( NameMapPair("K1", 24.0) );
+  c4params_.insert( NameMapPair("Rb1", 13.0) );
+  c4params_.insert( NameMapPair("Cs1", 16.0) );
+  c4params_.insert( NameMapPair("Tl1", 65.0) );
+  c4params_.insert( NameMapPair("Cu1", 21.0) );
+  c4params_.insert( NameMapPair("Ag1", 94.0) );
+  c4params_.insert( NameMapPair("F-1", -67.0) );
+  c4params_.insert( NameMapPair("Cl-1", -66.0) );
+  c4params_.insert( NameMapPair("Br-1", -68.0) );
+  c4params_.insert( NameMapPair("I-1", -62.0) );
+  c4params_.insert( NameMapPair("Be2", 228.5) );
+  c4params_.insert( NameMapPair("Cu2", 339.2) );
+  c4params_.insert( NameMapPair("Ni2", 259.2) );
+  c4params_.insert( NameMapPair("Zn2", 272.3) );
+  c4params_.insert( NameMapPair("Co2", 252.8) );
+  c4params_.insert( NameMapPair("Cr2", 177.4) );
+  c4params_.insert( NameMapPair("Fe2", 201.1) );
+  c4params_.insert( NameMapPair("Mg2", 180.5) );
+  c4params_.insert( NameMapPair("V2", 244.8) );
+  c4params_.insert( NameMapPair("Mn2", 192.3) );
+  c4params_.insert( NameMapPair("Hg2", 335.2) );
+  c4params_.insert( NameMapPair("Cd2", 233.7) );
+  c4params_.insert( NameMapPair("Ca2", 128.0) );
+  c4params_.insert( NameMapPair("Sn2", 231.4) );
+  c4params_.insert( NameMapPair("Sr2", 118.9) );
+  c4params_.insert( NameMapPair("Ba2", 112.5) );
+  c4params_.insert( NameMapPair("Al3", 488.0) );
+  c4params_.insert( NameMapPair("Fe3", 519.0) );
+  c4params_.insert( NameMapPair("Cr3", 322.0) );
+  c4params_.insert( NameMapPair("In3", 425.0) );
+  c4params_.insert( NameMapPair("Tl3", 535.0) );
+  c4params_.insert( NameMapPair("Y3", 294.0) );
+  c4params_.insert( NameMapPair("La3", 243.0) );
+  c4params_.insert( NameMapPair("Ce3", 315.0) );
+  c4params_.insert( NameMapPair("Pr3", 348.0) );
+  c4params_.insert( NameMapPair("Nd3", 297.0) );
+  c4params_.insert( NameMapPair("Sm3", 314.0) );
+  c4params_.insert( NameMapPair("Eu3", 345.0) );
+  c4params_.insert( NameMapPair("Gd3", 280.0) );
+  c4params_.insert( NameMapPair("Tb3", 313.0) );
+  c4params_.insert( NameMapPair("Dy3", 298.0) );
+  c4params_.insert( NameMapPair("Er3", 328.0) );
+  c4params_.insert( NameMapPair("Tm3", 356.0) );
+  c4params_.insert( NameMapPair("Lu3", 331.0) );
+  c4params_.insert( NameMapPair("Hf4", 956.0) );
+  c4params_.insert( NameMapPair("Zr4", 895.0) );
+  c4params_.insert( NameMapPair("Ce4", 835.0) );
+  c4params_.insert( NameMapPair("U4", 1183.0) );
+  c4params_.insert( NameMapPair("Pu4", 972.0) );
+  c4params_.insert( NameMapPair("Th4", 625.0) );
+}
+
+void LJ1264_Params::set_spce_params() {
+  c4params_.insert( NameMapPair("Li1", 33.0) );
+  c4params_.insert( NameMapPair("Na1", 6.0) );
+  c4params_.insert( NameMapPair("K1", 19.0) );
+  c4params_.insert( NameMapPair("Rb1", 7.0) );
+  c4params_.insert( NameMapPair("Cs1", 12.0) );
+  c4params_.insert( NameMapPair("Tl1", 61.0) );
+  c4params_.insert( NameMapPair("Cu1", 9.0) );
+  c4params_.insert( NameMapPair("Ag1", 92.0) );
+  c4params_.insert( NameMapPair("F-1", -53.0) );
+  c4params_.insert( NameMapPair("Cl-1", -55.0) );
+  c4params_.insert( NameMapPair("Br-1", -51.0) );
+  c4params_.insert( NameMapPair("I-1", -51.0) );
+  c4params_.insert( NameMapPair("Be2", 188.1) );
+  c4params_.insert( NameMapPair("Cu2", 304.4) );
+  c4params_.insert( NameMapPair("Ni2", 205.2) );
+  c4params_.insert( NameMapPair("Zn2", 231.2) );
+  c4params_.insert( NameMapPair("Co2", 209.2) );
+  c4params_.insert( NameMapPair("Cr2", 131.2) );
+  c4params_.insert( NameMapPair("Fe2", 155.4) );
+  c4params_.insert( NameMapPair("Mg2", 122.2) );
+  c4params_.insert( NameMapPair("V2", 206.6) );
+  c4params_.insert( NameMapPair("Mn2", 154.9) );
+  c4params_.insert( NameMapPair("Hg2", 300.2) );
+  c4params_.insert( NameMapPair("Cd2", 198.8) );
+  c4params_.insert( NameMapPair("Ca2", 89.0) );
+  c4params_.insert( NameMapPair("Sn2", 201.1) );
+  c4params_.insert( NameMapPair("Sr2", 96.3) );
+  c4params_.insert( NameMapPair("Ba2", 85.8) );
+  c4params_.insert( NameMapPair("Al3", 406.0) );
+  c4params_.insert( NameMapPair("Fe3", 442.0) );
+  c4params_.insert( NameMapPair("Cr3", 254.0) );
+  c4params_.insert( NameMapPair("In3", 349.0) );
+  c4params_.insert( NameMapPair("Tl3", 455.0) );
+  c4params_.insert( NameMapPair("Y3", 209.0) );
+  c4params_.insert( NameMapPair("La3", 165.0) );
+  c4params_.insert( NameMapPair("Ce3", 242.0) );
+  c4params_.insert( NameMapPair("Pr3", 272.0) );
+  c4params_.insert( NameMapPair("Nd3", 235.0) );
+  c4params_.insert( NameMapPair("Sm3", 224.0) );
+  c4params_.insert( NameMapPair("Eu3", 273.0) );
+  c4params_.insert( NameMapPair("Gd3", 186.0) );
+  c4params_.insert( NameMapPair("Tb3", 227.0) );
+  c4params_.insert( NameMapPair("Dy3", 206.0) );
+  c4params_.insert( NameMapPair("Er3", 247.0) );
+  c4params_.insert( NameMapPair("Tm3", 262.0) );
+  c4params_.insert( NameMapPair("Lu3", 247.0) );
+  c4params_.insert( NameMapPair("Hf4", 810.0) );
+  c4params_.insert( NameMapPair("Zr4", 760.0) );
+  c4params_.insert( NameMapPair("Ce4", 694.0) );
+  c4params_.insert( NameMapPair("U4", 1043.0) );
+  c4params_.insert( NameMapPair("Pu4", 828.0) );
+  c4params_.insert( NameMapPair("Th4", 513.0) );
+}
+
+void LJ1264_Params::set_opc3_params() {
+  c4params_.insert( NameMapPair("Li1", 29.0) );
+  c4params_.insert( NameMapPair("Na1", 2.0) );
+  c4params_.insert( NameMapPair("K1", 16.0) );
+  c4params_.insert( NameMapPair("Rb1", 8.0) );
+  c4params_.insert( NameMapPair("Cs1", 6.0) );
+  c4params_.insert( NameMapPair("Tl1", 63.0) );
+  c4params_.insert( NameMapPair("Cu1", 12.0) );
+  c4params_.insert( NameMapPair("Ag1", 83.0) );
+  c4params_.insert( NameMapPair("F-1", -40.0) );
+  c4params_.insert( NameMapPair("Cl-1", -47.0) );
+  c4params_.insert( NameMapPair("Br-1", -43.0) );
+  c4params_.insert( NameMapPair("I-1", -45.0) );
+  c4params_.insert( NameMapPair("Be2", 186.0) );
+  c4params_.insert( NameMapPair("Cu2", 269.0) );
+  c4params_.insert( NameMapPair("Ni2", 207.0) );
+  c4params_.insert( NameMapPair("Zn2", 199.0) );
+  c4params_.insert( NameMapPair("Co2", 182.0) );
+  c4params_.insert( NameMapPair("Cr2", 109.0) );
+  c4params_.insert( NameMapPair("Fe2", 131.0) );
+  c4params_.insert( NameMapPair("Mg2", 117.0) );
+  c4params_.insert( NameMapPair("V2", 201.0) );
+  c4params_.insert( NameMapPair("Mn2", 137.0) );
+  c4params_.insert( NameMapPair("Hg2", 276.0) );
+  c4params_.insert( NameMapPair("Cd2", 200.0) );
+  c4params_.insert( NameMapPair("Ca2", 76.0) );
+  c4params_.insert( NameMapPair("Sn2", 188.0) );
+  c4params_.insert( NameMapPair("Sr2", 85.0) );
+  c4params_.insert( NameMapPair("Ba2", 77.0) );
+  c4params_.insert( NameMapPair("Al3", 363.0) );
+  c4params_.insert( NameMapPair("Fe3", 429.0) );
+  c4params_.insert( NameMapPair("Cr3", 209.0) );
+  c4params_.insert( NameMapPair("In3", 330.0) );
+  c4params_.insert( NameMapPair("Tl3", 437.0) );
+  c4params_.insert( NameMapPair("Y3", 192.0) );
+  c4params_.insert( NameMapPair("La3", 131.0) );
+  c4params_.insert( NameMapPair("Ce3", 215.0) );
+  c4params_.insert( NameMapPair("Pr3", 255.0) );
+  c4params_.insert( NameMapPair("Nd3", 184.0) );
+  c4params_.insert( NameMapPair("Sm3", 188.0) );
+  c4params_.insert( NameMapPair("Eu3", 233.0) );
+  c4params_.insert( NameMapPair("Gd3", 164.0) );
+  c4params_.insert( NameMapPair("Tb3", 199.0) );
+  c4params_.insert( NameMapPair("Dy3", 183.0) );
+  c4params_.insert( NameMapPair("Er3", 228.0) );
+  c4params_.insert( NameMapPair("Tm3", 246.0) );
+  c4params_.insert( NameMapPair("Lu3", 222.0) );
+  c4params_.insert( NameMapPair("Hf4", 718.0) );
+  c4params_.insert( NameMapPair("Zr4", 707.0) );
+  c4params_.insert( NameMapPair("Ce4", 653.0) );
+  c4params_.insert( NameMapPair("U4", 980.0) );
+  c4params_.insert( NameMapPair("Pu4", 817.0) );
+  c4params_.insert( NameMapPair("Th4", 452.0) );
+}
+
+void LJ1264_Params::set_opc_params() {
+  c4params_.insert( NameMapPair("Li1", 29.0) );
+  c4params_.insert( NameMapPair("Na1", 0.0) );
+  c4params_.insert( NameMapPair("K1", 20.0) );
+  c4params_.insert( NameMapPair("Rb1", 6.0) );
+  c4params_.insert( NameMapPair("Cs1", 13.0) );
+  c4params_.insert( NameMapPair("Tl1", 60.0) );
+  c4params_.insert( NameMapPair("Cu1", 16.0) );
+  c4params_.insert( NameMapPair("Ag1", 83.0) );
+  c4params_.insert( NameMapPair("F-1", -67.0) );
+  c4params_.insert( NameMapPair("Cl-1", -69.0) );
+  c4params_.insert( NameMapPair("Br-1", -60.0) );
+  c4params_.insert( NameMapPair("I-1", -60.0) );
+  c4params_.insert( NameMapPair("Be2", 214.0) );
+  c4params_.insert( NameMapPair("Cu2", 291.0) );
+  c4params_.insert( NameMapPair("Ni2", 212.0) );
+  c4params_.insert( NameMapPair("Zn2", 225.0) );
+  c4params_.insert( NameMapPair("Co2", 204.0) );
+  c4params_.insert( NameMapPair("Cr2", 132.0) );
+  c4params_.insert( NameMapPair("Fe2", 154.0) );
+  c4params_.insert( NameMapPair("Mg2", 127.0) );
+  c4params_.insert( NameMapPair("V2", 239.0) );
+  c4params_.insert( NameMapPair("Mn2", 175.0) );
+  c4params_.insert( NameMapPair("Hg2", 289.0) );
+  c4params_.insert( NameMapPair("Cd2", 219.0) );
+  c4params_.insert( NameMapPair("Ca2", 86.0) );
+  c4params_.insert( NameMapPair("Sn2", 199.0) );
+  c4params_.insert( NameMapPair("Sr2", 87.0) );
+  c4params_.insert( NameMapPair("Ba2", 78.0) );
+  c4params_.insert( NameMapPair("Al3", 399.0) );
+  c4params_.insert( NameMapPair("Fe3", 531.0) );
+  c4params_.insert( NameMapPair("Cr3", 243.0) );
+  c4params_.insert( NameMapPair("In3", 413.0) );
+  c4params_.insert( NameMapPair("Tl3", 479.0) );
+  c4params_.insert( NameMapPair("Y3", 260.0) );
+  c4params_.insert( NameMapPair("La3", 165.0) );
+  c4params_.insert( NameMapPair("Ce3", 289.0) );
+  c4params_.insert( NameMapPair("Pr3", 311.0) );
+  c4params_.insert( NameMapPair("Nd3", 243.0) );
+  c4params_.insert( NameMapPair("Sm3", 236.0) );
+  c4params_.insert( NameMapPair("Eu3", 279.0) );
+  c4params_.insert( NameMapPair("Gd3", 222.0) );
+  c4params_.insert( NameMapPair("Tb3", 256.0) );
+  c4params_.insert( NameMapPair("Dy3", 243.0) );
+  c4params_.insert( NameMapPair("Er3", 298.0) );
+  c4params_.insert( NameMapPair("Tm3", 314.0) );
+  c4params_.insert( NameMapPair("Lu3", 289.0) );
+  c4params_.insert( NameMapPair("Hf4", 847.0) );
+  c4params_.insert( NameMapPair("Zr4", 804.0) );
+  c4params_.insert( NameMapPair("Ce4", 789.0) );
+  c4params_.insert( NameMapPair("U4", 1123.0) );
+  c4params_.insert( NameMapPair("Pu4", 941.0) );
+  c4params_.insert( NameMapPair("Th4", 598.0) );
+}
+
+void LJ1264_Params::set_fb3_params() {
+  c4params_.insert( NameMapPair("Li1", 30.0) );
+  c4params_.insert( NameMapPair("Na1", 2.0) );
+  c4params_.insert( NameMapPair("K1", 15.0) );
+  c4params_.insert( NameMapPair("Rb1", 7.0) );
+  c4params_.insert( NameMapPair("Cs1", 17.0) );
+  c4params_.insert( NameMapPair("Tl1", 65.0) );
+  c4params_.insert( NameMapPair("Cu1", 17.0) );
+  c4params_.insert( NameMapPair("Ag1", 85.0) );
+  c4params_.insert( NameMapPair("F-1", -45.0) );
+  c4params_.insert( NameMapPair("Cl-1", -49.0) );
+  c4params_.insert( NameMapPair("Br-1", -40.0) );
+  c4params_.insert( NameMapPair("I-1", -52.0) );
+  c4params_.insert( NameMapPair("Be2", 193.0) );
+  c4params_.insert( NameMapPair("Cu2", 279.0) );
+  c4params_.insert( NameMapPair("Ni2", 223.0) );
+  c4params_.insert( NameMapPair("Zn2", 217.0) );
+  c4params_.insert( NameMapPair("Co2", 192.0) );
+  c4params_.insert( NameMapPair("Cr2", 138.0) );
+  c4params_.insert( NameMapPair("Fe2", 157.0) );
+  c4params_.insert( NameMapPair("Mg2", 128.0) );
+  c4params_.insert( NameMapPair("V2", 212.0) );
+  c4params_.insert( NameMapPair("Mn2", 149.0) );
+  c4params_.insert( NameMapPair("Hg2", 289.0) );
+  c4params_.insert( NameMapPair("Cd2", 201.0) );
+  c4params_.insert( NameMapPair("Ca2", 92.0) );
+  c4params_.insert( NameMapPair("Sn2", 205.0) );
+  c4params_.insert( NameMapPair("Sr2", 91.0) );
+  c4params_.insert( NameMapPair("Ba2", 78.0) );
+  c4params_.insert( NameMapPair("Al3", 387.0) );
+  c4params_.insert( NameMapPair("Fe3", 446.0) );
+  c4params_.insert( NameMapPair("Cr3", 232.0) );
+  c4params_.insert( NameMapPair("In3", 343.0) );
+  c4params_.insert( NameMapPair("Tl3", 464.0) );
+  c4params_.insert( NameMapPair("Y3", 218.0) );
+  c4params_.insert( NameMapPair("La3", 155.0) );
+  c4params_.insert( NameMapPair("Ce3", 251.0) );
+  c4params_.insert( NameMapPair("Pr3", 291.0) );
+  c4params_.insert( NameMapPair("Nd3", 211.0) );
+  c4params_.insert( NameMapPair("Sm3", 218.0) );
+  c4params_.insert( NameMapPair("Eu3", 261.0) );
+  c4params_.insert( NameMapPair("Gd3", 191.0) );
+  c4params_.insert( NameMapPair("Tb3", 226.0) );
+  c4params_.insert( NameMapPair("Dy3", 219.0) );
+  c4params_.insert( NameMapPair("Er3", 256.0) );
+  c4params_.insert( NameMapPair("Tm3", 285.0) );
+  c4params_.insert( NameMapPair("Lu3", 250.0) );
+  c4params_.insert( NameMapPair("Hf4", 787.0) );
+  c4params_.insert( NameMapPair("Zr4", 769.0) );
+  c4params_.insert( NameMapPair("Ce4", 701.0) );
+  c4params_.insert( NameMapPair("U4", 1044.0) );
+  c4params_.insert( NameMapPair("Pu4", 817.0) );
+  c4params_.insert( NameMapPair("Th4", 507.0) );
+}
+
+void LJ1264_Params::set_fb4_params() {
+  c4params_.insert( NameMapPair("Li1", 33.0) );
+  c4params_.insert( NameMapPair("Na1", 8.0) );
+  c4params_.insert( NameMapPair("K1", 25.0) );
+  c4params_.insert( NameMapPair("Rb1", 9.0) );
+  c4params_.insert( NameMapPair("Cs1", 13.0) );
+  c4params_.insert( NameMapPair("Tl1", 68.0) );
+  c4params_.insert( NameMapPair("Cu1", 25.0) );
+  c4params_.insert( NameMapPair("Ag1", 90.0) );
+  c4params_.insert( NameMapPair("F-1", -57.0) );
+  c4params_.insert( NameMapPair("Cl-1", -55.0) );
+  c4params_.insert( NameMapPair("Br-1", -51.0) );
+  c4params_.insert( NameMapPair("I-1", -53.0) );
+  c4params_.insert( NameMapPair("Be2", 227.0) );
+  c4params_.insert( NameMapPair("Cu2", 313.0) );
+  c4params_.insert( NameMapPair("Ni2", 218.0) );
+  c4params_.insert( NameMapPair("Zn2", 239.0) );
+  c4params_.insert( NameMapPair("Co2", 206.0) );
+  c4params_.insert( NameMapPair("Cr2", 159.0) );
+  c4params_.insert( NameMapPair("Fe2", 187.0) );
+  c4params_.insert( NameMapPair("Mg2", 133.0) );
+  c4params_.insert( NameMapPair("V2", 234.0) );
+  c4params_.insert( NameMapPair("Mn2", 181.0) );
+  c4params_.insert( NameMapPair("Hg2", 331.0) );
+  c4params_.insert( NameMapPair("Cd2", 227.0) );
+  c4params_.insert( NameMapPair("Ca2", 109.0) );
+  c4params_.insert( NameMapPair("Sn2", 215.0) );
+  c4params_.insert( NameMapPair("Sr2", 103.0) );
+  c4params_.insert( NameMapPair("Ba2", 95.0) );
+  c4params_.insert( NameMapPair("Al3", 427.0) );
+  c4params_.insert( NameMapPair("Fe3", 502.0) );
+  c4params_.insert( NameMapPair("Cr3", 286.0) );
+  c4params_.insert( NameMapPair("In3", 403.0) );
+  c4params_.insert( NameMapPair("Tl3", 514.0) );
+  c4params_.insert( NameMapPair("Y3", 268.0) );
+  c4params_.insert( NameMapPair("La3", 211.0) );
+  c4params_.insert( NameMapPair("Ce3", 294.0) );
+  c4params_.insert( NameMapPair("Pr3", 326.0) );
+  c4params_.insert( NameMapPair("Nd3", 256.0) );
+  c4params_.insert( NameMapPair("Sm3", 257.0) );
+  c4params_.insert( NameMapPair("Eu3", 302.0) );
+  c4params_.insert( NameMapPair("Gd3", 238.0) );
+  c4params_.insert( NameMapPair("Tb3", 270.0) );
+  c4params_.insert( NameMapPair("Dy3", 253.0) );
+  c4params_.insert( NameMapPair("Er3", 304.0) );
+  c4params_.insert( NameMapPair("Tm3", 320.0) );
+  c4params_.insert( NameMapPair("Lu3", 303.0) );
+  c4params_.insert( NameMapPair("Hf4", 837.0) );
+  c4params_.insert( NameMapPair("Zr4", 845.0) );
+  c4params_.insert( NameMapPair("Ce4", 771.0) );
+  c4params_.insert( NameMapPair("U4", 1140.0) );
+  c4params_.insert( NameMapPair("Pu4", 919.0) );
+  c4params_.insert( NameMapPair("Th4", 601.0) );
+}
+
 /** Set up C4 parameters for given water model */
 void LJ1264_Params::setupForWaterModel(WaterModelType wmIn)
 {
@@ -72,6 +402,12 @@ void LJ1264_Params::setupForWaterModel(WaterModelType wmIn)
 
   switch (waterModel_) {
     case UNKNOWN_WATER_MODEL : break;
-    case TIP3P : set_tip3p_params(); break;
+    case TIP3P   : set_tip3p_params(); break;
+    case TIP4PEW : set_tip4pew_params(); break;
+    case SPCE    : set_spce_params(); break;
+    case OPC3    : set_opc3_params(); break;
+    case OPC     : set_opc_params(); break;
+    case FB3     : set_fb3_params(); break;
+    case FB4     : set_fb4_params(); break;
   }
 }
diff --git a/src/Parm/LJ1264_Params.h b/src/Parm/LJ1264_Params.h
index 1bdd038490..ee5a37b36a 100644
--- a/src/Parm/LJ1264_Params.h
+++ b/src/Parm/LJ1264_Params.h
@@ -17,6 +17,12 @@ class LJ1264_Params {
 
     /// Set C4 parameters for TIP3P
     void set_tip3p_params();
+    void set_tip4pew_params();
+    void set_spce_params();
+    void set_opc3_params();
+    void set_opc_params();
+    void set_fb3_params();
+    void set_fb4_params();
     /// Set C4 params for given water model
     void setupForWaterModel(WaterModelType);
 

From c118f3de11979521bccaddadc51f9e9df4b2fc8e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 7 Jan 2026 14:08:46 -0500
Subject: [PATCH 1186/1492] Read polarizabilities

---
 src/Parm/LJ1264_Params.cpp | 80 ++++++++++++++++++++++++++++++++++++++
 src/Parm/LJ1264_Params.h   |  4 ++
 src/Parm/parmdepend        |  2 +-
 3 files changed, 85 insertions(+), 1 deletion(-)

diff --git a/src/Parm/LJ1264_Params.cpp b/src/Parm/LJ1264_Params.cpp
index 1d586fff57..0370359b4d 100644
--- a/src/Parm/LJ1264_Params.cpp
+++ b/src/Parm/LJ1264_Params.cpp
@@ -1,4 +1,8 @@
 #include "LJ1264_Params.h"
+#include "../ArgList.h"
+#include "../BufferedLine.h"
+#include "../CpptrajStdio.h"
+#include <cstdlib> // atof
 
 using namespace Cpptraj::Parm;
 
@@ -411,3 +415,79 @@ void LJ1264_Params::setupForWaterModel(WaterModelType wmIn)
     case FB4     : set_fb4_params(); break;
   }
 }
+
+/** Read a 2 column file with format <name> <value> */
+int LJ1264_Params::read_2col_file(std::string const& infileName, NameMapType& mapIn)
+{
+  mapIn.clear();
+  BufferedLine infile;
+  if (infile.OpenFileRead(infileName)) {
+    mprinterr("Error: Could not open '%s'\n", infileName.c_str());
+    return 1;
+  }
+  const char* ptr = infile.Line();
+  while (ptr != 0) {
+    ArgList line(ptr, " \t");
+    if (line.Nargs() > 0 && line[0][0] != '#')
+    {
+      if (line.Nargs() < 2) {
+        mprinterr("Error: Expected a file with at least 2 columns. Line %i has %i: %s\n",
+                  infile.LineNumber(), line.Nargs(), ptr);
+        return 1;
+      }
+      double col2 = atof( line[1].c_str() );
+      // TODO report doubles
+      mapIn.insert( NameMapPair(line[0], col2) );
+    }
+    ptr = infile.Line();
+  }
+  infile.CloseFile();
+  return 0;
+}
+
+/** Read polarizabilities. */
+int LJ1264_Params::read_pol(std::string const& polfile)
+{
+  mprintf("\tReading atomic polarizabilities from '%s'\n", polfile.c_str());
+  return read_2col_file(polfile, pol_);
+}
+
+/** Initialize */
+int LJ1264_Params::Init_LJ1264(std::string const& maskIn, std::string const& c4fileIn, WaterModelType wmIn,
+                              std::string const& polfileIn, double tunfactorIn)
+{
+  tunfactor_ = tunfactorIn;
+
+  if (maskIn.empty())
+    mask_ = ":ZN";
+  else
+    mask_ = maskIn;
+
+  if (c4fileIn.empty())
+    setupForWaterModel( wmIn );
+  else {
+    // TODO
+    mprinterr("Internal Error: Not set up for reading external c4 params yet.\n");
+    return 1;
+  }
+
+  std::string polfile;
+  if (polfileIn.empty()) {
+    // First, need to determine where the Amber FF files are
+    const char* env = getenv("AMBERHOME");
+    if (env != 0)
+      polfile = std::string(env) + "/dat/leap/parm/lj_1264_pol.dat";
+    else {
+      mprinterr("Error: AMBERHOME not set. Cannot find 'lj_1264_pol.dat'.\n");
+      return 1;
+    }
+  } else
+    polfile = polfileIn;
+  if (!File::Exists(polfile)) {
+    mprinterr("Error: Polarizability file not found: %s\n", polfile.c_str());
+    return 1;
+  }
+  if (read_pol(polfile)) return 1;
+
+  return 0;
+}
diff --git a/src/Parm/LJ1264_Params.h b/src/Parm/LJ1264_Params.h
index ee5a37b36a..7dbf57adf0 100644
--- a/src/Parm/LJ1264_Params.h
+++ b/src/Parm/LJ1264_Params.h
@@ -26,10 +26,14 @@ class LJ1264_Params {
     /// Set C4 params for given water model
     void setupForWaterModel(WaterModelType);
 
+    int read_2col_file(std::string const&, NameMapType&);
+    int read_pol(std::string const&);
+
     WaterModelType waterModel_; ///< Water model that C3 parameters have been set for
     NameMapType c4params_; ///< C4 parameters
     NameMapType pol_; ///< Polarizabilities
     double tunfactor_; ///< Tuning factor
+    std::string mask_; ///< Mask for selecting metal centers
 };
 }
 }
diff --git a/src/Parm/parmdepend b/src/Parm/parmdepend
index c09005fe2e..528ccca2d4 100644
--- a/src/Parm/parmdepend
+++ b/src/Parm/parmdepend
@@ -1,6 +1,6 @@
 AssignParams.o : AssignParams.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/ParmEnum.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/GenerateConnectivityArrays.h ../SymbolExporting.h ../Timer.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h AssignParams.h DihedralParmHolder.h GetParams.h ImproperParmHolder.h ParameterSet.h ParmEnum.h ParmHolder.h
 GB_Params.o : GB_Params.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h GB_Params.h
 GetParams.o : GetParams.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/ParmEnum.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h DihedralParmHolder.h GetParams.h ImproperParmHolder.h ParameterSet.h ParmEnum.h ParmHolder.h
-LJ1264_Params.o : LJ1264_Params.cpp LJ1264_Params.h ParmEnum.h
+LJ1264_Params.o : LJ1264_Params.cpp ../ArgList.h ../BufferedLine.h ../CpptrajFile.h ../CpptrajStdio.h ../FileIO.h ../FileName.h ../Parallel.h LJ1264_Params.h ParmEnum.h
 Merge.o : Merge.cpp ../Atom.h ../Constants.h ../CpptrajStdio.h ../NameType.h ../ParameterTypes.h ../Residue.h ../StringRoutines.h ../SymbolExporting.h ../TypeNameHolder.h Merge.h ParmEnum.h ParmHolder.h
 ParameterSet.o : ParameterSet.cpp ../AtomType.h ../CmapParmHolder.h ../Constants.h ../CpptrajFile.h ../CpptrajStdio.h ../FileIO.h ../FileName.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/ParmEnum.h ../TypeNameHolder.h ../UpdateParameters.h DihedralParmHolder.h ImproperParmHolder.h ParameterSet.h ParmEnum.h ParmHolder.h

From e1abcd85f7eb0492b9e5d0320403ed4db9ac0d2e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 7 Jan 2026 14:12:06 -0500
Subject: [PATCH 1187/1492] Read c4 params from file

---
 src/Parm/LJ1264_Params.cpp | 16 ++++++++++++++--
 src/Parm/LJ1264_Params.h   |  1 +
 2 files changed, 15 insertions(+), 2 deletions(-)

diff --git a/src/Parm/LJ1264_Params.cpp b/src/Parm/LJ1264_Params.cpp
index 0370359b4d..819d95fd72 100644
--- a/src/Parm/LJ1264_Params.cpp
+++ b/src/Parm/LJ1264_Params.cpp
@@ -452,6 +452,14 @@ int LJ1264_Params::read_pol(std::string const& polfile)
   return read_2col_file(polfile, pol_);
 }
 
+/** Read C4 params */
+int LJ1264_Params::read_c4(std::string const& c4file)
+{
+  mprintf("\tReading C4 parameters from '%s'\n", c4file.c_str());
+  waterModel_ = UNKNOWN_WATER_MODEL;
+  return read_2col_file(c4file, c4params_);
+}
+
 /** Initialize */
 int LJ1264_Params::Init_LJ1264(std::string const& maskIn, std::string const& c4fileIn, WaterModelType wmIn,
                               std::string const& polfileIn, double tunfactorIn)
@@ -466,8 +474,12 @@ int LJ1264_Params::Init_LJ1264(std::string const& maskIn, std::string const& c4f
   if (c4fileIn.empty())
     setupForWaterModel( wmIn );
   else {
-    // TODO
-    mprinterr("Internal Error: Not set up for reading external c4 params yet.\n");
+    if (read_c4(c4fileIn)) return 1;
+  }
+
+  // Sanity check
+  if (c4params_.empty()) {
+    mprinterr("Error: No C4 parameters loaded.\n");
     return 1;
   }
 
diff --git a/src/Parm/LJ1264_Params.h b/src/Parm/LJ1264_Params.h
index 7dbf57adf0..819e7d91a0 100644
--- a/src/Parm/LJ1264_Params.h
+++ b/src/Parm/LJ1264_Params.h
@@ -28,6 +28,7 @@ class LJ1264_Params {
 
     int read_2col_file(std::string const&, NameMapType&);
     int read_pol(std::string const&);
+    int read_c4(std::string const&);
 
     WaterModelType waterModel_; ///< Water model that C3 parameters have been set for
     NameMapType c4params_; ///< C4 parameters

From e6e13a2414a9528b9d9778dc6e0c0b752c367b3e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 7 Jan 2026 14:17:50 -0500
Subject: [PATCH 1188/1492] Add strings for each water model

---
 src/Parm/CMakeLists.txt    |  1 +
 src/Parm/LJ1264_Params.cpp |  6 +++++-
 src/Parm/ParmEnum.cpp      | 15 +++++++++++++++
 src/Parm/ParmEnum.h        |  1 +
 src/Parm/parmdepend        |  1 +
 src/Parm/parmfiles         |  3 ++-
 6 files changed, 25 insertions(+), 2 deletions(-)
 create mode 100644 src/Parm/ParmEnum.cpp

diff --git a/src/Parm/CMakeLists.txt b/src/Parm/CMakeLists.txt
index 3683c011ad..7c5d2ae785 100644
--- a/src/Parm/CMakeLists.txt
+++ b/src/Parm/CMakeLists.txt
@@ -6,4 +6,5 @@ target_sources(cpptraj_common_obj PRIVATE
   ${CMAKE_CURRENT_LIST_DIR}/LJ1264_Params.cpp
   ${CMAKE_CURRENT_LIST_DIR}/Merge.cpp
   ${CMAKE_CURRENT_LIST_DIR}/ParameterSet.cpp
+  ${CMAKE_CURRENT_LIST_DIR}/ParmEnum.cpp
 )
diff --git a/src/Parm/LJ1264_Params.cpp b/src/Parm/LJ1264_Params.cpp
index 819d95fd72..7b9ff65b49 100644
--- a/src/Parm/LJ1264_Params.cpp
+++ b/src/Parm/LJ1264_Params.cpp
@@ -404,8 +404,9 @@ void LJ1264_Params::setupForWaterModel(WaterModelType wmIn)
   c4params_.clear();
   waterModel_ = wmIn;
 
+
   switch (waterModel_) {
-    case UNKNOWN_WATER_MODEL : break;
+    case UNKNOWN_WATER_MODEL : return;
     case TIP3P   : set_tip3p_params(); break;
     case TIP4PEW : set_tip4pew_params(); break;
     case SPCE    : set_spce_params(); break;
@@ -414,6 +415,8 @@ void LJ1264_Params::setupForWaterModel(WaterModelType wmIn)
     case FB3     : set_fb3_params(); break;
     case FB4     : set_fb4_params(); break;
   }
+
+  mprintf("\tUsing default C4 parameters for %s\n", WaterModelStr(waterModel_));
 }
 
 /** Read a 2 column file with format <name> <value> */
@@ -470,6 +473,7 @@ int LJ1264_Params::Init_LJ1264(std::string const& maskIn, std::string const& c4f
     mask_ = ":ZN";
   else
     mask_ = maskIn;
+  mprintf("\tLJ 12-6-4 mask: %s\n", mask_.c_str());
 
   if (c4fileIn.empty())
     setupForWaterModel( wmIn );
diff --git a/src/Parm/ParmEnum.cpp b/src/Parm/ParmEnum.cpp
new file mode 100644
index 0000000000..aba9d35618
--- /dev/null
+++ b/src/Parm/ParmEnum.cpp
@@ -0,0 +1,15 @@
+#include "ParmEnum.h"
+
+const char* Cpptraj::Parm::WaterModelStr(WaterModelType wm) {
+  switch (wm) {
+    case TIP3P : return "TIP3P"; 
+    case TIP4PEW : return "TIP4Pew"; 
+    case SPCE : return "SPCe"; 
+    case OPC3 : return "OPC3"; 
+    case OPC : return "OPC"; 
+    case FB3 : return "FB3"; 
+    case FB4 : return "FB4"; 
+    case UNKNOWN_WATER_MODEL: return "Unknown water model";
+  }
+  return 0;
+}
diff --git a/src/Parm/ParmEnum.h b/src/Parm/ParmEnum.h
index 141548e46f..301ac10094 100644
--- a/src/Parm/ParmEnum.h
+++ b/src/Parm/ParmEnum.h
@@ -5,6 +5,7 @@ namespace Parm {
   enum RetType { ADDED = 0, SAME, UPDATED, ERR };
 
   enum WaterModelType { TIP3P = 0, TIP4PEW, SPCE, OPC3, OPC, FB3, FB4, UNKNOWN_WATER_MODEL };
+  const char* WaterModelStr(WaterModelType);
 }
 }
 #endif
diff --git a/src/Parm/parmdepend b/src/Parm/parmdepend
index 528ccca2d4..791886d6e0 100644
--- a/src/Parm/parmdepend
+++ b/src/Parm/parmdepend
@@ -4,3 +4,4 @@ GetParams.o : GetParams.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Cm
 LJ1264_Params.o : LJ1264_Params.cpp ../ArgList.h ../BufferedLine.h ../CpptrajFile.h ../CpptrajStdio.h ../FileIO.h ../FileName.h ../Parallel.h LJ1264_Params.h ParmEnum.h
 Merge.o : Merge.cpp ../Atom.h ../Constants.h ../CpptrajStdio.h ../NameType.h ../ParameterTypes.h ../Residue.h ../StringRoutines.h ../SymbolExporting.h ../TypeNameHolder.h Merge.h ParmEnum.h ParmHolder.h
 ParameterSet.o : ParameterSet.cpp ../AtomType.h ../CmapParmHolder.h ../Constants.h ../CpptrajFile.h ../CpptrajStdio.h ../FileIO.h ../FileName.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/ParmEnum.h ../TypeNameHolder.h ../UpdateParameters.h DihedralParmHolder.h ImproperParmHolder.h ParameterSet.h ParmEnum.h ParmHolder.h
+ParmEnum.o : ParmEnum.cpp ParmEnum.h
diff --git a/src/Parm/parmfiles b/src/Parm/parmfiles
index 79b736579e..b8bb0e0754 100644
--- a/src/Parm/parmfiles
+++ b/src/Parm/parmfiles
@@ -5,4 +5,5 @@ PARM_SOURCES= \
   GetParams.cpp \
   LJ1264_Params.cpp \
   Merge.cpp \
-  ParameterSet.cpp
+  ParameterSet.cpp \
+  ParmEnum.cpp

From 0fb484c1a8e11b656dc39718d3ca9eb57624a7ba Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 7 Jan 2026 14:26:14 -0500
Subject: [PATCH 1189/1492] Start testing 1264

---
 src/Exec_Build.cpp         | 9 +++++++++
 src/Parm/LJ1264_Params.cpp | 2 +-
 src/cpptrajdepend          | 4 +++-
 3 files changed, 13 insertions(+), 2 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 0e6a3e9d64..0a63adfb6f 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -6,6 +6,7 @@
 #include "StringRoutines.h" // integerToString
 #include "Trajout_Single.h"
 #include "Parm/AssignParams.h"
+#include "Parm/LJ1264_Params.h"
 #include "Structure/AddIons.h"
 #include "Structure/Builder.h"
 #include "Structure/Creator.h"
@@ -1192,6 +1193,14 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
     ret = CpptrajState::ERR;
   }
 
+  // FIXME
+  // LJ 12-6-4
+  Cpptraj::Parm::LJ1264_Params lj1264;
+  if (lj1264.Init_LJ1264("", "", Cpptraj::Parm::TIP3P, "", 1.0)) {
+    mprinterr("Error: Init of LJ 12-6-4 failed.\n");
+    return CpptrajState::ERR;
+  }
+
   topOut.Summary();
   t_assign_.Stop();
 
diff --git a/src/Parm/LJ1264_Params.cpp b/src/Parm/LJ1264_Params.cpp
index 7b9ff65b49..5c366144a0 100644
--- a/src/Parm/LJ1264_Params.cpp
+++ b/src/Parm/LJ1264_Params.cpp
@@ -430,7 +430,7 @@ int LJ1264_Params::read_2col_file(std::string const& infileName, NameMapType& ma
   }
   const char* ptr = infile.Line();
   while (ptr != 0) {
-    ArgList line(ptr, " \t");
+    ArgList line(ptr, " \t\"'");
     if (line.Nargs() > 0 && line[0][0] != '#')
     {
       if (line.Nargs() < 2) {
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index df33162d9a..8778b054dc 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -316,7 +316,7 @@ EwaldOptions.o : EwaldOptions.cpp ArgList.h CpptrajStdio.h EwaldOptions.h
 ExclusionArray.o : ExclusionArray.cpp Atom.h AtomMask.h CharMask.h CpptrajStdio.h ExclusionArray.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Unit.h
 Exec_AddMissingRes.o : Exec_AddMissingRes.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h CharMask.h CompactFrameArray.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_AddMissingRes.h Exec_AddMissingRes_Pres.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h ParmFile.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h Trajout_Single.h Unit.h Vec3.h
 Exec_Analyze.o : Exec_Analyze.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Analyze.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_Build.o : Exec_Build.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h ExclusionArray.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PairList.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h ParmFile.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/AddIons.h Structure/Builder.h Structure/Creator.h Structure/Disulfide.h Structure/HisProt.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/RingFinder.h Structure/Solvate.h Structure/StructureEnum.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Build.o : Exec_Build.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h ExclusionArray.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PairList.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/ImproperParmHolder.h Parm/LJ1264_Params.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h ParmFile.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/AddIons.h Structure/Builder.h Structure/Creator.h Structure/Disulfide.h Structure/HisProt.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/RingFinder.h Structure/Solvate.h Structure/StructureEnum.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Calc.o : Exec_Calc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Calc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_CatCrd.o : Exec_CatCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CatCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_Change.o : Exec_Change.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Change.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
@@ -433,8 +433,10 @@ ParallelSetFrameNum.o : ParallelSetFrameNum.cpp AssociatedData.h CpptrajFile.h C
 Parm/AssignParams.o : Parm/AssignParams.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h GuessAtomHybridization.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/../Structure/GenerateConnectivityArrays.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GetParams.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Parm/GB_Params.o : Parm/GB_Params.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/GB_Params.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Parm/GetParams.o : Parm/GetParams.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/GetParams.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Parm/LJ1264_Params.o : Parm/LJ1264_Params.cpp ArgList.h BufferedLine.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Parallel.h Parm/LJ1264_Params.h Parm/ParmEnum.h
 Parm/Merge.o : Parm/Merge.cpp Atom.h Constants.h CpptrajStdio.h NameType.h ParameterTypes.h Parm/Merge.h Parm/ParmEnum.h Parm/ParmHolder.h Residue.h StringRoutines.h SymbolExporting.h TypeNameHolder.h
 Parm/ParameterSet.o : Parm/ParameterSet.cpp AtomType.h CmapParmHolder.h Constants.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h TypeNameHolder.h UpdateParameters.h
+Parm/ParmEnum.o : Parm/ParmEnum.cpp Parm/ParmEnum.h
 ParmFile.o : ParmFile.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h ParmFile.h ParmIO.h Parm_Amber.h Parm_CIF.h Parm_CharmmPsf.h Parm_Gromacs.h Parm_Mol2.h Parm_PDB.h Parm_SDF.h Parm_Tinker.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Parm_Amber.o : Parm_Amber.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h ExclusionArray.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/GetParams.h ParmIO.h Parm_Amber.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h Unit.h Vec3.h
 Parm_CIF.o : Parm_CIF.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h CIFfile.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmIO.h Parm_CIF.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h

From 5e531e6a0a493791a849abc937c21a1cb49bfd90 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 7 Jan 2026 20:29:56 -0500
Subject: [PATCH 1190/1492] Add lj1264 and related keywords

---
 src/Exec_Build.cpp | 20 ++++++++++++++------
 1 file changed, 14 insertions(+), 6 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 0a63adfb6f..9fabb91bb4 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -1009,6 +1009,20 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
   }
   mprintf("\tGB radii set: %s\n", Cpptraj::Parm::GbTypeStr(gbradii).c_str());
 
+  // LJ 12-6-4
+  Cpptraj::Parm::LJ1264_Params lj1264;
+  if (argIn.hasKey("lj1264")) {
+    mprintf("\tEnabling LJ 12-6-4 parameters.\n");
+    std::string lj1264mask = argIn.GetStringKey("lj1264mask");
+    std::string c4file = argIn.GetStringKey("c4file");
+    std::string polfile = argIn.GetStringKey("polfile");
+    double tunfactor = argIn.getKeyDouble("tunfactor", 1.0);
+    if (lj1264.Init_LJ1264(lj1264mask, c4file, Cpptraj::Parm::TIP3P, polfile, tunfactor)) {
+      mprinterr("Error: Init of LJ 12-6-4 failed.\n");
+      return CpptrajState::ERR;
+    }
+  }
+
   // Get templates and parameter sets.
   t_get_templates_.Start();
   Cpptraj::Structure::Creator creator( debug_ );
@@ -1194,12 +1208,6 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
   }
 
   // FIXME
-  // LJ 12-6-4
-  Cpptraj::Parm::LJ1264_Params lj1264;
-  if (lj1264.Init_LJ1264("", "", Cpptraj::Parm::TIP3P, "", 1.0)) {
-    mprinterr("Error: Init of LJ 12-6-4 failed.\n");
-    return CpptrajState::ERR;
-  }
 
   topOut.Summary();
   t_assign_.Stop();

From 3f78ed04f22344d348b6d0844bec8bd8aaa0bdce Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 8 Jan 2026 12:12:30 -0500
Subject: [PATCH 1191/1492] Start assigning parameters. Process the mask, find
 C4 params

---
 src/Exec_Build.cpp         |  9 ++++--
 src/Parm/LJ1264_Params.cpp | 59 +++++++++++++++++++++++++++++++++++---
 src/Parm/LJ1264_Params.h   | 11 +++++--
 src/Parm/parmdepend        |  2 +-
 src/cpptrajdepend          |  2 +-
 5 files changed, 73 insertions(+), 10 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 9fabb91bb4..8dd49dc0da 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -1206,8 +1206,13 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
     mprinterr("Error: Could not assign GB parameters for '%s'\n", topOut.c_str());
     ret = CpptrajState::ERR;
   }
-
-  // FIXME
+  // Assign LJ 12-6-4 parameters
+  if (lj1264.HasC4Params()) {
+    if (lj1264.AssignLJ1264(topOut)) {
+      mprinterr("Error: Could not assign LJ 12-6-4 parameters for '%s'\n", topOut.c_str());
+      ret = CpptrajState::ERR;
+    }
+  }
 
   topOut.Summary();
   t_assign_.Stop();
diff --git a/src/Parm/LJ1264_Params.cpp b/src/Parm/LJ1264_Params.cpp
index 5c366144a0..90588bde70 100644
--- a/src/Parm/LJ1264_Params.cpp
+++ b/src/Parm/LJ1264_Params.cpp
@@ -2,7 +2,10 @@
 #include "../ArgList.h"
 #include "../BufferedLine.h"
 #include "../CpptrajStdio.h"
+#include "../Topology.h"
 #include <cstdlib> // atof
+#include <cctype> // tolower
+#include "StringRoutines.h" // integerToString
 
 using namespace Cpptraj::Parm;
 
@@ -470,10 +473,14 @@ int LJ1264_Params::Init_LJ1264(std::string const& maskIn, std::string const& c4f
   tunfactor_ = tunfactorIn;
 
   if (maskIn.empty())
-    mask_ = ":ZN";
-  else
-    mask_ = maskIn;
-  mprintf("\tLJ 12-6-4 mask: %s\n", mask_.c_str());
+    mask_.SetMaskString(":ZN");
+  else {
+    if (mask_.SetMaskString(maskIn)) {
+      mprinterr("Error: Could not set mask string '%s'\n", maskIn.c_str());
+      return 1;
+    }
+  }
+  mprintf("\tLJ 12-6-4 mask: %s\n", mask_.MaskString());
 
   if (c4fileIn.empty())
     setupForWaterModel( wmIn );
@@ -507,3 +514,47 @@ int LJ1264_Params::Init_LJ1264(std::string const& maskIn, std::string const& c4f
 
   return 0;
 }
+
+/** Parameterize */
+int LJ1264_Params::AssignLJ1264(Topology& topOut)
+{
+  mprintf("\tAssigning LJ 12-6-4 parameters.\n");
+  if (topOut.SetupIntegerMask( mask_ )) {
+    mprinterr("Error: Could not set up mask '%s'\n", mask_.MaskString());
+    return 1;
+  }
+  mprintf("\t  Mask selection: ");
+  mask_.BriefMaskInfo();
+  mprintf("\n");
+  if (mask_.None()) {
+    mprintf("Warning: Nothing selected by mask '%s'\n", mask_.MaskString());
+    return 0;
+  }
+
+  // For each selected atom get the type index, element, charge
+  for (AtomMask::const_iterator at = mask_.begin(); at != mask_.end(); ++at)
+  {
+    int typeIdx = topOut[*at].TypeIndex();
+    // Sanity check
+    if (typeIdx < 0) {
+      mprinterr("Error: Atom %s does not have an atom type index.\n", topOut.AtomMaskName(*at).c_str());
+      return 1;
+    }
+    int iCharge = (int)topOut[*at].Charge();
+    std::string eltName = std::string(topOut[*at].ElementName());
+    // LJ 12-6-4 convention is element name second char is lower case
+    if (eltName.size() > 1) eltName[1] = tolower(eltName[1]);
+    // Append the integer charge
+    std::string ename = eltName + integerToString(iCharge);
+    // Get the C4 parameter
+    NameMapType::const_iterator c4it = c4params_.find( ename );
+    if (c4it == c4params_.end()) {
+      mprinterr("Error: Could not find a C4 parameter for atom %s, type index %i, charge %i, element %s\n",
+                topOut.AtomMaskName(*at).c_str(), typeIdx, iCharge, eltName.c_str());
+      return 1;
+    }
+    mprintf("DEBUG: %s : idx=%i  chg=%i  ename=%s  C4=%g\n", topOut.AtomMaskName(*at).c_str(), typeIdx, iCharge, ename.c_str(), c4it->second);
+  }
+
+  return 0;
+}
diff --git a/src/Parm/LJ1264_Params.h b/src/Parm/LJ1264_Params.h
index 819e7d91a0..1a7161af3a 100644
--- a/src/Parm/LJ1264_Params.h
+++ b/src/Parm/LJ1264_Params.h
@@ -1,8 +1,10 @@
 #ifndef INC_PARM_LJ1264_PARAMS_H
 #define INC_PARM_LJ1264_PARAMS_H
+#include "../AtomMask.h"
 #include "ParmEnum.h"
 #include <map>
 #include <string>
+class Topology;
 namespace Cpptraj {
 namespace Parm {
 /// Used to assign LJ 12-6-4 C coefficients
@@ -11,6 +13,11 @@ class LJ1264_Params {
     LJ1264_Params();
     /// Init - mask, c4 file, water model, polarization file, tuning factor
     int Init_LJ1264(std::string const&, std::string const&, WaterModelType, std::string const&, double);
+    /// Assign Topology with LJ 12-6-4 params
+    int AssignLJ1264(Topology&);
+
+    /// \return true if C4 parameters have been set up
+    bool HasC4Params() const { return !c4params_.empty(); }
   private:
     typedef std::pair<std::string, double> NameMapPair;
     typedef std::map<std::string, double> NameMapType;
@@ -30,11 +37,11 @@ class LJ1264_Params {
     int read_pol(std::string const&);
     int read_c4(std::string const&);
 
-    WaterModelType waterModel_; ///< Water model that C3 parameters have been set for
+    WaterModelType waterModel_; ///< Water model that C4 parameters have been set for
     NameMapType c4params_; ///< C4 parameters
     NameMapType pol_; ///< Polarizabilities
     double tunfactor_; ///< Tuning factor
-    std::string mask_; ///< Mask for selecting metal centers
+    AtomMask mask_; ///< Mask for selecting metal centers
 };
 }
 }
diff --git a/src/Parm/parmdepend b/src/Parm/parmdepend
index 791886d6e0..46b5ac63f4 100644
--- a/src/Parm/parmdepend
+++ b/src/Parm/parmdepend
@@ -1,7 +1,7 @@
 AssignParams.o : AssignParams.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/ParmEnum.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/GenerateConnectivityArrays.h ../SymbolExporting.h ../Timer.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h AssignParams.h DihedralParmHolder.h GetParams.h ImproperParmHolder.h ParameterSet.h ParmEnum.h ParmHolder.h
 GB_Params.o : GB_Params.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h GB_Params.h
 GetParams.o : GetParams.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/ParmEnum.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h DihedralParmHolder.h GetParams.h ImproperParmHolder.h ParameterSet.h ParmEnum.h ParmHolder.h
-LJ1264_Params.o : LJ1264_Params.cpp ../ArgList.h ../BufferedLine.h ../CpptrajFile.h ../CpptrajStdio.h ../FileIO.h ../FileName.h ../Parallel.h LJ1264_Params.h ParmEnum.h
+LJ1264_Params.o : LJ1264_Params.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../BufferedLine.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h LJ1264_Params.h ParmEnum.h StringRoutines.h
 Merge.o : Merge.cpp ../Atom.h ../Constants.h ../CpptrajStdio.h ../NameType.h ../ParameterTypes.h ../Residue.h ../StringRoutines.h ../SymbolExporting.h ../TypeNameHolder.h Merge.h ParmEnum.h ParmHolder.h
 ParameterSet.o : ParameterSet.cpp ../AtomType.h ../CmapParmHolder.h ../Constants.h ../CpptrajFile.h ../CpptrajStdio.h ../FileIO.h ../FileName.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/ParmEnum.h ../TypeNameHolder.h ../UpdateParameters.h DihedralParmHolder.h ImproperParmHolder.h ParameterSet.h ParmEnum.h ParmHolder.h
 ParmEnum.o : ParmEnum.cpp ParmEnum.h
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 8778b054dc..f2bd093252 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -433,7 +433,7 @@ ParallelSetFrameNum.o : ParallelSetFrameNum.cpp AssociatedData.h CpptrajFile.h C
 Parm/AssignParams.o : Parm/AssignParams.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h GuessAtomHybridization.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/../Structure/GenerateConnectivityArrays.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GetParams.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Parm/GB_Params.o : Parm/GB_Params.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/GB_Params.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Parm/GetParams.o : Parm/GetParams.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/GetParams.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Parm/LJ1264_Params.o : Parm/LJ1264_Params.cpp ArgList.h BufferedLine.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Parallel.h Parm/LJ1264_Params.h Parm/ParmEnum.h
+Parm/LJ1264_Params.o : Parm/LJ1264_Params.cpp ArgList.h Atom.h AtomMask.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/LJ1264_Params.h Parm/ParmEnum.h Parm/StringRoutines.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Parm/Merge.o : Parm/Merge.cpp Atom.h Constants.h CpptrajStdio.h NameType.h ParameterTypes.h Parm/Merge.h Parm/ParmEnum.h Parm/ParmHolder.h Residue.h StringRoutines.h SymbolExporting.h TypeNameHolder.h
 Parm/ParameterSet.o : Parm/ParameterSet.cpp AtomType.h CmapParmHolder.h Constants.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h TypeNameHolder.h UpdateParameters.h
 Parm/ParmEnum.o : Parm/ParmEnum.cpp Parm/ParmEnum.h

From 24d317393c49d381e3bc5deb74cd952b448b846c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 8 Jan 2026 13:41:28 -0500
Subject: [PATCH 1192/1492] Ensure LJC array gets allocated. Associate
 polaraization values with each atom type index. Start looping over type
 indices.

---
 src/ParameterTypes.h       |  2 +
 src/Parm/LJ1264_Params.cpp | 85 +++++++++++++++++++++++++++++++++++++-
 src/Parm/parmdepend        |  2 +-
 src/cpptrajdepend          |  2 +-
 4 files changed, 87 insertions(+), 4 deletions(-)

diff --git a/src/ParameterTypes.h b/src/ParameterTypes.h
index f87e32d61d..b17b3c7994 100644
--- a/src/ParameterTypes.h
+++ b/src/ParameterTypes.h
@@ -722,6 +722,8 @@ class NonbondParmType {
     void SetNLJ14terms(int n)    { lj14_.assign( n, NonbondType() ); }
     /// Set number of LJC terms
     void SetNLJCterms(int n)     { ccoef_.assign( n, 0 ); }
+    /// Create an array of LJC terms the same size as LJ A/B all set to zero
+    void AllocateLJC() { ccoef_.assign( nbarray_.size(), 0.0 ); }
     /// Set specified LJ term
     NonbondType& SetLJ(int i)    { return nbarray_[i];                  }
     /// Set specified LJ 1-4 term.
diff --git a/src/Parm/LJ1264_Params.cpp b/src/Parm/LJ1264_Params.cpp
index 90588bde70..600922ca04 100644
--- a/src/Parm/LJ1264_Params.cpp
+++ b/src/Parm/LJ1264_Params.cpp
@@ -1,11 +1,13 @@
 #include "LJ1264_Params.h"
 #include "../ArgList.h"
 #include "../BufferedLine.h"
+#include "../Constants.h" // SMALL
 #include "../CpptrajStdio.h"
+#include "../StringRoutines.h" // integerToString
 #include "../Topology.h"
 #include <cstdlib> // atof
 #include <cctype> // tolower
-#include "StringRoutines.h" // integerToString
+#include <cmath>
 
 using namespace Cpptraj::Parm;
 
@@ -519,6 +521,11 @@ int LJ1264_Params::Init_LJ1264(std::string const& maskIn, std::string const& c4f
 int LJ1264_Params::AssignLJ1264(Topology& topOut)
 {
   mprintf("\tAssigning LJ 12-6-4 parameters.\n");
+  // Must already have nonbond info
+  if (!topOut.Nonbond().HasNonbond()) {
+    mprinterr("Error: Topology %s does not have LJ A/B nonbond parameters; required before setting LJ 12-6-4 nonbond parameters.\n");
+    return 1;
+  }
   if (topOut.SetupIntegerMask( mask_ )) {
     mprinterr("Error: Could not set up mask '%s'\n", mask_.MaskString());
     return 1;
@@ -531,7 +538,12 @@ int LJ1264_Params::AssignLJ1264(Topology& topOut)
     return 0;
   }
 
-  // For each selected atom get the type index, element, charge
+  typedef std::pair<int, double> IdxParamMapPair;
+  typedef std::map<int, double> IdxParamMapType;
+  //typedef std::pair<IdxParamMapType::iterator, bool> IdxParamMapRet;
+  IdxParamMapType idxC4Map;
+
+  // For each selected atom get the type index, element, charge, C4 parameter
   for (AtomMask::const_iterator at = mask_.begin(); at != mask_.end(); ++at)
   {
     int typeIdx = topOut[*at].TypeIndex();
@@ -540,6 +552,12 @@ int LJ1264_Params::AssignLJ1264(Topology& topOut)
       mprinterr("Error: Atom %s does not have an atom type index.\n", topOut.AtomMaskName(*at).c_str());
       return 1;
     }
+    // Was this type index already seen?
+    IdxParamMapType::const_iterator ret = idxC4Map.find( typeIdx );
+    if (ret != idxC4Map.end()) {
+      continue; // TODO check that C4 param matches?
+    }
+    // Figure out charge and element
     int iCharge = (int)topOut[*at].Charge();
     std::string eltName = std::string(topOut[*at].ElementName());
     // LJ 12-6-4 convention is element name second char is lower case
@@ -553,8 +571,71 @@ int LJ1264_Params::AssignLJ1264(Topology& topOut)
                 topOut.AtomMaskName(*at).c_str(), typeIdx, iCharge, eltName.c_str());
       return 1;
     }
+    // Save the type index/C4 param pair
+    idxC4Map.insert( IdxParamMapPair(typeIdx, c4it->second) );
+
     mprintf("DEBUG: %s : idx=%i  chg=%i  ename=%s  C4=%g\n", topOut.AtomMaskName(*at).c_str(), typeIdx, iCharge, ename.c_str(), c4it->second);
   }
+  mprintf("\t  %zu unique C4 parameters for atoms selected by '%s'\n", idxC4Map.size(), mask_.MaskString());
+
+  // For each atom type index find the polarizability
+  IdxParamMapType idxPolMap;
+
+  for (int at = 0; at != topOut.Natom(); at++)
+  {
+    Atom const& ATM = topOut[at];
+    int typeIdx = ATM.TypeIndex();
+    // Sanity check
+    if (typeIdx < 0) {
+      mprinterr("Error: Atom %s does not have an atom type index.\n", topOut.AtomMaskName(at).c_str());
+      return 1;
+    }
+    // Find a polarization from the atom type
+    NameMapType::const_iterator polit = pol_.find( ATM.Type().Truncated() );
+    if (polit == pol_.end()) {
+      mprinterr("Error: Could not find LJ 12-6-4 polarization for atom type %s (%s)\n", *(ATM.Type()), topOut.AtomMaskName(at).c_str());
+      return 1;
+    }
+    // See if this type index was already seen
+    IdxParamMapType::const_iterator ret = idxPolMap.find( typeIdx );
+    if (ret != idxPolMap.end()) {
+      // Ensure polarization is a match
+      if ( fabs( polit->second - ret->second ) > Constants::SMALL ) {
+        // Find the previous atom type matching this index
+        int ii = 0;
+        for (; ii < topOut.Natom(); ii++) {
+          if (topOut[ii].TypeIndex() == typeIdx) break;
+        }
+        mprinterr("Error: Polarizability parameter of atom type %s is not the same as that of type %s,\n",
+                  *(ATM.Type()), *(topOut[ii].Type()));
+        mprinterr("Error:   but their VDW parameters are the same.\n");
+        return 1;
+      }
+    } else {
+      // New polarization
+      mprintf("DEBUG: idx= %i  type= %s  pol= %g\n", typeIdx, *(ATM.Type()), polit->second);
+      idxPolMap.insert( IdxParamMapPair(typeIdx, polit->second) );
+    }
+  }
+
+  // Allocate space for the LJC params
+  topOut.SetNonbond().AllocateLJC();
+
+  // Loop over all metal type indices
+  for (IdxParamMapType::const_iterator it = idxC4Map.begin(); it != idxC4Map.end(); ++it)
+  {
+    // Loop over all other atom type indices
+    for (int jidx = 0; jidx < topOut.Nonbond().Ntypes(); jidx++)
+    {
+      int ljidx = topOut.Nonbond().GetLJindex( it->first, jidx );
+      IdxParamMapType::const_iterator jt = idxPolMap.find( jidx );
+      mprintf("DEBUG: Type1= %i  Type2= %i  NBidx= %i  Pol= %g\n", it->first, jidx, ljidx, jt->second);
+      if (ljidx < 0) {
+        mprinterr("Error: Type pair %i -- %i is an LJ 10-12 pair, not LJ 6-12.\n", it->first, jidx);
+        return 1;
+      }
+    } // END loop over all atom types indices
+  } // END loop over all metal type indices
 
   return 0;
 }
diff --git a/src/Parm/parmdepend b/src/Parm/parmdepend
index 46b5ac63f4..7ad2488039 100644
--- a/src/Parm/parmdepend
+++ b/src/Parm/parmdepend
@@ -1,7 +1,7 @@
 AssignParams.o : AssignParams.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/ParmEnum.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/GenerateConnectivityArrays.h ../SymbolExporting.h ../Timer.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h AssignParams.h DihedralParmHolder.h GetParams.h ImproperParmHolder.h ParameterSet.h ParmEnum.h ParmHolder.h
 GB_Params.o : GB_Params.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h GB_Params.h
 GetParams.o : GetParams.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/ParmEnum.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h DihedralParmHolder.h GetParams.h ImproperParmHolder.h ParameterSet.h ParmEnum.h ParmHolder.h
-LJ1264_Params.o : LJ1264_Params.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../BufferedLine.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h LJ1264_Params.h ParmEnum.h StringRoutines.h
+LJ1264_Params.o : LJ1264_Params.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../BufferedLine.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../StringRoutines.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h LJ1264_Params.h ParmEnum.h
 Merge.o : Merge.cpp ../Atom.h ../Constants.h ../CpptrajStdio.h ../NameType.h ../ParameterTypes.h ../Residue.h ../StringRoutines.h ../SymbolExporting.h ../TypeNameHolder.h Merge.h ParmEnum.h ParmHolder.h
 ParameterSet.o : ParameterSet.cpp ../AtomType.h ../CmapParmHolder.h ../Constants.h ../CpptrajFile.h ../CpptrajStdio.h ../FileIO.h ../FileName.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/ParmEnum.h ../TypeNameHolder.h ../UpdateParameters.h DihedralParmHolder.h ImproperParmHolder.h ParameterSet.h ParmEnum.h ParmHolder.h
 ParmEnum.o : ParmEnum.cpp ParmEnum.h
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index f2bd093252..b4b701dac8 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -433,7 +433,7 @@ ParallelSetFrameNum.o : ParallelSetFrameNum.cpp AssociatedData.h CpptrajFile.h C
 Parm/AssignParams.o : Parm/AssignParams.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h GuessAtomHybridization.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/../Structure/GenerateConnectivityArrays.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GetParams.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Parm/GB_Params.o : Parm/GB_Params.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/GB_Params.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Parm/GetParams.o : Parm/GetParams.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/GetParams.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Parm/LJ1264_Params.o : Parm/LJ1264_Params.cpp ArgList.h Atom.h AtomMask.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/LJ1264_Params.h Parm/ParmEnum.h Parm/StringRoutines.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
+Parm/LJ1264_Params.o : Parm/LJ1264_Params.cpp ArgList.h Atom.h AtomMask.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/LJ1264_Params.h Parm/ParmEnum.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Parm/Merge.o : Parm/Merge.cpp Atom.h Constants.h CpptrajStdio.h NameType.h ParameterTypes.h Parm/Merge.h Parm/ParmEnum.h Parm/ParmHolder.h Residue.h StringRoutines.h SymbolExporting.h TypeNameHolder.h
 Parm/ParameterSet.o : Parm/ParameterSet.cpp AtomType.h CmapParmHolder.h Constants.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h TypeNameHolder.h UpdateParameters.h
 Parm/ParmEnum.o : Parm/ParmEnum.cpp Parm/ParmEnum.h

From cfd49b3b99096f160176e40d56ae7caeb6b4e5c7 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 8 Jan 2026 14:00:10 -0500
Subject: [PATCH 1193/1492] FInish initial lj 1264 calc

---
 src/Parm/LJ1264_Params.cpp | 54 +++++++++++++++++++++++++++-----------
 src/Parm/LJ1264_Params.h   |  3 +++
 2 files changed, 42 insertions(+), 15 deletions(-)

diff --git a/src/Parm/LJ1264_Params.cpp b/src/Parm/LJ1264_Params.cpp
index 600922ca04..acdcfc76f3 100644
--- a/src/Parm/LJ1264_Params.cpp
+++ b/src/Parm/LJ1264_Params.cpp
@@ -11,10 +11,13 @@
 
 using namespace Cpptraj::Parm;
 
+const double LJ1264_Params::DEFAULT_WATER_POL_ = 1.444; ///< Polarizability of water
+
 /** CONSTRUCTOR */
 LJ1264_Params::LJ1264_Params() :
   waterModel_(UNKNOWN_WATER_MODEL),
-  tunfactor_(1.0)
+  tunfactor_(1.0),
+  WATER_POL_(DEFAULT_WATER_POL_)
 {}
 
 void LJ1264_Params::set_tip3p_params() {
@@ -579,7 +582,18 @@ int LJ1264_Params::AssignLJ1264(Topology& topOut)
   mprintf("\t  %zu unique C4 parameters for atoms selected by '%s'\n", idxC4Map.size(), mask_.MaskString());
 
   // For each atom type index find the polarizability
-  IdxParamMapType idxPolMap;
+  //IdxParamMapType idxPolMap;
+  class TypePol {
+    public:
+      TypePol() : pol_(0) {}
+
+      bool IsSet() const { return typeName_.len() > 0; }
+
+      NameType typeName_;
+      double pol_;
+  };
+  typedef std::vector<TypePol> IdxPolArray;
+  IdxPolArray idxPol( topOut.Nonbond().Ntypes() );
 
   for (int at = 0; at != topOut.Natom(); at++)
   {
@@ -597,24 +611,23 @@ int LJ1264_Params::AssignLJ1264(Topology& topOut)
       return 1;
     }
     // See if this type index was already seen
-    IdxParamMapType::const_iterator ret = idxPolMap.find( typeIdx );
-    if (ret != idxPolMap.end()) {
+    if (idxPol[typeIdx].IsSet()) {
+
+//    IdxParamMapType::const_iterator ret = idxPolMap.find( typeIdx );
+//    if (ret != idxPolMap.end()) {
       // Ensure polarization is a match
-      if ( fabs( polit->second - ret->second ) > Constants::SMALL ) {
-        // Find the previous atom type matching this index
-        int ii = 0;
-        for (; ii < topOut.Natom(); ii++) {
-          if (topOut[ii].TypeIndex() == typeIdx) break;
-        }
-        mprinterr("Error: Polarizability parameter of atom type %s is not the same as that of type %s,\n",
-                  *(ATM.Type()), *(topOut[ii].Type()));
+      if ( fabs( polit->second - idxPol[typeIdx].pol_ ) > Constants::SMALL ) {
+        mprinterr("Error: Polarizability parameter of atom type %s (%g) is not the same as that of type %s (%g),\n",
+                  *(ATM.Type()), polit->second, *(idxPol[typeIdx].typeName_), idxPol[typeIdx].pol_);
         mprinterr("Error:   but their VDW parameters are the same.\n");
         return 1;
       }
     } else {
       // New polarization
       mprintf("DEBUG: idx= %i  type= %s  pol= %g\n", typeIdx, *(ATM.Type()), polit->second);
-      idxPolMap.insert( IdxParamMapPair(typeIdx, polit->second) );
+      idxPol[typeIdx].typeName_ = ATM.Type();
+      idxPol[typeIdx].pol_ = polit->second;
+      //idxPolMap.insert( IdxParamMapPair(typeIdx, polit->second) );
     }
   }
 
@@ -628,12 +641,23 @@ int LJ1264_Params::AssignLJ1264(Topology& topOut)
     for (int jidx = 0; jidx < topOut.Nonbond().Ntypes(); jidx++)
     {
       int ljidx = topOut.Nonbond().GetLJindex( it->first, jidx );
-      IdxParamMapType::const_iterator jt = idxPolMap.find( jidx );
-      mprintf("DEBUG: Type1= %i  Type2= %i  NBidx= %i  Pol= %g\n", it->first, jidx, ljidx, jt->second);
+      //IdxParamMapType::const_iterator jt = idxPolMap.find( jidx );
+      TypePol const& POL = idxPol[jidx];
+      mprintf("DEBUG: Type1= %i  C4= %g  Type2= %i  NBidx= %i  Pol= %g\n", it->first, it->second, jidx, ljidx, POL.pol_);
       if (ljidx < 0) {
         mprinterr("Error: Type pair %i -- %i is an LJ 10-12 pair, not LJ 6-12.\n", it->first, jidx);
         return 1;
       }
+      // Calculate final C4 term
+      double ljc;
+      if (POL.typeName_ == "OW")
+        // There is only one C4 term that exists between water and a certain ion
+        ljc = it->second;
+      else
+        // There are two C4 terms that need to add together between two different ions
+        ljc = topOut.Nonbond().LJC_Array( ljidx ) + (it->second / WATER_POL_ * POL.pol_ * tunfactor_);
+      mprintf("DEBUG:\t\tFinal LJC = %g\n", ljc);
+      topOut.SetNonbond().SetLJC( ljidx, ljc );
     } // END loop over all atom types indices
   } // END loop over all metal type indices
 
diff --git a/src/Parm/LJ1264_Params.h b/src/Parm/LJ1264_Params.h
index 1a7161af3a..09d02b4717 100644
--- a/src/Parm/LJ1264_Params.h
+++ b/src/Parm/LJ1264_Params.h
@@ -37,10 +37,13 @@ class LJ1264_Params {
     int read_pol(std::string const&);
     int read_c4(std::string const&);
 
+    static const double DEFAULT_WATER_POL_; ///< Default Polarizability of water
+
     WaterModelType waterModel_; ///< Water model that C4 parameters have been set for
     NameMapType c4params_; ///< C4 parameters
     NameMapType pol_; ///< Polarizabilities
     double tunfactor_; ///< Tuning factor
+    double WATER_POL_; ///< Polarizability of water
     AtomMask mask_; ///< Mask for selecting metal centers
 };
 }

From b059e023098f53f966155692624ff6bfa09465bc Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 8 Jan 2026 14:15:04 -0500
Subject: [PATCH 1194/1492] Guess the water model from the solvent box name

---
 src/Exec_Build.cpp      | 20 +++++++++++++++++++-
 src/Structure/Solvate.h |  3 ++-
 2 files changed, 21 insertions(+), 2 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 8dd49dc0da..3d8b8e63b1 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -1017,7 +1017,25 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
     std::string c4file = argIn.GetStringKey("c4file");
     std::string polfile = argIn.GetStringKey("polfile");
     double tunfactor = argIn.getKeyDouble("tunfactor", 1.0);
-    if (lj1264.Init_LJ1264(lj1264mask, c4file, Cpptraj::Parm::TIP3P, polfile, tunfactor)) {
+    // Try to guess the water model if we are solvating
+    Cpptraj::Parm::WaterModelType wm = Cpptraj::Parm::UNKNOWN_WATER_MODEL;
+    if (add_solvent == SOLVATEBOX) {
+      if (solvator.SolventBoxName() == "TIP3PBOX") wm = Cpptraj::Parm::TIP3P;
+      else if (solvator.SolventBoxName() == "TIP4PEWBOX") wm = Cpptraj::Parm::TIP4PEW;
+      else if (solvator.SolventBoxName() == "SPCBOX") wm = Cpptraj::Parm::SPCE;
+      else if (solvator.SolventBoxName() == "OPC3BOX") wm = Cpptraj::Parm::OPC3;
+      else if (solvator.SolventBoxName() == "OPCBOX") wm = Cpptraj::Parm::OPC;
+      else if (solvator.SolventBoxName() == "FB3BOX") wm = Cpptraj::Parm::FB3;
+      else if (solvator.SolventBoxName() == "FB4BOX") wm = Cpptraj::Parm::FB4;
+      else
+        mprintf("Warning: Unable to determine solvent model for LJ 12-6-4 from solvent box name %s\n",
+                solvator.SolventBoxName().c_str());
+    }
+    if (wm == Cpptraj::Parm::UNKNOWN_WATER_MODEL) {
+      mprintf("Warning: Unable to determine water model for LJ 12-6-4. Using TIP3P.\n");
+      wm = Cpptraj::Parm::TIP3P;
+    }
+    if (lj1264.Init_LJ1264(lj1264mask, c4file, wm, polfile, tunfactor)) {
       mprinterr("Error: Init of LJ 12-6-4 failed.\n");
       return CpptrajState::ERR;
     }
diff --git a/src/Structure/Solvate.h b/src/Structure/Solvate.h
index 75b0e0b6ee..b5f2e82d89 100644
--- a/src/Structure/Solvate.h
+++ b/src/Structure/Solvate.h
@@ -33,7 +33,8 @@ class Solvate {
 
     /// \return Solvent unit selected from given DataSetList
     DataSet_Coords* GetSolventUnit(DataSetList const&) const;
-    //std::string const& SolventBoxName() const { return solventBoxName_; }
+    /// \return Solvent box name
+    std::string const& SolventBoxName() const { return solventBoxName_; }
     /// Print solvate info to stdout
     void PrintSolvateInfo() const;
   private:

From 39dec41974b5004d832cadce1ab8589a51783e49 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 8 Jan 2026 14:42:52 -0500
Subject: [PATCH 1195/1492] Add code doc, use the text from parmed (has all the
 references)

---
 src/Parm/LJ1264_Params.h | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/src/Parm/LJ1264_Params.h b/src/Parm/LJ1264_Params.h
index 09d02b4717..6e11e3cb05 100644
--- a/src/Parm/LJ1264_Params.h
+++ b/src/Parm/LJ1264_Params.h
@@ -8,6 +8,32 @@ class Topology;
 namespace Cpptraj {
 namespace Parm {
 /// Used to assign LJ 12-6-4 C coefficients
+/** Adds the LENNARD_JONES_CCOEF term for the ion 12-6-4 Lennard-Jones potential
+  * term. If provided, the mask will allow you to specify which ions. If not
+  * provided, :ZN will be used for the mask by default. The C4 parameter between
+  * the ion and water can either be taken from the references for the requested
+  * [watermodel] (TIP3P, TIP4PEW, SPCE, OPC3, OPC, FB3, and FB4) or provided in
+  * the file specified by the c4file keyword. The polarizabilities must be
+  * present in the the polfile file. The chemical symbol of the element will be
+  * used to determine the atom type.
+  * Parameters are expected in a file with 2 columns:
+  *     <atom type>   <parameter>
+
+  * All defaults come from Ref. [1], [2], [3], [4], [5] and [6]
+
+  * [1] Pengfei Li and Kenneth M. Merz, J. Chem. Theory Comput., 2014, 10,
+  *     289-297.
+  * [2] Pengfei Li, Lin F. Song and Kenneth M. Merz, J. Phys. Chem. B, 2015,
+  *     119, 883-895.
+  * [3] Pengfei Li, Lin F. Song and Kenneth M. Merz, J. Chem. Theory Comput.,
+  *     2015, 11, 1645-1657.
+  * [4] Zhen Li, Lin Frank Song, Pengfei Li, and Kenneth M. Merz Jr. J. Chem.
+  *     Theory Comput., 2020, 16, 4429-4442.
+  * [5] Arkajyoti Sengupta, Zhen Li, Lin Frank Song, Pengfei Li, and Kenneth M.
+  *     Merz Jr., J. Chem. Inf. Model., 2021, 61, 869-880.
+  * [6] Zhen Li, Lin Frank Song, Pengfei Li, and Kenneth M. Merz Jr. J. Chem.
+  *     Theory Comput., 2021, 17, 2342-2354.
+  */
 class LJ1264_Params {
   public:
     LJ1264_Params();

From f75347748cbbeed93ef66504715b0d49ab0303d4 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 9 Jan 2026 08:38:30 -0500
Subject: [PATCH 1196/1492] Add debug level

---
 src/Exec_Build.cpp         |  2 +-
 src/Parm/LJ1264_Params.cpp | 12 ++++++++----
 src/Parm/LJ1264_Params.h   |  5 +++--
 3 files changed, 12 insertions(+), 7 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 3d8b8e63b1..2e8e6e9929 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -1035,7 +1035,7 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
       mprintf("Warning: Unable to determine water model for LJ 12-6-4. Using TIP3P.\n");
       wm = Cpptraj::Parm::TIP3P;
     }
-    if (lj1264.Init_LJ1264(lj1264mask, c4file, wm, polfile, tunfactor)) {
+    if (lj1264.Init_LJ1264(lj1264mask, c4file, wm, polfile, tunfactor, debug_)) {
       mprinterr("Error: Init of LJ 12-6-4 failed.\n");
       return CpptrajState::ERR;
     }
diff --git a/src/Parm/LJ1264_Params.cpp b/src/Parm/LJ1264_Params.cpp
index acdcfc76f3..70a26094c8 100644
--- a/src/Parm/LJ1264_Params.cpp
+++ b/src/Parm/LJ1264_Params.cpp
@@ -17,9 +17,11 @@ const double LJ1264_Params::DEFAULT_WATER_POL_ = 1.444; ///< Polarizability of w
 LJ1264_Params::LJ1264_Params() :
   waterModel_(UNKNOWN_WATER_MODEL),
   tunfactor_(1.0),
-  WATER_POL_(DEFAULT_WATER_POL_)
+  WATER_POL_(DEFAULT_WATER_POL_),
+  debug_(0)
 {}
 
+// ----- WATER MODEL LJC PARAMETERS GO HERE ------------------------------------
 void LJ1264_Params::set_tip3p_params() {
   c4params_.insert( NameMapPair("Li1", 27.0) );
   c4params_.insert( NameMapPair("Na1", 0.0) );
@@ -405,14 +407,15 @@ void LJ1264_Params::set_fb4_params() {
   c4params_.insert( NameMapPair("Th4", 601.0) );
 }
 
-/** Set up C4 parameters for given water model */
+// -----------------------------------------------------------------------------
+
+/** Set up default C4 parameters for given water model */
 void LJ1264_Params::setupForWaterModel(WaterModelType wmIn)
 {
   if (wmIn == waterModel_) return;
   c4params_.clear();
   waterModel_ = wmIn;
 
-
   switch (waterModel_) {
     case UNKNOWN_WATER_MODEL : return;
     case TIP3P   : set_tip3p_params(); break;
@@ -473,8 +476,9 @@ int LJ1264_Params::read_c4(std::string const& c4file)
 
 /** Initialize */
 int LJ1264_Params::Init_LJ1264(std::string const& maskIn, std::string const& c4fileIn, WaterModelType wmIn,
-                              std::string const& polfileIn, double tunfactorIn)
+                              std::string const& polfileIn, double tunfactorIn, int debugIn)
 {
+  debug_ = debugIn;
   tunfactor_ = tunfactorIn;
 
   if (maskIn.empty())
diff --git a/src/Parm/LJ1264_Params.h b/src/Parm/LJ1264_Params.h
index 6e11e3cb05..070f62cb2a 100644
--- a/src/Parm/LJ1264_Params.h
+++ b/src/Parm/LJ1264_Params.h
@@ -37,8 +37,8 @@ namespace Parm {
 class LJ1264_Params {
   public:
     LJ1264_Params();
-    /// Init - mask, c4 file, water model, polarization file, tuning factor
-    int Init_LJ1264(std::string const&, std::string const&, WaterModelType, std::string const&, double);
+    /// Init - mask, c4 file, water model, polarization file, tuning factor, debug
+    int Init_LJ1264(std::string const&, std::string const&, WaterModelType, std::string const&, double, int);
     /// Assign Topology with LJ 12-6-4 params
     int AssignLJ1264(Topology&);
 
@@ -71,6 +71,7 @@ class LJ1264_Params {
     double tunfactor_; ///< Tuning factor
     double WATER_POL_; ///< Polarizability of water
     AtomMask mask_; ///< Mask for selecting metal centers
+    int debug_;
 };
 }
 }

From 023284ced61d00fab62e908ee14fa291c39aa622 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 9 Jan 2026 08:43:38 -0500
Subject: [PATCH 1197/1492] Hide debug info. Clean up output

---
 src/Parm/LJ1264_Params.cpp | 30 +++++++++++++++++++-----------
 1 file changed, 19 insertions(+), 11 deletions(-)

diff --git a/src/Parm/LJ1264_Params.cpp b/src/Parm/LJ1264_Params.cpp
index 70a26094c8..d2d2849bd0 100644
--- a/src/Parm/LJ1264_Params.cpp
+++ b/src/Parm/LJ1264_Params.cpp
@@ -427,7 +427,7 @@ void LJ1264_Params::setupForWaterModel(WaterModelType wmIn)
     case FB4     : set_fb4_params(); break;
   }
 
-  mprintf("\tUsing default C4 parameters for %s\n", WaterModelStr(waterModel_));
+  mprintf("\t  Using default C4 parameters for %s\n", WaterModelStr(waterModel_));
 }
 
 /** Read a 2 column file with format <name> <value> */
@@ -462,14 +462,14 @@ int LJ1264_Params::read_2col_file(std::string const& infileName, NameMapType& ma
 /** Read polarizabilities. */
 int LJ1264_Params::read_pol(std::string const& polfile)
 {
-  mprintf("\tReading atomic polarizabilities from '%s'\n", polfile.c_str());
+  mprintf("\t  Reading atomic polarizabilities from '%s'\n", polfile.c_str());
   return read_2col_file(polfile, pol_);
 }
 
 /** Read C4 params */
 int LJ1264_Params::read_c4(std::string const& c4file)
 {
-  mprintf("\tReading C4 parameters from '%s'\n", c4file.c_str());
+  mprintf("\t  Reading C4 parameters from '%s'\n", c4file.c_str());
   waterModel_ = UNKNOWN_WATER_MODEL;
   return read_2col_file(c4file, c4params_);
 }
@@ -478,8 +478,10 @@ int LJ1264_Params::read_c4(std::string const& c4file)
 int LJ1264_Params::Init_LJ1264(std::string const& maskIn, std::string const& c4fileIn, WaterModelType wmIn,
                               std::string const& polfileIn, double tunfactorIn, int debugIn)
 {
+  mprintf("\tLJ 12-6-4 Init\n");
   debug_ = debugIn;
   tunfactor_ = tunfactorIn;
+  mprintf("\t  LJ 12-6-4 tuning factor: %g\n", tunfactor_);
 
   if (maskIn.empty())
     mask_.SetMaskString(":ZN");
@@ -489,7 +491,7 @@ int LJ1264_Params::Init_LJ1264(std::string const& maskIn, std::string const& c4f
       return 1;
     }
   }
-  mprintf("\tLJ 12-6-4 mask: %s\n", mask_.MaskString());
+  mprintf("\t  LJ 12-6-4 mask: %s\n", mask_.MaskString());
 
   if (c4fileIn.empty())
     setupForWaterModel( wmIn );
@@ -534,14 +536,14 @@ int LJ1264_Params::AssignLJ1264(Topology& topOut)
     return 1;
   }
   if (topOut.SetupIntegerMask( mask_ )) {
-    mprinterr("Error: Could not set up mask '%s'\n", mask_.MaskString());
+    mprinterr("Error: Could not set up LJ 12-6-4 mask '%s'\n", mask_.MaskString());
     return 1;
   }
-  mprintf("\t  Mask selection: ");
+  mprintf("\t  LJ 12-6-4 mask selection: ");
   mask_.BriefMaskInfo();
   mprintf("\n");
   if (mask_.None()) {
-    mprintf("Warning: Nothing selected by mask '%s'\n", mask_.MaskString());
+    mprintf("Warning: Nothing selected by LJ 12-6-4 mask '%s'\n", mask_.MaskString());
     return 0;
   }
 
@@ -581,7 +583,9 @@ int LJ1264_Params::AssignLJ1264(Topology& topOut)
     // Save the type index/C4 param pair
     idxC4Map.insert( IdxParamMapPair(typeIdx, c4it->second) );
 
-    mprintf("DEBUG: %s : idx=%i  chg=%i  ename=%s  C4=%g\n", topOut.AtomMaskName(*at).c_str(), typeIdx, iCharge, ename.c_str(), c4it->second);
+    if (debug_ > 0)
+       mprintf("DEBUG: %s : idx=%i  chg=%i  ename=%s  C4=%g\n", topOut.AtomMaskName(*at).c_str(),
+               typeIdx, iCharge, ename.c_str(), c4it->second);
   }
   mprintf("\t  %zu unique C4 parameters for atoms selected by '%s'\n", idxC4Map.size(), mask_.MaskString());
 
@@ -628,7 +632,8 @@ int LJ1264_Params::AssignLJ1264(Topology& topOut)
       }
     } else {
       // New polarization
-      mprintf("DEBUG: idx= %i  type= %s  pol= %g\n", typeIdx, *(ATM.Type()), polit->second);
+      if (debug_ > 0)
+        mprintf("DEBUG: idx= %i  type= %s  pol= %g\n", typeIdx, *(ATM.Type()), polit->second);
       idxPol[typeIdx].typeName_ = ATM.Type();
       idxPol[typeIdx].pol_ = polit->second;
       //idxPolMap.insert( IdxParamMapPair(typeIdx, polit->second) );
@@ -647,7 +652,9 @@ int LJ1264_Params::AssignLJ1264(Topology& topOut)
       int ljidx = topOut.Nonbond().GetLJindex( it->first, jidx );
       //IdxParamMapType::const_iterator jt = idxPolMap.find( jidx );
       TypePol const& POL = idxPol[jidx];
-      mprintf("DEBUG: Type1= %i  C4= %g  Type2= %i  NBidx= %i  Pol= %g\n", it->first, it->second, jidx, ljidx, POL.pol_);
+      if (debug_ > 0)
+        mprintf("DEBUG: Type1= %i  C4= %g  Type2= %i  NBidx= %i  Pol= %g\n", it->first, it->second,
+                jidx, ljidx, POL.pol_);
       if (ljidx < 0) {
         mprinterr("Error: Type pair %i -- %i is an LJ 10-12 pair, not LJ 6-12.\n", it->first, jidx);
         return 1;
@@ -660,7 +667,8 @@ int LJ1264_Params::AssignLJ1264(Topology& topOut)
       else
         // There are two C4 terms that need to add together between two different ions
         ljc = topOut.Nonbond().LJC_Array( ljidx ) + (it->second / WATER_POL_ * POL.pol_ * tunfactor_);
-      mprintf("DEBUG:\t\tFinal LJC = %g\n", ljc);
+      if (debug_ > 0)
+        mprintf("DEBUG:\t\tFinal LJC = %g\n", ljc);
       topOut.SetNonbond().SetLJC( ljidx, ljc );
     } // END loop over all atom types indices
   } // END loop over all metal type indices

From 76e7737098063b7a2811577b02fd9ba1d4ee6d31 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 9 Jan 2026 09:15:45 -0500
Subject: [PATCH 1198/1492] Clean up output. Do total system charge check

---
 src/Exec_Build.cpp         | 14 ++++++++++++--
 src/Parm/LJ1264_Params.cpp |  2 +-
 src/Structure/Solvate.cpp  | 16 ++++++++++++----
 3 files changed, 25 insertions(+), 7 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 2e8e6e9929..8f74568813 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -19,6 +19,7 @@
 #include "Structure/Sugar.h"
 #include "StructureCheck.h"
 #include <set> // For warning about missing residue templates
+#include <cmath> // fabs, modf
 
 /** CONSTRUCTOR */
 Exec_Build::Exec_Build() :
@@ -884,7 +885,7 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
   Topology topIn = coords.Top(); // FIXME do not work on the copy, work on the top itself
 
   std::string solventResName = argIn.GetStringKey("solventresname", "HOH");
-  mprintf("\tSolvent residue name: %s\n", solventResName.c_str());
+  mprintf("\tResidues named '%s' will be recognized as solvent.\n", solventResName.c_str());
 
   enum SolvateModeType { NO_SOLVATE = 0, SOLVATEBOX, SETBOX };
   SolvateModeType add_solvent = NO_SOLVATE;
@@ -1012,7 +1013,6 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
   // LJ 12-6-4
   Cpptraj::Parm::LJ1264_Params lj1264;
   if (argIn.hasKey("lj1264")) {
-    mprintf("\tEnabling LJ 12-6-4 parameters.\n");
     std::string lj1264mask = argIn.GetStringKey("lj1264mask");
     std::string c4file = argIn.GetStringKey("c4file");
     std::string polfile = argIn.GetStringKey("polfile");
@@ -1310,6 +1310,16 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
     t_check_.Stop();
   }
 
+  // Total charge check
+  double totalSystemCharge = crdout.Top().TotalCharge();
+  double q_frac, q_int;
+  q_frac = modf(totalSystemCharge, &q_int);
+  // NOTE: These cutoffs are the same as in LEaP
+  if ( fabs(q_frac) > 0.01 )
+   mprintf("Warning: The charge of the system (%f) is not integral.\n", totalSystemCharge);
+  if ( fabs(totalSystemCharge) > 0.01 )
+    mprintf("Warning: The charge of the system (%f) is not zero.\n", totalSystemCharge);
+
   if (!outputTopologyName.empty()) {
     ParmFile pfile;
     if (pfile.WriteTopology(crdout.Top(), outputTopologyName, argIn, ParmFile::UNKNOWN_PARM, debug_)) {
diff --git a/src/Parm/LJ1264_Params.cpp b/src/Parm/LJ1264_Params.cpp
index d2d2849bd0..b3b314e51c 100644
--- a/src/Parm/LJ1264_Params.cpp
+++ b/src/Parm/LJ1264_Params.cpp
@@ -478,7 +478,7 @@ int LJ1264_Params::read_c4(std::string const& c4file)
 int LJ1264_Params::Init_LJ1264(std::string const& maskIn, std::string const& c4fileIn, WaterModelType wmIn,
                               std::string const& polfileIn, double tunfactorIn, int debugIn)
 {
-  mprintf("\tLJ 12-6-4 Init\n");
+  mprintf("\tEnabling LJ 12-6-4 parameters.\n");
   debug_ = debugIn;
   tunfactor_ = tunfactorIn;
   mprintf("\t  LJ 12-6-4 tuning factor: %g\n", tunfactor_);
diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index 705b182c9f..6d23f2d6f6 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -103,10 +103,18 @@ int Solvate::InitSetbox(ArgList& argIn, int debugIn) {
 
 /** Print info to stdout */
 void Solvate::PrintSolvateInfo() const {
-  mprintf("\tSolvent buffer XYZ: %g %g %g Ang.\n", bufferX_, bufferY_, bufferZ_);
-  mprintf("\tSolvent closeness: %g Ang.\n", closeness_);
-  // FIXME improve output
-  mprintf("\tSolvent isotropic=%i  clip=%i  center_=%i  oct=%i\n", (int)isotropic_, (int)clip_, (int)center_, (int)doTruncatedOct_);
+  if (doTruncatedOct_)
+    mprintf("\tAdding solvent from %s using a truncated octahedral unit cell.\n", solventBoxName_.c_str());
+  else
+    mprintf("\tAdding solvent from %s using an orthorhombic unit cell.\n", solventBoxName_.c_str());
+  mprintf("\t  Solvent buffer XYZ: %g %g %g Ang.\n", bufferX_, bufferY_, bufferZ_);
+  mprintf("\t  Solvent closeness: %g Ang.\n", closeness_);
+  if (isotropic_)
+    mprintf("\t  Solute will be centered at the origin and principal-aligned before solvating.\n");
+  if (clip_)
+    mprintf("\t  Solvent outside the primary unit cell will be removed.\n");
+  if (center_)
+    mprintf("\t  Final system will be centered at box center after solvation.\n");
 } 
 
 /** Get solvent unit box from DataSetList */

From cabd93f021b3e62fc77e2c6a00e4d3438e40eb6e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 9 Jan 2026 09:27:45 -0500
Subject: [PATCH 1199/1492] CLean up solvate output

---
 src/Box.cpp               |  9 +++++++--
 src/Box.h                 |  4 +++-
 src/Exec_Build.cpp        |  2 +-
 src/Structure/Solvate.cpp | 38 +++++++++++++++++++-------------------
 4 files changed, 30 insertions(+), 23 deletions(-)

diff --git a/src/Box.cpp b/src/Box.cpp
index d7d67793eb..327d175fad 100644
--- a/src/Box.cpp
+++ b/src/Box.cpp
@@ -311,10 +311,15 @@ void Box::SetNoBox() {
   cellVolume_ = 0;
 }
 
+/** Print box info to STDOUT preceded by text. */
+void Box::PrintInfo(const char* desc) const {
+  mprintf("%sBox: '%s' XYZ= { %8.3f %8.3f %8.3f } ABG= { %6.2f %6.2f %6.2f }\n", desc,
+          CellShapeName(), box_[0], box_[1], box_[2], box_[3], box_[4], box_[5]);
+}
+
 /** Print box info to STDOUT. */
 void Box::PrintInfo() const {
-  mprintf("\tBox: '%s' XYZ= { %8.3f %8.3f %8.3f } ABG= { %6.2f %6.2f %6.2f }\n",
-          CellShapeName(), box_[0], box_[1], box_[2], box_[3], box_[4], box_[5]);
+  PrintInfo("\t");
 }
 
 // -----------------------------------------------------------------------------
diff --git a/src/Box.h b/src/Box.h
index 5ce56b23cd..b32c2abdf1 100644
--- a/src/Box.h
+++ b/src/Box.h
@@ -69,8 +69,10 @@ class Box {
     /// \return vector containing reciprocal lengths from fractional cell matrix
     Vec3 RecipLengths() const;
 
-    /// Print Box info to STDOUT
+    /// Print Box info to STDOUT preceded by a tab
     void PrintInfo() const;
+    /// Print Box info to STDOUT preceded by given text
+    void PrintInfo(const char*) const;
     /// Print box debug info to stdout
     void PrintDebug(const char*) const;
     /// \return Name of current cell shape
diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 8f74568813..2a15371e8f 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -1187,7 +1187,7 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
       mprinterr("Error: Adding solvent failed.\n");
       return CpptrajState::ERR;
     }
-    mprintf("\tAdded %i residues.\n", topOut.Nres() - initial_nres);
+    mprintf("\t  Added %i solvent residues.\n", topOut.Nres() - initial_nres);
     // Since by design the SolvateBox routine ensures solvent does not
     // clash with solute, just check the solute.
     checkMaskString.assign( "@1-" + integerToString(initial_natom) );
diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index 6d23f2d6f6..77468bf0dd 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -296,24 +296,24 @@ int Solvate::SetVdwBoundingBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm:
     mprinterr("Error: Setting vdw bounding box for %s failed.\n", topOut.c_str());
     return 1;
   }
-  mprintf("  Solute vdw bounding box:              %-5.3f %-5.3f %-5.3f\n", boxX, boxY, boxZ);
+  mprintf("\t  Solute vdw bounding box:              %-5.3f %-5.3f %-5.3f\n", boxX, boxY, boxZ);
 
   double dXWidth = boxX + bufferX_ * 2;
   double dYWidth = boxY + bufferY_ * 2;
   double dZWidth = boxZ + bufferZ_ * 2;
 
-    mprintf("  Total bounding box for atom centers:  %5.3f %5.3f %5.3f\n", 
+    mprintf("\t  Total bounding box for atom centers:  %5.3f %5.3f %5.3f\n", 
             dXWidth, dYWidth, dZWidth );
 
   // Setup box
   frameOut.ModifyBox().SetupFromXyzAbg(boxX, boxY, boxZ, 90.0, 90.0, 90.0);
   frameOut.BoxCrd().PrintInfo();
   topOut.SetParmBox( frameOut.BoxCrd() );
-  mprintf("  Total vdw box size:%s%5.3f %5.3f %5.3f angstroms.\n", "                   ",
+  mprintf("\t  Total vdw box size:%s%5.3f %5.3f %5.3f angstroms.\n", "                   ",
           frameOut.BoxCrd().Param(Box::X),
           frameOut.BoxCrd().Param(Box::Y),
           frameOut.BoxCrd().Param(Box::Z));
-  mprintf("  Volume: %5.3lf A^3\n", frameOut.BoxCrd().CellVolume());
+  mprintf("\t  Volume: %5.3f A^3\n", frameOut.BoxCrd().CellVolume());
   return 0;
 }
 
@@ -388,13 +388,13 @@ void Solvate::octBoxCheck(Frame const& frameOut) {
   dTmp = dMax + dPBuf[3];
   if ( dTmp <= dBmax ) {
     if ( dPBuf[3] == 0.0 )
-      mprintf("  (Diagonal clearance is %f)\n", dMax );
+      mprintf("\t  (Diagonal clearance is %f)\n", dMax );
     return;
   }
 
   //  not satisfied: scale up box
   dTmp /= dBmax;
-  mprintf("  Scaling up box by a factor of %f to meet diagonal cut criterion\n", dTmp );
+  mprintf("\t  Scaling up box by a factor of %f to meet diagonal cut criterion\n", dTmp );
 
   bufferX_ *= dTmp;
   bufferY_ *= dTmp;
@@ -478,7 +478,7 @@ int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::Parame
   // Check if buffers need to be increased for trunc oct.
   if (doTruncatedOct_)
     octBoxCheck( frameOut );
-  mprintf("  Solute vdw bounding box:              %-5.3f %-5.3f %-5.3f\n", boxX, boxY, boxZ);
+  mprintf("\t  Solute vdw bounding box:              %-5.3f %-5.3f %-5.3f\n", boxX, boxY, boxZ);
 
   double dXWidth = boxX + bufferX_ * 2;
   double dYWidth = boxY + bufferY_ * 2;
@@ -493,9 +493,9 @@ int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::Parame
 
     dTemp = (dMax * dMax * dMax - dTemp ) / dTemp;
 
-    mprintf("  Total bounding box for atom centers:  %5.3f %5.3f %5.3f\n", 
+    mprintf("\t  Total bounding box for atom centers:  %5.3f %5.3f %5.3f\n", 
             dXWidth, dYWidth, dZWidth );
-    mprintf("      (box expansion for 'iso' is %5.1lf%%)\n", dTemp * 100.0 );
+    mprintf("\t      (box expansion for 'iso' is %5.1lf%%)\n", dTemp * 100.0 );
 
      // To make the actual clip right, 'iso' the solute box
     dTemp = std::max(boxX, boxY);
@@ -503,7 +503,7 @@ int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::Parame
     //dXBox = dYBox = dZBox = dTemp;
     boxX = boxY = boxZ = dTemp;
   } else
-    mprintf("  Total bounding box for atom centers:  %5.3f %5.3f %5.3f\n", 
+    mprintf("\t  Total bounding box for atom centers:  %5.3f %5.3f %5.3f\n", 
             dXWidth, dYWidth, dZWidth );
 
   if (clip_) {
@@ -539,7 +539,7 @@ int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::Parame
       return 1;
     }
   }
-  mprintf("  Solvent unit box:                     %5.3f %5.3f %5.3f\n", solventX, solventY, solventZ);
+  mprintf("\t  Solvent unit box:                     %5.3f %5.3f %5.3f\n", solventX, solventY, solventZ);
 
   // See how many solvent boxes required in each dimension
 
@@ -594,13 +594,13 @@ int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::Parame
   }
   //mprintf("Max: %f %f %f\n", boxX, boxY, boxZ);
   frameOut.ModifyBox().SetupFromXyzAbg(boxX, boxY, boxZ, boxBeta, boxBeta, boxBeta);
-  frameOut.BoxCrd().PrintInfo();
+  frameOut.BoxCrd().PrintInfo("\t  ");
   topOut.SetParmBox( frameOut.BoxCrd() );
-  mprintf("  Total vdw box size:%s%5.3f %5.3f %5.3f angstroms.\n", "                   ",
-          frameOut.BoxCrd().Param(Box::X),
-          frameOut.BoxCrd().Param(Box::Y),
-          frameOut.BoxCrd().Param(Box::Z));
-  mprintf("  Volume: %5.3lf A^3\n", frameOut.BoxCrd().CellVolume());
+  //mprintf("\t  Total vdw box size:%s%5.3f %5.3f %5.3f angstroms.\n", "                   ",
+  //        frameOut.BoxCrd().Param(Box::X),
+  //        frameOut.BoxCrd().Param(Box::Y),
+  //        frameOut.BoxCrd().Param(Box::Z));
+  mprintf("\t  Volume: %5.3lf A^3\n", frameOut.BoxCrd().CellVolume());
   // Sum mass
   double sumMass = 0.0;
   for (int at = 0; at < topOut.Natom(); at++) {
@@ -612,7 +612,7 @@ int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::Parame
     }
   }
   if (sumMass > 0.0) {
-    mprintf("  Total mass %5.3f amu,  Density %5.3lf g/cc\n", sumMass, sumMass / (frameOut.BoxCrd().CellVolume() * 0.602204));
+    mprintf("\t  Total mass %5.3f amu,  Density %5.3lf g/cc\n", sumMass, sumMass / (frameOut.BoxCrd().CellVolume() * 0.602204));
   } else {
     mprintf("Warning: Mass could not be determined, so density unknown (i.e. type of all atoms could not be found)\n");
   }
@@ -779,7 +779,7 @@ const
   }
   int NboxesToAdd = numX * numY * numZ;
   int NatomsToAdd = NboxesToAdd * solventTop.Natom();
-  mprintf("  Will add %i solvent boxes, max %i atoms.\n", NboxesToAdd, NatomsToAdd);
+  mprintf("\t  Will add %i solvent boxes, max %i atoms.\n", NboxesToAdd, NatomsToAdd);
   frameOut.IncreaseX( NatomsToAdd );
 
   // Current solvent unit center

From 71d0bca08a0ff1d51335ccb2811648454024e32d Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 9 Jan 2026 11:47:10 -0500
Subject: [PATCH 1200/1492] Clean up add ions output. Fix fractional charge
 check

---
 src/Exec_Build.cpp        | 14 +++++++-------
 src/Structure/AddIons.cpp | 25 ++++++++++++++-----------
 src/Structure/Solvate.cpp |  1 +
 3 files changed, 22 insertions(+), 18 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 2a15371e8f..5736ba4034 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -19,7 +19,7 @@
 #include "Structure/Sugar.h"
 #include "StructureCheck.h"
 #include <set> // For warning about missing residue templates
-#include <cmath> // fabs, modf
+#include <cmath> // fabs
 
 /** CONSTRUCTOR */
 Exec_Build::Exec_Build() :
@@ -1312,13 +1312,13 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
 
   // Total charge check
   double totalSystemCharge = crdout.Top().TotalCharge();
-  double q_frac, q_int;
-  q_frac = modf(totalSystemCharge, &q_int);
+  double absSystemCharge = fabs(totalSystemCharge);
+  double q_frac = fabs( absSystemCharge - (double)(int)(absSystemCharge+0.5) );
   // NOTE: These cutoffs are the same as in LEaP
-  if ( fabs(q_frac) > 0.01 )
-   mprintf("Warning: The charge of the system (%f) is not integral.\n", totalSystemCharge);
-  if ( fabs(totalSystemCharge) > 0.01 )
-    mprintf("Warning: The charge of the system (%f) is not zero.\n", totalSystemCharge);
+  if ( q_frac > 0.01 )
+   mprintf("Warning: The charge of the system is not integral: %f\n", totalSystemCharge);
+  if ( absSystemCharge > 0.01 )
+    mprintf("Warning: The charge of the system is not zero: %f\n", totalSystemCharge);
 
   if (!outputTopologyName.empty()) {
     ParmFile pfile;
diff --git a/src/Structure/AddIons.cpp b/src/Structure/AddIons.cpp
index a8c9bb1fff..58a96b34b9 100644
--- a/src/Structure/AddIons.cpp
+++ b/src/Structure/AddIons.cpp
@@ -66,15 +66,16 @@ int AddIons::InitAddIons(std::string const& ion1nameIn, int Nion1,
 /** Print setup info to stdout */
 void AddIons::PrintAddIonsInfo() const {
   if (ion1name_.empty()) return;
+  mprintf("\tIon info:\n");
   if (Nion1_ < 1)
-    mprintf("\tAdding enough %s ions to neutralize.\n", ion1name_.c_str());
+    mprintf("\t  Adding enough %s ions to neutralize.\n", ion1name_.c_str());
   else
-    mprintf("\tAdding %i %s ions.\n", Nion1_, ion1name_.c_str());
+    mprintf("\t  Adding %i %s ions.\n", Nion1_, ion1name_.c_str());
   if (!ion2name_.empty())
-    mprintf("\tAdding %i %s ions.\n", Nion2_, ion2name_.c_str());
+    mprintf("\t  Adding %i %s ions.\n", Nion2_, ion2name_.c_str());
   if (separation_ > 0.0)
-    mprintf("\tMinimum ion separation is %g Ang.\n", separation_);
-  mprintf("\tIon RNG seed: %i\n", RNG_.Seed());
+    mprintf("\t  Minimum ion separation is %g Ang.\n", separation_);
+  mprintf("\t  Ion RNG seed: %i\n", RNG_.Seed());
 }
 
 /** Get ion unit box from DataSetList. */ // TODO consolidate with Solvate::GetSolventUnit()?
@@ -109,7 +110,7 @@ DataSet_Coords* AddIons::GetIonUnit(std::string const& ionname, DataSetList cons
     }
   }
   if (ionUnit != 0)
-    mprintf("\tIon unit: %s\n", ionUnit->legend());
+    mprintf("\t  Ion unit: %s\n", ionUnit->legend());
   else
     mprinterr("Error: Could not get ion unit named %s\n", ionname.c_str());
 
@@ -143,6 +144,7 @@ int AddIons::AddIonsRand(Topology& topOut, Frame& frameOut, DataSetList const& D
                          Cpptraj::Parm::ParameterSet const& set0)
 const
 {
+  mprintf("\tAdding ions by randomly swapping with solvent.\n");
   // Check that there are solvent molecules.
   int nsolvent = topOut.Nsolvent();
   if (nsolvent < 1) {
@@ -159,7 +161,7 @@ const
     }
     mprintf("Warning: Adding the ions anyway.\n");
   } else {
-    mprintf("\tTotal charge on %s is %g\n", topOut.c_str(), totalCharge);
+    mprintf("\t  Total charge on %s is %g\n", topOut.c_str(), totalCharge);
   }
 
   // Get first ion
@@ -205,7 +207,7 @@ const
     }
     // Get the nearest integer number of ions needed to neutralize the system.
     iIon1 = (int)lrint( fabs(totalCharge) / fabs(chargeIon1) );
-    mprintf("\tNumber of %s ions required to neutralize: %i\n", ion1name_.c_str(), iIon1);
+    mprintf("\t  Number of %s ions required to neutralize: %i\n", ion1name_.c_str(), iIon1);
   }
 
   // Check that there is enough solvent to swap
@@ -252,7 +254,7 @@ const
 
   //VstatArray solventStat(solventMolNums.size(), UNUSED);
 
-  mprintf("  Adding %d counter ions to \"%s\". %d solvent molecules will remain.\n",
+  mprintf("\t  Adding %d counter ions to \"%s\". %d solvent molecules will remain.\n",
           iIon1 + iIon2, topOut.c_str(), (int)topOut.SolventMolNums().size() - iIon1 - iIon2);
 
   typedef std::vector<Vec3> Varray;
@@ -370,8 +372,9 @@ const
     ionFrame.CenterOnPoint( pos, false ); // Use geometric center
     //Vec3 debugVec = ionFrame.VGeometricCenter();
     //debugVec.Print("DEBUG: check ion center");
-    mprintf("  %zu: Placed %s in %s at (%4.2lf, %4.2lf, %4.2lf).\n", iIon1, ionCrd->legend(), topOut.c_str(),
-            pos[0], pos[1], pos[2]);
+    if (debug_ > 0)
+      mprintf("\t  %zu: Placed %s in %s at (%4.2lf, %4.2lf, %4.2lf).\n", iIon1, ionCrd->legend(), topOut.c_str(),
+              pos[0], pos[1], pos[2]);
     if (separation_ > 0.0)
       ionPositions.push_back( pos );
     int ionAtoms0 = topOut.Natom();
diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index 77468bf0dd..8891981770 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -453,6 +453,7 @@ void Solvate::ewald_rotate(Frame& frameOut, double& dPAngle)
 int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::ParameterSet const& set0,
                         DataSet_Coords& SOLVENTBOX)
 {
+  mprintf("\tAdding solvent.\n");
   // Sanity check
   if (topOut.Natom() != frameOut.Natom()) {
     mprinterr("Internal Error: Solvate::SolvateBox(): Topology %s #atoms %i != frame #atoms %i\n",

From c1af1c55d86646e058411caf60b05499799727cf Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 9 Jan 2026 12:45:58 -0500
Subject: [PATCH 1201/1492] No longer assign default bond parameters every
 time. In the structure check routine (where it is really needed) generate Req
 parameters as needed when not present in the incoming topology. Put the
 routine inside Parm/Bond_Params.cpp in case we want to use it in the future

---
 src/Parm/Bond_Params.cpp | 42 ++++++++++++++++++++++++++++++
 src/Parm/Bond_Params.h   | 18 +++++++++++++
 src/Parm/CMakeLists.txt  |  1 +
 src/Parm/parmdepend      |  1 +
 src/Parm/parmfiles       |  1 +
 src/StructureCheck.cpp   | 18 ++++++++-----
 src/StructureCheck.h     |  2 +-
 src/Topology.cpp         | 56 +++-------------------------------------
 src/Topology.h           | 13 ++--------
 src/cpptrajdepend        |  1 +
 10 files changed, 81 insertions(+), 72 deletions(-)
 create mode 100644 src/Parm/Bond_Params.cpp
 create mode 100644 src/Parm/Bond_Params.h

diff --git a/src/Parm/Bond_Params.cpp b/src/Parm/Bond_Params.cpp
new file mode 100644
index 0000000000..af67e03395
--- /dev/null
+++ b/src/Parm/Bond_Params.cpp
@@ -0,0 +1,42 @@
+#include "Bond_Params.h"
+#include "../CpptrajStdio.h"
+#include "../ParameterTypes.h"
+#include "../Topology.h"
+#include <algorithm> // find
+
+/** Create parameters for given bond based on element types. */
+void Cpptraj::Parm::GenerateBondParam(BondParmArray& bondparm, BondType& bnd, BP_mapType& bpMap, std::vector<Atom> const& atoms)
+{
+  unsigned int bp_idx;
+  Atom::AtomicElementType a1Elt = atoms[bnd.A1()].Element();
+  Atom::AtomicElementType a2Elt = atoms[bnd.A2()].Element();
+  std::set<Atom::AtomicElementType> Eset;
+  Eset.insert( a1Elt );
+  Eset.insert( a2Elt );
+  // Has this bond parameter been defined?
+  BP_mapType::iterator bp = std::find(bpMap.begin(), bpMap.end(), Eset);
+  if (bp == bpMap.end()) { // Bond parameter Not defined
+    bp_idx = bondparm.size();
+    bpMap.push_back( Eset );
+    bondparm.push_back( BondParmType(0.0, Atom::GetBondLength(a1Elt, a2Elt)) );
+  } else
+    bp_idx = bp - bpMap.begin();
+  //mprintf("DEBUG:\t\t%i:[%s] -- %i:[%s] Cut=%f BPidx=%u\n",
+  //        bnd.A1()+1, atoms_[bnd.A1()].c_str(), bnd.A2()+1, atoms_[bnd.A2()].c_str(),
+  //        bondparm_[bp_idx].Req(), bp_idx);
+  bnd.SetIdx( bp_idx );
+}
+
+/** Fill in bond parameters based on atomic element types. */
+void Cpptraj::Parm::GenerateBondParameters(Topology& topOut)
+{
+  mprintf("\tDetermining bond length parameters from element types for '%s'.\n", topOut.c_str());
+  BondParmArray& bondparm = topOut.ModifyBondParm();
+  bondparm.clear();
+  // Hold indices into bondparm for unique element pairs
+  BP_mapType bpMap;
+  for (BondArray::iterator bnd = topOut.ModifyBondsH().begin(); bnd != topOut.ModifyBondsH().end(); ++bnd)
+    GenerateBondParam( bondparm, *bnd, bpMap, topOut.Atoms() ); 
+  for (BondArray::iterator bnd = topOut.ModifyBonds().begin();  bnd != topOut.ModifyBonds().end(); ++bnd)
+    GenerateBondParam( bondparm, *bnd, bpMap, topOut.Atoms() );
+}
diff --git a/src/Parm/Bond_Params.h b/src/Parm/Bond_Params.h
new file mode 100644
index 0000000000..423d0e4a9f
--- /dev/null
+++ b/src/Parm/Bond_Params.h
@@ -0,0 +1,18 @@
+#ifndef INC_PARM_BOND_PARAMS_H
+#define INC_PARM_BOND_PARAMS_H
+#include "../Atom.h"
+#include <vector>
+#include <set>
+class Topology;
+class BondType;
+class BondParmArray;
+namespace Cpptraj {
+namespace Parm {
+typedef std::vector< std::set<Atom::AtomicElementType> > BP_mapType;
+/// Generate bond parameters
+void GenerateBondParam(BondParmArray&, BondType&, BP_mapType&, std::vector<Atom> const&);
+/// Used to generate bond parameters (Req only) based on atomic element types.
+void GenerateBondParameters(Topology&);
+}
+}
+#endif
diff --git a/src/Parm/CMakeLists.txt b/src/Parm/CMakeLists.txt
index 7c5d2ae785..c8e8a81c32 100644
--- a/src/Parm/CMakeLists.txt
+++ b/src/Parm/CMakeLists.txt
@@ -1,6 +1,7 @@
 #CMake buildfile for CPPTRAJ Parm subdirectory.
 target_sources(cpptraj_common_obj PRIVATE
   ${CMAKE_CURRENT_LIST_DIR}/AssignParams.cpp
+  ${CMAKE_CURRENT_LIST_DIR}/Bond_Params.cpp
   ${CMAKE_CURRENT_LIST_DIR}/GB_Params.cpp
   ${CMAKE_CURRENT_LIST_DIR}/GetParams.cpp
   ${CMAKE_CURRENT_LIST_DIR}/LJ1264_Params.cpp
diff --git a/src/Parm/parmdepend b/src/Parm/parmdepend
index 7ad2488039..cf713aed50 100644
--- a/src/Parm/parmdepend
+++ b/src/Parm/parmdepend
@@ -1,4 +1,5 @@
 AssignParams.o : AssignParams.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/ParmEnum.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/GenerateConnectivityArrays.h ../SymbolExporting.h ../Timer.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h AssignParams.h DihedralParmHolder.h GetParams.h ImproperParmHolder.h ParameterSet.h ParmEnum.h ParmHolder.h
+Bond_Params.o : Bond_Params.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h Bond_Params.h
 GB_Params.o : GB_Params.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h GB_Params.h
 GetParams.o : GetParams.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/ParmEnum.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h DihedralParmHolder.h GetParams.h ImproperParmHolder.h ParameterSet.h ParmEnum.h ParmHolder.h
 LJ1264_Params.o : LJ1264_Params.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../BufferedLine.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../StringRoutines.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h LJ1264_Params.h ParmEnum.h
diff --git a/src/Parm/parmfiles b/src/Parm/parmfiles
index b8bb0e0754..4a8b0492c7 100644
--- a/src/Parm/parmfiles
+++ b/src/Parm/parmfiles
@@ -1,6 +1,7 @@
 # Files for Parm subdirectory.
 PARM_SOURCES= \
   AssignParams.cpp \
+  Bond_Params.cpp \
   GB_Params.cpp \
   GetParams.cpp \
   LJ1264_Params.cpp \
diff --git a/src/StructureCheck.cpp b/src/StructureCheck.cpp
index d9dd1408ab..f2e2546027 100644
--- a/src/StructureCheck.cpp
+++ b/src/StructureCheck.cpp
@@ -125,15 +125,19 @@ int StructureCheck::SetOptions(bool imageOn, bool checkBonds, bool saveProblemsI
   * the mask.
   */
 void StructureCheck::ProcessBondArray(BondArray const& Bonds, BondParmArray const& Parm,
-                                      CharMask const& cMask)
+                                      CharMask const& cMask, std::vector<Atom> const& Atoms)
 {
   for (BondArray::const_iterator bnd = Bonds.begin(); bnd != Bonds.end(); ++bnd)
   {
     if ( cMask.AtomInCharMask(bnd->A1()) && cMask.AtomInCharMask(bnd->A2()) ) {
-      if (bnd->Idx() < 0)
-        mprintf("Warning: Bond parameters not present for atoms %i-%i, skipping.\n",
-                bnd->A1()+1, bnd->A2()+1);
-      else {
+      if (bnd->Idx() < 0) {
+        //mprintf("Warning: Bond parameters not present for atoms %i-%i, skipping.\n",
+        //        bnd->A1()+1, bnd->A2()+1);
+        Atom::AtomicElementType a1Elt = Atoms[bnd->A1()].Element();
+        Atom::AtomicElementType a2Elt = Atoms[bnd->A2()].Element();
+        double Req_off = Atom::GetBondLength(a1Elt, a2Elt);
+        bondList_.push_back( Problem(bnd->A1(), bnd->A2(), Req_off) );
+      } else {
         double Req_off = Parm[ bnd->Idx() ].Req();// + bondoffset_;
         //bondList_.push_back( Problem(bnd->A1(), bnd->A2(), Req_off*Req_off) );
         bondList_.push_back( Problem(bnd->A1(), bnd->A2(), Req_off) );
@@ -146,8 +150,8 @@ void StructureCheck::ProcessBondArray(BondArray const& Bonds, BondParmArray cons
 void StructureCheck::SetupBondList(AtomMask const& iMask, Topology const& top) {
   CharMask cMask( iMask.ConvertToCharMask(), iMask.Nselected() );
  
-  ProcessBondArray(top.Bonds(),  top.BondParm(), cMask);
-  ProcessBondArray(top.BondsH(), top.BondParm(), cMask);
+  ProcessBondArray(top.Bonds(),  top.BondParm(), cMask, top.Atoms());
+  ProcessBondArray(top.BondsH(), top.BondParm(), cMask, top.Atoms());
   // Only look at bonds to heavy atoms for rings
   ringBonds_.clear();
   ringBonds_.reserve( top.Bonds().size() );
diff --git a/src/StructureCheck.h b/src/StructureCheck.h
index fa569f9305..51d4c7f2eb 100644
--- a/src/StructureCheck.h
+++ b/src/StructureCheck.h
@@ -119,7 +119,7 @@ class StructureCheck {
     /// \return mask string based on if extra points are being excluded
     std::string checkMaskStr(std::string const&) const;
     /// Add selected bonds in BondArray to list to be checked.
-    void ProcessBondArray(BondArray const&, BondParmArray const&, CharMask const&);
+    void ProcessBondArray(BondArray const&, BondParmArray const&, CharMask const&, std::vector<Atom> const&);
     /// Add selected bonds in topology to list to be checked.
     void SetupBondList(AtomMask const&, Topology const&);
     /// Check for intersection between bond and ring
diff --git a/src/Topology.cpp b/src/Topology.cpp
index a86caa9136..4fb8e963ae 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -1,4 +1,4 @@
-#include <algorithm> // find, copy, fill
+#include <algorithm> // copy, fill
 #include <stack> // For large system molecule search
 #include "Topology.h"
 #include "AtomMask.h"
@@ -599,24 +599,12 @@ const
   return false;
 }
 
-// Topology::CommonSetup()
-/** Set up common to all topologies. Assign bond lengths if none are present.
-  * \param molsearch If true, determine molecules based on bond info.
-  * \param renumberResidues If true, renumber residues if any residue is part of more than 1 molecule
-  *        e.g. when alternate locations are present.
-  */
-int Topology::CommonSetup(bool molsearch, bool renumberResidues)
-{
-  return CommonSetup(molsearch, renumberResidues, true);
-}
-
 /** Set up common to all topologies.
   * \param molsearch If true, determine molecules based on bond info.
   * \param renumberResidues If true, renumber residues if any residue is part of more than 1 molecule
   *        e.g. when alternate locations are present.
-  * \param assignBondParm If true, assign default bond lengths if no parameters present.
   */
-int Topology::CommonSetup(bool molsearch, bool renumberResidues, bool assignBondParm)
+int Topology::CommonSetup(bool molsearch, bool renumberResidues)
 {
   // Check the size of any "extra" arrays
   if (CheckExtraSize(tree_.size(), "Amber tree")) return 1;
@@ -626,10 +614,7 @@ int Topology::CommonSetup(bool molsearch, bool renumberResidues, bool assignBond
   if (CheckExtraSize(occupancy_.size(), "PDB occupancy")) return 1;
   if (CheckExtraSize(bfactor_.size(), "PDB Bfactor")) return 1;
   if (CheckExtraSize(pdbSerialNum_.size(), "PDB serial #")) return 1;
-  // TODO: Make bond parm assignment / molecule search optional?
-  // Assign default lengths if necessary (for e.g. CheckStructure)
-  if (assignBondParm && bondparm_.empty())
-    generateBondParameters();
+  // Molecule search
   if (molsearch) {
     // Determine molecule info from bonds
     if (DetermineMolecules())
@@ -865,41 +850,6 @@ int Topology::addBondParm(BondParmArray& bparray, BondParmType const& BPin)
   return pidx;
 }
 
-/** Create parameters for given bond based on element types. */
-void Topology::genBondParam(BondType& bnd, BP_mapType& bpMap)
-{
-  unsigned int bp_idx;
-  Atom::AtomicElementType a1Elt = atoms_[bnd.A1()].Element();
-  Atom::AtomicElementType a2Elt = atoms_[bnd.A2()].Element();
-  std::set<Atom::AtomicElementType> Eset;
-  Eset.insert( a1Elt );
-  Eset.insert( a2Elt );
-  // Has this bond parameter been defined?
-  BP_mapType::iterator bp = std::find(bpMap.begin(), bpMap.end(), Eset);
-  if (bp == bpMap.end()) { // Bond parameter Not defined
-    bp_idx = bondparm_.size();
-    bpMap.push_back( Eset );
-    bondparm_.push_back( BondParmType(0.0, Atom::GetBondLength(a1Elt, a2Elt)) );
-  } else
-    bp_idx = bp - bpMap.begin();
-  //mprintf("DEBUG:\t\t%i:[%s] -- %i:[%s] Cut=%f BPidx=%u\n",
-  //        bnd.A1()+1, atoms_[bnd.A1()].c_str(), bnd.A2()+1, atoms_[bnd.A2()].c_str(),
-  //        bondparm_[bp_idx].Req(), bp_idx);
-  bnd.SetIdx( bp_idx );
-}
-
-/** Fill in bond parameters based on atomic element types. */
-void Topology::generateBondParameters() {
-  mprintf("Warning: Determining bond length parameters from element types for '%s'.\n", c_str());
-  bondparm_.clear();
-  // Hold indices into bondparm for unique element pairs
-  BP_mapType bpMap;
-  for (BondArray::iterator bnd = bondsh_.begin(); bnd != bondsh_.end(); ++bnd)
-    genBondParam( *bnd, bpMap ); 
-  for (BondArray::iterator bnd = bonds_.begin(); bnd != bonds_.end(); ++bnd)
-    genBondParam( *bnd, bpMap );
-} 
-
 // Topology::AddBond()
 void Topology::AddBond(int atom1, int atom2, BondParmType const& BPin) {
   // See if the BondParm exists.
diff --git a/src/Topology.h b/src/Topology.h
index 7dd8dc9514..4ecfd8e505 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -1,7 +1,7 @@
 #ifndef INC_TOPOLOGY_H
 #define INC_TOPOLOGY_H
 #include <string>
-#include <set> // BP_mapType
+#include <set> // AtomDistance 
 #include "Atom.h"
 #include "Residue.h"
 #include "Molecule.h"
@@ -282,9 +282,7 @@ class Topology {
     //void StartNewMol();
     /// Perform common final setup: optional molecule determination, renumber residues by molecules
     int CommonSetup(bool, bool);
-    /// Perform common final setup: optional molecule determination, renumber residues by molecules, assign bond parameters
-    int CommonSetup(bool, bool, bool);
-    /// Perform common final setup with molecule determination on, renumber residues off, assign bond parameters on.
+    /// Perform common final setup with molecule determination on, renumber residues off
     int CommonSetup() { return CommonSetup(true, false); }
     /// Set up with no residue info TODO deprecate in favor of routine in CommonSetup?
     int Setup_NoResInfo();
@@ -329,13 +327,6 @@ class Topology {
   private:
     typedef std::vector<std::string> Sarray;
 
-    //void SetAtomBondInfo(BondArray const&);
-    // NOTE: Use set so that elements are always sorted.
-    typedef std::vector< std::set<Atom::AtomicElementType> > BP_mapType;
-    /// Generate a bond parameter for the given bond based on atom elements
-    void genBondParam(BondType&, BP_mapType&);
-    /// Fill in bond parameters with estimations based on atomic element types
-    void generateBondParameters();
     /// \return Index of existing/added bond parameter in given array
     static inline int addBondParm(BondParmArray&, BondParmType const&);
     /// \return Index of existing/added angle parameter in given array
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index b4b701dac8..96aec7b710 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -431,6 +431,7 @@ Parallel.o : Parallel.cpp Parallel.h
 ParallelNetcdf.o : ParallelNetcdf.cpp CpptrajStdio.h Parallel.h ParallelNetcdf.h
 ParallelSetFrameNum.o : ParallelSetFrameNum.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h ParallelSetFrameNum.h Range.h TextFormat.h
 Parm/AssignParams.o : Parm/AssignParams.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h GuessAtomHybridization.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/../Structure/GenerateConnectivityArrays.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GetParams.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Parm/Bond_Params.o : Parm/Bond_Params.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/Bond_Params.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Parm/GB_Params.o : Parm/GB_Params.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/GB_Params.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Parm/GetParams.o : Parm/GetParams.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/GetParams.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Parm/LJ1264_Params.o : Parm/LJ1264_Params.cpp ArgList.h Atom.h AtomMask.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/LJ1264_Params.h Parm/ParmEnum.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h

From f7086a2bedca500dfbdc8f3b92b6774fcdcf1cef Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 9 Jan 2026 12:46:54 -0500
Subject: [PATCH 1202/1492] CommonSetup interface change

---
 src/DataIO_AmberLib.cpp  | 4 ++--
 src/DataIO_AmberPrep.cpp | 2 +-
 src/Exec_Build.cpp       | 8 ++++----
 src/Exec_Graft.cpp       | 4 ++--
 src/Exec_Sequence.cpp    | 4 ++--
 5 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/src/DataIO_AmberLib.cpp b/src/DataIO_AmberLib.cpp
index 4d032d2995..7bc04c649b 100644
--- a/src/DataIO_AmberLib.cpp
+++ b/src/DataIO_AmberLib.cpp
@@ -270,8 +270,8 @@ class unitEntry {
     void AddBoxVal(double d) { boundbox_.push_back( d ); }
     /// Finish setting up the unit
     int FinishUnit(DataSet_Coords* crd, int debug_) {
-      // Set up topology; determine molecules, but no residue renumber or bond parm determination
-      top_.CommonSetup(true, false, false);
+      // Set up topology; determine molecules, but no residue renumber
+      top_.CommonSetup(true, false);
       if (debug_ > 1) top_.Summary();
       Frame frm;
       frm.SetupFrameV( top_.Atoms(), CoordinateInfo() );
diff --git a/src/DataIO_AmberPrep.cpp b/src/DataIO_AmberPrep.cpp
index 984d95c6de..58f785d0d8 100644
--- a/src/DataIO_AmberPrep.cpp
+++ b/src/DataIO_AmberPrep.cpp
@@ -376,7 +376,7 @@ int DataIO_AmberPrep::readAmberPrep(BufferedLine& infile, DataSetList& dsl, std:
     bondSearch.FindBonds( top, BondSearch::SEARCH_REGULAR, frm, 0.2, debug_ );
   }
   // Set up topology
-  top.CommonSetup(true, false, false);
+  top.CommonSetup(true, false);
   if (debug_ > 0)
     top.Summary();
   if (debug_ > 1)
diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 5736ba4034..1f7f43dc89 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -1167,8 +1167,8 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
   topOut.AllocTreeChainClassification( );
   topOut.AllocJoinArray();
   topOut.AllocRotateArray();
-    // Finalize topology - determine molecules, dont renumber residues, dont assign default bond params
-  topOut.CommonSetup(true, false, false);
+    // Finalize topology - determine molecules, dont renumber residues
+  topOut.CommonSetup(true, false);
 
   // Solvate/add ions
   std::string checkMaskString("*");
@@ -1640,8 +1640,8 @@ int Exec_Build::CleanAndFillStructure(DataSet* inCrdPtr, int tgtframe, std::stri
   topOut.AllocTreeChainClassification( );
   topOut.AllocJoinArray();
   topOut.AllocRotateArray();
-    // Finalize topology - determine molecules, dont renumber residues, dont assign default bond params
-  topOut.CommonSetup(true, false, false);
+    // Finalize topology - determine molecules, dont renumber residues
+  topOut.CommonSetup(true, false);
   topOut.Summary();
   t_assign_.Stop();
 
diff --git a/src/Exec_Graft.cpp b/src/Exec_Graft.cpp
index 23521c06b2..bb8c9b8ada 100644
--- a/src/Exec_Graft.cpp
+++ b/src/Exec_Graft.cpp
@@ -513,8 +513,8 @@ const
     return 1;
   }
 
-  // Finalize topology - determine molecules, dont renumber residues, assign default bond params
-  topOut.CommonSetup(true, false, true);
+  // Finalize topology - determine molecules, dont renumber residues
+  topOut.CommonSetup(true, false);
   topOut.Summary();
   // Add to output data set
   if (outCoords->CoordsSetup(topOut, frameOut.CoordsInfo())) return 1;
diff --git a/src/Exec_Sequence.cpp b/src/Exec_Sequence.cpp
index f3394a6ae4..14e8ce3c36 100644
--- a/src/Exec_Sequence.cpp
+++ b/src/Exec_Sequence.cpp
@@ -212,8 +212,8 @@ const
     }
   }
 
-  // Finalize topology - determine molecules, dont renumber residues, assign default bond params
-  topOut.CommonSetup(true, false, true);
+  // Finalize topology - determine molecules, dont renumber residues
+  topOut.CommonSetup(true, false);
   topOut.Summary();
 
   OUT->CoordsSetup(topOut, frameOut.CoordsInfo());

From 8d4cac0bc32b4a55ffeeaaf244216cdd5379d056 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 9 Jan 2026 14:27:52 -0500
Subject: [PATCH 1203/1492] Add more detailed timing for the fill step

---
 src/Exec_Build.cpp | 8 ++++++--
 src/Exec_Build.h   | 4 +++-
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 1f7f43dc89..5159db90fd 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -51,7 +51,6 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
                                        Topology const& topIn, Frame const& frameIn,
                                        Cpptraj::Structure::Creator const& creator,
                                        std::vector<BondType> const& topInBonds)
-const
 {
   // Array of head/tail connect atoms for each residue
   Iarray resHeadAtoms;
@@ -64,6 +63,7 @@ const
   std::vector<DataSet_Coords*> ResTemplates;
   ResTemplates.reserve( topIn.Nres() );
 
+  t_fill_template_.Start();
   // Initial loop to try to match residues to templates
   int newNatom = 0;
   unsigned int n_no_template_found = 0;
@@ -414,6 +414,7 @@ const
       topOut.AddBond(it->first, it->second);
     }
   } // END loop over source residues
+  t_fill_template_.Stop();
   if (nRefAtomsMissing > 0)
     mprintf("\t%i template atoms missing in source.\n", nRefAtomsMissing);
   if (nAtomsNotInTemplates > 0) {
@@ -661,6 +662,7 @@ const
 
   // -----------------------------------
   // Build using internal coords if needed.
+  t_fill_build_.Start();
   bool buildFailed = false;
   for (Iarray::const_iterator it = AtomOffsets.begin(); it != AtomOffsets.end(); ++it)
   {
@@ -733,6 +735,7 @@ const
       }
     }
   } // END loop over atom offsets
+  t_fill_build_.Stop();
 
   // DEBUG - Print new top/coords
   if (debug_ > 1) {
@@ -1667,5 +1670,6 @@ void Exec_Build::PrintTiming() const {
   t_disulfide_.WriteTiming    (2, "Disulfide detection :", t_total_.Total());
   t_sugar_.WriteTiming        (2, "Sugar preparation   :", t_total_.Total());
   t_fill_.WriteTiming         (2, "Fill missing atoms  :", t_total_.Total());
+  t_fill_template_.WriteTiming(3, "Get template atoms :", t_fill_.Total());
+  t_fill_build_.WriteTiming   (3, "Build atoms        :", t_fill_.Total());
 }
-
diff --git a/src/Exec_Build.h b/src/Exec_Build.h
index 3bde139f43..993fbffacb 100644
--- a/src/Exec_Build.h
+++ b/src/Exec_Build.h
@@ -39,7 +39,7 @@ class Exec_Build : public Exec {
     /// Create new topology/frame using templates
     int FillAtomsWithTemplates(Topology&, Frame&, Topology const&, Frame const&,
                                Cpptraj::Structure::Creator const&,
-                               std::vector<BondType> const&) const;
+                               std::vector<BondType> const&);
     /// Map atoms in topology to template
     static std::vector<int> MapAtomsToTemplate(Topology const&, int, DataSet_Coords*, Cpptraj::Structure::Creator const&, std::vector<NameType>&, int&);
     /// Transfer bonds from old topology to new topology
@@ -61,6 +61,8 @@ class Exec_Build : public Exec {
     Timer t_disulfide_;
     Timer t_sugar_;
     Timer t_fill_;
+    Timer t_fill_template_;
+    Timer t_fill_build_;
     Timer t_assign_;
     Timer t_check_;
     Timer t_solvate_;

From 3c4d51ef660fb15b9fb4f177acdc92d4a6ad72c7 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 9 Jan 2026 16:13:25 -0500
Subject: [PATCH 1204/1492] More timing

---
 src/Exec_Build.cpp | 9 +++++++++
 src/Exec_Build.h   | 3 +++
 2 files changed, 12 insertions(+)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 5159db90fd..82aa2b063c 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -678,6 +678,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
         structureBuilder.SetParameters( creator.MainParmSetPtr() );
       // Generate internals from the template, update indices to this topology.
       DataSet_Coords* resTemplate = ResTemplates[ires];
+      t_fill_build_internals_.Start();
       Frame templateFrame = resTemplate->AllocateFrame();
       resTemplate->GetFrame( 0, templateFrame );
       if (structureBuilder.GenerateInternals(templateFrame, resTemplate->Top(),
@@ -686,9 +687,11 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
         mprinterr("Error: Generate internals for residue template failed.\n");
         return 1;
       }
+      t_fill_build_internals_.Stop();
       structureBuilder.UpdateIndicesWithOffset( *it );
       //mprintf("DEBUG: Residue type: %s terminal\n", Cpptraj::Structure::terminalStr(*termType));
       // Is this residue connected to an earlier residue?
+      t_fill_build_link_.Start();
       for (IParray::const_iterator resBonds = resBondingAtoms[ires].begin();
                                    resBonds != resBondingAtoms[ires].end(); ++resBonds)
       {
@@ -709,16 +712,19 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
           }
         }
       }
+      t_fill_build_link_.Stop();
       // Update internal coords from known positions
       if (structureBuilder.UpdateICsFromFrame( frameOut, topOut, hasPosition )) {
         mprinterr("Error: Failed to update internals with values from existing positions.\n");
         return 1;
       }
+      t_fill_build_build_.Start();
       if (structureBuilder.BuildFromInternals(frameOut, topOut, hasPosition)) {
         mprinterr("Error: Building residue %s failed.\n",
                   topOut.TruncResNameOnumId(ires).c_str());
         buildFailed = true;
       }
+      t_fill_build_build_.Stop();
     } else {
       // All atoms present. Just connect
       // Is this residue connected to an earlier residue?
@@ -1672,4 +1678,7 @@ void Exec_Build::PrintTiming() const {
   t_fill_.WriteTiming         (2, "Fill missing atoms  :", t_total_.Total());
   t_fill_template_.WriteTiming(3, "Get template atoms :", t_fill_.Total());
   t_fill_build_.WriteTiming   (3, "Build atoms        :", t_fill_.Total());
+  t_fill_build_internals_.WriteTiming(4, "Internals :", t_fill_build_.Total());
+  t_fill_build_build_.WriteTiming    (4, "Build     :", t_fill_build_.Total());
+  t_fill_build_link_.WriteTiming     (4, "Link      :", t_fill_build_.Total());
 }
diff --git a/src/Exec_Build.h b/src/Exec_Build.h
index 993fbffacb..7f98aff403 100644
--- a/src/Exec_Build.h
+++ b/src/Exec_Build.h
@@ -63,6 +63,9 @@ class Exec_Build : public Exec {
     Timer t_fill_;
     Timer t_fill_template_;
     Timer t_fill_build_;
+    Timer t_fill_build_internals_;
+    Timer t_fill_build_build_;
+    Timer t_fill_build_link_;
     Timer t_assign_;
     Timer t_check_;
     Timer t_solvate_;

From 62b2dc08b496ed1268acbc64fb49bb2e08c8ead1 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 9 Jan 2026 22:24:46 -0500
Subject: [PATCH 1205/1492] When generating links around internals in the build
 command, keep track of what residue we are at so we dont have to keep setting
 the array up - becomes a bottleneck at higher atom counts.

---
 src/Exec_Build.cpp        | 14 ++++++++++++-
 src/Exec_Build.h          |  1 +
 src/Structure/Builder.cpp | 42 ++++++++++++++++++++++++++++++++++-----
 src/Structure/Builder.h   |  9 +++++++++
 4 files changed, 60 insertions(+), 6 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 82aa2b063c..406eea3033 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -664,6 +664,8 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
   // Build using internal coords if needed.
   t_fill_build_.Start();
   bool buildFailed = false;
+  Cpptraj::Structure::Builder::Barray tmpHasPosition(topOut.Natom(), false);
+  int nextTempHasPositionStart = 0;
   for (Iarray::const_iterator it = AtomOffsets.begin(); it != AtomOffsets.end(); ++it)
   {
     long int ires = it-AtomOffsets.begin();
@@ -700,10 +702,18 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
             mprintf("\t\tResidue connection: %s - %s\n",
                     topOut.AtomMaskName(resBonds->first).c_str(),
                     topOut.AtomMaskName(resBonds->second).c_str());
+          t_fill_build_link_bond_.Start();
           topOut.AddBond(resBonds->first, resBonds->second);
+          t_fill_build_link_bond_.Stop();
           // Generate internals around the link
+          Residue const& R0 = topIn.Res(topOut[resBonds->first].ResNum());
+          for (int at = nextTempHasPositionStart; at < R0.FirstAtom(); at++)
+            tmpHasPosition[at] = true;
+          nextTempHasPositionStart = R0.FirstAtom();
+
           if (structureBuilder.GenerateInternalsAroundLink(resBonds->first, resBonds->second,
-                                                            frameOut, topOut, hasPosition, Cpptraj::Structure::Builder::BUILD))
+                                                           frameOut, topOut, hasPosition, Cpptraj::Structure::Builder::BUILD,
+                                                           tmpHasPosition))
           {
             mprinterr("Error: Assign torsions around inter-residue link %s - %s failed.\n",
                       topOut.AtomMaskName(resBonds->first).c_str(),
@@ -1681,4 +1691,6 @@ void Exec_Build::PrintTiming() const {
   t_fill_build_internals_.WriteTiming(4, "Internals :", t_fill_build_.Total());
   t_fill_build_build_.WriteTiming    (4, "Build     :", t_fill_build_.Total());
   t_fill_build_link_.WriteTiming     (4, "Link      :", t_fill_build_.Total());
+  t_fill_build_link_bond_.WriteTiming(5, "Link Bond :", t_fill_build_link_.Total());
+  Cpptraj::Structure::Builder::PrintTiming(5, t_fill_build_link_.Total());
 }
diff --git a/src/Exec_Build.h b/src/Exec_Build.h
index 7f98aff403..c0b557f015 100644
--- a/src/Exec_Build.h
+++ b/src/Exec_Build.h
@@ -66,6 +66,7 @@ class Exec_Build : public Exec {
     Timer t_fill_build_internals_;
     Timer t_fill_build_build_;
     Timer t_fill_build_link_;
+    Timer t_fill_build_link_bond_;
     Timer t_assign_;
     Timer t_check_;
     Timer t_solvate_;
diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 16a497240b..548a314a7d 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -17,6 +17,10 @@
 using namespace Cpptraj::Structure;
 using namespace Cpptraj::Parm;
 
+Timer Builder::timeg_builder_IALsetup_ = Timer();
+Timer Builder::timeg_builder_IALgen_ = Timer();
+Timer Builder::timeg_builder_IALspan_ = Timer();
+
 /** CONSTRUCTOR */
 Builder::Builder() :
   debug_(0),
@@ -1592,7 +1596,20 @@ int Builder::generateAtomInternals(int at, Frame const& frameIn, Topology const&
 
   return 0;
 }
- 
+
+int Builder::GenerateInternalsAroundLink(int at0, int at1,
+                                         Frame const& frameIn, Topology const& topIn,
+                                         Barray const& hasPosition,
+                                         BuildType btype)
+{
+  Atom const& A0 = topIn[at0];
+  Residue const& R0 = topIn.Res(A0.ResNum());
+  Barray tmpHasPosition( topIn.Natom(), false );
+  for (int at = 0; at < R0.FirstAtom(); at++)
+    tmpHasPosition[at] = true;
+  return GenerateInternalsAroundLink(at0, at1, frameIn, topIn, hasPosition, btype, tmpHasPosition);
+}
+
 /** Generate internal coordinates around a bond linking two residues
   * in the same manner as LEaP.
   * \param zmatrix Hold output ICs
@@ -1602,12 +1619,14 @@ int Builder::generateAtomInternals(int at, Frame const& frameIn, Topology const&
 int Builder::GenerateInternalsAroundLink(int at0, int at1,
                                          Frame const& frameIn, Topology const& topIn,
                                          Barray const& hasPosition,
-                                         BuildType btype)
+                                         BuildType btype,
+                                         Barray const& tmpHasPosition)
 {
   if (debug_ > 0) {
     mprintf("DEBUG: ----- Entering Builder::GenerateInternalsAroundLink. -----\n");
     mprintf("DEBUG: Link: %s to %s\n", topIn.AtomMaskName(at0).c_str(), topIn.AtomMaskName(at1).c_str());
   }
+  timeg_builder_IALsetup_.Start();
   // Sanity check
   Atom const& A0 = topIn[at0];
   Atom const& A1 = topIn[at1];
@@ -1619,9 +1638,10 @@ int Builder::GenerateInternalsAroundLink(int at0, int at1,
   // this residue as having position, and all other atoms as not having
   // position.
   Residue const& R0 = topIn.Res(A0.ResNum());
-  Barray tmpHasPosition( topIn.Natom(), false );
-  for (int at = 0; at < R0.FirstAtom(); at++)
-    tmpHasPosition[at] = true;
+  //Barray tmpHasPosition( topIn.Natom(), false );
+  //for (int at = nextTempHasPositionStart_; at < R0.FirstAtom(); at++)
+  //  tmpHasPosition_[at] = true;
+  //nextTempHasPositionStart_ = R0.FirstAtom();
   // Create spanning tree across the link
   int actualAt1;
   if (btype == BUILD)
@@ -1630,7 +1650,11 @@ int Builder::GenerateInternalsAroundLink(int at0, int at1,
   else
     // Only want the 'forward' tree
     actualAt1 = at1;
+  timeg_builder_IALsetup_.Stop();
+  timeg_builder_IALspan_.Start();
   Iarray span_atoms = GenerateSpanningTree(at0, actualAt1, 4, topIn.Atoms());
+  timeg_builder_IALspan_.Stop();
+  timeg_builder_IALgen_.Start();
   for (Iarray::const_iterator it = span_atoms.begin(); it != span_atoms.end(); ++it)
   {
     //mprintf("SPANNING TREE ATOM: %s\n", *(topIn[*it].Name()));
@@ -1655,9 +1679,17 @@ int Builder::GenerateInternalsAroundLink(int at0, int at1,
   }
   if (debug_ > 0)
     mprintf("DEBUG: ----- Leaving Builder::GenerateInternalsAroundLink. -----\n");
+  timeg_builder_IALgen_.Stop();
   return 0;
 }
 
+void Builder::PrintTiming(int indent, double total)
+{
+  timeg_builder_IALsetup_.WriteTiming(indent, "Internals Around Link Setup : ", total);
+  timeg_builder_IALspan_.WriteTiming (indent, "Internals Around Link Span  : ", total);
+  timeg_builder_IALgen_.WriteTiming  (indent, "Internals Around Link Gen   : ", total);
+}
+
 /** For debugging, print all the complete internals associated with the given atom. */
 void Builder::printAllInternalsForAtom(int at, Topology const& topIn, Barray const& hasPosition) const
 {
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index a8d257457b..ce07693948 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -2,6 +2,8 @@
 #define INC_STRUCTURE_BUILDER_H
 #include <vector>
 #include "../AtomType.h"
+
+#include "../Timer.h" // DEBUG
 class Atom;
 class Topology;
 class Frame;
@@ -36,6 +38,7 @@ class Builder {
     /// Generate internal coordinates in the same manner as LEaP
     int GenerateInternals(Frame const&, Topology const&, Barray const&);
     /// Generate internal coordinates around a link between residues in same manner as LEaP
+    int GenerateInternalsAroundLink(int, int, Frame const&, Topology const&, Barray const&, BuildType, Barray const&);
     int GenerateInternalsAroundLink(int, int, Frame const&, Topology const&, Barray const&, BuildType);
     /// Update existing indices with given offset
     void UpdateIndicesWithOffset(int);
@@ -50,6 +53,8 @@ class Builder {
     //int GetZmatrixFromInternals(Zmatrix&, Topology const&) const;
     /// Adjust torsion around a bond so that atoms with longest 'depth' are trans
     int AdjustIcAroundLink(int, int, Frame const&, Topology const&);
+
+    static void PrintTiming(int, double);
   private:
     typedef std::vector<int> Iarray;
 
@@ -144,6 +149,10 @@ class Builder {
     Larray internalBonds_;
     Carray internalChirality_;
     Iarray Rnums_;               ///< Hold residue indices pertaining to current internals
+
+    static Timer timeg_builder_IALsetup_;
+    static Timer timeg_builder_IALspan_;
+    static Timer timeg_builder_IALgen_;
 };
 /// ----- Hold torsion internal ------------------
 class Cpptraj::Structure::Builder::InternalTorsion {

From 4a3ef53dd15410470ec94f6129d5059b1580b58f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Sat, 10 Jan 2026 10:34:52 -0500
Subject: [PATCH 1206/1492] Comment out old code

---
 src/Structure/Builder.cpp | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 548a314a7d..56a0e240e4 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -1604,6 +1604,9 @@ int Builder::GenerateInternalsAroundLink(int at0, int at1,
 {
   Atom const& A0 = topIn[at0];
   Residue const& R0 = topIn.Res(A0.ResNum());
+  // In order to mimic the way LEaP does things, mark all atoms before
+  // this residue as having position, and all other atoms as not having
+  // position.
   Barray tmpHasPosition( topIn.Natom(), false );
   for (int at = 0; at < R0.FirstAtom(); at++)
     tmpHasPosition[at] = true;
@@ -1634,10 +1637,8 @@ int Builder::GenerateInternalsAroundLink(int at0, int at1,
     mprintf("Warning: Builder::GenerateInternalsAroundLink(): Atoms are in the same residue.\n");
     //return 1;
   }
-  // In order to mimic the way LEaP does things, mark all atoms before
-  // this residue as having position, and all other atoms as not having
-  // position.
-  Residue const& R0 = topIn.Res(A0.ResNum());
+
+  //Residue const& R0 = topIn.Res(A0.ResNum());
   //Barray tmpHasPosition( topIn.Natom(), false );
   //for (int at = nextTempHasPositionStart_; at < R0.FirstAtom(); at++)
   //  tmpHasPosition_[at] = true;

From ded5e20ae1b8d79fa45e722918f381ed97837ad5 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Sat, 10 Jan 2026 15:02:37 -0500
Subject: [PATCH 1207/1492] Finding rings becomes expensive for lots of
 residues. Cache found ring atoms names for residues to speed things up.

---
 src/Structure/RingFinder.cpp | 52 +++++++++++++++++++++++++++++++++++-
 src/Structure/RingFinder.h   |  6 +++++
 2 files changed, 57 insertions(+), 1 deletion(-)

diff --git a/src/Structure/RingFinder.cpp b/src/Structure/RingFinder.cpp
index 486aff4060..2fc51d578f 100644
--- a/src/Structure/RingFinder.cpp
+++ b/src/Structure/RingFinder.cpp
@@ -3,6 +3,7 @@
 #include "../CharMask.h"
 #include "../CpptrajStdio.h"
 #include "../Topology.h"
+#include <map>
 
 using namespace Cpptraj::Structure;
 
@@ -75,16 +76,58 @@ static std::vector<int> findCycle(int at, int tgtAt, int previousAt, int res, To
   return std::vector<int>();
 }
 
+void RingFinder::useCachedRings(Topology const& topIn, int res, CharMask const& cmask, RingNamesType const& ringNamesArray)
+{
+  mprintf("DEBUG: Using cached values for residue %s, %zu rings.\n", topIn.TruncResNameNum(res).c_str(), ringNamesArray.size());
+  for (RingNamesType::const_iterator rnames = ringNamesArray.begin(); rnames != ringNamesArray.end(); ++rnames)
+  {
+    // Find all ring atoms. They must be present and selected.
+    bool allAtomsFound = true;
+    std::vector<int> ringAtoms;
+    ringAtoms.reserve(rnames->size());
+    for (AtomNameArray::const_iterator aname = rnames->begin(); aname != rnames->end(); ++aname)
+    {
+      NameType const& atmName = *aname;
+      int at = topIn.FindAtomInResidue(res, atmName);
+      if (at < 0) {
+        mprintf("Warning: Ring atom %s not found in residue %s\n", *atmName, topIn.TruncResNameNum(res).c_str());
+        allAtomsFound = false;
+        break;
+      }
+      if (!cmask.AtomInCharMask(at)) {
+        allAtomsFound = false;
+        break;
+      }
+      ringAtoms.push_back(at);
+    }
+    if (allAtomsFound)
+      rings_.push_back( AtomMask(ringAtoms, topIn.Natom()) );
+  } // END loop over rings in residue
+}
+
 /** Set up ring finder for topology. */
 int RingFinder::SetupRingFinder(Topology const& topIn, AtomMask const& maskIn) {
   rings_.clear();
 
+  typedef std::pair<NameType, RingNamesType> RingCachePair;
+  typedef std::map<NameType, RingNamesType> RingCacheType;
+  // Hold names of ring atoms for each unique type of residue.
+  RingCacheType RingCache;
+
   CharMask cmask( maskIn.ConvertToCharMask(), maskIn.Nselected() );
 
   std::vector<bool> Visited(topIn.Natom(), false); // TODO only have visited for residue atoms
   // Do not look for rings that span residues.
   for (int res = 0; res < topIn.Nres(); res++) {
     Residue const& currentRes = topIn.Res(res);
+    // Check the cache
+    RingCacheType::const_iterator it = RingCache.find( currentRes.Name() );
+    if ( it != RingCache.end() ) {
+      useCachedRings( topIn, res, cmask, it->second );
+      continue;
+    }
+    // First time this residue has been seen. Do the full ring search.
+    RingNamesType ringNamesArray;
     // Ignore solvent
     if (topIn.Mol( topIn[currentRes.FirstAtom()].MolNum() ).IsSolvent()) continue;
     std::vector<int> startAtoms;
@@ -155,8 +198,14 @@ int RingFinder::SetupRingFinder(Topology const& topIn, AtomMask const& maskIn) {
                     if (!cmask.AtomInCharMask( *rt )) allfound = false;
                   }
                   if (debug_ > 0) mprintf(" }\n");
-                  if (allfound)
+                  if (allfound) {
                     rings_.push_back( AtomMask(ringAtoms, topIn.Natom()) );
+                    AtomNameArray rnames;
+                    rnames.reserve( ringAtoms.size() );
+                    for (std::vector<int>::const_iterator zt = ringAtoms.begin(); zt != ringAtoms.end(); ++zt)
+                      rnames.push_back( topIn[*zt].Name() );
+                    ringNamesArray.push_back( rnames );
+                  }
                 }
               } // END bond atom 2 in residue
             } // END inner loop over bonds
@@ -164,6 +213,7 @@ int RingFinder::SetupRingFinder(Topology const& topIn, AtomMask const& maskIn) {
         } // END outer loop over bonds
       } // END # bonds > 1
     } // END loop over potential start atoms
+    RingCache.insert( RingCachePair( currentRes.Name(), ringNamesArray ) );
   } // END loop over all residues
 
   return 0;
diff --git a/src/Structure/RingFinder.h b/src/Structure/RingFinder.h
index 289caa5f6d..8225cea1ba 100644
--- a/src/Structure/RingFinder.h
+++ b/src/Structure/RingFinder.h
@@ -3,6 +3,8 @@
 #include <vector>
 class ArgList;
 class AtomMask;
+class CharMask;
+class NameType;
 class Topology;
 namespace Cpptraj {
 namespace Structure {
@@ -19,6 +21,10 @@ class RingFinder {
     AtomMask const& operator[](int idx) const { return rings_[idx]; }
   private:
     typedef std::vector<AtomMask> Marray;
+    typedef std::vector<NameType> AtomNameArray;
+    typedef std::vector<AtomNameArray> RingNamesType;
+
+    void useCachedRings(Topology const&, int, CharMask const&, RingNamesType const&);
 
     Marray rings_; ///< Array of masks corresponding to rings
     int debug_;

From 3299587459cbe8f63a6030aee232a59201dd9f04 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Sat, 10 Jan 2026 15:03:11 -0500
Subject: [PATCH 1208/1492] Add much more timing data

---
 src/Exec_Build.cpp     | 13 +++++++++++++
 src/Exec_Build.h       |  4 ++++
 src/StructureCheck.cpp | 18 +++++++++++++++++-
 src/StructureCheck.h   |  8 ++++++++
 4 files changed, 42 insertions(+), 1 deletion(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 406eea3033..7200bea462 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -1304,10 +1304,13 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
       }
       frameOut.BoxCrd().PrintInfo();
     }
+    t_check_setup_.Start();
     if (check.Setup( topOut, frameOut.BoxCrd() )) {
       mprinterr("Error: Structure check setup failed.\n");
       return CpptrajState::ERR;
     }
+    t_check_setup_.Stop();
+    check.PrintTiming(1, t_check_setup_.Total());
     check.Mask1().MaskInfo();
     if (check.ImageOpt().ImagingEnabled())
       mprintf("\tImaging on.\n");
@@ -1316,11 +1319,17 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
     // TODO make file a user option
     CpptrajFile check_output;
     check_output.OpenWrite("");
+    t_check_overlaps_.Start();
     int Ntotal_problems = check.CheckOverlaps( frameOut );
+    t_check_overlaps_.Stop();
     check.WriteProblemsToFile( &check_output, 1, topOut );
+    t_check_bonds_.Start();
     Ntotal_problems += check.CheckBonds( frameOut );
+    t_check_bonds_.Stop();
     check.WriteProblemsToFile( &check_output, 1, topOut );
+    t_check_rings_.Start();
     Ntotal_problems += check.CheckRings( frameOut );
+    t_check_rings_.Stop();
     check.WriteProblemsToFile( &check_output, 1, topOut );
     mprintf("\t%i total problems detected.\n", Ntotal_problems);
     // If box was added for check only, remove it
@@ -1367,6 +1376,10 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
   if (add_solvent)
     t_solvate_.WriteTiming    (2, "Solvate             :", t_total_.Total());
   t_check_.WriteTiming        (2, "Structure check     :", t_total_.Total());
+  t_check_overlaps_.WriteTiming(3, "Overlaps :", t_check_.Total());
+  t_check_bonds_.WriteTiming   (3, "Bonds    :", t_check_.Total());
+  t_check_rings_.WriteTiming   (3, "Rings    :", t_check_.Total());
+  t_check_setup_.WriteTiming   (3, "Setup    :", t_check_.Total());
   t_assign_.WriteTiming       (2, "Param./Top. gen.    :", t_total_.Total());
   AP.WriteAssignTiming(3, t_assign_.Total());
 
diff --git a/src/Exec_Build.h b/src/Exec_Build.h
index c0b557f015..91bb75beb8 100644
--- a/src/Exec_Build.h
+++ b/src/Exec_Build.h
@@ -69,6 +69,10 @@ class Exec_Build : public Exec {
     Timer t_fill_build_link_bond_;
     Timer t_assign_;
     Timer t_check_;
+    Timer t_check_bonds_;
+    Timer t_check_overlaps_;
+    Timer t_check_rings_;
+    Timer t_check_setup_;
     Timer t_solvate_;
 };
 #endif
diff --git a/src/StructureCheck.cpp b/src/StructureCheck.cpp
index f2e2546027..780c39f192 100644
--- a/src/StructureCheck.cpp
+++ b/src/StructureCheck.cpp
@@ -166,6 +166,7 @@ void StructureCheck::SetupBondList(AtomMask const& iMask, Topology const& top) {
 // StructureCheck::Setup()
 int StructureCheck::Setup(Topology const& topIn, Box const& boxIn)
 {
+  t_setup_.Start();
   imageOpt_.SetupImaging( boxIn.HasBox() );
   bondList_.clear();
   if (!checkExtraPts_)
@@ -178,7 +179,9 @@ int StructureCheck::Setup(Topology const& topIn, Box const& boxIn)
   }
   checkType_ = NO_PL_1_MASK;
   // Set up bonds if specified.
+  t_setup_bonds_.Start();
   if (bondcheck_ || ringcheck_) SetupBondList(Mask1_, topIn);
+  t_setup_bonds_.Stop();
   // Set up second mask if specified.
   if ( Mask2_.MaskStringSet() ) {
     if (topIn.SetupIntegerMask( Mask2_ ) ) return 1;
@@ -236,6 +239,7 @@ int StructureCheck::Setup(Topology const& topIn, Box const& boxIn)
     ex_list_opt = ExclusionArray::FULL;
   }
   // Set up exclusion list
+  t_setup_exclusion_.Start();
   if (checkType_ == PL_1_MASK || checkType_ == NO_PL_1_MASK) {
     mprintf("\tExcluding bond interactions.\n");
     // Set up atom exclusion list. Distance of 2 since we are not
@@ -246,9 +250,11 @@ int StructureCheck::Setup(Topology const& topIn, Box const& boxIn)
     }
   } else
     mprintf("\tNot using exclusions.\n");
+  t_setup_exclusion_.Stop();
   // Sort bond list
   if (bondcheck_ || ringcheck_) std::sort(bondList_.begin(), bondList_.end());
   // Find rings
+  t_setup_ringfinder_.Start();
   if (ringcheck_) {
     if (rings_.SetupRingFinder(topIn, Mask1_)) {
       mprinterr("Error: Could not set up ring finder.\n");
@@ -256,10 +262,20 @@ int StructureCheck::Setup(Topology const& topIn, Box const& boxIn)
     }
     if (debug_ > 0) rings_.PrintRings(topIn);
   }
-
+  t_setup_ringfinder_.Stop();
+  t_setup_.Stop();
   return 0;
 }
 
+void StructureCheck::PrintTiming(int indent, double total)
+const
+{
+  t_setup_.WriteTiming(indent, "Check Setup :", total);
+  t_setup_bonds_.WriteTiming     (indent+1, "Setup check bonds      :", t_setup_.Total());
+  t_setup_exclusion_.WriteTiming (indent+1, "Setup check exclusions :", t_setup_.Total());
+  t_setup_ringfinder_.WriteTiming(indent+1, "Setup check ringfinder :", t_setup_.Total());
+}
+
 /** Sort problem list. If OpenMP, combine problems from each thread
   * into problemAtoms_ first.
   */
diff --git a/src/StructureCheck.h b/src/StructureCheck.h
index 51d4c7f2eb..039c33a73c 100644
--- a/src/StructureCheck.h
+++ b/src/StructureCheck.h
@@ -6,6 +6,7 @@
 #include "AtomMask.h"
 #include "ParameterTypes.h"
 #include "Structure/RingFinder.h"
+#include "Timer.h"
 // Forward declares
 class Topology;
 class CharMask;
@@ -52,6 +53,8 @@ class StructureCheck {
     /// Write existing problems to the given file
     void WriteProblemsToFile(CpptrajFile*, int, Topology const&) const;
 
+
+    void PrintTiming(int, double) const;
     /// Format of problems currently stored in problemAtoms_
     enum FmtType { F_ATOM =0, F_BOND, F_RING };
 
@@ -181,5 +184,10 @@ class StructureCheck {
     bool saveProblems_;     ///< If true save problems in problemAtoms_
     bool checkExtraPts_;    ///< If true check extra points.
     FmtType lastFmt_;       ///< Format of problems currently stored in problemAtoms_
+
+    Timer t_setup_;
+    Timer t_setup_bonds_;
+    Timer t_setup_exclusion_;
+    Timer t_setup_ringfinder_;
 };
 #endif

From 7090aef7dba4e39c700b464fb15f4f6135a3d44b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Mon, 12 Jan 2026 09:09:32 -0500
Subject: [PATCH 1209/1492] Assume if the residue has a template that it will
 either be connected by the template's HEAD/TAIL atoms or by e.g. the sugar
 detection routines (i.e. do not rely on whatever bonds were in the input
 structure).

---
 src/Exec_Build.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 7200bea462..2eb8df1aa4 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -324,7 +324,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
           if (has_pdbn) topOut.AddPdbSerialNum( topIn.PdbSerialNum()[itgt] );
           //pdb[itgt-currentRes.FirstAtom()] = iref;
           // Check source atoms for inter-residue connections.
-          Atom const& sourceAtom = topIn[itgt];
+/*          Atom const& sourceAtom = topIn[itgt];
           for (Atom::bond_iterator bat = sourceAtom.bondbegin(); bat != sourceAtom.bondend(); ++bat) {
             if ( topIn[*bat].ResNum() < ires ) {
               // Use template atom names. Use saved names in case source name had an alias.
@@ -336,7 +336,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
                         *bat+1, *(topIn[*bat].Name()), topIn[*bat].ResNum()+1, *(SourceAtomNames[*bat]));
               }
             }
-          }
+          }*/
         }
       } // END loop over template atoms
       if (nTgtAtomsMissing > 0) {

From 38f7c24e0882f328ee21f9973b5dab1065a5f00a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Mon, 12 Jan 2026 09:11:37 -0500
Subject: [PATCH 1210/1492] Hide debug

---
 src/Structure/RingFinder.cpp | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/Structure/RingFinder.cpp b/src/Structure/RingFinder.cpp
index 2fc51d578f..e2575b3127 100644
--- a/src/Structure/RingFinder.cpp
+++ b/src/Structure/RingFinder.cpp
@@ -78,7 +78,8 @@ static std::vector<int> findCycle(int at, int tgtAt, int previousAt, int res, To
 
 void RingFinder::useCachedRings(Topology const& topIn, int res, CharMask const& cmask, RingNamesType const& ringNamesArray)
 {
-  mprintf("DEBUG: Using cached values for residue %s, %zu rings.\n", topIn.TruncResNameNum(res).c_str(), ringNamesArray.size());
+  if (debug_ > 0)
+    mprintf("DEBUG: Using cached values for residue %s, %zu rings.\n", topIn.TruncResNameNum(res).c_str(), ringNamesArray.size());
   for (RingNamesType::const_iterator rnames = ringNamesArray.begin(); rnames != ringNamesArray.end(); ++rnames)
   {
     // Find all ring atoms. They must be present and selected.

From 97d00b5f9ecb4f25a7de1ad8f3c80bb0bc704db0 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Tue, 13 Jan 2026 11:30:09 -0500
Subject: [PATCH 1211/1492] Add simplecheck keyword for apples to apples
 compare with leap timing

---
 src/Exec_Build.cpp | 49 +++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 48 insertions(+), 1 deletion(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 2eb8df1aa4..c2e0b4da22 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -811,7 +811,7 @@ void Exec_Build::Help() const
 {
   mprintf("\tname <output COORDS> crdset <COORDS set> [frame <#>]\n"
           "\t[title <title>] [gb <radii>] [verbose <#>] [keepmissingatoms]\n"
-          "\t[parmout <topology file>] [crdout <coord file>]\n"
+          "\t[parmout <topology file>] [crdout <coord file>] [simplecheck]\n"
           "\t[%s]\n"
           "\t[{%s} ...]\n"
           "\t[{%s} ...]\n"
@@ -883,6 +883,13 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
   std::string title = argIn.GetStringKey("title");
   std::string outputTopologyName = argIn.GetStringKey("parmout");
   std::string outputCoordsName = argIn.GetStringKey("crdout");
+  if (argIn.hasKey("simplecheck")) {
+    mprintf("\tSimple check: will only check bond lengths.\n");
+    check_structure_ = false;
+  } else {
+    mprintf("\tWill check bond lengths, atomic overlaps, and ring intersections.\n");
+    check_structure_ = true;
+  }
   if (!outputTopologyName.empty())
     mprintf("\tWill write topology to %s\n", outputTopologyName.c_str());
   if (!outputCoordsName.empty())
@@ -1336,6 +1343,46 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
     if (box_added)
       frameOut.ModifyBox().SetNoBox();
     t_check_.Stop();
+  } else {
+    // Just check bond lengths
+    t_check_.Start();
+    StructureCheck check;
+    if (check.SetOptions( false, // image 
+                          true,  // check bonds
+                          true,  // save problems
+                          debug_, // debug
+                          checkMaskString, // mask 1
+                          "", // mask 2
+                          0.8, // nonbond cut. NOTE: leap check cut is 1.5
+                          1.15, // bond long offset
+                          0.5, // bond short offset
+                          -1, // pairlist cut (-1 for heuristic)
+                          false, // ring check
+                          0, // 0 = default ring check short distance cut
+                          0, // 0 = default ring check long distance cut
+                          0  // 0 = default ring check angle cut
+        ))
+    {
+      mprinterr("Error: Structure check options failed.\n");
+      return CpptrajState::ERR;
+    }
+    t_check_setup_.Start();
+    if (check.Setup( topOut, frameOut.BoxCrd() )) {
+      mprinterr("Error: Structure check setup failed.\n");
+      return CpptrajState::ERR;
+    }
+    t_check_setup_.Stop();
+    check.PrintTiming(1, t_check_setup_.Total());
+    check.Mask1().MaskInfo();
+    // TODO make file a user option
+    CpptrajFile check_output;
+    check_output.OpenWrite("");
+    t_check_bonds_.Start();
+    int Ntotal_problems = check.CheckBonds( frameOut );
+    t_check_bonds_.Stop();
+    check.WriteProblemsToFile( &check_output, 1, topOut );
+    mprintf("\t%i total problems detected.\n", Ntotal_problems);
+    t_check_.Stop();
   }
 
   // Total charge check

From 1accaecfcf8608a12c4c48f45f82b1a4fa245d4a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 14 Jan 2026 12:52:53 -0500
Subject: [PATCH 1212/1492] Better error handling for topology files. Make sure
 we exit with an error if a write error or buffer overflow occurs. Handle
 large topologies by increasing the width of the diheral index FLAGs if
 needed.

---
 src/BufferedFrame.h |   4 ++
 src/Parm_Amber.cpp  | 168 ++++++++++++++++++++++++++------------------
 src/Parm_Amber.h    |  35 ++++-----
 3 files changed, 121 insertions(+), 86 deletions(-)

diff --git a/src/BufferedFrame.h b/src/BufferedFrame.h
index 1745ae30d2..309fba4f20 100644
--- a/src/BufferedFrame.h
+++ b/src/BufferedFrame.h
@@ -68,6 +68,10 @@ class BufferedFrame : public CpptrajFile {
     const char* Buffer() const { return buffer_;    }
     /// \return Total output file size for given number of frames.
     size_t OutputFileSize(unsigned int n) const { return offset_ + (frameSize_ * n); }
+    /// \return Number of errors since last time WriteFrame() was called.
+    int ErrorCount() const { return errorCount_; }
+    /// \return Number of character overflows since last time WriteFrame() was called.
+    int OverflowCount() const { return overflowCount_; }
   private:
     size_t CalcFrameSize(int) const;
     inline void AdvanceCol();
diff --git a/src/Parm_Amber.cpp b/src/Parm_Amber.cpp
index 158d16daa1..86300eaa98 100644
--- a/src/Parm_Amber.cpp
+++ b/src/Parm_Amber.cpp
@@ -147,6 +147,9 @@ const Parm_Amber::ParmFlag Parm_Amber::FLAGS_[] = {
   { "CMAP_RESOLUTION",             "%FORMAT(20I4)"},    // # steps along each Phi/Psi CMAP axis
   { "CMAP_PARAMETER_",             "%FORMAT(8F9.5)"},   // CMAP grid
   { "CMAP_INDEX",                  "%FORMAT(6I8)" },    // Atom i,j,k,l,m of cross term and idx
+  // Extended format flags
+  { "DIHEDRALS_INC_HYDROGEN",      "%FORMAT(8I10)" },   // For topologies with high atom counts
+  { "DIHEDRALS_WITHOUT_HYDROGEN",  "%FORMAT(8I10)" },   // For topologies with high atom counts
   { 0, 0 }
 };
 
@@ -1623,18 +1626,33 @@ int Parm_Amber::BufferAlloc(FlagType ftype, FortranData const& FMT, int nvals, i
   return 0;
 }
 
+/** Flush the current file buffer. Check for errors. */
+int Parm_Amber::flushFileBuffer(FlagType flagIn) {
+  int err = 0;
+  if (file_.ErrorCount() > 0) {
+    mprinterr("Error: Encountered %i errors writing FLAG %s\n", file_.ErrorCount(), FLAGS_[flagIn].Flag);
+    err += file_.ErrorCount();
+  }
+  if (file_.OverflowCount() > 0) {
+    mprinterr("Error: Encountered %i character overflows writing FLAG %s\n", file_.OverflowCount(), FLAGS_[flagIn].Flag);
+    err += file_.OverflowCount();
+  }
+  file_.FlushBuffer();
+  return err;
+}
+
 // Parm_Amber::WriteBondParm()
 int Parm_Amber::WriteBondParm(FlagType RKflag, FlagType REQflag, BondParmArray const& BP) {
   // BOND RK
   if (BufferAlloc(RKflag, BP.size())) return 1;
   for (BondParmArray::const_iterator it = BP.begin(); it != BP.end(); ++it)
     file_.DblToBuffer( it->Rk() );
-  file_.FlushBuffer();
+  if (flushFileBuffer( RKflag )) return 1;
   // BOND REQ
   if (BufferAlloc(REQflag, BP.size())) return 1;
   for (BondParmArray::const_iterator it = BP.begin(); it != BP.end(); ++it)
     file_.DblToBuffer( it->Req() );
-  file_.FlushBuffer();
+  if (flushFileBuffer( REQflag )) return 1;
   return 0;
 }
 
@@ -1644,12 +1662,12 @@ int Parm_Amber::WriteLJ(FlagType Aflag, FlagType Bflag, NonbondArray const& NB)
   if (BufferAlloc(Aflag, NB.size())) return 1;
   for (NonbondArray::const_iterator it = NB.begin(); it != NB.end(); ++it)
     file_.DblToBuffer( it->A() );
-  file_.FlushBuffer();
+  if (flushFileBuffer( Aflag )) return 1;
   // LJ B terms
   if (BufferAlloc(Bflag, NB.size())) return 1;
   for (NonbondArray::const_iterator it = NB.begin(); it != NB.end(); ++it)
     file_.DblToBuffer( it->B() );
-  file_.FlushBuffer();
+  if (flushFileBuffer( Bflag )) return 1;
   return 0;
 }
 
@@ -1661,7 +1679,7 @@ int Parm_Amber::WriteBonds(FlagType flag, BondArray const& BND) {
     file_.IntToBuffer( it->A2()*3 );
     file_.IntToBuffer( it->Idx()+1 );
   }
-  file_.FlushBuffer();
+  if (flushFileBuffer( flag )) return 1;
   return 0;
 }
 
@@ -1674,7 +1692,7 @@ int Parm_Amber::WriteAngles(FlagType flag, AngleArray const& ANG) {
     file_.IntToBuffer( it->A3()*3 );
     file_.IntToBuffer( it->Idx()+1 );
   }
-  file_.FlushBuffer();
+  if (flushFileBuffer( flag )) return 1;
   return 0;
 }
 
@@ -1717,7 +1735,7 @@ int Parm_Amber::WriteDihedrals(FlagType flag, DihedralArray const& DIH) {
       file_.IntToBuffer( dihIdxs[3] );
     file_.IntToBuffer( it->Idx()+1 );
   }
-  file_.FlushBuffer();
+  if (flushFileBuffer( flag )) return 1;
   return 0;
 }
 
@@ -1735,7 +1753,7 @@ int Parm_Amber::WriteTreeChainClassification(std::vector<NameType> const& tree)
   if (BufferAlloc(F_ITREE, tree.size())) return 1;
   for (std::vector<NameType>::const_iterator it = tree.begin(); it != tree.end(); ++it)
     file_.CharToBuffer( *(*it) );
-  file_.FlushBuffer();
+  if (flushFileBuffer( F_ITREE )) return 1;
   return 0;
 }
 
@@ -1744,7 +1762,7 @@ int Parm_Amber::WriteIjoin(std::vector<int> const& ijoin) {
   if (BufferAlloc(F_JOIN, ijoin.size())) return 1;
   for (std::vector<int>::const_iterator it = ijoin.begin(); it != ijoin.end(); ++it)
     file_.IntToBuffer( *it );
-  file_.FlushBuffer();
+  if (flushFileBuffer( F_JOIN )) return 1;
   return 0;
 }
 
@@ -1753,7 +1771,7 @@ int Parm_Amber::WriteIrotat(std::vector<int> const& irotat) {
   if (BufferAlloc(F_IROTAT, irotat.size())) return 1;
   for (std::vector<int>::const_iterator it = irotat.begin(); it != irotat.end(); ++it)
     file_.IntToBuffer( *it );
-  file_.FlushBuffer();
+  if (flushFileBuffer( F_IROTAT )) return 1;
   return 0;
 }
 
@@ -2000,7 +2018,7 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
   else
     file_.IntToBuffer( 0 );
   file_.IntToBuffer( TopOut.NextraPts() ); // NEXTRA
-  file_.FlushBuffer();
+  if (flushFileBuffer( F_POINTERS )) return 1;
  
   // CHAMBER only - FF type description
   if (ptype_ == CHAMBER) {
@@ -2023,31 +2041,31 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
   if (BufferAlloc(F_NAMES, TopOut.Natom())) return 1;
   for (Topology::atom_iterator atm = TopOut.begin(); atm != TopOut.end(); ++atm)
     file_.CharToBuffer( atm->c_str() );
-  file_.FlushBuffer();
+  if (flushFileBuffer( F_NAMES )) return 1;
 
   // CHARGES
   if (BufferAlloc(F_CHARGE, TopOut.Natom())) return 1;
   for (Topology::atom_iterator atm = TopOut.begin(); atm != TopOut.end(); ++atm)
     file_.DblToBuffer( atm->Charge() * elec_to_parm_ );
-  file_.FlushBuffer();
+  if (flushFileBuffer( F_CHARGE )) return 1;
 
   // ATOMIC NUMBER
   if (BufferAlloc(F_ATOMICNUM, TopOut.Natom())) return 1;
   for (Topology::atom_iterator atm = TopOut.begin(); atm != TopOut.end(); ++atm)
     file_.IntToBuffer( atm->AtomicNumber() );
-  file_.FlushBuffer();
+  if (flushFileBuffer( F_ATOMICNUM )) return 1;
 
   // MASS
   if (BufferAlloc(F_MASS, TopOut.Natom())) return 1;
   for (Topology::atom_iterator atm = TopOut.begin(); atm != TopOut.end(); ++atm)
     file_.DblToBuffer( atm->Mass() );
-  file_.FlushBuffer();
+  if (flushFileBuffer( F_MASS )) return 1;
 
   // TYPE INDEX
   if (BufferAlloc(F_ATYPEIDX, TopOut.Natom())) return 1;
   for (Topology::atom_iterator atm = TopOut.begin(); atm != TopOut.end(); ++atm)
     file_.IntToBuffer( atm->TypeIndex()+1 );
-  file_.FlushBuffer();
+  if (flushFileBuffer( F_ATYPEIDX )) return 1;
 
   // NUMEX
   if (BufferAlloc(F_NUMEX, TopOut.Natom())) return 1;
@@ -2059,7 +2077,7 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
     else
       file_.IntToBuffer( (int)exList->size() );
   }
-  file_.FlushBuffer();
+  if (flushFileBuffer( F_NUMEX )) return 1;
 
   // NONBONDED INDICES - positive needs to be shifted by +1 for fortran
   if (BufferAlloc(F_NB_INDEX, TopOut.Nonbond().NBindex().size())) return 1;
@@ -2069,19 +2087,19 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
       file_.IntToBuffer( *it + 1 );
     else
       file_.IntToBuffer( *it );
-  file_.FlushBuffer();
+  if (flushFileBuffer( F_NB_INDEX )) return 1;
 
   // RESIDUE NAME
   if (BufferAlloc(F_RESNAMES, TopOut.Nres())) return 1;
   for (Topology::res_iterator res = TopOut.ResStart(); res != TopOut.ResEnd(); ++res)
     file_.CharToBuffer( res->c_str() );
-  file_.FlushBuffer();
+  if (flushFileBuffer( F_RESNAMES )) return 1;
 
   // RESIDUE POINTERS
   if (BufferAlloc(F_RESNUMS, TopOut.Nres())) return 1;
   for (Topology::res_iterator res = TopOut.ResStart(); res != TopOut.ResEnd(); ++res)
     file_.IntToBuffer( res->FirstAtom()+1 );
-  file_.FlushBuffer();
+  if (flushFileBuffer( F_RESNUMS )) return 1;
 
   // BOND RK and REQ
   if (WriteBondParm(F_BONDRK, F_BONDREQ, TopOut.BondParm())) return 1;
@@ -2091,14 +2109,14 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
   for (AngleParmArray::const_iterator it = TopOut.AngleParm().begin();
                                       it != TopOut.AngleParm().end(); ++it)
     file_.DblToBuffer( it->Tk() );
-  file_.FlushBuffer();
+  if (flushFileBuffer( F_ANGLETK )) return 1;
 
   // ANGLE TEQ
   if (BufferAlloc(F_ANGLETEQ, TopOut.AngleParm().size())) return 1;
   for (AngleParmArray::const_iterator it = TopOut.AngleParm().begin();
                                       it != TopOut.AngleParm().end(); ++it)
     file_.DblToBuffer( it->Teq() );
-  file_.FlushBuffer();
+  if (flushFileBuffer( F_ANGLETEQ )) return 1;
 
   // CHARMM only - Urey-Bradley
   if (ptype_ == CHAMBER) {
@@ -2106,7 +2124,7 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
     if (BufferAlloc(F_CHM_UBC, 2)) return 1;
     file_.IntToBuffer( TopOut.UB().size() );
     file_.IntToBuffer( TopOut.UBparm().size() );
-    file_.FlushBuffer();
+    if (flushFileBuffer( F_CHM_UBC )) return 1;
     // UB terms
     if (BufferAlloc(F_CHM_UB, TopOut.UB().size()*3)) return 1;
     for (BondArray::const_iterator it = TopOut.UB().begin();
@@ -2116,7 +2134,7 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
       file_.IntToBuffer( it->A2()+1 );
       file_.IntToBuffer( it->Idx()+1 );
     }
-    file_.FlushBuffer();
+    if (flushFileBuffer( F_CHM_UB )) return 1;
     // UB FORCE CONSTANTS and EQ
     if (WriteBondParm(F_CHM_UBFC, F_CHM_UBEQ, TopOut.UBparm())) return 1;
   }
@@ -2126,42 +2144,42 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
   for (DihedralParmArray::const_iterator it = TopOut.DihedralParm().begin();
                                          it != TopOut.DihedralParm().end(); ++it)
     file_.DblToBuffer( it->Pk() );
-  file_.FlushBuffer();
+  if (flushFileBuffer( F_DIHPK )) return 1;
 
   // DIHEDRAL PN 
   if (BufferAlloc(F_DIHPN, TopOut.DihedralParm().size())) return 1;
   for (DihedralParmArray::const_iterator it = TopOut.DihedralParm().begin();
                                          it != TopOut.DihedralParm().end(); ++it)
     file_.DblToBuffer( it->Pn() );
-  file_.FlushBuffer();
+  if (flushFileBuffer( F_DIHPN )) return 1;
 
   // DIHEDRAL PHASE
   if (BufferAlloc(F_DIHPHASE, TopOut.DihedralParm().size())) return 1;
   for (DihedralParmArray::const_iterator it = TopOut.DihedralParm().begin();
                                          it != TopOut.DihedralParm().end(); ++it)
     file_.DblToBuffer( it->Phase() );
-  file_.FlushBuffer();
+  if (flushFileBuffer( F_DIHPHASE )) return 1;
 
   // DIHEDRAL SCEE
   if (BufferAlloc(F_SCEE, TopOut.DihedralParm().size())) return 1;
   for (DihedralParmArray::const_iterator it = TopOut.DihedralParm().begin();
                                          it != TopOut.DihedralParm().end(); ++it)
     file_.DblToBuffer( it->SCEE() );
-  file_.FlushBuffer();
+  if (flushFileBuffer( F_SCEE )) return 1;
 
   // DIHEDRAL SCNB
   if (BufferAlloc(F_SCNB, TopOut.DihedralParm().size())) return 1;
   for (DihedralParmArray::const_iterator it = TopOut.DihedralParm().begin();
                                          it != TopOut.DihedralParm().end(); ++it)
     file_.DblToBuffer( it->SCNB() );
-  file_.FlushBuffer();
+  if (flushFileBuffer( F_SCNB )) return 1;
 
   // CHAMBER only - Impropers
   if (ptype_ == CHAMBER) {
     // NUM IMPROPERS
     if (BufferAlloc(F_CHM_NIMP, 1)) return 1;
     file_.IntToBuffer( TopOut.Impropers().size() );
-    file_.FlushBuffer();
+    if (flushFileBuffer( F_CHM_NIMP )) return 1;
     // IMPROPER TERMS
     if (BufferAlloc(F_CHM_IMP, TopOut.Impropers().size()*5)) return 1;
     for (DihedralArray::const_iterator it = TopOut.Impropers().begin();
@@ -2179,30 +2197,30 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
         file_.IntToBuffer( it->A4() + 1 );
       file_.IntToBuffer( it->Idx() + 1 );
     }
-    file_.FlushBuffer();
+    if (flushFileBuffer( F_CHM_IMP )) return 1;
     // NUM IMPROPER PARAMS
     if (BufferAlloc(F_CHM_NIMPT, 1)) return 1;
     file_.IntToBuffer( TopOut.ImproperParm().size() );
-    file_.FlushBuffer();
+    if (flushFileBuffer( F_CHM_IMP )) return 1;
     // IMPROPER FORCE CONSTANTS
     if (BufferAlloc(F_CHM_IMPFC, TopOut.ImproperParm().size())) return 1;
     for (DihedralParmArray::const_iterator it = TopOut.ImproperParm().begin();
                                            it != TopOut.ImproperParm().end(); ++it)
       file_.DblToBuffer( it->Pk() );
-    file_.FlushBuffer();
+    if (flushFileBuffer( F_CHM_IMPFC )) return 1;
     // IMPROPER PHASES
     if (BufferAlloc(F_CHM_IMPP, TopOut.ImproperParm().size())) return 1;
     for (DihedralParmArray::const_iterator it = TopOut.ImproperParm().begin();
                                            it != TopOut.ImproperParm().end(); ++it)
       file_.DblToBuffer( it->Phase() );
-    file_.FlushBuffer();
+    if (flushFileBuffer( F_CHM_IMPP )) return 1;
   }
 
   // SOLTY - Currently unused but must be written.
   if (BufferAlloc(F_SOLTY, n_unique_atom_types)) return 1;
   for (unsigned int idx = 0; idx != n_unique_atom_types; idx++)
     file_.DblToBuffer( 0.0 );
-  file_.FlushBuffer();
+  if (flushFileBuffer( F_SOLTY )) return 1;
 
   // LJ A and B terms
   if (WriteLJ(F_LJ_A, F_LJ_B, TopOut.Nonbond().NBarray())) return 1;
@@ -2219,14 +2237,26 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
   if (WriteAngles(F_ANGLESH, TopOut.AnglesH())) return 1;
   if (WriteAngles(F_ANGLES,  TopOut.Angles()) ) return 1;
   // DIHEDRALSH and DIHEDRALS
-  if (WriteDihedrals(F_DIHH, TopOut.DihedralsH())) return 1;
-  if (WriteDihedrals(F_DIH,  TopOut.Dihedrals()) ) return 1;
+  FlagType flag_dihh, flag_dih;
+  // Check if the largest possible index will be greater than the default
+  // format width. If so, need a larger format.
+  if (TopOut.Natom()*3 < 10000000) {
+    flag_dihh = F_DIHH;
+    flag_dih  = F_DIH;
+  } else {
+    mprintf("Warning: Topology has >= 10M atoms. Using extended dihedral format strings.\n");
+    mprintf("Warning: This may confuse topology readers that do not actually read the FLAG format strings.\n");
+    flag_dihh = F_DIHH_LARGE;
+    flag_dih  = F_DIH_LARGE;
+  }
+  if (WriteDihedrals(flag_dihh, TopOut.DihedralsH())) return 1;
+  if (WriteDihedrals(flag_dih,  TopOut.Dihedrals()) ) return 1;
 
   // EXCLUDED ATOMS LIST
   if (BufferAlloc(F_EXCLUDE, Excluded.size())) return 1;
   for (Iarray::const_iterator it = Excluded.begin(); it != Excluded.end(); ++it)
     file_.IntToBuffer( *it );
-  file_.FlushBuffer();
+  if (flushFileBuffer( F_EXCLUDE )) return 1;
   Excluded.clear();
 
   // HBOND ASOL
@@ -2234,21 +2264,21 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
   for (HB_ParmArray::const_iterator it = TopOut.Nonbond().HBarray().begin();
                                     it != TopOut.Nonbond().HBarray().end(); ++it)
     file_.DblToBuffer( it->Asol() );
-  file_.FlushBuffer();
+  if (flushFileBuffer( F_ASOL )) return 1;
 
   // HBOND BSOL
   if (BufferAlloc(F_BSOL, TopOut.Nonbond().HBarray().size())) return 1;
   for (HB_ParmArray::const_iterator it = TopOut.Nonbond().HBarray().begin();
                                     it != TopOut.Nonbond().HBarray().end(); ++it)
     file_.DblToBuffer( it->Bsol() );
-  file_.FlushBuffer();
+  if (flushFileBuffer( F_BSOL )) return 1;
 
   // HBOND HBCUT 
   if (BufferAlloc(F_HBCUT, TopOut.Nonbond().HBarray().size())) return 1;
   for (HB_ParmArray::const_iterator it = TopOut.Nonbond().HBarray().begin();
                                     it != TopOut.Nonbond().HBarray().end(); ++it)
     file_.DblToBuffer( it->HBcut() );
-  file_.FlushBuffer();
+  if (flushFileBuffer( F_HBCUT )) return 1;
 
   // AMBER ATOM TYPES
   if (BufferAlloc(F_TYPES, TopOut.Natom())) return 1;
@@ -2258,7 +2288,7 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
     if (!atm->HasType()) ++NemptyTypes;
     file_.CharToBuffer( *(atm->Type()) );
   }
-  file_.FlushBuffer();
+  if (flushFileBuffer( F_TYPES )) return 1;
   if (NemptyTypes > 0) mprintf("Warning: %i empty atom type names.\n", NemptyTypes);
 
   // TODO: Generate automatically
@@ -2304,12 +2334,12 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
       file_.IntToBuffer( finalSoluteRes ); // Already +1
       file_.IntToBuffer( TopOut.Nmol() );
       file_.IntToBuffer( firstSolventMol + 1 );
-      file_.FlushBuffer();
+      if (flushFileBuffer( F_SOLVENT_POINTER )) return 1;
       // ATOMS PER MOLECULE
       if (BufferAlloc(F_ATOMSPERMOL, TopOut.Nmol())) return 1;
       for (Topology::mol_iterator mol = TopOut.MolStart(); mol != TopOut.MolEnd(); mol++)
         file_.IntToBuffer( mol->NumAtoms() );
-      file_.FlushBuffer();
+      if (flushFileBuffer( F_ATOMSPERMOL )) return 1;
     } else {
       // ----- Non-contiguous molecules ----------
       // Molecules are not contiguous. In order to ensure that #s in the
@@ -2359,12 +2389,12 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
       file_.IntToBuffer( finalSoluteRes ); // Already +1
       file_.IntToBuffer( segments.size() );
       file_.IntToBuffer( firstSolventMol + 1 );
-      file_.FlushBuffer();
+      if (flushFileBuffer( F_SOLVENT_POINTER )) return 1;
       // ATOMS PER MOLECULE
       if (BufferAlloc(F_ATOMSPERMOL, segments.size())) return 1;
       for (SegArray::const_iterator it = segments.begin(); it != segments.end(); ++it)
         file_.IntToBuffer( it->first.Size() );
-      file_.FlushBuffer();
+      if (flushFileBuffer( F_ATOMSPERMOL )) return 1;
     }
     // BOX DIMENSIONS
     if (BufferAlloc(F_PARMBOX, 4)) return 1;
@@ -2378,20 +2408,20 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
     file_.DblToBuffer( TopOut.ParmBox().Param(Box::X) );
     file_.DblToBuffer( TopOut.ParmBox().Param(Box::Y) );
     file_.DblToBuffer( TopOut.ParmBox().Param(Box::Z) );
-    file_.FlushBuffer();
+    if (flushFileBuffer( F_PARMBOX )) return 1;
   }
 
   // CAP info
   if (TopOut.Cap().NatCap() > 0) {
     if (BufferAlloc(F_CAP_INFO, 1)) return 1;
     file_.IntToBuffer( TopOut.Cap().NatCap()+1 );
-    file_.FlushBuffer();
+    if (flushFileBuffer( F_CAP_INFO )) return 1;
     if (BufferAlloc(F_CAP_INFO2, 4)) return 1;
     file_.DblToBuffer( TopOut.Cap().CutCap() );
     file_.DblToBuffer( TopOut.Cap().xCap() );
     file_.DblToBuffer( TopOut.Cap().yCap() );
     file_.DblToBuffer( TopOut.Cap().zCap() );
-    file_.FlushBuffer();
+    if (flushFileBuffer( F_CAP_INFO2 )) return 1;
   }
 
   // Only write GB params if actually present. At least one atom must have something.
@@ -2409,24 +2439,24 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
     if (BufferAlloc(F_RADII, TopOut.Natom())) return 1;
     for (Topology::atom_iterator atm = TopOut.begin(); atm != TopOut.end(); ++atm)
       file_.DblToBuffer( atm->GBRadius() );
-    file_.FlushBuffer();
+    if (flushFileBuffer( F_RADII )) return 1;
     // GB SCREENING PARAMS
     if (BufferAlloc(F_SCREEN, TopOut.Natom())) return 1;
     for (Topology::atom_iterator atm = TopOut.begin(); atm != TopOut.end(); ++atm)
       file_.DblToBuffer( atm->Screen() );
-    file_.FlushBuffer();
+    if (flushFileBuffer( F_SCREEN )) return 1;
   }
 
   // Polarizability
   if (BufferAlloc(F_IPOL, 1)) return 1;
   file_.IntToBuffer( TopOut.Ipol() );
-  file_.FlushBuffer();
+  if (flushFileBuffer( F_IPOL )) return 1;
   if (TopOut.Ipol() > 0) {
     // Only write polarizabilities if IPOL is set.
     if (BufferAlloc(F_POLAR, TopOut.Natom())) return 1;
     for (Topology::atom_iterator atm = TopOut.begin(); atm != TopOut.end(); ++atm)
       file_.DblToBuffer( atm->Polar() );
-    file_.FlushBuffer();
+    if (flushFileBuffer( F_POLAR )) return 1;
   }
 
   // Write CMAP parameters
@@ -2436,14 +2466,14 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
     if (BufferAlloc(f_count, 2)) return 1;
     file_.IntToBuffer( TopOut.Cmap().size() );     // CMAP terms
     file_.IntToBuffer( TopOut.CmapGrid().size() ); // CMAP grids
-    file_.FlushBuffer();
+    if (flushFileBuffer( f_count )) return 1;
     // CMAP GRID RESOLUTIONS
     const FlagType f_grid_res = (ptype_ == CHAMBER) ? F_CHM_CMAPR : F_CMAPR;
     if (BufferAlloc(f_grid_res, TopOut.CmapGrid().size())) return 1;
     for (CmapGridArray::const_iterator grid = TopOut.CmapGrid().begin();
                                        grid != TopOut.CmapGrid().end(); ++grid)
       file_.IntToBuffer( (int)grid->Resolution() );
-    file_.FlushBuffer();
+    if (flushFileBuffer( f_grid_res )) return 1;
     // CMAP GRIDS
     int ngrid = 1;
     const FlagType f_grid = (ptype_ == CHAMBER) ? F_CHM_CMAPP : F_CMAPP;
@@ -2466,7 +2496,7 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
       for (std::vector<double>::const_iterator it = grid->Grid().begin();
                                                it != grid->Grid().end(); ++it)
         file_.DblToBuffer( *it );
-      file_.FlushBuffer();
+      if (flushFileBuffer( f_grid )) return 1;
     }
     // CMAP terms
     const FlagType f_param = (ptype_ == CHAMBER) ? F_CHM_CMAPI : F_CMAPI;
@@ -2481,7 +2511,7 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
       file_.IntToBuffer( it->A5() + 1 );
       file_.IntToBuffer( it->Idx() + 1 );
     }
-    file_.FlushBuffer();
+    if (flushFileBuffer( f_param )) return 1;
   }
 
   // LES parameters
@@ -2489,7 +2519,7 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
     // LES NTYP
     if (BufferAlloc(F_LES_NTYP, 1)) return 1;
     file_.IntToBuffer( TopOut.LES().Ntypes() );
-    file_.FlushBuffer();
+    if (flushFileBuffer( F_LES_NTYP )) return 1;
     // Sanity check.
     if ( (int)TopOut.LES().Array().size() != TopOut.Natom() ) {
       mprinterr("Internal Error: # LES atoms (%zu) != # atoms in topology (%i).\n",
@@ -2501,25 +2531,25 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
     for (LES_Array::const_iterator les = TopOut.LES().Array().begin();
                                    les != TopOut.LES().Array().end(); ++les)
       file_.IntToBuffer( les->Type() );
-    file_.FlushBuffer();
+    if (flushFileBuffer( F_LES_TYPE )) return 1;
     // LES FAC
     if (BufferAlloc(F_LES_FAC, TopOut.LES().FAC().size())) return 1;
     for (std::vector<double>::const_iterator it = TopOut.LES().FAC().begin();
                                              it != TopOut.LES().FAC().end(); ++it)
       file_.DblToBuffer( *it );
-    file_.FlushBuffer();
+    if (flushFileBuffer( F_LES_FAC )) return 1;
     // LES CNUM
     if (BufferAlloc(F_LES_CNUM, TopOut.LES().Array().size())) return 1;
     for (LES_Array::const_iterator les = TopOut.LES().Array().begin();
                                    les != TopOut.LES().Array().end(); ++les)
       file_.IntToBuffer( les->Copy() );
-    file_.FlushBuffer();
+    if (flushFileBuffer( F_LES_CNUM )) return 1;
     // LES ID
     if (BufferAlloc(F_LES_ID, TopOut.LES().Array().size())) return 1;
     for (LES_Array::const_iterator les = TopOut.LES().Array().begin();
                                    les != TopOut.LES().Array().end(); ++les)
       file_.IntToBuffer( les->ID() );
-    file_.FlushBuffer();
+    if (flushFileBuffer( F_LES_ID )) return 1;
   }
 
   if (hasOrigResNums || hasChainID || hasIcodes) {
@@ -2543,7 +2573,7 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
     if (err != 0) return 1;
     for (Topology::res_iterator res = TopOut.ResStart(); res != TopOut.ResEnd(); ++res)
       file_.IntToBuffer( res->OriginalResNum() );
-    file_.FlushBuffer();
+    if (flushFileBuffer( F_PDB_RES )) return 1;
   }
   if (hasChainID) {
     // PDB chain IDs. Max # chars currently supported is 4.
@@ -2562,7 +2592,7 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
       }
       file_.CharToBuffer( cid );
     }
-    file_.FlushBuffer();
+    if (flushFileBuffer( F_PDB_CHAIN )) return 1;
   }
   if (hasIcodes) {
     // PDB residue insertion codes
@@ -2574,7 +2604,7 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
       icode[0] = res->Icode();
       file_.CharToBuffer( icode );
     }
-    file_.FlushBuffer();
+    if (flushFileBuffer( F_PDB_ICODE )) return 1;
   }
   if (hasOcc) {
     // PDB atomic occupancy
@@ -2583,7 +2613,7 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
     for (std::vector<float>::const_iterator it = TopOut.Occupancy().begin();
                                             it != TopOut.Occupancy().end(); ++it)
       file_.DblToBuffer( *it );
-    file_.FlushBuffer();
+    if (flushFileBuffer( F_PDB_OCC )) return 1;
   }
   if (hasBfac) {
     // PDB atomic B-factors
@@ -2592,7 +2622,7 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
     for (std::vector<float>::const_iterator it = TopOut.Bfactor().begin();
                                             it != TopOut.Bfactor().end(); ++it)
       file_.DblToBuffer( *it );
-    file_.FlushBuffer();
+    if (flushFileBuffer( F_PDB_BFAC )) return 1;
   }
   if (hasNum) {
     // PDB original serial numbers
@@ -2601,7 +2631,7 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
     for (std::vector<int>::const_iterator it = TopOut.PdbSerialNum().begin();
                                           it != TopOut.PdbSerialNum().end(); ++it)
       file_.IntToBuffer( *it );
-    file_.FlushBuffer();
+    if (flushFileBuffer( F_PDB_NUM )) return 1;
   }
 
   // LJ C terms.
@@ -2611,7 +2641,7 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
     if (BufferAlloc(F_LJ_C, ccoef.size())) return 1;
     for (std::vector<double>::const_iterator it = ccoef.begin(); it != ccoef.end(); ++it)
       file_.DblToBuffer( *it );
-    file_.FlushBuffer();
+    if (flushFileBuffer( F_LJ_C )) return 1;
   }
 
   return 0;
diff --git a/src/Parm_Amber.h b/src/Parm_Amber.h
index 482b7c0306..2b6d93f2d9 100644
--- a/src/Parm_Amber.h
+++ b/src/Parm_Amber.h
@@ -22,23 +22,23 @@ class Parm_Amber : public ParmIO {
     enum Type { UNKNOWN_FTYPE=0, FINT, FDOUBLE, FCHAR, FFLOAT };
     /// Enumerated type for Amber Parmtop Flags. KEEP IN SYNC WITH FLAGS_ ARRAY
     enum FlagType {
-      F_POINTERS = 0, F_NAMES,     F_CHARGE,    F_MASS,      F_RESNAMES,
-      F_RESNUMS,      F_TYPES,     F_BONDSH,    F_BONDS,     F_SOLVENT_POINTER,
-      F_ATOMSPERMOL,  F_PARMBOX,   F_ATYPEIDX,  F_NUMEX,     F_NB_INDEX,
-      F_LJ_A,         F_LJ_B,      F_LJ_C,      F_EXCLUDE,   F_RADII,
-      F_SCREEN,       F_BONDRK,    F_BONDREQ,   F_ANGLETK,   F_ANGLETEQ,
-      F_DIHPK,        F_DIHPN,     F_DIHPHASE,  F_SCEE,      F_SCNB,
-      F_SOLTY,        F_ANGLESH,   F_ANGLES,    F_DIHH,      F_DIH,
-      F_ASOL,         F_BSOL,      F_HBCUT,     F_ITREE,     F_JOIN,
-      F_IROTAT,       F_ATOMICNUM, F_TITLE,     F_RADSET,    F_LES_NTYP,
-      F_LES_TYPE,     F_LES_FAC,   F_LES_CNUM,  F_LES_ID,    F_CAP_INFO,
-      F_CAP_INFO2,    F_IPOL,      F_POLAR,     F_CTITLE,    F_CHM_UBC,
-      F_CHM_UB,       F_CHM_UBFC,  F_CHM_UBEQ,  F_CHM_NIMP,  F_CHM_IMP,
-      F_CHM_NIMPT,    F_CHM_IMPFC, F_CHM_IMPP,  F_LJ14A,     F_LJ14B,
-      F_CHM_CMAPC,    F_CHM_CMAPR, F_CHM_CMAPP, F_CHM_CMAPI, F_FF_TYPE,
-      F_PDB_RES,      F_PDB_CHAIN, F_PDB_ICODE, F_PDB_ALT,   F_PDB_BFAC,
-      F_PDB_OCC,      F_PDB_NUM,   F_CMAPC,     F_CMAPR,     F_CMAPP,
-      F_CMAPI
+      F_POINTERS = 0, F_NAMES,      F_CHARGE,    F_MASS,      F_RESNAMES,
+      F_RESNUMS,      F_TYPES,      F_BONDSH,    F_BONDS,     F_SOLVENT_POINTER,
+      F_ATOMSPERMOL,  F_PARMBOX,    F_ATYPEIDX,  F_NUMEX,     F_NB_INDEX,
+      F_LJ_A,         F_LJ_B,       F_LJ_C,      F_EXCLUDE,   F_RADII,
+      F_SCREEN,       F_BONDRK,     F_BONDREQ,   F_ANGLETK,   F_ANGLETEQ,
+      F_DIHPK,        F_DIHPN,      F_DIHPHASE,  F_SCEE,      F_SCNB,
+      F_SOLTY,        F_ANGLESH,    F_ANGLES,    F_DIHH,      F_DIH,
+      F_ASOL,         F_BSOL,       F_HBCUT,     F_ITREE,     F_JOIN,
+      F_IROTAT,       F_ATOMICNUM,  F_TITLE,     F_RADSET,    F_LES_NTYP,
+      F_LES_TYPE,     F_LES_FAC,    F_LES_CNUM,  F_LES_ID,    F_CAP_INFO,
+      F_CAP_INFO2,    F_IPOL,       F_POLAR,     F_CTITLE,    F_CHM_UBC,
+      F_CHM_UB,       F_CHM_UBFC,   F_CHM_UBEQ,  F_CHM_NIMP,  F_CHM_IMP,
+      F_CHM_NIMPT,    F_CHM_IMPFC,  F_CHM_IMPP,  F_LJ14A,     F_LJ14B,
+      F_CHM_CMAPC,    F_CHM_CMAPR,  F_CHM_CMAPP, F_CHM_CMAPI, F_FF_TYPE,
+      F_PDB_RES,      F_PDB_CHAIN,  F_PDB_ICODE, F_PDB_ALT,   F_PDB_BFAC,
+      F_PDB_OCC,      F_PDB_NUM,    F_CMAPC,     F_CMAPR,     F_CMAPP,
+      F_CMAPI,        F_DIHH_LARGE, F_DIH_LARGE
     };
     /// Used to hold %FLAG/FORMAT string pairs. Corresponds to FlagType.
     struct ParmFlag {
@@ -148,6 +148,7 @@ class Parm_Amber : public ParmIO {
     int BufferAlloc(FlagType, int, int);
     int BufferAlloc(FlagType, int, int, std::string const&);
     int BufferAlloc(FlagType f, int n) { return BufferAlloc(f, n, -1); }
+    int flushFileBuffer(FlagType);
     int WriteLJ(FlagType, FlagType, NonbondArray const&);
     int WriteBondParm(FlagType, FlagType, BondParmArray const&);
     int WriteBonds(FlagType, BondArray const&);

From cdc385b5f0b9913b921e76a9bdd81d168376aab3 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 14 Jan 2026 13:52:25 -0500
Subject: [PATCH 1213/1492] Instead of trapping CHAMBER related FLAGs in
 WriteFormat(), just create new format flags for them, which is consistent
 with how other CHAMBER flags are currently being handled.

---
 src/Parm_Amber.cpp | 25 +++++++++++++------------
 src/Parm_Amber.h   | 35 ++++++++++++++++++-----------------
 2 files changed, 31 insertions(+), 29 deletions(-)

diff --git a/src/Parm_Amber.cpp b/src/Parm_Amber.cpp
index 86300eaa98..2b58c6a529 100644
--- a/src/Parm_Amber.cpp
+++ b/src/Parm_Amber.cpp
@@ -134,6 +134,10 @@ const Parm_Amber::ParmFlag Parm_Amber::FLAGS_[] = {
   { "CHARMM_CMAP_PARAMETER_",             "%FORMAT(8(F9.5))"}, // CMAP grid
   { "CHARMM_CMAP_INDEX",                  "%FORMAT(6I8)" }, // Atom i,j,k,l,m of cross term and idx
   { "FORCE_FIELD_TYPE",                   "%FORMAT(i2,a78)"},// NOTE: Cannot use with SetFortranType
+  { "CHARGE",                             "%FORMAT(3E24.16)"}, // CHAMBER charge, F_CHM_CHARGE
+  { "ANGLE_EQUIL_VALUE",                  "%FORMAT(3E25.17)"}, // CHAMBER angle eq value, F_CHM_ANGLETEQ
+  { "LENNARD_JONES_ACOEF",                "%FORMAT(3E24.16)"}, // CHAMBER LJ A coef, F_CHM_LJ_A
+  { "LENNARD_JONES_BCOEF",                "%FORMAT(3E24.16)"}, // CHAMBER LJ B coef, F_CHM_LJ_B
   // PDB extra info
   { "RESIDUE_NUMBER", "%FORMAT(20I4)" },                // PDB residue number
   { "RESIDUE_CHAINID", F20a4 },                         // PDB chain ID
@@ -1549,13 +1553,6 @@ int Parm_Amber::processWriteArgs(ArgList& argIn) {
 /** \return Format for given flag. */
 Parm_Amber::FortranData Parm_Amber::WriteFormat(FlagType fflag) const {
   FortranData FMT;
-  // For chamber, certain flags have different format (boo).
-  if (ptype_ == CHAMBER) {
-    if      (fflag == F_CHARGE  ) FMT.ParseFortranFormat("%FORMAT(3E24.16)");
-    else if (fflag == F_ANGLETEQ) FMT.ParseFortranFormat("%FORMAT(3E25.17)");
-    else if (fflag == F_LJ_A    ) FMT.ParseFortranFormat("%FORMAT(3E24.16)");
-    else if (fflag == F_LJ_B    ) FMT.ParseFortranFormat("%FORMAT(3E24.16)");
-  }
   if (FMT.Ftype() == UNKNOWN_FTYPE)
     FMT.ParseFortranFormat( FLAGS_[fflag].Fmt );
   //mprintf("DEBUG: Flag '%s' format '%s'\n", FLAGS_[fflag].Flag, FMT.Fstr());
@@ -2044,10 +2041,11 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
   if (flushFileBuffer( F_NAMES )) return 1;
 
   // CHARGES
-  if (BufferAlloc(F_CHARGE, TopOut.Natom())) return 1;
+  const FlagType f_charge = (ptype_ == CHAMBER) ? F_CHM_CHARGE : F_CHARGE;
+  if (BufferAlloc(f_charge, TopOut.Natom())) return 1;
   for (Topology::atom_iterator atm = TopOut.begin(); atm != TopOut.end(); ++atm)
     file_.DblToBuffer( atm->Charge() * elec_to_parm_ );
-  if (flushFileBuffer( F_CHARGE )) return 1;
+  if (flushFileBuffer( f_charge )) return 1;
 
   // ATOMIC NUMBER
   if (BufferAlloc(F_ATOMICNUM, TopOut.Natom())) return 1;
@@ -2112,11 +2110,12 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
   if (flushFileBuffer( F_ANGLETK )) return 1;
 
   // ANGLE TEQ
-  if (BufferAlloc(F_ANGLETEQ, TopOut.AngleParm().size())) return 1;
+  const FlagType f_angleteq = (ptype_ == CHAMBER) ? F_CHM_ANGLETEQ : F_ANGLETEQ;
+  if (BufferAlloc(f_angleteq, TopOut.AngleParm().size())) return 1;
   for (AngleParmArray::const_iterator it = TopOut.AngleParm().begin();
                                       it != TopOut.AngleParm().end(); ++it)
     file_.DblToBuffer( it->Teq() );
-  if (flushFileBuffer( F_ANGLETEQ )) return 1;
+  if (flushFileBuffer( f_angleteq )) return 1;
 
   // CHARMM only - Urey-Bradley
   if (ptype_ == CHAMBER) {
@@ -2223,7 +2222,9 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
   if (flushFileBuffer( F_SOLTY )) return 1;
 
   // LJ A and B terms
-  if (WriteLJ(F_LJ_A, F_LJ_B, TopOut.Nonbond().NBarray())) return 1;
+  const FlagType f_lj_a = (ptype_ == CHAMBER) ? F_CHM_LJ_A : F_LJ_A;
+  const FlagType f_lj_b = (ptype_ == CHAMBER) ? F_CHM_LJ_B : F_LJ_B;
+  if (WriteLJ(f_lj_a, f_lj_b, TopOut.Nonbond().NBarray())) return 1;
  
   // CHAMBER only - LJ 1-4 terms
   if (ptype_ == CHAMBER) {
diff --git a/src/Parm_Amber.h b/src/Parm_Amber.h
index 2b6d93f2d9..25f021eecf 100644
--- a/src/Parm_Amber.h
+++ b/src/Parm_Amber.h
@@ -22,23 +22,24 @@ class Parm_Amber : public ParmIO {
     enum Type { UNKNOWN_FTYPE=0, FINT, FDOUBLE, FCHAR, FFLOAT };
     /// Enumerated type for Amber Parmtop Flags. KEEP IN SYNC WITH FLAGS_ ARRAY
     enum FlagType {
-      F_POINTERS = 0, F_NAMES,      F_CHARGE,    F_MASS,      F_RESNAMES,
-      F_RESNUMS,      F_TYPES,      F_BONDSH,    F_BONDS,     F_SOLVENT_POINTER,
-      F_ATOMSPERMOL,  F_PARMBOX,    F_ATYPEIDX,  F_NUMEX,     F_NB_INDEX,
-      F_LJ_A,         F_LJ_B,       F_LJ_C,      F_EXCLUDE,   F_RADII,
-      F_SCREEN,       F_BONDRK,     F_BONDREQ,   F_ANGLETK,   F_ANGLETEQ,
-      F_DIHPK,        F_DIHPN,      F_DIHPHASE,  F_SCEE,      F_SCNB,
-      F_SOLTY,        F_ANGLESH,    F_ANGLES,    F_DIHH,      F_DIH,
-      F_ASOL,         F_BSOL,       F_HBCUT,     F_ITREE,     F_JOIN,
-      F_IROTAT,       F_ATOMICNUM,  F_TITLE,     F_RADSET,    F_LES_NTYP,
-      F_LES_TYPE,     F_LES_FAC,    F_LES_CNUM,  F_LES_ID,    F_CAP_INFO,
-      F_CAP_INFO2,    F_IPOL,       F_POLAR,     F_CTITLE,    F_CHM_UBC,
-      F_CHM_UB,       F_CHM_UBFC,   F_CHM_UBEQ,  F_CHM_NIMP,  F_CHM_IMP,
-      F_CHM_NIMPT,    F_CHM_IMPFC,  F_CHM_IMPP,  F_LJ14A,     F_LJ14B,
-      F_CHM_CMAPC,    F_CHM_CMAPR,  F_CHM_CMAPP, F_CHM_CMAPI, F_FF_TYPE,
-      F_PDB_RES,      F_PDB_CHAIN,  F_PDB_ICODE, F_PDB_ALT,   F_PDB_BFAC,
-      F_PDB_OCC,      F_PDB_NUM,    F_CMAPC,     F_CMAPR,     F_CMAPP,
-      F_CMAPI,        F_DIHH_LARGE, F_DIH_LARGE
+      F_POINTERS = 0, F_NAMES,        F_CHARGE,    F_MASS,      F_RESNAMES,
+      F_RESNUMS,      F_TYPES,        F_BONDSH,    F_BONDS,     F_SOLVENT_POINTER,
+      F_ATOMSPERMOL,  F_PARMBOX,      F_ATYPEIDX,  F_NUMEX,     F_NB_INDEX,
+      F_LJ_A,         F_LJ_B,         F_LJ_C,      F_EXCLUDE,   F_RADII,
+      F_SCREEN,       F_BONDRK,       F_BONDREQ,   F_ANGLETK,   F_ANGLETEQ,
+      F_DIHPK,        F_DIHPN,        F_DIHPHASE,  F_SCEE,      F_SCNB,
+      F_SOLTY,        F_ANGLESH,      F_ANGLES,    F_DIHH,      F_DIH,
+      F_ASOL,         F_BSOL,         F_HBCUT,     F_ITREE,     F_JOIN,
+      F_IROTAT,       F_ATOMICNUM,    F_TITLE,     F_RADSET,    F_LES_NTYP,
+      F_LES_TYPE,     F_LES_FAC,      F_LES_CNUM,  F_LES_ID,    F_CAP_INFO,
+      F_CAP_INFO2,    F_IPOL,         F_POLAR,     F_CTITLE,    F_CHM_UBC,
+      F_CHM_UB,       F_CHM_UBFC,     F_CHM_UBEQ,  F_CHM_NIMP,  F_CHM_IMP,
+      F_CHM_NIMPT,    F_CHM_IMPFC,    F_CHM_IMPP,  F_LJ14A,     F_LJ14B,
+      F_CHM_CMAPC,    F_CHM_CMAPR,    F_CHM_CMAPP, F_CHM_CMAPI, F_FF_TYPE,
+      F_CHM_CHARGE,   F_CHM_ANGLETEQ, F_CHM_LJ_A,  F_CHM_LJ_B,
+      F_PDB_RES,      F_PDB_CHAIN,    F_PDB_ICODE, F_PDB_ALT,   F_PDB_BFAC,
+      F_PDB_OCC,      F_PDB_NUM,      F_CMAPC,     F_CMAPR,     F_CMAPP,
+      F_CMAPI,        F_DIHH_LARGE,   F_DIH_LARGE
     };
     /// Used to hold %FLAG/FORMAT string pairs. Corresponds to FlagType.
     struct ParmFlag {

From 877f1c1f22d4320f564e0485646c5b1c875d66b3 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 15 Jan 2026 09:13:29 -0500
Subject: [PATCH 1214/1492] Add more timers but put them behind TIMER define

---
 src/Structure/Builder.cpp | 101 +++++++++++++++++++++++++++++++++++---
 src/Structure/Builder.h   |  18 +++++--
 2 files changed, 110 insertions(+), 9 deletions(-)

diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
index 56a0e240e4..6a0a403b13 100644
--- a/src/Structure/Builder.cpp
+++ b/src/Structure/Builder.cpp
@@ -17,9 +17,21 @@
 using namespace Cpptraj::Structure;
 using namespace Cpptraj::Parm;
 
+#ifdef TIMER
 Timer Builder::timeg_builder_IALsetup_ = Timer();
-Timer Builder::timeg_builder_IALgen_ = Timer();
 Timer Builder::timeg_builder_IALspan_ = Timer();
+Timer Builder::timeg_builder_IALgen_ = Timer();
+Timer Builder::timeg_builder_IALgen_internals_ = Timer();
+Timer Builder::timeg_builder_IALgen_missing_ = Timer();
+Timer Builder::timeg_builder_torsions_ = Timer();
+Timer Builder::timeg_builder_angles_ = Timer();
+Timer Builder::timeg_builder_bonds_ = Timer();
+Timer Builder::timeg_builder_chirality_ = Timer();
+Timer Builder::timeg_ang_search_ = Timer();
+Timer Builder::timeg_ang_model_ = Timer();
+Timer Builder::timeg_MBA_getAngleParam_ = Timer();
+Timer Builder::timeg_MBA_getAtomHybrid_ = Timer();
+#endif
 
 /** CONSTRUCTOR */
 Builder::Builder() :
@@ -968,9 +980,18 @@ double Builder::ModelBondLength(int ai, int aj, Topology const& topIn) const {
 double Builder::ModelBondAngle(int ai, int aj, int ak, Topology const& topIn) const {
   // First look up parameter
   double theta = 0;
+# ifdef TIMER
+  timeg_MBA_getAngleParam_.Start();
+# endif
   if (getAngleParam(theta, ai, aj, ak, topIn)) {
+#   ifdef TIMER
+    timeg_MBA_getAngleParam_.Stop();
+#   endif
     return theta;
   }
+# ifdef TIMER
+  timeg_MBA_getAngleParam_.Stop();
+# endif
   Atom const& AJ = topIn[aj];
   // Figure out hybridization and chirality of atom j.
   if (debug_ > 0) {
@@ -978,8 +999,13 @@ double Builder::ModelBondAngle(int ai, int aj, int ak, Topology const& topIn) co
     mprintf("DEBUG:\t\tJ %s Nbonds: %i\n", AJ.ElementName(), AJ.Nbonds());
     mprintf("DEBUG:\t\tK %s Nbonds: %i\n", topIn[ak].ElementName(), topIn[ak].Nbonds());
   }
+# ifdef TIMER
+  timeg_MBA_getAtomHybrid_.Start();
+# endif
   AtomType::HybridizationType hybrid = getAtomHybridization( AJ, topIn.Atoms() );
-
+# ifdef TIMER
+  timeg_MBA_getAtomHybrid_.Stop();
+# endif
   // Guess hybrid if needed
   //if (hybrid == AtomType::UNKNOWN_HYBRIDIZATION)
   //  hybrid = GuessAtomHybridization(AJ, topIn.Atoms());
@@ -1484,6 +1510,9 @@ int Builder::generateAtomInternals(int at, Frame const& frameIn, Topology const&
   if (debug_ > 0)
     mprintf( "Building internals for: %s\n", topIn.LeapName(at).c_str());
   // Torsions
+# ifdef TIMER
+  timeg_builder_torsions_.Start();
+# endif
   Atom const& AtA = topIn[at];
   for (Atom::bond_iterator bat = AtA.bondbegin(); bat != AtA.bondend(); ++bat) {
     Atom const& AtB = topIn[*bat];
@@ -1506,7 +1535,13 @@ int Builder::generateAtomInternals(int at, Frame const& frameIn, Topology const&
       }
     }
   }
+# ifdef TIMER
+  timeg_builder_torsions_.Stop();
+# endif
   // Angles
+# ifdef TIMER
+  timeg_builder_angles_.Start();
+# endif
   for (Atom::bond_iterator bat = AtA.bondbegin(); bat != AtA.bondend(); ++bat) {
     Atom const& AtB = topIn[*bat];
     for (Atom::bond_iterator cat = AtB.bondbegin(); cat != AtB.bondend(); ++cat) {
@@ -1516,7 +1551,13 @@ int Builder::generateAtomInternals(int at, Frame const& frameIn, Topology const&
                   topIn.LeapName(at).c_str(),
                   topIn.LeapName(*bat).c_str(),
                   topIn.LeapName(*cat).c_str());
+#       ifdef TIMER
+        timeg_ang_search_.Start();
+#       endif
         int aidx = getExistingAngleIdx(at, *bat, *cat);
+#       ifdef TIMER
+        timeg_ang_search_.Stop();
+#       endif
         if (aidx < 0) {
           double dValue = 0;
           if (hasPosition[at] &&
@@ -1527,7 +1568,13 @@ int Builder::generateAtomInternals(int at, Frame const& frameIn, Topology const&
             dValue = CalcAngle(frameIn.XYZ(at), frameIn.XYZ(*bat), frameIn.XYZ(*cat));
           } else {
             if (debug_ > 1) mprintf("Got bond angle from model builder\n");
+#           ifdef TIMER
+            timeg_ang_model_.Start();
+#           endif
             dValue = ModelBondAngle(at, *bat, *cat, topIn);
+#           ifdef TIMER
+            timeg_ang_model_.Stop();
+#           endif
           }
           if (debug_ > 1)
             mprintf("++++Angle INTERNAL: %f  for %s - %s - %s\n", dValue*Constants::RADDEG,
@@ -1541,7 +1588,13 @@ int Builder::generateAtomInternals(int at, Frame const& frameIn, Topology const&
       }
     } // END loop over atoms bonded to B
   } // END loop over atoms bonded to A
+# ifdef TIMER
+  timeg_builder_angles_.Stop();
+# endif
   // Bonds
+# ifdef TIMER
+  timeg_builder_bonds_.Start();
+# endif
   for (Atom::bond_iterator bat = AtA.bondbegin(); bat != AtA.bondend(); ++bat) {
     if (debug_ > 1)
       mprintf("Building bond INTERNAL for: %s - %s\n",
@@ -1568,7 +1621,13 @@ int Builder::generateAtomInternals(int at, Frame const& frameIn, Topology const&
       if (debug_ > 1) mprintf( "Bond length INTERNAL already defined\n" );
     }
   } // END loop over atoms bonded to A
+# ifdef TIMER
+  timeg_builder_bonds_.Stop();
+# endif
   // Chirality
+# ifdef TIMER
+  timeg_builder_chirality_.Start();
+# endif
   double dChi = 0;
   int cidx = getExistingChiralityIdx(at);
   if (determineChirality(dChi, at, frameIn, topIn, hasPosition)) {
@@ -1593,7 +1652,9 @@ int Builder::generateAtomInternals(int at, Frame const& frameIn, Topology const&
         mprintf("Using already-defined chirality (%f).\n", internalChirality_[cidx].ChiralVal());
     }
   }
-
+# ifdef TIMER
+  timeg_builder_chirality_.Stop();
+# endif
   return 0;
 }
 
@@ -1629,7 +1690,9 @@ int Builder::GenerateInternalsAroundLink(int at0, int at1,
     mprintf("DEBUG: ----- Entering Builder::GenerateInternalsAroundLink. -----\n");
     mprintf("DEBUG: Link: %s to %s\n", topIn.AtomMaskName(at0).c_str(), topIn.AtomMaskName(at1).c_str());
   }
+# ifdef TIMER
   timeg_builder_IALsetup_.Start();
+# endif
   // Sanity check
   Atom const& A0 = topIn[at0];
   Atom const& A1 = topIn[at1];
@@ -1651,11 +1714,16 @@ int Builder::GenerateInternalsAroundLink(int at0, int at1,
   else
     // Only want the 'forward' tree
     actualAt1 = at1;
+# ifdef TIMER
   timeg_builder_IALsetup_.Stop();
   timeg_builder_IALspan_.Start();
+# endif
   Iarray span_atoms = GenerateSpanningTree(at0, actualAt1, 4, topIn.Atoms());
+# ifdef TIMER
   timeg_builder_IALspan_.Stop();
   timeg_builder_IALgen_.Start();
+  timeg_builder_IALgen_internals_.Start();
+# endif
   for (Iarray::const_iterator it = span_atoms.begin(); it != span_atoms.end(); ++it)
   {
     //mprintf("SPANNING TREE ATOM: %s\n", *(topIn[*it].Name()));
@@ -1664,6 +1732,10 @@ int Builder::GenerateInternalsAroundLink(int at0, int at1,
       return 1;
     }
   }
+# ifdef TIMER
+  timeg_builder_IALgen_internals_.Stop();
+  timeg_builder_IALgen_missing_.Start();
+# endif
   // FIXME this is a hack to make certain we have all the angle/bond terms we need
   if (debug_ > 0)
     mprintf("DEBUG: LOOKING FOR MISSING ANGLE/BOND PARAMS.\n");
@@ -1680,15 +1752,32 @@ int Builder::GenerateInternalsAroundLink(int at0, int at1,
   }
   if (debug_ > 0)
     mprintf("DEBUG: ----- Leaving Builder::GenerateInternalsAroundLink. -----\n");
+# ifdef TIMER
+  timeg_builder_IALgen_missing_.Stop();
   timeg_builder_IALgen_.Stop();
+# endif
   return 0;
 }
 
+/** Write timing data to stdout. Only availabe if TIMER was defined. */
 void Builder::PrintTiming(int indent, double total)
 {
-  timeg_builder_IALsetup_.WriteTiming(indent, "Internals Around Link Setup : ", total);
-  timeg_builder_IALspan_.WriteTiming (indent, "Internals Around Link Span  : ", total);
-  timeg_builder_IALgen_.WriteTiming  (indent, "Internals Around Link Gen   : ", total);
+# ifdef TIMER
+  timeg_builder_IALsetup_.WriteTiming(indent, "Internals Around Link Setup :", total);
+  timeg_builder_IALspan_.WriteTiming (indent, "Internals Around Link Span  :", total);
+  timeg_builder_IALgen_.WriteTiming  (indent, "Internals Around Link Gen   :", total);
+  timeg_builder_IALgen_missing_.WriteTiming  (indent+1, "Link Gen missing terms  :", timeg_builder_IALgen_.Total());
+  timeg_builder_IALgen_internals_.WriteTiming(indent+1, "Link Gen atom internals :", timeg_builder_IALgen_.Total());
+  timeg_builder_torsions_.WriteTiming (indent+2, "Torsions  :", timeg_builder_IALgen_internals_.Total());
+  timeg_builder_angles_.WriteTiming   (indent+2, "Angles    :", timeg_builder_IALgen_internals_.Total());
+  timeg_ang_search_.WriteTiming(indent+3, "Search :", timeg_builder_angles_.Total());
+  timeg_ang_model_.WriteTiming (indent+3, "Model  :", timeg_builder_angles_.Total());
+  timeg_MBA_getAngleParam_.WriteTiming(indent+4,"GetParam  :", timeg_ang_model_.Total());
+  timeg_MBA_getAtomHybrid_.WriteTiming(indent+4,"GetHybrid :", timeg_ang_model_.Total());
+  timeg_builder_bonds_.WriteTiming    (indent+2, "Bonds     :", timeg_builder_IALgen_internals_.Total());
+  timeg_builder_chirality_.WriteTiming(indent+2, "Chirality :", timeg_builder_IALgen_internals_.Total());
+# endif
+  return;
 }
 
 /** For debugging, print all the complete internals associated with the given atom. */
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
index ce07693948..2b9ec86946 100644
--- a/src/Structure/Builder.h
+++ b/src/Structure/Builder.h
@@ -2,8 +2,9 @@
 #define INC_STRUCTURE_BUILDER_H
 #include <vector>
 #include "../AtomType.h"
-
-#include "../Timer.h" // DEBUG
+#ifdef TIMER
+# include "../Timer.h" // DEBUG
+#endif
 class Atom;
 class Topology;
 class Frame;
@@ -149,10 +150,21 @@ class Builder {
     Larray internalBonds_;
     Carray internalChirality_;
     Iarray Rnums_;               ///< Hold residue indices pertaining to current internals
-
+#   ifdef TIMER
     static Timer timeg_builder_IALsetup_;
     static Timer timeg_builder_IALspan_;
     static Timer timeg_builder_IALgen_;
+    static Timer timeg_builder_IALgen_internals_;
+    static Timer timeg_builder_IALgen_missing_;
+    static Timer timeg_builder_torsions_;
+    static Timer timeg_builder_angles_;
+    static Timer timeg_builder_bonds_;
+    static Timer timeg_builder_chirality_;
+    static Timer timeg_ang_search_;
+    static Timer timeg_ang_model_;
+    static Timer timeg_MBA_getAngleParam_;
+    static Timer timeg_MBA_getAtomHybrid_;
+#   endif
 };
 /// ----- Hold torsion internal ------------------
 class Cpptraj::Structure::Builder::InternalTorsion {

From 19515a4ebb58e9a30e67c82ee4a45ed7310656a1 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 15 Jan 2026 09:21:35 -0500
Subject: [PATCH 1215/1492] Make solvent unit box selection happen inside
 SolvateBox()

---
 src/Exec_Build.cpp        | 8 +-------
 src/Structure/Solvate.cpp | 9 ++++++++-
 src/Structure/Solvate.h   | 6 +++---
 3 files changed, 12 insertions(+), 11 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index c2e0b4da22..7e05189036 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -1203,13 +1203,7 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
     // Record initial number of atoms and residues
     int initial_natom = topOut.Natom();
     int initial_nres = topOut.Nres();
-    // Get solvent unit box
-    DataSet_Coords* solventUnitBox = solvator.GetSolventUnit( DSL );
-    if (solventUnitBox == 0) {
-      mprinterr("Error: Getting solvent unit failed.\n");
-      return CpptrajState::ERR;
-    }
-    if (solvator.SolvateBox( topOut, frameOut, *(creator.MainParmSetPtr()), *solventUnitBox )) {
+    if (solvator.SolvateBox( topOut, frameOut, *(creator.MainParmSetPtr()), DSL )) {
       mprinterr("Error: Adding solvent failed.\n");
       return CpptrajState::ERR;
     }
diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index 8891981770..08bdf4ca78 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -451,7 +451,7 @@ void Solvate::ewald_rotate(Frame& frameOut, double& dPAngle)
 
 /** Create box, fill with solvent */
 int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::ParameterSet const& set0,
-                        DataSet_Coords& SOLVENTBOX)
+                        DataSetList const& DSL)
 {
   mprintf("\tAdding solvent.\n");
   // Sanity check
@@ -460,6 +460,13 @@ int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::Parame
               topOut.c_str(), topOut.Natom(), frameOut.Natom());
     return 1;
   }
+  // Get solvent unit box
+  DataSet_Coords* solventUnitBox = GetSolventUnit( DSL );
+  if (solventUnitBox == 0) {
+    mprinterr("Error: Getting solvent unit failed.\n");
+    return 1;
+  }
+  DataSet_Coords& SOLVENTBOX = static_cast<DataSet_Coords&>( *solventUnitBox );
 
   // TODO Remove any existing box info?
   //if (frameOut.BoxCrd.HasBox())
diff --git a/src/Structure/Solvate.h b/src/Structure/Solvate.h
index b5f2e82d89..2acca0d2a4 100644
--- a/src/Structure/Solvate.h
+++ b/src/Structure/Solvate.h
@@ -25,19 +25,19 @@ class Solvate {
     /// Set VDW bounding box
     int SetVdwBoundingBox(Topology&, Frame&, Cpptraj::Parm::ParameterSet const& set0);
     /// Solvate with box
-    int SolvateBox(Topology&, Frame&, Cpptraj::Parm::ParameterSet const&, DataSet_Coords&);
+    int SolvateBox(Topology&, Frame&, Cpptraj::Parm::ParameterSet const&, DataSetList const&);
 
     static const char* SetboxKeywords();
     static const char* SolvateKeywords1();
     static const char* SolvateKeywords2();
 
-    /// \return Solvent unit selected from given DataSetList
-    DataSet_Coords* GetSolventUnit(DataSetList const&) const;
     /// \return Solvent box name
     std::string const& SolventBoxName() const { return solventBoxName_; }
     /// Print solvate info to stdout
     void PrintSolvateInfo() const;
   private:
+    /// \return Solvent unit selected from given DataSetList
+    DataSet_Coords* GetSolventUnit(DataSetList const&) const;
     /// Get buffer arguments
     int getBufferArg(ArgList&, double);
     /// Get radii for atoms in topology

From 1d7c897beb6a314d7a1d2fb6b4bcc1536cd90ef5 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 15 Jan 2026 12:06:13 -0500
Subject: [PATCH 1216/1492] Start code for targeted number of waters, dont
 enable yet.

---
 src/Structure/Solvate.cpp | 145 ++++++++++++++++++++++++++++++++++++--
 src/Structure/Solvate.h   |   5 ++
 2 files changed, 144 insertions(+), 6 deletions(-)

diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index 08bdf4ca78..845ce60888 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -14,6 +14,7 @@ using namespace Cpptraj::Structure;
 /** CONSTRUCTOR */
 Solvate::Solvate() :
   debug_(0),
+  nsolvent_(0),
   bufferX_(0),
   bufferY_(0),
   bufferZ_(0),
@@ -30,7 +31,8 @@ const char* Solvate::SetboxKeywords() {
 }
 
 const char* Solvate::SolvateKeywords1() {
-  return "{buffer <buffer> | bufx <bufx> bufy <bufy> bufz <bufz>}";
+  //return "{buffer <buffer> | bufx <bufx> bufy <bufy> bufz <bufz> | nsolvent <#>}";
+  return "{buffer <buffer> | bufx <bufx> bufy <bufy> bufz <bufz> }";
 }
 
 const char* Solvate::SolvateKeywords2() {
@@ -50,9 +52,11 @@ int Solvate::getBufferArg(ArgList& argIn, double defaultBuffer) {
     bufferZ_ = argIn.getKeyDouble("bufz", defaultBuffer);
     bufferD_ = argIn.getKeyDouble("bufd", defaultBuffer);
   }
-  if (bufferX_ < 0 || bufferY_ < 0 || bufferZ_ < 0) {
-    mprinterr("Error: Either 'buffer' or 'bufx/bufy/bufx' must be specified and >= 0\n");
-    return 1;
+  if (nsolvent_ < 1) {
+    if (bufferX_ < 0 || bufferY_ < 0 || bufferZ_ < 0) {
+      mprinterr("Error: Either 'buffer' or 'bufx/bufy/bufx' must be specified and >= 0\n");
+      return 1;
+    }
   }
   return 0;
 }
@@ -61,6 +65,8 @@ int Solvate::getBufferArg(ArgList& argIn, double defaultBuffer) {
 int Solvate::InitSolvate(ArgList& argIn, bool octIn, int debugIn) {
   debug_ = debugIn;
   doTruncatedOct_ = octIn;
+  //nsolvent_ = (unsigned int)argIn.getKeyInt("nsolvent", 0);
+  nsolvent_ = 0; // TODO enable
 
   if (getBufferArg(argIn, -1.0)) return 1;
 
@@ -95,6 +101,7 @@ int Solvate::InitSolvate(ArgList& argIn, bool octIn, int debugIn) {
 /** Initialize args for setbox */
 int Solvate::InitSetbox(ArgList& argIn, int debugIn) {
   debug_ = debugIn;
+  nsolvent_ = 0;
 
   if (getBufferArg(argIn, 0.0)) return 1;
 
@@ -107,6 +114,8 @@ void Solvate::PrintSolvateInfo() const {
     mprintf("\tAdding solvent from %s using a truncated octahedral unit cell.\n", solventBoxName_.c_str());
   else
     mprintf("\tAdding solvent from %s using an orthorhombic unit cell.\n", solventBoxName_.c_str());
+  if (nsolvent_ > 0)
+    mprintf("\t  %u target number of solvent molecules.\n", nsolvent_);
   mprintf("\t  Solvent buffer XYZ: %g %g %g Ang.\n", bufferX_, bufferY_, bufferZ_);
   mprintf("\t  Solvent closeness: %g Ang.\n", closeness_);
   if (isotropic_)
@@ -149,7 +158,7 @@ DataSet_Coords* Solvate::GetSolventUnit(DataSetList const& DSL) const {
     }
   }
   if (solventUnit != 0)
-    mprintf("\tSolvent unit: %s\n", solventUnit->legend());
+    mprintf("\t  Solvent unit: %s\n", solventUnit->legend());
   else
     mprinterr("Error: Could not get solvent unit named %s\n", solventBoxName_.c_str());
 
@@ -449,10 +458,131 @@ void Solvate::ewald_rotate(Frame& frameOut, double& dPAngle)
   dPAngle = tetra_angl*180./pi;
 }
 
+/** Adjust box widths */
+void Solvate::adjustBoxWidths(double& dXWidth, double& dYWidth, double& dZWidth,
+                              double& boxX, double& boxY, double& boxZ)
+const
+{
+  if (isotropic_) {
+    double dTemp = dXWidth * dYWidth * dZWidth;
+
+    double dMax = std::max(dXWidth, dYWidth);
+    dMax = std::max(dMax, dZWidth);
+    dXWidth = dYWidth = dZWidth = dMax;
+
+    dTemp = (dMax * dMax * dMax - dTemp ) / dTemp;
+
+    mprintf("\t  Total bounding box for atom centers:  %5.3f %5.3f %5.3f\n", 
+            dXWidth, dYWidth, dZWidth );
+    mprintf("\t      (box expansion for 'iso' is %5.1lf%%)\n", dTemp * 100.0 );
+
+     // To make the actual clip right, 'iso' the solute box
+    dTemp = std::max(boxX, boxY);
+    dTemp = std::max(dTemp, boxZ);
+    //dXBox = dYBox = dZBox = dTemp;
+    boxX = boxY = boxZ = dTemp;
+  } else
+    mprintf("\t  Total bounding box for atom centers:  %5.3f %5.3f %5.3f\n", 
+            dXWidth, dYWidth, dZWidth );
+}
+
+/** Create box, fill with target number of solvent molecules. */
+int Solvate::SolvateBoxWithExactNumber(Topology& topOut, Frame& frameOut, Cpptraj::Parm::ParameterSet const& set0,
+                                       DataSetList const& DSL)
+{
+  mprintf("\tAdding %u solvent molecules.\n", nsolvent_);
+  if (nsolvent_ < 1) return 0;
+  // Sanity check
+  if (topOut.Natom() != frameOut.Natom()) {
+    mprinterr("Internal Error: Solvate::SolvateBox(): Topology %s #atoms %i != frame #atoms %i\n",
+              topOut.c_str(), topOut.Natom(), frameOut.Natom());
+    return 1;
+  }
+  // Get solvent unit box
+  DataSet_Coords* solventUnitBox = GetSolventUnit( DSL );
+  if (solventUnitBox == 0) {
+    mprinterr("Error: Getting solvent unit failed.\n");
+    return 1;
+  }
+  DataSet_Coords& SOLVENTBOX = static_cast<DataSet_Coords&>( *solventUnitBox );
+
+  // TODO check COORDS size
+  Frame solventFrame = SOLVENTBOX.AllocateFrame();
+  SOLVENTBOX.GetFrame(0, solventFrame);
+
+  // Set vdw box for solvent
+  double solventBoxVol = 0;
+  double solventMaxR;
+  std::vector<double> solventRadii = getAtomRadii(solventMaxR, SOLVENTBOX.Top(), set0);
+  double solventX, solventY, solventZ;
+  if (solventFrame.BoxCrd().HasBox()) {
+    // Use input box lengths
+    // TODO check ortho?
+    solventX = solventFrame.BoxCrd().Param(Box::X);
+    solventY = solventFrame.BoxCrd().Param(Box::Y);
+    solventZ = solventFrame.BoxCrd().Param(Box::Z);
+    solventBoxVol = solventFrame.BoxCrd().CellVolume();
+  } else {
+    if (setVdwBoundingBox(solventX, solventY, solventZ, solventRadii, solventFrame, false)) {
+      mprinterr("Error: Setting vdw bounding box for %s failed.\n", SOLVENTBOX.legend());
+      return 1;
+    }
+    solventBoxVol = solventX * solventY * solventZ;
+  }
+  mprintf("\t  Solvent unit box:                     %5.3f %5.3f %5.3f (%g Ang^3)\n", solventX, solventY, solventZ, solventBoxVol);
+
+  // Set solute box
+  double soluteMaxR;
+  std::vector<double> soluteRadii = getAtomRadii(soluteMaxR, topOut, set0);
+  double boxX, boxY, boxZ;
+  if (setVdwBoundingBox(boxX, boxY, boxZ, soluteRadii, frameOut, isotropic_)) {
+    mprinterr("Error: Setting vdw bounding box for %s failed.\n", topOut.c_str());
+    return 1;
+  }
+  // Check if buffers need to be increased for trunc oct.
+  if (doTruncatedOct_)
+    octBoxCheck( frameOut );
+  mprintf("\t  Solute vdw bounding box:              %-5.3f %-5.3f %-5.3f\n", boxX, boxY, boxZ);
+
+  // Ratio of solute box size to solvent box size 
+  double soluteFac = (boxX*boxY*boxZ) / solventBoxVol;
+  mprintf("\t  Solute is %g times the solvent box.\n", soluteFac);
+  // Estimate how many solvent molecules will be removed by solvent
+  unsigned int nMolsRemovedBySolute = (unsigned int)ceil( soluteFac * (double)SOLVENTBOX.Top().Nmol() );
+  mprintf("\t  Estimating approximately %u solvent molecules will be removed by solute.\n", nMolsRemovedBySolute);
+  //unsigned int nBoxesForSolvent = (unsigned int)ceil( (double)nsolvent / (double)SOLVENTBOX.Top().Nmol() );
+  // Calculate the solvent box density
+  double solventBoxDensity = (double)SOLVENTBOX.Top().Nmol() / solventBoxVol;
+  mprintf("\t  Solvent box density is %g mols/Ang^3\n", solventBoxDensity);
+  // Calculate how many solvent molecules we actually need to add given that solute will remove some
+  unsigned int neededNumberOfSolvent = nsolvent_ + nMolsRemovedBySolute;
+  // Calculate what volume of solvent is needed to hit the actual solvent molecule target
+  double tgtVol = (double)neededNumberOfSolvent / solventBoxDensity;
+  mprintf("\t  Target volume: %g Ang^3\n", tgtVol);
+  // Calculate number of solvent boxes needed
+  //unsigned int neededNumberOfBoxes = (unsigned int)ceil( tgtVol / solventBoxVol );
+  //mprintf("\t  Need %u solvent boxes.\n", neededNumberOfBoxes);
+  double tgtLen = pow(tgtVol, (1.0/3.0));
+  mprintf("\t  Target length: %g Ang\n", tgtLen);
+  double bX = (tgtLen - boxX) / 2.0;
+  double bY = (tgtLen - boxY) / 2.0;
+  double bZ = (tgtLen - boxZ) / 2.0;
+  mprintf("\t  Buffer: %g %g %g\n", bX, bY, bZ);
+  
+  //unsigned int nSolventBoxesNeeded = (unsigned int)ceil( (double)neededNumberOfSolvent / (double)SOLVENTBOX.Top().Nmol() );
+  //mprintf("\t  Estimating %u solvent boxes will be needed.\n", nSolventBoxesNeeded);
+
+
+  return 0;
+}
+
 /** Create box, fill with solvent */
 int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::ParameterSet const& set0,
                         DataSetList const& DSL)
 {
+  if (nsolvent_ > 0) {
+    return SolvateBoxWithExactNumber(topOut, frameOut, set0, DSL);
+  }
   mprintf("\tAdding solvent.\n");
   // Sanity check
   if (topOut.Natom() != frameOut.Natom()) {
@@ -492,6 +622,8 @@ int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::Parame
   double dYWidth = boxY + bufferY_ * 2;
   double dZWidth = boxZ + bufferZ_ * 2;
 
+  adjustBoxWidths(dXWidth, dYWidth, dZWidth, boxX, boxY, boxZ);
+/*
   if (isotropic_) {
     double dTemp = dXWidth * dYWidth * dZWidth;
 
@@ -513,6 +645,7 @@ int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::Parame
   } else
     mprintf("\t  Total bounding box for atom centers:  %5.3f %5.3f %5.3f\n", 
             dXWidth, dYWidth, dZWidth );
+*/
 
   if (clip_) {
     //  If the solvated system should be clipped to the exact
@@ -543,7 +676,7 @@ int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::Parame
     solventZ = solventFrame.BoxCrd().Param(Box::Z);
   } else {
     if (setVdwBoundingBox(solventX, solventY, solventZ, solventRadii, solventFrame, false)) {
-      mprinterr("Error: Setting vdw bounding box for %s failed.\n", topOut.c_str());
+      mprinterr("Error: Setting vdw bounding box for %s failed.\n", SOLVENTBOX.legend());
       return 1;
     }
   }
diff --git a/src/Structure/Solvate.h b/src/Structure/Solvate.h
index 2acca0d2a4..fcdf597685 100644
--- a/src/Structure/Solvate.h
+++ b/src/Structure/Solvate.h
@@ -38,6 +38,10 @@ class Solvate {
   private:
     /// \return Solvent unit selected from given DataSetList
     DataSet_Coords* GetSolventUnit(DataSetList const&) const;
+    /// Adjust box widths
+    void adjustBoxWidths(double&, double&, double&, double&, double&, double&) const;
+    /// Solvate with box and specified number of solvent
+    int SolvateBoxWithExactNumber(Topology&, Frame&, Cpptraj::Parm::ParameterSet const&, DataSetList const&);
     /// Get buffer arguments
     int getBufferArg(ArgList&, double);
     /// Get radii for atoms in topology
@@ -65,6 +69,7 @@ class Solvate {
                         std::vector<double> const&, std::vector<double> const&) const;
 
     int debug_;
+    unsigned int nsolvent_;
     double bufferX_;
     double bufferY_;
     double bufferZ_;

From c11afeda3df75e798fc08a47788b4c521e87267f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 15 Jan 2026 12:12:33 -0500
Subject: [PATCH 1217/1492] Hide debug

---
 src/DataSet_Coords.cpp | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/src/DataSet_Coords.cpp b/src/DataSet_Coords.cpp
index ce9a2777b8..ed097df7ac 100644
--- a/src/DataSet_Coords.cpp
+++ b/src/DataSet_Coords.cpp
@@ -21,6 +21,10 @@ void DataSet_Coords::UpdateCoordsInfoBox( Box const& boxIn ) {
 /** Copy the incoming topology if different from current topology. */
 void DataSet_Coords::set_topology(Topology const& topIn)
 {
+  if (&topIn != &top_) {
+    top_ = topIn;
+  }
+/*
   if (&topIn == &top_) {
     mprintf("DEBUG: set_topology called with existing topology (%s)\n", top_.c_str());
   } else {
@@ -28,4 +32,5 @@ void DataSet_Coords::set_topology(Topology const& topIn)
       mprintf("DEBUG: set_topology: overwriting top %s with top %s\n", top_.c_str(), topIn.c_str());
     top_ = topIn;
   }
+*/
 }

From b1ee7693607122e17a31e7edf5361922b7df6470 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 16 Jan 2026 09:46:29 -0500
Subject: [PATCH 1218/1492] Combine sugar terminel functional group check with
 the regular functional group check. Save the new residue numbers and types of
 detected functional groups

---
 src/Structure/FxnGroupBuilder.cpp | 24 ++++++++++++++++---
 src/Structure/FxnGroupBuilder.h   | 40 ++++++++++++++++++++++++-------
 src/Structure/SugarBuilder.cpp    | 26 +++++++++++---------
 3 files changed, 67 insertions(+), 23 deletions(-)

diff --git a/src/Structure/FxnGroupBuilder.cpp b/src/Structure/FxnGroupBuilder.cpp
index 1fe421aa12..7cdfb57624 100644
--- a/src/Structure/FxnGroupBuilder.cpp
+++ b/src/Structure/FxnGroupBuilder.cpp
@@ -285,9 +285,16 @@ const
 
 /** Check for functional groups that need to be separate residues. */
 int FxnGroupBuilder::CheckForFunctionalGroups(Sugar& sugar, Topology& topIn, Frame& frameIn)
-const
 {
+  resTypes_.clear();
   int rnum = sugar.ResNum(topIn);
+  // First check if there is a terminal group on the sugar anomeric carbon
+  if (CheckIfSugarIsTerminal( sugar, topIn, frameIn )) {
+    mprinterr("Error: Checking if if sugar %s has terminal functional groups failed.\n",
+              topIn.TruncResNameOnumId(sugar.ResNum(topIn)).c_str());
+    return 1;
+  }
+  // Check the rest of the sugar
   int original_at0 = topIn.Res(rnum).FirstAtom();
   int original_at1 = topIn.Res(rnum).LastAtom();
   std::string sugarName = topIn.TruncResNameOnumId(rnum);
@@ -385,8 +392,9 @@ const
                   sugarName.c_str());
         return 1;
       }
-      // Set the split residue as terminal
+      // Set the split residue as terminal, increment the residue offset
       topIn.SetRes(rnum+1).SetTerminal(true);
+      resTypes_.push_back( groupType );
       // Reorder the frame to match
       Frame oldFrame = frameIn;
       frameIn.SetCoordinatesByMap( oldFrame, atomMap );
@@ -398,6 +406,16 @@ const
     //atomsRemain = false; // DEBUG
   } // END while atoms remain
 
+  // Record new residue numbers for found types.
+  int resOffset = (int)resTypes_.size();
+  mprintf("DEBUG: Split off %i groups from residue %i: ", resOffset, rnum+1);
+  for (FTarray::const_iterator rt = resTypes_.begin(); rt != resTypes_.end(); ++rt) {
+    mprintf(" %i:%s", rnum+resOffset+1, FunctionalGroup::typeString(*rt)); // DEBUG
+    foundGroups_.push_back( FxnResType(rnum+resOffset, *rt) );
+    --resOffset;
+  }
+  mprintf("\n"); // DEBUG
+
   return 0;
 }
 
@@ -405,7 +423,6 @@ const
   * to be a separate ROH residue.
   */
 int FxnGroupBuilder::CheckIfSugarIsTerminal(Sugar& sugar, Topology& topIn, Frame& frameIn)
-const
 {
   int rnum = sugar.ResNum(topIn);
   int anomericAtom = sugar.AnomericAtom();
@@ -484,6 +501,7 @@ const
   }
   // Set the split residue as terminal
   topIn.SetRes(rnum+1).SetTerminal(true);
+  resTypes_.push_back( groupType );
   // DEBUG
   //for (int at = original_at0; at != original_at1; at++)
   //  mprintf("DEBUG:\t\tAtomMap[%i] = %i\n", at, atomMap[at]);
diff --git a/src/Structure/FxnGroupBuilder.h b/src/Structure/FxnGroupBuilder.h
index 3a1fb06c45..26379eaabd 100644
--- a/src/Structure/FxnGroupBuilder.h
+++ b/src/Structure/FxnGroupBuilder.h
@@ -9,18 +9,23 @@ namespace Structure {
 class Sugar;
 /// Class to help prepare recognized functional groups
 // TODO change function names, update help text
-// TODO combine CheckForFunctionalGroups and CheckIfSugarIsTerminal
 class FxnGroupBuilder {
- public:
-   /// CONSTRUCTOR - take debug level
-   FxnGroupBuilder(int);
-    /// Determine if sugar has sulfates that need SO3 residue(s)
-    int CheckForFunctionalGroups(Sugar&, Topology&, Frame&) const;
-    /// Determine if sugar is terminal and need an ROH residue
-    int CheckIfSugarIsTerminal(Sugar&, Topology&, Frame&) const;
+  public:
+    class FxnResType;
+    /// CONSTRUCTOR - take debug level
+    FxnGroupBuilder(int);
+    /// Determine if sugar has functional groups that need to be split off into separate residues
+    int CheckForFunctionalGroups(Sugar&, Topology&, Frame&);
+
+    typedef std::vector<FxnResType>::const_iterator const_iterator;
+    const_iterator begin() const { return foundGroups_.begin(); }
+    const_iterator end() const { return foundGroups_.end(); }
+    unsigned int NgroupsFound() const { return foundGroups_.size(); }
   private:
     typedef std::vector<int> Iarray;
     typedef std::vector<FunctionalGroup> FGarray;
+    typedef std::vector<FxnResType> FRarray;
+    typedef std::vector<FunctionalGroup::Type> FTarray;
     /// \return identity of the group bonded to given atom
     FunctionalGroup::Type IdFunctionalGroup_Silent(Iarray&, int, int, int, Topology const&) const;
     /// \return identity of the group bonded to given atom, print to stdout
@@ -31,10 +36,27 @@ class FxnGroupBuilder {
     /// \return Functional group if one is recognized
     FGarray::const_iterator GetGroup(Iarray&, Iarray const&, int, int, Topology const&) const;
 
-    FGarray functionalGroups_; ///< Recognized functional groups (FunctionalGroupType).
+    /// Determine if sugar anomeric carbon has a terminal functional group
+    int CheckIfSugarIsTerminal(Sugar&, Topology&, Frame&);
+
+    FGarray functionalGroups_; ///< Functional groups to search for (FunctionalGroupType).
+    FRarray foundGroups_;      ///< Groups that have been found
+    FTarray resTypes_;         ///< Groups that have been found in current call of CheckForFunctionalGroups()
     int debug_;                ///< Debug level
 
 };
+// -----------------------------------------------------------------------------
+/// Used to keep track of found functional groups
+class FxnGroupBuilder::FxnResType {
+  public:
+    FxnResType() : ires_(-1), ftype_(FunctionalGroup::UNRECOGNIZED_GROUP) {}
+    FxnResType(int ir, FunctionalGroup::Type ft) : ires_(ir), ftype_(ft) {}
+    int Ires() const { return ires_; }
+    FunctionalGroup::Type Ftype() const { return ftype_; }
+  private:
+    int ires_; ///< Residue # of the functional group
+    FunctionalGroup::Type ftype_; ///< Type of functional group
+};
 }
 }
 #endif
diff --git a/src/Structure/SugarBuilder.cpp b/src/Structure/SugarBuilder.cpp
index 46e359628c..069e3c736d 100644
--- a/src/Structure/SugarBuilder.cpp
+++ b/src/Structure/SugarBuilder.cpp
@@ -1887,16 +1887,16 @@ int SugarBuilder::FixSugarsStructure(Topology& topIn, Frame& frameIn,
   FxnGroupBuilder FGB(debug_);
   if (splitres) {
     // Loop over sugar indices to see if residues have ROH that must be split off
-    for (std::vector<Sugar>::iterator sugar = Sugars_.begin();
-                                      sugar != Sugars_.end(); ++sugar)
-    {
-      if (sugar->NotSet()) continue;
-      if (FGB.CheckIfSugarIsTerminal(*sugar, topIn, frameIn)) {
-        mprinterr("Error: Checking if sugar %s has terminal functional groups failed.\n",
-                  topIn.TruncResNameOnumId(sugar->ResNum(topIn)).c_str());
-        return 1;
-      }
-    } // End loop over sugar indices
+    //for (std::vector<Sugar>::iterator sugar = Sugars_.begin();
+    //                                  sugar != Sugars_.end(); ++sugar)
+    //{
+    //  if (sugar->NotSet()) continue;
+    //  if (FGB.CheckIfSugarIsTerminal(*sugar, topIn, frameIn)) {
+    //    mprinterr("Error: Checking if sugar %s has terminal functional groups failed.\n",
+    //              topIn.TruncResNameOnumId(sugar->ResNum(topIn)).c_str());
+    //    return 1;
+    //  }
+    //} // End loop over sugar indices
 
     // Loop over chain indices to see if residues need to be split
     for (std::vector<Sugar>::iterator sugar = Sugars_.begin();
@@ -1914,7 +1914,11 @@ int SugarBuilder::FixSugarsStructure(Topology& topIn, Frame& frameIn,
     //                                    sugar != sugarResidues.end(); ++sugar)
     //  sugar->PrintInfo(topIn);
   }
-
+  if (FGB.NgroupsFound() > 0) {
+    mprintf("\t  Found %u functional groups:\n", FGB.NgroupsFound());
+    for (FxnGroupBuilder::const_iterator it = FGB.begin(); it != FGB.end(); ++it)
+      mprintf("\t    %li : %s (%s)\n", it - FGB.begin(), topIn.TruncResNameNum(it->Ires()).c_str(), FunctionalGroup::typeString(it->Ftype()));
+  }
 
   return 0;
 }

From 95765c2599bb0d14a57c9be4032348986b7a640b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 16 Jan 2026 10:02:18 -0500
Subject: [PATCH 1219/1492] Make the functional group builder persistent

---
 src/Structure/FxnGroupBuilder.cpp | 14 ++++++-----
 src/Structure/SugarBuilder.cpp    | 39 ++++++++++++++-----------------
 src/Structure/SugarBuilder.h      |  4 ++++
 3 files changed, 30 insertions(+), 27 deletions(-)

diff --git a/src/Structure/FxnGroupBuilder.cpp b/src/Structure/FxnGroupBuilder.cpp
index 7cdfb57624..12c3fd2ae9 100644
--- a/src/Structure/FxnGroupBuilder.cpp
+++ b/src/Structure/FxnGroupBuilder.cpp
@@ -408,13 +408,15 @@ int FxnGroupBuilder::CheckForFunctionalGroups(Sugar& sugar, Topology& topIn, Fra
 
   // Record new residue numbers for found types.
   int resOffset = (int)resTypes_.size();
-  mprintf("DEBUG: Split off %i groups from residue %i: ", resOffset, rnum+1);
-  for (FTarray::const_iterator rt = resTypes_.begin(); rt != resTypes_.end(); ++rt) {
-    mprintf(" %i:%s", rnum+resOffset+1, FunctionalGroup::typeString(*rt)); // DEBUG
-    foundGroups_.push_back( FxnResType(rnum+resOffset, *rt) );
-    --resOffset;
+  if (resOffset > 0) {
+    mprintf("DEBUG: Split off %i groups from residue %i: ", resOffset, rnum+1);
+    for (FTarray::const_iterator rt = resTypes_.begin(); rt != resTypes_.end(); ++rt) {
+      mprintf(" %i:%s", rnum+resOffset+1, FunctionalGroup::typeString(*rt)); // DEBUG
+      foundGroups_.push_back( FxnResType(rnum+resOffset, *rt) );
+      --resOffset;
+    }
+    mprintf("\n"); // DEBUG
   }
-  mprintf("\n"); // DEBUG
 
   return 0;
 }
diff --git a/src/Structure/SugarBuilder.cpp b/src/Structure/SugarBuilder.cpp
index 069e3c736d..a8d92b3696 100644
--- a/src/Structure/SugarBuilder.cpp
+++ b/src/Structure/SugarBuilder.cpp
@@ -20,9 +20,15 @@ SugarBuilder::SugarBuilder(int debugIn) :
   offset_(0.2),
   hasGlycam_(false),
   useSugarName_(false),
-  debug_(debugIn)
+  debug_(debugIn),
+  FGB_(0)
 {}
 
+/** DESTRUCTOR */
+SugarBuilder::~SugarBuilder() {
+  if (FGB_ != 0) delete FGB_;
+}
+
 /** Initialize options. */
 int SugarBuilder::InitOptions(bool hasGlycamIn,
                               double rescutIn,
@@ -1884,26 +1890,17 @@ int SugarBuilder::FixSugarsStructure(Topology& topIn, Frame& frameIn,
   //for (std::vector<Sugar>::const_iterator sugar = sugarResidues.begin();
   //                                    sugar != sugarResidues.end(); ++sugar)
   //  sugar->PrintInfo(topIn);
-  FxnGroupBuilder FGB(debug_);
+
   if (splitres) {
-    // Loop over sugar indices to see if residues have ROH that must be split off
-    //for (std::vector<Sugar>::iterator sugar = Sugars_.begin();
-    //                                  sugar != Sugars_.end(); ++sugar)
-    //{
-    //  if (sugar->NotSet()) continue;
-    //  if (FGB.CheckIfSugarIsTerminal(*sugar, topIn, frameIn)) {
-    //    mprinterr("Error: Checking if sugar %s has terminal functional groups failed.\n",
-    //              topIn.TruncResNameOnumId(sugar->ResNum(topIn)).c_str());
-    //    return 1;
-    //  }
-    //} // End loop over sugar indices
-
-    // Loop over chain indices to see if residues need to be split
+    if (FGB_ != 0)
+      delete FGB_;
+    FGB_ = new FxnGroupBuilder(debug_);
+    // Loop over chain indices to see if functional groups should be split into separate residues
     for (std::vector<Sugar>::iterator sugar = Sugars_.begin();
                                       sugar != Sugars_.end(); ++sugar)
     {
       if (sugar->NotSet()) continue;
-      if (FGB.CheckForFunctionalGroups(*sugar, topIn, frameIn)) {
+      if (FGB_->CheckForFunctionalGroups(*sugar, topIn, frameIn)) {
         mprinterr("Error: Checking if sugar %s has functional groups failed.\n",
                  topIn.TruncResNameOnumId( sugar->ResNum(topIn) ).c_str());
         return 1;
@@ -1913,11 +1910,11 @@ int SugarBuilder::FixSugarsStructure(Topology& topIn, Frame& frameIn,
     //for (std::vector<Sugar>::const_iterator sugar = sugarResidues.begin();
     //                                    sugar != sugarResidues.end(); ++sugar)
     //  sugar->PrintInfo(topIn);
-  }
-  if (FGB.NgroupsFound() > 0) {
-    mprintf("\t  Found %u functional groups:\n", FGB.NgroupsFound());
-    for (FxnGroupBuilder::const_iterator it = FGB.begin(); it != FGB.end(); ++it)
-      mprintf("\t    %li : %s (%s)\n", it - FGB.begin(), topIn.TruncResNameNum(it->Ires()).c_str(), FunctionalGroup::typeString(it->Ftype()));
+    if (FGB_->NgroupsFound() > 0) {
+      mprintf("\t  Found %u functional groups:\n", FGB_->NgroupsFound());
+      for (FxnGroupBuilder::const_iterator it = FGB_->begin(); it != FGB_->end(); ++it)
+        mprintf("\t    %li : %s (%s)\n", it - FGB_->begin(), topIn.TruncResNameNum(it->Ires()).c_str(), FunctionalGroup::typeString(it->Ftype()));
+    }
   }
 
   return 0;
diff --git a/src/Structure/SugarBuilder.h b/src/Structure/SugarBuilder.h
index c2de4208b3..4c309e10f5 100644
--- a/src/Structure/SugarBuilder.h
+++ b/src/Structure/SugarBuilder.h
@@ -8,6 +8,7 @@ class NameType;
 namespace Cpptraj {
 namespace Structure {
 // Forward declares
+class FxnGroupBuilder;
 class Sugar;
 class ResStatArray;
 /// Class for preparing sugars in a topology
@@ -17,6 +18,8 @@ class SugarBuilder {
     typedef std::vector<Sugar> Array;
     /// CONSTRUCTOR - Take debug level
     SugarBuilder(int);
+    /// DESTRUCTOR
+    ~SugarBuilder();
     /// Init options: hasGlycam, residue cutoff, bond offset, sugar mask str, determineSugarsBy, resmapfile
     int InitOptions(bool, double, double, std::string const&, std::string const&, std::string const&);
     /// \return true if given res name is a recognized PDB sugar
@@ -118,6 +121,7 @@ class SugarBuilder {
     bool useSugarName_;        ///< If true, base form/chirality on name instead of geometry
     AtomMap myMap_;            ///< Used to determine unique atoms for chirality
     int debug_;
+    FxnGroupBuilder* FGB_;
 };
 }
 }

From 93daeb596261f5122f88d38dc36545218a8d149c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 16 Jan 2026 10:18:05 -0500
Subject: [PATCH 1220/1492] Leap function group warnings are now in
 FxnGroupBuilder

---
 src/Exec_PrepareForLeap.cpp       | 18 ++----------------
 src/Exec_PrepareForLeap.h         |  2 --
 src/Structure/FxnGroupBuilder.cpp | 18 ++++++++++++++++++
 src/Structure/FxnGroupBuilder.h   |  2 ++
 src/Structure/SugarBuilder.cpp    |  6 ++++++
 src/Structure/SugarBuilder.h      |  2 ++
 6 files changed, 30 insertions(+), 18 deletions(-)

diff --git a/src/Exec_PrepareForLeap.cpp b/src/Exec_PrepareForLeap.cpp
index 4e9719f948..689a2afcff 100644
--- a/src/Exec_PrepareForLeap.cpp
+++ b/src/Exec_PrepareForLeap.cpp
@@ -442,21 +442,6 @@ int Exec_PrepareForLeap::RunLeap(std::string const& ff_file,
   return 0;
 }
 
-/** Print warnings for residues that will need to be modified in leap. */
-void Exec_PrepareForLeap::LeapFxnGroupWarning(Topology const& topIn, int rnum) {
-  Residue const& res = topIn.Res(rnum);
-  if ( res.Name() == "SO3" ) {
-    mprintf("Warning: Residue '%s'; after LEaP, will need to adjust the charge on the link oxygen by +0.031.\n",
-            topIn.TruncResNameNum(rnum).c_str());
-  } else if ( res.Name() == "MEX" ) {
-    mprintf("Warning: Residue '%s'; after LEaP, will need to adjust the charge on the carbon bonded to link oxygen by -0.039.\n",
-            topIn.TruncResNameNum(rnum).c_str());
-  } else if ( res.Name() == "ACX" ) {
-    mprintf("Warning: Residue '%s'; after LEaP, will need to adjust the charge on the carbon bonded to link oxygen by +0.008.\n",
-            topIn.TruncResNameNum(rnum).c_str());
-  }
-}
-
 /** Try to download missing parameters. */
 int Exec_PrepareForLeap::DownloadParameters(ResStatArray& resStat, RmapType const& resNames,
                                             Topology const& topIn, CpptrajFile* leapInput,
@@ -1008,6 +993,8 @@ Exec::RetType Exec_PrepareForLeap::Execute(CpptrajState& State, ArgList& argIn)
     mprinterr("Internal Error: Could not allocate problemout file.\n");
     return CpptrajState::ERR;
   }
+  // Print warnings related to functional groups
+  sugarBuilder.PrintFxnGroupWarnings(topIn);
   //mprintf("\tResidues with potential problems:\n");
   int fatal_errors = 0;
   int potential_errors = 0;
@@ -1015,7 +1002,6 @@ Exec::RetType Exec_PrepareForLeap::Execute(CpptrajState& State, ArgList& argIn)
   static const char* msg2 = "Fatal problem     : ";
   for (ResStatArray::const_iterator it = resStat.begin(); it != resStat.end(); ++it)
   {
-    LeapFxnGroupWarning(topIn, it-resStat.begin());
     //if ( *it == VALIDATED )
     //  mprintf("\t\t%s VALIDATED\n", topIn.TruncResNameOnumId(it-resStat_.begin()).c_str());
     //else
diff --git a/src/Exec_PrepareForLeap.h b/src/Exec_PrepareForLeap.h
index a67f366d63..98feec0791 100644
--- a/src/Exec_PrepareForLeap.h
+++ b/src/Exec_PrepareForLeap.h
@@ -38,8 +38,6 @@ class Exec_PrepareForLeap : public Exec {
 
     /// Run leap to generate topology, perform any modifications
     int RunLeap(std::string const&, std::string const&) const;
-    /// Print a warning for residues that will need modification after leap
-    static void LeapFxnGroupWarning(Topology const&, int);
 
     /// Download missing parameters
     int DownloadParameters(Cpptraj::Structure::ResStatArray&, RmapType const&,
diff --git a/src/Structure/FxnGroupBuilder.cpp b/src/Structure/FxnGroupBuilder.cpp
index 12c3fd2ae9..63321cddf4 100644
--- a/src/Structure/FxnGroupBuilder.cpp
+++ b/src/Structure/FxnGroupBuilder.cpp
@@ -514,3 +514,21 @@ int FxnGroupBuilder::CheckIfSugarIsTerminal(Sugar& sugar, Topology& topIn, Frame
   sugar.RemapIndices( atomMap, original_at0, original_at1 );
   return 0;
 }
+
+/** Print out warnings related to found functional groups. */
+void FxnGroupBuilder::LeapFxnGroupWarning(Topology const& topIn) const {
+  for (FRarray::const_iterator it = foundGroups_.begin(); it != foundGroups_.end(); ++it)
+  {
+    int rnum = it->Ires();
+    if ( it->Ftype() == FunctionalGroup::G_SO3 ) {
+    mprintf("Warning: Residue '%s'; after LEaP, will need to adjust the charge on the link oxygen by +0.031.\n",
+            topIn.TruncResNameNum(rnum).c_str());
+    } else if ( it->Ftype() == FunctionalGroup::G_CH3 ) {
+      mprintf("Warning: Residue '%s'; after LEaP, will need to adjust the charge on the carbon bonded to link oxygen by -0.039.\n",
+              topIn.TruncResNameNum(rnum).c_str());
+    } else if ( it->Ftype() == FunctionalGroup::G_ACX ) {
+      mprintf("Warning: Residue '%s'; after LEaP, will need to adjust the charge on the carbon bonded to link oxygen by +0.008.\n",
+              topIn.TruncResNameNum(rnum).c_str());
+    }
+  }
+}
diff --git a/src/Structure/FxnGroupBuilder.h b/src/Structure/FxnGroupBuilder.h
index 26379eaabd..414a85938a 100644
--- a/src/Structure/FxnGroupBuilder.h
+++ b/src/Structure/FxnGroupBuilder.h
@@ -16,6 +16,8 @@ class FxnGroupBuilder {
     FxnGroupBuilder(int);
     /// Determine if sugar has functional groups that need to be split off into separate residues
     int CheckForFunctionalGroups(Sugar&, Topology&, Frame&);
+    /// Print LEAP-related warnings for found functional groups
+    void LeapFxnGroupWarning(Topology const&) const;
 
     typedef std::vector<FxnResType>::const_iterator const_iterator;
     const_iterator begin() const { return foundGroups_.begin(); }
diff --git a/src/Structure/SugarBuilder.cpp b/src/Structure/SugarBuilder.cpp
index a8d92b3696..21b784eed5 100644
--- a/src/Structure/SugarBuilder.cpp
+++ b/src/Structure/SugarBuilder.cpp
@@ -2000,3 +2000,9 @@ void SugarBuilder::SetEachSugarAsTerminal(Topology& topIn) const {
       topIn.SetRes(rnum-1).SetTerminal(true);
   }
 }
+
+/** Print warnings related to functional groups. */
+void SugarBuilder::PrintFxnGroupWarnings(Topology const& topIn) const {
+  if (FGB_ != 0)
+    FGB_->LeapFxnGroupWarning(topIn);
+}
diff --git a/src/Structure/SugarBuilder.h b/src/Structure/SugarBuilder.h
index 4c309e10f5..b1a619a25d 100644
--- a/src/Structure/SugarBuilder.h
+++ b/src/Structure/SugarBuilder.h
@@ -31,6 +31,8 @@ class SugarBuilder {
     int PrepareSugars(bool, ResStatArray&, Topology&, Frame const&, std::vector<BondType>&);
     /// Set each sugar as a terminal residue
     void SetEachSugarAsTerminal(Topology&) const;
+    /// Print any functional group warnings
+    void PrintFxnGroupWarnings(Topology const&) const;
   private:
     typedef std::vector<int> Iarray;
 

From 8304a802492c7a3ce6f418886d0a0c4b7f7a2f1e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 16 Jan 2026 10:36:17 -0500
Subject: [PATCH 1221/1492] Move functional group modifications into the
 function group builder

---
 src/Exec_PrepareForLeap.cpp       | 127 ++---------------------------
 src/Exec_PrepareForLeap.h         |   2 +-
 src/Structure/FxnGroupBuilder.cpp | 129 ++++++++++++++++++++++++++++++
 src/Structure/FxnGroupBuilder.h   |   2 +
 src/Structure/SugarBuilder.cpp    |   8 ++
 src/Structure/SugarBuilder.h      |   4 +-
 6 files changed, 149 insertions(+), 123 deletions(-)

diff --git a/src/Exec_PrepareForLeap.cpp b/src/Exec_PrepareForLeap.cpp
index 689a2afcff..d552cd173b 100644
--- a/src/Exec_PrepareForLeap.cpp
+++ b/src/Exec_PrepareForLeap.cpp
@@ -278,40 +278,10 @@ const
 
 // -----------------------------------------------------------------------------
 
-/// \return index of oxygen atom bonded to this atom but not in same residue
-static inline int getLinkOxygenIdx(Topology const& leaptop, int at, int rnum) {
-  int o_idx = -1;
-  for (Atom::bond_iterator bat = leaptop[at].bondbegin();
-                           bat != leaptop[at].bondend(); ++bat)
-  {
-    if (leaptop[*bat].Element() == Atom::OXYGEN && leaptop[*bat].ResNum() != rnum) {
-      o_idx = *bat;
-      break;
-    }
-  }
-  return o_idx;
-}
-
-/// \return index of carbon bonded to link oxygen not in same residue
-static inline int getLinkCarbonIdx(Topology const& leaptop, int at, int rnum)
-{
-  int o_idx = getLinkOxygenIdx(leaptop, at, rnum);
-  if (o_idx == -1) return o_idx;
-  int c_idx = -1;
-  for (Atom::bond_iterator bat = leaptop[o_idx].bondbegin();
-                           bat != leaptop[o_idx].bondend(); ++bat)
-  {
-    if (leaptop[*bat].Element() == Atom::CARBON && leaptop[*bat].ResNum() != rnum) {
-      c_idx = *bat;
-      break;
-    }
-  }
-  return c_idx;
-}
-
 /** Run leap to generate topology. Modify the topology if needed. */
 int Exec_PrepareForLeap::RunLeap(std::string const& ff_file,
-                                 std::string const& leapfilename) const
+                                 std::string const& leapfilename,
+                                 SugarBuilder const& sugarBuilder) const
 {
   if (leapfilename.empty()) {
     mprintf("Warning: No leap input file name was specified, not running leap.\n");
@@ -344,95 +314,10 @@ int Exec_PrepareForLeap::RunLeap(std::string const& ff_file,
 
   bool top_is_modified = false;
   // Go through each residue. Find ones that need to be adjusted.
-  // NOTE: If deoxy carbons are ever handled, need to add H1 hydrogen and
-  //       add the former -OH charge to the carbon.
-  for (int rnum = 0; rnum != leaptop.Nres(); rnum++)
-  {
-    Residue const& res = leaptop.Res(rnum);
-    if (res.Name() == "SO3") {
-      int o_idx = -1;
-      // Need to adjust the charge on the bonded oxygen by +0.031
-      for (int at = res.FirstAtom(); at != res.LastAtom(); at++) {
-        if (leaptop[at].Element() == Atom::SULFUR) {
-          o_idx = getLinkOxygenIdx( leaptop, at, rnum );
-          if (o_idx != -1) break;
-        }
-      }
-      if (o_idx == -1) {
-        mprinterr("Error: Could not find oxygen link atom for '%s'\n",
-                  leaptop.TruncResNameOnumId(rnum).c_str());
-        return 1;
-      }
-      double newcharge = leaptop[o_idx].Charge() + 0.031;
-      mprintf("\tFxn group '%s'; changing charge on %s from %f to %f\n", *(res.Name()),
-              leaptop.AtomMaskName(o_idx).c_str(), leaptop[o_idx].Charge(), newcharge);
-      leaptop.SetAtom(o_idx).SetCharge( newcharge );
-      top_is_modified = true;
-    } else if (res.Name() == "MEX") {
-      int c_idx = -1;
-      // Need to adjust the charge on the carbon bonded to link oxygen by -0.039
-      for (int at = res.FirstAtom(); at != res.LastAtom(); at++) {
-        if (leaptop[at].Element() == Atom::CARBON) {
-          c_idx = getLinkCarbonIdx( leaptop, at, rnum );
-          if (c_idx != -1) break;
-        }
-      }
-      if (c_idx == -1) {
-        mprinterr("Error: Could not find carbon bonded to oxygen link atom for '%s'\n",
-                  leaptop.TruncResNameOnumId(rnum).c_str());
-        return 1;
-      }
-      double newcharge = leaptop[c_idx].Charge() - 0.039;
-      mprintf("\tFxn group '%s'; changing charge on %s from %f to %f\n", *(res.Name()),
-              leaptop.AtomMaskName(c_idx).c_str(), leaptop[c_idx].Charge(), newcharge);
-      leaptop.SetAtom(c_idx).SetCharge( newcharge );
-      top_is_modified = true;
-    } else if (res.Name() == "ACX") {
-      int c_idx = -1;
-      // Need to adjust the charge on the carbon bonded to link oxygen by +0.008
-      for (int at = res.FirstAtom(); at != res.LastAtom(); at++) {
-        if (leaptop[at].Element() == Atom::CARBON) {
-          // This needs to be the acetyl carbon, ensure it is bonded to an oxygen
-          for (Atom::bond_iterator bat = leaptop[at].bondbegin();
-                                   bat != leaptop[at].bondend(); ++bat)
-          {
-            if (leaptop[*bat].Element() == Atom::OXYGEN) {
-              c_idx = getLinkCarbonIdx( leaptop, at, rnum );
-              if (c_idx != -1) break;
-            }
-          }
-          if (c_idx != -1) break;
-        }
-      }
-      if (c_idx == -1) {
-        mprinterr("Error: Could not find carbon bonded to oxygen link atom for '%s'\n",
-                  leaptop.TruncResNameOnumId(rnum).c_str());
-        return 1;
-      }
-      double newcharge = leaptop[c_idx].Charge() + 0.008;
-      mprintf("\tFxn group '%s'; changing charge on %s from %f to %f\n", *(res.Name()),
-              leaptop.AtomMaskName(c_idx).c_str(), leaptop[c_idx].Charge(), newcharge);
-      leaptop.SetAtom(c_idx).SetCharge( newcharge );
-      top_is_modified = true;
-    }
-  }
-
-  // DEBUG: Print out total charge on each residue
-  double total_q = 0;
-  for (Topology::res_iterator res = leaptop.ResStart(); res != leaptop.ResEnd(); ++res)
-  {
-    double tcharge = 0;
-    for (int at = res->FirstAtom(); at != res->LastAtom(); ++at) {
-      total_q += leaptop[at].Charge();
-      tcharge += leaptop[at].Charge();
-    }
-    if (debug_ > 0) {
-      mprintf("DEBUG:\tResidue %10s charge= %12.5f\n",
-              leaptop.TruncResNameOnumId(res-leaptop.ResStart()).c_str(), tcharge);
-    }
+  if (sugarBuilder.ModifyFoundFxnGroups( leaptop, top_is_modified )) {
+    mprinterr("Error: Could not make modifications to found functional groups.\n");
+    return 1;
   }
-  mprintf("\tTotal charge: %16.8f\n", total_q);
-
   // If topology was modified, write it back out
   if (top_is_modified) {
     mprintf("\tWriting modified topology back to '%s'\n", topname.c_str());
@@ -1107,7 +992,7 @@ Exec::RetType Exec_PrepareForLeap::Execute(CpptrajState& State, ArgList& argIn)
   }
   // Run leap if needed
   if (!leapffname.empty()) {
-    if (RunLeap( leapffname, leapfilename )) {
+    if (RunLeap( leapffname, leapfilename, sugarBuilder )) {
       mprinterr("Error: Running leap failed.\n");
       return CpptrajState::ERR;
     }
diff --git a/src/Exec_PrepareForLeap.h b/src/Exec_PrepareForLeap.h
index 98feec0791..50e43f14ed 100644
--- a/src/Exec_PrepareForLeap.h
+++ b/src/Exec_PrepareForLeap.h
@@ -37,7 +37,7 @@ class Exec_PrepareForLeap : public Exec {
     int FindTerByBonds(Topology&, CharMask const&) const;
 
     /// Run leap to generate topology, perform any modifications
-    int RunLeap(std::string const&, std::string const&) const;
+    int RunLeap(std::string const&, std::string const&, Cpptraj::Structure::SugarBuilder const&) const;
 
     /// Download missing parameters
     int DownloadParameters(Cpptraj::Structure::ResStatArray&, RmapType const&,
diff --git a/src/Structure/FxnGroupBuilder.cpp b/src/Structure/FxnGroupBuilder.cpp
index 63321cddf4..8ad678c8d6 100644
--- a/src/Structure/FxnGroupBuilder.cpp
+++ b/src/Structure/FxnGroupBuilder.cpp
@@ -532,3 +532,132 @@ void FxnGroupBuilder::LeapFxnGroupWarning(Topology const& topIn) const {
     }
   }
 }
+
+/// \return index of oxygen atom bonded to this atom but not in same residue
+static inline int getLinkOxygenIdx(Topology const& leaptop, int at, int rnum) {
+  int o_idx = -1;
+  for (Atom::bond_iterator bat = leaptop[at].bondbegin();
+                           bat != leaptop[at].bondend(); ++bat)
+  {
+    if (leaptop[*bat].Element() == Atom::OXYGEN && leaptop[*bat].ResNum() != rnum) {
+      o_idx = *bat;
+      break;
+    }
+  }
+  return o_idx;
+}
+
+/// \return index of carbon bonded to link oxygen not in same residue
+static inline int getLinkCarbonIdx(Topology const& leaptop, int at, int rnum)
+{
+  int o_idx = getLinkOxygenIdx(leaptop, at, rnum);
+  if (o_idx == -1) return o_idx;
+  int c_idx = -1;
+  for (Atom::bond_iterator bat = leaptop[o_idx].bondbegin();
+                           bat != leaptop[o_idx].bondend(); ++bat)
+  {
+    if (leaptop[*bat].Element() == Atom::CARBON && leaptop[*bat].ResNum() != rnum) {
+      c_idx = *bat;
+      break;
+    }
+  }
+  return c_idx;
+}
+
+/** Modify functional groups if needed. */
+int FxnGroupBuilder::ModifyFxnGroups(Topology& leaptop, bool& top_is_modified)
+const
+{
+  // Make necessary adjustments for found residues
+  // NOTE: If deoxy carbons are ever handled, need to add H1 hydrogen and
+  //       add the former -OH charge to the carbon.
+  for (FRarray::const_iterator it = foundGroups_.begin(); it != foundGroups_.end(); ++it)
+  {
+    int rnum = it->Ires();
+    Residue const& res = leaptop.Res(rnum);
+    if (it->Ftype() == FunctionalGroup::G_SO3) {
+      int o_idx = -1;
+      // Need to adjust the charge on the bonded oxygen by +0.031
+      for (int at = res.FirstAtom(); at != res.LastAtom(); at++) {
+        if (leaptop[at].Element() == Atom::SULFUR) {
+          o_idx = getLinkOxygenIdx( leaptop, at, rnum );
+          if (o_idx != -1) break;
+        }
+      }
+      if (o_idx == -1) {
+        mprinterr("Error: Could not find oxygen link atom for '%s'\n",
+                  leaptop.TruncResNameOnumId(rnum).c_str());
+        return 1;
+      }
+      double newcharge = leaptop[o_idx].Charge() + 0.031;
+      mprintf("\tFxn group '%s'; changing charge on %s from %f to %f\n", *(res.Name()),
+              leaptop.AtomMaskName(o_idx).c_str(), leaptop[o_idx].Charge(), newcharge);
+      leaptop.SetAtom(o_idx).SetCharge( newcharge );
+      top_is_modified = true;
+    } else if (it->Ftype() == FunctionalGroup::G_CH3) { // MEX
+      int c_idx = -1;
+      // Need to adjust the charge on the carbon bonded to link oxygen by -0.039
+      for (int at = res.FirstAtom(); at != res.LastAtom(); at++) {
+        if (leaptop[at].Element() == Atom::CARBON) {
+          c_idx = getLinkCarbonIdx( leaptop, at, rnum );
+          if (c_idx != -1) break;
+        }
+      }
+      if (c_idx == -1) {
+        mprinterr("Error: Could not find carbon bonded to oxygen link atom for '%s'\n",
+                  leaptop.TruncResNameOnumId(rnum).c_str());
+        return 1;
+      }
+      double newcharge = leaptop[c_idx].Charge() - 0.039;
+      mprintf("\tFxn group '%s'; changing charge on %s from %f to %f\n", *(res.Name()),
+              leaptop.AtomMaskName(c_idx).c_str(), leaptop[c_idx].Charge(), newcharge);
+      leaptop.SetAtom(c_idx).SetCharge( newcharge );
+      top_is_modified = true;
+    } else if (it->Ftype() == FunctionalGroup::G_ACX) {
+      int c_idx = -1;
+      // Need to adjust the charge on the carbon bonded to link oxygen by +0.008
+      for (int at = res.FirstAtom(); at != res.LastAtom(); at++) {
+        if (leaptop[at].Element() == Atom::CARBON) {
+          // This needs to be the acetyl carbon, ensure it is bonded to an oxygen
+          for (Atom::bond_iterator bat = leaptop[at].bondbegin();
+                                   bat != leaptop[at].bondend(); ++bat)
+          {
+            if (leaptop[*bat].Element() == Atom::OXYGEN) {
+              c_idx = getLinkCarbonIdx( leaptop, at, rnum );
+              if (c_idx != -1) break;
+            }
+          }
+          if (c_idx != -1) break;
+        }
+      }
+      if (c_idx == -1) {
+        mprinterr("Error: Could not find carbon bonded to oxygen link atom for '%s'\n",
+                  leaptop.TruncResNameOnumId(rnum).c_str());
+        return 1;
+      }
+      double newcharge = leaptop[c_idx].Charge() + 0.008;
+      mprintf("\tFxn group '%s'; changing charge on %s from %f to %f\n", *(res.Name()),
+              leaptop.AtomMaskName(c_idx).c_str(), leaptop[c_idx].Charge(), newcharge);
+      leaptop.SetAtom(c_idx).SetCharge( newcharge );
+      top_is_modified = true;
+    }
+  } // END loop over residues
+
+  // DEBUG: Print out total charge on each residue
+  double total_q = 0;
+  for (Topology::res_iterator res = leaptop.ResStart(); res != leaptop.ResEnd(); ++res)
+  {
+    double tcharge = 0;
+    for (int at = res->FirstAtom(); at != res->LastAtom(); ++at) {
+      total_q += leaptop[at].Charge();
+      tcharge += leaptop[at].Charge();
+    }
+    if (debug_ > 0) {
+      mprintf("DEBUG:\tResidue %10s charge= %12.5f\n",
+              leaptop.TruncResNameOnumId(res-leaptop.ResStart()).c_str(), tcharge);
+    }
+  }
+  mprintf("\tTotal charge: %16.8f\n", total_q);
+
+  return 0;
+}
diff --git a/src/Structure/FxnGroupBuilder.h b/src/Structure/FxnGroupBuilder.h
index 414a85938a..3108ecbb98 100644
--- a/src/Structure/FxnGroupBuilder.h
+++ b/src/Structure/FxnGroupBuilder.h
@@ -16,6 +16,8 @@ class FxnGroupBuilder {
     FxnGroupBuilder(int);
     /// Determine if sugar has functional groups that need to be split off into separate residues
     int CheckForFunctionalGroups(Sugar&, Topology&, Frame&);
+    /// Make any necessary modifications to found functional groups in Topology
+    int ModifyFxnGroups(Topology&, bool&) const;
     /// Print LEAP-related warnings for found functional groups
     void LeapFxnGroupWarning(Topology const&) const;
 
diff --git a/src/Structure/SugarBuilder.cpp b/src/Structure/SugarBuilder.cpp
index 21b784eed5..5c1a8d1ba5 100644
--- a/src/Structure/SugarBuilder.cpp
+++ b/src/Structure/SugarBuilder.cpp
@@ -2006,3 +2006,11 @@ void SugarBuilder::PrintFxnGroupWarnings(Topology const& topIn) const {
   if (FGB_ != 0)
     FGB_->LeapFxnGroupWarning(topIn);
 }
+
+/** Perform any necessary topology modifications for found functional groups. */
+int SugarBuilder::ModifyFoundFxnGroups(Topology& topIn, bool& top_is_modified) const {
+  int err = 0;
+  if (FGB_ != 0)
+    err = FGB_->ModifyFxnGroups(topIn, top_is_modified);
+  return err;
+}
diff --git a/src/Structure/SugarBuilder.h b/src/Structure/SugarBuilder.h
index b1a619a25d..87b56bd5bd 100644
--- a/src/Structure/SugarBuilder.h
+++ b/src/Structure/SugarBuilder.h
@@ -31,8 +31,10 @@ class SugarBuilder {
     int PrepareSugars(bool, ResStatArray&, Topology&, Frame const&, std::vector<BondType>&);
     /// Set each sugar as a terminal residue
     void SetEachSugarAsTerminal(Topology&) const;
-    /// Print any functional group warnings
+    /// Print any found functional group warnings
     void PrintFxnGroupWarnings(Topology const&) const;
+    /// Perform any necessary modifications for found functional groups
+    int ModifyFoundFxnGroups(Topology&, bool&) const;
   private:
     typedef std::vector<int> Iarray;
 

From f162e9ac702fde2149dd8928fec6e24a5c64a369 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 16 Jan 2026 10:46:49 -0500
Subject: [PATCH 1222/1492] Do sugar functional group modifications for build

---
 src/Exec_Build.cpp | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 7e05189036..20d8d26252 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -1189,6 +1189,13 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
     return CpptrajState::ERR;
   }
 
+  // Perform any modifications necessary for the sugar functional groups
+  bool top_is_modified = false;
+  if (sugarBuilder.ModifyFoundFxnGroups(topOut, top_is_modified)) {
+    mprinterr("Error: Could not make necessary modifications to detected sugar functional groups.\n");
+    return CpptrajState::ERR;
+  }
+
   // Create empty arrays for the TREE, JOIN, and IROTAT arrays
   topOut.AllocTreeChainClassification( );
   topOut.AllocJoinArray();

From 1d907f23daebb8a1d34959685025117e450d80ec Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 16 Jan 2026 11:18:35 -0500
Subject: [PATCH 1223/1492] Fix variable names and comments

---
 src/Structure/FxnGroupBuilder.cpp | 16 ++++++++--------
 src/Structure/FxnGroupBuilder.h   |  2 +-
 2 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/src/Structure/FxnGroupBuilder.cpp b/src/Structure/FxnGroupBuilder.cpp
index 8ad678c8d6..0a6fefc40c 100644
--- a/src/Structure/FxnGroupBuilder.cpp
+++ b/src/Structure/FxnGroupBuilder.cpp
@@ -303,11 +303,11 @@ int FxnGroupBuilder::CheckForFunctionalGroups(Sugar& sugar, Topology& topIn, Fra
   bool atomsRemain = true;
   while (atomsRemain) {
     // Even if the residue is split, rnum will always refer to the original
-    // sugar since the split SO3 will come AFTER this residue.
-    // Find an oxygen that is both bound to a chain carbon and an SO3 group
-    // in this residue.
+    // sugar since the split functional group will come AFTER this residue.
+    // Find an oxygen that is both bound to a chain carbon and a recognized
+    // functional group in this residue.
     int o_idx = -1;
-    int so3_idx = -1;
+    int hvy_idx = -1;
     Iarray selected;
     FunctionalGroup::Type groupType = FunctionalGroup::UNRECOGNIZED_GROUP;
     Iarray::const_iterator cat = sugar.ChainAtoms().begin();
@@ -333,20 +333,20 @@ int FxnGroupBuilder::CheckForFunctionalGroups(Sugar& sugar, Topology& topIn, Fra
             // DEBUG
             groupType = IdFunctionalGroup(selected, rnum, *sat, o_idx, topIn);
             if (groupType != FunctionalGroup::UNRECOGNIZED_GROUP) {
-              so3_idx = *sat;
+              hvy_idx = *sat;
               break;
             }
           } // END loop over bonds to oxygen
-          if (so3_idx != -1) break;
+          if (hvy_idx != -1) break;
         } // END atom is oxygen
       } // END loop over bonds to carbon
-      if (so3_idx != -1) break;
+      if (hvy_idx != -1) break;
     } // END loop over chain atoms
     if (cat == sugar.ChainAtoms().end())
       atomsRemain = false;
     else {
       // sanity check
-      if (so3_idx == -1 || o_idx == -1 || selected.empty()) {
+      if (hvy_idx == -1 || o_idx == -1 || selected.empty()) {
         mprinterr("Internal Error: Functional group index is negative.\n");
         return 1;
       }
diff --git a/src/Structure/FxnGroupBuilder.h b/src/Structure/FxnGroupBuilder.h
index 3108ecbb98..3e9f319c4e 100644
--- a/src/Structure/FxnGroupBuilder.h
+++ b/src/Structure/FxnGroupBuilder.h
@@ -8,7 +8,7 @@ namespace Cpptraj {
 namespace Structure {
 class Sugar;
 /// Class to help prepare recognized functional groups
-// TODO change function names, update help text
+// TODO Determine if we need GetGroup() 
 class FxnGroupBuilder {
   public:
     class FxnResType;

From c81dd67a0d62bf703e0fc638038e9e9f756e7cfd Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 16 Jan 2026 11:29:53 -0500
Subject: [PATCH 1224/1492] Consolidate GB parameter assignment in the
 GB_Params class

---
 src/Exec_Build.cpp     | 21 +++----------------
 src/Exec_Sequence.cpp  | 16 +++++----------
 src/Parm/GB_Params.cpp | 46 +++++++++++++++++++++++++++++++++---------
 src/Parm/GB_Params.h   | 18 +++++++++++++++--
 4 files changed, 61 insertions(+), 40 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 20d8d26252..0d74fc67a2 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -1018,23 +1018,8 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
   mprintf("\tOutput COORDS set: %s\n", crdout.legend());
 
   // GB radii set
-  Cpptraj::Parm::GB_RadiiType gbradii;
-  if (gbRadIn == Cpptraj::Parm::UNKNOWN_GB) {
-    // No radii set specified. Check for keyword.
-    gbradii = Cpptraj::Parm::MBONDI; // Default
-    std::string gbset = argIn.GetStringKey("gb");
-    if (!gbset.empty()) {
-      gbradii = Cpptraj::Parm::GbTypeFromKey( gbset );
-      if (gbradii == Cpptraj::Parm::UNKNOWN_GB) {
-        mprinterr("Error: Unknown GB radii set: %s\n", gbset.c_str());
-        return CpptrajState::ERR;
-      }
-    }
-  } else {
-    // Use passed-in GB radii set
-    gbradii = gbRadIn;
-  }
-  mprintf("\tGB radii set: %s\n", Cpptraj::Parm::GbTypeStr(gbradii).c_str());
+  Cpptraj::Parm::GB_Params gbradii;
+  if (gbradii.Init_GB_Radii(argIn, gbRadIn)) return CpptrajState::ERR;
 
   // LJ 12-6-4
   Cpptraj::Parm::LJ1264_Params lj1264;
@@ -1247,7 +1232,7 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
     ret = CpptrajState::ERR;
   }
   // Assign GB parameters
-  if (Cpptraj::Parm::Assign_GB_Radii( topOut, gbradii )) {
+  if (gbradii.Assign_GB_Radii(topOut)) {
     mprinterr("Error: Could not assign GB parameters for '%s'\n", topOut.c_str());
     ret = CpptrajState::ERR;
   }
diff --git a/src/Exec_Sequence.cpp b/src/Exec_Sequence.cpp
index 14e8ce3c36..4736435c3e 100644
--- a/src/Exec_Sequence.cpp
+++ b/src/Exec_Sequence.cpp
@@ -248,16 +248,10 @@ Exec::RetType Exec_Sequence::Execute(CpptrajState& State, ArgList& argIn)
 
   // Args
   int verbose = argIn.getKeyInt("verbose", 0);
-  // GB radii set.
-  Cpptraj::Parm::GB_RadiiType gbradii = Cpptraj::Parm::MBONDI; // Default
-  std::string gbset = argIn.GetStringKey("gb");
-  if (!gbset.empty()) {
-    gbradii = Cpptraj::Parm::GbTypeFromKey( gbset );
-    if (gbradii == Cpptraj::Parm::UNKNOWN_GB) {
-      mprinterr("Error: Unknown GB radii set: %s\n", gbset.c_str());
-      return CpptrajState::ERR;
-    }
-  }
+  // GB radii set. Default to mbondi
+  Cpptraj::Parm::GB_Params gbradii;
+  if (gbradii.Init_GB_Radii(argIn, Cpptraj::Parm::MBONDI)) return CpptrajState::ERR;
+
   // Creator args
   Cpptraj::Structure::Creator creator(debug_);
   if (creator.InitCreator(argIn, State.DSL(), debug_)) {
@@ -314,7 +308,7 @@ Exec::RetType Exec_Sequence::Execute(CpptrajState& State, ArgList& argIn)
       ret = CpptrajState::ERR;
     }
     // Assign GB parameters
-    if (Cpptraj::Parm::Assign_GB_Radii( topOut, gbradii )) {
+    if (gbradii.Assign_GB_Radii( topOut )) {
       mprinterr("Error: Could not assign GB parameters for '%s'\n", topOut.c_str());
       ret = CpptrajState::ERR;
     }
diff --git a/src/Parm/GB_Params.cpp b/src/Parm/GB_Params.cpp
index 854abf1b59..b1ace3918d 100644
--- a/src/Parm/GB_Params.cpp
+++ b/src/Parm/GB_Params.cpp
@@ -1,6 +1,7 @@
 #include "GB_Params.h"
-#include "../Topology.h"
+#include "../ArgList.h"
 #include "../CpptrajStdio.h"
+#include "../Topology.h"
 
 static const char* GB_RadiiTypeStr_[] = {
   "Bondi radii", // 0
@@ -80,8 +81,34 @@ static const int GB_RadiiTypeIGB_[] = {
   999999
 };
 
+// =============================================================================
+/** CONSTRUCTOR */
+Cpptraj::Parm::GB_Params::GB_Params() : gbradii_(Cpptraj::Parm::UNKNOWN_GB) {}
+
+/** Init radii set */
+int Cpptraj::Parm::GB_Params::Init_GB_Radii(ArgList& argIn, Cpptraj::Parm::GB_RadiiType gbRadIn)
+{
+  if (gbRadIn == Cpptraj::Parm::UNKNOWN_GB) {
+    // No radii set specified. Check for keyword.
+    gbradii_ = Cpptraj::Parm::MBONDI; // Default
+    std::string gbset = argIn.GetStringKey("gb");
+    if (!gbset.empty()) {
+      gbradii_ = Cpptraj::Parm::GbTypeFromKey( gbset );
+      if (gbradii_ == Cpptraj::Parm::UNKNOWN_GB) {
+        mprinterr("Error: Unknown GB radii set: %s\n", gbset.c_str());
+        return 1;
+      }
+    }
+  } else {
+    // Use passed-in GB radii set
+    gbradii_ = gbRadIn;
+  }
+  mprintf("\tGB radii set: %s\n", Cpptraj::Parm::GbTypeStr(gbradii_).c_str());
+  return 0;
+}
+
 /** Assign GB radii. */
-static void assign_gb_radii(Topology& top, Cpptraj::Parm::GB_RadiiType radiiSet)
+void Cpptraj::Parm::GB_Params::assign_gb_radii(Topology& top, Cpptraj::Parm::GB_RadiiType radiiSet)
 {
   int iGBparm = GB_RadiiTypeIGB_[radiiSet];
   for (int iat = 0; iat != top.Natom(); iat++)
@@ -318,7 +345,7 @@ static void assign_gb_radii(Topology& top, Cpptraj::Parm::GB_RadiiType radiiSet)
 }
 
 /** Assign GB screening parameters. */
-static void assign_gb_screen(Topology& top, Cpptraj::Parm::GB_RadiiType radiiSet)
+void Cpptraj::Parm::GB_Params::assign_gb_screen(Topology& top, Cpptraj::Parm::GB_RadiiType radiiSet)
 {
   int iGBparm = GB_RadiiTypeIGB_[radiiSet];
   for (int iat = 0; iat != top.Natom(); iat++)
@@ -424,16 +451,17 @@ static void assign_gb_screen(Topology& top, Cpptraj::Parm::GB_RadiiType radiiSet
 }
 
 /** Assign GB radii and screening parameters based on the given radius set. */
-int Cpptraj::Parm::Assign_GB_Radii(Topology& top, GB_RadiiType radiiSet)
+int Cpptraj::Parm::GB_Params::Assign_GB_Radii(Topology& top)
+const
 {
-  if (radiiSet == UNKNOWN_GB) {
+  if (gbradii_ == UNKNOWN_GB) {
     mprinterr("Error: Unknown GB radii set.\n");
     return 1;
   }
-  mprintf("\tUsing GB radii set: %s\n", GB_RadiiTypeStr_[radiiSet]);
-  top.SetGBradiiSet( std::string(GB_RadiiAmberFlag_[radiiSet]) );
-  assign_gb_radii( top, radiiSet );
-  assign_gb_screen( top, radiiSet );
+  mprintf("\tUsing GB radii set: %s\n", GB_RadiiTypeStr_[gbradii_]);
+  top.SetGBradiiSet( std::string(GB_RadiiAmberFlag_[gbradii_]) );
+  assign_gb_radii( top, gbradii_ );
+  assign_gb_screen( top, gbradii_ );
 
   return 0;
 }
diff --git a/src/Parm/GB_Params.h b/src/Parm/GB_Params.h
index 3e32c41af2..ef8a363089 100644
--- a/src/Parm/GB_Params.h
+++ b/src/Parm/GB_Params.h
@@ -1,6 +1,7 @@
 #ifndef INC_PARM_GBPARAMS_H
 #define INC_PARM_GBPARAMS_H
 #include <string>
+class ArgList;
 class Topology;
 namespace Cpptraj {
 namespace Parm {
@@ -25,8 +26,21 @@ std::string GbTypeStr(GB_RadiiType);
 GB_RadiiType GbTypeFromKey(std::string const&);
 /// Print GB radii keywords to stdout
 void PrintGbRadiiKeywords();
-/// Assign GB radii
-int Assign_GB_Radii(Topology&, GB_RadiiType);
+
+/// Used to assign GB radii to a Topology
+class GB_Params {
+  public:
+    /// CONSTRUCTOR
+    GB_Params();
+    /// Initialize 
+    int Init_GB_Radii(ArgList&, GB_RadiiType);
+    /// Assign GB radii
+    int Assign_GB_Radii(Topology&) const;
+  private:
+    static void assign_gb_radii(Topology&, GB_RadiiType);
+    static void assign_gb_screen(Topology&, GB_RadiiType);
+    GB_RadiiType gbradii_; ///< Type of GB radii to assign
+};
 }
 }
 #endif 

From f76388f0f3f40fd09ef877e039785a3b1f6b792d Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 16 Jan 2026 11:35:18 -0500
Subject: [PATCH 1225/1492] Add init from keywords to LJ 12-6-4

---
 src/Parm/LJ1264_Params.cpp | 31 +++++++++++++++++++++++++++++++
 src/Parm/LJ1264_Params.h   |  3 +++
 2 files changed, 34 insertions(+)

diff --git a/src/Parm/LJ1264_Params.cpp b/src/Parm/LJ1264_Params.cpp
index b3b314e51c..ef60e6149a 100644
--- a/src/Parm/LJ1264_Params.cpp
+++ b/src/Parm/LJ1264_Params.cpp
@@ -526,6 +526,37 @@ int LJ1264_Params::Init_LJ1264(std::string const& maskIn, std::string const& c4f
   return 0;
 }
 
+/** Init from argument list */
+int LJ1264_Params::Init_LJ1264(ArgList& argIn, int debugIn, std::string const& solventBoxName) {
+  std::string lj1264mask = argIn.GetStringKey("lj1264mask");
+  std::string c4file = argIn.GetStringKey("c4file");
+  std::string polfile = argIn.GetStringKey("polfile");
+  double tunfactor = argIn.getKeyDouble("tunfactor", 1.0);
+  // Try to guess the water model if we are solvating
+  Cpptraj::Parm::WaterModelType wm = Cpptraj::Parm::UNKNOWN_WATER_MODEL;
+  if (!solventBoxName.empty()) {
+    if (solventBoxName == "TIP3PBOX") wm = Cpptraj::Parm::TIP3P;
+    else if (solventBoxName == "TIP4PEWBOX") wm = Cpptraj::Parm::TIP4PEW;
+    else if (solventBoxName == "SPCBOX") wm = Cpptraj::Parm::SPCE;
+    else if (solventBoxName == "OPC3BOX") wm = Cpptraj::Parm::OPC3;
+    else if (solventBoxName == "OPCBOX") wm = Cpptraj::Parm::OPC;
+    else if (solventBoxName == "FB3BOX") wm = Cpptraj::Parm::FB3;
+    else if (solventBoxName == "FB4BOX") wm = Cpptraj::Parm::FB4;
+    else
+      mprintf("Warning: Unable to determine solvent model for LJ 12-6-4 from solvent box name %s\n",
+              solventBoxName.c_str());
+  }
+  if (wm == Cpptraj::Parm::UNKNOWN_WATER_MODEL) {
+    mprintf("Warning: Unable to determine water model for LJ 12-6-4. Using TIP3P.\n");
+    wm = Cpptraj::Parm::TIP3P;
+  }
+  if (Init_LJ1264(lj1264mask, c4file, wm, polfile, tunfactor, debugIn)) {
+    mprinterr("Error: Init of LJ 12-6-4 failed.\n");
+    return 1;
+  }
+  return 0;
+}
+
 /** Parameterize */
 int LJ1264_Params::AssignLJ1264(Topology& topOut)
 {
diff --git a/src/Parm/LJ1264_Params.h b/src/Parm/LJ1264_Params.h
index 070f62cb2a..8570c1245d 100644
--- a/src/Parm/LJ1264_Params.h
+++ b/src/Parm/LJ1264_Params.h
@@ -4,6 +4,7 @@
 #include "ParmEnum.h"
 #include <map>
 #include <string>
+class ArgList;
 class Topology;
 namespace Cpptraj {
 namespace Parm {
@@ -37,6 +38,8 @@ namespace Parm {
 class LJ1264_Params {
   public:
     LJ1264_Params();
+    /// Init from keywords
+    int Init_LJ1264(ArgList&, int, std::string const&);
     /// Init - mask, c4 file, water model, polarization file, tuning factor, debug
     int Init_LJ1264(std::string const&, std::string const&, WaterModelType, std::string const&, double, int);
     /// Assign Topology with LJ 12-6-4 params

From c08fec8dc0094ece0a1ea70096268d192044f3da Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 16 Jan 2026 11:40:49 -0500
Subject: [PATCH 1226/1492] Use new init function

---
 src/Exec_Build.cpp | 24 +-----------------------
 1 file changed, 1 insertion(+), 23 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 0d74fc67a2..4b9043d40c 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -1024,29 +1024,7 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
   // LJ 12-6-4
   Cpptraj::Parm::LJ1264_Params lj1264;
   if (argIn.hasKey("lj1264")) {
-    std::string lj1264mask = argIn.GetStringKey("lj1264mask");
-    std::string c4file = argIn.GetStringKey("c4file");
-    std::string polfile = argIn.GetStringKey("polfile");
-    double tunfactor = argIn.getKeyDouble("tunfactor", 1.0);
-    // Try to guess the water model if we are solvating
-    Cpptraj::Parm::WaterModelType wm = Cpptraj::Parm::UNKNOWN_WATER_MODEL;
-    if (add_solvent == SOLVATEBOX) {
-      if (solvator.SolventBoxName() == "TIP3PBOX") wm = Cpptraj::Parm::TIP3P;
-      else if (solvator.SolventBoxName() == "TIP4PEWBOX") wm = Cpptraj::Parm::TIP4PEW;
-      else if (solvator.SolventBoxName() == "SPCBOX") wm = Cpptraj::Parm::SPCE;
-      else if (solvator.SolventBoxName() == "OPC3BOX") wm = Cpptraj::Parm::OPC3;
-      else if (solvator.SolventBoxName() == "OPCBOX") wm = Cpptraj::Parm::OPC;
-      else if (solvator.SolventBoxName() == "FB3BOX") wm = Cpptraj::Parm::FB3;
-      else if (solvator.SolventBoxName() == "FB4BOX") wm = Cpptraj::Parm::FB4;
-      else
-        mprintf("Warning: Unable to determine solvent model for LJ 12-6-4 from solvent box name %s\n",
-                solvator.SolventBoxName().c_str());
-    }
-    if (wm == Cpptraj::Parm::UNKNOWN_WATER_MODEL) {
-      mprintf("Warning: Unable to determine water model for LJ 12-6-4. Using TIP3P.\n");
-      wm = Cpptraj::Parm::TIP3P;
-    }
-    if (lj1264.Init_LJ1264(lj1264mask, c4file, wm, polfile, tunfactor, debug_)) {
+    if (lj1264.Init_LJ1264( argIn, debug_, solvator.SolventBoxName())) {
       mprinterr("Error: Init of LJ 12-6-4 failed.\n");
       return CpptrajState::ERR;
     }

From 4431f73e13a7bddf9250bf98cfbc408f0fa95b3e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 16 Jan 2026 12:39:42 -0500
Subject: [PATCH 1227/1492] Fix GB help text

---
 src/Exec_Build.cpp     |  8 ++++----
 src/Exec_Sequence.cpp  |  9 ++++-----
 src/Parm/GB_Params.cpp | 18 ++++++++++--------
 src/Parm/GB_Params.h   |  4 ++--
 4 files changed, 20 insertions(+), 19 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 4b9043d40c..999e4634c9 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -810,9 +810,10 @@ const
 void Exec_Build::Help() const
 {
   mprintf("\tname <output COORDS> crdset <COORDS set> [frame <#>]\n"
-          "\t[title <title>] [gb <radii>] [verbose <#>] [keepmissingatoms]\n"
-          "\t[parmout <topology file>] [crdout <coord file>] [simplecheck]\n"
-          "\t[%s]\n"
+          "\t[title <title>] [verbose <#>] [keepmissingatoms]\n"
+          "\t[parmout <topology file>] [crdout <coord file>] [simplecheck]\n");
+  Cpptraj::Parm::GB_Params::HelpText();
+  mprintf("\t[%s]\n"
           "\t[{%s} ...]\n"
           "\t[{%s} ...]\n"
           "\t[{{solvatebox|solvateoct} %s\n"
@@ -829,7 +830,6 @@ void Exec_Build::Help() const
           Cpptraj::Structure::HisProt::keywords_,
           Cpptraj::Structure::Disulfide::keywords_
          );
-  Cpptraj::Parm::PrintGbRadiiKeywords();
   mprintf("  Build complete topology and parameters from given crdset.\n");
 }
 
diff --git a/src/Exec_Sequence.cpp b/src/Exec_Sequence.cpp
index 4736435c3e..7bc9eb21b9 100644
--- a/src/Exec_Sequence.cpp
+++ b/src/Exec_Sequence.cpp
@@ -227,15 +227,14 @@ const
 // Exec_Sequence::Help()
 void Exec_Sequence::Help() const
 {
-  mprintf("\tname <output set name> <unit0> <unit1> ...\n"
-          "\t[gb <radii>] [verbose <#>]\n" 
-          "\t[%s]\n"
+  mprintf("\tname <output set name> <unit0> <unit1> ... [verbose <#>]\n");
+  Cpptraj::Parm::GB_Params::HelpText();
+  mprintf("\t[%s]\n"
           "\t[{%s} ...]\n"
           "\t[{%s} ...]\n",
           Cpptraj::Structure::Creator::other_keywords_,
           Cpptraj::Structure::Creator::template_keywords_,
           Cpptraj::Structure::Creator::parm_keywords_);
-  Cpptraj::Parm::PrintGbRadiiKeywords();
   mprintf("  Create a molecule from a sequence of units.\n"
           "  If parameter sets are loaded, parameters will be assigned to <output set name>.\n");
 }
@@ -250,7 +249,7 @@ Exec::RetType Exec_Sequence::Execute(CpptrajState& State, ArgList& argIn)
   int verbose = argIn.getKeyInt("verbose", 0);
   // GB radii set. Default to mbondi
   Cpptraj::Parm::GB_Params gbradii;
-  if (gbradii.Init_GB_Radii(argIn, Cpptraj::Parm::MBONDI)) return CpptrajState::ERR;
+  if (gbradii.Init_GB_Radii(argIn, Cpptraj::Parm::UNKNOWN_GB)) return CpptrajState::ERR;
 
   // Creator args
   Cpptraj::Structure::Creator creator(debug_);
diff --git a/src/Parm/GB_Params.cpp b/src/Parm/GB_Params.cpp
index b1ace3918d..7c4e61248b 100644
--- a/src/Parm/GB_Params.cpp
+++ b/src/Parm/GB_Params.cpp
@@ -61,14 +61,6 @@ Cpptraj::Parm::GB_RadiiType Cpptraj::Parm::GbTypeFromKey(std::string const& key)
   return UNKNOWN_GB;
 }
 
-/** Print all recognized GB radii keywords to stdout */
-void Cpptraj::Parm::PrintGbRadiiKeywords() {
-  mprintf("    <radii> =");
-  for (int ig = 0; ig != (int)UNKNOWN_GB; ig++)
-    mprintf(" %s", GbTypeKey((GB_RadiiType)ig));
-  mprintf("\n");
-}
-
 /// These are the numeric iGBparm values used in LEaP
 static const int GB_RadiiTypeIGB_[] = {
   0, // bondi
@@ -85,6 +77,16 @@ static const int GB_RadiiTypeIGB_[] = {
 /** CONSTRUCTOR */
 Cpptraj::Parm::GB_Params::GB_Params() : gbradii_(Cpptraj::Parm::UNKNOWN_GB) {}
 
+/** Print keywords to stdout. */
+void Cpptraj::Parm::GB_Params::HelpText() {
+  mprintf("\t[gb {");
+  for (int ig = 0; ig != (int)UNKNOWN_GB; ig++) {
+    if (ig > 0) mprintf("|");
+    mprintf("%s", GbTypeKey((GB_RadiiType)ig));
+  }
+  mprintf("}]\n");
+}
+
 /** Init radii set */
 int Cpptraj::Parm::GB_Params::Init_GB_Radii(ArgList& argIn, Cpptraj::Parm::GB_RadiiType gbRadIn)
 {
diff --git a/src/Parm/GB_Params.h b/src/Parm/GB_Params.h
index ef8a363089..28edeafdec 100644
--- a/src/Parm/GB_Params.h
+++ b/src/Parm/GB_Params.h
@@ -24,14 +24,14 @@ std::string GbAmberFlag(GB_RadiiType);
 std::string GbTypeStr(GB_RadiiType);
 /// \return GB radii type corresponding to string
 GB_RadiiType GbTypeFromKey(std::string const&);
-/// Print GB radii keywords to stdout
-void PrintGbRadiiKeywords();
 
 /// Used to assign GB radii to a Topology
 class GB_Params {
   public:
     /// CONSTRUCTOR
     GB_Params();
+    /// Print Help text to stdout
+    static void HelpText();
     /// Initialize 
     int Init_GB_Radii(ArgList&, GB_RadiiType);
     /// Assign GB radii

From e2ea72e1c6cdbce5228b86eda14b043e72e3c678 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 16 Jan 2026 12:53:42 -0500
Subject: [PATCH 1228/1492] Make help text a string. Add the 'gb' keyword to
 the change command for changing GB radii sets

---
 src/Exec_Build.cpp     |  2 +-
 src/Exec_Change.cpp    | 19 +++++++++++++++++--
 src/Exec_Change.h      |  1 +
 src/Exec_Sequence.cpp  |  2 +-
 src/Parm/GB_Params.cpp | 11 ++++++-----
 src/Parm/GB_Params.h   |  4 ++--
 6 files changed, 28 insertions(+), 11 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 999e4634c9..7c30c626da 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -812,7 +812,7 @@ void Exec_Build::Help() const
   mprintf("\tname <output COORDS> crdset <COORDS set> [frame <#>]\n"
           "\t[title <title>] [verbose <#>] [keepmissingatoms]\n"
           "\t[parmout <topology file>] [crdout <coord file>] [simplecheck]\n");
-  Cpptraj::Parm::GB_Params::HelpText();
+  mprintf("\t[%s]\n", Cpptraj::Parm::GB_Params::HelpText().c_str());
   mprintf("\t[%s]\n"
           "\t[{%s} ...]\n"
           "\t[{%s} ...]\n"
diff --git a/src/Exec_Change.cpp b/src/Exec_Change.cpp
index 4aa3738e87..61a24ca8c0 100644
--- a/src/Exec_Change.cpp
+++ b/src/Exec_Change.cpp
@@ -5,6 +5,7 @@
 #include "ParameterTypes.h"
 #include "DataSet_1D.h"
 #include "DataSet_NameMap.h"
+#include "Parm/GB_Params.h"
 
 // Exec_Change::Help()
 void Exec_Change::Help() const
@@ -22,9 +23,12 @@ void Exec_Change::Help() const
           "\t  {mass|charge} [of <mask>] {to <value> |by <offset> |\n"
           "\t                             byfac <factor> |fromset <data set>} |\n"
           "\t  mergeres firstres <start res#> lastres <stop res#>\n"
+          "\t  %s\n"
           "\t}\n"
           "  Change specified parts of topology or topology of a COORDS data set.\n",
-          DataSetList::TopArgs);
+          DataSetList::TopArgs,
+          Cpptraj::Parm::GB_Params::HelpText().c_str()
+         );
 }
 
 // Exec_Change::Execute()
@@ -33,7 +37,7 @@ Exec::RetType Exec_Change::Execute(CpptrajState& State, ArgList& argIn)
   // Change type
   enum ChangeType { UNKNOWN = 0, RESNAME, CHAINID, ORESNUMS, ICODES,
                     ATOMNAME, ADDBOND, REMOVEBONDS, SPLITRES, BONDPARM,
-                    MASS, CHARGE, MERGERES };
+                    MASS, CHARGE, MERGERES, GBRADII };
   ChangeType type = UNKNOWN;
   if (argIn.hasKey("resname"))
     type = RESNAME;
@@ -59,6 +63,8 @@ Exec::RetType Exec_Change::Execute(CpptrajState& State, ArgList& argIn)
     type = CHARGE;
   else if (argIn.hasKey("mergeres"))
     type = MERGERES;
+  else if (argIn.Contains("gb"))
+    type = GBRADII;
   if (type == UNKNOWN) {
     mprinterr("Error: No change type specified.\n");
     return CpptrajState::ERR;
@@ -93,12 +99,21 @@ Exec::RetType Exec_Change::Execute(CpptrajState& State, ArgList& argIn)
     case MASS        : err = ChangeMassOrCharge(*parm, argIn, State.DSL(), 0); break;
     case CHARGE      : err = ChangeMassOrCharge(*parm, argIn, State.DSL(), 1); break;
     case MERGERES    : err = ChangeMergeRes(*parm, argIn); break;
+    case GBRADII     : err = ChangeGbRadii(*parm, argIn); break;
     case UNKNOWN  : err = 1; // sanity check
   }
   if (err != 0) return CpptrajState::ERR;
   return CpptrajState::OK;
 }
 
+/** Change the GB radii */
+int Exec_Change::ChangeGbRadii(Topology& parm, ArgList& argIn) const {
+  Cpptraj::Parm::GB_Params gbradii;
+  if (gbradii.Init_GB_Radii(argIn, Cpptraj::Parm::UNKNOWN_GB)) return 1;
+  if (gbradii.Assign_GB_Radii(parm)) return 1;
+  return 0;
+}
+
 // Exec_Change::ChangeSplitRes()
 int Exec_Change::ChangeSplitRes(Topology& topIn, ArgList& argIn)
 const
diff --git a/src/Exec_Change.h b/src/Exec_Change.h
index 9fa5dc9424..3ee401773d 100644
--- a/src/Exec_Change.h
+++ b/src/Exec_Change.h
@@ -14,6 +14,7 @@ class Exec_Change : public Exec {
     /// Change mass or charge
     static inline void changeTopVal(Topology&, int, ChangeType, double);
 
+    int ChangeGbRadii(Topology&, ArgList&) const;
     int ChangeSplitRes(Topology&, ArgList&) const;
     int ChangeResidueName(Topology&, ArgList&) const;
     int ChangeOresNums(Topology&, ArgList&) const;
diff --git a/src/Exec_Sequence.cpp b/src/Exec_Sequence.cpp
index 7bc9eb21b9..43b6ce8dde 100644
--- a/src/Exec_Sequence.cpp
+++ b/src/Exec_Sequence.cpp
@@ -228,7 +228,7 @@ const
 void Exec_Sequence::Help() const
 {
   mprintf("\tname <output set name> <unit0> <unit1> ... [verbose <#>]\n");
-  Cpptraj::Parm::GB_Params::HelpText();
+  mprintf("\t[%s]\n", Cpptraj::Parm::GB_Params::HelpText().c_str());
   mprintf("\t[%s]\n"
           "\t[{%s} ...]\n"
           "\t[{%s} ...]\n",
diff --git a/src/Parm/GB_Params.cpp b/src/Parm/GB_Params.cpp
index 7c4e61248b..5695f36825 100644
--- a/src/Parm/GB_Params.cpp
+++ b/src/Parm/GB_Params.cpp
@@ -78,13 +78,14 @@ static const int GB_RadiiTypeIGB_[] = {
 Cpptraj::Parm::GB_Params::GB_Params() : gbradii_(Cpptraj::Parm::UNKNOWN_GB) {}
 
 /** Print keywords to stdout. */
-void Cpptraj::Parm::GB_Params::HelpText() {
-  mprintf("\t[gb {");
+std::string Cpptraj::Parm::GB_Params::HelpText() {
+  std::string out("gb {");
   for (int ig = 0; ig != (int)UNKNOWN_GB; ig++) {
-    if (ig > 0) mprintf("|");
-    mprintf("%s", GbTypeKey((GB_RadiiType)ig));
+    if (ig > 0) out.append("|");
+    out.append(std::string( GbTypeKey((GB_RadiiType)ig) ));
   }
-  mprintf("}]\n");
+  out.append("}");
+  return out;
 }
 
 /** Init radii set */
diff --git a/src/Parm/GB_Params.h b/src/Parm/GB_Params.h
index 28edeafdec..443b0704fe 100644
--- a/src/Parm/GB_Params.h
+++ b/src/Parm/GB_Params.h
@@ -30,8 +30,8 @@ class GB_Params {
   public:
     /// CONSTRUCTOR
     GB_Params();
-    /// Print Help text to stdout
-    static void HelpText();
+    /// \return recognized GB radii keywords.
+    static std::string HelpText();
     /// Initialize 
     int Init_GB_Radii(ArgList&, GB_RadiiType);
     /// Assign GB radii

From 907881a81d72746d29addfcc6eb18d84bfb64313 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 16 Jan 2026 13:04:03 -0500
Subject: [PATCH 1229/1492] Add LJ 12-6-4 help text

---
 src/Exec_Build.cpp         |  1 +
 src/Parm/LJ1264_Params.cpp | 18 +++++++++++++++---
 src/Parm/LJ1264_Params.h   |  2 ++
 3 files changed, 18 insertions(+), 3 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 7c30c626da..29153930f3 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -813,6 +813,7 @@ void Exec_Build::Help() const
           "\t[title <title>] [verbose <#>] [keepmissingatoms]\n"
           "\t[parmout <topology file>] [crdout <coord file>] [simplecheck]\n");
   mprintf("\t[%s]\n", Cpptraj::Parm::GB_Params::HelpText().c_str());
+  mprintf("\t[lj1264 %s]\n", Cpptraj::Parm::LJ1264_Params::HelpText().c_str());
   mprintf("\t[%s]\n"
           "\t[{%s} ...]\n"
           "\t[{%s} ...]\n"
diff --git a/src/Parm/LJ1264_Params.cpp b/src/Parm/LJ1264_Params.cpp
index ef60e6149a..ac50d184cf 100644
--- a/src/Parm/LJ1264_Params.cpp
+++ b/src/Parm/LJ1264_Params.cpp
@@ -483,9 +483,10 @@ int LJ1264_Params::Init_LJ1264(std::string const& maskIn, std::string const& c4f
   tunfactor_ = tunfactorIn;
   mprintf("\t  LJ 12-6-4 tuning factor: %g\n", tunfactor_);
 
-  if (maskIn.empty())
+  if (maskIn.empty()) {
+    mprintf("Warning: No LJ 12-6-4 mask specified; using default.\n");
     mask_.SetMaskString(":ZN");
-  else {
+  } else {
     if (mask_.SetMaskString(maskIn)) {
       mprinterr("Error: Could not set mask string '%s'\n", maskIn.c_str());
       return 1;
@@ -526,12 +527,23 @@ int LJ1264_Params::Init_LJ1264(std::string const& maskIn, std::string const& c4f
   return 0;
 }
 
+/** \return Help text. */
+std::string LJ1264_Params::HelpText() {
+  std::string out("[lj1264mask <mask>] [tunfactor <fac>] [c4file <c4file>] [polfile <polfile>] [lj1264solvent <solvent>]");
+  return out;
+}
+
 /** Init from argument list */
-int LJ1264_Params::Init_LJ1264(ArgList& argIn, int debugIn, std::string const& solventBoxName) {
+int LJ1264_Params::Init_LJ1264(ArgList& argIn, int debugIn, std::string const& solventBoxNameIn) {
   std::string lj1264mask = argIn.GetStringKey("lj1264mask");
   std::string c4file = argIn.GetStringKey("c4file");
   std::string polfile = argIn.GetStringKey("polfile");
   double tunfactor = argIn.getKeyDouble("tunfactor", 1.0);
+  std::string solventBoxName;
+  if (solventBoxNameIn.empty())
+    solventBoxName = argIn.GetStringKey("lj1264solvent");
+  else
+    solventBoxName = solventBoxNameIn;
   // Try to guess the water model if we are solvating
   Cpptraj::Parm::WaterModelType wm = Cpptraj::Parm::UNKNOWN_WATER_MODEL;
   if (!solventBoxName.empty()) {
diff --git a/src/Parm/LJ1264_Params.h b/src/Parm/LJ1264_Params.h
index 8570c1245d..a31568d336 100644
--- a/src/Parm/LJ1264_Params.h
+++ b/src/Parm/LJ1264_Params.h
@@ -38,6 +38,8 @@ namespace Parm {
 class LJ1264_Params {
   public:
     LJ1264_Params();
+    /// \return Help text
+    static std::string HelpText();
     /// Init from keywords
     int Init_LJ1264(ArgList&, int, std::string const&);
     /// Init - mask, c4 file, water model, polarization file, tuning factor, debug

From 73c9e8b6d794c3803c1f45b84256420c4c199e2b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 16 Jan 2026 13:15:22 -0500
Subject: [PATCH 1230/1492] Start adding lj1264 to change

---
 src/Exec_Change.cpp | 18 ++++++++++++++++--
 src/Exec_Change.h   |  1 +
 src/cpptrajdepend   |  6 +++---
 3 files changed, 20 insertions(+), 5 deletions(-)

diff --git a/src/Exec_Change.cpp b/src/Exec_Change.cpp
index 61a24ca8c0..8d332b53d0 100644
--- a/src/Exec_Change.cpp
+++ b/src/Exec_Change.cpp
@@ -6,6 +6,7 @@
 #include "DataSet_1D.h"
 #include "DataSet_NameMap.h"
 #include "Parm/GB_Params.h"
+#include "Parm/LJ1264_Params.h"
 
 // Exec_Change::Help()
 void Exec_Change::Help() const
@@ -24,10 +25,12 @@ void Exec_Change::Help() const
           "\t                             byfac <factor> |fromset <data set>} |\n"
           "\t  mergeres firstres <start res#> lastres <stop res#>\n"
           "\t  %s\n"
+          "\t  lj1264 %s\n"
           "\t}\n"
           "  Change specified parts of topology or topology of a COORDS data set.\n",
           DataSetList::TopArgs,
-          Cpptraj::Parm::GB_Params::HelpText().c_str()
+          Cpptraj::Parm::GB_Params::HelpText().c_str(),
+          Cpptraj::Parm::LJ1264_Params::HelpText().c_str()
          );
 }
 
@@ -37,7 +40,7 @@ Exec::RetType Exec_Change::Execute(CpptrajState& State, ArgList& argIn)
   // Change type
   enum ChangeType { UNKNOWN = 0, RESNAME, CHAINID, ORESNUMS, ICODES,
                     ATOMNAME, ADDBOND, REMOVEBONDS, SPLITRES, BONDPARM,
-                    MASS, CHARGE, MERGERES, GBRADII };
+                    MASS, CHARGE, MERGERES, GBRADII, LJ1264 };
   ChangeType type = UNKNOWN;
   if (argIn.hasKey("resname"))
     type = RESNAME;
@@ -63,6 +66,8 @@ Exec::RetType Exec_Change::Execute(CpptrajState& State, ArgList& argIn)
     type = CHARGE;
   else if (argIn.hasKey("mergeres"))
     type = MERGERES;
+  else if (argIn.hasKey("lj1264"))
+    type = LJ1264;
   else if (argIn.Contains("gb"))
     type = GBRADII;
   if (type == UNKNOWN) {
@@ -100,12 +105,21 @@ Exec::RetType Exec_Change::Execute(CpptrajState& State, ArgList& argIn)
     case CHARGE      : err = ChangeMassOrCharge(*parm, argIn, State.DSL(), 1); break;
     case MERGERES    : err = ChangeMergeRes(*parm, argIn); break;
     case GBRADII     : err = ChangeGbRadii(*parm, argIn); break;
+    case LJ1264      : err = ChangeLJ1264(*parm, argIn, State.Debug()); break;
     case UNKNOWN  : err = 1; // sanity check
   }
   if (err != 0) return CpptrajState::ERR;
   return CpptrajState::OK;
 }
 
+/** Change the LJ 1264 params */
+int Exec_Change::ChangeLJ1264(Topology& parm, ArgList& argIn, int debugIn) const {
+  Cpptraj::Parm::LJ1264_Params lj1264;
+  if (lj1264.Init_LJ1264(argIn, debugIn, "")) return 1;
+  if (lj1264.AssignLJ1264(parm)) return 1;
+  return 0;
+}
+
 /** Change the GB radii */
 int Exec_Change::ChangeGbRadii(Topology& parm, ArgList& argIn) const {
   Cpptraj::Parm::GB_Params gbradii;
diff --git a/src/Exec_Change.h b/src/Exec_Change.h
index 3ee401773d..858531ce26 100644
--- a/src/Exec_Change.h
+++ b/src/Exec_Change.h
@@ -14,6 +14,7 @@ class Exec_Change : public Exec {
     /// Change mass or charge
     static inline void changeTopVal(Topology&, int, ChangeType, double);
 
+    int ChangeLJ1264(Topology&, ArgList&, int) const;
     int ChangeGbRadii(Topology&, ArgList&) const;
     int ChangeSplitRes(Topology&, ArgList&) const;
     int ChangeResidueName(Topology&, ArgList&) const;
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 96aec7b710..070462c069 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -319,7 +319,7 @@ Exec_Analyze.o : Exec_Analyze.cpp Action.h ActionList.h ActionState.h Analysis.h
 Exec_Build.o : Exec_Build.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h ExclusionArray.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PairList.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/ImproperParmHolder.h Parm/LJ1264_Params.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h ParmFile.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/AddIons.h Structure/Builder.h Structure/Creator.h Structure/Disulfide.h Structure/HisProt.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/RingFinder.h Structure/Solvate.h Structure/StructureEnum.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Calc.o : Exec_Calc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Calc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_CatCrd.o : Exec_CatCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CatCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_Change.o : Exec_Change.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Change.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Change.o : Exec_Change.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Change.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/GB_Params.h Parm/LJ1264_Params.h Parm/ParmEnum.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_ClusterMap.o : Exec_ClusterMap.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ClusterMap.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ClusterMap.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_CombineCoords.o : Exec_CombineCoords.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CombineCoords.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_Commands.o : Exec_Commands.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Commands.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
@@ -432,7 +432,7 @@ ParallelNetcdf.o : ParallelNetcdf.cpp CpptrajStdio.h Parallel.h ParallelNetcdf.h
 ParallelSetFrameNum.o : ParallelSetFrameNum.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h ParallelSetFrameNum.h Range.h TextFormat.h
 Parm/AssignParams.o : Parm/AssignParams.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h GuessAtomHybridization.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/../Structure/GenerateConnectivityArrays.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GetParams.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Parm/Bond_Params.o : Parm/Bond_Params.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/Bond_Params.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
-Parm/GB_Params.o : Parm/GB_Params.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/GB_Params.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
+Parm/GB_Params.o : Parm/GB_Params.cpp ArgList.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/GB_Params.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Parm/GetParams.o : Parm/GetParams.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/GetParams.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Parm/LJ1264_Params.o : Parm/LJ1264_Params.cpp ArgList.h Atom.h AtomMask.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/LJ1264_Params.h Parm/ParmEnum.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Parm/Merge.o : Parm/Merge.cpp Atom.h Constants.h CpptrajStdio.h NameType.h ParameterTypes.h Parm/Merge.h Parm/ParmEnum.h Parm/ParmHolder.h Residue.h StringRoutines.h SymbolExporting.h TypeNameHolder.h
@@ -483,7 +483,7 @@ SplineFxnTable.o : SplineFxnTable.cpp Constants.h CpptrajStdio.h Spline.h Spline
 Stats_Reduce.o : Stats_Reduce.cpp OnlineVarT.h Parallel.h Stats_Reduce.h
 StringRoutines.o : StringRoutines.cpp CpptrajStdio.h StringRoutines.h
 Structure/AddIons.o : Structure/AddIons.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DistRoutines.h FileIO.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/../Parm/../AtomType.h Structure/../Parm/../CmapParmHolder.h Structure/../Parm/../Constants.h Structure/../Parm/../NameType.h Structure/../Parm/../ParameterTypes.h Structure/../Parm/../Parm/ParmEnum.h Structure/../Parm/../TypeNameHolder.h Structure/../Parm/DihedralParmHolder.h Structure/../Parm/ImproperParmHolder.h Structure/../Parm/ParameterSet.h Structure/../Parm/ParmEnum.h Structure/../Parm/ParmHolder.h Structure/AddIons.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Structure/Builder.o : Structure/Builder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h GuessAtomHybridization.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/../Parm/../AtomType.h Structure/../Parm/../CmapParmHolder.h Structure/../Parm/../Constants.h Structure/../Parm/../NameType.h Structure/../Parm/../ParameterTypes.h Structure/../Parm/../Parm/ParmEnum.h Structure/../Parm/../TypeNameHolder.h Structure/../Parm/DihedralParmHolder.h Structure/../Parm/ImproperParmHolder.h Structure/../Parm/ParameterSet.h Structure/../Parm/ParmEnum.h Structure/../Parm/ParmHolder.h Structure/Builder.h Structure/Chirality.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Structure/Builder.o : Structure/Builder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h GuessAtomHybridization.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/../Parm/../AtomType.h Structure/../Parm/../CmapParmHolder.h Structure/../Parm/../Constants.h Structure/../Parm/../NameType.h Structure/../Parm/../ParameterTypes.h Structure/../Parm/../Parm/ParmEnum.h Structure/../Parm/../TypeNameHolder.h Structure/../Parm/DihedralParmHolder.h Structure/../Parm/ImproperParmHolder.h Structure/../Parm/ParameterSet.h Structure/../Parm/ParmEnum.h Structure/../Parm/ParmHolder.h Structure/Builder.h Structure/Chirality.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 Structure/Chirality.o : Structure/Chirality.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Chirality.h Structure/StructureEnum.h SymbolExporting.h Topology.h TorsionRoutines.h Unit.h Vec3.h
 Structure/Creator.o : Structure/Creator.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h DataSet_Parameters.h DataSet_PdbResMap.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h PdbResMapType.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/Creator.h Structure/GenerateConnectivityArrays.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/Disulfide.o : Structure/Disulfide.cpp ArgList.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Disulfide.h Structure/ResStatArray.h Structure/StructureRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h

From 68adf488355d0595b4b497e620ac059d68e66d74 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 16 Jan 2026 14:21:11 -0500
Subject: [PATCH 1231/1492] Add warning for adding LJ 12-6-4, requires specific
 nonbonds to already be present. Start a routine for this but do not yet
 enable.

---
 src/Exec_Change.cpp        |  2 ++
 src/Parm/LJ1264_Params.cpp | 20 ++++++++++++++++++++
 2 files changed, 22 insertions(+)

diff --git a/src/Exec_Change.cpp b/src/Exec_Change.cpp
index 8d332b53d0..3d42324578 100644
--- a/src/Exec_Change.cpp
+++ b/src/Exec_Change.cpp
@@ -114,6 +114,8 @@ Exec::RetType Exec_Change::Execute(CpptrajState& State, ArgList& argIn)
 
 /** Change the LJ 1264 params */
 int Exec_Change::ChangeLJ1264(Topology& parm, ArgList& argIn, int debugIn) const {
+  mprintf("Warning: If topology '%s' was not generated with the proper LJ 12-6-4 frcmod loaded\n"
+          "Warning:   this will not be adding the correct C coefficients!\n", parm.c_str());
   Cpptraj::Parm::LJ1264_Params lj1264;
   if (lj1264.Init_LJ1264(argIn, debugIn, "")) return 1;
   if (lj1264.AssignLJ1264(parm)) return 1;
diff --git a/src/Parm/LJ1264_Params.cpp b/src/Parm/LJ1264_Params.cpp
index ac50d184cf..130bdad224 100644
--- a/src/Parm/LJ1264_Params.cpp
+++ b/src/Parm/LJ1264_Params.cpp
@@ -526,6 +526,26 @@ int LJ1264_Params::Init_LJ1264(std::string const& maskIn, std::string const& c4f
 
   return 0;
 }
+/*
+int LJ1264_Params::LoadNonbonds(std::string const& frcmodNameIn) const {
+  std::string frcmodName;
+  if (frcmodNameIn.empty()) {
+    // Determine frcmod file from the water model
+    // First, need to determine where the Amber FF files are
+    const char* env = getenv("AMBERHOME");
+    if (env != 0)
+      frcmodName = std::string(env) + "/dat/leap/parm/frcmod.";
+    else {
+      mprinterr("Error: AMBERHOME not set. Cannot find LJ 12-6-4 frcmod files.\n");
+      return 1;
+    }
+
+    switch (waterModel_) {
+      case UNKNOWN_WATER_MODEL :
+        mprintf("Warning: Unknown water model; cannot determine LJ 12-6-4 frcmod file named.\n");
+        return 0;
+      case Cpptraj::Parm::TIP3P : frcmodName.append("ions234lm_1264_tip3p");
+*/
 
 /** \return Help text. */
 std::string LJ1264_Params::HelpText() {

From f81d7840bd969bb537daa64d438c8861fbfbf548 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 17 Jan 2026 18:44:49 -0500
Subject: [PATCH 1232/1492] Start improving output

---
 src/Exec_Build.cpp | 53 +++++++++++++++++++++++++++-------------------
 1 file changed, 31 insertions(+), 22 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 29153930f3..e55cac92d5 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -885,10 +885,8 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
   std::string outputTopologyName = argIn.GetStringKey("parmout");
   std::string outputCoordsName = argIn.GetStringKey("crdout");
   if (argIn.hasKey("simplecheck")) {
-    mprintf("\tSimple check: will only check bond lengths.\n");
     check_structure_ = false;
   } else {
-    mprintf("\tWill check bond lengths, atomic overlaps, and ring intersections.\n");
     check_structure_ = true;
   }
   if (!outputTopologyName.empty())
@@ -966,7 +964,27 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
     mprintf("\tRequire all input atoms to be found in templates.\n");
   else
     mprintf("\tInput atoms not found in templates will be ignored.\n");
+  // ---------------------------------------------
+  mprintf("    -----===== Getting templates and parameters ===== -----\n");
+  // Get templates and parameter sets.
+  t_get_templates_.Start();
+  Cpptraj::Structure::Creator creator( debug_ );
+  if (creator.InitCreator(argIn, DSL, debug_)) {
+    return CpptrajState::ERR;
+  }
+  if (!creator.HasTemplates()) {
+    mprintf("Warning: No residue templates loaded.\n");
+  }
+  if (!creator.HasMainParmSet()) {
+    mprinterr("Error: No parameter sets.\n");
+    return CpptrajState::ERR;
+  }
+  t_get_templates_.Stop();
+  // FIXME hide behind ifdef?
+  creator.TimingInfo(t_get_templates_.Total(), 2);
 
+  // ---------------------------------------------
+  mprintf("    -----===== Structure Prep ===== -----\n");
   // Do histidine detection before H atoms are removed
   t_hisDetect_.Start();
   if (!argIn.hasKey("nohisdetect")) {
@@ -1031,23 +1049,6 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
     }
   }
 
-  // Get templates and parameter sets.
-  t_get_templates_.Start();
-  Cpptraj::Structure::Creator creator( debug_ );
-  if (creator.InitCreator(argIn, DSL, debug_)) {
-    return CpptrajState::ERR;
-  }
-  if (!creator.HasTemplates()) {
-    mprintf("Warning: No residue templates loaded.\n");
-  }
-  if (!creator.HasMainParmSet()) {
-    mprinterr("Error: No parameter sets.\n");
-    return CpptrajState::ERR;
-  }
-  t_get_templates_.Stop();
-  // FIXME hide behind ifdef?
-  creator.TimingInfo(t_get_templates_.Total(), 2);
-
   // All residues start unknown
   Cpptraj::Structure::ResStatArray resStat( topIn.Nres() );
   std::vector<BondType> DisulfideBonds;
@@ -1123,6 +1124,7 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
   t_sugar_.Stop();
 
   // Fill in atoms with templates
+  mprintf("    -----===== Match residues to templates, fill missing atoms =====-----\n");
   t_fill_.Start();
   //Topology topOut;
   Topology& topOut = static_cast<Topology&>( *(crdout.TopPtr()) );
@@ -1170,6 +1172,7 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
   // Solvate/add ions
   std::string checkMaskString("*");
   if (add_solvent == SOLVATEBOX) {
+    mprintf("    -----===== Solvate =====-----\n");
     t_solvate_.Start();
     // Record initial number of atoms and residues
     int initial_natom = topOut.Natom();
@@ -1191,6 +1194,7 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
     }
     t_solvate_.Stop();
   } else if (add_solvent == SETBOX) {
+    mprintf("    -----===== Set Box =====-----\n");
     t_solvate_.Start();
     if (solvator.SetVdwBoundingBox( topOut, frameOut, *(creator.MainParmSetPtr()) )) {
       mprinterr("Error: Setting box failed.\n");
@@ -1201,6 +1205,7 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
 
   // Assign parameters. This will create the bond/angle/dihedral/improper
   // arrays as well.
+  mprintf("    -----===== Assign Parameters =====-----\n");
   t_assign_.Start();
   Exec::RetType ret = CpptrajState::OK;
   Cpptraj::Parm::AssignParams AP;
@@ -1228,15 +1233,17 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
 
   // Update coords 
   if (crdout.CoordsSetup( topOut, frameOut.CoordsInfo() )) { // FIXME better coordinate info
-    mprinterr("Error: Could not set up output COORDS.\n");
+    mprinterr("Error: Could not set up output COORDS data set.\n");
     return CpptrajState::ERR;
   }
   crdout.SetCRD(0, frameOut);
 
   // Structure check
+  mprintf("    -----===== Structure Check =====-----\n");
+  StructureCheck check;
   if (check_structure_) {
+    mprintf("\tWill check bond lengths, atomic overlaps, and ring intersections.\n");
     t_check_.Start();
-    StructureCheck check;
     if (check.SetOptions( true, // image 
                           true, // check bonds
                           true,  // save problems
@@ -1310,8 +1317,8 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
     t_check_.Stop();
   } else {
     // Just check bond lengths
+    mprintf("\tSimple check: will only check bond lengths.\n");
     t_check_.Start();
-    StructureCheck check;
     if (check.SetOptions( false, // image 
                           true,  // check bonds
                           true,  // save problems
@@ -1360,6 +1367,7 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
   if ( absSystemCharge > 0.01 )
     mprintf("Warning: The charge of the system is not zero: %f\n", totalSystemCharge);
 
+  mprintf("    -----===== File Output =====-----\n");
   if (!outputTopologyName.empty()) {
     ParmFile pfile;
     if (pfile.WriteTopology(crdout.Top(), outputTopologyName, argIn, ParmFile::UNKNOWN_PARM, debug_)) {
@@ -1384,6 +1392,7 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
   }
   t_total_.Stop();
 
+  mprintf("    -----===== Timing =====-----\n");
   PrintTiming();
   if (add_solvent)
     t_solvate_.WriteTiming    (2, "Solvate             :", t_total_.Total());

From 061428025a57d375de36f825cf864a2010370693 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 17 Jan 2026 18:51:39 -0500
Subject: [PATCH 1233/1492] Split off gb info

---
 src/Exec_Build.cpp     | 1 +
 src/Parm/GB_Params.cpp | 6 +++++-
 src/Parm/GB_Params.h   | 2 ++
 3 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index e55cac92d5..f44a2ffbc2 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -1216,6 +1216,7 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
     ret = CpptrajState::ERR;
   }
   // Assign GB parameters
+  gbradii.GB_Info();
   if (gbradii.Assign_GB_Radii(topOut)) {
     mprinterr("Error: Could not assign GB parameters for '%s'\n", topOut.c_str());
     ret = CpptrajState::ERR;
diff --git a/src/Parm/GB_Params.cpp b/src/Parm/GB_Params.cpp
index 5695f36825..f110d9f8f0 100644
--- a/src/Parm/GB_Params.cpp
+++ b/src/Parm/GB_Params.cpp
@@ -106,10 +106,14 @@ int Cpptraj::Parm::GB_Params::Init_GB_Radii(ArgList& argIn, Cpptraj::Parm::GB_Ra
     // Use passed-in GB radii set
     gbradii_ = gbRadIn;
   }
-  mprintf("\tGB radii set: %s\n", Cpptraj::Parm::GbTypeStr(gbradii_).c_str());
   return 0;
 }
 
+/** Print current setup. */
+void Cpptraj::Parm::GB_Params::GB_Info() const {
+  mprintf("\tGB radii set: %s\n", Cpptraj::Parm::GbTypeStr(gbradii_).c_str());
+}
+
 /** Assign GB radii. */
 void Cpptraj::Parm::GB_Params::assign_gb_radii(Topology& top, Cpptraj::Parm::GB_RadiiType radiiSet)
 {
diff --git a/src/Parm/GB_Params.h b/src/Parm/GB_Params.h
index 443b0704fe..36f955a928 100644
--- a/src/Parm/GB_Params.h
+++ b/src/Parm/GB_Params.h
@@ -34,6 +34,8 @@ class GB_Params {
     static std::string HelpText();
     /// Initialize 
     int Init_GB_Radii(ArgList&, GB_RadiiType);
+    // Print current setup
+    void GB_Info() const;
     /// Assign GB radii
     int Assign_GB_Radii(Topology&) const;
   private:

From 114db749331fa8acd93a9871499c3db80b78482c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 20 Jan 2026 08:47:54 -0500
Subject: [PATCH 1234/1492] Move gb/lj1264 param init and output coords setup
 to earlier

---
 src/Exec_Build.cpp | 59 +++++++++++++++++++++++-----------------------
 1 file changed, 30 insertions(+), 29 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index f44a2ffbc2..c3506628c1 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -964,6 +964,36 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
     mprintf("\tRequire all input atoms to be found in templates.\n");
   else
     mprintf("\tInput atoms not found in templates will be ignored.\n");
+
+  // Set up Output coords
+  if (!outset.empty()) {
+    // Separate output COORDS set.
+    outCrdPtr_ = DSL.AddSet( DataSet::COORDS, outset );
+  } else {
+    // In-place output COORDS
+    DSL.RemoveSet( inCrdPtr );
+    outCrdPtr_ = DSL.AddSet( DataSet::COORDS, inCrdPtr->Meta() );
+  }
+  if (outCrdPtr_ == 0) {
+    mprinterr("Error: Could not allocate output COORDS set with name '%s'\n", outset.c_str());
+    return CpptrajState::ERR;
+  }
+  DataSet_Coords& crdout = static_cast<DataSet_Coords&>( *((DataSet_Coords*)outCrdPtr_) );
+  mprintf("\tOutput COORDS set: %s\n", crdout.legend());
+
+  // GB radii set
+  Cpptraj::Parm::GB_Params gbradii;
+  if (gbradii.Init_GB_Radii(argIn, gbRadIn)) return CpptrajState::ERR;
+
+  // LJ 12-6-4
+  Cpptraj::Parm::LJ1264_Params lj1264;
+  if (argIn.hasKey("lj1264")) {
+    if (lj1264.Init_LJ1264( argIn, debug_, solvator.SolventBoxName())) {
+      mprinterr("Error: Init of LJ 12-6-4 failed.\n");
+      return CpptrajState::ERR;
+    }
+  }
+
   // ---------------------------------------------
   mprintf("    -----===== Getting templates and parameters ===== -----\n");
   // Get templates and parameter sets.
@@ -1020,35 +1050,6 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
   }
   t_clean_.Stop();
 
-  // Set up Output coords
-  if (!outset.empty()) {
-    // Separate output COORDS set.
-    outCrdPtr_ = DSL.AddSet( DataSet::COORDS, outset );
-  } else {
-    // In-place output COORDS
-    DSL.RemoveSet( inCrdPtr );
-    outCrdPtr_ = DSL.AddSet( DataSet::COORDS, inCrdPtr->Meta() );
-  }
-  if (outCrdPtr_ == 0) {
-    mprinterr("Error: Could not allocate output COORDS set with name '%s'\n", outset.c_str());
-    return CpptrajState::ERR;
-  }
-  DataSet_Coords& crdout = static_cast<DataSet_Coords&>( *((DataSet_Coords*)outCrdPtr_) );
-  mprintf("\tOutput COORDS set: %s\n", crdout.legend());
-
-  // GB radii set
-  Cpptraj::Parm::GB_Params gbradii;
-  if (gbradii.Init_GB_Radii(argIn, gbRadIn)) return CpptrajState::ERR;
-
-  // LJ 12-6-4
-  Cpptraj::Parm::LJ1264_Params lj1264;
-  if (argIn.hasKey("lj1264")) {
-    if (lj1264.Init_LJ1264( argIn, debug_, solvator.SolventBoxName())) {
-      mprinterr("Error: Init of LJ 12-6-4 failed.\n");
-      return CpptrajState::ERR;
-    }
-  }
-
   // All residues start unknown
   Cpptraj::Structure::ResStatArray resStat( topIn.Nres() );
   std::vector<BondType> DisulfideBonds;

From c28e8d4c1b9ab17a11397e876eaa70d6270cd118 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 20 Jan 2026 11:03:17 -0500
Subject: [PATCH 1235/1492] Protect against overwriting multiple frames when
 doing in-place build. Fix memory issue when doing in-place build.

---
 src/Exec_Build.cpp | 22 ++++++++++++----------
 1 file changed, 12 insertions(+), 10 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index c3506628c1..53a4aabfc8 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -849,10 +849,6 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
     return CpptrajState::ERR;
   }
   std::string outset = argIn.GetStringKey("name");
-  if (outset.empty()) {
-    mprinterr("Error: Must specify output COORDS set with 'name'\n");
-    return CpptrajState::ERR;
-  }
 
   return BuildStructure(inCrdPtr, outset, State.DSL(), State.Debug(), argIn, Cpptraj::Parm::UNKNOWN_GB);
 }
@@ -879,6 +875,11 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
     mprinterr("Error: Set '%s' is not coordinates, cannot use for building.\n", inCrdPtr->legend());
     return CpptrajState::ERR;
   }
+  if (outset.empty() && inCrdPtr->Size() > 1) {
+    mprinterr("Error: Set '%s' has more than 1 frame; must specify an output COORDS set in order to build.\n",
+              inCrdPtr->legend());
+    return CpptrajState::ERR;
+  }
   debug_ = debugIn;
   int verbose = argIn.getKeyInt("verbose", 0);
   std::string title = argIn.GetStringKey("title");
@@ -971,8 +972,9 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
     outCrdPtr_ = DSL.AddSet( DataSet::COORDS, outset );
   } else {
     // In-place output COORDS
+    MetaData inCrdMeta = inCrdPtr->Meta();
     DSL.RemoveSet( inCrdPtr );
-    outCrdPtr_ = DSL.AddSet( DataSet::COORDS, inCrdPtr->Meta() );
+    outCrdPtr_ = DSL.AddSet( DataSet::COORDS, inCrdMeta );
   }
   if (outCrdPtr_ == 0) {
     mprinterr("Error: Could not allocate output COORDS set with name '%s'\n", outset.c_str());
@@ -994,7 +996,7 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
     }
   }
 
-  // ---------------------------------------------
+  // =============================================
   mprintf("    -----===== Getting templates and parameters ===== -----\n");
   // Get templates and parameter sets.
   t_get_templates_.Start();
@@ -1013,7 +1015,6 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
   // FIXME hide behind ifdef?
   creator.TimingInfo(t_get_templates_.Total(), 2);
 
-  // ---------------------------------------------
   mprintf("    -----===== Structure Prep ===== -----\n");
   // Do histidine detection before H atoms are removed
   t_hisDetect_.Start();
@@ -1148,11 +1149,10 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
   }
   t_fill_.Stop();
 
-  // Add the disulfide/sugar bonds
+  // Add the disulfide bonds
   int addBondsErr = transfer_bonds( topOut, topIn, DisulfideBonds );
-  //addBondsErr += transfer_bonds( topOut, topIn, SugarBonds );
   if (addBondsErr != 0) {
-    mprinterr("Error: Adding disulfide/sugar bonds failed.\n");
+    mprinterr("Error: Adding disulfide bonds failed.\n");
     return CpptrajState::ERR;
   }
 
@@ -1170,6 +1170,8 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
     // Finalize topology - determine molecules, dont renumber residues
   topOut.CommonSetup(true, false);
 
+  // =============================================
+
   // Solvate/add ions
   std::string checkMaskString("*");
   if (add_solvent == SOLVATEBOX) {

From 483fa56bdc982fddb1792f6e1050147d2c469153 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 20 Jan 2026 11:14:21 -0500
Subject: [PATCH 1236/1492] Start trying to split off Parm set from Creator

---
 src/Parm/MainParmSet.cpp | 95 ++++++++++++++++++++++++++++++++++++++++
 src/Parm/MainParmSet.h   | 38 ++++++++++++++++
 2 files changed, 133 insertions(+)
 create mode 100644 src/Parm/MainParmSet.cpp
 create mode 100644 src/Parm/MainParmSet.h

diff --git a/src/Parm/MainParmSet.cpp b/src/Parm/MainParmSet.cpp
new file mode 100644
index 0000000000..3c9575ff08
--- /dev/null
+++ b/src/Parm/MainParmSet.cpp
@@ -0,0 +1,95 @@
+#include "MainParmSet.h"
+#include "../ArgList.h"
+#include "../CpptrajStdio.h"
+#include "../DataSet_Parameters.h"
+#include "../DataSetList.h"
+
+using namespace Cpptraj::Parm;
+
+/** CONSTRUCTOR */
+MainParmSet::MainParmSet() :
+  mainParmSet_(0),
+  free_parmset_mem_(false)
+{}
+
+/** DESTRUCTOR */
+MainParmSet::~MainParmSet() {
+  if (mainParmSet_ != 0 && free_parmset_mem_)
+    delete mainParmSet_;
+}
+
+const char* MainParmSet::parm_keywords_ = "parmset <parameter setname>";
+
+/** Initialize */
+int MainParmSet::InitMainParmSet(ArgList& argIn, DataSetList const& DSL, int debugIn)
+{
+  t_total_.Start();
+  debug_ = debugIn;
+
+  if (getParameterSets(argIn, DSL)) return 1;
+
+  t_total_.Stop();
+  return 0;
+}
+
+/** Write timing info to stdout. */
+void MainParmSet::TimingInfo(double total, int indent) const {
+  t_total_.WriteTiming(indent, "Get Parameters:", total);
+}
+
+/** Get parameter sets. */
+int MainParmSet::getParameterSets(ArgList& argIn, DataSetList const& DSL) {
+  // Clear any existing set
+  if (mainParmSet_ != 0) {
+    if (free_parmset_mem_) delete mainParmSet_;
+  }
+  mainParmSet_ = 0;
+  free_parmset_mem_ = false;
+  // Look for parmset args
+  typedef std::vector<DataSet_Parameters*> Parray;
+  Parray ParamSets;
+  std::string parmset = argIn.GetStringKey("parmset");
+  if (parmset.empty()) {
+    mprintf("\tNo parameter set(s) specified with 'parmset'; using any loaded sets.\n");
+    // See if there are any parameter sets.
+    DataSetList sets = DSL.GetSetsOfType( "*", DataSet::PARAMETERS );
+    for (DataSetList::const_iterator it = sets.begin(); it != sets.end(); ++it)
+      ParamSets.push_back( (DataSet_Parameters*)(*it) );
+  } else {
+    while (!parmset.empty()) {
+      DataSetList sets = DSL.GetSetsOfType( parmset, DataSet::PARAMETERS );
+      if (sets.empty()) {
+        mprintf("Warning: No parameter sets corresponding to '%s'\n", parmset.c_str());
+      } else {
+        for (DataSetList::const_iterator it = sets.begin(); it != sets.end(); ++it)
+          ParamSets.push_back( (DataSet_Parameters*)(*it) );
+      }
+      parmset = argIn.GetStringKey("parmset");
+    }
+  }
+  //if (ParamSets.empty()) {
+  //  mprinterr("Error: No parameter sets.\n");
+  //  return CpptrajState::ERR;
+  //}
+  if (!ParamSets.empty()) {
+    mprintf("\tParameter sets:\n"); // TODO put these names in the final combined parameter set
+    for (Parray::const_iterator it = ParamSets.begin(); it != ParamSets.end(); ++it)
+      mprintf("\t  %s\n", (*it)->legend());
+
+    // Combine parameters if needed
+
+    if (ParamSets.size() == 1)
+      mainParmSet_ = ParamSets.front();
+    else {
+      free_parmset_mem_ = true;
+      mprintf("\tCombining parameter sets.\n");
+      Parray::const_iterator it = ParamSets.begin();
+      mainParmSet_ = new DataSet_Parameters( *(*it) );
+      ++it;
+      Cpptraj::Parm::ParameterSet::UpdateCount UC;
+      for (; it != ParamSets.end(); ++it)
+        mainParmSet_->UpdateParamSet( *(*it), UC, debug_, debug_+1 ); // Make it so verbosity is at least 1 to report overwritten params 
+    }
+  }
+  return 0;
+}
diff --git a/src/Parm/MainParmSet.h b/src/Parm/MainParmSet.h
new file mode 100644
index 0000000000..bf1d8aeda6
--- /dev/null
+++ b/src/Parm/MainParmSet.h
@@ -0,0 +1,38 @@
+#ifndef INC_PARM_MAINPARMSET_H
+#define INC_PARM_MAINPARMSET_H
+#include "../Timer.h"
+class ArgList;
+class DataSetList;
+class DataSet_Parameters;
+namespace Cpptraj {
+namespace Parm {
+/// Hold any combination of parameter sets 
+class MainParmSet {
+  public:
+    /// CONSTRUCTOR
+    MainParmSet();
+    /// DESTRUCTOR
+    ~MainParmSet();
+    /// Associated parameter keywords for InitMainParmSet
+    static const char* parm_keywords_;
+    /// Initialize the MainParmSet
+    int InitMainParmSet(ArgList&, DataSetList const&, int);
+    /// Write timing info to stdout
+    void TimingInfo(double, int) const;
+
+    /// \return True if a parameter set is defined
+    bool HasMainParmSet() const { return (mainParmSet_ != 0); }
+    /// \return Main parm set
+    DataSet_Parameters const* MainParmSetPtr() const { return mainParmSet_; }
+  private:
+    /// Get parameter sets
+    int getParameterSets(ArgList&, DataSetList const&);
+
+    DataSet_Parameters* mainParmSet_; ///< Hold optional parameter set.
+    int debug_;                       ///< Debug level
+    bool free_parmset_mem_;           ///< True if main parm set is combined and should be freed
+    Timer t_total_;
+};
+}
+}
+#endif

From 19e547629ef3c38ed7ebe5c75e0d50a2060f1b55 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 20 Jan 2026 11:14:34 -0500
Subject: [PATCH 1237/1492] Update build infra.

---
 src/Parm/CMakeLists.txt | 1 +
 src/Parm/parmdepend     | 3 ++-
 src/Parm/parmfiles      | 1 +
 3 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/Parm/CMakeLists.txt b/src/Parm/CMakeLists.txt
index c8e8a81c32..212a39b333 100644
--- a/src/Parm/CMakeLists.txt
+++ b/src/Parm/CMakeLists.txt
@@ -5,6 +5,7 @@ target_sources(cpptraj_common_obj PRIVATE
   ${CMAKE_CURRENT_LIST_DIR}/GB_Params.cpp
   ${CMAKE_CURRENT_LIST_DIR}/GetParams.cpp
   ${CMAKE_CURRENT_LIST_DIR}/LJ1264_Params.cpp
+  ${CMAKE_CURRENT_LIST_DIR}/MainParmSet.cpp
   ${CMAKE_CURRENT_LIST_DIR}/Merge.cpp
   ${CMAKE_CURRENT_LIST_DIR}/ParameterSet.cpp
   ${CMAKE_CURRENT_LIST_DIR}/ParmEnum.cpp
diff --git a/src/Parm/parmdepend b/src/Parm/parmdepend
index cf713aed50..84a2eb4abe 100644
--- a/src/Parm/parmdepend
+++ b/src/Parm/parmdepend
@@ -1,8 +1,9 @@
 AssignParams.o : AssignParams.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/ParmEnum.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/GenerateConnectivityArrays.h ../SymbolExporting.h ../Timer.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h AssignParams.h DihedralParmHolder.h GetParams.h ImproperParmHolder.h ParameterSet.h ParmEnum.h ParmHolder.h
 Bond_Params.o : Bond_Params.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h Bond_Params.h
-GB_Params.o : GB_Params.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h GB_Params.h
+GB_Params.o : GB_Params.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h GB_Params.h
 GetParams.o : GetParams.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/ParmEnum.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h DihedralParmHolder.h GetParams.h ImproperParmHolder.h ParameterSet.h ParmEnum.h ParmHolder.h
 LJ1264_Params.o : LJ1264_Params.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../BufferedLine.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../StringRoutines.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h LJ1264_Params.h ParmEnum.h
+MainParmSet.o : MainParmSet.cpp ../ArgList.h ../AssociatedData.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../DataSet_Parameters.h ../Dimension.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/../AtomType.h ../Parm/../CmapParmHolder.h ../Parm/../Constants.h ../Parm/../NameType.h ../Parm/../ParameterTypes.h ../Parm/../Parm/ParmEnum.h ../Parm/../TypeNameHolder.h ../Parm/DihedralParmHolder.h ../Parm/ImproperParmHolder.h ../Parm/ParameterSet.h ../Parm/ParmEnum.h ../Parm/ParmHolder.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h MainParmSet.h
 Merge.o : Merge.cpp ../Atom.h ../Constants.h ../CpptrajStdio.h ../NameType.h ../ParameterTypes.h ../Residue.h ../StringRoutines.h ../SymbolExporting.h ../TypeNameHolder.h Merge.h ParmEnum.h ParmHolder.h
 ParameterSet.o : ParameterSet.cpp ../AtomType.h ../CmapParmHolder.h ../Constants.h ../CpptrajFile.h ../CpptrajStdio.h ../FileIO.h ../FileName.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/ParmEnum.h ../TypeNameHolder.h ../UpdateParameters.h DihedralParmHolder.h ImproperParmHolder.h ParameterSet.h ParmEnum.h ParmHolder.h
 ParmEnum.o : ParmEnum.cpp ParmEnum.h
diff --git a/src/Parm/parmfiles b/src/Parm/parmfiles
index 4a8b0492c7..157123f670 100644
--- a/src/Parm/parmfiles
+++ b/src/Parm/parmfiles
@@ -5,6 +5,7 @@ PARM_SOURCES= \
   GB_Params.cpp \
   GetParams.cpp \
   LJ1264_Params.cpp \
+  MainParmSet.cpp \
   Merge.cpp \
   ParameterSet.cpp \
   ParmEnum.cpp

From 0c41512a9ad172dfe753e9931a325186e15403a3 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 20 Jan 2026 11:37:45 -0500
Subject: [PATCH 1238/1492] Not ready to split up Creator yet.

---
 src/Parm/CMakeLists.txt  |  1 -
 src/Parm/MainParmSet.cpp | 95 ----------------------------------------
 src/Parm/MainParmSet.h   | 38 ----------------
 src/Parm/parmdepend      |  1 -
 src/Parm/parmfiles       |  1 -
 5 files changed, 136 deletions(-)
 delete mode 100644 src/Parm/MainParmSet.cpp
 delete mode 100644 src/Parm/MainParmSet.h

diff --git a/src/Parm/CMakeLists.txt b/src/Parm/CMakeLists.txt
index 212a39b333..c8e8a81c32 100644
--- a/src/Parm/CMakeLists.txt
+++ b/src/Parm/CMakeLists.txt
@@ -5,7 +5,6 @@ target_sources(cpptraj_common_obj PRIVATE
   ${CMAKE_CURRENT_LIST_DIR}/GB_Params.cpp
   ${CMAKE_CURRENT_LIST_DIR}/GetParams.cpp
   ${CMAKE_CURRENT_LIST_DIR}/LJ1264_Params.cpp
-  ${CMAKE_CURRENT_LIST_DIR}/MainParmSet.cpp
   ${CMAKE_CURRENT_LIST_DIR}/Merge.cpp
   ${CMAKE_CURRENT_LIST_DIR}/ParameterSet.cpp
   ${CMAKE_CURRENT_LIST_DIR}/ParmEnum.cpp
diff --git a/src/Parm/MainParmSet.cpp b/src/Parm/MainParmSet.cpp
deleted file mode 100644
index 3c9575ff08..0000000000
--- a/src/Parm/MainParmSet.cpp
+++ /dev/null
@@ -1,95 +0,0 @@
-#include "MainParmSet.h"
-#include "../ArgList.h"
-#include "../CpptrajStdio.h"
-#include "../DataSet_Parameters.h"
-#include "../DataSetList.h"
-
-using namespace Cpptraj::Parm;
-
-/** CONSTRUCTOR */
-MainParmSet::MainParmSet() :
-  mainParmSet_(0),
-  free_parmset_mem_(false)
-{}
-
-/** DESTRUCTOR */
-MainParmSet::~MainParmSet() {
-  if (mainParmSet_ != 0 && free_parmset_mem_)
-    delete mainParmSet_;
-}
-
-const char* MainParmSet::parm_keywords_ = "parmset <parameter setname>";
-
-/** Initialize */
-int MainParmSet::InitMainParmSet(ArgList& argIn, DataSetList const& DSL, int debugIn)
-{
-  t_total_.Start();
-  debug_ = debugIn;
-
-  if (getParameterSets(argIn, DSL)) return 1;
-
-  t_total_.Stop();
-  return 0;
-}
-
-/** Write timing info to stdout. */
-void MainParmSet::TimingInfo(double total, int indent) const {
-  t_total_.WriteTiming(indent, "Get Parameters:", total);
-}
-
-/** Get parameter sets. */
-int MainParmSet::getParameterSets(ArgList& argIn, DataSetList const& DSL) {
-  // Clear any existing set
-  if (mainParmSet_ != 0) {
-    if (free_parmset_mem_) delete mainParmSet_;
-  }
-  mainParmSet_ = 0;
-  free_parmset_mem_ = false;
-  // Look for parmset args
-  typedef std::vector<DataSet_Parameters*> Parray;
-  Parray ParamSets;
-  std::string parmset = argIn.GetStringKey("parmset");
-  if (parmset.empty()) {
-    mprintf("\tNo parameter set(s) specified with 'parmset'; using any loaded sets.\n");
-    // See if there are any parameter sets.
-    DataSetList sets = DSL.GetSetsOfType( "*", DataSet::PARAMETERS );
-    for (DataSetList::const_iterator it = sets.begin(); it != sets.end(); ++it)
-      ParamSets.push_back( (DataSet_Parameters*)(*it) );
-  } else {
-    while (!parmset.empty()) {
-      DataSetList sets = DSL.GetSetsOfType( parmset, DataSet::PARAMETERS );
-      if (sets.empty()) {
-        mprintf("Warning: No parameter sets corresponding to '%s'\n", parmset.c_str());
-      } else {
-        for (DataSetList::const_iterator it = sets.begin(); it != sets.end(); ++it)
-          ParamSets.push_back( (DataSet_Parameters*)(*it) );
-      }
-      parmset = argIn.GetStringKey("parmset");
-    }
-  }
-  //if (ParamSets.empty()) {
-  //  mprinterr("Error: No parameter sets.\n");
-  //  return CpptrajState::ERR;
-  //}
-  if (!ParamSets.empty()) {
-    mprintf("\tParameter sets:\n"); // TODO put these names in the final combined parameter set
-    for (Parray::const_iterator it = ParamSets.begin(); it != ParamSets.end(); ++it)
-      mprintf("\t  %s\n", (*it)->legend());
-
-    // Combine parameters if needed
-
-    if (ParamSets.size() == 1)
-      mainParmSet_ = ParamSets.front();
-    else {
-      free_parmset_mem_ = true;
-      mprintf("\tCombining parameter sets.\n");
-      Parray::const_iterator it = ParamSets.begin();
-      mainParmSet_ = new DataSet_Parameters( *(*it) );
-      ++it;
-      Cpptraj::Parm::ParameterSet::UpdateCount UC;
-      for (; it != ParamSets.end(); ++it)
-        mainParmSet_->UpdateParamSet( *(*it), UC, debug_, debug_+1 ); // Make it so verbosity is at least 1 to report overwritten params 
-    }
-  }
-  return 0;
-}
diff --git a/src/Parm/MainParmSet.h b/src/Parm/MainParmSet.h
deleted file mode 100644
index bf1d8aeda6..0000000000
--- a/src/Parm/MainParmSet.h
+++ /dev/null
@@ -1,38 +0,0 @@
-#ifndef INC_PARM_MAINPARMSET_H
-#define INC_PARM_MAINPARMSET_H
-#include "../Timer.h"
-class ArgList;
-class DataSetList;
-class DataSet_Parameters;
-namespace Cpptraj {
-namespace Parm {
-/// Hold any combination of parameter sets 
-class MainParmSet {
-  public:
-    /// CONSTRUCTOR
-    MainParmSet();
-    /// DESTRUCTOR
-    ~MainParmSet();
-    /// Associated parameter keywords for InitMainParmSet
-    static const char* parm_keywords_;
-    /// Initialize the MainParmSet
-    int InitMainParmSet(ArgList&, DataSetList const&, int);
-    /// Write timing info to stdout
-    void TimingInfo(double, int) const;
-
-    /// \return True if a parameter set is defined
-    bool HasMainParmSet() const { return (mainParmSet_ != 0); }
-    /// \return Main parm set
-    DataSet_Parameters const* MainParmSetPtr() const { return mainParmSet_; }
-  private:
-    /// Get parameter sets
-    int getParameterSets(ArgList&, DataSetList const&);
-
-    DataSet_Parameters* mainParmSet_; ///< Hold optional parameter set.
-    int debug_;                       ///< Debug level
-    bool free_parmset_mem_;           ///< True if main parm set is combined and should be freed
-    Timer t_total_;
-};
-}
-}
-#endif
diff --git a/src/Parm/parmdepend b/src/Parm/parmdepend
index 84a2eb4abe..c2c303deaa 100644
--- a/src/Parm/parmdepend
+++ b/src/Parm/parmdepend
@@ -3,7 +3,6 @@ Bond_Params.o : Bond_Params.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h
 GB_Params.o : GB_Params.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h GB_Params.h
 GetParams.o : GetParams.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/ParmEnum.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h DihedralParmHolder.h GetParams.h ImproperParmHolder.h ParameterSet.h ParmEnum.h ParmHolder.h
 LJ1264_Params.o : LJ1264_Params.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../BufferedLine.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../StringRoutines.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h LJ1264_Params.h ParmEnum.h
-MainParmSet.o : MainParmSet.cpp ../ArgList.h ../AssociatedData.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../DataSet_Parameters.h ../Dimension.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/../AtomType.h ../Parm/../CmapParmHolder.h ../Parm/../Constants.h ../Parm/../NameType.h ../Parm/../ParameterTypes.h ../Parm/../Parm/ParmEnum.h ../Parm/../TypeNameHolder.h ../Parm/DihedralParmHolder.h ../Parm/ImproperParmHolder.h ../Parm/ParameterSet.h ../Parm/ParmEnum.h ../Parm/ParmHolder.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h MainParmSet.h
 Merge.o : Merge.cpp ../Atom.h ../Constants.h ../CpptrajStdio.h ../NameType.h ../ParameterTypes.h ../Residue.h ../StringRoutines.h ../SymbolExporting.h ../TypeNameHolder.h Merge.h ParmEnum.h ParmHolder.h
 ParameterSet.o : ParameterSet.cpp ../AtomType.h ../CmapParmHolder.h ../Constants.h ../CpptrajFile.h ../CpptrajStdio.h ../FileIO.h ../FileName.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/ParmEnum.h ../TypeNameHolder.h ../UpdateParameters.h DihedralParmHolder.h ImproperParmHolder.h ParameterSet.h ParmEnum.h ParmHolder.h
 ParmEnum.o : ParmEnum.cpp ParmEnum.h
diff --git a/src/Parm/parmfiles b/src/Parm/parmfiles
index 157123f670..4a8b0492c7 100644
--- a/src/Parm/parmfiles
+++ b/src/Parm/parmfiles
@@ -5,7 +5,6 @@ PARM_SOURCES= \
   GB_Params.cpp \
   GetParams.cpp \
   LJ1264_Params.cpp \
-  MainParmSet.cpp \
   Merge.cpp \
   ParameterSet.cpp \
   ParmEnum.cpp

From 0035a0fd2a2fd35905b783961897c05b70e1d21c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 20 Jan 2026 15:21:57 -0500
Subject: [PATCH 1239/1492] Place some output topology code closer to where the
 output COORDS set is allocated. Start creating a stripped down version of the
 fill atoms with tempaltes and structure prep code.

---
 src/Exec_Build.cpp | 176 +++++++++++++++++++++++++++++++++++++++++----
 src/Exec_Build.h   |   2 +
 2 files changed, 164 insertions(+), 14 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 53a4aabfc8..7ae3adeb5b 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -982,6 +982,19 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
   }
   DataSet_Coords& crdout = static_cast<DataSet_Coords&>( *((DataSet_Coords*)outCrdPtr_) );
   mprintf("\tOutput COORDS set: %s\n", crdout.legend());
+  Topology& topOut = static_cast<Topology&>( *(crdout.TopPtr()) );
+  topOut.SetDebug( debug_ );
+  if (outset.empty()) {
+    // In-place output COORDS. Copy over existing topology metadata
+    topOut.CopyTopMetadata( topIn );
+  }
+  if (!title.empty())
+    topOut.SetParmName( title, FileName() );
+  else if (topOut.ParmName().empty()) {
+    // TODO better default
+    title.assign( topIn.c_str() );
+    topOut.SetParmName( title, FileName() );
+  }
 
   // GB radii set
   Cpptraj::Parm::GB_Params gbradii;
@@ -1128,20 +1141,6 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
   // Fill in atoms with templates
   mprintf("    -----===== Match residues to templates, fill missing atoms =====-----\n");
   t_fill_.Start();
-  //Topology topOut;
-  Topology& topOut = static_cast<Topology&>( *(crdout.TopPtr()) );
-  topOut.SetDebug( debug_ );
-  if (outset.empty()) {
-    // In-place output COORDS. Copy over existing topology metadata
-    topOut.CopyTopMetadata( topIn );
-  }
-  if (!title.empty())
-    topOut.SetParmName( title, FileName() );
-  else if (topOut.ParmName().empty()) {
-    // TODO better default
-    title.assign( topIn.c_str() );
-    topOut.SetParmName( title, FileName() );
-  }
   Frame frameOut;
   if (FillAtomsWithTemplates(topOut, frameOut, topIn, frameIn, creator, SugarBonds)) {
     mprinterr("Error: Could not fill in atoms using templates.\n");
@@ -1411,6 +1410,155 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
   return ret;
 }
 
+/** Prepare the structure, fill missing atoms from templates */ // NOTE: topIn/frameIn cant be const, SugarBuilder reorders during fxn group detect 
+int Exec_Build::StructurePrepAndFillTemplates(ArgList& argIn, Topology& topIn, Frame& frameIn,
+                                              Topology& topOut,
+                                              std::string const& solventResName,
+                                              Cpptraj::Structure::Creator const& creator)
+{
+  mprintf("    -----===== Structure Prep ===== -----\n");
+  // Do histidine detection before H atoms are removed
+  t_hisDetect_.Start();
+  if (!argIn.hasKey("nohisdetect")) {
+    Cpptraj::Structure::HisProt hisProt;
+    if (hisProt.InitHisProt( argIn, debug_ )) {
+      mprinterr("Error: Could not initialize histidine detection.\n");
+      return 1;
+    }
+    hisProt.HisProtInfo();
+    if (hisProt.DetermineHisProt( topIn )) {
+      mprinterr("Error: HIS protonation detection failed.\n");
+      return 1;
+    }
+  }
+  t_hisDetect_.Stop();
+
+  // Clean up structure
+  t_clean_.Start();
+  Cpptraj::Structure::PdbCleaner pdbCleaner;
+  pdbCleaner.SetDebug( debug_ );
+  if (pdbCleaner.InitPdbCleaner( argIn, solventResName, std::vector<int>() )) {
+    mprinterr("Error: Could not init PDB cleaner.\n");
+    return 1;
+  }
+  if (pdbCleaner.SetupPdbCleaner( topIn )) {
+    mprinterr("Error: Could not set up PDB cleaner.\n");
+    return 1;
+  }
+  pdbCleaner.PdbCleanerInfo();
+  if (pdbCleaner.ModifyCoords(topIn, frameIn)) {
+    mprinterr("Error: Could not clean PDB.\n");
+    return 1;
+  }
+  t_clean_.Stop();
+
+  // All residues start unknown
+  Cpptraj::Structure::ResStatArray resStat( topIn.Nres() );
+  std::vector<BondType> DisulfideBonds;
+  std::vector<BondType> SugarBonds;
+
+  // Disulfide search
+  t_disulfide_.Start();
+  if (!argIn.hasKey("nodisulfides")) {
+    Cpptraj::Structure::Disulfide disulfide;
+    if (disulfide.InitDisulfide( argIn, Cpptraj::Structure::Disulfide::ADD_BONDS, debug_ )) {
+      mprinterr("Error: Could not init disulfide search.\n");
+      return 1;
+    }
+    if (disulfide.SearchForDisulfides( resStat, topIn, frameIn, DisulfideBonds ))
+    {
+      mprinterr("Error: Disulfide search failed.\n");
+      return 1;
+    }
+  } else {
+    mprintf("\tNot searching for disulfides.\n");
+  }
+  t_disulfide_.Stop();
+
+  // Handle sugars.
+  t_sugar_.Start();
+  // TODO should be on a residue by residue basis in FillAtomsWithTemplates
+  bool prepare_sugars = !argIn.hasKey("nosugars");
+  if (!prepare_sugars)
+    mprintf("\tNot attempting to prepare sugars.\n");
+  else
+    mprintf("\tWill attempt to prepare sugars.\n");
+  Cpptraj::Structure::SugarBuilder sugarBuilder(debug_);
+  if (prepare_sugars) {
+    // Init options
+    if (sugarBuilder.InitOptions( argIn.hasKey("hasglycam"),
+                                  argIn.getKeyDouble("rescut", 8.0),
+                                  argIn.getKeyDouble("bondoffset", 0.2),
+                                  argIn.GetStringKey("sugarmask"),
+                                  argIn.GetStringKey("determinesugarsby", "geometry"),
+                                  argIn.GetStringKey("resmapfile") ))
+    {
+      mprinterr("Error: Sugar options init failed.\n");
+      return 1;
+    }
+    bool splitres = !argIn.hasKey("nosplitres");
+    if (splitres)
+      mprintf("\tWill split off recognized sugar functional groups into separate residues.\n");
+    else
+      mprintf("\tNot splitting recognized sugar functional groups into separate residues.\n");
+    bool c1bondsearch = !argIn.hasKey("noc1search");
+    if (c1bondsearch)
+      mprintf("\tWill search for missing bonds to sugar anomeric atoms.\n");
+    else
+      mprintf("\tNot searching for missing bonds to sugar anomeric atoms.\n");
+    // May need to modify sugar structure/topology, either by splitting
+    // C1 hydroxyls of terminal sugars into ROH residues, and/or by
+    // adding missing bonds to C1 atoms.
+    // This is done before any identification takes place since we want
+    // to identify based on the most up-to-date topology.
+    if (sugarBuilder.FixSugarsStructure(topIn, frameIn,
+                                        c1bondsearch, splitres, solventResName,
+                                        SugarBonds))
+    {
+      mprinterr("Error: Sugar structure modification failed.\n");
+      return 1;
+    }
+    if (sugarBuilder.PrepareSugars(true, resStat, topIn, frameIn, SugarBonds))
+    {
+      mprinterr("Error: Sugar preparation failed.\n");
+      return 1;
+    }
+  }
+  t_sugar_.Stop();
+
+  // Fill in atoms with templates
+  mprintf("    -----===== Match residues to templates, fill missing atoms =====-----\n");
+  t_fill_.Start();
+  Frame frameOut;
+  if (FillAtomsWithTemplates(topOut, frameOut, topIn, frameIn, creator, SugarBonds)) {
+    mprinterr("Error: Could not fill in atoms using templates.\n");
+    return 1;
+  }
+  t_fill_.Stop();
+
+  // Add the disulfide bonds
+  int addBondsErr = transfer_bonds( topOut, topIn, DisulfideBonds );
+  if (addBondsErr != 0) {
+    mprinterr("Error: Adding disulfide bonds failed.\n");
+    return 1;
+  }
+
+  // Perform any modifications necessary for the sugar functional groups
+  bool top_is_modified = false;
+  if (sugarBuilder.ModifyFoundFxnGroups(topOut, top_is_modified)) {
+    mprinterr("Error: Could not make necessary modifications to detected sugar functional groups.\n");
+    return 1;
+  }
+
+  // Create empty arrays for the TREE, JOIN, and IROTAT arrays
+  topOut.AllocTreeChainClassification( );
+  topOut.AllocJoinArray();
+  topOut.AllocRotateArray();
+    // Finalize topology - determine molecules, dont renumber residues
+  topOut.CommonSetup(true, false);
+  return 0;
+}
+
 /** Standalone execute. For DataIO_LeapRC. */
 int Exec_Build::CleanAndFillStructure(DataSet* inCrdPtr, int tgtframe, std::string const& outset, std::string const& title,
                                       DataSetList& DSL, int debugIn, Cpptraj::Structure::Creator const& creator)
diff --git a/src/Exec_Build.h b/src/Exec_Build.h
index 91bb75beb8..d685c84f25 100644
--- a/src/Exec_Build.h
+++ b/src/Exec_Build.h
@@ -47,6 +47,8 @@ class Exec_Build : public Exec {
 
     RetType BuildStructure(DataSet*, std::string const&, DataSetList&, int, ArgList&, Cpptraj::Parm::GB_RadiiType);
 
+    int StructurePrepAndFillTemplates(ArgList&, Topology&, Frame&, Topology&, std::string const&, Cpptraj::Structure::Creator const&); // NOTE not const bc of timers
+
     int debug_;
     int check_box_natom_;  ///< Systems larger than this will have box added so PL check can be used
     bool check_structure_; ///< If true check the resulting structure

From 2873a545b52ce2c0921fe0a195bef23e50d96dd6 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 20 Jan 2026 15:54:06 -0500
Subject: [PATCH 1240/1492] Make use of new StructurePrepAndFillTemplates
 routine

---
 src/Exec_Build.cpp | 14 +++++++++++---
 src/Exec_Build.h   |  2 +-
 2 files changed, 12 insertions(+), 4 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 7ae3adeb5b..6023df50cf 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -1028,6 +1028,13 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
   // FIXME hide behind ifdef?
   creator.TimingInfo(t_get_templates_.Total(), 2);
 
+  Frame frameOut;
+  if (StructurePrepAndFillTemplates(argIn, topIn, frameIn,
+                                    topOut, frameOut,
+                                    solventResName,
+                                    creator))
+    return CpptrajState::ERR;
+/*
   mprintf("    -----===== Structure Prep ===== -----\n");
   // Do histidine detection before H atoms are removed
   t_hisDetect_.Start();
@@ -1168,7 +1175,7 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
   topOut.AllocRotateArray();
     // Finalize topology - determine molecules, dont renumber residues
   topOut.CommonSetup(true, false);
-
+*/
   // =============================================
 
   // Solvate/add ions
@@ -1412,7 +1419,7 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
 
 /** Prepare the structure, fill missing atoms from templates */ // NOTE: topIn/frameIn cant be const, SugarBuilder reorders during fxn group detect 
 int Exec_Build::StructurePrepAndFillTemplates(ArgList& argIn, Topology& topIn, Frame& frameIn,
-                                              Topology& topOut,
+                                              Topology& topOut, Frame& frameOut,
                                               std::string const& solventResName,
                                               Cpptraj::Structure::Creator const& creator)
 {
@@ -1529,7 +1536,8 @@ int Exec_Build::StructurePrepAndFillTemplates(ArgList& argIn, Topology& topIn, F
   // Fill in atoms with templates
   mprintf("    -----===== Match residues to templates, fill missing atoms =====-----\n");
   t_fill_.Start();
-  Frame frameOut;
+  //Frame frameOut;
+  frameOut = Frame(); // TODO reserve?
   if (FillAtomsWithTemplates(topOut, frameOut, topIn, frameIn, creator, SugarBonds)) {
     mprinterr("Error: Could not fill in atoms using templates.\n");
     return 1;
diff --git a/src/Exec_Build.h b/src/Exec_Build.h
index d685c84f25..487bddeb26 100644
--- a/src/Exec_Build.h
+++ b/src/Exec_Build.h
@@ -47,7 +47,7 @@ class Exec_Build : public Exec {
 
     RetType BuildStructure(DataSet*, std::string const&, DataSetList&, int, ArgList&, Cpptraj::Parm::GB_RadiiType);
 
-    int StructurePrepAndFillTemplates(ArgList&, Topology&, Frame&, Topology&, std::string const&, Cpptraj::Structure::Creator const&); // NOTE not const bc of timers
+    int StructurePrepAndFillTemplates(ArgList&, Topology&, Frame&, Topology&, Frame&, std::string const&, Cpptraj::Structure::Creator const&); // NOTE not const bc of timers
 
     int debug_;
     int check_box_natom_;  ///< Systems larger than this will have box added so PL check can be used

From f6d1db82b8836c3a596267a6ab1ad57ea6327128 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 21 Jan 2026 11:16:51 -0500
Subject: [PATCH 1241/1492] Use inCrdPtr for setting topology title instead of
 topIn

---
 src/Exec_Build.cpp | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 6023df50cf..a67a2e3c4b 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -967,14 +967,19 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
     mprintf("\tInput atoms not found in templates will be ignored.\n");
 
   // Set up Output coords
+  std::string default_title( ((DataSet_Coords*)inCrdPtr)->Top().c_str() );
   if (!outset.empty()) {
     // Separate output COORDS set.
     outCrdPtr_ = DSL.AddSet( DataSet::COORDS, outset );
   } else {
     // In-place output COORDS
     MetaData inCrdMeta = inCrdPtr->Meta();
+    std::string originalParmName( ((DataSet_Coords*)inCrdPtr)->Top().ParmName() );
+    FileName    originalFileName( ((DataSet_Coords*)inCrdPtr)->Top().OriginalFilename() );
     DSL.RemoveSet( inCrdPtr );
     outCrdPtr_ = DSL.AddSet( DataSet::COORDS, inCrdMeta );
+    // Copy over existing topology name, file
+    ((DataSet_Coords*)outCrdPtr_)->TopPtr()->SetParmName( originalParmName, originalFileName );
   }
   if (outCrdPtr_ == 0) {
     mprinterr("Error: Could not allocate output COORDS set with name '%s'\n", outset.c_str());
@@ -984,16 +989,12 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
   mprintf("\tOutput COORDS set: %s\n", crdout.legend());
   Topology& topOut = static_cast<Topology&>( *(crdout.TopPtr()) );
   topOut.SetDebug( debug_ );
-  if (outset.empty()) {
-    // In-place output COORDS. Copy over existing topology metadata
-    topOut.CopyTopMetadata( topIn );
-  }
+
   if (!title.empty())
     topOut.SetParmName( title, FileName() );
   else if (topOut.ParmName().empty()) {
     // TODO better default
-    title.assign( topIn.c_str() );
-    topOut.SetParmName( title, FileName() );
+    topOut.SetParmName( default_title, topOut.OriginalFilename() );
   }
 
   // GB radii set

From d66869584322865f0c279f4243cbb501546fce67 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 21 Jan 2026 11:19:34 -0500
Subject: [PATCH 1242/1492] Add note

---
 src/Exec_Build.cpp | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index a67a2e3c4b..efd01aec1e 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -906,6 +906,7 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
   Frame frameIn = coords.AllocateFrame();
   coords.GetFrame(tgtframe, frameIn);
   // Get modifiable topology
+  // NOTE: Topology is copied here because it might be destroyed if doing in-place build.
   //Topology& topIn = *(coords.TopPtr());
   //Topology const& topIn = coords.Top();
   Topology topIn = coords.Top(); // FIXME do not work on the copy, work on the top itself

From 8bca0c70b8f3804f926ec90f24335ac2687140cd Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 21 Jan 2026 11:48:17 -0500
Subject: [PATCH 1243/1492] Create and use separate output coords setup routine

---
 src/Exec_Build.cpp | 48 ++++++++++++++++++++++++++++++++++++++++++++--
 src/Exec_Build.h   |  3 +++
 2 files changed, 49 insertions(+), 2 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index efd01aec1e..9072cea141 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -861,7 +861,43 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr,
   return BuildStructure(inCrdPtr, "", DSL, debugIn, argIn, gbRadIn);
 }
 
-/** Standalone execute. For DataIO_LeapRC. */
+/** Set up output COORDS (Topology) */
+int Exec_Build::setupOutputCoords(DataSet* inCrdPtr, std::string const& outset, std::string const& title, DataSetList& DSL)
+{
+  // Set up Output coords
+  std::string default_title( ((DataSet_Coords*)inCrdPtr)->Top().c_str() );
+  if (!outset.empty()) {
+    // Separate output COORDS set.
+    outCrdPtr_ = DSL.AddSet( DataSet::COORDS, outset );
+  } else {
+    // In-place output COORDS
+    MetaData inCrdMeta = inCrdPtr->Meta();
+    std::string originalParmName( ((DataSet_Coords*)inCrdPtr)->Top().ParmName() );
+    FileName    originalFileName( ((DataSet_Coords*)inCrdPtr)->Top().OriginalFilename() );
+    DSL.RemoveSet( inCrdPtr );
+    outCrdPtr_ = DSL.AddSet( DataSet::COORDS, inCrdMeta );
+    // Copy over existing topology name, file
+    ((DataSet_Coords*)outCrdPtr_)->TopPtr()->SetParmName( originalParmName, originalFileName );
+  }
+  if (outCrdPtr_ == 0) {
+    mprinterr("Error: Could not allocate output COORDS set with name '%s'\n", outset.c_str());
+    return 1;
+  }
+  DataSet_Coords& crdout = static_cast<DataSet_Coords&>( *((DataSet_Coords*)outCrdPtr_) );
+  mprintf("\tOutput COORDS set: %s\n", crdout.legend());
+  Topology& topOut = static_cast<Topology&>( *(crdout.TopPtr()) );
+  topOut.SetDebug( debug_ );
+
+  if (!title.empty())
+    topOut.SetParmName( title, FileName() );
+  else if (topOut.ParmName().empty()) {
+    // TODO better default
+    topOut.SetParmName( default_title, topOut.OriginalFilename() );
+  }
+  return 0;
+}
+
+/** Run the full build, parameterize, and check. */
 Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& outset,
                                          DataSetList& DSL, int debugIn, ArgList& argIn,
                                          Cpptraj::Parm::GB_RadiiType gbRadIn)
@@ -968,6 +1004,14 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
     mprintf("\tInput atoms not found in templates will be ignored.\n");
 
   // Set up Output coords
+  if (setupOutputCoords(inCrdPtr, outset, title, DSL)) {
+    mprinterr("Error: Could not set up OUTPUT coords for build.\n");
+    return CpptrajState::ERR;
+  }
+  DataSet_Coords& crdout = static_cast<DataSet_Coords&>( *((DataSet_Coords*)outCrdPtr_) );
+  Topology& topOut = static_cast<Topology&>( *(crdout.TopPtr()) );
+
+/*
   std::string default_title( ((DataSet_Coords*)inCrdPtr)->Top().c_str() );
   if (!outset.empty()) {
     // Separate output COORDS set.
@@ -996,7 +1040,7 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
   else if (topOut.ParmName().empty()) {
     // TODO better default
     topOut.SetParmName( default_title, topOut.OriginalFilename() );
-  }
+  }*/
 
   // GB radii set
   Cpptraj::Parm::GB_Params gbradii;
diff --git a/src/Exec_Build.h b/src/Exec_Build.h
index 487bddeb26..f7768347c0 100644
--- a/src/Exec_Build.h
+++ b/src/Exec_Build.h
@@ -45,6 +45,9 @@ class Exec_Build : public Exec {
     /// Transfer bonds from old topology to new topology
     int transfer_bonds(Topology&, Topology const&, std::vector<BondType> const&) const;
 
+    /// Set up output COORDS (outCrdPtr_) and Topology
+    int setupOutputCoords(DataSet*, std::string const&, std::string const&, DataSetList&);
+
     RetType BuildStructure(DataSet*, std::string const&, DataSetList&, int, ArgList&, Cpptraj::Parm::GB_RadiiType);
 
     int StructurePrepAndFillTemplates(ArgList&, Topology&, Frame&, Topology&, Frame&, std::string const&, Cpptraj::Structure::Creator const&); // NOTE not const bc of timers

From fa2c15566a3a428ffe86578030ab241475807669 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 21 Jan 2026 12:49:28 -0500
Subject: [PATCH 1244/1492] Make DataIO_LeapRC behavior more like leap: only
 fill in atom templates during the load commands; assign parameters right
 before saving

---
 src/DataIO_LeapRC.cpp  |  58 ++++--
 src/Exec_Build.cpp     | 399 +++++++++--------------------------------
 src/Exec_Build.h       |  24 ++-
 src/Parm/GB_Params.cpp |  13 ++
 src/Parm/GB_Params.h   |   2 +
 src/cpptrajdepend      |   2 +-
 6 files changed, 160 insertions(+), 338 deletions(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 7c0769ed49..c352c053a8 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -14,6 +14,8 @@
 #include "Parm_Amber.h"
 #include "StringRoutines.h" // ToLower
 #include "Trajout_Single.h"
+#include "Parm/AssignParams.h"
+#include "Structure/Creator.h"
 #include <cstdlib> //getenv
 #include <cstring> // strncmp
 
@@ -583,6 +585,20 @@ int DataIO_LeapRC::LoadMol2(ArgList const& argIn, DataSetList& dsl) const {
   }
   mprintf("\tLoaded file '%s' into '%s'\n",
           args[2].c_str(), args[0].c_str());
+
+  // Assume we want the remaining args to be passed to the builder.
+  args.MarkArg(0);
+  args.MarkArg(1);
+  args.MarkArg(2);
+  ArgList tmparg = args.RemainingArgs();
+
+  Exec_Build build;
+  Exec::RetType ret = build.BuildStructure( coordsIn.added_back(), dsl, debug_, "", "default_name" );
+  if (ret == CpptrajState::ERR) {
+    mprinterr("Error: Build of '%s' failed.\n", args[2].c_str());
+    return 1;
+  }
+
   return 0;
 }
 
@@ -619,14 +635,13 @@ int DataIO_LeapRC::LoadPDB(ArgList const& argIn, DataSetList& dsl) const {
   args.MarkArg(2);
   ArgList tmparg = args.RemainingArgs();
 
-/*  tmparg.AddArg("name " + args[0]);
-  DataSet_LeapOpts& OPTS = static_cast<DataSet_LeapOpts&>( *leapopts_ );
   Exec_Build build;
-  Exec::RetType ret = build.BuildStructure( coordsIn.added_back(), dsl, debug_, tmparg, OPTS.PbRadii() );
+  Exec::RetType ret = build.BuildStructure( coordsIn.added_back(), dsl, debug_, "", "default_name" );
   if (ret == CpptrajState::ERR) {
     mprinterr("Error: Build of '%s' failed.\n", args[2].c_str());
     return 1;
-  }*/
+  }
+
   return 0;
 }
 
@@ -723,18 +738,39 @@ const
     mprinterr("Error: '%s' is empty.\n", ds->legend());
     return 1;
   }
+  DataSet_Coords& crd = static_cast<DataSet_Coords&>( *ds ); // FIXME this really should be const
 
-  // Build
+  // Give the Topology parameters 
   ArgList buildarg = line.RemainingArgs();
+  // Default GB radii
   DataSet_LeapOpts& OPTS = static_cast<DataSet_LeapOpts&>( *leapopts_ );
-  Exec_Build build;
-  Exec::RetType ret = build.BuildStructure( ds, dsl, debug_, buildarg, OPTS.PbRadii() );
-  if (ret == CpptrajState::ERR) {
-    mprinterr("Error: Build of '%s' failed.\n", unitName.c_str());
+  Cpptraj::Parm::GB_Params gbradii;
+  if (gbradii.Init_GB_Radii(OPTS.PbRadii())) return 1;
+  // Get parameters
+  Cpptraj::Structure::Creator creator;
+  if (creator.InitCreator(buildarg, dsl, debug_)) {
     return 1;
   }
-
-  DataSet_Coords& crd = static_cast<DataSet_Coords&>( *(build.OutCrdPtr()) ); // FIXME this really should be const
+  if (!creator.HasMainParmSet()) {
+    mprinterr("Error: No parameter sets.\n");
+    return 1;
+  }
+  // Assign parameters
+  Cpptraj::Parm::AssignParams AP;
+  AP.SetDebug( debug_ );
+  AP.SetVerbose( debug_ );
+  Topology& topOut = *(crd.TopPtr());
+  if ( AP.AssignParameters( topOut, *(creator.MainParmSetPtr()) ) ) {
+    mprinterr("Error: Could not assign parameters for '%s'.\n", topOut.c_str());
+    return 1;
+  }
+  // Assign GB parameters
+  gbradii.GB_Info();
+  if (gbradii.Assign_GB_Radii(topOut)) {
+    mprinterr("Error: Could not assign GB parameters for '%s'\n", topOut.c_str());
+    return 1;
+  }
+ 
   Parm_Amber parmOut;
   parmOut.SetDebug( debug_ );
   if (parmOut.WriteParm( topName, crd.Top() )) {
diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 9072cea141..a3c8131803 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -850,17 +850,93 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
   }
   std::string outset = argIn.GetStringKey("name");
 
-  return BuildStructure(inCrdPtr, outset, State.DSL(), State.Debug(), argIn, Cpptraj::Parm::UNKNOWN_GB);
+  return BuildAndParmStructure(inCrdPtr, outset, State.DSL(), State.Debug(), argIn, Cpptraj::Parm::UNKNOWN_GB);
 }
 
 /** Standalone execute. For DataIO_LeapRC. Operate on inCrdPtr */
-Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, 
-                                         DataSetList& DSL, int debugIn, ArgList& argIn,
-                                         Cpptraj::Parm::GB_RadiiType gbRadIn)
+Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, int debugIn,
+                                         std::string const& outset, std::string const& title)
+                                         
 {
-  return BuildStructure(inCrdPtr, "", DSL, debugIn, argIn, gbRadIn);
+  t_total_.Start();
+  if (inCrdPtr == 0) {
+    mprinterr("Internal Error: Exec_Build::BuildStructure(): Null input coordinates.\n");
+    return CpptrajState::ERR;
+  }
+  if (inCrdPtr->Group() != DataSet::COORDINATES) {
+    mprinterr("Error: Set '%s' is not coordinates, cannot use for building.\n", inCrdPtr->legend());
+    return CpptrajState::ERR;
+  }
+  if (outset.empty() && inCrdPtr->Size() > 1) {
+    mprinterr("Error: Set '%s' has more than 1 frame; must specify an output COORDS set in order to build.\n",
+              inCrdPtr->legend());
+    return CpptrajState::ERR;
+  }
+  debug_ = debugIn;
+
+  // TODO make it so this can be const (cant bc GetFrame)
+  DataSet_Coords& coords = static_cast<DataSet_Coords&>( *((DataSet_Coords*)inCrdPtr) );
+  // Get frame from input coords
+  int tgtframe = 0;
+  //mprintf("\tUsing frame %i from COORDS set %s\n", tgtframe+1, coords.legend());
+  if (tgtframe < 0 || tgtframe >= (int)coords.Size()) {
+    mprinterr("Error: Frame is out of range.\n");
+    return CpptrajState::ERR;
+  }
+  Frame frameIn = coords.AllocateFrame();
+  coords.GetFrame(tgtframe, frameIn);
+  // Get modifiable topology
+  // NOTE: Topology is copied here because it might be destroyed if doing in-place build.
+  Topology topIn = coords.Top(); // FIXME do not work on the copy, work on the top itself
+
+  // Set some defaults
+  ArgList argIn;
+  std::string solventResName = "HOH"; //argIn.GetStringKey("solventresname", "HOH");
+  keepMissingSourceAtoms_ = false; //argIn.hasKey("keepmissingatoms");
+  requireAllInputAtoms_ = false; //argIn.hasKey("requireallinputatoms");
+
+  // Set up Output coords
+  if (setupOutputCoords(inCrdPtr, outset, title, DSL)) {
+    mprinterr("Error: Could not set up OUTPUT coords for build.\n");
+    return CpptrajState::ERR;
+  }
+  DataSet_Coords& crdout = static_cast<DataSet_Coords&>( *((DataSet_Coords*)outCrdPtr_) );
+  Topology& topOut = static_cast<Topology&>( *(crdout.TopPtr()) );
+
+  // Get templates.
+  t_get_templates_.Start();
+  Cpptraj::Structure::Creator creator;
+  if (creator.InitCreator(argIn, DSL, debug_)) {
+    return CpptrajState::ERR;
+  }
+  if (!creator.HasTemplates()) {
+    mprintf("Warning: No residue templates loaded.\n");
+  }
+  t_get_templates_.Stop();
+
+  Frame frameOut;
+  if (StructurePrepAndFillTemplates(argIn, topIn, frameIn,
+                                    topOut, frameOut,
+                                    solventResName,
+                                    creator))
+    return CpptrajState::ERR;
+
+  // Update coords 
+  if (crdout.CoordsSetup( topOut, frameOut.CoordsInfo() )) { // FIXME better coordinate info
+    mprinterr("Error: Could not set up output COORDS data set.\n");
+    return CpptrajState::ERR;
+  }
+  crdout.SetCRD(0, frameOut);
+
+  t_total_.Stop();
+
+  mprintf("    -----===== Timing =====-----\n");
+  PrintTiming();
+
+  return CpptrajState::OK;
 }
 
+// -----------------------------------------------------------------------------
 /** Set up output COORDS (Topology) */
 int Exec_Build::setupOutputCoords(DataSet* inCrdPtr, std::string const& outset, std::string const& title, DataSetList& DSL)
 {
@@ -898,9 +974,9 @@ int Exec_Build::setupOutputCoords(DataSet* inCrdPtr, std::string const& outset,
 }
 
 /** Run the full build, parameterize, and check. */
-Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& outset,
-                                         DataSetList& DSL, int debugIn, ArgList& argIn,
-                                         Cpptraj::Parm::GB_RadiiType gbRadIn)
+Exec::RetType Exec_Build::BuildAndParmStructure(DataSet* inCrdPtr, std::string const& outset,
+                                                DataSetList& DSL, int debugIn, ArgList& argIn,
+                                                Cpptraj::Parm::GB_RadiiType gbRadIn)
 {
   t_total_.Start();
   if (inCrdPtr == 0) {
@@ -1059,7 +1135,7 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, std::string const& o
   mprintf("    -----===== Getting templates and parameters ===== -----\n");
   // Get templates and parameter sets.
   t_get_templates_.Start();
-  Cpptraj::Structure::Creator creator( debug_ );
+  Cpptraj::Structure::Creator creator;
   if (creator.InitCreator(argIn, DSL, debug_)) {
     return CpptrajState::ERR;
   }
@@ -1613,310 +1689,7 @@ int Exec_Build::StructurePrepAndFillTemplates(ArgList& argIn, Topology& topIn, F
   return 0;
 }
 
-/** Standalone execute. For DataIO_LeapRC. */
-int Exec_Build::CleanAndFillStructure(DataSet* inCrdPtr, int tgtframe, std::string const& outset, std::string const& title,
-                                      DataSetList& DSL, int debugIn, Cpptraj::Structure::Creator const& creator)
-{
-  t_total_.Start();
-  if (inCrdPtr == 0) {
-    mprinterr("Internal Error: Exec_Build::BuildStructure(): Null input coordinates.\n");
-    return 1;
-  }
-  if (inCrdPtr->Group() != DataSet::COORDINATES) {
-    mprinterr("Error: Set '%s' is not coordinates, cannot use for building.\n", inCrdPtr->legend());
-    return 1;
-  }
-  debug_ = debugIn;
-//  int verbose = argIn.getKeyInt("verbose", 0);
-//  std::string title = argIn.GetStringKey("title");
-//  std::string outputTopologyName = argIn.GetStringKey("parmout");
-//  std::string outputCoordsName = argIn.GetStringKey("crdout");
-//  if (!outputTopologyName.empty())
-//    mprintf("\tWill write topology to %s\n", outputTopologyName.c_str());
-//  if (!outputCoordsName.empty())
-//    mprintf("\tWill write coords to %s\n", outputCoordsName.c_str());
-  // TODO make it so this can be const (cant bc GetFrame)
-  DataSet_Coords& coords = static_cast<DataSet_Coords&>( *((DataSet_Coords*)inCrdPtr) );
-  // Get frame from input coords
-  //int tgtframe = argIn.getKeyInt("frame", 1) - 1;
-  mprintf("\tUsing frame %i from COORDS set %s\n", tgtframe+1, coords.legend());
-  if (tgtframe < 0 || tgtframe >= (int)coords.Size()) {
-    mprinterr("Error: Frame is out of range.\n");
-    return 1;
-  }
-  Frame frameIn = coords.AllocateFrame();
-  coords.GetFrame(tgtframe, frameIn);
-  // Get modifiable topology
-  //Topology& topIn = *(coords.TopPtr());
-  //Topology const& topIn = coords.Top();
-  Topology topIn = coords.Top(); // FIXME do not work on the copy, work on the top itself
-
-  //std::string solventResName = argIn.GetStringKey("solventresname", "HOH");
-  //mprintf("\tSolvent residue name: %s\n", solventResName.c_str());
-
-//  enum SolvateModeType { NO_SOLVATE = 0, SOLVATEBOX, SETBOX };
-//  SolvateModeType add_solvent = NO_SOLVATE;
-//  Cpptraj::Structure::Solvate solvator;
-//  if (argIn.hasKey("solvatebox")) {
-//    add_solvent = SOLVATEBOX;
-//    if (solvator.InitSolvate(argIn, false, debug_)) {
-//      mprinterr("Error: Init solvatebox failed.\n");
-//      return CpptrajState::ERR;
-//    }
-//    solvator.PrintSolvateInfo();
-//  } else if (argIn.hasKey("solvateoct")) {
-//    add_solvent = SOLVATEBOX;
-//    if (solvator.InitSolvate(argIn, true, debug_)) {
-//      mprinterr("Error: Init solvateoct failed.\n");
-//      return CpptrajState::ERR;
-//    }
-//    solvator.PrintSolvateInfo();
-//  } else if (argIn.hasKey("setbox")) {
-//    add_solvent = SETBOX;
-//    if (solvator.InitSetbox(argIn, debug_)) {
-//      mprinterr("Error: Init setbox failed.\n");
-//      return CpptrajState::ERR;
-//    }
-//  }
-
-  keepMissingSourceAtoms_ = false; // FIXME
-//  keepMissingSourceAtoms_ = argIn.hasKey("keepmissingatoms");
-  if (keepMissingSourceAtoms_)
-    mprintf("\tInput atoms missing from templates will be kept.\n");
-  else
-    mprintf("\tInput atoms missing from templates will be ignored.\n");
-  requireAllInputAtoms_ = false; // FIXME
-//  requireAllInputAtoms_ = argIn.hasKey("requireallinputatoms");
-  if (requireAllInputAtoms_)
-    mprintf("\tRequire all input atoms to be found in templates.\n");
-  else
-    mprintf("\tInput atoms not found in templates will be ignored.\n");
-
-  // Do histidine detection before H atoms are removed
-  ArgList argIn; // FIXME
-  t_hisDetect_.Start();
-//  if (!argIn.hasKey("nohisdetect")) {
-    Cpptraj::Structure::HisProt hisProt;
-    if (hisProt.InitHisProt( argIn, debug_ )) {
-      mprinterr("Error: Could not initialize histidine detection.\n");
-      return 1;
-    }
-    hisProt.HisProtInfo();
-    if (hisProt.DetermineHisProt( topIn )) {
-      mprinterr("Error: HIS protonation detection failed.\n");
-      return 1;
-    }
-//  }
-  t_hisDetect_.Stop();
-
-  // Clean up structure
-  t_clean_.Start();
-  Cpptraj::Structure::PdbCleaner pdbCleaner;
-  pdbCleaner.SetDebug( debug_ );
-  std::string solventResName = "HOH"; //FIXME
-  if (pdbCleaner.InitPdbCleaner( argIn, solventResName, std::vector<int>() )) {
-    mprinterr("Error: Could not init PDB cleaner.\n");
-    return 1;
-  }
-  if (pdbCleaner.SetupPdbCleaner( topIn )) {
-    mprinterr("Error: Could not set up PDB cleaner.\n");
-    return 1;
-  }
-  pdbCleaner.PdbCleanerInfo();
-  if (pdbCleaner.ModifyCoords(topIn, frameIn)) {
-    mprinterr("Error: Could not clean PDB.\n");
-    return 1;
-  }
-  t_clean_.Stop();
-
-  // Set up Output coords
-  if (!outset.empty()) {
-    // Separate output COORDS set.
-    outCrdPtr_ = DSL.AddSet( DataSet::COORDS, outset );
-  } else {
-    // In-place output COORDS
-    DSL.RemoveSet( inCrdPtr );
-    outCrdPtr_ = DSL.AddSet( DataSet::COORDS, inCrdPtr->Meta() );
-  }
-  if (outCrdPtr_ == 0) {
-    mprinterr("Error: Could not allocate output COORDS set with name '%s'\n", outset.c_str());
-    return 1;
-  }
-  DataSet_Coords& crdout = static_cast<DataSet_Coords&>( *((DataSet_Coords*)outCrdPtr_) );
-  mprintf("\tOutput COORDS set: %s\n", crdout.legend());
-/*
-  // GB radii set
-  Cpptraj::Parm::GB_RadiiType gbradii;
-  if (gbRadIn == Cpptraj::Parm::UNKNOWN_GB) {
-    // No radii set specified. Check for keyword.
-    gbradii = Cpptraj::Parm::MBONDI; // Default
-    //std::string gbset = argIn.GetStringKey("gb");
-    //if (!gbset.empty()) {
-    //  gbradii = Cpptraj::Parm::GbTypeFromKey( gbset );
-    //  if (gbradii == Cpptraj::Parm::UNKNOWN_GB) {
-    //    mprinterr("Error: Unknown GB radii set: %s\n", gbset.c_str());
-    //    return CpptrajState::ERR;
-    //  }
-    //}
-  } else {
-    // Use passed-in GB radii set
-    gbradii = gbRadIn;
-  }
-  mprintf("\tGB radii set: %s\n", Cpptraj::Parm::GbTypeStr(gbradii).c_str());
-*/
-  // Get templates and parameter sets.
-/*  t_get_templates_.Start();
-  Cpptraj::Structure::Creator creator( debug_ );
-  if (creator.InitCreator(argIn, DSL, debug_)) {
-    return 1;
-  }
-  if (!creator.HasTemplates()) {
-    mprintf("Warning: No residue templates loaded.\n");
-  }
-  if (!creator.HasMainParmSet()) {
-    mprinterr("Error: No parameter sets.\n");
-    return 1;
-  }
-  t_get_templates_.Stop();
-  // FIXME hide behind ifdef?
-  creator.TimingInfo(t_get_templates_.Total(), 2);*/
-
-  // All residues start unknown
-  Cpptraj::Structure::ResStatArray resStat( topIn.Nres() );
-  std::vector<BondType> DisulfideBonds;
-  std::vector<BondType> SugarBonds;
-
-  // Disulfide search
-  t_disulfide_.Start();
-  //if (!argIn.hasKey("nodisulfides")) {
-    Cpptraj::Structure::Disulfide disulfide;
-    if (disulfide.InitDisulfide( argIn, Cpptraj::Structure::Disulfide::ADD_BONDS, debug_ )) {
-      mprinterr("Error: Could not init disulfide search.\n");
-      return 1;
-    }
-    if (disulfide.SearchForDisulfides( resStat, topIn, frameIn, DisulfideBonds ))
-    {
-      mprinterr("Error: Disulfide search failed.\n");
-      return 1;
-    }
-  //} else {
-  //  mprintf("\tNot searching for disulfides.\n");
-  //}
-  t_disulfide_.Stop();
-
-  // Handle sugars.
-  t_sugar_.Start();
-  // TODO should be on a residue by residue basis in FillAtomsWithTemplates
-  //bool prepare_sugars = !argIn.hasKey("nosugars");
-  bool prepare_sugars = true; //FIXME
-  if (!prepare_sugars)
-    mprintf("\tNot attempting to prepare sugars.\n");
-  else
-    mprintf("\tWill attempt to prepare sugars.\n");
-  Cpptraj::Structure::SugarBuilder sugarBuilder(debug_);
-  if (prepare_sugars) {
-    // Init options
-    // FIXME
-    bool hasglycam = false;
-    double rescut = 8.0;
-    double bondoffset = 0.2;
-    std::string sugarmask("");
-    std::string determinesugarsby("geometry");
-    std::string resmapfile("");
-    if (sugarBuilder.InitOptions( hasglycam,
-                                  rescut,
-                                  bondoffset,
-                                  sugarmask,
-                                  determinesugarsby,
-                                  resmapfile ))
-    {
-      mprinterr("Error: Sugar options init failed.\n");
-      return 1;
-    }
-    bool splitres = true; // FIXME
-    //bool splitres = !argIn.hasKey("nosplitres");
-    if (splitres)
-      mprintf("\tWill split off recognized sugar functional groups into separate residues.\n");
-    else
-      mprintf("\tNot splitting recognized sugar functional groups into separate residues.\n");
-    //bool c1bondsearch = !argIn.hasKey("noc1search");
-    bool c1bondsearch = true; // FIXME
-    if (c1bondsearch)
-      mprintf("\tWill search for missing bonds to sugar anomeric atoms.\n");
-    else
-      mprintf("\tNot searching for missing bonds to sugar anomeric atoms.\n");
-    // May need to modify sugar structure/topology, either by splitting
-    // C1 hydroxyls of terminal sugars into ROH residues, and/or by
-    // adding missing bonds to C1 atoms.
-    // This is done before any identification takes place since we want
-    // to identify based on the most up-to-date topology.
-    if (sugarBuilder.FixSugarsStructure(topIn, frameIn,
-                                        c1bondsearch, splitres, solventResName,
-                                        SugarBonds))
-    {
-      mprinterr("Error: Sugar structure modification failed.\n");
-      return 1;
-    }
-    if (sugarBuilder.PrepareSugars(true, resStat, topIn, frameIn, SugarBonds))
-    {
-      mprinterr("Error: Sugar preparation failed.\n");
-      return 1;
-    }
-  }
-  t_sugar_.Stop();
-
-  // Fill in atoms with templates
-  t_fill_.Start();
-  //Topology topOut;
-  Topology& topOut = static_cast<Topology&>( *(crdout.TopPtr()) );
-  topOut.SetDebug( debug_ );
-  if (outset.empty()) {
-    // In-place output COORDS. Copy over existing topology metadata
-    topOut.CopyTopMetadata( topIn );
-  }
-  if (!title.empty())
-    topOut.SetParmName( title, FileName() );
-  else if (topOut.ParmName().empty()) {
-    // TODO better default
-    topOut.SetParmName( std::string(topIn.c_str()), FileName() );
-  }
-  Frame frameOut;
-  if (FillAtomsWithTemplates(topOut, frameOut, topIn, frameIn, creator, SugarBonds)) {
-    mprinterr("Error: Could not fill in atoms using templates.\n");
-    return 1;
-  }
-  t_fill_.Stop();
-
-  // Add the disulfide/sugar bonds
-  int addBondsErr = transfer_bonds( topOut, topIn, DisulfideBonds );
-  //addBondsErr += transfer_bonds( topOut, topIn, SugarBonds );
-  if (addBondsErr != 0) {
-    mprinterr("Error: Adding disulfide/sugar bonds failed.\n");
-    return 1;
-  }
-
-  // Create empty arrays for the TREE, JOIN, and IROTAT arrays
-  topOut.AllocTreeChainClassification( );
-  topOut.AllocJoinArray();
-  topOut.AllocRotateArray();
-    // Finalize topology - determine molecules, dont renumber residues
-  topOut.CommonSetup(true, false);
-  topOut.Summary();
-  t_assign_.Stop();
-
-  // Update coords 
-  if (crdout.CoordsSetup( topOut, frameOut.CoordsInfo() )) { // FIXME better coordinate info
-    mprinterr("Error: Could not set up output COORDS.\n");
-    return CpptrajState::ERR;
-  }
-  crdout.SetCRD(0, frameOut);
-  t_total_.Stop();
-
-  PrintTiming();
-
-  return 0;
-}
-
+/** Write timing info to stdout */
 void Exec_Build::PrintTiming() const {
   t_total_.WriteTiming(1, "Build timing:");
   t_hisDetect_.WriteTiming    (2, "Histidine detection :", t_total_.Total());
diff --git a/src/Exec_Build.h b/src/Exec_Build.h
index f7768347c0..3e526f42e0 100644
--- a/src/Exec_Build.h
+++ b/src/Exec_Build.h
@@ -16,13 +16,11 @@ class Exec_Build : public Exec {
     DispatchObject* Alloc() const { return (DispatchObject*)new Exec_Build(); }
     RetType Execute(CpptrajState&, ArgList&);
 
-    /// Stand-alone execution
-    RetType BuildStructure(DataSet*, DataSetList&, int, ArgList&, Cpptraj::Parm::GB_RadiiType);
+    /// Stand-alone execution - only build, do not parameterize/solvate
+    RetType BuildStructure(DataSet*, DataSetList&, int, std::string const&, std::string const&);
     /// \return Output COORDS set
     DataSet* OutCrdPtr() const { return outCrdPtr_; }
-    /// Clean input coords, fill in missing atoms
-    int CleanAndFillStructure(DataSet*, int, std::string const&, std::string const&,
-                              DataSetList&, int, Cpptraj::Structure::Creator const&);
+    /// Print Timing data
     void PrintTiming() const;
   private:
     typedef std::vector<int> Iarray;
@@ -47,17 +45,17 @@ class Exec_Build : public Exec {
 
     /// Set up output COORDS (outCrdPtr_) and Topology
     int setupOutputCoords(DataSet*, std::string const&, std::string const&, DataSetList&);
-
-    RetType BuildStructure(DataSet*, std::string const&, DataSetList&, int, ArgList&, Cpptraj::Parm::GB_RadiiType);
-
+    /// Build, parameterize, solvate, and check
+    RetType BuildAndParmStructure(DataSet*, std::string const&, DataSetList&, int, ArgList&, Cpptraj::Parm::GB_RadiiType);
+    /// Do input structure clean/prep and fill in missing atoms from templates
     int StructurePrepAndFillTemplates(ArgList&, Topology&, Frame&, Topology&, Frame&, std::string const&, Cpptraj::Structure::Creator const&); // NOTE not const bc of timers
 
     int debug_;
-    int check_box_natom_;  ///< Systems larger than this will have box added so PL check can be used
-    bool check_structure_; ///< If true check the resulting structure
-    bool keepMissingSourceAtoms_;
-    bool requireAllInputAtoms_;
-    DataSet* outCrdPtr_; ///< Hold built COORDS
+    int check_box_natom_;         ///< Systems larger than this will have box added so PL check can be used
+    bool check_structure_;        ///< If true check the resulting structure
+    bool keepMissingSourceAtoms_; ///< If true, attempt to keep input atoms that are missing from templates
+    bool requireAllInputAtoms_;   ///< If true, require all input atoms to be found in templates.
+    DataSet* outCrdPtr_;          ///< Hold built (output) COORDS
 
     Timer t_total_;
     Timer t_hisDetect_;
diff --git a/src/Parm/GB_Params.cpp b/src/Parm/GB_Params.cpp
index f110d9f8f0..76eb0bbe9b 100644
--- a/src/Parm/GB_Params.cpp
+++ b/src/Parm/GB_Params.cpp
@@ -109,6 +109,19 @@ int Cpptraj::Parm::GB_Params::Init_GB_Radii(ArgList& argIn, Cpptraj::Parm::GB_Ra
   return 0;
 }
 
+/** Init radii set - no args */
+int Cpptraj::Parm::GB_Params::Init_GB_Radii(Cpptraj::Parm::GB_RadiiType gbRadIn)
+{
+  if (gbRadIn == Cpptraj::Parm::UNKNOWN_GB) {
+    // No radii set specified.
+    gbradii_ = Cpptraj::Parm::MBONDI; // Default
+  } else {
+    // Use passed-in GB radii set
+    gbradii_ = gbRadIn;
+  }
+  return 0;
+}
+
 /** Print current setup. */
 void Cpptraj::Parm::GB_Params::GB_Info() const {
   mprintf("\tGB radii set: %s\n", Cpptraj::Parm::GbTypeStr(gbradii_).c_str());
diff --git a/src/Parm/GB_Params.h b/src/Parm/GB_Params.h
index 36f955a928..3d63f42ed9 100644
--- a/src/Parm/GB_Params.h
+++ b/src/Parm/GB_Params.h
@@ -34,6 +34,8 @@ class GB_Params {
     static std::string HelpText();
     /// Initialize 
     int Init_GB_Radii(ArgList&, GB_RadiiType);
+    /// Initialize  no args
+    int Init_GB_Radii(GB_RadiiType);
     // Print current setup
     void GB_Info() const;
     /// Assign GB radii
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 070462c069..cc60b329ab 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -231,7 +231,7 @@ DataIO_Cpout.o : DataIO_Cpout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h B
 DataIO_Evecs.o : DataIO_Evecs.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Evecs.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Modes.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 DataIO_Gnuplot.o : DataIO_Gnuplot.cpp ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Gnuplot.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 DataIO_Grace.o : DataIO_Grace.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Grace.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_string.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-DataIO_LeapRC.o : DataIO_LeapRC.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_Coords.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_LeapOpts.h DataSet_NameMap.h DataSet_Parameters.h DataSet_PdbResMap.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h ParmIO.h Parm_Amber.h PdbResMapType.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_LeapRC.o : DataIO_LeapRC.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_Coords.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_LeapOpts.h DataSet_NameMap.h DataSet_Parameters.h DataSet_PdbResMap.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h ParmIO.h Parm_Amber.h PdbResMapType.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/Creator.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Mdout.o : DataIO_Mdout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Mdout.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 DataIO_NetCDF.o : DataIO_NetCDF.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cluster/Cframes.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_NetCDF.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_Mesh.h DataSet_Modes.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_Vector.h DataSet_Vector_Scalar.h DataSet_string.h DataSet_unsignedInt.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h Version.h
 DataIO_Numpy.o : DataIO_Numpy.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Numpy.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h libnpy/npy.hpp

From 058d1f72825ac389cf6affba820faba82bb4c255 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 21 Jan 2026 13:36:57 -0500
Subject: [PATCH 1245/1492] Allow the atom map in the sugar builder to be set
 up with a topology containing no bonds.

---
 src/AtomMap.cpp                | 8 +++++---
 src/AtomMap.h                  | 3 +++
 src/Structure/SugarBuilder.cpp | 1 +
 3 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/src/AtomMap.cpp b/src/AtomMap.cpp
index 92785acd58..a459e8d410 100644
--- a/src/AtomMap.cpp
+++ b/src/AtomMap.cpp
@@ -3,7 +3,7 @@
 #include "CpptrajStdio.h"
 
 // CONSTRUCTOR
-AtomMap::AtomMap() : debug_(0) {}
+AtomMap::AtomMap() : debug_(0), allowNoBonds_(false) {}
 
 /// Blank AtomMap for empty return of bracket operator
 MapAtom AtomMap::EMPTYMAPATOM = MapAtom();
@@ -294,8 +294,10 @@ int AtomMap::CheckBonds() {
     }
   }
   if (total_bonds == 0 && mapatoms_.size() > 1) {
-    mprinterr("Error: No bond information present, required by AtomMap.\n");
-    return 1;
+    if (!allowNoBonds_) {
+      mprinterr("Error: No bond information present, required by AtomMap.\n");
+      return 1;
+    }
   }
 
   // DEBUG
diff --git a/src/AtomMap.h b/src/AtomMap.h
index f39287d4c5..5543967ce1 100644
--- a/src/AtomMap.h
+++ b/src/AtomMap.h
@@ -13,6 +13,8 @@ class AtomMap {
     int Natom() const { return (int)mapatoms_.size(); }
     /// Set the debug level of the AtomMap.
     void SetDebug(int d) { debug_ = d; }
+    /// Set whether we are allowing no bonds during Setup or not.
+    void SetAllowNoBonds(bool b) { allowNoBonds_ = b; }
     /// Setup AtomMap with all atoms from input Topology.
     int Setup(Topology const&, Frame const&);
     /// Setup AtomMap with just atoms from specified Residue.
@@ -41,5 +43,6 @@ class AtomMap {
     typedef std::vector<MapAtom> Marray;
     Marray mapatoms_;
     int debug_;
+    bool allowNoBonds_; ///< If true, do not make having no bonds an error
 };
 #endif
diff --git a/src/Structure/SugarBuilder.cpp b/src/Structure/SugarBuilder.cpp
index 5c1a8d1ba5..3632806f0d 100644
--- a/src/Structure/SugarBuilder.cpp
+++ b/src/Structure/SugarBuilder.cpp
@@ -1821,6 +1821,7 @@ int SugarBuilder::FixSugarsStructure(Topology& topIn, Frame& frameIn,
   // Set up an AtomMap for this residue to help determine stereocenters.
   // This is required by the IdSugarRing() function.
   //myMap_.SetDebug(debug_); // DEBUG
+  myMap_.SetAllowNoBonds( true );
   if (myMap_.Setup(topIn, frameIn)) {
     mprinterr("Internal Error: FixSugarsStructure: Atom map setup failed.\n");
     return 1;

From 229aa2ecdb9c54429c082944ab028f3a348628f1 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 21 Jan 2026 14:04:27 -0500
Subject: [PATCH 1246/1492] When doing the build from a leaprc load command,
 turn off advanced prep features by default.

---
 src/DataIO_LeapRC.cpp |   4 +-
 src/Exec_Build.cpp    | 193 +++---------------------------------------
 src/Exec_Build.h      |   5 +-
 3 files changed, 20 insertions(+), 182 deletions(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index c352c053a8..5fa572a81a 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -593,7 +593,7 @@ int DataIO_LeapRC::LoadMol2(ArgList const& argIn, DataSetList& dsl) const {
   ArgList tmparg = args.RemainingArgs();
 
   Exec_Build build;
-  Exec::RetType ret = build.BuildStructure( coordsIn.added_back(), dsl, debug_, "", "default_name" );
+  Exec::RetType ret = build.BuildStructure( coordsIn.added_back(), dsl, debug_, "", "default_name", tmparg.hasKey("prepareforleap") );
   if (ret == CpptrajState::ERR) {
     mprinterr("Error: Build of '%s' failed.\n", args[2].c_str());
     return 1;
@@ -636,7 +636,7 @@ int DataIO_LeapRC::LoadPDB(ArgList const& argIn, DataSetList& dsl) const {
   ArgList tmparg = args.RemainingArgs();
 
   Exec_Build build;
-  Exec::RetType ret = build.BuildStructure( coordsIn.added_back(), dsl, debug_, "", "default_name" );
+  Exec::RetType ret = build.BuildStructure( coordsIn.added_back(), dsl, debug_, "", "default_name", tmparg.hasKey("prepareforleap") );
   if (ret == CpptrajState::ERR) {
     mprinterr("Error: Build of '%s' failed.\n", args[2].c_str());
     return 1;
diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index a3c8131803..a487537898 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -855,7 +855,8 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
 
 /** Standalone execute. For DataIO_LeapRC. Operate on inCrdPtr */
 Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, int debugIn,
-                                         std::string const& outset, std::string const& title)
+                                         std::string const& outset, std::string const& title,
+                                         bool enableExtraDetection)
                                          
 {
   t_total_.Start();
@@ -894,6 +895,9 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, in
   std::string solventResName = "HOH"; //argIn.GetStringKey("solventresname", "HOH");
   keepMissingSourceAtoms_ = false; //argIn.hasKey("keepmissingatoms");
   requireAllInputAtoms_ = false; //argIn.hasKey("requireallinputatoms");
+  doHisDetect_ = enableExtraDetection;
+  doDisulfide_ = enableExtraDetection;
+  doSugar_     = enableExtraDetection;
 
   // Set up Output coords
   if (setupOutputCoords(inCrdPtr, outset, title, DSL)) {
@@ -1002,6 +1006,9 @@ Exec::RetType Exec_Build::BuildAndParmStructure(DataSet* inCrdPtr, std::string c
   } else {
     check_structure_ = true;
   }
+  doHisDetect_ = !argIn.hasKey("nodisulfides");
+  doDisulfide_ = !argIn.hasKey("nohisdetect");
+  doSugar_ = !argIn.hasKey("nosugars");
   if (!outputTopologyName.empty())
     mprintf("\tWill write topology to %s\n", outputTopologyName.c_str());
   if (!outputCoordsName.empty())
@@ -1087,37 +1094,6 @@ Exec::RetType Exec_Build::BuildAndParmStructure(DataSet* inCrdPtr, std::string c
   DataSet_Coords& crdout = static_cast<DataSet_Coords&>( *((DataSet_Coords*)outCrdPtr_) );
   Topology& topOut = static_cast<Topology&>( *(crdout.TopPtr()) );
 
-/*
-  std::string default_title( ((DataSet_Coords*)inCrdPtr)->Top().c_str() );
-  if (!outset.empty()) {
-    // Separate output COORDS set.
-    outCrdPtr_ = DSL.AddSet( DataSet::COORDS, outset );
-  } else {
-    // In-place output COORDS
-    MetaData inCrdMeta = inCrdPtr->Meta();
-    std::string originalParmName( ((DataSet_Coords*)inCrdPtr)->Top().ParmName() );
-    FileName    originalFileName( ((DataSet_Coords*)inCrdPtr)->Top().OriginalFilename() );
-    DSL.RemoveSet( inCrdPtr );
-    outCrdPtr_ = DSL.AddSet( DataSet::COORDS, inCrdMeta );
-    // Copy over existing topology name, file
-    ((DataSet_Coords*)outCrdPtr_)->TopPtr()->SetParmName( originalParmName, originalFileName );
-  }
-  if (outCrdPtr_ == 0) {
-    mprinterr("Error: Could not allocate output COORDS set with name '%s'\n", outset.c_str());
-    return CpptrajState::ERR;
-  }
-  DataSet_Coords& crdout = static_cast<DataSet_Coords&>( *((DataSet_Coords*)outCrdPtr_) );
-  mprintf("\tOutput COORDS set: %s\n", crdout.legend());
-  Topology& topOut = static_cast<Topology&>( *(crdout.TopPtr()) );
-  topOut.SetDebug( debug_ );
-
-  if (!title.empty())
-    topOut.SetParmName( title, FileName() );
-  else if (topOut.ParmName().empty()) {
-    // TODO better default
-    topOut.SetParmName( default_title, topOut.OriginalFilename() );
-  }*/
-
   // GB radii set
   Cpptraj::Parm::GB_Params gbradii;
   if (gbradii.Init_GB_Radii(argIn, gbRadIn)) return CpptrajState::ERR;
@@ -1156,148 +1132,6 @@ Exec::RetType Exec_Build::BuildAndParmStructure(DataSet* inCrdPtr, std::string c
                                     solventResName,
                                     creator))
     return CpptrajState::ERR;
-/*
-  mprintf("    -----===== Structure Prep ===== -----\n");
-  // Do histidine detection before H atoms are removed
-  t_hisDetect_.Start();
-  if (!argIn.hasKey("nohisdetect")) {
-    Cpptraj::Structure::HisProt hisProt;
-    if (hisProt.InitHisProt( argIn, debug_ )) {
-      mprinterr("Error: Could not initialize histidine detection.\n");
-      return CpptrajState::ERR;
-    }
-    hisProt.HisProtInfo();
-    if (hisProt.DetermineHisProt( topIn )) {
-      mprinterr("Error: HIS protonation detection failed.\n");
-      return CpptrajState::ERR;
-    }
-  }
-  t_hisDetect_.Stop();
-
-  // Clean up structure
-  t_clean_.Start();
-  Cpptraj::Structure::PdbCleaner pdbCleaner;
-  pdbCleaner.SetDebug( debug_ );
-  if (pdbCleaner.InitPdbCleaner( argIn, solventResName, std::vector<int>() )) {
-    mprinterr("Error: Could not init PDB cleaner.\n");
-    return CpptrajState::ERR;
-  }
-  if (pdbCleaner.SetupPdbCleaner( topIn )) {
-    mprinterr("Error: Could not set up PDB cleaner.\n");
-    return CpptrajState::ERR;
-  }
-  pdbCleaner.PdbCleanerInfo();
-  if (pdbCleaner.ModifyCoords(topIn, frameIn)) {
-    mprinterr("Error: Could not clean PDB.\n");
-    return CpptrajState::ERR;
-  }
-  t_clean_.Stop();
-
-  // All residues start unknown
-  Cpptraj::Structure::ResStatArray resStat( topIn.Nres() );
-  std::vector<BondType> DisulfideBonds;
-  std::vector<BondType> SugarBonds;
-
-  // Disulfide search
-  t_disulfide_.Start();
-  if (!argIn.hasKey("nodisulfides")) {
-    Cpptraj::Structure::Disulfide disulfide;
-    if (disulfide.InitDisulfide( argIn, Cpptraj::Structure::Disulfide::ADD_BONDS, debug_ )) {
-      mprinterr("Error: Could not init disulfide search.\n");
-      return CpptrajState::ERR;
-    }
-    if (disulfide.SearchForDisulfides( resStat, topIn, frameIn, DisulfideBonds ))
-    {
-      mprinterr("Error: Disulfide search failed.\n");
-      return CpptrajState::ERR;
-    }
-  } else {
-    mprintf("\tNot searching for disulfides.\n");
-  }
-  t_disulfide_.Stop();
-
-  // Handle sugars.
-  t_sugar_.Start();
-  // TODO should be on a residue by residue basis in FillAtomsWithTemplates
-  bool prepare_sugars = !argIn.hasKey("nosugars");
-  if (!prepare_sugars)
-    mprintf("\tNot attempting to prepare sugars.\n");
-  else
-    mprintf("\tWill attempt to prepare sugars.\n");
-  Cpptraj::Structure::SugarBuilder sugarBuilder(debug_);
-  if (prepare_sugars) {
-    // Init options
-    if (sugarBuilder.InitOptions( argIn.hasKey("hasglycam"),
-                                  argIn.getKeyDouble("rescut", 8.0),
-                                  argIn.getKeyDouble("bondoffset", 0.2),
-                                  argIn.GetStringKey("sugarmask"),
-                                  argIn.GetStringKey("determinesugarsby", "geometry"),
-                                  argIn.GetStringKey("resmapfile") ))
-    {
-      mprinterr("Error: Sugar options init failed.\n");
-      return CpptrajState::ERR;
-    }
-    bool splitres = !argIn.hasKey("nosplitres");
-    if (splitres)
-      mprintf("\tWill split off recognized sugar functional groups into separate residues.\n");
-    else
-      mprintf("\tNot splitting recognized sugar functional groups into separate residues.\n");
-    bool c1bondsearch = !argIn.hasKey("noc1search");
-    if (c1bondsearch)
-      mprintf("\tWill search for missing bonds to sugar anomeric atoms.\n");
-    else
-      mprintf("\tNot searching for missing bonds to sugar anomeric atoms.\n");
-    // May need to modify sugar structure/topology, either by splitting
-    // C1 hydroxyls of terminal sugars into ROH residues, and/or by
-    // adding missing bonds to C1 atoms.
-    // This is done before any identification takes place since we want
-    // to identify based on the most up-to-date topology.
-    if (sugarBuilder.FixSugarsStructure(topIn, frameIn,
-                                        c1bondsearch, splitres, solventResName,
-                                        SugarBonds))
-    {
-      mprinterr("Error: Sugar structure modification failed.\n");
-      return CpptrajState::ERR;
-    }
-    if (sugarBuilder.PrepareSugars(true, resStat, topIn, frameIn, SugarBonds))
-    {
-      mprinterr("Error: Sugar preparation failed.\n");
-      return CpptrajState::ERR;
-    }
-  }
-  t_sugar_.Stop();
-
-  // Fill in atoms with templates
-  mprintf("    -----===== Match residues to templates, fill missing atoms =====-----\n");
-  t_fill_.Start();
-  Frame frameOut;
-  if (FillAtomsWithTemplates(topOut, frameOut, topIn, frameIn, creator, SugarBonds)) {
-    mprinterr("Error: Could not fill in atoms using templates.\n");
-    return CpptrajState::ERR;
-  }
-  t_fill_.Stop();
-
-  // Add the disulfide bonds
-  int addBondsErr = transfer_bonds( topOut, topIn, DisulfideBonds );
-  if (addBondsErr != 0) {
-    mprinterr("Error: Adding disulfide bonds failed.\n");
-    return CpptrajState::ERR;
-  }
-
-  // Perform any modifications necessary for the sugar functional groups
-  bool top_is_modified = false;
-  if (sugarBuilder.ModifyFoundFxnGroups(topOut, top_is_modified)) {
-    mprinterr("Error: Could not make necessary modifications to detected sugar functional groups.\n");
-    return CpptrajState::ERR;
-  }
-
-  // Create empty arrays for the TREE, JOIN, and IROTAT arrays
-  topOut.AllocTreeChainClassification( );
-  topOut.AllocJoinArray();
-  topOut.AllocRotateArray();
-    // Finalize topology - determine molecules, dont renumber residues
-  topOut.CommonSetup(true, false);
-*/
   // =============================================
 
   // Solvate/add ions
@@ -1548,7 +1382,7 @@ int Exec_Build::StructurePrepAndFillTemplates(ArgList& argIn, Topology& topIn, F
   mprintf("    -----===== Structure Prep ===== -----\n");
   // Do histidine detection before H atoms are removed
   t_hisDetect_.Start();
-  if (!argIn.hasKey("nohisdetect")) {
+  if (doHisDetect_) {
     Cpptraj::Structure::HisProt hisProt;
     if (hisProt.InitHisProt( argIn, debug_ )) {
       mprinterr("Error: Could not initialize histidine detection.\n");
@@ -1559,6 +1393,8 @@ int Exec_Build::StructurePrepAndFillTemplates(ArgList& argIn, Topology& topIn, F
       mprinterr("Error: HIS protonation detection failed.\n");
       return 1;
     }
+  } else {
+    mprintf("\tNot preparing histidines.\n");
   }
   t_hisDetect_.Stop();
 
@@ -1588,7 +1424,7 @@ int Exec_Build::StructurePrepAndFillTemplates(ArgList& argIn, Topology& topIn, F
 
   // Disulfide search
   t_disulfide_.Start();
-  if (!argIn.hasKey("nodisulfides")) {
+  if (doDisulfide_) {
     Cpptraj::Structure::Disulfide disulfide;
     if (disulfide.InitDisulfide( argIn, Cpptraj::Structure::Disulfide::ADD_BONDS, debug_ )) {
       mprinterr("Error: Could not init disulfide search.\n");
@@ -1607,13 +1443,12 @@ int Exec_Build::StructurePrepAndFillTemplates(ArgList& argIn, Topology& topIn, F
   // Handle sugars.
   t_sugar_.Start();
   // TODO should be on a residue by residue basis in FillAtomsWithTemplates
-  bool prepare_sugars = !argIn.hasKey("nosugars");
-  if (!prepare_sugars)
+  if (!doSugar_)
     mprintf("\tNot attempting to prepare sugars.\n");
   else
     mprintf("\tWill attempt to prepare sugars.\n");
   Cpptraj::Structure::SugarBuilder sugarBuilder(debug_);
-  if (prepare_sugars) {
+  if (doSugar_) {
     // Init options
     if (sugarBuilder.InitOptions( argIn.hasKey("hasglycam"),
                                   argIn.getKeyDouble("rescut", 8.0),
diff --git a/src/Exec_Build.h b/src/Exec_Build.h
index 3e526f42e0..2fa22120e3 100644
--- a/src/Exec_Build.h
+++ b/src/Exec_Build.h
@@ -17,7 +17,7 @@ class Exec_Build : public Exec {
     RetType Execute(CpptrajState&, ArgList&);
 
     /// Stand-alone execution - only build, do not parameterize/solvate
-    RetType BuildStructure(DataSet*, DataSetList&, int, std::string const&, std::string const&);
+    RetType BuildStructure(DataSet*, DataSetList&, int, std::string const&, std::string const&, bool);
     /// \return Output COORDS set
     DataSet* OutCrdPtr() const { return outCrdPtr_; }
     /// Print Timing data
@@ -55,6 +55,9 @@ class Exec_Build : public Exec {
     bool check_structure_;        ///< If true check the resulting structure
     bool keepMissingSourceAtoms_; ///< If true, attempt to keep input atoms that are missing from templates
     bool requireAllInputAtoms_;   ///< If true, require all input atoms to be found in templates.
+    bool doHisDetect_;
+    bool doDisulfide_;
+    bool doSugar_;
     DataSet* outCrdPtr_;          ///< Hold built (output) COORDS
 
     Timer t_total_;

From 6a1ea547edebe05cc406df3bdecfd52081212999 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 23 Jan 2026 15:10:27 -0500
Subject: [PATCH 1247/1492] Start improving error messages

---
 src/Exec_Build.cpp | 16 +++++++++++++++-
 src/Exec_Build.h   |  2 ++
 2 files changed, 17 insertions(+), 1 deletion(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index a487537898..2f32f3e31a 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -32,6 +32,11 @@ Exec_Build::Exec_Build() :
   outCrdPtr_(0)
 {}
 
+void Exec_Build::printErrMsgWebsites() {
+  mprinterr("Error: See https://ambermd.org/AmberModels.php for more information\n"
+             "Error: or email the Amber mailing list http://lists.ambermd.org/mailman/listinfo/amber\n");
+}
+
 /** Search in array of atom bonding pairs for given bonding pair. */
 bool Exec_Build::hasBondingPair(IParray const& bpairs, Ipair const& bpair) {
   for (IParray::const_iterator it = bpairs.begin(); it != bpairs.end(); ++it)
@@ -452,6 +457,11 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
           mprinterr("Error:\t%s missing types for%s\n", topOut.TruncResNameNum(ires).c_str(), missingTypes.c_str());
       }
     }
+    mprinterr("Error: Suggestions:\n"
+              "Error:   1) Load an Amber force field using 'source <leaprc file>', e.g. 'source leaprc.protein.ff19SB'\n"
+              "Error:   2) Load residue templates from library/coords files with 'readdata <file> as <type>', e.g. 'readdata amino19.lib as off'\n");
+    printErrMsgWebsites();
+
     return 1;
   }
 
@@ -1119,7 +1129,11 @@ Exec::RetType Exec_Build::BuildAndParmStructure(DataSet* inCrdPtr, std::string c
     mprintf("Warning: No residue templates loaded.\n");
   }
   if (!creator.HasMainParmSet()) {
-    mprinterr("Error: No parameter sets.\n");
+    mprinterr("Error: No parameter sets found.\n");
+    mprinterr("Error: Building a system requires that force field parameters be loaded. Suggestions:\n"
+              "Error:   1) Load an Amber force field using 'source <leaprc file>', e.g. 'source leaprc.protein.ff19SB'\n"
+              "Error:   2) Load individual parameter files with 'readdata <file> as <type>', e.g. 'readdata parm10.dat as amberff'\n");
+    printErrMsgWebsites();
     return CpptrajState::ERR;
   }
   t_get_templates_.Stop();
diff --git a/src/Exec_Build.h b/src/Exec_Build.h
index 2fa22120e3..2302d557cd 100644
--- a/src/Exec_Build.h
+++ b/src/Exec_Build.h
@@ -30,6 +30,8 @@ class Exec_Build : public Exec {
     typedef std::pair<int,int> Ipair;
     typedef std::vector<Ipair> IParray;
 
+    /// Print error message of websites to consult
+    static void printErrMsgWebsites();
     /// \return true if given IParray has the given Ipair
     static inline bool hasBondingPair(IParray const&, Ipair const&);
     /// \return true if given array of residue connections has target residue index.

From 9560cc30bcf0ea980655f34cf668bb33d62e49e6 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 23 Jan 2026 15:42:45 -0500
Subject: [PATCH 1248/1492] Fix error messages

---
 src/Exec_Build.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 2f32f3e31a..93e7c7c5a7 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -459,7 +459,7 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
     }
     mprinterr("Error: Suggestions:\n"
               "Error:   1) Load an Amber force field using 'source <leaprc file>', e.g. 'source leaprc.protein.ff19SB'\n"
-              "Error:   2) Load residue templates from library/coords files with 'readdata <file> as <type>', e.g. 'readdata amino19.lib as off'\n");
+              "Error:   2) Load residue templates with atom types from library/coords files with 'readdata <file> as <type>', e.g. 'readdata amino19.lib as off'\n");
     printErrMsgWebsites();
 
     return 1;

From 697889e2ccd693de7ed9b03c2a6fa3de575e0568 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 24 Jan 2026 11:24:34 -0500
Subject: [PATCH 1249/1492] New strategy for target number of waters

---
 src/Structure/Solvate.cpp | 62 +++++++++++++++++++++++++++------------
 src/Structure/Solvate.h   |  2 ++
 2 files changed, 45 insertions(+), 19 deletions(-)

diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index 845ce60888..cb42fe546e 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -65,8 +65,8 @@ int Solvate::getBufferArg(ArgList& argIn, double defaultBuffer) {
 int Solvate::InitSolvate(ArgList& argIn, bool octIn, int debugIn) {
   debug_ = debugIn;
   doTruncatedOct_ = octIn;
-  //nsolvent_ = (unsigned int)argIn.getKeyInt("nsolvent", 0);
-  nsolvent_ = 0; // TODO enable
+  nsolvent_ = (unsigned int)argIn.getKeyInt("nsolvent", 0);
+  //nsolvent_ = 0; // TODO enable
 
   if (getBufferArg(argIn, -1.0)) return 1;
 
@@ -486,6 +486,19 @@ const
             dXWidth, dYWidth, dZWidth );
 }
 
+/** Calculate the number of boxes needed to create a given layer */
+unsigned int Solvate::nBoxesInLayer(int n) {
+  // Special case; no layers is 1 cube
+  if (n < 1) return 1;
+  unsigned int nSide = (unsigned int)n + 2;
+  // Special case; 1 layer, center cube is surrounded by 26 boxes (3x3x3 cubes minus the center).
+  if (nSide == 3) return 26;
+  unsigned int nSidem1 = nSide - 1;
+  unsigned int cube = nSide * nSide * nSide;
+  unsigned int cubem1 = nSidem1 * nSidem1 * nSidem1;
+  return cube - cubem1;
+}
+
 /** Create box, fill with target number of solvent molecules. */
 int Solvate::SolvateBoxWithExactNumber(Topology& topOut, Frame& frameOut, Cpptraj::Parm::ParameterSet const& set0,
                                        DataSetList const& DSL)
@@ -550,24 +563,35 @@ int Solvate::SolvateBoxWithExactNumber(Topology& topOut, Frame& frameOut, Cpptra
   // Estimate how many solvent molecules will be removed by solvent
   unsigned int nMolsRemovedBySolute = (unsigned int)ceil( soluteFac * (double)SOLVENTBOX.Top().Nmol() );
   mprintf("\t  Estimating approximately %u solvent molecules will be removed by solute.\n", nMolsRemovedBySolute);
+
+  // How many "layers" are needed to be over the target number?
+  long int nSolventAdded = 0;
+  int layer = 0;
+  while (nSolventAdded < nsolvent_) {
+    nSolventAdded = (long int)(nBoxesInLayer(layer) * (unsigned int)SOLVENTBOX.Top().Nmol());
+    nSolventAdded = nSolventAdded - (long int)nMolsRemovedBySolute;
+    mprintf("DEBUG: Layer %i, # solvent added = %li\n", layer, nSolventAdded);
+    layer++;
+  }
+    
   //unsigned int nBoxesForSolvent = (unsigned int)ceil( (double)nsolvent / (double)SOLVENTBOX.Top().Nmol() );
-  // Calculate the solvent box density
-  double solventBoxDensity = (double)SOLVENTBOX.Top().Nmol() / solventBoxVol;
-  mprintf("\t  Solvent box density is %g mols/Ang^3\n", solventBoxDensity);
-  // Calculate how many solvent molecules we actually need to add given that solute will remove some
-  unsigned int neededNumberOfSolvent = nsolvent_ + nMolsRemovedBySolute;
-  // Calculate what volume of solvent is needed to hit the actual solvent molecule target
-  double tgtVol = (double)neededNumberOfSolvent / solventBoxDensity;
-  mprintf("\t  Target volume: %g Ang^3\n", tgtVol);
-  // Calculate number of solvent boxes needed
-  //unsigned int neededNumberOfBoxes = (unsigned int)ceil( tgtVol / solventBoxVol );
-  //mprintf("\t  Need %u solvent boxes.\n", neededNumberOfBoxes);
-  double tgtLen = pow(tgtVol, (1.0/3.0));
-  mprintf("\t  Target length: %g Ang\n", tgtLen);
-  double bX = (tgtLen - boxX) / 2.0;
-  double bY = (tgtLen - boxY) / 2.0;
-  double bZ = (tgtLen - boxZ) / 2.0;
-  mprintf("\t  Buffer: %g %g %g\n", bX, bY, bZ);
+//  // Calculate the solvent box density
+//  double solventBoxDensity = (double)SOLVENTBOX.Top().Nmol() / solventBoxVol;
+//  mprintf("\t  Solvent box density is %g mols/Ang^3\n", solventBoxDensity);
+//  // Calculate how many solvent molecules we actually need to add given that solute will remove some
+//  unsigned int neededNumberOfSolvent = nsolvent_ + nMolsRemovedBySolute;
+//  // Calculate what volume of solvent is needed to hit the actual solvent molecule target
+//  double tgtVol = (double)neededNumberOfSolvent / solventBoxDensity;
+//  mprintf("\t  Target volume: %g Ang^3\n", tgtVol);
+//  // Calculate number of solvent boxes needed
+//  //unsigned int neededNumberOfBoxes = (unsigned int)ceil( tgtVol / solventBoxVol );
+//  //mprintf("\t  Need %u solvent boxes.\n", neededNumberOfBoxes);
+//  double tgtLen = pow(tgtVol, (1.0/3.0));
+//  mprintf("\t  Target length: %g Ang\n", tgtLen);
+//  double bX = (tgtLen - boxX) / 2.0;
+//  double bY = (tgtLen - boxY) / 2.0;
+//  double bZ = (tgtLen - boxZ) / 2.0;
+//  mprintf("\t  Buffer: %g %g %g\n", bX, bY, bZ);
   
   //unsigned int nSolventBoxesNeeded = (unsigned int)ceil( (double)neededNumberOfSolvent / (double)SOLVENTBOX.Top().Nmol() );
   //mprintf("\t  Estimating %u solvent boxes will be needed.\n", nSolventBoxesNeeded);
diff --git a/src/Structure/Solvate.h b/src/Structure/Solvate.h
index fcdf597685..6a2d96f468 100644
--- a/src/Structure/Solvate.h
+++ b/src/Structure/Solvate.h
@@ -40,6 +40,8 @@ class Solvate {
     DataSet_Coords* GetSolventUnit(DataSetList const&) const;
     /// Adjust box widths
     void adjustBoxWidths(double&, double&, double&, double&, double&, double&) const;
+    /// \return number of boxes needed to create layer
+    static unsigned int nBoxesInLayer(int);
     /// Solvate with box and specified number of solvent
     int SolvateBoxWithExactNumber(Topology&, Frame&, Cpptraj::Parm::ParameterSet const&, DataSetList const&);
     /// Get buffer arguments

From 995dbb5ca65944a3b3d7a9252567319566cb8c57 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 24 Jan 2026 11:42:57 -0500
Subject: [PATCH 1250/1492] Add the solvent, no clipping. Might be
 overestimating the actual solvent needed

---
 src/Structure/Solvate.cpp | 34 ++++++++++++++++++++++++++++++++--
 1 file changed, 32 insertions(+), 2 deletions(-)

diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index cb42fe546e..4b0b8a37fe 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -67,6 +67,7 @@ int Solvate::InitSolvate(ArgList& argIn, bool octIn, int debugIn) {
   doTruncatedOct_ = octIn;
   nsolvent_ = (unsigned int)argIn.getKeyInt("nsolvent", 0);
   //nsolvent_ = 0; // TODO enable
+  if (nsolvent_ > 0) clip_ = false;
 
   if (getBufferArg(argIn, -1.0)) return 1;
 
@@ -573,7 +574,36 @@ int Solvate::SolvateBoxWithExactNumber(Topology& topOut, Frame& frameOut, Cpptra
     mprintf("DEBUG: Layer %i, # solvent added = %li\n", layer, nSolventAdded);
     layer++;
   }
-    
+  
+  // NOTE: layer is actually layer+1 right now
+  double dXWidth = ((double)layer * solventX);
+  double dYWidth = ((double)layer * solventY);
+  double dZWidth = ((double)layer * solventZ);
+  mprintf("DEBUG: Estimated size with buffer: %f %f %f\n", dXWidth, dYWidth, dZWidth);
+
+  // See how many solvent boxes required in each dimension
+  int iX = (int)( dXWidth / solventX ) + 1;
+  int iY = (int)( dYWidth / solventY ) + 1;
+  int iZ = (int)( dZWidth / solventZ ) + 1;
+
+  //  Calculate the center of the first solvent box 
+  //  (the one that goes in the max XYZ corner), given
+  //  that the solute is centered at 0,0,0
+  double dXStart = 0.5 * solventX * (double) (iX-1);
+  double dYStart = 0.5 * solventY * (double) (iY-1);
+  double dZStart = 0.5 * solventZ * (double) (iZ-1);
+
+  addSolventUnits(iX, iY, iZ, soluteMaxR, dXStart, dYStart, dZStart, solventX, solventY, solventZ,
+                  solventFrame, SOLVENTBOX.Top(), frameOut, topOut,
+                  soluteRadii, solventRadii);
+
+  // Define the size of the new solvent/solute system
+  soluteRadii = getAtomRadii(soluteMaxR, topOut, set0) ;
+  if (setVdwBoundingBox(boxX, boxY, boxZ, soluteRadii, frameOut, false)) {
+    mprinterr("Error: Setting vdw bounding box for solute/solvent system failed.\n", topOut.c_str());
+    return 1;
+  }
+
   //unsigned int nBoxesForSolvent = (unsigned int)ceil( (double)nsolvent / (double)SOLVENTBOX.Top().Nmol() );
 //  // Calculate the solvent box density
 //  double solventBoxDensity = (double)SOLVENTBOX.Top().Nmol() / solventBoxVol;
@@ -897,7 +927,7 @@ const
                  dZ = fabs( dZ - 0.5 );
           if ( ( dX + dY + dZ )  >  0.75 ) { collision = true; break; }
         }
-      }
+      } // END if clip
       double dR = solventRadii[vat] * closeness_ * CLOSENESSMODIFIER_;
       // Loop over close solute atoms, check for clash
       for (std::vector<int>::const_iterator uat = closeSoluteAtoms.begin(); uat != closeSoluteAtoms.end(); ++uat)

From 7f5996433c3d98aa26fd524987217b45454a65ca Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 24 Jan 2026 11:54:15 -0500
Subject: [PATCH 1251/1492] Better estimate of boxes needed

---
 src/Structure/Solvate.cpp | 18 ++++++++++++++++--
 src/Structure/Solvate.h   |  2 ++
 2 files changed, 18 insertions(+), 2 deletions(-)

diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index 4b0b8a37fe..89ce152338 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -500,6 +500,17 @@ unsigned int Solvate::nBoxesInLayer(int n) {
   return cube - cubem1;
 }
 
+/** Calculate the number of boxes needed to create a given cube */
+unsigned int Solvate::nBoxesInCube(int n) {
+  // Special case; no layers is 1 cube
+  if (n < 1) return 1;
+  unsigned int nSide = (unsigned int)n + 2;
+  // Special case; 1 layer, 27 boxes (3x3x3 cubes).
+  if (nSide == 3) return 27;
+  unsigned int cube = nSide * nSide * nSide;
+  return cube;
+}
+
 /** Create box, fill with target number of solvent molecules. */
 int Solvate::SolvateBoxWithExactNumber(Topology& topOut, Frame& frameOut, Cpptraj::Parm::ParameterSet const& set0,
                                        DataSetList const& DSL)
@@ -569,13 +580,16 @@ int Solvate::SolvateBoxWithExactNumber(Topology& topOut, Frame& frameOut, Cpptra
   long int nSolventAdded = 0;
   int layer = 0;
   while (nSolventAdded < nsolvent_) {
-    nSolventAdded = (long int)(nBoxesInLayer(layer) * (unsigned int)SOLVENTBOX.Top().Nmol());
+    nSolventAdded = (long int)(nBoxesInCube(layer) * (unsigned int)SOLVENTBOX.Top().Nmol());
     nSolventAdded = nSolventAdded - (long int)nMolsRemovedBySolute;
     mprintf("DEBUG: Layer %i, # solvent added = %li\n", layer, nSolventAdded);
     layer++;
   }
-  
   // NOTE: layer is actually layer+1 right now
+  if (layer > 1) {
+    layer = (layer - 1) + 2;
+  }
+
   double dXWidth = ((double)layer * solventX);
   double dYWidth = ((double)layer * solventY);
   double dZWidth = ((double)layer * solventZ);
diff --git a/src/Structure/Solvate.h b/src/Structure/Solvate.h
index 6a2d96f468..307e788b85 100644
--- a/src/Structure/Solvate.h
+++ b/src/Structure/Solvate.h
@@ -42,6 +42,8 @@ class Solvate {
     void adjustBoxWidths(double&, double&, double&, double&, double&, double&) const;
     /// \return number of boxes needed to create layer
     static unsigned int nBoxesInLayer(int);
+    /// \return number of boxes needed to create cube 
+    static unsigned int nBoxesInCube(int);
     /// Solvate with box and specified number of solvent
     int SolvateBoxWithExactNumber(Topology&, Frame&, Cpptraj::Parm::ParameterSet const&, DataSetList const&);
     /// Get buffer arguments

From a2d1a6b2c942f6885e0a0c64edf525db98023283 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 24 Jan 2026 14:51:30 -0500
Subject: [PATCH 1252/1492] Start adapting the solvate script

---
 src/Structure/Solvate.cpp | 119 +++++++++++++++++++++++++++++++++++++-
 1 file changed, 118 insertions(+), 1 deletion(-)

diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index 89ce152338..e3609143ad 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -511,6 +511,11 @@ unsigned int Solvate::nBoxesInCube(int n) {
   return cube;
 }
 
+static inline void checkBuffer(double& buf, double min, double max) {
+  if (buf < min) buf = min;
+  if (buf > max) buf = max;
+}
+
 /** Create box, fill with target number of solvent molecules. */
 int Solvate::SolvateBoxWithExactNumber(Topology& topOut, Frame& frameOut, Cpptraj::Parm::ParameterSet const& set0,
                                        DataSetList const& DSL)
@@ -607,17 +612,25 @@ int Solvate::SolvateBoxWithExactNumber(Topology& topOut, Frame& frameOut, Cpptra
   double dYStart = 0.5 * solventY * (double) (iY-1);
   double dZStart = 0.5 * solventZ * (double) (iZ-1);
 
+  int firstSolventRes = topOut.Nres();
+
   addSolventUnits(iX, iY, iZ, soluteMaxR, dXStart, dYStart, dZStart, solventX, solventY, solventZ,
                   solventFrame, SOLVENTBOX.Top(), frameOut, topOut,
                   soluteRadii, solventRadii);
 
   // Define the size of the new solvent/solute system
+  double maxX, maxY, maxZ;
   soluteRadii = getAtomRadii(soluteMaxR, topOut, set0) ;
-  if (setVdwBoundingBox(boxX, boxY, boxZ, soluteRadii, frameOut, false)) {
+  if (setVdwBoundingBox(maxX, maxY, maxZ, soluteRadii, frameOut, false)) {
     mprinterr("Error: Setting vdw bounding box for solute/solvent system failed.\n", topOut.c_str());
     return 1;
   }
 
+  if (firstSolventRes >= topOut.Nres()) {
+    mprinterr("Internal Error: Solvate::SolvateBoxWithExactNumber(): No solvent added.\n");
+    return 1;
+  }
+
   //unsigned int nBoxesForSolvent = (unsigned int)ceil( (double)nsolvent / (double)SOLVENTBOX.Top().Nmol() );
 //  // Calculate the solvent box density
 //  double solventBoxDensity = (double)SOLVENTBOX.Top().Nmol() / solventBoxVol;
@@ -640,6 +653,110 @@ int Solvate::SolvateBoxWithExactNumber(Topology& topOut, Frame& frameOut, Cpptra
   //unsigned int nSolventBoxesNeeded = (unsigned int)ceil( (double)neededNumberOfSolvent / (double)SOLVENTBOX.Top().Nmol() );
   //mprintf("\t  Estimating %u solvent boxes will be needed.\n", nSolventBoxesNeeded);
 
+  frameOut.CenterOnOrigin(false);
+
+  // FIXME make user-specifiable
+  double alpha = 90.0;
+  double beta  = 90.0;
+  double gamma = 90.0;
+
+  double bufX = boxX + ((maxX - boxX) / 2.0);
+  double bufY = boxY + ((maxY - boxY) / 2.0);
+  double bufZ = boxZ + ((maxZ - boxZ) / 2.0);
+  // This loop uses the same logic as my old Solvate.sh script
+  // (https://github.com/drroe/Solvate.sh/blob/master/Solvate.sh)
+  bool loop = true;
+  int ntries = 0;
+  double change = 0.001;
+  int lastdiff = 0;
+  Box newBox;
+  while (loop) {
+    mprintf("DEBUG: %i) Buffer %f %f %f\n", ntries, bufX, bufY, bufZ);
+    // Define the unit cell
+    newBox.SetupFromXyzAbg( bufX, bufY, bufZ, alpha, beta, gamma );
+    newBox.PrintInfo();
+    // Convert to fractional
+    int nSolventInCell = 0;
+    Matrix_3x3 const& recip = newBox.FracCell();
+    for (int ires = firstSolventRes; ires < topOut.Nres(); ires++) {
+      bool inCell = true;
+      Residue const& currentRes = topOut.Res(ires);
+      //mprintf("\t\t%s\n", topOut.TruncResNameNum(ires).c_str());
+      for (int at = currentRes.FirstAtom(); at != currentRes.LastAtom(); at++) {
+        const double* XYZ = frameOut.XYZ(at);
+        Vec3 fc = recip * Vec3( XYZ );
+        //mprintf("\t\t\t%s xyz={%f %f %f} frac={%f %f %f}\n", topOut.AtomMaskName(at).c_str(), XYZ[0], XYZ[1], XYZ[2], fc[0], fc[1], fc[2]);
+        if (fc[0] > 0.5) { inCell = false; break; }
+        if (fc[1] > 0.5) { inCell = false; break; }
+        if (fc[2] > 0.5) { inCell = false; break; }
+        if (fc[0] < -0.5) { inCell = false; break; }
+        if (fc[1] < -0.5) { inCell = false; break; }
+        if (fc[2] < -0.5) { inCell = false; break; }
+      }
+      //mprintf("\t\tInCell= %i\n", (int)inCell);
+      if (inCell)
+        nSolventInCell++;
+    } // END loop over solvent residues
+
+    // How far off is it?
+    int diff = nsolvent_ - nSolventInCell;
+    mprintf("DEBUG:\t%i solvent residues in cell. Diff: %i\n", nSolventInCell, diff);
+    // If this is the first time trhough choose an appropriate change val
+    if (ntries == 0) {
+      change = 0.001;
+    }
+    // See if we have tol more waters than the target TODO
+    if (diff == 0) {
+     loop = false;
+     mprintf("DEBUG: Found.\n");
+    } else {
+      double CHANGE_DIR = 0;
+      if ( lastdiff > 0 && diff < 0) {
+        change = change / 2.0;
+        CHANGE_DIR=-1;
+      } else if ( lastdiff < 0 && diff > 0) {
+        change = change / 2.0;
+        CHANGE_DIR=-1;
+      } else if (ntries > 0) {
+        // If we took a step and the size of the step we just took is smaller
+        // than the remaining distance to target, increase the step size.
+        int STEPSIZE = diff - lastdiff;
+        if (STEPSIZE < 0) {
+         STEPSIZE = -STEPSIZE;
+        } 
+        int ABSDIFF = diff;
+        if (ABSDIFF < 0) {
+          ABSDIFF = -ABSDIFF;
+        }
+        //printf " STEP=%i ABS=%i " $STEPSIZE $ABSDIFF
+        if ( STEPSIZE > 0 && STEPSIZE < ABSDIFF) {
+          change = change * 2.4;
+          CHANGE_DIR=1;
+        }
+      }
+      lastdiff = diff;
+      // Choose a new buffer value
+      double CD = change * (double)diff; // TODO should be minus?
+      double newbufX = bufX + CD; // TODO should be minus
+      double newbufY = bufY + CD; // TODO should be minus
+      double newbufZ = bufZ + CD; // TODO should be minus
+      //CheckBuffer $newbuffer;
+      //lastbuffer=$buffer
+      checkBuffer(newbufX, boxX, maxX);
+      checkBuffer(newbufY, boxY, maxY);
+      checkBuffer(newbufZ, boxZ, maxZ);
+      bufX = newbufX;
+      bufY = newbufY;
+      bufZ = newbufZ;
+      mprintf("DEBUG: Change: %G (%g) newBuf= %f %f %f\n", change, CHANGE_DIR, bufX, bufY, bufZ);
+    } // END change calc
+
+    // Safety valve
+    if (ntries > 100) {
+      mprintf("\tTaking too long - moving on...\n");
+      loop = false;
+    }
+  } // END cell loop
 
   return 0;
 }

From 8b5e4eda8550aba426c86c6410a37c5182ce613c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 24 Jan 2026 20:31:22 -0500
Subject: [PATCH 1253/1492] Start adding code to remove water molecules within
 a tolerance

---
 src/Structure/Solvate.cpp | 46 +++++++++++++++++++++++++++++++++++----
 1 file changed, 42 insertions(+), 4 deletions(-)

diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index e3609143ad..f5ad912e59 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -1,5 +1,6 @@
 #include "Solvate.h"
 #include "../ArgList.h"
+#include "../CharMask.h"
 #include "../CpptrajStdio.h"
 #include "../DataSet_Coords.h"
 #include "../DataSetList.h"
@@ -659,6 +660,7 @@ int Solvate::SolvateBoxWithExactNumber(Topology& topOut, Frame& frameOut, Cpptra
   double alpha = 90.0;
   double beta  = 90.0;
   double gamma = 90.0;
+  int negtol = -5;
 
   double bufX = boxX + ((maxX - boxX) / 2.0);
   double bufY = boxY + ((maxY - boxY) / 2.0);
@@ -675,6 +677,14 @@ int Solvate::SolvateBoxWithExactNumber(Topology& topOut, Frame& frameOut, Cpptra
     // Define the unit cell
     newBox.SetupFromXyzAbg( bufX, bufY, bufZ, alpha, beta, gamma );
     newBox.PrintInfo();
+    CharMask cmask( topOut.Natom() );
+    for (int ires = 0; ires < firstSolventRes; ires++) {
+      Residue const& currentRes = topOut.Res(ires);
+      //mprintf("\t\t%s\n", topOut.TruncResNameNum(ires).c_str());
+      for (int at = currentRes.FirstAtom(); at != currentRes.LastAtom(); at++) {
+        cmask.SelectAtom(at, true);
+      }
+    }
     // Convert to fractional
     int nSolventInCell = 0;
     Matrix_3x3 const& recip = newBox.FracCell();
@@ -694,8 +704,11 @@ int Solvate::SolvateBoxWithExactNumber(Topology& topOut, Frame& frameOut, Cpptra
         if (fc[2] < -0.5) { inCell = false; break; }
       }
       //mprintf("\t\tInCell= %i\n", (int)inCell);
-      if (inCell)
+      if (inCell) {
+        for (int at = currentRes.FirstAtom(); at != currentRes.LastAtom(); at++)
+          cmask.SelectAtom(at, true);
         nSolventInCell++;
+      }
     } // END loop over solvent residues
 
     // How far off is it?
@@ -706,9 +719,34 @@ int Solvate::SolvateBoxWithExactNumber(Topology& topOut, Frame& frameOut, Cpptra
       change = 0.001;
     }
     // See if we have tol more waters than the target TODO
-    if (diff == 0) {
-     loop = false;
-     mprintf("DEBUG: Found.\n");
+    if (diff < 0 && diff >= negtol) {
+      // Close enough, just remove the last water residue(s)
+      int nToRemove = -diff;
+      mprintf("\tOnly %i solvent molecules off, removing them.\n", nToRemove);
+      for (int ires = topOut.Nres() - 1; ires > firstSolventRes-1; ires--) {
+        Residue const& currentRes = topOut.Res(ires);
+        if (cmask.AtomInCharMask( currentRes.FirstAtom() )) {
+          mprintf("Removing %s\n", topOut.TruncResNameNum(ires).c_str());
+          for (int at = currentRes.FirstAtom(); at != currentRes.LastAtom(); at++)
+            cmask.SelectAtom(at, false);
+          nToRemove--;
+        }
+        if (nToRemove < 1) break;
+      }
+      if (nToRemove > 0) {
+        mprinterr("Error: Could not remove enough solvent residues.\n");
+        return 1;
+      }
+      //int LASTRES = firstSolventRes + nSolventInCell;
+      //int FIRSTRES = LASTRES + diff + 1;
+      //mprintf("\tOnly %i off, removing solvent residue(s) (%i-%i)", diff, FIRSTRES, LASTRES);
+      //for (int RRES = LASTRES; RRES >= FIRSTRES; RRES--) {
+      //  mprintf("DEBUG: remove $MOLNAME $MOLNAME.%i\n", RRES-1);
+      //}
+      loop = false;
+    } else if (diff == 0) {
+      loop = false;
+      mprintf("DEBUG: Found.\n");
     } else {
       double CHANGE_DIR = 0;
       if ( lastdiff > 0 && diff < 0) {

From e38e770545b8ee0b128aa860d4867165b7ee36c0 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 25 Jan 2026 10:34:06 -0500
Subject: [PATCH 1254/1492] Do the final strip to only retain the target number
 of waters

---
 src/Structure/Solvate.cpp | 48 +++++++++++++++++++++++++++++++--------
 1 file changed, 39 insertions(+), 9 deletions(-)

diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index f5ad912e59..4937208783 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -613,7 +613,9 @@ int Solvate::SolvateBoxWithExactNumber(Topology& topOut, Frame& frameOut, Cpptra
   double dYStart = 0.5 * solventY * (double) (iY-1);
   double dZStart = 0.5 * solventZ * (double) (iZ-1);
 
+//  int firstSolventAtom = topOut.Natom(); // DEBUG
   int firstSolventRes = topOut.Nres();
+//  mprintf("DEBUG: First solvent atom %i, first solvent res %i\n", topOut.Natom(), firstSolventRes);
 
   addSolventUnits(iX, iY, iZ, soluteMaxR, dXStart, dYStart, dZStart, solventX, solventY, solventZ,
                   solventFrame, SOLVENTBOX.Top(), frameOut, topOut,
@@ -665,6 +667,18 @@ int Solvate::SolvateBoxWithExactNumber(Topology& topOut, Frame& frameOut, Cpptra
   double bufX = boxX + ((maxX - boxX) / 2.0);
   double bufY = boxY + ((maxY - boxY) / 2.0);
   double bufZ = boxZ + ((maxZ - boxZ) / 2.0);
+
+  // Mask selecting everything that should be kept. Always keep solute
+  CharMask cmask( topOut.Natom() );
+  for (int ires = 0; ires < firstSolventRes; ires++) {
+    Residue const& currentRes = topOut.Res(ires);
+    //mprintf("\t\t%s\n", topOut.TruncResNameNum(ires).c_str());
+    for (int at = currentRes.FirstAtom(); at != currentRes.LastAtom(); at++) {
+      cmask.SelectAtom(at, true);
+    }
+  }
+//  cmask.MaskInfo(); // DEBUG
+
   // This loop uses the same logic as my old Solvate.sh script
   // (https://github.com/drroe/Solvate.sh/blob/master/Solvate.sh)
   bool loop = true;
@@ -677,14 +691,6 @@ int Solvate::SolvateBoxWithExactNumber(Topology& topOut, Frame& frameOut, Cpptra
     // Define the unit cell
     newBox.SetupFromXyzAbg( bufX, bufY, bufZ, alpha, beta, gamma );
     newBox.PrintInfo();
-    CharMask cmask( topOut.Natom() );
-    for (int ires = 0; ires < firstSolventRes; ires++) {
-      Residue const& currentRes = topOut.Res(ires);
-      //mprintf("\t\t%s\n", topOut.TruncResNameNum(ires).c_str());
-      for (int at = currentRes.FirstAtom(); at != currentRes.LastAtom(); at++) {
-        cmask.SelectAtom(at, true);
-      }
-    }
     // Convert to fractional
     int nSolventInCell = 0;
     Matrix_3x3 const& recip = newBox.FracCell();
@@ -705,16 +711,23 @@ int Solvate::SolvateBoxWithExactNumber(Topology& topOut, Frame& frameOut, Cpptra
       }
       //mprintf("\t\tInCell= %i\n", (int)inCell);
       if (inCell) {
+        // Keep solvent
         for (int at = currentRes.FirstAtom(); at != currentRes.LastAtom(); at++)
           cmask.SelectAtom(at, true);
         nSolventInCell++;
+      } else {
+        // Remove solvent
+        for (int at = currentRes.FirstAtom(); at != currentRes.LastAtom(); at++)
+          cmask.SelectAtom(at, false);
       }
     } // END loop over solvent residues
+    //cmask.MaskInfo(); // DEBUG
+    //mprintf("DEBUG: Should select %i atoms.\n", firstSolventAtom + (nSolventInCell*topOut.Res(firstSolventRes).NumAtoms()));
 
     // How far off is it?
     int diff = nsolvent_ - nSolventInCell;
     mprintf("DEBUG:\t%i solvent residues in cell. Diff: %i\n", nSolventInCell, diff);
-    // If this is the first time trhough choose an appropriate change val
+    // If this is the first time through choose an appropriate change val
     if (ntries == 0) {
       change = 0.001;
     }
@@ -796,6 +809,23 @@ int Solvate::SolvateBoxWithExactNumber(Topology& topOut, Frame& frameOut, Cpptra
     }
   } // END cell loop
 
+//  cmask.MaskInfo();
+  AtomMask imask( cmask.ConvertToIntMask(), topOut.Natom() );
+//  imask.MaskInfo();
+  Topology* newParm = topOut.modifyStateByMask( imask );
+  if (newParm == 0) {
+    mprinterr("Error: Could not create topology with the desired # of solvent.\n");
+    return 1;
+  }
+  topOut = *newParm;
+  delete newParm;
+  topOut.Brief("Topology with target # of solvent:");
+
+  Frame newFrame;
+  newFrame.SetupFrameV(topOut.Atoms(), frameOut.CoordsInfo());
+  newFrame.SetFrame( frameOut, imask );
+  frameOut = newFrame;
+
   return 0;
 }
 

From b2f1fd3c04c699fc3505dd8fcaa7fda1968633b6 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 25 Jan 2026 13:54:00 -0500
Subject: [PATCH 1255/1492] Do final cell construction

---
 src/Structure/Solvate.cpp | 71 ++++++++++++++++++++++++++++++++++++++-
 src/Structure/Solvate.h   |  2 ++
 2 files changed, 72 insertions(+), 1 deletion(-)

diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index 4937208783..8c151fc29e 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -826,7 +826,7 @@ int Solvate::SolvateBoxWithExactNumber(Topology& topOut, Frame& frameOut, Cpptra
   newFrame.SetFrame( frameOut, imask );
   frameOut = newFrame;
 
-  return 0;
+  return finishBox(topOut, frameOut, set0);
 }
 
 /** Create box, fill with solvent */
@@ -963,6 +963,8 @@ int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::Parame
                   solventFrame, SOLVENTBOX.Top(), frameOut, topOut,
                   soluteRadii, solventRadii);
 
+  return finishBox(topOut, frameOut, set0);
+/*
   // Define the size of the new solvent/solute system
   soluteRadii = getAtomRadii(soluteMaxR, topOut, set0) ;
   if (setVdwBoundingBox(boxX, boxY, boxZ, soluteRadii, frameOut, false)) {
@@ -1024,6 +1026,73 @@ int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::Parame
     }
   }
 
+  return 0;*/
+}
+
+/** Finish box */
+int Solvate::finishBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::ParameterSet const& set0) const {
+  // Define the size of the new solvent/solute system
+  double boxX, boxY, boxZ;
+  double soluteMaxR;
+  std::vector<double> soluteRadii = getAtomRadii(soluteMaxR, topOut, set0) ;
+  if (setVdwBoundingBox(boxX, boxY, boxZ, soluteRadii, frameOut, false)) {
+    mprinterr("Error: Setting vdw bounding box for solute/solvent system failed.\n", topOut.c_str());
+    return 1;
+  }
+  if (doTruncatedOct_) {
+    double dAngle = 0;
+    ewald_rotate(frameOut, dAngle);
+    //mprintf("EwaldRotate: %f\n", dAngle);
+    // Add an angstrom to the desired box size rather than using the bounding box size
+    dAngle = clipX_ + .5;
+    boxX = boxY = boxZ = dAngle * sqrt(3.0) * 0.5;
+  }
+
+  // Setup box
+  double boxBeta = 90.0;
+  if (doTruncatedOct_) {
+    boxBeta = Box::TruncatedOctAngle();
+    boxX *= 2.0;
+    boxY *= 2.0;
+    boxZ *= 2.0;
+  }
+  //mprintf("Max: %f %f %f\n", boxX, boxY, boxZ);
+  frameOut.ModifyBox().SetupFromXyzAbg(boxX, boxY, boxZ, boxBeta, boxBeta, boxBeta);
+  frameOut.BoxCrd().PrintInfo("\t  ");
+  topOut.SetParmBox( frameOut.BoxCrd() );
+  //mprintf("\t  Total vdw box size:%s%5.3f %5.3f %5.3f angstroms.\n", "                   ",
+  //        frameOut.BoxCrd().Param(Box::X),
+  //        frameOut.BoxCrd().Param(Box::Y),
+  //        frameOut.BoxCrd().Param(Box::Z));
+  mprintf("\t  Volume: %5.3lf A^3\n", frameOut.BoxCrd().CellVolume());
+  // Sum mass
+  double sumMass = 0.0;
+  for (int at = 0; at < topOut.Natom(); at++) {
+    if (topOut[at].HasType()) {
+      Cpptraj::Parm::ParmHolder<AtomType>::const_iterator it = set0.AT().GetParam( TypeNameHolder(topOut[at].Type()) );
+      if (it != set0.AT().end()) {
+        sumMass += it->second.Mass();
+      }
+    }
+  }
+  if (sumMass > 0.0) {
+    mprintf("\t  Total mass %5.3f amu,  Density %5.3lf g/cc\n", sumMass, sumMass / (frameOut.BoxCrd().CellVolume() * 0.602204));
+  } else {
+    mprintf("Warning: Mass could not be determined, so density unknown (i.e. type of all atoms could not be found)\n");
+  }
+  // Center if needed
+  if (center_) {
+    double dX2 = boxX * 0.5;
+    double dY2 = boxY * 0.5;
+    double dZ2 = boxZ * 0.5;
+    double* xptr = frameOut.xAddress();
+    for (int at = 0; at < frameOut.Natom(); at++, xptr += 3)
+    {
+      xptr[0] += dX2;
+      xptr[1] += dY2;
+      xptr[2] += dZ2;
+    }
+  }
   return 0;
 }
 
diff --git a/src/Structure/Solvate.h b/src/Structure/Solvate.h
index 307e788b85..a60750cb4e 100644
--- a/src/Structure/Solvate.h
+++ b/src/Structure/Solvate.h
@@ -46,6 +46,8 @@ class Solvate {
     static unsigned int nBoxesInCube(int);
     /// Solvate with box and specified number of solvent
     int SolvateBoxWithExactNumber(Topology&, Frame&, Cpptraj::Parm::ParameterSet const&, DataSetList const&);
+    // Finish box
+    int finishBox(Topology&, Frame&, Cpptraj::Parm::ParameterSet const&) const;
     /// Get buffer arguments
     int getBufferArg(ArgList&, double);
     /// Get radii for atoms in topology

From 016a028df566601aab4e9f88e4132c183276c573 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 25 Jan 2026 18:36:33 -0500
Subject: [PATCH 1256/1492] Start trying to do truncated octahedron

---
 src/Structure/Solvate.cpp | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index 8c151fc29e..6a5d4d59bb 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -91,7 +91,7 @@ int Solvate::InitSolvate(ArgList& argIn, bool octIn, int debugIn) {
   center_ = !argIn.hasKey("nocenter");
 
   if (doTruncatedOct_) {
-    if (!clip_) {
+    if (!clip_ && nsolvent_ < 1) {
       mprinterr("Error: Truncated octahedral box currently requires 'clip'.\n");
       return 1;
     }
@@ -659,9 +659,14 @@ int Solvate::SolvateBoxWithExactNumber(Topology& topOut, Frame& frameOut, Cpptra
   frameOut.CenterOnOrigin(false);
 
   // FIXME make user-specifiable
-  double alpha = 90.0;
-  double beta  = 90.0;
-  double gamma = 90.0;
+  double boxBeta;
+  if (doTruncatedOct_)
+    boxBeta = Box::TruncatedOctAngle();
+  else
+    boxBeta = 90.0;
+  double alpha = boxBeta;
+  double beta  = boxBeta;
+  double gamma = boxBeta;
   int negtol = -5;
 
   double bufX = boxX + ((maxX - boxX) / 2.0);

From 4afebfc00ff1a24d46e0c177814cbf68fda958b6 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 26 Jan 2026 13:40:18 -0500
Subject: [PATCH 1257/1492] Cannot finish box from Solvate with specified
 numbers the same way as the original since the method for determining waters
 out of the box is different. Just use the cell we have been using. Probably
 will require some imaging.

---
 src/Structure/Solvate.cpp | 104 +++++++++-----------------------------
 src/Structure/Solvate.h   |   2 -
 2 files changed, 24 insertions(+), 82 deletions(-)

diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index 6a5d4d59bb..e459b74c35 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -90,8 +90,8 @@ int Solvate::InitSolvate(ArgList& argIn, bool octIn, int debugIn) {
   closeness_ = argIn.getKeyDouble("closeness", 1.0);
   center_ = !argIn.hasKey("nocenter");
 
-  if (doTruncatedOct_) {
-    if (!clip_ && nsolvent_ < 1) {
+  if (doTruncatedOct_ && nsolvent_ < 1) {
+    if (!clip_) {
       mprinterr("Error: Truncated octahedral box currently requires 'clip'.\n");
       return 1;
     }
@@ -659,20 +659,28 @@ int Solvate::SolvateBoxWithExactNumber(Topology& topOut, Frame& frameOut, Cpptra
   frameOut.CenterOnOrigin(false);
 
   // FIXME make user-specifiable
-  double boxBeta;
-  if (doTruncatedOct_)
-    boxBeta = Box::TruncatedOctAngle();
-  else
-    boxBeta = 90.0;
-  double alpha = boxBeta;
-  double beta  = boxBeta;
-  double gamma = boxBeta;
+  double alpha, beta, gamma;
+  if (doTruncatedOct_) {
+    alpha = Box::TruncatedOctAngle();
+    beta = alpha;
+    gamma = alpha;
+  } else {
+    alpha = 90.0;
+    beta  = 90.0;
+    gamma = 90.0;
+  }
   int negtol = -5;
 
   double bufX = boxX + ((maxX - boxX) / 2.0);
   double bufY = boxY + ((maxY - boxY) / 2.0);
   double bufZ = boxZ + ((maxZ - boxZ) / 2.0);
 
+  if (doTruncatedOct_) {
+    if (bufX >= bufY && bufX >= bufZ) { bufY = bufX; bufZ = bufX; }
+    if (bufY >= bufX && bufY >= bufZ) { bufX = bufY; bufZ = bufY; }
+    if (bufZ >= bufX && bufZ >= bufY) { bufX = bufZ; bufY = bufZ; }
+  }
+
   // Mask selecting everything that should be kept. Always keep solute
   CharMask cmask( topOut.Natom() );
   for (int ires = 0; ires < firstSolventRes; ires++) {
@@ -831,7 +839,12 @@ int Solvate::SolvateBoxWithExactNumber(Topology& topOut, Frame& frameOut, Cpptra
   newFrame.SetFrame( frameOut, imask );
   frameOut = newFrame;
 
-  return finishBox(topOut, frameOut, set0);
+  frameOut.SetBox( newBox );
+  frameOut.BoxCrd().PrintInfo("\t  ");
+  topOut.SetParmBox( frameOut.BoxCrd() );
+  mprintf("\t  Volume: %5.3lf A^3\n", frameOut.BoxCrd().CellVolume());
+
+  return 0;
 }
 
 /** Create box, fill with solvent */
@@ -968,8 +981,6 @@ int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::Parame
                   solventFrame, SOLVENTBOX.Top(), frameOut, topOut,
                   soluteRadii, solventRadii);
 
-  return finishBox(topOut, frameOut, set0);
-/*
   // Define the size of the new solvent/solute system
   soluteRadii = getAtomRadii(soluteMaxR, topOut, set0) ;
   if (setVdwBoundingBox(boxX, boxY, boxZ, soluteRadii, frameOut, false)) {
@@ -1031,73 +1042,6 @@ int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::Parame
     }
   }
 
-  return 0;*/
-}
-
-/** Finish box */
-int Solvate::finishBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::ParameterSet const& set0) const {
-  // Define the size of the new solvent/solute system
-  double boxX, boxY, boxZ;
-  double soluteMaxR;
-  std::vector<double> soluteRadii = getAtomRadii(soluteMaxR, topOut, set0) ;
-  if (setVdwBoundingBox(boxX, boxY, boxZ, soluteRadii, frameOut, false)) {
-    mprinterr("Error: Setting vdw bounding box for solute/solvent system failed.\n", topOut.c_str());
-    return 1;
-  }
-  if (doTruncatedOct_) {
-    double dAngle = 0;
-    ewald_rotate(frameOut, dAngle);
-    //mprintf("EwaldRotate: %f\n", dAngle);
-    // Add an angstrom to the desired box size rather than using the bounding box size
-    dAngle = clipX_ + .5;
-    boxX = boxY = boxZ = dAngle * sqrt(3.0) * 0.5;
-  }
-
-  // Setup box
-  double boxBeta = 90.0;
-  if (doTruncatedOct_) {
-    boxBeta = Box::TruncatedOctAngle();
-    boxX *= 2.0;
-    boxY *= 2.0;
-    boxZ *= 2.0;
-  }
-  //mprintf("Max: %f %f %f\n", boxX, boxY, boxZ);
-  frameOut.ModifyBox().SetupFromXyzAbg(boxX, boxY, boxZ, boxBeta, boxBeta, boxBeta);
-  frameOut.BoxCrd().PrintInfo("\t  ");
-  topOut.SetParmBox( frameOut.BoxCrd() );
-  //mprintf("\t  Total vdw box size:%s%5.3f %5.3f %5.3f angstroms.\n", "                   ",
-  //        frameOut.BoxCrd().Param(Box::X),
-  //        frameOut.BoxCrd().Param(Box::Y),
-  //        frameOut.BoxCrd().Param(Box::Z));
-  mprintf("\t  Volume: %5.3lf A^3\n", frameOut.BoxCrd().CellVolume());
-  // Sum mass
-  double sumMass = 0.0;
-  for (int at = 0; at < topOut.Natom(); at++) {
-    if (topOut[at].HasType()) {
-      Cpptraj::Parm::ParmHolder<AtomType>::const_iterator it = set0.AT().GetParam( TypeNameHolder(topOut[at].Type()) );
-      if (it != set0.AT().end()) {
-        sumMass += it->second.Mass();
-      }
-    }
-  }
-  if (sumMass > 0.0) {
-    mprintf("\t  Total mass %5.3f amu,  Density %5.3lf g/cc\n", sumMass, sumMass / (frameOut.BoxCrd().CellVolume() * 0.602204));
-  } else {
-    mprintf("Warning: Mass could not be determined, so density unknown (i.e. type of all atoms could not be found)\n");
-  }
-  // Center if needed
-  if (center_) {
-    double dX2 = boxX * 0.5;
-    double dY2 = boxY * 0.5;
-    double dZ2 = boxZ * 0.5;
-    double* xptr = frameOut.xAddress();
-    for (int at = 0; at < frameOut.Natom(); at++, xptr += 3)
-    {
-      xptr[0] += dX2;
-      xptr[1] += dY2;
-      xptr[2] += dZ2;
-    }
-  }
   return 0;
 }
 
diff --git a/src/Structure/Solvate.h b/src/Structure/Solvate.h
index a60750cb4e..307e788b85 100644
--- a/src/Structure/Solvate.h
+++ b/src/Structure/Solvate.h
@@ -46,8 +46,6 @@ class Solvate {
     static unsigned int nBoxesInCube(int);
     /// Solvate with box and specified number of solvent
     int SolvateBoxWithExactNumber(Topology&, Frame&, Cpptraj::Parm::ParameterSet const&, DataSetList const&);
-    // Finish box
-    int finishBox(Topology&, Frame&, Cpptraj::Parm::ParameterSet const&) const;
     /// Get buffer arguments
     int getBufferArg(ArgList&, double);
     /// Get radii for atoms in topology

From 5bfe27992a7e4bb68908c17347969527c8ef8931 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 27 Jan 2026 10:11:16 -0500
Subject: [PATCH 1258/1492] Try to use autoimage. Still looks like there are
 visual artefacts

---
 src/Action_AutoImage.h    |  4 +++-
 src/Structure/Solvate.cpp | 24 ++++++++++++++++++++++++
 2 files changed, 27 insertions(+), 1 deletion(-)

diff --git a/src/Action_AutoImage.h b/src/Action_AutoImage.h
index 83b54c3226..475c60feb4 100644
--- a/src/Action_AutoImage.h
+++ b/src/Action_AutoImage.h
@@ -11,10 +11,12 @@ class Action_AutoImage : public Action {
     ~Action_AutoImage();
     DispatchObject* Alloc() const { return (DispatchObject*)new Action_AutoImage(); }
     void Help() const;
-  private:
+
     Action::RetType Init(ArgList&, ActionInit&, int);
     Action::RetType Setup(ActionSetup&);
     Action::RetType DoAction(int, ActionFrame&);
+
+  private:
     void Print() {}
 
     enum Mode { BY_DISTANCE=0, BY_VECTOR, UNSPECIFIED };
diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index e459b74c35..eec3398979 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -1,4 +1,5 @@
 #include "Solvate.h"
+#include "../Action_AutoImage.h"
 #include "../ArgList.h"
 #include "../CharMask.h"
 #include "../CpptrajStdio.h"
@@ -844,6 +845,29 @@ int Solvate::SolvateBoxWithExactNumber(Topology& topOut, Frame& frameOut, Cpptra
   topOut.SetParmBox( frameOut.BoxCrd() );
   mprintf("\t  Volume: %5.3lf A^3\n", frameOut.BoxCrd().CellVolume());
 
+  // Reimage FIXME create separate init routine for autoimage
+  Action_AutoImage autoimage;
+  ArgList actionargs;
+  DataSetList tempdsl;
+  DataFileList tempdfl;
+  ActionInit AI(tempdsl, tempdfl);
+  if (autoimage.Init(actionargs, AI, debug_) != Action::OK) {
+    mprinterr("Error: Could not initialize autoimage for post-solvate.\n");
+    return 1;
+  }
+  ActionSetup AS( &topOut, frameOut.CoordsInfo(), 1 );
+  Action::RetType ret = autoimage.Setup( AS );
+  if ( ret == Action::ERR || ret == Action::SKIP ) {
+    mprinterr("Error: Could not setup autoimage for post-solvate.\n");
+    return 1;
+  }
+  ActionFrame frm( &frameOut, 0 );
+  ret = autoimage.DoAction(0, frm);
+  if (ret == Action::ERR) {
+    mprinterr("Error: Could not autoimage post-solvate.\n");
+    return 1;
+  }
+
   return 0;
 }
 

From 8f6c85d33fec36469876a19498733ff0afe55bc8 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 27 Jan 2026 10:59:29 -0500
Subject: [PATCH 1259/1492] Make density calc separate

---
 src/Structure/Solvate.cpp | 31 +++++++++++++++++++++++++++----
 src/Structure/Solvate.h   |  2 ++
 2 files changed, 29 insertions(+), 4 deletions(-)

diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index eec3398979..f7d2c5b8b5 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -489,6 +489,26 @@ const
             dXWidth, dYWidth, dZWidth );
 }
 
+/** Calculate total density */
+void Solvate::calculateDensity(Topology const& topOut, Frame const& frameOut, Cpptraj::Parm::ParameterSet const& set0)
+{
+  // Sum mass
+  double sumMass = 0.0;
+  for (int at = 0; at < topOut.Natom(); at++) {
+    if (topOut[at].HasType()) {
+      Cpptraj::Parm::ParmHolder<AtomType>::const_iterator it = set0.AT().GetParam( TypeNameHolder(topOut[at].Type()) );
+      if (it != set0.AT().end()) {
+        sumMass += it->second.Mass();
+      }
+    }
+  }
+  if (sumMass > 0.0) {
+    mprintf("\t  Total mass %5.3f amu,  Density %5.3lf g/cc\n", sumMass, sumMass / (frameOut.BoxCrd().CellVolume() * 0.602204));
+  } else {
+    mprintf("Warning: Mass could not be determined, so density unknown (i.e. type of all atoms could not be found)\n");
+  }
+}
+
 /** Calculate the number of boxes needed to create a given layer */
 unsigned int Solvate::nBoxesInLayer(int n) {
   // Special case; no layers is 1 cube
@@ -846,7 +866,7 @@ int Solvate::SolvateBoxWithExactNumber(Topology& topOut, Frame& frameOut, Cpptra
   mprintf("\t  Volume: %5.3lf A^3\n", frameOut.BoxCrd().CellVolume());
 
   // Reimage FIXME create separate init routine for autoimage
-  Action_AutoImage autoimage;
+/*  Action_AutoImage autoimage;
   ArgList actionargs;
   DataSetList tempdsl;
   DataFileList tempdfl;
@@ -866,7 +886,9 @@ int Solvate::SolvateBoxWithExactNumber(Topology& topOut, Frame& frameOut, Cpptra
   if (ret == Action::ERR) {
     mprinterr("Error: Could not autoimage post-solvate.\n");
     return 1;
-  }
+  }*/
+
+  calculateDensity(topOut, frameOut, set0);
 
   return 0;
 }
@@ -1037,7 +1059,8 @@ int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::Parame
   //        frameOut.BoxCrd().Param(Box::Y),
   //        frameOut.BoxCrd().Param(Box::Z));
   mprintf("\t  Volume: %5.3lf A^3\n", frameOut.BoxCrd().CellVolume());
-  // Sum mass
+  calculateDensity(topOut, frameOut, set0);
+/*  // Sum mass
   double sumMass = 0.0;
   for (int at = 0; at < topOut.Natom(); at++) {
     if (topOut[at].HasType()) {
@@ -1051,7 +1074,7 @@ int Solvate::SolvateBox(Topology& topOut, Frame& frameOut, Cpptraj::Parm::Parame
     mprintf("\t  Total mass %5.3f amu,  Density %5.3lf g/cc\n", sumMass, sumMass / (frameOut.BoxCrd().CellVolume() * 0.602204));
   } else {
     mprintf("Warning: Mass could not be determined, so density unknown (i.e. type of all atoms could not be found)\n");
-  }
+  }*/
   // Center if needed
   if (center_) {
     double dX2 = boxX * 0.5;
diff --git a/src/Structure/Solvate.h b/src/Structure/Solvate.h
index 307e788b85..a3a2c5df3f 100644
--- a/src/Structure/Solvate.h
+++ b/src/Structure/Solvate.h
@@ -40,6 +40,8 @@ class Solvate {
     DataSet_Coords* GetSolventUnit(DataSetList const&) const;
     /// Adjust box widths
     void adjustBoxWidths(double&, double&, double&, double&, double&, double&) const;
+    /// Calculate density
+    static void calculateDensity(Topology const&, Frame const&, Cpptraj::Parm::ParameterSet const&);
     /// \return number of boxes needed to create layer
     static unsigned int nBoxesInLayer(int);
     /// \return number of boxes needed to create cube 

From cc594584048e492eec96366dddc5ce34d1ff6a42 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 27 Jan 2026 11:06:00 -0500
Subject: [PATCH 1260/1492] Add some debug

---
 src/Structure/Solvate.cpp | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index f7d2c5b8b5..aafaa4b5df 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -11,6 +11,9 @@
 #include <algorithm> //std::max
 #include <cmath> // cos, sin, sqrt
 
+// DEBUG
+//#inc lude "../Trajout_Single.h"
+
 using namespace Cpptraj::Structure;
 
 /** CONSTRUCTOR */
@@ -641,6 +644,13 @@ int Solvate::SolvateBoxWithExactNumber(Topology& topOut, Frame& frameOut, Cpptra
   addSolventUnits(iX, iY, iZ, soluteMaxR, dXStart, dYStart, dZStart, solventX, solventY, solventZ,
                   solventFrame, SOLVENTBOX.Top(), frameOut, topOut,
                   soluteRadii, solventRadii);
+  // DEBUG
+//  Trajout_Single trajout;
+//  trajout.InitTrajWrite("BigCube.mol2", ArgList(), DataSetList(), TrajectoryFile::MOL2FILE);
+//  trajout.SetupTrajWrite(&topOut, frameOut.CoordsInfo(), 1);
+//  trajout.WriteSingle(0, frameOut);
+//  trajout.EndTraj();
+  // END DEBUG
 
   // Define the size of the new solvent/solute system
   double maxX, maxY, maxZ;

From 0921ffa9259824157db8a67b998f130d1f29c8ba Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 27 Jan 2026 11:28:02 -0500
Subject: [PATCH 1261/1492] Actually increment ntries. Do the autoimage at the
 end

---
 src/Structure/Solvate.cpp | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index aafaa4b5df..4a651b9479 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -847,6 +847,7 @@ int Solvate::SolvateBoxWithExactNumber(Topology& topOut, Frame& frameOut, Cpptra
     } // END change calc
 
     // Safety valve
+    ntries++;
     if (ntries > 100) {
       mprintf("\tTaking too long - moving on...\n");
       loop = false;
@@ -876,7 +877,7 @@ int Solvate::SolvateBoxWithExactNumber(Topology& topOut, Frame& frameOut, Cpptra
   mprintf("\t  Volume: %5.3lf A^3\n", frameOut.BoxCrd().CellVolume());
 
   // Reimage FIXME create separate init routine for autoimage
-/*  Action_AutoImage autoimage;
+  Action_AutoImage autoimage;
   ArgList actionargs;
   DataSetList tempdsl;
   DataFileList tempdfl;
@@ -896,7 +897,7 @@ int Solvate::SolvateBoxWithExactNumber(Topology& topOut, Frame& frameOut, Cpptra
   if (ret == Action::ERR) {
     mprinterr("Error: Could not autoimage post-solvate.\n");
     return 1;
-  }*/
+  }
 
   calculateDensity(topOut, frameOut, set0);
 

From 80db09f543e82602d2c21a7d94faf07715bdcec2 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 27 Jan 2026 15:25:07 -0500
Subject: [PATCH 1262/1492] Put sugar options in SugarBuilder

---
 src/Exec_Build.cpp             | 11 ++++-------
 src/Exec_PrepareForLeap.cpp    | 17 ++++-------------
 src/Structure/Solvate.cpp      | 10 ++++++++++
 src/Structure/SugarBuilder.cpp | 19 +++++++++++++++++++
 src/Structure/SugarBuilder.h   |  8 ++++++--
 5 files changed, 43 insertions(+), 22 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 93e7c7c5a7..6bd4e0a1b2 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -831,6 +831,7 @@ void Exec_Build::Help() const
           "\t          %s |\n"
           "\t  setbox %s}]\n"
           "%s"
+          "%s"
           "%s",
           Cpptraj::Structure::Creator::other_keywords_,
           Cpptraj::Structure::Creator::template_keywords_,
@@ -839,7 +840,8 @@ void Exec_Build::Help() const
           Cpptraj::Structure::Solvate::SolvateKeywords2(),
           Cpptraj::Structure::Solvate::SetboxKeywords(),
           Cpptraj::Structure::HisProt::keywords_,
-          Cpptraj::Structure::Disulfide::keywords_
+          Cpptraj::Structure::Disulfide::keywords_,
+          Cpptraj::Structure::SugarBuilder::keywords_
          );
   mprintf("  Build complete topology and parameters from given crdset.\n");
 }
@@ -1464,12 +1466,7 @@ int Exec_Build::StructurePrepAndFillTemplates(ArgList& argIn, Topology& topIn, F
   Cpptraj::Structure::SugarBuilder sugarBuilder(debug_);
   if (doSugar_) {
     // Init options
-    if (sugarBuilder.InitOptions( argIn.hasKey("hasglycam"),
-                                  argIn.getKeyDouble("rescut", 8.0),
-                                  argIn.getKeyDouble("bondoffset", 0.2),
-                                  argIn.GetStringKey("sugarmask"),
-                                  argIn.GetStringKey("determinesugarsby", "geometry"),
-                                  argIn.GetStringKey("resmapfile") ))
+    if (sugarBuilder.InitSugarBuilder( argIn ))
     {
       mprinterr("Error: Sugar options init failed.\n");
       return 1;
diff --git a/src/Exec_PrepareForLeap.cpp b/src/Exec_PrepareForLeap.cpp
index d552cd173b..14591a1b00 100644
--- a/src/Exec_PrepareForLeap.cpp
+++ b/src/Exec_PrepareForLeap.cpp
@@ -413,12 +413,7 @@ void Exec_PrepareForLeap::Help() const
           "\t[molmask <molmask> ...] [determinemolmask <mask>]\n"
           "%s"
           "%s"
-          "\t[{nosugars |\n"
-          "\t  sugarmask <sugarmask> [noc1search] [nosplitres]\n"
-          "\t  [rescut <residue cutoff>] [bondoffset <offset>]\n"
-          "\t  [resmapfile <file>]\n"
-          "\t  [hasglycam] [determinesugarsby {geom|name}]\n"
-          "\t }]\n"
+          "%s"
           "  Prepare the structure in the given coords set for easier processing\n"
           "  with the LEaP program from AmberTools. Any existing/potential\n"
           "  disulfide bonds will be identified and the residue names changed\n"
@@ -431,7 +426,8 @@ void Exec_PrepareForLeap::Help() const
           "  The command will attempt to download parameters for unknown\n"
           "  residues unless 'nodlparams' is specified.\n",
           HisProt::keywords_,
-          Disulfide::keywords_
+          Disulfide::keywords_,
+          SugarBuilder::keywords_
          );
 }
 
@@ -572,12 +568,7 @@ Exec::RetType Exec_PrepareForLeap::Execute(CpptrajState& State, ArgList& argIn)
   SugarBuilder sugarBuilder(debug_);
   if (prepare_sugars) {
     // Init options
-    if (sugarBuilder.InitOptions( argIn.hasKey("hasglycam"),
-                                  argIn.getKeyDouble("rescut", 8.0),
-                                  argIn.getKeyDouble("bondoffset", 0.2),
-                                  argIn.GetStringKey("sugarmask"),
-                                  argIn.GetStringKey("determinesugarsby", "geometry"),
-                                  argIn.GetStringKey("resmapfile") ))
+    if (sugarBuilder.InitSugarBuilder( argIn ))
     {
       mprinterr("Error: Sugar options init failed.\n");
       return CpptrajState::ERR;
diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index 4a651b9479..8a2472f7e8 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -725,6 +725,8 @@ int Solvate::SolvateBoxWithExactNumber(Topology& topOut, Frame& frameOut, Cpptra
 
   // This loop uses the same logic as my old Solvate.sh script
   // (https://github.com/drroe/Solvate.sh/blob/master/Solvate.sh)
+  int smallestNegDiff = 0;
+  Vec3 smallestBuf(0.0);
   bool loop = true;
   int ntries = 0;
   double change = 0.001;
@@ -771,6 +773,13 @@ int Solvate::SolvateBoxWithExactNumber(Topology& topOut, Frame& frameOut, Cpptra
     // How far off is it?
     int diff = nsolvent_ - nSolventInCell;
     mprintf("DEBUG:\t%i solvent residues in cell. Diff: %i\n", nSolventInCell, diff);
+
+    if (diff < 0) {
+      if (smallestNegDiff == 0 || diff > smallestNegDiff) {
+        smallestNegDiff = diff;
+        smallestBuf = Vec3(bufX, bufY, bufZ);
+      }
+    }  
     // If this is the first time through choose an appropriate change val
     if (ntries == 0) {
       change = 0.001;
@@ -851,6 +860,7 @@ int Solvate::SolvateBoxWithExactNumber(Topology& topOut, Frame& frameOut, Cpptra
     if (ntries > 100) {
       mprintf("\tTaking too long - moving on...\n");
       loop = false;
+      mprintf("DEBUG: SmallestNegDiff %i : %f %f %f\n", smallestNegDiff, smallestBuf[0], smallestBuf[1], smallestBuf[2]);
     }
   } // END cell loop
 
diff --git a/src/Structure/SugarBuilder.cpp b/src/Structure/SugarBuilder.cpp
index 3632806f0d..bb733177eb 100644
--- a/src/Structure/SugarBuilder.cpp
+++ b/src/Structure/SugarBuilder.cpp
@@ -29,6 +29,25 @@ SugarBuilder::~SugarBuilder() {
   if (FGB_ != 0) delete FGB_;
 }
 
+/** Sugar options */
+const char* SugarBuilder::keywords_ =
+  "\t[{nosugars |\n"
+  "\t  sugarmask <sugarmask> [noc1search] [nosplitres]\n"
+  "\t  [rescut <residue cutoff>] [bondoffset <offset>]\n"
+  "\t  [resmapfile <file>]\n"
+  "\t  [hasglycam] [determinesugarsby {geom|name}]\n"
+  "\t }]\n";
+
+/** Get options from arglist */
+int SugarBuilder::InitSugarBuilder(ArgList& argIn) {
+  return InitOptions( argIn.hasKey("hasglycam"),
+                      argIn.getKeyDouble("rescut", 8.0),
+                      argIn.getKeyDouble("bondoffset", 0.2),
+                      argIn.GetStringKey("sugarmask"),
+                      argIn.GetStringKey("determinesugarsby", "geometry"),
+                      argIn.GetStringKey("resmapfile") );
+}
+
 /** Initialize options. */
 int SugarBuilder::InitOptions(bool hasGlycamIn,
                               double rescutIn,
diff --git a/src/Structure/SugarBuilder.h b/src/Structure/SugarBuilder.h
index 87b56bd5bd..b0e116069e 100644
--- a/src/Structure/SugarBuilder.h
+++ b/src/Structure/SugarBuilder.h
@@ -20,8 +20,10 @@ class SugarBuilder {
     SugarBuilder(int);
     /// DESTRUCTOR
     ~SugarBuilder();
-    /// Init options: hasGlycam, residue cutoff, bond offset, sugar mask str, determineSugarsBy, resmapfile
-    int InitOptions(bool, double, double, std::string const&, std::string const&, std::string const&);
+    /// Keywords
+    static const char* keywords_;
+    /// Initialize from ArgList
+    int InitSugarBuilder(ArgList&);
     /// \return true if given res name is a recognized PDB sugar
     bool IsRecognizedPdbSugar(NameType const&) const;
     /// ID sugar rings, find missing C1 links, split off functional groups
@@ -47,6 +49,8 @@ class SugarBuilder {
     typedef std::pair<std::string, int> ResIdxPairType;
     typedef std::map<std::string, int> ResIdxMapType;
 
+    /// Init options: hasGlycam, residue cutoff, bond offset, sugar mask str, determineSugarsBy, resmapfile
+    int InitOptions(bool, double, double, std::string const&, std::string const&, std::string const&);
     /// Set a reduced PDB res to glycam map when dat file not found.
     void SetGlycamPdbResMap();
     /// Load PDB res to glycam map from dat file

From 260fc8c68e37f5a35093398943c3a66bce5d04e8 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 27 Jan 2026 15:28:40 -0500
Subject: [PATCH 1263/1492] Add help text for adding ions

---
 src/Exec_Build.cpp | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 6bd4e0a1b2..3dd5db467b 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -830,6 +830,8 @@ void Exec_Build::Help() const
           "\t[{{solvatebox|solvateoct} %s\n"
           "\t          %s |\n"
           "\t  setbox %s}]\n"
+          "\t[addionsrand ion1 <name1> nion1 <num1> [ion2 <name2> nion2 <num2>]\n"
+          "\t  [minsep <dist>] [ionseed <seed>]]\n"
           "%s"
           "%s"
           "%s",

From 1b6a6bd022305f0bf00daf282b6b88dc55ac4f52 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 27 Jan 2026 15:40:03 -0500
Subject: [PATCH 1264/1492] Add another safety valve

---
 src/Structure/Solvate.cpp | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index 8a2472f7e8..abb6f5d176 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -727,6 +727,7 @@ int Solvate::SolvateBoxWithExactNumber(Topology& topOut, Frame& frameOut, Cpptra
   // (https://github.com/drroe/Solvate.sh/blob/master/Solvate.sh)
   int smallestNegDiff = 0;
   Vec3 smallestBuf(0.0);
+  int nTimesSmallestSeen = 0;
   bool loop = true;
   int ntries = 0;
   double change = 0.001;
@@ -778,6 +779,11 @@ int Solvate::SolvateBoxWithExactNumber(Topology& topOut, Frame& frameOut, Cpptra
       if (smallestNegDiff == 0 || diff > smallestNegDiff) {
         smallestNegDiff = diff;
         smallestBuf = Vec3(bufX, bufY, bufZ);
+        nTimesSmallestSeen = 1;
+      } else if (smallestNegDiff == diff) {
+        nTimesSmallestSeen++;
+        // Update smallest buffer; presumably is closer
+        smallestBuf = Vec3(bufX, bufY, bufZ);
       }
     }  
     // If this is the first time through choose an appropriate change val
@@ -785,7 +791,7 @@ int Solvate::SolvateBoxWithExactNumber(Topology& topOut, Frame& frameOut, Cpptra
       change = 0.001;
     }
     // See if we have tol more waters than the target TODO
-    if (diff < 0 && diff >= negtol) {
+    if ((diff < 0 && nTimesSmallestSeen > 4) || (diff < 0 && diff >= negtol)) {
       // Close enough, just remove the last water residue(s)
       int nToRemove = -diff;
       mprintf("\tOnly %i solvent molecules off, removing them.\n", nToRemove);
@@ -860,7 +866,7 @@ int Solvate::SolvateBoxWithExactNumber(Topology& topOut, Frame& frameOut, Cpptra
     if (ntries > 100) {
       mprintf("\tTaking too long - moving on...\n");
       loop = false;
-      mprintf("DEBUG: SmallestNegDiff %i : %f %f %f\n", smallestNegDiff, smallestBuf[0], smallestBuf[1], smallestBuf[2]);
+      mprintf("DEBUG: SmallestNegDiff %i (%i) : %f %f %f\n", smallestNegDiff, nTimesSmallestSeen, smallestBuf[0], smallestBuf[1], smallestBuf[2]);
     }
   } // END cell loop
 

From fe0ff27ceddd1afc5faa30e9a59df2f958bf8cbe Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 30 Jan 2026 10:58:27 -0500
Subject: [PATCH 1265/1492] Add function to sort typenames by making the first
 typename < last typename

---
 src/TypeNameHolder.h | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/src/TypeNameHolder.h b/src/TypeNameHolder.h
index b383ee43ee..67ce9e2399 100644
--- a/src/TypeNameHolder.h
+++ b/src/TypeNameHolder.h
@@ -118,6 +118,32 @@ class TypeNameHolder {
         tstr.append( " " + std::string( *(*it) ) );
       return tstr;
     }
+    /// Sort typenames so that the first typename < the last
+    void SortNames(NameType const& wc) {
+      if (types_.size() < 2) return;
+      unsigned int last = types_.size() - 1;
+      // Replace wildcards with spaces so they appear first
+      if (wc.len() > 0) {
+        if (types_[0]    == wc) types_[0]    = NameType(" ");
+        if (types_[last] == wc) types_[last] = NameType(" ");
+      }
+      if (types_[0] > types_[last]) {
+        // Need to swap TODO record if we swapped these names?
+        if (types_.size() < 4)
+          tswap(types_[0], types_[last]);
+        else {
+          unsigned int half = types_.size() / 2;
+          unsigned int jj = last;
+          for (unsigned int ii = 0; ii < half; ii++, jj--)
+            tswap(types_[ii], types_[jj]);
+        }
+      }
+      // Restore wildcards
+      if (wc.len() > 0) {
+        if (types_[0]    == " ") types_[0]    = wc;
+        if (types_[last] == " ") types_[last] = wc;
+      }
+    }
     /// Sort typenames alphabetically, preserving the 3rd position (for impropers)
     void SortImproperByAlpha(NameType const& wc) {
       if (types_.size() != 4) return;

From 5638841fdaafc84a708e7c0e814f13cb62468d29 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 30 Jan 2026 10:59:04 -0500
Subject: [PATCH 1266/1492] Test sorting typenames and using them in std::map

---
 unitTests/TypeNameHolder/main.cpp | 37 +++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

diff --git a/unitTests/TypeNameHolder/main.cpp b/unitTests/TypeNameHolder/main.cpp
index 2b84eb824a..d1f1630a6d 100644
--- a/unitTests/TypeNameHolder/main.cpp
+++ b/unitTests/TypeNameHolder/main.cpp
@@ -3,6 +3,7 @@
 #include <vector>
 #include <string>
 #include <algorithm>
+#include <map>
 #include "TypeNameHolder.h"
 
 static const int Err(const char* msg) {
@@ -16,6 +17,12 @@ static const int Err(const char* msg) {
   }
 } reverseSortObj;*/
 
+static inline void printTypes(TypeNameHolder const& types)
+{
+  for (unsigned int ii = 0; ii < types.Size(); ii++)
+    printf(" %4s", *types[ii]);
+}
+
 int main() {
   TypeNameHolder type1;
   type1.AddName("CT");
@@ -91,5 +98,35 @@ int main() {
   ismatch = ip2.Match_WC( ip1, "X" );
   if (!ismatch) return Err("TypeNameHolder improper WC match failed.");
 
+  typedef std::pair<TypeNameHolder, double> ParmPair;
+  typedef std::map<TypeNameHolder, double> ParmMap;
+  ParmMap parmMap;
+  parmMap.insert( ParmPair(ip1, 1.0) );
+  parmMap.insert( ParmPair(ip2, 3.0) );
+  dp1.SortNames("X");
+  dp2.SortNames("X");
+  parmMap.insert( ParmPair(dp1, 2.0) );
+  parmMap.insert( ParmPair(dp2, 0.0) );
+
+  for (ParmMap::const_iterator it = parmMap.begin(); it != parmMap.end(); ++it)
+  {
+    printTypes( it->first );
+    printf(" %f\n", it->second);
+  }
+
+  TypeNameHolder key(4);
+  key.AddName("HO");
+  key.AddName("O");
+  key.AddName("CX");
+  key.AddName("CT");
+
+  key.SortNames("X");
+  ParmMap::const_iterator ret = parmMap.find( key );
+  printTypes(key);
+  if ( ret == parmMap.end())
+    return Err("Using TypeNameHolder to find key in map failed.");
+  printf(" <->");
+  printTypes(ret->first);
+
   return 0;
 }

From 2a0c75f79b778e1488b26e0a624f854d3fe38a6d Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 30 Jan 2026 13:01:48 -0500
Subject: [PATCH 1267/1492] Have ParmHolder use std::map. Make the old class
 with std::vector into ParmArray; assigning nonbonds needs to be able to do
 addition with iterators, so std::map cannot be used in that case.

---
 src/Parm/AssignParams.cpp |  16 ++---
 src/Parm/ParameterSet.cpp |   5 +-
 src/Parm/ParmArray.h      | 124 ++++++++++++++++++++++++++++++++++++++
 src/Parm/ParmHolder.h     |  74 +++++++++--------------
 src/TypeNameHolder.h      |  19 ++++++
 5 files changed, 182 insertions(+), 56 deletions(-)
 create mode 100644 src/Parm/ParmArray.h

diff --git a/src/Parm/AssignParams.cpp b/src/Parm/AssignParams.cpp
index 3142dcdbb3..1b89781040 100644
--- a/src/Parm/AssignParams.cpp
+++ b/src/Parm/AssignParams.cpp
@@ -1,5 +1,6 @@
 #include "AssignParams.h"
 #include "GetParams.h"
+#include "ParmArray.h"
 #include "ParmHolder.h"
 #include "DihedralParmHolder.h"
 #include "ImproperParmHolder.h"
@@ -641,7 +642,8 @@ const
   bool hasLJ14 = !new14.empty();
   bool hasLJC = !newLJC.empty();
   // Generate array of only the types that are currently in Topology. TODO should this be a permanent part of Topology?
-  ParmHolder<AtomType> currentAtomTypes;
+  //ParmHolder<AtomType> currentAtomTypes;
+  ParmArray<AtomType> currentAtomTypes;
   for (AtArray::const_iterator atm = topOut.begin(); atm != topOut.end(); ++atm)
   {
     if (atm->HasType()) {
@@ -672,15 +674,15 @@ const
   NonbondParmType& nonbond = topOut.SetNonbond();
   nonbond.Clear();
   // Set type indices in order.
-  for (ParmHolder<AtomType>::iterator t1 = currentAtomTypes.begin(); t1 != currentAtomTypes.end(); ++t1)
+  for (ParmArray<AtomType>::iterator t1 = currentAtomTypes.begin(); t1 != currentAtomTypes.end(); ++t1)
     t1->second.SetTypeIdx( -1 );
   int n_unique_lj_types = 0;
-  for (ParmHolder<AtomType>::iterator t1 = currentAtomTypes.begin(); t1 != currentAtomTypes.end(); ++t1)
+  for (ParmArray<AtomType>::iterator t1 = currentAtomTypes.begin(); t1 != currentAtomTypes.end(); ++t1)
   {
     if (t1->second.OriginalIdx() == -1) {
       t1->second.SetTypeIdx( n_unique_lj_types );
       // Look for equivalent nonbond types
-      for (ParmHolder<AtomType>::iterator t2 = t1 + 1; t2 != currentAtomTypes.end(); ++t2) {
+      for (ParmArray<AtomType>::iterator t2 = t1 + 1; t2 != currentAtomTypes.end(); ++t2) {
         // Everything must match
         if (!hasLJ14) {
           if (t2->second.OriginalIdx() == -1 && t1->second.LJ() == t2->second.LJ()) {
@@ -710,12 +712,12 @@ const
   if (hasLJC)
     nonbond.SetNLJCterms( nonbond.NBarray().size() );
   // Loop over all atom type pairs
-  for (ParmHolder<AtomType>::const_iterator t1 = currentAtomTypes.begin(); t1 != currentAtomTypes.end(); ++t1)
+  for (ParmArray<AtomType>::const_iterator t1 = currentAtomTypes.begin(); t1 != currentAtomTypes.end(); ++t1)
   {
     NameType const& name1 = t1->first[0];
     //mprintf("DEBUG: Type1= %s (%i)\n", *name1, nidx1);
     AtomType const& type1 = t1->second;
-    for (ParmHolder<AtomType>::const_iterator t2 = t1; t2 != currentAtomTypes.end(); ++t2)
+    for (ParmArray<AtomType>::const_iterator t2 = t1; t2 != currentAtomTypes.end(); ++t2)
     {
       NameType const& name2 = t2->first[0];
       //mprintf("DEBUG:\t\tType2= %s (%i)\n", *name2, nidx2);
@@ -774,7 +776,7 @@ const
   for (AtArray::iterator atm = topOut.ModifyAtoms().begin(); atm != topOut.ModifyAtoms().end(); ++atm)
   {
     int tidx = -1;
-    ParmHolder<AtomType>::const_iterator it = currentAtomTypes.GetParam( TypeNameHolder(atm->Type()) );
+    ParmArray<AtomType>::const_iterator it = currentAtomTypes.GetParam( TypeNameHolder(atm->Type()) );
     if (it == currentAtomTypes.end()) {
       mprintf("Warning: Atom type not found for %s (type %s)\n",
               topOut.TruncResAtomNameNum( atm - topOut.ModifyAtoms().begin() ).c_str(),
diff --git a/src/Parm/ParameterSet.cpp b/src/Parm/ParameterSet.cpp
index 447509618b..a2399dc1d8 100644
--- a/src/Parm/ParameterSet.cpp
+++ b/src/Parm/ParameterSet.cpp
@@ -80,8 +80,9 @@ void ParameterSet::Print(CpptrajFile& Out) const {
   if (has_elements)
     Out.Printf(" %2s", "El");
   Out.Printf("\n");
-  for (ParmHolder<AtomType>::const_iterator at = atomTypes_.begin(); at != atomTypes_.end(); ++at) {
-    Out.Printf("\t%6s %8li %2i %12.4f %12.4f %12.4f %12.4f", *(at->first[0]), at - atomTypes_.begin(), (int)at->second.HasLJ(), at->second.LJ().Radius(), at->second.LJ().Depth(), at->second.Mass(), at->second.Polarizability());
+  unsigned int atidx = 0;
+  for (ParmHolder<AtomType>::const_iterator at = atomTypes_.begin(); at != atomTypes_.end(); ++at, atidx++) {
+    Out.Printf("\t%6s %8u %2i %12.4f %12.4f %12.4f %12.4f", *(at->first[0]), atidx, (int)at->second.HasLJ(), at->second.LJ().Radius(), at->second.LJ().Depth(), at->second.Mass(), at->second.Polarizability());
     if (has_hybridizations)
       Out.Printf(" %3s", hybStr[at->second.Hybridization()]);
     if (has_elements)
diff --git a/src/Parm/ParmArray.h b/src/Parm/ParmArray.h
new file mode 100644
index 0000000000..14d6f1ce74
--- /dev/null
+++ b/src/Parm/ParmArray.h
@@ -0,0 +1,124 @@
+#ifndef INC_PARM_PARMARRAY_H
+#define INC_PARM_PARMARRAY_H
+#include <vector>
+#include <utility> // std::pair
+#include "ParmEnum.h"
+#include "../TypeNameHolder.h"
+//#incl ude "CpptrajStdio.h" // DEBUG
+namespace Cpptraj {
+namespace Parm {
+/// Used to associate atom type names with an object (parameter etc)
+template <class T> class ParmArray {
+    // TODO may want to actually use a map one day for performance reasons.
+    typedef std::pair<TypeNameHolder,T> Bpair;
+    typedef std::vector<Bpair> Bmap;
+  public:
+    /// CONSTRUCTOR
+    ParmArray() {}
+    /// Clear all parameters
+    void clear()              { bpmap_.clear(); }
+    /// \return Number of parameters
+    size_t size()       const { return bpmap_.size(); }
+    /// \return true if no parameters
+    bool empty()        const { return bpmap_.empty(); }
+    /// \return Last parameter to be overwritten from AddParm()
+    T const& PreviousParm() const { return previousParm_; }
+    /// Set wildcard character
+    //void SetWildcard(char wc) { wc_ = NameType(std::string(1, wc)); }
+    /// Add (or update if allowed) given parameter to holder.
+    RetType AddParm(TypeNameHolder const& types, T const& bp, bool allowUpdate) {
+      // Check if parm for these types exist
+      typename Bmap::iterator it = bpmap_.begin();
+      for (; it != bpmap_.end(); ++it)
+        if (it->first.Match_NoWC( types )) break;
+      if (it == bpmap_.end()) {
+        // New parm
+        //mprintf("DEBUG: New parameter:");
+        //for (TypeNameHolder::const_iterator it = types.begin(); it != types.end(); ++it)
+        //  mprintf(" '%s'", *(*it));
+        //mprintf("\n");
+        bpmap_.push_back( Bpair(types, bp) );
+      } else {
+        if (bp < it->second || it->second < bp) {
+          //mprintf("DEBUG: Potential update of existing parameter:");
+          //for (TypeNameHolder::const_iterator it = types.begin(); it != types.end(); ++it)
+          //  mprintf(" '%s'", *(*it));
+          //mprintf("\n");
+          if (allowUpdate) {
+            previousParm_ = it->second;
+            it->second = bp;
+            return UPDATED;
+          } else {
+            return ERR;
+          }
+        } else {
+          //mprintf("DEBUG: Existing parameter:");
+          //for (TypeNameHolder::const_iterator it = types.begin(); it != types.end(); ++it)
+          //  mprintf(" '%s'", *(*it));
+          //mprintf("\n");
+          return SAME;
+        }
+      }
+      return ADDED;
+    }
+    /// Constant iterator
+    typedef typename Bmap::const_iterator const_iterator;
+    /// \return constant iterator to beginning
+    const_iterator begin() const { return bpmap_.begin(); }
+    /// \return constant iterator to end.
+    const_iterator end()   const { return bpmap_.end();   }
+    /// Iterator
+    typedef typename Bmap::iterator iterator;
+    /// \return iterator to beginning
+    iterator begin() { return bpmap_.begin(); }
+    /// \return iterator to end
+    iterator end()   { return bpmap_.end();   }
+    /// \return Parameter matching given types, or empty parameter if not found.
+//    T FindParam(TypeNameHolder const& types, bool& found) const { // TODO only use GetParam()?
+//      found = true;
+//      for (const_iterator it = begin(); it != end(); ++it)
+//        if (it->first.Match_NoWC( types )) return it->second;
+//      //if (wc_.len() > 0) {
+//      //  for (const_iterator it = begin(); it != end(); ++it)
+//      //    if (it->first.Match_WC( types, wc_)) return it->second;
+//      //}
+//      found = false;
+//      return T();
+//    }
+    /// \return iterator to parameter matching the given types.
+//    iterator GetParam(TypeNameHolder const& types) {
+//      for (iterator it = bpmap_.begin(); it != bpmap_.end(); ++it)
+//        if (it->first.Match_NoWC( types )) return it;
+//      //if (wc_.len() > 0) {
+//      //  for (iterator it = bpmap_.begin(); it != bpmap_.end(); ++it)
+//      //    if (it->first.Match_WC( types, wc_)) return it;
+//      //}
+//      return bpmap_.end();
+//    }
+    /// \return const iterator to parameter matching the given types.
+    const_iterator GetParam(TypeNameHolder const& types) const {
+      for (const_iterator it = bpmap_.begin(); it != bpmap_.end(); ++it)
+        if (it->first.Match_NoWC( types )) return it;
+      //if (wc_.len() > 0) {
+      //  for (const_iterator it = bpmap_.begin(); it != bpmap_.end(); ++it)
+      //    if (it->first.Match_WC( types, wc_)) return it;
+      //}
+      return bpmap_.end();
+    }
+    /// \return size in memory in bytes
+    size_t DataSize() const {
+      if (bpmap_.empty()) return 0;
+      const_iterator elt0 = begin();
+      // Assume all TypeNameHolders are the same size
+      return (bpmap_.size() * elt0->first.DataSize()) +
+             (bpmap_.size() * sizeof(T)) +
+             sizeof(Bmap);
+    }
+  private:
+    Bmap bpmap_;
+    T previousParm_; ///< When parameter is updated, store previous value.
+    //NameType wc_; ///< Wildcard character
+};
+} // END namespace Parm
+} // END namespace Cpptraj
+#endif
diff --git a/src/Parm/ParmHolder.h b/src/Parm/ParmHolder.h
index 183e7996c9..7ec2946427 100644
--- a/src/Parm/ParmHolder.h
+++ b/src/Parm/ParmHolder.h
@@ -1,17 +1,14 @@
 #ifndef INC_PARM_PARMHOLDER_H
 #define INC_PARM_PARMHOLDER_H
-#include <vector>
-#include <utility> // std::pair
+#include <map>
 #include "ParmEnum.h"
 #include "../TypeNameHolder.h"
-//#incl ude "CpptrajStdio.h" // DEBUG
 namespace Cpptraj {
 namespace Parm {
 /// Used to associate atom type names with an object (parameter etc)
 template <class T> class ParmHolder {
-    // TODO may want to actually use a map one day for performance reasons.
     typedef std::pair<TypeNameHolder,T> Bpair;
-    typedef std::vector<Bpair> Bmap;
+    typedef std::map<TypeNameHolder,T> Bmap;
   public:
     /// CONSTRUCTOR
     ParmHolder() {}
@@ -23,27 +20,19 @@ template <class T> class ParmHolder {
     bool empty()        const { return bpmap_.empty(); }
     /// \return Last parameter to be overwritten from AddParm()
     T const& PreviousParm() const { return previousParm_; }
-    /// Set wildcard character
-    //void SetWildcard(char wc) { wc_ = NameType(std::string(1, wc)); }
     /// Add (or update if allowed) given parameter to holder.
-    RetType AddParm(TypeNameHolder const& types, T const& bp, bool allowUpdate) {
+    RetType AddParm(TypeNameHolder const& typesIn, T const& bp, bool allowUpdate) {
+      // Ensure types are sorted
+      TypeNameHolder types = typesIn;
+      types.SortNames();
       // Check if parm for these types exist
-      typename Bmap::iterator it = bpmap_.begin();
-      for (; it != bpmap_.end(); ++it)
-        if (it->first.Match_NoWC( types )) break;
-      if (it == bpmap_.end()) {
+      typename Bmap::iterator it = bpmap_.lower_bound( types );
+      if (it == bpmap_.end() || it->first != types) {
         // New parm
-        //mprintf("DEBUG: New parameter:");
-        //for (TypeNameHolder::const_iterator it = types.begin(); it != types.end(); ++it)
-        //  mprintf(" '%s'", *(*it));
-        //mprintf("\n");
-        bpmap_.push_back( Bpair(types, bp) );
+        it = bpmap_.insert(it, Bpair(types, bp));
       } else {
         if (bp < it->second || it->second < bp) {
-          //mprintf("DEBUG: Potential update of existing parameter:");
-          //for (TypeNameHolder::const_iterator it = types.begin(); it != types.end(); ++it)
-          //  mprintf(" '%s'", *(*it));
-          //mprintf("\n");
+          // Potential update of existing parameter
           if (allowUpdate) {
             previousParm_ = it->second;
             it->second = bp;
@@ -74,36 +63,28 @@ template <class T> class ParmHolder {
     /// \return iterator to end
     iterator end()   { return bpmap_.end();   }
     /// \return Parameter matching given types, or empty parameter if not found.
-    T FindParam(TypeNameHolder const& types, bool& found) const { // TODO only use GetParam()?
+    T FindParam(TypeNameHolder const& typesIn, bool& found) const {
+      TypeNameHolder types = typesIn;
+      types.SortNames();
+      typename Bmap::const_iterator it = bpmap_.find( types );
+      if (it == bpmap_.end()) {
+        found = false;
+        return T();
+      }
       found = true;
-      for (const_iterator it = begin(); it != end(); ++it)
-        if (it->first.Match_NoWC( types )) return it->second;
-      //if (wc_.len() > 0) {
-      //  for (const_iterator it = begin(); it != end(); ++it)
-      //    if (it->first.Match_WC( types, wc_)) return it->second;
-      //}
-      found = false;
-      return T();
+      return it->second;
     }
     /// \return iterator to parameter matching the given types.
-    iterator GetParam(TypeNameHolder const& types) {
-      for (iterator it = bpmap_.begin(); it != bpmap_.end(); ++it)
-        if (it->first.Match_NoWC( types )) return it;
-      //if (wc_.len() > 0) {
-      //  for (iterator it = bpmap_.begin(); it != bpmap_.end(); ++it)
-      //    if (it->first.Match_WC( types, wc_)) return it;
-      //}
-      return bpmap_.end();
+    iterator GetParam(TypeNameHolder const& typesIn) {
+      TypeNameHolder types = typesIn;
+      types.SortNames();
+      return bpmap_.find( types );
     }
     /// \return const iterator to parameter matching the given types.
-    const_iterator GetParam(TypeNameHolder const& types) const {
-      for (const_iterator it = bpmap_.begin(); it != bpmap_.end(); ++it)
-        if (it->first.Match_NoWC( types )) return it;
-      //if (wc_.len() > 0) {
-      //  for (const_iterator it = bpmap_.begin(); it != bpmap_.end(); ++it)
-      //    if (it->first.Match_WC( types, wc_)) return it;
-      //}
-      return bpmap_.end();
+    const_iterator GetParam(TypeNameHolder const& typesIn) const {
+      TypeNameHolder types = typesIn;
+      types.SortNames();
+      return bpmap_.find( types );
     }
     /// \return size in memory in bytes
     size_t DataSize() const {
@@ -117,7 +98,6 @@ template <class T> class ParmHolder {
   private:
     Bmap bpmap_;
     T previousParm_; ///< When parameter is updated, store previous value.
-    //NameType wc_; ///< Wildcard character
 };
 } // END namespace Parm
 } // END namespace Cpptraj
diff --git a/src/TypeNameHolder.h b/src/TypeNameHolder.h
index 67ce9e2399..885fcefdcf 100644
--- a/src/TypeNameHolder.h
+++ b/src/TypeNameHolder.h
@@ -1,5 +1,6 @@
 #ifndef INC_TYPENAMEHOLDER_H
 #define INC_TYPENAMEHOLDER_H
+#include <vector>
 #include <cstddef> // size_t
 #include "NameType.h"
 /// Used to hold one or more atom type names.
@@ -55,6 +56,8 @@ class TypeNameHolder {
     }
     /// \return true if either direction is an exact match, no wildcard.
     bool operator==(TypeNameHolder const& rhs) const { return Match_NoWC(rhs); }
+    /// \return true if neither direction is an exact match.
+    bool operator!=(TypeNameHolder const& rhs) const { return !Match_NoWC(rhs); }
     /// \return true if either direction is a match, taking into account wildcard.
     bool Match_WC(TypeNameHolder const& rhs, NameType const& wildcard) const {
       // Sanity check
@@ -144,6 +147,22 @@ class TypeNameHolder {
         if (types_[last] == " ") types_[last] = wc;
       }
     }
+    /// Sort typenames so that the first typename < the last, no wildcard
+    void SortNames() {
+      if (types_.size() < 2) return;
+      unsigned int last = types_.size() - 1;
+      if (types_[0] > types_[last]) {
+        // Need to swap TODO record if we swapped these names?
+        if (types_.size() < 4)
+          tswap(types_[0], types_[last]);
+        else {
+          unsigned int half = types_.size() / 2;
+          unsigned int jj = last;
+          for (unsigned int ii = 0; ii < half; ii++, jj--)
+            tswap(types_[ii], types_[jj]);
+        }
+      }
+    }
     /// Sort typenames alphabetically, preserving the 3rd position (for impropers)
     void SortImproperByAlpha(NameType const& wc) {
       if (types_.size() != 4) return;

From 8891b8b111909ca8b8f4ac0934806e5b09fdc77f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 30 Jan 2026 13:03:08 -0500
Subject: [PATCH 1268/1492] Update dependencies

---
 src/Parm/parmdepend           | 2 +-
 src/Structure/structuredepend | 4 ++--
 src/cpptrajdepend             | 4 ++--
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/Parm/parmdepend b/src/Parm/parmdepend
index c2c303deaa..6d84d885d9 100644
--- a/src/Parm/parmdepend
+++ b/src/Parm/parmdepend
@@ -1,4 +1,4 @@
-AssignParams.o : AssignParams.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/ParmEnum.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/GenerateConnectivityArrays.h ../SymbolExporting.h ../Timer.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h AssignParams.h DihedralParmHolder.h GetParams.h ImproperParmHolder.h ParameterSet.h ParmEnum.h ParmHolder.h
+AssignParams.o : AssignParams.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/ParmEnum.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/GenerateConnectivityArrays.h ../SymbolExporting.h ../Timer.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h AssignParams.h DihedralParmHolder.h GetParams.h ImproperParmHolder.h ParameterSet.h ParmArray.h ParmEnum.h ParmHolder.h
 Bond_Params.o : Bond_Params.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h Bond_Params.h
 GB_Params.o : GB_Params.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h GB_Params.h
 GetParams.o : GetParams.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/ParmEnum.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h DihedralParmHolder.h GetParams.h ImproperParmHolder.h ParameterSet.h ParmEnum.h ParmHolder.h
diff --git a/src/Structure/structuredepend b/src/Structure/structuredepend
index ec20b595c1..d8794a81c6 100644
--- a/src/Structure/structuredepend
+++ b/src/Structure/structuredepend
@@ -1,5 +1,5 @@
 AddIons.o : AddIons.cpp ../AssociatedData.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../Dimension.h ../DistRoutines.h ../FileIO.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/../AtomType.h ../Parm/../CmapParmHolder.h ../Parm/../Constants.h ../Parm/../NameType.h ../Parm/../ParameterTypes.h ../Parm/../Parm/ParmEnum.h ../Parm/../TypeNameHolder.h ../Parm/DihedralParmHolder.h ../Parm/ImproperParmHolder.h ../Parm/ParameterSet.h ../Parm/ParmEnum.h ../Parm/ParmHolder.h ../Random.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h AddIons.h
-Builder.o : Builder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/../AtomType.h ../Parm/../CmapParmHolder.h ../Parm/../Constants.h ../Parm/../NameType.h ../Parm/../ParameterTypes.h ../Parm/../Parm/ParmEnum.h ../Parm/../TypeNameHolder.h ../Parm/DihedralParmHolder.h ../Parm/ImproperParmHolder.h ../Parm/ParameterSet.h ../Parm/ParmEnum.h ../Parm/ParmHolder.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Builder.h Chirality.h GenerateConnectivityArrays.h InternalCoords.h StructureEnum.h Zmatrix.h
+Builder.o : Builder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/../AtomType.h ../Parm/../CmapParmHolder.h ../Parm/../Constants.h ../Parm/../NameType.h ../Parm/../ParameterTypes.h ../Parm/../Parm/ParmEnum.h ../Parm/../TypeNameHolder.h ../Parm/DihedralParmHolder.h ../Parm/ImproperParmHolder.h ../Parm/ParameterSet.h ../Parm/ParmEnum.h ../Parm/ParmHolder.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Timer.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Builder.h Chirality.h GenerateConnectivityArrays.h InternalCoords.h StructureEnum.h Zmatrix.h
 Chirality.o : Chirality.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../Unit.h ../Vec3.h Chirality.h StructureEnum.h
 Creator.o : Creator.cpp ../ArgList.h ../AssociatedData.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../DataSet_NameMap.h ../DataSet_Parameters.h ../DataSet_PdbResMap.h ../Dimension.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/../AtomType.h ../Parm/../CmapParmHolder.h ../Parm/../Constants.h ../Parm/../NameType.h ../Parm/../ParameterTypes.h ../Parm/../Parm/ParmEnum.h ../Parm/../TypeNameHolder.h ../Parm/DihedralParmHolder.h ../Parm/ImproperParmHolder.h ../Parm/ParameterSet.h ../Parm/ParmEnum.h ../Parm/ParmHolder.h ../PdbResMapType.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/StructureEnum.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h Creator.h GenerateConnectivityArrays.h StructureEnum.h
 Disulfide.o : Disulfide.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h Disulfide.h ResStatArray.h StructureRoutines.h
@@ -12,7 +12,7 @@ LeastSquaresPlane.o : LeastSquaresPlane.cpp ../Atom.h ../AtomMask.h ../Box.h ../
 MetalCenterFinder.o : MetalCenterFinder.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h MetalCenterFinder.h
 PdbCleaner.o : PdbCleaner.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h PdbCleaner.h
 RingFinder.o : RingFinder.cpp ../Atom.h ../AtomMask.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h RingFinder.h
-Solvate.o : Solvate.cpp ../ArgList.h ../AssociatedData.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../Dimension.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/../AtomType.h ../Parm/../CmapParmHolder.h ../Parm/../Constants.h ../Parm/../NameType.h ../Parm/../ParameterTypes.h ../Parm/../Parm/ParmEnum.h ../Parm/../TypeNameHolder.h ../Parm/DihedralParmHolder.h ../Parm/ImproperParmHolder.h ../Parm/ParameterSet.h ../Parm/ParmEnum.h ../Parm/ParmHolder.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h Solvate.h
+Solvate.o : Solvate.cpp ../Action.h ../ActionState.h ../Action_AutoImage.h ../ArgList.h ../AssociatedData.h ../Atom.h ../AtomMask.h ../BaseIOtype.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataFile.h ../DataFileList.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../Dimension.h ../DispatchObject.h ../FileIO.h ../FileName.h ../FileTypes.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/../AtomType.h ../Parm/../CmapParmHolder.h ../Parm/../Constants.h ../Parm/../NameType.h ../Parm/../ParameterTypes.h ../Parm/../Parm/ParmEnum.h ../Parm/../TypeNameHolder.h ../Parm/DihedralParmHolder.h ../Parm/ImproperParmHolder.h ../Parm/ParameterSet.h ../Parm/ParmEnum.h ../Parm/ParmHolder.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h Solvate.h
 StructureEnum.o : StructureEnum.cpp StructureEnum.h
 StructureRoutines.o : StructureRoutines.cpp ../Atom.h ../CpptrajStdio.h ../NameType.h ../Residue.h ../SymbolExporting.h StructureRoutines.h
 Sugar.o : Sugar.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h Sugar.h SugarToken.h
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index cc60b329ab..94cc01c839 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -430,7 +430,7 @@ PairList.o : PairList.cpp Atom.h AtomMask.h Box.h CoordinateInfo.h CpptrajStdio.
 Parallel.o : Parallel.cpp Parallel.h
 ParallelNetcdf.o : ParallelNetcdf.cpp CpptrajStdio.h Parallel.h ParallelNetcdf.h
 ParallelSetFrameNum.o : ParallelSetFrameNum.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h ParallelSetFrameNum.h Range.h TextFormat.h
-Parm/AssignParams.o : Parm/AssignParams.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h GuessAtomHybridization.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/../Structure/GenerateConnectivityArrays.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GetParams.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Parm/AssignParams.o : Parm/AssignParams.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h GuessAtomHybridization.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/../Structure/GenerateConnectivityArrays.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GetParams.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmArray.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Parm/Bond_Params.o : Parm/Bond_Params.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/Bond_Params.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Parm/GB_Params.o : Parm/GB_Params.cpp ArgList.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/GB_Params.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Parm/GetParams.o : Parm/GetParams.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/GetParams.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
@@ -496,7 +496,7 @@ Structure/LeastSquaresPlane.o : Structure/LeastSquaresPlane.cpp Atom.h AtomMask.
 Structure/MetalCenterFinder.o : Structure/MetalCenterFinder.cpp ArgList.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/MetalCenterFinder.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Structure/PdbCleaner.o : Structure/PdbCleaner.cpp ArgList.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/PdbCleaner.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Structure/RingFinder.o : Structure/RingFinder.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/RingFinder.h SymbolExporting.h Topology.h Unit.h Vec3.h
-Structure/Solvate.o : Structure/Solvate.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/../Parm/../AtomType.h Structure/../Parm/../CmapParmHolder.h Structure/../Parm/../Constants.h Structure/../Parm/../NameType.h Structure/../Parm/../ParameterTypes.h Structure/../Parm/../Parm/ParmEnum.h Structure/../Parm/../TypeNameHolder.h Structure/../Parm/DihedralParmHolder.h Structure/../Parm/ImproperParmHolder.h Structure/../Parm/ParameterSet.h Structure/../Parm/ParmEnum.h Structure/../Parm/ParmHolder.h Structure/Solvate.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Structure/Solvate.o : Structure/Solvate.cpp Action.h ActionState.h Action_AutoImage.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/../Parm/../AtomType.h Structure/../Parm/../CmapParmHolder.h Structure/../Parm/../Constants.h Structure/../Parm/../NameType.h Structure/../Parm/../ParameterTypes.h Structure/../Parm/../Parm/ParmEnum.h Structure/../Parm/../TypeNameHolder.h Structure/../Parm/DihedralParmHolder.h Structure/../Parm/ImproperParmHolder.h Structure/../Parm/ParameterSet.h Structure/../Parm/ParmEnum.h Structure/../Parm/ParmHolder.h Structure/Solvate.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 Structure/StructureEnum.o : Structure/StructureEnum.cpp Structure/StructureEnum.h
 Structure/StructureRoutines.o : Structure/StructureRoutines.cpp Atom.h CpptrajStdio.h NameType.h Residue.h Structure/StructureRoutines.h SymbolExporting.h
 Structure/Sugar.o : Structure/Sugar.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h Unit.h Vec3.h

From 0c886125e1c26b32af97c8d2b84032fb4ef0bd65 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 30 Jan 2026 13:12:08 -0500
Subject: [PATCH 1269/1492] Remove unused code

---
 src/Parm/ParmArray.h | 32 +-------------------------------
 1 file changed, 1 insertion(+), 31 deletions(-)

diff --git a/src/Parm/ParmArray.h b/src/Parm/ParmArray.h
index 14d6f1ce74..99a8507148 100644
--- a/src/Parm/ParmArray.h
+++ b/src/Parm/ParmArray.h
@@ -7,9 +7,8 @@
 //#incl ude "CpptrajStdio.h" // DEBUG
 namespace Cpptraj {
 namespace Parm {
-/// Used to associate atom type names with an object (parameter etc)
+/// Used to associate atom type names with an object (parameter etc) in an array
 template <class T> class ParmArray {
-    // TODO may want to actually use a map one day for performance reasons.
     typedef std::pair<TypeNameHolder,T> Bpair;
     typedef std::vector<Bpair> Bmap;
   public:
@@ -23,8 +22,6 @@ template <class T> class ParmArray {
     bool empty()        const { return bpmap_.empty(); }
     /// \return Last parameter to be overwritten from AddParm()
     T const& PreviousParm() const { return previousParm_; }
-    /// Set wildcard character
-    //void SetWildcard(char wc) { wc_ = NameType(std::string(1, wc)); }
     /// Add (or update if allowed) given parameter to holder.
     RetType AddParm(TypeNameHolder const& types, T const& bp, bool allowUpdate) {
       // Check if parm for these types exist
@@ -73,36 +70,10 @@ template <class T> class ParmArray {
     iterator begin() { return bpmap_.begin(); }
     /// \return iterator to end
     iterator end()   { return bpmap_.end();   }
-    /// \return Parameter matching given types, or empty parameter if not found.
-//    T FindParam(TypeNameHolder const& types, bool& found) const { // TODO only use GetParam()?
-//      found = true;
-//      for (const_iterator it = begin(); it != end(); ++it)
-//        if (it->first.Match_NoWC( types )) return it->second;
-//      //if (wc_.len() > 0) {
-//      //  for (const_iterator it = begin(); it != end(); ++it)
-//      //    if (it->first.Match_WC( types, wc_)) return it->second;
-//      //}
-//      found = false;
-//      return T();
-//    }
-    /// \return iterator to parameter matching the given types.
-//    iterator GetParam(TypeNameHolder const& types) {
-//      for (iterator it = bpmap_.begin(); it != bpmap_.end(); ++it)
-//        if (it->first.Match_NoWC( types )) return it;
-//      //if (wc_.len() > 0) {
-//      //  for (iterator it = bpmap_.begin(); it != bpmap_.end(); ++it)
-//      //    if (it->first.Match_WC( types, wc_)) return it;
-//      //}
-//      return bpmap_.end();
-//    }
     /// \return const iterator to parameter matching the given types.
     const_iterator GetParam(TypeNameHolder const& types) const {
       for (const_iterator it = bpmap_.begin(); it != bpmap_.end(); ++it)
         if (it->first.Match_NoWC( types )) return it;
-      //if (wc_.len() > 0) {
-      //  for (const_iterator it = bpmap_.begin(); it != bpmap_.end(); ++it)
-      //    if (it->first.Match_WC( types, wc_)) return it;
-      //}
       return bpmap_.end();
     }
     /// \return size in memory in bytes
@@ -117,7 +88,6 @@ template <class T> class ParmArray {
   private:
     Bmap bpmap_;
     T previousParm_; ///< When parameter is updated, store previous value.
-    //NameType wc_; ///< Wildcard character
 };
 } // END namespace Parm
 } // END namespace Cpptraj

From 8ff13f016aac4e30520b49e1ab303cd24b3a80ea Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 30 Jan 2026 13:27:41 -0500
Subject: [PATCH 1270/1492] Everything but dihedrals/impropers is stored
 alphabetical now

---
 test/Test_ReadAmberFF/tip3pf.parm.dat.save    |   6 +-
 test/Test_ReadAmberFF/toyrna.parm.dat.save    | 144 ++++++++---------
 .../toyrna.tip3pf.parm.dat.save               | 152 +++++++++---------
 3 files changed, 151 insertions(+), 151 deletions(-)

diff --git a/test/Test_ReadAmberFF/tip3pf.parm.dat.save b/test/Test_ReadAmberFF/tip3pf.parm.dat.save
index 79c90293bb..3eb96e7c34 100644
--- a/test/Test_ReadAmberFF/tip3pf.parm.dat.save
+++ b/test/Test_ReadAmberFF/tip3pf.parm.dat.save
@@ -1,9 +1,9 @@
 Parameter set: This is TIP3P (model F) of Price and Brooks, JCP 121:10096, 2004 
 Atom Types:
 	  Name  TypeIdx LJ       Radius        Depth         Mass       Polar.
-	    OW        0  1       1.7926       0.0980      16.0000       0.0000
-	    HW        1  1       0.0000       0.0000       1.0080       0.0000
+	    HW        0  1       0.0000       0.0000       1.0080       0.0000
+	    OW        1  1       1.7926       0.0980      16.0000       0.0000
 Bond parameters:
 	 Type1  Type2 :           Rk          Req
-	    OW     HW :     553.0000       0.9572
 	    HW     HW :     553.0000       1.5136
+	    HW     OW :     553.0000       0.9572
diff --git a/test/Test_ReadAmberFF/toyrna.parm.dat.save b/test/Test_ReadAmberFF/toyrna.parm.dat.save
index 808f8a5bd1..874c7c2694 100644
--- a/test/Test_ReadAmberFF/toyrna.parm.dat.save
+++ b/test/Test_ReadAmberFF/toyrna.parm.dat.save
@@ -2,100 +2,100 @@ Parameter set: toyrna force field
 Nonbond parameters name: MOD4
 Atom Types:
 	  Name  TypeIdx LJ       Radius        Depth         Mass       Polar.
-	    CB        0  1       2.0000       0.2000      56.0000       0.0000
-	    CS        1  1       2.0000       0.2000      43.0000       0.0000
-	    G9        2  1       1.8000       0.3000      25.0000       0.0000
-	    G7        3  1       1.8000       0.2000      25.0000       0.0000
-	    G6        4  1       1.8000       0.2000      25.0000       0.0000
-	    G1        5  1       1.8000       0.2000      25.0000       0.0000
-	    G2        6  1       1.8000       0.2000      25.0000       0.0000
-	    G3        7  1       1.8000       0.2000      25.0000       0.0000
-	    A9        8  1       1.8000       0.3000      26.8000       0.0000
-	    A7        9  1       1.8000       0.2000      26.8000       0.0000
-	    A6       10  1       1.8000       0.2000      26.8000       0.0000
-	    A1       11  1       1.8000       0.2000      26.8000       0.0000
-	    A3       12  1       1.8000       0.2000      26.8000       0.0000
-	    U1       13  1       1.8000       0.3000      27.7500       0.0000
-	    U3       14  1       1.8000       0.2000      27.7500       0.0000
-	    U4       15  1       1.8000       0.2000      27.7500       0.0000
-	    U2       16  1       1.8000       0.2000      27.7500       0.0000
-	    C1       17  1       1.8000       0.3000      27.5000       0.0000
-	    C3       18  1       1.8000       0.2000      27.5000       0.0000
-	    C4       19  1       1.8000       0.2000      27.5000       0.0000
-	    C2       20  1       1.8000       0.2000      27.5000       0.0000
-	     P       21  1       3.0000       0.2000      95.0000       0.0000
+	    A1        0  1       1.8000       0.2000      26.8000       0.0000
+	    A3        1  1       1.8000       0.2000      26.8000       0.0000
+	    A6        2  1       1.8000       0.2000      26.8000       0.0000
+	    A7        3  1       1.8000       0.2000      26.8000       0.0000
+	    A9        4  1       1.8000       0.3000      26.8000       0.0000
+	    C1        5  1       1.8000       0.3000      27.5000       0.0000
+	    C2        6  1       1.8000       0.2000      27.5000       0.0000
+	    C3        7  1       1.8000       0.2000      27.5000       0.0000
+	    C4        8  1       1.8000       0.2000      27.5000       0.0000
+	    CB        9  1       2.0000       0.2000      56.0000       0.0000
+	    CS       10  1       2.0000       0.2000      43.0000       0.0000
+	    G1       11  1       1.8000       0.2000      25.0000       0.0000
+	    G2       12  1       1.8000       0.2000      25.0000       0.0000
+	    G3       13  1       1.8000       0.2000      25.0000       0.0000
+	    G6       14  1       1.8000       0.2000      25.0000       0.0000
+	    G7       15  1       1.8000       0.2000      25.0000       0.0000
+	    G9       16  1       1.8000       0.3000      25.0000       0.0000
+	     P       17  1       3.0000       0.2000      95.0000       0.0000
+	    U1       18  1       1.8000       0.3000      27.7500       0.0000
+	    U2       19  1       1.8000       0.2000      27.7500       0.0000
+	    U3       20  1       1.8000       0.2000      27.7500       0.0000
+	    U4       21  1       1.8000       0.2000      27.7500       0.0000
 HB LJ 10-12 parameters:
 	 Type1  Type2 :         Asol         Bsol        HBcut
-	    G6     C4 :       5.0000       3.0000       0.0000
-	    G1     C3 :       5.0000       3.0000       0.0000
-	    G2     C2 :       5.0000       3.0000       0.0000
-	    A6     U4 :       5.0000       3.0000       0.0000
 	    A1     U3 :       5.0000       3.0000       0.0000
-	    G7     C4 :       5.0000       6.0000       0.0000
-	    G3     C2 :       5.0000       5.2500       0.0000
+	    A6     U4 :       5.0000       3.0000       0.0000
+	    C2     G2 :       5.0000       3.0000       0.0000
+	    C2     G3 :       5.0000       5.2500       0.0000
+	    C3     G1 :       5.0000       3.0000       0.0000
+	    C4     G6 :       5.0000       3.0000       0.0000
+	    C4     G7 :       5.0000       6.0000       0.0000
 Bond parameters:
 	 Type1  Type2 :           Rk          Req
-	     P     CB :     150.0000       3.9000
+	    A1     A3 :     100.0000       2.3900
+	    A1     A6 :     100.0000       2.3100
+	    A3     A9 :     100.0000       2.4300
+	    A6     A7 :     100.0000       3.0800
+	    A7     A9 :     100.0000       2.2400
+	    A9     CS :     150.0000       1.4800
+	    C1     C2 :     100.0000       2.2700
+	    C1     C4 :     100.0000       4.0400
+	    C1     CS :     150.0000       1.4800
+	    C2     C3 :     100.0000       2.2600
+	    C3     C4 :     100.0000       2.3100
 	    CB     CS :     100.0000       2.3500
+	    CB      P :     150.0000       3.9000
 	    CS     G9 :     150.0000       1.4800
-	    CS     A9 :     150.0000       1.4800
 	    CS     U1 :     150.0000       1.4800
-	    CS     C1 :     150.0000       1.4800
-	    A9     A7 :     100.0000       2.2400
-	    A7     A6 :     100.0000       3.0800
-	    A6     A1 :     100.0000       2.3100
-	    A1     A3 :     100.0000       2.3900
-	    A3     A9 :     100.0000       2.4300
-	    G9     G7 :     100.0000       2.2500
-	    G7     G6 :     100.0000       3.0900
-	    G6     G1 :     100.0000       2.2700
 	    G1     G2 :     100.0000       2.2900
+	    G1     G6 :     100.0000       2.2700
 	    G2     G3 :     100.0000       2.3100
 	    G3     G9 :     100.0000       2.4200
+	    G6     G7 :     100.0000       3.0900
+	    G7     G9 :     100.0000       2.2500
+	    U1     U2 :     100.0000       2.2900
 	    U1     U4 :     100.0000       4.0400
-	    U4     U3 :     100.0000       2.2700
-	    U3     U2 :     100.0000       2.2800
-	    U2     U1 :     100.0000       2.2900
-	    C1     C4 :     100.0000       4.0400
-	    C4     C3 :     100.0000       2.3100
-	    C3     C2 :     100.0000       2.2600
-	    C2     C1 :     100.0000       2.2700
+	    U2     U3 :     100.0000       2.2800
+	    U3     U4 :     100.0000       2.2700
 Angle parameters:
 	 Type1  Type2  Type3 :           Tk          Teq
-	    CS     A9     A7 :      45.0000     160.9000
-	    A9     A7     A6 :      50.0000     118.9000
-	    A7     A6     A1 :      50.0000      85.4000
-	    A6     A1     A3 :      50.0000     123.9000
 	    A1     A3     A9 :      50.0000     112.1000
+	    A1     A6     A7 :      50.0000      85.4000
+	    A3     A1     A6 :      50.0000     123.9000
 	    A3     A9     A7 :      50.0000      99.7000
-	    CS     A9     A3 :      45.0000      99.1000
+	    A3     A9     CS :      45.0000      99.1000
+	    A6     A7     A9 :      50.0000     118.9000
+	    A7     A9     CS :      45.0000     160.9000
+	    A9     CS     CB :      30.0000     122.5000
+	    C1     C2     C3 :      50.0000      62.3000
+	    C1     C4     C3 :      50.0000      30.0000
+	    C1     CS     CB :      30.0000     122.5000
+	    C2     C1     C4 :      50.0000      87.7000
+	    C2     C1     CS :      45.0000      89.2000
+	    C2     C3     C4 :       0.0000     180.0000
+	    C4     C1     CS :       0.0000     180.0000
+	    CB     CS     G9 :      30.0000     122.5000
+	    CB     CS     U1 :      30.0000     122.5000
+	    CB      P     CB :      30.0000     103.0000
+	    CS     CB      P :      30.0000     104.0000
+	    CS     G9     G3 :      45.0000      97.9000
 	    CS     G9     G7 :      45.0000     161.2000
-	    G9     G7     G6 :      50.0000     117.7000
-	    G7     G6     G1 :      50.0000      85.2000
-	    G6     G1     G2 :      10.0000     175.1000
+	    CS     U1     U2 :      45.0000      90.8000
+	    CS     U1     U4 :       0.0000     180.0000
 	    G1     G2     G3 :      50.0000      62.2000
+	    G1     G6     G7 :      50.0000      85.2000
+	    G2     G1     G6 :      10.0000     175.1000
 	    G2     G3     G9 :      50.0000     169.6000
 	    G3     G9     G7 :      50.0000     100.3000
-	    CS     G9     G3 :      45.0000      97.9000
-	    CS     U1     U4 :       0.0000     180.0000
+	    G6     G7     G9 :      50.0000     117.7000
+	     P     CB      P :      22.0000      97.0000
+	    U1     U2     U3 :      50.0000      61.8000
 	    U1     U4     U3 :      50.0000      29.5000
-	    U4     U3     U2 :       0.0000     180.0000
-	    U3     U2     U1 :      50.0000      61.8000
 	    U2     U1     U4 :      50.0000      87.3000
-	    CS     U1     U2 :      45.0000      90.8000
-	    CS     C1     C4 :       0.0000     180.0000
-	    C1     C4     C3 :      50.0000      30.0000
-	    C4     C3     C2 :       0.0000     180.0000
-	    C3     C2     C1 :      50.0000      62.3000
-	    C2     C1     C4 :      50.0000      87.7000
-	    CS     C1     C2 :      45.0000      89.2000
-	     P     CB      P :      22.0000      97.0000
-	    CB      P     CB :      30.0000     103.0000
-	     P     CB     CS :      30.0000     104.0000
-	    CB     CS     G9 :      30.0000     122.5000
-	    CB     CS     A9 :      30.0000     122.5000
-	    CB     CS     U1 :      30.0000     122.5000
-	    CB     CS     C1 :      30.0000     122.5000
+	    U2     U3     U4 :       0.0000     180.0000
 Dihedral parameters:
 	 Type1  Type2  Type3  Type4           Pk   Pn    Phase   SCEE   SCNB
 	     X     CB     CS      X :       7.5000  1.0  -165.00   1.20   2.00
diff --git a/test/Test_ReadAmberFF/toyrna.tip3pf.parm.dat.save b/test/Test_ReadAmberFF/toyrna.tip3pf.parm.dat.save
index 15998a0a03..8aaa5c48c8 100644
--- a/test/Test_ReadAmberFF/toyrna.tip3pf.parm.dat.save
+++ b/test/Test_ReadAmberFF/toyrna.tip3pf.parm.dat.save
@@ -2,104 +2,104 @@ Parameter set: toyrna force field + This is TIP3P (model F) of Price and Brooks,
 Nonbond parameters name: MOD4
 Atom Types:
 	  Name  TypeIdx LJ       Radius        Depth         Mass       Polar.
-	    CB        0  1       2.0000       0.2000      56.0000       0.0000
-	    CS        1  1       2.0000       0.2000      43.0000       0.0000
-	    G9        2  1       1.8000       0.3000      25.0000       0.0000
-	    G7        3  1       1.8000       0.2000      25.0000       0.0000
-	    G6        4  1       1.8000       0.2000      25.0000       0.0000
-	    G1        5  1       1.8000       0.2000      25.0000       0.0000
-	    G2        6  1       1.8000       0.2000      25.0000       0.0000
-	    G3        7  1       1.8000       0.2000      25.0000       0.0000
-	    A9        8  1       1.8000       0.3000      26.8000       0.0000
-	    A7        9  1       1.8000       0.2000      26.8000       0.0000
-	    A6       10  1       1.8000       0.2000      26.8000       0.0000
-	    A1       11  1       1.8000       0.2000      26.8000       0.0000
-	    A3       12  1       1.8000       0.2000      26.8000       0.0000
-	    U1       13  1       1.8000       0.3000      27.7500       0.0000
-	    U3       14  1       1.8000       0.2000      27.7500       0.0000
-	    U4       15  1       1.8000       0.2000      27.7500       0.0000
-	    U2       16  1       1.8000       0.2000      27.7500       0.0000
-	    C1       17  1       1.8000       0.3000      27.5000       0.0000
-	    C3       18  1       1.8000       0.2000      27.5000       0.0000
-	    C4       19  1       1.8000       0.2000      27.5000       0.0000
-	    C2       20  1       1.8000       0.2000      27.5000       0.0000
-	     P       21  1       3.0000       0.2000      95.0000       0.0000
-	    OW       22  1       1.7926       0.0980      16.0000       0.0000
-	    HW       23  1       0.0000       0.0000       1.0080       0.0000
+	    A1        0  1       1.8000       0.2000      26.8000       0.0000
+	    A3        1  1       1.8000       0.2000      26.8000       0.0000
+	    A6        2  1       1.8000       0.2000      26.8000       0.0000
+	    A7        3  1       1.8000       0.2000      26.8000       0.0000
+	    A9        4  1       1.8000       0.3000      26.8000       0.0000
+	    C1        5  1       1.8000       0.3000      27.5000       0.0000
+	    C2        6  1       1.8000       0.2000      27.5000       0.0000
+	    C3        7  1       1.8000       0.2000      27.5000       0.0000
+	    C4        8  1       1.8000       0.2000      27.5000       0.0000
+	    CB        9  1       2.0000       0.2000      56.0000       0.0000
+	    CS       10  1       2.0000       0.2000      43.0000       0.0000
+	    G1       11  1       1.8000       0.2000      25.0000       0.0000
+	    G2       12  1       1.8000       0.2000      25.0000       0.0000
+	    G3       13  1       1.8000       0.2000      25.0000       0.0000
+	    G6       14  1       1.8000       0.2000      25.0000       0.0000
+	    G7       15  1       1.8000       0.2000      25.0000       0.0000
+	    G9       16  1       1.8000       0.3000      25.0000       0.0000
+	    HW       17  1       0.0000       0.0000       1.0080       0.0000
+	    OW       18  1       1.7926       0.0980      16.0000       0.0000
+	     P       19  1       3.0000       0.2000      95.0000       0.0000
+	    U1       20  1       1.8000       0.3000      27.7500       0.0000
+	    U2       21  1       1.8000       0.2000      27.7500       0.0000
+	    U3       22  1       1.8000       0.2000      27.7500       0.0000
+	    U4       23  1       1.8000       0.2000      27.7500       0.0000
 HB LJ 10-12 parameters:
 	 Type1  Type2 :         Asol         Bsol        HBcut
-	    G6     C4 :       5.0000       3.0000       0.0000
-	    G1     C3 :       5.0000       3.0000       0.0000
-	    G2     C2 :       5.0000       3.0000       0.0000
-	    A6     U4 :       5.0000       3.0000       0.0000
 	    A1     U3 :       5.0000       3.0000       0.0000
-	    G7     C4 :       5.0000       6.0000       0.0000
-	    G3     C2 :       5.0000       5.2500       0.0000
+	    A6     U4 :       5.0000       3.0000       0.0000
+	    C2     G2 :       5.0000       3.0000       0.0000
+	    C2     G3 :       5.0000       5.2500       0.0000
+	    C3     G1 :       5.0000       3.0000       0.0000
+	    C4     G6 :       5.0000       3.0000       0.0000
+	    C4     G7 :       5.0000       6.0000       0.0000
 Bond parameters:
 	 Type1  Type2 :           Rk          Req
-	     P     CB :     150.0000       3.9000
+	    A1     A3 :     100.0000       2.3900
+	    A1     A6 :     100.0000       2.3100
+	    A3     A9 :     100.0000       2.4300
+	    A6     A7 :     100.0000       3.0800
+	    A7     A9 :     100.0000       2.2400
+	    A9     CS :     150.0000       1.4800
+	    C1     C2 :     100.0000       2.2700
+	    C1     C4 :     100.0000       4.0400
+	    C1     CS :     150.0000       1.4800
+	    C2     C3 :     100.0000       2.2600
+	    C3     C4 :     100.0000       2.3100
 	    CB     CS :     100.0000       2.3500
+	    CB      P :     150.0000       3.9000
 	    CS     G9 :     150.0000       1.4800
-	    CS     A9 :     150.0000       1.4800
 	    CS     U1 :     150.0000       1.4800
-	    CS     C1 :     150.0000       1.4800
-	    A9     A7 :     100.0000       2.2400
-	    A7     A6 :     100.0000       3.0800
-	    A6     A1 :     100.0000       2.3100
-	    A1     A3 :     100.0000       2.3900
-	    A3     A9 :     100.0000       2.4300
-	    G9     G7 :     100.0000       2.2500
-	    G7     G6 :     100.0000       3.0900
-	    G6     G1 :     100.0000       2.2700
 	    G1     G2 :     100.0000       2.2900
+	    G1     G6 :     100.0000       2.2700
 	    G2     G3 :     100.0000       2.3100
 	    G3     G9 :     100.0000       2.4200
-	    U1     U4 :     100.0000       4.0400
-	    U4     U3 :     100.0000       2.2700
-	    U3     U2 :     100.0000       2.2800
-	    U2     U1 :     100.0000       2.2900
-	    C1     C4 :     100.0000       4.0400
-	    C4     C3 :     100.0000       2.3100
-	    C3     C2 :     100.0000       2.2600
-	    C2     C1 :     100.0000       2.2700
-	    OW     HW :     553.0000       0.9572
+	    G6     G7 :     100.0000       3.0900
+	    G7     G9 :     100.0000       2.2500
 	    HW     HW :     553.0000       1.5136
+	    HW     OW :     553.0000       0.9572
+	    U1     U2 :     100.0000       2.2900
+	    U1     U4 :     100.0000       4.0400
+	    U2     U3 :     100.0000       2.2800
+	    U3     U4 :     100.0000       2.2700
 Angle parameters:
 	 Type1  Type2  Type3 :           Tk          Teq
-	    CS     A9     A7 :      45.0000     160.9000
-	    A9     A7     A6 :      50.0000     118.9000
-	    A7     A6     A1 :      50.0000      85.4000
-	    A6     A1     A3 :      50.0000     123.9000
 	    A1     A3     A9 :      50.0000     112.1000
+	    A1     A6     A7 :      50.0000      85.4000
+	    A3     A1     A6 :      50.0000     123.9000
 	    A3     A9     A7 :      50.0000      99.7000
-	    CS     A9     A3 :      45.0000      99.1000
+	    A3     A9     CS :      45.0000      99.1000
+	    A6     A7     A9 :      50.0000     118.9000
+	    A7     A9     CS :      45.0000     160.9000
+	    A9     CS     CB :      30.0000     122.5000
+	    C1     C2     C3 :      50.0000      62.3000
+	    C1     C4     C3 :      50.0000      30.0000
+	    C1     CS     CB :      30.0000     122.5000
+	    C2     C1     C4 :      50.0000      87.7000
+	    C2     C1     CS :      45.0000      89.2000
+	    C2     C3     C4 :       0.0000     180.0000
+	    C4     C1     CS :       0.0000     180.0000
+	    CB     CS     G9 :      30.0000     122.5000
+	    CB     CS     U1 :      30.0000     122.5000
+	    CB      P     CB :      30.0000     103.0000
+	    CS     CB      P :      30.0000     104.0000
+	    CS     G9     G3 :      45.0000      97.9000
 	    CS     G9     G7 :      45.0000     161.2000
-	    G9     G7     G6 :      50.0000     117.7000
-	    G7     G6     G1 :      50.0000      85.2000
-	    G6     G1     G2 :      10.0000     175.1000
+	    CS     U1     U2 :      45.0000      90.8000
+	    CS     U1     U4 :       0.0000     180.0000
 	    G1     G2     G3 :      50.0000      62.2000
+	    G1     G6     G7 :      50.0000      85.2000
+	    G2     G1     G6 :      10.0000     175.1000
 	    G2     G3     G9 :      50.0000     169.6000
 	    G3     G9     G7 :      50.0000     100.3000
-	    CS     G9     G3 :      45.0000      97.9000
-	    CS     U1     U4 :       0.0000     180.0000
+	    G6     G7     G9 :      50.0000     117.7000
+	     P     CB      P :      22.0000      97.0000
+	    U1     U2     U3 :      50.0000      61.8000
 	    U1     U4     U3 :      50.0000      29.5000
-	    U4     U3     U2 :       0.0000     180.0000
-	    U3     U2     U1 :      50.0000      61.8000
 	    U2     U1     U4 :      50.0000      87.3000
-	    CS     U1     U2 :      45.0000      90.8000
-	    CS     C1     C4 :       0.0000     180.0000
-	    C1     C4     C3 :      50.0000      30.0000
-	    C4     C3     C2 :       0.0000     180.0000
-	    C3     C2     C1 :      50.0000      62.3000
-	    C2     C1     C4 :      50.0000      87.7000
-	    CS     C1     C2 :      45.0000      89.2000
-	     P     CB      P :      22.0000      97.0000
-	    CB      P     CB :      30.0000     103.0000
-	     P     CB     CS :      30.0000     104.0000
-	    CB     CS     G9 :      30.0000     122.5000
-	    CB     CS     A9 :      30.0000     122.5000
-	    CB     CS     U1 :      30.0000     122.5000
-	    CB     CS     C1 :      30.0000     122.5000
+	    U2     U3     U4 :       0.0000     180.0000
 Dihedral parameters:
 	 Type1  Type2  Type3  Type4           Pk   Pn    Phase   SCEE   SCNB
 	     X     CB     CS      X :       7.5000  1.0  -165.00   1.20   2.00

From c7f10b8ed0f14c6150929d4372ca22a9081cee7a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 30 Jan 2026 13:36:03 -0500
Subject: [PATCH 1271/1492] All parameters are alphabetical now execpt
 dihedral/improper

---
 test/Test_CharmmParams/testdata.prm.save | 66 ++++++++++++------------
 1 file changed, 33 insertions(+), 33 deletions(-)

diff --git a/test/Test_CharmmParams/testdata.prm.save b/test/Test_CharmmParams/testdata.prm.save
index ee1c3b25ff..f20208d07d 100644
--- a/test/Test_CharmmParams/testdata.prm.save
+++ b/test/Test_CharmmParams/testdata.prm.save
@@ -6,57 +6,57 @@ read param card flex append
 *
 
 ATOMS
-MASS  -1  NH1       14.00700
-MASS  -1  H          1.00800
+MASS  -1  C         12.01100
+MASS  -1  CC        12.01100
 MASS  -1  CT1       12.01100
-MASS  -1  HB1        1.00800
 MASS  -1  CT2       12.01100
-MASS  -1  HA2        1.00800
+MASS  -1  H          1.00800
 MASS  -1  HA         1.00800
+MASS  -1  HA2        1.00800
+MASS  -1  HB1        1.00800
 MASS  -1  NECA      14.00700
-MASS  -1  CC        12.01100
-MASS  -1  OC        15.99900
-MASS  -1  C         12.01100
+MASS  -1  NH1       14.00700
 MASS  -1  O         15.99900
+MASS  -1  OC        15.99900
 
 BONDS
-CT2      CT1       222.500     1.5380
-CT2      CT2       222.500     1.5300
-NECA     CT2       380.000     1.4300
-NH1      CT1       320.000     1.4300
 C        CT1       250.000     1.4900
-O        C         620.000     1.2300
-NECA     CC        320.000     1.4617
+C        O         620.000     1.2300
+CC       NECA      320.000     1.4617
 CC       OC        525.000     1.2600
-NH1      H         440.000     0.9970
+CT1      CT2       222.500     1.5380
 CT1      HB1       330.000     1.0800
-CT2      HA2       309.000     1.1110
+CT1      NH1       320.000     1.4300
+CT2      CT2       222.500     1.5300
 CT2      HA        309.000     1.1110
-NECA     H         440.000     1.0280
+CT2      HA2       309.000     1.1110
+CT2      NECA      380.000     1.4300
+H        NECA      440.000     1.0280
+H        NH1       440.000     0.9970
 
 ANGLES
-NH1      CT1      CT2        70.000     1.9809
-NH1      CT1      C          50.000     1.8675
-CT2      CT1      C          52.000     1.8850
-CT1      CT2      CT2        58.350     1.9809
-CT2      CT2      CT2        58.350     1.9827
-CT2      CT2      NECA       67.700     1.9361
+C        CT1      CT2        52.000     1.8850
+C        CT1      HB1        50.000     1.9111
+C        CT1      NH1        50.000     1.8675
+CC       NECA     CT2        50.000     2.0071
+CC       NECA     H          60.000     1.9199
 CT1      C        O          80.000     2.1118
-CT2      NECA     CC         50.000     2.0071
-NECA     CC       OC         80.000     1.9199
-OC       CC       OC          0.000     0.0000
-H        NH1      CT1        35.000     2.0420
-NH1      CT1      HB1        48.000     1.8850
-HB1      CT1      CT2        35.000     1.9373
-HB1      CT1      C          50.000     1.9111
+CT1      CT2      CT2        58.350     1.9809
 CT1      CT2      HA2        26.500     1.9216
-HA2      CT2      HA2        35.500     1.9024
-HA2      CT2      CT2        26.500     1.9216
+CT1      NH1      H          35.000     2.0420
+CT2      CT1      HB1        35.000     1.9373
+CT2      CT1      NH1        70.000     1.9809
+CT2      CT2      CT2        58.350     1.9827
 CT2      CT2      HA         26.500     1.9216
+CT2      CT2      HA2        26.500     1.9216
+CT2      CT2      NECA       67.700     1.9361
+CT2      NECA     H          60.000     1.9199
 HA       CT2      HA         35.500     1.9024
 HA       CT2      NECA       51.500     1.8762
-CT2      NECA     H          60.000     1.9199
-H        NECA     CC         60.000     1.9199
+HA2      CT2      HA2        35.500     1.9024
+HB1      CT1      NH1        48.000     1.8850
+NECA     CC       OC         80.000     1.9199
+OC       CC       OC          0.000     0.0000
 
 DIHEDRALS
 NH1      CT1      CT2      CT2          0.8800  1   180.00

From 366581a7f6649100ea4a0a003950c977adde6e07 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 2 Feb 2026 15:40:55 -0500
Subject: [PATCH 1272/1492] Start the version 7 changelog

---
 doc/ChangeLog.v7.md | 73 +++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 73 insertions(+)
 create mode 100644 doc/ChangeLog.v7.md

diff --git a/doc/ChangeLog.v7.md b/doc/ChangeLog.v7.md
new file mode 100644
index 0000000000..379952ad18
--- /dev/null
+++ b/doc/ChangeLog.v7.md
@@ -0,0 +1,73 @@
+Changes in version 7.0 of CPPTRAJ. 2026
+=======================================
+
+The major change in this version is the introduction of the ability of CPPTRAJ to fully build and parameterize systems in the same way that LEaP does.
+
+New Commands
+============
+- `build` - Allow full build and parameterization of systems for MD, including CMAP, LJ 12-6-4, solvation, and ions.
+
+- `source` - Read (limited) leaprc files.
+
+- `mutate` - Mutate residues from one kind to another, keeping only common atoms.
+
+- `desc` - DEBUG: describe a selection in the same manner as leap.
+
+New Keywords
+============
+- FIXME check this: Introduce the `byatom` keyword to `checkchirality` action to check the chirality of any atoms in specified mask that are chiral centers.
+
+- Introduce ring intersection check to `checkstructure` action.
+```
+{noringcheck | [ringshortdist <rsdist>] [ringdcut <ringdcut>]
+               [ringacut <ringacut>]}]
+```
+ Ring-bond intersections are detected when the ring center to bond center is less than <rsdist>, or less than <ringdcut> and the angle between the bond vector and ring perpendicular vector is less than <ringacut>.
+
+- Ignore extra points by default in the `checkstructure action.
+```
+[{checkxp | xpmask <xpmask>}]
+```
+If `checkxp` is specified, extra points will be included. By default, extra points will be ignored as determined by 'xpmask'; the default mask to select extra points is '&@\\XP'
+
+Add `namemap <mapset>` keywords for `change atomname from <mask>` to use an atom name map for determining new atom names.
+
+Add `gb` to `change` command to chang GB radii.
+
+Add `complete` keyword to `zmatrix` command to get complete zmatrix instead of minimal zmatrix.
+
+New functionality
+=================
+- Read topology/coordinates with the 'readdata' command.
+
+- More complete read of Amber library/prep files.
+
+- Read CMAP energy term from Amber MDOUT file.
+
+- The `permutedihedrals` command will now check rings.
+
+New file formats recognized
+===========================
+- Read Amber parameter (force field) files.
+
+- Read Amber force field modification (frcmod) files.
+
+- Read leaprc files (limited).
+
+- Read atom/pdb residue name maps.
+
+Misc Fixes
+==========
+- Fix timing percentage of solute-solvent hydrogen bonds in `hbond` action.
+
+- `replicatecell` action will correctly regenerate parameters as needed.
+
+- Fix small memory leak when calculating modes.
+
+- Ensure box information is properly updated if needed when using `crdaction`.
+
+- Improve memory allocation in the Frame class to avoid frequent reallocation of memory.
+
+- Improve handling of very large topology files.
+
+- Better handling of very small boxes with pairlist code.

From 9d97455e6a1568c2fb9e4c3fb432c2b7cee3973b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 3 Feb 2026 11:21:04 -0500
Subject: [PATCH 1273/1492] Add remove residue, graft on new one test

---
 test/Test_Graft/NALA.lib      | 105 ++++++++
 test/Test_Graft/Out.mol2.save | 474 ++++++++++++++++++++++++++++++++++
 test/Test_Graft/RunTest.sh    |  19 +-
 3 files changed, 597 insertions(+), 1 deletion(-)
 create mode 100644 test/Test_Graft/NALA.lib
 create mode 100644 test/Test_Graft/Out.mol2.save

diff --git a/test/Test_Graft/NALA.lib b/test/Test_Graft/NALA.lib
new file mode 100644
index 0000000000..f2eaa8bc3f
--- /dev/null
+++ b/test/Test_Graft/NALA.lib
@@ -0,0 +1,105 @@
+!!index array str
+ "NALA"
+!entry.NALA.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N3" 0 1 131072 1 7 0.141400
+ "H1" "H" 0 1 131072 2 1 0.199700
+ "H2" "H" 0 1 131072 3 1 0.199700
+ "H3" "H" 0 1 131072 4 1 0.199700
+ "CA" "CX" 0 1 131072 5 6 0.096200
+ "HA" "HP" 0 1 131072 6 1 0.088900
+ "CB" "CT" 0 1 131072 7 6 -0.059700
+ "HB1" "HC" 0 1 131072 8 1 0.030000
+ "HB2" "HC" 0 1 131072 9 1 0.030000
+ "HB3" "HC" 0 1 131072 10 1 0.030000
+ "C" "C" 0 1 131072 11 6 0.616300
+ "O" "O" 0 1 131072 12 8 -0.572200
+!entry.NALA.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N3" 0 -1 0.0
+ "H1" "H" 0 -1 0.0
+ "H2" "H" 0 -1 0.0
+ "H3" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "HP" 0 -1 0.0
+ "CB" "CT" 0 -1 0.0
+ "HB1" "HC" 0 -1 0.0
+ "HB2" "HC" 0 -1 0.0
+ "HB3" "HC" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O" 0 -1 0.0
+!entry.NALA.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.NALA.unit.childsequence single int
+ 2
+!entry.NALA.unit.connect array int
+ 0
+ 11
+!entry.NALA.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 1 4 1
+ 1 5 1
+ 5 6 1
+ 5 7 1
+ 5 11 1
+ 7 8 1
+ 7 9 1
+ 7 10 1
+ 11 12 1
+!entry.NALA.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+!entry.NALA.unit.name single str
+ "NALA"
+!entry.NALA.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 4.046154 0.839991 -2.855245E-06
+ 2.823094 1.499508 -0.874687
+ 2.823097 1.499507 0.874685
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 3.877484 3.115795 2.131197
+ 4.075059 4.623017 1.205786
+ 2.496995 3.801075 1.241379
+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+!entry.NALA.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 0 11 0 0 0 0
+!entry.NALA.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "NALA" 1 13 1 "p" 0
+!entry.NALA.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.NALA.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.NALA.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
diff --git a/test/Test_Graft/Out.mol2.save b/test/Test_Graft/Out.mol2.save
new file mode 100644
index 0000000000..40103bab8e
--- /dev/null
+++ b/test/Test_Graft/Out.mol2.save
@@ -0,0 +1,474 @@
+@<TRIPOS>MOLECULE
+Cpptraj Generated mol2 file.
+  222   229    13     0     0
+SMALL
+USER_CHARGES
+
+
+@<TRIPOS>ATOM
+      1 N          -0.3660   10.5720    5.0900 N          1 TRP     -0.415700
+      2 H           0.3440   10.6120    5.8080 H          1 TRP      0.271900
+      3 CA          0.1950   10.6970    3.7600 CT         1 TRP     -0.027500
+      4 HA         -0.2180   11.5690    3.2540 H1         1 TRP      0.112300
+      5 CB          1.7100   10.8790    3.7090 CT         1 TRP     -0.005000
+      6 HB2         2.2080    9.9860    4.0870 HC         1 TRP      0.033900
+      7 HB3         1.9270   11.6410    4.4580 HC         1 TRP      0.033900
+      8 CG          2.2650   11.2910    2.3840 C*         1 TRP     -0.141500
+      9 CD1         2.0320   12.5000    1.8270 CW         1 TRP     -0.163800
+     10 HD1         1.5380   13.3330    2.3050 H4         1 TRP      0.206200
+     11 NE1         2.8600   12.5800    0.7240 NA         1 TRP     -0.341800
+     12 HE1         2.9290   13.4040    0.1430 H          1 TRP      0.341200
+     13 CE2         3.6620   11.4600    0.6460 CN         1 TRP      0.138000
+     14 CZ2         4.6200   11.1600   -0.3300 CA         1 TRP     -0.260100
+     15 HZ2         5.0590   11.8630   -1.0230 HA         1 TRP      0.157200
+     16 CH2         5.0910    9.8430   -0.3770 CA         1 TRP     -0.113400
+     17 HH2         5.8540    9.6100   -1.1050 HA         1 TRP      0.141700
+     18 CZ3         4.5450    8.8500    0.4450 CA         1 TRP     -0.197200
+     19 HZ3         4.8230    7.8400    0.1820 HA         1 TRP      0.144700
+     20 CE3         3.5490    9.1590    1.3790 CA         1 TRP     -0.238700
+     21 HE3         3.1350    8.4300    2.0590 HA         1 TRP      0.170000
+     22 CD2         3.0750   10.4770    1.4830 CB         1 TRP      0.124300
+     23 C          -0.1900    9.6090    2.7680 C          1 TRP      0.597300
+     24 O          -0.4520    9.9630    1.6210 O          1 TRP     -0.567900
+     25 N          -0.2680    8.4020    3.3340 N          2 THR     -0.415700
+     26 H          -0.2600    8.2750    4.3360 H          2 THR      0.271900
+     27 CA         -0.6060    7.1720    2.6470 CT         2 THR     -0.038900
+     28 HA         -0.1800    7.2660    1.6480 H1         2 THR      0.100700
+     29 CB         -0.0930    5.9920    3.4680 CT         2 THR      0.365400
+     30 HB         -0.5860    5.0810    3.1280 H1         2 THR      0.004300
+     31 CG2         1.3430    5.6480    3.0810 CT         2 THR     -0.243800
+     32 HG21        1.3060    5.0050    2.2020 HC         2 THR      0.064200
+     33 HG22        1.9550    6.5430    2.9670 HC         2 THR      0.064200
+     34 HG23        1.8280    5.0680    3.8660 HC         2 THR      0.064200
+     35 OG1        -0.2730    6.2460    4.8430 OH         2 THR     -0.676100
+     36 HG1         0.4280    5.7500    5.2710 HO         2 THR      0.410200
+     37 C          -2.0730    6.8820    2.3630 C          2 THR      0.597300
+     38 O          -2.8840    6.6850    3.2650 O          2 THR     -0.567900
+     39 N          -2.4140    6.7960    1.0750 N          3 TRP     -0.415700
+     40 H          -1.6310    6.7560    0.4390 H          3 TRP      0.271900
+     41 CA         -3.6890    6.2860    0.6130 CT         3 TRP     -0.027500
+     42 HA         -4.2880    6.0200    1.4850 H1         3 TRP      0.112300
+     43 CB         -4.4650    7.2750   -0.2530 CT         3 TRP     -0.005000
+     44 HB2        -5.4500    6.8210   -0.3660 HC         3 TRP      0.033900
+     45 HB3        -4.0220    7.1620   -1.2420 HC         3 TRP      0.033900
+     46 CG         -4.6320    8.7230    0.0770 C*         3 TRP     -0.141500
+     47 CD1        -3.9020    9.7130   -0.4830 CW         3 TRP     -0.163800
+     48 HD1        -3.0890    9.5530   -1.1760 H4         3 TRP      0.206200
+     49 NE1        -4.4730   10.9230   -0.1410 NA         3 TRP     -0.341800
+     50 HE1        -4.1360   11.8610   -0.3060 H          3 TRP      0.341200
+     51 CE2        -5.4690   10.7460    0.7980 CN         3 TRP      0.138000
+     52 CZ2        -6.3300   11.6930    1.3650 CA         3 TRP     -0.260100
+     53 HZ2        -6.2760   12.7460    1.1300 HA         3 TRP      0.157200
+     54 CH2        -7.3740   11.1960    2.1540 CA         3 TRP     -0.113400
+     55 HH2        -8.2300   11.8220    2.3620 HA         3 TRP      0.141700
+     56 CZ3        -7.6300    9.8240    2.2590 CA         3 TRP     -0.197200
+     57 HZ3        -8.3790    9.4820    2.9590 HA         3 TRP      0.144700
+     58 CE3        -6.7760    8.9050    1.6380 CA         3 TRP     -0.238700
+     59 HE3        -6.9740    7.8720    1.8840 HA         3 TRP      0.170000
+     60 CD2        -5.7030    9.3470    0.8480 CB         3 TRP      0.124300
+     61 C          -3.6320    4.9260   -0.0680 C          3 TRP      0.597300
+     62 O          -4.2790    3.9520    0.3090 O          3 TRP     -0.567900
+     63 N          -2.7950    4.8720   -1.1060 N          4 GLU     -0.516300
+     64 H          -2.2780    5.7080   -1.3390 H          4 GLU      0.293600
+     65 CA         -2.5350    3.7230   -1.9500 CT         4 GLU      0.039700
+     66 HA         -3.0070    2.9480   -1.3460 H1         4 GLU      0.110500
+     67 CB         -3.4130    3.5240   -3.1830 CT         4 GLU      0.056000
+     68 HB2        -3.1390    4.1410   -4.0380 HC         4 GLU     -0.017300
+     69 HB3        -4.3860    3.7870   -2.7670 HC         4 GLU     -0.017300
+     70 CG         -3.4700    2.1080   -3.7480 CT         4 GLU      0.013600
+     71 HG2        -2.4470    1.7930   -3.9530 HC         4 GLU     -0.042500
+     72 HG3        -4.0390    2.4250   -4.6230 HC         4 GLU     -0.042500
+     73 CD         -4.1890    1.1230   -2.8370 C          4 GLU      0.805400
+     74 OE1        -3.8030    0.7710   -1.7020 O2         4 GLU     -0.818800
+     75 OE2        -5.2630    0.6010   -3.2070 O2         4 GLU     -0.818800
+     76 C          -1.0580    3.5180   -2.2550 C          4 GLU      0.536600
+     77 O          -0.3010    4.4140   -2.6190 O          4 GLU     -0.581900
+     78 N          -0.6680    2.2650   -2.0090 N          5 ASN     -0.415700
+     79 H          -1.3230    1.6560   -1.5390 H          5 ASN      0.271900
+     80 CA          0.6390    1.6960   -2.2670 CT         5 ASN      0.014300
+     81 HA          1.2390    2.4530   -2.7720 H1         5 ASN      0.104800
+     82 CB          1.4120    1.3660   -0.9930 CT         5 ASN     -0.204100
+     83 HB2         2.2240    0.7030   -1.2910 HC         5 ASN      0.079700
+     84 HB3         0.7120    0.8820   -0.3110 HC         5 ASN      0.079700
+     85 CG          2.1540    2.5500   -0.3910 C          5 ASN      0.713000
+     86 OD1         2.8090    3.3470   -1.0580 O          5 ASN     -0.593100
+     87 ND2         2.3590    2.5190    0.9280 N          5 ASN     -0.919100
+     88 HD21        1.8690    1.8970    1.5560 H          5 ASN      0.419600
+     89 HD22        3.0240    3.1960    1.2720 H          5 ASN      0.419600
+     90 C           0.5090    0.4880   -3.1850 C          5 ASN      0.597300
+     91 O          -0.4570   -0.2500   -3.0040 O          5 ASN     -0.567900
+     92 N           1.4630    0.2470   -4.0870 N          6 GLY     -0.415700
+     93 H           2.3720    0.6580   -3.9320 H          6 GLY      0.271900
+     94 CA          1.3990   -0.9020   -4.9670 CT         6 GLY     -0.025200
+     95 HA2         2.1800   -0.8820   -5.7280 H1         6 GLY      0.069800
+     96 HA3         0.5010   -0.7990   -5.5760 H1         6 GLY      0.069800
+     97 C           1.4480   -2.2750   -4.3130 C          6 GLY      0.597300
+     98 O           0.7270   -2.5760   -3.3640 O          6 GLY     -0.567900
+     99 N           2.3610   -3.1180   -4.8010 N          7 LYS     -0.347900
+    100 H           3.0800   -2.7840   -5.4260 H          7 LYS      0.274700
+    101 CA          2.5410   -4.5140   -4.4580 CT         7 LYS     -0.240000
+    102 HA          1.6270   -5.0150   -4.1380 H1         7 LYS      0.142600
+    103 CB          3.1230   -5.2830   -5.6410 CT         7 LYS     -0.009400
+    104 HB2         2.4350   -5.2430   -6.4860 HC         7 LYS      0.036200
+    105 HB3         3.3350   -6.3180   -5.3720 HC         7 LYS      0.036200
+    106 CG          4.4160   -4.7460   -6.2480 CT         7 LYS      0.018700
+    107 HG2         5.3080   -4.9600   -5.6600 HC         7 LYS      0.010300
+    108 HG3         4.3930   -3.6740   -6.4390 HC         7 LYS      0.010300
+    109 CD          4.7260   -5.5030   -7.5360 CT         7 LYS     -0.047900
+    110 HD2         3.9920   -5.2720   -8.3080 HC         7 LYS      0.062100
+    111 HD3         4.5840   -6.5430   -7.2410 HC         7 LYS      0.062100
+    112 CE          6.1480   -5.3380   -8.0660 CT         7 LYS     -0.014300
+    113 HE2         6.5210   -6.2900   -8.4440 HP         7 LYS      0.113500
+    114 HE3         6.8480   -5.0250   -7.2900 HP         7 LYS      0.113500
+    115 NZ          6.1770   -4.4200   -9.2140 N3         7 LYS     -0.385400
+    116 HZ1         6.0460   -3.5470   -8.7220 H          7 LYS      0.340000
+    117 HZ2         7.1310   -4.3920   -9.5460 H          7 LYS      0.340000
+    118 HZ3         5.4710   -4.5500   -9.9250 H          7 LYS      0.340000
+    119 C           3.5120   -4.5190   -3.2860 C          7 LYS      0.734100
+    120 O           4.6240   -5.0420   -3.2860 O          7 LYS     -0.589400
+    121 N           2.9250   -4.2560   -2.1160 N          8 TRP     -0.415700
+    122 H           2.0100   -3.8790   -2.3160 H          8 TRP      0.271900
+    123 CA          3.3410   -4.2620   -0.7280 CT         8 TRP     -0.027500
+    124 HA          4.4100   -4.0450   -0.7240 H1         8 TRP      0.112300
+    125 CB          2.6250   -3.0680   -0.1040 CT         8 TRP     -0.005000
+    126 HB2         1.5890   -3.2940    0.1480 HC         8 TRP      0.033900
+    127 HB3         2.8350   -2.1940   -0.7210 HC         8 TRP      0.033900
+    128 CG          3.2880   -2.4620    1.0910 C*         8 TRP     -0.141500
+    129 CD1         2.9250   -2.4360    2.3930 CW         8 TRP     -0.163800
+    130 HD1         1.9490   -2.7990    2.6780 H4         8 TRP      0.206200
+    131 NE1         3.8550   -1.8450    3.2240 NA         8 TRP     -0.341800
+    132 HE1         3.8850   -1.8480    4.2340 H          8 TRP      0.341200
+    133 CE2         4.8270   -1.3030    2.4080 CN         8 TRP      0.138000
+    134 CZ2         5.9110   -0.4710    2.7140 CA         8 TRP     -0.260100
+    135 HZ2         6.1390   -0.1560    3.7210 HA         8 TRP      0.157200
+    136 CH2         6.8410   -0.1410    1.7220 CA         8 TRP     -0.113400
+    137 HH2         7.7250    0.4050    2.0180 HA         8 TRP      0.141700
+    138 CZ3         6.5840   -0.5900    0.4210 CA         8 TRP     -0.197200
+    139 HZ3         7.2310   -0.2350   -0.3680 HA         8 TRP      0.144700
+    140 CE3         5.4240   -1.2970    0.0820 CA         8 TRP     -0.238700
+    141 HE3         5.1390   -1.4650   -0.9460 HA         8 TRP      0.170000
+    142 CD2         4.4790   -1.6200    1.0690 CB         8 TRP      0.124300
+    143 C           2.9450   -5.5930   -0.1050 C          8 TRP      0.597300
+    144 O           3.0220   -6.6750   -0.6820 O          8 TRP     -0.567900
+    145 N           2.5310   -5.6090    1.1640 N          9 THR     -0.415700
+    146 H           2.7110   -4.7940    1.7310 H          9 THR      0.271900
+    147 CA          2.2540   -6.8740    1.8150 CT         9 THR     -0.038900
+    148 HA          2.9820   -7.6670    1.6440 H1         9 THR      0.100700
+    149 CB          2.2070   -6.6220    3.3200 CT         9 THR      0.365400
+    150 HB          1.7220   -5.6670    3.5260 H1         9 THR      0.004300
+    151 CG2         1.4560   -7.6590    4.1490 CT         9 THR     -0.243800
+    152 HG21        1.5810   -7.4640    5.2140 HC         9 THR      0.064200
+    153 HG22        0.4020   -7.4680    3.9460 HC         9 THR      0.064200
+    154 HG23        1.7250   -8.6400    3.7550 HC         9 THR      0.064200
+    155 OG1         3.4600   -6.5010    3.9540 OH         9 THR     -0.676100
+    156 HG1         3.3850   -6.0970    4.8220 HO         9 THR      0.410200
+    157 C           0.8890   -7.3540    1.3440 C          9 THR      0.597300
+    158 O          -0.1720   -6.7600    1.5240 O          9 THR     -0.567900
+    159 N           0.9060   -8.5220    0.6990 N         10 TRP     -0.415700
+    160 H           1.7230   -9.1150    0.7340 H         10 TRP      0.271900
+    161 CA         -0.1880   -9.0660   -0.0800 CT        10 TRP     -0.027500
+    162 HA         -0.7370   -8.2200   -0.4950 H1        10 TRP      0.112300
+    163 CB          0.4120  -10.0100   -1.1170 CT        10 TRP     -0.005000
+    164 HB2         1.1130  -10.7100   -0.6610 HC        10 TRP      0.033900
+    165 HB3         0.8870   -9.3680   -1.8590 HC        10 TRP      0.033900
+    166 CG         -0.5390  -10.9280   -1.8160 C*        10 TRP     -0.141500
+    167 CD1        -1.3130  -10.6860   -2.8980 CW        10 TRP     -0.163800
+    168 HD1        -1.3370   -9.7640   -3.4600 H4        10 TRP      0.206200
+    169 NE1        -1.9710  -11.7860   -3.4110 NA        10 TRP     -0.341800
+    170 HE1        -2.3840  -11.8640   -4.3300 H         10 TRP      0.341200
+    171 CE2        -1.9570  -12.7630   -2.4370 CN        10 TRP      0.138000
+    172 CZ2        -2.7850  -13.8650   -2.1910 CA        10 TRP     -0.260100
+    173 HZ2        -3.6310  -14.0120   -2.8460 HA        10 TRP      0.157200
+    174 CH2        -2.6000  -14.7090   -1.0890 CA        10 TRP     -0.113400
+    175 HH2        -3.3150  -15.4730   -0.8230 HA        10 TRP      0.141700
+    176 CZ3        -1.5180  -14.3450   -0.2780 CA        10 TRP     -0.197200
+    177 HZ3        -1.3250  -14.9360    0.6040 HA        10 TRP      0.144700
+    178 CE3        -0.8090  -13.1460   -0.4190 CA        10 TRP     -0.238700
+    179 HE3        -0.0380  -12.8340    0.2700 HA        10 TRP      0.170000
+    180 CD2        -1.0340  -12.2590   -1.4840 CB        10 TRP      0.124300
+    181 C          -1.0790   -9.7520    0.9460 C         10 TRP      0.597300
+    182 O          -0.7100  -10.6730    1.6720 O         10 TRP     -0.567900
+    183 N          -2.3440   -9.3260    0.9490 N         11 LYS     -0.347900
+    184 H          -2.4560   -8.3390    0.7700 H         11 LYS      0.274700
+    185 CA         -3.4700   -9.9260    1.6360 CT        11 LYS     -0.240000
+    186 HA         -3.0970  -10.4390    2.5220 H1        11 LYS      0.142600
+    187 CB         -4.3840   -8.8140    2.1420 CT        11 LYS     -0.009400
+    188 HB2        -5.3890   -9.1120    2.4400 HC        11 LYS      0.036200
+    189 HB3        -4.4390   -8.0090    1.4090 HC        11 LYS      0.036200
+    190 CG         -3.7990   -8.0920    3.3520 CT        11 LYS      0.018700
+    191 HG2        -2.8890   -7.5660    3.0640 HC        11 LYS      0.010300
+    192 HG3        -3.6910   -8.7240    4.2330 HC        11 LYS      0.010300
+    193 CD         -4.8480   -7.0240    3.6500 CT        11 LYS     -0.047900
+    194 HD2        -5.6910   -7.4110    4.2220 HC        11 LYS      0.062100
+    195 HD3        -5.1300   -6.4950    2.7400 HC        11 LYS      0.062100
+    196 CE         -4.1080   -6.0190    4.5290 CT        11 LYS     -0.014300
+    197 HE2        -3.1830   -5.6350    4.0990 HP        11 LYS      0.113500
+    198 HE3        -3.8850   -6.5530    5.4520 HP        11 LYS      0.113500
+    199 NZ         -4.8770   -4.8020    4.8290 N3        11 LYS     -0.385400
+    200 HZ1        -5.1320   -4.3050    3.9870 H         11 LYS      0.340000
+    201 HZ2        -5.7180   -4.9680    5.3620 H         11 LYS      0.340000
+    202 HZ3        -4.2500   -4.2630    5.4100 H         11 LYS      0.340000
+    203 C          -4.3950  -10.7780    0.7790 C         11 LYS      0.734100
+    204 O          -4.4830  -11.9390    1.1720 O         11 LYS     -0.589400
+    205 N          -4.8320  -10.2020   -0.3440 N         12 NME     -0.415700
+    206 H          -4.6470   -9.2390   -0.5870 H         12 NME      0.271900
+    207 CH3        -5.7200  -10.8660   -1.2770 CT        12 NME     -0.149000
+    208 HH31       -5.5910  -11.9460   -1.3400 H1        12 NME      0.097600
+    209 HH32       -6.7570  -10.8860   -0.9420 H1        12 NME      0.097600
+    210 HH33       -5.7770  -10.3580   -2.2400 H1        12 NME      0.097600
+    211 N          -3.7277   10.1413    6.5932 N3        13 NALA     0.141400
+    212 H1         -4.0094   10.1591    5.6234 H         13 NALA     0.199700
+    213 H2         -4.0987   10.9599    7.0540 H         13 NALA     0.199700
+    214 H3         -3.9143    9.2223    6.9685 H         13 NALA     0.199700
+    215 CA         -2.2875   10.2915    6.6465 CX        13 NALA     0.096200
+    216 HA         -2.0359   11.1860    7.2162 HP        13 NALA     0.088900
+    217 CB         -1.6344    9.0873    7.3165 CT        13 NALA    -0.059700
+    218 HB1        -1.8698    8.1849    6.7523 HC        13 NALA     0.030000
+    219 HB2        -0.5538    9.2272    7.3427 HC        13 NALA     0.030000
+    220 HB3        -2.0122    8.9878    8.3341 HC        13 NALA     0.030000
+    221 C          -1.6982   10.4228    5.2494 C         13 NALA     0.616300
+    222 O          -2.4352   10.3930    4.2663 O         13 NALA    -0.572200
+@<TRIPOS>BOND
+    1     1     3 1
+    2     3     5 1
+    3     3    23 1
+    4     5     8 1
+    5     8     9 1
+    6     8    22 1
+    7     9    11 1
+    8    11    13 1
+    9    13    14 1
+   10    13    22 1
+   11    14    16 1
+   12    16    18 1
+   13    18    20 1
+   14    20    22 1
+   15    23    24 1
+   16    23    25 1
+   17    25    27 1
+   18    27    29 1
+   19    27    37 1
+   20    29    31 1
+   21    29    35 1
+   22    37    38 1
+   23    37    39 1
+   24    39    41 1
+   25    41    43 1
+   26    41    61 1
+   27    43    46 1
+   28    46    47 1
+   29    46    60 1
+   30    47    49 1
+   31    49    51 1
+   32    51    52 1
+   33    51    60 1
+   34    52    54 1
+   35    54    56 1
+   36    56    58 1
+   37    58    60 1
+   38    61    62 1
+   39    61    63 1
+   40    63    65 1
+   41    65    67 1
+   42    65    76 1
+   43    67    70 1
+   44    70    73 1
+   45    73    74 1
+   46    73    75 1
+   47    76    77 1
+   48    76    78 1
+   49    78    80 1
+   50    80    82 1
+   51    80    90 1
+   52    82    85 1
+   53    85    86 1
+   54    85    87 1
+   55    90    91 1
+   56    90    92 1
+   57    92    94 1
+   58    94    97 1
+   59    97    98 1
+   60    97    99 1
+   61    99   101 1
+   62   101   103 1
+   63   101   119 1
+   64   103   106 1
+   65   106   109 1
+   66   109   112 1
+   67   112   115 1
+   68   119   120 1
+   69   119   121 1
+   70   121   123 1
+   71   123   125 1
+   72   123   143 1
+   73   125   128 1
+   74   128   129 1
+   75   128   142 1
+   76   129   131 1
+   77   131   133 1
+   78   133   134 1
+   79   133   142 1
+   80   134   136 1
+   81   136   138 1
+   82   138   140 1
+   83   140   142 1
+   84   143   144 1
+   85   143   145 1
+   86   145   147 1
+   87   147   149 1
+   88   147   157 1
+   89   149   151 1
+   90   149   155 1
+   91   157   158 1
+   92   157   159 1
+   93   159   161 1
+   94   161   163 1
+   95   161   181 1
+   96   163   166 1
+   97   166   167 1
+   98   166   180 1
+   99   167   169 1
+  100   169   171 1
+  101   171   172 1
+  102   171   180 1
+  103   172   174 1
+  104   174   176 1
+  105   176   178 1
+  106   178   180 1
+  107   181   182 1
+  108   181   183 1
+  109   183   185 1
+  110   185   187 1
+  111   185   203 1
+  112   187   190 1
+  113   190   193 1
+  114   193   196 1
+  115   196   199 1
+  116   203   204 1
+  117   203   205 1
+  118   205   207 1
+  119   211   215 1
+  120   215   217 1
+  121   215   221 1
+  122   221   222 1
+  123   221     1 1
+  124     1     2 1
+  125     3     4 1
+  126     5     6 1
+  127     5     7 1
+  128     9    10 1
+  129    11    12 1
+  130    14    15 1
+  131    16    17 1
+  132    18    19 1
+  133    20    21 1
+  134    25    26 1
+  135    27    28 1
+  136    29    30 1
+  137    31    32 1
+  138    31    33 1
+  139    31    34 1
+  140    35    36 1
+  141    39    40 1
+  142    41    42 1
+  143    43    44 1
+  144    43    45 1
+  145    47    48 1
+  146    49    50 1
+  147    52    53 1
+  148    54    55 1
+  149    56    57 1
+  150    58    59 1
+  151    63    64 1
+  152    65    66 1
+  153    67    68 1
+  154    67    69 1
+  155    70    71 1
+  156    70    72 1
+  157    78    79 1
+  158    80    81 1
+  159    82    83 1
+  160    82    84 1
+  161    87    88 1
+  162    87    89 1
+  163    92    93 1
+  164    94    95 1
+  165    94    96 1
+  166    99   100 1
+  167   101   102 1
+  168   103   104 1
+  169   103   105 1
+  170   106   107 1
+  171   106   108 1
+  172   109   110 1
+  173   109   111 1
+  174   112   113 1
+  175   112   114 1
+  176   115   116 1
+  177   115   117 1
+  178   115   118 1
+  179   121   122 1
+  180   123   124 1
+  181   125   126 1
+  182   125   127 1
+  183   129   130 1
+  184   131   132 1
+  185   134   135 1
+  186   136   137 1
+  187   138   139 1
+  188   140   141 1
+  189   145   146 1
+  190   147   148 1
+  191   149   150 1
+  192   151   152 1
+  193   151   153 1
+  194   151   154 1
+  195   155   156 1
+  196   159   160 1
+  197   161   162 1
+  198   163   164 1
+  199   163   165 1
+  200   167   168 1
+  201   169   170 1
+  202   172   173 1
+  203   174   175 1
+  204   176   177 1
+  205   178   179 1
+  206   183   184 1
+  207   185   186 1
+  208   187   188 1
+  209   187   189 1
+  210   190   191 1
+  211   190   192 1
+  212   193   194 1
+  213   193   195 1
+  214   196   197 1
+  215   196   198 1
+  216   199   200 1
+  217   199   201 1
+  218   199   202 1
+  219   205   206 1
+  220   207   208 1
+  221   207   209 1
+  222   207   210 1
+  223   211   212 1
+  224   211   213 1
+  225   211   214 1
+  226   215   216 1
+  227   217   218 1
+  228   217   219 1
+  229   217   220 1
+@<TRIPOS>SUBSTRUCTURE
+      1 TRP               1 ****               0 ****  **** 
+      2 THR              25 ****               0 ****  **** 
+      3 TRP              39 ****               0 ****  **** 
+      4 GLU              63 ****               0 ****  **** 
+      5 ASN              78 ****               0 ****  **** 
+      6 GLY              92 ****               0 ****  **** 
+      7 LYS              99 ****               0 ****  **** 
+      8 TRP             121 ****               0 ****  **** 
+      9 THR             145 ****               0 ****  **** 
+     10 TRP             159 ****               0 ****  **** 
+     11 LYS             183 ****               0 ****  **** 
+     12 NME             205 ****               0 ****  **** 
+     13 NALA            211 ****               0 ****  **** 
diff --git a/test/Test_Graft/RunTest.sh b/test/Test_Graft/RunTest.sh
index e5b32c2f2b..d4129fde46 100755
--- a/test/Test_Graft/RunTest.sh
+++ b/test/Test_Graft/RunTest.sh
@@ -3,7 +3,8 @@
 . ../MasterTest.sh
 
 CleanFiles cpptraj.in Final.graft.mol2 Nucleotide.pdb Nucleotide.charge.mol2 \
-           IC.Final.graft.mol2 IC.Nucleotide.pdb
+           IC.Final.graft.mol2 IC.Nucleotide.pdb Out.mol2 \
+           zFinal.dat zicBaseSugar.dat zicFinal.dat
 TESTNAME='Graft test'
 Requires notparallel
 
@@ -185,11 +186,27 @@ EOF
   DoTest Nucleotide.charge.mol2.save Nucleotide.charge.mol2
 }
 
+# Remove existing N-terminal residue, graft another one on
+RemoveAndGraft() {
+  cat > cpptraj.in <<EOF
+parm ../tz2.parm7
+loadcrd ../tz2.rst7 name MyMol
+readdata NALA.lib name NALA
+crdaction MyMol strip :1
+graft src NALA[NALA] tgt MyMol ic bond :1@N,:1@C name Out
+crdout Out Out.mol2
+quit
+EOF
+  RunCpptraj "Remove an existing residue and graft on a new one."
+  DoTest Out.mol2.save Out.mol2
+}
+
 TyrPry
 TyrPryIC
 DNA
 DNAic
 DNAcharge
+RemoveAndGraft
 
 EndTest
 exit 0

From dfb6c28ac54af519b16abbdec35d11a2f1ddad22 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 3 Feb 2026 12:04:28 -0500
Subject: [PATCH 1274/1492] checkchirality byatom is not ready yet - disable
 for now

---
 src/Action_CheckChirality.cpp | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/src/Action_CheckChirality.cpp b/src/Action_CheckChirality.cpp
index 13af1a0c3b..514a88da38 100644
--- a/src/Action_CheckChirality.cpp
+++ b/src/Action_CheckChirality.cpp
@@ -6,10 +6,11 @@
 #include "Structure/Chirality.h"
 
 void Action_CheckChirality::Help() const {
-  mprintf("\t[<name>] [<mask1>] [out <filename>] [byatom]\n"
-          "  Check the chirality of amino acid residues in <mask1>.\n"
-          "  If 'byatom' is specified, check the chirality of any atoms in\n"
-          "  <mask1> that are chiral centers.\n");
+  //mprintf("\t[<name>] [<mask1>] [out <filename>] [byatom]\n"
+  mprintf("\t[<name>] [<mask1>] [out <filename>]\n"
+          "  Check the chirality of amino acid residues in <mask1>.\n");
+//          "  If 'byatom' is specified, check the chirality of any atoms in\n"
+//          "  <mask1> that are chiral centers.\n");
 }
 
 /** CONSTRUCTOR */
@@ -28,7 +29,8 @@ Action::RetType Action_CheckChirality::Init(ArgList& actionArgs, ActionInit& ini
   debug_ = debugIn;
   // Get keywords
   outfile_ = init.DFL().AddDataFile( actionArgs.GetStringKey("out"), actionArgs );
-  byatom_ = actionArgs.hasKey("byatom");
+  //byatom_ = actionArgs.hasKey("byatom");i //FIXME - not ready for primetime, needs more testing
+  byatom_ = false;
   // Get Masks
   if (Mask1_.SetMaskString( actionArgs.GetMaskNext() )) return Action::ERR;
   // Set up DataSets

From 18f8010c27be122accde4cc4925f9e0a7b1dbc51 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 3 Feb 2026 15:13:02 -0500
Subject: [PATCH 1275/1492] Add tests for grafting with connect atoms

---
 test/Test_Graft/ALA.ARG.lib       | 269 ++++++++++++++++++++++++++++++
 test/Test_Graft/RunTest.sh        |  17 +-
 test/Test_Graft/ala.arg.mol2.save |  79 +++++++++
 3 files changed, 364 insertions(+), 1 deletion(-)
 create mode 100644 test/Test_Graft/ALA.ARG.lib
 create mode 100644 test/Test_Graft/ala.arg.mol2.save

diff --git a/test/Test_Graft/ALA.ARG.lib b/test/Test_Graft/ALA.ARG.lib
new file mode 100644
index 0000000000..6322f534b0
--- /dev/null
+++ b/test/Test_Graft/ALA.ARG.lib
@@ -0,0 +1,269 @@
+!!index array str
+ "ALA"
+ "ARG"
+!entry.ALA.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N" 0 1 131072 1 7 -0.415700
+ "H" "H" 0 1 131072 2 1 0.271900
+ "CA" "XC" 0 1 131072 3 6 0.033700
+ "HA" "H1" 0 1 131072 4 1 0.082300
+ "CB" "CT" 0 1 131072 5 6 -0.182500
+ "HB1" "HC" 0 1 131072 6 1 0.060300
+ "HB2" "HC" 0 1 131072 7 1 0.060300
+ "HB3" "HC" 0 1 131072 8 1 0.060300
+ "C" "C" 0 1 131072 9 6 0.597300
+ "O" "O" 0 1 131072 10 8 -0.567900
+!entry.ALA.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
+ "H" "H" 0 -1 0.0
+ "CA" "XC" 0 -1 0.0
+ "HA" "H1" 0 -1 0.0
+ "CB" "CT" 0 -1 0.0
+ "HB1" "HC" 0 -1 0.0
+ "HB2" "HC" 0 -1 0.0
+ "HB3" "HC" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O" 0 -1 0.0
+!entry.ALA.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.ALA.unit.childsequence single int
+ 2
+!entry.ALA.unit.connect array int
+ 1
+ 9
+!entry.ALA.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 3 4 1
+ 3 5 1
+ 3 9 1
+ 5 6 1
+ 5 7 1
+ 5 8 1
+ 9 10 1
+!entry.ALA.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+!entry.ALA.unit.name single str
+ "ALA"
+!entry.ALA.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 3.909407 0.723611 -2.739882E-06
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 3.877484 3.115795 2.131197
+ 4.075059 4.623017 1.205786
+ 2.496995 3.801075 1.241379
+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+!entry.ALA.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 9 0 0 0 0
+!entry.ALA.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "ALA" 1 11 1 "p" 0
+!entry.ALA.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.ALA.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.ALA.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+!entry.ARG.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N" 0 1 131072 1 7 -0.347900
+ "H" "H" 0 1 131072 2 1 0.274700
+ "CA" "XC" 0 1 131072 3 6 -0.263700
+ "HA" "H1" 0 1 131072 4 1 0.156000
+ "CB" "C8" 0 1 131072 5 6 -0.000700
+ "HB2" "HC" 0 1 131072 6 1 0.032700
+ "HB3" "HC" 0 1 131072 7 1 0.032700
+ "CG" "C8" 0 1 131072 8 6 0.039000
+ "HG2" "HC" 0 1 131072 9 1 0.028500
+ "HG3" "HC" 0 1 131072 10 1 0.028500
+ "CD" "C8" 0 1 131072 11 6 0.048600
+ "HD2" "H1" 0 1 131072 12 1 0.068700
+ "HD3" "H1" 0 1 131072 13 1 0.068700
+ "NE" "N2" 0 1 131072 14 7 -0.529500
+ "HE" "H" 0 1 131072 15 1 0.345600
+ "CZ" "CA" 0 1 131072 16 6 0.807600
+ "NH1" "N2" 0 1 131072 17 7 -0.862700
+ "HH11" "H" 0 1 131072 18 1 0.447800
+ "HH12" "H" 0 1 131072 19 1 0.447800
+ "NH2" "N2" 0 1 131072 20 7 -0.862700
+ "HH21" "H" 0 1 131072 21 1 0.447800
+ "HH22" "H" 0 1 131072 22 1 0.447800
+ "C" "C" 0 1 131072 23 6 0.734100
+ "O" "O" 0 1 131072 24 8 -0.589400
+!entry.ARG.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
+ "H" "H" 0 -1 0.0
+ "CA" "XC" 0 -1 0.0
+ "HA" "H1" 0 -1 0.0
+ "CB" "C8" 0 -1 0.0
+ "HB2" "HC" 0 -1 0.0
+ "HB3" "HC" 0 -1 0.0
+ "CG" "C8" 0 -1 0.0
+ "HG2" "HC" 0 -1 0.0
+ "HG3" "HC" 0 -1 0.0
+ "CD" "C8" 0 -1 0.0
+ "HD2" "H1" 0 -1 0.0
+ "HD3" "H1" 0 -1 0.0
+ "NE" "N2" 0 -1 0.0
+ "HE" "H" 0 -1 0.0
+ "CZ" "CA" 0 -1 0.0
+ "NH1" "N2" 0 -1 0.0
+ "HH11" "H" 0 -1 0.0
+ "HH12" "H" 0 -1 0.0
+ "NH2" "N2" 0 -1 0.0
+ "HH21" "H" 0 -1 0.0
+ "HH22" "H" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O" 0 -1 0.0
+!entry.ARG.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.ARG.unit.childsequence single int
+ 2
+!entry.ARG.unit.connect array int
+ 1
+ 23
+!entry.ARG.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 3 4 1
+ 3 5 1
+ 3 23 1
+ 5 6 1
+ 5 7 1
+ 5 8 1
+ 8 9 1
+ 8 10 1
+ 8 11 1
+ 11 12 1
+ 11 13 1
+ 11 14 1
+ 14 15 1
+ 14 16 1
+ 16 17 1
+ 16 20 1
+ 17 18 1
+ 17 19 1
+ 20 21 1
+ 20 22 1
+ 23 24 1
+!entry.ARG.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+ "R" 1 "A" 14
+ "R" 1 "A" 15
+ "R" 1 "A" 16
+ "R" 1 "A" 17
+ "R" 1 "A" 18
+ "R" 1 "A" 19
+ "R" 1 "A" 20
+ "R" 1 "A" 21
+ "R" 1 "A" 22
+ "R" 1 "A" 23
+ "R" 1 "A" 24
+!entry.ARG.unit.name single str
+ "ARG"
+!entry.ARG.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 3.909407 0.723611 -2.739882E-06
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 2.496995 3.801075 1.241379
+ 3.877484 3.115795 2.131197
+ 4.274186 5.009602 1.194577
+ 5.354271 4.863178 1.185788
+ 3.973781 5.548460 0.295972
+ 3.881105 5.817645 2.426721
+ 2.801135 5.964881 2.435959
+ 4.181626 5.279602 3.325774
+ 4.540320 7.142723 2.424483
+ 5.151805 7.375492 1.655065
+ 4.364284 8.040989 3.389382
+ 3.575026 7.807606 4.434133
+ 3.088949 6.925423 4.508848
+ 3.465367 8.513631 5.147998
+ 5.006254 9.201287 3.286991
+ 5.604855 9.375325 2.492329
+ 4.892216 9.903045 4.004368
+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+!entry.ARG.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 23 0 0 0 0
+!entry.ARG.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "ARG" 1 25 1 "p" 0
+!entry.ARG.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.ARG.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.ARG.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
diff --git a/test/Test_Graft/RunTest.sh b/test/Test_Graft/RunTest.sh
index d4129fde46..da9faecb6a 100755
--- a/test/Test_Graft/RunTest.sh
+++ b/test/Test_Graft/RunTest.sh
@@ -3,7 +3,7 @@
 . ../MasterTest.sh
 
 CleanFiles cpptraj.in Final.graft.mol2 Nucleotide.pdb Nucleotide.charge.mol2 \
-           IC.Final.graft.mol2 IC.Nucleotide.pdb Out.mol2 \
+           IC.Final.graft.mol2 IC.Nucleotide.pdb Out.mol2 Out2.mol2 \
            zFinal.dat zicBaseSugar.dat zicFinal.dat
 TESTNAME='Graft test'
 Requires notparallel
@@ -193,12 +193,26 @@ parm ../tz2.parm7
 loadcrd ../tz2.rst7 name MyMol
 readdata NALA.lib name NALA
 crdaction MyMol strip :1
+dataset MyMol connect headmask :1@N
 graft src NALA[NALA] tgt MyMol ic bond :1@N,:1@C name Out
+graft src NALA[NALA] tgt MyMol ic name Out2
 crdout Out Out.mol2
+crdout Out2 Out2.mol2
 quit
 EOF
   RunCpptraj "Remove an existing residue and graft on a new one."
   DoTest Out.mol2.save Out.mol2
+  DoTest Out.mol2.save Out2.mol2
+}
+
+# Graft residues with CONNECT atoms
+GraftWithConnect() {
+  cat > cpptraj.in <<EOF
+readdata ALA.ARG.lib name LIB
+graft src LIB[ARG] tgt LIB[ALA] ic name Mol
+crdout Mol ala.arg.mol2
+EOF
+  RunCpptraj "Graft residues with CONNECT atoms"
 }
 
 TyrPry
@@ -207,6 +221,7 @@ DNA
 DNAic
 DNAcharge
 RemoveAndGraft
+GraftWithConnect
 
 EndTest
 exit 0
diff --git a/test/Test_Graft/ala.arg.mol2.save b/test/Test_Graft/ala.arg.mol2.save
new file mode 100644
index 0000000000..6e38838716
--- /dev/null
+++ b/test/Test_Graft/ala.arg.mol2.save
@@ -0,0 +1,79 @@
+@<TRIPOS>MOLECULE
+Cpptraj Generated mol2 file.
+   34    33     2     0     0
+SMALL
+USER_CHARGES
+
+
+@<TRIPOS>ATOM
+      1 N           3.3258    1.5479   -0.0000 N          1 ALA     -0.415700
+      2 H           3.9094    0.7236   -0.0000 H          1 ALA      0.271900
+      3 CA          3.9700    2.8458   -0.0000 XC         1 ALA      0.033700
+      4 HA          3.6717    3.4001   -0.8898 H1         1 ALA      0.082300
+      5 CB          3.5770    3.6538    1.2321 CT         1 ALA     -0.182500
+      6 HB1         3.8775    3.1158    2.1312 HC         1 ALA      0.060300
+      7 HB2         4.0751    4.6230    1.2058 HC         1 ALA      0.060300
+      8 HB3         2.4970    3.8011    1.2414 HC         1 ALA      0.060300
+      9 C           5.4855    2.7052   -0.0000 C          1 ALA      0.597300
+     10 O           6.0088    1.5932   -0.0000 O          1 ALA     -0.567900
+     11 N           6.2656    3.8070   -0.0000 N          2 ARG     -0.347900
+     12 H           5.8436    4.7246   -0.0000 H          2 ARG      0.274700
+     13 CA          7.7085    3.6731   -0.0000 XC         2 ARG     -0.263700
+     14 HA          8.0233    3.1280    0.8898 H1         2 ARG      0.156000
+     15 CB          8.1894    2.9141   -1.2322 C8         2 ARG     -0.000700
+     16 HB2         7.7472    1.9179   -1.2414 HC         2 ARG      0.032700
+     17 HB3         7.8895    3.4525   -2.1312 HC         2 ARG      0.032700
+     18 CG          9.7093    2.7949   -1.1946 C8         2 ARG      0.039000
+     19 HG2        10.1522    3.7908   -1.1858 HC         2 ARG      0.028500
+     20 HG3        10.0099    2.2561   -0.2960 HC         2 ARG      0.028500
+     21 CD         10.1902    2.0359   -2.4267 C8         2 ARG      0.048600
+     22 HD2         9.7480    1.0396   -2.4360 H1         2 ARG      0.068700
+     23 HD3         9.8903    2.5743   -3.3258 H1         2 ARG      0.068700
+     24 NE         11.6640    1.9004   -2.4245 N2         2 ARG     -0.529500
+     25 HE         12.1833    2.2984   -1.6551 H          2 ARG      0.345600
+     26 CZ         12.3357    1.2786   -3.3894 CA         2 ARG      0.807600
+     27 NH1        11.7224    0.7298   -4.4342 N2         2 ARG     -0.862700
+     28 HH11       10.7164    0.7798   -4.5089 H          2 ARG      0.447800
+     29 HH12       12.2655    0.2655   -5.1480 H          2 ARG      0.447800
+     30 NH2        13.6603    1.2151   -3.2870 N2         2 ARG     -0.862700
+     31 HH21       14.1229    1.6330   -2.4924 H          2 ARG      0.447800
+     32 HH22       14.1974    0.7494   -4.0044 H          2 ARG      0.447800
+     33 C           8.3852    5.0364   -0.0000 C          2 ARG      0.734100
+     34 O           7.7140    6.0660    0.0000 O          2 ARG     -0.589400
+@<TRIPOS>BOND
+    1     1     3 1
+    2     3     5 1
+    3     3     9 1
+    4     9    10 1
+    5    11    13 1
+    6    13    15 1
+    7    13    33 1
+    8    15    18 1
+    9    18    21 1
+   10    21    24 1
+   11    24    26 1
+   12    26    27 1
+   13    26    30 1
+   14    33    34 1
+   15    11     9 1
+   16     1     2 1
+   17     3     4 1
+   18     5     6 1
+   19     5     7 1
+   20     5     8 1
+   21    11    12 1
+   22    13    14 1
+   23    15    16 1
+   24    15    17 1
+   25    18    19 1
+   26    18    20 1
+   27    21    22 1
+   28    21    23 1
+   29    24    25 1
+   30    27    28 1
+   31    27    29 1
+   32    30    31 1
+   33    30    32 1
+@<TRIPOS>SUBSTRUCTURE
+      1 ALA               1 ****               0 ****  **** 
+      2 ARG              11 ****               0 ****  **** 

From f8b16d9bb6042842fd7c0d1db6f490160e49f5c1 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 3 Feb 2026 15:13:41 -0500
Subject: [PATCH 1276/1492] Automatically use connect atom information if
 grafting with internal coordinates

---
 src/Exec_Graft.cpp | 56 ++++++++++++++++++++++++++++++++++++++++++++++
 src/Exec_Graft.h   |  4 ++++
 src/cpptrajdepend  |  2 +-
 3 files changed, 61 insertions(+), 1 deletion(-)

diff --git a/src/Exec_Graft.cpp b/src/Exec_Graft.cpp
index bb8c9b8ada..7d9a43cac9 100644
--- a/src/Exec_Graft.cpp
+++ b/src/Exec_Graft.cpp
@@ -1,4 +1,5 @@
 #include "Exec_Graft.h"
+#include "AssociatedData_Connect.h"
 #include "CharMask.h"
 #include "CpptrajStdio.h"
 #include "DataSet_Coords.h"
@@ -89,6 +90,25 @@ int Exec_Graft::select_bond_idx(std::string const& bond0maskstr, Topology const&
   return bondmask0[0];
 }
 
+/** Get connect atoms from associated data */
+Exec_Graft::Iarray Exec_Graft::getConnectAtoms( AssociatedData* ad )
+{
+  if (ad == 0) return Iarray();
+  AssociatedData_Connect const& CONN = static_cast<AssociatedData_Connect const&>( *ad );
+  return CONN.Connect();
+}
+
+/** Print connect atoms to stdout */
+void Exec_Graft::print_connect(const char* desc, Iarray const& connect, Topology const& top)
+{
+  if (connect.empty()) return;
+  mprintf("\t  %s :", desc);
+  for (Iarray::const_iterator it = connect.begin(); it != connect.end(); ++it)
+    if (*it > -1)
+      mprintf(" %s", top.AtomMaskName(*it).c_str());
+  mprintf("\n");
+}
+
 // Exec_Graft::Help()
 void Exec_Graft::Help() const
 {
@@ -113,10 +133,14 @@ Exec::RetType Exec_Graft::Execute(CpptrajState& State, ArgList& argIn)
   Frame mol1frm;
   DataSet_Coords* mol1crd = get_crd(argIn, State.DSL(), "src", "Source COORDS", mol1frm, "srcframe");
   if (mol1crd == 0) return CpptrajState::ERR;
+  AssociatedData* ad1 = mol1crd->GetAssociatedData(AssociatedData::CONNECT);
+  Iarray connect1 = getConnectAtoms( ad1 );
   // Target (0, base)
   Frame mol0frm;
   DataSet_Coords* mol0crd = get_crd(argIn, State.DSL(), "tgt", "Target COORDS", mol0frm, "tgtframe");
   if (mol0crd == 0) return CpptrajState::ERR;
+  AssociatedData* ad0 = mol0crd->GetAssociatedData(AssociatedData::CONNECT);
+  Iarray connect0 = getConnectAtoms( ad0 );
 
   // Create output coords
   std::string kw = argIn.GetStringKey("name");
@@ -192,7 +216,9 @@ Exec::RetType Exec_Graft::Execute(CpptrajState& State, ArgList& argIn)
 
   // Info
   mprintf("\tSource coords   : %s\n", mol1crd->legend());
+  print_connect("Source connect atoms", connect1, mol1crd->Top());
   mprintf("\tTarget coords   : %s\n", mol0crd->legend());
+  print_connect("Target connect atoms", connect0, mol0crd->Top());
   mprintf("\tOutput coords   : %s\n", outCoords->legend());
   mprintf("\tSource mask     :");
   mol1Mask.BriefMaskInfo();
@@ -234,6 +260,36 @@ Exec::RetType Exec_Graft::Execute(CpptrajState& State, ArgList& argIn)
   }
 
   if (use_ic) {
+    if (bond0ArgStrings.empty()) {
+      // Do we have connect atoms?
+      if (!connect0.empty() && !connect1.empty()) {
+        // We have connect atoms.
+        int tail0 = -1;
+        int tail1 = -1;
+        int head0 = connect0[0];
+        int head1 = connect1[0];
+        if (connect0.size() > 1) tail0 = connect0[1];
+        if (connect1.size() > 1) tail1 = connect1[1];
+        // If we only have one of each that is easy
+        if (head0 != -1 && tail0 == -1 && head1 == -1 && tail1 != -1) {
+          // Head0, tail1
+          bond0ArgStrings.push_back( mol0crd->Top().AtomMaskName(head0) );
+          bond1ArgStrings.push_back( mol1crd->Top().AtomMaskName(tail1) );
+        } else if (head0 == -1 && tail0 != -1 && head1 != -1 && tail1 == -1) {
+          // Head1, tail0
+          bond0ArgStrings.push_back( mol0crd->Top().AtomMaskName(tail0) );
+          bond1ArgStrings.push_back( mol1crd->Top().AtomMaskName(head1) );
+        } else if (head0 != -1 && tail0 != -1 && head1 != -1 && tail1 != -1) {
+          // Default head of source (1) to tail of target (0)
+          bond0ArgStrings.push_back( mol0crd->Top().AtomMaskName(tail0) );
+          bond1ArgStrings.push_back( mol1crd->Top().AtomMaskName(head1) );
+        } else {
+          mprinterr("Error: No bonds specified and not enough CONNECT atoms:\n");
+          mprinterr("Error: head0 %i tail0 %i head1 %i tail1 %i\n", head0+1, tail0+1, head1+1, tail1+1);
+          return CpptrajState::ERR;
+        }
+      }
+    }
     // Get internals for both topologies before they are modified.
     get_original_orientations(mol0crd->Top(), mol0frm, mol1crd->Top(), mol1frm,
                               mol0Mask, mol1Mask, bond0ArgStrings, bond1ArgStrings);
diff --git a/src/Exec_Graft.h b/src/Exec_Graft.h
index 0440d4b198..1ae1a7da3d 100644
--- a/src/Exec_Graft.h
+++ b/src/Exec_Graft.h
@@ -12,6 +12,10 @@ class Exec_Graft : public Exec {
   private:
     typedef std::vector<int> Iarray;
     typedef std::vector<std::string> Sarray;
+    /// \return Array of connect atoms from associated data
+    static Iarray getConnectAtoms(AssociatedData*);
+    /// print connect atoms to stdout
+    static void print_connect(const char*, Iarray const&, Topology const&);
     /// Select bond index from expression in given topology
     static int select_bond_idx(std::string const&, Topology const&); 
     /// Modify topology and frame according to mask expression
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 94cc01c839..58aa9b5294 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -338,7 +338,7 @@ Exec_Emin.o : Exec_Emin.cpp Action.h ActionList.h ActionState.h Analysis.h Analy
 Exec_ExtendedComparison.o : Exec_ExtendedComparison.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ExtendedComparison.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_Flatten.o : Exec_Flatten.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Flatten.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_GenerateAmberRst.o : Exec_GenerateAmberRst.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_GenerateAmberRst.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_Graft.o : Exec_Graft.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Graft.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_Graft.o : Exec_Graft.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Graft.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_Help.o : Exec_Help.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Help.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_HmassRepartition.o : Exec_HmassRepartition.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_HmassRepartition.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_LoadCrd.o : Exec_LoadCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_LoadCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h Unit.h Vec3.h

From 5c536aaf7f666a14582b0ac1db654d3bbfc60616 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 3 Feb 2026 15:14:09 -0500
Subject: [PATCH 1277/1492] checkchirality byatom is not ready.

---
 doc/ChangeLog.v7.md | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/doc/ChangeLog.v7.md b/doc/ChangeLog.v7.md
index 379952ad18..2d5637cdc4 100644
--- a/doc/ChangeLog.v7.md
+++ b/doc/ChangeLog.v7.md
@@ -15,8 +15,6 @@ New Commands
 
 New Keywords
 ============
-- FIXME check this: Introduce the `byatom` keyword to `checkchirality` action to check the chirality of any atoms in specified mask that are chiral centers.
-
 - Introduce ring intersection check to `checkstructure` action.
 ```
 {noringcheck | [ringshortdist <rsdist>] [ringdcut <ringdcut>]
@@ -36,6 +34,8 @@ Add `gb` to `change` command to chang GB radii.
 
 Add `complete` keyword to `zmatrix` command to get complete zmatrix instead of minimal zmatrix.
 
+Add `atombondorder` keyword to mol2 output; sort bonds by first atom index (similar to how leap writes mol2 files).
+
 New functionality
 =================
 - Read topology/coordinates with the 'readdata' command.
@@ -71,3 +71,9 @@ Misc Fixes
 - Improve handling of very large topology files.
 
 - Better handling of very small boxes with pairlist code.
+
+Not Yet Ready
+=============
+- Introduce the `byatom` keyword to `checkchirality` action to check the chirality of any atoms in specified mask that are chiral centers.
+
+

From 0ffdc327bc5f9efcbf1e3bd27c6de4b5f40c0188 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 3 Feb 2026 15:15:51 -0500
Subject: [PATCH 1278/1492] Add note about connect atom information

---
 doc/ChangeLog.v7.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/doc/ChangeLog.v7.md b/doc/ChangeLog.v7.md
index 2d5637cdc4..61520172d7 100644
--- a/doc/ChangeLog.v7.md
+++ b/doc/ChangeLog.v7.md
@@ -46,6 +46,8 @@ New functionality
 
 - The `permutedihedrals` command will now check rings.
 
+- The `graft` command will now use CONNECT atom information if it is present.
+
 New file formats recognized
 ===========================
 - Read Amber parameter (force field) files.

From 1482ae19a5b561e69bd843f932d76fc2ad8d6e39 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 5 Feb 2026 14:11:32 -0500
Subject: [PATCH 1279/1492] Start LJ calculation for 1-4

---
 src/Energy.cpp    | 44 ++++++++++++++++++++++++++++++++++++++++++++
 src/Energy.h      |  2 ++
 src/Topology.h    | 12 ++++++++++++
 src/cpptrajdepend |  2 +-
 4 files changed, 59 insertions(+), 1 deletion(-)

diff --git a/src/Energy.cpp b/src/Energy.cpp
index 72255af143..07f3bfb0ae 100644
--- a/src/Energy.cpp
+++ b/src/Energy.cpp
@@ -10,6 +10,7 @@
 #include "Energy/Ene_Angle.h"
 #include "Energy/Ene_Bond.h"
 #include "Energy/Ene_LJ_6_12.h"
+#include "Energy/Ene_LJ_12_6_4.h"
 
 // CONSTRUCTOR
 Energy_Amber::Energy_Amber() : debug_(0) {}
@@ -201,6 +202,49 @@ double Energy_Amber::Calc_14_Energy(Frame const& fIn, DihedralArray const& Dihed
   return Evdw14;
 }
 
+// Energy_Amber::Calc_14_Energy_LJC()
+double Energy_Amber::Calc_14_Energy_LJC(Frame const& fIn, DihedralArray const& Dihedrals,
+                                        DihedralParmArray const& DPA, Topology const& tIn,
+                                        CharMask const& mask, double& Eq14)
+{
+  double Evdw14 = 0.0;
+  for (DihedralArray::const_iterator d = Dihedrals.begin(); d != Dihedrals.end(); d++)
+  {
+    if (d->Type() == DihedralType::NORMAL &&
+        mask.AtomInCharMask(d->A1()) && mask.AtomInCharMask(d->A4()))
+    {
+      int dpidx = d->Idx();
+      if (dpidx < 0) {
+        if (debug_ > 0)
+          mprintf("Warning: 1-4 pair %i -- %i has no parameters.\n", d->A1()+1, d->A4()+1);
+        continue;
+      }
+      DihedralParmType const& dp = DPA[dpidx];
+      double rij2 = DIST2_NoImage( fIn.XYZ(d->A1()), fIn.XYZ(d->A4()) );
+      double rij = sqrt( rij2 );
+      // VDW
+      double LJC = 0;
+      NonbondType const& LJ = tIn.GetLJCparam(LJC, d->A1(), d->A4());
+      double e_vdw = Cpptraj::Energy::Ene_LJ_12_6_4( rij2, LJ.A(), LJ.B(), LJC );
+      e_vdw /= dp.SCNB();
+      Evdw14 += e_vdw;
+      // Coulomb
+      double qiqj = Constants::COULOMBFACTOR * tIn[d->A1()].Charge() * tIn[d->A4()].Charge();
+      double e_elec = qiqj / rij;
+      e_elec /= dp.SCEE();
+      Eq14 += e_elec;
+#     ifdef DEBUG_ENERGY
+      mprintf("\tEVDW14  %4i -- %4i: A=  %12.5e  B=  %12.5e  C=  %12.5e  r2= %12.5f  E= %12.5e\n",
+              d->A1()+1, d->A4()+1, LJ.A(), LJ.B(), LJC, rij2, e_vdw);
+      mprintf("\tEELEC14 %4i -- %4i: q1= %12.5e  q2= %12.5e  r=  %12.5f  E= %12.5e\n",
+              d->A1()+1, d->A4()+1, tIn[d->A1()].Charge(), tIn[d->A4()].Charge(),
+              rij, e_elec);
+#     endif
+    }
+  }
+  return Evdw14;
+}
+
 // -----------------------------------------------------------------------------
 // Energy_Amber::E_Nonbond()
 double Energy_Amber::E_Nonbond(Frame const& fIn, Topology const& tIn, AtomMask const& mask,
diff --git a/src/Energy.h b/src/Energy.h
index 61a8b24eff..9a8c98358d 100644
--- a/src/Energy.h
+++ b/src/Energy.h
@@ -36,6 +36,8 @@ class Energy_Amber {
                              CharMask const&);
     double Calc_14_Energy(Frame const&, DihedralArray const&, DihedralParmArray const&,
                           Topology const&, CharMask const&, double&);
+    double Calc_14_Energy_LJC(Frame const&, DihedralArray const&, DihedralParmArray const&,
+                          Topology const&, CharMask const&, double&);
 
     int debug_;
 };
diff --git a/src/Topology.h b/src/Topology.h
index 4ecfd8e505..40bfeb5760 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -185,6 +185,8 @@ class Topology {
     double GetVDWdepth(int) const;
     /// \return Lennard-Jones 6-12 parameters for given pair of atoms
     inline NonbondType const& GetLJparam(int, int) const;
+    /// \return Lennard-Jones 6-12 parameters for given pair of atoms, set the LJC parameter
+    inline NonbondType const& GetLJCparam(double&, int, int) const;
     /// \return True if any charge is non-zero
     bool HasChargeInfo() const;
     /// \return Total charge
@@ -416,6 +418,16 @@ NonbondType const& Topology::GetLJparam(int a1, int a2) const {
     return LJ_EMPTY;
   return nonbond_.NBarray( nbindex );
 }
+NonbondType const& Topology::GetLJCparam(double& LJC, int a1, int a2) const {
+  int nbindex = nonbond_.GetLJindex( atoms_[a1].TypeIndex(), atoms_[a2].TypeIndex() );
+  if (nbindex < 0) // Means Amber Hbond, return A = B = 0.0
+    return LJ_EMPTY;
+  if (nonbond_.Has_C_Coeff())
+    LJC = nonbond_.LJC_Array(nbindex);
+  else
+    LJC = 0;
+  return nonbond_.NBarray( nbindex );
+}
 // -----------------------------------------------------------------------------
 class Topology::Pointers {
   public:
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 58aa9b5294..14c562a587 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -287,7 +287,7 @@ DiffusionResults.o : DiffusionResults.cpp ArgList.h AssociatedData.h Atom.h Atom
 DihedralSearch.o : DihedralSearch.cpp ArgList.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DihedralSearch.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h
 DistRoutines.o : DistRoutines.cpp Box.h DistRoutines.h ImageOption.h Matrix_3x3.h Parallel.h Vec3.h
 Dist_Imaged.o : Dist_Imaged.cpp Dist_Imaged.h Matrix_3x3.h Parallel.h Vec3.h
-Energy.o : Energy.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h Energy.h Energy/Ene_Angle.h Energy/Ene_Bond.h Energy/Ene_LJ_6_12.h Energy/Kernel_Harmonic.h ExclusionArray.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TorsionRoutines.h Unit.h Vec3.h
+Energy.o : Energy.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h Energy.h Energy/Ene_Angle.h Energy/Ene_Bond.h Energy/Ene_LJ_12_6_4.h Energy/Ene_LJ_6_12.h Energy/Kernel_Harmonic.h ExclusionArray.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TorsionRoutines.h Unit.h Vec3.h
 Energy/Ecalc_Nonbond.o : Energy/Ecalc_Nonbond.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy/Ecalc_Nonbond.h Energy/Ene_Decomp_Nonbond.h Energy/Ene_LJPME_6_12.h Energy/Ene_LJ_6_12.h Energy/Ene_Nonbond.h Energy/ErfcFxn.h Energy/EwaldCalc.h Energy/EwaldCalc_Decomp.h Energy/EwaldCalc_Decomp_LJPME.h Energy/EwaldCalc_Decomp_PME.h Energy/EwaldCalc_LJPME.h Energy/EwaldCalc_PME.h Energy/EwaldCalc_Regular.h Energy/EwaldParams.h Energy/EwaldParams_LJPME.h Energy/Ewald_Recip.h Energy/Kernel_EwaldAdjust.h Energy/Kernel_LJPME_Adjust.h Energy/PME_Recip.h Energy/PME_RecipParams.h Energy/VDW_LongRange_Correction.h EwaldOptions.h ExclusionArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h PairListEngine_Ewald_Decomp_LJLR.h PairListEngine_Ewald_Decomp_LJPME.h PairListEngine_Ewald_LJLR.h PairListEngine_Ewald_LJPME.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h Timer.h Topology.h Unit.h Vec3.h helpme_standalone.h
 Energy/EnergyDecomposer.o : Energy/EnergyDecomposer.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DistRoutines.h Energy/Ecalc_Nonbond.h Energy/Ene_Angle.h Energy/Ene_Bond.h Energy/Ene_LJ_6_12.h Energy/EnergyDecomposer.h Energy/Kernel_Fourier.h Energy/Kernel_Harmonic.h EwaldOptions.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h PairList.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h Stats_Reduce.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h Unit.h Vec3.h
 Energy/ErfcFxn.o : Energy/ErfcFxn.cpp CpptrajStdio.h Energy/ErfcFxn.h SplineFxnTable.h

From bb4051616d9d1ee9cc7baed521291989b4a28009 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 5 Feb 2026 14:21:57 -0500
Subject: [PATCH 1280/1492] Add LJ 12-6-4 energy routine

---
 src/Energy/Ene_LJ_12_6_4.h | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)
 create mode 100644 src/Energy/Ene_LJ_12_6_4.h

diff --git a/src/Energy/Ene_LJ_12_6_4.h b/src/Energy/Ene_LJ_12_6_4.h
new file mode 100644
index 0000000000..cd12d83514
--- /dev/null
+++ b/src/Energy/Ene_LJ_12_6_4.h
@@ -0,0 +1,21 @@
+#ifndef INC_ENERGY_ENE_LJ_12_6_4_H
+#define INC_ENERGY_ENE_LJ_12_6_4_H
+namespace Cpptraj {
+namespace Energy {
+/// \return LJ 12-6-4 energy
+template <typename T>
+T Ene_LJ_12_6_4(T const& rij2, T const& LJA, T const& LJB, T const& LJC)
+{
+  T r2    = 1.0 / rij2;
+  T r4    = r2  * r2;
+  T r6    = r4  * r2;
+  T r12   = r6  * r6;
+  T f12   = LJA * r12;  // A/r^12
+  T f6    = LJB * r6;   // B/r^6
+  T f4    = LJC * r4;   // C/r^4
+  T e_vdw = f12 - f6 - f4; // (A/r^12)-(B/r^6)-(C/r^4)
+  return e_vdw;
+}
+}
+}
+#endif

From c583ade6b1f714315bf719fc31af30ea55a318f4 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 5 Feb 2026 14:22:20 -0500
Subject: [PATCH 1281/1492] Add flag to turn on LJ 12-6-4 calc for 1-4

---
 src/Energy.cpp | 15 +++++++++++----
 src/Energy.h   |  2 +-
 2 files changed, 12 insertions(+), 5 deletions(-)

diff --git a/src/Energy.cpp b/src/Energy.cpp
index 07f3bfb0ae..0fe77c893d 100644
--- a/src/Energy.cpp
+++ b/src/Energy.cpp
@@ -145,12 +145,19 @@ double Energy_Amber::CalcTorsionEnergy(Frame const& fIn, DihedralArray const& Di
 // -----------------------------------------------------------------------------
 /** 1-4 nonbond energy */
 double Energy_Amber::E_14_Nonbond(Frame const& fIn, Topology const& tIn, CharMask const& mask,
-                                  double& Eq14)
+                                  double& Eq14, bool lj1264)
 {
   Eq14 = 0.0;
-  // Heavy atom dihedrals
-  double Evdw14 = Calc_14_Energy(fIn, tIn.Dihedrals(), tIn.DihedralParm(), tIn, mask, Eq14);
-  Evdw14 += Calc_14_Energy(fIn, tIn.DihedralsH(), tIn.DihedralParm(), tIn, mask, Eq14);
+  double Evdw14;
+  if (lj1264) {
+    Evdw14 = Calc_14_Energy_LJC(fIn, tIn.Dihedrals(), tIn.DihedralParm(), tIn, mask, Eq14);
+    Evdw14 += Calc_14_Energy_LJC(fIn, tIn.DihedralsH(), tIn.DihedralParm(), tIn, mask, Eq14);
+  } else {
+    // Heavy atom dihedrals
+    Evdw14 = Calc_14_Energy(fIn, tIn.Dihedrals(), tIn.DihedralParm(), tIn, mask, Eq14);
+    // Dihedrals including hydrogen
+    Evdw14 += Calc_14_Energy(fIn, tIn.DihedralsH(), tIn.DihedralParm(), tIn, mask, Eq14);
+  }
   return Evdw14;
 }
 
diff --git a/src/Energy.h b/src/Energy.h
index 9a8c98358d..2f52f778a1 100644
--- a/src/Energy.h
+++ b/src/Energy.h
@@ -15,7 +15,7 @@ class Energy_Amber {
     double E_bond(Frame const&, Topology const&, CharMask const&, bool);
     double E_angle(Frame const&, Topology const&, CharMask const&);
     double E_torsion(Frame const&, Topology const&, CharMask const&);
-    double E_14_Nonbond(Frame const&, Topology const&, CharMask const&, double&);
+    double E_14_Nonbond(Frame const&, Topology const&, CharMask const&, double&, bool);
     double E_Nonbond(Frame const&, Topology const&, AtomMask const&, double&, ExclusionArray const&);
     double E_VDW(Frame const&, Topology const&, AtomMask const&, ExclusionArray const&);
     double E_Elec(Frame const&, Topology const&, AtomMask const&, ExclusionArray const&);

From 3288fa4893a0f38f2b078f4e2d2b5cd687a1fe99 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 5 Feb 2026 14:22:50 -0500
Subject: [PATCH 1282/1492] Start adding LJ 12-6-4 keyword

---
 src/Action_Energy.cpp | 35 +++++++++++++++++++++++++++--------
 src/Action_Energy.h   |  2 ++
 2 files changed, 29 insertions(+), 8 deletions(-)

diff --git a/src/Action_Energy.cpp b/src/Action_Energy.cpp
index 2146d68be8..0b9f2326cb 100644
--- a/src/Action_Energy.cpp
+++ b/src/Action_Energy.cpp
@@ -18,7 +18,9 @@ Action_Energy::Action_Energy() :
   dt_(0),
   need_lj_params_(false),
   needs_exclList_(false),
-  bondsToH_(true)
+  bondsToH_(true),
+  lj1264_(false),
+  useLj1264_(false)
 {}
 
 /// DESTRUCTOR
@@ -29,7 +31,7 @@ Action_Energy::~Action_Energy() {
 void Action_Energy::Help() const {
   mprintf("\t[<name>] [<mask1>] [out <filename>] [nobondstoh] [openmm [<mdopts>]]\n"
           "\t[bond] [angle] [dihedral] {[nb14]|[e14]|[v14]} {[nonbond] | [elec] [vdw]}\n"
-          "\t[{nokinetic|kinetic [ketype {vel|vv}] [dt <dt>]}]\n"
+          "\t[{nokinetic|kinetic [ketype {vel|vv}] [dt <dt>]}] [lj1264]\n"
           "\t[ etype { simple |\n"
           "\t          directsum [npoints <N>] |\n"
           "\t          ewald %s\n"
@@ -99,6 +101,8 @@ Action::RetType Action_Energy::Init(ArgList& actionArgs, ActionInit& init, int d
     return Action::ERR;
 #   endif /* HAS_OPENMM */
   }
+  // LJ 12-6-4
+  useLj1264_ = actionArgs.hasKey("lj1264");
   // Determine which energy terms are active 
   std::vector<bool> termEnabled((int)TOTAL+1, false);
   if (use_openmm_) {
@@ -290,6 +294,8 @@ Action::RetType Action_Energy::Init(ArgList& actionArgs, ActionInit& init, int d
   } else {
     if (termEnabled[BOND] && !bondsToH_)
       mprintf("\tNot calculating energy of bonds to hydrogen.\n");
+    if (useLj1264_)
+      mprintf("\tWill use LJ 12-6-4 (C) coefficients if present.\n");
     if (elecType_ != NO_ELE)
       mprintf("\tElectrostatics method: %s\n", ElecStr[elecType_]);
     if (elecType_ == DIRECTSUM) {
@@ -343,11 +349,24 @@ Action::RetType Action_Energy::Setup(ActionSetup& setup) {
 
   Imask_ = AtomMask(Mask1_.ConvertToIntMask(), Mask1_.Natom());
   // Check for LJ terms
-  if (need_lj_params_ && !setup.Top().Nonbond().HasNonbond())
-  {
-    mprinterr("Error: LJ energy calc requested but topology '%s'\n"
-              "Error:   does not have LJ parameters.\n", setup.Top().c_str());
-    return Action::ERR;
+  lj1264_ = false;
+  if (need_lj_params_) {
+    if (!setup.Top().Nonbond().HasNonbond())
+    {
+      mprinterr("Error: LJ energy calc requested but topology '%s'\n"
+                "Error:   does not have LJ parameters.\n", setup.Top().c_str());
+      return Action::ERR;
+    }
+    if (useLj1264_) {
+      if (setup.Top().Nonbond().Has_C_Coeff())
+        lj1264_ = true;
+      else
+        mprintf("Warning: 'lj1264' specified but no LJ 12-6-4 (C) terms present in topology '%s'\n", setup.Top().c_str());
+    } else {
+      if (setup.Top().Nonbond().Has_C_Coeff()) {
+        mprintf("Warning: Topology has LJ C coefficients. To use these, specify 'lj1264'\n");
+      }
+    }
   }
   // Set up exclusion list if necessary.
   if (needs_exclList_) {
@@ -440,7 +459,7 @@ Action::RetType Action_Energy::DoAction(int frameNum, ActionFrame& frm) {
         break;
       case C_N14:
         time_14_.Start();
-        ene = ENE_.E_14_Nonbond(frm.Frm(), *currentParm_, Mask1_, ene2);
+        ene = ENE_.E_14_Nonbond(frm.Frm(), *currentParm_, Mask1_, ene2, lj1264_);
         time_14_.Stop();
         if (Energy_[V14] != 0) Energy_[V14]->Add(frameNum, &ene);
         if (Energy_[Q14] != 0) Energy_[Q14]->Add(frameNum, &ene2);
diff --git a/src/Action_Energy.h b/src/Action_Energy.h
index 7d47a6a07b..6c37b7e570 100644
--- a/src/Action_Energy.h
+++ b/src/Action_Energy.h
@@ -61,6 +61,8 @@ class Action_Energy: public Action {
     bool need_lj_params_;          ///< True if LJ parameters needed.
     bool needs_exclList_;          ///< True if Excluded_ needs to be set up.
     bool bondsToH_;                ///< True if we want to calculate energy of bonds with H
+    bool lj1264_;                  ///< True if LJ 12-6-4 (C) terms are active
+    bool useLj1264_;               ///< True if we want to use LJ 12-6-4 (C) terms if present
     Timer time_total_;
     Timer time_bond_;
     Timer time_angle_;

From 1559825be235239eed230bafaf4cf37d53982be8 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 5 Feb 2026 14:26:51 -0500
Subject: [PATCH 1283/1492] Improve feedback when LJC is active

---
 src/Action_Energy.cpp | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/Action_Energy.cpp b/src/Action_Energy.cpp
index 0b9f2326cb..a4ed51688d 100644
--- a/src/Action_Energy.cpp
+++ b/src/Action_Energy.cpp
@@ -358,9 +358,10 @@ Action::RetType Action_Energy::Setup(ActionSetup& setup) {
       return Action::ERR;
     }
     if (useLj1264_) {
-      if (setup.Top().Nonbond().Has_C_Coeff())
+      if (setup.Top().Nonbond().Has_C_Coeff()) {
         lj1264_ = true;
-      else
+        mprintf("\tLJ 12-6-4 (C) terms are active.\n");
+      } else
         mprintf("Warning: 'lj1264' specified but no LJ 12-6-4 (C) terms present in topology '%s'\n", setup.Top().c_str());
     } else {
       if (setup.Top().Nonbond().Has_C_Coeff()) {

From fc5db081b0829b7c797390f9b21165c991535d06 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 5 Feb 2026 14:32:24 -0500
Subject: [PATCH 1284/1492] Add LJC version of nonbond calc

---
 src/Energy.cpp | 68 +++++++++++++++++++++++++++++++++++++++++++++++++-
 src/Energy.h   |  4 ++-
 2 files changed, 70 insertions(+), 2 deletions(-)

diff --git a/src/Energy.cpp b/src/Energy.cpp
index 0fe77c893d..f11c8a318f 100644
--- a/src/Energy.cpp
+++ b/src/Energy.cpp
@@ -253,8 +253,17 @@ double Energy_Amber::Calc_14_Energy_LJC(Frame const& fIn, DihedralArray const& D
 }
 
 // -----------------------------------------------------------------------------
-// Energy_Amber::E_Nonbond()
 double Energy_Amber::E_Nonbond(Frame const& fIn, Topology const& tIn, AtomMask const& mask,
+                               double& EelecOut, ExclusionArray const& Excluded, bool lj1264)
+{
+  if (lj1264)
+    return E_Nonbond_LJC(fIn, tIn, mask, EelecOut, Excluded);
+  else
+    return E_Nonbond_6_12(fIn, tIn, mask, EelecOut, Excluded);
+}
+
+// Energy_Amber::E_Nonbond_6_12()
+double Energy_Amber::E_Nonbond_6_12(Frame const& fIn, Topology const& tIn, AtomMask const& mask,
                                double& EelecOut, ExclusionArray const& Excluded)
 {
   double Evdw = 0.0;
@@ -315,6 +324,63 @@ double Energy_Amber::E_Nonbond(Frame const& fIn, Topology const& tIn, AtomMask c
   return Evdw;
 }
 
+// Energy_Amber::E_Nonbond_LJC()
+double Energy_Amber::E_Nonbond_LJC(Frame const& fIn, Topology const& tIn, AtomMask const& mask,
+                               double& EelecOut, ExclusionArray const& Excluded)
+{
+  double Evdw = 0.0;
+  double Eelec = 0.0;
+  int idx1;
+# ifdef _OPENMP
+# pragma omp parallel private(idx1) reduction(+ : Eelec, Evdw)
+  {
+# pragma omp for
+# endif
+  for (idx1 = 0; idx1 < mask.Nselected(); idx1++)
+  {
+    int atom1 = mask[idx1];
+    // Set up coord for this atom
+    const double* crd1 = fIn.XYZ( atom1 );
+    // Set up exclusion list for this atom
+    // TODO refactor inner loop to be more like StructureCheck, more efficient.
+    ExclusionArray::ExListType::const_iterator excluded_idx = Excluded[idx1].begin();
+    for (int idx2 = idx1 + 1; idx2 < mask.Nselected(); idx2++)
+    {
+      int atom2 = mask[idx2];
+      // Advance excluded list up to current selected atom
+      while (excluded_idx != Excluded[idx1].end() && *excluded_idx < idx2) ++excluded_idx;
+      // If atom is excluded, just increment to next excluded atom.
+      if (excluded_idx != Excluded[idx1].end() && idx2 == *excluded_idx)
+        ++excluded_idx;
+      else {
+        double rij2 = DIST2_NoImage( crd1, fIn.XYZ( atom2 ) );
+        double rij = sqrt( rij2 );
+        // VDW
+        double LJC = 0;
+        NonbondType const& LJ = tIn.GetLJCparam(LJC, atom1, atom2);
+        double e_vdw = Cpptraj::Energy::Ene_LJ_12_6_4( rij2, LJ.A(), LJ.B(), LJC );
+        Evdw += e_vdw;
+        // Coulomb
+        double qiqj = Constants::COULOMBFACTOR * tIn[atom1].Charge() * tIn[atom2].Charge();
+        double e_elec = qiqj / rij;
+        Eelec += e_elec;
+#       ifdef DEBUG_ENERGY
+        mprintf("\tEVDW  %4i -- %4i: A=  %12.5e  B=  %12.5e  C=  %12.5e  r2= %12.5f  E= %12.5e\n",
+                atom1+1, atom2+1, LJ.A(), LJ.B(), LJC, rij2, e_vdw);
+        mprintf("\tEELEC %4i -- %4i: q1= %12.5e  q2= %12.5e  r=  %12.5f  E= %12.5e\n",
+                atom1+1, atom2+1, tIn[atom1].Charge(), tIn[atom2].Charge(),
+                rij, e_elec);
+#       endif
+      }
+    }
+  }
+# ifdef _OPENMP
+  } // END omp parallel
+# endif
+  EelecOut = Eelec;
+  return Evdw;
+}
+
 // -----------------------------------------------------------------------------
 double Energy_Amber::E_VDW(Frame const& fIn, Topology const& tIn, AtomMask const& mask,
                            ExclusionArray const& Excluded)
diff --git a/src/Energy.h b/src/Energy.h
index 2f52f778a1..113fc5b94a 100644
--- a/src/Energy.h
+++ b/src/Energy.h
@@ -16,7 +16,7 @@ class Energy_Amber {
     double E_angle(Frame const&, Topology const&, CharMask const&);
     double E_torsion(Frame const&, Topology const&, CharMask const&);
     double E_14_Nonbond(Frame const&, Topology const&, CharMask const&, double&, bool);
-    double E_Nonbond(Frame const&, Topology const&, AtomMask const&, double&, ExclusionArray const&);
+    double E_Nonbond(Frame const&, Topology const&, AtomMask const&, double&, ExclusionArray const&, bool);
     double E_VDW(Frame const&, Topology const&, AtomMask const&, ExclusionArray const&);
     double E_Elec(Frame const&, Topology const&, AtomMask const&, ExclusionArray const&);
 
@@ -38,6 +38,8 @@ class Energy_Amber {
                           Topology const&, CharMask const&, double&);
     double Calc_14_Energy_LJC(Frame const&, DihedralArray const&, DihedralParmArray const&,
                           Topology const&, CharMask const&, double&);
+    double E_Nonbond_6_12(Frame const&, Topology const&, AtomMask const&, double&, ExclusionArray const&);
+    double E_Nonbond_LJC(Frame const&, Topology const&, AtomMask const&, double&, ExclusionArray const&);
 
     int debug_;
 };

From 3b082dd5f2c166ca2c0038569ecfce76b6912721 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 5 Feb 2026 14:36:33 -0500
Subject: [PATCH 1285/1492] Pass in LJ 12-6-4

---
 src/Action_Energy.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Action_Energy.cpp b/src/Action_Energy.cpp
index a4ed51688d..9d8ff55f3b 100644
--- a/src/Action_Energy.cpp
+++ b/src/Action_Energy.cpp
@@ -468,7 +468,7 @@ Action::RetType Action_Energy::DoAction(int frameNum, ActionFrame& frm) {
         break;
       case C_NBD: // Both nonbond terms must be enabled 
         time_NB_.Start();
-        ene = ENE_.E_Nonbond(frm.Frm(), *currentParm_, Imask_, ene2, Excluded_);
+        ene = ENE_.E_Nonbond(frm.Frm(), *currentParm_, Imask_, ene2, Excluded_, lj1264_);
         time_NB_.Stop();
         Energy_[VDW]->Add(frameNum, &ene);
         Energy_[ELEC]->Add(frameNum, &ene2);

From fa16bf9dc1a14d41d3554df4fe65c67ddd5d02d3 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 5 Feb 2026 14:40:59 -0500
Subject: [PATCH 1286/1492] LJ 12-6-4 calc for standalone VDW

---
 src/Action_Energy.cpp |  2 +-
 src/Energy.cpp        | 57 +++++++++++++++++++++++++++++++++++++++++++
 src/Energy.h          |  4 ++-
 3 files changed, 61 insertions(+), 2 deletions(-)

diff --git a/src/Action_Energy.cpp b/src/Action_Energy.cpp
index 9d8ff55f3b..5a64d5cee4 100644
--- a/src/Action_Energy.cpp
+++ b/src/Action_Energy.cpp
@@ -476,7 +476,7 @@ Action::RetType Action_Energy::DoAction(int frameNum, ActionFrame& frm) {
         break;
       case C_LJ:
         time_NB_.Start();
-        ene = ENE_.E_VDW(frm.Frm(), *currentParm_, Imask_, Excluded_);
+        ene = ENE_.E_VDW(frm.Frm(), *currentParm_, Imask_, Excluded_, lj1264_);
         time_NB_.Stop();
         Energy_[VDW]->Add(frameNum, &ene);
         Etot += ene;
diff --git a/src/Energy.cpp b/src/Energy.cpp
index f11c8a318f..6763d08caa 100644
--- a/src/Energy.cpp
+++ b/src/Energy.cpp
@@ -383,6 +383,16 @@ double Energy_Amber::E_Nonbond_LJC(Frame const& fIn, Topology const& tIn, AtomMa
 
 // -----------------------------------------------------------------------------
 double Energy_Amber::E_VDW(Frame const& fIn, Topology const& tIn, AtomMask const& mask,
+                           ExclusionArray const& Excluded, bool lj1264)
+{
+  if (lj1264)
+    return E_VDW_LJC(fIn, tIn, mask, Excluded);
+  else
+    return E_VDW_6_12(fIn, tIn, mask, Excluded);
+}
+
+// E_VDW_6_12
+double Energy_Amber::E_VDW_6_12(Frame const& fIn, Topology const& tIn, AtomMask const& mask,
                            ExclusionArray const& Excluded)
 {
   double Evdw = 0.0;
@@ -433,6 +443,53 @@ double Energy_Amber::E_VDW(Frame const& fIn, Topology const& tIn, AtomMask const
   return Evdw;
 }
 
+// E_VDW_LJC
+double Energy_Amber::E_VDW_LJC(Frame const& fIn, Topology const& tIn, AtomMask const& mask,
+                           ExclusionArray const& Excluded)
+{
+  double Evdw = 0.0;
+  int idx1;
+# ifdef _OPENMP
+# pragma omp parallel private(idx1) reduction(+ : Evdw)
+  {
+# pragma omp for
+# endif
+  for (idx1 = 0; idx1 < mask.Nselected(); idx1++)
+  {
+    int atom1 = mask[idx1];
+    // Set up coord for this atom
+    const double* crd1 = fIn.XYZ( atom1 );
+    // Set up exclusion list for this atom
+    // TODO refactor inner loop to be more like StructureCheck
+    ExclusionArray::ExListType::const_iterator excluded_idx = Excluded[idx1].begin();
+    for (int idx2 = idx1 + 1; idx2 < mask.Nselected(); idx2++)
+    {
+      int atom2 = mask[idx2];
+      // Advance excluded list up to current selected atom
+      while (excluded_idx != Excluded[idx1].end() && *excluded_idx < idx2) ++excluded_idx;
+      // If atom is excluded, just increment to next excluded atom.
+      if (excluded_idx != Excluded[idx1].end() && idx2 == *excluded_idx)
+        ++excluded_idx;
+      else {
+        double rij2 = DIST2_NoImage( crd1, fIn.XYZ( atom2 ) );
+        // VDW
+        double LJC = 0;
+        NonbondType const& LJ = tIn.GetLJCparam(LJC, atom1, atom2);
+        double e_vdw = Cpptraj::Energy::Ene_LJ_12_6_4( rij2, LJ.A(), LJ.B(), LJC );
+        Evdw += e_vdw;
+#       ifdef DEBUG_ENERGY
+        mprintf("\tEVDW  %4i -- %4i: A=  %12.5e  B=  %12.5e  C=  %12.5e  r2= %12.5f  E= %12.5e\n",
+                atom1+1, atom2+1, LJ.A(), LJ.B(), LJC, rij2, e_vdw);
+#       endif
+      }
+    }
+  }
+# ifdef _OPENMP
+  } // END omp parallel
+# endif
+  return Evdw;
+}
+
 // -----------------------------------------------------------------------------
 double Energy_Amber::E_Elec(Frame const& fIn, Topology const& tIn, AtomMask const& mask,
                             ExclusionArray const& Excluded)
diff --git a/src/Energy.h b/src/Energy.h
index 113fc5b94a..e4093cbed0 100644
--- a/src/Energy.h
+++ b/src/Energy.h
@@ -17,7 +17,7 @@ class Energy_Amber {
     double E_torsion(Frame const&, Topology const&, CharMask const&);
     double E_14_Nonbond(Frame const&, Topology const&, CharMask const&, double&, bool);
     double E_Nonbond(Frame const&, Topology const&, AtomMask const&, double&, ExclusionArray const&, bool);
-    double E_VDW(Frame const&, Topology const&, AtomMask const&, ExclusionArray const&);
+    double E_VDW(Frame const&, Topology const&, AtomMask const&, ExclusionArray const&, bool);
     double E_Elec(Frame const&, Topology const&, AtomMask const&, ExclusionArray const&);
 
     double E_DirectSum(Frame const&, Topology const&, AtomMask const&, ExclusionArray const&,int);
@@ -40,6 +40,8 @@ class Energy_Amber {
                           Topology const&, CharMask const&, double&);
     double E_Nonbond_6_12(Frame const&, Topology const&, AtomMask const&, double&, ExclusionArray const&);
     double E_Nonbond_LJC(Frame const&, Topology const&, AtomMask const&, double&, ExclusionArray const&);
+    double E_VDW_6_12(Frame const&, Topology const&, AtomMask const&, ExclusionArray const&);
+    double E_VDW_LJC(Frame const&, Topology const&, AtomMask const&, ExclusionArray const&);
 
     int debug_;
 };

From 8037dc5e5c8c331add2eb920b032ffc1d90d51a7 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 6 Feb 2026 10:22:51 -0500
Subject: [PATCH 1287/1492] Add PME calc with LJC

---
 src/Energy/CMakeLists.txt        |   1 +
 src/Energy/EwaldCalc_LJCPME.cpp  | 106 +++++++++++++++++++++++++++++++
 src/Energy/EwaldCalc_LJCPME.h    |  29 +++++++++
 src/Energy/EwaldParams.h         |   2 +
 src/Energy/energydepend          |   1 +
 src/Energy/energyfiles           |   1 +
 src/PairListEngine_Ewald_LJCLR.h |  82 ++++++++++++++++++++++++
 src/cpptrajdepend                |   1 +
 8 files changed, 223 insertions(+)
 create mode 100644 src/Energy/EwaldCalc_LJCPME.cpp
 create mode 100644 src/Energy/EwaldCalc_LJCPME.h
 create mode 100644 src/PairListEngine_Ewald_LJCLR.h

diff --git a/src/Energy/CMakeLists.txt b/src/Energy/CMakeLists.txt
index d8fffe4717..6bfa915cf3 100644
--- a/src/Energy/CMakeLists.txt
+++ b/src/Energy/CMakeLists.txt
@@ -5,6 +5,7 @@ target_sources(cpptraj_common_obj PRIVATE
   ${CMAKE_CURRENT_LIST_DIR}/ErfcFxn.cpp
   ${CMAKE_CURRENT_LIST_DIR}/EwaldCalc_Decomp_LJPME.cpp
   ${CMAKE_CURRENT_LIST_DIR}/EwaldCalc_Decomp_PME.cpp
+  ${CMAKE_CURRENT_LIST_DIR}/EwaldCalc_LJCPME.cpp
   ${CMAKE_CURRENT_LIST_DIR}/EwaldCalc_LJPME.cpp
   ${CMAKE_CURRENT_LIST_DIR}/EwaldCalc_PME.cpp
   ${CMAKE_CURRENT_LIST_DIR}/EwaldCalc_Regular.cpp
diff --git a/src/Energy/EwaldCalc_LJCPME.cpp b/src/Energy/EwaldCalc_LJCPME.cpp
new file mode 100644
index 0000000000..4c10bc5296
--- /dev/null
+++ b/src/Energy/EwaldCalc_LJCPME.cpp
@@ -0,0 +1,106 @@
+#include "EwaldCalc_LJCPME.h"
+#ifdef LIBPME
+#include "../CpptrajStdio.h"
+#include "../EwaldOptions.h"
+#include "../Frame.h"
+#include "../PairListTemplate.h"
+#include "../Topology.h"
+
+using namespace Cpptraj::Energy;
+
+EwaldCalc_LJCPME::EwaldCalc_LJCPME() :
+  Recip_(PME_Recip::COULOMB)
+{}
+
+/** Set up PME parameters. */
+int EwaldCalc_LJCPME::Init(Box const& boxIn, EwaldOptions const& pmeOpts, int debugIn)
+{
+  // Sanity check
+  if (!pmeOpts.IsPmeType()) {
+    mprinterr("Internal Error: EwaldCalc_LJCPME::Init(): Options were not set up for PME.\n");
+    return 1;
+  }
+  mprintf("\tParticle Mesh Ewald (with LJC for VDW) params:\n");
+  if (NBengine_.ModifyEwaldParams().InitEwald(boxIn, pmeOpts, debugIn)) {
+    mprinterr("Error: PME with LJC calculation init failed.\n");
+    return 1;
+  }
+  VDW_LR_.SetDebug( debugIn );
+  if (Recip_.InitRecip(pmeOpts, debugIn)) {
+    mprinterr("Error: PME with LJC recip init failed.\n");
+    return 1;
+  }
+
+  return 0;
+}
+
+/** Setup PME calculation. */
+int EwaldCalc_LJCPME::Setup(Topology const& topIn, AtomMask const& maskIn) {
+  if (NBengine_.ModifyEwaldParams().SetupEwald(topIn, maskIn)) {
+    mprinterr("Error: PME with LJC calculation setup failed.\n");
+    return 1;
+  }
+  if (VDW_LR_.Setup_VDW_Correction( topIn, maskIn )) {
+    mprinterr("Error: PME with LJC calculation long range VDW correction setup failed.\n");
+    return 1;
+  }
+  if (!topIn.Nonbond().Has_C_Coeff()) {
+    mprinterr("Error: Cannot set up PME with LJC; topology '%s' does not have LJ 12-6-4 (C) terms.\n", topIn.c_str());
+    return 1;
+  }
+
+  return 0;
+}
+
+/** Calculate full nonbonded energy with PME */
+int EwaldCalc_LJCPME::CalcNonbondEnergy(Frame const& frameIn, AtomMask const& maskIn,
+                                     PairList const& pairList_, ExclusionArray const& Excluded_,
+                                     double& e_elec, double& e_vdw)
+{
+  t_total_.Start();
+  double volume = frameIn.BoxCrd().CellVolume();
+  double e_self = NBengine_.EwaldParams().SelfEnergy( volume );
+
+  // TODO make more efficient
+  NBengine_.ModifyEwaldParams().FillRecipCoords( frameIn, maskIn );
+
+  // FIXME helPME requires coords and charge arrays to be non-const
+  double e_recip = Recip_.Recip_ParticleMesh( NBengine_.ModifyEwaldParams().SelectedCoords(),
+                                              frameIn.BoxCrd(),
+                                              NBengine_.ModifyEwaldParams().SelectedCharges(),
+                                              NBengine_.EwaldParams().EwaldCoeff()
+                                            );
+
+  double e_vdw_lr_correction = VDW_LR_.Vdw_Correction( NBengine_.EwaldParams().Cutoff(), volume );
+
+  t_direct_.Start();
+  Cpptraj::PairListTemplate<double>(pairList_, Excluded_,
+                                    NBengine_.EwaldParams().Cut2(), NBengine_);
+  t_direct_.Stop();
+
+  if (NBengine_.EwaldParams().Debug() > 0) {
+    mprintf("DEBUG: Nonbond energy components:\n");
+    mprintf("     Evdw                   = %24.12f\n", NBengine_.Evdw() + e_vdw_lr_correction );
+    mprintf("     Ecoulomb               = %24.12f\n", e_self + e_recip +
+                                                       NBengine_.Eelec() +
+                                                       NBengine_.Eadjust());
+    mprintf("\n");
+    mprintf("     E electrostatic (self) = %24.12f\n", e_self);
+    mprintf("                     (rec)  = %24.12f\n", e_recip);
+    mprintf("                     (dir)  = %24.12f\n", NBengine_.Eelec());
+    mprintf("                     (adj)  = %24.12f\n", NBengine_.Eadjust());
+    mprintf("     E vanDerWaals   (dir)  = %24.12f\n", NBengine_.Evdw());
+    mprintf("                     (LR)   = %24.12f\n", e_vdw_lr_correction);
+  }
+  e_vdw = NBengine_.Evdw() + e_vdw_lr_correction;
+  e_elec = e_self + e_recip + NBengine_.Eelec() + NBengine_.Eadjust();
+  t_total_.Stop();
+  return 0;
+}
+
+void EwaldCalc_LJCPME::Timing(double total) const {
+  t_total_.WriteTiming(1,  "  PME Total:", total);
+  Recip_.Timing_Total().WriteTiming(2,  "Recip:     ", t_total_.Total());
+  t_direct_.WriteTiming(2, "Direct:    ", t_total_.Total());
+}
+#endif /* LIBPME */
diff --git a/src/Energy/EwaldCalc_LJCPME.h b/src/Energy/EwaldCalc_LJCPME.h
new file mode 100644
index 0000000000..e00528996b
--- /dev/null
+++ b/src/Energy/EwaldCalc_LJCPME.h
@@ -0,0 +1,29 @@
+#ifndef INC_ENERGY_EWALDCALC_LJCPME_H
+#define INC_ENERGY_EWALDCALC_LJCPME_H
+#ifdef LIBPME
+#include "EwaldCalc.h"
+#include "PME_Recip.h"
+#include "VDW_LongRange_Correction.h"
+#include "../PairListEngine_Ewald_LJCLR.h"
+namespace Cpptraj {
+namespace Energy {
+class EwaldCalc_LJCPME : public EwaldCalc {
+  public:
+    EwaldCalc_LJCPME();
+    /// Init with Box, EwaldOptions and debug level
+    int Init(Box const&, EwaldOptions const&, int);
+    int Setup(Topology const&, AtomMask const&);
+    int CalcNonbondEnergy(Frame const&, AtomMask const&,
+                          PairList const&, ExclusionArray const&,
+                          double&, double&);
+
+    void Timing(double) const;
+  private:
+    PairListEngine_Ewald_LJCLR<double> NBengine_;
+    PME_Recip Recip_;
+    VDW_LongRange_Correction VDW_LR_; ///< For calculating the long range VDW correction
+};
+}
+}
+#endif
+#endif
diff --git a/src/Energy/EwaldParams.h b/src/Energy/EwaldParams.h
index efdd4fb451..7aeae37ba8 100644
--- a/src/Energy/EwaldParams.h
+++ b/src/Energy/EwaldParams.h
@@ -51,6 +51,8 @@ class EwaldParams {
     int NbIndex(int idx0, int idx1) const { return NB_->GetLJindex(TypeIndices_[idx0], TypeIndices_[idx1]); }
     /// \return Nonbonded parameter at nonobonded parameter index
     NonbondType const& GetLJ(int nbindex) const { return NB_->NBarray()[ nbindex ]; }
+    /// \return Nonbonded LJC coefficient at nonbonded parameter index
+    double GetLJC(int nbindex) const { return NB_->LJC_Array( nbindex ); }
     /// \return Number of atoms (current size of charge array)
     unsigned int Natom() const { return Charge_.size(); }
 
diff --git a/src/Energy/energydepend b/src/Energy/energydepend
index 55290b47e4..8d5050fcfc 100644
--- a/src/Energy/energydepend
+++ b/src/Energy/energydepend
@@ -3,6 +3,7 @@ EnergyDecomposer.o : EnergyDecomposer.cpp ../ArgList.h ../AssociatedData.h ../At
 ErfcFxn.o : ErfcFxn.cpp ../CpptrajStdio.h ../SplineFxnTable.h ErfcFxn.h
 EwaldCalc_Decomp_LJPME.o : EwaldCalc_Decomp_LJPME.cpp ../Atom.h ../AtomMask.h ../Box.h ../CoordinateInfo.h ../CpptrajStdio.h ../Energy/../Constants.h ../Energy/../ParameterTypes.h ../Energy/../SplineFxnTable.h ../Energy/Ene_LJPME_6_12.h ../Energy/ErfcFxn.h ../Energy/EwaldParams.h ../Energy/EwaldParams_LJPME.h ../Energy/Kernel_EwaldAdjust.h ../Energy/Kernel_LJPME_Adjust.h ../EwaldOptions.h ../ExclusionArray.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../PairList.h ../PairListEngine_Ewald_Decomp_LJPME.h ../PairListTemplate.h ../Parallel.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Timer.h ../Unit.h ../Vec3.h ../helpme_standalone.h EwaldCalc.h EwaldCalc_Decomp.h EwaldCalc_Decomp_LJPME.h PME_Recip.h PME_RecipParams.h
 EwaldCalc_Decomp_PME.o : EwaldCalc_Decomp_PME.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../Energy/../Constants.h ../Energy/../ParameterTypes.h ../Energy/../SplineFxnTable.h ../Energy/Ene_LJ_6_12.h ../Energy/ErfcFxn.h ../Energy/EwaldParams.h ../Energy/Kernel_EwaldAdjust.h ../EwaldOptions.h ../ExclusionArray.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../PairList.h ../PairListEngine_Ewald_Decomp_LJLR.h ../PairListTemplate.h ../Parallel.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Timer.h ../Unit.h ../Vec3.h ../helpme_standalone.h EwaldCalc.h EwaldCalc_Decomp.h EwaldCalc_Decomp_PME.h PME_Recip.h PME_RecipParams.h VDW_LongRange_Correction.h
+EwaldCalc_LJCPME.o : EwaldCalc_LJCPME.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../Energy/../Constants.h ../Energy/../ParameterTypes.h ../Energy/../SplineFxnTable.h ../Energy/Ene_LJ_12_6_4.h ../Energy/ErfcFxn.h ../Energy/EwaldParams.h ../Energy/Kernel_EwaldAdjust.h ../EwaldOptions.h ../ExclusionArray.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../PairList.h ../PairListEngine_Ewald_LJCLR.h ../PairListTemplate.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h ../helpme_standalone.h EwaldCalc.h EwaldCalc_LJCPME.h PME_Recip.h PME_RecipParams.h VDW_LongRange_Correction.h
 EwaldCalc_LJPME.o : EwaldCalc_LJPME.cpp ../Atom.h ../AtomMask.h ../Box.h ../CoordinateInfo.h ../CpptrajStdio.h ../Energy/../Constants.h ../Energy/../ParameterTypes.h ../Energy/../SplineFxnTable.h ../Energy/Ene_LJPME_6_12.h ../Energy/ErfcFxn.h ../Energy/EwaldParams.h ../Energy/EwaldParams_LJPME.h ../Energy/Kernel_EwaldAdjust.h ../Energy/Kernel_LJPME_Adjust.h ../EwaldOptions.h ../ExclusionArray.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../PairList.h ../PairListEngine_Ewald_LJPME.h ../PairListTemplate.h ../Parallel.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Timer.h ../Unit.h ../Vec3.h ../helpme_standalone.h EwaldCalc.h EwaldCalc_LJPME.h PME_Recip.h PME_RecipParams.h
 EwaldCalc_PME.o : EwaldCalc_PME.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../Energy/../Constants.h ../Energy/../ParameterTypes.h ../Energy/../SplineFxnTable.h ../Energy/Ene_LJ_6_12.h ../Energy/ErfcFxn.h ../Energy/EwaldParams.h ../Energy/Kernel_EwaldAdjust.h ../EwaldOptions.h ../ExclusionArray.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../PairList.h ../PairListEngine_Ewald_LJLR.h ../PairListTemplate.h ../Parallel.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Timer.h ../Unit.h ../Vec3.h ../helpme_standalone.h EwaldCalc.h EwaldCalc_PME.h PME_Recip.h PME_RecipParams.h VDW_LongRange_Correction.h
 EwaldCalc_Regular.o : EwaldCalc_Regular.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../Energy/../Constants.h ../Energy/../ParameterTypes.h ../Energy/../SplineFxnTable.h ../Energy/Ene_LJ_6_12.h ../Energy/ErfcFxn.h ../Energy/EwaldParams.h ../Energy/Kernel_EwaldAdjust.h ../EwaldOptions.h ../ExclusionArray.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../PairList.h ../PairListEngine_Ewald_LJLR.h ../PairListTemplate.h ../Parallel.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Timer.h ../Unit.h ../Vec3.h EwaldCalc.h EwaldCalc_Regular.h Ewald_Recip.h VDW_LongRange_Correction.h
diff --git a/src/Energy/energyfiles b/src/Energy/energyfiles
index f60e63168b..d2858d0c64 100644
--- a/src/Energy/energyfiles
+++ b/src/Energy/energyfiles
@@ -5,6 +5,7 @@ ENERGY_SOURCES= \
   ErfcFxn.cpp \
   EwaldCalc_Decomp_LJPME.cpp \
   EwaldCalc_Decomp_PME.cpp \
+  EwaldCalc_LJCPME.cpp \
   EwaldCalc_LJPME.cpp \
   EwaldCalc_PME.cpp \
   EwaldCalc_Regular.cpp \
diff --git a/src/PairListEngine_Ewald_LJCLR.h b/src/PairListEngine_Ewald_LJCLR.h
new file mode 100644
index 0000000000..8505f2714e
--- /dev/null
+++ b/src/PairListEngine_Ewald_LJCLR.h
@@ -0,0 +1,82 @@
+#ifndef INC_PAIRLISTENGINE_EWALD_LJCLR_H
+#define INC_PAIRLISTENGINE_EWALD_LJCLR_H
+#include "Energy/Ene_LJ_12_6_4.h"
+#include "Energy/EwaldParams.h"
+#include "Energy/Kernel_EwaldAdjust.h"
+#include "PairList.h"
+namespace Cpptraj {
+/// Direct space nonbond calculation using pairlist with Ewald and LJ 12-6-4 VDW plus LR correction
+template <typename T>
+class PairListEngine_Ewald_LJCLR {
+  public:
+    PairListEngine_Ewald_LJCLR() {}
+    // -------------------------------------------
+    /// Call at the beginning of the frame calculation
+    void FrameBeginCalc() { Evdw_ = 0; Eelec_ = 0; Eadjust_ = 0; }
+    /// Call for atom 0 when looping over atoms of thisCell
+    void SetupAtom0( PairList::AtmType const& atom0 ) {
+      q0_ = EW_.Charge(atom0.Idx());
+    }
+    /// Call for atom 1 when looping over interaction atoms of this/other cell
+    void SetupAtom1( PairList::AtmType const& atom1 ) {
+      q1_ = EW_.Charge(atom1.Idx());
+    }
+    /// Call when cutoff is satisfied
+    void CutoffSatisfied(T const& rij2,
+                         PairList::AtmType const& atom0,
+                         PairList::AtmType const& atom1)
+    {
+      T rij = sqrt( rij2 );
+      T qiqj = q0_ * q1_;
+      //double erfc = erfc_func(ew_coeff_ * rij);
+      T erfcval = EW_.ErfcEW( rij );
+      T e_elec = qiqj * erfcval / rij;
+      Eelec_ += e_elec;
+
+      int nbindex = EW_.NbIndex(atom0.Idx(), atom1.Idx());
+      if (nbindex > -1) {
+        double vswitch = EW_.Switch_Fn(rij2);
+        double LJC = EW_.GetLJC( nbindex );
+        NonbondType const& LJ = EW_.GetLJ( nbindex );
+        T e_vdw = Cpptraj::Energy::Ene_LJ_12_6_4<T>(rij2, LJ.A(), LJ.B(), LJC);
+        Evdw_ += (e_vdw * vswitch);
+      }
+    }
+    /// Call when cutoff is not satisfied
+    void AtomPairExcluded(T const& rij2,
+                            PairList::AtmType const& atom0,
+                            PairList::AtmType const& atom1)
+    {
+      T rij = sqrt(rij2);
+      T erfcval = EW_.ErfcEW( rij );
+      Eadjust_ += Cpptraj::Energy::Kernel_EwaldAdjust<T>( q0_, q1_, rij, erfcval );
+    }
+    // -------------------------------------------
+    Cpptraj::Energy::EwaldParams& ModifyEwaldParams() { return EW_; }
+    Cpptraj::Energy::EwaldParams const& EwaldParams() const { return EW_; }
+
+    T Evdw() const { return Evdw_; }
+    T Eelec() const { return Eelec_; }
+    T Eadjust() const { return Eadjust_; }
+#   ifdef _OPENMP
+    /// To allow reduction of the energy terms
+    void operator+=(PairListEngine_Ewald_LJCLR const& rhs) {
+      Evdw_ += rhs.Evdw_;
+      Eelec_ += rhs.Eelec_;
+      Eadjust_ += rhs.Eadjust_;
+    }
+#   endif
+  private:
+    T q0_;                  ///< Charge on atom 0
+    T q1_;                  ///< Charge on atom 1
+    T Evdw_;                ///< VDW sum for current frame
+    T Eelec_;               ///< Coulomb sum for current frame
+    T Eadjust_;             ///< Adjust energy sum for current frame
+
+    Cpptraj::Energy::EwaldParams EW_;          ///< Hold Ewald parameters for PME
+};
+#ifdef _OPENMP
+#pragma omp declare reduction( + : PairListEngine_Ewald_LJCLR<double> : omp_out += omp_in ) initializer( omp_priv = omp_orig )
+#endif
+} // END namespace Cpptraj
+#endif
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 14c562a587..6e687707b2 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -293,6 +293,7 @@ Energy/EnergyDecomposer.o : Energy/EnergyDecomposer.cpp ArgList.h AssociatedData
 Energy/ErfcFxn.o : Energy/ErfcFxn.cpp CpptrajStdio.h Energy/ErfcFxn.h SplineFxnTable.h
 Energy/EwaldCalc_Decomp_LJPME.o : Energy/EwaldCalc_Decomp_LJPME.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy/Ene_LJPME_6_12.h Energy/ErfcFxn.h Energy/EwaldCalc.h Energy/EwaldCalc_Decomp.h Energy/EwaldCalc_Decomp_LJPME.h Energy/EwaldParams.h Energy/EwaldParams_LJPME.h Energy/Kernel_EwaldAdjust.h Energy/Kernel_LJPME_Adjust.h Energy/PME_Recip.h Energy/PME_RecipParams.h EwaldOptions.h ExclusionArray.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h PairListEngine_Ewald_Decomp_LJPME.h PairListTemplate.h Parallel.h ParameterTypes.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h Timer.h Unit.h Vec3.h helpme_standalone.h
 Energy/EwaldCalc_Decomp_PME.o : Energy/EwaldCalc_Decomp_PME.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy/Ene_LJ_6_12.h Energy/ErfcFxn.h Energy/EwaldCalc.h Energy/EwaldCalc_Decomp.h Energy/EwaldCalc_Decomp_PME.h Energy/EwaldParams.h Energy/Kernel_EwaldAdjust.h Energy/PME_Recip.h Energy/PME_RecipParams.h Energy/VDW_LongRange_Correction.h EwaldOptions.h ExclusionArray.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h PairListEngine_Ewald_Decomp_LJLR.h PairListTemplate.h Parallel.h ParameterTypes.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h Timer.h Unit.h Vec3.h helpme_standalone.h
+Energy/EwaldCalc_LJCPME.o : Energy/EwaldCalc_LJCPME.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy/Ene_LJ_12_6_4.h Energy/ErfcFxn.h Energy/EwaldCalc.h Energy/EwaldCalc_LJCPME.h Energy/EwaldParams.h Energy/Kernel_EwaldAdjust.h Energy/PME_Recip.h Energy/PME_RecipParams.h Energy/VDW_LongRange_Correction.h EwaldOptions.h ExclusionArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h PairListEngine_Ewald_LJCLR.h PairListTemplate.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h Timer.h Topology.h Unit.h Vec3.h helpme_standalone.h
 Energy/EwaldCalc_LJPME.o : Energy/EwaldCalc_LJPME.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy/Ene_LJPME_6_12.h Energy/ErfcFxn.h Energy/EwaldCalc.h Energy/EwaldCalc_LJPME.h Energy/EwaldParams.h Energy/EwaldParams_LJPME.h Energy/Kernel_EwaldAdjust.h Energy/Kernel_LJPME_Adjust.h Energy/PME_Recip.h Energy/PME_RecipParams.h EwaldOptions.h ExclusionArray.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h PairListEngine_Ewald_LJPME.h PairListTemplate.h Parallel.h ParameterTypes.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h Timer.h Unit.h Vec3.h helpme_standalone.h
 Energy/EwaldCalc_PME.o : Energy/EwaldCalc_PME.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy/Ene_LJ_6_12.h Energy/ErfcFxn.h Energy/EwaldCalc.h Energy/EwaldCalc_PME.h Energy/EwaldParams.h Energy/Kernel_EwaldAdjust.h Energy/PME_Recip.h Energy/PME_RecipParams.h Energy/VDW_LongRange_Correction.h EwaldOptions.h ExclusionArray.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h PairListEngine_Ewald_LJLR.h PairListTemplate.h Parallel.h ParameterTypes.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h Timer.h Unit.h Vec3.h helpme_standalone.h
 Energy/EwaldCalc_Regular.o : Energy/EwaldCalc_Regular.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy/Ene_LJ_6_12.h Energy/ErfcFxn.h Energy/EwaldCalc.h Energy/EwaldCalc_Regular.h Energy/EwaldParams.h Energy/Ewald_Recip.h Energy/Kernel_EwaldAdjust.h Energy/VDW_LongRange_Correction.h EwaldOptions.h ExclusionArray.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h PairListEngine_Ewald_LJLR.h PairListTemplate.h Parallel.h ParameterTypes.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h Timer.h Unit.h Vec3.h

From 501e026b3b6e2cf277475e6bc50cdb3b0cb95c25 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 6 Feb 2026 10:27:11 -0500
Subject: [PATCH 1288/1492] Add LJCPME calc type

---
 src/Energy/Ecalc_Nonbond.cpp | 5 +++++
 src/Energy/Ecalc_Nonbond.h   | 2 +-
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/src/Energy/Ecalc_Nonbond.cpp b/src/Energy/Ecalc_Nonbond.cpp
index 3de7a16a7f..2a08f0098b 100644
--- a/src/Energy/Ecalc_Nonbond.cpp
+++ b/src/Energy/Ecalc_Nonbond.cpp
@@ -3,6 +3,7 @@
 #ifdef LIBPME
 # include "EwaldCalc_LJPME.h"
 # include "EwaldCalc_PME.h"
+# include "EwaldCalc_LJCPME.h"
 # include "EwaldCalc_Decomp_LJPME.h"
 # include "EwaldCalc_Decomp_PME.h"
 #else
@@ -60,6 +61,10 @@ int Ecalc_Nonbond::InitNonbondCalc(CalcType typeIn, bool decompose_energyIn,
       else
         calc_ = new EwaldCalc_LJPME();
       break;
+    case LJCPME :
+      // FIXME do decompose energy
+      calc_ = new EwaldCalc_LJCPME();
+      break;
 #   else
     case PME : mprinterr("Error: PME requires compiling with LIBPME (FFTW3 and C++11 support).\n"); return 1;
     case LJPME : mprinterr("Error: LJPME requires compiling with LIBPME (FFTW3 and C++11 support).\n"); return 1;
diff --git a/src/Energy/Ecalc_Nonbond.h b/src/Energy/Ecalc_Nonbond.h
index aa1c792cb8..d9a6c16565 100644
--- a/src/Energy/Ecalc_Nonbond.h
+++ b/src/Energy/Ecalc_Nonbond.h
@@ -13,7 +13,7 @@ class Ecalc_Nonbond {
   public:
     typedef std::vector<double> Darray;
 
-    enum CalcType { SIMPLE = 0, PME, LJPME, REGULAR_EWALD, UNSPECIFIED };
+    enum CalcType { SIMPLE = 0, PME, LJPME, LJCPME, REGULAR_EWALD, UNSPECIFIED };
     /// CONSTRUCTOR
     Ecalc_Nonbond();
     /// DESTRUCTOR

From 2bad31abe338e2964601215cc0b83ab5c175ab4b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 6 Feb 2026 10:29:51 -0500
Subject: [PATCH 1289/1492] Enable LJC calc

---
 src/Action_Energy.cpp | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/src/Action_Energy.cpp b/src/Action_Energy.cpp
index 5a64d5cee4..f752366f1c 100644
--- a/src/Action_Energy.cpp
+++ b/src/Action_Energy.cpp
@@ -184,6 +184,13 @@ Action::RetType Action_Energy::Init(ArgList& actionArgs, ActionInit& init, int d
         return Action::ERR;
       if (ewaldOpts_.Type() == EwaldOptions::LJPME)
         nbCalcType_ = Ecalc_Nonbond::LJPME;
+      if (useLj1264_) {
+        if (nbCalcType_ != Ecalc_Nonbond::PME) {
+          mprinterr("Error: 'lj1264' is only compatible with regular PME.\n");
+          return Action::ERR;
+        }
+        nbCalcType_ = Ecalc_Nonbond::LJCPME;
+      }
 #     else
       mprinterr("Error: 'pme' requires compiling with LIBPME (FFTW3 and C++11 support).\n");
       return Action::ERR;

From eaf894b8e5bb6293c7d9a22f72d3ee80d9af8621 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 6 Feb 2026 10:33:05 -0500
Subject: [PATCH 1290/1492] Update dependencies

---
 src/Energy/energydepend | 2 +-
 src/cpptrajdepend       | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/Energy/energydepend b/src/Energy/energydepend
index 8d5050fcfc..b399ffa5d4 100644
--- a/src/Energy/energydepend
+++ b/src/Energy/energydepend
@@ -1,4 +1,4 @@
-Ecalc_Nonbond.o : Ecalc_Nonbond.cpp ../Atom.h ../AtomMask.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../Energy/../Constants.h ../Energy/../ParameterTypes.h ../Energy/../SplineFxnTable.h ../Energy/Ene_LJPME_6_12.h ../Energy/Ene_LJ_6_12.h ../Energy/ErfcFxn.h ../Energy/EwaldParams.h ../Energy/EwaldParams_LJPME.h ../Energy/Kernel_EwaldAdjust.h ../Energy/Kernel_LJPME_Adjust.h ../EwaldOptions.h ../ExclusionArray.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../PairList.h ../PairListEngine_Ewald_Decomp_LJLR.h ../PairListEngine_Ewald_Decomp_LJPME.h ../PairListEngine_Ewald_LJLR.h ../PairListEngine_Ewald_LJPME.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h ../helpme_standalone.h Ecalc_Nonbond.h Ene_Decomp_Nonbond.h Ene_LJ_6_12.h Ene_Nonbond.h EwaldCalc.h EwaldCalc_Decomp.h EwaldCalc_Decomp_LJPME.h EwaldCalc_Decomp_PME.h EwaldCalc_LJPME.h EwaldCalc_PME.h EwaldCalc_Regular.h Ewald_Recip.h PME_Recip.h PME_RecipParams.h VDW_LongRange_Correction.h
+Ecalc_Nonbond.o : Ecalc_Nonbond.cpp ../Atom.h ../AtomMask.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../Energy/../Constants.h ../Energy/../ParameterTypes.h ../Energy/../SplineFxnTable.h ../Energy/Ene_LJPME_6_12.h ../Energy/Ene_LJ_12_6_4.h ../Energy/Ene_LJ_6_12.h ../Energy/ErfcFxn.h ../Energy/EwaldParams.h ../Energy/EwaldParams_LJPME.h ../Energy/Kernel_EwaldAdjust.h ../Energy/Kernel_LJPME_Adjust.h ../EwaldOptions.h ../ExclusionArray.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../PairList.h ../PairListEngine_Ewald_Decomp_LJLR.h ../PairListEngine_Ewald_Decomp_LJPME.h ../PairListEngine_Ewald_LJCLR.h ../PairListEngine_Ewald_LJLR.h ../PairListEngine_Ewald_LJPME.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h ../helpme_standalone.h Ecalc_Nonbond.h Ene_Decomp_Nonbond.h Ene_LJ_6_12.h Ene_Nonbond.h EwaldCalc.h EwaldCalc_Decomp.h EwaldCalc_Decomp_LJPME.h EwaldCalc_Decomp_PME.h EwaldCalc_LJCPME.h EwaldCalc_LJPME.h EwaldCalc_PME.h EwaldCalc_Regular.h Ewald_Recip.h PME_Recip.h PME_RecipParams.h VDW_LongRange_Correction.h
 EnergyDecomposer.o : EnergyDecomposer.cpp ../ArgList.h ../AssociatedData.h ../Atom.h ../AtomMask.h ../BaseIOtype.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataFile.h ../DataFileList.h ../DataSet.h ../DataSetList.h ../DataSet_1D.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../DataSet_Mesh.h ../Dimension.h ../DistRoutines.h ../EwaldOptions.h ../ExclusionArray.h ../FileIO.h ../FileName.h ../FileTypes.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../OnlineVarT.h ../PairList.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Spline.h ../Stats_Reduce.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../TorsionRoutines.h ../Unit.h ../Vec3.h Ecalc_Nonbond.h Ene_Angle.h Ene_Bond.h Ene_LJ_6_12.h EnergyDecomposer.h Kernel_Fourier.h Kernel_Harmonic.h
 ErfcFxn.o : ErfcFxn.cpp ../CpptrajStdio.h ../SplineFxnTable.h ErfcFxn.h
 EwaldCalc_Decomp_LJPME.o : EwaldCalc_Decomp_LJPME.cpp ../Atom.h ../AtomMask.h ../Box.h ../CoordinateInfo.h ../CpptrajStdio.h ../Energy/../Constants.h ../Energy/../ParameterTypes.h ../Energy/../SplineFxnTable.h ../Energy/Ene_LJPME_6_12.h ../Energy/ErfcFxn.h ../Energy/EwaldParams.h ../Energy/EwaldParams_LJPME.h ../Energy/Kernel_EwaldAdjust.h ../Energy/Kernel_LJPME_Adjust.h ../EwaldOptions.h ../ExclusionArray.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../PairList.h ../PairListEngine_Ewald_Decomp_LJPME.h ../PairListTemplate.h ../Parallel.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Timer.h ../Unit.h ../Vec3.h ../helpme_standalone.h EwaldCalc.h EwaldCalc_Decomp.h EwaldCalc_Decomp_LJPME.h PME_Recip.h PME_RecipParams.h
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 6e687707b2..4b5185ffae 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -288,7 +288,7 @@ DihedralSearch.o : DihedralSearch.cpp ArgList.h Atom.h AtomMask.h Box.h Constant
 DistRoutines.o : DistRoutines.cpp Box.h DistRoutines.h ImageOption.h Matrix_3x3.h Parallel.h Vec3.h
 Dist_Imaged.o : Dist_Imaged.cpp Dist_Imaged.h Matrix_3x3.h Parallel.h Vec3.h
 Energy.o : Energy.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h Energy.h Energy/Ene_Angle.h Energy/Ene_Bond.h Energy/Ene_LJ_12_6_4.h Energy/Ene_LJ_6_12.h Energy/Kernel_Harmonic.h ExclusionArray.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TorsionRoutines.h Unit.h Vec3.h
-Energy/Ecalc_Nonbond.o : Energy/Ecalc_Nonbond.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy/Ecalc_Nonbond.h Energy/Ene_Decomp_Nonbond.h Energy/Ene_LJPME_6_12.h Energy/Ene_LJ_6_12.h Energy/Ene_Nonbond.h Energy/ErfcFxn.h Energy/EwaldCalc.h Energy/EwaldCalc_Decomp.h Energy/EwaldCalc_Decomp_LJPME.h Energy/EwaldCalc_Decomp_PME.h Energy/EwaldCalc_LJPME.h Energy/EwaldCalc_PME.h Energy/EwaldCalc_Regular.h Energy/EwaldParams.h Energy/EwaldParams_LJPME.h Energy/Ewald_Recip.h Energy/Kernel_EwaldAdjust.h Energy/Kernel_LJPME_Adjust.h Energy/PME_Recip.h Energy/PME_RecipParams.h Energy/VDW_LongRange_Correction.h EwaldOptions.h ExclusionArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h PairListEngine_Ewald_Decomp_LJLR.h PairListEngine_Ewald_Decomp_LJPME.h PairListEngine_Ewald_LJLR.h PairListEngine_Ewald_LJPME.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h Timer.h Topology.h Unit.h Vec3.h helpme_standalone.h
+Energy/Ecalc_Nonbond.o : Energy/Ecalc_Nonbond.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy/Ecalc_Nonbond.h Energy/Ene_Decomp_Nonbond.h Energy/Ene_LJPME_6_12.h Energy/Ene_LJ_12_6_4.h Energy/Ene_LJ_6_12.h Energy/Ene_Nonbond.h Energy/ErfcFxn.h Energy/EwaldCalc.h Energy/EwaldCalc_Decomp.h Energy/EwaldCalc_Decomp_LJPME.h Energy/EwaldCalc_Decomp_PME.h Energy/EwaldCalc_LJCPME.h Energy/EwaldCalc_LJPME.h Energy/EwaldCalc_PME.h Energy/EwaldCalc_Regular.h Energy/EwaldParams.h Energy/EwaldParams_LJPME.h Energy/Ewald_Recip.h Energy/Kernel_EwaldAdjust.h Energy/Kernel_LJPME_Adjust.h Energy/PME_Recip.h Energy/PME_RecipParams.h Energy/VDW_LongRange_Correction.h EwaldOptions.h ExclusionArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h PairListEngine_Ewald_Decomp_LJLR.h PairListEngine_Ewald_Decomp_LJPME.h PairListEngine_Ewald_LJCLR.h PairListEngine_Ewald_LJLR.h PairListEngine_Ewald_LJPME.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h Timer.h Topology.h Unit.h Vec3.h helpme_standalone.h
 Energy/EnergyDecomposer.o : Energy/EnergyDecomposer.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DistRoutines.h Energy/Ecalc_Nonbond.h Energy/Ene_Angle.h Energy/Ene_Bond.h Energy/Ene_LJ_6_12.h Energy/EnergyDecomposer.h Energy/Kernel_Fourier.h Energy/Kernel_Harmonic.h EwaldOptions.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h PairList.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h Stats_Reduce.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h Unit.h Vec3.h
 Energy/ErfcFxn.o : Energy/ErfcFxn.cpp CpptrajStdio.h Energy/ErfcFxn.h SplineFxnTable.h
 Energy/EwaldCalc_Decomp_LJPME.o : Energy/EwaldCalc_Decomp_LJPME.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy/Ene_LJPME_6_12.h Energy/ErfcFxn.h Energy/EwaldCalc.h Energy/EwaldCalc_Decomp.h Energy/EwaldCalc_Decomp_LJPME.h Energy/EwaldParams.h Energy/EwaldParams_LJPME.h Energy/Kernel_EwaldAdjust.h Energy/Kernel_LJPME_Adjust.h Energy/PME_Recip.h Energy/PME_RecipParams.h EwaldOptions.h ExclusionArray.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h PairListEngine_Ewald_Decomp_LJPME.h PairListTemplate.h Parallel.h ParameterTypes.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h Timer.h Unit.h Vec3.h helpme_standalone.h

From bac1d392143aba48975db5927a8e2ccb353285c1 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 6 Feb 2026 10:45:00 -0500
Subject: [PATCH 1291/1492] Add files for decomposing PME with LJCPME

---
 src/Energy/EwaldCalc_Decomp_LJCPME.cpp  | 132 ++++++++++++++++++++++++
 src/Energy/EwaldCalc_Decomp_LJCPME.h    |  32 ++++++
 src/PairListEngine_Ewald_Decomp_LJCLR.h | 112 ++++++++++++++++++++
 3 files changed, 276 insertions(+)
 create mode 100644 src/Energy/EwaldCalc_Decomp_LJCPME.cpp
 create mode 100644 src/Energy/EwaldCalc_Decomp_LJCPME.h
 create mode 100644 src/PairListEngine_Ewald_Decomp_LJCLR.h

diff --git a/src/Energy/EwaldCalc_Decomp_LJCPME.cpp b/src/Energy/EwaldCalc_Decomp_LJCPME.cpp
new file mode 100644
index 0000000000..7feff593ca
--- /dev/null
+++ b/src/Energy/EwaldCalc_Decomp_LJCPME.cpp
@@ -0,0 +1,132 @@
+#include "EwaldCalc_Decomp_LJCPME.h"
+#ifdef LIBPME
+#include "../CpptrajStdio.h"
+#include "../EwaldOptions.h"
+#include "../Frame.h"
+#include "../PairListTemplate.h"
+
+using namespace Cpptraj::Energy;
+
+EwaldCalc_Decomp_LJCPME::EwaldCalc_Decomp_LJCPME() :
+  Recip_(PME_Recip::COULOMB)
+{}
+
+/** Set up PME parameters. */
+int EwaldCalc_Decomp_LJCPME::Init(Box const& boxIn, EwaldOptions const& pmeOpts, int debugIn)
+{
+  // Sanity check
+  if (!pmeOpts.IsPmeType()) {
+    mprinterr("Internal Error: EwaldCalc_Decomp_LJCPME::Init(): Options were not set up for PME.\n");
+    return 1;
+  }
+  mprintf("\tDecomposed Particle Mesh Ewald params:\n");
+  if (NBengine_.ModifyEwaldParams().InitEwald(boxIn, pmeOpts, debugIn)) {
+    mprinterr("Error: Decomposable PME (with LJC for VDW) calculation init failed.\n");
+    return 1;
+  }
+  VDW_LR_.SetDebug( debugIn );
+  if (Recip_.InitRecip(pmeOpts, debugIn)) {
+    mprinterr("Error: PME (with LJC for VDW) recip init failed.\n");
+    return 1;
+  }
+
+  return 0;
+}
+
+/** Setup PME calculation. */
+int EwaldCalc_Decomp_LJCPME::Setup(Topology const& topIn, AtomMask const& maskIn) {
+  if (NBengine_.ModifyEwaldParams().SetupEwald(topIn, maskIn)) {
+    mprinterr("Error: PME (with LJC for VDW) calculation setup failed.\n");
+    return 1;
+  }
+  if (VDW_LR_.Setup_VDW_Correction( topIn, maskIn )) {
+    mprinterr("Error: PME (with LJC for VDW) calculation long range VDW correction setup failed.\n");
+    return 1;
+  }
+  // TODO reserve atom_elec and atom_vdw?
+
+  return 0;
+}
+
+/** Calculate full decomposed nonbonded energy with PME */
+int EwaldCalc_Decomp_LJCPME::CalcNonbondEnergy(Frame const& frameIn, AtomMask const& maskIn,
+                                            PairList const& pairList_, ExclusionArray const& Excluded_,
+                                            double& e_elec, double& e_vdw)
+{
+  t_total_.Start();
+  double volume = frameIn.BoxCrd().CellVolume();
+  Darray atom_self;
+  double e_self = NBengine_.EwaldParams().DecomposedSelfEnergy( atom_self, volume );
+# ifdef CPPTRAJ_DEBUG_ENEDECOMP
+  mprintf("DEBUG: Total self energy: %f\n", e_self);
+  mprintf("DEBUG: Sum of self array: %f\n", sumArray(atom_self));
+# endif
+  // TODO make more efficient
+  NBengine_.ModifyEwaldParams().FillRecipCoords( frameIn, maskIn );
+
+  Darray atom_recip;
+  // FIXME helPME requires coords and charge arrays to be non-const
+  double e_recip = Recip_.Recip_Decomp( atom_recip,
+                                        NBengine_.ModifyEwaldParams().SelectedCoords(),
+                                        frameIn.BoxCrd(),
+                                        NBengine_.ModifyEwaldParams().SelectedCharges(),
+                                        NBengine_.EwaldParams().EwaldCoeff()
+                                      );
+# ifdef CPPTRAJ_DEBUG_ENEDECOMP
+  mprintf("DEBUG: Recip energy      : %f\n", e_recip);
+  mprintf("DEBUG: Sum of recip array: %f\n", sumArray(atom_recip));
+# endif
+  // TODO distribute
+  Darray atom_vdwlr;
+  double e_vdw_lr_correction = VDW_LR_.Vdw_Decomp_Correction( atom_vdwlr,
+                                                       NBengine_.EwaldParams().Cutoff(), volume );
+# ifdef CPPTRAJ_DEBUG_ENEDECOMP
+  mprintf("DEBUG: VDW correction       : %f\n", e_vdw_lr_correction);
+  mprintf("DEBUG: Sum of VDW correction: %f\n", sumArray(atom_vdwlr));
+# endif
+  t_direct_.Start();
+  Cpptraj::PairListTemplate<double>(pairList_, Excluded_,
+                                    NBengine_.EwaldParams().Cut2(), NBengine_);
+  t_direct_.Stop();
+# ifdef CPPTRAJ_DEBUG_ENEDECOMP
+  mprintf("DEBUG: Direct Elec. energy : %f\n", NBengine_.Eelec());
+  mprintf("DEBUG: Sum of elec. energy : %f\n", sumArray(NBengine_.Eatom_Elec()));
+  mprintf("DEBUG: Direct VDW energy   : %f\n", NBengine_.Evdw());
+  mprintf("DEBUG: Sum of VDW energy   : %f\n", sumArray(NBengine_.Eatom_EVDW()));
+  mprintf("DEBUG: Direct Adjust energy: %f\n", NBengine_.Eadjust());
+  mprintf("DEBUG: Sum of Adjust energy: %f\n", sumArray(NBengine_.Eatom_EAdjust()));
+# endif
+  if (NBengine_.EwaldParams().Debug() > 0) {
+    mprintf("DEBUG: Nonbond energy components:\n");
+    mprintf("     Evdw                   = %24.12f\n", NBengine_.Evdw() + e_vdw_lr_correction );
+    mprintf("     Ecoulomb               = %24.12f\n", e_self + e_recip +
+                                                       NBengine_.Eelec() +
+                                                       NBengine_.Eadjust());
+    mprintf("\n");
+    mprintf("     E electrostatic (self) = %24.12f\n", e_self);
+    mprintf("                     (rec)  = %24.12f\n", e_recip);
+    mprintf("                     (dir)  = %24.12f\n", NBengine_.Eelec());
+    mprintf("                     (adj)  = %24.12f\n", NBengine_.Eadjust());
+    mprintf("     E vanDerWaals   (dir)  = %24.12f\n", NBengine_.Evdw());
+    mprintf("                     (LR)   = %24.12f\n", e_vdw_lr_correction);
+  }
+  e_vdw = NBengine_.Evdw() + e_vdw_lr_correction;
+  e_elec = e_self + e_recip + NBengine_.Eelec() + NBengine_.Eadjust();
+  // TODO preallocate?
+  atom_elec_.resize( NBengine_.Eatom_Elec().size() );
+  atom_vdw_.resize(  NBengine_.Eatom_EVDW().size() );
+  for (unsigned int idx = 0; idx != atom_elec_.size(); idx++)
+  {
+    atom_elec_[idx] = atom_self[idx] + atom_recip[idx] + NBengine_.Eatom_Elec()[idx] + NBengine_.Eatom_EAdjust()[idx];
+    atom_vdw_[idx]  = NBengine_.Eatom_EVDW()[idx] + atom_vdwlr[idx];
+  }
+  t_total_.Stop();
+  return 0;
+}
+
+void EwaldCalc_Decomp_LJCPME::Timing(double total) const {
+  t_total_.WriteTiming(1,  "  PME decomp Total:", total);
+  Recip_.Timing_Total().WriteTiming(2,  "Recip:     ", t_total_.Total());
+  t_direct_.WriteTiming(2, "Direct:    ", t_total_.Total());
+}
+#endif /* LIBPME */
diff --git a/src/Energy/EwaldCalc_Decomp_LJCPME.h b/src/Energy/EwaldCalc_Decomp_LJCPME.h
new file mode 100644
index 0000000000..57db9a58a6
--- /dev/null
+++ b/src/Energy/EwaldCalc_Decomp_LJCPME.h
@@ -0,0 +1,32 @@
+#ifndef INC_ENERGY_EWALDCALC_DECOMP_LJCPME_H
+#define INC_ENERGY_EWALDCALC_DECOMP_LJCPME_H
+#ifdef LIBPME
+#include "EwaldCalc_Decomp.h"
+#include "PME_Recip.h"
+#include "VDW_LongRange_Correction.h"
+#include "../PairListEngine_Ewald_Decomp_LJCLR.h"
+namespace Cpptraj {
+namespace Energy {
+/** Energy decomposition for nonbonded calculation using PME and LJC w/ VDW
+  * long-range correction.
+  * Comple with -DCPPTRAJ_DEBUG_ENEDECOMP for more details on the individual
+  * contributions.
+  */
+class EwaldCalc_Decomp_LJCPME : public EwaldCalc_Decomp {
+  public:
+    EwaldCalc_Decomp_LJCPME();
+    int Init(Box const&, EwaldOptions const&, int);
+    int Setup(Topology const&, AtomMask const&); // TODO CharMask?
+    int CalcNonbondEnergy(Frame const&, AtomMask const&,
+                          PairList const&, ExclusionArray const&,
+                          double&, double&);
+    void Timing(double) const;
+  private:
+    PairListEngine_Ewald_Decomp_LJCLR<double> NBengine_;
+    PME_Recip Recip_;
+    VDW_LongRange_Correction VDW_LR_; ///< For calculating the long range VDW correction
+};
+}
+}
+#endif /* LIBPME */
+#endif
diff --git a/src/PairListEngine_Ewald_Decomp_LJCLR.h b/src/PairListEngine_Ewald_Decomp_LJCLR.h
new file mode 100644
index 0000000000..3826adbe6c
--- /dev/null
+++ b/src/PairListEngine_Ewald_Decomp_LJCLR.h
@@ -0,0 +1,112 @@
+#ifndef INC_PAIRLISTENGINE_EWALD_DECOMP_LJLR_H
+#define INC_PAIRLISTENGINE_EWALD_DECOMP_LJLR_H
+#include "Energy/Ene_LJ_12_6_4.h"
+#include "Energy/EwaldParams.h"
+#include "Energy/Kernel_EwaldAdjust.h"
+#include "PairList.h"
+namespace Cpptraj {
+/// Direct space nonbond calculation using pairlist with decomposable Ewald and VDW LR correction
+template <typename T>
+class PairListEngine_Ewald_Decomp_LJLR {
+    typedef std::vector<T> Darray;
+  public:
+    PairListEngine_Ewald_Decomp_LJLR() {}
+    // -------------------------------------------
+    /// Call at the beginning of the frame calculation
+    void FrameBeginCalc() { Evdw_ = 0; Eelec_ = 0; Eadjust_ = 0; 
+                            atom_elec_.assign(EW_.Natom(), 0);
+                            atom_evdw_.assign(EW_.Natom(), 0);
+                            atom_eadj_.assign(EW_.Natom(), 0);
+                          }
+    /// Call for atom 0 when looping over atoms of thisCell
+    void SetupAtom0( PairList::AtmType const& atom0 ) {
+      q0_ = EW_.Charge(atom0.Idx());
+    }
+    /// Call for atom 1 when looping over interaction atoms of this/other cell
+    void SetupAtom1( PairList::AtmType const& atom1 ) {
+      q1_ = EW_.Charge(atom1.Idx());
+    }
+    /// Call when cutoff is satisfied
+    void CutoffSatisfied(T const& rij2,
+                         PairList::AtmType const& atom0,
+                         PairList::AtmType const& atom1)
+    {
+      T rij = sqrt( rij2 );
+      T qiqj = q0_ * q1_;
+      //double erfc = erfc_func(ew_coeff_ * rij);
+      T erfcval = EW_.ErfcEW( rij );
+      T e_elec = qiqj * erfcval / rij;
+      Eelec_ += e_elec;
+      T e_half = e_elec * 0.5;
+      atom_elec_[atom0.Idx()] += e_half;
+      atom_elec_[atom1.Idx()] += e_half;
+
+      int nbindex = EW_.NbIndex(atom0.Idx(), atom1.Idx());
+      if (nbindex > -1) {
+        double vswitch = EW_.Switch_Fn(rij2);
+        double LJC = EW_.GetLJC( nbindex );
+        NonbondType const& LJ = EW_.GetLJ( nbindex );
+        T e_vdw = Cpptraj::Energy::Ene_LJ_12_6_4<T>(rij2, LJ.A(), LJ.B(), LJC);
+        e_vdw *= vswitch;
+        Evdw_ += e_vdw;
+        e_half = e_vdw * 0.5;
+        atom_evdw_[atom0.Idx()] += e_half;
+        atom_evdw_[atom1.Idx()] += e_half;
+      }
+    }
+    /// Call when cutoff is not satisfied
+    void AtomPairExcluded(T const& rij2,
+                            PairList::AtmType const& atom0,
+                            PairList::AtmType const& atom1)
+    {
+      T rij = sqrt(rij2);
+      T erfcval = EW_.ErfcEW( rij );
+      T e_adj = Cpptraj::Energy::Kernel_EwaldAdjust<T>( q0_, q1_, rij, erfcval );
+      Eadjust_ += e_adj;
+      T e_half = e_adj * 0.5;
+      atom_eadj_[atom0.Idx()] += e_half;
+      atom_eadj_[atom1.Idx()] += e_half;
+    }
+    // -------------------------------------------
+    Cpptraj::Energy::EwaldParams& ModifyEwaldParams() { return EW_; }
+    Cpptraj::Energy::EwaldParams const& EwaldParams() const { return EW_; }
+
+    T Evdw() const { return Evdw_; }
+    T Eelec() const { return Eelec_; }
+    T Eadjust() const { return Eadjust_; }
+    Darray const& Eatom_Elec() const { return atom_elec_; }
+    Darray const& Eatom_EVDW() const { return atom_evdw_; }
+    Darray const& Eatom_EAdjust() const { return atom_eadj_; }
+#   ifdef _OPENMP
+    static void sum_Darray(Darray& lhs, Darray const& rhs) {
+      for (unsigned int idx = 0; idx != rhs.size(); ++idx)
+        lhs[idx] += rhs[idx];
+    }
+    /// To allow reduction of the energy terms
+    void operator+=(PairListEngine_Ewald_Decomp_LJLR const& rhs) {
+      Evdw_ += rhs.Evdw_;
+      Eelec_ += rhs.Eelec_;
+      Eadjust_ += rhs.Eadjust_;
+      sum_Darray(atom_elec_, rhs.atom_elec_);
+      sum_Darray(atom_evdw_, rhs.atom_evdw_);
+      sum_Darray(atom_eadj_, rhs.atom_eadj_);
+    }
+#   endif
+  private:
+    T q0_;                  ///< Charge on atom 0
+    T q1_;                  ///< Charge on atom 1
+    T Evdw_;                ///< VDW sum for current frame
+    T Eelec_;               ///< Coulomb sum for current frame
+    T Eadjust_;             ///< Adjust energy sum for current frame
+
+    Darray atom_elec_;      ///< Sum of Coulomb E on each atom for current frame
+    Darray atom_evdw_;      ///< Sum of VDW E on each atom for current frame
+    Darray atom_eadj_;      ///< Sum of excluded atom adjust E on each atom for current frame
+
+    Cpptraj::Energy::EwaldParams EW_;          ///< Hold Ewald parameters for PME
+};
+#ifdef _OPENMP
+#pragma omp declare reduction( + : PairListEngine_Ewald_Decomp_LJLR<double> : omp_out += omp_in ) initializer( omp_priv = omp_orig )
+#endif
+} // END namespace Cpptraj
+#endif

From 698493e97f5e518c54c91505bfe84f27757e5f04 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 6 Feb 2026 10:45:42 -0500
Subject: [PATCH 1292/1492] Update dependecies

---
 src/Energy/CMakeLists.txt | 1 +
 src/Energy/energydepend   | 1 +
 src/Energy/energyfiles    | 1 +
 3 files changed, 3 insertions(+)

diff --git a/src/Energy/CMakeLists.txt b/src/Energy/CMakeLists.txt
index 6bfa915cf3..cb15187320 100644
--- a/src/Energy/CMakeLists.txt
+++ b/src/Energy/CMakeLists.txt
@@ -3,6 +3,7 @@ target_sources(cpptraj_common_obj PRIVATE
   ${CMAKE_CURRENT_LIST_DIR}/Ecalc_Nonbond.cpp
   ${CMAKE_CURRENT_LIST_DIR}/EnergyDecomposer.cpp
   ${CMAKE_CURRENT_LIST_DIR}/ErfcFxn.cpp
+  ${CMAKE_CURRENT_LIST_DIR}/EwaldCalc_Decomp_LJCPME.cpp
   ${CMAKE_CURRENT_LIST_DIR}/EwaldCalc_Decomp_LJPME.cpp
   ${CMAKE_CURRENT_LIST_DIR}/EwaldCalc_Decomp_PME.cpp
   ${CMAKE_CURRENT_LIST_DIR}/EwaldCalc_LJCPME.cpp
diff --git a/src/Energy/energydepend b/src/Energy/energydepend
index b399ffa5d4..2d9f419f5a 100644
--- a/src/Energy/energydepend
+++ b/src/Energy/energydepend
@@ -1,6 +1,7 @@
 Ecalc_Nonbond.o : Ecalc_Nonbond.cpp ../Atom.h ../AtomMask.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../Energy/../Constants.h ../Energy/../ParameterTypes.h ../Energy/../SplineFxnTable.h ../Energy/Ene_LJPME_6_12.h ../Energy/Ene_LJ_12_6_4.h ../Energy/Ene_LJ_6_12.h ../Energy/ErfcFxn.h ../Energy/EwaldParams.h ../Energy/EwaldParams_LJPME.h ../Energy/Kernel_EwaldAdjust.h ../Energy/Kernel_LJPME_Adjust.h ../EwaldOptions.h ../ExclusionArray.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../PairList.h ../PairListEngine_Ewald_Decomp_LJLR.h ../PairListEngine_Ewald_Decomp_LJPME.h ../PairListEngine_Ewald_LJCLR.h ../PairListEngine_Ewald_LJLR.h ../PairListEngine_Ewald_LJPME.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h ../helpme_standalone.h Ecalc_Nonbond.h Ene_Decomp_Nonbond.h Ene_LJ_6_12.h Ene_Nonbond.h EwaldCalc.h EwaldCalc_Decomp.h EwaldCalc_Decomp_LJPME.h EwaldCalc_Decomp_PME.h EwaldCalc_LJCPME.h EwaldCalc_LJPME.h EwaldCalc_PME.h EwaldCalc_Regular.h Ewald_Recip.h PME_Recip.h PME_RecipParams.h VDW_LongRange_Correction.h
 EnergyDecomposer.o : EnergyDecomposer.cpp ../ArgList.h ../AssociatedData.h ../Atom.h ../AtomMask.h ../BaseIOtype.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataFile.h ../DataFileList.h ../DataSet.h ../DataSetList.h ../DataSet_1D.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../DataSet_Mesh.h ../Dimension.h ../DistRoutines.h ../EwaldOptions.h ../ExclusionArray.h ../FileIO.h ../FileName.h ../FileTypes.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../OnlineVarT.h ../PairList.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Spline.h ../Stats_Reduce.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../TorsionRoutines.h ../Unit.h ../Vec3.h Ecalc_Nonbond.h Ene_Angle.h Ene_Bond.h Ene_LJ_6_12.h EnergyDecomposer.h Kernel_Fourier.h Kernel_Harmonic.h
 ErfcFxn.o : ErfcFxn.cpp ../CpptrajStdio.h ../SplineFxnTable.h ErfcFxn.h
+EwaldCalc_Decomp_LJCPME.o : EwaldCalc_Decomp_LJCPME.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../Energy/../Constants.h ../Energy/../ParameterTypes.h ../Energy/../SplineFxnTable.h ../Energy/Ene_LJ_12_6_4.h ../Energy/ErfcFxn.h ../Energy/EwaldParams.h ../Energy/Kernel_EwaldAdjust.h ../EwaldOptions.h ../ExclusionArray.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../PairList.h ../PairListEngine_Ewald_Decomp_LJCLR.h ../PairListTemplate.h ../Parallel.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Timer.h ../Unit.h ../Vec3.h ../helpme_standalone.h EwaldCalc.h EwaldCalc_Decomp.h EwaldCalc_Decomp_LJCPME.h PME_Recip.h PME_RecipParams.h VDW_LongRange_Correction.h
 EwaldCalc_Decomp_LJPME.o : EwaldCalc_Decomp_LJPME.cpp ../Atom.h ../AtomMask.h ../Box.h ../CoordinateInfo.h ../CpptrajStdio.h ../Energy/../Constants.h ../Energy/../ParameterTypes.h ../Energy/../SplineFxnTable.h ../Energy/Ene_LJPME_6_12.h ../Energy/ErfcFxn.h ../Energy/EwaldParams.h ../Energy/EwaldParams_LJPME.h ../Energy/Kernel_EwaldAdjust.h ../Energy/Kernel_LJPME_Adjust.h ../EwaldOptions.h ../ExclusionArray.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../PairList.h ../PairListEngine_Ewald_Decomp_LJPME.h ../PairListTemplate.h ../Parallel.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Timer.h ../Unit.h ../Vec3.h ../helpme_standalone.h EwaldCalc.h EwaldCalc_Decomp.h EwaldCalc_Decomp_LJPME.h PME_Recip.h PME_RecipParams.h
 EwaldCalc_Decomp_PME.o : EwaldCalc_Decomp_PME.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../Energy/../Constants.h ../Energy/../ParameterTypes.h ../Energy/../SplineFxnTable.h ../Energy/Ene_LJ_6_12.h ../Energy/ErfcFxn.h ../Energy/EwaldParams.h ../Energy/Kernel_EwaldAdjust.h ../EwaldOptions.h ../ExclusionArray.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../PairList.h ../PairListEngine_Ewald_Decomp_LJLR.h ../PairListTemplate.h ../Parallel.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Timer.h ../Unit.h ../Vec3.h ../helpme_standalone.h EwaldCalc.h EwaldCalc_Decomp.h EwaldCalc_Decomp_PME.h PME_Recip.h PME_RecipParams.h VDW_LongRange_Correction.h
 EwaldCalc_LJCPME.o : EwaldCalc_LJCPME.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../Energy/../Constants.h ../Energy/../ParameterTypes.h ../Energy/../SplineFxnTable.h ../Energy/Ene_LJ_12_6_4.h ../Energy/ErfcFxn.h ../Energy/EwaldParams.h ../Energy/Kernel_EwaldAdjust.h ../EwaldOptions.h ../ExclusionArray.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../PairList.h ../PairListEngine_Ewald_LJCLR.h ../PairListTemplate.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h ../helpme_standalone.h EwaldCalc.h EwaldCalc_LJCPME.h PME_Recip.h PME_RecipParams.h VDW_LongRange_Correction.h
diff --git a/src/Energy/energyfiles b/src/Energy/energyfiles
index d2858d0c64..40fd8aa498 100644
--- a/src/Energy/energyfiles
+++ b/src/Energy/energyfiles
@@ -3,6 +3,7 @@ ENERGY_SOURCES= \
   Ecalc_Nonbond.cpp \
   EnergyDecomposer.cpp \
   ErfcFxn.cpp \
+  EwaldCalc_Decomp_LJCPME.cpp \
   EwaldCalc_Decomp_LJPME.cpp \
   EwaldCalc_Decomp_PME.cpp \
   EwaldCalc_LJCPME.cpp \

From 4f6396e2bad754c4d522676bc330246bb7d1c950 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 6 Feb 2026 10:49:57 -0500
Subject: [PATCH 1293/1492] Update depends

---
 src/cpptrajdepend | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 4b5185ffae..dc5c6f5e08 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -288,9 +288,10 @@ DihedralSearch.o : DihedralSearch.cpp ArgList.h Atom.h AtomMask.h Box.h Constant
 DistRoutines.o : DistRoutines.cpp Box.h DistRoutines.h ImageOption.h Matrix_3x3.h Parallel.h Vec3.h
 Dist_Imaged.o : Dist_Imaged.cpp Dist_Imaged.h Matrix_3x3.h Parallel.h Vec3.h
 Energy.o : Energy.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h Energy.h Energy/Ene_Angle.h Energy/Ene_Bond.h Energy/Ene_LJ_12_6_4.h Energy/Ene_LJ_6_12.h Energy/Kernel_Harmonic.h ExclusionArray.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TorsionRoutines.h Unit.h Vec3.h
-Energy/Ecalc_Nonbond.o : Energy/Ecalc_Nonbond.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy/Ecalc_Nonbond.h Energy/Ene_Decomp_Nonbond.h Energy/Ene_LJPME_6_12.h Energy/Ene_LJ_12_6_4.h Energy/Ene_LJ_6_12.h Energy/Ene_Nonbond.h Energy/ErfcFxn.h Energy/EwaldCalc.h Energy/EwaldCalc_Decomp.h Energy/EwaldCalc_Decomp_LJPME.h Energy/EwaldCalc_Decomp_PME.h Energy/EwaldCalc_LJCPME.h Energy/EwaldCalc_LJPME.h Energy/EwaldCalc_PME.h Energy/EwaldCalc_Regular.h Energy/EwaldParams.h Energy/EwaldParams_LJPME.h Energy/Ewald_Recip.h Energy/Kernel_EwaldAdjust.h Energy/Kernel_LJPME_Adjust.h Energy/PME_Recip.h Energy/PME_RecipParams.h Energy/VDW_LongRange_Correction.h EwaldOptions.h ExclusionArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h PairListEngine_Ewald_Decomp_LJLR.h PairListEngine_Ewald_Decomp_LJPME.h PairListEngine_Ewald_LJCLR.h PairListEngine_Ewald_LJLR.h PairListEngine_Ewald_LJPME.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h Timer.h Topology.h Unit.h Vec3.h helpme_standalone.h
+Energy/Ecalc_Nonbond.o : Energy/Ecalc_Nonbond.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy/Ecalc_Nonbond.h Energy/Ene_Decomp_Nonbond.h Energy/Ene_LJPME_6_12.h Energy/Ene_LJ_12_6_4.h Energy/Ene_LJ_6_12.h Energy/Ene_Nonbond.h Energy/ErfcFxn.h Energy/EwaldCalc.h Energy/EwaldCalc_Decomp.h Energy/EwaldCalc_Decomp_LJCPME.h Energy/EwaldCalc_Decomp_LJPME.h Energy/EwaldCalc_Decomp_PME.h Energy/EwaldCalc_LJCPME.h Energy/EwaldCalc_LJPME.h Energy/EwaldCalc_PME.h Energy/EwaldCalc_Regular.h Energy/EwaldParams.h Energy/EwaldParams_LJPME.h Energy/Ewald_Recip.h Energy/Kernel_EwaldAdjust.h Energy/Kernel_LJPME_Adjust.h Energy/PME_Recip.h Energy/PME_RecipParams.h Energy/VDW_LongRange_Correction.h EwaldOptions.h ExclusionArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h PairListEngine_Ewald_Decomp_LJCLR.h PairListEngine_Ewald_Decomp_LJLR.h PairListEngine_Ewald_Decomp_LJPME.h PairListEngine_Ewald_LJCLR.h PairListEngine_Ewald_LJLR.h PairListEngine_Ewald_LJPME.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h Timer.h Topology.h Unit.h Vec3.h helpme_standalone.h
 Energy/EnergyDecomposer.o : Energy/EnergyDecomposer.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DistRoutines.h Energy/Ecalc_Nonbond.h Energy/Ene_Angle.h Energy/Ene_Bond.h Energy/Ene_LJ_6_12.h Energy/EnergyDecomposer.h Energy/Kernel_Fourier.h Energy/Kernel_Harmonic.h EwaldOptions.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h PairList.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h Stats_Reduce.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h Unit.h Vec3.h
 Energy/ErfcFxn.o : Energy/ErfcFxn.cpp CpptrajStdio.h Energy/ErfcFxn.h SplineFxnTable.h
+Energy/EwaldCalc_Decomp_LJCPME.o : Energy/EwaldCalc_Decomp_LJCPME.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy/Ene_LJ_12_6_4.h Energy/ErfcFxn.h Energy/EwaldCalc.h Energy/EwaldCalc_Decomp.h Energy/EwaldCalc_Decomp_LJCPME.h Energy/EwaldParams.h Energy/Kernel_EwaldAdjust.h Energy/PME_Recip.h Energy/PME_RecipParams.h Energy/VDW_LongRange_Correction.h EwaldOptions.h ExclusionArray.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h PairListEngine_Ewald_Decomp_LJCLR.h PairListTemplate.h Parallel.h ParameterTypes.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h Timer.h Unit.h Vec3.h helpme_standalone.h
 Energy/EwaldCalc_Decomp_LJPME.o : Energy/EwaldCalc_Decomp_LJPME.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy/Ene_LJPME_6_12.h Energy/ErfcFxn.h Energy/EwaldCalc.h Energy/EwaldCalc_Decomp.h Energy/EwaldCalc_Decomp_LJPME.h Energy/EwaldParams.h Energy/EwaldParams_LJPME.h Energy/Kernel_EwaldAdjust.h Energy/Kernel_LJPME_Adjust.h Energy/PME_Recip.h Energy/PME_RecipParams.h EwaldOptions.h ExclusionArray.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h PairListEngine_Ewald_Decomp_LJPME.h PairListTemplate.h Parallel.h ParameterTypes.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h Timer.h Unit.h Vec3.h helpme_standalone.h
 Energy/EwaldCalc_Decomp_PME.o : Energy/EwaldCalc_Decomp_PME.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy/Ene_LJ_6_12.h Energy/ErfcFxn.h Energy/EwaldCalc.h Energy/EwaldCalc_Decomp.h Energy/EwaldCalc_Decomp_PME.h Energy/EwaldParams.h Energy/Kernel_EwaldAdjust.h Energy/PME_Recip.h Energy/PME_RecipParams.h Energy/VDW_LongRange_Correction.h EwaldOptions.h ExclusionArray.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h PairListEngine_Ewald_Decomp_LJLR.h PairListTemplate.h Parallel.h ParameterTypes.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h Timer.h Unit.h Vec3.h helpme_standalone.h
 Energy/EwaldCalc_LJCPME.o : Energy/EwaldCalc_LJCPME.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy/Ene_LJ_12_6_4.h Energy/ErfcFxn.h Energy/EwaldCalc.h Energy/EwaldCalc_LJCPME.h Energy/EwaldParams.h Energy/Kernel_EwaldAdjust.h Energy/PME_Recip.h Energy/PME_RecipParams.h Energy/VDW_LongRange_Correction.h EwaldOptions.h ExclusionArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h PairListEngine_Ewald_LJCLR.h PairListTemplate.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h Timer.h Topology.h Unit.h Vec3.h helpme_standalone.h

From af2b027c40ab4e259d316a29429b68a297466dff Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 6 Feb 2026 10:50:08 -0500
Subject: [PATCH 1294/1492] Fix class name

---
 src/PairListEngine_Ewald_Decomp_LJCLR.h | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/PairListEngine_Ewald_Decomp_LJCLR.h b/src/PairListEngine_Ewald_Decomp_LJCLR.h
index 3826adbe6c..d65466953e 100644
--- a/src/PairListEngine_Ewald_Decomp_LJCLR.h
+++ b/src/PairListEngine_Ewald_Decomp_LJCLR.h
@@ -1,5 +1,5 @@
-#ifndef INC_PAIRLISTENGINE_EWALD_DECOMP_LJLR_H
-#define INC_PAIRLISTENGINE_EWALD_DECOMP_LJLR_H
+#ifndef INC_PAIRLISTENGINE_EWALD_DECOMP_LJCLR_H
+#define INC_PAIRLISTENGINE_EWALD_DECOMP_LJCLR_H
 #include "Energy/Ene_LJ_12_6_4.h"
 #include "Energy/EwaldParams.h"
 #include "Energy/Kernel_EwaldAdjust.h"
@@ -7,10 +7,10 @@
 namespace Cpptraj {
 /// Direct space nonbond calculation using pairlist with decomposable Ewald and VDW LR correction
 template <typename T>
-class PairListEngine_Ewald_Decomp_LJLR {
+class PairListEngine_Ewald_Decomp_LJCLR {
     typedef std::vector<T> Darray;
   public:
-    PairListEngine_Ewald_Decomp_LJLR() {}
+    PairListEngine_Ewald_Decomp_LJCLR() {}
     // -------------------------------------------
     /// Call at the beginning of the frame calculation
     void FrameBeginCalc() { Evdw_ = 0; Eelec_ = 0; Eadjust_ = 0; 
@@ -83,7 +83,7 @@ class PairListEngine_Ewald_Decomp_LJLR {
         lhs[idx] += rhs[idx];
     }
     /// To allow reduction of the energy terms
-    void operator+=(PairListEngine_Ewald_Decomp_LJLR const& rhs) {
+    void operator+=(PairListEngine_Ewald_Decomp_LJCLR const& rhs) {
       Evdw_ += rhs.Evdw_;
       Eelec_ += rhs.Eelec_;
       Eadjust_ += rhs.Eadjust_;
@@ -106,7 +106,7 @@ class PairListEngine_Ewald_Decomp_LJLR {
     Cpptraj::Energy::EwaldParams EW_;          ///< Hold Ewald parameters for PME
 };
 #ifdef _OPENMP
-#pragma omp declare reduction( + : PairListEngine_Ewald_Decomp_LJLR<double> : omp_out += omp_in ) initializer( omp_priv = omp_orig )
+#pragma omp declare reduction( + : PairListEngine_Ewald_Decomp_LJCLR<double> : omp_out += omp_in ) initializer( omp_priv = omp_orig )
 #endif
 } // END namespace Cpptraj
 #endif

From 36a5f2f8d30d4a322dfd51832ddc7fe62c57481d Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 6 Feb 2026 10:50:18 -0500
Subject: [PATCH 1295/1492] Add decomposed LJC pme

---
 src/Energy/Ecalc_Nonbond.cpp | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/src/Energy/Ecalc_Nonbond.cpp b/src/Energy/Ecalc_Nonbond.cpp
index 2a08f0098b..434743c238 100644
--- a/src/Energy/Ecalc_Nonbond.cpp
+++ b/src/Energy/Ecalc_Nonbond.cpp
@@ -6,6 +6,7 @@
 # include "EwaldCalc_LJCPME.h"
 # include "EwaldCalc_Decomp_LJPME.h"
 # include "EwaldCalc_Decomp_PME.h"
+# include "EwaldCalc_Decomp_LJCPME.h"
 #else
 // TODO This is here for when LIBPME is not defined because there is
 //      currently no decomp version of regular Ewald. If there ever is
@@ -62,8 +63,10 @@ int Ecalc_Nonbond::InitNonbondCalc(CalcType typeIn, bool decompose_energyIn,
         calc_ = new EwaldCalc_LJPME();
       break;
     case LJCPME :
-      // FIXME do decompose energy
-      calc_ = new EwaldCalc_LJCPME();
+      if (decompose_energy_)
+        calc_ = new EwaldCalc_Decomp_LJCPME();
+      else
+        calc_ = new EwaldCalc_LJCPME();
       break;
 #   else
     case PME : mprinterr("Error: PME requires compiling with LIBPME (FFTW3 and C++11 support).\n"); return 1;

From c858536b069b56ab9d1376b84afecd2da4de2519 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 6 Feb 2026 11:03:32 -0500
Subject: [PATCH 1296/1492] Add test with/without LJC

---
 test/1d23.tip3p.lj1264.parm7          | 22191 ++++++++++++++++++++++++
 test/1d23.tip3p.rst7                  |  5032 ++++++
 test/Test_Energy/1d23.dat.save        |     2 +
 test/Test_Energy/1d23.lj1264.dat.save |     2 +
 test/Test_Energy/RunTest.sh           |    20 +-
 5 files changed, 27246 insertions(+), 1 deletion(-)
 create mode 100644 test/1d23.tip3p.lj1264.parm7
 create mode 100644 test/1d23.tip3p.rst7
 create mode 100644 test/Test_Energy/1d23.dat.save
 create mode 100644 test/Test_Energy/1d23.lj1264.dat.save

diff --git a/test/1d23.tip3p.lj1264.parm7 b/test/1d23.tip3p.lj1264.parm7
new file mode 100644
index 0000000000..3a4dcf3cef
--- /dev/null
+++ b/test/1d23.tip3p.lj1264.parm7
@@ -0,0 +1,22191 @@
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+       8       1       1       8       1       1       8       1       1       8
+       1       1       8       1       1       8       1       1
+%FLAG MASS
+%FORMAT(5E16.8)
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+  1.20100000E+01  1.40100000E+01  1.00800000E+00  1.00800000E+00  1.40100000E+01
+  1.20100000E+01  1.60000000E+01  1.20100000E+01  1.00800000E+00  1.20100000E+01
+  1.00800000E+00  1.00800000E+00  1.60000000E+01  3.09700000E+01  1.60000000E+01
+  1.60000000E+01  1.60000000E+01  1.20100000E+01  1.00800000E+00  1.00800000E+00
+  1.20100000E+01  1.00800000E+00  1.60000000E+01  1.20100000E+01  1.00800000E+00
+  1.40100000E+01  1.20100000E+01  1.00800000E+00  1.40100000E+01  1.20100000E+01
+  1.20100000E+01  1.60000000E+01  1.40100000E+01  1.00800000E+00  1.20100000E+01
+  1.40100000E+01  1.00800000E+00  1.00800000E+00  1.40100000E+01  1.20100000E+01
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+  1.60000000E+01  1.00800000E+00  1.00800000E+00  1.60000000E+01  1.00800000E+00
+  1.00800000E+00  1.60000000E+01  1.00800000E+00  1.00800000E+00  1.60000000E+01
+  1.00800000E+00  1.00800000E+00  1.60000000E+01  1.00800000E+00  1.00800000E+00
+  1.60000000E+01  1.00800000E+00  1.00800000E+00  1.60000000E+01  1.00800000E+00
+  1.00800000E+00  1.60000000E+01  1.00800000E+00  1.00800000E+00  1.60000000E+01
+  1.00800000E+00  1.00800000E+00  1.60000000E+01  1.00800000E+00  1.00800000E+00
+  1.60000000E+01  1.00800000E+00  1.00800000E+00  1.60000000E+01  1.00800000E+00
+  1.00800000E+00  1.60000000E+01  1.00800000E+00  1.00800000E+00  1.60000000E+01
+  1.00800000E+00  1.00800000E+00  1.60000000E+01  1.00800000E+00  1.00800000E+00
+  1.60000000E+01  1.00800000E+00  1.00800000E+00  1.60000000E+01  1.00800000E+00
+  1.00800000E+00  1.60000000E+01  1.00800000E+00  1.00800000E+00  1.60000000E+01
+  1.00800000E+00  1.00800000E+00  1.60000000E+01  1.00800000E+00  1.00800000E+00
+  1.60000000E+01  1.00800000E+00  1.00800000E+00  1.60000000E+01  1.00800000E+00
+  1.00800000E+00  1.60000000E+01  1.00800000E+00  1.00800000E+00  1.60000000E+01
+  1.00800000E+00  1.00800000E+00  1.60000000E+01  1.00800000E+00  1.00800000E+00
+  1.60000000E+01  1.00800000E+00  1.00800000E+00  1.60000000E+01  1.00800000E+00
+  1.00800000E+00  1.60000000E+01  1.00800000E+00  1.00800000E+00  1.60000000E+01
+  1.00800000E+00  1.00800000E+00  1.60000000E+01  1.00800000E+00  1.00800000E+00
+  1.60000000E+01  1.00800000E+00  1.00800000E+00  1.60000000E+01  1.00800000E+00
+  1.00800000E+00  1.60000000E+01  1.00800000E+00  1.00800000E+00  1.60000000E+01
+  1.00800000E+00  1.00800000E+00  1.60000000E+01  1.00800000E+00  1.00800000E+00
+  1.60000000E+01  1.00800000E+00  1.00800000E+00  1.60000000E+01  1.00800000E+00
+  1.00800000E+00  1.60000000E+01  1.00800000E+00  1.00800000E+00  1.60000000E+01
+  1.00800000E+00  1.00800000E+00  1.60000000E+01  1.00800000E+00  1.00800000E+00
+  1.60000000E+01  1.00800000E+00  1.00800000E+00  1.60000000E+01  1.00800000E+00
+  1.00800000E+00  1.60000000E+01  1.00800000E+00  1.00800000E+00  1.60000000E+01
+  1.00800000E+00  1.00800000E+00  1.60000000E+01  1.00800000E+00  1.00800000E+00
+  1.60000000E+01  1.00800000E+00  1.00800000E+00  1.60000000E+01  1.00800000E+00
+  1.00800000E+00  1.60000000E+01  1.00800000E+00  1.00800000E+00  1.60000000E+01
+  1.00800000E+00  1.00800000E+00  1.60000000E+01  1.00800000E+00  1.00800000E+00
+  1.60000000E+01  1.00800000E+00  1.00800000E+00  1.60000000E+01  1.00800000E+00
+  1.00800000E+00  1.60000000E+01  1.00800000E+00  1.00800000E+00  1.60000000E+01
+  1.00800000E+00  1.00800000E+00  1.60000000E+01  1.00800000E+00  1.00800000E+00
+  1.60000000E+01  1.00800000E+00  1.00800000E+00  1.60000000E+01  1.00800000E+00
+  1.00800000E+00  1.60000000E+01  1.00800000E+00  1.00800000E+00  1.60000000E+01
+  1.00800000E+00  1.00800000E+00  1.60000000E+01  1.00800000E+00  1.00800000E+00
+  1.60000000E+01  1.00800000E+00  1.00800000E+00  1.60000000E+01  1.00800000E+00
+  1.00800000E+00  1.60000000E+01  1.00800000E+00  1.00800000E+00  1.60000000E+01
+  1.00800000E+00  1.00800000E+00  1.60000000E+01  1.00800000E+00  1.00800000E+00
+  1.60000000E+01  1.00800000E+00  1.00800000E+00  1.60000000E+01  1.00800000E+00
+  1.00800000E+00  1.60000000E+01  1.00800000E+00  1.00800000E+00  1.60000000E+01
+  1.00800000E+00  1.00800000E+00  1.60000000E+01  1.00800000E+00  1.00800000E+00
+  1.60000000E+01  1.00800000E+00  1.00800000E+00  1.60000000E+01  1.00800000E+00
+  1.00800000E+00  1.60000000E+01  1.00800000E+00  1.00800000E+00  1.60000000E+01
+  1.00800000E+00  1.00800000E+00  1.60000000E+01  1.00800000E+00  1.00800000E+00
+  1.60000000E+01  1.00800000E+00  1.00800000E+00  1.60000000E+01  1.00800000E+00
+  1.00800000E+00  1.60000000E+01  1.00800000E+00  1.00800000E+00  1.60000000E+01
+  1.00800000E+00  1.00800000E+00  1.60000000E+01  1.00800000E+00  1.00800000E+00
+  1.60000000E+01  1.00800000E+00  1.00800000E+00  1.60000000E+01  1.00800000E+00
+  1.00800000E+00  1.60000000E+01  1.00800000E+00  1.00800000E+00  1.60000000E+01
+  1.00800000E+00  1.00800000E+00  1.60000000E+01  1.00800000E+00  1.00800000E+00
+  1.60000000E+01  1.00800000E+00  1.00800000E+00
+%FLAG ATOM_TYPE_INDEX
+%FORMAT(10I8)
+       1       2       3       4       4       3       4       5       3       6
+       7       8       9       8      10       8       7      11      11       7
+       8      12       3       4       3      13      13       5      14      12
+      12       5       3       4       4       3       4       5       3       6
+       7       8      15       7       8       8      12       7      11       8
+       7      11      11       7       8       3       4       3      13      13
+       5      14      12      12       5       3       4       4       3       4
+       5       3       6       7       8      15       7       8       8       7
+      11      11       7       8      15       7       8       3       4       3
+      13      13       5      14      12      12       5       3       4       4
+       3       4       5       3       6       7       8       9       8       3
+      13      13      13       8      12       7      11       8      12       3
+       4       3      13      13       5      14      12      12       5       3
+       4       4       3       4       5       3       6       7       8       9
+       8      10       8       7      11      11       7       8      12       3
+       4       3      13      13       5      14      12      12       5       3
+       4       4       3       4       5       3       6       7       8      15
+       7       8       8      12       7      11       8       7      11      11
+       7       8       3       4       3      13      13       5      14      12
+      12       5       3       4       4       3       4       5       3       6
+       7       8      15       7       8       8       7      11      11       7
+       8      15       7       8       3       4       3      13      13       5
+      14      12      12       5       3       4       4       3       4       5
+       3       6       7       8       9       8       3      13      13      13
+       8      12       7      11       8      12       3       4       3      13
+      13       5      14      12      12       5       3       4       4       3
+       4       5       3       6       7       8       9       8      10       8
+       7      11      11       7       8      12       3       4       3      13
+      13       5      14      12      12       5       3       4       4       3
+       4       5       3       6       7       8      15       7       8       8
+      12       7      11       8       7      11      11       7       8       3
+       4       3      13      13       2       1       1       2       3       4
+       4       3       4       5       3       6       7       8       9       8
+      10       8       7      11      11       7       8      12       3       4
+       3      13      13       5      14      12      12       5       3       4
+       4       3       4       5       3       6       7       8      15       7
+       8       8      12       7      11       8       7      11      11       7
+       8       3       4       3      13      13       5      14      12      12
+       5       3       4       4       3       4       5       3       6       7
+       8      15       7       8       8       7      11      11       7       8
+      15       7       8       3       4       3      13      13       5      14
+      12      12       5       3       4       4       3       4       5       3
+       6       7       8       9       8       3      13      13      13       8
+      12       7      11       8      12       3       4       3      13      13
+       5      14      12      12       5       3       4       4       3       4
+       5       3       6       7       8       9       8      10       8       7
+      11      11       7       8      12       3       4       3      13      13
+       5      14      12      12       5       3       4       4       3       4
+       5       3       6       7       8      15       7       8       8      12
+       7      11       8       7      11      11       7       8       3       4
+       3      13      13       5      14      12      12       5       3       4
+       4       3       4       5       3       6       7       8      15       7
+       8       8       7      11      11       7       8      15       7       8
+       3       4       3      13      13       5      14      12      12       5
+       3       4       4       3       4       5       3       6       7       8
+       9       8       3      13      13      13       8      12       7      11
+       8      12       3       4       3      13      13       5      14      12
+      12       5       3       4       4       3       4       5       3       6
+       7       8       9       8      10       8       7      11      11       7
+       8      12       3       4       3      13      13       5      14      12
+      12       5       3       4       4       3       4       5       3       6
+       7       8      15       7       8       8      12       7      11       8
+       7      11      11       7       8       3       4       3      13      13
+       2       1      16      16      16      16      16      16      16      16
+      16      17       1       1      17       1       1      17       1       1
+      17       1       1      17       1       1      17       1       1      17
+       1       1      17       1       1      17       1       1      17       1
+       1      17       1       1      17       1       1      17       1       1
+      17       1       1      17       1       1      17       1       1      17
+       1       1      17       1       1      17       1       1      17       1
+       1      17       1       1      17       1       1      17       1       1
+      17       1       1      17       1       1      17       1       1      17
+       1       1      17       1       1      17       1       1      17       1
+       1      17       1       1      17       1       1      17       1       1
+      17       1       1      17       1       1      17       1       1      17
+       1       1      17       1       1      17       1       1      17       1
+       1      17       1       1      17       1       1      17       1       1
+      17       1       1      17       1       1      17       1       1      17
+       1       1      17       1       1      17       1       1      17       1
+       1      17       1       1      17       1       1      17       1       1
+      17       1       1      17       1       1      17       1       1      17
+       1       1      17       1       1      17       1       1      17       1
+       1      17       1       1      17       1       1      17       1       1
+      17       1       1      17       1       1      17       1       1      17
+       1       1      17       1       1      17       1       1      17       1
+       1      17       1       1      17       1       1      17       1       1
+      17       1       1      17       1       1      17       1       1      17
+       1       1      17       1       1      17       1       1      17       1
+       1      17       1       1      17       1       1      17       1       1
+      17       1       1      17       1       1      17       1       1      17
+       1       1      17       1       1      17       1       1      17       1
+       1      17       1       1      17       1       1      17       1       1
+      17       1       1      17       1       1      17       1       1      17
+       1       1      17       1       1      17       1       1      17       1
+       1      17       1       1      17       1       1      17       1       1
+      17       1       1      17       1       1      17       1       1      17
+       1       1      17       1       1      17       1       1      17       1
+       1      17       1       1      17       1       1      17       1       1
+      17       1       1      17       1       1      17       1       1      17
+       1       1      17       1       1      17       1       1      17       1
+       1      17       1       1      17       1       1      17       1       1
+      17       1       1      17       1       1      17       1       1      17
+       1       1      17       1       1      17       1       1      17       1
+       1      17       1       1      17       1       1      17       1       1
+      17       1       1      17       1       1      17       1       1      17
+       1       1      17       1       1      17       1       1      17       1
+       1      17       1       1      17       1       1      17       1       1
+      17       1       1      17       1       1      17       1       1      17
+       1       1      17       1       1      17       1       1      17       1
+       1      17       1       1      17       1       1      17       1       1
+      17       1       1      17       1       1      17       1       1      17
+       1       1      17       1       1      17       1       1      17       1
+       1      17       1       1      17       1       1      17       1       1
+      17       1       1      17       1       1      17       1       1      17
+       1       1      17       1       1      17       1       1      17       1
+       1      17       1       1      17       1       1      17       1       1
+      17       1       1      17       1       1      17       1       1      17
+       1       1      17       1       1      17       1       1      17       1
+       1      17       1       1      17       1       1      17       1       1
+      17       1       1      17       1       1      17       1       1      17
+       1       1      17       1       1      17       1       1      17       1
+       1      17       1       1      17       1       1      17       1       1
+      17       1       1      17       1       1      17       1       1      17
+       1       1      17       1       1      17       1       1      17       1
+       1      17       1       1      17       1       1      17       1       1
+      17       1       1      17       1       1      17       1       1      17
+       1       1      17       1       1      17       1       1      17       1
+       1      17       1       1      17       1       1      17       1       1
+      17       1       1      17       1       1      17       1       1      17
+       1       1      17       1       1      17       1       1      17       1
+       1      17       1       1      17       1       1      17       1       1
+      17       1       1      17       1       1      17       1       1      17
+       1       1      17       1       1      17       1       1      17       1
+       1      17       1       1      17       1       1      17       1       1
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+      17       1       1      17       1       1      17       1       1      17
+       1       1      17       1       1      17       1       1      17       1
+       1      17       1       1      17       1       1      17       1       1
+      17       1       1      17       1       1      17       1       1      17
+       1       1      17       1       1      17       1       1      17       1
+       1      17       1       1      17       1       1      17       1       1
+      17       1       1      17       1       1      17       1       1      17
+       1       1      17       1       1      17       1       1      17       1
+       1      17       1       1      17       1       1      17       1       1
+      17       1       1      17       1       1      17       1       1      17
+       1       1      17       1       1      17       1       1      17       1
+       1      17       1       1      17       1       1      17       1       1
+      17       1       1      17       1       1      17       1       1      17
+       1       1      17       1       1      17       1       1      17       1
+       1      17       1       1      17       1       1      17       1       1
+      17       1       1      17       1       1      17       1       1      17
+       1       1      17       1       1      17       1       1      17       1
+       1      17       1       1      17       1       1      17       1       1
+      17       1       1      17       1       1      17       1       1      17
+       1       1      17       1       1      17       1       1      17       1
+       1      17       1       1      17       1       1      17       1       1
+      17       1       1      17       1       1      17       1       1      17
+       1       1      17       1       1      17       1       1      17       1
+       1      17       1       1      17       1       1      17       1       1
+      17       1       1      17       1       1      17       1       1      17
+       1       1      17       1       1      17       1       1      17       1
+       1      17       1       1      17       1       1      17       1       1
+      17       1       1      17       1       1      17       1       1      17
+       1       1      17       1       1      17       1       1      17       1
+       1      17       1       1      17       1       1      17       1       1
+      17       1       1      17       1       1      17       1       1      17
+       1       1      17       1       1      17       1       1      17       1
+       1      17       1       1      17       1       1      17       1       1
+      17       1       1      17       1       1      17       1       1      17
+       1       1      17       1       1      17       1       1      17       1
+       1      17       1       1      17       1       1      17       1       1
+      17       1       1      17       1       1      17       1       1      17
+       1       1      17       1       1      17       1       1      17       1
+       1      17       1       1      17       1       1      17       1       1
+      17       1       1      17       1       1      17       1       1      17
+       1       1      17       1       1      17       1       1      17       1
+       1      17       1       1      17       1       1      17       1       1
+      17       1       1      17       1       1      17       1       1      17
+       1       1      17       1       1      17       1       1
+%FLAG NUMBER_EXCLUDED_ATOMS
+%FORMAT(10I8)
+       5       7      10       5       4      12       6      11      14       7
+      12       9       4       7       3       6       4       2       1       2
+       2       1       9       5       4       2       1       5       7       3
+       2       7      10       5       4      12       6      11      14       7
+      12       7       3       6       7       7       4       7       3       5
+       4       2       1       1       1       9       5       4       2       1
+       5       7       3       2       7      10       5       4      12       6
+      11      14       7      12       7       3       6       8       8       5
+       2       1       4       3       2       1       1       9       5       4
+       2       1       5       7       3       2       7      10       5       4
+      12       6      11      14       7      13      12       4       9       6
+       3       2       1       5       3       3       2       2       1       9
+       5       4       2       1       5       7       3       2       7      10
+       5       4      12       6      11      14       7      12       9       4
+       7       3       6       4       2       1       2       2       1       9
+       5       4       2       1       5       7       3       2       7      10
+       5       4      12       6      11      14       7      12       7       3
+       6       7       7       4       7       3       5       4       2       1
+       1       1       9       5       4       2       1       5       7       3
+       2       7      10       5       4      12       6      11      14       7
+      12       7       3       6       8       8       5       2       1       4
+       3       2       1       1       9       5       4       2       1       5
+       7       3       2       7      10       5       4      12       6      11
+      14       7      13      12       4       9       6       3       2       1
+       5       3       3       2       2       1       9       5       4       2
+       1       5       7       3       2       7      10       5       4      12
+       6      11      14       7      12       9       4       7       3       6
+       4       2       1       2       2       1       9       5       4       2
+       1       5       7       3       2       7      10       5       4      12
+       6      11      14       7      12       7       3       6       7       7
+       4       7       3       5       4       2       1       1       1       6
+       5       4       2       1       1       1       5       7      10       5
+       4      12       6      11      14       7      12       9       4       7
+       3       6       4       2       1       2       2       1       9       5
+       4       2       1       5       7       3       2       7      10       5
+       4      12       6      11      14       7      12       7       3       6
+       7       7       4       7       3       5       4       2       1       1
+       1       9       5       4       2       1       5       7       3       2
+       7      10       5       4      12       6      11      14       7      12
+       7       3       6       8       8       5       2       1       4       3
+       2       1       1       9       5       4       2       1       5       7
+       3       2       7      10       5       4      12       6      11      14
+       7      13      12       4       9       6       3       2       1       5
+       3       3       2       2       1       9       5       4       2       1
+       5       7       3       2       7      10       5       4      12       6
+      11      14       7      12       9       4       7       3       6       4
+       2       1       2       2       1       9       5       4       2       1
+       5       7       3       2       7      10       5       4      12       6
+      11      14       7      12       7       3       6       7       7       4
+       7       3       5       4       2       1       1       1       9       5
+       4       2       1       5       7       3       2       7      10       5
+       4      12       6      11      14       7      12       7       3       6
+       8       8       5       2       1       4       3       2       1       1
+       9       5       4       2       1       5       7       3       2       7
+      10       5       4      12       6      11      14       7      13      12
+       4       9       6       3       2       1       5       3       3       2
+       2       1       9       5       4       2       1       5       7       3
+       2       7      10       5       4      12       6      11      14       7
+      12       9       4       7       3       6       4       2       1       2
+       2       1       9       5       4       2       1       5       7       3
+       2       7      10       5       4      12       6      11      14       7
+      12       7       3       6       7       7       4       7       3       5
+       4       2       1       1       1       6       5       4       2       1
+       1       1       1       1       1       1       1       1       1       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
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+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
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+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
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+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
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+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
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+       1       1       2       1       1       2       1       1       2       1
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+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
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+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
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+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
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+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
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+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
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+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
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+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
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+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
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+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
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+       1       2       1       1       2       1       1       2       1       1
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+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
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+       1       1       2       1       1       2       1       1       2       1
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+       1       2       1       1       2       1       1       2       1       1
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+       1       1       2       1       1       2       1       1       2       1
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+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
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+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
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+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1       2       1
+       1       2       1       1       2       1       1       2       1       1
+       2       1       1       2       1       1       2       1       1       2
+       1       1       2       1       1       2       1       1
+%FLAG NONBONDED_PARM_INDEX
+%FORMAT(10I8)
+       1       2       4       7      11      16      22      29      37      46
+      56      67      79      92     106     121     137       2       3       5
+       8      12      17      23      30      38      47      57      68      80
+      93     107     122     138       4       5       6       9      13      18
+      24      31      39      48      58      69      81      94     108     123
+     139       7       8       9      10      14      19      25      32      40
+      49      59      70      82      95     109     124     140      11      12
+      13      14      15      20      26      33      41      50      60      71
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+%FLAG LENNARD_JONES_BCOEF
+%FORMAT(5E16.8)
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+%FLAG BONDS_INC_HYDROGEN
+%FORMAT(10I8)
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+%FLAG BONDS_WITHOUT_HYDROGEN
+%FORMAT(10I8)
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+%FLAG ANGLES_WITHOUT_HYDROGEN
+%FORMAT(10I8)
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+    1800    1794    1803       1    1797    1794    1800      72    1797    1794
+    1803       1    1794    1803    1806      73
+%FLAG DIHEDRALS_INC_HYDROGEN
+%FORMAT(10I8)
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+      75      72      66      81       4      75      72     -66      81       5
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+      18      15      21      24      10      18      15      66      69       9
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+      18      15     -66      81       5      15      21      24      27      10
+      15      66      72      75      34      15      66      72      78      34
+      12       6      15      18       9      12       6      15      21       4
+      12       6      15      66       9       9       6      15      18       9
+       9       6      15      21       4       9       6      15      66       9
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+%FLAG EXCLUDED_ATOMS_LIST
+%FORMAT(10I8)
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+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+%FLAG JOIN_ARRAY
+%FORMAT(10I8)
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
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+%FLAG SOLVENT_POINTERS
+%FORMAT(3I8)
+      29    3150      12
+%FLAG ATOMS_PER_MOLECULE
+%FORMAT(10I8)
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+%FLAG BOX_DIMENSIONS
+%FORMAT(5E16.8)
+  9.00000000E+01  4.76861700E+01  4.67352440E+01  6.19964970E+01
+%FLAG RADIUS_SET
+%FORMAT(1a80)
+modified Bondi radii (mbondi)                                                   
+%FLAG RADII
+%FORMAT(5E16.8)
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+%FLAG IPOL
+%FORMAT(1I8)
+       0
+%FLAG LENNARD_JONES_CCOEF
+%COMMENT For 12-6-4 potential used for ions
+%FORMAT(5E16.8)
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diff --git a/test/1d23.tip3p.rst7 b/test/1d23.tip3p.rst7
new file mode 100644
index 0000000000..ff63face39
--- /dev/null
+++ b/test/1d23.tip3p.rst7
@@ -0,0 +1,5032 @@
+
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+   3.2942290   8.5655440   3.1852460  10.4328080  12.1010000   6.9586200
+   9.9558640  12.9082190   6.7658810   9.7489870  11.4488330   7.1112410
+   2.0612470  11.0794840  10.7313420   2.0327900  11.4837790   9.8641850
+   1.8977440  10.1505200  10.5685020  14.0127290  11.8621940  12.0277590
+  14.4887010  12.3404830  12.7066670  14.6334450  11.7939430  11.3023090
+  13.4160540   9.0534790   9.1877600  13.5423600   8.8146670   8.2694780
+  13.4581920   8.2219330   9.6599680   7.2777280  12.7562790   7.7572410
+   7.7921950  12.6670800   8.5594840   6.4346360  13.1022490   8.0500320
+   7.4253090   2.6669840  10.8484980   7.7506500   1.8333590  10.5087210
+   8.2133420   3.1898360  10.9963310   3.2742490   3.1009770  10.4095730
+   3.1786090   2.1604500  10.2596130   4.1174470   3.3224840  10.0143800
+   7.2561050   3.4356850   4.4680170   6.5242170   3.9443660   4.8170270
+   6.8585390   2.6186830   4.1668950   3.9946410   4.1712830   4.6198070
+   4.3616540   3.6971400   5.3659410   3.8051470   5.0454400   4.9606410
+   1.7845780   3.2121470   6.9382280   1.4802850   4.0913450   7.1632640
+   2.7392240   3.2721260   6.9739720  11.0715550   6.4147820   3.3275520
+  11.7914670   6.9103110   2.9371630  10.8697370   5.7365710   2.6829390
+   6.4534350   6.4856880   9.2144520   6.3871660   5.5652550   8.9602110
+   5.8239490   6.5832320   9.9289160   6.3851080   9.3077450   8.9648320
+   6.3995620   8.3758410   8.7467230   5.6776180   9.3937210   9.6038090
+  12.5962290   5.9484790   8.3116900  11.8710480   6.5413570   8.1146290
+  13.1237750   5.9408330   7.5130270   5.8184980  10.9495020   6.0588820
+   6.4627200  11.1554400   6.7362240   6.1814420  10.1883420   5.6059670
+   7.0917060   8.9527370   4.7766270   7.7339290   8.2520530   4.8898440
+   7.6166410   9.7325810   4.5963160   8.8654680   9.7522270   7.9802330
+   9.2010920  10.3388960   8.6580250   7.9455020   9.6214980   8.2100120
+   4.6943260   9.8013600  11.1490390   4.3740130   9.0822840  11.6936080
+   4.0201620  10.4768670  11.2226450   4.8698850   2.6879350   6.7365160
+   5.3684100   3.1625170   7.4017010   5.0121800   1.7642870   6.9435190
+  12.3713300  11.3189340   2.7009170  12.4960720  12.1420510   3.1732980
+  13.2378860  11.1080070   2.3533320   7.6853740   8.7046490  11.5087290
+   7.0791900   8.7278090  10.7683040   7.3807850   7.9729530  12.0454540
+   9.1154110  12.4326780  10.1196700  10.0675860  12.3484800  10.0696940
+   8.9682330  13.0968490  10.7930490   3.6224860   6.4911070  10.0383450
+   2.8570530   7.0596070   9.9538120   3.8040820   6.1987280   9.1451680
+  10.7648210   8.2216400  10.5958470  11.5057680   8.5592160  10.0925930
+  10.0020890   8.3908460  10.0428240   9.4393870   6.2731230   9.1313680
+   9.8534890   6.4276310   9.9804100   8.5044870   6.3986450   9.2939460
+   9.9116040   3.6127390  11.1352830  10.4936810   2.8579710  11.0473310
+  10.0877810   4.1434830  10.3584310   4.2009100   6.2251710   7.1009610
+   4.6197210   7.0684440   6.9285850   3.2817730   6.3623750   6.8716390
+   6.5373000   3.9567890   8.4847450   6.6569210   3.3609030   9.2242290
+   7.3967000   3.9937580   8.0648750   8.8760900   4.5105080   7.0609960
+   8.3496120   5.0347700   6.4575100   9.2192240   5.1432470   7.6919690
+   2.0516520  12.5304720   8.2167340   1.5137610  13.2550780   7.8976040
+   2.3050480  12.0535060   7.4264680   4.9078730  13.7655930   8.4753990
+   4.8337430  14.6691070   8.7826360   4.0057570  13.4467830   8.4476060
+  12.4358410  11.4618110   8.8046550  11.8360400  11.5210670   8.0610470
+  12.5652310  10.5223090   8.9343400  11.1210050   8.1870090   6.9022710
+  10.3069890   8.6167250   7.1648500  11.5284250   8.7988500   6.2891760
+  12.4700450   3.3258290   8.4291930  12.2386540   3.0971040   7.5289880
+  12.7305000   4.2457840   8.3836820  12.3551790   2.4044260   2.0959650
+  12.8789270   1.9106910   1.4649820  12.9411210   2.5394620   2.8407220
+  12.5341510   2.4884130   5.6179200  11.5844220   2.4547670   5.7324190
+  12.7154520   3.3984240   5.3828970   2.7854700  10.9266190   6.1791330
+   2.5446060  11.1940750   5.2921850   3.7257340  11.0971920   6.2342190
+  14.0458860  12.9460570   6.9801970  13.5517140  13.3429440   6.2629100
+  13.4372150  12.3209780   7.3739250  11.7298310  13.5883990   4.2588710
+  11.2701280  14.3399800   3.8846730  11.1010770  12.8690460   4.2003510
+   2.1594030  11.8972230   3.4336840   2.6759050  11.2859590   2.9085100
+   2.8091410  12.4001010   3.9247850   4.8989530  12.7880720   4.2605820
+   5.1867340  12.5335020   3.3838830   5.4112750  12.2358080   4.8511390
+   4.9661890  13.7096820  11.6274020   5.8929200  13.4741090  11.6709980
+   4.9512320  14.5368820  11.1460050  11.5339450  12.9366680  11.4515060
+  12.3264770  12.4415910  11.2441020  11.8272600  13.6156820  12.0590670
+  47.6861700  46.7352440  61.9964970  90.0000000  90.0000000  90.0000000
diff --git a/test/Test_Energy/1d23.dat.save b/test/Test_Energy/1d23.dat.save
new file mode 100644
index 0000000000..8417e29d5e
--- /dev/null
+++ b/test/Test_Energy/1d23.dat.save
@@ -0,0 +1,2 @@
+#Frame   No1264[bond] No1264[angle]  No1264[dih] No1264[vdw14] No1264[elec14]  No1264[vdw] No1264[elec] No1264[total]
+       1     107.3642      695.8765     550.8121      190.6375     -2269.9901    2819.5846  -29883.1151   -27788.8302
diff --git a/test/Test_Energy/1d23.lj1264.dat.save b/test/Test_Energy/1d23.lj1264.dat.save
new file mode 100644
index 0000000000..5807b3b93a
--- /dev/null
+++ b/test/Test_Energy/1d23.lj1264.dat.save
@@ -0,0 +1,2 @@
+#Frame     Cppt[bond]  Cppt[angle]    Cppt[dih]  Cppt[vdw14] Cppt[elec14]    Cppt[vdw]   Cppt[elec]  Cppt[total]
+       1     107.3642     695.8765     550.8121     190.6375   -2269.9901    2702.6284  -29883.1151  -27905.7865
diff --git a/test/Test_Energy/RunTest.sh b/test/Test_Energy/RunTest.sh
index 956fb318f9..6d61b28ec9 100755
--- a/test/Test_Energy/RunTest.sh
+++ b/test/Test_Energy/RunTest.sh
@@ -2,7 +2,7 @@
 
 . ../MasterTest.sh
 
-CleanFiles ene.in ene.agr short.dat tz2.dat strip.dat elec.dat vdw.dat
+CleanFiles ene.in ene.agr short.dat tz2.dat strip.dat elec.dat vdw.dat 1d23.lj1264.dat 1d23.dat
 
 INPUT="-i ene.in"
 
@@ -57,5 +57,23 @@ EOF
   DoTest vdw.dat.save vdw.dat
 fi
 
+UNITNAME='Test LJ 12-6-4 energy'
+CheckFor maxthreads 1
+if [ $? -eq 0 ] ; then
+  cat > ene.in <<EOF
+parm ../1d23.tip3p.lj1264.parm7
+trajin ../1d23.tip3p.rst7
+energy out 1d23.dat No1264 \
+  etype pme cut 8.0 dsumtol 0.00001 \
+  order 6 nfft 60,60,60
+energy out 1d23.lj1264.dat Cppt lj1264 \
+  etype pme cut 8.0 dsumtol 0.00001 \
+  order 6 nfft 60,60,60
+EOF
+  RunCpptraj "$UNITNAME"
+  DoTest 1d23.dat.save 1d23.dat
+  DoTest 1d23.lj1264.dat.save 1d23.lj1264.dat
+fi
+
 EndTest
 exit 0

From 47e84cd9aa6e69e145a2d2817e48b80ea76e0baa Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 6 Feb 2026 11:23:25 -0500
Subject: [PATCH 1297/1492] Add test save files

---
 test/Test_EneDecomp/1d23.dat.save        | 10059 +++++++++++++++++++++
 test/Test_EneDecomp/1d23.lj1264.dat.save | 10059 +++++++++++++++++++++
 2 files changed, 20118 insertions(+)
 create mode 100644 test/Test_EneDecomp/1d23.dat.save
 create mode 100644 test/Test_EneDecomp/1d23.lj1264.dat.save

diff --git a/test/Test_EneDecomp/1d23.dat.save b/test/Test_EneDecomp/1d23.dat.save
new file mode 100644
index 0000000000..44f761e323
--- /dev/null
+++ b/test/Test_EneDecomp/1d23.dat.save
@@ -0,0 +1,10059 @@
+#Atom          No1264
+    1.000      14.0031
+    2.000      -5.1290
+    3.000       1.7749
+    4.000       2.9266
+    5.000       3.0236
+    6.000      11.2244
+    7.000       1.1511
+    8.000       2.0522
+    9.000      11.5517
+   10.000      -2.3221
+   11.000       0.0802
+   12.000       3.2273
+   13.000       4.2836
+   14.000     -24.9597
+   15.000      -1.4566
+   16.000     -25.6457
+   17.000      -2.9492
+   18.000     -32.8356
+   19.000     -20.7753
+   20.000     -38.8836
+   21.000     -12.0486
+   22.000     -10.7543
+   23.000       2.7532
+   24.000       0.1475
+   25.000      10.5775
+   26.000       4.5999
+   27.000       2.1336
+   28.000     -15.9992
+   29.000      57.6372
+   30.000     -41.9195
+   31.000     -32.9408
+   32.000     -11.4824
+   33.000       2.8180
+   34.000       0.0596
+   35.000       0.1205
+   36.000       5.7240
+   37.000       0.6927
+   38.000      15.5885
+   39.000       7.0343
+   40.000      -8.4833
+   41.000      -0.7055
+   42.000      -3.5775
+   43.000      -7.9552
+   44.000      34.8147
+   45.000       2.7385
+   46.000     -31.9163
+   47.000      11.8272
+   48.000       9.1748
+   49.000     -44.9682
+   50.000     -63.4026
+   51.000      42.4003
+   52.000     -45.8146
+   53.000     -43.0596
+   54.000       3.7093
+   55.000     -12.4931
+   56.000       0.4115
+   57.000      -1.9119
+   58.000      12.7390
+   59.000       0.0072
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+   61.000     -11.6227
+   62.000      37.7545
+   63.000     -33.0964
+   64.000     -24.0258
+   65.000       0.3803
+   66.000       1.5333
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+   68.000      -3.7940
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+   71.000      29.1672
+   72.000       6.5983
+   73.000     -13.1529
+   74.000       2.2373
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+   76.000     -10.0040
+   77.000      53.0248
+   78.000       1.4422
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+   82.000     -40.1328
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diff --git a/test/Test_EneDecomp/1d23.lj1264.dat.save b/test/Test_EneDecomp/1d23.lj1264.dat.save
new file mode 100644
index 0000000000..344925fd91
--- /dev/null
+++ b/test/Test_EneDecomp/1d23.lj1264.dat.save
@@ -0,0 +1,10059 @@
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+ 9835.000      -8.2814
+ 9836.000     -10.4201
+ 9837.000      -0.9180
+ 9838.000      -0.5697
+ 9839.000      -7.2781
+ 9840.000       8.9161
+ 9841.000      -9.2467
+ 9842.000      -6.2580
+ 9843.000      -5.0698
+ 9844.000       1.8430
+ 9845.000      -3.1933
+ 9846.000      28.6242
+ 9847.000     -17.1122
+ 9848.000     -18.4950
+ 9849.000      -4.9857
+ 9850.000      -2.9178
+ 9851.000      -3.9748
+ 9852.000     -11.9829
+ 9853.000      -1.6113
+ 9854.000       0.1984
+ 9855.000      11.5378
+ 9856.000      -8.9527
+ 9857.000     -10.2953
+ 9858.000      18.5623
+ 9859.000     -12.1374
+ 9860.000     -17.2475
+ 9861.000     -10.5959
+ 9862.000       0.1187
+ 9863.000       0.6525
+ 9864.000     -15.7729
+ 9865.000       6.0989
+ 9866.000       2.5469
+ 9867.000      23.2242
+ 9868.000     -12.1661
+ 9869.000     -17.6900
+ 9870.000      -2.7386
+ 9871.000       1.7276
+ 9872.000      -4.2569
+ 9873.000      12.9124
+ 9874.000      -5.7006
+ 9875.000     -12.0452
+ 9876.000      12.6772
+ 9877.000      -9.7838
+ 9878.000      -9.9729
+ 9879.000       4.9620
+ 9880.000      -6.0744
+ 9881.000      -7.3309
+ 9882.000      40.4989
+ 9883.000     -22.6037
+ 9884.000     -21.4875
+ 9885.000      25.6374
+ 9886.000     -17.8941
+ 9887.000     -14.4926
+ 9888.000       5.8876
+ 9889.000      -4.0177
+ 9890.000      -5.5856
+ 9891.000       5.1782
+ 9892.000      -6.6364
+ 9893.000      -8.8755
+ 9894.000       6.3728
+ 9895.000      -6.8012
+ 9896.000      -7.5859
+ 9897.000       9.4241
+ 9898.000      -7.3455
+ 9899.000      -7.4003
+ 9900.000      23.3164
+ 9901.000     -18.0750
+ 9902.000     -16.3543
+ 9903.000     -29.8370
+ 9904.000      10.9206
+ 9905.000      12.6834
+ 9906.000     -26.5945
+ 9907.000      13.6146
+ 9908.000      10.5407
+ 9909.000     -20.0332
+ 9910.000       6.5495
+ 9911.000       4.9845
+ 9912.000     -28.3884
+ 9913.000      13.0928
+ 9914.000       8.7320
+ 9915.000     -26.0691
+ 9916.000       8.7574
+ 9917.000       9.5191
+ 9918.000     -30.3495
+ 9919.000      10.5853
+ 9920.000      11.8121
+ 9921.000     -29.6058
+ 9922.000      11.2073
+ 9923.000       9.8965
+ 9924.000     -29.4437
+ 9925.000      11.8250
+ 9926.000      10.8500
+ 9927.000     -24.9395
+ 9928.000      11.4979
+ 9929.000       7.4409
+ 9930.000     -24.0592
+ 9931.000       7.5043
+ 9932.000       9.0894
+ 9933.000     -23.6015
+ 9934.000       6.0125
+ 9935.000       9.8306
+ 9936.000      -6.9155
+ 9937.000      -2.4391
+ 9938.000      -1.3042
+ 9939.000     -20.0601
+ 9940.000       5.4452
+ 9941.000       6.2388
+ 9942.000     -21.3172
+ 9943.000       5.8876
+ 9944.000       2.3083
+ 9945.000     -23.9436
+ 9946.000      11.7840
+ 9947.000       5.0467
+ 9948.000     -19.6892
+ 9949.000      10.3541
+ 9950.000       9.2454
+ 9951.000     -27.7096
+ 9952.000      12.0863
+ 9953.000      13.2247
+ 9954.000     -25.4793
+ 9955.000       7.2837
+ 9956.000      10.5744
+ 9957.000     -19.3899
+ 9958.000       9.0880
+ 9959.000       7.7276
+ 9960.000     -42.3927
+ 9961.000      19.3040
+ 9962.000      18.6021
+ 9963.000     -24.2341
+ 9964.000       5.3731
+ 9965.000       8.2756
+ 9966.000     -21.9154
+ 9967.000       7.8717
+ 9968.000       5.0965
+ 9969.000     -16.1905
+ 9970.000       3.1356
+ 9971.000       6.2923
+ 9972.000     -25.3780
+ 9973.000       6.6539
+ 9974.000       8.1915
+ 9975.000     -32.6245
+ 9976.000       9.1685
+ 9977.000      15.5799
+ 9978.000     -25.2223
+ 9979.000       9.3117
+ 9980.000       4.3264
+ 9981.000     -22.5184
+ 9982.000       5.0337
+ 9983.000       7.1053
+ 9984.000     -33.2965
+ 9985.000       9.9443
+ 9986.000      15.1908
+ 9987.000     -27.1528
+ 9988.000       8.8571
+ 9989.000       9.1572
+ 9990.000      -8.6105
+ 9991.000       3.7123
+ 9992.000      -0.9186
+ 9993.000     -14.4299
+ 9994.000       2.3295
+ 9995.000       1.1772
+ 9996.000     -23.8273
+ 9997.000      11.8890
+ 9998.000       8.9263
+ 9999.000     -14.7630
+10000.000       4.8214
+10001.000       5.8224
+10002.000     -22.2246
+10003.000       5.7983
+10004.000       7.2551
+10005.000     -23.5550
+10006.000       9.2968
+10007.000       8.3773
+10008.000     -30.6896
+10009.000      12.3285
+10010.000      12.8488
+10011.000     -32.0056
+10012.000      11.4722
+10013.000       9.8315
+10014.000     -20.9583
+10015.000       7.3246
+10016.000       5.0020
+10017.000     -28.4153
+10018.000      13.3238
+10019.000       6.7102
+10020.000     -22.6972
+10021.000       6.7732
+10022.000       8.7874
+10023.000     -14.4234
+10024.000       4.7916
+10025.000       1.8526
+10026.000     -20.7082
+10027.000       6.5487
+10028.000       3.8850
+10029.000      -9.5152
+10030.000       4.8466
+10031.000      -0.6641
+10032.000     -37.8675
+10033.000      20.6640
+10034.000      15.9299
+10035.000     -24.1347
+10036.000      11.6939
+10037.000       7.7200
+10038.000     -23.3551
+10039.000       8.0194
+10040.000       7.5510
+10041.000     -24.9362
+10042.000       9.4686
+10043.000       6.3908
+10044.000     -22.6506
+10045.000       5.6495
+10046.000       7.5907
+10047.000     -18.7618
+10048.000       8.2680
+10049.000       8.6564
+10050.000     -32.3800
+10051.000      14.9235
+10052.000       9.4316
+10053.000     -19.9061
+10054.000       6.5517
+10055.000       6.5537
+10056.000      -8.7924
+10057.000      -1.4377
+10058.000      -1.2613

From b699ee2da9e30aa3d06c88dbbf6fe0c726297041 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 6 Feb 2026 11:23:37 -0500
Subject: [PATCH 1298/1492] Add 'lj1264' keyword for 'enedecomp'

---
 src/Energy/EnergyDecomposer.cpp | 41 ++++++++++++++++++++++++++++++++-
 src/Energy/EnergyDecomposer.h   |  2 ++
 2 files changed, 42 insertions(+), 1 deletion(-)

diff --git a/src/Energy/EnergyDecomposer.cpp b/src/Energy/EnergyDecomposer.cpp
index 71a644925c..a5e9e83953 100644
--- a/src/Energy/EnergyDecomposer.cpp
+++ b/src/Energy/EnergyDecomposer.cpp
@@ -32,12 +32,14 @@ EnergyDecomposer::EnergyDecomposer() :
   outfile_(0),
   debug_(0),
   saveComponents_(false),
+  lj1264_(false),
+  useLj1264_(false),
   currentTop_(0)
 { }
 
 void EnergyDecomposer::HelpText() {
   mprintf("\t[<name>] [<mask>] [out <filename>] [savecomponents]\n"
-          "\t[ pme %s\n"
+          "\t[ pme %s [lj1264]\n"
           "\t      %s\n"
           "\t      %s\n",
           EwaldOptions::KeywordsCommon1(),
@@ -53,6 +55,8 @@ int EnergyDecomposer::InitDecomposer(ArgList& argIn, DataSetList& DSLin, DataFil
   // Process keywords
   outfile_ = DFLin.AddDataFile( argIn.GetStringKey("out"), argIn );
   saveComponents_ = argIn.hasKey("savecomponents");
+  // LJ 12-6-4
+  useLj1264_ = argIn.hasKey("lj1264");
   nbcalctype_ = Ecalc_Nonbond::SIMPLE;
   if (argIn.hasKey("pme"))
     nbcalctype_ = Ecalc_Nonbond::PME;
@@ -63,10 +67,22 @@ int EnergyDecomposer::InitDecomposer(ArgList& argIn, DataSetList& DSLin, DataFil
       return 1;
     if (ewaldOpts_.Type() == EwaldOptions::LJPME)
       nbcalctype_ = Ecalc_Nonbond::LJPME;
+    if (useLj1264_) {
+      if (nbcalctype_ != Ecalc_Nonbond::PME) {
+        mprinterr("Error: 'lj1264' is only compatible with regular PME.\n");
+        return 1;
+      }
+      nbcalctype_ = Ecalc_Nonbond::LJCPME;
+    }
 #   else
     mprinterr("Error: 'pme' with energy decomposition requires compilation with LIBPME.\n");
     return 1;
 #   endif
+  } else {
+    if (useLj1264_) {
+      mprinterr("Error: 'lj1264' currently requires 'pme'.\n");
+      return 1;
+    }
   }
   // Get atom mask
   if (selectedAtoms_.SetMaskString( argIn.GetMaskNext() ))
@@ -142,6 +158,8 @@ void EnergyDecomposer::PrintOpts() const {
     mprintf("\tOutput file: %s\n", outfile_->DataFilename().full());
   if (nbcalctype_ != Ecalc_Nonbond::SIMPLE) {
     mprintf("\tUsing PME.\n");
+    if (useLj1264_)
+      mprintf("\tWill use LJ 12-6-4 (C) coefficients if present.\n");
     ewaldOpts_.PrintOptions();
   }
 }
@@ -218,6 +236,27 @@ int EnergyDecomposer::SetupDecomposer(Topology const& topIn, Box const& boxIn) {
     mprintf("Warning: Nothing selected by mask '%s'\n", selectedAtoms_.MaskString());
     return -1;
   }
+  // Check for LJ terms
+  lj1264_ = false;
+  if (topIn.Nonbond().HasNonbond())
+  {
+    if (useLj1264_) {
+      if (topIn.Nonbond().Has_C_Coeff()) {
+        lj1264_ = true;
+        mprintf("\tLJ 12-6-4 (C) terms are active.\n");
+      } else
+        mprintf("Warning: 'lj1264' specified but no LJ 12-6-4 (C) terms present in topology '%s'\n", topIn.c_str());
+    } else {
+      if (topIn.Nonbond().Has_C_Coeff()) {
+        mprintf("Warning: Topology has LJ C coefficients. To use these, specify 'lj1264'\n");
+      }
+    }
+  } else {
+    if (useLj1264_) {
+      mprinterr("Error: 'lj1264' specified but no nonbond parameters present.\n");
+      return 1;
+    }
+  }
   // Set up calculation arrays
   if (energies_.empty()) {
     // First time setup
diff --git a/src/Energy/EnergyDecomposer.h b/src/Energy/EnergyDecomposer.h
index d54b907761..a1fe8fc116 100644
--- a/src/Energy/EnergyDecomposer.h
+++ b/src/Energy/EnergyDecomposer.h
@@ -82,6 +82,8 @@ class EnergyDecomposer {
     DataFile* outfile_;      ///< Output file
     int debug_;              ///< Debug level
     bool saveComponents_;    ///< If true, save per-atom energies for individual energy components 
+    bool lj1264_;            ///< True if LJ 12-6-4 (C) terms are active
+    bool useLj1264_;         ///< True if we want to use LJ 12-6-4 (C) terms if present
     EwaldOptions ewaldOpts_; ///< Hold Ewald options
     Cpptraj::Energy::Ecalc_Nonbond::CalcType nbcalctype_;
 

From e68371410b9a8f797770dd1ee34e678b492ba657 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 6 Feb 2026 11:24:45 -0500
Subject: [PATCH 1299/1492] Add lj1264 decomp test

---
 test/Test_EneDecomp/RunTest.sh | 20 +++++++++++++++++++-
 1 file changed, 19 insertions(+), 1 deletion(-)

diff --git a/test/Test_EneDecomp/RunTest.sh b/test/Test_EneDecomp/RunTest.sh
index d5ebe7820a..887b13e6e7 100755
--- a/test/Test_EneDecomp/RunTest.sh
+++ b/test/Test_EneDecomp/RunTest.sh
@@ -4,7 +4,7 @@
 
 TESTNAME='Energy decomposition tests'
 
-CleanFiles enedecomp.in ene.*.dat decomp.*.dat Total.*.dat
+CleanFiles enedecomp.in ene.*.dat decomp.*.dat Total.*.dat 1d23.lj1264.dat 1d23.dat
 
 TESTNAME='Particle mesh Ewald tests'
 #Requires maxthreads 1 
@@ -72,4 +72,22 @@ EOF
   DoTest decomp.components.tz2.dat.save decomp.components.tz2.dat
 fi
 
+UNITNAME='LJ 12-6-4 decomposition'
+CheckFor maxthreads 1
+if [ $? -eq 0 ] ; then
+  cat > enedecomp.in <<EOF
+parm ../1d23.tip3p.lj1264.parm7
+trajin ../1d23.tip3p.rst7
+enedecomp out 1d23.dat No1264 \
+  pme cut 8.0 dsumtol 0.00001 \
+  order 6 nfft 60,60,60
+enedecomp out 1d23.lj1264.dat Cppt lj1264 \
+  pme cut 8.0 dsumtol 0.00001 \
+  order 6 nfft 60,60,60
+EOF
+  RunCpptraj "$UNITNAME"
+  DoTest 1d23.dat.save 1d23.dat
+  DoTest 1d23.lj1264.dat.save 1d23.lj1264.dat
+fi
+
 EndTest

From 9904c85373caa2facf63bd9aec10a3a826dff11a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sat, 7 Feb 2026 12:49:32 -0500
Subject: [PATCH 1300/1492] Start a class for calculating CMAP energies

---
 src/Energy/CMAP.cpp | 15 +++++++++++++++
 src/Energy/CMAP.h   | 13 +++++++++++++
 2 files changed, 28 insertions(+)
 create mode 100644 src/Energy/CMAP.cpp
 create mode 100644 src/Energy/CMAP.h

diff --git a/src/Energy/CMAP.cpp b/src/Energy/CMAP.cpp
new file mode 100644
index 0000000000..7b8f8c5229
--- /dev/null
+++ b/src/Energy/CMAP.cpp
@@ -0,0 +1,15 @@
+#include "CMAP.h"
+
+using namespace Cpptraj::Energy;
+
+/** CONSTRUCTOR */
+CMAP::CMAP() {}
+
+/** Calculate CMAP energy */
+double CMAP::Ene_CMAP(CmapArray const& Cmaps, Frame const& frameIn) {
+  double ene_cmap = 0.0;
+
+  for (CmapArray::const_iterator cmap = Cmaps.begin();
+                                 cmap != Cmaps.end(); ++cmap
+  {
+    
diff --git a/src/Energy/CMAP.h b/src/Energy/CMAP.h
new file mode 100644
index 0000000000..8fca59b9ae
--- /dev/null
+++ b/src/Energy/CMAP.h
@@ -0,0 +1,13 @@
+#ifndef INC_ENERGY_CMAP_H
+#define INC_ENERGY_CMAP_H
+namespace Cpptraj {
+namespace Energy {
+/// Implement CMAP energy term
+class CMAP {
+  public:
+    CMAP();
+  private:
+};
+}
+}
+#endif

From ac8ececcc9ccfaf99674bfa8bf06cf042b410d7b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 8 Feb 2026 20:09:30 -0500
Subject: [PATCH 1301/1492] Start the cmap torsion routine

---
 src/TorsionRoutines.cpp | 36 ++++++++++++++++++++++++++++++++++++
 src/TorsionRoutines.h   |  4 ++++
 2 files changed, 40 insertions(+)

diff --git a/src/TorsionRoutines.cpp b/src/TorsionRoutines.cpp
index 1abe27a97e..0bb2bf009b 100644
--- a/src/TorsionRoutines.cpp
+++ b/src/TorsionRoutines.cpp
@@ -40,6 +40,42 @@ double Torsion(const double *a1, const double *a2, const double *a3, const doubl
   return angle;
 }
 
+/** Calculate the torsion and partial derivative.
+  * From Tom Darden's generic torsion code in AM_VAL_GEOM_torsion in
+  * amoeba_valence.f.
+  * Adapted to C++ by DRR - any mistakes are mine!
+  */
+void Torsion_and_part_deriv(const double* XA, const double* XB, const double* XC, const double* XD,
+                            Vec3& dA, Vec3& dB, Vec3& dC, Vec3& dD,
+                            double& cosphi, double& sinphi)
+{
+  Vec3 rab( XA[0] - XB[0],
+            XA[1] - XB[1],
+            XA[2] - XB[2] );
+  Vec3 rcb( XC[0] - XB[0],
+            XC[1] - XB[1],
+            XC[2] - XB[2] );
+  Vec3 rdc( XD[0] - XC[0],
+            XD[1] - XC[1],
+            XD[2] - XC[2] );
+
+  double onesizcb = 1.0/sqrt(rcb[0]*rcb[0]+rcb[1]*rcb[1]+rcb[2]*rcb[2]);
+  Vec3 ucb = rcb*onesizcb;
+  double dotp_ab_cb = rab[0]*ucb[0]+rab[1]*ucb[1]+rab[2]*ucb[2];
+  // upab is unit vector along component rab perp to ucb
+  double dot = rab[0]*ucb[0]+rab[1]*ucb[1]+rab[2]*ucb[2];
+  Vec3 upab = rab - ucb*dot; //dot*ucb;
+  double onesizpab = 1.0/sqrt(upab[0]*upab[0]+upab[1]*upab[1]+upab[2]*upab[2]);
+       upab = upab * onesizpab;
+  double dotp_dc_cb = rdc[0]*ucb[0]+rdc[1]*ucb[1]+rdc[2]*ucb[2];
+  // updc is unit vector along component rdc perp to ucb
+         dot = rdc[0]*ucb[0]+rdc[1]*ucb[1]+rdc[2]*ucb[2];
+  Vec3 updc = rdc - ucb*dot; //dot*ucb;
+  double onesizpdc = 1.0/sqrt(updc[0]*updc[0]+updc[1]*updc[1]+updc[2]*updc[2]);
+       updc = updc * onesizpdc;
+  // cosine of phi is given by dot product of upab and updc
+}
+
 /// Constant used in AS pucker calc
 static const double pi_over_5 = Constants::PI / 5.0;
 
diff --git a/src/TorsionRoutines.h b/src/TorsionRoutines.h
index 1cebe0e829..d9f86fe141 100644
--- a/src/TorsionRoutines.h
+++ b/src/TorsionRoutines.h
@@ -3,8 +3,12 @@
 /*! \file TorsionRoutines.h
     \brief A collection of routines used to calculate angles and torsions
  */
+class Vec3;
 double Torsion(const double *, const double *, const double *, const double *);
 
+void Torsion_and_part_deriv(const double*, const double*, const double*, const double*,
+                            Vec3&, Vec3&, Vec3&, Vec3&, double&, double&);
+
 double Pucker_AS(const double*, const double*, const double*, const double*, 
                  const double*, double&);
 double Pucker_CP(const double*, const double*, const double*, const double*, 

From 4f49da81b6c9fd9c86f6d395ac7e76316e283645 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 8 Feb 2026 20:10:24 -0500
Subject: [PATCH 1302/1492] Get coords

---
 src/Energy/CMAP.cpp | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/src/Energy/CMAP.cpp b/src/Energy/CMAP.cpp
index 7b8f8c5229..ce33c911f4 100644
--- a/src/Energy/CMAP.cpp
+++ b/src/Energy/CMAP.cpp
@@ -12,4 +12,12 @@ double CMAP::Ene_CMAP(CmapArray const& Cmaps, Frame const& frameIn) {
   for (CmapArray::const_iterator cmap = Cmaps.begin();
                                  cmap != Cmaps.end(); ++cmap
   {
-    
+    const double* ixyz = frameIn.XYZ( cmap->A1() );
+    const double* jxyz = frameIn.XYZ( cmap->A2() );
+    const double* kxyz = frameIn.XYZ( cmap->A3() );
+    const double* lxyz = frameIn.XYZ( cmap->A4() );
+    const double* mxyz = frameIn.XYZ( cmap->A5() );
+
+  }
+  return ene_cmap;
+}

From 19c1e34d737d50b52d8f72272293db4fdba5990d Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 9 Feb 2026 08:59:25 -0500
Subject: [PATCH 1303/1492] Add more of the torsion code

---
 src/TorsionRoutines.cpp | 39 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)

diff --git a/src/TorsionRoutines.cpp b/src/TorsionRoutines.cpp
index 0bb2bf009b..ba5a74f091 100644
--- a/src/TorsionRoutines.cpp
+++ b/src/TorsionRoutines.cpp
@@ -1,6 +1,7 @@
 /*! \file TorsionRoutines.cpp
     \brief Routines used to calculate torsions and angles.
  */
+#include <algorithm>
 #include <cmath>
 #include "TorsionRoutines.h"
 #include "Constants.h" // PI, TWOPI
@@ -74,6 +75,44 @@ void Torsion_and_part_deriv(const double* XA, const double* XB, const double* XC
   double onesizpdc = 1.0/sqrt(updc[0]*updc[0]+updc[1]*updc[1]+updc[2]*updc[2]);
        updc = updc * onesizpdc;
   // cosine of phi is given by dot product of upab and updc
+
+  // cosphi must be returned in the range -1.d0 to 1.d0
+  // small rounding issues in the 16th decimal place of the
+  // folloing sum can cause this value to lie outside of this range
+  // by 1E-16 when:
+  //  upab[0] = updc[0] and upab[1] = updc[1] and upab[2] = updc[2]
+
+  double cosphi_pre = upab[0]*updc[0]+upab[1]*updc[1]+upab[2]*updc[2];
+         cosphi = std::min( std::max(cosphi_pre, -1.0), 1.0);
+
+  // sine of phi is given by dot product of ucb and upab x updc
+  Vec3 rcross(upab[1]*updc[2] - upab[2]*updc[1],
+              upab[2]*updc[0] - upab[0]*updc[2],
+              upab[0]*updc[1] - upab[1]*updc[0]);
+
+  //See note above of cosphi_pre
+  double sinphi_pre = rcross[0]*ucb[0]+rcross[1]*ucb[1]+rcross[2]*ucb[2];
+         sinphi = std::min( std::max(sinphi_pre, -1.0), 1.0);
+
+  // gradient of phi wrt ra is perp to abc plane---movement of ra by dr perp
+  // to abc plane results in dphi of dr/sizpab
+  // perp to abc given by upab x ucb  (these are orthogonal unit vectors)
+  Vec3 upabc(upab[1]*ucb[2] - upab[2]*ucb[1],
+             upab[2]*ucb[0] - upab[0]*ucb[2],
+             upab[0]*ucb[1] - upab[1]*ucb[0]);
+  // grad of phi wrt rd is perp to bcd plane--calc sim to grad phi wrt ra
+  // perp given by updc x ucb or ucb x updc
+  Vec3 upbcd(ucb[1]*updc[2] - ucb[2]*updc[1],
+             ucb[2]*updc[0] - ucb[0]*updc[2],
+             ucb[0]*updc[1] - ucb[1]*updc[0]);
+  // now have enough for gradphi for a and d
+  dA = upabc * onesizpab;
+  dD = upbcd * onesizpdc;
+  //do m = 1,3
+  //  gradphi_abcd(m) = upabc(m) * onesizpab
+  //  gradphi_abcd(9+m) = upbcd(m) * onesizpdc
+  //enddo
+  
 }
 
 /// Constant used in AS pucker calc

From 32a7e63cc1b0341fd7dcd24e6d1700bb1041cab6 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 9 Feb 2026 09:13:11 -0500
Subject: [PATCH 1304/1492] Finish torsion routine for cmap

---
 src/TorsionRoutines.cpp | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/src/TorsionRoutines.cpp b/src/TorsionRoutines.cpp
index ba5a74f091..87fbe21d23 100644
--- a/src/TorsionRoutines.cpp
+++ b/src/TorsionRoutines.cpp
@@ -112,7 +112,20 @@ void Torsion_and_part_deriv(const double* XA, const double* XB, const double* XC
   //  gradphi_abcd(m) = upabc(m) * onesizpab
   //  gradphi_abcd(9+m) = upbcd(m) * onesizpdc
   //enddo
-  
+  // following chap 5 of thesis of Bekker we have grad phi wrt b = -grad phi wrt a
+  // plus some vec S and rad phi wrt c = -grad phi wrt d - S
+  // S is perp to rcb; using simple torque rule and identity for
+  // triple cross product he derives S (eqn 5.20)
+  for (int m = 0; m < 3; m++) {
+    double vecS = (dotp_ab_cb*onesizcb)*dA[m] + (dotp_dc_cb*onesizcb)*dD[m];
+    dB[m] = vecS - dA[m];
+    dC[m] = -vecS - dD[m];
+  }
+  //do m = 1,3
+  //  vecS(m) = (dotp_ab_cb*onesizcb)*gradphi_abcd(m) + (dotp_dc_cb*onesizcb)*gradphi_abcd(m+9)
+  //  gradphi_abcd(m+3) = vecS(m) - gradphi_abcd(m)
+  //  gradphi_abcd(m+6) = -vecS(m) - gradphi_abcd(m+9)
+  //enddo
 }
 
 /// Constant used in AS pucker calc

From 4de2184d7a99101a76a3afb1780fff3441b3623e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 9 Feb 2026 11:28:41 -0500
Subject: [PATCH 1305/1492] Add to build framework, add missing depends

---
 src/Energy/CMAP.cpp       | 21 +++++++++++++++++++--
 src/Energy/CMAP.h         |  5 +++++
 src/Energy/CMakeLists.txt |  1 +
 src/Energy/energydepend   |  3 ++-
 src/Energy/energyfiles    |  1 +
 src/cpptrajdepend         |  1 +
 6 files changed, 29 insertions(+), 3 deletions(-)

diff --git a/src/Energy/CMAP.cpp b/src/Energy/CMAP.cpp
index ce33c911f4..59a9ae7cc4 100644
--- a/src/Energy/CMAP.cpp
+++ b/src/Energy/CMAP.cpp
@@ -1,4 +1,8 @@
 #include "CMAP.h"
+#include "../CpptrajStdio.h" // DEBUG
+#include "../Frame.h"
+#include "../ParameterTypes.h"
+#include "../TorsionRoutines.h"
 
 using namespace Cpptraj::Energy;
 
@@ -6,11 +10,13 @@ using namespace Cpptraj::Energy;
 CMAP::CMAP() {}
 
 /** Calculate CMAP energy */
-double CMAP::Ene_CMAP(CmapArray const& Cmaps, Frame const& frameIn) {
+double CMAP::Ene_CMAP(CmapArray const& Cmaps, Frame const& frameIn)
+const
+{
   double ene_cmap = 0.0;
 
   for (CmapArray::const_iterator cmap = Cmaps.begin();
-                                 cmap != Cmaps.end(); ++cmap
+                                 cmap != Cmaps.end(); ++cmap)
   {
     const double* ixyz = frameIn.XYZ( cmap->A1() );
     const double* jxyz = frameIn.XYZ( cmap->A2() );
@@ -18,6 +24,17 @@ double CMAP::Ene_CMAP(CmapArray const& Cmaps, Frame const& frameIn) {
     const double* lxyz = frameIn.XYZ( cmap->A4() );
     const double* mxyz = frameIn.XYZ( cmap->A5() );
 
+    // Calculate the dihedral angle (phi) and the derivatives of the
+    // four coordinates with respect to phi. Remember this subroutine is
+    // operating in radians.
+    Vec3 dA, dB, dC, dD;
+    double cosphi_ijkl, sinphi_ijkl;
+    Torsion_and_part_deriv( ixyz, jxyz, kxyz, lxyz,
+                            dA, dB, dC, dD,
+                            cosphi_ijkl, sinphi_ijkl );
+    double phi = copysign(acos(cosphi_ijkl),sinphi_ijkl) * Constants::RADDEG;
+    mprintf("DEBUG: Dihedral 1 %i %i %i %i = %g deg.\n", cmap->A1()+1, cmap->A2()+1, cmap->A3()+1, cmap->A4()+1, phi);
+
   }
   return ene_cmap;
 }
diff --git a/src/Energy/CMAP.h b/src/Energy/CMAP.h
index 8fca59b9ae..e096e943bf 100644
--- a/src/Energy/CMAP.h
+++ b/src/Energy/CMAP.h
@@ -1,11 +1,16 @@
 #ifndef INC_ENERGY_CMAP_H
 #define INC_ENERGY_CMAP_H
+class CmapArray;
+class Frame;
 namespace Cpptraj {
 namespace Energy {
 /// Implement CMAP energy term
 class CMAP {
   public:
     CMAP();
+
+    /// Calculate CMAP energy
+    double Ene_CMAP(CmapArray const&, Frame const&) const;
   private:
 };
 }
diff --git a/src/Energy/CMakeLists.txt b/src/Energy/CMakeLists.txt
index cb15187320..524a784d0f 100644
--- a/src/Energy/CMakeLists.txt
+++ b/src/Energy/CMakeLists.txt
@@ -1,5 +1,6 @@
 #CMake buildfile for CPPTRAJ Energy subdirectory.
 target_sources(cpptraj_common_obj PRIVATE
+  ${CMAKE_CURRENT_LIST_DIR}/CMAP.cpp
   ${CMAKE_CURRENT_LIST_DIR}/Ecalc_Nonbond.cpp
   ${CMAKE_CURRENT_LIST_DIR}/EnergyDecomposer.cpp
   ${CMAKE_CURRENT_LIST_DIR}/ErfcFxn.cpp
diff --git a/src/Energy/energydepend b/src/Energy/energydepend
index 2d9f419f5a..6c2dd78b72 100644
--- a/src/Energy/energydepend
+++ b/src/Energy/energydepend
@@ -1,4 +1,5 @@
-Ecalc_Nonbond.o : Ecalc_Nonbond.cpp ../Atom.h ../AtomMask.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../Energy/../Constants.h ../Energy/../ParameterTypes.h ../Energy/../SplineFxnTable.h ../Energy/Ene_LJPME_6_12.h ../Energy/Ene_LJ_12_6_4.h ../Energy/Ene_LJ_6_12.h ../Energy/ErfcFxn.h ../Energy/EwaldParams.h ../Energy/EwaldParams_LJPME.h ../Energy/Kernel_EwaldAdjust.h ../Energy/Kernel_LJPME_Adjust.h ../EwaldOptions.h ../ExclusionArray.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../PairList.h ../PairListEngine_Ewald_Decomp_LJLR.h ../PairListEngine_Ewald_Decomp_LJPME.h ../PairListEngine_Ewald_LJCLR.h ../PairListEngine_Ewald_LJLR.h ../PairListEngine_Ewald_LJPME.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h ../helpme_standalone.h Ecalc_Nonbond.h Ene_Decomp_Nonbond.h Ene_LJ_6_12.h Ene_Nonbond.h EwaldCalc.h EwaldCalc_Decomp.h EwaldCalc_Decomp_LJPME.h EwaldCalc_Decomp_PME.h EwaldCalc_LJCPME.h EwaldCalc_LJPME.h EwaldCalc_PME.h EwaldCalc_Regular.h Ewald_Recip.h PME_Recip.h PME_RecipParams.h VDW_LongRange_Correction.h
+CMAP.o : CMAP.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../TorsionRoutines.h ../Unit.h ../Vec3.h CMAP.h
+Ecalc_Nonbond.o : Ecalc_Nonbond.cpp ../Atom.h ../AtomMask.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../Energy/../Constants.h ../Energy/../ParameterTypes.h ../Energy/../SplineFxnTable.h ../Energy/Ene_LJPME_6_12.h ../Energy/Ene_LJ_12_6_4.h ../Energy/Ene_LJ_6_12.h ../Energy/ErfcFxn.h ../Energy/EwaldParams.h ../Energy/EwaldParams_LJPME.h ../Energy/Kernel_EwaldAdjust.h ../Energy/Kernel_LJPME_Adjust.h ../EwaldOptions.h ../ExclusionArray.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../PairList.h ../PairListEngine_Ewald_Decomp_LJCLR.h ../PairListEngine_Ewald_Decomp_LJLR.h ../PairListEngine_Ewald_Decomp_LJPME.h ../PairListEngine_Ewald_LJCLR.h ../PairListEngine_Ewald_LJLR.h ../PairListEngine_Ewald_LJPME.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h ../helpme_standalone.h Ecalc_Nonbond.h Ene_Decomp_Nonbond.h Ene_LJ_6_12.h Ene_Nonbond.h EwaldCalc.h EwaldCalc_Decomp.h EwaldCalc_Decomp_LJCPME.h EwaldCalc_Decomp_LJPME.h EwaldCalc_Decomp_PME.h EwaldCalc_LJCPME.h EwaldCalc_LJPME.h EwaldCalc_PME.h EwaldCalc_Regular.h Ewald_Recip.h PME_Recip.h PME_RecipParams.h VDW_LongRange_Correction.h
 EnergyDecomposer.o : EnergyDecomposer.cpp ../ArgList.h ../AssociatedData.h ../Atom.h ../AtomMask.h ../BaseIOtype.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataFile.h ../DataFileList.h ../DataSet.h ../DataSetList.h ../DataSet_1D.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../DataSet_Mesh.h ../Dimension.h ../DistRoutines.h ../EwaldOptions.h ../ExclusionArray.h ../FileIO.h ../FileName.h ../FileTypes.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../OnlineVarT.h ../PairList.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Spline.h ../Stats_Reduce.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../TorsionRoutines.h ../Unit.h ../Vec3.h Ecalc_Nonbond.h Ene_Angle.h Ene_Bond.h Ene_LJ_6_12.h EnergyDecomposer.h Kernel_Fourier.h Kernel_Harmonic.h
 ErfcFxn.o : ErfcFxn.cpp ../CpptrajStdio.h ../SplineFxnTable.h ErfcFxn.h
 EwaldCalc_Decomp_LJCPME.o : EwaldCalc_Decomp_LJCPME.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../Energy/../Constants.h ../Energy/../ParameterTypes.h ../Energy/../SplineFxnTable.h ../Energy/Ene_LJ_12_6_4.h ../Energy/ErfcFxn.h ../Energy/EwaldParams.h ../Energy/Kernel_EwaldAdjust.h ../EwaldOptions.h ../ExclusionArray.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../PairList.h ../PairListEngine_Ewald_Decomp_LJCLR.h ../PairListTemplate.h ../Parallel.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Timer.h ../Unit.h ../Vec3.h ../helpme_standalone.h EwaldCalc.h EwaldCalc_Decomp.h EwaldCalc_Decomp_LJCPME.h PME_Recip.h PME_RecipParams.h VDW_LongRange_Correction.h
diff --git a/src/Energy/energyfiles b/src/Energy/energyfiles
index 40fd8aa498..1a607eeadf 100644
--- a/src/Energy/energyfiles
+++ b/src/Energy/energyfiles
@@ -1,5 +1,6 @@
 # Files for Energy subdirectory.
 ENERGY_SOURCES= \
+  CMAP.cpp \
   Ecalc_Nonbond.cpp \
   EnergyDecomposer.cpp \
   ErfcFxn.cpp \
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index dc5c6f5e08..57b1c56661 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -288,6 +288,7 @@ DihedralSearch.o : DihedralSearch.cpp ArgList.h Atom.h AtomMask.h Box.h Constant
 DistRoutines.o : DistRoutines.cpp Box.h DistRoutines.h ImageOption.h Matrix_3x3.h Parallel.h Vec3.h
 Dist_Imaged.o : Dist_Imaged.cpp Dist_Imaged.h Matrix_3x3.h Parallel.h Vec3.h
 Energy.o : Energy.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h Energy.h Energy/Ene_Angle.h Energy/Ene_Bond.h Energy/Ene_LJ_12_6_4.h Energy/Ene_LJ_6_12.h Energy/Kernel_Harmonic.h ExclusionArray.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TorsionRoutines.h Unit.h Vec3.h
+Energy/CMAP.o : Energy/CMAP.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy/CMAP.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TorsionRoutines.h Unit.h Vec3.h
 Energy/Ecalc_Nonbond.o : Energy/Ecalc_Nonbond.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy/Ecalc_Nonbond.h Energy/Ene_Decomp_Nonbond.h Energy/Ene_LJPME_6_12.h Energy/Ene_LJ_12_6_4.h Energy/Ene_LJ_6_12.h Energy/Ene_Nonbond.h Energy/ErfcFxn.h Energy/EwaldCalc.h Energy/EwaldCalc_Decomp.h Energy/EwaldCalc_Decomp_LJCPME.h Energy/EwaldCalc_Decomp_LJPME.h Energy/EwaldCalc_Decomp_PME.h Energy/EwaldCalc_LJCPME.h Energy/EwaldCalc_LJPME.h Energy/EwaldCalc_PME.h Energy/EwaldCalc_Regular.h Energy/EwaldParams.h Energy/EwaldParams_LJPME.h Energy/Ewald_Recip.h Energy/Kernel_EwaldAdjust.h Energy/Kernel_LJPME_Adjust.h Energy/PME_Recip.h Energy/PME_RecipParams.h Energy/VDW_LongRange_Correction.h EwaldOptions.h ExclusionArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h PairListEngine_Ewald_Decomp_LJCLR.h PairListEngine_Ewald_Decomp_LJLR.h PairListEngine_Ewald_Decomp_LJPME.h PairListEngine_Ewald_LJCLR.h PairListEngine_Ewald_LJLR.h PairListEngine_Ewald_LJPME.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h Timer.h Topology.h Unit.h Vec3.h helpme_standalone.h
 Energy/EnergyDecomposer.o : Energy/EnergyDecomposer.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DistRoutines.h Energy/Ecalc_Nonbond.h Energy/Ene_Angle.h Energy/Ene_Bond.h Energy/Ene_LJ_6_12.h Energy/EnergyDecomposer.h Energy/Kernel_Fourier.h Energy/Kernel_Harmonic.h EwaldOptions.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h PairList.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h Stats_Reduce.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h Unit.h Vec3.h
 Energy/ErfcFxn.o : Energy/ErfcFxn.cpp CpptrajStdio.h Energy/ErfcFxn.h SplineFxnTable.h

From 15c718c2aae0e3a18384b68f8994ac4814549092 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 9 Feb 2026 11:36:46 -0500
Subject: [PATCH 1306/1492] Enable cmap for testing

---
 src/Action_Energy.cpp | 20 ++++++++++++++++++--
 src/Action_Energy.h   |  6 ++++--
 src/cpptrajdepend     |  2 +-
 3 files changed, 23 insertions(+), 5 deletions(-)

diff --git a/src/Action_Energy.cpp b/src/Action_Energy.cpp
index f752366f1c..140e9cd7dc 100644
--- a/src/Action_Energy.cpp
+++ b/src/Action_Energy.cpp
@@ -2,6 +2,7 @@
 #include "CpptrajStdio.h"
 #include "PotentialFunction.h"
 #include "MdOpts.h"
+#include "Energy/CMAP.h"
 
 using namespace Cpptraj::Energy;
 
@@ -31,6 +32,7 @@ Action_Energy::~Action_Energy() {
 void Action_Energy::Help() const {
   mprintf("\t[<name>] [<mask1>] [out <filename>] [nobondstoh] [openmm [<mdopts>]]\n"
           "\t[bond] [angle] [dihedral] {[nb14]|[e14]|[v14]} {[nonbond] | [elec] [vdw]}\n"
+          "\t[cmap]\n"
           "\t[{nokinetic|kinetic [ketype {vel|vv}] [dt <dt>]}] [lj1264]\n"
           "\t[ etype { simple |\n"
           "\t          directsum [npoints <N>] |\n"
@@ -63,11 +65,11 @@ void Action_Energy::Help(ArgList& argIn) const {
 }
 
 /// Corresponds to Etype 
-static const char* AspectStr[] = {"bond", "angle", "dih", "vdw14", "elec14",
+static const char* AspectStr[] = {"bond", "angle", "dih", "cmap", "vdw14", "elec14",
                                   "vdw", "elec", "kinetic", "total"};
 
 /// Corresponds to Etype
-static const char* EtypeStr[] = {"Bonds", "Angles", "Dihedrals", "1-4 VDW", "1-4 Elec.",
+static const char* EtypeStr[] = {"Bonds", "Angles", "Dihedrals", "CMAP", "1-4 VDW", "1-4 Elec.",
                                  "VDW", "Elec.", "Kinetic", "Total"};
 
 /// Corresponds to ElecType 
@@ -112,6 +114,7 @@ Action::RetType Action_Energy::Init(ArgList& actionArgs, ActionInit& init, int d
     termEnabled[BOND] = actionArgs.hasKey("bond");
     termEnabled[ANGLE] = actionArgs.hasKey("angle");
     termEnabled[DIHEDRAL] = actionArgs.hasKey("dihedral");
+    termEnabled[CMAP] = actionArgs.hasKey("cmap");
     termEnabled[V14] = actionArgs.hasKey("v14");
     termEnabled[Q14] = actionArgs.hasKey("e14");
     termEnabled[VDW] = actionArgs.hasKey("vdw");
@@ -213,6 +216,8 @@ Action::RetType Action_Energy::Init(ArgList& actionArgs, ActionInit& init, int d
     Ecalcs_.push_back(C_ANG);
   if (termEnabled[DIHEDRAL])
     Ecalcs_.push_back(C_DIH);
+  if (termEnabled[CMAP])
+    Ecalcs_.push_back(C_CMAP);
   if (termEnabled[KE]) {
     if (KEtype_ == KE_AUTO)
       Ecalcs_.push_back(C_KEAUTO);
@@ -436,6 +441,8 @@ Action::RetType Action_Energy::DoAction(int frameNum, ActionFrame& frm) {
   double Etot = 0.0, ene, ene2;
   int err = 0;
 
+  Cpptraj::Energy::CMAP cmap;
+
   if (use_openmm_) {
     if (potential_->CalculateEnergy( frm.Frm() )) return Action::ERR;
     Etot = potential_->Energy().Ene( EnergyArray::E_OPENMM ); 
@@ -465,6 +472,13 @@ Action::RetType Action_Energy::DoAction(int frameNum, ActionFrame& frm) {
         Energy_[DIHEDRAL]->Add(frameNum, &ene);
         Etot += ene;
         break;
+      case C_CMAP:
+        time_cmap_.Start();
+        ene = cmap.Ene_CMAP(currentParm_->Cmap(), frm.Frm());
+        time_cmap_.Stop();
+        Energy_[CMAP]->Add(frameNum, &ene);
+        Etot += ene;
+        break;
       case C_N14:
         time_14_.Start();
         ene = ENE_.E_14_Nonbond(frm.Frm(), *currentParm_, Mask1_, ene2, lj1264_);
@@ -558,6 +572,8 @@ void Action_Energy::Print() {
     time_angle_.WriteTiming(1, "ANGLE       :", time_total_.Total());
   if (time_tors_.Total() > 0.0)
     time_tors_.WriteTiming(1,  "TORSION     :", time_total_.Total());
+  if (time_cmap_.Total() > 0.0)
+    time_cmap_.WriteTiming(1,  "CMAP        :", time_total_.Total());
   if (time_14_.Total() > 0.0)
     time_14_.WriteTiming(1,    "1-4_NONBOND :", time_total_.Total());
   if (nbCalcType_ != Ecalc_Nonbond::UNSPECIFIED)
diff --git a/src/Action_Energy.h b/src/Action_Energy.h
index 6c37b7e570..f8fc2bb9d1 100644
--- a/src/Action_Energy.h
+++ b/src/Action_Energy.h
@@ -23,14 +23,15 @@ class Action_Energy: public Action {
     void Print();
 
     /// Corresponds to data sets.
-    enum Etype { BOND = 0, ANGLE, DIHEDRAL, V14, Q14, VDW, ELEC, KE, TOTAL};
+    enum Etype { BOND = 0, ANGLE, DIHEDRAL, CMAP, V14, Q14, VDW, ELEC, KE, TOTAL};
     /// Add energy data set of specified type.
     int AddSet(Etype, DataSetList&, DataFile*, std::string const&);
     /// For debugging the direct sum convergence
     double Dbg_Direct(Frame const&,int);
     /// Corresponds to calculations.
     enum CalcType { C_BND = 0, C_ANG, C_DIH, C_N14, C_NBD, C_LJ,
-                    C_COULOMB, C_DIRECT, C_EWALD, C_PME, C_KEAUTO, C_KEVEL, C_KEVV };
+                    C_COULOMB, C_DIRECT, C_EWALD, C_PME, C_KEAUTO, C_KEVEL, C_KEVV,
+                    C_CMAP };
     /// Corresponds to type of electrostatics.
     enum ElecType { NO_ELE = 0, SIMPLE, DIRECTSUM, EWALD, PME };
     /// Corresponds to type of KE calc.
@@ -70,5 +71,6 @@ class Action_Energy: public Action {
     Timer time_14_;
     Timer time_NB_;
     Timer time_ke_;
+    Timer time_cmap_;
 };
 #endif
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 57b1c56661..c5362fb3f6 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -33,7 +33,7 @@ Action_Dipole.o : Action_Dipole.cpp Action.h ActionState.h Action_Dipole.h ArgLi
 Action_DistRmsd.o : Action_DistRmsd.cpp Action.h ActionState.h Action_DistRmsd.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 Action_Distance.o : Action_Distance.cpp Action.h ActionState.h Action_Distance.h ArgList.h AssociatedData.h AssociatedData_NOE.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 Action_EneDecomp.o : Action_EneDecomp.cpp Action.h ActionState.h Action_EneDecomp.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h Energy/Ecalc_Nonbond.h Energy/EnergyDecomposer.h EwaldOptions.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h PairList.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_Energy.o : Action_Energy.cpp Action.h ActionState.h Action_Energy.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h Energy.h Energy/Ecalc_Nonbond.h EnergyArray.h EwaldOptions.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Molecule.h NameType.h PairList.h Parallel.h ParameterTypes.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Energy.o : Action_Energy.cpp Action.h ActionState.h Action_Energy.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h Energy.h Energy/CMAP.h Energy/Ecalc_Nonbond.h EnergyArray.h EwaldOptions.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Molecule.h NameType.h PairList.h Parallel.h ParameterTypes.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 Action_Esander.o : Action_Esander.cpp Action.h ActionState.h Action_Esander.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h Energy_Sander.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 Action_FilterByData.o : Action_FilterByData.cpp Action.h ActionState.h Action_FilterByData.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 Action_FixAtomOrder.o : Action_FixAtomOrder.cpp Action.h ActionState.h ActionTopWriter.h Action_FixAtomOrder.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomTopType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h

From f58ea7294608f89df47ab364bb237159c4ae4dad Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 9 Feb 2026 11:44:47 -0500
Subject: [PATCH 1307/1492] Calc psi

---
 src/Energy/CMAP.cpp | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/src/Energy/CMAP.cpp b/src/Energy/CMAP.cpp
index 59a9ae7cc4..ddc1b5d7a3 100644
--- a/src/Energy/CMAP.cpp
+++ b/src/Energy/CMAP.cpp
@@ -27,14 +27,24 @@ const
     // Calculate the dihedral angle (phi) and the derivatives of the
     // four coordinates with respect to phi. Remember this subroutine is
     // operating in radians.
-    Vec3 dA, dB, dC, dD;
+    Vec3 dAphi, dBphi, dCphi, dDphi;
     double cosphi_ijkl, sinphi_ijkl;
     Torsion_and_part_deriv( ixyz, jxyz, kxyz, lxyz,
-                            dA, dB, dC, dD,
+                            dAphi, dBphi, dCphi, dDphi,
                             cosphi_ijkl, sinphi_ijkl );
     double phi = copysign(acos(cosphi_ijkl),sinphi_ijkl) * Constants::RADDEG;
     mprintf("DEBUG: Dihedral 1 %i %i %i %i = %g deg.\n", cmap->A1()+1, cmap->A2()+1, cmap->A3()+1, cmap->A4()+1, phi);
 
+    // Calculate the dihedral angle (psi) and the derivatives of the
+    // four coordinates with respect to psi. Remember this subroutine is
+    // operating in radians.
+    Vec3 dApsi, dBpsi, dCpsi, dDpsi;
+    double cospsi_jklm, sinpsi_jklm;
+    Torsion_and_part_deriv( jxyz, kxyz, lxyz, mxyz,
+                            dApsi, dBpsi, dCpsi, dDpsi,
+                            cospsi_jklm, sinpsi_jklm );
+    double psi = copysign(acos(cospsi_jklm),sinpsi_jklm) * Constants::RADDEG;
+    mprintf("DEBUG: Dihedral 2 %i %i %i %i = %g deg.\n", cmap->A2()+1, cmap->A3()+1, cmap->A4()+1, cmap->A5()+1, psi);
   }
   return ene_cmap;
 }

From 4df80cf165a111a2a1ff94cca79333783863ec6a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 9 Feb 2026 14:46:41 -0500
Subject: [PATCH 1308/1492] Add debug code to print gradients

---
 src/Energy/CMAP.cpp | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/src/Energy/CMAP.cpp b/src/Energy/CMAP.cpp
index ddc1b5d7a3..4f65f26842 100644
--- a/src/Energy/CMAP.cpp
+++ b/src/Energy/CMAP.cpp
@@ -9,6 +9,13 @@ using namespace Cpptraj::Energy;
 /** CONSTRUCTOR */
 CMAP::CMAP() {}
 
+/// DEBUG - print gradients
+static inline void print_grad(Vec3 const& dA, Vec3 const& dB, Vec3 const& dC, Vec3 const& dD)
+{
+  for (int i = 0; i < 3; i++)
+    mprintf("DEBUG:\t\tdX %12.4f%12.4f%12.4f%12.4f\n", dA[i], dB[i], dC[i], dD[i]);
+}
+
 /** Calculate CMAP energy */
 double CMAP::Ene_CMAP(CmapArray const& Cmaps, Frame const& frameIn)
 const
@@ -32,6 +39,7 @@ const
     Torsion_and_part_deriv( ixyz, jxyz, kxyz, lxyz,
                             dAphi, dBphi, dCphi, dDphi,
                             cosphi_ijkl, sinphi_ijkl );
+    print_grad(dAphi, dBphi, dCphi, dDphi);
     double phi = copysign(acos(cosphi_ijkl),sinphi_ijkl) * Constants::RADDEG;
     mprintf("DEBUG: Dihedral 1 %i %i %i %i = %g deg.\n", cmap->A1()+1, cmap->A2()+1, cmap->A3()+1, cmap->A4()+1, phi);
 
@@ -43,6 +51,7 @@ const
     Torsion_and_part_deriv( jxyz, kxyz, lxyz, mxyz,
                             dApsi, dBpsi, dCpsi, dDpsi,
                             cospsi_jklm, sinpsi_jklm );
+    print_grad(dApsi, dBpsi, dCpsi, dDpsi);
     double psi = copysign(acos(cospsi_jklm),sinpsi_jklm) * Constants::RADDEG;
     mprintf("DEBUG: Dihedral 2 %i %i %i %i = %g deg.\n", cmap->A2()+1, cmap->A3()+1, cmap->A4()+1, cmap->A5()+1, psi);
   }

From 9d0122858afbbba78f4c296e029a346c596ddeb7 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 9 Feb 2026 15:00:55 -0500
Subject: [PATCH 1309/1492] Add reduced version of the spline routine

---
 src/Energy/CMAP.cpp | 48 +++++++++++++++++++++++++++++++++++++++++++++
 src/Energy/CMAP.h   |  2 ++
 2 files changed, 50 insertions(+)

diff --git a/src/Energy/CMAP.cpp b/src/Energy/CMAP.cpp
index 4f65f26842..1ff5321e9d 100644
--- a/src/Energy/CMAP.cpp
+++ b/src/Energy/CMAP.cpp
@@ -57,3 +57,51 @@ const
   }
   return ene_cmap;
 }
+
+/** This is reduced version of a typical cubic spline routine
+  * that one may find in a recipe book of a numerical flavour.
+  *
+  * It is "reduced" since it is used here to obtain smooth derivatives
+  * ONLY at discrete points on the CMAP grid, hence it never interpolates
+  * between the points, therefore the coefficient a is always 1.0 and b is
+  * always 0.0. In addition,  there is never a need to return the
+  * interpolated value since it will be aways the same as the value passed to it.
+  */
+double CMAP::evaluate_cubic_spline(int step_size, std::vector<double> const& y,
+                                   std::vector<double> const& y2,
+                                   int grid_point)
+{
+  //Work out nearest complete grid point on the CMAP grid from xin
+  //lo =  int( (xin - gridOrigin)/(step_size) ) + 1
+
+  int lo = grid_point;
+  //!write(6,'(a,I4)'),"Lo is: ",lo
+
+  //!b = ( xin - ( (lo-1)*step_size + gridOrigin)  )/step_size
+  //!a = 1-b
+
+  //!write(6,'(a,f15.6)'),"a is : ",a
+  //!write(6,'(a,f15.6)'),"b is : ",b
+
+  double a = 1.0;
+  double b = 0.0;
+  //DEBUG
+
+  //yout =   a*y(lo)                                        &
+  //       + b*y(lo+1)                                      &
+  //!      + (1/6)*(a*a*a-a)*(step_size*step_size)*y2(lo)   &
+  //!      + (1/6)*(b*b*b-b)*(step_size*step_size)*y2(lo+1)
+
+  double dyout =  (y[lo+1]-y[lo])/step_size
+                - ((3*a*a-1)/6)*step_size*y2[lo]
+                + ((3*b*b-1)/6)*step_size*y2[lo+1];
+
+  //DEBUG
+  //write(6,'(a,f15.6)'),"y(lo) is :", y(lo)
+  //write(6,'(a,f15.6)'),"y(lo+1) is :", y(lo+1)
+  //write(6,'(a,f15.6)'),"y2(lo) is :", y2(lo)
+  //write(6,'(a,f15.6)'),"y2(lo+1) is :", y2(lo+1)
+  //write(6,'(a,f15.6)'),"yout is :", yout
+  //write(6,'(a)'),""
+  return dyout;
+}
diff --git a/src/Energy/CMAP.h b/src/Energy/CMAP.h
index e096e943bf..dd03a026d8 100644
--- a/src/Energy/CMAP.h
+++ b/src/Energy/CMAP.h
@@ -1,5 +1,6 @@
 #ifndef INC_ENERGY_CMAP_H
 #define INC_ENERGY_CMAP_H
+#include <vector>
 class CmapArray;
 class Frame;
 namespace Cpptraj {
@@ -12,6 +13,7 @@ class CMAP {
     /// Calculate CMAP energy
     double Ene_CMAP(CmapArray const&, Frame const&) const;
   private:
+    static double evaluate_cubic_spline(int, std::vector<double> const&, std::vector<double> const&, int);
 };
 }
 }

From 16021c819d02ce64f31ba91017fd895eb4d0f8f3 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 9 Feb 2026 15:55:31 -0500
Subject: [PATCH 1310/1492] Start CMAP setup. Add function to get CMAP grid
 terms

---
 src/Energy/CMAP.cpp  | 64 ++++++++++++++++++++++++++++++++++++++++++++
 src/Energy/CMAP.h    |  2 ++
 src/ParameterTypes.h | 16 +++++++++++
 3 files changed, 82 insertions(+)

diff --git a/src/Energy/CMAP.cpp b/src/Energy/CMAP.cpp
index 1ff5321e9d..43f7ac8003 100644
--- a/src/Energy/CMAP.cpp
+++ b/src/Energy/CMAP.cpp
@@ -2,6 +2,7 @@
 #include "../CpptrajStdio.h" // DEBUG
 #include "../Frame.h"
 #include "../ParameterTypes.h"
+#include "../Topology.h"
 #include "../TorsionRoutines.h"
 
 using namespace Cpptraj::Energy;
@@ -105,3 +106,66 @@ double CMAP::evaluate_cubic_spline(int step_size, std::vector<double> const& y,
   //write(6,'(a)'),""
   return dyout;
 }
+
+/** Called once after CMAP parameters have been read. This populates
+  * various partial derivatives in the cmapParameter%{dPsi,dPhi,dPsi_dPhi}
+  * object. It does this using a cubic spline on the read in CMAP grid.
+  *
+  * Later, this information is used to evaluate an arbitary phi/phi angle
+  * for a given crossterm.
+  */
+int CMAP::generate_cmap_derivatives(Topology const& topIn)
+{
+  if (!topIn.HasCmap()) {
+    mprinterr("Internal Error: CMAP::generate_cmap_derivatives(): Topology '%s' does not have CMAP parameters.\n", topIn.c_str());
+    return 1;
+  }
+  // Loop over all grids
+  for (CmapGridArray::const_iterator grid = topIn.CmapGrid().begin();
+                                     grid != topIn.CmapGrid().end(); ++grid)
+  {
+    int res = grid->Resolution();
+    int halfRes = res / 2;
+    int twoRes = res * 2;
+    int step_size = 360 / res;
+
+    std::vector<double> tmpy(twoRes);
+    std::vector<double> tmpy2(twoRes);
+
+    // 1) calculate dE/dPhi
+    for (int row = 0; row < res; row++)
+    {
+      // Step up one row each cycle, splining across all columns
+
+      // Fill an *extended* tmp array (tmpy) for with CMAP values
+      // for the 1D splining like CHARMM.
+      // It is possible CHARMM does this to avoid edge issues.
+
+      unsigned int k=0; //interal offset counter for tmp array
+      mprintf("DEBUG: Row %6i from %6i to %6i\n", row, -halfRes, res+halfRes-1);
+      for (int col = -halfRes; col < res+halfRes; col++) { // -12 to 35
+        tmpy[k] = grid->Grid(col, row);
+        mprintf("DEBUG:\t\t%6i%12.4f\n", k, tmpy[k]);
+        k++;
+      }
+
+/*
+      !Calculate spline coeffients (tmpy2) for each of the 1D
+      !horizontal rows in the CMAP table
+      call generate_cubic_spline(twoRes, step_size, tmpy, tmpy2)
+     
+      !Calculate %dPhi for using each row
+      !of energies and corresponding splines in tmpy and tmpy2
+      do j=1,res
+        !evaluate_cubic_spline(n,step_size, gridOrigin, y,y2,xin,yout)
+
+        !offset array passed to evaluate_cubic_spline
+        call evaluate_cubic_spline(step_size, tmpy, tmpy2, &
+                                   j+12, gbl_cmap_dPhi(i,row,j))
+      enddo
+*/
+    } // END loop over rows
+  } // END loop over grids
+
+  return 0;
+}
diff --git a/src/Energy/CMAP.h b/src/Energy/CMAP.h
index dd03a026d8..30271633b4 100644
--- a/src/Energy/CMAP.h
+++ b/src/Energy/CMAP.h
@@ -3,6 +3,7 @@
 #include <vector>
 class CmapArray;
 class Frame;
+class Topology;
 namespace Cpptraj {
 namespace Energy {
 /// Implement CMAP energy term
@@ -14,6 +15,7 @@ class CMAP {
     double Ene_CMAP(CmapArray const&, Frame const&) const;
   private:
     static double evaluate_cubic_spline(int, std::vector<double> const&, std::vector<double> const&, int);
+    int generate_cmap_derivatives(Topology const&);
 };
 }
 }
diff --git a/src/ParameterTypes.h b/src/ParameterTypes.h
index b17b3c7994..6d0e9bf9bc 100644
--- a/src/ParameterTypes.h
+++ b/src/ParameterTypes.h
@@ -877,6 +877,15 @@ class CapParmType {
 // ----- CHAMBER PARAMETERS ----------------------------------------------------
 /// Hold CMAP grid parameters // FIXME use NameType
 class CmapGridType {
+    static inline int wrap_grid(int iin, int res) {
+      int iout = iin;
+      if (iout < 0) {
+        while (iout < 0) iout += res;
+      } else if (iout >= res) {
+        while (iout >= res) iout -= res;
+      }
+      return iout;
+    }
   public:
     CmapGridType() : nCmapRes_(0), resolution_(0) {}
     CmapGridType(unsigned int r) : nCmapRes_(0), resolution_(r), grid_(r*r, 0.0) {}
@@ -884,6 +893,13 @@ class CmapGridType {
     unsigned int Resolution()                const { return resolution_;       }
     /// \return CMAP grid
     std::vector<double> const& Grid()        const { return grid_;             }
+    /// \return CMAP grid point for specified column and row.
+    double Grid(int col, int row) const {
+      // NOTE : CMAPs are read in from Amber topologys in COLUMN-MAJOR order
+      int ix = wrap_grid(col, resolution_);
+      int iy = wrap_grid(row, resolution_);
+      return ( (ix * resolution_) + iy );
+    }
     /// \return array of residue names this CMAP applies to
     std::vector<std::string> const& ResNames() const { return resNames_; }
     /// \return true if given name matches a residue name

From a0e17c841df7a6f728aef97eba810a6dc7b58be9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 9 Feb 2026 16:17:21 -0500
Subject: [PATCH 1311/1492] Start adding CMAP setup code

---
 src/Action_Energy.cpp | 17 +++++++++++++----
 src/Action_Energy.h   |  7 +++++++
 src/Energy/CMAP.cpp   | 14 ++++++++++++++
 src/Energy/CMAP.h     |  2 ++
 src/ParameterTypes.h  |  2 +-
 5 files changed, 37 insertions(+), 5 deletions(-)

diff --git a/src/Action_Energy.cpp b/src/Action_Energy.cpp
index 140e9cd7dc..ed4a4dbed0 100644
--- a/src/Action_Energy.cpp
+++ b/src/Action_Energy.cpp
@@ -14,6 +14,7 @@ Action_Energy::Action_Energy() :
   npoints_(0),
   debug_(0),
   nbCalcType_(Ecalc_Nonbond::UNSPECIFIED),
+  cmap_(0),
   potential_(0),
   use_openmm_(false),
   dt_(0),
@@ -27,6 +28,7 @@ Action_Energy::Action_Energy() :
 /// DESTRUCTOR
 Action_Energy::~Action_Energy() {
   if (potential_ != 0) delete potential_;
+  if (cmap_ != 0) delete cmap_;
 }
 
 void Action_Energy::Help() const {
@@ -216,8 +218,10 @@ Action::RetType Action_Energy::Init(ArgList& actionArgs, ActionInit& init, int d
     Ecalcs_.push_back(C_ANG);
   if (termEnabled[DIHEDRAL])
     Ecalcs_.push_back(C_DIH);
-  if (termEnabled[CMAP])
+  if (termEnabled[CMAP]) {
     Ecalcs_.push_back(C_CMAP);
+    cmap_ = new Cpptraj::Energy::CMAP();
+  }
   if (termEnabled[KE]) {
     if (KEtype_ == KE_AUTO)
       Ecalcs_.push_back(C_KEAUTO);
@@ -360,6 +364,13 @@ Action::RetType Action_Energy::Setup(ActionSetup& setup) {
   }
 
   Imask_ = AtomMask(Mask1_.ConvertToIntMask(), Mask1_.Natom());
+  // CMAP
+  if (cmap_ != 0) {
+    if (cmap_->Setup_CMAP_Ene(setup.Top())) {
+      mprinterr("Error: CMAP setup failed.\n");
+      return Action::ERR;
+    }
+  }
   // Check for LJ terms
   lj1264_ = false;
   if (need_lj_params_) {
@@ -441,8 +452,6 @@ Action::RetType Action_Energy::DoAction(int frameNum, ActionFrame& frm) {
   double Etot = 0.0, ene, ene2;
   int err = 0;
 
-  Cpptraj::Energy::CMAP cmap;
-
   if (use_openmm_) {
     if (potential_->CalculateEnergy( frm.Frm() )) return Action::ERR;
     Etot = potential_->Energy().Ene( EnergyArray::E_OPENMM ); 
@@ -474,7 +483,7 @@ Action::RetType Action_Energy::DoAction(int frameNum, ActionFrame& frm) {
         break;
       case C_CMAP:
         time_cmap_.Start();
-        ene = cmap.Ene_CMAP(currentParm_->Cmap(), frm.Frm());
+        ene = cmap_->Ene_CMAP(currentParm_->Cmap(), frm.Frm());
         time_cmap_.Stop();
         Energy_[CMAP]->Add(frameNum, &ene);
         Etot += ene;
diff --git a/src/Action_Energy.h b/src/Action_Energy.h
index f8fc2bb9d1..c0026dc577 100644
--- a/src/Action_Energy.h
+++ b/src/Action_Energy.h
@@ -7,6 +7,11 @@
 #include "ExclusionArray.h"
 #include "EwaldOptions.h"
 #include "Energy/Ecalc_Nonbond.h"
+namespace Cpptraj {
+namespace Energy {
+class CMAP;
+}
+}
 class PotentialFunction;
 /// Calculate energy 
 class Action_Energy: public Action {
@@ -55,6 +60,8 @@ class Action_Energy: public Action {
     Cpptraj::Energy::Ecalc_Nonbond::CalcType nbCalcType_; ///< Nonbond calculation type
     EwaldOptions ewaldOpts_;       ///< Ewald options
 
+    Cpptraj::Energy::CMAP* cmap_;  ///< For calculating cmap energies
+
     PotentialFunction* potential_; ///< TODO currently just for openmm, use for everything
     bool use_openmm_;              ///< If true use openmm for calculating total E
 
diff --git a/src/Energy/CMAP.cpp b/src/Energy/CMAP.cpp
index 43f7ac8003..34ed89aca7 100644
--- a/src/Energy/CMAP.cpp
+++ b/src/Energy/CMAP.cpp
@@ -169,3 +169,17 @@ int CMAP::generate_cmap_derivatives(Topology const& topIn)
 
   return 0;
 }
+
+/** Set up CMAP-related terms */
+int CMAP::Setup_CMAP_Ene(Topology const& topIn) {
+  if (!topIn.HasCmap()) {
+    mprintf("Warning: No CMAP parameters in '%s'\n", topIn.c_str());
+    return 0;
+  }
+  if (generate_cmap_derivatives(topIn)) {
+    mprinterr("Error: Could not set up CMAP derivatives.\n");
+    return 1;
+  }
+
+  return 0;
+}
diff --git a/src/Energy/CMAP.h b/src/Energy/CMAP.h
index 30271633b4..b8cdb8a47d 100644
--- a/src/Energy/CMAP.h
+++ b/src/Energy/CMAP.h
@@ -11,6 +11,8 @@ class CMAP {
   public:
     CMAP();
 
+    /// Setup CMAP splines etc
+    int Setup_CMAP_Ene(Topology const&);
     /// Calculate CMAP energy
     double Ene_CMAP(CmapArray const&, Frame const&) const;
   private:
diff --git a/src/ParameterTypes.h b/src/ParameterTypes.h
index 6d0e9bf9bc..8847e09d7a 100644
--- a/src/ParameterTypes.h
+++ b/src/ParameterTypes.h
@@ -898,7 +898,7 @@ class CmapGridType {
       // NOTE : CMAPs are read in from Amber topologys in COLUMN-MAJOR order
       int ix = wrap_grid(col, resolution_);
       int iy = wrap_grid(row, resolution_);
-      return ( (ix * resolution_) + iy );
+      return grid_[(ix * resolution_) + iy];
     }
     /// \return array of residue names this CMAP applies to
     std::vector<std::string> const& ResNames() const { return resNames_; }

From 93a9adc0f54e9a4f671e7e94ac4023b2ee9f8768 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 10 Feb 2026 07:56:01 -0500
Subject: [PATCH 1312/1492] Add generate_cubic_spline

---
 src/Energy/CMAP.cpp | 65 +++++++++++++++++++++++++++++++++++----------
 src/Energy/CMAP.h   |  1 +
 2 files changed, 52 insertions(+), 14 deletions(-)

diff --git a/src/Energy/CMAP.cpp b/src/Energy/CMAP.cpp
index 34ed89aca7..a82f2ba0fa 100644
--- a/src/Energy/CMAP.cpp
+++ b/src/Energy/CMAP.cpp
@@ -107,6 +107,48 @@ double CMAP::evaluate_cubic_spline(int step_size, std::vector<double> const& y,
   return dyout;
 }
 
+/** Generates the set cubic splining coefficients from a 1D array with
+  * the assumption that the distance between the points is constant. This
+  * interpolation method ensures that the derivative of this spline is
+  * continuous across the boundary of two intervals.
+  *
+  * These coefficients are only calculated *once*, but are later used on
+  * multiple occassions by another subroutine to interpolate anywhere
+  * between two points in this 1D array.
+  */
+void CMAP::generate_cubic_spline(int n, int step_size, std::vector<double> const& y, std::vector<double>& y2)
+{
+  // tmp array used internally for the decomposition loop
+  std::vector<double> tmp(n);
+  // Lower and upper boundaries are natural
+  y2[0]  = 0.0;
+  tmp[0] = 0.0;
+
+  for (int i = 1; i < n-1; i++)
+  {
+    // y2 is used initially as a temp storage array
+    double p = 0.5*y2[i-1] + 2.0;
+    //Debug
+    y2[i]  = -0.5/p;
+    tmp[i] = ( y[i+1]-2.0*y[i] + y[i-1] ) / (double)step_size;
+    tmp[i] = ( 3.0* (tmp[i]/(double)step_size) - 0.5 *tmp[ i-1 ] )/p;
+    mprintf("%6i y2= %16.8f  tmp= %16.8f\n", i, y2[i], tmp[i]);
+  }
+
+  // Set the upper boundary
+  y2[n-1] = 0.0;
+
+  for (int i = n-2; i > -1; i--)
+  {
+    y2[i]=y2[i]*y2[i+1]+tmp[i];
+    mprintf("%6i %16.8f\n", i, y2[i]);
+    //mprintf("\t\t\tn is %i:\n",n);
+    //mprintf("\t\t\tStep size is : %i\n",step_size);
+    //mprintf("\t\t\ty is : %f\n",y[i]);
+    //mprintf("\t\t\ty2 is : %f\n",y2[i]);
+  }
+}
+
 /** Called once after CMAP parameters have been read. This populates
   * various partial derivatives in the cmapParameter%{dPsi,dPhi,dPsi_dPhi}
   * object. It does this using a cubic spline on the read in CMAP grid.
@@ -149,21 +191,16 @@ int CMAP::generate_cmap_derivatives(Topology const& topIn)
         k++;
       }
 
-/*
-      !Calculate spline coeffients (tmpy2) for each of the 1D
-      !horizontal rows in the CMAP table
-      call generate_cubic_spline(twoRes, step_size, tmpy, tmpy2)
+      // Calculate spline coeffients (tmpy2) for each of the 1D
+      // horizontal rows in the CMAP table
+      generate_cubic_spline(twoRes, step_size, tmpy, tmpy2);
      
-      !Calculate %dPhi for using each row
-      !of energies and corresponding splines in tmpy and tmpy2
-      do j=1,res
-        !evaluate_cubic_spline(n,step_size, gridOrigin, y,y2,xin,yout)
-
-        !offset array passed to evaluate_cubic_spline
-        call evaluate_cubic_spline(step_size, tmpy, tmpy2, &
-                                   j+12, gbl_cmap_dPhi(i,row,j))
-      enddo
-*/
+      // Calculate %dPhi for using each row
+      // of energies and corresponding splines in tmpy and tmpy2
+      for (int j = 0; j < res; j++) {
+        // offset array passed to evaluate_cubic_spline
+        double dPhi = evaluate_cubic_spline(step_size, tmpy, tmpy2, j+halfRes); //gbl_cmap_dPhi(i,row,j))
+      }
     } // END loop over rows
   } // END loop over grids
 
diff --git a/src/Energy/CMAP.h b/src/Energy/CMAP.h
index b8cdb8a47d..66a83a8090 100644
--- a/src/Energy/CMAP.h
+++ b/src/Energy/CMAP.h
@@ -18,6 +18,7 @@ class CMAP {
   private:
     static double evaluate_cubic_spline(int, std::vector<double> const&, std::vector<double> const&, int);
     int generate_cmap_derivatives(Topology const&);
+    static void generate_cubic_spline(int, int, std::vector<double> const&, std::vector<double>&);
 };
 }
 }

From b8facd0441f2e8d2e129d1b17027f89880f7f9f7 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 10 Feb 2026 08:09:46 -0500
Subject: [PATCH 1313/1492] Add variables to hold partial deriv for each grid

---
 src/Energy/CMAP.cpp     | 11 +++++++++++
 src/Energy/CMAP.h       |  7 +++++++
 src/Energy/energydepend |  2 +-
 src/cpptrajdepend       |  4 ++--
 4 files changed, 21 insertions(+), 3 deletions(-)

diff --git a/src/Energy/CMAP.cpp b/src/Energy/CMAP.cpp
index a82f2ba0fa..315cf8ab9b 100644
--- a/src/Energy/CMAP.cpp
+++ b/src/Energy/CMAP.cpp
@@ -162,10 +162,20 @@ int CMAP::generate_cmap_derivatives(Topology const& topIn)
     mprinterr("Internal Error: CMAP::generate_cmap_derivatives(): Topology '%s' does not have CMAP parameters.\n", topIn.c_str());
     return 1;
   }
+  // Allocate partial derivative matrices
+  cmap_dPhi_.resize( topIn.CmapGrid().size() );
+  cmap_dPsi_.resize( topIn.CmapGrid().size() );
+  for (unsigned int idx = 0; idx != topIn.CmapGrid().size(); idx++) {
+    unsigned int res = topIn.CmapGrid()[idx].Resolution();
+    cmap_dPhi_[idx].resize( res, res );
+    cmap_dPsi_[idx].resize( res, res );
+  } 
   // Loop over all grids
   for (CmapGridArray::const_iterator grid = topIn.CmapGrid().begin();
                                      grid != topIn.CmapGrid().end(); ++grid)
   {
+    // gidx is the cmap grid index
+    long int gidx = grid - topIn.CmapGrid().begin();
     int res = grid->Resolution();
     int halfRes = res / 2;
     int twoRes = res * 2;
@@ -200,6 +210,7 @@ int CMAP::generate_cmap_derivatives(Topology const& topIn)
       for (int j = 0; j < res; j++) {
         // offset array passed to evaluate_cubic_spline
         double dPhi = evaluate_cubic_spline(step_size, tmpy, tmpy2, j+halfRes); //gbl_cmap_dPhi(i,row,j))
+        cmap_dPhi_[gidx].setElement(row, j, dPhi);
       }
     } // END loop over rows
   } // END loop over grids
diff --git a/src/Energy/CMAP.h b/src/Energy/CMAP.h
index 66a83a8090..0c688b56b3 100644
--- a/src/Energy/CMAP.h
+++ b/src/Energy/CMAP.h
@@ -1,6 +1,7 @@
 #ifndef INC_ENERGY_CMAP_H
 #define INC_ENERGY_CMAP_H
 #include <vector>
+#include "../Matrix.h"
 class CmapArray;
 class Frame;
 class Topology;
@@ -19,6 +20,12 @@ class CMAP {
     static double evaluate_cubic_spline(int, std::vector<double> const&, std::vector<double> const&, int);
     int generate_cmap_derivatives(Topology const&);
     static void generate_cubic_spline(int, int, std::vector<double> const&, std::vector<double>&);
+
+    typedef Matrix<double> Dmatrix;
+    typedef std::vector<Dmatrix> DMarray;
+
+    DMarray cmap_dPhi_; ///< Hold dE/dPhi for each CMAP grid
+    DMarray cmap_dPsi_; ///< Hold dE/dPsi for each CMAP grid
 };
 }
 }
diff --git a/src/Energy/energydepend b/src/Energy/energydepend
index 6c2dd78b72..33d57d250a 100644
--- a/src/Energy/energydepend
+++ b/src/Energy/energydepend
@@ -1,4 +1,4 @@
-CMAP.o : CMAP.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../TorsionRoutines.h ../Unit.h ../Vec3.h CMAP.h
+CMAP.o : CMAP.cpp ../ArrayIterator.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../Unit.h ../Vec3.h CMAP.h
 Ecalc_Nonbond.o : Ecalc_Nonbond.cpp ../Atom.h ../AtomMask.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../Energy/../Constants.h ../Energy/../ParameterTypes.h ../Energy/../SplineFxnTable.h ../Energy/Ene_LJPME_6_12.h ../Energy/Ene_LJ_12_6_4.h ../Energy/Ene_LJ_6_12.h ../Energy/ErfcFxn.h ../Energy/EwaldParams.h ../Energy/EwaldParams_LJPME.h ../Energy/Kernel_EwaldAdjust.h ../Energy/Kernel_LJPME_Adjust.h ../EwaldOptions.h ../ExclusionArray.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../PairList.h ../PairListEngine_Ewald_Decomp_LJCLR.h ../PairListEngine_Ewald_Decomp_LJLR.h ../PairListEngine_Ewald_Decomp_LJPME.h ../PairListEngine_Ewald_LJCLR.h ../PairListEngine_Ewald_LJLR.h ../PairListEngine_Ewald_LJPME.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h ../helpme_standalone.h Ecalc_Nonbond.h Ene_Decomp_Nonbond.h Ene_LJ_6_12.h Ene_Nonbond.h EwaldCalc.h EwaldCalc_Decomp.h EwaldCalc_Decomp_LJCPME.h EwaldCalc_Decomp_LJPME.h EwaldCalc_Decomp_PME.h EwaldCalc_LJCPME.h EwaldCalc_LJPME.h EwaldCalc_PME.h EwaldCalc_Regular.h Ewald_Recip.h PME_Recip.h PME_RecipParams.h VDW_LongRange_Correction.h
 EnergyDecomposer.o : EnergyDecomposer.cpp ../ArgList.h ../AssociatedData.h ../Atom.h ../AtomMask.h ../BaseIOtype.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataFile.h ../DataFileList.h ../DataSet.h ../DataSetList.h ../DataSet_1D.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../DataSet_Mesh.h ../Dimension.h ../DistRoutines.h ../EwaldOptions.h ../ExclusionArray.h ../FileIO.h ../FileName.h ../FileTypes.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../OnlineVarT.h ../PairList.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Spline.h ../Stats_Reduce.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../TorsionRoutines.h ../Unit.h ../Vec3.h Ecalc_Nonbond.h Ene_Angle.h Ene_Bond.h Ene_LJ_6_12.h EnergyDecomposer.h Kernel_Fourier.h Kernel_Harmonic.h
 ErfcFxn.o : ErfcFxn.cpp ../CpptrajStdio.h ../SplineFxnTable.h ErfcFxn.h
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index c5362fb3f6..4e5d1cb6f4 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -33,7 +33,7 @@ Action_Dipole.o : Action_Dipole.cpp Action.h ActionState.h Action_Dipole.h ArgLi
 Action_DistRmsd.o : Action_DistRmsd.cpp Action.h ActionState.h Action_DistRmsd.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 Action_Distance.o : Action_Distance.cpp Action.h ActionState.h Action_Distance.h ArgList.h AssociatedData.h AssociatedData_NOE.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 Action_EneDecomp.o : Action_EneDecomp.cpp Action.h ActionState.h Action_EneDecomp.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h Energy/Ecalc_Nonbond.h Energy/EnergyDecomposer.h EwaldOptions.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h PairList.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_Energy.o : Action_Energy.cpp Action.h ActionState.h Action_Energy.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h Energy.h Energy/CMAP.h Energy/Ecalc_Nonbond.h EnergyArray.h EwaldOptions.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Molecule.h NameType.h PairList.h Parallel.h ParameterTypes.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Energy.o : Action_Energy.cpp Action.h ActionState.h Action_Energy.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h Energy.h Energy/CMAP.h Energy/Ecalc_Nonbond.h EnergyArray.h EwaldOptions.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MdOpts.h MetaData.h Molecule.h NameType.h PairList.h Parallel.h ParameterTypes.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 Action_Esander.o : Action_Esander.cpp Action.h ActionState.h Action_Esander.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h Energy_Sander.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 Action_FilterByData.o : Action_FilterByData.cpp Action.h ActionState.h Action_FilterByData.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 Action_FixAtomOrder.o : Action_FixAtomOrder.cpp Action.h ActionState.h ActionTopWriter.h Action_FixAtomOrder.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomTopType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
@@ -288,7 +288,7 @@ DihedralSearch.o : DihedralSearch.cpp ArgList.h Atom.h AtomMask.h Box.h Constant
 DistRoutines.o : DistRoutines.cpp Box.h DistRoutines.h ImageOption.h Matrix_3x3.h Parallel.h Vec3.h
 Dist_Imaged.o : Dist_Imaged.cpp Dist_Imaged.h Matrix_3x3.h Parallel.h Vec3.h
 Energy.o : Energy.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h Energy.h Energy/Ene_Angle.h Energy/Ene_Bond.h Energy/Ene_LJ_12_6_4.h Energy/Ene_LJ_6_12.h Energy/Kernel_Harmonic.h ExclusionArray.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TorsionRoutines.h Unit.h Vec3.h
-Energy/CMAP.o : Energy/CMAP.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy/CMAP.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TorsionRoutines.h Unit.h Vec3.h
+Energy/CMAP.o : Energy/CMAP.cpp ArrayIterator.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy/CMAP.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TorsionRoutines.h Unit.h Vec3.h
 Energy/Ecalc_Nonbond.o : Energy/Ecalc_Nonbond.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy/Ecalc_Nonbond.h Energy/Ene_Decomp_Nonbond.h Energy/Ene_LJPME_6_12.h Energy/Ene_LJ_12_6_4.h Energy/Ene_LJ_6_12.h Energy/Ene_Nonbond.h Energy/ErfcFxn.h Energy/EwaldCalc.h Energy/EwaldCalc_Decomp.h Energy/EwaldCalc_Decomp_LJCPME.h Energy/EwaldCalc_Decomp_LJPME.h Energy/EwaldCalc_Decomp_PME.h Energy/EwaldCalc_LJCPME.h Energy/EwaldCalc_LJPME.h Energy/EwaldCalc_PME.h Energy/EwaldCalc_Regular.h Energy/EwaldParams.h Energy/EwaldParams_LJPME.h Energy/Ewald_Recip.h Energy/Kernel_EwaldAdjust.h Energy/Kernel_LJPME_Adjust.h Energy/PME_Recip.h Energy/PME_RecipParams.h Energy/VDW_LongRange_Correction.h EwaldOptions.h ExclusionArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h PairListEngine_Ewald_Decomp_LJCLR.h PairListEngine_Ewald_Decomp_LJLR.h PairListEngine_Ewald_Decomp_LJPME.h PairListEngine_Ewald_LJCLR.h PairListEngine_Ewald_LJLR.h PairListEngine_Ewald_LJPME.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h Timer.h Topology.h Unit.h Vec3.h helpme_standalone.h
 Energy/EnergyDecomposer.o : Energy/EnergyDecomposer.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DistRoutines.h Energy/Ecalc_Nonbond.h Energy/Ene_Angle.h Energy/Ene_Bond.h Energy/Ene_LJ_6_12.h Energy/EnergyDecomposer.h Energy/Kernel_Fourier.h Energy/Kernel_Harmonic.h EwaldOptions.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h PairList.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h Stats_Reduce.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h Unit.h Vec3.h
 Energy/ErfcFxn.o : Energy/ErfcFxn.cpp CpptrajStdio.h Energy/ErfcFxn.h SplineFxnTable.h

From c83a1877bdb2e6db10d08672068a0037f58e83a9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 10 Feb 2026 09:14:09 -0500
Subject: [PATCH 1314/1492] Calculate dE/dPsi

---
 src/Energy/CMAP.cpp | 29 ++++++++++++++++++++++++++++-
 1 file changed, 28 insertions(+), 1 deletion(-)

diff --git a/src/Energy/CMAP.cpp b/src/Energy/CMAP.cpp
index 315cf8ab9b..0d7927e6ce 100644
--- a/src/Energy/CMAP.cpp
+++ b/src/Energy/CMAP.cpp
@@ -193,7 +193,7 @@ int CMAP::generate_cmap_derivatives(Topology const& topIn)
       // for the 1D splining like CHARMM.
       // It is possible CHARMM does this to avoid edge issues.
 
-      unsigned int k=0; //interal offset counter for tmp array
+      unsigned int k=0; // index for tmpy array
       mprintf("DEBUG: Row %6i from %6i to %6i\n", row, -halfRes, res+halfRes-1);
       for (int col = -halfRes; col < res+halfRes; col++) { // -12 to 35
         tmpy[k] = grid->Grid(col, row);
@@ -213,6 +213,33 @@ int CMAP::generate_cmap_derivatives(Topology const& topIn)
         cmap_dPhi_[gidx].setElement(row, j, dPhi);
       }
     } // END loop over rows
+
+    // 2) calculate dE/dPsi
+    for (int col = 0; col < res; col++)
+    {
+      // Step across one column each cycle, splining up each column
+
+      unsigned int k=0; // index for tmpy array
+      mprintf("DEBUG: Col %6i from %6i to %6i\n", col, -halfRes, res+halfRes-1);
+      for (int row = -halfRes; row < res+halfRes; row++) { // -12 to 35
+        tmpy[k] = grid->Grid(col, row);
+        mprintf("DEBUG:\t\t%6i%12.4f\n", k, tmpy[k]);
+        k++;
+      }
+
+      // Calculate spline coeffients (tmpy2) for each of the 1D
+      // vertical columns in the CMAP table
+      generate_cubic_spline(twoRes, step_size, tmpy, tmpy2);
+     
+      // Calculate %dPsi for using each column of energies and
+      // corresponding splines in tmpy and tmpy2
+      for (int j = 0; j < res; j++) {
+        // offset array passed to evaluate_cubic_spline
+        double dPsi = evaluate_cubic_spline(step_size, tmpy, tmpy2, j+halfRes); //gbl_cmap_dPsi(i,j,col))
+        cmap_dPsi_[gidx].setElement(j, col, dPsi);
+      }
+    } // END loop over cols
+
   } // END loop over grids
 
   return 0;

From 92f25c90170efa43fd3226b1c784b080bc6e885c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 10 Feb 2026 09:41:53 -0500
Subject: [PATCH 1315/1492] Calculate d^2E/dPhiPsi

---
 src/Energy/CMAP.cpp | 22 ++++++++++++++++++++++
 src/Energy/CMAP.h   |  1 +
 src/Matrix.h        | 20 ++++++++++++++++++++
 3 files changed, 43 insertions(+)

diff --git a/src/Energy/CMAP.cpp b/src/Energy/CMAP.cpp
index 0d7927e6ce..1dc000e9ac 100644
--- a/src/Energy/CMAP.cpp
+++ b/src/Energy/CMAP.cpp
@@ -165,10 +165,12 @@ int CMAP::generate_cmap_derivatives(Topology const& topIn)
   // Allocate partial derivative matrices
   cmap_dPhi_.resize( topIn.CmapGrid().size() );
   cmap_dPsi_.resize( topIn.CmapGrid().size() );
+  cmap_dPhi_dPsi_.resize( topIn.CmapGrid().size() );
   for (unsigned int idx = 0; idx != topIn.CmapGrid().size(); idx++) {
     unsigned int res = topIn.CmapGrid()[idx].Resolution();
     cmap_dPhi_[idx].resize( res, res );
     cmap_dPsi_[idx].resize( res, res );
+    cmap_dPhi_dPsi_[idx].resize( res, res );
   } 
   // Loop over all grids
   for (CmapGridArray::const_iterator grid = topIn.CmapGrid().begin();
@@ -240,6 +242,26 @@ int CMAP::generate_cmap_derivatives(Topology const& topIn)
       }
     } // END loop over cols
 
+    // 3) calculate d^2E/dPhidPsi
+    // TODO Interpolate partitial derivative of psi; dE/dPhi ?
+    for (int col = 0; col < res; col++)
+    {
+      unsigned int k=0;
+      mprintf("DEBUG: D2 %6i from %6i to %6i\n", col, -halfRes, res+halfRes-1);
+      for (int row = -halfRes; row < res+halfRes; row++) { // -12 to 35
+        tmpy[k] = cmap_dPhi_[gidx].element_wrapped(row, col);
+        mprintf("DEBUG:\t\t%6i%12.4f\n", k, tmpy[k]);
+        k++;
+      }
+
+      generate_cubic_spline(twoRes, step_size, tmpy, tmpy2);
+     
+      for (int j = 0; j < res; j++) {
+        double dPhiPsi = evaluate_cubic_spline(step_size, tmpy, tmpy2, j+halfRes); //gbl_cmap_dPhi_dPsi(i,j,col))
+        cmap_dPhi_dPsi_[gidx].setElement(j, col, dPhiPsi);
+      }
+    } // END loop over cols
+
   } // END loop over grids
 
   return 0;
diff --git a/src/Energy/CMAP.h b/src/Energy/CMAP.h
index 0c688b56b3..e8331fa7ee 100644
--- a/src/Energy/CMAP.h
+++ b/src/Energy/CMAP.h
@@ -26,6 +26,7 @@ class CMAP {
 
     DMarray cmap_dPhi_; ///< Hold dE/dPhi for each CMAP grid
     DMarray cmap_dPsi_; ///< Hold dE/dPsi for each CMAP grid
+    DMarray cmap_dPhi_dPsi_; ///< Hold d^2E/dPhidPsi for each CMAP grid
 };
 }
 }
diff --git a/src/Matrix.h b/src/Matrix.h
index 99c63c7df4..ad2e0b17a2 100644
--- a/src/Matrix.h
+++ b/src/Matrix.h
@@ -34,6 +34,8 @@ template <class T> class Matrix {
     /// \return element at specified col and row.
     const T& element(size_t,size_t) const;
     T&       element(size_t,size_t);
+    /// \return element at specified col and row. Out-of-bound indices will be wrapped.
+    const T& element_wrapped(long int, long int) const;
     /// \return number of rows (Y).
     size_t Nrows()     const { return nrows_;     }
     /// \return number of cols (X).
@@ -118,6 +120,16 @@ template <class T> class Matrix {
       size_t i1 = i + 1UL;
       return (long int)(( (nX * i) - ((i1 * i) / 2UL) ) + j - i1);
     }
+    /// If an index is out of bounds, wrap it
+    static inline long int wrap_grid(long int iin, long int res) {
+      long int iout = iin;
+      if (iout < 0) {
+        while (iout < 0) iout += res;
+      } else if (iout >= res) {
+        while (iout >= res) iout -= res;
+      }
+      return iout;
+    }
 };
 // COPY CONSTRUCTOR
 template<class T> Matrix<T>::Matrix(const Matrix& rhs) :
@@ -254,6 +266,14 @@ template<class T> T& Matrix<T>::element(size_t xIn, size_t yIn) {
   if (idx < 0) return diagElt_; // In case of xIn == yIn for TRIANGLE
   return elements_[idx];
 }
+/** \return element at specified col and row. Out-of-bound indices will be wrapped. */
+template<class T> const T& Matrix<T>::element_wrapped(long int xIn, long int yIn) const {
+  long int ix = wrap_grid(xIn, ncols_);
+  long int iy = wrap_grid(yIn, nrows_);
+  long int idx = indexFxn_(ncols_, ix, iy);
+  if (idx < 0) return diagElt_; // In case of xIn == yIn for TRIANGLE
+  return elements_[idx];
+}
 // Matrix::LinearLeastSquares()
 /** Produce a vector containing the solution to an over-determined system of linear equations
   * represented by the matrix itself and an input vector.  This will work for float and

From 55413fb277902e9dfb0943e769d92e75bf261a43 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 10 Feb 2026 11:55:34 -0500
Subject: [PATCH 1316/1492] Start doing the interpolation to actually get the
 energy

---
 src/Energy/CMAP.cpp | 42 +++++++++++++++++++++++++++++++++++++++---
 src/Energy/CMAP.h   |  4 ++++
 2 files changed, 43 insertions(+), 3 deletions(-)

diff --git a/src/Energy/CMAP.cpp b/src/Energy/CMAP.cpp
index 1dc000e9ac..7e64bed346 100644
--- a/src/Energy/CMAP.cpp
+++ b/src/Energy/CMAP.cpp
@@ -8,7 +8,8 @@
 using namespace Cpptraj::Energy;
 
 /** CONSTRUCTOR */
-CMAP::CMAP() {}
+CMAP::CMAP() : cmapGridPtr_(0)
+{}
 
 /// DEBUG - print gradients
 static inline void print_grad(Vec3 const& dA, Vec3 const& dB, Vec3 const& dC, Vec3 const& dD)
@@ -41,8 +42,9 @@ const
                             dAphi, dBphi, dCphi, dDphi,
                             cosphi_ijkl, sinphi_ijkl );
     print_grad(dAphi, dBphi, dCphi, dDphi);
+    mprintf("%30.15f\n", acos(cosphi_ijkl));
     double phi = copysign(acos(cosphi_ijkl),sinphi_ijkl) * Constants::RADDEG;
-    mprintf("DEBUG: Dihedral 1 %i %i %i %i = %g deg.\n", cmap->A1()+1, cmap->A2()+1, cmap->A3()+1, cmap->A4()+1, phi);
+    mprintf("DEBUG: Dihedral 1 %i %i %i %i = %30.15f%30.15f%30.15f\n", cmap->A1()+1, cmap->A2()+1, cmap->A3()+1, cmap->A4()+1, phi, cosphi_ijkl, sinphi_ijkl);
 
     // Calculate the dihedral angle (psi) and the derivatives of the
     // four coordinates with respect to psi. Remember this subroutine is
@@ -54,11 +56,44 @@ const
                             cospsi_jklm, sinpsi_jklm );
     print_grad(dApsi, dBpsi, dCpsi, dDpsi);
     double psi = copysign(acos(cospsi_jklm),sinpsi_jklm) * Constants::RADDEG;
-    mprintf("DEBUG: Dihedral 2 %i %i %i %i = %g deg.\n", cmap->A2()+1, cmap->A3()+1, cmap->A4()+1, cmap->A5()+1, psi);
+    mprintf("DEBUG: Dihedral 2 %i %i %i %i = %30.15f%30.15f%30.15f\n", cmap->A2()+1, cmap->A3()+1, cmap->A4()+1, cmap->A5()+1, psi, cospsi_jklm, sinpsi_jklm);
+
+    double dPhi, dPsi;
+    ene_cmap = charmm_calc_cmap_from_phi_psi(phi, psi, (*(cmapGridPtr_))[cmap->Idx()], dPhi, dPsi);
   }
   return ene_cmap;
 }
 
+/// Used to mimic Fortran modulo with REAL arguments
+static inline double dmodulo(double a, double p) {
+  return ( a - floor(a / p) * p );
+}
+
+/** Calculate the CMAP energy given psi,phi and the cmap parameter */
+double CMAP::charmm_calc_cmap_from_phi_psi(double phi, double psi, CmapGridType const& cmapGrid, double& dPhi, double& dPsi)
+const
+{
+  static const int gridOrigin = -180; ///< Where the 2D grid starts in degrees
+  int step_size = 360 / cmapGrid.Resolution();
+  double ene_cmap = 0.0;
+  // Work out nearest complete grid point on the CMAP grid from
+  // phi and psi and use this to form a 2x2 stencil
+  mprintf("x= %16.8f  y= %16.8f\n", (phi - gridOrigin)/(step_size),(psi - gridOrigin)/(step_size) );
+  int x = (int)( (phi - gridOrigin)/(step_size) );
+  int y = (int)( (psi - gridOrigin)/(step_size) );
+  mprintf("x= %6i  y= %6i\n", x, y);
+
+  // Work out the fraction of the CMAP grid step that the interpolated
+  // point takes up.
+  // This will give the remainder part and then it is divided by the step size
+  double phiFrac = dmodulo((phi - gridOrigin), step_size) / step_size;
+  double psiFrac = dmodulo((psi - gridOrigin), step_size) / step_size;
+  mprintf("phiFrac %16.8f  psiFrac %16.8f\n", phiFrac, psiFrac);
+
+  return ene_cmap;
+}
+
+// -----------------------------------------------------------------------------
 /** This is reduced version of a typical cubic spline routine
   * that one may find in a recipe book of a numerical flavour.
   *
@@ -273,6 +308,7 @@ int CMAP::Setup_CMAP_Ene(Topology const& topIn) {
     mprintf("Warning: No CMAP parameters in '%s'\n", topIn.c_str());
     return 0;
   }
+  cmapGridPtr_ = &(topIn.CmapGrid());
   if (generate_cmap_derivatives(topIn)) {
     mprinterr("Error: Could not set up CMAP derivatives.\n");
     return 1;
diff --git a/src/Energy/CMAP.h b/src/Energy/CMAP.h
index e8331fa7ee..2befee0855 100644
--- a/src/Energy/CMAP.h
+++ b/src/Energy/CMAP.h
@@ -3,6 +3,8 @@
 #include <vector>
 #include "../Matrix.h"
 class CmapArray;
+class CmapGridArray;
+class CmapGridType;
 class Frame;
 class Topology;
 namespace Cpptraj {
@@ -17,6 +19,7 @@ class CMAP {
     /// Calculate CMAP energy
     double Ene_CMAP(CmapArray const&, Frame const&) const;
   private:
+    double charmm_calc_cmap_from_phi_psi(double, double, CmapGridType const&, double&, double&) const;
     static double evaluate_cubic_spline(int, std::vector<double> const&, std::vector<double> const&, int);
     int generate_cmap_derivatives(Topology const&);
     static void generate_cubic_spline(int, int, std::vector<double> const&, std::vector<double>&);
@@ -27,6 +30,7 @@ class CMAP {
     DMarray cmap_dPhi_; ///< Hold dE/dPhi for each CMAP grid
     DMarray cmap_dPsi_; ///< Hold dE/dPsi for each CMAP grid
     DMarray cmap_dPhi_dPsi_; ///< Hold d^2E/dPhidPsi for each CMAP grid
+    CmapGridArray const* cmapGridPtr_; ///< Pointer to CMAP grids this was set up with.
 };
 }
 }

From 9c9da4e0bb82d47f3043d3b4d45a8d24c0c8de96 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 10 Feb 2026 12:14:00 -0500
Subject: [PATCH 1317/1492] Start filling in stencils

---
 src/Energy/CMAP.cpp | 23 +++++++++++++++++++++--
 src/Energy/CMAP.h   |  3 +--
 2 files changed, 22 insertions(+), 4 deletions(-)

diff --git a/src/Energy/CMAP.cpp b/src/Energy/CMAP.cpp
index 7e64bed346..72489f2d2f 100644
--- a/src/Energy/CMAP.cpp
+++ b/src/Energy/CMAP.cpp
@@ -59,7 +59,7 @@ const
     mprintf("DEBUG: Dihedral 2 %i %i %i %i = %30.15f%30.15f%30.15f\n", cmap->A2()+1, cmap->A3()+1, cmap->A4()+1, cmap->A5()+1, psi, cospsi_jklm, sinpsi_jklm);
 
     double dPhi, dPsi;
-    ene_cmap = charmm_calc_cmap_from_phi_psi(phi, psi, (*(cmapGridPtr_))[cmap->Idx()], dPhi, dPsi);
+    ene_cmap = charmm_calc_cmap_from_phi_psi(phi, psi, cmap->Idx(), dPhi, dPsi);
   }
   return ene_cmap;
 }
@@ -70,9 +70,10 @@ static inline double dmodulo(double a, double p) {
 }
 
 /** Calculate the CMAP energy given psi,phi and the cmap parameter */
-double CMAP::charmm_calc_cmap_from_phi_psi(double phi, double psi, CmapGridType const& cmapGrid, double& dPhi, double& dPsi)
+double CMAP::charmm_calc_cmap_from_phi_psi(double phi, double psi, int cidx, double& dPhi, double& dPsi)
 const
 {
+  CmapGridType const& cmapGrid = (*(cmapGridPtr_))[cidx];
   static const int gridOrigin = -180; ///< Where the 2D grid starts in degrees
   int step_size = 360 / cmapGrid.Resolution();
   double ene_cmap = 0.0;
@@ -90,6 +91,24 @@ const
   double psiFrac = dmodulo((psi - gridOrigin), step_size) / step_size;
   mprintf("phiFrac %16.8f  psiFrac %16.8f\n", phiFrac, psiFrac);
 
+  double E_stencil[2][2];
+  double dPhi_stencil[2][2];
+  double dPsi_stencil[2][2];
+  double dPhi_dPsi_stencil[2][2];
+
+  for (int i = 0; i < 2; i++) {
+    for (int j = 0; j < 2; j++) {
+      E_stencil[i][j] = cmapGrid.Grid(x+j, y+i);
+
+      dPhi_stencil[i][j] = cmap_dPhi_[cidx].element_wrapped(x+j, y+i);
+
+      dPsi_stencil[i][j] = cmap_dPsi_[cidx].element_wrapped(x+j, y+i);
+
+      dPhi_dPsi_stencil[i][j] = cmap_dPhi_dPsi_[cidx].element_wrapped(x+j, y+i);
+    }
+  }
+
+
   return ene_cmap;
 }
 
diff --git a/src/Energy/CMAP.h b/src/Energy/CMAP.h
index 2befee0855..46f60b77c0 100644
--- a/src/Energy/CMAP.h
+++ b/src/Energy/CMAP.h
@@ -4,7 +4,6 @@
 #include "../Matrix.h"
 class CmapArray;
 class CmapGridArray;
-class CmapGridType;
 class Frame;
 class Topology;
 namespace Cpptraj {
@@ -19,7 +18,7 @@ class CMAP {
     /// Calculate CMAP energy
     double Ene_CMAP(CmapArray const&, Frame const&) const;
   private:
-    double charmm_calc_cmap_from_phi_psi(double, double, CmapGridType const&, double&, double&) const;
+    double charmm_calc_cmap_from_phi_psi(double, double, int, double&, double&) const;
     static double evaluate_cubic_spline(int, std::vector<double> const&, std::vector<double> const&, int);
     int generate_cmap_derivatives(Topology const&);
     static void generate_cubic_spline(int, int, std::vector<double> const&, std::vector<double>&);

From 05c534cc3b1d8431f42998865c9613f61b8932de Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 10 Feb 2026 14:32:15 -0500
Subject: [PATCH 1318/1492] Add the weight matrix

---
 src/Energy/CMAP.cpp | 101 ++++++++++++++++++++++++++++++++++++++++++--
 src/Energy/CMAP.h   |   2 +
 2 files changed, 99 insertions(+), 4 deletions(-)

diff --git a/src/Energy/CMAP.cpp b/src/Energy/CMAP.cpp
index 72489f2d2f..6c9931a991 100644
--- a/src/Energy/CMAP.cpp
+++ b/src/Energy/CMAP.cpp
@@ -11,6 +11,26 @@ using namespace Cpptraj::Energy;
 CMAP::CMAP() : cmapGridPtr_(0)
 {}
 
+/** The weight matrix */
+const int CMAP::wt_[16][16] = {
+  {1, 0, -3,  2, 0, 0,  0,  0, -3,  0,  9, -6,  2,  0, -6,  4},
+  {0, 0,  0,  0, 0, 0,  0,  0,  3,  0, -9,  6, -2,  0,  6, -4},
+  {0, 0,  0,  0, 0, 0,  0,  0,  0,  0,  9, -6,  0,  0, -6,  4},
+  {0, 0,  3, -2, 0, 0,  0,  0,  0,  0, -9,  6,  0,  0,  6, -4},
+  {0, 0,  0,  0, 1, 0, -3,  2, -2,  0,  6, -4,  1,  0, -3,  2},
+  {0, 0,  0,  0, 0, 0,  0,  0, -1,  0,  3, -2,  1,  0, -3,  2},
+  {0, 0,  0,  0, 0, 0,  0,  0,  0,  0, -3,  2,  0,  0,  3, -2},
+  {0, 0,  0,  0, 0, 0,  3, -2,  0,  0, -6,  4,  0,  0,  3, -2},
+  {0, 1, -2,  1, 0, 0,  0,  0,  0, -3,  6, -3,  0,  2, -4,  2},
+  {0, 0,  0,  0, 0, 0,  0,  0,  0,  3, -6,  3,  0, -2,  4, -2},
+  {0, 0,  0,  0, 0, 0,  0,  0,  0,  0, -3,  3,  0,  0,  2, -2},
+  {0, 0, -1,  1, 0, 0,  0,  0,  0,  0,  3, -3,  0,  0, -2,  2},
+  {0, 0,  0,  0, 0, 1, -2,  1,  0, -2,  4, -2,  0,  1, -2,  1},
+  {0, 0,  0,  0, 0, 0,  0,  0,  0, -1,  2, -1,  0,  1, -2,  1},
+  {0, 0,  0,  0, 0, 0,  0,  0,  0,  0,  1, -1,  0,  0, -1,  1},
+  {0, 0,  0,  0, 0, 0, -1,  1,  0,  0,  2, -2,  0,  0, -1,  1}
+};
+
 /// DEBUG - print gradients
 static inline void print_grad(Vec3 const& dA, Vec3 const& dB, Vec3 const& dC, Vec3 const& dD)
 {
@@ -69,6 +89,22 @@ static inline double dmodulo(double a, double p) {
   return ( a - floor(a / p) * p );
 }
 
+static inline void print_stencil(const char* desc, const double (&matrix)[2][2])
+{
+  mprintf("%s:\n", desc);
+  mprintf("%9.6f %9.6f\n", matrix[1][0], matrix[1][1]);
+  mprintf("%9.6f %9.6f\n", matrix[0][0], matrix[0][1]);
+  mprintf("\n");
+}
+
+static inline void flatten_stencil(double(&out)[4], const double(&matrix)[2][2])
+{
+  out[0] = matrix[0][0];
+  out[1] = matrix[0][1];
+  out[2] = matrix[1][1];
+  out[3] = matrix[1][0];
+}
+
 /** Calculate the CMAP energy given psi,phi and the cmap parameter */
 double CMAP::charmm_calc_cmap_from_phi_psi(double phi, double psi, int cidx, double& dPhi, double& dPsi)
 const
@@ -100,15 +136,72 @@ const
     for (int j = 0; j < 2; j++) {
       E_stencil[i][j] = cmapGrid.Grid(x+j, y+i);
 
-      dPhi_stencil[i][j] = cmap_dPhi_[cidx].element_wrapped(x+j, y+i);
+      dPhi_stencil[i][j] = cmap_dPhi_[cidx].element_wrapped(y+i, x+j);
 
-      dPsi_stencil[i][j] = cmap_dPsi_[cidx].element_wrapped(x+j, y+i);
+      dPsi_stencil[i][j] = cmap_dPsi_[cidx].element_wrapped(y+i, x+j);
 
-      dPhi_dPsi_stencil[i][j] = cmap_dPhi_dPsi_[cidx].element_wrapped(x+j, y+i);
+      dPhi_dPsi_stencil[i][j] = cmap_dPhi_dPsi_[cidx].element_wrapped(y+i, x+j);
     }
   }
 
-
+  print_stencil("CMAP", E_stencil);
+  print_stencil("dPhi", dPhi_stencil);
+  print_stencil("dPsi", dPsi_stencil);
+  print_stencil("dPhi_dPsi", dPhi_dPsi_stencil);
+
+  // Convert the 2x2 stencils into a 1D array for processing
+  // by weight_stencil.
+  // The array starts at the bottom left of the 2x2, working
+  // around counterclockwise:
+  //
+  //          4 3
+  //          1 2
+  //
+  //There may be a cleaner/better way of doing this
+  double E_stencil_1D[4];
+  double dPhi_stencil_1D[4];
+  double dPsi_stencil_1D[4];
+  double dPhi_dPsi_stencil_1D[4];
+
+  flatten_stencil(E_stencil_1D, E_stencil);
+  mprintf("%9.6f %9.6f %9.6f %9.6f\n", E_stencil_1D[0], E_stencil_1D[1], E_stencil_1D[2], E_stencil_1D[3]);
+  flatten_stencil(dPhi_stencil_1D, dPhi_stencil);
+  flatten_stencil(dPsi_stencil_1D, dPsi_stencil);
+  flatten_stencil(dPhi_dPsi_stencil_1D, dPhi_dPsi_stencil);
+/*
+  E_stencil_1D(0) = E_stencil(0,0)
+  E_stencil_1D(1) = E_stencil(0,1)
+  E_stencil_1D(2) = E_stencil(1,1)
+  E_stencil_1D(3) = E_stencil(1,0)
+
+  !DEBUG
+  !write(6,'(f9.6)'),E_stencil_1D
+
+  dPhi_stencil_1D(1) = dPhi_stencil(1,1)
+  dPhi_stencil_1D(2) = dPhi_stencil(1,2)
+  dPhi_stencil_1D(3) = dPhi_stencil(2,2)
+  dPhi_stencil_1D(4) = dPhi_stencil(2,1)
+
+  dPsi_stencil_1D(1) = dPsi_stencil(1,1)
+  dPsi_stencil_1D(2) = dPsi_stencil(1,2)
+  dPsi_stencil_1D(3) = dPsi_stencil(2,2)
+  dPsi_stencil_1D(4) = dPsi_stencil(2,1)
+
+  dPhi_dPsi_stencil_1D(1) = dPhi_dPsi_stencil(1,1)
+  dPhi_dPsi_stencil_1D(2) = dPhi_dPsi_stencil(1,2)
+  dPhi_dPsi_stencil_1D(3) = dPhi_dPsi_stencil(2,2)
+  dPhi_dPsi_stencil_1D(4) = dPhi_dPsi_stencil(2,1)
+
+  !Weight d{Psi,dPhi,dPhidPsi}_stencil
+  call weight_stencil(gbl_cmap_grid_step_size(cmap_idx), &
+                      E_stencil_1D,              &
+                      dPhi_stencil_1D,           &
+                      dPsi_stencil_1D,           &
+                      dPhi_dPsi_stencil_1D,      &
+                      c )
+
+  call bicubic_interpolation(phiFrac, psiFrac, c, E, dphi, dpsi)
+*/
   return ene_cmap;
 }
 
diff --git a/src/Energy/CMAP.h b/src/Energy/CMAP.h
index 46f60b77c0..bd43b76970 100644
--- a/src/Energy/CMAP.h
+++ b/src/Energy/CMAP.h
@@ -30,6 +30,8 @@ class CMAP {
     DMarray cmap_dPsi_; ///< Hold dE/dPsi for each CMAP grid
     DMarray cmap_dPhi_dPsi_; ///< Hold d^2E/dPhidPsi for each CMAP grid
     CmapGridArray const* cmapGridPtr_; ///< Pointer to CMAP grids this was set up with.
+
+    static const int wt_[16][16]; ///< Weight matrix
 };
 }
 }

From 8844575cb68be6e3d2d4fae4037121aacc0ea80a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 10 Feb 2026 14:53:11 -0500
Subject: [PATCH 1319/1492] Generate the bicubic coefficients

---
 src/Energy/CMAP.cpp | 48 ++++++++++++++++++++++++++++++---------------
 1 file changed, 32 insertions(+), 16 deletions(-)

diff --git a/src/Energy/CMAP.cpp b/src/Energy/CMAP.cpp
index 6c9931a991..6738ec1cfe 100644
--- a/src/Energy/CMAP.cpp
+++ b/src/Energy/CMAP.cpp
@@ -97,12 +97,12 @@ static inline void print_stencil(const char* desc, const double (&matrix)[2][2])
   mprintf("\n");
 }
 
-static inline void flatten_stencil(double(&out)[4], const double(&matrix)[2][2])
+static inline void flatten_stencil(double* out, const double(&matrix)[2][2], double step_size)
 {
-  out[0] = matrix[0][0];
-  out[1] = matrix[0][1];
-  out[2] = matrix[1][1];
-  out[3] = matrix[1][0];
+  out[0] = matrix[0][0] * step_size;
+  out[1] = matrix[0][1] * step_size;
+  out[2] = matrix[1][1] * step_size;
+  out[3] = matrix[1][0] * step_size;
 }
 
 /** Calculate the CMAP energy given psi,phi and the cmap parameter */
@@ -158,16 +158,18 @@ const
   //          1 2
   //
   //There may be a cleaner/better way of doing this
-  double E_stencil_1D[4];
-  double dPhi_stencil_1D[4];
-  double dPsi_stencil_1D[4];
-  double dPhi_dPsi_stencil_1D[4];
-
-  flatten_stencil(E_stencil_1D, E_stencil);
-  mprintf("%9.6f %9.6f %9.6f %9.6f\n", E_stencil_1D[0], E_stencil_1D[1], E_stencil_1D[2], E_stencil_1D[3]);
-  flatten_stencil(dPhi_stencil_1D, dPhi_stencil);
-  flatten_stencil(dPsi_stencil_1D, dPsi_stencil);
-  flatten_stencil(dPhi_dPsi_stencil_1D, dPhi_dPsi_stencil);
+  //double E_stencil_1D[4];
+  //double dPhi_stencil_1D[4];
+  //double dPsi_stencil_1D[4];
+  //double dPhi_dPsi_stencil_1D[4];
+
+  std::vector<double> E_stencil_1D(16);
+  double* dptr = &(E_stencil_1D[0]);
+  flatten_stencil(dptr, E_stencil, 1);
+  //mprintf("%9.6f %9.6f %9.6f %9.6f\n", E_stencil_1D[0], E_stencil_1D[1], E_stencil_1D[2], E_stencil_1D[3]);
+  flatten_stencil(dptr+4, dPhi_stencil, step_size);
+  flatten_stencil(dptr+8, dPsi_stencil, step_size);
+  flatten_stencil(dptr+12, dPhi_dPsi_stencil, step_size*step_size);
 /*
   E_stencil_1D(0) = E_stencil(0,0)
   E_stencil_1D(1) = E_stencil(0,1)
@@ -199,7 +201,21 @@ const
                       dPsi_stencil_1D,           &
                       dPhi_dPsi_stencil_1D,      &
                       c )
-
+*/
+  // Generate coefficients for bicubic interpolation
+  for (std::vector<double>::const_iterator it = E_stencil_1D.begin(); it != E_stencil_1D.end(); ++it)
+    mprintf("%16.8f\n", *it);
+  
+  std::vector<double> coeff(16);
+  for (int i = 0; i < 16; i++) {
+    coeff[i] = 0.0;
+    for (int k = 0; k < 16; k++) {
+      coeff[i] += wt_[k][i] * E_stencil_1D[k];
+    }
+  }
+  for (std::vector<double>::const_iterator it = coeff.begin(); it != coeff.end(); ++it)
+    mprintf("%16.8f\n", *it);
+/*
   call bicubic_interpolation(phiFrac, psiFrac, c, E, dphi, dpsi)
 */
   return ene_cmap;

From 4fbc97200e2c79661e68eb839c9ee184a24c0092 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 10 Feb 2026 15:14:26 -0500
Subject: [PATCH 1320/1492] Do bicubic interpolation

---
 src/Energy/CMAP.cpp | 29 ++++++++++++++++++++++++++---
 1 file changed, 26 insertions(+), 3 deletions(-)

diff --git a/src/Energy/CMAP.cpp b/src/Energy/CMAP.cpp
index 6738ec1cfe..6bc9b7b143 100644
--- a/src/Energy/CMAP.cpp
+++ b/src/Energy/CMAP.cpp
@@ -113,6 +113,8 @@ const
   static const int gridOrigin = -180; ///< Where the 2D grid starts in degrees
   int step_size = 360 / cmapGrid.Resolution();
   double ene_cmap = 0.0;
+  dPhi = 0.0;
+  dPsi = 0.0;
   // Work out nearest complete grid point on the CMAP grid from
   // phi and psi and use this to form a 2x2 stencil
   mprintf("x= %16.8f  y= %16.8f\n", (phi - gridOrigin)/(step_size),(psi - gridOrigin)/(step_size) );
@@ -170,6 +172,9 @@ const
   flatten_stencil(dptr+4, dPhi_stencil, step_size);
   flatten_stencil(dptr+8, dPsi_stencil, step_size);
   flatten_stencil(dptr+12, dPhi_dPsi_stencil, step_size*step_size);
+  for (std::vector<double>::const_iterator it = E_stencil_1D.begin(); it != E_stencil_1D.end(); ++it)
+    mprintf("%16.8f\n", *it);
+ 
 /*
   E_stencil_1D(0) = E_stencil(0,0)
   E_stencil_1D(1) = E_stencil(0,1)
@@ -203,9 +208,8 @@ const
                       c )
 */
   // Generate coefficients for bicubic interpolation
-  for (std::vector<double>::const_iterator it = E_stencil_1D.begin(); it != E_stencil_1D.end(); ++it)
-    mprintf("%16.8f\n", *it);
-  
+  // NOTE: This is based on routine weight_stencil in cmap.F90
+ 
   std::vector<double> coeff(16);
   for (int i = 0; i < 16; i++) {
     coeff[i] = 0.0;
@@ -218,6 +222,25 @@ const
 /*
   call bicubic_interpolation(phiFrac, psiFrac, c, E, dphi, dpsi)
 */
+  // Bicubic interpolation
+  // NOTE: This is based on routine bicubic_interpolation in cmap.F90
+  std::vector<double>::const_reverse_iterator Cit = coeff.rbegin();
+  std::vector<double>::const_reverse_iterator Dit = coeff.rbegin();
+  for (int i = 3; i > -1; i--, Cit += 4, Dit++) {
+    mprintf("BICUBIC %i %16.8f %16.8f %16.8f %16.8f\n", i, *(Cit), *(Cit+1), *(Cit+2), *(Cit+3));
+    mprintf("BICUBIC2 %i %16.8f %16.8f %16.8f\n", i, *(Dit), *(Dit+4), *(Dit+8));
+    double c4 = *(Cit);
+    double c3 = *(Cit+1);
+    double c2 = *(Cit+2);
+    double c1 = *(Cit+3);
+    double d4 = *(Dit);
+    double d3 = *(Dit+4);
+    double d2 = *(Dit+8);
+    ene_cmap =  ene_cmap*phiFrac +( (c4*psiFrac + c3)*psiFrac + c2 )*psiFrac + c1;
+    dPhi = dPhi*psiFrac +( 3.0*d4*phiFrac + 2.0*d3 )*phiFrac + d2;
+    dPsi = dPsi*phiFrac +( 3.0*c4*psiFrac + 2.0*c3 )*psiFrac + c2;
+  }
+  mprintf("FINAL %16.8f %16.8f %16.8f\n", ene_cmap, dPhi, dPsi);
   return ene_cmap;
 }
 

From f78d09804f4b656581c09388f01f6b8c16e206fa Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 10 Feb 2026 15:38:14 -0500
Subject: [PATCH 1321/1492] Refactor to make it easier to create a routine that
 also caluclates forces

---
 src/Energy/CMAP.cpp | 25 +++++++++++++++++--------
 src/Energy/CMAP.h   |  4 ++++
 2 files changed, 21 insertions(+), 8 deletions(-)

diff --git a/src/Energy/CMAP.cpp b/src/Energy/CMAP.cpp
index 6bc9b7b143..c609766209 100644
--- a/src/Energy/CMAP.cpp
+++ b/src/Energy/CMAP.cpp
@@ -41,6 +41,18 @@ static inline void print_grad(Vec3 const& dA, Vec3 const& dB, Vec3 const& dC, Ve
 /** Calculate CMAP energy */
 double CMAP::Ene_CMAP(CmapArray const& Cmaps, Frame const& frameIn)
 const
+{
+    Vec3 dPhi_dijkl[4];
+    Vec3 dPsi_djklm[4];
+    double dPhi, dPsi;
+  return get_cmap_energy(Cmaps, frameIn, dPhi, dPsi, dPhi_dijkl, dPsi_djklm);
+}
+
+/** Calculate CMAP energy and partial derivatives */
+double CMAP::get_cmap_energy(CmapArray const& Cmaps, Frame const& frameIn,
+                             double& dPhi, double& dPsi,
+                             Vec3(&dPhi_dijkl)[4], Vec3(&dPsi_djklm)[4])
+const
 {
   double ene_cmap = 0.0;
 
@@ -56,29 +68,26 @@ const
     // Calculate the dihedral angle (phi) and the derivatives of the
     // four coordinates with respect to phi. Remember this subroutine is
     // operating in radians.
-    Vec3 dAphi, dBphi, dCphi, dDphi;
     double cosphi_ijkl, sinphi_ijkl;
     Torsion_and_part_deriv( ixyz, jxyz, kxyz, lxyz,
-                            dAphi, dBphi, dCphi, dDphi,
+                            dPhi_dijkl[0], dPhi_dijkl[1], dPhi_dijkl[2], dPhi_dijkl[3],
                             cosphi_ijkl, sinphi_ijkl );
-    print_grad(dAphi, dBphi, dCphi, dDphi);
-    mprintf("%30.15f\n", acos(cosphi_ijkl));
+    print_grad(dPhi_dijkl[0], dPhi_dijkl[1], dPhi_dijkl[2], dPhi_dijkl[3]);
+//    mprintf("%30.15f\n", acos(cosphi_ijkl));
     double phi = copysign(acos(cosphi_ijkl),sinphi_ijkl) * Constants::RADDEG;
     mprintf("DEBUG: Dihedral 1 %i %i %i %i = %30.15f%30.15f%30.15f\n", cmap->A1()+1, cmap->A2()+1, cmap->A3()+1, cmap->A4()+1, phi, cosphi_ijkl, sinphi_ijkl);
 
     // Calculate the dihedral angle (psi) and the derivatives of the
     // four coordinates with respect to psi. Remember this subroutine is
     // operating in radians.
-    Vec3 dApsi, dBpsi, dCpsi, dDpsi;
     double cospsi_jklm, sinpsi_jklm;
     Torsion_and_part_deriv( jxyz, kxyz, lxyz, mxyz,
-                            dApsi, dBpsi, dCpsi, dDpsi,
+                            dPsi_djklm[0], dPsi_djklm[1], dPsi_djklm[2], dPsi_djklm[3],
                             cospsi_jklm, sinpsi_jklm );
-    print_grad(dApsi, dBpsi, dCpsi, dDpsi);
+    print_grad(dPsi_djklm[0], dPsi_djklm[1], dPsi_djklm[2], dPsi_djklm[3]);
     double psi = copysign(acos(cospsi_jklm),sinpsi_jklm) * Constants::RADDEG;
     mprintf("DEBUG: Dihedral 2 %i %i %i %i = %30.15f%30.15f%30.15f\n", cmap->A2()+1, cmap->A3()+1, cmap->A4()+1, cmap->A5()+1, psi, cospsi_jklm, sinpsi_jklm);
 
-    double dPhi, dPsi;
     ene_cmap = charmm_calc_cmap_from_phi_psi(phi, psi, cmap->Idx(), dPhi, dPsi);
   }
   return ene_cmap;
diff --git a/src/Energy/CMAP.h b/src/Energy/CMAP.h
index bd43b76970..d123afb68e 100644
--- a/src/Energy/CMAP.h
+++ b/src/Energy/CMAP.h
@@ -6,6 +6,7 @@ class CmapArray;
 class CmapGridArray;
 class Frame;
 class Topology;
+class Vec3;
 namespace Cpptraj {
 namespace Energy {
 /// Implement CMAP energy term
@@ -18,6 +19,9 @@ class CMAP {
     /// Calculate CMAP energy
     double Ene_CMAP(CmapArray const&, Frame const&) const;
   private:
+    double get_cmap_energy(CmapArray const&, Frame const&, double&, double&,
+                             Vec3(&dPhi_dijkl)[4], Vec3(&dPsi_djklm)[4]) const;
+
     double charmm_calc_cmap_from_phi_psi(double, double, int, double&, double&) const;
     static double evaluate_cubic_spline(int, std::vector<double> const&, std::vector<double> const&, int);
     int generate_cmap_derivatives(Topology const&);

From 6a09e3a49b790838ac8cbf8b1f293f27a2bf10ee Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 10 Feb 2026 16:20:05 -0500
Subject: [PATCH 1322/1492] DO the force calc

---
 src/Energy/CMAP.cpp | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/src/Energy/CMAP.cpp b/src/Energy/CMAP.cpp
index c609766209..9d0ab0952e 100644
--- a/src/Energy/CMAP.cpp
+++ b/src/Energy/CMAP.cpp
@@ -89,6 +89,35 @@ const
     mprintf("DEBUG: Dihedral 2 %i %i %i %i = %30.15f%30.15f%30.15f\n", cmap->A2()+1, cmap->A3()+1, cmap->A4()+1, cmap->A5()+1, psi, cospsi_jklm, sinpsi_jklm);
 
     ene_cmap = charmm_calc_cmap_from_phi_psi(phi, psi, cmap->Idx(), dPhi, dPsi);
+
+    // Do force calc
+    // Convert over to degrees per interval
+    CmapGridType const& cmapGrid = (*(cmapGridPtr_))[cmap->Idx()];
+    double rad_to_deg_coeff = Constants::RADDEG * 1 / (double)(360.0 / cmapGrid.Resolution());
+    for (unsigned int i = 0; i < 4; i++) {
+      dPhi_dijkl[i] *= rad_to_deg_coeff;
+      dPsi_djklm[i] *= rad_to_deg_coeff;
+      // Use chain rule to obtain the energy gradient wrt to coordinate
+      dPhi_dijkl[i] *= dPhi;
+      dPsi_djklm[i] *= dPsi;
+    }
+    mprintf("FINAL PHI\n");
+    for (unsigned int i = 0; i < 4; i++)
+      for (unsigned int j = 0; j < 3; j++)
+        mprintf("%16.8f\n", dPhi_dijkl[i][j]);
+    mprintf("FINAL PSI\n");
+    for (unsigned int i = 0; i < 4; i++)
+      for (unsigned int j = 0; j < 3; j++)
+        mprintf("%16.8f\n", dPsi_djklm[i][j]);
+
+    std::vector<Vec3> frc(5, Vec3(0.0));
+    for (int n = 0; n < 3; n++) {
+      frc[0][n] = -dPhi_dijkl[0][n];
+      frc[1][n] = -dPhi_dijkl[1][n] - dPsi_djklm[0][n];
+      frc[2][n] = -dPhi_dijkl[2][n] - dPsi_djklm[1][n];
+      frc[3][n] = -dPhi_dijkl[3][n] - dPsi_djklm[2][n];
+      frc[4][n] =                   - dPsi_djklm[3][n];
+    }
   }
   return ene_cmap;
 }
@@ -250,6 +279,7 @@ const
     dPsi = dPsi*phiFrac +( 3.0*c4*psiFrac + 2.0*c3 )*psiFrac + c2;
   }
   mprintf("FINAL %16.8f %16.8f %16.8f\n", ene_cmap, dPhi, dPsi);
+
   return ene_cmap;
 }
 

From 78dbd11d2db59076ce4a37448f3fab30ca1028cc Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 10 Feb 2026 18:42:50 -0500
Subject: [PATCH 1323/1492] Debug force write

---
 src/Energy/CMAP.cpp | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/src/Energy/CMAP.cpp b/src/Energy/CMAP.cpp
index 9d0ab0952e..3e96909107 100644
--- a/src/Energy/CMAP.cpp
+++ b/src/Energy/CMAP.cpp
@@ -117,6 +117,11 @@ const
       frc[2][n] = -dPhi_dijkl[2][n] - dPsi_djklm[1][n];
       frc[3][n] = -dPhi_dijkl[3][n] - dPsi_djklm[2][n];
       frc[4][n] =                   - dPsi_djklm[3][n];
+      mprintf("i %3i %16.8f\n", n, frc[0][n]);
+      mprintf("j %3i %16.8f\n", n, frc[1][n]);
+      mprintf("k %3i %16.8f\n", n, frc[2][n]);
+      mprintf("l %3i %16.8f\n", n, frc[3][n]);
+      mprintf("m %3i %16.8f\n", n, frc[4][n]);
     }
   }
   return ene_cmap;

From f012339a9d8d262e289a640c96e7e6b77e734f69 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 10 Feb 2026 18:49:55 -0500
Subject: [PATCH 1324/1492] Need to sum energy

---
 src/Energy/CMAP.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Energy/CMAP.cpp b/src/Energy/CMAP.cpp
index 3e96909107..051b6be2a7 100644
--- a/src/Energy/CMAP.cpp
+++ b/src/Energy/CMAP.cpp
@@ -88,7 +88,7 @@ const
     double psi = copysign(acos(cospsi_jklm),sinpsi_jklm) * Constants::RADDEG;
     mprintf("DEBUG: Dihedral 2 %i %i %i %i = %30.15f%30.15f%30.15f\n", cmap->A2()+1, cmap->A3()+1, cmap->A4()+1, cmap->A5()+1, psi, cospsi_jklm, sinpsi_jklm);
 
-    ene_cmap = charmm_calc_cmap_from_phi_psi(phi, psi, cmap->Idx(), dPhi, dPsi);
+    ene_cmap += charmm_calc_cmap_from_phi_psi(phi, psi, cmap->Idx(), dPhi, dPsi);
 
     // Do force calc
     // Convert over to degrees per interval

From 4439baa73ab485f7f2dc7b7b525e01524f3f2c43 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 11 Feb 2026 09:13:34 -0500
Subject: [PATCH 1325/1492] Create separate routines for force and force+energy

---
 src/Energy/CMAP.cpp | 60 ++++++++++++++++++++++++++++++++++++++++++---
 src/Energy/CMAP.h   |  6 +++--
 2 files changed, 60 insertions(+), 6 deletions(-)

diff --git a/src/Energy/CMAP.cpp b/src/Energy/CMAP.cpp
index 051b6be2a7..adeece144c 100644
--- a/src/Energy/CMAP.cpp
+++ b/src/Energy/CMAP.cpp
@@ -39,22 +39,74 @@ static inline void print_grad(Vec3 const& dA, Vec3 const& dB, Vec3 const& dC, Ve
 }
 
 /** Calculate CMAP energy */
-double CMAP::Ene_CMAP(CmapArray const& Cmaps, Frame const& frameIn)
+/*double CMAP::Ene_CMAP(CmapArray const& Cmaps, Frame const& frameIn)
 const
 {
     Vec3 dPhi_dijkl[4];
     Vec3 dPsi_djklm[4];
     double dPhi, dPsi;
   return get_cmap_energy(Cmaps, frameIn, dPhi, dPsi, dPhi_dijkl, dPsi_djklm);
-}
+}*/
 
 /** Calculate CMAP energy and partial derivatives */
-double CMAP::get_cmap_energy(CmapArray const& Cmaps, Frame const& frameIn,
+/*double CMAP::get_cmap_energy(CmapArray const& Cmaps, Frame const& frameIn,
                              double& dPhi, double& dPsi,
-                             Vec3(&dPhi_dijkl)[4], Vec3(&dPsi_djklm)[4])
+                             Vec3(&dPhi_dijkl)[4], Vec3(&dPsi_djklm)[4])*/
+
+/** Calculate CMAP energy */
+double CMAP::Ene_CMAP(CmapArray const& Cmaps, Frame const& frameIn)
+const
+{
+  double ene_cmap = 0.0;
+  Vec3 dPhi_dijkl[4];
+  Vec3 dPsi_djklm[4];
+  double dPhi, dPsi;
+
+  for (CmapArray::const_iterator cmap = Cmaps.begin();
+                                 cmap != Cmaps.end(); ++cmap)
+  {
+    const double* ixyz = frameIn.XYZ( cmap->A1() );
+    const double* jxyz = frameIn.XYZ( cmap->A2() );
+    const double* kxyz = frameIn.XYZ( cmap->A3() );
+    const double* lxyz = frameIn.XYZ( cmap->A4() );
+    const double* mxyz = frameIn.XYZ( cmap->A5() );
+
+    // Calculate the dihedral angle (phi) and the derivatives of the
+    // four coordinates with respect to phi. Remember this subroutine is
+    // operating in radians.
+    double cosphi_ijkl, sinphi_ijkl;
+    Torsion_and_part_deriv( ixyz, jxyz, kxyz, lxyz,
+                            dPhi_dijkl[0], dPhi_dijkl[1], dPhi_dijkl[2], dPhi_dijkl[3],
+                            cosphi_ijkl, sinphi_ijkl );
+    print_grad(dPhi_dijkl[0], dPhi_dijkl[1], dPhi_dijkl[2], dPhi_dijkl[3]);
+//    mprintf("%30.15f\n", acos(cosphi_ijkl));
+    double phi = copysign(acos(cosphi_ijkl),sinphi_ijkl) * Constants::RADDEG;
+    mprintf("DEBUG: Dihedral 1 %i %i %i %i = %30.15f%30.15f%30.15f\n", cmap->A1()+1, cmap->A2()+1, cmap->A3()+1, cmap->A4()+1, phi, cosphi_ijkl, sinphi_ijkl);
+
+    // Calculate the dihedral angle (psi) and the derivatives of the
+    // four coordinates with respect to psi. Remember this subroutine is
+    // operating in radians.
+    double cospsi_jklm, sinpsi_jklm;
+    Torsion_and_part_deriv( jxyz, kxyz, lxyz, mxyz,
+                            dPsi_djklm[0], dPsi_djklm[1], dPsi_djklm[2], dPsi_djklm[3],
+                            cospsi_jklm, sinpsi_jklm );
+    print_grad(dPsi_djklm[0], dPsi_djklm[1], dPsi_djklm[2], dPsi_djklm[3]);
+    double psi = copysign(acos(cospsi_jklm),sinpsi_jklm) * Constants::RADDEG;
+    mprintf("DEBUG: Dihedral 2 %i %i %i %i = %30.15f%30.15f%30.15f\n", cmap->A2()+1, cmap->A3()+1, cmap->A4()+1, cmap->A5()+1, psi, cospsi_jklm, sinpsi_jklm);
+
+    ene_cmap += charmm_calc_cmap_from_phi_psi(phi, psi, cmap->Idx(), dPhi, dPsi);
+  } // END loop over CMAPs
+  return ene_cmap;
+}
+
+/** Calculate CMAP energy and force */
+double CMAP::Ene_Frc_CMAP(CmapArray const& Cmaps, Frame const& frameIn)
 const
 {
   double ene_cmap = 0.0;
+  Vec3 dPhi_dijkl[4];
+  Vec3 dPsi_djklm[4];
+  double dPhi, dPsi;
 
   for (CmapArray::const_iterator cmap = Cmaps.begin();
                                  cmap != Cmaps.end(); ++cmap)
diff --git a/src/Energy/CMAP.h b/src/Energy/CMAP.h
index d123afb68e..2b5f644aec 100644
--- a/src/Energy/CMAP.h
+++ b/src/Energy/CMAP.h
@@ -18,9 +18,11 @@ class CMAP {
     int Setup_CMAP_Ene(Topology const&);
     /// Calculate CMAP energy
     double Ene_CMAP(CmapArray const&, Frame const&) const;
+    /// Calculate CMAP energy and force
+    double Ene_Frc_CMAP(CmapArray const&, Frame const&) const;
   private:
-    double get_cmap_energy(CmapArray const&, Frame const&, double&, double&,
-                             Vec3(&dPhi_dijkl)[4], Vec3(&dPsi_djklm)[4]) const;
+    //double get_cmap_energy(CmapArray const&, Frame const&, double&, double&,
+    //                         Vec3(&dPhi_dijkl)[4], Vec3(&dPsi_djklm)[4]) const;
 
     double charmm_calc_cmap_from_phi_psi(double, double, int, double&, double&) const;
     static double evaluate_cubic_spline(int, std::vector<double> const&, std::vector<double> const&, int);

From 0cf5ce162bcc08bcf7f7093b566f892a36c6811f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 11 Feb 2026 09:22:03 -0500
Subject: [PATCH 1326/1492] Make a common function to return number of possible
 selected atoms in mask, Natom(). Create function to check if all atoms are
 selected.

---
 src/Action_HydrogenBond.cpp | 2 +-
 src/AtomMask.h              | 2 +-
 src/MaskToken.h             | 4 ++++
 3 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/src/Action_HydrogenBond.cpp b/src/Action_HydrogenBond.cpp
index adbe7f7f95..65a116f539 100644
--- a/src/Action_HydrogenBond.cpp
+++ b/src/Action_HydrogenBond.cpp
@@ -379,7 +379,7 @@ Action::RetType Action_HydrogenBond::Setup(ActionSetup& setup) {
       if (!setup.Top().Mol(molnum).IsSolvent() && IsFON( setup.Top()[*at] ))
         AcceptorMask_.AddSelectedAtom( *at );
     }
-    AcceptorMask_.SetNatoms( Mask_.NmaskAtoms() );
+    AcceptorMask_.SetNatoms( Mask_.Natom() );
   }
   int lastAcceptor = -1;
   if (!AcceptorMask_.None())
diff --git a/src/AtomMask.h b/src/AtomMask.h
index 2d4d8000f1..ff1f73df14 100644
--- a/src/AtomMask.h
+++ b/src/AtomMask.h
@@ -45,7 +45,7 @@ class AtomMask : public MaskTokenArray {
     /// \return selected atom at idx
     const int& operator[](int idx)      const { return Selected_[idx];        }
     /// \return Number of atoms from corresponding topology.
-    int NmaskAtoms()                    const { return Natom_;                }
+    int Natom()                         const { return Natom_;                }
     /// Flip current mask expression.
     void InvertMaskExpression();
     /// Invert current mask
diff --git a/src/MaskToken.h b/src/MaskToken.h
index e7d9972b3f..a21990f8ff 100644
--- a/src/MaskToken.h
+++ b/src/MaskToken.h
@@ -84,9 +84,13 @@ class MaskTokenArray {
     virtual void InvertMask() = 0;
     /// \return Number of selected atoms.
     virtual int Nselected() const = 0;
+    /// \return Max number of potentially selected atoms (# atoms in topology).
+    virtual int Natom() const = 0;
     // -------------------------------------------
     /// \return true if no atoms selected
     bool None() const { return Nselected() == 0; }
+    /// \return true if all possible atoms selected
+    bool All()  const { return Nselected() == Natom(); }
   protected:
     void ClearTokens() { maskTokens_.clear(); maskExpression_.clear(); }
     /// \return array of characters with selected atoms marked with SelectedChar_

From 368cff67c5b942483f210d70f6e2abdc5da72798 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 11 Feb 2026 09:38:55 -0500
Subject: [PATCH 1327/1492] Respect mask selection

---
 src/Energy/CMAP.cpp     | 66 +++++++++++++++++++++++++++++++++++++++--
 src/Energy/CMAP.h       | 14 +++++++--
 src/Energy/energydepend |  2 +-
 src/cpptrajdepend       |  2 +-
 4 files changed, 76 insertions(+), 8 deletions(-)

diff --git a/src/Energy/CMAP.cpp b/src/Energy/CMAP.cpp
index adeece144c..c06f92f7e8 100644
--- a/src/Energy/CMAP.cpp
+++ b/src/Energy/CMAP.cpp
@@ -1,5 +1,6 @@
 #include "CMAP.h"
-#include "../CpptrajStdio.h" // DEBUG
+#include "../CharMask.h"
+#include "../CpptrajStdio.h"
 #include "../Frame.h"
 #include "../ParameterTypes.h"
 #include "../Topology.h"
@@ -8,9 +9,17 @@
 using namespace Cpptraj::Energy;
 
 /** CONSTRUCTOR */
-CMAP::CMAP() : cmapGridPtr_(0)
+CMAP::CMAP() :
+  cmapGridPtr_(0),
+  selected_cmaps_(0),
+  all_cmaps_(0)
 {}
 
+/** DESTRUCTOR */
+CMAP::~CMAP() {
+  if (selected_cmaps_ != 0) delete selected_cmaps_;
+}
+
 /** The weight matrix */
 const int CMAP::wt_[16][16] = {
   {1, 0, -3,  2, 0, 0,  0,  0, -3,  0,  9, -6,  2,  0, -6,  4},
@@ -53,6 +62,16 @@ const
                              double& dPhi, double& dPsi,
                              Vec3(&dPhi_dijkl)[4], Vec3(&dPsi_djklm)[4])*/
 
+/** Calculate CMAP energy */
+double CMAP::Ene_CMAP(Frame const& frameIn)
+const
+{
+  if ( all_cmaps_ != 0)
+    return Ene_CMAP( *all_cmaps_, frameIn );
+  else
+    return Ene_CMAP( *selected_cmaps_, frameIn );
+}
+
 /** Calculate CMAP energy */
 double CMAP::Ene_CMAP(CmapArray const& Cmaps, Frame const& frameIn)
 const
@@ -99,6 +118,16 @@ const
   return ene_cmap;
 }
 
+/** Calculate CMAP energy and force */
+double CMAP::Ene_Frc_CMAP(Frame const& frameIn)
+const
+{
+  if ( all_cmaps_ != 0)
+    return Ene_Frc_CMAP( *all_cmaps_, frameIn );
+  else
+    return Ene_Frc_CMAP( *selected_cmaps_, frameIn );
+}
+
 /** Calculate CMAP energy and force */
 double CMAP::Ene_Frc_CMAP(CmapArray const& Cmaps, Frame const& frameIn)
 const
@@ -550,7 +579,11 @@ int CMAP::generate_cmap_derivatives(Topology const& topIn)
 }
 
 /** Set up CMAP-related terms */
-int CMAP::Setup_CMAP_Ene(Topology const& topIn) {
+int CMAP::Setup_CMAP_Ene(Topology const& topIn, CharMask const& cmask) {
+  if (selected_cmaps_ != 0) delete selected_cmaps_;
+  selected_cmaps_ = 0;
+  all_cmaps_ = 0;
+
   if (!topIn.HasCmap()) {
     mprintf("Warning: No CMAP parameters in '%s'\n", topIn.c_str());
     return 0;
@@ -561,5 +594,32 @@ int CMAP::Setup_CMAP_Ene(Topology const& topIn) {
     return 1;
   }
 
+  if (cmask.All()) {
+    mprintf("\tAll CMAPs will be selected.\n");
+    all_cmaps_ = &(topIn.Cmap());
+    mprintf("\t%zu CMAPs.\n", all_cmaps_->size());
+  } else {
+    selected_cmaps_ = new CmapArray();
+    for (CmapArray::const_iterator cmap = topIn.Cmap().begin();
+                                   cmap != topIn.Cmap().end(); ++cmap)
+    {
+      if ( cmask.AtomInCharMask(cmap->A1()) &&
+           cmask.AtomInCharMask(cmap->A2()) &&
+           cmask.AtomInCharMask(cmap->A3()) &&
+           cmask.AtomInCharMask(cmap->A4()) &&
+           cmask.AtomInCharMask(cmap->A5()) )
+      {
+        mprintf("\t\tSelecting CMAP %s - %s - %s - %s - %s\n",
+                topIn.AtomMaskName(cmap->A1()).c_str(),
+                topIn.AtomMaskName(cmap->A2()).c_str(),
+                topIn.AtomMaskName(cmap->A3()).c_str(),
+                topIn.AtomMaskName(cmap->A4()).c_str(),
+                topIn.AtomMaskName(cmap->A5()).c_str());
+        selected_cmaps_->push_back( *cmap );
+      }
+    }
+    mprintf("\t%zu CMAPs.\n", selected_cmaps_->size());
+  }
+
   return 0;
 }
diff --git a/src/Energy/CMAP.h b/src/Energy/CMAP.h
index 2b5f644aec..fca888aa3a 100644
--- a/src/Energy/CMAP.h
+++ b/src/Energy/CMAP.h
@@ -2,6 +2,7 @@
 #define INC_ENERGY_CMAP_H
 #include <vector>
 #include "../Matrix.h"
+class CharMask;
 class CmapArray;
 class CmapGridArray;
 class Frame;
@@ -13,16 +14,21 @@ namespace Energy {
 class CMAP {
   public:
     CMAP();
+    ~CMAP();
 
     /// Setup CMAP splines etc
-    int Setup_CMAP_Ene(Topology const&);
+    int Setup_CMAP_Ene(Topology const&, CharMask const&);
     /// Calculate CMAP energy
-    double Ene_CMAP(CmapArray const&, Frame const&) const;
+    double Ene_CMAP(Frame const&) const;
     /// Calculate CMAP energy and force
-    double Ene_Frc_CMAP(CmapArray const&, Frame const&) const;
+    double Ene_Frc_CMAP(Frame const&) const;
   private:
     //double get_cmap_energy(CmapArray const&, Frame const&, double&, double&,
     //                         Vec3(&dPhi_dijkl)[4], Vec3(&dPsi_djklm)[4]) const;
+    /// Calculate CMAP energy
+    double Ene_CMAP(CmapArray const&, Frame const&) const;
+    /// Calculate CMAP energy and force
+    double Ene_Frc_CMAP(CmapArray const&, Frame const&) const;
 
     double charmm_calc_cmap_from_phi_psi(double, double, int, double&, double&) const;
     static double evaluate_cubic_spline(int, std::vector<double> const&, std::vector<double> const&, int);
@@ -36,6 +42,8 @@ class CMAP {
     DMarray cmap_dPsi_; ///< Hold dE/dPsi for each CMAP grid
     DMarray cmap_dPhi_dPsi_; ///< Hold d^2E/dPhidPsi for each CMAP grid
     CmapGridArray const* cmapGridPtr_; ///< Pointer to CMAP grids this was set up with.
+    CmapArray* selected_cmaps_; ///< Hold cmaps to calculate energy for if not all selected.
+    CmapArray const* all_cmaps_; ///< Pointer to CMAP array in Topology when all selected.
 
     static const int wt_[16][16]; ///< Weight matrix
 };
diff --git a/src/Energy/energydepend b/src/Energy/energydepend
index 33d57d250a..59677fcaf9 100644
--- a/src/Energy/energydepend
+++ b/src/Energy/energydepend
@@ -1,4 +1,4 @@
-CMAP.o : CMAP.cpp ../ArrayIterator.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../Unit.h ../Vec3.h CMAP.h
+CMAP.o : CMAP.cpp ../ArrayIterator.h ../Atom.h ../AtomMask.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../Unit.h ../Vec3.h CMAP.h
 Ecalc_Nonbond.o : Ecalc_Nonbond.cpp ../Atom.h ../AtomMask.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../Energy/../Constants.h ../Energy/../ParameterTypes.h ../Energy/../SplineFxnTable.h ../Energy/Ene_LJPME_6_12.h ../Energy/Ene_LJ_12_6_4.h ../Energy/Ene_LJ_6_12.h ../Energy/ErfcFxn.h ../Energy/EwaldParams.h ../Energy/EwaldParams_LJPME.h ../Energy/Kernel_EwaldAdjust.h ../Energy/Kernel_LJPME_Adjust.h ../EwaldOptions.h ../ExclusionArray.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../PairList.h ../PairListEngine_Ewald_Decomp_LJCLR.h ../PairListEngine_Ewald_Decomp_LJLR.h ../PairListEngine_Ewald_Decomp_LJPME.h ../PairListEngine_Ewald_LJCLR.h ../PairListEngine_Ewald_LJLR.h ../PairListEngine_Ewald_LJPME.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h ../helpme_standalone.h Ecalc_Nonbond.h Ene_Decomp_Nonbond.h Ene_LJ_6_12.h Ene_Nonbond.h EwaldCalc.h EwaldCalc_Decomp.h EwaldCalc_Decomp_LJCPME.h EwaldCalc_Decomp_LJPME.h EwaldCalc_Decomp_PME.h EwaldCalc_LJCPME.h EwaldCalc_LJPME.h EwaldCalc_PME.h EwaldCalc_Regular.h Ewald_Recip.h PME_Recip.h PME_RecipParams.h VDW_LongRange_Correction.h
 EnergyDecomposer.o : EnergyDecomposer.cpp ../ArgList.h ../AssociatedData.h ../Atom.h ../AtomMask.h ../BaseIOtype.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataFile.h ../DataFileList.h ../DataSet.h ../DataSetList.h ../DataSet_1D.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../DataSet_Mesh.h ../Dimension.h ../DistRoutines.h ../EwaldOptions.h ../ExclusionArray.h ../FileIO.h ../FileName.h ../FileTypes.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../OnlineVarT.h ../PairList.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Spline.h ../Stats_Reduce.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../TorsionRoutines.h ../Unit.h ../Vec3.h Ecalc_Nonbond.h Ene_Angle.h Ene_Bond.h Ene_LJ_6_12.h EnergyDecomposer.h Kernel_Fourier.h Kernel_Harmonic.h
 ErfcFxn.o : ErfcFxn.cpp ../CpptrajStdio.h ../SplineFxnTable.h ErfcFxn.h
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 4e5d1cb6f4..6d81805955 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -288,7 +288,7 @@ DihedralSearch.o : DihedralSearch.cpp ArgList.h Atom.h AtomMask.h Box.h Constant
 DistRoutines.o : DistRoutines.cpp Box.h DistRoutines.h ImageOption.h Matrix_3x3.h Parallel.h Vec3.h
 Dist_Imaged.o : Dist_Imaged.cpp Dist_Imaged.h Matrix_3x3.h Parallel.h Vec3.h
 Energy.o : Energy.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h Energy.h Energy/Ene_Angle.h Energy/Ene_Bond.h Energy/Ene_LJ_12_6_4.h Energy/Ene_LJ_6_12.h Energy/Kernel_Harmonic.h ExclusionArray.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TorsionRoutines.h Unit.h Vec3.h
-Energy/CMAP.o : Energy/CMAP.cpp ArrayIterator.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy/CMAP.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TorsionRoutines.h Unit.h Vec3.h
+Energy/CMAP.o : Energy/CMAP.cpp ArrayIterator.h Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy/CMAP.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TorsionRoutines.h Unit.h Vec3.h
 Energy/Ecalc_Nonbond.o : Energy/Ecalc_Nonbond.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy/Ecalc_Nonbond.h Energy/Ene_Decomp_Nonbond.h Energy/Ene_LJPME_6_12.h Energy/Ene_LJ_12_6_4.h Energy/Ene_LJ_6_12.h Energy/Ene_Nonbond.h Energy/ErfcFxn.h Energy/EwaldCalc.h Energy/EwaldCalc_Decomp.h Energy/EwaldCalc_Decomp_LJCPME.h Energy/EwaldCalc_Decomp_LJPME.h Energy/EwaldCalc_Decomp_PME.h Energy/EwaldCalc_LJCPME.h Energy/EwaldCalc_LJPME.h Energy/EwaldCalc_PME.h Energy/EwaldCalc_Regular.h Energy/EwaldParams.h Energy/EwaldParams_LJPME.h Energy/Ewald_Recip.h Energy/Kernel_EwaldAdjust.h Energy/Kernel_LJPME_Adjust.h Energy/PME_Recip.h Energy/PME_RecipParams.h Energy/VDW_LongRange_Correction.h EwaldOptions.h ExclusionArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h PairListEngine_Ewald_Decomp_LJCLR.h PairListEngine_Ewald_Decomp_LJLR.h PairListEngine_Ewald_Decomp_LJPME.h PairListEngine_Ewald_LJCLR.h PairListEngine_Ewald_LJLR.h PairListEngine_Ewald_LJPME.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h Timer.h Topology.h Unit.h Vec3.h helpme_standalone.h
 Energy/EnergyDecomposer.o : Energy/EnergyDecomposer.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DistRoutines.h Energy/Ecalc_Nonbond.h Energy/Ene_Angle.h Energy/Ene_Bond.h Energy/Ene_LJ_6_12.h Energy/EnergyDecomposer.h Energy/Kernel_Fourier.h Energy/Kernel_Harmonic.h EwaldOptions.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h PairList.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h Stats_Reduce.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h Unit.h Vec3.h
 Energy/ErfcFxn.o : Energy/ErfcFxn.cpp CpptrajStdio.h Energy/ErfcFxn.h SplineFxnTable.h

From a0af5104e7a837543e5b28acd2af7575270b1bdd Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 11 Feb 2026 09:47:34 -0500
Subject: [PATCH 1328/1492] Print selected cmaps

---
 src/Action_Energy.cpp |  4 ++--
 src/Energy/CMAP.cpp   | 19 ++++++++++++-------
 2 files changed, 14 insertions(+), 9 deletions(-)

diff --git a/src/Action_Energy.cpp b/src/Action_Energy.cpp
index ed4a4dbed0..724f57a1d0 100644
--- a/src/Action_Energy.cpp
+++ b/src/Action_Energy.cpp
@@ -366,7 +366,7 @@ Action::RetType Action_Energy::Setup(ActionSetup& setup) {
   Imask_ = AtomMask(Mask1_.ConvertToIntMask(), Mask1_.Natom());
   // CMAP
   if (cmap_ != 0) {
-    if (cmap_->Setup_CMAP_Ene(setup.Top())) {
+    if (cmap_->Setup_CMAP_Ene(setup.Top(), Mask1_)) {
       mprinterr("Error: CMAP setup failed.\n");
       return Action::ERR;
     }
@@ -483,7 +483,7 @@ Action::RetType Action_Energy::DoAction(int frameNum, ActionFrame& frm) {
         break;
       case C_CMAP:
         time_cmap_.Start();
-        ene = cmap_->Ene_CMAP(currentParm_->Cmap(), frm.Frm());
+        ene = cmap_->Ene_CMAP(frm.Frm());
         time_cmap_.Stop();
         Energy_[CMAP]->Add(frameNum, &ene);
         Etot += ene;
diff --git a/src/Energy/CMAP.cpp b/src/Energy/CMAP.cpp
index c06f92f7e8..f57b95ace1 100644
--- a/src/Energy/CMAP.cpp
+++ b/src/Energy/CMAP.cpp
@@ -594,12 +594,15 @@ int CMAP::Setup_CMAP_Ene(Topology const& topIn, CharMask const& cmask) {
     return 1;
   }
 
+  CmapArray const* cmaparray = 0;
   if (cmask.All()) {
     mprintf("\tAll CMAPs will be selected.\n");
     all_cmaps_ = &(topIn.Cmap());
+    cmaparray = all_cmaps_;
     mprintf("\t%zu CMAPs.\n", all_cmaps_->size());
   } else {
     selected_cmaps_ = new CmapArray();
+    cmaparray = (CmapArray const*)selected_cmaps_;
     for (CmapArray::const_iterator cmap = topIn.Cmap().begin();
                                    cmap != topIn.Cmap().end(); ++cmap)
     {
@@ -609,17 +612,19 @@ int CMAP::Setup_CMAP_Ene(Topology const& topIn, CharMask const& cmask) {
            cmask.AtomInCharMask(cmap->A4()) &&
            cmask.AtomInCharMask(cmap->A5()) )
       {
-        mprintf("\t\tSelecting CMAP %s - %s - %s - %s - %s\n",
-                topIn.AtomMaskName(cmap->A1()).c_str(),
-                topIn.AtomMaskName(cmap->A2()).c_str(),
-                topIn.AtomMaskName(cmap->A3()).c_str(),
-                topIn.AtomMaskName(cmap->A4()).c_str(),
-                topIn.AtomMaskName(cmap->A5()).c_str());
         selected_cmaps_->push_back( *cmap );
       }
     }
     mprintf("\t%zu CMAPs.\n", selected_cmaps_->size());
   }
-
+  for (CmapArray::const_iterator cmap = cmaparray->begin(); cmap != cmaparray->end(); ++cmap)
+  {
+    mprintf("\t\tSelecting CMAP %s - %s - %s - %s - %s\n",
+            topIn.AtomMaskName(cmap->A1()).c_str(),
+            topIn.AtomMaskName(cmap->A2()).c_str(),
+            topIn.AtomMaskName(cmap->A3()).c_str(),
+            topIn.AtomMaskName(cmap->A4()).c_str(),
+            topIn.AtomMaskName(cmap->A5()).c_str());
+  }
   return 0;
 }

From 90c809588063b105e53ca6f4bce525274bad0fd4 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 11 Feb 2026 10:10:55 -0500
Subject: [PATCH 1329/1492] Improve code docs. Hide some debug info. Pass in
 force array for force calc

---
 src/Energy/CMAP.cpp | 63 ++++++++++++++++++++++++++++++++++++++-------
 src/Energy/CMAP.h   | 12 ++++++---
 2 files changed, 63 insertions(+), 12 deletions(-)

diff --git a/src/Energy/CMAP.cpp b/src/Energy/CMAP.cpp
index f57b95ace1..2c78c804e1 100644
--- a/src/Energy/CMAP.cpp
+++ b/src/Energy/CMAP.cpp
@@ -40,12 +40,14 @@ const int CMAP::wt_[16][16] = {
   {0, 0,  0,  0, 0, 0, -1,  1,  0,  0,  2, -2,  0,  0, -1,  1}
 };
 
+#ifdef DEBUG_CPPTRAJ_CMAP
 /// DEBUG - print gradients
 static inline void print_grad(Vec3 const& dA, Vec3 const& dB, Vec3 const& dC, Vec3 const& dD)
 {
   for (int i = 0; i < 3; i++)
     mprintf("DEBUG:\t\tdX %12.4f%12.4f%12.4f%12.4f\n", dA[i], dB[i], dC[i], dD[i]);
 }
+#endif
 
 /** Calculate CMAP energy */
 /*double CMAP::Ene_CMAP(CmapArray const& Cmaps, Frame const& frameIn)
@@ -97,11 +99,14 @@ const
     Torsion_and_part_deriv( ixyz, jxyz, kxyz, lxyz,
                             dPhi_dijkl[0], dPhi_dijkl[1], dPhi_dijkl[2], dPhi_dijkl[3],
                             cosphi_ijkl, sinphi_ijkl );
+#   ifdef DEBUG_CPPTRAJ_CMAP
     print_grad(dPhi_dijkl[0], dPhi_dijkl[1], dPhi_dijkl[2], dPhi_dijkl[3]);
+#   endif
 //    mprintf("%30.15f\n", acos(cosphi_ijkl));
     double phi = copysign(acos(cosphi_ijkl),sinphi_ijkl) * Constants::RADDEG;
+#   ifdef DEBUG_CPPTRAJ_CMAP
     mprintf("DEBUG: Dihedral 1 %i %i %i %i = %30.15f%30.15f%30.15f\n", cmap->A1()+1, cmap->A2()+1, cmap->A3()+1, cmap->A4()+1, phi, cosphi_ijkl, sinphi_ijkl);
-
+#   endif
     // Calculate the dihedral angle (psi) and the derivatives of the
     // four coordinates with respect to psi. Remember this subroutine is
     // operating in radians.
@@ -109,27 +114,30 @@ const
     Torsion_and_part_deriv( jxyz, kxyz, lxyz, mxyz,
                             dPsi_djklm[0], dPsi_djklm[1], dPsi_djklm[2], dPsi_djklm[3],
                             cospsi_jklm, sinpsi_jklm );
+#   ifdef DEBUG_CPPTRAJ_CMAP
     print_grad(dPsi_djklm[0], dPsi_djklm[1], dPsi_djklm[2], dPsi_djklm[3]);
+#   endif
     double psi = copysign(acos(cospsi_jklm),sinpsi_jklm) * Constants::RADDEG;
+#   ifdef DEBUG_CPPTRAJ_CMAP
     mprintf("DEBUG: Dihedral 2 %i %i %i %i = %30.15f%30.15f%30.15f\n", cmap->A2()+1, cmap->A3()+1, cmap->A4()+1, cmap->A5()+1, psi, cospsi_jklm, sinpsi_jklm);
-
+#   endif
     ene_cmap += charmm_calc_cmap_from_phi_psi(phi, psi, cmap->Idx(), dPhi, dPsi);
   } // END loop over CMAPs
   return ene_cmap;
 }
 
 /** Calculate CMAP energy and force */
-double CMAP::Ene_Frc_CMAP(Frame const& frameIn)
+double CMAP::Ene_Frc_CMAP(Frame const& frameIn, double* forcePtr)
 const
 {
   if ( all_cmaps_ != 0)
-    return Ene_Frc_CMAP( *all_cmaps_, frameIn );
+    return Ene_Frc_CMAP( *all_cmaps_, frameIn, forcePtr );
   else
-    return Ene_Frc_CMAP( *selected_cmaps_, frameIn );
+    return Ene_Frc_CMAP( *selected_cmaps_, frameIn, forcePtr );
 }
 
 /** Calculate CMAP energy and force */
-double CMAP::Ene_Frc_CMAP(CmapArray const& Cmaps, Frame const& frameIn)
+double CMAP::Ene_Frc_CMAP(CmapArray const& Cmaps, Frame const& frameIn, double* forcePtr)
 const
 {
   double ene_cmap = 0.0;
@@ -153,11 +161,14 @@ const
     Torsion_and_part_deriv( ixyz, jxyz, kxyz, lxyz,
                             dPhi_dijkl[0], dPhi_dijkl[1], dPhi_dijkl[2], dPhi_dijkl[3],
                             cosphi_ijkl, sinphi_ijkl );
+#   ifdef DEBUG_CPPTRAJ_CMAP
     print_grad(dPhi_dijkl[0], dPhi_dijkl[1], dPhi_dijkl[2], dPhi_dijkl[3]);
+#   endif
 //    mprintf("%30.15f\n", acos(cosphi_ijkl));
     double phi = copysign(acos(cosphi_ijkl),sinphi_ijkl) * Constants::RADDEG;
+#   ifdef DEBUG_CPPTRAJ_CMAP
     mprintf("DEBUG: Dihedral 1 %i %i %i %i = %30.15f%30.15f%30.15f\n", cmap->A1()+1, cmap->A2()+1, cmap->A3()+1, cmap->A4()+1, phi, cosphi_ijkl, sinphi_ijkl);
-
+#   endif
     // Calculate the dihedral angle (psi) and the derivatives of the
     // four coordinates with respect to psi. Remember this subroutine is
     // operating in radians.
@@ -165,10 +176,13 @@ const
     Torsion_and_part_deriv( jxyz, kxyz, lxyz, mxyz,
                             dPsi_djklm[0], dPsi_djklm[1], dPsi_djklm[2], dPsi_djklm[3],
                             cospsi_jklm, sinpsi_jklm );
+#   ifdef DEBUG_CPPTRAJ_CMAP
     print_grad(dPsi_djklm[0], dPsi_djklm[1], dPsi_djklm[2], dPsi_djklm[3]);
+#   endif
     double psi = copysign(acos(cospsi_jklm),sinpsi_jklm) * Constants::RADDEG;
+#   ifdef DEBUG_CPPTRAJ_CMAP
     mprintf("DEBUG: Dihedral 2 %i %i %i %i = %30.15f%30.15f%30.15f\n", cmap->A2()+1, cmap->A3()+1, cmap->A4()+1, cmap->A5()+1, psi, cospsi_jklm, sinpsi_jklm);
-
+#   endif
     ene_cmap += charmm_calc_cmap_from_phi_psi(phi, psi, cmap->Idx(), dPhi, dPsi);
 
     // Do force calc
@@ -182,6 +196,7 @@ const
       dPhi_dijkl[i] *= dPhi;
       dPsi_djklm[i] *= dPsi;
     }
+#   ifdef DEBUG_CPPTRAJ_CMAP
     mprintf("FINAL PHI\n");
     for (unsigned int i = 0; i < 4; i++)
       for (unsigned int j = 0; j < 3; j++)
@@ -190,7 +205,8 @@ const
     for (unsigned int i = 0; i < 4; i++)
       for (unsigned int j = 0; j < 3; j++)
         mprintf("%16.8f\n", dPsi_djklm[i][j]);
-
+#   endif
+#   ifdef DEBUG_CPPTRAJ_CMAP
     std::vector<Vec3> frc(5, Vec3(0.0));
     for (int n = 0; n < 3; n++) {
       frc[0][n] = -dPhi_dijkl[0][n];
@@ -204,6 +220,19 @@ const
       mprintf("l %3i %16.8f\n", n, frc[3][n]);
       mprintf("m %3i %16.8f\n", n, frc[4][n]);
     }
+#   endif
+    double* fi = forcePtr + (cmap->A1() * 3);
+    double* fj = forcePtr + (cmap->A1() * 3);
+    double* fk = forcePtr + (cmap->A1() * 3);
+    double* fl = forcePtr + (cmap->A1() * 3);
+    double* fm = forcePtr + (cmap->A1() * 3);
+    for (int n = 0; n < 3; n++) {
+      fi[n] += -dPhi_dijkl[0][n];
+      fj[n] += -dPhi_dijkl[1][n] - dPsi_djklm[0][n];
+      fk[n] += -dPhi_dijkl[2][n] - dPsi_djklm[1][n];
+      fl[n] += -dPhi_dijkl[3][n] - dPsi_djklm[2][n];
+      fm[n] +=                   - dPsi_djklm[3][n];
+    }
   }
   return ene_cmap;
 }
@@ -443,7 +472,9 @@ void CMAP::generate_cubic_spline(int n, int step_size, std::vector<double> const
     y2[i]  = -0.5/p;
     tmp[i] = ( y[i+1]-2.0*y[i] + y[i-1] ) / (double)step_size;
     tmp[i] = ( 3.0* (tmp[i]/(double)step_size) - 0.5 *tmp[ i-1 ] )/p;
+#   ifdef DEBUG_CPPTRAJ_CMAP
     mprintf("%6i y2= %16.8f  tmp= %16.8f\n", i, y2[i], tmp[i]);
+#   endif
   }
 
   // Set the upper boundary
@@ -452,7 +483,9 @@ void CMAP::generate_cubic_spline(int n, int step_size, std::vector<double> const
   for (int i = n-2; i > -1; i--)
   {
     y2[i]=y2[i]*y2[i+1]+tmp[i];
+#   ifdef DEBUG_CPPTRAJ_CMAP
     mprintf("%6i %16.8f\n", i, y2[i]);
+#   endif
     //mprintf("\t\t\tn is %i:\n",n);
     //mprintf("\t\t\tStep size is : %i\n",step_size);
     //mprintf("\t\t\ty is : %f\n",y[i]);
@@ -507,10 +540,14 @@ int CMAP::generate_cmap_derivatives(Topology const& topIn)
       // It is possible CHARMM does this to avoid edge issues.
 
       unsigned int k=0; // index for tmpy array
+#     ifdef DEBUG_CPPTRAJ_CMAP
       mprintf("DEBUG: Row %6i from %6i to %6i\n", row, -halfRes, res+halfRes-1);
+#     endif
       for (int col = -halfRes; col < res+halfRes; col++) { // -12 to 35
         tmpy[k] = grid->Grid(col, row);
+#       ifdef DEBUG_CPPTRAJ_CMAP
         mprintf("DEBUG:\t\t%6i%12.4f\n", k, tmpy[k]);
+#       endif
         k++;
       }
 
@@ -533,10 +570,14 @@ int CMAP::generate_cmap_derivatives(Topology const& topIn)
       // Step across one column each cycle, splining up each column
 
       unsigned int k=0; // index for tmpy array
+#     ifdef DEBUG_CPPTRAJ_CMAP
       mprintf("DEBUG: Col %6i from %6i to %6i\n", col, -halfRes, res+halfRes-1);
+#     endif
       for (int row = -halfRes; row < res+halfRes; row++) { // -12 to 35
         tmpy[k] = grid->Grid(col, row);
+#       ifdef DEBUG_CPPTRAJ_CMAP
         mprintf("DEBUG:\t\t%6i%12.4f\n", k, tmpy[k]);
+#       endif
         k++;
       }
 
@@ -558,10 +599,14 @@ int CMAP::generate_cmap_derivatives(Topology const& topIn)
     for (int col = 0; col < res; col++)
     {
       unsigned int k=0;
+#     ifdef DEBUG_CPPTRAJ_CMAP
       mprintf("DEBUG: D2 %6i from %6i to %6i\n", col, -halfRes, res+halfRes-1);
+#     endif
       for (int row = -halfRes; row < res+halfRes; row++) { // -12 to 35
         tmpy[k] = cmap_dPhi_[gidx].element_wrapped(row, col);
+#       ifdef DEBUG_CPPTRAJ_CMAP
         mprintf("DEBUG:\t\t%6i%12.4f\n", k, tmpy[k]);
+#       endif
         k++;
       }
 
diff --git a/src/Energy/CMAP.h b/src/Energy/CMAP.h
index fca888aa3a..d906d2bed5 100644
--- a/src/Energy/CMAP.h
+++ b/src/Energy/CMAP.h
@@ -11,24 +11,30 @@ class Vec3;
 namespace Cpptraj {
 namespace Energy {
 /// Implement CMAP energy term
+/** This class implements the 2D dihedral energy grid correction map (CMAP)
+  * energy and force calculations: see MacKerell et. al JACS 2004 126 698-699.
+  * The code in this class is largely based off of the cmap.F90 file
+  * from the pmemd program of Amber, adapted to C++ by DRR.
+  * Compile with DEBUG_CPPTRAJ_CMAP for more detailed debug output.
+  */
 class CMAP {
   public:
     CMAP();
     ~CMAP();
 
-    /// Setup CMAP splines etc
+    /// Setup CMAP terms to be calculated, splines, etc
     int Setup_CMAP_Ene(Topology const&, CharMask const&);
     /// Calculate CMAP energy
     double Ene_CMAP(Frame const&) const;
     /// Calculate CMAP energy and force
-    double Ene_Frc_CMAP(Frame const&) const;
+    double Ene_Frc_CMAP(Frame const&, double*) const;
   private:
     //double get_cmap_energy(CmapArray const&, Frame const&, double&, double&,
     //                         Vec3(&dPhi_dijkl)[4], Vec3(&dPsi_djklm)[4]) const;
     /// Calculate CMAP energy
     double Ene_CMAP(CmapArray const&, Frame const&) const;
     /// Calculate CMAP energy and force
-    double Ene_Frc_CMAP(CmapArray const&, Frame const&) const;
+    double Ene_Frc_CMAP(CmapArray const&, Frame const&, double*) const;
 
     double charmm_calc_cmap_from_phi_psi(double, double, int, double&, double&) const;
     static double evaluate_cubic_spline(int, std::vector<double> const&, std::vector<double> const&, int);

From d114a1ff92f3340f6a0cc138a48422072ce95092 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 11 Feb 2026 10:16:42 -0500
Subject: [PATCH 1330/1492] Hide more debug info and remove old code

---
 src/Energy/CMAP.cpp | 83 +++++++++++++++------------------------------
 1 file changed, 27 insertions(+), 56 deletions(-)

diff --git a/src/Energy/CMAP.cpp b/src/Energy/CMAP.cpp
index 2c78c804e1..7ef7c95ad6 100644
--- a/src/Energy/CMAP.cpp
+++ b/src/Energy/CMAP.cpp
@@ -242,6 +242,7 @@ static inline double dmodulo(double a, double p) {
   return ( a - floor(a / p) * p );
 }
 
+#ifdef DEBUG_CPPTRAJ_CMAP
 static inline void print_stencil(const char* desc, const double (&matrix)[2][2])
 {
   mprintf("%s:\n", desc);
@@ -249,7 +250,17 @@ static inline void print_stencil(const char* desc, const double (&matrix)[2][2])
   mprintf("%9.6f %9.6f\n", matrix[0][0], matrix[0][1]);
   mprintf("\n");
 }
+#endif
 
+/// Convert the 2x2 stencils into a 1D array for processing by weight_stencil.
+/** The array starts at the bottom left of the 2x2, working
+  * around counterclockwise:
+  *
+  *          4 3
+  *          1 2
+  *
+  * NOTE: There may be a cleaner/better way of doing this
+  */
 static inline void flatten_stencil(double* out, const double(&matrix)[2][2], double step_size)
 {
   out[0] = matrix[0][0] * step_size;
@@ -270,18 +281,20 @@ const
   dPsi = 0.0;
   // Work out nearest complete grid point on the CMAP grid from
   // phi and psi and use this to form a 2x2 stencil
-  mprintf("x= %16.8f  y= %16.8f\n", (phi - gridOrigin)/(step_size),(psi - gridOrigin)/(step_size) );
+//  mprintf("x= %16.8f  y= %16.8f\n", (phi - gridOrigin)/(step_size),(psi - gridOrigin)/(step_size) );
   int x = (int)( (phi - gridOrigin)/(step_size) );
   int y = (int)( (psi - gridOrigin)/(step_size) );
+# ifdef DEBUG_CPPTRAJ_CMAP
   mprintf("x= %6i  y= %6i\n", x, y);
-
+# endif
   // Work out the fraction of the CMAP grid step that the interpolated
   // point takes up.
   // This will give the remainder part and then it is divided by the step size
   double phiFrac = dmodulo((phi - gridOrigin), step_size) / step_size;
   double psiFrac = dmodulo((psi - gridOrigin), step_size) / step_size;
+# ifdef DEBUG_CPPTRAJ_CMAP
   mprintf("phiFrac %16.8f  psiFrac %16.8f\n", phiFrac, psiFrac);
-
+# endif
   double E_stencil[2][2];
   double dPhi_stencil[2][2];
   double dPsi_stencil[2][2];
@@ -298,26 +311,14 @@ const
       dPhi_dPsi_stencil[i][j] = cmap_dPhi_dPsi_[cidx].element_wrapped(y+i, x+j);
     }
   }
-
+# ifdef DEBUG_CPPTRAJ_CMAP
   print_stencil("CMAP", E_stencil);
   print_stencil("dPhi", dPhi_stencil);
   print_stencil("dPsi", dPsi_stencil);
   print_stencil("dPhi_dPsi", dPhi_dPsi_stencil);
-
+# endif
   // Convert the 2x2 stencils into a 1D array for processing
-  // by weight_stencil.
-  // The array starts at the bottom left of the 2x2, working
-  // around counterclockwise:
-  //
-  //          4 3
-  //          1 2
-  //
-  //There may be a cleaner/better way of doing this
-  //double E_stencil_1D[4];
-  //double dPhi_stencil_1D[4];
-  //double dPsi_stencil_1D[4];
-  //double dPhi_dPsi_stencil_1D[4];
-
+  // by the below weight_stencil code.
   std::vector<double> E_stencil_1D(16);
   double* dptr = &(E_stencil_1D[0]);
   flatten_stencil(dptr, E_stencil, 1);
@@ -325,44 +326,12 @@ const
   flatten_stencil(dptr+4, dPhi_stencil, step_size);
   flatten_stencil(dptr+8, dPsi_stencil, step_size);
   flatten_stencil(dptr+12, dPhi_dPsi_stencil, step_size*step_size);
+# ifdef DEBUG_CPPTRAJ_CMAP
   for (std::vector<double>::const_iterator it = E_stencil_1D.begin(); it != E_stencil_1D.end(); ++it)
     mprintf("%16.8f\n", *it);
- 
-/*
-  E_stencil_1D(0) = E_stencil(0,0)
-  E_stencil_1D(1) = E_stencil(0,1)
-  E_stencil_1D(2) = E_stencil(1,1)
-  E_stencil_1D(3) = E_stencil(1,0)
-
-  !DEBUG
-  !write(6,'(f9.6)'),E_stencil_1D
-
-  dPhi_stencil_1D(1) = dPhi_stencil(1,1)
-  dPhi_stencil_1D(2) = dPhi_stencil(1,2)
-  dPhi_stencil_1D(3) = dPhi_stencil(2,2)
-  dPhi_stencil_1D(4) = dPhi_stencil(2,1)
-
-  dPsi_stencil_1D(1) = dPsi_stencil(1,1)
-  dPsi_stencil_1D(2) = dPsi_stencil(1,2)
-  dPsi_stencil_1D(3) = dPsi_stencil(2,2)
-  dPsi_stencil_1D(4) = dPsi_stencil(2,1)
-
-  dPhi_dPsi_stencil_1D(1) = dPhi_dPsi_stencil(1,1)
-  dPhi_dPsi_stencil_1D(2) = dPhi_dPsi_stencil(1,2)
-  dPhi_dPsi_stencil_1D(3) = dPhi_dPsi_stencil(2,2)
-  dPhi_dPsi_stencil_1D(4) = dPhi_dPsi_stencil(2,1)
-
-  !Weight d{Psi,dPhi,dPhidPsi}_stencil
-  call weight_stencil(gbl_cmap_grid_step_size(cmap_idx), &
-                      E_stencil_1D,              &
-                      dPhi_stencil_1D,           &
-                      dPsi_stencil_1D,           &
-                      dPhi_dPsi_stencil_1D,      &
-                      c )
-*/
+# endif
   // Generate coefficients for bicubic interpolation
   // NOTE: This is based on routine weight_stencil in cmap.F90
- 
   std::vector<double> coeff(16);
   for (int i = 0; i < 16; i++) {
     coeff[i] = 0.0;
@@ -370,18 +339,19 @@ const
       coeff[i] += wt_[k][i] * E_stencil_1D[k];
     }
   }
+# ifdef DEBUG_CPPTRAJ_CMAP
   for (std::vector<double>::const_iterator it = coeff.begin(); it != coeff.end(); ++it)
     mprintf("%16.8f\n", *it);
-/*
-  call bicubic_interpolation(phiFrac, psiFrac, c, E, dphi, dpsi)
-*/
+# endif
   // Bicubic interpolation
   // NOTE: This is based on routine bicubic_interpolation in cmap.F90
   std::vector<double>::const_reverse_iterator Cit = coeff.rbegin();
   std::vector<double>::const_reverse_iterator Dit = coeff.rbegin();
   for (int i = 3; i > -1; i--, Cit += 4, Dit++) {
+#   ifdef DEBUG_CPPTRAJ_CMAP
     mprintf("BICUBIC %i %16.8f %16.8f %16.8f %16.8f\n", i, *(Cit), *(Cit+1), *(Cit+2), *(Cit+3));
     mprintf("BICUBIC2 %i %16.8f %16.8f %16.8f\n", i, *(Dit), *(Dit+4), *(Dit+8));
+#   endif
     double c4 = *(Cit);
     double c3 = *(Cit+1);
     double c2 = *(Cit+2);
@@ -393,8 +363,9 @@ const
     dPhi = dPhi*psiFrac +( 3.0*d4*phiFrac + 2.0*d3 )*phiFrac + d2;
     dPsi = dPsi*phiFrac +( 3.0*c4*psiFrac + 2.0*c3 )*psiFrac + c2;
   }
+# ifdef DEBUG_CPPTRAJ_CMAP
   mprintf("FINAL %16.8f %16.8f %16.8f\n", ene_cmap, dPhi, dPsi);
-
+# endif
   return ene_cmap;
 }
 

From 59e219cb1d88a7271d0b55ea665e594128923f69 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 11 Feb 2026 10:27:36 -0500
Subject: [PATCH 1331/1492] Add a debug level

---
 src/Energy/CMAP.cpp | 26 +++++++++++++++++---------
 src/Energy/CMAP.h   |  3 +++
 2 files changed, 20 insertions(+), 9 deletions(-)

diff --git a/src/Energy/CMAP.cpp b/src/Energy/CMAP.cpp
index 7ef7c95ad6..7b3dacc549 100644
--- a/src/Energy/CMAP.cpp
+++ b/src/Energy/CMAP.cpp
@@ -12,7 +12,8 @@ using namespace Cpptraj::Energy;
 CMAP::CMAP() :
   cmapGridPtr_(0),
   selected_cmaps_(0),
-  all_cmaps_(0)
+  all_cmaps_(0),
+  debug_(0)
 {}
 
 /** DESTRUCTOR */
@@ -20,6 +21,11 @@ CMAP::~CMAP() {
   if (selected_cmaps_ != 0) delete selected_cmaps_;
 }
 
+/** Set debug level */
+void CMAP::SetDebug(int debugIn) {
+  debug_ = debugIn;
+}
+
 /** The weight matrix */
 const int CMAP::wt_[16][16] = {
   {1, 0, -3,  2, 0, 0,  0,  0, -3,  0,  9, -6,  2,  0, -6,  4},
@@ -633,14 +639,16 @@ int CMAP::Setup_CMAP_Ene(Topology const& topIn, CharMask const& cmask) {
     }
     mprintf("\t%zu CMAPs.\n", selected_cmaps_->size());
   }
-  for (CmapArray::const_iterator cmap = cmaparray->begin(); cmap != cmaparray->end(); ++cmap)
-  {
-    mprintf("\t\tSelecting CMAP %s - %s - %s - %s - %s\n",
-            topIn.AtomMaskName(cmap->A1()).c_str(),
-            topIn.AtomMaskName(cmap->A2()).c_str(),
-            topIn.AtomMaskName(cmap->A3()).c_str(),
-            topIn.AtomMaskName(cmap->A4()).c_str(),
-            topIn.AtomMaskName(cmap->A5()).c_str());
+  if (debug_ > 0) {
+    for (CmapArray::const_iterator cmap = cmaparray->begin(); cmap != cmaparray->end(); ++cmap)
+    {
+      mprintf("\t\tSelecting CMAP %s - %s - %s - %s - %s\n",
+              topIn.AtomMaskName(cmap->A1()).c_str(),
+              topIn.AtomMaskName(cmap->A2()).c_str(),
+              topIn.AtomMaskName(cmap->A3()).c_str(),
+              topIn.AtomMaskName(cmap->A4()).c_str(),
+              topIn.AtomMaskName(cmap->A5()).c_str());
+    }
   }
   return 0;
 }
diff --git a/src/Energy/CMAP.h b/src/Energy/CMAP.h
index d906d2bed5..131b98415c 100644
--- a/src/Energy/CMAP.h
+++ b/src/Energy/CMAP.h
@@ -22,6 +22,8 @@ class CMAP {
     CMAP();
     ~CMAP();
 
+    /// Set debug level
+    void SetDebug(int);
     /// Setup CMAP terms to be calculated, splines, etc
     int Setup_CMAP_Ene(Topology const&, CharMask const&);
     /// Calculate CMAP energy
@@ -50,6 +52,7 @@ class CMAP {
     CmapGridArray const* cmapGridPtr_; ///< Pointer to CMAP grids this was set up with.
     CmapArray* selected_cmaps_; ///< Hold cmaps to calculate energy for if not all selected.
     CmapArray const* all_cmaps_; ///< Pointer to CMAP array in Topology when all selected.
+    int debug_;
 
     static const int wt_[16][16]; ///< Weight matrix
 };

From 2031bd3b877e7d1e5279544f5ba72c2683e216bd Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 11 Feb 2026 10:33:15 -0500
Subject: [PATCH 1332/1492] Add CMAP test

---
 test/Test_Energy/RunTest.sh        |   16 +-
 test/Test_Energy/tz2.cmap.dat.save |    2 +
 test/Test_Energy/tz2.cmap.parm7    | 1950 ++++++++++++++++++++++++++++
 3 files changed, 1967 insertions(+), 1 deletion(-)
 create mode 100644 test/Test_Energy/tz2.cmap.dat.save
 create mode 100644 test/Test_Energy/tz2.cmap.parm7

diff --git a/test/Test_Energy/RunTest.sh b/test/Test_Energy/RunTest.sh
index 6d61b28ec9..9cb4dd0e82 100755
--- a/test/Test_Energy/RunTest.sh
+++ b/test/Test_Energy/RunTest.sh
@@ -2,7 +2,8 @@
 
 . ../MasterTest.sh
 
-CleanFiles ene.in ene.agr short.dat tz2.dat strip.dat elec.dat vdw.dat 1d23.lj1264.dat 1d23.dat
+CleanFiles ene.in ene.agr short.dat tz2.dat strip.dat elec.dat vdw.dat \
+           1d23.lj1264.dat 1d23.dat tz2.cmap.dat
 
 INPUT="-i ene.in"
 
@@ -75,5 +76,18 @@ EOF
   DoTest 1d23.lj1264.dat.save 1d23.lj1264.dat
 fi
 
+UNITNAME='Test CMAP energy'
+CheckFor maxthreads 1
+if [ $? -eq 0 ] ; then
+  cat > ene.in <<EOF
+parm tz2.cmap.parm7
+trajin ../tz2.rst7
+energy Cppt out tz2.cmap.dat
+EOF
+  RunCpptraj "$UNITNAME"
+  DoTest tz2.cmap.dat.save tz2.cmap.dat
+fi
+
+
 EndTest
 exit 0
diff --git a/test/Test_Energy/tz2.cmap.dat.save b/test/Test_Energy/tz2.cmap.dat.save
new file mode 100644
index 0000000000..f95d048fc9
--- /dev/null
+++ b/test/Test_Energy/tz2.cmap.dat.save
@@ -0,0 +1,2 @@
+#Frame     Cppt[bond]  Cppt[angle]    Cppt[dih]   Cppt[cmap]  Cppt[vdw14] Cppt[elec14]    Cppt[vdw]   Cppt[elec] Cppt[kinetic]  Cppt[total]
+       1       0.0153     135.7030      98.7527      18.1603      52.5576     720.6593     -44.9812    -781.5956        0.0000     199.2714
diff --git a/test/Test_Energy/tz2.cmap.parm7 b/test/Test_Energy/tz2.cmap.parm7
new file mode 100644
index 0000000000..ac83bb3a81
--- /dev/null
+++ b/test/Test_Energy/tz2.cmap.parm7
@@ -0,0 +1,1950 @@
+%VERSION  VERSION_STAMP = V0001.000  DATE = 02/11/26 10:25:45                  
+%FLAG TITLE                                                                     
+%FORMAT(20a4)                                                                   
+default_name                                                                    
+%FLAG POINTERS                                                                  
+%FORMAT(10I8)                                                                   
+     223      12     106     124     238     170     494     477       0       0
+    1226      13     124     170     477      45      97     100      26       0
+       0       0       0       0       0       0       0       0      24       0
+       0
+%FLAG ATOM_NAME                                                                 
+%FORMAT(20a4)                                                                   
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+HB2 HB3 CG  HG2 HG3 CD  HD2 HD3 CE  HE2 HE3 NZ  HZ1 HZ2 HZ3 C   O   N   H   C   
+H1  H2  H3  
+%FLAG CHARGE                                                                    
+%FORMAT(5E16.8)                                                                 
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+%FLAG ATOMIC_NUMBER                                                             
+%FORMAT(10I8)                                                                   
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+%FLAG MASS                                                                      
+%FORMAT(5E16.8)                                                                 
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+%FLAG ATOM_TYPE_INDEX                                                           
+%FORMAT(10I8)                                                                   
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+%FLAG NUMBER_EXCLUDED_ATOMS                                                     
+%FORMAT(10I8)                                                                   
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+       7      10       7       6       3       2       1       2       1       7
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+       4       7       3       8       7       4       6       3       4       3
+       2       1       1       7       3      10       4      13       7      12
+       6       5      10       5       4       9       5       4       6       5
+       4       3       2       1       1       7       3       5       4       3
+       2       1       1
+%FLAG NONBONDED_PARM_INDEX                                                      
+%FORMAT(10I8)                                                                   
+       1       2       4       7      11      16      22      29      37      46
+      56      67       2       3       5       8      12      17      23      30
+      38      47      57      68       4       5       6       9      13      18
+      24      31      39      48      58      69       7       8       9      10
+      14      19      25      32      40      49      59      70      11      12
+      13      14      15      20      26      33      41      50      60      71
+      16      17      18      19      20      21      27      34      42      51
+      61      72      22      23      24      25      26      27      28      35
+      43      52      62      73      29      30      31      32      33      34
+      35      36      44      53      63      74      37      38      39      40
+      41      42      43      44      45      54      64      75      46      47
+      48      49      50      51      52      53      54      55      65      76
+      56      57      58      59      60      61      62      63      64      65
+      66      77      67      68      69      70      71      72      73      74
+      75      76      77      78
+%FLAG RESIDUE_LABEL                                                             
+%FORMAT(20a4)                                                                   
+SER TRP THR TRP GLU ASN GLY LYS TRP THR TRP LYS NME 
+%FLAG RESIDUE_POINTER                                                           
+%FORMAT(10I8)                                                                   
+       1      14      38      52      76      91     105     112     134     158
+     172     196     218
+%FLAG BOND_FORCE_CONSTANT                                                       
+%FORMAT(5E16.8)                                                                 
+  5.70000000E+02  4.90000000E+02  5.53000000E+02  3.40000000E+02  3.20000000E+02
+  3.40000000E+02  3.10000000E+02  3.17000000E+02  4.34000000E+02  3.67000000E+02
+  3.67000000E+02  4.69000000E+02  4.69000000E+02  4.69000000E+02  4.47000000E+02
+  4.34000000E+02  4.28000000E+02  3.67000000E+02  4.27000000E+02  5.46000000E+02
+  3.88000000E+02  3.40000000E+02  3.17000000E+02  3.40000000E+02  3.10000000E+02
+  3.17000000E+02  4.34000000E+02  3.37000000E+02  3.40000000E+02  3.10000000E+02
+  3.20000000E+02  3.10000000E+02  6.56000000E+02  3.40000000E+02  3.17000000E+02
+  3.10000000E+02  3.10000000E+02  3.17000000E+02  3.40000000E+02  3.67000000E+02
+  3.40000000E+02  3.10000000E+02  3.10000000E+02  3.40000000E+02  3.37000000E+02
+%FLAG BOND_EQUIL_VALUE                                                          
+%FORMAT(5E16.8)                                                                 
+  1.22900000E+00  1.33500000E+00  9.60000000E-01  1.09000000E+00  1.41000000E+00
+  1.09000000E+00  1.52600000E+00  1.52200000E+00  1.01000000E+00  1.47100000E+00
+  1.08000000E+00  1.40400000E+00  1.40000000E+00  1.40000000E+00  1.41900000E+00
+  1.01000000E+00  1.38000000E+00  1.08000000E+00  1.38100000E+00  1.35200000E+00
+  1.45900000E+00  1.09000000E+00  1.49500000E+00  1.09000000E+00  1.52600000E+00
+  1.52200000E+00  1.01000000E+00  1.44900000E+00  1.09000000E+00  1.52600000E+00
+  1.41000000E+00  1.52600000E+00  1.25000000E+00  1.09000000E+00  1.52200000E+00
+  1.52600000E+00  1.52600000E+00  1.52200000E+00  1.09000000E+00  1.47100000E+00
+  1.09000000E+00  1.52600000E+00  1.52600000E+00  1.09000000E+00  1.44900000E+00
+%FLAG ANGLE_FORCE_CONSTANT                                                      
+%FORMAT(5E16.8)                                                                 
+  8.00000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01  3.50000000E+01
+  6.30000000E+01  5.50000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01
+  5.00000000E+01  8.00000000E+01  7.00000000E+01  5.00000000E+01  3.50000000E+01
+  5.00000000E+01  8.00000000E+01  8.00000000E+01  5.00000000E+01  5.00000000E+01
+  6.30000000E+01  6.30000000E+01  6.30000000E+01  5.00000000E+01  6.30000000E+01
+  6.30000000E+01  5.00000000E+01  7.00000000E+01  7.00000000E+01  5.00000000E+01
+  6.30000000E+01  5.00000000E+01  7.00000000E+01  5.00000000E+01  7.00000000E+01
+  6.30000000E+01  6.30000000E+01  5.00000000E+01  3.50000000E+01  6.30000000E+01
+  7.00000000E+01  7.00000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01
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+  8.00000000E+01  6.30000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01
+  6.30000000E+01  5.00000000E+01  5.50000000E+01  5.00000000E+01  5.00000000E+01
+  4.00000000E+01  5.00000000E+01  8.00000000E+01  8.00000000E+01  5.00000000E+01
+  3.50000000E+01  7.00000000E+01  5.00000000E+01  6.30000000E+01  6.30000000E+01
+  5.00000000E+01  5.00000000E+01  4.00000000E+01  8.00000000E+01  3.50000000E+01
+  5.00000000E+01  8.00000000E+01  7.00000000E+01  6.30000000E+01  3.50000000E+01
+  5.00000000E+01  3.50000000E+01  5.00000000E+01  5.00000000E+01  3.50000000E+01
+  5.00000000E+01  8.00000000E+01  4.00000000E+01  6.30000000E+01  5.00000000E+01
+  5.00000000E+01  4.00000000E+01  8.00000000E+01  5.00000000E+01  3.50000000E+01
+  5.00000000E+01  5.00000000E+01
+%FLAG ANGLE_EQUIL_VALUE                                                         
+%FORMAT(5E16.8)                                                                 
+  2.14501057E+00  2.09439600E+00  2.12755727E+00  1.91113635E+00  1.91113635E+00
+  1.93906163E+00  1.89368305E+00  1.91113635E+00  1.91113635E+00  1.91113635E+00
+  1.91113635E+00  2.10137732E+00  2.03505478E+00  1.91113635E+00  1.91113635E+00
+  1.91113635E+00  1.94080696E+00  1.94080696E+00  2.09439600E+00  2.09439600E+00
+  2.09439600E+00  2.09439600E+00  2.14151991E+00  2.09439600E+00  2.09439600E+00
+  2.02807346E+00  2.14850123E+00  2.31779824E+00  1.82212452E+00  2.09439600E+00
+  1.85703112E+00  2.09439600E+00  1.94778828E+00  2.09439600E+00  1.89717371E+00
+  1.89891904E+00  2.35445017E+00  1.91113635E+00  1.91113635E+00  1.93906163E+00
+  2.18166250E+00  2.24449438E+00  1.91113635E+00  1.91113635E+00  1.91113635E+00
+  2.01760148E+00  2.10137732E+00  2.03505478E+00  2.06018753E+00  1.91113635E+00
+  1.91462701E+00  1.92160833E+00  1.91113635E+00  1.91113635E+00  1.91113635E+00
+  1.93906163E+00  1.91113635E+00  1.89368305E+00  1.91113635E+00  1.91113635E+00
+  1.91113635E+00  1.91113635E+00  1.91462701E+00  2.19911580E+00  1.91113635E+00
+  1.91113635E+00  2.04203610E+00  1.91113635E+00  1.93906163E+00  1.93906163E+00
+  1.91113635E+00  1.91113635E+00  1.91113635E+00  1.91462701E+00  2.09439600E+00
+  1.91113635E+00  2.10137732E+00  2.03505478E+00  1.93906163E+00  1.91113635E+00
+  1.91113635E+00  1.91113635E+00  1.91113635E+00  1.91113635E+00  1.91113635E+00
+  1.91113635E+00  1.94080696E+00  1.91113635E+00  1.93906163E+00  1.91113635E+00
+  1.91113635E+00  1.91113635E+00  1.91462701E+00  2.12755727E+00  1.91113635E+00
+  2.06018753E+00  1.91113635E+00
+%FLAG DIHEDRAL_FORCE_CONSTANT                                                   
+%FORMAT(5E16.8)                                                                 
+  2.00000000E+00  2.50000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  6.61000000E-01  2.18000000E-01  4.01000000E-01  1.29000000E-01
+  1.55555556E-01  1.66666667E-01  2.00000000E-01  2.00000000E-01  4.00000000E-01
+  2.11000000E-01  4.44000000E-01  2.67000000E-01  7.00000000E-03  6.66000000E-01
+  2.46000000E-01  1.60000000E-01  3.62500000E+00  3.00000000E+00  3.50000000E+00
+  1.52500000E+00  6.52500000E+00  1.50000000E+00  1.67500000E+00  1.70000000E-02
+  3.53000000E-01  2.34000000E-01  7.40000000E-02  0.00000000E+00  3.65000000E-01
+  4.08000000E-01  8.19000000E-01  9.50000000E-02  7.90000000E-02  3.13000000E-01
+  3.10000000E-02  0.00000000E+00  0.00000000E+00  6.97000000E-01  1.19000000E-01
+  3.15000000E-01  1.56000000E-01  2.50000000E-01  4.06000000E-01  2.89000000E-01
+  1.48000000E-01  1.12000000E-01  6.43000000E-01  7.90000000E-02  2.36000000E-01
+  4.80000000E-02  1.60000000E-01  6.00000000E-03  2.51000000E-01  1.30000000E-02
+  3.37000000E-01  2.16000000E-01  1.00000000E-03  6.74000000E-01  6.00000000E-03
+  9.50000000E-02  4.21000000E-01  3.93000000E-01  1.44000000E-01  1.45000000E-01
+  1.50000000E-01  3.90000000E-01  6.40000000E-02  1.36700000E+00  2.22000000E-01
+  6.08000000E-01  5.60000000E-02  1.00000000E-01  1.84000000E-01  7.80000000E-02
+  1.04600000E+00  3.03000000E-01  3.30000000E-02  1.07000000E-01  8.00000000E-01
+  8.00000000E-02  8.28000000E-01  4.85000000E-01  3.01000000E-01  8.00000000E-03
+  6.88000000E-01  2.97000000E-01  5.90000000E-02  2.00000000E-01  2.50000000E-01
+  1.80000000E-01  1.05000000E+01  0.00000000E+00  1.10000000E+00  1.00000000E+00
+%FLAG DIHEDRAL_PERIODICITY                                                      
+%FORMAT(5E16.8)                                                                 
+  1.00000000E+00  2.00000000E+00  2.00000000E+00  1.00000000E+00  3.00000000E+00
+  4.00000000E+00  1.00000000E+00  2.00000000E+00  3.00000000E+00  4.00000000E+00
+  3.00000000E+00  3.00000000E+00  1.00000000E+00  2.00000000E+00  3.00000000E+00
+  1.00000000E+00  2.00000000E+00  3.00000000E+00  4.00000000E+00  1.00000000E+00
+  2.00000000E+00  4.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
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+  2.00000000E+00  3.00000000E+00  4.00000000E+00  3.00000000E+00  1.00000000E+00
+  2.00000000E+00  3.00000000E+00  4.00000000E+00  1.00000000E+00  2.00000000E+00
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+  1.00000000E+00  2.00000000E+00  4.00000000E+00  1.00000000E+00  2.00000000E+00
+  4.00000000E+00  1.00000000E+00  2.00000000E+00  3.00000000E+00  4.00000000E+00
+  3.00000000E+00  2.00000000E+00  4.00000000E+00  1.00000000E+00  2.00000000E+00
+  3.00000000E+00  4.00000000E+00  1.00000000E+00  2.00000000E+00  4.00000000E+00
+  1.00000000E+00  2.00000000E+00  3.00000000E+00  4.00000000E+00  1.00000000E+00
+  3.00000000E+00  1.00000000E+00  2.00000000E+00  3.00000000E+00  4.00000000E+00
+  1.00000000E+00  2.00000000E+00  4.00000000E+00  1.00000000E+00  2.00000000E+00
+  3.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+%FLAG DIHEDRAL_PHASE                                                            
+%FORMAT(5E16.8)                                                                 
+  0.00000000E+00  3.14159400E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  3.14159400E+00  3.14159400E+00  0.00000000E+00  0.00000000E+00
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+  3.14159400E+00  0.00000000E+00  3.14159400E+00  3.14159400E+00  3.14159400E+00
+  3.14159400E+00  3.14159400E+00  3.14159400E+00  3.14159400E+00  3.14159400E+00
+  3.14159400E+00  0.00000000E+00  0.00000000E+00  3.14159400E+00  0.00000000E+00
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+  0.00000000E+00  0.00000000E+00  0.00000000E+00  3.14159400E+00  0.00000000E+00
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+  3.14159400E+00  3.14159400E+00  3.14159400E+00  3.14159400E+00  0.00000000E+00
+  3.14159400E+00  3.14159400E+00  0.00000000E+00  3.14159400E+00  3.14159400E+00
+  0.00000000E+00  3.14159400E+00  3.14159400E+00  3.14159400E+00  3.14159400E+00
+%FLAG SCEE_SCALE_FACTOR                                                         
+%FORMAT(5E16.8)                                                                 
+  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00
+  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00
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+  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00
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+  1.20000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+%FLAG SCNB_SCALE_FACTOR                                                         
+%FORMAT(5E16.8)                                                                 
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
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+  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
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+  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
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+  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  2.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+%FLAG SOLTY                                                                     
+%FORMAT(5E16.8)                                                                 
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
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+  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00
+%FLAG LENNARD_JONES_ACOEF                                                       
+%FORMAT(5E16.8)                                                                 
+  9.44293233E+05  2.12601181E+03  1.39982777E-01  9.95480466E+05  2.56678134E+03
+  1.04308023E+06  2.01791425E+04  9.14716912E+00  2.27401052E+04  2.01823541E+02
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+  9.24822270E+05  2.01619733E+04  6.01816484E+04  7.01803794E+05  0.00000000E+00
+  8.19971662E+05  6.06829342E+05  1.02595236E+03  6.47841731E+05  1.12780457E+04
+  3.69471530E+04  4.71003287E+05  0.00000000E+00  5.74393458E+05  3.79876399E+05
+  8.96776989E+04  1.07193646E+02  9.71708117E+04  1.41077189E+03  4.98586848E+03
+  6.82786631E+04  0.00000000E+00  8.61541883E+04  5.44261042E+04  7.51607703E+03
+  6.58473870E+04  6.63368273E+01  7.18621074E+04  9.55000044E+02  3.50301067E+03
+  4.96707306E+04  0.00000000E+00  6.37148278E+04  3.93690817E+04  5.34045360E+03
+  3.76169105E+03  7.91627154E+04  8.90987508E+01  8.59947003E+04  1.21014911E+03
+  4.33325458E+03  6.00750218E+04  0.00000000E+00  7.62451550E+04  4.77908183E+04
+  6.55825601E+03  4.64559155E+03  5.71629601E+03
+%FLAG LENNARD_JONES_BCOEF                                                       
+%FORMAT(5E16.8)                                                                 
+  8.01323529E+02  2.09604198E+01  9.37598976E-02  7.36907417E+02  2.06278363E+01
+  6.75612247E+02  6.45756063E+01  7.57919667E-01  6.13981767E+01  3.56012899E+00
+  1.13252061E+02  1.93248820E+00  1.06076943E+02  7.42992380E+00  1.43076527E+01
+  7.50714425E+02  1.79702257E+01  6.93079947E+02  5.79323581E+01  1.03606917E+02
+  6.99746810E+02  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  6.53361429E+02  1.82891803E+01
+  5.99015525E+02  5.44372326E+01  9.40505980E+01  6.14502845E+02  0.00000000E+00
+  5.31102864E+02  6.77220874E+02  1.53505284E+01  6.26720080E+02  5.08951803E+01
+  9.21192136E+01  6.29300710E+02  0.00000000E+00  5.55666448E+02  5.64885984E+02
+  1.36131731E+02  2.59456373E+00  1.26919150E+02  9.41257003E+00  1.76949863E+01
+  1.25287818E+02  0.00000000E+00  1.12529845E+02  1.11805549E+02  2.17257828E+01
+  1.15327881E+02  2.01792524E+00  1.07908863E+02  7.65648470E+00  1.46638650E+01
+  1.05648788E+02  0.00000000E+00  9.56748258E+01  9.40124296E+01  1.81057616E+01
+  1.50233639E+01  1.26451907E+02  2.33864085E+00  1.18043746E+02  8.61880722E+00
+  1.63092814E+01  1.16187983E+02  0.00000000E+00  1.04660679E+02  1.03580945E+02
+  2.00642027E+01  1.66953734E+01  1.85196588E+01
+%FLAG BONDS_INC_HYDROGEN                                                        
+%FORMAT(10I8)                                                                   
+      27      30       3      18      21       4      18      24       4      12
+      15       6       0       3       9       0       6       9       0       9
+       9      96      99      11      90      93      11      84      87      11
+      78      81      11      69      72      16      63      66      18      51
+      54      22      51      57      22      45      48      24      39      42
+      27     141     144       3     129     132      22     129     135      22
+     129     138      22     123     126      29     117     120      24     111
+     114      27     210     213      11     204     207      11     198     201
+      11     192     195      11     183     186      16     177     180      18
+     165     168      22     165     171      22     159     162      24     153
+     156      27     246     249      34     246     252      34     237     240
+      34     237     243      34     231     234      24     225     228      27
+     297     300      27     297     303      27     282     285      34     282
+     288      34     276     279      24     270     273      27     318     321
+      24     318     324      24     312     315      27     381     384       9
+     381     387       9     381     390       9     372     375      39     372
+     378      39     363     366      41     363     369      41     354     357
+      41     354     360      41     345     348      41     345     351      41
+     339     342      24     333     336      27     456     459      11     450
+     453      11     444     447      11     438     441      11     429     432
+      16     423     426      18     411     414      22     411     417      22
+     405     408      24     399     402      27     501     504       3     489
+     492      22     489     495      22     489     498      22     483     486
+      29     477     480      24     471     474      27     570     573      11
+     564     567      11     558     561      11     552     555      11     543
+     546      16     537     540      18     525     528      22     525     531
+      22     519     522      24     513     516      27     633     636       9
+     633     639       9     633     642       9     624     627      39     624
+     630      39     615     618      41     615     621      41     606     609
+      41     606     612      41     597     600      41     597     603      41
+     591     594      24     585     588      27     657     660      44     657
+     663      44     657     666      44     651     654      27
+%FLAG BONDS_WITHOUT_HYDROGEN                                                    
+%FORMAT(10I8)                                                                   
+      33      36       1      33      39       2      18      27       5      12
+      18       7      12      33       8       0      12      10     105     108
+       1     105     111       2      96     102      12      90      96      13
+      84      90      13      78      84      13      75      78      14      75
+     102      15      69      75      17      63      69      19      60      63
+      20      60     102      21      51      60      23      45      51      25
+      45     105      26      39      45      28     147     150       1     147
+     153       2     123     129      30     123     141      31     117     123
+      32     117     147      26     111     117      28     219     222       1
+     219     225       2     210     216      12     204     210      13     198
+     204      13     192     198      13     189     192      14     189     216
+      15     183     189      17     177     183      19     174     177      20
+     174     216      21     165     174      23     159     165      25     159
+     219      26     153     159      28     264     267       1     264     270
+       2     255     258      33     255     261      33     246     255      35
+     237     246      36     231     237      37     231     264      26     225
+     231      28     306     309       1     306     312       2     291     294
+       1     291     297       2     282     291      38     276     282      37
+     276     306      26     270     276      28     327     330       1     327
+     333       2     318     327      26     312     318      28     393     396
+       1     393     399       2     372     381      40     363     372      42
+     354     363      42     345     354      42     339     345      43     339
+     393      26     333     339      28     465     468       1     465     471
+       2     456     462      12     450     456      13     444     450      13
+     438     444      13     435     438      14     435     462      15     429
+     435      17     423     429      19     420     423      20     420     462
+      21     411     420      23     405     411      25     405     465      26
+     399     405      28     507     510       1     507     513       2     483
+     489      30     483     501      31     477     483      32     477     507
+      26     471     477      28     579     582       1     579     585       2
+     570     576      12     564     570      13     558     564      13     552
+     558      13     549     552      14     549     576      15     543     549
+      17     537     543      19     534     537      20     534     576      21
+     525     534      23     519     525      25     519     579      26     513
+     519      28     645     648       1     645     651       2     624     633
+      40     615     624      42     606     615      42     597     606      42
+     591     597      43     591     645      26     585     591      28     651
+     657      45
+%FLAG ANGLES_INC_HYDROGEN                                                       
+%FORMAT(10I8)                                                                   
+      33      39      42       2      24      18      27       4      21      18
+      24       5      21      18      27       4      18      27      30       7
+      15      12      18       8      15      12      33       9      12      18
+      21      10      12      18      24      10       9       0      12      14
+       6       0       9      15       6       0      12      14       3       0
+       6      15       3       0       9      15       3       0      12      14
+       0      12      15      16     105     111     114       2      99      96
+     102      19      93      90      96      20      90      96      99      20
+      87      84      90      20      84      90      93      20      81      78
+      84      20      78      84      87      20      75      78      81      24
+      72      69      75      27      66      63      69      30      63      69
+      72      32      60      63      66      34      57      51      60      38
+      54      51      57      39      54      51      60      38      48      45
+      51      43      48      45     105      44      45      51      54      45
+      45      51      57      45      42      39      45      49      39      45
+      48      50     147     153     156       2     135     129     138      39
+     132     129     135      39     132     129     138      39     126     123
+     129      54     126     123     141      55     123     129     132      57
+     123     129     135      57     123     129     138      57     123     141
+     144      58     120     117     123      59     120     117     147      44
+     117     123     126      60     114     111     117      49     111     117
+     120      50     219     225     228       2     213     210     216      19
+     207     204     210      20     204     210     213      20     201     198
+     204      20     198     204     207      20     195     192     198      20
+     192     198     201      20     189     192     195      24     186     183
+     189      27     180     177     183      30     177     183     186      32
+     174     177     180      34     171     165     174      38     168     165
+     171      39     168     165     174      38     162     159     165      43
+     162     159     219      44     159     165     168      45     159     165
+     171      45     156     153     159      49     153     159     162      50
+     264     270     273       2     252     246     255      65     249     246
+     252      66     249     246     255      65     243     237     246      68
+     240     237     243      66     240     237     246      68     237     246
+     249      68     237     246     252      68     234     231     237      71
+     234     231     264      44     231     237     240      72     231     237
+     243      72     228     225     231      49     225     231     234      50
+     306     312     315       2     300     297     303      75     291     297
+     300       2     291     297     303       2     288     282     291      76
+     285     282     288      66     285     282     291      76     279     276
+     282      71     279     276     306      44     276     282     285      72
+     276     282     288      72     273     270     276      49     270     276
+     279      50     327     333     336       2     324     318     327      44
+     321     318     324      80     321     318     327      44     315     312
+     318      49     312     318     321      50     312     318     324      50
+     393     399     402       2     387     381     390      15     384     381
+     387      15     384     381     390      15     378     372     381      81
+     375     372     378      82     375     372     381      81     372     381
+     384      83     372     381     387      83     372     381     390      83
+     369     363     372      84     366     363     369      85     366     363
+     372      84     363     372     375      86     363     372     378      86
+     360     354     363      84     357     354     360      85     357     354
+     363      84     354     363     366      84     354     363     369      84
+     351     345     354      84     348     345     351      85     348     345
+     354      84     345     354     357      84     345     354     360      84
+     342     339     345      90     342     339     393      44     339     345
+     348      91     339     345     351      91     336     333     339      49
+     333     339     342      50     465     471     474       2     459     456
+     462      19     453     450     456      20     450     456     459      20
+     447     444     450      20     444     450     453      20     441     438
+     444      20     438     444     447      20     435     438     441      24
+     432     429     435      27     426     423     429      30     423     429
+     432      32     420     423     426      34     417     411     420      38
+     414     411     417      39     414     411     420      38     408     405
+     411      43     408     405     465      44     405     411     414      45
+     405     411     417      45     402     399     405      49     399     405
+     408      50     507     513     516       2     495     489     498      39
+     492     489     495      39     492     489     498      39     486     483
+     489      54     486     483     501      55     483     489     492      57
+     483     489     495      57     483     489     498      57     483     501
+     504      58     480     477     483      59     480     477     507      44
+     477     483     486      60     474     471     477      49     471     477
+     480      50     579     585     588       2     573     570     576      19
+     567     564     570      20     564     570     573      20     561     558
+     564      20     558     564     567      20     555     552     558      20
+     552     558     561      20     549     552     555      24     546     543
+     549      27     540     537     543      30     537     543     546      32
+     534     537     540      34     531     525     534      38     528     525
+     531      39     528     525     534      38     522     519     525      43
+     522     519     579      44     519     525     528      45     519     525
+     531      45     516     513     519      49     513     519     522      50
+     645     651     654       2     639     633     642      15     636     633
+     639      15     636     633     642      15     630     624     633      81
+     627     624     630      82     627     624     633      81     624     633
+     636      83     624     633     639      83     624     633     642      83
+     621     615     624      84     618     615     621      85     618     615
+     624      84     615     624     627      86     615     624     630      86
+     612     606     615      84     609     606     612      85     609     606
+     615      84     606     615     618      84     606     615     621      84
+     603     597     606      84     600     597     603      85     600     597
+     606      84     597     606     609      84     597     606     612      84
+     594     591     597      90     594     591     645      44     591     597
+     600      91     591     597     603      91     588     585     591      49
+     585     591     594      50     663     657     666      95     660     657
+     663      95     660     657     666      95     654     651     657      96
+     651     657     660      97     651     657     663      97     651     657
+     666      97
+%FLAG ANGLES_WITHOUT_HYDROGEN                                                   
+%FORMAT(10I8)                                                                   
+      36      33      39       1      33      39      45       3      18      12
+      33       6      12      18      27      11      12      33      36      12
+      12      33      39      13       0      12      18      17       0      12
+      33      18     108     105     111       1     105     111     117       3
+      90      96     102      21      84      90      96      22      78      75
+     102      23      78      84      90      22      75      78      84      25
+      75     102      96      26      69      75      78      28      69      75
+     102      29      63      60     102      31      63      69      75      33
+      60      63      69      35      60     102      75      36      60     102
+      96      37      51      45     105      40      51      60      63      41
+      51      60     102      42      45      51      60      46      45     105
+     108      47      45     105     111      48      39      45      51      51
+      39      45     105      52     150     147     153       1     147     153
+     159       3     129     123     141      53     123     117     147      56
+     117     123     129      61     117     123     141      62     117     147
+     150      47     117     147     153      48     111     117     123      63
+     111     117     147      52     222     219     225       1     219     225
+     231       3     204     210     216      21     198     204     210      22
+     192     189     216      23     192     198     204      22     189     192
+     198      25     189     216     210      26     183     189     192      28
+     183     189     216      29     177     174     216      31     177     183
+     189      33     174     177     183      35     174     216     189      36
+     174     216     210      37     165     159     219      40     165     174
+     177      41     165     174     216      42     159     165     174      46
+     159     219     222      47     159     219     225      48     153     159
+     165      51     153     159     219      52     267     264     270       1
+     264     270     276       3     258     255     261      64     246     255
+     258      67     246     255     261      67     237     231     264      69
+     237     246     255      70     231     237     246      73     231     264
+     267      47     231     264     270      48     225     231     237      74
+     225     231     264      52     309     306     312       1     306     312
+     318       3     294     291     297       1     282     276     306      69
+     282     291     294      77     282     291     297      78     276     282
+     291      79     276     306     309      47     276     306     312      48
+     270     276     282      74     270     276     306      52     330     327
+     333       1     327     333     339       3     318     327     330      47
+     318     327     333      48     312     318     327      52     396     393
+     399       1     393     399     405       3     363     372     381      87
+     354     363     372      88     345     339     393      89     345     354
+     363      88     339     345     354      92     339     393     396      47
+     339     393     399      48     333     339     345      93     333     339
+     393      52     468     465     471       1     465     471     477       3
+     450     456     462      21     444     450     456      22     438     435
+     462      23     438     444     450      22     435     438     444      25
+     435     462     456      26     429     435     438      28     429     435
+     462      29     423     420     462      31     423     429     435      33
+     420     423     429      35     420     462     435      36     420     462
+     456      37     411     405     465      40     411     420     423      41
+     411     420     462      42     405     411     420      46     405     465
+     468      47     405     465     471      48     399     405     411      51
+     399     405     465      52     510     507     513       1     507     513
+     519       3     489     483     501      53     483     477     507      56
+     477     483     489      61     477     483     501      62     477     507
+     510      47     477     507     513      48     471     477     483      63
+     471     477     507      52     582     579     585       1     579     585
+     591       3     564     570     576      21     558     564     570      22
+     552     549     576      23     552     558     564      22     549     552
+     558      25     549     576     570      26     543     549     552      28
+     543     549     576      29     537     534     576      31     537     543
+     549      33     534     537     543      35     534     576     549      36
+     534     576     570      37     525     519     579      40     525     534
+     537      41     525     534     576      42     519     525     534      46
+     519     579     582      47     519     579     585      48     513     519
+     525      51     513     519     579      52     648     645     651       1
+     645     651     657      94     615     624     633      87     606     615
+     624      88     597     591     645      89     597     606     615      88
+     591     597     606      92     591     645     648      47     591     645
+     651      48     585     591     597      93     585     591     645      52
+%FLAG DIHEDRALS_INC_HYDROGEN                                                    
+%FORMAT(10I8)                                                                   
+      36      33      39      42       1      36      33     -39      42       2
+      33      39      45      48       3      24      18      12      33      11
+      24      18      27      30      12      21      18      12      33      11
+      21      18      27      30      12      15      12      18      21      11
+      15      12      18      24      11      15      12      18      27      11
+      15      12      33      36       3      15      12      33      39       3
+      12      18      27      30      16      12      18     -27      30      17
+      12      18     -27      30      18      12      18     -27      30      19
+      12      33      39      42       2       9       0      12      15      11
+       9       0      12      18      11       9       0      12      33      11
+       6       0      12      15      11       6       0      12      18      11
+       6       0      12      33      11       3       0      12      15      11
+       3       0      12      18      11       3       0      12      33      11
+       0      12      18      21      11       0      12      18      24      11
+     108     105     111     114       1     108     105    -111     114       2
+     105     111     117     120       3      93      90      96      99      23
+      93      90      96     102      23      87      84      90      93      23
+      87      84      90      96      23      84      90      96      99      23
+      81      78      75     102      23      81      78      84      87      23
+      81      78      84      90      23      78      84      90      93      23
+      75      78      84      87      23      75     102      96      99      25
+      72      69      75      78      26      72      69      75     102      26
+      69      75      78      81      23      66      63      60     102      27
+      66      63      69      72      28      66      63      69      75      28
+      60      63      69      72      28      60     102      96      99      25
+      57      51      45     105      11      57      51      60      63       3
+      57      51      60     102       3      54      51      45     105      11
+      54      51      60      63       3      54      51      60     102       3
+      51      60      63      66      27      48      45      51      54      11
+      48      45      51      57      11      48      45      51      60      11
+      48      45     105     108       4      48      45    -105     108       3
+      48      45    -105     108      34      48      45     105     111       3
+      45     105     111     114       2      42      39      45      48       3
+      42      39      45      51       3      42      39      45     105       3
+      39      45      51      54      11      39      45      51      57      11
+     150     147     153     156       1     150     147    -153     156       2
+     147     153     159     162       3     138     129     123     141      48
+     138     129    -123     141       5     135     129     123     141      48
+     135     129    -123     141       5     132     129     123     141      48
+     132     129    -123     141       5     129     123     141     144      53
+     129     123    -141     144      54     129     123    -141     144      55
+     129     123    -141     144      56     126     123     117     147      11
+     126     123     129     132      11     126     123     129     135      11
+     126     123     129     138      11     126     123     141     144      12
+     120     117     123     126      11     120     117     123     129      11
+     120     117     123     141      48     120     117    -123     141       5
+     120     117     147     150       4     120     117    -147     150       3
+     120     117    -147     150      34     120     117     147     153       3
+     117     123     129     132      57     117     123     129     135      57
+     117     123     129     138      57     117     123     141     144      58
+     117     123    -141     144      59     117     123    -141     144      55
+     117     123    -141     144      60     117     147     153     156       2
+     114     111     117     120       3     114     111     117     123       3
+     114     111     117     147       3     111     117     123     126      11
+     222     219     225     228       1     222     219    -225     228       2
+     219     225     231     234       3     207     204     210     213      23
+     207     204     210     216      23     201     198     204     207      23
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+%FLAG DIHEDRALS_WITHOUT_HYDROGEN                                                
+%FORMAT(10I8)                                                                   
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+     423     420    -462     435      29     423     420     462     456      29
+     423     429     435     438      26     423     429    -435     462      26
+     420     411     405     465      30     420     411    -405     465      31
+     420     411    -405     465      32     420     411    -405     465      33
+     420     423    -429     435      28     420     462    -435     429      24
+     420     462     435     438      24     420     462     456     450      25
+     411     405     465     468       3     411     405     465     471       4
+     411     405    -465     471       3     411     405    -465     471       5
+     411     405    -465     471       6     411     420     423     429      27
+     411     420     462     435      29     411     420     462     456      29
+     405     411     420     423       4     405     411    -420     423       3
+     405     411    -420     423       5     405     411    -420     423       6
+     405     411     420     462      35     405     411    -420     462      36
+     405     411    -420     462      37     405     411    -420     462      38
+     405     465     471     477       2     399     405     411     420      39
+     399     405    -411     420      40     399     405    -411     420      32
+     399     405    -411     420      41     399     405     465     468       3
+     399     405     465     471      42     399     405    -465     471      43
+     399     405    -465     471      34     399     405    -465     471       6
+     510     507     513     519       2     507     513     519     525       4
+     507     513    -519     525       3     507     513    -519     525       5
+     507     513    -519     525       6     507     513     519     579       4
+     507     513    -519     579       3     507     513    -519     579       5
+     507     513    -519     579       6     501     483     477     507      44
+     501     483    -477     507      45     501     483    -477     507      46
+     501     483    -477     507      47     489     483     477     507      49
+     489     483    -477     507      50     489     483    -477     507      51
+     489     483    -477     507      52     483     477     507     510       3
+     483     477     507     513       4     483     477    -507     513       3
+     483     477    -507     513       5     483     477    -507     513       6
+     477     507     513     519       2     471     477     483     489      61
+     471     477    -483     489      62     471     477    -483     489      51
+     471     477    -483     489      63     471     477     483     501      64
+     471     477    -483     501      65     471     477    -483     501      46
+     471     477    -483     501      66     471     477     507     510       3
+     471     477     507     513      42     471     477    -507     513      43
+     471     477    -507     513      34     471     477    -507     513       6
+     582     579     585     591       2     579     585     591     597       4
+     579     585    -591     597       3     579     585    -591     597       5
+     579     585    -591     597       6     579     585     591     645       4
+     579     585    -591     645       3     579     585    -591     645       5
+     579     585    -591     645       6     558     552     549     576      23
+     558     564    -570     576      23     552     549     576     570      24
+     552     558    -564     570      23     549     552     558     564      23
+     549     576    -570     564      25     543     537    -534     576      27
+     543     549     552     558      23     543     549     576     570      24
+     537     534    -576     549      29     537     534     576     570      29
+     537     543     549     552      26     537     543    -549     576      26
+     534     525     519     579      30     534     525    -519     579      31
+     534     525    -519     579      32     534     525    -519     579      33
+     534     537    -543     549      28     534     576    -549     543      24
+     534     576     549     552      24     534     576     570     564      25
+     525     519     579     582       3     525     519     579     585       4
+     525     519    -579     585       3     525     519    -579     585       5
+     525     519    -579     585       6     525     534     537     543      27
+     525     534     576     549      29     525     534     576     570      29
+     519     525     534     537       4     519     525    -534     537       3
+     519     525    -534     537       5     519     525    -534     537       6
+     519     525     534     576      35     519     525    -534     576      36
+     519     525    -534     576      37     519     525    -534     576      38
+     519     579     585     591       2     513     519     525     534      39
+     513     519    -525     534      40     513     519    -525     534      32
+     513     519    -525     534      41     513     519     579     582       3
+     513     519     579     585      42     513     519    -579     585      43
+     513     519    -579     585      34     513     519    -579     585       6
+     648     645     651     657       2     606     597     591     645      11
+     606     615     624     633      11     597     591     645     648       3
+     597     591     645     651       4     597     591    -645     651       3
+     597     591    -645     651       5     597     591    -645     651       6
+     597     606     615     624      94     597     606    -615     624      95
+     597     606    -615     624      96     591     597     606     615      94
+     591     597    -606     615      95     591     597    -606     615      96
+     591     645     651     657       2     585     591     597     606      11
+     585     591     645     648       3     585     591     645     651      42
+     585     591    -645     651      43     585     591    -645     651      34
+     585     591    -645     651       6      12      39     -33     -36      97
+      45     111    -105    -108      97      60      75    -102     -96      98
+      69      78     -75    -102      98     102      51     -60     -63      99
+     117     153    -147    -150      97     159     225    -219    -222      97
+     174     210    -216    -189      98     192     216    -189    -183      98
+     216     165    -174    -177      99     231     270    -264    -267      97
+     246     258    -255    -261      97     276     312    -306    -309      97
+     282     297    -291    -294      97     318     333    -327    -330      97
+     339     399    -393    -396      97     405     471    -465    -468      97
+     420     456    -462    -435      98     438     462    -435    -429      98
+     462     411    -420    -423      99     477     513    -507    -510      97
+     519     585    -579    -582      97     534     570    -576    -549      98
+     552     576    -549    -543      98     576     525    -534    -537      99
+     591     651    -645    -648      97
+%FLAG EXCLUDED_ATOMS_LIST                                                       
+%FORMAT(10I8)                                                                   
+       2       3       4       5       6       7       8       9      10      12
+      13      14       3       4       5       6       7      12       4       5
+       6       7      12       5       6       7      12       6       7       8
+       9      10      11      12      13      14      15      16       7       8
+       9      10      12      13      14       8       9      10      11      12
+      13      14       9      10      11      12      10      11      12      11
+      12       0      13      14      15      16      17      18      36      14
+      15      16      15      16      17      18      19      20      21      36
+      37      38      16      17      18      36      17      18      19      20
+      21      22      35      36      37      38      39      40      18      19
+      20      21      36      37      38      19      20      21      22      23
+      24      26      33      35      36      37      38      20      21      22
+      35      36      21      22      35      36      22      23      24      25
+      26      27      31      33      34      35      36      23      24      25
+      26      27      33      35      24      25      26      35      25      26
+      27      28      29      33      35      26      27      35      27      28
+      29      30      31      33      34      35      28      29      30      31
+      32      33      35      29      30      31      35      30      31      32
+      33      34      35      31      32      33      32      33      34      35
+      33      34      35      34      35      35       0      37      38      39
+      40      41      42      50      38      39      40      39      40      41
+      42      43      44      48      50      51      52      40      41      42
+      50      41      42      43      44      45      46      47      48      49
+      50      51      52      53      54      42      43      44      48      50
+      51      52      43      44      45      46      47      48      49      50
+      51      52      44      45      46      47      48      49      50      45
+      46      47      48      49      50      46      47      48      47      48
+      48      49      50       0      51      52      53      54      55      56
+      74      52      53      54      53      54      55      56      57      58
+      59      74      75      76      54      55      56      74      55      56
+      57      58      59      60      73      74      75      76      77      78
+      56      57      58      59      74      75      76      57      58      59
+      60      61      62      64      71      73      74      75      76      58
+      59      60      73      74      59      60      73      74      60      61
+      62      63      64      65      69      71      72      73      74      61
+      62      63      64      65      71      73      62      63      64      73
+      63      64      65      66      67      71      73      64      65      73
+      65      66      67      68      69      71      72      73      66      67
+      68      69      70      71      73      67      68      69      73      68
+      69      70      71      72      73      69      70      71      70      71
+      72      73      71      72      73      72      73      73       0      75
+      76      77      78      79      80      89      76      77      78      77
+      78      79      80      81      82      83      89      90      91      78
+      79      80      89      79      80      81      82      83      84      85
+      86      89      90      91      92      93      80      81      82      83
+      89      90      91      81      82      83      84      85      86      87
+      88      89      90      91      82      83      84      85      86      89
+      83      84      85      86      89      84      85      86      87      88
+      89      85      86      87      88      86      87      88      87      88
+      88       0      90      91      92      93      94      95     103      91
+      92      93      92      93      94      95      96      97      98     103
+     104     105      93      94      95     103      94      95      96      97
+      98      99     100     103     104     105     106     107      95      96
+      97      98     103     104     105      96      97      98      99     100
+     101     102     103     104     105      97      98      99     100     103
+      98      99     100     103      99     100     101     102     103     100
+     101     102     101     102     102       0     104     105     106     107
+     108     109     110     105     106     107     106     107     108     109
+     110     111     112     107     108     109     110     108     109     110
+     111     112     113     114     109     110     111     112     110     111
+     112     111     112     113     114     115     116     132     112     113
+     114     113     114     115     116     117     118     119     132     133
+     134     114     115     116     132     115     116     117     118     119
+     120     121     122     132     133     134     135     136     116     117
+     118     119     132     133     134     117     118     119     120     121
+     122     123     124     125     132     133     134     118     119     120
+     121     122     132     119     120     121     122     132     120     121
+     122     123     124     125     126     127     128     132     121     122
+     123     124     125     122     123     124     125     123     124     125
+     126     127     128     129     130     131     124     125     126     127
+     128     125     126     127     128     126     127     128     129     130
+     131     127     128     129     130     131     128     129     130     131
+     129     130     131     130     131     131       0     133     134     135
+     136     137     138     156     134     135     136     135     136     137
+     138     139     140     141     156     157     158     136     137     138
+     156     137     138     139     140     141     142     155     156     157
+     158     159     160     138     139     140     141     156     157     158
+     139     140     141     142     143     144     146     153     155     156
+     157     158     140     141     142     155     156     141     142     155
+     156     142     143     144     145     146     147     151     153     154
+     155     156     143     144     145     146     147     153     155     144
+     145     146     155     145     146     147     148     149     153     155
+     146     147     155     147     148     149     150     151     153     154
+     155     148     149     150     151     152     153     155     149     150
+     151     155     150     151     152     153     154     155     151     152
+     153     152     153     154     155     153     154     155     154     155
+     155       0     157     158     159     160     161     162     170     158
+     159     160     159     160     161     162     163     164     168     170
+     171     172     160     161     162     170     161     162     163     164
+     165     166     167     168     169     170     171     172     173     174
+     162     163     164     168     170     171     172     163     164     165
+     166     167     168     169     170     171     172     164     165     166
+     167     168     169     170     165     166     167     168     169     170
+     166     167     168     167     168     168     169     170       0     171
+     172     173     174     175     176     194     172     173     174     173
+     174     175     176     177     178     179     194     195     196     174
+     175     176     194     175     176     177     178     179     180     193
+     194     195     196     197     198     176     177     178     179     194
+     195     196     177     178     179     180     181     182     184     191
+     193     194     195     196     178     179     180     193     194     179
+     180     193     194     180     181     182     183     184     185     189
+     191     192     193     194     181     182     183     184     185     191
+     193     182     183     184     193     183     184     185     186     187
+     191     193     184     185     193     185     186     187     188     189
+     191     192     193     186     187     188     189     190     191     193
+     187     188     189     193     188     189     190     191     192     193
+     189     190     191     190     191     192     193     191     192     193
+     192     193     193       0     195     196     197     198     199     200
+     216     196     197     198     197     198     199     200     201     202
+     203     216     217     218     198     199     200     216     199     200
+     201     202     203     204     205     206     216     217     218     219
+     220     200     201     202     203     216     217     218     201     202
+     203     204     205     206     207     208     209     216     217     218
+     202     203     204     205     206     216     203     204     205     206
+     216     204     205     206     207     208     209     210     211     212
+     216     205     206     207     208     209     206     207     208     209
+     207     208     209     210     211     212     213     214     215     208
+     209     210     211     212     209     210     211     212     210     211
+     212     213     214     215     211     212     213     214     215     212
+     213     214     215     213     214     215     214     215     215       0
+     217     218     219     220     221     222     223     218     219     220
+     219     220     221     222     223     220     221     222     223     221
+     222     223     222     223     223       0
+%FLAG HBOND_ACOEF                                                               
+%FORMAT(5E16.8)                                                                 
+
+%FLAG HBOND_BCOEF                                                               
+%FORMAT(5E16.8)                                                                 
+
+%FLAG HBCUT                                                                     
+%FORMAT(5E16.8)                                                                 
+
+%FLAG AMBER_ATOM_TYPE                                                           
+%FORMAT(20a4)                                                                   
+N3  H   H   H   CX  HP  2C  H1  H1  OH  HO  C   O   N   H   XC  H1  CT  HC  HC  
+C*  CW  H4  NA  H   CN  CA  HA  CA  HA  CA  HA  CA  HA  CB  C   O   N   H   XC  
+H1  3C  H1  CT  HC  HC  HC  OH  HO  C   O   N   H   XC  H1  CT  HC  HC  C*  CW  
+H4  NA  H   CN  CA  HA  CA  HA  CA  HA  CA  HA  CB  C   O   N   H   XC  H1  2C  
+HC  HC  2C  HC  HC  CO  O2  O2  C   O   N   H   XC  H1  2C  HC  HC  C   O   N   
+H   H   C   O   N   H   XC  H1  H1  C   O   N   H   XC  H1  C8  HC  HC  C8  HC  
+HC  C8  HC  HC  C8  HP  HP  N3  H   H   H   C   O   N   H   XC  H1  CT  HC  HC  
+C*  CW  H4  NA  H   CN  CA  HA  CA  HA  CA  HA  CA  HA  CB  C   O   N   H   XC  
+H1  3C  H1  CT  HC  HC  HC  OH  HO  C   O   N   H   XC  H1  CT  HC  HC  C*  CW  
+H4  NA  H   CN  CA  HA  CA  HA  CA  HA  CA  HA  CB  C   O   N   H   XC  H1  C8  
+HC  HC  C8  HC  HC  C8  HC  HC  C8  HP  HP  N3  H   H   H   C   O   N   H   CT  
+H1  H1  H1  
+%FLAG TREE_CHAIN_CLASSIFICATION                                                 
+%FORMAT(20a4)                                                                   
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA 
+%FLAG JOIN_ARRAY                                                                
+%FORMAT(10I8)                                                                   
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0
+%FLAG IROTAT                                                                    
+%FORMAT(10I8)                                                                   
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0
+%FLAG RADIUS_SET                                                                
+%FORMAT(1a80)                                                                   
+modified Bondi radii (mbondi)                                                   
+%FLAG RADII                                                                     
+%FORMAT(5E16.8)                                                                 
+  1.55000000E+00  1.30000000E+00  1.30000000E+00  1.30000000E+00  1.70000000E+00
+  1.30000000E+00  1.70000000E+00  1.30000000E+00  1.30000000E+00  1.50000000E+00
+  8.00000000E-01  1.70000000E+00  1.50000000E+00  1.55000000E+00  1.30000000E+00
+  1.70000000E+00  1.30000000E+00  1.70000000E+00  1.30000000E+00  1.30000000E+00
+  1.70000000E+00  1.70000000E+00  1.30000000E+00  1.55000000E+00  1.30000000E+00
+  1.70000000E+00  1.70000000E+00  1.30000000E+00  1.70000000E+00  1.30000000E+00
+  1.70000000E+00  1.30000000E+00  1.70000000E+00  1.30000000E+00  1.70000000E+00
+  1.70000000E+00  1.50000000E+00  1.55000000E+00  1.30000000E+00  1.70000000E+00
+  1.30000000E+00  1.70000000E+00  1.30000000E+00  1.70000000E+00  1.30000000E+00
+  1.30000000E+00  1.30000000E+00  1.50000000E+00  8.00000000E-01  1.70000000E+00
+  1.50000000E+00  1.55000000E+00  1.30000000E+00  1.70000000E+00  1.30000000E+00
+  1.70000000E+00  1.30000000E+00  1.30000000E+00  1.70000000E+00  1.70000000E+00
+  1.30000000E+00  1.55000000E+00  1.30000000E+00  1.70000000E+00  1.70000000E+00
+  1.30000000E+00  1.70000000E+00  1.30000000E+00  1.70000000E+00  1.30000000E+00
+  1.70000000E+00  1.30000000E+00  1.70000000E+00  1.70000000E+00  1.50000000E+00
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+%FLAG SCREEN                                                                    
+%FORMAT(5E16.8)                                                                 
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+%FLAG IPOL                                                                      
+%FORMAT(1I8)                                                                    
+       0
+%FLAG CMAP_COUNT                                                                
+%FORMAT(2I8)                                                                    
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+%FLAG CMAP_RESOLUTION                                                           
+%FORMAT(20I4)                                                                   
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+%FLAG CMAP_PARAMETER_01                                                         
+%COMMENT  Gly CMAP                                                              
+%FORMAT(8F9.5)                                                                  
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+%FLAG CMAP_PARAMETER_02                                                         
+%COMMENT  Thr CMAP                                                              
+%FORMAT(8F9.5)                                                                  
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+%FLAG CMAP_PARAMETER_03                                                         
+%COMMENT  Asn CMAP                                                              
+%FORMAT(8F9.5)                                                                  
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+%FLAG CMAP_PARAMETER_04                                                         
+%COMMENT  Glu CMAP                                                              
+%FORMAT(8F9.5)                                                                  
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+%FLAG CMAP_PARAMETER_05                                                         
+%COMMENT  Lys CMAP                                                              
+%FORMAT(8F9.5)                                                                  
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+ -0.64060 -0.32893  0.02012  0.02118  0.47137  1.14861  1.91913  2.36069
+  2.22229  1.95149  1.20614 -0.57017 -1.75076 -2.03501 -1.58763 -0.64877
+  0.30096  0.62023  0.45342  0.04313 -0.46090 -0.79564 -0.82334 -0.74223
+ -0.24137 -0.11209  0.08544  0.05425  0.40854  1.14888  2.02651  2.38762
+  2.30421  2.65775  0.84980 -0.58949 -1.42718 -1.56969 -1.12474 -0.27600
+  0.57048  0.92694  0.75506  0.36313  0.41248 -0.25267 -0.29508 -0.30702
+  0.15784  0.16124  0.21528  0.19125  0.52652  1.17640  2.01822  2.39523
+  2.25697  1.97743  0.85670 -0.29822 -0.64315 -0.71138 -0.30686  0.45873
+  0.81134  1.29671  1.19500  0.84969  0.46708  0.29043  0.21746  0.16500
+  0.89392  0.71753  0.57115  0.43890  0.76485  1.44400  2.31824  2.67943
+  2.58376  2.16804  1.23014  0.82763 -0.51969 -0.73656 -0.32147  0.44935
+  1.20995  1.60156  1.65872  1.41868  1.06413  0.88918  1.40765  0.89807
+  1.39127  1.14527  0.83908  0.62088  1.03137  2.44461  3.61122  3.03639
+  2.93037  2.34216  1.25412  0.23792 -0.42524 -0.47841  0.12423  0.77695
+  1.18318  1.45904  1.64051  1.57482  1.43824  1.35338  1.42422  1.50599
+  1.03940  0.78129  0.55141  0.59044  1.11541  1.93195  3.28135  3.10600
+  2.87709  2.08673  0.97761 -0.07189 -0.55989 -0.15343  0.59138  0.86483
+  1.13795  1.36979  1.55187  1.49198  1.31001  1.19377  1.27168  1.26717
+  0.31570  0.32645  0.43538  0.89961  1.65773  2.35060  2.92667  3.00795
+  2.52682  1.60328  0.45969  0.23113 -0.28882  1.23655  1.15894  1.54835
+  1.88547  1.93525  1.86074  1.72151  1.65432  0.72519  0.57772  0.96376
+  0.01270  0.24227  0.76959  1.64854  2.60813  3.46061  3.69061  3.18918
+  2.22863  1.15788  0.39483  0.21073  0.68040  2.18832  1.80572  2.24818
+  2.70988  2.86880  2.79105  2.41410  2.01156  0.35940  0.00000  0.00646
+  0.35073  0.90201  2.00003  3.08122  4.18056  4.93815  4.63514  3.60238
+  2.75114  1.43898  1.23584  1.46770  2.07827  2.18651  2.36403  2.96159
+  3.67909  4.13912  4.10653  3.18582  1.51669  0.18861 -0.06191  0.04962
+  1.53826  2.58483  4.03310  5.05092  6.11295  6.14815  5.20647  3.81976
+  2.76531  2.50097  2.69420  2.97134  2.67683  2.45579  2.69794  3.72189
+  4.88760  5.73443  5.25225  3.32794  1.50262  0.37839  0.90315  0.93349
+  3.53826  4.97003  5.16584  4.77571  4.97699  4.94501  4.73810  4.10406
+  3.72549  4.11352  4.26970  3.27545  2.15952  2.71722  2.87070  4.71124
+  5.93638  5.07391  4.12244  2.88828  2.59390  1.43687  1.95877  2.78313
+  5.77443  4.46997  3.56825  3.21013  3.29175  3.88737  4.64985  4.86020
+  5.40449  5.58649  3.52430  1.95498  2.12058  1.64132  3.18061  4.76232
+  4.12981  3.48929  3.28524  2.96613  2.82022  3.09461  3.81784  4.80706
+  4.81125  3.11064  2.19879  1.79413  2.26340  3.62230  5.03506  6.19526
+  6.42134  4.54813  2.74872  2.01212  1.67501  2.46391  3.72853  3.32011
+  2.54393  2.64930  4.53517  3.65435  4.11000  4.43677  5.16380  5.36330
+  2.40638  1.42733  0.83483  0.72279  1.83113  3.87438  5.88103  6.54537
+  5.44021  4.07584  2.89687  2.46565  2.57255  2.85706  2.48850  1.54075
+  1.55152  2.30832  3.47039  4.36402  4.62076  5.24285  4.48773  3.44960
+  1.10697  0.48844  0.05413  0.22301  1.84021  4.72185  5.44366  5.35532
+  4.78976  3.85091  3.07756  2.70321  2.41981  1.79438  0.82855  0.52195
+  1.15697  2.28904  3.44297  4.00628  3.92284  3.44623  2.77364  1.79239
+  0.57707  0.21457  0.12757  0.11426  1.68939  3.35709  3.67419  3.88209
+  3.86371  3.22634  2.49647  1.84377  1.15687  0.09138 -0.36996 -0.04023
+  1.02408  2.05775  2.68926  2.74955  2.42499  2.04678  1.55711  1.00697
+  0.05163  0.00299 -0.17038  0.08753  1.18689  2.24636  2.73093  2.76323
+  2.65887  2.14045  1.40562  0.50704 -0.61236 -1.29634 -1.05969 -0.13291
+  0.96124  1.48528  1.46883  1.23917  0.87082  0.57255  0.35700  0.19011
+ -0.10233  0.05477 -0.00840  0.09387  0.67551  1.37869  1.72925  1.53428
+  1.31553  0.82680  0.14475 -0.97642 -1.85541 -1.92868 -1.09786  0.07237
+  0.91454  0.97238  0.58573  0.26675 -0.11967 -0.34550 -0.35246 -0.32802
+  0.52160  0.15688 -0.09909 -0.06538  0.41444  1.10954  1.57762  1.58789
+  1.28279  0.65634 -0.44715 -1.51329 -2.08018 -1.90600 -1.01779  0.15231
+  0.91178  1.43560  0.45842  0.08514 -0.30926 -0.44935 -0.25988 -0.05601
+  0.17976  0.55827 -0.34578 -0.27097  0.25407  1.08656  1.80718  1.95109
+  1.58890  0.72912 -0.40442 -1.34979 -1.91684 -1.87165 -0.98156  0.28439
+  0.89099  0.90274  0.79523  0.40138  0.02081  0.00907  0.23280  0.31097
+ -0.44608 -0.50159 -0.63851 -0.46568  0.06284  0.89854  2.27207  2.66185
+  2.06789  0.75765 -0.37406 -1.13229 -1.70425 -1.63652 -0.60650  0.74288
+  0.97450  0.83959  0.77625  0.54584  0.23025  0.14501  0.19838  0.06330
+ -1.11297 -1.28309 -1.07056 -0.72163 -0.11182  1.28275  1.90578  2.41469
+  1.97238  0.84092  0.11079 -0.94101 -1.15465 -0.94939  0.64316  0.56647
+  0.70355  0.74958  1.63039  0.63838  0.25608  0.41040 -0.50836 -0.80252
+ -1.72473 -1.92912 -1.10012 -1.05519 -0.10274  0.90677  2.05671  2.58075
+  2.16667  1.05344  0.03573 -0.05773 -0.58287 -1.40318 -1.58072 -0.87231
+  0.01980  0.51998  0.63491  0.37020 -0.25344 -0.90749 -1.16574 -1.34771
+%FLAG CMAP_PARAMETER_06                                                         
+%COMMENT  Leu CMAP                                                              
+%FORMAT(8F9.5)                                                                  
+ -0.86694 -0.26821  0.11903  0.36257  0.95573  1.67477  2.43156  2.60365
+  2.27204  1.80613  1.46886  1.61233 -0.96663 -1.49770 -1.08239 -0.09973
+  0.68400  0.98069  0.74771  0.20585 -0.44627 -0.94569 -1.07455 -1.03710
+ -0.32646  0.18654  0.61372  0.67096  1.01304  1.68958  2.59064  2.69380
+  2.62711  2.28315  1.55874 -0.12149 -1.21885 -1.44423 -0.97001 -0.05369
+  0.80796  1.12834  0.84158  0.41540 -0.05618 -0.48333 -0.57243 -0.49018
+ -0.00270  0.44349  0.67720  0.69907  0.96098  1.51827  2.31922  2.59766
+  2.46815  2.10040  1.01494 -0.35138 -1.06078 -0.51379 -0.69064  0.13405
+  0.94764  1.25044  1.05896  0.70807  1.27955  0.00478 -0.14861 -0.13199
+  0.46773  1.06122  0.84151  0.87321  1.53577  2.26717  2.28379  2.61533
+  2.48323  2.10062  0.99888 -0.16216 -0.70927 -0.70653 -0.29305  0.40855
+  1.21244  1.57878  1.45953  1.15294  0.73992  0.44830  0.51887  0.42642
+  1.08264  1.22032  1.01432  0.92883  1.19777  1.89909  2.63517  2.91989
+  2.71483  2.15712  1.13870  0.10970 -0.35319 -0.45575 -0.07314  0.71696
+  1.39933  1.70190  1.76612  1.54603  1.28907  0.96167  1.05593  0.99887
+  1.28886  1.08719  1.25509  0.61945  1.07490  1.93759  3.19207  3.05501
+  2.85024  2.25228  1.28855  0.30319 -0.32580 -0.33934  0.94330  1.01391
+  1.36742  1.55398  1.68291  1.69903  1.58878  1.35670  1.38167  1.38984
+  0.98482  0.77092  0.58293  0.75254  1.33157  2.19094  2.97361  3.31530
+  2.98261  2.34181  1.68188  0.20860 -0.18920  0.15129  0.97347  1.18438
+  1.41087  2.18263  1.74084  1.83977  2.49337  1.40782  1.29872  1.23230
+  0.48495  0.51375  0.72118  1.16071  2.03516  2.76085  3.33781  3.33714
+  3.21881  1.91348  0.71654 -0.06047  0.05722  0.95499  1.57463  1.97846
+  2.20669  2.25753  2.16240  2.05082  1.46338  0.92763  0.63950  0.52464
+  0.07954  0.44680  1.02424  2.02016  2.99245  3.73027  3.90871  3.36270
+  2.34980  1.21384  0.31676  0.22259  0.86998  1.74017  2.65575  2.56314
+  2.94846  3.04800  2.92362  2.53858  1.53008  0.44000  0.00000 -0.00769
+  0.24993  1.09492  2.17567  3.43132  4.50566  5.05694  4.64546  3.50848
+  2.15393  1.27464  0.97041  1.34987  2.11323  2.30548  2.56683  3.12183
+  3.71616  4.15639  4.02019  3.11381  1.50702  0.51912 -0.20195 -0.08615
+  1.52978  2.82371  4.12062  5.09490  6.15608  6.08176  5.03421  3.52597
+  2.34959  2.18514  2.44731  2.85399  2.64346  2.42082  2.71715  3.68263
+  4.79352  5.66725  5.08137  3.19151  1.34349  0.25042  0.36715  0.82954
+  3.49877  5.10429  4.80281  4.54651  4.68704  4.66098  4.37663  3.68363
+  3.39535  3.95518  3.96235  2.85930  2.21248  2.20453  2.53736  4.31396
+  5.52110  4.69616  3.78755  2.61424  1.52261  1.35018  1.75048  2.53707
+  5.65682  4.15269  3.35229  3.00261  3.08500  3.54523  4.16460  4.62833
+  5.13779  5.01177  3.02054  1.47096  1.36914  1.36431  2.92161  6.08683
+  3.79124  3.26901  3.87628  3.15138  2.56586  2.96443  3.52026  4.83005
+  4.54702  3.10593  2.16146  1.79107  2.10872  3.47796  4.87594  5.92625
+  6.01846  4.12483  2.27314  1.85210  1.40705  2.31574  3.63083  3.28348
+  2.48395  2.41514  2.93210  3.56664  3.83230  4.13078  4.61915  5.21000
+  2.54403  1.68952  0.97521  0.88413  2.02670  4.01998  5.83129  6.49399
+  5.45501  4.03342  2.72981  3.04219  2.43764  2.97586  2.73313  1.73379
+  1.55615  2.30112  3.86657  4.36600  4.57747  4.78312  4.62251  3.65331
+  1.39094  0.80730  0.29380  0.53655  2.14327  4.35364  5.64162  5.52871
+  4.81227  3.89474  3.02138  2.56961  2.36903  1.91970  1.04584  0.61644
+  1.26738  2.48009  3.51320  4.14947  3.98350  3.59513  2.95805  2.05137
+  0.59467  0.26702 -0.00118  0.34338  1.95569  3.71282  4.31538  4.26902
+  3.93382  3.80334  2.45012  1.80769  1.23485  0.28708 -0.16539  0.11408
+  1.10892  2.16939  3.27563  2.90643  2.66635  2.32593  1.63311  1.04332
+ -0.00101 -0.07278 -0.15248  0.39936  1.35477  2.58696  2.88424  2.91922
+  2.69118  2.08752  1.30318  0.53921 -0.47040 -1.05688 -0.84349  0.07495
+  1.13508  1.90971  1.60384  1.52061  1.19284  0.82628  0.49692  0.18749
+  0.52653 -0.01117  0.01170  0.35019  0.99208  1.68051  1.85145  1.71415
+  1.38754  0.91039  0.24804 -0.73699 -1.51069 -1.53963 -0.72203  0.43100
+  1.18026  1.23810  0.97321  0.69525  0.29409 -0.04217 -0.12688 -0.18077
+  0.41738  0.42830  0.25395  0.41670  0.84705  1.54378  1.90242  1.75429
+  1.39459  0.87970 -0.19758 -1.19662 -1.65765 -1.41581 -0.57110  0.57555
+  1.30161  1.37911  1.15311  0.73096  0.18428  0.11942  0.12025  0.23185
+  0.51056  0.47767  0.30339  0.39748  0.84570  1.55327  2.29045  2.38960
+  1.92281  1.05703  0.33844 -0.94589 -1.40734 -1.22267 -0.28396  0.91594
+  1.42889  1.47580  1.35177  1.37396  0.53214  0.53898  0.61490  0.64450
+ -0.24761 -0.32226 -0.19849 -0.08985  1.01997  1.40580  2.20658  2.50290
+  1.91878  0.83859 -0.21275 -0.98048 -1.44651 -1.19821  0.00869  1.25483
+  1.43243  1.66446  1.63593  0.87150  0.53192  0.38847  0.31803  0.05867
+ -0.50737 -1.45363 -0.79190  0.11592  0.23743  1.27007  2.22830  3.43018
+  2.03991  0.82982 -0.28204 -0.30716 -1.28098 -0.47386  0.89069  1.08272
+  1.18900  1.30124  1.20693  0.90441  0.47681 -0.17330 -0.62574 -1.08723
+ -1.62255 -1.96136 -0.83933 -0.65406  0.11828  1.42624  2.54120  2.90447
+  2.24826  1.86505 -0.18930 -0.85728 -0.87693 -1.06001 -1.16287  0.46816
+  0.39155  1.80618  1.14253  0.79781  0.04909 -0.40498 -1.27362 -1.36635
+%FLAG CMAP_INDEX                                                                
+%FORMAT(6I8)                                                                    
+      12      14      16      36      38       6
+      36      38      40      50      52       2
+      50      52      54      74      76       6
+      74      76      78      89      91       4
+      89      91      93     103     105       3
+     103     105     107     110     112       1
+     110     112     114     132     134       5
+     132     134     136     156     158       6
+     156     158     160     170     172       2
+     170     172     174     194     196       6
+     194     196     198     216     218       5

From 6bbb2f8ea98dced36c9b0fdb697910a633e15b6f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 11 Feb 2026 10:41:39 -0500
Subject: [PATCH 1333/1492] Do not try to calculate CMAP energy if no CMAP
 terms/parameters are present

---
 src/Action_Energy.cpp | 12 +++++++-----
 src/Energy/CMAP.h     |  2 ++
 2 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/src/Action_Energy.cpp b/src/Action_Energy.cpp
index 724f57a1d0..6c98b9a569 100644
--- a/src/Action_Energy.cpp
+++ b/src/Action_Energy.cpp
@@ -482,11 +482,13 @@ Action::RetType Action_Energy::DoAction(int frameNum, ActionFrame& frm) {
         Etot += ene;
         break;
       case C_CMAP:
-        time_cmap_.Start();
-        ene = cmap_->Ene_CMAP(frm.Frm());
-        time_cmap_.Stop();
-        Energy_[CMAP]->Add(frameNum, &ene);
-        Etot += ene;
+        if (cmap_->HasCMAPs()) {
+          time_cmap_.Start();
+          ene = cmap_->Ene_CMAP(frm.Frm());
+          time_cmap_.Stop();
+          Energy_[CMAP]->Add(frameNum, &ene);
+          Etot += ene;
+        }
         break;
       case C_N14:
         time_14_.Start();
diff --git a/src/Energy/CMAP.h b/src/Energy/CMAP.h
index 131b98415c..8bfac72272 100644
--- a/src/Energy/CMAP.h
+++ b/src/Energy/CMAP.h
@@ -30,6 +30,8 @@ class CMAP {
     double Ene_CMAP(Frame const&) const;
     /// Calculate CMAP energy and force
     double Ene_Frc_CMAP(Frame const&, double*) const;
+    /// \return True if there are CMAP terms
+    bool HasCMAPs() const { return (selected_cmaps_ != 0 || all_cmaps_ != 0); }
   private:
     //double get_cmap_energy(CmapArray const&, Frame const&, double&, double&,
     //                         Vec3(&dPhi_dijkl)[4], Vec3(&dPsi_djklm)[4]) const;

From a132b7f1e4ba47df4ab2623305a5c2a72f2a4d46 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 11 Feb 2026 12:12:36 -0500
Subject: [PATCH 1334/1492] Have topology report whether non-contiguous mols
 are present

---
 src/Topology.cpp |  5 ++++-
 src/Topology.h   | 11 +++++++----
 2 files changed, 11 insertions(+), 5 deletions(-)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index 4fb8e963ae..9ce8bb3d00 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -21,7 +21,8 @@ Topology::Topology() :
   ipol_(0),
   NsolventMolecules_(0),
   pindex_(0),
-  n_extra_pts_(0)
+  n_extra_pts_(0),
+  hasNonContiguousMols_(false)
 { }
 
 /** Copy the metadata from another Topology. */
@@ -1282,6 +1283,7 @@ int Topology::NresInMol(int idx) const {
   * recursive search over the bonds of each atom.
   */
 int Topology::DetermineMolecules() {
+  hasNonContiguousMols_ = false;
   // Since this is always done only print when debugging
   if (debug_>0) mprintf("\t%s: determining molecule info from bonds.\n",c_str());
   // Reset molecule info for each atom
@@ -1339,6 +1341,7 @@ int Topology::DetermineMolecules() {
     }
   }
   if (!nonContiguousMols.empty()) {
+    hasNonContiguousMols_ = true;
     mprintf("Warning: %zu molecules have non-contiguous segments of atoms.\n", nonContiguousMols.size());
     for (std::vector< std::vector<Molecule>::const_iterator >::const_iterator it = nonContiguousMols.begin();
                                                                               it != nonContiguousMols.end(); ++it)
diff --git a/src/Topology.h b/src/Topology.h
index 40bfeb5760..6387269338 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -121,6 +121,8 @@ class Topology {
     int DetermineMolecules();
     /// Designate all atoms as part of a single molecule.
     int SetSingleMolecule();
+    /// \return True if molecules with non-contiguous residues are present
+    bool HasNoncontiguousMols() const { return hasNonContiguousMols_; }
     // ----- Bond-specific routines --------------
     size_t Nbonds()                            const { return bonds_.size()+bondsh_.size(); }
     BondArray         const& Bonds()        const { return bonds_;        }
@@ -406,10 +408,11 @@ class Topology {
     Frame refCoords_;       ///< Internal reference coords for distance-based masks
 
     int debug_;
-    int ipol_;              ///< 0 if fixed charge, 1 if polarizable
-    int NsolventMolecules_; ///< Number of molecules marked SOLVENT
-    int pindex_;            ///< Internal index used to ID Topology 
-    int n_extra_pts_;       ///< Number of extra points.
+    int ipol_;                  ///< 0 if fixed charge, 1 if polarizable
+    int NsolventMolecules_;     ///< Number of molecules marked SOLVENT
+    int pindex_;                ///< Internal index used to ID Topology 
+    int n_extra_pts_;           ///< Number of extra points.
+    bool hasNonContiguousMols_; ///< Set to true during DetermineMolecules() if there are molecules with non-contiguous residues
 };
 // ----- INLINE FUNCTIONS ------------------------------------------------------
 NonbondType const& Topology::GetLJparam(int a1, int a2) const {

From 8446471316e84300458d432696233ca5654bf417 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 11 Feb 2026 12:22:15 -0500
Subject: [PATCH 1335/1492] Pass in just the Topology

---
 src/Action_FixAtomOrder.cpp | 24 ++++++++++++------------
 src/Action_FixAtomOrder.h   |  4 ++--
 2 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/src/Action_FixAtomOrder.cpp b/src/Action_FixAtomOrder.cpp
index 7fedf1f9da..db610a6ec0 100644
--- a/src/Action_FixAtomOrder.cpp
+++ b/src/Action_FixAtomOrder.cpp
@@ -59,9 +59,9 @@ Action::RetType Action_FixAtomOrder::Init(ArgList& actionArgs, ActionInit& init,
 Action::RetType Action_FixAtomOrder::Setup(ActionSetup& setup) {
   Action::RetType ret;
   if (mode_ == FIX_MOLECULES)
-    ret = FixMolecules(setup);
+    ret = FixMolecules(setup.Top());
   else if (mode_ == PDB_ORDER)
-    ret = PdbOrder(setup);
+    ret = PdbOrder(setup.Top());
   else
     return Action::ERR;
 
@@ -98,18 +98,18 @@ Action::RetType Action_FixAtomOrder::Setup(ActionSetup& setup) {
 }
 
 /** Try to make the order match original PDB info. */
-Action::RetType Action_FixAtomOrder::PdbOrder(ActionSetup& setup) {
+Action::RetType Action_FixAtomOrder::PdbOrder(Topology const& topIn) {
   if (hetatm_.MaskStringSet()) {
-    if (setup.Top().SetupCharMask( hetatm_ )) return Action::ERR;
+    if (topIn.SetupCharMask( hetatm_ )) return Action::ERR;
     hetatm_.MaskInfo();
   } else {
-    hetatm_ = CharMask( setup.Top().Natom() );
+    hetatm_ = CharMask( topIn.Natom() );
   }
   // Create array with PDB info.
   std::vector<AtomTopType> atoms;
-  for (int idx = 0; idx != setup.Top().Natom(); idx++)
+  for (int idx = 0; idx != topIn.Natom(); idx++)
   {
-    Residue const& res = setup.Top().Res( setup.Top()[idx].ResNum() );
+    Residue const& res = topIn.Res( topIn[idx].ResNum() );
     AtomTopType::PdbType pt;
     if (hetatm_.AtomInCharMask(idx))
       pt = AtomTopType::HETATM;
@@ -122,7 +122,7 @@ Action::RetType Action_FixAtomOrder::PdbOrder(ActionSetup& setup) {
   std::sort(atoms.begin(), atoms.end());
   // Put indices in atomMap_
   atomMap_.clear();
-  atomMap_.reserve( setup.Top().Natom() );
+  atomMap_.reserve( topIn.Natom() );
   for (std::vector<AtomTopType>::const_iterator it = atoms.begin();
                                                 it != atoms.end(); ++it)
     atomMap_.push_back( it->AtomIdx() );
@@ -131,11 +131,11 @@ Action::RetType Action_FixAtomOrder::PdbOrder(ActionSetup& setup) {
 }
 
 /** Fix molecules that are not contiguous. */
-Action::RetType Action_FixAtomOrder::FixMolecules(ActionSetup& setup) {
+Action::RetType Action_FixAtomOrder::FixMolecules(Topology const& topIn) {
   atomMap_.clear();
-  atomMap_.reserve( setup.Top().Natom() );
-  for (Topology::mol_iterator mol = setup.Top().MolStart();
-                              mol != setup.Top().MolEnd(); ++mol)
+  atomMap_.reserve( topIn.Natom() );
+  for (Topology::mol_iterator mol = topIn.MolStart();
+                              mol != topIn.MolEnd(); ++mol)
   {
     for (Unit::const_iterator seg = mol->MolUnit().segBegin();
                               seg != mol->MolUnit().segEnd(); ++seg)
diff --git a/src/Action_FixAtomOrder.h b/src/Action_FixAtomOrder.h
index 926ed668a1..443c28678a 100644
--- a/src/Action_FixAtomOrder.h
+++ b/src/Action_FixAtomOrder.h
@@ -18,8 +18,8 @@ class Action_FixAtomOrder: public Action {
     void Print() {}
 
     void VisitAtom(int,int,Topology const&);
-    Action::RetType PdbOrder(ActionSetup&);
-    Action::RetType FixMolecules(ActionSetup&);
+    Action::RetType PdbOrder(Topology const&);
+    Action::RetType FixMolecules(Topology const&);
 
     enum ModeType {FIX_MOLECULES = 0, PDB_ORDER};
 

From 4f2e25ab6b6a90497cc2facd5d6ec38ef89f7d0c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 11 Feb 2026 12:31:58 -0500
Subject: [PATCH 1336/1492] Create separate routine for fixing atom ordering

---
 src/Action_FixAtomOrder.cpp | 32 ++++++++++++++++++++++++++++++++
 src/Action_FixAtomOrder.h   |  2 ++
 2 files changed, 34 insertions(+)

diff --git a/src/Action_FixAtomOrder.cpp b/src/Action_FixAtomOrder.cpp
index db610a6ec0..5f77388272 100644
--- a/src/Action_FixAtomOrder.cpp
+++ b/src/Action_FixAtomOrder.cpp
@@ -55,6 +55,38 @@ Action::RetType Action_FixAtomOrder::Init(ArgList& actionArgs, ActionInit& init,
   return Action::OK;
 }
 
+/** Separate routine that will just fix the atom order. */
+int Action_FixAtomOrder::FixMoleculeOrder(Topology& topOut, Frame& frameOut, int debugIn)
+{
+  debug_ = debugIn;
+  mode_ = FIX_MOLECULES;
+  if (FixMolecules(topOut) != Action::OK) {
+    mprinterr("Error: Fixing molecule order failed.\n");
+    return 1;
+  }
+  if (debug_ > 0) {
+    mprintf("\tNew atom mapping:\n");
+    for (MapType::const_iterator atom = atomMap_.begin();
+                                 atom != atomMap_.end(); ++atom)
+      mprintf("\t\tNew atom %8li => old atom %8i\n", atom - atomMap_.begin() + 1, *atom + 1);
+  }
+  // Create new topology based on map
+  if (newParm_ != 0) delete newParm_;
+  newParm_ = topOut.ModifyByMap( atomMap_ );
+  if (newParm_ == 0) {
+    mprinterr("Error: Could not create re-ordered topology.\n");
+    return Action::ERR;
+  }
+  topOut = *newParm_;
+  
+  // Allocate space for new frame and reorder coords
+  newFrame_.SetupFrameV( newParm_->Atoms(), frameOut.CoordsInfo() );
+  newFrame_.SetCoordinatesByMap( frameOut, atomMap_ );
+  frameOut = newFrame_;
+
+  return 0;
+}
+
 // Action_FixAtomOrder::setup()
 Action::RetType Action_FixAtomOrder::Setup(ActionSetup& setup) {
   Action::RetType ret;
diff --git a/src/Action_FixAtomOrder.h b/src/Action_FixAtomOrder.h
index 443c28678a..7b570ad756 100644
--- a/src/Action_FixAtomOrder.h
+++ b/src/Action_FixAtomOrder.h
@@ -11,6 +11,8 @@ class Action_FixAtomOrder: public Action {
     ~Action_FixAtomOrder();
     DispatchObject* Alloc() const { return (DispatchObject*)new Action_FixAtomOrder(); }
     void Help() const;
+    /// Standalone routine for e.g. the Exec_Build command
+    int FixMoleculeOrder(Topology&, Frame&, int);
   private:
     Action::RetType Init(ArgList&, ActionInit&, int);
     Action::RetType Setup(ActionSetup&);

From a9f9ec562ad355b97aed72fb9f8bf41ad893f70b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 11 Feb 2026 12:51:53 -0500
Subject: [PATCH 1337/1492] If residues in molecules are not contiguous, fix
 the ordering by default unless nofixorder is specified.

---
 src/Exec_Build.cpp | 26 +++++++++++++++++++++++++-
 src/Exec_Build.h   |  1 +
 2 files changed, 26 insertions(+), 1 deletion(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 3dd5db467b..ce01b16a1b 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -1,4 +1,5 @@
 #include "Exec_Build.h"
+#include "Action_FixAtomOrder.h"
 #include "AssociatedData_Connect.h"
 #include "CpptrajStdio.h"
 #include "DataSet_Parameters.h" // For casting DataSet_Parameters to ParameterSet
@@ -29,6 +30,10 @@ Exec_Build::Exec_Build() :
   check_structure_(true),
   keepMissingSourceAtoms_(false),
   requireAllInputAtoms_(false),
+  doHisDetect_(true),
+  doDisulfide_(true),
+  doSugar_(true),
+  fixAtomOrder_(true),
   outCrdPtr_(0)
 {}
 
@@ -820,7 +825,7 @@ const
 void Exec_Build::Help() const
 {
   mprintf("\tname <output COORDS> crdset <COORDS set> [frame <#>]\n"
-          "\t[title <title>] [verbose <#>] [keepmissingatoms]\n"
+          "\t[title <title>] [verbose <#>] [keepmissingatoms] [nofixorder]\n"
           "\t[parmout <topology file>] [crdout <coord file>] [simplecheck]\n");
   mprintf("\t[%s]\n", Cpptraj::Parm::GB_Params::HelpText().c_str());
   mprintf("\t[lj1264 %s]\n", Cpptraj::Parm::LJ1264_Params::HelpText().c_str());
@@ -912,6 +917,7 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, in
   doHisDetect_ = enableExtraDetection;
   doDisulfide_ = enableExtraDetection;
   doSugar_     = enableExtraDetection;
+  fixAtomOrder_ = enableExtraDetection;
 
   // Set up Output coords
   if (setupOutputCoords(inCrdPtr, outset, title, DSL)) {
@@ -1013,6 +1019,10 @@ Exec::RetType Exec_Build::BuildAndParmStructure(DataSet* inCrdPtr, std::string c
   debug_ = debugIn;
   int verbose = argIn.getKeyInt("verbose", 0);
   std::string title = argIn.GetStringKey("title");
+  if (argIn.hasKey("nofixorder"))
+    fixAtomOrder_ = false;
+  else
+    fixAtomOrder_ = true;
   std::string outputTopologyName = argIn.GetStringKey("parmout");
   std::string outputCoordsName = argIn.GetStringKey("crdout");
   if (argIn.hasKey("simplecheck")) {
@@ -1534,6 +1544,20 @@ int Exec_Build::StructurePrepAndFillTemplates(ArgList& argIn, Topology& topIn, F
   topOut.AllocRotateArray();
     // Finalize topology - determine molecules, dont renumber residues
   topOut.CommonSetup(true, false);
+
+  if (topOut.HasNoncontiguousMols()) {
+    mprintf("\tMolecules with non-contiguous stretches of residues are present.\n");
+    if (fixAtomOrder_) {
+      mprintf("\tReordering topology/coords so that molecules are contiguous.\n");
+      Action_FixAtomOrder fixOrder;
+      if (fixOrder.FixMoleculeOrder(topOut, frameOut, debug_)) {
+        mprinterr("Error: Could not fix molecule order.\n");
+        return 1;
+      }
+    } else {
+      mprintf("\t'nofixorder' was specified - not reordering molecules.\n");
+    }
+  }
   return 0;
 }
 
diff --git a/src/Exec_Build.h b/src/Exec_Build.h
index 2302d557cd..293b1608f3 100644
--- a/src/Exec_Build.h
+++ b/src/Exec_Build.h
@@ -60,6 +60,7 @@ class Exec_Build : public Exec {
     bool doHisDetect_;
     bool doDisulfide_;
     bool doSugar_;
+    bool fixAtomOrder_;           ///< If true will attempt to make sure residues in molecules are contiguous
     DataSet* outCrdPtr_;          ///< Hold built (output) COORDS
 
     Timer t_total_;

From cbe5acd42a0e17ec7d6a279ca0529d91aeaea0d8 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 11 Feb 2026 13:52:51 -0500
Subject: [PATCH 1338/1492] Add CMAP to new stuff. Note that fixatomorder now
 baked into the build command

---
 doc/ChangeLog.v7.md | 30 +++++++++++++++++-------------
 1 file changed, 17 insertions(+), 13 deletions(-)

diff --git a/doc/ChangeLog.v7.md b/doc/ChangeLog.v7.md
index 61520172d7..a6f7f6d5e2 100644
--- a/doc/ChangeLog.v7.md
+++ b/doc/ChangeLog.v7.md
@@ -5,7 +5,7 @@ The major change in this version is the introduction of the ability of CPPTRAJ t
 
 New Commands
 ============
-- `build` - Allow full build and parameterization of systems for MD, including CMAP, LJ 12-6-4, solvation, and ions.
+- `build` - Allow full build and parameterization of systems for MD, including CMAP, LJ 12-6-4, solvation, and ions. Includes `prepareforleap` and `fixatomorder` functionality.
 
 - `source` - Read (limited) leaprc files.
 
@@ -13,6 +13,20 @@ New Commands
 
 - `desc` - DEBUG: describe a selection in the same manner as leap.
 
+New functionality
+=================
+- Read topology/coordinates with the 'readdata' command.
+
+- More complete read of Amber library/prep files.
+
+- Read CMAP energy term from Amber MDOUT file.
+
+- The `permutedihedrals` command will now check rings.
+
+- The `graft` command will now use CONNECT atom information if it is present.
+
+- The `energy` command will now calculate CMAP energies (if CMAP parameters are present) and/or LJ 12-6-4 contributions to VDW energy (if `lj1264` is specified).
+
 New Keywords
 ============
 - Introduce ring intersection check to `checkstructure` action.
@@ -30,23 +44,13 @@ If `checkxp` is specified, extra points will be included. By default, extra poin
 
 Add `namemap <mapset>` keywords for `change atomname from <mask>` to use an atom name map for determining new atom names.
 
-Add `gb` to `change` command to chang GB radii.
+Add `gb` to `change` command to change GB radii.
 
 Add `complete` keyword to `zmatrix` command to get complete zmatrix instead of minimal zmatrix.
 
 Add `atombondorder` keyword to mol2 output; sort bonds by first atom index (similar to how leap writes mol2 files).
 
-New functionality
-=================
-- Read topology/coordinates with the 'readdata' command.
-
-- More complete read of Amber library/prep files.
-
-- Read CMAP energy term from Amber MDOUT file.
-
-- The `permutedihedrals` command will now check rings.
-
-- The `graft` command will now use CONNECT atom information if it is present.
+Add `lj1264` keyword to the `energy` command to enable LJ 12-6-4 energy calculation.
 
 New file formats recognized
 ===========================

From 83240d49d9e6593803736f924dc26557ca8c3034 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 12 Feb 2026 10:14:07 -0500
Subject: [PATCH 1339/1492] Fix up help

---
 src/Exec_Build.cpp        | 5 +++--
 src/Structure/Solvate.cpp | 4 +---
 2 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index ce01b16a1b..25f08ab7f6 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -824,8 +824,9 @@ const
 // Exec_Build::Help()
 void Exec_Build::Help() const
 {
-  mprintf("\tname <output COORDS> crdset <COORDS set> [frame <#>]\n"
-          "\t[title <title>] [verbose <#>] [keepmissingatoms] [nofixorder]\n"
+  mprintf("\tname <output COORDS> crdset <COORDS set> [frame <#>]\n");
+  Cpptraj::Structure::PdbCleaner::Help();
+  mprintf("\t[title <title>] [verbose <#>] [keepmissingatoms] [nofixorder]\n"
           "\t[parmout <topology file>] [crdout <coord file>] [simplecheck]\n");
   mprintf("\t[%s]\n", Cpptraj::Parm::GB_Params::HelpText().c_str());
   mprintf("\t[lj1264 %s]\n", Cpptraj::Parm::LJ1264_Params::HelpText().c_str());
diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index abb6f5d176..20795c7250 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -36,8 +36,7 @@ const char* Solvate::SetboxKeywords() {
 }
 
 const char* Solvate::SolvateKeywords1() {
-  //return "{buffer <buffer> | bufx <bufx> bufy <bufy> bufz <bufz> | nsolvent <#>}";
-  return "{buffer <buffer> | bufx <bufx> bufy <bufy> bufz <bufz> }";
+  return "{buffer <buffer> | bufx <bufx> bufy <bufy> bufz <bufz> | nsolvent <#>}";
 }
 
 const char* Solvate::SolvateKeywords2() {
@@ -71,7 +70,6 @@ int Solvate::InitSolvate(ArgList& argIn, bool octIn, int debugIn) {
   debug_ = debugIn;
   doTruncatedOct_ = octIn;
   nsolvent_ = (unsigned int)argIn.getKeyInt("nsolvent", 0);
-  //nsolvent_ = 0; // TODO enable
   if (nsolvent_ > 0) clip_ = false;
 
   if (getBufferArg(argIn, -1.0)) return 1;

From c052dffc3479b39e1ab1850751d715ff059e21a2 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 13 Feb 2026 08:36:49 -0500
Subject: [PATCH 1340/1492]  I can't believe I got these backwards...

---
 src/Exec_Build.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 25f08ab7f6..ca5a4eac4b 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -1031,8 +1031,8 @@ Exec::RetType Exec_Build::BuildAndParmStructure(DataSet* inCrdPtr, std::string c
   } else {
     check_structure_ = true;
   }
-  doHisDetect_ = !argIn.hasKey("nodisulfides");
-  doDisulfide_ = !argIn.hasKey("nohisdetect");
+  doHisDetect_ = !argIn.hasKey("nohisdetect");
+  doDisulfide_ = !argIn.hasKey("nodisulfides");
   doSugar_ = !argIn.hasKey("nosugars");
   if (!outputTopologyName.empty())
     mprintf("\tWill write topology to %s\n", outputTopologyName.c_str());

From f397bcf6a0fd03c2b013f4a68eb7c684c180593f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 13 Feb 2026 08:47:51 -0500
Subject: [PATCH 1341/1492] Add TODO for renumbering after adding ions

---
 src/Structure/AddIons.cpp | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/Structure/AddIons.cpp b/src/Structure/AddIons.cpp
index 58a96b34b9..abb7014f3c 100644
--- a/src/Structure/AddIons.cpp
+++ b/src/Structure/AddIons.cpp
@@ -315,6 +315,8 @@ const
   Frame frameOutCopy = frameOut;
   frameOut.ModifyByMap( frameOutCopy, atomMap );
 
+  // TODO if PDB original residue number/atom number is present, it needs to be regenerated for ions/waters 
+
   return 0;
 }
 

From bb889596e6531f6a5ac0b1792f432be6aa386df8 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 13 Feb 2026 13:53:49 -0500
Subject: [PATCH 1342/1492] Give build the ability to just work directly on an
 input file

---
 src/Exec_Build.cpp | 25 ++++++++++++++++++++-----
 src/cpptrajdepend  |  2 +-
 2 files changed, 21 insertions(+), 6 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index ca5a4eac4b..bab9c105c4 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -2,6 +2,7 @@
 #include "Action_FixAtomOrder.h"
 #include "AssociatedData_Connect.h"
 #include "CpptrajStdio.h"
+#include "DataIO_Coords.h"
 #include "DataSet_Parameters.h" // For casting DataSet_Parameters to ParameterSet
 #include "ParmFile.h"
 #include "StringRoutines.h" // integerToString
@@ -857,18 +858,32 @@ void Exec_Build::Help() const
 // Exec_Build::Execute()
 Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
 {
+  std::string outset = argIn.GetStringKey("name");
   // Get input coords
+  DataSet* inCrdPtr = 0;
   std::string crdset = argIn.GetStringKey("crdset");
   if (crdset.empty()) {
-    mprinterr("Error: Must specify input COORDS set with 'crdset'\n");
-    return CpptrajState::ERR;
+    // Try to load a file
+    FileName fname(argIn.GetStringNext());
+    if (File::Exists( fname )) {
+      DataIO_Coords crdin;
+      if (crdin.ReadData(fname, State.DSL(), fname.Base())) {
+        mprinterr("Error: Could not read top/coords from '%s'\n", fname.full());
+        return CpptrajState::ERR;
+      }
+      inCrdPtr = crdin.added_back();
+    }
+  } else {
+    inCrdPtr = State.DSL().FindSetOfGroup( crdset, DataSet::COORDINATES );
+    if (inCrdPtr == 0) {
+      mprinterr("Error: No COORDS set found matching %s\n", crdset.c_str());
+      return CpptrajState::ERR;
+    }
   }
-  DataSet* inCrdPtr = State.DSL().FindSetOfGroup( crdset, DataSet::COORDINATES );
   if (inCrdPtr == 0) {
-    mprinterr("Error: No COORDS set found matching %s\n", crdset.c_str());
+    mprinterr("Error: Must specify file to build or COORDS set with 'crdset'\n");
     return CpptrajState::ERR;
   }
-  std::string outset = argIn.GetStringKey("name");
 
   return BuildAndParmStructure(inCrdPtr, outset, State.DSL(), State.Debug(), argIn, Cpptraj::Parm::UNKNOWN_GB);
 }
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 6d81805955..3f7ee67e2b 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -319,7 +319,7 @@ EwaldOptions.o : EwaldOptions.cpp ArgList.h CpptrajStdio.h EwaldOptions.h
 ExclusionArray.o : ExclusionArray.cpp Atom.h AtomMask.h CharMask.h CpptrajStdio.h ExclusionArray.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Unit.h
 Exec_AddMissingRes.o : Exec_AddMissingRes.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h CharMask.h CompactFrameArray.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_AddMissingRes.h Exec_AddMissingRes_Pres.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h ParmFile.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h Trajout_Single.h Unit.h Vec3.h
 Exec_Analyze.o : Exec_Analyze.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Analyze.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_Build.o : Exec_Build.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h ExclusionArray.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PairList.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/ImproperParmHolder.h Parm/LJ1264_Params.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h ParmFile.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/AddIons.h Structure/Builder.h Structure/Creator.h Structure/Disulfide.h Structure/HisProt.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/RingFinder.h Structure/Solvate.h Structure/StructureEnum.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Build.o : Exec_Build.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h ActionTopWriter.h Action_FixAtomOrder.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_Coords.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h ExclusionArray.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PairList.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/ImproperParmHolder.h Parm/LJ1264_Params.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h ParmFile.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/AddIons.h Structure/Builder.h Structure/Creator.h Structure/Disulfide.h Structure/HisProt.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/RingFinder.h Structure/Solvate.h Structure/StructureEnum.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Calc.o : Exec_Calc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Calc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_CatCrd.o : Exec_CatCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CatCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_Change.o : Exec_Change.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Change.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/GB_Params.h Parm/LJ1264_Params.h Parm/ParmEnum.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h

From 5496306b1bdf79f11a623a523ded6c18d6f36697 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 13 Feb 2026 13:54:36 -0500
Subject: [PATCH 1343/1492] Update help

---
 src/Exec_Build.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index bab9c105c4..48b96cb61a 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -825,7 +825,7 @@ const
 // Exec_Build::Help()
 void Exec_Build::Help() const
 {
-  mprintf("\tname <output COORDS> crdset <COORDS set> [frame <#>]\n");
+  mprintf("\t[name <output COORDS>] {crdset <COORDS set>|<file>} [frame <#>]\n");
   Cpptraj::Structure::PdbCleaner::Help();
   mprintf("\t[title <title>] [verbose <#>] [keepmissingatoms] [nofixorder]\n"
           "\t[parmout <topology file>] [crdout <coord file>] [simplecheck]\n");

From 36501acdfa5e0f36e53426f477cfcd3d86df5cf8 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 16 Feb 2026 15:48:01 -0500
Subject: [PATCH 1344/1492] Allow the second ion to also be 0 for
 neutralization. This allows one to specify both positive and negative counter
 ions and use whatever ion is suitable for neutralization. It also allows one
 to add a specified number of positive or negative counter ions and
 automatically have the opposite charge counter ion neutralize.

---
 src/Structure/AddIons.cpp | 59 +++++++++++++++++++++++++++++++--------
 1 file changed, 47 insertions(+), 12 deletions(-)

diff --git a/src/Structure/AddIons.cpp b/src/Structure/AddIons.cpp
index abb7014f3c..c131d5d1c1 100644
--- a/src/Structure/AddIons.cpp
+++ b/src/Structure/AddIons.cpp
@@ -45,11 +45,14 @@ int AddIons::InitAddIons(std::string const& ion1nameIn, int Nion1,
     Nion2_ = 0;
   } else {
     ion2name_ = ion2nameIn;
-    if (Nion2 < 1) {
-      mprinterr("Error: Number of second %s ions cannot be less than 1 (%i)\n", ion2nameIn.c_str(), Nion2);
-      return 1;
-    }
-    Nion2_ = Nion2;
+    //if (Nion2 < 1) {
+    //  mprinterr("Error: Number of second %s ions cannot be less than 1 (%i)\n", ion2nameIn.c_str(), Nion2);
+    //  return 1;
+    //}
+    if (Nion2_ < 0)
+      Nion2_ = 0;
+    else
+      Nion2_ = Nion2;
   }
 
   separation_ = separationIn;
@@ -71,8 +74,12 @@ void AddIons::PrintAddIonsInfo() const {
     mprintf("\t  Adding enough %s ions to neutralize.\n", ion1name_.c_str());
   else
     mprintf("\t  Adding %i %s ions.\n", Nion1_, ion1name_.c_str());
-  if (!ion2name_.empty())
-    mprintf("\t  Adding %i %s ions.\n", Nion2_, ion2name_.c_str());
+  if (!ion2name_.empty()) {
+    if (Nion2_ < 1)
+      mprintf("\t  Adding enough %s ions to neutralize.\n", ion2name_.c_str());
+    else
+      mprintf("\t  Adding %i %s ions.\n", Nion2_, ion2name_.c_str());
+  }
   if (separation_ > 0.0)
     mprintf("\t  Minimum ion separation is %g Ang.\n", separation_);
   mprintf("\t  Ion RNG seed: %i\n", RNG_.Seed());
@@ -197,19 +204,47 @@ const
   // Check that ion can actually neutralize
   int iIon1 = Nion1_;
   int iIon2 = Nion2_; 
+  bool can_neutralize1 = true;
+  bool is_neutralized = false;
   if (Nion1_ < 1) {
     if ( (chargeIon1 < 0 && totalCharge < 0) ||
          (chargeIon1 > 0 && totalCharge > 0) )
     {
-      mprinterr("Error: First ion and system charges have same sign (%g and %g); can't neutralize.\n",
+      mprintf("Warning: First ion and system charges have same sign (%g and %g); can't neutralize.\n",
                 chargeIon1, totalCharge);
-      return 1;
+      can_neutralize1 = false;
+    } else {
+      // Get the nearest integer number of ions needed to neutralize the system.
+      iIon1 = (int)lrint( fabs(totalCharge+(chargeIon2*Nion2_)) / fabs(chargeIon1) );
+      mprintf("\t  Number of %s ions required to neutralize: %i\n", ion1name_.c_str(), iIon1);
+      is_neutralized = true;
+    }
+  }
+
+  bool can_neutralize2 = true;
+  if (Ion2 != 0 && Nion2_ < 1 && !is_neutralized) {
+    if ( (chargeIon2 < 0 && totalCharge < 0) ||
+         (chargeIon2 > 0 && totalCharge > 0) )
+    {
+      mprintf("Warning: Second ion and system charges have same sign (%g and %g); can't neutralize.\n",
+                chargeIon2, totalCharge);
+      can_neutralize2 = false;
+    } else {
+      // Get the nearest integer number of ions needed to neutralize the system.
+      iIon2 = (int)lrint( fabs(totalCharge+(chargeIon1*iIon1)) / fabs(chargeIon2) );
+      mprintf("\t  Number of %s ions required to neutralize: %i\n", ion2name_.c_str(), iIon2);
     }
-    // Get the nearest integer number of ions needed to neutralize the system.
-    iIon1 = (int)lrint( fabs(totalCharge) / fabs(chargeIon1) );
-    mprintf("\t  Number of %s ions required to neutralize: %i\n", ion1name_.c_str(), iIon1);
   }
 
+  if (!can_neutralize1 && !can_neutralize2) {
+    mprinterr("Error: Could not automatically neutralize system charge with specified ions.\n");
+    return 1;
+  }
+  if (iIon1 > 0)
+    mprintf("\t  Adding %i %s ions\n", iIon1, ion1name_.c_str());
+  if (iIon2 > 0)
+    mprintf("\t  Adding %i %s ions\n", iIon2, ion2name_.c_str());
+
   // Check that there is enough solvent to swap
   int nIons = iIon1 + iIon2;
   if ( nIons == nsolvent )

From d6b14b17b15aab72ef5557f6d0d175fa952de712 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 17 Feb 2026 14:50:39 -0500
Subject: [PATCH 1345/1492] Read IPOL section

---
 src/AmberParamFile.cpp | 17 +++++++++++++++++
 src/AmberParamFile.h   |  4 +++-
 2 files changed, 20 insertions(+), 1 deletion(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 2e52066f72..777ff777ff 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -408,6 +408,20 @@ const
   return 0;
 }
 
+/** Read IPOL section */
+int AmberParamFile::read_ipol(ParameterSet& prm, const char* ptr)
+const
+{
+  mprintf("DEBUG: Read IPOL.\n");
+  int ipolIn = -1;
+  if (sscanf(ptr, "%i", &ipolIn) != 1) {
+    mprinterr("Error: Could not read IPOL value from line: %s\n", ptr);
+    return 1;
+  }
+  mprintf("DEBUG: IPOL value is %i\n", ipolIn);
+  return 0;
+}
+
 /** Read radius/depth input for LJ 6-12 nonbond. */
 int AmberParamFile::read_nb_RE(NonbondSet& nbset, const char* ptr)
 const
@@ -694,6 +708,7 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname) const
       else if (line.compare(0, 4, "IMPR") == 0) section = IMPROPER;
       else if (line.compare(0, 4, "HBON") == 0) section = LJ1012;
       else if (line.compare(0, 4, "CMAP") == 0) section = CMAP;
+      else if (line.compare(0, 4, "IPOL") == 0) section = IPOL;
       else if (line.compare(0, 6, "LJEDIT") == 0) {
         section = LJEDIT;
         prm.SetHasLJparams( true );
@@ -722,6 +737,8 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname) const
           err = read_ljedit(Offdiag, ptr);
         else if (section == CMAP)
           err = read_cmap(currentCmap, prm, currentCmapFlag, line);
+        else if (section == IPOL)
+          err = read_ipol(prm, ptr);
         if (err != 0) {
           mprinterr("Error: Reading line: %s\n", ptr);
           return 1;
diff --git a/src/AmberParamFile.h b/src/AmberParamFile.h
index d2ac4c5216..fadd29df8d 100644
--- a/src/AmberParamFile.h
+++ b/src/AmberParamFile.h
@@ -27,7 +27,7 @@ class AmberParamFile {
     static const int MAXSYMLEN;
 
     enum SectionType { ATYPE = 0, HYDROPHILIC, BOND, ANGLE, DIHEDRAL, IMPROPER, 
-                       LJ1012, NB_EQUIV, NONBOND, LJEDIT, CMAP, UNKNOWN };
+                       LJ1012, NB_EQUIV, NONBOND, LJEDIT, CMAP, IPOL, UNKNOWN };
     enum CmapType { CMAP_INITIAL, CMAP_TITLE, CMAP_RESLIST, CMAP_PARAMETER };
 
     class NonbondSet;
@@ -47,6 +47,8 @@ class AmberParamFile {
     int read_improper(ParameterSet&, const char*) const;
     /// Read LJ 10-12 hbond line
     int read_lj1012(ParameterSet&, const char*) const;
+    /// Read IPOL line
+    int read_ipol(ParameterSet&, const char*) const;
     /// Read LJ 6-12 R/depth line
     int read_nb_RE(NonbondSet&, const char*) const;
     /// Read LJ 6-12 A/C coefficient line

From 0cdd3c935c6dca6e9aff7f7340ed995fe169f1bb Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 17 Feb 2026 15:26:28 -0500
Subject: [PATCH 1346/1492] Start fixing CMAP for the pol FF

---
 src/AmberParamFile.cpp | 55 +++++++++++++++++++++++++++++++++---------
 src/AmberParamFile.h   |  4 +--
 2 files changed, 45 insertions(+), 14 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 777ff777ff..f804666235 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -553,30 +553,55 @@ static inline void add_cmap_default_atoms(CmapGridType& cmap) {
   * Atom : C - N - CA - C - N
   */ 
 int AmberParamFile::read_cmap(CmapGridType& currentCmap, ParameterSet& prm, CmapType& currentCmapFlag,
-                              std::string const& line)
+                              std::string const& line, int& cmap_count_is_index)
 const
 {
   ArgList argline(line);
   if (argline.Nargs() > 1)
   {
+    // NOTE: CMAP_COUNT is used differently in different files. For example,
+    //       in ff19SB it is used as an index of the current CMAP parameter
+    //       being read. However, in ff12polL it is used to give a total
+    //       count of CMAP parameters
     if (argline[0] == "%FLAG") {
       if (argline[1] == "CMAP_COUNT") {
         // New CMAP term. Ignore the index for now. If a previous CMAP
         // was read make sure its OK.
-        if (!currentCmap.empty()) {
-          if (currentCmap.AtomNames().empty()) add_cmap_default_atoms( currentCmap );
-          if (check_cmap(prm.CMAP().size()+1, currentCmap)) return 1;
-          prm.CMAP().AddParm( currentCmap, true, debug_ );
-          currentCmap = CmapGridType();
-        }
+        //if (!currentCmap.empty()) {
+        //  if (currentCmap.AtomNames().empty()) add_cmap_default_atoms( currentCmap );
+        //  if (check_cmap(prm.CMAP().size()+1, currentCmap)) return 1;
+        //  prm.CMAP().AddParm( currentCmap, true, debug_ );
+        //  currentCmap = CmapGridType();
+        //}
         int cmapcount = argline.getKeyInt("CMAP_COUNT", -1);
-        //mprintf("DEBUG: Cmap count: %i\n", cmapcount);
-        if ( cmapcount != (int)prm.CMAP().size()+1 )
+        mprintf("DEBUG: Cmap count: %i\n", cmapcount);
+        //if ( cmapcount != (int)prm.CMAP().size()+1 )
+        //  mprintf("Warning: CMAP term is not in numerical order. CMAP_COUNT %i, expected %zu\n",
+        //          cmapcount, prm.CMAP().size());
+        if (cmap_count_is_index == -1) {
+          if  (cmapcount == (int)prm.CMAP().size()) {
+            mprintf("DEBUG: Assuming CMAP count is based on index.\n");
+            cmap_count_is_index = 1;
+          } else {
+            mprintf("DEBUG: Assuming CMAP count is the total number of CMAPS\n");
+            cmap_count_is_index = 0;
+          }
+        } else if (cmap_count_is_index == 1 && cmapcount != (int)prm.CMAP().size()) {
           mprintf("Warning: CMAP term is not in numerical order. CMAP_COUNT %i, expected %zu\n",
                   cmapcount, prm.CMAP().size());
+
+        }
         return 0;
       } else if (argline[1] == "CMAP_TITLE") {
         currentCmapFlag = CMAP_TITLE;
+        // New CMAP term. If a previous CMAP was read make sure it is OK.
+        if (!currentCmap.empty()) {
+          if (currentCmap.AtomNames().empty()) add_cmap_default_atoms( currentCmap );
+          if (check_cmap(prm.CMAP().size()+1, currentCmap)) return 1;
+          prm.CMAP().AddParm( currentCmap, true, debug_ );
+          currentCmap = CmapGridType();
+        }
+
         return 0;
       } else if (argline[1] == "CMAP_RESLIST") {
         currentCmapFlag = CMAP_RESLIST;
@@ -589,7 +614,7 @@ const
         return 0;
       } else if (argline[1] == "CMAP_RESOLUTION") {
         int cmapres = argline.getKeyInt("CMAP_RESOLUTION", -1);
-        //mprintf("DEBUG: Cmap res: %i\n", cmapres);
+        mprintf("DEBUG: Cmap res: %i\n", cmapres);
         if (cmapres < 1) {
           mprinterr("Error: Bad CMAP resolution: %s\n", line.c_str());
           return 1;
@@ -600,6 +625,10 @@ const
         currentCmapFlag = CMAP_PARAMETER;
         return 0;
       }
+    } else if (argline[0][0] == '%' && argline[0][1] == 'C' && argline[0][2] == 'O') {
+      // Assume comment
+      currentCmapFlag = CMAP_COMMENT;
+      mprintf("DEBUG: CMAP comment: %s\n", line.c_str());
     }
   }
 
@@ -609,7 +638,7 @@ const
                         terms, terms+1, terms+2, terms+3,
                         terms+4, terms+5, terms+6, terms+7);
     for (int i = 0; i != nterms; i++) {
-      //mprintf("DEBUG: cmap term %f\n", terms[i] );
+      mprintf("DEBUG: cmap term %f\n", terms[i] );
       currentCmap.AddToGrid( terms[i] );
     }
   } else if (currentCmapFlag == CMAP_RESLIST) {
@@ -620,6 +649,7 @@ const
       rn = resnames.GetStringNext();
     }
   } else if (currentCmapFlag == CMAP_TITLE) {
+    mprintf("DEBUG: CMAP TITLE: %s\n", line.c_str());
     currentCmap.SetTitle( line );
   }
   return 0;
@@ -668,6 +698,7 @@ int AmberParamFile::assign_offdiag(ParameterSet& prm, Oarray const& Offdiag) con
 /** Read parametrers from Amber frcmod file. */
 int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname) const
 {
+  int cmap_count_is_index = -1;
   // Set wildcard character for dihedrals and impropers
   prm.DP().SetWildcard('X');
   prm.IP().SetWildcard('X');
@@ -736,7 +767,7 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname) const
         else if (section == LJEDIT)
           err = read_ljedit(Offdiag, ptr);
         else if (section == CMAP)
-          err = read_cmap(currentCmap, prm, currentCmapFlag, line);
+          err = read_cmap(currentCmap, prm, currentCmapFlag, line, cmap_count_is_index);
         else if (section == IPOL)
           err = read_ipol(prm, ptr);
         if (err != 0) {
diff --git a/src/AmberParamFile.h b/src/AmberParamFile.h
index fadd29df8d..9fc9ec5f3f 100644
--- a/src/AmberParamFile.h
+++ b/src/AmberParamFile.h
@@ -28,7 +28,7 @@ class AmberParamFile {
 
     enum SectionType { ATYPE = 0, HYDROPHILIC, BOND, ANGLE, DIHEDRAL, IMPROPER, 
                        LJ1012, NB_EQUIV, NONBOND, LJEDIT, CMAP, IPOL, UNKNOWN };
-    enum CmapType { CMAP_INITIAL, CMAP_TITLE, CMAP_RESLIST, CMAP_PARAMETER };
+    enum CmapType { CMAP_INITIAL, CMAP_TITLE, CMAP_RESLIST, CMAP_PARAMETER, CMAP_COMMENT };
 
     class NonbondSet;
     class OffdiagNB;
@@ -58,7 +58,7 @@ class AmberParamFile {
     /// Check for issues in CMAP section
     inline int check_cmap(int, CmapGridType const&) const;
     /// Read CMAP section
-    int read_cmap(CmapGridType&, ParameterSet&, CmapType&, std::string const&) const;
+    int read_cmap(CmapGridType&, ParameterSet&, CmapType&, std::string const&, int&) const;
     /// Assign parameters from NonbondSet to ParameterSet
     int assign_nb(ParameterSet&, NonbondSet const&) const;
     /// Assign parameters from OffdiagNB array to ParameterSet

From 28679f9060027411c9e7147f5deebfe2fba60748 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 17 Feb 2026 19:00:00 -0500
Subject: [PATCH 1347/1492] Start handling formerly unhandled CMAP flags

---
 src/AmberParamFile.cpp | 175 ++++++++++++++++++++++++-----------------
 src/AmberParamFile.h   |   3 +-
 2 files changed, 107 insertions(+), 71 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index f804666235..01ff410011 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -556,81 +556,116 @@ int AmberParamFile::read_cmap(CmapGridType& currentCmap, ParameterSet& prm, Cmap
                               std::string const& line, int& cmap_count_is_index)
 const
 {
-  ArgList argline(line);
-  if (argline.Nargs() > 1)
-  {
-    // NOTE: CMAP_COUNT is used differently in different files. For example,
-    //       in ff19SB it is used as an index of the current CMAP parameter
-    //       being read. However, in ff12polL it is used to give a total
-    //       count of CMAP parameters
-    if (argline[0] == "%FLAG") {
-      if (argline[1] == "CMAP_COUNT") {
-        // New CMAP term. Ignore the index for now. If a previous CMAP
-        // was read make sure its OK.
-        //if (!currentCmap.empty()) {
-        //  if (currentCmap.AtomNames().empty()) add_cmap_default_atoms( currentCmap );
-        //  if (check_cmap(prm.CMAP().size()+1, currentCmap)) return 1;
-        //  prm.CMAP().AddParm( currentCmap, true, debug_ );
-        //  currentCmap = CmapGridType();
-        //}
-        int cmapcount = argline.getKeyInt("CMAP_COUNT", -1);
-        mprintf("DEBUG: Cmap count: %i\n", cmapcount);
-        //if ( cmapcount != (int)prm.CMAP().size()+1 )
-        //  mprintf("Warning: CMAP term is not in numerical order. CMAP_COUNT %i, expected %zu\n",
-        //          cmapcount, prm.CMAP().size());
-        if (cmap_count_is_index == -1) {
-          if  (cmapcount == (int)prm.CMAP().size()) {
-            mprintf("DEBUG: Assuming CMAP count is based on index.\n");
-            cmap_count_is_index = 1;
-          } else {
-            mprintf("DEBUG: Assuming CMAP count is the total number of CMAPS\n");
-            cmap_count_is_index = 0;
-          }
-        } else if (cmap_count_is_index == 1 && cmapcount != (int)prm.CMAP().size()) {
-          mprintf("Warning: CMAP term is not in numerical order. CMAP_COUNT %i, expected %zu\n",
-                  cmapcount, prm.CMAP().size());
+  if (line.empty()) return 0;
+  // At this point, line should have no leading whitespace
 
-        }
-        return 0;
-      } else if (argline[1] == "CMAP_TITLE") {
-        currentCmapFlag = CMAP_TITLE;
-        // New CMAP term. If a previous CMAP was read make sure it is OK.
-        if (!currentCmap.empty()) {
-          if (currentCmap.AtomNames().empty()) add_cmap_default_atoms( currentCmap );
-          if (check_cmap(prm.CMAP().size()+1, currentCmap)) return 1;
-          prm.CMAP().AddParm( currentCmap, true, debug_ );
-          currentCmap = CmapGridType();
-        }
+  if (line[0] == '%') {
+    ArgList argline(line);
+    if (argline.Nargs() > 1) {
+      // NOTE: CMAP_COUNT is used differently in different files. For example,
+      //       in ff19SB it is used as an index of the current CMAP parameter
+      //       being read. However, in ff12polL it is used to give a total
+      //       count of CMAP parameters
+      if (argline[0] == "%FLAG") {
+        if (argline[1] == "CMAP_COUNT") {
+          // New CMAP term. Ignore the index for now. If a previous CMAP
+          // was read make sure its OK.
+          //if (!currentCmap.empty()) {
+          //  if (currentCmap.AtomNames().empty()) add_cmap_default_atoms( currentCmap );
+          //  if (check_cmap(prm.CMAP().size()+1, currentCmap)) return 1;
+          //  prm.CMAP().AddParm( currentCmap, true, debug_ );
+          //  currentCmap = CmapGridType();
+          //}
+          int cmapcount = argline.getKeyInt("CMAP_COUNT", -1);
+          mprintf("DEBUG: Cmap count: %i\n", cmapcount);
+          //if ( cmapcount != (int)prm.CMAP().size()+1 )
+          //  mprintf("Warning: CMAP term is not in numerical order. CMAP_COUNT %i, expected %zu\n",
+          //          cmapcount, prm.CMAP().size());
+          if (cmap_count_is_index == -1) {
+            if  (cmapcount == (int)prm.CMAP().size()) {
+              mprintf("DEBUG: Assuming CMAP count is based on index.\n");
+              cmap_count_is_index = 1;
+            } else {
+              mprintf("DEBUG: Assuming CMAP count is the total number of CMAPS\n");
+              cmap_count_is_index = 0;
+            }
+          } else if (cmap_count_is_index == 1 && cmapcount != (int)prm.CMAP().size()) {
+            mprintf("Warning: CMAP term is not in numerical order. CMAP_COUNT %i, expected %zu\n",
+                    cmapcount, prm.CMAP().size());
+  
+          }
+          return 0;
+        } else if (argline[1] == "CMAP_TITLE") {
+          currentCmapFlag = CMAP_TITLE;
+          // New CMAP term. If a previous CMAP was read make sure it is OK.
+          if (!currentCmap.empty()) {
+            if (currentCmap.AtomNames().empty()) add_cmap_default_atoms( currentCmap );
+            if (check_cmap(prm.CMAP().size()+1, currentCmap)) return 1;
+            prm.CMAP().AddParm( currentCmap, true, debug_ );
+            currentCmap = CmapGridType();
+          }
 
-        return 0;
-      } else if (argline[1] == "CMAP_RESLIST") {
-        currentCmapFlag = CMAP_RESLIST;
-        int nres = argline.getKeyInt("CMAP_RESLIST", -1);
-        if (nres < 1) {
-          mprinterr("Error: Bad CMAP # residues: %s\n", line.c_str());
-          return 1;
-        }
-        currentCmap.SetNumCmapRes( nres );
-        return 0;
-      } else if (argline[1] == "CMAP_RESOLUTION") {
-        int cmapres = argline.getKeyInt("CMAP_RESOLUTION", -1);
-        mprintf("DEBUG: Cmap res: %i\n", cmapres);
-        if (cmapres < 1) {
-          mprinterr("Error: Bad CMAP resolution: %s\n", line.c_str());
-          return 1;
+          return 0;
+        } else if (argline[1] == "CMAP_RESLIST") {
+          currentCmapFlag = CMAP_RESLIST;
+          int nres = argline.getKeyInt("CMAP_RESLIST", -1);
+          if (nres < 1) {
+            mprinterr("Error: Bad CMAP # residues: %s\n", line.c_str());
+            return 1;
+          }
+          mprintf("DEBUG: CMAP_RESLIST expect %i residues.\n", nres);
+          currentCmap.SetNumCmapRes( nres );
+          return 0;
+        } else if (argline[1] == "CMAP_RESOLUTION") {
+          int cmapres = argline.getKeyInt("CMAP_RESOLUTION", -1);
+          mprintf("DEBUG: Cmap resolution: %i\n", cmapres);
+          if (cmapres < 1) {
+            mprinterr("Error: Bad CMAP resolution: %s\n", line.c_str());
+            return 1;
+          }
+          currentCmap.SetResolution( cmapres );
+          return 0;
+        } else if (argline[1] == "CMAP_PARAMETER") {
+          currentCmapFlag = CMAP_PARAMETER;
+          return 0;
+        } else if (argline[1] == "CMAP_ATMLIST") {
+          currentCmapFlag = CMAP_ATMLIST;
+          // Remove any dashes as well
+          ArgList atmArgs(line, " -");
+          if (atmArgs.Nargs() < 7) {
+            mprinterr("Error: Malformed CMAP_ATMLIST line; expected 5 elements, got %i\n", atmArgs.Nargs() - 2);
+            mprinterr("Error: %s\n", line.c_str());
+            return 1;
+          }
+          mprintf("DEBUG: Atom names: %s %s %s %s %s\n",
+                  atmArgs[2].c_str(),
+                  atmArgs[3].c_str(),
+                  atmArgs[4].c_str(),
+                  atmArgs[5].c_str(),
+                  atmArgs[6].c_str());
+        } else if (argline[1] == "CMAP_RESIDX") {
+          currentCmapFlag = CMAP_RESIDX;
+          if (argline.Nargs() < 7) {
+            mprinterr("Error: Malformed CMAP_RESIDX line; expected 5 elements, got %i\n", argline.Nargs() - 2);
+            mprinterr("Error: %s\n", line.c_str());
+            return 1;
+          }
+          int residxs[5];
+          for (int i = 0; i < 5; i++)
+            residxs[i] = argline.getNextInteger(0);
+          mprintf("DEBUG: Residue offsets: %i %i %i %i %i\n",
+                  residxs[0], residxs[1], residxs[2], residxs[3], residxs[4]);
+        } else {
+          mprintf("Warning: Unhandled CMAP FLAG %s\n", argline[1].c_str());
         }
-        currentCmap.SetResolution( cmapres );
-        return 0;
-      } else if (argline[1] == "CMAP_PARAMETER") {
-        currentCmapFlag = CMAP_PARAMETER;
+      } else if (argline[0][0] == '%' && argline[0][1] == 'C' && argline[0][2] == 'O') {
+        // Assume comment
+        currentCmapFlag = CMAP_COMMENT;
+        mprintf("DEBUG: CMAP comment: %s\n", line.c_str());
         return 0;
       }
-    } else if (argline[0][0] == '%' && argline[0][1] == 'C' && argline[0][2] == 'O') {
-      // Assume comment
-      currentCmapFlag = CMAP_COMMENT;
-      mprintf("DEBUG: CMAP comment: %s\n", line.c_str());
-    }
-  }
+    } // END line args > 1
+  } // END line starts with %
 
   if (currentCmapFlag == CMAP_PARAMETER) {
     double terms[8];
diff --git a/src/AmberParamFile.h b/src/AmberParamFile.h
index 9fc9ec5f3f..1dc750cd2f 100644
--- a/src/AmberParamFile.h
+++ b/src/AmberParamFile.h
@@ -28,7 +28,8 @@ class AmberParamFile {
 
     enum SectionType { ATYPE = 0, HYDROPHILIC, BOND, ANGLE, DIHEDRAL, IMPROPER, 
                        LJ1012, NB_EQUIV, NONBOND, LJEDIT, CMAP, IPOL, UNKNOWN };
-    enum CmapType { CMAP_INITIAL, CMAP_TITLE, CMAP_RESLIST, CMAP_PARAMETER, CMAP_COMMENT };
+    enum CmapType { CMAP_INITIAL, CMAP_TITLE, CMAP_RESLIST, CMAP_PARAMETER, CMAP_COMMENT,
+                    CMAP_RESIDX,  CMAP_ATMLIST };
 
     class NonbondSet;
     class OffdiagNB;

From 71573a3b829b559bc8efeb91eb393ae7312142b9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 17 Feb 2026 19:19:57 -0500
Subject: [PATCH 1348/1492] Better error message when a CMAP is invalid. CMAP
 PARAMETER line is not always 8 floats. Sometimes apparently there are
 commas...

---
 src/AmberParamFile.cpp | 30 +++++++++++++++++++++++-------
 1 file changed, 23 insertions(+), 7 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 01ff410011..6ea44d9d51 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -526,6 +526,11 @@ int AmberParamFile::check_cmap(int currentCmapIdx, CmapGridType const& cmap) con
   }
   if (!cmap.CmapIsValid()) {
     mprinterr("Error: CMAP term %i '%s' is not valid.\n", currentCmapIdx, cmap.Title().c_str());
+    // Why not?
+    if (cmap.Resolution() < 1) mprinterr("Error: Resolution is 0.\n");
+    if ((int)(cmap.Resolution() * cmap.Resolution()) != cmap.Size()) mprinterr("Error: Resolution %u*%u != grid size %i\n",cmap.Resolution(), cmap.Resolution(), cmap.Size());
+    if (cmap.AtomNames().size() != 5) mprinterr("Error: Expected 5 atom names (got %zu)\n", cmap.AtomNames().size());
+    if (cmap.NcmapResNames() < 1) mprinterr("Error: No residue names set up.\n");
     return 1;
   }
   if (!cmap.CmapNresIsValid()) {
@@ -643,6 +648,11 @@ const
                   atmArgs[4].c_str(),
                   atmArgs[5].c_str(),
                   atmArgs[6].c_str());
+          currentCmap.AddAtomName( atmArgs[2] );
+          currentCmap.AddAtomName( atmArgs[3] );
+          currentCmap.AddAtomName( atmArgs[4] );
+          currentCmap.AddAtomName( atmArgs[5] );
+          currentCmap.AddAtomName( atmArgs[6] );
         } else if (argline[1] == "CMAP_RESIDX") {
           currentCmapFlag = CMAP_RESIDX;
           if (argline.Nargs() < 7) {
@@ -668,14 +678,20 @@ const
   } // END line starts with %
 
   if (currentCmapFlag == CMAP_PARAMETER) {
-    double terms[8];
-    int nterms = sscanf(line.c_str(), "%lf %lf %lf %lf %lf %lf %lf %lf",
-                        terms, terms+1, terms+2, terms+3,
-                        terms+4, terms+5, terms+6, terms+7);
-    for (int i = 0; i != nterms; i++) {
-      mprintf("DEBUG: cmap term %f\n", terms[i] );
-      currentCmap.AddToGrid( terms[i] );
+    ArgList termArgs(line, " ,\t\r");
+    for (int i = 0; i != termArgs.Nargs(); i++) {
+      double term = termArgs.getNextDouble(0.0);
+      mprintf("DEBUG: cmap term %f\n", term);
+      currentCmap.AddToGrid( term );
     }
+    //double terms[8];
+    //int nterms = sscanf(line.c_str(), "%lf %lf %lf %lf %lf %lf %lf %lf",
+    //                    terms, terms+1, terms+2, terms+3,
+    //                    terms+4, terms+5, terms+6, terms+7);
+    //for (int i = 0; i != nterms; i++) {
+    //  mprintf("DEBUG: cmap term %f\n", terms[i] );
+    //  currentCmap.AddToGrid( terms[i] );
+    //}
   } else if (currentCmapFlag == CMAP_RESLIST) {
     ArgList resnames( line );
     std::string rn = resnames.GetStringNext();

From 18547c6bcf198558a472a702a36bb9ea51eda6f6 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 17 Feb 2026 23:22:39 -0500
Subject: [PATCH 1349/1492] Handle 9.5 and comma CMAP parameters

---
 src/AmberParamFile.cpp | 34 +++++++++++++++++++++-------------
 1 file changed, 21 insertions(+), 13 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 6ea44d9d51..cab263307e 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -678,20 +678,28 @@ const
   } // END line starts with %
 
   if (currentCmapFlag == CMAP_PARAMETER) {
-    ArgList termArgs(line, " ,\t\r");
-    for (int i = 0; i != termArgs.Nargs(); i++) {
-      double term = termArgs.getNextDouble(0.0);
-      mprintf("DEBUG: cmap term %f\n", term);
-      currentCmap.AddToGrid( term );
+    // Another annoyance; CMAP parameters can be in regular formatted 
+    // 8 column F9.5, or comma-separated list
+    size_t found = line.find_first_of(",");
+    if (found != std::string::npos) {
+      // Comma-separated
+      ArgList termArgs(line, " ,\t\r");
+      for (int i = 0; i != termArgs.Nargs(); i++) {
+        double term = termArgs.getNextDouble(0.0);
+        mprintf("DEBUG: cmap term %f\n", term);
+        currentCmap.AddToGrid( term );
+      }
+    } else {
+      // Assume 8F9.5
+      double terms[8];
+      int nterms = sscanf(line.c_str(), "%9lf%9lf%9lf%9lf%9lf%9lf%9lf%9lf",
+                          terms, terms+1, terms+2, terms+3,
+                          terms+4, terms+5, terms+6, terms+7);
+      for (int i = 0; i != nterms; i++) {
+        mprintf("DEBUG: cmap term %f\n", terms[i] );
+        currentCmap.AddToGrid( terms[i] );
+      }
     }
-    //double terms[8];
-    //int nterms = sscanf(line.c_str(), "%lf %lf %lf %lf %lf %lf %lf %lf",
-    //                    terms, terms+1, terms+2, terms+3,
-    //                    terms+4, terms+5, terms+6, terms+7);
-    //for (int i = 0; i != nterms; i++) {
-    //  mprintf("DEBUG: cmap term %f\n", terms[i] );
-    //  currentCmap.AddToGrid( terms[i] );
-    //}
   } else if (currentCmapFlag == CMAP_RESLIST) {
     ArgList resnames( line );
     std::string rn = resnames.GetStringNext();

From b2f1ade97b1f7da9556a362fc528ec50eb7b6210 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 18 Feb 2026 00:54:48 -0500
Subject: [PATCH 1350/1492] Hide debug info

---
 src/AmberParamFile.cpp | 50 ++++++++++++++++++++++++++----------------
 src/ParameterTypes.h   |  1 +
 2 files changed, 32 insertions(+), 19 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index cab263307e..a08047732b 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -412,13 +412,14 @@ const
 int AmberParamFile::read_ipol(ParameterSet& prm, const char* ptr)
 const
 {
-  mprintf("DEBUG: Read IPOL.\n");
+  //mprintf("DEBUG: Read IPOL.\n");
   int ipolIn = -1;
   if (sscanf(ptr, "%i", &ipolIn) != 1) {
     mprinterr("Error: Could not read IPOL value from line: %s\n", ptr);
     return 1;
   }
-  mprintf("DEBUG: IPOL value is %i\n", ipolIn);
+  if (debug_ > 0)
+    mprintf("DEBUG: IPOL value is %i\n", ipolIn);
   return 0;
 }
 
@@ -582,16 +583,19 @@ const
           //  currentCmap = CmapGridType();
           //}
           int cmapcount = argline.getKeyInt("CMAP_COUNT", -1);
-          mprintf("DEBUG: Cmap count: %i\n", cmapcount);
+          if (debug_ > 0)
+            mprintf("DEBUG: Cmap count: %i\n", cmapcount);
           //if ( cmapcount != (int)prm.CMAP().size()+1 )
           //  mprintf("Warning: CMAP term is not in numerical order. CMAP_COUNT %i, expected %zu\n",
           //          cmapcount, prm.CMAP().size());
           if (cmap_count_is_index == -1) {
             if  (cmapcount == (int)prm.CMAP().size()) {
-              mprintf("DEBUG: Assuming CMAP count is based on index.\n");
+              if (debug_ > 0)
+                mprintf("DEBUG: Assuming CMAP count is based on index.\n");
               cmap_count_is_index = 1;
             } else {
-              mprintf("DEBUG: Assuming CMAP count is the total number of CMAPS\n");
+              if (debug_ > 0)
+                mprintf("DEBUG: Assuming CMAP count is the total number of CMAPS\n");
               cmap_count_is_index = 0;
             }
           } else if (cmap_count_is_index == 1 && cmapcount != (int)prm.CMAP().size()) {
@@ -618,12 +622,14 @@ const
             mprinterr("Error: Bad CMAP # residues: %s\n", line.c_str());
             return 1;
           }
-          mprintf("DEBUG: CMAP_RESLIST expect %i residues.\n", nres);
+          if (debug_ > 0)
+            mprintf("DEBUG: CMAP_RESLIST expect %i residues.\n", nres);
           currentCmap.SetNumCmapRes( nres );
           return 0;
         } else if (argline[1] == "CMAP_RESOLUTION") {
           int cmapres = argline.getKeyInt("CMAP_RESOLUTION", -1);
-          mprintf("DEBUG: Cmap resolution: %i\n", cmapres);
+          if (debug_ > 0)
+            mprintf("DEBUG: Cmap resolution: %i\n", cmapres);
           if (cmapres < 1) {
             mprinterr("Error: Bad CMAP resolution: %s\n", line.c_str());
             return 1;
@@ -642,12 +648,13 @@ const
             mprinterr("Error: %s\n", line.c_str());
             return 1;
           }
-          mprintf("DEBUG: Atom names: %s %s %s %s %s\n",
-                  atmArgs[2].c_str(),
-                  atmArgs[3].c_str(),
-                  atmArgs[4].c_str(),
-                  atmArgs[5].c_str(),
-                  atmArgs[6].c_str());
+          if (debug_ > 0)
+            mprintf("DEBUG: Atom names: %s %s %s %s %s\n",
+                    atmArgs[2].c_str(),
+                    atmArgs[3].c_str(),
+                    atmArgs[4].c_str(),
+                    atmArgs[5].c_str(),
+                    atmArgs[6].c_str());
           currentCmap.AddAtomName( atmArgs[2] );
           currentCmap.AddAtomName( atmArgs[3] );
           currentCmap.AddAtomName( atmArgs[4] );
@@ -663,15 +670,16 @@ const
           int residxs[5];
           for (int i = 0; i < 5; i++)
             residxs[i] = argline.getNextInteger(0);
-          mprintf("DEBUG: Residue offsets: %i %i %i %i %i\n",
-                  residxs[0], residxs[1], residxs[2], residxs[3], residxs[4]);
+          if (debug_ > 0)
+            mprintf("DEBUG: Residue offsets: %i %i %i %i %i\n",
+                    residxs[0], residxs[1], residxs[2], residxs[3], residxs[4]);
         } else {
           mprintf("Warning: Unhandled CMAP FLAG %s\n", argline[1].c_str());
         }
       } else if (argline[0][0] == '%' && argline[0][1] == 'C' && argline[0][2] == 'O') {
         // Assume comment
         currentCmapFlag = CMAP_COMMENT;
-        mprintf("DEBUG: CMAP comment: %s\n", line.c_str());
+        if (debug_ > 0) mprintf("DEBUG: CMAP comment: %s\n", line.c_str());
         return 0;
       }
     } // END line args > 1
@@ -686,7 +694,7 @@ const
       ArgList termArgs(line, " ,\t\r");
       for (int i = 0; i != termArgs.Nargs(); i++) {
         double term = termArgs.getNextDouble(0.0);
-        mprintf("DEBUG: cmap term %f\n", term);
+        if (debug_ > 1) mprintf("DEBUG: cmap term %f\n", term);
         currentCmap.AddToGrid( term );
       }
     } else {
@@ -695,8 +703,11 @@ const
       int nterms = sscanf(line.c_str(), "%9lf%9lf%9lf%9lf%9lf%9lf%9lf%9lf",
                           terms, terms+1, terms+2, terms+3,
                           terms+4, terms+5, terms+6, terms+7);
+      if (debug_ > 1) {
+        for (int i = 0; i != nterms; i++)
+          mprintf("DEBUG: cmap term %f\n", terms[i] );
+      }
       for (int i = 0; i != nterms; i++) {
-        mprintf("DEBUG: cmap term %f\n", terms[i] );
         currentCmap.AddToGrid( terms[i] );
       }
     }
@@ -708,7 +719,8 @@ const
       rn = resnames.GetStringNext();
     }
   } else if (currentCmapFlag == CMAP_TITLE) {
-    mprintf("DEBUG: CMAP TITLE: %s\n", line.c_str());
+    if (debug_ > 0)
+      mprintf("DEBUG: CMAP TITLE: %s\n", line.c_str());
     currentCmap.SetTitle( line );
   }
   return 0;
diff --git a/src/ParameterTypes.h b/src/ParameterTypes.h
index 8847e09d7a..e45d3e9b8f 100644
--- a/src/ParameterTypes.h
+++ b/src/ParameterTypes.h
@@ -976,6 +976,7 @@ class CmapGridType {
     std::string title_;        ///< CMAP title (from parameter file)
     std::vector<std::string> resNames_;  ///< Residue name(s) this CMAP will apply to
     std::vector<std::string> atomNames_; ///< 5x atom names this CMAP will apply to
+    std::vector<int> resOffsets_; ///< 5x residue offset corresponding to each atom name
 };
 /// Hold an array of CMAP grids
 class CmapGridArray {

From 7350b229d2fa6fafd9263523bc218b8307984bd2 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 18 Feb 2026 11:45:54 -0500
Subject: [PATCH 1351/1492] Save residue offsets for CMAP

---
 src/AmberParamFile.cpp | 7 +++++++
 src/ParameterTypes.h   | 6 ++++++
 2 files changed, 13 insertions(+)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index a08047732b..b741f49d2f 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -551,6 +551,11 @@ static inline void add_cmap_default_atoms(CmapGridType& cmap) {
   cmap.AddAtomName("CA");
   cmap.AddAtomName("C");
   cmap.AddAtomName("N");
+  cmap.AddResOffset( -1 );
+  cmap.AddResOffset(  0 );
+  cmap.AddResOffset(  0 );
+  cmap.AddResOffset(  0 );
+  cmap.AddResOffset(  1 );
 }
 
 /** Read CMAP section
@@ -673,6 +678,8 @@ const
           if (debug_ > 0)
             mprintf("DEBUG: Residue offsets: %i %i %i %i %i\n",
                     residxs[0], residxs[1], residxs[2], residxs[3], residxs[4]);
+          for (int i = 0; i < 5; i++)
+            currentCmap.AddResOffset( residxs[i] );
         } else {
           mprintf("Warning: Unhandled CMAP FLAG %s\n", argline[1].c_str());
         }
diff --git a/src/ParameterTypes.h b/src/ParameterTypes.h
index e45d3e9b8f..9bc25ccd8f 100644
--- a/src/ParameterTypes.h
+++ b/src/ParameterTypes.h
@@ -910,6 +910,8 @@ class CmapGridType {
     }*/
     /// \return array of atom names this CMAP applies to
     std::vector<std::string> const& AtomNames() const { return atomNames_; }
+    /// \return array of residue offsets corresponding to atom names
+    std::vector<int> ResOffsets() const { return resOffsets_; }
     /// \return Expected number of CMAP residue names
     int NcmapResNames()                      const { return nCmapRes_; }
     /// \return Grid size as integer, used for topology write
@@ -940,12 +942,16 @@ class CmapGridType {
     void AddResName(std::string const& n) { resNames_.push_back( n ); }
     /// Add atom name this CMAP will apply to
     void AddAtomName(std::string const& n) { atomNames_.push_back( n ); }
+    /// Add residue offset for each atom name
+    void AddResOffset(int i) { resOffsets_.push_back( i ); }
     /// \return True if the CMAP is valid
     bool CmapIsValid() const {
       if (resolution_ == 0 || resolution_*resolution_ != grid_.size())
         return false;
       if (atomNames_.size() != 5)
         return false;
+      if (resOffsets_.size() != 5)
+        return false;
       if (resNames_.empty())
         return false;
       return true;

From e00b3b953042015ae25f15913a41c444d8846c62 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 18 Feb 2026 12:25:57 -0500
Subject: [PATCH 1352/1492] Ensure cmap residue offsets match before assignment

---
 src/Parm/AssignParams.cpp | 61 ++++++++++++++++++++++++++++++++-------
 1 file changed, 50 insertions(+), 11 deletions(-)

diff --git a/src/Parm/AssignParams.cpp b/src/Parm/AssignParams.cpp
index 1b89781040..d08c4c5d73 100644
--- a/src/Parm/AssignParams.cpp
+++ b/src/Parm/AssignParams.cpp
@@ -968,6 +968,31 @@ const
   return remap_cmap_indices(topOut, originalCmapIndices, cmapGrids, cmapTerms, cmapIn);
 }
 
+/// Calculate the residue offsets for atoms
+static inline void calc_res_offsets(int* resoffsets, Topology const& topOut, int rnum2, DihedralType const& dih, int a5)
+{
+  resoffsets[0] = topOut[dih.A1()].ResNum() - rnum2;
+  resoffsets[1] = topOut[dih.A2()].ResNum() - rnum2;
+  resoffsets[2] = topOut[dih.A3()].ResNum() - rnum2;
+  resoffsets[3] = topOut[dih.A4()].ResNum() - rnum2;
+  resoffsets[4] = topOut[a5      ].ResNum() - rnum2;
+//  mprintf("DEBUG: Cmap res offsets: %i %i %i %i %i\n",
+//          resoffsets[0],
+//          resoffsets[1],
+//          resoffsets[2],
+//          resoffsets[3],
+//          resoffsets[4]);
+}
+
+/// \return true if residue offsets match
+static inline bool res_offsets_match(const int* resoffsets, std::vector<int> const& cmapResOffsets)
+{
+  for (int i = 0; i < 5; i++) {
+    if (resoffsets[i] != cmapResOffsets[i]) return false;
+  }
+  return true;
+}
+
 /** Assign CMAP parameters. Also generates CMAP terms from dihedrals. */
 int AssignParams::AssignCmapParams(Topology const& topOut, DihedralArray const& allDih, CmapParmHolder const& cmapIn,
                                CmapGridArray& cmapGrids, CmapArray& cmapTerms)
@@ -979,6 +1004,8 @@ const
   typedef std::vector<std::string> Sarray;
   std::vector<Sarray> CmapResNames;
   std::vector<Sarray> CmapAtomNames;
+  typedef std::vector<int> Iarray;
+  std::vector<Iarray> CmapResOffsets;
   // The LEaP convention is to number the CMAP parameters in the same
   // order as they are listed in the original parameter file. This
   // variable keeps track of those indices.
@@ -990,6 +1017,7 @@ const
     if (dih->IsImproper() || dih->Skip14()) continue;
     // Get residue name for A2
     Atom const& A2 = topOut[dih->A2()];
+    int rnum2 = A2.ResNum();
     // TODO make sure A2-A4 in same residue?
     NameType const& rn2 = topOut.Res( A2.ResNum() ).Name();
     // Is this residue already in cmapGrids?
@@ -1002,9 +1030,14 @@ const
         //a5 = cmap_anames_match(*dih, atoms_, cmapGrids[idx]);
         a5 = cmap_anames_match(*dih, topOut.Atoms(), CmapAtomNames[idx]);
         if (a5 > -1) {
-          //cidx = (int)idx;
-          cidx = originalCmapIndices[idx];
-          break;
+          // Calc offsets
+          int resoffsets[5];
+          calc_res_offsets(resoffsets, topOut, rnum2, *dih, a5);
+          if (res_offsets_match(resoffsets, CmapResOffsets[idx])) {
+            //cidx = (int)idx;
+            cidx = originalCmapIndices[idx];
+            break;
+          }
         }
       }
     }
@@ -1030,14 +1063,20 @@ const
           //a5 = cmap_anames_match(*dih, atoms_, cmapIn[idx]);
           a5 = cmap_anames_match(*dih, topOut.Atoms(), cmapIn[idx].AtomNames());
           if (a5 > -1) {
-            //cidx = (int)cmapGrids.size();
-            cidx = (int)idx;
-            //cmapGrids.push_back( cmapIn[idx] );
-            CmapResNames.push_back( cmapIn[idx].ResNames() );
-            CmapAtomNames.push_back( cmapIn[idx].AtomNames() );
-            originalCmapIndices.push_back( idx );
-            //nidx = (int)idx;
-            break;
+            // Calc offsets
+            int resoffsets[5];
+            calc_res_offsets(resoffsets, topOut, rnum2, *dih, a5);
+            if (res_offsets_match(resoffsets, cmapIn[idx].ResOffsets())) {
+              //cidx = (int)cmapGrids.size();
+              cidx = (int)idx;
+              //cmapGrids.push_back( cmapIn[idx] );
+              CmapResNames.push_back( cmapIn[idx].ResNames() );
+              CmapAtomNames.push_back( cmapIn[idx].AtomNames() );
+              CmapResOffsets.push_back( cmapIn[idx].ResOffsets() );
+              originalCmapIndices.push_back( idx );
+              //nidx = (int)idx;
+              break;
+            }
           }
         }
       }

From 15ea458c4db1a84a5705a1d2c9178c7b92125c9d Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 18 Feb 2026 14:33:01 -0500
Subject: [PATCH 1353/1492] Do not report mass/pol if they arent actually
 different

---
 src/AmberParamFile.cpp | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index b741f49d2f..d148633db5 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -129,9 +129,14 @@ const
   if (ret == Cpptraj::Parm::SAME)
     mprintf("Warning: Duplicated %s\n", typeNameStr(types, "atom").c_str());
   else if (ret == Cpptraj::Parm::UPDATED) {
-    mprintf("Warning: Redefining %s from mass= %g pol= %g to mass= %g pol= %g\n",
-             typeNameStr(types, "atom").c_str(),
-             prm.AT().PreviousParm().Mass(), prm.AT().PreviousParm().Polarizability(), amass, atpol);
+    AtomType const& prev = prm.AT().PreviousParm();
+    bool diff_mass = (prev.Mass() != amass);
+    bool diff_pol  = (prev.Polarizability() != atpol);
+    mprintf("Warning: Redefining %s", typeNameStr(types, "atom").c_str());
+             //prm.AT().PreviousParm().Mass(), prm.AT().PreviousParm().Polarizability(), amass, atpol);
+    if (diff_mass) mprintf(" from mass %g to %g", prev.Mass(), amass);
+    if (diff_pol)  mprintf(" from pol %g to %g", prev.Polarizability(), atpol);
+    mprintf("\n");
   } else if (ret == Cpptraj::Parm::ERR) {
     mprinterr("Error: Reading %s\n", typeNameStr(types, "atom").c_str());
     return 1;

From 9ab18bfec30636cfa96b969c438d4a88b63d2559 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 18 Feb 2026 16:20:57 -0500
Subject: [PATCH 1354/1492] Report when LJ parameters are changed within a FF
 load

---
 src/AmberParamFile.cpp | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index d148633db5..8f31fa7efe 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -749,7 +749,11 @@ int AmberParamFile::assign_nb(ParameterSet& prm, NonbondSet const& nbset) const
       mprinterr("Error: Nonbond parameters defined for previously undefined type '%s'.\n",
                 *(it->first[0]));
       return 1;
-    } 
+    }
+    if (at->second.LJ() != it->second)
+      mprintf("Warning: Changing type %s radius from %g to %g, depth from %g to %g\n", *(it->first[0]),
+              at->second.LJ().Radius(), it->second.Radius(),
+              at->second.LJ().Depth(), it->second.Depth());
     at->second.SetLJ( it->second );
   }
   return 0;

From 26323009b6c16622cabc954358cf2eeb60f2fe14 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 18 Feb 2026 17:14:45 -0500
Subject: [PATCH 1355/1492] Add copy constructor

---
 src/AtomType.h | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/src/AtomType.h b/src/AtomType.h
index e25b408fc0..ef2407ba42 100644
--- a/src/AtomType.h
+++ b/src/AtomType.h
@@ -88,6 +88,21 @@ class AtomType {
       hasLJ14_ = rhs.hasLJ14_;
       return *this;
     }
+    /// COPY CONSTRUCTOR
+    AtomType(AtomType const& rhs) :
+      lj_(rhs.lj_),
+      lj14_(rhs.lj14_),
+      mass_(rhs.mass_),
+      polarizability_(rhs.polarizability_),
+      oidx_(rhs.oidx_),
+      hybrid_(rhs.hybrid_),
+      hasLJ_(rhs.hasLJ_),
+      hasLJ14_(rhs.hasLJ14_)
+    {
+      elt_[0] = rhs.elt_[0];
+      elt_[1] = rhs.elt_[1];
+      elt_[2] = '\0';
+    }
   private:
     LJparmType lj_;         ///< Default Lennard-Jones parameters (always valid for self).
     LJparmType lj14_;       ///< Lennard-Jones 1-4 parameters (optional).

From b65bfc1b3fec909624cb1b5a3cd4a18ccc34e02c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 18 Feb 2026 17:30:31 -0500
Subject: [PATCH 1356/1492] Be more verbose when updating parameters by saying
 what we are changing the parameters from

---
 src/UpdateParameters.h | 21 ++++++++++++++-------
 1 file changed, 14 insertions(+), 7 deletions(-)

diff --git a/src/UpdateParameters.h b/src/UpdateParameters.h
index 79838e64ec..51b35d073b 100644
--- a/src/UpdateParameters.h
+++ b/src/UpdateParameters.h
@@ -4,17 +4,17 @@
 //       classes, e.g. ParameterSet and/or Topology. Therefore there are
 //       no 'include' statements or forward declares as it is assumed
 //       those files have already been included prior to this one.
-static inline void PrintParmType(BondParmType const& bp) { mprintf(" %12.4f %12.4f\n", bp.Rk(), bp.Req()); }
-static inline void PrintParmType(AngleParmType const& ap) { mprintf(" %12.4f %12.4f\n", ap.Tk(), ap.Teq()*Constants::RADDEG); }
-static inline void PrintParmType(DihedralParmType const& dp) { mprintf(" %12.4f %12.4f %12.4f\n", dp.Pk(), dp.Pn(), dp.Phase()*Constants::RADDEG); }
+static inline void PrintParmType(BondParmType const& bp) { mprintf(" %12.4f %12.4f", bp.Rk(), bp.Req()); }
+static inline void PrintParmType(AngleParmType const& ap) { mprintf(" %12.4f %12.4f", ap.Tk(), ap.Teq()*Constants::RADDEG); }
+static inline void PrintParmType(DihedralParmType const& dp) { mprintf(" %12.4f %12.4f %12.4f", dp.Pk(), dp.Pn(), dp.Phase()*Constants::RADDEG); }
 static inline void PrintParmType(DihedralParmArray const& dpa) {
   mprintf("\n");
   for (DihedralParmArray::const_iterator it = dpa.begin(); it != dpa.end(); ++it)
     mprintf("\t\t%12.4f %12.4f %12.4f\n", it->Pk(), it->Pn(), it->Phase()*Constants::RADDEG);
 }
-static inline void PrintParmType(AtomType const& at) { mprintf(" %12.4f %12.4f %12.4f\n", at.LJ().Radius(), at.LJ().Depth(), at.Mass()); }
-static inline void PrintParmType(NonbondType const& nb) { mprintf(" %12.4E %12.4E\n", nb.A(), nb.B()); }
-static inline void PrintParmType(HB_ParmType const& hb) { mprintf(" %12.4E %12.4E %12.4E\n", hb.Asol(), hb.Bsol(), hb.HBcut()); }
+static inline void PrintParmType(AtomType const& at) { mprintf(" R=%g Depth=%g Mass=%g", at.LJ().Radius(), at.LJ().Depth(), at.Mass()); }
+static inline void PrintParmType(NonbondType const& nb) { mprintf(" %12.4E %12.4E", nb.A(), nb.B()); }
+static inline void PrintParmType(HB_ParmType const& hb) { mprintf(" %12.4E %12.4E %12.4E", hb.Asol(), hb.Bsol(), hb.HBcut()); }
 
 /** Add update parameters.
   * \param0 Parameters to add to/update.
@@ -50,7 +50,14 @@ template <typename T> int UpdateParameters(T& param0, T const& param1, const cha
         // NOTE: For AtomType its possible only a partial update occurred.
         //       Get the new parameter explicitly.
         typename T::const_iterator newIt = param0.GetParam( newp->first );
-        PrintParmType( newIt->second );
+        if (ret == Cpptraj::Parm::UPDATED) {
+          mprintf(" From");
+          PrintParmType( param0.PreviousParm() );
+          mprintf(" to");
+          PrintParmType( newIt->second );
+        } else
+          PrintParmType( newIt->second );
+        mprintf("\n");
       }
       //mprintf(" %s %s %12.4f %12.4f\n", 
       //        *(newp->first[0]), *(newp->first[1]), newp->second.Rk(), newp->second.Req());

From 4334156c46e2eb34261851b5f55d47ea6438e3a3 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 18 Feb 2026 17:55:10 -0500
Subject: [PATCH 1357/1492] If AtomType has LJ params do not overwrite the
 hasLJ flag

---
 src/AtomType.h | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/AtomType.h b/src/AtomType.h
index ef2407ba42..b616e1256d 100644
--- a/src/AtomType.h
+++ b/src/AtomType.h
@@ -73,8 +73,8 @@ class AtomType {
     AtomType& operator=(AtomType const& rhs) {
       if (this == &rhs) return *this;
       //mprintf("DEBUG: Assign elt %c%c oldHasLj=%i oldR=%f newHasLj=%i newR=%f\n", elt_[0], elt_[1], (int)hasLJ_, lj_.Radius(), (int)rhs.hasLJ_, rhs.lj_.Radius());
-      if (rhs.hasLJ_) lj_ = rhs.lj_;
-      if (rhs.hasLJ14_) lj14_ = rhs.lj14_;
+      if (rhs.hasLJ_)   { lj_   = rhs.lj_;   hasLJ_ = true; }
+      if (rhs.hasLJ14_) { lj14_ = rhs.lj14_; hasLJ14_ = true; }
       //mprintf("DEBUG: After Assign elt %c%c newR=%f\n", elt_[0], elt_[1], lj_.Radius());
       mass_ = rhs.mass_;
       polarizability_ = rhs.polarizability_;
@@ -84,8 +84,8 @@ class AtomType {
       elt_[0] = rhs.elt_[0];
       elt_[1] = rhs.elt_[1];
       //elt_[2] = rhs.elt_[2];
-      hasLJ_ = rhs.hasLJ_;
-      hasLJ14_ = rhs.hasLJ14_;
+      //hasLJ_ = rhs.hasLJ_;
+      //hasLJ14_ = rhs.hasLJ14_;
       return *this;
     }
     /// COPY CONSTRUCTOR

From ea8ab78f05e840605d1c7bedf5f334fd424dacf9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 18 Feb 2026 17:55:45 -0500
Subject: [PATCH 1358/1492] Only report if the LJ type is changing if there
 were already params

---
 src/AmberParamFile.cpp | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 8f31fa7efe..11a135b13b 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -750,7 +750,8 @@ int AmberParamFile::assign_nb(ParameterSet& prm, NonbondSet const& nbset) const
                 *(it->first[0]));
       return 1;
     }
-    if (at->second.LJ() != it->second)
+    //mprintf("DEBUG: searched type %s hasLJ=%i\n", *(at->first[0]), (int)at->second.HasLJ());
+    if (at->second.HasLJ() && at->second.LJ() != it->second)
       mprintf("Warning: Changing type %s radius from %g to %g, depth from %g to %g\n", *(it->first[0]),
               at->second.LJ().Radius(), it->second.Radius(),
               at->second.LJ().Depth(), it->second.Depth());

From ac275ac6c760513366c984b320867dd910d9bead Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 18 Feb 2026 19:32:58 -0500
Subject: [PATCH 1359/1492] Save file name as well as title

---
 src/AmberParamFile.cpp        |  2 ++
 src/Parm/ParameterSet.cpp     | 17 +++++++++++++++++
 src/Parm/ParameterSet.h       |  8 ++++++++
 src/Structure/structuredepend |  8 ++++----
 src/cpptrajdepend             |  8 ++++----
 5 files changed, 35 insertions(+), 8 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 11a135b13b..1067645871 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -806,6 +806,7 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname) const
   std::string title(ptr);
   mprintf("\tTitle: %s\n", title.c_str());
   prm.SetParamSetName( title );
+  prm.SetParamSetFile( fname );
   NonbondSet nbset(title);
   Oarray Offdiag;
   // Read file
@@ -914,6 +915,7 @@ int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
   std::string title(ptr);
   mprintf("\tTitle: %s\n", title.c_str());
   prm.SetParamSetName( title );
+  prm.SetParamSetFile( fname );
   std::vector<std::string> last_symbols;
   last_symbols.reserve(4);
   // Read file
diff --git a/src/Parm/ParameterSet.cpp b/src/Parm/ParameterSet.cpp
index a2399dc1d8..b58dfc25fc 100644
--- a/src/Parm/ParameterSet.cpp
+++ b/src/Parm/ParameterSet.cpp
@@ -37,6 +37,12 @@ void ParameterSet::Debug(const char* fnameIn) const {
 /** Write summary to stdout. */
 void ParameterSet::Summary() const {
   mprintf("\tParameter set: %s\n", ParamSetName().c_str());
+  if (!fname_.empty()) {
+    mprintf("\tFiles:");
+    for (FNarray::const_iterator fn = fname_.begin(); fn != fname_.end(); ++fn)
+      mprintf(" %s", fn->base());
+    mprintf("\n");
+  }
   mprintf("\t  %zu atom types:", atomTypes_.size());
   for (ParmHolder<AtomType>::const_iterator at = atomTypes_.begin(); at != atomTypes_.end(); ++at)
     mprintf(" %s", *(at->first[0]));
@@ -58,6 +64,12 @@ void ParameterSet::Summary() const {
 void ParameterSet::Print(CpptrajFile& Out) const {
   if (!name_.empty())
     Out.Printf("Parameter set: %s\n", ParamSetName().c_str());
+  if (!fname_.empty()) {
+    Out.Printf("\tFiles:");
+    for (FNarray::const_iterator fn = fname_.begin(); fn != fname_.end(); ++fn)
+      Out.Printf(" %s", fn->base());
+    Out.Printf("\n");
+  }
   if (!NBname_.empty())
     Out.Printf("Nonbond parameters name: %s\n", NBname_.c_str());
   static const char* hybStr[] = {"SP ", "SP2", "SP3", "UNK"};
@@ -281,6 +293,11 @@ void ParameterSet::SetParamSetName(std::string const& nameIn) {
   name_.push_back( nameIn );
 }
 
+/** Set parameter set file */
+void ParameterSet::SetParamSetFile(FileName const& fnameIn) {
+  fname_.push_back( fnameIn );
+}
+
 /** Set nonbond parameter set name. */
 void ParameterSet::SetNbParamName(std::string const& nameIn) {
   NBname_ = nameIn;
diff --git a/src/Parm/ParameterSet.h b/src/Parm/ParameterSet.h
index 6d070275dc..9e154ebb39 100644
--- a/src/Parm/ParameterSet.h
+++ b/src/Parm/ParameterSet.h
@@ -5,6 +5,7 @@
 #include "ImproperParmHolder.h"
 #include "../AtomType.h"
 #include "../CmapParmHolder.h"
+#include "../FileName.h"
 #include "../ParameterTypes.h"
 class CpptrajFile;
 /// Hold a set of parameters for atom types, bonds, angles, etc.
@@ -18,6 +19,8 @@ class ParameterSet {
   public:
     ParameterSet() : hasLJparams_(false) {}
 
+    typedef std::vector<FileName> FNarray;
+
     ParmHolder<AtomType>& AT()         { return atomTypes_; }
     ParmHolder<NonbondType>& NB()      { return nbParm_;    }
     ParmHolder<NonbondType>& NB14()    { return nb14Parm_;  }
@@ -49,6 +52,8 @@ class ParameterSet {
     std::string const& NbParamName()         const { return NBname_;    }
     /// \return Parameter set names as a single line
     std::string ParamSetName()        const;
+    /// \return File name array
+    FNarray const& ParamSetFile() const { return fname_; }
     /// Write parameters to file with given name
     void Debug(const char*) const;
     /// Write parameters to stdout
@@ -85,6 +90,8 @@ class ParameterSet {
     int AddHydrophilicAtomType(NameType const&);
     /// Set parameter set name
     void SetParamSetName(std::string const&);
+    /// Set parameter set file name
+    void SetParamSetFile(FileName const&);
     /// Set nonbond parameter set name
     void SetNbParamName(std::string const&);
     /// \return Size in memory in bytes
@@ -99,6 +106,7 @@ class ParameterSet {
     int updateCmapParams(CmapParmHolder const&, int, int);
 
     Sarray name_;                          ///< Parameter set name(s)
+    FNarray fname_;                        ///< Parameter set file(s)
     std::string NBname_;                   ///< Nonbond set name
 
     ParmHolder<AtomType> atomTypes_;       ///< Atom types
diff --git a/src/Structure/structuredepend b/src/Structure/structuredepend
index d8794a81c6..f564485165 100644
--- a/src/Structure/structuredepend
+++ b/src/Structure/structuredepend
@@ -1,7 +1,7 @@
-AddIons.o : AddIons.cpp ../AssociatedData.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../Dimension.h ../DistRoutines.h ../FileIO.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/../AtomType.h ../Parm/../CmapParmHolder.h ../Parm/../Constants.h ../Parm/../NameType.h ../Parm/../ParameterTypes.h ../Parm/../Parm/ParmEnum.h ../Parm/../TypeNameHolder.h ../Parm/DihedralParmHolder.h ../Parm/ImproperParmHolder.h ../Parm/ParameterSet.h ../Parm/ParmEnum.h ../Parm/ParmHolder.h ../Random.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h AddIons.h
-Builder.o : Builder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/../AtomType.h ../Parm/../CmapParmHolder.h ../Parm/../Constants.h ../Parm/../NameType.h ../Parm/../ParameterTypes.h ../Parm/../Parm/ParmEnum.h ../Parm/../TypeNameHolder.h ../Parm/DihedralParmHolder.h ../Parm/ImproperParmHolder.h ../Parm/ParameterSet.h ../Parm/ParmEnum.h ../Parm/ParmHolder.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Timer.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Builder.h Chirality.h GenerateConnectivityArrays.h InternalCoords.h StructureEnum.h Zmatrix.h
+AddIons.o : AddIons.cpp ../AssociatedData.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../Dimension.h ../DistRoutines.h ../FileIO.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/../AtomType.h ../Parm/../CmapParmHolder.h ../Parm/../Constants.h ../Parm/../FileName.h ../Parm/../NameType.h ../Parm/../ParameterTypes.h ../Parm/../Parm/ParmEnum.h ../Parm/../TypeNameHolder.h ../Parm/DihedralParmHolder.h ../Parm/ImproperParmHolder.h ../Parm/ParameterSet.h ../Parm/ParmEnum.h ../Parm/ParmHolder.h ../Random.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h AddIons.h
+Builder.o : Builder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/../AtomType.h ../Parm/../CmapParmHolder.h ../Parm/../Constants.h ../Parm/../FileName.h ../Parm/../NameType.h ../Parm/../ParameterTypes.h ../Parm/../Parm/ParmEnum.h ../Parm/../TypeNameHolder.h ../Parm/DihedralParmHolder.h ../Parm/ImproperParmHolder.h ../Parm/ParameterSet.h ../Parm/ParmEnum.h ../Parm/ParmHolder.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Timer.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Builder.h Chirality.h GenerateConnectivityArrays.h InternalCoords.h StructureEnum.h Zmatrix.h
 Chirality.o : Chirality.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../Unit.h ../Vec3.h Chirality.h StructureEnum.h
-Creator.o : Creator.cpp ../ArgList.h ../AssociatedData.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../DataSet_NameMap.h ../DataSet_Parameters.h ../DataSet_PdbResMap.h ../Dimension.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/../AtomType.h ../Parm/../CmapParmHolder.h ../Parm/../Constants.h ../Parm/../NameType.h ../Parm/../ParameterTypes.h ../Parm/../Parm/ParmEnum.h ../Parm/../TypeNameHolder.h ../Parm/DihedralParmHolder.h ../Parm/ImproperParmHolder.h ../Parm/ParameterSet.h ../Parm/ParmEnum.h ../Parm/ParmHolder.h ../PdbResMapType.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/StructureEnum.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h Creator.h GenerateConnectivityArrays.h StructureEnum.h
+Creator.o : Creator.cpp ../ArgList.h ../AssociatedData.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../DataSet_NameMap.h ../DataSet_Parameters.h ../DataSet_PdbResMap.h ../Dimension.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/../AtomType.h ../Parm/../CmapParmHolder.h ../Parm/../Constants.h ../Parm/../FileName.h ../Parm/../NameType.h ../Parm/../ParameterTypes.h ../Parm/../Parm/ParmEnum.h ../Parm/../TypeNameHolder.h ../Parm/DihedralParmHolder.h ../Parm/ImproperParmHolder.h ../Parm/ParameterSet.h ../Parm/ParmEnum.h ../Parm/ParmHolder.h ../PdbResMapType.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/StructureEnum.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h Creator.h GenerateConnectivityArrays.h StructureEnum.h
 Disulfide.o : Disulfide.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h Disulfide.h ResStatArray.h StructureRoutines.h
 FunctionalGroup.o : FunctionalGroup.cpp ../Atom.h ../AtomMap.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h FunctionalGroup.h
 FxnGroupBuilder.o : FxnGroupBuilder.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h FunctionalGroup.h FxnGroupBuilder.h StructureRoutines.h Sugar.h SugarToken.h
@@ -12,7 +12,7 @@ LeastSquaresPlane.o : LeastSquaresPlane.cpp ../Atom.h ../AtomMask.h ../Box.h ../
 MetalCenterFinder.o : MetalCenterFinder.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h MetalCenterFinder.h
 PdbCleaner.o : PdbCleaner.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h PdbCleaner.h
 RingFinder.o : RingFinder.cpp ../Atom.h ../AtomMask.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h RingFinder.h
-Solvate.o : Solvate.cpp ../Action.h ../ActionState.h ../Action_AutoImage.h ../ArgList.h ../AssociatedData.h ../Atom.h ../AtomMask.h ../BaseIOtype.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataFile.h ../DataFileList.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../Dimension.h ../DispatchObject.h ../FileIO.h ../FileName.h ../FileTypes.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/../AtomType.h ../Parm/../CmapParmHolder.h ../Parm/../Constants.h ../Parm/../NameType.h ../Parm/../ParameterTypes.h ../Parm/../Parm/ParmEnum.h ../Parm/../TypeNameHolder.h ../Parm/DihedralParmHolder.h ../Parm/ImproperParmHolder.h ../Parm/ParameterSet.h ../Parm/ParmEnum.h ../Parm/ParmHolder.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h Solvate.h
+Solvate.o : Solvate.cpp ../Action.h ../ActionState.h ../Action_AutoImage.h ../ArgList.h ../AssociatedData.h ../Atom.h ../AtomMask.h ../BaseIOtype.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataFile.h ../DataFileList.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../Dimension.h ../DispatchObject.h ../FileIO.h ../FileName.h ../FileTypes.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/../AtomType.h ../Parm/../CmapParmHolder.h ../Parm/../Constants.h ../Parm/../FileName.h ../Parm/../NameType.h ../Parm/../ParameterTypes.h ../Parm/../Parm/ParmEnum.h ../Parm/../TypeNameHolder.h ../Parm/DihedralParmHolder.h ../Parm/ImproperParmHolder.h ../Parm/ParameterSet.h ../Parm/ParmEnum.h ../Parm/ParmHolder.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h Solvate.h
 StructureEnum.o : StructureEnum.cpp StructureEnum.h
 StructureRoutines.o : StructureRoutines.cpp ../Atom.h ../CpptrajStdio.h ../NameType.h ../Residue.h ../SymbolExporting.h StructureRoutines.h
 Sugar.o : Sugar.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h Sugar.h SugarToken.h
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 6d81805955..71c559d837 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -319,7 +319,7 @@ EwaldOptions.o : EwaldOptions.cpp ArgList.h CpptrajStdio.h EwaldOptions.h
 ExclusionArray.o : ExclusionArray.cpp Atom.h AtomMask.h CharMask.h CpptrajStdio.h ExclusionArray.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Unit.h
 Exec_AddMissingRes.o : Exec_AddMissingRes.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h CharMask.h CompactFrameArray.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_AddMissingRes.h Exec_AddMissingRes_Pres.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h ParmFile.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h Trajout_Single.h Unit.h Vec3.h
 Exec_Analyze.o : Exec_Analyze.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Analyze.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_Build.o : Exec_Build.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h ExclusionArray.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PairList.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/ImproperParmHolder.h Parm/LJ1264_Params.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h ParmFile.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/AddIons.h Structure/Builder.h Structure/Creator.h Structure/Disulfide.h Structure/HisProt.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/RingFinder.h Structure/Solvate.h Structure/StructureEnum.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Build.o : Exec_Build.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h ActionTopWriter.h Action_FixAtomOrder.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h ExclusionArray.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PairList.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/ImproperParmHolder.h Parm/LJ1264_Params.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h ParmFile.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/AddIons.h Structure/Builder.h Structure/Creator.h Structure/Disulfide.h Structure/HisProt.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/RingFinder.h Structure/Solvate.h Structure/StructureEnum.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Calc.o : Exec_Calc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Calc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_CatCrd.o : Exec_CatCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CatCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_Change.o : Exec_Change.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Change.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/GB_Params.h Parm/LJ1264_Params.h Parm/ParmEnum.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
@@ -485,8 +485,8 @@ Spline.o : Spline.cpp CpptrajStdio.h Spline.h
 SplineFxnTable.o : SplineFxnTable.cpp Constants.h CpptrajStdio.h Spline.h SplineFxnTable.h StringRoutines.h
 Stats_Reduce.o : Stats_Reduce.cpp OnlineVarT.h Parallel.h Stats_Reduce.h
 StringRoutines.o : StringRoutines.cpp CpptrajStdio.h StringRoutines.h
-Structure/AddIons.o : Structure/AddIons.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DistRoutines.h FileIO.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/../Parm/../AtomType.h Structure/../Parm/../CmapParmHolder.h Structure/../Parm/../Constants.h Structure/../Parm/../NameType.h Structure/../Parm/../ParameterTypes.h Structure/../Parm/../Parm/ParmEnum.h Structure/../Parm/../TypeNameHolder.h Structure/../Parm/DihedralParmHolder.h Structure/../Parm/ImproperParmHolder.h Structure/../Parm/ParameterSet.h Structure/../Parm/ParmEnum.h Structure/../Parm/ParmHolder.h Structure/AddIons.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Structure/Builder.o : Structure/Builder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h GuessAtomHybridization.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/../Parm/../AtomType.h Structure/../Parm/../CmapParmHolder.h Structure/../Parm/../Constants.h Structure/../Parm/../NameType.h Structure/../Parm/../ParameterTypes.h Structure/../Parm/../Parm/ParmEnum.h Structure/../Parm/../TypeNameHolder.h Structure/../Parm/DihedralParmHolder.h Structure/../Parm/ImproperParmHolder.h Structure/../Parm/ParameterSet.h Structure/../Parm/ParmEnum.h Structure/../Parm/ParmHolder.h Structure/Builder.h Structure/Chirality.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Structure/AddIons.o : Structure/AddIons.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DistRoutines.h FileIO.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/../Parm/../AtomType.h Structure/../Parm/../CmapParmHolder.h Structure/../Parm/../Constants.h Structure/../Parm/../FileName.h Structure/../Parm/../NameType.h Structure/../Parm/../ParameterTypes.h Structure/../Parm/../Parm/ParmEnum.h Structure/../Parm/../TypeNameHolder.h Structure/../Parm/DihedralParmHolder.h Structure/../Parm/ImproperParmHolder.h Structure/../Parm/ParameterSet.h Structure/../Parm/ParmEnum.h Structure/../Parm/ParmHolder.h Structure/AddIons.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Structure/Builder.o : Structure/Builder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h GuessAtomHybridization.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/../Parm/../AtomType.h Structure/../Parm/../CmapParmHolder.h Structure/../Parm/../Constants.h Structure/../Parm/../FileName.h Structure/../Parm/../NameType.h Structure/../Parm/../ParameterTypes.h Structure/../Parm/../Parm/ParmEnum.h Structure/../Parm/../TypeNameHolder.h Structure/../Parm/DihedralParmHolder.h Structure/../Parm/ImproperParmHolder.h Structure/../Parm/ParameterSet.h Structure/../Parm/ParmEnum.h Structure/../Parm/ParmHolder.h Structure/Builder.h Structure/Chirality.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 Structure/Chirality.o : Structure/Chirality.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Chirality.h Structure/StructureEnum.h SymbolExporting.h Topology.h TorsionRoutines.h Unit.h Vec3.h
 Structure/Creator.o : Structure/Creator.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h DataSet_Parameters.h DataSet_PdbResMap.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h PdbResMapType.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/Creator.h Structure/GenerateConnectivityArrays.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/Disulfide.o : Structure/Disulfide.cpp ArgList.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Disulfide.h Structure/ResStatArray.h Structure/StructureRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h
@@ -499,7 +499,7 @@ Structure/LeastSquaresPlane.o : Structure/LeastSquaresPlane.cpp Atom.h AtomMask.
 Structure/MetalCenterFinder.o : Structure/MetalCenterFinder.cpp ArgList.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/MetalCenterFinder.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Structure/PdbCleaner.o : Structure/PdbCleaner.cpp ArgList.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/PdbCleaner.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Structure/RingFinder.o : Structure/RingFinder.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/RingFinder.h SymbolExporting.h Topology.h Unit.h Vec3.h
-Structure/Solvate.o : Structure/Solvate.cpp Action.h ActionState.h Action_AutoImage.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/../Parm/../AtomType.h Structure/../Parm/../CmapParmHolder.h Structure/../Parm/../Constants.h Structure/../Parm/../NameType.h Structure/../Parm/../ParameterTypes.h Structure/../Parm/../Parm/ParmEnum.h Structure/../Parm/../TypeNameHolder.h Structure/../Parm/DihedralParmHolder.h Structure/../Parm/ImproperParmHolder.h Structure/../Parm/ParameterSet.h Structure/../Parm/ParmEnum.h Structure/../Parm/ParmHolder.h Structure/Solvate.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Structure/Solvate.o : Structure/Solvate.cpp Action.h ActionState.h Action_AutoImage.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/../Parm/../AtomType.h Structure/../Parm/../CmapParmHolder.h Structure/../Parm/../Constants.h Structure/../Parm/../FileName.h Structure/../Parm/../NameType.h Structure/../Parm/../ParameterTypes.h Structure/../Parm/../Parm/ParmEnum.h Structure/../Parm/../TypeNameHolder.h Structure/../Parm/DihedralParmHolder.h Structure/../Parm/ImproperParmHolder.h Structure/../Parm/ParameterSet.h Structure/../Parm/ParmEnum.h Structure/../Parm/ParmHolder.h Structure/Solvate.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 Structure/StructureEnum.o : Structure/StructureEnum.cpp Structure/StructureEnum.h
 Structure/StructureRoutines.o : Structure/StructureRoutines.cpp Atom.h CpptrajStdio.h NameType.h Residue.h Structure/StructureRoutines.h SymbolExporting.h
 Structure/Sugar.o : Structure/Sugar.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h Unit.h Vec3.h

From 169286d31391676b413cfa7ebbdca477ac29457c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Wed, 18 Feb 2026 19:49:15 -0500
Subject: [PATCH 1360/1492] Was referencing the wrong var. Can lead to
 segfaults

---
 src/Structure/AddIons.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Structure/AddIons.cpp b/src/Structure/AddIons.cpp
index c131d5d1c1..ba21b86416 100644
--- a/src/Structure/AddIons.cpp
+++ b/src/Structure/AddIons.cpp
@@ -49,7 +49,7 @@ int AddIons::InitAddIons(std::string const& ion1nameIn, int Nion1,
     //  mprinterr("Error: Number of second %s ions cannot be less than 1 (%i)\n", ion2nameIn.c_str(), Nion2);
     //  return 1;
     //}
-    if (Nion2_ < 0)
+    if (Nion2 < 0)
       Nion2_ = 0;
     else
       Nion2_ = Nion2;

From 1861e845dd25302e79a05dfc3ed93b43a9d7ed58 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 19 Feb 2026 11:44:50 -0500
Subject: [PATCH 1361/1492] When combining parm sets, combine names and file
 names as well

---
 src/Parm/ParameterSet.cpp | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/src/Parm/ParameterSet.cpp b/src/Parm/ParameterSet.cpp
index b58dfc25fc..4165a7ec12 100644
--- a/src/Parm/ParameterSet.cpp
+++ b/src/Parm/ParameterSet.cpp
@@ -235,6 +235,16 @@ int ParameterSet::UpdateParamSet(ParameterSet const& set1, UpdateCount& uc, int
     set0.Debug("originalp.dat");
     set1.Debug("incomingp.dat");
   }
+  // Save names/files
+  for (Sarray::const_iterator it = set1.name_.begin(); it != set1.name_.end(); ++it)
+    name_.push_back( *it );
+  for (FNarray::const_iterator it = set1.fname_.begin(); it != set1.fname_.end(); ++it)
+    fname_.push_back( *it );
+  if (debugIn > 0) {
+    mprintf("DEBUG: Combined name: %s\n", ParamSetName().c_str());
+    for (FNarray::const_iterator it = fname_.begin(); it != fname_.end(); ++it)
+      mprintf("\t%s\n", it->base());
+  }
 
   // Bond parameters
   uc.nBondsUpdated_ = UpdateParameters< ParmHolder<BondParmType> >(set0.BP(), set1.BP(), "bond", verbose);

From 9aba32b80c94eb63c4ed49cf4e5b9e99168e6ca7 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 19 Feb 2026 12:07:18 -0500
Subject: [PATCH 1362/1492] Add files used in parameterization as comments

---
 src/Exec_Build.cpp | 6 +++++-
 src/Parm_Amber.cpp | 5 +++++
 2 files changed, 10 insertions(+), 1 deletion(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 48b96cb61a..293d1dce7c 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -1558,7 +1558,11 @@ int Exec_Build::StructurePrepAndFillTemplates(ArgList& argIn, Topology& topIn, F
   topOut.AllocTreeChainClassification( );
   topOut.AllocJoinArray();
   topOut.AllocRotateArray();
-    // Finalize topology - determine molecules, dont renumber residues
+  for (Cpptraj::Parm::ParameterSet::FNarray::const_iterator
+         fn = creator.MainParmSetPtr()->ParamSetFile().begin();
+         fn != creator.MainParmSetPtr()->ParamSetFile().end(); ++fn)
+    topOut.AddDescription( fn->Base() );
+  // Finalize topology - determine molecules, dont renumber residues
   topOut.CommonSetup(true, false);
 
   if (topOut.HasNoncontiguousMols()) {
diff --git a/src/Parm_Amber.cpp b/src/Parm_Amber.cpp
index 2b58c6a529..3a11940a67 100644
--- a/src/Parm_Amber.cpp
+++ b/src/Parm_Amber.cpp
@@ -2032,6 +2032,11 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
       // No description. Write a placeholder.
       file_.Printf("%2i%78s\n", 1, "CHARMM:");
     }
+  } else if (!TopOut.Description().empty()) {
+    // Add as comments
+    for (std::vector<std::string>::const_iterator it = TopOut.Description().begin();
+                                                  it != TopOut.Description().end(); ++it)
+      file_.Printf("%%COMMENT %s\n", it->c_str());
   }
 
   // NAMES

From 645dc9db87f688bb8b9a8e6d90bbc248d2688abb Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 19 Feb 2026 12:39:31 -0500
Subject: [PATCH 1363/1492] Use FF description flag instead

---
 src/Parm_Amber.cpp | 11 +++--------
 1 file changed, 3 insertions(+), 8 deletions(-)

diff --git a/src/Parm_Amber.cpp b/src/Parm_Amber.cpp
index 3a11940a67..ac0ad5726d 100644
--- a/src/Parm_Amber.cpp
+++ b/src/Parm_Amber.cpp
@@ -2017,12 +2017,12 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
   file_.IntToBuffer( TopOut.NextraPts() ); // NEXTRA
   if (flushFileBuffer( F_POINTERS )) return 1;
  
-  // CHAMBER only - FF type description
-  if (ptype_ == CHAMBER) {
+  // FF type description
+  if (ptype_ == CHAMBER || !TopOut.Description().empty()) {
     file_.Printf("%%FLAG %-74s\n%-80s\n", FLAGS_[F_FF_TYPE].Flag, FLAGS_[F_FF_TYPE].Fmt);
     int nlines = (int)TopOut.Description().size();
     if (nlines > 99) {
-      mprintf("Warning: Number of CHAMBER description lines > 99. Only writing 99.\n", nlines);
+      mprintf("Warning: Number of %s description lines > 99 (%i). Only writing 99.\n", FLAGS_[F_FF_TYPE].Flag, nlines);
       nlines = 99;
     }
     if (nlines > 0) {
@@ -2032,11 +2032,6 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
       // No description. Write a placeholder.
       file_.Printf("%2i%78s\n", 1, "CHARMM:");
     }
-  } else if (!TopOut.Description().empty()) {
-    // Add as comments
-    for (std::vector<std::string>::const_iterator it = TopOut.Description().begin();
-                                                  it != TopOut.Description().end(); ++it)
-      file_.Printf("%%COMMENT %s\n", it->c_str());
   }
 
   // NAMES

From 04489f9b45d35442acc2b9d06c5b98715d6d44e3 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 19 Feb 2026 13:01:55 -0500
Subject: [PATCH 1364/1492] Report the parameter set being combined so we know
 what is actually overwriting what

---
 src/Structure/Creator.cpp | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/src/Structure/Creator.cpp b/src/Structure/Creator.cpp
index 12b657e333..7b4a42ecc2 100644
--- a/src/Structure/Creator.cpp
+++ b/src/Structure/Creator.cpp
@@ -346,7 +346,7 @@ int Creator::getParameterSets(ArgList& argIn, DataSetList const& DSL) {
   //  return CpptrajState::ERR;
   //}
   if (!ParamSets.empty()) {
-    mprintf("\tParameter sets:\n"); // TODO put these names in the final combined parameter set
+    mprintf("\tParameter sets:\n");
     for (Parray::const_iterator it = ParamSets.begin(); it != ParamSets.end(); ++it)
       mprintf("\t  %s\n", (*it)->legend());
 
@@ -358,11 +358,14 @@ int Creator::getParameterSets(ArgList& argIn, DataSetList const& DSL) {
       free_parmset_mem_ = true;
       mprintf("\tCombining parameter sets.\n");
       Parray::const_iterator it = ParamSets.begin();
+      mprintf("\t  Initial parameter set: %s\n", (*it)->legend());
       mainParmSet_ = new DataSet_Parameters( *(*it) );
       ++it;
       Cpptraj::Parm::ParameterSet::UpdateCount UC;
-      for (; it != ParamSets.end(); ++it)
-        mainParmSet_->UpdateParamSet( *(*it), UC, debug_, debug_+1 ); // Make it so verbosity is at least 1 to report overwritten params 
+      for (; it != ParamSets.end(); ++it) {
+        mprintf("\t  Adding parameter set: %s\n", (*it)->legend());
+        mainParmSet_->UpdateParamSet( *(*it), UC, debug_, debug_+1 ); // Make it so verbosity is at least 1 to report overwritten params
+      }
     }
   }
   return 0;

From 06f7ca66a71d24608a4a12c110ff3ce2adbd9257 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 19 Feb 2026 15:44:08 -0500
Subject: [PATCH 1365/1492] Add large indices for angles and bonds

---
 src/Parm_Amber.cpp | 29 +++++++++++++++++++++++------
 src/Parm_Amber.h   | 35 ++++++++++++++++++-----------------
 2 files changed, 41 insertions(+), 23 deletions(-)

diff --git a/src/Parm_Amber.cpp b/src/Parm_Amber.cpp
index ac0ad5726d..98ecd8ee8a 100644
--- a/src/Parm_Amber.cpp
+++ b/src/Parm_Amber.cpp
@@ -154,6 +154,10 @@ const Parm_Amber::ParmFlag Parm_Amber::FLAGS_[] = {
   // Extended format flags
   { "DIHEDRALS_INC_HYDROGEN",      "%FORMAT(8I10)" },   // For topologies with high atom counts
   { "DIHEDRALS_WITHOUT_HYDROGEN",  "%FORMAT(8I10)" },   // For topologies with high atom counts
+  { "BONDS_INC_HYDROGEN",          "%FORMAT(8I10)" }, ///< Bonds to hydrogen
+  { "BONDS_WITHOUT_HYDROGEN",      "%FORMAT(8I10)" }, ///< Bonds not including hydrogen
+  { "ANGLES_INC_HYDROGEN",         "%FORMAT(8I10)" },
+  { "ANGLES_WITHOUT_HYDROGEN",     "%FORMAT(8I10)" },
   { 0, 0 }
 };
 
@@ -2231,12 +2235,25 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
     if (WriteLJ(F_LJ14A, F_LJ14B, TopOut.Nonbond().LJ14())) return 1;
   }
 
-  // BONDSH and BONDS
-  if (WriteBonds(F_BONDSH, TopOut.BondsH())) return 1;
-  if (WriteBonds(F_BONDS,  TopOut.Bonds()) ) return 1;
-  // ANGLESH and ANGLES
-  if (WriteAngles(F_ANGLESH, TopOut.AnglesH())) return 1;
-  if (WriteAngles(F_ANGLES,  TopOut.Angles()) ) return 1;
+  // BONDSH and BONDS, ANGLESH and ANGLES
+  FlagType flag_bndh, flag_bnd, flag_angh, flag_ang;
+  if (TopOut.Natom()*3 < 100000000) {
+    flag_bndh = F_BONDSH;
+    flag_bnd  = F_BONDS;
+    flag_angh = F_ANGLESH;
+    flag_ang  = F_ANGLES;
+  } else {
+    mprintf("Warning: Topology has >= 100M atoms. Using extended bond/angle format strings.\n");
+    mprintf("Warning: This may confuse topology readers that do not actually read the FLAG format strings.\n");
+    flag_bndh = F_BNDH_LARGE;
+    flag_bnd  = F_BND_LARGE;
+    flag_angh = F_ANGH_LARGE;
+    flag_ang  = F_ANG_LARGE;
+  }
+  if (WriteBonds(flag_bndh, TopOut.BondsH())) return 1;
+  if (WriteBonds(flag_bnd,  TopOut.Bonds()) ) return 1;
+  if (WriteAngles(flag_angh, TopOut.AnglesH())) return 1;
+  if (WriteAngles(flag_ang,  TopOut.Angles()) ) return 1;
   // DIHEDRALSH and DIHEDRALS
   FlagType flag_dihh, flag_dih;
   // Check if the largest possible index will be greater than the default
diff --git a/src/Parm_Amber.h b/src/Parm_Amber.h
index 25f021eecf..5ad193c05a 100644
--- a/src/Parm_Amber.h
+++ b/src/Parm_Amber.h
@@ -22,24 +22,25 @@ class Parm_Amber : public ParmIO {
     enum Type { UNKNOWN_FTYPE=0, FINT, FDOUBLE, FCHAR, FFLOAT };
     /// Enumerated type for Amber Parmtop Flags. KEEP IN SYNC WITH FLAGS_ ARRAY
     enum FlagType {
-      F_POINTERS = 0, F_NAMES,        F_CHARGE,    F_MASS,      F_RESNAMES,
-      F_RESNUMS,      F_TYPES,        F_BONDSH,    F_BONDS,     F_SOLVENT_POINTER,
-      F_ATOMSPERMOL,  F_PARMBOX,      F_ATYPEIDX,  F_NUMEX,     F_NB_INDEX,
-      F_LJ_A,         F_LJ_B,         F_LJ_C,      F_EXCLUDE,   F_RADII,
-      F_SCREEN,       F_BONDRK,       F_BONDREQ,   F_ANGLETK,   F_ANGLETEQ,
-      F_DIHPK,        F_DIHPN,        F_DIHPHASE,  F_SCEE,      F_SCNB,
-      F_SOLTY,        F_ANGLESH,      F_ANGLES,    F_DIHH,      F_DIH,
-      F_ASOL,         F_BSOL,         F_HBCUT,     F_ITREE,     F_JOIN,
-      F_IROTAT,       F_ATOMICNUM,    F_TITLE,     F_RADSET,    F_LES_NTYP,
-      F_LES_TYPE,     F_LES_FAC,      F_LES_CNUM,  F_LES_ID,    F_CAP_INFO,
-      F_CAP_INFO2,    F_IPOL,         F_POLAR,     F_CTITLE,    F_CHM_UBC,
-      F_CHM_UB,       F_CHM_UBFC,     F_CHM_UBEQ,  F_CHM_NIMP,  F_CHM_IMP,
-      F_CHM_NIMPT,    F_CHM_IMPFC,    F_CHM_IMPP,  F_LJ14A,     F_LJ14B,
-      F_CHM_CMAPC,    F_CHM_CMAPR,    F_CHM_CMAPP, F_CHM_CMAPI, F_FF_TYPE,
+      F_POINTERS = 0, F_NAMES,        F_CHARGE,    F_MASS,       F_RESNAMES,
+      F_RESNUMS,      F_TYPES,        F_BONDSH,    F_BONDS,      F_SOLVENT_POINTER,
+      F_ATOMSPERMOL,  F_PARMBOX,      F_ATYPEIDX,  F_NUMEX,      F_NB_INDEX,
+      F_LJ_A,         F_LJ_B,         F_LJ_C,      F_EXCLUDE,    F_RADII,
+      F_SCREEN,       F_BONDRK,       F_BONDREQ,   F_ANGLETK,    F_ANGLETEQ,
+      F_DIHPK,        F_DIHPN,        F_DIHPHASE,  F_SCEE,       F_SCNB,
+      F_SOLTY,        F_ANGLESH,      F_ANGLES,    F_DIHH,       F_DIH,
+      F_ASOL,         F_BSOL,         F_HBCUT,     F_ITREE,      F_JOIN,
+      F_IROTAT,       F_ATOMICNUM,    F_TITLE,     F_RADSET,     F_LES_NTYP,
+      F_LES_TYPE,     F_LES_FAC,      F_LES_CNUM,  F_LES_ID,     F_CAP_INFO,
+      F_CAP_INFO2,    F_IPOL,         F_POLAR,     F_CTITLE,     F_CHM_UBC,
+      F_CHM_UB,       F_CHM_UBFC,     F_CHM_UBEQ,  F_CHM_NIMP,   F_CHM_IMP,
+      F_CHM_NIMPT,    F_CHM_IMPFC,    F_CHM_IMPP,  F_LJ14A,      F_LJ14B,
+      F_CHM_CMAPC,    F_CHM_CMAPR,    F_CHM_CMAPP, F_CHM_CMAPI,  F_FF_TYPE,
       F_CHM_CHARGE,   F_CHM_ANGLETEQ, F_CHM_LJ_A,  F_CHM_LJ_B,
-      F_PDB_RES,      F_PDB_CHAIN,    F_PDB_ICODE, F_PDB_ALT,   F_PDB_BFAC,
-      F_PDB_OCC,      F_PDB_NUM,      F_CMAPC,     F_CMAPR,     F_CMAPP,
-      F_CMAPI,        F_DIHH_LARGE,   F_DIH_LARGE
+      F_PDB_RES,      F_PDB_CHAIN,    F_PDB_ICODE, F_PDB_ALT,    F_PDB_BFAC,
+      F_PDB_OCC,      F_PDB_NUM,      F_CMAPC,     F_CMAPR,      F_CMAPP,
+      F_CMAPI,        F_DIHH_LARGE,   F_DIH_LARGE, F_BNDH_LARGE, F_BND_LARGE,
+      F_ANGH_LARGE,   F_ANG_LARGE
     };
     /// Used to hold %FLAG/FORMAT string pairs. Corresponds to FlagType.
     struct ParmFlag {

From 692a9dce16461c1901067d675d05b0ac096a1d89 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 19 Feb 2026 17:02:51 -0500
Subject: [PATCH 1366/1492] No longer CHAMBER-specific.

---
 src/Parm_Amber.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Parm_Amber.cpp b/src/Parm_Amber.cpp
index 98ecd8ee8a..5225b9d06f 100644
--- a/src/Parm_Amber.cpp
+++ b/src/Parm_Amber.cpp
@@ -1263,7 +1263,7 @@ static inline int fftype_err(const char* ptr, const char* Flag) {
   *       If this fails print a warning and try to continue.
   */
 int Parm_Amber::ReadChamberFFtype(Topology& TopIn, FortranData const& FMT) {
-  mprintf("\tCHAMBER topology:\n");
+  mprintf("\tForce field description:\n");
   if (FMT.Ftype() != FINT)
     mprintf("Warning: In '%s' expected format to begin with integer. Skipping.\n",
             FLAGS_[F_FF_TYPE].Flag);

From ef698ee8da25a91d66acde56459260a79bba44df Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 19 Feb 2026 17:46:52 -0500
Subject: [PATCH 1367/1492] Convert index limits to # atom limits

---
 src/Parm_Amber.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/Parm_Amber.cpp b/src/Parm_Amber.cpp
index 5225b9d06f..a3cb730ce6 100644
--- a/src/Parm_Amber.cpp
+++ b/src/Parm_Amber.cpp
@@ -2243,7 +2243,7 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
     flag_angh = F_ANGLESH;
     flag_ang  = F_ANGLES;
   } else {
-    mprintf("Warning: Topology has >= 100M atoms. Using extended bond/angle format strings.\n");
+    mprintf("Warning: Topology has > 33M atoms. Using extended bond/angle format strings.\n");
     mprintf("Warning: This may confuse topology readers that do not actually read the FLAG format strings.\n");
     flag_bndh = F_BNDH_LARGE;
     flag_bnd  = F_BND_LARGE;
@@ -2262,7 +2262,7 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
     flag_dihh = F_DIHH;
     flag_dih  = F_DIH;
   } else {
-    mprintf("Warning: Topology has >= 10M atoms. Using extended dihedral format strings.\n");
+    mprintf("Warning: Topology has > 3M atoms. Using extended dihedral format strings.\n");
     mprintf("Warning: This may confuse topology readers that do not actually read the FLAG format strings.\n");
     flag_dihh = F_DIHH_LARGE;
     flag_dih  = F_DIH_LARGE;

From ccabe264988b7bca9ded07d24f8df7d8767d24a8 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 19 Feb 2026 19:06:47 -0500
Subject: [PATCH 1368/1492] When appending top, only print warning for no atom
 types when assignin nonbonds if verbose

---
 src/Topology.cpp | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/src/Topology.cpp b/src/Topology.cpp
index 9ce8bb3d00..4592d10517 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -2395,7 +2395,12 @@ int Topology::AppendTop(Topology const& NewTop, int verbose_, bool reduce_bond_p
   AssignParams assign;
   assign.SetDebug( debug_ );
   assign.SetVerbose( verbose_ );
-  assign.AssignNonbondParams( topOut, myAtomTypes, myNB, my14, myLJC, myHB );
+  if ( myAtomTypes.size() < 1) {
+    if (verbose_ > 1)
+      mprintf("Warning: No atom types; cannot assign nonbond parameters.\n");
+  } else {
+    assign.AssignNonbondParams( topOut, myAtomTypes, myNB, my14, myLJC, myHB );
+  }
 
   // The version of AddTopAtom() with molecule number already determines
   // molecules and number of solvent molecules.

From 03383255bed6fb5b77e5f31de173c473577855b9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 19 Feb 2026 19:07:14 -0500
Subject: [PATCH 1369/1492] Only put a warning about no atom types found if all
 the types are blank. Maybe should be if any are blank?

---
 src/Parm/Merge.cpp | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/src/Parm/Merge.cpp b/src/Parm/Merge.cpp
index 70b49ac209..c3670d045d 100644
--- a/src/Parm/Merge.cpp
+++ b/src/Parm/Merge.cpp
@@ -121,6 +121,11 @@ static inline DihedralType idxWithOffset(DihedralType const& dih1, int idx, unsi
 
 // -------------------------------------
 static inline void noParmWarning(TypeNameHolder const& types) {
+  bool all_empty = true;
+  for (unsigned int idx = 0; idx < types.Size(); idx++) {
+    if (types[idx].len() > 0) { all_empty = false; break; }
+  }
+  if (all_empty) return;
   if (types.Size() == 2)
     mprintf("Warning: No bond parameters for types %s - %s\n", *(types[0]), *(types[1]));
   else if (types.Size() == 3)

From 00c5b7cdc33cf78af63a2a54258bae792d9c18f5 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 19 Feb 2026 19:09:05 -0500
Subject: [PATCH 1370/1492] Add doassembly keyword for automatically creating
 assemblies from PDB MODELs

---
 src/Exec_Build.cpp | 78 ++++++++++++++++++++++++++++++++++++----------
 src/Exec_Build.h   |  2 ++
 2 files changed, 63 insertions(+), 17 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 293d1dce7c..57f7a398b7 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -825,7 +825,7 @@ const
 // Exec_Build::Help()
 void Exec_Build::Help() const
 {
-  mprintf("\t[name <output COORDS>] {crdset <COORDS set>|<file>} [frame <#>]\n");
+  mprintf("\t[name <output COORDS>] {crdset <COORDS set>|<file>} [{frame <#>|doassembly}]\n");
   Cpptraj::Structure::PdbCleaner::Help();
   mprintf("\t[title <title>] [verbose <#>] [keepmissingatoms] [nofixorder]\n"
           "\t[parmout <topology file>] [crdout <coord file>] [simplecheck]\n");
@@ -888,6 +888,39 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
   return BuildAndParmStructure(inCrdPtr, outset, State.DSL(), State.Debug(), argIn, Cpptraj::Parm::UNKNOWN_GB);
 }
 
+/** Create an assembly from all the frames in the input coordinates. */
+int Exec_Build::createAssembly(Topology& topIn, Frame& frameIn,
+                               DataSet_Coords& CRDIN)
+const
+{
+  if (CRDIN.Size() < 2) {
+    mprintf("Warning: Only %zu frames in COORDS set '%s'; no assembly needed.\n");
+    frameIn = CRDIN.AllocateFrame();
+    CRDIN.GetFrame(0, frameIn);
+    topIn = CRDIN.Top();
+  } else {
+    mprintf("\tCreating assembly from %zu structures:", CRDIN.Size());
+    for (unsigned int idx = 0; idx < CRDIN.Size(); idx++) {
+      mprintf(" %u", idx+1);
+      topIn.AppendTop( CRDIN.Top(), debug_, false, false );
+    }
+    frameIn.SetupFrameV( topIn.Atoms(), CRDIN.CoordsInfo() );
+    Frame frm = CRDIN.AllocateFrame();
+    mprintf("\n\tCopying coordinates for assembly:");
+    double *output = frameIn.xAddress();
+    for (unsigned int idx = 0; idx < CRDIN.Size(); idx++) {
+      // Coords
+      mprintf(" %u", idx+1);
+      CRDIN.GetFrame(idx, frm);
+      std::copy(frm.xAddress(), frm.xAddress()+frm.size(), output);
+      output += frm.size();
+    }
+    mprintf("\n");
+    topIn.Brief("Assembly");
+  }
+  return 0;
+}
+
 /** Standalone execute. For DataIO_LeapRC. Operate on inCrdPtr */
 Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, int debugIn,
                                          std::string const& outset, std::string const& title,
@@ -1019,6 +1052,8 @@ Exec::RetType Exec_Build::BuildAndParmStructure(DataSet* inCrdPtr, std::string c
                                                 Cpptraj::Parm::GB_RadiiType gbRadIn)
 {
   t_total_.Start();
+  debug_ = debugIn;
+  int verbose = argIn.getKeyInt("verbose", 0);
   if (inCrdPtr == 0) {
     mprinterr("Internal Error: Exec_Build::BuildStructure(): Null input coordinates.\n");
     return CpptrajState::ERR;
@@ -1027,13 +1062,12 @@ Exec::RetType Exec_Build::BuildAndParmStructure(DataSet* inCrdPtr, std::string c
     mprinterr("Error: Set '%s' is not coordinates, cannot use for building.\n", inCrdPtr->legend());
     return CpptrajState::ERR;
   }
-  if (outset.empty() && inCrdPtr->Size() > 1) {
+  bool doassembly = argIn.hasKey("doassembly");
+  if (!doassembly && outset.empty() && inCrdPtr->Size() > 1) {
     mprinterr("Error: Set '%s' has more than 1 frame; must specify an output COORDS set in order to build.\n",
               inCrdPtr->legend());
     return CpptrajState::ERR;
   }
-  debug_ = debugIn;
-  int verbose = argIn.getKeyInt("verbose", 0);
   std::string title = argIn.GetStringKey("title");
   if (argIn.hasKey("nofixorder"))
     fixAtomOrder_ = false;
@@ -1053,22 +1087,32 @@ Exec::RetType Exec_Build::BuildAndParmStructure(DataSet* inCrdPtr, std::string c
     mprintf("\tWill write topology to %s\n", outputTopologyName.c_str());
   if (!outputCoordsName.empty())
     mprintf("\tWill write coords to %s\n", outputCoordsName.c_str());
+
+  Frame frameIn;
+  Topology topIn;
   // TODO make it so this can be const (cant bc GetFrame)
   DataSet_Coords& coords = static_cast<DataSet_Coords&>( *((DataSet_Coords*)inCrdPtr) );
-  // Get frame from input coords
-  int tgtframe = argIn.getKeyInt("frame", 1) - 1;
-  mprintf("\tUsing frame %i from COORDS set %s\n", tgtframe+1, coords.legend());
-  if (tgtframe < 0 || tgtframe >= (int)coords.Size()) {
-    mprinterr("Error: Frame is out of range.\n");
-    return CpptrajState::ERR;
+  if (doassembly) {
+    if (createAssembly(topIn, frameIn, coords)) {
+      mprinterr("Error: Assembly creation failed.\n");
+      return CpptrajState::ERR;
+    }
+  } else {
+    // Get frame from input coords
+    int tgtframe = argIn.getKeyInt("frame", 1) - 1;
+    mprintf("\tUsing frame %i from COORDS set %s\n", tgtframe+1, coords.legend());
+    if (tgtframe < 0 || tgtframe >= (int)coords.Size()) {
+      mprinterr("Error: Frame is out of range.\n");
+      return CpptrajState::ERR;
+    }
+    frameIn = coords.AllocateFrame();
+    coords.GetFrame(tgtframe, frameIn);
+    // Get modifiable topology
+    // NOTE: Topology is copied here because it might be destroyed if doing in-place build.
+    //Topology& topIn = *(coords.TopPtr());
+    //Topology const& topIn = coords.Top();
+    topIn = coords.Top(); // FIXME do not work on the copy, work on the top itself
   }
-  Frame frameIn = coords.AllocateFrame();
-  coords.GetFrame(tgtframe, frameIn);
-  // Get modifiable topology
-  // NOTE: Topology is copied here because it might be destroyed if doing in-place build.
-  //Topology& topIn = *(coords.TopPtr());
-  //Topology const& topIn = coords.Top();
-  Topology topIn = coords.Top(); // FIXME do not work on the copy, work on the top itself
 
   std::string solventResName = argIn.GetStringKey("solventresname", "HOH");
   mprintf("\tResidues named '%s' will be recognized as solvent.\n", solventResName.c_str());
diff --git a/src/Exec_Build.h b/src/Exec_Build.h
index 293b1608f3..45fc9d712f 100644
--- a/src/Exec_Build.h
+++ b/src/Exec_Build.h
@@ -36,6 +36,8 @@ class Exec_Build : public Exec {
     static inline bool hasBondingPair(IParray const&, Ipair const&);
     /// \return true if given array of residue connections has target residue index.
     static inline bool resIsConnected(Iarray const&, int);
+    /// Create assembly from input COORDS
+    int createAssembly(Topology&, Frame&, DataSet_Coords&) const;
     /// Create new topology/frame using templates
     int FillAtomsWithTemplates(Topology&, Frame&, Topology const&, Frame const&,
                                Cpptraj::Structure::Creator const&,

From f9602e48c653c6407c99fa708364abe9e48276c2 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 19 Feb 2026 19:44:23 -0500
Subject: [PATCH 1371/1492] Handle large pointers

---
 src/Parm_Amber.cpp | 80 +++++++++++++++++++++++++++++++++++++++-------
 src/Parm_Amber.h   |  3 +-
 2 files changed, 71 insertions(+), 12 deletions(-)

diff --git a/src/Parm_Amber.cpp b/src/Parm_Amber.cpp
index a3cb730ce6..2e29930487 100644
--- a/src/Parm_Amber.cpp
+++ b/src/Parm_Amber.cpp
@@ -61,6 +61,7 @@ static const char* F5E16 = "%FORMAT(5E16.8)";
 static const char* F3I8  = "%FORMAT(3I8)";
 static const char* F1a80 = "%FORMAT(1a80)";
 static const char* F1I8  = "%FORMAT(1I8)";
+static const char* F8I10 = "%FORMAT(8I10)";
 /// Constant strings for Amber parm flags and fortran formats. Enumerated by FlagType
 const Parm_Amber::ParmFlag Parm_Amber::FLAGS_[] = {
   { "POINTERS",                   F10I8 }, ///< Described above in topValues
@@ -152,12 +153,13 @@ const Parm_Amber::ParmFlag Parm_Amber::FLAGS_[] = {
   { "CMAP_PARAMETER_",             "%FORMAT(8F9.5)"},   // CMAP grid
   { "CMAP_INDEX",                  "%FORMAT(6I8)" },    // Atom i,j,k,l,m of cross term and idx
   // Extended format flags
-  { "DIHEDRALS_INC_HYDROGEN",      "%FORMAT(8I10)" },   // For topologies with high atom counts
-  { "DIHEDRALS_WITHOUT_HYDROGEN",  "%FORMAT(8I10)" },   // For topologies with high atom counts
-  { "BONDS_INC_HYDROGEN",          "%FORMAT(8I10)" }, ///< Bonds to hydrogen
-  { "BONDS_WITHOUT_HYDROGEN",      "%FORMAT(8I10)" }, ///< Bonds not including hydrogen
-  { "ANGLES_INC_HYDROGEN",         "%FORMAT(8I10)" },
-  { "ANGLES_WITHOUT_HYDROGEN",     "%FORMAT(8I10)" },
+  { "DIHEDRALS_INC_HYDROGEN",      F8I10 },   // For topologies with high atom counts
+  { "DIHEDRALS_WITHOUT_HYDROGEN",  F8I10 },   // For topologies with high atom counts
+  { "BONDS_INC_HYDROGEN",          F8I10 }, ///< Bonds to hydrogen
+  { "BONDS_WITHOUT_HYDROGEN",      F8I10 }, ///< Bonds not including hydrogen
+  { "ANGLES_INC_HYDROGEN",         F8I10 },
+  { "ANGLES_WITHOUT_HYDROGEN",     F8I10 },
+  { "POINTERS",                    F8I10 }, ///< Described above in topValues
   { 0, 0 }
 };
 
@@ -1841,6 +1843,61 @@ static inline int check_array_size(unsigned int expectedSize, unsigned int actua
   return 0;
 }
 
+/// \return true if incoming value will overflow the default POINTERS width (8 digits)
+template <typename T> bool GT_MAX_PTR(T valIn) { return (valIn > (T)99999999); } 
+
+/** Check the pointers from the input Topology and return a flag big enough
+  * to accommodate them.
+  */
+Parm_Amber::FlagType Parm_Amber::check_pointers(Topology const& TopOut, unsigned int excludedSize, unsigned int n_unique_atom_types, unsigned int maxResSize ) const {
+  FlagType flag_pointers = F_POINTERS;
+
+  if (GT_MAX_PTR( TopOut.Natom() )) flag_pointers = F_PNT_LARGE; // NATOM
+  if (GT_MAX_PTR( TopOut.Nonbond().Ntypes() )) flag_pointers = F_PNT_LARGE; // NTYPES
+  if (GT_MAX_PTR( TopOut.BondsH().size() )) flag_pointers = F_PNT_LARGE; // NBONH
+  if (GT_MAX_PTR( TopOut.Bonds().size() )) flag_pointers = F_PNT_LARGE; // NBONA
+  if (GT_MAX_PTR( TopOut.AnglesH().size() )) flag_pointers = F_PNT_LARGE; // NTHETH
+  if (GT_MAX_PTR( TopOut.Angles().size() )) flag_pointers = F_PNT_LARGE; // NTHETA
+  if (GT_MAX_PTR( TopOut.DihedralsH().size() )) flag_pointers = F_PNT_LARGE; // NPHIH
+  if (GT_MAX_PTR( TopOut.Dihedrals().size() )) flag_pointers = F_PNT_LARGE; // NPHIA
+  //if (GT_MAX_PTR( 0 )) flag_pointers = F_PNT_LARGE; // NHPARM, not used
+  //if (TopOut.LES().HasLES()) { // NPARM
+  //  mprintf("Warning: Excluded atom list for LES info is not correct.\n");
+  //  file_.IntToBuffer( 1 );
+  //} else
+  //  file_.IntToBuffer( 0 );
+  if (GT_MAX_PTR( excludedSize )) flag_pointers = F_PNT_LARGE; // NNB
+  if (GT_MAX_PTR( TopOut.Nres() )) flag_pointers = F_PNT_LARGE; // NRES
+  //   NOTE: Assuming MBONA == NBONA etc
+  if (GT_MAX_PTR( TopOut.Bonds().size() )) flag_pointers = F_PNT_LARGE; // MBONA
+  if (GT_MAX_PTR( TopOut.Angles().size() )) flag_pointers = F_PNT_LARGE; // MTHETA
+  if (GT_MAX_PTR( TopOut.Dihedrals().size() )) flag_pointers = F_PNT_LARGE; // MPHIA
+  if (GT_MAX_PTR( TopOut.BondParm().size() )) flag_pointers = F_PNT_LARGE; // NUMBND
+  if (GT_MAX_PTR( TopOut.AngleParm().size() )) flag_pointers = F_PNT_LARGE; // NUMANG
+  if (GT_MAX_PTR( TopOut.DihedralParm().size() )) flag_pointers = F_PNT_LARGE; // NPTRA
+  if (GT_MAX_PTR( n_unique_atom_types )) flag_pointers = F_PNT_LARGE; // NATYP, only for SOLTY
+  if (GT_MAX_PTR( TopOut.Nonbond().HBarray().size() )) flag_pointers = F_PNT_LARGE; // NPHB
+  //file_.IntToBuffer( 0 ); // IFPERT
+  //file_.IntToBuffer( 0 ); // NBPER
+  //file_.IntToBuffer( 0 ); // NGPER
+  //file_.IntToBuffer( 0 ); // NDPER
+  //file_.IntToBuffer( 0 ); // MBPER
+  //file_.IntToBuffer( 0 ); // MGPER
+  //file_.IntToBuffer( 0 ); // MDPER
+  //file_.IntToBuffer( ifbox ); // IFBOX
+  if (GT_MAX_PTR( maxResSize )) flag_pointers = F_PNT_LARGE; // NMXRS
+  //if (TopOut.Cap().NatCap() > 0) // IFCAP
+  //  file_.IntToBuffer( 1 );
+  //else
+  //  file_.IntToBuffer( 0 );
+  if (GT_MAX_PTR( TopOut.NextraPts() )) flag_pointers = F_PNT_LARGE; // NEXTRA
+
+  if (flag_pointers != F_POINTERS)
+    mprintf("Warning: Very large values detected; using extended format string for POINTERS.\n");
+
+  return flag_pointers;
+}
+
 // Parm_Amber::WriteParm()
 int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
   if (file_.OpenWrite( fname )) return 1;
@@ -1975,7 +2032,11 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
   }
 
   // POINTERS
-  if (BufferAlloc(F_POINTERS, AMBERPOINTERS_)) return 1;
+  Cpptraj::Parm::GetParams GP;
+  GP.SetDebug( debug_ );
+  unsigned int n_unique_atom_types = GP.NuniqueAtomTypes( TopOut );
+  FlagType flag_pointers = check_pointers( TopOut, Excluded.size(), n_unique_atom_types, maxResSize );
+  if (BufferAlloc(flag_pointers, AMBERPOINTERS_)) return 1;
   file_.IntToBuffer( TopOut.Natom() ); // NATOM
   file_.IntToBuffer( TopOut.Nonbond().Ntypes() ); // NTYPES
   file_.IntToBuffer( TopOut.BondsH().size() ); // NBONH
@@ -2000,9 +2061,6 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
   file_.IntToBuffer( TopOut.BondParm().size() ); // NUMBND
   file_.IntToBuffer( TopOut.AngleParm().size() ); // NUMANG
   file_.IntToBuffer( TopOut.DihedralParm().size() ); // NPTRA
-  Cpptraj::Parm::GetParams GP;
-  GP.SetDebug( debug_ );
-  unsigned int n_unique_atom_types = GP.NuniqueAtomTypes( TopOut );
   file_.IntToBuffer( n_unique_atom_types ); // NATYP, only for SOLTY
   file_.IntToBuffer( TopOut.Nonbond().HBarray().size() ); // NPHB
   file_.IntToBuffer( 0 ); // IFPERT
@@ -2019,7 +2077,7 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
   else
     file_.IntToBuffer( 0 );
   file_.IntToBuffer( TopOut.NextraPts() ); // NEXTRA
-  if (flushFileBuffer( F_POINTERS )) return 1;
+  if (flushFileBuffer( flag_pointers )) return 1;
  
   // FF type description
   if (ptype_ == CHAMBER || !TopOut.Description().empty()) {
diff --git a/src/Parm_Amber.h b/src/Parm_Amber.h
index 5ad193c05a..dd3a975e56 100644
--- a/src/Parm_Amber.h
+++ b/src/Parm_Amber.h
@@ -40,7 +40,7 @@ class Parm_Amber : public ParmIO {
       F_PDB_RES,      F_PDB_CHAIN,    F_PDB_ICODE, F_PDB_ALT,    F_PDB_BFAC,
       F_PDB_OCC,      F_PDB_NUM,      F_CMAPC,     F_CMAPR,      F_CMAPP,
       F_CMAPI,        F_DIHH_LARGE,   F_DIH_LARGE, F_BNDH_LARGE, F_BND_LARGE,
-      F_ANGH_LARGE,   F_ANG_LARGE
+      F_ANGH_LARGE,   F_ANG_LARGE,    F_PNT_LARGE
     };
     /// Used to hold %FLAG/FORMAT string pairs. Corresponds to FlagType.
     struct ParmFlag {
@@ -161,6 +161,7 @@ class Parm_Amber : public ParmIO {
     int WriteIjoin(std::vector<int> const&);
     int WriteIrotat(std::vector<int> const&);
     int WriteExtra(Topology const&, int);
+    FlagType check_pointers(Topology const&, unsigned int, unsigned int, unsigned int) const;
  
     static const int AMBERPOINTERS_;
     /// Contain topology flags enumerated by FlagType

From 87de649902f55790a8de71919b586ed0119c7e9c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 20 Feb 2026 11:47:00 -0500
Subject: [PATCH 1372/1492] Change the tolerance for number of times smallest
 diff seen to > 2 instead of > 4

---
 src/Structure/Solvate.cpp | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index 20795c7250..a943ceb164 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -783,13 +783,14 @@ int Solvate::SolvateBoxWithExactNumber(Topology& topOut, Frame& frameOut, Cpptra
         // Update smallest buffer; presumably is closer
         smallestBuf = Vec3(bufX, bufY, bufZ);
       }
-    }  
+    } 
+    mprintf("DEBUG: SmallestNegDiff= %i  nTimesSmallestSeen= %i\n", smallestNegDiff, nTimesSmallestSeen);
     // If this is the first time through choose an appropriate change val
     if (ntries == 0) {
       change = 0.001;
     }
     // See if we have tol more waters than the target TODO
-    if ((diff < 0 && nTimesSmallestSeen > 4) || (diff < 0 && diff >= negtol)) {
+    if ((diff < 0 && nTimesSmallestSeen > 2) || (diff < 0 && diff >= negtol)) {
       // Close enough, just remove the last water residue(s)
       int nToRemove = -diff;
       mprintf("\tOnly %i solvent molecules off, removing them.\n", nToRemove);

From ec878336206a930e1e88b81737ec02927a5e824a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 20 Feb 2026 12:02:38 -0500
Subject: [PATCH 1373/1492] Note the 'doassembly' keyword

---
 doc/ChangeLog.v7.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/ChangeLog.v7.md b/doc/ChangeLog.v7.md
index a6f7f6d5e2..109a0ae734 100644
--- a/doc/ChangeLog.v7.md
+++ b/doc/ChangeLog.v7.md
@@ -5,7 +5,7 @@ The major change in this version is the introduction of the ability of CPPTRAJ t
 
 New Commands
 ============
-- `build` - Allow full build and parameterization of systems for MD, including CMAP, LJ 12-6-4, solvation, and ions. Includes `prepareforleap` and `fixatomorder` functionality.
+- `build` - Allow full build and parameterization of systems for MD, including CMAP, LJ 12-6-4, solvation, and ions. Includes `prepareforleap` and `fixatomorder` functionality. Can create macromolecular assemblies from PDBs with multiple models.
 
 - `source` - Read (limited) leaprc files.
 

From 246fea6beba55286c3c9dcab7c65303517c9f9fe Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 20 Feb 2026 12:03:12 -0500
Subject: [PATCH 1374/1492] Note nsolvent keyword

---
 doc/ChangeLog.v7.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/ChangeLog.v7.md b/doc/ChangeLog.v7.md
index 109a0ae734..f6324df32b 100644
--- a/doc/ChangeLog.v7.md
+++ b/doc/ChangeLog.v7.md
@@ -5,7 +5,7 @@ The major change in this version is the introduction of the ability of CPPTRAJ t
 
 New Commands
 ============
-- `build` - Allow full build and parameterization of systems for MD, including CMAP, LJ 12-6-4, solvation, and ions. Includes `prepareforleap` and `fixatomorder` functionality. Can create macromolecular assemblies from PDBs with multiple models.
+- `build` - Allow full build and parameterization of systems for MD, including CMAP, LJ 12-6-4, solvation, and ions. Includes `prepareforleap` and `fixatomorder` functionality. Can create macromolecular assemblies from PDBs with multiple models. Can solvate with a target # of solvent molecules.
 
 - `source` - Read (limited) leaprc files.
 

From 5f0aa8816ce1cbfc86c000c6bb04631710e6e66b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 24 Feb 2026 14:12:14 -0500
Subject: [PATCH 1375/1492] Wildcard is not in TypeNameHolder anymore, remove
 from DataSize

---
 src/TypeNameHolder.h | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/TypeNameHolder.h b/src/TypeNameHolder.h
index 885fcefdcf..410f55ccfc 100644
--- a/src/TypeNameHolder.h
+++ b/src/TypeNameHolder.h
@@ -184,7 +184,7 @@ class TypeNameHolder {
       }
     }
     /// \return size in bytes
-    size_t DataSize() const { return (types_.size()*NameType::DataSize()) + NameType::DataSize(); }
+    size_t DataSize() const { return (types_.size()*NameType::DataSize()); }
   private:
     Narray types_;
     //NameType wildcard_;

From 3f431606e3326b43276eb87e9d50d60c6513bc1c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 24 Feb 2026 14:28:13 -0500
Subject: [PATCH 1376/1492] Start the DihedralParmSet class

---
 src/Parm/DihedralParmSet.h | 83 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 83 insertions(+)
 create mode 100644 src/Parm/DihedralParmSet.h

diff --git a/src/Parm/DihedralParmSet.h b/src/Parm/DihedralParmSet.h
new file mode 100644
index 0000000000..8a14a898e6
--- /dev/null
+++ b/src/Parm/DihedralParmSet.h
@@ -0,0 +1,83 @@
+#ifndef INC_PARM_DIHEDRALPARMSET_H
+#define INC_PARM_DIHEDRALPARMSET_H
+#include <map>
+#include "ParmEnum.h"
+#include "../ParameterTypes.h"
+#include "../TypeNameHolder.h"
+namespace Cpptraj {
+namespace Parm {
+/// Used for reading in dihedral parameters.
+/** When dihedral parameters are read in one at a time it is not
+  * guaranteed that parameters for all multiplcities will be
+  * present. This allows dihedral parameters to be read in
+  * one multiplicit at a time and then be checked for
+  * consistency afterwards.
+  */
+class DihedralParmSet {
+    typedef std::pair<TypeNameHolder, DihedralParmArray> Dpair;
+    typedef std::map<TypeNameHolder, DihedralParmArray> Dmap;
+  public:
+    DihedralParmSet() {}
+    /// Add (or update) a single dihedral parameter for given atom types.
+    RetType AddDihParm(TypeNameHolder const& types, DihedralParmType const& dp, bool allowUpdate) {
+      // Check if dihedral parm for these types exist
+      Dmap::iterator it0 = dihparm_.lower_bound( types );
+      if (it0 == dihparm_.end() || it0->first != types) {
+        // Brand new dihedral for these types
+        it0 = dihparm_.insert(it0, Dpair(types, DihedralParmArray(1, dp)));
+      } else {
+        // If we are here types match - check multiplicity
+        DihedralParmArray::iterator it1 = it0->second.begin();
+        for (; it1 != it0->second.end(); ++it1)
+        {
+          if (FEQ(it1->Pn(), dp.Pn()))
+            break;
+        }
+        if (it1 == it0->second.end()) {
+          // Brand new multiplicity for this dihedral.
+          //mprintf("DEBUG: Dihedral new mult: %s %s %s %s pk=%12.4f pn=%12.4f pp=%12.4f\n",
+          //        *types[0], *types[1], *types[2], *types[3], dp.Pk(), dp.Pn(), dp.Phase());
+          if (it0->second.empty())
+            it0->second.push_back( dp );
+          else if (dp.Pn() > it0->second.back().Pn())
+            it0->second.push_back( dp );
+          else {
+            // Try to keep multiplicities in order.
+            DihedralParmArray sorted;
+            bool isInserted = false;
+            for (DihedralParmArray::const_iterator jt = it0->second.begin(); jt != it0->second.end(); ++jt) {
+              if (!isInserted) {
+                if (dp.Pn() < jt->Pn()) {
+                  sorted.push_back( dp );
+                  isInserted = true;
+                }
+              }
+              sorted.push_back( *jt );
+            }
+            it0->second = sorted;
+          }
+        } else {
+          // Multiplicity already exists for this dihedral.
+          if (dp < *it1 || *it1 < dp) {
+            //mprintf("DEBUG: Attempt dihedral update mult (allow=%i): %s %s %s %s pk=%6.2f pn=%3.1f pp=%6.3f (orig pk=%6.2f pn=%3.1f pp=%6.3f )\n",
+            //        (int)allowUpdate, *types[0], *types[1], *types[2], *types[3], dp.Pk(), dp.Pn(), dp.Phase(), it1->Pk(), it1->Pn(), it1->Phase());
+            if (allowUpdate) {
+              previousParm_ = *it1;
+              *it1 = dp;
+              return UPDATED;
+            } else {
+              return ERR;
+            }
+          } else
+            return SAME;
+        }
+      }
+      return ADDED;
+    }
+  private:
+    Dmap dihparm_;
+    DihedralParmType previousParm_; ///< When parameter is updated, store previous value.
+};
+}
+}
+#endif

From 1ea8a8929dbebed9089ae64a1a8a62cfa335a4d5 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 24 Feb 2026 14:30:23 -0500
Subject: [PATCH 1377/1492] Add PreviousParm

---
 src/Parm/DihedralParmSet.h | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/Parm/DihedralParmSet.h b/src/Parm/DihedralParmSet.h
index 8a14a898e6..f9e2f0ec0c 100644
--- a/src/Parm/DihedralParmSet.h
+++ b/src/Parm/DihedralParmSet.h
@@ -18,6 +18,8 @@ class DihedralParmSet {
     typedef std::map<TypeNameHolder, DihedralParmArray> Dmap;
   public:
     DihedralParmSet() {}
+    /// \return Last parameter to be overwritten from AddParm()
+    DihedralParmType const& PreviousParm() const { return previousParm_; }
     /// Add (or update) a single dihedral parameter for given atom types.
     RetType AddDihParm(TypeNameHolder const& types, DihedralParmType const& dp, bool allowUpdate) {
       // Check if dihedral parm for these types exist

From 1c9bec57be67c90906bd0ab721a203f2144cd6ef Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 24 Feb 2026 14:56:50 -0500
Subject: [PATCH 1378/1492] Put the dihedrals from Dihedral parm set into the
 main parameter set

---
 src/AmberParamFile.cpp     | 31 +++++++++++++++++++++++++------
 src/AmberParamFile.h       |  5 ++++-
 src/Parm/DihedralParmSet.h | 10 +++++++++-
 src/TypeNameHolder.h       | 11 +++++++----
 src/cpptrajdepend          |  2 +-
 5 files changed, 46 insertions(+), 13 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 1067645871..04f1885dc7 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -3,6 +3,7 @@
 #include "CpptrajStdio.h"
 #include "BufferedLine.h"
 #include "StringRoutines.h"
+#include "Parm/DihedralParmSet.h"
 #include "Parm/ParameterSet.h"
 #include "Parm/ParmHolder.h"
 #include "Constants.h"
@@ -246,7 +247,7 @@ const
   * of pn is used only for identifying the existence of the next term and 
   * only the absolute value of PN is kept.
   */
-int AmberParamFile::read_dihedral(ParameterSet& prm, const char* ptr,
+int AmberParamFile::read_dihedral(DihedralParmSet& prm, const char* ptr,
                                   std::vector<std::string>& last_symbols,
                                   bool first_char_is_space)
 const
@@ -299,13 +300,13 @@ const
   types.AddName( symbols[2] );
   types.AddName( symbols[3] );
   Cpptraj::Parm::RetType ret =
-    prm.DP().AddParm(types, DihedralParmType(PK / (double)IDIVF, PN, PHASE*Constants::DEGRAD, scee, scnb), true);
+    prm.AddDihParm(types, DihedralParmType(PK / (double)IDIVF, PN, PHASE*Constants::DEGRAD, scee, scnb), true);
   if (ret == Cpptraj::Parm::SAME)
     mprintf("Warning: Duplicated %s\n", typeNameStr(types, "dihedral").c_str());
   else if (ret == Cpptraj::Parm::UPDATED) // TODO SCEE/SCNB?
     mprintf("Warning: Redefining %s (PN=%g) from PK= %g Phase= %g to PK= %g Phase= %g\n",
              typeNameStr(types, "dihedral").c_str(), PN,
-             prm.DP().PreviousParm().Pk(), prm.DP().PreviousParm().Phase()*Constants::RADDEG, PK/(double)IDIVF, PHASE);
+             prm.PreviousParm().Pk(), prm.PreviousParm().Phase()*Constants::RADDEG, PK/(double)IDIVF, PHASE);
   else if (ret == Cpptraj::Parm::ERR) {
     mprinterr("Error: Reading %s\n", typeNameStr(types, "dihedral").c_str());
     return 1;
@@ -319,6 +320,17 @@ const
   return 0;
 }
 
+/** Put read-in dihedral parameters into the given ParameterSet.
+  * Warn about missing multiplicities.
+  */
+int AmberParamFile::dihparm_to_parmset(ParameterSet& prm, DihedralParmSet const& dihPrm)
+const
+{
+  for (DihedralParmSet::const_iterator it = dihPrm.begin(); it != dihPrm.end(); ++it)
+    prm.DP().AddParm( it->first, it->second, true );
+  return 0;
+}
+
 /** Read input for improper. */
 int AmberParamFile::read_improper(ParameterSet& prm, const char* ptr)
 const
@@ -783,7 +795,7 @@ int AmberParamFile::assign_offdiag(ParameterSet& prm, Oarray const& Offdiag) con
   return 0;
 }
 
-/** Read parametrers from Amber frcmod file. */
+/** Read parameters from Amber frcmod file. */
 int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname) const
 {
   int cmap_count_is_index = -1;
@@ -809,6 +821,7 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname) const
   prm.SetParamSetFile( fname );
   NonbondSet nbset(title);
   Oarray Offdiag;
+  DihedralParmSet dihPrm;
   // Read file
   SectionType section = UNKNOWN;
   CmapType currentCmapFlag = CMAP_INITIAL;
@@ -846,7 +859,7 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname) const
         else if (section == ANGLE)
           err = read_angle(prm, ptr);
         else if (section == DIHEDRAL)
-          err = read_dihedral(prm, ptr, last_symbols, first_char_is_space);
+          err = read_dihedral(dihPrm, ptr, last_symbols, first_char_is_space);
         else if (section == IMPROPER)
           err = read_improper(prm, ptr);
         else if (section == LJ1012)
@@ -873,6 +886,8 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname) const
     if (check_cmap(prm.CMAP().size(), currentCmap)) return 1;
     prm.CMAP().AddParm( currentCmap, true, debug_ );
   }
+  // Add dihedrals
+  if (dihparm_to_parmset(prm, dihPrm)) return 1;
   // Nonbonds
   if (assign_nb(prm, nbset)) return 1;
   // Off-diagonal NB modifications
@@ -918,6 +933,7 @@ int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
   prm.SetParamSetFile( fname );
   std::vector<std::string> last_symbols;
   last_symbols.reserve(4);
+  DihedralParmSet dihPrm;
   // Read file
   int readNbType = 0;
   SectionType section = ATYPE;
@@ -1006,7 +1022,7 @@ int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
     } else if (section == ANGLE) {
       read_err = read_angle(prm, ptr);
     } else if (section == DIHEDRAL) {
-      read_err = read_dihedral(prm, ptr, last_symbols, first_char_is_space);
+      read_err = read_dihedral(dihPrm, ptr, last_symbols, first_char_is_space);
     } else if (section == IMPROPER) {
       read_err = read_improper(prm, ptr);
     } else if (section == LJ1012) {
@@ -1042,6 +1058,9 @@ int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
     ptr = infile.Line();
   } // END loop over file.
 
+  // Add dihedrals
+  if (dihparm_to_parmset(prm, dihPrm)) return 1;
+
   // Deal with nonbond and equivalence
   if (!NBsets.empty()) {
     int nbsetidx = 0;
diff --git a/src/AmberParamFile.h b/src/AmberParamFile.h
index 1dc750cd2f..081f1e02f2 100644
--- a/src/AmberParamFile.h
+++ b/src/AmberParamFile.h
@@ -7,12 +7,14 @@ class CmapGridType;
 class FileName;
 namespace Cpptraj {
 namespace Parm {
+class DihedralParmSet;
 class ParameterSet;
 }
 }
 /// Used to read in Amber parameters from Amber FF/FRCMOD file.
 class AmberParamFile {
     typedef Cpptraj::Parm::ParameterSet ParameterSet;
+    typedef Cpptraj::Parm::DihedralParmSet DihedralParmSet;
   public:
     AmberParamFile();
     /// Read main Amber FF file
@@ -43,7 +45,8 @@ class AmberParamFile {
     /// Read angle line
     int read_angle(ParameterSet&, const char*) const;
     /// Read dihedral line
-    int read_dihedral(ParameterSet&, const char*, std::vector<std::string>&, bool) const;
+    int read_dihedral(DihedralParmSet&, const char*, std::vector<std::string>&, bool) const;
+    int dihparm_to_parmset(ParameterSet&, DihedralParmSet const&) const;
     /// Read improper line
     int read_improper(ParameterSet&, const char*) const;
     /// Read LJ 10-12 hbond line
diff --git a/src/Parm/DihedralParmSet.h b/src/Parm/DihedralParmSet.h
index f9e2f0ec0c..e983653483 100644
--- a/src/Parm/DihedralParmSet.h
+++ b/src/Parm/DihedralParmSet.h
@@ -20,8 +20,16 @@ class DihedralParmSet {
     DihedralParmSet() {}
     /// \return Last parameter to be overwritten from AddParm()
     DihedralParmType const& PreviousParm() const { return previousParm_; }
+
+    typedef Dmap::const_iterator const_iterator;
+    const_iterator begin() const { return dihparm_.begin(); }
+    const_iterator end()   const { return dihparm_.end(); }
+
     /// Add (or update) a single dihedral parameter for given atom types.
-    RetType AddDihParm(TypeNameHolder const& types, DihedralParmType const& dp, bool allowUpdate) {
+    RetType AddDihParm(TypeNameHolder const& typesIn, DihedralParmType const& dp, bool allowUpdate) {
+      // Ensure types are sorted
+      TypeNameHolder types = typesIn;
+      types.SortNames();
       // Check if dihedral parm for these types exist
       Dmap::iterator it0 = dihparm_.lower_bound( types );
       if (it0 == dihparm_.end() || it0->first != types) {
diff --git a/src/TypeNameHolder.h b/src/TypeNameHolder.h
index 410f55ccfc..52c0ed14eb 100644
--- a/src/TypeNameHolder.h
+++ b/src/TypeNameHolder.h
@@ -16,11 +16,11 @@ class TypeNameHolder {
     typedef Narray::const_iterator const_iterator;
     TypeNameHolder() {}
     /// CONSTRUCTOR - Take single atom type name
-    TypeNameHolder(NameType const& nameIn) : types_(1, nameIn) {}
+    TypeNameHolder(NameType const& nameIn) : types_(1, nameIn), is_swapped_(false) {}
     /// CONSTRUCTOR - Take array of atom type names
-    TypeNameHolder(Narray const& namesIn) : types_(namesIn) {}
+    TypeNameHolder(Narray const& namesIn) : types_(namesIn), is_swapped_(false) {}
     /// CONSTRUCTOR - Reserve space for given number of type names
-    TypeNameHolder(int size) { types_.clear(); types_.reserve(size); }
+    TypeNameHolder(int size) : is_swapped_(false) { types_.clear(); types_.reserve(size); }
 /*    /// CONSTRUCTOR - Set wildcard name and reserve space for given number of type names.
     TypeNameHolder(int size, NameType const& wc) : wildcard_(wc) { types_.clear(); types_.reserve(size); }*/
     /// Add atom type name.
@@ -132,6 +132,7 @@ class TypeNameHolder {
       }
       if (types_[0] > types_[last]) {
         // Need to swap TODO record if we swapped these names?
+        is_swapped_ = true;
         if (types_.size() < 4)
           tswap(types_[0], types_[last]);
         else {
@@ -140,7 +141,8 @@ class TypeNameHolder {
           for (unsigned int ii = 0; ii < half; ii++, jj--)
             tswap(types_[ii], types_[jj]);
         }
-      }
+      } else
+        is_swapped_ = false;
       // Restore wildcards
       if (wc.len() > 0) {
         if (types_[0]    == " ") types_[0]    = wc;
@@ -188,5 +190,6 @@ class TypeNameHolder {
   private:
     Narray types_;
     //NameType wildcard_;
+    bool is_swapped_;
 };
 #endif
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 686c765a3d..cf9b10c96a 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -96,7 +96,7 @@ Action_Volmap.o : Action_Volmap.cpp Action.h ActionState.h Action_Volmap.h ArgLi
 Action_Volume.o : Action_Volume.cpp Action.h ActionState.h Action_Volume.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 Action_Watershell.o : Action_Watershell.cpp Action.h ActionState.h Action_Watershell.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h ImageRoutines.h ImageTypes.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h cuda_kernels/kernel_wrappers.cuh
 Action_XtalSymm.o : Action_XtalSymm.cpp Action.h ActionState.h Action_XtalSymm.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SpaceGroup.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-AmberParamFile.o : AmberParamFile.cpp AmberParamFile.h ArgList.h AtomType.h BufferedLine.h CmapParmHolder.h Constants.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h StringRoutines.h TypeNameHolder.h
+AmberParamFile.o : AmberParamFile.cpp AmberParamFile.h ArgList.h AtomType.h BufferedLine.h CmapParmHolder.h Constants.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/DihedralParmSet.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h StringRoutines.h TypeNameHolder.h
 AnalysisList.o : AnalysisList.cpp ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 Analysis_AmdBias.o : Analysis_AmdBias.cpp ActionState.h Analysis.h AnalysisState.h Analysis_AmdBias.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 Analysis_AutoCorr.o : Analysis_AutoCorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_AutoCorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h

From b32369809fe237576f6deffc75b2bb2d60266bb7 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 24 Feb 2026 15:05:14 -0500
Subject: [PATCH 1379/1492] Convert back to a vector to preserve parameter
 ordering for now

---
 src/Parm/DihedralParmSet.h | 31 ++++++++++++++++++++++---------
 1 file changed, 22 insertions(+), 9 deletions(-)

diff --git a/src/Parm/DihedralParmSet.h b/src/Parm/DihedralParmSet.h
index e983653483..3162da7fbe 100644
--- a/src/Parm/DihedralParmSet.h
+++ b/src/Parm/DihedralParmSet.h
@@ -1,6 +1,6 @@
 #ifndef INC_PARM_DIHEDRALPARMSET_H
 #define INC_PARM_DIHEDRALPARMSET_H
-#include <map>
+//#include <map>
 #include "ParmEnum.h"
 #include "../ParameterTypes.h"
 #include "../TypeNameHolder.h"
@@ -15,7 +15,8 @@ namespace Parm {
   */
 class DihedralParmSet {
     typedef std::pair<TypeNameHolder, DihedralParmArray> Dpair;
-    typedef std::map<TypeNameHolder, DihedralParmArray> Dmap;
+    //typedef std::map<TypeNameHolder, DihedralParmArray> Dmap;
+    typedef std::vector<Dpair> Dmap;
   public:
     DihedralParmSet() {}
     /// \return Last parameter to be overwritten from AddParm()
@@ -26,15 +27,27 @@ class DihedralParmSet {
     const_iterator end()   const { return dihparm_.end(); }
 
     /// Add (or update) a single dihedral parameter for given atom types.
-    RetType AddDihParm(TypeNameHolder const& typesIn, DihedralParmType const& dp, bool allowUpdate) {
+    RetType AddDihParm(TypeNameHolder const& types, DihedralParmType const& dp, bool allowUpdate) {
       // Ensure types are sorted
-      TypeNameHolder types = typesIn;
-      types.SortNames();
+      //TypeNameHolder types = typesIn;
+      //types.SortNames();
       // Check if dihedral parm for these types exist
-      Dmap::iterator it0 = dihparm_.lower_bound( types );
-      if (it0 == dihparm_.end() || it0->first != types) {
-        // Brand new dihedral for these types
-        it0 = dihparm_.insert(it0, Dpair(types, DihedralParmArray(1, dp)));
+      //Dmap::iterator it0 = dihparm_.lower_bound( types );
+      //if (it0 == dihparm_.end() || it0->first != types) {
+      //  // Brand new dihedral for these types
+      //  it0 = dihparm_.insert(it0, Dpair(types, DihedralParmArray(1, dp)));
+      // Check if parm for these types exist
+      Dmap::iterator it0 = dihparm_.begin();
+      for (; it0 != dihparm_.end(); ++it0)
+      {
+        if (it0->first.Match_NoWC( types ))
+          break;
+      }
+      if (it0 == dihparm_.end()) {
+        // Brand new dihedral for these types.
+        //mprintf("DEBUG: New dihedral parm: %s %s %s %s pk=%12.4f pn=%12.4f pp=%12.4f\n",
+        //        *types[0], *types[1], *types[2], *types[3], dp.Pk(), dp.Pn(), dp.Phase());
+        dihparm_.push_back( Dpair(types, DihedralParmArray(1, dp)) );
       } else {
         // If we are here types match - check multiplicity
         DihedralParmArray::iterator it1 = it0->second.begin();

From edae9e346d34988f45069f94ceae56fd8a6d0210 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 24 Feb 2026 15:44:10 -0500
Subject: [PATCH 1380/1492] Add back the warnings; are there too many now?

---
 src/AmberParamFile.cpp        | 33 ++++++++++++++++++++++++++++++++-
 src/Parm/DihedralParmHolder.h |  5 ++++-
 2 files changed, 36 insertions(+), 2 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 04f1885dc7..c4aea75828 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -320,6 +320,12 @@ const
   return 0;
 }
 
+static inline void printdih(DihedralParmArray const& dpa)
+{
+  for (DihedralParmArray::const_iterator it = dpa.begin(); it != dpa.end(); ++it)
+    mprintf("Warning:\t\t%3g PK= %g Phase= %g\n", it->Pn(), it->Pk(), it->Phase()*Constants::RADDEG);
+}
+
 /** Put read-in dihedral parameters into the given ParameterSet.
   * Warn about missing multiplicities.
   */
@@ -327,7 +333,32 @@ int AmberParamFile::dihparm_to_parmset(ParameterSet& prm, DihedralParmSet const&
 const
 {
   for (DihedralParmSet::const_iterator it = dihPrm.begin(); it != dihPrm.end(); ++it)
-    prm.DP().AddParm( it->first, it->second, true );
+  {
+    // Check multiplicites; warn if one seems missing
+    if (it->second.size() > 1) {
+      DihedralParmArray::const_iterator dp = it->second.begin();
+      unsigned int next_expected_mult = (unsigned int)dp->Pn() + 1;
+      dp++;
+      for (; dp != it->second.end(); dp++) {
+        if ((unsigned int)dp->Pn() != next_expected_mult)
+          mprintf("Warning: %s does not have dihedral term for multiplicity %u\n",
+                  typeNameStr(it->first, "dihedral").c_str(), next_expected_mult);
+        next_expected_mult = (unsigned int)dp->Pn() + 1;
+      }
+    }
+    Cpptraj::Parm::RetType ret = prm.DP().AddParm( it->first, it->second, true );
+    if (ret == Cpptraj::Parm::SAME)
+      mprintf("Warning: Duplicated %s\n", typeNameStr(it->first, "dihedral").c_str());
+    else if (ret == Cpptraj::Parm::UPDATED) {// TODO SCEE/SCNB?
+      mprintf("Warning: Redefining %s from\n", typeNameStr(it->first, "dihedral").c_str());
+      printdih(prm.DP().PreviousArray());
+      mprintf("Warning: to\n");
+      printdih(it->second);
+    } else if (ret == Cpptraj::Parm::ERR) {
+      mprinterr("Error: Reading %s\n", typeNameStr(it->first, "dihedral").c_str());
+      return 1;
+    }
+  }
   return 0;
 }
 
diff --git a/src/Parm/DihedralParmHolder.h b/src/Parm/DihedralParmHolder.h
index e297f10963..13c4e23739 100644
--- a/src/Parm/DihedralParmHolder.h
+++ b/src/Parm/DihedralParmHolder.h
@@ -31,6 +31,7 @@ class DihedralParmHolder {
     bool empty()        const { return bpmap_.empty(); }
     /// \return Last parameter to be overwritten from AddParm()
     DihedralParmType const& PreviousParm() const { return previousParm_; }
+    DihedralParmArray const& PreviousArray() const { return previousArray_; }
     /// Set wildcard character
     void SetWildcard(char wc) { wc_ = NameType(std::string(1, wc)); }
     /// Add (or update) a single dihedral parameter for given atom types.
@@ -123,6 +124,7 @@ class DihedralParmHolder {
           }
         }
         if (update) {
+          previousArray_ = it0->second;
           it0->second = dpa;
           return UPDATED;
         } else
@@ -171,7 +173,8 @@ class DihedralParmHolder {
     NameType wc_; ///< Wildcard character
   private:
     Bmap bpmap_;
-    DihedralParmType previousParm_; ///< When parameter is updated, store previous value.
+    DihedralParmType previousParm_; ///< When parameter is updated, store previous value. TODO remove?
+    DihedralParmArray previousArray_; ///< When array is updated, store previous value
 };
 } // END namespace Parm
 } // END namespace Cpptraj

From 4bbd3f30236f5d8dcb3802fd469744087db2b26c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 26 Feb 2026 08:12:21 -0500
Subject: [PATCH 1381/1492] Put the function to transfer dihedral params from
 the set to the holder in the set

---
 src/Parm/DihedralParmSet.cpp | 45 ++++++++++++++++++++++++++++++++++++
 src/Parm/DihedralParmSet.h   |  4 ++++
 src/Parm/parmdepend          |  2 ++
 src/Parm/parmfiles           |  4 +++-
 src/cpptrajdepend            |  2 ++
 5 files changed, 56 insertions(+), 1 deletion(-)
 create mode 100644 src/Parm/DihedralParmSet.cpp

diff --git a/src/Parm/DihedralParmSet.cpp b/src/Parm/DihedralParmSet.cpp
new file mode 100644
index 0000000000..5c964407c9
--- /dev/null
+++ b/src/Parm/DihedralParmSet.cpp
@@ -0,0 +1,45 @@
+#include "DihedralParmSet.h"
+#include "ParameterSet.h"
+#include "../CpptrajStdio.h"
+
+using namespace Cpptraj::Parm;
+
+/// Print all dihedral multiplicities to stdout
+static inline void printdih(DihedralParmArray const& dpa)
+{
+  for (DihedralParmArray::const_iterator it = dpa.begin(); it != dpa.end(); ++it)
+    mprintf("Warning:\t\t%3g PK= %g Phase= %g\n", it->Pn(), it->Pk(), it->Phase()*Constants::RADDEG);
+}
+
+/** Add all dihedral parameters into the given parameter set. */
+int DihedralParmSet::ToDihParm(ParameterSet& prm) const
+{
+  for (DihedralParmSet::const_iterator it = begin(); it != end(); ++it)
+  {
+    // Check multiplicites; warn if one seems missing
+    if (it->second.size() > 1) {
+      DihedralParmArray::const_iterator dp = it->second.begin();
+      unsigned int next_expected_mult = (unsigned int)dp->Pn() + 1;
+      dp++;
+      for (; dp != it->second.end(); dp++) {
+        if ((unsigned int)dp->Pn() != next_expected_mult)
+          mprintf("Warning: %s does not have dihedral term for multiplicity %u\n",
+                  it->first.TypeNameStr("dihedral").c_str(), next_expected_mult);
+        next_expected_mult = (unsigned int)dp->Pn() + 1;
+      }
+    }
+    Cpptraj::Parm::RetType ret = prm.DP().AddParm( it->first, it->second, true );
+    if (ret == Cpptraj::Parm::SAME)
+      mprintf("Warning: Duplicated %s\n", it->first.TypeNameStr("dihedral").c_str());
+    else if (ret == Cpptraj::Parm::UPDATED) {// TODO SCEE/SCNB?
+      mprintf("Warning: Redefining %s from\n", it->first.TypeNameStr("dihedral").c_str());
+      printdih(prm.DP().PreviousArray());
+      mprintf("Warning: to\n");
+      printdih(it->second);
+    } else if (ret == Cpptraj::Parm::ERR) {
+      mprinterr("Error: Reading %s\n", it->first.TypeNameStr("dihedral").c_str());
+      return 1;
+    }
+  }
+  return 0;
+}
diff --git a/src/Parm/DihedralParmSet.h b/src/Parm/DihedralParmSet.h
index 3162da7fbe..143bf06630 100644
--- a/src/Parm/DihedralParmSet.h
+++ b/src/Parm/DihedralParmSet.h
@@ -6,6 +6,7 @@
 #include "../TypeNameHolder.h"
 namespace Cpptraj {
 namespace Parm {
+class ParameterSet;
 /// Used for reading in dihedral parameters.
 /** When dihedral parameters are read in one at a time it is not
   * guaranteed that parameters for all multiplcities will be
@@ -26,6 +27,9 @@ class DihedralParmSet {
     const_iterator begin() const { return dihparm_.begin(); }
     const_iterator end()   const { return dihparm_.end(); }
 
+    /// Put all dihedral parameters into given dihedral parameter holder.
+    int ToDihParm(ParameterSet&) const;
+
     /// Add (or update) a single dihedral parameter for given atom types.
     RetType AddDihParm(TypeNameHolder const& types, DihedralParmType const& dp, bool allowUpdate) {
       // Ensure types are sorted
diff --git a/src/Parm/parmdepend b/src/Parm/parmdepend
index 6d84d885d9..df3a1af846 100644
--- a/src/Parm/parmdepend
+++ b/src/Parm/parmdepend
@@ -1,8 +1,10 @@
 AssignParams.o : AssignParams.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/ParmEnum.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/GenerateConnectivityArrays.h ../SymbolExporting.h ../Timer.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h AssignParams.h DihedralParmHolder.h GetParams.h ImproperParmHolder.h ParameterSet.h ParmArray.h ParmEnum.h ParmHolder.h
 Bond_Params.o : Bond_Params.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h Bond_Params.h
+DihedralParmSet.o : DihedralParmSet.cpp ../AtomType.h ../CmapParmHolder.h ../Constants.h ../CpptrajStdio.h ../FileName.h ../NameType.h ../ParameterTypes.h ../Parm/ParmEnum.h ../TypeNameHolder.h DihedralParmHolder.h DihedralParmSet.h ImproperParmHolder.h ParameterSet.h ParmEnum.h ParmHolder.h
 GB_Params.o : GB_Params.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h GB_Params.h
 GetParams.o : GetParams.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/ParmEnum.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h DihedralParmHolder.h GetParams.h ImproperParmHolder.h ParameterSet.h ParmEnum.h ParmHolder.h
 LJ1264_Params.o : LJ1264_Params.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../BufferedLine.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../StringRoutines.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h LJ1264_Params.h ParmEnum.h
 Merge.o : Merge.cpp ../Atom.h ../Constants.h ../CpptrajStdio.h ../NameType.h ../ParameterTypes.h ../Residue.h ../StringRoutines.h ../SymbolExporting.h ../TypeNameHolder.h Merge.h ParmEnum.h ParmHolder.h
 ParameterSet.o : ParameterSet.cpp ../AtomType.h ../CmapParmHolder.h ../Constants.h ../CpptrajFile.h ../CpptrajStdio.h ../FileIO.h ../FileName.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/ParmEnum.h ../TypeNameHolder.h ../UpdateParameters.h DihedralParmHolder.h ImproperParmHolder.h ParameterSet.h ParmEnum.h ParmHolder.h
 ParmEnum.o : ParmEnum.cpp ParmEnum.h
+test.o : test.cpp ../Constants.h ../NameType.h ../ParameterTypes.h ../TypeNameHolder.h DihedralParmSet.h ParmEnum.h
diff --git a/src/Parm/parmfiles b/src/Parm/parmfiles
index 4a8b0492c7..71f9a08add 100644
--- a/src/Parm/parmfiles
+++ b/src/Parm/parmfiles
@@ -2,9 +2,11 @@
 PARM_SOURCES= \
   AssignParams.cpp \
   Bond_Params.cpp \
+  DihedralParmSet.cpp \
   GB_Params.cpp \
   GetParams.cpp \
   LJ1264_Params.cpp \
   Merge.cpp \
   ParameterSet.cpp \
-  ParmEnum.cpp
+  ParmEnum.cpp \
+  test.cpp
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index cf9b10c96a..4e6a3c84a9 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -435,12 +435,14 @@ ParallelNetcdf.o : ParallelNetcdf.cpp CpptrajStdio.h Parallel.h ParallelNetcdf.h
 ParallelSetFrameNum.o : ParallelSetFrameNum.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h ParallelSetFrameNum.h Range.h TextFormat.h
 Parm/AssignParams.o : Parm/AssignParams.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h GuessAtomHybridization.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/../Structure/GenerateConnectivityArrays.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GetParams.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmArray.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Parm/Bond_Params.o : Parm/Bond_Params.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/Bond_Params.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
+Parm/DihedralParmSet.o : Parm/DihedralParmSet.cpp AtomType.h CmapParmHolder.h Constants.h CpptrajStdio.h FileName.h NameType.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/DihedralParmSet.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h TypeNameHolder.h
 Parm/GB_Params.o : Parm/GB_Params.cpp ArgList.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/GB_Params.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Parm/GetParams.o : Parm/GetParams.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/GetParams.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Parm/LJ1264_Params.o : Parm/LJ1264_Params.cpp ArgList.h Atom.h AtomMask.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/LJ1264_Params.h Parm/ParmEnum.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Parm/Merge.o : Parm/Merge.cpp Atom.h Constants.h CpptrajStdio.h NameType.h ParameterTypes.h Parm/Merge.h Parm/ParmEnum.h Parm/ParmHolder.h Residue.h StringRoutines.h SymbolExporting.h TypeNameHolder.h
 Parm/ParameterSet.o : Parm/ParameterSet.cpp AtomType.h CmapParmHolder.h Constants.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h TypeNameHolder.h UpdateParameters.h
 Parm/ParmEnum.o : Parm/ParmEnum.cpp Parm/ParmEnum.h
+Parm/test.o : Parm/test.cpp Constants.h NameType.h ParameterTypes.h Parm/DihedralParmSet.h Parm/ParmEnum.h TypeNameHolder.h
 ParmFile.o : ParmFile.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h ParmFile.h ParmIO.h Parm_Amber.h Parm_CIF.h Parm_CharmmPsf.h Parm_Gromacs.h Parm_Mol2.h Parm_PDB.h Parm_SDF.h Parm_Tinker.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Parm_Amber.o : Parm_Amber.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h ExclusionArray.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/GetParams.h ParmIO.h Parm_Amber.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h Unit.h Vec3.h
 Parm_CIF.o : Parm_CIF.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h CIFfile.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmIO.h Parm_CIF.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h

From 0116a033d902724ee2a3409b4751d4007f03d3e4 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 26 Feb 2026 08:12:52 -0500
Subject: [PATCH 1382/1492] Put the type name string function that was in
 AmberParamFile in TypeNameHolder

---
 src/TypeNameHolder.h | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/src/TypeNameHolder.h b/src/TypeNameHolder.h
index 52c0ed14eb..fd360414e4 100644
--- a/src/TypeNameHolder.h
+++ b/src/TypeNameHolder.h
@@ -121,6 +121,18 @@ class TypeNameHolder {
         tstr.append( " " + std::string( *(*it) ) );
       return tstr;
     }
+    /// \return string containing a description and atom type names
+    std::string TypeNameStr(std::string const& desc) const {
+      std::string OUT(desc);
+      switch (Size()) {
+        case 1 : OUT.append(" type " + types_[0].Truncated()); break;
+        case 2 : OUT.append(" type " + types_[0].Truncated() + " - " + types_[1].Truncated()); break;
+        case 3 : OUT.append(" type " + types_[0].Truncated() + " - " + types_[1].Truncated() + " - " + types_[2].Truncated()); break;
+        case 4 : OUT.append(" type " + types_[0].Truncated() + " - " + types_[1].Truncated() + " - " + types_[2].Truncated() + " - " + types_[3].Truncated());
+        default: OUT.append(" type " + TypeString());
+      }
+      return OUT;
+    }
     /// Sort typenames so that the first typename < the last
     void SortNames(NameType const& wc) {
       if (types_.size() < 2) return;

From e27260b54d8d1ae112a753746499e2c5f6e087f6 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 26 Feb 2026 08:13:15 -0500
Subject: [PATCH 1383/1492] Update CMakeLists

---
 src/Parm/CMakeLists.txt | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/Parm/CMakeLists.txt b/src/Parm/CMakeLists.txt
index c8e8a81c32..b7885ef92c 100644
--- a/src/Parm/CMakeLists.txt
+++ b/src/Parm/CMakeLists.txt
@@ -2,10 +2,12 @@
 target_sources(cpptraj_common_obj PRIVATE
   ${CMAKE_CURRENT_LIST_DIR}/AssignParams.cpp
   ${CMAKE_CURRENT_LIST_DIR}/Bond_Params.cpp
+  ${CMAKE_CURRENT_LIST_DIR}/DihedralParmSet.cpp
   ${CMAKE_CURRENT_LIST_DIR}/GB_Params.cpp
   ${CMAKE_CURRENT_LIST_DIR}/GetParams.cpp
   ${CMAKE_CURRENT_LIST_DIR}/LJ1264_Params.cpp
   ${CMAKE_CURRENT_LIST_DIR}/Merge.cpp
   ${CMAKE_CURRENT_LIST_DIR}/ParameterSet.cpp
   ${CMAKE_CURRENT_LIST_DIR}/ParmEnum.cpp
+  ${CMAKE_CURRENT_LIST_DIR}/test.cpp
 )

From a45a18397ec75fe8fb15b22208aa8c8fb1a97a14 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 26 Feb 2026 08:25:26 -0500
Subject: [PATCH 1384/1492] Add function for putting parameters in dihedral set
 into improper holder

---
 src/Parm/DihedralParmSet.cpp | 43 +++++++++++++++++++++++++++++++-----
 src/Parm/DihedralParmSet.h   |  9 +++++---
 2 files changed, 44 insertions(+), 8 deletions(-)

diff --git a/src/Parm/DihedralParmSet.cpp b/src/Parm/DihedralParmSet.cpp
index 5c964407c9..c5bf212d3c 100644
--- a/src/Parm/DihedralParmSet.cpp
+++ b/src/Parm/DihedralParmSet.cpp
@@ -4,15 +4,15 @@
 
 using namespace Cpptraj::Parm;
 
-/// Print all dihedral multiplicities to stdout
+/// Print all multiplicities to stdout
 static inline void printdih(DihedralParmArray const& dpa)
 {
   for (DihedralParmArray::const_iterator it = dpa.begin(); it != dpa.end(); ++it)
     mprintf("Warning:\t\t%3g PK= %g Phase= %g\n", it->Pn(), it->Pk(), it->Phase()*Constants::RADDEG);
 }
 
-/** Add all dihedral parameters into the given parameter set. */
-int DihedralParmSet::ToDihParm(ParameterSet& prm) const
+/** Add all dihedral parameters into the given dihedral parameter holder. */
+int DihedralParmSet::ToDihParm(DihedralParmHolder& DP) const
 {
   for (DihedralParmSet::const_iterator it = begin(); it != end(); ++it)
   {
@@ -28,12 +28,12 @@ int DihedralParmSet::ToDihParm(ParameterSet& prm) const
         next_expected_mult = (unsigned int)dp->Pn() + 1;
       }
     }
-    Cpptraj::Parm::RetType ret = prm.DP().AddParm( it->first, it->second, true );
+    Cpptraj::Parm::RetType ret = DP.AddParm( it->first, it->second, true );
     if (ret == Cpptraj::Parm::SAME)
       mprintf("Warning: Duplicated %s\n", it->first.TypeNameStr("dihedral").c_str());
     else if (ret == Cpptraj::Parm::UPDATED) {// TODO SCEE/SCNB?
       mprintf("Warning: Redefining %s from\n", it->first.TypeNameStr("dihedral").c_str());
-      printdih(prm.DP().PreviousArray());
+      printdih(DP.PreviousArray());
       mprintf("Warning: to\n");
       printdih(it->second);
     } else if (ret == Cpptraj::Parm::ERR) {
@@ -43,3 +43,36 @@ int DihedralParmSet::ToDihParm(ParameterSet& prm) const
   }
   return 0;
 }
+
+/** Add all improper parameters into the given improper parameter holder. */
+int DihedralParmSet::ToImpParm(ImproperParmHolder& IP) const
+{
+  for (DihedralParmSet::const_iterator it = begin(); it != end(); ++it)
+  {
+    // Check multiplicites; warn if one seems missing
+    if (it->second.size() > 1) {
+      DihedralParmArray::const_iterator dp = it->second.begin();
+      unsigned int next_expected_mult = (unsigned int)dp->Pn() + 1;
+      dp++;
+      for (; dp != it->second.end(); dp++) {
+        if ((unsigned int)dp->Pn() != next_expected_mult)
+          mprintf("Warning: %s does not have improper term for multiplicity %u\n",
+                  it->first.TypeNameStr("improper").c_str(), next_expected_mult);
+        next_expected_mult = (unsigned int)dp->Pn() + 1;
+      }
+    }
+    Cpptraj::Parm::RetType ret = IP.AddParm( it->first, it->second, true );
+    if (ret == Cpptraj::Parm::SAME)
+      mprintf("Warning: Duplicated %s\n", it->first.TypeNameStr("improper").c_str());
+    else if (ret == Cpptraj::Parm::UPDATED) {
+      mprintf("Warning: Redefining %s from\n", it->first.TypeNameStr("improper").c_str());
+      printdih(IP.PreviousArray());
+      mprintf("Warning: to\n");
+      printdih(it->second);
+    } else if (ret == Cpptraj::Parm::ERR) {
+      mprinterr("Error: Reading %s\n", it->first.TypeNameStr("improper").c_str());
+      return 1;
+    }
+  }
+  return 0;
+}
diff --git a/src/Parm/DihedralParmSet.h b/src/Parm/DihedralParmSet.h
index 143bf06630..4461be04ea 100644
--- a/src/Parm/DihedralParmSet.h
+++ b/src/Parm/DihedralParmSet.h
@@ -6,7 +6,8 @@
 #include "../TypeNameHolder.h"
 namespace Cpptraj {
 namespace Parm {
-class ParameterSet;
+class DihedralParmHolder;
+class ImproperParmHolder;
 /// Used for reading in dihedral parameters.
 /** When dihedral parameters are read in one at a time it is not
   * guaranteed that parameters for all multiplcities will be
@@ -28,9 +29,11 @@ class DihedralParmSet {
     const_iterator end()   const { return dihparm_.end(); }
 
     /// Put all dihedral parameters into given dihedral parameter holder.
-    int ToDihParm(ParameterSet&) const;
+    int ToDihParm(DihedralParmHolder&) const;
+    /// Put all improper parameters into given improper parameter holder.
+    int ToImpParm(ImproperParmHolder&) const;
 
-    /// Add (or update) a single dihedral parameter for given atom types.
+    /// Add (or update) a single dihedral or improper parameter for given atom types.
     RetType AddDihParm(TypeNameHolder const& types, DihedralParmType const& dp, bool allowUpdate) {
       // Ensure types are sorted
       //TypeNameHolder types = typesIn;

From 3f0eec2b859f21a8af410a5fae78b0880b022ebf Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 26 Feb 2026 08:40:03 -0500
Subject: [PATCH 1385/1492] Remove single multiplicity dihedral parameter add
 from the Dihedral/Improper parm holders. Use DihedralParmSet routines in
 AmberParamFile, and make use of DihedralParmSet for impropers

---
 src/AmberParamFile.cpp        | 117 +++++++++-------------------------
 src/AmberParamFile.h          |   4 +-
 src/Parm/DihedralParmHolder.h |  11 ++--
 src/Parm/ImproperParmHolder.h |   5 +-
 4 files changed, 40 insertions(+), 97 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index c4aea75828..7c4e4313b6 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -68,26 +68,6 @@ class AmberParamFile::OffdiagNB {
     LJparmType LJ2_;
 };
 
-/*static inline void printTypes(TypeNameHolder const& types) {
-  switch (types.Size()) {
-    case 1 : mprintf("%s", *(types[0])); break;
-    case 2 : mprintf("%s - %s", *(types[0]), *(types[1])); break;
-    case 3 : mprintf("%s - %s - %s", *(types[0]), *(types[1]), *(types[2])); break;
-    case 4 : mprintf("%s - %s - %s - %s", *(types[0]), *(types[1]), *(types[2]), *(types[3])); break;
-  }
-}*/
-
-static inline std::string typeNameStr(TypeNameHolder const& types, std::string const& desc) {
-  std::string OUT(desc);
-  switch (types.Size()) {
-    case 1 : OUT.append(" type " + types[0].Truncated()); break;
-    case 2 : OUT.append(" type " + types[0].Truncated() + " - " + types[1].Truncated()); break;
-    case 3 : OUT.append(" type " + types[0].Truncated() + " - " + types[1].Truncated() + " - " + types[2].Truncated()); break;
-    case 4 : OUT.append(" type " + types[0].Truncated() + " - " + types[1].Truncated() + " - " + types[2].Truncated() + " - " + types[3].Truncated());
-  }
-  return OUT;
-}
-
 /** Read input for atom symbols and masses. */
 int AmberParamFile::read_atype(ParameterSet& prm, const char* ptr)
 const
@@ -128,18 +108,18 @@ const
     return 1;
   }
   if (ret == Cpptraj::Parm::SAME)
-    mprintf("Warning: Duplicated %s\n", typeNameStr(types, "atom").c_str());
+    mprintf("Warning: Duplicated %s\n", types.TypeNameStr("atom").c_str());
   else if (ret == Cpptraj::Parm::UPDATED) {
     AtomType const& prev = prm.AT().PreviousParm();
     bool diff_mass = (prev.Mass() != amass);
     bool diff_pol  = (prev.Polarizability() != atpol);
-    mprintf("Warning: Redefining %s", typeNameStr(types, "atom").c_str());
+    mprintf("Warning: Redefining %s", types.TypeNameStr("atom").c_str());
              //prm.AT().PreviousParm().Mass(), prm.AT().PreviousParm().Polarizability(), amass, atpol);
     if (diff_mass) mprintf(" from mass %g to %g", prev.Mass(), amass);
     if (diff_pol)  mprintf(" from pol %g to %g", prev.Polarizability(), atpol);
     mprintf("\n");
   } else if (ret == Cpptraj::Parm::ERR) {
-    mprinterr("Error: Reading %s\n", typeNameStr(types, "atom").c_str());
+    mprinterr("Error: Reading %s\n", types.TypeNameStr("atom").c_str());
     return 1;
   }
 
@@ -175,13 +155,13 @@ const
   Cpptraj::Parm::RetType ret = prm.BP().AddParm(types, BondParmType(RK, REQ), true);
 
   if (ret == Cpptraj::Parm::SAME)
-    mprintf("Warning: Duplicated %s\n", typeNameStr(types, "bond").c_str());
+    mprintf("Warning: Duplicated %s\n", types.TypeNameStr("bond").c_str());
   else if (ret == Cpptraj::Parm::UPDATED)
     mprintf("Warning: Redefining %s from RK= %g REQ= %g to RK= %g REQ= %g\n",
-            typeNameStr(types, "bond").c_str(),
+            types.TypeNameStr("bond").c_str(),
             prm.BP().PreviousParm().Rk(), prm.BP().PreviousParm().Req(), RK, REQ);
   else if (ret == Cpptraj::Parm::ERR) {
-    mprinterr("Error: Reading %s\n", typeNameStr(types, "bond").c_str());
+    mprinterr("Error: Reading %s\n", types.TypeNameStr("bond").c_str());
     return 1;
   }
 
@@ -215,13 +195,13 @@ const
   types.AddName( symbols[2] );
   Cpptraj::Parm::RetType ret = prm.AP().AddParm(types, AngleParmType(TK, TEQ*Constants::DEGRAD), true);
   if (ret == Cpptraj::Parm::SAME)
-    mprintf("Warning: Duplicated %s\n", typeNameStr(types, "angle").c_str());
+    mprintf("Warning: Duplicated %s\n", types.TypeNameStr("angle").c_str());
   else if (ret == Cpptraj::Parm::UPDATED)
     mprintf("Warning: Redefining %s from TK= %g TEQ= %g to RK= %g REQ= %g\n",
-             typeNameStr(types, "angle").c_str(),
+             types.TypeNameStr("angle").c_str(),
              prm.AP().PreviousParm().Tk(), prm.AP().PreviousParm().Teq()*Constants::RADDEG, TK, TEQ);
   else if (ret == Cpptraj::Parm::ERR) {
-    mprinterr("Error: Reading %s\n", typeNameStr(types, "angle").c_str());
+    mprinterr("Error: Reading %s\n", types.TypeNameStr("angle").c_str());
     return 1;
   }
   //if (ret == Cpptraj::Parm::UPDATED)
@@ -302,13 +282,13 @@ const
   Cpptraj::Parm::RetType ret =
     prm.AddDihParm(types, DihedralParmType(PK / (double)IDIVF, PN, PHASE*Constants::DEGRAD, scee, scnb), true);
   if (ret == Cpptraj::Parm::SAME)
-    mprintf("Warning: Duplicated %s\n", typeNameStr(types, "dihedral").c_str());
+    mprintf("Warning: Duplicated %s\n", types.TypeNameStr("dihedral").c_str());
   else if (ret == Cpptraj::Parm::UPDATED) // TODO SCEE/SCNB?
     mprintf("Warning: Redefining %s (PN=%g) from PK= %g Phase= %g to PK= %g Phase= %g\n",
-             typeNameStr(types, "dihedral").c_str(), PN,
+             types.TypeNameStr("dihedral").c_str(), PN,
              prm.PreviousParm().Pk(), prm.PreviousParm().Phase()*Constants::RADDEG, PK/(double)IDIVF, PHASE);
   else if (ret == Cpptraj::Parm::ERR) {
-    mprinterr("Error: Reading %s\n", typeNameStr(types, "dihedral").c_str());
+    mprinterr("Error: Reading %s\n", types.TypeNameStr("dihedral").c_str());
     return 1;
   }
   //if (ret == Cpptraj::Parm::UPDATED) {
@@ -320,50 +300,8 @@ const
   return 0;
 }
 
-static inline void printdih(DihedralParmArray const& dpa)
-{
-  for (DihedralParmArray::const_iterator it = dpa.begin(); it != dpa.end(); ++it)
-    mprintf("Warning:\t\t%3g PK= %g Phase= %g\n", it->Pn(), it->Pk(), it->Phase()*Constants::RADDEG);
-}
-
-/** Put read-in dihedral parameters into the given ParameterSet.
-  * Warn about missing multiplicities.
-  */
-int AmberParamFile::dihparm_to_parmset(ParameterSet& prm, DihedralParmSet const& dihPrm)
-const
-{
-  for (DihedralParmSet::const_iterator it = dihPrm.begin(); it != dihPrm.end(); ++it)
-  {
-    // Check multiplicites; warn if one seems missing
-    if (it->second.size() > 1) {
-      DihedralParmArray::const_iterator dp = it->second.begin();
-      unsigned int next_expected_mult = (unsigned int)dp->Pn() + 1;
-      dp++;
-      for (; dp != it->second.end(); dp++) {
-        if ((unsigned int)dp->Pn() != next_expected_mult)
-          mprintf("Warning: %s does not have dihedral term for multiplicity %u\n",
-                  typeNameStr(it->first, "dihedral").c_str(), next_expected_mult);
-        next_expected_mult = (unsigned int)dp->Pn() + 1;
-      }
-    }
-    Cpptraj::Parm::RetType ret = prm.DP().AddParm( it->first, it->second, true );
-    if (ret == Cpptraj::Parm::SAME)
-      mprintf("Warning: Duplicated %s\n", typeNameStr(it->first, "dihedral").c_str());
-    else if (ret == Cpptraj::Parm::UPDATED) {// TODO SCEE/SCNB?
-      mprintf("Warning: Redefining %s from\n", typeNameStr(it->first, "dihedral").c_str());
-      printdih(prm.DP().PreviousArray());
-      mprintf("Warning: to\n");
-      printdih(it->second);
-    } else if (ret == Cpptraj::Parm::ERR) {
-      mprinterr("Error: Reading %s\n", typeNameStr(it->first, "dihedral").c_str());
-      return 1;
-    }
-  }
-  return 0;
-}
-
 /** Read input for improper. */
-int AmberParamFile::read_improper(ParameterSet& prm, const char* ptr)
+int AmberParamFile::read_improper(DihedralParmSet& prm, const char* ptr)
 const
 {
   // Improper parameters
@@ -395,15 +333,15 @@ const
   types.AddName( symbols[3] );
   //types.SortImproperByAlpha("X"); // FIXME wildcard should be a static var
   Cpptraj::Parm::RetType ret =
-    prm.IP().AddParm(types, DihedralParmType(PK, PN, PHASE*Constants::DEGRAD), true);
+    prm.AddDihParm(types, DihedralParmType(PK, PN, PHASE*Constants::DEGRAD), true);
   if (ret == Cpptraj::Parm::SAME)
-    mprintf("Warning: Duplicated %s\n", typeNameStr(types, "improper").c_str());
+    mprintf("Warning: Duplicated %s\n", types.TypeNameStr("improper").c_str());
   else if (ret == Cpptraj::Parm::UPDATED)
     mprintf("Warning: Redefining %s from PK= %g Phase= %g to PK= %g Phase= %g\n",
-             typeNameStr(types, "improper").c_str(),
-             prm.IP().PreviousParm().Pk(), prm.IP().PreviousParm().Phase()*Constants::RADDEG, PK, PHASE);
+             types.TypeNameStr("improper").c_str(),
+             prm.PreviousParm().Pk(), prm.PreviousParm().Phase()*Constants::RADDEG, PK, PHASE);
   else if (ret == Cpptraj::Parm::ERR) {
-    mprinterr("Error: Reading %s\n", typeNameStr(types, "improper").c_str());
+    mprinterr("Error: Reading %s\n", types.TypeNameStr("improper").c_str());
     return 1;
   }
 
@@ -440,14 +378,14 @@ const
   types.AddName( KT2 );
   Cpptraj::Parm::RetType ret = prm.HB().AddParm(types, HB_ParmType(A, B, HCUT), true);
   if (ret == Cpptraj::Parm::SAME)
-    mprintf("Warning: Duplicated %s\n", typeNameStr(types, "LJ 10-12 hbond").c_str());
+    mprintf("Warning: Duplicated %s\n", types.TypeNameStr("LJ 10-12 hbond").c_str());
   else if (ret == Cpptraj::Parm::UPDATED) {
     mprintf("Warning: Redefining %s from Asol= %g Bsol= %g Cut= %g to Asol= %g Bsol= %g Cut=%g\n",
-            typeNameStr(types, "LJ 10-12 hbond").c_str(),
+            types.TypeNameStr("LJ 10-12 hbond").c_str(),
             prm.HB().PreviousParm().Asol(), prm.HB().PreviousParm().Bsol(), prm.HB().PreviousParm().HBcut(),
             A, B, HCUT);
   } else if (ret == Cpptraj::Parm::ERR) {
-    mprinterr("Error: Reading %s\n", typeNameStr(types, "LJ 10-12 hbond").c_str());
+    mprinterr("Error: Reading %s\n", types.TypeNameStr("LJ 10-12 hbond").c_str());
     return 1;
   }
 
@@ -853,6 +791,7 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname) const
   NonbondSet nbset(title);
   Oarray Offdiag;
   DihedralParmSet dihPrm;
+  DihedralParmSet impPrm;
   // Read file
   SectionType section = UNKNOWN;
   CmapType currentCmapFlag = CMAP_INITIAL;
@@ -892,7 +831,7 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname) const
         else if (section == DIHEDRAL)
           err = read_dihedral(dihPrm, ptr, last_symbols, first_char_is_space);
         else if (section == IMPROPER)
-          err = read_improper(prm, ptr);
+          err = read_improper(impPrm, ptr);
         else if (section == LJ1012)
           err = read_lj1012(prm, ptr);
         else if (section == NONBOND)
@@ -918,7 +857,8 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname) const
     prm.CMAP().AddParm( currentCmap, true, debug_ );
   }
   // Add dihedrals
-  if (dihparm_to_parmset(prm, dihPrm)) return 1;
+  if (dihPrm.ToDihParm(prm.DP())) return 1;
+  if (impPrm.ToImpParm(prm.IP())) return 1;
   // Nonbonds
   if (assign_nb(prm, nbset)) return 1;
   // Off-diagonal NB modifications
@@ -965,6 +905,7 @@ int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
   std::vector<std::string> last_symbols;
   last_symbols.reserve(4);
   DihedralParmSet dihPrm;
+  DihedralParmSet impPrm;
   // Read file
   int readNbType = 0;
   SectionType section = ATYPE;
@@ -1055,7 +996,7 @@ int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
     } else if (section == DIHEDRAL) {
       read_err = read_dihedral(dihPrm, ptr, last_symbols, first_char_is_space);
     } else if (section == IMPROPER) {
-      read_err = read_improper(prm, ptr);
+      read_err = read_improper(impPrm, ptr);
     } else if (section == LJ1012) {
       read_err = read_lj1012(prm, ptr);
     } else if (section == NB_EQUIV) {
@@ -1090,8 +1031,8 @@ int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
   } // END loop over file.
 
   // Add dihedrals
-  if (dihparm_to_parmset(prm, dihPrm)) return 1;
-
+  if (dihPrm.ToDihParm(prm.DP())) return 1;
+  if (impPrm.ToImpParm(prm.IP())) return 1;
   // Deal with nonbond and equivalence
   if (!NBsets.empty()) {
     int nbsetidx = 0;
diff --git a/src/AmberParamFile.h b/src/AmberParamFile.h
index 081f1e02f2..0ccb83a825 100644
--- a/src/AmberParamFile.h
+++ b/src/AmberParamFile.h
@@ -46,9 +46,9 @@ class AmberParamFile {
     int read_angle(ParameterSet&, const char*) const;
     /// Read dihedral line
     int read_dihedral(DihedralParmSet&, const char*, std::vector<std::string>&, bool) const;
-    int dihparm_to_parmset(ParameterSet&, DihedralParmSet const&) const;
+//    int dihparm_to_parmset(ParameterSet&, DihedralParmSet const&) const;
     /// Read improper line
-    int read_improper(ParameterSet&, const char*) const;
+    int read_improper(DihedralParmSet&, const char*) const;
     /// Read LJ 10-12 hbond line
     int read_lj1012(ParameterSet&, const char*) const;
     /// Read IPOL line
diff --git a/src/Parm/DihedralParmHolder.h b/src/Parm/DihedralParmHolder.h
index 13c4e23739..4d8183185d 100644
--- a/src/Parm/DihedralParmHolder.h
+++ b/src/Parm/DihedralParmHolder.h
@@ -10,10 +10,7 @@ namespace Cpptraj {
 namespace Parm {
 // -----------------------------------------------------------------------------
 /// Specialized class for associating atom types with dihedral parameters.
-/** NOTE: Instead of using a specialize template here I'm creating a new
-  *       class because while I want AddParm() to accept DihedralParmType,
-  *       I want FindParam to return an array of DihedralParmType, one for
-  *       each unique multiplicity.
+/** Dihedrals are specialized because you may need to do wildcard matching.
   */
 class DihedralParmHolder {
     typedef std::pair<TypeNameHolder,DihedralParmArray> Bpair;
@@ -30,10 +27,11 @@ class DihedralParmHolder {
     /// \return true if no dihedral parameters
     bool empty()        const { return bpmap_.empty(); }
     /// \return Last parameter to be overwritten from AddParm()
-    DihedralParmType const& PreviousParm() const { return previousParm_; }
+//    DihedralParmType const& PreviousParm() const { return previousParm_; }
     DihedralParmArray const& PreviousArray() const { return previousArray_; }
     /// Set wildcard character
     void SetWildcard(char wc) { wc_ = NameType(std::string(1, wc)); }
+/*
     /// Add (or update) a single dihedral parameter for given atom types.
     RetType AddParm(TypeNameHolder const& types, DihedralParmType const& dp, bool allowUpdate) {
       // Check if parm for these types exist
@@ -96,6 +94,7 @@ class DihedralParmHolder {
       }
       return ADDED;
     }
+*/
     /// Add array of dihedral parameters with unique multiplicities
     RetType AddParm(TypeNameHolder const& types, DihedralParmArray const& dpa, bool allowUpdate) {
       // Check if parm for these types exist
@@ -173,7 +172,7 @@ class DihedralParmHolder {
     NameType wc_; ///< Wildcard character
   private:
     Bmap bpmap_;
-    DihedralParmType previousParm_; ///< When parameter is updated, store previous value. TODO remove?
+//    DihedralParmType previousParm_; ///< When parameter is updated, store previous value. TODO remove?
     DihedralParmArray previousArray_; ///< When array is updated, store previous value
 };
 } // END namespace Parm
diff --git a/src/Parm/ImproperParmHolder.h b/src/Parm/ImproperParmHolder.h
index 4d388ba330..f24b62b4a9 100644
--- a/src/Parm/ImproperParmHolder.h
+++ b/src/Parm/ImproperParmHolder.h
@@ -36,7 +36,8 @@ class ImproperParmHolder : private DihedralParmHolder {
     /// \return True if no parameters
     bool empty()               const { return DihedralParmHolder::empty(); }
     /// \return Last parameter to be overwritten from AddParm()
-    DihedralParmType const& PreviousParm() const { return DihedralParmHolder::PreviousParm(); }
+//    DihedralParmType const& PreviousParm() const { return DihedralParmHolder::PreviousParm(); }
+    DihedralParmArray const& PreviousArray() const { return DihedralParmHolder::PreviousArray(); }
     /// \return Wildcard
     NameType const& Wildcard() const { return wc_; }
     /// \return True if an exact match is required to find a parameter
@@ -53,10 +54,12 @@ class ImproperParmHolder : private DihedralParmHolder {
     void SetWildcard(NameType const& wc) { wc_ = wc; }
     /// Indicate whether exact type matches are required to find parameters
     void SetRequireExactMatch(bool b) { require_exact_match_ = b; }
+/*
     /// Add (or update) a single improper parameter for given atom types.
     RetType AddParm(TypeNameHolder const& types, DihedralParmType const& dp, bool allowUpdate) {
       return DihedralParmHolder::AddParm( types, dp, allowUpdate );
     }
+*/
     /// Add array of improper parameters, one for each multiplicity.
     RetType AddParm(TypeNameHolder const& types, DihedralParmArray const& dpa, bool allowUpdate) {
       return DihedralParmHolder::AddParm( types, dpa, allowUpdate );

From f49ded992a92a1dab54320fa712cf5e561671930 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 26 Feb 2026 08:45:58 -0500
Subject: [PATCH 1386/1492] Use DihedralParmSet

---
 src/CharmmParamFile.cpp | 16 +++++++++++-----
 src/cpptrajdepend       |  2 +-
 2 files changed, 12 insertions(+), 6 deletions(-)

diff --git a/src/CharmmParamFile.cpp b/src/CharmmParamFile.cpp
index 544dba4178..b872c82f6d 100644
--- a/src/CharmmParamFile.cpp
+++ b/src/CharmmParamFile.cpp
@@ -1,9 +1,10 @@
 #include "CharmmParamFile.h"
-#include "CpptrajStdio.h"
-#include "StringRoutines.h" // RemoveTrailingWhitespace()
 #include "ArgList.h"
-#include "Constants.h"
 #include "BufferedLine.h"
+#include "Constants.h"
+#include "CpptrajStdio.h"
+#include "StringRoutines.h" // RemoveTrailingWhitespace()
+#include "Parm/DihedralParmSet.h"
 #include "Parm/ParameterSet.h"
 
 static inline std::string Input(const char* line) {
@@ -86,6 +87,8 @@ int CharmmParamFile::ReadParams(Cpptraj::Parm::ParameterSet& prm, FileName const
   // Set wildcard character for dihedrals and impropers
   prm.DP().SetWildcard('X');
   prm.IP().SetWildcard('X');
+  DihedralParmSet dihPrm;
+  DihedralParmSet impPrm;
 
   while (ReadInput(input, infile)) {
     if (input.empty()) continue;
@@ -235,9 +238,9 @@ int CharmmParamFile::ReadParams(Cpptraj::Parm::ParameterSet& prm, FileName const
               double pn = args.getNextDouble(0);
               double phase = args.getNextDouble(0) * Constants::DEGRAD;
               if (currentSection == DIHEDRALS)
-                prm.DP().AddParm(types, DihedralParmType(pk, pn, phase, 1.0, 1.0), false);
+                dihPrm.AddDihParm(types, DihedralParmType(pk, pn, phase, 1.0, 1.0), false);
               else
-                prm.IP().AddParm(types, DihedralParmType(pk, pn, phase), false);
+                impPrm.AddDihParm(types, DihedralParmType(pk, pn, phase), false);
             }
           } else if (currentSection == NONBONDED) {
             // NONBONDED PARAMETERS TODO do not add if not already present
@@ -290,6 +293,9 @@ int CharmmParamFile::ReadParams(Cpptraj::Parm::ParameterSet& prm, FileName const
       }  // END line not blank
     } // END if not title or comment 
   } // END loop over file read
+  // Add dihedrals/impropers
+  if (dihPrm.ToDihParm(prm.DP())) return 1;
+  if (impPrm.ToImpParm(prm.IP())) return 1;
   if (debugIn > 0) 
     prm.Debug();
 
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 4e6a3c84a9..4f8233f18a 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -158,7 +158,7 @@ BufferedLine.o : BufferedLine.cpp BufferedLine.h CpptrajFile.h CpptrajStdio.h Fi
 ByteRoutines.o : ByteRoutines.cpp
 CIFfile.o : CIFfile.cpp ArgList.h Atom.h BufferedLine.h CIFfile.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h StringRoutines.h SymbolExporting.h
 CharMask.o : CharMask.cpp Atom.h CharMask.h CpptrajStdio.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h SymbolExporting.h Unit.h
-CharmmParamFile.o : CharmmParamFile.cpp ArgList.h AtomType.h BufferedLine.h CharmmParamFile.h CmapParmHolder.h Constants.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h StringRoutines.h TypeNameHolder.h
+CharmmParamFile.o : CharmmParamFile.cpp ArgList.h AtomType.h BufferedLine.h CharmmParamFile.h CmapParmHolder.h Constants.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/DihedralParmSet.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h StringRoutines.h TypeNameHolder.h
 Cluster/Algorithm.o : Cluster/Algorithm.cpp Cluster/Algorithm.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h CpptrajStdio.h
 Cluster/Algorithm_DBscan.o : Cluster/Algorithm_DBscan.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cluster/Algorithm.h Cluster/Algorithm_DBscan.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 Cluster/Algorithm_DPeaks.o : Cluster/Algorithm_DPeaks.cpp ArgList.h AssociatedData.h Cluster/Algorithm.h Cluster/Algorithm_DPeaks.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_Mesh.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h ProgressBar.h Range.h Spline.h TextFormat.h

From 66e20a308216624dcfac4e43ea88dec5b381194b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 26 Feb 2026 08:59:53 -0500
Subject: [PATCH 1387/1492] Remove references to temporary file

---
 src/Parm/CMakeLists.txt | 1 -
 src/Parm/parmdepend     | 1 -
 src/Parm/parmfiles      | 3 +--
 3 files changed, 1 insertion(+), 4 deletions(-)

diff --git a/src/Parm/CMakeLists.txt b/src/Parm/CMakeLists.txt
index b7885ef92c..268e981bfc 100644
--- a/src/Parm/CMakeLists.txt
+++ b/src/Parm/CMakeLists.txt
@@ -9,5 +9,4 @@ target_sources(cpptraj_common_obj PRIVATE
   ${CMAKE_CURRENT_LIST_DIR}/Merge.cpp
   ${CMAKE_CURRENT_LIST_DIR}/ParameterSet.cpp
   ${CMAKE_CURRENT_LIST_DIR}/ParmEnum.cpp
-  ${CMAKE_CURRENT_LIST_DIR}/test.cpp
 )
diff --git a/src/Parm/parmdepend b/src/Parm/parmdepend
index df3a1af846..f2e7d5e2db 100644
--- a/src/Parm/parmdepend
+++ b/src/Parm/parmdepend
@@ -7,4 +7,3 @@ LJ1264_Params.o : LJ1264_Params.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.
 Merge.o : Merge.cpp ../Atom.h ../Constants.h ../CpptrajStdio.h ../NameType.h ../ParameterTypes.h ../Residue.h ../StringRoutines.h ../SymbolExporting.h ../TypeNameHolder.h Merge.h ParmEnum.h ParmHolder.h
 ParameterSet.o : ParameterSet.cpp ../AtomType.h ../CmapParmHolder.h ../Constants.h ../CpptrajFile.h ../CpptrajStdio.h ../FileIO.h ../FileName.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/ParmEnum.h ../TypeNameHolder.h ../UpdateParameters.h DihedralParmHolder.h ImproperParmHolder.h ParameterSet.h ParmEnum.h ParmHolder.h
 ParmEnum.o : ParmEnum.cpp ParmEnum.h
-test.o : test.cpp ../Constants.h ../NameType.h ../ParameterTypes.h ../TypeNameHolder.h DihedralParmSet.h ParmEnum.h
diff --git a/src/Parm/parmfiles b/src/Parm/parmfiles
index 71f9a08add..b9e06f928b 100644
--- a/src/Parm/parmfiles
+++ b/src/Parm/parmfiles
@@ -8,5 +8,4 @@ PARM_SOURCES= \
   LJ1264_Params.cpp \
   Merge.cpp \
   ParameterSet.cpp \
-  ParmEnum.cpp \
-  test.cpp
+  ParmEnum.cpp

From 7328c3c34019fe14fcce3cc33b76006e68756dd1 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 26 Feb 2026 09:11:41 -0500
Subject: [PATCH 1388/1492] Use DihedralParmSet

---
 src/Parm/GetParams.cpp | 19 ++++++++++++++++---
 src/Parm/parmdepend    |  2 +-
 src/cpptrajdepend      |  3 +--
 3 files changed, 18 insertions(+), 6 deletions(-)

diff --git a/src/Parm/GetParams.cpp b/src/Parm/GetParams.cpp
index 2c7b5979ca..a092acd650 100644
--- a/src/Parm/GetParams.cpp
+++ b/src/Parm/GetParams.cpp
@@ -1,4 +1,5 @@
 #include "GetParams.h"
+#include "DihedralParmSet.h"
 #include "ParameterSet.h"
 #include "../Atom.h"
 #include "../AtomType.h"
@@ -62,6 +63,7 @@ void GetParams::GetAngleParams(ParmHolder<AngleParmType>& AP, std::vector<Atom>
 // GetImproperParams()
 void GetParams::GetImproperParams(ImproperParmHolder& IP, std::vector<Atom> const& atoms, DihedralArray const& imp, DihedralParmArray const& ipa) {
   IP.SetRequireExactMatch(true);
+  DihedralParmSet impPrm;
   for (DihedralArray::const_iterator b = imp.begin(); b != imp.end(); ++b)
   {
     if (b->Idx() != -1) {
@@ -70,16 +72,21 @@ void GetParams::GetImproperParams(ImproperParmHolder& IP, std::vector<Atom> cons
       types.AddName( atoms[b->A2()].Type() );
       types.AddName( atoms[b->A3()].Type() );
       types.AddName( atoms[b->A4()].Type() );
-      Cpptraj::Parm::RetType ret = IP.AddParm( types, ipa[b->Idx()], false );
+      Cpptraj::Parm::RetType ret = impPrm.AddDihParm( types, ipa[b->Idx()], false );
       if (ret == Cpptraj::Parm::ERR)
         paramOverwriteWarning("improper");
     }
   }
+  if (impPrm.ToImpParm(IP)) {
+    mprinterr("Internal Error: GetParams::GetImproperParams(): Could not transfer parameters from set to holder.\n");
+  }
 }
 
 // GetDihedralParams()
 void GetParams::GetDihedralParams(DihedralParmHolder& DP, ImproperParmHolder& IP, std::vector<Atom> const& atoms, DihedralArray const& dih, DihedralParmArray const& dpa) {
   IP.SetRequireExactMatch(true);
+  DihedralParmSet dihPrm;
+  DihedralParmSet impPrm;
   for (DihedralArray::const_iterator b = dih.begin(); b != dih.end(); ++b)
   {
     if (b->Idx() != -1) {
@@ -94,9 +101,9 @@ void GetParams::GetDihedralParams(DihedralParmHolder& DP, ImproperParmHolder& IP
       //        dpa[b->Idx()].Pk(), dpa[b->Idx()].Pn(), dpa[b->Idx()].Phase(), dpa[b->Idx()].SCEE(), dpa[b->Idx()].SCNB());
       Cpptraj::Parm::RetType ret;
       if (b->IsImproper()) {
-        ret = IP.AddParm( types, dpa[b->Idx()], false );
+        ret = impPrm.AddDihParm( types, dpa[b->Idx()], false );
       } else {
-        ret = DP.AddParm( types, dpa[b->Idx()], false );
+        ret = dihPrm.AddDihParm( types, dpa[b->Idx()], false );
       }
       // DEBUG
       //if (ret == Cpptraj::Parm::ADDED) {
@@ -116,6 +123,12 @@ void GetParams::GetDihedralParams(DihedralParmHolder& DP, ImproperParmHolder& IP
       }
     }
   }
+  if (impPrm.ToImpParm(IP)) {
+    mprinterr("Internal Error: GetParams::GetImproperParams(): Could not transfer parameters from set to holder.\n");
+  }
+  if (dihPrm.ToDihParm(DP)) {
+    mprinterr("Internal Error: GetParams::GetDihedralParams(): Could not transfer parameters from set to holder.\n");
+  }
 }
 
 /// \return an error if cmap atom names do not match
diff --git a/src/Parm/parmdepend b/src/Parm/parmdepend
index f2e7d5e2db..a1541e66c1 100644
--- a/src/Parm/parmdepend
+++ b/src/Parm/parmdepend
@@ -2,7 +2,7 @@ AssignParams.o : AssignParams.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h
 Bond_Params.o : Bond_Params.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h Bond_Params.h
 DihedralParmSet.o : DihedralParmSet.cpp ../AtomType.h ../CmapParmHolder.h ../Constants.h ../CpptrajStdio.h ../FileName.h ../NameType.h ../ParameterTypes.h ../Parm/ParmEnum.h ../TypeNameHolder.h DihedralParmHolder.h DihedralParmSet.h ImproperParmHolder.h ParameterSet.h ParmEnum.h ParmHolder.h
 GB_Params.o : GB_Params.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h GB_Params.h
-GetParams.o : GetParams.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/ParmEnum.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h DihedralParmHolder.h GetParams.h ImproperParmHolder.h ParameterSet.h ParmEnum.h ParmHolder.h
+GetParams.o : GetParams.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/ParmEnum.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h DihedralParmHolder.h DihedralParmSet.h GetParams.h ImproperParmHolder.h ParameterSet.h ParmEnum.h ParmHolder.h
 LJ1264_Params.o : LJ1264_Params.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../BufferedLine.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../StringRoutines.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h LJ1264_Params.h ParmEnum.h
 Merge.o : Merge.cpp ../Atom.h ../Constants.h ../CpptrajStdio.h ../NameType.h ../ParameterTypes.h ../Residue.h ../StringRoutines.h ../SymbolExporting.h ../TypeNameHolder.h Merge.h ParmEnum.h ParmHolder.h
 ParameterSet.o : ParameterSet.cpp ../AtomType.h ../CmapParmHolder.h ../Constants.h ../CpptrajFile.h ../CpptrajStdio.h ../FileIO.h ../FileName.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/ParmEnum.h ../TypeNameHolder.h ../UpdateParameters.h DihedralParmHolder.h ImproperParmHolder.h ParameterSet.h ParmEnum.h ParmHolder.h
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 4f8233f18a..f24db85897 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -437,12 +437,11 @@ Parm/AssignParams.o : Parm/AssignParams.cpp Atom.h AtomMask.h AtomType.h Box.h C
 Parm/Bond_Params.o : Parm/Bond_Params.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/Bond_Params.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Parm/DihedralParmSet.o : Parm/DihedralParmSet.cpp AtomType.h CmapParmHolder.h Constants.h CpptrajStdio.h FileName.h NameType.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/DihedralParmSet.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h TypeNameHolder.h
 Parm/GB_Params.o : Parm/GB_Params.cpp ArgList.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/GB_Params.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
-Parm/GetParams.o : Parm/GetParams.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/GetParams.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Parm/GetParams.o : Parm/GetParams.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/DihedralParmSet.h Parm/GetParams.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Parm/LJ1264_Params.o : Parm/LJ1264_Params.cpp ArgList.h Atom.h AtomMask.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/LJ1264_Params.h Parm/ParmEnum.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Parm/Merge.o : Parm/Merge.cpp Atom.h Constants.h CpptrajStdio.h NameType.h ParameterTypes.h Parm/Merge.h Parm/ParmEnum.h Parm/ParmHolder.h Residue.h StringRoutines.h SymbolExporting.h TypeNameHolder.h
 Parm/ParameterSet.o : Parm/ParameterSet.cpp AtomType.h CmapParmHolder.h Constants.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h TypeNameHolder.h UpdateParameters.h
 Parm/ParmEnum.o : Parm/ParmEnum.cpp Parm/ParmEnum.h
-Parm/test.o : Parm/test.cpp Constants.h NameType.h ParameterTypes.h Parm/DihedralParmSet.h Parm/ParmEnum.h TypeNameHolder.h
 ParmFile.o : ParmFile.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h ParmFile.h ParmIO.h Parm_Amber.h Parm_CIF.h Parm_CharmmPsf.h Parm_Gromacs.h Parm_Mol2.h Parm_PDB.h Parm_SDF.h Parm_Tinker.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Parm_Amber.o : Parm_Amber.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h ExclusionArray.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/GetParams.h ParmIO.h Parm_Amber.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h Unit.h Vec3.h
 Parm_CIF.o : Parm_CIF.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h CIFfile.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmIO.h Parm_CIF.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h

From 2212ddc9e8821acf374b09a3d211cb7323ec3a25 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 26 Feb 2026 09:12:12 -0500
Subject: [PATCH 1389/1492] Go back to PreviousParm instead of PreviousArray to
 be consistent with other parameter holders; important for UpdateParameters.h

---
 src/Parm/DihedralParmHolder.h | 8 +++-----
 src/Parm/DihedralParmSet.cpp  | 4 ++--
 src/Parm/ImproperParmHolder.h | 3 +--
 3 files changed, 6 insertions(+), 9 deletions(-)

diff --git a/src/Parm/DihedralParmHolder.h b/src/Parm/DihedralParmHolder.h
index 4d8183185d..1a2a16b53f 100644
--- a/src/Parm/DihedralParmHolder.h
+++ b/src/Parm/DihedralParmHolder.h
@@ -27,8 +27,7 @@ class DihedralParmHolder {
     /// \return true if no dihedral parameters
     bool empty()        const { return bpmap_.empty(); }
     /// \return Last parameter to be overwritten from AddParm()
-//    DihedralParmType const& PreviousParm() const { return previousParm_; }
-    DihedralParmArray const& PreviousArray() const { return previousArray_; }
+    DihedralParmArray const& PreviousParm() const { return previousParm_; }
     /// Set wildcard character
     void SetWildcard(char wc) { wc_ = NameType(std::string(1, wc)); }
 /*
@@ -123,7 +122,7 @@ class DihedralParmHolder {
           }
         }
         if (update) {
-          previousArray_ = it0->second;
+          previousParm_ = it0->second;
           it0->second = dpa;
           return UPDATED;
         } else
@@ -172,8 +171,7 @@ class DihedralParmHolder {
     NameType wc_; ///< Wildcard character
   private:
     Bmap bpmap_;
-//    DihedralParmType previousParm_; ///< When parameter is updated, store previous value. TODO remove?
-    DihedralParmArray previousArray_; ///< When array is updated, store previous value
+    DihedralParmArray previousParm_; ///< When parameter is updated, store previous value.
 };
 } // END namespace Parm
 } // END namespace Cpptraj
diff --git a/src/Parm/DihedralParmSet.cpp b/src/Parm/DihedralParmSet.cpp
index c5bf212d3c..de6673d3cf 100644
--- a/src/Parm/DihedralParmSet.cpp
+++ b/src/Parm/DihedralParmSet.cpp
@@ -33,7 +33,7 @@ int DihedralParmSet::ToDihParm(DihedralParmHolder& DP) const
       mprintf("Warning: Duplicated %s\n", it->first.TypeNameStr("dihedral").c_str());
     else if (ret == Cpptraj::Parm::UPDATED) {// TODO SCEE/SCNB?
       mprintf("Warning: Redefining %s from\n", it->first.TypeNameStr("dihedral").c_str());
-      printdih(DP.PreviousArray());
+      printdih(DP.PreviousParm());
       mprintf("Warning: to\n");
       printdih(it->second);
     } else if (ret == Cpptraj::Parm::ERR) {
@@ -66,7 +66,7 @@ int DihedralParmSet::ToImpParm(ImproperParmHolder& IP) const
       mprintf("Warning: Duplicated %s\n", it->first.TypeNameStr("improper").c_str());
     else if (ret == Cpptraj::Parm::UPDATED) {
       mprintf("Warning: Redefining %s from\n", it->first.TypeNameStr("improper").c_str());
-      printdih(IP.PreviousArray());
+      printdih(IP.PreviousParm());
       mprintf("Warning: to\n");
       printdih(it->second);
     } else if (ret == Cpptraj::Parm::ERR) {
diff --git a/src/Parm/ImproperParmHolder.h b/src/Parm/ImproperParmHolder.h
index f24b62b4a9..8464033074 100644
--- a/src/Parm/ImproperParmHolder.h
+++ b/src/Parm/ImproperParmHolder.h
@@ -36,8 +36,7 @@ class ImproperParmHolder : private DihedralParmHolder {
     /// \return True if no parameters
     bool empty()               const { return DihedralParmHolder::empty(); }
     /// \return Last parameter to be overwritten from AddParm()
-//    DihedralParmType const& PreviousParm() const { return DihedralParmHolder::PreviousParm(); }
-    DihedralParmArray const& PreviousArray() const { return DihedralParmHolder::PreviousArray(); }
+    DihedralParmArray const& PreviousParm() const { return DihedralParmHolder::PreviousParm(); }
     /// \return Wildcard
     NameType const& Wildcard() const { return wc_; }
     /// \return True if an exact match is required to find a parameter

From 4ff040f654d7e4520d0ee1e18c45bc98038c54b5 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 26 Feb 2026 09:17:02 -0500
Subject: [PATCH 1390/1492] Allow multiplicity > 1 for impropers

---
 src/Parm/AssignParams.cpp | 17 ++++++++++-------
 1 file changed, 10 insertions(+), 7 deletions(-)

diff --git a/src/Parm/AssignParams.cpp b/src/Parm/AssignParams.cpp
index d08c4c5d73..830df02f23 100644
--- a/src/Parm/AssignParams.cpp
+++ b/src/Parm/AssignParams.cpp
@@ -456,22 +456,25 @@ const
           mprintf("Warning: No improper parameters for SP2 hybridized atom %s\n", topOut.AtomMaskName(dih->A3()).c_str());
         }
       } else {
-        if (ipa.size() > 1)
-          mprintf("Warning: %zu improper parameters found for types %s - %s - %s - %s, expected only one."
-                  "Warning: Only using first parameter.\n", ipa.size(), *(types[0]), *(types[1]), *(types[2]), *(types[3]));
+        //if (ipa.size() > 1)
+        //  mprintf("Warning: %zu improper parameters found for types %s - %s - %s - %s, expected only one."
+        //          "Warning: Only using first parameter.\n", ipa.size(), *(types[0]), *(types[1]), *(types[2]), *(types[3]));
         if (reordered) warn_improper_reorder( topOut.Atoms(), *dih, mydih );
-        idx = topOut.addTorsionParm( topOut.ModifyDihedralParm(), ipa.front() );
-        mydih.SetIdx( idx );
         mydih.SetImproper( true );
         // Always skip 1-4 for impropers
         mydih.SetSkip14( true );
-        dihedralsIn.push_back( mydih );
+        for (DihedralParmArray::const_iterator it = ipa.begin(); it != ipa.end(); ++it)
+        {
+          idx = topOut.addTorsionParm( topOut.ModifyDihedralParm(), *it );
+          mydih.SetIdx( idx );
+          dihedralsIn.push_back( mydih );
+        }
         // Add to the cache
         if (is_new_improper) {
           // To match leap behavior, make sure paramTypes are sorted alphabetically.
           //mprintf("DEBUG: Improper wildcard: %s\n", *(newImproperParams.Wildcard()));
           if (sort_improper_cache) paramTypes.SortImproperByAlpha( newImproperParams.Wildcard() );
-          improperCache.AddParm( paramTypes, ipa.front(), false );
+          improperCache.AddParm( paramTypes, ipa, false );
         }
       }
 #     ifdef TIMER

From d34630a9712d2e202583d29ad03563d1ebdb9532 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 26 Feb 2026 09:19:20 -0500
Subject: [PATCH 1391/1492] Remove code that is now in DihedralParmSet

---
 src/Parm/DihedralParmHolder.h | 65 -----------------------------------
 1 file changed, 65 deletions(-)

diff --git a/src/Parm/DihedralParmHolder.h b/src/Parm/DihedralParmHolder.h
index 1a2a16b53f..f2751e133e 100644
--- a/src/Parm/DihedralParmHolder.h
+++ b/src/Parm/DihedralParmHolder.h
@@ -5,7 +5,6 @@
 #include "ParmEnum.h"
 #include "../ParameterTypes.h"
 #include "../TypeNameHolder.h"
-//#incl ude "CpptrajStdio.h" // DEBUG
 namespace Cpptraj {
 namespace Parm {
 // -----------------------------------------------------------------------------
@@ -30,70 +29,6 @@ class DihedralParmHolder {
     DihedralParmArray const& PreviousParm() const { return previousParm_; }
     /// Set wildcard character
     void SetWildcard(char wc) { wc_ = NameType(std::string(1, wc)); }
-/*
-    /// Add (or update) a single dihedral parameter for given atom types.
-    RetType AddParm(TypeNameHolder const& types, DihedralParmType const& dp, bool allowUpdate) {
-      // Check if parm for these types exist
-      Bmap::iterator it0 = bpmap_.begin();
-      for (; it0 != bpmap_.end(); ++it0)
-      {
-        if (it0->first.Match_NoWC( types ))
-          break;
-      }
-      if (it0 == bpmap_.end()) {
-        // Brand new dihedral for these types.
-        //mprintf("DEBUG: New dihedral parm: %s %s %s %s pk=%12.4f pn=%12.4f pp=%12.4f\n",
-        //        *types[0], *types[1], *types[2], *types[3], dp.Pk(), dp.Pn(), dp.Phase());
-        bpmap_.push_back( Bpair(types, DihedralParmArray(1, dp)) );
-      } else {
-        // If we are here types match - check multiplicity.
-        DihedralParmArray::iterator it1 = it0->second.begin();
-        for (; it1 != it0->second.end(); ++it1)
-        {
-          if (FEQ(it1->Pn(), dp.Pn()))
-            break;
-        }
-        if (it1 == it0->second.end()) {
-          // Brand new multiplicity for this dihedral.
-          //mprintf("DEBUG: Dihedral new mult: %s %s %s %s pk=%12.4f pn=%12.4f pp=%12.4f\n",
-          //        *types[0], *types[1], *types[2], *types[3], dp.Pk(), dp.Pn(), dp.Phase());
-          if (it0->second.empty())
-            it0->second.push_back( dp );
-          else if (dp.Pn() > it0->second.back().Pn())
-            it0->second.push_back( dp );
-          else {
-            // Try to keep multiplicities in order.
-            DihedralParmArray sorted;
-            bool isInserted = false;
-            for (DihedralParmArray::const_iterator jt = it0->second.begin(); jt != it0->second.end(); ++jt) {
-              if (!isInserted) {
-                if (dp.Pn() < jt->Pn()) {
-                  sorted.push_back( dp );
-                  isInserted = true;
-                }
-              }
-              sorted.push_back( *jt );
-            }
-            it0->second = sorted;
-          }
-        } else {
-          if (dp < *it1 || *it1 < dp) {
-            //mprintf("DEBUG: Attempt dihedral update mult (allow=%i): %s %s %s %s pk=%6.2f pn=%3.1f pp=%6.3f (orig pk=%6.2f pn=%3.1f pp=%6.3f )\n",
-            //        (int)allowUpdate, *types[0], *types[1], *types[2], *types[3], dp.Pk(), dp.Pn(), dp.Phase(), it1->Pk(), it1->Pn(), it1->Phase());
-            if (allowUpdate) {
-              previousParm_ = *it1;
-              *it1 = dp;
-              return UPDATED;
-            } else {
-              return ERR;
-            }
-          } else
-            return SAME;
-        }
-      }
-      return ADDED;
-    }
-*/
     /// Add array of dihedral parameters with unique multiplicities
     RetType AddParm(TypeNameHolder const& types, DihedralParmArray const& dpa, bool allowUpdate) {
       // Check if parm for these types exist

From de91348fdbdfe1f1e80fc59c7b73650a20ad17ef Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 26 Feb 2026 09:29:51 -0500
Subject: [PATCH 1392/1492] Consolidate the multiplicity check

---
 src/Parm/DihedralParmSet.cpp | 41 +++++++++++++++++-------------------
 src/Parm/DihedralParmSet.h   |  2 ++
 2 files changed, 21 insertions(+), 22 deletions(-)

diff --git a/src/Parm/DihedralParmSet.cpp b/src/Parm/DihedralParmSet.cpp
index de6673d3cf..0ee681b269 100644
--- a/src/Parm/DihedralParmSet.cpp
+++ b/src/Parm/DihedralParmSet.cpp
@@ -11,23 +11,29 @@ static inline void printdih(DihedralParmArray const& dpa)
     mprintf("Warning:\t\t%3g PK= %g Phase= %g\n", it->Pn(), it->Pk(), it->Phase()*Constants::RADDEG);
 }
 
+/** Print multiplicity warning */
+void DihedralParmSet::check_mult(std::string const& desc, TypeNameHolder const& types, DihedralParmArray const& DPA) {
+  if (DPA.size() > 1) {
+    DihedralParmArray::const_iterator dp = DPA.begin();
+    unsigned int next_expected_mult = (unsigned int)dp->Pn() + 1;
+    dp++;
+    for (; dp != DPA.end(); dp++) {
+      if ((unsigned int)dp->Pn() != next_expected_mult)
+        mprintf("Warning: %s does not have term for multiplicity %u\n",
+                types.TypeNameStr(desc).c_str(), next_expected_mult);
+      next_expected_mult = (unsigned int)dp->Pn() + 1;
+    }
+  }
+}
+
 /** Add all dihedral parameters into the given dihedral parameter holder. */
 int DihedralParmSet::ToDihParm(DihedralParmHolder& DP) const
 {
   for (DihedralParmSet::const_iterator it = begin(); it != end(); ++it)
   {
     // Check multiplicites; warn if one seems missing
-    if (it->second.size() > 1) {
-      DihedralParmArray::const_iterator dp = it->second.begin();
-      unsigned int next_expected_mult = (unsigned int)dp->Pn() + 1;
-      dp++;
-      for (; dp != it->second.end(); dp++) {
-        if ((unsigned int)dp->Pn() != next_expected_mult)
-          mprintf("Warning: %s does not have dihedral term for multiplicity %u\n",
-                  it->first.TypeNameStr("dihedral").c_str(), next_expected_mult);
-        next_expected_mult = (unsigned int)dp->Pn() + 1;
-      }
-    }
+    check_mult("dihedral", it->first, it->second);
+
     Cpptraj::Parm::RetType ret = DP.AddParm( it->first, it->second, true );
     if (ret == Cpptraj::Parm::SAME)
       mprintf("Warning: Duplicated %s\n", it->first.TypeNameStr("dihedral").c_str());
@@ -50,17 +56,8 @@ int DihedralParmSet::ToImpParm(ImproperParmHolder& IP) const
   for (DihedralParmSet::const_iterator it = begin(); it != end(); ++it)
   {
     // Check multiplicites; warn if one seems missing
-    if (it->second.size() > 1) {
-      DihedralParmArray::const_iterator dp = it->second.begin();
-      unsigned int next_expected_mult = (unsigned int)dp->Pn() + 1;
-      dp++;
-      for (; dp != it->second.end(); dp++) {
-        if ((unsigned int)dp->Pn() != next_expected_mult)
-          mprintf("Warning: %s does not have improper term for multiplicity %u\n",
-                  it->first.TypeNameStr("improper").c_str(), next_expected_mult);
-        next_expected_mult = (unsigned int)dp->Pn() + 1;
-      }
-    }
+    check_mult("improper", it->first, it->second);
+
     Cpptraj::Parm::RetType ret = IP.AddParm( it->first, it->second, true );
     if (ret == Cpptraj::Parm::SAME)
       mprintf("Warning: Duplicated %s\n", it->first.TypeNameStr("improper").c_str());
diff --git a/src/Parm/DihedralParmSet.h b/src/Parm/DihedralParmSet.h
index 4461be04ea..7ae7232a1d 100644
--- a/src/Parm/DihedralParmSet.h
+++ b/src/Parm/DihedralParmSet.h
@@ -105,6 +105,8 @@ class DihedralParmSet {
       return ADDED;
     }
   private:
+    static inline void check_mult(std::string const&, TypeNameHolder const&, DihedralParmArray const&);
+
     Dmap dihparm_;
     DihedralParmType previousParm_; ///< When parameter is updated, store previous value.
 };

From feaf994427e1f0d322f751815ec70972165d3f66 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 26 Feb 2026 09:39:32 -0500
Subject: [PATCH 1393/1492] By default do not report dihedrals with "missing"
 multiplicities since it seems like it happens a lot and there is nothing in
 the force field description that says you have to have a term for every
 multiplicity

---
 src/AmberParamFile.cpp       | 8 ++++----
 src/CharmmParamFile.cpp      | 4 ++--
 src/Parm/DihedralParmSet.cpp | 6 ++++--
 src/Parm/DihedralParmSet.h   | 6 +++++-
 4 files changed, 15 insertions(+), 9 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 7c4e4313b6..bf2cf477d6 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -790,8 +790,8 @@ int AmberParamFile::ReadFrcmod(ParameterSet& prm, FileName const& fname) const
   prm.SetParamSetFile( fname );
   NonbondSet nbset(title);
   Oarray Offdiag;
-  DihedralParmSet dihPrm;
-  DihedralParmSet impPrm;
+  DihedralParmSet dihPrm( debug_ );
+  DihedralParmSet impPrm( debug_ );
   // Read file
   SectionType section = UNKNOWN;
   CmapType currentCmapFlag = CMAP_INITIAL;
@@ -904,8 +904,8 @@ int AmberParamFile::ReadParams(ParameterSet& prm, FileName const& fname,
   prm.SetParamSetFile( fname );
   std::vector<std::string> last_symbols;
   last_symbols.reserve(4);
-  DihedralParmSet dihPrm;
-  DihedralParmSet impPrm;
+  DihedralParmSet dihPrm( debug_ );
+  DihedralParmSet impPrm( debug_ );
   // Read file
   int readNbType = 0;
   SectionType section = ATYPE;
diff --git a/src/CharmmParamFile.cpp b/src/CharmmParamFile.cpp
index b872c82f6d..27f32dc43a 100644
--- a/src/CharmmParamFile.cpp
+++ b/src/CharmmParamFile.cpp
@@ -87,8 +87,8 @@ int CharmmParamFile::ReadParams(Cpptraj::Parm::ParameterSet& prm, FileName const
   // Set wildcard character for dihedrals and impropers
   prm.DP().SetWildcard('X');
   prm.IP().SetWildcard('X');
-  DihedralParmSet dihPrm;
-  DihedralParmSet impPrm;
+  DihedralParmSet dihPrm( debugIn );
+  DihedralParmSet impPrm( debugIn );
 
   while (ReadInput(input, infile)) {
     if (input.empty()) continue;
diff --git a/src/Parm/DihedralParmSet.cpp b/src/Parm/DihedralParmSet.cpp
index 0ee681b269..98c52fb384 100644
--- a/src/Parm/DihedralParmSet.cpp
+++ b/src/Parm/DihedralParmSet.cpp
@@ -32,7 +32,8 @@ int DihedralParmSet::ToDihParm(DihedralParmHolder& DP) const
   for (DihedralParmSet::const_iterator it = begin(); it != end(); ++it)
   {
     // Check multiplicites; warn if one seems missing
-    check_mult("dihedral", it->first, it->second);
+    if (debug_ > 0)
+      check_mult("dihedral", it->first, it->second);
 
     Cpptraj::Parm::RetType ret = DP.AddParm( it->first, it->second, true );
     if (ret == Cpptraj::Parm::SAME)
@@ -56,7 +57,8 @@ int DihedralParmSet::ToImpParm(ImproperParmHolder& IP) const
   for (DihedralParmSet::const_iterator it = begin(); it != end(); ++it)
   {
     // Check multiplicites; warn if one seems missing
-    check_mult("improper", it->first, it->second);
+    if (debug_ > 0)
+      check_mult("improper", it->first, it->second);
 
     Cpptraj::Parm::RetType ret = IP.AddParm( it->first, it->second, true );
     if (ret == Cpptraj::Parm::SAME)
diff --git a/src/Parm/DihedralParmSet.h b/src/Parm/DihedralParmSet.h
index 7ae7232a1d..d9adcc3e50 100644
--- a/src/Parm/DihedralParmSet.h
+++ b/src/Parm/DihedralParmSet.h
@@ -20,7 +20,10 @@ class DihedralParmSet {
     //typedef std::map<TypeNameHolder, DihedralParmArray> Dmap;
     typedef std::vector<Dpair> Dmap;
   public:
-    DihedralParmSet() {}
+    /// CONSTRUCTOR
+    DihedralParmSet() : debug_(0) {}
+    /// CONSTRUCTOR - with debug level
+    DihedralParmSet(int debugIn) : debug_(debugIn) {}
     /// \return Last parameter to be overwritten from AddParm()
     DihedralParmType const& PreviousParm() const { return previousParm_; }
 
@@ -109,6 +112,7 @@ class DihedralParmSet {
 
     Dmap dihparm_;
     DihedralParmType previousParm_; ///< When parameter is updated, store previous value.
+    int debug_; ///< Debug level
 };
 }
 }

From 4bc6bee9d4341f7fe7191e64054057a4b443c68a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 26 Feb 2026 13:17:24 -0500
Subject: [PATCH 1394/1492] Add missing break

---
 src/TypeNameHolder.h | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/TypeNameHolder.h b/src/TypeNameHolder.h
index fd360414e4..1d0a721200 100644
--- a/src/TypeNameHolder.h
+++ b/src/TypeNameHolder.h
@@ -128,7 +128,7 @@ class TypeNameHolder {
         case 1 : OUT.append(" type " + types_[0].Truncated()); break;
         case 2 : OUT.append(" type " + types_[0].Truncated() + " - " + types_[1].Truncated()); break;
         case 3 : OUT.append(" type " + types_[0].Truncated() + " - " + types_[1].Truncated() + " - " + types_[2].Truncated()); break;
-        case 4 : OUT.append(" type " + types_[0].Truncated() + " - " + types_[1].Truncated() + " - " + types_[2].Truncated() + " - " + types_[3].Truncated());
+        case 4 : OUT.append(" type " + types_[0].Truncated() + " - " + types_[1].Truncated() + " - " + types_[2].Truncated() + " - " + types_[3].Truncated()); break
         default: OUT.append(" type " + TypeString());
       }
       return OUT;

From 68b672bd9b59ca6137053e8629d1679df4f80224 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 26 Feb 2026 13:20:47 -0500
Subject: [PATCH 1395/1492] Add missing ;

---
 src/TypeNameHolder.h | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/TypeNameHolder.h b/src/TypeNameHolder.h
index 1d0a721200..5f1c8a7a61 100644
--- a/src/TypeNameHolder.h
+++ b/src/TypeNameHolder.h
@@ -128,7 +128,7 @@ class TypeNameHolder {
         case 1 : OUT.append(" type " + types_[0].Truncated()); break;
         case 2 : OUT.append(" type " + types_[0].Truncated() + " - " + types_[1].Truncated()); break;
         case 3 : OUT.append(" type " + types_[0].Truncated() + " - " + types_[1].Truncated() + " - " + types_[2].Truncated()); break;
-        case 4 : OUT.append(" type " + types_[0].Truncated() + " - " + types_[1].Truncated() + " - " + types_[2].Truncated() + " - " + types_[3].Truncated()); break
+        case 4 : OUT.append(" type " + types_[0].Truncated() + " - " + types_[1].Truncated() + " - " + types_[2].Truncated() + " - " + types_[3].Truncated()); break;
         default: OUT.append(" type " + TypeString());
       }
       return OUT;

From 488882846f250783d1675232c40b0716ad50e0ef Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 26 Feb 2026 14:46:02 -0500
Subject: [PATCH 1396/1492] Keep track of the number of missing parameters, and
 make it an error on build

---
 src/DataIO_LeapRC.cpp     |  7 +++++-
 src/Exec_Build.cpp        |  7 +++++-
 src/Exec_Sequence.cpp     |  7 +++++-
 src/Parm/AssignParams.cpp | 48 ++++++++++++++++++++++++++-------------
 src/Parm/AssignParams.h   | 12 +++++-----
 5 files changed, 56 insertions(+), 25 deletions(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 5fa572a81a..83656e1be4 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -760,10 +760,15 @@ const
   AP.SetDebug( debug_ );
   AP.SetVerbose( debug_ );
   Topology& topOut = *(crd.TopPtr());
-  if ( AP.AssignParameters( topOut, *(creator.MainParmSetPtr()) ) ) {
+  int nmissing = 0;
+  if ( AP.AssignParameters( topOut, *(creator.MainParmSetPtr()), nmissing ) ) {
     mprinterr("Error: Could not assign parameters for '%s'.\n", topOut.c_str());
     return 1;
   }
+  if (nmissing != 0) {
+    mprinterr("Error: Missing %i parameters for '%s'\n", nmissing, topOut.c_str());
+    return 1;
+  }
   // Assign GB parameters
   gbradii.GB_Info();
   if (gbradii.Assign_GB_Radii(topOut)) {
diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 57f7a398b7..04348f7267 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -1264,10 +1264,15 @@ Exec::RetType Exec_Build::BuildAndParmStructure(DataSet* inCrdPtr, std::string c
   Cpptraj::Parm::AssignParams AP;
   AP.SetDebug( debug_ );
   AP.SetVerbose( verbose );
-  if ( AP.AssignParameters( topOut, *(creator.MainParmSetPtr()) ) ) {
+  int nmissing = 0;
+  if ( AP.AssignParameters( topOut, *(creator.MainParmSetPtr()), nmissing ) ) {
     mprinterr("Error: Could not assign parameters for '%s'.\n", topOut.c_str());
     ret = CpptrajState::ERR;
   }
+  if (nmissing != 0) {
+    mprinterr("Error: Missing %i parameters for '%s'\n", nmissing, topOut.c_str());
+    ret = CpptrajState::ERR;
+  }
   // Assign GB parameters
   gbradii.GB_Info();
   if (gbradii.Assign_GB_Radii(topOut)) {
diff --git a/src/Exec_Sequence.cpp b/src/Exec_Sequence.cpp
index 43b6ce8dde..775dbe0819 100644
--- a/src/Exec_Sequence.cpp
+++ b/src/Exec_Sequence.cpp
@@ -302,10 +302,15 @@ Exec::RetType Exec_Sequence::Execute(CpptrajState& State, ArgList& argIn)
     Cpptraj::Parm::AssignParams AP;
     AP.SetDebug( debug_ );
     AP.SetVerbose( verbose );
-    if ( AP.AssignParameters( topOut, *(creator.MainParmSetPtr()) ) ) {
+    int nmissing = 0;
+    if ( AP.AssignParameters( topOut, *(creator.MainParmSetPtr()), nmissing ) ) {
       mprinterr("Error: Could not assign parameters for '%s'.\n", topOut.c_str());
       ret = CpptrajState::ERR;
     }
+    if (nmissing != 0) {
+      mprinterr("Error: Missing %i parameters for '%s'\n", nmissing, topOut.c_str());
+      ret = CpptrajState::ERR;
+    }
     // Assign GB parameters
     if (gbradii.Assign_GB_Radii( topOut )) {
       mprinterr("Error: Could not assign GB parameters for '%s'\n", topOut.c_str());
diff --git a/src/Parm/AssignParams.cpp b/src/Parm/AssignParams.cpp
index 830df02f23..ef35a443af 100644
--- a/src/Parm/AssignParams.cpp
+++ b/src/Parm/AssignParams.cpp
@@ -37,9 +37,10 @@ void AssignParams::SetVerbose(int verboseIn) {
 }
 
 /** Set parameters for atoms via given atom type parameter holder. */
-void AssignParams::AssignAtomTypeParm(AtArray& atoms, ParmHolder<AtomType> const& newAtomTypeParams)
+int AssignParams::AssignAtomTypeParm(AtArray& atoms, ParmHolder<AtomType> const& newAtomTypeParams)
 const
 {
+  int nmissing = 0;
   for (AtArray::iterator iat = atoms.begin(); iat != atoms.end(); ++iat)
   {
     bool found;
@@ -50,17 +51,21 @@ const
       iat->SetMass( AT.Mass() );
       // Update polarizability
       iat->SetPolar( AT.Polarizability() );
-    } else
+    } else {
       mprintf("Warning: Atom type parameter not found for %s\n", *atype[0]);
+      nmissing++;
+    }
   }
+  return nmissing;
 }
 
 /** Set parameters for bonds in given bond array. */
-void AssignParams::AssignBondParm(Topology const& topOut,
+int AssignParams::AssignBondParm(Topology const& topOut,
                                   ParmHolder<BondParmType> const& newBondParams,
                                   BondArray& bonds, BondParmArray& bpa, const char* desc)
 const
 {
+  int nmissing = 0;
   ParmHolder<int> currentTypes;
   for (BondArray::iterator bnd = bonds.begin(); bnd != bonds.end(); ++bnd) {
     TypeNameHolder types(2);
@@ -78,6 +83,7 @@ const
                 topOut.TruncResAtomNameNum(bnd->A1()).c_str(),
                 topOut.TruncResAtomNameNum(bnd->A2()).c_str(),
                 *types[0], *types[1]);
+        nmissing++;
       } else {
         //idx = addBondParm( bpa, bp ); TODO handle array packing
         idx = (int)bpa.size();
@@ -106,6 +112,7 @@ const
     }
     bnd->SetIdx( idx );
   }*/
+  return nmissing;
 }
 
 /** Replace any current bond parameters with given bond parameters. */
@@ -124,7 +131,8 @@ void AssignParams::AssignUBParams(Topology& topOut, ParmHolder<BondParmType> con
 /** Set parameters for angles in given angle array. */
 AngleArray AssignParams::AssignAngleParm(Topology const& topOut,
                                          ParmHolder<AngleParmType> const& newAngleParams,
-                                         AngleArray const& angles, AngleParmArray& apa)
+                                         AngleArray const& angles, AngleParmArray& apa,
+                                         int& nmissing)
 const
 {
   AngleArray newAngles;
@@ -189,6 +197,7 @@ const
                 topOut.TruncResAtomNameNum(ang->A2()).c_str(),
                 topOut.TruncResAtomNameNum(ang->A3()).c_str(),
                 *types[0], *types[1], *types[2]);
+        nmissing++;
       } else {
         //idx = addAngleParm( angleparm_, ap ); // TODO uncomment for array packing
         idx = (int)apa.size();
@@ -227,8 +236,9 @@ const
 /** Replace any current angle parameters with given angle parameters. */
 void AssignParams::AssignAngleParams(Topology& topOut, ParmHolder<AngleParmType> const& newAngleParams) const {
   topOut.ModifyAngleParm().clear();
-  topOut.ModifyAngles() = AssignAngleParm( topOut, newAngleParams, topOut.Angles(), topOut.ModifyAngleParm() );
-  topOut.ModifyAnglesH() = AssignAngleParm( topOut, newAngleParams, topOut.AnglesH(), topOut.ModifyAngleParm() );
+  int nmissing = 0;
+  topOut.ModifyAngles() = AssignAngleParm( topOut, newAngleParams, topOut.Angles(), topOut.ModifyAngleParm(), nmissing );
+  topOut.ModifyAnglesH() = AssignAngleParm( topOut, newAngleParams, topOut.AnglesH(), topOut.ModifyAngleParm(), nmissing );
 }
 
 /** Warn if improper atoms have been reordered so they match the parameter. */
@@ -304,7 +314,8 @@ DihedralArray AssignParams::AssignDihedralParm(Topology& topOut,
                                                ImproperParmHolder const& newImproperParams,
                                                ParmHolder<AtomType> const& AT,
                                                DihedralArray const& dihedrals,
-                                               bool sort_improper_cache)
+                                               bool sort_improper_cache,
+                                               int& nmissing)
 #ifndef TIMER
 const
 #endif
@@ -515,6 +526,7 @@ const
         DihedralType mydih = *dih;
         mydih.SetIdx( -1 );
         dihedralsIn.push_back( mydih );
+        nmissing++;
       } else {
         // Actually add parameters for this dihedral.
         // Determine if this is actually a 1-4 interaction by making
@@ -626,10 +638,11 @@ const
   // multiplicities for a single dihedral type. In case multiplicities
   // change, start with a fresh dihedral array containing only unique
   // dihedrals.
+  int nmissing = 0;
   topOut.ModifyDihedrals()  = AssignDihedralParm( topOut, newDihedralParams, newImproperParams,
-                                                  AT, get_unique_dihedrals(topOut.Dihedrals()), false  );
+                                                  AT, get_unique_dihedrals(topOut.Dihedrals()), false, nmissing  );
   topOut.ModifyDihedralsH() = AssignDihedralParm( topOut, newDihedralParams, newImproperParams,
-                                                  AT, get_unique_dihedrals(topOut.DihedralsH()), false );
+                                                  AT, get_unique_dihedrals(topOut.DihedralsH()), false, nmissing );
 }
 
 /** Replace current nonbond parameters with given nonbond parameters. */
@@ -1140,13 +1153,16 @@ void AssignParams::AddToDihedralArrays(Topology& topOut, DihedralType const& dih
 
 /** Replace existing parameters with the given parameter set. */
 #ifdef TIMER
-int AssignParams::AssignParameters(Topology& topOut, ParameterSet const& set0)
+int AssignParams::AssignParameters(Topology& topOut, ParameterSet const& set0, int& nmissing)
 #else
-int AssignParams::AssignParameters(Topology& topOut, ParameterSet const& set0) const
+int AssignParams::AssignParameters(Topology& topOut, ParameterSet const& set0, int& nmissing) const
 #endif
 {
 # ifdef TIMER
   t_total_.Start();
+#endif
+  nmissing = 0;
+# ifdef TIMER
   t_bonds_.Start();
 # endif
   // Bond parameters
@@ -1156,7 +1172,7 @@ int AssignParams::AssignParameters(Topology& topOut, ParameterSet const& set0) c
   topOut.ModifyBonds().clear();
   topOut.ModifyBondsH().clear();
   BondArray allBonds = Cpptraj::Structure::GenerateBondArray(topOut.Residues(), topOut.Atoms());
-  AssignBondParm( topOut, set0.BP(), allBonds, topOut.ModifyBondParm(), "bond" );
+  nmissing += AssignBondParm( topOut, set0.BP(), allBonds, topOut.ModifyBondParm(), "bond" );
   for (BondArray::const_iterator bnd = allBonds.begin(); bnd != allBonds.end(); ++bnd)
     AddToBondArrays( topOut, *bnd );
 # ifdef TIMER
@@ -1170,7 +1186,7 @@ int AssignParams::AssignParameters(Topology& topOut, ParameterSet const& set0) c
   topOut.ModifyAngles().clear();
   topOut.ModifyAnglesH().clear();
   AngleArray allAngles = Cpptraj::Structure::GenerateAngleArray(topOut.Residues(), topOut.Atoms());
-  allAngles = AssignAngleParm( topOut, set0.AP(), allAngles, topOut.ModifyAngleParm() );
+  allAngles = AssignAngleParm( topOut, set0.AP(), allAngles, topOut.ModifyAngleParm(), nmissing );
   for (AngleArray::const_iterator ang = allAngles.begin(); ang != allAngles.end(); ++ang)
     AddToAngleArrays( topOut, *ang );
 # ifdef TIMER
@@ -1204,7 +1220,7 @@ int AssignParams::AssignParameters(Topology& topOut, ParameterSet const& set0) c
 # ifdef TIMER
   t_multi_.Start();
 # endif
-  allDihedrals = AssignDihedralParm( topOut, set0.DP(), set0.IP(), set0.AT(), allDihedrals, false );
+  allDihedrals = AssignDihedralParm( topOut, set0.DP(), set0.IP(), set0.AT(), allDihedrals, false, nmissing );
   for (DihedralArray::const_iterator dih = allDihedrals.begin(); dih != allDihedrals.end(); ++dih)
     AddToDihedralArrays( topOut, *dih );
 # ifdef TIMER
@@ -1226,7 +1242,7 @@ int AssignParams::AssignParameters(Topology& topOut, ParameterSet const& set0) c
     // Amber improper parameters
     mprintf("\tAssigning improper parameters.\n");
     DihedralArray allImpropers = Cpptraj::Structure::GenerateImproperArray(topOut.Residues(), topOut.Atoms());
-    allImpropers = AssignDihedralParm( topOut, set0.DP(), set0.IP(), set0.AT(), allImpropers, true );
+    allImpropers = AssignDihedralParm( topOut, set0.DP(), set0.IP(), set0.AT(), allImpropers, true, nmissing );
     for (DihedralArray::const_iterator imp = allImpropers.begin(); imp != allImpropers.end(); ++imp)
       AddToDihedralArrays( topOut, *imp );
   }
@@ -1236,7 +1252,7 @@ int AssignParams::AssignParameters(Topology& topOut, ParameterSet const& set0) c
 # endif
   // Atom types
   mprintf("\tAssigning atom type parameters.\n");
-  AssignAtomTypeParm( topOut.ModifyAtoms(), set0.AT() );
+  nmissing += AssignAtomTypeParm( topOut.ModifyAtoms(), set0.AT() );
 # ifdef TIMER
   t_atype_.Stop();
   t_nonbond_.Start();
diff --git a/src/Parm/AssignParams.h b/src/Parm/AssignParams.h
index 8269720a57..327ad7bd48 100644
--- a/src/Parm/AssignParams.h
+++ b/src/Parm/AssignParams.h
@@ -41,9 +41,9 @@ class AssignParams {
     void SetVerbose(int);
     /// Replace existing parameters with those from given set
 #   ifdef TIMER
-    int AssignParameters(Topology&, ParameterSet const&);
+    int AssignParameters(Topology&, ParameterSet const&, int&);
 #   else
-    int AssignParameters(Topology&, ParameterSet const&) const;
+    int AssignParameters(Topology&, ParameterSet const&, int&) const;
 #   endif
     /// Update existing parameters with given parameter set
     int UpdateParameters(Topology&, ParameterSet const&)
@@ -61,14 +61,14 @@ class AssignParams {
   private:
     typedef std::vector<Atom> AtArray;
 
-    void AssignAtomTypeParm(AtArray&, ParmHolder<AtomType> const&) const;
-    void AssignBondParm(Topology const&, ParmHolder<BondParmType> const&,
+    int AssignAtomTypeParm(AtArray&, ParmHolder<AtomType> const&) const;
+    int AssignBondParm(Topology const&, ParmHolder<BondParmType> const&,
                         BondArray&, BondParmArray&, const char*) const;
     void AssignBondParams(Topology&, ParmHolder<BondParmType> const&) const;
     void AssignUBParams(Topology&, ParmHolder<BondParmType> const&) const;
 
     AngleArray AssignAngleParm(Topology const&, ParmHolder<AngleParmType> const&,
-                               AngleArray const&, AngleParmArray&) const;
+                               AngleArray const&, AngleParmArray&, int&) const;
     void AssignAngleParams(Topology&, ParmHolder<AngleParmType> const&) const;
 
     void warn_improper_reorder(AtArray const&, DihedralType const&, DihedralType const&) const;
@@ -79,7 +79,7 @@ class AssignParams {
     DihedralArray AssignDihedralParm(Topology&,
                                      DihedralParmHolder const&, ImproperParmHolder const&,
                                      ParmHolder<AtomType> const&, DihedralArray const&,
-                                     bool)  // TODO make the bool a class var?
+                                     bool, int&)  // TODO make the bool a class var?
 #   ifdef TIMER
       ;
 #   else

From e45b8054ad4bafab0e5dd013bc2383b10514a573 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 27 Feb 2026 08:42:48 -0500
Subject: [PATCH 1397/1492] Have make depend trigger subdirectory make depend
 as well

---
 src/Makefile | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/Makefile b/src/Makefile
index 386e0b5794..9ba86b1096 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -155,6 +155,10 @@ findDepend: FindDepend.cpp FindDepend.o
 	$(CXX) -o findDepend FindDepend.o
 
 depend: findDepend
+	cd Cluster && $(MAKE) depend
+	cd Structure && $(MAKE) depend
+	cd Parm && $(MAKE) depend
+	cd Energy && $(MAKE) depend
 	./findDepend $(SOURCES) $(CSOURCES) $(CLUSTER_SOURCEFILES) $(STRUCTURE_SOURCEFILES) $(PARM_SOURCEFILES) $(ENERGY_SOURCEFILES) > cpptrajdepend
 
 dependclean:

From e4d97359b9d907e1cebda9baf6bf054c8deb3bb0 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 27 Feb 2026 08:47:00 -0500
Subject: [PATCH 1398/1492] Add small note about system build capability.
 Upgrade to lyx 2.4.

---
 doc/cpptraj.lyx | 10181 +++++++++++++++++++++++++---------------------
 1 file changed, 5509 insertions(+), 4672 deletions(-)

diff --git a/doc/cpptraj.lyx b/doc/cpptraj.lyx
index db07f2c5fd..13d137fefc 100644
--- a/doc/cpptraj.lyx
+++ b/doc/cpptraj.lyx
@@ -1,5 +1,5 @@
-#LyX 2.3 created this file. For more info see http://www.lyx.org/
-\lyxformat 544
+#LyX 2.4 created this file. For more info see https://www.lyx.org/
+\lyxformat 620
 \begin_document
 \begin_header
 \save_transient_properties true
@@ -9,11 +9,11 @@
 \usepackage{varwidth}
 \end_preamble
 \use_default_options true
-\maintain_unincluded_children false
+\maintain_unincluded_children no
 \language english
 \language_package default
-\inputencoding auto
-\fontencoding global
+\inputencoding auto-legacy
+\fontencoding auto
 \font_roman "default" "default"
 \font_sans "default" "default"
 \font_typewriter "default" "default"
@@ -21,7 +21,9 @@
 \font_default_family default
 \use_non_tex_fonts false
 \font_sc false
-\font_osf false
+\font_roman_osf false
+\font_sans_osf false
+\font_typewriter_osf false
 \font_sf_scale 100 100
 \font_tt_scale 100 100
 \use_microtype false
@@ -65,7 +67,9 @@
 \suppress_date false
 \justification true
 \use_refstyle 1
+\use_formatted_ref 0
 \use_minted 0
+\use_lineno 0
 \index Index
 \shortcut idx
 \color #008000
@@ -81,11 +85,16 @@
 \papercolumns 1
 \papersides 1
 \paperpagestyle default
+\tablestyle default
 \tracking_changes false
 \output_changes false
+\change_bars false
+\postpone_fragile_content false
 \html_math_output 0
 \html_css_as_file 0
 \html_be_strict false
+\docbook_table_output 0
+\docbook_mathml_prefix 1
 \end_header
 
 \begin_body
@@ -111,15 +120,14 @@ literal "true"
 \emph on
 ptraj
 \emph default
-) is the main program in Amber for processing coordinate trajectories and
- data files.
+) is the main program in Amber for processing coordinate trajectories and data files.
  
 \shape italic
 Cpptraj
 \shape default
- has a wide range of functionality, and makes use of OpenMP/MPI to speed
- up many calculations, including processing ensembles of trajectories and/or
- conducting multiple analyses in parallel with MPI.
+ has a wide range of functionality,
+ and makes use of OpenMP/MPI to speed up many calculations,
+ including processing ensembles of trajectories and/or conducting multiple analyses in parallel with MPI.
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Roe2018"
@@ -147,50 +155,65 @@ Several actions/analyses in
 \emph on
 cpptraj
 \emph default
- are OpenMP parallelized; see section 
+ are OpenMP parallelized;
+ see section 
 \begin_inset CommandInset ref
 LatexCommand ref
 reference "subsec:CpptrajOpenMP"
+nolink "false"
 
 \end_inset
 
  for more details.
 \end_layout
 
+\begin_layout Enumerate
+In addition to processing single trajectories,
+ can read,
+ process,
+ and write ensembles of trajectories at the same time (from e.g.
+ REMD).
+\end_layout
+
 \begin_layout Enumerate
 Trajectory and ensemble reads can be MPI parallelized.
 \end_layout
 
+\begin_layout Enumerate
+As of version 7.0 has the ability to fully build and parameterize systems for MD simulations,
+ including the addition of solvent and ions (similar to the LEaP program from AmberTools).
+\end_layout
+
 \begin_layout Enumerate
 Almost any file read or written by 
 \emph on
 cpptraj
 \emph default
  can be compressed (with the exception of the NetCDF trajectory format).
- So for example gzipped/bzipped topology files can be read, and data files
- can be written out as gzip/bzip2 files.
- Compression is detected automatically when reading, and is determined by
- the filename extension (.gz and .bz2 respectively) on writing.
+ So for example gzipped/bzipped topology files can be read,
+ and data files can be written out as gzip/bzip2 files.
+ Compression is detected automatically when reading,
+ and is determined by the filename extension (.gz and .bz2 respectively) on writing.
 \end_layout
 
 \begin_layout Enumerate
 The format of output data files can be specified by extension.
- For example, data files can be written in xmgrace format if the filename
- given has a '.agr' extension.
+ For example,
+ data files can be written in xmgrace format if the filename given has a '.agr' extension.
  A trajectory can be written in DCD format if the '.dcd' extension is used.
 \end_layout
 
 \begin_layout Enumerate
-Multiple output trajectories can be specified, and can be written during
- action processing (as opposed to only after) via the 
+Multiple output trajectories can be specified,
+ and can be written during action processing (as opposed to only after) via the 
 \series bold
 \shape italic
 outtraj
 \series default
 \shape default
  command.
- In addition, output files can be directed to write only specific frames
- from the input trajectories.
+ In addition,
+ output files can be directed to write only specific frames from the input trajectories.
 \end_layout
 
 \begin_layout Enumerate
@@ -206,7 +229,8 @@ rmsd
 \series default
 \shape default
  action allows specification of a separate mask for the reference structure.
- In addition, per-residue RMSD can be calculated easily.
+ In addition,
+ per-residue RMSD can be calculated easily.
  
 \end_layout
 
@@ -223,14 +247,12 @@ strip
 closest
 \series default
 \shape default
- actions can often write an accompanying fully-functional stripped topology
- file.
+ actions can often write an accompanying fully-functional stripped topology file.
  
 \end_layout
 
 \begin_layout Enumerate
-Users usually are able to fine-tune the output format of data files declared
- in actions using the 
+Users usually are able to fine-tune the output format of data files declared in actions using the 
 \begin_inset Quotes eld
 \end_inset
 
@@ -242,19 +264,21 @@ out
 \begin_inset Quotes erd
 \end_inset
 
- keyword (for example, the precision of the numbers can be changed).
- In addition, users can control which data sets are written to which files
- (e.g.
- if two actions specify the same data file with the 'out' keyword, data
- from both actions will be written to that data file).
+ keyword (for example,
+ the precision of the numbers can be changed).
+ In addition,
+ users can control which data sets are written to which files (e.g.
+ if two actions specify the same data file with the 'out' keyword,
+ data from both actions will be written to that data file).
 \end_layout
 
 \begin_layout Enumerate
-Users can manipulate data sets using mathematical expressions (with some
- limitations), see 
+Users can manipulate data sets using mathematical expressions (with some limitations),
+ see 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-Data-Set-Math"
+nolink "false"
 
 \end_inset
 
@@ -269,13 +293,15 @@ There is some support for creating internal loops over e.g.
 for
 \series default
 \emph default
-, 
+,
+ 
 \series bold
 \emph on
 set
 \series default
 \emph default
-, and 
+,
+ and 
 \series bold
 \emph on
 show
@@ -289,7 +315,9 @@ See the README.md file in the
 \emph on
 cpptraj
 \emph default
- home directory for information on how to build, authors, and so on.
+ home directory for information on how to build,
+ authors,
+ and so on.
 \end_layout
 
 \begin_layout Subsection
@@ -309,8 +337,8 @@ The syntax presented in this manual uses the following conventions:
 \end_layout
 
 \begin_layout Description
-{|} Denotes several choices separated by the '|' character; one of the choices
- must be specified.
+{|} Denotes several choices separated by the '|' character;
+ one of the choices must be specified.
 \end_layout
 
 \begin_layout Description
@@ -328,8 +356,8 @@ Installation
 \end_layout
 
 \begin_layout Standard
-See instructions in the CPPTRAJ GitHub repository README.md file under 'Installat
-ion & Testing': 
+See instructions in the CPPTRAJ GitHub repository README.md file under 'Installation & Testing':
+ 
 \begin_inset Flex URL
 status open
 
@@ -455,7 +483,8 @@ cpptraj [-p <Top0>] [-i <Input0>] [-y <trajin>] [-x <trajout>]
 \begin_inset space ~
 \end_inset
 
-<trajin>* Read from trajectory file <trajin>; same as input 'trajin <trajin>'.
+<trajin>* Read from trajectory file <trajin>;
+ same as input 'trajin <trajin>'.
 \end_layout
 
 \begin_layout Description
@@ -463,7 +492,8 @@ cpptraj [-p <Top0>] [-i <Input0>] [-y <trajin>] [-x <trajout>]
 \begin_inset space ~
 \end_inset
 
-<trajout>* Write trajectory file <trajout>; same as input 'trajout <trajout>'.
+<trajout>* Write trajectory file <trajout>;
+ same as input 'trajout <trajout>'.
 \end_layout
 
 \begin_layout Description
@@ -483,7 +513,9 @@ cpptraj [-p <Top0>] [-i <Input0>] [-y <trajin>] [-x <trajout>]
 \end_layout
 
 \begin_layout Description
-<file>* A topology, input trajectory, or file containing cpptraj input.
+<file>* A topology,
+ input trajectory,
+ or file containing cpptraj input.
 \end_layout
 
 \begin_layout Description
@@ -491,8 +523,8 @@ cpptraj [-p <Top0>] [-i <Input0>] [-y <trajin>] [-x <trajout>]
 \begin_inset space ~
 \end_inset
 
-<reference>* Read <reference> as reference coordinates; same as input 'reference
- <reference>'.
+<reference>* Read <reference> as reference coordinates;
+ same as input 'reference <reference>'.
 \end_layout
 
 \begin_layout Description
@@ -552,7 +584,8 @@ cpptraj [-p <Top0>] [-i <Input0>] [-y <trajin>] [-x <trajout>]
 \begin_inset space ~
 \end_inset
 
-<#> Set global debug level to <#>; same as input 'debug <#>'.
+<#> Set global debug level to <#>;
+ same as input 'debug <#>'.
 \end_layout
 
 \begin_layout Description
@@ -570,7 +603,8 @@ cpptraj [-p <Top0>] [-i <Input0>] [-y <trajin>] [-x <trajout>]
 
 \begin_layout Description
 -tl Print length of trajectories specified with '-y' to STDOUT.
- The total number of frames is written out as 'Frames: <X>'
+ The total number of frames is written out as 'Frames:
+ <X>'
 \end_layout
 
 \begin_layout Description
@@ -587,7 +621,8 @@ cpptraj [-p <Top0>] [-i <Input0>] [-y <trajin>] [-x <trajout>]
 \begin_inset space ~
 \end_inset
 
-<mask> : Print selected residue numbers to STDOUT.
+<mask> :
+ Print selected residue numbers to STDOUT.
  Selected residues are written out as 'Selected= 1 2 3 ...'
 \end_layout
 
@@ -629,14 +664,13 @@ Note that unlike
 \shape italic
 ptraj
 \shape default
-, in 
+,
+ in 
 \shape italic
 cpptraj
 \shape default
- it is not required that a topology file be specified on the command line
- as long as one is specified in the input file with the 'parm' keyword.
- Multiple topology/input files can be specified by use of multiple '-p'
- and '-i' flags.
+ it is not required that a topology file be specified on the command line as long as one is specified in the input file with the 'parm' keyword.
+ Multiple topology/input files can be specified by use of multiple '-p' and '-i' flags.
  All topology and coordinate flags will be processed before any input flags.
 \end_layout
 
@@ -649,11 +683,12 @@ Input to
 \shape italic
 cpptraj
 \shape default
- is in the form of commands, which can be categorized in to 2 types: immediate
- and queued.
+ is in the form of commands,
+ which can be categorized in to 2 types:
+ immediate and queued.
  Immediate commands are executed as soon as they are encountered.
- Queued commands are initialized when they are encountered, but are not
- executed until a Run is executed via a 
+ Queued commands are initialized when they are encountered,
+ but are not executed until a Run is executed via a 
 \series bold
 \shape italic
 run
@@ -666,19 +701,23 @@ go
 \series default
 \shape default
  command.
- Actions, Analyses, and Trajectory commands (except 
+ Actions,
+ Analyses,
+ and Trajectory commands (except 
 \series bold
 \emph on
 reference
 \series default
 \emph default
-) are queued commands; however, they can also be run immediately via commands
- such as 
+) are queued commands;
+ however,
+ they can also be run immediately via commands such as 
 \series bold
 \shape italic
 crdaction
 \series default
 ,
+
 \shape default
  
 \series bold
@@ -686,6 +725,7 @@ crdaction
 runanalysis
 \series default
 ,
+
 \shape default
  
 \series bold
@@ -693,11 +733,13 @@ runanalysis
 loadcrd
 \series default
 \emph default
-, etc.
+,
+ etc.
  See 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "sec:Coordinates-as-a"
+nolink "false"
 
 \end_inset
 
@@ -714,7 +756,9 @@ General (Immediate) These commands are executed immediately when entered.
 
 \begin_layout Description
 System (Immediate) These are unix system commands (e.g.
- 'ls', 'pwd', etc).
+ 'ls',
+ 'pwd',
+ etc).
 \end_layout
 
 \begin_layout Description
@@ -723,6 +767,7 @@ Coords (Immediate) These commands are used to manipulate COORDS data sets;
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "sec:Coordinates-as-a"
+nolink "false"
 
 \end_inset
 
@@ -730,43 +775,41 @@ reference "sec:Coordinates-as-a"
 \end_layout
 
 \begin_layout Description
-Trajectory (Queued) These commands prepare cpptraj for reading or writing
- trajectories during a Run.
+Trajectory (Queued) These commands prepare cpptraj for reading or writing trajectories during a Run.
 \end_layout
 
 \begin_layout Description
-Topology (Immediate) These commands are used to read, write, and modify
- topology information.
+Topology (Immediate) These commands are used to read,
+ write,
+ and modify topology information.
 \end_layout
 
 \begin_layout Description
-Action (Queued) These commands specify actions that will be performed on
- coordinate frames read in from trajectories during a Run.
+Action (Queued) These commands specify actions that will be performed on coordinate frames read in from trajectories during a Run.
 \end_layout
 
 \begin_layout Description
-Analysis (Queued) These commands specify analyses that will be performed
- on data that has been either generated from a Run or read in from an external
- source.
+Analysis (Queued) These commands specify analyses that will be performed on data that has been either generated from a Run or read in from an external source.
 \end_layout
 
 \begin_layout Description
-Control (Immediate) These commands set up control blocks that can be used
- to e.g.
+Control (Immediate) These commands set up control blocks that can be used to e.g.
  loop over a set of commands.
 \end_layout
 
 \begin_layout Standard
-In addition to normal commands, 
+In addition to normal commands,
+ 
 \emph on
 cpptraj
 \emph default
- now has the ability to perform certain basic math operations, even on data
- sets.
+ now has the ability to perform certain basic math operations,
+ even on data sets.
  See 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-Data-Set-Math"
+nolink "false"
 
 \end_inset
 
@@ -779,12 +822,13 @@ Commands in
 cpptraj
 \shape default
  can be read in from an input file or from the interactive command prompt.
- A '#' anywhere on a line denotes a comment; anything after '#' will be
- ignored no matter where it occurs.
+ A '#' anywhere on a line denotes a comment;
+ anything after '#' will be ignored no matter where it occurs.
  A '
 \backslash
 ' allows the continuation of one line to another.
- For example, the input:
+ For example,
+ the input:
 \end_layout
 
 \begin_layout LyX-Code
@@ -822,13 +866,11 @@ Getting Help
 \end_layout
 
 \begin_layout Standard
-If in interactive mode, the 'help' command can be used to list recognized
- commands and topics; topics (such as mask syntax) start with uppercase
- letters.
- 'help <command>' can be used to get the associated keywords as well as
- an abbreviated description of the command.
- Most commands have a corresponding test which also serves as an example
- of how to use the command.
+If in interactive mode,
+ the 'help' command can be used to list recognized commands and topics;
+ topics (such as mask syntax) start with uppercase letters.
+ 'help <command>' can be used to get the associated keywords as well as an abbreviated description of the command.
+ Most commands have a corresponding test which also serves as an example of how to use the command.
  See $AMBERHOME/AmberTools/test/cpptraj/README for more details.
 \end_layout
 
@@ -845,8 +887,8 @@ batch
 \begin_inset Quotes erd
 \end_inset
 
- mode, cpptraj is executed from the command line with one or more input
- files containing commands to be processed or STDIN.
+ mode,
+ cpptraj is executed from the command line with one or more input files containing commands to be processed or STDIN.
  The syntax of <input file> is similar to that of 
 \shape italic
 ptraj
@@ -874,13 +916,14 @@ interactive mode
 \end_inset
 
  users can enter commands in a UNIX-like shell.
- Interactive mode is useful for running short and simple analyses or for
- trying out new kinds of analyses.
+ Interactive mode is useful for running short and simple analyses or for trying out new kinds of analyses.
  If 
 \emph on
 cpptraj
 \emph default
- is run with '–interactive', no arguments, or no specified input file:
+ is run with '–interactive',
+ no arguments,
+ or no specified input file:
 \end_layout
 
 \begin_layout LyX-Code
@@ -901,13 +944,12 @@ cpptraj -p <parm file>
 
 \begin_layout Standard
 this brings up the interactive interface.
- This interface supports command history (via the up and down arrows) and
- tab completion for commands and file names.
- If no log file name has been given (with '–log <logfile>'), all commands
- used in interactive mode will be logged to a file named 'cpptraj.log', which
- can subsequently be used as input if desired.
- When starting cpptraj, command histories will be read from any existing
- logs.
+ This interface supports command history (via the up and down arrows) and tab completion for commands and file names.
+ If no log file name has been given (with '–log <logfile>'),
+ all commands used in interactive mode will be logged to a file named 'cpptraj.log',
+ which can subsequently be used as input if desired.
+ When starting cpptraj,
+ command histories will be read from any existing logs.
 \end_layout
 
 \begin_layout Subsection
@@ -927,7 +969,8 @@ Like
 \shape italic
 ptraj
 \shape default
-, a trajectory processing 
+,
+ a trajectory processing 
 \begin_inset Quotes eld
 \end_inset
 
@@ -940,14 +983,13 @@ Run
 cpptraj
 \shape default
 .
- First the Run is set up via commands read in from an input file or the
- interactive prompt.
- Trajectories are then read in one frame at a time (or in the case of ensemble
- processing all frames from a given step are read).
- Actions are performed on the coordinates stored in the frame, after which
- any output coordinates are written.
- At the end of the run, any data sets generated are written, and any queued
- Analyses are performed.
+ First the Run is set up via commands read in from an input file or the interactive prompt.
+ Trajectories are then read in one frame at a time (or in the case of ensemble processing all frames from a given step are read).
+ Actions are performed on the coordinates stored in the frame,
+ after which any output coordinates are written.
+ At the end of the run,
+ any data sets generated are written,
+ and any queued Analyses are performed.
 \end_layout
 
 \begin_layout Subsubsection
@@ -959,14 +1001,12 @@ Since
 \emph on
 cpptraj
 \emph default
- supports multiple topology files, during a Run actions are set up every
- time the topology changes in order to recalculate things like what atoms
- are in a mask etc.
- Actions that are not valid for the current topology are skipped for that
- topology.
- So for example given two topology files with 100 residues, if the first
- topology file processed includes a ligand named MOL and the second one
- does not, the action:
+ supports multiple topology files,
+ during a Run actions are set up every time the topology changes in order to recalculate things like what atoms are in a mask etc.
+ Actions that are not valid for the current topology are skipped for that topology.
+ So for example given two topology files with 100 residues,
+ if the first topology file processed includes a ligand named MOL and the second one does not,
+ the action:
 \end_layout
 
 \begin_layout LyX-Code
@@ -974,8 +1014,8 @@ distance :80 :MOL out D_80-to-MOL.dat
 \end_layout
 
 \begin_layout Standard
-will be valid for the first topology but not for the second, so it will
- be skipped as long as the second topology is active.
+will be valid for the first topology but not for the second,
+ so it will be skipped as long as the second topology is active.
 \end_layout
 
 \begin_layout Subsection
@@ -988,20 +1028,22 @@ Parallelization
 Cpptraj
 \emph default
  has many levels of parallelization that can be enabled via the '-mpi',
- '-openmp', and/or '-cuda' configure flags for MPI, OpenMP, and CUDA paralleliza
-tion respectively.
- At the highest level, trajectory and ensemble reads are parallelized with
- MPI.
- In addition, certain time consuming actions have been parallelized with
- OpenMP and/or CUDA.
+ '-openmp',
+ and/or '-cuda' configure flags for MPI,
+ OpenMP,
+ and CUDA parallelization respectively.
+ At the highest level,
+ trajectory and ensemble reads are parallelized with MPI.
+ In addition,
+ certain time consuming actions have been parallelized with OpenMP and/or CUDA.
 \end_layout
 
 \begin_layout Standard
-Note that any combination of the '-openmp', '-cuda', and '-mpi' flags may
- be used to generate a hybrid MPI/OpenMP/CUDA binary; however this may require
- additional runtime setup (e.g.
- setting OMP_NUM_THREADS for OpenMP) to work properly and not oversubscribe
- cores.
+Note that any combination of the '-openmp',
+ '-cuda',
+ and '-mpi' flags may be used to generate a hybrid MPI/OpenMP/CUDA binary;
+ however this may require additional runtime setup (e.g.
+ setting OMP_NUM_THREADS for OpenMP) to work properly and not oversubscribe cores.
 \end_layout
 
 \begin_layout Subsubsection
@@ -1027,62 +1069,72 @@ Cpptraj
 trajin
 \series default
 \emph default
-' trajectory input, where the trajectory read is divided as evenly as possible
- among all input frames (across-trajectory parallelism).
- For example, if given two trajectories of 1000 frames each and 4 MPI processes,
- process 0 reads frames 1-500 of trajectory 1, process 1 reads frames 501-1000
- of trajectory 1, process 2 reads frames 1-500 of trajectory 2, and process
- 3 reads frames 501-1000 of trajectory 2.
- Most Actions will work with across-trajectory parallelization with the
- exception of the following: 
+' trajectory input,
+ where the trajectory read is divided as evenly as possible among all input frames (across-trajectory parallelism).
+ For example,
+ if given two trajectories of 1000 frames each and 4 MPI processes,
+ process 0 reads frames 1-500 of trajectory 1,
+ process 1 reads frames 501-1000 of trajectory 1,
+ process 2 reads frames 1-500 of trajectory 2,
+ and process 3 reads frames 501-1000 of trajectory 2.
+ Most Actions will work with across-trajectory parallelization with the exception of the following:
+ 
 \series bold
 \emph on
 'clusterdihedral'
 \series default
 \emph default
-, 
+,
+ 
 \series bold
 \emph on
 'contacts'
 \series default
 \emph default
-, 
+,
+ 
 \series bold
 \emph on
 'createreservoir'
 \series default
 \emph default
-, 
+,
+ 
 \series bold
 \emph on
 'lipidorder'
 \series default
 \emph default
-, 
+,
+ 
 \series bold
 \emph on
 'pairwise'
 \series default
 \emph default
-, 
+,
+ 
 \series bold
 \emph on
 'stfcdiffusion'
 \series default
 \emph default
-, 
+,
+ 
 \series bold
 \emph on
 'tordiff'
 \series default
 \emph default
-, 
+,
+ 
 \series bold
 \emph on
 'unwrap'
 \series default
 \emph default
-, and 
+,
+ and 
 \series bold
 \emph on
 'xtalsymm'
@@ -1095,19 +1147,18 @@ trajin
 'diffusion'
 \series default
 \emph default
- Action will only work with across-trajectory parallelism if no imaging
- is to be performed.
+ Action will only work with across-trajectory parallelism if no imaging is to be performed.
 \end_layout
 
 \begin_layout Standard
-In addition to across-trajectory parallelism, the 
+In addition to across-trajectory parallelism,
+ the 
 \series bold
 \emph on
 'gist'
 \series default
 \emph default
- command will also MPI-parallelize the entropy calculation that occurs after
- trajectory processing.
+ command will also MPI-parallelize the entropy calculation that occurs after trajectory processing.
 \end_layout
 
 \begin_layout Standard
@@ -1120,28 +1171,28 @@ The second is for
 'ensemble'
 \series default
 \shape default
- trajectory input, where the reading/processing/writing of each member of
- the ensemble is divided up among MPI processes.
+ trajectory input,
+ where the reading/processing/writing of each member of the ensemble is divided up among MPI processes.
  The number of MPI processes must be a multiple of the ensemble size.
- If the number of processes is greater than the ensemble size then the processin
-g of each ensemble member will be divided among MPI processes (i.e.
+ If the number of processes is greater than the ensemble size then the processing of each ensemble member will be divided among MPI processes (i.e.
  across-trajectory parallelism will be used).
- For example, given an ensemble of 4 trajectories and 8 processes, processes
- 0 and 1 are assigned to the first ensemble trajectory, processes 2 and
- 3 are assigned to the second ensemble trajectory, and so on.
+ For example,
+ given an ensemble of 4 trajectories and 8 processes,
+ processes 0 and 1 are assigned to the first ensemble trajectory,
+ processes 2 and 3 are assigned to the second ensemble trajectory,
+ and so on.
  When using ensemble mode in parallel it is recommended that the 
 \series bold
 \emph on
 ensemblesize
 \series default
 \emph default
- command be used prior to any ensemble command as this will make set up
- far more efficient.
+ command be used prior to any ensemble command as this will make set up far more efficient.
 \end_layout
 
 \begin_layout Standard
-Note that most Analyses are not MPI-parallelized, with the exception of
- the 
+Note that most Analyses are not MPI-parallelized,
+ with the exception of the 
 \series bold
 \emph on
 calcdiffusion
@@ -1154,6 +1205,7 @@ reference "subsec:cpptraj-calcdiffusion"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
@@ -1161,7 +1213,8 @@ noprefix "false"
 \end_layout
 
 \begin_layout Standard
-In order to use the MPI version, Amber/
+In order to use the MPI version,
+ Amber/
 \emph on
 cpptraj
 \emph default
@@ -1170,8 +1223,9 @@ cpptraj
 \emph on
 cpptraj
 \emph default
- has been compiled with MPI as it will print 'MPI' in the title, and/or
- by calling 'cpptraj —defines' and looking for '-DMPI'.
+ has been compiled with MPI as it will print 'MPI' in the title,
+ and/or by calling 'cpptraj —
+defines' and looking for '-DMPI'.
  
 \end_layout
 
@@ -1191,8 +1245,7 @@ Some of the more time-consuming actions/analyses in
 \shape italic
 cpptraj
 \shape default
- have been parallelized with OpenMP to take advantage of machines with multiple
- cores.
+ have been parallelized with OpenMP to take advantage of machines with multiple cores.
  In order to use OpenMP parallelization Amber/
 \emph on
 cpptraj
@@ -1202,8 +1255,9 @@ cpptraj
 \shape italic
 cpptraj
 \shape default
- has been compiled with OpenMP as it will print 'OpenMP' in the title, and/or
- by calling 'cpptraj —defines' and looking for '-D_OPENMP'.
+ has been compiled with OpenMP as it will print 'OpenMP' in the title,
+ and/or by calling 'cpptraj —
+defines' and looking for '-D_OPENMP'.
  The following actions/analyses have been OpenMP parallelized:
 \end_layout
 
@@ -1325,8 +1379,7 @@ By default OpenMP
 cpptraj
 \shape default
  will use all available cores.
- The number of OpenMP threads can be controlled by setting the OMP_NUM_THREADS
- environment variable.
+ The number of OpenMP threads can be controlled by setting the OMP_NUM_THREADS environment variable.
 \end_layout
 
 \begin_layout Subsubsection
@@ -1334,13 +1387,11 @@ CUDA Parallelization
 \end_layout
 
 \begin_layout Standard
-Some time-consuming actions in cpptraj have been parallelized with CUDA
- to take advantage of machines with NVIDIA GPUs.
- In order to use CUDA parallelization Amber/cpptraj should be configured
- with the '-cuda' flag.
- You can easily tell if cpptraj has been compiled with CUDA as it will print
- 'CUDA' and details on the current graphics device in the title, and/or
- by calling 'cpptraj —defines' and looking for '-DCUDA'.
+Some time-consuming actions in cpptraj have been parallelized with CUDA to take advantage of machines with NVIDIA GPUs.
+ In order to use CUDA parallelization Amber/cpptraj should be configured with the '-cuda' flag.
+ You can easily tell if cpptraj has been compiled with CUDA as it will print 'CUDA' and details on the current graphics device in the title,
+ and/or by calling 'cpptraj —
+defines' and looking for '-DCUDA'.
  The following actions have been CUDA parallelized:
 \end_layout
 
@@ -1370,8 +1421,8 @@ Units
 
 \begin_layout Standard
 Cpptraj uses the AKMA system of units.
- The execption is time, which is typically expressed in ps (except where
- noted).
+ The execption is time,
+ which is typically expressed in ps (except where noted).
 \begin_inset Separator latexpar
 \end_inset
 
@@ -1550,16 +1601,17 @@ ptraj
 \family typewriter
 :
 \family default
-', '
+',
+ '
 \family typewriter
 @
 \family default
-', and '
+',
+ and '
 \family typewriter
 *
 \family default
-' are reserved for masks and should not be used in output file or data set
- names.
+' are reserved for masks and should not be used in output file or data set names.
  All masks are case-sensitive.
  Either names or numbers can be used.
  Masks can contain ranges (denoted with '
@@ -1571,11 +1623,13 @@ ptraj
 \family typewriter
 &
 \family default
-' (and), '
+' (and),
+ '
 \family typewriter
 |
 \family default
-' (or), and '
+' (or),
+ and '
 \family typewriter
 !
 \family default
@@ -1593,7 +1647,9 @@ The syntax for elementary selections is the following:
 \end_inset
 
 numlist} e.g.
- '@12,17', '@54-85', '@12,54-85,90'
+ '@12,17',
+ '@54-85',
+ '@12,54-85,90'
 \end_layout
 
 \begin_layout Description
@@ -1602,7 +1658,8 @@ numlist} e.g.
 \end_inset
 
 namelist} e.g.
- '@CA', '@CA,C,O,N,H'
+ '@CA',
+ '@CA,C,O,N,H'
 \end_layout
 
 \begin_layout Description
@@ -1629,7 +1686,9 @@ name} e.g.
 \end_inset
 
 numlist} e.g.
- ':1-10', ':1,3,5', ':1-3,5,7-9'
+ ':1-10',
+ ':1,3,5',
+ ':1-3,5,7-9'
 \end_layout
 
 \begin_layout Description
@@ -1638,7 +1697,8 @@ numlist} e.g.
 \end_inset
 
 namelist} e.g.
- ':LYS', ':ARG,ALA,GLY'
+ ':LYS',
+ ':ARG,ALA,GLY'
 \end_layout
 
 \begin_layout Description
@@ -1647,7 +1707,8 @@ namelist} e.g.
 \end_inset
 
 id} e.g.
- '::B', '::A,D'.
+ '::B',
+ '::A,D'.
  Requires chain ID information be present in the topology.
 \end_layout
 
@@ -1662,11 +1723,12 @@ residue
 
 number} e.g.
  ':;2-4,8'.
- Requires a PDB loaded as topology, or Amber topology with embedded PDB
- information (see 
+ Requires a PDB loaded as topology,
+ or Amber topology with embedded PDB information (see 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:parmed_addPDB"
+nolink "false"
 
 \end_inset
 
@@ -1679,7 +1741,8 @@ reference "subsec:parmed_addPDB"
 \end_inset
 
 numlist} e.g.
- '^1-10', ':23,84,111'
+ '^1-10',
+ ':23,84,111'
 \end_layout
 
 \begin_layout Description
@@ -1687,7 +1750,8 @@ numlist} e.g.
 \begin_inset space ~
 \end_inset
 
-operator><distance> Selection by distance, see below.
+operator><distance> Selection by distance,
+ see below.
 \end_layout
 
 \begin_layout Standard
@@ -1707,7 +1771,8 @@ Several wildcard characters are supported:
 \end_layout
 
 \begin_layout Standard
-The wildcards can also be used with numbers or other mask characters, e.g.
+The wildcards can also be used with numbers or other mask characters,
+ e.g.
  ':?0' means 
 \begin_inset Quotes eld
 \end_inset
@@ -1716,7 +1781,8 @@ The wildcards can also be used with numbers or other mask characters, e.g.
 \begin_inset Quotes erd
 \end_inset
 
-, ':*' means all residues and '@*' means all atoms.
+,
+ ':*' means all residues and '@*' means all atoms.
  If the atom name (or type name) contains a wildcard character like an asterisk,
  it can be explictly selected by escaping (i.e.
  preceding) the wildcard character with a backslash '
@@ -1730,7 +1796,11 @@ atoms @C?*
 \end_layout
 
 \begin_layout Standard
-would select atoms named C5, C4*, C422, etc., but:
+would select atoms named C5,
+ C4*,
+ C422,
+ etc.,
+ but:
 \end_layout
 
 \begin_layout LyX-Code
@@ -1752,7 +1822,8 @@ Compound expressions of the following type are allowed:
 \end_layout
 
 \begin_layout Standard
-and are processed as: 
+and are processed as:
+ 
 \end_layout
 
 \begin_layout LyX-Code
@@ -1773,7 +1844,8 @@ e.g.
 \end_layout
 
 \begin_layout Standard
-More examples: 
+More examples:
+ 
 \end_layout
 
 \begin_layout Description
@@ -1801,8 +1873,8 @@ More examples:
 \end_layout
 
 \begin_layout Description
-:1-500@O&!(:WAT|:LYS,ARG) All backbone oxygens in residues 1-500 but not
- in water, lysine or arginine residues.
+:1-500@O&!(:WAT|:LYS,ARG) All backbone oxygens in residues 1-500 but not in water,
+ lysine or arginine residues.
 \end_layout
 
 \begin_layout Description
@@ -1855,11 +1927,13 @@ operator> Distance operator.
 \end_layout
 
 \begin_layout Description
-: Any atom within a residue.
+:
+ Any atom within a residue.
 \end_layout
 
 \begin_layout Description
-; Residue geometric center.
+;
+ Residue geometric center.
 \end_layout
 
 \begin_layout Description
@@ -1873,8 +1947,7 @@ operator> Distance operator.
 
 \end_deeper
 \begin_layout Standard
-There are two very important things to keep in mind when using distance
- based masks:
+There are two very important things to keep in mind when using distance based masks:
 \end_layout
 
 \begin_layout Enumerate
@@ -1904,7 +1977,8 @@ mask
 reference
 \series default
 \shape default
-; distances are then calculated using the 
+;
+ distances are then calculated using the 
 \bar under
 specified reference frame only
 \bar default
@@ -1936,7 +2010,8 @@ The syntax for selection by distance is a
 \series bold
 <distance operator>
 \series default
- consists of 2 characters: '
+ consists of 2 characters:
+ '
 \series bold
 <
 \series default
@@ -1948,16 +2023,20 @@ The syntax for selection by distance is a
 \series bold
 ^
 \series default
-' (molecules), '
+' (molecules),
+ '
 \series bold
 :
 \series default
-' (residues), ';' (residue centers), or '
+' (residues),
+ ';' (residue centers),
+ or '
 \series bold
 @
 \series default
 ' (atoms).
- For example, '
+ For example,
+ '
 \series bold
 <:
 \series default
@@ -1970,15 +2049,16 @@ residues within 3.0 Angstroms
 \end_inset
 
  etc.
- For ':' residue- and '^' molecule-based distance selection, if any atom
- in that residue/molecule meets the given distance criterion, the entire
- residue/molecule is selected.
- For ';' residue center, the geometric center of the residue must meet the
- given distance criterion in order to be selected.
+ For ':' residue- and '^' molecule-based distance selection,
+ if any atom in that residue/molecule meets the given distance criterion,
+ the entire residue/molecule is selected.
+ For ';' residue center,
+ the geometric center of the residue must meet the given distance criterion in order to be selected.
 \end_layout
 
 \begin_layout Standard
-In plain language, the entire distance mask can be read as 
+In plain language,
+ the entire distance mask can be read as 
 \begin_inset Quotes eld
 \end_inset
 
@@ -1999,7 +2079,8 @@ Select
 \end_inset
 
 .
- So for example, the mask expression:
+ So for example,
+ the mask expression:
 \end_layout
 
 \begin_layout LyX-Code
@@ -2011,8 +2092,7 @@ Means
 \begin_inset Quotes eld
 \end_inset
 
-Select atoms within 2.4 Å distance of atoms selected by ':11-17' (residues
- numbered 11 through 17)
+Select atoms within 2.4 Å distance of atoms selected by ':11-17' (residues numbered 11 through 17)
 \begin_inset Quotes erd
 \end_inset
 
@@ -2043,15 +2123,19 @@ Ranges
 
 \begin_layout Standard
 For several commands some arguments are ranges (e.g.
- 'trajout onlyframes <range>', 'nastruct resrange <range>', 'rmsd perres
- range <range>'); 
+ 'trajout onlyframes <range>',
+ 'nastruct resrange <range>',
+ 'rmsd perres range <range>');
+ 
 \series bold
 THESE ARE NOT ATOM MASKS
 \series default
 .
- They are simple number ranges using '-' to specify a range and ',' to separate
- different ranges.
- For example 1-2,4-6,9 specifies 1 to 2, 4 to 6, and 9, i.e.
+ They are simple number ranges using '-' to specify a range and ',' to separate different ranges.
+ For example 1-2,4-6,9 specifies 1 to 2,
+ 4 to 6,
+ and 9,
+ i.e.
  '1 2 4 5 6 9'.
 \end_layout
 
@@ -2068,16 +2152,16 @@ name "subsec:Parameter/Reference-Tagging"
 
 \begin_layout Standard
 Parameter and reference files may be 'tagged' (i.e.
- given a nickname); these tags can then be used in place of the file name
- itself.
+ given a nickname);
+ these tags can then be used in place of the file name itself.
  A tag in 
 \shape italic
 cpptraj
 \shape default
  is recognized by being bounded by brackets ('[' and ']').
- This can be particularly useful when reading in many parameter or reference
- files.
- For example, when reading in multiple reference structures:
+ This can be particularly useful when reading in many parameter or reference files.
+ For example,
+ when reading in multiple reference structures:
 \end_layout
 
 \begin_layout LyX-Code
@@ -2109,15 +2193,15 @@ rms Open ref [open] :2-12@CA out rmsd.dat
 \end_layout
 
 \begin_layout Standard
-This defines three reference structures and gives them tags [xray], [last],
+This defines three reference structures and gives them tags [xray],
+ [last],
  and [open].
- These reference structures can then be referred to by their tags instead
- of their filenames by any action that uses reference structures (in this
- case the RMSD action).
+ These reference structures can then be referred to by their tags instead of their filenames by any action that uses reference structures (in this case the RMSD action).
 \end_layout
 
 \begin_layout Standard
-Similarly, this can be useful when reading in multiple parameter files:
+Similarly,
+ this can be useful when reading in multiple parameter files:
 \end_layout
 
 \begin_layout LyX-Code
@@ -2142,12 +2226,11 @@ rms ref [tz2] !(:WAT) out rmsd.dat
 
 \begin_layout Standard
 This defines two parm files and gives them tags [tz2-water] and [tz2-nowater],
- then reads in a trajectory associated with one, and a reference structure
- associated with the other.
- Note that in the 'reference' command there are two tags; the first goes
- along with the 'parm' keyword and specifies what parameter file the reference
- should use, the second is the tag given to the reference itself (as in
- the previous example) and is referred to in the subsequent RMSD action.
+ then reads in a trajectory associated with one,
+ and a reference structure associated with the other.
+ Note that in the 'reference' command there are two tags;
+ the first goes along with the 'parm' keyword and specifies what parameter file the reference should use,
+ the second is the tag given to the reference itself (as in the previous example) and is referred to in the subsequent RMSD action.
 \end_layout
 
 \begin_layout Section
@@ -2155,7 +2238,8 @@ Variables and Control Structures
 \end_layout
 
 \begin_layout Standard
-As of version 18, CPPTRAJ has limited support for 
+As of version 18,
+ CPPTRAJ has limited support for 
 \begin_inset Quotes eld
 \end_inset
 
@@ -2164,10 +2248,8 @@ script
 \end_inset
 
  variables and 'for' loops.
- Script variables are referred to by a dollar sign ('$') prefix and are
- replaced when they are processed.
- These are stored in the master data set list like other data and are assigned
- the type 
+ Script variables are referred to by a dollar sign ('$') prefix and are replaced when they are processed.
+ These are stored in the master data set list like other data and are assigned the type 
 \begin_inset Quotes eld
 \end_inset
 
@@ -2178,11 +2260,12 @@ string variable
 .
  
 \series bold
-Note that to use script variables in CPPTRAJ input that is inside another
- script (e.g.
- a BASH script), they must be escaped with the '
+Note that to use script variables in CPPTRAJ input that is inside another script (e.g.
+ a BASH script),
+ they must be escaped with the '
 \backslash
 ' character,
+
 \series default
  e.g.
 \end_layout
@@ -2214,9 +2297,7 @@ EOF
 \end_layout
 
 \begin_layout Standard
-Note that regular CPPTRAJ 1D Data Sets that contain a single value can be
- used as script variables (if the Data Set contains more than 1 value only
- the first value will be used).
+Note that regular CPPTRAJ 1D Data Sets that contain a single value can be used as script variables (if the Data Set contains more than 1 value only the first value will be used).
 \end_layout
 
 \begin_layout Standard
@@ -2354,15 +2435,21 @@ for { {atoms|residues|molecules|molfirstres|mollastres}
 \end_layout
 
 \begin_layout LyX-Code
-	END KEYWORD: 'done'
+	END KEYWORD:
+ 'done'
 \end_layout
 
 \begin_layout LyX-Code
-  Available 'end OP'       : '<' '>' '<=' '>='
+  Available 'end OP'       :
+ '<' '>' '<=' '>='
 \end_layout
 
 \begin_layout LyX-Code
-  Available 'increment OP' : '++', '--', '+=', '-='
+  Available 'increment OP' :
+ '++',
+ '--',
+ '+=',
+ '-='
 \end_layout
 
 \begin_deeper
@@ -2379,9 +2466,8 @@ inmask
 \begin_inset space ~
 \end_inset
 
-<mask> Loop over atoms/residues/molecules/first residue in molecules/last
- residue in molecules selected by the given mask expression, set as script
- variable 
+<mask> Loop over atoms/residues/molecules/first residue in molecules/last residue in molecules selected by the given mask expression,
+ set as script variable 
 \series bold
 <var>
 \series default
@@ -2495,8 +2581,8 @@ blocksize
 \end_layout
 
 \begin_layout Description
-[cumulative] Instead of blocks of fixed size, use blocks of increasing size
- incremented by blocksize.
+[cumulative] Instead of blocks of fixed size,
+ use blocks of increasing size incremented by blocksize.
 \end_layout
 
 \begin_deeper
@@ -2505,8 +2591,8 @@ blocksize
 \begin_inset space ~
 \end_inset
 
-<#>] When cumulative, the size of the first block (default is first data
- set element).
+<#>] When cumulative,
+ the size of the first block (default is first data set element).
 \end_layout
 
 \end_deeper
@@ -2528,11 +2614,13 @@ OP>[<value>] Loop over integer script variable
 \series bold
 <start>
 \series default
-, optionally ending at 
+,
+ optionally ending at 
 \series bold
 <end>
 \series default
-, increment by 
+,
+ increment by 
 \series bold
 <value>
 \series default
@@ -2548,8 +2636,7 @@ Data Sets Created (datasetblocks loops):
 \begin_inset space \space{}
 \end_inset
 
-idx> (Data set blocks only) Data set block of blocksize starting at <start
- idx>.
+idx> (Data set blocks only) Data set block of blocksize starting at <start idx>.
 \end_layout
 
 \begin_layout Description
@@ -2557,17 +2644,17 @@ idx> (Data set blocks only) Data set block of blocksize starting at <start
 \begin_inset space ~
 \end_inset
 
-idx> (Cumulative data set blocks only) Data set block starting at firstblock
- and ending at <end idx>.
+idx> (Cumulative data set blocks only) Data set block starting at firstblock and ending at <end idx>.
 \end_layout
 
 \end_deeper
 \begin_layout Standard
-Create a for loop using one or more mask expressions, integers, etc.
+Create a for loop using one or more mask expressions,
+ integers,
+ etc.
  Loops can be nested inside each other.
- Integer loops may be used without an end condition, but in that case at
- least one descriptor in the loop should have an end condition or refer
- to a mask.
+ Integer loops may be used without an end condition,
+ but in that case at least one descriptor in the loop should have an end condition or refer to a mask.
  Loops are ended by the 
 \series bold
 done
@@ -2578,7 +2665,8 @@ done
 
 \begin_layout Standard
 Note that non-integer variables (e.g.
- 'inmask' loops) are NOT incremented after the final loop iteration, i.e.
+ 'inmask' loops) are NOT incremented after the final loop iteration,
+ i.e.
  these loop variables always retain their final value.
 \end_layout
 
@@ -2599,10 +2687,9 @@ done
 \end_layout
 
 \begin_layout Standard
-This loops over all atoms in the mask expression ':1-3@CA' (all atoms named
- CA in residues 1 to 3) and creates a variable named 'i' that starts from
- 1 and is incremented by 1 each iteration.
- Inside the loop, the mask selection is referred to by 
+This loops over all atoms in the mask expression ':1-3@CA' (all atoms named CA in residues 1 to 3) and creates a variable named 'i' that starts from 1 and is incremented by 1 each iteration.
+ Inside the loop,
+ the mask selection is referred to by 
 \series bold
 $A0
 \series default
@@ -2671,7 +2758,9 @@ set { <variable> <OP> <value> |
 \end_layout
 
 \begin_layout LyX-Code
-  Available <OP> : '=', '+='
+  Available <OP> :
+ '=',
+ '+='
 \end_layout
 
 \begin_deeper
@@ -2708,10 +2797,9 @@ inmask
 \begin_inset space ~
 \end_inset
 
-<mask> Set/append a script variable to/by the total number of atoms/residues/mol
-ecules in, a range expression of selected atom #s/residue #s/original residue
- #s/molecule #s in, or the total charge/mass of atoms selected by the given
- mask expression.
+<mask> Set/append a script variable to/by the total number of atoms/residues/molecules in,
+ a range expression of selected atom #s/residue #s/original residue #s/molecule #s in,
+ or the total charge/mass of atoms selected by the given mask expression.
 \end_layout
 
 \begin_deeper
@@ -2753,8 +2841,7 @@ parmindex
 \begin_inset space ~
 \end_inset
 
-trajinframes Set/append a script variable to/by the total number of frames
- in trajectories currently loaded by 
+trajinframes Set/append a script variable to/by the total number of frames in trajectories currently loaded by 
 \series bold
 \emph on
 trajin
@@ -2766,12 +2853,13 @@ trajin
 \end_deeper
 \begin_layout Standard
 Set (<OP> = '=') or append (<OP> = '+=') a script variable.
- Script variables are character strings, and are referred to in CPPTRAJ
- input by using a dollar sign '$' prefix.
+ Script variables are character strings,
+ and are referred to in CPPTRAJ input by using a dollar sign '$' prefix.
 \end_layout
 
 \begin_layout Standard
-For example, the following input will load files my.parm7 and my.rst7:
+For example,
+ the following input will load files my.parm7 and my.rst7:
 \end_layout
 
 \begin_layout LyX-Code
@@ -2787,8 +2875,8 @@ trajin $PREFIX.rst7
 \end_layout
 
 \begin_layout Standard
-For example, the following input will print info for the last 10 atoms in
- a topology to 'last10.dat':
+For example,
+ the following input will print info for the last 10 atoms in a topology to 'last10.dat':
 \end_layout
 
 \begin_layout LyX-Code
@@ -2816,7 +2904,8 @@ The following input will put a range of residues selected by :LYS:
 \end_layout
 
 \begin_layout LyX-Code
-	Using topology: FtuFabI.NAD.TCL.parm7
+	Using topology:
+ FtuFabI.NAD.TCL.parm7
 \end_layout
 
 \begin_layout LyX-Code
@@ -2832,9 +2921,10 @@ show [<var1> ...]
 \end_layout
 
 \begin_layout Standard
-If no variable names specified, show all current script variables and their
- values.
- Otherwise, show the values of the specified script variables.
+If no variable names specified,
+ show all current script variables and their values.
+ Otherwise,
+ show the values of the specified script variables.
 \end_layout
 
 \begin_layout Section
@@ -2846,19 +2936,19 @@ In
 \shape italic
 cpptraj
 \shape default
-, Actions and Analyses can generate one or more data sets which are available
- for further processing.
- For example, the 
+,
+ Actions and Analyses can generate one or more data sets which are available for further processing.
+ For example,
+ the 
 \series bold
 \shape italic
 distance
 \series default
 \shape default
  command creates a data set containing distances vs time.
- The data set can be named by the user simply by specifying a non-keyword
- string as an additional argument.
- If no name is given, a default one will be generated based on the action
- name and data set number.
+ The data set can be named by the user simply by specifying a non-keyword string as an additional argument.
+ If no name is given,
+ a default one will be generated based on the action name and data set number.
  For example:
 \end_layout
 
@@ -2876,7 +2966,8 @@ d1-2
 \end_inset
 
 .
- If a name is not specified, e.g.:
+ If a name is not specified,
+ e.g.:
 \end_layout
 
 \begin_layout LyX-Code
@@ -2896,7 +2987,8 @@ Dis_00000
 \end_layout
 
 \begin_layout Standard
-Data files are created automatically by most commands, usually via the 
+Data files are created automatically by most commands,
+ usually via the 
 \begin_inset Quotes eld
 \end_inset
 
@@ -2937,34 +3029,38 @@ readdata
 \begin_inset CommandInset ref
 LatexCommand ref
 reference "tab:cpptraj-DataFile-formats"
+nolink "false"
 
 \end_inset
 
-, although it cannot write in all formats.
- In addition, a data set must be valid for the data file format.
- For example, 3D data (such as a grid) can be written to an OpenDX format
- file but not a Grace format file.
+,
+ although it cannot write in all formats.
+ In addition,
+ a data set must be valid for the data file format.
+ For example,
+ 3D data (such as a grid) can be written to an OpenDX format file but not a Grace format file.
  
 \end_layout
 
 \begin_layout Standard
-The default file format is called 'Standard', which simply has data in columns,
+The default file format is called 'Standard',
+ which simply has data in columns,
  like 
 \shape italic
 ptraj
 \shape default
-, although multiple data sets can be directed to the same output file.
- The format of a file can be changed either by specifying a recognized keyword
- (either on the command line itself or later via a 'datafile' command) or
- by giving the file an extension corresponding to te format, so 'filename.agr'
- will output in Grace format, and 'filename.gnu' will output in Gnuplot contour,
+,
+ although multiple data sets can be directed to the same output file.
+ The format of a file can be changed either by specifying a recognized keyword (either on the command line itself or later via a 'datafile' command) or by giving the file an extension corresponding to te format,
+ so 'filename.agr' will output in Grace format,
+ and 'filename.gnu' will output in Gnuplot contour,
  and so on.
- The xmgrace/gnuplot output is particularly nice for the secstruct sumout
- and rmsd perresout files.
+ The xmgrace/gnuplot output is particularly nice for the secstruct sumout and rmsd perresout files.
  Additional options for data files can be found in 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "sec:Datafile-Commands"
+nolink "false"
 
 \end_inset
 
@@ -2980,9 +3076,9 @@ out
 \begin_inset Quotes erd
 \end_inset
 
- keyword will allow data sets from separate commands to be written into
- the same file.
- For example, the commands:
+ keyword will allow data sets from separate commands to be written into the same file.
+ For example,
+ the commands:
 \end_layout
 
 \begin_layout LyX-Code
@@ -3026,12 +3122,14 @@ phipsi.dat
 \end_layout
 
 \begin_layout Standard
-Note that when reading the Amber Prep and Amber OFF Library formats, a COORDS
- data set will be created for each unit present in these files.
+Note that when reading the Amber Prep and Amber OFF Library formats,
+ a COORDS data set will be created for each unit present in these files.
 \end_layout
 
 \begin_layout Standard
 \begin_inset Float table
+placement document
+alignment document
 wide false
 sideways false
 status open
@@ -3135,7 +3233,9 @@ dat
 \begin_inset Text
 
 \begin_layout Plain Layout
-1D, 2D, 3D
+1D,
+ 2D,
+ 3D
 \end_layout
 
 \end_inset
@@ -3164,7 +3264,8 @@ Grace
 \begin_inset Text
 
 \begin_layout Plain Layout
-.agr, .xmgr
+.agr,
+ .xmgr
 \end_layout
 
 \end_inset
@@ -3229,7 +3330,8 @@ gnu
 \begin_inset Text
 
 \begin_layout Plain Layout
-1D, 2D
+1D,
+ 2D
 \end_layout
 
 \end_inset
@@ -3258,7 +3360,8 @@ Xplor
 \begin_inset Text
 
 \begin_layout Plain Layout
-.xplor, .grid
+.xplor,
+ .grid
 \end_layout
 
 \end_inset
@@ -3426,7 +3529,8 @@ mdout
 \begin_inset Text
 
 \begin_layout Plain Layout
-Energy information, Read Only
+Energy information,
+ Read Only
 \end_layout
 
 \end_inset
@@ -3849,7 +3953,8 @@ charmmout
 \begin_inset Text
 
 \begin_layout Plain Layout
-Energy information, Read Only
+Energy information,
+ Read Only
 \end_layout
 
 \end_inset
@@ -4057,7 +4162,8 @@ Amber OFF Library File
 \begin_inset Text
 
 \begin_layout Plain Layout
-.off, .lib
+.off,
+ .lib
 \end_layout
 
 \end_inset
@@ -4151,8 +4257,10 @@ entire
 
 \series bold
 <name>:
+
 \series default
- The data set name, usually specified in the action (e.g.
+ The data set name,
+ usually specified in the action (e.g.
  in 'distance d0 @1 @2' the data set name is 
 \begin_inset Quotes eld
 \end_inset
@@ -4168,16 +4276,18 @@ d0
 
 \series bold
 <aspect>:
+
 \series default
- Optional; this is set for certain data sets internally in order to easily
- select subsets of data.
+ Optional;
+ this is set for certain data sets internally in order to easily select subsets of data.
  
 \series bold
 The brackets are required
 \series default
 .
- For example, when using 'hbond series', both solute-solute and solute-solvent
- hydrogen bond time series may be generated.
+ For example,
+ when using 'hbond series',
+ both solute-solute and solute-solvent hydrogen bond time series may be generated.
  To select all solute-solute hydrogen bonds one would use the aspect 
 \begin_inset Quotes eld
 \end_inset
@@ -4186,7 +4296,8 @@ The brackets are required
 \begin_inset Quotes erd
 \end_inset
 
-; to select solute-solvent hydrogen bonds the aspect 
+;
+ to select solute-solvent hydrogen bonds the aspect 
 \begin_inset Quotes eld
 \end_inset
 
@@ -4202,16 +4313,20 @@ The brackets are required
 
 \series bold
 <index>:
+
 \series default
- Optional; for actions that generate many data sets (such as 'rmsd perres')
- an index is used.
- Depending on the action, the index may correspond to atom #s, residue #s,
+ Optional;
+ for actions that generate many data sets (such as 'rmsd perres') an index is used.
+ Depending on the action,
+ the index may correspond to atom #s,
+ residue #s,
  etc.
  A number range (comma and/or dash separated) may be used.
 \end_layout
 
 \begin_layout Standard
-For example: to select all data sets with aspect 
+For example:
+ to select all data sets with aspect 
 \begin_inset Quotes eld
 \end_inset
 
@@ -4235,7 +4350,8 @@ To select all data sets with aspect
 \begin_inset Quotes erd
 \end_inset
 
- with any name, indices 1 and 3:
+ with any name,
+ indices 1 and 3:
 \end_layout
 
 \begin_layout LyX-Code
@@ -4243,7 +4359,8 @@ To select all data sets with aspect
 \end_layout
 
 \begin_layout Standard
-In ensemble mode, data set selection has additional syntax:
+In ensemble mode,
+ data set selection has additional syntax:
 \end_layout
 
 \begin_layout LyX-Code
@@ -4266,11 +4383,13 @@ name "subsec:cpptraj-Data-Set-Math"
 \end_layout
 
 \begin_layout Standard
-As of version 15, 
+As of version 15,
+ 
 \emph on
 cpptraj
 \emph default
- can perform basic math operations, even on data sets (with some limitations).
+ can perform basic math operations,
+ even on data sets (with some limitations).
  Currently recognized operations are:
 \begin_inset Separator latexpar
 \end_inset
@@ -4751,11 +4870,13 @@ E
 \begin_inset Quotes erd
 \end_inset
 
- notation, e.g.
+ notation,
+ e.g.
  1E-5 = 0.00001.
  The parser also recognizes PI as the number pi.
  Expressions can also be enclosed in parentheses.
- So for example, the following expression is valid:
+ So for example,
+ the following expression is valid:
 \end_layout
 
 \begin_layout LyX-Code
@@ -4763,12 +4884,12 @@ E
 \end_layout
 
 \begin_layout LyX-Code
-Result: 0.879887
+Result:
+ 0.879887
 \end_layout
 
 \begin_layout Standard
-Results of numerical calculations like the above can be assigned to a variable
- (essentially a data set of size 1) for use in subsequent calculations,
+Results of numerical calculations like the above can be assigned to a variable (essentially a data set of size 1) for use in subsequent calculations,
  e.g.
 \end_layout
 
@@ -4781,15 +4902,18 @@ Result stored in 'R'
 \end_layout
 
 \begin_layout LyX-Code
-> R + 1 Result: 1.879887
+> R + 1 Result:
+ 1.879887
 \end_layout
 
 \begin_layout Standard
 Data sets can be specified in expressions as well.
- Currently data sets in an expression must be of the same type and only
- 1D, 2D, and 3D data sets are supported.
+ Currently data sets in an expression must be of the same type and only 1D,
+ 2D,
+ and 3D data sets are supported.
  Functions are applied to each member of the data set.
- So for example, given two 1D data sets of the same size named D0 and D1,
+ So for example,
+ given two 1D data sets of the same size named D0 and D1,
  the following expression:
 \end_layout
 
@@ -4798,8 +4922,9 @@ Data sets can be specified in expressions as well.
 \end_layout
 
 \begin_layout Standard
-would take the square root of each member of D0, add it to the corresponding
- member of D1, and assign the result to D2.
+would take the square root of each member of D0,
+ add it to the corresponding member of D1,
+ and assign the result to D2.
  The following table lists which operations are valid for data set types.
  If a type is not listed it is not supported:
 \begin_inset Separator latexpar
@@ -4868,7 +4993,9 @@ Notes
 \begin_inset Text
 
 \begin_layout Plain Layout
-1D (integer, double, float)
+1D (integer,
+ double,
+ float)
 \end_layout
 
 \end_inset
@@ -4915,7 +5042,11 @@ All
 \begin_inset Text
 
 \begin_layout Plain Layout
-+, -, *, /, =
++,
+ -,
+ *,
+ /,
+ =
 \end_layout
 
 \end_inset
@@ -4953,7 +5084,11 @@ None
 \begin_inset Text
 
 \begin_layout Plain Layout
-+, -, /, *, =
++,
+ -,
+ /,
+ *,
+ =
 \end_layout
 
 \end_inset
@@ -4962,7 +5097,11 @@ None
 \begin_inset Text
 
 \begin_layout Plain Layout
-sum, avg, stdev, min, max
+sum,
+ avg,
+ stdev,
+ min,
+ max
 \end_layout
 
 \end_inset
@@ -4991,7 +5130,11 @@ sum, avg, stdev, min, max
 \begin_inset Text
 
 \begin_layout Plain Layout
-+, -, /, *, =
++,
+ -,
+ /,
+ *,
+ =
 \end_layout
 
 \end_inset
@@ -5000,7 +5143,11 @@ sum, avg, stdev, min, max
 \begin_inset Text
 
 \begin_layout Plain Layout
-sum, avg, stdev, min, max
+sum,
+ avg,
+ stdev,
+ min,
+ max
 \end_layout
 
 \end_inset
@@ -5035,8 +5182,8 @@ name "sec:Datafile-Commands"
 
 \begin_layout Standard
 Data file output can be handled multiple ways in cpptraj.
- Output data files can be created by Actions/Analyses/Commands, or can be
- explicitly created with 
+ Output data files can be created by Actions/Analyses/Commands,
+ or can be explicitly created with 
 \series bold
 \emph on
 writedata
@@ -5046,6 +5193,7 @@ writedata
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_writedata"
+nolink "false"
 
 \end_inset
 
@@ -5059,6 +5207,7 @@ create
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_create"
+nolink "false"
 
 \end_inset
 
@@ -5073,6 +5222,7 @@ readdata
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_readdata"
+nolink "false"
 
 \end_inset
 
@@ -5080,12 +5230,14 @@ reference "subsec:cpptraj_readdata"
 \end_layout
 
 \begin_layout Standard
-In general, data files which have been declared with an 
+In general,
+ data files which have been declared with an 
 \series bold
 'out'
 \series default
  keyword will recognize data file write keywords on the same command line.
- For example, the 
+ For example,
+ the 
 \series bold
 'time'
 \series default
@@ -5103,10 +5255,8 @@ distance d0 :1 :2 out d0.agr time 0.001
 \end_layout
 
 \begin_layout Standard
-The data file format can be changed from standard implicitly by using specific
- filename extensions or keywords.
- If the extension is not recognized or no keyword is give the default format
- is 'Standard'.
+The data file format can be changed from standard implicitly by using specific filename extensions or keywords.
+ If the extension is not recognized or no keyword is give the default format is 'Standard'.
  Keywords and extensions for data file formats recognized by 
 \shape italic
 cpptraj
@@ -5115,12 +5265,12 @@ cpptraj
 \begin_inset CommandInset ref
 LatexCommand ref
 reference "tab:cpptraj-DataFile-formats"
+nolink "false"
 
 \end_inset
 
 .
- Note that the use of certain options may be restricted for certain data
- file formats.
+ Note that the use of certain options may be restricted for certain data file formats.
  These options can also be passed to data files via the 
 \series bold
 \emph on
@@ -5131,6 +5281,7 @@ datafile
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_datafile_command"
+nolink "false"
 
 \end_inset
 
@@ -5181,8 +5332,7 @@ zlabel}
 
 <label> Set the x-axis label for the specified datafile to <label>.
  For regular data files this is the header for the first column of data.
- If the data is at least 2-dimensional 'datafile ylabel <label>' will likewise
- set the y-axis label.
+ If the data is at least 2-dimensional 'datafile ylabel <label>' will likewise set the y-axis label.
 \end_layout
 
 \begin_layout Description
@@ -5207,13 +5357,14 @@ zmin}
 \end_inset
 
 <min> Set the starting X coordinate value to <min>.
- If the data is at least 2-dimensional 'datafile ymin <min>' will likewise
- set the starting Y coordinate value.
+ If the data is at least 2-dimensional 'datafile ymin <min>' will likewise set the starting Y coordinate value.
 \end_layout
 
 \begin_layout Description
 sort Sort data sets prior to write.
- Ordering is by name, aspect, then index (all descending).
+ Ordering is by name,
+ aspect,
+ then index (all descending).
 \end_layout
 
 \begin_layout Description
@@ -5238,8 +5389,7 @@ zstep}
 \end_inset
 
 <step> Multiply each frame number by <step> (x coordinates).
- If the data is at least 2-dimensional 'datafile ystep <step>' will likewise
- multiply y coordinates by <step>.
+ If the data is at least 2-dimensional 'datafile ystep <step>' will likewise multiply y coordinates by <step>.
 \end_layout
 
 \begin_layout Description
@@ -5260,8 +5410,7 @@ prec
 \begin_inset space ~
 \end_inset
 
-<width>[.<precision>] Change the output format width (and optionally precision)
- of all sets 
+<width>[.<precision>] Change the output format width (and optionally precision) of all sets 
 \shape italic
 subsequently
 \shape default
@@ -5298,7 +5447,8 @@ xfmt
 [noensextension] Omit ensemble extension in ensemble processing mode.
  
 \series bold
-NOTE: THIS OPTION HAS NOT BEEN FULLY TESTED IN PARALLEL.
+NOTE:
+ THIS OPTION HAS NOT BEEN FULLY TESTED IN PARALLEL.
 \end_layout
 
 \end_deeper
@@ -5324,11 +5474,10 @@ Write
 
 \begin_deeper
 \begin_layout Description
-invert Normally, data is written out with X-values pertaining to frames
- (i.e.
+invert Normally,
+ data is written out with X-values pertaining to frames (i.e.
  data over all trajectories is printed in columns).
- This command flips that behavior so that X-values pertain to data sets
- (i.e.
+ This command flips that behavior so that X-values pertain to data sets (i.e.
  data over all trajectories is printed in rows).
 \end_layout
 
@@ -5372,7 +5521,8 @@ noxcol Prevent printing of indices (i.e.
  the #Frame column in most datafiles) for the specified datafile.
  Useful e.g.
  if one would like a 2D plot such as phi vs psi.
- For example, given the input:
+ For example,
+ given the input:
 \begin_inset Separator latexpar
 \end_inset
 
@@ -5397,8 +5547,8 @@ datafile phipsi.dat noxcol
 \shape italic
 Cpptraj
 \shape default
- will write a 2 column datafile containing only phi and psi, no frame numbers
- will be written.
+ will write a 2 column datafile containing only phi and psi,
+ no frame numbers will be written.
 \end_layout
 
 \end_deeper
@@ -5429,7 +5579,8 @@ D1') at the beginning of data file.
 \end_layout
 
 \begin_layout Description
-square2d Write 2D data as a square matrix, e.g.:
+square2d Write 2D data as a square matrix,
+ e.g.:
 \begin_inset Separator latexpar
 \end_inset
 
@@ -5470,7 +5621,8 @@ cut
 \begin_inset space ~
 \end_inset
 
-<cut> Cutoff for 'sparse'; default 0.
+<cut> Cutoff for 'sparse';
+ default 0.
 \end_layout
 
 \end_deeper
@@ -5533,7 +5685,8 @@ prec
 \begin_inset space ~
 \end_inset
 
-{flt|dbl} Read 2d/3d data as single (flt) or double (dbl, default) precision.
+{flt|dbl} Read 2d/3d data as single (flt) or double (dbl,
+ default) precision.
 \end_layout
 
 \begin_layout Description
@@ -5600,21 +5753,27 @@ nosquare2d Read data as XYZ matrix (i.e.
 \begin_layout Description
 vector Read data as vector.
  If indices are present they will be skipped.
- Assume first 3 columns after the index column are vector X, Y, and Z, and
- (if present) the next 3 columns contain vector origin X, Y, and Z.
+ Assume first 3 columns after the index column are vector X,
+ Y,
+ and Z,
+ and (if present) the next 3 columns contain vector origin X,
+ Y,
+ and Z.
 \end_layout
 
 \begin_deeper
 \begin_layout Description
-magnitude If specified, assume vector file last column contains vector magnitude
-s; read these into a set with Aspect 'Mag'.
+magnitude If specified,
+ assume vector file last column contains vector magnitudes;
+ read these into a set with Aspect 'Mag'.
 \end_layout
 
 \end_deeper
 \begin_layout Description
 mat3x3 Read data as 3x3 matrix.
  If indices are present they will be skipped.
- Assume matrices are in row major order on each line, i.e.
+ Assume matrices are in row major order on each line,
+ i.e.
  M(1,1) M(1,2) ...
  M(3,2) M(3,3).
 \end_layout
@@ -5654,7 +5813,8 @@ prec
 \begin_inset space ~
 \end_inset
 
-{dbl|flt} Grid precision, double or float (default float).
+{dbl|flt} Grid precision,
+ double or float (default float).
 \end_layout
 
 \begin_layout Description
@@ -5668,21 +5828,17 @@ bin
 \end_deeper
 \end_deeper
 \begin_layout Standard
-By default, standard data files are assumed to contain 1D data in columns.
- Data set legends will be read in if the file has a header line (denoted
- by '#').
- Columns labeled '#Frame' are automatically considered the 'index' column
- and skipped.
- Data sets are stored as <name>:<idx> where <name> is the given data set
- name (the file name if not specified) and <idx> corresponds to the column
- the data was read from starting from 1.
+By default,
+ standard data files are assumed to contain 1D data in columns.
+ Data set legends will be read in if the file has a header line (denoted by '#').
+ Columns labeled '#Frame' are automatically considered the 'index' column and skipped.
+ Data sets are stored as <name>:<idx> where <name> is the given data set name (the file name if not specified) and <idx> corresponds to the column the data was read from starting from 1.
  
 \shape italic
 Cpptraj
 \shape default
- assumes the data increases monotonically and will automatically attempt
- to determine the dimensions of the data set(s); a warning will be printed
- if this is not successful.
+ assumes the data increases monotonically and will automatically attempt to determine the dimensions of the data set(s);
+ a warning will be printed if this is not successful.
 \end_layout
 
 \begin_layout Standard
@@ -5695,8 +5851,8 @@ If a file contains the header:
 
 \begin_layout Standard
 CPPTRAJ will assume the file contains pairwise distances for clustering,
- where the F1 and F2 columns contain the frame numbers, and the <name> column
- contains the distance.
+ where the F1 and F2 columns contain the frame numbers,
+ and the <name> column contains the distance.
 \end_layout
 
 \begin_layout Subsection
@@ -5730,8 +5886,8 @@ Write
 
 \begin_deeper
 \begin_layout Description
-invert Normally, data is written out with X-values pertaining to frames
- (i.e.
+invert Normally,
+ data is written out with X-values pertaining to frames (i.e.
  data over all trajectories is printed in columns).
  This command flips that behavior so that X-values pertain to data sets.
 \end_layout
@@ -5753,13 +5909,14 @@ noxydy Do not combine consecutuve pairs of sets into XYDY sets (default).
 \begin_inset space ~
 \end_inset
 
-set> If a string dataset is specified, assume it has data point labels.
+set> If a string dataset is specified,
+ assume it has data point labels.
 \end_layout
 
 \end_deeper
 \begin_layout Standard
-If a single string data set is specified when writing Grace format, it is
- assumed they are data point labels.
+If a single string data set is specified when writing Grace format,
+ it is assumed they are data point labels.
 \end_layout
 
 \begin_layout Subsubsection*
@@ -5767,10 +5924,8 @@ Read
 \end_layout
 
 \begin_layout Standard
-Cpptraj will read set legends from grace files, and data sets are stored
- as <name>:<idx> where <name> is the given data set name (the file name
- if not specified) and <idx> corresponds to the set number the data was
- read from starting from 0.
+Cpptraj will read set legends from grace files,
+ and data sets are stored as <name>:<idx> where <name> is the given data set name (the file name if not specified) and <idx> corresponds to the set number the data was read from starting from 0.
 \end_layout
 
 \begin_layout Subsection
@@ -5778,8 +5933,7 @@ Gnuplot Data File Options
 \end_layout
 
 \begin_layout Standard
-For more information on these options it helps to look at the PM3D options
- in the Gnuplot manual (see 
+For more information on these options it helps to look at the PM3D options in the Gnuplot manual (see 
 \begin_inset CommandInset href
 LatexCommand href
 name "http://www.gnuplot.info/"
@@ -5850,7 +6004,8 @@ header Format the plot so it can be directly processed by gnuplot.
 \end_layout
 
 \begin_layout Description
-noheader Do not format plot; data output only.
+noheader Do not format plot;
+ data output only.
 \end_layout
 
 \begin_layout Description
@@ -5863,15 +6018,28 @@ palette
 
 \begin_deeper
 \begin_layout Description
-'rgb' Red, yellow, green, cyan, blue, magenta, red.
+'rgb' Red,
+ yellow,
+ green,
+ cyan,
+ blue,
+ magenta,
+ red.
 \end_layout
 
 \begin_layout Description
-'kbvyw' Black, blue, violet, yellow, white.
+'kbvyw' Black,
+ blue,
+ violet,
+ yellow,
+ white.
 \end_layout
 
 \begin_layout Description
-'bgyr' Blue, green, yellow, red.
+'bgyr' Blue,
+ green,
+ yellow,
+ red.
 \end_layout
 
 \begin_layout Description
@@ -5885,7 +6053,10 @@ xlabels|ylabels|zlabels
 \begin_inset space ~
 \end_inset
 
-<labellist> Set x, y, or z axis labels with comma-separated list, e.g.
+<labellist> Set x,
+ y,
+ or z axis labels with comma-separated list,
+ e.g.
  'xlabels X1,X2,X3'.
 \end_layout
 
@@ -5906,6 +6077,7 @@ readdata
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-remlog"
+nolink "false"
 
 \end_inset
 
@@ -5926,8 +6098,7 @@ Read
 
 \begin_deeper
 \begin_layout Description
-[nosearch] If specified do not automatically search for MREMD dimension
- logs.
+[nosearch] If specified do not automatically search for MREMD dimension logs.
 \end_layout
 
 \begin_layout Description
@@ -5947,8 +6118,7 @@ Read
 \begin_inset space ~
 \end_inset
 
-indices>] Use comma-separated list of indices as the initial coordinate
- indices (H-REMD only).
+indices>] Use comma-separated list of indices as the initial coordinate indices (H-REMD only).
  For example (4 replicas):
 \begin_inset Separator latexpar
 \end_inset
@@ -5999,8 +6169,7 @@ ibeg
 \begin_inset space ~
 \end_inset
 
-<firstmode> Number of the first mode (or principal component) to read from
- evecs file.
+<firstmode> Number of the first mode (or principal component) to read from evecs file.
  Default 1.
 \end_layout
 
@@ -6009,13 +6178,13 @@ iend
 \begin_inset space ~
 \end_inset
 
-<lastmode> Number of the last mode (or principal component) to read from
- evecs file.
+<lastmode> Number of the last mode (or principal component) to read from evecs file.
  Default is to read all for newer evecs files (generated by 
 \shape italic
 cpptraj
 \shape default
- version > 12), 50 for older evecs files.
+ version > 12),
+ 50 for older evecs files.
 \end_layout
 
 \end_deeper
@@ -6024,12 +6193,12 @@ Vector psuedo-traj Options
 \end_layout
 
 \begin_layout Standard
-This can be used to write out a representation of a vector data set which
- can then be visualized.
+This can be used to write out a representation of a vector data set which can then be visualized.
  See 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-vector"
+nolink "false"
 
 \end_inset
 
@@ -6059,6 +6228,7 @@ trajfmt
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "tab:cpptraj-trajformats"
+nolink "false"
 
 \end_inset
 
@@ -6122,7 +6292,8 @@ gridwrap Like
 \series bold
 'bincenter'
 \series default
-, but also wrap grid density.
+,
+ but also wrap grid density.
  Useful when grid encompasses unit cell.
 \end_layout
 
@@ -6131,7 +6302,8 @@ gridext Like
 \series bold
 'bincenter'
 \series default
-, but also print extra layer of empty bins.
+,
+ but also print extra layer of empty bins.
 \end_layout
 
 \end_deeper
@@ -6225,13 +6397,13 @@ cpin
 
 \end_deeper
 \begin_layout Standard
-Note that when reading in constant pH data the data set aspect will be set
- to the residue name and the index will be set to the residue number.
- When reading in constant pH REMD data the data is unsorted, and sortensembledat
-a should be used to create sorted constant pH data sets (see 
+Note that when reading in constant pH data the data set aspect will be set to the residue name and the index will be set to the residue number.
+ When reading in constant pH REMD data the data is unsorted,
+ and sortensembledata should be used to create sorted constant pH data sets (see 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_sortensembledata"
+nolink "false"
 
 \end_inset
 
@@ -6251,10 +6423,10 @@ name "sec:Coordinates-as-a"
 
 \begin_layout Standard
 Coordinate I/O tends to be the most time-consuming part of trajectory analysis.
- In addition, many types of analyses (for example two-dimensional RMSD and
- cluster analysis) require using coordinate frames multiple times.
- To simplify this, trajectory coordinates may be saved as a separate data
- set via the 
+ In addition,
+ many types of analyses (for example two-dimensional RMSD and cluster analysis) require using coordinate frames multiple times.
+ To simplify this,
+ trajectory coordinates may be saved as a separate data set via the 
 \series bold
 \shape italic
 loadcrd
@@ -6280,8 +6452,7 @@ crdaction
 crdout
 \series default
 \shape default
- command can be used to write coordinates to an output trajectory (similar
- to 
+ command can be used to write coordinates to an output trajectory (similar to 
 \series bold
 \shape italic
 trajout
@@ -6293,9 +6464,8 @@ trajout
 \begin_layout Standard
 Although COORDS data sets store everything internally with single-precision,
  they can still use a large amount of memory.
- Because of this there is a specialized type of COORDS data set called a
- TRAJ data set (trajectory), which functions exactly like a COORDS data
- set except all data is stored on disk.
+ Because of this there is a specialized type of COORDS data set called a TRAJ data set (trajectory),
+ which functions exactly like a COORDS data set except all data is stored on disk.
  TRAJ data sets can be created with the 
 \series bold
 \shape italic
@@ -6318,8 +6488,8 @@ runanalysis
 \shape default
  command.
  Note that while these analyses can be run on specified COORDS data sets,
- if one is not specified a default COORDS data set will be created, made
- up of frames from 
+ if one is not specified a default COORDS data set will be created,
+ made up of frames from 
 \series bold
 \shape italic
 trajin
@@ -6329,11 +6499,10 @@ trajin
 \end_layout
 
 \begin_layout Standard
-As an example of where this might be useful is in the calculation of atomic
- positional fluctuations.
- Previously this required two steps: one to generate an average structure,
- then a second to rms-fit to that average structure prior to calculating
- the fluctuations.
+As an example of where this might be useful is in the calculation of atomic positional fluctuations.
+ Previously this required two steps:
+ one to generate an average structure,
+ then a second to rms-fit to that average structure prior to calculating the fluctuations.
  This can now be done in one pass with the following input:
 \end_layout
 
@@ -6346,7 +6515,8 @@ loadcrd mdcrd.nc
 \end_layout
 
 \begin_layout LyX-Code
-# Generate average structure PDB, @CA only
+# Generate average structure PDB,
+ @CA only
 \end_layout
 
 \begin_layout LyX-Code
@@ -6574,8 +6744,7 @@ extendedcomp
 \begin_inset Text
 
 \begin_layout Plain Layout
-Calculate extended comparison similarity values for each frame in COORDS
- set.
+Calculate extended comparison similarity values for each frame in COORDS set.
 \end_layout
 
 \end_inset
@@ -6655,8 +6824,7 @@ permutedihedrals
 \begin_inset Text
 
 \begin_layout Plain Layout
-Rotate specified dihedral(s) in given COORDS set by specific interval or
- to random values.
+Rotate specified dihedral(s) in given COORDS set by specific interval or to random values.
 \end_layout
 
 \end_inset
@@ -6676,8 +6844,7 @@ prepareforleap
 \begin_inset Text
 
 \begin_layout Plain Layout
-Prepare a structure (usually loaded from a PDB) for processing with LEaP
- from Amber.
+Prepare a structure (usually loaded from a PDB) for processing with LEaP from Amber.
 \end_layout
 
 \end_inset
@@ -6777,8 +6944,7 @@ zmatrix
 \begin_inset Text
 
 \begin_layout Plain Layout
-Apply Z-matrix to a COORDS set or calculate Z-matrix for a molecule/frame
- in a COORDS set.
+Apply Z-matrix to a COORDS set or calculate Z-matrix for a molecule/frame in a COORDS set.
 \end_layout
 
 \end_inset
@@ -6802,7 +6968,8 @@ catcrd <crd1> <crd2> ...
 
 \begin_deeper
 \begin_layout Description
-<crdX> COORDS data sets to concatentate, specify 2 or more.
+<crdX> COORDS data sets to concatentate,
+ specify 2 or more.
 \end_layout
 
 \begin_layout Description
@@ -6817,8 +6984,8 @@ name
 \begin_layout Standard
 Concatentate two or more COORDS data sets into a single COORDS data set.
  The topologies must have the same number of atoms for this to work.
- If the topologies differ in other ways, the topology of the first COORDS
- set takes priority.
+ If the topologies differ in other ways,
+ the topology of the first COORDS set takes priority.
 \end_layout
 
 \begin_layout Subsection
@@ -6840,7 +7007,8 @@ combinecrd <crd1> <crd2> ...
 
 \begin_deeper
 \begin_layout Description
-<crdX> COORDS data sets to combine, specify 2 or more.
+<crdX> COORDS data sets to combine,
+ specify 2 or more.
 \end_layout
 
 \begin_layout Description
@@ -6883,8 +7051,10 @@ not
 \end_layout
 
 \begin_layout Standard
-For example, to load two MOL2 files as COORDS data sets, combine them, and
- write them out as a single MOL2:
+For example,
+ to load two MOL2 files as COORDS data sets,
+ combine them,
+ and write them out as a single MOL2:
 \end_layout
 
 \begin_layout LyX-Code
@@ -6915,8 +7085,7 @@ name "subsec:cpptraj_crdaction"
 \end_layout
 
 \begin_layout LyX-Code
-crdaction <crd set> <actioncmd> [<action args>] [crdframes <start>,<stop>,<offse
-t>]
+crdaction <crd set> <actioncmd> [<action args>] [crdframes <start>,<stop>,<offset>]
 \end_layout
 
 \begin_layout Standard
@@ -6925,8 +7094,9 @@ Perform action <actioncmd> on COORDS data set <crd set>.
 \end_layout
 
 \begin_layout Standard
-For example, to calculate RMSD for a previously created COORDS data set
- named crd1 using frames 1 to the last, skipping every 10:
+For example,
+ to calculate RMSD for a previously created COORDS data set named crd1 using frames 1 to the last,
+ skipping every 10:
 \end_layout
 
 \begin_layout LyX-Code
@@ -6947,8 +7117,8 @@ Write COORDS data set <crd set> to trajectory named <filename>.
 \end_layout
 
 \begin_layout Standard
-For example, to write frames 1 to 10 from a previously created COORDS data
- set named 
+For example,
+ to write frames 1 to 10 from a previously created COORDS data set named 
 \begin_inset Quotes eld
 \end_inset
 
@@ -7017,7 +7187,8 @@ crd
 \begin_inset space ~
 \end_inset
 
-set>] COORDS set to create; if not specified <input crd set> will be modified.
+set>] COORDS set to create;
+ if not specified <input crd set> will be modified.
 \end_layout
 
 \begin_layout Description
@@ -7047,8 +7218,7 @@ rmsrefine Do iterative RMS refinement.
 
 \end_deeper
 \begin_layout Description
-normcoords Normalize coordinates between 0.0 and 1.0 using the minimum and
- maximum coordinate values.
+normcoords Normalize coordinates between 0.0 and 1.0 using the minimum and maximum coordinate values.
 \end_layout
 
 \begin_layout Description
@@ -7061,7 +7231,8 @@ trim Remove trajectory frames using extended similarity metrics.
 \begin_inset space ~
 \end_inset
 
-<metric>] Metric to use; default MSD.
+<metric>] Metric to use;
+ default MSD.
 \end_layout
 
 \begin_layout Description
@@ -7091,17 +7262,21 @@ trim Remove trajectory frames using extended similarity metrics.
 \begin_layout Standard
 Transform a COORDS set in one of several ways.
  Does not yet work with TRAJ data sets.
- The iterative RMS refinement is similar to the procedure outlined by Klem
- et al.
+ The iterative RMS refinement is similar to the procedure outlined by Klem et al.
  (J.
  Chem.
  Theory Comput.
- 2022, 18, 3218−3230).
+ 2022,
+ 18,
+ 3218−3230).
  The extended similarity metrics are those defined by Racz et al.
  (J.
  Comp.-Aid.
  Mol.
- Design, 2022, 36, 157-173).
+ Design,
+ 2022,
+ 36,
+ 157-173).
 \end_layout
 
 \begin_layout Subsection
@@ -7109,11 +7284,12 @@ createcrd
 \end_layout
 
 \begin_layout Standard
-This command is actually an Action that can be used to create COORDS data
- sets during trajectory processing, see 
+This command is actually an Action that can be used to create COORDS data sets during trajectory processing,
+ see 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_createcrd"
+nolink "false"
 
 \end_inset
 
@@ -7209,17 +7385,18 @@ crdset
 \begin_inset space ~
 \end_inset
 
-<setname>] If specified, create an energy per step data set.
+<setname>] If specified,
+ create an energy per step data set.
 \end_layout
 
 \begin_layout Description
-[nonbond] If specified, use simple nonbonded potential term in additon to
- bonded terms.
+[nonbond] If specified,
+ use simple nonbonded potential term in additon to bonded terms.
 \end_layout
 
 \begin_layout Description
-[openmm] If specified and if CPPTRAJ was compiled with OpenMM support, use
- OpenMM to calculate the forces.
+[openmm] If specified and if CPPTRAJ was compiled with OpenMM support,
+ use OpenMM to calculate the forces.
 \end_layout
 
 \begin_layout Standard
@@ -7320,8 +7497,9 @@ THIS COMMAND IS STILL IN DEVELOPMENT AS OF VERSION 5.0.2.
 \end_layout
 
 \begin_layout Standard
-Perform steepest descent minimization on a frame in a COORDS set using a
- very basic force field (bonds, angles, dihedrals).
+Perform steepest descent minimization on a frame in a COORDS set using a very basic force field (bonds,
+ angles,
+ dihedrals).
  A simple nonbonded term can be added as well if desired.
 \end_layout
 
@@ -7411,13 +7589,15 @@ name> Set containing similarity values for each COORDS frame.
 
 \end_deeper
 \begin_layout Standard
-Calculate extended comparison similarity values for each frame in a COORDS
- set.
+Calculate extended comparison similarity values for each frame in a COORDS set.
  The extended similarity metrics are those defined by Racz et al.
  (J.
  Comp.-Aid.
  Mol.
- Design, 2022, 36, 157-173).
+ Design,
+ 2022,
+ 36,
+ 157-173).
  The metrics are as follows:
 \end_layout
 
@@ -7683,13 +7863,11 @@ graft
 \end_layout
 
 \begin_layout LyX-Code
-graft src <source COORDS> [srcframe <#>] [srcmask <srcmask> [srccharge <srccharg
-e>]]
+graft src <source COORDS> [srcframe <#>] [srcmask <srcmask> [srccharge <srccharge>]]
 \end_layout
 
 \begin_layout LyX-Code
-  	tgt <target COORDS> [tgtframe <#>] [tgtmask <tgtmask> [tgtcharge <tgtcharge>]
-]
+  	tgt <target COORDS> [tgtframe <#>] [tgtmask <tgtmask> [tgtcharge <tgtcharge>]]
 \end_layout
 
 \begin_layout LyX-Code
@@ -7735,8 +7913,8 @@ COORDS> Source coordinates.
 \begin_inset space ~
 \end_inset
 
-<charge>] If trimming atoms from source, ensure sum of charges on remaining
- atoms equals <charge> via scaling.
+<charge>] If trimming atoms from source,
+ ensure sum of charges on remaining atoms equals <charge> via scaling.
 \end_layout
 
 \end_deeper
@@ -7774,8 +7952,8 @@ COORDS> Target coordinates that will be grafted onto.
 \begin_inset space ~
 \end_inset
 
-<charge>] If trimming atoms from target, ensure sum of charges on remaining
- atoms equals <charge> via scaling.
+<charge>] If trimming atoms from target,
+ ensure sum of charges on remaining atoms equals <charge> via scaling.
 \end_layout
 
 \end_deeper
@@ -7824,10 +8002,9 @@ COORDS> Name of output COORDS set containing source grafted onto target.
 \begin_inset space ~
 \end_inset
 
-<tgt>,<src>] Create a bond between target atom selected by <tgt> and source
- atoms selected by <src> in the final structure.
- Must be specified only once if connecting via internal coordinates, otherwise
- may be specified multiple times.
+<tgt>,<src>] Create a bond between target atom selected by <tgt> and source atoms selected by <src> in the final structure.
+ Must be specified only once if connecting via internal coordinates,
+ otherwise may be specified multiple times.
 \end_layout
 
 \end_deeper
@@ -7841,8 +8018,8 @@ srcfitmask
 \series bold
 tgtfitmask
 \series default
- is specified, the source coordinates will be RMS best-fit onto target using
- the specified atoms.
+ is specified,
+ the source coordinates will be RMS best-fit onto target using the specified atoms.
  Only the atoms specified by 
 \series bold
 srcmask
@@ -7856,10 +8033,9 @@ tgtmask
 \series bold
 bond
 \series default
- keyword can be used to create bonds between target and source in the final
- structure.
- If using internal coordinates to connect the units, exactly one bond must
- be specified.
+ keyword can be used to create bonds between target and source in the final structure.
+ If using internal coordinates to connect the units,
+ exactly one bond must be specified.
 \end_layout
 
 \begin_layout Subsection
@@ -7884,8 +8060,7 @@ loadcrd <filename> [parm <parm> | parmindex<#>] [<trajin args>] [name <name>]
 \begin_inset space ~
 \end_inset
 
-<parmfile/tag>] Topology filename/tag to associate with trajectory (default
- first topology).
+<parmfile/tag>] Topology filename/tag to associate with trajectory (default first topology).
 \end_layout
 
 \begin_layout Description
@@ -7893,7 +8068,8 @@ loadcrd <filename> [parm <parm> | parmindex<#>] [<trajin args>] [name <name>]
 \begin_inset space ~
 \end_inset
 
-<#>] Index of Topology to associate with trajectory (default 0, first topology).
+<#>] Index of Topology to associate with trajectory (default 0,
+ first topology).
 \end_layout
 
 \begin_layout Description
@@ -7901,13 +8077,15 @@ loadcrd <filename> [parm <parm> | parmindex<#>] [<trajin args>] [name <name>]
 \begin_inset space ~
 \end_inset
 
-args>] Additional 'trajin' args; see 
+args>] Additional 'trajin' args;
+ see 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_trajin"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
@@ -7927,21 +8105,18 @@ noprefix "false"
 \begin_inset space ~
 \end_inset
 
-{single|double}] Load as either a single-precision COORDS set (the default)
- or a double-precision FRAMES set (which will use much more memory).
+{single|double}] Load as either a single-precision COORDS set (the default) or a double-precision FRAMES set (which will use much more memory).
 \end_layout
 
 \end_deeper
 \begin_layout Standard
-Immediately load trajectory <filename> as a COORDS data set named <name>
- (default base name of <filename>).
- If <name> is already present the coordinates will be appended to the existing
- data set.
+Immediately load trajectory <filename> as a COORDS data set named <name> (default base name of <filename>).
+ If <name> is already present the coordinates will be appended to the existing data set.
 \end_layout
 
 \begin_layout Standard
-For example, to load frames from trajectories named 'traj1.nc' and 'traj2.nc'
- into a COORDS data set named Crd1:
+For example,
+ to load frames from trajectories named 'traj1.nc' and 'traj2.nc' into a COORDS data set named Crd1:
 \end_layout
 
 \begin_layout LyX-Code
@@ -7977,14 +8152,15 @@ name
 \end_layout
 
 \begin_layout Description
-[<filename>] If specified, trajectory to add to the TRAJ set.
+[<filename>] If specified,
+ trajectory to add to the TRAJ set.
 \end_layout
 
 \end_deeper
 \begin_layout Standard
 This command functions in two ways.
- If <filename> is not provided, all currently loaded input trajectories
- (from 
+ If <filename> is not provided,
+ all currently loaded input trajectories (from 
 \series bold
 \shape italic
 trajin
@@ -7993,11 +8169,11 @@ trajin
  commands) are added to TRAJ data set named <setname>.
  
 \series bold
-Note that if the input trajectory list is cleared (via 'clear trajin') this
- will invalidate the TRAJ data set.
+Note that if the input trajectory list is cleared (via 'clear trajin') this will invalidate the TRAJ data set.
 
 \series default
- In addition, currently all trajectories must have the same number of atoms.
+ In addition,
+ currently all trajectories must have the same number of atoms.
  Otherwise add trajectory <filename> to TRAJ data set <setname>.
 \end_layout
 
@@ -8057,8 +8233,7 @@ permutedihedrals crdset <COORDS set> resrange <range> [{interval | random}]
 \end_layout
 
 \begin_layout LyX-Code
-  <dihedral types> =  alpha beta gamma delta epsilon zeta nu1 nu2 h1p c2p
- chin 
+  <dihedral types> =  alpha beta gamma delta epsilon zeta nu1 nu2 h1p c2p chin 
 \end_layout
 
 \begin_layout LyX-Code
@@ -8092,8 +8267,7 @@ resrange
 
 \begin_layout Description
 interval Rotate found dihedrals by <interval>.
- This is done in an ordered fashion so that every combination of dihedral
- rotations is sampled at least once.
+ This is done in an ordered fashion so that every combination of dihedral rotations is sampled at least once.
 \end_layout
 
 \begin_layout Description
@@ -8246,8 +8420,7 @@ name>] Number of problems data set name.
 \begin_inset space ~
 \end_inset
 
-<max_factor>] The maximum number of total attempted rotations will be <max_facto
-r> * <total # of dihedrals> (default 2).
+<max_factor>] The maximum number of total attempted rotations will be <max_factor> * <total # of dihedrals> (default 2).
 \end_layout
 
 \begin_layout Description
@@ -8263,14 +8436,14 @@ r> * <total # of dihedrals> (default 2).
 \end_inset
 
 <backtrack>] (No longer recommended as of version 5.1.0).
- If a clash is encountered at dihedral N and cannot be resolved, go to dihedral
- N-<backtrack> to try and resolve the clash (default is no backtracking).
+ If a clash is encountered at dihedral N and cannot be resolved,
+ go to dihedral N-<backtrack> to try and resolve the clash (default is no backtracking).
 \end_layout
 
 \begin_deeper
 \begin_layout Description
-[checkallresidues] If specified all residues checked for clashes, otherwise
- only residues up to the currently rotated dihedral check.
+[checkallresidues] If specified all residues checked for clashes,
+ otherwise only residues up to the currently rotated dihedral check.
 \end_layout
 
 \begin_layout Description
@@ -8278,9 +8451,9 @@ r> * <total # of dihedrals> (default 2).
 \begin_inset space ~
 \end_inset
 
-<increment>] If a clash is encountered, first attempt to rotate dihedral
- by increment to resolve it; if it cannot be resolved by a full rotation
- the calculation will backtrack (default 1).
+<increment>] If a clash is encountered,
+ first attempt to rotate dihedral by increment to resolve it;
+ if it cannot be resolved by a full rotation the calculation will backtrack (default 1).
  
 \end_layout
 
@@ -8288,12 +8461,12 @@ r> * <total # of dihedrals> (default 2).
 \end_deeper
 \end_deeper
 \begin_layout Standard
-Create a trajectory by rotating specified dihedrals in a structure by regular
- intervals (
+Create a trajectory by rotating specified dihedrals in a structure by regular intervals (
 \series bold
 interval
 \series default
-), or create 1 structure by randomly rotating specified dihedrals (
+),
+ or create 1 structure by randomly rotating specified dihedrals (
 \series bold
 random
 \series default
@@ -8312,10 +8485,9 @@ crdout
 \series bold
 check
 \series default
- is specified; in such cases the algorithm will attempt to resolve the clash
- as best it can.
- If clashes are not being resolved you can increase the number of rotation
- attempts 
+ is specified;
+ in such cases the algorithm will attempt to resolve the clash as best it can.
+ If clashes are not being resolved you can increase the number of rotation attempts 
 \family typewriter
 \shape italic
 cpptraj
@@ -8329,9 +8501,8 @@ maxfactor
 \end_layout
 
 \begin_layout Standard
-For example, to rotate all backbone dihedrals in a protein with coordinates
- in a file named tz2.rst7 in -120 degree intervals and write the resulting
- trajectory in Amber format to rotations.mdcrd:
+For example,
+ to rotate all backbone dihedrals in a protein with coordinates in a file named tz2.rst7 in -120 degree intervals and write the resulting trajectory in Amber format to rotations.mdcrd:
 \end_layout
 
 \begin_layout LyX-Code
@@ -8343,8 +8514,7 @@ permutedihedrals crdset [TZ2] interval -120 outtraj rotations.mdcrd phi psi
 \end_layout
 
 \begin_layout Standard
-To randomly rotate backbone dihedrals for the same structure and write to
- file random.mol2 in MOL2 format:
+To randomly rotate backbone dihedrals for the same structure and write to file random.mol2 in MOL2 format:
 \end_layout
 
 \begin_layout LyX-Code
@@ -8352,8 +8522,7 @@ reference tz2.rst7 [TZ2]
 \end_layout
 
 \begin_layout LyX-Code
-permutedihedrals crdset [TZ2] random rseed 1 check maxfactor 10 phi psi
- 
+permutedihedrals crdset [TZ2] random rseed 1 check maxfactor 10 phi psi 
 \backslash
 
 \end_layout
@@ -8375,8 +8544,7 @@ prepareforleap crdset <coords set> [frame <#>] name <out coords set>
 \end_layout
 
 \begin_layout LyX-Code
-                  	[leapunitname <unit>] [out <leap input file> [runleap
- <ff file>]]
+                  	[leapunitname <unit>] [out <leap input file> [runleap <ff file>]]
 \end_layout
 
 \begin_layout LyX-Code
@@ -8420,8 +8588,7 @@ prepareforleap crdset <coords set> [frame <#>] name <out coords set>
 \end_layout
 
 \begin_layout LyX-Code
-                  	  [cysmask <cysmask>] [disulfidecut <cut>] [newcysname
- <name>]}]
+                  	  [cysmask <cysmask>] [disulfidecut <cut>] [newcysname <name>]}]
 \end_layout
 
 \begin_layout LyX-Code
@@ -8495,7 +8662,8 @@ set> Output COORDS set containing prepared topology/coordinates.
 
 \begin_deeper
 \begin_layout Description
-[terbymol] If specified, base TER cards on molecules instead of PDB chains.
+[terbymol] If specified,
+ base TER cards on molecules instead of PDB chains.
 \end_layout
 
 \end_deeper
@@ -8533,8 +8701,9 @@ input
 \begin_inset space ~
 \end_inset
 
-file>] File containing LEaP input needed to read in the prepared system
- (loadpdb, bond commands for disulfides, etc).
+file>] File containing LEaP input needed to read in the prepared system (loadpdb,
+ bond commands for disulfides,
+ etc).
 \end_layout
 
 \begin_layout Description
@@ -8546,23 +8715,25 @@ file>] File containing LEaP input needed to read in the prepared system
 \begin_inset space ~
 \end_inset
 
-file>] If specified, CPPTRAJ will attempt to run LEaP directly to generate
- a topology and coordinates; <ff
+file>] If specified,
+ CPPTRAJ will attempt to run LEaP directly to generate a topology and coordinates;
+ <ff
 \begin_inset space ~
 \end_inset
 
-file> should contain the appropriate 'source' commands for loading the desired
- force field parameters.
+file> should contain the appropriate 'source' commands for loading the desired force field parameters.
  Will attempt to produce topology <unit>.parm7 and coordinates <unit>.rst7.
 \end_layout
 
 \begin_layout Description
-[skiperrors] If specified, the command will try to ignore any errors encountered.
+[skiperrors] If specified,
+ the command will try to ignore any errors encountered.
  Can be useful for debugging.
 \end_layout
 
 \begin_layout Description
-[nowat] If specified, remove waters from the system.
+[nowat] If specified,
+ remove waters from the system.
 \end_layout
 
 \begin_deeper
@@ -8576,7 +8747,8 @@ file> should contain the appropriate 'source' commands for loading the desired
 
 \end_deeper
 \begin_layout Description
-[noh] If specified, strip all hydrogen atoms from the system (recommended).
+[noh] If specified,
+ strip all hydrogen atoms from the system (recommended).
 \end_layout
 
 \begin_layout Description
@@ -8592,8 +8764,8 @@ loc
 \begin_inset space ~
 \end_inset
 
-ID>|highestocc}] LEaP cannot handle alternate atom locations, so the command
- will choose location 'A' by default.
+ID>|highestocc}] LEaP cannot handle alternate atom locations,
+ so the command will choose location 'A' by default.
  This can be changed to either <alt
 \begin_inset space ~
 \end_inset
@@ -8630,8 +8802,8 @@ id> or the location with the highest occupancy if
 \begin_inset space ~
 \end_inset
 
-<mask>] If specified, atoms in <mask> will be considered all part of one
- molecule.
+<mask>] If specified,
+ atoms in <mask> will be considered all part of one molecule.
  May be specified multiple times.
 \end_layout
 
@@ -8640,8 +8812,8 @@ id> or the location with the highest occupancy if
 \begin_inset space ~
 \end_inset
 
-<mask>] If specified, determine if atoms selected in <mask> are in the same
- molecule via bonds.
+<mask>] If specified,
+ determine if atoms selected in <mask> are in the same molecule via bonds.
 \end_layout
 
 \begin_layout Standard
@@ -8709,8 +8881,8 @@ Disulfide Handling:
 \end_layout
 
 \begin_layout Description
-[existingdisulfides] Only handle disulfides already present; do not search
- for additional disulfides.
+[existingdisulfides] Only handle disulfides already present;
+ do not search for additional disulfides.
 \end_layout
 
 \begin_layout Description
@@ -8726,8 +8898,7 @@ Disulfide Handling:
 \begin_inset space ~
 \end_inset
 
-<cut>] Sulfur to sulfur atom distance cutoff for forming a disulfide (default
- 2.5 Ang).
+<cut>] Sulfur to sulfur atom distance cutoff for forming a disulfide (default 2.5 Ang).
 \end_layout
 
 \begin_layout Description
@@ -8735,8 +8906,7 @@ Disulfide Handling:
 \begin_inset space ~
 \end_inset
 
-<name>] Name to change cysteine residues that participate in a disulfide
- bond to (default 'CYX').
+<name>] Name to change cysteine residues that participate in a disulfide bond to (default 'CYX').
 \end_layout
 
 \begin_layout Standard
@@ -8761,13 +8931,13 @@ resmapfile
 \end_layout
 
 \begin_layout Description
-[noc1search] If specified, disable search for missing linkages to sugar
- C1 atom bonds.
+[noc1search] If specified,
+ disable search for missing linkages to sugar C1 atom bonds.
 \end_layout
 
 \begin_layout Description
-[nosplitres] If specified, do not attempt to split off functional groups
- from sugars into separate residues.
+[nosplitres] If specified,
+ do not attempt to split off functional groups from sugars into separate residues.
 \end_layout
 
 \begin_layout Description
@@ -8779,8 +8949,7 @@ resmapfile
 \begin_inset space ~
 \end_inset
 
-cutoff>] Initial distance cutoff (default 8 Ang.) for residue center to residue
- center distance when looking for missing sugar linkages.
+cutoff>] Initial distance cutoff (default 8 Ang.) for residue center to residue center distance when looking for missing sugar linkages.
 \end_layout
 
 \begin_layout Description
@@ -8810,7 +8979,8 @@ ideal
 \end_layout
 
 \begin_layout Description
-[hasglycam] If specified, assume sugars already have GLYCAM residue names;
+[hasglycam] If specified,
+ assume sugars already have GLYCAM residue names;
  just check sugar anomer type/configuration/linkage.
 \end_layout
 
@@ -8819,18 +8989,13 @@ ideal
 \begin_inset space ~
 \end_inset
 
-{geometry|name}] Determine whether sugar anomer type/configuration should
- be chosen based on sugar geometry (default) or the residue name.
- CPPTRAJ will report when a mismatch is detected between the sugar anomer
- type/configuration based on geometry and anomer type/configuration based
- on the residue name.
+{geometry|name}] Determine whether sugar anomer type/configuration should be chosen based on sugar geometry (default) or the residue name.
+ CPPTRAJ will report when a mismatch is detected between the sugar anomer type/configuration based on geometry and anomer type/configuration based on the residue name.
 \end_layout
 
 \end_deeper
 \begin_layout Standard
-This command will prepare a structure (usually from a PDB) for processing
- with the Amber program LEaP to generate topology and coordinates files
- for MD simulations.
+This command will prepare a structure (usually from a PDB) for processing with the Amber program LEaP to generate topology and coordinates files for MD simulations.
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Roe2022"
@@ -8838,54 +9003,52 @@ literal "true"
 
 \end_inset
 
- It will handle things like choosing alternate atom locations, removing
- waters/hydrogen atoms from the structure, renaming residues and generating
- 'bond' commands for disulfide bonds, change histidine names based on any
- existing protonation, and renaming residues/atoms and generating 'bond'
- commands for carbohydrates.
- The command can also call LEaP directly to generate the parameters once
- the structure is prepared.
+ It will handle things like choosing alternate atom locations,
+ removing waters/hydrogen atoms from the structure,
+ renaming residues and generating 'bond' commands for disulfide bonds,
+ change histidine names based on any existing protonation,
+ and renaming residues/atoms and generating 'bond' commands for carbohydrates.
+ The command can also call LEaP directly to generate the parameters once the structure is prepared.
 \end_layout
 
 \begin_layout Standard
-If hydrogen atoms are present in the structure, the command will attempt
- a simple and straightforward determination of the protonation state of
- any histidine residues based on where hydrogens are bonded, and assign
- the appropriate residue name.
- The command will also identify any existing disulfide bonds as well as
- potential disulfide bonds and generate the corresponding LEaP ‘bond’ commands
- which can be applied after the structure is loaded in LEaP.
- Potential disulfide bonding atoms can be identified via a user-specifiable
- mask expression.
+If hydrogen atoms are present in the structure,
+ the command will attempt a simple and straightforward determination of the protonation state of any histidine residues based on where hydrogens are bonded,
+ and assign the appropriate residue name.
+ The command will also identify any existing disulfide bonds as well as potential disulfide bonds and generate the corresponding LEaP ‘bond’ commands which can be applied after the structure is loaded in LEaP.
+ Potential disulfide bonding atoms can be identified via a user-specifiable mask expression.
 \end_layout
 
 \begin_layout Standard
-By default, sugars will have their residue names changed to those compatible
- with the GLYCAM force field based on their anomer type (alpha/beta), configurat
-ion (D/L), and linkages (glycosidic and covalent sugar to non-sugar).
+By default,
+ sugars will have their residue names changed to those compatible with the GLYCAM force field based on their anomer type (alpha/beta),
+ configuration (D/L),
+ and linkages (glycosidic and covalent sugar to non-sugar).
  Any recognized functional groups that are part of sugar residues (hydroxyl,
- acetyl, sulfate, etc) will be split into separate residues as required
- by GLYCAM.
- If this happens and 'runleap' has not been specified, CPPTRAJ will warn
- about any residues/atoms that require charge to be adjusted.
- If 'runleap' has not been specified the command will warn about any atoms
- that need to have their charges adjusted after LEaP is run.
+ acetyl,
+ sulfate,
+ etc) will be split into separate residues as required by GLYCAM.
+ If this happens and 'runleap' has not been specified,
+ CPPTRAJ will warn about any residues/atoms that require charge to be adjusted.
+ If 'runleap' has not been specified the command will warn about any atoms that need to have their charges adjusted after LEaP is run.
 \end_layout
 
 \begin_layout Standard
 The command will try to report any potential problems that LEaP might encounter.
- These include residue names that may be unrecognized (and therefore may
- not have parameters), mismatches between detected sugar anomer type/configurati
-on and anomer type/configuration based on the sugar residue name, unrecognized
- sugar linkages, and so on.
+ These include residue names that may be unrecognized (and therefore may not have parameters),
+ mismatches between detected sugar anomer type/configuration and anomer type/configuration based on the sugar residue name,
+ unrecognized sugar linkages,
+ and so on.
  
 \end_layout
 
 \begin_layout Standard
-For example, the following input prepares PDB 4zzw for processing with PDB,
- putting the proper leap commands in leap.4zzw.in, writing the prepared PDB
- to 4zzw.cpptraj.pdb, removing waters and hydrogen atoms, and keeping alternate
- atom locations with the highest occupancy:
+For example,
+ the following input prepares PDB 4zzw for processing with PDB,
+ putting the proper leap commands in leap.4zzw.in,
+ writing the prepared PDB to 4zzw.cpptraj.pdb,
+ removing waters and hydrogen atoms,
+ and keeping alternate atom locations with the highest occupancy:
 \end_layout
 
 \begin_layout LyX-Code
@@ -8911,31 +9074,36 @@ Sugar Residue/Atom Name Mapping File
 \end_layout
 
 \begin_layout Standard
-This file controls how CPPTRAJ will name sugars based on sugar form/chirality
- linkage.
+This file controls how CPPTRAJ will name sugars based on sugar form/chirality linkage.
  It consists of three sections separated by a blank line.
- The first section defines sugar PDB residue names and how they are mapped
- to GLYCAM residue characters:
+ The first section defines sugar PDB residue names and how they are mapped to GLYCAM residue characters:
 \end_layout
 
 \begin_layout LyX-Code
-Format: <ResName> <GlycamCode> <Anomer> <Config> <RingType> "<Name>"
+Format:
+ <ResName> <GlycamCode> <Anomer> <Config> <RingType> "<Name>"
 \end_layout
 
 \begin_layout LyX-Code
-Anomer: A=alpha, B=beta
+Anomer:
+ A=alpha,
+ B=beta
 \end_layout
 
 \begin_layout LyX-Code
-Config: D/L
+Config:
+ D/L
 \end_layout
 
 \begin_layout LyX-Code
-RingType: P=pyranose, F=furanose
+RingType:
+ P=pyranose,
+ F=furanose
 \end_layout
 
 \begin_layout LyX-Code
-Example: 64K A A D P "alpha-D-arabinopyranose" 
+Example:
+ 64K A A D P "alpha-D-arabinopyranose" 
 \end_layout
 
 \begin_layout Standard
@@ -8943,17 +9111,19 @@ The second section contains PDB to GLYCAM atom name maps for residues:
 \end_layout
 
 \begin_layout LyX-Code
-Format: <GLYCAM residue codes> <PDB atom name>,<GLYCAM atom name>[,<anomer>]
- … 
+Format:
+ <GLYCAM residue codes> <PDB atom name>,<GLYCAM atom name>[,<anomer>] … 
 \end_layout
 
 \begin_layout LyX-Code
-If <anomer> (A=alpha, B=beta) is specified, the atom name map is only valid
- for that specific form.
+If <anomer> (A=alpha,
+ B=beta) is specified,
+ the atom name map is only valid for that specific form.
 \end_layout
 
 \begin_layout LyX-Code
-Example: V,W,Y C7,C2N O7,O2N C8,CME 
+Example:
+ V,W,Y C7,C2N O7,O2N C8,CME 
 \end_layout
 
 \begin_layout Standard
@@ -8962,11 +9132,13 @@ The third section contains PDB to GLYCAM linkage residue (i.e.
 \end_layout
 
 \begin_layout LyX-Code
-Format: <PDB residue name> <GLYCAM residue name>
+Format:
+ <PDB residue name> <GLYCAM residue name>
 \end_layout
 
 \begin_layout LyX-Code
-Example: SER OLS 
+Example:
+ SER OLS 
 \end_layout
 
 \begin_layout Subsection
@@ -8979,6 +9151,7 @@ Reference coordinates can now be used and manipulated like COORDS data sets.
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_reference"
+nolink "false"
 
 \end_inset
 
@@ -9024,7 +9197,8 @@ crdset
 \end_inset
 
 set> Coordinates data set to work on.
- If a TRAJ data set is specified, 
+ If a TRAJ data set is specified,
+ 
 \series bold
 name
 \series default
@@ -9111,10 +9285,9 @@ type> Dihedral type to rotate in specified residue.
 
 \end_deeper
 \begin_layout Standard
-Rotate the specified dihedral in given COORDS set to a target value or by
- given increment.
- For example, to set the protein chi dihedral in residue 8 to 35 degrees
- and write out to a mol2 file:
+Rotate the specified dihedral in given COORDS set to a target value or by given increment.
+ For example,
+ to set the protein chi dihedral in residue 8 to 35 degrees and write out to a mol2 file:
 \end_layout
 
 \begin_layout LyX-Code
@@ -9208,10 +9381,9 @@ name> COORDS set containing final molecule.
 \end_deeper
 \begin_layout Standard
 Connect units in different COORDS sets together to form a single molecule.
- Internal coordinates are used to try to determine the correct geometry
- around connection sites.
- The COORDS sets must have connection information set, either from reading
- in an Amber OFF library file or set manually via 
+ Internal coordinates are used to try to determine the correct geometry around connection sites.
+ The COORDS sets must have connection information set,
+ either from reading in an Amber OFF library file or set manually via 
 \series bold
 \emph on
 dataset
@@ -9228,6 +9400,7 @@ reference "subsec:cpptraj-datasetcmd"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
@@ -9235,8 +9408,10 @@ noprefix "false"
 \end_layout
 
 \begin_layout Standard
-For example, the following reads in two Mol2 files as COORDS sets, sets
- up connection atoms, then creates a molecule via 
+For example,
+ the following reads in two Mol2 files as COORDS sets,
+ sets up connection atoms,
+ then creates a molecule via 
 \series bold
 \emph on
 sequence:
@@ -9311,7 +9486,8 @@ name> Name of new set to create.
 \begin_layout Standard
 Split trajectory specified by <crd set> by molecule into a new COORDS set.
  All molecules in <crd set> must be the same size.
- For example, if there are 10 molecules and 10 frames in COORDS set 
+ For example,
+ if there are 10 molecules and 10 frames in COORDS set 
 \begin_inset Quotes eld
 \end_inset
 
@@ -9319,8 +9495,10 @@ Set0
 \begin_inset Quotes erd
 \end_inset
 
-, the following would create a new COORDS set with 100 frames (original
- molecules 1-10 frame 1, original molecules 1-10 frame 2, etc):
+,
+ the following would create a new COORDS set with 100 frames (original molecules 1-10 frame 1,
+ original molecules 1-10 frame 2,
+ etc):
 \end_layout
 
 \begin_layout LyX-Code
@@ -9353,8 +9531,7 @@ set
 \begin_inset space ~
 \end_inset
 
-name> COORDS set to calculate Z-matrix from or use as topology for applied
- Z-matrix.
+name> COORDS set to calculate Z-matrix from or use as topology for applied Z-matrix.
 \end_layout
 
 \begin_layout Description
@@ -9420,8 +9597,7 @@ parmindex
 \begin_inset space ~
 \end_inset
 
-<frame#>] Calculate Z-matrix from specified molecule in specified frame
- (default first frame).
+<frame#>] Calculate Z-matrix from specified molecule in specified frame (default first frame).
 \end_layout
 
 \begin_layout Description
@@ -9449,17 +9625,18 @@ set
 \begin_inset space ~
 \end_inset
 
-name> If 'zset', COORDS set containing final coordinates.
+name> If 'zset',
+ COORDS set containing final coordinates.
  Otherwise contains Z-matrix data.
 \end_layout
 
 \end_deeper
 \begin_layout Standard
 Command for working with Z-matrices.
- If 'zset' is specified, generate coordinates from the specified Z-matrix
- data set and topology.
- Otherwise, calculate a Z-matrix for a single molecule from the specified
- frame of given COORDS data set.
+ If 'zset' is specified,
+ generate coordinates from the specified Z-matrix data set and topology.
+ Otherwise,
+ calculate a Z-matrix for a single molecule from the specified frame of given COORDS data set.
 \end_layout
 
 \begin_layout Section
@@ -9940,7 +10117,8 @@ random
 \begin_inset Text
 
 \begin_layout Plain Layout
-Change default random number generator, create random sets.
+Change default random number generator,
+ create random sets.
 \end_layout
 
 \end_inset
@@ -10200,6 +10378,8 @@ activeref
 \begin_layout LyX-Code
 activeref
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -10212,10 +10392,11 @@ activeref
 \end_layout
 
 \begin_layout Standard
-Set which reference structure should be used when setting up distance-based
- masks for everything but the 'mask' action.
- Numbering starts from 0, so 'activeref 0' selects the first reference structure
- read in, 'activeref 1' selects the second, and so on.
+Set which reference structure should be used when setting up distance-based masks for everything but the 'mask' action.
+ Numbering starts from 0,
+ so 'activeref 0' selects the first reference structure read in,
+ 'activeref 1' selects the second,
+ and so on.
 \end_layout
 
 \begin_layout Subsection
@@ -10237,6 +10418,7 @@ calc <expression>
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-Data-Set-Math"
+nolink "false"
 
 \end_inset
 
@@ -10278,9 +10460,10 @@ clear [{all | <type>}]
 \end_layout
 
 \begin_layout Standard
-Clear list of indicated type, or all lists if 'all' specified.
- Note that when clearing actions or analyses, associated data sets and data
- files are not cleared and vice versa.
+Clear list of indicated type,
+ or all lists if 'all' specified.
+ Note that when clearing actions or analyses,
+ associated data sets and data files are not cleared and vice versa.
 \end_layout
 
 \begin_layout Subsection
@@ -10297,6 +10480,8 @@ name "subsec:cpptraj_create"
 \begin_layout LyX-Code
 create
 \begin_inset Index idx
+range none
+pageformat default
 status open
 
 \begin_layout Plain Layout
@@ -10309,10 +10494,12 @@ create
 \end_layout
 
 \begin_layout Standard
-Add specified data sets to the data file named <filename>; if the file does
- not exist, it will be added to the DataFileList.
- Data files created in this way are only written at the end of coordinate
- processing, analyses, or via the 
+Add specified data sets to the data file named <filename>;
+ if the file does not exist,
+ it will be added to the DataFileList.
+ Data files created in this way are only written at the end of coordinate processing,
+ analyses,
+ or via the 
 \series bold
 \emph on
 'writedata'
@@ -10323,6 +10510,7 @@ Add specified data sets to the data file named <filename>; if the file does
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "sec:Datafile-Commands"
+nolink "false"
 
 \end_inset
 
@@ -10339,8 +10527,9 @@ createset <expression> [xmin <min>] xstep <step> nx <nxvals>
 
 \begin_deeper
 \begin_layout Description
-expression Simple mathematical expression, must contain equals sign, can
- contain X (e.g.
+expression Simple mathematical expression,
+ must contain equals sign,
+ can contain X (e.g.
  Y=2*X).
  If not enclosed in quotes must not contain whitespace.
 \end_layout
@@ -10388,6 +10577,8 @@ name "subsec:cpptraj_datafile_command"
 \begin_layout LyX-Code
 datafile
 \begin_inset Index idx
+range none
+pageformat default
 status open
 
 \begin_layout Plain Layout
@@ -10405,6 +10596,7 @@ Pass <datafile arg> to data file <filename>.
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "sec:Datafile-Commands"
+nolink "false"
 
 \end_inset
 
@@ -10431,8 +10623,7 @@ datafilter {<dataset arg> min <min> max <max> ...} [out <file>] [name <setname>]
 \end_layout
 
 \begin_layout LyX-Code
-           {[multi] | [filterset <set> [newset <newname>]] [countout <countfile>
-]}
+           {[multi] | [filterset <set> [newset <newname>]] [countout <countfile>]}
 \end_layout
 
 \begin_deeper
@@ -10457,7 +10648,8 @@ max
 \begin_inset space ~
 \end_inset
 
-<max> Data set name and min/max cutoffs to use; can specify more than one.
+<max> Data set name and min/max cutoffs to use;
+ can specify more than one.
 \end_layout
 
 \begin_layout Description
@@ -10478,8 +10670,7 @@ max
 \end_layout
 
 \begin_layout Description
-[multi] Filter each set separately instead of all together (creates filter
- set for each input set).
+[multi] Filter each set separately instead of all together (creates filter set for each input set).
  Cannot be used with 'filterset'.
 \end_layout
 
@@ -10488,8 +10679,8 @@ max
 \begin_inset space ~
 \end_inset
 
-<set>] If specified, <set> will be filtered to only contain data that satisfies
- cutoffs.
+<set>] If specified,
+ <set> will be filtered to only contain data that satisfies cutoffs.
  Cannot be used with 'multi'.
 \end_layout
 
@@ -10499,8 +10690,7 @@ max
 \begin_inset space ~
 \end_inset
 
-<newname>] If specified a new set will be created from 'filterset' instead
- of replacing 'filterset'.
+<newname>] If specified a new set will be created from 'filterset' instead of replacing 'filterset'.
 \end_layout
 
 \end_deeper
@@ -10509,8 +10699,8 @@ max
 \begin_inset space ~
 \end_inset
 
-<count>] If specified, write number of elements passed and filtered to <countfil
-e>.
+<count>] If specified,
+ write number of elements passed and filtered to <countfile>.
  Cannot be used with 'multi'.
 \end_layout
 
@@ -10527,7 +10717,8 @@ passed
 \begin_inset Quotes erd
 \end_inset
 
-, 0 otherwise.
+,
+ 0 otherwise.
 \end_layout
 
 \begin_layout Description
@@ -10543,8 +10734,8 @@ Sets Created ('multi')
 \end_layout
 
 \begin_layout Description
-<setname>:<idx> For each input set (number with <idx>, starting from 0)
- contains 1 for elements that 
+<setname>:<idx> For each input set (number with <idx>,
+ starting from 0) contains 1 for elements that 
 \begin_inset Quotes eld
 \end_inset
 
@@ -10552,13 +10743,13 @@ passed
 \begin_inset Quotes erd
 \end_inset
 
-, 0 otherwise.
+,
+ 0 otherwise.
 \end_layout
 
 \end_deeper
 \begin_layout Standard
-Create a data set (optionally named <setname>) containing 1 for data within
- given 
+Create a data set (optionally named <setname>) containing 1 for data within given 
 \series bold
 <min>
 \series default
@@ -10575,22 +10766,24 @@ Create a data set (optionally named <setname>) containing 1 for data within
 \series bold
 <max>
 \series default
- argument, and can be as many as there are specified data sets.
+ argument,
+ and can be as many as there are specified data sets.
  If 
 \series bold
 'multi'
 \series default
- is specified then only filter data sets will be created for each data set
- instead.
+ is specified then only filter data sets will be created for each data set instead.
  If 
 \series bold
 'filterset'
 \series default
- is specified, the specified 
+ is specified,
+ the specified 
 \series bold
 <set>
 \series default
- will be modified to only contain '1' frames; cannot be used with 
+ will be modified to only contain '1' frames;
+ cannot be used with 
 \series bold
 'multi'
 \series default
@@ -10599,21 +10792,20 @@ Create a data set (optionally named <setname>) containing 1 for data within
 \series bold
 'newset'
 \series default
- is also specified, a new set will be created containing the '1' frames
- instead.
+ is also specified,
+ a new set will be created containing the '1' frames instead.
  The 'filterset' functionality only works for 1D scalar sets.
  If 
 \series bold
 'countout'
 \series default
- is specified, the final number of elements passed and filtered out will
- be written to <countfile>.
+ is specified,
+ the final number of elements passed and filtered out will be written to <countfile>.
 \end_layout
 
 \begin_layout Standard
-For example, to read in data from two separate files (d1.dat and a1.dat) and
- generate a filter data set named FILTER having 1 when d1 is between 0.0
- and 3.0 and a1 is between 135.0 and 180.0:
+For example,
+ to read in data from two separate files (d1.dat and a1.dat) and generate a filter data set named FILTER having 1 when d1 is between 0.0 and 3.0 and a1 is between 135.0 and 180.0:
 \end_layout
 
 \begin_layout LyX-Code
@@ -10629,8 +10821,7 @@ datafilter d1 min 0.0 max 3.0 a1 min 135.0 max 180.0 out filter.dat name FILTER
 \end_layout
 
 \begin_layout Standard
-Note that a similar command that can be used with data generated by Actions
- during trajectory processing is 
+Note that a similar command that can be used with data generated by Actions during trajectory processing is 
 \series bold
 \shape italic
 filter
@@ -10640,6 +10831,7 @@ filter
 \begin_inset CommandInset ref
 LatexCommand pageref
 reference "subsec:cpptraj-filter"
+nolink "false"
 
 \end_inset
 
@@ -10679,8 +10871,7 @@ dataset { legend <legend> <set> |
 \end_layout
 
 \begin_layout LyX-Code
-          {drop|keep}points {range <range arg> | [start <#>] [stop <#>]
- [offset <#>]}
+          {drop|keep}points {range <range arg> | [start <#>] [stop <#>] [offset <#>]}
 \end_layout
 
 \begin_layout LyX-Code
@@ -10689,23 +10880,19 @@ dataset { legend <legend> <set> |
 \end_layout
 
 \begin_layout LyX-Code
-          remove <criterion> <select> <value> [and <value2>] [<set selection>]
- |
+          remove <criterion> <select> <value> [and <value2>] [<set selection>] |
 \end_layout
 
 \begin_layout LyX-Code
-          connect {[head <head atom>] [tail <tail atom>]|[headmask <headmask>]
- [tailmask <tailmask>]}
+          connect {[head <head atom>] [tail <tail atom>]|[headmask <headmask>] [tailmask <tailmask>]}
 \end_layout
 
 \begin_layout LyX-Code
-          dim {xdim|ydim|zdim|ndim <#>} [label <label>] [min <min>] [step
- <step>] |
+          dim {xdim|ydim|zdim|ndim <#>} [label <label>] [min <min>] [step <step>] |
 \end_layout
 
 \begin_layout LyX-Code
-          outformat {double|scientific|general} <set arg1> [<set arg 2>
- ...] |
+          outformat {double|scientific|general} <set arg1> [<set arg 2> ...] |
 \end_layout
 
 \begin_layout LyX-Code
@@ -10714,8 +10901,7 @@ dataset { legend <legend> <set> |
 \end_layout
 
 \begin_layout LyX-Code
-          shift [above <value> by <offset>] [below <value> by <offset>]
- <set arg0> ...
+          shift [above <value> by <offset>] [below <value> by <offset>] <set arg0> ...
 \end_layout
 
 \begin_layout LyX-Code
@@ -10727,27 +10913,25 @@ dataset { legend <legend> <set> |
 \end_layout
 
 \begin_layout LyX-Code
-  <mode>:  'distance' 'angle' 'torsion' 'pucker' 'rms' 'matrix' 'vector'
+  <mode>:
+  'distance' 'angle' 'torsion' 'pucker' 'rms' 'matrix' 'vector'
 \end_layout
 
 \begin_layout LyX-Code
-  <type>:  'alpha' 'beta' 'gamma' 'delta' 'epsilon' 'zeta' 'nu0' 'nu1' 'nu2'
- 'nu3'
+  <type>:
+  'alpha' 'beta' 'gamma' 'delta' 'epsilon' 'zeta' 'nu0' 'nu1' 'nu2' 'nu3'
 \end_layout
 
 \begin_layout LyX-Code
-           'nu4' 'h1p' 'c2p' 'chin' 'phi' 'psi' 'chip' 'omega' 'chi2' 'chi3'
- 'chi4'
+           'nu4' 'h1p' 'c2p' 'chin' 'phi' 'psi' 'chip' 'omega' 'chi2' 'chi3' 'chi4'
 \end_layout
 
 \begin_layout LyX-Code
-           'chi5' 'pucker' 'noe' 'distance' 'covariance' 'mass-weighted
- covariance'
+           'chi5' 'pucker' 'noe' 'distance' 'covariance' 'mass-weighted covariance'
 \end_layout
 
 \begin_layout LyX-Code
-           'correlation' 'distance covariance' 'IDEA' 'IRED' 'dihedral covarianc
-e'
+           'correlation' 'distance covariance' 'IDEA' 'IRED' 'dihedral covariance'
 \end_layout
 
 \begin_layout LyX-Code
@@ -10816,8 +11000,7 @@ makexy
 \begin_inset space ~
 \end_inset
 
-<Yset> Create a new data set (optionally named <name>) with X values from
- <Xset> and Y values from <Yset>.
+<Yset> Create a new data set (optionally named <name>) with X values from <Xset> and Y values from <Yset>.
 \end_layout
 
 \begin_layout Description
@@ -10829,8 +11012,7 @@ vectorcoord
 \begin_inset space ~
 \end_inset
 
-<set> Extract X/Y/Z coordinates from vector data set into a new 1D data
- set.
+<set> Extract X/Y/Z coordinates from vector data set into a new 1D data set.
 \end_layout
 
 \begin_layout Description
@@ -10847,8 +11029,7 @@ cat
 \end_inset
 
 ...
- Concatenate two or more data sets into a new data set (optionally named
- <name>).
+ Concatenate two or more data sets into a new data set (optionally named <name>).
  Only works for scalar 1D and string sets.
 \end_layout
 
@@ -10877,8 +11058,7 @@ rows
 \begin_inset space ~
 \end_inset
 
-<nrows> Convert 1D data set into row-major 2D data set with specified number
- of rows and columns.
+<nrows> Convert 1D data set into row-major 2D data set with specified number of rows and columns.
 \end_layout
 
 \begin_layout Description
@@ -10895,8 +11075,8 @@ arg1>
 \end_inset
 
 ...
- Drop or keep specified points from data set(s), optionally creating a new
- data set.
+ Drop or keep specified points from data set(s),
+ optionally creating a new data set.
 \end_layout
 
 \begin_deeper
@@ -10966,16 +11146,17 @@ remove
 \begin_inset space ~
 \end_inset
 
-selection>] Remove data sets from <set selection> according to specified
- criterion and selection.
+selection>] Remove data sets from <set selection> according to specified criterion and selection.
 \end_layout
 
 \begin_layout LyX-Code
-<criterion>:  'ifaverage' 'ifsize' 'ifmode' 'iftype'
+<criterion>:
+  'ifaverage' 'ifsize' 'ifmode' 'iftype'
 \end_layout
 
 \begin_layout LyX-Code
-<select>   :  'equal' '==' 'notequal' '!=' 'lessthan' '<' 
+<select>   :
+  'equal' '==' 'notequal' '!=' 'lessthan' '<' 
 \end_layout
 
 \begin_layout LyX-Code
@@ -10999,11 +11180,13 @@ reference "subsec:cpptraj-sequence"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
 ) to COORDS set(s).
- Head atoms connect to previous residue, tail atoms connect to next residue.
+ Head atoms connect to previous residue,
+ tail atoms connect to next residue.
  Can use either absolute atom numbers or atom mask expressions.
 \end_layout
 
@@ -11226,7 +11409,8 @@ arg0>
 \begin_inset space ~
 \end_inset
 
-<type>] Set data set(s) type to 'type', useful for e.g.
+<type>] Set data set(s) type to 'type',
+ useful for e.g.
  analysis with 
 \series bold
 \shape italic
@@ -11240,13 +11424,15 @@ statistics
 distance
 \series default
 \shape default
-, 
+,
+ 
 \series bold
 \shape italic
 dihedral
 \series default
 \shape default
-, 
+,
+ 
 \series bold
 \shape italic
 pucker
@@ -11273,7 +11459,8 @@ bound
 \begin_inset space ~
 \end_inset
 
-<upper>] Lower and upper bounds for NOE (in Angstroms); must specify both.
+<upper>] Lower and upper bounds for NOE (in Angstroms);
+ must specify both.
 \end_layout
 
 \begin_layout Description
@@ -11281,8 +11468,8 @@ bound
 \begin_inset space ~
 \end_inset
 
-<expected>] Expected value for NOE (in Angstroms); if not given '(<lower>
- + <upper>)' / 2.0 is used.
+<expected>] Expected value for NOE (in Angstroms);
+ if not given '(<lower> + <upper>)' / 2.0 is used.
 \end_layout
 
 \begin_layout Description
@@ -11299,16 +11486,17 @@ bound
 
 \end_deeper
 \begin_layout Standard
-Either set the legend for a single data set, create a new set with X values
- from one set and Y values from another, concatenate 2 or more sets, make
- a 2D set from 1D set, remove sets according to a certain criterion, or
- change the mode/type for one or more data sets.
+Either set the legend for a single data set,
+ create a new set with X values from one set and Y values from another,
+ concatenate 2 or more sets,
+ make a 2D set from 1D set,
+ remove sets according to a certain criterion,
+ or change the mode/type for one or more data sets.
 \end_layout
 
 \begin_layout Standard
-Setting the mode/type can be useful for cases where the data set is being
- read in from a file; for example when reading in a dihedral data set the
- type can be set to 'dihedral' so that various Analysis routines like 
+Setting the mode/type can be useful for cases where the data set is being read in from a file;
+ for example when reading in a dihedral data set the type can be set to 'dihedral' so that various Analysis routines like 
 \series bold
 \shape italic
 statistics
@@ -12185,11 +12373,11 @@ IRED vector.
 \end_layout
 
 \begin_layout Standard
-The invert mode takes a group of M 1D data sets of size N and create N new
- "inverted" data sets of size M.
- This is similar to the invert keyword already available for standard and
- Grace data writes, but operates directly on data sets.
- For example, given the following two data sets:
+The invert mode takes a group of M 1D data sets of size N and create N new "inverted" data sets of size M.
+ This is similar to the invert keyword already available for standard and Grace data writes,
+ but operates directly on data sets.
+ For example,
+ given the following two data sets:
 \end_layout
 
 \begin_layout LyX-Code
@@ -12225,10 +12413,9 @@ N0 N1 N2
 \end_layout
 
 \begin_layout Standard
-The dataset invert command can be useful if you want to easily view output
- from multiple analysis commands in a single graph.
- For example, to view state counts from two different simulations side by
- side:
+The dataset invert command can be useful if you want to easily view output from multiple analysis commands in a single graph.
+ For example,
+ to view state counts from two different simulations side by side:
 \end_layout
 
 \begin_layout LyX-Code
@@ -12252,10 +12439,10 @@ writedata statecount.agr Inverted*
 \end_layout
 
 \begin_layout Standard
-The dataset shift command can be used for wrapping circular values, such
- as torsions.
- For example, to ensure a pucker has a range from 0 to 360 instead of -180
- to 180:
+The dataset shift command can be used for wrapping circular values,
+ such as torsions.
+ For example,
+ to ensure a pucker has a range from 0 to 360 instead of -180 to 180:
 \end_layout
 
 \begin_layout LyX-Code
@@ -12277,6 +12464,8 @@ debug | prnlev
 \begin_layout LyX-Code
 debug
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -12295,8 +12484,7 @@ debug
 \begin_layout Standard
 Set the level of debug information to print.
  In general the higher the <#> the more information that is printed.
- If <type> is specified only set the debug level for a specific area of
- 
+ If <type> is specified only set the debug level for a specific area of 
 \shape italic
 cpptraj.
 \end_layout
@@ -12317,8 +12505,8 @@ Turn printing of ensemble member number filename extensions on or off.
 \begin_layout Standard
 
 \series bold
-NOTE: THE 'ensextension off' OPTION HAS NOT BEEN FULLY TESTED IN PARALLEL
- AND IS NOT CURRENTLY RECOMMENDED.
+NOTE:
+ THE 'ensextension off' OPTION HAS NOT BEEN FULLY TESTED IN PARALLEL AND IS NOT CURRENTLY RECOMMENDED.
 \end_layout
 
 \begin_layout Subsection
@@ -12367,8 +12555,10 @@ mode
 \begin_inset space ~
 \end_inset
 
-{sum|avg} If sum, matrix elements will be summed.
- If avg, matrix elements will be averaged.
+{sum|avg} If sum,
+ matrix elements will be summed.
+ If avg,
+ matrix elements will be averaged.
 \end_layout
 
 \begin_layout Description
@@ -12416,14 +12606,15 @@ set
 \begin_inset space ~
 \end_inset
 
-name>:<idx> Flattened 1D sets when more than one input matrix; index starts
- from 1.
+name>:<idx> Flattened 1D sets when more than one input matrix;
+ index starts from 1.
 \end_layout
 
 \end_deeper
 \begin_layout Standard
 Flatten 1 or more matrices into 1D array(s) by summing or averaging elements.
- For example, given a matrix with values like this:
+ For example,
+ given a matrix with values like this:
 \end_layout
 
 \begin_layout LyX-Code
@@ -12499,7 +12690,8 @@ go | run
 \end_layout
 
 \begin_layout Standard
-Begin trajectory processing, followed by analysis and datafile write.
+Begin trajectory processing,
+ followed by analysis and datafile write.
 \end_layout
 
 \begin_layout Subsection
@@ -12509,6 +12701,8 @@ help
 \begin_layout LyX-Code
 help
 \begin_inset Index idx
+range none
+pageformat default
 status open
 
 \begin_layout Plain Layout
@@ -12533,8 +12727,7 @@ help
 \end_layout
 
 \begin_layout LyX-Code
- 	    Form[ats] [{trajin|trajout|readdata|writedata|parm|parmwrite} [<fmt
- key>]] |
+ 	    Form[ats] [{trajin|trajout|readdata|writedata|parm|parmwrite} [<fmt key>]] |
 \end_layout
 
 \begin_layout LyX-Code
@@ -12542,7 +12735,8 @@ help
 \end_layout
 
 \begin_layout LyX-Code
-	Command Categories: Gen[eral] Sys[tem] Coor[ds] Traj[ectory] Top[ology]
+	Command Categories:
+ Gen[eral] Sys[tem] Coor[ds] Traj[ectory] Top[ology]
 \end_layout
 
 \begin_layout LyX-Code
@@ -12550,35 +12744,50 @@ help
 \end_layout
 
 \begin_layout LyX-Code
-  All                : Print all known commands.
+  All                :
+ Print all known commands.
 \end_layout
 
 \begin_layout LyX-Code
-  <cmd>              : Print help for command <cmd>.
+  <cmd>              :
+ Print help for command <cmd>.
 \end_layout
 
 \begin_layout LyX-Code
-  <command category> : Print all commands in specified category.
+  <command category> :
+ Print all commands in specified category.
 \end_layout
 
 \begin_layout LyX-Code
-  Form[ats]          : Help for file formats.
+  Form[ats]          :
+ Help for file formats.
 \end_layout
 
 \begin_layout LyX-Code
-  Mask               : Help for mask syntax.
+  Mask               :
+ Help for mask syntax.
 \end_layout
 
 \begin_layout Standard
-If 'All' is specifed, list all commands known to 
+If 'All' is specifed,
+ list all commands known to 
 \shape italic
 cpptraj
 \shape default
 .
- If given with a command, print help for that command.
- Otherwise, list all commands of a certain category (General, System, Coords,
- Trajectory, Topology, Action, Analysis, or Control), help for various file
- formats, or help with atom mask syntax.
+ If given with a command,
+ print help for that command.
+ Otherwise,
+ list all commands of a certain category (General,
+ System,
+ Coords,
+ Trajectory,
+ Topology,
+ Action,
+ Analysis,
+ or Control),
+ help for various file formats,
+ or help with atom mask syntax.
 \end_layout
 
 \begin_layout Subsection
@@ -12605,6 +12814,8 @@ noexitonerror
 \begin_layout LyX-Code
 noexitonerror
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -12628,7 +12839,8 @@ cpptraj
 noexitonerror
 \series default
 \shape default
- is specified, 
+ is specified,
+ 
 \shape italic
 cpptraj
 \shape default
@@ -12643,6 +12855,8 @@ noprogress
 \begin_layout LyX-Code
 noprogress
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -12668,8 +12882,7 @@ parallelanalysis [sync]
 
 \begin_layout Standard
 MPI only.
- Divide all currently set up analyses as evenly as possible among available
- MPI processes and execute.
+ Divide all currently set up analyses as evenly as possible among available MPI processes and execute.
  Each analysis will get a single MPI process.
  If 
 \series bold
@@ -12677,13 +12890,15 @@ sync
 \series default
  is specified all data will be synced back to the master process (for e.g.
  subsequent analysis).
- For an example of how to use the parallelanalysis command, see 
+ For an example of how to use the parallelanalysis command,
+ see 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_hausdorff"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
@@ -12741,18 +12956,20 @@ args> Files containing CPPTRAJ output to get timing data from.
 \begin_inset space ~
 \end_inset
 
-{time|cores|filename}] Sort timing data sets by either time, number of cores
- (MPI processes * OpenMP threads), or file name.
+{time|cores|filename}] Sort timing data sets by either time,
+ number of cores (MPI processes * OpenMP threads),
+ or file name.
 \end_layout
 
 \begin_layout Description
-[includebad] If specified, include run output for which timing data cannot
- be extracted (e.g.
+[includebad] If specified,
+ include run output for which timing data cannot be extracted (e.g.
  an incomplete/failed run).
 \end_layout
 
 \begin_layout Description
-[showdetails] If specified, details about each run will be printed to STDOUT.
+[showdetails] If specified,
+ details about each run will be printed to STDOUT.
 \end_layout
 
 \begin_layout Description
@@ -12760,30 +12977,27 @@ args> Files containing CPPTRAJ output to get timing data from.
 \begin_inset space ~
 \end_inset
 
-{trajproc|trajread|actframe} If specified, report time other than the total
- time (which is the default):
+{trajproc|trajread|actframe} If specified,
+ report time other than the total time (which is the default):
 \end_layout
 
 \begin_deeper
 \begin_layout Description
-trajproc Total trajectory processing time (trajectory I/O plus action frame
- time).
+trajproc Total trajectory processing time (trajectory I/O plus action frame time).
 \end_layout
 
 \begin_layout Description
-trajread Trajectory read time (requires compiling with '-timer' configure
- option/-DTIMER compiler define).
+trajread Trajectory read time (requires compiling with '-timer' configure option/-DTIMER compiler define).
 \end_layout
 
 \begin_layout Description
-actframe Action frame time (requires compiling with '-timer' configure option/-D
-TIMER compiler define).
+actframe Action frame time (requires compiling with '-timer' configure option/-DTIMER compiler define).
 \end_layout
 
 \end_deeper
 \begin_layout Description
-[reverse] Instead of longest time to shortest time, sort shortest time to
- longest time.
+[reverse] Instead of longest time to shortest time,
+ sort shortest time to longest time.
 \end_layout
 
 \begin_layout Description
@@ -12792,8 +13006,7 @@ TIMER compiler define).
 \end_inset
 
 <file>] Group run output by a property and write to a file.
- Additional details will be written like speedup and efficiency (relative
- to the slowest run).
+ Additional details will be written like speedup and efficiency (relative to the slowest run).
 \end_layout
 
 \begin_deeper
@@ -12819,8 +13032,8 @@ name Group by run type name (see
 \end_layout
 
 \begin_layout Description
-kind Group by run type name; OpenMP runs are separated by number of OpenMP
- threads.
+kind Group by run type name;
+ OpenMP runs are separated by number of OpenMP threads.
 \end_layout
 
 \end_deeper
@@ -12835,17 +13048,22 @@ DataSets Created:
 
 \begin_layout Description
 <setname>[name] Set containing shortedhand run names.
- Consists of a prefix (S for serial, O for OpenMP, M for MPI, H for hybrid
- MPI/OpenMP) followed by numbers indicating number of MPI processes 'x'
- OpenMP threads; e.g., H16x4 means a hybrid run consisting of 16 MPI processes
- and 4 OpenMP threads per process.
- If CUDA is active, the name will be wrapped in 'G()', e.g.
+ Consists of a prefix (S for serial,
+ O for OpenMP,
+ M for MPI,
+ H for hybrid MPI/OpenMP) followed by numbers indicating number of MPI processes 'x' OpenMP threads;
+ e.g.,
+ H16x4 means a hybrid run consisting of 16 MPI processes and 4 OpenMP threads per process.
+ If CUDA is active,
+ the name will be wrapped in 'G()',
+ e.g.
  G(H16x4).
 \end_layout
 
 \begin_layout Description
 <setname>[dir] Set containing output directory prefixes.
- If no directory prefix, just contains output file name.
+ If no directory prefix,
+ just contains output file name.
 \end_layout
 
 \end_deeper
@@ -12866,6 +13084,8 @@ precision
 \begin_layout LyX-Code
 precision
 \begin_inset Index idx
+range none
+pageformat default
 status open
 
 \begin_layout Plain Layout
@@ -12878,20 +13098,19 @@ precision
 \end_layout
 
 \begin_layout Standard
-Set the precision for all data sets in data file <filename> or data set(s)
- specified by <dataset arg> to 
+Set the precision for all data sets in data file <filename> or data set(s) specified by <dataset arg> to 
 \shape italic
 width.precision
 \shape default
-, where width is the column width and precision is the number of digits
- after the decimal point.
- Note that the <precision> argument only applies to floating-point data
- sets.
+,
+ where width is the column width and precision is the number of digits after the decimal point.
+ Note that the <precision> argument only applies to floating-point data sets.
 \end_layout
 
 \begin_layout Standard
-For example, if one wanted to set the precision of the output of an Rmsd
- calculation to 8.3, the input could be:
+For example,
+ if one wanted to set the precision of the output of an Rmsd calculation to 8.3,
+ the input could be:
 \end_layout
 
 \begin_layout LyX-Code
@@ -12940,13 +13159,13 @@ random [setdefault {marsaglia|stdlib|mt|pcg32|xo128}]
 
 \begin_deeper
 \begin_layout Description
-setdefault If specified, change the default random number generator (RNG).
+setdefault If specified,
+ change the default random number generator (RNG).
 \end_layout
 
 \begin_deeper
 \begin_layout Description
-marsaglia Use the Marsaglia RNG that is used in the Amber MD programs sander/pme
-md.
+marsaglia Use the Marsaglia RNG that is used in the Amber MD programs sander/pmemd.
 \end_layout
 
 \begin_layout Description
@@ -12954,8 +13173,8 @@ stdlib Use the C standard library RNG.
 \end_layout
 
 \begin_layout Description
-mt Use the C++11 implementation of the Mersenne twister (mt19937); only
- available with C++11 support.
+mt Use the C++11 implementation of the Mersenne twister (mt19937);
+ only available with C++11 support.
 \end_layout
 
 \begin_layout Description
@@ -12984,8 +13203,8 @@ literal "true"
 
 \end_deeper
 \begin_layout Description
-createset If specified, create a 1D data set filled with random numbers
- of the specified type.
+createset If specified,
+ create a 1D data set filled with random numbers of the specified type.
 \end_layout
 
 \begin_deeper
@@ -13006,8 +13225,10 @@ settype
 \begin_inset space ~
 \end_inset
 
-{int|float01|gauss} Type of numbers to use; integer, floating point between
- 0 and 1, Gaussian distribution.
+{int|float01|gauss} Type of numbers to use;
+ integer,
+ floating point between 0 and 1,
+ Gaussian distribution.
 \end_layout
 
 \begin_deeper
@@ -13039,8 +13260,8 @@ seed
 \end_deeper
 \end_deeper
 \begin_layout Standard
-This command can be used to set the default random number generator used
- in CPPTRAJ, and/or create a 1D data set filled with random values.
+This command can be used to set the default random number generator used in CPPTRAJ,
+ and/or create a 1D data set filled with random values.
 \end_layout
 
 \begin_layout Subsection
@@ -13057,6 +13278,8 @@ name "subsec:cpptraj_readdata"
 \begin_layout LyX-Code
 readdata
 \begin_inset Index idx
+range none
+pageformat default
 status open
 
 \begin_layout Plain Layout
@@ -13087,8 +13310,7 @@ as
 \begin_inset space ~
 \end_inset
 
-<fmt> Force <filename> to be read as a specific format using given format
- keyword.
+<fmt> Force <filename> to be read as a specific format using given format keyword.
 \end_layout
 
 \begin_layout Description
@@ -13102,6 +13324,7 @@ Read data from file <filename> and store as data sets.
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "tab:cpptraj-DataFile-formats"
+nolink "false"
 
 \end_inset
 
@@ -13110,11 +13333,13 @@ reference "tab:cpptraj-DataFile-formats"
 \begin_inset CommandInset ref
 LatexCommand ref
 reference "sec:Datafile-Commands"
+nolink "false"
 
 \end_inset
 
 .
- For example, given the file calc.dat:
+ For example,
+ given the file calc.dat:
 \end_layout
 
 \begin_layout LyX-Code
@@ -13130,7 +13355,8 @@ The command '
 \family typewriter
 readdata calc.dat
 \family default
-' would read data into two data sets, calc.dat:2 (legend set to 
+' would read data into two data sets,
+ calc.dat:2 (legend set to 
 \begin_inset Quotes eld
 \end_inset
 
@@ -13192,14 +13418,16 @@ args> Additional data file arguments.
 
 \end_deeper
 \begin_layout Standard
-Read data sets as an ensemble, i.e.
+Read data sets as an ensemble,
+ i.e.
  each file is a different member of an ensemble.
  This command is MPI-aware.
 \end_layout
 
 \begin_layout Standard
-If one filename is given, it is assumed it is the "lowest" member of an
- ensemble with a numerical extension, e.g.
+If one filename is given,
+ it is assumed it is the "lowest" member of an ensemble with a numerical extension,
+ e.g.
  'file.001' and the remaining files are searched for automatically.
  Otherwise all other members of the ensemble can be specified with 
 \series bold
@@ -13211,6 +13439,7 @@ If one filename is given, it is assumed it is the "lowest" member of an
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "sec:Datafile-Commands"
+nolink "false"
 
 \end_inset
 
@@ -13218,7 +13447,8 @@ reference "sec:Datafile-Commands"
 \end_layout
 
 \begin_layout Standard
-For example, to read in data files named cpout.001 to cpout.006 automatically:
+For example,
+ to read in data files named cpout.001 to cpout.006 automatically:
 \end_layout
 
 \begin_layout LyX-Code
@@ -13236,8 +13466,7 @@ readensembledata cpout.001
 \end_layout
 
 \begin_layout LyX-Code
-                 filenames cpout.002,cpout.003,cpout.004,cpout.005,cpout.006
- 
+                 filenames cpout.002,cpout.003,cpout.004,cpout.005,cpout.006 
 \backslash
 
 \end_layout
@@ -13253,6 +13482,8 @@ readinput
 \begin_layout LyX-Code
 readinput
 \begin_inset Index idx
+range none
+pageformat default
 status open
 
 \begin_layout Plain Layout
@@ -13337,7 +13568,8 @@ rX
 \begin_inset space ~
 \end_inset
 
-<rX> Value of RX (X=1-4, default 0.0)
+<rX> Value of RX (X=1-4,
+ default 0.0)
 \end_layout
 
 \begin_layout Description
@@ -13409,10 +13641,14 @@ refindex
 \begin_inset space ~
 \end_inset
 
-reference} Use distance/angle/dihedral in reference structure to determine
- values for r1, r2, r3, and r4.
- The value of r2 is set to <r2> + <off>, r3 = r2, r1 = r2 - <width>, r4
- = r3 + <width>.
+reference} Use distance/angle/dihedral in reference structure to determine values for r1,
+ r2,
+ r3,
+ and r4.
+ The value of r2 is set to <r2> + <off>,
+ r3 = r2,
+ r1 = r2 - <width>,
+ r4 = r3 + <width>.
 \end_layout
 
 \begin_layout Description
@@ -13420,8 +13656,7 @@ reference} Use distance/angle/dihedral in reference structure to determine
 \begin_inset space ~
 \end_inset
 
-<off>] (Reference only) Value to offset distance/angle/torsion in reference
- by (default 0.0).
+<off>] (Reference only) Value to offset distance/angle/torsion in reference by (default 0.0).
 \end_layout
 
 \begin_layout Description
@@ -13429,7 +13664,8 @@ reference} Use distance/angle/dihedral in reference structure to determine
 \begin_inset space ~
 \end_inset
 
-<width>] (Reference only) Width between r1 and r2, r3 and r4 (default 0.5).
+<width>] (Reference only) Width between r1 and r2,
+ r3 and r4 (default 0.5).
 \end_layout
 
 \begin_layout Description
@@ -13438,17 +13674,16 @@ reference} Use distance/angle/dihedral in reference structure to determine
 \end_inset
 
 <outfile>] Write restraints to outfile.
- If not specified, write to STDOUT.
+ If not specified,
+ write to STDOUT.
 \end_layout
 
 \end_deeper
 \begin_layout Standard
 Generate Amber-style distance restraints for use with nmropt=1.
- This is particularly useful for generating distance restraints based off
- of reference coordinates.
- For example to generate a distance restraint between two C5' atoms using
- the current distance between them in a reference structure, offsetting
- the distance by 1.0 Ang.:
+ This is particularly useful for generating distance restraints based off of reference coordinates.
+ For example to generate a distance restraint between two C5' atoms using the current distance between them in a reference structure,
+ offsetting the distance by 1.0 Ang.:
 \end_layout
 
 \begin_layout LyX-Code
@@ -13481,9 +13716,10 @@ runanalysis [<analysiscmd> [<analysis args>]]
 \begin_layout Standard
 Run given analysis command immediately and write any data generated.
  If no command is given run any analysis currently set up.
- NOTE: When 'runanalysis' is specified alone, data is not automatically
- written; to write data generated with 'runanalysis' use the 'writedata'
- command (this allows multiple analysis runs between output if desired).
+ NOTE:
+ When 'runanalysis' is specified alone,
+ data is not automatically written;
+ to write data generated with 'runanalysis' use the 'writedata' command (this allows multiple analysis runs between output if desired).
 \end_layout
 
 \begin_layout Subsection
@@ -13493,6 +13729,8 @@ select
 \begin_layout LyX-Code
 select
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -13505,8 +13743,8 @@ select
 \end_layout
 
 \begin_layout Standard
-Prints the number of selected atoms corresponding to the given mask, as
- well as the atom numbers with format:
+Prints the number of selected atoms corresponding to the given mask,
+ as well as the atom numbers with format:
 \end_layout
 
 \begin_layout LyX-Code
@@ -13514,8 +13752,8 @@ Selected= <#atom1> <#atom2> ...
 \end_layout
 
 \begin_layout Standard
-This does not affect the state in any way, but is intended for use in scripts
- etc.
+This does not affect the state in any way,
+ but is intended for use in scripts etc.
  for testing the results of a mask expression.
 \end_layout
 
@@ -13539,13 +13777,12 @@ Show the results of a data set selection.
 \begin_layout Standard
 Either the [<aspect>] or the <index> arguments may be omitted.
  A '*' can be used in place of <name> or [<aspect>] as a wildcard.
- The <index> argument can be a single number or a range separated by '-'
- and ','.
+ The <index> argument can be a single number or a range separated by '-' and ','.
 \end_layout
 
 \begin_layout Standard
-This command does not affect the state in any way, but is particularly useful
- in interactive mode for determining the results of a dataset argument.
+This command does not affect the state in any way,
+ but is particularly useful in interactive mode for determining the results of a dataset argument.
 \end_layout
 
 \begin_layout Subsection
@@ -13599,7 +13836,8 @@ usediskcache {on|off}
 \end_layout
 
 \begin_layout Standard
-If on, CPPTRAJ will attempt to cache data sets to disk if possible.
+If on,
+ CPPTRAJ will attempt to cache data sets to disk if possible.
  This currently only works for integer data sets (e.g.
  
 \series bold
@@ -13611,7 +13849,8 @@ hbond
 \series bold
 series
 \series default
- data sets, etc).
+ data sets,
+ etc).
 \end_layout
 
 \begin_layout Subsection
@@ -13630,14 +13869,17 @@ write [<filename> <datasetname0> [<datasetname1> ...]] [<DataFile Options>]
 \end_layout
 
 \begin_layout Standard
-With no arguments, write all files currently in the data file list.
- Otherwise, write specified data set(s) to <filename>.
- This is like the 'create' command except a data file is not added to the
- data file list; it is written immediately.
+With no arguments,
+ write all files currently in the data file list.
+ Otherwise,
+ write specified data set(s) to <filename>.
+ This is like the 'create' command except a data file is not added to the data file list;
+ it is written immediately.
  See 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "sec:Datafile-Commands"
+nolink "false"
 
 \end_inset
 
@@ -13674,7 +13916,8 @@ head
 \family typewriter
 head
 \family default
-, which lists the first few lines of a file.
+,
+ which lists the first few lines of a file.
 \end_layout
 
 \begin_layout Description
@@ -13686,7 +13929,8 @@ less
 \family typewriter
 less
 \family default
-, which can be used to view the contents of a file.
+,
+ which can be used to view the contents of a file.
 \end_layout
 
 \begin_layout Description
@@ -14112,7 +14356,9 @@ parm
 \begin_inset space ~
 \end_inset
 
-[<name>] Select topology corresponding to given file name, tag, or name.
+[<name>] Select topology corresponding to given file name,
+ tag,
+ or name.
 \end_layout
 
 \begin_layout Description
@@ -14120,7 +14366,8 @@ parmindex
 \begin_inset space ~
 \end_inset
 
-[<#>] Select topology by order in which it was loaded, starting from 0.
+[<#>] Select topology by order in which it was loaded,
+ starting from 0.
 \end_layout
 
 \begin_layout Standard
@@ -14167,7 +14414,9 @@ Description
 \begin_inset Text
 
 \begin_layout Plain Layout
-angleinfo, angles, printangles
+angleinfo,
+ angles,
+ printangles
 \end_layout
 
 \end_inset
@@ -14187,7 +14436,9 @@ Print angle info for selected atoms.
 \begin_inset Text
 
 \begin_layout Plain Layout
-atominfo, atoms, printatoms
+atominfo,
+ atoms,
+ printatoms
 \end_layout
 
 \end_inset
@@ -14207,7 +14458,9 @@ Print details for selected atoms.
 \begin_inset Text
 
 \begin_layout Plain Layout
-bondinfo, bonds, printbonds
+bondinfo,
+ bonds,
+ printbonds
 \end_layout
 
 \end_inset
@@ -14307,7 +14560,9 @@ Compare two topologies and report differences.
 \begin_inset Text
 
 \begin_layout Plain Layout
-dihedralinfo, dihedrals, printdihedrals
+dihedralinfo,
+ dihedrals,
+ printdihedrals
 \end_layout
 
 \end_inset
@@ -14347,7 +14602,9 @@ Perform hydrogen mass repartitioning.
 \begin_inset Text
 
 \begin_layout Plain Layout
-improperinfo, impropers, printimpropers
+improperinfo,
+ impropers,
+ printimpropers
 \end_layout
 
 \end_inset
@@ -14507,7 +14764,8 @@ Write selected topology to file.
 \begin_inset Text
 
 \begin_layout Plain Layout
-printub, ubinfo
+printub,
+ ubinfo
 \end_layout
 
 \end_inset
@@ -14664,7 +14922,8 @@ parmindex
 \begin_inset space ~
 \end_inset
 
-<mask3>] If specified, angles must match all masks.
+<mask3>] If specified,
+ angles must match all masks.
 \end_layout
 
 \begin_layout Description
@@ -14681,8 +14940,7 @@ parmindex
 
 \end_deeper
 \begin_layout Standard
-Print angle information of atoms in <mask> for selected topology (first
- loaded topology by default) with format:
+Print angle information of atoms in <mask> for selected topology (first loaded topology by default) with format:
 \end_layout
 
 \begin_layout LyX-Code
@@ -14694,15 +14952,18 @@ Where
 \family typewriter
 Angle
 \family default
- is the internal angle index, 
+ is the internal angle index,
+ 
 \family typewriter
 Kthet
 \family default
- is the angle force constant, 
+ is the angle force constant,
+ 
 \family typewriter
 degrees
 \family default
- is the angle equilibrium value, 
+ is the angle equilibrium value,
+ 
 \family typewriter
 atom names
 \family default
@@ -14710,7 +14971,8 @@ atom names
 \family typewriter
 :<residue num>@<atom name>
 \family default
-, and 
+,
+ and 
 \family typewriter
 (numbers)
 \family default
@@ -14719,8 +14981,10 @@ atom names
 \end_layout
 
 \begin_layout Standard
-If 3 masks are given instead of 1, print info for angles with first atom
- in <mask1>, second atom in <mask2>, and third atom in <mask3>.
+If 3 masks are given instead of 1,
+ print info for angles with first atom in <mask1>,
+ second atom in <mask2>,
+ and third atom in <mask3>.
 \end_layout
 
 \begin_layout Subsection
@@ -14775,8 +15039,7 @@ parmindex
 
 \end_deeper
 \begin_layout Standard
-Print information on atoms in <mask> for selected topology (first loaded
- topology by default) with format:
+Print information on atoms in <mask> for selected topology (first loaded topology by default) with format:
 \end_layout
 
 \begin_layout LyX-Code
@@ -14788,46 +15051,54 @@ where
 \family typewriter
 #Atom
 \family default
- is the internal atom index, the first 
+ is the internal atom index,
+ the first 
 \family typewriter
 Name
 \family default
- column is the atom name, 
+ column is the atom name,
+ 
 \family typewriter
 #Res
 \family default
- is the atom's residue number, the second 
+ is the atom's residue number,
+ the second 
 \family typewriter
 Name
 \family default
- column is residue name, 
+ column is residue name,
+ 
 \family typewriter
 #Mol
 \family default
- is the atom's molecule number, 
+ is the atom's molecule number,
+ 
 \family typewriter
 Type
 \family default
- is the atom's type (certain topologies only), 
+ is the atom's type (certain topologies only),
+ 
 \family typewriter
 Charge
 \family default
- is the atom charge (in units of electron charge), 
+ is the atom charge (in units of electron charge),
+ 
 \family typewriter
 Mass
 \family default
- is the atom's mass (in amu), 
+ is the atom's mass (in amu),
+ 
 \family typewriter
 GBradius
 \family default
- is the generalized Born radius of the atom (Amber topologies only), and
- 
+ is the generalized Born radius of the atom (Amber topologies only),
+ and 
 \family typewriter
 El
 \family default
  is the 2 character element string.
- The final two columns are only shown if the topology contains non-bonded
- parameters: 
+ The final two columns are only shown if the topology contains non-bonded parameters:
+ 
 \family typewriter
 rVDW
 \family default
@@ -14885,7 +15156,8 @@ parmindex
 \end_layout
 
 \begin_layout Description
-[<mask2>] If specified, bonds must match both masks.
+[<mask2>] If specified,
+ bonds must match both masks.
 \end_layout
 
 \begin_layout Description
@@ -14906,8 +15178,7 @@ parmindex
 
 \end_deeper
 \begin_layout Standard
-Print bond information for atoms in <mask> for selected topology (first
- loaded topology by default) with format:
+Print bond information for atoms in <mask> for selected topology (first loaded topology by default) with format:
 \end_layout
 
 \begin_layout LyX-Code
@@ -14919,15 +15190,18 @@ where
 \family typewriter
 Bond
 \family default
- is the internal bond index, 
+ is the internal bond index,
+ 
 \family typewriter
 Kb
 \family default
- is the bond force constant, 
+ is the bond force constant,
+ 
 \family typewriter
 Req
 \family default
- is the bond equilibrium value (in Angstroms), 
+ is the bond equilibrium value (in Angstroms),
+ 
 \family typewriter
 atom names
 \family default
@@ -14935,7 +15209,8 @@ atom names
 \family typewriter
 :<residue num>@<atom name>
 \family default
-, and 
+,
+ and 
 \family typewriter
 (numbers)
 \family default
@@ -14944,8 +15219,8 @@ atom names
 \end_layout
 
 \begin_layout Standard
-If 2 masks are given instead of 1, print info for bonds with first atom
- in <mask1> and second atom in <mask2>.
+If 2 masks are given instead of 1,
+ print info for bonds with first atom in <mask1> and second atom in <mask2>.
 \end_layout
 
 \begin_layout Subsection
@@ -15004,8 +15279,9 @@ Print the bond parameter table with format:
 \end_layout
 
 \begin_layout Standard
-Where Idx is the internal bond parameter index, Rk is the bond force constant
- (in kcal/mol*Ang^2), and Req is the bond equilibrium value (in Ang.).
+Where Idx is the internal bond parameter index,
+ Rk is the bond force constant (in kcal/mol*Ang^2),
+ and Req is the bond equilibrium value (in Ang.).
 \end_layout
 
 \begin_layout Subsection
@@ -15049,8 +15325,7 @@ change [parm <name> | parmindex <#> | <#> |
 \end_layout
 
 \begin_layout LyX-Code
-      bondparm <mask1> [<mask2>] {setrk|scalerk|setreq|scalereq} <value>
- |
+      bondparm <mask1> [<mask2>] {setrk|scalerk|setreq|scalereq} <value> |
 \end_layout
 
 \begin_layout LyX-Code
@@ -15188,8 +15463,7 @@ max
 \end_inset
 
 max> Change original residue numbers (to e.g.
- original PDB numbers) of residues in <mask> to a range starting from <min>
- and ending with <max>.
+ original PDB numbers) of residues in <mask> to a range starting from <min> and ending with <max>.
 \end_layout
 
 \begin_layout Description
@@ -15233,9 +15507,8 @@ max>
 \begin_inset space ~
 \end_inset
 
-<#> Change residue insertion codes of residues in <mask> to a range of character
-s starting from <min> and ending with <max>; set the original residue number
- to <resnum>.
+<#> Change residue insertion codes of residues in <mask> to a range of characters starting from <min> and ending with <max>;
+ set the original residue number to <resnum>.
 \end_layout
 
 \begin_layout Description
@@ -15267,8 +15540,7 @@ addbond
 \begin_inset space ~
 \end_inset
 
-<mask2> Add bond between atom specified by <mask1> and atom specified by
- <mask2>.
+<mask2> Add bond between atom specified by <mask1> and atom specified by <mask2>.
 \end_layout
 
 \begin_deeper
@@ -15303,8 +15575,8 @@ removebonds
 \end_inset
 
 [<mask2>] Remove bonds from atoms in <mask1>.
- If <mask2> also given, remove bonds between atoms in <mask1> and atoms
- in <mask2>.
+ If <mask2> also given,
+ remove bonds between atoms in <mask1> and atoms in <mask2>.
 \end_layout
 
 \begin_deeper
@@ -15313,8 +15585,8 @@ removebonds
 \begin_inset space ~
 \end_inset
 
-<file>] If specified, write removed bonds to <file> with format '<residue
- name> <residue num> <atom name> <atom num>'.
+<file>] If specified,
+ write removed bonds to <file> with format '<residue name> <residue num> <atom name> <atom num>'.
 \end_layout
 
 \end_deeper
@@ -15335,8 +15607,7 @@ bondparm
 \begin_inset space ~
 \end_inset
 
-<value> Modify bond parameters in bonds selected by <mask1> (and <mask2>
- if specified) by specified <value>.
+<value> Modify bond parameters in bonds selected by <mask1> (and <mask2> if specified) by specified <value>.
 \end_layout
 
 \begin_deeper
@@ -15403,8 +15674,8 @@ fromset
 \begin_inset space ~
 \end_inset
 
-set> Use values in <data set> for mass/charge; must have the same number
- of values as atoms selected by <mask>.
+set> Use values in <data set> for mass/charge;
+ must have the same number of values as atoms selected by <mask>.
 \end_layout
 
 \end_deeper
@@ -15446,7 +15717,8 @@ firstres
 \end_deeper
 \begin_layout Standard
 Change specified parts of the specified topology.
- For example, to change atoms named 'HN' to 'H' in topology 0:
+ For example,
+ to change atoms named 'HN' to 'H' in topology 0:
 \end_layout
 
 \begin_layout LyX-Code
@@ -15499,14 +15771,13 @@ parmindex
 \begin_inset space ~
 \end_inset
 
-<set>] If specified, a data set named <set> will be cretaed containing total
- charge.
+<set>] If specified,
+ a data set named <set> will be cretaed containing total charge.
 \end_layout
 
 \end_deeper
 \begin_layout Standard
-Print the total charge of atoms in <mask> (in units of electron charge)
- for selected topology (first loaded topology by default).
+Print the total charge of atoms in <mask> (in units of electron charge) for selected topology (first loaded topology by default).
 \end_layout
 
 \begin_layout Subsection
@@ -15514,8 +15785,7 @@ comparetop
 \end_layout
 
 \begin_layout LyX-Code
-comparetop {parm <name> | parmindex <#>} {parm <name> | parmindex <#>} [out
- <file>]
+comparetop {parm <name> | parmindex <#>} {parm <name> | parmindex <#>} [out <file>]
 \end_layout
 
 \begin_layout LyX-Code
@@ -15578,9 +15848,8 @@ out
 \end_deeper
 \begin_layout Standard
 Compare and report differences in atoms/parameters between two topologies.
- Differences are reported in standard 'diff' format, with '<' prefix indicating
- the parameter is from the first topology and '>' prefix indicating the
- parameter is from the second topology.
+ Differences are reported in standard 'diff' format,
+ with '<' prefix indicating the parameter is from the first topology and '>' prefix indicating the parameter is from the second topology.
 \end_layout
 
 \begin_layout Subsection
@@ -15588,8 +15857,7 @@ dihedralinfo | dihedrals | printdihedrals
 \end_layout
 
 \begin_layout LyX-Code
-dihedralinfo [parm <name> | parmindex <#> | <#>] [<mask1>] [<mask2> <mask3>
- <mask4>]
+dihedralinfo [parm <name> | parmindex <#> | <#>] [<mask1>] [<mask2> <mask3> <mask4>]
 \end_layout
 
 \begin_layout LyX-Code
@@ -15643,7 +15911,8 @@ parmindex
 \begin_inset space ~
 \end_inset
 
-<mask4>] If specified, dihedrals must match all masks.
+<mask4>] If specified,
+ dihedrals must match all masks.
 \end_layout
 
 \begin_layout Description
@@ -15673,8 +15942,7 @@ tgtidx
 
 \end_deeper
 \begin_layout Standard
-Print dihedral information of atoms in <mask> for selected topology (first
- loaded topology by default) with format:
+Print dihedral information of atoms in <mask> for selected topology (first loaded topology by default) with format:
 \end_layout
 
 \begin_layout LyX-Code
@@ -15686,19 +15954,23 @@ where
 \family typewriter
 #Dihedral
 \family default
- is the internal dihedral index, 
+ is the internal dihedral index,
+ 
 \family typewriter
 pk
 \family default
- is the dihedral force constant, 
+ is the dihedral force constant,
+ 
 \family typewriter
 phase
 \family default
- is the dihedral phase, 
+ is the dihedral phase,
+ 
 \family typewriter
 pn
 \family default
- is the dihedral periodicity, and 
+ is the dihedral periodicity,
+ and 
 \family typewriter
 atoms
 \family default
@@ -15706,17 +15978,21 @@ atoms
 \family typewriter
 :<residue num>@<atom name>
 \family default
-, followed by the atom indices involved in a comma-separated list.
- In addition if the dihedral is an end dihedral, improper dihedral, or both
- it will be prefaced with an 
+,
+ followed by the atom indices involved in a comma-separated list.
+ In addition if the dihedral is an end dihedral,
+ improper dihedral,
+ or both it will be prefaced with an 
 \family typewriter
 E
 \family default
-, 
+,
+ 
 \family typewriter
 I
 \family default
-, or 
+,
+ or 
 \family typewriter
 B
 \family default
@@ -15725,9 +16001,11 @@ B
 \end_layout
 
 \begin_layout Standard
-If 4 masks are given instead of 1, print info for dihedrals with first atom
- in <mask1>, second atom in <mask2>, third atom in <mask3>, and fourth atom
- in <mask4>.
+If 4 masks are given instead of 1,
+ print info for dihedrals with first atom in <mask1>,
+ second atom in <mask2>,
+ third atom in <mask3>,
+ and fourth atom in <mask4>.
 \end_layout
 
 \begin_layout Subsection
@@ -15796,18 +16074,16 @@ mass> Mass to change hydrogens to (3.024 u by default).
 \end_layout
 
 \begin_layout Description
-dowater If specified, modify water hydrogen mass as well.
+dowater If specified,
+ modify water hydrogen mass as well.
 \end_layout
 
 \end_deeper
 \begin_layout Standard
 Perform hydrogen mass repartitioning on the specified topology.
- Hydrogen mass repartitioning means that for a given heavy atom, the mass
- of all bonded hydrogens are increased (to 3.024 u by default) and the mass
- of that heavy atom is decreased so as to maintain the same overall mass.
- The main use case is to allow longer time steps for molecular dynamics
- integration due to reduced frequency of vibration of bonds to hydrogen
- atoms.
+ Hydrogen mass repartitioning means that for a given heavy atom,
+ the mass of all bonded hydrogens are increased (to 3.024 u by default) and the mass of that heavy atom is decreased so as to maintain the same overall mass.
+ The main use case is to allow longer time steps for molecular dynamics integration due to reduced frequency of vibration of bonds to hydrogen atoms.
 \end_layout
 
 \begin_layout Subsection
@@ -15815,8 +16091,7 @@ improperinfo | impropers | printimpropers
 \end_layout
 
 \begin_layout LyX-Code
-improperinfo [parm <name> | parmindex <#> | <#>] [<mask1>] [<mask2> <mask3>
- <mask4>]
+improperinfo [parm <name> | parmindex <#> | <#>] [<mask1>] [<mask2> <mask3> <mask4>]
 \end_layout
 
 \begin_layout LyX-Code
@@ -15866,7 +16141,8 @@ parmindex
 \begin_inset space ~
 \end_inset
 
-<mask4>] If specified, impropers must match all masks.
+<mask4>] If specified,
+ impropers must match all masks.
 \end_layout
 
 \begin_layout Description
@@ -15892,10 +16168,11 @@ tgtidx
 
 \end_deeper
 \begin_layout Standard
-For specified topology (first by default) either print CHARMM improper info
- for all atoms in <mask1>, or print info for dihedrals with first atom in
- <mask1>, second atom in <mask2>, third atom in <mask3>, and fourth atom
- in <mask4>.
+For specified topology (first by default) either print CHARMM improper info for all atoms in <mask1>,
+ or print info for dihedrals with first atom in <mask1>,
+ second atom in <mask2>,
+ third atom in <mask3>,
+ and fourth atom in <mask4>.
 \end_layout
 
 \begin_layout Subsection
@@ -15903,8 +16180,7 @@ mass
 \end_layout
 
 \begin_layout LyX-Code
-[<parmindex>] [parm <name> | parmindex <#> | <#>] <mask> [out <file>] [name
- <set>]
+[<parmindex>] [parm <name> | parmindex <#> | <#>] <mask> [out <file>] [name <set>]
 \end_layout
 
 \begin_deeper
@@ -15945,14 +16221,13 @@ parmindex
 \begin_inset space ~
 \end_inset
 
-<set>] If specified, a data set named <set> will be cretaed containing total
- mass.
+<set>] If specified,
+ a data set named <set> will be cretaed containing total mass.
 \end_layout
 
 \end_deeper
 \begin_layout Standard
-Print the total mass of atoms in <mask> (in amu) for selected topology (first
- loaded topology by default).
+Print the total mass of atoms in <mask> (in amu) for selected topology (first loaded topology by default).
 \end_layout
 
 \begin_layout Subsection
@@ -16007,8 +16282,7 @@ parmindex
 
 \end_deeper
 \begin_layout Standard
-Print molecule information for atoms in <mask> for selected topology (first
- loaded topology by default) with format:
+Print molecule information for atoms in <mask> for selected topology (first loaded topology by default) with format:
 \end_layout
 
 \begin_layout LyX-Code
@@ -16020,11 +16294,13 @@ where
 \family typewriter
 #Mol
 \family default
- is the molecule number, 
+ is the molecule number,
+ 
 \family typewriter
 Natom
 \family default
- is the number of atoms in the molecule, 
+ is the number of atoms in the molecule,
+ 
 \family typewriter
 #Res
 \family default
@@ -16032,21 +16308,24 @@ Natom
 \family typewriter
 Name
 \family default
- are the residue number and residue name of the first residue in the molecule
- respectively, and 
+ are the residue number and residue name of the first residue in the molecule respectively,
+ and 
 \family typewriter
 C
 \family default
  is the chain ID of the first residue.
- If the molecule is composed on non-consecutive fragments, 
+ If the molecule is composed on non-consecutive fragments,
+ 
 \family typewriter
 #Res
 \family default
-, 
+,
+ 
 \family typewriter
 Name
 \family default
-, and 
+,
+ and 
 \family typewriter
 C
 \family default
@@ -16065,6 +16344,8 @@ parm
 \begin_layout LyX-Code
 parm
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -16098,7 +16379,8 @@ parm
 \series bold
 <filename>
 \series default
- Parameter file to read in; format is auto-detected.
+ Parameter file to read in;
+ format is auto-detected.
 \end_layout
 
 \begin_layout Description
@@ -16106,11 +16388,11 @@ parm
 \series bold
 '[TAG]'
 \series default
- Optional tag (bounded in brackets) which can be referred to in place of
- the topology file name in order to simplify references to it (see 
+ Optional tag (bounded in brackets) which can be referred to in place of the topology file name in order to simplify references to it (see 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:Parameter/Reference-Tagging"
+nolink "false"
 
 \end_inset
 
@@ -16122,8 +16404,7 @@ reference "subsec:Parameter/Reference-Tagging"
 \begin_inset space ~
 \end_inset
 
-<setname>] Optional name that can be used to refer to the topology in place
- of the file name.
+<setname>] Optional name that can be used to refer to the topology in place of the file name.
 \end_layout
 
 \begin_layout Description
@@ -16131,8 +16412,8 @@ reference "subsec:Parameter/Reference-Tagging"
 \series bold
 [bondsearch <offset>]
 \series default
- Optional; when searching for bonds via geometry search (default for Topologies
- without bond information) add <offset> to distances (default 0.2 Å).
+ Optional;
+ when searching for bonds via geometry search (default for Topologies without bond information) add <offset> to distances (default 0.2 Å).
  Increase this if your system includes unusually long bonds.
 \end_layout
 
@@ -16141,8 +16422,7 @@ reference "subsec:Parameter/Reference-Tagging"
 \begin_inset space ~
 \end_inset
 
-{grid|pairlist}] Change search algorithm from the default search between
- residues algorithm:
+{grid|pairlist}] Change search algorithm from the default search between residues algorithm:
 \end_layout
 
 \begin_deeper
@@ -16154,8 +16434,8 @@ grid Uses a grid when searching for bonds between residues.
 
 \begin_layout Description
 pairlist Uses a pair list to search for bonds between atoms.
- This can potentially find bonds across periodic boundaries, but is the
- more experimental of the two.
+ This can potentially find bonds across periodic boundaries,
+ but is the more experimental of the two.
 \end_layout
 
 \end_deeper
@@ -16170,8 +16450,7 @@ Advanced Options - Not recommended for general use
 \series bold
 [nobondsearch]
 \series default
- If specified do not search for bonds via geometry if Topology does not
- include bond information.
+ If specified do not search for bonds via geometry if Topology does not include bond information.
  May cause some Actions to fail.
 \end_layout
 
@@ -16181,8 +16460,8 @@ Advanced Options - Not recommended for general use
 \end_layout
 
 \begin_layout Description
-[renumresidues] If specified, ensure that any residue cannot be part of
- more than 1 molecule (can occur with e.g.
+[renumresidues] If specified,
+ ensure that any residue cannot be part of more than 1 molecule (can occur with e.g.
  alternate sites).
  Residues will be renumbered according to molecule information in that case.
 \end_layout
@@ -16195,15 +16474,15 @@ Read in parameter file.
 \begin_inset CommandInset ref
 LatexCommand vpageref
 reference "tab:cpptraj-Topology-formats"
+nolink "false"
 
 \end_inset
 
 .
- If the file does not contain bond information, cpptraj will attempt to
- assign bonds based on a simple distance search of atoms within and between
- residues.
- The distance cutoff for determining bonds between atoms depends on the
- elements of the two atoms in question, augmented by <offset>.
+ If the file does not contain bond information,
+ cpptraj will attempt to assign bonds based on a simple distance search of atoms within and between residues.
+ The distance cutoff for determining bonds between atoms depends on the elements of the two atoms in question,
+ augmented by <offset>.
  Molecule information is then determined from bond information.
 \end_layout
 
@@ -16230,8 +16509,7 @@ name "subsec:cpptraj-parm-pdb"
 
 \begin_deeper
 \begin_layout Description
-[pqr] Read charge and radius information from the occupancy and B-factor
- columns.
+[pqr] Read charge and radius information from the occupancy and B-factor columns.
 \end_layout
 
 \begin_layout Description
@@ -16260,8 +16538,8 @@ name "subsec:cpptraj-parm-pdb"
 \begin_inset space ~
 \end_inset
 
-<char>] If specified, only keep alternate atom location IDs matching the
- specified character 
+<char>] If specified,
+ only keep alternate atom location IDs matching the specified character 
 \series bold
 <char>
 \series default
@@ -16276,8 +16554,8 @@ IMPORTANT NOTES FOR PDB FILES
 \end_layout
 
 \begin_layout Standard
-Sometimes PDB files can contain alternate coordinates for the same atom
- in a residue, e.g.:
+Sometimes PDB files can contain alternate coordinates for the same atom in a residue,
+ e.g.:
 \end_layout
 
 \begin_layout LyX-Code
@@ -16301,11 +16579,10 @@ If this is the case
 \shape italic
 cpptraj
 \shape default
- will print a warning about alternate location IDs being present but will
- take no other action.
- Both residues are considered 'CYS' and the mask ':CYS@CA' would select
- both atom 806 and 808.
- If desired, a specific location ID can be kept via the 
+ will print a warning about alternate location IDs being present but will take no other action.
+ Both residues are considered 'CYS' and the mask ':CYS@CA' would select both atom 806 and 808.
+ If desired,
+ a specific location ID can be kept via the 
 \series bold
 keepaltloc
 \series default
@@ -16314,7 +16591,8 @@ keepaltloc
 \series bold
 keepaltloc
 \series default
- is specified, it should also be specified for any 
+ is specified,
+ it should also be specified for any 
 \series bold
 trajin
 \series default
@@ -16325,6 +16603,7 @@ reference "subsec:cpptraj-trajin-pdb"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
@@ -16356,9 +16635,9 @@ Gromacs Top
 \end_layout
 
 \begin_layout Standard
-By default cpptraj will look for Gromacs topology data (that is not in the
- same directory) in the directory defined by the GMXDATA environment variable;
- specifically, it expects things to be in the "$GMXDATA/top" directory.
+By default cpptraj will look for Gromacs topology data (that is not in the same directory) in the directory defined by the GMXDATA environment variable;
+ specifically,
+ it expects things to be in the "$GMXDATA/top" directory.
  
 \end_layout
 
@@ -16369,6 +16648,8 @@ parmbox
 \begin_layout LyX-Code
 parmbox
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -16477,8 +16758,8 @@ parmindex
 \end_deeper
 \begin_layout Standard
 Modify the box information for specified topology.
- Overwrites any box information if present with specified values; any that
- are not specified will remain unchanged.
+ Overwrites any box information if present with specified values;
+ any that are not specified will remain unchanged.
  Note that unlike the 
 \series bold
 \shape italic
@@ -16513,6 +16794,8 @@ parminfo
 \begin_layout LyX-Code
 parminfo
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -16525,8 +16808,7 @@ parminfo
 \end_layout
 
 \begin_layout Standard
-Print a summary of information contained in the specified topology (first
- loaded topology by default) .
+Print a summary of information contained in the specified topology (first loaded topology by default) .
 \end_layout
 
 \begin_layout Subsection
@@ -16536,6 +16818,8 @@ parmstrip
 \begin_layout LyX-Code
 parmstrip
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -16559,12 +16843,13 @@ Strip atoms in
 strip
 \series default
 \emph default
- Action, this permanently modifies the topology for as long as 
+ Action,
+ this permanently modifies the topology for as long as 
 \emph on
 cpptraj
 \emph default
- is running, so this should not be used if the topology is being used to
- read or write a trajectory via 
+ is running,
+ so this should not be used if the topology is being used to read or write a trajectory via 
 \series bold
 \emph on
 trajin
@@ -16578,8 +16863,8 @@ trajout
 \emph default
 .
  This command can be used to quickly created stripped Amber topology files.
- For example, to strip all residues name WAT from a topology and write a
- new topology:
+ For example,
+ to strip all residues name WAT from a topology and write a new topology:
 \end_layout
 
 \begin_layout LyX-Code
@@ -16601,6 +16886,8 @@ parmwrite
 \begin_layout LyX-Code
 parmwrite
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -16668,8 +16955,7 @@ parmindex
 \end_layout
 
 \begin_layout Description
-[nochamber] (Amber topology only) Remove any CHAMBER information from the
- topology.
+[nochamber] (Amber topology only) Remove any CHAMBER information from the topology.
 \end_layout
 
 \end_deeper
@@ -16683,8 +16969,7 @@ Write out specified topology (first topology loaded by default) to
 <fmt>
 \series default
  (Amber topology if not specified).
- Note that the Amber topology format is the only fully supported format
- for topology writes.
+ Note that the Amber topology format is the only fully supported format for topology writes.
 \end_layout
 
 \begin_layout Subsubsection
@@ -16702,12 +16987,16 @@ Amber Topology
 \end_layout
 
 \begin_layout Description
-[writeempty] Write Amber tree, join, and rotate info even if not present.
+[writeempty] Write Amber tree,
+ join,
+ and rotate info even if not present.
 \end_layout
 
 \begin_layout Description
 [nopdbinfo] Do not write "PDB" info (e.g.
- chain IDs, original res #s, etc).
+ chain IDs,
+ original res #s,
+ etc).
 \end_layout
 
 \end_deeper
@@ -16776,7 +17065,8 @@ parmindex
 \end_layout
 
 \begin_layout Description
-[<mask2>] If specified, UB info must match both masks.
+[<mask2>] If specified,
+ UB info must match both masks.
 \end_layout
 
 \begin_layout Description
@@ -16793,9 +17083,8 @@ parmindex
 
 \end_deeper
 \begin_layout Standard
-For specified topology (first by default) either print CHARMM Urey-Bradley
- info for all atoms in <mask1>, or print info for bonds with first atom
- in <mask1> and second atom in <mask2>.
+For specified topology (first by default) either print CHARMM Urey-Bradley info for all atoms in <mask1>,
+ or print info for bonds with first atom in <mask1> and second atom in <mask2>.
 \end_layout
 
 \begin_layout Subsection
@@ -16805,6 +17094,8 @@ resinfo
 \begin_layout LyX-Code
 resinfo
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -16895,8 +17186,7 @@ parmindex
 
 \end_deeper
 \begin_layout Standard
-Print residue information for atoms in <mask> for selected topology (first
- loaded topology by default) with format:
+Print residue information for atoms in <mask> for selected topology (first loaded topology by default) with format:
 \end_layout
 
 \begin_layout LyX-Code
@@ -16908,11 +17198,13 @@ where
 \family typewriter
 #Res
 \family default
- is the residue number, 
+ is the residue number,
+ 
 \family typewriter
 Name
 \family default
- is the residue name, 
+ is the residue name,
+ 
 \family typewriter
 First
 \family default
@@ -16920,15 +17212,18 @@ First
 \family typewriter
 Last
 \family default
- are the first and last atom numbers of the residue, 
+ are the first and last atom numbers of the residue,
+ 
 \family typewriter
 Natom
 \family default
- is the total number of atoms in the residue, 
+ is the total number of atoms in the residue,
+ 
 \family typewriter
 #Orig
 \family default
- is the original residue number (in PDB files), #Mol is the molecule number,
+ is the original residue number (in PDB files),
+ #Mol is the molecule number,
  and C is the chain ID.
 \end_layout
 
@@ -16938,9 +17233,11 @@ If
 short
 \series default
  is specified then residues will be printed out in a condensed format.
- Each residue name will be shortened to 1 character, and residues are printed
- out in groups of 10, 5 groups to a line, with each line beginning with
- a residue number, e.g.
+ Each residue name will be shortened to 1 character,
+ and residues are printed out in groups of 10,
+ 5 groups to a line,
+ with each line beginning with a residue number,
+ e.g.
 \end_layout
 
 \begin_layout LyX-Code
@@ -16956,8 +17253,7 @@ short
 \end_layout
 
 \begin_layout Standard
-If the 1 character name for a residue is unknown it will be shown as the
- first letter of the residue name in lower-case.
+If the 1 character name for a residue is unknown it will be shown as the first letter of the residue name in lower-case.
 \end_layout
 
 \begin_layout Subsection
@@ -16969,8 +17265,7 @@ scaledihedralk [parm <name> | parmindex <#>] <scale factor> [<mask> [useall]]
 \end_layout
 
 \begin_layout Standard
-Scale dihedral force constants for dihderals selected by <mask> for specified
- topology.
+Scale dihedral force constants for dihderals selected by <mask> for specified topology.
  If 
 \series bold
 useall
@@ -16995,12 +17290,12 @@ solvent [parm <name> | parmindex <#> | <#>] { <mask> | none }
 \end_layout
 
 \begin_layout Standard
-Set solvent for selected topology (first loaded topology by default) based
- on 
+Set solvent for selected topology (first loaded topology by default) based on 
 \series bold
 <mask>
 \series default
-, or set nothing as solvent if 
+,
+ or set nothing as solvent if 
 \series bold
 none
 \series default
@@ -17060,20 +17355,21 @@ set> Topology or parameter data set containing parameters to use.
 \begin_layout Standard
 
 \emph on
-NOTE: This command is provided for convenience only.
- For editing topology files, ParmEd is a much better alternative.
+NOTE:
+ This command is provided for convenience only.
+ For editing topology files,
+ ParmEd is a much better alternative.
 \end_layout
 
 \begin_layout Standard
 Update parameters in specified topology with those from <parm set>.
  <parm set> can either be a parameter set or a topology.
- If a parameter from <parm set> does not exist in the topology it will be
- added.
+ If a parameter from <parm set> does not exist in the topology it will be added.
 \end_layout
 
 \begin_layout Standard
-For example, to modify parameters in a topology file named lys.parm7 with
- those from parameter file kcx.str:
+For example,
+ to modify parameters in a topology file named lys.parm7 with those from parameter file kcx.str:
 \end_layout
 
 \begin_layout LyX-Code
@@ -17118,15 +17414,18 @@ These commands control the reading and writing of trajectory files.
 \shape italic
 cpptraj
 \shape default
-: input, output, and reference.
+:
+ input,
+ output,
+ and reference.
  In 
 \shape italic
 cpptraj
 \shape default
-, trajectories are always associated with a topology file.
- If a topology file is not specified, a trajectory file will be associated
- with the first topology file loaded by default (this is true for both input
- and output trajectories.
+,
+ trajectories are always associated with a topology file.
+ If a topology file is not specified,
+ a trajectory file will be associated with the first topology file loaded by default (this is true for both input and output trajectories.
 \end_layout
 
 \begin_layout Standard
@@ -17244,7 +17543,8 @@ Amber NetCDF
 \begin_inset Text
 
 \begin_layout Plain Layout
-cdf, netcdf
+cdf,
+ netcdf
 \end_layout
 
 \end_inset
@@ -17291,7 +17591,8 @@ restart
 \begin_inset Text
 
 \begin_layout Plain Layout
-.rst7, .rst
+.rst7,
+ .rst
 \end_layout
 
 \end_inset
@@ -17320,7 +17621,8 @@ Amber NetCDF Restart
 \begin_inset Text
 
 \begin_layout Plain Layout
-ncrestart, restartnc
+ncrestart,
+ restartnc
 \end_layout
 
 \end_inset
@@ -17366,7 +17668,8 @@ DCD
 \begin_inset Text
 
 \begin_layout Plain Layout
-dcd, charmm
+dcd,
+ charmm
 \end_layout
 
 \end_inset
@@ -17992,7 +18295,8 @@ conflib
 \begin_inset Text
 
 \begin_layout Plain Layout
-Read Only, Detection by extension
+Read Only,
+ Detection by extension
 \end_layout
 
 \end_inset
@@ -18290,7 +18594,8 @@ ensemble <file0> {[<start>] [<stop> | last] [offset]} | lastframe
 \begin_inset space ~
 \end_inset
 
-last] Frame to stop reading ensemble at; if not specified or 'last' specified,
+last] Frame to stop reading ensemble at;
+ if not specified or 'last' specified,
  end of trajectories.
 \end_layout
 
@@ -18307,8 +18612,7 @@ last] Frame to stop reading ensemble at; if not specified or 'last' specified,
 \begin_inset space ~
 \end_inset
 
-<parmfile>] Topology filename/tag to associate with trajectories (default
- first topology).
+<parmfile>] Topology filename/tag to associate with trajectories (default first topology).
 \end_layout
 
 \begin_layout Description
@@ -18316,8 +18620,8 @@ last] Frame to stop reading ensemble at; if not specified or 'last' specified,
 \begin_inset space ~
 \end_inset
 
-<#>] Index of Topology to associate with trajectories (default 0, first
- topology).
+<#>] Index of Topology to associate with trajectories (default 0,
+ first topology).
 \end_layout
 
 \begin_layout Description
@@ -18325,8 +18629,8 @@ last] Frame to stop reading ensemble at; if not specified or 'last' specified,
 \begin_inset space ~
 \end_inset
 
-<file1>,...,<fileN>] Do not automatically search for additional replica trajectorie
-s; use comma-separated list of trajectory names.
+<file1>,...,<fileN>] Do not automatically search for additional replica trajectories;
+ use comma-separated list of trajectory names.
 \end_layout
 
 \begin_layout Description
@@ -18336,8 +18640,8 @@ s; use comma-separated list of trajectory names.
 \end_layout
 
 \begin_layout Description
-[bycrdidx] For H-REMD trajectories, sort by coordinate indices stored in
- trajectory files.
+[bycrdidx] For H-REMD trajectories,
+ sort by coordinate indices stored in trajectory files.
  This is preferred over sorting via 'remlog'.
 \end_layout
 
@@ -18346,8 +18650,8 @@ s; use comma-separated list of trajectory names.
 \begin_inset space ~
 \end_inset
 
-<remlogfile>] For H-REMD trajectories only, use specified REMD log file
- to sort trajectories by coordinate index (instead of by replica/Hamiltonian).
+<remlogfile>] For H-REMD trajectories only,
+ use specified REMD log file to sort trajectories by coordinate index (instead of by replica/Hamiltonian).
 \begin_inset Separator latexpar
 \end_inset
 
@@ -18368,9 +18672,8 @@ ntwx
 \begin_inset space ~
 \end_inset
 
-<ntwx>] If trajectory and REMD log were not written at the same rate, these
- are the values for nstlim (steps between each exchange) and ntwx (steps
- between trajectory write) used in the REMD simulation.
+<ntwx>] If trajectory and REMD log were not written at the same rate,
+ these are the values for nstlim (steps between each exchange) and ntwx (steps between trajectory write) used in the REMD simulation.
 \end_layout
 
 \end_deeper
@@ -18383,7 +18686,8 @@ Read in and process trajectories as an ensemble.
 trajin
 \series default
 \shape default
- remdtraj', except instead of processing one frame at a target temperature,
+ remdtraj',
+ except instead of processing one frame at a target temperature,
  process all frames.
  This means that action and trajout commands apply to the entire ensemble;
  note however that not all actions currently function in 
@@ -18393,8 +18697,10 @@ trajin
 \series default
 \shape default
  mode.
- For example, to read in a replica ensemble, convert it to temperature trajector
-ies, and calculate a distance at each temperature:
+ For example,
+ to read in a replica ensemble,
+ convert it to temperature trajectories,
+ and calculate a distance at each temperature:
 \end_layout
 
 \begin_layout LyX-Code
@@ -18414,10 +18720,12 @@ distance d1 out d1.ensemble.dat @1 @21
 \end_layout
 
 \begin_layout Standard
-This will output 4 temperature trajectories named 'temp.crd.X', where X ranges
- from 0 to 3 with 0 corresponding to the lowest temperature, and 'd1.ensemble.dat'
- containing 4 columns, each corresponding to a temperature.
- If run with MPI, data will be written to separate files named 'd1.ensemble.dat.X',
+This will output 4 temperature trajectories named 'temp.crd.X',
+ where X ranges from 0 to 3 with 0 corresponding to the lowest temperature,
+ and 'd1.ensemble.dat' containing 4 columns,
+ each corresponding to a temperature.
+ If run with MPI,
+ data will be written to separate files named 'd1.ensemble.dat.X',
  similar to the output trajectories.
 \end_layout
 
@@ -18439,12 +18747,9 @@ ensemble
 \end_layout
 
 \begin_layout Standard
-H-REMD trajectories which are typically already sorted by replica/Hamiltonian
- can be sorted by coordinate index instead with 'bycrdidx' (if the trajectory
- contains coordinate indices) or by REMD log data specified with the 'remlog'
- keyword.
- For example, to sort by coordinate index using a REMD log and write sorted
- trajectories:
+H-REMD trajectories which are typically already sorted by replica/Hamiltonian can be sorted by coordinate index instead with 'bycrdidx' (if the trajectory contains coordinate indices) or by REMD log data specified with the 'remlog' keyword.
+ For example,
+ to sort by coordinate index using a REMD log and write sorted trajectories:
 \end_layout
 
 \begin_layout LyX-Code
@@ -18499,7 +18804,8 @@ This command is MPI only.
 ensemble
 \series default
 \emph default
- command, which dramatically improves set up efficiency.
+ command,
+ which dramatically improves set up efficiency.
 \end_layout
 
 \begin_layout Subsection
@@ -18516,6 +18822,8 @@ name "subsec:cpptraj_reference"
 \begin_layout LyX-Code
 reference
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -18537,8 +18845,8 @@ reference
 
 \begin_deeper
 \begin_layout Description
-<name> File name (or COORDS set name if 'crdset' specified) to read in as
- reference; any trajectory recognized by 'trajin' can be used.
+<name> File name (or COORDS set name if 'crdset' specified) to read in as reference;
+ any trajectory recognized by 'trajin' can be used.
 \end_layout
 
 \begin_layout Description
@@ -18550,7 +18858,8 @@ reference
 \end_layout
 
 \begin_layout Description
-([tag]) Tag to give this reference file, e.g.
+([tag]) Tag to give this reference file,
+ e.g.
  
 \begin_inset Quotes eld
 \end_inset
@@ -18559,7 +18868,8 @@ reference
 \begin_inset Quotes erd
 \end_inset
 
-; BRACKETS MUST BE INCLUDED.
+;
+ BRACKETS MUST BE INCLUDED.
 \end_layout
 
 \begin_layout Description
@@ -18575,8 +18885,7 @@ reference
 \begin_inset space ~
 \end_inset
 
-<parmfile/tag>] Topology filename/tag to associate with reference (default
- first topology).
+<parmfile/tag>] Topology filename/tag to associate with reference (default first topology).
 \end_layout
 
 \begin_layout Description
@@ -18584,33 +18893,33 @@ reference
 \begin_inset space ~
 \end_inset
 
-<#>] Index of Topology to associate with reference (default 0, first topology).
+<#>] Index of Topology to associate with reference (default 0,
+ first topology).
 \end_layout
 
 \end_deeper
 \begin_layout Standard
 Use specified trajectory as reference coordinates.
- For trajectories with multiple frames, the first frame is used if a specific
- frame is not specified.
- An optional tag can be given (bounded in brackets) which can then be used
- in place of the name (see 
+ For trajectories with multiple frames,
+ the first frame is used if a specific frame is not specified.
+ An optional tag can be given (bounded in brackets) which can then be used in place of the name (see 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:Parameter/Reference-Tagging"
+nolink "false"
 
 \end_inset
 
  for examples of how to use tags).
- If desired, an atom mask can be used to read in only specified atoms from
- a reference.
+ If desired,
+ an atom mask can be used to read in only specified atoms from a reference.
 \end_layout
 
 \begin_layout Standard
-Reference coordinates are now considered COORDS data sets and can be used
- anywhere a COORDS data set could, which allows reference structures to
- be manipulated once they are loaded.
- For example, a reference structure could be centered on the origin like
- so:
+Reference coordinates are now considered COORDS data sets and can be used anywhere a COORDS data set could,
+ which allows reference structures to be manipulated once they are loaded.
+ For example,
+ a reference structure could be centered on the origin like so:
 \end_layout
 
 \begin_layout LyX-Code
@@ -18623,8 +18932,8 @@ crdaction [MyRef] center origin
 
 \begin_layout Standard
 Note that the 'average' keyword has been deprecated for reference.
- If desired, an averaged reference COORDS data set can be created from a
- trajectory using the 'average' command like so:
+ If desired,
+ an averaged reference COORDS data set can be created from a trajectory using the 'average' command like so:
 \end_layout
 
 \begin_layout LyX-Code
@@ -18665,6 +18974,8 @@ name "subsec:cpptraj_trajin"
 \begin_layout LyX-Code
 trajin
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -18689,8 +19000,7 @@ trajin
 \end_layout
 
 \begin_layout LyX-Code
-       [ remdtraj {remdtrajtemp <Temperature> | remdtrajidx <idx1,idx2,...>
- 
+       [ remdtraj {remdtrajtemp <Temperature> | remdtrajidx <idx1,idx2,...> 
 \end_layout
 
 \begin_layout LyX-Code
@@ -18732,8 +19042,9 @@ trajin
 \begin_inset space ~
 \end_inset
 
-last] Frame to stop reading at; if not specified or 'last' specified, end
- of trajectory.
+last] Frame to stop reading at;
+ if not specified or 'last' specified,
+ end of trajectory.
 \end_layout
 
 \begin_layout Description
@@ -18749,8 +19060,7 @@ last] Frame to stop reading at; if not specified or 'last' specified, end
 \begin_inset space ~
 \end_inset
 
-<parmfile/tag>] Topology filename/tag to associate with trajectory (default
- first topology).
+<parmfile/tag>] Topology filename/tag to associate with trajectory (default first topology).
 \end_layout
 
 \begin_layout Description
@@ -18758,7 +19068,8 @@ last] Frame to stop reading at; if not specified or 'last' specified, end
 \begin_inset space ~
 \end_inset
 
-<#>] Index of Topology to associate with trajectory (default 0, first topology).
+<#>] Index of Topology to associate with trajectory (default 0,
+ first topology).
 \end_layout
 
 \begin_layout Description
@@ -18786,8 +19097,8 @@ last] Frame to stop reading at; if not specified or 'last' specified, end
 \begin_inset space ~
 \end_inset
 
-keyword>] Force file to be read as specified format; overrides file autodetectio
-n.
+keyword>] Force file to be read as specified format;
+ overrides file autodetection.
 \end_layout
 
 \begin_layout Description
@@ -18799,8 +19110,7 @@ Options>] See below.
 \end_layout
 
 \begin_layout Description
-[remdtraj] Read <filename> as the first replica in a group of replica trajectori
-es.
+[remdtraj] Read <filename> as the first replica in a group of replica trajectories.
 \begin_inset Separator latexpar
 \end_inset
 
@@ -18825,9 +19135,9 @@ remdtrajidx
 \begin_inset space ~
 \end_inset
 
-<idx1,idx2,...> Use frames at <Temperature> (for temperature replica trajectories)
- or index <idx1,idx2,...> (for Hamiltonian replica trajectories); For Multidimensio
-nal REMD simulations, multiple values are comma-separated.
+<idx1,idx2,...> Use frames at <Temperature> (for temperature replica trajectories) or index <idx1,idx2,...> (for Hamiltonian replica trajectories);
+ For Multidimensional REMD simulations,
+ multiple values are comma-separated.
 \end_layout
 
 \begin_layout Description
@@ -18835,15 +19145,15 @@ remdtrajvalues
 \begin_inset space ~
 \end_inset
 
-<value1,value2,...> Use frames at <value1,value2,...> (for Multidimensional REMD
- trajectories).
- Each value may correspond to either temperature, pH, Redox Potential or
- Hamiltonian index.
- The values need to be entered in the same order as the dimensions in the
- Multidimensional REMD simulation.
- For example, for T,pH-REMD value1 would correspond to a temperature and
- value2 to a pH.
- In the command, the values are comma-separated.
+<value1,value2,...> Use frames at <value1,value2,...> (for Multidimensional REMD trajectories).
+ Each value may correspond to either temperature,
+ pH,
+ Redox Potential or Hamiltonian index.
+ The values need to be entered in the same order as the dimensions in the Multidimensional REMD simulation.
+ For example,
+ for T,pH-REMD value1 would correspond to a temperature and value2 to a pH.
+ In the command,
+ the values are comma-separated.
 \end_layout
 
 \begin_layout Description
@@ -18851,8 +19161,8 @@ remdtrajvalues
 \begin_inset space ~
 \end_inset
 
-<file1>,...,<fileN>] Do not automatically search for additional replica trajectorie
-s; use comma-separated list of trajectory names.
+<file1>,...,<fileN>] Do not automatically search for additional replica trajectories;
+ use comma-separated list of trajectory names.
 \end_layout
 
 \end_deeper
@@ -18863,18 +19173,20 @@ Read in trajectory specified by filename.
 \begin_inset CommandInset ref
 LatexCommand pageref
 reference "tab:cpptraj-trajformats"
+nolink "false"
 
 \end_inset
 
  for currently recognized trajectory file formats.
- If just the <start> argument is given, all frames from <start> to the last
- frame of the trajectory will be read.
+ If just the <start> argument is given,
+ all frames from <start> to the last frame of the trajectory will be read.
  To read in a trajectory with offsets where the last frame # is not known,
  specify the 
 \series bold
 last
 \series default
- keyword instead of a <stop> argument, e.g.
+ keyword instead of a <stop> argument,
+ e.g.
 \end_layout
 
 \begin_layout LyX-Code
@@ -18882,9 +19194,10 @@ trajin Test1.crd 10 last 2
 \end_layout
 
 \begin_layout Standard
-This will process Test1.crd from frame 10 to the last frame, skipping by
- 2 frames.
- To explicitly select only the last frame, specify the 
+This will process Test1.crd from frame 10 to the last frame,
+ skipping by 2 frames.
+ To explicitly select only the last frame,
+ specify the 
 \series bold
 lastframe
 \series default
@@ -18896,8 +19209,7 @@ trajin Test1.crd lastframe
 \end_layout
 
 \begin_layout Standard
-Here is an example of loading in multiple trajectories which have difference
- topology files:
+Here is an example of loading in multiple trajectories which have difference topology files:
 \end_layout
 
 \begin_layout LyX-Code
@@ -18933,11 +19245,11 @@ trajin Test3.crd parmindex 3
 \end_layout
 
 \begin_layout Standard
-Test0.crd is associated with top0.parm7; since no parm was specified it defaulted
- to the first parm read in.
- Test1.crd was associated with top1.parm7 by filename, Test2.crd was associated
- with top2.parm7 by its tag, and finally Test3.crd was associated with top3.parm7
- by its index (based on the order it was read in).
+Test0.crd is associated with top0.parm7;
+ since no parm was specified it defaulted to the first parm read in.
+ Test1.crd was associated with top1.parm7 by filename,
+ Test2.crd was associated with top2.parm7 by its tag,
+ and finally Test3.crd was associated with top3.parm7 by its index (based on the order it was read in).
 \end_layout
 
 \begin_layout Subsubsection*
@@ -18949,17 +19261,16 @@ If the
 \series bold
 remdtraj
 \series default
- keyword is specified the trajectory is treated as belonging to the lowest
- # replica of a group of REMD trajectories.
- The remaining replicas can be either automatically detected by following
- a naming convention of <REMDFILENAME>.X, where X is the replica number,
+ keyword is specified the trajectory is treated as belonging to the lowest # replica of a group of REMD trajectories.
+ The remaining replicas can be either automatically detected by following a naming convention of <REMDFILENAME>.X,
+ where X is the replica number,
  or explicitly specified in a comma-separated list following the 
 \series bold
 trajnames
 \series default
  keyword.
- All trajectories will be processed at the same time, but only frames with
- a temperature matching the one specified by 
+ All trajectories will be processed at the same time,
+ but only frames with a temperature matching the one specified by 
 \series bold
 remdtrajtemp
 \series default
@@ -18968,9 +19279,12 @@ remdtrajtemp
 remdtrajidx
 \series default
  will be processed.
- For example, to process replica trajectories rem.001, rem.002, rem.003, and
- rem.004, grabbing only the frames at temperature 300.0 (assuming that this
- is a temperature in the ensemble):
+ For example,
+ to process replica trajectories rem.001,
+ rem.002,
+ rem.003,
+ and rem.004,
+ grabbing only the frames at temperature 300.0 (assuming that this is a temperature in the ensemble):
 \end_layout
 
 \begin_layout LyX-Code
@@ -19001,7 +19315,9 @@ ensemble
 \begin_layout Subsubsection
 
 \emph on
-Options for Amber NetCDF, Amber NC Restart, Amber Restart:
+Options for Amber NetCDF,
+ Amber NC Restart,
+ Amber Restart:
 \end_layout
 
 \begin_layout LyX-Code
@@ -19046,27 +19362,29 @@ shape Force reading of box info as CHARMM shape matrix (XX XY YY XZ YZ ZZ).
 \end_layout
 
 \begin_layout Description
-namdcell Force reading of box info as NAMD unit cell (X cos(g) Y cos(b)
- cos(a) Z).
+namdcell Force reading of box info as NAMD unit cell (X cos(g) Y cos(b) cos(a) Z).
  
 \end_layout
 
 \begin_layout Description
-charmmcell Force reading of box info as old CHARMM unit cell (X Y Z a b
- g).
+charmmcell Force reading of box info as old CHARMM unit cell (X Y Z a b g).
  
 \end_layout
 
 \end_deeper
 \begin_layout Standard
-Note that CHARMM trajectories can have unit cell data stored in one of two
- ways.
- Older versions (<22) of charmm store the 3x lengths (X Y Z, in Angstroms)
- and 3x angles (alpha beta gamma, in degrees).
+Note that CHARMM trajectories can have unit cell data stored in one of two ways.
+ Older versions (<22) of charmm store the 3x lengths (X Y Z,
+ in Angstroms) and 3x angles (alpha beta gamma,
+ in degrees).
  Newer versions (>=22) store elements of the symmetric shape matrix (XX,
- XY, YY, XZ, YZ, ZZ).
- CPPTRAJ will attempt to automatically detect which type of parameters are
- present, but this can be overridden with the 
+ XY,
+ YY,
+ XZ,
+ YZ,
+ ZZ).
+ CPPTRAJ will attempt to automatically detect which type of parameters are present,
+ but this can be overridden with the 
 \series bold
 shape
 \series default
@@ -19079,9 +19397,8 @@ charmmcell
 \series bold
 namdcell
 \series default
- keyword is provided for compatibility with DCD trajectories produced by
- VMD/NAMD, but note these trajectories only store a version of the shape
- matrix that is correct if the unit cell is also X-aligned.
+ keyword is provided for compatibility with DCD trajectories produced by VMD/NAMD,
+ but note these trajectories only store a version of the shape matrix that is correct if the unit cell is also X-aligned.
 \end_layout
 
 \begin_layout Subsubsection
@@ -19105,8 +19422,8 @@ name "subsec:cpptraj-trajin-pdb"
 \begin_inset space ~
 \end_inset
 
-<char>] If specified, only keep alternate atom location IDs matching the
- specified character 
+<char>] If specified,
+ only keep alternate atom location IDs matching the specified character 
 \series bold
 <char>
 \series default
@@ -19119,8 +19436,9 @@ Note that if
 \series bold
 keepaltloc
 \series default
- is specified, the associated topology should not have alternate location
- IDs, i.e.
+ is specified,
+ the associated topology should not have alternate location IDs,
+ i.e.
  if the topology is from a PDB the 
 \series bold
 keepaltloc
@@ -19136,6 +19454,7 @@ reference "subsec:cpptraj-parm-pdb"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
@@ -19156,6 +19475,8 @@ name "subsec:cpptraj-trajout"
 \begin_layout LyX-Code
 trajout
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -19201,16 +19522,18 @@ trajout
 \begin_inset CommandInset ref
 LatexCommand vpageref
 reference "tab:cpptraj-trajformats"
+nolink "false"
 
 \end_inset
 
 ).
- If not specified format will be determined from extension, otherwise default
- to Amber trajectory.
+ If not specified format will be determined from extension,
+ otherwise default to Amber trajectory.
 \end_layout
 
 \begin_layout Description
-[append] If <filename> exists, frames will be appended to <filename>.
+[append] If <filename> exists,
+ frames will be appended to <filename>.
 \end_layout
 
 \begin_layout Description
@@ -19238,8 +19561,7 @@ reference "tab:cpptraj-trajformats"
 \begin_inset space ~
 \end_inset
 
-<parmfile>] Topology filename/tag to associate with trajectory (default
- first topology).
+<parmfile>] Topology filename/tag to associate with trajectory (default first topology).
 \end_layout
 
 \begin_layout Description
@@ -19247,7 +19569,8 @@ reference "tab:cpptraj-trajformats"
 \begin_inset space ~
 \end_inset
 
-<#>] Index of Topology to associate with trajectory (default 0, first topology).
+<#>] Index of Topology to associate with trajectory (default 0,
+ first topology).
 \end_layout
 
 \begin_layout Description
@@ -19271,8 +19594,8 @@ reference "tab:cpptraj-trajformats"
 \begin_inset space ~
 \end_inset
 
-<memberlist>] Ensemble processing only; only write from specified members
- (starting from 0).
+<memberlist>] Ensemble processing only;
+ only write from specified members (starting from 0).
 \end_layout
 
 \begin_layout Description
@@ -19301,14 +19624,13 @@ reference "tab:cpptraj-trajformats"
 
 \end_deeper
 \begin_layout Standard
-During a run, write frames to trajectory specified by filename in specified
- file format (Amber trajectory if none specified) after all Action processing
- has occurred.
- To write out trajectories within the Action queue see the outtraj Action
- (
+During a run,
+ write frames to trajectory specified by filename in specified file format (Amber trajectory if none specified) after all Action processing has occurred.
+ To write out trajectories within the Action queue see the outtraj Action (
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_outtraj"
+nolink "false"
 
 \end_inset
 
@@ -19317,13 +19639,12 @@ reference "subsec:cpptraj_outtraj"
 \begin_inset CommandInset ref
 LatexCommand pageref
 reference "tab:cpptraj-trajformats"
+nolink "false"
 
 \end_inset
 
- for currently recognized output trajectory formats and their associated
- keyword(s).
- Note that now the file type can be determined from the output extension
- if not specified by a keyword.
+ for currently recognized output trajectory formats and their associated keyword(s).
+ Note that now the file type can be determined from the output extension if not specified by a keyword.
  Multiple output trajectories of any format can be specified.
  
 \end_layout
@@ -19331,9 +19652,7 @@ reference "tab:cpptraj-trajformats"
 \begin_layout Standard
 
 \series bold
-Frames will be written to the output trajectory when the parameter file
- being processed matches the parameter file the output trajectory was set
- up with.
+Frames will be written to the output trajectory when the parameter file being processed matches the parameter file the output trajectory was set up with.
 
 \series default
  So given the input:
@@ -19360,11 +19679,9 @@ trajout output.crd parm [top1]
 \end_layout
 
 \begin_layout Standard
-only frames read in from input1.crd (which is associated with top1.parm7)
- will be written to output.crd.
- The trajectory input0.crd is associated with top0.parm7; since no output
- trajectory is associated with top0.parm7 no frames will be written when
- processing top0.parm7/input0.crd.
+only frames read in from input1.crd (which is associated with top1.parm7) will be written to output.crd.
+ The trajectory input0.crd is associated with top0.parm7;
+ since no output trajectory is associated with top0.parm7 no frames will be written when processing top0.parm7/input0.crd.
 \end_layout
 
 \begin_layout Standard
@@ -19372,9 +19689,10 @@ If
 \series bold
 onlyframes
 \series default
- is specified, only input frames matching the specified range will be written
- out.
- For example, given the input:
+ is specified,
+ only input frames matching the specified range will be written out.
+ For example,
+ given the input:
 \end_layout
 
 \begin_layout LyX-Code
@@ -19386,7 +19704,10 @@ trajout output.crd onlyframes 2,5-7
 \end_layout
 
 \begin_layout Standard
-only frames 2, 5, 6, and 7 from input.crd will be written to output.crd.
+only frames 2,
+ 5,
+ 6,
+ and 7 from input.crd will be written to output.crd.
 \end_layout
 
 \begin_layout Subsubsection*
@@ -19401,22 +19722,24 @@ Certain Actions (e.g.
 align
 \series default
 \emph default
-, 
+,
+ 
 \series bold
 \emph on
 rms
 \series default
 \emph default
-, 
+,
+ 
 \series bold
 \emph on
 principal
 \series default
 \emph default
-, etc.) can rotate the unit cell vectors (i.e.
+,
+ etc.) can rotate the unit cell vectors (i.e.
  the box) if they are present.
- Some trajectory formats do not support writing out box coordinates if the
- unit cell is not 
+ Some trajectory formats do not support writing out box coordinates if the unit cell is not 
 \begin_inset Quotes eld
 \end_inset
 
@@ -19424,7 +19747,9 @@ X-aligned
 \begin_inset Quotes erd
 \end_inset
 
-; in other words, if the unit cell 
+;
+ in other words,
+ if the unit cell 
 \begin_inset Quotes eld
 \end_inset
 
@@ -19441,36 +19766,40 @@ B
 \end_inset
 
  vector is not in the X-Y plane.
- If this is the case, the following warnings may appear:
+ If this is the case,
+ the following warnings may appear:
 \end_layout
 
 \begin_layout LyX-Code
-Warning: Unit cell is not X-aligned.
+Warning:
+ Unit cell is not X-aligned.
  Box cannot be properly stored as <format>.
 \end_layout
 
 \begin_layout LyX-Code
-Warning: Set <#>; unit cell is not X-aligned.
+Warning:
+ Set <#>;
+ unit cell is not X-aligned.
  Box cannot be properly stored as <format>.
 \end_layout
 
 \begin_layout Standard
-This means that the frame will be written with the X-aligned unit cell instead
- of the actual unit cell.
+This means that the frame will be written with the X-aligned unit cell instead of the actual unit cell.
  Imaging will not be possible with a trajectory written this way.
- Currently the only trajectory formats that support writing non-X-aligned
- cells are the Gromacs TRR and XTC formats.
+ Currently the only trajectory formats that support writing non-X-aligned cells are the Gromacs TRR and XTC formats.
 \end_layout
 
 \begin_layout Standard
-If unit cell information is no longer needed, it can be removed (via e.g.
+If unit cell information is no longer needed,
+ it can be removed (via e.g.
  the 
 \series bold
 \emph on
 box
 \series default
 \emph default
- action, the 
+ action,
+ the 
 \series bold
 \emph on
 strip
@@ -19480,7 +19809,8 @@ strip
 \series bold
 'nobox'
 \series default
- keyword, etc.) to prevent these warnings from triggering.
+ keyword,
+ etc.) to prevent these warnings from triggering.
 \end_layout
 
 \begin_layout Subsubsection
@@ -19523,22 +19853,23 @@ Options for pdb format
 
 \begin_deeper
 \begin_layout Description
-dumpq PQR format; write charges (in units of e-) and GB radii to occupancy
- and B-factor columns respectively.
+dumpq PQR format;
+ write charges (in units of e-) and GB radii to occupancy and B-factor columns respectively.
 \end_layout
 
 \begin_layout Description
-parse PQR format; write charges and PARSE radii to occupancy/B-factor columns.
+parse PQR format;
+ write charges and PARSE radii to occupancy/B-factor columns.
 \end_layout
 
 \begin_layout Description
-vdw PQR format; write charges and vdW radii to occupancy/B-factor columns.
+vdw PQR format;
+ write charges and vdW radii to occupancy/B-factor columns.
 \end_layout
 
 \begin_layout Description
 pdbres Use PDB V3 residue names.
- Will write a default chain ID ('Z') for each residue if the corresponding
- topology does not have chain ID information.
+ Will write a default chain ID ('Z') for each residue if the corresponding topology does not have chain ID information.
 \end_layout
 
 \begin_layout Description
@@ -19551,7 +19882,8 @@ pdbv3 Use PDB V3 residue/atom names.
 \end_layout
 
 \begin_layout Description
-topresnum Use topology residue numbers; otherwise use original residue numbers.
+topresnum Use topology residue numbers;
+ otherwise use original residue numbers.
 \end_layout
 
 \begin_layout Description
@@ -19571,13 +19903,11 @@ noter Do not write TER cards.
 \end_layout
 
 \begin_layout Description
-model (Default) Frames will be written to a single PDB file separated by
- MODEL/ENDMDL keywords.
+model (Default) Frames will be written to a single PDB file separated by MODEL/ENDMDL keywords.
 \end_layout
 
 \begin_layout Description
-multi Each frame will be written to a separate file with the frame # appended
- to <filename>.
+multi Each frame will be written to a separate file with the frame # appended to <filename>.
 \end_layout
 
 \begin_layout Description
@@ -19593,7 +19923,8 @@ sg
 \begin_inset space ~
 \end_inset
 
-<group> Space group for CRYST1 record; only used if box coordinates written.
+<group> Space group for CRYST1 record;
+ only used if box coordinates written.
 \end_layout
 
 \begin_layout Description
@@ -19609,13 +19940,14 @@ conectmode
 \begin_inset space ~
 \end_inset
 
-<m> Write CONECT records for <m>='all' (all bonds), 'het' (HETATM only),
+<m> Write CONECT records for <m>='all' (all bonds),
+ 'het' (HETATM only),
  'none' (no CONECT).
 \end_layout
 
 \begin_layout Description
-keepext Keep filename extension; write '<name>.<num>.<ext>' instead (implies
- 'multi').
+keepext Keep filename extension;
+ write '<name>.<num>.<ext>' instead (implies 'multi').
 \end_layout
 
 \begin_layout Description
@@ -19655,13 +19987,11 @@ occdata
 \end_layout
 
 \begin_layout Description
-bfacbyres If specified assume X values in B-factor data set are residue
- numbers.
+bfacbyres If specified assume X values in B-factor data set are residue numbers.
 \end_layout
 
 \begin_layout Description
-occbyres If specified assume X values in occupancy data set are residue
- numbers.
+occbyres If specified assume X values in occupancy data set are residue numbers.
 \end_layout
 
 \begin_layout Description
@@ -19700,13 +20030,15 @@ adpdata
 atomicfluct
 \series default
 \emph default
- command, 
+ command,
+ 
 \begin_inset CommandInset ref
 LatexCommand vpageref
 reference "subsec:cpptraj_atomicfluct"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
@@ -19730,20 +20062,21 @@ Options for Amber ASCII format:
 
 \begin_deeper
 \begin_layout Description
-remdtraj Write REMD header to trajectory that includes temperature: 'REMD
- <Replica> <Step> <Total_Steps> <Temperature>'.
+remdtraj Write REMD header to trajectory that includes temperature:
+ 'REMD <Replica> <Step> <Total_Steps> <Temperature>'.
  Since 
 \shape italic
 cpptraj
 \shape default
- has no concept of replica number, 0 is printed for <Replica>.
+ has no concept of replica number,
+ 0 is printed for <Replica>.
  <Step> and <Total_Steps> are set to the current frame #.
 \end_layout
 
 \begin_layout Description
 highprecision (EXPERT USE ONLY) Write with 8.6 precision instead of 8.3.
- Note that since the width does not change, the precision of large coords
- may be lower than 6.
+ Note that since the width does not change,
+ the precision of large coords may be lower than 6.
 \end_layout
 
 \begin_layout Description
@@ -19814,8 +20147,7 @@ Options for Amber Restart/NetCDF Restart format:
 \end_layout
 
 \begin_layout LyX-Code
-  [remdtraj] [novelocity] [notime] [time0 <initial time>] [dt <timestep>]
- [keepext]
+  [remdtraj] [novelocity] [notime] [time0 <initial time>] [dt <timestep>] [keepext]
 \begin_inset Separator latexpar
 \end_inset
 
@@ -19825,8 +20157,7 @@ Options for Amber Restart/NetCDF Restart format:
 \begin_deeper
 \begin_layout Description
 remdtraj Write replica temperature to restart.
- Note that this will automatically include time in the restart file (see
- the 
+ Note that this will automatically include time in the restart file (see the 
 \series bold
 time0
 \family typewriter
@@ -19858,7 +20189,8 @@ dt
 \end_layout
 
 \begin_layout Description
-keepext Keep filename extension; write '<name>.<num>.<ext>' instead.
+keepext Keep filename extension;
+ write '<name>.<num>.<ext>' instead.
 \end_layout
 
 \end_deeper
@@ -19874,7 +20206,8 @@ Options for CHARMM COORdinates:
 
 \begin_deeper
 \begin_layout Description
-keepext Keep filename extension; write '<name>.<num>.<ext>'
+keepext Keep filename extension;
+ write '<name>.<num>.<ext>'
 \end_layout
 
 \begin_layout Description
@@ -19939,8 +20272,7 @@ shape Force writing box info as CHARMM shape matrix (XX XY YY XZ YZ ZZ).
 \end_layout
 
 \begin_layout Description
-namdcell Force writing box info as NAMD unit cell (X cos(g) Y cos(b) cos(a)
- Z).
+namdcell Force writing box info as NAMD unit cell (X cos(g) Y cos(b) cos(a) Z).
  
 \end_layout
 
@@ -19950,10 +20282,9 @@ charmmcell Force writing box info as old CHARMM unit cell (X Y Z a b g).
 
 \end_deeper
 \begin_layout Standard
-Note that by default CPPTRAJ will try to write the symmetric shape matrix
- if box information is present.
- If this is not possible, CPPTRAJ will fall back to writing unit cell parameters
- (lengths and angles) as long as the cell is X-aligned.
+Note that by default CPPTRAJ will try to write the symmetric shape matrix if box information is present.
+ If this is not possible,
+ CPPTRAJ will fall back to writing unit cell parameters (lengths and angles) as long as the cell is X-aligned.
  For more information see 
 \begin_inset CommandInset ref
 LatexCommand vref
@@ -19961,6 +20292,7 @@ reference "subsec:cpptraj-Options-for-CHARMM"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
@@ -19985,7 +20317,8 @@ dt Time step tp multiply set numbers by (default 1.0).
 
 \end_deeper
 \begin_layout Standard
-Note: these formats can write rotated (i.e.
+Note:
+ these formats can write rotated (i.e.
  non-X-aligned) unit cells.
 \end_layout
 
@@ -20005,13 +20338,11 @@ Options for mol2 format:
 
 \begin_deeper
 \begin_layout Description
-single (Default) Frames will be written to a single Mol2 file separated
- by MOLECULE keywords.
+single (Default) Frames will be written to a single Mol2 file separated by MOLECULE keywords.
 \end_layout
 
 \begin_layout Description
-multi Each frame will be written to a separate file with the frame # appended
- to <filename>.
+multi Each frame will be written to a separate file with the frame # appended to <filename>.
 \end_layout
 
 \begin_layout Description
@@ -20028,8 +20359,8 @@ sybylbond File containing Amber to SYBYL bond type correspondance (optional).
 \end_layout
 
 \begin_layout Description
-keepext Keep filename extension; write '<name>.<num>.<ext>' instead (implies
- 'multi').
+keepext Keep filename extension;
+ write '<name>.<num>.<ext>' instead (implies 'multi').
 \end_layout
 
 \end_deeper
@@ -20061,8 +20392,7 @@ Options for XYZ format:
 \end_layout
 
 \begin_layout LyX-Code
-[ftype {namexyz|atomxyz|xyz}] [titletype {none|single|perframe}] [width
- <#>] [prec <#>]
+[ftype {namexyz|atomxyz|xyz}] [titletype {none|single|perframe}] [width <#>] [prec <#>]
 \end_layout
 
 \begin_deeper
@@ -20071,16 +20401,16 @@ ftype
 \begin_inset space ~
 \end_inset
 
-{atomxyz|xyz} Choose either 'NAME X Y Z' (default), 'ATOM X Y Z', or 'X
- Y Z' output format.
+{atomxyz|xyz} Choose either 'NAME X Y Z' (default),
+ 'ATOM X Y Z',
+ or 'X Y Z' output format.
  
 \series bold
 'namexyz'
 \series default
- format is the standard XYZ format, where each frame is preceded by the
- number of atoms and a comment.
- The comment written by CPPTRAJ will include the set number and box information
- (if present).
+ format is the standard XYZ format,
+ where each frame is preceded by the number of atoms and a comment.
+ The comment written by CPPTRAJ will include the set number and box information (if present).
 \end_layout
 
 \begin_layout Description
@@ -20088,8 +20418,9 @@ titletype
 \begin_inset space ~
 \end_inset
 
-{none|single|perframe} No title, one title (default), or title before every
- frame.
+{none|single|perframe} No title,
+ one title (default),
+ or title before every frame.
  Only applies if not 
 \series bold
 'namexyz'
@@ -20142,8 +20473,9 @@ trajin
 ensemble
 \series default
 \emph default
- commands one at a time and extract derived data, modify the coordinates/topolog
-y in some way, or both.
+ commands one at a time and extract derived data,
+ modify the coordinates/topology in some way,
+ or both.
  Most Actions in 
 \shape italic
 cpptraj
@@ -20167,15 +20499,15 @@ ptraj
 rmsd
 \series default
 \emph default
- Action, or the ability to write out stripped topologies for visualization
- in the 
+ Action,
+ or the ability to write out stripped topologies for visualization in the 
 \series bold
 \emph on
 strip
 \series default
 \emph default
- Action), while other Actions produce slightly different output (like the
- 
+ Action),
+ while other Actions produce slightly different output (like the 
 \series bold
 \emph on
 hbond
@@ -20191,9 +20523,8 @@ secstruct
 \end_layout
 
 \begin_layout Standard
-Unlike some other command types, when an Action command is issued it is
- by default added to the Action queue and is not executed until trajectory
- processing is started (e.g.
+Unlike some other command types,
+ when an Action command is issued it is by default added to the Action queue and is not executed until trajectory processing is started (e.g.
  by a 
 \series bold
 \emph on
@@ -20207,8 +20538,8 @@ go
 \series default
 \emph default
  command).
- However, Actions can be executed immediately on COORDS data sets via the
- 
+ However,
+ Actions can be executed immediately on COORDS data sets via the 
 \series bold
 \emph on
 crdaction
@@ -20218,6 +20549,7 @@ crdaction
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_crdaction"
+nolink "false"
 
 \end_inset
 
@@ -20225,10 +20557,10 @@ reference "subsec:cpptraj_crdaction"
 \end_layout
 
 \begin_layout Standard
-When a frame is modified by an Action, it is modified for every Action that
- follows them during trajectory processing.
- For example, given a solvated system with water residues named WAT and
- the following Action commands:
+When a frame is modified by an Action,
+ it is modified for every Action that follows them during trajectory processing.
+ For example,
+ given a solvated system with water residues named WAT and the following Action commands:
 \end_layout
 
 \begin_layout LyX-Code
@@ -20250,14 +20582,14 @@ the first
 rms
 \series default
 \emph default
- command will be valid, but the second 
+ command will be valid,
+ but the second 
 \series bold
 \emph on
 rms
 \series default
 \emph default
- command will not since all residues named WAT are removed from the state
- by the 
+ command will not since all residues named WAT are removed from the state by the 
 \series bold
 \emph on
 strip
@@ -20267,27 +20599,29 @@ strip
 \end_layout
 
 \begin_layout Standard
-Note that for commands which can use a reference mask as well as a target
- mask (e.g.
+Note that for commands which can use a reference mask as well as a target mask (e.g.
  
 \series bold
 \emph on
 rms
 \series default
 \emph default
-, 
+,
+ 
 \series bold
 \emph on
 drmsd
 \series default
 \emph default
-, 
+,
+ 
 \series bold
 \emph on
 symmrmsd
 \series default
 \emph default
-, etc.) there must be a 1 to 1 correspondence between the atoms in each mask,
+,
+ etc.) there must be a 1 to 1 correspondence between the atoms in each mask,
  i.e.
  the 
 \emph on
@@ -20298,8 +20632,7 @@ number of atoms and the ordering of selected atoms must be the same
 
 \begin_layout Standard
 The following Actions are available.
- If an Action may modify coordinate/topology information for subsequent
- Actions it is denoted with an X in the 
+ If an Action may modify coordinate/topology information for subsequent Actions it is denoted with an X in the 
 \family typewriter
 \series bold
 Mod
@@ -20505,7 +20838,8 @@ Calculate average correlation between motions of specified atoms.
 \begin_inset Text
 
 \begin_layout Plain Layout
-atomicfluct, rmsf
+atomicfluct,
+ rmsf
 \end_layout
 
 \end_inset
@@ -20630,7 +20964,8 @@ avgbox
 \begin_inset Text
 
 \begin_layout Plain Layout
-Calculate average unit cell (box), primarily for unwrapping NPT trajectories.
+Calculate average unit cell (box),
+ primarily for unwrapping NPT trajectories.
 \end_layout
 
 \end_inset
@@ -20738,7 +21073,8 @@ X
 \begin_inset Text
 
 \begin_layout Plain Layout
-check, checkoverlap,
+check,
+ checkoverlap,
 \end_layout
 
 \end_inset
@@ -20806,7 +21142,8 @@ checkchirality
 \begin_inset Text
 
 \begin_layout Plain Layout
-Report chirality around alpha carbons in amino acids (L, D).
+Report chirality around alpha carbons in amino acids (L,
+ D).
 \end_layout
 
 \end_inset
@@ -20826,7 +21163,8 @@ Report chirality around alpha carbons in amino acids (L, D).
 \begin_inset Text
 
 \begin_layout Plain Layout
-closest, closestwaters
+closest,
+ closestwaters
 \end_layout
 
 \end_inset
@@ -20835,8 +21173,7 @@ closest, closestwaters
 \begin_inset Text
 
 \begin_layout Plain Layout
-Retain only the specified number of solvent molecules closest to specified
- solute.
+Retain only the specified number of solvent molecules closest to specified solute.
 \end_layout
 
 \end_inset
@@ -20865,8 +21202,7 @@ clusterdihedral
 \begin_inset Text
 
 \begin_layout Plain Layout
-Assign frames into clusters based on binning of backbone dihedral angles
- in amino acids.
+Assign frames into clusters based on binning of backbone dihedral angles in amino acids.
 \end_layout
 
 \end_inset
@@ -20901,7 +21237,8 @@ Older version of
 nativecontacts
 \series default
 \emph default
-, retained for backwards compatibility.
+,
+ retained for backwards compatibility.
 \end_layout
 
 \end_inset
@@ -21066,7 +21403,8 @@ Calculate the dihedral angle using four points.
 \begin_inset Text
 
 \begin_layout Plain Layout
-dihrms, 
+dihrms,
+ 
 \end_layout
 
 \begin_layout Plain Layout
@@ -21109,7 +21447,8 @@ dipole
 
 \begin_layout Plain Layout
 Bin dipoles of solvent molecules in 3D grid.
- Not well tested, may be obsolete.
+ Not well tested,
+ may be obsolete.
 \end_layout
 
 \end_inset
@@ -21158,7 +21497,8 @@ Calculate the distance between two points.
 \begin_inset Text
 
 \begin_layout Plain Layout
-drms, drmsd
+drms,
+ drmsd
 \end_layout
 
 \end_inset
@@ -21187,7 +21527,8 @@ Calculate the RMSD of distance pairs within selected atoms.
 \begin_inset Text
 
 \begin_layout Plain Layout
-dssp, secstruct
+dssp,
+ secstruct
 \end_layout
 
 \end_inset
@@ -21254,8 +21595,10 @@ energy
 \begin_inset Text
 
 \begin_layout Plain Layout
-Calculate simple bond, angle, dihedral, and non-bonded energy terms (no
- PME).
+Calculate simple bond,
+ angle,
+ dihedral,
+ and non-bonded energy terms (no PME).
 \end_layout
 
 \end_inset
@@ -21284,8 +21627,8 @@ esander
 \begin_inset Text
 
 \begin_layout Plain Layout
-Calculate energies using via SANDER; requires compilation with the SANDER
- API.
+Calculate energies using via SANDER;
+ requires compilation with the SANDER API.
 \end_layout
 
 \end_inset
@@ -21611,8 +21954,7 @@ lie
 \begin_inset Text
 
 \begin_layout Plain Layout
-Calculate linear interaction energy between user-specified ligand and surroundin
-gs.
+Calculate linear interaction energy between user-specified ligand and surroundings.
 \end_layout
 
 \end_inset
@@ -21788,8 +22130,7 @@ mindist/maxdist
 \begin_inset Text
 
 \begin_layout Plain Layout
-Calculate the minimum or maximum distance between pairs of atoms/residues/molecu
-les.
+Calculate the minimum or maximum distance between pairs of atoms/residues/molecules.
 \end_layout
 
 \end_inset
@@ -21964,8 +22305,7 @@ nativecontacts
 \begin_inset Text
 
 \begin_layout Plain Layout
-Calculate native contacts within a region or between two regions using a
- given reference.
+Calculate native contacts within a region or between two regions using a given reference.
  
 \end_layout
 
@@ -22189,7 +22529,8 @@ Calculate ring pucker using five or six points.
 \begin_inset Text
 
 \begin_layout Plain Layout
-radgyr, rog
+radgyr,
+ rog
 \end_layout
 
 \end_inset
@@ -22218,7 +22559,8 @@ Calculate radius of gyration (and optionally tensor) for specified atoms.
 \begin_inset Text
 
 \begin_layout Plain Layout
-radial, rdf
+radial,
+ rdf
 \end_layout
 
 \end_inset
@@ -22314,8 +22656,7 @@ replicatecell
 \begin_inset Text
 
 \begin_layout Plain Layout
-Replicate unit cell in specified (or all) directions for specfied atoms
- and write to trajectory.
+Replicate unit cell in specified (or all) directions for specfied atoms and write to trajectory.
 \end_layout
 
 \end_inset
@@ -22335,7 +22676,8 @@ Replicate unit cell in specified (or all) directions for specfied atoms
 \begin_inset Text
 
 \begin_layout Plain Layout
-rms, rmsd
+rms,
+ rmsd
 \end_layout
 
 \end_inset
@@ -22402,8 +22744,9 @@ rotate
 \begin_inset Text
 
 \begin_layout Plain Layout
-Rotate the system around X/Y/Z axes, a specified axis, or via given rotation
- matrices.
+Rotate the system around X/Y/Z axes,
+ a specified axis,
+ or via given rotation matrices.
 \end_layout
 
 \end_inset
@@ -22423,7 +22766,8 @@ X
 \begin_inset Text
 
 \begin_layout Plain Layout
-runavg, 
+runavg,
+ 
 \end_layout
 
 \end_inset
@@ -22572,8 +22916,7 @@ spam
 \begin_inset Text
 
 \begin_layout Plain Layout
-SPAM method for estimating relative free energies of waters in hydration
- shell around proteins.
+SPAM method for estimating relative free energies of waters in hydration shell around proteins.
 \end_layout
 
 \end_inset
@@ -22602,8 +22945,7 @@ stfcdiffusion
 \begin_inset Text
 
 \begin_layout Plain Layout
-Alternative translational diffusion calculation which can calculate diffusion
- in specified regions.
+Alternative translational diffusion calculation which can calculate diffusion in specified regions.
 \end_layout
 
 \end_inset
@@ -22798,7 +23140,8 @@ Calculate diffusion using the toroidal-view-preserving scheme.
 \begin_inset Text
 
 \begin_layout Plain Layout
-trans, translate
+trans,
+ translate
 \end_layout
 
 \end_inset
@@ -22877,7 +23220,8 @@ Reverse of
 image
 \series default
 \emph default
-; unwrap selected atoms so they have continuous trajectories.
+;
+ unwrap selected atoms so they have continuous trajectories.
 \end_layout
 
 \end_inset
@@ -22964,7 +23308,8 @@ volmap
 \begin_inset Text
 
 \begin_layout Plain Layout
-Create volumetric map for specified coordinates; similar to 
+Create volumetric map for specified coordinates;
+ similar to 
 \series bold
 \emph on
 grid
@@ -23064,8 +23409,7 @@ watershell
 \begin_inset Text
 
 \begin_layout Plain Layout
-Calculate the number of waters in the first and second solvation shells
- based on distance critera.
+Calculate the number of waters in the first and second solvation shells based on distance critera.
 \end_layout
 
 \end_inset
@@ -23094,8 +23438,7 @@ xtalsymm
 \begin_inset Text
 
 \begin_layout Plain Layout
-Re-image coordinates based on crystal space group symmetry operations and
- asymmetric unit volume.
+Re-image coordinates based on crystal space group symmetry operations and asymmetric unit volume.
 \end_layout
 
 \end_inset
@@ -23210,8 +23553,7 @@ name>] New residue name for the new atom.
 \begin_inset space ~
 \end_inset
 
-<prefix>] Write out modified topology file with name '<prefix>.<Original
- Topology Name>'.
+<prefix>] Write out modified topology file with name '<prefix>.<Original Topology Name>'.
 \end_layout
 
 \begin_layout Description
@@ -23246,16 +23588,18 @@ dummy
 \end_inset
 
  atom for subsequent actions to use.
- For example, this can be used in conjunction with the 
+ For example,
+ this can be used in conjunction with the 
 \series bold
 \emph on
 'mask'
 \series default
 \emph default
- command in order to get a list of atoms within a certain distance of a
- specified point in space.
- For example, the following input gets a list of atoms within 3.0 Angstroms
- of coordinates 1, 1, 1:
+ command in order to get a list of atoms within a certain distance of a specified point in space.
+ For example,
+ the following input gets a list of atoms within 3.0 Angstroms of coordinates 1,
+ 1,
+ 1:
 \end_layout
 
 \begin_layout LyX-Code
@@ -23352,8 +23696,7 @@ refindex
 
 <#>
 \series default
- Use previously read in reference structure specified by <#> (based on order
- read in).
+ Use previously read in reference structure specified by <#> (based on order read in).
 \end_layout
 
 \begin_layout Description
@@ -23369,13 +23712,12 @@ reftraj
 \begin_inset space ~
 \end_inset
 
-<name> Use frames from COORDS set <name> or read in from trajectory file
- <name> as references.
- Each frame from <name> is used in turn, so that frame 1 is compared to
- frame 1 from <name>, frame 2 is compared to frame 2 from <name> and so
- on.
- If <trajname> runs out of frames before processing is complete, the last
- frame of <trajname> continues to be used as the reference.
+<name> Use frames from COORDS set <name> or read in from trajectory file <name> as references.
+ Each frame from <name> is used in turn,
+ so that frame 1 is compared to frame 1 from <name>,
+ frame 2 is compared to frame 2 from <name> and so on.
+ If <trajname> runs out of frames before processing is complete,
+ the last frame of <trajname> continues to be used as the reference.
 \begin_inset Separator latexpar
 \end_inset
 
@@ -23404,15 +23746,17 @@ parmindex
 \series bold
 reftraj
 \series default
- specifies a trajectory file, associate it with specified topology; if not
- specified the first topology is used.
+ specifies a trajectory file,
+ associate it with specified topology;
+ if not specified the first topology is used.
 \end_layout
 
 \end_deeper
 \end_deeper
 \begin_layout Standard
 Align structure using specified <mask> onto reference.
- If 'move' is specified, only move atoms in the move mask.
+ If 'move' is specified,
+ only move atoms in the move mask.
 \end_layout
 
 \begin_layout Subsection
@@ -23422,6 +23766,8 @@ angle
 \begin_layout LyX-Code
 angle
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -23464,9 +23810,11 @@ name>] Output data set name.
 
 \end_deeper
 \begin_layout Standard
-Calculate angle (in degrees) between atoms in <mask1>, <mask2>, and <mask3>.
- For example, to calculate the angle between the first three atoms in the
- system:
+Calculate angle (in degrees) between atoms in <mask1>,
+ <mask2>,
+ and <mask3>.
+ For example,
+ to calculate the angle between the first three atoms in the system:
 \end_layout
 
 \begin_layout LyX-Code
@@ -23513,8 +23861,8 @@ areapermol [<name>] {[<mask1>] [nlayers <#>] | nmols <#>} [out <filename>]
 \begin_inset space ~
 \end_inset
 
-<#>] If <mask1> is not specified, the number of molecules to use when calculatin
-g area per molecule.
+<#>] If <mask1> is not specified,
+ the number of molecules to use when calculating area per molecule.
 \end_layout
 
 \begin_layout Description
@@ -23533,11 +23881,10 @@ g area per molecule.
 \end_deeper
 \begin_layout Standard
 Calculate area per molecule as Area / # molecules.
- The area is determined from the specified cross-section of the box (X-Y
- by default).
- Currently the calculation is only guaranteed to work properly with orthorhombic
- unit cells.
- For example, to get the area per molecule of residues named 
+ The area is determined from the specified cross-section of the box (X-Y by default).
+ Currently the calculation is only guaranteed to work properly with orthorhombic unit cells.
+ For example,
+ to get the area per molecule of residues named 
 \begin_inset Quotes eld
 \end_inset
 
@@ -23598,24 +23945,23 @@ min
 \begin_inset space ~
 \end_inset
 
-spacing> Only calculate correlations for motion vectors spaced <min spacing>
- apart.
+spacing> Only calculate correlations for motion vectors spaced <min spacing> apart.
 \end_layout
 
 \begin_layout Description
-byatom Default; calculate atomic motion vectors.
+byatom Default;
+ calculate atomic motion vectors.
 \end_layout
 
 \begin_layout Description
-byres Calculate motion vectors for entire residues (selected atoms in residues
- only).
+byres Calculate motion vectors for entire residues (selected atoms in residues only).
 \end_layout
 
 \end_deeper
 \begin_layout Standard
 Calculate average correlations between the motion of atoms in <mask>.
- For each frame, a motion vector is calculated for each selected atom from
- its previous position to its current position.
+ For each frame,
+ a motion vector is calculated for each selected atom from its previous position to its current position.
  For each pair of motion vectors 
 \shape italic
 Va
@@ -23624,8 +23970,8 @@ Va
 \shape italic
 Vb
 \shape default
-, the average correlation between those vectors is calculated as the average
- of the dot product of those vectors over all 
+,
+ the average correlation between those vectors is calculated as the average of the dot product of those vectors over all 
 \shape italic
 N
 \shape default
@@ -23646,10 +23992,10 @@ N
 \end_layout
 
 \begin_layout Standard
-The value of AvgCorr can range from 1.0 (correlated) to 0.0 (no correlation)
- to -1.0 (anti-correlated).
- For example, to calculate the correlation of motion vectors between residues
- 1 to 13, writing to a Gnuplot-readable formatted file:
+The value of AvgCorr can range from 1.0 (correlated) to 0.0 (no correlation) to -1.0 (anti-correlated).
+ For example,
+ to calculate the correlation of motion vectors between residues 1 to 13,
+ writing to a Gnuplot-readable formatted file:
 \end_layout
 
 \begin_layout LyX-Code
@@ -23670,6 +24016,8 @@ name "subsec:cpptraj_atomicfluct"
 \begin_layout LyX-Code
 atomicfluct
 \begin_inset Index idx
+range none
+pageformat default
 status open
 
 \begin_layout Plain Layout
@@ -23711,13 +24059,12 @@ out
 \end_layout
 
 \begin_layout Description
-[bfactor] Calculate atomic positional fluctuations squared and weight by
- 
+[bfactor] Calculate atomic positional fluctuations squared and weight by 
 \begin_inset Formula $\frac{8}{3}\pi^{2}$
 \end_inset
 
-; this is similar but not necessarily equivalent to the calculation of crystallo
-graphic B-factors.
+;
+ this is similar but not necessarily equivalent to the calculation of crystallographic B-factors.
 \end_layout
 
 \begin_layout Description
@@ -23729,8 +24076,7 @@ graphic B-factors.
 \begin_inset space ~
 \end_inset
 
-<file>]] Calculate anisotropic displacement parameters and optionally output
- them to <file>.
+<file>]] Calculate anisotropic displacement parameters and optionally output them to <file>.
 \end_layout
 
 \begin_layout Description
@@ -23739,7 +24085,8 @@ byres [pdbres] Output the average (mass-weighted) fluctuation by residue.
 
 \begin_deeper
 \begin_layout Description
-pdbres If specified, the original residue numbering will be used.
+pdbres If specified,
+ the original residue numbering will be used.
 \end_layout
 
 \begin_layout Description
@@ -23748,8 +24095,7 @@ resrange
 \end_inset
 
 <range> Calculate fluctuations for residues in the given range argument.
- The residues selected by <mask> must be a subset of residues specified
- with <range>.
+ The residues selected by <mask> must be a subset of residues specified with <range>.
  Unselected residues will get a fluctuation of 0.0.
 \end_layout
 
@@ -23792,8 +24138,8 @@ DataSets created
 
 \end_deeper
 \begin_layout Standard
-Compute the atomic positional fluctuations (also referred to as root-mean-square
- fluctuations, RMSF) for atoms specified in the 
+Compute the atomic positional fluctuations (also referred to as root-mean-square fluctuations,
+ RMSF) for atoms specified in the 
 \series bold
 <mask>
 \series default
@@ -23823,9 +24169,8 @@ x
 
 \begin_layout Standard
 Note that RMS fitting is not done implicitly.
- If you want fluctuations without rotations or translations (for example
- to the average structure), perform an RMS fit to the average structure
- (best) or the first structure (see 
+ If you want fluctuations without rotations or translations (for example to the average structure),
+ perform an RMS fit to the average structure (best) or the first structure (see 
 \series bold
 \shape italic
 rmsd
@@ -23860,9 +24205,8 @@ byres
 \series bold
 bymask
 \series default
- are specified, the mass-weighted average of atomic fluctuations of each
- atom for either each residue or the entire mask will be calculated respectively
-:
+ are specified,
+ the mass-weighted average of atomic fluctuations of each atom for either each residue or the entire mask will be calculated respectively:
 \begin_inset Separator latexpar
 \end_inset
 
@@ -23882,8 +24226,8 @@ If
 \series bold
 calcadp
 \series default
- is specified, anisotropic displacement factors for atoms will be calculated
- and written to the file specified by 
+ is specified,
+ anisotropic displacement factors for atoms will be calculated and written to the file specified by 
 \series bold
 adpout
 \series default
@@ -23905,7 +24249,8 @@ With
 \emph on
 cpptraj
 \emph default
- it is possible to perform coordinate averaging, the fit to average coordinates,
+ it is possible to perform coordinate averaging,
+ the fit to average coordinates,
  and the atomic fluctuation calculation in a single execution like so:
 \end_layout
 
@@ -23938,8 +24283,10 @@ atomicfluct out fluct.agr
 \end_layout
 
 \begin_layout Standard
-To write the mass-weighted B-factors for the protein backbone atoms C, CA,
- and N, averaged by residue use the command:
+To write the mass-weighted B-factors for the protein backbone atoms C,
+ CA,
+ and N,
+ averaged by residue use the command:
 \end_layout
 
 \begin_layout LyX-Code
@@ -23947,8 +24294,8 @@ atomicfluct out back.agr @C,CA,N byres bfactor
 \end_layout
 
 \begin_layout Standard
-To write the RMSF or atomic positional fluctuations of the same atoms, use
- the command:
+To write the RMSF or atomic positional fluctuations of the same atoms,
+ use the command:
 \end_layout
 
 \begin_layout LyX-Code
@@ -23956,8 +24303,7 @@ atomicfluct out backbone-atoms.agr @C,CA,N
 \end_layout
 
 \begin_layout Standard
-To write a PDB of averaged coordinates (after fitting to the first frame)
- with both B-factors and anisotropic temperature factors:
+To write a PDB of averaged coordinates (after fitting to the first frame) with both B-factors and anisotropic temperature factors:
 \end_layout
 
 \begin_layout LyX-Code
@@ -23995,6 +24341,8 @@ atommap
 \begin_layout LyX-Code
 atommap
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -24049,6 +24397,7 @@ Target atoms that cannot be mapped to a reference atom are denoted
 \end_inset
 
 —
+
 \begin_inset Quotes erd
 \end_inset
 
@@ -24060,8 +24409,7 @@ maponly Write atom map but do not reorder atoms.
 \end_layout
 
 \begin_layout Description
-rmsfit Any input frames using the same topology as <target> will be RMS
- fit to <reference> using whatever atoms could be mapped.
+rmsfit Any input frames using the same topology as <target> will be RMS fit to <reference> using whatever atoms could be mapped.
 \begin_inset Separator latexpar
 \end_inset
 
@@ -24074,13 +24422,14 @@ rmsout
 \begin_inset space ~
 \end_inset
 
-<rmsout> If rmsfit specified, write resulting RMSDs to <rmsout>.
+<rmsout> If rmsfit specified,
+ write resulting RMSDs to <rmsout>.
 \end_layout
 
 \end_deeper
 \begin_layout Description
-changenames If specified, change names of mapped atoms in <target> to match
- those in <reference>.
+changenames If specified,
+ change names of mapped atoms in <target> to match those in <reference>.
 \end_layout
 
 \begin_layout Description
@@ -24088,45 +24437,39 @@ chiralimpcut
 \begin_inset space ~
 \end_inset
 
-<cut> sets the improper dihedral angle cutoff for determining mapping via
- chirality (default 10 deg.).
+<cut> sets the improper dihedral angle cutoff for determining mapping via chirality (default 10 deg.).
 \end_layout
 
 \end_deeper
 \begin_layout Standard
-Attempt to map the atoms of <target> to those of <reference> based on structural
- similarity.
+Attempt to map the atoms of <target> to those of <reference> based on structural similarity.
  This is useful e.g.
- when there are two files containing the same structure but with different
- atom names or atom ordering.
- Both <target> and <reference> need to have been read in with a previous
- 
+ when there are two files containing the same structure but with different atom names or atom ordering.
+ Both <target> and <reference> need to have been read in with a previous 
 \series bold
 \shape italic
 reference
 \series default
 \shape default
  command.
- The state will then be modified so that any trajectory read in with the
- same parameter file as <target> will have its atoms mapped (i.e.
+ The state will then be modified so that any trajectory read in with the same parameter file as <target> will have its atoms mapped (i.e.
  reordered) to match those of <reference>.
- If the number of atoms that can be mapped in <target> are less than those
- in <reference>, the reference structure specified by <reference> will be
- modified to include only mapped atoms; this is useful if for example the
- reference structure is protonated with respect to the target.
+ If the number of atoms that can be mapped in <target> are less than those in <reference>,
+ the reference structure specified by <reference> will be modified to include only mapped atoms;
+ this is useful if for example the reference structure is protonated with respect to the target.
  The 
 \series bold
 rmsfit
 \series default
- keyword is useful in cases where the atom mapping will not be complete
- (e.g.
+ keyword is useful in cases where the atom mapping will not be complete (e.g.
  two ligands with the same scaffold but different substituents).
  If 
 \series bold
 changenames
 \series default
- is specified, in addition to remapping, the target atom names will be changed
- to match the reference atom names.
+ is specified,
+ in addition to remapping,
+ the target atom names will be changed to match the reference atom names.
 \end_layout
 
 \begin_layout Standard
@@ -24140,22 +24483,22 @@ improper
 \end_inset
 
  dihedral angles to determine the orientation of the bonded atoms.
- By default the code assumes the orientation of the atoms around the chiral
- centers are fairly close, hence there is a small improper dihedral angle
- cutoff of 10 degrees.
- However, this can be increased via the 
+ By default the code assumes the orientation of the atoms around the chiral centers are fairly close,
+ hence there is a small improper dihedral angle cutoff of 10 degrees.
+ However,
+ this can be increased via the 
 \series bold
 chiralimpcut
 \series default
- keyword to handle cases where one structure is distorted with respect to
- the other.
+ keyword to handle cases where one structure is distorted with respect to the other.
 \end_layout
 
 \begin_layout Standard
-For example, say you have the same ligand structure in two files, Ref.mol2
- and Lig.mol2, but the atom ordering in each file is different.
- To map the atoms in Lig.mol2 onto those of Ref.mol2 so that Lig.mol2 has the
- same ordering as Ref.mol2:
+For example,
+ say you have the same ligand structure in two files,
+ Ref.mol2 and Lig.mol2,
+ but the atom ordering in each file is different.
+ To map the atoms in Lig.mol2 onto those of Ref.mol2 so that Lig.mol2 has the same ordering as Ref.mol2:
 \end_layout
 
 \begin_layout LyX-Code
@@ -24216,7 +24559,8 @@ anchor
 \begin_inset space ~
 \end_inset
 
-<mask>] Atoms to image around; this is the region that will be centered.
+<mask>] Atoms to image around;
+ this is the region that will be centered.
  Default is the entire first molecule.
 \end_layout
 
@@ -24225,8 +24569,8 @@ anchor
 \begin_inset space ~
 \end_inset
 
-<mask>] Molecules that should remain 'fixed' to the anchor region; default
- is all non-ion/non-solvent molecules.
+<mask>] Molecules that should remain 'fixed' to the anchor region;
+ default is all non-ion/non-solvent molecules.
 \end_layout
 
 \begin_layout Description
@@ -24234,23 +24578,24 @@ anchor
 \begin_inset space ~
 \end_inset
 
-<mask>] Molecules that can be freely imaged; default is all ion/solvent
- molecules.
+<mask>] Molecules that can be freely imaged;
+ default is all ion/solvent molecules.
 \end_layout
 
 \begin_layout Description
-[origin] Center anchor region at the origin; if not specified, center at
- box center.
+[origin] Center anchor region at the origin;
+ if not specified,
+ center at box center.
 \end_layout
 
 \begin_layout Description
-[firstatom] Image based on molecule first atom; default is to image by molecule
- center of mass.
+[firstatom] Image based on molecule first atom;
+ default is to image by molecule center of mass.
 \end_layout
 
 \begin_layout Description
-[familiar] Image to familiar truncated-octahedral shape; this is on by default
- if the original cell is truncated octahedron.
+[familiar] Image to familiar truncated-octahedral shape;
+ this is on by default if the original cell is truncated octahedron.
 \end_layout
 
 \begin_layout Description
@@ -24266,9 +24611,9 @@ fixed
 \begin_inset Quotes erd
 \end_inset
 
- molecules, the anchor point will be set to the previous "fixed" molecule;
- this is only expected to work well when "fixed" molecules that are sequential
- are also geometrically close.
+ molecules,
+ the anchor point will be set to the previous "fixed" molecule;
+ this is only expected to work well when "fixed" molecules that are sequential are also geometrically close.
  Most useful in more condensed systems like those containing membranes.
 \end_layout
 
@@ -24287,8 +24632,7 @@ bydist The default.
 \end_layout
 
 \begin_layout Description
-byvec Fixed molecules will use the image closest to their orientation with
- respect to the anchor in the first frame.
+byvec Fixed molecules will use the image closest to their orientation with respect to the anchor in the first frame.
  May work better than 
 \series bold
 'bydist'
@@ -24299,8 +24643,7 @@ byvec Fixed molecules will use the image closest to their orientation with
 \end_deeper
 \end_deeper
 \begin_layout Standard
-Automatically center and image (by molecule) a trajectory with periodic
- boundaries.
+Automatically center and image (by molecule) a trajectory with periodic boundaries.
  For most cases just specifying 
 \series bold
 \shape italic
@@ -24312,7 +24655,8 @@ Automatically center and image (by molecule) a trajectory with periodic
 \series bold
 'anchor'
 \series default
- region (default the entire first molecule) will be centered; all 
+ region (default the entire first molecule) will be centered;
+ all 
 \series bold
 'fixed'
 \series default
@@ -24333,13 +24677,13 @@ Automatically center and image (by molecule) a trajectory with periodic
 \end_layout
 
 \begin_layout Standard
-The autoimage command works for the majority of systems; however, for very
- densely packed systems the default anchor (entire first molecule) may not
- be appropriate.
- In these cases, it is recommended to choose as the anchor a small region
- which should lie near the center of your system.
- For example, in a protein dimer system one could choose a single residue
- that is near the center of the interface between the two monomers.
+The autoimage command works for the majority of systems;
+ however,
+ for very densely packed systems the default anchor (entire first molecule) may not be appropriate.
+ In these cases,
+ it is recommended to choose as the anchor a small region which should lie near the center of your system.
+ For example,
+ in a protein dimer system one could choose a single residue that is near the center of the interface between the two monomers.
  The 
 \series bold
 'moveanchor'
@@ -24352,8 +24696,8 @@ The autoimage command works for the majority of systems; however, for very
 \series bold
 byvec'
 \series default
- options may also help in cases where the system is more condensed, such
- as those containing membranes.
+ options may also help in cases where the system is more condensed,
+ such as those containing membranes.
 \end_layout
 
 \begin_layout Subsection
@@ -24370,6 +24714,8 @@ name "subsec:cpptraj-average"
 \begin_layout LyX-Code
 average
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -24395,8 +24741,8 @@ average
 
 \begin_deeper
 \begin_layout Description
-<filename> If specified, write averaged coordinates to <filename> (not compatibl
-e with crdset).
+<filename> If specified,
+ write averaged coordinates to <filename> (not compatible with crdset).
 \end_layout
 
 \begin_layout Description
@@ -24408,8 +24754,8 @@ crdset
 \begin_inset space ~
 \end_inset
 
-name> If specified, save averaged coordinates to COORDS set <set name> (not
- compatible with <filename>).
+name> If specified,
+ save averaged coordinates to COORDS set <set name> (not compatible with <filename>).
 \end_layout
 
 \begin_layout Description
@@ -24455,8 +24801,8 @@ cpptraj
 \series bold
 <mask>
 \series default
- are less than the total number of atoms, the topology will be stripped
- to match 
+ are less than the total number of atoms,
+ the topology will be stripped to match 
 \series bold
 <mask>
 \series default
@@ -24465,13 +24811,11 @@ cpptraj
 \end_layout
 
 \begin_layout Standard
-Note that since coordinates are being averaged over many frames, resulting
- structures may appear distorted.
- For example, if one averages the coordinates of a freely rotating methyl
- group the average position of the hydrogen atoms will be close to the center
- of rotation.
- Also note that typically one will want to remove global rotational and
- translation movement prior to this command by using e.g.
+Note that since coordinates are being averaged over many frames,
+ resulting structures may appear distorted.
+ For example,
+ if one averages the coordinates of a freely rotating methyl group the average position of the hydrogen atoms will be close to the center of rotation.
+ Also note that typically one will want to remove global rotational and translation movement prior to this command by using e.g.
  the 
 \series bold
 \emph on
@@ -24482,6 +24826,7 @@ rms
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-rmsd"
+nolink "false"
 
 \end_inset
 
@@ -24499,13 +24844,13 @@ trajout
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-trajout"
+nolink "false"
 
 \end_inset
 
-) can be passed to this command in order to control the format of the output
- coordinates.
- For example, to write out a PDB file containing the averaged coordinates
- over all frames:
+) can be passed to this command in order to control the format of the output coordinates.
+ For example,
+ to write out a PDB file containing the averaged coordinates over all frames:
 \end_layout
 
 \begin_layout LyX-Code
@@ -24513,8 +24858,7 @@ average test.pdb pdb
 \end_layout
 
 \begin_layout Standard
-To write out a mol2 file containing only the averaged coordinates of residues
- 1 to 10 for frames 1 to 100:
+To write out a mol2 file containing only the averaged coordinates of residues 1 to 10 for frames 1 to 100:
 \end_layout
 
 \begin_layout LyX-Code
@@ -24522,8 +24866,7 @@ average test.mol2 mol2 start 1 stop 100 :1-10
 \end_layout
 
 \begin_layout Standard
-To create an average structure of atoms named CA and then use it as a reference
- for an rms command in a subsequent run:
+To create an average structure of atoms named CA and then use it as a reference for an rms command in a subsequent run:
 \end_layout
 
 \begin_layout LyX-Code
@@ -24588,22 +24931,22 @@ DataSets created:
 
 \end_deeper
 \begin_layout Standard
-Calculate the average unit cell vectors for incoming frames and store them
- in a 3x3 matrix data set, The average unit cell is particularly useful
- when unwrapping trajectories from NPT simulations where the box size fluctuates
- (see the 
+Calculate the average unit cell vectors for incoming frames and store them in a 3x3 matrix data set,
+ The average unit cell is particularly useful when unwrapping trajectories from NPT simulations where the box size fluctuates (see the 
 \series bold
 \emph on
 unwrap
 \series default
 \emph default
- command, 
+ command,
+ 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_unwrap"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
@@ -24611,23 +24954,22 @@ noprefix "false"
 \end_layout
 
 \begin_layout Standard
-If writing to a .dat file, the output will look something like:
+If writing to a .dat file,
+ the output will look something like:
 \end_layout
 
 \begin_layout LyX-Code
-#Frame                                                                 
-                                            MyBox[avg]
+#Frame                                                                                                             MyBox[avg]
 \end_layout
 
 \begin_layout LyX-Code
-       1 42.433046075  0.000000000  0.000000000 -14.144347550 40.006259905  0.00000000
-0 -14.144347550 -20.003127532 34.646438786
+       1 42.433046075  0.000000000  0.000000000 -14.144347550 40.006259905  0.000000000 -14.144347550 -20.003127532 34.646438786
 \end_layout
 
 \begin_layout Standard
 Where the first 3 floating point numbers are the average X unit cell vector,
- the next 3 floating point numbers are the average Y unit cell vector, and
- the last 3 floating point numbers are the average Z unit cell vector.
+ the next 3 floating point numbers are the average Y unit cell vector,
+ and the last 3 floating point numbers are the average Z unit cell vector.
 \end_layout
 
 \begin_layout Subsection
@@ -24698,7 +25040,8 @@ bounds [<mask>] [out <filename>]
 \end_inset
 
 <dz>]] Triggers creation of a grid data set from bounds.
- Spacings of generated grid in the X, Y and Z directions.
+ Spacings of generated grid in the X,
+ Y and Z directions.
  If only dx is specified <dx> will be used for <dy> and <dz> as well.
 \end_layout
 
@@ -24772,8 +25115,8 @@ Calculate the boundaries (i.e.
 grid
 \series default
 \shape default
- command, and can be used to generate a grid data set that can be used by
- 
+ command,
+ and can be used to generate a grid data set that can be used by 
 \series bold
 \shape italic
 grid
@@ -24783,6 +25126,7 @@ grid
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_grid"
+nolink "false"
 
 \end_inset
 
@@ -24794,8 +25138,7 @@ box
 \end_layout
 
 \begin_layout LyX-Code
-box {[x <xval>] [y <yval>] [z <zval>] {[alpha <a>] [beta <b>] [gamma <g>]
- |
+box {[x <xval>] [y <yval>] [z <zval>] {[alpha <a>] [beta <b>] [gamma <g>] |
 \end_layout
 
 \begin_layout LyX-Code
@@ -24888,8 +25231,7 @@ Change box length(s) to specified value(s).
 \end_layout
 
 \begin_layout Description
-auto Set an orthogonal bounding box enclosing all atoms by the specified
- radii and an optional offset.
+auto Set an orthogonal bounding box enclosing all atoms by the specified radii and an optional offset.
 \end_layout
 
 \begin_deeper
@@ -24906,8 +25248,11 @@ radii
 \begin_inset space ~
 \end_inset
 
-{vdw|gb|parse|none} Radii to use for each atom: van der Waals, generalized
- Born, PARSE, or no radii.
+{vdw|gb|parse|none} Radii to use for each atom:
+ van der Waals,
+ generalized Born,
+ PARSE,
+ or no radii.
 \end_layout
 
 \end_deeper
@@ -24917,15 +25262,18 @@ getbox Save existing box information to a 3x3 matrix data set.
 
 \begin_deeper
 \begin_layout Description
-{ucell|frac|shape} Specify the kind of box information to save: 
+{ucell|frac|shape} Specify the kind of box information to save:
+ 
 \series bold
 ucell
 \series default
- saves the unit cell vectors, 
+ saves the unit cell vectors,
+ 
 \series bold
 frac
 \series default
- saves the fractional unit cell vectors, and 
+ saves the fractional unit cell vectors,
+ and 
 \series bold
 shape
 \series default
@@ -24952,19 +25300,17 @@ out
 \end_deeper
 \begin_layout Standard
 Modify box information during trajectory processing.
- Note that this will permanently modify the box information for topology
- files during trajectory processing as well.
+ Note that this will permanently modify the box information for topology files during trajectory processing as well.
  It is possible to modify any number of the box parameters (e.g.
- only the Z length can be modified if desired while leaving all other parameters
- intact).
- If no box is present, an orthogonal bounding box enclosing all atoms can
- be created with the 
+ only the Z length can be modified if desired while leaving all other parameters intact).
+ If no box is present,
+ an orthogonal bounding box enclosing all atoms can be created with the 
 \series bold
 auto
 \series default
  keyword.
- If 'getbox' is specified, the existing box information will be saved to
- a data set.
+ If 'getbox' is specified,
+ the existing box information will be saved to a data set.
 \end_layout
 
 \begin_layout Subsection
@@ -24974,6 +25320,8 @@ center
 \begin_layout LyX-Code
 center
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -24995,12 +25343,17 @@ center
 
 \begin_deeper
 \begin_layout Description
-[<mask>] Center based on atoms in mask; default is all atoms.
+[<mask>] Center based on atoms in mask;
+ default is all atoms.
 \end_layout
 
 \begin_layout Description
-[origin] Center to origin (0, 0, 0); default is center to box center (X/2,
- Y/2, Z/2).
+[origin] Center to origin (0,
+ 0,
+ 0);
+ default is center to box center (X/2,
+ Y/2,
+ Z/2).
 \end_layout
 
 \begin_layout Description
@@ -25036,8 +25389,7 @@ refindex
 \begin_inset space ~
 \end_inset
 
-[<refmask]] Center using coordinates in specified reference structure selected
- by <refmask> (<mask> if not specified.
+[<refmask]] Center using coordinates in specified reference structure selected by <refmask> (<mask> if not specified.
 \end_layout
 
 \end_deeper
@@ -25046,13 +25398,15 @@ Move all atoms so that the center of the atoms in
 \series bold
 <mask>
 \series default
- is centered at the specified location: box center (default), coordinate
- origin, or reference coordinates.
+ is centered at the specified location:
+ box center (default),
+ coordinate origin,
+ or reference coordinates.
 \end_layout
 
 \begin_layout Standard
-For example, to move all coordinates so that the center of mass of residue
- 1 is at the center of the box:
+For example,
+ to move all coordinates so that the center of mass of residue 1 is at the center of the box:
 \end_layout
 
 \begin_layout LyX-Code
@@ -25066,6 +25420,8 @@ check | checkoverlap | checkstructure
 \begin_layout LyX-Code
 check
 \begin_inset Index idx
+range none
+pageformat default
 status open
 
 \begin_layout Plain Layout
@@ -25107,8 +25463,8 @@ check
 \begin_inset space ~
 \end_inset
 
-<mask2>] If specified, only check for problems between atoms in <mask> and
- atoms in <mask2>.
+<mask2>] If specified,
+ only check for problems between atoms in <mask> and atoms in <mask2>.
 \end_layout
 
 \begin_layout Description
@@ -25124,8 +25480,8 @@ check
 \end_layout
 
 \begin_layout Description
-[skipbadframes] If errors are encountered for a frame, subsequent actions/trajec
-tory output will be skipped.
+[skipbadframes] If errors are encountered for a frame,
+ subsequent actions/trajectory output will be skipped.
 \end_layout
 
 \begin_layout Description
@@ -25133,8 +25489,7 @@ tory output will be skipped.
 \begin_inset space ~
 \end_inset
 
-<offset>] Report bond lengths greater than the equilibrium value plus <offset>
- (default 1.15 Å).
+<offset>] Report bond lengths greater than the equilibrium value plus <offset> (default 1.15 Å).
 \end_layout
 
 \begin_layout Description
@@ -25142,8 +25497,7 @@ tory output will be skipped.
 \begin_inset space ~
 \end_inset
 
-<minoffset>] Report bond lengths less than the equilibrium value minus <minoffse
-t> (default 0.5 Å).
+<minoffset>] Report bond lengths less than the equilibrium value minus <minoffset> (default 0.5 Å).
 \end_layout
 
 \begin_layout Description
@@ -25159,8 +25513,7 @@ t> (default 0.5 Å).
 \end_layout
 
 \begin_layout Description
-[silent] Do not print information for bad frames - useful in conjunction
- with the 
+[silent] Do not print information for bad frames - useful in conjunction with the 
 \series bold
 skipbadframes
 \series default
@@ -25172,7 +25525,8 @@ skipbadframes
 \begin_inset space ~
 \end_inset
 
-<cut>] Pair list cutoff (default 4.0 Å); only matters if box is present.
+<cut>] Pair list cutoff (default 4.0 Å);
+ only matters if box is present.
 \end_layout
 
 \begin_layout Description
@@ -25239,13 +25593,13 @@ Check the structure and report problems related to atomic overlap/unusual bond l
 \series bold
 <cut>
 \series default
-; atoms that are bonded to each other are ignored (except if using the 
+;
+ atoms that are bonded to each other are ignored (except if using the 
 \series bold
 'around'
 \series default
  mask).
- If bonds are being checked then bond lengths greater than their equilibrium
- value plus 
+ If bonds are being checked then bond lengths greater than their equilibrium value plus 
 \series bold
 <offset>
 \series default
@@ -25272,17 +25626,20 @@ Check the structure and report problems related to atomic overlap/unusual bond l
 \series bold
 'around'
 \series default
- mask, a pairlist will be used to speed up the calculation.
+ mask,
+ a pairlist will be used to speed up the calculation.
 \end_layout
 
 \begin_layout Standard
-This command can also be used to skip corrupted frames in a trajectory during
- processing.
- For example, if this message is encountered:
+This command can also be used to skip corrupted frames in a trajectory during processing.
+ For example,
+ if this message is encountered:
 \end_layout
 
 \begin_layout LyX-Code
-Warning: Frame 10 coords 1 & 2 overlap at origin; may be corrupt.
+Warning:
+ Frame 10 coords 1 & 2 overlap at origin;
+ may be corrupt.
 \end_layout
 
 \begin_layout Standard
@@ -25311,12 +25668,11 @@ distance d1 :1 :10
 \end_layout
 
 \begin_layout Standard
-Usually frame corruption can be detected using only a few atoms, but this
- may not catch all types of corruption.
+Usually frame corruption can be detected using only a few atoms,
+ but this may not catch all types of corruption.
  The more atoms that are used the better the corruption detection will be,
  but the slower it will be to process the command.
- Typically a good procedure to follow when corruption is suspected is to
- run 
+ Typically a good procedure to follow when corruption is suspected is to run 
 \series bold
 \shape italic
 check
@@ -25333,7 +25689,8 @@ skipbadframes
 trajout
 \series default
 \shape default
- command to write all non-corrupt frames, for example:
+ command to write all non-corrupt frames,
+ for example:
 \end_layout
 
 \begin_layout LyX-Code
@@ -25391,14 +25748,16 @@ DataSet Aspects:
 
 \end_deeper
 \begin_layout Standard
-Check the chirality around the alpha carbon in amino acid residues selected
- by <mask>.
+Check the chirality around the alpha carbon in amino acid residues selected by <mask>.
  Note that cpptraj expects atom names to correspond to the PDB V3 standard:
- N, CA, C, CB.
- For each residue, the number of frames in which the amino acid is 'L' or
- 'D' will be recorded.
- For example, to check the chirality of all amino acids in a system and
- write to a file named chiral.dat with data set name DPDP:
+ N,
+ CA,
+ C,
+ CB.
+ For each residue,
+ the number of frames in which the amino acid is 'L' or 'D' will be recorded.
+ For example,
+ to check the chirality of all amino acids in a system and write to a file named chiral.dat with data set name DPDP:
 \end_layout
 
 \begin_layout LyX-Code
@@ -25428,6 +25787,8 @@ closest | closestwaters
 \begin_layout LyX-Code
 closest
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -25478,7 +25839,8 @@ keep> Number of solvent molecules to keep around <mask>
 \end_inset
 
 mask>] Optional mask for selecting solvent atoms.
- If not specified, atoms in all molecules marked as 
+ If not specified,
+ atoms in all molecules marked as 
 \begin_inset Quotes eld
 \end_inset
 
@@ -25490,8 +25852,8 @@ solvent
 \end_layout
 
 \begin_layout Description
-[noimage] Do not perform imaging; only recommended if trajectory has previously
- been imaged.
+[noimage] Do not perform imaging;
+ only recommended if trajectory has previously been imaged.
 \end_layout
 
 \begin_layout Description
@@ -25507,8 +25869,7 @@ oxygen] Calculate distances between all atoms in
 \series bold
 <mask>
 \series default
- and the first atom of solvent only (recommended for standard water models
- as it will increase speed of calculation).
+ and the first atom of solvent only (recommended for standard water models as it will increase speed of calculation).
 \end_layout
 
 \begin_layout Description
@@ -25599,15 +25960,16 @@ Similar to the
 strip
 \series default
 \shape default
- command, but modify coordinate frame and topology by keeping only the specified
- number of closest solvent molecules to the region specified by the given
- mask.
+ command,
+ but modify coordinate frame and topology by keeping only the specified number of closest solvent molecules to the region specified by the given mask.
  Solvent molecules can be determined automatically by 
 \shape italic
 cpptraj
 \shape default
- (by default residues named WAT, HOH, or TIP3), can be specified prior via
- the 
+ (by default residues named WAT,
+ HOH,
+ or TIP3),
+ can be specified prior via the 
 \series bold
 \shape italic
 solvent
@@ -25617,10 +25979,12 @@ solvent
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_solvent"
+nolink "false"
 
 \end_inset
 
-), or can be selected by 
+),
+ or can be selected by 
 \series bold
 solventmask
 \series default
@@ -25640,9 +26004,9 @@ Frame    Molecule    Distance    FirstAtom#
 \end_layout
 
 \begin_layout Standard
-For example, to obtain the 10 closest waters to residues 1-268 by distance
- to the first atom of the waters, write out which waters were closest for
- each frame to a file called 
+For example,
+ to obtain the 10 closest waters to residues 1-268 by distance to the first atom of the waters,
+ write out which waters were closest for each frame to a file called 
 \begin_inset Quotes eld
 \end_inset
 
@@ -25650,7 +26014,8 @@ closestmols.dat
 \begin_inset Quotes erd
 \end_inset
 
-, and write out the stripped topology with prefix 
+,
+ and write out the stripped topology with prefix 
 \begin_inset Quotes eld
 \end_inset
 
@@ -25678,11 +26043,13 @@ Although the
 \series bold
 'cluster'
 \series default
- command can still be specified as an action, it is now considered an analysis.
+ command can still be specified as an action,
+ it is now considered an analysis.
  See 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-cluster-analysis"
+nolink "false"
 
 \end_inset
 
@@ -25696,6 +26063,8 @@ clusterdihedral
 \begin_layout LyX-Code
 clusterdihedral
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -25721,14 +26090,13 @@ clusterdihedral
 
 \begin_layout Standard
 Cluster frames in a trajectory using dihedral angles.
- To define which dihedral angles will be used for clustering either an atom
- mask or an input file specified by the 
+ To define which dihedral angles will be used for clustering either an atom mask or an input file specified by the 
 \series bold
 dihedralfile
 \series default
  keyword should be used.
- If dihedral file is used, each line in the file should contain a dihedral
- to be binned with format:
+ If dihedral file is used,
+ each line in the file should contain a dihedral to be binned with format:
 \end_layout
 
 \begin_layout LyX-Code
@@ -25736,13 +26104,10 @@ ATOM#1 ATOM#2 ATOM#3 ATOM#4 #BINS
 \end_layout
 
 \begin_layout Standard
-where the ATOM arguments are the atom numbers (starting from 1) defining
- the dihedral and #BINS is the number of bins to be used (so if #BINS=10
- the width of each bin will be 36º).
- If an atom mask is specified, only protein backbone dihedrals (Phi and
- Psi defined using atom names C-N-CA-C and N-CA-C-N) within the mask will
- be used, with the bin sizes specified by the phibins and psibins keywords
- (default for each is 10 bins).
+where the ATOM arguments are the atom numbers (starting from 1) defining the dihedral and #BINS is the number of bins to be used (so if #BINS=10 the width of each bin will be 36º).
+ If an atom mask is specified,
+ only protein backbone dihedrals (Phi and Psi defined using atom names C-N-CA-C and N-CA-C-N) within the mask will be used,
+ with the bin sizes specified by the phibins and psibins keywords (default for each is 10 bins).
 \end_layout
 
 \begin_layout Standard
@@ -25751,15 +26116,17 @@ Output will either be written to STDOUT or the file specified by the
 out
 \series default
  keyword.
- First, information about which dihedrals were clustered will be printed.
- Then the number of clusters will be printed, followed by detailed information
- of each cluster.
+ First,
+ information about which dihedrals were clustered will be printed.
+ Then the number of clusters will be printed,
+ followed by detailed information of each cluster.
  The clusters are sorted from most populated to least populated.
  Each cluster line has format
 \end_layout
 
 \begin_layout LyX-Code
-Cluster CLUSTERNUM CLUSTERPOP [ dihedral1bin, dihedral2bin ...
+Cluster CLUSTERNUM CLUSTERPOP [ dihedral1bin,
+ dihedral2bin ...
  dihedralNbin ]
 \end_layout
 
@@ -25769,7 +26136,8 @@ followed by a list of frame numbers that belong to that cluster.
 \series bold
 cut
 \series default
-, only clusters with population greater than CUT will be printed.
+,
+ only clusters with population greater than CUT will be printed.
 \end_layout
 
 \begin_layout Standard
@@ -25777,13 +26145,14 @@ If specified by the
 \series bold
 clustervtime
 \series default
- keyword, the number of clusters for each frame will be printed to <cvtfile>.
+ keyword,
+ the number of clusters for each frame will be printed to <cvtfile>.
  If specified by the 
 \series bold
 framefile
 \series default
- keyword, a file containing cluster information for each frame will be written
- with format
+ keyword,
+ a file containing cluster information for each frame will be written with format
 \end_layout
 
 \begin_layout LyX-Code
@@ -25791,9 +26160,7 @@ Frame CLUSTERNUM CLUSTERSIZE DIHEDRALBINID
 \end_layout
 
 \begin_layout Standard
-where DIHEDRALBINID is a number that identifies the unique combination of
- dihedral bins this cluster belongs to (specifically it is a 3*number-of-dihedra
-l-characters long number composed of the individual dihedral bins).
+where DIHEDRALBINID is a number that identifies the unique combination of dihedral bins this cluster belongs to (specifically it is a 3*number-of-dihedral-characters long number composed of the individual dihedral bins).
 \end_layout
 
 \begin_layout Standard
@@ -25801,12 +26168,12 @@ If specified by the
 \series bold
 clusterinfo
 \series default
- keyword, a file containing information on each dihedral and each cluster
- will be printed.
- This file can be read by SANDER for use with REMD with a structure reservoir
- (-rremd=3).
- The file, which is essentially a simplified version of the main output
- file, has the following format:
+ keyword,
+ a file containing information on each dihedral and each cluster will be printed.
+ This file can be read by SANDER for use with REMD with a structure reservoir (-rremd=3).
+ The file,
+ which is essentially a simplified version of the main output file,
+ has the following format:
 \end_layout
 
 \begin_layout LyX-Code
@@ -25846,7 +26213,8 @@ contacts [ first | reference | ref <ref> | refindex <#> ] [byresidue]
 \end_layout
 
 \begin_layout Standard
-NOTE: Users are encouraged to try the 
+NOTE:
+ Users are encouraged to try the 
 \series bold
 \emph on
 nativecontacts
@@ -25856,10 +26224,12 @@ nativecontacts
 \begin_inset CommandInset ref
 LatexCommand vpageref
 reference "subsec:cpptraj-nativecontacts"
+nolink "false"
 
 \end_inset
 
-), an update version of this command.
+),
+ an update version of this command.
 \end_layout
 
 \begin_layout Standard
@@ -25867,7 +26237,8 @@ For each atom given in
 \shape italic
 mask
 \shape default
-, calculate the number of other atoms (contacts) within the distance 
+,
+ calculate the number of other atoms (contacts) within the distance 
 \shape italic
 cutoff
 \shape default
@@ -25877,8 +26248,8 @@ cutoff
 \shape italic
 mask
 \shape default
- are potential interaction partners (e.g., a mask @CA will evaluate only contacts
- between CA atoms).
+ are potential interaction partners (e.g.,
+ a mask @CA will evaluate only contacts between CA atoms).
  The results are dumped to 
 \shape italic
 filename
@@ -25896,15 +26267,15 @@ out
 \end_inset
 
  is specified.
- Thereby, the time between snapshots is taken to be 
+ Thereby,
+ the time between snapshots is taken to be 
 \shape italic
 interval
 \shape default
 .
- In addition to the number of overall contacts, the number of native contacts
- is also determined.
- Native contacts are those that have been found either in the first snapshot
- of the trajectory (if the keyword 
+ In addition to the number of overall contacts,
+ the number of native contacts is also determined.
+ Native contacts are those that have been found either in the first snapshot of the trajectory (if the keyword 
 \begin_inset Quotes eld
 \end_inset
 
@@ -25929,7 +26300,8 @@ reference
 \end_inset
 
  is specified).
- Finally, if the keyword 
+ Finally,
+ if the keyword 
 \begin_inset Quotes eld
 \end_inset
 
@@ -25941,7 +26313,8 @@ byresidue
 \begin_inset Quotes erd
 \end_inset
 
- is provided, results are output on a per-residue basis for each snapshot,
+ is provided,
+ results are output on a per-residue basis for each snapshot,
  whereby the number of native contacts is written to 
 \shape italic
 filename
@@ -25965,13 +26338,12 @@ createcrd [<name>] [ parm <name> | parmindex <#> ]
 \end_layout
 
 \begin_layout Standard
-This command creates a COORDS data set named <name> using trajectory frames
- that are associated with the specified topology.
+This command creates a COORDS data set named <name> using trajectory frames that are associated with the specified topology.
 \end_layout
 
 \begin_layout Standard
-For example, to save frames that have been previously RMS-fit to a reference
- structure into a COORDS set named MyCrd you would use the input:
+For example,
+ to save frames that have been previously RMS-fit to a reference structure into a COORDS set named MyCrd you would use the input:
 \end_layout
 
 \begin_layout LyX-Code
@@ -25993,8 +26365,7 @@ Note that here the
 strip
 \series default
 \emph default
- command will have no effect on the coordinates saved in MyCrd since it
- occurs after the 
+ command will have no effect on the coordinates saved in MyCrd since it occurs after the 
 \series bold
 \emph on
 createcrd
@@ -26008,8 +26379,7 @@ createreservoir
 \end_layout
 
 \begin_layout LyX-Code
-createreservoir <filename> ene <energy data set> [bin <cluster bin data
- set>]
+createreservoir <filename> ene <energy data set> [bin <cluster bin data set>]
 \end_layout
 
 \begin_layout LyX-Code
@@ -26115,12 +26485,11 @@ parmindex
 
 \end_deeper
 \begin_layout Standard
-Create structure reservoir for use with reservoir REMD simulations using
- energies in <energy data set>, temperature <temp0> and random seed <iseed>
- Include velocities if [velocity] is specified.
+Create structure reservoir for use with reservoir REMD simulations using energies in <energy data set>,
+ temperature <temp0> and random seed <iseed> Include velocities if [velocity] is specified.
  If <cluster bin data set> is specified from e.g.
- a previous 'clusterdihedral' command, the reservoir can be used for non-Boltzma
-nn reservoir REMD (rremd==3).
+ a previous 'clusterdihedral' command,
+ the reservoir can be used for non-Boltzmann reservoir REMD (rremd==3).
 \end_layout
 
 \begin_layout Subsection
@@ -26179,8 +26548,8 @@ name>] Output data set name.
 \begin_inset space ~
 \end_inset
 
-<maskN> Arbitrary number of masks for atom selection; a dataset is created
- and the output will contain entries for each mask.
+<maskN> Arbitrary number of masks for atom selection;
+ a dataset is created and the output will contain entries for each mask.
 \end_layout
 
 \begin_deeper
@@ -26189,7 +26558,8 @@ name>] Output data set name.
 \begin_inset space ~
 \end_inset
 
-<resolution>] Resolution, i.e.
+<resolution>] Resolution,
+ i.e.
  determines number of slices (i.e.
  histogram bins).
  (default 0.25 Å)
@@ -26201,16 +26571,15 @@ name>] Output data set name.
 \end_layout
 
 \begin_layout Description
-[{number|mass|charge|electron}] Number, mass, partial charge (q) or electron
- (Ne - q) density.
- Electron density will be converted to e-/Å3 by dividing the average area
- spanned by the other two dimensions.
+[{number|mass|charge|electron}] Number,
+ mass,
+ partial charge (q) or electron (Ne - q) density.
+ Electron density will be converted to e-/Å3 by dividing the average area spanned by the other two dimensions.
  (default number)
 \end_layout
 
 \begin_layout Description
-[{bincenter|binedge}] Determine whether histogram bin coordinates will be
- based on bin center (default) or bin edges.
+[{bincenter|binedge}] Determine whether histogram bin coordinates will be based on bin center (default) or bin edges.
 \end_layout
 
 \begin_layout Description
@@ -26222,8 +26591,8 @@ name>] Output data set name.
 \series bold
 'restrict'
 \series default
- is specified, only calculate the density that is within a cylinder or square
- shape from the specified axis as defined by a distance cutoff.
+ is specified,
+ only calculate the density that is within a cylinder or square shape from the specified axis as defined by a distance cutoff.
 \end_layout
 
 \begin_deeper
@@ -26258,8 +26627,7 @@ name>[avg]:<idx> Average density over coordinate for mask number <idx>.
 \begin_inset space ~
 \end_inset
 
-name>[sd]:<idx> Standard deviation of density over coordinate for mask number
- <idx>.
+name>[sd]:<idx> Standard deviation of density over coordinate for mask number <idx>.
 \end_layout
 
 \begin_layout Standard
@@ -26276,14 +26644,14 @@ name> Total system density each frame.
 
 \end_deeper
 \begin_layout Standard
-If no atom masks are specified, calculate the total system density.
- Otherwise, calculate specified density along the given axis for atoms in
- specified mask(s).
+If no atom masks are specified,
+ calculate the total system density.
+ Otherwise,
+ calculate specified density along the given axis for atoms in specified mask(s).
  Defaults are shown in parentheses above.
  The format of the file is as follows.
  Comments are lines starting with '#' or empty lines.
- All other lines must contain the atom type followed by an integer number
- for the electron number.
+ All other lines must contain the atom type followed by an integer number for the electron number.
  Entries must be separated by spaces or '='.
  Example input:
 \end_layout
@@ -26343,8 +26711,8 @@ See also $AMBERHOME/AmberTools/test/cpptraj/Test_Density.
 \end_layout
 
 \begin_layout Standard
-It can be useful to write out the average and standard deviation as an XYDY
- set to a Grace data file, e.g.
+It can be useful to write out the average and standard deviation as an XYDY set to a Grace data file,
+ e.g.
 \end_layout
 
 \begin_layout LyX-Code
@@ -26369,12 +26737,12 @@ Note that although the syntax for
 \series bold
 diffusion
 \series default
- has changed as of version 16, the old syntax is still supported.
+ has changed as of version 16,
+ the old syntax is still supported.
 \end_layout
 
 \begin_layout LyX-Code
-diffusion [{out <filename>|separateout <suffix>}] [time <time per frame>]
- [noimage]
+diffusion [{out <filename>|separateout <suffix>}] [time <time per frame>] [noimage]
 \end_layout
 
 \begin_layout LyX-Code
@@ -26399,8 +26767,7 @@ diffusion [{out <filename>|separateout <suffix>}] [time <time per frame>]
 \begin_inset space ~
 \end_inset
 
-<filename>] Write mean-square displacement (MSD) data set output to file
- specified by <filename>.
+<filename>] Write mean-square displacement (MSD) data set output to file specified by <filename>.
 \end_layout
 
 \begin_layout Description
@@ -26408,8 +26775,8 @@ diffusion [{out <filename>|separateout <suffix>}] [time <time per frame>]
 \begin_inset space ~
 \end_inset
 
-<suffix>] Write each MSD data set type to files with suffix <suffix>; see
- description below.
+<suffix>] Write each MSD data set type to files with suffix <suffix>;
+ see description below.
 \end_layout
 
 \begin_layout Description
@@ -26417,8 +26784,8 @@ diffusion [{out <filename>|separateout <suffix>}] [time <time per frame>]
 \begin_inset space ~
 \end_inset
 
-<time_per_frame>] Time in-between each coordinate frame in ps; default is
- 1.0.
+<time_per_frame>] Time in-between each coordinate frame in ps;
+ default is 1.0.
 \end_layout
 
 \begin_layout Description
@@ -26427,7 +26794,8 @@ diffusion [{out <filename>|separateout <suffix>}] [time <time per frame>]
 \end_layout
 
 \begin_layout Description
-[<mask>] Mask of atoms to calculate diffusion for; default all atoms.
+[<mask>] Mask of atoms to calculate diffusion for;
+ default all atoms.
 \end_layout
 
 \begin_layout Description
@@ -26439,8 +26807,7 @@ name>] MSD data set name.
 \end_layout
 
 \begin_layout Description
-[individual] Write diffusion for each individual atom as well as average
- diffusion for atoms in mask.
+[individual] Write diffusion for each individual atom as well as average diffusion for atoms in mask.
 \end_layout
 
 \begin_layout Description
@@ -26448,8 +26815,7 @@ name>] MSD data set name.
 \begin_inset space ~
 \end_inset
 
-<filename>] Write diffusion contants calculated from fits of MSD data sets
- to <filename>.
+<filename>] Write diffusion contants calculated from fits of MSD data sets to <filename>.
 \end_layout
 
 \begin_layout Description
@@ -26457,14 +26823,13 @@ name>] MSD data set name.
 \end_layout
 
 \begin_layout Description
-[avgucell] Remove periodic box fluctuations from imaged NPT trajectories
- using average unit cell vectors.
+[avgucell] Remove periodic box fluctuations from imaged NPT trajectories using average unit cell vectors.
 \end_layout
 
 \begin_layout Description
 [allowmultipleorigins] (MPI only).
- For imaged trajectories in parallel, calculate diffusion by averaging over
- multiple time origins.
+ For imaged trajectories in parallel,
+ calculate diffusion by averaging over multiple time origins.
  Should be used with caution.
 \end_layout
 
@@ -26572,8 +26937,8 @@ individual
 
 \end_deeper
 \begin_layout Standard
-Compute mean-squared displacement (MSD, in Angstroms squared) plots (using
- distance traveled from initial position) for the atoms in 
+Compute mean-squared displacement (MSD,
+ in Angstroms squared) plots (using distance traveled from initial position) for the atoms in 
 \series bold
 <mask>
 \series default
@@ -26582,7 +26947,8 @@ Compute mean-squared displacement (MSD, in Angstroms squared) plots (using
 \series bold
 <mask>
 \series default
- is calculated; if 
+ is calculated;
+ if 
 \series bold
 individual
 \series default
@@ -26591,10 +26957,9 @@ individual
 \end_layout
 
 \begin_layout Standard
-In order to correctly calculate diffusion molecules should take continuous
- paths, so imaging of atoms is autoimatically performed.
- If the trajectory is already unwrapped (or the unwrap command is used prior
- to this command) the 
+In order to correctly calculate diffusion molecules should take continuous paths,
+ so imaging of atoms is autoimatically performed.
+ If the trajectory is already unwrapped (or the unwrap command is used prior to this command) the 
 \series bold
 noimage
 \series default
@@ -26607,12 +26972,13 @@ noise
 \begin_inset Quotes erd
 \end_inset
 
- caused by box fluctuations in NPT trajectories, the average unit cell vectors
- describing the average box can be provided with the 
+ caused by box fluctuations in NPT trajectories,
+ the average unit cell vectors describing the average box can be provided with the 
 \series bold
 avgucell
 \series default
- keyword; see the 
+ keyword;
+ see the 
 \series bold
 \emph on
 avgbox
@@ -26625,28 +26991,33 @@ reference "subsec:cpptraj_avgbox"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
 ).
- Alternatively, the trajectory can be unwrapped prior using the 
+ Alternatively,
+ the trajectory can be unwrapped prior using the 
 \series bold
 \emph on
 unwrap
 \series default
 \emph default
- command, 
+ command,
+ 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_unwrap"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
 .
- If the trajectory is unwrapped, the 
+ If the trajectory is unwrapped,
+ the 
 \series bold
 noimage
 \series default
@@ -26654,10 +27025,9 @@ noimage
 \end_layout
 
 \begin_layout Standard
-Note that in parallel, imaging becomes difficult because there is no way
- to correct for any wrapping that has been done on preceding MPI ranks.
- Therefore this command will not work on imaged trajectories in parallel
- by default.
+Note that in parallel,
+ imaging becomes difficult because there is no way to correct for any wrapping that has been done on preceding MPI ranks.
+ Therefore this command will not work on imaged trajectories in parallel by default.
  There are two workarounds.
  1) Unwrap the trajectory prior to 
 \series bold
@@ -26671,19 +27041,20 @@ diffusion
 unwrap
 \series default
 \emph default
- command, then run the diffusion calculation with the 
+ command,
+ then run the diffusion calculation with the 
 \series bold
 noimage
 \series default
- keyword (this is the recommended way), or 2) specify the 
+ keyword (this is the recommended way),
+ or 2) specify the 
 \series bold
 allowmultipleorigins
 \series default
- keyword to calculate MSD separately on each MPI rank, then averaging over
- all MSD plots.
- This means the maximum length of any given MSD plot will be <# frames>
- / <# MPI ranks>, and the calculated diffusion constants will not be as
- accurate.
+ keyword to calculate MSD separately on each MPI rank,
+ then averaging over all MSD plots.
+ This means the maximum length of any given MSD plot will be <# frames> / <# MPI ranks>,
+ and the calculated diffusion constants will not be as accurate.
 \end_layout
 
 \begin_layout Standard
@@ -26759,15 +27130,17 @@ Where
 n
 \series default
 \shape default
- is the number of dimensions; for overall MSD n = 3, for single dimension
- MSD (e.g.
- X) n = 1, etc.
+ is the number of dimensions;
+ for overall MSD n = 3,
+ for single dimension MSD (e.g.
+ X) n = 1,
+ etc.
  Unless 
 \series bold
 nocalc
 \series default
- is specified, the diffusion constant is calculated automatically from MSD
- data sets (and written to the file specified by 
+ is specified,
+ the diffusion constant is calculated automatically from MSD data sets (and written to the file specified by 
 \series bold
 diffout
 \series default
@@ -26795,18 +27168,19 @@ diffout
 
 \end_inset
 
-/s, the slope is multiplied by 10.0/(2n).
- Both the calculated diffusion constants as well as the results of the fit
- are reported.
+/s,
+ the slope is multiplied by 10.0/(2n).
+ Both the calculated diffusion constants as well as the results of the fit are reported.
 \end_layout
 
 \begin_layout Standard
-Due to the fact that diffusion is currently calculated from initial positions
- only, diffusion calculated for small numbers of atoms will be inherently
- stochastic, so the results are most sensible when averaged over many atoms;
- for example, the diffusion of water should be calculated using all waters
- in the system.
- If more averaging is needed, the 
+Due to the fact that diffusion is currently calculated from initial positions only,
+ diffusion calculated for small numbers of atoms will be inherently stochastic,
+ so the results are most sensible when averaged over many atoms;
+ for example,
+ the diffusion of water should be calculated using all waters in the system.
+ If more averaging is needed,
+ the 
 \series bold
 \emph on
 calcdiffusion
@@ -26819,6 +27193,7 @@ reference "subsec:cpptraj-calcdiffusion"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
@@ -26826,7 +27201,8 @@ noprefix "false"
 \end_layout
 
 \begin_layout Standard
-For example, to calculate the diffusion of water in a system:
+For example,
+ to calculate the diffusion of water in a system:
 \end_layout
 
 \begin_layout LyX-Code
@@ -26840,6 +27216,8 @@ dihedral
 \begin_layout LyX-Code
 dihedral
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -26852,8 +27230,7 @@ dihedral
 \end_layout
 
 \begin_layout LyX-Code
-         [type {alpha|beta|gamma|delta|epsilon|zeta|chi|c2p|h1p|phi|psi|omega|pc
-hi}]
+         [type {alpha|beta|gamma|delta|epsilon|zeta|chi|c2p|h1p|phi|psi|omega|pchi}]
 \end_layout
 
 \begin_layout LyX-Code
@@ -26882,12 +27259,12 @@ hi}]
 \end_layout
 
 \begin_layout Description
-[mass] Use center of mass of atoms in <maskX>; default is geometric center.
+[mass] Use center of mass of atoms in <maskX>;
+ default is geometric center.
 \end_layout
 
 \begin_layout Description
-[range360] Output dihedral angle values from 0 to 360 degrees instead of
- -180 to 180 degrees.
+[range360] Output dihedral angle values from 0 to 360 degrees instead of -180 to 180 degrees.
 \end_layout
 
 \begin_layout Description
@@ -26901,13 +27278,17 @@ hi}]
 statistics
 \series default
 \shape default
- analysis; note 'chi' is nucleic acid chi and 'pchi' is protein chi.
+ analysis;
+ note 'chi' is nucleic acid chi and 'pchi' is protein chi.
 \end_layout
 
 \end_deeper
 \begin_layout Standard
-Calculate dihedral angle (in degrees) between the planes defined by atoms
- in <mask1>, <mask2>, <mask3> and <mask2>, <mask3>, <mask4>.
+Calculate dihedral angle (in degrees) between the planes defined by atoms in <mask1>,
+ <mask2>,
+ <mask3> and <mask2>,
+ <mask3>,
+ <mask4>.
  To calculate multiple dihedral angles see the 
 \series bold
 \emph on
@@ -26921,6 +27302,7 @@ reference "subsec:cpptraj_multidihedral"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
@@ -26936,8 +27318,7 @@ dihedralrms | dihrms
 \end_layout
 
 \begin_layout LyX-Code
-            	[ first | reference | ref <name> | refindex <#> | previous
- |
+            	[ first | reference | ref <name> | refindex <#> | previous |
 \end_layout
 
 \begin_layout LyX-Code
@@ -26963,7 +27344,8 @@ dihedralrms | dihrms
 \end_inset
 
 types> Dihedral types to look for.
- Note that chip is 'protein chi', chin is 'nucleic chi'.
+ Note that chip is 'protein chi',
+ chin is 'nucleic chi'.
 \end_layout
 
 \begin_layout Description
@@ -26979,8 +27361,10 @@ types> Dihedral types to look for.
 \begin_inset space ~
 \end_inset
 
-<name>:<a0>:<a1>:<a2>:<a3>[:<offset>] Search for a custom dihedral type
- called <name> using atom names <a0>, <a1>, <a2>, and <a3>.
+<name>:<a0>:<a1>:<a2>:<a3>[:<offset>] Search for a custom dihedral type called <name> using atom names <a0>,
+ <a1>,
+ <a2>,
+ and <a3>.
 \begin_inset Separator latexpar
 \end_inset
 
@@ -26989,8 +27373,12 @@ types> Dihedral types to look for.
 
 \begin_deeper
 \begin_layout Standard
-Offset: -2=<a0><a1> in previous res, -1=<a0> in previous res, 0=All <aX>
- in single res, 1=<a3> in next res, 2=<a2><a3> in next res.
+Offset:
+ -2=<a0><a1> in previous res,
+ -1=<a0> in previous res,
+ 0=All <aX> in single res,
+ 1=<a3> in next res,
+ 2=<a2><a3> in next res.
 \end_layout
 
 \end_deeper
@@ -27009,7 +27397,8 @@ Offset: -2=<a0><a1> in previous res, -1=<a0> in previous res, 0=All <aX>
 \end_inset
 
 <range>] Residues range to look for reference dihedrals in.
- If not specified, use target range.
+ If not specified,
+ use target range.
 \end_layout
 
 \end_deeper
@@ -27028,6 +27417,7 @@ reference "subsec:cpptraj_multidihedral"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
@@ -27045,10 +27435,12 @@ This command has been replaced by
 permutedihedrals
 \series default
 \emph default
-; see 
+;
+ see 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_permutedihedrals"
+nolink "false"
 
 \end_inset
 
@@ -27118,7 +27510,8 @@ dipole [out <filename>]
 \begin_inset Quotes erd
 \end_inset
 
- extension for XPLOR format, 
+ extension for XPLOR format,
+ 
 \begin_inset Quotes eld
 \end_inset
 
@@ -27163,8 +27556,7 @@ name/tag>
 \begin_inset space ~
 \end_inset
 
-<nz> Set up grid using box information from a previously loaded reference
- structure.
+<nz> Set up grid using box information from a previously loaded reference structure.
  Currently the only way to set up non-orthogonal grids.
 \end_layout
 
@@ -27205,7 +27597,10 @@ name/tag>
 \begin_inset space ~
 \end_inset
 
-<cz>] Location of grid center, default is origin (0.0, 0.0, 0.0).
+<cz>] Location of grid center,
+ default is origin (0.0,
+ 0.0,
+ 0.0).
 \end_layout
 
 \begin_layout Description
@@ -27225,16 +27620,14 @@ name/tag>
 \begin_inset space ~
 \end_inset
 
-<mask>] Perform a best-fit rotation of the grid using the coordinates selected
- by <mask>.
+<mask>] Perform a best-fit rotation of the grid using the coordinates selected by <mask>.
 \end_layout
 
 \begin_deeper
 \begin_layout Description
-[noxalign] If specified, grid will not be re-oriented to align with Cartesian
- axes once binning is finished.
- Will affect file formats that do not store full unit cell vectors (like
- Xplor).
+[noxalign] If specified,
+ grid will not be re-oriented to align with Cartesian axes once binning is finished.
+ Will affect file formats that do not store full unit cell vectors (like Xplor).
 \end_layout
 
 \end_deeper
@@ -27294,7 +27687,8 @@ percent>] Only keep density >= to <max_percent> of the maximum density.
 
 \end_deeper
 \begin_layout Standard
-NOTE: This command is not well-tested and may be obsolete.
+NOTE:
+ This command is not well-tested and may be obsolete.
 \end_layout
 
 \begin_layout Standard
@@ -27308,12 +27702,12 @@ grid
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_grid"
+nolink "false"
 
 \end_inset
 
  below) except that dipoles of the solvent molecules are binned.
- The output file format is for Chris Bayly's discern delegate program that
- comes with Midas/Plus.
+ The output file format is for Chris Bayly's discern delegate program that comes with Midas/Plus.
  Consult the code in Action_Dipole.cpp for more information.
 
 \shape italic
@@ -27327,6 +27721,8 @@ distance
 \begin_layout LyX-Code
 distance
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -27351,8 +27747,7 @@ distance
 \end_layout
 
 \begin_layout LyX-Code
-	  [bound <lower> bound <upper>] [rexp <expected>] [noe_strong] [noe_medium]
- [noe_weak]
+	  [bound <lower> bound <upper>] [rexp <expected>] [noe_strong] [noe_medium] [noe_weak]
 \begin_inset Separator latexpar
 \end_inset
 
@@ -27369,8 +27764,8 @@ distance
 \end_layout
 
 \begin_layout Description
-<mask2> If specified, second atom mask selection atom(s) to calculate distance
- from <mask1>.
+<mask2> If specified,
+ second atom mask selection atom(s) to calculate distance from <mask1>.
 \end_layout
 
 \begin_layout Description
@@ -27386,8 +27781,8 @@ point
 \begin_inset space ~
 \end_inset
 
-<Z> If specified instead of second mask, calculate distance between <mask1>
- and specified XYZ coordinates.
+<Z> If specified instead of second mask,
+ calculate distance between <mask1> and specified XYZ coordinates.
 \end_layout
 
 \begin_layout Description
@@ -27415,8 +27810,8 @@ refindex
 \begin_inset space ~
 \end_inset
 
-<#> If specified, calculate distance between <mask1> in each input frame
- and <mask2> in the specified reference.
+<#> If specified,
+ calculate distance between <mask1> in each input frame and <mask2> in the specified reference.
 \end_layout
 
 \begin_layout Description
@@ -27428,8 +27823,8 @@ refindex
 \end_layout
 
 \begin_layout Description
-[geom] Use geometric center of atoms in <mask1>/<mask2>; default is to use
- center of mass.
+[geom] Use geometric center of atoms in <mask1>/<mask2>;
+ default is to use center of mass.
 \end_layout
 
 \begin_layout Description
@@ -27468,7 +27863,8 @@ bound
 \begin_inset space ~
 \end_inset
 
-<upper>] Lower and upper bounds for NOE (in Angstroms); must specify both.
+<upper>] Lower and upper bounds for NOE (in Angstroms);
+ must specify both.
 \end_layout
 
 \begin_layout Description
@@ -27476,8 +27872,8 @@ bound
 \begin_inset space ~
 \end_inset
 
-<expected>] Expected value for NOE (in Angstroms); if not given '(<lower>
- + <upper>)' / 2.0 is used.
+<expected>] Expected value for NOE (in Angstroms);
+ if not given '(<lower> + <upper>)' / 2.0 is used.
 \end_layout
 
 \begin_layout Description
@@ -27495,15 +27891,16 @@ bound
 \end_deeper
 \end_deeper
 \begin_layout Standard
-Calculate distance between the center of mass of atoms in <mask1> to atoms
- in <mask2>, between atoms in <mask1> from each input frame and atoms in
- <mask2> in specified reference, or atoms in <mask1> and the specified point.
+Calculate distance between the center of mass of atoms in <mask1> to atoms in <mask2>,
+ between atoms in <mask1> from each input frame and atoms in <mask2> in specified reference,
+ or atoms in <mask1> and the specified point.
  If 
 \series bold
 geom
 \series default
  is specified use the geometric center instead.
- For periodic systems imaging is turned on by default; the 
+ For periodic systems imaging is turned on by default;
+ the 
 \series bold
 noimage
 \series default
@@ -27525,6 +27922,7 @@ type noe
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_statistics"
+nolink "false"
 
 \end_inset
 
@@ -27538,6 +27936,8 @@ drms | drmsd (distance RMSD)
 \begin_layout LyX-Code
 drmsd
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -27575,7 +27975,8 @@ name>] Output data set name.
 \end_layout
 
 \begin_layout Description
-[<refmask>] Mask corresponding to atoms in reference; if not specified,
+[<refmask>] Mask corresponding to atoms in reference;
+ if not specified,
  <mask> is used.
 \end_layout
 
@@ -27620,8 +28021,7 @@ name>] Output data set name.
 \begin_inset space ~
 \end_inset
 
-<#>] Use previously read in reference structure specified by <#> (based
- on order read in).
+<#>] Use previously read in reference structure specified by <#> (based on order read in).
 \end_layout
 
 \begin_layout Description
@@ -27637,13 +28037,12 @@ reftraj
 \begin_inset space ~
 \end_inset
 
-<name> Use frames from COORDS set <name> or read in from trajectory file
- <name> as references.
- Each frame from <name> is used in turn, so that frame 1 is compared to
- frame 1 from <name>, frame 2 is compared to frame 2 from <name> and so
- on.
- If <trajname> runs out of frames before processing is complete, the last
- frame of <trajname> continues to be used as the reference.
+<name> Use frames from COORDS set <name> or read in from trajectory file <name> as references.
+ Each frame from <name> is used in turn,
+ so that frame 1 is compared to frame 1 from <name>,
+ frame 2 is compared to frame 2 from <name> and so on.
+ If <trajname> runs out of frames before processing is complete,
+ the last frame of <trajname> continues to be used as the reference.
 \begin_inset Separator latexpar
 \end_inset
 
@@ -27672,16 +28071,15 @@ parmindex
 \series bold
 reftraj
 \series default
- specifies a file associate trajectory <name> with specified topology; if
- not specified the first topology is used.
+ specifies a file associate trajectory <name> with specified topology;
+ if not specified the first topology is used.
 \end_layout
 
 \end_deeper
 \end_deeper
 \begin_layout Standard
 Calculate the distance RMSD (i.e.
- the RMSD of all pairs of internal distances) between atoms in the frame
- defined by 
+ the RMSD of all pairs of internal distances) between atoms in the frame defined by 
 \series bold
 <mask>
 \series default
@@ -27710,15 +28108,16 @@ Calculate the distance RMSD (i.e.
 \series bold
 <refmask>
 \series default
- must specify the same number of atoms, otherwise an error will occur.
+ must specify the same number of atoms,
+ otherwise an error will occur.
  
 \end_layout
 
 \begin_layout Standard
-Because this method compares pairs of internal distances and not absolute
- coordinates, it is not sensitive to translations and rotations the way
- that a no-fit RMSD calculation is.
- It can be more time consuming however, as (N
+Because this method compares pairs of internal distances and not absolute coordinates,
+ it is not sensitive to translations and rotations the way that a no-fit RMSD calculation is.
+ It can be more time consuming however,
+ as (N
 \begin_inset script superscript
 
 \begin_layout Plain Layout
@@ -27727,14 +28126,13 @@ Because this method compares pairs of internal distances and not absolute
 
 \end_inset
 
--N)/2 distances must be calculated and compared for both the target and
- reference structures.
+-N)/2 distances must be calculated and compared for both the target and reference structures.
  
 \end_layout
 
 \begin_layout Standard
-For example, to get the DRMSD of a residue named LIG to its structure in
- the first frame read in:
+For example,
+ to get the DRMSD of a residue named LIG to its structure in the first frame read in:
 \end_layout
 
 \begin_layout LyX-Code
@@ -27750,6 +28148,7 @@ See
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-secstruct"
+nolink "false"
 
 \end_inset
 
@@ -27794,13 +28193,16 @@ enedecomp [<name>] [<mask>] [out <filename>] [savecomponents]
 \end_layout
 
 \begin_layout Description
-[savecomponents] If specified, also save the individual components of the
- total energy (bond, angle, dihedral, etc.).
+[savecomponents] If specified,
+ also save the individual components of the total energy (bond,
+ angle,
+ dihedral,
+ etc.).
 \end_layout
 
 \begin_layout Description
-[pme] Use particle mesh Ewald for electrostatics; van der Waals energy will
- be calculated using a long-range correction for periodicity.
+[pme] Use particle mesh Ewald for electrostatics;
+ van der Waals energy will be calculated using a long-range correction for periodicity.
 \end_layout
 
 \begin_deeper
@@ -27838,8 +28240,8 @@ erfcdx
 \end_layout
 
 \begin_layout Description
-skinnb Used to determine pairlist atoms (added to cut, so pairlist cutoff
- is 
+skinnb Used to determine pairlist atoms (added to cut,
+ so pairlist cutoff is 
 \series bold
 cut
 \series default
@@ -27847,7 +28249,8 @@ cut
 \series bold
 skinnb
 \series default
-); included in order to maintain consistency with results from sander.
+);
+ included in order to maintain consistency with results from sander.
 \end_layout
 
 \begin_layout Description
@@ -27855,8 +28258,8 @@ ljswidth
 \begin_inset space ~
 \end_inset
 
-<width> If specified, use a force-switching form for the Lennard-Jones calculati
-on from <cutoff>-<width> to <cutoff>.
+<width> If specified,
+ use a force-switching form for the Lennard-Jones calculation from <cutoff>-<width> to <cutoff>.
 \end_layout
 
 \begin_layout Description
@@ -27872,8 +28275,7 @@ nfft
 \begin_inset space ~
 \end_inset
 
-<nfft1>,<nfft2>,<nfft3> Explicitly set the number of FFT grid points in
- each dimension.
+<nfft1>,<nfft2>,<nfft3> Explicitly set the number of FFT grid points in each dimension.
  Will be determined automatically from unit cell dimensions if not specified.
 \end_layout
 
@@ -27883,8 +28285,7 @@ DataSets created:
 \end_layout
 
 \begin_layout Description
-<name> Set containing atom index and the corresponding average total energy
- over frames.
+<name> Set containing atom index and the corresponding average total energy over frames.
 \end_layout
 
 \begin_layout Standard
@@ -27908,45 +28309,42 @@ If
 \end_layout
 
 \begin_layout Description
-<name>[vdw14] Set containing atom index and average 1-4 van der Waals energy
- over frames.
+<name>[vdw14] Set containing atom index and average 1-4 van der Waals energy over frames.
 \end_layout
 
 \begin_layout Description
-<name>[elec14] Set containing atom index and average 1-4 electrostatic energy
- over frames.
+<name>[elec14] Set containing atom index and average 1-4 electrostatic energy over frames.
 \end_layout
 
 \begin_layout Description
-<name>[elec] Set containing atom index and average electrostatic energy
- over frames.
+<name>[elec] Set containing atom index and average electrostatic energy over frames.
 \end_layout
 
 \begin_layout Description
-<name>[vdw] Set containing atom index and average van der Waals energy over
- frames.
+<name>[vdw] Set containing atom index and average van der Waals energy over frames.
 \end_layout
 
 \end_deeper
 \begin_layout Standard
 Perform per-atom energy decomposition for selected atoms.
- The energy is calculated for the entire system but only the energies for
- selected atoms will be reported.
- The energy is composed of the regular bond, angle, torsion, 1-4 nonbonded,
+ The energy is calculated for the entire system but only the energies for selected atoms will be reported.
+ The energy is composed of the regular bond,
+ angle,
+ torsion,
+ 1-4 nonbonded,
  and nonbonded terms.
  If 
 \series bold
 'savecomponents'
 \series default
- is specified, each of the energy components will be saved in addition to
- the total energy for each atom.
+ is specified,
+ each of the energy components will be saved in addition to the total energy for each atom.
  If 
 \series bold
 'pme'
 \series default
- is specified the non-bonded terms will us PME for electrostatics and a
- long-range periodic correction for van der Waals, otherwise a simple model
- with no cutoff will be used.
+ is specified the non-bonded terms will us PME for electrostatics and a long-range periodic correction for van der Waals,
+ otherwise a simple model with no cutoff will be used.
 \end_layout
 
 \begin_layout Subsection
@@ -27958,8 +28356,7 @@ energy [<name>] [<mask1>] [out <filename>] [nobondstoh] [openmm [<mdopts>]]
 \end_layout
 
 \begin_layout LyX-Code
-   	[bond] [angle] [dihedral] {[nb14]|[e14]|[v14]} {[nonbond]|[elec] [vdw]}
- 
+   	[bond] [angle] [dihedral] {[nb14]|[e14]|[v14]} {[nonbond]|[elec] [vdw]} 
 \end_layout
 
 \begin_layout LyX-Code
@@ -27983,8 +28380,7 @@ energy [<name>] [<mask1>] [out <filename>] [nobondstoh] [openmm [<mdopts>]]
 \end_layout
 
 \begin_layout LyX-Code
-   	                [rsumtol <rtol>] [maxexp <max>] [mlimits <X>,<Y>,<Z>]
- |
+   	                [rsumtol <rtol>] [maxexp <max>] [mlimits <X>,<Y>,<Z>] |
 \end_layout
 
 \begin_layout LyX-Code
@@ -28033,17 +28429,19 @@ energy [<name>] [<mask1>] [out <filename>] [nobondstoh] [openmm [<mdopts>]]
 \end_layout
 
 \begin_layout Description
-[openmm] If specified and CPPTRAJ is compiled with OpenMM support, use OpenMM
- to calculate energy.
- Note this will only calculate total energy; any keywords pertaining to
- individual energy components are not available.
- For a list of potential options that can be used with 'openmm', see 
+[openmm] If specified and CPPTRAJ is compiled with OpenMM support,
+ use OpenMM to calculate energy.
+ Note this will only calculate total energy;
+ any keywords pertaining to individual energy components are not available.
+ For a list of potential options that can be used with 'openmm',
+ see 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-emin"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
@@ -28087,8 +28485,7 @@ noprefix "false"
 \end_layout
 
 \begin_layout Description
-[nokinetic] Do not calculate kinetic energy even if velocity/force information
- present.
+[nokinetic] Do not calculate kinetic energy even if velocity/force information present.
 \end_layout
 
 \begin_layout Description
@@ -28103,15 +28500,16 @@ ketype
 \end_inset
 
 {vel|vv} Specify kinetic energy type.
- If not specified, if velocity and force information use a velocity verlet-type
- calculation (
+ If not specified,
+ if velocity and force information use a velocity verlet-type calculation (
 \series bold
 vv
 \series default
-), i.e.
+),
+ i.e.
  assume velocities are a half-step ahead of the forces.
- If only velocity information is present, calculate from on-step velocities
- (
+ If only velocity information is present,
+ calculate from on-step velocities (
 \series bold
 vel
 \series default
@@ -28140,7 +28538,8 @@ vv
 \end_layout
 
 \begin_layout Description
-[simple] Use simple Coulomb term for electrostatics, no cutoff.
+[simple] Use simple Coulomb term for electrostatics,
+ no cutoff.
 \end_layout
 
 \begin_layout Description
@@ -28159,8 +28558,7 @@ vv
 \end_deeper
 \begin_layout Description
 [ewald] Use Ewald summation for electrostatics.
- If van der Waals energy will be calculated a long-range correction for
- periodicity will be applied.
+ If van der Waals energy will be calculated a long-range correction for periodicity will be applied.
 \end_layout
 
 \begin_deeper
@@ -28198,8 +28596,8 @@ erfcdx
 \end_layout
 
 \begin_layout Description
-skinnb Used to determine pairlist atoms (added to cut, so pairlist cutoff
- is 
+skinnb Used to determine pairlist atoms (added to cut,
+ so pairlist cutoff is 
 \series bold
 cut
 \series default
@@ -28207,7 +28605,8 @@ cut
 \series bold
 skinnb
 \series default
-); included in order to maintain consistency with results from sander.
+);
+ included in order to maintain consistency with results from sander.
 \end_layout
 
 \begin_layout Description
@@ -28215,8 +28614,8 @@ ljswidth
 \begin_inset space ~
 \end_inset
 
-<width> If specified, use a force-switching form for the Lennard-Jones calculati
-on from <cutoff>-<width> to <cutoff>.
+<width> If specified,
+ use a force-switching form for the Lennard-Jones calculation from <cutoff>-<width> to <cutoff>.
 \end_layout
 
 \begin_layout Description
@@ -28233,16 +28632,14 @@ mlimits
 \begin_inset space ~
 \end_inset
 
-<X>,<Y>,<Z> Explicitly set the number of reciprocal space vectors in each
- dimension.
+<X>,<Y>,<Z> Explicitly set the number of reciprocal space vectors in each dimension.
  Will be determined automatically if not specified.
 \end_layout
 
 \end_deeper
 \begin_layout Description
 [pme] Use particle mesh Ewald for electrostatics.
- If van der Waals energy will be calculated a long-range correction for
- periodicity will be applied.
+ If van der Waals energy will be calculated a long-range correction for periodicity will be applied.
 \end_layout
 
 \begin_deeper
@@ -28280,8 +28677,8 @@ erfcdx
 \end_layout
 
 \begin_layout Description
-skinnb Used to determine pairlist atoms (added to cut, so pairlist cutoff
- is 
+skinnb Used to determine pairlist atoms (added to cut,
+ so pairlist cutoff is 
 \series bold
 cut
 \series default
@@ -28289,7 +28686,8 @@ cut
 \series bold
 skinnb
 \series default
-); included in order to maintain consistency with results from sander.
+);
+ included in order to maintain consistency with results from sander.
 \end_layout
 
 \begin_layout Description
@@ -28297,8 +28695,8 @@ ljswidth
 \begin_inset space ~
 \end_inset
 
-<width> If specified, use a force-switching form for the Lennard-Jones calculati
-on from <cutoff>-<width> to <cutoff>.
+<width> If specified,
+ use a force-switching form for the Lennard-Jones calculation from <cutoff>-<width> to <cutoff>.
 \end_layout
 
 \begin_layout Description
@@ -28314,14 +28712,12 @@ nfft
 \begin_inset space ~
 \end_inset
 
-<nfft1>,<nfft2>,<nfft3> Explicitly set the number of FFT grid points in
- each dimension.
+<nfft1>,<nfft2>,<nfft3> Explicitly set the number of FFT grid points in each dimension.
  Will be determined automatically from unit cell dimensions if not specified.
 \end_layout
 
 \begin_layout Description
-ljpme If specified use particle mesh Ewald for calculating Lennard-Jones
- interactions.
+ljpme If specified use particle mesh Ewald for calculating Lennard-Jones interactions.
 \end_layout
 
 \begin_layout Description
@@ -28376,22 +28772,23 @@ DataSet Aspects:
 \end_deeper
 \begin_layout Standard
 Calculate the energy for atoms in <mask>.
- If no terms are specified, all terms are calculated.
+ If no terms are specified,
+ all terms are calculated.
  Note that the non-bonded energy terms for 
 \series bold
 'simple'
 \series default
  do not take into account periodicity and there is no distance cut-off.
- Electrostatics can also be determined via the direct sum, Ewald, or particle-me
-sh Ewald summation procedures.
- The particle mesh Ewald functionality requires that CPPTRAJ be compiled
- with FFTW and a C++11 compliant compiler.
+ Electrostatics can also be determined via the direct sum,
+ Ewald,
+ or particle-mesh Ewald summation procedures.
+ The particle mesh Ewald functionality requires that CPPTRAJ be compiled with FFTW and a C++11 compliant compiler.
 \end_layout
 
 \begin_layout Standard
-Calculation of energy terms requires that the associated topology file have
- parameters for any of the calculated terms, so for example angle calculations
- are not possible when using a PDB file as a topology, etc.
+Calculation of energy terms requires that the associated topology file have parameters for any of the calculated terms,
+ so for example angle calculations are not possible when using a PDB file as a topology,
+ etc.
  All nonbonded calculations methods other than 
 \series bold
 simple
@@ -28400,7 +28797,8 @@ simple
 \end_layout
 
 \begin_layout Standard
-For example, to calculate all energy terms and write to a Grace-format file:
+For example,
+ to calculate all energy terms and write to a Grace-format file:
 \end_layout
 
 \begin_layout LyX-Code
@@ -28445,7 +28843,8 @@ esander [<name>] [out <filename>] [saveforces] [parmname <file>] [keepfiles]
 \end_layout
 
 \begin_layout Description
-[saveforces] If specified, save forces to frames.
+[saveforces] If specified,
+ save forces to frames.
  Requires writing frames in NetCDF format.
 \end_layout
 
@@ -28454,7 +28853,8 @@ esander [<name>] [out <filename>] [saveforces] [parmname <file>] [keepfiles]
 \begin_inset space ~
 \end_inset
 
-<file>] Name of temporary topology file (default: 'CpptrajEsander.parm7').
+<file>] Name of temporary topology file (default:
+ 'CpptrajEsander.parm7').
 \end_layout
 
 \begin_layout Description
@@ -28474,73 +28874,89 @@ vars>] Namelist variables supported by the sander API in format 'var <value>';
 \begin_layout Standard
 Calculate energies for input frames using the sander API.
  It requires compilation with the SANDER API (sanderlib).
- This can be considered as a faster alternative to energy post-processing
- with sander (imin = 5).
- Currently the following sander namelist variables are supported: 
+ This can be considered as a faster alternative to energy post-processing with sander (imin = 5).
+ Currently the following sander namelist variables are supported:
+ 
 \series bold
 extidel
 \series default
-, 
+,
+ 
 \series bold
 intdiel
 \series default
-, 
+,
+ 
 \series bold
 rgbmax
 \series default
-, 
+,
+ 
 \series bold
 saltcon
 \series default
-, 
+,
+ 
 \series bold
 cut
 \series default
-, 
+,
+ 
 \series bold
 dielc
 \series default
-, 
+,
+ 
 \series bold
 igb
 \series default
-, 
+,
+ 
 \series bold
 alpb
 \series default
-, 
+,
+ 
 \series bold
 gbsa
 \series default
-, 
+,
+ 
 \series bold
 lj1264
 \series default
-, 
+,
+ 
 \series bold
 ipb
 \series default
-, 
+,
+ 
 \series bold
 inp
 \series default
-, 
+,
+ 
 \series bold
 vdwmeth
 \series default
-, 
+,
+ 
 \series bold
 ew_type
 \series default
-, 
+,
+ 
 \series bold
 ntb
 \series default
-, 
+,
+ 
 \series bold
 ntf
 \series default
-, 
+,
+ 
 \series bold
 ntc
 \series default
@@ -28549,6 +28965,7 @@ ntc
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "chap:sander"
+nolink "false"
 
 \end_inset
 
@@ -28556,12 +28973,15 @@ reference "chap:sander"
 \end_layout
 
 \begin_layout Standard
-If ntb/cut/igb are not specified cpptraj will attempt to pick reasonable
- values based on the input system.
- The defaults for a non-periodic system are ntb=0, cut=9999.0, igb=1.
- The defaults for a periodic system are ntb=1, cut=8.0, igb=0.
- This currently requires writing a temporary Amber topology, the name of
- which can be set by 
+If ntb/cut/igb are not specified cpptraj will attempt to pick reasonable values based on the input system.
+ The defaults for a non-periodic system are ntb=0,
+ cut=9999.0,
+ igb=1.
+ The defaults for a periodic system are ntb=1,
+ cut=8.0,
+ igb=0.
+ This currently requires writing a temporary Amber topology,
+ the name of which can be set by 
 \series bold
 parmname
 \series default
@@ -28574,8 +28994,8 @@ keepfiles
 \end_layout
 
 \begin_layout Standard
-For example, to calculate energies for a non-periodic system using igb=1
- (the default) with GB surface area turned on (gbsa=1):
+For example,
+ to calculate energies for a non-periodic system using igb=1 (the default) with GB surface area turned on (gbsa=1):
 \end_layout
 
 \begin_layout LyX-Code
@@ -28643,8 +29063,8 @@ max
 \begin_inset space ~
 \end_inset
 
-<file>] File containing 1 for frames that were allowed, 0 for frames that
- were filtered.
+<file>] File containing 1 for frames that were allowed,
+ 0 for frames that were filtered.
 \end_layout
 
 \begin_layout Description
@@ -28652,13 +29072,12 @@ max
 \begin_inset space ~
 \end_inset
 
-<setname>] Filtered data set name containing 1 for allowed frames, 0 for
- filtered frames.
+<setname>] Filtered data set name containing 1 for allowed frames,
+ 0 for filtered frames.
 \end_layout
 
 \begin_layout Description
-[multi] Filter each set separately instead of all together (creates filter
- set for each input set).
+[multi] Filter each set separately instead of all together (creates filter set for each input set).
  Cannot be used with 'filterset'.
 \end_layout
 
@@ -28667,8 +29086,8 @@ max
 \begin_inset space ~
 \end_inset
 
-<set>] If specified, <set> will be filtered to only contain data that satisfies
- cutoffs.
+<set>] If specified,
+ <set> will be filtered to only contain data that satisfies cutoffs.
  Cannot be used with 'multi'.
 \end_layout
 
@@ -28678,8 +29097,7 @@ max
 \begin_inset space ~
 \end_inset
 
-<newname>] If specified a new set will be created from 'filterset' instead
- of replacing 'filterset'.
+<newname>] If specified a new set will be created from 'filterset' instead of replacing 'filterset'.
 \end_layout
 
 \end_deeper
@@ -28688,8 +29106,8 @@ max
 \begin_inset space ~
 \end_inset
 
-<count>] If specified, write number of elements passed and filtered to <countfil
-e>.
+<count>] If specified,
+ write number of elements passed and filtered to <countfile>.
  Cannot be used with 'multi'.
 \end_layout
 
@@ -28706,7 +29124,8 @@ passed
 \begin_inset Quotes erd
 \end_inset
 
-, 0 otherwise.
+,
+ 0 otherwise.
 \end_layout
 
 \begin_layout Description
@@ -28722,8 +29141,8 @@ Sets Created ('multi')
 \end_layout
 
 \begin_layout Description
-<setname>:<idx> For each input set (number with <idx>, starting from 0)
- contains 1 for elements that 
+<setname>:<idx> For each input set (number with <idx>,
+ starting from 0) contains 1 for elements that 
 \begin_inset Quotes eld
 \end_inset
 
@@ -28731,12 +29150,14 @@ passed
 \begin_inset Quotes erd
 \end_inset
 
-, 0 otherwise.
+,
+ 0 otherwise.
 \end_layout
 
 \end_deeper
 \begin_layout Standard
-For all following actions, only include frames that are between 
+For all following actions,
+ only include frames that are between 
 \series bold
 <min>
 \series default
@@ -28757,7 +29178,8 @@ For all following actions, only include frames that are between
 \series bold
 <max>
 \series default
- argument, and there must be as many 
+ argument,
+ and there must be as many 
 \series bold
 <min>
 \series default
@@ -28770,14 +29192,14 @@ For all following actions, only include frames that are between
 \series bold
 'multi'
 \series default
- is specified then only filter data sets will be created for each data set
- instead.
+ is specified then only filter data sets will be created for each data set instead.
  If 
 \series bold
 'filterset'
 \series default
- is specified, the specified <set> will be modified to only contain '1'
- frames; cannot be used with 
+ is specified,
+ the specified <set> will be modified to only contain '1' frames;
+ cannot be used with 
 \series bold
 'multi'
 \series default
@@ -28786,8 +29208,8 @@ For all following actions, only include frames that are between
 \series bold
 'newset'
 \series default
- is also specified, a new set will be created containing the '1' frames
- instead.
+ is also specified,
+ a new set will be created containing the '1' frames instead.
  The 
 \series bold
 'filterset'
@@ -28797,13 +29219,13 @@ For all following actions, only include frames that are between
 \series bold
 'countout'
 \series default
- is specified, the final number of elements passed and filtered out will
- be written to <countfile>.
+ is specified,
+ the final number of elements passed and filtered out will be written to <countfile>.
 \end_layout
 
 \begin_layout Standard
-For example, to write only frames in-between an RMSD of 0.7-0.8 Angstroms
- for a given input trajectory:
+For example,
+ to write only frames in-between an RMSD of 0.7-0.8 Angstroms for a given input trajectory:
 \end_layout
 
 \begin_layout LyX-Code
@@ -28849,6 +29271,7 @@ datafilter
 \begin_inset CommandInset ref
 LatexCommand pageref
 reference "subsec:cpptraj-datafilter"
+nolink "false"
 
 \end_inset
 
@@ -28910,21 +29333,22 @@ hetatm
 \begin_inset space ~
 \end_inset
 
-<mask> Mark atoms in mask as HETATM, order them after other atoms.
+<mask> Mark atoms in mask as HETATM,
+ order them after other atoms.
 \end_layout
 
 \end_deeper
 \end_deeper
 \begin_layout Standard
-Cpptraj (and most of Amber) expects that atom indices in molecules to increase
- monotonically.
- However, occasionally atom indices in molecules can become disordered or
- non-sequential, in which case cpptraj will print an error message such
- as the following:
+Cpptraj (and most of Amber) expects that atom indices in molecules to increase monotonically.
+ However,
+ occasionally atom indices in molecules can become disordered or non-sequential,
+ in which case cpptraj will print an error message such as the following:
 \end_layout
 
 \begin_layout LyX-Code
-Error: Atom 45 was assigned a lower molecule # (1) than previous atom (2).
+Error:
+ Atom 45 was assigned a lower molecule # (1) than previous atom (2).
 \end_layout
 
 \begin_layout Standard
@@ -28932,7 +29356,8 @@ and:
 \end_layout
 
 \begin_layout LyX-Code
-Error: Could not determine molecule information for <topology file>.
+Error:
+ Could not determine molecule information for <topology file>.
 \end_layout
 
 \begin_layout Standard
@@ -28950,10 +29375,9 @@ outprefix
 \end_layout
 
 \begin_layout Standard
-For example, given an out of order topology named 'outoforder.parm7' and
- a corresponding trajectory 'min1.crd', the following will produce a reordered
- topology named 'reorder.outoforder.parm7' and a reordered trajectory named
- 'reorder.mdcrd':
+For example,
+ given an out of order topology named 'outoforder.parm7' and a corresponding trajectory 'min1.crd',
+ the following will produce a reordered topology named 'reorder.outoforder.parm7' and a reordered trajectory named 'reorder.mdcrd':
 \end_layout
 
 \begin_layout LyX-Code
@@ -28977,8 +29401,11 @@ If
 \series bold
 'pdborder'
 \series default
- is specified, attempt to organize atoms by PDB information (i.e.
- Chain ID, original residue numbering, and insertion codes).
+ is specified,
+ attempt to organize atoms by PDB information (i.e.
+ Chain ID,
+ original residue numbering,
+ and insertion codes).
  Atoms optionally specified by 
 \series bold
 'hetatm
@@ -28990,8 +29417,8 @@ If
 ' will be placed after all other atoms.
  
 \emph on
-Note that the 'pdborder' keyword is still experimental, and requires that
- the Topology have PDB-type information present.
+Note that the 'pdborder' keyword is still experimental,
+ and requires that the Topology have PDB-type information present.
 \end_layout
 
 \begin_layout Subsection
@@ -29026,6 +29453,8 @@ gist (Grid Inhomogeneous Solvation Theory)
 \begin_layout LyX-Code
 gist
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -29058,8 +29487,7 @@ gist
 \end_layout
 
 \begin_layout LyX-Code
-     [floatfmt {double|scientific|general}] [floatwidth <fw>] [floatprec
- <fp>]
+     [floatfmt {double|scientific|general}] [floatwidth <fw>] [floatprec <fp>]
 \end_layout
 
 \begin_layout LyX-Code
@@ -29113,8 +29541,8 @@ literal "true"
 
 \begin_deeper
 \begin_layout Description
-[nopl] If specified, do not use the pair list for the order calculation
- (may be much slower).
+[nopl] If specified,
+ do not use the pair list for the order calculation (may be much slower).
 \end_layout
 
 \begin_layout Description
@@ -29131,8 +29559,7 @@ literal "true"
 \series bold
 [doeij]
 \series default
- Calculate the triangular matrix representing the water-water interactions
- between pairs of voxels (see below).
+ Calculate the triangular matrix representing the water-water interactions between pairs of voxels (see below).
 \end_layout
 
 \begin_layout Description
@@ -29156,15 +29583,18 @@ literal "true"
 
 rdval>]
 \series default
- Reference density of bulk water, used in computing
+ Reference density of bulk water,
+ used in computing
 \series bold
  g_O
 \series default
 ,
+
 \series bold
  g_H
 \series default
-, and the translational entropy.
+,
+ and the translational entropy.
  Default is 0.0334 molecules/Å
 \begin_inset Formula $^{3}$
 \end_inset
@@ -29201,7 +29631,9 @@ rdval>]
 
 <zval>]
 \series default
- Coordinates (Å) of the center of the grid (default 0.0, 0.0, 0.0).
+ Coordinates (Å) of the center of the grid (default 0.0,
+ 0.0,
+ 0.0).
 \end_layout
 
 \begin_layout Description
@@ -29209,8 +29641,8 @@ rdval>]
 \begin_inset space ~
 \end_inset
 
-<fitmask>] If specified, grid will be centered and rotated to follow atoms
- selected by <fitmask>.
+<fitmask>] If specified,
+ grid will be centered and rotated to follow atoms selected by <fitmask>.
 \end_layout
 
 \begin_layout Description
@@ -29230,8 +29662,9 @@ rdval>]
 
 <nz>]
 \series default
- Grid dimensions (number of bins/voxels) along each coordinate axis (default
- 40, 40, 40).
+ Grid dimensions (number of bins/voxels) along each coordinate axis (default 40,
+ 40,
+ 40).
 \end_layout
 
 \begin_layout Description
@@ -29305,7 +29738,8 @@ extension>] Output grid file name extension (default
 <output suffix>]
 \series default
  Suffix for main GIST output file name.
- If not specified, output file will be set to '<prefix>-output.dat'.
+ If not specified,
+ output file will be set to '<prefix>-output.dat'.
 \end_layout
 
 \begin_layout Description
@@ -29313,9 +29747,12 @@ extension>] Output grid file name extension (default
 \begin_inset space ~
 \end_inset
 
-{double|scientific|general}] Format for floating point values in GIST output
- file: double (regular fixed decimal point), scientific, or general (default,
- chooses fixed or scientific, whichever fits better).
+{double|scientific|general}] Format for floating point values in GIST output file:
+ double (regular fixed decimal point),
+ scientific,
+ or general (default,
+ chooses fixed or scientific,
+ whichever fits better).
 \end_layout
 
 \begin_layout Description
@@ -29355,7 +29792,8 @@ extension>] Output grid file name extension (default
 \end_inset
 
 suffix>] Suffix for main GIST info file name.
- If not specified, info will be written to standard output.
+ If not specified,
+ info will be written to standard output.
 \end_layout
 
 \begin_layout Description
@@ -29368,12 +29806,10 @@ suffix>] Suffix for main GIST info file name.
 \begin_inset space ~
 \end_inset
 
-<nlayers>] Number of layers of neighboring voxels that should be used when
- searching for nearest neighbors.
+<nlayers>] Number of layers of neighboring voxels that should be used when searching for nearest neighbors.
  This has to be at least 1 to obtain the correct entropy.
- Higher values can help to obtain better convergence of the translational
- and 6D entropy with little sampling or fine grid spacings, but increase
- the calculation time (default 1).
+ Higher values can help to obtain better convergence of the translational and 6D entropy with little sampling or fine grid spacings,
+ but increase the calculation time (default 1).
 \end_layout
 
 \begin_layout Description
@@ -29383,7 +29819,8 @@ suffix>] Suffix for main GIST info file name.
 
 <mask>] Selection mask for the solute.
  All other molecules will be solvent.
- If this is omitted, the standard solute/solvent assignment will be used.
+ If this is omitted,
+ the standard solute/solvent assignment will be used.
 \end_layout
 
 \begin_layout Description
@@ -29393,8 +29830,11 @@ suffix>] Suffix for main GIST info file name.
 
 <MOLS>] Comma-separated list of names of solvent molecules.
  Energies will be computed per solvent molecule.
- For the entropy, only the main solvent (the first one) will be used.
- Use, e.g., 
+ For the entropy,
+ only the main solvent (the first one) will be used.
+ Use,
+ e.g.,
+ 
 \series bold
 solventmols WAT,NA,CL
 \series default
@@ -29404,7 +29844,8 @@ solventmols WAT,NA,CL
 
 \begin_layout Description
 [nocom] Do not use the center of mass to define the molecular position.
- Instead, use the first atom in 
+ Instead,
+ use the first atom in 
 \series bold
 rigidatoms
 \series default
@@ -29426,16 +29867,19 @@ rigidatoms
 \end_inset
 
 <SUBST2>] Specifies how to define the molecular orientation for the entropy.
- By default, a simple heuristic will be used.
- This works for water, but not for all solvents.
- The atoms should be representative of the molecular orientation and should
- not be collinear.
+ By default,
+ a simple heuristic will be used.
+ This works for water,
+ but not for all solvents.
+ The atoms should be representative of the molecular orientation and should not be collinear.
  Note that the central atom goes first.
- For water, the default is equivalent to 
+ For water,
+ the default is equivalent to 
 \series bold
 rigidatoms O H1 H2
 \series default
-, corresponding to H1-O-H2 as the rigid substructure.
+,
+ corresponding to H1-O-H2 as the rigid substructure.
 \end_layout
 
 \begin_layout Description
@@ -29444,8 +29888,7 @@ rigidatoms O H1 H2
 
 \begin_layout Description
 [pme] Use particle mesh Ewald for the non-bonded electrostatics calculation.
- The van der Waals energy will be calculated using a long-range correction
- for periodicity.
+ The van der Waals energy will be calculated using a long-range correction for periodicity.
  Does not support 
 \series bold
 doeij
@@ -29488,8 +29931,8 @@ erfcdx
 \end_layout
 
 \begin_layout Description
-skinnb Used to determine pairlist atoms (added to cut, so pairlist cutoff
- is 
+skinnb Used to determine pairlist atoms (added to cut,
+ so pairlist cutoff is 
 \series bold
 cut
 \series default
@@ -29497,7 +29940,8 @@ cut
 \series bold
 skinnb
 \series default
-); included in order to maintain consistency with results from sander.
+);
+ included in order to maintain consistency with results from sander.
 \end_layout
 
 \begin_layout Description
@@ -29505,8 +29949,8 @@ ljswidth
 \begin_inset space ~
 \end_inset
 
-<width> If specified, use a force-switching form for the Lennard-Jones calculati
-on from <cutoff>-<width> to <cutoff>.
+<width> If specified,
+ use a force-switching form for the Lennard-Jones calculation from <cutoff>-<width> to <cutoff>.
 \end_layout
 
 \begin_layout Description
@@ -29522,8 +29966,7 @@ nfft
 \begin_inset space ~
 \end_inset
 
-<nfft1>,<nfft2>,<nfft3> Explicitly set the number of FFT grid points in
- each dimension.
+<nfft1>,<nfft2>,<nfft3> Explicitly set the number of FFT grid points in each dimension.
  Will be determined automatically if not specified.
 \end_layout
 
@@ -29533,13 +29976,12 @@ DataSet Aspects:
 \end_layout
 
 \begin_layout Description
-[gO] Number density of oxygen centers found in the voxel, in units of the
- bulk density.
+[gO] Number density of oxygen centers found in the voxel,
+ in units of the bulk density.
 \end_layout
 
 \begin_layout Description
-[gH] Number density of hydrogen centers found in the voxel in units of the
- reference bulk density.
+[gH] Number density of hydrogen centers found in the voxel in units of the reference bulk density.
 \end_layout
 
 \begin_layout Description
@@ -29563,8 +30005,7 @@ DataSet Aspects:
 \end_layout
 
 \begin_layout Description
-[neighbor] Mean number of waters neighboring the water molecules found in
- this voxel multiplied by the voxel number density.
+[neighbor] Mean number of waters neighboring the water molecules found in this voxel multiplied by the voxel number density.
 \end_layout
 
 \begin_layout Description
@@ -29608,7 +30049,9 @@ DataSets if the main solvent is not water:
 \series bold
 ELEM
 \series default
- in the main solvent, the atomic density relative to rho0 (e.g., 
+ in the main solvent,
+ the atomic density relative to rho0 (e.g.,
+ 
 \series bold
 gC
 \series default
@@ -29628,7 +30071,8 @@ DataSets if there are multiple solvents:
 \series bold
 NAME
 \series default
- (e.g., 
+ (e.g.,
+ 
 \series bold
 g_mol_WAT
 \series default
@@ -29648,7 +30092,8 @@ solventmols WAT,NA
 \series bold
 NAME
 \series default
- (e.g., 
+ (e.g.,
+ 
 \series bold
 Esw_mol_WAT
 \series default
@@ -29668,7 +30113,8 @@ solventmols WAT,NA
 \series bold
 NAME
 \series default
- (e.g., 
+ (e.g.,
+ 
 \series bold
 Eww_mol_WAT
 \series default
@@ -29693,21 +30139,20 @@ literal "true"
 
 \end_inset
 
- (GIST) is a method for analyzing the structure and thermodynamics of solvent
- in the vicinity of a solute molecule.
- The current implementation works for only water, but the method can be
- generalized to other solvents whose molecules are rigid like water, such
- as chloroform or dimethylsulfoxide (DMSO).
- GIST post-processes explicit solvent simulation data to create a three-dimensio
-nal mapping of water density and thermodynamic properties within a region
- of interest, which is defined by a user-specified 3D rectangular grid.
- The small grid boxes are referred to as voxels, and each voxel is associated
- with solvent properties.
+ (GIST) is a method for analyzing the structure and thermodynamics of solvent in the vicinity of a solute molecule.
+ The current implementation works for only water,
+ but the method can be generalized to other solvents whose molecules are rigid like water,
+ such as chloroform or dimethylsulfoxide (DMSO).
+ GIST post-processes explicit solvent simulation data to create a three-dimensional mapping of water density and thermodynamic properties within a region of interest,
+ which is defined by a user-specified 3D rectangular grid.
+ The small grid boxes are referred to as voxels,
+ and each voxel is associated with solvent properties.
  (See Fig.
  
 \begin_inset CommandInset ref
 LatexCommand ref
 reference "gist-1-1"
+nolink "false"
 
 \end_inset
 
@@ -29715,30 +30160,32 @@ reference "gist-1-1"
 \emph on
 cpptraj
 \emph default
- also calculates a number of other local water properties, as listed below.
+ also calculates a number of other local water properties,
+ as listed below.
  GIST works for the nonpolarizable water models currently supported by AMBER.
 \end_layout
 
 \begin_layout Standard
-In order to carry out a GIST calculation, you must have a trajectory file
- generated with explicit water, as well as the corresponding topology file.
- To generate the most readily interpretable results, it is recommended that
- the solute (e.g., a protein) be restrained into essentially one conformation.
- GIST will then provide information about the structure and thermodynamics
- of the solvent for that conformation.
- For a room-temperature simulation of a solvent-exposed binding site, and
- a grid-spacing of 0.5 Å, it is recommended that the simulation be at least
- 10-20 ns in duration, and it is also a good idea to check for convergence
- of the GIST properties you are interested in by loading and then processing
- successively more frames of your trajectory file.
- Because GIST assumes that the solute of interest comprises all molecules
- in the simulation that are not waters, it is a good idea to remove all
- counterions and cosolutes with cpptraj's strip command before running GIST.
+In order to carry out a GIST calculation,
+ you must have a trajectory file generated with explicit water,
+ as well as the corresponding topology file.
+ To generate the most readily interpretable results,
+ it is recommended that the solute (e.g.,
+ a protein) be restrained into essentially one conformation.
+ GIST will then provide information about the structure and thermodynamics of the solvent for that conformation.
+ For a room-temperature simulation of a solvent-exposed binding site,
+ and a grid-spacing of 0.5 Å,
+ it is recommended that the simulation be at least 10-20 ns in duration,
+ and it is also a good idea to check for convergence of the GIST properties you are interested in by loading and then processing successively more frames of your trajectory file.
+ Because GIST assumes that the solute of interest comprises all molecules in the simulation that are not waters,
+ it is a good idea to remove all counterions and cosolutes with cpptraj's strip command before running GIST.
  A sample series of cpptraj commands for running GIST is provided below.
 \end_layout
 
 \begin_layout Standard
 \begin_inset Float figure
+placement document
+alignment document
 wide false
 sideways false
 status open
@@ -29767,7 +30214,9 @@ centering
 \begin_inset Caption Standard
 
 \begin_layout Plain Layout
-Diagram, in 2D, of GIST's gridded water properties in a binding site.
+Diagram,
+ in 2D,
+ of GIST's gridded water properties in a binding site.
 \end_layout
 
 \end_inset
@@ -29795,7 +30244,8 @@ Although it is not mandatory to supply values of
 \series bold
 gridcntr
 \series default
-, 
+,
+ 
 \series bold
 griddim
 \series default
@@ -29803,8 +30253,9 @@ griddim
 \series bold
 gridspcn
 \series default
-, these parameters should be carefully chosen, because they determine the
- region to be analyzed (
+,
+ these parameters should be carefully chosen,
+ because they determine the region to be analyzed (
 \series bold
 gridcntr
 \series default
@@ -29817,13 +30268,13 @@ griddim
 gridspcn
 \series default
 ).
- In particular, although smaller grid spacings will give finer spatial resolutio
-n, longer simulation times will be needed to converge the properties in
- the smaller voxels that result.
- A larger grid spacing will allow earlier convergence, but will smooth the
- spatial distributions.
- When computing the sum over voxel values in a larger region, the result
- is independent of the grid spacing as long as 
+ In particular,
+ although smaller grid spacings will give finer spatial resolution,
+ longer simulation times will be needed to converge the properties in the smaller voxels that result.
+ A larger grid spacing will allow earlier convergence,
+ but will smooth the spatial distributions.
+ When computing the sum over voxel values in a larger region,
+ the result is independent of the grid spacing as long as 
 \series bold
 nlayers
 \series default
@@ -29835,38 +30286,45 @@ The reference density of water (
 \series bold
 rdval
 \series default
-) is taken by default to be the experimental number density of pure water
- at 300 K and 1 atm.
- However, different water models may yield slightly different bulk densities
- under these conditions, and the density also depends on T and P.
- If you know that the bulk density of the water model you are using, at
- the T and P of your simulation, deviates significantly from 0.0334 water
- molecules/Å
+) is taken by default to be the experimental number density of pure water at 300 K and 1 atm.
+ However,
+ different water models may yield slightly different bulk densities under these conditions,
+ and the density also depends on T and P.
+ If you know that the bulk density of the water model you are using,
+ at the T and P of your simulation,
+ deviates significantly from 0.0334 water molecules/Å
 \begin_inset Formula $^{3}$
 \end_inset
 
-, it would be advisable to supply the actual value with the 
+,
+ it would be advisable to supply the actual value with the 
 \series bold
 refdens
 \series default
- keyword, instead of allowing GIST to supply the default value.
+ keyword,
+ instead of allowing GIST to supply the default value.
 \end_layout
 
 \begin_layout Standard
-For GIST, a GPU accelerated version is available, in which the interaction
- energy is calculated using CUDA.
- When using the GPU accelerated version of GIST, the 
+For GIST,
+ a GPU accelerated version is available,
+ in which the interaction energy is calculated using CUDA.
+ When using the GPU accelerated version of GIST,
+ the 
 \series bold
 doeij 
 \series default
 keyword is not available.
- It is recommended to use a grid covering the entire box, when using the
- GPU implementation.
- You may also choose a smaller grid, but all interaction energies, i.e., each
- atom with each atom, will always be calculated independent of the chosen
- grid.
+ It is recommended to use a grid covering the entire box,
+ when using the GPU implementation.
+ You may also choose a smaller grid,
+ but all interaction energies,
+ i.e.,
+ each atom with each atom,
+ will always be calculated independent of the chosen grid.
  This ensures optimum performance when calculating the interaction energies.
- Thus, the additional time required to calculate the order parameters (
+ Thus,
+ the additional time required to calculate the order parameters (
 \series bold
 doorder
 \series default
@@ -29874,8 +30332,7 @@ doorder
 \end_layout
 
 \begin_layout Standard
-The nonbonded energy calculation can also be accelerated using particle
- mesh Ewald via the pme keyword (CPU only).
+The nonbonded energy calculation can also be accelerated using particle mesh Ewald via the pme keyword (CPU only).
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Chen2021"
@@ -29897,9 +30354,8 @@ GIST Output
 \end_layout
 
 \begin_layout Standard
-GIST generates a main output file and a collection of grid data files that
- by default are in Data Explorer format (.dx); this can be changed via the
- 
+GIST generates a main output file and a collection of grid data files that by default are in Data Explorer format (.dx);
+ this can be changed via the 
 \series bold
 ext
 \series default
@@ -29918,47 +30374,53 @@ literal "true"
 \series bold
 doeij
 \series default
- keyword is provided, GIST also writes out a matrix of water-water interactions
- between pairs of voxels.
- In addition, run details are written to stdout, which can be redirected
- into a log file.
+ keyword is provided,
+ GIST also writes out a matrix of water-water interactions between pairs of voxels.
+ In addition,
+ run details are written to stdout,
+ which can be redirected into a log file.
  
 \end_layout
 
 \begin_layout Standard
-Note that a number of quantities are written out as both densities and normalize
-d quantities.
- For example, the output file includes both the solute-water energy density
- and the normalized (per water) solute-water energy.
- In all cases, the normalized quantity at voxel 
+Note that a number of quantities are written out as both densities and normalized quantities.
+ For example,
+ the output file includes both the solute-water energy density and the normalized (per water) solute-water energy.
+ In all cases,
+ the normalized quantity at voxel 
 \begin_inset Formula $i$
 \end_inset
 
-, 
+,
+ 
 \begin_inset Formula $X_{i,norm}$
 \end_inset
 
- is related to the corresponding density, 
+ is related to the corresponding density,
+ 
 \begin_inset Formula $X_{i,dens}$
 \end_inset
 
-, by the relationship 
+,
+ by the relationship 
 \begin_inset Formula $X_{i,norm}=\rho_{i}X_{i,dens}$
 \end_inset
 
-, where 
+,
+ where 
 \begin_inset Formula $\rho_{i}$
 \end_inset
 
  is the number density of water in the voxel.
- The normalized quantity provides information regarding the nature of the
- water found in the voxel.
- The density has the property that, if the grid extended over the entire
- simulation volume, the total system quantity would be given by 
+ The normalized quantity provides information regarding the nature of the water found in the voxel.
+ The density has the property that,
+ if the grid extended over the entire simulation volume,
+ the total system quantity would be given by 
 \begin_inset Formula $X_{tot}=V_{voxel}\sum_{i}X_{i,dens}$
 \end_inset
 
-, where 
+,
+ where 
 \begin_inset Formula $V_{voxel}$
 \end_inset
 
@@ -29969,8 +30431,7 @@ d quantities.
 \begin_layout Standard
 The main output file takes the form of a space-delimited-variable file,
  where each row corresponds to one voxel of the grid.
- This file can easily be opened with and manipulated with spreadsheet programs
- like Excel and LibreOffice Calc.
+ This file can easily be opened with and manipulated with spreadsheet programs like Excel and LibreOffice Calc.
  The columns are as follows.
  
 \end_layout
@@ -29980,7 +30441,8 @@ The main output file takes the form of a space-delimited-variable file,
 \series bold
 index
 \series default
- - A unique, sequential integer assigned to each voxel
+ - A unique,
+ sequential integer assigned to each voxel
 \end_layout
 
 \begin_layout Itemize
@@ -30012,15 +30474,15 @@ zcoord
 \series bold
 population 
 \series default
-- Number of water molecule, 
+- Number of water molecule,
+ 
 \begin_inset Formula $n_{i}$
 \end_inset
 
-, found in the voxel over the entire simulation.
- A water molecule is deemed to populate a voxel if its oxygen coordinates
- are inside the voxel.
- The expectation value of this quantity increases in proportion to the length
- of the simulation.
+,
+ found in the voxel over the entire simulation.
+ A water molecule is deemed to populate a voxel if its oxygen coordinates are inside the voxel.
+ The expectation value of this quantity increases in proportion to the length of the simulation.
 \end_layout
 
 \begin_layout Itemize
@@ -30028,9 +30490,10 @@ population
 \series bold
 g_O
 \series default
- - Number density of oxygen centers found in the voxel, in units of the
- bulk density (rdval).
- Thus, the expectation value of 
+ - Number density of oxygen centers found in the voxel,
+ in units of the bulk density (rdval).
+ Thus,
+ the expectation value of 
 \series bold
 g_O
 \series default
@@ -30042,13 +30505,13 @@ g_O
 \series bold
 g_H
 \series default
- - Number density of hydrogen centers found in the voxel in units of the
- reference bulk density (2
+ - Number density of hydrogen centers found in the voxel in units of the reference bulk density (2
 \begin_inset Formula $\times$
 \end_inset
 
 rdval).
- Thus, the expectation value of 
+ Thus,
+ the expectation value of 
 \series bold
 g_H
 \series default
@@ -30073,8 +30536,7 @@ ELEM
 \series bold
 g_mol_NAME
 \series default
- - (if there is more than one solvent) Density of every solvent species
- 
+ - (if there is more than one solvent) Density of every solvent species 
 \series bold
 NAME
 \series default
@@ -30095,8 +30557,9 @@ dTStrans-dens
 \begin_inset Formula $^{3}$
 \end_inset
 
-), referenced to the translational entropy of bulk water, based on the value
- rdval.
+),
+ referenced to the translational entropy of bulk water,
+ based on the value rdval.
 \end_layout
 
 \begin_layout Itemize
@@ -30105,8 +30568,8 @@ dTStrans-dens
 dTStrans-norm
 \series default
  - First order translational entropy per water molecule (kcal/mole/molecule),
- referenced to the translational entropy of bulk water, based on the value
- rdval.
+ referenced to the translational entropy of bulk water,
+ based on the value rdval.
  The quantity
 \series bold
  dTStrans-norm
@@ -30131,7 +30594,8 @@ dTSorient-dens
 \begin_inset Formula $^{3}$
 \end_inset
 
-), referenced to bulk solvent (see below).
+),
+ referenced to bulk solvent (see below).
 \end_layout
 
 \begin_layout Itemize
@@ -30158,12 +30622,11 @@ Esw-dens
 \end_inset
 
 ).
- This is the interaction of the solvent in a given voxel with the entire
- solute.
- Both Lennard-Jones and electrostatic interactions are computed without
- any cutoff, within the minimum image convention but without Ewald summation.
- This quantity is referenced to bulk, in the trivial sense that the solute-solve
-nt interaction energy is zero in bulk.
+ This is the interaction of the solvent in a given voxel with the entire solute.
+ Both Lennard-Jones and electrostatic interactions are computed without any cutoff,
+ within the minimum image convention but without Ewald summation.
+ This quantity is referenced to bulk,
+ in the trivial sense that the solute-solvent interaction energy is zero in bulk.
 \end_layout
 
 \begin_layout Itemize
@@ -30184,18 +30647,19 @@ Esw-norm
 \series bold
 Eww-dens
 \series default
- - Mean water-water interaction energy density, scaled by ½ to prevent double-co
-unting, and not referenced to the corresponding bulk value of this quantity
- (see below).
- This quantity is one half of the mean interaction energy of the water in
- a given voxel with all other waters in the system, both on and off the
- GIST grid, divided by the volume of the voxel (kcal/mole/Å
+ - Mean water-water interaction energy density,
+ scaled by ½ to prevent double-counting,
+ and not referenced to the corresponding bulk value of this quantity (see below).
+ This quantity is one half of the mean interaction energy of the water in a given voxel with all other waters in the system,
+ both on and off the GIST grid,
+ divided by the volume of the voxel (kcal/mole/Å
 \begin_inset Formula $^{3}$
 \end_inset
 
 ).
- Unless PME is used, both Lennard-Jones and electrostatic interactions are
- computed without any cutoff, within the minimum image convention.
+ Unless PME is used,
+ both Lennard-Jones and electrostatic interactions are computed without any cutoff,
+ within the minimum image convention.
 \end_layout
 
 \begin_layout Itemize
@@ -30207,12 +30671,12 @@ Esw_mol_NAME-dens
 \series bold
 Esw_mol_NAME-norm
 \series default
- - (if there are multiple solvent species) Mean solute-solvent energy per
- molecule of species 
+ - (if there are multiple solvent species) Mean solute-solvent energy per molecule of species 
 \series bold
 NAME
 \series default
-, for each solvent specified in 
+,
+ for each solvent specified in 
 \series bold
 solventmols
 \series default
@@ -30233,12 +30697,12 @@ Eww_mol_NAME-dens
 \series bold
 Eww_mol_NAME-norm
 \series default
- - (if there are multiple solvent species) Mean solvent-solvent energy per
- molecule of species 
+ - (if there are multiple solvent species) Mean solvent-solvent energy per molecule of species 
 \series bold
 NAME
 \series default
-, for each solvent specified in 
+,
+ for each solvent specified in 
 \series bold
 solventmols
 \series default
@@ -30255,8 +30719,7 @@ Eww
 \series bold
 PME-norm
 \series default
- - (Only if PME was used) Mean PME solvent energy per water molecule (kcal/mole/
-molecule).
+ - (Only if PME was used) Mean PME solvent energy per water molecule (kcal/mole/molecule).
  This equals 
 \series bold
 PME-dens
@@ -30291,8 +30754,8 @@ Esw-norm
 \series bold
 Eww-norm
 \series default
- - Mean water-water interaction energy, normalized to the mean number of
- water molecules in the voxel (kcal/mole/water).
+ - Mean water-water interaction energy,
+ normalized to the mean number of water molecules in the voxel (kcal/mole/water).
  See prior column definition for details.
 \end_layout
 
@@ -30349,12 +30812,10 @@ Dipole-dens
 \series bold
 Neighbor-dens
 \series default
- - Mean number of waters neighboring the water molecules found in this voxel
- multiplied by the voxel number density.
- Two waters are considered neighbors if their oxygens are within 3.5 angstroms
- of each other.
- For any given frame, the contribution to the average is set to zero if
- no water is found in the voxel (units of number/Å
+ - Mean number of waters neighboring the water molecules found in this voxel multiplied by the voxel number density.
+ Two waters are considered neighbors if their oxygens are within 3.5 angstroms of each other.
+ For any given frame,
+ the contribution to the average is set to zero if no water is found in the voxel (units of number/Å
 \begin_inset Formula $^{3}$
 \end_inset
 
@@ -30366,8 +30827,8 @@ Neighbor-dens
 \series bold
 Neighbor-norm
 \series default
- - Mean number of neighboring water molecules, per water molecule found
- in the voxel (units of number per water).
+ - Mean number of neighboring water molecules,
+ per water molecule found in the voxel (units of number per water).
 \end_layout
 
 \begin_layout Itemize
@@ -30383,17 +30844,20 @@ literal "true"
 
 \end_inset
 
-, 
+,
+ 
 \begin_inset Formula $q_{tet}$
 \end_inset
 
-, for water molecules found in the voxel, normalized by the number of waters
- in the voxel.
+,
+ for water molecules found in the voxel,
+ normalized by the number of waters in the voxel.
  The order parameter for water 
 \begin_inset Formula $i$
 \end_inset
 
- in a given frame is given by: 
+ in a given frame is given by:
+ 
 \begin_inset Formula $q_{tet}(i)=1-\frac{3}{8}\sum_{j=1}^{3}\sum_{k=j+1}^{4}(cos\phi_{ijk}+\frac{1}{3})^{2}$
 \end_inset
 
@@ -30409,7 +30873,8 @@ literal "true"
 \begin_inset Formula $i$
 \end_inset
 
-, and 
+,
+ and 
 \begin_inset Formula $\phi_{ijk}$
 \end_inset
 
@@ -30417,34 +30882,48 @@ literal "true"
 \begin_inset Formula $i$
 \end_inset
 
-, 
+,
+ 
 \begin_inset Formula $j$
 \end_inset
 
-, and 
+,
+ and 
 \begin_inset Formula $k$
 \end_inset
 
 .
- If the doorder keyword is not provided or is set to FALSE, then this calculatio
-n will not be done, and the entries in this column will be set to zero.
-\end_layout
-
-\begin_layout Standard
-Grid files are provided for all computed quantities listed above, except
- that the normalized quantities are not included.
- The filenames are as follows: gist-gO.dx, gist-gH.dx, gist-dTStrans-dens.dx,
- gist-dTSorient-dens.dx, gist-Esw-dens.dx, gist-Eww-dens.dx, gist-dipolex-dens.dx,
- gist-dipoley-dens.dx, gist-dipolez-dens.dx, gist-dipole-dens.dx, gist-neighbor-den
-s.dx, gist-neighbor-norm.dx, gist-order-norm.dx.
+ If the doorder keyword is not provided or is set to FALSE,
+ then this calculation will not be done,
+ and the entries in this column will be set to zero.
+\end_layout
+
+\begin_layout Standard
+Grid files are provided for all computed quantities listed above,
+ except that the normalized quantities are not included.
+ The filenames are as follows:
+ gist-gO.dx,
+ gist-gH.dx,
+ gist-dTStrans-dens.dx,
+ gist-dTSorient-dens.dx,
+ gist-Esw-dens.dx,
+ gist-Eww-dens.dx,
+ gist-dipolex-dens.dx,
+ gist-dipoley-dens.dx,
+ gist-dipolez-dens.dx,
+ gist-dipole-dens.dx,
+ gist-neighbor-dens.dx,
+ gist-neighbor-norm.dx,
+ gist-order-norm.dx.
  If the 
 \series bold
 doorder
 \series default
- keyword is not provided, then the data in gist-order-norm.dx will all be
- zeroes.
- Note that the file of voxel water densities, gist-gO.dx, can be used as
- input to the program Placevent 
+ keyword is not provided,
+ then the data in gist-order-norm.dx will all be zeroes.
+ Note that the file of voxel water densities,
+ gist-gO.dx,
+ can be used as input to the program Placevent 
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Sindhikara"
@@ -30452,7 +30931,8 @@ literal "true"
 
 \end_inset
 
-, in order to define spherical hydration sites based on the density distribution.
+,
+ in order to define spherical hydration sites based on the density distribution.
  More detailed descriptions of the files follows:
 \end_layout
 
@@ -30494,10 +30974,10 @@ gist-dipolez-dens.dx
 gist-dTSorient-dens.dx
 \series default
  - Density weighted first order orientational entropy (kcal/mole/Å3).
- The more negative the isovalue, the more restricted or unfavorable the
- orientation of the water is.
- The value at bulk density is expected to be zero, most values will fall
- between 0 and -1.
+ The more negative the isovalue,
+ the more restricted or unfavorable the orientation of the water is.
+ The value at bulk density is expected to be zero,
+ most values will fall between 0 and -1.
 \end_layout
 
 \begin_layout Itemize
@@ -30506,9 +30986,10 @@ gist-dTSorient-dens.dx
 gist-dTStrans-dens.dx
 \series default
  - Density weighted first order tranlational entropy (kcal/mole/Å3).
- The more negative isovalue, the more restricted the water is positionally.
- The value at bulk density is expected to be zero, most values will fall
- between 0 and -1.
+ The more negative isovalue,
+ the more restricted the water is positionally.
+ The value at bulk density is expected to be zero,
+ most values will fall between 0 and -1.
  
 \end_layout
 
@@ -30519,10 +31000,10 @@ gist-Esw-dens.dx
 \series default
  - Density weighted Solute-Water interaction energy (kcal/mole/Å3).
  This is the interaction of the water with the entire solute.
- Both Lennard-Jones and electrostatic interactions are computed without
- any cutoff, within the minimum image convention.
- The more negative the number, the more favorable the interaction between
- the water and solute is.
+ Both Lennard-Jones and electrostatic interactions are computed without any cutoff,
+ within the minimum image convention.
+ The more negative the number,
+ the more favorable the interaction between the water and solute is.
  Isovalues will be negative numbers.
  
 \end_layout
@@ -30534,10 +31015,10 @@ gist-Eww-dens.dx
 \series default
  - Density weighted Water-Water interaction energy (kcal/mole/Å3).
  This is the interaction of the water with the entire solvent.
- Both Lennard-Jones and electrostatic interactions are computed without
- any cutoff, within the minimum image convention.
- The more negative the number, the more favorable the interaction between
- water within this voxel and all other water molucules is.
+ Both Lennard-Jones and electrostatic interactions are computed without any cutoff,
+ within the minimum image convention.
+ The more negative the number,
+ the more favorable the interaction between water within this voxel and all other water molucules is.
  Isovalues will be negative numbers.
  
 \end_layout
@@ -30547,12 +31028,11 @@ gist-Eww-dens.dx
 \series bold
 gist-gH.dx
 \series default
- - Number density of hydrogen centers found in the voxel, in units of the
- bulk density.
+ - Number density of hydrogen centers found in the voxel,
+ in units of the bulk density.
  The expectation value of g_H for a neat water system is unity.
  The units of this dx file are the density/bulk density.
- Therefore an isovalue of 1 represents every voxel at or greater than bulk
- density.
+ Therefore an isovalue of 1 represents every voxel at or greater than bulk density.
  
 \end_layout
 
@@ -30561,12 +31041,11 @@ gist-gH.dx
 \series bold
 gist-gO.dx
 \series default
- - Number density of oxygen centers found in the voxel, in units of the
- bulk density.
+ - Number density of oxygen centers found in the voxel,
+ in units of the bulk density.
  The expectation value of g_O for a neat water system is unity.
  The units of this dx file are the density/bulk density.
- Therefore an isovalue of 1 represents every voxel at or greater than bulk
- density.
+ Therefore an isovalue of 1 represents every voxel at or greater than bulk density.
  
 \end_layout
 
@@ -30575,10 +31054,9 @@ gist-gO.dx
 \series bold
 gist-neighbor-norm.dx
 \series default
- - Mean number of neighboring water molecules, per water molecule found
- in the voxel (units of number per water).
- Two waters are considered neighbors if their oxygens are within 3.5 Angstroms
- of each other.
+ - Mean number of neighboring water molecules,
+ per water molecule found in the voxel (units of number per water).
+ Two waters are considered neighbors if their oxygens are within 3.5 Angstroms of each other.
  
 \end_layout
 
@@ -30587,8 +31065,8 @@ gist-neighbor-norm.dx
 \series bold
 gist-order-norm.dx
 \series default
- - Average Tetrahedral Order Parameter for water molecules found in the
- voxel, normalized by the number of waters in the voxel.
+ - Average Tetrahedral Order Parameter for water molecules found in the voxel,
+ normalized by the number of waters in the voxel.
  
 \series bold
 doorder
@@ -30597,14 +31075,16 @@ doorder
 \end_layout
 
 \begin_layout Standard
-Similar grid files with other computed quantities can be generated by reading
- the gist.out file into a spreadsheet program, processing the numbers to
- generate a new column of voxel data of interest, and writing this column
- to an ascii text file.
- Then the Perl script write_dx_file.pl, which should be available on the
- GIST tutorial web-site, may be used to read in the column of data and create
- the corresponding dx file.
- The input format, and an example, are as follows: 
+Similar grid files with other computed quantities can be generated by reading the gist.out file into a spreadsheet program,
+ processing the numbers to generate a new column of voxel data of interest,
+ and writing this column to an ascii text file.
+ Then the Perl script write_dx_file.pl,
+ which should be available on the GIST tutorial web-site,
+ may be used to read in the column of data and create the corresponding dx file.
+ The input format,
+ and an example,
+ are as follows:
+ 
 \end_layout
 
 \begin_layout LyX-Code
@@ -30620,24 +31100,30 @@ Similar grid files with other computed quantities can be generated by reading
 \end_layout
 
 \begin_layout Standard
-If the doeij keyword is provided, GIST also writes a large file, Eww_ij.dat,
+If the doeij keyword is provided,
+ GIST also writes a large file,
+ Eww_ij.dat,
  containing the mean water-water interaction energies between pairs of voxels,
  scaled by ½.
  (See below.) This file has three columns.
- The first two columns are voxel indexes, 
+ The first two columns are voxel indexes,
+ 
 \begin_inset Formula $i$
 \end_inset
 
-, 
+,
+ 
 \begin_inset Formula $j$
 \end_inset
 
-, where 
+,
+ where 
 \begin_inset Formula $j>i$
 \end_inset
 
-, so that no pair appears more than once, and the third column is the mean
- interaction energy (kcal/mole) of water in voxels 
+,
+ so that no pair appears more than once,
+ and the third column is the mean interaction energy (kcal/mole) of water in voxels 
 \begin_inset Formula $i$
 \end_inset
 
@@ -30645,10 +31131,13 @@ If the doeij keyword is provided, GIST also writes a large file, Eww_ij.dat,
 \begin_inset Formula $j$
 \end_inset
 
-, scaled by ½.
- If the occupancy of either voxel is 0, such as for voxels covered by solute
- atoms, then the interaction energy is zero.
- In order to save space, such interactions are omitted from the file.
+,
+ scaled by ½.
+ If the occupancy of either voxel is 0,
+ such as for voxels covered by solute atoms,
+ then the interaction energy is zero.
+ In order to save space,
+ such interactions are omitted from the file.
  
 \end_layout
 
@@ -30661,16 +31150,21 @@ Sample cpptraj input file to run GIST
 \end_layout
 
 \begin_layout Standard
-The following input file, gist.in, causes cpptraj to read a parameter file
- named topology.top; read in the first 5000 frames of the trajectory file
- named trajectoryfile.mdcrd; strip out all Na and Cl ions; and carry out
- a GIST run which computes order parameters, uses a 41x41x45 grid centered
- at (25.0, 31.0, 30.0) with a spacing of 0.5 Å, uses the default bulk water
- density of 0.0334 molecules/Å
+The following input file,
+ gist.in,
+ causes cpptraj to read a parameter file named topology.top;
+ read in the first 5000 frames of the trajectory file named trajectoryfile.mdcrd;
+ strip out all Na and Cl ions;
+ and carry out a GIST run which computes order parameters,
+ uses a 41x41x45 grid centered at (25.0,
+ 31.0,
+ 30.0) with a spacing of 0.5 Å,
+ uses the default bulk water density of 0.0334 molecules/Å
 \begin_inset Formula $^{3}$
 \end_inset
 
-, and generates the main output file gist.out.
+,
+ and generates the main output file gist.out.
  
 \end_layout
 
@@ -30703,7 +31197,8 @@ go
 \end_layout
 
 \begin_layout Standard
-To execute this run in the background, use 
+To execute this run in the background,
+ use 
 \end_layout
 
 \begin_layout LyX-Code
@@ -30721,31 +31216,34 @@ Referencing GIST results to unperturbed (bulk) water
 \end_layout
 
 \begin_layout Standard
-Inhomogeneous fluid solvation theory, which is the basis of GIST, is designed
- to provide information on how water structure and thermodynamics around
- a solute molecule, such as a protein, are changed relative to the structure
- and thermodynamics of unperturbed (bulk) water.
- Accordingly, the quantities reported by GIST are most informative when
- the results are referenced to the corresponding bulk water properties.
- For the orientational entropy, the reference value is the same regardless
- of water model or conditions, because the first order orientational distributio
-n of water in the bulk is always uniform.
- Therefore, the GIST results for orientational entropies are already referenced
- to bulk.
- However, cpptraj reports unreferenced values for those GIST quantities
- whose reference values depend upon the water model and the simulation condition
-s; i.e., the energies.
- The translational entropy as well as the number densities will be referenced
- to bulk using the input referenced density or the default density value
- of 0.0334.
+Inhomogeneous fluid solvation theory,
+ which is the basis of GIST,
+ is designed to provide information on how water structure and thermodynamics around a solute molecule,
+ such as a protein,
+ are changed relative to the structure and thermodynamics of unperturbed (bulk) water.
+ Accordingly,
+ the quantities reported by GIST are most informative when the results are referenced to the corresponding bulk water properties.
+ For the orientational entropy,
+ the reference value is the same regardless of water model or conditions,
+ because the first order orientational distribution of water in the bulk is always uniform.
+ Therefore,
+ the GIST results for orientational entropies are already referenced to bulk.
+ However,
+ cpptraj reports unreferenced values for those GIST quantities whose reference values depend upon the water model and the simulation conditions;
+ i.e.,
+ the energies.
+ The translational entropy as well as the number densities will be referenced to bulk using the input referenced density or the default density value of 0.0334.
  The table below provides useful reference values for these quantities,
- computed for various water models at P=1atm, T=300K, using GIST in order
- to ensure a consistent minimum image treatment of periodic boundary conditions.
+ computed for various water models at P=1atm,
+ T=300K,
+ using GIST in order to ensure a consistent minimum image treatment of periodic boundary conditions.
  
 \end_layout
 
 \begin_layout Standard
 \begin_inset Float table
+placement document
+alignment document
 wide false
 sideways false
 status open
@@ -31025,21 +31523,22 @@ Water model energy and density.
 \end_layout
 
 \begin_layout Standard
-Users running calculations under significantly different conditions, or
- with different water models, should consider generating their own reference
- quantities by applying GIST to a simulation of pure water under their condition
-s of interest.
- The quantities of interest can then be obtained in their most precise available
- form by averaging over voxels, for the pure water simulation.
+Users running calculations under significantly different conditions,
+ or with different water models,
+ should consider generating their own reference quantities by applying GIST to a simulation of pure water under their conditions of interest.
+ The quantities of interest can then be obtained in their most precise available form by averaging over voxels,
+ for the pure water simulation.
  If the quantity of interest is 
 \begin_inset Formula $Q$
 \end_inset
 
-, then its average reference value is 
+,
+ then its average reference value is 
 \begin_inset Formula $Q_{reference}=\frac{\sum n_{i}Q_{i}}{\sum n_{i}}$
 \end_inset
 
-, where 
+,
+ where 
 \begin_inset Formula $Q_{i}$
 \end_inset
 
@@ -31047,31 +31546,35 @@ s of interest.
 \begin_inset Formula $n_{i}$
 \end_inset
 
- are, respectively, GIST's reported values of the quantity and the population
- in voxel 
+ are,
+ respectively,
+ GIST's reported values of the quantity and the population in voxel 
 \begin_inset Formula $i$
 \end_inset
 
 .
- The densities, 
+ The densities,
+ 
 \begin_inset Formula $\rho_{i}$
 \end_inset
 
-, are referenced to the corresponding bulk densities, 
+,
+ are referenced to the corresponding bulk densities,
+ 
 \begin_inset Formula $\rho^{o}$
 \end_inset
 
-, as 
+,
+ as 
 \begin_inset Formula $g_{i}=\rho_{i}/\rho^{o}$
 \end_inset
 
-, while the energy and entropy terms are referenced by subtracting their
- bulk values.
+,
+ while the energy and entropy terms are referenced by subtracting their bulk values.
 \end_layout
 
 \begin_layout Standard
-Note that the Eww reference needs to be subtracted from the normalized water-wat
-er energy 
+Note that the Eww reference needs to be subtracted from the normalized water-water energy 
 \series bold
 Eww-norm
 \series default
@@ -31088,7 +31591,8 @@ Eww-norm
 \begin_inset Formula $\rho=g_{O}\rho^{o}=\frac{N_{w}}{N_{f}V_{vox}}$
 \end_inset
 
-, where 
+,
+ where 
 \begin_inset Formula $N_{w}$
 \end_inset
 
@@ -31096,11 +31600,13 @@ Eww-norm
 \series bold
 population
 \series default
-), 
+),
+ 
 \begin_inset Formula $N_{f}$
 \end_inset
 
- is the number of frames, and 
+ is the number of frames,
+ and 
 \begin_inset Formula $V_{vox}$
 \end_inset
 
@@ -31118,28 +31624,31 @@ Interpreting GIST results
 \end_layout
 
 \begin_layout Standard
-GIST provides access to the first order entropies and the first- and second-orde
-r energies of inhomogeneous fluid solvation theory.
- Non-zero higher-order entropies exist but are not yet computationally accessibl
-e.
- However, for a pairwise additive force-field, such as those listed in the
- Table above, the energy is fully described at the second order provided
- by GIST.
+GIST provides access to the first order entropies and the first- and second-order energies of inhomogeneous fluid solvation theory.
+ Non-zero higher-order entropies exist but are not yet computationally accessible.
+ However,
+ for a pairwise additive force-field,
+ such as those listed in the Table above,
+ the energy is fully described at the second order provided by GIST.
  
 \end_layout
 
 \begin_layout Standard
-GIST is a research tool, and its applications (to, for example, protein-ligand
- binding and protein function) are still being explored.
+GIST is a research tool,
+ and its applications (to,
+ for example,
+ protein-ligand binding and protein function) are still being explored.
  The following general comments may be helpful to users studying GIST results.
  
 \end_layout
 
 \begin_layout Standard
 1.
- The water in voxels near a solute (e.g., a protein) almost always has unfavorable
- water-water interaction energies, relative to bulk, simply because the
- solute displaces water, resulting in fewer proximal water-water interactions.
+ The water in voxels near a solute (e.g.,
+ a protein) almost always has unfavorable water-water interaction energies,
+ relative to bulk,
+ simply because the solute displaces water,
+ resulting in fewer proximal water-water interactions.
  
 \end_layout
 
@@ -31154,10 +31663,11 @@ literal "true"
 \end_inset
 
  may be balanced by favorable water-solute interactions.
- If they are not, as may occur especially for voxels in small, hydrophobic
- pockets, then the net energy of the water in the voxel may be unfavorable
- relative to bulk, in which case a ligand which displaces water from the
- voxel into bulk may get a boost in affinity.
+ If they are not,
+ as may occur especially for voxels in small,
+ hydrophobic pockets,
+ then the net energy of the water in the voxel may be unfavorable relative to bulk,
+ in which case a ligand which displaces water from the voxel into bulk may get a boost in affinity.
  
 \end_layout
 
@@ -31165,51 +31675,49 @@ literal "true"
 3.
  Because the first order orientational distribution of bulk water is uniform,
  and a nonuniform distribution always has lower entropy than a uniform one,
- the solute can only lower the orientational entropy of water, relative
- to bulk.
- Thus, this term always opposes solvation, and displacing oriented water
- into the bulk is always favorable from the standpoint of orientational
- entropy.
+ the solute can only lower the orientational entropy of water,
+ relative to bulk.
+ Thus,
+ this term always opposes solvation,
+ and displacing oriented water into the bulk is always favorable from the standpoint of orientational entropy.
  
 \end_layout
 
 \begin_layout Standard
 4.
- Localized water, which corresponds to voxels with high water density, has
- a low first order translational entropy, and the translational entropy
- around a solute is lower than that in bulk, as a nonuniform translational
- distribution takes the place of the uniform translational distribution
- of bulk water.
+ Localized water,
+ which corresponds to voxels with high water density,
+ has a low first order translational entropy,
+ and the translational entropy around a solute is lower than that in bulk,
+ as a nonuniform translational distribution takes the place of the uniform translational distribution of bulk water.
  
 \end_layout
 
 \begin_layout Standard
 5.
- The displacement of highly oriented (low orientational entropy) and localized
- (low translational entropy) water into bulk leads to a favorable increase
- in these entropy terms.
+ The displacement of highly oriented (low orientational entropy) and localized (low translational entropy) water into bulk leads to a favorable increase in these entropy terms.
  
 \end_layout
 
 \begin_layout Standard
 6.
- However, highly oriented and localized water is often the consequence of
- strongly favorable polar interactions, such as hydrogen-bonding, between
- water and the solute.
- As a consequence, the net favorability of displacing such water is frequently
- a balance between favorable entropic consequences and unfavorable energetic
- consequences.
+ However,
+ highly oriented and localized water is often the consequence of strongly favorable polar interactions,
+ such as hydrogen-bonding,
+ between water and the solute.
+ As a consequence,
+ the net favorability of displacing such water is frequently a balance between favorable entropic consequences and unfavorable energetic consequences.
  
 \end_layout
 
 \begin_layout Standard
 7.
- The water-water energy associated with a given voxel accounts for the interacti
-ons of the waters in this voxel with all other waters in the system, including
- waters in other voxels.
- This quantity is multiplied by ½, so that, in a pure-water system where
- the GIST grid covers the entire simulation box, the sum over all voxels
- equals the correct mean water-water interaction energy.
+ The water-water energy associated with a given voxel accounts for the interactions of the waters in this voxel with all other waters in the system,
+ including waters in other voxels.
+ This quantity is multiplied by ½,
+ so that,
+ in a pure-water system where the GIST grid covers the entire simulation box,
+ the sum over all voxels equals the correct mean water-water interaction energy.
  Note that Reference 
 \begin_inset CommandInset citation
 LatexCommand citep
@@ -31224,9 +31732,10 @@ literal "true"
 
 \begin_layout Standard
 8.
- For a typical GIST application, in which the grid occupies only part of
- the simulation box, the energy bookkeeping can become complicated, as discussed
- in Section II.B.3 (page 044101-6) of Reference 
+ For a typical GIST application,
+ in which the grid occupies only part of the simulation box,
+ the energy bookkeeping can become complicated,
+ as discussed in Section II.B.3 (page 044101-6) of Reference 
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Nguyen-gist"
@@ -31235,18 +31744,19 @@ literal "true"
 \end_inset
 
 .
- That section also explains how one can compute the water-water energy associate
-d with a region 
+ That section also explains how one can compute the water-water energy associated with a region 
 \begin_inset Formula $R$
 \end_inset
 
- defined by a set of voxels, 
+ defined by a set of voxels,
+ 
 \begin_inset Formula $E_{WW}^{R}$
 \end_inset
 
 .
- The regional water-water energy, on a normalized (per water) basis, is
- given by 
+ The regional water-water energy,
+ on a normalized (per water) basis,
+ is given by 
 \begin_inset Formula $E_{WW}^{R}=2(\sum_{i\in R}E_{i,WW}-\sum_{i\in R}\sum_{j\in R,j>i}E_{i,j,WW})$
 \end_inset
 
@@ -31262,7 +31772,8 @@ d with a region
 \begin_inset Formula $R$
 \end_inset
 
-, 
+,
+ 
 \begin_inset Formula $E_{i,WW}$
 \end_inset
 
@@ -31270,7 +31781,8 @@ d with a region
 \begin_inset Formula $i$
 \end_inset
 
-, and 
+,
+ and 
 \begin_inset Formula $E_{i,j,WW}$
 \end_inset
 
@@ -31282,27 +31794,28 @@ d with a region
 \begin_inset Formula $j$
 \end_inset
 
-, taken from the file Eww_ij.dat.
- The extra factor of 2 in the present formula, relative to that in the paper,
- results from application of an extra factor of ½ to the reported water-water
- interaction energies here.
+,
+ taken from the file Eww_ij.dat.
+ The extra factor of 2 in the present formula,
+ relative to that in the paper,
+ results from application of an extra factor of ½ to the reported water-water interaction energies here.
  
 \end_layout
 
 \begin_layout Standard
 9.
- If the GIST grid contains the entire solute and the calculation is sufficently
- converged, the energy and first-order entropy of hydration can be calculated
- by numerical integration.
- E.g., the energy of hydration is 
+ If the GIST grid contains the entire solute and the calculation is sufficently converged,
+ the energy and first-order entropy of hydration can be calculated by numerical integration.
+ E.g.,
+ the energy of hydration is 
 \begin_inset Formula $\Delta E_{hyd}=\sum^{voxels}(E_{sw}^{dens}+E_{ww}^{dens})\times V_{vox}$
 \end_inset
 
 .
- For this, Eww has to be referenced carefully, since numerical inaccuracies
- can add up quickly.
- It can be advisable to omit all voxels above a certain distance to the
- solute to obtain more stable results.
+ For this,
+ Eww has to be referenced carefully,
+ since numerical inaccuracies can add up quickly.
+ It can be advisable to omit all voxels above a certain distance to the solute to obtain more stable results.
  
 \end_layout
 
@@ -31388,7 +31901,8 @@ grid [out <filename>]
 \begin_inset Quotes erd
 \end_inset
 
- extension for XPLOR format, 
+ extension for XPLOR format,
+ 
 \begin_inset Quotes eld
 \end_inset
 
@@ -31433,8 +31947,7 @@ name/tag>
 \begin_inset space ~
 \end_inset
 
-<nz> Set up grid using box information from a previously loaded reference
- structure.
+<nz> Set up grid using box information from a previously loaded reference structure.
  Currently the only way to set up non-orthogonal grids.
 \end_layout
 
@@ -31475,7 +31988,10 @@ name/tag>
 \begin_inset space ~
 \end_inset
 
-<cz>] Location of grid center, default is origin (0.0, 0.0, 0.0).
+<cz>] Location of grid center,
+ default is origin (0.0,
+ 0.0,
+ 0.0).
 \end_layout
 
 \begin_layout Description
@@ -31495,16 +32011,14 @@ name/tag>
 \begin_inset space ~
 \end_inset
 
-<mask>] Perform a best-fit rotation of the grid using the coordinates selected
- by <mask>.
+<mask>] Perform a best-fit rotation of the grid using the coordinates selected by <mask>.
 \end_layout
 
 \begin_deeper
 \begin_layout Description
-[noxalign] If specified, grid will not be re-oriented to align with Cartesian
- axes once binning is finished.
- Will affect file formats that do not store full unit cell vectors (like
- Xplor).
+[noxalign] If specified,
+ grid will not be re-oriented to align with Cartesian axes once binning is finished.
+ Will affect file formats that do not store full unit cell vectors (like Xplor).
 \end_layout
 
 \end_deeper
@@ -31563,8 +32077,8 @@ Other options:
 \begin_inset space ~
 \end_inset
 
-<density>]] Normalize grid bins by density: GridBin = GridBin / (Nframes
- * BinVolume * density).
+<density>]] Normalize grid bins by density:
+ GridBin = GridBin / (Nframes * BinVolume * density).
  Default particle density (molecules/Ang^3) for water based on 1.0 g/mL.
 \end_layout
 
@@ -31581,13 +32095,11 @@ Other options:
 \begin_inset space ~
 \end_inset
 
-<fraction>]] Write a pseudo-PDB of grid points that have density greater
- than <fraction> (default 0.80) of the grid max value.
+<fraction>]] Write a pseudo-PDB of grid points that have density greater than <fraction> (default 0.80) of the grid max value.
 \end_layout
 
 \begin_layout Description
-[{byres|bymol}] Grid the centers of mass of residues or molecules selected
- by <mask>.
+[{byres|bymol}] Grid the centers of mass of residues or molecules selected by <mask>.
 \end_layout
 
 \begin_layout Standard
@@ -31600,8 +32112,8 @@ Less common options:
 \end_inset
 
 <smooth>] Used to smooth density.
- The smoothing takes the form of GridBin = 0 if GridBin < smooth, otherwise
- GridBin = GridBin - (GridBin * exp[-(GridBin - smooth)^2 / (0.2 * smooth^2)]).
+ The smoothing takes the form of GridBin = 0 if GridBin < smooth,
+ otherwise GridBin = GridBin - (GridBin * exp[-(GridBin - smooth)^2 / (0.2 * smooth^2)]).
 \end_layout
 
 \begin_layout Description
@@ -31614,8 +32126,8 @@ Less common options:
 \begin_inset space ~
 \end_inset
 
-<madura>] Grid values lower than <madura> become flipped in sign, exposes
- low density.
+<madura>] Grid values lower than <madura> become flipped in sign,
+ exposes low density.
 \end_layout
 
 \begin_layout Standard
@@ -31670,8 +32182,8 @@ box
 \series bold
 center <mask>
 \series default
-); if either of these options are used the grid must be centered at the
- origin.
+);
+ if either of these options are used the grid must be centered at the origin.
  Note that the 
 \series bold
 \shape italic
@@ -31682,6 +32194,7 @@ bounds
 \begin_inset CommandInset ref
 LatexCommand vpageref
 reference "subsec:cpptraj-bounds"
+nolink "false"
 
 \end_inset
 
@@ -31690,8 +32203,8 @@ reference "subsec:cpptraj-bounds"
 
 \begin_layout Standard
 Note that when calculating grid densities for things like solvent/ions,
- the solute of interest (about which the atomic densities are binned) should
- be rms fit, centered and imaged prior to the 
+ the solute of interest (about which the atomic densities are binned) should be rms fit,
+ centered and imaged prior to the 
 \family sans
 \series bold
 \shape italic
@@ -31706,7 +32219,8 @@ grid
 negative
 \family default
 \series default
- is also specified, then these density will be stored as negative numbers.
+ is also specified,
+ then these density will be stored as negative numbers.
  Output can be in the XPLOR or OpenDX data formats.
 \end_layout
 
@@ -31715,7 +32229,8 @@ Examples
 \end_layout
 
 \begin_layout Standard
-Example 1: Grid water density around a solute.
+Example 1:
+ Grid water density around a solute.
  The solute is imaged to the origin and rms fit to the first frame.
  The grid will be centered on the origin as well.
 \end_layout
@@ -31745,7 +32260,8 @@ grid out.dx 20 0.5 20 0.5 20 0.5 :WAT@O
 \end_layout
 
 \begin_layout Standard
-Example 2: Grid water density around a solute.
+Example 2:
+ Grid water density around a solute.
  The grid is centered on the solute.
 \end_layout
 
@@ -31762,7 +32278,8 @@ grid out.dx 20 0.5 20 0.5 20 0.5 :WAT@O maskcenter :1-13
 \end_layout
 
 \begin_layout Standard
-Example 3: Grid water density around a solute.
+Example 3:
+ Grid water density around a solute.
  The grid is centered on the solute and rms-fit.
  The density obtained should be equivalent to the first example.
 \end_layout
@@ -31780,7 +32297,8 @@ grid out.dx 20 0.5 20 0.5 20 0.5 :WAT@O rmsfit :1-13
 \end_layout
 
 \begin_layout Standard
-Example 4: Generate grid from bounds command.
+Example 4:
+ Generate grid from bounds command.
 \end_layout
 
 \begin_layout LyX-Code
@@ -31824,7 +32342,8 @@ crdaction MyCoords grid bounds.xplor data MyGrid :WAT@O
 \end_layout
 
 \begin_layout Standard
-Example 5: Create non-orthogonal grid based on the box.
+Example 5:
+ Create non-orthogonal grid based on the box.
 \end_layout
 
 \begin_layout LyX-Code
@@ -31857,6 +32376,8 @@ name "subsec:cpptraj-hbond"
 \begin_layout LyX-Code
 hbond
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -31914,13 +32435,10 @@ hbond
 \begin_inset space ~
 \end_inset
 
-<filename>] Write # of solute-solute hydrogen bonds (aspect [UU]) vs time
- to this file.
- If searching for solute-solvent hydrogen bonds, write # of solute-solvent
- hydrogen bonds (aspect [UV]) and # of bridging solvent molecules (aspect
- [Bridge]), as well as the residue # of the bridging solvent and the solute
- residues being bridged with format '<solvent resnum>(<solute res1>+<solute
- res2>+...+),...' (aspect [ID]).
+<filename>] Write # of solute-solute hydrogen bonds (aspect [UU]) vs time to this file.
+ If searching for solute-solvent hydrogen bonds,
+ write # of solute-solvent hydrogen bonds (aspect [UV]) and # of bridging solvent molecules (aspect [Bridge]),
+ as well as the residue # of the bridging solvent and the solute residues being bridged with format '<solvent resnum>(<solute res1>+<solute res2>+...+),...' (aspect [ID]).
 \end_layout
 
 \begin_layout Description
@@ -31951,8 +32469,7 @@ hbond
 \end_inset
 
 <dmask>] Use atoms in <dmask> as solute donor heavy atoms.
- If 'donorhmask' not specified only atoms bonded to hydrogen will be considered
- donors.
+ If 'donorhmask' not specified only atoms bonded to hydrogen will be considered donors.
 \end_layout
 
 \begin_layout Description
@@ -31982,7 +32499,8 @@ hbond
 \end_layout
 
 \begin_layout Description
-[printatomnum] Add atom numbers to the output, in addtion to residue name,
+[printatomnum] Add atom numbers to the output,
+ in addtion to residue name,
  residue number and atom name.
 \end_layout
 
@@ -32018,8 +32536,8 @@ hbond
 \end_inset
 
 <filename>] Write solute-solvent hydrogen bond averages to <filename>.
- If not specified and 'avgout' is, solute-solvent hydrogen bonds averages
- will be written to that file.
+ If not specified and 'avgout' is,
+ solute-solvent hydrogen bonds averages will be written to that file.
 \end_layout
 
 \begin_layout Description
@@ -32028,7 +32546,8 @@ hbond
 \end_inset
 
 <filename>] Write information on detected solvent bridges to <filename>.
- If not specified, will be written to same place as 'solvout'.
+ If not specified,
+ will be written to same place as 'solvout'.
 \end_layout
 
 \begin_layout Description
@@ -32036,10 +32555,9 @@ hbond
 \end_layout
 
 \begin_layout Description
-[series] Save hydrogen bond formed (1.0) or not formed (0.0) per frame for
- any detected hydrogen bond.
- Solute-solute hydrogen bonds are saved with aspect [solutehb], solute-solvent
- hydrogen bonds are saved with aspect [solventhb].
+[series] Save hydrogen bond formed (1.0) or not formed (0.0) per frame for any detected hydrogen bond.
+ Solute-solute hydrogen bonds are saved with aspect [solutehb],
+ solute-solvent hydrogen bonds are saved with aspect [solventhb].
 \begin_inset Separator latexpar
 \end_inset
 
@@ -32065,11 +32583,9 @@ hbond
 
 \end_deeper
 \begin_layout Description
-[bseries] Save bridge formed (1.0) or not formed (0.0) per frame for any detected
- bridge.
- Bridges are saved with aspect [bridge_<indexlist>], where <indexlist> is
- an underscore ('_') delimited list of bridged atom/residue numbers (depending
- on 
+[bseries] Save bridge formed (1.0) or not formed (0.0) per frame for any detected bridge.
+ Bridges are saved with aspect [bridge_<indexlist>],
+ where <indexlist> is an underscore ('_') delimited list of bridged atom/residue numbers (depending on 
 \series bold
 bridgebyatom
 \series default
@@ -32087,8 +32603,8 @@ bridgebyatom
 
 \end_deeper
 \begin_layout Description
-[uuresmatrix] If specified, create a matrix with aspect [UUresmat] containing
- # of hydrogen bonds between each possible solute residue pair.
+[uuresmatrix] If specified,
+ create a matrix with aspect [UUresmat] containing # of hydrogen bonds between each possible solute residue pair.
 \end_layout
 
 \begin_deeper
@@ -32097,7 +32613,8 @@ bridgebyatom
 \begin_inset space ~
 \end_inset
 
-{none|frames}] Control how matrix is normalized: none=no normalization,
+{none|frames}] Control how matrix is normalized:
+ none=no normalization,
  frames=normalize by total # frames.
 \end_layout
 
@@ -32106,7 +32623,8 @@ bridgebyatom
 \begin_inset space ~
 \end_inset
 
-<file>] If specified, write matrix data to specified file.
+<file>] If specified,
+ write matrix data to specified file.
 \end_layout
 
 \end_deeper
@@ -32115,21 +32633,27 @@ bridgebyatom
 \begin_inset space ~
 \end_inset
 
-<comma-separated-list>] If specified, aplit the average hydrogen bond (
+<comma-separated-list>] If specified,
+ aplit the average hydrogen bond (
 \series bold
 avgout
 \series default
-, 
+,
+ 
 \series bold
 solvout
 \series default
-, 
+,
+ 
 \series bold
 bridgeout
 \series default
 ) analysis into sections delimited by the frame numbers.
- For example, 'splitframe 250,500,1000' will divide analysis into frames
- 1-249, 250-499, 500-999, and 1000 to end.
+ For example,
+ 'splitframe 250,500,1000' will divide analysis into frames 1-249,
+ 250-499,
+ 500-999,
+ and 1000 to end.
 \end_layout
 
 \begin_layout Standard
@@ -32173,8 +32697,7 @@ solventdonor
 \series bold
 solventacceptor
 \series default
-) String identifying bridging solvent residues and the solute residues they
- bridge.
+) String identifying bridging solvent residues and the solute residues they bridge.
 \end_layout
 
 \begin_layout Description
@@ -32182,8 +32705,9 @@ solventacceptor
 \series bold
 series
 \series default
- only) Time series for solute-solute hydrogen bonds; 1 for present, 0 for
- not present.
+ only) Time series for solute-solute hydrogen bonds;
+ 1 for present,
+ 0 for not present.
 \end_layout
 
 \begin_layout Description
@@ -32191,8 +32715,9 @@ series
 \series bold
 series
 \series default
- only) Time series for solute-solvent hydrogen bonds; 1 for present, 0 for
- not present.
+ only) Time series for solute-solvent hydrogen bonds;
+ 1 for present,
+ 0 for not present.
 \end_layout
 
 \begin_layout Description
@@ -32200,9 +32725,10 @@ series
 \series bold
 bseries
 \series default
- only) Time series for bridge; 1 for present, 0 for not present.
- The <indexlist> is an underscore ('_') delimited list of bridged atom/residue
- numbers (depending on 
+ only) Time series for bridge;
+ 1 for present,
+ 0 for not present.
+ The <indexlist> is an underscore ('_') delimited list of bridged atom/residue numbers (depending on 
 \series bold
 bridgebyatom
 \series default
@@ -32225,8 +32751,7 @@ Note that
 \series bold
 series
 \series default
- data sets are not generated until hydrogen bonds are actually determined
- (i.e.
+ data sets are not generated until hydrogen bonds are actually determined (i.e.
  
 \series bold
 run
@@ -32235,15 +32760,13 @@ run
 \end_layout
 
 \begin_layout Standard
-Determine hydrogen bonds in each coordinate frame using simple geometric
- criteria.
- A hydrogen bond is defined as being between an acceptor heavy atom A, a
- donor hydrogen atom H, and a donor heavy atom D.
- If the A to D distance is less than or equal to the distance cutoff and
- the A-H-D angle is greater than or equal to the angle cutoff a hydrogen
- bond is considered formed.
- Imaging of distances/angles is not performed by default, but can be turned
- on using the 
+Determine hydrogen bonds in each coordinate frame using simple geometric criteria.
+ A hydrogen bond is defined as being between an acceptor heavy atom A,
+ a donor hydrogen atom H,
+ and a donor heavy atom D.
+ If the A to D distance is less than or equal to the distance cutoff and the A-H-D angle is greater than or equal to the angle cutoff a hydrogen bond is considered formed.
+ Imaging of distances/angles is not performed by default,
+ but can be turned on using the 
 \series bold
 image
 \series default
@@ -32259,8 +32782,7 @@ If just
 \series bold
 <mask>
 \series default
- is specified donors and acceptors will be automatically determined from
- 
+ is specified donors and acceptors will be automatically determined from 
 \series bold
 <mask>
 \series default
@@ -32277,7 +32799,8 @@ donormask
 <dmask>
 \series default
  (only atoms bonded to hydrogen will be considered valid).
- Optionally, 
+ Optionally,
+ 
 \series bold
 donorhmask
 \series default
@@ -32327,7 +32850,8 @@ donormask
 \series bold
 <dmask>
 \series default
- will be used; no searching will occur in 
+ will be used;
+ no searching will occur in 
 \series bold
 <mask>
 \series default
@@ -32335,8 +32859,7 @@ donormask
 \end_layout
 
 \begin_layout Standard
-Automatic determination of hydrogen bond donors/acceptors uses the simplistic
- criterion that 
+Automatic determination of hydrogen bond donors/acceptors uses the simplistic criterion that 
 \begin_inset Quotes eld
 \end_inset
 
@@ -32344,8 +32867,14 @@ hydrogen bonds are FON
 \begin_inset Quotes erd
 \end_inset
 
-, i.e., hydrogens bonded to F, O, and N atoms are considered donors, and F,
- O, and N atoms are considered acceptors.
+,
+ i.e.,
+ hydrogens bonded to F,
+ O,
+ and N atoms are considered donors,
+ and F,
+ O,
+ and N atoms are considered acceptors.
  Intra-molecular hydrogen bonds can be ignored using the 
 \series bold
 nointramol
@@ -32354,13 +32883,13 @@ nointramol
 \end_layout
 
 \begin_layout Standard
-The number of hydrogen bonds present at each frame will be determined and
- written to the file specified by 
+The number of hydrogen bonds present at each frame will be determined and written to the file specified by 
 \series bold
 out
 \series default
 .
- If desired, the bridge [ID] data can be used in conjunction with the 
+ If desired,
+ the bridge [ID] data can be used in conjunction with the 
 \series bold
 \emph on
 keep
@@ -32373,6 +32902,7 @@ reference "subsec:cpptraj-keep"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
@@ -32389,19 +32919,20 @@ series
 lifetime
 \series default
 \shape default
-, see 
+,
+ see 
 \begin_inset CommandInset ref
 LatexCommand vpageref
 reference "subsec:cpptraj-lifetime"
+nolink "false"
 
 \end_inset
 
-); solute-solute hydrogen bonds will be saved to '<dataset name>[solutehb]'
- and solute-solvent hydrogen bonds will be saved to '<dataset name>[solventhb]'.
- The data set legends are set with the residues and atoms involved in the
- hydrogen bonds.
- In the case of solute to non-specific solvent hydrogen bonds, a V is used
- in place of solvent.
+);
+ solute-solute hydrogen bonds will be saved to '<dataset name>[solutehb]' and solute-solvent hydrogen bonds will be saved to '<dataset name>[solventhb]'.
+ The data set legends are set with the residues and atoms involved in the hydrogen bonds.
+ In the case of solute to non-specific solvent hydrogen bonds,
+ a V is used in place of solvent.
 \end_layout
 
 \begin_layout Standard
@@ -32409,9 +32940,7 @@ If
 \series bold
 avgout
 \series default
- is specified the average of each solute-solute hydrogen bond (sorted by
- population) formed over the course of the trajectory is printed with the
- format:
+ is specified the average of each solute-solute hydrogen bond (sorted by population) formed over the course of the trajectory is printed with the format:
 \end_layout
 
 \begin_layout LyX-Code
@@ -32423,11 +32952,13 @@ where
 \shape italic
 Acceptor
 \shape default
-, 
+,
+ 
 \shape italic
 DonorH
 \shape default
-, and 
+,
+ and 
 \shape italic
 Donor
 \shape default
@@ -32436,15 +32967,18 @@ Donor
 \shape italic
 Frames
 \shape default
- is the number of frames the bond is present, 
+ is the number of frames the bond is present,
+ 
 \shape italic
 Frac
 \shape default
- is the fraction of frames the bond is present, 
+ is the fraction of frames the bond is present,
+ 
 \shape italic
 AvgDist
 \shape default
- is the average distance of the bond when present, and 
+ is the average distance of the bond when present,
+ and 
 \shape italic
 AvgAng
 \shape default
@@ -32457,8 +32991,7 @@ printatomnum
 \end_layout
 
 \begin_layout Standard
-Solute to non-specific solvent hydrogen bonds can be tracked by using the
- 
+Solute to non-specific solvent hydrogen bonds can be tracked by using the 
 \series bold
 solventdonor
 \series default
@@ -32476,14 +33009,12 @@ bridging
 \end_inset
 
  solvent molecules (i.e.
- solvent that is hydrogen bonded to two or more different solute residues
- at the same time) will also be written to the file specified by 
+ solvent that is hydrogen bonded to two or more different solute residues at the same time) will also be written to the file specified by 
 \series bold
 out
 \series default
 .
- These keywords can also be used to track non-specific interactions with
- ions.
+ These keywords can also be used to track non-specific interactions with ions.
  If 
 \series bold
 avgout
@@ -32492,8 +33023,7 @@ avgout
 \series bold
 solvavg
 \series default
- is specified the average of each solute solvent hydrogen bond will be printed
- with the format:
+ is specified the average of each solute solvent hydrogen bond will be printed with the format:
 \end_layout
 
 \begin_layout LyX-Code
@@ -32505,11 +33035,13 @@ where
 \shape italic
 Acceptor
 \shape default
-, 
+,
+ 
 \shape italic
 DonorH
 \shape default
-, and 
+,
+ and 
 \shape italic
 Donor
 \shape default
@@ -32537,18 +33069,18 @@ SolventDnr
 \begin_inset Quotes erd
 \end_inset
 
- representing solvent, 
+ representing solvent,
+ 
 \shape italic
 Count
 \shape default
- is the total number of interactions between solute and solvent (note this
- can be greater than the total number of frames since for any given frame
- more than one solvent molecule can hydrogen bond to the same place on solute
- and vice versa), 
+ is the total number of interactions between solute and solvent (note this can be greater than the total number of frames since for any given frame more than one solvent molecule can hydrogen bond to the same place on solute and vice versa),
+ 
 \shape italic
 AvgDist
 \shape default
- is the average distance of the bond when present, and 
+ is the average distance of the bond when present,
+ and 
 \shape italic
 AvgAng
 \shape default
@@ -32561,18 +33093,17 @@ avgout
 \series bold
 bridgeout
 \series default
- is specified information on residues that were bridged by a solvent molecule
- over the course of the trajectory will be written to <bfilename> with format:
+ is specified information on residues that were bridged by a solvent molecule over the course of the trajectory will be written to <bfilename> with format:
 \end_layout
 
 \begin_layout LyX-Code
 Bridge Res <N0:RES0> <N1:RES1> ...
- , <X> frames.
+ ,
+ <X> frames.
 \end_layout
 
 \begin_layout Standard
-where '<N0:RES0> ...' is a list of residues that were bridged (residue # followed
- by residue name) and <X> is the number of frames the residues were bridged.
+where '<N0:RES0> ...' is a list of residues that were bridged (residue # followed by residue name) and <X> is the number of frames the residues were bridged.
 \end_layout
 
 \begin_layout Subsubsection*
@@ -32580,8 +33111,8 @@ hbond Examples
 \end_layout
 
 \begin_layout Standard
-To search for all hydrogen bonds within residues 1-22, writing the number
- of hydrogen bonds per frame to 
+To search for all hydrogen bonds within residues 1-22,
+ writing the number of hydrogen bonds per frame to 
 \begin_inset Quotes eld
 \end_inset
 
@@ -32605,8 +33136,7 @@ hbond :1-22 out nhb.dat avgout avghb.dat
 \end_layout
 
 \begin_layout Standard
-To search for all hydrogen bonds formed between donors in residue 1 and
- acceptors in residue 2:
+To search for all hydrogen bonds formed between donors in residue 1 and acceptors in residue 2:
 \end_layout
 
 \begin_layout LyX-Code
@@ -32614,8 +33144,8 @@ hbond donormask :1 acceptormask :2 out nhb.dat avgout avghb.dat
 \end_layout
 
 \begin_layout Standard
-To search for all intermolecular hydrogen bonds only and solute-solvent
- hydrogen bonds, saving time series data to HB:
+To search for all intermolecular hydrogen bonds only and solute-solvent hydrogen bonds,
+ saving time series data to HB:
 \end_layout
 
 \begin_layout LyX-Code
@@ -32641,8 +33171,7 @@ hbond HB out nhb.dat avgout solute_avg.dat
 \end_layout
 
 \begin_layout Standard
-To search for non-specific hydrogen bonds between solute and ions named
- Na+:
+To search for non-specific hydrogen bonds between solute and ions named Na+:
 \end_layout
 
 \begin_layout LyX-Code
@@ -32662,6 +33191,8 @@ image
 \begin_layout LyX-Code
 image
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -32683,13 +33214,16 @@ image
 
 \begin_deeper
 \begin_layout Description
-[origin] Image to coordinate origin (0.0, 0.0, 0.0); default is to image to
- box center.
+[origin] Image to coordinate origin (0.0,
+ 0.0,
+ 0.0);
+ default is to image to box center.
 \end_layout
 
 \begin_layout Description
-[center] For bymol/byres, image by center of mass; default is to image by
- first atom position.
+[center] For bymol/byres,
+ image by center of mass;
+ default is to image by first atom position.
 \end_layout
 
 \begin_layout Description
@@ -32707,8 +33241,8 @@ image
 \end_inset
 
 <commask>]] Image to truncated octahedron shape.
- If 'com <commask>' is given, image with respect to the center of mass of
- atoms in <commask>.
+ If 'com <commask>' is given,
+ image with respect to the center of mass of atoms in <commask>.
 \end_layout
 
 \begin_layout Description
@@ -32753,7 +33287,8 @@ image
 
 \end_deeper
 \begin_layout Standard
-Note this command is intended for advanced use; for most cases the 
+Note this command is intended for advanced use;
+ for most cases the 
 \series bold
 \shape italic
 autoimage
@@ -32763,8 +33298,8 @@ autoimage
 \end_layout
 
 \begin_layout Standard
-For periodic systems only, image molecules/residues/atoms that are outside
- of the box back into the box.
+For periodic systems only,
+ image molecules/residues/atoms that are outside of the box back into the box.
  Currently both orthorhombic and non-orthorhombic boxes are supported.
  A typical use of 
 \series bold
@@ -32779,9 +33314,9 @@ center
 \series default
 \shape default
 .
- For example, the following commands move all atoms so that the center of
- residue 1 is at the center of the box, then image so that all molecules
- that are outside the box after centering are wrapped back inside:
+ For example,
+ the following commands move all atoms so that the center of residue 1 is at the center of the box,
+ then image so that all molecules that are outside the box after centering are wrapped back inside:
 \end_layout
 
 \begin_layout LyX-Code
@@ -32794,11 +33329,11 @@ image
 
 \begin_layout Standard
 The xoffset etc.
- keywords can be used to shift the entire unit cell in a certain direction
- by the given factor, which can be useful for visualizing trajectories with
- periodic boundary conditions.
- For example, to generate a trajectory that is offset by 1.0 box length in
- the X direction, one could use:
+ keywords can be used to shift the entire unit cell in a certain direction by the given factor,
+ which can be useful for visualizing trajectories with periodic boundary conditions.
+ For example,
+ to generate a trajectory that is offset by 1.0 box length in the X direction,
+ one could use:
 \end_layout
 
 \begin_layout LyX-Code
@@ -32816,6 +33351,8 @@ jcoupling
 \begin_layout LyX-Code
 jcoupling
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -32858,8 +33395,9 @@ jcoupling
 \end_inset
 
 file>] File containing Karplus parameters.
- If not specified will check CPPTRAJHOME, AMBERHOME, and KARPLUS environment
- variables (see below).
+ If not specified will check CPPTRAJHOME,
+ AMBERHOME,
+ and KARPLUS environment variables (see below).
 \end_layout
 
 \begin_layout Description
@@ -32895,14 +33433,14 @@ Calculate J-coupling values for all dihedrals found within
 <mask>
 \series default
  (all atoms if no mask given).
- In order to use this function, Karplus parameters for all dihedrals which
- will be calculated must be loaded.
+ In order to use this function,
+ Karplus parameters for all dihedrals which will be calculated must be loaded.
  By default 
 \shape italic
 cpptraj
 \shape default
- will use the data found in either $CPPTRAJHOME/dat/Karplus.txt or $AMBERHOME/dat
-/Karplus.txt; if this is not found 
+ will use the data found in either $CPPTRAJHOME/dat/Karplus.txt or $AMBERHOME/dat/Karplus.txt;
+ if this is not found 
 \shape italic
 cpptraj
 \shape default
@@ -32911,8 +33449,7 @@ cpptraj
 \end_layout
 
 \begin_layout Standard
-In the Karplus parameter file each parameter set consists of two lines for
- each dihedral with the format:
+In the Karplus parameter file each parameter set consists of two lines for each dihedral with the format:
 \end_layout
 
 \begin_layout LyX-Code
@@ -32925,8 +33462,8 @@ In the Karplus parameter file each parameter set consists of two lines for
 
 \begin_layout Standard
 The first line defines the parameter set for a dihedral.
- <Type> is optional; if not given the form for calculating the J-coupling
- will be as described by Chou et al.
+ <Type> is optional;
+ if not given the form for calculating the J-coupling will be as described by Chou et al.
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Chou03"
@@ -32934,7 +33471,8 @@ literal "true"
 
 \end_inset
 
-; if 'C' the form will be as described by Perez et al.
+;
+ if 'C' the form will be as described by Perez et al.
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Perez01"
@@ -32944,16 +33482,23 @@ literal "true"
 
 .
  The <NameX> parameters define the four atoms involved in the dihedral.
- Each <NameX> parameter is 5 characters wide, starting with a plus '+',
+ Each <NameX> parameter is 5 characters wide,
+ starting with a plus '+',
  minus '-' or space ' ' character indicating the atom belongs to the next,
- previous, or current residue.
+ previous,
+ or current residue.
  The remaining 4 characters are the atom name.
- The parameters <A>, <B>, <C>, and <D> are floating point values 6 characters
- wide describing the Karplus parameters.
- For the 'C' form A, B, and C correspond to C0, C1, and C2; D is unused
- and should not be specified.
- The second line is a list of residue names (4 characters each) to which
- the dihedral applies.
+ The parameters <A>,
+ <B>,
+ <C>,
+ and <D> are floating point values 6 characters wide describing the Karplus parameters.
+ For the 'C' form A,
+ B,
+ and C correspond to C0,
+ C1,
+ and C2;
+ D is unused and should not be specified.
+ The second line is a list of residue names (4 characters each) to which the dihedral applies.
  For example:
 \end_layout
 
@@ -32967,7 +33512,9 @@ ILE VAL
 
 \begin_layout Standard
 Describes a dihedral between atoms HA-CA-CB-HB using the Perez et al.
- form with constants C0=5.40, C1=-1.37, C2=3.61 applied to ILE and VAL residues.
+ form with constants C0=5.40,
+ C1=-1.37,
+ C2=3.61 applied to ILE and VAL residues.
 \end_layout
 
 \begin_layout Standard
@@ -32984,7 +33531,8 @@ out <filename>
 \series bold
 <mask1>
 \series default
- printed along with its calculated J-coupling value for each frame, e.g.:
+ printed along with its calculated J-coupling value for each frame,
+ e.g.:
 \end_layout
 
 \begin_layout LyX-Code
@@ -33004,8 +33552,12 @@ out <filename>
 \end_layout
 
 \begin_layout Standard
-First the frame number is printed, then for each dihedral: Residue number,
- residue name, atom names 1-4 in the dihedral, the value of the dihedral,
+First the frame number is printed,
+ then for each dihedral:
+ Residue number,
+ residue name,
+ atom names 1-4 in the dihedral,
+ the value of the dihedral,
  the J-coupling value.
 \end_layout
 
@@ -33016,7 +33568,8 @@ In
 cpptraj
 \family default
 \shape default
- format, only the J-coupling value is written.
+ format,
+ only the J-coupling value is written.
 \end_layout
 
 \begin_layout Subsection
@@ -33077,6 +33630,7 @@ reference "subsec:cpptraj-hbond"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
@@ -33093,8 +33647,8 @@ nbridge
 \end_layout
 
 \begin_layout Description
-nobridgewarn If specified, suppress warnings for when active # bridges does
- not equal requested number.
+nobridgewarn If specified,
+ suppress warnings for when active # bridges does not equal requested number.
 \end_layout
 
 \begin_layout Description
@@ -33114,8 +33668,8 @@ bridgeresonly
 \begin_inset space ~
 \end_inset
 
-<range> If specified, only keep bridges that bridge residues in the <resrange>
- list.
+<range> If specified,
+ only keep bridges that bridge residues in the <resrange> list.
 \end_layout
 
 \end_deeper
@@ -33144,8 +33698,7 @@ charge
 \begin_inset space ~
 \end_inset
 
-charge> Scale charges so total charge of remaining atoms matches the specified
- <new charge>.
+charge> Scale charges so total charge of remaining atoms matches the specified <new charge>.
 \end_layout
 
 \begin_layout Description
@@ -33193,14 +33746,15 @@ hbond
 \emph default
  command to retain solute and only bridging residues (e.g.
  bridging waters).
- For example, the following run generates bridging data with the 
+ For example,
+ the following run generates bridging data with the 
 \series bold
 \emph on
 'hbond'
 \series default
 \emph default
- command in a first pass, then uses the bridge ID data to retain only 1
- single bridging water between residues 10 and 11:
+ command in a first pass,
+ then uses the bridge ID data to retain only 1 single bridging water between residues 10 and 11:
 \end_layout
 
 \begin_layout LyX-Code
@@ -33212,7 +33766,8 @@ trajin tz2.ortho.nc
 \end_layout
 
 \begin_layout LyX-Code
-# First pass, generate bridge time series 
+# First pass,
+ generate bridge time series 
 \end_layout
 
 \begin_layout LyX-Code
@@ -33224,7 +33779,8 @@ run
 \end_layout
 
 \begin_layout LyX-Code
-# Second pass, retain only frames where the bridge is present
+# Second pass,
+ retain only frames where the bridge is present
 \end_layout
 
 \begin_layout LyX-Code
@@ -33248,8 +33804,9 @@ run
 \end_layout
 
 \begin_layout Standard
-This run reads in bridge ID data from a previous hbond run and uses it to
- keep only residues 10, 11, and a bridging water:
+This run reads in bridge ID data from a previous hbond run and uses it to keep only residues 10,
+ 11,
+ and a bridging water:
 \end_layout
 
 \begin_layout LyX-Code
@@ -33304,8 +33861,8 @@ lessplit [out <filename prefix>] [average <avg filename>] <trajout args>
 \begin_inset space ~
 \end_inset
 
-prefix>] Write split LES trajectories to <filename prefix>.X, where X is
- an integer.
+prefix>] Write split LES trajectories to <filename prefix>.X,
+ where X is an integer.
 \end_layout
 
 \begin_layout Description
@@ -33350,6 +33907,8 @@ lie
 \begin_layout LyX-Code
 lie
 \begin_inset Index idx
+range none
+pageformat default
 status open
 
 \begin_layout Plain Layout
@@ -33384,17 +33943,15 @@ DataSet Aspects:
 
 \end_deeper
 \begin_layout Standard
-For each frame, calculate the non-bonded interactions between all atoms
- in <Ligand mask> with all atoms in <Surroundings mask>.
- Electrostatic and van der Waals interactions will be calculated for all
- atom pairs.
- A separate electrostatic and van der Waals cutoff can be applied, the default
- is 12.0 Angstroms for both.
+For each frame,
+ calculate the non-bonded interactions between all atoms in <Ligand mask> with all atoms in <Surroundings mask>.
+ Electrostatic and van der Waals interactions will be calculated for all atom pairs.
+ A separate electrostatic and van der Waals cutoff can be applied,
+ the default is 12.0 Angstroms for both.
  <dielc> is an optional dielectric constant.
- Either the electrostatic or van der Waals calculations can be suppressed
- via the keywords noelec and novdw, respectively.
- Periodic boundary conditions (and the minimum image convention) can be
- abandoned with the 
+ Either the electrostatic or van der Waals calculations can be suppressed via the keywords noelec and novdw,
+ respectively.
+ Periodic boundary conditions (and the minimum image convention) can be abandoned with the 
 \begin_inset Quotes eld
 \end_inset
 
@@ -33403,19 +33960,18 @@ nopbc
 \end_inset
 
  keyword.
- Note, however, that no prior imaging is performed if the frames contain
- periodic boundaries.
- This may be useful for instances when you are simulating a microscopic
- droplets.
+ Note,
+ however,
+ that no prior imaging is performed if the frames contain periodic boundaries.
+ This may be useful for instances when you are simulating a microscopic droplets.
 \end_layout
 
 \begin_layout Standard
-The electrostatic interactions are calculated according to a simple shifting
- function shown below.
- The data file will contain two data sets—one for electrostatic interactions
- and one for van der Waals interactions.
- Periodic topologies and trajectories are required (i.e., explicit solvent
- is necessary).
+The electrostatic interactions are calculated according to a simple shifting function shown below.
+ The data file will contain two data sets—
+one for electrostatic interactions and one for van der Waals interactions.
+ Periodic topologies and trajectories are required (i.e.,
+ explicit solvent is necessary).
  The minimum image convention is followed.
 \end_layout
 
@@ -33453,11 +34009,12 @@ order out <filename> [x|y|z] [scd] [unsat <mask>]
 
 \begin_deeper
 \begin_layout Description
-out Output file for order parameters: Sx, Sy, Sz (each succeeded by the
- standard deviation), and two estimates for the deuterium-order parameter
- |SCD| = 0.5Sz and |SCD| = -(2Sx + Sy)/3.
- If scd is set then the order parameter directly computed from the C-H vectors
- is output.
+out Output file for order parameters:
+ Sx,
+ Sy,
+ Sz (each succeeded by the standard deviation),
+ and two estimates for the deuterium-order parameter |SCD| = 0.5Sz and |SCD| = -(2Sx + Sy)/3.
+ If scd is set then the order parameter directly computed from the C-H vectors is output.
 \end_layout
 
 \begin_layout Description
@@ -33468,16 +34025,16 @@ x|y|z Reference axis.
 \begin_layout Description
 unsat Mask for unsaturated bonds.
  Sz is calculated for vector Cn-Cn+1.
- This is only relevant if scd (below) is not set, i.e.
+ This is only relevant if scd (below) is not set,
+ i.e.
  order parameters are calculated from carbon position only.
  
 \end_layout
 
 \begin_layout Description
-scd Calculate the deuterium-order parameter |SCD| directly from the C-H
- vectors (masks must contain C-H-H triplets, see below).
- Otherwise the order parameter is estimated from carbon positions only (masks
- must contain only relevant carbons).
+scd Calculate the deuterium-order parameter |SCD| directly from the C-H vectors (masks must contain C-H-H triplets,
+ see below).
+ Otherwise the order parameter is estimated from carbon positions only (masks must contain only relevant carbons).
  (false) 
 \end_layout
 
@@ -33514,11 +34071,13 @@ The order parameters
 \begin_inset Formula $S_{x}$
 \end_inset
 
-, 
+,
+ 
 \begin_inset Formula $S_{y}$
 \end_inset
 
-, 
+,
+ 
 \begin_inset Formula $S_{z}$
 \end_inset
 
@@ -33528,9 +34087,8 @@ The order parameters
 \series bold
 scd
 \series default
- the masks must be made up of C-H-H triples, hence hydrogens to double bonds
- must be enumerated twice while methyl groups require an additional mask
- which will also create two entries in the output.
+ the masks must be made up of C-H-H triples,
+ hence hydrogens to double bonds must be enumerated twice while methyl groups require an additional mask which will also create two entries in the output.
 \end_layout
 
 \begin_layout Standard
@@ -33545,7 +34103,8 @@ is the vector joining carbons
 \begin_inset Formula $C_{n+1}$
 \end_inset
 
-, 
+,
+ 
 \begin_inset Formula $S_{x}$
 \end_inset
 
@@ -33566,7 +34125,8 @@ is the vector joining carbons
 \begin_inset Formula $Sc=0.5<3\cos(2\theta)>-1$
 \end_inset
 
-, where 
+,
+ where 
 \begin_inset Formula $\theta$
 \end_inset
 
@@ -33580,15 +34140,18 @@ Example input (all atom names according to CHARMM27 force field for POPC).
 \end_layout
 
 \begin_layout Standard
-sn1 chain: order parameters 
+sn1 chain:
+ order parameters 
 \begin_inset Formula $S_{x}$
 \end_inset
 
-, 
+,
+ 
 \begin_inset Formula $S_{y}$
 \end_inset
 
-, 
+,
+ 
 \begin_inset Formula $S_{z}$
 \end_inset
 
@@ -33675,7 +34238,8 @@ out
 \end_layout
 
 \begin_layout Description
-p2 If specified, report raw <P2> values.
+p2 If specified,
+ report raw <P2> values.
 \end_layout
 
 \begin_layout Standard
@@ -33689,28 +34253,28 @@ DataSets Generated:
 
 \begin_layout Description
 <name>[H2]:<idx> Hold lipid order parameters for each C-H2.
- If no H2, the C-H1 value will be used.
+ If no H2,
+ the C-H1 value will be used.
 \end_layout
 
 \begin_layout Description
 <name>[H3]:<idx> Hold lipid order parameters for each C-H3.
- If no H3, the C-H2/C-H1 value will be used.
+ If no H3,
+ the C-H2/C-H1 value will be used.
 \end_layout
 
 \begin_layout Description
-<name>[SDHX]:<idx> Hold standard deviation of lipid order parameters for
- each C-HX.
+<name>[SDHX]:<idx> Hold standard deviation of lipid order parameters for each C-HX.
 \end_layout
 
 \end_deeper
 \begin_layout Standard
-Calculate lipid order parameters SCD (|<P2>|) for lipid chains in mask 
-  <mask>.
- Lipid chains are identified by carboxyl groups, i.e.
-   O-(C=O)-C1-...-CN, where C1 is the first carbon in the acyl chain   and
- CN is the last.
- Order parameters will be determined for each   hydrogen bonded to each
- carbon.
+Calculate lipid order parameters SCD (|<P2>|) for lipid chains in mask   <mask>.
+ Lipid chains are identified by carboxyl groups,
+ i.e.
+   O-(C=O)-C1-...-CN,
+ where C1 is the first carbon in the acyl chain   and CN is the last.
+ Order parameters will be determined for each   hydrogen bonded to each carbon.
  If 'p2' is specified the raw <P2>   values will be reported.
 \end_layout
 
@@ -33723,8 +34287,9 @@ makestructure <List of Args>
 \end_layout
 
 \begin_layout Standard
-Apply dihedrals to specified residues using arguments found in <List of
- Args>, where an argument is 1 or more of the following arg types: 
+Apply dihedrals to specified residues using arguments found in <List of Args>,
+ where an argument is 1 or more of the following arg types:
+ 
 \end_layout
 
 \begin_layout Subsubsection*
@@ -33736,10 +34301,9 @@ range>
 \end_layout
 
 \begin_layout Standard
-Apply secondary structure type (via phi/psi backbone angles) to residues
- in given range.
- If the secondary structure type is a turn, the residue range must correspond
- to a multiple of 2 residues.
+Apply secondary structure type (via phi/psi backbone angles) to residues in given range.
+ If the secondary structure type is a turn,
+ the residue range must correspond to a multiple of 2 residues.
 \end_layout
 
 \begin_layout Standard
@@ -33768,7 +34332,8 @@ Keyword
 \begin_layout Plain Layout
 
 \series bold
-phi, psi (deg.)
+phi,
+ psi (deg.)
 \end_layout
 
 \end_inset
@@ -33799,7 +34364,8 @@ alpha
 \begin_inset Text
 
 \begin_layout Plain Layout
--57.8, -47.0
+-57.8,
+ -47.0
 \end_layout
 
 \end_inset
@@ -33828,7 +34394,8 @@ left
 \begin_inset Text
 
 \begin_layout Plain Layout
--57.8, 47.0
+-57.8,
+ 47.0
 \end_layout
 
 \end_inset
@@ -33857,7 +34424,8 @@ pp2
 \begin_inset Text
 
 \begin_layout Plain Layout
--75.0, 145.0
+-75.0,
+ 145.0
 \end_layout
 
 \end_inset
@@ -33886,7 +34454,8 @@ hairpin
 \begin_inset Text
 
 \begin_layout Plain Layout
--100.0, 130.0
+-100.0,
+ 130.0
 \end_layout
 
 \end_inset
@@ -33915,7 +34484,8 @@ extended
 \begin_inset Text
 
 \begin_layout Plain Layout
--150.0, 155.0
+-150.0,
+ 155.0
 \end_layout
 
 \end_inset
@@ -33944,7 +34514,9 @@ typeI
 \begin_inset Text
 
 \begin_layout Plain Layout
--60.0, -30.0 | -90.0, 0.0
+-60.0,
+ -30.0 | -90.0,
+ 0.0
 \end_layout
 
 \end_inset
@@ -33973,7 +34545,9 @@ typeII
 \begin_inset Text
 
 \begin_layout Plain Layout
--60.0, 120.0 | 80.0, 0.0
+-60.0,
+ 120.0 | 80.0,
+ 0.0
 \end_layout
 
 \end_inset
@@ -34002,7 +34576,9 @@ typeVIII
 \begin_inset Text
 
 \begin_layout Plain Layout
--60.0, -30.0 | -120.0, 120.0
+-60.0,
+ -30.0 | -120.0,
+ 120.0
 \end_layout
 
 \end_inset
@@ -34031,7 +34607,9 @@ typeI'
 \begin_inset Text
 
 \begin_layout Plain Layout
-60.0, 30.0 | 90.0, 0.0
+60.0,
+ 30.0 | 90.0,
+ 0.0
 \end_layout
 
 \end_inset
@@ -34060,7 +34638,9 @@ typeII
 \begin_inset Text
 
 \begin_layout Plain Layout
-60.0, -120.0 | -80.0, 0.0
+60.0,
+ -120.0 | -80.0,
+ 0.0
 \end_layout
 
 \end_inset
@@ -34089,7 +34669,9 @@ typeVIa1
 \begin_inset Text
 
 \begin_layout Plain Layout
--60.0, 120.0 | -90.0, 0.0
+-60.0,
+ 120.0 | -90.0,
+ 0.0
 \end_layout
 
 \end_inset
@@ -34118,7 +34700,9 @@ typeVIa2
 \begin_inset Text
 
 \begin_layout Plain Layout
--120.0, 120.0 | -60.0, 0.0
+-120.0,
+ 120.0 | -60.0,
+ 0.0
 \end_layout
 
 \end_inset
@@ -34147,7 +34731,9 @@ typeVIb
 \begin_inset Text
 
 \begin_layout Plain Layout
--135.0, 135.0 | -75.0, 160.0
+-135.0,
+ 135.0 | -75.0,
+ 160.0
 \end_layout
 
 \end_inset
@@ -34186,10 +34772,9 @@ range>[:<phi>:<psi>]
 \end_layout
 
 \begin_layout Standard
-If <phi> and <psi> are given, define a custom secondary structure conformation
- named <custom_ss> and apply to residues in range.
- If <custom_ss> has been previously defined then apply it to residues in
- range.
+If <phi> and <psi> are given,
+ define a custom secondary structure conformation named <custom_ss> and apply to residues in range.
+ If <custom_ss> has been previously defined then apply it to residues in range.
 \end_layout
 
 \begin_layout Subsubsection*
@@ -34209,11 +34794,12 @@ range>[:<phi1>:<psi1>:<phi2>:<psi2>]
 \end_layout
 
 \begin_layout Standard
-If <phi1>, <psi1>, <phi2>, and <psi2> are given, defined a custom turn conformat
-ion named <custom_turn> and apply to residues in range (range must correspond
- to a multiple of 2 residues).
- If <custom_turn> has been previously defined then apply it to residues
- in range.
+If <phi1>,
+ <psi1>,
+ <phi2>,
+ and <psi2> are given,
+ defined a custom turn conformation named <custom_turn> and apply to residues in range (range must correspond to a multiple of 2 residues).
+ If <custom_turn> has been previously defined then apply it to residues in range.
 \end_layout
 
 \begin_layout Subsubsection*
@@ -34245,10 +34831,9 @@ type>:<angle>]
 \end_layout
 
 \begin_layout Standard
-If <dih type> and <angle> are given, apply <angle> to selected dihedrals
- of type in range.
- If <custom dih> has been previously defined then apply it to residues in
- range.
+If <dih type> and <angle> are given,
+ apply <angle> to selected dihedrals of type in range.
+ If <custom dih> has been previously defined then apply it to residues in range.
 \end_layout
 
 \begin_layout Subsubsection*
@@ -34268,7 +34853,10 @@ range>[:<at0>:<at1>:<at2>:<at3>:<angle>[:<offset>]]
 \end_layout
 
 \begin_layout Standard
-Apply <angle> to dihedral defined by atoms <at1>, <at2>, <at3>, and <at4>,
+Apply <angle> to dihedral defined by atoms <at1>,
+ <at2>,
+ <at3>,
+ and <at4>,
  or use previously defined <custom_dih>.
 \end_layout
 
@@ -34414,17 +35002,18 @@ range>[:<dih types>]] [refvalsout <file>] [founddihout <file>]
 \end_layout
 
 \begin_layout Standard
-Apply dihedrals from residues <ref_range> in previously loaded reference
- structure <refname> to dihedrals in <range>.
- If <ref range> is specified, use those residues from reference.
+Apply dihedrals from residues <ref_range> in previously loaded reference structure <refname> to dihedrals in <range>.
+ If <ref range> is specified,
+ use those residues from reference.
  The dihedral types to be used (see 
 \series bold
 <dih_type>
 \series default
- above) can be specified in a comma-separated list; default is phi/psi.
- Note that in order to specify <dih types>, <ref range> must be specified.
- The 'refvalsout' and 'founddihout' keywords can be used to print dihedrals
- found in the reference and target structures respectively to files.
+ above) can be specified in a comma-separated list;
+ default is phi/psi.
+ Note that in order to specify <dih types>,
+ <ref range> must be specified.
+ The 'refvalsout' and 'founddihout' keywords can be used to print dihedrals found in the reference and target structures respectively to files.
 \end_layout
 
 \begin_layout Subsubsection*
@@ -34440,9 +35029,11 @@ makestructure pp2:1-13
 \end_layout
 
 \begin_layout Standard
-Make residues 1 and 12 'extended', residues 6 and 7 a type I' turn, and
- two custom assignments, one (custom1) for residues 2-5, the other (custom2)
- for residues 8-11:
+Make residues 1 and 12 'extended',
+ residues 6 and 7 a type I' turn,
+ and two custom assignments,
+ one (custom1) for residues 2-5,
+ the other (custom2) for residues 8-11:
 \end_layout
 
 \begin_layout LyX-Code
@@ -34468,7 +35059,8 @@ makestructure extended:1,12
 \end_layout
 
 \begin_layout Standard
-Assign residue 5 phi 90 degrees, residues 6 and 7 phi=-70 and psi=60 degrees:
+Assign residue 5 phi 90 degrees,
+ residues 6 and 7 phi=-70 and psi=60 degrees:
 \end_layout
 
 \begin_layout LyX-Code
@@ -34476,8 +35068,7 @@ makestructure customdih:5:phi:90 custom:6,7:-70:60
 \end_layout
 
 \begin_layout Standard
-Create a new dihedral named chi1 and assign it a value of 35 degrees in
- residue 8:
+Create a new dihedral named chi1 and assign it a value of 35 degrees in residue 8:
 \end_layout
 
 \begin_layout LyX-Code
@@ -34485,8 +35076,9 @@ makestructure chi1:8:N:CA:CB:CG:35
 \end_layout
 
 \begin_layout Standard
-Assign 'extended' structure to residues 1 and 12, a custom turn to residues
- 2-5 and 8-11, and a typeI' turn to residues 6-7:
+Assign 'extended' structure to residues 1 and 12,
+ a custom turn to residues 2-5 and 8-11,
+ and a typeI' turn to residues 6-7:
 \end_layout
 
 \begin_layout LyX-Code
@@ -34542,6 +35134,8 @@ mask
 \begin_layout LyX-Code
 mask
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -34579,8 +35173,12 @@ out
 \begin_inset space ~
 \end_inset
 
-<filename> Write the frame, atom number, atom name, residue number, residue
- name, and molecule number for each selected atom to file.
+<filename> Write the frame,
+ atom number,
+ atom name,
+ residue number,
+ residue name,
+ and molecule number for each selected atom to file.
 \end_layout
 
 \begin_layout Description
@@ -34624,8 +35222,8 @@ trajargs
 \begin_inset space ~
 \end_inset
 
-args> When writing output PDB/Mol2, additional trajectory arguments to pass
- to the output trajectory.
+args> When writing output PDB/Mol2,
+ additional trajectory arguments to pass to the output trajectory.
 \end_layout
 
 \begin_layout Standard
@@ -34667,14 +35265,13 @@ For each frame determine all atoms that correspond to
 <mask>
 \series default
 .
- This is most useful when using distance-based masks, since the atoms in
- the mask are updated for every frame read in.
+ This is most useful when using distance-based masks,
+ since the atoms in the mask are updated for every frame read in.
  If 
 \series bold
 maskout
 \series default
- is specified information on all atoms in <mask> will be written to <filename>
- with format:
+ is specified information on all atoms in <mask> will be written to <filename> with format:
 \end_layout
 
 \begin_layout LyX-Code
@@ -34686,23 +35283,28 @@ where
 \family typewriter
 #Frame
 \family default
- is the frame number, 
+ is the frame number,
+ 
 \family typewriter
 AtomNum
 \family default
- is the number of the selected atom, 
+ is the number of the selected atom,
+ 
 \family typewriter
 Atom
 \family default
- is the name of the selected atom, 
+ is the name of the selected atom,
+ 
 \family typewriter
 ResNum
 \family default
- is the residue number of the selected atom, 
+ is the residue number of the selected atom,
+ 
 \family typewriter
 Res
 \family default
- is the residue name, and 
+ is the residue name,
+ and 
 \family typewriter
 MolNum
 \family default
@@ -34718,8 +35320,7 @@ maskpdb
 \series bold
 maskmol2
 \series default
- are specified a PDB/Mol2 file corresponding to <mask> will be written out
- every frame with name 
+ are specified a PDB/Mol2 file corresponding to <mask> will be written out every frame with name 
 \begin_inset Quotes eld
 \end_inset
 
@@ -34735,8 +35336,8 @@ maskmol2
 \end_layout
 
 \begin_layout Standard
-For example, to write out all residues within 3.0 Angstroms of residue 195
- that are named WAT to 
+For example,
+ to write out all residues within 3.0 Angstroms of residue 195 that are named WAT to 
 \begin_inset Quotes eld
 \end_inset
 
@@ -34744,7 +35345,8 @@ Res195WAT.dat
 \begin_inset Quotes erd
 \end_inset
 
-, as well as write out corresponding PDB files:
+,
+ as well as write out corresponding PDB files:
 \end_layout
 
 \begin_layout LyX-Code
@@ -34760,8 +35362,7 @@ mask
 \end_layout
 
 \begin_layout Standard
-To write all out atoms outside of 5.0 Angstroms of residues named ARG to
- PDB files with a chain ID of 'B':
+To write all out atoms outside of 5.0 Angstroms of residues named ARG to PDB files with a chain ID of 'B':
 \end_layout
 
 \begin_layout LyX-Code
@@ -34818,7 +35419,8 @@ matrix [out <filename>] [start <#>] [stop|end <#>] [offset <#>]
 
 <filename>]
 \series default
- If specified, write matrix to <filename>.
+ If specified,
+ write matrix to <filename>.
 \end_layout
 
 \begin_layout Description
@@ -34846,7 +35448,9 @@ matrix [out <filename>] [start <#>] [stop|end <#>] [offset <#>]
 
 <#>]
 \series default
- Start, stop, and offset frames to use (as a subset of all frames read in).
+ Start,
+ stop,
+ and offset frames to use (as a subset of all frames read in).
 \end_layout
 
 \begin_layout Description
@@ -34871,11 +35475,13 @@ byatom
 \family typewriter
 covar
 \family default
-, 
+,
+ 
 \family typewriter
 mwcovar
 \family default
-, and 
+,
+ and 
 \family typewriter
 ired
 \family default
@@ -34887,8 +35493,7 @@ ired
 \series bold
 byres
 \series default
- Write results by calculating an average for each residue (mass weighted
- if 
+ Write results by calculating an average for each residue (mass weighted if 
 \series bold
 mass
 \series default
@@ -34900,8 +35505,8 @@ mass
 \series bold
 bymask
 \series default
- Write average over <mask1>, and if <mask2> is specified <mask1> x <mask2>
- and <mask2> as well (mass weighted if 
+ Write average over <mask1>,
+ and if <mask2> is specified <mask1> x <mask2> and <mask2> as well (mass weighted if 
 \series bold
 mass
 \series default
@@ -35026,6 +35631,7 @@ ired
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-vector"
+nolink "false"
 
 \end_inset
 
@@ -35073,23 +35679,28 @@ Matrix dimensions will be of the order of N x M for
 \series bold
 dist
 \series default
-, 
+,
+ 
 \series bold
 correl
 \series default
-, 
+,
+ 
 \series bold
 idea
 \series default
-, and 
+,
+ and 
 \series bold
 ired
 \series default
-, 2N x 2N for 
+,
+ 2N x 2N for 
 \series bold
 dihcovar
 \series default
-, 3N x 3M for 
+,
+ 3N x 3M for 
 \series bold
 covar
 \series default
@@ -35097,7 +35708,8 @@ covar
 \series bold
 mwcovar
 \series default
-, and N(N-1) x N(N-1) / 4 for 
+,
+ and N(N-1) x N(N-1) / 4 for 
 \series bold
 distcovar
 \series default
@@ -35117,7 +35729,8 @@ dihcovar
 \series default
 \shape default
 \emph default
- otherwise, and M being the number of atoms in 
+ otherwise,
+ and M being the number of atoms in 
 \series bold
 <mask2>
 \series default
@@ -35134,8 +35747,8 @@ dihcovar
 \series bold
 ired
 \series default
-; the matrix will be made up of previously defined IRED vectors (see the
- 
+;
+ the matrix will be made up of previously defined IRED vectors (see the 
 \series bold
 \shape italic
 vector
@@ -35145,12 +35758,13 @@ vector
 \begin_inset CommandInset ref
 LatexCommand vpageref
 reference "subsec:cpptraj-vector"
+nolink "false"
 
 \end_inset
 
 ).
- Similarly no mask is required for dihcovar; dihedral data sets must have
- been previously defined.
+ Similarly no mask is required for dihcovar;
+ dihedral data sets must have been previously defined.
  Only one mask can be used with 
 \series bold
 distcovar
@@ -35160,8 +35774,8 @@ distcovar
 idea
 \series default
  matrices (i.e.
- they can be symmetric only), otherwise one or two masks can be used (for
- symmetric and full matrices respectively).
+ they can be symmetric only),
+ otherwise one or two masks can be used (for symmetric and full matrices respectively).
  If two masks are specified the number of atoms covered by 
 \shape italic
 mask1
@@ -35169,6 +35783,7 @@ mask1
  must be greater than or equal to the number of atoms covered by 
 \shape italic
 mask2,
+
 \shape default
  and on output 
 \series bold
@@ -35185,7 +35800,8 @@ corresponds to columns while
 \end_layout
 
 \begin_layout Standard
-Note that for backwards compatibility, output files written with '
+Note that for backwards compatibility,
+ output files written with '
 \series bold
 out <filename>
 \series default
@@ -35200,19 +35816,23 @@ reference "sec:Datafile-Commands"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
  for more details).
- To prevent any of these from taking effect, simply specify '
+ To prevent any of these from taking effect,
+ simply specify '
 \series bold
 header
 \series default
-', '
+',
+ '
 \series bold
 xcol
 \series default
-', and/or '
+',
+ and/or '
 \series bold
 nosquare2d
 \series default
@@ -35224,8 +35844,8 @@ out <filename>
 \end_layout
 
 \begin_layout Standard
-As a simple example, a distance matrix of all CA atoms is generated and
- output to 'distmat.dat'.
+As a simple example,
+ a distance matrix of all CA atoms is generated and output to 'distmat.dat'.
 \end_layout
 
 \begin_layout LyX-Code
@@ -35267,14 +35887,13 @@ mask1
 
 \begin_deeper
 \begin_layout Description
-byatom Report the minimum or maximum distance between atoms in <mask1> or
- between atoms in <mask1> and atoms in <mask2>.
+byatom Report the minimum or maximum distance between atoms in <mask1> or between atoms in <mask1> and atoms in <mask2>.
 \end_layout
 
 \begin_layout Description
-byres Report the minimum or maximum distance between all residue pairs selected
- by <mask1>, or pairs of residues selected by <mask1> and residues selected
- by <mask2> (excluding certain pairs, see 
+byres Report the minimum or maximum distance between all residue pairs selected by <mask1>,
+ or pairs of residues selected by <mask1> and residues selected by <mask2> (excluding certain pairs,
+ see 
 \series bold
 resoffset
 \series default
@@ -35282,9 +35901,8 @@ resoffset
 \end_layout
 
 \begin_layout Description
-bymol Report the minimum or maximum distance between all molecule pairs
- selected by <mask1>, or pairs of molecules selected by <mask1> and molecules
- selected by <mask2>.
+bymol Report the minimum or maximum distance between all molecule pairs selected by <mask1>,
+ or pairs of molecules selected by <mask1> and molecules selected by <mask2>.
 \end_layout
 
 \end_deeper
@@ -35317,8 +35935,8 @@ bymol Report the minimum or maximum distance between all molecule pairs
 \series bold
 byres
 \series default
-, ignore residue pairs if the difference in residue numbers is greater than
- the cutoff (default 1).
+,
+ ignore residue pairs if the difference in residue numbers is greater than the cutoff (default 1).
 \end_layout
 
 \begin_layout Standard
@@ -35330,7 +35948,8 @@ Data Sets Created:
 \series bold
 byatom
 \series default
-, a set containing the minimum or maximum distance for each frame.
+,
+ a set containing the minimum or maximum distance for each frame.
 \end_layout
 
 \begin_layout Description
@@ -35342,8 +35961,9 @@ byres
 \series bold
 b
 \series default
-ymol, a set containing the minimum or maximum distance between the residue/molec
-ule pair specified by the numbers in the aspect, e.g.
+ymol,
+ a set containing the minimum or maximum distance between the residue/molecule pair specified by the numbers in the aspect,
+ e.g.
  '<name>[1_3]' for 
 \series bold
 byres
@@ -35353,8 +35973,7 @@ byres
 
 \end_deeper
 \begin_layout Standard
-Calculate the minimum or maximum distance in Angstroms between atoms or
- residue/molecule pairs.
+Calculate the minimum or maximum distance in Angstroms between atoms or residue/molecule pairs.
 \end_layout
 
 \begin_layout Subsection
@@ -35395,12 +36014,12 @@ geom (
 \series bold
 maskcenter
 \series default
- only) If specified, use geometric center instead of center of mass.
+ only) If specified,
+ use geometric center instead of center of mass.
 \end_layout
 
 \begin_layout Description
-maskcenter Calculate distance from center of masks instead of between each
- atom.
+maskcenter Calculate distance from center of masks instead of between each atom.
 \end_layout
 
 \begin_layout Standard
@@ -35421,17 +36040,18 @@ Data Sets Created:
 
 \end_deeper
 \begin_layout Standard
-Calculate the shortest distance to an image, i.e.
- the distance to a neighboring unit cell, as well as the numbers of the
- atoms involved in the distance.
+Calculate the shortest distance to an image,
+ i.e.
+ the distance to a neighboring unit cell,
+ as well as the numbers of the atoms involved in the distance.
  By default the distance between each atom in <mask1> and <mask2> is considered;
  if 
 \series bold
 maskcenter
 \series default
  is specified the center of the masks is used.
- By convention, the lower atom number is saved as A1 and the higher is saved
- as A2.
+ By convention,
+ the lower atom number is saved as A1 and the higher is saved as A2.
 \end_layout
 
 \begin_layout Subsection
@@ -35441,6 +36061,8 @@ molsurf
 \begin_layout LyX-Code
 molsurf
 \begin_inset Index idx
+range none
+pageformat default
 status open
 
 \begin_layout Plain Layout
@@ -35529,15 +36151,14 @@ literal "true"
 
 \end_inset
 
- of atoms in <mask> (default all atoms if no mask specified) using routines
- from molsurf (originally developed by Paul Beroza) using the probe radius
- specified by 
+ of atoms in <mask> (default all atoms if no mask specified) using routines from molsurf (originally developed by Paul Beroza) using the probe radius specified by 
 \series bold
 probe
 \series default
  (1.4 Å if not specified).
  Note that if GB/VDW radii are not present in the topology file (e.g.
- for PDB files), then PARSE
+ for PDB files),
+ then PARSE
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Sitkoff94"
@@ -35546,9 +36167,10 @@ literal "true"
 \end_inset
 
  radii can be used.
- Also note that this routine only calculate absolute surface areas, i.e.
- it cannot be used to get the contribution of a subset of atoms to overall
- surface area; if such functionality is needed try the 
+ Also note that this routine only calculate absolute surface areas,
+ i.e.
+ it cannot be used to get the contribution of a subset of atoms to overall surface area;
+ if such functionality is needed try the 
 \series bold
 \emph on
 surf
@@ -35558,6 +36180,7 @@ surf
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_surf"
+nolink "false"
 
 \end_inset
 
@@ -35576,8 +36199,7 @@ name "subsec:cpptraj_multidihedral"
 \end_layout
 
 \begin_layout LyX-Code
-multidihedral [<name>] <dihedral types> [resrange <range/mask>] [out <filename>]
- [range360]
+multidihedral [<name>] <dihedral types> [resrange <range/mask>] [out <filename>] [range360]
 \end_layout
 
 \begin_layout LyX-Code
@@ -35585,8 +36207,8 @@ multidihedral [<name>] <dihedral types> [resrange <range/mask>] [out <filename>]
 \end_layout
 
 \begin_layout LyX-Code
-                  Offset -2=<at0><at1> in previous res, -1=<at0> in previous
- res,
+                  Offset -2=<at0><at1> in previous res,
+ -1=<at0> in previous res,
 \end_layout
 
 \begin_layout LyX-Code
@@ -35594,7 +36216,8 @@ multidihedral [<name>] <dihedral types> [resrange <range/mask>] [out <filename>]
 \end_layout
 
 \begin_layout LyX-Code
-                          1=<at3> in next res, 2=<at2><at3> in next res.
+                          1=<at3> in next res,
+ 2=<at2><at3> in next res.
 \end_layout
 
 \begin_layout LyX-Code
@@ -35624,7 +36247,8 @@ multidihedral [<name>] <dihedral types> [resrange <range/mask>] [out <filename>]
 \end_inset
 
 types> Dihedral types to look for.
- Note that chip is 'protein chi', chin is 'nucleic chi'.
+ Note that chip is 'protein chi',
+ chin is 'nucleic chi'.
 \end_layout
 
 \begin_layout Description
@@ -35634,7 +36258,8 @@ types> Dihedral types to look for.
 
 <range/mask>] Residue range to look for dihedrals in.
  Default is all solute residues.
- If a mask expression is given, use residues selected by the mask expression;
+ If a mask expression is given,
+ use residues selected by the mask expression;
  if any part of a residue is selcted it will be used.
 \end_layout
 
@@ -35655,8 +36280,10 @@ types> Dihedral types to look for.
 \begin_inset space ~
 \end_inset
 
-<name>:<a0>:<a1>:<a2>:<a3>[:<offset>] Search for a custom dihedral type
- called <name> using atom names <a0>, <a1>, <a2>, and <a3>.
+<name>:<a0>:<a1>:<a2>:<a3>[:<offset>] Search for a custom dihedral type called <name> using atom names <a0>,
+ <a1>,
+ <a2>,
+ and <a3>.
 \begin_inset Separator latexpar
 \end_inset
 
@@ -35665,8 +36292,12 @@ types> Dihedral types to look for.
 
 \begin_deeper
 \begin_layout Standard
-Offset: -2=<a0><a1> in previous res, -1=<a0> in previous res, 0=All <aX>
- in single res, 1=<a3> in next res, 2=<a2><a3> in next res.
+Offset:
+ -2=<a0><a1> in previous res,
+ -1=<a0> in previous res,
+ 0=All <aX> in single res,
+ 1=<a3> in next res,
+ 2=<a2><a3> in next res.
 \end_layout
 
 \end_deeper
@@ -35680,7 +36311,9 @@ DataSets Generated:
 \end_inset
 
 type>]:<#> Aspect corresponds to the dihedral type name (e.g.
- [phi], [psi], etc).
+ [phi],
+ [psi],
+ etc).
  The index is the residue number.
 \end_layout
 
@@ -35697,13 +36330,13 @@ run
 
 \begin_layout Standard
 Calculate specified dihedral angle types for residues in given range/mask.
- By default, dihedral angles are identified based on standard Amber atom
- names.
- The resulting data sets will have aspect equal to [<dihedral type>] and
- index equal to residue #.
- To differentiate the chi angle, chip is used for proteins and chin for
- nucleic acids.
- For example, to calculate all phi/psi dihedrals for residues 6 to 9:
+ By default,
+ dihedral angles are identified based on standard Amber atom names.
+ The resulting data sets will have aspect equal to [<dihedral type>] and index equal to residue #.
+ To differentiate the chi angle,
+ chip is used for proteins and chin for nucleic acids.
+ For example,
+ to calculate all phi/psi dihedrals for residues 6 to 9:
 \end_layout
 
 \begin_layout LyX-Code
@@ -35711,8 +36344,10 @@ multidihedral MyTorsions phi psi resrange 6-9 out PhiPsi_6-9.dat
 \end_layout
 
 \begin_layout Standard
-This will generate data sets named MyTorsions[phi]:6, MyTorsions[psi]:6,
- MyTorsions[phi]:7, etc.
+This will generate data sets named MyTorsions[phi]:6,
+ MyTorsions[psi]:6,
+ MyTorsions[phi]:7,
+ etc.
  Dihedrals other than those defined in 
 \series bold
 <dihedral types>
@@ -35723,8 +36358,10 @@ dihtype
 \series default
 .
  For example to create a custom dihedral type called chi1 using atoms N,
- CA, CB, and CG (all in the same residue), then search for and calculate
- the dihedral in all residues:
+ CA,
+ CB,
+ and CG (all in the same residue),
+ then search for and calculate the dihedral in all residues:
 \end_layout
 
 \begin_layout LyX-Code
@@ -35740,8 +36377,7 @@ multipucker [<name>] [<pucker types>] [out <filename>] [resrange <range>]
 \end_layout
 
 \begin_layout LyX-Code
-            [altona|cremer] [puckertype <name>:<a0>:<a1>:<a2>:<a3>:<a4>[:<a5>]
- ...]
+            [altona|cremer] [puckertype <name>:<a0>:<a1>:<a2>:<a3>:<a4>[:<a5>] ...]
 \end_layout
 
 \begin_layout LyX-Code
@@ -35792,9 +36428,11 @@ types> Pucker types to look for.
 \begin_inset space ~
 \end_inset
 
-<name>:<a0>:<a1>:<a2>:<a3>:<a4>[:<a5>] Search for a custom pucker type called
- <name> using atom names <a0>, <a1>, <a2>, <a3>, and <a4> (also <a5> for
- 6 atom puckers).
+<name>:<a0>:<a1>:<a2>:<a3>:<a4>[:<a5>] Search for a custom pucker type called <name> using atom names <a0>,
+ <a1>,
+ <a2>,
+ <a3>,
+ and <a4> (also <a5> for 6 atom puckers).
 \end_layout
 
 \begin_layout Description
@@ -35857,7 +36495,9 @@ DataSets Generated:
 \end_inset
 
 type>]:<#> Aspect corresponds to the pucker type name (e.g.
- [nucleic], [furanose], etc).
+ [nucleic],
+ [furanose],
+ etc).
  The index is the residue number.
 \end_layout
 
@@ -35900,16 +36540,17 @@ run
 
 \begin_layout Standard
 Calculate specified pucker types for residues in given range.
- By default, puckers are identified based on standard Amber atom names.
- The resulting data sets will have aspect equal to [<pucker type>] and index
- equal to residue #.
- In order to be identified as a pucker, all consecutive atoms in the pucker
- must be bonded, and the last atom of the pucker must be bonded to the first.
+ By default,
+ puckers are identified based on standard Amber atom names.
+ The resulting data sets will have aspect equal to [<pucker type>] and index equal to residue #.
+ In order to be identified as a pucker,
+ all consecutive atoms in the pucker must be bonded,
+ and the last atom of the pucker must be bonded to the first.
 \end_layout
 
 \begin_layout Standard
-For example, to calculate all nucleic acid ribose puckers for residues 6
- to 9:
+For example,
+ to calculate all nucleic acid ribose puckers for residues 6 to 9:
 \end_layout
 
 \begin_layout LyX-Code
@@ -35917,7 +36558,8 @@ multipucker MyPuckers nucleic resrange 6-9 out Pucker_6-9.dat
 \end_layout
 
 \begin_layout Standard
-This will generate data sets named MyPuckers[nucleic]:6, MyPuckers[nucleic]:7,
+This will generate data sets named MyPuckers[nucleic]:6,
+ MyPuckers[nucleic]:7,
  etc.
  Puckers other than those defined in 
 \series bold
@@ -35928,9 +36570,12 @@ This will generate data sets named MyPuckers[nucleic]:6, MyPuckers[nucleic]:7,
 puckertype
 \series default
 .
- For example to create a custom pucker type called furanoid using atoms
- C2, C3, C4, C5, and O2, then search for and calculate that pucker (with
- amplitudes) using the method of Cremer and Pople in all residues:
+ For example to create a custom pucker type called furanoid using atoms C2,
+ C3,
+ C4,
+ C5,
+ and O2,
+ then search for and calculate that pucker (with amplitudes) using the method of Cremer and Pople in all residues:
 \end_layout
 
 \begin_layout LyX-Code
@@ -35948,8 +36593,7 @@ multivector
 \end_layout
 
 \begin_layout LyX-Code
-multivector [<name>] [resrange <range>] name1 <name1> name2 <name2> [out
- <filename>]
+multivector [<name>] [resrange <range>] name1 <name1> name2 <name2> [out <filename>]
 \end_layout
 
 \begin_layout LyX-Code
@@ -35999,9 +36643,8 @@ name2
 
 \end_deeper
 \begin_layout Standard
-Search for and calculate atomic vectors between atoms named <name1> and
- <name2> in residues specified by the given <range>; each one is equivalent
- to the command '
+Search for and calculate atomic vectors between atoms named <name1> and <name2> in residues specified by the given <range>;
+ each one is equivalent to the command '
 \family typewriter
 \series bold
 vector
@@ -36009,9 +36652,9 @@ vector
  <name1> <name2>
 \family default
 '.
- For example, to calculate all vectors between atoms named 'N' and atoms
- named 'H' in residues 5-20, storing the results in data sets named NH and
- writing to NH.dat:
+ For example,
+ to calculate all vectors between atoms named 'N' and atoms named 'H' in residues 5-20,
+ storing the results in data sets named NH and writing to NH.dat:
 \end_layout
 
 \begin_layout LyX-Code
@@ -36025,6 +36668,8 @@ nastruct
 \begin_layout LyX-Code
 nastruct
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -36069,8 +36714,7 @@ nastruct
 \end_layout
 
 \begin_layout LyX-Code
-         [axisnameo <name>] [axisnamex <name>] [axisnamey <name>] [axisnamez
- <name>]
+         [axisnameo <name>] [axisnamex <name>] [axisnamey <name>] [axisnamez <name>]
 \end_layout
 
 \begin_layout LyX-Code
@@ -36112,14 +36756,16 @@ name>] Output data set name.
 \begin_inset space ~
 \end_inset
 
-<suffix>] File name suffix for output files; BP.<suffix> for base pair parameters
-, BPstep.<suffix> for base pair step parameters, and Helix.<suffix> for base
- pair step helical parameters.
+<suffix>] File name suffix for output files;
+ BP.<suffix> for base pair parameters,
+ BPstep.<suffix> for base pair step parameters,
+ and Helix.<suffix> for base pair step helical parameters.
  If 
 \series bold
 sscalc
 \series default
- is specified, also SS.<suffix> for parameters of consecutive bases in strands.
+ is specified,
+ also SS.<suffix> for parameters of consecutive bases in strands.
 \end_layout
 
 \begin_layout Description
@@ -36135,20 +36781,21 @@ naout
 \begin_inset space ~
 \end_inset
 
-<ResName>:{A,C,G,T,U}] Attempt to treat residues named <ResName> as if it
- were A, C, G, T, or U; useful for residues with modifications or non-standard
- residue names.
+<ResName>:{A,C,G,T,U}] Attempt to treat residues named <ResName> as if it were A,
+ C,
+ G,
+ T,
+ or U;
+ useful for residues with modifications or non-standard residue names.
  This will only work if enough reference atoms are present in <ResName>.
 \end_layout
 
 \begin_layout Description
-[calcnohb] Calculate parameters between bases in base pairs even if no hydrogen
- bonds present between them.
+[calcnohb] Calculate parameters between bases in base pairs even if no hydrogen bonds present between them.
 \end_layout
 
 \begin_layout Description
-[noframespaces] If specified there will be no spaces between frames in the
- 
+[noframespaces] If specified there will be no spaces between frames in the 
 \series bold
 naout
 \series default
@@ -36161,7 +36808,8 @@ naout
 \end_inset
 
 <file>] Specify a custom nucleic acid base reference.
- One file per custom residue; multiple 'baseref' keywords may be present.
+ One file per custom residue;
+ multiple 'baseref' keywords may be present.
  See below for details.
 \end_layout
 
@@ -36171,7 +36819,8 @@ naout
 \end_inset
 
 {3dna|babcock}] Specify axis conventions for calculating base pair parameters.
- If '3dna' (default), use conventions of 3DNA
+ If '3dna' (default),
+ use conventions of 3DNA
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Lu2003"
@@ -36179,8 +36828,10 @@ literal "true"
 
 \end_inset
 
-; flip Y and Z of complimentary base for antiparallel.
- If 'babcock', use conventions of Babcock et al.
+;
+ flip Y and Z of complimentary base for antiparallel.
+ If 'babcock',
+ use conventions of Babcock et al.
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Babcock94"
@@ -36188,13 +36839,13 @@ literal "true"
 
 \end_inset
 
- ; flip Y and Z of complimentary base for antiparallel, flip X and Y for
- parallel.
+ ;
+ flip Y and Z of complimentary base for antiparallel,
+ flip X and Y for parallel.
 \end_layout
 
 \begin_layout Description
-[allhb] Report the total number of hydrogen bonds detected instead of just
- the number of Watson-Crick-Franklin hydrogen bonds.
+[allhb] Report the total number of hydrogen bonds detected instead of just the number of Watson-Crick-Franklin hydrogen bonds.
 \end_layout
 
 \begin_layout Description
@@ -36202,8 +36853,7 @@ literal "true"
 \begin_inset space ~
 \end_inset
 
-<hbcut>] Distance cutoff (in Angstroms) for determining hydrogen bonds between
- bases (default 3.5).
+<hbcut>] Distance cutoff (in Angstroms) for determining hydrogen bonds between bases (default 3.5).
 \end_layout
 
 \begin_layout Description
@@ -36211,13 +36861,12 @@ literal "true"
 \begin_inset space ~
 \end_inset
 
-<origincut>] Distance cutoff (in Angstroms) between base pair axis origins
- for determining which bases are eligible for base-pairing (default 2.5).
+<origincut>] Distance cutoff (in Angstroms) between base pair axis origins for determining which bases are eligible for base-pairing (default 2.5).
 \end_layout
 
 \begin_layout Description
-[altona] Use method of Altona & Sundaralingam to calculate sugar pucker
- (default, see 
+[altona] Use method of Altona & Sundaralingam to calculate sugar pucker (default,
+ see 
 \series bold
 \shape italic
 pucker
@@ -36237,14 +36886,12 @@ pucker
 \end_layout
 
 \begin_layout Description
-[zcut] Distance cutoff (in Angstroms) between base reference axes along
- the Z axis (i.e.
+[zcut] Distance cutoff (in Angstroms) between base reference axes along the Z axis (i.e.
  stagger) for determining base pairing (default 2).
 \end_layout
 
 \begin_layout Description
-[zanglecut] Angle cutoff (in degrees) between base reference Z axes for
- determining base pairing (default 65).
+[zanglecut] Angle cutoff (in degrees) between base reference Z axes for determining base pairing (default 65).
 \end_layout
 
 \begin_layout Description
@@ -36257,7 +36904,8 @@ pucker
 
 \begin_deeper
 \begin_layout Description
-simple Use P-P distance for major groove, O4-O4 distance for minor groove.
+simple Use P-P distance for major groove,
+ O4-O4 distance for minor groove.
  Output to 'BP.<suffix>'.
 \end_layout
 
@@ -36289,8 +36937,7 @@ literal "true"
 \begin_inset space ~
 \end_inset
 
-<arg>] Trajectory argument to pass to base axes trajectory file (can specify
- more than once).
+<arg>] Trajectory argument to pass to base axes trajectory file (can specify more than once).
 \end_layout
 
 \begin_layout Description
@@ -36316,8 +36963,7 @@ literal "true"
 \begin_inset space ~
 \end_inset
 
-<arg>] Trajectory argument to pass to base pair axes trajectory file (can
- specify more than once).
+<arg>] Trajectory argument to pass to base pair axes trajectory file (can specify more than once).
 \end_layout
 
 \begin_layout Description
@@ -36343,8 +36989,7 @@ literal "true"
 \begin_inset space ~
 \end_inset
 
-<arg>] Trajectory argument to pass to base pair step axes trajectory file
- (can specify more than once).
+<arg>] Trajectory argument to pass to base pair step axes trajectory file (can specify more than once).
 \end_layout
 
 \begin_layout Description
@@ -36438,9 +37083,9 @@ pairs
 \end_inset
 
 <b1>-<b2>,...] User specified base pairing.
- Base pairs are specified in a comma-separated list after the 'pairs' keyword
- as <b1>-<b2>, where <b1> and <b2> are the residue numbers of bases in the
- base pair, e.g.
+ Base pairs are specified in a comma-separated list after the 'pairs' keyword as <b1>-<b2>,
+ where <b1> and <b2> are the residue numbers of bases in the base pair,
+ e.g.
  'pairs 1-16,2-15,3-14,4-13'.
  Can specify 'pairs' multiple times.
 \end_layout
@@ -36486,17 +37131,16 @@ Base pairs:
 \end_layout
 
 \begin_layout Description
-<name>[bp]:X Contain 1 if bases are base paired, 0 otherwise.
+<name>[bp]:X Contain 1 if bases are base paired,
+ 0 otherwise.
 \end_layout
 
 \begin_layout Description
-<name>[major]:X (If groovecalc simple) Major groove width calculated between
- P atoms of each base.
+<name>[major]:X (If groovecalc simple) Major groove width calculated between P atoms of each base.
 \end_layout
 
 \begin_layout Description
-<name>[minor]:X (If groovecalc simple) Minor groove width calculated between
- O4 atoms of each base.
+<name>[minor]:X (If groovecalc simple) Minor groove width calculated between O4 atoms of each base.
 \end_layout
 
 \begin_layout Standard
@@ -36532,11 +37176,13 @@ Base pair steps:
 \end_layout
 
 \begin_layout Description
-<name>[major]:X (If groovecalc 3dna) Major groove width, El Hassan and Calladine.
+<name>[major]:X (If groovecalc 3dna) Major groove width,
+ El Hassan and Calladine.
 \end_layout
 
 \begin_layout Description
-<name>[minor]:X (If groovecalc 3dna) Minor groove width, El Hassan and Calladine.
+<name>[minor]:X (If groovecalc 3dna) Minor groove width,
+ El Hassan and Calladine.
 \end_layout
 
 \begin_layout Standard
@@ -36603,22 +37249,37 @@ Note that base pair data sets are not created until base pairing is determined.
 \end_layout
 
 \begin_layout Standard
-Calculate basic nucleic acid (NA) structure parameters for all residues
- in the range specified by 
+Calculate basic nucleic acid (NA) structure parameters for all residues in the range specified by 
 \series bold
 resrange
 \series default
  (or all NA residues if no range specified).
- Residue names are recognized with the following priority: standard Amber
- residue names DA, DG, DC, DT, RA, RG, RC, and RU; 3 letter residue names
- ADE, GUA, CYT, THY, and URA; and finally 1 letter residue names A, G, C,
- T, and U.
+ Residue names are recognized with the following priority:
+ standard Amber residue names DA,
+ DG,
+ DC,
+ DT,
+ RA,
+ RG,
+ RC,
+ and RU;
+ 3 letter residue names ADE,
+ GUA,
+ CYT,
+ THY,
+ and URA;
+ and finally 1 letter residue names A,
+ G,
+ C,
+ T,
+ and U.
  Non-standard/modified NA bases can be recognized by using the 
 \series bold
 resmap
 \series default
  keyword.
- For example, to make 
+ For example,
+ to make 
 \shape italic
 cpptraj
 \shape default
@@ -36634,19 +37295,18 @@ The
 \series bold
 resmap
 \series default
- keyword can be specified multiple times, but only one mapping per unique
- residue name is allowed.
+ keyword can be specified multiple times,
+ but only one mapping per unique residue name is allowed.
  Note that 
 \series bold
 resmap
 \series default
- may fail if the residue is missing heavy atoms normally present in the
- specified base type.
+ may fail if the residue is missing heavy atoms normally present in the specified base type.
 \end_layout
 
 \begin_layout Standard
-Base pairs are determined either once from the first frame or from a reference
- structure, or can be determined each frame if 
+Base pairs are determined either once from the first frame or from a reference structure,
+ or can be determined each frame if 
 \series bold
 allframes
 \series default
@@ -36661,17 +37321,17 @@ pairs
 \series default
  keywords.
  Base pairing is determined first by base reference axis origin distance,
- then by stagger, then by angle between base Z axes, then finally by hydrogen
- bonding (at least one hydrogen bond must be present).
+ then by stagger,
+ then by angle between base Z axes,
+ then finally by hydrogen bonding (at least one hydrogen bond must be present).
  Base pair parameters will only be written for determined base pairs.
  Both Watson-Crick and other types of base pairing can be detected.
- Note that although all possible hydrogen bonds are searched for, only WC
- hydrogen bonds are reported in the BP.<suffix> file.
+ Note that although all possible hydrogen bonds are searched for,
+ only WC hydrogen bonds are reported in the BP.<suffix> file.
 \end_layout
 
 \begin_layout Standard
-The procedure used to calculate NA structural parameters is the same as
- 3DNA
+The procedure used to calculate NA structural parameters is the same as 3DNA
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Lu2003"
@@ -36679,7 +37339,8 @@ literal "true"
 
 \end_inset
 
-, with algorithms adapted from Babcok et al.
+,
+ with algorithms adapted from Babcok et al.
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Babcock94"
@@ -36696,7 +37357,8 @@ literal "true"
 \end_inset
 
 .
- Given the same base pairs are determined, 
+ Given the same base pairs are determined,
+ 
 \shape italic
 cpptraj
 \shape default
@@ -36717,22 +37379,39 @@ Calculated NA structure parameters are written to three separate files,
 naout
 \series default
 .
- Base pair parameters (shear, stretch, stagger, buckle, propeller twist,
- opening, # WC hydrogen bonds, base pairing, and simple groove widths) are
- written to BP.<suffix>, along with the number of WC hydrogen bonds detected.
- Base pair step parameters (shift, slide, rise, tilt, roll, twist, Zp, and
- El Hassan and Calladine groove widths) are written to BPstep.<suffix>, and
- helical parameters (X-displacement, Y-displacement, rise, inclination,
- tip, and twist) are written to Helix.<suffix>.
+ Base pair parameters (shear,
+ stretch,
+ stagger,
+ buckle,
+ propeller twist,
+ opening,
+ # WC hydrogen bonds,
+ base pairing,
+ and simple groove widths) are written to BP.<suffix>,
+ along with the number of WC hydrogen bonds detected.
+ Base pair step parameters (shift,
+ slide,
+ rise,
+ tilt,
+ roll,
+ twist,
+ Zp,
+ and El Hassan and Calladine groove widths) are written to BPstep.<suffix>,
+ and helical parameters (X-displacement,
+ Y-displacement,
+ rise,
+ inclination,
+ tip,
+ and twist) are written to Helix.<suffix>.
  If 
 \series bold
 noheader
 \series default
  is specified a header will not be written to the output files.
- Note that although base puckering is calculated, it is not written to an
- output file by default.
- You can output pucker to a file via the create or write/writedata commands
- after the data has been generated, e.g.:
+ Note that although base puckering is calculated,
+ it is not written to an output file by default.
+ You can output pucker to a file via the create or write/writedata commands after the data has been generated,
+ e.g.:
 \end_layout
 
 \begin_layout LyX-Code
@@ -36748,9 +37427,8 @@ writedata NApucker.dat NA[pucker]
 \end_layout
 
 \begin_layout Standard
-Note that while the underlying procedure is geared towards calculating parameter
-s for base pairs, the code can be made to calculate parameters between consecuti
-ve bases in single strands by specifying 
+Note that while the underlying procedure is geared towards calculating parameters for base pairs,
+ the code can be made to calculate parameters between consecutive bases in single strands by specifying 
 \series bold
 sscalc
 \series default
@@ -36758,35 +37436,42 @@ sscalc
 \end_layout
 
 \begin_layout Standard
-Base axes, base pair axes, and base pair step axes can be written to trajectory
- files using the 
+Base axes,
+ base pair axes,
+ and base pair step axes can be written to trajectory files using the 
 \series bold
 axesout
 \series default
-, 
+,
+ 
 \series bold
 bpaxesout
 \series default
-, and 
+,
+ and 
 \series bold
 stepaxesout
 \series default
  and related keywords.
- The axes are written using 4 points: an origin, and X Y and Z which are
- bonded to the origin.
+ The axes are written using 4 points:
+ an origin,
+ and X Y and Z which are bonded to the origin.
  The names of these pseudo atoms can be changed using the 
 \series bold
 axisnameo
 \series default
-, 
+,
+ 
 \series bold
 axisnamex
 \series default
-, 
+,
+ 
 \series bold
 axisnamey
 \series default
-, and 
+,
+ and 
 \series bold
 axisnamez
 \series default
@@ -36803,8 +37488,9 @@ Users can now specify
 baseref <file>
 \series default
  to load a custom nucleic acid base reference.
- The base reference files are white-space delimited, begin with the line
- NASTRUCT REFERENCE, and have the following format:
+ The base reference files are white-space delimited,
+ begin with the line NASTRUCT REFERENCE,
+ and have the following format:
 \end_layout
 
 \begin_layout LyX-Code
@@ -36833,9 +37519,10 @@ There is a line for each reference atom.
 \begin_inset space ~
 \end_inset
 
-character> Used to identify the underlying base type: A G C T or U.
- If none of these, it will be considered an unknown residue (which just
- means WC hydrogen bonding will not be identified).
+character> Used to identify the underlying base type:
+ A G C T or U.
+ If none of these,
+ it will be considered an unknown residue (which just means WC hydrogen bonding will not be identified).
 \end_layout
 
 \begin_layout Description
@@ -36878,7 +37565,11 @@ name> A reference atom name.
 \end_inset
 
 type> Denotes if and how the atom participates in hydrogen bonding.
- Can be 'd'onor, 'a'cceptor, or 'n'one (or the numbers 1, 2, 0 respectively).
+ Can be 'd'onor,
+ 'a'cceptor,
+ or 'n'one (or the numbers 1,
+ 2,
+ 0 respectively).
  Only the first character of the word actually matters.
 \end_layout
 
@@ -36978,8 +37669,7 @@ nativecontacts [<mask1> [<mask2>]] [writecontacts <outfile>] [resout <resfile>]
 \end_layout
 
 \begin_layout LyX-Code
-               [resoffset <n>] [contactpdb <file>] [pdbcut <cut>] [mindist]
- [maxdist]
+               [resoffset <n>] [contactpdb <file>] [pdbcut <cut>] [mindist] [maxdist]
 \end_layout
 
 \begin_layout LyX-Code
@@ -37040,8 +37730,7 @@ nativecontacts [<mask1> [<mask2>]] [writecontacts <outfile>] [resout <resfile>]
 \begin_inset space ~
 \end_inset
 
-<cut>] Distance cutoff for determining native contacts in Angstroms (default
- 7.0 Ang).
+<cut>] Distance cutoff for determining native contacts in Angstroms (default 7.0 Ang).
 \end_layout
 
 \begin_layout Description
@@ -37053,8 +37742,8 @@ nativecontacts [<mask1> [<mask2>]] [writecontacts <outfile>] [resout <resfile>]
 \end_layout
 
 \begin_layout Description
-[includesolvent] By default solvent molecules are ignored; this will explicitly
- include solvent molecules.
+[includesolvent] By default solvent molecules are ignored;
+ this will explicitly include solvent molecules.
 \end_layout
 
 \begin_layout Description
@@ -37102,8 +37791,7 @@ refindex
 \series bold
 byresidue
 \series default
- only) Ignore contacts between residues spaced less than <n> residues apart
- in sequence.
+ only) Ignore contacts between residues spaced less than <n> residues apart in sequence.
 \end_layout
 
 \begin_layout Description
@@ -37111,8 +37799,7 @@ byresidue
 \begin_inset space ~
 \end_inset
 
-<file>] Write PDB with B-factor column containing relative contact strength
- for native contacts (strongest is 100.0).
+<file>] Write PDB with B-factor column containing relative contact strength for native contacts (strongest is 100.0).
 \end_layout
 
 \begin_layout Description
@@ -37124,7 +37811,8 @@ byresidue
 \series bold
 contactpdb
 \series default
-, only write contacts with relative contact strength greater than 
+,
+ only write contacts with relative contact strength greater than 
 \series bold
 <cut>
 \series default
@@ -37132,13 +37820,13 @@ contactpdb
 \end_layout
 
 \begin_layout Description
-[mindist] If specified, determine the minimum distance between any atoms
- in the mask(s).
+[mindist] If specified,
+ determine the minimum distance between any atoms in the mask(s).
 \end_layout
 
 \begin_layout Description
-[maxdist] If specified, determine the maximum distance between any atoms
- in the mask(s).
+[maxdist] If specified,
+ determine the maximum distance between any atoms in the mask(s).
 \end_layout
 
 \begin_layout Description
@@ -37154,10 +37842,9 @@ contactpdb
 \end_layout
 
 \begin_layout Description
-[map] Calculate matrices of native contacts ([nativemap]) and non-native
- contacts ([nonnatmap]).
- These matrices are normalized by the total number of frames, so that a
- value of 1.0 means 
+[map] Calculate matrices of native contacts ([nativemap]) and non-native contacts ([nonnatmap]).
+ These matrices are normalized by the total number of frames,
+ so that a value of 1.0 means 
 \begin_inset Quotes eld
 \end_inset
 
@@ -37170,8 +37857,8 @@ contact always present
 \series bold
 byresidue
 \series default
- specified, the values for each individual atom pair are summed over the
- residues they belong to (this means for 
+ specified,
+ the values for each individual atom pair are summed over the residues they belong to (this means for 
 \series bold
 byresidue
 \series default
@@ -37183,13 +37870,12 @@ byresidue
 \begin_inset space ~
 \end_inset
 
-<mapfile>] Write native/non-native matrices to 'native.<mapfile>' and 'nonnative.<
-mapfile>' respectively.
+<mapfile>] Write native/non-native matrices to 'native.<mapfile>' and 'nonnative.<mapfile>' respectively.
 \end_layout
 
 \begin_layout Description
-[series] Calculate native contact time series data, 1 for contact present
- and 0 otherwise.
+[series] Calculate native contact time series data,
+ 1 for contact present and 0 otherwise.
 \end_layout
 
 \begin_layout Description
@@ -37201,7 +37887,8 @@ mapfile>' respectively.
 \end_layout
 
 \begin_layout Description
-[savenonnative] Save non-native contacts; 
+[savenonnative] Save non-native contacts;
+ 
 \series bold
 series
 \series default
@@ -37227,8 +37914,7 @@ skipnative
 \begin_inset space ~
 \end_inset
 
-<file>] Write PDB with B-factor column containing relative contact strength
- for non-native contacts (strongest is 100.0).
+<file>] Write PDB with B-factor column containing relative contact strength for non-native contacts (strongest is 100.0).
 \end_layout
 
 \end_deeper
@@ -37245,7 +37931,8 @@ skipnative
 \begin_inset space ~
 \end_inset
 
-sum} Create contacts time series by residue; 
+sum} Create contacts time series by residue;
+ 
 \series bold
 series
 \series default
@@ -37275,7 +37962,9 @@ sum The sum of all individual contacts is recorded for the residue pair.
 
 \end_deeper
 \begin_layout Description
-[skipnative] If specified, skip native contacts determination, i.e.
+[skipnative] If specified,
+ skip native contacts determination,
+ i.e.
  treat all sonctacts as non-native contacts.
  Implies 
 \series bold
@@ -37336,18 +38025,21 @@ native
 \begin_inset Quotes erd
 \end_inset
 
- contacts as determined by a simple distance cut-off, i.e.
+ contacts as determined by a simple distance cut-off,
+ i.e.
  any atoms which are closer than 
 \series bold
 <cut>
 \series default
- in the specified reference frame (the first frame if no reference specified)
- are considered a native contact.
- If one mask is provided, contacts are looked for within 
+ in the specified reference frame (the first frame if no reference specified) are considered a native contact.
+ If one mask is provided,
+ contacts are looked for within 
 \series bold
 <mask1>
 \series default
-; if two masks are provided, only contacts between atoms in 
+;
+ if two masks are provided,
+ only contacts between atoms in 
 \series bold
 <mask1>
 \series default
@@ -37370,19 +38062,18 @@ skipnative
 \series bold
 series
 \series default
- keyword; these can be further consolidated by residue using the 
+ keyword;
+ these can be further consolidated by residue using the 
 \series bold
 resseries
 \series default
  keyword.
- When using <resseries> the data set index is calculated as (r2 * nres)
- + r1 so that indices can be matched between native/non-native contact pairs.
+ When using <resseries> the data set index is calculated as (r2 * nres) + r1 so that indices can be matched between native/non-native contact pairs.
  Non-native residue contact legends have an nn_ prefix.
 \end_layout
 
 \begin_layout Standard
-Native contacts that are found are written to the file specified by writecontact
-s (or STDOUT) with format:
+Native contacts that are found are written to the file specified by writecontacts (or STDOUT) with format:
 \end_layout
 
 \begin_layout LyX-Code
@@ -37400,16 +38091,19 @@ Contact
 \family typewriter
 Nframes
 \family default
- is the number of frames the contact is present, 
+ is the number of frames the contact is present,
+ 
 \family typewriter
 Frac.
 
 \family default
- is the total fraction of frames the contact is present, 
+ is the total fraction of frames the contact is present,
+ 
 \family typewriter
 Avg
 \family default
- is the average distance of the contact when present, and 
+ is the average distance of the contact when present,
+ and 
 \family typewriter
 Stdev
 \family default
@@ -37418,8 +38112,7 @@ Stdev
 \series bold
 resout
 \series default
- is specified the total fraction of contacts is printed for all residue
- pairs having native contacts with format:
+ is specified the total fraction of contacts is printed for all residue pairs having native contacts with format:
 \end_layout
 
 \begin_layout LyX-Code
@@ -37431,15 +38124,18 @@ Where
 \family typewriter
 #Res1
 \family default
- is the first residue number, 
+ is the first residue number,
+ 
 \family typewriter
 #Res2
 \family default
- is the second residue number, 
+ is the second residue number,
+ 
 \family typewriter
 TotalFrac
 \family default
- is the total fraction of contacts for the residue pair, and 
+ is the total fraction of contacts for the residue pair,
+ and 
 \family typewriter
 Contacts
 \family default
@@ -37448,8 +38144,8 @@ Contacts
 \family typewriter
 TotalFrac
 \family default
- is calculated for each pair as the sum of each contact involving that pair
- divided by the total number of frames, it is possible to have 
+ is calculated for each pair as the sum of each contact involving that pair divided by the total number of frames,
+ it is possible to have 
 \family typewriter
 TotalFrac
 \family default
@@ -37457,11 +38153,11 @@ TotalFrac
 \end_layout
 
 \begin_layout Standard
-During trajectory processing, non-native contacts (i.e.
- any pair satisfying the distance cut-off which is not already a native
- contact) are also searched for.
- The time series for native contacts can be saved as well, with 1 for contact
- present and 0 otherwise (similar to the 
+During trajectory processing,
+ non-native contacts (i.e.
+ any pair satisfying the distance cut-off which is not already a native contact) are also searched for.
+ The time series for native contacts can be saved as well,
+ with 1 for contact present and 0 otherwise (similar to the 
 \series bold
 \emph on
 hbond
@@ -37472,6 +38168,7 @@ hbond
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-lifetime"
+nolink "false"
 
 \end_inset
 
@@ -37484,8 +38181,9 @@ Contact maps (matrices) are generated for native and non-native contacts.
 \series bold
 byresidue
 \series default
- is specified, contact maps are summed over residues, and contacts between
- residues spaced 
+ is specified,
+ contact maps are summed over residues,
+ and contacts between residues spaced 
 \series bold
 <resoffset>
 \series default
@@ -37497,15 +38195,13 @@ If
 \series bold
 contactpdb
 \series default
- is specified a PDB is generated containing relative contact strengths in
- the B-factor column.
- The relative contact strength is normalized so that a value of 100 means
- that atom participated in the most contacts with other atoms.
+ is specified a PDB is generated containing relative contact strengths in the B-factor column.
+ The relative contact strength is normalized so that a value of 100 means that atom participated in the most contacts with other atoms.
 \end_layout
 
 \begin_layout Standard
-Example command looking for contacts between residues 210 to 260 and residue
- named NDP, using reference structure 'FtuFabI.WT.pdb' to define native contacts:
+Example command looking for contacts between residues 210 to 260 and residue named NDP,
+ using reference structure 'FtuFabI.WT.pdb' to define native contacts:
 \end_layout
 
 \begin_layout LyX-Code
@@ -37562,6 +38258,8 @@ name "subsec:cpptraj_outtraj"
 \begin_layout LyX-Code
 outtraj
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -37595,6 +38293,7 @@ args] Output trajectory arguments (see
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-trajout"
+nolink "false"
 
 \end_inset
 
@@ -37622,8 +38321,7 @@ max
 \begin_inset space ~
 \end_inset
 
-<max>] Only write frames to <filename> if values in <dataset> for those
- frames are between <min> and <max>.
+<max>] Only write frames to <filename> if values in <dataset> for those frames are between <min> and <max>.
  Can be specified for one or more data sets.
 \end_layout
 
@@ -37635,10 +38333,12 @@ The outtraj command is similar in function to
 trajout
 \series default
 \emph default
-, and takes all of the same arguments.
- However, instead of writing a trajectory frame after all actions are complete
- outtraj writes the trajectory frame at its position in the Action queue.
- For example, given the input:
+,
+ and takes all of the same arguments.
+ However,
+ instead of writing a trajectory frame after all actions are complete outtraj writes the trajectory frame at its position in the Action queue.
+ For example,
+ given the input:
 \end_layout
 
 \begin_layout LyX-Code
@@ -37662,17 +38362,18 @@ outtraj AfterRmsd.crd
 \end_layout
 
 \begin_layout Standard
-three trajectories will be written: output.crd, BeforeRmsd.crd, and AfterRmsd.crd.
- The output.crd and AfterRmsd.crd trajectories will be identical, but the
- BeforeRmsd.crd trajectory will contain the coordinates of mdcrd.crd before
- they are RMS-fit.
+three trajectories will be written:
+ output.crd,
+ BeforeRmsd.crd,
+ and AfterRmsd.crd.
+ The output.crd and AfterRmsd.crd trajectories will be identical,
+ but the BeforeRmsd.crd trajectory will contain the coordinates of mdcrd.crd before they are RMS-fit.
 \end_layout
 
 \begin_layout Standard
-The maxmin keyword can be used to restrict output using one more more data
- sets.
- For example, to only write frames for which the RMSD value is between 0.7
- and 0.8:
+The maxmin keyword can be used to restrict output using one more more data sets.
+ For example,
+ to only write frames for which the RMSD value is between 0.7 and 0.8:
 \end_layout
 
 \begin_layout LyX-Code
@@ -37697,12 +38398,16 @@ pairdist out <filename> mask <mask> [delta <resolution>]
 
 \begin_layout Standard
 Calculate pair distribution function.
- In the following, defaults are given in parentheses.
+ In the following,
+ defaults are given in parentheses.
  The 
 \series bold
 out
 \series default
- keyword specifies output file for histogram: distance, P(r), s(P(r)).
+ keyword specifies output file for histogram:
+ distance,
+ P(r),
+ s(P(r)).
  The 
 \series bold
 mask
@@ -37721,8 +38426,7 @@ pairwise
 \end_layout
 
 \begin_layout LyX-Code
-pairwise [<name>] [<mask>] [out <filename>] [cuteelec <ecut>] [cutevdw <vcut>]
- 	
+pairwise [<name>] [<mask>] [out <filename>] [cuteelec <ecut>] [cutevdw <vcut>] 	
 \end_layout
 
 \begin_layout LyX-Code
@@ -37734,8 +38438,7 @@ pairwise [<name>] [<mask>] [out <filename>] [cuteelec <ecut>] [cutevdw <vcut>]
 \end_layout
 
 \begin_layout LyX-Code
-     	[eout <eout file>] [pdbout <pdb file>] [scalepdbe] [printmode {only|or|and
-|}]
+     	[eout <eout file>] [pdbout <pdb file>] [scalepdbe] [printmode {only|or|and|}]
 \begin_inset Separator latexpar
 \end_inset
 
@@ -37744,8 +38447,8 @@ pairwise [<name>] [<mask>] [out <filename>] [cuteelec <ecut>] [cutevdw <vcut>]
 
 \begin_deeper
 \begin_layout Description
-[<name>] Data set name; van der Waals energy will get aspect [EVDW] and
- electrostatic energy will get aspect [EELEC].
+[<name>] Data set name;
+ van der Waals energy will get aspect [EVDW] and electrostatic energy will get aspect [EELEC].
 \end_layout
 
 \begin_layout Description
@@ -37810,8 +38513,7 @@ refindex
 \begin_inset space ~
 \end_inset
 
-<cut>] Only report interaction EELEC (or delta EELEC) if absolute value
- is greater than <ecut> (default 1.0 kcal/mol).
+<cut>] Only report interaction EELEC (or delta EELEC) if absolute value is greater than <ecut> (default 1.0 kcal/mol).
 \end_layout
 
 \begin_layout Description
@@ -37819,8 +38521,7 @@ refindex
 \begin_inset space ~
 \end_inset
 
-<cutv>] Only report interaction EVDW (or delta EVDW) if absolute value is
- greater than <vcut> (default 1.0 kcal/mol).
+<cutv>] Only report interaction EVDW (or delta EVDW) if absolute value is greater than <vcut> (default 1.0 kcal/mol).
 \end_layout
 
 \begin_layout Description
@@ -37836,8 +38537,7 @@ mol2
 \begin_inset space ~
 \end_inset
 
-prefix>] Write out mol2 containing only atom pairs which satisfy <ecut>
- and <vcut>.
+prefix>] Write out mol2 containing only atom pairs which satisfy <ecut> and <vcut>.
 \end_layout
 
 \begin_layout Description
@@ -37861,8 +38561,7 @@ map>] Write out interaction EVDW (or delta EVDW) matrix to file <vdw map>.
 \begin_inset space ~
 \end_inset
 
-map>] Write out interaction EELEC (or delta EELEC) matrix to file <elec
- map>.
+map>] Write out interaction EELEC (or delta EELEC) matrix to file <elec map>.
 \end_layout
 
 \begin_layout Description
@@ -37874,8 +38573,7 @@ map>] Write out interaction EELEC (or delta EELEC) matrix to file <elec
 \begin_inset space ~
 \end_inset
 
-file>] Print average interaction EVDW|EELEC (or average delta EVDW|EELC)
- to <avg file>.
+file>] Print average interaction EVDW|EELEC (or average delta EVDW|EELC) to <avg file>.
 \end_layout
 
 \begin_layout Description
@@ -37924,22 +38622,26 @@ Data Sets Created:
 
 \end_deeper
 \begin_layout Standard
-This action has two related functions: 1) Calculate pairwise (i.e.
+This action has two related functions:
+ 1) Calculate pairwise (i.e.
  non-bonded) energy (in kcal/mol) for atoms in 
 \series bold
 <mask>
 \series default
-, or 2) Compare pairwise energy of frames to a reference frame.
+,
+ or 2) Compare pairwise energy of frames to a reference frame.
  This calculation does use an exclusion list but is not periodic.
 \end_layout
 
 \begin_layout Standard
-When comparing to a reference frame, the 
+When comparing to a reference frame,
+ the 
 \series bold
 eout
 \series default
  file will contain the differences for each individual interaction (i.e.
- Eref - Eframe), otherwise the 
+ Eref - Eframe),
+ otherwise the 
 \series bold
 eout
 \series default
@@ -37952,21 +38654,20 @@ cuteelc
 \series bold
 cutevdw
 \series default
- keywords can be used to restrict printing of individual interactions to
- those for which the absolute value is above a cutoff.
- The VMAP and EMAP matrix elements will contain these values as well (difference
-s for reference, absolute value otherwise) averaged over all frames.
+ keywords can be used to restrict printing of individual interactions to those for which the absolute value is above a cutoff.
+ The VMAP and EMAP matrix elements will contain these values as well (differences for reference,
+ absolute value otherwise) averaged over all frames.
  The 
 \series bold
 avgout
 \series default
- file will contain only these values averaged over all frames that satisfy
- the cutoffs.
+ file will contain only these values averaged over all frames that satisfy the cutoffs.
  The 
 \series bold
 printmode
 \series default
- keyword controls when the average energies are written: 
+ keyword controls when the average energies are written:
+ 
 \series bold
 only
 \series default
@@ -37975,13 +38676,12 @@ only
 \series bold
 or
 \series default
- means that both energy components will be printed if either satistfy a
- cutoff, and 
+ means that both energy components will be printed if either satistfy a cutoff,
+ and 
 \series bold
 and
 \series default
- means that both energy components will be written only if both satisfy
- the cutoffs.
+ means that both energy components will be written only if both satisfy the cutoffs.
 \end_layout
 
 \begin_layout Standard
@@ -37989,17 +38689,15 @@ The
 \series bold
 cutout
 \series default
- keyword can be used to write out MOL2 files each frame named '<cut mol2
- prefix>.evdw.mol2.X' and '<cut mol2 prefix>.eelec.mol2.X' (where X is the frame
- number) containing only atoms with energies that satisfy the cutoffs.
- Similarly, the 
+ keyword can be used to write out MOL2 files each frame named '<cut mol2 prefix>.evdw.mol2.X' and '<cut mol2 prefix>.eelec.mol2.X' (where X is the frame number) containing only atoms with energies that satisfy the cutoffs.
+ Similarly,
+ the 
 \series bold
 pdbout
 \series default
  keyword can be used to write out a PDB file (with 1 MODEL per frame).
- The occupancy and B-factor columns will contain the total van der Waals
- and electrostatic energy for each atom if cutoffs are satisfied, or 0.0
- otherwise.
+ The occupancy and B-factor columns will contain the total van der Waals and electrostatic energy for each atom if cutoffs are satisfied,
+ or 0.0 otherwise.
 \end_layout
 
 \begin_layout Subsection
@@ -38048,7 +38746,8 @@ name
 \end_layout
 
 \begin_layout Description
-<dsname>[evec] Eigenvectors (3x3 matrix, row-major).
+<dsname>[evec] Eigenvectors (3x3 matrix,
+ row-major).
 \end_layout
 
 \begin_layout Description
@@ -38057,17 +38756,18 @@ name
 
 \end_deeper
 \begin_layout Standard
-Determine principal axes of each frame determined by diagonalization of
- the inertial matrix from the coordinates of the specified atoms.
+Determine principal axes of each frame determined by diagonalization of the inertial matrix from the coordinates of the specified atoms.
  At least one of 
 \series bold
 dorotation
 \series default
-, 
+,
+ 
 \series bold
 out
 \series default
-, or 
+,
+ or 
 \series bold
 name
 \series default
@@ -38088,28 +38788,32 @@ vector
 principal
 \series default
 ').
- If out is specified the eigenvectors and eigenvalues will be written for
- each frame N with format:
+ If out is specified the eigenvectors and eigenvalues will be written for each frame N with format:
 \end_layout
 
 \begin_layout LyX-Code
-<N> EIGENVALUES: <EX> <EY> <EZ>
+<N> EIGENVALUES:
+ <EX> <EY> <EZ>
 \end_layout
 
 \begin_layout LyX-Code
-<N> EIGENVECTOR 0: <Xx> <Xy> <Xz>
+<N> EIGENVECTOR 0:
+ <Xx> <Xy> <Xz>
 \end_layout
 
 \begin_layout LyX-Code
-<N> EIGENVECTOR 1: <Yx> <Yy> <Yz>
+<N> EIGENVECTOR 1:
+ <Yx> <Yy> <Yz>
 \end_layout
 
 \begin_layout LyX-Code
-<N> EIGENVECTOR 2: <Zx> <Zy> <Zz>
+<N> EIGENVECTOR 2:
+ <Zx> <Zy> <Zz>
 \end_layout
 
 \begin_layout Standard
-NOTE: The eigenvector 3x3 matrix data set could subsequently be used e.g.
+NOTE:
+ The eigenvector 3x3 matrix data set could subsequently be used e.g.
  with the 
 \series bold
 \emph on
@@ -38120,7 +38824,8 @@ rotate
 \end_layout
 
 \begin_layout Standard
-Example: Align system (residues 1-76) along principle axes:
+Example:
+ Align system (residues 1-76) along principle axes:
 \end_layout
 
 \begin_layout LyX-Code
@@ -38147,8 +38852,7 @@ name "subsec:cpptraj-projection"
 \end_layout
 
 \begin_layout LyX-Code
-projection [<name>] evecs <dataset name> [out <outfile>] [beg <beg>] [end
- <end>]
+projection [<name>] evecs <dataset name> [out <outfile>] [beg <beg>] [end <end>]
 \end_layout
 
 \begin_layout LyX-Code
@@ -38205,8 +38909,8 @@ name> Data set containing eigenvectors (modes).
 \end_layout
 
 \begin_layout Description
-[<mask>] (Not dihedral covariance) Mask of atoms to use in projection; MUST
- CORRESPOND TO HOW EIGENVECTORS WERE GENERATED.
+[<mask>] (Not dihedral covariance) Mask of atoms to use in projection;
+ MUST CORRESPOND TO HOW EIGENVECTORS WERE GENERATED.
 \end_layout
 
 \begin_layout Description
@@ -38231,10 +38935,11 @@ arg>] (Dihedral covariance only) Dihedral data sets to use in projection;
 \begin_inset space ~
 \end_inset
 
-arg>] (Data covariance only, e.g.
+arg>] (Data covariance only,
+ e.g.
  from TICA).
- 1D data sets to use in projection; MUST CORRESPOND TO HOW EIGENVECTORS
- WERE GENERATED.
+ 1D data sets to use in projection;
+ MUST CORRESPOND TO HOW EIGENVECTORS WERE GENERATED.
 \end_layout
 
 \begin_layout Description
@@ -38291,8 +38996,7 @@ DataSet indices correspond to mode #.
 
 \end_deeper
 \begin_layout Standard
-Projects snapshots onto eigenvectors obtained by diagonalizing covariance
- or mass-weighted covariance matrices.
+Projects snapshots onto eigenvectors obtained by diagonalizing covariance or mass-weighted covariance matrices.
  Eigenvectors are taken from previously generated (e.g.
  with 
 \series bold
@@ -38318,8 +39022,8 @@ readdata
 \series bold
 <mask>
 \series default
- agree with the ones used to calculate the modes (i.e., if mask = '@CA' was
- used in the 
+ agree with the ones used to calculate the modes (i.e.,
+ if mask = '@CA' was used in the 
 \begin_inset Quotes eld
 \end_inset
 
@@ -38335,11 +39039,13 @@ matrix
 \begin_inset Quotes erd
 \end_inset
 
- command, mask = '@CA' needs to be set here as well).
+ command,
+ mask = '@CA' needs to be set here as well).
  See 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "sec:cpptraj-Matrix-Vector-Analysis-Examples"
+nolink "false"
 
 \end_inset
 
@@ -38350,19 +39056,22 @@ projection
 \series default
 \emph default
  command.
- If only 1D data sets need to be projected, see the 
+ If only 1D data sets need to be projected,
+ see the 
 \series bold
 \emph on
 projectdata
 \series default
 \emph default
- analysis command, 
+ analysis command,
+ 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-projectdata"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
@@ -38376,6 +39085,8 @@ pucker
 \begin_layout LyX-Code
 pucker
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -38405,8 +39116,7 @@ pucker
 \end_layout
 
 \begin_layout Description
-<maskX> Five (optionally six) atom masks selecting atom(s) to calculate
- pucker for.
+<maskX> Five (optionally six) atom masks selecting atom(s) to calculate pucker for.
 \end_layout
 
 \begin_layout Description
@@ -38476,8 +39186,11 @@ theta
 
 \end_deeper
 \begin_layout Standard
-Calculate the pucker (in degrees) for atoms in <mask1>, <mask2>, <mask3>,
- <mask4>, <mask5> using the method of Altona & Sundarlingam
+Calculate the pucker (in degrees) for atoms in <mask1>,
+ <mask2>,
+ <mask3>,
+ <mask4>,
+ <mask5> using the method of Altona & Sundarlingam
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Altona1972,Harvey1986"
@@ -38485,11 +39198,13 @@ literal "true"
 
 \end_inset
 
- (default for 5 masks, or if 
+ (default for 5 masks,
+ or if 
 \series bold
 altona
 \series default
- specified), or the method of Cremer & Pople
+ specified),
+ or the method of Cremer & Pople
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Cremer1975"
@@ -38497,7 +39212,8 @@ literal "true"
 
 \end_inset
 
- (default for 6 masks, or if 
+ (default for 6 masks,
+ or if 
 \series bold
 cremer
 \series default
@@ -38510,8 +39226,8 @@ amplitude
 \series bold
 theta
 \series default
- keywords are given, amplitudes/thetas (also in degrees) will be calculated
- in addition to pucker.
+ keywords are given,
+ amplitudes/thetas (also in degrees) will be calculated in addition to pucker.
  The results from 
 \series bold
 \shape italic
@@ -38528,20 +39244,21 @@ statistics
 \end_layout
 
 \begin_layout Standard
-By default, pucker values are wrapped to range from -180 to 180 degrees.
+By default,
+ pucker values are wrapped to range from -180 to 180 degrees.
  If the 
 \series bold
 range360
 \series default
  keyword is specified values will be wrapped to range from 0 to 360 degrees.
- Note that the Cremer & Pople convention is offset from Altona & Sundarlingam
- convention (with nucleic acids) by +90.0 degrees; the 
+ Note that the Cremer & Pople convention is offset from Altona & Sundarlingam convention (with nucleic acids) by +90.0 degrees;
+ the 
 \series bold
 offset
 \series default
- keyword will add an offset to the final value and so can be used to convert
- between the two.
- For example, to convert from Cremer to Altona specify 
+ keyword will add an offset to the final value and so can be used to convert between the two.
+ For example,
+ to convert from Cremer to Altona specify 
 \begin_inset Quotes eld
 \end_inset
 
@@ -38557,11 +39274,13 @@ offset
 \end_layout
 
 \begin_layout Standard
-To calculate nucleic acid pucker specify C1' first, followed by C2', C3',
+To calculate nucleic acid pucker specify C1' first,
+ followed by C2',
+ C3',
  C4' and O4'.
- For example, to calculate the sugar pucker for nucleic acid residues 1
- and 2 using the method of Altona & Sundarlingam, with final pseudorotation
- values ranging from 0 to 360:
+ For example,
+ to calculate the sugar pucker for nucleic acid residues 1 and 2 using the method of Altona & Sundarlingam,
+ with final pseudorotation values ranging from 0 to 360:
 \end_layout
 
 \begin_layout LyX-Code
@@ -38579,6 +39298,8 @@ radgyr | rog
 \begin_layout LyX-Code
 radgyr
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -38600,7 +39321,8 @@ radgyr
 \end_layout
 
 \begin_layout Description
-[<mask>] Atoms to calculate radius of gyration for; default all atoms.
+[<mask>] Atoms to calculate radius of gyration for;
+ default all atoms.
 \end_layout
 
 \begin_layout Description
@@ -38620,8 +39342,8 @@ radgyr
 \end_layout
 
 \begin_layout Description
-[tensor] Calculate radius of gyration tensor, output format 'XX YY ZZ XY
- XZ YZ'.
+[tensor] Calculate radius of gyration tensor,
+ output format 'XX YY ZZ XY XZ YZ'.
 \end_layout
 
 \begin_layout Standard
@@ -38637,15 +39359,15 @@ Data Sets Created:
 \end_layout
 
 \begin_layout Description
-<name>[Tensor] Radius of gyration tensor; format 'XX YY ZZ XY XZ YZ'.
+<name>[Tensor] Radius of gyration tensor;
+ format 'XX YY ZZ XY XZ YZ'.
 \end_layout
 
 \end_deeper
 \begin_layout Standard
 Calculate the radius of gyration of specified atoms.
- For example, to calculate only the mass-weighted radius of gyration (not
- the maximum) of the non-hydrogen atoms of residues 4 to 10 and print the
- results to 
+ For example,
+ to calculate only the mass-weighted radius of gyration (not the maximum) of the non-hydrogen atoms of residues 4 to 10 and print the results to 
 \begin_inset Quotes eld
 \end_inset
 
@@ -38667,6 +39389,8 @@ radial | rdf
 \begin_layout LyX-Code
 radial
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -38683,8 +39407,7 @@ radial
 \end_layout
 
 \begin_layout LyX-Code
-   	[density <density> | volume] [<dataset name>] [intrdf <file>] [rawrdf
- <file>]
+   	[density <density> | volume] [<dataset name>] [intrdf <file>] [rawrdf <file>]
 \end_layout
 
 \begin_layout LyX-Code
@@ -38709,11 +39432,13 @@ radial
 \end_layout
 
 \begin_layout Description
-<spacing> Bin spacing, required.
+<spacing> Bin spacing,
+ required.
 \end_layout
 
 \begin_layout Description
-<maximum> Max bin value, required.
+<maximum> Max bin value,
+ required.
 \end_layout
 
 \begin_layout Description
@@ -38721,7 +39446,8 @@ radial
 \begin_inset space ~
 \end_inset
 
-mask1> Atoms to calculate RDF for, required.
+mask1> Atoms to calculate RDF for,
+ required.
 \end_layout
 
 \begin_layout Description
@@ -38729,8 +39455,7 @@ mask1> Atoms to calculate RDF for, required.
 \begin_inset space ~
 \end_inset
 
-mask2>] (Optional) If specified calculate RDF of all atoms in <solvent mask1>
- to each atom in <solute mask2>.
+mask2>] (Optional) If specified calculate RDF of all atoms in <solvent mask1> to each atom in <solute mask2>.
 \end_layout
 
 \begin_layout Description
@@ -38738,8 +39463,8 @@ mask2>] (Optional) If specified calculate RDF of all atoms in <solvent mask1>
 \end_layout
 
 \begin_layout Description
-[mass] Use center of mass for centerX/byresX/bymolX keywords, otherwise
- use geometric center.
+[mass] Use center of mass for centerX/byresX/bymolX keywords,
+ otherwise use geometric center.
 \end_layout
 
 \begin_layout Description
@@ -38747,8 +39472,7 @@ mask2>] (Optional) If specified calculate RDF of all atoms in <solvent mask1>
 \begin_inset space ~
 \end_inset
 
-<density>] Use density value of <density> for normalization (default 0.033456
- molecules
+<density>] Use density value of <density> for normalization (default 0.033456 molecules
 \begin_inset space ~
 \end_inset
 
@@ -38760,8 +39484,7 @@ mask2>] (Optional) If specified calculate RDF of all atoms in <solvent mask1>
 \end_layout
 
 \begin_layout Description
-[volume] Determine density for normalization from average volume of input
- frames.
+[volume] Determine density for normalization from average volume of input frames.
 \end_layout
 
 \begin_layout Description
@@ -38773,9 +39496,7 @@ mask2>] (Optional) If specified calculate RDF of all atoms in <solvent mask1>
 \begin_inset space ~
 \end_inset
 
-<file>] Calculate integral of RDF bin values (averaged over # of frames
- but otherwise not normalized) and write to <file> (can be same as <output_filen
-ame>).
+<file>] Calculate integral of RDF bin values (averaged over # of frames but otherwise not normalized) and write to <file> (can be same as <output_filename>).
 \end_layout
 
 \begin_layout Description
@@ -38787,13 +39508,11 @@ ame>).
 \end_layout
 
 \begin_layout Description
-[center1] Calculate RDF from center of atoms in <solvent mask1> to all atoms
- in <solute mask2>.
+[center1] Calculate RDF from center of atoms in <solvent mask1> to all atoms in <solute mask2>.
 \end_layout
 
 \begin_layout Description
-[center2] Calculate RDF from center of atoms in <solute mask2> to all atoms
- in <solvent mask1>.
+[center2] Calculate RDF from center of atoms in <solute mask2> to all atoms in <solvent mask1>.
 \end_layout
 
 \begin_layout Description
@@ -38805,8 +39524,7 @@ ame>).
 \begin_inset space ~
 \end_inset
 
-<x>,<y>,<z>] Calculate RDF from atoms selected by <solvent mask1> to point
- specified by <x> <y> and <z> (in Ang.).
+<x>,<y>,<z>] Calculate RDF from atoms selected by <solvent mask1> to point specified by <x> <y> and <z> (in Ang.).
 \end_layout
 
 \begin_layout Description
@@ -38851,18 +39569,19 @@ rawrdf
 
 \end_deeper
 \begin_layout Standard
-Calculate the radial distribution function (RDF, aka pair correlation function)
- of atoms in 
+Calculate the radial distribution function (RDF,
+ aka pair correlation function) of atoms in 
 \series bold
 <solvent mask1>
 \series default
- (note that this mask does not need to be solvent, but this nomenclature
- is used for clarity).
+ (note that this mask does not need to be solvent,
+ but this nomenclature is used for clarity).
  If an optional second mask (
 \series bold
 <solute mask2>
 \series default
-) is given, calculate the RDF of ALL atoms in 
+) is given,
+ calculate the RDF of ALL atoms in 
 \series bold
 <solvent mask1>
 \series default
@@ -38871,7 +39590,8 @@ Calculate the radial distribution function (RDF, aka pair correlation function)
 <solute mask2>
 \series default
 .
- If desired, the geometric center of atoms in 
+ If desired,
+ the geometric center of atoms in 
 \series bold
 <solvent mask1>
 \series default
@@ -38887,8 +39607,8 @@ center1
 \series bold
 center2
 \series default
- keywords respectively, or alternatively intra-molecular distances can be
- ignored by specifying the 
+ keywords respectively,
+ or alternatively intra-molecular distances can be ignored by specifying the 
 \series bold
 nointramol
 \series default
@@ -38901,8 +39621,8 @@ byresX
 \series bold
 bymolX
 \series default
- are specified, distances will be between the centers of residues/molecules
- selected by 
+ are specified,
+ distances will be between the centers of residues/molecules selected by 
 \series bold
 <solvent mask1>
 \series default
@@ -38927,13 +39647,13 @@ byresX
 \series bold
 bymolX
 \series default
-, otherwise use geometric center.
+,
+ otherwise use geometric center.
 \end_layout
 
 \begin_layout Standard
-The RDF is calculated from the histogram of the number of particles found
- as a function of distance R, normalized by the expected number of particles
- at that distance.
+The RDF is calculated from the histogram of the number of particles found as a function of distance R,
+ normalized by the expected number of particles at that distance.
  The normalization is calculated from:
 \begin_inset Separator latexpar
 \end_inset
@@ -38960,7 +39680,8 @@ where dR is equal to the bin spacing.
 \begin_inset Formula $^{-\text{3}}$
 \end_inset
 
-, which corresponds to a density of water approximately equal to 1.0 g
+,
+ which corresponds to a density of water approximately equal to 1.0 g
 \begin_inset space ~
 \end_inset
 
@@ -38977,37 +39698,37 @@ mL
 \begin_inset Formula $^{-\text{1}}$
 \end_inset
 
-, multiply the density by 
+,
+ multiply the density by 
 \begin_inset Formula $\frac{0.6022}{M_{r}}$
 \end_inset
 
-, where 
+,
+ where 
 \begin_inset Formula $M_{r}$
 \end_inset
 
  is the mass of the molecule in atomic mass units.
- Alternatively, if the 
+ Alternatively,
+ if the 
 \series bold
 volume
 \series default
- keyword is specified the density is determined from the average volume
- of the system over all Frames.
+ keyword is specified the density is determined from the average volume of the system over all Frames.
  
 \end_layout
 
 \begin_layout Standard
-Note that correct normalization of the RDF depends on the number of atoms
- in each mask; if multiple topology files are being processed that result
- in changes in the number of atoms in each mask, the normalization will
- be off.
+Note that correct normalization of the RDF depends on the number of atoms in each mask;
+ if multiple topology files are being processed that result in changes in the number of atoms in each mask,
+ the normalization will be off.
 \end_layout
 
 \begin_layout Standard
 The basic (i.e.
- no center1/center2/byres1/byres2/bymol1/bymol2) RDF calculations are now
- CUDA parallelized.
- However, the calculation is done in single-precision on GPUs so the resulting
- histograms may differ slightly from the CPU (on the order of 0.0002 - 0.0004).
+ no center1/center2/byres1/byres2/bymol1/bymol2) RDF calculations are now CUDA parallelized.
+ However,
+ the calculation is done in single-precision on GPUs so the resulting histograms may differ slightly from the CPU (on the order of 0.0002 - 0.0004).
 \end_layout
 
 \begin_layout Subsection
@@ -39015,8 +39736,7 @@ randomizeions
 \end_layout
 
 \begin_layout LyX-Code
-randomizeions <mask> [around <ardoundmask> by <distance>] [{allowoverlap|overlap
- <value>}]
+randomizeions <mask> [around <ardoundmask> by <distance>] [{allowoverlap|overlap <value>}]
 \end_layout
 
 \begin_layout LyX-Code
@@ -39071,14 +39791,13 @@ overlap
 \end_layout
 
 \begin_layout Description
-[originalalgorithm] Use the original, slower algorithm (from versions before
- 5.1.0).
+[originalalgorithm] Use the original,
+ slower algorithm (from versions before 5.1.0).
 \end_layout
 
 \end_deeper
 \begin_layout Standard
-This can be used to randomly swap the positions of solvent and single atom
- ions.
+This can be used to randomly swap the positions of solvent and single atom ions.
  The 
 \begin_inset Quotes eld
 \end_inset
@@ -39091,7 +39810,8 @@ overlap
 \begin_inset Quotes erd
 \end_inset
 
- specifies the minimum distance between ions, and the 
+ specifies the minimum distance between ions,
+ and the 
 \begin_inset Quotes eld
 \end_inset
 
@@ -39103,8 +39823,7 @@ around
 \begin_inset Quotes erd
 \end_inset
 
- keyword can be used to specify a solute (or set of atoms) around which
- the ions can get no closer than the distance specified.
+ keyword can be used to specify a solute (or set of atoms) around which the ions can get no closer than the distance specified.
  The optional keywords 
 \begin_inset Quotes eld
 \end_inset
@@ -39182,8 +39901,9 @@ data
 \begin_inset space ~
 \end_inset
 
-<setname> Data set to use for remapping; should be a 1D integer data set
- with X= reference (old) atom index, Y = target (new) atom index.
+<setname> Data set to use for remapping;
+ should be a 1D integer data set with X= reference (old) atom index,
+ Y = target (new) atom index.
 \end_layout
 
 \begin_layout Description
@@ -39293,8 +40013,9 @@ dir
 \end_inset
 
 <XYZ> Repicate cell once in specified directions.
- <XYZ> should consist of 3 numbers with no spaces in between them and are
- restricted to values of -1, 1, and 0.
+ <XYZ> should consist of 3 numbers with no spaces in between them and are restricted to values of -1,
+ 1,
+ and 0.
  May be specified more than once.
 \end_layout
 
@@ -39332,10 +40053,8 @@ parmopts
 
 \end_deeper
 \begin_layout Standard
-Create a trajectory where the unit cell is replicated in 1 or more directions
- (up to 27).
- The resulting coordinates and topology can be written to a trajectory/topology
- file.
+Create a trajectory where the unit cell is replicated in 1 or more directions (up to 27).
+ The resulting coordinates and topology can be written to a trajectory/topology file.
  They can also be saved as a COORDS data set for subsequent processing.
  Currently replication is only allowed 1 axis length in either direction.
  The 
@@ -39347,17 +40066,20 @@ all
 \series bold
 dir
 \series default
- keyword can be used to restrict replication to specific directions, e.g.
+ keyword can be used to restrict replication to specific directions,
+ e.g.
  '
 \family typewriter
 dir 10-1
 \family default
-' would replicate the cell once in the +X, -Z directions.
+' would replicate the cell once in the +X,
+ -Z directions.
 \end_layout
 
 \begin_layout Standard
-For example, to replicate a cell in all directions, writing out to NetCDF
- trajectory cell.nc:
+For example,
+ to replicate a cell in all directions,
+ writing out to NetCDF trajectory cell.nc:
 \end_layout
 
 \begin_layout LyX-Code
@@ -39386,6 +40108,8 @@ name "subsec:cpptraj-rmsd"
 \begin_layout LyX-Code
 rmsd
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -39439,12 +40163,15 @@ rmsd
 \end_layout
 
 \begin_layout Description
-[<mask>] Mask of atoms to calculate RMSD for; if not specified, calculate
- for all atoms.
+[<mask>] Mask of atoms to calculate RMSD for;
+ if not specified,
+ calculate for all atoms.
 \end_layout
 
 \begin_layout Description
-[<refmask>] Reference mask; if not specified, use 
+[<refmask>] Reference mask;
+ if not specified,
+ use 
 \series bold
 <mask>
 \series default
@@ -39468,16 +40195,17 @@ rmsd
 \end_layout
 
 \begin_layout Description
-[norotate] If calculating best-fit RMSD, translate but do not rotate coordinates.
+[norotate] If calculating best-fit RMSD,
+ translate but do not rotate coordinates.
 \end_layout
 
 \begin_layout Description
-[nomod] If calculating best-fit RMSD, do not modify coordinates.
+[nomod] If calculating best-fit RMSD,
+ do not modify coordinates.
 \end_layout
 
 \begin_layout Description
-[savematrices] If specified save rotation matrices to data set with aspect
- [RM].
+[savematrices] If specified save rotation matrices to data set with aspect [RM].
 \end_layout
 
 \begin_deeper
@@ -39495,7 +40223,8 @@ matricesout
 \begin_inset space ~
 \end_inset
 
-{combined|separate}] If specified save translation vectors: 
+{combined|separate}] If specified save translation vectors:
+ 
 \series bold
 combined
 \series default
@@ -39504,8 +40233,9 @@ combined
 \series bold
 separate
 \series default
- means save target-to-origin as Vx, Vy, Vz and save origin-to-reference
- as Ox Oy Oz in the output vector data set.
+ means save target-to-origin as Vx,
+ Vy,
+ Vz and save origin-to-reference as Ox Oy Oz in the output vector data set.
 \end_layout
 
 \begin_deeper
@@ -39559,8 +40289,7 @@ refindex
 
 <#>
 \series default
- Use previously read in reference structure specified by <#> (based on order
- read in).
+ Use previously read in reference structure specified by <#> (based on order read in).
 \end_layout
 
 \begin_layout Description
@@ -39576,13 +40305,12 @@ reftraj
 \begin_inset space ~
 \end_inset
 
-<name> Use frames from COORDS set <name> or read in from trajectory file
- <name> as references.
- Each frame from <name> is used in turn, so that frame 1 is compared to
- frame 1 from <name>, frame 2 is compared to frame 2 from <name> and so
- on.
- If <trajname> runs out of frames before processing is complete, the last
- frame of <trajname> continues to be used as the reference.
+<name> Use frames from COORDS set <name> or read in from trajectory file <name> as references.
+ Each frame from <name> is used in turn,
+ so that frame 1 is compared to frame 1 from <name>,
+ frame 2 is compared to frame 2 from <name> and so on.
+ If <trajname> runs out of frames before processing is complete,
+ the last frame of <trajname> continues to be used as the reference.
 \begin_inset Separator latexpar
 \end_inset
 
@@ -39611,8 +40339,9 @@ parmindex
 \series bold
 reftraj
 \series default
- specifies a trajectory file, associate it with specified topology; if not
- specified the first topology is used.
+ specifies a trajectory file,
+ associate it with specified topology;
+ if not specified the first topology is used.
 \end_layout
 
 \end_deeper
@@ -39649,8 +40378,7 @@ range
 \begin_inset space ~
 \end_inset
 
-range> Calculate per-residue RMSDs for residues in <res range> (default
- all solute residues).
+range> Calculate per-residue RMSDs for residues in <res range> (default all solute residues).
 \end_layout
 
 \begin_layout Description
@@ -39662,8 +40390,7 @@ refrange
 \begin_inset space ~
 \end_inset
 
-range> Calculate per-residue RMSDs to reference residues in <ref range>
- (use <res range> if not specified).
+range> Calculate per-residue RMSDs to reference residues in <ref range> (use <res range> if not specified).
 \end_layout
 
 \begin_layout Description
@@ -39675,13 +40402,12 @@ perresmask
 \begin_inset space ~
 \end_inset
 
-mask> By default residues are selected using the mask ':X' where X is residue
- number; this appends <additional mask> to the mask expression.
+mask> By default residues are selected using the mask ':X' where X is residue number;
+ this appends <additional mask> to the mask expression.
 \end_layout
 
 \begin_layout Description
-perrescenter Translate residues to a common center of mass prior to calculating
- RMSD.
+perrescenter Translate residues to a common center of mass prior to calculating RMSD.
 \end_layout
 
 \begin_layout Description
@@ -39709,7 +40435,8 @@ Data Sets Created:
 \series bold
 perres
 \series default
- only) Per-residue RMSDs; index is residue number.
+ only) Per-residue RMSDs;
+ index is residue number.
 \end_layout
 
 \begin_layout Description
@@ -39744,21 +40471,22 @@ run
 \end_layout
 
 \begin_layout Standard
-Calculate the coordinate RMSD of input frames to a reference frame (or reference
- trajectory).
- Both <mask> and <refmask> must specify the same number of atoms, otherwise
- an error will occur.
+Calculate the coordinate RMSD of input frames to a reference frame (or reference trajectory).
+ Both <mask> and <refmask> must specify the same number of atoms,
+ otherwise an error will occur.
  
 \end_layout
 
 \begin_layout Standard
-For example, say you have a trajectory and you want to calculate RMSD to
- two separate reference structures.
- To calculate the best-fit RMSD of the C, CA, and N atoms of residues 1
- to 20 in each frame to the C, CA, and N atoms of residues 3 to 23 in StructX.crd
-, and then calculate the no-fit RMSD of residue 7 to residue 7 in another
- structure named Struct-begin.rst7, writing both results to Grace-format
- file 
+For example,
+ say you have a trajectory and you want to calculate RMSD to two separate reference structures.
+ To calculate the best-fit RMSD of the C,
+ CA,
+ and N atoms of residues 1 to 20 in each frame to the C,
+ CA,
+ and N atoms of residues 3 to 23 in StructX.crd,
+ and then calculate the no-fit RMSD of residue 7 to residue 7 in another structure named Struct-begin.rst7,
+ writing both results to Grace-format file 
 \begin_inset Quotes eld
 \end_inset
 
@@ -39796,27 +40524,28 @@ If the
 perres
 \series default
 \color inherit
- keyword is specified, after the initial RMSD calculation the no-fit RMSD
- of specified residues is also calculated.
+ keyword is specified,
+ after the initial RMSD calculation the no-fit RMSD of specified residues is also calculated.
  So for example:
 \end_layout
 
 \begin_layout LyX-Code
-rmsd :10-260 reference perres perresout PRMS.dat range 190-211 perresmask
- &!(@H=)
+rmsd :10-260 reference perres perresout PRMS.dat range 190-211 perresmask &!(@H=)
 \end_layout
 
 \begin_layout Standard
 
 \family roman
-will first perform a best-fit RMSD calculation to the first specified reference
- structure using residues 10 to 260, then calculate the no-fit RMSD of residues
- 190 to 211 (excluding any hydrogen atoms), writing the results to PRMS.dat.
- Two additional recommendations for the 'perres' option: 1) try not including
- backbone atoms by using the 'perresmask' keyword, e.g.
- "perresmask &!@H,N,CA,HA,C,O", and 2) try using the 'perrescenter' keyword,
- which centers each residue prior to the 'nofit' calculation; this is useful
- for isolating changes in residue conformation.
+will first perform a best-fit RMSD calculation to the first specified reference structure using residues 10 to 260,
+ then calculate the no-fit RMSD of residues 190 to 211 (excluding any hydrogen atoms),
+ writing the results to PRMS.dat.
+ Two additional recommendations for the 'perres' option:
+ 1) try not including backbone atoms by using the 'perresmask' keyword,
+ e.g.
+ "perresmask &!@H,N,CA,HA,C,O",
+ and 2) try using the 'perrescenter' keyword,
+ which centers each residue prior to the 'nofit' calculation;
+ this is useful for isolating changes in residue conformation.
 \end_layout
 
 \begin_layout Subsection
@@ -39830,11 +40559,13 @@ Although the
 'rms2d'
 \series default
 \emph default
- command can still be specified as an action, it is now considered an analysis.
+ command can still be specified as an action,
+ it is now considered an analysis.
  See 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-rms2d"
+nolink "false"
 
 \end_inset
 
@@ -39852,11 +40583,13 @@ Although the
 'rmsavgcorr'
 \series default
 \emph default
- command can still be specified as an action, it is now considered an analysis.
+ command can still be specified as an action,
+ it is now considered an analysis.
  See 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-rmsavgcorr"
+nolink "false"
 
 \end_inset
 
@@ -39872,6 +40605,7 @@ See
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_atomicfluct"
+nolink "false"
 
 \end_inset
 
@@ -39966,8 +40700,8 @@ usedata
 \begin_inset space ~
 \end_inset
 
-name> If specified, use 3x3 rotation matrices in specified data set to rotate
- coordinates.
+name> If specified,
+ use 3x3 rotation matrices in specified data set to rotate coordinates.
 \end_layout
 
 \begin_deeper
@@ -39985,9 +40719,8 @@ calcfrom
 \begin_inset space ~
 \end_inset
 
-name> Instead of rotating coordinates, calculate rotations around the X
- Y and Z axes (as well as total rotation) in degrees from existing rotation
- matrices specified by <set name>.
+name> Instead of rotating coordinates,
+ calculate rotations around the X Y and Z axes (as well as total rotation) in degrees from existing rotation matrices specified by <set name>.
 \end_layout
 
 \begin_deeper
@@ -40070,13 +40803,16 @@ name>[T] (caclfrom only) Total rotation in degrees.
 
 \end_deeper
 \begin_layout Standard
-Rotate specified atoms around the X, Y, and/or Z axes by the specified amounts,
- around a user-defined axis (specified by <mask0> and <mask1>), or use a
- previously read in or generated data set of 3x3 matrices to perform rotations.
+Rotate specified atoms around the X,
+ Y,
+ and/or Z axes by the specified amounts,
+ around a user-defined axis (specified by <mask0> and <mask1>),
+ or use a previously read in or generated data set of 3x3 matrices to perform rotations.
 \end_layout
 
 \begin_layout Standard
-For example, to rotate the entire system 90 degrees around the X axis:
+For example,
+ to rotate the entire system 90 degrees around the X axis:
 \end_layout
 
 \begin_layout LyX-Code
@@ -40085,13 +40821,20 @@ rotate x 90
 
 \begin_layout Standard
 To rotate residue 270 90 degrees around the axis defined between atoms C1,
- C2, C3, C4, C5, and C6 in residue 270 and atoms C7, C8, C9, C10, C11, and
- C12 in residue 270:
+ C2,
+ C3,
+ C4,
+ C5,
+ and C6 in residue 270 and atoms C7,
+ C8,
+ C9,
+ C10,
+ C11,
+ and C12 in residue 270:
 \end_layout
 
 \begin_layout LyX-Code
-rotate :270 axis0 :270@C1,C2,C3,C4,C5,C6 axis1 :270@C7,C8,C9,C10,C11,C12
- 90.0
+rotate :270 axis0 :270@C1,C2,C3,C4,C5,C6 axis1 :270@C7,C8,C9,C10,C11,C12 90.0
 \end_layout
 
 \begin_layout Standard
@@ -40111,8 +40854,7 @@ rotate usedata RM
 \end_layout
 
 \begin_layout Standard
-To calculate rotations from rotation matrices generated by a previous RMSD
- calculation:
+To calculate rotations from rotation matrices generated by a previous RMSD calculation:
 \end_layout
 
 \begin_layout LyX-Code
@@ -40150,10 +40892,12 @@ The
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-rotdif"
+nolink "false"
 
 \end_inset
 
-), and requires that rotation matrices be generated via an 
+),
+ and requires that rotation matrices be generated via an 
 \series bold
 \emph on
 rmsd
@@ -40198,6 +40942,8 @@ runavg | runningaverage
 \begin_layout LyX-Code
 runavg
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -40224,15 +40970,13 @@ runningaverage
 \end_layout
 
 \begin_layout Standard
-Replaces the current frame with a running average over a number of frames
- specified by 
+Replaces the current frame with a running average over a number of frames specified by 
 \series bold
 window
 \series default
  <window_size> (5 if not specified).
- This means that in order to build up the correct number of frames to calculate
- the average, the first <window_size> minus one frames will not be processed
- by subsequent actions.
+ This means that in order to build up the correct number of frames to calculate the average,
+ the first <window_size> minus one frames will not be processed by subsequent actions.
  So for example given the input:
 \end_layout
 
@@ -40245,9 +40989,13 @@ rms first out rmsd.dat
 \end_layout
 
 \begin_layout Standard
-the rms command will not take effect until frame 3 since that is the first
- time 3 frames are available for averaging (1, 2, and 3).
- The next frame processed would be an average of frames 2, 3, and 4, etc.
+the rms command will not take effect until frame 3 since that is the first time 3 frames are available for averaging (1,
+ 2,
+ and 3).
+ The next frame processed would be an average of frames 2,
+ 3,
+ and 4,
+ etc.
 \end_layout
 
 \begin_layout Subsection
@@ -40276,6 +41024,8 @@ name "subsec:cpptraj-secstruct"
 \begin_layout LyX-Code
 secstruct
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -40329,8 +41079,8 @@ secstruct
 \begin_inset space ~
 \end_inset
 
-<sumfilename>] Write average secondary structure values for each residue
- to <sumfilename>; if not specified <filename>.sum is used.
+<sumfilename>] Write average secondary structure values for each residue to <sumfilename>;
+ if not specified <filename>.sum is used.
 \end_layout
 
 \begin_layout Description
@@ -40338,18 +41088,16 @@ secstruct
 \begin_inset space ~
 \end_inset
 
-<filename>] Write overall secondary structure assignment (based on dominant
- secondary structure type for each residue) to file.
+<filename>] Write overall secondary structure assignment (based on dominant secondary structure type for each residue) to file.
 \end_layout
 
 \begin_layout Description
-[ptrajformat] Write secondary structure as a string of characters for each
- frame, similar to ptraj output.
+[ptrajformat] Write secondary structure as a string of characters for each frame,
+ similar to ptraj output.
 \end_layout
 
 \begin_layout Description
-[betadetail] Record anti-parallel beta and parallel beta in place of extended
- and bridge secondary structure.
+[betadetail] Record anti-parallel beta and parallel beta in place of extended and bridge secondary structure.
  If a residue could be both only anti-parallel is reported.
 \end_layout
 
@@ -40422,8 +41170,8 @@ name>] Backbone carbonyl oxygen atom name (default 'O').
 \begin_inset space ~
 \end_inset
 
-name>] Cysteine sulfur atom name, used to ignore disulfide connectivity
- (default 'SG').
+name>] Cysteine sulfur atom name,
+ used to ignore disulfide connectivity (default 'SG').
 \end_layout
 
 \begin_layout Standard
@@ -40431,18 +41179,20 @@ Data Sets Created:
 \end_layout
 
 \begin_layout Description
-<name>[res] Residue secondary structure per frame; index corresponds to
- residue number.
+<name>[res] Residue secondary structure per frame;
+ index corresponds to residue number.
  If 
 \series bold
 ptrajformat
 \series default
- specified these will be characters, otherwise integers (see table below).
+ specified these will be characters,
+ otherwise integers (see table below).
 \end_layout
 
 \begin_layout Description
-<name>[avgss] Average of each type of secondary structure; index corresponds
- to secondary structure type (see table below; no index for 
+<name>[avgss] Average of each type of secondary structure;
+ index corresponds to secondary structure type (see table below;
+ no index for 
 \begin_inset Quotes eld
 \end_inset
 
@@ -40458,13 +41208,11 @@ None
 \end_layout
 
 \begin_layout Description
-<name>[Para] Total fraction of residues with parallel beta structure vs
- time.
+<name>[Para] Total fraction of residues with parallel beta structure vs time.
 \end_layout
 
 \begin_layout Description
-<name>[Anti] Total fraction of residues with anti-parallel beta structure
- vs time.
+<name>[Anti] Total fraction of residues with anti-parallel beta structure vs time.
 \end_layout
 
 \begin_layout Description
@@ -40491,12 +41239,11 @@ None
 \begin_layout Standard
 
 \series bold
-As of version 4.18.0, this command now produces output that better conforms
- with the original definitions in Kabsch and Sander 1983; namely that Extended
- beta (i.e.
+As of version 4.18.0,
+ this command now produces output that better conforms with the original definitions in Kabsch and Sander 1983;
+ namely that Extended beta (i.e.
  2 or more consecutive beta bridges of the same type) and beta Bridge (i.e.
- an isolated beta bridge) are now reported instead of anti-parallel and
- parallel beta.
+ an isolated beta bridge) are now reported instead of anti-parallel and parallel beta.
  To restore the original behavior the 'betadetail' keyword must be specified.
 \end_layout
 
@@ -40515,8 +41262,7 @@ Calculate secondary structural propensities for residues in
 \series bold
 <mask>
 \series default
- (or all solute residues if no mask given) using the DSSP method of Kabsch
- and Sander
+ (or all solute residues if no mask given) using the DSSP method of Kabsch and Sander
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Kabsch83"
@@ -40524,8 +41270,8 @@ literal "true"
 
 \end_inset
 
-, which assigns secondary structure types for residues based on backbone
- amide (N-H) and carbonyl (C=O) atom positions.
+,
+ which assigns secondary structure types for residues based on backbone amide (N-H) and carbonyl (C=O) atom positions.
  By default 
 \shape italic
 cpptraj
@@ -40538,7 +41284,8 @@ N
 \begin_inset Quotes erd
 \end_inset
 
-, 
+,
+ 
 \begin_inset Quotes eld
 \end_inset
 
@@ -40546,7 +41293,8 @@ H
 \begin_inset Quotes erd
 \end_inset
 
-, 
+,
+ 
 \begin_inset Quotes eld
 \end_inset
 
@@ -40554,7 +41302,8 @@ C
 \begin_inset Quotes erd
 \end_inset
 
-, and 
+,
+ and 
 \begin_inset Quotes eld
 \end_inset
 
@@ -40578,14 +41327,15 @@ nameX
 \series default
  keywords (e.g.
  'nameH HN').
- Note that it is expected that some residues will not have all of these
- atoms (such as proline); in this case 
+ Note that it is expected that some residues will not have all of these atoms (such as proline);
+ in this case 
 \shape italic
 cpptraj
 \shape default
  will print an informational message but the calculation will proceed normally.
  If a residue has no atoms selected it will be skipped.
- When determining residue connecivity, disulfide bonds will be ignored;
+ When determining residue connecivity,
+ disulfide bonds will be ignored;
  
 \emph on
 cpptraj
@@ -40619,13 +41369,13 @@ out
 \end_layout
 
 \begin_layout Standard
-where <#Frame> is the frame number and <ResX SS> is an integer representing
- the calculated secondary structure type for residue X.
+where <#Frame> is the frame number and <ResX SS> is an integer representing the calculated secondary structure type for residue X.
  If the keyword 
 \series bold
 ptrajformat
 \series default
- is specified, the output format will instead be:
+ is specified,
+ the output format will instead be:
 \end_layout
 
 \begin_layout LyX-Code
@@ -40633,17 +41383,13 @@ ptrajformat
 \end_layout
 
 \begin_layout Standard
-where STRING is a string of characters (one for each residue) where each
- character represents a different structural type (this format is similar
- to what 
+where STRING is a string of characters (one for each residue) where each character represents a different structural type (this format is similar to what 
 \shape italic
 ptraj
 \shape default
  had outputed and is retained for backwards compatibility).
- The various secondary structure types and their corresponding integer/character
- are listed below.
- If 'betadetail' is specified what is reported and the characters used change
- slightly.
+ The various secondary structure types and their corresponding integer/character are listed below.
+ If 'betadetail' is specified what is reported and the characters used change slightly.
 \begin_inset Separator latexpar
 \end_inset
 
@@ -41009,8 +41755,7 @@ Bend
 \end_layout
 
 \begin_layout Standard
-Average structural propensities over all frames for each residue will be
- written to the file specified by 
+Average structural propensities over all frames for each residue will be written to the file specified by 
 \series bold
 sumout
 \series default
@@ -41031,17 +41776,16 @@ sumout
 sumout
 \series default
  is not specified).
- The total structural propensity over all residues for each secondary structure
- type will be written to the file specified by 
+ The total structural propensity over all residues for each secondary structure type will be written to the file specified by 
 \series bold
 totalout
 \series default
 .
- If assignout is specified, the overall secondary structure assignment for
- each residue will be printed in two line chunks of 50 residues, with the
- first line containing the residue number the line starts with and one character
- residue names, and the second line containing secondary structure assignment
- using DSSP-style characters, like so:
+ If assignout is specified,
+ the overall secondary structure assignment for each residue will be printed in two line chunks of 50 residues,
+ with the first line containing the residue number the line starts with and one character residue names,
+ and the second line containing secondary structure assignment using DSSP-style characters,
+ like so:
 \end_layout
 
 \begin_layout LyX-Code
@@ -41054,8 +41798,8 @@ totalout
 
 \begin_layout Standard
 The output of secstruct command is amenable to visualization with gnuplot.
- To generate a 2D map-style plot of secondary structure vs time, with each
- residue on the Y axis simply give the output file a 
+ To generate a 2D map-style plot of secondary structure vs time,
+ with each residue on the Y axis simply give the output file a 
 \begin_inset Quotes eld
 \end_inset
 
@@ -41064,9 +41808,9 @@ The output of secstruct command is amenable to visualization with gnuplot.
 \end_inset
 
  extension.
- For example, to generate a 2D map of secondary structure vs time, with
- different colors representing different secondary structure types for residues
- 1-22:
+ For example,
+ to generate a 2D map of secondary structure vs time,
+ with different colors representing different secondary structure types for residues 1-22:
 \end_layout
 
 \begin_layout LyX-Code
@@ -41082,7 +41826,8 @@ gnuplot dssp.gnu
 \end_layout
 
 \begin_layout Standard
-Similarly, the 
+Similarly,
+ the 
 \series bold
 sumout
 \series default
@@ -41118,8 +41863,7 @@ dgbulk
 \series bold
 dhbulk
 \series default
- for different water models can be calculated from pure water simulations
- with the 
+ for different water models can be calculated from pure water simulations with the 
 \series bold
 purewater
 \series default
@@ -41139,8 +41883,7 @@ setvelocity [<mask>]
 \end_layout
 
 \begin_layout LyX-Code
-               scale [factor <fac>] [sx <xfac>] [sy <yfac>] [sz <zfac>]
- |
+               scale [factor <fac>] [sx <xfac>] [sy <yfac>] [sz <zfac>] |
 \end_layout
 
 \begin_layout LyX-Code
@@ -41257,8 +42000,9 @@ none Remove any velocities.
 \end_layout
 
 \begin_layout Description
-modify If specified, do not set, just modify any existing velocities (via
- 'ntc' or 'zeromomentum').
+modify If specified,
+ do not set,
+ just modify any existing velocities (via 'ntc' or 'zeromomentum').
 \end_layout
 
 \begin_layout Description
@@ -41279,8 +42023,10 @@ ntc
 \end_inset
 
 <#> Correct set velocities for SHAKE constraints.
- Numbers match sander/pmemd: 1 = no SHAKE, 2 = SHAKE on hydrogens, 3 = SHAKE
- on all atoms.
+ Numbers match sander/pmemd:
+ 1 = no SHAKE,
+ 2 = SHAKE on hydrogens,
+ 3 = SHAKE on all atoms.
 \end_layout
 
 \begin_layout Description
@@ -41300,17 +42046,16 @@ epsilon
 \end_layout
 
 \begin_layout Description
-zeromomentum If specified adjust velocities so the total momentum of atoms
- in <mask> is zero.
+zeromomentum If specified adjust velocities so the total momentum of atoms in <mask> is zero.
 \end_layout
 
 \end_deeper
 \begin_layout Standard
-Set velocities in frame for atoms in <mask> using Maxwellian distribution
- based on given temperature, optionally adjusted for SHAKE constraints.
+Set velocities in frame for atoms in <mask> using Maxwellian distribution based on given temperature,
+ optionally adjusted for SHAKE constraints.
  Can also be used to modify existing velocity information or remove it entirely.
- The total momentum of the system can be set to zero as well, which can
- be useful for NVE simulations.
+ The total momentum of the system can be set to zero as well,
+ which can be useful for NVE simulations.
 \end_layout
 
 \begin_layout Subsection
@@ -41373,18 +42118,18 @@ solv
 \begin_layout Description
 [purewater] The system is pure water.
  Used to parametrize the bulk values.
- If this is specified, none of the below options are relevant.
+ If this is specified,
+ none of the below options are relevant.
 \end_layout
 
 \begin_layout Description
-<peaksname> Data set or file (XYZ- format: see below) with the peak locations
- present .
+<peaksname> Data set or file (XYZ- format:
+ see below) with the peak locations present .
  
 \end_layout
 
 \begin_layout Description
-[reorder] The solvent should be re-ordered so the same solvent molecule
- is always in the same site.
+[reorder] The solvent should be re-ordered so the same solvent molecule is always in the same site.
 \end_layout
 
 \begin_layout Description
@@ -41401,12 +42146,12 @@ summary
 \end_inset
 
 <summary> File with the summary of all SPAM results.
- If not specified, no SPAM energies will be calculated.
+ If not specified,
+ no SPAM energies will be calculated.
 \end_layout
 
 \begin_layout Description
-site_size <size> Size of the water site around each density peak (sphere
- diameter/box edge length) in Ang.
+site_size <size> Size of the water site around each density peak (sphere diameter/box edge length) in Ang.
 \end_layout
 
 \begin_layout Description
@@ -41426,8 +42171,8 @@ dgbulk
 \begin_inset space ~
 \end_inset
 
-<dgbulk> SPAM free energy of the bulk solvent in kcal/mol; default is -30.3
- kcal/mol (SPC/E water).
+<dgbulk> SPAM free energy of the bulk solvent in kcal/mol;
+ default is -30.3 kcal/mol (SPC/E water).
 \end_layout
 
 \begin_layout Description
@@ -41435,8 +42180,8 @@ dhbulk
 \begin_inset space ~
 \end_inset
 
-<dhbulk> SPAM enthalpy of the bulk solvent in kcal/mol; default is -22.2
- kcal/mol (SPC/E water).
+<dhbulk> SPAM enthalpy of the bulk solvent in kcal/mol;
+ default is -22.2 kcal/mol (SPC/E water).
 \end_layout
 
 \begin_layout Standard
@@ -41478,18 +42223,17 @@ literal "true"
 \end_inset
 
 .
- Briefly, this method identifies and estimates the free energy profiles
- of bound waters via calculation of the distribution of interaction energies
- between the water and it's environment from explicit solvent MD trajectories.
- The interaction energies are calculated using a force- and energy-shifted
- electrostatic term with a hard cutoff.
- For a given peak, SPAM energies will only be calculated for peaks where
- the peak is singly-occupied (i.e.
+ Briefly,
+ this method identifies and estimates the free energy profiles of bound waters via calculation of the distribution of interaction energies between the water and it's environment from explicit solvent MD trajectories.
+ The interaction energies are calculated using a force- and energy-shifted electrostatic term with a hard cutoff.
+ For a given peak,
+ SPAM energies will only be calculated for peaks where the peak is singly-occupied (i.e.
  a multiple-occupied peak is not considered valid).
 \end_layout
 
 \begin_layout Standard
-Prior to this command, the 
+Prior to this command,
+ the 
 \series bold
 \emph on
 volmap
@@ -41503,6 +42247,7 @@ peakfile
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_volmap"
+nolink "false"
 
 \end_inset
 
@@ -41513,7 +42258,8 @@ reference "subsec:cpptraj_volmap"
 volmap
 \series default
 \emph default
- command, the peaks file should have one line per peak with format:
+ command,
+ the peaks file should have one line per peak with format:
 \end_layout
 
 \begin_layout LyX-Code
@@ -41566,7 +42312,8 @@ mask Atoms for which MSDs will be computed.
 \end_layout
 
 \begin_layout Description
-out Output file: time vs.
+out Output file:
+ time vs.
  MSD.
  
 \end_layout
@@ -41578,7 +42325,9 @@ time Time step in the trajectory.
 
 \begin_layout Description
 mask2 Compute MSDs only within the lower and upper limit of mask2.
- IMPORTANT: may be very slow!!! 
+ IMPORTANT:
+ may be very slow!!!
+ 
 \end_layout
 
 \begin_layout Description
@@ -41603,8 +42352,7 @@ avout Output file containing average distances.
 \end_layout
 
 \begin_layout Description
-x|y|z|xy|xz|yz|xyz Computation of the mean square displacement in the chosen
- dimension.
+x|y|z|xy|xz|yz|xyz Computation of the mean square displacement in the chosen dimension.
  (xyz) 
 \end_layout
 
@@ -41621,8 +42369,7 @@ com Calculate MSD for centre of mass.
 
 \end_deeper
 \begin_layout Standard
-Calculate diffusion for selected atoms using code based on the 'diffusion'
- routine developed by Hannes Loeffler at STFC (http://www.stfc.ac.uk/CSE).
+Calculate diffusion for selected atoms using code based on the 'diffusion' routine developed by Hannes Loeffler at STFC (http://www.stfc.ac.uk/CSE).
 \end_layout
 
 \begin_layout Subsection
@@ -41632,6 +42379,8 @@ strip
 \begin_layout LyX-Code
 strip
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -41669,8 +42418,7 @@ charge
 \begin_inset space ~
 \end_inset
 
-charge> Scale charges so total charge of remaining atoms matches the specified
- <new charge>.
+charge> Scale charges so total charge of remaining atoms matches the specified <new charge>.
 \end_layout
 
 \begin_layout Description
@@ -41678,8 +42426,7 @@ charge> Scale charges so total charge of remaining atoms matches the specified
 \begin_inset space ~
 \end_inset
 
-<prefix>] Write out stripped topology file with name '<prefix>.<Original
- Topology Name>'.
+<prefix>] Write out stripped topology file with name '<prefix>.<Original Topology Name>'.
 \end_layout
 
 \begin_layout Description
@@ -41713,8 +42460,8 @@ Strip all atoms specified by
 \series bold
 outprefix
 \series default
- keyword can be used to write stripped topologies; stripped Amber topologies
- are fully-functional.
+ keyword can be used to write stripped topologies;
+ stripped Amber topologies are fully-functional.
  Available options for 
 \series bold
 <parmopts>
@@ -41730,8 +42477,8 @@ help Formats parmwrite
 \end_layout
 
 \begin_layout Standard
-Note that stripping a system renumbers all atoms and residues, so for example
- after this command:
+Note that stripping a system renumbers all atoms and residues,
+ so for example after this command:
 \end_layout
 
 \begin_layout LyX-Code
@@ -41739,13 +42486,14 @@ strip :1
 \end_layout
 
 \begin_layout Standard
-residue 1 will be gone, and the former second residue will now be the first,
+residue 1 will be gone,
+ and the former second residue will now be the first,
  and so on.
 \end_layout
 
 \begin_layout Standard
-For example, to strip all residues named WAT from each topology/coordinate
- frame:
+For example,
+ to strip all residues named WAT from each topology/coordinate frame:
 \end_layout
 
 \begin_layout LyX-Code
@@ -41760,9 +42508,10 @@ The next example uses a distance-based mask to strip atoms in a single frame.
 mask
 \series default
 \shape default
- command, distance-based masks do not update on a per-frame basis.
- To strip all residues outside of 6.0 from any atom in residues 1 to 14 and
- write out the stripped topology and coordinates, both with no box information:
+ command,
+ distance-based masks do not update on a per-frame basis.
+ To strip all residues outside of 6.0 from any atom in residues 1 to 14 and write out the stripped topology and coordinates,
+ both with no box information:
 \end_layout
 
 \begin_layout LyX-Code
@@ -41799,6 +42548,8 @@ name "subsec:cpptraj_surf"
 \begin_layout LyX-Code
 surf
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -41836,7 +42587,8 @@ solutemask
 \begin_inset space ~
 \end_inset
 
-<mask> If specified, calculate the contribution of <mask1> to <mask>.
+<mask> If specified,
+ calculate the contribution of <mask1> to <mask>.
 \end_layout
 
 \begin_layout Description
@@ -41844,7 +42596,8 @@ offset
 \begin_inset space ~
 \end_inset
 
-<offset> Increment van der Waals radii by <offset>; 1.4 Ang.
+<offset> Increment van der Waals radii by <offset>;
+ 1.4 Ang.
  is the default (as used by Amber).
 \end_layout
 
@@ -41853,8 +42606,7 @@ nbrcut
 \begin_inset space ~
 \end_inset
 
-<cut> Only atoms with van der Waals radii greater than <cut> are considered
- to have neighbors (2.5 Ang Amber default).
+<cut> Only atoms with van der Waals radii greater than <cut> are considered to have neighbors (2.5 Ang Amber default).
 \end_layout
 
 \end_deeper
@@ -41863,9 +42615,8 @@ Calculate the surface area in Å
 \begin_inset Formula $^{\text{2}}$
 \end_inset
 
- of atoms in <mask> (if no mask specified, all atoms not marked as 'solvent'
- that are part of a molecule > 1 atom in size) using the LCPO algorithm
- of Weiser et al.
+ of atoms in <mask> (if no mask specified,
+ all atoms not marked as 'solvent' that are part of a molecule > 1 atom in size) using the LCPO algorithm of Weiser et al.
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Weiser99"
@@ -41874,24 +42625,24 @@ literal "true"
 \end_inset
 
 .
- In order for this to work, the topology needs to have bond information
- and atom type information.
+ In order for this to work,
+ the topology needs to have bond information and atom type information.
  
 \end_layout
 
 \begin_layout Standard
-Note that even if <mask> does not include all solute atoms, the neighbor
- list is still calculated for all solute atoms so the surface area calculated
- reflects the contribution of atoms in <mask> to the overall surface area,
+Note that even if <mask> does not include all solute atoms,
+ the neighbor list is still calculated for all solute atoms so the surface area calculated reflects the contribution of atoms in <mask> to the overall surface area,
  not the surface area of <mask> as an isolated system.
- As a result, it may be possible to obtain a negative surface area if only
- a small fraction of the solute is selected.
+ As a result,
+ it may be possible to obtain a negative surface area if only a small fraction of the solute is selected.
 \end_layout
 
 \begin_layout Standard
-For example, to calculate the overall surface area of all solute atoms,
- as well as the contribution of residue 1 to the overall surface area, writing
- both results to 
+For example,
+ to calculate the overall surface area of all solute atoms,
+ as well as the contribution of residue 1 to the overall surface area,
+ writing both results to 
 \begin_inset Quotes eld
 \end_inset
 
@@ -41922,8 +42673,7 @@ name "subsec:cpptraj_symmrmsd"
 \end_layout
 
 \begin_layout LyX-Code
-symmrmsd  [<name>] [<mask>] [<refmask>] [out <filename>] [nofit] [mass]
- [remap]
+symmrmsd  [<name>] [<mask>] [<refmask>] [out <filename>] [nofit] [mass] [remap]
 \end_layout
 
 \begin_layout LyX-Code
@@ -41944,12 +42694,15 @@ symmrmsd  [<name>] [<mask>] [<refmask>] [out <filename>] [nofit] [mass]
 \end_layout
 
 \begin_layout Description
-[<mask>] Mask of atoms to calculate RMSD for; if not specified, calculate
- for all atoms.
+[<mask>] Mask of atoms to calculate RMSD for;
+ if not specified,
+ calculate for all atoms.
 \end_layout
 
 \begin_layout Description
-[<refmask>] Reference mask; if not specified, use 
+[<refmask>] Reference mask;
+ if not specified,
+ use 
 \series bold
 <mask>
 \series default
@@ -42018,8 +42771,7 @@ refindex
 
 <#>
 \series default
- Use previously read in reference structure specified by <#> (based on order
- read in).
+ Use previously read in reference structure specified by <#> (based on order read in).
 \end_layout
 
 \begin_layout Description
@@ -42035,13 +42787,12 @@ reftraj
 \begin_inset space ~
 \end_inset
 
-<name> Use frames from COORDS set <name> or read in from trajectory file
- <name> as references.
- Each frame from <name> is used in turn, so that frame 1 is compared to
- frame 1 from <name>, frame 2 is compared to frame 2 from <name> and so
- on.
- If <trajname> runs out of frames before processing is complete, the last
- frame of <trajname> continues to be used as the reference.
+<name> Use frames from COORDS set <name> or read in from trajectory file <name> as references.
+ Each frame from <name> is used in turn,
+ so that frame 1 is compared to frame 1 from <name>,
+ frame 2 is compared to frame 2 from <name> and so on.
+ If <trajname> runs out of frames before processing is complete,
+ the last frame of <trajname> continues to be used as the reference.
 \begin_inset Separator latexpar
 \end_inset
 
@@ -42070,8 +42821,8 @@ parmindex
 \series bold
 reftraj
 \series default
- specifies a file associate trajectory <name> with specified topology; if
- not specified the first topology is used.
+ specifies a file associate trajectory <name> with specified topology;
+ if not specified the first topology is used.
 \end_layout
 
 \end_deeper
@@ -42079,25 +42830,22 @@ reftraj
 \begin_layout Standard
 Perform symmetry-corrected RMSD calculation.
  This is done by identifying potential symmetric atoms in each residue,
- performing an initial best-fit, then determining which configuration of
- symmetric atoms will give the lowest RMSD using atomic distance to reference
- atoms.
+ performing an initial best-fit,
+ then determining which configuration of symmetric atoms will give the lowest RMSD using atomic distance to reference atoms.
  
 \end_layout
 
 \begin_layout Standard
 
 \series bold
-Note that when re-mapping, all atoms in the residues of interest should
- be selected to prevent cases where selected symmetric atoms are swapped
- but the atoms they are bonded to are not
+Note that when re-mapping,
+ all atoms in the residues of interest should be selected to prevent cases where selected symmetric atoms are swapped but the atoms they are bonded to are not
 \series default
 .
- Also, occasionally larger symmetric structures (e.g.
- 6 membered rings) may become distorted due to only part of the residue
- being corrected for symmetry.
- This appears to happen about 4% of the time but does not overly inflate
- the RMSD.
+ Also,
+ occasionally larger symmetric structures (e.g.
+ 6 membered rings) may become distorted due to only part of the residue being corrected for symmetry.
+ This appears to happen about 4% of the time but does not overly inflate the RMSD.
  The 
 \series bold
 \shape italic
@@ -42114,9 +42862,9 @@ symmrmsd
 \end_layout
 
 \begin_layout Standard
-Warning: the symmetry correction is generally robust enough to account for
- symmetries in the standard amino and nucleic acid residues, but has not
- been extensively tested on residues with more extended types of symmetry.
+Warning:
+ the symmetry correction is generally robust enough to account for symmetries in the standard amino and nucleic acid residues,
+ but has not been extensively tested on residues with more extended types of symmetry.
 \end_layout
 
 \begin_layout Subsection
@@ -42153,7 +42901,8 @@ temperature [<name>] [out <filename>]
 \end_layout
 
 \begin_layout Description
-frame Do not calculate temperature; use existing frame temperature.
+frame Do not calculate temperature;
+ use existing frame temperature.
 \end_layout
 
 \begin_layout Description
@@ -42165,8 +42914,10 @@ frame Do not calculate temperature; use existing frame temperature.
 \begin_inset space ~
 \end_inset
 
-<#>] Value of SHAKE bond constraint: 1 - none, 2 - bonds to H, 3- all bonds
- (equivalent to SANDER/PMEMD).
+<#>] Value of SHAKE bond constraint:
+ 1 - none,
+ 2 - bonds to H,
+ 3- all bonds (equivalent to SANDER/PMEMD).
 \end_layout
 
 \begin_layout Description
@@ -42178,8 +42929,9 @@ frame Do not calculate temperature; use existing frame temperature.
 \begin_inset space ~
 \end_inset
 
-{trans|rot|both}] Correct for removed translational, rotational, or both
- kinds of degrees of freedom.
+{trans|rot|both}] Correct for removed translational,
+ rotational,
+ or both kinds of degrees of freedom.
 \end_layout
 
 \end_deeper
@@ -42189,7 +42941,8 @@ Calculate temperature in frame based on velocity information.
 \series bold
 update
 \series default
-' is specified, update frame temperature too.
+' is specified,
+ update frame temperature too.
  If '
 \series bold
 frame
@@ -42199,16 +42952,17 @@ frame
 \end_layout
 
 \begin_layout Standard
-The 'ntc' keyword can be used to correct for lost degrees of freedom due
- to SHAKE constraints (2 = bonds to hydrogen, 3 = all bonds).
- The 'remove' keyword can be used to account for removed translational and/or
- rotational degrees of freedom.
+The 'ntc' keyword can be used to correct for lost degrees of freedom due to SHAKE constraints (2 = bonds to hydrogen,
+ 3 = all bonds).
+ The 'remove' keyword can be used to account for removed translational and/or rotational degrees of freedom.
 \end_layout
 
 \begin_layout Standard
-For example, if using a trajectory that has been generated with SHAKE on
- hydrogens, no periodic boundary conditions (i.e.
- no box), and has had the center of mass periodically removed:
+For example,
+ if using a trajectory that has been generated with SHAKE on hydrogens,
+ no periodic boundary conditions (i.e.
+ no box),
+ and has had the center of mass periodically removed:
 \end_layout
 
 \begin_layout LyX-Code
@@ -42216,9 +42970,10 @@ temperature T1 ntc 2 remove both out T1.dat
 \end_layout
 
 \begin_layout Standard
-If using a trajectory that has been generated with SHAKE on hydrogens, periodic
- boundary conditions (i.e.
- with a box), and has had the center of mass periodically removed:
+If using a trajectory that has been generated with SHAKE on hydrogens,
+ periodic boundary conditions (i.e.
+ with a box),
+ and has had the center of mass periodically removed:
 \end_layout
 
 \begin_layout LyX-Code
@@ -42226,8 +42981,9 @@ temperature T1 ntc 2 remove trans out T1.dat
 \end_layout
 
 \begin_layout Standard
-If using a trajectory that has been generated with SHAKE on all bonds, periodic
- boundary conditions, and no center of mass motion removal:
+If using a trajectory that has been generated with SHAKE on all bonds,
+ periodic boundary conditions,
+ and no center of mass motion removal:
 \end_layout
 
 \begin_layout LyX-Code
@@ -42264,7 +43020,8 @@ dt
 \end_layout
 
 \begin_layout Description
-[update] If specified, modify any existing time info.
+[update] If specified,
+ modify any existing time info.
 \end_layout
 
 \begin_layout Description
@@ -42273,10 +43030,11 @@ remove Remove any time info from frame.
 
 \end_deeper
 \begin_layout Standard
-Either add time information to frames, modify existing time information
- in frames, or remove existing time information from frames.
- Note that currently COORDS data sets do not store time information, so
- using this command with the 
+Either add time information to frames,
+ modify existing time information in frames,
+ or remove existing time information from frames.
+ Note that currently COORDS data sets do not store time information,
+ so using this command with the 
 \series bold
 \emph on
 crdaction
@@ -42290,8 +43048,7 @@ tordiff
 \end_layout
 
 \begin_layout LyX-Code
-tordiff [<set name>] [<mask>] [mass] [out <file>] [diffout <file>] [time
- <dt>]
+tordiff [<set name>] [<mask>] [mass] [out <file>] [diffout <file>] [time <dt>]
 \end_layout
 
 \begin_deeper
@@ -42324,8 +43081,7 @@ name>] Output mean-squared-displacement data sets name.
 \begin_inset space ~
 \end_inset
 
-<file>] Write diffusion contants calculated from fits of mean-squared-displacent
- data sets to <filename>.
+<file>] Write diffusion contants calculated from fits of mean-squared-displacent data sets to <filename>.
 \end_layout
 
 \begin_layout Description
@@ -42404,8 +43160,7 @@ Calculate the diffusion via mean-squared displacement (in Å
 \begin_inset Formula $^{\text{2}}$
 \end_inset
 
-/ps) of specified molecules using the toroidal-view-preserving (TOR) scheme
- of Hummer et al.
+/ps) of specified molecules using the toroidal-view-preserving (TOR) scheme of Hummer et al.
  
 \series bold
 Note that currently this only works for orthogonal boxes
@@ -42436,6 +43191,7 @@ reference "subsec:cpptraj-diffusion"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
@@ -42452,13 +43208,12 @@ reference "subsec:cpptraj_unwrap"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
 ) commands which correct for box fluctuations via fractional coordinates,
- the TOR scheme corrects for box fluctuations by tracking the displacement
- of each molecule with respect to its position in the previous frame in
- Cartesian space.
+ the TOR scheme corrects for box fluctuations by tracking the displacement of each molecule with respect to its position in the previous frame in Cartesian space.
 \end_layout
 
 \begin_layout Standard
@@ -42468,13 +43223,15 @@ Diffusion constants are calculated in the same manner as the
 diffusion
 \series default
 \emph default
- command; for more details see 
+ command;
+ for more details see 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-diffusion"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
@@ -42482,8 +43239,8 @@ noprefix "false"
 \end_layout
 
 \begin_layout Standard
-For example, to calculate the diffusion (with data set name TOR) of waters
- (name WAT) in an orthogonal box using the toroidal scheme:
+For example,
+ to calculate the diffusion (with data set name TOR) of waters (name WAT) in an orthogonal box using the toroidal scheme:
 \end_layout
 
 \begin_layout LyX-Code
@@ -42540,14 +43297,16 @@ topoint
 \begin_inset space ~
 \end_inset
 
-<x>,<y>,<z> If specified, translate center of specified atoms to a specific
- point defined by <x>, <y>, and <z> in the given comma-separated list instead
- of by deltas.
+<x>,<y>,<z> If specified,
+ translate center of specified atoms to a specific point defined by <x>,
+ <y>,
+ and <z> in the given comma-separated list instead of by deltas.
 \end_layout
 
 \begin_deeper
 \begin_layout Description
-mass If specified, translate center of mass of specified atoms (
+mass If specified,
+ translate center of mass of specified atoms (
 \series bold
 topoint
 \series default
@@ -42565,11 +43324,13 @@ Translate atoms in
 \series bold
 <dx>
 \series default
- Å in the X direction, 
+ Å in the X direction,
+ 
 \series bold
 <dy>
 \series default
- Å in the Y direction, and 
+ Å in the Y direction,
+ and 
 \series bold
 <dz>
 \series default
@@ -42578,8 +43339,8 @@ Translate atoms in
 \series bold
 'topoint
 \series default
-' is specified, translate atoms in <mask> to the specified coordinates (also
- in Å).
+' is specified,
+ translate atoms in <mask> to the specified coordinates (also in Å).
 \end_layout
 
 \begin_layout Subsection
@@ -42589,6 +43350,8 @@ unstrip
 \begin_layout LyX-Code
 unstrip
 \begin_inset Index idx
+range none
+pageformat default
 status open
 
 \begin_layout Plain Layout
@@ -42601,13 +43364,14 @@ unstrip
 \end_layout
 
 \begin_layout Standard
-Requests that the original topology and frame be used for all following
- actions.
- This has the effect of undoing any command that modifies the state (such
- as strip).
- For example, the following code takes a solvated complex and uses a combination
- of strip, unstrip, and outtraj commands to write out separate dry complex,
- receptor, and ligand files:
+Requests that the original topology and frame be used for all following actions.
+ This has the effect of undoing any command that modifies the state (such as strip).
+ For example,
+ the following code takes a solvated complex and uses a combination of strip,
+ unstrip,
+ and outtraj commands to write out separate dry complex,
+ receptor,
+ and ligand files:
 \end_layout
 
 \begin_layout LyX-Code
@@ -42619,7 +43383,8 @@ trajin Complex.WAT.pdb
 \end_layout
 
 \begin_layout LyX-Code
-# Remove water, write complex
+# Remove water,
+ write complex
 \end_layout
 
 \begin_layout LyX-Code
@@ -42639,7 +43404,8 @@ unstrip
 \end_layout
 
 \begin_layout LyX-Code
-# Remove water and ligand, write receptor
+# Remove water and ligand,
+ write receptor
 \end_layout
 
 \begin_layout LyX-Code
@@ -42659,7 +43425,8 @@ unstrip
 \end_layout
 
 \begin_layout LyX-Code
-# Remove water and receptor, write ligand
+# Remove water and receptor,
+ write ligand
 \end_layout
 
 \begin_layout LyX-Code
@@ -42703,8 +43470,8 @@ unwrap [center] [{byatom | byres | bymol}] [avgucell <avg ucell set>]
 
 \begin_deeper
 \begin_layout Description
-[center] Unwrap by center of mass; otherwise unwrap by first atom position
- (byres and bymol).
+[center] Unwrap by center of mass;
+ otherwise unwrap by first atom position (byres and bymol).
 \end_layout
 
 \begin_layout Description
@@ -42732,7 +43499,8 @@ ucell
 \begin_inset space ~
 \end_inset
 
-set>] Average unit cell data set; useful when unwrapping NPT trajectories.
+set>] Average unit cell data set;
+ useful when unwrapping NPT trajectories.
 \end_layout
 
 \begin_layout Description
@@ -42793,15 +43561,18 @@ oidal-view-preserving scheme (orthogonal boxes only).
 
 \end_deeper
 \begin_layout Standard
-Under periodic boundary conditions, MD trajectories are not continuous if
- molecules are wrapped(imaged) into the central unit cell.
- Especially, in sander, with 
+Under periodic boundary conditions,
+ MD trajectories are not continuous if molecules are wrapped(imaged) into the central unit cell.
+ Especially,
+ in sander,
+ with 
 \emph on
 iwrap
 \emph default
-=1, molecular trajectories become discontinuous when a molecule crosses
- the boundary of the unit cell.
- This command, 
+=1,
+ molecular trajectories become discontinuous when a molecule crosses the boundary of the unit cell.
+ This command,
+ 
 \family sans
 \series bold
 \emph on
@@ -42813,8 +43584,7 @@ unwrap
 \shape italic
 mask
 \shape default
-ed molecules continuous by translating the molecules into the neighboring
- unit cells.
+ed molecules continuous by translating the molecules into the neighboring unit cells.
  It is the opposite function of 
 \family sans
 \series bold
@@ -42823,20 +43593,25 @@ image
 \family default
 \series default
 \emph default
-, but this command can also be used to place molecules side by side, for
- example, two strands of a DNA duplex.
- However, this command may fail if the 
+,
+ but this command can also be used to place molecules side by side,
+ for example,
+ two strands of a DNA duplex.
+ However,
+ this command may fail if the 
 \shape italic
 mask
 \shape default
 ed entities travel more than half of the box size within a single frame.
- Note that uwrapping by atom (the default behavior) is slower than unwrapping
- by residue or molecule, but is usually the safer method, especially if
- it is unknown if the original imaging was done by atom, by residue, or
- by molecule.
- If the optional reference arguments are specified, then the first frame
- is unwrapped according to the reference structure.
- Otherwise, the first frame is not modified.
+ Note that uwrapping by atom (the default behavior) is slower than unwrapping by residue or molecule,
+ but is usually the safer method,
+ especially if it is unknown if the original imaging was done by atom,
+ by residue,
+ or by molecule.
+ If the optional reference arguments are specified,
+ then the first frame is unwrapped according to the reference structure.
+ Otherwise,
+ the first frame is not modified.
 \end_layout
 
 \begin_layout Standard
@@ -42848,12 +43623,13 @@ noise
 \begin_inset Quotes erd
 \end_inset
 
- caused by box fluctuations in NPT trajectories, the average unit cell vectors
- describing the average box can be provided with the 
+ caused by box fluctuations in NPT trajectories,
+ the average unit cell vectors describing the average box can be provided with the 
 \series bold
 avgucell
 \series default
- keyword; see the 
+ keyword;
+ see the 
 \series bold
 \emph on
 avgbox
@@ -42866,6 +43642,7 @@ reference "subsec:cpptraj_avgbox"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
@@ -42891,20 +43668,18 @@ https://arxiv.org/abs/2303.09418
 scheme tor.
 
 \series default
- However, note that this currently 
+ However,
+ note that this currently 
 \series bold
 only works for orthogonal boxes
 \series default
- and may result in unrealistic trajectories (particularly at long times
- when molecules have had the chance to traverse multiple box lengths) and
- is only currently recommended for calculating diffusion.
+ and may result in unrealistic trajectories (particularly at long times when molecules have had the chance to traverse multiple box lengths) and is only currently recommended for calculating diffusion.
 \end_layout
 
 \begin_layout Standard
-As an example, assume that :1-10 is the first strand of a DNA duplex and
- :11-20 is the other strand of the duplex.
- Then the following commands could be used to create system where the two
- strands are not separated artificially:
+As an example,
+ assume that :1-10 is the first strand of a DNA duplex and :11-20 is the other strand of the duplex.
+ Then the following commands could be used to create system where the two strands are not separated artificially:
 \end_layout
 
 \begin_layout LyX-Code
@@ -42920,8 +43695,8 @@ image origin center familiar
 \end_layout
 
 \begin_layout Standard
-To unwrap an NPT trajectory by using the average unit cell (box), the calculate
- diffusion from the unwrapped trajectory:
+To unwrap an NPT trajectory by using the average unit cell (box),
+ the calculate diffusion from the unwrapped trajectory:
 \end_layout
 
 \begin_layout LyX-Code
@@ -43005,7 +43780,8 @@ vector [<name>] <Type> [out <filename> [ptrajoutput]] [<mask1>] [<mask2>]
 \end_layout
 
 \begin_layout Description
-<Type> Vector type; see below.
+<Type> Vector type;
+ see below.
 \end_layout
 
 \begin_layout Description
@@ -43017,8 +43793,7 @@ vector [<name>] <Type> [out <filename> [ptrajoutput]] [<mask1>] [<mask2>]
 \series bold
 <filename>
 \series default
- with format 'Vx Vy Vz Ox Oy Oz' where V denotes vector coordinates and
- 'O' denotes origin coordinates.
+ with format 'Vx Vy Vz Ox Oy Oz' where V denotes vector coordinates and 'O' denotes origin coordinates.
 \end_layout
 
 \begin_layout Description
@@ -43039,7 +43814,8 @@ ptraj
 \end_layout
 
 \begin_layout Description
-[<mask1>] Atom mask, required for all types except 
+[<mask1>] Atom mask,
+ required for all types except 
 \series bold
 'box'
 \series default
@@ -43047,7 +43823,8 @@ ptraj
 \end_layout
 
 \begin_layout Description
-[<mask2>] Second atom mask, only required for type 
+[<mask2>] Second atom mask,
+ only required for type 
 \series bold
 'mask'
 \series default
@@ -43059,12 +43836,12 @@ ptraj
 \end_layout
 
 \begin_layout Description
-[geom] If specified, use geometric centers instead of centers of mass.
+[geom] If specified,
+ use geometric centers instead of centers of mass.
 \end_layout
 
 \begin_layout Description
-[ired] Mark this vector for subsequent IRED analysis with commands 'matrix
- ired' and 'ired'.
+[ired] Mark this vector for subsequent IRED analysis with commands 'matrix ired' and 'ired'.
 \end_layout
 
 \begin_layout Description
@@ -43072,16 +43849,17 @@ ptraj
 \begin_inset space ~
 \end_inset
 
-<grid>] Name of grid data set to get box info from instead of frame for
- 
+<grid>] Name of grid data set to get box info from instead of frame for 
 \series bold
 box
 \series default
-, 
+,
+ 
 \series bold
 boxcenter
 \series default
-, and 
+,
+ and 
 \series bold
 ucell[x|y|z]
 \series default
@@ -43114,8 +43892,8 @@ magnitude
 
 \end_deeper
 \begin_layout Standard
-This command will keep track of a vector value (and its origin) over the
- trajectory; the data can be referenced for later use based on the 
+This command will keep track of a vector value (and its origin) over the trajectory;
+ the data can be referenced for later use based on the 
 \shape italic
 name
 \shape default
@@ -43159,8 +43937,7 @@ dipole Store the dipole and center of mass of the atoms specified in
 \series default
  is specified for units of Debye.
  The center is always stored as simply Ang (since it is just coordinates).
- Note that the value may not be well-defined if the atoms in the mask are
- not overall charge neutral.
+ Note that the value may not be well-defined if the atoms in the mask are not overall charge neutral.
 \end_layout
 
 \begin_layout Description
@@ -43169,12 +43946,13 @@ center Store the center of mass of atoms in
 <mask1>
 \series default
 .
- The reference point is the origin (0.0, 0.0, 0.0).
+ The reference point is the origin (0.0,
+ 0.0,
+ 0.0).
 \end_layout
 
 \begin_layout Description
-corrplane This defines a vector perpendicular to the (least-squares best)
- plane through the atoms in 
+corrplane This defines a vector perpendicular to the (least-squares best) plane through the atoms in 
 \series bold
 <mask1>
 \series default
@@ -43188,7 +43966,9 @@ corrplane This defines a vector perpendicular to the (least-squares best)
 
 \begin_layout Description
 box (No mask needed) Store the box lengths of the trajectory.
- The reference point is the origin (0.0, 0.0, 0.0).
+ The reference point is the origin (0.0,
+ 0.0,
+ 0.0).
  
 \end_layout
 
@@ -43197,7 +43977,8 @@ boxcenter (No mask needed) Store the center of the box as a vector.
 \end_layout
 
 \begin_layout Description
-ucell{x|y|z}: (No mask needed) Store specified unit cell (i.e.
+ucell{x|y|z}:
+ (No mask needed) Store specified unit cell (i.e.
  box) vector.
 \end_layout
 
@@ -43210,8 +43991,7 @@ principal
 \begin_inset space ~
 \end_inset
 
-[x|y|z] Store one of the principal axis vectors determined by diagonalization
- of the inertial matrix from the coordinates of the atoms specified by 
+[x|y|z] Store one of the principal axis vectors determined by diagonalization of the inertial matrix from the coordinates of the atoms specified by 
 \series bold
 <mask1>
 \series default
@@ -43228,8 +44008,8 @@ x
 \begin_inset Quotes erd
 \end_inset
 
- (i.e., the hardest axis to rotate around) and the eigenvector with the smallest
- eigenvalue is considered 
+ (i.e.,
+ the hardest axis to rotate around) and the eigenvector with the smallest eigenvalue is considered 
 \begin_inset Quotes eld
 \end_inset
 
@@ -43254,7 +44034,8 @@ y
 \family typewriter
 z
 \family default
- are specified, then the 
+ are specified,
+ then the 
 \begin_inset Quotes eld
 \end_inset
 
@@ -43279,21 +44060,20 @@ force Store force of atoms in <mask1> (requires forces).
 \end_layout
 
 \begin_layout Standard
-Cpptraj supports writing out vector data in a pseudo-trajectory format for
- easy visualization.
- Once a vector data set has been generated the writedata command can be
- used with the vectraj keyword (see 
+Cpptraj supports writing out vector data in a pseudo-trajectory format for easy visualization.
+ Once a vector data set has been generated the writedata command can be used with the vectraj keyword (see 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "sec:Datafile-Commands"
+nolink "false"
 
 \end_inset
 
  for more details) to write a pseudo trajectory consisting of two atoms,
  one for the vector origin and one for the vector from the origin (i.e.
  V+O).
- For example, to create a MOL2 containing a pseudo-trajectory of the minimum-ima
-ged vector from residue 4 to residue 11:
+ For example,
+ to create a MOL2 containing a pseudo-trajectory of the minimum-imaged vector from residue 4 to residue 11:
 \end_layout
 
 \begin_layout LyX-Code
@@ -43313,8 +44093,7 @@ writedata v8.mol2 vectraj v8 trajfmt mol2
 \end_layout
 
 \begin_layout Standard
-Auto-correlation or cross-correlation functions can be calculated subsequently
- for vectors using either the 
+Auto-correlation or cross-correlation functions can be calculated subsequently for vectors using either the 
 \series bold
 \emph on
 corr
@@ -43334,8 +44113,7 @@ velocityautocorr
 \end_layout
 
 \begin_layout LyX-Code
-velocityautocorr [<set name>] [<mask>] [usevelocity] [out <filename>] [diffout
- <file>]
+velocityautocorr [<set name>] [<mask>] [usevelocity] [out <filename>] [diffout <file>]
 \end_layout
 
 \begin_layout LyX-Code
@@ -43361,8 +44139,7 @@ name>] Data set name.
 
 \begin_layout Description
 [usevelocity] Use velocity information in frame if present.
- This will only give sensible results if the velocities are recorded close
- to the order of the simulation time step.
+ This will only give sensible results if the velocities are recorded close to the order of the simulation time step.
 \end_layout
 
 \begin_layout Description
@@ -43399,8 +44176,7 @@ name>] Data set name.
 \end_layout
 
 \begin_layout Description
-[direct] Calculate VAC function directly instead of via FFT (will be much
- slower).
+[direct] Calculate VAC function directly instead of via FFT (will be much slower).
 \end_layout
 
 \begin_layout Description
@@ -43435,15 +44211,12 @@ DataSet Aspects:
 
 \end_deeper
 \begin_layout Standard
-Calculate the velocity autocorrelation (VAC) function averaged over the
- atoms in <mask>.
- Pseudo-velocities are calculated using coordinates and the specified time
- step.
- As with all time correlation functions the statistical noise will increase
- if the maximum lag is greater than half the total number of frames.
- In addition to calculating the velocity autocorrelation function, the self-diff
-usion coefficient will be reported in the output, calculated from the integral
- over the VAC function.
+Calculate the velocity autocorrelation (VAC) function averaged over the atoms in <mask>.
+ Pseudo-velocities are calculated using coordinates and the specified time step.
+ As with all time correlation functions the statistical noise will increase if the maximum lag is greater than half the total number of frames.
+ In addition to calculating the velocity autocorrelation function,
+ the self-diffusion coefficient will be reported in the output,
+ calculated from the integral over the VAC function.
 \end_layout
 
 \begin_layout Subsection
@@ -43524,8 +44297,8 @@ radscale
 <factor> 
 \family default
 Factor by which to scale radii (by division).
- To match the atomic radius of Oxygen used by the VMD volmap tool, a scaling
- factor of 1.36 should be used.
+ To match the atomic radius of Oxygen used by the VMD volmap tool,
+ a scaling factor of 1.36 should be used.
  Default 1.0.
 \end_layout
 
@@ -43534,8 +44307,8 @@ stepfac
 \begin_inset space ~
 \end_inset
 
-<factor> Factor for determining how many voxels to smear Gaussian (default
- 4.1, 1.0 for 
+<factor> Factor for determining how many voxels to smear Gaussian (default 4.1,
+ 1.0 for 
 \series bold
 sphere
 \series default
@@ -43543,7 +44316,8 @@ sphere
 \end_layout
 
 \begin_layout Description
-sphere When smearing Gaussian, skip voxels farther than radii/2.
+sphere When smearing Gaussian,
+ skip voxels farther than radii/2.
 \end_layout
 
 \begin_layout Description
@@ -43551,8 +44325,7 @@ radii
 \begin_inset space ~
 \end_inset
 
-{vdw|element} Specify either van der Waals radii (default) or elemental
- radii.
+{vdw|element} Specify either van der Waals radii (default) or elemental radii.
 \end_layout
 
 \begin_layout Description
@@ -43564,8 +44337,8 @@ splinedx
 \end_layout
 
 \begin_layout Description
-calcpeaks If specified, peaks in the grid density will be calculated and
- saved to set <setname> with aspect 
+calcpeaks If specified,
+ peaks in the grid density will be calculated and saved to set <setname> with aspect 
 \begin_inset Quotes eld
 \end_inset
 
@@ -43585,8 +44358,7 @@ peakcut
 
 <cutoff> 
 \family default
-The minimum density required to consider a local maximum a 'density peak'
- in the outputted peak file (default 0.05).
+The minimum density required to consider a local maximum a 'density peak' in the outputted peak file (default 0.05).
 \end_layout
 
 \begin_layout Description
@@ -43598,8 +44370,7 @@ peakfile
 
 <xyzfile> 
 \family default
-A file in XYZ-format that contains a carbon atom centered at the grid point
- of every local density maximum.
+A file in XYZ-format that contains a carbon atom centered at the grid point of every local density maximum.
  This file is necessary input to the spam action command.
 \end_layout
 
@@ -43640,7 +44411,10 @@ dy,
 
 dz 
 \family default
-The grid spacing (Angstroms) in the X-, Y-, and Z-dimensions, respectively.
+The grid spacing (Angstroms) in the X-,
+ Y-,
+ and Z-dimensions,
+ respectively.
 \end_layout
 
 \begin_layout Description
@@ -43652,7 +44426,9 @@ size
 
 <x,y,z> 
 \family default
-Specify the size of the grid in the X-, Y-, and Z-dimensions.
+Specify the size of the grid in the X-,
+ Y-,
+ and Z-dimensions.
  Must be used alongside the center argument.
 \end_layout
 
@@ -43667,7 +44443,8 @@ center
 <x,y,z> 
 \family default
 Specify the grid center explicitly.
- Note, the size argument must be present in this case.
+ Note,
+ the size argument must be present in this case.
  Default is the origin.
 \end_layout
 
@@ -43682,8 +44459,8 @@ centermask
 <mask> 
 \family default
 The mask around which the grid should be centered (via geometric center).
- If this is omitted and the center and size are not specified, the default
- <mask> entered (see above) is used in its place.
+ If this is omitted and the center and size are not specified,
+ the default <mask> entered (see above) is used in its place.
 \end_layout
 
 \begin_deeper
@@ -43696,9 +44473,9 @@ buffer
 
 <buffer> 
 \family default
-A buffer distance, in Angstroms, by which the edges of the grid should clear
- every atom of the centermask (or default mask if centermask is omitted)
- in every direction.
+A buffer distance,
+ in Angstroms,
+ by which the edges of the grid should clear every atom of the centermask (or default mask if centermask is omitted) in every direction.
  The default value is 3.
  The buffer is ignored if the center and size are specified (see below).
 \end_layout
@@ -43730,17 +44507,17 @@ calcpeaks
 
 \end_deeper
 \begin_layout Standard
-Grid data as a volumetric map, similar to the 'volmap' command in VMD.
- The density is calculated by treating each atom as a 3-dimensional Gaussian
- function whose standard deviation is equal to the van der Waals radius.
- The density calculated is the number density averaged over the entire simulatio
-n.
+Grid data as a volumetric map,
+ similar to the 'volmap' command in VMD.
+ The density is calculated by treating each atom as a 3-dimensional Gaussian function whose standard deviation is equal to the van der Waals radius.
+ The density calculated is the number density averaged over the entire simulation.
  The grid can be specified in one of three ways:
 \end_layout
 
 \begin_layout Enumerate
 An existing grid data set (from e.g.
- bounds), specified with the 
+ bounds),
+ specified with the 
 \series bold
 data
 \series default
@@ -43756,7 +44533,8 @@ size
 \series bold
 center
 \series default
- keywords (comma-separated strings, e.g.
+ keywords (comma-separated strings,
+ e.g.
  '20,20,20').
 \end_layout
 
@@ -43773,8 +44551,7 @@ buffer
 \end_layout
 
 \begin_layout Standard
-The calculation is sped up by using cubic splines to interpolate the exponential
- function when calculating the Gaussians.
+The calculation is sped up by using cubic splines to interpolate the exponential function when calculating the Gaussians.
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Roe2021"
@@ -43820,8 +44597,7 @@ watershell
 \end_layout
 
 \begin_layout LyX-Code
-watershell <solutemask> [out <filename>] [lower <lower cut>] [upper <upper
- cut>]
+watershell <solutemask> [out <filename>] [lower <lower cut>] [upper <upper cut>]
 \end_layout
 
 \begin_layout LyX-Code
@@ -43891,9 +44667,7 @@ DataSet Aspects:
 
 \end_deeper
 \begin_layout Standard
-This option will count the number of waters within a certain distance of
- the atoms in the <solutemask> in order to represent the first and second
- solvation shells.
+This option will count the number of waters within a certain distance of the atoms in the <solutemask> in order to represent the first and second solvation shells.
  The optional <solventmask> can be used to consider other atoms as the solvent;
  the default is 
 \begin_inset Quotes eld
@@ -43913,8 +44687,7 @@ This action is often used prior to the
 closest
 \series default
 \shape default
- command in order to determine how many waters around a solute should be
- retained to maintain the first and/or second water shells.
+ command in order to determine how many waters around a solute should be retained to maintain the first and/or second water shells.
 \end_layout
 
 \begin_layout Standard
@@ -43939,8 +44712,7 @@ xtalsymm <mask> group <space group> [collect [centroid]]
 
 \begin_deeper
 \begin_layout Description
-<mask> Atom mask defining the asymmetric unit within the larger system (required
-).
+<mask> Atom mask defining the asymmetric unit within the larger system (required).
 \end_layout
 
 \begin_layout Description
@@ -43954,7 +44726,8 @@ group
 
 group> The space group to which the system belongs.
  Omit spaces in the name.
- Example: 
+ Example:
+ 
 \begin_inset Quotes eld
 \end_inset
 
@@ -43966,10 +44739,10 @@ P22(1)2(1)
 \end_layout
 
 \begin_layout Description
-[collect] Optional flag to have all solvent particles, not just the asymmetric
- units, re-imaged.
- This will trigger cpptraj to compute the unit cell volume that constitutes
- the aymmetric unit and thereby classify all particles for re-imaging.
+[collect] Optional flag to have all solvent particles,
+ not just the asymmetric units,
+ re-imaged.
+ This will trigger cpptraj to compute the unit cell volume that constitutes the aymmetric unit and thereby classify all particles for re-imaging.
 \end_layout
 
 \begin_deeper
@@ -43978,7 +44751,9 @@ P22(1)2(1)
 \series bold
 collect
 \series default
-, re-image solvent molecules by centroids, not individual atom coordinates.
+,
+ re-image solvent molecules by centroids,
+ not individual atom coordinates.
  This is useful for keeping water molecules intact.
 \end_layout
 
@@ -44040,41 +44815,38 @@ refindex
 \begin_inset space ~
 \end_inset
 
-<nc>] The number of times the crystal unit cell is replicated along the
- “a,” “b,” or “c” axes (for orthorhombic unti cells, these are the x, y,
- and z axes) of the simulation; default is 1.
- Many crystal unit cells are too small in one or more dimensions for our
- simulation cutoffs, and replicating the unit cell is an effective way to
- counter imaging artifacts even for larger unit cells.
+<nc>] The number of times the crystal unit cell is replicated along the “a,” “b,” or “c” axes (for orthorhombic unti cells,
+ these are the x,
+ y,
+ and z axes) of the simulation;
+ default is 1.
+ Many crystal unit cells are too small in one or more dimensions for our simulation cutoffs,
+ and replicating the unit cell is an effective way to counter imaging artifacts even for larger unit cells.
 \end_layout
 
 \end_deeper
 \begin_layout Standard
-Calculate the optimal approach for superimposing symmetry-related subunits
- of the simulation back onto one another.
- The calculation assumes that the system is a simulation of an X-ray structure
- in its native crystal lattice, finds all copies of the asymmetric unit
- among the entire system, and devises plans for re-imagining their coordinates
- to superimpose them back on the original asymmetric unit.
- The space group information can be found in a PDB X-ray structure used
- as the initial coordinates for a simulation.
- All 230 space groups are supported, and a scan of the PDB was made to ensure
- that common variants of the names are included (P2(1)22(1) is the same
- as P22(1)2(1), but with different axis conventions).
- If your space group is not understood, contact the Amber mailing list.
- This command is compute intensive, especially for simulations that are
- “supercells” containing many crystallographic unit cells.
+Calculate the optimal approach for superimposing symmetry-related subunits of the simulation back onto one another.
+ The calculation assumes that the system is a simulation of an X-ray structure in its native crystal lattice,
+ finds all copies of the asymmetric unit among the entire system,
+ and devises plans for re-imagining their coordinates to superimpose them back on the original asymmetric unit.
+ The space group information can be found in a PDB X-ray structure used as the initial coordinates for a simulation.
+ All 230 space groups are supported,
+ and a scan of the PDB was made to ensure that common variants of the names are included (P2(1)22(1) is the same as P22(1)2(1),
+ but with different axis conventions).
+ If your space group is not understood,
+ contact the Amber mailing list.
+ This command is compute intensive,
+ especially for simulations that are “supercells” containing many crystallographic unit cells.
 \end_layout
 
 \begin_layout Standard
-This command will cause cpptraj to locate all asymmetric units from within
- the topology, then determine what wrapping, if any, has occurred in order
- to bring about an optimal re-alignment based on the space group symmetry
- operations.
- The user need not worry about wrapping or drift of the simulation over
- time–the asymmetric units will be re-imaged frame by frame.
- Coordinate modifications due to this action are permanent and will affect
- the results of subsequent actions and analyses.
+This command will cause cpptraj to locate all asymmetric units from within the topology,
+ then determine what wrapping,
+ if any,
+ has occurred in order to bring about an optimal re-alignment based on the space group symmetry operations.
+ The user need not worry about wrapping or drift of the simulation over time–the asymmetric units will be re-imaged frame by frame.
+ Coordinate modifications due to this action are permanent and will affect the results of subsequent actions and analyses.
 \end_layout
 
 \begin_layout Section
@@ -44086,8 +44858,7 @@ Analyses in
 \emph on
 cpptraj
 \emph default
- operate on data sets which have been generated by Actions in a prior Run
- or read in with a 
+ operate on data sets which have been generated by Actions in a prior Run or read in with a 
 \series bold
 \emph on
 readdata
@@ -44097,6 +44868,7 @@ readdata
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_readdata"
+nolink "false"
 
 \end_inset
 
@@ -44105,7 +44877,8 @@ reference "subsec:cpptraj_readdata"
 \emph on
 ptraj
 \emph default
-, Analysis commands in 
+,
+ Analysis commands in 
 \emph on
 cpptraj
 \emph default
@@ -44126,7 +44899,8 @@ analyze matrix
 matrix
 \series default
 \emph default
- Action command; users are encouraged to use the new command 
+ Action command;
+ users are encouraged to use the new command 
 \series bold
 \emph on
 diagmatrix
@@ -44136,11 +44910,9 @@ diagmatrix
 \end_layout
 
 \begin_layout Standard
-Like Actions, when an Analysis command is issued it is by default added
- to the Analysis queue and is not executed until after trajectory processing
- is completed; a complete list of data sets available for analysis is shown
- after trajectory processing (prefaced by 'DATASETS') or can be shown with
- the '
+Like Actions,
+ when an Analysis command is issued it is by default added to the Analysis queue and is not executed until after trajectory processing is completed;
+ a complete list of data sets available for analysis is shown after trajectory processing (prefaced by 'DATASETS') or can be shown with the '
 \series bold
 \emph on
 list dataset
@@ -44157,6 +44929,7 @@ runanalysis
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_runanalysis"
+nolink "false"
 
 \end_inset
 
@@ -44164,9 +44937,8 @@ reference "subsec:cpptraj_runanalysis"
 \end_layout
 
 \begin_layout Standard
-Note that for Analysis commands that use COORDS data sets, if no COORDS
- data set is specified then a default one will be automatically created
- from frames read in by 
+Note that for Analysis commands that use COORDS data sets,
+ if no COORDS data set is specified then a default one will be automatically created from frames read in by 
 \series bold
 \emph on
 trajin
@@ -44265,7 +45037,10 @@ avg
 \begin_inset Text
 
 \begin_layout Plain Layout
-Calculate average, standard deviation, min, and max for (or over) data sets.
+Calculate average,
+ standard deviation,
+ min,
+ and max for (or over) data sets.
 \end_layout
 
 \end_inset
@@ -44361,7 +45136,8 @@ Perform cluster analysis.
 \begin_inset Text
 
 \begin_layout Plain Layout
-COORDS, N 1D scalar
+COORDS,
+ N 1D scalar
 \end_layout
 
 \end_inset
@@ -44390,7 +45166,8 @@ Calculate auto or cross correlation for 1 or 2 data sets.
 \begin_inset Text
 
 \begin_layout Plain Layout
-1D scalar, vector
+1D scalar,
+ vector
 \end_layout
 
 \end_inset
@@ -44459,7 +45236,8 @@ pH data sets
 \begin_inset Text
 
 \begin_layout Plain Layout
-crank, 
+crank,
+ 
 \end_layout
 
 \end_inset
@@ -44778,7 +45556,8 @@ N 2D matrices
 \begin_inset Text
 
 \begin_layout Plain Layout
-hist, histogram
+hist,
+ histogram
 \end_layout
 
 \end_inset
@@ -44990,7 +45769,8 @@ lowestcurve
 \begin_inset Text
 
 \begin_layout Plain Layout
-For each given data set, calculate a curve that traces 
+For each given data set,
+ calculate a curve that traces 
 \end_layout
 
 \end_inset
@@ -45200,8 +45980,7 @@ phipsi
 \begin_inset Text
 
 \begin_layout Plain Layout
-Calculate and plot the average phi and psi values from input dihedral data
- sets.
+Calculate and plot the average phi and psi values from input dihedral data sets.
 \end_layout
 
 \end_inset
@@ -45239,7 +46018,8 @@ Project data along eigenmodes.
 \begin_inset Text
 
 \begin_layout Plain Layout
-eigenmodes, N 1D scalar
+eigenmodes,
+ N 1D scalar
 \end_layout
 
 \end_inset
@@ -45308,7 +46088,8 @@ replica log
 \begin_inset Text
 
 \begin_layout Plain Layout
-rms2d, 2drms
+rms2d,
+ 2drms
 \end_layout
 
 \end_inset
@@ -45460,7 +46241,8 @@ N 1D scalar
 \begin_inset Text
 
 \begin_layout Plain Layout
-stat, statistics
+stat,
+ statistics
 \end_layout
 
 \end_inset
@@ -45536,7 +46318,8 @@ Perform time-independent correlation analysis.
 \begin_inset Text
 
 \begin_layout Plain Layout
-COORDS, N 1D scalar
+COORDS,
+ N 1D scalar
 \end_layout
 
 \end_inset
@@ -45748,14 +46531,16 @@ autocorr [name <dsetname>] <dsetarg0> [<dsetarg1> ...] [out <filename>]
 \series bold
 [direct]
 \series default
- Do not use FFTs to calculate correlation; this will be much slower.
+ Do not use FFTs to calculate correlation;
+ this will be much slower.
 \end_layout
 
 \end_deeper
 \begin_layout Standard
 
 \shape italic
-This is for integer/double/float datasets only; for vectors see the 
+This is for integer/double/float datasets only;
+ for vectors see the 
 \series bold
 'timecorr'
 \series default
@@ -45763,8 +46548,7 @@ This is for integer/double/float datasets only; for vectors see the
 \end_layout
 
 \begin_layout Standard
-Calculate auto-correlation (actually auto-covariance by default) function
- for datasets specified by one or more dataset arguments.
+Calculate auto-correlation (actually auto-covariance by default) function for datasets specified by one or more dataset arguments.
  The datasets must have the same # of data points.
 \end_layout
 
@@ -45791,7 +46575,8 @@ avg <dset0> [<dset1> ...] [torsion] [out <file>] [oversets]
 
 \begin_layout Description
 [torsion] If the data sets are not already marked periodic (e.g.
- if read in via 'readdata'), treat them as periodic torsion.
+ if read in via 'readdata'),
+ treat them as periodic torsion.
 \end_layout
 
 \begin_layout Description
@@ -45803,8 +46588,8 @@ avg <dset0> [<dset1> ...] [torsion] [out <file>] [oversets]
 \end_layout
 
 \begin_layout Description
-[oversets] If specified, calculate the average over all inpout sets instead
- of each input set.
+[oversets] If specified,
+ calculate the average over all inpout sets instead of each input set.
 \end_layout
 
 \begin_layout Description
@@ -45816,8 +46601,7 @@ avg <dset0> [<dset1> ...] [torsion] [out <file>] [oversets]
 \end_layout
 
 \begin_layout Description
-[nostdout] If 'nostdout' specified do not write averages to STDOUT when
- 'out' not specified.
+[nostdout] If 'nostdout' specified do not write averages to STDOUT when 'out' not specified.
 \end_layout
 
 \begin_layout Standard
@@ -45874,19 +46658,22 @@ DataSets Created (oversets)
 \end_layout
 
 \begin_layout Standard
-Calculate the average, standard deviation, min, and max of given 1D data
- sets.
- Alternatively, if 
+Calculate the average,
+ standard deviation,
+ min,
+ and max of given 1D data sets.
+ Alternatively,
+ if 
 \series bold
 oversets
 \series default
- is specified the average over each set for each point is calculated; this
- requires all input sets be the same size.
+ is specified the average over each set for each point is calculated;
+ this requires all input sets be the same size.
 \end_layout
 
 \begin_layout Standard
-For example, to read in data from a file named perres.peptide.dat and calculate
- the averages etc for all the input sets:
+For example,
+ to read in data from a file named perres.peptide.dat and calculate the averages etc for all the input sets:
 \end_layout
 
 \begin_layout LyX-Code
@@ -45967,8 +46754,7 @@ set>] Input COORDS set to calculate diffusion for.
 \begin_inset space ~
 \end_inset
 
-<file>] Write diffusion contants calculated from fits of MSD data sets to
- <filename>.
+<file>] Write diffusion contants calculated from fits of MSD data sets to <filename>.
 \end_layout
 
 \begin_layout Standard
@@ -46049,25 +46835,28 @@ reference "subsec:cpptraj-diffusion"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
-), which calculates MSD from a single time origin, the 
+),
+ which calculates MSD from a single time origin,
+ the 
 \series bold
 \emph on
 calcdiffusion
 \series default
 \emph default
- command calculates diffusion from multiple time origins up to a user-specified
- lag (in frames).
- Note that no imaging is performed for this command, so any unwrapping should
- be performed prior to this command (see 
+ command calculates diffusion from multiple time origins up to a user-specified lag (in frames).
+ Note that no imaging is performed for this command,
+ so any unwrapping should be performed prior to this command (see 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_unwrap"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
@@ -46078,13 +46867,15 @@ noprefix "false"
 diffusion
 \series default
 \emph default
- command; for more details see 
+ command;
+ for more details see 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-diffusion"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
@@ -46092,18 +46883,18 @@ noprefix "false"
 \end_layout
 
 \begin_layout Standard
-This command is both OpenMP- and MPI-parallelized; either or both can be
- active.
- In order to keep per-process memory requirements low, it is recommended
- that TRAJ (i.e.
- on-disk) data sets be used with MPI instead of CRD (in-memory) sets (see
- 
+This command is both OpenMP- and MPI-parallelized;
+ either or both can be active.
+ In order to keep per-process memory requirements low,
+ it is recommended that TRAJ (i.e.
+ on-disk) data sets be used with MPI instead of CRD (in-memory) sets (see 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-loadtraj"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
@@ -46111,9 +46902,8 @@ noprefix "false"
 \end_layout
 
 \begin_layout Standard
-For example, to calculate diffusion from multiple time origins (with a maximum
- lag of half the number of trajectrory frames) from an input trajectory
- in memory (unwrapping first):
+For example,
+ to calculate diffusion from multiple time origins (with a maximum lag of half the number of trajectrory frames) from an input trajectory in memory (unwrapping first):
 \end_layout
 
 \begin_layout LyX-Code
@@ -46133,9 +46923,9 @@ runanalysis calcdiffusion crdset TZ2 out tz2.diff.dat :WAT@O
 \end_layout
 
 \begin_layout Standard
-To do the same calculation using MPI parallelism, it will first be necessary
- to unwrap the trajectory (non-MPI parallel, but OpenMP parallelism can
- be used):
+To do the same calculation using MPI parallelism,
+ it will first be necessary to unwrap the trajectory (non-MPI parallel,
+ but OpenMP parallelism can be used):
 \end_layout
 
 \begin_layout LyX-Code
@@ -46175,8 +46965,7 @@ calcstate
 \end_layout
 
 \begin_layout LyX-Code
-calcstate {state <ID>,<dataset>,<min>,<max>[,<dataset1>,<min1>,<max1>]}
- ...
+calcstate {state <ID>,<dataset>,<min>,<max>[,<dataset1>,<min1>,<max1>]} ...
 \end_layout
 
 \begin_layout LyX-Code
@@ -46201,13 +46990,13 @@ state
 \begin_inset space ~
 \end_inset
 
-<ID>,<dataset>,<min>,<max> Define a state according to given data set and
- criteria.
- Multiple states can be given, and each state can have multiple criteria.
- If multiple criteria are specified, each one must be satisfied in order
- to assign the state.
- If the same state is defined multiple times, the state will be assigned
- if either criteria match.
+<ID>,<dataset>,<min>,<max> Define a state according to given data set and criteria.
+ Multiple states can be given,
+ and each state can have multiple criteria.
+ If multiple criteria are specified,
+ each one must be satisfied in order to assign the state.
+ If the same state is defined multiple times,
+ the state will be assigned if either criteria match.
 \begin_inset Separator latexpar
 \end_inset
 
@@ -46234,8 +47023,7 @@ undefined state
 \end_layout
 
 \begin_layout Description
-<min>,<max> Frames with data set value above <min> and below <max> will
- be assigned <ID>.
+<min>,<max> Frames with data set value above <min> and below <max> will be assigned <ID>.
 \end_layout
 
 \end_deeper
@@ -46353,22 +47141,20 @@ DataSets Created:
 \end_layout
 
 \begin_layout Description
-<setname>[Xlifetimes] Number of times each state transitioned to each other
- state.
+<setname>[Xlifetimes] Number of times each state transitioned to each other state.
 \end_layout
 
 \begin_layout Description
-<setname>[Xavglife] Average lifetime of each state before transitioning
- to each other state.
+<setname>[Xavglife] Average lifetime of each state before transitioning to each other state.
 \end_layout
 
 \begin_layout Description
-<setname>[Xmaxlife] Maximum lifetime of each state before transitioning
- to each other state.
+<setname>[Xmaxlife] Maximum lifetime of each state before transitioning to each other state.
 \end_layout
 
 \begin_layout Description
-<setname>[Xname] Name of each transition, format 
+<setname>[Xname] Name of each transition,
+ format 
 \begin_inset Quotes eld
 \end_inset
 
@@ -46380,19 +47166,18 @@ StateA->StateB
 \end_layout
 
 \begin_layout Description
-<setname>[sCurve]:X State curves; lifetime curve for transitions from given
- state to any other state.
+<setname>[sCurve]:X State curves;
+ lifetime curve for transitions from given state to any other state.
 \end_layout
 
 \begin_layout Description
-<setname>[tCurve]:X Transition curves; lifetime curve for transitions from
- given state to other specific state.
+<setname>[tCurve]:X Transition curves;
+ lifetime curve for transitions from given state to other specific state.
 \end_layout
 
 \end_deeper
 \begin_layout Standard
-Data for the specified data set(s) that matches the given criteria will
- be assigned a state index.
+Data for the specified data set(s) that matches the given criteria will be assigned a state index.
  State indices start from 0 and match the order in which 
 \series bold
 state
@@ -46407,7 +47192,8 @@ undefined state
 \end_inset
 
 .
- For example, the following input:
+ For example,
+ the following input:
 \end_layout
 
 \begin_layout LyX-Code
@@ -46427,8 +47213,7 @@ angle a1 :19@O :12@H :12@N
 \end_layout
 
 \begin_layout LyX-Code
-calcstate state D,d1,3.0,4.0 state A,a1,100,120 out state.dat curveout curve.agr
- 
+calcstate state D,d1,3.0,4.0 state A,a1,100,120 out state.dat curveout curve.agr 
 \backslash
 
 \end_layout
@@ -46451,8 +47236,7 @@ D
 \begin_inset Quotes erd
 \end_inset
 
- based on the distance from ':19@O' to ':12@N' (data set d1) being between
- 3 and 4 Angstroms.
+ based on the distance from ':19@O' to ':12@N' (data set d1) being between 3 and 4 Angstroms.
  State index 1 is defined as a state named 
 \begin_inset Quotes eld
 \end_inset
@@ -46461,8 +47245,9 @@ A
 \begin_inset Quotes erd
 \end_inset
 
- based on the angle between ':19@O', ':12@H', and ':12@N' (data set a1)
- being between 100 and 120 degrees.
+ based on the angle between ':19@O',
+ ':12@H',
+ and ':12@N' (data set a1) being between 100 and 120 degrees.
  The output in state.dat might look like:
 \end_layout
 
@@ -46511,7 +47296,8 @@ A
 \end_layout
 
 \begin_layout Standard
-where the values in column d1_a1 refer to state index: -1 is undefined,
+where the values in column d1_a1 refer to state index:
+ -1 is undefined,
  0 is state 
 \begin_inset Quotes eld
 \end_inset
@@ -46520,7 +47306,8 @@ D
 \begin_inset Quotes erd
 \end_inset
 
-, and 1 is state 
+,
+ and 1 is state 
 \begin_inset Quotes eld
 \end_inset
 
@@ -46575,46 +47362,51 @@ Lifetime curves (see
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-lifetime"
+nolink "false"
 
 \end_inset
 
- for further explanation) are calculated for transitions from each state
- to any other state (aspect [sCurve]) and each state to each other state
- (aspect [tCurve]).
+ for further explanation) are calculated for transitions from each state to any other state (aspect [sCurve]) and each state to each other state (aspect [tCurve]).
  In this case there will be 3 sCurves and 4 tCurves:
 \end_layout
 
 \begin_layout LyX-Code
-d1_a1[sCurve]:0 "Undefined" (double), size is 10 
+d1_a1[sCurve]:0 "Undefined" (double),
+ size is 10 
 \end_layout
 
 \begin_layout LyX-Code
-d1_a1[sCurve]:1 "D" (double), size is 3 
+d1_a1[sCurve]:1 "D" (double),
+ size is 3 
 \end_layout
 
 \begin_layout LyX-Code
-d1_a1[sCurve]:2 "A" (double), size is 1 
+d1_a1[sCurve]:2 "A" (double),
+ size is 1 
 \end_layout
 
 \begin_layout LyX-Code
-d1_a1[tCurve]:0 "Undefined->D" (double), size is 10
+d1_a1[tCurve]:0 "Undefined->D" (double),
+ size is 10
 \end_layout
 
 \begin_layout LyX-Code
-d1_a1[tCurve]:1 "D->Undefined" (double), size is 3
+d1_a1[tCurve]:1 "D->Undefined" (double),
+ size is 3
 \end_layout
 
 \begin_layout LyX-Code
-d1_a1[tCurve]:2 "Undefined->A" (double), size is 1
+d1_a1[tCurve]:2 "Undefined->A" (double),
+ size is 1
 \end_layout
 
 \begin_layout LyX-Code
-d1_a1[tCurve]:3 "A->Undefined" (double), size is 1
+d1_a1[tCurve]:3 "A->Undefined" (double),
+ size is 1
 \end_layout
 
 \begin_layout Standard
-Lifetime analysis from each state to any other state is directed to the
- file specified by 
+Lifetime analysis from each state to any other state is directed to the file specified by 
 \series bold
 stateout
 \series default
@@ -46630,15 +47422,18 @@ Where
 \family typewriter
 #Index
 \family default
- is the state index, 
+ is the state index,
+ 
 \family typewriter
 N
 \family default
- is the number of lifetimes in that state, 
+ is the number of lifetimes in that state,
+ 
 \family typewriter
 Average
 \family default
- is the average lifetime while in that state (in frames), 
+ is the average lifetime while in that state (in frames),
+ 
 \family typewriter
 Max
 \family default
@@ -46650,8 +47445,8 @@ State
 \end_layout
 
 \begin_layout Standard
-Finally, lifetime analysis of transitions from each state to each other
- state is directory to the file specified by transout and has format:
+Finally,
+ lifetime analysis of transitions from each state to each other state is directory to the file specified by transout and has format:
 \end_layout
 
 \begin_layout LyX-Code
@@ -46663,12 +47458,13 @@ Where
 \family typewriter
 #N
 \family default
- is the number of transitions, 
+ is the number of transitions,
+ 
 \family typewriter
 Average
 \family default
- is the average lifetime (in frames) in the first state before transitioning
- to the second state, 
+ is the average lifetime (in frames) in the first state before transitioning to the second state,
+ 
 \family typewriter
 Max
 \family default
@@ -46693,6 +47489,8 @@ cluster
 \begin_layout LyX-Code
 cluster
 \begin_inset Index idx
+range none
+pageformat default
 status open
 
 \begin_layout Plain Layout
@@ -46722,7 +47520,8 @@ cluster
 \end_layout
 
 \begin_layout LyX-Code
-  Algorithm Args: [{hieragglo|dbscan|kmeans|dpeaks}]
+  Algorithm Args:
+ [{hieragglo|dbscan|kmeans|dpeaks}]
 \end_layout
 
 \begin_layout LyX-Code
@@ -46762,8 +47561,7 @@ cluster
 \end_layout
 
 \begin_layout LyX-Code
-	[{dme|rms|srmsd|qrmsd} [mass] [nofit] [<mask>]] [{euclid|manhattan}] [wgt
- <list>]
+	[{dme|rms|srmsd|qrmsd} [mass] [nofit] [<mask>]] [{euclid|manhattan}] [wgt <list>]
 \end_layout
 
 \begin_layout LyX-Code
@@ -46865,8 +47663,7 @@ cluster
 \end_inset
 
 set>] Name of COORDS data set to cluster on and/or use for coordinate output.
- If not specified the default COORDS set will be generated and used unless
- 
+ If not specified the default COORDS set will be generated and used unless 
 \series bold
 nocoords
 \series default
@@ -46878,15 +47675,14 @@ nocoords
 \begin_inset space ~
 \end_inset
 
-<dset0>[,<dset1>,...] Distance between frames calculated using specified data
- set(s).
+<dset0>[,<dset1>,...] Distance between frames calculated using specified data set(s).
  Currently 1D scalar sets and COORDS sets are supported.
 \end_layout
 
 \begin_deeper
 \begin_layout Description
-[nocoords] Do not use a COORDS data set; distance metrics that require coordinat
-es and coordinate output will be disabled.
+[nocoords] Do not use a COORDS data set;
+ distance metrics that require coordinates and coordinate output will be disabled.
 \end_layout
 
 \end_deeper
@@ -46927,8 +47723,8 @@ cnvtset
 
 \end_deeper
 \begin_layout Description
-[useframesincache] If a pairwise cache is specified, cluster on the frames
- stored in the cache.
+[useframesincache] If a pairwise cache is specified,
+ cluster on the frames stored in the cache.
 \end_layout
 
 \begin_layout Standard
@@ -46949,8 +47745,7 @@ hieragglo (Default) Use hierarchical agglomerative (bottom-up) approach.
 \begin_inset space ~
 \end_inset
 
-<e>] Finish clustering when minimum distance between clusters is greater
- than 
+<e>] Finish clustering when minimum distance between clusters is greater than 
 \series bold
 <e>
 \series default
@@ -46974,7 +47769,8 @@ hieragglo (Default) Use hierarchical agglomerative (bottom-up) approach.
 \series bold
 linkage]
 \series default
- Single-linkage; use the shortest distance between members of two clusters.
+ Single-linkage;
+ use the shortest distance between members of two clusters.
 \end_layout
 
 \begin_layout Description
@@ -46982,8 +47778,8 @@ linkage]
 \series bold
 averagelinkage]
 \series default
- Average-linkage (default); use the average distance between members of
- two clusters.
+ Average-linkage (default);
+ use the average distance between members of two clusters.
 \end_layout
 
 \begin_layout Description
@@ -46991,7 +47787,8 @@ averagelinkage]
 \series bold
 [complete]
 \series default
- Complete-linkage; use the maximum distance between members of two clusters.
+ Complete-linkage;
+ use the maximum distance between members of two clusters.
 \end_layout
 
 \begin_layout Description
@@ -47045,8 +47842,7 @@ epsilon
 \begin_inset space ~
 \end_inset
 
-<k>] Generate K-dist plot for help in determining DBSCAN parameters (see
- below).
+<k>] Generate K-dist plot for help in determining DBSCAN parameters (see below).
 \end_layout
 
 \begin_layout Description
@@ -47084,8 +47880,8 @@ epsilon
 \end_layout
 
 \begin_layout Description
-[noise] If specified, treat all points within epsilon of another cluster
- as noise.
+[noise] If specified,
+ treat all points within epsilon of another cluster as noise.
 \end_layout
 
 \begin_layout Description
@@ -47093,10 +47889,8 @@ epsilon
 \begin_inset space ~
 \end_inset
 
-<density_vs_dist_file>] File to write density versus minimum distance to
- point with next highest density.
- This can be used to determine appropriate cutoffs for distance and density
- in a subsequent step with 
+<density_vs_dist_file>] File to write density versus minimum distance to point with next highest density.
+ This can be used to determine appropriate cutoffs for distance and density in a subsequent step with 
 \series bold
 choosepoints
 \series default
@@ -47120,10 +47914,9 @@ manual
 \begin_inset space ~
 \end_inset
 
-auto}] Specify whether clusters will be chosen based on specified distance/densi
-ty cutoffs, or automatically.
- If not specified only the density vs distance file will be written and
- no clustering will be performed.
+auto}] Specify whether clusters will be chosen based on specified distance/density cutoffs,
+ or automatically.
+ If not specified only the density vs distance file will be written and no clustering will be performed.
  Currently 
 \series bold
 manual
@@ -47152,8 +47945,8 @@ choosepoints
 \series bold
 manual
 \series default
-, points with minimum distance greather than or equal to <distcut> and density
- greater than or equal to <densitycut> will be chosen.
+,
+ points with minimum distance greather than or equal to <distcut> and density greater than or equal to <densitycut> will be chosen.
 \end_layout
 
 \begin_layout Description
@@ -47173,8 +47966,8 @@ choosepoints
 \series bold
 automatic
 \series default
-, the calculated running average of density versus distance will be written
- to <runavg file>.
+,
+ the calculated running average of density versus distance will be written to <runavg file>.
 \end_layout
 
 \begin_layout Description
@@ -47190,13 +47983,12 @@ choosepoints
 \series bold
 automatic
 \series default
-, distance minus the running average for each point will be written to this
- file.
+,
+ distance minus the running average for each point will be written to this file.
 \end_layout
 
 \begin_layout Description
-[gauss] Calculate density with Gaussian kernels instead of using discrete
- density.
+[gauss] Calculate density with Gaussian kernels instead of using discrete density.
 \end_layout
 
 \end_deeper
@@ -47242,8 +48034,7 @@ randompoint
 \begin_inset space ~
 \end_inset
 
-<iteration>] Algorithm will run until frames no longer change clusters of
- <iteration> iterations are reached (default 100).
+<iteration>] Algorithm will run until frames no longer change clusters of <iteration> iterations are reached (default 100).
 \end_layout
 
 \end_deeper
@@ -47268,8 +48059,8 @@ srmsd}
 \series bold
 rms
 \series default
-) For COORDS data, distance between coordinate frames calculated via best-fit
- coordinate RMSD using atoms in 
+) For COORDS data,
+ distance between coordinate frames calculated via best-fit coordinate RMSD using atoms in 
 \series bold
 <mask>
 \series default
@@ -47282,6 +48073,7 @@ srmsd
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_symmrmsd"
+nolink "false"
 
 \end_inset
 
@@ -47307,9 +48099,8 @@ qrmsd
 \begin_inset space ~
 \end_inset
 
-[<mask>] For COORDS data, distance between coordinate frames calculated
- using best-fit quaternion RMSD (can be 15-20% faster than regular RMSD)
- using atoms in 
+[<mask>] For COORDS data,
+ distance between coordinate frames calculated using best-fit quaternion RMSD (can be 15-20% faster than regular RMSD) using atoms in 
 \series bold
 <mask>
 \series default
@@ -47327,8 +48118,9 @@ dme
 \begin_inset space ~
 \end_inset
 
-[<mask>] For COORDS data, distance between coordinate frames calculated
- using distance-RMSD (aka DME, 
+[<mask>] For COORDS data,
+ distance between coordinate frames calculated using distance-RMSD (aka DME,
+ 
 \series bold
 \emph on
 distrmsd
@@ -47342,13 +48134,11 @@ distrmsd
 \end_layout
 
 \begin_layout Description
-euclid Use Euclidean distance (sqrt(SUM(distance^2))) when more than one
- data set has been specified (default).
+euclid Use Euclidean distance (sqrt(SUM(distance^2))) when more than one data set has been specified (default).
 \end_layout
 
 \begin_layout Description
-manhatttan Use Manhattan distance (SUM(distance)) when more than one data
- set has been specified.
+manhatttan Use Manhattan distance (SUM(distance)) when more than one data set has been specified.
 \end_layout
 
 \begin_layout Description
@@ -47356,16 +48146,14 @@ wgt
 \begin_inset space ~
 \end_inset
 
-<list> Factor to multiply distances from each metric by in a comma-separated
- list.
+<list> Factor to multiply distances from each metric by in a comma-separated list.
  Can be used to adjust the contribution from each metric.
  Default is 1 for each metric.
  Output from the 
 \series bold
 metricstats
 \series default
- keyword can be used to determine the relative contribution of each metric
- to the distance.
+ keyword can be used to determine the relative contribution of each metric to the distance.
 \end_layout
 
 \begin_layout Standard
@@ -47377,8 +48165,7 @@ Pairwise Distance Matrix Options:
 \begin_inset space ~
 \end_inset
 
-<name>] Pairwise cache DataSet/File name to use for loading/saving pairwise
- distances.
+<name>] Pairwise cache DataSet/File name to use for loading/saving pairwise distances.
 \end_layout
 
 \begin_deeper
@@ -47387,11 +48174,13 @@ Pairwise Distance Matrix Options:
 \begin_inset space ~
 \end_inset
 
-<file>] File name to use for pairwise cache; if not specified and 
+<file>] File name to use for pairwise cache;
+ if not specified and 
 \series bold
 'pairdist'
 \series default
- specified, uses 
+ specified,
+ uses 
 \series bold
 'pairdist'
 \series default
@@ -47400,8 +48189,8 @@ Pairwise Distance Matrix Options:
 
 \end_deeper
 \begin_layout Description
-[pwrecalc] If the loaded pairwise distance matrix does not match the current
- setup, force recalculation.
+[pwrecalc] If the loaded pairwise distance matrix does not match the current setup,
+ force recalculation.
 \end_layout
 
 \begin_layout Description
@@ -47426,7 +48215,8 @@ pairdist
 pairdist
 \series default
  not specified).
- NOTE: If sieving was performed only the calculated distances are saved.
+ NOTE:
+ If sieving was performed only the calculated distances are saved.
 \end_layout
 
 \begin_layout Description
@@ -47450,11 +48240,11 @@ disk
 \begin_inset space ~
 \end_inset
 
-none}] Cache pairwise distance data in memory (default), to disk, or disable
- pairwise caching.
+none}] Cache pairwise distance data in memory (default),
+ to disk,
+ or disable pairwise caching.
  No caching will save memory but be extremely slow.
- Caching to disk will likely be slow unless writing to a fast storage device
- (e.g.
+ Caching to disk will likely be slow unless writing to a fast storage device (e.g.
  SSD) - data is saved to a file named 'CpptrajPairwiseCache'.
 \end_layout
 
@@ -47472,7 +48262,8 @@ Sieving Options:
 <#>
 \series default
  frame.
- After clustering, all other frames will be added to clusters.
+ After clustering,
+ all other frames will be added to clusters.
 \end_layout
 
 \begin_layout Description
@@ -47480,7 +48271,8 @@ Sieving Options:
 \series bold
 sieve
 \series default
- is specified, select initial frames to cluster randomly.
+ is specified,
+ select initial frames to cluster randomly.
 \end_layout
 
 \begin_layout Description
@@ -47488,12 +48280,12 @@ sieve
 \begin_inset space ~
 \end_inset
 
-<#>] Seed for random sieving; if not set the wallclock time will be used.
+<#>] Seed for random sieving;
+ if not set the wallclock time will be used.
 \end_layout
 
 \begin_layout Description
-[includesieved_cdist] Include sieved frames in final cluster distance calculatio
-n (
+[includesieved_cdist] Include sieved frames in final cluster distance calculation (
 \bar under
 may be very slow
 \bar default
@@ -47501,8 +48293,7 @@ may be very slow
 \end_layout
 
 \begin_layout Description
-[includesieveincalc] Include sieved frames when calculating within-cluster
- average (
+[includesieveincalc] Include sieved frames when calculating within-cluster average (
 \bar under
 may be very slow
 \bar default
@@ -47510,8 +48301,8 @@ may be very slow
 \end_layout
 
 \begin_layout Description
-[sievetoframe] When restoring sieved frames, compare frame to every frame
- in a cluster using a cutoff of 
+[sievetoframe] When restoring sieved frames,
+ compare frame to every frame in a cluster using a cutoff of 
 \series bold
 <restore epsilon>
 \series default
@@ -47519,12 +48310,13 @@ may be very slow
 \series bold
 epsilon
 \series default
- when using DPeaks/DBscan) instead of the centroid; slower but more accurate.
+ when using DPeaks/DBscan) instead of the centroid;
+ slower but more accurate.
 \end_layout
 
 \begin_layout Description
-[sievetocentroid] When restoring sieved frames, compare frame to cluster
- centroid using a cutoff of 
+[sievetocentroid] When restoring sieved frames,
+ compare frame to cluster centroid using a cutoff of 
 \series bold
 <restore epsilon>
 \series default
@@ -47537,8 +48329,8 @@ epsilon
 \end_layout
 
 \begin_layout Description
-[closestcentroid] When restoring sieved frames, add each frame to its closest
- centroid.
+[closestcentroid] When restoring sieved frames,
+ add each frame to its closest centroid.
  Default method for hieragglo/kmeans.
 \end_layout
 
@@ -47551,8 +48343,7 @@ epsilon
 \begin_inset space ~
 \end_inset
 
-epsilon>] Epsilon to use for sievetoframe/sievetocentroid (default is algorithm
- 
+epsilon>] Epsilon to use for sievetoframe/sievetocentroid (default is algorithm 
 \series bold
 epsilon
 \series default
@@ -47568,8 +48359,7 @@ Best Representative Options:
 \begin_inset space ~
 \end_inset
 
-{cumulative|centroid|cumulative_nosieve}] Method for choosing cluster representa
-tive frames.
+{cumulative|centroid|cumulative_nosieve}] Method for choosing cluster representative frames.
 \end_layout
 
 \begin_deeper
@@ -47617,8 +48407,8 @@ Output Options:
 
 \begin_deeper
 \begin_layout Description
-[gracecolor] Instead of cluster # vs frame, write cluster# + 1 (corresponding
- to colors used by XMGRACE) vs frame.
+[gracecolor] Instead of cluster # vs frame,
+ write cluster# + 1 (corresponding to colors used by XMGRACE) vs frame.
  Cluster #s larger than 15 are given the same color.
  Algorithms that calculate noise (e.g.
  DBSCAN) will assign noise points a color of 0 (blank).
@@ -47630,8 +48420,7 @@ Output Options:
 \begin_inset space ~
 \end_inset
 
-<summaryfile>] Summarize each cluster with format '#Cluster Frames Frac
- AvgDist Stdev Centroid AvgCDist':
+<summaryfile>] Summarize each cluster with format '#Cluster Frames Frac AvgDist Stdev Centroid AvgCDist':
 \begin_inset Separator latexpar
 \end_inset
 
@@ -47660,11 +48449,9 @@ Stdev Standard deviation of points in the cluster.
 \end_layout
 
 \begin_layout Description
-Centroid Frame # of structure in cluster that has the lowest cumulative
- distance to every other point.
- If multiple representatives are being saved this column is replaced with
- two columns for each representative, 'Rep' (representative frame #) and
- 'RepScore' (score according to current best representative metric).
+Centroid Frame # of structure in cluster that has the lowest cumulative distance to every other point.
+ If multiple representatives are being saved this column is replaced with two columns for each representative,
+ 'Rep' (representative frame #) and 'RepScore' (score according to current best representative metric).
 \end_layout
 
 \begin_layout Description
@@ -47686,7 +48473,8 @@ AvgCDist Average distance of this cluster to every other cluster.
 \begin_inset Newline newline
 \end_inset
 
-#Clustering: <X> clusters <N> frames
+#Clustering:
+ <X> clusters <N> frames
 \begin_inset Newline newline
 \end_inset
 
@@ -47698,19 +48486,23 @@ AvgCDist Average distance of this cluster to every other cluster.
 \begin_inset Newline newline
 \end_inset
 
-#DBI: <DBI>
+#DBI:
+ <DBI>
 \begin_inset Newline newline
 \end_inset
 
-#pSF: <PSF>
+#pSF:
+ <PSF>
 \begin_inset Newline newline
 \end_inset
 
-#SSR/SST: <SSR/SST>
+#SSR/SST:
+ <SSR/SST>
 \begin_inset Newline newline
 \end_inset
 
-#Algorithm: <algorithm-specific info>
+#Algorithm:
+ <algorithm-specific info>
 \begin_inset Newline newline
 \end_inset
 
@@ -47722,18 +48514,21 @@ AvgCDist Average distance of this cluster to every other cluster.
 \begin_inset Newline newline
 \end_inset
 
-#Representative frames: <representative frame list>
+#Representative frames:
+ <representative frame list>
 \begin_inset Newline newline
 \end_inset
 
-Where <X> is the number of clusters, <N> is the number of frames clustered,
- <I> ranges from 0 to <X>-1, <AVG> is the average distance of all frames
- in that cluster to the centroid, <DBI> is the Davies-Bouldin Index, <pSF>
- is the pseudo-F statistic, <SSR/SST> is the SSR/SST ratio, and <representative
- frame list> contains the frame # of the representative frame (i.e.
+Where <X> is the number of clusters,
+ <N> is the number of frames clustered,
+ <I> ranges from 0 to <X>-1,
+ <AVG> is the average distance of all frames in that cluster to the centroid,
+ <DBI> is the Davies-Bouldin Index,
+ <pSF> is the pseudo-F statistic,
+ <SSR/SST> is the SSR/SST ratio,
+ and <representative frame list> contains the frame # of the representative frame (i.e.
  closest to the centroid) for each cluster.
- Each cluster has a line made up of characters (one for each frame) where
- '.' means 'not in cluster' and 'X' means 'in cluster'.
+ Each cluster has a line made up of characters (one for each frame) where '.' means 'not in cluster' and 'X' means 'in cluster'.
 \end_layout
 
 \begin_layout Description
@@ -47745,9 +48540,7 @@ Where <X> is the number of clusters, <N> is the number of frames clustered,
 \begin_inset space ~
 \end_inset
 
-<splitfile>] Summarize each cluster based on which of its frames fall in
- portions of the trajectory specified by splitframe with format '#Cluster
- Total Frac C# Color NumInX ...
+<splitfile>] Summarize each cluster based on which of its frames fall in portions of the trajectory specified by splitframe with format '#Cluster Total Frac C# Color NumInX ...
  FracX ...
  FirstX ...
  RepX':
@@ -47787,13 +48580,11 @@ FracX Fraction of frames in Xth portion of the trajectory.
 \end_layout
 
 \begin_layout Description
-FirstX Frame in the Xth portion of the trajectory where the cluster is first
- observed.
+FirstX Frame in the Xth portion of the trajectory where the cluster is first observed.
 \end_layout
 
 \begin_layout Description
-RepX Best representative frame in the Xth portion of the trajectory for
- that cluster.
+RepX Best representative frame in the Xth portion of the trajectory for that cluster.
 \end_layout
 
 \end_deeper
@@ -47806,7 +48597,9 @@ RepX Best representative frame in the Xth portion of the trajectory for
 \series bold
 summarysplit
 \series default
-, frame or comma-separated list of frames to split the trajectory at, e.g.
+,
+ frame or comma-separated list of frames to split the trajectory at,
+ e.g.
  '100,200,300'.
 \end_layout
 
@@ -47815,8 +48608,7 @@ summarysplit
 \begin_inset space ~
 \end_inset
 
-<filename>] Write number of unique clusters observed in a given time window
- to <filename>.
+<filename>] Write number of unique clusters observed in a given time window to <filename>.
 \end_layout
 
 \begin_deeper
@@ -47838,9 +48630,7 @@ clustersvtime
 \begin_inset space ~
 \end_inset
 
-<prefix>] Write average cluster silhouette value for each cluster to '<prefix>.cl
-uster.dat' and cluster silhouette value for each individual frame to '<prefix>.fra
-me.dat'.
+<prefix>] Write average cluster silhouette value for each cluster to '<prefix>.cluster.dat' and cluster silhouette value for each individual frame to '<prefix>.frame.dat'.
 \end_layout
 
 \begin_deeper
@@ -47849,12 +48639,13 @@ me.dat'.
 \begin_inset space ~
 \end_inset
 
-{idx|frm}] Choose what indices to write to the cluster silhouette frame
- file: 
+{idx|frm}] Choose what indices to write to the cluster silhouette frame file:
+ 
 \series bold
 idx
 \series default
- (the default) specifies the sorted index (starting from 0), 
+ (the default) specifies the sorted index (starting from 0),
+ 
 \series bold
 frm
 \series default
@@ -47867,8 +48658,8 @@ frm
 \begin_inset space ~
 \end_inset
 
-<file>] When more than one metric in use, print the fraction contribution
- of each metric to the total distance.
+<file>] When more than one metric in use,
+ print the fraction contribution of each metric to the total distance.
  This information can be used in conjunction with the 
 \series bold
 wgt
@@ -47882,14 +48673,18 @@ wgt
 \begin_inset Newline newline
 \end_inset
 
-Where #Metric is the metric number, FracAv and FracSD are the average and
- standard devation of the fraction contribution of that metric to the total
- distance (taking into account distance type and weights), Avg, SD, Min,
- and Max are the average, standard devation, minimum, and maximum of the
- unmodified distance contribution from that metric, and Description is the
- metric description.
- This may be slow for large numbers of frames, so it is advisable to run
- this on a smaller (potentially sieved) number of frames.
+Where #Metric is the metric number,
+ FracAv and FracSD are the average and standard devation of the fraction contribution of that metric to the total distance (taking into account distance type and weights),
+ Avg,
+ SD,
+ Min,
+ and Max are the average,
+ standard devation,
+ minimum,
+ and maximum of the unmodified distance contribution from that metric,
+ and Description is the metric description.
+ This may be slow for large numbers of frames,
+ so it is advisable to run this on a smaller (potentially sieved) number of frames.
 \end_layout
 
 \begin_layout Description
@@ -47913,11 +48708,13 @@ normframe]] Write cluster population vs time to
 \series bold
 <file>
 \series default
-; if 
+;
+ if 
 \series bold
 normpop
 \series default
- specified normalize each cluster to 1.0; if 
+ specified normalize each cluster to 1.0;
+ if 
 \series bold
 normframe
 \series default
@@ -47929,8 +48726,9 @@ normframe
 \emph on
 [Lifetime]
 \emph default
- for each cluster; for each frame, have 1 if the cluster is present and
- 0 otherwise.
+ for each cluster;
+ for each frame,
+ have 1 if the cluster is present and 0 otherwise.
  Can be used with 
 \series bold
 \emph on
@@ -47944,6 +48742,7 @@ reference "subsec:cpptraj-lifetime"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
@@ -47978,8 +48777,7 @@ singlerepout
 \begin_inset space ~
 \end_inset
 
-<trajfilename> Write all representative frames to single trajectory named
- <trajfilename>.
+<trajfilename> Write all representative frames to single trajectory named <trajfilename>.
 \end_layout
 
 \begin_deeper
@@ -47997,9 +48795,8 @@ repout
 \begin_inset space ~
 \end_inset
 
-<repprefix> Write representative frames to separate files named <repprefix>.X.<ext
->, where X is the cluster number and <ext> is a format-specific filename
- extension.
+<repprefix> Write representative frames to separate files named <repprefix>.X.<ext>,
+ where X is the cluster number and <ext> is a format-specific filename extension.
 \end_layout
 
 \begin_deeper
@@ -48025,9 +48822,8 @@ avgout
 \begin_inset space ~
 \end_inset
 
-<avgprefix> Write average structure for each cluster to separate files named
- <avgprefix>.X.<ext>, where X is the cluster number and <ext> is a format-specific
- filename extension.
+<avgprefix> Write average structure for each cluster to separate files named <avgprefix>.X.<ext>,
+ where X is the cluster number and <ext> is a format-specific filename extension.
 \end_layout
 
 \begin_deeper
@@ -48049,8 +48845,8 @@ summary
 \series bold
 summarysplit
 \series default
-, assign clusters to loaded reference structures if RMSD to that reference
- is less than specified cutoff.
+,
+ assign clusters to loaded reference structures if RMSD to that reference is less than specified cutoff.
  This will be printed in 
 \series bold
 summary
@@ -48059,8 +48855,8 @@ summary
 \series bold
 summarysplit
 \series default
- files as 2 extra columns: 'Name' (reference name) and 'RMS' (RMS to cluster
- centroid).
+ files as 2 extra columns:
+ 'Name' (reference name) and 'RMS' (RMS to cluster centroid).
 \end_layout
 
 \begin_deeper
@@ -48116,8 +48912,8 @@ clustersvtime
 \end_layout
 
 \begin_layout Description
-<name>[Pop]:<X> Cluster X population vs time; index X corresponds to cluster
- number.
+<name>[Pop]:<X> Cluster X population vs time;
+ index X corresponds to cluster number.
 \end_layout
 
 \begin_layout Description
@@ -48126,36 +48922,37 @@ clustersvtime
 lifetime
 \series default
  only).
- For each cluster X, contain 1 if cluster present that frame, 0 otherwise.
+ For each cluster X,
+ contain 1 if cluster present that frame,
+ 0 otherwise.
 \end_layout
 
 \end_deeper
 \begin_layout Standard
 
 \shape italic
-Note cluster population vs time data sets are not generated until the analysis
- has been run.
+Note cluster population vs time data sets are not generated until the analysis has been run.
 \end_layout
 
 \begin_layout Standard
-Cluster input frames using the specified input data sets (can be any combination
- of coordinates/COORDS and/or 1D scalar data) with the specified clustering
- algorithm.
- For COORDS sets, the distance metric can be RMSD, symmetry-corrected RMSD,
+Cluster input frames using the specified input data sets (can be any combination of coordinates/COORDS and/or 1D scalar data) with the specified clustering algorithm.
+ For COORDS sets,
+ the distance metric can be RMSD,
+ symmetry-corrected RMSD,
  or DME.
- When multiple data sets are present, the total distance can be determined
- either via the Euclidean (default) or Manhattan method.
+ When multiple data sets are present,
+ the total distance can be determined either via the Euclidean (default) or Manhattan method.
 \end_layout
 
 \begin_layout Standard
-In order to speed up clustering of large trajectories, the 
+In order to speed up clustering of large trajectories,
+ the 
 \series bold
 sieve
 \series default
  keyword can be used.
- In addition, subsequent clustering calculations can be sped up by writing/readi
-ng calculated pair distances between each frame to/from a file specified
- by 
+ In addition,
+ subsequent clustering calculations can be sped up by writing/reading calculated pair distances between each frame to/from a file specified by 
 \series bold
 pairdist
 \series default
@@ -48175,7 +48972,8 @@ pairdist
 \end_layout
 
 \begin_layout Standard
-Example: cluster on a specific distance:
+Example:
+ cluster on a specific distance:
 \end_layout
 
 \begin_layout LyX-Code
@@ -48187,10 +48985,10 @@ cluster data endToEnd clusters 10 epsilon 3.0 summary summary.dat info info.dat
 \end_layout
 
 \begin_layout Standard
-Example: two clustering commands on the CA atoms of residues 2-10 using
- average-linkage, stopping when either 3 clusters are reached or the minimum
- distance between clusters is 4.0 for the first, and 8 clusters or minimum
- distance 2.0 for the second.
+Example:
+ two clustering commands on the CA atoms of residues 2-10 using average-linkage,
+ stopping when either 3 clusters are reached or the minimum distance between clusters is 4.0 for the first,
+ and 8 clusters or minimum distance 2.0 for the second.
  The first command will write the cluster number vs time to 
 \begin_inset Quotes eld
 \end_inset
@@ -48208,13 +49006,11 @@ avg.summary.dat
 \end_inset
 
 .
- The second clustering command will use the pairwise distance matrix from
- the first to speed things up:
+ The second clustering command will use the pairwise distance matrix from the first to speed things up:
 \end_layout
 
 \begin_layout LyX-Code
-cluster C1 :2-10 clusters 3 epsilon 4.0 info C1.info out cnumvtime.dat summary
- avg.summary.dat pairdist PW
+cluster C1 :2-10 clusters 3 epsilon 4.0 info C1.info out cnumvtime.dat summary avg.summary.dat pairdist PW
 \end_layout
 
 \begin_layout LyX-Code
@@ -48226,43 +49022,54 @@ Clustering Success Metrics
 \end_layout
 
 \begin_layout Standard
-The Davies-Bouldin Index (DBI, reported in the 
+The Davies-Bouldin Index (DBI,
+ reported in the 
 \series bold
 info
 \series default
- file) measures sum over all clusters of the within cluster scatter to the
- between cluster separation; 
+ file) measures sum over all clusters of the within cluster scatter to the between cluster separation;
+ 
 \series bold
-the smaller the DBI, the better
+the smaller the DBI,
+ the better
 \series default
 .
- The DBI is defined as the average, for all clusters X, of fred, where fred(X)
- = max, across other clusters Y, of (Cx + Cy)/dXY.
- Here Cx is the average distance from points in X to the centroid, similarly
- Cy, and dXY is the distance between cluster centroids.
+ The DBI is defined as the average,
+ for all clusters X,
+ of fred,
+ where fred(X) = max,
+ across other clusters Y,
+ of (Cx + Cy)/dXY.
+ Here Cx is the average distance from points in X to the centroid,
+ similarly Cy,
+ and dXY is the distance between cluster centroids.
  
 \end_layout
 
 \begin_layout Standard
-The pseudo-F statistic (pSF, reported in the 
+The pseudo-F statistic (pSF,
+ reported in the 
 \series bold
 info
 \series default
  file) is another measure of clustering goodness.
- It is intended to capture the 'tightness' of clusters, and is in essence
- a ratio of the mean sum of squares between groups to the mean sum of squares
- within group.
+ It is intended to capture the 'tightness' of clusters,
+ and is in essence a ratio of the mean sum of squares between groups to the mean sum of squares within group.
  
 \series bold
 Higher values of pseudo-F are good
 \series default
 .
- Generally, one selects a cluster-count that gives a peak in the pseudo-f
- statistic.
- Formula: A/B, where A = (T - P)/(G-1), and B = P / (n-G).
- Here n is the number of points, G is the number of clusters, T is the total
- distance from the all-data centroid, and P is the sum (for all clusters)
- of the distances from the cluster centroid.
+ Generally,
+ one selects a cluster-count that gives a peak in the pseudo-f statistic.
+ Formula:
+ A/B,
+ where A = (T - P)/(G-1),
+ and B = P / (n-G).
+ Here n is the number of points,
+ G is the number of clusters,
+ T is the total distance from the all-data centroid,
+ and P is the sum (for all clusters) of the distances from the cluster centroid.
  
 \end_layout
 
@@ -48271,23 +49078,19 @@ The SSR/SST (reported in the
 \series bold
 info
 \series default
- file) is the ratio of the sum of squares regression (SSR or between sum
- of squares) and the total sum of squares (SST).
- The SSR is calculated via the sum of the squared distances of all points
- within a given cluster to its centroid, and summed together for all clusters.
- The total sum of squares is the sum of squared distances for all frames
- to the overall mean.
- The ratio lies between 0 and 1 and is supposed to give the fraction of
- explained variance by the data.
+ file) is the ratio of the sum of squares regression (SSR or between sum of squares) and the total sum of squares (SST).
+ The SSR is calculated via the sum of the squared distances of all points within a given cluster to its centroid,
+ and summed together for all clusters.
+ The total sum of squares is the sum of squared distances for all frames to the overall mean.
+ The ratio lies between 0 and 1 and is supposed to give the fraction of explained variance by the data.
  The ratio should increase with cluster count.
  
 \series bold
-There should be a point at which adding more clusters does not substantially
- increase SSR/SST
+There should be a point at which adding more clusters does not substantially increase SSR/SST
 \series default
-, i.e.
- the point where increasing the cluster count does not add new information
- and should not increase further.
+,
+ i.e.
+ the point where increasing the cluster count does not add new information and should not increase further.
 \end_layout
 
 \begin_layout Standard
@@ -48303,15 +49106,16 @@ silidx
  Values of 1 indicate the point is very similar to other points in the cluster,
  i.e.
  it is well-clustered.
- Values of -1 indicate the point is dissimilar and may fit better in a neighbori
-ng cluster.
+ Values of -1 indicate the point is dissimilar and may fit better in a neighboring cluster.
  Values of 0 indicate the point is on a border between two clusters.
  The 
 \series bold
 sil <prefix>
 \series default
  keyword will write two files.
- The first, <prefix>.cluster.dat, which has the format:
+ The first,
+ <prefix>.cluster.dat,
+ which has the format:
 \end_layout
 
 \begin_layout LyX-Code
@@ -48319,15 +49123,18 @@ sil <prefix>
 \end_layout
 
 \begin_layout Standard
-Where #Cluster is the cluster number, <Si> is the average silhouette value
- for all frames in the cluster, and StdDev is the standard deviation of
- the silhouette value for all frames in the cluster.
- The second, <prefix>.frame.dat, will contain the silhouette value for each
- frame grouped by cluster, with indices controlled by the 
+Where #Cluster is the cluster number,
+ <Si> is the average silhouette value for all frames in the cluster,
+ and StdDev is the standard deviation of the silhouette value for all frames in the cluster.
+ The second,
+ <prefix>.frame.dat,
+ will contain the silhouette value for each frame grouped by cluster,
+ with indices controlled by the 
 \series bold
 silidx
 \series default
- keyword (default sorted by ascending silhouette value), e.g.:
+ keyword (default sorted by ascending silhouette value),
+ e.g.:
 \end_layout
 
 \begin_layout LyX-Code
@@ -48401,11 +49208,10 @@ silidx
 \begin_layout Standard
 The last two lines will contain the overall average silhouette value twice,
  one at the lowest index and one at the highest.
- The file is formatted in this way to make it easy to visualize each cluster
- silhouette relative to the average value in e.g.
+ The file is formatted in this way to make it easy to visualize each cluster silhouette relative to the average value in e.g.
  the XMGRACE plotting program.
- If the clustering results in one or more cluster with silhouette values
- completely below the average line, the clustering is likely poor.
+ If the clustering results in one or more cluster with silhouette values completely below the average line,
+ the clustering is likely poor.
 \end_layout
 
 \begin_layout Subsubsection*
@@ -48421,30 +49227,26 @@ name "subsec:cpptraj_dbscan_Hints"
 
 \begin_layout Standard
 It is not always obvious what parameters to set for DBSCAN.
- You can get a rough idea of what to set 'mindist' and 'epsilon' to by generatin
-g a so-called "K-dist" plot with the 'kidst <k>' option.
- The K-dist plot shows for each point (X axis) the Kth farthest distance
- (Y axis), sorted by decreasing distance.
- You supply the same distance metric and sieve parameters you want to use
- for the actual clustering, but nothing else.
+ You can get a rough idea of what to set 'mindist' and 'epsilon' to by generating a so-called "K-dist" plot with the 'kidst <k>' option.
+ The K-dist plot shows for each point (X axis) the Kth farthest distance (Y axis),
+ sorted by decreasing distance.
+ You supply the same distance metric and sieve parameters you want to use for the actual clustering,
+ but nothing else.
  For example:
 \end_layout
 
 \begin_layout LyX-Code
-cluster C0 dbscan kdist 4 rms :1-4@CA sieve 10 loadpairdist pairdist CpptrajPair
-Dist
+cluster C0 dbscan kdist 4 rms :1-4@CA sieve 10 loadpairdist pairdist CpptrajPairDist
 \end_layout
 
 \begin_layout Standard
-The K-dist plot will be named <prefix>.<k>.dat, with the default prefix being
- 'Kdist' (in this case the file name would be Kdist.4.dat).
- The K-dist plot usually looks like a curve with an initially steep slope
- that gradually decreases.
- Around where the initial part of the curve starts to flatten out (indicating
- an increase in density) is around where epsilon should be set; minpoints
- is set to whatever <k> was.
- It has been suggested that the shape of the K-dist curve doesn't change
- too much after Kdist=4, but users are encouraged to experiment.
+The K-dist plot will be named <prefix>.<k>.dat,
+ with the default prefix being 'Kdist' (in this case the file name would be Kdist.4.dat).
+ The K-dist plot usually looks like a curve with an initially steep slope that gradually decreases.
+ Around where the initial part of the curve starts to flatten out (indicating an increase in density) is around where epsilon should be set;
+ minpoints is set to whatever <k> was.
+ It has been suggested that the shape of the K-dist curve doesn't change too much after Kdist=4,
+ but users are encouraged to experiment.
 \end_layout
 
 \begin_layout Subsubsection*
@@ -48452,9 +49254,7 @@ Using 'dpeaks' clustering
 \end_layout
 
 \begin_layout Standard
-The 'dpeaks' (density peaks) algorithm attempts to find clusters by identifying
- points in high density regions which are far from other points of high
- density
+The 'dpeaks' (density peaks) algorithm attempts to find clusters by identifying points in high density regions which are far from other points of high density
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Rodriguez2014"
@@ -48465,16 +49265,14 @@ literal "true"
 .
  There are two ways these points can be chosen.
  The first and recommended way is manually.
- In this method, clustering if first run with 
+ In this method,
+ clustering if first run with 
 \series bold
 choosepoints
 \series default
- not specified to generate a plot containing density versus minimum distance
- to point with next highest density (the decision graph).
- Appropriate cut offs for distance and density can then be chosen based
- on visual inspection; cutoffs should be chosen so that they select points
- that have both a high density and a high distance to point with next highest
- density.
+ not specified to generate a plot containing density versus minimum distance to point with next highest density (the decision graph).
+ Appropriate cut offs for distance and density can then be chosen based on visual inspection;
+ cutoffs should be chosen so that they select points that have both a high density and a high distance to point with next highest density.
  Clustering can then be run again with 
 \series bold
 distancecut
@@ -48487,10 +49285,10 @@ densitycut
 \end_layout
 
 \begin_layout Standard
-The second way is automatically; cpptraj will attempt to identify outliers
- in the density vs distance plot based on distance from the running average.
- Although this only requires a single pass, this method of choosing points
- is not well-tested and currently not recommended.
+The second way is automatically;
+ cpptraj will attempt to identify outliers in the density vs distance plot based on distance from the running average.
+ Although this only requires a single pass,
+ this method of choosing points is not well-tested and currently not recommended.
 \end_layout
 
 \begin_layout Subsubsection*
@@ -48498,14 +49296,12 @@ The Binary pairwise matrix file format
 \end_layout
 
 \begin_layout Standard
-When NetCDF is not present, the pairwise matrix file will be written in
- binary.
- The exact format depends on what version of cpptraj generated the file
- (since earlier versions had no concept of 'sieve').
- The CpptrajPairDist file starts with a 4 byte header containing the characters
- 'C' 'T' 'M' followed by the version number.
- A quick way to figure out the version is to use the linux 'od' command
- to output the first 4 bytes as hexadecimal, e.g.:
+When NetCDF is not present,
+ the pairwise matrix file will be written in binary.
+ The exact format depends on what version of cpptraj generated the file (since earlier versions had no concept of 'sieve').
+ The CpptrajPairDist file starts with a 4 byte header containing the characters 'C' 'T' 'M' followed by the version number.
+ A quick way to figure out the version is to use the linux 'od' command to output the first 4 bytes as hexadecimal,
+ e.g.:
 \end_layout
 
 \begin_layout LyX-Code
@@ -48525,7 +49321,9 @@ Version
 \begin_inset space ~
 \end_inset
 
-0: Two 4-byte integers: # of rows and # of elements.
+0:
+ Two 4-byte integers:
+ # of rows and # of elements.
  
 \end_layout
 
@@ -48534,7 +49332,8 @@ Version
 \begin_inset space ~
 \end_inset
 
-1: Two 8-byte unsigned integers (equivalent to size_t on most systems):
+1:
+ Two 8-byte unsigned integers (equivalent to size_t on most systems):
  # of rows and # of elements.
  
 \end_layout
@@ -48544,15 +49343,19 @@ Version
 \begin_inset space ~
 \end_inset
 
-2: Three 8 byte unsigned integers: original # of rows, actual # of rows,
+2:
+ Three 8 byte unsigned integers:
+ original # of rows,
+ actual # of rows,
  and sieve value.
 \end_layout
 
 \begin_layout Standard
-This is followed by the actual matrix data, stored as a single array of
- floats (4 bytes).
+This is followed by the actual matrix data,
+ stored as a single array of floats (4 bytes).
  For versions 1 and 2 the number of elements is explicitly stored.
- For version 2, to calculate the number of matrix elements you need to read:
+ For version 2,
+ to calculate the number of matrix elements you need to read:
 \end_layout
 
 \begin_layout LyX-Code
@@ -48560,22 +49363,22 @@ Elements = (actual_rows * (actual_rows - 1)) / 2
 \end_layout
 
 \begin_layout Standard
-The cluster pair-distance matrix is an upper-right triangle matrix without
- the diagonal (in row-major order), so the first element is the distance
- between elements 0 and 1, the second is between elements 0 and 2, etc.
+The cluster pair-distance matrix is an upper-right triangle matrix without the diagonal (in row-major order),
+ so the first element is the distance between elements 0 and 1,
+ the second is between elements 0 and 2,
+ etc.
 \end_layout
 
 \begin_layout Standard
-In version 2 files, if the sieve value is greater than 1 that means original_row
-s > actual_rows and there is an additional array of characters original_nrows
- long, with 'T' if the row is being ignored (i.e.
+In version 2 files,
+ if the sieve value is greater than 1 that means original_rows > actual_rows and there is an additional array of characters original_nrows long,
+ with 'T' if the row is being ignored (i.e.
  it was sieved out) and 'F' if the row is active (i.e.
  is active in the actual pairwise-distance matrix).
 \end_layout
 
 \begin_layout Standard
-The code that cpptraj uses to read in CpptrajPairDist files is in ClusterMatrix:
-:LoadFile() (ClusterMatrix.cpp).
+The code that cpptraj uses to read in CpptrajPairDist files is in ClusterMatrix::LoadFile() (ClusterMatrix.cpp).
 \end_layout
 
 \begin_layout Subsubsection*
@@ -48583,8 +49386,7 @@ The NetCDF pairwise matrix format
 \end_layout
 
 \begin_layout Standard
-The default way to write pairwise matrix files as of version 6.0.0 is with
- NetCDF.
+The default way to write pairwise matrix files as of version 6.0.0 is with NetCDF.
  This will be set up with the following parameters:
 \end_layout
 
@@ -48629,7 +49431,8 @@ n_rows Number of rows in the upper-triangle pairwise matrix.
 \end_layout
 
 \begin_layout Description
-msize Actual size of the matrix; should be (nRows_ * (nRows_-1)) / 2;
+msize Actual size of the matrix;
+ should be (nRows_ * (nRows_-1)) / 2;
 \end_layout
 
 \end_deeper
@@ -48639,15 +49442,19 @@ Variables:
 
 \begin_deeper
 \begin_layout Description
-sieve (integer, no dimension).
+sieve (integer,
+ no dimension).
  Sieve value.
 \end_layout
 
 \begin_layout Description
-matrix (float, dimension msize).
- The pairwise matrix, flattened to 1 dimension.
- Index calc is: i1 = i + 1; index = (((nRows_ * i) - ((i1 * i) / 2)) + j
- - i1);
+matrix (float,
+ dimension msize).
+ The pairwise matrix,
+ flattened to 1 dimension.
+ Index calc is:
+ i1 = i + 1;
+ index = (((nRows_ * i) - ((i1 * i) / 2)) + j - i1);
 \end_layout
 
 \begin_layout Description
@@ -48655,7 +49462,8 @@ actual
 \begin_inset space ~
 \end_inset
 
-frames (integer, dimension n_rows).
+frames (integer,
+ dimension n_rows).
  The actual frame numbers for which pairwise distances were calculated.
 \end_layout
 
@@ -48698,11 +49506,13 @@ statsout
 \end_layout
 
 \begin_layout Description
-deprot If specified, calculate fraction deprotonated instead of protonated.
+deprot If specified,
+ calculate fraction deprotonated instead of protonated.
 \end_layout
 
 \begin_layout Description
-fracplot If specified, calculate fraction protonated/deprotonated vs pH.
+fracplot If specified,
+ calculate fraction protonated/deprotonated vs pH.
 \end_layout
 
 \begin_deeper
@@ -48725,8 +49535,7 @@ Data Sets Generated
 
 \end_deeper
 \begin_layout Standard
-Calculate statistics for constant pH simulation data previously read in
- with 
+Calculate statistics for constant pH simulation data previously read in with 
 \series bold
 \emph on
 readdata
@@ -48736,6 +49545,7 @@ readdata
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_cphdatafile"
+nolink "false"
 
 \end_inset
 
@@ -48749,8 +49559,8 @@ Solvent pH is <pH>
 \end_layout
 
 \begin_layout LyX-Code
-<res name> <res num> : Offset <off> Pred <pred> Frac Prot <frac> Transitions
- <#trans>
+<res name> <res num> :
+ Offset <off> Pred <pred> Frac Prot <frac> Transitions <#trans>
 \end_layout
 
 \begin_layout LyX-Code
@@ -48762,7 +49572,8 @@ Solvent pH is <pH>
 \end_layout
 
 \begin_layout LyX-Code
-Average total molecular protonation: <avg>
+Average total molecular protonation:
+ <avg>
 \end_layout
 
 \begin_layout Standard
@@ -48770,11 +49581,13 @@ Where
 \series bold
 <off>
 \series default
- is offset from predicted, 
+ is offset from predicted,
+ 
 \series bold
 <pred>
 \series default
- is predicted pH, and <#trans> is the number of transitions.
+ is predicted pH,
+ and <#trans> is the number of transitions.
  A line is printed for each residue.
  This functionality is similar to the 
 \series bold
@@ -48784,6 +49597,7 @@ cphstats
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "sec:cphstats"
+nolink "false"
 
 \end_inset
 
@@ -48808,6 +49622,7 @@ readensembledata
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_readensembledata"
+nolink "false"
 
 \end_inset
 
@@ -48821,6 +49636,7 @@ sortensembledata
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_sortensembledata"
+nolink "false"
 
 \end_inset
 
@@ -48828,8 +49644,9 @@ reference "subsec:cpptraj_sortensembledata"
 \end_layout
 
 \begin_layout Standard
-For example, to read in constant pH data from constant pH REMD, sort and
- analyze:
+For example,
+ to read in constant pH data from constant pH REMD,
+ sort and analyze:
 \end_layout
 
 \begin_layout LyX-Code
@@ -48841,8 +49658,7 @@ sortensembledata PH
 \end_layout
 
 \begin_layout LyX-Code
-runanalysis cphstats PH[*] statsout stats.dat fracplot fracplotout frac.agr
- deprot
+runanalysis cphstats PH[*] statsout stats.dat fracplot fracplotout frac.agr deprot
 \end_layout
 
 \begin_layout Subsection
@@ -48852,6 +49668,8 @@ corr | correlationcoe
 \begin_layout LyX-Code
 corr
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -48895,8 +49713,9 @@ out
 [<dataset2>]
 \series default
  Data set(s) to calculate correlation for.
- If one dataset or the same dataset is given twice, the auto-correlation
- will be calculated, otherwise cross-correlation.
+ If one dataset or the same dataset is given twice,
+ the auto-correlation will be calculated,
+ otherwise cross-correlation.
 \end_layout
 
 \begin_layout Description
@@ -48921,7 +49740,8 @@ out
 \series bold
 [direct]
 \series default
- Do not use FFTs to calculate correlation; this will be much slower.
+ Do not use FFTs to calculate correlation;
+ this will be much slower.
 \end_layout
 
 \begin_layout Standard
@@ -48929,13 +49749,11 @@ DataSet Aspects:
 \end_layout
 
 \begin_layout Description
-[<dataset1>] (Auto-correlation) The aspect will be the name of each of the
- input data set.
+[<dataset1>] (Auto-correlation) The aspect will be the name of each of the input data set.
 \end_layout
 
 \begin_layout Description
-[<dataset1>-<dataset2>] (Cross-correlation) The aspect will be the names
- of each of the input data sets joined by a dash ('-').
+[<dataset1>-<dataset2>] (Cross-correlation) The aspect will be the names of each of the input data sets joined by a dash ('-').
 \end_layout
 
 \begin_layout Standard
@@ -48948,13 +49766,12 @@ DataSet Aspects:
 
 \end_deeper
 \begin_layout Standard
-Calculate the auto-correlation function for data set named <dataset1> or
- the cross-correlation function for data sets named <dataset1> and <dataset2>
- up to <lagmax> frames (all if 
+Calculate the auto-correlation function for data set named <dataset1> or the cross-correlation function for data sets named <dataset1> and <dataset2> up to <lagmax> frames (all if 
 \series bold
 lagmax
 \series default
- not specified), writing the result to file specified by 
+ not specified),
+ writing the result to file specified by 
 \series bold
 out
 \series default
@@ -49047,13 +49864,14 @@ Calculate atomic positional fluctuations for atoms in
 \series bold
 bfactor
 \series default
- is specified, the fluctuations are weighted by 
+ is specified,
+ the fluctuations are weighted by 
 \begin_inset Formula $\frac{8}{3}\pi^{2}$
 \end_inset
 
-(similar but not necessarily equivalent to crystallographic B-factor calculation
-).
- Units are Å, or Å
+(similar but not necessarily equivalent to crystallographic B-factor calculation).
+ Units are Å,
+ or Å
 \begin_inset script superscript
 
 \begin_layout Plain Layout
@@ -49128,8 +49946,7 @@ crosscorr [name <dsetname>] <dsetarg0> [<dsetarg1> ...] [out <filename>]
 
 \end_deeper
 \begin_layout Standard
-Calculate the Pearson product-moment correlation coefficients between all
- specified datasets.
+Calculate the Pearson product-moment correlation coefficients between all specified datasets.
 \end_layout
 
 \begin_layout Subsection
@@ -49148,8 +49965,7 @@ curvefit <dset> { <equation>  |
 \end_layout
 
 \begin_layout LyX-Code
-                  name <dsname> {gauss | nexp <m> [form {mexp|mexpk|mexpk_penalt
-y}} }
+                  name <dsname> {gauss | nexp <m> [form {mexp|mexpk|mexpk_penalty}} }
 \end_layout
 
 \begin_layout LyX-Code
@@ -49179,6 +49995,7 @@ y}} }
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-Data-Set-Math"
+nolink "false"
 
 \end_inset
 
@@ -49236,23 +50053,23 @@ form
 
 \begin_deeper
 \begin_layout Description
-mexp Multi-exponential, SUM(m)[ An * exp(An+1 * X)]
+mexp Multi-exponential,
+ SUM(m)[ An * exp(An+1 * X)]
 \end_layout
 
 \begin_layout Description
-mexpk Multi-exponential plus constant, A0 + SUM(m)[An * exp(An+1 * X)]
+mexpk Multi-exponential plus constant,
+ A0 + SUM(m)[An * exp(An+1 * X)]
 \end_layout
 
 \begin_layout Description
-mexpk_penalty Same as mexpk except sum of prefactors constrained to 1.0 and
- exponential constants constrained to < 0.0.
+mexpk_penalty Same as mexpk except sum of prefactors constrained to 1.0 and exponential constants constrained to < 0.0.
 \end_layout
 
 \end_deeper
 \end_deeper
 \begin_layout Description
-AX=<value> Value of any constants in specified equation with X starting
- from 0 (can specify more than one).
+AX=<value> Value of any constants in specified equation with X starting from 0 (can specify more than one).
 \end_layout
 
 \begin_layout Description
@@ -49280,8 +50097,7 @@ maxit
 \begin_inset space ~
 \end_inset
 
-iterations> Number of iterations to run curve fitting algorithm (default
- 50).
+iterations> Number of iterations to run curve fitting algorithm (default 50).
 \end_layout
 
 \begin_layout Description
@@ -49297,8 +50113,7 @@ outxbins
 \begin_inset space ~
 \end_inset
 
-<NX> Number of points to use when generating final curve (default same number
- of points as input data set).
+<NX> Number of points to use when generating final curve (default same number of points as input data set).
 \end_layout
 
 \begin_layout Description
@@ -49306,8 +50121,7 @@ outxmin
 \begin_inset space ~
 \end_inset
 
-<xmin> Minimum X value to use for final curve (default same number of points
- as input data set).
+<xmin> Minimum X value to use for final curve (default same number of points as input data set).
 \end_layout
 
 \begin_layout Description
@@ -49315,28 +50129,28 @@ outxmax
 \begin_inset space ~
 \end_inset
 
-<xmax> Maximum X value to use for final curve (default same number of points
- as input data set).
+<xmax> Maximum X value to use for final curve (default same number of points as input data set).
 \end_layout
 
 \end_deeper
 \begin_layout Standard
-Perform non-linear curve fitting for the specified data set using the Levenberg-
-Marquardt algorithm.
+Perform non-linear curve fitting for the specified data set using the Levenberg-Marquardt algorithm.
  Any equation form that cpptraj understands (see 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-Data-Set-Math"
+nolink "false"
 
 \end_inset
 
-) can be used, or several preset forms can be used.
- Similar to Grace (http://plasma-gate.weizmann.ac.il/Grace/), an equation can
- contain constants for curve fitting termed AX (with X being a numerical
- digit, one for each constant), and is assigned to a variable which then
- becomes a data set.
- For example, to fit a curve to data from a file named Data.dat to a data
- set named 'FitY':
+) can be used,
+ or several preset forms can be used.
+ Similar to Grace (http://plasma-gate.weizmann.ac.il/Grace/),
+ an equation can contain constants for curve fitting termed AX (with X being a numerical digit,
+ one for each constant),
+ and is assigned to a variable which then becomes a data set.
+ For example,
+ to fit a curve to data from a file named Data.dat to a data set named 'FitY':
 \end_layout
 
 \begin_layout LyX-Code
@@ -49455,15 +50269,15 @@ name>
 <filename>]]
 \series default
  Mass-weighted covariance (mwcovar) matrix only.
- Calculate entropy, heat capacity, and internal energy from the structure
- of a molecule (average coordinates, see above) and its vibrational frequencies
- using standard statistical mechanical formulas for an ideal gas.
- Results are written to <filename> if specified, otherwise results are written
- to STDOUT.
+ Calculate entropy,
+ heat capacity,
+ and internal energy from the structure of a molecule (average coordinates,
+ see above) and its vibrational frequencies using standard statistical mechanical formulas for an ideal gas.
+ Results are written to <filename> if specified,
+ otherwise results are written to STDOUT.
  
 \series bold
-Note that this converts the units of the calculated eigenvalues to frequencies
- (cm
+Note that this converts the units of the calculated eigenvalues to frequencies (cm
 \begin_inset script superscript
 
 \begin_layout Plain Layout
@@ -49487,7 +50301,8 @@ Note that this converts the units of the calculated eigenvalues to frequencies
 <#>]
 \series default
  Number of eigenvectors to calculate.
- Default is 0, which is only allowed when 'thermo' is specified.
+ Default is 0,
+ which is only allowed when 'thermo' is specified.
 \end_layout
 
 \begin_layout Description
@@ -49508,13 +50323,14 @@ Note that this converts the units of the calculated eigenvalues to frequencies
 [reduce]
 \series default
  Covariance (covar/mwcovar/distcovar) matrices only.
- For coordinate covariance (covar/mwcovar) matrices, each eigenvector element
- is reduced via Ei = Eix^2 + Eiy^2 + Eiz^2.
- For distance covariance (distcovar) the eigenvectors are reduced by taking
- the sum of the squares of each row.
- See Abseher & Nilges, JMB 1998, 279, 911-920 for further details.
- They may be used to compare results from PCA in distance space with those
- from PCA in cartesian-coordinate space.
+ For coordinate covariance (covar/mwcovar) matrices,
+ each eigenvector element is reduced via Ei = Eix^2 + Eiy^2 + Eiz^2.
+ For distance covariance (distcovar) the eigenvectors are reduced by taking the sum of the squares of each row.
+ See Abseher & Nilges,
+ JMB 1998,
+ 279,
+ 911-920 for further details.
+ They may be used to compare results from PCA in distance space with those from PCA in cartesian-coordinate space.
 \end_layout
 
 \begin_layout Description
@@ -49544,8 +50360,8 @@ literal "true"
 \begin_inset space ~
 \end_inset
 
-<#>] Number of vectors to write out for nmwiz output, starting with the
- lowest frequency mode (default 20).
+<#>] Number of vectors to write out for nmwiz output,
+ starting with the lowest frequency mode (default 20).
 \end_layout
 
 \begin_layout Description
@@ -49561,38 +50377,37 @@ literal "true"
 \begin_inset space ~
 \end_inset
 
-<mask>] Mask of atoms corresponding to eigenvectors - should be the same
- one used to generate the matrix.
+<mask>] Mask of atoms corresponding to eigenvectors - should be the same one used to generate the matrix.
 \end_layout
 
 \end_deeper
 \end_deeper
 \begin_layout Standard
 Calculate eigenvectors and eigenvalues for the specified symmetric matrix.
- This is followed by Principal Component Analysis (in cartesian coordinate
- space in the case of a covariance matrix or in distance space in the case
- of a distance-covariance matrix), or Quasiharmonic Analysis (in the case
- of a mass-weighted covariance matrix).
- Diagonalization of distance, correlation, idea, and ired matrices are also
- possible.
+ This is followed by Principal Component Analysis (in cartesian coordinate space in the case of a covariance matrix or in distance space in the case of a distance-covariance matrix),
+ or Quasiharmonic Analysis (in the case of a mass-weighted covariance matrix).
+ Diagonalization of distance,
+ correlation,
+ idea,
+ and ired matrices are also possible.
  Eigenvalues are given in cm
 \begin_inset Formula $^{-1}$
 \end_inset
 
- in the case of a mass-weighted covariance matrix and in the units of the
- matrix elements in all other cases.
- In the case of a mass-weighted covariance matrix, the eigenvectors are
- mass-weighted.
+ in the case of a mass-weighted covariance matrix and in the units of the matrix elements in all other cases.
+ In the case of a mass-weighted covariance matrix,
+ the eigenvectors are mass-weighted.
 \end_layout
 
 \begin_layout Standard
-For quasi-harmonic analysis the input must be a mass-weighted covariance
- matrix.
- Thermodynamic quantities are calculated based on statistical mechanical
- formulae that assume the input system is oscillating in a single energy
- well: see Statistical Thermodynamics by D.
+For quasi-harmonic analysis the input must be a mass-weighted covariance matrix.
+ Thermodynamic quantities are calculated based on statistical mechanical formulae that assume the input system is oscillating in a single energy well:
+ see Statistical Thermodynamics by D.
  A.
- McQuarrie, particularly chapters 4, 5, and 6 for more details.
+ McQuarrie,
+ particularly chapters 4,
+ 5,
+ and 6 for more details.
 \begin_inset CommandInset citation
 LatexCommand citep
 key "McQuarrie1973"
@@ -49600,8 +50415,7 @@ literal "true"
 
 \end_inset
 
- For an in-depth discussion of the accuracy of thermodynamic parameters
- obtained via quasi-harmonic analysis see Chang et al..
+ For an in-depth discussion of the accuracy of thermodynamic parameters obtained via quasi-harmonic analysis see Chang et al..
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Chang2005"
@@ -49613,24 +50427,27 @@ literal "true"
 \end_layout
 
 \begin_layout Standard
-Note that the maximum number of non-zero eigenvalues obtainable depends
- on the number of frames used to generate the input matrix; the number of
- frames should be equal to or greater than the number of columns in the
- matrix in order to obtain all eigenmodes.
+Note that the maximum number of non-zero eigenvalues obtainable depends on the number of frames used to generate the input matrix;
+ the number of frames should be equal to or greater than the number of columns in the matrix in order to obtain all eigenmodes.
 \end_layout
 
 \begin_layout Standard
-Results may include average coordinates (in the case of covar, mwcovar,
- correl), average distances (in the case of distcovar), main diagonal elements
- (in the case of idea and ired), eigenvalues, and eigenvectors.
+Results may include average coordinates (in the case of covar,
+ mwcovar,
+ correl),
+ average distances (in the case of distcovar),
+ main diagonal elements (in the case of idea and ired),
+ eigenvalues,
+ and eigenvectors.
 \end_layout
 
 \begin_layout Standard
-For example, in the following a mass-weighted covariance matrix of all atoms
- is generated and stored internally with the name mwcvmat; the matrix itself
- is written to mwcvmat.dat.
- Subsequently, the first 20 eigenmodes of the matrix are calculated and
- written to evecs.dat, and quasiharmonic analysis is performed at 300.0 K,
+For example,
+ in the following a mass-weighted covariance matrix of all atoms is generated and stored internally with the name mwcvmat;
+ the matrix itself is written to mwcvmat.dat.
+ Subsequently,
+ the first 20 eigenmodes of the matrix are calculated and written to evecs.dat,
+ and quasiharmonic analysis is performed at 300.0 K,
  with the results written to thermo.dat.
 \end_layout
 
@@ -49673,7 +50490,8 @@ evecs
 \end_layout
 
 \begin_layout LyX-Code
- [Reduced] Eigenvector file: <Type> nmodes <#> width <width>
+ [Reduced] Eigenvector file:
+ <Type> nmodes <#> width <width>
 \end_layout
 
 \begin_layout LyX-Code
@@ -49685,10 +50503,10 @@ evecs
 \end_layout
 
 \begin_layout Standard
-Where <Type> is a string identifying what kind of matrix the eigenvectors/eigenv
-alues were determined from, nmodes is how many eigenvectors are in the file,
- and <Average Coordinates> are in lines 7 columns wide, with each element
- having width specified by <width>.
+Where <Type> is a string identifying what kind of matrix the eigenvectors/eigenvalues were determined from,
+ nmodes is how many eigenvectors are in the file,
+ and <Average Coordinates> are in lines 7 columns wide,
+ with each element having width specified by <width>.
  Then for each eigenvector:
 \end_layout
 
@@ -49709,8 +50527,8 @@ alues were determined from, nmodes is how many eigenvectors are in the file,
 \end_layout
 
 \begin_layout Standard
-Where <Eigenvector Coordinates> are in lines 7 columns wide, with each element
- having width specified by <width>.
+Where <Eigenvector Coordinates> are in lines 7 columns wide,
+ with each element having width specified by <width>.
 \end_layout
 
 \begin_layout Subsection
@@ -49905,8 +50723,7 @@ Data Sets Created
 \end_layout
 
 \begin_layout Description
-<name>[vala] Difference between last half average of data vs final density
- (A2).
+<name>[vala] Difference between last half average of data vs final density (A2).
 \end_layout
 
 \begin_layout Description
@@ -49926,7 +50743,10 @@ Data Sets Created
 \end_layout
 
 \begin_layout Description
-<name>[result] Final result: yes, no, err (error).
+<name>[result] Final result:
+ yes,
+ no,
+ err (error).
 \end_layout
 
 \end_deeper
@@ -49939,10 +50759,10 @@ plateaued
 \begin_inset Quotes erd
 \end_inset
 
-, i.e.
+,
+ i.e.
  stopped changing significantly by the end of the set.
- Currently the defaults are set up to evaluate density data as part of the
- system preparation protocol described by Roe & Brooks.
+ Currently the defaults are set up to evaluate density data as part of the system preparation protocol described by Roe & Brooks.
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Roe2020"
@@ -50021,7 +50841,8 @@ fft <dset0> [<dset1> ...] [out <outfile>] [name <outsetname>] [dt <samp_int>]
 \end_deeper
 \begin_layout Standard
 Perform fast Fourier transform (FFT) on specified data set(s).
- If more than 1 data set, they must all have the same size.
+ If more than 1 data set,
+ they must all have the same size.
 \end_layout
 
 \begin_layout Subsection
@@ -50040,13 +50861,11 @@ hausdorff <set arg0> [<set arg1> ...]
 \end_layout
 
 \begin_layout LyX-Code
-          [outtype {basic|trimatrix nrows <#>|fullmatrix nrows <#> [ncols
- <#>]}]
+          [outtype {basic|trimatrix nrows <#>|fullmatrix nrows <#> [ncols <#>]}]
 \end_layout
 
 \begin_layout LyX-Code
-      	[name <output set name>] [out <file>] [outab <file>] [outba <file>]
- 
+      	[name <output set name>] [out <file>] [outab <file>] [outba <file>] 
 \end_layout
 
 \begin_deeper
@@ -50081,8 +50900,7 @@ nrows
 \begin_inset space ~
 \end_inset
 
-<#> Output Hausdorff distances for each input matrix as a 2D upper-triangular
- matrix with the given number of rows.
+<#> Output Hausdorff distances for each input matrix as a 2D upper-triangular matrix with the given number of rows.
  Must have (nrows * (nrows-1)) / 2 input sets.
 \end_layout
 
@@ -50103,13 +50921,13 @@ ncols
 \begin_inset space ~
 \end_inset
 
-<#> Output Hausdorff distances for each input matrix as a full matrix with
- the given number of columns and rows.
+<#> Output Hausdorff distances for each input matrix as a full matrix with the given number of columns and rows.
  If 
 \series bold
 ncols
 \series default
- is not given, use 
+ is not given,
+ use 
 \series bold
 nrows
 \series default
@@ -50161,24 +50979,24 @@ name>] Name of output data sets.
 \end_deeper
 \begin_layout Standard
 Calculate the symmetric Hausdorff distance for one or more matrices.
- The results can be saved as an array or as a full or upper-triangular matrix
- with the specified dimensions.
+ The results can be saved as an array or as a full or upper-triangular matrix with the specified dimensions.
  The Hausdorff distance H is determined from:
 \end_layout
 
 \begin_layout LyX-Code
-H = max{dH(A,B), dH(B,A)]
+H = max{dH(A,B),
+ dH(B,A)]
 \end_layout
 
 \begin_layout Standard
-Where dH(A,B) is the directed Hausdorff distance between sets A and B, etc.
- Colloquially speaking, the directed Hausdorff distance between A and B
- is determined as follows:
+Where dH(A,B) is the directed Hausdorff distance between sets A and B,
+ etc.
+ Colloquially speaking,
+ the directed Hausdorff distance between A and B is determined as follows:
 \end_layout
 
 \begin_layout Enumerate
-What is the closest approach (distance) of each point in A to any point
- in B?
+What is the closest approach (distance) of each point in A to any point in B?
 \end_layout
 
 \begin_layout Enumerate
@@ -50186,12 +51004,14 @@ Choose the largest distance from among those distances.
 \end_layout
 
 \begin_layout Standard
-If desired, the output can be formed into a matrix, which can be useful
- e.g.
+If desired,
+ the output can be formed into a matrix,
+ which can be useful e.g.
  when doing multiple 2D rms calculations on different regions of a trajectory.
- For example, the following input divides a 100 frame trajectory into 10
- frame chunks, calcultes the 2D RMS matrix for each chunk, then performs
- Hausdorff analysis on the resulting matrices and forms a full output matrix.
+ For example,
+ the following input divides a 100 frame trajectory into 10 frame chunks,
+ calcultes the 2D RMS matrix for each chunk,
+ then performs Hausdorff analysis on the resulting matrices and forms a full output matrix.
 \end_layout
 
 \begin_layout LyX-Code
@@ -50334,8 +51154,7 @@ parallelanalysis sync
 \end_layout
 
 \begin_layout LyX-Code
-runanalysis hausdorff M* out hausdorff.fullmatrix.gnu title hausdorff.matrix.gnu
- 
+runanalysis hausdorff M* out hausdorff.fullmatrix.gnu title hausdorff.matrix.gnu 
 \backslash
 
 \end_layout
@@ -50351,6 +51170,8 @@ hist | histogram
 \begin_layout LyX-Code
 hist
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -50389,10 +51210,13 @@ hist
 <dataset_name>[,<min>,<max>,<step>,<bins>]
 \series default
  Dataset(s) to be histogrammed.
- Optionally, the min, max, step, and/or number of bins can be specified
- for this dimension after the dataset name separated by commas.
- It is only necessary to specify the step or number of bins, an asterisk
- '*' indicates the value should be calculated from available data.
+ Optionally,
+ the min,
+ max,
+ step,
+ and/or number of bins can be specified for this dimension after the dataset name separated by commas.
+ It is only necessary to specify the step or number of bins,
+ an asterisk '*' indicates the value should be calculated from available data.
  
 \end_layout
 
@@ -50405,11 +51229,13 @@ hist
 
 <temperature>]
 \series default
- If specified, estimate free energy from bin populations using 
+ If specified,
+ estimate free energy from bin populations using 
 \begin_inset Formula $G_{i}=-k_{B}T\ln\left(\frac{N_{i}}{N_{Max}}\right)$
 \end_inset
 
-, where K
+,
+ where K
 \begin_inset script subscript
 
 \begin_layout Plain Layout
@@ -50418,7 +51244,8 @@ B
 
 \end_inset
 
- is Boltzmann's constant, T is the temperature specified by <temperature>,
+ is Boltzmann's constant,
+ T is the temperature specified by <temperature>,
  N
 \begin_inset script subscript
 
@@ -50438,8 +51265,7 @@ Max
 \end_inset
 
  is the population of the most populated bin.
- Bins with no population are given an artificial barrier equivalent to a
- population of 0.5.
+ Bins with no population are given an artificial barrier equivalent to a population of 0.5.
 \end_layout
 
 \begin_layout Description
@@ -50447,8 +51273,8 @@ Max
 \series bold
 [norm]
 \series default
- If specified, normalize bin populations so the sum over all bins equals
- 1.0.
+ If specified,
+ normalize bin populations so the sum over all bins equals 1.0.
 \end_layout
 
 \begin_layout Description
@@ -50460,7 +51286,9 @@ Max
 \series bold
 [gnu]
 \series default
- Internal output only; data will be gnuplot-readable, i.e.
+ Internal output only;
+ data will be gnuplot-readable,
+ i.e.
  a space will be printed after the highest order coordinate cycles.
 \end_layout
 
@@ -50469,7 +51297,9 @@ Max
 \series bold
 [circular]
 \series default
- Internal output only; data will wrap, i.e.
+ Internal output only;
+ data will wrap,
+ i.e.
  an extra bin will be printed before min and after max in each direction.
  Useful for e.g.
  dihedral angles.
@@ -50492,8 +51322,7 @@ out
 \begin_inset space ~
 \end_inset
 
-<amdboost_data>] Reweight bins using AMD boost energies in data set <amdboost_da
-ta> (in KT).
+<amdboost_data>] Reweight bins using AMD boost energies in data set <amdboost_data> (in KT).
 \end_layout
 
 \begin_layout Description
@@ -50521,8 +51350,7 @@ name>] Output histogram data set name.
 \begin_inset space ~
 \end_inset
 
-<format>]] (3D histograms only) Write a pseudo-trajectory of the 3 data
- sets (1 atom) to <file> with format <format>.
+<format>]] (3D histograms only) Write a pseudo-trajectory of the 3 data sets (1 atom) to <file> with format <format>.
 \end_layout
 
 \begin_layout Description
@@ -50530,8 +51358,7 @@ name>] Output histogram data set name.
 \begin_inset space ~
 \end_inset
 
-<file>] (3D histograms only) Write a topology corresponding to the pseudo-trajec
-tory to <file>.
+<file>] (3D histograms only) Write a topology corresponding to the pseudo-trajectory to <file>.
 \end_layout
 
 \begin_layout Description
@@ -50583,17 +51410,18 @@ tory to <file>.
 \end_layout
 
 \begin_layout Description
-[nativeout] Do not use cpptraj data file framework; only necessary for writing
- out histograms with > 3 dimensions.
+[nativeout] Do not use cpptraj data file framework;
+ only necessary for writing out histograms with > 3 dimensions.
 \end_layout
 
 \end_deeper
 \begin_layout Standard
-Create an N-dimensional histrogram, where N is the number of datasets specified.
+Create an N-dimensional histrogram,
+ where N is the number of datasets specified.
  For 1-dimensional histograms the xmgrace '.agr' file format is recommended;
  for 2-dimensional hisograms the gnuplot '.gnu' file format is recommended;
- for all other dimensions plot formatting is disabled and the routine uses
- its own internal output format; this is also enabled if 
+ for all other dimensions plot formatting is disabled and the routine uses its own internal output format;
+ this is also enabled if 
 \series bold
 gnu
 \series default
@@ -50605,8 +51433,8 @@ circular
 \end_layout
 
 \begin_layout Standard
-For example, to create a two dimensional histogram of two datasets 'phi'
- and 'psi':
+For example,
+ to create a two dimensional histogram of two datasets 'phi' and 'psi':
 \end_layout
 
 \begin_layout LyX-Code
@@ -50622,9 +51450,8 @@ hist phi,-180,180,*,72 psi,-180,180,*,72 out hist.gnu
 \end_layout
 
 \begin_layout Standard
-In this case the number of bins (72) has been specified for each dimension
- and '*' has been given for the step size, indicating it should be calculated
- based on min/max/bins.
+In this case the number of bins (72) has been specified for each dimension and '*' has been given for the step size,
+ indicating it should be calculated based on min/max/bins.
  The following 'hist' command is equivalent:
 \end_layout
 
@@ -50662,7 +51489,8 @@ integrate <dset0> [<dset1> ...] [out <outfile>] [intout <intfile>]
 \begin_inset space ~
 \end_inset
 
-<outfile>] If specified, write cumulative sum curves to <outfile>.
+<outfile>] If specified,
+ write cumulative sum curves to <outfile>.
 \end_layout
 
 \begin_layout Description
@@ -50670,7 +51498,8 @@ integrate <dset0> [<dset1> ...] [out <outfile>] [intout <intfile>]
 \begin_inset space ~
 \end_inset
 
-<intfile>] If specified, write final integral values to <intfile>.
+<intfile>] If specified,
+ write final integral values to <intfile>.
 \end_layout
 
 \begin_layout Description
@@ -50686,7 +51515,8 @@ DataSets Created:
 \end_layout
 
 \begin_layout Description
-<name> Final integral values, 1 for each input data set (indexed from 0).
+<name> Final integral values,
+ 1 for each input data set (indexed from 0).
 \end_layout
 
 \begin_layout Description
@@ -50694,7 +51524,8 @@ DataSets Created:
 \series bold
 out
 \series default
- was specified, 1 for each input data set (indexed from 0).
+ was specified,
+ 1 for each input data set (indexed from 0).
 \end_layout
 
 \end_deeper
@@ -50750,8 +51581,8 @@ freq
 
 <MHz>]
 \series default
- Should only be used when ired vectors represent N-H bonds; calculate correlatio
-n times 
+ Should only be used when ired vectors represent N-H bonds;
+ calculate correlation times 
 \family roman
 \series medium
 \shape up
@@ -50794,7 +51625,9 @@ for each eigenmode and relaxation rates and NOEs for each N-H vector.
 \begin_inset space ~
 \end_inset
 
-<noefilename>] File to write the T1, T2, and NOE data to.
+<noefilename>] File to write the T1,
+ T2,
+ and NOE data to.
 \end_layout
 
 \end_deeper
@@ -50803,8 +51636,7 @@ for each eigenmode and relaxation rates and NOEs for each N-H vector.
 \begin_inset space ~
 \end_inset
 
-<order>] Order of the Legendre polynomials to use when calculating spherical
- harmonics (default 2).
+<order>] Order of the Legendre polynomials to use when calculating spherical harmonics (default 2).
 \end_layout
 
 \begin_layout Description
@@ -50857,7 +51689,9 @@ for each eigenmode and relaxation rates and NOEs for each N-H vector.
 \series bold
 [norm]
 \series default
- Normalize all correlation functions, i.e., 
+ Normalize all correlation functions,
+ i.e.,
+ 
 \begin_inset Formula $C_{l}(t=0)=P_{l}(t=0)=1.0$
 \end_inset
 
@@ -50869,8 +51703,8 @@ for each eigenmode and relaxation rates and NOEs for each N-H vector.
 \series bold
 [drct]
 \series default
- Use the direct method to calculate correlations instead of FFT; this will
- be much slower.
+ Use the direct method to calculate correlations instead of FFT;
+ this will be much slower.
 \end_layout
 
 \begin_layout Description
@@ -50898,8 +51732,8 @@ modes
 \begin_inset space ~
 \end_inset
 
-<file>] If specified, write full delta*S^2 matrix (# IRED vector rows by
- # eigenmodes columns) to <file>.
+<file>] If specified,
+ write full delta*S^2 matrix (# IRED vector rows by # eigenmodes columns) to <file>.
 \end_layout
 
 \begin_layout Standard
@@ -50952,12 +51786,9 @@ literal "true"
 
 \end_inset
 
- analysis on previously defined IRED vectors (see vector ired) using eigenmodes
- calculated from those vectors with a previous 'diagmatrix' command.
- The number of defined IRED vectors should match the number of eigenmodes
- calculated.
- Autocorrelation functions for each mode and the corresponding correlation
- time 
+ analysis on previously defined IRED vectors (see vector ired) using eigenmodes calculated from those vectors with a previous 'diagmatrix' command.
+ The number of defined IRED vectors should match the number of eigenmodes calculated.
+ Autocorrelation functions for each mode and the corresponding correlation time 
 \family roman
 \series medium
 \shape up
@@ -50984,8 +51815,7 @@ literal "true"
 \lang english
 will be written to <filename>.cmt.
  Autocorrelation functions for each vector will be written to <filename>.cjt.
- Relaxation rates and NOEs for each N-H vector will be written to <filename>
- or added to the the end of the standard output.
+ Relaxation rates and NOEs for each N-H vector will be written to <filename> or added to the the end of the standard output.
  For the calculation of
 \lang american
  
@@ -51014,10 +51844,11 @@ will be written to <filename>.cmt.
 \lang american
  
 \lang english
-the normalized correlation functions and only the first third of the analyzed
- time steps will be used.
- For further information on the convergence of correlation functions see
- [Schneider, Brünger, Nilges, 
+the normalized correlation functions and only the first third of the analyzed time steps will be used.
+ For further information on the convergence of correlation functions see [Schneider,
+ Brünger,
+ Nilges,
+ 
 \emph on
 J.
  Mol.
@@ -51028,7 +51859,8 @@ J.
 \series bold
 285
 \series default
-, 727 (1999)].
+,
+ 727 (1999)].
 \end_layout
 
 \begin_layout Subsubsection*
@@ -51040,7 +51872,8 @@ In
 \shape italic
 cpptraj
 \shape default
-, IRED analysis
+,
+ IRED analysis
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Prompers02a"
@@ -51048,16 +51881,14 @@ literal "true"
 
 \end_inset
 
- can now be performed in one pass (as opposed to the two passes previously
- required in 
+ can now be performed in one pass (as opposed to the two passes previously required in 
 \shape italic
 ptraj
 \shape default
 ).
- First, IRED vectors are defined (in this case for N-H bonds) and an IRED
- matrix is calculated and analyzed.
- The IRED vectors are then projected onto the calculated IRED eigenvectors
- in the 
+ First,
+ IRED vectors are defined (in this case for N-H bonds) and an IRED matrix is calculated and analyzed.
+ The IRED vectors are then projected onto the calculated IRED eigenvectors in the 
 \series bold
 \shape italic
 ired
@@ -51068,14 +51899,15 @@ ired
 \shape italic
 order
 \shape default
- is specified, order parameters based on IRED are calculated.
+ is specified,
+ order parameters based on IRED are calculated.
  By specifying the 
 \shape italic
 relax
 \shape default
- parameter, relaxation rates and NOEs can be obtained for each N-H vector.
- Note that the order of the IRED matrix should be the same as the one specified
- for IRED analysis.
+ parameter,
+ relaxation rates and NOEs can be obtained for each N-H vector.
+ Note that the order of the IRED matrix should be the same as the one specified for IRED analysis.
 \end_layout
 
 \begin_layout LyX-Code
@@ -51158,8 +51990,8 @@ kde <dataset> [bandwidth <bw>] [out <file>] [name <dsname>]
 \begin_inset space ~
 \end_inset
 
-<bw>] Bandwidth to use for KDE; if not specified bandwidth will be estimated
- using the normal distribution approximation.
+<bw>] Bandwidth to use for KDE;
+ if not specified bandwidth will be estimated using the normal distribution approximation.
 \end_layout
 
 \begin_layout Description
@@ -51227,8 +52059,7 @@ kde <dataset> [bandwidth <bw>] [out <file>] [name <dsname>]
 \begin_inset space ~
 \end_inset
 
-<outfile>]] Calculate Kullback-Leibler divergence over time of <dataset>
- distribution to <dsname2> distribution.
+<outfile>]] Calculate Kullback-Leibler divergence over time of <dataset> distribution to <dsname2> distribution.
  Output to <outfile> if 
 \series bold
 klout
@@ -51241,8 +52072,7 @@ klout
 \begin_inset space ~
 \end_inset
 
-<amdboost_data>] Reweight histogram using AMD boost data from data set <amdboost
-_data> (in KT).
+<amdboost_data>] Reweight histogram using AMD boost data from data set <amdboost_data> (in KT).
 \end_layout
 
 \end_deeper
@@ -51292,11 +52122,15 @@ lifetime [out <filename>] <dsetarg0> [ <dsetarg1> ...
 
 <filename>]
 \series default
- Write results to file named <filename>, and lifetime curves to 'crv.<filename>'.
- If performing windowed lifetime analysis, <filename> contains the fraction
- present over time windows, and 2 additional files are written: 'max.<filename>',
- containing max lifetime over windows, and 'avg.<filename>', containing average
- lifetime over windows.
+ Write results to file named <filename>,
+ and lifetime curves to 'crv.<filename>'.
+ If performing windowed lifetime analysis,
+ <filename> contains the fraction present over time windows,
+ and 2 additional files are written:
+ 'max.<filename>',
+ containing max lifetime over windows,
+ and 'avg.<filename>',
+ containing average lifetime over windows.
 \end_layout
 
 \begin_layout Description
@@ -51389,8 +52223,7 @@ Just calculate averages (no lifetime analysis).
 \begin_inset space ~
 \end_inset
 
-<fuzzcut>] Ignore changes in lifetime state that are less than <fuzzcut>
- frames.
+<fuzzcut>] Ignore changes in lifetime state that are less than <fuzzcut> frames.
 \end_layout
 
 \begin_layout Description
@@ -51402,7 +52235,8 @@ Data Sets Created:
 \end_layout
 
 \begin_layout Description
-<setname> Number of lifetimes for each set, or if 
+<setname> Number of lifetimes for each set,
+ or if 
 \series bold
 window
 \series default
@@ -51410,7 +52244,8 @@ window
 \end_layout
 
 \begin_layout Description
-<setname>[max] Maximum lifetime for each set, or if 
+<setname>[max] Maximum lifetime for each set,
+ or if 
 \series bold
 window
 \series default
@@ -51418,7 +52253,8 @@ window
 \end_layout
 
 \begin_layout Description
-<setname>[avg] Average lifetime for each set, or if 
+<setname>[avg] Average lifetime for each set,
+ or if 
 \series bold
 window
 \series default
@@ -51448,8 +52284,8 @@ window
 \end_deeper
 \begin_layout Standard
 Perform lifetime analysis for specified data sets.
- Lifetime data can either be determined for the entire set, or for time
- windows of specified size within the set if 
+ Lifetime data can either be determined for the entire set,
+ or for time windows of specified size within the set if 
 \series bold
 window
 \series default
@@ -51465,26 +52301,33 @@ lifetime
 \begin_inset Quotes erd
 \end_inset
 
- is defined as the length of time something remains 'present'; data is considere
-d present when above or below a certain cutoff (the default is greater than
- 0.5, useful for analysis of 
+ is defined as the length of time something remains 'present';
+ data is considered present when above or below a certain cutoff (the default is greater than 0.5,
+ useful for analysis of 
 \series bold
 \shape italic
 hbond
 \series default
 \shape default
  time series data).
- For example, in the case of a hydrogen bond 
+ For example,
+ in the case of a hydrogen bond 
 \series bold
 'series'
 \series default
- data set, if a hydrogen bond is present during a frame the value is 1,
+ data set,
+ if a hydrogen bond is present during a frame the value is 1,
  otherwise it is 0.
- Given the hbond time series data set {1 1 1 0 1 0 0 0 1 1}, the overall
- fraction present is 0.6.
- However, there are 3 lifetimes of lengths 3, 1, and 2 ({1 1 1}, {1}, and
- {1 1}).
- The maximum lifetime is 3 and the average lifetime is 2.0, i.e.
+ Given the hbond time series data set {1 1 1 0 1 0 0 0 1 1},
+ the overall fraction present is 0.6.
+ However,
+ there are 3 lifetimes of lengths 3,
+ 1,
+ and 2 ({1 1 1},
+ {1},
+ and {1 1}).
+ The maximum lifetime is 3 and the average lifetime is 2.0,
+ i.e.
  (3 + 1 + 2) / 3 lifetimes = 2.0.
  One can also construct a 
 \begin_inset Quotes eld
@@ -51494,15 +52337,15 @@ lifetime curve
 \begin_inset Quotes erd
 \end_inset
 
-, which is constructed as the sum of all individual lifetimes.
- By default these curves are normalized to 1.0, but the raw curve can be
- obtained using the 
+,
+ which is constructed as the sum of all individual lifetimes.
+ By default these curves are normalized to 1.0,
+ but the raw curve can be obtained using the 
 \series bold
 rawcurve
 \series default
  keyword.
- For the example data set here the raw lifetime curve would be 3 frames
- long:
+ For the example data set here the raw lifetime curve would be 3 frames long:
 \end_layout
 
 \begin_layout LyX-Code
@@ -51518,7 +52361,8 @@ rawcurve
 \end_layout
 
 \begin_layout LyX-Code
-Curve: 3 2 1
+Curve:
+ 3 2 1
 \end_layout
 
 \begin_layout Standard
@@ -51527,16 +52371,14 @@ By default data sets are sorted by name unless
 nosort
 \series default
  is specified.
- The lifetime command can calculate lifetimes over specific time windows
- by using the 
+ The lifetime command can calculate lifetimes over specific time windows by using the 
 \series bold
 window
 \series default
  keyword.
- This can be particularly useful if one wants to get a sense for how lifetimes
- are changing over the course of very long time series data.
- In addition, averages can be calculated instead of lifetimes by specifying
- 
+ This can be particularly useful if one wants to get a sense for how lifetimes are changing over the course of very long time series data.
+ In addition,
+ averages can be calculated instead of lifetimes by specifying 
 \series bold
 averageonly
 \series default
@@ -51545,8 +52387,8 @@ averageonly
 \series bold
 cumulative
 \series default
- keyword, or the change from the average value in the previous window can
- be obtained using the 
+ keyword,
+ or the change from the average value in the previous window can be obtained using the 
 \series bold
 delta
 \series default
@@ -51558,16 +52400,13 @@ The
 \series bold
 fuzz
 \series default
- keyword can be used to try and smooth the input data by ignoring changes
- in state that occur for fewer frames than <fuzzcut>.
- For example, in the above example hbond time series data set there is a
- one frame change in state between the first and second lifetimes which
- could be interpreted as a transient breaking of the hydrogen bond.
- Using a <fuzzcut> value of 1, this one frame change in state would be ignored,
- and the data set would effectively appear to lifetime as {1 1 1 1 1 0 0
- 0 1 1}.
- The state change between the second and third lifetimes is longer than
- <fuzzcut> (3 frames) and so it would remain.
+ keyword can be used to try and smooth the input data by ignoring changes in state that occur for fewer frames than <fuzzcut>.
+ For example,
+ in the above example hbond time series data set there is a one frame change in state between the first and second lifetimes which could be interpreted as a transient breaking of the hydrogen bond.
+ Using a <fuzzcut> value of 1,
+ this one frame change in state would be ignored,
+ and the data set would effectively appear to lifetime as {1 1 1 1 1 0 0 0 1 1}.
+ The state change between the second and third lifetimes is longer than <fuzzcut> (3 frames) and so it would remain.
 \end_layout
 
 \begin_layout Standard
@@ -51575,7 +52414,9 @@ If
 \series bold
 window
 \series default
- is not specified, two files are output: <filename> and crv.<filename>.
+ is not specified,
+ two files are output:
+ <filename> and crv.<filename>.
  The file <filename> contains overall lifetime stats for each set with format:
 \end_layout
 
@@ -51588,19 +52429,23 @@ where
 \family typewriter
 <setname>
 \family default
- denotes the total number of lifetimes, 
+ denotes the total number of lifetimes,
+ 
 \family typewriter
 <setname>[max]
 \family default
- denotes the maximum lifetime, 
+ denotes the maximum lifetime,
+ 
 \family typewriter
 <setname>[avg] 
 \family default
-denotes the average lifetime, 
+denotes the average lifetime,
+ 
 \family typewriter
 <setname>[frames]
 \family default
- denotes the total number of frames present in all lifetimes, and 
+ denotes the total number of frames present in all lifetimes,
+ and 
 \family typewriter
 <setname>[name] 
 \family default
@@ -51613,7 +52458,11 @@ If
 \series bold
 window
 \series default
- is specified, four files are output: <filename>, max.<filename>, avg.<filename>,
+ is specified,
+ four files are output:
+ <filename>,
+ max.<filename>,
+ avg.<filename>,
  and crv.<filename>.
  <filename> contains the fraction 
 \begin_inset Quotes eld
@@ -51623,15 +52472,17 @@ present
 \begin_inset Quotes erd
 \end_inset
 
- over each time window for each set, max.<filename> contains the maximum
- lifetime in each time window for each set, avg.<filename> contains the average
- lifetime over each window for each set, and crv.<filename> contains the
- overall lifetime curves for each set.
- For window output, Gnuplot format is recommended.
+ over each time window for each set,
+ max.<filename> contains the maximum lifetime in each time window for each set,
+ avg.<filename> contains the average lifetime over each window for each set,
+ and crv.<filename> contains the overall lifetime curves for each set.
+ For window output,
+ Gnuplot format is recommended.
 \end_layout
 
 \begin_layout Subsubsection*
-Example: hbond lifetime analysis
+Example:
+ hbond lifetime analysis
 \end_layout
 
 \begin_layout LyX-Code
@@ -51748,8 +52599,8 @@ lowest> Number of lowest points in each bin to average over.
 \end_deeper
 \begin_layout Standard
 Calculate a curve of the average of the # lowest points in bins of stepsize.
- Essentially each input data set is binned over bins of stepsize, then the
- lowest <#> points are averaged over for each bin.
+ Essentially each input data set is binned over bins of stepsize,
+ then the lowest <#> points are averaged over for each bin.
 \end_layout
 
 \begin_layout Subsection
@@ -51762,8 +52613,8 @@ meltcurve <dset0> [<dset1> ...] [out <outfile>] [name <outsetname>] cut <cut>
 
 \begin_layout Standard
 Calculate melting curve from input data sets (i.e.
- fraction 'folded' for each data set) assuming a simple 2-state transition
- model, using data below <cut>as 'folded' and data above <cut> as 'unfolded'.
+ fraction 'folded' for each data set) assuming a simple 2-state transition model,
+ using data below <cut>as 'folded' and data above <cut> as 'unfolded'.
 \end_layout
 
 \begin_layout Subsection
@@ -51771,8 +52622,7 @@ modes
 \end_layout
 
 \begin_layout LyX-Code
-modes {fluct|displ|corr|eigenval|trajout|rmsip} name <modesname> [name2
- <modesname>]
+modes {fluct|displ|corr|eigenval|trajout|rmsip} name <modesname> [name2 <modesname>]
 \end_layout
 
 \begin_layout LyX-Code
@@ -51784,7 +52634,8 @@ modes {fluct|displ|corr|eigenval|trajout|rmsip} name <modesname> [name2
 \end_layout
 
 \begin_layout LyX-Code
-    Options for 'trajout': (Generate pseudo-trajectory)
+    Options for 'trajout':
+ (Generate pseudo-trajectory)
 \end_layout
 
 \begin_layout LyX-Code
@@ -51800,7 +52651,8 @@ modes {fluct|displ|corr|eigenval|trajout|rmsip} name <modesname> [name2
 \end_layout
 
 \begin_layout LyX-Code
-    Options for 'corr': (Calculate dipole correlation)
+    Options for 'corr':
+ (Calculate dipole correlation)
 \end_layout
 
 \begin_layout LyX-Code
@@ -51825,8 +52677,10 @@ Types of Calculations:
 \series bold
 fluct
 \series default
- RMS fluctuations (X, Y, Z, and total) for each atom across specified normal
- modes.
+ RMS fluctuations (X,
+ Y,
+ Z,
+ and total) for each atom across specified normal modes.
 \end_layout
 
 \begin_layout Description
@@ -51834,8 +52688,8 @@ fluct
 \series bold
 displ
 \series default
- Displacement of cartesian coordinates in the X, Y and Z directions for
- each atom across specified normal modes.
+ Displacement of cartesian coordinates in the X,
+ Y and Z directions for each atom across specified normal modes.
 \end_layout
 
 \begin_layout Description
@@ -51856,13 +52710,11 @@ eigenval Calculate eigenvalue fractions.
 \end_layout
 
 \begin_layout Description
-trajout Create a pseudo-trajectory along the given mode from the average
- structure.
+trajout Create a pseudo-trajectory along the given mode from the average structure.
 \end_layout
 
 \begin_layout Description
-rmsip Calculate the root-mean-square inner product between modes specified
- by 
+rmsip Calculate the root-mean-square inner product between modes specified by 
 \series bold
 name
 \series default
@@ -51906,13 +52758,14 @@ name
 
 <end>]
 \series default
- If modes taken from datafile, beginning and end modes to read.
+ If modes taken from datafile,
+ beginning and end modes to read.
  Default for 
 \shape italic
 beg
 \shape default
- is 7 (which skips the first 6 zero-frequency modes in the case of a normal
- mode analysis); for 
+ is 7 (which skips the first 6 zero-frequency modes in the case of a normal mode analysis);
+ for 
 \shape italic
 end
 \shape default
@@ -51941,8 +52794,8 @@ end
 \end_layout
 
 \begin_layout Description
-[calcall] If specified use all eigenvectors; otherwise eigenvectors associated
- with zero or negative eigenvalues will be skipped.
+[calcall] If specified use all eigenvectors;
+ otherwise eigenvectors associated with zero or negative eigenvalues will be skipped.
 \end_layout
 
 \begin_layout Description
@@ -52007,8 +52860,7 @@ Options for 'trajout':
 \begin_inset space ~
 \end_inset
 
-<pcmin>] Lowest principal component projection value to use for output trajector
-y.
+<pcmin>] Lowest principal component projection value to use for output trajectory.
 \end_layout
 
 \begin_layout Description
@@ -52016,8 +52868,7 @@ y.
 \begin_inset space ~
 \end_inset
 
-<pcmax>] Highest principal component projection value to use for output
- trajectory.
+<pcmax>] Highest principal component projection value to use for output trajectory.
 \end_layout
 
 \begin_layout Description
@@ -52053,15 +52904,18 @@ Options for 'corr':
 \series bold
 corr
 \series default
-, pairs of atom masks (
+,
+ pairs of atom masks (
 \shape italic
 mask1
 \shape default
-, 
+,
+ 
 \shape italic
 mask2
 \shape default
-; each pair preceded by 
+;
+ each pair preceded by 
 \begin_inset Quotes eld
 \end_inset
 
@@ -52073,8 +52927,7 @@ maskp
 \begin_inset Quotes erd
 \end_inset
 
- and each mask defining only a single atom) have to be given that specify
- the atoms for which the correlation functions are desired.
+ and each mask defining only a single atom) have to be given that specify the atoms for which the correlation functions are desired.
 \end_layout
 
 \begin_layout Description
@@ -52094,8 +52947,9 @@ mask2
 \series bold
 maskp
 \series default
-, specify two masks; atoms from the first mask will be paired up with atoms
- from the second mask.
+,
+ specify two masks;
+ atoms from the first mask will be paired up with atoms from the second mask.
 \end_layout
 
 \begin_layout Standard
@@ -52160,9 +53014,7 @@ DataSets Created (rmsip)
 
 \end_deeper
 \begin_layout Standard
-Analyze previously calculated eigenmodes obtained from principal component
- analyses (of covariance matrices) or quasiharmonic analyses (diagmatrix
- analysis command).
+Analyze previously calculated eigenmodes obtained from principal component analyses (of covariance matrices) or quasiharmonic analyses (diagmatrix analysis command).
  Modes are taken from a previously generated data set (i.e.
  from 
 \series bold
@@ -52177,8 +53029,8 @@ readdata
 \series default
 \shape default
 .
- By default, classical (Boltzmann) statistics are used in populating the
- modes.
+ By default,
+ classical (Boltzmann) statistics are used in populating the modes.
  A possible series of commands would be 
 \begin_inset Quotes eld
 \end_inset
@@ -52203,7 +53055,8 @@ mwcovar
 \begin_inset Quotes erd
 \end_inset
 
- to generate the matrix, 
+ to generate the matrix,
+ 
 \begin_inset Quotes eld
 \end_inset
 
@@ -52217,7 +53070,10 @@ diagmatrix
 \begin_inset Quotes erd
 \end_inset
 
- to calculate the modes, and, finally, 
+ to calculate the modes,
+ and,
+ finally,
+ 
 \begin_inset Quotes eld
 \end_inset
 
@@ -52236,8 +53092,8 @@ modes
 \end_layout
 
 \begin_layout Standard
-For example, to calculate the RMS fluctuations or displacements of the first
- 3 eigenmodes caluclated from a mass-weighted covariance matrix:
+For example,
+ to calculate the RMS fluctuations or displacements of the first 3 eigenmodes caluclated from a mass-weighted covariance matrix:
 \end_layout
 
 \begin_layout LyX-Code
@@ -52257,8 +53113,8 @@ modes displ out resdispl.dat name evecs beg 1 end 3
 \end_layout
 
 \begin_layout Standard
-Additionally, dipole-dipole correlation functions for modes obtained from
- principle component analysis or quasiharmonic analysis can be computed.
+Additionally,
+ dipole-dipole correlation functions for modes obtained from principle component analysis or quasiharmonic analysis can be computed.
 \end_layout
 
 \begin_layout LyX-Code
@@ -52284,8 +53140,8 @@ If
 \series bold
 eigenval
 \series default
- is specified, the fraction contribution of each eigenvector to the total
- motion is calculated and output with format:
+ is specified,
+ the fraction contribution of each eigenvector to the total motion is calculated and output with format:
 \end_layout
 
 \begin_layout LyX-Code
@@ -52298,12 +53154,14 @@ where
 \family typewriter
 #Mode
 \family default
- is the eigenvector number, 
+ is the eigenvector number,
+ 
 \family typewriter
 Frac.
 
 \family default
- is the eigenvalue over the sum of all eigenvalues, 
+ is the eigenvalue over the sum of all eigenvalues,
+ 
 \family typewriter
 Cumulative
 \family default
@@ -52311,27 +53169,25 @@ Cumulative
 \family typewriter
 Frac.
 \family default
-, and 
+,
+ and 
 \family typewriter
 Eigenval
 \family default
  is the eigenvalue itself.
- Note that in order to get an idea for how much each eigenvector contributes
- to all motion, this is best used when all possible eigenvectors have been
- determined for a system.
+ Note that in order to get an idea for how much each eigenvector contributes to all motion,
+ this is best used when all possible eigenvectors have been determined for a system.
 \end_layout
 
 \begin_layout Standard
-In order to visualize eigenvectors, pseudo-trajectories along eigenvectors
- can be created using average coordinates with the 
+In order to visualize eigenvectors,
+ pseudo-trajectories along eigenvectors can be created using average coordinates with the 
 \series bold
 trajout
 \series default
  keyword.
- For example, to write a pseudo-trajectory of the first principal component
- from principal component value of -100 to 100 for a previously calculated
- Modes data set corresponding to heavy atoms (no hydrogens) for residues
- 1 to 36:
+ For example,
+ to write a pseudo-trajectory of the first principal component from principal component value of -100 to 100 for a previously calculated Modes data set corresponding to heavy atoms (no hydrogens) for residues 1 to 36:
 \end_layout
 
 \begin_layout LyX-Code
@@ -52365,8 +53221,7 @@ multicurve set <dset> [set <dset> ...]
 \end_layout
 
 \begin_layout LyX-Code
-                    name <dsname> nexp <m> [form {mexp|mexpk|mexpk_penalty}
- }
+                    name <dsname> nexp <m> [form {mexp|mexpk|mexpk_penalty} }
 \end_layout
 
 \begin_layout LyX-Code
@@ -52412,6 +53267,7 @@ set
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-Data-Set-Math"
+nolink "false"
 
 \end_inset
 
@@ -52456,22 +53312,22 @@ form
 
 \begin_deeper
 \begin_layout Description
-mexp Multi-exponential, SUM(m)[ An * exp(An+1 * X)]
+mexp Multi-exponential,
+ SUM(m)[ An * exp(An+1 * X)]
 \end_layout
 
 \begin_layout Description
-mexpk Multi-exponential plus constant, A0 + SUM(m)[An * exp(An+1 * X)]
+mexpk Multi-exponential plus constant,
+ A0 + SUM(m)[An * exp(An+1 * X)]
 \end_layout
 
 \begin_layout Description
-mexpk_penalty Same as mexpk except sum of prefactors constrained to 1.0 and
- exponential constants constrained to < 0.0.
+mexpk_penalty Same as mexpk except sum of prefactors constrained to 1.0 and exponential constants constrained to < 0.0.
 \end_layout
 
 \end_deeper
 \begin_layout Description
-AX=<value> Value of any constants in specified equation with X starting
- from 0 (can specify more than one).
+AX=<value> Value of any constants in specified equation with X starting from 0 (can specify more than one).
 \end_layout
 
 \begin_layout Description
@@ -52499,8 +53355,7 @@ maxit
 \begin_inset space ~
 \end_inset
 
-iterations> Number of iterations to run curve fitting algotrithm (default
- 50).
+iterations> Number of iterations to run curve fitting algotrithm (default 50).
 \end_layout
 
 \begin_layout Description
@@ -52516,8 +53371,7 @@ outxbins
 \begin_inset space ~
 \end_inset
 
-<NX> Number of points to use when generating final curve (default same number
- of points as input data set).
+<NX> Number of points to use when generating final curve (default same number of points as input data set).
 \end_layout
 
 \begin_layout Description
@@ -52525,8 +53379,7 @@ outxmin
 \begin_inset space ~
 \end_inset
 
-<xmin> Minimum X value to use for final curve (default same number of points
- as input data set).
+<xmin> Minimum X value to use for final curve (default same number of points as input data set).
 \end_layout
 
 \begin_layout Description
@@ -52534,8 +53387,7 @@ outxmax
 \begin_inset space ~
 \end_inset
 
-<xmax> Maximum X value to use for final curve (default same number of points
- as input data set).
+<xmax> Maximum X value to use for final curve (default same number of points as input data set).
 \end_layout
 
 \end_deeper
@@ -52551,6 +53403,7 @@ curvefit
 \begin_inset CommandInset ref
 LatexCommand vpageref
 reference "subsec:cpptraj_curvefit"
+nolink "false"
 
 \end_inset
 
@@ -52644,8 +53497,7 @@ free
 \begin_inset space ~
 \end_inset
 
-<T> Calculate free energy from bin populations as G = -R * <T> * ln( Ni
- / Nmax ).
+<T> Calculate free energy from bin populations as G = -R * <T> * ln( Ni / Nmax ).
 \end_layout
 
 \begin_layout Description
@@ -52702,8 +53554,8 @@ resrange
 
 \end_deeper
 \begin_layout Standard
-Calculate the average and standard deviation of [phi] and [psi] data set
- pairs, write to <file> with format:
+Calculate the average and standard deviation of [phi] and [psi] data set pairs,
+ write to <file> with format:
 \end_layout
 
 \begin_layout LyX-Code
@@ -52711,14 +53563,13 @@ Calculate the average and standard deviation of [phi] and [psi] data set
 \end_layout
 
 \begin_layout Standard
-Where Phi is the average value of phi, Psi is the average value of psi,
- SD(Phi) is the standard deviation of phi, SD(psi) is the standard deviation
- of psi, and Legend contains text describing the phi and psi data sets used
- in the calculation.
+Where Phi is the average value of phi,
+ Psi is the average value of psi,
+ SD(Phi) is the standard deviation of phi,
+ SD(psi) is the standard deviation of psi,
+ and Legend contains text describing the phi and psi data sets used in the calculation.
  Periodicity is taken into account during averaging.
- The data sets must have been internally labeled as type 'phi'/'psi' and
- must have a data set index set (actions like dihedral and multidihedral
- do this automatically).
+ The data sets must have been internally labeled as type 'phi'/'psi' and must have a data set index set (actions like dihedral and multidihedral do this automatically).
  For example:
 \end_layout
 
@@ -52754,8 +53605,7 @@ name "subsec:cpptraj-projectdata"
 \end_layout
 
 \begin_layout LyX-Code
-projectdata evecs <evecs dataset> [name <name>] [out <outfile>] [beg <beg>]
- [end <end>]
+projectdata evecs <evecs dataset> [name <name>] [out <outfile>] [beg <beg>] [end <end>]
 \end_layout
 
 \begin_layout LyX-Code
@@ -52829,10 +53679,11 @@ arg>] (Dihedral covariance only) Dihedral data sets to use in projection;
 \begin_inset space ~
 \end_inset
 
-arg>] (Data covariance only, e.g.
+arg>] (Data covariance only,
+ e.g.
  from TICA).
- 1D data sets to use in projection; MUST CORRESPOND TO HOW EIGENVECTORS
- WERE GENERATED.
+ 1D data sets to use in projection;
+ MUST CORRESPOND TO HOW EIGENVECTORS WERE GENERATED.
 \end_layout
 
 \begin_layout Standard
@@ -52860,6 +53711,7 @@ reference "subsec:cpptraj-projection"
 plural "false"
 caps "false"
 noprefix "false"
+nolink "false"
 
 \end_inset
 
@@ -52900,9 +53752,9 @@ nx
 \begin_inset space ~
 \end_inset
 
-<nxvals> Number of X values to use in output data set(s) (ranging from input
- set min to max X).
- If not specified, input X values used.
+<nxvals> Number of X values to use in output data set(s) (ranging from input set min to max X).
+ If not specified,
+ input X values used.
 \end_layout
 
 \begin_layout Description
@@ -52926,8 +53778,7 @@ DataSets Generated:
 \end_layout
 
 \begin_layout Description
-<name>:<idx> Output fit line(s) (indexed by input set order if more than
- one input set).
+<name>:<idx> Output fit line(s) (indexed by input set order if more than one input set).
 \end_layout
 
 \begin_layout Description
@@ -52955,8 +53806,8 @@ statsout
 \end_layout
 
 \begin_layout Standard
-For example, to fit data read in from a file and then create a set using
- the fit parameters:
+For example,
+ to fit data read in from a file and then create a set using the fit parameters:
 \end_layout
 
 \begin_layout LyX-Code
@@ -52987,8 +53838,7 @@ name "subsec:cpptraj-remlog"
 \end_layout
 
 \begin_layout LyX-Code
-remlog {<remlog dataset> | <remlog filename>} [out <filename>] [crdidx |
- repidx]
+remlog {<remlog dataset> | <remlog filename>} [out <filename>] [crdidx | repidx]
 \end_layout
 
 \begin_layout LyX-Code
@@ -52996,8 +53846,7 @@ remlog {<remlog dataset> | <remlog filename>} [out <filename>] [crdidx |
 \end_layout
 
 \begin_layout LyX-Code
-   	[reptimeslope <n> reptimeslopeout <file>] [acceptout <file>] [name <setname>
-]
+   	[reptimeslope <n> reptimeslopeout <file>] [acceptout <file>] [name <setname>]
 \begin_inset Separator latexpar
 \end_inset
 
@@ -53039,12 +53888,14 @@ filename> REM log file name to read in.
 
 \begin_deeper
 \begin_layout Description
-crdidx Print coordinate index vs exchange; output sets contain replica indices.
+crdidx Print coordinate index vs exchange;
+ output sets contain replica indices.
  
 \end_layout
 
 \begin_layout Description
-repidx Print replica index vs exchange; output sets contain coordinate indices.
+repidx Print replica index vs exchange;
+ output sets contain coordinate indices.
  
 \end_layout
 
@@ -53126,7 +53977,8 @@ reptimeslope
 \begin_inset space ~
 \end_inset
 
-<file>]] Extract energy data from replica log, optionally write to file.
+<file>]] Extract energy data from replica log,
+ optionally write to file.
 \end_layout
 
 \begin_layout Standard
@@ -53138,7 +53990,8 @@ DataSets created:
 \end_layout
 
 \begin_layout Description
-<setname>[E]:<idx> If 'edata' specified, energy data from replica log.
+<setname>[E]:<idx> If 'edata' specified,
+ energy data from replica log.
 \end_layout
 
 \end_deeper
@@ -53150,11 +54003,11 @@ readdata
 \series default
 \emph default
 ) M-REMD/T-REMD/H-REMD replica log data.
- Statistics calculated include round-trip time, which is the time needed
- for a coordinate set to travel from the lowest replica to the highest and
- back, and the number of exchanges each coordinate spent at each replica.
- For example, to read in REM log data from an Amber M-REMD run and analyze
- it:
+ Statistics calculated include round-trip time,
+ which is the time needed for a coordinate set to travel from the lowest replica to the highest and back,
+ and the number of exchanges each coordinate spent at each replica.
+ For example,
+ to read in REM log data from an Amber M-REMD run and analyze it:
 \end_layout
 
 \begin_layout LyX-Code
@@ -53172,7 +54025,8 @@ For an example of
 remlog
 \series default
 \emph default
- analysis applied to actual REMD data, see Roe et al.
+ analysis applied to actual REMD data,
+ see Roe et al.
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Roe2014"
@@ -53197,6 +54051,8 @@ name "subsec:cpptraj-rms2d"
 \begin_layout LyX-Code
 rms2d
 \begin_inset Index idx
+range none
+pageformat default
 status collapsed
 
 \begin_layout Plain Layout
@@ -53252,8 +54108,8 @@ set>] Name of previously generated COORDS DataSet.
 \end_layout
 
 \begin_layout Description
-[dme] Calculate distance RMSD instead of coordinate RMSD; this is substantially
- slower.
+[dme] Calculate distance RMSD instead of coordinate RMSD;
+ this is substantially slower.
 \end_layout
 
 \begin_layout Description
@@ -53265,6 +54121,7 @@ set>] Name of previously generated COORDS DataSet.
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_symmrmsd"
+nolink "false"
 
 \end_inset
 
@@ -53284,8 +54141,7 @@ reference "subsec:cpptraj_symmrmsd"
 \begin_inset space ~
 \end_inset
 
-<traj>] Calculate 2D RMSD to frames in trajectory <traj> instead (can also
- be another COORDS set).
+<traj>] Calculate 2D RMSD to frames in trajectory <traj> instead (can also be another COORDS set).
 \end_layout
 
 \begin_layout Description
@@ -53305,7 +54161,8 @@ parmindex
 \begin_inset space ~
 \end_inset
 
-<#>] Topology to use for <traj>; only useful in conjunction with 
+<#>] Topology to use for <traj>;
+ only useful in conjunction with 
 \series bold
 reftraj
 \series default
@@ -53313,8 +54170,8 @@ reftraj
 \end_layout
 
 \begin_layout Description
-[<refmask>] Mask of atoms in reference; only useful in conjunction with
- 
+[<refmask>] Mask of atoms in reference;
+ only useful in conjunction with 
 \series bold
 reftraj
 \series default
@@ -53334,21 +54191,23 @@ C
 \begin_inset Formula $C(i)=\frac{\sum_{j=0}^{j<N-i}\exp(-RMSD(j,j+i))}{N-i}$
 \end_inset
 
-, where 
+,
+ where 
 \shape italic
 i
 \shape default
- is the lag, 
+ is the lag,
+ 
 \shape italic
 j
 \shape default
- is the frame #, and 
+ is the frame #,
+ and 
 \shape italic
 N
 \shape default
  is the total number of frames.
- An exponential is used to weight the RMSD since 0.0 RMSD is equivalent to
- correlation of 1.0.
+ An exponential is used to weight the RMSD since 0.0 RMSD is equivalent to correlation of 1.0.
  This can only be done if 
 \series bold
 reftraj
@@ -53372,23 +54231,21 @@ corr
 \begin_layout Standard
 
 \shape italic
-Note: For backwards compatibility with ptraj the command '2drms' will also
- work.
+Note:
+ For backwards compatibility with ptraj the command '2drms' will also work.
 \end_layout
 
 \begin_layout Standard
-Calculate the best-fit RMSD of each frame in <crd set> (the default COORDS
- set if none specified) to each other frame.
- This creates an upper-triangle matrix named <name> (or a full matrix if
- 
+Calculate the best-fit RMSD of each frame in <crd set> (the default COORDS set if none specified) to each other frame.
+ This creates an upper-triangle matrix named <name> (or a full matrix if 
 \series bold
 reftraj
 \series default
  specified).
- The output of the rms2d command can be best-viewed using gnuplot; a gnuplot-for
-matted file can be produced by giving <filename> a '.gnu' extension.
- For example, to calculate the RMSD of non-hydrogen atoms of each frame
- in trajectory 
+ The output of the rms2d command can be best-viewed using gnuplot;
+ a gnuplot-formatted file can be produced by giving <filename> a '.gnu' extension.
+ For example,
+ to calculate the RMSD of non-hydrogen atoms of each frame in trajectory 
 \begin_inset Quotes eld
 \end_inset
 
@@ -53396,7 +54253,8 @@ test.nc
 \begin_inset Quotes erd
 \end_inset
 
- to each other frame, writing to a gnuplot-viewable file 
+ to each other frame,
+ writing to a gnuplot-viewable file 
 \begin_inset Quotes eld
 \end_inset
 
@@ -53457,6 +54315,8 @@ name "subsec:cpptraj-rmsavgcorr"
 \begin_layout LyX-Code
 rmsavgcorr
 \begin_inset Index idx
+range none
+pageformat default
 status open
 
 \begin_layout Plain Layout
@@ -53490,8 +54350,7 @@ rmsavgcorr
 \begin_inset space ~
 \end_inset
 
-set>] COORDS data set to use (if not specified the default COORDS set will
- be used).
+set>] COORDS data set to use (if not specified the default COORDS set will be used).
 \end_layout
 
 \begin_layout Description
@@ -53551,8 +54410,7 @@ file>
 \begin_inset space ~
 \end_inset
 
-<parmfile>] Use reference file (with specified parm) as reference for each
- window.
+<parmfile>] Use reference file (with specified parm) as reference for each window.
 \end_layout
 
 \end_deeper
@@ -53565,8 +54423,7 @@ literal "true"
 
 \end_inset
 
- (RAC) is calculated as the average RMSD of running-averaged coordinates
- over increasing window sizes (or lag).
+ (RAC) is calculated as the average RMSD of running-averaged coordinates over increasing window sizes (or lag).
  Output has format:
 \end_layout
 
@@ -53575,27 +54432,26 @@ literal "true"
 \end_layout
 
 \begin_layout Standard
-The first entry has a window size of 1, and so is just the average RMSD
- of all frames to the specified reference structure.
- The second entry has a window size of two, so it is the average RMSD of
- all frames averaged over two adjacent windows to the specified reference,
+The first entry has a window size of 1,
+ and so is just the average RMSD of all frames to the specified reference structure.
+ The second entry has a window size of two,
+ so it is the average RMSD of all frames averaged over two adjacent windows to the specified reference,
  and so on.
- The RAC will be calculated up to the number of frames minus 1 or the value
- specified by 
+ The RAC will be calculated up to the number of frames minus 1 or the value specified by 
 \series bold
 stop
 \series default
-, whichever is lower.
+,
+ whichever is lower.
  The offset can be used to speed up the calculation by skipping window sizes.
  To calculate mass-weighted RMSD specify 
 \series bold
 mass
 \series default
 .
- Note that to reduce memory costs it can be useful to strip all coordinates
- not involved in the RMS fit from the system prior to specifying 'rmsavgcorr'.
- For example, to calculate the correlation of C-alpha RMSD of residues 2
- to 12:
+ Note that to reduce memory costs it can be useful to strip all coordinates not involved in the RMS fit from the system prior to specifying 'rmsavgcorr'.
+ For example,
+ to calculate the correlation of C-alpha RMSD of residues 2 to 12:
 \end_layout
 
 \begin_layout LyX-Code
@@ -53608,27 +54464,23 @@ rmsavgcorr out rmscorr.dat
 
 \begin_layout Standard
 The curve generated by RAC decays towards zero due to the way RAC is defined.
- By the time the "lag" is N-1 (where N is the total number of frames) you
- have only two averaged coordinates: call them Avg1 (averaged over 1 though
- N-1 frames) and Avg2 (averaged over 2 through N frames).
- Barring any extraordinary circumstances the RMSD between Avg1 and Avg2
- will almost certainly be quite low.
+ By the time the "lag" is N-1 (where N is the total number of frames) you have only two averaged coordinates:
+ call them Avg1 (averaged over 1 though N-1 frames) and Avg2 (averaged over 2 through N frames).
+ Barring any extraordinary circumstances the RMSD between Avg1 and Avg2 will almost certainly be quite low.
  
 \end_layout
 
 \begin_layout Standard
 The RAC is a way to probe the time scales of interesting events.
- Any deviation from a smoothly decaying curve is an indication that there
- are some significant structural differences occurring over that time interval.
- RAC curves can be particularly useful when comparing independent simulations
- of the same system.
+ Any deviation from a smoothly decaying curve is an indication that there are some significant structural differences occurring over that time interval.
+ RAC curves can be particularly useful when comparing independent simulations of the same system.
 \end_layout
 
 \begin_layout Standard
-One thing to keep in mind that since the underlying metric is RMSD, it can
- be sensitive to the reference frame you choose.
- It may be useful to try looking at both RAC from the first frame, as well
- as an averaged reference frame.
+One thing to keep in mind that since the underlying metric is RMSD,
+ it can be sensitive to the reference frame you choose.
+ It may be useful to try looking at both RAC from the first frame,
+ as well as an averaged reference frame.
  For an example of use see Galindo-Murillo et al.
 \begin_inset CommandInset citation
 LatexCommand citep
@@ -53637,7 +54489,8 @@ literal "true"
 
 \end_inset
 
-, in particular Figure 2.
+,
+ in particular Figure 2.
 \end_layout
 
 \begin_layout Subsection
@@ -53681,7 +54534,8 @@ rotdif [outfile <outfilename>] [usefft]
 \end_layout
 
 \begin_layout LyX-Code
-  Options for calculating local effective D, small anisotropy:
+  Options for calculating local effective D,
+ small anisotropy:
 \end_layout
 
 \begin_layout LyX-Code
@@ -53758,7 +54612,8 @@ rvecin
 \begin_inset space ~
 \end_inset
 
-<randvecIn> File to read random vectors from (format is 1 per line, 4 columns,
+<randvecIn> File to read random vectors from (format is 1 per line,
+ 4 columns,
  <#> <VX> <VY> <VZ>).
 \end_layout
 
@@ -53780,7 +54635,8 @@ rvecout
 \begin_inset space ~
 \end_inset
 
-<randvecOut> File to write random vectors to (format is 1 per line, 4 columns,
+<randvecOut> File to write random vectors to (format is 1 per line,
+ 4 columns,
  <#> <VX> <VY> <VZ>).
 \end_layout
 
@@ -53802,8 +54658,9 @@ rmout
 \begin_inset space ~
 \end_inset
 
-<rmOut> Write rotation matrices to file, 1 per line, frame # followed by
- matrix in row-major order.
+<rmOut> Write rotation matrices to file,
+ 1 per line,
+ frame # followed by matrix in row-major order.
 \end_layout
 
 \end_deeper
@@ -53826,8 +54683,7 @@ order
 \begin_inset space ~
 \end_inset
 
-<olegendre> The order of Legendre polynomials to use when calculating vector
- time correlation functions (default 2).
+<olegendre> The order of Legendre polynomials to use when calculating vector time correlation functions (default 2).
 \end_layout
 
 \begin_layout Description
@@ -53856,8 +54712,8 @@ corrout
 \begin_inset space ~
 \end_inset
 
-<corrOut> If specified write vector time correlation functions to <corrOut>.X
- with format: <Time> <Px>
+<corrOut> If specified write vector time correlation functions to <corrOut>.X with format:
+ <Time> <Px>
 \end_layout
 
 \end_deeper
@@ -53865,7 +54721,8 @@ corrout
 
 \family roman
 \emph on
-Options for calculating local effective D, small anisotropy:
+Options for calculating local effective D,
+ small anisotropy:
 \family default
 
 \begin_inset Separator latexpar
@@ -53880,8 +54737,7 @@ deffout
 \begin_inset space ~
 \end_inset
 
-<deffOut> File to write out local effective diffusion constants determined
- in the limit of small anisotropy.
+<deffOut> File to write out local effective diffusion constants determined in the limit of small anisotropy.
 \end_layout
 
 \begin_layout Description
@@ -53889,9 +54745,7 @@ itmax
 \begin_inset space ~
 \end_inset
 
-<itmax> Maximum number of iterations to determine each local effective diffusion
- constant (small anisotropy) assuming fit to single exponential form (default
- 500).
+<itmax> Maximum number of iterations to determine each local effective diffusion constant (small anisotropy) assuming fit to single exponential form (default 500).
 \end_layout
 
 \begin_layout Description
@@ -53899,8 +54753,7 @@ tol
 \begin_inset space ~
 \end_inset
 
-<tolerance> Tolerance for determining local effective diffusion constant
- (small anisotropy) assuming fit to single exponential form (default 1E-6).
+<tolerance> Tolerance for determining local effective diffusion constant (small anisotropy) assuming fit to single exponential form (default 1E-6).
 \end_layout
 
 \begin_layout Description
@@ -53908,8 +54761,7 @@ d0
 \begin_inset space ~
 \end_inset
 
-<d0> Initial guess for small anisotropy diffusion constant in radians^2/ns
- (default 0.03).
+<d0> Initial guess for small anisotropy diffusion constant in radians^2/ns (default 0.03).
 \end_layout
 
 \begin_layout Description
@@ -53917,8 +54769,7 @@ nmesh
 \begin_inset space ~
 \end_inset
 
-<NmeshPoints> Number of points per frame to use when creating cubic-splined-smoo
-thed forms of vector time correlation curves (default 2).
+<NmeshPoints> Number of points per frame to use when creating cubic-splined-smoothed forms of vector time correlation curves (default 2).
 \end_layout
 
 \begin_layout Description
@@ -53926,8 +54777,7 @@ dt
 \begin_inset space ~
 \end_inset
 
-<tfac> Time interval between frames (used in integrating vector time correlation
- curves) in ns.
+<tfac> Time interval between frames (used in integrating vector time correlation curves) in ns.
 \end_layout
 
 \begin_layout Description
@@ -53935,8 +54785,7 @@ ti
 \begin_inset space ~
 \end_inset
 
-<ti> Initial time value in ns for integrating the time correlation functions
- (default 0.0).
+<ti> Initial time value in ns for integrating the time correlation functions (default 0.0).
 \end_layout
 
 \begin_layout Description
@@ -53945,8 +54794,7 @@ tf
 \end_inset
 
 <tf> Final time value in ns for integrating the time correlation functions.
- It is recommended this be less than the maximum simulation time since the
- tails of time correlation functions tend to be noisy.
+ It is recommended this be less than the maximum simulation time since the tails of time correlation functions tend to be noisy.
 \end_layout
 
 \end_deeper
@@ -53977,8 +54825,7 @@ amoeba_itmax
 \begin_inset space ~
 \end_inset
 
-<iterations> Number of iterations to run downhill-simplex minimizer (default
- 10000).
+<iterations> Number of iterations to run downhill-simplex minimizer (default 10000).
 \end_layout
 
 \begin_layout Description
@@ -53986,8 +54833,7 @@ amoeba_nsearch
 \begin_inset space ~
 \end_inset
 
-<n> Number of searches to perform with downhill-simplex minimizer (default
- 1).
+<n> Number of searches to perform with downhill-simplex minimizer (default 1).
 \end_layout
 
 \begin_layout Description
@@ -53999,15 +54845,13 @@ scalesimplex
 \end_layout
 
 \begin_layout Description
-gridsearch If specified, perform a brute-force grid search to attempt to
- find a better solution for diffusion tensor with full anisotropy (may be
- expensive).
+gridsearch If specified,
+ perform a brute-force grid search to attempt to find a better solution for diffusion tensor with full anisotropy (may be expensive).
 \end_layout
 
 \end_deeper
 \begin_layout Standard
-Evaluate rotational diffusion properties of a molecule over a trajectory
- according to an expanded version of the procedure laid out by Wong & Case
+Evaluate rotational diffusion properties of a molecule over a trajectory according to an expanded version of the procedure laid out by Wong & Case
 \begin_inset CommandInset citation
 LatexCommand citep
 key "wong2008"
@@ -54016,48 +54860,42 @@ literal "true"
 \end_inset
 
 .
- Briefly, random vectors (representing the orientation of the molecule)
- are rotated according to rotation matrices obtained from an RMS fit to
- a reference structure (typically an averaged structure).
- For each random vector the time correlation function of the rotated vector
- is calculated using Legendre polynomials of the specified order.
- The integral over this time correlation function (which may be smoothed
- using cubic splines to improve the integration) is then used to find the
- effective diffusion constant (D) in the limit of small anisotropy.
- Then, using each calculated D, the diffusion tensor is determined with
- full anisotropy.
- Finally, a downhill simplex minimizer is used to optimize D with full anisotrop
-y; (this last step is not described in the original paper).
-\end_layout
-
-\begin_layout Standard
-Rotation matrices are generated via an RMS fit to a reference structure
- (see 
+ Briefly,
+ random vectors (representing the orientation of the molecule) are rotated according to rotation matrices obtained from an RMS fit to a reference structure (typically an averaged structure).
+ For each random vector the time correlation function of the rotated vector is calculated using Legendre polynomials of the specified order.
+ The integral over this time correlation function (which may be smoothed using cubic splines to improve the integration) is then used to find the effective diffusion constant (D) in the limit of small anisotropy.
+ Then,
+ using each calculated D,
+ the diffusion tensor is determined with full anisotropy.
+ Finally,
+ a downhill simplex minimizer is used to optimize D with full anisotropy;
+ (this last step is not described in the original paper).
+\end_layout
+
+\begin_layout Standard
+Rotation matrices are generated via an RMS fit to a reference structure (see 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-rmsd"
+nolink "false"
 
 \end_inset
 
 ).
- It is recommended that the RMS fit be done to an average structure (see
- 
+ It is recommended that the RMS fit be done to an average structure (see 
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj-average"
+nolink "false"
 
 \end_inset
 
 ).
- These rotation matrices are used to rotate each random vector M times (where
- M is the total number of frames), which creates a time series for each
- random vector.
- The time correlation functions are calculated for each random vector time
- series using Legendre polynomials of the specified order (default 2).
- Calculation of time correlation functions can be sped up by using the OpenMP
- version of CPPTRAJ.
- The maximum length of the correlation function (or lag) can be specified
- by 
+ These rotation matrices are used to rotate each random vector M times (where M is the total number of frames),
+ which creates a time series for each random vector.
+ The time correlation functions are calculated for each random vector time series using Legendre polynomials of the specified order (default 2).
+ Calculation of time correlation functions can be sped up by using the OpenMP version of CPPTRAJ.
+ The maximum length of the correlation function (or lag) can be specified by 
 \series bold
 ncorr
 \series default
@@ -54066,26 +54904,27 @@ ncorr
 \series bold
 ncorr
 \series default
- is not specified it will be set internally based on the specified values
- of 
+ is not specified it will be set internally based on the specified values of 
 \series bold
 ti
 \series default
-, 
+,
+ 
 \series bold
 tf
 \series default
-, and 
+,
+ and 
 \series bold
 dt
 \series default
-; this is recommended.
+;
+ this is recommended.
  Note that if 
 \series bold
 ncorr
 \series default
- is specified it should be set to a number less than the total number of
- frames since noise in time correlation functions increases as 
+ is specified it should be set to a number less than the total number of frames since noise in time correlation functions increases as 
 \series bold
 ncorr
 \series default
@@ -54098,7 +54937,9 @@ ti
 \series bold
 dt
 \series default
-, generally ns; 0.0 ns if not specified) to 
+,
+ generally ns;
+ 0.0 ns if not specified) to 
 \series bold
 tf
 \series default
@@ -54106,14 +54947,14 @@ tf
 \series bold
 ti
 \series default
-), with the time between frames specified by 
+),
+ with the time between frames specified by 
 \series bold
 dt
 \series default
-; the final time should be less than the total simulation time (see example
- below).
- The relative size of the mesh used with cubic spline interpolation for
- integration is controlled by 
+;
+ the final time should be less than the total simulation time (see example below).
+ The relative size of the mesh used with cubic spline interpolation for integration is controlled by 
 \series bold
 nmesh
 \series default
@@ -54125,46 +54966,49 @@ ncorr
 \series bold
 nmesh
 \series default
-); 
+);
+ 
 \series bold
 nmesh
 \series default
- = 1 means no interpolation, default is 2.
+ = 1 means no interpolation,
+ default is 2.
  Note that if the integral of the correlation function for a vector is negative,
- that vector will be skipped in subsequent calculations (since it would
- imply a negative value for effective diffusion).
+ that vector will be skipped in subsequent calculations (since it would imply a negative value for effective diffusion).
 \end_layout
 
 \begin_layout Standard
-The iterative solver for effective value of the diffusion constant from
- the correlation functions is controlled by 
+The iterative solver for effective value of the diffusion constant from the correlation functions is controlled by 
 \series bold
 itmax
 \series default
-, 
+,
+ 
 \series bold
 tol
 \series default
-, and 
+,
+ and 
 \series bold
 d0
 \series default
-, where 
+,
+ where 
 \series bold
 itmax
 \series default
- specifies the number of iterations to perform (default 500), 
+ specifies the number of iterations to perform (default 500),
+ 
 \series bold
 tol
 \series default
- specifies the tolerance (default 1E-6), and 
+ specifies the tolerance (default 1E-6),
+ and 
 \series bold
 d0
 \series default
- specifies the initial guess for the diffusion constant in radians^2 / ns
- (default 0.03).
- Effective diffusion constants for each random vector can be written out
- to a file specified by 
+ specifies the initial guess for the diffusion constant in radians^2 / ns (default 0.03).
+ Effective diffusion constants for each random vector can be written out to a file specified by 
 \series bold
 deffout
 \series default
@@ -54174,13 +55018,14 @@ deffout
 outfile
 \series default
 .
- Details on the Q and D tensors are given, as well as observed and calculated
- tau for each random vector.
- First, results are printed for analysis in the limit of small anisotropy.
- Next, results are printed for analysis with full anisotropy.
- The results of the full anisotropic calculation are first given using results
- from the small anisotropic analysis as an initial guess, followed by the
- final results after minimization using the downhill simplex (amoeba) minimizer.
+ Details on the Q and D tensors are given,
+ as well as observed and calculated tau for each random vector.
+ First,
+ results are printed for analysis in the limit of small anisotropy.
+ Next,
+ results are printed for analysis with full anisotropy.
+ The results of the full anisotropic calculation are first given using results from the small anisotropic analysis as an initial guess,
+ followed by the final results after minimization using the downhill simplex (amoeba) minimizer.
 \end_layout
 
 \begin_layout Subsubsection*
@@ -54192,27 +55037,22 @@ There are two important things to keep in mind when using rotdif analysis:
 \end_layout
 
 \begin_layout Enumerate
-When calculating any kind of diffusive property it is best to simulate in
- the microcanonical (NVE) ensemble with a shorter time step and increased
- SHAKE tolerance; thermostats and barostats will effect diffusion calculations.
+When calculating any kind of diffusive property it is best to simulate in the microcanonical (NVE) ensemble with a shorter time step and increased SHAKE tolerance;
+ thermostats and barostats will effect diffusion calculations.
 \end_layout
 
 \begin_layout Enumerate
-Time correlation functions become noisier as the length of the function
- approaches the maximum.
- Therefore in general one should choose parameters for the time correlation
- function that are much shorter than the total simulation length.
+Time correlation functions become noisier as the length of the function approaches the maximum.
+ Therefore in general one should choose parameters for the time correlation function that are much shorter than the total simulation length.
  
 \end_layout
 
 \begin_layout Standard
-For example, given a trajectory 'mdcrd.nc' containing 10000 frames with a
- total simulation time of 200 ns (so the time between frames is 0.02 ns),
- to calculate rotational diffusion using 100 vectors using rotation matrices
- generated via an RMS fit to 'avgstruct.pdb', computing and integrating the
- time correlation function for each vector from 0 to 5 ns (1/40th of the
- simulation), and writing out the effective diffusion constants and results
- to 'deffs.dat' and 'rotdif.out' respectively:
+For example,
+ given a trajectory 'mdcrd.nc' containing 10000 frames with a total simulation time of 200 ns (so the time between frames is 0.02 ns),
+ to calculate rotational diffusion using 100 vectors using rotation matrices generated via an RMS fit to 'avgstruct.pdb',
+ computing and integrating the time correlation function for each vector from 0 to 5 ns (1/40th of the simulation),
+ and writing out the effective diffusion constants and results to 'deffs.dat' and 'rotdif.out' respectively:
 \end_layout
 
 \begin_layout LyX-Code
@@ -54302,8 +55142,7 @@ runningavg <dset1> [<dset2> ...] [name <dsetname>] [out <filename>]
 
 \end_deeper
 \begin_layout Standard
-Calculate running average over windows of given size for data in selected
- data set(s).
+Calculate running average over windows of given size for data in selected data set(s).
 \end_layout
 
 \begin_layout Subsection
@@ -54352,8 +55191,7 @@ slope <dset0> [<dset1> ...] [out <outfile>] [name <name>]
 \begin_inset space ~
 \end_inset
 
-{forward|backward|central}] Specify type of finite difference to calculate
- (default forward).
+{forward|backward|central}] Specify type of finite difference to calculate (default forward).
 \end_layout
 
 \begin_layout Standard
@@ -54361,8 +55199,7 @@ DataSets generated:
 \end_layout
 
 \begin_layout Description
-<name>:<idx> Output finite difference curves for each input data set (indexed
- from 0).
+<name>:<idx> Output finite difference curves for each input data set (indexed from 0).
 \end_layout
 
 \end_deeper
@@ -54408,7 +55245,8 @@ spline <dset0> [<dset1> ...] [out <outfile>] [meshsize <n> | meshfactor <x>]
 \begin_inset space ~
 \end_inset
 
-<x>] If meshsize is not given, use a mesh of data set size * <x>.
+<x>] If meshsize is not given,
+ use a mesh of data set size * <x>.
 \end_layout
 
 \begin_layout Description
@@ -54535,23 +55373,26 @@ distance for each set.
 
 \end_deeper
 \begin_layout Standard
-Analyze angles, dihedrals, distances, and/or puckers and calculate various
- properties.
- More specific analyses can be obtained by labelling distances/dihedrals/puckers
- (from e.g.
+Analyze angles,
+ dihedrals,
+ distances,
+ and/or puckers and calculate various properties.
+ More specific analyses can be obtained by labelling distances/dihedrals/puckers (from e.g.
  the 
 \series bold
 \shape italic
 distance
 \series default
 \shape default
-, 
+,
+ 
 \series bold
 \shape italic
 dihedral
 \series default
 \shape default
-, 
+,
+ 
 \series bold
 \shape italic
 pucker
@@ -54575,8 +55416,19 @@ type
 \begin_inset space ~
 \end_inset
 
-labels: alpha, beta, gamma, delta, epsilon, zeta, chi, c2p h1p, phi, psi,
- omega, pchi
+labels:
+ alpha,
+ beta,
+ gamma,
+ delta,
+ epsilon,
+ zeta,
+ chi,
+ c2p h1p,
+ phi,
+ psi,
+ omega,
+ pchi
 \end_layout
 
 \begin_layout Description
@@ -54588,7 +55440,8 @@ type
 \begin_inset space ~
 \end_inset
 
-labels: noe
+labels:
+ noe
 \end_layout
 
 \begin_layout Description
@@ -54600,14 +55453,16 @@ type
 \begin_inset space ~
 \end_inset
 
-labels: pucker
+labels:
+ pucker
 \end_layout
 
 \begin_layout Standard
-For each input data set, the average, standard deviation, initial and final
- values will be reported.
- The cyclic nature of dihedral/pucker data sets is taken into consideration
- when averaging.
+For each input data set,
+ the average,
+ standard deviation,
+ initial and final values will be reported.
+ The cyclic nature of dihedral/pucker data sets is taken into consideration when averaging.
 \end_layout
 
 \begin_layout Subsubsection
@@ -54615,10 +55470,10 @@ Torsion Analysis
 \end_layout
 
 \begin_layout Standard
-A table will be written in ASCII format showing the distribution of torsion
- values for each data set.
+A table will be written in ASCII format showing the distribution of torsion values for each data set.
  More specific information may be printed based on the set type.
- Values in the output marked SNB are from those defined by Schneider, Neidle,
+ Values in the output marked SNB are from those defined by Schneider,
+ Neidle,
  and Berman.
 \begin_inset CommandInset citation
 LatexCommand citep
@@ -54627,8 +55482,7 @@ literal "true"
 
 \end_inset
 
- For more information on nucleic acid torsion as pertains to RNA see further
- work by Schneider et al..
+ For more information on nucleic acid torsion as pertains to RNA see further work by Schneider et al..
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Schneider2004"
@@ -54640,8 +55494,8 @@ literal "true"
 \end_layout
 
 \begin_layout Standard
-For example, to perform in-depth analysis on some nucleic acid dihedral
- angles:
+For example,
+ to perform in-depth analysis on some nucleic acid dihedral angles:
 \end_layout
 
 \begin_layout LyX-Code
@@ -54665,17 +55519,18 @@ Distance Analysis
 \end_layout
 
 \begin_layout Standard
-A table will be written in ASCII format showing the distribution of distance
- values < 6.5.
- If a distance is labled as 'type noe' a compact time series will be printed
- in ASCII format showing the NOE as strong, medium, or weak.
- In addition the <r^-6>^(-1/6) averaged value will be reported, as well
- as the number of upper/lower bound violations.
+A table will be written in ASCII format showing the distribution of distance values < 6.5.
+ If a distance is labled as 'type noe' a compact time series will be printed in ASCII format showing the NOE as strong,
+ medium,
+ or weak.
+ In addition the <r^-6>^(-1/6) averaged value will be reported,
+ as well as the number of upper/lower bound violations.
  If 
 \series bold
 'noeout'
 \series default
- is specified, a summary of these results will be written with format:
+ is specified,
+ a summary of these results will be written with format:
 \end_layout
 
 \begin_layout LyX-Code
@@ -54683,23 +55538,26 @@ A table will be written in ASCII format showing the distribution of distance
 \end_layout
 
 \begin_layout Standard
-Where <#NOE> is an index, <R6> is the <r^-6>^(-1/6) averaged distance, <Nviolati
-on> is the total number of bounds violations, <AvgViolation> is the average
- difference from expected distance 
+Where <#NOE> is an index,
+ <R6> is the <r^-6>^(-1/6) averaged distance,
+ <Nviolation> is the total number of bounds violations,
+ <AvgViolation> is the average difference from expected distance 
 \shape italic
 Rexp
 \shape default
- when the distance is violated (note that if not explicitly set, 
+ when the distance is violated (note that if not explicitly set,
+ 
 \shape italic
 Rexp
 \shape default
- is set to the upper bound when the lower bound is 0.0, or the average of
- upper and lower bounds otherwise), and <Name> is the data set legend.
+ is set to the upper bound when the lower bound is 0.0,
+ or the average of upper and lower bounds otherwise),
+ and <Name> is the data set legend.
 \end_layout
 
 \begin_layout Standard
-For example, the following input could be used to check certain distances
- for NOE violations:
+For example,
+ the following input could be used to check certain distances for NOE violations:
 \end_layout
 
 \begin_layout LyX-Code
@@ -54731,8 +55589,7 @@ Pucker Analysis
 \end_layout
 
 \begin_layout Standard
-A table will be written in ASCII format showing the distribution of pucker
- phases for each data set.
+A table will be written in ASCII format showing the distribution of pucker phases for each data set.
 \end_layout
 
 \begin_layout Subsection
@@ -54856,7 +55713,8 @@ to
 \end_inset
 
 skip> Comma separated list of number of points to skip.
- For each number given, the TI integration will be repeated.
+ For each number given,
+ the TI integration will be repeated.
 \end_layout
 
 \begin_layout Description
@@ -54880,9 +55738,11 @@ avgincrement
 \begin_inset space ~
 \end_inset
 
-<#>] Starting from point 'avgskip' (default 0), repeat the TI integration
- calculation in increments of <#> up to 'avgmax' (default all points), so
- 'avgincrement 10' will do points 0-10, 0-20, etc.
+<#>] Starting from point 'avgskip' (default 0),
+ repeat the TI integration calculation in increments of <#> up to 'avgmax' (default all points),
+ so 'avgincrement 10' will do points 0-10,
+ 0-20,
+ etc.
 \end_layout
 
 \begin_layout Description
@@ -54910,9 +55770,8 @@ bs_samples
 \begin_inset space ~
 \end_inset
 
-<factor>] Estimate error via bootstrap analysis, repeating the TI integration
- <samples> times using <points> points or <factor> times the total number
- of points.
+<factor>] Estimate error via bootstrap analysis,
+ repeating the TI integration <samples> times using <points> points or <factor> times the total number of points.
  Randomize with given seed.
 \end_layout
 
@@ -54923,13 +55782,14 @@ DataSet Aspects:
 \begin_layout Description
 [TIcurve] Raw TI curve.
  If 'nskip' index is number of points skipped.
- If bootstrapping, index is sample index.
+ If bootstrapping,
+ index is sample index.
  If 'avgincrement' the index is the number of points.
 \end_layout
 
 \begin_layout Description
-[SD] For bootstrap analysis, standard deviation of average free energy over
- samples.
+[SD] For bootstrap analysis,
+ standard deviation of average free energy over samples.
 \end_layout
 
 \end_deeper
@@ -54939,7 +55799,8 @@ Calculate free energy using DV/DL energies from thermodynamic integration.
 \series bold
 <file>
 \series default
-, while the curves themselves will be written to 
+,
+ while the curves themselves will be written to 
 \series bold
 <ti curve file>
 \series default
@@ -54948,12 +55809,13 @@ Calculate free energy using DV/DL energies from thermodynamic integration.
 \series bold
 nq
 \series default
- to specify number of Gaussian quadrature points; otherwise the lambda values
- should be specified by 
+ to specify number of Gaussian quadrature points;
+ otherwise the lambda values should be specified by 
 \series bold
 xvals
 \series default
-, where 
+,
+ where 
 \series bold
 <x values>
 \series default
@@ -54961,14 +55823,13 @@ xvals
 \end_layout
 
 \begin_layout Standard
-For example, to perform Gaussian quadrature integration using data sets
- named 'TIdata', repeating the calculation for various number of skipped
- data points:
+For example,
+ to perform Gaussian quadrature integration using data sets named 'TIdata',
+ repeating the calculation for various number of skipped data points:
 \end_layout
 
 \begin_layout LyX-Code
-ti TIdata nq 9 name Curve out skip.agr curveout curve.agr nskip 0,5,10,15,20,30,40
-,50
+ti TIdata nq 9 name Curve out skip.agr curveout curve.agr nskip 0,5,10,15,20,30,40,50
 \end_layout
 
 \begin_layout Subsection
@@ -55032,8 +55893,10 @@ set
 \begin_inset space ~
 \end_inset
 
-arg1> Input 1D data set name(s), may specify more than once.
- If any data set is periodic, all need to be periodic.
+arg1> Input 1D data set name(s),
+ may specify more than once.
+ If any data set is periodic,
+ all need to be periodic.
 \end_layout
 
 \begin_layout Description
@@ -55058,15 +55921,14 @@ map
 
 \begin_deeper
 \begin_layout Description
-kinetic (default) Scale eigenvectors by eigenvalues so that distances in
- the transformed data approximate kinetic distances; particularly useful
- if using the projections to cluster.
+kinetic (default) Scale eigenvectors by eigenvalues so that distances in the transformed data approximate kinetic distances;
+ particularly useful if using the projections to cluster.
 \end_layout
 
 \begin_layout Description
-commute Scale eigenvectors by regularized time scales, sqrt(timescale_i
- / 2), so that distances in the transformed data will approximate commute
- distances.
+commute Scale eigenvectors by regularized time scales,
+ sqrt(timescale_i / 2),
+ so that distances in the transformed data will approximate commute distances.
  Timescales smaller than the lag time are dampened.
 \begin_inset CommandInset citation
 LatexCommand citep
@@ -55118,13 +55980,11 @@ cumvarout
 \end_deeper
 \begin_layout Standard
 Perform time-independent correlation analysis (TICA).
- Similar to principal component analysis (PCA), TICA calculates eigenvectors/eig
-envalues (i.e.
- eigenmodes) from input data sets (either coordinates or a combination of
- other 1D data sets).
+ Similar to principal component analysis (PCA),
+ TICA calculates eigenvectors/eigenvalues (i.e.
+ eigenmodes) from input data sets (either coordinates or a combination of other 1D data sets).
  Whereas the eigenvectors from PCA describe the variance in the input data,
- the eigenvectors from TICA describe the maximal autocorrelation in the
- input data at the given lag time.
+ the eigenvectors from TICA describe the maximal autocorrelation in the input data at the given lag time.
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Perez2013"
@@ -55132,9 +55992,8 @@ literal "true"
 
 \end_inset
 
- The analysis can be performed on either coordinates or 1D data sets; the
- data sets can either be all periodic (in which case they will be converted
- to cos/sin form) or not.
+ The analysis can be performed on either coordinates or 1D data sets;
+ the data sets can either be all periodic (in which case they will be converted to cos/sin form) or not.
 \end_layout
 
 \begin_layout Subsection
@@ -55176,9 +56035,8 @@ vec1
 <vecname2>]
 \series default
  Vector(s) on which to operate.
- By default the auto-correlation function will be calculated if one vector
- is specified, and the cross-correlation function will be calculated if
- two vectors are specified.
+ By default the auto-correlation function will be calculated if one vector is specified,
+ and the cross-correlation function will be calculated if two vectors are specified.
 \end_layout
 
 \begin_layout Description
@@ -55210,7 +56068,8 @@ out
 
 <order>]
 \series default
- Order of Legendre polynomials to use; default 2.
+ Order of Legendre polynomials to use;
+ default 2.
 \end_layout
 
 \begin_layout Description
@@ -55262,7 +56121,9 @@ out
 \series bold
 [norm]
 \series default
- Normalize all correlation functions, i.e., 
+ Normalize all correlation functions,
+ i.e.,
+ 
 \begin_inset Formula $C_{l}(t=0)=P_{l}(t=0)=1.0$
 \end_inset
 
@@ -55274,8 +56135,8 @@ out
 \series bold
 [drct]
 \series default
- Use the direct method to calculate correlations instead of FFT; this will
- be much slower.
+ Use the direct method to calculate correlations instead of FFT;
+ this will be much slower.
 \end_layout
 
 \begin_layout Description
@@ -55291,8 +56152,7 @@ dplr
 \end_layout
 
 \begin_layout Description
-[ptrajformat] Write output in ptraj style (prevents use of data formatting
- options).
+[ptrajformat] Write output in ptraj style (prevents use of data formatting options).
 \end_layout
 
 \begin_layout Standard
@@ -55363,10 +56223,9 @@ r(t)
 
 \end_deeper
 \begin_layout Standard
-Calculate time auto/cross-correlation functions for vectors using spherical
- harmonics theory.
- NOTE: To calculate direct correlation functions for vectors just use the
- 
+Calculate time auto/cross-correlation functions for vectors using spherical harmonics theory.
+ NOTE:
+ To calculate direct correlation functions for vectors just use the 
 \series bold
 \emph on
 corr
@@ -55382,9 +56241,12 @@ norm
 \series bold
 dplr
 \series default
- is specified, several additional data sets with aspects [R], [RRIG], [R3],
- [R6], and [Name] will be created containing either 1 or 2 values depending
- on how many vectors were specified.
+ is specified,
+ several additional data sets with aspects [R],
+ [RRIG],
+ [R3],
+ [R6],
+ and [Name] will be created containing either 1 or 2 values depending on how many vectors were specified.
  
 \end_layout
 
@@ -55393,8 +56255,8 @@ Examples
 \end_layout
 
 \begin_layout Standard
-Vectors between atoms 5 and 6 as well as 7 and 8 are calculated below, for
- which auto and cross time correlation functions are obtained.
+Vectors between atoms 5 and 6 as well as 7 and 8 are calculated below,
+ for which auto and cross time correlation functions are obtained.
 \end_layout
 
 \begin_layout LyX-Code
@@ -55418,8 +56280,10 @@ timecorr vec1 v0 vec2 v1 tstep 1.0 tcorr 100.0 out v0_v1.out order 2
 \end_layout
 
 \begin_layout Standard
-Similarly, a vector perpendicular to the plane through atoms 18, 19, and
- 20 is obtained and further analyzed.
+Similarly,
+ a vector perpendicular to the plane through atoms 18,
+ 19,
+ and 20 is obtained and further analyzed.
 \end_layout
 
 \begin_layout LyX-Code
@@ -55435,13 +56299,11 @@ vectormath
 \end_layout
 
 \begin_layout LyX-Code
-vectormath vec1 <vecname1> vec2 <vecname2> [out <filename>] [norm] [name
- <setname>]
+vectormath vec1 <vecname1> vec2 <vecname2> [out <filename>] [norm] [name <setname>]
 \end_layout
 
 \begin_layout LyX-Code
-           [ dotproduct | dotangle | crossproduct | magnitude | average
- ]
+           [ dotproduct | dotangle | crossproduct | magnitude | average ]
 \begin_inset Separator latexpar
 \end_inset
 
@@ -55482,8 +56344,8 @@ vec2
 \end_layout
 
 \begin_layout Description
-[norm] Normalize the vectors; this will affect any subsequent calculations
- with the vectors.
+[norm] Normalize the vectors;
+ this will affect any subsequent calculations with the vectors.
  This is turned on automatically if 
 \series bold
 dotangle/magnitude
@@ -55504,8 +56366,8 @@ dotangle/magnitude
 \end_layout
 
 \begin_layout Description
-[dotangle] Calculate angle from dot-product between the two vectors; vectors
- will be normalized.
+[dotangle] Calculate angle from dot-product between the two vectors;
+ vectors will be normalized.
 \end_layout
 
 \begin_layout Description
@@ -55582,14 +56444,15 @@ average
 
 \end_deeper
 \begin_layout Standard
-Calculate dot product, angle from dot product (degrees), or cross product
- for specified vectors.
+Calculate dot product,
+ angle from dot product (degrees),
+ or cross product for specified vectors.
  Note that 
 \series bold
 norm
 \series default
- normalizes the vectors themselves; the vectors will remain normalized for
- subsequent calculations or output.
+ normalizes the vectors themselves;
+ the vectors will remain normalized for subsequent calculations or output.
  Either 
 \series bold
 vec1
@@ -55598,9 +56461,10 @@ vec1
 \series bold
 vec2
 \series default
- can be of size 1; in that case each vector in the set with N frames operates
- on the single vector.
- For example, if 
+ can be of size 1;
+ in that case each vector in the set with N frames operates on the single vector.
+ For example,
+ if 
 \series bold
 vec1
 \series default
@@ -55608,13 +56472,13 @@ vec1
 \series bold
 vec2
 \series default
- is size 1, then each frame of vec1 is operated on the single vector from
- vec2.
+ is size 1,
+ then each frame of vec1 is operated on the single vector from vec2.
 \end_layout
 
 \begin_layout Standard
-For example, to get the angles between two previously calculated vectors
- v1 and v2:
+For example,
+ to get the angles between two previously calculated vectors v1 and v2:
 \end_layout
 
 \begin_layout LyX-Code
@@ -55680,7 +56544,8 @@ scaling
 \end_inset
 
 vals> Number of scales.
- The smaller the number the better resolution, but slower to plot.
+ The smaller the number the better resolution,
+ but slower to plot.
  
 \end_layout
 
@@ -55689,8 +56554,7 @@ vals> Number of scales.
 \begin_inset space ~
 \end_inset
 
-<s0>] The smallest scale of the wavelet function (default 2dt where dt is
- time between snapshots in ps ) 
+<s0>] The smallest scale of the wavelet function (default 2dt where dt is time between snapshots in ps ) 
 \end_layout
 
 \begin_layout Description
@@ -55701,8 +56565,8 @@ vals> Number of scales.
 <ds>] Spacing between discrete scales.
  (Default is 0.25.
  Smaller value of ds gives finer resolution.
- The largest values that give adequate sampling in scale for Morlet and
- Paul are 0.5 and 1.5, respectively)
+ The largest values that give adequate sampling in scale for Morlet and Paul are 0.5 and 1.5,
+ respectively)
 \end_layout
 
 \begin_layout Description
@@ -55710,8 +56574,8 @@ vals> Number of scales.
 \begin_inset space ~
 \end_inset
 
-<correction>] The scale-to-wavelength parameter (1.01 for Morlet, 1.389 for
- Paul).
+<correction>] The scale-to-wavelength parameter (1.01 for Morlet,
+ 1.389 for Paul).
  Automatically set based on wavelet if not otherwise specified.
  
 \end_layout
@@ -55787,12 +56651,13 @@ at a particular confidence level
 \begin_inset space ~
 \end_inset
 
-<file>] Output cluster map (recommended gnuplot format, see below).
+<file>] Output cluster map (recommended gnuplot format,
+ see below).
 \end_layout
 
 \begin_layout Description
-[cmapdetail] Instead of the map being smoothed to cluster regions, show
- full detail.
+[cmapdetail] Instead of the map being smoothed to cluster regions,
+ show full detail.
 \end_layout
 
 \begin_layout Description
@@ -55808,8 +56673,7 @@ at a particular confidence level
 \begin_inset space ~
 \end_inset
 
-prefix>] Output cluster region PDBs (only containing from minimum to maximum
- atom and minimum to maximum frame) with given prefix.
+prefix>] Output cluster region PDBs (only containing from minimum to maximum atom and minimum to maximum frame) with given prefix.
 \end_layout
 
 \begin_layout Description
@@ -55817,10 +56681,8 @@ prefix>] Output cluster region PDBs (only containing from minimum to maximum
 \begin_inset space ~
 \end_inset
 
-<trajfile>] Create a trajectory that can be overlaid with the original trajector
-y to highlight atoms of interest.
- Atoms in cluster regions will get their normal coordinates - all others
- are set to the common center of mass.
+<trajfile>] Create a trajectory that can be overlaid with the original trajectory to highlight atoms of interest.
+ Atoms in cluster regions will get their normal coordinates - all others are set to the common center of mass.
  
 \end_layout
 
@@ -55834,31 +56696,28 @@ y to highlight atoms of interest.
 
 \end_deeper
 \begin_layout Standard
-<wavelet>: morlet, paul
+<wavelet>:
+ morlet,
+ paul
 \end_layout
 
 \end_deeper
 \begin_layout Standard
-Perform the wavelet analysis using fast Fourier transform (FFT) algorithm
- on specified trajectory and write out to a gnuplot-formatted file named
- <name.gnu>.
- The created Wavelet map provides a clear picture of the significant motions
- which are characterized both in time and space.
- Note that typically the trajectory in question should have rotational and
- translational movement removed (via e.g.
+Perform the wavelet analysis using fast Fourier transform (FFT) algorithm on specified trajectory and write out to a gnuplot-formatted file named <name.gnu>.
+ The created Wavelet map provides a clear picture of the significant motions which are characterized both in time and space.
+ Note that typically the trajectory in question should have rotational and translational movement removed (via e.g.
  the 
 \series bold
 \emph on
 rms
 \series default
 \emph default
- command); otherwise these will be reflected in the wavelet analysis results.
+ command);
+ otherwise these will be reflected in the wavelet analysis results.
 \end_layout
 
 \begin_layout Standard
-Wavelet analysis contains two main steps which performs continues wavelet
- transform (CWT) and statistical significance testing as proposed by Torrence
- and Compo
+Wavelet analysis contains two main steps which performs continues wavelet transform (CWT) and statistical significance testing as proposed by Torrence and Compo
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Torrence1998"
@@ -55867,10 +56726,9 @@ literal "true"
 \end_inset
 
 .
- Analysis is executed on one dimensional (1-D) coordinate which is defined
- as the displacement from the starting position.
- For each atom, CWT is calculated over a specified range of scales from
- 
+ Analysis is executed on one dimensional (1-D) coordinate which is defined as the displacement from the starting position.
+ For each atom,
+ CWT is calculated over a specified range of scales from 
 \begin_inset Formula $S_{0}$
 \end_inset
 
@@ -55879,22 +56737,17 @@ up to
 \end_inset
 
 .
- To obtain the CWT of the trajectory the Fourier transform of atom's displacemen
-t and wavelets which scaled by S ( S is calculated from: 
+ To obtain the CWT of the trajectory the Fourier transform of atom's displacement and wavelets which scaled by S ( S is calculated from:
+ 
 \begin_inset Formula $S=S_{0}2^{jds};\:j=0,1,2,\ldots,nb-1$
 \end_inset
 
-) is computed and then the inverse Fourier transform of the product of Fourier
- transforms will be calculated as the CWT.
- After calculating the wavelet coordinates for all atoms, a significance
- testing is performed to determine the significance of each wavelet coordinate.
- For doing this test we need to have an appropriate background spectrum
- to consider as a mean or expected spectrum and compare our wavelet coordinates
- against this background.
- In order to calculate the background spectrum since wavelet spectrum (according
- to the convolution theorem) follows the Fourier spectrum, the Fourier coefficie
-nts over every atom's displacement is calculated using the following formula
- and a model (
+) is computed and then the inverse Fourier transform of the product of Fourier transforms will be calculated as the CWT.
+ After calculating the wavelet coordinates for all atoms,
+ a significance testing is performed to determine the significance of each wavelet coordinate.
+ For doing this test we need to have an appropriate background spectrum to consider as a mean or expected spectrum and compare our wavelet coordinates against this background.
+ In order to calculate the background spectrum since wavelet spectrum (according to the convolution theorem) follows the Fourier spectrum,
+ the Fourier coefficients over every atom's displacement is calculated using the following formula and a model (
 \begin_inset Formula $\mu_{k}$
 \end_inset
 
@@ -55902,8 +56755,7 @@ nts over every atom's displacement is calculated using the following formula
 \begin_inset Formula $X_{n}$
 \end_inset
 
-) is the time series which is the atom’s displacement and k is the frequency
- index
+) is the time series which is the atom’s displacement and k is the frequency index
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Benson2012"
@@ -55926,12 +56778,10 @@ f_{k=\frac{1}{N}}\sum_{n=0}^{N-1}\exp\left(\frac{-2\pi ikn}{N}\right)X_{n}
 \end_layout
 
 \begin_layout Standard
-This test is implemented based on the null hypothesis that the assumption
- is that Fourier coordinates normally distributed around the expected value,
+This test is implemented based on the null hypothesis that the assumption is that Fourier coordinates normally distributed around the expected value,
  then the wavelet coordinates should also be normally distributed.
- Assuming the expected background spectrum and since the square of a normally
- distributed variable is chi-square distributed, then the distribution for
- the square of the absolute values of wavelet coordinates (
+ Assuming the expected background spectrum and since the square of a normally distributed variable is chi-square distributed,
+ then the distribution for the square of the absolute values of wavelet coordinates (
 \begin_inset Formula $|W_{i,k}|^{2}$
 \end_inset
 
@@ -55954,21 +56804,17 @@ is the variance of the atom's displacement).
 \end_layout
 
 \begin_layout Standard
-Then choosing a confidence level we can determine the minimum acceptable
- value for 
+Then choosing a confidence level we can determine the minimum acceptable value for 
 \begin_inset Formula $|W_{i,k}|^{2}$
 \end_inset
 
-to be considered as a significant coordinates at that certain confidence
- level.
- In the final map the scales of only those wavelet coordinates which are
- significantly above the expected distribution are stored.
+to be considered as a significant coordinates at that certain confidence level.
+ In the final map the scales of only those wavelet coordinates which are significantly above the expected distribution are stored.
 \end_layout
 
 \begin_layout Standard
-For example, to perform wavelet analysis on residues 1 to 17 with 40 scaling
- values starting from scaling of 0.2 with a spacing of 0.25 using the Morlet
- wavelet:
+For example,
+ to perform wavelet analysis on residues 1 to 17 with 40 scaling values starting from scaling of 0.2 with a spacing of 0.25 using the Morlet wavelet:
 \end_layout
 
 \begin_layout LyX-Code
@@ -56006,12 +56852,8 @@ literal "true"
 
 \end_inset
 
- uses a density-based clustering algorithm (a modified version of the DBSCAN
- algorithm) to highlight physical and temporal regions that have significant
- motions from wavelet mapsand can extract the specific atoms and frames
- involved in these motions for further analysis.
- Cluster regions shown in the map will be smoother by default for easier
- visualization (unless 
+ uses a density-based clustering algorithm (a modified version of the DBSCAN algorithm) to highlight physical and temporal regions that have significant motions from wavelet mapsand can extract the specific atoms and frames involved in these motions for further analysis.
+ Cluster regions shown in the map will be smoother by default for easier visualization (unless 
 \series bold
 cmapdetail
 \series default
@@ -56058,8 +56900,8 @@ avgval Average value of points in the region.
 
 \end_deeper
 \begin_layout Standard
-For example, to create a 2D gnuplot map highlight regions of interest called
- 'cluster.gnu' one could use the following input.
+For example,
+ to create a 2D gnuplot map highlight regions of interest called 'cluster.gnu' one could use the following input.
 \end_layout
 
 \begin_layout LyX-Code
@@ -56118,6 +56960,7 @@ epsilon
 \begin_inset CommandInset ref
 LatexCommand vref
 reference "subsec:cpptraj_dbscan_Hints"
+nolink "false"
 
 \end_inset
 
@@ -56136,9 +56979,7 @@ name "sec:cpptraj-Matrix-Vector-Analysis-Examples"
 \end_layout
 
 \begin_layout Standard
-Please note that typically for principal component analysis (PCA) the trajectory
- needs to be aligned against a reference structure to remove overall global
- and translation motion.
+Please note that typically for principal component analysis (PCA) the trajectory needs to be aligned against a reference structure to remove overall global and translation motion.
  Use the 
 \family sans
 \series bold
@@ -56158,12 +56999,10 @@ Cartesian covariance matrix calculation and projection (PCA)
 \end_layout
 
 \begin_layout Standard
-After calculating modes, snapshots can be projected onto these in an additional
- pass through the trajectory.
- It is very important that the snapshots used when projecting are exactly
- the same as those used to generate the original covariance matrix.
- This example takes advantage of the COORDS data set functionality in cpptraj
- to save snapshots for the purposes of projection.
+After calculating modes,
+ snapshots can be projected onto these in an additional pass through the trajectory.
+ It is very important that the snapshots used when projecting are exactly the same as those used to generate the original covariance matrix.
+ This example takes advantage of the COORDS data set functionality in cpptraj to save snapshots for the purposes of projection.
 \end_layout
 
 \begin_layout LyX-Code
@@ -56252,8 +57091,7 @@ crdaction CRD1 projection evecs MyEvecs !@H= out project.dat beg 1 end 2
 \end_layout
 
 \begin_layout Subsection
-Dihedral covariance matrix calculation and projection for backbone phi/psi
- (PCA)
+Dihedral covariance matrix calculation and projection for backbone phi/psi (PCA)
 \end_layout
 
 \begin_layout LyX-Code
@@ -56303,8 +57141,7 @@ run
 \end_layout
 
 \begin_layout LyX-Code
-projection evecs DIHMODES out dih.project.dat beg 1 end 4 dihedrals BB[*]
- 
+projection evecs DIHMODES out dih.project.dat beg 1 end 4 dihedrals BB[*] 
 \end_layout
 
 \begin_layout LyX-Code

From 43b9fa01383f5ddae19d5cf72a456dcfd3d5fa78 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 27 Feb 2026 08:58:19 -0500
Subject: [PATCH 1399/1492] Add some notes about namespaces. Update to lyx 2.4.

---
 doc/CpptrajDevelopmentGuide.lyx | 1742 ++++++++++++++++++-------------
 1 file changed, 1005 insertions(+), 737 deletions(-)

diff --git a/doc/CpptrajDevelopmentGuide.lyx b/doc/CpptrajDevelopmentGuide.lyx
index ced87ea271..8d11d03287 100644
--- a/doc/CpptrajDevelopmentGuide.lyx
+++ b/doc/CpptrajDevelopmentGuide.lyx
@@ -1,16 +1,16 @@
-#LyX 2.3 created this file. For more info see http://www.lyx.org/
-\lyxformat 544
+#LyX 2.4 created this file. For more info see https://www.lyx.org/
+\lyxformat 620
 \begin_document
 \begin_header
 \save_transient_properties true
 \origin unavailable
 \textclass article
 \use_default_options true
-\maintain_unincluded_children false
+\maintain_unincluded_children no
 \language english
 \language_package default
-\inputencoding auto
-\fontencoding global
+\inputencoding auto-legacy
+\fontencoding auto
 \font_roman "default" "default"
 \font_sans "default" "default"
 \font_typewriter "default" "default"
@@ -18,7 +18,9 @@
 \font_default_family default
 \use_non_tex_fonts false
 \font_sc false
-\font_osf false
+\font_roman_osf false
+\font_sans_osf false
+\font_typewriter_osf false
 \font_sf_scale 100 100
 \font_tt_scale 100 100
 \use_microtype false
@@ -61,7 +63,9 @@
 \suppress_date false
 \justification true
 \use_refstyle 0
+\use_formatted_ref 0
 \use_minted 0
+\use_lineno 0
 \index Index
 \shortcut idx
 \color #008000
@@ -77,11 +81,16 @@
 \papercolumns 1
 \papersides 1
 \paperpagestyle default
+\tablestyle default
 \tracking_changes false
 \output_changes false
+\change_bars false
+\postpone_fragile_content false
 \html_math_output 0
 \html_css_as_file 0
 \html_be_strict false
+\docbook_table_output 0
+\docbook_mathml_prefix 1
 \end_header
 
 \begin_body
@@ -105,7 +114,8 @@ Jason M.
 \begin_inset Newline newline
 \end_inset
 
-Last Updated: 2019-12-13
+Last Updated:
+ 2026-02-27
 \begin_inset Newpage pagebreak
 \end_inset
 
@@ -113,21 +123,19 @@ Last Updated: 2019-12-13
 \end_layout
 
 \begin_layout Abstract
-CPPTRAJ is code used for processing MD trajectory data as well as other
- types of data, derived from trajectories or otherwise.
- CPPTRAJ is a complete rewrite of the PTRAJ code in primarily C++, with
- the intent being to make the code more readable, leak-free, and thread-safe.
- The biggest functional change from PTRAJ is the ability to load and process
- trajectories with different topology files in the same run.
+CPPTRAJ is code used for processing MD trajectory data as well as other types of data,
+ derived from trajectories or otherwise.
+ CPPTRAJ is a complete rewrite of the PTRAJ code in primarily C++,
+ with the intent being to make the code more readable,
+ leak-free,
+ and thread-safe.
+ The biggest functional change from PTRAJ is the ability to load and process trajectories with different topology files in the same run.
 \end_layout
 
 \begin_layout Abstract
-This guide assumes that the reader has at least a basic familiarity with
- C and C++ object-oriented programming.
- If you aren't sure what a constructor is or how pointers work you may have
- a difficult time coding in Cpptraj.
- There are several good introduction to C/C++ tutorials on the web that
- may be helpful.
+This guide assumes that the reader has at least a basic familiarity with C and C++ object-oriented programming.
+ If you aren't sure what a constructor is or how pointers work you may have a difficult time coding in Cpptraj.
+ There are several good introduction to C/C++ tutorials on the web that may be helpful.
  
 \begin_inset Newpage pagebreak
 \end_inset
@@ -164,10 +172,9 @@ Coding Conventions
 \end_layout
 
 \begin_layout Standard
-It is important to maintain a consistent coding style within cpptraj so
- that it remains easy to modify and understand.
- By following code conventions, it will be easier to read code written by
- anybody and determine what is happening.
+It is important to maintain a consistent coding style within cpptraj so that it remains easy to modify and understand.
+ By following code conventions,
+ it will be easier to read code written by anybody and determine what is happening.
 \end_layout
 
 \begin_layout Itemize
@@ -180,38 +187,43 @@ DO NOT USE TABS
 \end_layout
 
 \begin_layout Itemize
-Try to keep the maximum length of lines between 80 and 100 characters long.
+Try to keep the maximum length of lines between 80 and 120 characters long.
 \end_layout
 
 \begin_layout Itemize
-Whenever possible, put separate code on separate lines.
- Exceptions can be made for very simple statements such as logic evaluations
- and simple initializations.
+Whenever possible,
+ put separate code on separate lines.
+ Exceptions can be made for very simple statements such as logic evaluations and simple initializations.
  For example,
 \end_layout
 
 \begin_layout LyX-Code
-double x1 = 0.0; x2 = 0.0; x3 = 0.0;
+double x1 = 0.0;
+ x2 = 0.0;
+ x3 = 0.0;
 \end_layout
 
 \begin_layout Standard
-is OK, but
+is OK,
+ but
 \end_layout
 
 \begin_layout LyX-Code
-double x1 = var1 * var2; double x2 = var3 / var4;
+double x1 = var1 * var2;
+ double x2 = var3 / var4;
 \end_layout
 
 \begin_layout Standard
 is not.
- There are two reasons: 1) When separate statements share a line it makes
- using debuggers more difficult, and 2) when separate statements share a
- line it is harder to read.
+ There are two reasons:
+ 1) When separate statements share a line it makes using debuggers more difficult,
+ and 2) when separate statements share a line it is harder to read.
 \end_layout
 
 \begin_layout Itemize
-C++ files have '.cpp' suffix, C files have '.c' suffix, header files have
- '.h' suffix.
+C++ files have '.cpp' suffix,
+ C files have '.c' suffix,
+ header files have '.h' suffix.
 \end_layout
 
 \begin_layout Itemize
@@ -237,33 +249,37 @@ All header files should have a '#define' guard to prevent multiple inclusion.
 
 \begin_layout Itemize
 'using namespace' should be used sparingly and NEVER in a header file.
+ If a class occurs in a subdirectory,
+ it is fine to put 'using namespace Cpptraj::<subdirectory>' in the implementation (i.e.
+ .cpp) file.
 \end_layout
 
 \begin_layout Itemize
-The order of #include directives should be (in general): C includes, C++
- includes, class definition, any other Cpptraj includes.
+The order of #include directives should be (in general):
+ C includes,
+ C++ includes,
+ class definition,
+ any other Cpptraj includes.
 \end_layout
 
 \begin_layout Itemize
-Use of STL classes/methods is acceptable; use C99 conventions to maximize
- portability.
- The only external libraries that should be used are NetCDF and ARPACK/LAPACK/BL
-AS (both included with AmberTools), i.e.
+Use of STL classes/methods is acceptable;
+ use C99 conventions to maximize portability.
+ The only external libraries that should be used are NetCDF and ARPACK/LAPACK/BLAS (both included with AmberTools),
+ i.e.
  no Boost etc.
 \end_layout
 
 \begin_layout Itemize
 Do not use iostream for basic IO.
- All console output should be performed with the functions in CpptrajStdio.h
- (chiefly mprintf() and mprinterr() for STDOUT and STDERR respectively).
- All file IO should be performed with CpptrajFile or the derived classes
- BufferedLine and BufferedFrame.
- This choice has been made mainly for performance reasons (C file routines
- are in general much faster than iostream), but also so that all IO is centraliz
-ed (e.g.
+ All console output should be performed with the functions in CpptrajStdio.h (chiefly mprintf() and mprinterr() for STDOUT and STDERR respectively).
+ All file IO should be performed with CpptrajFile or the derived classes BufferedLine and BufferedFrame.
+ This choice has been made mainly for performance reasons (C file routines are in general much faster than iostream),
+ but also so that all IO is centralized (e.g.
  CpptrajFile will automatically detect if an input file is compressed).
- This is also so output can be easily controlled; for example, using mprintf
- will make sure that during MPI only the master writes.
+ This is also so output can be easily controlled;
+ for example,
+ using mprintf will make sure that during MPI only the master writes.
 \end_layout
 
 \begin_layout Itemize
@@ -285,7 +301,8 @@ Class types are named using
 \emph on
 CapWords
 \emph default
- (no spaces or underscores, start of each word is a capital letter).
+ (no spaces or underscores,
+ start of each word is a capital letter).
 \end_layout
 
 \begin_layout Itemize
@@ -295,12 +312,14 @@ Files containing a class should be named after the class (e.g.
 
 \begin_layout Itemize
 Classes which inherit should be named after their base class (e.g.
- 'class Action_Distance : public Action { };').
+ 'class Action_Distance :
+ public Action { };').
 \end_layout
 
 \begin_layout Itemize
-Public class methods should be listed first; protected methods/variables
- second; private methods/variables last.
+Public class methods should be listed first;
+ protected methods/variables second;
+ private methods/variables last.
  All class member variables should be private if possible.
 \end_layout
 
@@ -336,8 +355,10 @@ mixedCase_
 
 \end_deeper
 \begin_layout Itemize
-Abbreviations: 1st letter in each word is capitalized.
- For instance, 
+Abbreviations:
+ 1st letter in each word is capitalized.
+ For instance,
+ 
 \family typewriter
 Data File List
 \family default
@@ -351,8 +372,7 @@ DFL.
 \end_layout
 
 \begin_layout Itemize
-Variables that have function scope (or lower) and all public variables for
- classes are named using 
+Variables that have function scope (or lower) and all public variables for classes are named using 
 \emph on
 mixedCase
 \emph default
@@ -365,8 +385,10 @@ CapWords
 
 \begin_layout Itemize
 No one-letter variable names except in loop scopes (e.g.
- for (int i = 0; i < N; ++i) { } ), and even then they should be short loops
- (no more than 10 lines or so).
+ for (int i = 0;
+ i < N;
+ ++i) { } ),
+ and even then they should be short loops (no more than 10 lines or so).
 \end_layout
 
 \begin_layout Itemize
@@ -374,8 +396,11 @@ All identifiers in an enumerated type are named using all
 \emph on
 CAPS
 \emph default
-, and the first identifier should be explicitly initialized (e.g.
- enum DirectionType { DX = 0, DY, DZ };).
+,
+ and the first identifier should be explicitly initialized (e.g.
+ enum DirectionType { DX = 0,
+ DY,
+ DZ };).
 \end_layout
 
 \begin_layout Itemize
@@ -387,7 +412,8 @@ doxygen
 \emph on
 doxygen
 \emph default
-, so please construct comments in such a doxygen-compatible manner (e.g.
+,
+ so please construct comments in such a doxygen-compatible manner (e.g.
  JavaDoc etc).
  See http://www.stack.nl/~dimitri/doxygen/manual.html for instructions.
 \end_layout
@@ -397,7 +423,8 @@ Versioning
 \end_layout
 
 \begin_layout Standard
-The internal versioning for CPPTRAJ is supposed to go like this: 
+The internal versioning for CPPTRAJ is supposed to go like this:
+ 
 \end_layout
 
 \begin_layout LyX-Code
@@ -405,13 +432,18 @@ V<major>.<minor>.<revision>
 \end_layout
 
 \begin_layout Description
-<major> Incremented whenever there is a major API change, e.g.
- changing the Action base class, etc.
+<major> Incremented whenever there is a major API change,
+ e.g.
+ changing the Action base class,
+ etc.
 \end_layout
 
 \begin_layout Description
-<minor> Incremented whenever there are changes to behavior, e.g.
- syntax, functionality, or output.
+<minor> Incremented whenever there are changes to behavior,
+ e.g.
+ syntax,
+ functionality,
+ or output.
 \end_layout
 
 \begin_layout Description
@@ -419,8 +451,8 @@ V<major>.<minor>.<revision>
 \end_layout
 
 \begin_layout Standard
-Whenever a number that precedes <revision> is incremented, all subsequent
- numbers should be reset to 0.
+Whenever a number that precedes <revision> is incremented,
+ all subsequent numbers should be reset to 0.
 \end_layout
 
 \begin_layout Section
@@ -428,8 +460,8 @@ Building Cpptraj and Documentation
 \end_layout
 
 \begin_layout Standard
-Cpptraj is automatically built as part of AmberTools, or it can be built
- standalone using the configure script in the 
+Cpptraj is automatically built as part of AmberTools,
+ or it can be built standalone using the configure script in the 
 \family typewriter
 $AMBERHOME/AmberTools/src/cpptraj
 \family default
@@ -440,9 +472,11 @@ $CPPTRAJHOME
  directory.
  The standalone build is particularly useful for development and testing.
  Type './configure –help' for a list of configure options.
- In order to build Cpptraj standalone one needs to specify the location
- of the NetCDF, zlib, bzlib2, and BLAS/LAPACK/ARPACK libraries if they aren't
- in your system path; configure will use the ones in $AMBERHOME if 
+ In order to build Cpptraj standalone one needs to specify the location of the NetCDF,
+ zlib,
+ bzlib2,
+ and BLAS/LAPACK/ARPACK libraries if they aren't in your system path;
+ configure will use the ones in $AMBERHOME if 
 \family typewriter
 '-amberlib'
 \family default
@@ -452,7 +486,8 @@ $CPPTRAJHOME
 \end_layout
 
 \begin_layout Standard
-For example, to build cpptraj standalone:
+For example,
+ to build cpptraj standalone:
 \end_layout
 
 \begin_layout LyX-Code
@@ -468,11 +503,13 @@ To build the documentation using
 \emph on
 doxygen
 \emph default
-, you must have 
+,
+ you must have 
 \emph on
 doxygen
 \emph default
- installed, and you must have configured AmberTools.
+ installed,
+ and you must have configured AmberTools.
  Run the command:
 \end_layout
 
@@ -482,8 +519,8 @@ make docs
 
 \begin_layout Standard
 to build the documentation.
- PDF files and HTML files are generated during this process, showing class
- inheritance and descriptions from comments written in doxy-format.
+ PDF files and HTML files are generated during this process,
+ showing class inheritance and descriptions from comments written in doxy-format.
  Open the file 
 \family typewriter
 $AMBERHOME/AmberTools/src/cpptraj/doc/html/index.html
@@ -504,9 +541,9 @@ Cpptraj currently lives in 3 key classes:
 \series bold
 Cpptraj
 \series default
- Defined in main.cpp, controls overall flow (e.g.
- it is responsible for deciding whether to execute in batch mode or interactive
- mode).
+ Defined in main.cpp,
+ controls overall flow (e.g.
+ it is responsible for deciding whether to execute in batch mode or interactive mode).
 \end_layout
 
 \begin_layout Description
@@ -518,7 +555,11 @@ CpptrajState
 \series bold
 Cpptraj
 \series default
-, holds all of the data, Actions, Analyses, etc.
+,
+ holds all of the data,
+ Actions,
+ Analyses,
+ etc.
  
 \end_layout
 
@@ -556,10 +597,12 @@ DataSetList
 \begin_inset space ~
 \end_inset
 
-DSL_; Hold all DataSets.
- This is essentially how different components can talk to each other, e.g.
- an Action creates a DataSet in the DataSetList, which can then be used
- by a subsequent Analysis.
+DSL_;
+ Hold all DataSets.
+ This is essentially how different components can talk to each other,
+ e.g.
+ an Action creates a DataSet in the DataSetList,
+ which can then be used by a subsequent Analysis.
 \end_layout
 
 \begin_layout Description
@@ -567,9 +610,10 @@ DataFileList
 \begin_inset space ~
 \end_inset
 
-DFL_; Hold all DataFiles.
- These are either for writing out DataSets or general text output, primarily
- from Actions/Analyses.
+DFL_;
+ Hold all DataFiles.
+ These are either for writing out DataSets or general text output,
+ primarily from Actions/Analyses.
 \end_layout
 
 \begin_layout Description
@@ -577,11 +621,12 @@ TrajinList
 \begin_inset space ~
 \end_inset
 
-trajinList_; Hold all input trajectories to be processed during a run.
- Whenever a user inputs a 'trajin' or 'ensemble' command, the trajectory/ensembl
-e in question is added to this list.
- When a 'run' command is executed, these are the trajectories that are read
- in a frame at a time so that Actions in the ActionList can process them.
+trajinList_;
+ Hold all input trajectories to be processed during a run.
+ Whenever a user inputs a 'trajin' or 'ensemble' command,
+ the trajectory/ensemble in question is added to this list.
+ When a 'run' command is executed,
+ these are the trajectories that are read in a frame at a time so that Actions in the ActionList can process them.
 \end_layout
 
 \begin_layout Description
@@ -589,7 +634,8 @@ TrajoutList
 \begin_inset space ~
 \end_inset
 
-trajoutList_; Hold output trajectories to be written during a run.
+trajoutList_;
+ Hold output trajectories to be written during a run.
  This output occurs after all Actions have been processed.
 \end_layout
 
@@ -598,10 +644,11 @@ ActionList
 \begin_inset space ~
 \end_inset
 
-actionList_; Hold all Actions to be executed during a run.
- By default, whenver an Action command is issued the Action in question
- is initialized and queued up in the ActionList, to be processed during
- the next run.
+actionList_;
+ Hold all Actions to be executed during a run.
+ By default,
+ whenver an Action command is issued the Action in question is initialized and queued up in the ActionList,
+ to be processed during the next run.
 \end_layout
 
 \begin_layout Description
@@ -609,10 +656,10 @@ AnalysisList
 \begin_inset space ~
 \end_inset
 
-analysisList_; Hold all Analyses to be executed after a run or when a 'runanalys
-is' command is given.
- Similar to ActionList, whenever an Analysis command is issued the Analysis
- in question is initialized and queued up in the AnalysisList.
+analysisList_;
+ Hold all Analyses to be executed after a run or when a 'runanalysis' command is given.
+ Similar to ActionList,
+ whenever an Analysis command is issued the Analysis in question is initialized and queued up in the AnalysisList.
 \end_layout
 
 \begin_layout Section
@@ -634,20 +681,25 @@ The abstract base class that defines the Action interface.
 \end_layout
 
 \begin_layout Description
-Init(): Initialize Action, set up DataSets/DataFiles, etc.
+Init():
+ Initialize Action,
+ set up DataSets/DataFiles,
+ etc.
 \end_layout
 
 \begin_layout Description
-Setup(): Set up Action for a given Topology.
+Setup():
+ Set up Action for a given Topology.
 \end_layout
 
 \begin_layout Description
-DoAction(): Perform Action on given Frame.
+DoAction():
+ Perform Action on given Frame.
 \end_layout
 
 \begin_layout Description
-Print(): Perform any post-processing or output that occurs outside the main
- DataSet/DataFile framework.
+Print():
+ Perform any post-processing or output that occurs outside the main DataSet/DataFile framework.
 \end_layout
 
 \begin_layout Subsection
@@ -655,8 +707,8 @@ ActionInit (ActionState.h)
 \end_layout
 
 \begin_layout Standard
-Used to interface with Init(); contains pointers to the master DataSetList
- and DataFileList in CpptrajState.
+Used to interface with Init();
+ contains pointers to the master DataSetList and DataFileList in CpptrajState.
 \end_layout
 
 \begin_layout Description
@@ -689,11 +741,10 @@ DataSetList*
 \begin_inset space ~
 \end_inset
 
-DslPtr() For Actions that require access to the master DataSetList after
- Init() (e.g.
- hbond, which cannot set up hbond time series until hbonds are actually
- detected in DoAction()), they can store a pointer to the master DataSetList
- like so:
+DslPtr() For Actions that require access to the master DataSetList after Init() (e.g.
+ hbond,
+ which cannot set up hbond time series until hbonds are actually detected in DoAction()),
+ they can store a pointer to the master DataSetList like so:
 \begin_inset Separator latexpar
 \end_inset
 
@@ -702,11 +753,13 @@ DslPtr() For Actions that require access to the master DataSetList after
 
 \begin_deeper
 \begin_layout Standard
-(In header): DataSetList* masterDSL_;
+(In header):
+ DataSetList* masterDSL_;
 \end_layout
 
 \begin_layout Standard
-(In Action::Init): masterDSL_ = init.DslPtr();
+(In Action::Init):
+ masterDSL_ = init.DslPtr();
 \end_layout
 
 \end_deeper
@@ -740,9 +793,9 @@ ActionSetup (ActionState.h)
 \end_layout
 
 \begin_layout Standard
-Used to interface with Setup(); contains pointers to current Topology and
- CoordinateInfo, as well as expected number of frames associated with current
- Topology.
+Used to interface with Setup();
+ contains pointers to current Topology and CoordinateInfo,
+ as well as expected number of frames associated with current Topology.
 \end_layout
 
 \begin_layout Subsection
@@ -750,7 +803,8 @@ ActionFrame (ActionState.h)
 \end_layout
 
 \begin_layout Standard
-Used to interface with DoAction(); contains pointer to current Frame.
+Used to interface with DoAction();
+ contains pointer to current Frame.
 \end_layout
 
 \begin_layout Part
@@ -766,7 +820,8 @@ Vec3
 \end_layout
 
 \begin_layout Standard
-An array of 3 doubles, used to hold XYZ coords.
+An array of 3 doubles,
+ used to hold XYZ coords.
  Used for vector math.
 \end_layout
 
@@ -775,10 +830,10 @@ Matrix_3x3
 \end_layout
 
 \begin_layout Standard
-A 3x3 array of doubles, useful for performing rotations etc.
+A 3x3 array of doubles,
+ useful for performing rotations etc.
  Used for basic matrix math.
- Can be diagonalized via an internal routine (no need for external math
- library).
+ Can be diagonalized via an internal routine (no need for external math library).
 \end_layout
 
 \begin_layout Subsection
@@ -787,8 +842,7 @@ ComplexArray
 
 \begin_layout Standard
 Used to hold an array of complex numbers.
- Implemented as a double array instead of using the STL Complex class so
- that it easily interface with external routines.
+ Implemented as a double array instead of using the STL Complex class so that it easily interface with external routines.
 \end_layout
 
 \begin_layout Subsection
@@ -796,19 +850,21 @@ PubFFT
 \end_layout
 
 \begin_layout Standard
-Interface to FFT routines (either pubfft, which are the FFT routines used
- by Amber, or FFTW depending on how CPPTRAJ is configured).
+Interface to FFT routines (either pubfft,
+ which are the FFT routines used by Amber,
+ or FFTW depending on how CPPTRAJ is configured).
  Currently only 1D forward and backwards FFTs are supported.
  Makes use of ComplexArray.
 \end_layout
 
 \begin_layout Subsection
-Corr.h: CorrF_Direct, CorrF_FFT
+Corr.h:
+ CorrF_Direct,
+ CorrF_FFT
 \end_layout
 
 \begin_layout Standard
-Classes used to calculate auto/cross correlation functions from arrays of
- complex numbers (ComplexArray).
+Classes used to calculate auto/cross correlation functions from arrays of complex numbers (ComplexArray).
 \end_layout
 
 \begin_layout Section
@@ -816,10 +872,9 @@ Some Key Classes and Functions
 \end_layout
 
 \begin_layout Standard
-The following is a brief list of some of the more commonly-used classes
- and functions in Cpptraj.
- Classes are more or less self-documented to a certain extent; this section
- will be focused on how these classes are/should be used.
+The following is a brief list of some of the more commonly-used classes and functions in Cpptraj.
+ Classes are more or less self-documented to a certain extent;
+ this section will be focused on how these classes are/should be used.
 \end_layout
 
 \begin_layout Subsection
@@ -828,11 +883,14 @@ ArgList
 
 \begin_layout Standard
 The ArgList class is used throughout Cpptraj.
- It is the main way that user input is translated to actions, analyses,
- trajectory IO, etc.
- Basically, the ArgList class takes a string and separates it into tokens
- based on a given delimiter or delimiters.
- For example, the string:
+ It is the main way that user input is translated to actions,
+ analyses,
+ trajectory IO,
+ etc.
+ Basically,
+ the ArgList class takes a string and separates it into tokens based on a given delimiter or delimiters.
+ For example,
+ the string:
 \end_layout
 
 \begin_layout LyX-Code
@@ -848,8 +906,7 @@ trajin mytraj.nc 1 100 10
 \end_layout
 
 \begin_layout Standard
-can be separated via a space (' ') delimeter (the default) into 5 tokens
- like so:
+can be separated via a space (' ') delimeter (the default) into 5 tokens like so:
 \end_layout
 
 \begin_layout LyX-Code
@@ -861,28 +918,34 @@ The resulting ArgList internally looks something like:
 \end_layout
 
 \begin_layout LyX-Code
-0: trajin
+0:
+ trajin
 \end_layout
 
 \begin_layout LyX-Code
-1: mytraj.nc
+1:
+ mytraj.nc
 \end_layout
 
 \begin_layout LyX-Code
-2: 1
+2:
+ 1
 \end_layout
 
 \begin_layout LyX-Code
-3: 100
+3:
+ 100
 \end_layout
 
 \begin_layout LyX-Code
-4: 10
+4:
+ 10
 \end_layout
 
 \begin_layout Standard
 A custom delimeter string containing 1 or more characters can also be used.
- For example, the following string:
+ For example,
+ the following string:
 \end_layout
 
 \begin_layout LyX-Code
@@ -902,7 +965,8 @@ can be separated via a comma (',') delimiter into 4 tokens like so:
 \end_layout
 
 \begin_layout LyX-Code
-ArgList myArgs(myString, 
+ArgList myArgs(myString,
+ 
 \begin_inset Quotes eld
 \end_inset
 
@@ -918,28 +982,33 @@ The resulting ArgList internall lookws something like:
 \end_layout
 
 \begin_layout LyX-Code
-0: d01
+0:
+ d01
 \end_layout
 
 \begin_layout LyX-Code
-1: d02
+1:
+ d02
 \end_layout
 
 \begin_layout LyX-Code
-2: d03
+2:
+ d03
 \end_layout
 
 \begin_layout LyX-Code
-3: d04
+3:
+ d04
 \end_layout
 
 \begin_layout Standard
 These tokens (or arguments) are stored internally as an STL vector of strings.
  ArgList provides many functions to access user arguments.
  A second array of boolean values records whether an argument has been accessed.
- This concept is functionally similar to the argumentStack in Ptraj; however,
- it avoids the constant memory allocation/deallocation when arguments are
- added/accessed, and allows an argument list to be re-used if desired.
+ This concept is functionally similar to the argumentStack in Ptraj;
+ however,
+ it avoids the constant memory allocation/deallocation when arguments are added/accessed,
+ and allows an argument list to be re-used if desired.
  The two main ways arguments are usually accessed are through 
 \begin_inset Quotes eld
 \end_inset
@@ -969,7 +1038,8 @@ GetNext
 \end_inset
 
  functions return the next argument of the desired type.
- For example, using the ArgList created in the first example from 
+ For example,
+ using the ArgList created in the first example from 
 \begin_inset Quotes eld
 \end_inset
 
@@ -977,7 +1047,8 @@ trajin mytraj.nc 1 100 10
 \begin_inset Quotes erd
 \end_inset
 
- and assuming all arguments are unmarked, GetStringNext() would return 
+ and assuming all arguments are unmarked,
+ GetStringNext() would return 
 \begin_inset Quotes eld
 \end_inset
 
@@ -985,7 +1056,8 @@ trajin
 \begin_inset Quotes erd
 \end_inset
 
-, while getNextInteger() would return 
+,
+ while getNextInteger() would return 
 \begin_inset Quotes eld
 \end_inset
 
@@ -993,8 +1065,9 @@ trajin
 \begin_inset Quotes erd
 \end_inset
 
-; in both cases the argument returned would be marked, so that a subsequent
- call to GetStringNext() would return 
+;
+ in both cases the argument returned would be marked,
+ so that a subsequent call to GetStringNext() would return 
 \begin_inset Quotes eld
 \end_inset
 
@@ -1019,8 +1092,11 @@ GetMaskNext()
 \begin_inset Quotes erd
 \end_inset
 
- function, which returns the next atom mask expression (so noted because
- it will begin with ':', '@', '*'); an example of this will be shown below.
+ function,
+ which returns the next atom mask expression (so noted because it will begin with ':',
+ '@',
+ '*');
+ an example of this will be shown below.
 \end_layout
 
 \begin_layout Standard
@@ -1052,35 +1128,43 @@ rmsd R1 @CA ref [myref] out rmsd.dat
 \end_layout
 
 \begin_layout LyX-Code
-0: rmsd
+0:
+ rmsd
 \end_layout
 
 \begin_layout LyX-Code
-1: R1
+1:
+ R1
 \end_layout
 
 \begin_layout LyX-Code
-2: @CA
+2:
+ @CA
 \end_layout
 
 \begin_layout LyX-Code
-2: ref
+2:
+ ref
 \end_layout
 
 \begin_layout LyX-Code
-3: [myref]
+3:
+ [myref]
 \end_layout
 
 \begin_layout LyX-Code
-4: out
+4:
+ out
 \end_layout
 
 \begin_layout LyX-Code
-5: rmsd.dat
+5:
+ rmsd.dat
 \end_layout
 
 \begin_layout Standard
-If we want to access a specific argument, we use a 
+If we want to access a specific argument,
+ we use a 
 \begin_inset Quotes eld
 \end_inset
 
@@ -1089,8 +1173,9 @@ GetKey
 \end_inset
 
  function.
- For example, if we want to know the filename specified by 'out', we would
- use GetStringKey(
+ For example,
+ if we want to know the filename specified by 'out',
+ we would use GetStringKey(
 \begin_inset Quotes eld
 \end_inset
 
@@ -1098,7 +1183,8 @@ out
 \begin_inset Quotes erd
 \end_inset
 
-); this would return 
+);
+ this would return 
 \begin_inset Quotes eld
 \end_inset
 
@@ -1106,7 +1192,8 @@ rmsd.dat
 \begin_inset Quotes erd
 \end_inset
 
-, and mark both 
+,
+ and mark both 
 \begin_inset Quotes eld
 \end_inset
 
@@ -1123,7 +1210,8 @@ rmsd.dat
 \end_inset
 
 .
- Similarly, GetStringKey(
+ Similarly,
+ GetStringKey(
 \begin_inset Quotes eld
 \end_inset
 
@@ -1140,8 +1228,7 @@ ref
 \end_inset
 
 .
- At this point we could also use the GetMaskNext() function to get the atom
- mask expression 
+ At this point we could also use the GetMaskNext() function to get the atom mask expression 
 \begin_inset Quotes eld
 \end_inset
 
@@ -1181,7 +1268,9 @@ cutoff
 \begin_inset Quotes erd
 \end_inset
 
-, 0.0); // Value 2.0
+,
+ 0.0);
+ // Value 2.0
 \end_layout
 
 \begin_layout LyX-Code
@@ -1193,7 +1282,9 @@ nval
 \begin_inset Quotes erd
 \end_inset
 
-, 0);      // Value 3
+,
+ 0);
+      // Value 3
 \end_layout
 
 \begin_layout LyX-Code
@@ -1205,7 +1296,9 @@ ntypes
 \begin_inset Quotes erd
 \end_inset
 
-, 0);  // Value 0
+,
+ 0);
+  // Value 0
 \end_layout
 
 \begin_layout LyX-Code
@@ -1217,7 +1310,8 @@ name
 \begin_inset Quotes erd
 \end_inset
 
-);  // Value 
+);
+  // Value 
 \begin_inset Quotes eld
 \end_inset
 
@@ -1237,11 +1331,13 @@ out
 \begin_inset Quotes erd
 \end_inset
 
-);    // Empty
+);
+    // Empty
 \end_layout
 
 \begin_layout LyX-Code
-std::string maskExp = myArgs.GetMaskNext();      // Value 
+std::string maskExp = myArgs.GetMaskNext();
+      // Value 
 \begin_inset Quotes eld
 \end_inset
 
@@ -1253,7 +1349,8 @@ std::string maskExp = myArgs.GetMaskNext();      // Value
 \end_layout
 
 \begin_layout LyX-Code
-std::string mask2Exp = myArgs.GetMaskNext();     // Empty
+std::string mask2Exp = myArgs.GetMaskNext();
+     // Empty
 \end_layout
 
 \begin_layout LyX-Code
@@ -1274,16 +1371,18 @@ Topology
 
 \begin_layout Standard
 The Topology class describes how a system is laid out in terms of Atoms,
- Residues, and Molecules (all of which are classes themselves).
+ Residues,
+ and Molecules (all of which are classes themselves).
  It may also hold parameters which describe interactions between Atoms (e.g.
- bonds, angles, dihedrals, etc).
- The Topology class is chiefly used in Trajectory input/output and setting
- up atom masks (see below).
+ bonds,
+ angles,
+ dihedrals,
+ etc).
+ The Topology class is chiefly used in Trajectory input/output and setting up atom masks (see below).
 \end_layout
 
 \begin_layout Standard
-The Topology class has several routines that return strings of atom and
- residue names:
+The Topology class has several routines that return strings of atom and residue names:
 \end_layout
 
 \begin_layout Description
@@ -1295,7 +1394,8 @@ TruncResAtomName(int
 \begin_inset space ~
 \end_inset
 
-atom) Format: 
+atom) Format:
+ 
 \begin_inset Quotes eld
 \end_inset
 
@@ -1315,7 +1415,8 @@ AtomMaskName(int
 \begin_inset space ~
 \end_inset
 
-atom) Format: 
+atom) Format:
+ 
 \begin_inset Quotes eld
 \end_inset
 
@@ -1335,7 +1436,8 @@ TruncAtomNameNum(int
 \begin_inset space ~
 \end_inset
 
-atom) Format: 
+atom) Format:
+ 
 \begin_inset Quotes eld
 \end_inset
 
@@ -1355,7 +1457,8 @@ TruncResNameNum(int
 \begin_inset space ~
 \end_inset
 
-residue) Format: 
+residue) Format:
+ 
 \begin_inset Quotes eld
 \end_inset
 
@@ -1376,7 +1479,8 @@ Iterate over all atoms in a certain residue.
 \end_layout
 
 \begin_layout LyX-Code
-// Iterate over all atoms in residue 4, print charge.
+// Iterate over all atoms in residue 4,
+ print charge.
 \end_layout
 
 \begin_layout LyX-Code
@@ -1402,7 +1506,9 @@ n
 \begin_inset Quotes erd
 \end_inset
 
-, atom_index+1, Top[atom_index].Charge());
+,
+ atom_index+1,
+ Top[atom_index].Charge());
 \end_layout
 
 \begin_layout Standard
@@ -1456,35 +1562,32 @@ AtomMask/CharMask
 \end_layout
 
 \begin_layout Standard
-The AtomMask and CharMask classes keep track of what atoms for a given Topology
- are selected based on a given mask expression.
- The AtomMask class holds information on selected atoms only, while CharMask
- has the state of all atoms (selected/not selected).
- AtomMask is as an integer mask, where the atom numbers currently selected
- are stored as an array of integers.
- Since one is usually only interested in selected atoms, most times AtomMask
- is all that is needed and so is the most used mask class in Cpptraj; for
- example, all routines that take masks in the Frame class use the AtomMask
- class.
+The AtomMask and CharMask classes keep track of what atoms for a given Topology are selected based on a given mask expression.
+ The AtomMask class holds information on selected atoms only,
+ while CharMask has the state of all atoms (selected/not selected).
+ AtomMask is as an integer mask,
+ where the atom numbers currently selected are stored as an array of integers.
+ Since one is usually only interested in selected atoms,
+ most times AtomMask is all that is needed and so is the most used mask class in Cpptraj;
+ for example,
+ all routines that take masks in the Frame class use the AtomMask class.
  
 \end_layout
 
 \begin_layout Standard
-The CharMask class has an internal character array where the state of each
- atom is stored.
- It has functions that can then be used to interrogate if a certain atom
- or atoms are selected or not.
+The CharMask class has an internal character array where the state of each atom is stored.
+ It has functions that can then be used to interrogate if a certain atom or atoms are selected or not.
 \end_layout
 
 \begin_layout Standard
-In typical use, there are 3 phases to using AtomMask or CharMask: 1) initializat
-ion with a mask expression, 2) setup via a Topology class, and 3) iteration
- over the mask/interrogation of the mask.
- Initialization with a mask expression performs all necessary tokenization
- of the mask expression string and prepares the mask to be set up, but does
- not actually select atoms.
- The mask expression can be used during AtomMask construction or passed
- in via SetMaskString():
+In typical use,
+ there are 3 phases to using AtomMask or CharMask:
+ 1) initialization with a mask expression,
+ 2) setup via a Topology class,
+ and 3) iteration over the mask/interrogation of the mask.
+ Initialization with a mask expression performs all necessary tokenization of the mask expression string and prepares the mask to be set up,
+ but does not actually select atoms.
+ The mask expression can be used during AtomMask construction or passed in via SetMaskString():
 \end_layout
 
 \begin_layout LyX-Code
@@ -1512,7 +1615,8 @@ AtomMask Mask(
 \end_layout
 
 \begin_layout LyX-Code
-AtomMask Mask; Mask.SetMaskString(
+AtomMask Mask;
+ Mask.SetMaskString(
 \begin_inset Quotes eld
 \end_inset
 
@@ -1524,10 +1628,9 @@ AtomMask Mask; Mask.SetMaskString(
 \end_layout
 
 \begin_layout Standard
-Setup occurs via a Topology class (since in order to set up a mask you need
- to know atom names/numbers, residue name/number/types etc).
- This can be done using SetupIntegerMask() or SetupCharMask() to set up
- an integer mask (more common) or a char mask:
+Setup occurs via a Topology class (since in order to set up a mask you need to know atom names/numbers,
+ residue name/number/types etc).
+ This can be done using SetupIntegerMask() or SetupCharMask() to set up an integer mask (more common) or a char mask:
 \end_layout
 
 \begin_layout LyX-Code
@@ -1563,26 +1666,25 @@ Top.SetupCharMask( Mask );
 \end_layout
 
 \begin_layout Standard
-Once a mask has been setup the Nselected() function returns the number of
- selected atoms, while the None() function returns true if no atoms were
- selected.
- If necessary, one can convert between the mask types post-setup by using
- AtomMask::ConvertToCharMask() / CharMask::ConvertToIntMask() routines:
+Once a mask has been setup the Nselected() function returns the number of selected atoms,
+ while the None() function returns true if no atoms were selected.
+ If necessary,
+ one can convert between the mask types post-setup by using AtomMask::ConvertToCharMask() / CharMask::ConvertToIntMask() routines:
 \end_layout
 
 \begin_layout LyX-Code
-AtomMask mask( CharMask.ConvertToIntMask(), CharMask.Natom() )
+AtomMask mask( CharMask.ConvertToIntMask(),
+ CharMask.Natom() )
 \end_layout
 
 \begin_layout LyX-Code
-CharMask mask( AtomMask.ConvertToCharMask(), AtomMask.Nselected() )
+CharMask mask( AtomMask.ConvertToCharMask(),
+ AtomMask.Nselected() )
 \end_layout
 
 \begin_layout Standard
 The final stage is to make use of the atom mask.
- One can iterate over selected atoms in an integer atom mask using the STL-like
- const_iterator variable and begin() and end() functions - this is the recommend
-ed way to use atom masks:
+ One can iterate over selected atoms in an integer atom mask using the STL-like const_iterator variable and begin() and end() functions - this is the recommended way to use atom masks:
 \end_layout
 
 \begin_layout LyX-Code
@@ -1590,7 +1692,8 @@ for (AtomMask::const_iterator atomnum = Mask.begin();
 \end_layout
 
 \begin_layout LyX-Code
-                              atomnum != Mask.end(); 
+                              atomnum != Mask.end();
+ 
 \end_layout
 
 \begin_layout LyX-Code
@@ -1608,16 +1711,18 @@ n
 \begin_inset Quotes erd
 \end_inset
 
-, *atomnum);
+,
+ *atomnum);
 \end_layout
 
 \begin_layout Standard
-One can also access members of the integer array directly via the bracket
- ('[]') operator:
+One can also access members of the integer array directly via the bracket ('[]') operator:
 \end_layout
 
 \begin_layout LyX-Code
-for (int maskidx = 0; maskidx < Mask.Nselected(); ++maskidx)
+for (int maskidx = 0;
+ maskidx < Mask.Nselected();
+ ++maskidx)
 \end_layout
 
 \begin_layout LyX-Code
@@ -1631,19 +1736,22 @@ n
 \begin_inset Quotes erd
 \end_inset
 
-, Mask[atomidx]);
+,
+ Mask[atomidx]);
 \end_layout
 
 \begin_layout Standard
-To see if atom(s) are selected in a CharMask, use the AtomInCharMask() and
- AtomsInCharMask() functions.
- The former returns true if a specified atom is selected, the latter returns
- true if any atoms within a given range are selected.
+To see if atom(s) are selected in a CharMask,
+ use the AtomInCharMask() and AtomsInCharMask() functions.
+ The former returns true if a specified atom is selected,
+ the latter returns true if any atoms within a given range are selected.
  For example:
 \end_layout
 
 \begin_layout LyX-Code
-for (int atom = 0; atom < Top.Natom(); ++atom)
+for (int atom = 0;
+ atom < Top.Natom();
+ ++atom)
 \end_layout
 
 \begin_layout LyX-Code
@@ -1661,11 +1769,14 @@ n
 \begin_inset Quotes erd
 \end_inset
 
-, atom);
+,
+ atom);
 \end_layout
 
 \begin_layout LyX-Code
-for (int rnum = 0; rnum < Top.Nres(); ++res)
+for (int rnum = 0;
+ rnum < Top.Nres();
+ ++res)
 \end_layout
 
 \begin_layout LyX-Code
@@ -1687,7 +1798,8 @@ n
 \begin_inset Quotes erd
 \end_inset
 
-, rnum);
+,
+ rnum);
 \end_layout
 
 \begin_layout Subsection
@@ -1695,29 +1807,36 @@ Frame
 \end_layout
 
 \begin_layout Standard
-The Frame class is in many ways the workhorse of Cpptraj, as it holds all
- XYZ coordinates for a given input frame, and optionally box coordinates,
- masses, replica indices, temperature, time, and/or velocities.
- Note that although mass is stored in Topology, it is also stored in Frame
- since many calculations require it (center of mass, mass-weighted RMSD,
+The Frame class is in many ways the workhorse of Cpptraj,
+ as it holds all XYZ coordinates for a given input frame,
+ and optionally box coordinates,
+ masses,
+ replica indices,
+ temperature,
+ time,
+ and/or velocities.
+ Note that although mass is stored in Topology,
+ it is also stored in Frame since many calculations require it (center of mass,
+ mass-weighted RMSD,
  etc).
  Coordinates and velocities are stored with double precision.
- Many routines are available to do things like calculate the center of mass
- of atoms, rotate, translate, scale, and so on.
+ Many routines are available to do things like calculate the center of mass of atoms,
+ rotate,
+ translate,
+ scale,
+ and so on.
  A major use of the Frame class is to perform RMSD calculations.
 \end_layout
 
 \begin_layout Standard
 Frames are typically set up in two phases.
- The first phase is memory allocation, which occurs via constructors or
- the SetupFrameX routines.
- This should be done as little as possible since memory allocation is relatively
- expensive.
- The second phase is actually setting the coordinates, which occurs via
- the SetX routines.
- For example, the following code will set up a Frame (newFrame) with the
- coordinates from another Frame (oldFrame) based on a previously set up
- AtomMask (mask) and Topology (top) corresponding to oldFrame:
+ The first phase is memory allocation,
+ which occurs via constructors or the SetupFrameX routines.
+ This should be done as little as possible since memory allocation is relatively expensive.
+ The second phase is actually setting the coordinates,
+ which occurs via the SetX routines.
+ For example,
+ the following code will set up a Frame (newFrame) with the coordinates from another Frame (oldFrame) based on a previously set up AtomMask (mask) and Topology (top) corresponding to oldFrame:
 \end_layout
 
 \begin_layout LyX-Code
@@ -1725,11 +1844,13 @@ Frame newFrame;
 \end_layout
 
 \begin_layout LyX-Code
-// Allocate memory, copy in masses based on mask.
+// Allocate memory,
+ copy in masses based on mask.
 \end_layout
 
 \begin_layout LyX-Code
-newFrame.SetupFrameFromMask( mask, top.Atoms() );
+newFrame.SetupFrameFromMask( mask,
+ top.Atoms() );
 \end_layout
 
 \begin_layout LyX-Code
@@ -1737,22 +1858,24 @@ newFrame.SetupFrameFromMask( mask, top.Atoms() );
 \end_layout
 
 \begin_layout LyX-Code
-newFrame.SetCoordinates( oldFrame, mask );
+newFrame.SetCoordinates( oldFrame,
+ mask );
 \end_layout
 
 \begin_layout Standard
-Alternatively, this can be done in one step with a constructor:
+Alternatively,
+ this can be done in one step with a constructor:
 \end_layout
 
 \begin_layout LyX-Code
-Frame newFrame( oldFrame, mask );
+Frame newFrame( oldFrame,
+ mask );
 \end_layout
 
 \begin_layout Standard
-The advantage of separating out Setup and Set is that memory reallocation
- is kept to a minimum.
- For example, if we wanted to use newFrame to hold a different set of coordinate
-s (of the same size as newFrame or smaller) we might do something like:
+The advantage of separating out Setup and Set is that memory reallocation is kept to a minimum.
+ For example,
+ if we wanted to use newFrame to hold a different set of coordinates (of the same size as newFrame or smaller) we might do something like:
 \end_layout
 
 \begin_layout LyX-Code
@@ -1761,10 +1884,10 @@ newFrame.SetCoordinates( differentFrame );
 
 \begin_layout Standard
 If the new coordinates might be bigger than the current size of newFrame,
- we could explicitly call a SetupFrameX routine; this will only reallocate
- if the new size is greater than the current maximum size.
- A Frame remembers the largest size it was ever allocated for, so reallocation
- is kept to a minimum.
+ we could explicitly call a SetupFrameX routine;
+ this will only reallocate if the new size is greater than the current maximum size.
+ A Frame remembers the largest size it was ever allocated for,
+ so reallocation is kept to a minimum.
 \end_layout
 
 \begin_layout Standard
@@ -1780,8 +1903,7 @@ double*
 \begin_inset space ~
 \end_inset
 
-XYZ(atom) return pointer to beginning of XYZ coordinates for given atom
- (max Natom()).
+XYZ(atom) return pointer to beginning of XYZ coordinates for given atom (max Natom()).
 \end_layout
 
 \begin_layout Description
@@ -1797,8 +1919,8 @@ CRD(coord) return pointer to given coordinate (max size()).
 \end_layout
 
 \begin_layout Standard
-Note that you can get pointers to the raw coordinates, but it is not recommened
- to use these in general.
+Note that you can get pointers to the raw coordinates,
+ but it is not recommened to use these in general.
 \end_layout
 
 \begin_layout Subsubsection
@@ -1806,16 +1928,15 @@ Using Frame for RMSD calculations
 \end_layout
 
 \begin_layout Standard
-Unlike some of the other functions of Frame, the RMSD functions do not take
- a mask - it is assumed all atoms in the Frame are involved in the RMSD
- calculation.
+Unlike some of the other functions of Frame,
+ the RMSD functions do not take a mask - it is assumed all atoms in the Frame are involved in the RMSD calculation.
  This is done for performance reasons.
- If a subset of atoms is desired for an RMSD calculation the reference and
- target Frames should be modified beforehand.
- Since the reference structure usually does not change it is often beneficial
- to pre-center the reference at the origin.
- For example, given a reference Frame (Ref), a Farget frame (Tgt), and an
- AtomMask (mask):
+ If a subset of atoms is desired for an RMSD calculation the reference and target Frames should be modified beforehand.
+ Since the reference structure usually does not change it is often beneficial to pre-center the reference at the origin.
+ For example,
+ given a reference Frame (Ref),
+ a Farget frame (Tgt),
+ and an AtomMask (mask):
 \end_layout
 
 \begin_layout LyX-Code
@@ -1827,7 +1948,8 @@ top.SetupIntegerMask( mask );
 \end_layout
 
 \begin_layout LyX-Code
-Frame selectedRef, selectedTgt;
+Frame selectedRef,
+ selectedTgt;
 \end_layout
 
 \begin_layout LyX-Code
@@ -1835,11 +1957,13 @@ Frame selectedRef, selectedTgt;
 \end_layout
 
 \begin_layout LyX-Code
-selectedRef.SetupFrameFromMask( mask, top.Atoms() );
+selectedRef.SetupFrameFromMask( mask,
+ top.Atoms() );
 \end_layout
 
 \begin_layout LyX-Code
-selectedRef.SetCoordinates( Ref, mask );
+selectedRef.SetCoordinates( Ref,
+ mask );
 \end_layout
 
 \begin_layout LyX-Code
@@ -1855,11 +1979,13 @@ Vec3 refTrans = selectedRef.CenterOnOrigin( useMass );
 \end_layout
 
 \begin_layout LyX-Code
-selectedTgt.SetupFrameFromMask( mask, top.Atoms() );
+selectedTgt.SetupFrameFromMask( mask,
+ top.Atoms() );
 \end_layout
 
 \begin_layout LyX-Code
-selectedTgt.SetCoordinates( Tgt, mask );
+selectedTgt.SetCoordinates( Tgt,
+ mask );
 \end_layout
 
 \begin_layout LyX-Code
@@ -1896,20 +2022,24 @@ double rmsd = selectedTgt.RMSD_CenteredRef( selectedRef,
 \end_layout
 
 \begin_layout LyX-Code
-Tgt.Trans_Rot_Trans( tgtTrans, rot_matrix, refTrans );
+Tgt.Trans_Rot_Trans( tgtTrans,
+ rot_matrix,
+ refTrans );
 \end_layout
 
 \begin_layout Standard
-Now for subsequent RMS calculations to the same Reference, only the selected
- Target frame needs to have its coordinates set:
+Now for subsequent RMS calculations to the same Reference,
+ only the selected Target frame needs to have its coordinates set:
 \end_layout
 
 \begin_layout LyX-Code
-selectedTgt.SetCoordinates( Tgt2, mask );
+selectedTgt.SetCoordinates( Tgt2,
+ mask );
 \end_layout
 
 \begin_layout LyX-Code
-rmsd = selectedTgt.RMSD_CenteredRef( selectedRef, ...
+rmsd = selectedTgt.RMSD_CenteredRef( selectedRef,
+ ...
 \end_layout
 
 \begin_layout Subsection
@@ -1918,33 +2048,32 @@ Box
 
 \begin_layout Standard
 The Box class holds all unit cell information.
- It has the unit cell vectors (stored in a Matrix_3x3 class in row-major
- order), as well as the fractional cell matrix (for converting from Cartesian
- to fractional coordinates), the box lengths and angles, and the unit cell
- volume.
+ It has the unit cell vectors (stored in a Matrix_3x3 class in row-major order),
+ as well as the fractional cell matrix (for converting from Cartesian to fractional coordinates),
+ the box lengths and angles,
+ and the unit cell volume.
  There are in general two ways to set up Box with unit cell information:
  the SetupX routines (e.g.
  SetupFromXyzAbg()) and AssignX routines (e.g.
  AssignFromXyzAbg()).
- The SetupX routines perform some extra checks and will return 1 if something
- is wrong with the box.
- The AssignX routines do not perform these checks and so should be used
- where performance is needed (or the state of the box doesn't matter).
+ The SetupX routines perform some extra checks and will return 1 if something is wrong with the box.
+ The AssignX routines do not perform these checks and so should be used where performance is needed (or the state of the box doesn't matter).
 \end_layout
 
 \begin_layout Standard
 Both the SetupX and AssignX will set the unit and fractional cell matrices,
- the box lengths and angles, and the cell volume each time they are called.
- The ImageOption class can then be used to determine what kind of imaging
- can be performed on the unit cell using the distance calculation routines
- (DIST2(), DIST()) found in DistRoutines.h.
- For example, this is how distances are calculated using ImageOption imageOpt_
- in the distance action.
+ the box lengths and angles,
+ and the cell volume each time they are called.
+ The ImageOption class can then be used to determine what kind of imaging can be performed on the unit cell using the distance calculation routines (DIST2(),
+ DIST()) found in DistRoutines.h.
+ For example,
+ this is how distances are calculated using ImageOption imageOpt_ in the distance action.
 \end_layout
 
 \begin_layout Standard
 1.
- In Init(), determine if imaging should be used if possible:
+ In Init(),
+ determine if imaging should be used if possible:
 \end_layout
 
 \begin_layout LyX-Code
@@ -1953,8 +2082,8 @@ imageOpt_.InitImaging( !(actionArgs.hasKey("noimage")) );
 
 \begin_layout Standard
 2.
- In Setup(), determine if imaging will be possible based on if box info
- is present:
+ In Setup(),
+ determine if imaging will be possible based on if box info is present:
 \end_layout
 
 \begin_layout LyX-Code
@@ -1963,8 +2092,8 @@ imageOpt_.SetupImaging( setup.CoordInfo().TrajBox().HasBox() );
 
 \begin_layout Standard
 3.
- In DoAction(), determine what imaging to use and then calculate distance
- using DIST() from DistRoutines.h:
+ In DoAction(),
+ determine what imaging to use and then calculate distance using DIST() from DistRoutines.h:
 \end_layout
 
 \begin_layout LyX-Code
@@ -1976,7 +2105,10 @@ if (imageOpt_.ImagingEnabled())
 \end_layout
 
 \begin_layout LyX-Code
-double Dist = DIST(imageOpt_.ImagingType(), a1, a2_, frm.Frm().BoxCrd());
+double Dist = DIST(imageOpt_.ImagingType(),
+ a1,
+ a2_,
+ frm.Frm().BoxCrd());
 \end_layout
 
 \begin_layout Section
@@ -1984,22 +2116,25 @@ Console and File Input/Output
 \end_layout
 
 \begin_layout Subsection
-Output to STDOUT/STDERR: CpptrajStdio.h
+Output to STDOUT/STDERR:
+ CpptrajStdio.h
 \end_layout
 
 \begin_layout Standard
-The file CpptrajStdio.cpp contains functions used to write output to standard
- output (STDOUT) and standard error (STDERR).
- This is accomplished with the C printf-like functions mprintf() and mprinterr()
- respectively:
+The file CpptrajStdio.cpp contains functions used to write output to standard output (STDOUT) and standard error (STDERR).
+ This is accomplished with the C printf-like functions mprintf() and mprinterr() respectively:
 \end_layout
 
 \begin_layout LyX-Code
-mprintf(const char* format, ...); // STDOUT
+mprintf(const char* format,
+ ...);
+ // STDOUT
 \end_layout
 
 \begin_layout LyX-Code
-mprinterr(const char* format, ...); // STDERR
+mprinterr(const char* format,
+ ...);
+ // STDERR
 \end_layout
 
 \begin_layout Standard
@@ -2011,11 +2146,9 @@ master
 \begin_inset Quotes erd
 \end_inset
 
-, and ensures that when CPPTRAJ is running via MPI that only the master
- thread is able to write with these functions (note the same does NOT apply
- for OpenMP).
- The syntax is the same as basic printf - a format string followed by any
- variables.
+,
+ and ensures that when CPPTRAJ is running via MPI that only the master thread is able to write with these functions (note the same does NOT apply for OpenMP).
+ The syntax is the same as basic printf - a format string followed by any variables.
  There are numerous resources that describe printf syntax in detail.
  Some useful syntax is listed here:
 \end_layout
@@ -2029,7 +2162,8 @@ master
 \end_layout
 
 \begin_layout Description
-%g Use scientific or floating point representation, whichever is shorter.
+%g Use scientific or floating point representation,
+ whichever is shorter.
 \end_layout
 
 \begin_layout Description
@@ -2093,7 +2227,8 @@ mprintf(
 \begin_inset Quotes eld
 \end_inset
 
-Using printf is %s; %i is an integer and %f is a double.
+Using printf is %s;
+ %i is an integer and %f is a double.
 \backslash
 n
 \begin_inset Quotes erd
@@ -2103,7 +2238,9 @@ n
 \end_layout
 
 \begin_layout LyX-Code
-        myString.c_str(), myInteger, myDouble);
+        myString.c_str(),
+ myInteger,
+ myDouble);
 \end_layout
 
 \begin_layout Standard
@@ -2112,7 +2249,8 @@ Note that the string function c_str() must be used to print C++ strings.
 \end_layout
 
 \begin_layout LyX-Code
-Using printf is easy; 3 is an integer and 5.430000 is a double.
+Using printf is easy;
+ 3 is an integer and 5.430000 is a double.
 \end_layout
 
 \begin_layout Subsection
@@ -2122,13 +2260,13 @@ CpptrajFile
 \begin_layout Standard
 The CpptrajFile class provides basic file input and output operations.
  It can handle reading and writing both Gzip and Bzip2 compressed files,
- and through the FileName class performs tilde-expansion on file names (via
- globbing) as well as separates the file name into its base name, extension,
+ and through the FileName class performs tilde-expansion on file names (via globbing) as well as separates the file name into its base name,
+ extension,
  and compressed extension.
- The file can be opened immediately, or set up first and then opened later.
+ The file can be opened immediately,
+ or set up first and then opened later.
  Once it has been set up it can be opened or closed multiple times.
- The CpptrajFile class destructor will automatically close the file if it
- is open at time of destruction.
+ The CpptrajFile class destructor will automatically close the file if it is open at time of destruction.
  
 \end_layout
 
@@ -2137,16 +2275,14 @@ BufferedLine
 \end_layout
 
 \begin_layout Standard
-The BufferedLine class is a child of CpptrajFile used for text files that
- will be read in line by line (note that writing is not possible with this
- class).
- The class has an internal buffer, which chunks of the input file are read
- into.
- The Line() routine can be used to read that chunk line by line; this avoids
- potentially expensive file IO.
+The BufferedLine class is a child of CpptrajFile used for text files that will be read in line by line (note that writing is not possible with this class).
+ The class has an internal buffer,
+ which chunks of the input file are read into.
+ The Line() routine can be used to read that chunk line by line;
+ this avoids potentially expensive file IO.
  When the chunk is empty a new chunk is read in.
- The line can be further split into Tokens (similar to ArgList) and read
- one token at a time; this can be useful for e.g.
+ The line can be further split into Tokens (similar to ArgList) and read one token at a time;
+ this can be useful for e.g.
  determining the number of columns in a file.
 \end_layout
 
@@ -2155,26 +2291,24 @@ BufferedFrame
 \end_layout
 
 \begin_layout Standard
-The BufferedFrame class is a child of CpptrajFile used for highly-formatted
- text files that will be read/written multiple lines at a time (such as
- the Amber ASCII trajectory format).
- This class is set up for a certain total number of elements of a certain
- character width with a certain number of elements per line, which can then
- be read to or written from a character buffer in one entire chunk.
+The BufferedFrame class is a child of CpptrajFile used for highly-formatted text files that will be read/written multiple lines at a time (such as the Amber ASCII trajectory format).
+ This class is set up for a certain total number of elements of a certain character width with a certain number of elements per line,
+ which can then be read to or written from a character buffer in one entire chunk.
  
 \end_layout
 
 \begin_layout Subsection
-FileName, FileName.h
+FileName,
+ FileName.h
 \end_layout
 
 \begin_layout Standard
 The FileName class is used by all file-related classes.
- It is more powerful than a string and will automatically do tilde expansion
- and split the name into path, base name, extension, etc.
- FileName.h also contains the File namespace which includes File::Exists()
- for testing whether a file can be opened and File::NameArray and File::ExpandTo
-Filenames() for getting an array of files using wildcard matching.
+ It is more powerful than a string and will automatically do tilde expansion and split the name into path,
+ base name,
+ extension,
+ etc.
+ FileName.h also contains the File namespace which includes File::Exists() for testing whether a file can be opened and File::NameArray and File::ExpandToFilenames() for getting an array of files using wildcard matching.
 \end_layout
 
 \begin_layout Section
@@ -2182,24 +2316,19 @@ Trajectory Input/Output
 \end_layout
 
 \begin_layout Standard
-Trajectory input and output (IO) is handled via high-level and low-level
- classes.
- At the highest level trajectory input is provided by Trajin-derived classes
- (Trajin_Single and Trajin_Multi) for reading one frame at a time (i.e.
+Trajectory input and output (IO) is handled via high-level and low-level classes.
+ At the highest level trajectory input is provided by Trajin-derived classes (Trajin_Single and Trajin_Multi) for reading one frame at a time (i.e.
  during 'trajin' runs) and EnsembleIn-derived classes (EnsembleIn_Single,
- which is experimental currently, and EnsembleIn_Multi) for reading multiple
- frames at a time (i.e.
+ which is experimental currently,
+ and EnsembleIn_Multi) for reading multiple frames at a time (i.e.
  during 'ensemble' runs).
- Trajectory output is currently handled by Trajout_Single for writing one
- frame at a time to a single file, and EnsembleOut-dervived classes for
- writing multiple frames out at a time.
- At the lower level IO is handled by format-specific classes which inherit
- from TrajectoryIO (TrajectoryIO.h), which are called Traj_X by convention
- (e.g.
+ Trajectory output is currently handled by Trajout_Single for writing one frame at a time to a single file,
+ and EnsembleOut-dervived classes for writing multiple frames out at a time.
+ At the lower level IO is handled by format-specific classes which inherit from TrajectoryIO (TrajectoryIO.h),
+ which are called Traj_X by convention (e.g.
  Traj_AmberNetcdf for Amber NetCDF trajectories).
  TrajectoryIO classes are contained and set up within the higher level classes.
- Note that there is currently no Trajout_Multi (write a single frame to
- multiple files) since this functionality is already handled by TrajoutList.
+ Note that there is currently no Trajout_Multi (write a single frame to multiple files) since this functionality is already handled by TrajoutList.
 \end_layout
 
 \begin_layout Subsection
@@ -2233,8 +2362,8 @@ EnsembleIn_Multi
 \end_layout
 
 \begin_layout Standard
-For reading in multiple frames at a time from multiple files, optionally
- sort the frames.
+For reading in multiple frames at a time from multiple files,
+ optionally sort the frames.
 \end_layout
 
 \begin_layout Subsection
@@ -2273,8 +2402,7 @@ The
 ParmIO
 \emph default
  class is a base class for all topology file formats.
- This provides an easy mechanism for extracting the system topology from
- any number of file formats.
+ This provides an easy mechanism for extracting the system topology from any number of file formats.
  The 
 \emph on
 ParmFile
@@ -2283,8 +2411,7 @@ ParmFile
 \emph on
 ParmIO
 \emph default
- classes that hides the implementation details for each data file type from
- you.
+ classes that hides the implementation details for each data file type from you.
  You should interact with 
 \emph on
 ParmIO
@@ -2298,8 +2425,7 @@ ParmFile
 \emph on
 ParmFile
 \emph default
- provides the ability to both read and write topology file objects of any
- class.
+ provides the ability to both read and write topology file objects of any class.
 \end_layout
 
 \begin_layout Standard
@@ -2328,9 +2454,7 @@ Topology
 \emph on
 Topology
 \emph default
- objects contain as much of the information in the Amber topology file as
- can be parsed from the information present in the ParmIO object (and figured
- out based on atomic arrangements).
+ objects contain as much of the information in the Amber topology file as can be parsed from the information present in the ParmIO object (and figured out based on atomic arrangements).
  A 
 \emph on
 Topology
@@ -2339,7 +2463,8 @@ Topology
 \emph on
 ParmFile::Read
 \emph default
- function, followed by the name of the topology file.
+ function,
+ followed by the name of the topology file.
  Unlike the 
 \emph on
 DataFile
@@ -2348,7 +2473,8 @@ DataFile
 \emph on
 TrajectoryFile
 \emph default
- classes, 
+ classes,
+ 
 \emph on
 ParmFile
 \emph default
@@ -2366,9 +2492,8 @@ Topology
 \emph on
 Topology
 \emph default
- class is format-independent, providing a layer of abstraction to make other
- parts of the code that require topology information less error-prone while
- coding.
+ class is format-independent,
+ providing a layer of abstraction to make other parts of the code that require topology information less error-prone while coding.
 \end_layout
 
 \begin_layout Standard
@@ -2384,16 +2509,14 @@ ReadParm
 \emph on
 Topology
 \emph default
- instance as the first argument and fills as much of the information there
- as possible.
- Afterwards, the CommonSetup method of the Topology class is called to finish
- setup and determine bond information (from atom distances if not present
- directly in the file format) and molecule information (based on the bonded
- structure).
+ instance as the first argument and fills as much of the information there as possible.
+ Afterwards,
+ the CommonSetup method of the Topology class is called to finish setup and determine bond information (from atom distances if not present directly in the file format) and molecule information (based on the bonded structure).
  The currently available types of topologies are summarized in 
 \begin_inset CommandInset ref
 LatexCommand formatted
 reference "tbl:Cpptraj-Parm-Formats"
+nolink "false"
 
 \end_inset
 
@@ -2402,6 +2525,8 @@ reference "tbl:Cpptraj-Parm-Formats"
 
 \begin_layout Standard
 \begin_inset Float table
+placement document
+alignment document
 wide false
 sideways false
 status open
@@ -2500,7 +2625,8 @@ Parm_CharmmPsf (CHARMMPSF)
 \begin_inset Text
 
 \begin_layout Plain Layout
-CHARMM PSF topology file format (used by NAMD, too)
+CHARMM PSF topology file format (used by NAMD,
+ too)
 \end_layout
 
 \end_inset
@@ -2573,21 +2699,22 @@ The DataSet and DataFile Framework
 \end_layout
 
 \begin_layout Standard
-One of the goals in writing cpptraj was to try and generalize data collection
- and output, so that any action could output any generated data in any format
- known to cpptraj without having to write any extra code.
- For example, data generated by a distance calculation can be output in
- columns, as a Grace file, as a Gnuplot file, or as all three.
- To that end Actions and Analyses have access to the main DataSetList in
- CpptrajState (usually named DSL inside Actions) and the main DataFileList
- (usually named DFL inside actions).
- A DataSet can be generated by an Action, but because it is held outside
- the Action in the master DataSetList it can persist after the Action that
- generated it has been destroyed and be used in subsequent Analyses etc.
+One of the goals in writing cpptraj was to try and generalize data collection and output,
+ so that any action could output any generated data in any format known to cpptraj without having to write any extra code.
+ For example,
+ data generated by a distance calculation can be output in columns,
+ as a Grace file,
+ as a Gnuplot file,
+ or as all three.
+ To that end Actions and Analyses have access to the main DataSetList in CpptrajState (usually named DSL inside Actions) and the main DataFileList (usually named DFL inside actions).
+ A DataSet can be generated by an Action,
+ but because it is held outside the Action in the master DataSetList it can persist after the Action that generated it has been destroyed and be used in subsequent Analyses etc.
  DataSets have a base type which determines what kind of data it can hold,
- and can also belong to a group; DataSets in the same group behave in a
- similar fashion.
- For example, all DataSets in the COORDINATES group hold coordinates, etc.
+ and can also belong to a group;
+ DataSets in the same group behave in a similar fashion.
+ For example,
+ all DataSets in the COORDINATES group hold coordinates,
+ etc.
 \end_layout
 
 \begin_layout Subsection
@@ -2595,25 +2722,31 @@ The MetaData class
 \end_layout
 
 \begin_layout Standard
-DataSets are associated with meta data which is used to both describe and
- categorize the data.
- DataSet selection uses meta data; meta data is also used to sort DataSets.
+DataSets are associated with meta data which is used to both describe and categorize the data.
+ DataSet selection uses meta data;
+ meta data is also used to sort DataSets.
  This information is contained within the MetaData class.
- A DataSet can have a name, aspect, index, type etc.
+ A DataSet can have a name,
+ aspect,
+ index,
+ type etc.
  This allows for DataSets to e.g.
- be marked as an alpha torsion (M_TORSION, ALPHA).
+ be marked as an alpha torsion (M_TORSION,
+ ALPHA).
  There are currently 9 MetaData variables:
 \end_layout
 
 \begin_layout Description
-name_ The DataSet name; this is the most general level of classification.
+name_ The DataSet name;
+ this is the most general level of classification.
  Used in searches.
 \end_layout
 
 \begin_layout Description
-fileName_ If the data was read in from a file, the name of that file.
- Used in searches; both the full path and base name can be used to match
- (e.g.
+fileName_ If the data was read in from a file,
+ the name of that file.
+ Used in searches;
+ both the full path and base name can be used to match (e.g.
  for reference frame data sets).
 \end_layout
 
@@ -2626,9 +2759,10 @@ sub-name
 \begin_inset Quotes erd
 \end_inset
 
-, used to differentiate between different aspects of similar data.
- For example, DataSets generated by the 'nastruct' Action have different
- aspects for nucleic acid 
+,
+ used to differentiate between different aspects of similar data.
+ For example,
+ DataSets generated by the 'nastruct' Action have different aspects for nucleic acid 
 \begin_inset Quotes eld
 \end_inset
 
@@ -2636,7 +2770,8 @@ stretch
 \begin_inset Quotes erd
 \end_inset
 
-, 
+,
+ 
 \begin_inset Quotes eld
 \end_inset
 
@@ -2644,7 +2779,8 @@ shear
 \begin_inset Quotes erd
 \end_inset
 
-, 
+,
+ 
 \begin_inset Quotes eld
 \end_inset
 
@@ -2652,7 +2788,8 @@ stagger
 \begin_inset Quotes erd
 \end_inset
 
-, etc.
+,
+ etc.
  Used in searches.
 \end_layout
 
@@ -2664,38 +2801,44 @@ legend_ This is the name that will be used when writing data out to a file.
 
 \begin_layout Description
 idx_ (Index) A number which can be used to further differentiate data.
- It could correspond to residue, atom, etc.
+ It could correspond to residue,
+ atom,
+ etc.
  Used in searches.
 \end_layout
 
 \begin_layout Description
-ensembleNum_ (Ensemble number) For use during ensemble processing; this
- is set by the DataSetList to differentiate data from different ensembles.
+ensembleNum_ (Ensemble number) For use during ensemble processing;
+ this is set by the DataSetList to differentiate data from different ensembles.
 \end_layout
 
 \begin_layout Description
-scalarmode_ Internal categorization of the type of data, e.g.
- a distance, angle, torsion, etc.
- Certain functions will use this data - for example data sets marked as
- angle, torsion, or pucker will take periodicity into account when averaging
- (DataSet_1D::Avg()).
+scalarmode_ Internal categorization of the type of data,
+ e.g.
+ a distance,
+ angle,
+ torsion,
+ etc.
+ Certain functions will use this data - for example data sets marked as angle,
+ torsion,
+ or pucker will take periodicity into account when averaging (DataSet_1D::Avg()).
 \end_layout
 
 \begin_layout Description
-scalartype_ Internal sub-type; so in the case of a torison what type of
- torsion it is (phi, psi etc) or in the case of a matrix what kind of matrix,
+scalartype_ Internal sub-type;
+ so in the case of a torison what type of torsion it is (phi,
+ psi etc) or in the case of a matrix what kind of matrix,
  etc.
 \end_layout
 
 \begin_layout Description
-timeSeries_ Whether the DataSet is a time series; used by DataSetList to
- determine whether to call the Allocate() function.
+timeSeries_ Whether the DataSet is a time series;
+ used by DataSetList to determine whether to call the Allocate() function.
 \end_layout
 
 \begin_layout Standard
-MetaData can be set using the DataSet::SetMeta() routine, but it is recommended
- that this be done sparingly once a DataSet is part of the master DataSetList
- since this could create conflicts.
+MetaData can be set using the DataSet::SetMeta() routine,
+ but it is recommended that this be done sparingly once a DataSet is part of the master DataSetList since this could create conflicts.
 \end_layout
 
 \begin_layout Subsection
@@ -2704,8 +2847,7 @@ The TextFormat class
 
 \begin_layout Standard
 This class is used when writing the data set out to text files.
- It creates a printf-like format string of a given type with specified width
- and precision.
+ It creates a printf-like format string of a given type with specified width and precision.
 \end_layout
 
 \begin_layout Subsection
@@ -2719,11 +2861,13 @@ A simple usage example is given here.
 \end_layout
 
 \begin_layout LyX-Code
-dist_ = DSL->AddSet(DataSet::DOUBLE, MetaData(actionArgs.GetStringNext(),
+dist_ = DSL->AddSet(DataSet::DOUBLE,
+ MetaData(actionArgs.GetStringNext(),
 \end_layout
 
 \begin_layout LyX-Code
-                                              MetaData::M_DISTANCE), "Dis");
+                                              MetaData::M_DISTANCE),
+ "Dis");
 \end_layout
 
 \begin_layout LyX-Code
@@ -2731,18 +2875,15 @@ if (dist_==0) return 1;
 \end_layout
 
 \begin_layout Standard
-In the first line a DataSet class of type DOUBLE is added to the master
- DataSetList.
+In the first line a DataSet class of type DOUBLE is added to the master DataSetList.
  The various types are enumerated in DataSet::DataType (DataSet.h).
- The DataSet will be named whatever the next string is in the actionArgs
- ArgList.
- If there is no name, a default one will be created based on the given default
- "Dis" and the DataSet's overall position in the DataSetList (so in this
- case the default could be something like Dis_00000).
- The DataSet is also given the scalarMode M_DISTANCE, which is information
- that other Actions/Analyses can use (like Analysis_Statistics).
- What is returned is a pointer to the DataSet; DataSet is actually a base
- class that specific DataSet types inherit (in this case DataSet_double).
+ The DataSet will be named whatever the next string is in the actionArgs ArgList.
+ If there is no name,
+ a default one will be created based on the given default "Dis" and the DataSet's overall position in the DataSetList (so in this case the default could be something like Dis_00000).
+ The DataSet is also given the scalarMode M_DISTANCE,
+ which is information that other Actions/Analyses can use (like Analysis_Statistics).
+ What is returned is a pointer to the DataSet;
+ DataSet is actually a base class that specific DataSet types inherit (in this case DataSet_double).
  In this way the interface is generalized.
 \end_layout
 
@@ -2751,7 +2892,8 @@ The next step is to add the DataSet to the DataFileList.
 \end_layout
 
 \begin_layout LyX-Code
-DataFile* outfile = DFL->AddFile(distanceFile, actionArgs);
+DataFile* outfile = DFL->AddFile(distanceFile,
+ actionArgs);
 \end_layout
 
 \begin_layout LyX-Code
@@ -2759,16 +2901,12 @@ if (outfile != 0) outfile->AddDataSet( dist_ );
 \end_layout
 
 \begin_layout Standard
-In the first line a pointer to a new or exsiting (if already created somewhere
- else) DataFile is returned only if the string distanceFile is not empty;
+In the first line a pointer to a new or exsiting (if already created somewhere else) DataFile is returned only if the string distanceFile is not empty;
  this allows specification of output files to be optional.
- The actionsArgs ArgList is passed in so that the DataFile outfile can process
- any DataFile-related arguments.
+ The actionsArgs ArgList is passed in so that the DataFile outfile can process any DataFile-related arguments.
  In the second line the DataSet is added to the DataFile.
- In this way output from multiple actions can be combined rather than overwritte
-n.
- The machinery of the DataFileList takes care of output (formatting etc)
- from there.
+ In this way output from multiple actions can be combined rather than overwritten.
+ The machinery of the DataFileList takes care of output (formatting etc) from there.
 \end_layout
 
 \begin_layout Standard
@@ -2777,26 +2915,29 @@ The final phase is actually adding data to the DataSet.
 \end_layout
 
 \begin_layout LyX-Code
-double distance = sqrt( DIST2_NoImage( V1, V2 ) );
+double distance = sqrt( DIST2_NoImage( V1,
+ V2 ) );
 \end_layout
 
 \begin_layout LyX-Code
-dist_->Add(frameNum, &distance);
+dist_->Add(frameNum,
+ &distance);
 \end_layout
 
 \begin_layout Standard
 In the first line the value 'distance' is being calculated.
- In the next line the value from 'distance' is being added to DataSet dist_
- with frame number 'frameNum' (automatically set within Action).
+ In the next line the value from 'distance' is being added to DataSet dist_ with frame number 'frameNum' (automatically set within Action).
  Notice that the address of 'distance' is passed rather than the value;
  this is a necessity from the generalization of the DataSet interface.
- DataSet has no idea a prior what the data type might be, so in the Add
- routine the value is cast to what the underlying DataSet implementation
- expects.
- This allows the Add routine to be used for double, float, int, string,
+ DataSet has no idea a prior what the data type might be,
+ so in the Add routine the value is cast to what the underlying DataSet implementation expects.
+ This allows the Add routine to be used for double,
+ float,
+ int,
+ string,
  etc.
- This DataSet could also be cast back to it's actual type to access other
- routines, e.g.:
+ This DataSet could also be cast back to it's actual type to access other routines,
+ e.g.:
 \end_layout
 
 \begin_layout LyX-Code
@@ -2808,7 +2949,9 @@ DataSet_1D / SCALAR_1D
 \end_layout
 
 \begin_layout Standard
-Base class for 1D scalar data sets (like DataSet_double, DataSet_Mesh, etc).
+Base class for 1D scalar data sets (like DataSet_double,
+ DataSet_Mesh,
+ etc).
  Basically hold a series of numbers.
 \end_layout
 
@@ -2842,27 +2985,31 @@ Adding New Functionality
 
 \begin_layout Standard
 Most development for Cpptraj will likely be in adding new functionality;
- actions, analyses, and trajectory/topology/data file formats.
- This part of the manual will provide guidance and some helpful hints to
- this end.
- In general, adding new functionality is done by writing an implementation
- of the desired class type (e.g.
- for actions, inherit from the Action class) and then adding that class
- to the container for that specific functionality (e,g, in the case of actions,
+ actions,
+ analyses,
+ and trajectory/topology/data file formats.
+ This part of the manual will provide guidance and some helpful hints to this end.
+ In general,
+ adding new functionality is done by writing an implementation of the desired class type (e.g.
+ for actions,
+ inherit from the Action class) and then adding that class to the container for that specific functionality (e,g,
+ in the case of actions,
  ActionList).
 \end_layout
 
 \begin_layout Standard
-Note that there is a script provided that can generate default templates
- for various class types, located at $CPPTRAJHOME/devtools/Template.sh:
+Note that there is a script provided that can generate default templates for various class types,
+ located at $CPPTRAJHOME/devtools/Template.sh:
 \end_layout
 
 \begin_layout LyX-Code
-Usage: ./devtools/Template.sh <name> [<type>] 
+Usage:
+ ./devtools/Template.sh <name> [<type>] 
 \end_layout
 
 \begin_layout LyX-Code
-  <type>: Action Analysis Exec Traj DataIO DataSet
+  <type>:
+ Action Analysis Exec Traj DataIO DataSet
 \end_layout
 
 \begin_layout Section
@@ -2871,20 +3018,25 @@ Adding Actions - Example
 
 \begin_layout Standard
 All actions inherit from the Action abstract base class.
- The Action class itself inherits from the DispatchObject class so that
- it can be associated with an allocator (to create the action) and a help
- function.
- There are four functions that every action must implement: Init(), Setup(),
- DoAction(), and Print().
- Init() is called when the action is first created, and processes input
- arguments, sets up DataSets/DataFiles, deals with reference frames, and
- sets the debug level.
- Setup() is called to set the action up for a specific topology, and so
- handles anything Topology-related (such as parsing atom masks).
- The DoAction() function is called to actually perform the action on input
- coordinate frames.
- The Init(), Setup(), and DoAction() functions return a special type of
- integer, Action::RetType, which described the result of the action:
+ The Action class itself inherits from the DispatchObject class so that it can be associated with an allocator (to create the action) and a help function.
+ There are four functions that every action must implement:
+ Init(),
+ Setup(),
+ DoAction(),
+ and Print().
+ Init() is called when the action is first created,
+ and processes input arguments,
+ sets up DataSets/DataFiles,
+ deals with reference frames,
+ and sets the debug level.
+ Setup() is called to set the action up for a specific topology,
+ and so handles anything Topology-related (such as parsing atom masks).
+ The DoAction() function is called to actually perform the action on input coordinate frames.
+ The Init(),
+ Setup(),
+ and DoAction() functions return a special type of integer,
+ Action::RetType,
+ which described the result of the action:
 \end_layout
 
 \begin_layout Description
@@ -2896,20 +3048,18 @@ Action::ERR Action is not successful.
 \end_layout
 
 \begin_layout Description
-Action::USE_ORIGINAL_FRAME Action requests that the original unmodified
- topology/frame be used (see e.g.
+Action::USE_ORIGINAL_FRAME Action requests that the original unmodified topology/frame be used (see e.g.
  Action_Unstrip in Action_Strip.h).
 \end_layout
 
 \begin_layout Description
-Action::SUPPRESS_COORD_OUTPUT Action requests that further processing of
- the current coordinate frame be skipped (see e.g.
+Action::SUPPRESS_COORD_OUTPUT Action requests that further processing of the current coordinate frame be skipped (see e.g.
  Action_RunningAvg).
 \end_layout
 
 \begin_layout Description
-Action::SKIP Non-fatal problem occurred during setup; skip Action until
- next Setup call.
+Action::SKIP Non-fatal problem occurred during setup;
+ skip Action until next Setup call.
 \end_layout
 
 \begin_layout Description
@@ -2921,25 +3071,27 @@ Action::MODIFY_COORDS DoAction routine has modified the Frame.
 \end_layout
 
 \begin_layout Standard
-The final function is Print(), which is called after all trajectory processing
- is complete and performs any additional calculation or output necessary.
- This function can be blank if such functionality is not needed, but it
- still must be implemented.
+The final function is Print(),
+ which is called after all trajectory processing is complete and performs any additional calculation or output necessary.
+ This function can be blank if such functionality is not needed,
+ but it still must be implemented.
 \end_layout
 
 \begin_layout Standard
-In addition to Action, there are currently two additional action-related
- classes that actions may want to inherit from.
- The ImagedAction class is for classes that may need to calculate imaged
- distances, and the ActionFrameCounter class is for actions that may want
- to process subsets of input frames (see e.g.
+In addition to Action,
+ there are currently two additional action-related classes that actions may want to inherit from.
+ The ImagedAction class is for classes that may need to calculate imaged distances,
+ and the ActionFrameCounter class is for actions that may want to process subsets of input frames (see e.g.
  the Action_Matrix action).
 \end_layout
 
 \begin_layout Standard
-As an example, we will go through the creation of a simplified version of
- the Action_Distance class for calculating distances; this will cover using
- the DataSet, DataFile, AtomMask, and ImagedAction classes as well.
+As an example,
+ we will go through the creation of a simplified version of the Action_Distance class for calculating distances;
+ this will cover using the DataSet,
+ DataFile,
+ AtomMask,
+ and ImagedAction classes as well.
 \end_layout
 
 \begin_layout Subsection
@@ -2947,8 +3099,9 @@ Create the Class Header
 \end_layout
 
 \begin_layout Standard
-As mentioned in the style guide, header files should be named after the
- class, so the Action_Distance class will go in a file named 
+As mentioned in the style guide,
+ header files should be named after the class,
+ so the Action_Distance class will go in a file named 
 \begin_inset Quotes eld
 \end_inset
 
@@ -2966,8 +3119,8 @@ header guard
 \end_inset
 
  - this will prevent issues with multiple inclusion.
- The header guard should be named after the class and header file, so for
- Action_Distance.h:
+ The header guard should be named after the class and header file,
+ so for Action_Distance.h:
 \end_layout
 
 \begin_layout LyX-Code
@@ -2978,22 +3131,60 @@ header guard
 #define INC_ACTION_DISTANCE_H
 \end_layout
 
+\begin_layout Standard
+New classes should be put in the Cpptraj namespace if it does not conflict with the Cpptraj class (this will be fixed in a future release).
+ If the class is in a subdirectory,
+ it should be put in the Cpptraj::<subdirectory> namespace.
+ For example,
+ the GB_Params class definition is located in $CPPTRAJHOME/src/Parm/GB_Params.h.
+ The header begins like this:
+\end_layout
+
+\begin_layout LyX-Code
+#ifndef INC_PARM_GBPARAMS_H
+\end_layout
+
+\begin_layout LyX-Code
+#define INC_PARM_GBPARAMS_H
+\end_layout
+
+\begin_layout LyX-Code
+#include <string>
+\end_layout
+
+\begin_layout LyX-Code
+class ArgList;
+\end_layout
+
+\begin_layout LyX-Code
+class Topology;
+\end_layout
+
+\begin_layout LyX-Code
+namespace Cpptraj {
+\end_layout
+
+\begin_layout LyX-Code
+namespace Parm {
+\end_layout
+
 \begin_layout Standard
 Next comes the class description.
- Since distance calculations may involve imaging we also include the ImagedActio
-n class as a variable to simplify image handling:
+ Since distance calculations may involve imaging we also include the ImagedAction class as a variable to simplify image handling:
 \end_layout
 
 \begin_layout LyX-Code
-class Action_Distance: public Action {
+class Action_Distance:
+ public Action {
 \end_layout
 
 \begin_layout Standard
-Following the style guide, we first implement any public methods.
- For actions this is at least the constructor, the allocator (named Alloc()
- by convention), and the Help() function.
- The allocator and help functions need to be static so that they can be
- called without instantiating the class.
+Following the style guide,
+ we first implement any public methods.
+ For actions this is at least the constructor,
+ the allocator (named Alloc() by convention),
+ and the Help() function.
+ The allocator and help functions need to be static so that they can be called without instantiating the class.
  
 \end_layout
 
@@ -3002,7 +3193,8 @@ public:
 \end_layout
 
 \begin_layout LyX-Code
-  Action_Distance();  ///< Constructor
+  Action_Distance();
+  ///< Constructor
 \end_layout
 
 \begin_layout LyX-Code
@@ -3010,30 +3202,35 @@ public:
 \end_layout
 
 \begin_layout LyX-Code
-  static DispatchObject* Alloc() { return (DispatchObject*)new Action_Distance()
-; }
+  static DispatchObject* Alloc() { return (DispatchObject*)new Action_Distance();
+ }
 \end_layout
 
 \begin_layout LyX-Code
-  static void Help(); ///< Help function
+  static void Help();
+ ///< Help function
 \end_layout
 
 \begin_layout Standard
-The implemented functions Init(), Setup(), DoAction(), and Print() can be
- either public or private, although the preference is private.
+The implemented functions Init(),
+ Setup(),
+ DoAction(),
+ and Print() can be either public or private,
+ although the preference is private.
 \end_layout
 
 \begin_layout Standard
-The private section is where all functions and variables specific to the
- class will go.
- First, we add entries for the functions inherited from the Action base
- class which must be implemented.
- Since we will not need to do any post-processing for this action, the Print()
- function is empty:
+The private section is where all functions and variables specific to the class will go.
+ First,
+ we add entries for the functions inherited from the Action base class which must be implemented.
+ Since we will not need to do any post-processing for this action,
+ the Print() function is empty:
 \end_layout
 
 \begin_layout LyX-Code
-  Action::RetType Init(ArgList&, ActionInit&, int);
+  Action::RetType Init(ArgList&,
+ ActionInit&,
+ int);
 \end_layout
 
 \begin_layout LyX-Code
@@ -3041,7 +3238,8 @@ The private section is where all functions and variables specific to the
 \end_layout
 
 \begin_layout LyX-Code
-  Action::RetType DoAction(int, ActionFrame&);
+  Action::RetType DoAction(int,
+ ActionFrame&);
 \end_layout
 
 \begin_layout LyX-Code
@@ -3051,9 +3249,8 @@ The private section is where all functions and variables specific to the
 \begin_layout Standard
 Next we define the class variables.
  For Action_Distance we will want a DataSet to hold the calculated distances,
- two AtomMasks to describe the points between which the distance should
- be calculated, and a variable to indicate whether the distance should be
- mass-weighted.
+ two AtomMasks to describe the points between which the distance should be calculated,
+ and a variable to indicate whether the distance should be mass-weighted.
 \end_layout
 
 \begin_layout LyX-Code
@@ -3061,39 +3258,51 @@ private:
 \end_layout
 
 \begin_layout LyX-Code
-  DataSet* dist_;      ///< Will hold DataSet of calculated distances.
+  DataSet* dist_;
+      ///< Will hold DataSet of calculated distances.
 \end_layout
 
 \begin_layout LyX-Code
-  bool useMass_;       ///< If true, mass-weight distances.
+  bool useMass_;
+       ///< If true,
+ mass-weight distances.
 \end_layout
 
 \begin_layout LyX-Code
-  AtomMask Mask1_;     ///< First atom selection.
+  AtomMask Mask1_;
+     ///< First atom selection.
 \end_layout
 
 \begin_layout LyX-Code
-  AtomMask Mask2_;     ///< Second atom selection
+  AtomMask Mask2_;
+     ///< Second atom selection
 \end_layout
 
 \begin_layout LyX-Code
-  ImagedAction image_; ///< Holds imaging info
+  ImagedAction image_;
+ ///< Holds imaging info
 \end_layout
 
 \begin_layout Standard
-All variables related to imaging are already include via the ImagedAction
- class.
+All variables related to imaging are already include via the ImagedAction class.
  
 \end_layout
 
 \begin_layout Standard
-Last, end the class definition and finish the header guard:
+End the class definition with a closed bracket and semicolon:
 \end_layout
 
 \begin_layout LyX-Code
 };
 \end_layout
 
+\begin_layout Standard
+If the class is located in one or more namespaces,
+ don't forget to close them off with a bracket '}'.
+ Finally,
+ and finish the header guard:
+\end_layout
+
 \begin_layout LyX-Code
 #endif
 \end_layout
@@ -3103,11 +3312,12 @@ Create the Class Implementation
 \end_layout
 
 \begin_layout Standard
-Following the naming scheme, the class implementation will go into Action_Distan
-ce.cpp.
+Following the naming scheme,
+ the class implementation will go into Action_Distance.cpp.
  The first part of this file will have the necessary #include directives.
- We need <cmath> for the square root function, Action_Distance.h for the
- class definition, and CpptrajStdio.h for wiriting to the console.
+ We need <cmath> for the square root function,
+ Action_Distance.h for the class definition,
+ and CpptrajStdio.h for wiriting to the console.
  
 \end_layout
 
@@ -3125,18 +3335,23 @@ ce.cpp.
 
 \begin_layout Standard
 First we will need to create the class constructor.
- It is encouraged that users make use of initalizer lists (which tend to
- be more efficient) for this purpose.
- In this case we have two non-class variables: dist_, which is a pointer
- to a DataSet, and useMass_, which is boolean:
+ It is encouraged that users make use of initalizer lists (which tend to be more efficient) for this purpose.
+ In this case we have two non-class variables:
+ dist_,
+ which is a pointer to a DataSet,
+ and useMass_,
+ which is boolean:
 \end_layout
 
 \begin_layout LyX-Code
-Action_Distance::Action_Distance() : dist_(0), useMass_(true) {}
+Action_Distance::Action_Distance() :
+ dist_(0),
+ useMass_(true) {}
 \end_layout
 
 \begin_layout Standard
-Next, ensure that the Help() function has an implementation.
+Next,
+ ensure that the Help() function has an implementation.
  Note that in cpptraj 
 \begin_inset Quotes eld
 \end_inset
@@ -3171,12 +3386,12 @@ n");
 \end_layout
 
 \begin_layout Subsubsection
-Init() - Parse user arguments, set up DataSets/DataFiles etc
+Init() - Parse user arguments,
+ set up DataSets/DataFiles etc
 \end_layout
 
 \begin_layout Standard
-Init() is called when the action is created and is responsible for parsing
- the Argument list (ArgList) and inital setup.
+Init() is called when the action is created and is responsible for parsing the Argument list (ArgList) and inital setup.
  Init() has the same input arguments for every action:
 \end_layout
 
@@ -3185,7 +3400,9 @@ Action::RetType
 \end_layout
 
 \begin_layout LyX-Code
-  Action_Distance::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
+  Action_Distance::Init(ArgList& actionArgs,
+ ActionInit& init,
+ int debugIn)
 \end_layout
 
 \begin_layout LyX-Code
@@ -3193,11 +3410,13 @@ Action::RetType
 \end_layout
 
 \begin_layout Standard
-The input arguments are as follows: 
+The input arguments are as follows:
+ 
 \series bold
 actionArgs
 \series default
- (ArgList class) contains arguments from user input, 
+ (ArgList class) contains arguments from user input,
+ 
 \series bold
 init
 \series default
@@ -3207,18 +3426,20 @@ init
 debugIn
 \series default
  is the current debug level for all actions.
- It is up to the action implementation whether it wants to record the debug
- level or not.
+ It is up to the action implementation whether it wants to record the debug level or not.
 \end_layout
 
 \begin_layout Standard
-Typical order of argument processing is keywords, masks, DataSet name.
- First we will process the keywords 'noimage', 'geom', and 'out <filename>'.
+Typical order of argument processing is keywords,
+ masks,
+ DataSet name.
+ First we will process the keywords 'noimage',
+ 'geom',
+ and 'out <filename>'.
 \end_layout
 
 \begin_layout Standard
-In order to determine whether the action will try to use imaging we call
- the InitImaging() function (inherited from the ImagedAction class).
+In order to determine whether the action will try to use imaging we call the InitImaging() function (inherited from the ImagedAction class).
  If the ArgList actionArgs contains the string 
 \begin_inset Quotes eld
 \end_inset
@@ -3227,7 +3448,8 @@ noimage
 \begin_inset Quotes erd
 \end_inset
 
-, false will be sent to InitImaging to disable imaging:
+,
+ false will be sent to InitImaging to disable imaging:
 \end_layout
 
 \begin_layout LyX-Code
@@ -3244,7 +3466,8 @@ geom
 \begin_inset Quotes erd
 \end_inset
 
-, useMass_ will be set to false:
+,
+ useMass_ will be set to false:
 \end_layout
 
 \begin_layout LyX-Code
@@ -3252,7 +3475,8 @@ geom
 \end_layout
 
 \begin_layout Standard
-Next, we will try to create an output DataFile:
+Next,
+ we will try to create an output DataFile:
 \end_layout
 
 \begin_layout LyX-Code
@@ -3264,8 +3488,8 @@ Next, we will try to create an output DataFile:
 \end_layout
 
 \begin_layout Standard
-The behavior of AddDataFile() depends on the result from actionArgs.GetStringKey(
-); if 
+The behavior of AddDataFile() depends on the result from actionArgs.GetStringKey();
+ if 
 \begin_inset Quotes eld
 \end_inset
 
@@ -3273,9 +3497,9 @@ out
 \begin_inset Quotes erd
 \end_inset
 
- is present in actionArgs, the next string (presumably <filename>) is returned
- and passed to AddDataFile(), and a DataFile will be returned corresponding
- to <filename>.
+ is present in actionArgs,
+ the next string (presumably <filename>) is returned and passed to AddDataFile(),
+ and a DataFile will be returned corresponding to <filename>.
  If 
 \begin_inset Quotes eld
 \end_inset
@@ -3284,15 +3508,17 @@ out
 \begin_inset Quotes erd
 \end_inset
 
- is not present nothing will be returned, no file will be set up, and outfile
- will be null (0).
+ is not present nothing will be returned,
+ no file will be set up,
+ and outfile will be null (0).
  
 \end_layout
 
 \begin_layout Standard
-Next, we will get two atom mask expressions.
- We will require that the user must specify two masks, so if either of the
- strings is empty return an error:
+Next,
+ we will get two atom mask expressions.
+ We will require that the user must specify two masks,
+ so if either of the strings is empty return an error:
 \end_layout
 
 \begin_layout LyX-Code
@@ -3308,7 +3534,9 @@ Next, we will get two atom mask expressions.
 \end_layout
 
 \begin_layout LyX-Code
-    mprinterr("Error: distance: Requires 2 masks
+    mprinterr("Error:
+ distance:
+ Requires 2 masks
 \backslash
 n");
 \end_layout
@@ -3322,9 +3550,7 @@ n");
 \end_layout
 
 \begin_layout Standard
-Now we can use the mask expression strings to initialize the two AtomMask
- classes (note that this tokenizes the mask expressions but does not yet
- set them up since we need topology information to do that):
+Now we can use the mask expression strings to initialize the two AtomMask classes (note that this tokenizes the mask expressions but does not yet set them up since we need topology information to do that):
 \end_layout
 
 \begin_layout LyX-Code
@@ -3336,11 +3562,10 @@ Now we can use the mask expression strings to initialize the two AtomMask
 \end_layout
 
 \begin_layout Standard
-Next we will use the master DataSetList (init.DSL()) to create a DataSet
- to store the calculated distances.
- We will use a version of DataSetList::AddSet() that allows us to specify
- the DataSet type, MetaData, and a default name if no name is specified
- (
+Next we will use the master DataSetList (init.DSL()) to create a DataSet to store the calculated distances.
+ We will use a version of DataSetList::AddSet() that allows us to specify the DataSet type,
+ MetaData,
+ and a default name if no name is specified (
 \begin_inset Quotes eld
 \end_inset
 
@@ -3349,13 +3574,15 @@ Dis
 \end_inset
 
 ).
- If any errors occur in creating the DataSet, NULL (0) will be returned.
- Note that the string returned by actionArgs.GetStringNext() is implicitly
- converted to a MetaData class.
+ If any errors occur in creating the DataSet,
+ NULL (0) will be returned.
+ Note that the string returned by actionArgs.GetStringNext() is implicitly converted to a MetaData class.
 \end_layout
 
 \begin_layout LyX-Code
-  dist_ = init.DSL().AddSet(DataSet::DOUBLE, actionArgs.GetStringNext(), "Dis");
+  dist_ = init.DSL().AddSet(DataSet::DOUBLE,
+ actionArgs.GetStringNext(),
+ "Dis");
 \end_layout
 
 \begin_layout LyX-Code
@@ -3363,7 +3590,8 @@ Dis
 \end_layout
 
 \begin_layout Standard
-If a DataFile was previously set up, we now add the DataSet to this DataFile:
+If a DataFile was previously set up,
+ we now add the DataSet to this DataFile:
 \end_layout
 
 \begin_layout LyX-Code
@@ -3371,12 +3599,14 @@ If a DataFile was previously set up, we now add the DataSet to this DataFile:
 \end_layout
 
 \begin_layout Standard
-Last, we print out some information regarding how the Action has been initialize
-d and return Action::OK to indicate successful intialization:
+Last,
+ we print out some information regarding how the Action has been initialized and return Action::OK to indicate successful intialization:
 \end_layout
 
 \begin_layout LyX-Code
-  mprintf("    DISTANCE: %s to %s",Mask1_.MaskString(), Mask2_.MaskString());
+  mprintf("    DISTANCE:
+ %s to %s",Mask1_.MaskString(),
+ Mask2_.MaskString());
 \end_layout
 
 \begin_layout LyX-Code
@@ -3384,7 +3614,8 @@ d and return Action::OK to indicate successful intialization:
 \end_layout
 
 \begin_layout LyX-Code
-    mprintf(", non-imaged");
+    mprintf(",
+ non-imaged");
 \end_layout
 
 \begin_layout LyX-Code
@@ -3392,7 +3623,8 @@ d and return Action::OK to indicate successful intialization:
 \end_layout
 
 \begin_layout LyX-Code
-    mprintf(", center of mass");
+    mprintf(",
+ center of mass");
 \end_layout
 
 \begin_layout LyX-Code
@@ -3400,7 +3632,9 @@ d and return Action::OK to indicate successful intialization:
 \end_layout
 
 \begin_layout LyX-Code
-   mprintf(", geometric center");   mprintf(".
+   mprintf(",
+ geometric center");
+   mprintf(".
 \backslash
 n");
 \end_layout
@@ -3417,22 +3651,24 @@ n");
 
 \series bold
 IMPORTANT:
+
 \series default
- Note that this is the only time in which the master DataSetList is passed
- to the Action.
+ Note that this is the only time in which the master DataSetList is passed to the Action.
  If the Action will need to set up DataSets later (because e.g.
- they may depend on what's in the Topology, like in the case of the 
+ they may depend on what's in the Topology,
+ like in the case of the 
 \series bold
 \emph on
 multidihedral
 \series default
 \emph default
- command), it should save a pointer to the master DataSetList using the
- 
+ command),
+ it should save a pointer to the master DataSetList using the 
 \series bold
 init.DslPtr()
 \series default
- function, e.g.
+ function,
+ e.g.
 \end_layout
 
 \begin_layout LyX-Code
@@ -3444,10 +3680,8 @@ Setup() - Set up Topology-related parts of the Action
 \end_layout
 
 \begin_layout Standard
-Setup() is called whenever the action needs to be set up for a given Topology
- file.
- Any component of the action that depends on Topology (in this case the
- AtomMasks and the Imaging) is handled here.
+Setup() is called whenever the action needs to be set up for a given Topology file.
+ Any component of the action that depends on Topology (in this case the AtomMasks and the Imaging) is handled here.
  The arguments to Setup() are:
 \end_layout
 
@@ -3460,11 +3694,9 @@ Note that the
 \series bold
 setup
 \series default
- variable (ActionSetup class) contains a pointer to the current Topology
- and current trajectory CoordinateInfo, as well as the number of expected
- frames associated with this Topology during the current run.
- Actions that want to modify the current Topology or CoordinateInfo for
- subsequent Actions can do so using the 
+ variable (ActionSetup class) contains a pointer to the current Topology and current trajectory CoordinateInfo,
+ as well as the number of expected frames associated with this Topology during the current run.
+ Actions that want to modify the current Topology or CoordinateInfo for subsequent Actions can do so using the 
 \series bold
 setup
 \series default
@@ -3474,12 +3706,11 @@ setup
 \end_layout
 
 \begin_layout Standard
-First, we setup the AtomMasks.
- Each AtomMask is passed to the current topology using the SetupIntegerMask()
- function, which will create an integer array containing only the selected
- atoms based on the mask expression.
- If we needed to know both selected and unselected atoms we could use the
- SetupCharMask() function instead.
+First,
+ we setup the AtomMasks.
+ Each AtomMask is passed to the current topology using the SetupIntegerMask() function,
+ which will create an integer array containing only the selected atoms based on the mask expression.
+ If we needed to know both selected and unselected atoms we could use the SetupCharMask() function instead.
 \end_layout
 
 \begin_layout LyX-Code
@@ -3491,20 +3722,20 @@ First, we setup the AtomMasks.
 \end_layout
 
 \begin_layout Standard
-After this, we print some information about what atoms are selected (note
- we could also use the MaskInfo() function of AtomMask for this).
- For calculating distance, we need to make sure atoms were actually selected
- (using the None() function of AtomMask).
- If no atoms were selected this may be because the mask is only valid for
- certain Topologies during the run, so in that case make it a non-fatal
- error (i.e.
+After this,
+ we print some information about what atoms are selected (note we could also use the MaskInfo() function of AtomMask for this).
+ For calculating distance,
+ we need to make sure atoms were actually selected (using the None() function of AtomMask).
+ If no atoms were selected this may be because the mask is only valid for certain Topologies during the run,
+ so in that case make it a non-fatal error (i.e.
  a Warning) and return Action::SKIP:
 \end_layout
 
 \begin_layout LyX-Code
   mprintf("
 \backslash
-t%s (%i atoms) to %s (%i atoms)",Mask1_.MaskString(), Mask1_.Nselected(),
+t%s (%i atoms) to %s (%i atoms)",Mask1_.MaskString(),
+ Mask1_.Nselected(),
 \end_layout
 
 \begin_layout LyX-Code
@@ -3518,7 +3749,9 @@ t%s (%i atoms) to %s (%i atoms)",Mask1_.MaskString(), Mask1_.Nselected(),
 \begin_layout LyX-Code
     mprintf("
 \backslash
-nWarning: distance: One or both masks have no atoms.
+nWarning:
+ distance:
+ One or both masks have no atoms.
 \backslash
 n");
 \end_layout
@@ -3532,12 +3765,10 @@ n");
 \end_layout
 
 \begin_layout Standard
-Next we determine if imaging can actually be performed based on the box
- information present in the current trajectory's CoordinateInfo; if there
- is no box information imaging cannot be performed.
+Next we determine if imaging can actually be performed based on the box information present in the current trajectory's CoordinateInfo;
+ if there is no box information imaging cannot be performed.
  We do this with the image_.SetupImaging() function (ImagedAction class).
- The image_.ImagingEnabled() function will let us know if imaging for this
- Topology is possible or not:
+ The image_.ImagingEnabled() function will let us know if imaging for this Topology is possible or not:
 \end_layout
 
 \begin_layout LyX-Code
@@ -3549,7 +3780,8 @@ Next we determine if imaging can actually be performed based on the box
 \end_layout
 
 \begin_layout LyX-Code
-    mprintf(", imaged");
+    mprintf(",
+ imaged");
 \end_layout
 
 \begin_layout LyX-Code
@@ -3557,7 +3789,8 @@ Next we determine if imaging can actually be performed based on the box
 \end_layout
 
 \begin_layout LyX-Code
-    mprintf(", imaging off");
+    mprintf(",
+ imaging off");
 \end_layout
 
 \begin_layout LyX-Code
@@ -3583,14 +3816,15 @@ Now all Topology-dependent aspects of the action are set up.
 
 \series bold
 IMPORTANT:
+
 \series default
  Note that this is the only time in which a Topology is passed to the Action.
- If the Action requires Topology information later (such as in DoAction()
- or Print()) it should save a pointer to the Topology using the 
+ If the Action requires Topology information later (such as in DoAction() or Print()) it should save a pointer to the Topology using the 
 \series bold
 setup.TopAddress()
 \series default
- function, e.g.
+ function,
+ e.g.
 \end_layout
 
 \begin_layout LyX-Code
@@ -3603,25 +3837,28 @@ Modification of Topology Info
 
 \begin_layout Standard
 If there will be a modification of Topology/Frame information (e.g.
- removing atoms, adding velocity information to the Frame, etc) the Action
- must return Action::MODIFY_TOPOLOGY.
- If the CoordinateInfo will be modified, the Action should have a copy of
- the CoordinateInfo in the Action class itself; 
+ removing atoms,
+ adding velocity information to the Frame,
+ etc) the Action must return Action::MODIFY_TOPOLOGY.
+ If the CoordinateInfo will be modified,
+ the Action should have a copy of the CoordinateInfo in the Action class itself;
+ 
 \series bold
-it must not reside only in Action::Setup(), otherwise it will be lost when
- setup exits
+it must not reside only in Action::Setup(),
+ otherwise it will be lost when setup exits
 \series default
 .
 \end_layout
 
 \begin_layout Standard
-For example, say we are adding time information to a frame that currently
- does not have it.
+For example,
+ say we are adding time information to a frame that currently does not have it.
  The code might look something like:
 \end_layout
 
 \begin_layout LyX-Code
-cInfo_ = setup.CoordInfo(); 
+cInfo_ = setup.CoordInfo();
+ 
 \end_layout
 
 \begin_layout LyX-Code
@@ -3637,7 +3874,8 @@ setup.SetCoordInfo( &cInfo_ );
 \end_layout
 
 \begin_layout Standard
-Here, cInfo_ is a CoordinateInfo variable in the Action class.
+Here,
+ cInfo_ is a CoordinateInfo variable in the Action class.
 \end_layout
 
 \begin_layout Subsubsection
@@ -3645,15 +3883,15 @@ DoAction() - Process input Frame
 \end_layout
 
 \begin_layout Standard
-Coordinates are read in a frame at a time and stored in a Frame class, which
- is then passed to each action in the ActionList.
+Coordinates are read in a frame at a time and stored in a Frame class,
+ which is then passed to each action in the ActionList.
  The DoAction() function is called to process a coordinate Frame.
  The arguments are:
 \end_layout
 
 \begin_layout LyX-Code
-Action::RetType Action_Distance::DoAction(int frameNum, ActionFrame& frm)
- {
+Action::RetType Action_Distance::DoAction(int frameNum,
+ ActionFrame& frm) {
 \end_layout
 
 \begin_layout Standard
@@ -3667,10 +3905,8 @@ frameNum
 frm
 \series default
  variable (ActionFrame class) contains a pointer to the current Frame.
- Actions that want to alter the current Frame beyond just manipulating coordinat
-es for subsequent Actions (e.g.
- changing the Frame size or adding velocity info etc) can do so via the
- 
+ Actions that want to alter the current Frame beyond just manipulating coordinates for subsequent Actions (e.g.
+ changing the Frame size or adding velocity info etc) can do so via the 
 \series bold
 frm
 \series default
@@ -3681,29 +3917,31 @@ frm
 
 \begin_layout Standard
 There are several variables needed for calculating the distance.
- First, we have two Vec3 classes (Vec3.h, which is already included from
- other headers) to store the XYZ coordinates of the points:
+ First,
+ we have two Vec3 classes (Vec3.h,
+ which is already included from other headers) to store the XYZ coordinates of the points:
 \end_layout
 
 \begin_layout LyX-Code
-  Vec3 a1, a2;
+  Vec3 a1,
+ a2;
 \end_layout
 
 \begin_layout Standard
-If we are performing non-orthorhombic imaging we need to store the matrices
- which perform conversion from Cartesian to fractional coordinates and vice
- versa (using Matrix_3x3 classes, Matrix_3x3.h).
- Note that these are called 'ucell' and 'recip' respectively throughout
- CPPTRAJ, as these were the names used for the analogous structures in PTRAJ.
+If we are performing non-orthorhombic imaging we need to store the matrices which perform conversion from Cartesian to fractional coordinates and vice versa (using Matrix_3x3 classes,
+ Matrix_3x3.h).
+ Note that these are called 'ucell' and 'recip' respectively throughout CPPTRAJ,
+ as these were the names used for the analogous structures in PTRAJ.
 \end_layout
 
 \begin_layout LyX-Code
-  Matrix_3x3 ucell, recip;
+  Matrix_3x3 ucell,
+ recip;
 \end_layout
 
 \begin_layout Standard
-Finally, we need a double to store the actual result of the distance calculation
-:
+Finally,
+ we need a double to store the actual result of the distance calculation:
 \end_layout
 
 \begin_layout LyX-Code
@@ -3711,9 +3949,10 @@ Finally, we need a double to store the actual result of the distance calculation
 \end_layout
 
 \begin_layout Standard
-In the first part of the actual calculation, we calculate the centers of
- the coordinates in Mask1_ and Mask2_, either mass-weighted or not depending
- on useMass_, using the appropriate functions from the Frame class (Frame.h):
+In the first part of the actual calculation,
+ we calculate the centers of the coordinates in Mask1_ and Mask2_,
+ either mass-weighted or not depending on useMass_,
+ using the appropriate functions from the Frame class (Frame.h):
 \end_layout
 
 \begin_layout LyX-Code
@@ -3745,22 +3984,20 @@ In the first part of the actual calculation, we calculate the centers of
 \end_layout
 
 \begin_layout Standard
-Note that here we are using the Frm() function, which returns a constant
- (i.e.
- non-modifiable) reference to the current Frame; if we wanted to actually
- manipulate the coordinates we would have to call ModifyFrm().
+Note that here we are using the Frm() function,
+ which returns a constant (i.e.
+ non-modifiable) reference to the current Frame;
+ if we wanted to actually manipulate the coordinates we would have to call ModifyFrm().
  
 \end_layout
 
 \begin_layout Standard
-Next, we get the distance between the coordinates stored in a1 and a2.
- For non-orthorhombic imaging we first need to convert the current box coordinat
-es (stored in the Frame class in double precision as 3 lengths and 3 angles)
- into the coordinate conversion matrices using the ToRecip() function of
- the Box class (Box.h).
- Then, depending on the type of imaging that needs to be performed we call
- the appropriate distance calculation routine (DIST2_XXX, found in DistRoutines.h
-):
+Next,
+ we get the distance between the coordinates stored in a1 and a2.
+ For non-orthorhombic imaging we first need to convert the current box coordinates (stored in the Frame class in double precision as 3 lengths and 3 angles) into the coordinate conversion matrices using the ToRecip() function of the Box class (Box.h).
+ Then,
+ depending on the type of imaging that needs to be performed we call the appropriate distance calculation routine (DIST2_XXX,
+ found in DistRoutines.h):
 \end_layout
 
 \begin_layout LyX-Code
@@ -3772,11 +4009,15 @@ es (stored in the Frame class in double precision as 3 lengths and 3 angles)
 \end_layout
 
 \begin_layout LyX-Code
-      frm.Frm().BoxCrd().ToRecip(ucell, recip);
+      frm.Frm().BoxCrd().ToRecip(ucell,
+ recip);
 \end_layout
 
 \begin_layout LyX-Code
-      Dist = DIST2_ImageNonOrtho(a1, a2, ucell, recip);
+      Dist = DIST2_ImageNonOrtho(a1,
+ a2,
+ ucell,
+ recip);
 \end_layout
 
 \begin_layout LyX-Code
@@ -3788,7 +4029,9 @@ es (stored in the Frame class in double precision as 3 lengths and 3 angles)
 \end_layout
 
 \begin_layout LyX-Code
-      Dist = DIST2_ImageOrtho(a1, a2, frm.Frm().BoxCrd());
+      Dist = DIST2_ImageOrtho(a1,
+ a2,
+ frm.Frm().BoxCrd());
 \end_layout
 
 \begin_layout LyX-Code
@@ -3800,7 +4043,9 @@ es (stored in the Frame class in double precision as 3 lengths and 3 angles)
 \end_layout
 
 \begin_layout LyX-Code
-      Dist = DIST2_NoImage(a1, a2);       break;
+      Dist = DIST2_NoImage(a1,
+ a2);
+       break;
 \end_layout
 
 \begin_layout LyX-Code
@@ -3812,14 +4057,14 @@ es (stored in the Frame class in double precision as 3 lengths and 3 angles)
 \end_layout
 
 \begin_layout Standard
-Last, we add the result to the DataSet and return Action::OK.
- Since DataSet is just an interface we pass in the address of Dist (&Dist)
- to let the underlying DataSet framework take care of the fact that it is
- a double.
+Last,
+ we add the result to the DataSet and return Action::OK.
+ Since DataSet is just an interface we pass in the address of Dist (&Dist) to let the underlying DataSet framework take care of the fact that it is a double.
 \end_layout
 
 \begin_layout LyX-Code
-  dist_->Add(frameNum, &Dist);
+  dist_->Add(frameNum,
+ &Dist);
 \end_layout
 
 \begin_layout LyX-Code
@@ -3836,14 +4081,12 @@ Print() - Any post-processing
 
 \begin_layout Standard
 The Print() function is called once all input frames have been read in,
- and is used if there is anything that should be printed outside the normal
- DataFile/DataSet framework (e.g.
- hydrogen bond averages in the hbond action) or if there are any additional
- calculations that need to be performed (e.g.
+ and is used if there is anything that should be printed outside the normal DataFile/DataSet framework (e.g.
+ hydrogen bond averages in the hbond action) or if there are any additional calculations that need to be performed (e.g.
  finishing up matrix calculations in the matrix action).
- In this example we're only calculating a simple distance; the output is
- handled by the DataFile/DataSet framework, so we implement a blank Print()
- function in the header:
+ In this example we're only calculating a simple distance;
+ the output is handled by the DataFile/DataSet framework,
+ so we implement a blank Print() function in the header:
 \end_layout
 
 \begin_layout LyX-Code
@@ -3855,8 +4098,8 @@ Add the Action to the Command class
 \end_layout
 
 \begin_layout Standard
-Now that the class implementation is complete, we need to let cpptraj know
- how to call it.
+Now that the class implementation is complete,
+ we need to let cpptraj know how to call it.
  This is currently done using a 
 \begin_inset Quotes eld
 \end_inset
@@ -3865,15 +4108,19 @@ static
 \begin_inset Quotes erd
 \end_inset
 
- Class, Command (Command.cpp), which is initialized by the Cpptraj class
- via Command::Init() when the program starts.
- Command::Init() makes use of the Command::AddCmd() function to add the
- Command, set its destination, and any associated keywords.
+ Class,
+ Command (Command.cpp),
+ which is initialized by the Cpptraj class via Command::Init() when the program starts.
+ Command::Init() makes use of the Command::AddCmd() function to add the Command,
+ set its destination,
+ and any associated keywords.
  The Command::AddCmd() function looks like:
 \end_layout
 
 \begin_layout LyX-Code
-void Command::AddCmd(DispatchObject* oIn, Cmd::DestType dIn, int nKeys,
+void Command::AddCmd(DispatchObject* oIn,
+ Cmd::DestType dIn,
+ int nKeys,
  ...)
 \end_layout
 
@@ -3882,27 +4129,37 @@ where
 \series bold
 oIn
 \series default
- is a pointer to the DispatchObject (Exec-, Action-, Analysis-, or Deprecated-de
-rived class), 
+ is a pointer to the DispatchObject (Exec-,
+ Action-,
+ Analysis-,
+ or Deprecated-derived class),
+ 
 \series bold
 dIn
 \series default
- determines how the Command will be processed, 
+ determines how the Command will be processed,
+ 
 \series bold
 nKeys
 \series default
- is the number of keywords associated with the command, and the remaining
- arguments are the command keywords.
+ is the number of keywords associated with the command,
+ and the remaining arguments are the command keywords.
  For example:
 \end_layout
 
 \begin_layout LyX-Code
-Command::AddCmd( new Action_Rmsd(), Cmd::ACT, 2, "rms", "rmsd" );
+Command::AddCmd( new Action_Rmsd(),
+ Cmd::ACT,
+ 2,
+ "rms",
+ "rmsd" );
 \end_layout
 
 \begin_layout Standard
-Adds a new instance of the Action-derived class Action_Rmsd, sets its destinatio
-n as Action (Cmd::ACT), and sets 2 associated command keys, 
+Adds a new instance of the Action-derived class Action_Rmsd,
+ sets its destination as Action (Cmd::ACT),
+ and sets 2 associated command keys,
+ 
 \begin_inset Quotes eld
 \end_inset
 
@@ -3922,8 +4179,8 @@ rmsd
 \end_layout
 
 \begin_layout Standard
-To make navigation of Commands.cpp easier, you can search for ACTION (or
- ANALYSIS if adding an Analysis) to go where things need to be added.
+To make navigation of Commands.cpp easier,
+ you can search for ACTION (or ANALYSIS if adding an Analysis) to go where things need to be added.
  First add the class to Commands.cpp with the appropriate '#include'.
  Includes should be in alphabetical order within their given section.
 \end_layout
@@ -3943,21 +4200,32 @@ To make navigation of Commands.cpp easier, you can search for ACTION (or
 \end_layout
 
 \begin_layout Standard
-Then add the command to Command::Init() using Command::AddCmd(), e.g.:
+Then add the command to Command::Init() using Command::AddCmd(),
+ e.g.:
 \end_layout
 
 \begin_layout LyX-Code
-Command::AddCmd( new Action_Dipole(), Cmd::ACT, 1, "dipole" );
+Command::AddCmd( new Action_Dipole(),
+ Cmd::ACT,
+ 1,
+ "dipole" );
 \end_layout
 
 \begin_layout LyX-Code
 
 \series bold
-Command::AddCmd( new Action_Distance(), Cmd::ACT, 1, "distance" );
+Command::AddCmd( new Action_Distance(),
+ Cmd::ACT,
+ 1,
+ "distance" );
 \end_layout
 
 \begin_layout LyX-Code
-Command::AddCmd( new Action_DistRmsd(), Cmd::ACT, 2, "drms", "drmsd" );
+Command::AddCmd( new Action_DistRmsd(),
+ Cmd::ACT,
+ 2,
+ "drms",
+ "drmsd" );
  
 \end_layout
 

From 5a7deb4743028fc54f81a110690377605761c370 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 27 Feb 2026 09:04:22 -0500
Subject: [PATCH 1400/1492] Update the doxyfile

---
 src/cpptraj.Doxyfile | 2778 ++++++++++++++++++++++++++++--------------
 1 file changed, 1832 insertions(+), 946 deletions(-)

diff --git a/src/cpptraj.Doxyfile b/src/cpptraj.Doxyfile
index add3c6ae5a..68bbacd487 100644
--- a/src/cpptraj.Doxyfile
+++ b/src/cpptraj.Doxyfile
@@ -1,110 +1,150 @@
-# Doxyfile 1.8.1.1
+# Doxyfile 1.9.4
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
 #
-# All text after a hash (#) is considered a comment and will be ignored.
+# All text after a double hash (##) is considered a comment and is placed in
+# front of the TAG it is preceding.
+#
+# All text after a single hash (#) is considered a comment and will be ignored.
 # The format is:
-#       TAG = value [value, ...]
-# For lists items can also be appended using:
-#       TAG += value [value, ...]
-# Values that contain spaces should be placed between quotes (" ").
+# TAG = value [value, ...]
+# For lists, items can also be appended using:
+# TAG += value [value, ...]
+# Values that contain spaces should be placed between quotes (\" \").
+#
+# Note:
+#
+# Use doxygen to compare the used configuration file with the template
+# configuration file:
+# doxygen -x [configFile]
+# Use doxygen to compare the used configuration file with the template
+# configuration file without replacing the environment variables:
+# doxygen -x_noenv [configFile]
 
 #---------------------------------------------------------------------------
 # Project related configuration options
 #---------------------------------------------------------------------------
 
-# This tag specifies the encoding used for all characters in the config file
-# that follow. The default is UTF-8 which is also the encoding used for all
+# This tag specifies the encoding used for all characters in the configuration
+# file that follow. The default is UTF-8 which is also the encoding used for all
 # text before the first occurrence of this tag. Doxygen uses libiconv (or the
 # iconv built into libc) for the transcoding. See
-# http://www.gnu.org/software/libiconv for the list of possible encodings.
+# https://www.gnu.org/software/libiconv/ for the list of possible encodings.
+# The default value is: UTF-8.
 
 DOXYFILE_ENCODING      = UTF-8
 
-# The PROJECT_NAME tag is a single word (or sequence of words) that should
-# identify the project. Note that if you do not use Doxywizard you need
-# to put quotes around the project name if it contains spaces.
+# The PROJECT_NAME tag is a single word (or a sequence of words surrounded by
+# double-quotes, unless you are using Doxywizard) that should identify the
+# project for which the documentation is generated. This name is used in the
+# title of most generated pages and in a few other places.
+# The default value is: My Project.
 
 PROJECT_NAME           = Cpptraj
 
-# The PROJECT_NUMBER tag can be used to enter a project or revision number.
-# This could be handy for archiving the generated documentation or
-# if some version control system is used.
+# The PROJECT_NUMBER tag can be used to enter a project or revision number. This
+# could be handy for archiving the generated documentation or if some version
+# control system is used.
 
-PROJECT_NUMBER         = 13 
+PROJECT_NUMBER         = 13
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
-# for a project that appears at the top of each page and should give viewer
-# a quick idea about the purpose of the project. Keep the description short.
+# for a project that appears at the top of each page and should give viewer a
+# quick idea about the purpose of the project. Keep the description short.
 
 PROJECT_BRIEF          = "Trajectory Analysis Written in C++"
 
-# With the PROJECT_LOGO tag one can specify an logo or icon that is
-# included in the documentation. The maximum height of the logo should not
-# exceed 55 pixels and the maximum width should not exceed 200 pixels.
-# Doxygen will copy the logo to the output directory.
+# With the PROJECT_LOGO tag one can specify a logo or an icon that is included
+# in the documentation. The maximum height of the logo should not exceed 55
+# pixels and the maximum width should not exceed 200 pixels. Doxygen will copy
+# the logo to the output directory.
 
 PROJECT_LOGO           =
 
-# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
-# base path where the generated documentation will be put.
-# If a relative path is entered, it will be relative to the location
-# where doxygen was started. If left blank the current directory will be used.
+# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path
+# into which the generated documentation will be written. If a relative path is
+# entered, it will be relative to the location where doxygen was started. If
+# left blank the current directory will be used.
 
 OUTPUT_DIRECTORY       = ../doc/
 
-# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create
-# 4096 sub-directories (in 2 levels) under the output directory of each output
-# format and will distribute the generated files over these directories.
-# Enabling this option can be useful when feeding doxygen a huge amount of
-# source files, where putting all generated files in the same directory would
-# otherwise cause performance problems for the file system.
+# If the CREATE_SUBDIRS tag is set to YES then doxygen will create up to 4096
+# sub-directories (in 2 levels) under the output directory of each output format
+# and will distribute the generated files over these directories. Enabling this
+# option can be useful when feeding doxygen a huge amount of source files, where
+# putting all generated files in the same directory would otherwise causes
+# performance problems for the file system. Adapt CREATE_SUBDIRS_LEVEL to
+# control the number of sub-directories.
+# The default value is: NO.
 
 CREATE_SUBDIRS         = NO
 
+# Controls the number of sub-directories that will be created when
+# CREATE_SUBDIRS tag is set to YES. Level 0 represents 16 directories, and every
+# level increment doubles the number of directories, resulting in 4096
+# directories at level 8 which is the default and also the maximum value. The
+# sub-directories are organized in 2 levels, the first level always has a fixed
+# numer of 16 directories.
+# Minimum value: 0, maximum value: 8, default value: 8.
+# This tag requires that the tag CREATE_SUBDIRS is set to YES.
+
+CREATE_SUBDIRS_LEVEL   = 8
+
+# If the ALLOW_UNICODE_NAMES tag is set to YES, doxygen will allow non-ASCII
+# characters to appear in the names of generated files. If set to NO, non-ASCII
+# characters will be escaped, for example _xE3_x81_x84 will be used for Unicode
+# U+3044.
+# The default value is: NO.
+
+ALLOW_UNICODE_NAMES    = NO
+
 # The OUTPUT_LANGUAGE tag is used to specify the language in which all
 # documentation generated by doxygen is written. Doxygen will use this
 # information to generate all constant output in the proper language.
-# The default language is English, other supported languages are:
-# Afrikaans, Arabic, Brazilian, Catalan, Chinese, Chinese-Traditional,
-# Croatian, Czech, Danish, Dutch, Esperanto, Farsi, Finnish, French, German,
-# Greek, Hungarian, Italian, Japanese, Japanese-en (Japanese with English
-# messages), Korean, Korean-en, Lithuanian, Norwegian, Macedonian, Persian,
-# Polish, Portuguese, Romanian, Russian, Serbian, Serbian-Cyrillic, Slovak,
-# Slovene, Spanish, Swedish, Ukrainian, and Vietnamese.
+# Possible values are: Afrikaans, Arabic, Armenian, Brazilian, Bulgarian,
+# Catalan, Chinese, Chinese-Traditional, Croatian, Czech, Danish, Dutch, English
+# (United States), Esperanto, Farsi (Persian), Finnish, French, German, Greek,
+# Hindi, Hungarian, Indonesian, Italian, Japanese, Japanese-en (Japanese with
+# English messages), Korean, Korean-en (Korean with English messages), Latvian,
+# Lithuanian, Macedonian, Norwegian, Persian (Farsi), Polish, Portuguese,
+# Romanian, Russian, Serbian, Serbian-Cyrillic, Slovak, Slovene, Spanish,
+# Swedish, Turkish, Ukrainian and Vietnamese.
+# The default value is: English.
 
 OUTPUT_LANGUAGE        = English
 
-# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will
-# include brief member descriptions after the members that are listed in
-# the file and class documentation (similar to JavaDoc).
-# Set to NO to disable this.
+# If the BRIEF_MEMBER_DESC tag is set to YES, doxygen will include brief member
+# descriptions after the members that are listed in the file and class
+# documentation (similar to Javadoc). Set to NO to disable this.
+# The default value is: YES.
 
 BRIEF_MEMBER_DESC      = YES
 
-# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend
-# the brief description of a member or function before the detailed description.
-# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the
+# If the REPEAT_BRIEF tag is set to YES, doxygen will prepend the brief
+# description of a member or function before the detailed description
+#
+# Note: If both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the
 # brief descriptions will be completely suppressed.
+# The default value is: YES.
 
 REPEAT_BRIEF           = YES
 
-# This tag implements a quasi-intelligent brief description abbreviator
-# that is used to form the text in various listings. Each string
-# in this list, if found as the leading text of the brief description, will be
-# stripped from the text and the result after processing the whole list, is
-# used as the annotated text. Otherwise, the brief description is used as-is.
-# If left blank, the following values are used ("$name" is automatically
-# replaced with the name of the entity): "The $name class" "The $name widget"
-# "The $name file" "is" "provides" "specifies" "contains"
-# "represents" "a" "an" "the"
+# This tag implements a quasi-intelligent brief description abbreviator that is
+# used to form the text in various listings. Each string in this list, if found
+# as the leading text of the brief description, will be stripped from the text
+# and the result, after processing the whole list, is used as the annotated
+# text. Otherwise, the brief description is used as-is. If left blank, the
+# following values are used ($name is automatically replaced with the name of
+# the entity):The $name class, The $name widget, The $name file, is, provides,
+# specifies, contains, represents, a, an and the.
 
 ABBREVIATE_BRIEF       =
 
 # If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then
-# Doxygen will generate a detailed section even if there is only a brief
+# doxygen will generate a detailed section even if there is only a brief
 # description.
+# The default value is: NO.
 
 ALWAYS_DETAILED_SEC    = NO
 
@@ -112,578 +152,791 @@ ALWAYS_DETAILED_SEC    = NO
 # inherited members of a class in the documentation of that class as if those
 # members were ordinary class members. Constructors, destructors and assignment
 # operators of the base classes will not be shown.
+# The default value is: NO.
 
 INLINE_INHERITED_MEMB  = NO
 
-# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full
-# path before files name in the file list and in the header files. If set
-# to NO the shortest path that makes the file name unique will be used.
+# If the FULL_PATH_NAMES tag is set to YES, doxygen will prepend the full path
+# before files name in the file list and in the header files. If set to NO the
+# shortest path that makes the file name unique will be used
+# The default value is: YES.
 
 FULL_PATH_NAMES        = YES
 
-# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag
-# can be used to strip a user-defined part of the path. Stripping is
-# only done if one of the specified strings matches the left-hand part of
-# the path. The tag can be used to show relative paths in the file list.
-# If left blank the directory from which doxygen is run is used as the
-# path to strip.
+# The STRIP_FROM_PATH tag can be used to strip a user-defined part of the path.
+# Stripping is only done if one of the specified strings matches the left-hand
+# part of the path. The tag can be used to show relative paths in the file list.
+# If left blank the directory from which doxygen is run is used as the path to
+# strip.
+#
+# Note that you can specify absolute paths here, but also relative paths, which
+# will be relative from the directory where doxygen is started.
+# This tag requires that the tag FULL_PATH_NAMES is set to YES.
 
 STRIP_FROM_PATH        =
 
-# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of
-# the path mentioned in the documentation of a class, which tells
-# the reader which header file to include in order to use a class.
-# If left blank only the name of the header file containing the class
-# definition is used. Otherwise one should specify the include paths that
-# are normally passed to the compiler using the -I flag.
+# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of the
+# path mentioned in the documentation of a class, which tells the reader which
+# header file to include in order to use a class. If left blank only the name of
+# the header file containing the class definition is used. Otherwise one should
+# specify the list of include paths that are normally passed to the compiler
+# using the -I flag.
 
 STRIP_FROM_INC_PATH    =
 
-# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter
-# (but less readable) file names. This can be useful if your file system
-# doesn't support long names like on DOS, Mac, or CD-ROM.
+# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter (but
+# less readable) file names. This can be useful is your file systems doesn't
+# support long names like on DOS, Mac, or CD-ROM.
+# The default value is: NO.
 
 SHORT_NAMES            = NO
 
-# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen
-# will interpret the first line (until the first dot) of a JavaDoc-style
-# comment as the brief description. If set to NO, the JavaDoc
-# comments will behave just like regular Qt-style comments
-# (thus requiring an explicit @brief command for a brief description.)
+# If the JAVADOC_AUTOBRIEF tag is set to YES then doxygen will interpret the
+# first line (until the first dot) of a Javadoc-style comment as the brief
+# description. If set to NO, the Javadoc-style will behave just like regular Qt-
+# style comments (thus requiring an explicit @brief command for a brief
+# description.)
+# The default value is: NO.
 
 JAVADOC_AUTOBRIEF      = NO
 
-# If the QT_AUTOBRIEF tag is set to YES then Doxygen will
-# interpret the first line (until the first dot) of a Qt-style
-# comment as the brief description. If set to NO, the comments
-# will behave just like regular Qt-style comments (thus requiring
-# an explicit \brief command for a brief description.)
+# If the JAVADOC_BANNER tag is set to YES then doxygen will interpret a line
+# such as
+# /***************
+# as being the beginning of a Javadoc-style comment "banner". If set to NO, the
+# Javadoc-style will behave just like regular comments and it will not be
+# interpreted by doxygen.
+# The default value is: NO.
+
+JAVADOC_BANNER         = NO
+
+# If the QT_AUTOBRIEF tag is set to YES then doxygen will interpret the first
+# line (until the first dot) of a Qt-style comment as the brief description. If
+# set to NO, the Qt-style will behave just like regular Qt-style comments (thus
+# requiring an explicit \brief command for a brief description.)
+# The default value is: NO.
 
 QT_AUTOBRIEF           = NO
 
-# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen
-# treat a multi-line C++ special comment block (i.e. a block of //! or ///
-# comments) as a brief description. This used to be the default behaviour.
-# The new default is to treat a multi-line C++ comment block as a detailed
-# description. Set this tag to YES if you prefer the old behaviour instead.
+# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make doxygen treat a
+# multi-line C++ special comment block (i.e. a block of //! or /// comments) as
+# a brief description. This used to be the default behavior. The new default is
+# to treat a multi-line C++ comment block as a detailed description. Set this
+# tag to YES if you prefer the old behavior instead.
+#
+# Note that setting this tag to YES also means that rational rose comments are
+# not recognized any more.
+# The default value is: NO.
 
 MULTILINE_CPP_IS_BRIEF = NO
 
-# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented
-# member inherits the documentation from any documented member that it
-# re-implements.
+# By default Python docstrings are displayed as preformatted text and doxygen's
+# special commands cannot be used. By setting PYTHON_DOCSTRING to NO the
+# doxygen's special commands can be used and the contents of the docstring
+# documentation blocks is shown as doxygen documentation.
+# The default value is: YES.
+
+PYTHON_DOCSTRING       = YES
+
+# If the INHERIT_DOCS tag is set to YES then an undocumented member inherits the
+# documentation from any documented member that it re-implements.
+# The default value is: YES.
 
 INHERIT_DOCS           = YES
 
-# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce
-# a new page for each member. If set to NO, the documentation of a member will
-# be part of the file/class/namespace that contains it.
+# If the SEPARATE_MEMBER_PAGES tag is set to YES then doxygen will produce a new
+# page for each member. If set to NO, the documentation of a member will be part
+# of the file/class/namespace that contains it.
+# The default value is: NO.
 
 SEPARATE_MEMBER_PAGES  = NO
 
-# The TAB_SIZE tag can be used to set the number of spaces in a tab.
-# Doxygen uses this value to replace tabs by spaces in code fragments.
+# The TAB_SIZE tag can be used to set the number of spaces in a tab. Doxygen
+# uses this value to replace tabs by spaces in code fragments.
+# Minimum value: 1, maximum value: 16, default value: 4.
 
 TAB_SIZE               = 8
 
-# This tag can be used to specify a number of aliases that acts
-# as commands in the documentation. An alias has the form "name=value".
-# For example adding "sideeffect=\par Side Effects:\n" will allow you to
-# put the command \sideeffect (or @sideeffect) in the documentation, which
-# will result in a user-defined paragraph with heading "Side Effects:".
-# You can put \n's in the value part of an alias to insert newlines.
+# This tag can be used to specify a number of aliases that act as commands in
+# the documentation. An alias has the form:
+# name=value
+# For example adding
+# "sideeffect=@par Side Effects:^^"
+# will allow you to put the command \sideeffect (or @sideeffect) in the
+# documentation, which will result in a user-defined paragraph with heading
+# "Side Effects:". Note that you cannot put \n's in the value part of an alias
+# to insert newlines (in the resulting output). You can put ^^ in the value part
+# of an alias to insert a newline as if a physical newline was in the original
+# file. When you need a literal { or } or , in the value part of an alias you
+# have to escape them by means of a backslash (\), this can lead to conflicts
+# with the commands \{ and \} for these it is advised to use the version @{ and
+# @} or use a double escape (\\{ and \\})
 
 ALIASES                =
 
-# This tag can be used to specify a number of word-keyword mappings (TCL only).
-# A mapping has the form "name=value". For example adding
-# "class=itcl::class" will allow you to use the command class in the
-# itcl::class meaning.
-
-TCL_SUBST              =
-
-# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C
-# sources only. Doxygen will then generate output that is more tailored for C.
-# For instance, some of the names that are used will be different. The list
-# of all members will be omitted, etc.
+# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources
+# only. Doxygen will then generate output that is more tailored for C. For
+# instance, some of the names that are used will be different. The list of all
+# members will be omitted, etc.
+# The default value is: NO.
 
 OPTIMIZE_OUTPUT_FOR_C  = NO
 
-# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java
-# sources only. Doxygen will then generate output that is more tailored for
-# Java. For instance, namespaces will be presented as packages, qualified
-# scopes will look different, etc.
+# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java or
+# Python sources only. Doxygen will then generate output that is more tailored
+# for that language. For instance, namespaces will be presented as packages,
+# qualified scopes will look different, etc.
+# The default value is: NO.
 
 OPTIMIZE_OUTPUT_JAVA   = NO
 
 # Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran
-# sources only. Doxygen will then generate output that is more tailored for
-# Fortran.
+# sources. Doxygen will then generate output that is tailored for Fortran.
+# The default value is: NO.
 
 OPTIMIZE_FOR_FORTRAN   = NO
 
 # Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL
-# sources. Doxygen will then generate output that is tailored for
-# VHDL.
+# sources. Doxygen will then generate output that is tailored for VHDL.
+# The default value is: NO.
 
 OPTIMIZE_OUTPUT_VHDL   = NO
 
+# Set the OPTIMIZE_OUTPUT_SLICE tag to YES if your project consists of Slice
+# sources only. Doxygen will then generate output that is more tailored for that
+# language. For instance, namespaces will be presented as modules, types will be
+# separated into more groups, etc.
+# The default value is: NO.
+
+OPTIMIZE_OUTPUT_SLICE  = NO
+
 # Doxygen selects the parser to use depending on the extension of the files it
-# parses. With this tag you can assign which parser to use for a given extension.
-# Doxygen has a built-in mapping, but you can override or extend it using this
-# tag. The format is ext=language, where ext is a file extension, and language
-# is one of the parsers supported by doxygen: IDL, Java, Javascript, CSharp, C,
-# C++, D, PHP, Objective-C, Python, Fortran, VHDL, C, C++. For instance to make
-# doxygen treat .inc files as Fortran files (default is PHP), and .f files as C
-# (default is Fortran), use: inc=Fortran f=C. Note that for custom extensions
-# you also need to set FILE_PATTERNS otherwise the files are not read by doxygen.
+# parses. With this tag you can assign which parser to use for a given
+# extension. Doxygen has a built-in mapping, but you can override or extend it
+# using this tag. The format is ext=language, where ext is a file extension, and
+# language is one of the parsers supported by doxygen: IDL, Java, JavaScript,
+# Csharp (C#), C, C++, Lex, D, PHP, md (Markdown), Objective-C, Python, Slice,
+# VHDL, Fortran (fixed format Fortran: FortranFixed, free formatted Fortran:
+# FortranFree, unknown formatted Fortran: Fortran. In the later case the parser
+# tries to guess whether the code is fixed or free formatted code, this is the
+# default for Fortran type files). For instance to make doxygen treat .inc files
+# as Fortran files (default is PHP), and .f files as C (default is Fortran),
+# use: inc=Fortran f=C.
+#
+# Note: For files without extension you can use no_extension as a placeholder.
+#
+# Note that for custom extensions you also need to set FILE_PATTERNS otherwise
+# the files are not read by doxygen. When specifying no_extension you should add
+# * to the FILE_PATTERNS.
+#
+# Note see also the list of default file extension mappings.
 
 EXTENSION_MAPPING      =
 
-# If MARKDOWN_SUPPORT is enabled (the default) then doxygen pre-processes all
-# comments according to the Markdown format, which allows for more readable
-# documentation. See http://daringfireball.net/projects/markdown/ for details.
-# The output of markdown processing is further processed by doxygen, so you
-# can mix doxygen, HTML, and XML commands with Markdown formatting.
-# Disable only in case of backward compatibilities issues.
+# If the MARKDOWN_SUPPORT tag is enabled then doxygen pre-processes all comments
+# according to the Markdown format, which allows for more readable
+# documentation. See https://daringfireball.net/projects/markdown/ for details.
+# The output of markdown processing is further processed by doxygen, so you can
+# mix doxygen, HTML, and XML commands with Markdown formatting. Disable only in
+# case of backward compatibilities issues.
+# The default value is: YES.
 
 MARKDOWN_SUPPORT       = YES
 
+# When the TOC_INCLUDE_HEADINGS tag is set to a non-zero value, all headings up
+# to that level are automatically included in the table of contents, even if
+# they do not have an id attribute.
+# Note: This feature currently applies only to Markdown headings.
+# Minimum value: 0, maximum value: 99, default value: 5.
+# This tag requires that the tag MARKDOWN_SUPPORT is set to YES.
+
+TOC_INCLUDE_HEADINGS   = 5
+
+# When enabled doxygen tries to link words that correspond to documented
+# classes, or namespaces to their corresponding documentation. Such a link can
+# be prevented in individual cases by putting a % sign in front of the word or
+# globally by setting AUTOLINK_SUPPORT to NO.
+# The default value is: YES.
+
+AUTOLINK_SUPPORT       = YES
+
 # If you use STL classes (i.e. std::string, std::vector, etc.) but do not want
-# to include (a tag file for) the STL sources as input, then you should
-# set this tag to YES in order to let doxygen match functions declarations and
-# definitions whose arguments contain STL classes (e.g. func(std::string); v.s.
-# func(std::string) {}). This also makes the inheritance and collaboration
+# to include (a tag file for) the STL sources as input, then you should set this
+# tag to YES in order to let doxygen match functions declarations and
+# definitions whose arguments contain STL classes (e.g. func(std::string);
+# versus func(std::string) {}). This also make the inheritance and collaboration
 # diagrams that involve STL classes more complete and accurate.
+# The default value is: NO.
 
 BUILTIN_STL_SUPPORT    = NO
 
 # If you use Microsoft's C++/CLI language, you should set this option to YES to
 # enable parsing support.
+# The default value is: NO.
 
 CPP_CLI_SUPPORT        = NO
 
-# Set the SIP_SUPPORT tag to YES if your project consists of sip sources only.
-# Doxygen will parse them like normal C++ but will assume all classes use public
-# instead of private inheritance when no explicit protection keyword is present.
+# Set the SIP_SUPPORT tag to YES if your project consists of sip (see:
+# https://www.riverbankcomputing.com/software/sip/intro) sources only. Doxygen
+# will parse them like normal C++ but will assume all classes use public instead
+# of private inheritance when no explicit protection keyword is present.
+# The default value is: NO.
 
 SIP_SUPPORT            = NO
 
-# For Microsoft's IDL there are propget and propput attributes to indicate getter
-# and setter methods for a property. Setting this option to YES (the default)
-# will make doxygen replace the get and set methods by a property in the
-# documentation. This will only work if the methods are indeed getting or
-# setting a simple type. If this is not the case, or you want to show the
-# methods anyway, you should set this option to NO.
+# For Microsoft's IDL there are propget and propput attributes to indicate
+# getter and setter methods for a property. Setting this option to YES will make
+# doxygen to replace the get and set methods by a property in the documentation.
+# This will only work if the methods are indeed getting or setting a simple
+# type. If this is not the case, or you want to show the methods anyway, you
+# should set this option to NO.
+# The default value is: YES.
 
 IDL_PROPERTY_SUPPORT   = YES
 
 # If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
-# tag is set to YES, then doxygen will reuse the documentation of the first
+# tag is set to YES then doxygen will reuse the documentation of the first
 # member in the group (if any) for the other members of the group. By default
 # all members of a group must be documented explicitly.
+# The default value is: NO.
 
 DISTRIBUTE_GROUP_DOC   = NO
 
-# Set the SUBGROUPING tag to YES (the default) to allow class member groups of
-# the same type (for instance a group of public functions) to be put as a
-# subgroup of that type (e.g. under the Public Functions section). Set it to
-# NO to prevent subgrouping. Alternatively, this can be done per class using
-# the \nosubgrouping command.
+# If one adds a struct or class to a group and this option is enabled, then also
+# any nested class or struct is added to the same group. By default this option
+# is disabled and one has to add nested compounds explicitly via \ingroup.
+# The default value is: NO.
+
+GROUP_NESTED_COMPOUNDS = NO
+
+# Set the SUBGROUPING tag to YES to allow class member groups of the same type
+# (for instance a group of public functions) to be put as a subgroup of that
+# type (e.g. under the Public Functions section). Set it to NO to prevent
+# subgrouping. Alternatively, this can be done per class using the
+# \nosubgrouping command.
+# The default value is: YES.
 
 SUBGROUPING            = YES
 
-# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and
-# unions are shown inside the group in which they are included (e.g. using
-# @ingroup) instead of on a separate page (for HTML and Man pages) or
-# section (for LaTeX and RTF).
+# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and unions
+# are shown inside the group in which they are included (e.g. using \ingroup)
+# instead of on a separate page (for HTML and Man pages) or section (for LaTeX
+# and RTF).
+#
+# Note that this feature does not work in combination with
+# SEPARATE_MEMBER_PAGES.
+# The default value is: NO.
 
 INLINE_GROUPED_CLASSES = NO
 
-# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and
-# unions with only public data fields will be shown inline in the documentation
-# of the scope in which they are defined (i.e. file, namespace, or group
-# documentation), provided this scope is documented. If set to NO (the default),
-# structs, classes, and unions are shown on a separate page (for HTML and Man
-# pages) or section (for LaTeX and RTF).
+# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and unions
+# with only public data fields or simple typedef fields will be shown inline in
+# the documentation of the scope in which they are defined (i.e. file,
+# namespace, or group documentation), provided this scope is documented. If set
+# to NO, structs, classes, and unions are shown on a separate page (for HTML and
+# Man pages) or section (for LaTeX and RTF).
+# The default value is: NO.
 
 INLINE_SIMPLE_STRUCTS  = NO
 
-# When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum
-# is documented as struct, union, or enum with the name of the typedef. So
+# When TYPEDEF_HIDES_STRUCT tag is enabled, a typedef of a struct, union, or
+# enum is documented as struct, union, or enum with the name of the typedef. So
 # typedef struct TypeS {} TypeT, will appear in the documentation as a struct
 # with name TypeT. When disabled the typedef will appear as a member of a file,
-# namespace, or class. And the struct will be named TypeS. This can typically
-# be useful for C code in case the coding convention dictates that all compound
+# namespace, or class. And the struct will be named TypeS. This can typically be
+# useful for C code in case the coding convention dictates that all compound
 # types are typedef'ed and only the typedef is referenced, never the tag name.
+# The default value is: NO.
 
 TYPEDEF_HIDES_STRUCT   = NO
 
-# The SYMBOL_CACHE_SIZE determines the size of the internal cache use to
-# determine which symbols to keep in memory and which to flush to disk.
-# When the cache is full, less often used symbols will be written to disk.
-# For small to medium size projects (<1000 input files) the default value is
-# probably good enough. For larger projects a too small cache size can cause
-# doxygen to be busy swapping symbols to and from disk most of the time
-# causing a significant performance penalty.
-# If the system has enough physical memory increasing the cache will improve the
-# performance by keeping more symbols in memory. Note that the value works on
-# a logarithmic scale so increasing the size by one will roughly double the
-# memory usage. The cache size is given by this formula:
-# 2^(16+SYMBOL_CACHE_SIZE). The valid range is 0..9, the default is 0,
-# corresponding to a cache size of 2^16 = 65536 symbols.
-
-SYMBOL_CACHE_SIZE      = 0
-
-# Similar to the SYMBOL_CACHE_SIZE the size of the symbol lookup cache can be
-# set using LOOKUP_CACHE_SIZE. This cache is used to resolve symbols given
-# their name and scope. Since this can be an expensive process and often the
-# same symbol appear multiple times in the code, doxygen keeps a cache of
-# pre-resolved symbols. If the cache is too small doxygen will become slower.
-# If the cache is too large, memory is wasted. The cache size is given by this
-# formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range is 0..9, the default is 0,
-# corresponding to a cache size of 2^16 = 65536 symbols.
+# The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This
+# cache is used to resolve symbols given their name and scope. Since this can be
+# an expensive process and often the same symbol appears multiple times in the
+# code, doxygen keeps a cache of pre-resolved symbols. If the cache is too small
+# doxygen will become slower. If the cache is too large, memory is wasted. The
+# cache size is given by this formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range
+# is 0..9, the default is 0, corresponding to a cache size of 2^16=65536
+# symbols. At the end of a run doxygen will report the cache usage and suggest
+# the optimal cache size from a speed point of view.
+# Minimum value: 0, maximum value: 9, default value: 0.
 
 LOOKUP_CACHE_SIZE      = 0
 
+# The NUM_PROC_THREADS specifies the number of threads doxygen is allowed to use
+# during processing. When set to 0 doxygen will based this on the number of
+# cores available in the system. You can set it explicitly to a value larger
+# than 0 to get more control over the balance between CPU load and processing
+# speed. At this moment only the input processing can be done using multiple
+# threads. Since this is still an experimental feature the default is set to 1,
+# which effectively disables parallel processing. Please report any issues you
+# encounter. Generating dot graphs in parallel is controlled by the
+# DOT_NUM_THREADS setting.
+# Minimum value: 0, maximum value: 32, default value: 1.
+
+NUM_PROC_THREADS       = 1
+
 #---------------------------------------------------------------------------
 # Build related configuration options
 #---------------------------------------------------------------------------
 
-# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in
-# documentation are documented, even if no documentation was available.
-# Private class members and static file members will be hidden unless
-# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES
+# If the EXTRACT_ALL tag is set to YES, doxygen will assume all entities in
+# documentation are documented, even if no documentation was available. Private
+# class members and static file members will be hidden unless the
+# EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES.
+# Note: This will also disable the warnings about undocumented members that are
+# normally produced when WARNINGS is set to YES.
+# The default value is: NO.
 
 EXTRACT_ALL            = NO
 
-# If the EXTRACT_PRIVATE tag is set to YES all private members of a class
-# will be included in the documentation.
+# If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will
+# be included in the documentation.
+# The default value is: NO.
 
 EXTRACT_PRIVATE        = YES
 
-# If the EXTRACT_PACKAGE tag is set to YES all members with package or internal scope will be included in the documentation.
+# If the EXTRACT_PRIV_VIRTUAL tag is set to YES, documented private virtual
+# methods of a class will be included in the documentation.
+# The default value is: NO.
+
+EXTRACT_PRIV_VIRTUAL   = NO
+
+# If the EXTRACT_PACKAGE tag is set to YES, all members with package or internal
+# scope will be included in the documentation.
+# The default value is: NO.
 
 EXTRACT_PACKAGE        = NO
 
-# If the EXTRACT_STATIC tag is set to YES all static members of a file
-# will be included in the documentation.
+# If the EXTRACT_STATIC tag is set to YES, all static members of a file will be
+# included in the documentation.
+# The default value is: NO.
 
 EXTRACT_STATIC         = YES
 
-# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs)
-# defined locally in source files will be included in the documentation.
-# If set to NO only classes defined in header files are included.
+# If the EXTRACT_LOCAL_CLASSES tag is set to YES, classes (and structs) defined
+# locally in source files will be included in the documentation. If set to NO,
+# only classes defined in header files are included. Does not have any effect
+# for Java sources.
+# The default value is: YES.
 
 EXTRACT_LOCAL_CLASSES  = YES
 
-# This flag is only useful for Objective-C code. When set to YES local
-# methods, which are defined in the implementation section but not in
-# the interface are included in the documentation.
-# If set to NO (the default) only methods in the interface are included.
+# This flag is only useful for Objective-C code. If set to YES, local methods,
+# which are defined in the implementation section but not in the interface are
+# included in the documentation. If set to NO, only methods in the interface are
+# included.
+# The default value is: NO.
 
 EXTRACT_LOCAL_METHODS  = NO
 
 # If this flag is set to YES, the members of anonymous namespaces will be
 # extracted and appear in the documentation as a namespace called
-# 'anonymous_namespace{file}', where file will be replaced with the base
-# name of the file that contains the anonymous namespace. By default
-# anonymous namespaces are hidden.
+# 'anonymous_namespace{file}', where file will be replaced with the base name of
+# the file that contains the anonymous namespace. By default anonymous namespace
+# are hidden.
+# The default value is: NO.
 
 EXTRACT_ANON_NSPACES   = NO
 
-# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all
-# undocumented members of documented classes, files or namespaces.
-# If set to NO (the default) these members will be included in the
-# various overviews, but no documentation section is generated.
-# This option has no effect if EXTRACT_ALL is enabled.
+# If this flag is set to YES, the name of an unnamed parameter in a declaration
+# will be determined by the corresponding definition. By default unnamed
+# parameters remain unnamed in the output.
+# The default value is: YES.
+
+RESOLVE_UNNAMED_PARAMS = YES
+
+# If the HIDE_UNDOC_MEMBERS tag is set to YES, doxygen will hide all
+# undocumented members inside documented classes or files. If set to NO these
+# members will be included in the various overviews, but no documentation
+# section is generated. This option has no effect if EXTRACT_ALL is enabled.
+# The default value is: NO.
 
 HIDE_UNDOC_MEMBERS     = NO
 
-# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all
-# undocumented classes that are normally visible in the class hierarchy.
-# If set to NO (the default) these classes will be included in the various
-# overviews. This option has no effect if EXTRACT_ALL is enabled.
+# If the HIDE_UNDOC_CLASSES tag is set to YES, doxygen will hide all
+# undocumented classes that are normally visible in the class hierarchy. If set
+# to NO, these classes will be included in the various overviews. This option
+# has no effect if EXTRACT_ALL is enabled.
+# The default value is: NO.
 
 HIDE_UNDOC_CLASSES     = NO
 
-# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all
-# friend (class|struct|union) declarations.
-# If set to NO (the default) these declarations will be included in the
+# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, doxygen will hide all friend
+# declarations. If set to NO, these declarations will be included in the
 # documentation.
+# The default value is: NO.
 
 HIDE_FRIEND_COMPOUNDS  = NO
 
-# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any
-# documentation blocks found inside the body of a function.
-# If set to NO (the default) these blocks will be appended to the
-# function's detailed documentation block.
+# If the HIDE_IN_BODY_DOCS tag is set to YES, doxygen will hide any
+# documentation blocks found inside the body of a function. If set to NO, these
+# blocks will be appended to the function's detailed documentation block.
+# The default value is: NO.
 
 HIDE_IN_BODY_DOCS      = NO
 
-# The INTERNAL_DOCS tag determines if documentation
-# that is typed after a \internal command is included. If the tag is set
-# to NO (the default) then the documentation will be excluded.
-# Set it to YES to include the internal documentation.
+# The INTERNAL_DOCS tag determines if documentation that is typed after a
+# \internal command is included. If the tag is set to NO then the documentation
+# will be excluded. Set it to YES to include the internal documentation.
+# The default value is: NO.
 
 INTERNAL_DOCS          = NO
 
-# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate
-# file names in lower-case letters. If set to YES upper-case letters are also
-# allowed. This is useful if you have classes or files whose names only differ
-# in case and if your file system supports case sensitive file names. Windows
-# and Mac users are advised to set this option to NO.
+# With the correct setting of option CASE_SENSE_NAMES doxygen will better be
+# able to match the capabilities of the underlying filesystem. In case the
+# filesystem is case sensitive (i.e. it supports files in the same directory
+# whose names only differ in casing), the option must be set to YES to properly
+# deal with such files in case they appear in the input. For filesystems that
+# are not case sensitive the option should be set to NO to properly deal with
+# output files written for symbols that only differ in casing, such as for two
+# classes, one named CLASS and the other named Class, and to also support
+# references to files without having to specify the exact matching casing. On
+# Windows (including Cygwin) and MacOS, users should typically set this option
+# to NO, whereas on Linux or other Unix flavors it should typically be set to
+# YES.
+# The default value is: system dependent.
 
 CASE_SENSE_NAMES       = YES
 
-# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen
-# will show members with their full class and namespace scopes in the
-# documentation. If set to YES the scope will be hidden.
+# If the HIDE_SCOPE_NAMES tag is set to NO then doxygen will show members with
+# their full class and namespace scopes in the documentation. If set to YES, the
+# scope will be hidden.
+# The default value is: NO.
 
 HIDE_SCOPE_NAMES       = NO
 
-# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen
-# will put a list of the files that are included by a file in the documentation
-# of that file.
+# If the HIDE_COMPOUND_REFERENCE tag is set to NO (default) then doxygen will
+# append additional text to a page's title, such as Class Reference. If set to
+# YES the compound reference will be hidden.
+# The default value is: NO.
+
+HIDE_COMPOUND_REFERENCE= NO
+
+# If the SHOW_HEADERFILE tag is set to YES then the documentation for a class
+# will show which file needs to be included to use the class.
+# The default value is: YES.
+
+SHOW_HEADERFILE        = YES
+
+# If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of
+# the files that are included by a file in the documentation of that file.
+# The default value is: YES.
 
 SHOW_INCLUDE_FILES     = YES
 
-# If the FORCE_LOCAL_INCLUDES tag is set to YES then Doxygen
-# will list include files with double quotes in the documentation
-# rather than with sharp brackets.
+# If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each
+# grouped member an include statement to the documentation, telling the reader
+# which file to include in order to use the member.
+# The default value is: NO.
+
+SHOW_GROUPED_MEMB_INC  = NO
+
+# If the FORCE_LOCAL_INCLUDES tag is set to YES then doxygen will list include
+# files with double quotes in the documentation rather than with sharp brackets.
+# The default value is: NO.
 
 FORCE_LOCAL_INCLUDES   = NO
 
-# If the INLINE_INFO tag is set to YES (the default) then a tag [inline]
-# is inserted in the documentation for inline members.
+# If the INLINE_INFO tag is set to YES then a tag [inline] is inserted in the
+# documentation for inline members.
+# The default value is: YES.
 
 INLINE_INFO            = YES
 
-# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen
-# will sort the (detailed) documentation of file and class members
-# alphabetically by member name. If set to NO the members will appear in
-# declaration order.
+# If the SORT_MEMBER_DOCS tag is set to YES then doxygen will sort the
+# (detailed) documentation of file and class members alphabetically by member
+# name. If set to NO, the members will appear in declaration order.
+# The default value is: YES.
 
 SORT_MEMBER_DOCS       = YES
 
-# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the
-# brief documentation of file, namespace and class members alphabetically
-# by member name. If set to NO (the default) the members will appear in
-# declaration order.
+# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the brief
+# descriptions of file, namespace and class members alphabetically by member
+# name. If set to NO, the members will appear in declaration order. Note that
+# this will also influence the order of the classes in the class list.
+# The default value is: NO.
 
 SORT_BRIEF_DOCS        = NO
 
-# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen
-# will sort the (brief and detailed) documentation of class members so that
-# constructors and destructors are listed first. If set to NO (the default)
-# the constructors will appear in the respective orders defined by
-# SORT_MEMBER_DOCS and SORT_BRIEF_DOCS.
-# This tag will be ignored for brief docs if SORT_BRIEF_DOCS is set to NO
-# and ignored for detailed docs if SORT_MEMBER_DOCS is set to NO.
+# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the
+# (brief and detailed) documentation of class members so that constructors and
+# destructors are listed first. If set to NO the constructors will appear in the
+# respective orders defined by SORT_BRIEF_DOCS and SORT_MEMBER_DOCS.
+# Note: If SORT_BRIEF_DOCS is set to NO this option is ignored for sorting brief
+# member documentation.
+# Note: If SORT_MEMBER_DOCS is set to NO this option is ignored for sorting
+# detailed member documentation.
+# The default value is: NO.
 
 SORT_MEMBERS_CTORS_1ST = NO
 
-# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the
-# hierarchy of group names into alphabetical order. If set to NO (the default)
-# the group names will appear in their defined order.
+# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the hierarchy
+# of group names into alphabetical order. If set to NO the group names will
+# appear in their defined order.
+# The default value is: NO.
 
 SORT_GROUP_NAMES       = NO
 
-# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be
-# sorted by fully-qualified names, including namespaces. If set to
-# NO (the default), the class list will be sorted only by class name,
-# not including the namespace part.
+# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be sorted by
+# fully-qualified names, including namespaces. If set to NO, the class list will
+# be sorted only by class name, not including the namespace part.
 # Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
-# Note: This option applies only to the class list, not to the
-# alphabetical list.
+# Note: This option applies only to the class list, not to the alphabetical
+# list.
+# The default value is: NO.
 
 SORT_BY_SCOPE_NAME     = NO
 
-# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to
-# do proper type resolution of all parameters of a function it will reject a
-# match between the prototype and the implementation of a member function even
-# if there is only one candidate or it is obvious which candidate to choose
-# by doing a simple string match. By disabling STRICT_PROTO_MATCHING doxygen
-# will still accept a match between prototype and implementation in such cases.
+# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to do proper
+# type resolution of all parameters of a function it will reject a match between
+# the prototype and the implementation of a member function even if there is
+# only one candidate or it is obvious which candidate to choose by doing a
+# simple string match. By disabling STRICT_PROTO_MATCHING doxygen will still
+# accept a match between prototype and implementation in such cases.
+# The default value is: NO.
 
 STRICT_PROTO_MATCHING  = NO
 
-# The GENERATE_TODOLIST tag can be used to enable (YES) or
-# disable (NO) the todo list. This list is created by putting \todo
-# commands in the documentation.
+# The GENERATE_TODOLIST tag can be used to enable (YES) or disable (NO) the todo
+# list. This list is created by putting \todo commands in the documentation.
+# The default value is: YES.
 
 GENERATE_TODOLIST      = YES
 
-# The GENERATE_TESTLIST tag can be used to enable (YES) or
-# disable (NO) the test list. This list is created by putting \test
-# commands in the documentation.
+# The GENERATE_TESTLIST tag can be used to enable (YES) or disable (NO) the test
+# list. This list is created by putting \test commands in the documentation.
+# The default value is: YES.
 
 GENERATE_TESTLIST      = YES
 
-# The GENERATE_BUGLIST tag can be used to enable (YES) or
-# disable (NO) the bug list. This list is created by putting \bug
-# commands in the documentation.
+# The GENERATE_BUGLIST tag can be used to enable (YES) or disable (NO) the bug
+# list. This list is created by putting \bug commands in the documentation.
+# The default value is: YES.
 
 GENERATE_BUGLIST       = YES
 
-# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or
-# disable (NO) the deprecated list. This list is created by putting
-# \deprecated commands in the documentation.
+# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or disable (NO)
+# the deprecated list. This list is created by putting \deprecated commands in
+# the documentation.
+# The default value is: YES.
 
 GENERATE_DEPRECATEDLIST= YES
 
-# The ENABLED_SECTIONS tag can be used to enable conditional
-# documentation sections, marked by \if sectionname ... \endif.
+# The ENABLED_SECTIONS tag can be used to enable conditional documentation
+# sections, marked by \if <section_label> ... \endif and \cond <section_label>
+# ... \endcond blocks.
 
 ENABLED_SECTIONS       =
 
-# The MAX_INITIALIZER_LINES tag determines the maximum number of lines
-# the initial value of a variable or macro consists of for it to appear in
-# the documentation. If the initializer consists of more lines than specified
-# here it will be hidden. Use a value of 0 to hide initializers completely.
-# The appearance of the initializer of individual variables and macros in the
-# documentation can be controlled using \showinitializer or \hideinitializer
-# command in the documentation regardless of this setting.
+# The MAX_INITIALIZER_LINES tag determines the maximum number of lines that the
+# initial value of a variable or macro / define can have for it to appear in the
+# documentation. If the initializer consists of more lines than specified here
+# it will be hidden. Use a value of 0 to hide initializers completely. The
+# appearance of the value of individual variables and macros / defines can be
+# controlled using \showinitializer or \hideinitializer command in the
+# documentation regardless of this setting.
+# Minimum value: 0, maximum value: 10000, default value: 30.
 
 MAX_INITIALIZER_LINES  = 30
 
-# Set the SHOW_USED_FILES tag to NO to disable the list of files generated
-# at the bottom of the documentation of classes and structs. If set to YES the
+# Set the SHOW_USED_FILES tag to NO to disable the list of files generated at
+# the bottom of the documentation of classes and structs. If set to YES, the
 # list will mention the files that were used to generate the documentation.
+# The default value is: YES.
 
 SHOW_USED_FILES        = YES
 
-# Set the SHOW_FILES tag to NO to disable the generation of the Files page.
-# This will remove the Files entry from the Quick Index and from the
-# Folder Tree View (if specified). The default is YES.
+# Set the SHOW_FILES tag to NO to disable the generation of the Files page. This
+# will remove the Files entry from the Quick Index and from the Folder Tree View
+# (if specified).
+# The default value is: YES.
 
 SHOW_FILES             = YES
 
-# Set the SHOW_NAMESPACES tag to NO to disable the generation of the
-# Namespaces page.
-# This will remove the Namespaces entry from the Quick Index
-# and from the Folder Tree View (if specified). The default is YES.
+# Set the SHOW_NAMESPACES tag to NO to disable the generation of the Namespaces
+# page. This will remove the Namespaces entry from the Quick Index and from the
+# Folder Tree View (if specified).
+# The default value is: YES.
 
 SHOW_NAMESPACES        = YES
 
 # The FILE_VERSION_FILTER tag can be used to specify a program or script that
 # doxygen should invoke to get the current version for each file (typically from
 # the version control system). Doxygen will invoke the program by executing (via
-# popen()) the command <command> <input-file>, where <command> is the value of
-# the FILE_VERSION_FILTER tag, and <input-file> is the name of an input file
-# provided by doxygen. Whatever the program writes to standard output
-# is used as the file version. See the manual for examples.
+# popen()) the command command input-file, where command is the value of the
+# FILE_VERSION_FILTER tag, and input-file is the name of an input file provided
+# by doxygen. Whatever the program writes to standard output is used as the file
+# version. For an example see the documentation.
 
 FILE_VERSION_FILTER    =
 
 # The LAYOUT_FILE tag can be used to specify a layout file which will be parsed
 # by doxygen. The layout file controls the global structure of the generated
 # output files in an output format independent way. To create the layout file
-# that represents doxygen's defaults, run doxygen with the -l option.
-# You can optionally specify a file name after the option, if omitted
-# DoxygenLayout.xml will be used as the name of the layout file.
+# that represents doxygen's defaults, run doxygen with the -l option. You can
+# optionally specify a file name after the option, if omitted DoxygenLayout.xml
+# will be used as the name of the layout file. See also section "Changing the
+# layout of pages" for information.
+#
+# Note that if you run doxygen from a directory containing a file called
+# DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE
+# tag is left empty.
 
 LAYOUT_FILE            =
 
-# The CITE_BIB_FILES tag can be used to specify one or more bib files
-# containing the references data. This must be a list of .bib files. The
-# .bib extension is automatically appended if omitted. Using this command
-# requires the bibtex tool to be installed. See also
-# http://en.wikipedia.org/wiki/BibTeX for more info. For LaTeX the style
-# of the bibliography can be controlled using LATEX_BIB_STYLE. To use this
-# feature you need bibtex and perl available in the search path.
+# The CITE_BIB_FILES tag can be used to specify one or more bib files containing
+# the reference definitions. This must be a list of .bib files. The .bib
+# extension is automatically appended if omitted. This requires the bibtex tool
+# to be installed. See also https://en.wikipedia.org/wiki/BibTeX for more info.
+# For LaTeX the style of the bibliography can be controlled using
+# LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the
+# search path. See also \cite for info how to create references.
 
 CITE_BIB_FILES         =
 
 #---------------------------------------------------------------------------
-# configuration options related to warning and progress messages
+# Configuration options related to warning and progress messages
 #---------------------------------------------------------------------------
 
-# The QUIET tag can be used to turn on/off the messages that are generated
-# by doxygen. Possible values are YES and NO. If left blank NO is used.
+# The QUIET tag can be used to turn on/off the messages that are generated to
+# standard output by doxygen. If QUIET is set to YES this implies that the
+# messages are off.
+# The default value is: NO.
 
 QUIET                  = NO
 
 # The WARNINGS tag can be used to turn on/off the warning messages that are
-# generated by doxygen. Possible values are YES and NO. If left blank
-# NO is used.
+# generated to standard error (stderr) by doxygen. If WARNINGS is set to YES
+# this implies that the warnings are on.
+#
+# Tip: Turn warnings on while writing the documentation.
+# The default value is: YES.
 
 WARNINGS               = YES
 
-# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings
-# for undocumented members. If EXTRACT_ALL is set to YES then this flag will
-# automatically be disabled.
+# If the WARN_IF_UNDOCUMENTED tag is set to YES then doxygen will generate
+# warnings for undocumented members. If EXTRACT_ALL is set to YES then this flag
+# will automatically be disabled.
+# The default value is: YES.
 
 WARN_IF_UNDOCUMENTED   = YES
 
-# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for
-# potential errors in the documentation, such as not documenting some
-# parameters in a documented function, or documenting parameters that
-# don't exist or using markup commands wrongly.
+# If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for
+# potential errors in the documentation, such as documenting some parameters in
+# a documented function twice, or documenting parameters that don't exist or
+# using markup commands wrongly.
+# The default value is: YES.
 
 WARN_IF_DOC_ERROR      = YES
 
-# The WARN_NO_PARAMDOC option can be enabled to get warnings for
-# functions that are documented, but have no documentation for their parameters
-# or return value. If set to NO (the default) doxygen will only warn about
-# wrong or incomplete parameter documentation, but not about the absence of
-# documentation.
+# If WARN_IF_INCOMPLETE_DOC is set to YES, doxygen will warn about incomplete
+# function parameter documentation. If set to NO, doxygen will accept that some
+# parameters have no documentation without warning.
+# The default value is: YES.
+
+WARN_IF_INCOMPLETE_DOC = YES
+
+# This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that
+# are documented, but have no documentation for their parameters or return
+# value. If set to NO, doxygen will only warn about wrong parameter
+# documentation, but not about the absence of documentation. If EXTRACT_ALL is
+# set to YES then this flag will automatically be disabled. See also
+# WARN_IF_INCOMPLETE_DOC
+# The default value is: NO.
 
 WARN_NO_PARAMDOC       = NO
 
-# The WARN_FORMAT tag determines the format of the warning messages that
-# doxygen can produce. The string should contain the $file, $line, and $text
-# tags, which will be replaced by the file and line number from which the
-# warning originated and the warning text. Optionally the format may contain
-# $version, which will be replaced by the version of the file (if it could
-# be obtained via FILE_VERSION_FILTER)
+# If the WARN_AS_ERROR tag is set to YES then doxygen will immediately stop when
+# a warning is encountered. If the WARN_AS_ERROR tag is set to FAIL_ON_WARNINGS
+# then doxygen will continue running as if WARN_AS_ERROR tag is set to NO, but
+# at the end of the doxygen process doxygen will return with a non-zero status.
+# Possible values are: NO, YES and FAIL_ON_WARNINGS.
+# The default value is: NO.
+
+WARN_AS_ERROR          = NO
+
+# The WARN_FORMAT tag determines the format of the warning messages that doxygen
+# can produce. The string should contain the $file, $line, and $text tags, which
+# will be replaced by the file and line number from which the warning originated
+# and the warning text. Optionally the format may contain $version, which will
+# be replaced by the version of the file (if it could be obtained via
+# FILE_VERSION_FILTER)
+# See also: WARN_LINE_FORMAT
+# The default value is: $file:$line: $text.
 
 WARN_FORMAT            = "$file:$line: $text"
 
-# The WARN_LOGFILE tag can be used to specify a file to which warning
-# and error messages should be written. If left blank the output is written
-# to stderr.
+# In the $text part of the WARN_FORMAT command it is possible that a reference
+# to a more specific place is given. To make it easier to jump to this place
+# (outside of doxygen) the user can define a custom "cut" / "paste" string.
+# Example:
+# WARN_LINE_FORMAT = "'vi $file +$line'"
+# See also: WARN_FORMAT
+# The default value is: at line $line of file $file.
+
+WARN_LINE_FORMAT       = "at line $line of file $file"
+
+# The WARN_LOGFILE tag can be used to specify a file to which warning and error
+# messages should be written. If left blank the output is written to standard
+# error (stderr). In case the file specified cannot be opened for writing the
+# warning and error messages are written to standard error. When as file - is
+# specified the warning and error messages are written to standard output
+# (stdout).
 
 WARN_LOGFILE           =
 
 #---------------------------------------------------------------------------
-# configuration options related to the input files
+# Configuration options related to the input files
 #---------------------------------------------------------------------------
 
-# The INPUT tag can be used to specify the files and/or directories that contain
-# documented source files. You may enter file names like "myfile.cpp" or
-# directories like "/usr/src/myproject". Separate the files or directories
-# with spaces.
+# The INPUT tag is used to specify the files and/or directories that contain
+# documented source files. You may enter file names like myfile.cpp or
+# directories like /usr/src/myproject. Separate the files or directories with
+# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
+# Note: If this tag is empty the current directory is searched.
 
 INPUT                  =
 
 # This tag can be used to specify the character encoding of the source files
-# that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is
-# also the default input encoding. Doxygen uses libiconv (or the iconv built
-# into libc) for the transcoding. See http://www.gnu.org/software/libiconv for
-# the list of possible encodings.
+# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
+# libiconv (or the iconv built into libc) for the transcoding. See the libiconv
+# documentation (see:
+# https://www.gnu.org/software/libiconv/) for the list of possible encodings.
+# The default value is: UTF-8.
 
 INPUT_ENCODING         = UTF-8
 
 # If the value of the INPUT tag contains directories, you can use the
-# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
-# and *.h) to filter out the source-files in the directories. If left
-# blank the following patterns are tested:
-# *.c *.cc *.cxx *.cpp *.c++ *.d *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh
-# *.hxx *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.dox *.py
-# *.f90 *.f *.for *.vhd *.vhdl
+# FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and
+# *.h) to filter out the source-files in the directories.
+#
+# Note that for custom extensions or not directly supported extensions you also
+# need to set EXTENSION_MAPPING for the extension otherwise the files are not
+# read by doxygen.
+#
+# Note the list of default checked file patterns might differ from the list of
+# default file extension mappings.
+#
+# If left blank the following patterns are tested:*.c, *.cc, *.cxx, *.cpp,
+# *.c++, *.java, *.ii, *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h,
+# *.hh, *.hxx, *.hpp, *.h++, *.l, *.cs, *.d, *.php, *.php4, *.php5, *.phtml,
+# *.inc, *.m, *.markdown, *.md, *.mm, *.dox (to be provided as doxygen C
+# comment), *.py, *.pyw, *.f90, *.f95, *.f03, *.f08, *.f18, *.f, *.for, *.vhd,
+# *.vhdl, *.ucf, *.qsf and *.ice.
 
 FILE_PATTERNS          =
 
-# The RECURSIVE tag can be used to turn specify whether or not subdirectories
-# should be searched for input files as well. Possible values are YES and NO.
-# If left blank NO is used.
+# The RECURSIVE tag can be used to specify whether or not subdirectories should
+# be searched for input files as well.
+# The default value is: NO.
 
 RECURSIVE              = NO
 
 # The EXCLUDE tag can be used to specify files and/or directories that should be
 # excluded from the INPUT source files. This way you can easily exclude a
 # subdirectory from a directory tree whose root is specified with the INPUT tag.
+#
 # Note that relative paths are relative to the directory from which doxygen is
 # run.
 
@@ -692,14 +945,16 @@ EXCLUDE                =
 # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
 # directories that are symbolic links (a Unix file system feature) are excluded
 # from the input.
+# The default value is: NO.
 
 EXCLUDE_SYMLINKS       = NO
 
 # If the value of the INPUT tag contains directories, you can use the
 # EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
-# certain files from those directories. Note that the wildcards are matched
-# against the file with absolute path, so to exclude all test directories
-# for example use the pattern */test/*
+# certain files from those directories.
+#
+# Note that the wildcards are matched against the file with absolute path, so to
+# exclude all test directories for example use the pattern */test/*
 
 EXCLUDE_PATTERNS       =
 
@@ -707,756 +962,1254 @@ EXCLUDE_PATTERNS       =
 # (namespaces, classes, functions, etc.) that should be excluded from the
 # output. The symbol name can be a fully qualified name, a word, or if the
 # wildcard * is used, a substring. Examples: ANamespace, AClass,
-# AClass::ANamespace, ANamespace::*Test
+# ANamespace::AClass, ANamespace::*Test
+#
+# Note that the wildcards are matched against the file with absolute path, so to
+# exclude all test directories use the pattern */test/*
 
 EXCLUDE_SYMBOLS        =
 
-# The EXAMPLE_PATH tag can be used to specify one or more files or
-# directories that contain example code fragments that are included (see
-# the \include command).
+# The EXAMPLE_PATH tag can be used to specify one or more files or directories
+# that contain example code fragments that are included (see the \include
+# command).
 
 EXAMPLE_PATH           =
 
 # If the value of the EXAMPLE_PATH tag contains directories, you can use the
-# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
-# and *.h) to filter out the source-files in the directories. If left
-# blank all files are included.
+# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and
+# *.h) to filter out the source-files in the directories. If left blank all
+# files are included.
 
 EXAMPLE_PATTERNS       =
 
 # If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
-# searched for input files to be used with the \include or \dontinclude
-# commands irrespective of the value of the RECURSIVE tag.
-# Possible values are YES and NO. If left blank NO is used.
+# searched for input files to be used with the \include or \dontinclude commands
+# irrespective of the value of the RECURSIVE tag.
+# The default value is: NO.
 
 EXAMPLE_RECURSIVE      = NO
 
-# The IMAGE_PATH tag can be used to specify one or more files or
-# directories that contain image that are included in the documentation (see
-# the \image command).
+# The IMAGE_PATH tag can be used to specify one or more files or directories
+# that contain images that are to be included in the documentation (see the
+# \image command).
 
 IMAGE_PATH             =
 
 # The INPUT_FILTER tag can be used to specify a program that doxygen should
 # invoke to filter for each input file. Doxygen will invoke the filter program
-# by executing (via popen()) the command <filter> <input-file>, where <filter>
-# is the value of the INPUT_FILTER tag, and <input-file> is the name of an
-# input file. Doxygen will then use the output that the filter program writes
-# to standard output.
-# If FILTER_PATTERNS is specified, this tag will be
-# ignored.
+# by executing (via popen()) the command:
+#
+# <filter> <input-file>
+#
+# where <filter> is the value of the INPUT_FILTER tag, and <input-file> is the
+# name of an input file. Doxygen will then use the output that the filter
+# program writes to standard output. If FILTER_PATTERNS is specified, this tag
+# will be ignored.
+#
+# Note that the filter must not add or remove lines; it is applied before the
+# code is scanned, but not when the output code is generated. If lines are added
+# or removed, the anchors will not be placed correctly.
+#
+# Note that for custom extensions or not directly supported extensions you also
+# need to set EXTENSION_MAPPING for the extension otherwise the files are not
+# properly processed by doxygen.
 
 INPUT_FILTER           =
 
 # The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
-# basis.
-# Doxygen will compare the file name with each pattern and apply the
-# filter if there is a match.
-# The filters are a list of the form:
-# pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further
-# info on how filters are used. If FILTER_PATTERNS is empty or if
-# non of the patterns match the file name, INPUT_FILTER is applied.
+# basis. Doxygen will compare the file name with each pattern and apply the
+# filter if there is a match. The filters are a list of the form: pattern=filter
+# (like *.cpp=my_cpp_filter). See INPUT_FILTER for further information on how
+# filters are used. If the FILTER_PATTERNS tag is empty or if none of the
+# patterns match the file name, INPUT_FILTER is applied.
+#
+# Note that for custom extensions or not directly supported extensions you also
+# need to set EXTENSION_MAPPING for the extension otherwise the files are not
+# properly processed by doxygen.
 
 FILTER_PATTERNS        =
 
 # If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
-# INPUT_FILTER) will be used to filter the input files when producing source
-# files to browse (i.e. when SOURCE_BROWSER is set to YES).
+# INPUT_FILTER) will also be used to filter the input files that are used for
+# producing the source files to browse (i.e. when SOURCE_BROWSER is set to YES).
+# The default value is: NO.
 
 FILTER_SOURCE_FILES    = NO
 
 # The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file
-# pattern. A pattern will override the setting for FILTER_PATTERN (if any)
-# and it is also possible to disable source filtering for a specific pattern
-# using *.ext= (so without naming a filter). This option only has effect when
-# FILTER_SOURCE_FILES is enabled.
+# pattern. A pattern will override the setting for FILTER_PATTERN (if any) and
+# it is also possible to disable source filtering for a specific pattern using
+# *.ext= (so without naming a filter).
+# This tag requires that the tag FILTER_SOURCE_FILES is set to YES.
 
 FILTER_SOURCE_PATTERNS =
 
+# If the USE_MDFILE_AS_MAINPAGE tag refers to the name of a markdown file that
+# is part of the input, its contents will be placed on the main page
+# (index.html). This can be useful if you have a project on for instance GitHub
+# and want to reuse the introduction page also for the doxygen output.
+
+USE_MDFILE_AS_MAINPAGE =
+
 #---------------------------------------------------------------------------
-# configuration options related to source browsing
+# Configuration options related to source browsing
 #---------------------------------------------------------------------------
 
-# If the SOURCE_BROWSER tag is set to YES then a list of source files will
-# be generated. Documented entities will be cross-referenced with these sources.
-# Note: To get rid of all source code in the generated output, make sure also
-# VERBATIM_HEADERS is set to NO.
+# If the SOURCE_BROWSER tag is set to YES then a list of source files will be
+# generated. Documented entities will be cross-referenced with these sources.
+#
+# Note: To get rid of all source code in the generated output, make sure that
+# also VERBATIM_HEADERS is set to NO.
+# The default value is: NO.
 
 SOURCE_BROWSER         = NO
 
-# Setting the INLINE_SOURCES tag to YES will include the body
-# of functions and classes directly in the documentation.
+# Setting the INLINE_SOURCES tag to YES will include the body of functions,
+# classes and enums directly into the documentation.
+# The default value is: NO.
 
 INLINE_SOURCES         = NO
 
-# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct
-# doxygen to hide any special comment blocks from generated source code
-# fragments. Normal C, C++ and Fortran comments will always remain visible.
+# Setting the STRIP_CODE_COMMENTS tag to YES will instruct doxygen to hide any
+# special comment blocks from generated source code fragments. Normal C, C++ and
+# Fortran comments will always remain visible.
+# The default value is: YES.
 
 STRIP_CODE_COMMENTS    = YES
 
-# If the REFERENCED_BY_RELATION tag is set to YES
-# then for each documented function all documented
-# functions referencing it will be listed.
+# If the REFERENCED_BY_RELATION tag is set to YES then for each documented
+# entity all documented functions referencing it will be listed.
+# The default value is: NO.
 
 REFERENCED_BY_RELATION = NO
 
-# If the REFERENCES_RELATION tag is set to YES
-# then for each documented function all documented entities
-# called/used by that function will be listed.
+# If the REFERENCES_RELATION tag is set to YES then for each documented function
+# all documented entities called/used by that function will be listed.
+# The default value is: NO.
 
 REFERENCES_RELATION    = NO
 
-# If the REFERENCES_LINK_SOURCE tag is set to YES (the default)
-# and SOURCE_BROWSER tag is set to YES, then the hyperlinks from
-# functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will
-# link to the source code.
-# Otherwise they will link to the documentation.
+# If the REFERENCES_LINK_SOURCE tag is set to YES and SOURCE_BROWSER tag is set
+# to YES then the hyperlinks from functions in REFERENCES_RELATION and
+# REFERENCED_BY_RELATION lists will link to the source code. Otherwise they will
+# link to the documentation.
+# The default value is: YES.
 
 REFERENCES_LINK_SOURCE = YES
 
-# If the USE_HTAGS tag is set to YES then the references to source code
-# will point to the HTML generated by the htags(1) tool instead of doxygen
-# built-in source browser. The htags tool is part of GNU's global source
-# tagging system (see http://www.gnu.org/software/global/global.html). You
-# will need version 4.8.6 or higher.
+# If SOURCE_TOOLTIPS is enabled (the default) then hovering a hyperlink in the
+# source code will show a tooltip with additional information such as prototype,
+# brief description and links to the definition and documentation. Since this
+# will make the HTML file larger and loading of large files a bit slower, you
+# can opt to disable this feature.
+# The default value is: YES.
+# This tag requires that the tag SOURCE_BROWSER is set to YES.
+
+SOURCE_TOOLTIPS        = YES
+
+# If the USE_HTAGS tag is set to YES then the references to source code will
+# point to the HTML generated by the htags(1) tool instead of doxygen built-in
+# source browser. The htags tool is part of GNU's global source tagging system
+# (see https://www.gnu.org/software/global/global.html). You will need version
+# 4.8.6 or higher.
+#
+# To use it do the following:
+# - Install the latest version of global
+# - Enable SOURCE_BROWSER and USE_HTAGS in the configuration file
+# - Make sure the INPUT points to the root of the source tree
+# - Run doxygen as normal
+#
+# Doxygen will invoke htags (and that will in turn invoke gtags), so these
+# tools must be available from the command line (i.e. in the search path).
+#
+# The result: instead of the source browser generated by doxygen, the links to
+# source code will now point to the output of htags.
+# The default value is: NO.
+# This tag requires that the tag SOURCE_BROWSER is set to YES.
 
 USE_HTAGS              = NO
 
-# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen
-# will generate a verbatim copy of the header file for each class for
-# which an include is specified. Set to NO to disable this.
+# If the VERBATIM_HEADERS tag is set the YES then doxygen will generate a
+# verbatim copy of the header file for each class for which an include is
+# specified. Set to NO to disable this.
+# See also: Section \class.
+# The default value is: YES.
 
 VERBATIM_HEADERS       = YES
 
+# If the CLANG_ASSISTED_PARSING tag is set to YES then doxygen will use the
+# clang parser (see:
+# http://clang.llvm.org/) for more accurate parsing at the cost of reduced
+# performance. This can be particularly helpful with template rich C++ code for
+# which doxygen's built-in parser lacks the necessary type information.
+# Note: The availability of this option depends on whether or not doxygen was
+# generated with the -Duse_libclang=ON option for CMake.
+# The default value is: NO.
+
+CLANG_ASSISTED_PARSING = NO
+
+# If the CLANG_ASSISTED_PARSING tag is set to YES and the CLANG_ADD_INC_PATHS
+# tag is set to YES then doxygen will add the directory of each input to the
+# include path.
+# The default value is: YES.
+# This tag requires that the tag CLANG_ASSISTED_PARSING is set to YES.
+
+CLANG_ADD_INC_PATHS    = YES
+
+# If clang assisted parsing is enabled you can provide the compiler with command
+# line options that you would normally use when invoking the compiler. Note that
+# the include paths will already be set by doxygen for the files and directories
+# specified with INPUT and INCLUDE_PATH.
+# This tag requires that the tag CLANG_ASSISTED_PARSING is set to YES.
+
+CLANG_OPTIONS          =
+
+# If clang assisted parsing is enabled you can provide the clang parser with the
+# path to the directory containing a file called compile_commands.json. This
+# file is the compilation database (see:
+# http://clang.llvm.org/docs/HowToSetupToolingForLLVM.html) containing the
+# options used when the source files were built. This is equivalent to
+# specifying the -p option to a clang tool, such as clang-check. These options
+# will then be passed to the parser. Any options specified with CLANG_OPTIONS
+# will be added as well.
+# Note: The availability of this option depends on whether or not doxygen was
+# generated with the -Duse_libclang=ON option for CMake.
+
+CLANG_DATABASE_PATH    =
+
 #---------------------------------------------------------------------------
-# configuration options related to the alphabetical class index
+# Configuration options related to the alphabetical class index
 #---------------------------------------------------------------------------
 
-# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index
-# of all compounds will be generated. Enable this if the project
-# contains a lot of classes, structs, unions or interfaces.
+# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index of all
+# compounds will be generated. Enable this if the project contains a lot of
+# classes, structs, unions or interfaces.
+# The default value is: YES.
 
 ALPHABETICAL_INDEX     = YES
 
-# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then
-# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns
-# in which this list will be split (can be a number in the range [1..20])
-
-COLS_IN_ALPHA_INDEX    = 5
-
-# In case all classes in a project start with a common prefix, all
-# classes will be put under the same header in the alphabetical index.
-# The IGNORE_PREFIX tag can be used to specify one or more prefixes that
-# should be ignored while generating the index headers.
+# In case all classes in a project start with a common prefix, all classes will
+# be put under the same header in the alphabetical index. The IGNORE_PREFIX tag
+# can be used to specify a prefix (or a list of prefixes) that should be ignored
+# while generating the index headers.
+# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
 
 IGNORE_PREFIX          =
 
 #---------------------------------------------------------------------------
-# configuration options related to the HTML output
+# Configuration options related to the HTML output
 #---------------------------------------------------------------------------
 
-# If the GENERATE_HTML tag is set to YES (the default) Doxygen will
-# generate HTML output.
+# If the GENERATE_HTML tag is set to YES, doxygen will generate HTML output
+# The default value is: YES.
 
 GENERATE_HTML          = YES
 
-# The HTML_OUTPUT tag is used to specify where the HTML docs will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
-# put in front of it. If left blank `html' will be used as the default path.
+# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: html.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 HTML_OUTPUT            = html
 
-# The HTML_FILE_EXTENSION tag can be used to specify the file extension for
-# each generated HTML page (for example: .htm,.php,.asp). If it is left blank
-# doxygen will generate files with .html extension.
+# The HTML_FILE_EXTENSION tag can be used to specify the file extension for each
+# generated HTML page (for example: .htm, .php, .asp).
+# The default value is: .html.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 HTML_FILE_EXTENSION    = .html
 
-# The HTML_HEADER tag can be used to specify a personal HTML header for
-# each generated HTML page. If it is left blank doxygen will generate a
-# standard header. Note that when using a custom header you are responsible
-#  for the proper inclusion of any scripts and style sheets that doxygen
-# needs, which is dependent on the configuration options used.
-# It is advised to generate a default header using "doxygen -w html
-# header.html footer.html stylesheet.css YourConfigFile" and then modify
-# that header. Note that the header is subject to change so you typically
-# have to redo this when upgrading to a newer version of doxygen or when
-# changing the value of configuration settings such as GENERATE_TREEVIEW!
+# The HTML_HEADER tag can be used to specify a user-defined HTML header file for
+# each generated HTML page. If the tag is left blank doxygen will generate a
+# standard header.
+#
+# To get valid HTML the header file that includes any scripts and style sheets
+# that doxygen needs, which is dependent on the configuration options used (e.g.
+# the setting GENERATE_TREEVIEW). It is highly recommended to start with a
+# default header using
+# doxygen -w html new_header.html new_footer.html new_stylesheet.css
+# YourConfigFile
+# and then modify the file new_header.html. See also section "Doxygen usage"
+# for information on how to generate the default header that doxygen normally
+# uses.
+# Note: The header is subject to change so you typically have to regenerate the
+# default header when upgrading to a newer version of doxygen. For a description
+# of the possible markers and block names see the documentation.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 HTML_HEADER            =
 
-# The HTML_FOOTER tag can be used to specify a personal HTML footer for
-# each generated HTML page. If it is left blank doxygen will generate a
-# standard footer.
+# The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each
+# generated HTML page. If the tag is left blank doxygen will generate a standard
+# footer. See HTML_HEADER for more information on how to generate a default
+# footer and what special commands can be used inside the footer. See also
+# section "Doxygen usage" for information on how to generate the default footer
+# that doxygen normally uses.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 HTML_FOOTER            =
 
-# The HTML_STYLESHEET tag can be used to specify a user-defined cascading
-# style sheet that is used by each HTML page. It can be used to
-# fine-tune the look of the HTML output. If the tag is left blank doxygen
-# will generate a default style sheet. Note that doxygen will try to copy
-# the style sheet file to the HTML output directory, so don't put your own
-# style sheet in the HTML output directory as well, or it will be erased!
+# The HTML_STYLESHEET tag can be used to specify a user-defined cascading style
+# sheet that is used by each HTML page. It can be used to fine-tune the look of
+# the HTML output. If left blank doxygen will generate a default style sheet.
+# See also section "Doxygen usage" for information on how to generate the style
+# sheet that doxygen normally uses.
+# Note: It is recommended to use HTML_EXTRA_STYLESHEET instead of this tag, as
+# it is more robust and this tag (HTML_STYLESHEET) will in the future become
+# obsolete.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 HTML_STYLESHEET        =
 
+# The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined
+# cascading style sheets that are included after the standard style sheets
+# created by doxygen. Using this option one can overrule certain style aspects.
+# This is preferred over using HTML_STYLESHEET since it does not replace the
+# standard style sheet and is therefore more robust against future updates.
+# Doxygen will copy the style sheet files to the output directory.
+# Note: The order of the extra style sheet files is of importance (e.g. the last
+# style sheet in the list overrules the setting of the previous ones in the
+# list). For an example see the documentation.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_EXTRA_STYLESHEET  =
+
 # The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
 # other source files which should be copied to the HTML output directory. Note
 # that these files will be copied to the base HTML output directory. Use the
-# $relpath$ marker in the HTML_HEADER and/or HTML_FOOTER files to load these
-# files. In the HTML_STYLESHEET file, use the file name only. Also note that
-# the files will be copied as-is; there are no commands or markers available.
+# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these
+# files. In the HTML_STYLESHEET file, use the file name only. Also note that the
+# files will be copied as-is; there are no commands or markers available.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 HTML_EXTRA_FILES       =
 
-# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output.
-# Doxygen will adjust the colors in the style sheet and background images
-# according to this color. Hue is specified as an angle on a colorwheel,
-# see http://en.wikipedia.org/wiki/Hue for more information.
-# For instance the value 0 represents red, 60 is yellow, 120 is green,
-# 180 is cyan, 240 is blue, 300 purple, and 360 is red again.
-# The allowed range is 0 to 359.
+# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen
+# will adjust the colors in the style sheet and background images according to
+# this color. Hue is specified as an angle on a color-wheel, see
+# https://en.wikipedia.org/wiki/Hue for more information. For instance the value
+# 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300
+# purple, and 360 is red again.
+# Minimum value: 0, maximum value: 359, default value: 220.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 HTML_COLORSTYLE_HUE    = 220
 
-# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of
-# the colors in the HTML output. For a value of 0 the output will use
-# grayscales only. A value of 255 will produce the most vivid colors.
+# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors
+# in the HTML output. For a value of 0 the output will use gray-scales only. A
+# value of 255 will produce the most vivid colors.
+# Minimum value: 0, maximum value: 255, default value: 100.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 HTML_COLORSTYLE_SAT    = 100
 
-# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to
-# the luminance component of the colors in the HTML output. Values below
-# 100 gradually make the output lighter, whereas values above 100 make
-# the output darker. The value divided by 100 is the actual gamma applied,
-# so 80 represents a gamma of 0.8, The value 220 represents a gamma of 2.2,
-# and 100 does not change the gamma.
+# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to the
+# luminance component of the colors in the HTML output. Values below 100
+# gradually make the output lighter, whereas values above 100 make the output
+# darker. The value divided by 100 is the actual gamma applied, so 80 represents
+# a gamma of 0.8, The value 220 represents a gamma of 2.2, and 100 does not
+# change the gamma.
+# Minimum value: 40, maximum value: 240, default value: 80.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 HTML_COLORSTYLE_GAMMA  = 80
 
 # If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
-# page will contain the date and time when the page was generated. Setting
-# this to NO can help when comparing the output of multiple runs.
+# page will contain the date and time when the page was generated. Setting this
+# to YES can help to show when doxygen was last run and thus if the
+# documentation is up to date.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 HTML_TIMESTAMP         = YES
 
+# If the HTML_DYNAMIC_MENUS tag is set to YES then the generated HTML
+# documentation will contain a main index with vertical navigation menus that
+# are dynamically created via JavaScript. If disabled, the navigation index will
+# consists of multiple levels of tabs that are statically embedded in every HTML
+# page. Disable this option to support browsers that do not have JavaScript,
+# like the Qt help browser.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_DYNAMIC_MENUS     = YES
+
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 HTML_DYNAMIC_SECTIONS  = NO
 
-# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
-# entries shown in the various tree structured indices initially; the user
-# can expand and collapse entries dynamically later on. Doxygen will expand
-# the tree to such a level that at most the specified number of entries are
-# visible (unless a fully collapsed tree already exceeds this amount).
-# So setting the number of entries 1 will produce a full collapsed tree by
-# default. 0 is a special value representing an infinite number of entries
-# and will result in a full expanded tree by default.
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries
+# shown in the various tree structured indices initially; the user can expand
+# and collapse entries dynamically later on. Doxygen will expand the tree to
+# such a level that at most the specified number of entries are visible (unless
+# a fully collapsed tree already exceeds this amount). So setting the number of
+# entries 1 will produce a full collapsed tree by default. 0 is a special value
+# representing an infinite number of entries and will result in a full expanded
+# tree by default.
+# Minimum value: 0, maximum value: 9999, default value: 100.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 HTML_INDEX_NUM_ENTRIES = 100
 
-# If the GENERATE_DOCSET tag is set to YES, additional index files
-# will be generated that can be used as input for Apple's Xcode 3
-# integrated development environment, introduced with OSX 10.5 (Leopard).
-# To create a documentation set, doxygen will generate a Makefile in the
-# HTML output directory. Running make will produce the docset in that
-# directory and running "make install" will install the docset in
-# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find
-# it at startup.
-# See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html
-# for more information.
+# If the GENERATE_DOCSET tag is set to YES, additional index files will be
+# generated that can be used as input for Apple's Xcode 3 integrated development
+# environment (see:
+# https://developer.apple.com/xcode/), introduced with OSX 10.5 (Leopard). To
+# create a documentation set, doxygen will generate a Makefile in the HTML
+# output directory. Running make will produce the docset in that directory and
+# running make install will install the docset in
+# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find it at
+# startup. See https://developer.apple.com/library/archive/featuredarticles/Doxy
+# genXcode/_index.html for more information.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 GENERATE_DOCSET        = NO
 
-# When GENERATE_DOCSET tag is set to YES, this tag determines the name of the
-# feed. A documentation feed provides an umbrella under which multiple
-# documentation sets from a single provider (such as a company or product suite)
-# can be grouped.
+# This tag determines the name of the docset feed. A documentation feed provides
+# an umbrella under which multiple documentation sets from a single provider
+# (such as a company or product suite) can be grouped.
+# The default value is: Doxygen generated docs.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
 
 DOCSET_FEEDNAME        = "Doxygen generated docs"
 
-# When GENERATE_DOCSET tag is set to YES, this tag specifies a string that
-# should uniquely identify the documentation set bundle. This should be a
-# reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen
-# will append .docset to the name.
+# This tag determines the URL of the docset feed. A documentation feed provides
+# an umbrella under which multiple documentation sets from a single provider
+# (such as a company or product suite) can be grouped.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_FEEDURL         =
+
+# This tag specifies a string that should uniquely identify the documentation
+# set bundle. This should be a reverse domain-name style string, e.g.
+# com.mycompany.MyDocSet. Doxygen will append .docset to the name.
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
 
 DOCSET_BUNDLE_ID       = org.doxygen.Project
 
-# When GENERATE_PUBLISHER_ID tag specifies a string that should uniquely identify
+# The DOCSET_PUBLISHER_ID tag specifies a string that should uniquely identify
 # the documentation publisher. This should be a reverse domain-name style
 # string, e.g. com.mycompany.MyDocSet.documentation.
+# The default value is: org.doxygen.Publisher.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
 
 DOCSET_PUBLISHER_ID    = org.doxygen.Publisher
 
-# The GENERATE_PUBLISHER_NAME tag identifies the documentation publisher.
+# The DOCSET_PUBLISHER_NAME tag identifies the documentation publisher.
+# The default value is: Publisher.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
 
 DOCSET_PUBLISHER_NAME  = Publisher
 
-# If the GENERATE_HTMLHELP tag is set to YES, additional index files
-# will be generated that can be used as input for tools like the
-# Microsoft HTML help workshop to generate a compiled HTML help file (.chm)
-# of the generated HTML documentation.
+# If the GENERATE_HTMLHELP tag is set to YES then doxygen generates three
+# additional HTML index files: index.hhp, index.hhc, and index.hhk. The
+# index.hhp is a project file that can be read by Microsoft's HTML Help Workshop
+# on Windows. In the beginning of 2021 Microsoft took the original page, with
+# a.o. the download links, offline the HTML help workshop was already many years
+# in maintenance mode). You can download the HTML help workshop from the web
+# archives at Installation executable (see:
+# http://web.archive.org/web/20160201063255/http://download.microsoft.com/downlo
+# ad/0/A/9/0A939EF6-E31C-430F-A3DF-DFAE7960D564/htmlhelp.exe).
+#
+# The HTML Help Workshop contains a compiler that can convert all HTML output
+# generated by doxygen into a single compiled HTML file (.chm). Compiled HTML
+# files are now used as the Windows 98 help format, and will replace the old
+# Windows help format (.hlp) on all Windows platforms in the future. Compressed
+# HTML files also contain an index, a table of contents, and you can search for
+# words in the documentation. The HTML workshop also contains a viewer for
+# compressed HTML files.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 GENERATE_HTMLHELP      = NO
 
-# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can
-# be used to specify the file name of the resulting .chm file. You
-# can add a path in front of the file if the result should not be
+# The CHM_FILE tag can be used to specify the file name of the resulting .chm
+# file. You can add a path in front of the file if the result should not be
 # written to the html output directory.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
 
 CHM_FILE               =
 
-# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can
-# be used to specify the location (absolute path including file name) of
-# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run
-# the HTML help compiler on the generated index.hhp.
+# The HHC_LOCATION tag can be used to specify the location (absolute path
+# including file name) of the HTML help compiler (hhc.exe). If non-empty,
+# doxygen will try to run the HTML help compiler on the generated index.hhp.
+# The file has to be specified with full path.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
 
 HHC_LOCATION           =
 
-# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag
-# controls if a separate .chi index file is generated (YES) or that
-# it should be included in the master .chm file (NO).
+# The GENERATE_CHI flag controls if a separate .chi index file is generated
+# (YES) or that it should be included in the main .chm file (NO).
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
 
 GENERATE_CHI           = NO
 
-# If the GENERATE_HTMLHELP tag is set to YES, the CHM_INDEX_ENCODING
-# is used to encode HtmlHelp index (hhk), content (hhc) and project file
-# content.
+# The CHM_INDEX_ENCODING is used to encode HtmlHelp index (hhk), content (hhc)
+# and project file content.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
 
 CHM_INDEX_ENCODING     =
 
-# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag
-# controls whether a binary table of contents is generated (YES) or a
-# normal table of contents (NO) in the .chm file.
+# The BINARY_TOC flag controls whether a binary table of contents is generated
+# (YES) or a normal table of contents (NO) in the .chm file. Furthermore it
+# enables the Previous and Next buttons.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
 
 BINARY_TOC             = NO
 
-# The TOC_EXPAND flag can be set to YES to add extra items for group members
-# to the contents of the HTML help documentation and to the tree view.
+# The TOC_EXPAND flag can be set to YES to add extra items for group members to
+# the table of contents of the HTML help documentation and to the tree view.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
 
 TOC_EXPAND             = NO
 
 # If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and
-# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated
-# that can be used as input for Qt's qhelpgenerator to generate a
-# Qt Compressed Help (.qch) of the generated HTML documentation.
+# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated that
+# can be used as input for Qt's qhelpgenerator to generate a Qt Compressed Help
+# (.qch) of the generated HTML documentation.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 GENERATE_QHP           = NO
 
-# If the QHG_LOCATION tag is specified, the QCH_FILE tag can
-# be used to specify the file name of the resulting .qch file.
-# The path specified is relative to the HTML output folder.
+# If the QHG_LOCATION tag is specified, the QCH_FILE tag can be used to specify
+# the file name of the resulting .qch file. The path specified is relative to
+# the HTML output folder.
+# This tag requires that the tag GENERATE_QHP is set to YES.
 
 QCH_FILE               =
 
-# The QHP_NAMESPACE tag specifies the namespace to use when generating
-# Qt Help Project output. For more information please see
-# http://doc.trolltech.com/qthelpproject.html#namespace
+# The QHP_NAMESPACE tag specifies the namespace to use when generating Qt Help
+# Project output. For more information please see Qt Help Project / Namespace
+# (see:
+# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#namespace).
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_QHP is set to YES.
 
 QHP_NAMESPACE          = org.doxygen.Project
 
-# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating
-# Qt Help Project output. For more information please see
-# http://doc.trolltech.com/qthelpproject.html#virtual-folders
+# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating Qt
+# Help Project output. For more information please see Qt Help Project / Virtual
+# Folders (see:
+# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#virtual-folders).
+# The default value is: doc.
+# This tag requires that the tag GENERATE_QHP is set to YES.
 
 QHP_VIRTUAL_FOLDER     = doc
 
-# If QHP_CUST_FILTER_NAME is set, it specifies the name of a custom filter to
-# add. For more information please see
-# http://doc.trolltech.com/qthelpproject.html#custom-filters
+# If the QHP_CUST_FILTER_NAME tag is set, it specifies the name of a custom
+# filter to add. For more information please see Qt Help Project / Custom
+# Filters (see:
+# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#custom-filters).
+# This tag requires that the tag GENERATE_QHP is set to YES.
 
 QHP_CUST_FILTER_NAME   =
 
-# The QHP_CUST_FILT_ATTRS tag specifies the list of the attributes of the
-# custom filter to add. For more information please see
-# <a href="http://doc.trolltech.com/qthelpproject.html#custom-filters">
-# Qt Help Project / Custom Filters</a>.
+# The QHP_CUST_FILTER_ATTRS tag specifies the list of the attributes of the
+# custom filter to add. For more information please see Qt Help Project / Custom
+# Filters (see:
+# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#custom-filters).
+# This tag requires that the tag GENERATE_QHP is set to YES.
 
 QHP_CUST_FILTER_ATTRS  =
 
 # The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this
-# project's
-# filter section matches.
-# <a href="http://doc.trolltech.com/qthelpproject.html#filter-attributes">
-# Qt Help Project / Filter Attributes</a>.
+# project's filter section matches. Qt Help Project / Filter Attributes (see:
+# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#filter-attributes).
+# This tag requires that the tag GENERATE_QHP is set to YES.
 
 QHP_SECT_FILTER_ATTRS  =
 
-# If the GENERATE_QHP tag is set to YES, the QHG_LOCATION tag can
-# be used to specify the location of Qt's qhelpgenerator.
-# If non-empty doxygen will try to run qhelpgenerator on the generated
-# .qhp file.
+# The QHG_LOCATION tag can be used to specify the location (absolute path
+# including file name) of Qt's qhelpgenerator. If non-empty doxygen will try to
+# run qhelpgenerator on the generated .qhp file.
+# This tag requires that the tag GENERATE_QHP is set to YES.
 
 QHG_LOCATION           =
 
-# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files
-#  will be generated, which together with the HTML files, form an Eclipse help
-# plugin. To install this plugin and make it available under the help contents
-# menu in Eclipse, the contents of the directory containing the HTML and XML
-# files needs to be copied into the plugins directory of eclipse. The name of
-# the directory within the plugins directory should be the same as
-# the ECLIPSE_DOC_ID value. After copying Eclipse needs to be restarted before
-# the help appears.
+# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files will be
+# generated, together with the HTML files, they form an Eclipse help plugin. To
+# install this plugin and make it available under the help contents menu in
+# Eclipse, the contents of the directory containing the HTML and XML files needs
+# to be copied into the plugins directory of eclipse. The name of the directory
+# within the plugins directory should be the same as the ECLIPSE_DOC_ID value.
+# After copying Eclipse needs to be restarted before the help appears.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 GENERATE_ECLIPSEHELP   = NO
 
-# A unique identifier for the eclipse help plugin. When installing the plugin
-# the directory name containing the HTML and XML files should also have
-# this name.
+# A unique identifier for the Eclipse help plugin. When installing the plugin
+# the directory name containing the HTML and XML files should also have this
+# name. Each documentation set should have its own identifier.
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_ECLIPSEHELP is set to YES.
 
 ECLIPSE_DOC_ID         = org.doxygen.Project
 
-# The DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs)
-# at top of each HTML page. The value NO (the default) enables the index and
-# the value YES disables it. Since the tabs have the same information as the
-# navigation tree you can set this option to NO if you already set
-# GENERATE_TREEVIEW to YES.
+# If you want full control over the layout of the generated HTML pages it might
+# be necessary to disable the index and replace it with your own. The
+# DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) at top
+# of each HTML page. A value of NO enables the index and the value YES disables
+# it. Since the tabs in the index contain the same information as the navigation
+# tree, you can set this option to YES if you also set GENERATE_TREEVIEW to YES.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 DISABLE_INDEX          = NO
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
-# structure should be generated to display hierarchical information.
-# If the tag value is set to YES, a side panel will be generated
-# containing a tree-like index structure (just like the one that
-# is generated for HTML Help). For this to work a browser that supports
-# JavaScript, DHTML, CSS and frames is required (i.e. any modern browser).
-# Windows users are probably better off using the HTML help feature.
-# Since the tree basically has the same information as the tab index you
-# could consider to set DISABLE_INDEX to NO when enabling this option.
+# structure should be generated to display hierarchical information. If the tag
+# value is set to YES, a side panel will be generated containing a tree-like
+# index structure (just like the one that is generated for HTML Help). For this
+# to work a browser that supports JavaScript, DHTML, CSS and frames is required
+# (i.e. any modern browser). Windows users are probably better off using the
+# HTML help feature. Via custom style sheets (see HTML_EXTRA_STYLESHEET) one can
+# further fine tune the look of the index (see "Fine-tuning the output"). As an
+# example, the default style sheet generated by doxygen has an example that
+# shows how to put an image at the root of the tree instead of the PROJECT_NAME.
+# Since the tree basically has the same information as the tab index, you could
+# consider setting DISABLE_INDEX to YES when enabling this option.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 GENERATE_TREEVIEW      = NO
 
-# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values
-# (range [0,1..20]) that doxygen will group on one line in the generated HTML
-# documentation. Note that a value of 0 will completely suppress the enum
-# values from appearing in the overview section.
+# When both GENERATE_TREEVIEW and DISABLE_INDEX are set to YES, then the
+# FULL_SIDEBAR option determines if the side bar is limited to only the treeview
+# area (value NO) or if it should extend to the full height of the window (value
+# YES). Setting this to YES gives a layout similar to
+# https://docs.readthedocs.io with more room for contents, but less room for the
+# project logo, title, and description. If either GENERATE_TREEVIEW or
+# DISABLE_INDEX is set to NO, this option has no effect.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+FULL_SIDEBAR           = NO
+
+# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that
+# doxygen will group on one line in the generated HTML documentation.
+#
+# Note that a value of 0 will completely suppress the enum values from appearing
+# in the overview section.
+# Minimum value: 0, maximum value: 20, default value: 4.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 ENUM_VALUES_PER_LINE   = 4
 
-# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
-# used to set the initial width (in pixels) of the frame in which the tree
-# is shown.
+# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be used
+# to set the initial width (in pixels) of the frame in which the tree is shown.
+# Minimum value: 0, maximum value: 1500, default value: 250.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 TREEVIEW_WIDTH         = 250
 
-# When the EXT_LINKS_IN_WINDOW option is set to YES doxygen will open
-# links to external symbols imported via tag files in a separate window.
+# If the EXT_LINKS_IN_WINDOW option is set to YES, doxygen will open links to
+# external symbols imported via tag files in a separate window.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 EXT_LINKS_IN_WINDOW    = NO
 
-# Use this tag to change the font size of Latex formulas included
-# as images in the HTML documentation. The default is 10. Note that
-# when you change the font size after a successful doxygen run you need
-# to manually remove any form_*.png images from the HTML output directory
-# to force them to be regenerated.
+# If the OBFUSCATE_EMAILS tag is set to YES, doxygen will obfuscate email
+# addresses.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+OBFUSCATE_EMAILS       = YES
+
+# If the HTML_FORMULA_FORMAT option is set to svg, doxygen will use the pdf2svg
+# tool (see https://github.com/dawbarton/pdf2svg) or inkscape (see
+# https://inkscape.org) to generate formulas as SVG images instead of PNGs for
+# the HTML output. These images will generally look nicer at scaled resolutions.
+# Possible values are: png (the default) and svg (looks nicer but requires the
+# pdf2svg or inkscape tool).
+# The default value is: png.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_FORMULA_FORMAT    = png
+
+# Use this tag to change the font size of LaTeX formulas included as images in
+# the HTML documentation. When you change the font size after a successful
+# doxygen run you need to manually remove any form_*.png images from the HTML
+# output directory to force them to be regenerated.
+# Minimum value: 8, maximum value: 50, default value: 10.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 FORMULA_FONTSIZE       = 10
 
-# Use the FORMULA_TRANPARENT tag to determine whether or not the images
-# generated for formulas are transparent PNGs. Transparent PNGs are
-# not supported properly for IE 6.0, but are supported on all modern browsers.
-# Note that when changing this option you need to delete any form_*.png files
-# in the HTML output before the changes have effect.
+# Use the FORMULA_TRANSPARENT tag to determine whether or not the images
+# generated for formulas are transparent PNGs. Transparent PNGs are not
+# supported properly for IE 6.0, but are supported on all modern browsers.
+#
+# Note that when changing this option you need to delete any form_*.png files in
+# the HTML output directory before the changes have effect.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 FORMULA_TRANSPARENT    = YES
 
-# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax
-# (see http://www.mathjax.org) which uses client side Javascript for the
-# rendering instead of using prerendered bitmaps. Use this if you do not
-# have LaTeX installed or if you want to formulas look prettier in the HTML
-# output. When enabled you may also need to install MathJax separately and
-# configure the path to it using the MATHJAX_RELPATH option.
+# The FORMULA_MACROFILE can contain LaTeX \newcommand and \renewcommand commands
+# to create new LaTeX commands to be used in formulas as building blocks. See
+# the section "Including formulas" for details.
+
+FORMULA_MACROFILE      =
+
+# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax (see
+# https://www.mathjax.org) which uses client side JavaScript for the rendering
+# instead of using pre-rendered bitmaps. Use this if you do not have LaTeX
+# installed or if you want to formulas look prettier in the HTML output. When
+# enabled you may also need to install MathJax separately and configure the path
+# to it using the MATHJAX_RELPATH option.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 USE_MATHJAX            = NO
 
-# When MathJax is enabled you need to specify the location relative to the
-# HTML output directory using the MATHJAX_RELPATH option. The destination
-# directory should contain the MathJax.js script. For instance, if the mathjax
-# directory is located at the same level as the HTML output directory, then
-# MATHJAX_RELPATH should be ../mathjax. The default value points to
-# the MathJax Content Delivery Network so you can quickly see the result without
-# installing MathJax.
-# However, it is strongly recommended to install a local
-# copy of MathJax from http://www.mathjax.org before deployment.
+# With MATHJAX_VERSION it is possible to specify the MathJax version to be used.
+# Note that the different versions of MathJax have different requirements with
+# regards to the different settings, so it is possible that also other MathJax
+# settings have to be changed when switching between the different MathJax
+# versions.
+# Possible values are: MathJax_2 and MathJax_3.
+# The default value is: MathJax_2.
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_VERSION        = MathJax_2
+
+# When MathJax is enabled you can set the default output format to be used for
+# the MathJax output. For more details about the output format see MathJax
+# version 2 (see:
+# http://docs.mathjax.org/en/v2.7-latest/output.html) and MathJax version 3
+# (see:
+# http://docs.mathjax.org/en/latest/web/components/output.html).
+# Possible values are: HTML-CSS (which is slower, but has the best
+# compatibility. This is the name for Mathjax version 2, for MathJax version 3
+# this will be translated into chtml), NativeMML (i.e. MathML. Only supported
+# for NathJax 2. For MathJax version 3 chtml will be used instead.), chtml (This
+# is the name for Mathjax version 3, for MathJax version 2 this will be
+# translated into HTML-CSS) and SVG.
+# The default value is: HTML-CSS.
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_FORMAT         = HTML-CSS
+
+# When MathJax is enabled you need to specify the location relative to the HTML
+# output directory using the MATHJAX_RELPATH option. The destination directory
+# should contain the MathJax.js script. For instance, if the mathjax directory
+# is located at the same level as the HTML output directory, then
+# MATHJAX_RELPATH should be ../mathjax. The default value points to the MathJax
+# Content Delivery Network so you can quickly see the result without installing
+# MathJax. However, it is strongly recommended to install a local copy of
+# MathJax from https://www.mathjax.org before deployment. The default value is:
+# - in case of MathJax version 2: https://cdn.jsdelivr.net/npm/mathjax@2
+# - in case of MathJax version 3: https://cdn.jsdelivr.net/npm/mathjax@3
+# This tag requires that the tag USE_MATHJAX is set to YES.
 
 MATHJAX_RELPATH        = http://www.mathjax.org/mathjax
 
-# The MATHJAX_EXTENSIONS tag can be used to specify one or MathJax extension
-# names that should be enabled during MathJax rendering.
+# The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax
+# extension names that should be enabled during MathJax rendering. For example
+# for MathJax version 2 (see
+# https://docs.mathjax.org/en/v2.7-latest/tex.html#tex-and-latex-extensions):
+# MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols
+# For example for MathJax version 3 (see
+# http://docs.mathjax.org/en/latest/input/tex/extensions/index.html):
+# MATHJAX_EXTENSIONS = ams
+# This tag requires that the tag USE_MATHJAX is set to YES.
 
 MATHJAX_EXTENSIONS     =
 
-# When the SEARCHENGINE tag is enabled doxygen will generate a search box
-# for the HTML output. The underlying search engine uses javascript
-# and DHTML and should work on any modern browser. Note that when using
-# HTML help (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets
-# (GENERATE_DOCSET) there is already a search function so this one should
-# typically be disabled. For large projects the javascript based search engine
-# can be slow, then enabling SERVER_BASED_SEARCH may provide a better solution.
+# The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces
+# of code that will be used on startup of the MathJax code. See the MathJax site
+# (see:
+# http://docs.mathjax.org/en/v2.7-latest/output.html) for more details. For an
+# example see the documentation.
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_CODEFILE       =
+
+# When the SEARCHENGINE tag is enabled doxygen will generate a search box for
+# the HTML output. The underlying search engine uses javascript and DHTML and
+# should work on any modern browser. Note that when using HTML help
+# (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets (GENERATE_DOCSET)
+# there is already a search function so this one should typically be disabled.
+# For large projects the javascript based search engine can be slow, then
+# enabling SERVER_BASED_SEARCH may provide a better solution. It is possible to
+# search using the keyboard; to jump to the search box use <access key> + S
+# (what the <access key> is depends on the OS and browser, but it is typically
+# <CTRL>, <ALT>/<option>, or both). Inside the search box use the <cursor down
+# key> to jump into the search results window, the results can be navigated
+# using the <cursor keys>. Press <Enter> to select an item or <escape> to cancel
+# the search. The filter options can be selected when the cursor is inside the
+# search box by pressing <Shift>+<cursor down>. Also here use the <cursor keys>
+# to select a filter and <Enter> or <escape> to activate or cancel the filter
+# option.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 SEARCHENGINE           = YES
 
 # When the SERVER_BASED_SEARCH tag is enabled the search engine will be
-# implemented using a PHP enabled web server instead of at the web client
-# using Javascript. Doxygen will generate the search PHP script and index
-# file to put on the web server. The advantage of the server
-# based approach is that it scales better to large projects and allows
-# full text search. The disadvantages are that it is more difficult to setup
-# and does not have live searching capabilities.
+# implemented using a web server instead of a web client using JavaScript. There
+# are two flavors of web server based searching depending on the EXTERNAL_SEARCH
+# setting. When disabled, doxygen will generate a PHP script for searching and
+# an index file used by the script. When EXTERNAL_SEARCH is enabled the indexing
+# and searching needs to be provided by external tools. See the section
+# "External Indexing and Searching" for details.
+# The default value is: NO.
+# This tag requires that the tag SEARCHENGINE is set to YES.
 
 SERVER_BASED_SEARCH    = NO
 
+# When EXTERNAL_SEARCH tag is enabled doxygen will no longer generate the PHP
+# script for searching. Instead the search results are written to an XML file
+# which needs to be processed by an external indexer. Doxygen will invoke an
+# external search engine pointed to by the SEARCHENGINE_URL option to obtain the
+# search results.
+#
+# Doxygen ships with an example indexer (doxyindexer) and search engine
+# (doxysearch.cgi) which are based on the open source search engine library
+# Xapian (see:
+# https://xapian.org/).
+#
+# See the section "External Indexing and Searching" for details.
+# The default value is: NO.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+EXTERNAL_SEARCH        = NO
+
+# The SEARCHENGINE_URL should point to a search engine hosted by a web server
+# which will return the search results when EXTERNAL_SEARCH is enabled.
+#
+# Doxygen ships with an example indexer (doxyindexer) and search engine
+# (doxysearch.cgi) which are based on the open source search engine library
+# Xapian (see:
+# https://xapian.org/). See the section "External Indexing and Searching" for
+# details.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+SEARCHENGINE_URL       =
+
+# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the unindexed
+# search data is written to a file for indexing by an external tool. With the
+# SEARCHDATA_FILE tag the name of this file can be specified.
+# The default file is: searchdata.xml.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+SEARCHDATA_FILE        = searchdata.xml
+
+# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the
+# EXTERNAL_SEARCH_ID tag can be used as an identifier for the project. This is
+# useful in combination with EXTRA_SEARCH_MAPPINGS to search through multiple
+# projects and redirect the results back to the right project.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+EXTERNAL_SEARCH_ID     =
+
+# The EXTRA_SEARCH_MAPPINGS tag can be used to enable searching through doxygen
+# projects other than the one defined by this configuration file, but that are
+# all added to the same external search index. Each project needs to have a
+# unique id set via EXTERNAL_SEARCH_ID. The search mapping then maps the id of
+# to a relative location where the documentation can be found. The format is:
+# EXTRA_SEARCH_MAPPINGS = tagname1=loc1 tagname2=loc2 ...
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+EXTRA_SEARCH_MAPPINGS  =
+
 #---------------------------------------------------------------------------
-# configuration options related to the LaTeX output
+# Configuration options related to the LaTeX output
 #---------------------------------------------------------------------------
 
-# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will
-# generate Latex output.
+# If the GENERATE_LATEX tag is set to YES, doxygen will generate LaTeX output.
+# The default value is: YES.
 
 GENERATE_LATEX         = YES
 
-# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
-# put in front of it. If left blank `latex' will be used as the default path.
+# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: latex.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
 
 LATEX_OUTPUT           = latex
 
 # The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
-# invoked. If left blank `latex' will be used as the default command name.
-# Note that when enabling USE_PDFLATEX this option is only used for
-# generating bitmaps for formulas in the HTML output, but not in the
-# Makefile that is written to the output directory.
+# invoked.
+#
+# Note that when not enabling USE_PDFLATEX the default is latex when enabling
+# USE_PDFLATEX the default is pdflatex and when in the later case latex is
+# chosen this is overwritten by pdflatex. For specific output languages the
+# default can have been set differently, this depends on the implementation of
+# the output language.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
 
 LATEX_CMD_NAME         = latex
 
-# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to
-# generate index for LaTeX. If left blank `makeindex' will be used as the
-# default command name.
+# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to generate
+# index for LaTeX.
+# Note: This tag is used in the Makefile / make.bat.
+# See also: LATEX_MAKEINDEX_CMD for the part in the generated output file
+# (.tex).
+# The default file is: makeindex.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
 
 MAKEINDEX_CMD_NAME     = makeindex
 
-# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact
-# LaTeX documents. This may be useful for small projects and may help to
-# save some trees in general.
+# The LATEX_MAKEINDEX_CMD tag can be used to specify the command name to
+# generate index for LaTeX. In case there is no backslash (\) as first character
+# it will be automatically added in the LaTeX code.
+# Note: This tag is used in the generated output file (.tex).
+# See also: MAKEINDEX_CMD_NAME for the part in the Makefile / make.bat.
+# The default value is: makeindex.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_MAKEINDEX_CMD    = makeindex
+
+# If the COMPACT_LATEX tag is set to YES, doxygen generates more compact LaTeX
+# documents. This may be useful for small projects and may help to save some
+# trees in general.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
 
 COMPACT_LATEX          = NO
 
-# The PAPER_TYPE tag can be used to set the paper type that is used
-# by the printer. Possible values are: a4, letter, legal and
-# executive. If left blank a4wide will be used.
+# The PAPER_TYPE tag can be used to set the paper type that is used by the
+# printer.
+# Possible values are: a4 (210 x 297 mm), letter (8.5 x 11 inches), legal (8.5 x
+# 14 inches) and executive (7.25 x 10.5 inches).
+# The default value is: a4.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
 
 PAPER_TYPE             = a4
 
-# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX
-# packages that should be included in the LaTeX output.
+# The EXTRA_PACKAGES tag can be used to specify one or more LaTeX package names
+# that should be included in the LaTeX output. The package can be specified just
+# by its name or with the correct syntax as to be used with the LaTeX
+# \usepackage command. To get the times font for instance you can specify :
+# EXTRA_PACKAGES=times or EXTRA_PACKAGES={times}
+# To use the option intlimits with the amsmath package you can specify:
+# EXTRA_PACKAGES=[intlimits]{amsmath}
+# If left blank no extra packages will be included.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
 
 EXTRA_PACKAGES         =
 
-# The LATEX_HEADER tag can be used to specify a personal LaTeX header for
-# the generated latex document. The header should contain everything until
-# the first chapter. If it is left blank doxygen will generate a
-# standard header. Notice: only use this tag if you know what you are doing!
+# The LATEX_HEADER tag can be used to specify a user-defined LaTeX header for
+# the generated LaTeX document. The header should contain everything until the
+# first chapter. If it is left blank doxygen will generate a standard header. It
+# is highly recommended to start with a default header using
+# doxygen -w latex new_header.tex new_footer.tex new_stylesheet.sty
+# and then modify the file new_header.tex. See also section "Doxygen usage" for
+# information on how to generate the default header that doxygen normally uses.
+#
+# Note: Only use a user-defined header if you know what you are doing!
+# Note: The header is subject to change so you typically have to regenerate the
+# default header when upgrading to a newer version of doxygen. The following
+# commands have a special meaning inside the header (and footer): For a
+# description of the possible markers and block names see the documentation.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
 
 LATEX_HEADER           =
 
-# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for
-# the generated latex document. The footer should contain everything after
-# the last chapter. If it is left blank doxygen will generate a
-# standard footer. Notice: only use this tag if you know what you are doing!
+# The LATEX_FOOTER tag can be used to specify a user-defined LaTeX footer for
+# the generated LaTeX document. The footer should contain everything after the
+# last chapter. If it is left blank doxygen will generate a standard footer. See
+# LATEX_HEADER for more information on how to generate a default footer and what
+# special commands can be used inside the footer. See also section "Doxygen
+# usage" for information on how to generate the default footer that doxygen
+# normally uses. Note: Only use a user-defined footer if you know what you are
+# doing!
+# This tag requires that the tag GENERATE_LATEX is set to YES.
 
 LATEX_FOOTER           =
 
-# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated
-# is prepared for conversion to pdf (using ps2pdf). The pdf file will
-# contain links (just like the HTML output) instead of page references
-# This makes the output suitable for online browsing using a pdf viewer.
+# The LATEX_EXTRA_STYLESHEET tag can be used to specify additional user-defined
+# LaTeX style sheets that are included after the standard style sheets created
+# by doxygen. Using this option one can overrule certain style aspects. Doxygen
+# will copy the style sheet files to the output directory.
+# Note: The order of the extra style sheet files is of importance (e.g. the last
+# style sheet in the list overrules the setting of the previous ones in the
+# list).
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_EXTRA_STYLESHEET =
+
+# The LATEX_EXTRA_FILES tag can be used to specify one or more extra images or
+# other source files which should be copied to the LATEX_OUTPUT output
+# directory. Note that the files will be copied as-is; there are no commands or
+# markers available.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_EXTRA_FILES      =
+
+# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated is
+# prepared for conversion to PDF (using ps2pdf or pdflatex). The PDF file will
+# contain links (just like the HTML output) instead of page references. This
+# makes the output suitable for online browsing using a PDF viewer.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
 
 PDF_HYPERLINKS         = YES
 
-# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of
-# plain latex in the generated Makefile. Set this option to YES to get a
-# higher quality PDF documentation.
+# If the USE_PDFLATEX tag is set to YES, doxygen will use the engine as
+# specified with LATEX_CMD_NAME to generate the PDF file directly from the LaTeX
+# files. Set this option to YES, to get a higher quality PDF documentation.
+#
+# See also section LATEX_CMD_NAME for selecting the engine.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
 
 USE_PDFLATEX           = YES
 
-# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode.
-# command to the generated LaTeX files. This will instruct LaTeX to keep
-# running if errors occur, instead of asking the user for help.
-# This option is also used when generating formulas in HTML.
+# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \batchmode
+# command to the generated LaTeX files. This will instruct LaTeX to keep running
+# if errors occur, instead of asking the user for help.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
 
 LATEX_BATCHMODE        = NO
 
-# If LATEX_HIDE_INDICES is set to YES then doxygen will not
-# include the index chapters (such as File Index, Compound Index, etc.)
-# in the output.
+# If the LATEX_HIDE_INDICES tag is set to YES then doxygen will not include the
+# index chapters (such as File Index, Compound Index, etc.) in the output.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
 
 LATEX_HIDE_INDICES     = NO
 
-# If LATEX_SOURCE_CODE is set to YES then doxygen will include
-# source code with syntax highlighting in the LaTeX output.
-# Note that which sources are shown also depends on other settings
-# such as SOURCE_BROWSER.
-
-LATEX_SOURCE_CODE      = NO
-
 # The LATEX_BIB_STYLE tag can be used to specify the style to use for the
-# bibliography, e.g. plainnat, or ieeetr. The default style is "plain". See
-# http://en.wikipedia.org/wiki/BibTeX for more info.
+# bibliography, e.g. plainnat, or ieeetr. See
+# https://en.wikipedia.org/wiki/BibTeX and \cite for more info.
+# The default value is: plain.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
 
 LATEX_BIB_STYLE        = plain
 
+# If the LATEX_TIMESTAMP tag is set to YES then the footer of each generated
+# page will contain the date and time when the page was generated. Setting this
+# to NO can help when comparing the output of multiple runs.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_TIMESTAMP        = NO
+
+# The LATEX_EMOJI_DIRECTORY tag is used to specify the (relative or absolute)
+# path from which the emoji images will be read. If a relative path is entered,
+# it will be relative to the LATEX_OUTPUT directory. If left blank the
+# LATEX_OUTPUT directory will be used.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_EMOJI_DIRECTORY  =
+
 #---------------------------------------------------------------------------
-# configuration options related to the RTF output
+# Configuration options related to the RTF output
 #---------------------------------------------------------------------------
 
-# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output
-# The RTF output is optimized for Word 97 and may not look very pretty with
-# other RTF readers or editors.
+# If the GENERATE_RTF tag is set to YES, doxygen will generate RTF output. The
+# RTF output is optimized for Word 97 and may not look too pretty with other RTF
+# readers/editors.
+# The default value is: NO.
 
 GENERATE_RTF           = NO
 
-# The RTF_OUTPUT tag is used to specify where the RTF docs will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
-# put in front of it. If left blank `rtf' will be used as the default path.
+# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: rtf.
+# This tag requires that the tag GENERATE_RTF is set to YES.
 
 RTF_OUTPUT             = rtf
 
-# If the COMPACT_RTF tag is set to YES Doxygen generates more compact
-# RTF documents. This may be useful for small projects and may help to
-# save some trees in general.
+# If the COMPACT_RTF tag is set to YES, doxygen generates more compact RTF
+# documents. This may be useful for small projects and may help to save some
+# trees in general.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_RTF is set to YES.
 
 COMPACT_RTF            = NO
 
-# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated
-# will contain hyperlink fields. The RTF file will
-# contain links (just like the HTML output) instead of page references.
-# This makes the output suitable for online browsing using WORD or other
-# programs which support those fields.
-# Note: wordpad (write) and others do not support links.
+# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated will
+# contain hyperlink fields. The RTF file will contain links (just like the HTML
+# output) instead of page references. This makes the output suitable for online
+# browsing using Word or some other Word compatible readers that support those
+# fields.
+#
+# Note: WordPad (write) and others do not support links.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_RTF is set to YES.
 
 RTF_HYPERLINKS         = NO
 
-# Load style sheet definitions from file. Syntax is similar to doxygen's
-# config file, i.e. a series of assignments. You only have to provide
+# Load stylesheet definitions from file. Syntax is similar to doxygen's
+# configuration file, i.e. a series of assignments. You only have to provide
 # replacements, missing definitions are set to their default value.
+#
+# See also section "Doxygen usage" for information on how to generate the
+# default style sheet that doxygen normally uses.
+# This tag requires that the tag GENERATE_RTF is set to YES.
 
 RTF_STYLESHEET_FILE    =
 
-# Set optional variables used in the generation of an rtf document.
-# Syntax is similar to doxygen's config file.
+# Set optional variables used in the generation of an RTF document. Syntax is
+# similar to doxygen's configuration file. A template extensions file can be
+# generated using doxygen -e rtf extensionFile.
+# This tag requires that the tag GENERATE_RTF is set to YES.
 
 RTF_EXTENSIONS_FILE    =
 
 #---------------------------------------------------------------------------
-# configuration options related to the man page output
+# Configuration options related to the man page output
 #---------------------------------------------------------------------------
 
-# If the GENERATE_MAN tag is set to YES (the default) Doxygen will
-# generate man pages
+# If the GENERATE_MAN tag is set to YES, doxygen will generate man pages for
+# classes and files.
+# The default value is: NO.
 
 GENERATE_MAN           = NO
 
-# The MAN_OUTPUT tag is used to specify where the man pages will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
-# put in front of it. If left blank `man' will be used as the default path.
+# The MAN_OUTPUT tag is used to specify where the man pages will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it. A directory man3 will be created inside the directory specified by
+# MAN_OUTPUT.
+# The default directory is: man.
+# This tag requires that the tag GENERATE_MAN is set to YES.
 
 MAN_OUTPUT             = man
 
-# The MAN_EXTENSION tag determines the extension that is added to
-# the generated man pages (default is the subroutine's section .3)
+# The MAN_EXTENSION tag determines the extension that is added to the generated
+# man pages. In case the manual section does not start with a number, the number
+# 3 is prepended. The dot (.) at the beginning of the MAN_EXTENSION tag is
+# optional.
+# The default value is: .3.
+# This tag requires that the tag GENERATE_MAN is set to YES.
 
 MAN_EXTENSION          = .3
 
-# If the MAN_LINKS tag is set to YES and Doxygen generates man output,
-# then it will generate one additional man file for each entity
-# documented in the real man page(s). These additional files
-# only source the real man page, but without them the man command
-# would be unable to find the correct page. The default is NO.
+# The MAN_SUBDIR tag determines the name of the directory created within
+# MAN_OUTPUT in which the man pages are placed. If defaults to man followed by
+# MAN_EXTENSION with the initial . removed.
+# This tag requires that the tag GENERATE_MAN is set to YES.
+
+MAN_SUBDIR             =
+
+# If the MAN_LINKS tag is set to YES and doxygen generates man output, then it
+# will generate one additional man file for each entity documented in the real
+# man page(s). These additional files only source the real man page, but without
+# them the man command would be unable to find the correct page.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_MAN is set to YES.
 
 MAN_LINKS              = NO
 
 #---------------------------------------------------------------------------
-# configuration options related to the XML output
+# Configuration options related to the XML output
 #---------------------------------------------------------------------------
 
-# If the GENERATE_XML tag is set to YES Doxygen will
-# generate an XML file that captures the structure of
-# the code including all documentation.
+# If the GENERATE_XML tag is set to YES, doxygen will generate an XML file that
+# captures the structure of the code including all documentation.
+# The default value is: NO.
 
 GENERATE_XML           = NO
 
-# The XML_OUTPUT tag is used to specify where the XML pages will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
-# put in front of it. If left blank `xml' will be used as the default path.
+# The XML_OUTPUT tag is used to specify where the XML pages will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: xml.
+# This tag requires that the tag GENERATE_XML is set to YES.
 
 XML_OUTPUT             = xml
 
-# The XML_SCHEMA tag can be used to specify an XML schema,
-# which can be used by a validating XML parser to check the
-# syntax of the XML files.
+# If the XML_PROGRAMLISTING tag is set to YES, doxygen will dump the program
+# listings (including syntax highlighting and cross-referencing information) to
+# the XML output. Note that enabling this will significantly increase the size
+# of the XML output.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_XML is set to YES.
 
-XML_SCHEMA             =
+XML_PROGRAMLISTING     = YES
 
-# The XML_DTD tag can be used to specify an XML DTD,
-# which can be used by a validating XML parser to check the
-# syntax of the XML files.
+# If the XML_NS_MEMB_FILE_SCOPE tag is set to YES, doxygen will include
+# namespace members in file scope as well, matching the HTML output.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_XML is set to YES.
 
-XML_DTD                =
+XML_NS_MEMB_FILE_SCOPE = NO
 
-# If the XML_PROGRAMLISTING tag is set to YES Doxygen will
-# dump the program listings (including syntax highlighting
-# and cross-referencing information) to the XML output. Note that
-# enabling this will significantly increase the size of the XML output.
+#---------------------------------------------------------------------------
+# Configuration options related to the DOCBOOK output
+#---------------------------------------------------------------------------
 
-XML_PROGRAMLISTING     = YES
+# If the GENERATE_DOCBOOK tag is set to YES, doxygen will generate Docbook files
+# that can be used to generate PDF.
+# The default value is: NO.
+
+GENERATE_DOCBOOK       = NO
+
+# The DOCBOOK_OUTPUT tag is used to specify where the Docbook pages will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be put in
+# front of it.
+# The default directory is: docbook.
+# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
+
+DOCBOOK_OUTPUT         = docbook
 
 #---------------------------------------------------------------------------
-# configuration options for the AutoGen Definitions output
+# Configuration options for the AutoGen Definitions output
 #---------------------------------------------------------------------------
 
-# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will
-# generate an AutoGen Definitions (see autogen.sf.net) file
-# that captures the structure of the code including all
-# documentation. Note that this feature is still experimental
-# and incomplete at the moment.
+# If the GENERATE_AUTOGEN_DEF tag is set to YES, doxygen will generate an
+# AutoGen Definitions (see http://autogen.sourceforge.net/) file that captures
+# the structure of the code including all documentation. Note that this feature
+# is still experimental and incomplete at the moment.
+# The default value is: NO.
 
 GENERATE_AUTOGEN_DEF   = NO
 
 #---------------------------------------------------------------------------
-# configuration options related to the Perl module output
+# Configuration options related to the Perl module output
 #---------------------------------------------------------------------------
 
-# If the GENERATE_PERLMOD tag is set to YES Doxygen will
-# generate a Perl module file that captures the structure of
-# the code including all documentation. Note that this
-# feature is still experimental and incomplete at the
-# moment.
+# If the GENERATE_PERLMOD tag is set to YES, doxygen will generate a Perl module
+# file that captures the structure of the code including all documentation.
+#
+# Note that this feature is still experimental and incomplete at the moment.
+# The default value is: NO.
 
 GENERATE_PERLMOD       = NO
 
-# If the PERLMOD_LATEX tag is set to YES Doxygen will generate
-# the necessary Makefile rules, Perl scripts and LaTeX code to be able
-# to generate PDF and DVI output from the Perl module output.
+# If the PERLMOD_LATEX tag is set to YES, doxygen will generate the necessary
+# Makefile rules, Perl scripts and LaTeX code to be able to generate PDF and DVI
+# output from the Perl module output.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_PERLMOD is set to YES.
 
 PERLMOD_LATEX          = NO
 
-# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be
-# nicely formatted so it can be parsed by a human reader.
-# This is useful
-# if you want to understand what is going on.
-# On the other hand, if this
-# tag is set to NO the size of the Perl module output will be much smaller
-# and Perl will parse it just the same.
+# If the PERLMOD_PRETTY tag is set to YES, the Perl module output will be nicely
+# formatted so it can be parsed by a human reader. This is useful if you want to
+# understand what is going on. On the other hand, if this tag is set to NO, the
+# size of the Perl module output will be much smaller and Perl will parse it
+# just the same.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_PERLMOD is set to YES.
 
 PERLMOD_PRETTY         = YES
 
-# The names of the make variables in the generated doxyrules.make file
-# are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX.
-# This is useful so different doxyrules.make files included by the same
-# Makefile don't overwrite each other's variables.
+# The names of the make variables in the generated doxyrules.make file are
+# prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. This is useful
+# so different doxyrules.make files included by the same Makefile don't
+# overwrite each other's variables.
+# This tag requires that the tag GENERATE_PERLMOD is set to YES.
 
 PERLMOD_MAKEVAR_PREFIX =
 
@@ -1464,332 +2217,465 @@ PERLMOD_MAKEVAR_PREFIX =
 # Configuration options related to the preprocessor
 #---------------------------------------------------------------------------
 
-# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will
-# evaluate all C-preprocessor directives found in the sources and include
-# files.
+# If the ENABLE_PREPROCESSING tag is set to YES, doxygen will evaluate all
+# C-preprocessor directives found in the sources and include files.
+# The default value is: YES.
 
 ENABLE_PREPROCESSING   = YES
 
-# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro
-# names in the source code. If set to NO (the default) only conditional
-# compilation will be performed. Macro expansion can be done in a controlled
-# way by setting EXPAND_ONLY_PREDEF to YES.
+# If the MACRO_EXPANSION tag is set to YES, doxygen will expand all macro names
+# in the source code. If set to NO, only conditional compilation will be
+# performed. Macro expansion can be done in a controlled way by setting
+# EXPAND_ONLY_PREDEF to YES.
+# The default value is: NO.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
 MACRO_EXPANSION        = NO
 
-# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES
-# then the macro expansion is limited to the macros specified with the
-# PREDEFINED and EXPAND_AS_DEFINED tags.
+# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES then
+# the macro expansion is limited to the macros specified with the PREDEFINED and
+# EXPAND_AS_DEFINED tags.
+# The default value is: NO.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
 EXPAND_ONLY_PREDEF     = NO
 
-# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files
-# pointed to by INCLUDE_PATH will be searched when a #include is found.
+# If the SEARCH_INCLUDES tag is set to YES, the include files in the
+# INCLUDE_PATH will be searched if a #include is found.
+# The default value is: YES.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
 SEARCH_INCLUDES        = YES
 
 # The INCLUDE_PATH tag can be used to specify one or more directories that
-# contain include files that are not input files but should be processed by
-# the preprocessor.
+# contain include files that are not input files but should be processed by the
+# preprocessor. Note that the INCLUDE_PATH is not recursive, so the setting of
+# RECURSIVE has no effect here.
+# This tag requires that the tag SEARCH_INCLUDES is set to YES.
 
 INCLUDE_PATH           =
 
 # You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
 # patterns (like *.h and *.hpp) to filter out the header-files in the
-# directories. If left blank, the patterns specified with FILE_PATTERNS will
-# be used.
+# directories. If left blank, the patterns specified with FILE_PATTERNS will be
+# used.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
 INCLUDE_FILE_PATTERNS  =
 
-# The PREDEFINED tag can be used to specify one or more macro names that
-# are defined before the preprocessor is started (similar to the -D option of
-# gcc). The argument of the tag is a list of macros of the form: name
-# or name=definition (no spaces). If the definition and the = are
-# omitted =1 is assumed. To prevent a macro definition from being
-# undefined via #undef or recursively expanded use the := operator
-# instead of the = operator.
+# The PREDEFINED tag can be used to specify one or more macro names that are
+# defined before the preprocessor is started (similar to the -D option of e.g.
+# gcc). The argument of the tag is a list of macros of the form: name or
+# name=definition (no spaces). If the definition and the "=" are omitted, "=1"
+# is assumed. To prevent a macro definition from being undefined via #undef or
+# recursively expanded use the := operator instead of the = operator.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
 PREDEFINED             = BINTRAJ \
                          MPI \
                          HASGZ \
                          HASBZ2
 
-# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then
-# this tag can be used to specify a list of macro names that should be expanded.
-# The macro definition that is found in the sources will be used.
-# Use the PREDEFINED tag if you want to use a different macro definition that
-# overrules the definition found in the source code.
+# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then this
+# tag can be used to specify a list of macro names that should be expanded. The
+# macro definition that is found in the sources will be used. Use the PREDEFINED
+# tag if you want to use a different macro definition that overrules the
+# definition found in the source code.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
 EXPAND_AS_DEFINED      =
 
-# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then
-# doxygen's preprocessor will remove all references to function-like macros
-# that are alone on a line, have an all uppercase name, and do not end with a
-# semicolon, because these will confuse the parser if not removed.
+# If the SKIP_FUNCTION_MACROS tag is set to YES then doxygen's preprocessor will
+# remove all references to function-like macros that are alone on a line, have
+# an all uppercase name, and do not end with a semicolon. Such function macros
+# are typically used for boiler-plate code, and will confuse the parser if not
+# removed.
+# The default value is: YES.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
 SKIP_FUNCTION_MACROS   = YES
 
 #---------------------------------------------------------------------------
-# Configuration::additions related to external references
+# Configuration options related to external references
 #---------------------------------------------------------------------------
 
-# The TAGFILES option can be used to specify one or more tagfiles. For each
-# tag file the location of the external documentation should be added. The
-# format of a tag file without this location is as follows:
-#
+# The TAGFILES tag can be used to specify one or more tag files. For each tag
+# file the location of the external documentation should be added. The format of
+# a tag file without this location is as follows:
 # TAGFILES = file1 file2 ...
 # Adding location for the tag files is done as follows:
-#
 # TAGFILES = file1=loc1 "file2 = loc2" ...
-# where "loc1" and "loc2" can be relative or absolute paths
-# or URLs. Note that each tag file must have a unique name (where the name does
-# NOT include the path). If a tag file is not located in the directory in which
-# doxygen is run, you must also specify the path to the tagfile here.
+# where loc1 and loc2 can be relative or absolute paths or URLs. See the
+# section "Linking to external documentation" for more information about the use
+# of tag files.
+# Note: Each tag file must have a unique name (where the name does NOT include
+# the path). If a tag file is not located in the directory in which doxygen is
+# run, you must also specify the path to the tagfile here.
 
 TAGFILES               =
 
-# When a file name is specified after GENERATE_TAGFILE, doxygen will create
-# a tag file that is based on the input files it reads.
+# When a file name is specified after GENERATE_TAGFILE, doxygen will create a
+# tag file that is based on the input files it reads. See section "Linking to
+# external documentation" for more information about the usage of tag files.
 
 GENERATE_TAGFILE       =
 
-# If the ALLEXTERNALS tag is set to YES all external classes will be listed
-# in the class index. If set to NO only the inherited external classes
-# will be listed.
+# If the ALLEXTERNALS tag is set to YES, all external class will be listed in
+# the class index. If set to NO, only the inherited external classes will be
+# listed.
+# The default value is: NO.
 
 ALLEXTERNALS           = NO
 
-# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed
-# in the modules index. If set to NO, only the current project's groups will
-# be listed.
+# If the EXTERNAL_GROUPS tag is set to YES, all external groups will be listed
+# in the modules index. If set to NO, only the current project's groups will be
+# listed.
+# The default value is: YES.
 
 EXTERNAL_GROUPS        = YES
 
-# The PERL_PATH should be the absolute path and name of the perl script
-# interpreter (i.e. the result of `which perl').
+# If the EXTERNAL_PAGES tag is set to YES, all external pages will be listed in
+# the related pages index. If set to NO, only the current project's pages will
+# be listed.
+# The default value is: YES.
 
-PERL_PATH              = /usr/bin/perl
+EXTERNAL_PAGES         = YES
 
 #---------------------------------------------------------------------------
 # Configuration options related to the dot tool
 #---------------------------------------------------------------------------
 
-# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will
-# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base
-# or super classes. Setting the tag to NO turns the diagrams off. Note that
-# this option also works with HAVE_DOT disabled, but it is recommended to
-# install and use dot, since it yields more powerful graphs.
-
-CLASS_DIAGRAMS         = YES
+# You can include diagrams made with dia in doxygen documentation. Doxygen will
+# then run dia to produce the diagram and insert it in the documentation. The
+# DIA_PATH tag allows you to specify the directory where the dia binary resides.
+# If left empty dia is assumed to be found in the default search path.
 
-# You can define message sequence charts within doxygen comments using the \msc
-# command. Doxygen will then run the mscgen tool (see
-# http://www.mcternan.me.uk/mscgen/) to produce the chart and insert it in the
-# documentation. The MSCGEN_PATH tag allows you to specify the directory where
-# the mscgen tool resides. If left empty the tool is assumed to be found in the
-# default search path.
+DIA_PATH               =
 
-MSCGEN_PATH            =
-
-# If set to YES, the inheritance and collaboration graphs will hide
-# inheritance and usage relations if the target is undocumented
-# or is not a class.
+# If set to YES the inheritance and collaboration graphs will hide inheritance
+# and usage relations if the target is undocumented or is not a class.
+# The default value is: YES.
 
 HIDE_UNDOC_RELATIONS   = YES
 
 # If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is
-# available from the path. This tool is part of Graphviz, a graph visualization
-# toolkit from AT&T and Lucent Bell Labs. The other options in this section
-# have no effect if this option is set to NO (the default)
+# available from the path. This tool is part of Graphviz (see:
+# http://www.graphviz.org/), a graph visualization toolkit from AT&T and Lucent
+# Bell Labs. The other options in this section have no effect if this option is
+# set to NO
+# The default value is: YES.
 
 HAVE_DOT               = NO
 
-# The DOT_NUM_THREADS specifies the number of dot invocations doxygen is
-# allowed to run in parallel. When set to 0 (the default) doxygen will
-# base this on the number of processors available in the system. You can set it
-# explicitly to a value larger than 0 to get control over the balance
-# between CPU load and processing speed.
+# The DOT_NUM_THREADS specifies the number of dot invocations doxygen is allowed
+# to run in parallel. When set to 0 doxygen will base this on the number of
+# processors available in the system. You can set it explicitly to a value
+# larger than 0 to get control over the balance between CPU load and processing
+# speed.
+# Minimum value: 0, maximum value: 32, default value: 0.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 DOT_NUM_THREADS        = 0
 
-# By default doxygen will use the Helvetica font for all dot files that
-# doxygen generates. When you want a differently looking font you can specify
-# the font name using DOT_FONTNAME. You need to make sure dot is able to find
-# the font, which can be done by putting it in a standard location or by setting
-# the DOTFONTPATH environment variable or by setting DOT_FONTPATH to the
-# directory containing the font.
+# When you want a differently looking font in the dot files that doxygen
+# generates you can specify the font name using DOT_FONTNAME. You need to make
+# sure dot is able to find the font, which can be done by putting it in a
+# standard location or by setting the DOTFONTPATH environment variable or by
+# setting DOT_FONTPATH to the directory containing the font.
+# The default value is: Helvetica.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 DOT_FONTNAME           = Helvetica
 
-# The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs.
-# The default size is 10pt.
+# The DOT_FONTSIZE tag can be used to set the size (in points) of the font of
+# dot graphs.
+# Minimum value: 4, maximum value: 24, default value: 10.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 DOT_FONTSIZE           = 10
 
-# By default doxygen will tell dot to use the Helvetica font.
-# If you specify a different font using DOT_FONTNAME you can use DOT_FONTPATH to
-# set the path where dot can find it.
+# By default doxygen will tell dot to use the default font as specified with
+# DOT_FONTNAME. If you specify a different font using DOT_FONTNAME you can set
+# the path where dot can find it using this tag.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 DOT_FONTPATH           =
 
-# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen
-# will generate a graph for each documented class showing the direct and
-# indirect inheritance relations. Setting this tag to YES will force the
-# CLASS_DIAGRAMS tag to NO.
+# If the CLASS_GRAPH tag is set to YES (or GRAPH) then doxygen will generate a
+# graph for each documented class showing the direct and indirect inheritance
+# relations. In case HAVE_DOT is set as well dot will be used to draw the graph,
+# otherwise the built-in generator will be used. If the CLASS_GRAPH tag is set
+# to TEXT the direct and indirect inheritance relations will be shown as texts /
+# links.
+# Possible values are: NO, YES, TEXT and GRAPH.
+# The default value is: YES.
 
 CLASS_GRAPH            = YES
 
-# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen
-# will generate a graph for each documented class showing the direct and
-# indirect implementation dependencies (inheritance, containment, and
-# class references variables) of the class with other documented classes.
+# If the COLLABORATION_GRAPH tag is set to YES then doxygen will generate a
+# graph for each documented class showing the direct and indirect implementation
+# dependencies (inheritance, containment, and class references variables) of the
+# class with other documented classes.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 COLLABORATION_GRAPH    = YES
 
-# If the GROUP_GRAPHS and HAVE_DOT tags are set to YES then doxygen
-# will generate a graph for groups, showing the direct groups dependencies
+# If the GROUP_GRAPHS tag is set to YES then doxygen will generate a graph for
+# groups, showing the direct groups dependencies. See also the chapter Grouping
+# in the manual.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 GROUP_GRAPHS           = YES
 
-# If the UML_LOOK tag is set to YES doxygen will generate inheritance and
+# If the UML_LOOK tag is set to YES, doxygen will generate inheritance and
 # collaboration diagrams in a style similar to the OMG's Unified Modeling
 # Language.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 UML_LOOK               = NO
 
-# If the UML_LOOK tag is enabled, the fields and methods are shown inside
-# the class node. If there are many fields or methods and many nodes the
-# graph may become too big to be useful. The UML_LIMIT_NUM_FIELDS
-# threshold limits the number of items for each type to make the size more
-# managable. Set this to 0 for no limit. Note that the threshold may be
-# exceeded by 50% before the limit is enforced.
+# If the UML_LOOK tag is enabled, the fields and methods are shown inside the
+# class node. If there are many fields or methods and many nodes the graph may
+# become too big to be useful. The UML_LIMIT_NUM_FIELDS threshold limits the
+# number of items for each type to make the size more manageable. Set this to 0
+# for no limit. Note that the threshold may be exceeded by 50% before the limit
+# is enforced. So when you set the threshold to 10, up to 15 fields may appear,
+# but if the number exceeds 15, the total amount of fields shown is limited to
+# 10.
+# Minimum value: 0, maximum value: 100, default value: 10.
+# This tag requires that the tag UML_LOOK is set to YES.
 
 UML_LIMIT_NUM_FIELDS   = 10
 
-# If set to YES, the inheritance and collaboration graphs will show the
-# relations between templates and their instances.
+# If the DOT_UML_DETAILS tag is set to NO, doxygen will show attributes and
+# methods without types and arguments in the UML graphs. If the DOT_UML_DETAILS
+# tag is set to YES, doxygen will add type and arguments for attributes and
+# methods in the UML graphs. If the DOT_UML_DETAILS tag is set to NONE, doxygen
+# will not generate fields with class member information in the UML graphs. The
+# class diagrams will look similar to the default class diagrams but using UML
+# notation for the relationships.
+# Possible values are: NO, YES and NONE.
+# The default value is: NO.
+# This tag requires that the tag UML_LOOK is set to YES.
+
+DOT_UML_DETAILS        = NO
+
+# The DOT_WRAP_THRESHOLD tag can be used to set the maximum number of characters
+# to display on a single line. If the actual line length exceeds this threshold
+# significantly it will wrapped across multiple lines. Some heuristics are apply
+# to avoid ugly line breaks.
+# Minimum value: 0, maximum value: 1000, default value: 17.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_WRAP_THRESHOLD     = 17
+
+# If the TEMPLATE_RELATIONS tag is set to YES then the inheritance and
+# collaboration graphs will show the relations between templates and their
+# instances.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 TEMPLATE_RELATIONS     = NO
 
-# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT
-# tags are set to YES then doxygen will generate a graph for each documented
-# file showing the direct and indirect include dependencies of the file with
-# other documented files.
+# If the INCLUDE_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are set to
+# YES then doxygen will generate a graph for each documented file showing the
+# direct and indirect include dependencies of the file with other documented
+# files.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 INCLUDE_GRAPH          = YES
 
-# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and
-# HAVE_DOT tags are set to YES then doxygen will generate a graph for each
-# documented header file showing the documented files that directly or
-# indirectly include this file.
+# If the INCLUDED_BY_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are
+# set to YES then doxygen will generate a graph for each documented file showing
+# the direct and indirect include dependencies of the file with other documented
+# files.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 INCLUDED_BY_GRAPH      = YES
 
-# If the CALL_GRAPH and HAVE_DOT options are set to YES then
-# doxygen will generate a call dependency graph for every global function
-# or class method. Note that enabling this option will significantly increase
-# the time of a run. So in most cases it will be better to enable call graphs
-# for selected functions only using the \callgraph command.
+# If the CALL_GRAPH tag is set to YES then doxygen will generate a call
+# dependency graph for every global function or class method.
+#
+# Note that enabling this option will significantly increase the time of a run.
+# So in most cases it will be better to enable call graphs for selected
+# functions only using the \callgraph command. Disabling a call graph can be
+# accomplished by means of the command \hidecallgraph.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 CALL_GRAPH             = NO
 
-# If the CALLER_GRAPH and HAVE_DOT tags are set to YES then
-# doxygen will generate a caller dependency graph for every global function
-# or class method. Note that enabling this option will significantly increase
-# the time of a run. So in most cases it will be better to enable caller
-# graphs for selected functions only using the \callergraph command.
+# If the CALLER_GRAPH tag is set to YES then doxygen will generate a caller
+# dependency graph for every global function or class method.
+#
+# Note that enabling this option will significantly increase the time of a run.
+# So in most cases it will be better to enable caller graphs for selected
+# functions only using the \callergraph command. Disabling a caller graph can be
+# accomplished by means of the command \hidecallergraph.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 CALLER_GRAPH           = NO
 
-# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen
-# will generate a graphical hierarchy of all classes instead of a textual one.
+# If the GRAPHICAL_HIERARCHY tag is set to YES then doxygen will graphical
+# hierarchy of all classes instead of a textual one.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 GRAPHICAL_HIERARCHY    = YES
 
-# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
-# then doxygen will show the dependencies a directory has on other directories
-# in a graphical way. The dependency relations are determined by the #include
-# relations between the files in the directories.
+# If the DIRECTORY_GRAPH tag is set to YES then doxygen will show the
+# dependencies a directory has on other directories in a graphical way. The
+# dependency relations are determined by the #include relations between the
+# files in the directories.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 DIRECTORY_GRAPH        = YES
 
+# The DIR_GRAPH_MAX_DEPTH tag can be used to limit the maximum number of levels
+# of child directories generated in directory dependency graphs by dot.
+# Minimum value: 1, maximum value: 25, default value: 1.
+# This tag requires that the tag DIRECTORY_GRAPH is set to YES.
+
+DIR_GRAPH_MAX_DEPTH    = 1
+
 # The DOT_IMAGE_FORMAT tag can be used to set the image format of the images
-# generated by dot. Possible values are svg, png, jpg, or gif.
-# If left blank png will be used. If you choose svg you need to set
-# HTML_FILE_EXTENSION to xhtml in order to make the SVG files
-# visible in IE 9+ (other browsers do not have this requirement).
+# generated by dot. For an explanation of the image formats see the section
+# output formats in the documentation of the dot tool (Graphviz (see:
+# http://www.graphviz.org/)).
+# Note: If you choose svg you need to set HTML_FILE_EXTENSION to xhtml in order
+# to make the SVG files visible in IE 9+ (other browsers do not have this
+# requirement).
+# Possible values are: png, jpg, jpg:cairo, jpg:cairo:gd, jpg:gd, jpg:gd:gd,
+# gif, gif:cairo, gif:cairo:gd, gif:gd, gif:gd:gd, svg, png:gd, png:gd:gd,
+# png:cairo, png:cairo:gd, png:cairo:cairo, png:cairo:gdiplus, png:gdiplus and
+# png:gdiplus:gdiplus.
+# The default value is: png.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 DOT_IMAGE_FORMAT       = png
 
 # If DOT_IMAGE_FORMAT is set to svg, then this option can be set to YES to
 # enable generation of interactive SVG images that allow zooming and panning.
-# Note that this requires a modern browser other than Internet Explorer.
-# Tested and working are Firefox, Chrome, Safari, and Opera. For IE 9+ you
-# need to set HTML_FILE_EXTENSION to xhtml in order to make the SVG files
-# visible. Older versions of IE do not have SVG support.
+#
+# Note that this requires a modern browser other than Internet Explorer. Tested
+# and working are Firefox, Chrome, Safari, and Opera.
+# Note: For IE 9+ you need to set HTML_FILE_EXTENSION to xhtml in order to make
+# the SVG files visible. Older versions of IE do not have SVG support.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 INTERACTIVE_SVG        = NO
 
-# The tag DOT_PATH can be used to specify the path where the dot tool can be
+# The DOT_PATH tag can be used to specify the path where the dot tool can be
 # found. If left blank, it is assumed the dot tool can be found in the path.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 DOT_PATH               =
 
 # The DOTFILE_DIRS tag can be used to specify one or more directories that
-# contain dot files that are included in the documentation (see the
-# \dotfile command).
+# contain dot files that are included in the documentation (see the \dotfile
+# command).
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 DOTFILE_DIRS           =
 
 # The MSCFILE_DIRS tag can be used to specify one or more directories that
-# contain msc files that are included in the documentation (see the
-# \mscfile command).
+# contain msc files that are included in the documentation (see the \mscfile
+# command).
 
 MSCFILE_DIRS           =
 
-# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of
-# nodes that will be shown in the graph. If the number of nodes in a graph
-# becomes larger than this value, doxygen will truncate the graph, which is
-# visualized by representing a node as a red box. Note that doxygen if the
-# number of direct children of the root node in a graph is already larger than
-# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note
-# that the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH.
+# The DIAFILE_DIRS tag can be used to specify one or more directories that
+# contain dia files that are included in the documentation (see the \diafile
+# command).
+
+DIAFILE_DIRS           =
+
+# When using plantuml, the PLANTUML_JAR_PATH tag should be used to specify the
+# path where java can find the plantuml.jar file or to the filename of jar file
+# to be used. If left blank, it is assumed PlantUML is not used or called during
+# a preprocessing step. Doxygen will generate a warning when it encounters a
+# \startuml command in this case and will not generate output for the diagram.
+
+PLANTUML_JAR_PATH      =
+
+# When using plantuml, the PLANTUML_CFG_FILE tag can be used to specify a
+# configuration file for plantuml.
+
+PLANTUML_CFG_FILE      =
+
+# When using plantuml, the specified paths are searched for files specified by
+# the !include statement in a plantuml block.
+
+PLANTUML_INCLUDE_PATH  =
+
+# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of nodes
+# that will be shown in the graph. If the number of nodes in a graph becomes
+# larger than this value, doxygen will truncate the graph, which is visualized
+# by representing a node as a red box. Note that doxygen if the number of direct
+# children of the root node in a graph is already larger than
+# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note that
+# the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH.
+# Minimum value: 0, maximum value: 10000, default value: 50.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 DOT_GRAPH_MAX_NODES    = 50
 
-# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the
-# graphs generated by dot. A depth value of 3 means that only nodes reachable
-# from the root by following a path via at most 3 edges will be shown. Nodes
-# that lay further from the root node will be omitted. Note that setting this
-# option to 1 or 2 may greatly reduce the computation time needed for large
-# code bases. Also note that the size of a graph can be further restricted by
+# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the graphs
+# generated by dot. A depth value of 3 means that only nodes reachable from the
+# root by following a path via at most 3 edges will be shown. Nodes that lay
+# further from the root node will be omitted. Note that setting this option to 1
+# or 2 may greatly reduce the computation time needed for large code bases. Also
+# note that the size of a graph can be further restricted by
 # DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction.
+# Minimum value: 0, maximum value: 1000, default value: 0.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 MAX_DOT_GRAPH_DEPTH    = 0
 
 # Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
-# background. This is disabled by default, because dot on Windows does not
-# seem to support this out of the box. Warning: Depending on the platform used,
-# enabling this option may lead to badly anti-aliased labels on the edges of
-# a graph (i.e. they become hard to read).
+# background. This is disabled by default, because dot on Windows does not seem
+# to support this out of the box.
+#
+# Warning: Depending on the platform used, enabling this option may lead to
+# badly anti-aliased labels on the edges of a graph (i.e. they become hard to
+# read).
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 DOT_TRANSPARENT        = NO
 
-# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output
+# Set the DOT_MULTI_TARGETS tag to YES to allow dot to generate multiple output
 # files in one run (i.e. multiple -o and -T options on the command line). This
-# makes dot run faster, but since only newer versions of dot (>1.8.10)
-# support this, this feature is disabled by default.
+# makes dot run faster, but since only newer versions of dot (>1.8.10) support
+# this, this feature is disabled by default.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 DOT_MULTI_TARGETS      = NO
 
-# If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will
-# generate a legend page explaining the meaning of the various boxes and
-# arrows in the dot generated graphs.
+# If the GENERATE_LEGEND tag is set to YES doxygen will generate a legend page
+# explaining the meaning of the various boxes and arrows in the dot generated
+# graphs.
+# Note: This tag requires that UML_LOOK isn't set, i.e. the doxygen internal
+# graphical representation for inheritance and collaboration diagrams is used.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 GENERATE_LEGEND        = YES
 
-# If the DOT_CLEANUP tag is set to YES (the default) Doxygen will
-# remove the intermediate dot files that are used to generate
-# the various graphs.
+# If the DOT_CLEANUP tag is set to YES, doxygen will remove the intermediate
+# files that are used to generate the various graphs.
+#
+# Note: This setting is not only used for dot files but also for msc temporary
+# files.
+# The default value is: YES.
 
 DOT_CLEANUP            = YES

From ece35a71f033c3123d2a4f4997b14080a56532fd Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 27 Feb 2026 09:30:36 -0500
Subject: [PATCH 1401/1492] Add subdirectories

---
 src/cpptraj.Doxyfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/cpptraj.Doxyfile b/src/cpptraj.Doxyfile
index 68bbacd487..5249ebf4e8 100644
--- a/src/cpptraj.Doxyfile
+++ b/src/cpptraj.Doxyfile
@@ -896,7 +896,7 @@ WARN_LOGFILE           =
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  =
+INPUT                  = . ./Cluster ./Energy ./Parm ./Structure
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses

From 600ed7e6d0c5719398e1d8a8267fe4825eed4e67 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 27 Feb 2026 09:31:34 -0500
Subject: [PATCH 1402/1492] Add some namespace documentation

---
 src/Cluster/Control.h         | 4 ++++
 src/Energy/Ecalc_Nonbond.h    | 4 ++++
 src/MaskArray.h               | 7 +++++++
 src/Parm/ParmEnum.h           | 5 +++++
 src/Structure/StructureEnum.h | 4 ++++
 5 files changed, 24 insertions(+)

diff --git a/src/Cluster/Control.h b/src/Cluster/Control.h
index 557da5a7e1..27e0262a9d 100644
--- a/src/Cluster/Control.h
+++ b/src/Cluster/Control.h
@@ -15,6 +15,10 @@ class DataFile;
 class DataFileList;
 class DataSetList;
 namespace Cpptraj {
+/** @brief The namespace for all clustering-related classes.
+  *
+  * All cluster classes and related functions belong in this namespace.
+  */
 namespace Cluster {
 class Algorithm;
 class Results;
diff --git a/src/Energy/Ecalc_Nonbond.h b/src/Energy/Ecalc_Nonbond.h
index d9a6c16565..d2b7eb230a 100644
--- a/src/Energy/Ecalc_Nonbond.h
+++ b/src/Energy/Ecalc_Nonbond.h
@@ -6,6 +6,10 @@ class CharMask;
 class EwaldOptions;
 class Topology;
 namespace Cpptraj {
+/** @brief The namespace that all energy-related classes should be in.
+  *
+  * Namespace for all classes and functions related to calculating energy/forces.
+  */
 namespace Energy {
 class EwaldCalc;
 /// Calculate nonbonded energy for atoms
diff --git a/src/MaskArray.h b/src/MaskArray.h
index 1a74c6250c..d79b46a1d5 100644
--- a/src/MaskArray.h
+++ b/src/MaskArray.h
@@ -4,6 +4,13 @@
 // Forward declarations
 class Topology;
 class AtomMask;
+/** @brief The main Cpptraj namespace.
+  *
+  * This is the namespace that all CPPTRAJ classes should be in.
+  * NOTE: When CPPTRAJ was first developed, classes were not in any particular
+  *       namespace. Since it conflicts with the Cpptraj class, care should
+  *       be taken when putting new classes in the Cpptraj namespace.
+  */
 namespace Cpptraj {
 
 /// Hold array of atom masks, intended for 'bymol' or 'byres' type selection
diff --git a/src/Parm/ParmEnum.h b/src/Parm/ParmEnum.h
index 301ac10094..5a5d067a02 100644
--- a/src/Parm/ParmEnum.h
+++ b/src/Parm/ParmEnum.h
@@ -1,6 +1,11 @@
 #ifndef INC_PARM_PARMENUM_H
 #define INC_PARM_PARMENUM_H
 namespace Cpptraj {
+/** @brief Namespace containing classes related to parameters.
+  *
+  * This namespace contains classes/functions related to assigning, updating, and
+  * manipulating paramters.
+  */
 namespace Parm {
   enum RetType { ADDED = 0, SAME, UPDATED, ERR };
 
diff --git a/src/Structure/StructureEnum.h b/src/Structure/StructureEnum.h
index 3014a56b0b..a860a4befd 100644
--- a/src/Structure/StructureEnum.h
+++ b/src/Structure/StructureEnum.h
@@ -1,6 +1,10 @@
 #ifndef INC_STRUCTURE_STRUCTUREENUM_H
 #define INC_STRUCTURE_STRUCTUREENUM_H
 namespace Cpptraj {
+/** @brief The namespace for all structure related classes.
+  *
+  * This namespace holds all classes related to building systems.
+  */
 namespace Structure {
 
 enum ChiralType { CHIRALITY_ERR = 0, IS_S, IS_R, IS_UNKNOWN_CHIRALITY };

From 3298e71b717ce171c2cc23908cfce7987a333748 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 27 Feb 2026 09:42:29 -0500
Subject: [PATCH 1403/1492] Script to extract current version number no matter
 where you are

---
 devtools/GetVersionNum.sh | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)
 create mode 100755 devtools/GetVersionNum.sh

diff --git a/devtools/GetVersionNum.sh b/devtools/GetVersionNum.sh
new file mode 100755
index 0000000000..6ff603c44e
--- /dev/null
+++ b/devtools/GetVersionNum.sh
@@ -0,0 +1,20 @@
+#!/bin/bash
+
+EXEDIR=`dirname $0`
+
+if [ ! -d "$EXEDIR" ] ; then
+  echo "Error: Could not determine execution directory."
+  exit 1
+fi
+
+cd $EXEDIR
+
+VFILE=../src/Version.h
+if [ ! -f "$VFILE" ] ; then
+  echo "Version file $VFILE not found."
+  exit 1
+fi
+
+VERSION=`awk '{if ($2 == "CPPTRAJ_INTERNAL_VERSION") {gsub(/\"/,""); printf ("%s", $3);}}' $VFILE`
+echo $VERSION
+exit 0

From aec23442aa8fb091417f7032d7c3c5b086ab6c17 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 27 Feb 2026 09:48:30 -0500
Subject: [PATCH 1404/1492] Script for automatically updating the version
 string in the Doxyfile

---
 devtools/UpdateDoxyVersion.sh | 36 +++++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)
 create mode 100755 devtools/UpdateDoxyVersion.sh

diff --git a/devtools/UpdateDoxyVersion.sh b/devtools/UpdateDoxyVersion.sh
new file mode 100755
index 0000000000..36edd7277b
--- /dev/null
+++ b/devtools/UpdateDoxyVersion.sh
@@ -0,0 +1,36 @@
+#!/bin/bash
+
+# Update the cpptraj.Doxyfile version number
+
+EXEDIR=`dirname $0`
+
+if [ ! -d "$EXEDIR" ] ; then
+  echo "Error: Could not determine execution directory."
+  exit 1
+fi
+
+cd $EXEDIR
+DFILE=../src/cpptraj.Doxyfile
+if [ ! -f "$DFILE" ] ; then
+  echo "Doxygen file $DFILE not found."
+  exit 1
+fi
+
+VERSION=`./GetVersionNum.sh`
+if [ $? -ne 0 ] ; then
+  echo "Error: Could not get version number."
+  exit 1
+fi
+
+if [ -f 'tmp.cpptraj.Doxyfile' ] ; then
+  rm tmp.cpptraj.Doxyfile
+fi
+awk -v vstring="$VERSION" '{
+  if ($1 == "PROJECT_NUMBER")
+    printf("PROJECT_NUMBER         = %s\n", vstring);
+  else
+    print $0;
+}' $DFILE > tmp.cpptraj.Doxyfile
+mv tmp.cpptraj.Doxyfile $DFILE
+
+exit 0

From 80553ad2de277daf87752b3516a52646a71782aa Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 27 Feb 2026 10:07:06 -0500
Subject: [PATCH 1405/1492] Automatically update doxygen version number when
 doing make docs

---
 Makefile             | 2 +-
 src/cpptraj.Doxyfile | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/Makefile b/Makefile
index 55e0de5497..ec91548749 100644
--- a/Makefile
+++ b/Makefile
@@ -38,7 +38,7 @@ clean: config.h
 
 docs: src/cpptraj.Doxyfile
 	cd doc && make docs
-	cd src && doxygen cpptraj.Doxyfile
+	cd src && ../devtools/UpdateDoxyVersion.sh && doxygen cpptraj.Doxyfile
 
 # Remove cpptraj binary
 uninstall: config.h
diff --git a/src/cpptraj.Doxyfile b/src/cpptraj.Doxyfile
index 5249ebf4e8..57f0a6de18 100644
--- a/src/cpptraj.Doxyfile
+++ b/src/cpptraj.Doxyfile
@@ -47,7 +47,7 @@ PROJECT_NAME           = Cpptraj
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = 13
+PROJECT_NUMBER         = V6.30.1
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a

From a89f34c87890028d4abfd4a4a406a1a4fb7a3b29 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 27 Feb 2026 10:07:36 -0500
Subject: [PATCH 1406/1492] Have make docs call GeneratePDFs.sh

---
 doc/Makefile | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/doc/Makefile b/doc/Makefile
index 4f8141c076..d80a87382f 100644
--- a/doc/Makefile
+++ b/doc/Makefile
@@ -1,4 +1,5 @@
-docs: CpptrajManual.pdf CpptrajDevelopmentGuide.pdf 
+docs: GeneratePDFs.sh
+	./GeneratePDFs.sh
 
 .lyx.pdf:
 	lyx -batch --export pdf2 $<

From 19e1ea6f03a30ee5d850af28a36b525f5642e967 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 27 Feb 2026 10:55:44 -0500
Subject: [PATCH 1407/1492] Cpptraj needs to be modified if unhandled radii set

---
 src/Parm/GB_Params.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Parm/GB_Params.cpp b/src/Parm/GB_Params.cpp
index 76eb0bbe9b..6e35e841b1 100644
--- a/src/Parm/GB_Params.cpp
+++ b/src/Parm/GB_Params.cpp
@@ -33,7 +33,7 @@ static const char* GB_RadiiAmberFlag_[] = {
   "H(N)-modified Bondi radii (mbondi2)",              // 6
   "Parse radii (parse)",                              // 7
   "ArgH and AspGluO modified Bondi2 radii (mbondi3)", // 8
-  "Unknown radius set (leap needs to be modified!)"
+  "Unknown radius set (cpptraj needs to be modified!)"
 };
 
 /** \return key corresponding to type. */

From 59dd580e42618236554f7315b0225827ce64b88b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 27 Feb 2026 13:37:23 -0500
Subject: [PATCH 1408/1492] Add help for the source command

---
 src/DataIO_LeapRC.cpp | 7 +++++++
 src/DataIO_LeapRC.h   | 2 ++
 src/Exec_Source.cpp   | 7 ++++++-
 3 files changed, 15 insertions(+), 1 deletion(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 83656e1be4..7e79c31135 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -43,6 +43,13 @@ DataIO_LeapRC::LeapEltHybrid& DataIO_LeapRC::LeapEltHybrid::operator=(const Leap
   return *this;
 }
 
+/** Print a list of supported leap commands to stdout. */
+void DataIO_LeapRC::PrintSupportedLeapCommands() {
+  mprintf("  Supported leap commands: addatomtypes, addpath, addpdbatommap, addpdbresmap,\n"
+          "                           loadamberparams, loadamberprep, loadmol2, loadoff,\n"
+          "                           loadpdb, quit, saveamberparm, set, source\n");
+}
+
 /// \return true if not equal.
 bool DataIO_LeapRC::LeapEltHybrid::operator!=(const LeapEltHybrid& rhs) const {
   return ( hybrid_ != rhs.hybrid_ ||
diff --git a/src/DataIO_LeapRC.h b/src/DataIO_LeapRC.h
index f440ee4463..925bc16c79 100644
--- a/src/DataIO_LeapRC.h
+++ b/src/DataIO_LeapRC.h
@@ -16,6 +16,8 @@ class DataIO_LeapRC : public DataIO {
     int processWriteArgs(ArgList&);
     int WriteData(FileName const&, DataSetList const&);
     bool ID_DataFormat(CpptrajFile&);
+
+    static void PrintSupportedLeapCommands();
   private:
     /// Store atom type hybridization and element from leaprc addAtomTypes
     class LeapEltHybrid {
diff --git a/src/Exec_Source.cpp b/src/Exec_Source.cpp
index 2e842bc0b6..dca4fa11d4 100644
--- a/src/Exec_Source.cpp
+++ b/src/Exec_Source.cpp
@@ -5,7 +5,12 @@
 // Exec_Source::Help()
 void Exec_Source::Help() const
 {
-
+  mprintf("\t<filename>\n"
+          " Process <filename> as a leaprc file, mostly intended for loading\n"
+          " force field parameters from Amber leaprc files. If AMBERHOME\n"
+          " is set CPPTRAJ will look for leaprc files in\n"
+          " $AMBERHOME/dat/leap/cmd, otherwise the full path must be specified.\n");
+  DataIO_LeapRC::PrintSupportedLeapCommands();
 }
 
 // Exec_Source::Execute()

From df8ae75e70551209b74684cf80b6155c5bd1e646 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 27 Feb 2026 14:04:11 -0500
Subject: [PATCH 1409/1492] Update PDFs. Start adding section to manual for
 building systems, containing the build, sequence, and source commands.

---
 doc/CpptrajDevelopmentGuide.pdf |  Bin 349093 -> 245303 bytes
 doc/CpptrajManual.pdf           |  Bin 1102679 -> 965026 bytes
 doc/DocumentChecksums.txt       |    4 +-
 doc/cpptraj.lyx                 | 1121 +++++++++++++++++++++++++++++++
 4 files changed, 1123 insertions(+), 2 deletions(-)

diff --git a/doc/CpptrajDevelopmentGuide.pdf b/doc/CpptrajDevelopmentGuide.pdf
index 2a583ad7c7b69510f833953f63faf6be054c9243..de4a52c7205039f573c3846174f326008ae4b191 100644
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diff --git a/doc/CpptrajManual.pdf b/doc/CpptrajManual.pdf
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diff --git a/doc/DocumentChecksums.txt b/doc/DocumentChecksums.txt
index 9077af46e2..4b96f6cbff 100644
--- a/doc/DocumentChecksums.txt
+++ b/doc/DocumentChecksums.txt
@@ -1,3 +1,3 @@
-b37726e7a841f6fc695ecd7fb040ffbf  CpptrajDevelopmentGuide.lyx
-30abc9d08551e23061abcb780f78b02a  cpptraj.lyx
+f6f8cb1a79951d80a9d2656fd9c30f55  CpptrajDevelopmentGuide.lyx
+07a6da1d65a59267a00a79d76fad6ecf  cpptraj.lyx
 5d9b5b5ed47a3ded57b6464df99b3585  CpptrajManual.lyx
diff --git a/doc/cpptraj.lyx b/doc/cpptraj.lyx
index 13d137fefc..a17cf45cd7 100644
--- a/doc/cpptraj.lyx
+++ b/doc/cpptraj.lyx
@@ -6410,6 +6410,1120 @@ nolink "false"
 ).
 \end_layout
 
+\begin_layout Section
+System Build and Parameterization Commands
+\begin_inset CommandInset label
+LatexCommand label
+name "sec:Cpptraj-System-Build"
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+As of version 7.0,
+ CPPTRAJ has the ability to create full coordinates and Amber Topology files for MD simulations.
+\end_layout
+
+\begin_layout Standard
+The following build and parameterization commands are available:
+\end_layout
+
+\begin_layout Standard
+\begin_inset Tabular
+<lyxtabular version="3" rows="4" columns="2">
+<features tabularvalignment="middle">
+<column alignment="center" valignment="top" width="50text%">
+<column alignment="center" valignment="top" width="25text%">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\series bold
+Command
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\series bold
+Description
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+build
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Fully build and parameterize a COORDS set or input file using template libraries and force field parameter sets.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+sequence
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Create and parameterize a COORDS set using specified residues from template libraries and force field parameter sets.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+source
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Limited version of the LEaP 'source' command,
+ intended to load Amber force field 
+\begin_inset Quotes eld
+\end_inset
+
+leaprc
+\begin_inset Quotes erd
+\end_inset
+
+ files.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+</lyxtabular>
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+build
+\begin_inset CommandInset label
+LatexCommand label
+name "subsec:cpptraj-build"
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout LyX-Code
+build [name <output COORDS>] {crdset <COORDS set>|<file>} [{frame <#>|doassembly}]
+\end_layout
+
+\begin_layout LyX-Code
+	[nowat [watermask <watermask>] [noh]
+\end_layout
+
+\begin_layout LyX-Code
+	[keepaltloc {<alt loc ID>|highestocc}]
+\end_layout
+
+\begin_layout LyX-Code
+	[stripmask <stripmask>]
+\end_layout
+
+\begin_layout LyX-Code
+	[title <title>] [verbose <#>] [keepmissingatoms] [nofixorder]
+\end_layout
+
+\begin_layout LyX-Code
+	[parmout <topology file>] [crdout <coord file>] [simplecheck]
+\end_layout
+
+\begin_layout LyX-Code
+	[gb {bondi|amber6|mbondi|pbamber|mbondi2|parse|mbondi3}]
+\end_layout
+
+\begin_deeper
+\begin_layout Standard
+LJ 12-6-4 options:
+\end_layout
+
+\end_deeper
+\begin_layout LyX-Code
+	[lj1264 [lj1264mask <mask>] [tunfactor <fac>] [c4file <c4file>] [polfile <polfile>]
+\end_layout
+
+\begin_layout LyX-Code
+    [lj1264solvent <solvent>]]
+\end_layout
+
+\begin_deeper
+\begin_layout Standard
+Atom Scan direction:
+\end_layout
+
+\end_deeper
+\begin_layout LyX-Code
+	[atomscandir {f|b}]
+\end_layout
+
+\begin_deeper
+\begin_layout Standard
+Residue Templates and Parameters to use:
+\end_layout
+
+\end_deeper
+\begin_layout LyX-Code
+	[{lib <template setname>} ...]
+\end_layout
+
+\begin_layout LyX-Code
+	[{parmset <parameter setname>} ...]
+\end_layout
+
+\begin_deeper
+\begin_layout Standard
+Solvation/box:
+\end_layout
+
+\end_deeper
+\begin_layout LyX-Code
+	[{{solvatebox|solvateoct} {buffer <buffer> | bufx <bufx> bufy <bufy> bufz <bufz> |
+\end_layout
+
+\begin_layout LyX-Code
+                               nsolvent <#>}
+\end_layout
+
+\begin_layout LyX-Code
+	          solventbox <unit> [closeness <closeness>] [{iso|aniso}] [nocenter] |
+\end_layout
+
+\begin_layout LyX-Code
+	  setbox [{buffer <buffer> | bufx <bufx> bufy <bufy> bufz <bufz>}]}]
+\end_layout
+
+\begin_deeper
+\begin_layout Standard
+Adding ions:
+\end_layout
+
+\end_deeper
+\begin_layout LyX-Code
+	[addionsrand ion1 <name1> nion1 <num1> [ion2 <name2> nion2 <num2>]
+\end_layout
+
+\begin_layout LyX-Code
+	  [minsep <dist>] [ionseed <seed>]]
+\end_layout
+
+\begin_deeper
+\begin_layout Standard
+
+\series bold
+\emph on
+prepareforleap
+\series default
+\emph default
+ options:
+\end_layout
+
+\end_deeper
+\begin_layout LyX-Code
+	[{nohisdetect |
+\end_layout
+
+\begin_layout LyX-Code
+	  [nd1 <nd1>] [ne2 <ne2] [hisname <his>] [hiename <hie>]
+\end_layout
+
+\begin_layout LyX-Code
+	  [hidname <hid>] [hipname <hip]} [defaulthis <default>]]
+\end_layout
+
+\begin_layout LyX-Code
+	[{nodisulfides |
+\end_layout
+
+\begin_layout LyX-Code
+	  existingdisulfides |
+\end_layout
+
+\begin_layout LyX-Code
+	  [cysmask <cysmask>] [disulfidecut <cut>] [newcysname <name>]}]
+\end_layout
+
+\begin_layout LyX-Code
+	[{nosugars |
+\end_layout
+
+\begin_layout LyX-Code
+	  sugarmask <sugarmask> [noc1search] [nosplitres]
+\end_layout
+
+\begin_layout LyX-Code
+	  [rescut <residue cutoff>] [bondoffset <offset>]
+\end_layout
+
+\begin_layout LyX-Code
+	  [resmapfile <file>]
+\end_layout
+
+\begin_layout LyX-Code
+	  [hasglycam] [determinesugarsby {geom|name}]
+\end_layout
+
+\begin_layout LyX-Code
+	 }]
+\end_layout
+
+\begin_deeper
+\begin_layout Description
+[name
+\begin_inset space ~
+\end_inset
+
+<OUTPUT
+\begin_inset space ~
+\end_inset
+
+COORDS>] Optional name of the output COORDS set to create.
+ If not specified the input structure will be altered.
+\end_layout
+
+\begin_layout Description
+{crdset
+\begin_inset space ~
+\end_inset
+
+<COORDS
+\begin_inset space ~
+\end_inset
+
+set>|<file>} REQUIRED.
+ Name of the input COORDS set to build,
+ or name of the input file to build directly.
+ The input 
+\series bold
+<file>
+\series default
+ if specified must be a format that contains some topology information (like atom names and residue numbers).
+\end_layout
+
+\begin_layout Description
+[{frame
+\begin_inset space ~
+\end_inset
+
+<#>|doassembly}] If the input structure contains multiple frames/models,
+ specify the one to use with 
+\series bold
+frame
+\series default
+,
+ or if the frames/models are part of an assembly 
+\series bold
+doassembly
+\series default
+ will put them all into a single output structure.
+\end_layout
+
+\begin_layout Description
+[nowat] Remove any input residues identified as solvent (by watermask).
+\end_layout
+
+\begin_deeper
+\begin_layout Description
+[watermask
+\begin_inset space ~
+\end_inset
+
+<watermask>] Mask for identifying input residues as solvent;
+ default 
+\begin_inset Quotes eld
+\end_inset
+
+:HOH
+\begin_inset Quotes erd
+\end_inset
+
+.
+\end_layout
+
+\end_deeper
+\begin_layout Description
+[noh] Remove any input atoms identified as hydrogen.
+\end_layout
+
+\begin_layout Description
+[keepaltloc
+\begin_inset space ~
+\end_inset
+
+{<alt
+\begin_inset space ~
+\end_inset
+
+loc
+\begin_inset space ~
+\end_inset
+
+ID>|highestocc}] When input atoms have alternate location specifiers,
+ specify how to choose.
+ If 
+\series bold
+highestocc
+\series default
+ is specified and input coordinates includes occupancy,
+ choose the atom with the highest occupancy.
+ Otherwise use the specified alternate location identifier.
+\end_layout
+
+\begin_layout Description
+[stripmask
+\begin_inset space ~
+\end_inset
+
+<stripmask>] If specified,
+ remove input atoms selected by 
+\series bold
+<stripmask>
+\series default
+.
+\end_layout
+
+\begin_layout Description
+[title
+\begin_inset space ~
+\end_inset
+
+<title>] Optional title to give the output topology.
+\end_layout
+
+\begin_layout Description
+[verbose
+\begin_inset space ~
+\end_inset
+
+<#>] Parameter assignment verbosity;
+ higher values will provide more output.
+\end_layout
+
+\begin_layout Description
+[keepmissingatoms] By default,
+ input atoms not found in residue templates will be removed.
+ If this option is specified those atoms will be kept (like LEaP).
+\end_layout
+
+\begin_layout Description
+[nofixorder] By default,
+ CPPTRAJ will rearrange atoms so that atoms in the same molecule are contiguous.
+ If this option is specified no rearrangement will occur.
+\end_layout
+
+\begin_layout Description
+[parmout
+\begin_inset space ~
+\end_inset
+
+<topology
+\begin_inset space ~
+\end_inset
+
+file>] Name of the output topology file.
+\end_layout
+
+\begin_layout Description
+[crdout
+\begin_inset space ~
+\end_inset
+
+<coord
+\begin_inset space ~
+\end_inset
+
+file>] Name of the output coordinates file.
+ Format can be chosen based on filename extension.
+\end_layout
+
+\begin_layout Description
+[gb
+\begin_inset space ~
+\end_inset
+
+{bondi|amber6|mbondi|pbamber|mbondi2|parse|mbondi3}] Select with GB radii set to use.
+ Default is mbondi.
+\end_layout
+
+\begin_deeper
+\begin_layout Description
+bondi Bondi radii.
+\end_layout
+
+\begin_layout Description
+amber6 Amber6 modified Bondi radii.
+\end_layout
+
+\begin_layout Description
+mbondi Modified Bondi radii (default).
+\end_layout
+
+\begin_layout Description
+pbamber Huo and Kollman optimized radii.
+\end_layout
+
+\begin_layout Description
+mbondi2 H(N)-modified Bondi radii.
+\end_layout
+
+\begin_layout Description
+parse PARSE radii.
+\end_layout
+
+\begin_layout Description
+mbondi3 ArgH and AspGluO modified Bondi2 radii.
+\end_layout
+
+\end_deeper
+\begin_layout Standard
+LJ 12-6-4 options:
+\end_layout
+
+\begin_layout Description
+[lj1264] Option to activate LJ 12-6-4 parameters.
+\end_layout
+
+\begin_deeper
+\begin_layout Description
+[lj1264mask
+\begin_inset space ~
+\end_inset
+
+<mask>] Mask of atoms to assign LJ 12-6-4 parameters to (default 
+\begin_inset Quotes eld
+\end_inset
+
+:ZN
+\begin_inset Quotes erd
+\end_inset
+
+).
+\end_layout
+
+\begin_layout Description
+[tunfactor
+\begin_inset space ~
+\end_inset
+
+<fac>] Scaling factor to adjust interaction between two different ions (default 1.0).
+\end_layout
+
+\begin_layout Description
+[c4file
+\begin_inset space ~
+\end_inset
+
+<c4file>] File containing C4 parameters for each element.
+ If not specified,
+ use default parameters for whatever solvent model is in use.
+\end_layout
+
+\begin_layout Description
+[polfile
+\begin_inset space ~
+\end_inset
+
+<polfile>] File containing polarizabilities for each atom type.
+ Default is '$AMBERHOME/dat/leap/parm/lj_1264_pol.dat'.
+\end_layout
+
+\begin_layout Description
+[lj1264solvent
+\begin_inset space ~
+\end_inset
+
+<solvent>]] Name of water box unit containing water model to set up for.
+ If not specified,
+ 'build' will try to guess based on the specified solvent box.
+\end_layout
+
+\begin_deeper
+\begin_layout Description
+TIP3PBOX TIP3P water model.
+\end_layout
+
+\begin_layout Description
+TIP4PEWBOX TIP4P Ewald water model.
+\end_layout
+
+\begin_layout Description
+SPCBOX SPC Ewald water model.
+\end_layout
+
+\begin_layout Description
+OPC3BOX OPC 3 point water model.
+\end_layout
+
+\begin_layout Description
+OPCBOX OPC 4 point water model.
+\end_layout
+
+\begin_layout Description
+FB3BOX FB3 water model.
+\end_layout
+
+\begin_layout Description
+FB4BOX FB4 water model.
+\end_layout
+
+\end_deeper
+\end_deeper
+\begin_layout Standard
+Atom Scan direction:
+\end_layout
+
+\begin_layout Description
+[atomscandir
+\begin_inset space ~
+\end_inset
+
+{f|b}] Mostly intended for debugging when compared to LEaP.
+ LEaP generates bond/angle/dihedral lists within residues differently depending on where the residue was read from.
+ For PDBs the scanning goes from back to front ('
+\series bold
+b
+\series default
+'),
+ while for Mol2s the scanning is from front to back ('
+\series bold
+f
+\series default
+').
+ In CPPTRAJ the default scan direction is back to front since the assumption is that most systems built with LEaP have been read in from PDB files.
+\end_layout
+
+\begin_layout Standard
+Residue templates and Parameters to use:
+\end_layout
+
+\begin_layout Description
+[{lib
+\begin_inset space ~
+\end_inset
+
+<template
+\begin_inset space ~
+\end_inset
+
+setname>}
+\begin_inset space ~
+\end_inset
+
+...] Name of residue template set(s) to use.
+ If not specified use all loaded templates.
+ Can be specified multiple times.
+\end_layout
+
+\begin_layout Description
+[{parmset
+\begin_inset space ~
+\end_inset
+
+<parameter
+\begin_inset space ~
+\end_inset
+
+setname>}
+\begin_inset space ~
+\end_inset
+
+...] Name of parameters set(s) to use.
+ If not specified use all loaded parameters.
+ Can be specified multiple times.
+\end_layout
+
+\begin_layout Standard
+Solvation/box:
+\end_layout
+
+\begin_layout Description
+solvatebox|solvateoct Solvate the system in either an orthorhombic or truncated octadedral box.
+\end_layout
+
+\begin_deeper
+\begin_layout Description
+buffer
+\begin_inset space ~
+\end_inset
+
+<buffer>
+\begin_inset space ~
+\end_inset
+
+|
+\begin_inset space ~
+\end_inset
+
+bufx
+\begin_inset space ~
+\end_inset
+
+<bufx>
+\begin_inset space ~
+\end_inset
+
+bufy
+\begin_inset space ~
+\end_inset
+
+<bufy>
+\begin_inset space ~
+\end_inset
+
+bufz
+\begin_inset space ~
+\end_inset
+
+<bufz> Buffer distance (in Angstroms) between solute and the edge of the box.
+ Can either specify one uniform value or separate X Y and Z values.
+ The separate X Y and Z values will not work for truncated octahedrons.
+\end_layout
+
+\begin_layout Description
+nsolvent
+\begin_inset space ~
+\end_inset
+
+<#> EXPERIMENTAL.
+ Instead of a buffer,
+ specify a target number of waters to solvate the system with.
+\end_layout
+
+\end_deeper
+\begin_layout Description
+	solventbox
+\begin_inset space ~
+\end_inset
+
+<unit> Name of the solvent box to use (e.g.
+ OPCBOX,
+ TIP4PEWBOX,
+ SPCBOX etc).
+\end_layout
+
+\begin_deeper
+\begin_layout Description
+[closeness
+\begin_inset space ~
+\end_inset
+
+<closeness>] Specify how close solute and solvent are allowed to get (in Angstroms).
+ Default is 1.0.
+\end_layout
+
+\begin_layout Description
+[{iso|aniso}] Specify if solute should be treated as isotropic (centered and aligned along principal axes) before solvating or not.
+ Note that 
+\series bold
+solvatebox
+\series default
+ is default 
+\series bold
+aniso
+\series default
+,
+ while 
+\series bold
+solvateoct
+\series default
+ is default 
+\series bold
+iso
+\series default
+.
+\end_layout
+
+\begin_layout Description
+[nocenter] If specified,
+ do not center system in the center of the solvent box after solvating.
+\end_layout
+
+\end_deeper
+\begin_layout Description
+setbox
+\begin_inset space ~
+\end_inset
+
+[{buffer
+\begin_inset space ~
+\end_inset
+
+<buffer>
+\begin_inset space ~
+\end_inset
+
+|
+\begin_inset space ~
+\end_inset
+
+bufx
+\begin_inset space ~
+\end_inset
+
+<bufx>
+\begin_inset space ~
+\end_inset
+
+bufy
+\begin_inset space ~
+\end_inset
+
+<bufy>
+\begin_inset space ~
+\end_inset
+
+bufz
+\begin_inset space ~
+\end_inset
+
+<bufz>}] If this is specified,
+ do not solvate,
+ just create an orthorhombic box with the given buffer.
+\end_layout
+
+\begin_layout Standard
+Adding ions:
+\end_layout
+
+\begin_layout Description
+addionsrand Add specified number of ions to the system.
+\end_layout
+
+\begin_deeper
+\begin_layout Description
+ion1
+\begin_inset space ~
+\end_inset
+
+<name1>
+\begin_inset space ~
+\end_inset
+
+nion1
+\begin_inset space ~
+\end_inset
+
+<num1> Residue name of the first ion to use along with the number of ions to add.
+ If a number of 0 is specified a number of ions required to neutralize the system will be added (if the system charge and ion charges are opposite).
+\end_layout
+
+\begin_layout Description
+[ion2
+\begin_inset space ~
+\end_inset
+
+<name2>
+\begin_inset space ~
+\end_inset
+
+nion2
+\begin_inset space ~
+\end_inset
+
+<num2>] Optional residue name of second ion to use along with number of ions to add.
+ If a number of 0 is specified a number of ions required to neutralize the system will be added,
+ factoring in ions added by 
+\series bold
+ion1
+\series default
+ (and again if the system charge and ion charges are opposite).
+\end_layout
+
+\begin_layout Description
+[minsep
+\begin_inset space ~
+\end_inset
+
+<dist>] Minimum separation between any two ions in Angstroms.
+\end_layout
+
+\begin_layout Description
+[ionseed
+\begin_inset space ~
+\end_inset
+
+<seed>]] Random number generator seed to use (default is system time).
+\end_layout
+
+\end_deeper
+\begin_layout Standard
+
+\series bold
+\emph on
+prepareforleap
+\series default
+\emph default
+ options:
+ See 
+\begin_inset CommandInset ref
+LatexCommand vref
+reference "subsec:cpptraj-prepareforleap"
+plural "false"
+caps "false"
+noprefix "false"
+nolink "false"
+
+\end_inset
+
+
+\end_layout
+
+\end_deeper
+\begin_layout Standard
+Build the full coordinates and topology of a system for MD simulations using residue templates and force field parameters,
+ including CMAP and LJ 12-6-4 parameters.
+ Also includes the ability to add explicit solvent and ions,
+ including the ability to solvate with a target number of water molecules.
+ This command effectively includes `
+\series bold
+\emph on
+prepareforleap
+\series default
+\emph default
+`,
+ `
+\series bold
+\emph on
+checkstructure
+\series default
+\emph default
+`,
+ and `
+\series bold
+\emph on
+fixatomorder
+\series default
+\emph default
+` functionality.
+ If the 
+\series bold
+'doassembly'
+\series default
+ keyword is specified it can create macromolecular assemblies from PDBs with multiple models.
+\end_layout
+
+\begin_layout Subsection
+sequence
+\end_layout
+
+\begin_layout LyX-Code
+sequence name <output set name> <unit0> <unit1> ...
+ [verbose <#>]
+\end_layout
+
+\begin_layout LyX-Code
+	[gb {bondi|amber6|mbondi|pbamber|mbondi2|parse|mbondi3}]
+\end_layout
+
+\begin_layout LyX-Code
+	[atomscandir {f|b}]
+\end_layout
+
+\begin_layout LyX-Code
+	[{lib <template setname>} ...]
+\end_layout
+
+\begin_layout LyX-Code
+	[{parmset <parameter setname>} ...]
+\end_layout
+
+\begin_deeper
+\begin_layout Description
+name
+\begin_inset space ~
+\end_inset
+
+<output
+\begin_inset space ~
+\end_inset
+
+set
+\begin_inset space ~
+\end_inset
+
+name> Name of output COORDS set.
+\end_layout
+
+\begin_layout Description
+<unit0>
+\begin_inset space ~
+\end_inset
+
+<unit1>
+\begin_inset space ~
+\end_inset
+
+...
+ Names of the residues/units to connect together in sequence.
+\end_layout
+
+\begin_layout Description
+[verbose
+\begin_inset space ~
+\end_inset
+
+<#>] Parameter assignment verbosity;
+ higher values will provide more output.
+\end_layout
+
+\begin_layout Description
+[gb
+\begin_inset space ~
+\end_inset
+
+{bondi|amber6|mbondi|pbamber|mbondi2|parse|mbondi3}] Select with GB radii set to use.
+ Default is mbondi.
+ See 
+\begin_inset CommandInset ref
+LatexCommand vref
+reference "subsec:cpptraj-build"
+plural "false"
+caps "false"
+noprefix "false"
+nolink "false"
+
+\end_inset
+
+ for specific details on the GB radii set keywords.
+\end_layout
+
+\begin_layout Description
+[atomscandir
+\begin_inset space ~
+\end_inset
+
+{f|b}] Mostly intended for debugging when compared to LEaP.
+ See 
+\begin_inset CommandInset ref
+LatexCommand vref
+reference "subsec:cpptraj-build"
+plural "false"
+caps "false"
+noprefix "false"
+nolink "false"
+
+\end_inset
+
+ for specific details on the atom scan direction.
+\end_layout
+
+\begin_layout Description
+[{lib
+\begin_inset space ~
+\end_inset
+
+<template
+\begin_inset space ~
+\end_inset
+
+setname>}
+\begin_inset space ~
+\end_inset
+
+...] Name of residue template set(s) to use.
+ If not specified use all loaded templates.
+ Can be specified multiple times.
+\end_layout
+
+\begin_layout Description
+[{parmset
+\begin_inset space ~
+\end_inset
+
+<parameter
+\begin_inset space ~
+\end_inset
+
+setname>}
+\begin_inset space ~
+\end_inset
+
+...] Name of parameters set(s) to use.
+ If not specified use all loaded parameters.
+ Can be specified multiple times.
+\end_layout
+
+\end_deeper
+\begin_layout Standard
+Create a molecule from a sequence of units.
+ If parameter sets are loaded,
+ parameters will be assigned to <output set name>.
+\end_layout
+
+\begin_layout Subsection
+source
+\end_layout
+
+\begin_layout LyX-Code
+source <filename>
+\end_layout
+
+\begin_layout Standard
+Process <filename> as a leaprc file,
+ mostly intended for loading force field parameters from Amber leaprc files.
+ If AMBERHOME is set CPPTRAJ will look for leaprc files in $AMBERHOME/dat/leap/cmd,
+ otherwise the full path must be specified.
+\end_layout
+
+\begin_layout Standard
+Supported leap commands:
+ addatomtypes,
+ addpath,
+ addpdbatommap,
+ addpdbresmap,
+ loadamberparams,
+ loadamberprep,
+ loadmol2,
+ loadoff,
+ loadpdb,
+ quit,
+ saveamberparm,
+ set,
+ source.
+\end_layout
+
 \begin_layout Section
 Coordinates (COORDS) Data Set Commands
 \begin_inset CommandInset label
@@ -8533,6 +9647,13 @@ permutedihedrals crdset [TZ2] random rseed 1 check maxfactor 10 phi psi
 
 \begin_layout Subsection
 prepareforleap
+\begin_inset CommandInset label
+LatexCommand label
+name "subsec:cpptraj-prepareforleap"
+
+\end_inset
+
+
 \end_layout
 
 \begin_layout LyX-Code

From de978face9f3d5a181efa1adcdbc64a8d79da222 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 27 Feb 2026 14:07:52 -0500
Subject: [PATCH 1410/1492] Add note about improved sequence command

---
 doc/ChangeLog.v7.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/doc/ChangeLog.v7.md b/doc/ChangeLog.v7.md
index f6324df32b..a381366652 100644
--- a/doc/ChangeLog.v7.md
+++ b/doc/ChangeLog.v7.md
@@ -27,6 +27,8 @@ New functionality
 
 - The `energy` command will now calculate CMAP energies (if CMAP parameters are present) and/or LJ 12-6-4 contributions to VDW energy (if `lj1264` is specified).
 
+- The `sequence` command now generates better geometries around bonds linking residues.
+
 New Keywords
 ============
 - Introduce ring intersection check to `checkstructure` action.

From a17a4f2227e5fe8265fa52658369487470acc6ed Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 27 Feb 2026 14:13:36 -0500
Subject: [PATCH 1411/1492] The sequence command is now located in the system
 build part of the manual.

---
 doc/CpptrajManual.pdf     | Bin 965026 -> 964643 bytes
 doc/DocumentChecksums.txt |   2 +-
 doc/cpptraj.lyx           | 226 +++++++++++++-------------------------
 3 files changed, 79 insertions(+), 149 deletions(-)

diff --git a/doc/CpptrajManual.pdf b/doc/CpptrajManual.pdf
index 6b81b3ee5e584c45afdac6a2bac5762d8aaf45d1..563863eaed620e08c18d9e06afe77441b40598bb 100644
GIT binary patch
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zJfmU{kpC~%t;IMCFWqx84x1C^ZM@LK9si`>O)^06HMaprFLB4fPwEOqeZ+2YTcjqV
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zYt#a?1^}YFrp?reah9`uugx+nnUt?lRv+hG{0W$H+<V_S`>eLasxp}8L$K5h3aS{g
zM=>Dg8$maQLtzd?)-6VYbnuXeg6!%<46P3YnbnDVEO{M>hg!S@Nozt<Eg>o3l^`)e
zraz<v$De*WNC?4`&WJ>+MF&j_qu_&`gDk#PQ~72@U&t@GVw#fA>ghPB;bLOcTwKq!
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diff --git a/doc/DocumentChecksums.txt b/doc/DocumentChecksums.txt
index 4b96f6cbff..49ab11ff36 100644
--- a/doc/DocumentChecksums.txt
+++ b/doc/DocumentChecksums.txt
@@ -1,3 +1,3 @@
 f6f8cb1a79951d80a9d2656fd9c30f55  CpptrajDevelopmentGuide.lyx
-07a6da1d65a59267a00a79d76fad6ecf  cpptraj.lyx
+ad83256a537dde12e3067e100b2e6a3a  cpptraj.lyx
 5d9b5b5ed47a3ded57b6464df99b3585  CpptrajManual.lyx
diff --git a/doc/cpptraj.lyx b/doc/cpptraj.lyx
index a17cf45cd7..f928df1f1e 100644
--- a/doc/cpptraj.lyx
+++ b/doc/cpptraj.lyx
@@ -7346,6 +7346,13 @@ fixatomorder
 
 \begin_layout Subsection
 sequence
+\begin_inset CommandInset label
+LatexCommand label
+name "subsec:cpptraj-sequence"
+
+\end_inset
+
+
 \end_layout
 
 \begin_layout LyX-Code
@@ -7487,9 +7494,75 @@ setname>}
 
 \end_deeper
 \begin_layout Standard
-Create a molecule from a sequence of units.
+Create a single molecule from a sequence of units.
  If parameter sets are loaded,
  parameters will be assigned to <output set name>.
+ Internal coordinates are used to try to determine the correct geometry around connection sites.
+ The COORDS sets must have connection information set,
+ either from reading in an Amber OFF library file or set manually via 
+\series bold
+\emph on
+dataset
+\series default
+\emph default
+ 
+\series bold
+connect
+\series default
+ (see 
+\begin_inset CommandInset ref
+LatexCommand vref
+reference "subsec:cpptraj-datasetcmd"
+plural "false"
+caps "false"
+noprefix "false"
+nolink "false"
+
+\end_inset
+
+).
+\end_layout
+
+\begin_layout Standard
+For example,
+ the following reads in two Mol2 files as COORDS sets,
+ sets up connection atoms,
+ then creates a molecule via 
+\series bold
+\emph on
+sequence:
+\end_layout
+
+\begin_layout LyX-Code
+parm MOC.mol2
+\end_layout
+
+\begin_layout LyX-Code
+loadcrd MOC.mol2 parm MOC.mol2 name MOC
+\end_layout
+
+\begin_layout LyX-Code
+dataset connect MOC tailmask @O5
+\end_layout
+
+\begin_layout LyX-Code
+parm CNALA.mol2 
+\end_layout
+
+\begin_layout LyX-Code
+loadcrd CNALA.mol2 parm CNALA.mol2 name CNALA
+\end_layout
+
+\begin_layout LyX-Code
+dataset connect CNALA headmask @N
+\end_layout
+
+\begin_layout LyX-Code
+sequence MOC CNALA name Mol
+\end_layout
+
+\begin_layout LyX-Code
+crdout Mol Mol.mol2
 \end_layout
 
 \begin_layout Subsection
@@ -7676,7 +7749,7 @@ The following COORDS data set commands are available:
 \begin_layout Standard
 \align center
 \begin_inset Tabular
-<lyxtabular version="3" rows="19" columns="2">
+<lyxtabular version="3" rows="18" columns="2">
 <features tabularvalignment="middle">
 <column alignment="center" valignment="top" width="25text%">
 <column alignment="center" valignment="top" width="75text%">
@@ -8008,26 +8081,6 @@ Rotate specified dihedral to specified value or by given increment.
 <cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
 \begin_inset Text
 
-\begin_layout Plain Layout
-sequence
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Plain Layout
-Create a new molecule from a sequence of COORDS sets.
-\end_layout
-
-\end_inset
-</cell>
-</row>
-<row>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
 \begin_layout Plain Layout
 splitcoords
 \end_layout
@@ -10429,95 +10482,14 @@ crdout TZ2 tz2.rotate.1.mol2
 
 \begin_layout Subsection
 sequence
-\begin_inset CommandInset label
-LatexCommand label
-name "subsec:cpptraj-sequence"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout LyX-Code
-sequence name <output set name> <unit0> <unit1> ...
-\end_layout
-
-\begin_layout LyX-Code
-         [{libset <libsetname>} ...]
 \end_layout
 
-\begin_deeper
-\begin_layout Description
-name
-\begin_inset space ~
-\end_inset
-
-<output
-\begin_inset space ~
-\end_inset
-
-set
-\begin_inset space ~
-\end_inset
-
-name> Name of final molecule.
-\end_layout
-
-\begin_layout Description
-<unit0>
-\begin_inset space ~
-\end_inset
-
-<unit1> Name of COORDS set (with connection info).
-\end_layout
-
-\begin_layout Description
-[{libset
-\begin_inset space ~
-\end_inset
-
-<libsetname>}
-\begin_inset space ~
-\end_inset
-
-...} One or more set name prefixes of data sets (libraries) containing units.
-\end_layout
-
-\begin_layout Standard
-Data sets created:
-\end_layout
-
-\begin_layout Description
-<output
-\begin_inset space ~
-\end_inset
-
-set
-\begin_inset space ~
-\end_inset
-
-name> COORDS set containing final molecule.
-\end_layout
-
-\end_deeper
 \begin_layout Standard
-Connect units in different COORDS sets together to form a single molecule.
- Internal coordinates are used to try to determine the correct geometry around connection sites.
- The COORDS sets must have connection information set,
- either from reading in an Amber OFF library file or set manually via 
-\series bold
-\emph on
-dataset
-\series default
-\emph default
+Syntax for this command is now located here:
  
-\series bold
-connect
-\series default
- (see 
 \begin_inset CommandInset ref
-LatexCommand vref
-reference "subsec:cpptraj-datasetcmd"
+LatexCommand ref
+reference "subsec:cpptraj-sequence"
 plural "false"
 caps "false"
 noprefix "false"
@@ -10525,49 +10497,7 @@ nolink "false"
 
 \end_inset
 
-).
-\end_layout
-
-\begin_layout Standard
-For example,
- the following reads in two Mol2 files as COORDS sets,
- sets up connection atoms,
- then creates a molecule via 
-\series bold
-\emph on
-sequence:
-\end_layout
-
-\begin_layout LyX-Code
-parm MOC.mol2
-\end_layout
 
-\begin_layout LyX-Code
-loadcrd MOC.mol2 parm MOC.mol2 name MOC
-\end_layout
-
-\begin_layout LyX-Code
-dataset connect MOC tailmask @O5
-\end_layout
-
-\begin_layout LyX-Code
-parm CNALA.mol2 
-\end_layout
-
-\begin_layout LyX-Code
-loadcrd CNALA.mol2 parm CNALA.mol2 name CNALA
-\end_layout
-
-\begin_layout LyX-Code
-dataset connect CNALA headmask @N
-\end_layout
-
-\begin_layout LyX-Code
-sequence MOC CNALA name Mol
-\end_layout
-
-\begin_layout LyX-Code
-crdout Mol Mol.mol2
 \end_layout
 
 \begin_layout Subsection

From a794bcf0c2a4e01b981201be123bdcc883a1f521 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 1 Mar 2026 08:49:31 -0500
Subject: [PATCH 1412/1492] Make desc a hidden command since its primary use is
 debugging against leap

---
 src/Command.cpp   | 2 +-
 src/Exec_Desc.cpp | 5 +++++
 src/Exec_Desc.h   | 2 +-
 3 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/src/Command.cpp b/src/Command.cpp
index f0562af6ae..5fb2f4d163 100644
--- a/src/Command.cpp
+++ b/src/Command.cpp
@@ -311,7 +311,7 @@ void Command::Init() {
   Command::AddCmd( new Exec_Change(),        Cmd::EXE, 1, "change" );
   Command::AddCmd( new Exec_ChargeInfo(),    Cmd::EXE, 1, "charge" );
   Command::AddCmd( new Exec_CompareTop(),    Cmd::EXE, 1, "comparetop" );
-  Command::AddCmd( new Exec_Desc(),          Cmd::EXE, 1, "desc" );
+  Command::AddCmd( new Exec_Desc(),          Cmd::EXE, 1, "desc" ); // HIDDEN
   Command::AddCmd( new Exec_DihedralInfo(),Cmd::EXE, 3,"dihedrals","dihedralinfo","printdihedrals");
   Command::AddCmd( new Exec_HmassRepartition(),Cmd::EXE, 1, "hmassrepartition" );
   Command::AddCmd( new Exec_ImproperInfo(),Cmd::EXE, 3,"impropers","improperinfo","printimpropers");
diff --git a/src/Exec_Desc.cpp b/src/Exec_Desc.cpp
index 56aa0dd763..25ba06e56f 100644
--- a/src/Exec_Desc.cpp
+++ b/src/Exec_Desc.cpp
@@ -1,6 +1,11 @@
 #include "Exec_Desc.h"
 #include "CpptrajStdio.h"
 
+/** CONSTRUCTOR */
+Exec_Desc::Exec_Desc() : Exec(PARM) {
+  SetHidden(true);
+}
+
 int Exec_Desc::desc_atom(Topology const& topIn, int iat) {
   Atom const& AT = topIn[iat];
 
diff --git a/src/Exec_Desc.h b/src/Exec_Desc.h
index 2bf830a71d..b698cf3758 100644
--- a/src/Exec_Desc.h
+++ b/src/Exec_Desc.h
@@ -4,7 +4,7 @@
 /// <Enter description of Exec_Desc here>
 class Exec_Desc : public Exec {
   public:
-    Exec_Desc() : Exec(PARM) {}
+    Exec_Desc();
     void Help() const;
     DispatchObject* Alloc() const { return (DispatchObject*)new Exec_Desc(); }
     RetType Execute(CpptrajState&, ArgList&);

From 445d89ec6d4d3b6e4adebe9028f769bab2151e83 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Sun, 1 Mar 2026 09:04:31 -0500
Subject: [PATCH 1413/1492] Add more readdata formats to manual

---
 doc/cpptraj.lyx | 197 +++++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 193 insertions(+), 4 deletions(-)

diff --git a/doc/cpptraj.lyx b/doc/cpptraj.lyx
index f928df1f1e..20fa1da08c 100644
--- a/doc/cpptraj.lyx
+++ b/doc/cpptraj.lyx
@@ -3137,7 +3137,7 @@ status open
 \begin_layout Plain Layout
 \align center
 \begin_inset Tabular
-<lyxtabular version="3" rows="22" columns="5">
+<lyxtabular version="3" rows="26" columns="5">
 <features tabularvalignment="middle">
 <column alignment="center" valignment="top" width="20text%">
 <column alignment="center" valignment="top" width="20text%">
@@ -4149,7 +4149,7 @@ Read Only
 </cell>
 </row>
 <row>
-<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
 \begin_inset Text
 
 \begin_layout Plain Layout
@@ -4158,7 +4158,7 @@ Amber OFF Library File
 
 \end_inset
 </cell>
-<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
 \begin_inset Text
 
 \begin_layout Plain Layout
@@ -4168,13 +4168,202 @@ Amber OFF Library File
 
 \end_inset
 </cell>
-<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
 \begin_inset Text
 
 \begin_layout Plain Layout
 off,lib
 \end_layout
 
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+COORDS
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Read Only
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Amber Force Field
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+.parm
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+amberff
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Parameters
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Read Only
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Amber Force Mod
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+.frcmod
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+frcmod
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Parameters
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Read Only
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Amber leaprc File
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+.leaprc
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+leaprc
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Parameters,
+ COORDS
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Read Only
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Numpy array
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+.npy
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+numpy
+\end_layout
+
 \end_inset
 </cell>
 <cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">

From b659cb2860f020300311f3b88f990dc77c3d7233 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Mon, 2 Mar 2026 12:54:12 -0500
Subject: [PATCH 1414/1492] Fix up help text

---
 src/DataIO_AmberFF.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/DataIO_AmberFF.cpp b/src/DataIO_AmberFF.cpp
index 086e4f6e32..300bb66b5b 100644
--- a/src/DataIO_AmberFF.cpp
+++ b/src/DataIO_AmberFF.cpp
@@ -23,7 +23,7 @@ bool DataIO_AmberFF::ID_DataFormat(CpptrajFile& infile)
 // DataIO_AmberFF::ReadHelp()
 void DataIO_AmberFF::ReadHelp()
 {
-  mprintf("\tnbset <nonbond set name> : Nonbonded set name to use when multiple nonbond parameter sets.\n");
+  mprintf("\tnbset <nonbond set name> : Nonbonded set name to use when multiple nonbond parameter sets are present.\n");
 }
 
 // DataIO_AmberFF::processReadArgs()

From c7155a3d627125c729189c64435ea7af233b0627 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Mon, 2 Mar 2026 12:54:46 -0500
Subject: [PATCH 1415/1492] Add documentation for some datafile options

---
 doc/cpptraj.lyx | 67 +++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 67 insertions(+)

diff --git a/doc/cpptraj.lyx b/doc/cpptraj.lyx
index 20fa1da08c..2b6c81d38d 100644
--- a/doc/cpptraj.lyx
+++ b/doc/cpptraj.lyx
@@ -6599,6 +6599,73 @@ nolink "false"
 ).
 \end_layout
 
+\begin_layout Subsection
+Amber prep file options
+\end_layout
+
+\begin_layout Subsubsection*
+Read
+\end_layout
+
+\begin_layout LyX-Code
+[keepdummyatoms]
+\end_layout
+
+\begin_deeper
+\begin_layout Description
+keepdummyatoms Keep dummy atoms instead of removing them.
+\end_layout
+
+\end_deeper
+\begin_layout Subsection
+Amber Library (OFF) file options
+\end_layout
+
+\begin_layout Subsubsection*
+Read
+\end_layout
+
+\begin_layout LyX-Code
+[allowoverwrite]
+\end_layout
+
+\begin_deeper
+\begin_layout Description
+allowoverwrite If specified,
+ allow existing sets to be overwritten.
+\end_layout
+
+\end_deeper
+\begin_layout Subsection
+Amber Parameter (main force field) file options
+\end_layout
+
+\begin_layout Subsubsection*
+Read
+\end_layout
+
+\begin_layout LyX-Code
+[nbset <nonbond set name>]
+\end_layout
+
+\begin_deeper
+\begin_layout Description
+nbset
+\begin_inset space ~
+\end_inset
+
+<nonbond
+\begin_inset space ~
+\end_inset
+
+set
+\begin_inset space ~
+\end_inset
+
+name> Nonbonded set name to use when multiple nonbond parameters sets are present.
+\end_layout
+
+\end_deeper
 \begin_layout Section
 System Build and Parameterization Commands
 \begin_inset CommandInset label

From cc207fd4e800c680bea459f04e0c34f24c3f4901 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Mon, 2 Mar 2026 19:11:29 -0500
Subject: [PATCH 1416/1492] Add link to leaprc source

---
 doc/cpptraj.lyx | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/doc/cpptraj.lyx b/doc/cpptraj.lyx
index 2b6c81d38d..ea04168729 100644
--- a/doc/cpptraj.lyx
+++ b/doc/cpptraj.lyx
@@ -6666,6 +6666,26 @@ name> Nonbonded set name to use when multiple nonbond parameters sets are presen
 \end_layout
 
 \end_deeper
+\begin_layout Subsection
+Amber leaprc file options
+\end_layout
+
+\begin_layout Standard
+For a list of supported LEaP commands in leaprc files,
+ see 
+\begin_inset CommandInset ref
+LatexCommand vref
+reference "subsec:cpptraj-source"
+plural "false"
+caps "false"
+noprefix "false"
+nolink "false"
+
+\end_inset
+
+.
+\end_layout
+
 \begin_layout Section
 System Build and Parameterization Commands
 \begin_inset CommandInset label
@@ -7823,6 +7843,13 @@ crdout Mol Mol.mol2
 
 \begin_layout Subsection
 source
+\begin_inset CommandInset label
+LatexCommand label
+name "subsec:cpptraj-source"
+
+\end_inset
+
+
 \end_layout
 
 \begin_layout LyX-Code

From 9f847cd6ced5887b5bb3249dd54564eb2b5655b9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 3 Mar 2026 08:48:41 -0500
Subject: [PATCH 1417/1492] Add a build Example

---
 doc/cpptraj.lyx | 50 +++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 50 insertions(+)

diff --git a/doc/cpptraj.lyx b/doc/cpptraj.lyx
index ea04168729..a9ee37e7ba 100644
--- a/doc/cpptraj.lyx
+++ b/doc/cpptraj.lyx
@@ -7620,6 +7620,56 @@ fixatomorder
  keyword is specified it can create macromolecular assemblies from PDBs with multiple models.
 \end_layout
 
+\begin_layout Subsubsection*
+Example - Solvate and add ions,
+ system charge not known a priori
+\end_layout
+
+\begin_layout Standard
+This example loads a PDB as a COORDS data set,
+ then builds it and generates a topology and restart file.
+ Solvent is added with a 10 Angstrom buffer,
+ and enough Na+ or Cl- ions are added to neutralize the system depending on what the solute charge is.
+\end_layout
+
+\begin_layout LyX-Code
+source leaprc.protein.ff19SB
+\end_layout
+
+\begin_layout LyX-Code
+source leaprc.water.opc
+\end_layout
+
+\begin_layout LyX-Code
+parm 6g37.pdb 
+\end_layout
+
+\begin_layout LyX-Code
+loadcrd 6g37.pdb name MyMol
+\end_layout
+
+\begin_layout LyX-Code
+build crdset MyMol name Out title 6g37 
+\backslash
+
+\end_layout
+
+\begin_layout LyX-Code
+  parmout cpptraj.parm7 crdout cpptraj.rst7 
+\backslash
+
+\end_layout
+
+\begin_layout LyX-Code
+  solvateoct solventbox TIP3PBOX buffer 10.0 
+\backslash
+
+\end_layout
+
+\begin_layout LyX-Code
+  addionsrand ion1 Na+ nion1 0 ion2 Cl- nion2 0
+\end_layout
+
 \begin_layout Subsection
 sequence
 \begin_inset CommandInset label

From e5ba702d0c3e59032ffe685c76b93c010bed74bc Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 3 Mar 2026 08:56:15 -0500
Subject: [PATCH 1418/1492] Add entry about reading files as top/coords with
 readdata

---
 doc/cpptraj.lyx | 107 ++++++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 103 insertions(+), 4 deletions(-)

diff --git a/doc/cpptraj.lyx b/doc/cpptraj.lyx
index a9ee37e7ba..567484e445 100644
--- a/doc/cpptraj.lyx
+++ b/doc/cpptraj.lyx
@@ -3137,7 +3137,7 @@ status open
 \begin_layout Plain Layout
 \align center
 \begin_inset Tabular
-<lyxtabular version="3" rows="26" columns="5">
+<lyxtabular version="3" rows="27" columns="5">
 <features tabularvalignment="middle">
 <column alignment="center" valignment="top" width="20text%">
 <column alignment="center" valignment="top" width="20text%">
@@ -4339,7 +4339,7 @@ Read Only
 </cell>
 </row>
 <row>
-<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
 \begin_inset Text
 
 \begin_layout Plain Layout
@@ -4348,7 +4348,7 @@ Numpy array
 
 \end_inset
 </cell>
-<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
 \begin_inset Text
 
 \begin_layout Plain Layout
@@ -4357,13 +4357,60 @@ Numpy array
 
 \end_inset
 </cell>
-<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
 \begin_inset Text
 
 \begin_layout Plain Layout
 numpy
 \end_layout
 
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+COORDS
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Read Only
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Topology/Coordinates
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Various
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+coords
+\end_layout
+
 \end_inset
 </cell>
 <cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
@@ -6686,6 +6733,58 @@ nolink "false"
 .
 \end_layout
 
+\begin_layout Subsection
+Coords file options
+\end_layout
+
+\begin_layout Standard
+The 
+\series bold
+\emph on
+readdata
+\series default
+\emph default
+ command can be used to read in a file format that contains Topology 
+\series bold
+and
+\series default
+ Coordinate info (e.g.
+ PDB,
+ Mol2,
+ CIF,
+ etc.).
+ For a list of topology formats recognized by CPPTRAJ see 
+\begin_inset CommandInset ref
+LatexCommand vref
+reference "tab:cpptraj-Topology-formats"
+plural "false"
+caps "false"
+noprefix "false"
+nolink "false"
+
+\end_inset
+
+,
+ and for a list of coordinate formats recognized by CPPTRAJ see 
+\begin_inset CommandInset ref
+LatexCommand vref
+reference "tab:cpptraj-trajformats"
+plural "false"
+caps "false"
+noprefix "false"
+nolink "false"
+
+\end_inset
+
+.
+ For example,
+ to read in a PDB file as COORDS set named 'MyCrd':
+\end_layout
+
+\begin_layout LyX-Code
+readdata Mypdb.pdb as coords name MyCrd
+\end_layout
+
 \begin_layout Section
 System Build and Parameterization Commands
 \begin_inset CommandInset label

From d2887a39df86f3828e196e9c42f4e051c9444076 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 3 Mar 2026 10:01:33 -0500
Subject: [PATCH 1419/1492] Add information about CONNECT atoms with graft ic

---
 doc/cpptraj.lyx | 59 ++++++++++++++++++++++++++++++++++++++++++++++---
 1 file changed, 56 insertions(+), 3 deletions(-)

diff --git a/doc/cpptraj.lyx b/doc/cpptraj.lyx
index 567484e445..078d13d7b5 100644
--- a/doc/cpptraj.lyx
+++ b/doc/cpptraj.lyx
@@ -9558,6 +9558,19 @@ COORDS> Target coordinates that will be grafted onto.
 \end_deeper
 \begin_layout Description
 [ic] Connect source and target using internal coordinates.
+ If source and target contain CONNECT information (see 
+\begin_inset CommandInset ref
+LatexCommand vref
+reference "subsec:cpptraj-datasetcmd"
+plural "false"
+caps "false"
+noprefix "false"
+nolink "false"
+
+\end_inset
+
+),
+ that will be used to create a bond between source and target if a bond has not otherwise been specified.
 \end_layout
 
 \begin_layout Description
@@ -9633,8 +9646,24 @@ tgtmask
 bond
 \series default
  keyword can be used to create bonds between target and source in the final structure.
- If using internal coordinates to connect the units,
- exactly one bond must be specified.
+ 
+\end_layout
+
+\begin_layout Standard
+If using internal coordinates to connect the units,
+ a bond will be created between the source and target automatically if they contain CONNECT information (see 
+\begin_inset CommandInset ref
+LatexCommand vref
+reference "subsec:cpptraj-datasetcmd"
+plural "false"
+caps "false"
+noprefix "false"
+nolink "false"
+
+\end_inset
+
+).
+ Otherwise exactly one bond must be specified.
 \end_layout
 
 \begin_layout Subsection
@@ -10084,7 +10113,24 @@ crdout
 \series bold
 check
 \series default
- is specified;
+ is specified using the same algorithm used by the 
+\series bold
+\emph on
+check
+\series default
+\emph default
+ action (see 
+\begin_inset CommandInset ref
+LatexCommand vref
+reference "subsec:cpptraj-check"
+plural "false"
+caps "false"
+noprefix "false"
+nolink "false"
+
+\end_inset
+
+);
  in such cases the algorithm will attempt to resolve the clash as best it can.
  If clashes are not being resolved you can increase the number of rotation attempts 
 \family typewriter
@@ -26898,6 +26944,13 @@ center :1 mass
 
 \begin_layout Subsection
 check | checkoverlap | checkstructure
+\begin_inset CommandInset label
+LatexCommand label
+name "subsec:cpptraj-check"
+
+\end_inset
+
+
 \end_layout
 
 \begin_layout LyX-Code

From 74e59e1c24a7dee37845b088e2f8040190ece816 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 3 Mar 2026 10:13:03 -0500
Subject: [PATCH 1420/1492] Do not print warning for readdata coords if set not
 already present

---
 src/DataIO_Coords.cpp | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/src/DataIO_Coords.cpp b/src/DataIO_Coords.cpp
index 8ef1b0b27a..eb6389c8a6 100644
--- a/src/DataIO_Coords.cpp
+++ b/src/DataIO_Coords.cpp
@@ -72,11 +72,13 @@ int DataIO_Coords::ReadData(FileName const& fname, DataSetList& dsl, std::string
 
   DataSet* dset = 0;
   if (!dsname.empty()) {
-    // Is this set already present? TODO search without warning
-    dset = dsl.GetDataSet( dsname );
-    //if (dset == 0) {
-    //  dset = dsl.GetDataSet(fname.Base());
-    //}
+    // Is this set already present?
+    DataSetList selectedDS = dsl.SelectSets( dsname );
+    if (!selectedDS.empty()) {
+      dset = selectedDS[0];
+      if (selectedDS.size() > 1)
+        mprintf("Warning: %s selects multiple data sets, only using the first (%s)\n", dsname.c_str(), dset->legend());
+    }
     if (dset != 0) {
       if (!can_append(dset->Type())) {
         mprinterr("Error: Cannot append coordinates to existing set '%s'\n", dset->legend());

From a4f6e764694759ce4977b519f3b41c90ec2d54d4 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 3 Mar 2026 10:42:41 -0500
Subject: [PATCH 1421/1492] File names are now printed

---
 test/Test_ReadAmberFF/tip3pf.parm.dat.save        | 1 +
 test/Test_ReadAmberFF/toyrna.parm.dat.save        | 1 +
 test/Test_ReadAmberFF/toyrna.tip3pf.parm.dat.save | 1 +
 3 files changed, 3 insertions(+)

diff --git a/test/Test_ReadAmberFF/tip3pf.parm.dat.save b/test/Test_ReadAmberFF/tip3pf.parm.dat.save
index 3eb96e7c34..fa1afc17ab 100644
--- a/test/Test_ReadAmberFF/tip3pf.parm.dat.save
+++ b/test/Test_ReadAmberFF/tip3pf.parm.dat.save
@@ -1,4 +1,5 @@
 Parameter set: This is TIP3P (model F) of Price and Brooks, JCP 121:10096, 2004 
+	Files: frcmod.tip3pf
 Atom Types:
 	  Name  TypeIdx LJ       Radius        Depth         Mass       Polar.
 	    HW        0  1       0.0000       0.0000       1.0080       0.0000
diff --git a/test/Test_ReadAmberFF/toyrna.parm.dat.save b/test/Test_ReadAmberFF/toyrna.parm.dat.save
index 874c7c2694..13e2391f90 100644
--- a/test/Test_ReadAmberFF/toyrna.parm.dat.save
+++ b/test/Test_ReadAmberFF/toyrna.parm.dat.save
@@ -1,4 +1,5 @@
 Parameter set: toyrna force field
+	Files: toyrna.dat
 Nonbond parameters name: MOD4
 Atom Types:
 	  Name  TypeIdx LJ       Radius        Depth         Mass       Polar.
diff --git a/test/Test_ReadAmberFF/toyrna.tip3pf.parm.dat.save b/test/Test_ReadAmberFF/toyrna.tip3pf.parm.dat.save
index 8aaa5c48c8..1f684e8116 100644
--- a/test/Test_ReadAmberFF/toyrna.tip3pf.parm.dat.save
+++ b/test/Test_ReadAmberFF/toyrna.tip3pf.parm.dat.save
@@ -1,4 +1,5 @@
 Parameter set: toyrna force field + This is TIP3P (model F) of Price and Brooks, JCP 121:10096, 2004 
+	Files: toyrna.dat frcmod.tip3pf
 Nonbond parameters name: MOD4
 Atom Types:
 	  Name  TypeIdx LJ       Radius        Depth         Mass       Polar.

From 4d7ce7748a40cadaa11089b1801bcfd9e5fbeeae Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 3 Mar 2026 11:11:40 -0500
Subject: [PATCH 1422/1492] Fix up check help

---
 doc/cpptraj.lyx               | 98 ++++++++++++++++++++++++++++++++++-
 src/Action_CheckStructure.cpp |  2 +-
 2 files changed, 97 insertions(+), 3 deletions(-)

diff --git a/doc/cpptraj.lyx b/doc/cpptraj.lyx
index 078d13d7b5..b3b74cf3fd 100644
--- a/doc/cpptraj.lyx
+++ b/doc/cpptraj.lyx
@@ -9666,6 +9666,74 @@ nolink "false"
  Otherwise exactly one bond must be specified.
 \end_layout
 
+\begin_layout Standard
+Graft using RMSD and removing atoms.
+\end_layout
+
+\begin_layout LyX-Code
+readdata Tyr.mol2 as coords name TYR
+\end_layout
+
+\begin_layout LyX-Code
+readdata PRY.mol2 as coords name PRY
+\end_layout
+
+\begin_layout LyX-Code
+graft 
+\backslash
+
+\end_layout
+
+\begin_layout LyX-Code
+  tgt TYR 
+\backslash
+
+\end_layout
+
+\begin_layout LyX-Code
+  src PRY 
+\backslash
+
+\end_layout
+
+\begin_layout LyX-Code
+  name Final 
+\backslash
+
+\end_layout
+
+\begin_layout LyX-Code
+  srcfitmask @O1,C5,C6,C4,H6,H5,C7,C3,H7,H4,C2 
+\backslash
+
+\end_layout
+
+\begin_layout LyX-Code
+  tgtfitmask @OH,CZ,CE1,CE2,HE1,HE2,CD1,CD2,HD1,HD2,CG 
+\backslash
+
+\end_layout
+
+\begin_layout LyX-Code
+  srcmask !(@1-4) 
+\backslash
+
+\end_layout
+
+\begin_layout LyX-Code
+  tgtmask @C,O,CA,HA,N,H,CB,HB2,HB3 
+\backslash
+
+\end_layout
+
+\begin_layout LyX-Code
+  bond :1@CB,:1@C2
+\end_layout
+
+\begin_layout LyX-Code
+crdout Final Final.graft.mol2
+\end_layout
+
 \begin_layout Subsection
 loadcrd
 \end_layout
@@ -26982,11 +27050,15 @@ check
 \end_layout
 
 \begin_layout LyX-Code
-       [{noringcheck | [ringshortdist <rsdist>] [ringdcut <ringdcut>]
+      [{noringcheck | [ringshortdist <rsdist>] [ringdcut <ringdcut>]
 \end_layout
 
 \begin_layout LyX-Code
-                       [ringacut <ringacut>]}]
+                      [ringacut <ringacut>]}]
+\end_layout
+
+\begin_layout LyX-Code
+      [{checkxp | xpmask <xpmask>}]
 \end_layout
 
 \begin_deeper
@@ -27106,9 +27178,31 @@ skipbadframes
  (default 65 degrees).
 \end_layout
 
+\begin_layout Description
+[checkxp] If specified,
+ check extra points as well.
+\end_layout
+
+\begin_deeper
+\begin_layout Description
+xpmask
+\begin_inset space ~
+\end_inset
+
+<xpmask> Specify mask to select extra points;
+ default is '&@/XP' (atom element XP).
+\end_layout
+
+\end_deeper
 \end_deeper
 \begin_layout Standard
 Check the structure and report problems related to atomic overlap/unusual bond length/ring-bond intersections.
+ By default extra points are skipped because by design they are quite close to some atoms.
+ The 
+\series bold
+checkxp
+\series default
+ keyword can be specified to check extra points as well.
  Problems are reported when any two atoms in 
 \series bold
 <mask>
diff --git a/src/Action_CheckStructure.cpp b/src/Action_CheckStructure.cpp
index 08c12de7ac..299fe0a3f1 100644
--- a/src/Action_CheckStructure.cpp
+++ b/src/Action_CheckStructure.cpp
@@ -38,7 +38,7 @@ void Action_CheckStructure::Help() const {
           "  between the bond vector and ring perpendicular vector is less than\n"
           "  <ringacut>.\n"
           "  By default, extra points will be ignored as determined by 'xpmask'; the\n"
-          "  default mask to select extra points is '&@\\XP'. If 'checkxp' is specified\n",
+          "  default mask to select extra points is '&@/XP'. If 'checkxp' is specified\n",
           "  extra points will also be checked.\n"
           "  Warnings will go to the file specified by 'reportfile', STDOUT,\n"
           "  or will be suppressed if 'silent' is specified. If 'skipbadframes'\n"

From b195bf24d393895455dedf3762177dc0a85403ae Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 3 Mar 2026 14:12:59 -0500
Subject: [PATCH 1423/1492] Start build test

---
 test/Test_Build/RunTest.sh     |   24 +
 test/Test_Build/amino12.lib    | 3570 ++++++++++++++++++++++++++++++++
 test/Test_Build/aminoct12.lib  | 3344 ++++++++++++++++++++++++++++++
 test/Test_Build/aminont12.lib  | 3303 +++++++++++++++++++++++++++++
 test/Test_Build/frcmod.ff14SB  |  514 +++++
 test/Test_Build/parm10.dat     | 1005 +++++++++
 test/Test_Build/tz2.parm7.save | 1562 ++++++++++++++
 test/Test_Build/tz2.rst7.save  |  114 +
 8 files changed, 13436 insertions(+)
 create mode 100755 test/Test_Build/RunTest.sh
 create mode 100644 test/Test_Build/amino12.lib
 create mode 100644 test/Test_Build/aminoct12.lib
 create mode 100644 test/Test_Build/aminont12.lib
 create mode 100644 test/Test_Build/frcmod.ff14SB
 create mode 100644 test/Test_Build/parm10.dat
 create mode 100644 test/Test_Build/tz2.parm7.save
 create mode 100644 test/Test_Build/tz2.rst7.save

diff --git a/test/Test_Build/RunTest.sh b/test/Test_Build/RunTest.sh
new file mode 100755
index 0000000000..042825eefe
--- /dev/null
+++ b/test/Test_Build/RunTest.sh
@@ -0,0 +1,24 @@
+#!/bin/bash
+
+. ../MasterTest.sh
+
+CleanFiles cpptraj.in tz2.parm7 tz2.rst7
+
+TESTNAME='Build tests'
+
+INPUT='-i cpptraj.in'
+
+if [ ! -z "$AMBERHOME" ] ; then
+  echo "Warning: AMBERHOME is set; temporarily unsetting for $TESTNAME"
+  unset AMBERHOME
+fi
+
+cat > cpptraj.in <<EOF
+source leaprc.protein.ff14SB
+build ../tz2.pdb parmout tz2.parm7 crdout tz2.rst7
+EOF
+RunCpptraj "$TESTNAME"
+DoTest tz2.parm7.save tz2.parm7 -I %VERSION
+DoTest tz2.rst7.save tz2.rst7
+
+EndTest
diff --git a/test/Test_Build/amino12.lib b/test/Test_Build/amino12.lib
new file mode 100644
index 0000000000..c1b2f3bf90
--- /dev/null
+++ b/test/Test_Build/amino12.lib
@@ -0,0 +1,3570 @@
+!!index array str
+ "ALA"
+ "ARG"
+ "ASH"
+ "ASN"
+ "ASP"
+ "CYM"
+ "CYS"
+ "CYX"
+ "GLH"
+ "GLN"
+ "GLU"
+ "GLY"
+ "HID"
+ "HIE"
+ "HIP"
+ "HYP"
+ "ILE"
+ "LEU"
+ "LYN"
+ "LYS"
+ "MET"
+ "PHE"
+ "PRO"
+ "SER"
+ "THR"
+ "TRP"
+ "TYR"
+ "VAL"
+!entry.ALA.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N" 0 1 131072 1 7 -0.415700
+ "H" "H" 0 1 131072 2 1 0.271900
+ "CA" "CX" 0 1 131072 3 6 0.033700
+ "HA" "H1" 0 1 131072 4 1 0.082300
+ "CB" "CT" 0 1 131072 5 6 -0.182500
+ "HB1" "HC" 0 1 131072 6 1 0.060300
+ "HB2" "HC" 0 1 131072 7 1 0.060300
+ "HB3" "HC" 0 1 131072 8 1 0.060300
+ "C" "C" 0 1 131072 9 6 0.597300
+ "O" "O" 0 1 131072 10 8 -0.567900
+!entry.ALA.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
+ "H" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "H1" 0 -1 0.0
+ "CB" "CT" 0 -1 0.0
+ "HB1" "HC" 0 -1 0.0
+ "HB2" "HC" 0 -1 0.0
+ "HB3" "HC" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O" 0 -1 0.0
+!entry.ALA.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.ALA.unit.childsequence single int
+ 2
+!entry.ALA.unit.connect array int
+ 1
+ 9
+!entry.ALA.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 3 4 1
+ 3 5 1
+ 3 9 1
+ 5 6 1
+ 5 7 1
+ 5 8 1
+ 9 10 1
+!entry.ALA.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+!entry.ALA.unit.name single str
+ "ALA"
+!entry.ALA.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 3.909407 0.723611 -2.739882E-06
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 3.877484 3.115795 2.131197
+ 4.075059 4.623017 1.205786
+ 2.496995 3.801075 1.241379
+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+!entry.ALA.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 9 0 0 0 0
+!entry.ALA.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "ALA" 1 11 1 "p" 0
+!entry.ALA.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.ALA.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.ALA.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+!entry.ARG.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N" 0 1 131072 1 7 -0.347900
+ "H" "H" 0 1 131072 2 1 0.274700
+ "CA" "CX" 0 1 131072 3 6 -0.263700
+ "HA" "H1" 0 1 131072 4 1 0.156000
+ "CB" "C8" 0 1 131072 5 6 -0.000700
+ "HB2" "HC" 0 1 131072 6 1 0.032700
+ "HB3" "HC" 0 1 131072 7 1 0.032700
+ "CG" "C8" 0 1 131072 8 6 0.039000
+ "HG2" "HC" 0 1 131072 9 1 0.028500
+ "HG3" "HC" 0 1 131072 10 1 0.028500
+ "CD" "C8" 0 1 131072 11 6 0.048600
+ "HD2" "H1" 0 1 131072 12 1 0.068700
+ "HD3" "H1" 0 1 131072 13 1 0.068700
+ "NE" "N2" 0 1 131072 14 7 -0.529500
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+ "NH1" "N2" 0 1 131072 17 7 -0.862700
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+ "C" "C" 0 1 131072 23 6 0.734100
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+ "ASH"
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+ 1 12 0 0 0 0
+!entry.ASH.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "ASH" 1 14 1 "p" 0
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+ "C" "C" 0 1 131072 13 6 0.597300
+ "O" "O" 0 1 131072 14 8 -0.567900
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+ "HD22" "H" 0 -1 0.0
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+ 13
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+ "R" 1 "A" 13
+ "R" 1 "A" 14
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+ 3.325770 1.547909 -1.607204E-06
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+ 3.970048 2.845795 -1.311163E-07
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+ 5.485541 2.705207 -4.398755E-06
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+!entry.ASN.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 13 0 0 0 0
+!entry.ASN.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "ASN" 1 15 1 "p" 0
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+ "OD2" "O2" 0 1 131072 10 8 -0.801400
+ "C" "C" 0 1 131072 11 6 0.536600
+ "O" "O" 0 1 131072 12 8 -0.581900
+!entry.ASP.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
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+ 5 8 1
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+!entry.ASP.unit.name single str
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+!entry.ASP.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 11 0 0 0 0
+!entry.ASP.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
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+ 0
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+ "C" "C" 0 1 131072 9 6 0.597300
+ "O" "O" 0 1 131072 10 8 -0.567900
+!entry.CYM.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
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+ 1 2 1
+ 1 3 1
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+ 3 9 1
+ 5 6 1
+ 5 7 1
+ 5 8 1
+ 9 10 1
+!entry.CYM.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
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+!entry.CYM.unit.name single str
+ "CYM"
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+ 3.909407 0.723611 -2.739882E-06
+ 3.970048 2.845795 -1.311163E-07
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+ 5.485541 2.705207 -4.398755E-06
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+!entry.CYM.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 9 0 0 0 0
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+!entry.CYM.unit.velocities table  dbl x  dbl y  dbl z
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+!entry.CYS.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N" 0 1 131072 1 7 -0.415700
+ "H" "H" 0 1 131072 2 1 0.271900
+ "CA" "CX" 0 1 131072 3 6 0.021300
+ "HA" "H1" 0 1 131072 4 1 0.112400
+ "CB" "2C" 0 1 131072 5 6 -0.123100
+ "HB2" "H1" 0 1 131072 6 1 0.111200
+ "HB3" "H1" 0 1 131072 7 1 0.111200
+ "SG" "SH" 0 1 131072 8 16 -0.311900
+ "HG" "HS" 0 1 131072 9 1 0.193300
+ "C" "C" 0 1 131072 10 6 0.597300
+ "O" "O" 0 1 131072 11 8 -0.567900
+!entry.CYS.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
+ "H" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "H1" 0 -1 0.0
+ "CB" "2C" 0 -1 0.0
+ "HB2" "H1" 0 -1 0.0
+ "HB3" "H1" 0 -1 0.0
+ "SG" "SH" 0 -1 0.0
+ "HG" "HS" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O" 0 -1 0.0
+!entry.CYS.unit.boundbox array dbl
+ -1.000000
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+ 0.0
+ 0.0
+ 0.0
+!entry.CYS.unit.childsequence single int
+ 2
+!entry.CYS.unit.connect array int
+ 1
+ 10
+!entry.CYS.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 3 4 1
+ 3 5 1
+ 3 10 1
+ 5 6 1
+ 5 7 1
+ 5 8 1
+ 8 9 1
+ 10 11 1
+!entry.CYS.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+!entry.CYS.unit.name single str
+ "CYS"
+!entry.CYS.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 3.909407 0.723611 -2.739882E-06
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 2.496995 3.801075 1.241379
+ 3.877484 3.115795 2.131197
+ 4.309573 5.303523 1.366036
+ 3.725392 5.622018 2.517640
+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+!entry.CYS.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 10 0 0 0 0
+!entry.CYS.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "CYS" 1 12 1 "p" 0
+!entry.CYS.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.CYS.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.CYS.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
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+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+!entry.CYX.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N" 0 1 131072 1 7 -0.415700
+ "H" "H" 0 1 131072 2 1 0.271900
+ "CA" "CX" 0 1 131072 3 6 0.042900
+ "HA" "H1" 0 1 131072 4 1 0.076600
+ "CB" "2C" 0 1 131072 5 6 -0.079000
+ "HB2" "H1" 0 1 131072 6 1 0.091000
+ "HB3" "H1" 0 1 131072 7 1 0.091000
+ "SG" "S" 0 1 131072 8 16 -0.108100
+ "C" "C" 0 1 131072 9 6 0.597300
+ "O" "O" 0 1 131072 10 8 -0.567900
+!entry.CYX.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
+ "H" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "H1" 0 -1 0.0
+ "CB" "2C" 0 -1 0.0
+ "HB2" "H1" 0 -1 0.0
+ "HB3" "H1" 0 -1 0.0
+ "SG" "S" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O" 0 -1 0.0
+!entry.CYX.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.CYX.unit.childsequence single int
+ 2
+!entry.CYX.unit.connect array int
+ 1
+ 9
+!entry.CYX.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 3 4 1
+ 3 5 1
+ 3 9 1
+ 5 6 1
+ 5 7 1
+ 5 8 1
+ 9 10 1
+!entry.CYX.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+!entry.CYX.unit.name single str
+ "CYX"
+!entry.CYX.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 3.909407 0.723611 -2.739882E-06
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 2.496995 3.801075 1.241379
+ 3.877484 3.115795 2.131197
+ 4.309573 5.303523 1.366036
+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+!entry.CYX.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 9 8 0 0 0
+!entry.CYX.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "CYX" 1 11 1 "p" 0
+!entry.CYX.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.CYX.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.CYX.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
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+ 0.0 0.0 0.0
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+!entry.GLH.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N" 0 1 131072 1 7 -0.415700
+ "H" "H" 0 1 131072 2 1 0.271900
+ "CA" "CX" 0 1 131072 3 6 0.014500
+ "HA" "H1" 0 1 131072 4 1 0.077900
+ "CB" "2C" 0 1 131072 5 6 -0.007100
+ "HB2" "HC" 0 1 131072 6 1 0.025600
+ "HB3" "HC" 0 1 131072 7 1 0.025600
+ "CG" "2C" 0 1 131072 8 6 -0.017400
+ "HG2" "HC" 0 1 131072 9 1 0.043000
+ "HG3" "HC" 0 1 131072 10 1 0.043000
+ "CD" "C" 0 1 131072 11 6 0.680100
+ "OE1" "O" 0 1 131072 12 8 -0.583800
+ "OE2" "OH" 0 1 131072 13 8 -0.651100
+ "HE2" "HO" 0 1 131072 14 1 0.464100
+ "C" "C" 0 1 131072 15 6 0.597300
+ "O" "O" 0 1 131072 16 8 -0.567900
+!entry.GLH.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
+ "H" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "H1" 0 -1 0.0
+ "CB" "2C" 0 -1 0.0
+ "HB2" "HC" 0 -1 0.0
+ "HB3" "HC" 0 -1 0.0
+ "CG" "2C" 0 -1 0.0
+ "HG2" "HC" 0 -1 0.0
+ "HG3" "HC" 0 -1 0.0
+ "CD" "C" 0 -1 0.0
+ "OE1" "O" 0 -1 0.0
+ "OE2" "OH" 0 -1 0.0
+ "HE2" "HO" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O" 0 -1 0.0
+!entry.GLH.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.GLH.unit.childsequence single int
+ 2
+!entry.GLH.unit.connect array int
+ 1
+ 15
+!entry.GLH.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 3 4 1
+ 3 5 1
+ 3 15 1
+ 5 6 1
+ 5 7 1
+ 5 8 1
+ 8 9 1
+ 8 10 1
+ 8 11 1
+ 11 12 1
+ 11 13 1
+ 13 14 1
+ 15 16 1
+!entry.GLH.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+ "R" 1 "A" 14
+ "R" 1 "A" 15
+ "R" 1 "A" 16
+!entry.GLH.unit.name single str
+ "GLH"
+!entry.GLH.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 3.909407 0.723611 -2.739882E-06
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 2.496995 3.801075 1.241379
+ 3.877484 3.115795 2.131197
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+ 3.966923 5.535124 0.296342
+ 3.873732 5.805369 2.428706
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+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+!entry.GLH.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 15 0 0 0 0
+!entry.GLH.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "GLH" 1 17 1 "p" 0
+!entry.GLH.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.GLH.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.GLH.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
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+ 0.0 0.0 0.0
+!entry.GLN.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N" 0 1 131072 1 7 -0.415700
+ "H" "H" 0 1 131072 2 1 0.271900
+ "CA" "CX" 0 1 131072 3 6 -0.003100
+ "HA" "H1" 0 1 131072 4 1 0.085000
+ "CB" "2C" 0 1 131072 5 6 -0.003600
+ "HB2" "HC" 0 1 131072 6 1 0.017100
+ "HB3" "HC" 0 1 131072 7 1 0.017100
+ "CG" "2C" 0 1 131072 8 6 -0.064500
+ "HG2" "HC" 0 1 131072 9 1 0.035200
+ "HG3" "HC" 0 1 131072 10 1 0.035200
+ "CD" "C" 0 1 131072 11 6 0.695100
+ "OE1" "O" 0 1 131072 12 8 -0.608600
+ "NE2" "N" 0 1 131072 13 7 -0.940700
+ "HE21" "H" 0 1 131072 14 1 0.425100
+ "HE22" "H" 0 1 131072 15 1 0.425100
+ "C" "C" 0 1 131072 16 6 0.597300
+ "O" "O" 0 1 131072 17 8 -0.567900
+!entry.GLN.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
+ "H" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "H1" 0 -1 0.0
+ "CB" "2C" 0 -1 0.0
+ "HB2" "HC" 0 -1 0.0
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+ "CG" "2C" 0 -1 0.0
+ "HG2" "HC" 0 -1 0.0
+ "HG3" "HC" 0 -1 0.0
+ "CD" "C" 0 -1 0.0
+ "OE1" "O" 0 -1 0.0
+ "NE2" "N" 0 -1 0.0
+ "HE21" "H" 0 -1 0.0
+ "HE22" "H" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O" 0 -1 0.0
+!entry.GLN.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.GLN.unit.childsequence single int
+ 2
+!entry.GLN.unit.connect array int
+ 1
+ 16
+!entry.GLN.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 3 4 1
+ 3 5 1
+ 3 16 1
+ 5 6 1
+ 5 7 1
+ 5 8 1
+ 8 9 1
+ 8 10 1
+ 8 11 1
+ 11 12 1
+ 11 13 1
+ 13 14 1
+ 13 15 1
+ 16 17 1
+!entry.GLN.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+ "R" 1 "A" 14
+ "R" 1 "A" 15
+ "R" 1 "A" 16
+ "R" 1 "A" 17
+!entry.GLN.unit.name single str
+ "GLN"
+!entry.GLN.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 3.909407 0.723611 -2.739882E-06
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 2.496995 3.801075 1.241379
+ 3.877484 3.115795 2.131197
+ 4.274186 5.009602 1.194577
+ 5.354271 4.863178 1.185788
+ 3.973781 5.548460 0.295972
+ 3.906976 5.848443 2.410302
+ 3.138962 5.408349 3.262893
+ 4.458856 7.061523 2.488333
+ 4.248434 7.659045 3.274966
+ 5.084281 7.376210 1.760379
+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+!entry.GLN.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 16 0 0 0 0
+!entry.GLN.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "GLN" 1 18 1 "p" 0
+!entry.GLN.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.GLN.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.GLN.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
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+ 0.0 0.0 0.0
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+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+!entry.GLU.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N" 0 1 131072 1 7 -0.516300
+ "H" "H" 0 1 131072 2 1 0.293600
+ "CA" "CX" 0 1 131072 3 6 0.039700
+ "HA" "H1" 0 1 131072 4 1 0.110500
+ "CB" "2C" 0 1 131072 5 6 0.056000
+ "HB2" "HC" 0 1 131072 6 1 -0.017300
+ "HB3" "HC" 0 1 131072 7 1 -0.017300
+ "CG" "2C" 0 1 131072 8 6 0.013600
+ "HG2" "HC" 0 1 131072 9 1 -0.042500
+ "HG3" "HC" 0 1 131072 10 1 -0.042500
+ "CD" "CO" 0 1 131072 11 6 0.805400
+ "OE1" "O2" 0 1 131072 12 8 -0.818800
+ "OE2" "O2" 0 1 131072 13 8 -0.818800
+ "C" "C" 0 1 131072 14 6 0.536600
+ "O" "O" 0 1 131072 15 8 -0.581900
+!entry.GLU.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
+ "H" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
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+ "CG" "2C" 0 -1 0.0
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+ "HG3" "HC" 0 -1 0.0
+ "CD" "CO" 0 -1 0.0
+ "OE1" "O2" 0 -1 0.0
+ "OE2" "O2" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O" 0 -1 0.0
+!entry.GLU.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.GLU.unit.childsequence single int
+ 2
+!entry.GLU.unit.connect array int
+ 1
+ 14
+!entry.GLU.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 3 4 1
+ 3 5 1
+ 3 14 1
+ 5 6 1
+ 5 7 1
+ 5 8 1
+ 8 9 1
+ 8 10 1
+ 8 11 1
+ 11 12 1
+ 11 13 1
+ 14 15 1
+!entry.GLU.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+ "R" 1 "A" 14
+ "R" 1 "A" 15
+!entry.GLU.unit.name single str
+ "GLU"
+!entry.GLU.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 3.909407 0.723611 -2.739882E-06
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 2.496995 3.801075 1.241379
+ 3.877484 3.115795 2.131197
+ 4.267328 4.996267 1.194946
+ 5.347413 4.849843 1.186158
+ 3.966923 5.535124 0.296342
+ 3.873732 5.805369 2.428706
+ 4.594590 5.679012 3.454376
+ 2.855965 6.542070 2.333721
+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+!entry.GLU.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 14 0 0 0 0
+!entry.GLU.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "GLU" 1 16 1 "p" 0
+!entry.GLU.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.GLU.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.GLU.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
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+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+!entry.GLY.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N" 0 1 131072 1 7 -0.415700
+ "H" "H" 0 1 131072 2 1 0.271900
+ "CA" "CX" 0 1 131072 3 6 -0.025200
+ "HA2" "H1" 0 1 131072 4 1 0.069800
+ "HA3" "H1" 0 1 131072 5 1 0.069800
+ "C" "C" 0 1 131072 6 6 0.597300
+ "O" "O" 0 1 131072 7 8 -0.567900
+!entry.GLY.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
+ "H" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA2" "H1" 0 -1 0.0
+ "HA3" "H1" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O" 0 -1 0.0
+!entry.GLY.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.GLY.unit.childsequence single int
+ 2
+!entry.GLY.unit.connect array int
+ 1
+ 6
+!entry.GLY.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 3 4 1
+ 3 5 1
+ 3 6 1
+ 6 7 1
+!entry.GLY.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+!entry.GLY.unit.name single str
+ "GLY"
+!entry.GLY.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 3.909407 0.723611 -2.739882E-06
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.671668 3.400125 0.889824
+ 5.483710 2.686702 -4.438857E-06
+ 5.993369 1.568360 -8.469843E-06
+!entry.GLY.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 6 0 0 0 0
+!entry.GLY.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "GLY" 1 8 1 "p" 0
+!entry.GLY.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.GLY.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.GLY.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+!entry.HID.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N" 0 1 131072 1 7 -0.415700
+ "H" "H" 0 1 131072 2 1 0.271900
+ "CA" "CX" 0 1 131072 3 6 0.018800
+ "HA" "H1" 0 1 131072 4 1 0.088100
+ "CB" "CT" 0 1 131072 5 6 -0.046200
+ "HB2" "HC" 0 1 131072 6 1 0.040200
+ "HB3" "HC" 0 1 131072 7 1 0.040200
+ "CG" "CC" 0 1 131072 8 6 -0.026600
+ "ND1" "NA" 0 1 131072 9 7 -0.381100
+ "HD1" "H" 0 1 131072 10 1 0.364900
+ "CE1" "CR" 0 1 131072 11 6 0.205700
+ "HE1" "H5" 0 1 131072 12 1 0.139200
+ "NE2" "NB" 0 1 131072 13 7 -0.572700
+ "CD2" "CV" 0 1 131072 14 6 0.129200
+ "HD2" "H4" 0 1 131072 15 1 0.114700
+ "C" "C" 0 1 131072 16 6 0.597300
+ "O" "O" 0 1 131072 17 8 -0.567900
+!entry.HID.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
+ "H" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "H1" 0 -1 0.0
+ "CB" "CT" 0 -1 0.0
+ "HB2" "HC" 0 -1 0.0
+ "HB3" "HC" 0 -1 0.0
+ "CG" "CC" 0 -1 0.0
+ "ND1" "NA" 0 -1 0.0
+ "HD1" "H" 0 -1 0.0
+ "CE1" "CR" 0 -1 0.0
+ "HE1" "H5" 0 -1 0.0
+ "NE2" "NB" 0 -1 0.0
+ "CD2" "CV" 0 -1 0.0
+ "HD2" "H4" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O" 0 -1 0.0
+!entry.HID.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.HID.unit.childsequence single int
+ 2
+!entry.HID.unit.connect array int
+ 1
+ 16
+!entry.HID.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 3 4 1
+ 3 5 1
+ 3 16 1
+ 5 6 1
+ 5 7 1
+ 5 8 1
+ 8 9 1
+ 8 14 1
+ 9 10 1
+ 9 11 1
+ 11 12 1
+ 11 13 1
+ 13 14 1
+ 14 15 1
+ 16 17 1
+!entry.HID.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+ "R" 1 "A" 14
+ "R" 1 "A" 15
+ "R" 1 "A" 16
+ "R" 1 "A" 17
+!entry.HID.unit.name single str
+ "HID"
+!entry.HID.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 3.909407 0.723611 -2.739882E-06
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 2.496995 3.801075 1.241379
+ 3.877484 3.115795 2.131197
+ 4.200813 5.026064 1.321087
+ 3.942782 5.885086 2.382972
+ 3.339725 5.691913 3.169805
+ 4.624274 6.997642 2.182500
+ 4.563048 7.811875 2.904563
+ 5.294011 6.891451 1.061663
+ 5.058974 5.678868 0.492453
+ 5.537741 5.417846 -0.451343
+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+!entry.HID.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 16 0 0 0 0
+!entry.HID.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "HID" 1 18 1 "p" 0
+!entry.HID.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.HID.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.HID.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
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+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+!entry.HIE.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N" 0 1 131072 1 7 -0.415700
+ "H" "H" 0 1 131072 2 1 0.271900
+ "CA" "CX" 0 1 131072 3 6 -0.058100
+ "HA" "H1" 0 1 131072 4 1 0.136000
+ "CB" "CT" 0 1 131072 5 6 -0.007400
+ "HB2" "HC" 0 1 131072 6 1 0.036700
+ "HB3" "HC" 0 1 131072 7 1 0.036700
+ "CG" "CC" 0 1 131072 8 6 0.186800
+ "ND1" "NB" 0 1 131072 9 7 -0.543200
+ "CE1" "CR" 0 1 131072 10 6 0.163500
+ "HE1" "H5" 0 1 131072 11 1 0.143500
+ "NE2" "NA" 0 1 131072 12 7 -0.279500
+ "HE2" "H" 0 1 131072 13 1 0.333900
+ "CD2" "CW" 0 1 131072 14 6 -0.220700
+ "HD2" "H4" 0 1 131072 15 1 0.186200
+ "C" "C" 0 1 131072 16 6 0.597300
+ "O" "O" 0 1 131072 17 8 -0.567900
+!entry.HIE.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
+ "H" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "H1" 0 -1 0.0
+ "CB" "CT" 0 -1 0.0
+ "HB2" "HC" 0 -1 0.0
+ "HB3" "HC" 0 -1 0.0
+ "CG" "CC" 0 -1 0.0
+ "ND1" "NB" 0 -1 0.0
+ "CE1" "CR" 0 -1 0.0
+ "HE1" "H5" 0 -1 0.0
+ "NE2" "NA" 0 -1 0.0
+ "HE2" "H" 0 -1 0.0
+ "CD2" "CW" 0 -1 0.0
+ "HD2" "H4" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O" 0 -1 0.0
+!entry.HIE.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.HIE.unit.childsequence single int
+ 2
+!entry.HIE.unit.connect array int
+ 1
+ 16
+!entry.HIE.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 3 4 1
+ 3 5 1
+ 3 16 1
+ 5 6 1
+ 5 7 1
+ 5 8 1
+ 8 9 1
+ 8 14 1
+ 9 10 1
+ 10 11 1
+ 10 12 1
+ 12 13 1
+ 12 14 1
+ 14 15 1
+ 16 17 1
+!entry.HIE.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+ "R" 1 "A" 14
+ "R" 1 "A" 15
+ "R" 1 "A" 16
+ "R" 1 "A" 17
+!entry.HIE.unit.name single str
+ "HIE"
+!entry.HIE.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 3.909407 0.723611 -2.739882E-06
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 2.496995 3.801075 1.241379
+ 3.877484 3.115795 2.131197
+ 4.200813 5.026064 1.321087
+ 3.942782 5.885086 2.382972
+ 4.624274 6.997642 2.182500
+ 4.563048 7.811875 2.904563
+ 5.294011 6.891451 1.061663
+ 5.896297 7.605085 0.676854
+ 5.058974 5.678868 0.492453
+ 5.537741 5.417846 -0.451343
+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+!entry.HIE.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 16 0 0 0 0
+!entry.HIE.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "HIE" 1 18 1 "p" 0
+!entry.HIE.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.HIE.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.HIE.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+!entry.HIP.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N" 0 1 131072 1 7 -0.347900
+ "H" "H" 0 1 131072 2 1 0.274700
+ "CA" "CX" 0 1 131072 3 6 -0.135400
+ "HA" "H1" 0 1 131072 4 1 0.121200
+ "CB" "CT" 0 1 131072 5 6 -0.041400
+ "HB2" "HC" 0 1 131072 6 1 0.081000
+ "HB3" "HC" 0 1 131072 7 1 0.081000
+ "CG" "CC" 0 1 131072 8 6 -0.001200
+ "ND1" "NA" 0 1 131072 9 7 -0.151300
+ "HD1" "H" 0 1 131072 10 1 0.386600
+ "CE1" "CR" 0 1 131072 11 6 -0.017000
+ "HE1" "H5" 0 1 131072 12 1 0.268100
+ "NE2" "NA" 0 1 131072 13 7 -0.171800
+ "HE2" "H" 0 1 131072 14 1 0.391100
+ "CD2" "CW" 0 1 131072 15 6 -0.114100
+ "HD2" "H4" 0 1 131072 16 1 0.231700
+ "C" "C" 0 1 131072 17 6 0.734100
+ "O" "O" 0 1 131072 18 8 -0.589400
+!entry.HIP.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
+ "H" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "H1" 0 -1 0.0
+ "CB" "CT" 0 -1 0.0
+ "HB2" "HC" 0 -1 0.0
+ "HB3" "HC" 0 -1 0.0
+ "CG" "CC" 0 -1 0.0
+ "ND1" "NA" 0 -1 0.0
+ "HD1" "H" 0 -1 0.0
+ "CE1" "CR" 0 -1 0.0
+ "HE1" "H5" 0 -1 0.0
+ "NE2" "NA" 0 -1 0.0
+ "HE2" "H" 0 -1 0.0
+ "CD2" "CW" 0 -1 0.0
+ "HD2" "H4" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O" 0 -1 0.0
+!entry.HIP.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.HIP.unit.childsequence single int
+ 2
+!entry.HIP.unit.connect array int
+ 1
+ 17
+!entry.HIP.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 3 4 1
+ 3 5 1
+ 3 17 1
+ 5 6 1
+ 5 7 1
+ 5 8 1
+ 8 9 1
+ 8 15 1
+ 9 10 1
+ 9 11 1
+ 11 12 1
+ 11 13 1
+ 13 14 1
+ 13 15 1
+ 15 16 1
+ 17 18 1
+!entry.HIP.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+ "R" 1 "A" 14
+ "R" 1 "A" 15
+ "R" 1 "A" 16
+ "R" 1 "A" 17
+ "R" 1 "A" 18
+!entry.HIP.unit.name single str
+ "HIP"
+!entry.HIP.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 3.909407 0.723611 -2.739882E-06
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 2.496995 3.801075 1.241379
+ 3.877484 3.115795 2.131197
+ 4.200813 5.026064 1.321087
+ 3.942782 5.885086 2.382972
+ 3.339725 5.691913 3.169805
+ 4.624274 6.997642 2.182500
+ 4.563048 7.811875 2.904563
+ 5.294011 6.891451 1.061663
+ 5.896297 7.605085 0.676854
+ 5.058974 5.678868 0.492453
+ 5.537741 5.417846 -0.451343
+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+!entry.HIP.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 17 0 0 0 0
+!entry.HIP.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "HIP" 1 19 1 "p" 0
+!entry.HIP.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.HIP.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.HIP.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+!entry.HYP.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N" 0 1 131072 1 7 -0.254800
+ "CD" "CT" 0 1 131072 2 6 0.059500
+ "HD22" "H1" 0 1 131072 3 1 0.070000
+ "HD23" "H1" 0 1 131072 4 1 0.070000
+ "CG" "CT" 0 1 131072 5 6 0.040000
+ "HG" "H1" 0 1 131072 6 1 0.041600
+ "OD1" "OH" 0 1 131072 7 8 -0.613400
+ "HD1" "HO" 0 1 131072 8 1 0.385100
+ "CB" "CT" 0 1 131072 9 6 0.020300
+ "HB2" "HC" 0 1 131072 10 1 0.042600
+ "HB3" "HC" 0 1 131072 11 1 0.042600
+ "CA" "CX" 0 1 131072 12 6 0.004700
+ "HA" "H1" 0 1 131072 13 1 0.077000
+ "C" "C" 0 1 131072 14 6 0.589600
+ "O" "O" 0 1 131072 15 8 -0.574800
+!entry.HYP.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
+ "CD" "CT" 0 -1 0.0
+ "HD22" "H1" 0 -1 0.0
+ "HD23" "H1" 0 -1 0.0
+ "CG" "CT" 0 -1 0.0
+ "HG" "H1" 0 -1 0.0
+ "OD1" "OH" 0 -1 0.0
+ "HD1" "HO" 0 -1 0.0
+ "CB" "CT" 0 -1 0.0
+ "HB2" "HC" 0 -1 0.0
+ "HB3" "HC" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "H1" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O" 0 -1 0.0
+!entry.HYP.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.HYP.unit.childsequence single int
+ 2
+!entry.HYP.unit.connect array int
+ 1
+ 14
+!entry.HYP.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 12 1
+ 2 3 1
+ 2 4 1
+ 2 5 1
+ 5 6 1
+ 5 7 1
+ 5 9 1
+ 7 8 1
+ 9 10 1
+ 9 11 1
+ 9 12 1
+ 12 13 1
+ 12 14 1
+ 14 15 1
+!entry.HYP.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+ "R" 1 "A" 14
+ "R" 1 "A" 15
+!entry.HYP.unit.name single str
+ "HYP"
+!entry.HYP.unit.positions table  dbl x  dbl y  dbl z
+ 3.326834 1.557389 -1.603945E-06
+ 4.302147 0.476598 0.080119
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+ 3.955888 -0.274040 0.790574
+ 5.547126 1.172441 0.544693
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+ 5.687901 1.006813 1.978308
+ 6.219605 0.169859 2.170401
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+ 5.969289 2.861861 -0.694123
+ 5.690642 3.251038 1.019947
+ 3.933610 2.871277 -0.104508
+ 3.611470 3.488570 0.734106
+ 3.505164 3.526392 -1.409783
+ 2.754240 2.939065 -2.185412
+!entry.HYP.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 14 0 0 0 0
+!entry.HYP.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "HYP" 1 16 1 "p" 0
+!entry.HYP.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.HYP.unit.solventcap array dbl
+ -1.000000
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+ "N" "N" 0 1 131072 1 7 -0.415700
+ "H" "H" 0 1 131072 2 1 0.271900
+ "CA" "CX" 0 1 131072 3 6 -0.059700
+ "HA" "H1" 0 1 131072 4 1 0.086900
+ "CB" "3C" 0 1 131072 5 6 0.130300
+ "HB" "HC" 0 1 131072 6 1 0.018700
+ "CG2" "CT" 0 1 131072 7 6 -0.320400
+ "HG21" "HC" 0 1 131072 8 1 0.088200
+ "HG22" "HC" 0 1 131072 9 1 0.088200
+ "HG23" "HC" 0 1 131072 10 1 0.088200
+ "CG1" "2C" 0 1 131072 11 6 -0.043000
+ "HG12" "HC" 0 1 131072 12 1 0.023600
+ "HG13" "HC" 0 1 131072 13 1 0.023600
+ "CD1" "CT" 0 1 131072 14 6 -0.066000
+ "HD11" "HC" 0 1 131072 15 1 0.018600
+ "HD12" "HC" 0 1 131072 16 1 0.018600
+ "HD13" "HC" 0 1 131072 17 1 0.018600
+ "C" "C" 0 1 131072 18 6 0.597300
+ "O" "O" 0 1 131072 19 8 -0.567900
+!entry.ILE.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
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+ "HG21" "HC" 0 -1 0.0
+ "HG22" "HC" 0 -1 0.0
+ "HG23" "HC" 0 -1 0.0
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+ "HG12" "HC" 0 -1 0.0
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+ "HD13" "HC" 0 -1 0.0
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+!entry.ILE.unit.childsequence single int
+ 2
+!entry.ILE.unit.connect array int
+ 1
+ 18
+!entry.ILE.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 3 4 1
+ 3 5 1
+ 3 18 1
+ 5 6 1
+ 5 7 1
+ 5 11 1
+ 7 8 1
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+ 14 15 1
+ 14 16 1
+ 14 17 1
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+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+ "R" 1 "A" 14
+ "R" 1 "A" 15
+ "R" 1 "A" 16
+ "R" 1 "A" 17
+ "R" 1 "A" 18
+ "R" 1 "A" 19
+!entry.ILE.unit.name single str
+ "ILE"
+!entry.ILE.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 3.909407 0.723611 -2.739882E-06
+ 3.970048 2.845795 -1.311163E-07
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+ 3.552136 3.620733 1.245168
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+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+!entry.ILE.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 18 0 0 0 0
+!entry.ILE.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "ILE" 1 20 1 "p" 0
+!entry.ILE.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.ILE.unit.solventcap array dbl
+ -1.000000
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+!entry.ILE.unit.velocities table  dbl x  dbl y  dbl z
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+ "N" "N" 0 1 131072 1 7 -0.415700
+ "H" "H" 0 1 131072 2 1 0.271900
+ "CA" "CX" 0 1 131072 3 6 -0.051800
+ "HA" "H1" 0 1 131072 4 1 0.092200
+ "CB" "2C" 0 1 131072 5 6 -0.110200
+ "HB2" "HC" 0 1 131072 6 1 0.045700
+ "HB3" "HC" 0 1 131072 7 1 0.045700
+ "CG" "3C" 0 1 131072 8 6 0.353100
+ "HG" "HC" 0 1 131072 9 1 -0.036100
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+ "HD11" "HC" 0 1 131072 11 1 0.100000
+ "HD12" "HC" 0 1 131072 12 1 0.100000
+ "HD13" "HC" 0 1 131072 13 1 0.100000
+ "CD2" "CT" 0 1 131072 14 6 -0.412100
+ "HD21" "HC" 0 1 131072 15 1 0.100000
+ "HD22" "HC" 0 1 131072 16 1 0.100000
+ "HD23" "HC" 0 1 131072 17 1 0.100000
+ "C" "C" 0 1 131072 18 6 0.597300
+ "O" "O" 0 1 131072 19 8 -0.567900
+!entry.LEU.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
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+ "HD23" "HC" 0 -1 0.0
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+!entry.LEU.unit.boundbox array dbl
+ -1.000000
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+ 0.0
+!entry.LEU.unit.childsequence single int
+ 2
+!entry.LEU.unit.connect array int
+ 1
+ 18
+!entry.LEU.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 3 4 1
+ 3 5 1
+ 3 18 1
+ 5 6 1
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+ 5 8 1
+ 8 9 1
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+ 10 13 1
+ 14 15 1
+ 14 16 1
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+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
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+ "R" 1 "A" 14
+ "R" 1 "A" 15
+ "R" 1 "A" 16
+ "R" 1 "A" 17
+ "R" 1 "A" 18
+ "R" 1 "A" 19
+!entry.LEU.unit.name single str
+ "LEU"
+!entry.LEU.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 3.909407 0.723611 -2.739882E-06
+ 3.970048 2.845795 -1.311163E-07
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+ 3.576965 3.653838 1.232143
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+ 4.274186 5.009602 1.194577
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+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+!entry.LEU.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 18 0 0 0 0
+!entry.LEU.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "LEU" 1 20 1 "p" 0
+!entry.LEU.unit.residuesPdbSequenceNumber array int
+ 0
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+ -1.000000
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+ "H" "H" 0 1 131072 2 1 0.271900
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+ "HA" "H1" 0 1 131072 4 1 0.099400
+ "CB" "CT" 0 1 131072 5 6 -0.048450
+ "HB2" "HC" 0 1 131072 6 1 0.034000
+ "HB3" "HC" 0 1 131072 7 1 0.034000
+ "CG" "CT" 0 1 131072 8 6 0.066120
+ "HG2" "HC" 0 1 131072 9 1 0.010410
+ "HG3" "HC" 0 1 131072 10 1 0.010410
+ "CD" "CT" 0 1 131072 11 6 -0.037680
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+ "HD3" "HC" 0 1 131072 13 1 0.011550
+ "CE" "CT" 0 1 131072 14 6 0.326040
+ "HE2" "HP" 0 1 131072 15 1 -0.033580
+ "HE3" "HP" 0 1 131072 16 1 -0.033580
+ "NZ" "N3" 0 1 131072 17 7 -1.035810
+ "HZ2" "H" 0 1 131072 18 1 0.386040
+ "HZ3" "H" 0 1 131072 19 1 0.386040
+ "C" "C" 0 1 131072 20 6 0.597300
+ "O" "O" 0 1 131072 21 8 -0.567900
+!entry.LYN.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
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+ "HB2" "HC" 0 -1 0.0
+ "HB3" "HC" 0 -1 0.0
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+ "HD3" "HC" 0 -1 0.0
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+ "C" "C" 0 -1 0.0
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+!entry.LYN.unit.boundbox array dbl
+ -1.000000
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+ 0.0
+!entry.LYN.unit.childsequence single int
+ 2
+!entry.LYN.unit.connect array int
+ 1
+ 20
+!entry.LYN.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 3 4 1
+ 3 5 1
+ 3 20 1
+ 5 6 1
+ 5 7 1
+ 5 8 1
+ 8 9 1
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+ 11 13 1
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+ 14 15 1
+ 14 16 1
+ 14 17 1
+ 17 18 1
+ 17 19 1
+ 20 21 1
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+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
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+ "R" 1 "A" 14
+ "R" 1 "A" 15
+ "R" 1 "A" 16
+ "R" 1 "A" 17
+ "R" 1 "A" 18
+ "R" 1 "A" 19
+ "R" 1 "A" 20
+ "R" 1 "A" 21
+!entry.LYN.unit.name single str
+ "LYN"
+!entry.LYN.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 3.909407 0.723611 -2.739882E-06
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 2.496995 3.801075 1.241379
+ 3.877484 3.115795 2.131197
+ 4.274186 5.009602 1.194577
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+ 3.973781 5.548460 0.295972
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+ 3.198675 8.088466 3.584971
+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+!entry.LYN.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 20 0 0 0 0
+!entry.LYN.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "LYN" 1 22 1 "p" 0
+!entry.LYN.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.LYN.unit.solventcap array dbl
+ -1.000000
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+ 0.0
+ 0.0
+!entry.LYN.unit.velocities table  dbl x  dbl y  dbl z
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+ "H" "H" 0 1 131072 2 1 0.274700
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+ "HG2" "HC" 0 1 131072 9 1 0.010300
+ "HG3" "HC" 0 1 131072 10 1 0.010300
+ "CD" "C8" 0 1 131072 11 6 -0.047900
+ "HD2" "HC" 0 1 131072 12 1 0.062100
+ "HD3" "HC" 0 1 131072 13 1 0.062100
+ "CE" "C8" 0 1 131072 14 6 -0.014300
+ "HE2" "HP" 0 1 131072 15 1 0.113500
+ "HE3" "HP" 0 1 131072 16 1 0.113500
+ "NZ" "N3" 0 1 131072 17 7 -0.385400
+ "HZ1" "H" 0 1 131072 18 1 0.340000
+ "HZ2" "H" 0 1 131072 19 1 0.340000
+ "HZ3" "H" 0 1 131072 20 1 0.340000
+ "C" "C" 0 1 131072 21 6 0.734100
+ "O" "O" 0 1 131072 22 8 -0.589400
+!entry.LYS.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
+ "H" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
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+ "HE2" "HP" 0 -1 0.0
+ "HE3" "HP" 0 -1 0.0
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+ "HZ2" "H" 0 -1 0.0
+ "HZ3" "H" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O" 0 -1 0.0
+!entry.LYS.unit.boundbox array dbl
+ -1.000000
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+ 0.0
+ 0.0
+!entry.LYS.unit.childsequence single int
+ 2
+!entry.LYS.unit.connect array int
+ 1
+ 21
+!entry.LYS.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 3 4 1
+ 3 5 1
+ 3 21 1
+ 5 6 1
+ 5 7 1
+ 5 8 1
+ 8 9 1
+ 8 10 1
+ 8 11 1
+ 11 12 1
+ 11 13 1
+ 11 14 1
+ 14 15 1
+ 14 16 1
+ 14 17 1
+ 17 18 1
+ 17 19 1
+ 17 20 1
+ 21 22 1
+!entry.LYS.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+ "R" 1 "A" 14
+ "R" 1 "A" 15
+ "R" 1 "A" 16
+ "R" 1 "A" 17
+ "R" 1 "A" 18
+ "R" 1 "A" 19
+ "R" 1 "A" 20
+ "R" 1 "A" 21
+ "R" 1 "A" 22
+!entry.LYS.unit.name single str
+ "LYS"
+!entry.LYS.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 3.909407 0.723611 -2.739882E-06
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 2.496995 3.801075 1.241379
+ 3.877484 3.115795 2.131197
+ 4.274186 5.009602 1.194577
+ 5.354271 4.863178 1.185788
+ 3.973781 5.548460 0.295972
+ 3.881105 5.817645 2.426721
+ 2.801135 5.964881 2.435959
+ 4.181626 5.279602 3.325774
+ 4.578325 7.173410 2.389153
+ 5.658410 7.026987 2.380363
+ 4.277917 7.712267 1.490550
+ 4.199422 7.952309 3.576860
+ 4.478085 7.453366 4.409628
+ 4.661186 8.850226 3.551979
+ 3.198675 8.088466 3.584971
+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+!entry.LYS.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 21 0 0 0 0
+!entry.LYS.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "LYS" 1 23 1 "p" 0
+!entry.LYS.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.LYS.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
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+!entry.LYS.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
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+!entry.MET.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N" 0 1 131072 1 7 -0.415700
+ "H" "H" 0 1 131072 2 1 0.271900
+ "CA" "CX" 0 1 131072 3 6 -0.023700
+ "HA" "H1" 0 1 131072 4 1 0.088000
+ "CB" "2C" 0 1 131072 5 6 0.034200
+ "HB2" "HC" 0 1 131072 6 1 0.024100
+ "HB3" "HC" 0 1 131072 7 1 0.024100
+ "CG" "2C" 0 1 131072 8 6 0.001800
+ "HG2" "H1" 0 1 131072 9 1 0.044000
+ "HG3" "H1" 0 1 131072 10 1 0.044000
+ "SD" "S" 0 1 131072 11 16 -0.273700
+ "CE" "CT" 0 1 131072 12 6 -0.053600
+ "HE1" "H1" 0 1 131072 13 1 0.068400
+ "HE2" "H1" 0 1 131072 14 1 0.068400
+ "HE3" "H1" 0 1 131072 15 1 0.068400
+ "C" "C" 0 1 131072 16 6 0.597300
+ "O" "O" 0 1 131072 17 8 -0.567900
+!entry.MET.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
+ "H" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "H1" 0 -1 0.0
+ "CB" "2C" 0 -1 0.0
+ "HB2" "HC" 0 -1 0.0
+ "HB3" "HC" 0 -1 0.0
+ "CG" "2C" 0 -1 0.0
+ "HG2" "H1" 0 -1 0.0
+ "HG3" "H1" 0 -1 0.0
+ "SD" "S" 0 -1 0.0
+ "CE" "CT" 0 -1 0.0
+ "HE1" "H1" 0 -1 0.0
+ "HE2" "H1" 0 -1 0.0
+ "HE3" "H1" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O" 0 -1 0.0
+!entry.MET.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.MET.unit.childsequence single int
+ 2
+!entry.MET.unit.connect array int
+ 1
+ 16
+!entry.MET.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 3 4 1
+ 3 5 1
+ 3 16 1
+ 5 6 1
+ 5 7 1
+ 5 8 1
+ 8 9 1
+ 8 10 1
+ 8 11 1
+ 11 12 1
+ 12 13 1
+ 12 14 1
+ 12 15 1
+ 16 17 1
+!entry.MET.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+ "R" 1 "A" 14
+ "R" 1 "A" 15
+ "R" 1 "A" 16
+ "R" 1 "A" 17
+!entry.MET.unit.name single str
+ "MET"
+!entry.MET.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 3.909407 0.723611 -2.739882E-06
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 2.496995 3.801075 1.241379
+ 3.877484 3.115795 2.131197
+ 4.274186 5.009602 1.194577
+ 5.354271 4.863178 1.185788
+ 3.973781 5.548460 0.295972
+ 3.817309 5.981266 2.651708
+ 4.753212 7.463128 2.340949
+ 4.433582 7.904044 1.396741
+ 4.585907 8.175299 3.148985
+ 5.814074 7.218763 2.286554
+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+!entry.MET.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 16 0 0 0 0
+!entry.MET.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "MET" 1 18 1 "p" 0
+!entry.MET.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.MET.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.MET.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
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+ 0.0 0.0 0.0
+!entry.PHE.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N" 0 1 131072 1 7 -0.415700
+ "H" "H" 0 1 131072 2 1 0.271900
+ "CA" "CX" 0 1 131072 3 6 -0.002400
+ "HA" "H1" 0 1 131072 4 1 0.097800
+ "CB" "CT" 0 1 131072 5 6 -0.034300
+ "HB2" "HC" 0 1 131072 6 1 0.029500
+ "HB3" "HC" 0 1 131072 7 1 0.029500
+ "CG" "CA" 0 1 131072 8 6 0.011800
+ "CD1" "CA" 0 1 131072 9 6 -0.125600
+ "HD1" "HA" 0 1 131072 10 1 0.133000
+ "CE1" "CA" 0 1 131072 11 6 -0.170400
+ "HE1" "HA" 0 1 131072 12 1 0.143000
+ "CZ" "CA" 0 1 131072 13 6 -0.107200
+ "HZ" "HA" 0 1 131072 14 1 0.129700
+ "CE2" "CA" 0 1 131072 15 6 -0.170400
+ "HE2" "HA" 0 1 131072 16 1 0.143000
+ "CD2" "CA" 0 1 131072 17 6 -0.125600
+ "HD2" "HA" 0 1 131072 18 1 0.133000
+ "C" "C" 0 1 131072 19 6 0.597300
+ "O" "O" 0 1 131072 20 8 -0.567900
+!entry.PHE.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
+ "H" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "H1" 0 -1 0.0
+ "CB" "CT" 0 -1 0.0
+ "HB2" "HC" 0 -1 0.0
+ "HB3" "HC" 0 -1 0.0
+ "CG" "CA" 0 -1 0.0
+ "CD1" "CA" 0 -1 0.0
+ "HD1" "HA" 0 -1 0.0
+ "CE1" "CA" 0 -1 0.0
+ "HE1" "HA" 0 -1 0.0
+ "CZ" "CA" 0 -1 0.0
+ "HZ" "HA" 0 -1 0.0
+ "CE2" "CA" 0 -1 0.0
+ "HE2" "HA" 0 -1 0.0
+ "CD2" "CA" 0 -1 0.0
+ "HD2" "HA" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O" 0 -1 0.0
+!entry.PHE.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.PHE.unit.childsequence single int
+ 2
+!entry.PHE.unit.connect array int
+ 1
+ 19
+!entry.PHE.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 3 4 1
+ 3 5 1
+ 3 19 1
+ 5 6 1
+ 5 7 1
+ 5 8 1
+ 8 9 1
+ 8 17 1
+ 9 10 1
+ 9 11 1
+ 11 12 1
+ 11 13 1
+ 13 14 1
+ 13 15 1
+ 15 16 1
+ 15 17 1
+ 17 18 1
+ 19 20 1
+!entry.PHE.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+ "R" 1 "A" 14
+ "R" 1 "A" 15
+ "R" 1 "A" 16
+ "R" 1 "A" 17
+ "R" 1 "A" 18
+ "R" 1 "A" 19
+ "R" 1 "A" 20
+!entry.PHE.unit.name single str
+ "PHE"
+!entry.PHE.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 3.909407 0.723611 -2.739882E-06
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 2.496995 3.801075 1.241379
+ 3.877484 3.115795 2.131197
+ 4.200813 5.026064 1.321087
+ 3.911613 5.857250 2.409890
+ 3.236123 5.513843 3.193398
+ 4.490014 7.129513 2.492354
+ 4.264853 7.776651 3.340066
+ 5.357616 7.570591 1.486016
+ 5.807943 8.561138 1.550220
+ 5.646818 6.739407 0.397211
+ 6.322309 7.082817 -0.386295
+ 5.068419 5.467143 0.314744
+ 5.293584 4.820007 -0.532968
+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+!entry.PHE.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 19 0 0 0 0
+!entry.PHE.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "PHE" 1 21 1 "p" 0
+!entry.PHE.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.PHE.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.PHE.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
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+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+!entry.PRO.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N" 0 1 131072 1 7 -0.254800
+ "CD" "CT" 0 1 131072 2 6 0.019200
+ "HD2" "H1" 0 1 131072 3 1 0.039100
+ "HD3" "H1" 0 1 131072 4 1 0.039100
+ "CG" "CT" 0 1 131072 5 6 0.018900
+ "HG2" "HC" 0 1 131072 6 1 0.021300
+ "HG3" "HC" 0 1 131072 7 1 0.021300
+ "CB" "CT" 0 1 131072 8 6 -0.007000
+ "HB2" "HC" 0 1 131072 9 1 0.025300
+ "HB3" "HC" 0 1 131072 10 1 0.025300
+ "CA" "CX" 0 1 131072 11 6 -0.026600
+ "HA" "H1" 0 1 131072 12 1 0.064100
+ "C" "C" 0 1 131072 13 6 0.589600
+ "O" "O" 0 1 131072 14 8 -0.574800
+!entry.PRO.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
+ "CD" "CT" 0 -1 0.0
+ "HD2" "H1" 0 -1 0.0
+ "HD3" "H1" 0 -1 0.0
+ "CG" "CT" 0 -1 0.0
+ "HG2" "HC" 0 -1 0.0
+ "HG3" "HC" 0 -1 0.0
+ "CB" "CT" 0 -1 0.0
+ "HB2" "HC" 0 -1 0.0
+ "HB3" "HC" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "H1" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O" 0 -1 0.0
+!entry.PRO.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.PRO.unit.childsequence single int
+ 2
+!entry.PRO.unit.connect array int
+ 1
+ 13
+!entry.PRO.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 11 1
+ 2 3 1
+ 2 4 1
+ 2 5 1
+ 5 6 1
+ 5 7 1
+ 5 8 1
+ 8 9 1
+ 8 10 1
+ 8 11 1
+ 11 12 1
+ 11 13 1
+ 13 14 1
+!entry.PRO.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+ "R" 1 "A" 14
+!entry.PRO.unit.name single str
+ "PRO"
+!entry.PRO.unit.positions table  dbl x  dbl y  dbl z
+ 3.326834 1.557389 -1.603945E-06
+ 4.302147 0.476598 0.080119
+ 4.419998 0.019283 -0.902263
+ 3.955888 -0.274040 0.790574
+ 5.547126 1.172441 0.544693
+ 6.413549 0.741636 0.042879
+ 5.652950 1.047934 1.622376
+ 5.369091 2.628184 0.185227
+ 5.969289 2.861861 -0.694123
+ 5.690642 3.251038 1.019947
+ 3.933610 2.871277 -0.104508
+ 3.611470 3.488570 0.734106
+ 3.505164 3.526392 -1.409783
+ 2.754240 2.939065 -2.185412
+!entry.PRO.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 13 0 0 0 0
+!entry.PRO.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "PRO" 1 15 1 "p" 0
+!entry.PRO.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.PRO.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.PRO.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
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+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+!entry.SER.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N" 0 1 131072 1 7 -0.415700
+ "H" "H" 0 1 131072 2 1 0.271900
+ "CA" "CX" 0 1 131072 3 6 -0.024900
+ "HA" "H1" 0 1 131072 4 1 0.084300
+ "CB" "2C" 0 1 131072 5 6 0.211700
+ "HB2" "H1" 0 1 131072 6 1 0.035200
+ "HB3" "H1" 0 1 131072 7 1 0.035200
+ "OG" "OH" 0 1 131072 8 8 -0.654600
+ "HG" "HO" 0 1 131072 9 1 0.427500
+ "C" "C" 0 1 131072 10 6 0.597300
+ "O" "O" 0 1 131072 11 8 -0.567900
+!entry.SER.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
+ "H" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "H1" 0 -1 0.0
+ "CB" "2C" 0 -1 0.0
+ "HB2" "H1" 0 -1 0.0
+ "HB3" "H1" 0 -1 0.0
+ "OG" "OH" 0 -1 0.0
+ "HG" "HO" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O" 0 -1 0.0
+!entry.SER.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.SER.unit.childsequence single int
+ 2
+!entry.SER.unit.connect array int
+ 1
+ 10
+!entry.SER.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 3 4 1
+ 3 5 1
+ 3 10 1
+ 5 6 1
+ 5 7 1
+ 5 8 1
+ 8 9 1
+ 10 11 1
+!entry.SER.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+!entry.SER.unit.name single str
+ "SER"
+!entry.SER.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 3.909407 0.723611 -2.739882E-06
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 2.496995 3.801075 1.241379
+ 3.877484 3.115795 2.131197
+ 4.230753 4.925145 1.196917
+ 3.983305 5.433814 1.972562
+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+!entry.SER.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 10 0 0 0 0
+!entry.SER.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "SER" 1 12 1 "p" 0
+!entry.SER.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.SER.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.SER.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
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+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
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+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+!entry.THR.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N" 0 1 131072 1 7 -0.415700
+ "H" "H" 0 1 131072 2 1 0.271900
+ "CA" "CX" 0 1 131072 3 6 -0.038900
+ "HA" "H1" 0 1 131072 4 1 0.100700
+ "CB" "3C" 0 1 131072 5 6 0.365400
+ "HB" "H1" 0 1 131072 6 1 0.004300
+ "CG2" "CT" 0 1 131072 7 6 -0.243800
+ "HG21" "HC" 0 1 131072 8 1 0.064200
+ "HG22" "HC" 0 1 131072 9 1 0.064200
+ "HG23" "HC" 0 1 131072 10 1 0.064200
+ "OG1" "OH" 0 1 131072 11 8 -0.676100
+ "HG1" "HO" 0 1 131072 12 1 0.410200
+ "C" "C" 0 1 131072 13 6 0.597300
+ "O" "O" 0 1 131072 14 8 -0.567900
+!entry.THR.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
+ "H" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "H1" 0 -1 0.0
+ "CB" "3C" 0 -1 0.0
+ "HB" "H1" 0 -1 0.0
+ "CG2" "CT" 0 -1 0.0
+ "HG21" "HC" 0 -1 0.0
+ "HG22" "HC" 0 -1 0.0
+ "HG23" "HC" 0 -1 0.0
+ "OG1" "OH" 0 -1 0.0
+ "HG1" "HO" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O" 0 -1 0.0
+!entry.THR.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.THR.unit.childsequence single int
+ 2
+!entry.THR.unit.connect array int
+ 1
+ 13
+!entry.THR.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 3 4 1
+ 3 5 1
+ 3 13 1
+ 5 6 1
+ 5 7 1
+ 5 11 1
+ 7 8 1
+ 7 9 1
+ 7 10 1
+ 11 12 1
+ 13 14 1
+!entry.THR.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+ "R" 1 "A" 14
+!entry.THR.unit.name single str
+ "THR"
+!entry.THR.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 3.909407 0.723611 -2.739882E-06
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 4.075059 4.623017 1.205786
+ 2.065936 3.859425 1.244383
+ 1.567127 2.890627 1.271209
+ 1.784431 4.436953 2.124903
+ 1.764699 4.397847 0.345796
+ 3.971501 2.947413 2.411212
+ 3.724052 3.456082 3.186857
+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+!entry.THR.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 13 0 0 0 0
+!entry.THR.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "THR" 1 15 1 "p" 0
+!entry.THR.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.THR.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.THR.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
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+ 0.0 0.0 0.0
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+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+!entry.TRP.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N" 0 1 131072 1 7 -0.415700
+ "H" "H" 0 1 131072 2 1 0.271900
+ "CA" "CX" 0 1 131072 3 6 -0.027500
+ "HA" "H1" 0 1 131072 4 1 0.112300
+ "CB" "CT" 0 1 131072 5 6 -0.005000
+ "HB2" "HC" 0 1 131072 6 1 0.033900
+ "HB3" "HC" 0 1 131072 7 1 0.033900
+ "CG" "C*" 0 1 131072 8 6 -0.141500
+ "CD1" "CW" 0 1 131072 9 6 -0.163800
+ "HD1" "H4" 0 1 131072 10 1 0.206200
+ "NE1" "NA" 0 1 131072 11 7 -0.341800
+ "HE1" "H" 0 1 131072 12 1 0.341200
+ "CE2" "CN" 0 1 131072 13 6 0.138000
+ "CZ2" "CA" 0 1 131072 14 6 -0.260100
+ "HZ2" "HA" 0 1 131072 15 1 0.157200
+ "CH2" "CA" 0 1 131072 16 6 -0.113400
+ "HH2" "HA" 0 1 131072 17 1 0.141700
+ "CZ3" "CA" 0 1 131072 18 6 -0.197200
+ "HZ3" "HA" 0 1 131072 19 1 0.144700
+ "CE3" "CA" 0 1 131072 20 6 -0.238700
+ "HE3" "HA" 0 1 131072 21 1 0.170000
+ "CD2" "CB" 0 1 131072 22 6 0.124300
+ "C" "C" 0 1 131072 23 6 0.597300
+ "O" "O" 0 1 131072 24 8 -0.567900
+!entry.TRP.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
+ "H" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "H1" 0 -1 0.0
+ "CB" "CT" 0 -1 0.0
+ "HB2" "HC" 0 -1 0.0
+ "HB3" "HC" 0 -1 0.0
+ "CG" "C*" 0 -1 0.0
+ "CD1" "CW" 0 -1 0.0
+ "HD1" "H4" 0 -1 0.0
+ "NE1" "NA" 0 -1 0.0
+ "HE1" "H" 0 -1 0.0
+ "CE2" "CN" 0 -1 0.0
+ "CZ2" "CA" 0 -1 0.0
+ "HZ2" "HA" 0 -1 0.0
+ "CH2" "CA" 0 -1 0.0
+ "HH2" "HA" 0 -1 0.0
+ "CZ3" "CA" 0 -1 0.0
+ "HZ3" "HA" 0 -1 0.0
+ "CE3" "CA" 0 -1 0.0
+ "HE3" "HA" 0 -1 0.0
+ "CD2" "CB" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O" 0 -1 0.0
+!entry.TRP.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.TRP.unit.childsequence single int
+ 2
+!entry.TRP.unit.connect array int
+ 1
+ 23
+!entry.TRP.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 3 4 1
+ 3 5 1
+ 3 23 1
+ 5 6 1
+ 5 7 1
+ 5 8 1
+ 8 9 1
+ 8 22 1
+ 9 10 1
+ 9 11 1
+ 11 12 1
+ 11 13 1
+ 13 14 1
+ 13 22 1
+ 14 15 1
+ 14 16 1
+ 16 17 1
+ 16 18 1
+ 18 19 1
+ 18 20 1
+ 20 21 1
+ 20 22 1
+ 23 24 1
+!entry.TRP.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+ "R" 1 "A" 14
+ "R" 1 "A" 15
+ "R" 1 "A" 16
+ "R" 1 "A" 17
+ "R" 1 "A" 18
+ "R" 1 "A" 19
+ "R" 1 "A" 20
+ "R" 1 "A" 21
+ "R" 1 "A" 22
+ "R" 1 "A" 23
+ "R" 1 "A" 24
+!entry.TRP.unit.name single str
+ "TRP"
+!entry.TRP.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 3.909407 0.723611 -2.739882E-06
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 2.496995 3.801075 1.241379
+ 3.877484 3.115795 2.131197
+ 4.200813 5.026064 1.321087
+ 4.023453 5.931084 2.293240
+ 3.368841 5.705466 3.135071
+ 4.811943 7.073555 1.949808
+ 4.882921 7.922010 2.493118
+ 5.427347 6.842060 0.816764
+ 6.297161 7.689052 0.119605
+ 6.531230 8.676649 0.517050
+ 6.814091 7.187011 -1.069023
+ 7.498074 7.791857 -1.664362
+ 6.482659 5.953119 -1.505101
+ 6.897660 5.575648 -2.439654
+ 5.604041 5.117355 -0.785636
+ 5.358720 4.126570 -1.168080
+ 5.083390 5.623004 0.411545
+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+!entry.TRP.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 23 0 0 0 0
+!entry.TRP.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "TRP" 1 25 1 "p" 0
+!entry.TRP.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.TRP.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.TRP.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
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+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+!entry.TYR.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N" 0 1 131072 1 7 -0.415700
+ "H" "H" 0 1 131072 2 1 0.271900
+ "CA" "CX" 0 1 131072 3 6 -0.001400
+ "HA" "H1" 0 1 131072 4 1 0.087600
+ "CB" "CT" 0 1 131072 5 6 -0.015200
+ "HB2" "HC" 0 1 131072 6 1 0.029500
+ "HB3" "HC" 0 1 131072 7 1 0.029500
+ "CG" "CA" 0 1 131072 8 6 -0.001100
+ "CD1" "CA" 0 1 131072 9 6 -0.190600
+ "HD1" "HA" 0 1 131072 10 1 0.169900
+ "CE1" "CA" 0 1 131072 11 6 -0.234100
+ "HE1" "HA" 0 1 131072 12 1 0.165600
+ "CZ" "C" 0 1 131072 13 6 0.322600
+ "OH" "OH" 0 1 131072 14 8 -0.557900
+ "HH" "HO" 0 1 131072 15 1 0.399200
+ "CE2" "CA" 0 1 131072 16 6 -0.234100
+ "HE2" "HA" 0 1 131072 17 1 0.165600
+ "CD2" "CA" 0 1 131072 18 6 -0.190600
+ "HD2" "HA" 0 1 131072 19 1 0.169900
+ "C" "C" 0 1 131072 20 6 0.597300
+ "O" "O" 0 1 131072 21 8 -0.567900
+!entry.TYR.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
+ "H" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "H1" 0 -1 0.0
+ "CB" "CT" 0 -1 0.0
+ "HB2" "HC" 0 -1 0.0
+ "HB3" "HC" 0 -1 0.0
+ "CG" "CA" 0 -1 0.0
+ "CD1" "CA" 0 -1 0.0
+ "HD1" "HA" 0 -1 0.0
+ "CE1" "CA" 0 -1 0.0
+ "HE1" "HA" 0 -1 0.0
+ "CZ" "C" 0 -1 0.0
+ "OH" "OH" 0 -1 0.0
+ "HH" "HO" 0 -1 0.0
+ "CE2" "CA" 0 -1 0.0
+ "HE2" "HA" 0 -1 0.0
+ "CD2" "CA" 0 -1 0.0
+ "HD2" "HA" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O" 0 -1 0.0
+!entry.TYR.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.TYR.unit.childsequence single int
+ 2
+!entry.TYR.unit.connect array int
+ 1
+ 20
+!entry.TYR.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 3 4 1
+ 3 5 1
+ 3 20 1
+ 5 6 1
+ 5 7 1
+ 5 8 1
+ 8 9 1
+ 8 18 1
+ 9 10 1
+ 9 11 1
+ 11 12 1
+ 11 13 1
+ 13 14 1
+ 13 16 1
+ 14 15 1
+ 16 17 1
+ 16 18 1
+ 18 19 1
+ 20 21 1
+!entry.TYR.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+ "R" 1 "A" 14
+ "R" 1 "A" 15
+ "R" 1 "A" 16
+ "R" 1 "A" 17
+ "R" 1 "A" 18
+ "R" 1 "A" 19
+ "R" 1 "A" 20
+ "R" 1 "A" 21
+!entry.TYR.unit.name single str
+ "TYR"
+!entry.TYR.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 3.909407 0.723611 -2.739882E-06
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 2.496995 3.801075 1.241379
+ 3.877484 3.115795 2.131197
+ 4.267328 4.996267 1.194946
+ 4.059927 5.918911 2.227280
+ 3.400108 5.668218 3.057877
+ 4.699998 7.163547 2.192791
+ 4.538522 7.881891 2.996538
+ 5.547471 7.485542 1.125970
+ 6.169255 8.694617 1.092468
+ 5.956327 9.246984 1.848214
+ 5.754875 6.562900 0.093635
+ 6.414694 6.813595 -0.736962
+ 5.114806 5.318263 0.128119
+ 5.276286 4.599920 -0.675627
+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+!entry.TYR.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 20 0 0 0 0
+!entry.TYR.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "TYR" 1 22 1 "p" 0
+!entry.TYR.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.TYR.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.TYR.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
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+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
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+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+!entry.VAL.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N" 0 1 131072 1 7 -0.415700
+ "H" "H" 0 1 131072 2 1 0.271900
+ "CA" "CX" 0 1 131072 3 6 -0.087500
+ "HA" "H1" 0 1 131072 4 1 0.096900
+ "CB" "3C" 0 1 131072 5 6 0.298500
+ "HB" "HC" 0 1 131072 6 1 -0.029700
+ "CG1" "CT" 0 1 131072 7 6 -0.319200
+ "HG11" "HC" 0 1 131072 8 1 0.079100
+ "HG12" "HC" 0 1 131072 9 1 0.079100
+ "HG13" "HC" 0 1 131072 10 1 0.079100
+ "CG2" "CT" 0 1 131072 11 6 -0.319200
+ "HG21" "HC" 0 1 131072 12 1 0.079100
+ "HG22" "HC" 0 1 131072 13 1 0.079100
+ "HG23" "HC" 0 1 131072 14 1 0.079100
+ "C" "C" 0 1 131072 15 6 0.597300
+ "O" "O" 0 1 131072 16 8 -0.567900
+!entry.VAL.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
+ "H" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "H1" 0 -1 0.0
+ "CB" "3C" 0 -1 0.0
+ "HB" "HC" 0 -1 0.0
+ "CG1" "CT" 0 -1 0.0
+ "HG11" "HC" 0 -1 0.0
+ "HG12" "HC" 0 -1 0.0
+ "HG13" "HC" 0 -1 0.0
+ "CG2" "CT" 0 -1 0.0
+ "HG21" "HC" 0 -1 0.0
+ "HG22" "HC" 0 -1 0.0
+ "HG23" "HC" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O" 0 -1 0.0
+!entry.VAL.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.VAL.unit.childsequence single int
+ 2
+!entry.VAL.unit.connect array int
+ 1
+ 15
+!entry.VAL.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 3 4 1
+ 3 5 1
+ 3 15 1
+ 5 6 1
+ 5 7 1
+ 5 11 1
+ 7 8 1
+ 7 9 1
+ 7 10 1
+ 11 12 1
+ 11 13 1
+ 11 14 1
+ 15 16 1
+!entry.VAL.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+ "R" 1 "A" 14
+ "R" 1 "A" 15
+ "R" 1 "A" 16
+!entry.VAL.unit.name single str
+ "VAL"
+!entry.VAL.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 3.909407 0.723611 -2.739882E-06
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 2.496995 3.801075 1.241379
+ 3.997712 2.900483 2.489542
+ 5.077693 2.753265 2.481244
+ 3.716972 3.477628 3.370558
+ 3.499630 1.931323 2.516834
+ 4.274186 5.009602 1.194577
+ 3.973781 5.548460 0.295972
+ 3.993559 5.587585 2.075079
+ 5.354271 4.863178 1.185788
+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+!entry.VAL.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 15 0 0 0 0
+!entry.VAL.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "VAL" 1 17 1 "p" 0
+!entry.VAL.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.VAL.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.VAL.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
diff --git a/test/Test_Build/aminoct12.lib b/test/Test_Build/aminoct12.lib
new file mode 100644
index 0000000000..c6bb0f1a12
--- /dev/null
+++ b/test/Test_Build/aminoct12.lib
@@ -0,0 +1,3344 @@
+!!index array str
+ "CALA"
+ "CARG"
+ "CASN"
+ "CASP"
+ "CCYS"
+ "CCYX"
+ "CGLN"
+ "CGLU"
+ "CGLY"
+ "CHID"
+ "CHIE"
+ "CHIP"
+ "CHYP"
+ "CILE"
+ "CLEU"
+ "CLYS"
+ "CMET"
+ "CPHE"
+ "CPRO"
+ "CSER"
+ "CTHR"
+ "CTRP"
+ "CTYR"
+ "CVAL"
+ "NHE"
+ "NME"
+!entry.CALA.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N" 0 1 131072 1 7 -0.382100
+ "H" "H" 0 1 131072 2 1 0.268100
+ "CA" "CX" 0 1 131072 3 6 -0.174700
+ "HA" "H1" 0 1 131072 4 1 0.106700
+ "CB" "CT" 0 1 131072 5 6 -0.209300
+ "HB1" "HC" 0 1 131072 6 1 0.076400
+ "HB2" "HC" 0 1 131072 7 1 0.076400
+ "HB3" "HC" 0 1 131072 8 1 0.076400
+ "C" "C" 0 1 131072 9 6 0.773100
+ "O" "O2" 0 1 131072 10 8 -0.805500
+ "OXT" "O2" 0 1 131072 11 8 -0.805500
+!entry.CALA.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
+ "H" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "H1" 0 -1 0.0
+ "CB" "CT" 0 -1 0.0
+ "HB1" "HC" 0 -1 0.0
+ "HB2" "HC" 0 -1 0.0
+ "HB3" "HC" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O2" 0 -1 0.0
+ "OXT" "O2" 0 -1 0.0
+!entry.CALA.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.CALA.unit.childsequence single int
+ 2
+!entry.CALA.unit.connect array int
+ 1
+ 0
+!entry.CALA.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 3 4 1
+ 3 5 1
+ 3 9 1
+ 5 6 1
+ 5 7 1
+ 5 8 1
+ 9 10 1
+ 9 11 1
+!entry.CALA.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+!entry.CALA.unit.name single str
+ "CALA"
+!entry.CALA.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 3.909407 0.723611 -2.739882E-06
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 3.877484 3.115795 2.131197
+ 4.075059 4.623017 1.205786
+ 2.496995 3.801075 1.241379
+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+ 6.204455 3.702003 -2.420005E-06
+!entry.CALA.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 0 0 0 0 0
+!entry.CALA.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "CALA" 1 12 1 "p" 0
+!entry.CALA.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.CALA.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.CALA.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+!entry.CARG.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N" 0 1 131072 1 7 -0.348100
+ "H" "H" 0 1 131072 2 1 0.276400
+ "CA" "CX" 0 1 131072 3 6 -0.306800
+ "HA" "H1" 0 1 131072 4 1 0.144700
+ "CB" "C8" 0 1 131072 5 6 -0.037400
+ "HB2" "HC" 0 1 131072 6 1 0.037100
+ "HB3" "HC" 0 1 131072 7 1 0.037100
+ "CG" "C8" 0 1 131072 8 6 0.074400
+ "HG2" "HC" 0 1 131072 9 1 0.018500
+ "HG3" "HC" 0 1 131072 10 1 0.018500
+ "CD" "C8" 0 1 131072 11 6 0.111400
+ "HD2" "H1" 0 1 131072 12 1 0.046800
+ "HD3" "H1" 0 1 131072 13 1 0.046800
+ "NE" "N2" 0 1 131072 14 7 -0.556400
+ "HE" "H" 0 1 131072 15 1 0.347900
+ "CZ" "CA" 0 1 131072 16 6 0.836800
+ "NH1" "N2" 0 1 131072 17 7 -0.873700
+ "HH11" "H" 0 1 131072 18 1 0.449300
+ "HH12" "H" 0 1 131072 19 1 0.449300
+ "NH2" "N2" 0 1 131072 20 7 -0.873700
+ "HH21" "H" 0 1 131072 21 1 0.449300
+ "HH22" "H" 0 1 131072 22 1 0.449300
+ "C" "C" 0 1 131072 23 6 0.855700
+ "O" "O2" 0 1 131072 24 8 -0.826600
+ "OXT" "O2" 0 1 131072 25 8 -0.826600
+!entry.CARG.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
+ "H" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "H1" 0 -1 0.0
+ "CB" "C8" 0 -1 0.0
+ "HB2" "HC" 0 -1 0.0
+ "HB3" "HC" 0 -1 0.0
+ "CG" "C8" 0 -1 0.0
+ "HG2" "HC" 0 -1 0.0
+ "HG3" "HC" 0 -1 0.0
+ "CD" "C8" 0 -1 0.0
+ "HD2" "H1" 0 -1 0.0
+ "HD3" "H1" 0 -1 0.0
+ "NE" "N2" 0 -1 0.0
+ "HE" "H" 0 -1 0.0
+ "CZ" "CA" 0 -1 0.0
+ "NH1" "N2" 0 -1 0.0
+ "HH11" "H" 0 -1 0.0
+ "HH12" "H" 0 -1 0.0
+ "NH2" "N2" 0 -1 0.0
+ "HH21" "H" 0 -1 0.0
+ "HH22" "H" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O2" 0 -1 0.0
+ "OXT" "O2" 0 -1 0.0
+!entry.CARG.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.CARG.unit.childsequence single int
+ 2
+!entry.CARG.unit.connect array int
+ 1
+ 0
+!entry.CARG.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 3 4 1
+ 3 5 1
+ 3 23 1
+ 5 6 1
+ 5 7 1
+ 5 8 1
+ 8 9 1
+ 8 10 1
+ 8 11 1
+ 11 12 1
+ 11 13 1
+ 11 14 1
+ 14 15 1
+ 14 16 1
+ 16 17 1
+ 16 20 1
+ 17 18 1
+ 17 19 1
+ 20 21 1
+ 20 22 1
+ 23 24 1
+ 23 25 1
+!entry.CARG.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+ "R" 1 "A" 14
+ "R" 1 "A" 15
+ "R" 1 "A" 16
+ "R" 1 "A" 17
+ "R" 1 "A" 18
+ "R" 1 "A" 19
+ "R" 1 "A" 20
+ "R" 1 "A" 21
+ "R" 1 "A" 22
+ "R" 1 "A" 23
+ "R" 1 "A" 24
+ "R" 1 "A" 25
+!entry.CARG.unit.name single str
+ "CARG"
+!entry.CARG.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 3.909407 0.723611 -2.739882E-06
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 2.496995 3.801075 1.241379
+ 3.877484 3.115795 2.131197
+ 4.274186 5.009602 1.194577
+ 5.354271 4.863178 1.185788
+ 3.973781 5.548460 0.295972
+ 3.881105 5.817645 2.426721
+ 2.801135 5.964881 2.435959
+ 4.181626 5.279602 3.325774
+ 4.540320 7.142723 2.424483
+ 5.151805 7.375492 1.655065
+ 4.364284 8.040989 3.389382
+ 3.575026 7.807606 4.434133
+ 3.088949 6.925423 4.508848
+ 3.465367 8.513631 5.147998
+ 5.006254 9.201287 3.286991
+ 5.604855 9.375325 2.492329
+ 4.892216 9.903045 4.004368
+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+ 6.204455 3.702003 -2.420005E-06
+!entry.CARG.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 0 0 0 0 0
+!entry.CARG.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "CARG" 1 26 1 "p" 0
+!entry.CARG.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.CARG.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.CARG.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+!entry.CASN.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N" 0 1 131072 1 7 -0.382100
+ "H" "H" 0 1 131072 2 1 0.268100
+ "CA" "CX" 0 1 131072 3 6 -0.208000
+ "HA" "H1" 0 1 131072 4 1 0.135800
+ "CB" "2C" 0 1 131072 5 6 -0.229900
+ "HB2" "HC" 0 1 131072 6 1 0.102300
+ "HB3" "HC" 0 1 131072 7 1 0.102300
+ "CG" "C" 0 1 131072 8 6 0.715300
+ "OD1" "O" 0 1 131072 9 8 -0.601000
+ "ND2" "N" 0 1 131072 10 7 -0.908400
+ "HD21" "H" 0 1 131072 11 1 0.415000
+ "HD22" "H" 0 1 131072 12 1 0.415000
+ "C" "C" 0 1 131072 13 6 0.805000
+ "O" "O2" 0 1 131072 14 8 -0.814700
+ "OXT" "O2" 0 1 131072 15 8 -0.814700
+!entry.CASN.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
+ "H" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "H1" 0 -1 0.0
+ "CB" "2C" 0 -1 0.0
+ "HB2" "HC" 0 -1 0.0
+ "HB3" "HC" 0 -1 0.0
+ "CG" "C" 0 -1 0.0
+ "OD1" "O" 0 -1 0.0
+ "ND2" "N" 0 -1 0.0
+ "HD21" "H" 0 -1 0.0
+ "HD22" "H" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O2" 0 -1 0.0
+ "OXT" "O2" 0 -1 0.0
+!entry.CASN.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.CASN.unit.childsequence single int
+ 2
+!entry.CASN.unit.connect array int
+ 1
+ 0
+!entry.CASN.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 3 4 1
+ 3 5 1
+ 3 13 1
+ 5 6 1
+ 5 7 1
+ 5 8 1
+ 8 9 1
+ 8 10 1
+ 10 11 1
+ 10 12 1
+ 13 14 1
+ 13 15 1
+!entry.CASN.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+ "R" 1 "A" 14
+ "R" 1 "A" 15
+!entry.CASN.unit.name single str
+ "CASN"
+!entry.CASN.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 3.909407 0.723611 -2.739882E-06
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 2.496995 3.801075 1.241379
+ 3.877484 3.115795 2.131197
+ 4.253700 5.017112 1.232144
+ 5.005299 5.340406 0.315072
+ 3.984885 5.817909 2.265917
+ 4.408015 6.733702 2.314743
+ 3.359611 5.504297 2.994464
+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+ 6.204455 3.702003 -2.420005E-06
+!entry.CASN.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 0 0 0 0 0
+!entry.CASN.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "CASN" 1 16 1 "p" 0
+!entry.CASN.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.CASN.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.CASN.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+!entry.CASP.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N" 0 1 131072 1 7 -0.519200
+ "H" "H" 0 1 131072 2 1 0.305500
+ "CA" "CX" 0 1 131072 3 6 -0.181700
+ "HA" "H1" 0 1 131072 4 1 0.104600
+ "CB" "2C" 0 1 131072 5 6 -0.067700
+ "HB2" "HC" 0 1 131072 6 1 -0.021200
+ "HB3" "HC" 0 1 131072 7 1 -0.021200
+ "CG" "CO" 0 1 131072 8 6 0.885100
+ "OD1" "O2" 0 1 131072 9 8 -0.816200
+ "OD2" "O2" 0 1 131072 10 8 -0.816200
+ "C" "C" 0 1 131072 11 6 0.725600
+ "O" "O2" 0 1 131072 12 8 -0.788700
+ "OXT" "O2" 0 1 131072 13 8 -0.788700
+!entry.CASP.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
+ "H" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "H1" 0 -1 0.0
+ "CB" "2C" 0 -1 0.0
+ "HB2" "HC" 0 -1 0.0
+ "HB3" "HC" 0 -1 0.0
+ "CG" "CO" 0 -1 0.0
+ "OD1" "O2" 0 -1 0.0
+ "OD2" "O2" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O2" 0 -1 0.0
+ "OXT" "O2" 0 -1 0.0
+!entry.CASP.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.CASP.unit.childsequence single int
+ 2
+!entry.CASP.unit.connect array int
+ 1
+ 0
+!entry.CASP.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 3 4 1
+ 3 5 1
+ 3 11 1
+ 5 6 1
+ 5 7 1
+ 5 8 1
+ 8 9 1
+ 8 10 1
+ 11 12 1
+ 11 13 1
+!entry.CASP.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+!entry.CASP.unit.name single str
+ "CASP"
+!entry.CASP.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 3.909407 0.723611 -2.739882E-06
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 2.496995 3.801075 1.241379
+ 3.877484 3.115795 2.131197
+ 4.275101 5.011380 1.194527
+ 3.669108 5.954940 0.620011
+ 5.407731 5.091879 1.740667
+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+ 6.204455 3.702003 -2.420005E-06
+!entry.CASP.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 0 0 0 0 0
+!entry.CASP.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "CASP" 1 14 1 "p" 0
+!entry.CASP.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.CASP.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.CASP.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+!entry.CCYS.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N" 0 1 131072 1 7 -0.382100
+ "H" "H" 0 1 131072 2 1 0.268100
+ "CA" "CX" 0 1 131072 3 6 -0.163500
+ "HA" "H1" 0 1 131072 4 1 0.139600
+ "CB" "2C" 0 1 131072 5 6 -0.199600
+ "HB2" "H1" 0 1 131072 6 1 0.143700
+ "HB3" "H1" 0 1 131072 7 1 0.143700
+ "SG" "SH" 0 1 131072 8 16 -0.310200
+ "HG" "HS" 0 1 131072 9 1 0.206800
+ "C" "C" 0 1 131072 10 6 0.749700
+ "O" "O2" 0 1 131072 11 8 -0.798100
+ "OXT" "O2" 0 1 131072 12 8 -0.798100
+!entry.CCYS.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
+ "H" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "H1" 0 -1 0.0
+ "CB" "2C" 0 -1 0.0
+ "HB2" "H1" 0 -1 0.0
+ "HB3" "H1" 0 -1 0.0
+ "SG" "SH" 0 -1 0.0
+ "HG" "HS" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O2" 0 -1 0.0
+ "OXT" "O2" 0 -1 0.0
+!entry.CCYS.unit.boundbox array dbl
+ -1.000000
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+ 0.0
+!entry.CCYS.unit.childsequence single int
+ 2
+!entry.CCYS.unit.connect array int
+ 1
+ 0
+!entry.CCYS.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 3 4 1
+ 3 5 1
+ 3 10 1
+ 5 6 1
+ 5 7 1
+ 5 8 1
+ 8 9 1
+ 10 11 1
+ 10 12 1
+!entry.CCYS.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+!entry.CCYS.unit.name single str
+ "CCYS"
+!entry.CCYS.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 3.909407 0.723611 -2.739882E-06
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
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+ 3.877484 3.115795 2.131197
+ 4.309573 5.303523 1.366036
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+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+ 6.204455 3.702003 -2.420005E-06
+!entry.CCYS.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 0 0 0 0 0
+!entry.CCYS.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "CCYS" 1 13 1 "p" 0
+!entry.CCYS.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.CCYS.unit.solventcap array dbl
+ -1.000000
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+ 0.0
+ 0.0
+!entry.CCYS.unit.velocities table  dbl x  dbl y  dbl z
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+!entry.CCYX.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N" 0 1 131072 1 7 -0.382100
+ "H" "H" 0 1 131072 2 1 0.268100
+ "CA" "CX" 0 1 131072 3 6 -0.131800
+ "HA" "H1" 0 1 131072 4 1 0.093800
+ "CB" "2C" 0 1 131072 5 6 -0.194300
+ "HB2" "H1" 0 1 131072 6 1 0.122800
+ "HB3" "H1" 0 1 131072 7 1 0.122800
+ "SG" "S" 0 1 131072 8 16 -0.052900
+ "C" "C" 0 1 131072 9 6 0.761800
+ "O" "O2" 0 1 131072 10 8 -0.804100
+ "OXT" "O2" 0 1 131072 11 8 -0.804100
+!entry.CCYX.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
+ "H" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
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+ "HB3" "H1" 0 -1 0.0
+ "SG" "S" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O2" 0 -1 0.0
+ "OXT" "O2" 0 -1 0.0
+!entry.CCYX.unit.boundbox array dbl
+ -1.000000
+ 0.0
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+ 0.0
+!entry.CCYX.unit.childsequence single int
+ 2
+!entry.CCYX.unit.connect array int
+ 1
+ 0
+!entry.CCYX.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 3 4 1
+ 3 5 1
+ 3 9 1
+ 5 6 1
+ 5 7 1
+ 5 8 1
+ 9 10 1
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+!entry.CCYX.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+!entry.CCYX.unit.name single str
+ "CCYX"
+!entry.CCYX.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 3.909407 0.723611 -2.739882E-06
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
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+ 3.877484 3.115795 2.131197
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+ 6.008824 1.593175 -8.449768E-06
+ 6.204455 3.702003 -2.420005E-06
+!entry.CCYX.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 0 8 0 0 0
+!entry.CCYX.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "CCYX" 1 12 1 "p" 0
+!entry.CCYX.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.CCYX.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.CCYX.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
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+ 0.0 0.0 0.0
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+ 0.0 0.0 0.0
+!entry.CGLN.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N" 0 1 131072 1 7 -0.382100
+ "H" "H" 0 1 131072 2 1 0.268100
+ "CA" "CX" 0 1 131072 3 6 -0.224800
+ "HA" "H1" 0 1 131072 4 1 0.123200
+ "CB" "2C" 0 1 131072 5 6 -0.066400
+ "HB2" "HC" 0 1 131072 6 1 0.045200
+ "HB3" "HC" 0 1 131072 7 1 0.045200
+ "CG" "2C" 0 1 131072 8 6 -0.021000
+ "HG2" "HC" 0 1 131072 9 1 0.020300
+ "HG3" "HC" 0 1 131072 10 1 0.020300
+ "CD" "C" 0 1 131072 11 6 0.709300
+ "OE1" "O" 0 1 131072 12 8 -0.609800
+ "NE2" "N" 0 1 131072 13 7 -0.957400
+ "HE21" "H" 0 1 131072 14 1 0.430400
+ "HE22" "H" 0 1 131072 15 1 0.430400
+ "C" "C" 0 1 131072 16 6 0.777500
+ "O" "O2" 0 1 131072 17 8 -0.804200
+ "OXT" "O2" 0 1 131072 18 8 -0.804200
+!entry.CGLN.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
+ "H" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "H1" 0 -1 0.0
+ "CB" "2C" 0 -1 0.0
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+ "HB3" "HC" 0 -1 0.0
+ "CG" "2C" 0 -1 0.0
+ "HG2" "HC" 0 -1 0.0
+ "HG3" "HC" 0 -1 0.0
+ "CD" "C" 0 -1 0.0
+ "OE1" "O" 0 -1 0.0
+ "NE2" "N" 0 -1 0.0
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+ "HE22" "H" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O2" 0 -1 0.0
+ "OXT" "O2" 0 -1 0.0
+!entry.CGLN.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.CGLN.unit.childsequence single int
+ 2
+!entry.CGLN.unit.connect array int
+ 1
+ 0
+!entry.CGLN.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 3 4 1
+ 3 5 1
+ 3 16 1
+ 5 6 1
+ 5 7 1
+ 5 8 1
+ 8 9 1
+ 8 10 1
+ 8 11 1
+ 11 12 1
+ 11 13 1
+ 13 14 1
+ 13 15 1
+ 16 17 1
+ 16 18 1
+!entry.CGLN.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+ "R" 1 "A" 14
+ "R" 1 "A" 15
+ "R" 1 "A" 16
+ "R" 1 "A" 17
+ "R" 1 "A" 18
+!entry.CGLN.unit.name single str
+ "CGLN"
+!entry.CGLN.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 3.909407 0.723611 -2.739882E-06
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 2.496995 3.801075 1.241379
+ 3.877484 3.115795 2.131197
+ 4.274186 5.009602 1.194577
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+ 3.138962 5.408349 3.262893
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+ 6.008824 1.593175 -8.449768E-06
+ 6.204455 3.702003 -2.420005E-06
+!entry.CGLN.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 0 0 0 0 0
+!entry.CGLN.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "CGLN" 1 19 1 "p" 0
+!entry.CGLN.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.CGLN.unit.solventcap array dbl
+ -1.000000
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+!entry.CGLN.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
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+!entry.CGLU.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N" 0 1 131072 1 7 -0.519200
+ "H" "H" 0 1 131072 2 1 0.305500
+ "CA" "CX" 0 1 131072 3 6 -0.205900
+ "HA" "H1" 0 1 131072 4 1 0.139900
+ "CB" "2C" 0 1 131072 5 6 0.007100
+ "HB2" "HC" 0 1 131072 6 1 -0.007800
+ "HB3" "HC" 0 1 131072 7 1 -0.007800
+ "CG" "2C" 0 1 131072 8 6 0.067500
+ "HG2" "HC" 0 1 131072 9 1 -0.054800
+ "HG3" "HC" 0 1 131072 10 1 -0.054800
+ "CD" "CO" 0 1 131072 11 6 0.818300
+ "OE1" "O2" 0 1 131072 12 8 -0.822000
+ "OE2" "O2" 0 1 131072 13 8 -0.822000
+ "C" "C" 0 1 131072 14 6 0.742000
+ "O" "O2" 0 1 131072 15 8 -0.793000
+ "OXT" "O2" 0 1 131072 16 8 -0.793000
+!entry.CGLU.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
+ "H" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
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+ "CB" "2C" 0 -1 0.0
+ "HB2" "HC" 0 -1 0.0
+ "HB3" "HC" 0 -1 0.0
+ "CG" "2C" 0 -1 0.0
+ "HG2" "HC" 0 -1 0.0
+ "HG3" "HC" 0 -1 0.0
+ "CD" "CO" 0 -1 0.0
+ "OE1" "O2" 0 -1 0.0
+ "OE2" "O2" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O2" 0 -1 0.0
+ "OXT" "O2" 0 -1 0.0
+!entry.CGLU.unit.boundbox array dbl
+ -1.000000
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+ 0.0
+!entry.CGLU.unit.childsequence single int
+ 2
+!entry.CGLU.unit.connect array int
+ 1
+ 0
+!entry.CGLU.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 3 4 1
+ 3 5 1
+ 3 14 1
+ 5 6 1
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+ 5 8 1
+ 8 9 1
+ 8 10 1
+ 8 11 1
+ 11 12 1
+ 11 13 1
+ 14 15 1
+ 14 16 1
+!entry.CGLU.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+ "R" 1 "A" 14
+ "R" 1 "A" 15
+ "R" 1 "A" 16
+!entry.CGLU.unit.name single str
+ "CGLU"
+!entry.CGLU.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 3.909407 0.723611 -2.739882E-06
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 2.496995 3.801075 1.241379
+ 3.877484 3.115795 2.131197
+ 4.267328 4.996267 1.194946
+ 5.347413 4.849843 1.186158
+ 3.966923 5.535124 0.296342
+ 3.873732 5.805369 2.428706
+ 4.594590 5.679012 3.454376
+ 2.855965 6.542070 2.333721
+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+ 6.204455 3.702003 -2.420005E-06
+!entry.CGLU.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 0 0 0 0 0
+!entry.CGLU.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "CGLU" 1 17 1 "p" 0
+!entry.CGLU.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.CGLU.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.CGLU.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
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+!entry.CGLY.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N" 0 1 131072 1 7 -0.382100
+ "H" "H" 0 1 131072 2 1 0.268100
+ "CA" "CX" 0 1 131072 3 6 -0.249300
+ "HA2" "H1" 0 1 131072 4 1 0.105600
+ "HA3" "H1" 0 1 131072 5 1 0.105600
+ "C" "C" 0 1 131072 6 6 0.723100
+ "O" "O2" 0 1 131072 7 8 -0.785500
+ "OXT" "O2" 0 1 131072 8 8 -0.785500
+!entry.CGLY.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
+ "H" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA2" "H1" 0 -1 0.0
+ "HA3" "H1" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O2" 0 -1 0.0
+ "OXT" "O2" 0 -1 0.0
+!entry.CGLY.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.CGLY.unit.childsequence single int
+ 2
+!entry.CGLY.unit.connect array int
+ 1
+ 0
+!entry.CGLY.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 3 4 1
+ 3 5 1
+ 3 6 1
+ 6 7 1
+ 6 8 1
+!entry.CGLY.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+!entry.CGLY.unit.name single str
+ "CGLY"
+!entry.CGLY.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 3.909407 0.723611 -2.739882E-06
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.671668 3.400125 0.889824
+ 5.483710 2.686702 -4.438857E-06
+ 5.993369 1.568360 -8.469843E-06
+ 6.214748 3.674642 -2.512987E-06
+!entry.CGLY.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 0 0 0 0 0
+!entry.CGLY.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "CGLY" 1 9 1 "p" 0
+!entry.CGLY.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.CGLY.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.CGLY.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+!entry.CHID.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N" 0 1 131072 1 7 -0.382100
+ "H" "H" 0 1 131072 2 1 0.268100
+ "CA" "CX" 0 1 131072 3 6 -0.173900
+ "HA" "H1" 0 1 131072 4 1 0.110000
+ "CB" "CT" 0 1 131072 5 6 -0.104600
+ "HB2" "HC" 0 1 131072 6 1 0.056500
+ "HB3" "HC" 0 1 131072 7 1 0.056500
+ "CG" "CC" 0 1 131072 8 6 0.029300
+ "ND1" "NA" 0 1 131072 9 7 -0.389200
+ "HD1" "H" 0 1 131072 10 1 0.375500
+ "CE1" "CR" 0 1 131072 11 6 0.192500
+ "HE1" "H5" 0 1 131072 12 1 0.141800
+ "NE2" "NB" 0 1 131072 13 7 -0.562900
+ "CD2" "CV" 0 1 131072 14 6 0.100100
+ "HD2" "H4" 0 1 131072 15 1 0.124100
+ "C" "C" 0 1 131072 16 6 0.761500
+ "O" "O2" 0 1 131072 17 8 -0.801600
+ "OXT" "O2" 0 1 131072 18 8 -0.801600
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+ "N" "N" 0 -1 0.0
+ "H" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "H1" 0 -1 0.0
+ "CB" "CT" 0 -1 0.0
+ "HB2" "HC" 0 -1 0.0
+ "HB3" "HC" 0 -1 0.0
+ "CG" "CC" 0 -1 0.0
+ "ND1" "NA" 0 -1 0.0
+ "HD1" "H" 0 -1 0.0
+ "CE1" "CR" 0 -1 0.0
+ "HE1" "H5" 0 -1 0.0
+ "NE2" "NB" 0 -1 0.0
+ "CD2" "CV" 0 -1 0.0
+ "HD2" "H4" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O2" 0 -1 0.0
+ "OXT" "O2" 0 -1 0.0
+!entry.CHID.unit.boundbox array dbl
+ -1.000000
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+ 0.0
+ 0.0
+!entry.CHID.unit.childsequence single int
+ 2
+!entry.CHID.unit.connect array int
+ 1
+ 0
+!entry.CHID.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 3 4 1
+ 3 5 1
+ 3 16 1
+ 5 6 1
+ 5 7 1
+ 5 8 1
+ 8 9 1
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+ 9 10 1
+ 9 11 1
+ 11 12 1
+ 11 13 1
+ 13 14 1
+ 14 15 1
+ 16 17 1
+ 16 18 1
+!entry.CHID.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+ "R" 1 "A" 14
+ "R" 1 "A" 15
+ "R" 1 "A" 16
+ "R" 1 "A" 17
+ "R" 1 "A" 18
+!entry.CHID.unit.name single str
+ "CHID"
+!entry.CHID.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 3.909407 0.723611 -2.739882E-06
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 2.496995 3.801075 1.241379
+ 3.877484 3.115795 2.131197
+ 4.200813 5.026064 1.321087
+ 3.942782 5.885086 2.382972
+ 3.339725 5.691913 3.169805
+ 4.624274 6.997642 2.182500
+ 4.563048 7.811875 2.904563
+ 5.294011 6.891451 1.061663
+ 5.058974 5.678868 0.492453
+ 5.537741 5.417846 -0.451343
+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+ 6.204455 3.702003 -2.420005E-06
+!entry.CHID.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 0 0 0 0 0
+!entry.CHID.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "CHID" 1 19 1 "p" 0
+!entry.CHID.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.CHID.unit.solventcap array dbl
+ -1.000000
+ 0.0
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+ 0.0
+ 0.0
+!entry.CHID.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
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+!entry.CHIE.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N" 0 1 131072 1 7 -0.382100
+ "H" "H" 0 1 131072 2 1 0.268100
+ "CA" "CX" 0 1 131072 3 6 -0.269900
+ "HA" "H1" 0 1 131072 4 1 0.165000
+ "CB" "CT" 0 1 131072 5 6 -0.106800
+ "HB2" "HC" 0 1 131072 6 1 0.062000
+ "HB3" "HC" 0 1 131072 7 1 0.062000
+ "CG" "CC" 0 1 131072 8 6 0.272400
+ "ND1" "NB" 0 1 131072 9 7 -0.551700
+ "CE1" "CR" 0 1 131072 10 6 0.155800
+ "HE1" "H5" 0 1 131072 11 1 0.144800
+ "NE2" "NA" 0 1 131072 12 7 -0.267000
+ "HE2" "H" 0 1 131072 13 1 0.331900
+ "CD2" "CW" 0 1 131072 14 6 -0.258800
+ "HD2" "H4" 0 1 131072 15 1 0.195700
+ "C" "C" 0 1 131072 16 6 0.791600
+ "O" "O2" 0 1 131072 17 8 -0.806500
+ "OXT" "O2" 0 1 131072 18 8 -0.806500
+!entry.CHIE.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
+ "H" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "H1" 0 -1 0.0
+ "CB" "CT" 0 -1 0.0
+ "HB2" "HC" 0 -1 0.0
+ "HB3" "HC" 0 -1 0.0
+ "CG" "CC" 0 -1 0.0
+ "ND1" "NB" 0 -1 0.0
+ "CE1" "CR" 0 -1 0.0
+ "HE1" "H5" 0 -1 0.0
+ "NE2" "NA" 0 -1 0.0
+ "HE2" "H" 0 -1 0.0
+ "CD2" "CW" 0 -1 0.0
+ "HD2" "H4" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O2" 0 -1 0.0
+ "OXT" "O2" 0 -1 0.0
+!entry.CHIE.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.CHIE.unit.childsequence single int
+ 2
+!entry.CHIE.unit.connect array int
+ 1
+ 0
+!entry.CHIE.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 3 4 1
+ 3 5 1
+ 3 16 1
+ 5 6 1
+ 5 7 1
+ 5 8 1
+ 8 9 1
+ 8 14 1
+ 9 10 1
+ 10 11 1
+ 10 12 1
+ 12 13 1
+ 12 14 1
+ 14 15 1
+ 16 17 1
+ 16 18 1
+!entry.CHIE.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+ "R" 1 "A" 14
+ "R" 1 "A" 15
+ "R" 1 "A" 16
+ "R" 1 "A" 17
+ "R" 1 "A" 18
+!entry.CHIE.unit.name single str
+ "CHIE"
+!entry.CHIE.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 3.909407 0.723611 -2.739882E-06
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 2.496995 3.801075 1.241379
+ 3.877484 3.115795 2.131197
+ 4.200813 5.026064 1.321087
+ 3.942782 5.885086 2.382972
+ 4.624274 6.997642 2.182500
+ 4.563048 7.811875 2.904563
+ 5.294011 6.891451 1.061663
+ 5.896297 7.605085 0.676854
+ 5.058974 5.678868 0.492453
+ 5.537741 5.417846 -0.451343
+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+ 6.204455 3.702003 -2.420005E-06
+!entry.CHIE.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 0 0 0 0 0
+!entry.CHIE.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "CHIE" 1 19 1 "p" 0
+!entry.CHIE.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.CHIE.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.CHIE.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
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+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+!entry.CHIP.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N" 0 1 131072 1 7 -0.348100
+ "H" "H" 0 1 131072 2 1 0.276400
+ "CA" "CX" 0 1 131072 3 6 -0.144500
+ "HA" "H1" 0 1 131072 4 1 0.111500
+ "CB" "CT" 0 1 131072 5 6 -0.080000
+ "HB2" "HC" 0 1 131072 6 1 0.086800
+ "HB3" "HC" 0 1 131072 7 1 0.086800
+ "CG" "CC" 0 1 131072 8 6 0.029800
+ "ND1" "NA" 0 1 131072 9 7 -0.150100
+ "HD1" "H" 0 1 131072 10 1 0.388300
+ "CE1" "CR" 0 1 131072 11 6 -0.025100
+ "HE1" "H5" 0 1 131072 12 1 0.269400
+ "NE2" "NA" 0 1 131072 13 7 -0.168300
+ "HE2" "H" 0 1 131072 14 1 0.391300
+ "CD2" "CW" 0 1 131072 15 6 -0.125600
+ "HD2" "H4" 0 1 131072 16 1 0.233600
+ "C" "C" 0 1 131072 17 6 0.803200
+ "O" "O2" 0 1 131072 18 8 -0.817700
+ "OXT" "O2" 0 1 131072 19 8 -0.817700
+!entry.CHIP.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
+ "H" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "H1" 0 -1 0.0
+ "CB" "CT" 0 -1 0.0
+ "HB2" "HC" 0 -1 0.0
+ "HB3" "HC" 0 -1 0.0
+ "CG" "CC" 0 -1 0.0
+ "ND1" "NA" 0 -1 0.0
+ "HD1" "H" 0 -1 0.0
+ "CE1" "CR" 0 -1 0.0
+ "HE1" "H5" 0 -1 0.0
+ "NE2" "NA" 0 -1 0.0
+ "HE2" "H" 0 -1 0.0
+ "CD2" "CW" 0 -1 0.0
+ "HD2" "H4" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O2" 0 -1 0.0
+ "OXT" "O2" 0 -1 0.0
+!entry.CHIP.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.CHIP.unit.childsequence single int
+ 2
+!entry.CHIP.unit.connect array int
+ 1
+ 0
+!entry.CHIP.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 3 4 1
+ 3 5 1
+ 3 17 1
+ 5 6 1
+ 5 7 1
+ 5 8 1
+ 8 9 1
+ 8 15 1
+ 9 10 1
+ 9 11 1
+ 11 12 1
+ 11 13 1
+ 13 14 1
+ 13 15 1
+ 15 16 1
+ 17 18 1
+ 17 19 1
+!entry.CHIP.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+ "R" 1 "A" 14
+ "R" 1 "A" 15
+ "R" 1 "A" 16
+ "R" 1 "A" 17
+ "R" 1 "A" 18
+ "R" 1 "A" 19
+!entry.CHIP.unit.name single str
+ "CHIP"
+!entry.CHIP.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 3.909407 0.723611 -2.739882E-06
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 2.496995 3.801075 1.241379
+ 3.877484 3.115795 2.131197
+ 4.200813 5.026064 1.321087
+ 3.942782 5.885086 2.382972
+ 3.339725 5.691913 3.169805
+ 4.624274 6.997642 2.182500
+ 4.563048 7.811875 2.904563
+ 5.294011 6.891451 1.061663
+ 5.896297 7.605085 0.676854
+ 5.058974 5.678868 0.492453
+ 5.537741 5.417846 -0.451343
+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+ 6.204455 3.702003 -2.420005E-06
+!entry.CHIP.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 0 0 0 0 0
+!entry.CHIP.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "CHIP" 1 20 1 "p" 0
+!entry.CHIP.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.CHIP.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.CHIP.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
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+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
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+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+!entry.CHYP.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N" 0 1 131072 1 7 -0.280200
+ "CD" "CT" 0 1 131072 2 6 0.077800
+ "HD22" "H1" 0 1 131072 3 1 0.033100
+ "HD23" "H1" 0 1 131072 4 1 0.033100
+ "CG" "CT" 0 1 131072 5 6 0.081000
+ "HG" "H1" 0 1 131072 6 1 0.041600
+ "OD1" "OH" 0 1 131072 7 8 -0.613400
+ "HD1" "HO" 0 1 131072 8 1 0.385100
+ "CB" "CT" 0 1 131072 9 6 0.054700
+ "HB2" "HC" 0 1 131072 10 1 0.042600
+ "HB3" "HC" 0 1 131072 11 1 0.042600
+ "CA" "CX" 0 1 131072 12 6 -0.099300
+ "HA" "H1" 0 1 131072 13 1 0.077600
+ "C" "C" 0 1 131072 14 6 0.663100
+ "O" "O2" 0 1 131072 15 8 -0.769700
+ "OXT" "O2" 0 1 131072 16 8 -0.769700
+!entry.CHYP.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
+ "CD" "CT" 0 -1 0.0
+ "HD22" "H1" 0 -1 0.0
+ "HD23" "H1" 0 -1 0.0
+ "CG" "CT" 0 -1 0.0
+ "HG" "H1" 0 -1 0.0
+ "OD1" "OH" 0 -1 0.0
+ "HD1" "HO" 0 -1 0.0
+ "CB" "CT" 0 -1 0.0
+ "HB2" "HC" 0 -1 0.0
+ "HB3" "HC" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "H1" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O2" 0 -1 0.0
+ "OXT" "O2" 0 -1 0.0
+!entry.CHYP.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.CHYP.unit.childsequence single int
+ 2
+!entry.CHYP.unit.connect array int
+ 1
+ 0
+!entry.CHYP.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 12 1
+ 2 3 1
+ 2 4 1
+ 2 5 1
+ 5 6 1
+ 5 7 1
+ 5 9 1
+ 7 8 1
+ 9 10 1
+ 9 11 1
+ 9 12 1
+ 12 13 1
+ 12 14 1
+ 14 15 1
+ 14 16 1
+!entry.CHYP.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+ "R" 1 "A" 14
+ "R" 1 "A" 15
+ "R" 1 "A" 16
+!entry.CHYP.unit.name single str
+ "CHYP"
+!entry.CHYP.unit.positions table  dbl x  dbl y  dbl z
+ 3.326834 1.557389 -1.603945E-06
+ 4.302147 0.476598 0.080119
+ 4.419998 0.019283 -0.902263
+ 3.955888 -0.274040 0.790574
+ 5.547126 1.172441 0.544693
+ 6.413549 0.741636 0.042879
+ 5.687901 1.006813 1.978308
+ 6.219605 0.169859 2.170401
+ 5.369091 2.628184 0.185227
+ 5.969289 2.861861 -0.694123
+ 5.690642 3.251038 1.019947
+ 3.933610 2.871277 -0.104508
+ 3.611470 3.488570 0.734106
+ 3.505164 3.526392 -1.409783
+ 2.754240 2.939065 -2.185412
+ 3.904907 4.650696 -1.704043
+!entry.CHYP.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 0 0 0 0 0
+!entry.CHYP.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "CHYP" 1 17 1 "p" 0
+!entry.CHYP.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.CHYP.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.CHYP.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
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+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+!entry.CILE.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N" 0 1 131072 1 7 -0.382100
+ "H" "H" 0 1 131072 2 1 0.268100
+ "CA" "CX" 0 1 131072 3 6 -0.310000
+ "HA" "H1" 0 1 131072 4 1 0.137500
+ "CB" "3C" 0 1 131072 5 6 0.036300
+ "HB" "HC" 0 1 131072 6 1 0.076600
+ "CG2" "CT" 0 1 131072 7 6 -0.349800
+ "HG21" "HC" 0 1 131072 8 1 0.102100
+ "HG22" "HC" 0 1 131072 9 1 0.102100
+ "HG23" "HC" 0 1 131072 10 1 0.102100
+ "CG1" "2C" 0 1 131072 11 6 -0.032300
+ "HG12" "HC" 0 1 131072 12 1 0.032100
+ "HG13" "HC" 0 1 131072 13 1 0.032100
+ "CD1" "CT" 0 1 131072 14 6 -0.069900
+ "HD11" "HC" 0 1 131072 15 1 0.019600
+ "HD12" "HC" 0 1 131072 16 1 0.019600
+ "HD13" "HC" 0 1 131072 17 1 0.019600
+ "C" "C" 0 1 131072 18 6 0.834300
+ "O" "O2" 0 1 131072 19 8 -0.819000
+ "OXT" "O2" 0 1 131072 20 8 -0.819000
+!entry.CILE.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
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+ "CA" "CX" 0 -1 0.0
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+ "HB" "HC" 0 -1 0.0
+ "CG2" "CT" 0 -1 0.0
+ "HG21" "HC" 0 -1 0.0
+ "HG22" "HC" 0 -1 0.0
+ "HG23" "HC" 0 -1 0.0
+ "CG1" "2C" 0 -1 0.0
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+ "CD1" "CT" 0 -1 0.0
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+ "C" "C" 0 -1 0.0
+ "O" "O2" 0 -1 0.0
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+ 2
+!entry.CILE.unit.connect array int
+ 1
+ 0
+!entry.CILE.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 3 4 1
+ 3 5 1
+ 3 18 1
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+ 11 12 1
+ 11 13 1
+ 11 14 1
+ 14 15 1
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+ 14 17 1
+ 18 19 1
+ 18 20 1
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+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
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+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+ "R" 1 "A" 14
+ "R" 1 "A" 15
+ "R" 1 "A" 16
+ "R" 1 "A" 17
+ "R" 1 "A" 18
+ "R" 1 "A" 19
+ "R" 1 "A" 20
+!entry.CILE.unit.name single str
+ "CILE"
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+ 3.325770 1.547909 -1.607204E-06
+ 3.909407 0.723611 -2.739882E-06
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.552136 3.620733 1.245168
+ 2.470128 3.752486 1.245640
+ 3.970045 2.845728 2.490296
+ 5.052053 2.713974 2.490763
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+ 3.485650 1.869275 2.490737
+ 4.230204 4.986694 1.245169
+ 5.312310 4.855746 1.245164
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+ 6.008824 1.593175 -8.449768E-06
+ 6.204455 3.702003 -2.420005E-06
+!entry.CILE.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 0 0 0 0 0
+!entry.CILE.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "CILE" 1 21 1 "p" 0
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+!entry.CILE.unit.velocities table  dbl x  dbl y  dbl z
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+ "N" "N" 0 1 131072 1 7 -0.382100
+ "H" "H" 0 1 131072 2 1 0.268100
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+ "HA" "H1" 0 1 131072 4 1 0.134600
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+ "HB3" "HC" 0 1 131072 7 1 0.097400
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+ "HG" "HC" 0 1 131072 9 1 -0.037400
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+ "CD2" "CT" 0 1 131072 14 6 -0.416300
+ "HD21" "HC" 0 1 131072 15 1 0.103800
+ "HD22" "HC" 0 1 131072 16 1 0.103800
+ "HD23" "HC" 0 1 131072 17 1 0.103800
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+ "O" "O2" 0 1 131072 19 8 -0.819900
+ "OXT" "O2" 0 1 131072 20 8 -0.819900
+!entry.CLEU.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
+ "H" "H" 0 -1 0.0
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+!entry.CLEU.unit.childsequence single int
+ 2
+!entry.CLEU.unit.connect array int
+ 1
+ 0
+!entry.CLEU.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 3 4 1
+ 3 5 1
+ 3 18 1
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+ 10 13 1
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+ 14 17 1
+ 18 19 1
+ 18 20 1
+!entry.CLEU.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
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+ "R" 1 "A" 6
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+ "R" 1 "A" 9
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+ "R" 1 "A" 17
+ "R" 1 "A" 18
+ "R" 1 "A" 19
+ "R" 1 "A" 20
+!entry.CLEU.unit.name single str
+ "CLEU"
+!entry.CLEU.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 3.909407 0.723611 -2.739882E-06
+ 3.970048 2.845795 -1.311163E-07
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+ 3.576965 3.653838 1.232143
+ 2.496995 3.801075 1.241379
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+ 4.274186 5.009602 1.194577
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+ 2.773449 5.910113 -0.054557
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+ 6.008824 1.593175 -8.449768E-06
+ 6.204455 3.702003 -2.420005E-06
+!entry.CLEU.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 0 0 0 0 0
+!entry.CLEU.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "CLEU" 1 21 1 "p" 0
+!entry.CLEU.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.CLEU.unit.solventcap array dbl
+ -1.000000
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+!entry.CLEU.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
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+!entry.CLYS.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N" 0 1 131072 1 7 -0.348100
+ "H" "H" 0 1 131072 2 1 0.276400
+ "CA" "CX" 0 1 131072 3 6 -0.290300
+ "HA" "H1" 0 1 131072 4 1 0.143800
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+ "HG3" "HC" 0 1 131072 10 1 0.013400
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+ "HD2" "HC" 0 1 131072 12 1 0.061100
+ "HD3" "HC" 0 1 131072 13 1 0.061100
+ "CE" "C8" 0 1 131072 14 6 -0.017600
+ "HE2" "HP" 0 1 131072 15 1 0.112100
+ "HE3" "HP" 0 1 131072 16 1 0.112100
+ "NZ" "N3" 0 1 131072 17 7 -0.374100
+ "HZ1" "H" 0 1 131072 18 1 0.337400
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+ "HZ3" "H" 0 1 131072 20 1 0.337400
+ "C" "C" 0 1 131072 21 6 0.848800
+ "O" "O2" 0 1 131072 22 8 -0.825200
+ "OXT" "O2" 0 1 131072 23 8 -0.825200
+!entry.CLYS.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
+ "H" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
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+ "CB" "C8" 0 -1 0.0
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+ "HD2" "HC" 0 -1 0.0
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+ "CE" "C8" 0 -1 0.0
+ "HE2" "HP" 0 -1 0.0
+ "HE3" "HP" 0 -1 0.0
+ "NZ" "N3" 0 -1 0.0
+ "HZ1" "H" 0 -1 0.0
+ "HZ2" "H" 0 -1 0.0
+ "HZ3" "H" 0 -1 0.0
+ "C" "C" 0 -1 0.0
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+ "OXT" "O2" 0 -1 0.0
+!entry.CLYS.unit.boundbox array dbl
+ -1.000000
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+ 0.0
+!entry.CLYS.unit.childsequence single int
+ 2
+!entry.CLYS.unit.connect array int
+ 1
+ 0
+!entry.CLYS.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 3 4 1
+ 3 5 1
+ 3 21 1
+ 5 6 1
+ 5 7 1
+ 5 8 1
+ 8 9 1
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+ 14 15 1
+ 14 16 1
+ 14 17 1
+ 17 18 1
+ 17 19 1
+ 17 20 1
+ 21 22 1
+ 21 23 1
+!entry.CLYS.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
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+ "R" 1 "A" 6
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+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+ "R" 1 "A" 14
+ "R" 1 "A" 15
+ "R" 1 "A" 16
+ "R" 1 "A" 17
+ "R" 1 "A" 18
+ "R" 1 "A" 19
+ "R" 1 "A" 20
+ "R" 1 "A" 21
+ "R" 1 "A" 22
+ "R" 1 "A" 23
+!entry.CLYS.unit.name single str
+ "CLYS"
+!entry.CLYS.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 3.909407 0.723611 -2.739882E-06
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 2.496995 3.801075 1.241379
+ 3.877484 3.115795 2.131197
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+ 6.008824 1.593175 -8.449768E-06
+ 6.204455 3.702003 -2.420005E-06
+!entry.CLYS.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 0 0 0 0 0
+!entry.CLYS.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "CLYS" 1 24 1 "p" 0
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+ 0
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+ -1.000000
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+ 0.0
+ 0.0
+!entry.CLYS.unit.velocities table  dbl x  dbl y  dbl z
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+!entry.CMET.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N" 0 1 131072 1 7 -0.382100
+ "H" "H" 0 1 131072 2 1 0.268100
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+ "CG" "2C" 0 1 131072 8 6 0.049200
+ "HG2" "H1" 0 1 131072 9 1 0.031700
+ "HG3" "H1" 0 1 131072 10 1 0.031700
+ "SD" "S" 0 1 131072 11 16 -0.269200
+ "CE" "CT" 0 1 131072 12 6 -0.037600
+ "HE1" "H1" 0 1 131072 13 1 0.062500
+ "HE2" "H1" 0 1 131072 14 1 0.062500
+ "HE3" "H1" 0 1 131072 15 1 0.062500
+ "C" "C" 0 1 131072 16 6 0.801300
+ "O" "O2" 0 1 131072 17 8 -0.810500
+ "OXT" "O2" 0 1 131072 18 8 -0.810500
+!entry.CMET.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
+ "H" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
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+ "CG" "2C" 0 -1 0.0
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+ "C" "C" 0 -1 0.0
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+!entry.CMET.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.CMET.unit.childsequence single int
+ 2
+!entry.CMET.unit.connect array int
+ 1
+ 0
+!entry.CMET.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 3 4 1
+ 3 5 1
+ 3 16 1
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+ 5 7 1
+ 5 8 1
+ 8 9 1
+ 8 10 1
+ 8 11 1
+ 11 12 1
+ 12 13 1
+ 12 14 1
+ 12 15 1
+ 16 17 1
+ 16 18 1
+!entry.CMET.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
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+ "R" 1 "A" 11
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+ "R" 1 "A" 15
+ "R" 1 "A" 16
+ "R" 1 "A" 17
+ "R" 1 "A" 18
+!entry.CMET.unit.name single str
+ "CMET"
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+ 3.325770 1.547909 -1.607204E-06
+ 3.909407 0.723611 -2.739882E-06
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
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+ 3.877484 3.115795 2.131197
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+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+ 6.204455 3.702003 -2.420005E-06
+!entry.CMET.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 0 0 0 0 0
+!entry.CMET.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "CMET" 1 19 1 "p" 0
+!entry.CMET.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.CMET.unit.solventcap array dbl
+ -1.000000
+ 0.0
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+ 0.0
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+!entry.CMET.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
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+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+!entry.CPHE.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N" 0 1 131072 1 7 -0.382100
+ "H" "H" 0 1 131072 2 1 0.268100
+ "CA" "CX" 0 1 131072 3 6 -0.182500
+ "HA" "H1" 0 1 131072 4 1 0.109800
+ "CB" "CT" 0 1 131072 5 6 -0.095900
+ "HB2" "HC" 0 1 131072 6 1 0.044300
+ "HB3" "HC" 0 1 131072 7 1 0.044300
+ "CG" "CA" 0 1 131072 8 6 0.055200
+ "CD1" "CA" 0 1 131072 9 6 -0.130000
+ "HD1" "HA" 0 1 131072 10 1 0.140800
+ "CE1" "CA" 0 1 131072 11 6 -0.184700
+ "HE1" "HA" 0 1 131072 12 1 0.146100
+ "CZ" "CA" 0 1 131072 13 6 -0.094400
+ "HZ" "HA" 0 1 131072 14 1 0.128000
+ "CE2" "CA" 0 1 131072 15 6 -0.184700
+ "HE2" "HA" 0 1 131072 16 1 0.146100
+ "CD2" "CA" 0 1 131072 17 6 -0.130000
+ "HD2" "HA" 0 1 131072 18 1 0.140800
+ "C" "C" 0 1 131072 19 6 0.766000
+ "O" "O2" 0 1 131072 20 8 -0.802600
+ "OXT" "O2" 0 1 131072 21 8 -0.802600
+!entry.CPHE.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
+ "H" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "H1" 0 -1 0.0
+ "CB" "CT" 0 -1 0.0
+ "HB2" "HC" 0 -1 0.0
+ "HB3" "HC" 0 -1 0.0
+ "CG" "CA" 0 -1 0.0
+ "CD1" "CA" 0 -1 0.0
+ "HD1" "HA" 0 -1 0.0
+ "CE1" "CA" 0 -1 0.0
+ "HE1" "HA" 0 -1 0.0
+ "CZ" "CA" 0 -1 0.0
+ "HZ" "HA" 0 -1 0.0
+ "CE2" "CA" 0 -1 0.0
+ "HE2" "HA" 0 -1 0.0
+ "CD2" "CA" 0 -1 0.0
+ "HD2" "HA" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O2" 0 -1 0.0
+ "OXT" "O2" 0 -1 0.0
+!entry.CPHE.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.CPHE.unit.childsequence single int
+ 2
+!entry.CPHE.unit.connect array int
+ 1
+ 0
+!entry.CPHE.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 3 4 1
+ 3 5 1
+ 3 19 1
+ 5 6 1
+ 5 7 1
+ 5 8 1
+ 8 9 1
+ 8 17 1
+ 9 10 1
+ 9 11 1
+ 11 12 1
+ 11 13 1
+ 13 14 1
+ 13 15 1
+ 15 16 1
+ 15 17 1
+ 17 18 1
+ 19 20 1
+ 19 21 1
+!entry.CPHE.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+ "R" 1 "A" 14
+ "R" 1 "A" 15
+ "R" 1 "A" 16
+ "R" 1 "A" 17
+ "R" 1 "A" 18
+ "R" 1 "A" 19
+ "R" 1 "A" 20
+ "R" 1 "A" 21
+!entry.CPHE.unit.name single str
+ "CPHE"
+!entry.CPHE.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 3.909407 0.723611 -2.739882E-06
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 2.496995 3.801075 1.241379
+ 3.877484 3.115795 2.131197
+ 4.200813 5.026064 1.321087
+ 3.911613 5.857250 2.409890
+ 3.236123 5.513843 3.193398
+ 4.490014 7.129513 2.492354
+ 4.264853 7.776651 3.340066
+ 5.357616 7.570591 1.486016
+ 5.807943 8.561138 1.550220
+ 5.646818 6.739407 0.397211
+ 6.322309 7.082817 -0.386295
+ 5.068419 5.467143 0.314744
+ 5.293584 4.820007 -0.532968
+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+ 6.204455 3.702003 -2.420005E-06
+!entry.CPHE.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 0 0 0 0 0
+!entry.CPHE.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "CPHE" 1 22 1 "p" 0
+!entry.CPHE.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.CPHE.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.CPHE.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
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+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
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+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+!entry.CPRO.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N" 0 1 131072 1 7 -0.280200
+ "CD" "CT" 0 1 131072 2 6 0.043400
+ "HD2" "H1" 0 1 131072 3 1 0.033100
+ "HD3" "H1" 0 1 131072 4 1 0.033100
+ "CG" "CT" 0 1 131072 5 6 0.046600
+ "HG2" "HC" 0 1 131072 6 1 0.017200
+ "HG3" "HC" 0 1 131072 7 1 0.017200
+ "CB" "CT" 0 1 131072 8 6 -0.054300
+ "HB2" "HC" 0 1 131072 9 1 0.038100
+ "HB3" "HC" 0 1 131072 10 1 0.038100
+ "CA" "CX" 0 1 131072 11 6 -0.133600
+ "HA" "H1" 0 1 131072 12 1 0.077600
+ "C" "C" 0 1 131072 13 6 0.663100
+ "O" "O2" 0 1 131072 14 8 -0.769700
+ "OXT" "O2" 0 1 131072 15 8 -0.769700
+!entry.CPRO.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
+ "CD" "CT" 0 -1 0.0
+ "HD2" "H1" 0 -1 0.0
+ "HD3" "H1" 0 -1 0.0
+ "CG" "CT" 0 -1 0.0
+ "HG2" "HC" 0 -1 0.0
+ "HG3" "HC" 0 -1 0.0
+ "CB" "CT" 0 -1 0.0
+ "HB2" "HC" 0 -1 0.0
+ "HB3" "HC" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "H1" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O2" 0 -1 0.0
+ "OXT" "O2" 0 -1 0.0
+!entry.CPRO.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.CPRO.unit.childsequence single int
+ 2
+!entry.CPRO.unit.connect array int
+ 1
+ 0
+!entry.CPRO.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 11 1
+ 2 3 1
+ 2 4 1
+ 2 5 1
+ 5 6 1
+ 5 7 1
+ 5 8 1
+ 8 9 1
+ 8 10 1
+ 8 11 1
+ 11 12 1
+ 11 13 1
+ 13 14 1
+ 13 15 1
+!entry.CPRO.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+ "R" 1 "A" 14
+ "R" 1 "A" 15
+!entry.CPRO.unit.name single str
+ "CPRO"
+!entry.CPRO.unit.positions table  dbl x  dbl y  dbl z
+ 3.326834 1.557389 -1.603945E-06
+ 4.302147 0.476598 0.080119
+ 4.419998 0.019283 -0.902263
+ 3.955888 -0.274040 0.790574
+ 5.547126 1.172441 0.544693
+ 6.413549 0.741636 0.042879
+ 5.652950 1.047934 1.622376
+ 5.369091 2.628184 0.185227
+ 5.969289 2.861861 -0.694123
+ 5.690642 3.251038 1.019947
+ 3.933610 2.871277 -0.104508
+ 3.611470 3.488570 0.734106
+ 3.505164 3.526392 -1.409783
+ 2.754240 2.939065 -2.185412
+ 3.904907 4.650696 -1.704043
+!entry.CPRO.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 0 0 0 0 0
+!entry.CPRO.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "CPRO" 1 16 1 "p" 0
+!entry.CPRO.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.CPRO.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.CPRO.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+!entry.CSER.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N" 0 1 131072 1 7 -0.382100
+ "H" "H" 0 1 131072 2 1 0.268100
+ "CA" "CX" 0 1 131072 3 6 -0.272200
+ "HA" "H1" 0 1 131072 4 1 0.130400
+ "CB" "2C" 0 1 131072 5 6 0.112300
+ "HB2" "H1" 0 1 131072 6 1 0.081300
+ "HB3" "H1" 0 1 131072 7 1 0.081300
+ "OG" "OH" 0 1 131072 8 8 -0.651400
+ "HG" "HO" 0 1 131072 9 1 0.447400
+ "C" "C" 0 1 131072 10 6 0.811300
+ "O" "O2" 0 1 131072 11 8 -0.813200
+ "OXT" "O2" 0 1 131072 12 8 -0.813200
+!entry.CSER.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
+ "H" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "H1" 0 -1 0.0
+ "CB" "2C" 0 -1 0.0
+ "HB2" "H1" 0 -1 0.0
+ "HB3" "H1" 0 -1 0.0
+ "OG" "OH" 0 -1 0.0
+ "HG" "HO" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O2" 0 -1 0.0
+ "OXT" "O2" 0 -1 0.0
+!entry.CSER.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.CSER.unit.childsequence single int
+ 2
+!entry.CSER.unit.connect array int
+ 1
+ 0
+!entry.CSER.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 3 4 1
+ 3 5 1
+ 3 10 1
+ 5 6 1
+ 5 7 1
+ 5 8 1
+ 8 9 1
+ 10 11 1
+ 10 12 1
+!entry.CSER.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+!entry.CSER.unit.name single str
+ "CSER"
+!entry.CSER.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 3.909407 0.723611 -2.739882E-06
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 2.496995 3.801075 1.241379
+ 3.877484 3.115795 2.131197
+ 4.230753 4.925145 1.196917
+ 3.983305 5.433814 1.972562
+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+ 6.204455 3.702003 -2.420005E-06
+!entry.CSER.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 0 0 0 0 0
+!entry.CSER.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "CSER" 1 13 1 "p" 0
+!entry.CSER.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.CSER.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.CSER.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+!entry.CTHR.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N" 0 1 131072 1 7 -0.382100
+ "H" "H" 0 1 131072 2 1 0.268100
+ "CA" "CX" 0 1 131072 3 6 -0.242000
+ "HA" "H1" 0 1 131072 4 1 0.120700
+ "CB" "3C" 0 1 131072 5 6 0.302500
+ "HB" "H1" 0 1 131072 6 1 0.007800
+ "CG2" "CT" 0 1 131072 7 6 -0.185300
+ "HG21" "HC" 0 1 131072 8 1 0.058600
+ "HG22" "HC" 0 1 131072 9 1 0.058600
+ "HG23" "HC" 0 1 131072 10 1 0.058600
+ "OG1" "OH" 0 1 131072 11 8 -0.649600
+ "HG1" "HO" 0 1 131072 12 1 0.411900
+ "C" "C" 0 1 131072 13 6 0.781000
+ "O" "O2" 0 1 131072 14 8 -0.804400
+ "OXT" "O2" 0 1 131072 15 8 -0.804400
+!entry.CTHR.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
+ "H" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "H1" 0 -1 0.0
+ "CB" "3C" 0 -1 0.0
+ "HB" "H1" 0 -1 0.0
+ "CG2" "CT" 0 -1 0.0
+ "HG21" "HC" 0 -1 0.0
+ "HG22" "HC" 0 -1 0.0
+ "HG23" "HC" 0 -1 0.0
+ "OG1" "OH" 0 -1 0.0
+ "HG1" "HO" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O2" 0 -1 0.0
+ "OXT" "O2" 0 -1 0.0
+!entry.CTHR.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.CTHR.unit.childsequence single int
+ 2
+!entry.CTHR.unit.connect array int
+ 1
+ 0
+!entry.CTHR.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 3 4 1
+ 3 5 1
+ 3 13 1
+ 5 6 1
+ 5 7 1
+ 5 11 1
+ 7 8 1
+ 7 9 1
+ 7 10 1
+ 11 12 1
+ 13 14 1
+ 13 15 1
+!entry.CTHR.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+ "R" 1 "A" 14
+ "R" 1 "A" 15
+!entry.CTHR.unit.name single str
+ "CTHR"
+!entry.CTHR.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 3.909407 0.723611 -2.739882E-06
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 4.075059 4.623017 1.205786
+ 2.065936 3.859425 1.244383
+ 1.567127 2.890627 1.271209
+ 1.784431 4.436953 2.124903
+ 1.764699 4.397847 0.345796
+ 3.971501 2.947413 2.411212
+ 3.724052 3.456082 3.186857
+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+ 6.204455 3.702003 -2.420005E-06
+!entry.CTHR.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 0 0 0 0 0
+!entry.CTHR.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "CTHR" 1 16 1 "p" 0
+!entry.CTHR.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.CTHR.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.CTHR.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+!entry.CTRP.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N" 0 1 131072 1 7 -0.382100
+ "H" "H" 0 1 131072 2 1 0.268100
+ "CA" "CX" 0 1 131072 3 6 -0.208400
+ "HA" "H1" 0 1 131072 4 1 0.127200
+ "CB" "CT" 0 1 131072 5 6 -0.074200
+ "HB2" "HC" 0 1 131072 6 1 0.049700
+ "HB3" "HC" 0 1 131072 7 1 0.049700
+ "CG" "C*" 0 1 131072 8 6 -0.079600
+ "CD1" "CW" 0 1 131072 9 6 -0.180800
+ "HD1" "H4" 0 1 131072 10 1 0.204300
+ "NE1" "NA" 0 1 131072 11 7 -0.331600
+ "HE1" "H" 0 1 131072 12 1 0.341300
+ "CE2" "CN" 0 1 131072 13 6 0.122200
+ "CZ2" "CA" 0 1 131072 14 6 -0.259400
+ "HZ2" "HA" 0 1 131072 15 1 0.156700
+ "CH2" "CA" 0 1 131072 16 6 -0.102000
+ "HH2" "HA" 0 1 131072 17 1 0.140100
+ "CZ3" "CA" 0 1 131072 18 6 -0.228700
+ "HZ3" "HA" 0 1 131072 19 1 0.150700
+ "CE3" "CA" 0 1 131072 20 6 -0.183700
+ "HE3" "HA" 0 1 131072 21 1 0.149100
+ "CD2" "CB" 0 1 131072 22 6 0.107800
+ "C" "C" 0 1 131072 23 6 0.765800
+ "O" "O2" 0 1 131072 24 8 -0.801100
+ "OXT" "O2" 0 1 131072 25 8 -0.801100
+!entry.CTRP.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
+ "H" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "H1" 0 -1 0.0
+ "CB" "CT" 0 -1 0.0
+ "HB2" "HC" 0 -1 0.0
+ "HB3" "HC" 0 -1 0.0
+ "CG" "C*" 0 -1 0.0
+ "CD1" "CW" 0 -1 0.0
+ "HD1" "H4" 0 -1 0.0
+ "NE1" "NA" 0 -1 0.0
+ "HE1" "H" 0 -1 0.0
+ "CE2" "CN" 0 -1 0.0
+ "CZ2" "CA" 0 -1 0.0
+ "HZ2" "HA" 0 -1 0.0
+ "CH2" "CA" 0 -1 0.0
+ "HH2" "HA" 0 -1 0.0
+ "CZ3" "CA" 0 -1 0.0
+ "HZ3" "HA" 0 -1 0.0
+ "CE3" "CA" 0 -1 0.0
+ "HE3" "HA" 0 -1 0.0
+ "CD2" "CB" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O2" 0 -1 0.0
+ "OXT" "O2" 0 -1 0.0
+!entry.CTRP.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.CTRP.unit.childsequence single int
+ 2
+!entry.CTRP.unit.connect array int
+ 1
+ 0
+!entry.CTRP.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 3 4 1
+ 3 5 1
+ 3 23 1
+ 5 6 1
+ 5 7 1
+ 5 8 1
+ 8 9 1
+ 8 22 1
+ 9 10 1
+ 9 11 1
+ 11 12 1
+ 11 13 1
+ 13 14 1
+ 13 22 1
+ 14 15 1
+ 14 16 1
+ 16 17 1
+ 16 18 1
+ 18 19 1
+ 18 20 1
+ 20 21 1
+ 20 22 1
+ 23 24 1
+ 23 25 1
+!entry.CTRP.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+ "R" 1 "A" 14
+ "R" 1 "A" 15
+ "R" 1 "A" 16
+ "R" 1 "A" 17
+ "R" 1 "A" 18
+ "R" 1 "A" 19
+ "R" 1 "A" 20
+ "R" 1 "A" 21
+ "R" 1 "A" 22
+ "R" 1 "A" 23
+ "R" 1 "A" 24
+ "R" 1 "A" 25
+!entry.CTRP.unit.name single str
+ "CTRP"
+!entry.CTRP.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 3.909407 0.723611 -2.739882E-06
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 2.496995 3.801075 1.241379
+ 3.877484 3.115795 2.131197
+ 4.200813 5.026064 1.321087
+ 4.023453 5.931084 2.293240
+ 3.368841 5.705466 3.135071
+ 4.811943 7.073555 1.949808
+ 4.882921 7.922010 2.493118
+ 5.427347 6.842060 0.816764
+ 6.297161 7.689052 0.119605
+ 6.531230 8.676649 0.517050
+ 6.814091 7.187011 -1.069023
+ 7.498074 7.791857 -1.664362
+ 6.482659 5.953119 -1.505101
+ 6.897660 5.575648 -2.439654
+ 5.604041 5.117355 -0.785636
+ 5.358720 4.126570 -1.168080
+ 5.083390 5.623004 0.411545
+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+ 6.204455 3.702003 -2.420005E-06
+!entry.CTRP.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 0 0 0 0 0
+!entry.CTRP.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "CTRP" 1 26 1 "p" 0
+!entry.CTRP.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.CTRP.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.CTRP.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+!entry.CTYR.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N" 0 1 131072 1 7 -0.382100
+ "H" "H" 0 1 131072 2 1 0.268100
+ "CA" "CX" 0 1 131072 3 6 -0.201500
+ "HA" "H1" 0 1 131072 4 1 0.109200
+ "CB" "CT" 0 1 131072 5 6 -0.075200
+ "HB2" "HC" 0 1 131072 6 1 0.049000
+ "HB3" "HC" 0 1 131072 7 1 0.049000
+ "CG" "CA" 0 1 131072 8 6 0.024300
+ "CD1" "CA" 0 1 131072 9 6 -0.192200
+ "HD1" "HA" 0 1 131072 10 1 0.178000
+ "CE1" "CA" 0 1 131072 11 6 -0.245800
+ "HE1" "HA" 0 1 131072 12 1 0.167300
+ "CZ" "C" 0 1 131072 13 6 0.339500
+ "OH" "OH" 0 1 131072 14 8 -0.564300
+ "HH" "HO" 0 1 131072 15 1 0.401700
+ "CE2" "CA" 0 1 131072 16 6 -0.245800
+ "HE2" "HA" 0 1 131072 17 1 0.167300
+ "CD2" "CA" 0 1 131072 18 6 -0.192200
+ "HD2" "HA" 0 1 131072 19 1 0.178000
+ "C" "C" 0 1 131072 20 6 0.781700
+ "O" "O2" 0 1 131072 21 8 -0.807000
+ "OXT" "O2" 0 1 131072 22 8 -0.807000
+!entry.CTYR.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
+ "H" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "H1" 0 -1 0.0
+ "CB" "CT" 0 -1 0.0
+ "HB2" "HC" 0 -1 0.0
+ "HB3" "HC" 0 -1 0.0
+ "CG" "CA" 0 -1 0.0
+ "CD1" "CA" 0 -1 0.0
+ "HD1" "HA" 0 -1 0.0
+ "CE1" "CA" 0 -1 0.0
+ "HE1" "HA" 0 -1 0.0
+ "CZ" "C" 0 -1 0.0
+ "OH" "OH" 0 -1 0.0
+ "HH" "HO" 0 -1 0.0
+ "CE2" "CA" 0 -1 0.0
+ "HE2" "HA" 0 -1 0.0
+ "CD2" "CA" 0 -1 0.0
+ "HD2" "HA" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O2" 0 -1 0.0
+ "OXT" "O2" 0 -1 0.0
+!entry.CTYR.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.CTYR.unit.childsequence single int
+ 2
+!entry.CTYR.unit.connect array int
+ 1
+ 0
+!entry.CTYR.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 3 4 1
+ 3 5 1
+ 3 20 1
+ 5 6 1
+ 5 7 1
+ 5 8 1
+ 8 9 1
+ 8 18 1
+ 9 10 1
+ 9 11 1
+ 11 12 1
+ 11 13 1
+ 13 14 1
+ 13 16 1
+ 14 15 1
+ 16 17 1
+ 16 18 1
+ 18 19 1
+ 20 21 1
+ 20 22 1
+!entry.CTYR.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+ "R" 1 "A" 14
+ "R" 1 "A" 15
+ "R" 1 "A" 16
+ "R" 1 "A" 17
+ "R" 1 "A" 18
+ "R" 1 "A" 19
+ "R" 1 "A" 20
+ "R" 1 "A" 21
+ "R" 1 "A" 22
+!entry.CTYR.unit.name single str
+ "CTYR"
+!entry.CTYR.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 3.909407 0.723611 -2.739882E-06
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 2.496995 3.801075 1.241379
+ 3.877484 3.115795 2.131197
+ 4.267328 4.996267 1.194946
+ 4.059927 5.918911 2.227280
+ 3.400108 5.668218 3.057877
+ 4.699998 7.163547 2.192791
+ 4.538522 7.881891 2.996538
+ 5.547471 7.485542 1.125970
+ 6.169255 8.694617 1.092468
+ 5.956327 9.246984 1.848214
+ 5.754875 6.562900 0.093635
+ 6.414694 6.813595 -0.736962
+ 5.114806 5.318263 0.128119
+ 5.276286 4.599920 -0.675627
+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+ 6.204455 3.702003 -2.420005E-06
+!entry.CTYR.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 0 0 0 0 0
+!entry.CTYR.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "CTYR" 1 23 1 "p" 0
+!entry.CTYR.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.CTYR.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.CTYR.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+!entry.CVAL.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N" 0 1 131072 1 7 -0.382100
+ "H" "H" 0 1 131072 2 1 0.268100
+ "CA" "CX" 0 1 131072 3 6 -0.343800
+ "HA" "H1" 0 1 131072 4 1 0.143800
+ "CB" "3C" 0 1 131072 5 6 0.194000
+ "HB" "HC" 0 1 131072 6 1 0.030800
+ "CG1" "CT" 0 1 131072 7 6 -0.306400
+ "HG11" "HC" 0 1 131072 8 1 0.083600
+ "HG12" "HC" 0 1 131072 9 1 0.083600
+ "HG13" "HC" 0 1 131072 10 1 0.083600
+ "CG2" "CT" 0 1 131072 11 6 -0.306400
+ "HG21" "HC" 0 1 131072 12 1 0.083600
+ "HG22" "HC" 0 1 131072 13 1 0.083600
+ "HG23" "HC" 0 1 131072 14 1 0.083600
+ "C" "C" 0 1 131072 15 6 0.835000
+ "O" "O2" 0 1 131072 16 8 -0.817300
+ "OXT" "O2" 0 1 131072 17 8 -0.817300
+!entry.CVAL.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
+ "H" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "H1" 0 -1 0.0
+ "CB" "3C" 0 -1 0.0
+ "HB" "HC" 0 -1 0.0
+ "CG1" "CT" 0 -1 0.0
+ "HG11" "HC" 0 -1 0.0
+ "HG12" "HC" 0 -1 0.0
+ "HG13" "HC" 0 -1 0.0
+ "CG2" "CT" 0 -1 0.0
+ "HG21" "HC" 0 -1 0.0
+ "HG22" "HC" 0 -1 0.0
+ "HG23" "HC" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O2" 0 -1 0.0
+ "OXT" "O2" 0 -1 0.0
+!entry.CVAL.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.CVAL.unit.childsequence single int
+ 2
+!entry.CVAL.unit.connect array int
+ 1
+ 0
+!entry.CVAL.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 3 4 1
+ 3 5 1
+ 3 15 1
+ 5 6 1
+ 5 7 1
+ 5 11 1
+ 7 8 1
+ 7 9 1
+ 7 10 1
+ 11 12 1
+ 11 13 1
+ 11 14 1
+ 15 16 1
+ 15 17 1
+!entry.CVAL.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+ "R" 1 "A" 14
+ "R" 1 "A" 15
+ "R" 1 "A" 16
+ "R" 1 "A" 17
+!entry.CVAL.unit.name single str
+ "CVAL"
+!entry.CVAL.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 3.909407 0.723611 -2.739882E-06
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 2.496995 3.801075 1.241379
+ 3.997712 2.900483 2.489542
+ 5.077693 2.753265 2.481244
+ 3.716972 3.477628 3.370558
+ 3.499630 1.931323 2.516834
+ 4.274186 5.009602 1.194577
+ 3.973781 5.548460 0.295972
+ 3.993559 5.587585 2.075079
+ 5.354271 4.863178 1.185788
+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+ 6.204455 3.702003 -2.420005E-06
+!entry.CVAL.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 0 0 0 0 0
+!entry.CVAL.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "CVAL" 1 18 1 "p" 0
+!entry.CVAL.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.CVAL.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.CVAL.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+!entry.NHE.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N" 0 1 131072 1 7 -0.463000
+ "HN1" "H" 0 1 131072 2 1 0.231500
+ "HN2" "H" 0 1 131072 3 1 0.231500
+!entry.NHE.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
+ "HN1" "H" 0 -1 0.0
+ "HN2" "H" 0 -1 0.0
+!entry.NHE.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.NHE.unit.childsequence single int
+ 2
+!entry.NHE.unit.connect array int
+ 1
+ 0
+!entry.NHE.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+!entry.NHE.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+!entry.NHE.unit.name single str
+ "NHE"
+!entry.NHE.unit.positions table  dbl x  dbl y  dbl z
+ 2.193696 1.597759 -1.607204E-06
+ 3.034948 1.038834 -2.739928E-06
+ 2.250077 2.606184 -5.030662E-07
+!entry.NHE.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 1 0 0 0 0
+!entry.NHE.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "NHE" 1 4 1 "p" 0
+!entry.NHE.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.NHE.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.NHE.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+!entry.NME.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N" 0 1 131072 1 7 -0.415700
+ "H" "H" 0 1 131072 2 1 0.271900
+ "C" "CT" 0 1 131072 3 6 -0.149000
+ "H1" "H1" 0 1 131072 4 1 0.097600
+ "H2" "H1" 0 1 131072 5 1 0.097600
+ "H3" "H1" 0 1 131072 6 1 0.097600
+!entry.NME.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
+ "H" "H" 0 -1 0.0
+ "C" "CT" 0 -1 0.0
+ "H1" "H1" 0 -1 0.0
+ "H2" "H1" 0 -1 0.0
+ "H3" "H1" 0 -1 0.0
+!entry.NME.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.NME.unit.childsequence single int
+ 2
+!entry.NME.unit.connect array int
+ 1
+ 0
+!entry.NME.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 3 4 1
+ 3 5 1
+ 3 6 1
+!entry.NME.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+!entry.NME.unit.name single str
+ "NME"
+!entry.NME.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 3.909407 0.723611 -2.739882E-06
+ 3.970048 2.845795 -1.311163E-07
+ 3.211504 3.628554 2.348065E-06
+ 4.591993 2.943271 0.889822
+ 4.591988 2.943275 -0.889825
+!entry.NME.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 3 0 0 0 0
+!entry.NME.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "NME" 1 7 1 "p" 0
+!entry.NME.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.NME.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.NME.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
diff --git a/test/Test_Build/aminont12.lib b/test/Test_Build/aminont12.lib
new file mode 100644
index 0000000000..adaac9fa60
--- /dev/null
+++ b/test/Test_Build/aminont12.lib
@@ -0,0 +1,3303 @@
+!!index array str
+ "ACE"
+ "NALA"
+ "NARG"
+ "NASN"
+ "NASP"
+ "NCYS"
+ "NCYX"
+ "NGLN"
+ "NGLU"
+ "NGLY"
+ "NHID"
+ "NHIE"
+ "NHIP"
+ "NILE"
+ "NLEU"
+ "NLYS"
+ "NMET"
+ "NPHE"
+ "NPRO"
+ "NSER"
+ "NTHR"
+ "NTRP"
+ "NTYR"
+ "NVAL"
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+ "H1" "HC" 0 1 131072 1 1 0.112300
+ "CH3" "CT" 0 1 131072 2 6 -0.366200
+ "H2" "HC" 0 1 131072 3 1 0.112300
+ "H3" "HC" 0 1 131072 4 1 0.112300
+ "C" "C" 0 1 131072 5 6 0.597200
+ "O" "O" 0 1 131072 6 8 -0.567900
+!entry.ACE.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "H1" "HC" 0 -1 0.0
+ "CH3" "CT" 0 -1 0.0
+ "H2" "HC" 0 -1 0.0
+ "H3" "HC" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O" 0 -1 0.0
+!entry.ACE.unit.boundbox array dbl
+ -1.000000
+ 0.0
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+ 0.0
+ 0.0
+!entry.ACE.unit.childsequence single int
+ 2
+!entry.ACE.unit.connect array int
+ 0
+ 5
+!entry.ACE.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 2 3 1
+ 2 4 1
+ 2 5 1
+ 5 6 1
+!entry.ACE.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+!entry.ACE.unit.name single str
+ "ACE"
+!entry.ACE.unit.positions table  dbl x  dbl y  dbl z
+ 2.000001 1.000000 -1.346410E-06
+ 2.000001 2.090000 1.211769E-07
+ 1.486264 2.453849 0.889824
+ 1.486259 2.453852 -0.889820
+ 3.427420 2.640795 -2.981008E-06
+ 4.390580 1.877406 -6.602451E-06
+!entry.ACE.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 5 0 0 0 0
+!entry.ACE.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "ACE" 1 7 1 "p" 0
+!entry.ACE.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.ACE.unit.solventcap array dbl
+ -1.000000
+ 0.0
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+ 0.0
+ 0.0
+!entry.ACE.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
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+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+!entry.NALA.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N3" 0 1 131072 1 7 0.141400
+ "H1" "H" 0 1 131072 2 1 0.199700
+ "H2" "H" 0 1 131072 3 1 0.199700
+ "H3" "H" 0 1 131072 4 1 0.199700
+ "CA" "CX" 0 1 131072 5 6 0.096200
+ "HA" "HP" 0 1 131072 6 1 0.088900
+ "CB" "CT" 0 1 131072 7 6 -0.059700
+ "HB1" "HC" 0 1 131072 8 1 0.030000
+ "HB2" "HC" 0 1 131072 9 1 0.030000
+ "HB3" "HC" 0 1 131072 10 1 0.030000
+ "C" "C" 0 1 131072 11 6 0.616300
+ "O" "O" 0 1 131072 12 8 -0.572200
+!entry.NALA.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N3" 0 -1 0.0
+ "H1" "H" 0 -1 0.0
+ "H2" "H" 0 -1 0.0
+ "H3" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "HP" 0 -1 0.0
+ "CB" "CT" 0 -1 0.0
+ "HB1" "HC" 0 -1 0.0
+ "HB2" "HC" 0 -1 0.0
+ "HB3" "HC" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O" 0 -1 0.0
+!entry.NALA.unit.boundbox array dbl
+ -1.000000
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+ 0.0
+ 0.0
+ 0.0
+!entry.NALA.unit.childsequence single int
+ 2
+!entry.NALA.unit.connect array int
+ 0
+ 11
+!entry.NALA.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 1 4 1
+ 1 5 1
+ 5 6 1
+ 5 7 1
+ 5 11 1
+ 7 8 1
+ 7 9 1
+ 7 10 1
+ 11 12 1
+!entry.NALA.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+!entry.NALA.unit.name single str
+ "NALA"
+!entry.NALA.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 4.046154 0.839991 -2.855245E-06
+ 2.823094 1.499508 -0.874687
+ 2.823097 1.499507 0.874685
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 3.877484 3.115795 2.131197
+ 4.075059 4.623017 1.205786
+ 2.496995 3.801075 1.241379
+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+!entry.NALA.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 0 11 0 0 0 0
+!entry.NALA.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "NALA" 1 13 1 "p" 0
+!entry.NALA.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.NALA.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.NALA.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
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+ 0.0 0.0 0.0
+!entry.NARG.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N3" 0 1 131072 1 7 0.130500
+ "H1" "H" 0 1 131072 2 1 0.208300
+ "H2" "H" 0 1 131072 3 1 0.208300
+ "H3" "H" 0 1 131072 4 1 0.208300
+ "CA" "CX" 0 1 131072 5 6 -0.022300
+ "HA" "HP" 0 1 131072 6 1 0.124200
+ "CB" "C8" 0 1 131072 7 6 0.011800
+ "HB2" "HC" 0 1 131072 8 1 0.022600
+ "HB3" "HC" 0 1 131072 9 1 0.022600
+ "CG" "C8" 0 1 131072 10 6 0.023600
+ "HG2" "HC" 0 1 131072 11 1 0.030900
+ "HG3" "HC" 0 1 131072 12 1 0.030900
+ "CD" "C8" 0 1 131072 13 6 0.093500
+ "HD2" "H1" 0 1 131072 14 1 0.052700
+ "HD3" "H1" 0 1 131072 15 1 0.052700
+ "NE" "N2" 0 1 131072 16 7 -0.565000
+ "HE" "H" 0 1 131072 17 1 0.359200
+ "CZ" "CA" 0 1 131072 18 6 0.828100
+ "NH1" "N2" 0 1 131072 19 7 -0.869300
+ "HH11" "H" 0 1 131072 20 1 0.449400
+ "HH12" "H" 0 1 131072 21 1 0.449400
+ "NH2" "N2" 0 1 131072 22 7 -0.869300
+ "HH21" "H" 0 1 131072 23 1 0.449400
+ "HH22" "H" 0 1 131072 24 1 0.449400
+ "C" "C" 0 1 131072 25 6 0.721400
+ "O" "O" 0 1 131072 26 8 -0.601300
+!entry.NARG.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N3" 0 -1 0.0
+ "H1" "H" 0 -1 0.0
+ "H2" "H" 0 -1 0.0
+ "H3" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "HP" 0 -1 0.0
+ "CB" "C8" 0 -1 0.0
+ "HB2" "HC" 0 -1 0.0
+ "HB3" "HC" 0 -1 0.0
+ "CG" "C8" 0 -1 0.0
+ "HG2" "HC" 0 -1 0.0
+ "HG3" "HC" 0 -1 0.0
+ "CD" "C8" 0 -1 0.0
+ "HD2" "H1" 0 -1 0.0
+ "HD3" "H1" 0 -1 0.0
+ "NE" "N2" 0 -1 0.0
+ "HE" "H" 0 -1 0.0
+ "CZ" "CA" 0 -1 0.0
+ "NH1" "N2" 0 -1 0.0
+ "HH11" "H" 0 -1 0.0
+ "HH12" "H" 0 -1 0.0
+ "NH2" "N2" 0 -1 0.0
+ "HH21" "H" 0 -1 0.0
+ "HH22" "H" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O" 0 -1 0.0
+!entry.NARG.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.NARG.unit.childsequence single int
+ 2
+!entry.NARG.unit.connect array int
+ 0
+ 25
+!entry.NARG.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 1 4 1
+ 1 5 1
+ 5 6 1
+ 5 7 1
+ 5 25 1
+ 7 8 1
+ 7 9 1
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+ 16 17 1
+ 16 18 1
+ 18 19 1
+ 18 22 1
+ 19 20 1
+ 19 21 1
+ 22 23 1
+ 22 24 1
+ 25 26 1
+!entry.NARG.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+ "R" 1 "A" 14
+ "R" 1 "A" 15
+ "R" 1 "A" 16
+ "R" 1 "A" 17
+ "R" 1 "A" 18
+ "R" 1 "A" 19
+ "R" 1 "A" 20
+ "R" 1 "A" 21
+ "R" 1 "A" 22
+ "R" 1 "A" 23
+ "R" 1 "A" 24
+ "R" 1 "A" 25
+ "R" 1 "A" 26
+!entry.NARG.unit.name single str
+ "NARG"
+!entry.NARG.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 4.046154 0.839991 -2.855245E-06
+ 2.823094 1.499508 -0.874687
+ 2.823097 1.499507 0.874685
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
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+ 4.274186 5.009602 1.194577
+ 5.354271 4.863178 1.185788
+ 3.973781 5.548460 0.295972
+ 3.881105 5.817645 2.426721
+ 2.801135 5.964881 2.435959
+ 4.181626 5.279602 3.325774
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+ 5.151805 7.375492 1.655065
+ 4.364284 8.040989 3.389382
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+ 4.892216 9.903045 4.004368
+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+!entry.NARG.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 0 25 0 0 0 0
+!entry.NARG.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "NARG" 1 27 1 "p" 0
+!entry.NARG.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.NARG.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.NARG.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
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+!entry.NASN.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N3" 0 1 131072 1 7 0.180100
+ "H1" "H" 0 1 131072 2 1 0.192100
+ "H2" "H" 0 1 131072 3 1 0.192100
+ "H3" "H" 0 1 131072 4 1 0.192100
+ "CA" "CX" 0 1 131072 5 6 0.036800
+ "HA" "HP" 0 1 131072 6 1 0.123100
+ "CB" "2C" 0 1 131072 7 6 -0.028300
+ "HB2" "HC" 0 1 131072 8 1 0.051500
+ "HB3" "HC" 0 1 131072 9 1 0.051500
+ "CG" "C" 0 1 131072 10 6 0.583300
+ "OD1" "O" 0 1 131072 11 8 -0.574400
+ "ND2" "N" 0 1 131072 12 7 -0.863400
+ "HD21" "H" 0 1 131072 13 1 0.409700
+ "HD22" "H" 0 1 131072 14 1 0.409700
+ "C" "C" 0 1 131072 15 6 0.616300
+ "O" "O" 0 1 131072 16 8 -0.572200
+!entry.NASN.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N3" 0 -1 0.0
+ "H1" "H" 0 -1 0.0
+ "H2" "H" 0 -1 0.0
+ "H3" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "HP" 0 -1 0.0
+ "CB" "2C" 0 -1 0.0
+ "HB2" "HC" 0 -1 0.0
+ "HB3" "HC" 0 -1 0.0
+ "CG" "C" 0 -1 0.0
+ "OD1" "O" 0 -1 0.0
+ "ND2" "N" 0 -1 0.0
+ "HD21" "H" 0 -1 0.0
+ "HD22" "H" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O" 0 -1 0.0
+!entry.NASN.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.NASN.unit.childsequence single int
+ 2
+!entry.NASN.unit.connect array int
+ 0
+ 15
+!entry.NASN.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 1 4 1
+ 1 5 1
+ 5 6 1
+ 5 7 1
+ 5 15 1
+ 7 8 1
+ 7 9 1
+ 7 10 1
+ 10 11 1
+ 10 12 1
+ 12 13 1
+ 12 14 1
+ 15 16 1
+!entry.NASN.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+ "R" 1 "A" 14
+ "R" 1 "A" 15
+ "R" 1 "A" 16
+!entry.NASN.unit.name single str
+ "NASN"
+!entry.NASN.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 4.046154 0.839991 -2.855245E-06
+ 2.823094 1.499508 -0.874687
+ 2.823097 1.499507 0.874685
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 2.496995 3.801075 1.241379
+ 3.877484 3.115795 2.131197
+ 4.253700 5.017112 1.232144
+ 5.005299 5.340406 0.315072
+ 3.984885 5.817909 2.265917
+ 4.408015 6.733702 2.314743
+ 3.359611 5.504297 2.994464
+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+!entry.NASN.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 0 15 0 0 0 0
+!entry.NASN.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "NASN" 1 17 1 "p" 0
+!entry.NASN.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.NASN.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.NASN.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
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+ 0.0 0.0 0.0
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+ 0.0 0.0 0.0
+!entry.NASP.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N3" 0 1 131072 1 7 0.078200
+ "H1" "H" 0 1 131072 2 1 0.220000
+ "H2" "H" 0 1 131072 3 1 0.220000
+ "H3" "H" 0 1 131072 4 1 0.220000
+ "CA" "CX" 0 1 131072 5 6 0.029200
+ "HA" "HP" 0 1 131072 6 1 0.114100
+ "CB" "2C" 0 1 131072 7 6 -0.023500
+ "HB2" "HC" 0 1 131072 8 1 -0.016900
+ "HB3" "HC" 0 1 131072 9 1 -0.016900
+ "CG" "CO" 0 1 131072 10 6 0.819400
+ "OD1" "O2" 0 1 131072 11 8 -0.808400
+ "OD2" "O2" 0 1 131072 12 8 -0.808400
+ "C" "C" 0 1 131072 13 6 0.562100
+ "O" "O" 0 1 131072 14 8 -0.588900
+!entry.NASP.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N3" 0 -1 0.0
+ "H1" "H" 0 -1 0.0
+ "H2" "H" 0 -1 0.0
+ "H3" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "HP" 0 -1 0.0
+ "CB" "2C" 0 -1 0.0
+ "HB2" "HC" 0 -1 0.0
+ "HB3" "HC" 0 -1 0.0
+ "CG" "CO" 0 -1 0.0
+ "OD1" "O2" 0 -1 0.0
+ "OD2" "O2" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O" 0 -1 0.0
+!entry.NASP.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.NASP.unit.childsequence single int
+ 2
+!entry.NASP.unit.connect array int
+ 0
+ 13
+!entry.NASP.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 1 4 1
+ 1 5 1
+ 5 6 1
+ 5 7 1
+ 5 13 1
+ 7 8 1
+ 7 9 1
+ 7 10 1
+ 10 11 1
+ 10 12 1
+ 13 14 1
+!entry.NASP.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+ "R" 1 "A" 14
+!entry.NASP.unit.name single str
+ "NASP"
+!entry.NASP.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 4.046154 0.839991 -2.855245E-06
+ 2.823094 1.499508 -0.874687
+ 2.823097 1.499507 0.874685
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
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+ "N" "N3" 0 1 131072 1 7 0.132500
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+ "HB3" "H1" 0 1 131072 9 1 0.118800
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+ "C" "C" 0 1 131072 12 6 0.612300
+ "O" "O" 0 1 131072 13 8 -0.571300
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+ 1 2 1
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+ 3.325770 1.547909 -1.607204E-06
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+!entry.NCYS.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 0 12 0 0 0 0
+!entry.NCYS.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
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+ 0
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+ "C" "C" 0 1 131072 11 6 0.612300
+ "O" "O" 0 1 131072 12 8 -0.571300
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+ 2
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+ 1 2 1
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+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
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+ "R" 1 "A" 11
+ "R" 1 "A" 12
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+ "NCYX"
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+ 0 11 10 0 0 0
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+ "NCYX" 1 13 1 "p" 0
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+ 0
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+ "H1" "H" 0 1 131072 2 1 0.199600
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+ "HA" "HP" 0 1 131072 6 1 0.101500
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+ "CD" "C" 0 1 131072 13 6 0.735400
+ "OE1" "O" 0 1 131072 14 8 -0.613300
+ "NE2" "N" 0 1 131072 15 7 -1.003100
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+ "HE22" "H" 0 1 131072 17 1 0.442900
+ "C" "C" 0 1 131072 18 6 0.612300
+ "O" "O" 0 1 131072 19 8 -0.571300
+!entry.NGLN.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
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+!entry.NGLN.unit.boundbox array dbl
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+ 2
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+ 0
+ 18
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+ 1 2 1
+ 1 3 1
+ 1 4 1
+ 1 5 1
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+ "U" 0 "R" 1
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+ "R" 1 "A" 15
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+ "R" 1 "A" 17
+ "R" 1 "A" 18
+ "R" 1 "A" 19
+!entry.NGLN.unit.name single str
+ "NGLN"
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+ 3.325770 1.547909 -1.607204E-06
+ 4.046154 0.839991 -2.855245E-06
+ 2.823094 1.499508 -0.874687
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+ 6.008824 1.593175 -8.449768E-06
+!entry.NGLN.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 0 18 0 0 0 0
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+ "NGLN" 1 20 1 "p" 0
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+!entry.NGLN.unit.velocities table  dbl x  dbl y  dbl z
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+ "N" "N3" 0 1 131072 1 7 0.001700
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+ "HG3" "HC" 0 1 131072 12 1 -0.031500
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+ "OE2" "O2" 0 1 131072 15 8 -0.818900
+ "C" "C" 0 1 131072 16 6 0.562100
+ "O" "O" 0 1 131072 17 8 -0.588900
+!entry.NGLU.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
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+!entry.NGLU.unit.boundbox array dbl
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+ 2
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+ 0
+ 16
+!entry.NGLU.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 1 4 1
+ 1 5 1
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+ 7 8 1
+ 7 9 1
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+ 10 11 1
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+ 16 17 1
+!entry.NGLU.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
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+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
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+ "R" 1 "A" 7
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+ "R" 1 "A" 13
+ "R" 1 "A" 14
+ "R" 1 "A" 15
+ "R" 1 "A" 16
+ "R" 1 "A" 17
+!entry.NGLU.unit.name single str
+ "NGLU"
+!entry.NGLU.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 4.046154 0.839991 -2.855245E-06
+ 2.823094 1.499508 -0.874687
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+ 3.970048 2.845795 -1.311163E-07
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+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+!entry.NGLU.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 0 16 0 0 0 0
+!entry.NGLU.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "NGLU" 1 18 1 "p" 0
+!entry.NGLU.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.NGLU.unit.solventcap array dbl
+ -1.000000
+ 0.0
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+ 0.0
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+!entry.NGLU.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
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+!entry.NGLY.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N3" 0 1 131072 1 7 0.294300
+ "H1" "H" 0 1 131072 2 1 0.164200
+ "H2" "H" 0 1 131072 3 1 0.164200
+ "H3" "H" 0 1 131072 4 1 0.164200
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+ "HA2" "HP" 0 1 131072 6 1 0.089500
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+ "C" "C" 0 1 131072 8 6 0.616300
+ "O" "O" 0 1 131072 9 8 -0.572200
+!entry.NGLY.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N3" 0 -1 0.0
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+ "H2" "H" 0 -1 0.0
+ "H3" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA2" "HP" 0 -1 0.0
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+ "C" "C" 0 -1 0.0
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+!entry.NGLY.unit.boundbox array dbl
+ -1.000000
+ 0.0
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+!entry.NGLY.unit.childsequence single int
+ 2
+!entry.NGLY.unit.connect array int
+ 0
+ 8
+!entry.NGLY.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 1 4 1
+ 1 5 1
+ 5 6 1
+ 5 7 1
+ 5 8 1
+ 8 9 1
+!entry.NGLY.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+!entry.NGLY.unit.name single str
+ "NGLY"
+!entry.NGLY.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 4.046154 0.839991 -2.855245E-06
+ 2.823094 1.499508 -0.874687
+ 2.823097 1.499507 0.874685
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.671668 3.400125 0.889824
+ 5.483710 2.686702 -4.438857E-06
+ 5.993369 1.568360 -8.469843E-06
+!entry.NGLY.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 0 8 0 0 0 0
+!entry.NGLY.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "NGLY" 1 10 1 "p" 0
+!entry.NGLY.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.NGLY.unit.solventcap array dbl
+ -1.000000
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+ 0.0
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+!entry.NGLY.unit.velocities table  dbl x  dbl y  dbl z
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+ "N" "N3" 0 1 131072 1 7 0.154200
+ "H1" "H" 0 1 131072 2 1 0.196300
+ "H2" "H" 0 1 131072 3 1 0.196300
+ "H3" "H" 0 1 131072 4 1 0.196300
+ "CA" "CX" 0 1 131072 5 6 0.096400
+ "HA" "HP" 0 1 131072 6 1 0.095800
+ "CB" "CT" 0 1 131072 7 6 0.025900
+ "HB2" "HC" 0 1 131072 8 1 0.020900
+ "HB3" "HC" 0 1 131072 9 1 0.020900
+ "CG" "CC" 0 1 131072 10 6 -0.039900
+ "ND1" "NA" 0 1 131072 11 7 -0.381900
+ "HD1" "H" 0 1 131072 12 1 0.363200
+ "CE1" "CR" 0 1 131072 13 6 0.212700
+ "HE1" "H5" 0 1 131072 14 1 0.138500
+ "NE2" "NB" 0 1 131072 15 7 -0.571100
+ "CD2" "CV" 0 1 131072 16 6 0.104600
+ "HD2" "H4" 0 1 131072 17 1 0.129900
+ "C" "C" 0 1 131072 18 6 0.612300
+ "O" "O" 0 1 131072 19 8 -0.571300
+!entry.NHID.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N3" 0 -1 0.0
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+ "HA" "HP" 0 -1 0.0
+ "CB" "CT" 0 -1 0.0
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+ "HB3" "HC" 0 -1 0.0
+ "CG" "CC" 0 -1 0.0
+ "ND1" "NA" 0 -1 0.0
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+ "HE1" "H5" 0 -1 0.0
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+ "CD2" "CV" 0 -1 0.0
+ "HD2" "H4" 0 -1 0.0
+ "C" "C" 0 -1 0.0
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+ -1.000000
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+ 0.0
+!entry.NHID.unit.childsequence single int
+ 2
+!entry.NHID.unit.connect array int
+ 0
+ 18
+!entry.NHID.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 1 4 1
+ 1 5 1
+ 5 6 1
+ 5 7 1
+ 5 18 1
+ 7 8 1
+ 7 9 1
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+ 10 16 1
+ 11 12 1
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+ 13 14 1
+ 13 15 1
+ 15 16 1
+ 16 17 1
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+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+ "R" 1 "A" 14
+ "R" 1 "A" 15
+ "R" 1 "A" 16
+ "R" 1 "A" 17
+ "R" 1 "A" 18
+ "R" 1 "A" 19
+!entry.NHID.unit.name single str
+ "NHID"
+!entry.NHID.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 4.046154 0.839991 -2.855245E-06
+ 2.823094 1.499508 -0.874687
+ 2.823097 1.499507 0.874685
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 2.496995 3.801075 1.241379
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+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+!entry.NHID.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 0 18 0 0 0 0
+!entry.NHID.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "NHID" 1 20 1 "p" 0
+!entry.NHID.unit.residuesPdbSequenceNumber array int
+ 0
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+ -1.000000
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+ "N" "N3" 0 1 131072 1 7 0.147200
+ "H1" "H" 0 1 131072 2 1 0.201600
+ "H2" "H" 0 1 131072 3 1 0.201600
+ "H3" "H" 0 1 131072 4 1 0.201600
+ "CA" "CX" 0 1 131072 5 6 0.023600
+ "HA" "HP" 0 1 131072 6 1 0.138000
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+ "CE1" "CR" 0 1 131072 12 6 0.180400
+ "HE1" "H5" 0 1 131072 13 1 0.139700
+ "NE2" "NA" 0 1 131072 14 7 -0.278100
+ "HE2" "H" 0 1 131072 15 1 0.332400
+ "CD2" "CW" 0 1 131072 16 6 -0.234900
+ "HD2" "H4" 0 1 131072 17 1 0.196300
+ "C" "C" 0 1 131072 18 6 0.612300
+ "O" "O" 0 1 131072 19 8 -0.571300
+!entry.NHIE.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N3" 0 -1 0.0
+ "H1" "H" 0 -1 0.0
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+ "HD2" "H4" 0 -1 0.0
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+!entry.NHIE.unit.boundbox array dbl
+ -1.000000
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+ 0.0
+!entry.NHIE.unit.childsequence single int
+ 2
+!entry.NHIE.unit.connect array int
+ 0
+ 18
+!entry.NHIE.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 1 4 1
+ 1 5 1
+ 5 6 1
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+ 5 18 1
+ 7 8 1
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+ 10 16 1
+ 11 12 1
+ 12 13 1
+ 12 14 1
+ 14 15 1
+ 14 16 1
+ 16 17 1
+ 18 19 1
+!entry.NHIE.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+ "R" 1 "A" 14
+ "R" 1 "A" 15
+ "R" 1 "A" 16
+ "R" 1 "A" 17
+ "R" 1 "A" 18
+ "R" 1 "A" 19
+!entry.NHIE.unit.name single str
+ "NHIE"
+!entry.NHIE.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 4.046154 0.839991 -2.855245E-06
+ 2.823094 1.499508 -0.874687
+ 2.823097 1.499507 0.874685
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 2.496995 3.801075 1.241379
+ 3.877484 3.115795 2.131197
+ 4.200813 5.026064 1.321087
+ 3.942782 5.885086 2.382972
+ 4.624274 6.997642 2.182500
+ 4.563048 7.811875 2.904563
+ 5.294011 6.891451 1.061663
+ 5.896297 7.605085 0.676854
+ 5.058974 5.678868 0.492453
+ 5.537741 5.417846 -0.451343
+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+!entry.NHIE.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 0 18 0 0 0 0
+!entry.NHIE.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "NHIE" 1 20 1 "p" 0
+!entry.NHIE.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.NHIE.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.NHIE.unit.velocities table  dbl x  dbl y  dbl z
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+ "N" "N3" 0 1 131072 1 7 0.256000
+ "H1" "H" 0 1 131072 2 1 0.170400
+ "H2" "H" 0 1 131072 3 1 0.170400
+ "H3" "H" 0 1 131072 4 1 0.170400
+ "CA" "CX" 0 1 131072 5 6 0.058100
+ "HA" "HP" 0 1 131072 6 1 0.104700
+ "CB" "CT" 0 1 131072 7 6 0.048400
+ "HB2" "HC" 0 1 131072 8 1 0.053100
+ "HB3" "HC" 0 1 131072 9 1 0.053100
+ "CG" "CC" 0 1 131072 10 6 -0.023600
+ "ND1" "NA" 0 1 131072 11 7 -0.151000
+ "HD1" "H" 0 1 131072 12 1 0.382100
+ "CE1" "CR" 0 1 131072 13 6 -0.001100
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+ "NE2" "NA" 0 1 131072 15 7 -0.173900
+ "HE2" "H" 0 1 131072 16 1 0.392100
+ "CD2" "CW" 0 1 131072 17 6 -0.143300
+ "HD2" "H4" 0 1 131072 18 1 0.249500
+ "C" "C" 0 1 131072 19 6 0.721400
+ "O" "O" 0 1 131072 20 8 -0.601300
+!entry.NHIP.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N3" 0 -1 0.0
+ "H1" "H" 0 -1 0.0
+ "H2" "H" 0 -1 0.0
+ "H3" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "HP" 0 -1 0.0
+ "CB" "CT" 0 -1 0.0
+ "HB2" "HC" 0 -1 0.0
+ "HB3" "HC" 0 -1 0.0
+ "CG" "CC" 0 -1 0.0
+ "ND1" "NA" 0 -1 0.0
+ "HD1" "H" 0 -1 0.0
+ "CE1" "CR" 0 -1 0.0
+ "HE1" "H5" 0 -1 0.0
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+ "HD2" "H4" 0 -1 0.0
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+ "O" "O" 0 -1 0.0
+!entry.NHIP.unit.boundbox array dbl
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+ 0.0
+!entry.NHIP.unit.childsequence single int
+ 2
+!entry.NHIP.unit.connect array int
+ 0
+ 19
+!entry.NHIP.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 1 4 1
+ 1 5 1
+ 5 6 1
+ 5 7 1
+ 5 19 1
+ 7 8 1
+ 7 9 1
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+ 11 12 1
+ 11 13 1
+ 13 14 1
+ 13 15 1
+ 15 16 1
+ 15 17 1
+ 17 18 1
+ 19 20 1
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+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+ "R" 1 "A" 14
+ "R" 1 "A" 15
+ "R" 1 "A" 16
+ "R" 1 "A" 17
+ "R" 1 "A" 18
+ "R" 1 "A" 19
+ "R" 1 "A" 20
+!entry.NHIP.unit.name single str
+ "NHIP"
+!entry.NHIP.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 4.046154 0.839991 -2.855245E-06
+ 2.823094 1.499508 -0.874687
+ 2.823097 1.499507 0.874685
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 2.496995 3.801075 1.241379
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+ 4.200813 5.026064 1.321087
+ 3.942782 5.885086 2.382972
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+ 4.563048 7.811875 2.904563
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+ 5.058974 5.678868 0.492453
+ 5.537741 5.417846 -0.451343
+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+!entry.NHIP.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 0 19 0 0 0 0
+!entry.NHIP.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "NHIP" 1 21 1 "p" 0
+!entry.NHIP.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.NHIP.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.NHIP.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
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+ 0.0 0.0 0.0
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+!entry.NILE.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N3" 0 1 131072 1 7 0.031100
+ "H1" "H" 0 1 131072 2 1 0.232900
+ "H2" "H" 0 1 131072 3 1 0.232900
+ "H3" "H" 0 1 131072 4 1 0.232900
+ "CA" "CX" 0 1 131072 5 6 0.025700
+ "HA" "HP" 0 1 131072 6 1 0.103100
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+ "HB" "HC" 0 1 131072 8 1 0.021300
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+ "HG22" "HC" 0 1 131072 11 1 0.094700
+ "HG23" "HC" 0 1 131072 12 1 0.094700
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+ "HG12" "HC" 0 1 131072 14 1 0.020100
+ "HG13" "HC" 0 1 131072 15 1 0.020100
+ "CD1" "CT" 0 1 131072 16 6 -0.090800
+ "HD11" "HC" 0 1 131072 17 1 0.022600
+ "HD12" "HC" 0 1 131072 18 1 0.022600
+ "HD13" "HC" 0 1 131072 19 1 0.022600
+ "C" "C" 0 1 131072 20 6 0.612300
+ "O" "O" 0 1 131072 21 8 -0.571300
+!entry.NILE.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N3" 0 -1 0.0
+ "H1" "H" 0 -1 0.0
+ "H2" "H" 0 -1 0.0
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+ "CA" "CX" 0 -1 0.0
+ "HA" "HP" 0 -1 0.0
+ "CB" "3C" 0 -1 0.0
+ "HB" "HC" 0 -1 0.0
+ "CG2" "CT" 0 -1 0.0
+ "HG21" "HC" 0 -1 0.0
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+ "CD1" "CT" 0 -1 0.0
+ "HD11" "HC" 0 -1 0.0
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+ "O" "O" 0 -1 0.0
+!entry.NILE.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.NILE.unit.childsequence single int
+ 2
+!entry.NILE.unit.connect array int
+ 0
+ 20
+!entry.NILE.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 1 4 1
+ 1 5 1
+ 5 6 1
+ 5 7 1
+ 5 20 1
+ 7 8 1
+ 7 9 1
+ 7 13 1
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+ 13 15 1
+ 13 16 1
+ 16 17 1
+ 16 18 1
+ 16 19 1
+ 20 21 1
+!entry.NILE.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+ "R" 1 "A" 14
+ "R" 1 "A" 15
+ "R" 1 "A" 16
+ "R" 1 "A" 17
+ "R" 1 "A" 18
+ "R" 1 "A" 19
+ "R" 1 "A" 20
+ "R" 1 "A" 21
+!entry.NILE.unit.name single str
+ "NILE"
+!entry.NILE.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 4.046154 0.839991 -2.855245E-06
+ 2.823094 1.499508 -0.874687
+ 2.823097 1.499507 0.874685
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.552136 3.620733 1.245168
+ 2.470128 3.752486 1.245640
+ 3.970045 2.845728 2.490296
+ 5.052053 2.713974 2.490763
+ 3.671561 3.399208 3.380615
+ 3.485650 1.869275 2.490737
+ 4.230204 4.986694 1.245169
+ 3.931820 5.541027 0.355348
+ 5.312310 4.855746 1.245164
+ 3.812294 5.761632 2.490339
+ 4.110777 5.208104 3.380628
+ 4.296689 6.738085 2.490833
+ 2.730286 5.893383 2.490813
+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+!entry.NILE.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 0 20 0 0 0 0
+!entry.NILE.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "NILE" 1 22 1 "p" 0
+!entry.NILE.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.NILE.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.NILE.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
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+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+!entry.NLEU.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N3" 0 1 131072 1 7 0.101000
+ "H1" "H" 0 1 131072 2 1 0.214800
+ "H2" "H" 0 1 131072 3 1 0.214800
+ "H3" "H" 0 1 131072 4 1 0.214800
+ "CA" "CX" 0 1 131072 5 6 0.010400
+ "HA" "HP" 0 1 131072 6 1 0.105300
+ "CB" "2C" 0 1 131072 7 6 -0.024400
+ "HB2" "HC" 0 1 131072 8 1 0.025600
+ "HB3" "HC" 0 1 131072 9 1 0.025600
+ "CG" "3C" 0 1 131072 10 6 0.342100
+ "HG" "HC" 0 1 131072 11 1 -0.038000
+ "CD1" "CT" 0 1 131072 12 6 -0.410600
+ "HD11" "HC" 0 1 131072 13 1 0.098000
+ "HD12" "HC" 0 1 131072 14 1 0.098000
+ "HD13" "HC" 0 1 131072 15 1 0.098000
+ "CD2" "CT" 0 1 131072 16 6 -0.410400
+ "HD21" "HC" 0 1 131072 17 1 0.098000
+ "HD22" "HC" 0 1 131072 18 1 0.098000
+ "HD23" "HC" 0 1 131072 19 1 0.098000
+ "C" "C" 0 1 131072 20 6 0.612300
+ "O" "O" 0 1 131072 21 8 -0.571300
+!entry.NLEU.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N3" 0 -1 0.0
+ "H1" "H" 0 -1 0.0
+ "H2" "H" 0 -1 0.0
+ "H3" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "HP" 0 -1 0.0
+ "CB" "2C" 0 -1 0.0
+ "HB2" "HC" 0 -1 0.0
+ "HB3" "HC" 0 -1 0.0
+ "CG" "3C" 0 -1 0.0
+ "HG" "HC" 0 -1 0.0
+ "CD1" "CT" 0 -1 0.0
+ "HD11" "HC" 0 -1 0.0
+ "HD12" "HC" 0 -1 0.0
+ "HD13" "HC" 0 -1 0.0
+ "CD2" "CT" 0 -1 0.0
+ "HD21" "HC" 0 -1 0.0
+ "HD22" "HC" 0 -1 0.0
+ "HD23" "HC" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O" 0 -1 0.0
+!entry.NLEU.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.NLEU.unit.childsequence single int
+ 2
+!entry.NLEU.unit.connect array int
+ 0
+ 20
+!entry.NLEU.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 1 4 1
+ 1 5 1
+ 5 6 1
+ 5 7 1
+ 5 20 1
+ 7 8 1
+ 7 9 1
+ 7 10 1
+ 10 11 1
+ 10 12 1
+ 10 16 1
+ 12 13 1
+ 12 14 1
+ 12 15 1
+ 16 17 1
+ 16 18 1
+ 16 19 1
+ 20 21 1
+!entry.NLEU.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+ "R" 1 "A" 14
+ "R" 1 "A" 15
+ "R" 1 "A" 16
+ "R" 1 "A" 17
+ "R" 1 "A" 18
+ "R" 1 "A" 19
+ "R" 1 "A" 20
+ "R" 1 "A" 21
+!entry.NLEU.unit.name single str
+ "NLEU"
+!entry.NLEU.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 4.046154 0.839991 -2.855245E-06
+ 2.823094 1.499508 -0.874687
+ 2.823097 1.499507 0.874685
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 2.496995 3.801075 1.241379
+ 3.877484 3.115795 2.131197
+ 4.274186 5.009602 1.194577
+ 5.354271 4.863178 1.185788
+ 3.853429 5.762895 -0.062857
+ 2.773449 5.910113 -0.054557
+ 4.351513 6.732052 -0.090203
+ 4.134159 5.185704 -0.943846
+ 3.881105 5.817645 2.426721
+ 4.181626 5.279602 3.325774
+ 4.379198 6.786825 2.400363
+ 2.801135 5.964881 2.435959
+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+!entry.NLEU.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 0 20 0 0 0 0
+!entry.NLEU.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "NLEU" 1 22 1 "p" 0
+!entry.NLEU.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.NLEU.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.NLEU.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
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+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+!entry.NLYS.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N3" 0 1 131072 1 7 0.096600
+ "H1" "H" 0 1 131072 2 1 0.216500
+ "H2" "H" 0 1 131072 3 1 0.216500
+ "H3" "H" 0 1 131072 4 1 0.216500
+ "CA" "CX" 0 1 131072 5 6 -0.001500
+ "HA" "HP" 0 1 131072 6 1 0.118000
+ "CB" "C8" 0 1 131072 7 6 0.021200
+ "HB2" "HC" 0 1 131072 8 1 0.028300
+ "HB3" "HC" 0 1 131072 9 1 0.028300
+ "CG" "C8" 0 1 131072 10 6 -0.004800
+ "HG2" "HC" 0 1 131072 11 1 0.012100
+ "HG3" "HC" 0 1 131072 12 1 0.012100
+ "CD" "C8" 0 1 131072 13 6 -0.060800
+ "HD2" "HC" 0 1 131072 14 1 0.063300
+ "HD3" "HC" 0 1 131072 15 1 0.063300
+ "CE" "C8" 0 1 131072 16 6 -0.018100
+ "HE2" "HP" 0 1 131072 17 1 0.117100
+ "HE3" "HP" 0 1 131072 18 1 0.117100
+ "NZ" "N3" 0 1 131072 19 7 -0.376400
+ "HZ1" "H" 0 1 131072 20 1 0.338200
+ "HZ2" "H" 0 1 131072 21 1 0.338200
+ "HZ3" "H" 0 1 131072 22 1 0.338200
+ "C" "C" 0 1 131072 23 6 0.721400
+ "O" "O" 0 1 131072 24 8 -0.601300
+!entry.NLYS.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N3" 0 -1 0.0
+ "H1" "H" 0 -1 0.0
+ "H2" "H" 0 -1 0.0
+ "H3" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "HP" 0 -1 0.0
+ "CB" "C8" 0 -1 0.0
+ "HB2" "HC" 0 -1 0.0
+ "HB3" "HC" 0 -1 0.0
+ "CG" "C8" 0 -1 0.0
+ "HG2" "HC" 0 -1 0.0
+ "HG3" "HC" 0 -1 0.0
+ "CD" "C8" 0 -1 0.0
+ "HD2" "HC" 0 -1 0.0
+ "HD3" "HC" 0 -1 0.0
+ "CE" "C8" 0 -1 0.0
+ "HE2" "HP" 0 -1 0.0
+ "HE3" "HP" 0 -1 0.0
+ "NZ" "N3" 0 -1 0.0
+ "HZ1" "H" 0 -1 0.0
+ "HZ2" "H" 0 -1 0.0
+ "HZ3" "H" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O" 0 -1 0.0
+!entry.NLYS.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.NLYS.unit.childsequence single int
+ 2
+!entry.NLYS.unit.connect array int
+ 0
+ 23
+!entry.NLYS.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 1 4 1
+ 1 5 1
+ 5 6 1
+ 5 7 1
+ 5 23 1
+ 7 8 1
+ 7 9 1
+ 7 10 1
+ 10 11 1
+ 10 12 1
+ 10 13 1
+ 13 14 1
+ 13 15 1
+ 13 16 1
+ 16 17 1
+ 16 18 1
+ 16 19 1
+ 19 20 1
+ 19 21 1
+ 19 22 1
+ 23 24 1
+!entry.NLYS.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+ "R" 1 "A" 14
+ "R" 1 "A" 15
+ "R" 1 "A" 16
+ "R" 1 "A" 17
+ "R" 1 "A" 18
+ "R" 1 "A" 19
+ "R" 1 "A" 20
+ "R" 1 "A" 21
+ "R" 1 "A" 22
+ "R" 1 "A" 23
+ "R" 1 "A" 24
+!entry.NLYS.unit.name single str
+ "NLYS"
+!entry.NLYS.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 4.046154 0.839991 -2.855245E-06
+ 2.823094 1.499508 -0.874687
+ 2.823097 1.499507 0.874685
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 2.496995 3.801075 1.241379
+ 3.877484 3.115795 2.131197
+ 4.274186 5.009602 1.194577
+ 5.354271 4.863178 1.185788
+ 3.973781 5.548460 0.295972
+ 3.881105 5.817645 2.426721
+ 2.801135 5.964881 2.435959
+ 4.181626 5.279602 3.325774
+ 4.578325 7.173410 2.389153
+ 5.658410 7.026987 2.380363
+ 4.277917 7.712267 1.490550
+ 4.199422 7.952309 3.576860
+ 4.478085 7.453366 4.409628
+ 4.661186 8.850226 3.551979
+ 3.198675 8.088466 3.584971
+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+!entry.NLYS.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 0 23 0 0 0 0
+!entry.NLYS.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "NLYS" 1 25 1 "p" 0
+!entry.NLYS.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.NLYS.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.NLYS.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
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+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+!entry.NMET.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N3" 0 1 131072 1 7 0.159200
+ "H1" "H" 0 1 131072 2 1 0.198400
+ "H2" "H" 0 1 131072 3 1 0.198400
+ "H3" "H" 0 1 131072 4 1 0.198400
+ "CA" "CX" 0 1 131072 5 6 0.022100
+ "HA" "HP" 0 1 131072 6 1 0.111600
+ "CB" "2C" 0 1 131072 7 6 0.086500
+ "HB2" "HC" 0 1 131072 8 1 0.012500
+ "HB3" "HC" 0 1 131072 9 1 0.012500
+ "CG" "2C" 0 1 131072 10 6 0.033400
+ "HG2" "H1" 0 1 131072 11 1 0.029200
+ "HG3" "H1" 0 1 131072 12 1 0.029200
+ "SD" "S" 0 1 131072 13 16 -0.277400
+ "CE" "CT" 0 1 131072 14 6 -0.034100
+ "HE1" "H1" 0 1 131072 15 1 0.059700
+ "HE2" "H1" 0 1 131072 16 1 0.059700
+ "HE3" "H1" 0 1 131072 17 1 0.059700
+ "C" "C" 0 1 131072 18 6 0.612300
+ "O" "O" 0 1 131072 19 8 -0.571300
+!entry.NMET.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N3" 0 -1 0.0
+ "H1" "H" 0 -1 0.0
+ "H2" "H" 0 -1 0.0
+ "H3" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "HP" 0 -1 0.0
+ "CB" "2C" 0 -1 0.0
+ "HB2" "HC" 0 -1 0.0
+ "HB3" "HC" 0 -1 0.0
+ "CG" "2C" 0 -1 0.0
+ "HG2" "H1" 0 -1 0.0
+ "HG3" "H1" 0 -1 0.0
+ "SD" "S" 0 -1 0.0
+ "CE" "CT" 0 -1 0.0
+ "HE1" "H1" 0 -1 0.0
+ "HE2" "H1" 0 -1 0.0
+ "HE3" "H1" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O" 0 -1 0.0
+!entry.NMET.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.NMET.unit.childsequence single int
+ 2
+!entry.NMET.unit.connect array int
+ 0
+ 18
+!entry.NMET.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 1 4 1
+ 1 5 1
+ 5 6 1
+ 5 7 1
+ 5 18 1
+ 7 8 1
+ 7 9 1
+ 7 10 1
+ 10 11 1
+ 10 12 1
+ 10 13 1
+ 13 14 1
+ 14 15 1
+ 14 16 1
+ 14 17 1
+ 18 19 1
+!entry.NMET.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+ "R" 1 "A" 14
+ "R" 1 "A" 15
+ "R" 1 "A" 16
+ "R" 1 "A" 17
+ "R" 1 "A" 18
+ "R" 1 "A" 19
+!entry.NMET.unit.name single str
+ "NMET"
+!entry.NMET.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 4.046154 0.839991 -2.855245E-06
+ 2.823094 1.499508 -0.874687
+ 2.823097 1.499507 0.874685
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 2.496995 3.801075 1.241379
+ 3.877484 3.115795 2.131197
+ 4.274186 5.009602 1.194577
+ 5.354271 4.863178 1.185788
+ 3.973781 5.548460 0.295972
+ 3.817309 5.981266 2.651708
+ 4.753212 7.463128 2.340949
+ 4.433582 7.904044 1.396741
+ 4.585907 8.175299 3.148985
+ 5.814074 7.218763 2.286554
+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+!entry.NMET.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 0 18 0 0 0 0
+!entry.NMET.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "NMET" 1 20 1 "p" 0
+!entry.NMET.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.NMET.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.NMET.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
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+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
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+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+!entry.NPHE.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N3" 0 1 131072 1 7 0.173700
+ "H1" "H" 0 1 131072 2 1 0.192100
+ "H2" "H" 0 1 131072 3 1 0.192100
+ "H3" "H" 0 1 131072 4 1 0.192100
+ "CA" "CX" 0 1 131072 5 6 0.073300
+ "HA" "HP" 0 1 131072 6 1 0.104100
+ "CB" "CT" 0 1 131072 7 6 0.033000
+ "HB2" "HC" 0 1 131072 8 1 0.010400
+ "HB3" "HC" 0 1 131072 9 1 0.010400
+ "CG" "CA" 0 1 131072 10 6 0.003100
+ "CD1" "CA" 0 1 131072 11 6 -0.139200
+ "HD1" "HA" 0 1 131072 12 1 0.137400
+ "CE1" "CA" 0 1 131072 13 6 -0.160200
+ "HE1" "HA" 0 1 131072 14 1 0.143300
+ "CZ" "CA" 0 1 131072 15 6 -0.120800
+ "HZ" "HA" 0 1 131072 16 1 0.132900
+ "CE2" "CA" 0 1 131072 17 6 -0.160300
+ "HE2" "HA" 0 1 131072 18 1 0.143300
+ "CD2" "CA" 0 1 131072 19 6 -0.139100
+ "HD2" "HA" 0 1 131072 20 1 0.137400
+ "C" "C" 0 1 131072 21 6 0.612300
+ "O" "O" 0 1 131072 22 8 -0.571300
+!entry.NPHE.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N3" 0 -1 0.0
+ "H1" "H" 0 -1 0.0
+ "H2" "H" 0 -1 0.0
+ "H3" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "HP" 0 -1 0.0
+ "CB" "CT" 0 -1 0.0
+ "HB2" "HC" 0 -1 0.0
+ "HB3" "HC" 0 -1 0.0
+ "CG" "CA" 0 -1 0.0
+ "CD1" "CA" 0 -1 0.0
+ "HD1" "HA" 0 -1 0.0
+ "CE1" "CA" 0 -1 0.0
+ "HE1" "HA" 0 -1 0.0
+ "CZ" "CA" 0 -1 0.0
+ "HZ" "HA" 0 -1 0.0
+ "CE2" "CA" 0 -1 0.0
+ "HE2" "HA" 0 -1 0.0
+ "CD2" "CA" 0 -1 0.0
+ "HD2" "HA" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O" 0 -1 0.0
+!entry.NPHE.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.NPHE.unit.childsequence single int
+ 2
+!entry.NPHE.unit.connect array int
+ 0
+ 21
+!entry.NPHE.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 1 4 1
+ 1 5 1
+ 5 6 1
+ 5 7 1
+ 5 21 1
+ 7 8 1
+ 7 9 1
+ 7 10 1
+ 10 11 1
+ 10 19 1
+ 11 12 1
+ 11 13 1
+ 13 14 1
+ 13 15 1
+ 15 16 1
+ 15 17 1
+ 17 18 1
+ 17 19 1
+ 19 20 1
+ 21 22 1
+!entry.NPHE.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+ "R" 1 "A" 14
+ "R" 1 "A" 15
+ "R" 1 "A" 16
+ "R" 1 "A" 17
+ "R" 1 "A" 18
+ "R" 1 "A" 19
+ "R" 1 "A" 20
+ "R" 1 "A" 21
+ "R" 1 "A" 22
+!entry.NPHE.unit.name single str
+ "NPHE"
+!entry.NPHE.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 4.046154 0.839991 -2.855245E-06
+ 2.823094 1.499508 -0.874687
+ 2.823097 1.499507 0.874685
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 2.496995 3.801075 1.241379
+ 3.877484 3.115795 2.131197
+ 4.200813 5.026064 1.321087
+ 3.911613 5.857250 2.409890
+ 3.236123 5.513843 3.193398
+ 4.490014 7.129513 2.492354
+ 4.264853 7.776651 3.340066
+ 5.357616 7.570591 1.486016
+ 5.807943 8.561138 1.550220
+ 5.646818 6.739407 0.397211
+ 6.322309 7.082817 -0.386295
+ 5.068419 5.467143 0.314744
+ 5.293584 4.820007 -0.532968
+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+!entry.NPHE.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 0 21 0 0 0 0
+!entry.NPHE.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "NPHE" 1 23 1 "p" 0
+!entry.NPHE.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.NPHE.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.NPHE.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
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+!entry.NPRO.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N3" 0 1 131072 1 7 -0.202000
+ "H2" "H" 0 1 131072 2 1 0.312000
+ "H3" "H" 0 1 131072 3 1 0.312000
+ "CD" "CT" 0 1 131072 4 6 -0.012000
+ "HD2" "HP" 0 1 131072 5 1 0.100000
+ "HD3" "HP" 0 1 131072 6 1 0.100000
+ "CG" "CT" 0 1 131072 7 6 -0.121000
+ "HG2" "HC" 0 1 131072 8 1 0.100000
+ "HG3" "HC" 0 1 131072 9 1 0.100000
+ "CB" "CT" 0 1 131072 10 6 -0.115000
+ "HB2" "HC" 0 1 131072 11 1 0.100000
+ "HB3" "HC" 0 1 131072 12 1 0.100000
+ "CA" "CX" 0 1 131072 13 6 0.100000
+ "HA" "HP" 0 1 131072 14 1 0.100000
+ "C" "C" 0 1 131072 15 6 0.526000
+ "O" "O" 0 1 131072 16 8 -0.500000
+!entry.NPRO.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N3" 0 -1 0.0
+ "H2" "H" 0 -1 0.0
+ "H3" "H" 0 -1 0.0
+ "CD" "CT" 0 -1 0.0
+ "HD2" "HP" 0 -1 0.0
+ "HD3" "HP" 0 -1 0.0
+ "CG" "CT" 0 -1 0.0
+ "HG2" "HC" 0 -1 0.0
+ "HG3" "HC" 0 -1 0.0
+ "CB" "CT" 0 -1 0.0
+ "HB2" "HC" 0 -1 0.0
+ "HB3" "HC" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "HP" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O" 0 -1 0.0
+!entry.NPRO.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.NPRO.unit.childsequence single int
+ 2
+!entry.NPRO.unit.connect array int
+ 0
+ 15
+!entry.NPRO.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 1 4 1
+ 1 13 1
+ 4 5 1
+ 4 6 1
+ 4 7 1
+ 7 8 1
+ 7 9 1
+ 7 10 1
+ 10 11 1
+ 10 12 1
+ 10 13 1
+ 13 14 1
+ 13 15 1
+ 15 16 1
+!entry.NPRO.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+ "R" 1 "A" 14
+ "R" 1 "A" 15
+ "R" 1 "A" 16
+!entry.NPRO.unit.name single str
+ "NPRO"
+!entry.NPRO.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 2.823094 1.499508 -0.874687
+ 2.823097 1.499507 0.874685
+ 4.293514 0.460336 0.080119
+ 4.408169 0.002209 -0.902263
+ 3.942023 -0.287867 0.790574
+ 5.543321 1.147470 0.544693
+ 6.406715 0.710627 0.042879
+ 5.648273 1.022228 1.622376
+ 5.375453 2.604421 0.185227
+ 5.977268 2.833902 -0.694123
+ 5.701345 3.225015 1.019947
+ 3.941704 2.857529 -0.104508
+ 3.623882 3.477056 0.734106
+ 3.517842 3.515620 -1.409783
+ 2.762837 2.933549 -2.185412
+!entry.NPRO.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 0 15 0 0 0 0
+!entry.NPRO.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "NPRO" 1 17 1 "p" 0
+!entry.NPRO.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.NPRO.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.NPRO.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
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+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
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+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+!entry.NSER.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N3" 0 1 131072 1 7 0.184900
+ "H1" "H" 0 1 131072 2 1 0.189800
+ "H2" "H" 0 1 131072 3 1 0.189800
+ "H3" "H" 0 1 131072 4 1 0.189800
+ "CA" "CX" 0 1 131072 5 6 0.056700
+ "HA" "HP" 0 1 131072 6 1 0.078200
+ "CB" "2C" 0 1 131072 7 6 0.259600
+ "HB2" "H1" 0 1 131072 8 1 0.027300
+ "HB3" "H1" 0 1 131072 9 1 0.027300
+ "OG" "OH" 0 1 131072 10 8 -0.671400
+ "HG" "HO" 0 1 131072 11 1 0.423900
+ "C" "C" 0 1 131072 12 6 0.616300
+ "O" "O" 0 1 131072 13 8 -0.572200
+!entry.NSER.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N3" 0 -1 0.0
+ "H1" "H" 0 -1 0.0
+ "H2" "H" 0 -1 0.0
+ "H3" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "HP" 0 -1 0.0
+ "CB" "2C" 0 -1 0.0
+ "HB2" "H1" 0 -1 0.0
+ "HB3" "H1" 0 -1 0.0
+ "OG" "OH" 0 -1 0.0
+ "HG" "HO" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O" 0 -1 0.0
+!entry.NSER.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.NSER.unit.childsequence single int
+ 2
+!entry.NSER.unit.connect array int
+ 0
+ 12
+!entry.NSER.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 1 4 1
+ 1 5 1
+ 5 6 1
+ 5 7 1
+ 5 12 1
+ 7 8 1
+ 7 9 1
+ 7 10 1
+ 10 11 1
+ 12 13 1
+!entry.NSER.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+!entry.NSER.unit.name single str
+ "NSER"
+!entry.NSER.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 4.046154 0.839991 -2.855245E-06
+ 2.823094 1.499508 -0.874687
+ 2.823097 1.499507 0.874685
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 2.496995 3.801075 1.241379
+ 3.877484 3.115795 2.131197
+ 4.230753 4.925145 1.196917
+ 3.983305 5.433814 1.972562
+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+!entry.NSER.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 0 12 0 0 0 0
+!entry.NSER.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "NSER" 1 14 1 "p" 0
+!entry.NSER.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.NSER.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.NSER.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
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+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+!entry.NTHR.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N3" 0 1 131072 1 7 0.181200
+ "H1" "H" 0 1 131072 2 1 0.193400
+ "H2" "H" 0 1 131072 3 1 0.193400
+ "H3" "H" 0 1 131072 4 1 0.193400
+ "CA" "CX" 0 1 131072 5 6 0.003400
+ "HA" "HP" 0 1 131072 6 1 0.108700
+ "CB" "3C" 0 1 131072 7 6 0.451400
+ "HB" "H1" 0 1 131072 8 1 -0.032300
+ "CG2" "CT" 0 1 131072 9 6 -0.255400
+ "HG21" "HC" 0 1 131072 10 1 0.062700
+ "HG22" "HC" 0 1 131072 11 1 0.062700
+ "HG23" "HC" 0 1 131072 12 1 0.062700
+ "OG1" "OH" 0 1 131072 13 8 -0.676400
+ "HG1" "HO" 0 1 131072 14 1 0.407000
+ "C" "C" 0 1 131072 15 6 0.616300
+ "O" "O" 0 1 131072 16 8 -0.572200
+!entry.NTHR.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N3" 0 -1 0.0
+ "H1" "H" 0 -1 0.0
+ "H2" "H" 0 -1 0.0
+ "H3" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "HP" 0 -1 0.0
+ "CB" "3C" 0 -1 0.0
+ "HB" "H1" 0 -1 0.0
+ "CG2" "CT" 0 -1 0.0
+ "HG21" "HC" 0 -1 0.0
+ "HG22" "HC" 0 -1 0.0
+ "HG23" "HC" 0 -1 0.0
+ "OG1" "OH" 0 -1 0.0
+ "HG1" "HO" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O" 0 -1 0.0
+!entry.NTHR.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.NTHR.unit.childsequence single int
+ 2
+!entry.NTHR.unit.connect array int
+ 0
+ 15
+!entry.NTHR.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 1 4 1
+ 1 5 1
+ 5 6 1
+ 5 7 1
+ 5 15 1
+ 7 8 1
+ 7 9 1
+ 7 13 1
+ 9 10 1
+ 9 11 1
+ 9 12 1
+ 13 14 1
+ 15 16 1
+!entry.NTHR.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+ "R" 1 "A" 14
+ "R" 1 "A" 15
+ "R" 1 "A" 16
+!entry.NTHR.unit.name single str
+ "NTHR"
+!entry.NTHR.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 4.046154 0.839991 -2.855245E-06
+ 2.823094 1.499508 -0.874687
+ 2.823097 1.499507 0.874685
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 4.075059 4.623017 1.205786
+ 2.065936 3.859425 1.244383
+ 1.567127 2.890627 1.271209
+ 1.784431 4.436953 2.124903
+ 1.764699 4.397847 0.345796
+ 3.971501 2.947413 2.411212
+ 3.724052 3.456082 3.186857
+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+!entry.NTHR.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 0 15 0 0 0 0
+!entry.NTHR.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "NTHR" 1 17 1 "p" 0
+!entry.NTHR.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.NTHR.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.NTHR.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
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+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
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+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+!entry.NTRP.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N3" 0 1 131072 1 7 0.191300
+ "H1" "H" 0 1 131072 2 1 0.188800
+ "H2" "H" 0 1 131072 3 1 0.188800
+ "H3" "H" 0 1 131072 4 1 0.188800
+ "CA" "CX" 0 1 131072 5 6 0.042100
+ "HA" "HP" 0 1 131072 6 1 0.116200
+ "CB" "CT" 0 1 131072 7 6 0.054300
+ "HB2" "HC" 0 1 131072 8 1 0.022200
+ "HB3" "HC" 0 1 131072 9 1 0.022200
+ "CG" "C*" 0 1 131072 10 6 -0.165400
+ "CD1" "CW" 0 1 131072 11 6 -0.178800
+ "HD1" "H4" 0 1 131072 12 1 0.219500
+ "NE1" "NA" 0 1 131072 13 7 -0.344400
+ "HE1" "H" 0 1 131072 14 1 0.341200
+ "CE2" "CN" 0 1 131072 15 6 0.157500
+ "CZ2" "CA" 0 1 131072 16 6 -0.271000
+ "HZ2" "HA" 0 1 131072 17 1 0.158900
+ "CH2" "CA" 0 1 131072 18 6 -0.108000
+ "HH2" "HA" 0 1 131072 19 1 0.141100
+ "CZ3" "CA" 0 1 131072 20 6 -0.203400
+ "HZ3" "HA" 0 1 131072 21 1 0.145800
+ "CE3" "CA" 0 1 131072 22 6 -0.226500
+ "HE3" "HA" 0 1 131072 23 1 0.164600
+ "CD2" "CB" 0 1 131072 24 6 0.113200
+ "C" "C" 0 1 131072 25 6 0.612300
+ "O" "O" 0 1 131072 26 8 -0.571300
+!entry.NTRP.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N3" 0 -1 0.0
+ "H1" "H" 0 -1 0.0
+ "H2" "H" 0 -1 0.0
+ "H3" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "HP" 0 -1 0.0
+ "CB" "CT" 0 -1 0.0
+ "HB2" "HC" 0 -1 0.0
+ "HB3" "HC" 0 -1 0.0
+ "CG" "C*" 0 -1 0.0
+ "CD1" "CW" 0 -1 0.0
+ "HD1" "H4" 0 -1 0.0
+ "NE1" "NA" 0 -1 0.0
+ "HE1" "H" 0 -1 0.0
+ "CE2" "CN" 0 -1 0.0
+ "CZ2" "CA" 0 -1 0.0
+ "HZ2" "HA" 0 -1 0.0
+ "CH2" "CA" 0 -1 0.0
+ "HH2" "HA" 0 -1 0.0
+ "CZ3" "CA" 0 -1 0.0
+ "HZ3" "HA" 0 -1 0.0
+ "CE3" "CA" 0 -1 0.0
+ "HE3" "HA" 0 -1 0.0
+ "CD2" "CB" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O" 0 -1 0.0
+!entry.NTRP.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.NTRP.unit.childsequence single int
+ 2
+!entry.NTRP.unit.connect array int
+ 0
+ 25
+!entry.NTRP.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 1 4 1
+ 1 5 1
+ 5 6 1
+ 5 7 1
+ 5 25 1
+ 7 8 1
+ 7 9 1
+ 7 10 1
+ 10 11 1
+ 10 24 1
+ 11 12 1
+ 11 13 1
+ 13 14 1
+ 13 15 1
+ 15 16 1
+ 15 24 1
+ 16 17 1
+ 16 18 1
+ 18 19 1
+ 18 20 1
+ 20 21 1
+ 20 22 1
+ 22 23 1
+ 22 24 1
+ 25 26 1
+!entry.NTRP.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+ "R" 1 "A" 14
+ "R" 1 "A" 15
+ "R" 1 "A" 16
+ "R" 1 "A" 17
+ "R" 1 "A" 18
+ "R" 1 "A" 19
+ "R" 1 "A" 20
+ "R" 1 "A" 21
+ "R" 1 "A" 22
+ "R" 1 "A" 23
+ "R" 1 "A" 24
+ "R" 1 "A" 25
+ "R" 1 "A" 26
+!entry.NTRP.unit.name single str
+ "NTRP"
+!entry.NTRP.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 4.046154 0.839991 -2.855245E-06
+ 2.823094 1.499508 -0.874687
+ 2.823097 1.499507 0.874685
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 2.496995 3.801075 1.241379
+ 3.877484 3.115795 2.131197
+ 4.200813 5.026064 1.321087
+ 4.023453 5.931084 2.293240
+ 3.368841 5.705466 3.135071
+ 4.811943 7.073555 1.949808
+ 4.882921 7.922010 2.493118
+ 5.427347 6.842060 0.816764
+ 6.297161 7.689052 0.119605
+ 6.531230 8.676649 0.517050
+ 6.814091 7.187011 -1.069023
+ 7.498074 7.791857 -1.664362
+ 6.482659 5.953119 -1.505101
+ 6.897660 5.575648 -2.439654
+ 5.604041 5.117355 -0.785636
+ 5.358720 4.126570 -1.168080
+ 5.083390 5.623004 0.411545
+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+!entry.NTRP.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 0 25 0 0 0 0
+!entry.NTRP.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "NTRP" 1 27 1 "p" 0
+!entry.NTRP.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.NTRP.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.NTRP.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+!entry.NTYR.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N3" 0 1 131072 1 7 0.194000
+ "H1" "H" 0 1 131072 2 1 0.187300
+ "H2" "H" 0 1 131072 3 1 0.187300
+ "H3" "H" 0 1 131072 4 1 0.187300
+ "CA" "CX" 0 1 131072 5 6 0.057000
+ "HA" "HP" 0 1 131072 6 1 0.098300
+ "CB" "CT" 0 1 131072 7 6 0.065900
+ "HB2" "HC" 0 1 131072 8 1 0.010200
+ "HB3" "HC" 0 1 131072 9 1 0.010200
+ "CG" "CA" 0 1 131072 10 6 -0.020500
+ "CD1" "CA" 0 1 131072 11 6 -0.200200
+ "HD1" "HA" 0 1 131072 12 1 0.172000
+ "CE1" "CA" 0 1 131072 13 6 -0.223900
+ "HE1" "HA" 0 1 131072 14 1 0.165000
+ "CZ" "C" 0 1 131072 15 6 0.313900
+ "OH" "OH" 0 1 131072 16 8 -0.557800
+ "HH" "HO" 0 1 131072 17 1 0.400100
+ "CE2" "CA" 0 1 131072 18 6 -0.223900
+ "HE2" "HA" 0 1 131072 19 1 0.165000
+ "CD2" "CA" 0 1 131072 20 6 -0.200200
+ "HD2" "HA" 0 1 131072 21 1 0.172000
+ "C" "C" 0 1 131072 22 6 0.612300
+ "O" "O" 0 1 131072 23 8 -0.571300
+!entry.NTYR.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N3" 0 -1 0.0
+ "H1" "H" 0 -1 0.0
+ "H2" "H" 0 -1 0.0
+ "H3" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "HP" 0 -1 0.0
+ "CB" "CT" 0 -1 0.0
+ "HB2" "HC" 0 -1 0.0
+ "HB3" "HC" 0 -1 0.0
+ "CG" "CA" 0 -1 0.0
+ "CD1" "CA" 0 -1 0.0
+ "HD1" "HA" 0 -1 0.0
+ "CE1" "CA" 0 -1 0.0
+ "HE1" "HA" 0 -1 0.0
+ "CZ" "C" 0 -1 0.0
+ "OH" "OH" 0 -1 0.0
+ "HH" "HO" 0 -1 0.0
+ "CE2" "CA" 0 -1 0.0
+ "HE2" "HA" 0 -1 0.0
+ "CD2" "CA" 0 -1 0.0
+ "HD2" "HA" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O" 0 -1 0.0
+!entry.NTYR.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.NTYR.unit.childsequence single int
+ 2
+!entry.NTYR.unit.connect array int
+ 0
+ 22
+!entry.NTYR.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 1 4 1
+ 1 5 1
+ 5 6 1
+ 5 7 1
+ 5 22 1
+ 7 8 1
+ 7 9 1
+ 7 10 1
+ 10 11 1
+ 10 20 1
+ 11 12 1
+ 11 13 1
+ 13 14 1
+ 13 15 1
+ 15 16 1
+ 15 18 1
+ 16 17 1
+ 18 19 1
+ 18 20 1
+ 20 21 1
+ 22 23 1
+!entry.NTYR.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+ "R" 1 "A" 14
+ "R" 1 "A" 15
+ "R" 1 "A" 16
+ "R" 1 "A" 17
+ "R" 1 "A" 18
+ "R" 1 "A" 19
+ "R" 1 "A" 20
+ "R" 1 "A" 21
+ "R" 1 "A" 22
+ "R" 1 "A" 23
+!entry.NTYR.unit.name single str
+ "NTYR"
+!entry.NTYR.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 4.046154 0.839991 -2.855245E-06
+ 2.823094 1.499508 -0.874687
+ 2.823097 1.499507 0.874685
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 2.496995 3.801075 1.241379
+ 3.877484 3.115795 2.131197
+ 4.267328 4.996267 1.194946
+ 4.059927 5.918911 2.227280
+ 3.400108 5.668218 3.057877
+ 4.699998 7.163547 2.192791
+ 4.538522 7.881891 2.996538
+ 5.547471 7.485542 1.125970
+ 6.169255 8.694617 1.092468
+ 5.956327 9.246984 1.848214
+ 5.754875 6.562900 0.093635
+ 6.414694 6.813595 -0.736962
+ 5.114806 5.318263 0.128119
+ 5.276286 4.599920 -0.675627
+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+!entry.NTYR.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 0 22 0 0 0 0
+!entry.NTYR.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "NTYR" 1 24 1 "p" 0
+!entry.NTYR.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.NTYR.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.NTYR.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+!entry.NVAL.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "N" "N3" 0 1 131072 1 7 0.057700
+ "H1" "H" 0 1 131072 2 1 0.227200
+ "H2" "H" 0 1 131072 3 1 0.227200
+ "H3" "H" 0 1 131072 4 1 0.227200
+ "CA" "CX" 0 1 131072 5 6 -0.005400
+ "HA" "HP" 0 1 131072 6 1 0.109300
+ "CB" "3C" 0 1 131072 7 6 0.319600
+ "HB" "HC" 0 1 131072 8 1 -0.022100
+ "CG1" "CT" 0 1 131072 9 6 -0.312900
+ "HG11" "HC" 0 1 131072 10 1 0.073500
+ "HG12" "HC" 0 1 131072 11 1 0.073500
+ "HG13" "HC" 0 1 131072 12 1 0.073500
+ "CG2" "CT" 0 1 131072 13 6 -0.312900
+ "HG21" "HC" 0 1 131072 14 1 0.073500
+ "HG22" "HC" 0 1 131072 15 1 0.073500
+ "HG23" "HC" 0 1 131072 16 1 0.073500
+ "C" "C" 0 1 131072 17 6 0.616300
+ "O" "O" 0 1 131072 18 8 -0.572200
+!entry.NVAL.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N3" 0 -1 0.0
+ "H1" "H" 0 -1 0.0
+ "H2" "H" 0 -1 0.0
+ "H3" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "HP" 0 -1 0.0
+ "CB" "3C" 0 -1 0.0
+ "HB" "HC" 0 -1 0.0
+ "CG1" "CT" 0 -1 0.0
+ "HG11" "HC" 0 -1 0.0
+ "HG12" "HC" 0 -1 0.0
+ "HG13" "HC" 0 -1 0.0
+ "CG2" "CT" 0 -1 0.0
+ "HG21" "HC" 0 -1 0.0
+ "HG22" "HC" 0 -1 0.0
+ "HG23" "HC" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O" 0 -1 0.0
+!entry.NVAL.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.NVAL.unit.childsequence single int
+ 2
+!entry.NVAL.unit.connect array int
+ 0
+ 17
+!entry.NVAL.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 1 4 1
+ 1 5 1
+ 5 6 1
+ 5 7 1
+ 5 17 1
+ 7 8 1
+ 7 9 1
+ 7 13 1
+ 9 10 1
+ 9 11 1
+ 9 12 1
+ 13 14 1
+ 13 15 1
+ 13 16 1
+ 17 18 1
+!entry.NVAL.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+ "R" 1 "A" 13
+ "R" 1 "A" 14
+ "R" 1 "A" 15
+ "R" 1 "A" 16
+ "R" 1 "A" 17
+ "R" 1 "A" 18
+!entry.NVAL.unit.name single str
+ "NVAL"
+!entry.NVAL.unit.positions table  dbl x  dbl y  dbl z
+ 3.325770 1.547909 -1.607204E-06
+ 4.046154 0.839991 -2.855245E-06
+ 2.823094 1.499508 -0.874687
+ 2.823097 1.499507 0.874685
+ 3.970048 2.845795 -1.311163E-07
+ 3.671663 3.400129 -0.889820
+ 3.576965 3.653838 1.232143
+ 2.496995 3.801075 1.241379
+ 3.997712 2.900483 2.489542
+ 5.077693 2.753265 2.481244
+ 3.716972 3.477628 3.370558
+ 3.499630 1.931323 2.516834
+ 4.274186 5.009602 1.194577
+ 3.973781 5.548460 0.295972
+ 3.993559 5.587585 2.075079
+ 5.354271 4.863178 1.185788
+ 5.485541 2.705207 -4.398755E-06
+ 6.008824 1.593175 -8.449768E-06
+!entry.NVAL.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 0 17 0 0 0 0
+!entry.NVAL.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "NVAL" 1 19 1 "p" 0
+!entry.NVAL.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.NVAL.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.NVAL.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
diff --git a/test/Test_Build/frcmod.ff14SB b/test/Test_Build/frcmod.ff14SB
new file mode 100644
index 0000000000..5fee412e6e
--- /dev/null
+++ b/test/Test_Build/frcmod.ff14SB
@@ -0,0 +1,514 @@
+ff14SB protein backbone and sidechain parameters
+MASS
+CO 12.01         0.616  !            sp2 C carboxylate group 
+2C 12.01         0.878               sp3 aliphatic C with two (duo) heavy atoms
+3C 12.01         0.878               sp3 aliphatic C with three (tres) heavy atoms
+C8 12.01         0.878               sp3 aliphatic C basic AA side chain
+
+BOND
+C -2C  317.0    1.5220
+C*-2C  317.0    1.4950
+C8-C8  310.0    1.5260
+C8-CX  310.0    1.5260
+C8-H1  340.0    1.0900
+C8-HC  340.0    1.0900
+C8-HP  340.0    1.0900
+C8-N2  337.0    1.4630
+C8-N3  367.0    1.4710
+CA-2C  317.0    1.5100
+CC-2C  317.0    1.5040
+CO-O2  656.0    1.2500
+CO-2C  317.0    1.5220
+CT-2C  310.0    1.5260
+CT-3C  310.0    1.5260
+CX-2C  310.0    1.5260
+CX-3C  310.0    1.5260
+H1-2C  340.0    1.0900
+H1-3C  340.0    1.0900
+HC-2C  340.0    1.0900
+HC-3C  340.0    1.0900
+OH-2C  320.0    1.4100
+OH-3C  320.0    1.4100
+S -2C  227.0    1.8100
+SH-2C  237.0    1.8100
+2C-2C  310.0    1.5260
+2C-3C  310.0    1.5260
+
+ANGL
+N -C -2C    70.0      116.60
+O -C -2C    80.0      120.40
+OH-C -2C    80.0      110.00
+CB-C*-2C    70.0      128.60
+CW-C*-2C    70.0      125.00
+C8-C8-C8    40.0      109.50
+C8-C8-CX    40.0      109.50
+C8-C8-H1    50.0      109.50
+C8-C8-HC    50.0      109.50
+C8-C8-HP    50.0      109.50
+C8-C8-N2    80.0      111.20
+C8-C8-N3    80.0      111.20
+CX-C8-HC    50.0      109.50
+H1-C8-H1    35.0      109.50
+H1-C8-N2    50.0      109.50
+HC-C8-HC    35.0      109.50
+HP-C8-HP    35.0      109.50
+HP-C8-N3    50.0      109.50
+CA-CA-2C    70.0      120.00
+CV-CC-2C    70.0      120.00
+CW-CC-2C    70.0      120.00
+NA-CC-2C    70.0      120.00
+NB-CC-2C    70.0      120.00
+O2-CO-O2    80.0      126.00
+O2-CO-2C    70.0      117.00
+HC-CT-2C    50.0      109.50
+HC-CT-3C    50.0      109.50
+C -CX-C8    63.0      111.10
+C -CX-2C    63.0      111.10
+C -CX-3C    63.0      111.10
+C8-CX-H1    50.0      109.50
+C8-CX-N     80.0      109.70
+C8-CX-N3    80.0      111.20
+H1-CX-2C    50.0      109.50
+H1-CX-3C    50.0      109.50
+HP-CX-C8    50.0      109.50    changed based on NMA nmodes (was CT-CT-HP)
+HP-CX-2C    50.0      109.50    changed based on NMA nmodes (was CT-CT-HP)
+HP-CX-3C    50.0      109.50    changed based on NMA nmodes (was CT-CT-HP)
+N -CX-2C    80.0      109.70
+N -CX-3C    80.0      109.70
+N3-CX-2C    80.0      111.20
+N3-CX-3C    80.0      111.20
+C8-N2-CA    50.0      123.20
+C8-N2-H     50.0      118.40
+C8-N3-H     50.0      109.50
+HO-OH-2C    55.0      108.50
+HO-OH-3C    55.0      108.50
+CT-S -2C    62.0       98.90
+2C-S -S     68.0      103.70
+HS-SH-2C    43.0       96.00
+C -2C-CX    63.0      111.10
+C -2C-HC    50.0      109.50
+C -2C-2C    63.0      111.10
+C*-2C-CX    63.0      115.60
+C*-2C-HC    50.0      109.50
+CA-2C-CX    63.0      114.00
+CA-2C-HC    50.0      109.50
+CC-2C-CX    63.0      113.10
+CC-2C-HC    50.0      109.50
+CO-2C-CX    63.0      111.10
+CO-2C-HC    50.0      109.50
+CO-2C-2C    63.0      111.10
+CT-2C-HC    50.0      109.50
+CT-2C-3C    40.0      109.50
+CX-2C-H1    50.0      109.50
+CX-2C-HC    50.0      109.50
+CX-2C-OH    50.0      109.50
+CX-2C-S     50.0      114.70
+CX-2C-SH    50.0      108.60
+CX-2C-2C    40.0      109.50
+CX-2C-3C    40.0      109.50
+H1-2C-H1    35.0      109.50
+H1-2C-OH    50.0      109.50
+H1-2C-S     50.0      109.50
+H1-2C-SH    50.0      109.50
+H1-2C-2C    50.0      109.50
+HC-2C-HC    35.0      109.50
+HC-2C-2C    50.0      109.50
+HC-2C-3C    50.0      109.50
+S -2C-2C    50.0      114.70
+CT-3C-CT    40.0      109.50
+CT-3C-CX    40.0      109.50
+CT-3C-H1    50.0      109.50
+CT-3C-HC    50.0      109.50
+CT-3C-OH    50.0      109.50
+CT-3C-2C    40.0      109.50
+CX-3C-H1    50.0      109.50
+CX-3C-HC    50.0      109.50
+CX-3C-OH    50.0      109.50
+CX-3C-2C    40.0      109.50
+H1-3C-OH    50.0      109.50
+HC-3C-2C    50.0      109.50
+
+DIHE
+C8-CX-N -C    1    0.000         0.0            -4.    phi'
+C8-CX-N -C    1    0.800         0.0            -3.
+C8-CX-N -C    1    1.800         0.0            -2.
+C8-CX-N -C    1    2.000         0.0             1.
+CT-CX-N -C    1    0.000         0.0            -4.
+CT-CX-N -C    1    0.800         0.0            -3.
+CT-CX-N -C    1    1.800         0.0            -2.
+CT-CX-N -C    1    2.000         0.0             1.
+2C-CX-N -C    1    0.000         0.0            -4.
+2C-CX-N -C    1    0.800         0.0            -3.
+2C-CX-N -C    1    1.800         0.0            -2.
+2C-CX-N -C    1    2.000         0.0             1.
+3C-CX-N -C    1    0.000         0.0            -4.
+3C-CX-N -C    1    0.800         0.0            -3.
+3C-CX-N -C    1    1.800         0.0            -2.
+3C-CX-N -C    1    2.000         0.0             1.
+N -C -CX-C8   1    0.000         0.0            -4.    psi'
+N -C -CX-C8   1    0.400         0.0            -3.
+N -C -CX-C8   1    0.200         0.0            -2.
+N -C -CX-C8   1    0.200         0.0             1.
+N -C -CX-CT   1    0.000         0.0            -4.
+N -C -CX-CT   1    0.400         0.0            -3.
+N -C -CX-CT   1    0.200         0.0            -2.
+N -C -CX-CT   1    0.200         0.0             1.
+N -C -CX-2C   1    0.000         0.0            -4.
+N -C -CX-2C   1    0.400         0.0            -3.
+N -C -CX-2C   1    0.200         0.0            -2.
+N -C -CX-2C   1    0.200         0.0             1.
+N -C -CX-3C   1    0.000         0.0            -4.
+N -C -CX-3C   1    0.400         0.0            -3.
+N -C -CX-3C   1    0.200         0.0            -2.
+N -C -CX-3C   1    0.200         0.0             1.
+N -C -2C-HC   1    0.000         0.0             2.    JCC,7,(1986),230 (X -C -CT-X )
+O -C -2C-HC   1    0.080       180.0            -3.    Junmei et al, 1999 (HC-CT-C -O )
+O -C -2C-HC   1    0.000         0.0            -2.
+O -C -2C-HC   1    0.800         0.0             1.
+OH-C -2C-HC   1    0.000         0.0             2.
+CB-C*-2C-HC   1    0.000         0.0             2.    JCC,7,(1986),230 (X -C*-CT-X )
+CW-C*-2C-HC   1    0.000         0.0             2.
+X -C8-C8-X    9    1.400         0.0             3.    JCC,7,(1986),230 (X -CT-CT-X )
+C8-C8-C8-HC   1    0.160         0.0             3.    Junmei et al, 1999 (was HC-CT-CT-CT)
+CX-C8-C8-HC   1    0.160         0.0             3.
+HC-C8-C8-HC   1    0.150         0.0             3.    Junmei et al, 1999 (HC-CT-CT-HC)
+X -C8-CX-X    9    1.400         0.0             3.
+X -C8-N2-X    6    0.000         0.0             3.    JCC,7,(1986),230 (X -CT-N2-X )
+X -C8-N3-X    9    1.400         0.0             3.    JCC,7,(1986),230 (was X -CT-N3-X )
+X -CA-2C-X    1    0.000         0.0             2.    JCC,7,(1986),230 (was X -CA-CT-X )
+2C-CC-CV-H4   1    5.150       180.0             2.
+2C-CC-CV-NB   1    5.150       180.0             2.
+2C-CC-CW-H4   1    5.375       180.0             2.
+2C-CC-CW-NA   1    5.375       180.0             2.
+2C-CC-NA-CR   1    1.400       180.0             2.
+2C-CC-NA-H    1    1.400       180.0             2.
+2C-CC-NB-CR   1    2.400       180.0             2.
+CV-CC-2C-HC   1    0.000         0.0             2.
+CW-CC-2C-HC   1    0.000         0.0             2.
+NA-CC-2C-HC   1    0.000         0.0             2.
+NB-CC-2C-HC   1    0.000         0.0             2.
+O2-CO-2C-HC   1    0.000         0.0             2.
+H1-CT-S -2C   3    1.000         0.0             3.
+HC-CT-2C-HC   1    0.150         0.0             3.
+HC-CT-2C-3C   1    0.160         0.0             3.
+HC-CT-3C-CT   1    0.160         0.0             3.
+HC-CT-3C-CX   1    0.160         0.0             3.
+HC-CT-3C-H1   9    1.400         0.0             3.
+HC-CT-3C-HC   1    0.150         0.0             3.
+HC-CT-3C-OH   1    0.000         0.0            -3.
+HC-CT-3C-OH   1    0.250         0.0             1.
+HC-CT-3C-2C   1    0.160         0.0             3.
+X -CX-2C-X    9    1.400         0.0             3.
+H1-CX-2C-OH   1    0.000         0.0            -3.
+H1-CX-2C-OH   1    0.250         0.0             1.
+X -CX-3C-X    9    1.400         0.0             3.
+H1-CX-3C-OH   1    0.000         0.0            -3.
+H1-CX-3C-OH   1    0.250         0.0             1.
+HO-OH-2C-H1   3    0.500         0.0             3.         JCC,7,(1986),230
+HO-OH-3C-H1   3    0.500         0.0             3.
+EP-S -S -2C   1    0.000         0.0             3.    cyx (dac)
+X -S -2C-X    3    1.000         0.0             3.    JCC,7,(1986),230 (X -CT-S -X )
+X -SH-2C-X    3    0.750         0.0             3.    JCC,7,(1986),230 (X -CT-SH-X )
+X -2C-2C-X    9    1.400         0.0             3.
+CX-2C-2C-HC   1    0.160         0.0             3.    Junmei et al, 1999
+HC-2C-2C-HC   1    0.150         0.0             3.    Junmei et al, 1999
+CT-2C-3C-HC   1    0.160         0.0             3.    Junmei et al, 1999
+CX-2C-3C-HC   1    0.160         0.0             3.
+HC-2C-3C-CT   1    0.160         0.0             3.
+HC-2C-3C-CX   1    0.160         0.0             3.
+HC-2C-3C-HC   1    0.150         0.0             3.
+C -CX-C8-C8   9    1.400         0.0             3.    Arg Lys
+N -CX-C8-C8   9    1.400         0.0             3.
+N3-CX-C8-C8   9    1.400         0.0             3.
+CX-C8-C8-C8   1    0.180         0.0            -3.
+CX-C8-C8-C8   1    0.250       180.0            -2.
+CX-C8-C8-C8   1    0.200       180.0             1.
+C8-C8-C8-N2   9    1.400         0.0             3.
+C8-C8-N2-CA   1    0.000         0.0            -3.
+C8-C8-N2-CA   1    0.000         0.0             1.
+C8-C8-C8-C8   1    0.180         0.0            -3.
+C8-C8-C8-C8   1    0.250       180.0            -2.
+C8-C8-C8-C8   1    0.200       180.0             1.
+C8-C8-C8-N3   9    1.400         0.0             3.
+C8-N2-CA-N2   1    0.000         0.0            -4.    Arg Lys copied
+C8-N2-CA-N2   1    2.400       180.0             2.
+H -N2-CA-N2   1    0.000         0.0            -4.
+H -N2-CA-N2   1    2.400       180.0             2.
+C8-C8-N3-H    9    1.400         0.0             3.
+C -CX-2C-SH   1    0.075         0.0            -4.       C
+C -CX-2C-SH   1    0.251         0.0            -3.
+C -CX-2C-SH   1    0.337       180.0            -2.
+C -CX-2C-SH   1    0.269       180.0             1.
+N -CX-2C-SH   1    0.033         0.0            -4.
+N -CX-2C-SH   1    0.251         0.0            -3.
+N -CX-2C-SH   1    0.486       180.0            -2.
+N -CX-2C-SH   1    0.154         0.0             1.
+N3-CX-2C-SH   1    0.033         0.0            -4.
+N3-CX-2C-SH   1    0.251         0.0            -3.
+N3-CX-2C-SH   1    0.486       180.0            -2.
+N3-CX-2C-SH   1    0.154         0.0             1.
+CX-2C-SH-HS   1    0.030         0.0            -4.
+CX-2C-SH-HS   1    0.252         0.0            -3.
+CX-2C-SH-HS   1    0.612         0.0            -2.
+CX-2C-SH-HS   1    0.092         0.0             1.
+C -CX-2C-CO   1    0.154         0.0            -4.       D
+C -CX-2C-CO   1    0.058         0.0            -3.
+C -CX-2C-CO   1    0.459       180.0            -2.
+C -CX-2C-CO   1    0.424         0.0             1.
+N -CX-2C-CO   1    0.089         0.0            -4.
+N -CX-2C-CO   1    0.058         0.0            -3.
+N -CX-2C-CO   1    0.647       180.0            -2.
+N -CX-2C-CO   1    2.154       180.0             1.
+N3-CX-2C-CO   1    0.089         0.0            -4.
+N3-CX-2C-CO   1    0.058         0.0            -3.
+N3-CX-2C-CO   1    0.647       180.0            -2.
+N3-CX-2C-CO   1    2.154       180.0             1.
+CX-2C-CO-O2   1    0.031       180.0            -4.
+CX-2C-CO-O2   1    0.000         0.0            -3.
+CX-2C-CO-O2   1    0.769       180.0            -2.
+CX-2C-CO-O2   1    0.000         0.0             1.
+C -CX-2C-C    1    0.107         0.0            -4.       DhN
+C -CX-2C-C    1    0.033         0.0            -3.
+C -CX-2C-C    1    0.303       180.0            -2.
+C -CX-2C-C    1    1.046         0.0             1.
+N -CX-2C-C    1    0.059         0.0            -4.
+N -CX-2C-C    1    0.033         0.0            -3.
+N -CX-2C-C    1    0.297       180.0            -2.
+N -CX-2C-C    1    0.688       180.0             1.
+N3-CX-2C-C    1    0.059         0.0            -4.
+N3-CX-2C-C    1    0.033         0.0            -3.
+N3-CX-2C-C    1    0.297       180.0            -2.
+N3-CX-2C-C    1    0.688       180.0             1.
+CX-2C-C -O    1    0.000         0.0             1.
+CX-2C-C -OH   1    0.199       180.0            -4.
+CX-2C-C -OH   1    0.008         0.0            -3.
+CX-2C-C -OH   1    0.575       180.0            -2.
+CX-2C-C -OH   1    1.199       180.0             1.
+2C-C -OH-HO   1    0.113         0.0            -4.
+2C-C -OH-HO   1    0.479         0.0            -3.
+2C-C -OH-HO   1    2.706       180.0            -2.
+2C-C -OH-HO   1    0.448       180.0             1.
+CX-2C-C -N    1    0.008         0.0            -4.
+CX-2C-C -N    1    0.301       180.0            -3.
+CX-2C-C -N    1    0.485       180.0            -2.
+CX-2C-C -N    1    0.828       180.0             1.
+C -CX-CT-CC   1    0.025         0.0            -4.       Hie,dp
+C -CX-CT-CC   1    0.219         0.0            -3.
+C -CX-CT-CC   1    0.244       180.0            -2.
+C -CX-CT-CC   1    0.143       180.0             1.
+N -CX-CT-CC   1    0.089         0.0            -4.
+N -CX-CT-CC   1    0.219         0.0            -3.
+N -CX-CT-CC   1    0.221       180.0            -2.
+N -CX-CT-CC   1    0.306       180.0             1.
+N3-CX-CT-CC   1    0.089         0.0            -4.
+N3-CX-CT-CC   1    0.219         0.0            -3.
+N3-CX-CT-CC   1    0.221       180.0            -2.
+N3-CX-CT-CC   1    0.306       180.0             1.
+CX-CT-CC-NA   1    0.037       180.0            -4.
+CX-CT-CC-NA   1    0.686         0.0            -3.
+CX-CT-CC-NA   1    0.392       180.0            -2.
+CX-CT-CC-NA   1    0.160       180.0             1.
+CX-CT-CC-CV   1    0.010       180.0            -4.
+CX-CT-CC-CV   1    0.122       180.0            -3.
+CX-CT-CC-CV   1    0.750         0.0            -2.
+CX-CT-CC-CV   1    0.674       180.0             1.
+CX-CT-CC-NB   1    0.047       180.0            -4.
+CX-CT-CC-NB   1    0.740         0.0            -3.
+CX-CT-CC-NB   1    0.204         0.0            -2.
+CX-CT-CC-NB   1    0.690         0.0             1.
+C -CX-3C-CT   1    0.112         0.0            -4.       ITV
+C -CX-3C-CT   1    0.148         0.0            -3.
+C -CX-3C-CT   1    0.289       180.0            -2.
+C -CX-3C-CT   1    0.406       180.0             1.
+C -CX-3C-2C   1    0.115         0.0            -4.
+C -CX-3C-2C   1    0.113         0.0            -3.
+C -CX-3C-2C   1    0.735       180.0            -2.
+C -CX-3C-2C   1    0.162         0.0             1.
+N -CX-3C-CT   1    0.001       180.0            -4.
+N -CX-3C-CT   1    0.148         0.0            -3.
+N -CX-3C-CT   1    0.216       180.0            -2.
+N -CX-3C-CT   1    0.337         0.0             1.
+N -CX-3C-2C   1    0.097       180.0            -4.
+N -CX-3C-2C   1    0.113         0.0            -3.
+N -CX-3C-2C   1    0.144       180.0            -2.
+N -CX-3C-2C   1    0.310         0.0             1.
+N3-CX-3C-CT   1    0.001       180.0            -4.
+N3-CX-3C-CT   1    0.148         0.0            -3.
+N3-CX-3C-CT   1    0.216       180.0            -2.
+N3-CX-3C-CT   1    0.337         0.0             1.
+N3-CX-3C-2C   1    0.097       180.0            -4.
+N3-CX-3C-2C   1    0.113         0.0            -3.
+N3-CX-3C-2C   1    0.144       180.0            -2.
+N3-CX-3C-2C   1    0.310         0.0             1.
+CX-3C-2C-CT   1    0.230         0.0            -4.
+CX-3C-2C-CT   1    0.107         0.0            -3.
+CX-3C-2C-CT   1    0.053         0.0            -2.
+CX-3C-2C-CT   1    0.447         0.0             1.
+CT-3C-2C-CT   1    0.224         0.0            -4.
+CT-3C-2C-CT   1    0.107         0.0            -3.
+CT-3C-2C-CT   1    0.077       180.0            -2.
+CT-3C-2C-CT   1    0.202         0.0             1.
+C -CX-3C-OH   1    0.156         0.0            -4.
+C -CX-3C-OH   1    0.315         0.0            -3.
+C -CX-3C-OH   1    0.119       180.0            -2.
+C -CX-3C-OH   1    0.697       180.0             1.
+N -CX-3C-OH   1    0.095         0.0            -4.
+N -CX-3C-OH   1    0.315         0.0            -3.
+N -CX-3C-OH   1    0.006         0.0            -2.
+N -CX-3C-OH   1    0.674         0.0             1.
+N3-CX-3C-OH   1    0.095         0.0            -4.
+N3-CX-3C-OH   1    0.315         0.0            -3.
+N3-CX-3C-OH   1    0.006         0.0            -2.
+N3-CX-3C-OH   1    0.674         0.0             1.
+CX-3C-OH-HO   1    0.013         0.0            -4.
+CX-3C-OH-HO   1    0.236         0.0            -3.
+CX-3C-OH-HO   1    0.251         0.0            -2.
+CX-3C-OH-HO   1    0.006       180.0             1.
+CT-3C-OH-HO   1    0.048         0.0            -4.
+CT-3C-OH-HO   1    0.236         0.0            -3.
+CT-3C-OH-HO   1    0.079       180.0            -2.
+CT-3C-OH-HO   1    0.643         0.0             1.
+C -CX-2C-3C   1    0.190         0.0            -4.       L
+C -CX-2C-3C   1    0.144         0.0            -3.
+C -CX-2C-3C   1    0.620       180.0            -2.
+C -CX-2C-3C   1    0.706         0.0             1.
+N -CX-2C-3C   1    0.073         0.0            -4.
+N -CX-2C-3C   1    0.144         0.0            -3.
+N -CX-2C-3C   1    0.259       180.0            -2.
+N -CX-2C-3C   1    0.098         0.0             1.
+N3-CX-2C-3C   1    0.073         0.0            -4.
+N3-CX-2C-3C   1    0.144         0.0            -3.
+N3-CX-2C-3C   1    0.259       180.0            -2.
+N3-CX-2C-3C   1    0.098         0.0             1.
+CX-2C-3C-CT   1    0.179         0.0            -4.
+CX-2C-3C-CT   1    0.142         0.0            -3.
+CX-2C-3C-CT   1    0.027       180.0            -2.
+CX-2C-3C-CT   1    0.379         0.0             1.
+C -CX-2C-OH   1    0.129         0.0            -4.       S
+C -CX-2C-OH   1    0.401         0.0            -3.
+C -CX-2C-OH   1    0.218       180.0            -2.
+C -CX-2C-OH   1    0.661       180.0             1.
+N -CX-2C-OH   1    0.160         0.0            -4.
+N -CX-2C-OH   1    0.401         0.0            -3.
+N -CX-2C-OH   1    0.246       180.0            -2.
+N -CX-2C-OH   1    0.666         0.0             1.
+N3-CX-2C-OH   1    0.160         0.0            -4.
+N3-CX-2C-OH   1    0.401         0.0            -3.
+N3-CX-2C-OH   1    0.246       180.0            -2.
+N3-CX-2C-OH   1    0.666         0.0             1.
+CX-2C-OH-HO   1    0.007         0.0            -4.
+CX-2C-OH-HO   1    0.267         0.0            -3.
+CX-2C-OH-HO   1    0.444         0.0            -2.
+CX-2C-OH-HO   1    0.211         0.0             1.
+C -CX-CT-C*   1    0.074         0.0            -4.       W_CB
+C -CX-CT-C*   1    0.234         0.0            -3.
+C -CX-CT-C*   1    0.353       180.0            -2.
+C -CX-CT-C*   1    0.017       180.0             1.
+N -CX-CT-C*   1    0.031         0.0            -4.
+N -CX-CT-C*   1    0.234         0.0            -3.
+N -CX-CT-C*   1    0.313       180.0            -2.
+N -CX-CT-C*   1    0.079         0.0             1.
+N3-CX-CT-C*   1    0.031         0.0            -4.
+N3-CX-CT-C*   1    0.234         0.0            -3.
+N3-CX-CT-C*   1    0.313       180.0            -2.
+N3-CX-CT-C*   1    0.079         0.0             1.
+CX-CT-C*-CB   1    0.095       180.0            -4.
+CX-CT-C*-CB   1    0.819         0.0            -3.
+CX-CT-C*-CB   1    0.408         0.0            -2.
+CX-CT-C*-CB   1    0.365         0.0             1.
+CX-CT-C*-CW   1    0.000         0.0            -4.
+CX-CT-C*-CW   1    0.000         0.0            -3.
+CX-CT-C*-CW   1    0.000         0.0            -2.
+CX-CT-C*-CW   1    0.000         0.0             1.
+C -CX-CT-CA   1    0.012       180.0            -4.       FY
+C -CX-CT-CA   1    0.192         0.0            -3.
+C -CX-CT-CA   1    0.469       180.0            -2.
+C -CX-CT-CA   1    0.055         0.0             1.
+N -CX-CT-CA   1    0.007       180.0            -4.
+N -CX-CT-CA   1    0.192         0.0            -3.
+N -CX-CT-CA   1    0.290       180.0            -2.
+N -CX-CT-CA   1    0.012       180.0             1.
+N3-CX-CT-CA   1    0.007       180.0            -4.
+N3-CX-CT-CA   1    0.192         0.0            -3.
+N3-CX-CT-CA   1    0.290       180.0            -2.
+N3-CX-CT-CA   1    0.012       180.0             1.
+CX-CT-CA-CA   1    0.048       180.0            -4.
+CX-CT-CA-CA   1    0.000         0.0            -3.
+CX-CT-CA-CA   1    0.069       180.0            -2.
+CX-CT-CA-CA   1    0.000         0.0             1.
+CA-C -OH-HO   1    0.065         0.0            -4.
+CA-C -OH-HO   1    0.000         0.0            -3.
+CA-C -OH-HO   1    0.883       180.0            -2.
+CA-C -OH-HO   1    0.000         0.0             1.
+C -CX-2C-2C   1    0.145         0.0            -4.    Glh Gln Glu Met
+C -CX-2C-2C   1    0.144         0.0            -3.
+C -CX-2C-2C   1    0.393       180.0            -2.
+C -CX-2C-2C   1    0.421       180.0             1.
+N -CX-2C-2C   1    0.078         0.0            -4.
+N -CX-2C-2C   1    0.144         0.0            -3.
+N -CX-2C-2C   1    0.184       180.0            -2.
+N -CX-2C-2C   1    0.100       180.0             1.
+N3-CX-2C-2C   1    0.078         0.0            -4.
+N3-CX-2C-2C   1    0.144         0.0            -3.
+N3-CX-2C-2C   1    0.184       180.0            -2.
+N3-CX-2C-2C   1    0.100       180.0             1.
+CX-2C-2C-C    1    0.138         0.0            -4.
+CX-2C-2C-C    1    0.412       180.0            -3.
+CX-2C-2C-C    1    0.083         0.0            -2.
+CX-2C-2C-C    1    0.196       180.0             1.
+2C-2C-C -O    1    0.000         0.0             1.
+2C-2C-C -OH   1    0.066       180.0            -4.
+2C-2C-C -OH   1    0.025       180.0            -3.
+2C-2C-C -OH   1    1.104       180.0            -2.
+2C-2C-C -OH   1    0.824       180.0             1.
+2C-2C-C -N    1    0.042         0.0            -4.
+2C-2C-C -N    1    0.085       180.0            -3.
+2C-2C-C -N    1    0.845       180.0            -2.
+2C-2C-C -N    1    0.609       180.0             1.
+CX-2C-2C-CO   1    0.056       180.0            -4.
+CX-2C-2C-CO   1    0.608       180.0            -3.
+CX-2C-2C-CO   1    0.222       180.0            -2.
+CX-2C-2C-CO   1    1.367       180.0             1.
+2C-2C-CO-O2   1    0.064         0.0            -4.
+2C-2C-CO-O2   1    0.390       180.0             2.
+CX-2C-2C-S    1    0.028         0.0            -4.
+CX-2C-2C-S    1    0.016         0.0            -3.
+CX-2C-2C-S    1    0.245         0.0            -2.
+CX-2C-2C-S    1    0.417         0.0             1.
+2C-2C-S -CT   1    0.057         0.0            -4.
+2C-2C-S -CT   1    0.414         0.0            -3.
+2C-2C-S -CT   1    0.442         0.0            -2.
+2C-2C-S -CT   1    0.247       180.0             1.
+C -CX-2C-S    1    0.278         0.0            -4.     C-C
+C -CX-2C-S    1    0.323         0.0            -3.
+C -CX-2C-S    1    0.394       180.0            -2.
+C -CX-2C-S    1    0.602         0.0             1.
+N -CX-2C-S    1    0.064         0.0            -4.
+N -CX-2C-S    1    0.323         0.0            -3.
+N -CX-2C-S    1    0.021       180.0            -2.
+N -CX-2C-S    1    0.469         0.0             1.
+N3-CX-2C-S    1    0.064         0.0            -4.
+N3-CX-2C-S    1    0.323         0.0            -3.
+N3-CX-2C-S    1    0.021       180.0            -2.
+N3-CX-2C-S    1    0.469         0.0             1.
+CX-2C-S -S    1    0.135       180.0            -4.
+CX-2C-S -S    1    0.302         0.0            -3.
+CX-2C-S -S    1    0.666         0.0            -2.
+CX-2C-S -S    1    0.056         0.0             1.
+2C-S -S -2C   1    0.379         0.0            -4.
+2C-S -S -2C   1    0.682         0.0            -3.
+2C-S -S -2C   1    4.480         0.0            -2.
+2C-S -S -2C   1    0.420         0.0             1.
+
+IMPR
+X -O2-CO-O2        10.5          180.          2.
+2C-O -C -OH        10.5          180.          2.
+CA-CA-CA-2C         1.1          180.          2.
+
+NONB
+  2C          1.9080  0.1094             Spellmeyer
+  3C          1.9080  0.1094             Spellmeyer
+  C8          1.9080  0.1094             Spellmeyer
+  CO          1.9080  0.0860             OPLS
+
+
diff --git a/test/Test_Build/parm10.dat b/test/Test_Build/parm10.dat
new file mode 100644
index 0000000000..cb5815c94f
--- /dev/null
+++ b/test/Test_Build/parm10.dat
@@ -0,0 +1,1005 @@
+PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
+C  12.01         0.616  !            sp2 C carbonyl group 
+CA 12.01         0.360               sp2 C pure aromatic (benzene)
+CB 12.01         0.360               sp2 aromatic C, 5&6 membered ring junction
+CC 12.01         0.360               sp2 aromatic C, 5 memb. ring HIS
+CD 12.01         0.360               sp2 C atom in the middle of: C=CD-CD=C
+CI 12.01                             parmbsc0
+CK 12.01         0.360               sp2 C 5 memb.ring in purines (dA,dG)
+CP 12.01         0.360               sp2 C 5 memb.ring in purines (G)
+CM 12.01         0.360               sp2 C  pyrimidines in pos. 5 & 6 (dT,dC)
+CS 12.01         0.360               sp2 C  pyrimidines in pos. 5 & 6 (U)
+CN 12.01         0.360               sp2 C aromatic 5&6 memb.ring junct.(TRP)
+CQ 12.01         0.360               sp2 C in 5 mem.ring of purines between 2 N
+CR 12.01         0.360               sp2 arom as CQ but in HIS
+CT 12.01         0.878               sp3 aliphatic C
+CV 12.01         0.360               sp2 arom. 5 memb.ring w/1 N and 1 H (HIS)
+CW 12.01         0.360               sp2 arom. 5 memb.ring w/1 N-H and 1 H (HIS)
+C* 12.01         0.360               sp2 arom. 5 memb.ring w/1 subst. (TRP)
+CX 12.01         0.360               protein C-alpha (new to ff10)
+CY 12.01         0.360               nitrile C (Howard et al.JCC,16,243,1995)
+CZ 12.01         0.360               sp C (Howard et al.JCC,16,243,1995)
+C5 12.01         0.360               sp2 C 5 memb.ring in purines (A)
+C4 12.01         0.360               sp2 C  pyrimidines in pos. 5 & 6 (C)
+C0 40.08                             calcium
+H  1.008         0.161               H bonded to nitrogen atoms
+HC 1.008         0.135               H aliph. bond. to C without electrwd.group
+H1 1.008         0.135               H aliph. bond. to C with 1 electrwd. group
+H2 1.008         0.135               H aliph. bond. to C with 2 electrwd.groups
+H3 1.008         0.135               H aliph. bond. to C with 3 eletrwd.groups
+HA 1.008         0.167               H arom. bond. to C without elctrwd. groups
+H4 1.008         0.167               H arom. bond. to C with 1 electrwd. group
+H5 1.008         0.167               H arom.at C with 2 elctrwd. gr,+HCOO group
+HO 1.008         0.135               hydroxyl group
+HS 1.008         0.135               hydrogen bonded to sulphur (pol?)
+HP 1.008         0.135               H bonded to C next to positively charged gr
+HZ 1.008         0.161               H bond sp C (Howard et al.JCC,16,243,1995)
+F  19.00         0.320               fluorine (not fluoride!)
+Cl 35.45         1.910               chlorine  (Applequist) (not chloride!)
+Br 79.90         2.880               bromine  (Applequist) (not bromide!)
+I  126.9         4.690               iodine   (Applequist) (not iodide!)
+MG 24.305        0.120               magnesium
+N  14.01         0.530               sp2 nitrogen in amide groups
+NA 14.01         0.530               sp2 N in 5 memb.ring w/H atom (HIS)
+NB 14.01         0.530               sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA)
+NC 14.01         0.530               sp2 N in 6 memb.ring w/LP (ADE,GUA)
+N2 14.01         0.530               sp2 N in amino groups
+N3 14.01         0.530               sp3 N for charged amino groups (Lys, etc)
+NT 14.01         0.530               sp3 N for amino groups amino groups 
+N* 14.01         0.530               sp2 N 
+NY 14.01         0.530               nitrile N (Howard et al.JCC,16,243,1995)
+O  16.00         0.434               carbonyl group oxygen
+O2 16.00         0.434               carboxyl and phosphate group oxygen
+OH 16.00         0.465               oxygen in hydroxyl group
+OS 16.00         0.465               ether and ester oxygen
+OP 16.00         0.465               2- phosphate oxygen
+P  30.97         1.538               phosphate,pol:JACS,112,8543,90,K.J.Miller
+S  32.06         2.900               S in disulfide linkage,pol:JPC,102,2399,98
+SH 32.06         2.900               S in cystine
+CU 63.55                             copper
+FE 55.00                             iron
+
+C   H   HO  N   NA  NB  NC  N2  NT  N2  N3  N*  O   OH  OS  P   O2 
+C -C   310.0    1.525       Junmei et al, 1999
+C -CA  469.0    1.409       JCC,7,(1986),230; (not used any more in TYR)
+C -CB  447.0    1.419       JCC,7,(1986),230; GUA
+C -CM  410.0    1.444       JCC,7,(1986),230; THY,URA
+C -CS  410.0    1.444       JCC,7,(1986),230; THY,URA
+C -CT  317.0    1.522       JCC,7,(1986),230; AA
+C -CX  317.0    1.522       JCC,7,(1986),230; AA (was C-CT)
+C -N   490.0    1.335       JCC,7,(1986),230; AA
+C -N*  424.0    1.383       JCC,7,(1986),230; CYT,URA
+C -NA  418.0    1.388       JCC,7,(1986),230; GUA.URA
+C -NC  457.0    1.358       JCC,7,(1986),230; CYT
+C -O   570.0    1.229       JCC,7,(1986),230; AA,CYT,GUA,THY,URA
+C -O2  656.0    1.250       JCC,7,(1986),230; GLU,ASP
+C -OH  450.0    1.364       JCC,7,(1986),230; (not used any more for TYR) 
+C -OS  450.0    1.323       Junmei et al, 1999
+C -H4  367.0    1.080       Junmei et al, 1999
+C -H5  367.0    1.080       Junmei et al, 1999
+CA-CA  469.0    1.400       JCC,7,(1986),230; BENZENE,PHE,TRP,TYR
+CA-CB  469.0    1.404       JCC,7,(1986),230; ADE,TRP
+CA-CM  427.0    1.433       JCC,7,(1986),230; CYT
+CA-CS  427.0    1.433       JCC,7,(1986),230; CYT
+CA-CN  469.0    1.400       JCC,7,(1986),230; TRP
+CA-CT  317.0    1.510       JCC,7,(1986),230; PHE,TYR
+CA-HA  367.0    1.080       changed from 340. bsd on C6H6 nmodes; PHE,TRP,TYR
+CA-H4  367.0    1.080       changed from 340. bsd on C6H6 nmodes; no assigned
+CA-N2  481.0    1.340       JCC,7,(1986),230; ARG,CYT,GUA
+CA-NA  427.0    1.381       JCC,7,(1986),230; GUA
+CA-NC  483.0    1.339       JCC,7,(1986),230; ADE,CYT,GUA
+CA-OH  450.0    1.364       substituted for C-OH in tyr 
+CB-CB  520.0    1.370       JCC,7,(1986),230; ADE,GUA
+CB-N*  436.0    1.374       JCC,7,(1986),230; ADE,GUA
+CB-NB  414.0    1.391       JCC,7,(1986),230; ADE,GUA
+CB-NC  461.0    1.354       JCC,7,(1986),230; ADE,GUA
+CD-HA  367.0    1.080       Junmei et al, 1999 
+CD-CD  469.0    1.400       Junmei et al, 1999
+CD-CM  549.0    1.350       Junmei et al, 1999
+CD-CS  549.0    1.350       Junmei et al, 1999
+CD-CT  317.0    1.510       Junmei et al, 1999
+CK-H5  367.0    1.080       changed from 340. bsd on C6H6 nmodes; ADE,GUA
+CK-N*  440.0    1.371       JCC,7,(1986),230; ADE,GUA
+CK-NB  529.0    1.304       JCC,7,(1986),230; ADE,GUA
+CP-H5  367.0    1.080       changed from 340. bsd on C6H6 nmodes; ADE,GUA
+CP-N*  440.0    1.371       JCC,7,(1986),230; ADE,GUA
+CP-NB  529.0    1.304       JCC,7,(1986),230; ADE,GUA
+CM-CM  549.0    1.350       JCC,7,(1986),230; CYT,THY,URA
+CM-CT  317.0    1.510       JCC,7,(1986),230; THY
+CM-HA  367.0    1.080       changed from 340. bsd on C6H6 nmodes; CYT,URA
+CM-H4  367.0    1.080       changed from 340. bsd on C6H6 nmodes; CYT,URA
+CM-H5  367.0    1.080       changed from 340. bsd on C6H6 nmodes; not assigned
+CM-N*  448.0    1.365       JCC,7,(1986),230; CYT,THY,URA
+CM-OS  480.0    1.240       Junmei et al, 1999
+CS-CS  549.0    1.350       JCC,7,(1986),230; CYT,THY,URA
+CS-CT  317.0    1.510       JCC,7,(1986),230; THY
+CS-HA  367.0    1.080       changed from 340. bsd on C6H6 nmodes; CYT,URA
+CS-H4  367.0    1.080       changed from 340. bsd on C6H6 nmodes; CYT,URA
+CS-H5  367.0    1.080       changed from 340. bsd on C6H6 nmodes; not assigned
+CS-N*  448.0    1.365       JCC,7,(1986),230; CYT,THY,URA
+CS-OS  480.0    1.240       Junmei et al, 1999
+CQ-H5  367.0    1.080       changed from 340. bsd on C6H6 nmodes; ADE
+CQ-NC  502.0    1.324       JCC,7,(1986),230; ADE
+CT-CT  310.0    1.526       JCC,7,(1986),230; AA, SUGARS
+CX-CT  310.0    1.526       JCC,7,(1986),230; AA, SUGARS (was CT-CT)
+CT-HC  340.0    1.090       changed from 331 bsd on NMA nmodes; AA, SUGARS
+CT-H1  340.0    1.090       changed from 331 bsd on NMA nmodes; AA, RIBOSE
+CX-H1  340.0    1.090       changed from 331 bsd on NMA nmodes; AA, RIBOSE (was CT-H1)
+CT-H2  340.0    1.090       changed from 331 bsd on NMA nmodes; SUGARS
+CT-H3  340.0    1.090       changed from 331 bsd on NMA nmodes; not assigned
+CT-HP  340.0    1.090       changed from 331; AA-lysine, methyl ammonium cation
+CX-HP  340.0    1.090       changed from 331; AA-lysine, methyl ammonium cation (was CT-HP)
+CT-N*  337.0    1.475       JCC,7,(1986),230; ADE,CYT,GUA,THY,URA
+CT-N2  337.0    1.463       JCC,7,(1986),230; ARG
+CT-OH  320.0    1.410       JCC,7,(1986),230; SUGARS
+CT-OS  320.0    1.410       JCC,7,(1986),230; NUCLEIC ACIDS
+C*-HC  367.0    1.080       changed from 340. bsd on C6H6 nmodes, not needed AA
+C*-CB  388.0    1.459       JCC,7,(1986),230; TRP
+C*-CT  317.0    1.495       JCC,7,(1986),230; TRP
+C*-CW  546.0    1.352       JCC,7,(1986),230; TRP
+CB-CN  447.0    1.419       JCC,7,(1986),230; TRP
+CC-CT  317.0    1.504       JCC,7,(1986),230; HIS
+CC-CV  512.0    1.375       JCC,7,(1986),230; HIS(delta)
+CC-CW  518.0    1.371       JCC,7,(1986),230; HIS(epsilon)
+CC-NA  422.0    1.385       JCC,7,(1986),230; HIS
+CC-NB  410.0    1.394       JCC,7,(1986),230; HIS
+CN-NA  428.0    1.380       JCC,7,(1986),230; TRP
+CR-H5  367.0    1.080       changed from 340. bsd on C6H6 nmodes;HIS
+CR-NA  477.0    1.343       JCC,7,(1986),230; HIS
+CR-NB  488.0    1.335       JCC,7,(1986),230; HIS
+CT-N   337.0    1.449       JCC,7,(1986),230; AA
+CX-N   337.0    1.449       JCC,7,(1986),230; AA  (was CT-N)
+CT-N3  367.0    1.471       JCC,7,(1986),230; LYS
+CX-N3  367.0    1.471       JCC,7,(1986),230; LYS (was CT-N3)
+CT-NT  367.0    1.471       for neutral amines 
+CT-S   227.0    1.810       changed from 222.0 based on dimethylS nmodes
+CT-SH  237.0    1.810       changed from 222.0 based on methanethiol nmodes
+CT-CY  400.0    1.458       Howard et al JCC.16,243,1995
+CT-CZ  400.0    1.459       Howard et al JCC,16,243,1995
+CV-H4  367.0    1.080       changed from 340. bsd on C6H6 nmodes; HIS
+CV-NB  410.0    1.394       JCC,7,(1986),230; HIS
+CW-H4  367.0    1.080       changed from 340. bsd on C6H6 nmodes;HIS(epsilon,+)
+CW-NA  427.0    1.381       JCC,7,(1986),230; HIS,TRP
+CY-NY  600.0    1.150       Howard et al JCC,16,243,1995
+CZ-CZ  600.0    1.206       Howard et al JCC,16,243,1995
+CZ-HZ  400.0    1.056       Howard et al JCC,16,243,1995
+OP-P   525.0    1.480       JCC,7,(1986),230; NA PHOSPHATES
+O2-P   525.0    1.480       JCC,7,(1986),230; NA PHOSPHATES
+OH-P   230.0    1.610       JCC,7,(1986),230; NA PHOSPHATES
+OS-P   230.0    1.610       JCC,7,(1986),230; NA PHOSPHATES
+NA-P   250.0    1.840       phosphohistidine
+H -N2  434.0    1.010       JCC,7,(1986),230; ADE,CYT,GUA,ARG
+H -N*  434.0    1.010       for plain unmethylated bases ADE,CYT,GUA,ARG
+H -NA  434.0    1.010       JCC,7,(1986),230; GUA,URA,HIS
+H -N   434.0    1.010       JCC,7,(1986),230; AA
+H -N3  434.0    1.010       JCC,7,(1986),230; LYS    
+H -NT  434.0    1.010       for neutral amines 
+HO-OH  553.0    0.960       JCC,7,(1986),230; SUGARS,SER,TYR
+HO-OS  553.0    0.960       JCC,7,(1986),230; NUCLEOTIDE ENDS
+HS-SH  274.0    1.336       JCC,7,(1986),230; CYS
+S -S   166.0    2.038       JCC,7,(1986),230; CYX   (SCHERAGA)
+F -CT  367.0    1.380       JCC,13,(1992),963;CF4; R0=1.332 FOR CHF3
+Cl-CT  232.0    1.766       6-31g* opt
+Br-CT  159.0    1.944       Junmei et al,99 
+I -CT  148.0    2.166       Junmei et al,99 
+F -CA  386.0    1.359       Junmei et al,99 
+Cl-CA  193.0    1.727       Junmei et al,99 
+I -CA  171.0    2.075       Junmei et al,99 
+Br-CA  172.0    1.890       Junmei et al,99
+EP-O   600.0    0.200       or 0.35
+EP-OH  600.0    0.200       or 0.35
+EP-OS  600.0    0.200       or 0.35
+EP-N3  600.0    0.200       or 0.35
+EP-NT  600.0    0.200       or 0.35
+EP-NB  600.0    0.200       or 0.35 histidines, nucleic acids
+EP-NC  600.0    0.200       or 0.35 nucleic acids
+EP-S   600.0    0.700       cys,cyx,met
+EP-SH  600.0    0.700       cys,cyx
+CI-H1  340.0    1.090       parmbsc0
+CI-CT  310.0    1.526       parmbsc0
+OS-CI  320.0    1.410       parmbsc0
+OH-CI  320.0    1.410       parmbsc0
+C5-H5  367.0    1.080       changed from 340. bsd on C6H6 nmodes; ADE,GUA
+C5-N*  440.0    1.371       JCC,7,(1986),230; ADE,GUA
+C5-NB  529.0    1.304       JCC,7,(1986),230; ADE,GUA
+C -C4  410.0    1.444       JCC,7,(1986),230; THY,URA
+CA-C4  427.0    1.433       JCC,7,(1986),230; CYT
+C4-C4  549.0    1.350       JCC,7,(1986),230; CYT,THY,URA
+C4-CT  317.0    1.510       JCC,7,(1986),230; THY
+C4-HA  367.0    1.080       changed from 340. bsd on C6H6 nmodes; CYT,URA
+C4-H4  367.0    1.080       changed from 340. bsd on C6H6 nmodes; CYT,URA
+C4-N*  448.0    1.365       JCC,7,(1986),230; CYT,THY,URA
+
+C -C -O     80.0      120.00    Junmei et al, 1999 acrolein
+C -C -OH    80.0      120.00    Junmei et al, 1999
+CA-C -CA    63.0      120.00    changed from 85.0  bsd on C6H6 nmodes; AA
+CA-C -OH    70.0      120.00    AA (not used in tyr)
+CA-C -OS    70.0      120.00    phosphotyrosine
+CC-NA-P     76.7      125.10    phosphohistidine
+CR-NA-P     76.7      125.10    phosphohistidine
+NA-P -OP    42.9      102.38    phosphohistidine
+CB-C -NA    70.0      111.30    NA
+CB-C -O     80.0      128.80
+CM-C -NA    70.0      114.10
+CM-C -O     80.0      125.30
+CS-C -NA    70.0      114.10
+CS-C -O     80.0      125.30
+CT-C -O     80.0      120.40
+CX-C -O     80.0      120.40    (was CT-C-O)
+CT-C -O2    70.0      117.00
+CX-C -O2    70.0      117.00    (was CT-C -O2)
+CT-C -N     70.0      116.60    AA general
+CX-C -N     70.0      116.60    AA general  (was CT-C-N)
+CT-C -CT    63.0      117.00    Junmei et al, 1999
+CT-C -OS    80.0      115.00    Junmei et al, 1999
+CT-C -OH    80.0      110.00    Junmei et al, 1999
+CX-C -OH    80.0      110.00    Junmei et al, 1999 (was CT-C-OH)
+N*-C -NA    70.0      115.40
+N*-C -NC    70.0      118.60
+N*-C -O     80.0      120.90
+NA-C -O     80.0      120.60
+NC-C -O     80.0      122.50
+N -C -O     80.0      122.90    AA general
+O -C -O     80.0      126.00    AA COO- terminal residues
+O -C -OH    80.0      120.00    (check with Junmei for: theta0:120.0?)
+O -C -OS    80.0      125.00    Junmei et al, 1999
+O2-C -O2    80.0      126.00    AA GLU            (SCH JPC 79,2379)
+H4-C -C     50.0      120.00    Junmei et al, 1999 
+H4-C -CM    50.0      115.00    Junmei et al, 1999 
+H4-C -CS    50.0      115.00    Junmei et al, 1999 
+H4-C -CT    50.0      115.00    Junmei et al, 1999
+H4-C -O     50.0      120.00    Junmei et al, 1999
+H4-C -OH    50.0      120.00    Junmei et al, 1999
+H5-C -N     50.0      120.00    Junmei et al, 1999
+H5-C -O     50.0      119.00    Junmei et al, 1999
+H5-C -OH    50.0      107.00    Junmei et al, 1999
+H5-C -OS    50.0      107.00    Junmei et al, 1999
+C -CA-CA    63.0      120.00    changed from 85.0  bsd on C6H6 nmodes
+C -CA-HA    50.0      120.00    AA (not used in tyr)
+CA-CA-CA    63.0      120.00    changed from 85.0  bsd on C6H6 nmodes
+CA-CA-CB    63.0      120.00    changed from 85.0  bsd on C6H6 nmodes
+CA-CA-CT    70.0      120.00
+CA-CA-HA    50.0      120.00
+CA-CA-H4    50.0      120.00
+CA-CA-OH    70.0      120.00    replacement in tyr
+CA-CA-CN    63.0      120.00    changed from 85.0  bsd on C6H6 nmodes; AA trp
+CB-CA-HA    50.0      120.00
+CB-CA-H4    50.0      120.00
+CB-CA-N2    70.0      123.50
+CB-CA-NC    70.0      117.30
+CM-CA-N2    70.0      120.10
+CM-CA-NC    70.0      121.50
+CS-CA-N2    70.0      120.10
+CS-CA-NC    70.0      121.50
+CN-CA-HA    50.0      120.00    AA trp
+NA-CA-NC    70.0      123.30
+N2-CA-NA    70.0      116.00
+N2-CA-NC    70.0      119.30
+N2-CA-N2    70.0      120.00    AA arg
+F -CA-CA    70.0      121.00    Junmei et al,99 
+Cl-CA-CA    70.0      118.80    Junmei et al,99 
+Br-CA-CA    70.0      118.80    Junmei et al,99
+I -CA-CA    70.0      118.80    Junmei et al,99 
+C -CB-CB    63.0      119.20    changed from 85.0  bsd on C6H6 nmodes; NA gua
+C -CB-NB    70.0      130.00
+CA-CB-CB    63.0      117.30    changed from 85.0  bsd on C6H6 nmodes; NA ade
+CA-CB-NB    70.0      132.40    
+CB-CB-N*    70.0      106.20
+CB-CB-NB    70.0      110.40
+CB-CB-NC    70.0      127.70
+C*-CB-CA    63.0      134.90    changed from 85.0  bsd on C6H6 nmodes; AA trp
+C*-CB-CN    63.0      108.80    changed from 85.0  bsd on C6H6 nmodes; AA trp
+CA-CB-CN    63.0      116.20    changed from 85.0  bsd on C6H6 nmodes; AA trp
+N*-CB-NC    70.0      126.20
+CD-CD-CM    63.0      120.00    Junmei et al, 1999
+CD-CD-CS    63.0      120.00    Junmei et al, 1999
+CD-CD-CT    70.0      120.00    Junmei et al, 1999
+CM-CD-CT    70.0      120.00    Junmei et al, 1999
+CS-CD-CT    70.0      120.00    Junmei et al, 1999
+HA-CD-HA    35.0      119.00    Junmei et al, 1999
+HA-CD-CD    50.0      120.00    Junmei et al, 1999
+HA-CD-CM    50.0      120.00    Junmei et al, 1999
+HA-CD-CS    50.0      120.00    Junmei et al, 1999
+H5-CK-N*    50.0      123.05
+H5-CK-NB    50.0      123.05
+N*-CK-NB    70.0      113.90
+H5-CP-N*    50.0      123.05
+H5-CP-NB    50.0      123.05
+N*-CP-NB    70.0      113.90
+C -CM-CM    63.0      120.70    changed from 85.0  bsd on C6H6 nmodes; NA thy
+C -CM-CT    70.0      119.70
+C -CM-HA    50.0      119.70
+C -CM-H4    50.0      119.70
+CA-CM-CM    63.0      117.00    changed from 85.0  bsd on C6H6 nmodes; NA cyt
+CA-CM-HA    50.0      123.30
+CA-CM-H4    50.0      123.30
+CM-CM-CT    70.0      119.70
+CM-CM-HA    50.0      119.70
+CM-CM-H4    50.0      119.70
+CM-CM-N*    70.0      121.20
+CM-CM-OS    80.0      125.00    Junmei et al, 1999
+H4-CM-N*    50.0      119.10
+H4-CM-OS    50.0      113.00    Junmei et al, 1999
+HA-CM-HA    35.0      120.00    Junmei et al, 1999
+HA-CM-CD    50.0      120.00    Junmei et al, 1999
+HA-CM-CT    50.0      120.00    Junmei et al, 1999
+C -CS-CS    63.0      120.70    changed from 85.0  bsd on C6H6 nmodes; NA thy
+C -CS-CT    70.0      119.70
+C -CS-HA    50.0      119.70
+C -CS-H4    50.0      119.70
+CA-CS-CS    63.0      117.00    changed from 85.0  bsd on C6H6 nmodes; NA cyt
+CA-CS-HA    50.0      123.30
+CA-CS-H4    50.0      123.30
+CM-CS-CT    70.0      119.70
+CS-CS-HA    50.0      119.70
+CS-CS-H4    50.0      119.70
+CS-CS-N*    70.0      121.20
+CS-CS-OS    80.0      125.00    Junmei et al, 1999
+H4-CS-N*    50.0      119.10
+H4-CS-OS    50.0      113.00    Junmei et al, 1999
+HA-CS-HA    35.0      120.00    Junmei et al, 1999
+HA-CS-CD    50.0      120.00    Junmei et al, 1999
+HA-CS-CT    50.0      120.00    Junmei et al, 1999
+NC-CQ-NC    70.0      129.10
+H5-CQ-NC    50.0      115.45
+H1-CT-H1    35.0      109.50
+H1-CX-H1    35.0      109.50    (was H1-CT-H1)
+H1-CT-N*    50.0      109.50    changed based on NMA nmodes
+H1-CT-OH    50.0      109.50    changed based on NMA nmodes 
+H1-CT-OS    50.0      109.50    changed based on NMA nmodes 
+H1-CT-CM    50.0      109.50    Junmei et al, 1999 
+H1-CT-CS    50.0      109.50    Junmei et al, 1999 
+H1-CT-CY    50.0      110.00    Junmei et al, 1999
+H1-CT-CZ    50.0      110.00    Junmei et al, 1999
+H1-CT-N     50.0      109.50    AA general  changed based on NMA nmodes
+H1-CX-N     50.0      109.50    AA general  (was H1-CT-N)
+H1-CT-S     50.0      109.50    AA cys     changed based on NMA nmodes
+H1-CT-SH    50.0      109.50    AA cyx     changed based on NMA nmodes
+H1-CT-N2    50.0      109.50    AA arg     changed based on NMA nmodes
+H1-CT-NT    50.0      109.50    neutral amines 
+H2-CT-H2    35.0      109.50    AA lys
+H2-CT-N*    50.0      109.50    changed based on NMA nmodes
+H2-CT-OS    50.0      109.50    changed based on NMA nmodes
+HP-CT-HP    35.0      109.50    AA lys, ch3nh4+
+HP-CX-HP    35.0      109.50    AA lys, ch3nh4+ (was HP-CT-HP)
+HP-CT-N3    50.0      109.50    AA lys, ch3nh3+, changed based on NMA nmodes
+HP-CX-N3    50.0      109.50    AA lys, ch3nh3+, changed based on NMA nmodes (was HP-CT-N3)
+HC-CT-HC    35.0      109.50
+HC-CT-CM    50.0      109.50    changed based on NMA nmodes
+HC-CT-CS    50.0      109.50    changed based on NMA nmodes
+HC-CT-CD    50.0      109.50    Junmei et al, 1999
+HC-CT-CZ    50.0      110.00    Junmei et al, 1999
+C -CT-H1    50.0      109.50    AA general  changed based on NMA nmodes
+C -CX-H1    50.0      109.50    AA general  (was C-CT-H1)
+C -CT-HP    50.0      109.50    AA zwitterion  changed based on NMA nmodes
+C -CX-HP    50.0      109.50    AA zwitterion  changed based on NMA nmodes (was C -CT-HP)
+C -CT-HC    50.0      109.50    AA gln      changed based on NMA nmodes
+C -CT-N     63.0      110.10    AA general
+C -CX-N     63.0      110.10    AA general  (was C-CT-N)
+C -CT-N3    80.0      111.20    AA amino terminal residues
+C -CX-N3    80.0      111.20    AA amino terminal residues (was C -CT-N3)
+C -CT-CT    63.0      111.10    AA general
+C -CT-CX    63.0      111.10    AA general (was C -CT-CT)
+C -CX-CT    63.0      111.10    AA general  (was C-CT-CT)
+C -CT-OS    60.0      109.50    Junmei et al, 1999
+CA-CT-HC    50.0      109.50    AA tyr     changed based on NMA nmodes
+CC-CT-CT    63.0      113.10    AA his
+CC-CT-CX    63.0      113.10    AA his (was CC-CT-CT)
+CC-CT-HC    50.0      109.50    AA his     changed based on NMA nmodes
+CM-CT-CT    63.0      111.00    Junmei et al, 1999 (last change: Mar24,99)
+CM-CT-OS    50.0      109.50    Junmei et al, 1999
+CS-CT-CT    63.0      111.00    Junmei et al, 1999 (last change: Mar24,99)
+CS-CT-OS    50.0      109.50    Junmei et al, 1999
+CT-CT-CT    40.0      109.50
+CT-CT-CX    40.0      109.50    (was CT-CT-CT)
+CT-CT-HC    50.0      109.50    changed based on NMA nmodes
+CX-CT-HC    50.0      109.50    changed based on NMA nmodes (was CT-CT-HC)
+CT-CT-H1    50.0      109.50    changed based on NMA nmodes
+CT-CX-H1    50.0      109.50    changed based on NMA nmodes (was CT-CT-H1)
+CX-CT-H1    50.0      109.50    changed based on NMA nmodes (was CT-CT-H1)
+CT-CT-H2    50.0      109.50    changed based on NMA nmodes
+CT-CT-HP    50.0      109.50    changed based on NMA nmodes
+CT-CX-HP    50.0      109.50    changed based on NMA nmodes (was CT-CT-HP)
+CT-CT-N*    50.0      109.50
+CT-CT-OH    50.0      109.50
+CX-CT-OH    50.0      109.50    (was CT-CT-OH)
+CT-CT-OS    50.0      109.50
+CT-CT-S     50.0      114.70    AA cyx            (SCHERAGA  JPC 79,1428)
+CX-CT-S     50.0      114.70    AA cyx            (SCHERAGA  JPC 79,1428) (was CT-CT-S )
+CT-CT-SH    50.0      108.60    AA cys
+CX-CT-SH    50.0      108.60    AA cys (was CT-CT-SH)
+CT-CT-CA    63.0      114.00    AA phe tyr          (SCH JPC  79,2379)
+CX-CT-CA    63.0      114.00    AA phe tyr          (SCH JPC  79,2379) (was CT-CT-CA)
+CT-CT-N2    80.0      111.20    AA arg             (JCP 76, 1439)
+CT-CT-N     80.0      109.70    AA ala, general    (JACS 94, 2657)
+CT-CX-N     80.0      109.70    AA ala, general    (was CT-CT-N)
+CT-CT-N3    80.0      111.20    AA lys             (JCP 76, 1439)
+CT-CX-N3    80.0      111.20    AA lys             (JCP 76, 1439) (was CT-CT-N3)
+CT-CT-NT    80.0      111.20    neutral amines 
+CT-CT-CY    63.0      110.00    Junmei et al, 1999    
+CT-CT-CZ    63.0      110.00    Junmei et al, 1999
+C*-CT-CT    63.0      115.60    AA trp
+C*-CT-CX    63.0      115.60    AA trp (was C*-CT-CT)
+C*-CT-HC    50.0      109.50    AA trp    changed based on NMA nmodes
+OS-CT-OS   160.0      101.00    Junmei et al, 1999
+OS-CT-CY    50.0      110.00    Junmei et al, 1999
+OS-CT-CZ    50.0      110.00    Junmei et al, 1999
+OS-CT-N*    50.0      109.50
+F -CT-F     77.0      109.10    JCC,13,(1992),963;
+F -CT-H1    50.0      109.50    JCC,13,(1992),963;
+F -CT-CT    50.0      109.00    
+F -CT-H2    50.0      109.50  
+Cl-CT-CT    50.0      108.50    (6-31g* opt value)
+Cl-CT-H1    50.0      108.50    (6-31g* opt value)  
+Br-CT-CT    50.0      108.00    Junmei et al 99 
+Br-CT-H1    50.0      106.50    Junmei et al 99 
+I -CT-CT    50.0      106.00    Junmei et al,99 
+CT-CC-NA    70.0      120.00    AA his
+CT-CC-CV    70.0      120.00    AA his
+CT-CC-NB    70.0      120.00    AA his
+CV-CC-NA    70.0      120.00    AA his
+CW-CC-NA    70.0      120.00    AA his
+CW-CC-NB    70.0      120.00    AA his
+CT-CC-CW    70.0      120.00    AA his
+H5-CR-NA    50.0      120.00    AA his
+H5-CR-NB    50.0      120.00    AA his
+NA-CR-NA    70.0      120.00    AA his
+NA-CR-NB    70.0      120.00    AA his
+CC-CV-H4    50.0      120.00    AA his
+CC-CV-NB    70.0      120.00    AA his
+H4-CV-NB    50.0      120.00    AA his
+CC-CW-H4    50.0      120.00    AA his
+CC-CW-NA    70.0      120.00    AA his
+C*-CW-H4    50.0      120.00    AA trp
+C*-CW-NA    70.0      108.70    AA trp
+H4-CW-NA    50.0      120.00    AA his
+CB-C*-CT    70.0      128.60    AA trp
+CB-C*-CW    63.0      106.40    changed from 85.0  bsd on C6H6 nmodes; AA trp
+CT-C*-CW    70.0      125.00    AA trp
+CA-CN-CB    63.0      122.70    changed from 85.0  bsd on C6H6 nmodes; AA trp
+CA-CN-NA    70.0      132.80    AA trp
+CB-CN-NA    70.0      104.40    AA trp
+CT-CY-NY    80.0      180.00    Junmei et al, 1999
+CT-CZ-CZ    80.0      180.00    Junmei et al, 1999
+CZ-CZ-HZ    50.0      180.00    Junmei et al, 1999
+C -N -CT    50.0      121.90    AA general
+C -N -CX    50.0      121.90    AA general  (was C-N-CT)
+C -N -H     50.0      120.00    AA general, gln, asn,changed based on NMA nmodes
+CT-N -H     50.0      118.04    AA general,     changed based on NMA nmodes
+CX-N -H     50.0      118.04    AA general,     (was CT-N-H)
+CT-N -CT    50.0      118.00    AA pro             (DETAR JACS 99,1232)
+CT-N -CX    50.0      118.00    AA pro             (DETAR JACS 99,1232) (was CT-N -CT)
+H -N -H     35.0      120.00    ade,cyt,gua,gln,asn     **
+C -N*-CM    70.0      121.60
+C -N*-CS    70.0      121.60
+C -N*-CT    70.0      117.60
+C -N*-H     50.0      119.20    changed based on NMA nmodes
+CB-N*-CK    70.0      105.40
+CB-N*-CP    70.0      105.40
+CB-N*-CT    70.0      125.80
+CB-N*-H     50.0      125.80    for unmethylated n.a. bases,chngd bsd NMA nmodes
+CK-N*-CT    70.0      128.80
+CK-N*-H     50.0      128.80    for unmethylated n.a. bases,chngd bsd NMA nmodes
+CP-N*-CT    70.0      128.80
+CP-N*-H     50.0      128.80    for unmethylated n.a. bases,chngd bsd NMA nmodes
+CM-N*-CT    70.0      121.20
+CM-N*-H     50.0      121.20    for unmethylated n.a. bases,chngd bsd NMA nmodes
+CS-N*-CT    70.0      121.20
+CS-N*-H     50.0      121.20    for unmethylated n.a. bases,chngd bsd NMA nmodes
+CA-N2-H     50.0      120.00    
+CA-N2-CT    50.0      123.20    AA arg
+CT-N2-H     50.0      118.40    AA arg
+H -N2-H     35.0      120.00    
+CT-N3-H     50.0      109.50    AA lys,     changed based on NMA nmodes
+CX-N3-H     50.0      109.50    AA lys,     changed based on NMA nmodes (was CT-N3-H )
+CT-N3-CT    50.0      109.50    AA pro/nt
+CT-N3-CX    50.0      109.50    AA pro/nt (was CT-N3-CT)
+H -N3-H     35.0      109.50    AA lys, AA(end)
+CT-NT-H     50.0      109.50    neutral amines 
+CT-NT-CT    50.0      109.50    neutral amines 
+H -NT-H     35.0      109.50    neutral amines 
+C -NA-C     70.0      126.40
+C -NA-CA    70.0      125.20
+C -NA-H     50.0      116.80    changed based on NMA nmodes
+CA-NA-H     50.0      118.00    changed based on NMA nmodes
+CC-NA-CR    70.0      120.00    AA his
+CC-NA-H     50.0      120.00    AA his,    changed based on NMA nmodes
+CR-NA-CW    70.0      120.00    AA his
+CR-NA-H     50.0      120.00    AA his,    changed based on NMA nmodes
+CW-NA-H     50.0      120.00    AA his,    changed based on NMA nmodes
+CN-NA-CW    70.0      111.60    AA trp
+CN-NA-H     50.0      123.10    AA trp,    changed based on NMA nmodes
+CB-NB-CK    70.0      103.80
+CB-NB-CP    70.0      103.80
+CC-NB-CR    70.0      117.00    AA his
+CR-NB-CV    70.0      117.00    AA his
+C -NC-CA    70.0      120.50
+CA-NC-CB    70.0      112.20
+CA-NC-CQ    70.0      118.60
+CB-NC-CQ    70.0      111.00
+C -OH-HO    50.0      113.00    (not used in tyr anymore)
+CA-OH-HO    50.0      113.00    replacement in tyr
+CT-OH-HO    55.0      108.50
+HO-OH-P     45.0      108.50
+C -OS-CT    60.0      117.00    Junmei et al, 1999
+CM-OS-CT    60.0      117.00    Junmei et al, 1999
+CS-OS-CT    60.0      117.00    Junmei et al, 1999
+CT-OS-CT    60.0      109.50
+CT-OS-P    100.0      120.50
+C -OS-P    100.0      120.50    phosphotyrosine
+P -OS-P    100.0      120.50
+O2-P -OH    45.0      108.23
+O2-P -O2   140.0      119.90
+OP-P -OP   140.0      119.90
+OP-P -OS   100.0      108.23
+O2-P -OS   100.0      108.23
+OH-P -OS    45.0      102.60
+OS-P -OS    45.0      102.60
+CT-S -CT    62.0       98.90    AA met
+CT-S -S     68.0      103.70    AA cyx             (SCHERAGA  JPC 79,1428)
+CT-SH-HS    43.0       96.00    changed from 44.0 based on methanethiol nmodes
+HS-SH-HS    35.0       92.07    AA cys
+CB-NB-EP   150.0       126.0    NA
+CC-NB-EP   150.0       126.0    his,NA
+CK-NB-EP   150.0       126.0    NA
+CP-NB-EP   150.0       126.0    NA
+CR-NB-EP   150.0       126.0    his,NA
+CV-NB-EP   150.0       126.0    his,NA
+C -NC-EP   150.0       120.0    NA
+CA-NC-EP   150.0       120.0    NA
+CB-NC-EP   150.0       120.0    NA
+CQ-NC-EP   150.0       120.0    NA
+CT-N3-EP   150.0       109.5    in neutral lysine
+H -N3-EP   150.0       109.5    in neutral lysine
+CT-NT-EP   150.0       109.5
+H -NT-EP   150.0       109.5
+C -O -EP   150.0       120.0
+EP-O -EP   150.0       120.0
+C -OH-EP   150.0       120.0
+CT-OH-EP   150.0       109.5
+HO-OH-EP   150.0       109.5
+EP-OH-EP   150.0       109.5
+C -OS-EP   150.0       109.5 
+CM-OS-EP   150.0       109.5    methyl vinyl ether
+CS-OS-EP   150.0       109.5    methyl vinyl ether
+CT-OS-EP   150.0       109.5
+EP-OS-EP   150.0       109.5
+CT-S -EP   150.0        90.0    cys,cyx,met
+CT-SH-EP   150.0        90.0    cys,cyx,met
+P -OS-EP   150.0       109.5    NA
+EP-S -EP   150.0       180.0    cys,cyx,met
+EP-SH-EP   150.0       180.0    cys,cyx,met
+HS-SH-EP   150.0        90.0    cys  
+H1-CI-CT    50.0      109.50    parmbsc0
+H1-CI-H1    35.0      109.50    parmbsc0
+CI-CT-H1    50.0      109.50    parmbsc0
+CI-CT-OS    50.0      109.50    parmbsc0
+CI-CT-CT    40.0      109.50    parmbsc0
+OS-CI-H1    50.0      109.50   parmbsc0
+OS-CI-CT    50.0      109.50   parmbsc0
+P -OS-CI   100.0      120.50   parmbsc0
+OH-CI-H1    50.0      109.50   parmbsc0
+OH-CI-CT    50.0      109.50   parmbsc0
+HO-OH-CI    55.0      108.50   parmbsc0
+H5-C5-N*    50.0      123.05
+H5-C5-NB    50.0      123.05
+N*-C5-NB    70.0      113.90
+CB-N*-C5    70.0      105.40
+C5-N*-CT    70.0      128.80
+CB-NB-C5    70.0      103.80
+C4-C -NA    70.0      114.10
+C4-C -O     80.0      125.30
+C4-CA-N2    70.0      120.10
+C4-CA-NC    70.0      121.50
+C -C4-C4    63.0      120.70    changed from 85.0  bsd on C6H6 nmodes; NA thy
+C -C4-CT    70.0      119.70
+C -C4-HA    50.0      119.70
+C -C4-H4    50.0      119.70
+CA-C4-C4    63.0      117.00    changed from 85.0  bsd on C6H6 nmodes; NA cyt
+CA-C4-HA    50.0      123.30
+CA-C4-H4    50.0      123.30
+C4-C4-CT    70.0      119.70
+C4-C4-HA    50.0      119.70
+C4-C4-H4    50.0      119.70
+C4-C4-N*    70.0      121.20
+H4-C4-N*    50.0      119.10
+H1-CT-C4    50.0      109.50    Junmei et al, 1999 
+HC-CT-C4    50.0      109.50    changed based on NMA nmodes
+C -N*-C4    70.0      121.60
+C4-N*-CT    70.0      121.20
+EP-S -S    150.0       96.70    AA cyx (dac, from parm91 LP-S-S)
+
+X -C -C -X    4   14.50        180.0             2.         Junmei et al, 1999
+X -C -CA-X    4   14.50        180.0             2.         intrpol.bsd.on C6H6
+X -C -CB-X    4   12.00        180.0             2.         intrpol.bsd.on C6H6
+X -C -CM-X    4    8.70        180.0             2.         intrpol.bsd.on C6H6
+X -C -CS-X    4    8.70        180.0             2.         intrpol.bsd.on C6H6
+X -C -CT-X    6    0.00          0.0             2.         JCC,7,(1986),230
+X -C -CX-X    6    0.00          0.0             2.         JCC,7,(1986),230 (was X -C -CT-X )
+X -C -N -X    4   10.00        180.0             2.         AA,NMA
+X -C -N*-X    4    5.80        180.0             2.         JCC,7,(1986),230
+X -C -NA-X    4    5.40        180.0             2.         JCC,7,(1986),230
+X -C -NC-X    2    8.00        180.0             2.         JCC,7,(1986),230
+X -C -O -X    4   11.20        180.0             2.         Junmei et al, 1999
+X -C -OH-X    2    4.60        180.0             2.         Junmei et al, 1999
+X -C -OS-X    2    5.40        180.0             2.         Junmei et al, 1999
+X -CA-CA-X    4   14.50        180.0             2.         intrpol.bsd.on C6H6
+X -CA-CB-X    4   14.00        180.0             2.         intrpol.bsd.on C6H6
+X -CA-CM-X    4   10.20        180.0             2.         intrpol.bsd.on C6H6
+X -CA-CS-X    4   10.20        180.0             2.         intrpol.bsd.on C6H6
+X -CA-CN-X    4   14.50        180.0             2.         reinterpolated 93'
+X -CA-CT-X    6    0.00          0.0             2.         JCC,7,(1986),230
+X -CA-N2-X    4    9.60        180.0             2.         reinterpolated 93'
+X -CA-NA-X    4    6.00        180.0             2.         JCC,7,(1986),230
+X -CA-NC-X    2    9.60        180.0             2.         JCC,7,(1986),230
+X -CA-OH-X    2    1.80        180.0             2.         Junmei et al, 99
+X -CB-CB-X    4   21.80        180.0             2.         intrpol.bsd.on C6H6
+X -CB-CN-X    4   12.00        180.0             2.         reinterpolated 93'
+X -CB-N*-X    4    6.60        180.0             2.         JCC,7,(1986),230
+X -CB-NB-X    2    5.10        180.0             2.         JCC,7,(1986),230
+X -CB-NC-X    2    8.30        180.0             2.         JCC,7,(1986),230
+X -CC-CT-X    6    0.00          0.0             2.         JCC,7,(1986),230
+X -CC-CV-X    4   20.60        180.0             2.         intrpol.bsd.on C6H6
+X -CC-CW-X    4   21.50        180.0             2.         intrpol.bsd.on C6H6
+X -CC-NA-X    4    5.60        180.0             2.         JCC,7,(1986),230
+X -CC-NB-X    2    4.80        180.0             2.         JCC,7,(1986),230
+X -CD-CD-X    4    4.00        180.0             2.         Junmei et al, 1999
+X -CD-CT-X    6    0.00          0.0             2.         Junmei et al, 1999
+X -CD-CM-X    4   26.60        180.0             2.         Junmei et al, 1999
+X -CD-CS-X    4   26.60        180.0             2.         Junmei et al, 1999
+X -CK-N*-X    4    6.80        180.0             2.         JCC,7,(1986),230
+X -CK-NB-X    2   20.00        180.0             2.         JCC,7,(1986),230
+X -CP-N*-X    4    6.80        180.0             2.         JCC,7,(1986),230
+X -CP-NB-X    2   20.00        180.0             2.         JCC,7,(1986),230
+X -CM-CM-X    4   26.60        180.0             2.         intrpol.bsd.on C6H6
+X -CM-CT-X    6    0.00          0.0             3.         JCC,7,(1986),230
+X -CM-N*-X    4    7.40        180.0             2.         JCC,7,(1986),230
+X -CM-OS-X    2    2.10        180.0             2.         Junmei et al, 1999
+X -CS-CS-X    4   26.60        180.0             2.         intrpol.bsd.on C6H6
+X -CS-CT-X    6    0.00          0.0             3.         JCC,7,(1986),230
+X -CS-N*-X    4    7.40        180.0             2.         JCC,7,(1986),230
+X -CS-OS-X    2    2.10        180.0             2.         Junmei et al, 1999
+X -CN-NA-X    4    6.10        180.0             2.         reinterpolated 93'
+X -CQ-NC-X    2   13.60        180.0             2.         JCC,7,(1986),230
+X -CT-CT-X    9    1.40          0.0             3.         JCC,7,(1986),230
+X -CT-CX-X    9    1.40          0.0             3.         JCC,7,(1986),230 (was X -CT-CT-X )
+X -CT-CY-X    3    0.00          0.0             1.         Junmei et al, 1999
+X -CT-CZ-X    3    0.00          0.0             1.         Junmei et al, 1999
+X -CT-N -X    6    0.00          0.0             2.         JCC,7,(1986),230
+X -CX-N -X    6    0.00          0.0             2.         JCC,7,(1986),230 (was X -CT-N -X )
+X -CT-N*-X    6    0.00          0.0             2.         JCC,7,(1986),230
+X -CT-N2-X    6    0.00          0.0             3.         JCC,7,(1986),230
+X -CT-NT-X    6    1.80          0.0             3.         Junmei et al, 1999
+X -CT-N3-X    9    1.40          0.0             3.         JCC,7,(1986),230
+X -CX-N3-X    9    1.40          0.0             3.         JCC,7,(1986),230 (was X -CT-N3-X )
+X -CT-OH-X    3    0.50          0.0             3.         JCC,7,(1986),230
+X -CT-OS-X    3    1.15          0.0             3.         JCC,7,(1986),230
+X -CT-S -X    3    1.00          0.0             3.         JCC,7,(1986),230
+X -CT-SH-X    3    0.75          0.0             3.         JCC,7,(1986),230
+X -C*-CB-X    4    6.70        180.0             2.         intrpol.bsd.onC6H6aa
+X -C*-CT-X    6    0.00          0.0             2.         JCC,7,(1986),230
+X -C*-CW-X    4   26.10        180.0             2.         intrpol.bsd.on C6H6
+X -CR-NA-X    4    9.30        180.0             2.         JCC,7,(1986),230
+X -CR-NB-X    2   10.00        180.0             2.         JCC,7,(1986),230
+X -CV-NB-X    2    4.80        180.0             2.         JCC,7,(1986),230
+X -CW-NA-X    4    6.00        180.0             2.         JCC,7,(1986),230
+X -OH-P -X    3    0.75          0.0             3.         JCC,7,(1986),230
+X -OS-P -X    3    0.75          0.0             3.         JCC,7,(1986),230
+X -CI-OS-X    3    1.150         0.0             3.
+X -CI-OH-X    3    0.500         0.0             3.
+X -CI-CT-X    9    1.400         0.0             3.
+X -C5-N*-X    4    6.80        180.0             2.         JCC,7,(1986),230
+X -C5-NB-X    2   20.00        180.0             2.         JCC,7,(1986),230
+X -C -C4-X    4    8.70        180.0             2.         intrpol.bsd.on C6H6
+X -CA-C4-X    4   10.20        180.0             2.         intrpol.bsd.on C6H6
+X -C4-C4-X    4   26.60        180.0             2.         intrpol.bsd.on C6H6
+X -C4-CT-X    6    0.00          0.0             3.         JCC,7,(1986),230
+X -C4-N*-X    4    7.40        180.0             2.         JCC,7,(1986),230
+CT-OS-CT-CI   1    0.383         0.0            -3.
+CT-OS-CT-CI   1    0.100       180.0             2.
+H1-CI-CT-OS   1    0.00          0.0            -3.
+H1-CI-CT-OS   1    0.250         0.0             1.
+H1-CI-CT-OH   1    0.000         0.0            -3.
+H1-CI-CT-OH   1    0.250         0.0             1.
+H1-CT-CI-OS   1    0.00          0.0            -3.
+H1-CT-CI-OS   1    0.250         0.0             1.
+H1-CT-CI-OH   1    0.00          0.0            -3.
+H1-CT-CI-OH   1    0.250         0.0             1.
+CI-CT-CT-CT   1    0.180         0.0            -3.
+CI-CT-CT-CT   1    0.250       180.0            -2.
+CI-CT-CT-CT   1    0.200       180.0             1.
+OP-P -OS-CA   1    0.0         180.0            -3.         phosphotyrosine
+OP-P -OS-CA   1    0.0         180.0             1.         phosphotyrosine
+CC-NA-P -OP   1    0.24          0.0             3.         phosphohistidine
+CR-NA-P -OP   1    0.00          0.0             3.         phosphohistidine
+OS-P -OS-CI   1    0.185181     31.79508        -1.         alfa
+OS-P -OS-CI   1    1.256531    351.95960        -2.         alfa
+OS-P -OS-CI   1    0.354858    357.24748         3.         alfa
+OH-P -OS-CI   1    0.185181     31.79508        -1.         alfa
+OH-P -OS-CI   1    1.256531    351.95960        -2.         alfa
+OH-P -OS-CI   1    0.354858    357.24748         3.         alfa
+CT-CT-CI-OS   1    1.178040    190.97653        -1.         gamma
+CT-CT-CI-OS   1    0.092102    295.63279        -2.         gamma
+CT-CT-CI-OS   1    0.962830    348.09535         3.         gamma
+CT-CT-CI-OH   1    1.178040    190.97653        -1.         gamma
+CT-CT-CI-OH   1    0.092102    295.63279        -2.         gamma
+CT-CT-CI-OH   1    0.962830    348.09535         3.         gamma
+HC-CT-C4-C4   1    0.38        180.0            -3.         Junmei et al, 1999
+HC-CT-C4-C4   1    1.15          0.0             1.         Junmei et al, 1999
+C4-C4-C -O    1    2.175       180.0            -2.         Junmei et al, 1999
+C4-C4-C -O    1    0.30          0.0             3.         Junmei et al, 1999
+OS-CT-N*-C5   1    0.96561      68.7902         -1.         ol3 chi ade
+OS-CT-N*-C5   1    1.07403      15.6360         -2.         ol3 chi ade
+OS-CT-N*-C5   1    0.45754     171.5787         -3.         ol3 chi ade
+OS-CT-N*-C5   1    0.30917      19.0921          4.         ol3 chi ade
+OS-CT-N*-CP   1    0.70510      74.7558         -1.         ol3 chi gua
+OS-CT-N*-CP   1    1.06546       6.2286         -2.         ol3 chi gua
+OS-CT-N*-CP   1    0.44273     168.6503         -3.         ol3 chi gua
+OS-CT-N*-CP   1    0.25602       3.9746          4.         ol3 chi gua
+OS-CT-N*-C4   1    1.22506     146.9892         -1.         ol3 chi cyt
+OS-CT-N*-C4   1    1.63459      16.4766         -2.         ol3 chi cyt
+OS-CT-N*-C4   1    0.93747     185.8774         -3.         ol3 chi cyt
+OS-CT-N*-C4   1    0.31033      32.1590          4.         ol3 chi cyt
+OS-CT-N*-CS   1    1.02514     149.8583         -1.         ol3 chi ura
+OS-CT-N*-CS   1    1.74876      16.7648         -2.         ol3 chi ura
+OS-CT-N*-CS   1    0.58150     179.3474         -3.         ol3 chi ura
+OS-CT-N*-CS   1    0.35148      16.0016          4.         ol3 chi ura
+C -N -CX-C    1    0.00          0.0            -4.         four amplitudes and
+C -N -CX-C    1    0.42          0.0            -3.         phases for phi
+C -N -CX-C    1    0.27          0.0            -2.
+C -N -CX-C    1    0.00          0.0             1.
+N -CX-C -N    1    0.00          0.0            -4.         four amplitudes and
+N -CX-C -N    1    0.55        180.0            -3.         phases for psi
+N -CX-C -N    1    1.58        180.0            -2.
+N -CX-C -N    1    0.45        180.0             1.
+CT-CT-N -C    1    0.00          0.0            -4.         four amplitudes and
+CT-CT-N -C    1    0.40          0.0            -3.         phases for phi'
+CT-CT-N -C    1    2.00          0.0            -2.
+CT-CT-N -C    1    2.00          0.0             1.
+CT-CX-N -C    1    0.00          0.0            -4.         four amplitudes and
+CT-CX-N -C    1    0.40          0.0            -3.         phases for phi'
+CT-CX-N -C    1    2.00          0.0            -2.
+CT-CX-N -C    1    2.00          0.0             1.
+CT-CT-C -N    1    0.00          0.0            -4.         four amplitudes and
+CT-CT-C -N    1    0.40          0.0            -3.         phases for psi'
+CT-CT-C -N    1    0.20          0.0            -2.
+CT-CT-C -N    1    0.20          0.0             1.
+CT-CX-C -N    1    0.00          0.0            -4.         four amplitudes and
+CT-CX-C -N    1    0.40          0.0            -3.         phases for psi'
+CT-CX-C -N    1    0.20          0.0            -2.
+CT-CX-C -N    1    0.20          0.0             1.
+CX-CT-C -N    1    0.00          0.0            -4.         four amplitudes and
+CX-CT-C -N    1    0.40          0.0            -3.         phases for psi'
+CX-CT-C -N    1    0.20          0.0            -2.
+CX-CT-C -N    1    0.20          0.0             1.
+H -N -C -O    1    2.50        180.0            -2.         JCC,7,(1986),230
+H -N -C -O    1    2.00          0.0             1.         J.C.cistrans-NMA DE
+CT-S -S -CT   1    3.50          0.0            -2.         JCC,7,(1986),230
+CT-S -S -CT   1    0.60          0.0             3.         JCC,7,(1986),230
+OH-P -OS-CT   1    0.25          0.0            -3.         JCC,7,(1986),230
+OH-P -OS-CT   1    1.20          0.0             2.         gg&gt ene.631g*/mp2
+OS-P -OS-CT   1    0.25          0.0            -3.         JCC,7,(1986),230
+OS-P -OS-CT   1    1.20          0.0             2.         gg&gt ene.631g*/mp2
+H1-CT-C -O    1    0.80          0.0            -1.         Junmei et al, 1999
+H1-CT-C -O    1    0.00          0.0            -2.         Explicit of wild card X-C-CT-X
+H1-CT-C -O    1    0.08        180.0             3.         Junmei et al, 1999
+H1-CX-C -O    1    0.80          0.0            -1.         Junmei et al, 1999 (was H1-CT-C -O )
+H1-CX-C -O    1    0.00          0.0            -2.         Explicit of wild card X-C-CT-X
+H1-CX-C -O    1    0.08        180.0             3.         Junmei et al, 1999 (was H1-CT-C -O )
+HC-CT-C -O    1    0.80          0.0            -1.         Junmei et al, 1999
+HC-CT-C -O    1    0.00          0.0            -2.         Explicit of wild card X-C-CT-X
+HC-CT-C -O    1    0.08        180.0             3.         Junmei et al, 1999
+HC-CT-CT-HC   1    0.15          0.0             3.         Junmei et al, 1999
+HC-CT-CT-CT   1    0.16          0.0             3.         Junmei et al, 1999
+HC-CT-CT-CX   1    0.16          0.0             3.         Junmei et al, 1999 (was HC-CT-CT-CT)
+HC-CT-CM-CM   1    0.38        180.0            -3.         Junmei et al, 1999
+HC-CT-CM-CM   1    1.15          0.0             1.         Junmei et al, 1999
+HC-CT-CS-CS   1    0.38        180.0            -3.         Junmei et al, 1999
+HC-CT-CS-CS   1    1.15          0.0             1.         Junmei et al, 1999
+HO-OH-CT-CT   1    0.16          0.0            -3.         Junmei et al, 1999
+HO-OH-CT-CT   1    0.25          0.0             1.         Junmei et al, 1999
+HO-OH-CT-CX   1    0.16          0.0            -3.         Junmei et al, 1999 (was HO-OH-CT-CT)
+HO-OH-CT-CX   1    0.25          0.0             1.         Junmei et al, 1999 (was HO-OH-CT-CT)
+HO-OH-C -O    1    2.30        180.0            -2.         Junmei et al, 1999
+HO-OH-C -O    1    1.90          0.0             1.         Junmei et al, 1999
+CM-CM-C -O    1    2.175       180.0            -2.         Junmei et al, 1999
+CM-CM-C -O    1    0.30          0.0             3.         Junmei et al, 1999
+CT-CM-CM-CT   1    6.65        180.0            -2.         Junmei et al, 1999
+CT-CM-CM-CT   1    1.90        180.0             1.         Junmei et al, 1999
+CS-CS-C -O    1    2.175       180.0            -2.         Junmei et al, 1999
+CS-CS-C -O    1    0.30          0.0             3.         Junmei et al, 1999
+CT-CS-CS-CT   1    6.65        180.0            -2.         Junmei et al, 1999
+CT-CS-CS-CT   1    1.90        180.0             1.         Junmei et al, 1999
+CT-CT-CT-CT   1    0.18          0.0            -3.         Junmei et al, 1999
+CT-CT-CT-CT   1    0.25        180.0            -2.         Junmei et al, 1999
+CT-CT-CT-CT   1    0.20        180.0             1.         Junmei et al, 1999
+CX-CT-CT-CT   1    0.18          0.0            -3.         Junmei et al, 1999 (was CT-CT-CT-CT)
+CX-CT-CT-CT   1    0.25        180.0            -2.         Junmei et al, 1999 (was CT-CT-CT-CT)
+CX-CT-CT-CT   1    0.20        180.0             1.         Junmei et al, 1999 (was CT-CT-CT-CT)
+CT-CT-NT-CT   1    0.30          0.0            -3.         Junmei et al, 1999
+CT-CT-NT-CT   1    0.48        180.0             2.         Junmei et al, 1999
+CT-CT-OS-CT   1    0.383         0.0            -3.
+CT-CT-OS-CT   1    0.1         180.0             2.
+CT-CT-OS-C    1    0.383         0.0            -3.         Junmei et al, 1999
+CT-CT-OS-C    1    0.80        180.0             1.         Junmei et al, 1999
+CT-OS-CT-OS   1    0.10          0.0            -3.         Junmei et al, 1999
+CT-OS-CT-OS   1    0.85        180.0            -2.         Junmei et al, 1999
+CT-OS-CT-OS   1    1.35        180.0             1.         Junmei et al, 1999
+CT-OS-CT-N*   1    0.383         0.0            -3.         parm98.dat, TC,PC,PAK
+CT-OS-CT-N*   1    0.65          0.0             2.         Piotr et al.
+CT-CZ-CZ-HZ   1    0.00          0.0             1.         Junmei et al, 1999
+O -C -OS-CT   1    2.70        180.0            -2.         Junmei et al, 1999
+O -C -OS-CT   1    1.40        180.0             1.         Junmei et al, 1999
+OS-CT-N*-CK   1    0.00        000.0            -2.         parm98, TC,PC,PAK
+OS-CT-N*-CK   1    2.50          0.0             1.         parm98, TC,PC,PAK
+OS-CT-N*-CM   1    0.00        000.0            -2.         parm98, TC,PC,PAK
+OS-CT-N*-CM   1    2.50          0.0             1.         parm98, TC,PC,PAK
+OS-CT-CT-OS   1    0.144         0.0            -3.         parm98, TC,PC,PAK
+OS-CT-CT-OS   1    1.175         0.0             2.         Piotr et al.     
+OS-CT-CT-OH   1    0.144         0.0            -3.         parm98, TC,PC,PAK
+OS-CT-CT-OH   1    1.175         0.0             2.         parm98, TC,PC,PAK
+OH-CT-CT-OH   1    0.144         0.0            -3.         parm98, TC,PC,PAK
+OH-CT-CT-OH   1    1.175         0.0             2.         parm98, TC,PC,PAK 
+F -CT-CT-F    1    0.000         0.0            -3.         JCC,7,(1986),230
+F -CT-CT-F    1    1.20        180.0             1.         Junmei et al, 1999
+Cl-CT-CT-Cl   1    0.000         0.0            -3.         JCC,7,(1986),230
+Cl-CT-CT-Cl   1    0.45        180.0             1.         Junmei et al, 1999
+Br-CT-CT-Br   1    0.000         0.0            -3.         JCC,7,(1986),230
+Br-CT-CT-Br   1    0.00        180.0             1.         Junmei et al, 1999
+H1-CT-CT-OS   1    0.000         0.0            -3.         JCC,7,(1986),230
+H1-CT-CT-OS   1    0.25          0.0             1.         Junmei et al, 1999
+H1-CT-CT-OH   1    0.000         0.0            -3.         JCC,7,(1986),230
+H1-CT-CT-OH   1    0.25          0.0             1.         Junmei et al, 1999
+H1-CX-CT-OH   1    0.000         0.0            -3.         JCC,7,(1986),230 (was H1-CT-CT-OH)
+H1-CX-CT-OH   1    0.25          0.0             1.         Junmei et al, 1999 (was H1-CT-CT-OH)
+H1-CT-CT-F    1    0.000         0.0            -3.         JCC,7,(1986),230
+H1-CT-CT-F    1    0.19          0.0             1.         Junmei et al, 1999
+H1-CT-CT-Cl   1    0.000         0.0            -3.         JCC,7,(1986),230
+H1-CT-CT-Cl   1    0.25          0.0             1.         Junmei et al, 1999
+H1-CT-CT-Br   1    0.000         0.0            -3.         JCC,7,(1986),230
+H1-CT-CT-Br   1    0.55          0.0             1.         Junmei et al, 1999
+HC-CT-CT-OS   1    0.000         0.0            -3.         JCC,7,(1986),230
+HC-CT-CT-OS   1    0.25          0.0             1.         Junmei et al, 1999
+HC-CT-CT-OH   1    0.000         0.0            -3.         JCC,7,(1986),230
+HC-CT-CT-OH   1    0.25          0.0             1.         Junmei et al, 1999
+HC-CT-CT-F    1    0.000         0.0            -3.         JCC,7,(1986),230
+HC-CT-CT-F    1    0.19          0.0             1.         Junmei et al, 1999
+HC-CT-CT-Cl   1    0.000         0.0            -3.         JCC,7,(1986),230
+HC-CT-CT-Cl   1    0.25          0.0             1.         Junmei et al, 1999
+HC-CT-CT-Br   1    0.000         0.0            -3.         JCC,7,(1986),230
+HC-CT-CT-Br   1    0.55          0.0             1.         Junmei et al, 1999
+H1-CT-NT-EP   1    0.000         0.000           3.000
+CT-CT-NT-EP   1    0.000         0.000           3.000
+CT-C -N -EP   1    0.000       180.000           2.000
+O -C -N -EP   1    0.000       180.000           2.000
+H1-CT-OH-EP   1    0.000         0.000           3.000
+CT-CT-OH-EP   1    0.000         0.000           3.000
+H1-CT-OS-EP   1    0.000         0.000           3.000
+H2-CT-OS-EP   1    0.000         0.000           3.000
+CT-CT-OS-EP   1    0.000         0.000           3.000
+CM-CM-OS-EP   1    0.000       180.000           2.000
+HA-CM-OS-EP   1    0.000       180.000           2.000
+H4-CM-OS-EP   1    0.000       180.000           2.000
+CS-CS-OS-EP   1    0.000       180.000           2.000
+HA-CS-OS-EP   1    0.000       180.000           2.000
+H4-CS-OS-EP   1    0.000       180.000           2.000
+N -CT-CT-OH   1    0.000         0.000          -1.         HYP
+N -CT-CT-OH   1    1.490         0.000          -2.         HYP  (JCC 26:1612,2005)
+N -CT-CT-OH   1    0.156         0.000          -3.         HYP
+N -CT-CT-OH   1    0.000         0.000           4.         HYP
+EP-S -S -CT   1    0.00          0.0             3.         cyx (dac)
+EP-S -S -EP   1    0.00          0.0             3.         cyx (dac)
+
+X -X -C -O          10.5         180.          2.           JCC,7,(1986),230
+X -O2-C -O2         10.5         180.          2.           JCC,7,(1986),230
+X -X -N -H          1.0          180.          2.           JCC,7,(1986),230
+X -X -N2-H          1.0          180.          2.           JCC,7,(1986),230
+X -X -NA-H          1.0          180.          2.           JCC,7,(1986),230
+X -N2-CA-N2         10.5         180.          2.           JCC,7,(1986),230
+X -CT-N -CT         1.0          180.          2.           JCC,7,(1986),230
+X -CT-N -CX         1.0          180.          2.           JCC,7,(1986),230 (was X -CT-N -CT)
+X -X -CA-HA         1.1          180.          2.           bsd.on C6H6 nmodes
+X -X -CW-H4         1.1          180.          2.
+X -X -CR-H5         1.1          180.          2.
+X -X -CV-H4         1.1          180.          2.
+X -X -CQ-H5         1.1          180.          2.
+X -X -CK-H5         1.1          180.          2.
+X -X -CP-H5         1.1          180.          2.
+X -X -CM-H4         1.1          180.          2.
+X -X -CM-HA         1.1          180.          2.
+X -X -CS-H4         1.1          180.          2.
+X -X -CS-HA         1.1          180.          2.
+X -X -CA-H4         1.1          180.          2.           bsd.on C6H6 nmodes 
+X -X -CA-H5         1.1          180.          2.           bsd.on C6H6 nmodes
+CB-CK-N*-CT         1.0          180.          2.
+CB-CP-N*-CT         1.0          180.          2.
+C -CM-N*-CT         1.0          180.          2.           dac guess, 9/94
+C -CS-N*-CT         1.0          180.          2.           dac guess, 9/94
+C -CS-CM-CT         1.1          180.          2. 
+CT-O -C -OH         10.5         180.          2.
+CT-CV-CC-NA         1.1          180.          2.
+CT-CW-CC-NB         1.1          180.          2.
+CT-CW-CC-NA         1.1          180.          2.
+CB-CT-C*-CW         1.1          180.          2.
+CA-CA-CA-CT         1.1          180.          2. 
+C -CM-CM-CT         1.1          180.          2.           dac guess, 9/94
+C -CS-CS-CT         1.1          180.          2.           dac guess, 9/94
+CM-N2-CA-NC         1.1          180.          2.           dac guess, 9/94
+CS-N2-CA-NC         1.1          180.          2.           dac guess, 9/94
+CB-N2-CA-NC         1.1          180.          2.           dac, 10/94
+N2-NA-CA-NC         1.1          180.          2.           dac, 10/94
+CA-CA-C -OH         1.1          180.          2.           (not used in tyr!)
+CA-CA-CA-OH         1.1          180.          2.           in tyr
+H5-O -C -OH         1.1          180.          2.           Junmei et al.1999
+H5-O -C -OS         1.1          180.          2.           
+CM-CT-CM-HA         1.1          180.          2.           Junmei et al.1999
+CS-CT-CS-HA         1.1          180.          2.           Junmei et al.1999
+Br-CA-CA-CA         1.1          180.          2.           Junmei et al.1999
+CM-H4-C -O          1.1          180.          2.           Junmei et al.1999
+CS-H4-C -O          1.1          180.          2.           Junmei et al.1999
+C -CT-N -H          1.1          180.          2.           Junmei et al.1999
+C -CX-N -H          1.1          180.          2.           Junmei et al.1999 (was C -CT-N -H )
+C -CT-N -O          1.1          180.          2.           Junmei et al.1999
+X -X -C5-H5         1.1          180.          2.
+CB-C5-N*-CT         1.0          180.          2.
+X -X -C4-H4         1.1          180.          2.
+X -X -C4-HA         1.1          180.          2.
+C -C4-N*-CT         1.0          180.          2.           dac guess, 9/94
+C -C4-C4-CT         1.1          180.          2.           dac guess, 9/94
+C4-N2-CA-NC         1.1          180.          2.           dac guess, 9/94
+CA-CA-C -OS         1.1          180.          2.           phosphotyrosine
+CR-CC-NA-P          1.1          180.          2.           phosphohistine
+C*-CN-CB-CA         0.0          180.          2.           # zero improper for rings
+NA-CA-CN-CB         0.0          180.          2.           # that were not defined 
+N*-CB-CB-NC         0.0          180.          2.           # before
+NB-C -CB-CB         0.0          180.          2.
+NB-CA-CB-CB         0.0          180.          2.
+OH-H1-CJ-H1         0.0          180.          2.
+OH-H1-CJ-CT         0.0          180.          2.
+H1-H1-CJ-CT         0.0          180.          2.
+OS-H1-CJ-H1         0.0          180.          2.
+OS-H1-CJ-CT         0.0          180.          2.
+ 
+
+N   NA  N2  N*  NC  NB  NT  NY
+C*  CA  CB  CC  CD  CK  CM  CN  CQ  CR  CV  CW  CY  CZ  CP  CS
+
+MOD4      RE
+  H           0.6000  0.0157            !Ferguson base pair geom.
+  HO          0.0000  0.0000             OPLS Jorgensen, JACS,110,(1988),1657
+  HS          0.6000  0.0157             W. Cornell CH3SH --> CH3OH FEP
+  HC          1.4870  0.0157             OPLS
+  H1          1.3870  0.0157             Veenstra et al JCC,8,(1992),963 
+  H2          1.2870  0.0157             Veenstra et al JCC,8,(1992),963 
+  H3          1.1870  0.0157             Veenstra et al JCC,8,(1992),963 
+  HP          1.1000  0.0157             Veenstra et al JCC,8,(1992),963
+  HA          1.4590  0.0150             Spellmeyer 
+  H4          1.4090  0.0150             Spellmeyer, one electrowithdr. neighbor
+  H5          1.3590  0.0150             Spellmeyer, two electrowithdr. neighbor
+  HZ          1.4590  0.0150             H bonded to sp C (Howard et al JCC 16)
+  O           1.6612  0.2100             OPLS
+  O2          1.6612  0.2100             OPLS
+  OH          1.7210  0.2104             OPLS 
+  OS          1.6837  0.1700             OPLS ether
+  OP          1.8500  0.1700             Steinbrecher/Latzer for 2- phosphate
+  C*          1.9080  0.0860             Spellmeyer
+  CI          1.9080  0.1094             parmbsc0
+  C5          1.9080  0.0860             Spellmeyer
+  C4          1.9080  0.0860             Spellmeyer
+  CT          1.9080  0.1094             Spellmeyer
+  CX          1.9080  0.1094             Spellmeyer  (was CT)
+  C           1.9080  0.0860             OPLS
+  N           1.8240  0.1700             OPLS
+  N3          1.8240  0.1700             OPLS
+  S           2.0000  0.2500             W. Cornell CH3SH and CH3SCH3 FEP's
+  SH          2.0000  0.2500             W. Cornell CH3SH and CH3SCH3 FEP's
+  P           2.1000  0.2000             JCC,7,(1986),230; 
+  MG          0.7926  0.8947             Mg2+ Aqvist JPC 1990,94,8021.(adapted)
+  C0          1.7131  0.459789           Ca2+ Aqvist JPC 1990,94,8021.(adapted)
+  F           1.75    0.061              Gough et al. JCC 13,(1992),963.
+  Cl          1.948   0.265              Fox, JPCB,102,8070,(98),flex.mdl CHCl3
+  Br          2.22    0.320              Junmei(?)
+  I           2.35    0.40               JCC,7,(1986),230;  
+ 
+END
+
diff --git a/test/Test_Build/tz2.parm7.save b/test/Test_Build/tz2.parm7.save
new file mode 100644
index 0000000000..7a32d0acd6
--- /dev/null
+++ b/test/Test_Build/tz2.parm7.save
@@ -0,0 +1,1562 @@
+%VERSION  VERSION_STAMP = V0001.000  DATE = 03/03/26 14:08:41                  
+%FLAG TITLE                                                                     
+%FORMAT(20a4)                                                                   
+tz2.pdb                                                                         
+%FLAG POINTERS                                                                  
+%FORMAT(10I8)                                                                   
+     223      12     106     124     238     170     494     477       0       0
+    1226      13     124     170     477      43      94     104      25       0
+       0       0       0       0       0       0       0       0      24       0
+       0
+%FLAG FORCE_FIELD_TYPE                                                          
+%FORMAT(i2,a78)                                                                 
+ 2                                                                    parm10.dat
+ 2                                                                 frcmod.ff14SB
+%FLAG ATOM_NAME                                                                 
+%FORMAT(20a4)                                                                   
+N   H1  H2  H3  CA  HA  CB  HB2 HB3 OG  HG  C   O   N   H   CA  HA  CB  HB2 HB3 
+CG  CD1 HD1 NE1 HE1 CE2 CZ2 HZ2 CH2 HH2 CZ3 HZ3 CE3 HE3 CD2 C   O   N   H   CA  
+HA  CB  HB  CG2 HG21HG22HG23OG1 HG1 C   O   N   H   CA  HA  CB  HB2 HB3 CG  CD1 
+HD1 NE1 HE1 CE2 CZ2 HZ2 CH2 HH2 CZ3 HZ3 CE3 HE3 CD2 C   O   N   H   CA  HA  CB  
+HB2 HB3 CG  HG2 HG3 CD  OE1 OE2 C   O   N   H   CA  HA  CB  HB2 HB3 CG  OD1 ND2 
+HD21HD22C   O   N   H   CA  HA2 HA3 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 
+HG3 CD  HD2 HD3 CE  HE2 HE3 NZ  HZ1 HZ2 HZ3 C   O   N   H   CA  HA  CB  HB2 HB3 
+CG  CD1 HD1 NE1 HE1 CE2 CZ2 HZ2 CH2 HH2 CZ3 HZ3 CE3 HE3 CD2 C   O   N   H   CA  
+HA  CB  HB  CG2 HG21HG22HG23OG1 HG1 C   O   N   H   CA  HA  CB  HB2 HB3 CG  CD1 
+HD1 NE1 HE1 CE2 CZ2 HZ2 CH2 HH2 CZ3 HZ3 CE3 HE3 CD2 C   O   N   H   CA  HA  CB  
+HB2 HB3 CG  HG2 HG3 CD  HD2 HD3 CE  HE2 HE3 NZ  HZ1 HZ2 HZ3 C   O   N   H   C   
+H1  H2  H3  
+%FLAG CHARGE                                                                    
+%FORMAT(5E16.8)                                                                 
+  3.36930327E+00  3.45859254E+00  3.45859254E+00  3.45859254E+00  1.03320441E+00
+  1.42498386E+00  4.73050908E+00  4.97468790E-01  4.97468790E-01 -1.22344522E+01
+  7.72443297E+00  1.12304035E+01 -1.04268001E+01 -7.57501011E+00  4.95464337E+00
+ -5.01113250E-01  2.04636429E+00 -9.11115000E-02  6.17735970E-01  6.17735970E-01
+ -2.57845545E+00 -2.98481274E+00  3.75743826E+00 -6.22838214E+00  6.21744876E+00
+  2.51467740E+00 -4.73962023E+00  2.86454556E+00 -2.06640882E+00  2.58209991E+00
+ -3.59343756E+00  2.63676681E+00 -4.34966301E+00  3.09779100E+00  2.26503189E+00
+  1.08841798E+01 -1.03484442E+01 -7.57501011E+00  4.95464337E+00 -7.08847470E-01
+  1.83498561E+00  6.65842842E+00  7.83558900E-02 -4.44259674E+00  1.16987166E+00
+  1.16987166E+00  1.16987166E+00 -1.23200970E+01  7.47478746E+00  1.08841798E+01
+ -1.03484442E+01 -7.57501011E+00  4.95464337E+00 -5.01113250E-01  2.04636429E+00
+ -9.11115000E-02  6.17735970E-01  6.17735970E-01 -2.57845545E+00 -2.98481274E+00
+  3.75743826E+00 -6.22838214E+00  6.21744876E+00  2.51467740E+00 -4.73962023E+00
+  2.86454556E+00 -2.06640882E+00  2.58209991E+00 -3.59343756E+00  2.63676681E+00
+ -4.34966301E+00  3.09779100E+00  2.26503189E+00  1.08841798E+01 -1.03484442E+01
+ -9.40817349E+00  5.35006728E+00  7.23425310E-01  2.01356415E+00  1.02044880E+00
+ -3.15245790E-01 -3.15245790E-01  2.47823280E-01 -7.74447750E-01 -7.74447750E-01
+  1.46762404E+01 -1.49204192E+01 -1.49204192E+01  9.77808618E+00 -1.06035564E+01
+ -7.57501011E+00  4.95464337E+00  2.60578890E-01  1.90969704E+00 -3.71917143E+00
+  1.45231731E+00  1.45231731E+00  1.29924999E+01 -1.08076461E+01 -1.67481159E+01
+  7.64607708E+00  7.64607708E+00  1.08841798E+01 -1.03484442E+01 -7.57501011E+00
+  4.95464337E+00 -4.59201960E-01  1.27191654E+00  1.27191654E+00  1.08841798E+01
+ -1.03484442E+01 -6.33953817E+00  5.00566581E+00 -4.37335200E+00  2.59849998E+00
+ -1.71289620E-01  6.59647260E-01  6.59647260E-01  3.40757010E-01  1.87689690E-01
+  1.87689690E-01 -8.72848170E-01  1.13160483E+00  1.13160483E+00 -2.60578890E-01
+  2.06823105E+00  2.06823105E+00 -7.02287442E+00  6.19558200E+00  6.19558200E+00
+  6.19558200E+00  1.33769904E+01 -1.07402236E+01 -7.57501011E+00  4.95464337E+00
+ -5.01113250E-01  2.04636429E+00 -9.11115000E-02  6.17735970E-01  6.17735970E-01
+ -2.57845545E+00 -2.98481274E+00  3.75743826E+00 -6.22838214E+00  6.21744876E+00
+  2.51467740E+00 -4.73962023E+00  2.86454556E+00 -2.06640882E+00  2.58209991E+00
+ -3.59343756E+00  2.63676681E+00 -4.34966301E+00  3.09779100E+00  2.26503189E+00
+  1.08841798E+01 -1.03484442E+01 -7.57501011E+00  4.95464337E+00 -7.08847470E-01
+  1.83498561E+00  6.65842842E+00  7.83558900E-02 -4.44259674E+00  1.16987166E+00
+  1.16987166E+00  1.16987166E+00 -1.23200970E+01  7.47478746E+00  1.08841798E+01
+ -1.03484442E+01 -7.57501011E+00  4.95464337E+00 -5.01113250E-01  2.04636429E+00
+ -9.11115000E-02  6.17735970E-01  6.17735970E-01 -2.57845545E+00 -2.98481274E+00
+  3.75743826E+00 -6.22838214E+00  6.21744876E+00  2.51467740E+00 -4.73962023E+00
+  2.86454556E+00 -2.06640882E+00  2.58209991E+00 -3.59343756E+00  2.63676681E+00
+ -4.34966301E+00  3.09779100E+00  2.26503189E+00  1.08841798E+01 -1.03484442E+01
+ -6.33953817E+00  5.00566581E+00 -4.37335200E+00  2.59849998E+00 -1.71289620E-01
+  6.59647260E-01  6.59647260E-01  3.40757010E-01  1.87689690E-01  1.87689690E-01
+ -8.72848170E-01  1.13160483E+00  1.13160483E+00 -2.60578890E-01  2.06823105E+00
+  2.06823105E+00 -7.02287442E+00  6.19558200E+00  6.19558200E+00  6.19558200E+00
+  1.33769904E+01 -1.07402236E+01 -7.57501011E+00  4.95464337E+00 -2.71512270E+00
+  1.77849648E+00  1.77849648E+00  1.77849648E+00
+%FLAG ATOMIC_NUMBER                                                             
+%FORMAT(10I8)                                                                   
+       7       1       1       1       6       1       6       1       1       8
+       1       6       8       7       1       6       1       6       1       1
+       6       6       1       7       1       6       6       1       6       1
+       6       1       6       1       6       6       8       7       1       6
+       1       6       1       6       1       1       1       8       1       6
+       8       7       1       6       1       6       1       1       6       6
+       1       7       1       6       6       1       6       1       6       1
+       6       1       6       6       8       7       1       6       1       6
+       1       1       6       1       1       6       8       8       6       8
+       7       1       6       1       6       1       1       6       8       7
+       1       1       6       8       7       1       6       1       1       6
+       8       7       1       6       1       6       1       1       6       1
+       1       6       1       1       6       1       1       7       1       1
+       1       6       8       7       1       6       1       6       1       1
+       6       6       1       7       1       6       6       1       6       1
+       6       1       6       1       6       6       8       7       1       6
+       1       6       1       6       1       1       1       8       1       6
+       8       7       1       6       1       6       1       1       6       6
+       1       7       1       6       6       1       6       1       6       1
+       6       1       6       6       8       7       1       6       1       6
+       1       1       6       1       1       6       1       1       6       1
+       1       7       1       1       1       6       8       7       1       6
+       1       1       1
+%FLAG MASS                                                                      
+%FORMAT(5E16.8)                                                                 
+  1.40100000E+01  1.00800000E+00  1.00800000E+00  1.00800000E+00  1.20100000E+01
+  1.00800000E+00  1.20100000E+01  1.00800000E+00  1.00800000E+00  1.60000000E+01
+  1.00800000E+00  1.20100000E+01  1.60000000E+01  1.40100000E+01  1.00800000E+00
+  1.20100000E+01  1.00800000E+00  1.20100000E+01  1.00800000E+00  1.00800000E+00
+  1.20100000E+01  1.20100000E+01  1.00800000E+00  1.40100000E+01  1.00800000E+00
+  1.20100000E+01  1.20100000E+01  1.00800000E+00  1.20100000E+01  1.00800000E+00
+  1.20100000E+01  1.00800000E+00  1.20100000E+01  1.00800000E+00  1.20100000E+01
+  1.20100000E+01  1.60000000E+01  1.40100000E+01  1.00800000E+00  1.20100000E+01
+  1.00800000E+00  1.20100000E+01  1.00800000E+00  1.20100000E+01  1.00800000E+00
+  1.00800000E+00  1.00800000E+00  1.60000000E+01  1.00800000E+00  1.20100000E+01
+  1.60000000E+01  1.40100000E+01  1.00800000E+00  1.20100000E+01  1.00800000E+00
+  1.20100000E+01  1.00800000E+00  1.00800000E+00  1.20100000E+01  1.20100000E+01
+  1.00800000E+00  1.40100000E+01  1.00800000E+00  1.20100000E+01  1.20100000E+01
+  1.00800000E+00  1.20100000E+01  1.00800000E+00  1.20100000E+01  1.00800000E+00
+  1.20100000E+01  1.00800000E+00  1.20100000E+01  1.20100000E+01  1.60000000E+01
+  1.40100000E+01  1.00800000E+00  1.20100000E+01  1.00800000E+00  1.20100000E+01
+  1.00800000E+00  1.00800000E+00  1.20100000E+01  1.00800000E+00  1.00800000E+00
+  1.20100000E+01  1.60000000E+01  1.60000000E+01  1.20100000E+01  1.60000000E+01
+  1.40100000E+01  1.00800000E+00  1.20100000E+01  1.00800000E+00  1.20100000E+01
+  1.00800000E+00  1.00800000E+00  1.20100000E+01  1.60000000E+01  1.40100000E+01
+  1.00800000E+00  1.00800000E+00  1.20100000E+01  1.60000000E+01  1.40100000E+01
+  1.00800000E+00  1.20100000E+01  1.00800000E+00  1.00800000E+00  1.20100000E+01
+  1.60000000E+01  1.40100000E+01  1.00800000E+00  1.20100000E+01  1.00800000E+00
+  1.20100000E+01  1.00800000E+00  1.00800000E+00  1.20100000E+01  1.00800000E+00
+  1.00800000E+00  1.20100000E+01  1.00800000E+00  1.00800000E+00  1.20100000E+01
+  1.00800000E+00  1.00800000E+00  1.40100000E+01  1.00800000E+00  1.00800000E+00
+  1.00800000E+00  1.20100000E+01  1.60000000E+01  1.40100000E+01  1.00800000E+00
+  1.20100000E+01  1.00800000E+00  1.20100000E+01  1.00800000E+00  1.00800000E+00
+  1.20100000E+01  1.20100000E+01  1.00800000E+00  1.40100000E+01  1.00800000E+00
+  1.20100000E+01  1.20100000E+01  1.00800000E+00  1.20100000E+01  1.00800000E+00
+  1.20100000E+01  1.00800000E+00  1.20100000E+01  1.00800000E+00  1.20100000E+01
+  1.20100000E+01  1.60000000E+01  1.40100000E+01  1.00800000E+00  1.20100000E+01
+  1.00800000E+00  1.20100000E+01  1.00800000E+00  1.20100000E+01  1.00800000E+00
+  1.00800000E+00  1.00800000E+00  1.60000000E+01  1.00800000E+00  1.20100000E+01
+  1.60000000E+01  1.40100000E+01  1.00800000E+00  1.20100000E+01  1.00800000E+00
+  1.20100000E+01  1.00800000E+00  1.00800000E+00  1.20100000E+01  1.20100000E+01
+  1.00800000E+00  1.40100000E+01  1.00800000E+00  1.20100000E+01  1.20100000E+01
+  1.00800000E+00  1.20100000E+01  1.00800000E+00  1.20100000E+01  1.00800000E+00
+  1.20100000E+01  1.00800000E+00  1.20100000E+01  1.20100000E+01  1.60000000E+01
+  1.40100000E+01  1.00800000E+00  1.20100000E+01  1.00800000E+00  1.20100000E+01
+  1.00800000E+00  1.00800000E+00  1.20100000E+01  1.00800000E+00  1.00800000E+00
+  1.20100000E+01  1.00800000E+00  1.00800000E+00  1.20100000E+01  1.00800000E+00
+  1.00800000E+00  1.40100000E+01  1.00800000E+00  1.00800000E+00  1.00800000E+00
+  1.20100000E+01  1.60000000E+01  1.40100000E+01  1.00800000E+00  1.20100000E+01
+  1.00800000E+00  1.00800000E+00  1.00800000E+00
+%FLAG ATOM_TYPE_INDEX                                                           
+%FORMAT(10I8)                                                                   
+       1       2       2       2       3       4       3       5       5       6
+       7       8       9       1       2       3       5       3      10      10
+       8       8      11       1       2       8       8      12       8      12
+       8      12       8      12       8       8       9       1       2       3
+       5       3       5       3      10      10      10       6       7       8
+       9       1       2       3       5       3      10      10       8       8
+      11       1       2       8       8      12       8      12       8      12
+       8      12       8       8       9       1       2       3       5       3
+      10      10       3      10      10       8       9       9       8       9
+       1       2       3       5       3      10      10       8       9       1
+       2       2       8       9       1       2       3       5       5       8
+       9       1       2       3       5       3      10      10       3      10
+      10       3      10      10       3       4       4       1       2       2
+       2       8       9       1       2       3       5       3      10      10
+       8       8      11       1       2       8       8      12       8      12
+       8      12       8      12       8       8       9       1       2       3
+       5       3       5       3      10      10      10       6       7       8
+       9       1       2       3       5       3      10      10       8       8
+      11       1       2       8       8      12       8      12       8      12
+       8      12       8       8       9       1       2       3       5       3
+      10      10       3      10      10       3      10      10       3       4
+       4       1       2       2       2       8       9       1       2       3
+       5       5       5
+%FLAG NUMBER_EXCLUDED_ATOMS                                                     
+%FORMAT(10I8)                                                                   
+      12       6       5       4      11       7       7       4       3       2
+       1       7       3      10       4      12       7      12       5       4
+      11       7       4       7       3       8       7       4       6       3
+       4       3       2       1       1       7       3      10       4      14
+       7      10       7       6       3       2       1       2       1       7
+       3      10       4      12       7      12       5       4      11       7
+       4       7       3       8       7       4       6       3       4       3
+       2       1       1       7       3      10       4      13       7      11
+       6       5       6       4       3       2       1       1       7       3
+      10       4      12       7      10       5       4       5       3       2
+       1       1       7       3       7       4       7       4       3       7
+       3      10       4      13       7      12       6       5      10       5
+       4       9       5       4       6       5       4       3       2       1
+       1       7       3      10       4      12       7      12       5       4
+      11       7       4       7       3       8       7       4       6       3
+       4       3       2       1       1       7       3      10       4      14
+       7      10       7       6       3       2       1       2       1       7
+       3      10       4      12       7      12       5       4      11       7
+       4       7       3       8       7       4       6       3       4       3
+       2       1       1       7       3      10       4      13       7      12
+       6       5      10       5       4       9       5       4       6       5
+       4       3       2       1       1       7       3       5       4       3
+       2       1       1
+%FLAG NONBONDED_PARM_INDEX                                                      
+%FORMAT(10I8)                                                                   
+       1       2       4       7      11      16      22      29      37      46
+      56      67       2       3       5       8      12      17      23      30
+      38      47      57      68       4       5       6       9      13      18
+      24      31      39      48      58      69       7       8       9      10
+      14      19      25      32      40      49      59      70      11      12
+      13      14      15      20      26      33      41      50      60      71
+      16      17      18      19      20      21      27      34      42      51
+      61      72      22      23      24      25      26      27      28      35
+      43      52      62      73      29      30      31      32      33      34
+      35      36      44      53      63      74      37      38      39      40
+      41      42      43      44      45      54      64      75      46      47
+      48      49      50      51      52      53      54      55      65      76
+      56      57      58      59      60      61      62      63      64      65
+      66      77      67      68      69      70      71      72      73      74
+      75      76      77      78
+%FLAG RESIDUE_LABEL                                                             
+%FORMAT(20a4)                                                                   
+SER TRP THR TRP GLU ASN GLY LYS TRP THR TRP LYS NME 
+%FLAG RESIDUE_POINTER                                                           
+%FORMAT(10I8)                                                                   
+       1      14      38      52      76      91     105     112     134     158
+     172     196     218
+%FLAG BOND_FORCE_CONSTANT                                                       
+%FORMAT(5E16.8)                                                                 
+  5.70000000E+02  4.90000000E+02  5.53000000E+02  3.40000000E+02  3.20000000E+02
+  3.40000000E+02  3.10000000E+02  3.17000000E+02  4.34000000E+02  3.67000000E+02
+  3.67000000E+02  4.69000000E+02  4.69000000E+02  4.69000000E+02  4.47000000E+02
+  4.34000000E+02  4.28000000E+02  3.67000000E+02  4.27000000E+02  5.46000000E+02
+  3.88000000E+02  3.40000000E+02  3.17000000E+02  3.40000000E+02  3.10000000E+02
+  4.34000000E+02  3.37000000E+02  3.40000000E+02  3.10000000E+02  3.20000000E+02
+  3.10000000E+02  6.56000000E+02  3.40000000E+02  3.17000000E+02  3.10000000E+02
+  3.17000000E+02  3.40000000E+02  3.67000000E+02  3.40000000E+02  3.10000000E+02
+  3.10000000E+02  3.40000000E+02  3.37000000E+02
+%FLAG BOND_EQUIL_VALUE                                                          
+%FORMAT(5E16.8)                                                                 
+  1.22900000E+00  1.33500000E+00  9.60000000E-01  1.09000000E+00  1.41000000E+00
+  1.09000000E+00  1.52600000E+00  1.52200000E+00  1.01000000E+00  1.47100000E+00
+  1.08000000E+00  1.40400000E+00  1.40000000E+00  1.40000000E+00  1.41900000E+00
+  1.01000000E+00  1.38000000E+00  1.08000000E+00  1.38100000E+00  1.35200000E+00
+  1.45900000E+00  1.09000000E+00  1.49500000E+00  1.09000000E+00  1.52600000E+00
+  1.01000000E+00  1.44900000E+00  1.09000000E+00  1.52600000E+00  1.41000000E+00
+  1.52600000E+00  1.25000000E+00  1.09000000E+00  1.52200000E+00  1.52600000E+00
+  1.52200000E+00  1.09000000E+00  1.47100000E+00  1.09000000E+00  1.52600000E+00
+  1.52600000E+00  1.09000000E+00  1.44900000E+00
+%FLAG ANGLE_FORCE_CONSTANT                                                      
+%FORMAT(5E16.8)                                                                 
+  8.00000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01  3.50000000E+01
+  6.30000000E+01  5.50000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01
+  5.00000000E+01  8.00000000E+01  7.00000000E+01  5.00000000E+01  3.50000000E+01
+  5.00000000E+01  8.00000000E+01  8.00000000E+01  5.00000000E+01  5.00000000E+01
+  6.30000000E+01  6.30000000E+01  6.30000000E+01  5.00000000E+01  6.30000000E+01
+  6.30000000E+01  5.00000000E+01  7.00000000E+01  7.00000000E+01  5.00000000E+01
+  6.30000000E+01  5.00000000E+01  7.00000000E+01  5.00000000E+01  7.00000000E+01
+  6.30000000E+01  6.30000000E+01  5.00000000E+01  3.50000000E+01  6.30000000E+01
+  7.00000000E+01  7.00000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01
+  6.30000000E+01  5.00000000E+01  5.00000000E+01  8.00000000E+01  6.30000000E+01
+  5.00000000E+01  5.00000000E+01  5.00000000E+01  6.30000000E+01  5.00000000E+01
+  5.50000000E+01  5.00000000E+01  5.00000000E+01  4.00000000E+01  5.00000000E+01
+  8.00000000E+01  8.00000000E+01  5.00000000E+01  3.50000000E+01  7.00000000E+01
+  5.00000000E+01  6.30000000E+01  5.00000000E+01  5.00000000E+01  4.00000000E+01
+  8.00000000E+01  3.50000000E+01  5.00000000E+01  8.00000000E+01  7.00000000E+01
+  6.30000000E+01  3.50000000E+01  5.00000000E+01  3.50000000E+01  5.00000000E+01
+  5.00000000E+01  3.50000000E+01  5.00000000E+01  8.00000000E+01  4.00000000E+01
+  6.30000000E+01  5.00000000E+01  5.00000000E+01  4.00000000E+01  8.00000000E+01
+  5.00000000E+01  3.50000000E+01  5.00000000E+01  5.00000000E+01
+%FLAG ANGLE_EQUIL_VALUE                                                         
+%FORMAT(5E16.8)                                                                 
+  2.14500965E+00  2.09439510E+00  2.12755636E+00  1.91113553E+00  1.91113553E+00
+  1.93906080E+00  1.89368224E+00  1.91113553E+00  1.91113553E+00  1.91113553E+00
+  1.91113553E+00  2.10137642E+00  2.03505391E+00  1.91113553E+00  1.91113553E+00
+  1.91113553E+00  1.94080613E+00  1.94080613E+00  2.09439510E+00  2.09439510E+00
+  2.09439510E+00  2.09439510E+00  2.14151899E+00  2.09439510E+00  2.09439510E+00
+  2.02807259E+00  2.14850031E+00  2.31779725E+00  1.82212374E+00  2.09439510E+00
+  1.85703032E+00  2.09439510E+00  1.94778745E+00  2.09439510E+00  1.89717290E+00
+  1.89891823E+00  2.35444916E+00  1.91113553E+00  1.91113553E+00  1.93906080E+00
+  2.18166156E+00  2.24449342E+00  1.91113553E+00  1.91113553E+00  1.91113553E+00
+  2.01760062E+00  2.06018665E+00  1.91113553E+00  1.91462619E+00  1.92160751E+00
+  1.91113553E+00  1.91113553E+00  1.91113553E+00  1.93906080E+00  1.91113553E+00
+  1.89368224E+00  1.91113553E+00  1.91113553E+00  1.91113553E+00  1.91113553E+00
+  1.91462619E+00  2.19911486E+00  1.91113553E+00  1.91113553E+00  2.04203522E+00
+  1.91113553E+00  1.93906080E+00  1.91113553E+00  1.91113553E+00  1.91113553E+00
+  1.91462619E+00  2.09439510E+00  1.91113553E+00  2.10137642E+00  2.03505391E+00
+  1.93906080E+00  1.91113553E+00  1.91113553E+00  1.91113553E+00  1.91113553E+00
+  1.91113553E+00  1.91113553E+00  1.91113553E+00  1.94080613E+00  1.91113553E+00
+  1.93906080E+00  1.91113553E+00  1.91113553E+00  1.91113553E+00  1.91462619E+00
+  2.12755636E+00  1.91113553E+00  2.06018665E+00  1.91113553E+00
+%FLAG DIHEDRAL_FORCE_CONSTANT                                                   
+%FORMAT(5E16.8)                                                                 
+  2.00000000E+00  2.50000000E+00  0.00000000E+00  1.80000000E+00  8.00000000E-01
+  0.00000000E+00  0.00000000E+00  2.70000000E-01  4.20000000E-01  6.61000000E-01
+  2.18000000E-01  4.01000000E-01  1.29000000E-01  1.55555556E-01  1.66666667E-01
+  2.00000000E-01  2.00000000E-01  4.00000000E-01  2.11000000E-01  4.44000000E-01
+  2.67000000E-01  7.00000000E-03  6.66000000E-01  2.46000000E-01  1.60000000E-01
+  3.62500000E+00  3.00000000E+00  3.50000000E+00  1.52500000E+00  6.52500000E+00
+  1.50000000E+00  1.67500000E+00  1.70000000E-02  3.53000000E-01  2.34000000E-01
+  7.40000000E-02  8.00000000E-01  8.00000000E-02  0.00000000E+00  3.65000000E-01
+  4.08000000E-01  8.19000000E-01  9.50000000E-02  7.90000000E-02  3.13000000E-01
+  3.10000000E-02  4.50000000E-01  1.58000000E+00  5.50000000E-01  6.97000000E-01
+  1.19000000E-01  3.15000000E-01  1.56000000E-01  2.50000000E-01  4.06000000E-01
+  2.89000000E-01  1.48000000E-01  1.12000000E-01  6.43000000E-01  7.90000000E-02
+  2.36000000E-01  4.80000000E-02  1.60000000E-01  6.00000000E-03  2.51000000E-01
+  1.30000000E-02  3.37000000E-01  2.16000000E-01  1.00000000E-03  6.74000000E-01
+  6.00000000E-03  9.50000000E-02  4.21000000E-01  3.93000000E-01  1.44000000E-01
+  1.45000000E-01  1.50000000E-01  3.90000000E-01  6.40000000E-02  1.36700000E+00
+  2.22000000E-01  6.08000000E-01  5.60000000E-02  1.00000000E-01  1.84000000E-01
+  7.80000000E-02  1.04600000E+00  3.03000000E-01  3.30000000E-02  1.07000000E-01
+  8.28000000E-01  4.85000000E-01  3.01000000E-01  8.00000000E-03  6.88000000E-01
+  2.97000000E-01  5.90000000E-02  2.00000000E-01  2.50000000E-01  1.80000000E-01
+  1.05000000E+01  0.00000000E+00  1.10000000E+00  1.00000000E+00
+%FLAG DIHEDRAL_PERIODICITY                                                      
+%FORMAT(5E16.8)                                                                 
+  1.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  3.00000000E+00
+  4.00000000E+00  1.00000000E+00  2.00000000E+00  3.00000000E+00  1.00000000E+00
+  2.00000000E+00  3.00000000E+00  4.00000000E+00  3.00000000E+00  3.00000000E+00
+  1.00000000E+00  2.00000000E+00  3.00000000E+00  1.00000000E+00  2.00000000E+00
+  3.00000000E+00  4.00000000E+00  1.00000000E+00  2.00000000E+00  4.00000000E+00
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  2.00000000E+00  2.00000000E+00  1.00000000E+00  2.00000000E+00  3.00000000E+00
+  4.00000000E+00  1.00000000E+00  3.00000000E+00  3.00000000E+00  1.00000000E+00
+  2.00000000E+00  3.00000000E+00  4.00000000E+00  1.00000000E+00  2.00000000E+00
+  4.00000000E+00  1.00000000E+00  2.00000000E+00  3.00000000E+00  1.00000000E+00
+  2.00000000E+00  3.00000000E+00  4.00000000E+00  1.00000000E+00  1.00000000E+00
+  2.00000000E+00  3.00000000E+00  4.00000000E+00  1.00000000E+00  2.00000000E+00
+  3.00000000E+00  4.00000000E+00  3.00000000E+00  1.00000000E+00  2.00000000E+00
+  4.00000000E+00  1.00000000E+00  2.00000000E+00  4.00000000E+00  1.00000000E+00
+  2.00000000E+00  4.00000000E+00  1.00000000E+00  2.00000000E+00  3.00000000E+00
+  4.00000000E+00  3.00000000E+00  2.00000000E+00  4.00000000E+00  1.00000000E+00
+  2.00000000E+00  3.00000000E+00  4.00000000E+00  1.00000000E+00  2.00000000E+00
+  4.00000000E+00  1.00000000E+00  2.00000000E+00  3.00000000E+00  4.00000000E+00
+  1.00000000E+00  2.00000000E+00  3.00000000E+00  4.00000000E+00  1.00000000E+00
+  2.00000000E+00  4.00000000E+00  1.00000000E+00  2.00000000E+00  3.00000000E+00
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+%FLAG DIHEDRAL_PHASE                                                            
+%FORMAT(5E16.8)                                                                 
+  0.00000000E+00  3.14159265E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  3.14159265E+00
+  3.14159265E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  3.14159265E+00  0.00000000E+00
+  3.14159265E+00  3.14159265E+00  3.14159265E+00  3.14159265E+00  3.14159265E+00
+  3.14159265E+00  3.14159265E+00  3.14159265E+00  3.14159265E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  3.14159265E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  3.14159265E+00  0.00000000E+00  3.14159265E+00
+  0.00000000E+00  3.14159265E+00  3.14159265E+00  3.14159265E+00  3.14159265E+00
+  3.14159265E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  3.14159265E+00
+  3.14159265E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  3.14159265E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  3.14159265E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  3.14159265E+00  3.14159265E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  3.14159265E+00  3.14159265E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  3.14159265E+00  0.00000000E+00  3.14159265E+00
+  3.14159265E+00  3.14159265E+00  3.14159265E+00  3.14159265E+00  3.14159265E+00
+  0.00000000E+00  0.00000000E+00  3.14159265E+00  0.00000000E+00  0.00000000E+00
+  3.14159265E+00  3.14159265E+00  3.14159265E+00  0.00000000E+00  3.14159265E+00
+  3.14159265E+00  0.00000000E+00  3.14159265E+00  3.14159265E+00  0.00000000E+00
+  3.14159265E+00  3.14159265E+00  3.14159265E+00  3.14159265E+00
+%FLAG SCEE_SCALE_FACTOR                                                         
+%FORMAT(5E16.8)                                                                 
+  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00
+  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00
+  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00
+  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00
+  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00
+  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00
+  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00
+  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00
+  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00
+  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00
+  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00
+  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00
+  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00
+  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00
+  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00
+  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00
+  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00
+  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00
+  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00
+  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+%FLAG SCNB_SCALE_FACTOR                                                         
+%FORMAT(5E16.8)                                                                 
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+%FLAG SOLTY                                                                     
+%FORMAT(5E16.8)                                                                 
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+%FLAG LENNARD_JONES_ACOEF                                                       
+%FORMAT(5E16.8)                                                                 
+  9.44293233E+05  2.12601181E+03  1.39982777E-01  9.95480466E+05  2.56678134E+03
+  1.04308023E+06  2.01791425E+04  9.14716912E+00  2.27401052E+04  2.01823541E+02
+  6.20665997E+04  5.94667300E+01  6.78771368E+04  8.79040886E+02  3.25969625E+03
+  7.44975864E+05  1.40467023E+03  7.91544157E+05  1.45985502E+04  4.66922514E+04
+  5.81803229E+05  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  8.82619071E+05  2.27577561E+03
+  9.24822270E+05  2.01619733E+04  6.01816484E+04  7.01803794E+05  0.00000000E+00
+  8.19971662E+05  6.06829342E+05  1.02595236E+03  6.47841731E+05  1.12780457E+04
+  3.69471530E+04  4.71003287E+05  0.00000000E+00  5.74393458E+05  3.79876399E+05
+  8.96776989E+04  1.07193646E+02  9.71708117E+04  1.41077189E+03  4.98586848E+03
+  6.82786631E+04  0.00000000E+00  8.61541883E+04  5.44261042E+04  7.51607703E+03
+  6.58473870E+04  6.63368273E+01  7.18621074E+04  9.55000044E+02  3.50301067E+03
+  4.96707306E+04  0.00000000E+00  6.37148278E+04  3.93690817E+04  5.34045360E+03
+  3.76169105E+03  7.91627154E+04  8.90987508E+01  8.59947003E+04  1.21014911E+03
+  4.33325458E+03  6.00750218E+04  0.00000000E+00  7.62451550E+04  4.77908183E+04
+  6.55825601E+03  4.64559155E+03  5.71629601E+03
+%FLAG LENNARD_JONES_BCOEF                                                       
+%FORMAT(5E16.8)                                                                 
+  8.01323529E+02  2.09604198E+01  9.37598976E-02  7.36907417E+02  2.06278363E+01
+  6.75612247E+02  6.45756063E+01  7.57919667E-01  6.13981767E+01  3.56012899E+00
+  1.13252061E+02  1.93248820E+00  1.06076943E+02  7.42992380E+00  1.43076527E+01
+  7.50714425E+02  1.79702257E+01  6.93079947E+02  5.79323581E+01  1.03606917E+02
+  6.99746810E+02  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  6.53361429E+02  1.82891803E+01
+  5.99015525E+02  5.44372326E+01  9.40505980E+01  6.14502845E+02  0.00000000E+00
+  5.31102864E+02  6.77220874E+02  1.53505284E+01  6.26720080E+02  5.08951803E+01
+  9.21192136E+01  6.29300710E+02  0.00000000E+00  5.55666448E+02  5.64885984E+02
+  1.36131731E+02  2.59456373E+00  1.26919150E+02  9.41257003E+00  1.76949863E+01
+  1.25287818E+02  0.00000000E+00  1.12529845E+02  1.11805549E+02  2.17257828E+01
+  1.15327881E+02  2.01792524E+00  1.07908863E+02  7.65648470E+00  1.46638650E+01
+  1.05648788E+02  0.00000000E+00  9.56748258E+01  9.40124296E+01  1.81057616E+01
+  1.50233639E+01  1.26451907E+02  2.33864085E+00  1.18043746E+02  8.61880722E+00
+  1.63092814E+01  1.16187983E+02  0.00000000E+00  1.04660679E+02  1.03580945E+02
+  2.00642027E+01  1.66953734E+01  1.85196588E+01
+%FLAG BONDS_INC_HYDROGEN                                                        
+%FORMAT(10I8)                                                                   
+      27      30       3      18      21       4      18      24       4      12
+      15       6       0       3       9       0       6       9       0       9
+       9      96      99      11      90      93      11      84      87      11
+      78      81      11      69      72      16      63      66      18      51
+      54      22      51      57      22      45      48      24      39      42
+      26     141     144       3     129     132      22     129     135      22
+     129     138      22     123     126      28     117     120      24     111
+     114      26     210     213      11     204     207      11     198     201
+      11     192     195      11     183     186      16     177     180      18
+     165     168      22     165     171      22     159     162      24     153
+     156      26     246     249      33     246     252      33     237     240
+      33     237     243      33     231     234      24     225     228      26
+     297     300      26     297     303      26     282     285      33     282
+     288      33     276     279      24     270     273      26     318     321
+      24     318     324      24     312     315      26     381     384       9
+     381     387       9     381     390       9     372     375      37     372
+     378      37     363     366      39     363     369      39     354     357
+      39     354     360      39     345     348      39     345     351      39
+     339     342      24     333     336      26     456     459      11     450
+     453      11     444     447      11     438     441      11     429     432
+      16     423     426      18     411     414      22     411     417      22
+     405     408      24     399     402      26     501     504       3     489
+     492      22     489     495      22     489     498      22     483     486
+      28     477     480      24     471     474      26     570     573      11
+     564     567      11     558     561      11     552     555      11     543
+     546      16     537     540      18     525     528      22     525     531
+      22     519     522      24     513     516      26     633     636       9
+     633     639       9     633     642       9     624     627      37     624
+     630      37     615     618      39     615     621      39     606     609
+      39     606     612      39     597     600      39     597     603      39
+     591     594      24     585     588      26     657     660      42     657
+     663      42     657     666      42     651     654      26
+%FLAG BONDS_WITHOUT_HYDROGEN                                                    
+%FORMAT(10I8)                                                                   
+      33      36       1      33      39       2      18      27       5      12
+      18       7      12      33       8       0      12      10     105     108
+       1     105     111       2      96     102      12      90      96      13
+      84      90      13      78      84      13      75      78      14      75
+     102      15      69      75      17      63      69      19      60      63
+      20      60     102      21      51      60      23      45      51      25
+      45     105       8      39      45      27     147     150       1     147
+     153       2     123     129      29     123     141      30     117     123
+      31     117     147       8     111     117      27     219     222       1
+     219     225       2     210     216      12     204     210      13     198
+     204      13     192     198      13     189     192      14     189     216
+      15     183     189      17     177     183      19     174     177      20
+     174     216      21     165     174      23     159     165      25     159
+     219       8     153     159      27     264     267       1     264     270
+       2     255     258      32     255     261      32     246     255      34
+     237     246      35     231     237       7     231     264       8     225
+     231      27     306     309       1     306     312       2     291     294
+       1     291     297       2     282     291      36     276     282       7
+     276     306       8     270     276      27     327     330       1     327
+     333       2     318     327       8     312     318      27     393     396
+       1     393     399       2     372     381      38     363     372      40
+     354     363      40     345     354      40     339     345      41     339
+     393       8     333     339      27     465     468       1     465     471
+       2     456     462      12     450     456      13     444     450      13
+     438     444      13     435     438      14     435     462      15     429
+     435      17     423     429      19     420     423      20     420     462
+      21     411     420      23     405     411      25     405     465       8
+     399     405      27     507     510       1     507     513       2     483
+     489      29     483     501      30     477     483      31     477     507
+       8     471     477      27     579     582       1     579     585       2
+     570     576      12     564     570      13     558     564      13     552
+     558      13     549     552      14     549     576      15     543     549
+      17     537     543      19     534     537      20     534     576      21
+     525     534      23     519     525      25     519     579       8     513
+     519      27     645     648       1     645     651       2     624     633
+      38     615     624      40     606     615      40     597     606      40
+     591     597      41     591     645       8     585     591      27     651
+     657      43
+%FLAG ANGLES_INC_HYDROGEN                                                       
+%FORMAT(10I8)                                                                   
+      33      39      42       2      24      18      27       4      21      18
+      24       5      21      18      27       4      18      27      30       7
+      15      12      18       8      15      12      33       9      12      18
+      21      10      12      18      24      10       9       0      12      14
+       6       0       9      15       6       0      12      14       3       0
+       6      15       3       0       9      15       3       0      12      14
+       0      12      15      16     105     111     114       2      99      96
+     102      19      93      90      96      20      90      96      99      20
+      87      84      90      20      84      90      93      20      81      78
+      84      20      78      84      87      20      75      78      81      24
+      72      69      75      27      66      63      69      30      63      69
+      72      32      60      63      66      34      57      51      60      38
+      54      51      57      39      54      51      60      38      48      45
+      51      43      48      45     105      44      45      51      54      45
+      45      51      57      45      42      39      45      47      39      45
+      48      48     147     153     156       2     135     129     138      39
+     132     129     135      39     132     129     138      39     126     123
+     129      52     126     123     141      53     123     129     132      55
+     123     129     135      55     123     129     138      55     123     141
+     144      56     120     117     123      57     120     117     147      44
+     117     123     126      58     114     111     117      47     111     117
+     120      48     219     225     228       2     213     210     216      19
+     207     204     210      20     204     210     213      20     201     198
+     204      20     198     204     207      20     195     192     198      20
+     192     198     201      20     189     192     195      24     186     183
+     189      27     180     177     183      30     177     183     186      32
+     174     177     180      34     171     165     174      38     168     165
+     171      39     168     165     174      38     162     159     165      43
+     162     159     219      44     159     165     168      45     159     165
+     171      45     156     153     159      47     153     159     162      48
+     264     270     273       2     252     246     255      63     249     246
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+     240     237     243      64     240     237     246      66     237     246
+     249      66     237     246     252      66     234     231     237      68
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+     243      69     228     225     231      47     225     231     234      48
+     306     312     315       2     300     297     303      72     291     297
+     300       2     291     297     303       2     288     282     291      73
+     285     282     288      64     285     282     291      73     279     276
+     282      68     279     276     306      44     276     282     285      69
+     276     282     288      69     273     270     276      47     270     276
+     279      48     327     333     336       2     324     318     327      44
+     321     318     324      77     321     318     327      44     315     312
+     318      47     312     318     321      48     312     318     324      48
+     393     399     402       2     387     381     390      15     384     381
+     387      15     384     381     390      15     378     372     381      78
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+     384      80     372     381     387      80     372     381     390      80
+     369     363     372      81     366     363     369      82     366     363
+     372      81     363     372     375      83     363     372     378      83
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+     363      81     354     363     366      81     354     363     369      81
+     351     345     354      81     348     345     351      82     348     345
+     354      81     345     354     357      81     345     354     360      81
+     342     339     345      87     342     339     393      44     339     345
+     348      88     339     345     351      88     336     333     339      47
+     333     339     342      48     465     471     474       2     459     456
+     462      19     453     450     456      20     450     456     459      20
+     447     444     450      20     444     450     453      20     441     438
+     444      20     438     444     447      20     435     438     441      24
+     432     429     435      27     426     423     429      30     423     429
+     432      32     420     423     426      34     417     411     420      38
+     414     411     417      39     414     411     420      38     408     405
+     411      43     408     405     465      44     405     411     414      45
+     405     411     417      45     402     399     405      47     399     405
+     408      48     507     513     516       2     495     489     498      39
+     492     489     495      39     492     489     498      39     486     483
+     489      52     486     483     501      53     483     489     492      55
+     483     489     495      55     483     489     498      55     483     501
+     504      56     480     477     483      57     480     477     507      44
+     477     483     486      58     474     471     477      47     471     477
+     480      48     579     585     588       2     573     570     576      19
+     567     564     570      20     564     570     573      20     561     558
+     564      20     558     564     567      20     555     552     558      20
+     552     558     561      20     549     552     555      24     546     543
+     549      27     540     537     543      30     537     543     546      32
+     534     537     540      34     531     525     534      38     528     525
+     531      39     528     525     534      38     522     519     525      43
+     522     519     579      44     519     525     528      45     519     525
+     531      45     516     513     519      47     513     519     522      48
+     645     651     654       2     639     633     642      15     636     633
+     639      15     636     633     642      15     630     624     633      78
+     627     624     630      79     627     624     633      78     624     633
+     636      80     624     633     639      80     624     633     642      80
+     621     615     624      81     618     615     621      82     618     615
+     624      81     615     624     627      83     615     624     630      83
+     612     606     615      81     609     606     612      82     609     606
+     615      81     606     615     618      81     606     615     621      81
+     603     597     606      81     600     597     603      82     600     597
+     606      81     597     606     609      81     597     606     612      81
+     594     591     597      87     594     591     645      44     591     597
+     600      88     591     597     603      88     588     585     591      47
+     585     591     594      48     663     657     666      92     660     657
+     663      92     660     657     666      92     654     651     657      93
+     651     657     660      94     651     657     663      94     651     657
+     666      94
+%FLAG ANGLES_WITHOUT_HYDROGEN                                                   
+%FORMAT(10I8)                                                                   
+      36      33      39       1      33      39      45       3      18      12
+      33       6      12      18      27      11      12      33      36      12
+      12      33      39      13       0      12      18      17       0      12
+      33      18     108     105     111       1     105     111     117       3
+      90      96     102      21      84      90      96      22      78      75
+     102      23      78      84      90      22      75      78      84      25
+      75     102      96      26      69      75      78      28      69      75
+     102      29      63      60     102      31      63      69      75      33
+      60      63      69      35      60     102      75      36      60     102
+      96      37      51      45     105      40      51      60      63      41
+      51      60     102      42      45      51      60      46      45     105
+     108      12      45     105     111      13      39      45      51      49
+      39      45     105      50     150     147     153       1     147     153
+     159       3     129     123     141      51     123     117     147      54
+     117     123     129      59     117     123     141      60     117     147
+     150      12     117     147     153      13     111     117     123      61
+     111     117     147      50     222     219     225       1     219     225
+     231       3     204     210     216      21     198     204     210      22
+     192     189     216      23     192     198     204      22     189     192
+     198      25     189     216     210      26     183     189     192      28
+     183     189     216      29     177     174     216      31     177     183
+     189      33     174     177     183      35     174     216     189      36
+     174     216     210      37     165     159     219      40     165     174
+     177      41     165     174     216      42     159     165     174      46
+     159     219     222      12     159     219     225      13     153     159
+     165      49     153     159     219      50     267     264     270       1
+     264     270     276       3     258     255     261      62     246     255
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+%FLAG DIHEDRALS_INC_HYDROGEN                                                    
+%FORMAT(10I8)                                                                   
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+%FLAG DIHEDRALS_WITHOUT_HYDROGEN                                                
+%FORMAT(10I8)                                                                   
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+     585     591    -645     651       6      12      39     -33     -36     101
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+      69      78     -75    -102     102     102      51     -60     -63     103
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+     216     165    -174    -177     103     231     270    -264    -267     101
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+     552     576    -549    -543     102     576     525    -534    -537     103
+     591     651    -645    -648     101
+%FLAG EXCLUDED_ATOMS_LIST                                                       
+%FORMAT(10I8)                                                                   
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+      13      14       3       4       5       6       7      12       4       5
+       6       7      12       5       6       7      12       6       7       8
+       9      10      11      12      13      14      15      16       7       8
+       9      10      12      13      14       8       9      10      11      12
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+      12       0      13      14      15      16      17      18      36      14
+      15      16      15      16      17      18      19      20      21      36
+      37      38      16      17      18      36      17      18      19      20
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+      20      21      36      37      38      19      20      21      22      23
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+      35      36      21      22      35      36      22      23      24      25
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+      26      27      33      35      24      25      26      35      25      26
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+     121     122     132     119     120     121     122     132     120     121
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+     123     124     125     122     123     124     125     123     124     125
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+     129     130     131     130     131     131       0     133     134     135
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+     158     159     160     138     139     140     141     156     157     158
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+     157     158     140     141     142     155     156     141     142     155
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+     155     148     149     150     151     152     153     155     149     150
+     151     155     150     151     152     153     154     155     151     152
+     153     152     153     154     155     153     154     155     154     155
+     155       0     157     158     159     160     161     162     170     158
+     159     160     159     160     161     162     163     164     168     170
+     171     172     160     161     162     170     161     162     163     164
+     165     166     167     168     169     170     171     172     173     174
+     162     163     164     168     170     171     172     163     164     165
+     166     167     168     169     170     171     172     164     165     166
+     167     168     169     170     165     166     167     168     169     170
+     166     167     168     167     168     168     169     170       0     171
+     172     173     174     175     176     194     172     173     174     173
+     174     175     176     177     178     179     194     195     196     174
+     175     176     194     175     176     177     178     179     180     193
+     194     195     196     197     198     176     177     178     179     194
+     195     196     177     178     179     180     181     182     184     191
+     193     194     195     196     178     179     180     193     194     179
+     180     193     194     180     181     182     183     184     185     189
+     191     192     193     194     181     182     183     184     185     191
+     193     182     183     184     193     183     184     185     186     187
+     191     193     184     185     193     185     186     187     188     189
+     191     192     193     186     187     188     189     190     191     193
+     187     188     189     193     188     189     190     191     192     193
+     189     190     191     190     191     192     193     191     192     193
+     192     193     193       0     195     196     197     198     199     200
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+     203     216     217     218     198     199     200     216     199     200
+     201     202     203     204     205     206     216     217     218     219
+     220     200     201     202     203     216     217     218     201     202
+     203     204     205     206     207     208     209     216     217     218
+     202     203     204     205     206     216     203     204     205     206
+     216     204     205     206     207     208     209     210     211     212
+     216     205     206     207     208     209     206     207     208     209
+     207     208     209     210     211     212     213     214     215     208
+     209     210     211     212     209     210     211     212     210     211
+     212     213     214     215     211     212     213     214     215     212
+     213     214     215     213     214     215     214     215     215       0
+     217     218     219     220     221     222     223     218     219     220
+     219     220     221     222     223     220     221     222     223     221
+     222     223     222     223     223       0
+%FLAG HBOND_ACOEF                                                               
+%FORMAT(5E16.8)                                                                 
+
+%FLAG HBOND_BCOEF                                                               
+%FORMAT(5E16.8)                                                                 
+
+%FLAG HBCUT                                                                     
+%FORMAT(5E16.8)                                                                 
+
+%FLAG AMBER_ATOM_TYPE                                                           
+%FORMAT(20a4)                                                                   
+N3  H   H   H   CX  HP  2C  H1  H1  OH  HO  C   O   N   H   CX  H1  CT  HC  HC  
+C*  CW  H4  NA  H   CN  CA  HA  CA  HA  CA  HA  CA  HA  CB  C   O   N   H   CX  
+H1  3C  H1  CT  HC  HC  HC  OH  HO  C   O   N   H   CX  H1  CT  HC  HC  C*  CW  
+H4  NA  H   CN  CA  HA  CA  HA  CA  HA  CA  HA  CB  C   O   N   H   CX  H1  2C  
+HC  HC  2C  HC  HC  CO  O2  O2  C   O   N   H   CX  H1  2C  HC  HC  C   O   N   
+H   H   C   O   N   H   CX  H1  H1  C   O   N   H   CX  H1  C8  HC  HC  C8  HC  
+HC  C8  HC  HC  C8  HP  HP  N3  H   H   H   C   O   N   H   CX  H1  CT  HC  HC  
+C*  CW  H4  NA  H   CN  CA  HA  CA  HA  CA  HA  CA  HA  CB  C   O   N   H   CX  
+H1  3C  H1  CT  HC  HC  HC  OH  HO  C   O   N   H   CX  H1  CT  HC  HC  C*  CW  
+H4  NA  H   CN  CA  HA  CA  HA  CA  HA  CA  HA  CB  C   O   N   H   CX  H1  C8  
+HC  HC  C8  HC  HC  C8  HC  HC  C8  HP  HP  N3  H   H   H   C   O   N   H   CT  
+H1  H1  H1  
+%FLAG TREE_CHAIN_CLASSIFICATION                                                 
+%FORMAT(20a4)                                                                   
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA 
+%FLAG JOIN_ARRAY                                                                
+%FORMAT(10I8)                                                                   
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
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+       0       0       0       0       0       0       0       0       0       0
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+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
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+       0       0       0       0       0       0       0       0       0       0
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+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0
+%FLAG IROTAT                                                                    
+%FORMAT(10I8)                                                                   
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
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+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
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+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
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+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0
+%FLAG RADIUS_SET                                                                
+%FORMAT(1a80)                                                                   
+modified Bondi radii (mbondi)                                                   
+%FLAG RADII                                                                     
+%FORMAT(5E16.8)                                                                 
+  1.55000000E+00  1.30000000E+00  1.30000000E+00  1.30000000E+00  1.70000000E+00
+  1.30000000E+00  1.70000000E+00  1.30000000E+00  1.30000000E+00  1.50000000E+00
+  8.00000000E-01  1.70000000E+00  1.50000000E+00  1.55000000E+00  1.30000000E+00
+  1.70000000E+00  1.30000000E+00  1.70000000E+00  1.30000000E+00  1.30000000E+00
+  1.70000000E+00  1.70000000E+00  1.30000000E+00  1.55000000E+00  1.30000000E+00
+  1.70000000E+00  1.70000000E+00  1.30000000E+00  1.70000000E+00  1.30000000E+00
+  1.70000000E+00  1.30000000E+00  1.70000000E+00  1.30000000E+00  1.70000000E+00
+  1.70000000E+00  1.50000000E+00  1.55000000E+00  1.30000000E+00  1.70000000E+00
+  1.30000000E+00  1.70000000E+00  1.30000000E+00  1.70000000E+00  1.30000000E+00
+  1.30000000E+00  1.30000000E+00  1.50000000E+00  8.00000000E-01  1.70000000E+00
+  1.50000000E+00  1.55000000E+00  1.30000000E+00  1.70000000E+00  1.30000000E+00
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+  1.30000000E+00  1.70000000E+00  1.30000000E+00  1.70000000E+00  1.30000000E+00
+  1.70000000E+00  1.30000000E+00  1.70000000E+00  1.70000000E+00  1.50000000E+00
+  1.55000000E+00  1.30000000E+00  1.70000000E+00  1.30000000E+00  1.70000000E+00
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+  1.70000000E+00  1.50000000E+00  1.50000000E+00  1.70000000E+00  1.50000000E+00
+  1.55000000E+00  1.30000000E+00  1.70000000E+00  1.30000000E+00  1.70000000E+00
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+  1.30000000E+00  1.70000000E+00  1.30000000E+00  1.30000000E+00  1.70000000E+00
+  1.50000000E+00  1.55000000E+00  1.30000000E+00  1.70000000E+00  1.30000000E+00
+  1.70000000E+00  1.30000000E+00  1.30000000E+00  1.70000000E+00  1.30000000E+00
+  1.30000000E+00  1.70000000E+00  1.30000000E+00  1.30000000E+00  1.70000000E+00
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+  1.30000000E+00  1.70000000E+00  1.50000000E+00  1.55000000E+00  1.30000000E+00
+  1.70000000E+00  1.30000000E+00  1.70000000E+00  1.30000000E+00  1.30000000E+00
+  1.70000000E+00  1.70000000E+00  1.30000000E+00  1.55000000E+00  1.30000000E+00
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+  1.70000000E+00  1.30000000E+00  1.70000000E+00  1.30000000E+00  1.70000000E+00
+  1.70000000E+00  1.50000000E+00  1.55000000E+00  1.30000000E+00  1.70000000E+00
+  1.30000000E+00  1.70000000E+00  1.30000000E+00  1.70000000E+00  1.30000000E+00
+  1.30000000E+00  1.30000000E+00  1.50000000E+00  8.00000000E-01  1.70000000E+00
+  1.50000000E+00  1.55000000E+00  1.30000000E+00  1.70000000E+00  1.30000000E+00
+  1.70000000E+00  1.30000000E+00  1.30000000E+00  1.70000000E+00  1.70000000E+00
+  1.30000000E+00  1.55000000E+00  1.30000000E+00  1.70000000E+00  1.70000000E+00
+  1.30000000E+00  1.70000000E+00  1.30000000E+00  1.70000000E+00  1.30000000E+00
+  1.70000000E+00  1.30000000E+00  1.70000000E+00  1.70000000E+00  1.50000000E+00
+  1.55000000E+00  1.30000000E+00  1.70000000E+00  1.30000000E+00  1.70000000E+00
+  1.30000000E+00  1.30000000E+00  1.70000000E+00  1.30000000E+00  1.30000000E+00
+  1.70000000E+00  1.30000000E+00  1.30000000E+00  1.70000000E+00  1.30000000E+00
+  1.30000000E+00  1.55000000E+00  1.30000000E+00  1.30000000E+00  1.30000000E+00
+  1.70000000E+00  1.50000000E+00  1.55000000E+00  1.30000000E+00  1.70000000E+00
+  1.30000000E+00  1.30000000E+00  1.30000000E+00
+%FLAG SCREEN                                                                    
+%FORMAT(5E16.8)                                                                 
+  7.90000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01  7.20000000E-01
+  8.50000000E-01  7.20000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01
+  8.50000000E-01  7.20000000E-01  8.50000000E-01  7.90000000E-01  8.50000000E-01
+  7.20000000E-01  8.50000000E-01  7.20000000E-01  8.50000000E-01  8.50000000E-01
+  7.20000000E-01  7.20000000E-01  8.50000000E-01  7.90000000E-01  8.50000000E-01
+  7.20000000E-01  7.20000000E-01  8.50000000E-01  7.20000000E-01  8.50000000E-01
+  7.20000000E-01  8.50000000E-01  7.20000000E-01  8.50000000E-01  7.20000000E-01
+  7.20000000E-01  8.50000000E-01  7.90000000E-01  8.50000000E-01  7.20000000E-01
+  8.50000000E-01  7.20000000E-01  8.50000000E-01  7.20000000E-01  8.50000000E-01
+  8.50000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01  7.20000000E-01
+  8.50000000E-01  7.90000000E-01  8.50000000E-01  7.20000000E-01  8.50000000E-01
+  7.20000000E-01  8.50000000E-01  8.50000000E-01  7.20000000E-01  7.20000000E-01
+  8.50000000E-01  7.90000000E-01  8.50000000E-01  7.20000000E-01  7.20000000E-01
+  8.50000000E-01  7.20000000E-01  8.50000000E-01  7.20000000E-01  8.50000000E-01
+  7.20000000E-01  8.50000000E-01  7.20000000E-01  7.20000000E-01  8.50000000E-01
+  7.90000000E-01  8.50000000E-01  7.20000000E-01  8.50000000E-01  7.20000000E-01
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+  8.50000000E-01  8.50000000E-01  7.20000000E-01  8.50000000E-01  7.90000000E-01
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+  8.50000000E-01  7.90000000E-01  8.50000000E-01  7.20000000E-01  8.50000000E-01
+  7.20000000E-01  8.50000000E-01  8.50000000E-01  7.20000000E-01  8.50000000E-01
+  8.50000000E-01  7.20000000E-01  8.50000000E-01  8.50000000E-01  7.20000000E-01
+  8.50000000E-01  8.50000000E-01  7.90000000E-01  8.50000000E-01  8.50000000E-01
+  8.50000000E-01  7.20000000E-01  8.50000000E-01  7.90000000E-01  8.50000000E-01
+  7.20000000E-01  8.50000000E-01  7.20000000E-01  8.50000000E-01  8.50000000E-01
+  7.20000000E-01  7.20000000E-01  8.50000000E-01  7.90000000E-01  8.50000000E-01
+  7.20000000E-01  7.20000000E-01  8.50000000E-01  7.20000000E-01  8.50000000E-01
+  7.20000000E-01  8.50000000E-01  7.20000000E-01  8.50000000E-01  7.20000000E-01
+  7.20000000E-01  8.50000000E-01  7.90000000E-01  8.50000000E-01  7.20000000E-01
+  8.50000000E-01  7.20000000E-01  8.50000000E-01  7.20000000E-01  8.50000000E-01
+  8.50000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01  7.20000000E-01
+  8.50000000E-01  7.90000000E-01  8.50000000E-01  7.20000000E-01  8.50000000E-01
+  7.20000000E-01  8.50000000E-01  8.50000000E-01  7.20000000E-01  7.20000000E-01
+  8.50000000E-01  7.90000000E-01  8.50000000E-01  7.20000000E-01  7.20000000E-01
+  8.50000000E-01  7.20000000E-01  8.50000000E-01  7.20000000E-01  8.50000000E-01
+  7.20000000E-01  8.50000000E-01  7.20000000E-01  7.20000000E-01  8.50000000E-01
+  7.90000000E-01  8.50000000E-01  7.20000000E-01  8.50000000E-01  7.20000000E-01
+  8.50000000E-01  8.50000000E-01  7.20000000E-01  8.50000000E-01  8.50000000E-01
+  7.20000000E-01  8.50000000E-01  8.50000000E-01  7.20000000E-01  8.50000000E-01
+  8.50000000E-01  7.90000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01
+  7.20000000E-01  8.50000000E-01  7.90000000E-01  8.50000000E-01  7.20000000E-01
+  8.50000000E-01  8.50000000E-01  8.50000000E-01
+%FLAG IPOL                                                                      
+%FORMAT(1I8)                                                                    
+       0
+%FLAG ATOM_OCCUPANCY                                                            
+%FORMAT(10F8.2)                                                                 
+    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00
+    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00
+    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00
+    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00
+    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00
+    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00
+    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00
+    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00
+    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00
+    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00
+    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00
+    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00
+    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00
+    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00
+    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00
+    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00
+    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00
+    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00
+    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00
+    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00
+    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00
+    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00    1.00    0.00
+    0.00    0.00    0.00
+%FLAG ATOM_BFACTOR                                                              
+%FORMAT(10F8.2)                                                                 
+    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
+    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
+    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
+    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
+    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
+    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
+    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
+    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
+    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
+    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
+    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
+    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
+    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
+    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
+    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
+    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
+    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
+    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
+    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
+    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
+    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
+    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
+    0.00    0.00    0.00
+%FLAG ATOM_NUMBER                                                               
+%FORMAT(10I8)                                                                   
+       1       2       3       4       5       6       7       8       9      10
+      11      12      13      14      15      16      17      18      19      20
+      21      22      23      24      25      26      27      28      29      30
+      31      32      33      34      35      36      37      38      39      40
+      41      42      43      44      45      46      47      48      49      50
+      51      52      53      54      55      56      57      58      59      60
+      61      62      63      64      65      66      67      68      69      70
+      71      72      73      74      75      76      77      78      79      80
+      81      82      83      84      85      86      87      88      89      90
+      91      92      93      94      95      96      97      98      99     100
+     101     102     103     104     105     106     107     108     109     110
+     111     112     113     114     115     116     117     118     119     120
+     121     122     123     124     125     126     127     128     129     130
+     131     132     133     134     135     136     137     138     139     140
+     141     142     143     144     145     146     147     148     149     150
+     151     152     153     154     155     156     157     158     159     160
+     161     162     163     164     165     166     167     168     169     170
+     171     172     173     174     175     176     177     178     179     180
+     181     182     183     184     185     186     187     188     189     190
+     191     192     193     194     195     196     197     198     199     200
+     201     202     203     204     205     206     207     208     209     210
+     211     212     213     214     215     216     217     218     219       0
+       0       0       0
diff --git a/test/Test_Build/tz2.rst7.save b/test/Test_Build/tz2.rst7.save
new file mode 100644
index 0000000000..c58ccf35ff
--- /dev/null
+++ b/test/Test_Build/tz2.rst7.save
@@ -0,0 +1,114 @@
+Cpptraj Generated Restart                                                       
+  223
+  -1.8890001   9.1590004   7.5689998  -1.0369999   8.6910000   7.2960000
+  -1.9000000   9.2980003   8.5690002  -2.5380001   8.4469995   7.2649999
+  -2.0639999  10.5010004   6.9930000  -3.0999999  10.8240004   7.1020002
+  -1.2300000  11.5609999   7.7069998  -1.6700000  11.8109999   8.6730003
+  -1.2480000  12.5030003   7.1589999   0.1230000  11.2159996   7.9039998
+   0.2740000  11.7279997   8.7010002  -1.6130000  10.4180002   5.5419998
+  -2.4979999  10.4329996   4.6890001  -0.3660000  10.5719995   5.0900002
+   0.3440000  10.6120005   5.8080001   0.1950000  10.6969995   3.7600000
+  -0.2180000  11.5690002   3.2539999   1.7100000  10.8789997   3.7090001
+   2.2079999   9.9860001   4.0869999   1.9270000  11.6409998   4.4580002
+   2.2650001  11.2910004   2.3840001   2.0320001  12.5000000   1.8270000
+   1.5380000  13.3330002   2.3050001   2.8599999  12.5799999   0.7240000
+   2.9289999  13.4040003   0.1430000   3.6619999  11.4600000   0.6460000
+   4.6199999  11.1599998  -0.3300000   5.0590000  11.8629999  -1.0230000
+   5.0910001   9.8430004  -0.3770000   5.8540001   9.6099997  -1.1050000
+   4.5450001   8.8500004   0.4450000   4.8230000   7.8400002   0.1820000
+   3.5490000   9.1590004   1.3789999   3.1350000   8.4300003   2.0590000
+   3.0750000  10.4770002   1.4830000  -0.1900000   9.6090002   2.7679999
+  -0.4520000   9.9630003   1.6210001  -0.2680000   8.4020004   3.3340001
+  -0.2600000   8.2749996   4.3360000  -0.6060000   7.1719999   2.6470001
+  -0.1800000   7.2659998   1.6480000  -0.0930000   5.9920001   3.4679999
+  -0.5860000   5.0809999   3.1280000   1.3430001   5.6479998   3.0810001
+   1.3060000   5.0050001   2.2019999   1.9550000   6.5430002   2.9670000
+   1.8279999   5.0679998   3.8659999  -0.2730000   6.2459998   4.8429999
+   0.4280000   5.7500000   5.2709999  -2.0730000   6.8820000   2.3629999
+  -2.8840001   6.6849999   3.2650001  -2.4140000   6.7960000   1.0750000
+  -1.6310000   6.7560000   0.4390000  -3.6889999   6.2859998   0.6130000
+  -4.2880001   6.0200000   1.4850000  -4.4650002   7.2750001  -0.2530000
+  -5.4499998   6.8210001  -0.3660000  -4.0219998   7.1620002  -1.2420000
+  -4.6320000   8.7229996   0.0770000  -3.9020000   9.7130003  -0.4830000
+  -3.0890000   9.5530005  -1.1760000  -4.4730000  10.9230003  -0.1410000
+  -4.1360002  11.8610001  -0.3060000  -5.4689999  10.7460003   0.7980000
+  -6.3299999  11.6929998   1.3650000  -6.2760000  12.7460003   1.1300000
+  -7.3740001  11.1960001   2.1540000  -8.2299995  11.8219995   2.3620000
+  -7.6300001   9.8240004   2.2590001  -8.3789997   9.4820004   2.9590001
+  -6.7760000   8.9049997   1.6380000  -6.9740000   7.8720002   1.8839999
+  -5.7030001   9.3470001   0.8480000  -3.6320000   4.9260001  -0.0680000
+  -4.2789998   3.9519999   0.3090000  -2.7950001   4.8720002  -1.1059999
+  -2.2780001   5.7080002  -1.3390000  -2.5350001   3.7230000  -1.9500000
+  -3.0070000   2.9480000  -1.3460000  -3.4130001   3.5239999  -3.1830001
+  -3.1389999   4.1409998  -4.0380001  -4.3860002   3.7869999  -2.7670000
+  -3.4700000   2.1080000  -3.7479999  -2.4470000   1.7930000  -3.9530001
+  -4.0390000   2.4250000  -4.6230001  -4.1890001   1.1230000  -2.8369999
+  -3.8030000   0.7710000  -1.7020000  -5.2630000   0.6010000  -3.2070000
+  -1.0580000   3.5179999  -2.2550001  -0.3010000   4.4140000  -2.6190000
+  -0.6680000   2.2650001  -2.0090001  -1.3230000   1.6560000  -1.5390000
+   0.6390000   1.6960000  -2.2670000   1.2390000   2.4530001  -2.7720001
+   1.4119999   1.3660001  -0.9930000   2.2240000   0.7030000  -1.2910000
+   0.7120000   0.8820000  -0.3110000   2.1540000   2.5500000  -0.3910000
+   2.8090000   3.3469999  -1.0580000   2.3590000   2.5190001   0.9280000
+   1.8690000   1.8970000   1.5560000   3.0239999   3.1960001   1.2720000
+   0.5090000   0.4880000  -3.1849999  -0.4570000  -0.2500000  -3.0039999
+   1.4630001   0.2470000  -4.0869999   2.3720000   0.6580000  -3.9319999
+   1.3990000  -0.9020000  -4.9670000   2.1800001  -0.8820000  -5.7280002
+   0.5010000  -0.7990000  -5.5760002   1.4480000  -2.2750001  -4.3130002
+   0.7270000  -2.5760000  -3.3640001   2.3610001  -3.1180000  -4.8010001
+   3.0799999  -2.7839999  -5.4260001   2.5409999  -4.5139999  -4.4580002
+   1.6270000  -5.0149999  -4.1380000   3.1229999  -5.2830000  -5.6409998
+   2.4349999  -5.2430000  -6.4860001   3.3350000  -6.3179998  -5.3720002
+   4.4159999  -4.7459998  -6.2480001   5.3080001  -4.9600000  -5.6599998
+   4.3930001  -3.6740000  -6.4390001   4.7259998  -5.5029998  -7.5359998
+   3.9920001  -5.2719998  -8.3079996   4.5840001  -6.5430002  -7.2410002
+   6.1479998  -5.3379998  -8.0660000   6.5209999  -6.2900000  -8.4440002
+   6.8480000  -5.0250001  -7.2900000   6.1770000  -4.4200001  -9.2139997
+   6.0460000  -3.5469999  -8.7220001   7.1310000  -4.3920002  -9.5459995
+   5.4710002  -4.5500002  -9.9250002   3.5120001  -4.5190001  -3.2860000
+   4.6240001  -5.0419998  -3.2860000   2.9250000  -4.2560000  -2.1159999
+   2.0100000  -3.8789999  -2.3160000   3.3410001  -4.2620001  -0.7280000
+   4.4099998  -4.0450001  -0.7240000   2.6250000  -3.0680001  -0.1040000
+   1.5890000  -3.2939999   0.1480000   2.8350000  -2.1940000  -0.7210000
+   3.2880001  -2.4619999   1.0910000   2.9250000  -2.4360001   2.3929999
+   1.9490000  -2.7990000   2.6780000   3.8550000  -1.8450000   3.2240000
+   3.8850000  -1.8480000   4.2340002   4.8270001  -1.3030000   2.4080000
+   5.9109998  -0.4710000   2.7140000   6.1389999  -0.1560000   3.7210000
+   6.8410001  -0.1410000   1.7220000   7.7249999   0.4050000   2.0179999
+   6.5840001  -0.5900000   0.4210000   7.2309999  -0.2350000  -0.3680000
+   5.4239998  -1.2970001   0.0820000   5.1389999  -1.4650000  -0.9460000
+   4.4790001  -1.6200000   1.0690000   2.9449999  -5.5929999  -0.1050000
+   3.0220001  -6.6750002  -0.6820000   2.5309999  -5.6090002   1.1640000
+   2.7110000  -4.7940001   1.7309999   2.2539999  -6.8740001   1.8150001
+   2.9820001  -7.6669998   1.6440001   2.2070000  -6.6220002   3.3199999
+   1.7220000  -5.6669998   3.5260000   1.4560000  -7.6589999   4.1490002
+   1.5810000  -7.4640002   5.2140002   0.4020000  -7.4679999   3.9460001
+   1.7250000  -8.6400003   3.7550001   3.4600000  -6.5009999   3.9540000
+   3.3850000  -6.0970001   4.8220000   0.8890000  -7.3540001   1.3440000
+  -0.1720000  -6.7600002   1.5240000   0.9060000  -8.5220003   0.6990000
+   1.7230000  -9.1149998   0.7340000  -0.1880000  -9.0660000  -0.0800000
+  -0.7370000  -8.2200003  -0.4950000   0.4120000 -10.0100002  -1.1170000
+   1.1130000 -10.7100000  -0.6610000   0.8870000  -9.3680000  -1.8590000
+  -0.5390000 -10.9280005  -1.8160000  -1.3130000 -10.6859999  -2.8980000
+  -1.3370000  -9.7639999  -3.4600000  -1.9710000 -11.7860003  -3.4110000
+  -2.3840001 -11.8640003  -4.3299999  -1.9570000 -12.7629995  -2.4370000
+  -2.7850001 -13.8649998  -2.1910000  -3.6310000 -14.0120001  -2.8460000
+  -2.5999999 -14.7089996  -1.0890000  -3.3150001 -15.4729996  -0.8230000
+  -1.5180000 -14.3450003  -0.2780000  -1.3250000 -14.9359999   0.6040000
+  -0.8090000 -13.1459999  -0.4190000  -0.0380000 -12.8339996   0.2700000
+  -1.0340000 -12.2589998  -1.4840000  -1.0790000  -9.7519999   0.9460000
+  -0.7100000 -10.6730003   1.6720001  -2.3440001  -9.3260002   0.9490000
+  -2.4560001  -8.3389997   0.7700000  -3.4700000  -9.9259996   1.6360000
+  -3.0969999 -10.4390001   2.5220001  -4.3839998  -8.8140001   2.1420000
+  -5.3889999  -9.1120005   2.4400001  -4.4390001  -8.0089998   1.4090000
+  -3.7990000  -8.0920000   3.3520000  -2.8889999  -7.5660000   3.0639999
+  -3.6910000  -8.7240000   4.2329998  -4.8480000  -7.0240002   3.6500001
+  -5.6910000  -7.4109998   4.2220001  -5.1300001  -6.4949999   2.7400000
+  -4.1079998  -6.0190001   4.5289998  -3.1830001  -5.6350002   4.0990000
+  -3.8850000  -6.5530000   5.4520001  -4.8769999  -4.8020000   4.8290000
+  -5.1320000  -4.3049998   3.9870000  -5.7179999  -4.9679999   5.3620000
+  -4.2500000  -4.2630000   5.4099998  -4.3950000 -10.7779999   0.7790000
+  -4.4829998 -11.9390001   1.1720001  -4.8319998 -10.2019997  -0.3440000
+  -4.6469998  -9.2390003  -0.5870000  -5.7864748 -10.8540745  -1.2177150
+  -5.9324884 -11.8842255  -0.8928001  -6.7375435 -10.3230082  -1.1785067
+  -5.4084096 -10.8462084  -2.2400188

From 3816a0cbfdab1e34705ca99d712b05fa7cb54541 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 3 Mar 2026 14:16:09 -0500
Subject: [PATCH 1424/1492] Add build from COORDS test

---
 test/Test_Build/RunTest.sh | 15 +++++++++++++--
 1 file changed, 13 insertions(+), 2 deletions(-)

diff --git a/test/Test_Build/RunTest.sh b/test/Test_Build/RunTest.sh
index 042825eefe..7a8d6d071d 100755
--- a/test/Test_Build/RunTest.sh
+++ b/test/Test_Build/RunTest.sh
@@ -2,7 +2,7 @@
 
 . ../MasterTest.sh
 
-CleanFiles cpptraj.in tz2.parm7 tz2.rst7
+CleanFiles cpptraj.in tz2.parm7 tz2.rst7 tz2.coords.parm7 tz2.coords.rst7
 
 TESTNAME='Build tests'
 
@@ -13,12 +13,23 @@ if [ ! -z "$AMBERHOME" ] ; then
   unset AMBERHOME
 fi
 
+UNITNAME='Build test, direct'
 cat > cpptraj.in <<EOF
 source leaprc.protein.ff14SB
 build ../tz2.pdb parmout tz2.parm7 crdout tz2.rst7
 EOF
-RunCpptraj "$TESTNAME"
+RunCpptraj "$UNITNAME"
 DoTest tz2.parm7.save tz2.parm7 -I %VERSION
 DoTest tz2.rst7.save tz2.rst7
 
+UNITNAME='Build test, COORDS'
+cat > cpptraj.in <<EOF
+source leaprc.protein.ff14SB
+readdata ../tz2.pdb as coords name MyCrd
+build crdset MyCrd parmout tz2.coords.parm7 crdout tz2.coords.rst7
+EOF
+RunCpptraj "$UNITNAME"
+DoTest tz2.parm7.save tz2.coords.parm7 -I %VERSION
+DoTest tz2.rst7.save tz2.coords.rst7
+
 EndTest

From 502d8f5ce7416b47fb9b3ad3b2b2ab70b5fcbaab Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 3 Mar 2026 14:17:57 -0500
Subject: [PATCH 1425/1492] Enable the build test

---
 test/Makefile              | 6 +++++-
 test/Test_Build/RunTest.sh | 6 +++---
 2 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/test/Makefile b/test/Makefile
index 17f2214e01..b781b9f8f0 100644
--- a/test/Makefile
+++ b/test/Makefile
@@ -564,6 +564,9 @@ test.watershellclosest:
 test.mutate:
 	@-cd Test_Mutate && ./RunTest.sh $(OPT)
 
+test.build:
+	@-cd Test_Build && ./RunTest.sh $(OPT)
+
 # Only GPU-specific tests should go here
 GPUTESTS=test.closest \
          test.solvent \
@@ -749,7 +752,8 @@ COMPLETETESTS=test.general \
               test.addatom \
               test.minmaxdist \
               test.watershellclosest \
-              test.mutate
+              test.mutate \
+              test.build
 
 test.all:
 	$(MAKE) test.complete summary
diff --git a/test/Test_Build/RunTest.sh b/test/Test_Build/RunTest.sh
index 7a8d6d071d..724d93de0a 100755
--- a/test/Test_Build/RunTest.sh
+++ b/test/Test_Build/RunTest.sh
@@ -4,7 +4,7 @@
 
 CleanFiles cpptraj.in tz2.parm7 tz2.rst7 tz2.coords.parm7 tz2.coords.rst7
 
-TESTNAME='Build tests'
+TESTNAME='Build/Source tests'
 
 INPUT='-i cpptraj.in'
 
@@ -13,7 +13,7 @@ if [ ! -z "$AMBERHOME" ] ; then
   unset AMBERHOME
 fi
 
-UNITNAME='Build test, direct'
+UNITNAME='Source and Build test, direct'
 cat > cpptraj.in <<EOF
 source leaprc.protein.ff14SB
 build ../tz2.pdb parmout tz2.parm7 crdout tz2.rst7
@@ -22,7 +22,7 @@ RunCpptraj "$UNITNAME"
 DoTest tz2.parm7.save tz2.parm7 -I %VERSION
 DoTest tz2.rst7.save tz2.rst7
 
-UNITNAME='Build test, COORDS'
+UNITNAME='Source and Build test, COORDS'
 cat > cpptraj.in <<EOF
 source leaprc.protein.ff14SB
 readdata ../tz2.pdb as coords name MyCrd

From 129fb99e3db42b01be49feaa7175453f1f6d25e0 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 3 Mar 2026 14:41:31 -0500
Subject: [PATCH 1426/1492] Add test for change atomname with namemap

---
 test/Test_Change/RunTest.sh  | 19 ++++++++++++++++++-
 test/Test_Change/namemap.dat |  1 +
 2 files changed, 19 insertions(+), 1 deletion(-)
 create mode 100644 test/Test_Change/namemap.dat

diff --git a/test/Test_Change/RunTest.sh b/test/Test_Change/RunTest.sh
index 8b42a8c8a1..c4b9bb1ee1 100755
--- a/test/Test_Change/RunTest.sh
+++ b/test/Test_Change/RunTest.sh
@@ -4,7 +4,8 @@
 
 CleanFiles change.in ala3.mod.pdb ala3.chain.pdb crdala3.chain.pdb \
            AFV.zeroHmass.dat AFV.fluctMass.dat merged.?-?.mol2 \
-           AFV.zeroHcharge.dat AFV.1.offset.dat AFV.1.byfac.dat
+           AFV.zeroHcharge.dat AFV.1.offset.dat AFV.1.byfac.dat \
+           ala3.mod.namemap.pdb
 
 TESTNAME='Change command test'
 
@@ -25,6 +26,22 @@ EOF
   DoTest ala3.mod.pdb.save ala3.mod.pdb
 fi
 
+UNITNAME='Change atom name using name map test'
+CheckFor maxthreads 1
+if [ $? -eq 0 ] ; then
+  cat > change.in <<EOF
+parm ../Test_Charmm/ala3.psf
+trajin ../Test_Charmm/ala3.dcd 1 1
+change parmindex 0 resname from :1 to NALA
+change parmindex 0 resname from :3 to CALA
+readdata namemap.dat namemap
+change parmindex 0 atomname from @HN namemap namemap.dat
+trajout ala3.mod.namemap.pdb chainid " "
+EOF
+  RunCpptraj "$UNITNAME"
+  DoTest ala3.mod.pdb.save ala3.mod.namemap.pdb
+fi
+
 UNITNAME='Change chain ID test'
 CheckFor maxthreads 1
 if [ $? -eq 0 ] ; then
diff --git a/test/Test_Change/namemap.dat b/test/Test_Change/namemap.dat
new file mode 100644
index 0000000000..65b23bbdea
--- /dev/null
+++ b/test/Test_Change/namemap.dat
@@ -0,0 +1 @@
+H HN

From 73d920758c52b9af3f97384c1234e0edf2b88eac Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 3 Mar 2026 14:41:59 -0500
Subject: [PATCH 1427/1492] Update energy help. Fix change help text, and add
 entry for change gb/lj1264.

---
 doc/cpptraj.lyx     | 193 ++++++++++++++++++++++++++++++++++----------
 src/Exec_Change.cpp |   4 +-
 2 files changed, 154 insertions(+), 43 deletions(-)

diff --git a/doc/cpptraj.lyx b/doc/cpptraj.lyx
index b3b74cf3fd..28495106f3 100644
--- a/doc/cpptraj.lyx
+++ b/doc/cpptraj.lyx
@@ -5892,11 +5892,6 @@ Read
 \end_layout
 
 \begin_layout LyX-Code
- [vector [magnitude]] |
-\end_layout
-
-\begin_layout LyX-Code
- [mat3x3] |
 \begin_inset Separator latexpar
 \end_inset
 
@@ -5904,13 +5899,25 @@ Read
 \end_layout
 
 \begin_layout LyX-Code
- [read3d [dims <nx>,<ny>,<nz>] [origin <ox>,<oy>,<oz>]
+ [read3d [dims <nx>,<ny>,<nz>] [origin <ox>,<oy>,<oz>] |
 \end_layout
 
 \begin_layout LyX-Code
          [delta <dx>,<dy>,dz>] [prec {dbl|flt}] [bin {center|corner} ]
 \end_layout
 
+\begin_layout LyX-Code
+ [vector [magnitude]] |
+\end_layout
+
+\begin_layout LyX-Code
+ [mat3x3] |
+\end_layout
+
+\begin_layout LyX-Code
+ [namemap]
+\end_layout
+
 \begin_layout LyX-Code
 }
 \end_layout
@@ -5986,34 +5993,6 @@ nosquare2d Read data as XYZ matrix (i.e.
 \end_layout
 
 \end_deeper
-\begin_layout Description
-vector Read data as vector.
- If indices are present they will be skipped.
- Assume first 3 columns after the index column are vector X,
- Y,
- and Z,
- and (if present) the next 3 columns contain vector origin X,
- Y,
- and Z.
-\end_layout
-
-\begin_deeper
-\begin_layout Description
-magnitude If specified,
- assume vector file last column contains vector magnitudes;
- read these into a set with Aspect 'Mag'.
-\end_layout
-
-\end_deeper
-\begin_layout Description
-mat3x3 Read data as 3x3 matrix.
- If indices are present they will be skipped.
- Assume matrices are in row major order on each line,
- i.e.
- M(1,1) M(1,2) ...
- M(3,2) M(3,3).
-\end_layout
-
 \begin_layout Description
 read3d Read data as 3D grid.
  If no dimension data in file must also speify 'dims'.
@@ -6062,6 +6041,45 @@ bin
 \end_layout
 
 \end_deeper
+\begin_layout Description
+vector Read data as vector.
+ If indices are present they will be skipped.
+ Assume first 3 columns after the index column are vector X,
+ Y,
+ and Z,
+ and (if present) the next 3 columns contain vector origin X,
+ Y,
+ and Z.
+\end_layout
+
+\begin_deeper
+\begin_layout Description
+magnitude If specified,
+ assume vector file last column contains vector magnitudes;
+ read these into a set with Aspect 'Mag'.
+\end_layout
+
+\end_deeper
+\begin_layout Description
+mat3x3 Read data as 3x3 matrix.
+ If indices are present they will be skipped.
+ Assume matrices are in row major order on each line,
+ i.e.
+ M(1,1) M(1,2) ...
+ M(3,2) M(3,3).
+\end_layout
+
+\begin_layout Description
+namemap
+\begin_inset CommandInset label
+LatexCommand label
+name "cpptraj-readdata-dat-namemap"
+
+\end_inset
+
+ Read data as atom name map ('#TgtAt Tgt RefAt Ref' or '#Tgt Ref')
+\end_layout
+
 \end_deeper
 \begin_layout Standard
 By default,
@@ -16910,7 +16928,7 @@ change [parm <name> | parmindex <#> | <#> |
 \end_layout
 
 \begin_layout LyX-Code
-	  atomname from <mask> to <value> |
+	  atomname from <mask> {to <value>|namemap <mapset>} | |
 \end_layout
 
 \begin_layout LyX-Code
@@ -16934,7 +16952,19 @@ change [parm <name> | parmindex <#> | <#> |
 \end_layout
 
 \begin_layout LyX-Code
-      mergeres firstres <start res#> lastres <stop res#>
+      mergeres firstres <start res#> lastres <stop res#> |
+\end_layout
+
+\begin_layout LyX-Code
+      gb {bondi|amber6|mbondi|pbamber|mbondi2|parse|mbondi3} |
+\end_layout
+
+\begin_layout LyX-Code
+      lj1264 [lj1264mask <mask>] [tunfactor <fac>] [c4file <c4file>]
+\end_layout
+
+\begin_layout LyX-Code
+             [polfile <polfile>] [lj1264solvent <solvent>]
 \end_layout
 
 \begin_layout LyX-Code
@@ -17117,10 +17147,11 @@ from
 \begin_inset space ~
 \end_inset
 
-<mask>
-\begin_inset space ~
-\end_inset
+<mask> Change atoms names for atoms in <mask>.
+\end_layout
 
+\begin_deeper
+\begin_layout Description
 to
 \begin_inset space ~
 \end_inset
@@ -17128,6 +17159,27 @@ to
 <value> Change atom names for atoms in <mask> to the given <value>.
 \end_layout
 
+\begin_layout Description
+namemap
+\begin_inset space ~
+\end_inset
+
+<mapset> Change atom names according to the given name map set.
+ See 
+\begin_inset CommandInset ref
+LatexCommand vref
+reference "cpptraj-readdata-dat-namemap"
+plural "false"
+caps "false"
+noprefix "false"
+nolink "false"
+
+\end_inset
+
+ for details on reading in atom name maps.
+\end_layout
+
+\end_deeper
 \begin_layout Description
 addbond
 \begin_inset space ~
@@ -17311,6 +17363,43 @@ firstres
 \end_layout
 
 \end_deeper
+\begin_layout Description
+gb
+\begin_inset space ~
+\end_inset
+
+{bondi|amber6|mbondi|pbamber|mbondi2|parse|mbondi3} Add/change the GB radii set.
+ Default is mbondi.
+ See 
+\begin_inset CommandInset ref
+LatexCommand vref
+reference "subsec:cpptraj-build"
+plural "false"
+caps "false"
+noprefix "false"
+nolink "false"
+
+\end_inset
+
+ for details on the GB keywords.
+\end_layout
+
+\begin_layout Description
+[lj1264] Option to add LJ 12-6-4 parameters.
+ See 
+\begin_inset CommandInset ref
+LatexCommand vref
+reference "subsec:cpptraj-build"
+plural "false"
+caps "false"
+noprefix "false"
+nolink "false"
+
+\end_inset
+
+ for details on LJ 12-6-4 keywords.
+\end_layout
+
 \end_deeper
 \begin_layout Standard
 Change specified parts of the specified topology.
@@ -29986,11 +30075,15 @@ energy [<name>] [<mask1>] [out <filename>] [nobondstoh] [openmm [<mdopts>]]
 \end_layout
 
 \begin_layout LyX-Code
-   	[bond] [angle] [dihedral] {[nb14]|[e14]|[v14]} {[nonbond]|[elec] [vdw]} 
+   	[bond] [angle] [dihedral] {[nb14]|[e14]|[v14]} {[nonbond]|[elec] [vdw]}
+\end_layout
+
+\begin_layout LyX-Code
+       [cmap]
 \end_layout
 
 \begin_layout LyX-Code
-   	[{nokinetic|kinetic [ketype {vel|vv}] [dt <dt>]}]
+   	[{nokinetic|kinetic [ketype {vel|vv}] [dt <dt>]}] [lj1264]
 \end_layout
 
 \begin_layout LyX-Code
@@ -30114,6 +30207,10 @@ nolink "false"
 [vdw] Calculate van der Waals energy (Lennard-Jones 6-12 potential).
 \end_layout
 
+\begin_layout Description
+[cmap] Calculate CMAP energy.
+\end_layout
+
 \begin_layout Description
 [nokinetic] Do not calculate kinetic energy even if velocity/force information present.
 \end_layout
@@ -30159,6 +30256,10 @@ vv
 \end_layout
 
 \end_deeper
+\begin_layout Description
+[lj1264] Turn on LJ 12-6-4 contribution if topology contains LJ C coefficients.
+\end_layout
+
 \begin_layout Description
 [etype
 \begin_inset space ~
@@ -30375,6 +30476,10 @@ DataSet Aspects:
 [dih] Dihedral energy.
 \end_layout
 
+\begin_layout Description
+[cmap] CMAP energy.
+\end_layout
+
 \begin_layout Description
 [vdw14] 1-4 van der Waals energy.
 \end_layout
@@ -30424,6 +30529,12 @@ Calculation of energy terms requires that the associated topology file have para
 simple
 \series default
  require unit cell parameters.
+ By default,
+ to match SANDER/PMEMD behavior the LJ 12-6-4 contribution is not included in the van der Waals energy term unless the 
+\series bold
+lj1264
+\series default
+ keyword is specified.
 \end_layout
 
 \begin_layout Standard
diff --git a/src/Exec_Change.cpp b/src/Exec_Change.cpp
index 3d42324578..7f817e42f3 100644
--- a/src/Exec_Change.cpp
+++ b/src/Exec_Change.cpp
@@ -23,8 +23,8 @@ void Exec_Change::Help() const
           "\t  bondparm <mask1> [<mask2>] {setrk|scalerk|setreq|scalereq} <value> |\n"
           "\t  {mass|charge} [of <mask>] {to <value> |by <offset> |\n"
           "\t                             byfac <factor> |fromset <data set>} |\n"
-          "\t  mergeres firstres <start res#> lastres <stop res#>\n"
-          "\t  %s\n"
+          "\t  mergeres firstres <start res#> lastres <stop res#> |\n"
+          "\t  %s |\n"
           "\t  lj1264 %s\n"
           "\t}\n"
           "  Change specified parts of topology or topology of a COORDS data set.\n",

From 9de52ffd6e157fffd8315632166af166bb3a415d Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 3 Mar 2026 14:47:47 -0500
Subject: [PATCH 1428/1492] Add zmatrix complete test

---
 test/Test_Zmatrix/RunTest.sh                  |   6 +-
 .../zmatrix.0SB.complete.dat.save             | 195 ++++++++++++++++++
 2 files changed, 200 insertions(+), 1 deletion(-)
 create mode 100644 test/Test_Zmatrix/zmatrix.0SB.complete.dat.save

diff --git a/test/Test_Zmatrix/RunTest.sh b/test/Test_Zmatrix/RunTest.sh
index 4c88a0ff5b..1236c84c5d 100755
--- a/test/Test_Zmatrix/RunTest.sh
+++ b/test/Test_Zmatrix/RunTest.sh
@@ -3,7 +3,8 @@
 . ../MasterTest.sh
 
 CleanFiles cpptraj.in zmatrix.dat zmatrix.0SB.dat fromZmatrix.0SB.mol2 \
-           zmatrix.MEX.dat fromZmatrix.MEX.mol2
+           zmatrix.MEX.dat fromZmatrix.MEX.mol2 zmatrix.MEX.complete.dat \
+           zmatrix.0SB.complete.dat
 
 INPUT='-i cpptraj.in'
 
@@ -23,12 +24,14 @@ Sugar() {
   cat > cpptraj.in <<EOF
 parm 0SB.mol2
 loadcrd 0SB.mol2 name 0SB
+zmatrix 0SB complete out zmatrix.0SB.complete.dat name MyC
 zmatrix 0SB out zmatrix.0SB.dat name MyZ
 zmatrix 0SB zset MyZ name MyCrd
 crdout MyCrd fromZmatrix.0SB.mol2
 EOF
   RunCpptraj "$TESTNAME, Sugar"
   DoTest zmatrix.0SB.dat.save zmatrix.0SB.dat
+  DoTest zmatrix.0SB.complete.dat.save zmatrix.0SB.complete.dat
   DoTest 0SB.mol2 fromZmatrix.0SB.mol2
 }
 
@@ -36,6 +39,7 @@ MEX() {
   cat > cpptraj.in <<EOF
 parm MEX.mol2
 loadcrd MEX.mol2 name MEX
+#zmatrix complete MEX out zmatrix.MEX.complete.dat name MyComplete
 zmatrix MEX out zmatrix.MEX.dat name MyZ
 zmatrix MEX zset MyZ name MyCrd
 crdout MyCrd fromZmatrix.MEX.mol2
diff --git a/test/Test_Zmatrix/zmatrix.0SB.complete.dat.save b/test/Test_Zmatrix/zmatrix.0SB.complete.dat.save
new file mode 100644
index 0000000000..a299fb7693
--- /dev/null
+++ b/test/Test_Zmatrix/zmatrix.0SB.complete.dat.save
@@ -0,0 +1,195 @@
+#IC                                                                 MyC
+       1    1.000    2.000    3.000    5.000    1.445  119.813  172.109
+       2    5.000    3.000    2.000    1.000    1.547  109.628  172.109
+       3    1.000    2.000    3.000   18.000    1.445  119.813  -58.369
+       4   18.000    3.000    2.000    1.000    1.541  109.366  -58.369
+       5    1.000    2.000    3.000    4.000    1.445  119.813   57.481
+       6    4.000    3.000    2.000    1.000    1.092  107.320   57.481
+       7    1.000   32.000   28.000   18.000    1.549  112.519   54.054
+       8   18.000   28.000   32.000    1.000    1.555  110.763   54.054
+       9    1.000   32.000   28.000   30.000    1.549  112.519  177.651
+      10   30.000   28.000   32.000    1.000    1.460  108.777  177.651
+      11    1.000   32.000   28.000   29.000    1.549  112.519  -65.433
+      12   29.000   28.000   32.000    1.000    1.092  108.527  -65.433
+      13    2.000    1.000   35.000   36.000    1.445  112.883  125.259
+      14   36.000   35.000    1.000    2.000    1.259  115.055  125.259
+      15    2.000    1.000   35.000   37.000    1.445  112.883  -56.528
+      16   37.000   35.000    1.000    2.000    1.254  119.483  -56.528
+      17    2.000    1.000   32.000   28.000    1.445  106.898  -52.470
+      18   28.000   32.000    1.000    2.000    1.538  112.519  -52.470
+      19    2.000    1.000   32.000   33.000    1.445  106.898 -175.086
+      20   33.000   32.000    1.000    2.000    1.093  109.955 -175.086
+      21    2.000    1.000   32.000   34.000    1.445  106.898   69.077
+      22   34.000   32.000    1.000    2.000    1.093  110.143   69.077
+      23    2.000    3.000    5.000    7.000    1.443  109.628   78.456
+      24    7.000    5.000    3.000    2.000    1.449  109.776   78.456
+      25    2.000    3.000    5.000    9.000    1.443  109.628  -45.455
+      26    9.000    5.000    3.000    2.000    1.556  114.437  -45.455
+      27    2.000    3.000    5.000    6.000    1.443  109.628 -165.180
+      28    6.000    5.000    3.000    2.000    1.091  107.454 -165.180
+      29    2.000    3.000   18.000   20.000    1.443  109.366  173.191
+      30   20.000   18.000    3.000    2.000    1.475  109.673  173.191
+      31    2.000    3.000   18.000   28.000    1.443  109.366   52.047
+      32   28.000   18.000    3.000    2.000    1.555  110.258   52.047
+      33    2.000    3.000   18.000   19.000    1.443  109.366  -66.569
+      34   19.000   18.000    3.000    2.000    1.092  109.164  -66.569
+      35    3.000    2.000    1.000   35.000    1.443  119.813  173.396
+      36   35.000    1.000    2.000    3.000    1.623  112.883  173.396
+      37    3.000    2.000    1.000   32.000    1.443  119.813   57.190
+      38   32.000    1.000    2.000    3.000    1.549  106.898   57.190
+      39    3.000    5.000    7.000    8.000    1.547  109.776   69.177
+      40    8.000    7.000    5.000    3.000    0.974  109.637   69.177
+      41    3.000    5.000    9.000   11.000    1.547  114.437  -50.185
+      42   11.000    9.000    5.000    3.000    1.460  109.032  -50.185
+      43    3.000    5.000    9.000   13.000    1.547  114.437 -170.254
+      44   13.000    9.000    5.000    3.000    1.547  112.392 -170.254
+      45    3.000    5.000    9.000   10.000    1.547  114.437   68.196
+      46   10.000    9.000    5.000    3.000    1.091  109.581   68.196
+      47    3.000   18.000   20.000   22.000    1.541  109.673   97.438
+      48   22.000   20.000   18.000    3.000    1.332  123.257   97.438
+      49    3.000   18.000   20.000   21.000    1.541  109.673  -78.719
+      50   21.000   20.000   18.000    3.000    1.005  117.087  -78.719
+      51    3.000   18.000   28.000   30.000    1.541  110.258 -174.457
+      52   30.000   28.000   18.000    3.000    1.460  112.071 -174.457
+      53    3.000   18.000   28.000   32.000    1.541  110.258  -52.775
+      54   32.000   28.000   18.000    3.000    1.538  110.763  -52.775
+      55    3.000   18.000   28.000   29.000    1.541  110.258   66.493
+      56   29.000   28.000   18.000    3.000    1.092  108.890   66.493
+      57    4.000    3.000    5.000    7.000    1.092  105.944 -166.038
+      58    7.000    5.000    3.000    4.000    1.449  109.776 -166.038
+      59    4.000    3.000    5.000    9.000    1.092  105.944   70.051
+      60    9.000    5.000    3.000    4.000    1.556  114.437   70.051
+      61    4.000    3.000    5.000    6.000    1.092  105.944  -49.674
+      62    6.000    5.000    3.000    4.000    1.091  107.454  -49.674
+      63    4.000    3.000   18.000   20.000    1.092  107.097   57.198
+      64   20.000   18.000    3.000    4.000    1.475  109.673   57.198
+      65    4.000    3.000   18.000   28.000    1.092  107.097  -63.946
+      66   28.000   18.000    3.000    4.000    1.555  110.258  -63.946
+      67    4.000    3.000   18.000   19.000    1.092  107.097  177.439
+      68   19.000   18.000    3.000    4.000    1.092  109.164  177.439
+      69    5.000    3.000   18.000   20.000    1.547  117.007  -61.444
+      70   20.000   18.000    3.000    5.000    1.475  109.673  -61.444
+      71    5.000    3.000   18.000   28.000    1.547  117.007  177.412
+      72   28.000   18.000    3.000    5.000    1.555  110.258  177.412
+      73    5.000    3.000   18.000   19.000    1.547  117.007   58.796
+      74   19.000   18.000    3.000    5.000    1.092  109.164   58.796
+      75    5.000    9.000   11.000   12.000    1.556  109.032   66.841
+      76   12.000   11.000    9.000    5.000    0.967  107.041   66.841
+      77    5.000    9.000   13.000   16.000    1.556  112.392 -179.231
+      78   16.000   13.000    9.000    5.000    1.445  110.975 -179.231
+      79    5.000    9.000   13.000   14.000    1.556  112.392  -58.947
+      80   14.000   13.000    9.000    5.000    1.090  110.244  -58.947
+      81    5.000    9.000   13.000   15.000    1.556  112.392   60.184
+      82   15.000   13.000    9.000    5.000    1.091  110.082   60.184
+      83    6.000    5.000    3.000   18.000    1.091  107.454   69.587
+      84   18.000    3.000    5.000    6.000    1.541  117.007   69.587
+      85    6.000    5.000    7.000    8.000    1.091  107.287  -47.292
+      86    8.000    7.000    5.000    6.000    0.974  109.637  -47.292
+      87    6.000    5.000    9.000   11.000    1.091  107.851   69.317
+      88   11.000    9.000    5.000    6.000    1.460  109.032   69.317
+      89    6.000    5.000    9.000   13.000    1.091  107.851  -50.752
+      90   13.000    9.000    5.000    6.000    1.547  112.392  -50.752
+      91    6.000    5.000    9.000   10.000    1.091  107.851 -172.302
+      92   10.000    9.000    5.000    6.000    1.091  109.581 -172.302
+      93    7.000    5.000    3.000   18.000    1.449  109.776  -46.778
+      94   18.000    3.000    5.000    7.000    1.541  117.007  -46.778
+      95    7.000    5.000    9.000   11.000    1.449  109.755 -174.107
+      96   11.000    9.000    5.000    7.000    1.460  109.032 -174.107
+      97    7.000    5.000    9.000   13.000    1.449  109.755   65.824
+      98   13.000    9.000    5.000    7.000    1.547  112.392   65.824
+      99    7.000    5.000    9.000   10.000    1.449  109.755  -55.726
+     100   10.000    9.000    5.000    7.000    1.091  109.581  -55.726
+     101    8.000    7.000    5.000    9.000    0.974  109.637 -164.222
+     102    9.000    5.000    7.000    8.000    1.556  109.755 -164.222
+     103    9.000    5.000    3.000   18.000    1.556  114.437 -170.688
+     104   18.000    3.000    5.000    9.000    1.541  117.007 -170.688
+     105    9.000   13.000   16.000   17.000    1.547  110.975  -44.062
+     106   17.000   16.000   13.000    9.000    0.965  106.902  -44.062
+     107   10.000    9.000   11.000   12.000    1.091  108.305  -52.337
+     108   12.000   11.000    9.000   10.000    0.967  107.041  -52.337
+     109   10.000    9.000   13.000   16.000    1.091  109.157  -57.439
+     110   16.000   13.000    9.000   10.000    1.445  110.975  -57.439
+     111   10.000    9.000   13.000   14.000    1.091  109.157   62.845
+     112   14.000   13.000    9.000   10.000    1.090  110.244   62.845
+     113   10.000    9.000   13.000   15.000    1.091  109.157 -178.024
+     114   15.000   13.000    9.000   10.000    1.091  110.082 -178.024
+     115   11.000    9.000   13.000   16.000    1.460  108.283   60.267
+     116   16.000   13.000    9.000   11.000    1.445  110.975   60.267
+     117   11.000    9.000   13.000   14.000    1.460  108.283 -179.449
+     118   14.000   13.000    9.000   11.000    1.090  110.244 -179.449
+     119   11.000    9.000   13.000   15.000    1.460  108.283  -60.318
+     120   15.000   13.000    9.000   11.000    1.091  110.082  -60.318
+     121   12.000   11.000    9.000   13.000    0.967  107.041 -170.587
+     122   13.000    9.000   11.000   12.000    1.547  108.283 -170.587
+     123   14.000   13.000   16.000   17.000    1.090  108.537 -165.355
+     124   17.000   16.000   13.000   14.000    0.965  106.902 -165.355
+     125   15.000   13.000   16.000   17.000    1.091  108.863   77.241
+     126   17.000   16.000   13.000   15.000    0.965  106.902   77.241
+     127   18.000   20.000   22.000   23.000    1.475  123.257   -3.821
+     128   23.000   22.000   20.000   18.000    1.226  121.726   -3.821
+     129   18.000   20.000   22.000   24.000    1.475  123.257  176.070
+     130   24.000   22.000   20.000   18.000    1.541  116.620  176.070
+     131   18.000   28.000   30.000   31.000    1.555  112.071  -59.820
+     132   31.000   30.000   28.000   18.000    0.961  110.371  -59.820
+     133   18.000   28.000   32.000   33.000    1.555  110.763  176.806
+     134   33.000   32.000   28.000   18.000    1.093  109.712  176.806
+     135   18.000   28.000   32.000   34.000    1.555  110.763  -68.268
+     136   34.000   32.000   28.000   18.000    1.093  108.775  -68.268
+     137   19.000   18.000   20.000   22.000    1.092  109.721  -22.463
+     138   22.000   20.000   18.000   19.000    1.332  123.257  -22.463
+     139   19.000   18.000   20.000   21.000    1.092  109.721  161.380
+     140   21.000   20.000   18.000   19.000    1.005  117.087  161.380
+     141   19.000   18.000   28.000   30.000    1.092  108.104  -55.195
+     142   30.000   28.000   18.000   19.000    1.460  112.071  -55.195
+     143   19.000   18.000   28.000   32.000    1.092  108.104   66.487
+     144   32.000   28.000   18.000   19.000    1.538  110.763   66.487
+     145   19.000   18.000   28.000   29.000    1.092  108.104 -174.245
+     146   29.000   28.000   18.000   19.000    1.092  108.890 -174.245
+     147   20.000   18.000   28.000   30.000    1.475  109.896   64.532
+     148   30.000   28.000   18.000   20.000    1.460  112.071   64.532
+     149   20.000   18.000   28.000   32.000    1.475  109.896 -173.786
+     150   32.000   28.000   18.000   20.000    1.538  110.763 -173.786
+     151   20.000   18.000   28.000   29.000    1.475  109.896  -54.518
+     152   29.000   28.000   18.000   20.000    1.092  108.890  -54.518
+     153   20.000   22.000   24.000   25.000    1.332  116.620   23.276
+     154   25.000   24.000   22.000   20.000    1.092  111.126   23.276
+     155   20.000   22.000   24.000   26.000    1.332  116.620  -97.180
+     156   26.000   24.000   22.000   20.000    1.091  109.294  -97.180
+     157   20.000   22.000   24.000   27.000    1.332  116.620  143.390
+     158   27.000   24.000   22.000   20.000    1.091  109.699  143.390
+     159   21.000   20.000   18.000   28.000    1.005  117.087   42.643
+     160   28.000   18.000   20.000   21.000    1.555  109.896   42.643
+     161   21.000   20.000   22.000   23.000    1.005  119.545  172.247
+     162   23.000   22.000   20.000   21.000    1.226  121.726  172.247
+     163   21.000   20.000   22.000   24.000    1.005  119.545   -7.862
+     164   24.000   22.000   20.000   21.000    1.541  116.620   -7.862
+     165   22.000   20.000   18.000   28.000    1.332  123.257 -141.200
+     166   28.000   18.000   20.000   22.000    1.555  109.896 -141.200
+     167   23.000   22.000   24.000   25.000    1.226  121.654 -156.833
+     168   25.000   24.000   22.000   23.000    1.092  111.126 -156.833
+     169   23.000   22.000   24.000   26.000    1.226  121.654   82.711
+     170   26.000   24.000   22.000   23.000    1.091  109.294   82.711
+     171   23.000   22.000   24.000   27.000    1.226  121.654  -36.719
+     172   27.000   24.000   22.000   23.000    1.091  109.699  -36.719
+     173   28.000   32.000    1.000   35.000    1.538  112.519 -173.146
+     174   35.000    1.000   32.000   28.000    1.623  106.036 -173.146
+     175   29.000   28.000   30.000   31.000    1.092  107.704   59.926
+     176   31.000   30.000   28.000   29.000    0.961  110.371   59.926
+     177   29.000   28.000   32.000   33.000    1.092  108.527   57.319
+     178   33.000   32.000   28.000   29.000    1.093  109.712   57.319
+     179   29.000   28.000   32.000   34.000    1.092  108.527  172.245
+     180   34.000   32.000   28.000   29.000    1.093  108.775  172.245
+     181   30.000   28.000   32.000   33.000    1.460  108.777  -59.597
+     182   33.000   32.000   28.000   30.000    1.093  109.712  -59.597
+     183   30.000   28.000   32.000   34.000    1.460  108.777   55.329
+     184   34.000   32.000   28.000   30.000    1.093  108.775   55.329
+     185   31.000   30.000   28.000   32.000    0.961  110.371  177.367
+     186   32.000   28.000   30.000   31.000    1.538  108.777  177.367
+     187   32.000    1.000   35.000   36.000    1.549  106.036 -118.024
+     188   36.000   35.000    1.000   32.000    1.259  115.055 -118.024
+     189   32.000    1.000   35.000   37.000    1.549  106.036   60.190
+     190   37.000   35.000    1.000   32.000    1.254  119.483   60.190
+     191   33.000   32.000    1.000   35.000    1.093  109.955   64.239
+     192   35.000    1.000   32.000   33.000    1.623  106.036   64.239
+     193   34.000   32.000    1.000   35.000    1.093  110.143  -51.599
+     194   35.000    1.000   32.000   34.000    1.623  106.036  -51.599

From 63c7cfa5e10b6f7edd7c86e375ceb5191ba0ece1 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 3 Mar 2026 14:50:53 -0500
Subject: [PATCH 1429/1492] Fix up entry for zmatrix complete

---
 doc/cpptraj.lyx      | 12 +++++++++---
 src/Exec_Zmatrix.cpp |  4 ++--
 2 files changed, 11 insertions(+), 5 deletions(-)

diff --git a/doc/cpptraj.lyx b/doc/cpptraj.lyx
index 28495106f3..8abad59e97 100644
--- a/doc/cpptraj.lyx
+++ b/doc/cpptraj.lyx
@@ -11129,11 +11129,11 @@ zmatrix <COORDS set name> [name <output set name>]
 \end_layout
 
 \begin_layout LyX-Code
-        { zset <input zmatrix set> [parm <top>|parmindex <#>] |
+        { zset <input zmatrix set> [parm <top>|parmindex <#>]|
 \end_layout
 
 \begin_layout LyX-Code
-          [molnum <mol#>] [frame <frame#>] [out <zmatrix file>] }
+          [complete][molnum <mol#>] [frame <frame#>] [out <zmatrix file>] }
 \end_layout
 
 \begin_deeper
@@ -11199,6 +11199,12 @@ parmindex
 \end_layout
 
 \end_deeper
+\begin_layout Description
+complete If specified,
+ generate all possible internal coordinates,
+ otherwise generate a minimal set.
+\end_layout
+
 \begin_layout Description
 [molnum
 \begin_inset space ~
@@ -17164,7 +17170,7 @@ namemap
 \begin_inset space ~
 \end_inset
 
-<mapset> Change atom names according to the given name map set.
+<mapset> Change atom names from reference name to target name according to the given name map set (#Tgt Ref).
  See 
 \begin_inset CommandInset ref
 LatexCommand vref
diff --git a/src/Exec_Zmatrix.cpp b/src/Exec_Zmatrix.cpp
index c4e8158e9e..0a109eebba 100644
--- a/src/Exec_Zmatrix.cpp
+++ b/src/Exec_Zmatrix.cpp
@@ -116,8 +116,8 @@ const
 void Exec_Zmatrix::Help() const
 {
   mprintf("\t<COORDS set name> [name <output set name>]\n"
-          "\t{ zset <input zmatrix set> [parm <top>|parmindex <#>] [complete]|\n"
-          "\t  [molnum <mol#>] [frame <frame#>] [out <zmatrix file>] }\n"
+          "\t{ zset <input zmatrix set> [parm <top>|parmindex <#>]|\n"
+          "\t  [complete] [molnum <mol#>] [frame <frame#>] [out <zmatrix file>] }\n"
           "  If 'zset' is specified, use Z-matrix to generate coordinates using\n"
           "  a specified topology or topology from specified COORDS set;\n"
           "  output is a new COORDS set. If 'complete is specified, generate\n"

From 255d3a7258baed7e411e73be6df8e97bc6fbf554 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 3 Mar 2026 14:52:42 -0500
Subject: [PATCH 1430/1492] Add entry for mol2 write atombondorder

---
 doc/cpptraj.lyx | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/doc/cpptraj.lyx b/doc/cpptraj.lyx
index 8abad59e97..72c9a9c7af 100644
--- a/doc/cpptraj.lyx
+++ b/doc/cpptraj.lyx
@@ -22055,6 +22055,10 @@ keepext Keep filename extension;
  write '<name>.<num>.<ext>' instead (implies 'multi').
 \end_layout
 
+\begin_layout Description
+atombondorder Sort bonds by first atom index (will produce Mol2 files similar to LEaP).
+\end_layout
+
 \end_deeper
 \begin_layout Subsubsection
 Options for SQM input format:

From 7e56dd46ea6457504e85246cd7327d014a44e830 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 3 Mar 2026 16:04:02 -0500
Subject: [PATCH 1431/1492] Make nodlparams the default

---
 src/Exec_PrepareForLeap.cpp | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/Exec_PrepareForLeap.cpp b/src/Exec_PrepareForLeap.cpp
index 14591a1b00..4cf99549a7 100644
--- a/src/Exec_PrepareForLeap.cpp
+++ b/src/Exec_PrepareForLeap.cpp
@@ -423,8 +423,8 @@ void Exec_PrepareForLeap::Help() const
           "  have any inter-residue bonds removed, and the appropriate LEaP\n"
           "  input to add the bonds back once the structure has been loaded\n"
           "  into LEaP will be written to <leap input file>.\n"
-          "  The command will attempt to download parameters for unknown\n"
-          "  residues unless 'nodlparams' is specified.\n",
+          "  If 'dlparams' is specified, the command will attempt to download\n"
+          "  parameters for unknown residues.\n",
           HisProt::keywords_,
           Disulfide::keywords_,
           SugarBuilder::keywords_
@@ -445,7 +445,7 @@ Exec::RetType Exec_PrepareForLeap::Execute(CpptrajState& State, ArgList& argIn)
   else if (argIn.hasKey("nodlparams"))
     downloadParams_ = false;
   else
-    downloadParams_ = true;
+    downloadParams_ = false;
   if (argIn.hasKey("bondunknown"))
     bondUnknownResidues_ = true;
   else if (argIn.hasKey("nobondunknown"))

From 6690b766494ea917ac31dea5e639adfd20cc0724 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Tue, 3 Mar 2026 16:09:10 -0500
Subject: [PATCH 1432/1492] Fix up prepareforleap help

---
 doc/cpptraj.lyx | 40 ++++++++++++++++++++++++++++++++++++++--
 1 file changed, 38 insertions(+), 2 deletions(-)

diff --git a/doc/cpptraj.lyx b/doc/cpptraj.lyx
index 72c9a9c7af..254d7c7cdf 100644
--- a/doc/cpptraj.lyx
+++ b/doc/cpptraj.lyx
@@ -10278,7 +10278,7 @@ prepareforleap crdset <coords set> [frame <#>] name <out coords set>
 \end_layout
 
 \begin_layout LyX-Code
-                  	[pdbout <pdbfile> [terbymol]]
+                  	[pdbout <pdbfile> [terbymol]] [problemout <file>]
 \end_layout
 
 \begin_layout LyX-Code
@@ -10286,7 +10286,7 @@ prepareforleap crdset <coords set> [frame <#>] name <out coords set>
 \end_layout
 
 \begin_layout LyX-Code
-                  	[skiperrors]
+                  	[skiperrors] [{dlparams|nodlparams}] [{bondunknown|nobondunknown}]
 \end_layout
 
 \begin_layout LyX-Code
@@ -10405,6 +10405,14 @@ set> Output COORDS set containing prepared topology/coordinates.
 \end_layout
 
 \end_deeper
+\begin_layout Description
+[problemout
+\begin_inset space ~
+\end_inset
+
+<file>] If specified redirect found problems to <file> instead of stdout.
+\end_layout
+
 \begin_layout Description
 [leapunitname
 \begin_inset space ~
@@ -10469,6 +10477,34 @@ file> should contain the appropriate 'source' commands for loading the desired f
  Can be useful for debugging.
 \end_layout
 
+\begin_layout Description
+[{dlparams|nodlparams}] If 
+\series bold
+'dlparams'
+\series default
+ is specified,
+ try to download parameters for unknown residues (default is to not do this,
+ 
+\series bold
+'nodlparams'
+\series default
+).
+\end_layout
+
+\begin_layout Description
+[{bondunknown|nobondunknown}] If 
+\series bold
+'bondunknown'
+\series default
+ is specified,
+ try to determine bonds to unknown residues (default is to not do this,
+ 
+\series bold
+'nobondunknown'
+\series default
+).
+\end_layout
+
 \begin_layout Description
 [nowat] If specified,
  remove waters from the system.

From 8e7f11788eb7583f173274de65d35c2c0f94ea61 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 4 Mar 2026 08:32:16 -0500
Subject: [PATCH 1433/1492] Add warning about missing residues to build

---
 src/Exec_Build.cpp | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 04348f7267..7e0cc5b916 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -1068,6 +1068,7 @@ Exec::RetType Exec_Build::BuildAndParmStructure(DataSet* inCrdPtr, std::string c
               inCrdPtr->legend());
     return CpptrajState::ERR;
   }
+  unsigned int input_has_missing_res = ((DataSet_Coords*)inCrdPtr)->Top().MissingRes().size();
   std::string title = argIn.GetStringKey("title");
   if (argIn.hasKey("nofixorder"))
     fixAtomOrder_ = false;
@@ -1415,6 +1416,15 @@ Exec::RetType Exec_Build::BuildAndParmStructure(DataSet* inCrdPtr, std::string c
     mprintf("\t%i total problems detected.\n", Ntotal_problems);
     t_check_.Stop();
   }
+  if (input_has_missing_res > 0) {
+    mprintf("Warning: Input coordinates had %u missing residues.\n", input_has_missing_res);
+    mprintf("Warning: If long bond lengths were reported above it may be due to these\n"
+            "Warning:  missing residues. If the missing residues are non-terminal\n"
+            "Warning:  they should probably be modeled in.\n"
+            "Warning: The 'addmissingres' command could be used to create a simple\n"
+            "Warning:  model for these missing residues, but note THAT COMMAND\n"
+            "Warning:  IS STILL EXPERIMENTAL. Results should be carefully checked.\n");
+  }
 
   // Total charge check
   double totalSystemCharge = crdout.Top().TotalCharge();

From 94e13570cfeea7e8c155e934c1e68c877b9fac26 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 4 Mar 2026 08:45:29 -0500
Subject: [PATCH 1434/1492] Start code for allowing redirection of all problem
 details to a file.

---
 src/Exec_Build.cpp | 37 +++++++++++++++++++++----------------
 src/Exec_Build.h   |  1 +
 2 files changed, 22 insertions(+), 16 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 7e0cc5b916..44dae00de0 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -1301,6 +1301,10 @@ Exec::RetType Exec_Build::BuildAndParmStructure(DataSet* inCrdPtr, std::string c
   // Structure check
   mprintf("    -----===== Structure Check =====-----\n");
   StructureCheck check;
+  // TODO make file a user option
+  CpptrajFile check_output;
+  check_output.OpenWrite(reportfile_);
+  int Ntotal_problems = 0;
   if (check_structure_) {
     mprintf("\tWill check bond lengths, atomic overlaps, and ring intersections.\n");
     t_check_.Start();
@@ -1355,11 +1359,8 @@ Exec::RetType Exec_Build::BuildAndParmStructure(DataSet* inCrdPtr, std::string c
       mprintf("\tImaging on.\n");
     else
       mprintf("\timaging off.\n");
-    // TODO make file a user option
-    CpptrajFile check_output;
-    check_output.OpenWrite("");
     t_check_overlaps_.Start();
-    int Ntotal_problems = check.CheckOverlaps( frameOut );
+    Ntotal_problems = check.CheckOverlaps( frameOut );
     t_check_overlaps_.Stop();
     check.WriteProblemsToFile( &check_output, 1, topOut );
     t_check_bonds_.Start();
@@ -1370,7 +1371,6 @@ Exec::RetType Exec_Build::BuildAndParmStructure(DataSet* inCrdPtr, std::string c
     Ntotal_problems += check.CheckRings( frameOut );
     t_check_rings_.Stop();
     check.WriteProblemsToFile( &check_output, 1, topOut );
-    mprintf("\t%i total problems detected.\n", Ntotal_problems);
     // If box was added for check only, remove it
     if (box_added)
       frameOut.ModifyBox().SetNoBox();
@@ -1406,19 +1406,17 @@ Exec::RetType Exec_Build::BuildAndParmStructure(DataSet* inCrdPtr, std::string c
     t_check_setup_.Stop();
     check.PrintTiming(1, t_check_setup_.Total());
     check.Mask1().MaskInfo();
-    // TODO make file a user option
-    CpptrajFile check_output;
-    check_output.OpenWrite("");
     t_check_bonds_.Start();
-    int Ntotal_problems = check.CheckBonds( frameOut );
+    Ntotal_problems = check.CheckBonds( frameOut );
     t_check_bonds_.Stop();
     check.WriteProblemsToFile( &check_output, 1, topOut );
-    mprintf("\t%i total problems detected.\n", Ntotal_problems);
     t_check_.Stop();
   }
   if (input_has_missing_res > 0) {
-    mprintf("Warning: Input coordinates had %u missing residues.\n", input_has_missing_res);
-    mprintf("Warning: If long bond lengths were reported above it may be due to these\n"
+    Ntotal_problems++;
+    check_output.Printf("Warning: Input coordinates had %u missing residues.\n", input_has_missing_res);
+    check_output.Printf(
+            "Warning: If long bond lengths were reported above it may be due to these\n"
             "Warning:  missing residues. If the missing residues are non-terminal\n"
             "Warning:  they should probably be modeled in.\n"
             "Warning: The 'addmissingres' command could be used to create a simple\n"
@@ -1431,10 +1429,17 @@ Exec::RetType Exec_Build::BuildAndParmStructure(DataSet* inCrdPtr, std::string c
   double absSystemCharge = fabs(totalSystemCharge);
   double q_frac = fabs( absSystemCharge - (double)(int)(absSystemCharge+0.5) );
   // NOTE: These cutoffs are the same as in LEaP
-  if ( q_frac > 0.01 )
-   mprintf("Warning: The charge of the system is not integral: %f\n", totalSystemCharge);
-  if ( absSystemCharge > 0.01 )
-    mprintf("Warning: The charge of the system is not zero: %f\n", totalSystemCharge);
+  if ( q_frac > 0.01 ) {
+   check_output.Printf("Warning: The charge of the system is not integral: %f\n", totalSystemCharge);
+   Ntotal_problems++;
+  }
+  if ( absSystemCharge > 0.01 ) {
+    check_output.Printf("Warning: The charge of the system is not zero: %f\n", totalSystemCharge);
+    Ntotal_problems++;
+  }
+  check_output.Printf("\t%i total problems detected.\n", Ntotal_problems);
+  if (!reportfile_.empty())
+    mprintf("\t%i total problems detected. See '%s' for details.\n", Ntotal_problems, reportfile_.c_str());
 
   mprintf("    -----===== File Output =====-----\n");
   if (!outputTopologyName.empty()) {
diff --git a/src/Exec_Build.h b/src/Exec_Build.h
index 45fc9d712f..b6f8dcd84a 100644
--- a/src/Exec_Build.h
+++ b/src/Exec_Build.h
@@ -64,6 +64,7 @@ class Exec_Build : public Exec {
     bool doSugar_;
     bool fixAtomOrder_;           ///< If true will attempt to make sure residues in molecules are contiguous
     DataSet* outCrdPtr_;          ///< Hold built (output) COORDS
+    std::string reportfile_;      ///< File for reporting problems with the final structure
 
     Timer t_total_;
     Timer t_hisDetect_;

From cde9674f9fc06d843dab65c8501293218fbde56e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 4 Mar 2026 08:50:18 -0500
Subject: [PATCH 1435/1492] Add reportfile keyword

---
 src/Exec_Build.cpp | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 44dae00de0..430643af08 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -828,7 +828,8 @@ void Exec_Build::Help() const
   mprintf("\t[name <output COORDS>] {crdset <COORDS set>|<file>} [{frame <#>|doassembly}]\n");
   Cpptraj::Structure::PdbCleaner::Help();
   mprintf("\t[title <title>] [verbose <#>] [keepmissingatoms] [nofixorder]\n"
-          "\t[parmout <topology file>] [crdout <coord file>] [simplecheck]\n");
+          "\t[parmout <topology file>] [crdout <coord file>] [simplecheck]\n"
+          "\t[reportfile <check file>]\n");
   mprintf("\t[%s]\n", Cpptraj::Parm::GB_Params::HelpText().c_str());
   mprintf("\t[lj1264 %s]\n", Cpptraj::Parm::LJ1264_Params::HelpText().c_str());
   mprintf("\t[%s]\n"
@@ -1081,6 +1082,9 @@ Exec::RetType Exec_Build::BuildAndParmStructure(DataSet* inCrdPtr, std::string c
   } else {
     check_structure_ = true;
   }
+  reportfile_ = argIn.GetStringKey("reportfile");
+  if (!reportfile_.empty())
+    mprintf("\tProblems with the final structure will be written to '%s'\n", reportfile_.c_str());
   doHisDetect_ = !argIn.hasKey("nohisdetect");
   doDisulfide_ = !argIn.hasKey("nodisulfides");
   doSugar_ = !argIn.hasKey("nosugars");
@@ -1301,7 +1305,6 @@ Exec::RetType Exec_Build::BuildAndParmStructure(DataSet* inCrdPtr, std::string c
   // Structure check
   mprintf("    -----===== Structure Check =====-----\n");
   StructureCheck check;
-  // TODO make file a user option
   CpptrajFile check_output;
   check_output.OpenWrite(reportfile_);
   int Ntotal_problems = 0;

From 5dd6692b3f6591be0a5081bf777d2f97d7afd3d7 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 4 Mar 2026 09:01:47 -0500
Subject: [PATCH 1436/1492] Add manual entry for reportfile keyword

---
 doc/cpptraj.lyx | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/doc/cpptraj.lyx b/doc/cpptraj.lyx
index 254d7c7cdf..6dd6f2d1a6 100644
--- a/doc/cpptraj.lyx
+++ b/doc/cpptraj.lyx
@@ -6964,6 +6964,10 @@ build [name <output COORDS>] {crdset <COORDS set>|<file>} [{frame <#>|doassembly
 	[parmout <topology file>] [crdout <coord file>] [simplecheck]
 \end_layout
 
+\begin_layout LyX-Code
+    [reportfile <check file>]
+\end_layout
+
 \begin_layout LyX-Code
 	[gb {bondi|amber6|mbondi|pbamber|mbondi2|parse|mbondi3}]
 \end_layout
@@ -7271,6 +7275,24 @@ file>] Name of the output coordinates file.
  Format can be chosen based on filename extension.
 \end_layout
 
+\begin_layout Description
+[simplecheck] (Not recommended) Do not check for overlaps or ring intersections;
+ only check for abnormal bond lengths.
+\end_layout
+
+\begin_layout Description
+[reportfile
+\begin_inset space ~
+\end_inset
+
+<check
+\begin_inset space ~
+\end_inset
+
+file>] File to write details on problems with the final structure;
+ if not specified write to STDOUT.
+\end_layout
+
 \begin_layout Description
 [gb
 \begin_inset space ~

From 19d5038688871cccd7a01cbc92dc8a6d13918686 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 4 Mar 2026 09:06:07 -0500
Subject: [PATCH 1437/1492] Add sections for build help

---
 src/Exec_Build.cpp | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 430643af08..c5c8686ab0 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -831,15 +831,21 @@ void Exec_Build::Help() const
           "\t[parmout <topology file>] [crdout <coord file>] [simplecheck]\n"
           "\t[reportfile <check file>]\n");
   mprintf("\t[%s]\n", Cpptraj::Parm::GB_Params::HelpText().c_str());
+  mprintf("    LJ 12-6-4 options:\n");
   mprintf("\t[lj1264 %s]\n", Cpptraj::Parm::LJ1264_Params::HelpText().c_str());
+  mprintf("    Atom Scan direction:\n");
   mprintf("\t[%s]\n"
+          "    Residue Templates and Parameters to use:\n"
           "\t[{%s} ...]\n"
           "\t[{%s} ...]\n"
+          "    Solvation/box:\n"
           "\t[{{solvatebox|solvateoct} %s\n"
           "\t          %s |\n"
           "\t  setbox %s}]\n"
+          "    Adding ions:\n"
           "\t[addionsrand ion1 <name1> nion1 <num1> [ion2 <name2> nion2 <num2>]\n"
           "\t  [minsep <dist>] [ionseed <seed>]]\n"
+          "    'prepareforleap' options:\n"
           "%s"
           "%s"
           "%s",

From 128728c4c5b02c2ebcd18a1cf9625d2d8339962a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 4 Mar 2026 09:07:30 -0500
Subject: [PATCH 1438/1492] Simplify the build example

---
 doc/cpptraj.lyx | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/doc/cpptraj.lyx b/doc/cpptraj.lyx
index 6dd6f2d1a6..5a58db53a7 100644
--- a/doc/cpptraj.lyx
+++ b/doc/cpptraj.lyx
@@ -7780,11 +7780,7 @@ source leaprc.water.opc
 \end_layout
 
 \begin_layout LyX-Code
-parm 6g37.pdb 
-\end_layout
-
-\begin_layout LyX-Code
-loadcrd 6g37.pdb name MyMol
+readdata 6g37.pdb as coords name MyMol
 \end_layout
 
 \begin_layout LyX-Code

From d0aefa2a495dcc149806cb03c0ff1932337756ae Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 4 Mar 2026 09:12:55 -0500
Subject: [PATCH 1439/1492] Hide check setup timing behind TIMER ifdef

---
 src/StructureCheck.cpp | 16 ++++++++++++++++
 src/StructureCheck.h   |  3 ++-
 2 files changed, 18 insertions(+), 1 deletion(-)

diff --git a/src/StructureCheck.cpp b/src/StructureCheck.cpp
index 780c39f192..236efc04e6 100644
--- a/src/StructureCheck.cpp
+++ b/src/StructureCheck.cpp
@@ -166,7 +166,9 @@ void StructureCheck::SetupBondList(AtomMask const& iMask, Topology const& top) {
 // StructureCheck::Setup()
 int StructureCheck::Setup(Topology const& topIn, Box const& boxIn)
 {
+# ifdef TIMER
   t_setup_.Start();
+# endif
   imageOpt_.SetupImaging( boxIn.HasBox() );
   bondList_.clear();
   if (!checkExtraPts_)
@@ -179,9 +181,13 @@ int StructureCheck::Setup(Topology const& topIn, Box const& boxIn)
   }
   checkType_ = NO_PL_1_MASK;
   // Set up bonds if specified.
+# ifdef TIMER
   t_setup_bonds_.Start();
+# endif
   if (bondcheck_ || ringcheck_) SetupBondList(Mask1_, topIn);
+# ifdef TIMER
   t_setup_bonds_.Stop();
+# endif
   // Set up second mask if specified.
   if ( Mask2_.MaskStringSet() ) {
     if (topIn.SetupIntegerMask( Mask2_ ) ) return 1;
@@ -239,7 +245,9 @@ int StructureCheck::Setup(Topology const& topIn, Box const& boxIn)
     ex_list_opt = ExclusionArray::FULL;
   }
   // Set up exclusion list
+# ifdef TIMER
   t_setup_exclusion_.Start();
+# endif
   if (checkType_ == PL_1_MASK || checkType_ == NO_PL_1_MASK) {
     mprintf("\tExcluding bond interactions.\n");
     // Set up atom exclusion list. Distance of 2 since we are not
@@ -250,11 +258,15 @@ int StructureCheck::Setup(Topology const& topIn, Box const& boxIn)
     }
   } else
     mprintf("\tNot using exclusions.\n");
+# ifdef TIMER
   t_setup_exclusion_.Stop();
+# endif
   // Sort bond list
   if (bondcheck_ || ringcheck_) std::sort(bondList_.begin(), bondList_.end());
   // Find rings
+# ifdef TIMER
   t_setup_ringfinder_.Start();
+# endif
   if (ringcheck_) {
     if (rings_.SetupRingFinder(topIn, Mask1_)) {
       mprinterr("Error: Could not set up ring finder.\n");
@@ -262,18 +274,22 @@ int StructureCheck::Setup(Topology const& topIn, Box const& boxIn)
     }
     if (debug_ > 0) rings_.PrintRings(topIn);
   }
+# ifdef TIMER
   t_setup_ringfinder_.Stop();
   t_setup_.Stop();
+# endif
   return 0;
 }
 
 void StructureCheck::PrintTiming(int indent, double total)
 const
 {
+# ifdef TIMER
   t_setup_.WriteTiming(indent, "Check Setup :", total);
   t_setup_bonds_.WriteTiming     (indent+1, "Setup check bonds      :", t_setup_.Total());
   t_setup_exclusion_.WriteTiming (indent+1, "Setup check exclusions :", t_setup_.Total());
   t_setup_ringfinder_.WriteTiming(indent+1, "Setup check ringfinder :", t_setup_.Total());
+# endif
 }
 
 /** Sort problem list. If OpenMP, combine problems from each thread
diff --git a/src/StructureCheck.h b/src/StructureCheck.h
index 039c33a73c..42066f3d6d 100644
--- a/src/StructureCheck.h
+++ b/src/StructureCheck.h
@@ -184,10 +184,11 @@ class StructureCheck {
     bool saveProblems_;     ///< If true save problems in problemAtoms_
     bool checkExtraPts_;    ///< If true check extra points.
     FmtType lastFmt_;       ///< Format of problems currently stored in problemAtoms_
-
+#  ifdef TIMER
     Timer t_setup_;
     Timer t_setup_bonds_;
     Timer t_setup_exclusion_;
     Timer t_setup_ringfinder_;
+#   endif
 };
 #endif

From 2ed91e08876c8c6a6c778c06c5abf8a2ed26c13c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 4 Mar 2026 09:18:45 -0500
Subject: [PATCH 1440/1492] Hide detailed template/parm load behind ifdef

---
 src/Exec_Build.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index c5c8686ab0..916d714179 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -1222,9 +1222,9 @@ Exec::RetType Exec_Build::BuildAndParmStructure(DataSet* inCrdPtr, std::string c
     return CpptrajState::ERR;
   }
   t_get_templates_.Stop();
-  // FIXME hide behind ifdef?
+# ifdef TIMER
   creator.TimingInfo(t_get_templates_.Total(), 2);
-
+# endif
   Frame frameOut;
   if (StructurePrepAndFillTemplates(argIn, topIn, frameIn,
                                     topOut, frameOut,

From 17e9be3640689a0dd2514706b162ac9802aec2da Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 4 Mar 2026 09:31:56 -0500
Subject: [PATCH 1441/1492] Hide the leap prompt as debug info when loading
 leaprc files

---
 src/DataIO_LeapRC.cpp | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 7e79c31135..1d2946d981 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -968,7 +968,8 @@ int DataIO_LeapRC::Source(FileName const& fname, DataSetList& dsl, std::string c
 
       //ArgList line( ptr, " =\t" );
       ArgList line( lineBuf, " =\t" );
-      mprintf("\tLEAP> %s\n", ptr);
+      if (debug_ > 0)
+        mprintf("\tLEAP> %s\n", ptr);
       //line.PrintDebug(); // DEBUG
 
       LeapCmdType leapcmd = UNKNOWN_CMD;

From 8ee43ccb01912c975ac15acd17362e1aebff0dce Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 4 Mar 2026 09:32:21 -0500
Subject: [PATCH 1442/1492] Update Cluster build files

---
 src/Cluster/CMakeLists.txt | 2 +-
 src/Cluster/Makefile       | 5 +++++
 src/Cluster/clusterfiles   | 2 +-
 3 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/src/Cluster/CMakeLists.txt b/src/Cluster/CMakeLists.txt
index d15bf6c1ed..81f908344b 100644
--- a/src/Cluster/CMakeLists.txt
+++ b/src/Cluster/CMakeLists.txt
@@ -21,8 +21,8 @@ target_sources(cpptraj_common_obj PRIVATE
   ${CMAKE_CURRENT_LIST_DIR}/Metric_Matrix2D.cpp
   ${CMAKE_CURRENT_LIST_DIR}/Metric_QuatRMSD.cpp
   ${CMAKE_CURRENT_LIST_DIR}/Metric_RMS.cpp
-  ${CMAKE_CURRENT_LIST_DIR}/Metric_SRMSD.cpp
   ${CMAKE_CURRENT_LIST_DIR}/Metric_Scalar.cpp
+  ${CMAKE_CURRENT_LIST_DIR}/Metric_SRMSD.cpp
   ${CMAKE_CURRENT_LIST_DIR}/Metric_Torsion.cpp
   ${CMAKE_CURRENT_LIST_DIR}/Node.cpp
   ${CMAKE_CURRENT_LIST_DIR}/Output.cpp
diff --git a/src/Cluster/Makefile b/src/Cluster/Makefile
index b437803b63..7d7838da1f 100644
--- a/src/Cluster/Makefile
+++ b/src/Cluster/Makefile
@@ -8,6 +8,11 @@ DEL_FILE = /bin/rm -f
 # Objects
 OBJECTS=$(CLUSTER_SOURCES:.cpp=.o)
 
+# General rules
+.cpp.o:
+	$(VB)echo CXX $<
+	$(VB)$(CXX) $(DIRECTIVES) $(CPPTRAJ_INC) $(CXXFLAGS) -c -o $@ $<
+
 # Default target: objects
 all: $(OBJECTS)
 
diff --git a/src/Cluster/clusterfiles b/src/Cluster/clusterfiles
index f32ae977db..4706ea9a0b 100644
--- a/src/Cluster/clusterfiles
+++ b/src/Cluster/clusterfiles
@@ -21,8 +21,8 @@ CLUSTER_SOURCES= \
   Metric_Matrix2D.cpp \
   Metric_QuatRMSD.cpp \
   Metric_RMS.cpp \
-  Metric_SRMSD.cpp \
   Metric_Scalar.cpp \
+  Metric_SRMSD.cpp \
   Metric_Torsion.cpp \
   Node.cpp \
   Output.cpp \

From 2492187dd6bcbb7458e25c5aafc8f604bf4c7ef4 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 4 Mar 2026 09:36:44 -0500
Subject: [PATCH 1443/1492] Fix ParameterSet location

---
 src/cpptrajfiles | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/cpptrajfiles b/src/cpptrajfiles
index e0eea7842a..16c9cae7c1 100644
--- a/src/cpptrajfiles
+++ b/src/cpptrajfiles
@@ -627,7 +627,7 @@ LIBCPPTRAJ_PARM_OBJECTS= \
   CharmmParamFile.o \
   ExclusionArray.o \
   Mol.o \
-  ParameterSet.o \
+  Parm/ParameterSet.o \
   ParmFile.o \
   Parm_Amber.o \
   Parm_CharmmPsf.o \

From f467052e3a50c9aa6fec60f05c2c040c0e3b9fba Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 4 Mar 2026 10:02:13 -0500
Subject: [PATCH 1444/1492] Fix reporting overwritten addatomtypes entries, and
 report duplicate entries by default - it's useful info

---
 src/DataIO_LeapRC.cpp | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 1d2946d981..876087b17e 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -425,16 +425,16 @@ const
   if (!duplicateEntries.empty()) {
     mprintf("Warning: %zu duplicate entries in addAtomTypes; this is expected if other leaprc files have been loaded.\n",
             duplicateEntries.size());
-    if (debug_ > 0) {
+    //if (debug_ > 0) {
       mprintf("Warning: Duplicates:");
       for (Sarray::const_iterator it = duplicateEntries.begin(); it != duplicateEntries.end(); ++it)
         mprintf(" %s", it->c_str());
       mprintf("\n");
-    }
+    //}
   }
   if (!overwrittenEntries.empty()) {
-    mprintf("Warning: %zu entries were overwritten in addAtomTypes:", duplicateEntries.size());
-    for (Sarray::const_iterator it = duplicateEntries.begin(); it != duplicateEntries.end(); ++it)
+    mprintf("Warning: %zu entries were overwritten in addAtomTypes:", overwrittenEntries.size());
+    for (Sarray::const_iterator it = overwrittenEntries.begin(); it != overwrittenEntries.end(); ++it)
       mprintf(" %s", it->c_str());
     mprintf("\n");
   }

From 219d97137ee638915a1bd973563346a4599557df Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 4 Mar 2026 10:20:14 -0500
Subject: [PATCH 1445/1492] Do not recommend addmissingres command yet because
 it is so not ready for prime time

---
 src/Exec_Build.cpp | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 916d714179..783a725140 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -1428,9 +1428,10 @@ Exec::RetType Exec_Build::BuildAndParmStructure(DataSet* inCrdPtr, std::string c
             "Warning: If long bond lengths were reported above it may be due to these\n"
             "Warning:  missing residues. If the missing residues are non-terminal\n"
             "Warning:  they should probably be modeled in.\n"
-            "Warning: The 'addmissingres' command could be used to create a simple\n"
-            "Warning:  model for these missing residues, but note THAT COMMAND\n"
-            "Warning:  IS STILL EXPERIMENTAL. Results should be carefully checked.\n");
+            //"Warning: The 'addmissingres' command could be used to create a simple\n"
+            //"Warning:  model for these missing residues, but note THAT COMMAND\n"
+            //"Warning:  IS STILL EXPERIMENTAL. Results should be carefully checked.\n"
+           );
   }
 
   // Total charge check

From 5bf3cbfbc39265f812087f249c865ddc2c699984 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 4 Mar 2026 10:27:04 -0500
Subject: [PATCH 1446/1492] Move hint about fixatomorder from Topology to
 ParmFile since we really should only need it after a topology is loaded

---
 src/ParmFile.cpp | 7 +++++--
 src/Topology.cpp | 4 ++--
 2 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/src/ParmFile.cpp b/src/ParmFile.cpp
index 268e8da2d9..970179c672 100644
--- a/src/ParmFile.cpp
+++ b/src/ParmFile.cpp
@@ -176,9 +176,12 @@ int ParmFile::ReadTopology(Topology& Top, FileName const& fnameIn,
   if (parmio->processReadArgs(argIn)) return 1;
   int err = parmio->ReadParm( parmName_.Full(), Top);
   // Perform setup common to all parm files.
-  if (err == 0) 
+  if (err == 0) {
     err = Top.CommonSetup( molsearch, renumberResidues );
-  else
+    if (Top.HasNoncontiguousMols())
+      mprintf("Warning: The 'fixatomorder' command can be used to reorder the topology and any\n"
+              "Warning:  associated coordinates.\n");
+  } else
     mprinterr("Error reading topology file '%s'\n", parmName_.full());
   delete parmio;
   if (err > 0) return 1;
diff --git a/src/Topology.cpp b/src/Topology.cpp
index 4592d10517..e1077dbdd3 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -1352,8 +1352,8 @@ int Topology::DetermineMolecules() {
         mprintf(" %i-%i (%i) ", seg->Begin()+1, seg->End(), seg->Size());
       mprintf("\n");
     }
-    mprintf("Warning: The 'fixatomorder' command can be used to reorder the topology and any\n"
-            "Warning:  associated coordinates.\n");
+    //mprintf("Warning: The 'fixatomorder' command can be used to reorder the topology and any\n"
+    //        "Warning:  associated coordinates.\n");
   } 
 /*
   std::vector<Molecule>::iterator molecule = molecules_.begin();

From 34f9080995a2ac29d1788fc8626cff8918ae75ec Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 4 Mar 2026 10:38:16 -0500
Subject: [PATCH 1447/1492] Add StructureCheck report mode without leading
 frame arg

---
 src/Exec_Build.cpp     |  8 ++++----
 src/StructureCheck.cpp | 17 +++++++++++++++++
 src/StructureCheck.h   |  7 +++++--
 3 files changed, 26 insertions(+), 6 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 783a725140..8fbaab2084 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -1371,15 +1371,15 @@ Exec::RetType Exec_Build::BuildAndParmStructure(DataSet* inCrdPtr, std::string c
     t_check_overlaps_.Start();
     Ntotal_problems = check.CheckOverlaps( frameOut );
     t_check_overlaps_.Stop();
-    check.WriteProblemsToFile( &check_output, 1, topOut );
+    check.WriteProblemsToFile( &check_output, topOut );
     t_check_bonds_.Start();
     Ntotal_problems += check.CheckBonds( frameOut );
     t_check_bonds_.Stop();
-    check.WriteProblemsToFile( &check_output, 1, topOut );
+    check.WriteProblemsToFile( &check_output, topOut );
     t_check_rings_.Start();
     Ntotal_problems += check.CheckRings( frameOut );
     t_check_rings_.Stop();
-    check.WriteProblemsToFile( &check_output, 1, topOut );
+    check.WriteProblemsToFile( &check_output, topOut );
     // If box was added for check only, remove it
     if (box_added)
       frameOut.ModifyBox().SetNoBox();
@@ -1418,7 +1418,7 @@ Exec::RetType Exec_Build::BuildAndParmStructure(DataSet* inCrdPtr, std::string c
     t_check_bonds_.Start();
     Ntotal_problems = check.CheckBonds( frameOut );
     t_check_bonds_.Stop();
-    check.WriteProblemsToFile( &check_output, 1, topOut );
+    check.WriteProblemsToFile( &check_output, topOut );
     t_check_.Stop();
   }
   if (input_has_missing_res > 0) {
diff --git a/src/StructureCheck.cpp b/src/StructureCheck.cpp
index 236efc04e6..7ed1ea3ffb 100644
--- a/src/StructureCheck.cpp
+++ b/src/StructureCheck.cpp
@@ -1011,6 +1011,13 @@ const char* StructureCheck::Fmt_[] = {
   "%i\t Warning: Bond involving atom %i:%s intersects ring involving atom %i:%s (%.2f)\n" ///< F_RING
 };
 
+/** Write formats for problems, no frame number. */
+const char* StructureCheck::NoFrameFmt_[] = {
+  "Warning: Atoms %i:%s and %i:%s are close (%.2f)\n",    ///< F_ATOM
+  "Warning: Unusual bond length %i:%s to %i:%s (%.2f)\n", ///< F_BOND
+  "Warning: Bond involving atom %i:%s intersects ring involving atom %i:%s (%.2f)\n" ///< F_RING
+};
+
 /** Write current problems to the given file. */
 void StructureCheck::WriteProblemsToFile(CpptrajFile* outfile, int frameNum, Topology const& top) const {
   if (outfile == 0) return;
@@ -1020,3 +1027,13 @@ void StructureCheck::WriteProblemsToFile(CpptrajFile* outfile, int frameNum, Top
                     p->A2()+1, top.TruncResAtomName(p->A2()).c_str(), p->D());
   }
 }
+
+/** Write current problems to the given file, no frame number. */
+void StructureCheck::WriteProblemsToFile(CpptrajFile* outfile, Topology const& top) const {
+  if (outfile == 0) return;
+  for (const_iterator p = begin(); p != end(); ++p) {
+    outfile->Printf(NoFrameFmt_[lastFmt_],
+                    p->A1()+1, top.TruncResAtomName(p->A1()).c_str(),
+                    p->A2()+1, top.TruncResAtomName(p->A2()).c_str(), p->D());
+  }
+}
diff --git a/src/StructureCheck.h b/src/StructureCheck.h
index 42066f3d6d..d3ea7ed9ad 100644
--- a/src/StructureCheck.h
+++ b/src/StructureCheck.h
@@ -52,8 +52,9 @@ class StructureCheck {
     int CheckRings(Frame const&, Cpptraj::Structure::RingFinder const&, std::vector<Btype> const&);
     /// Write existing problems to the given file
     void WriteProblemsToFile(CpptrajFile*, int, Topology const&) const;
-
-
+    /// Write existing problems to the given file, no frame number
+    void WriteProblemsToFile(CpptrajFile*, Topology const&) const;
+    /// Print timing data to stdout
     void PrintTiming(int, double) const;
     /// Format of problems currently stored in problemAtoms_
     enum FmtType { F_ATOM =0, F_BOND, F_RING };
@@ -117,6 +118,8 @@ class StructureCheck {
   private:
     /// Format strings corresponding to FmtType
     static const char* Fmt_[];
+    /// Format strings corresponding to FmtType, no frame number
+    static const char* NoFrameFmt_[];
     /// Type of overlap check
     enum CheckType { NO_PL_1_MASK=0, NO_PL_2_MASKS, PL_1_MASK };
     /// \return mask string based on if extra points are being excluded

From e9fd5f84373277bf564933748c5d98c7f03ebf8b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 4 Mar 2026 10:45:08 -0500
Subject: [PATCH 1448/1492] Hide some build timers behind ifdef TIMER

---
 src/Exec_Build.cpp | 18 ++++++++++++++++++
 src/Exec_Build.h   |  2 ++
 2 files changed, 20 insertions(+)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 8fbaab2084..a74fdaa5ef 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -696,7 +696,9 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
         structureBuilder.SetParameters( creator.MainParmSetPtr() );
       // Generate internals from the template, update indices to this topology.
       DataSet_Coords* resTemplate = ResTemplates[ires];
+#     ifdef TIMER
       t_fill_build_internals_.Start();
+#     endif
       Frame templateFrame = resTemplate->AllocateFrame();
       resTemplate->GetFrame( 0, templateFrame );
       if (structureBuilder.GenerateInternals(templateFrame, resTemplate->Top(),
@@ -705,11 +707,15 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
         mprinterr("Error: Generate internals for residue template failed.\n");
         return 1;
       }
+#     ifdef TIMER
       t_fill_build_internals_.Stop();
+#     endif
       structureBuilder.UpdateIndicesWithOffset( *it );
       //mprintf("DEBUG: Residue type: %s terminal\n", Cpptraj::Structure::terminalStr(*termType));
       // Is this residue connected to an earlier residue?
+#     ifdef TIMER
       t_fill_build_link_.Start();
+#     endif
       for (IParray::const_iterator resBonds = resBondingAtoms[ires].begin();
                                    resBonds != resBondingAtoms[ires].end(); ++resBonds)
       {
@@ -718,9 +724,13 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
             mprintf("\t\tResidue connection: %s - %s\n",
                     topOut.AtomMaskName(resBonds->first).c_str(),
                     topOut.AtomMaskName(resBonds->second).c_str());
+#         ifdef TIMER
           t_fill_build_link_bond_.Start();
+#         endif
           topOut.AddBond(resBonds->first, resBonds->second);
+#         ifdef TIMER
           t_fill_build_link_bond_.Stop();
+#         endif
           // Generate internals around the link
           Residue const& R0 = topIn.Res(topOut[resBonds->first].ResNum());
           for (int at = nextTempHasPositionStart; at < R0.FirstAtom(); at++)
@@ -738,19 +748,25 @@ int Exec_Build::FillAtomsWithTemplates(Topology& topOut, Frame& frameOut,
           }
         }
       }
+#     ifdef TIMER
       t_fill_build_link_.Stop();
+#     endif
       // Update internal coords from known positions
       if (structureBuilder.UpdateICsFromFrame( frameOut, topOut, hasPosition )) {
         mprinterr("Error: Failed to update internals with values from existing positions.\n");
         return 1;
       }
+#     ifdef TIMER
       t_fill_build_build_.Start();
+#     endif
       if (structureBuilder.BuildFromInternals(frameOut, topOut, hasPosition)) {
         mprinterr("Error: Building residue %s failed.\n",
                   topOut.TruncResNameOnumId(ires).c_str());
         buildFailed = true;
       }
+#     ifdef TIMER
       t_fill_build_build_.Stop();
+#     endif
     } else {
       // All atoms present. Just connect
       // Is this residue connected to an earlier residue?
@@ -1667,9 +1683,11 @@ void Exec_Build::PrintTiming() const {
   t_fill_.WriteTiming         (2, "Fill missing atoms  :", t_total_.Total());
   t_fill_template_.WriteTiming(3, "Get template atoms :", t_fill_.Total());
   t_fill_build_.WriteTiming   (3, "Build atoms        :", t_fill_.Total());
+# ifdef TIMER
   t_fill_build_internals_.WriteTiming(4, "Internals :", t_fill_build_.Total());
   t_fill_build_build_.WriteTiming    (4, "Build     :", t_fill_build_.Total());
   t_fill_build_link_.WriteTiming     (4, "Link      :", t_fill_build_.Total());
   t_fill_build_link_bond_.WriteTiming(5, "Link Bond :", t_fill_build_link_.Total());
   Cpptraj::Structure::Builder::PrintTiming(5, t_fill_build_link_.Total());
+# endif
 }
diff --git a/src/Exec_Build.h b/src/Exec_Build.h
index b6f8dcd84a..f31e8ac673 100644
--- a/src/Exec_Build.h
+++ b/src/Exec_Build.h
@@ -75,10 +75,12 @@ class Exec_Build : public Exec {
     Timer t_fill_;
     Timer t_fill_template_;
     Timer t_fill_build_;
+#   ifdef TIMER
     Timer t_fill_build_internals_;
     Timer t_fill_build_build_;
     Timer t_fill_build_link_;
     Timer t_fill_build_link_bond_;
+#   endif
     Timer t_assign_;
     Timer t_check_;
     Timer t_check_bonds_;

From 99d11e7d6c5517a32e1abc2e47f1c8a07ee8c003 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 4 Mar 2026 10:50:23 -0500
Subject: [PATCH 1449/1492] Add file output timer

---
 src/Exec_Build.cpp | 3 +++
 src/Exec_Build.h   | 1 +
 2 files changed, 4 insertions(+)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index a74fdaa5ef..13a945ddc4 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -1467,6 +1467,7 @@ Exec::RetType Exec_Build::BuildAndParmStructure(DataSet* inCrdPtr, std::string c
   if (!reportfile_.empty())
     mprintf("\t%i total problems detected. See '%s' for details.\n", Ntotal_problems, reportfile_.c_str());
 
+  t_output_.Start();
   mprintf("    -----===== File Output =====-----\n");
   if (!outputTopologyName.empty()) {
     ParmFile pfile;
@@ -1490,6 +1491,7 @@ Exec::RetType Exec_Build::BuildAndParmStructure(DataSet* inCrdPtr, std::string c
       return CpptrajState::ERR;
     }
   }
+  t_output_.Stop();
   t_total_.Stop();
 
   mprintf("    -----===== Timing =====-----\n");
@@ -1503,6 +1505,7 @@ Exec::RetType Exec_Build::BuildAndParmStructure(DataSet* inCrdPtr, std::string c
   t_check_setup_.WriteTiming   (3, "Setup    :", t_check_.Total());
   t_assign_.WriteTiming       (2, "Param./Top. gen.    :", t_total_.Total());
   AP.WriteAssignTiming(3, t_assign_.Total());
+  t_output_.WriteTiming       (2, "File output         :", t_total_.Total());
 
   return ret;
 }
diff --git a/src/Exec_Build.h b/src/Exec_Build.h
index f31e8ac673..18d98c7008 100644
--- a/src/Exec_Build.h
+++ b/src/Exec_Build.h
@@ -88,5 +88,6 @@ class Exec_Build : public Exec {
     Timer t_check_rings_;
     Timer t_check_setup_;
     Timer t_solvate_;
+    Timer t_output_;
 };
 #endif

From 78472a607a5c4f359aeb550c70186fa7b8fbb551 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 4 Mar 2026 10:51:26 -0500
Subject: [PATCH 1450/1492] Add missing leaprc

---
 test/Test_Build/leaprc.protein.ff14SB | 127 ++++++++++++++++++++++++++
 1 file changed, 127 insertions(+)
 create mode 100644 test/Test_Build/leaprc.protein.ff14SB

diff --git a/test/Test_Build/leaprc.protein.ff14SB b/test/Test_Build/leaprc.protein.ff14SB
new file mode 100644
index 0000000000..cfb292f1fd
--- /dev/null
+++ b/test/Test_Build/leaprc.protein.ff14SB
@@ -0,0 +1,127 @@
+logFile leap.log
+#
+# ----- leaprc for loading the ff14SB force field
+# ----- NOTE: this is designed for PDB format 3!
+#
+#	load atom type hybridizations
+#
+addAtomTypes {
+	{ "H"   "H" "sp3" }
+	{ "HO"  "H" "sp3" }
+	{ "HS"  "H" "sp3" }
+	{ "H1"  "H" "sp3" }
+	{ "H2"  "H" "sp3" }
+	{ "H3"  "H" "sp3" }
+	{ "H4"  "H" "sp3" }
+	{ "H5"  "H" "sp3" }
+	{ "HW"  "H" "sp3" }
+	{ "HC"  "H" "sp3" }
+	{ "HA"  "H" "sp3" }
+	{ "HP"  "H" "sp3" }
+	{ "HZ"  "H" "sp3" }
+	{ "OH"  "O" "sp3" }
+	{ "OS"  "O" "sp3" }
+	{ "O"   "O" "sp2" }
+	{ "O2"  "O" "sp2" }
+	{ "OP"  "O" "sp2" }
+	{ "OW"  "O" "sp3" }
+	{ "CT"  "C" "sp3" }
+	{ "CX"  "C" "sp3" }
+	{ "C8"  "C" "sp3" }
+	{ "2C"  "C" "sp3" }
+	{ "3C"  "C" "sp3" }
+	{ "CH"  "C" "sp3" }
+	{ "CS"  "C" "sp2" }
+	{ "C"   "C" "sp2" }
+	{ "CO"   "C" "sp2" }
+	{ "C*"  "C" "sp2" }
+	{ "CA"  "C" "sp2" }
+	{ "CB"  "C" "sp2" }
+	{ "CC"  "C" "sp2" }
+	{ "CN"  "C" "sp2" }
+	{ "CM"  "C" "sp2" }
+	{ "CK"  "C" "sp2" }
+	{ "CQ"  "C" "sp2" }
+	{ "CD"  "C" "sp2" }
+	{ "C5"  "C" "sp2" }
+	{ "C4"  "C" "sp2" }
+	{ "CP"  "C" "sp2" }
+	{ "CI"  "C" "sp3" }
+	{ "CJ"  "C" "sp2" }
+	{ "CW"  "C" "sp2" }
+	{ "CV"  "C" "sp2" }
+	{ "CR"  "C" "sp2" }
+	{ "CA"  "C" "sp2" }
+	{ "CY"  "C" "sp2" }
+	{ "C0"  "Ca" "sp3" }
+	{ "MG"  "Mg" "sp3" }
+	{ "N"   "N" "sp2" }
+	{ "NA"  "N" "sp2" }
+	{ "N2"  "N" "sp2" }
+	{ "N*"  "N" "sp2" }
+	{ "NP"  "N" "sp2" }
+	{ "NQ"  "N" "sp2" }
+	{ "NB"  "N" "sp2" }
+	{ "NC"  "N" "sp2" }
+	{ "NT"  "N" "sp3" }
+	{ "NY"  "N" "sp2" }
+	{ "N3"  "N" "sp3" }
+	{ "S"   "S" "sp3" }
+	{ "SH"  "S" "sp3" }
+	{ "P"   "P" "sp3" }
+	{ "LP"  ""  "sp3" }
+	{ "EP"  ""  "sp3" }
+	{ "F"   "F" "sp3" }
+	{ "Cl"  "Cl" "sp3" }
+	{ "Br"  "Br" "sp3" }
+	{ "I"   "I"  "sp3" }
+}
+#
+#	Load the main parameter set.
+#
+parm10 = loadamberparams parm10.dat
+frcmod14SB = loadamberparams frcmod.ff14SB
+#
+#	Load main chain and terminating amino acid libraries
+#
+loadOff amino12.lib
+loadOff aminoct12.lib
+loadOff aminont12.lib
+
+#
+#	Define the PDB name map for the amino acids
+#
+addPdbResMap {
+  { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" }
+  { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
+  { 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
+  { 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
+  { 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
+  { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
+  { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
+  { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
+  { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
+  { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
+  { 0 "HID" "NHID" } { 1 "HID" "CHID" }
+  { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
+  { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
+  { 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
+  { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
+  { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
+  { 0 "MET" "NMET" } { 1 "MET" "CMET" }
+  { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
+  { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
+  { 0 "SER" "NSER" } { 1 "SER" "CSER" }
+  { 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
+  { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
+  { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
+  { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
+  { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
+}
+
+#
+# assume that most often proteins use HIE
+#
+NHIS = NHIE
+HIS = HIE
+CHIS = CHIE

From 589030498a45c1114e3a9ce21cf5781f9d1673cc Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 4 Mar 2026 11:17:01 -0500
Subject: [PATCH 1451/1492] Previously, specifying '-shared' would silently
 disable libsander support in cpptraj. Create a new category of linked
 libraries that is cpptraj-only that will not be linked to libcpptraj so that
 libsander can be supported with -shared

---
 configure    | 11 ++++++++---
 src/Makefile |  2 +-
 2 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/configure b/configure
index d02ba5a106..c5bea5a1a0 100755
--- a/configure
+++ b/configure
@@ -259,7 +259,7 @@ LIB_STTC[$LNETCDF]='libnetcdf.a'     # Expected static location relative to home
 LIB_D_ON[$LNETCDF]='-DBINTRAJ'       # Directive if library on
 LIB_DOFF[$LNETCDF]=''                # Directive if library off
 LIB_LINK[$LNETCDF]='dynamic'         # How to link the library
-LIB_TYPE[$LNETCDF]='ld'              # ld = LDFLAGS, cpp = cpptraj, blank = special
+LIB_TYPE[$LNETCDF]='ld'              # ld = LDFLAGS, cpp = cpptraj/libcpptraj, cpptraj=cpptraj only, blank = special
 
 LIB_STAT[$LPARANC]='off'
 LIB_CKEY[$LPARANC]='pnetcdf'
@@ -349,7 +349,7 @@ LIB_FLAG[$LSANDER]='-lsander'
 LIB_STTC[$LSANDER]=''
 LIB_D_ON[$LSANDER]='-DUSE_SANDERLIB'
 LIB_DOFF[$LSANDER]=''
-LIB_TYPE[$LSANDER]='ld'
+LIB_TYPE[$LSANDER]='cpptraj'
 
 LIB_STAT[$LTIMER]='off'
 LIB_CKEY[$LTIMER]='timer'
@@ -1387,6 +1387,7 @@ SetupFinalFlags() {
   # Set up include and linking flags
   ldf=''
   CPPTRAJ_LIB=''
+  CPPTRAJONLY_LIB=''
   CPPTRAJ_INC=''
   nincl=0
   for ((i=0; i < $NLIB; i++)) ; do
@@ -1423,6 +1424,8 @@ SetupFinalFlags() {
         ldf="$ldf ${LIB_FLAG[$i]}"
       elif [ "${LIB_TYPE[$i]}" = 'cpp' ] ; then
         CPPTRAJ_LIB="$CPPTRAJ_LIB ${LIB_FLAG[$i]}"
+      elif [ "${LIB_TYPE[$i]}" = 'cpptraj' ] ; then
+        CPPTRAJONLY_LIB="$CPPTRAJONLY_LIB ${LIB_FLAG[$i]}"
       fi
     fi
   done
@@ -2855,7 +2858,7 @@ while [ ! -z "$1" ] ; do
     '-libstatic'        ) USE_STATIC=2 ;;
     '-shared'           )
       USE_SHARED=1
-      LIB_STAT[$LSANDER]='off'
+#      LIB_STAT[$LSANDER]='off'
       ;;
     '-amberlib'         )
       if [ -z "$AMBERHOME" ] ; then
@@ -3077,6 +3080,7 @@ fi
 #echo FFLAGS $FFLAGS
 #echo LDFLAGS $LDFLAGS
 #echo CPPTRAJ_LIB $CPPTRAJ_LIB
+#echo CPPTRAJONLY_LIB $CPPTRAJONLY_LIB
 #echo CPPTRAJ_INC $CPPTRAJ_INC
 #echo REQUIRES_FLINK $REQUIRES_FLINK FLINK $FLINK
 echo ""
@@ -3186,6 +3190,7 @@ ARPACK_TARGET=$ARPACK_TARGET
 FFT_TARGET=$FFT_TARGET
 
 CPPTRAJ_LIB=$CPPTRAJ_LIB
+CPPTRAJONLY_LIB=$CPPTRAJONLY_LIB
 LDFLAGS=$LDFLAGS
 SFX=$SFX
 EXE=$EXE
diff --git a/src/Makefile b/src/Makefile
index 9ba86b1096..6095a12832 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -52,7 +52,7 @@ install_cpptraj: cpptraj$(SFX)$(EXE)
 
 cpptraj$(SFX)$(EXE): $(OBJECTS) $(FFT_TARGET) $(READLINE_TARGET) $(CUDA_TARGET) $(XDRFILE_TARGET) $(ARPACK_TARGET) $(TNGFILE_TARGET)
 	$(VB)echo Link cpptraj$(SFX)$(EXE)
-	$(VB)$(CXX) -o cpptraj$(SFX)$(EXE) $(OBJECTS) $(CUDA_TARGET) $(FFT_TARGET) $(READLINE_LIB) $(CPPTRAJ_LIB) $(LDFLAGS)
+	$(VB)$(CXX) -o cpptraj$(SFX)$(EXE) $(OBJECTS) $(CUDA_TARGET) $(FFT_TARGET) $(READLINE_LIB) $(CPPTRAJ_LIB) $(LDFLAGS) $(CPPTRAJONLY_LIB)
 
 # libcpptraj ---------------------------
 # Rule to make libcpptraj-specific objects

From 4b127264bc567188a9a1a2a3c3aa1415ac081863 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 4 Mar 2026 11:29:14 -0500
Subject: [PATCH 1452/1492] Add warning about leaps value of PI

---
 src/Cpptraj.cpp    |  5 +++++
 src/Exec_Build.cpp | 12 ++++++++++++
 2 files changed, 17 insertions(+)

diff --git a/src/Cpptraj.cpp b/src/Cpptraj.cpp
index 03b4c3c1f9..12f1f5ca78 100644
--- a/src/Cpptraj.cpp
+++ b/src/Cpptraj.cpp
@@ -139,6 +139,11 @@ void Cpptraj::Intro() const {
   }
 # endif
   mprintf("\n");
+#ifdef CPPTRAJ_USE_LEAP_PI
+  mprintf("Warning: CPPTRAJ was compiled with LEaP's value of PI.\n"
+          "Warning: This should only be used to compare directly to LEaP.\n"
+          "Warning: This will cause some test cases to fail.\n\n");
+#endif
 }
 
 void Cpptraj::Finalize() {
diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 13a945ddc4..3ad61451cc 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -881,6 +881,12 @@ void Exec_Build::Help() const
 // Exec_Build::Execute()
 Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
 {
+#ifndef CPPTRAJ_USE_LEAP_PI
+  mprintf("Warning: CPPTRAJ was not compiled with LEaP's value of PI.\n"
+          "Warning: Output Topology and Coordinates are expected to differ slightly from LEaP.\n"
+          "Warning: To obtain an exact match to LEaP CPPTRAJ must be compiled with\n"
+          "Warning: -DCPPTRAJ_USE_LEAP_PI (configure flag '-leappi').\n");
+# endif
   std::string outset = argIn.GetStringKey("name");
   // Get input coords
   DataSet* inCrdPtr = 0;
@@ -950,6 +956,12 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, in
                                          bool enableExtraDetection)
                                          
 {
+#ifndef CPPTRAJ_USE_LEAP_PI
+  mprintf("Warning: CPPTRAJ was not compiled with LEaP's value of PI.\n"
+          "Warning: Output Topology and Coordinates are expected to differ slightly from LEaP.\n"
+          "Warning: To obtain an exact match to LEaP CPPTRAJ must be compiled with\n"
+          "Warning: -DCPPTRAJ_USE_LEAP_PI (configure flag '-leappi').\n");
+# endif
   t_total_.Start();
   if (inCrdPtr == 0) {
     mprinterr("Internal Error: Exec_Build::BuildStructure(): Null input coordinates.\n");

From b387963279caaa697a9e9c57364f7f6446a36156 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 4 Mar 2026 12:06:15 -0500
Subject: [PATCH 1453/1492] Just report split off groups

---
 src/Structure/FxnGroupBuilder.cpp | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/Structure/FxnGroupBuilder.cpp b/src/Structure/FxnGroupBuilder.cpp
index 0a6fefc40c..4699890d99 100644
--- a/src/Structure/FxnGroupBuilder.cpp
+++ b/src/Structure/FxnGroupBuilder.cpp
@@ -409,13 +409,13 @@ int FxnGroupBuilder::CheckForFunctionalGroups(Sugar& sugar, Topology& topIn, Fra
   // Record new residue numbers for found types.
   int resOffset = (int)resTypes_.size();
   if (resOffset > 0) {
-    mprintf("DEBUG: Split off %i groups from residue %i: ", resOffset, rnum+1);
+    mprintf("Info: Split off %i groups from residue %i: ", resOffset, rnum+1);
     for (FTarray::const_iterator rt = resTypes_.begin(); rt != resTypes_.end(); ++rt) {
-      mprintf(" %i:%s", rnum+resOffset+1, FunctionalGroup::typeString(*rt)); // DEBUG
+      mprintf(" %i:%s", rnum+resOffset+1, FunctionalGroup::typeString(*rt));
       foundGroups_.push_back( FxnResType(rnum+resOffset, *rt) );
       --resOffset;
     }
-    mprintf("\n"); // DEBUG
+    mprintf("\n");
   }
 
   return 0;

From 7cc5372ddaf96d4a24facf30f173bdf2ac3ad31c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 4 Mar 2026 12:06:25 -0500
Subject: [PATCH 1454/1492] Warn about ignoring set default cmap on/off

---
 src/DataIO_LeapRC.cpp | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 876087b17e..84fc97fab0 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -682,6 +682,14 @@ int DataIO_LeapRC::LeapSet(ArgList const& argIn, DataSetList& dsl) const {
         mprinterr("Error: Could not set default pbradii %s\n", argIn[3].c_str());
         return 1;
       }
+    } else if ( ToLower(argIn[2]) == "cmap" ) {
+      if ( ToLower(argIn[3]) == "on" ) {
+        mprintf("Warning: LEaP 'set default cmap on' command ignored; CMAP terms will always be added if present.\n");
+      } else if ( ToLower(argIn[3]) == "off" ) {
+        mprinterr("Error: LEaP 'set default cmap off' is not supported; CMAP terms will always be added if present.\n");
+        return 1;
+      } else
+        mprintf("Warning: Skipping unrecognized 'set default cmap' mode: %s\n", argIn[3].c_str());
     } else {
       mprintf("Warning: Unhandled 'set default' command: %s\n", argIn.ArgLine());
     }

From 2061bb7aeac1f6599568e3f089de64ac6e517439 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 4 Mar 2026 13:45:33 -0500
Subject: [PATCH 1455/1492] Make sure the box isnt too small when doing
 nsolvent to prevent clashes across unit cell boundaries. Disable truncoct for
 now

---
 src/Structure/Solvate.cpp | 33 ++++++++++++++++++++++++++++++++-
 1 file changed, 32 insertions(+), 1 deletion(-)

diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index a943ceb164..67033be121 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -70,7 +70,13 @@ int Solvate::InitSolvate(ArgList& argIn, bool octIn, int debugIn) {
   debug_ = debugIn;
   doTruncatedOct_ = octIn;
   nsolvent_ = (unsigned int)argIn.getKeyInt("nsolvent", 0);
-  if (nsolvent_ > 0) clip_ = false;
+  if (nsolvent_ > 0) {
+    if (doTruncatedOct_) {
+      mprinterr("Error: 'nsolvent' currently does not work for truncated octahedral cells.\n");
+      return 1;
+    }
+    clip_ = false;
+  }
 
   if (getBufferArg(argIn, -1.0)) return 1;
 
@@ -885,7 +891,32 @@ int Solvate::SolvateBoxWithExactNumber(Topology& topOut, Frame& frameOut, Cpptra
   newFrame.SetupFrameV(topOut.Atoms(), frameOut.CoordsInfo());
   newFrame.SetFrame( frameOut, imask );
   frameOut = newFrame;
+  // ---------------------------------------------
+  // Define the size of the new solvent/solute system
+  soluteRadii = getAtomRadii(soluteMaxR, topOut, set0) ;
+  if (setVdwBoundingBox(boxX, boxY, boxZ, soluteRadii, frameOut, false)) {
+    mprinterr("Error: Setting vdw bounding box for solute/solvent system failed.\n", topOut.c_str());
+    return 1;
+  }
+  if (doTruncatedOct_) {
+    double dAngle = 0;
+    ewald_rotate(frameOut, dAngle);
+    //mprintf("EwaldRotate: %f\n", dAngle);
+    // Add an angstrom to the desired box size rather than using the bounding box size
+    dAngle = clipX_ + .5;
+    boxX = boxY = boxZ = dAngle * sqrt(3.0) * 0.5;
+  }
 
+  // Setup box
+  double boxBeta = 90.0;
+  if (doTruncatedOct_) {
+    boxBeta = Box::TruncatedOctAngle();
+    boxX *= 2.0;
+    boxY *= 2.0;
+    boxZ *= 2.0;
+  }
+  newBox.SetupFromXyzAbg( boxX, boxY, boxZ, boxBeta, boxBeta, boxBeta );
+  // ---------------------------------------------
   frameOut.SetBox( newBox );
   frameOut.BoxCrd().PrintInfo("\t  ");
   topOut.SetParmBox( frameOut.BoxCrd() );

From 38396644b671ee1922d60e1cab8f63260383f4c9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 4 Mar 2026 13:57:21 -0500
Subject: [PATCH 1456/1492] Add note about clipX being 0 if truncoct is ever
 enabled for nsolvent

---
 src/Structure/Solvate.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index 67033be121..d9c3a937c0 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -903,7 +903,7 @@ int Solvate::SolvateBoxWithExactNumber(Topology& topOut, Frame& frameOut, Cpptra
     ewald_rotate(frameOut, dAngle);
     //mprintf("EwaldRotate: %f\n", dAngle);
     // Add an angstrom to the desired box size rather than using the bounding box size
-    dAngle = clipX_ + .5;
+    dAngle = clipX_ + .5; // NOTE: If truncoct is enabled for nsolvent, clipX_ will be 0
     boxX = boxY = boxZ = dAngle * sqrt(3.0) * 0.5;
   }
 

From a89153063ca7e6702b50e3c842055f6df5fb8c3d Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 4 Mar 2026 13:58:29 -0500
Subject: [PATCH 1457/1492] Add note about nsolvent not working for truncoct
 yet

---
 doc/cpptraj.lyx | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/doc/cpptraj.lyx b/doc/cpptraj.lyx
index 5a58db53a7..f2b4b1c154 100644
--- a/doc/cpptraj.lyx
+++ b/doc/cpptraj.lyx
@@ -7544,6 +7544,8 @@ nsolvent
 <#> EXPERIMENTAL.
  Instead of a buffer,
  specify a target number of waters to solvate the system with.
+ Currently only works for orthorhombic cells (i.e.
+ not truncated octahedron).
 \end_layout
 
 \end_deeper

From b35e5eea064cc5c16c516b535df0fb2d0f5cba0a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Wed, 4 Mar 2026 14:26:49 -0500
Subject: [PATCH 1458/1492] Add note about nsolvent functionality being
 experimental

---
 src/Structure/Solvate.cpp | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/Structure/Solvate.cpp b/src/Structure/Solvate.cpp
index d9c3a937c0..ae5029ba53 100644
--- a/src/Structure/Solvate.cpp
+++ b/src/Structure/Solvate.cpp
@@ -76,6 +76,7 @@ int Solvate::InitSolvate(ArgList& argIn, bool octIn, int debugIn) {
       return 1;
     }
     clip_ = false;
+    mprintf("Warning: The 'nsolvent' functionality is currently EXPERIMENTAL.\n");
   }
 
   if (getBufferArg(argIn, -1.0)) return 1;

From f85eac9a9b11d34cb9315c4c0ac28feb4f0dc427 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 5 Mar 2026 08:43:26 -0500
Subject: [PATCH 1459/1492] Start modxna info class

---
 src/Structure/ModXNA_Info.cpp | 48 +++++++++++++++++++++++++++++++++++
 src/Structure/ModXNA_Info.h   | 39 ++++++++++++++++++++++++++++
 2 files changed, 87 insertions(+)
 create mode 100644 src/Structure/ModXNA_Info.cpp
 create mode 100644 src/Structure/ModXNA_Info.h

diff --git a/src/Structure/ModXNA_Info.cpp b/src/Structure/ModXNA_Info.cpp
new file mode 100644
index 0000000000..d490c82f6b
--- /dev/null
+++ b/src/Structure/ModXNA_Info.cpp
@@ -0,0 +1,48 @@
+#include "ModXNA_Info.h"
+#include "../ArgList.h"
+#include "../CpptrajStdio.h"
+
+using namespace Cpptraj::Structure;
+
+/** CONSTRUCTOR */
+ModXNA_Info::ModXNA_Info() {}
+
+/** Parse ModXNA info from given string. */
+ModXNA_Info::StatType ModXNA_Info::ParseModxnaStr(std::string const& line) {
+  if (line.empty()) return NOT_MODXNA;
+  ArgList args(line, ":");
+
+  if (args.GetStringNext() != "modXNA-fragment") return NOT_MODXNA;
+
+  if (args.Nargs() < 2) {
+    mprinterr("Error: modXNA string is too short.\n"
+              "Error: '%s'\n", line.c_str());
+    return ERR;
+  }
+  fragmentName_ = args[1];
+
+  if (args.Nargs() >= 4) head_ = args[3];
+  if (args.Nargs() >= 6) headStrip_ = args[5];
+  if (args.Nargs() >= 8) tail_ = args[7];
+  if (args.Nargs() >= 10) tailStrip_ = args[9];
+  if (args.Nargs() >= 12) anchor_ = args[11];
+  if (args.Nargs() >= 14) anchorStrip_ = args[13];
+
+  return OK;
+}
+
+static inline void printmxna(const char* desc, std::string const& str) {
+  if (!str.empty()) mprintf("%s: %s\n", desc, str.c_str());
+}
+
+/** Print info to stdout */
+void ModXNA_Info::PrintModxna() const {
+  if (!HasModxna()) return;
+  mprintf("\tFragment: %s\n", fragmentName_.c_str());
+  printmxna("\tHead        ", head_);
+  printmxna("\tHeadStrip   ", headStrip_);
+  printmxna("\tTail        ", tail_);
+  printmxna("\tTailStrip   ", tailStrip_);
+  printmxna("\tAnchor      ", anchor_);
+  printmxna("\tAnchorStrip ", anchorStrip_);
+}
diff --git a/src/Structure/ModXNA_Info.h b/src/Structure/ModXNA_Info.h
new file mode 100644
index 0000000000..52bf4df496
--- /dev/null
+++ b/src/Structure/ModXNA_Info.h
@@ -0,0 +1,39 @@
+#ifndef INC_STRUCTURE_MODXNA_INFO_H
+#define INC_STRUCTURE_MODXNA_INFO_H
+#include <string>
+namespace Cpptraj {
+namespace Structure {
+/// Hold info used by the modXNA FF for joining fragments
+class ModXNA_Info {
+  public:
+    /// CONSTRUCTOR
+    ModXNA_Info();
+
+    enum StatType { OK = 0, NOT_MODXNA, ERR };
+
+    /// Parse the given modXNA title string
+    StatType ParseModxnaStr(std::string const&);
+    /// \return true if there is modXNA info
+    bool HasModxna() const { return (!fragmentName_.empty()); }
+    /// Print to stdout
+    void PrintModxna() const;
+
+    std::string const& FragmentName() const { return fragmentName_; }
+    std::string const& Head()         const { return head_; }
+    std::string const& HeadStrip()    const { return headStrip_; }
+    std::string const& Tail()         const { return tail_; }
+    std::string const& TailStrip()    const { return tailStrip_; }
+    std::string const& Anchor()       const { return anchor_; }
+    std::string const& AnchorStrip()  const { return anchorStrip_; }
+  private:
+    std::string fragmentName_;
+    std::string head_;
+    std::string headStrip_;
+    std::string tail_;
+    std::string tailStrip_;
+    std::string anchor_;
+    std::string anchorStrip_;
+};
+}
+}
+#endif

From b5a2bc8a396f40f2cb4faee27036216864c20afd Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 5 Mar 2026 08:43:48 -0500
Subject: [PATCH 1460/1492] Add to build

---
 src/Structure/CMakeLists.txt  | 1 +
 src/Structure/structuredepend | 1 +
 src/Structure/structurefiles  | 1 +
 3 files changed, 3 insertions(+)

diff --git a/src/Structure/CMakeLists.txt b/src/Structure/CMakeLists.txt
index a98547d991..62fa481b5c 100644
--- a/src/Structure/CMakeLists.txt
+++ b/src/Structure/CMakeLists.txt
@@ -12,6 +12,7 @@ target_sources(cpptraj_common_obj PRIVATE
   ${CMAKE_CURRENT_LIST_DIR}/InternalCoords.cpp
   ${CMAKE_CURRENT_LIST_DIR}/LeastSquaresPlane.cpp
   ${CMAKE_CURRENT_LIST_DIR}/MetalCenterFinder.cpp
+  ${CMAKE_CURRENT_LIST_DIR}/ModXNA_Info.cpp
   ${CMAKE_CURRENT_LIST_DIR}/PdbCleaner.cpp
   ${CMAKE_CURRENT_LIST_DIR}/RingFinder.cpp
   ${CMAKE_CURRENT_LIST_DIR}/Solvate.cpp
diff --git a/src/Structure/structuredepend b/src/Structure/structuredepend
index f564485165..0b600969dd 100644
--- a/src/Structure/structuredepend
+++ b/src/Structure/structuredepend
@@ -10,6 +10,7 @@ HisProt.o : HisProt.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../Constan
 InternalCoords.o : InternalCoords.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h InternalCoords.h
 LeastSquaresPlane.o : LeastSquaresPlane.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Unit.h ../Vec3.h LeastSquaresPlane.h
 MetalCenterFinder.o : MetalCenterFinder.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h MetalCenterFinder.h
+ModXNA_Info.o : ModXNA_Info.cpp ../ArgList.h ../CpptrajStdio.h ModXNA_Info.h
 PdbCleaner.o : PdbCleaner.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h PdbCleaner.h
 RingFinder.o : RingFinder.cpp ../Atom.h ../AtomMask.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h RingFinder.h
 Solvate.o : Solvate.cpp ../Action.h ../ActionState.h ../Action_AutoImage.h ../ArgList.h ../AssociatedData.h ../Atom.h ../AtomMask.h ../BaseIOtype.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataFile.h ../DataFileList.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../Dimension.h ../DispatchObject.h ../FileIO.h ../FileName.h ../FileTypes.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/../AtomType.h ../Parm/../CmapParmHolder.h ../Parm/../Constants.h ../Parm/../FileName.h ../Parm/../NameType.h ../Parm/../ParameterTypes.h ../Parm/../Parm/ParmEnum.h ../Parm/../TypeNameHolder.h ../Parm/DihedralParmHolder.h ../Parm/ImproperParmHolder.h ../Parm/ParameterSet.h ../Parm/ParmEnum.h ../Parm/ParmHolder.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h Solvate.h
diff --git a/src/Structure/structurefiles b/src/Structure/structurefiles
index 3f53f820b1..6073081a65 100644
--- a/src/Structure/structurefiles
+++ b/src/Structure/structurefiles
@@ -12,6 +12,7 @@ STRUCTURE_SOURCES= \
   InternalCoords.cpp \
   LeastSquaresPlane.cpp \
   MetalCenterFinder.cpp \
+  ModXNA_Info.cpp \
   PdbCleaner.cpp \
   RingFinder.cpp \
   Solvate.cpp \

From 2b7f8ec2922ddf27379e8bda7fe97f11fe72ca3b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 5 Mar 2026 09:06:15 -0500
Subject: [PATCH 1461/1492] Get modxna info from mol2 file

---
 src/Mol2File.cpp  | 22 ++++++++++++++++++++++
 src/Mol2File.h    |  8 ++++++++
 src/Parm_Mol2.cpp |  3 +++
 3 files changed, 33 insertions(+)

diff --git a/src/Mol2File.cpp b/src/Mol2File.cpp
index 887e82272e..9ad61e170f 100644
--- a/src/Mol2File.cpp
+++ b/src/Mol2File.cpp
@@ -6,6 +6,7 @@
 #include "Residue.h"
 #include "CpptrajStdio.h" // To print debug info
 #include "StringRoutines.h" // RemoveTrailingWhitespace
+#include "Structure/ModXNA_Info.h"
 
 // CONSTRUCTOR
 Mol2File::Mol2File() : 
@@ -63,6 +64,27 @@ void Mol2File::WriteHeader( Mol2File::TRIPOSTAG tag ) {
   Printf("%s\n", TRIPOSTAGTEXT[tag] );
 }
 
+/** Check for ModXNA info in the title. */
+Cpptraj::Structure::ModXNA_Info* Mol2File::CheckForModxna() {
+  // Check for modxna info
+  using namespace Cpptraj::Structure;
+  size_t pos = mol2title_.find_first_of( "modXNA-fragment" );
+  if (pos != std::string::npos) {
+    ModXNA_Info* minfo = new ModXNA_Info();
+    ModXNA_Info::StatType ret = minfo->ParseModxnaStr( mol2title_ );
+    if (ret == ModXNA_Info::OK) {
+      mprintf("\tMol2 file has ModXNA info:\n");
+      minfo->PrintModxna();
+      return minfo;
+    } else {
+      delete minfo;
+      if (ret == ModXNA_Info::ERR)
+        mprinterr("Error: Could not parse modxna string '%s'\n", mol2title_.c_str());
+    }
+  }
+  return 0;
+}
+
 // Mol2File::ReadMolecule()
 /** Set title, number of atoms, and number of bonds. */
 bool Mol2File::ReadMolecule( ) {
diff --git a/src/Mol2File.h b/src/Mol2File.h
index 0599952cee..035ae2b376 100644
--- a/src/Mol2File.h
+++ b/src/Mol2File.h
@@ -5,6 +5,11 @@
 #include <map>
 class Atom;
 class Residue;
+namespace Cpptraj {
+namespace Structure {
+class ModXNA_Info;
+}
+}
 /// Used to access mol2 files.
 class Mol2File : private CpptrajFile {
   public: 
@@ -19,6 +24,9 @@ class Mol2File : private CpptrajFile {
     void WriteHeader( TRIPOSTAG );
     /// Read in MOLECULE section of mol2file.
     bool ReadMolecule();
+    /// Check for modXNA info in the title
+    Cpptraj::Structure::ModXNA_Info* CheckForModxna();
+    /// Write Mol2 info
     bool WriteMolecule(bool,int);
     //// Used to only read # atoms in next MOLECULE record.
     int NextMolecule();
diff --git a/src/Parm_Mol2.cpp b/src/Parm_Mol2.cpp
index 2ea4054ae5..5597a5e8b3 100644
--- a/src/Parm_Mol2.cpp
+++ b/src/Parm_Mol2.cpp
@@ -2,6 +2,7 @@
 #include "Mol2File.h"
 #include "BondSearch.h"
 #include "CpptrajStdio.h"
+#include "Structure/ModXNA_Info.h"
 
 // Parm_Mol2::ID_ParmFormat() 
 bool Parm_Mol2::ID_ParmFormat(CpptrajFile& fileIn) {
@@ -16,6 +17,8 @@ int Parm_Mol2::ReadParm(FileName const& fname, Topology &parmOut) {
   mprintf("    Reading Mol2 file %s as topology file.\n",infile.Filename().base());
   // Get @<TRIPOS>MOLECULE information
   if (infile.ReadMolecule()) return 1;
+  Cpptraj::Structure::ModXNA_Info* modxna = infile.CheckForModxna();
+  if (modxna != 0) delete modxna;
   parmOut.SetParmName( infile.Mol2Title(), infile.Filename() );
 
   // Get @<TRIPOS>ATOM information

From 3dfcef1854daa74fd088551e94aeab510e46322e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 5 Mar 2026 09:12:57 -0500
Subject: [PATCH 1462/1492] Cant be in the Cpptraj namespace because if
 included in Topology will clash with the Cpptraj class.

---
 src/{Structure => }/ModXNA_Info.cpp | 0
 src/{Structure => }/ModXNA_Info.h   | 0
 2 files changed, 0 insertions(+), 0 deletions(-)
 rename src/{Structure => }/ModXNA_Info.cpp (100%)
 rename src/{Structure => }/ModXNA_Info.h (100%)

diff --git a/src/Structure/ModXNA_Info.cpp b/src/ModXNA_Info.cpp
similarity index 100%
rename from src/Structure/ModXNA_Info.cpp
rename to src/ModXNA_Info.cpp
diff --git a/src/Structure/ModXNA_Info.h b/src/ModXNA_Info.h
similarity index 100%
rename from src/Structure/ModXNA_Info.h
rename to src/ModXNA_Info.h

From f932bf38065e509e832685137183d0fac549e05f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 5 Mar 2026 09:15:12 -0500
Subject: [PATCH 1463/1492] Move out of the Structure namespace

---
 src/ModXNA_Info.cpp | 2 --
 src/ModXNA_Info.h   | 8 ++++----
 2 files changed, 4 insertions(+), 6 deletions(-)

diff --git a/src/ModXNA_Info.cpp b/src/ModXNA_Info.cpp
index d490c82f6b..e76cbeb450 100644
--- a/src/ModXNA_Info.cpp
+++ b/src/ModXNA_Info.cpp
@@ -2,8 +2,6 @@
 #include "../ArgList.h"
 #include "../CpptrajStdio.h"
 
-using namespace Cpptraj::Structure;
-
 /** CONSTRUCTOR */
 ModXNA_Info::ModXNA_Info() {}
 
diff --git a/src/ModXNA_Info.h b/src/ModXNA_Info.h
index 52bf4df496..3b7714163f 100644
--- a/src/ModXNA_Info.h
+++ b/src/ModXNA_Info.h
@@ -1,8 +1,8 @@
 #ifndef INC_STRUCTURE_MODXNA_INFO_H
 #define INC_STRUCTURE_MODXNA_INFO_H
 #include <string>
-namespace Cpptraj {
-namespace Structure {
+//namespace Cpptraj {
+//namespace Structure {
 /// Hold info used by the modXNA FF for joining fragments
 class ModXNA_Info {
   public:
@@ -34,6 +34,6 @@ class ModXNA_Info {
     std::string anchor_;
     std::string anchorStrip_;
 };
-}
-}
+//}
+//}
 #endif

From a6496d3f99de560155fd5eeba821fdee919b1d00 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 5 Mar 2026 09:16:30 -0500
Subject: [PATCH 1464/1492] Remove references to ModXNA_Info

---
 src/Structure/CMakeLists.txt  |  1 -
 src/Structure/structuredepend | 35 +++++++++++++++++------------------
 src/Structure/structurefiles  |  1 -
 3 files changed, 17 insertions(+), 20 deletions(-)

diff --git a/src/Structure/CMakeLists.txt b/src/Structure/CMakeLists.txt
index 62fa481b5c..a98547d991 100644
--- a/src/Structure/CMakeLists.txt
+++ b/src/Structure/CMakeLists.txt
@@ -12,7 +12,6 @@ target_sources(cpptraj_common_obj PRIVATE
   ${CMAKE_CURRENT_LIST_DIR}/InternalCoords.cpp
   ${CMAKE_CURRENT_LIST_DIR}/LeastSquaresPlane.cpp
   ${CMAKE_CURRENT_LIST_DIR}/MetalCenterFinder.cpp
-  ${CMAKE_CURRENT_LIST_DIR}/ModXNA_Info.cpp
   ${CMAKE_CURRENT_LIST_DIR}/PdbCleaner.cpp
   ${CMAKE_CURRENT_LIST_DIR}/RingFinder.cpp
   ${CMAKE_CURRENT_LIST_DIR}/Solvate.cpp
diff --git a/src/Structure/structuredepend b/src/Structure/structuredepend
index 0b600969dd..4f7a6a8765 100644
--- a/src/Structure/structuredepend
+++ b/src/Structure/structuredepend
@@ -1,23 +1,22 @@
-AddIons.o : AddIons.cpp ../AssociatedData.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../Dimension.h ../DistRoutines.h ../FileIO.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/../AtomType.h ../Parm/../CmapParmHolder.h ../Parm/../Constants.h ../Parm/../FileName.h ../Parm/../NameType.h ../Parm/../ParameterTypes.h ../Parm/../Parm/ParmEnum.h ../Parm/../TypeNameHolder.h ../Parm/DihedralParmHolder.h ../Parm/ImproperParmHolder.h ../Parm/ParameterSet.h ../Parm/ParmEnum.h ../Parm/ParmHolder.h ../Random.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h AddIons.h
-Builder.o : Builder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/../AtomType.h ../Parm/../CmapParmHolder.h ../Parm/../Constants.h ../Parm/../FileName.h ../Parm/../NameType.h ../Parm/../ParameterTypes.h ../Parm/../Parm/ParmEnum.h ../Parm/../TypeNameHolder.h ../Parm/DihedralParmHolder.h ../Parm/ImproperParmHolder.h ../Parm/ParameterSet.h ../Parm/ParmEnum.h ../Parm/ParmHolder.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Timer.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Builder.h Chirality.h GenerateConnectivityArrays.h InternalCoords.h StructureEnum.h Zmatrix.h
-Chirality.o : Chirality.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../Unit.h ../Vec3.h Chirality.h StructureEnum.h
-Creator.o : Creator.cpp ../ArgList.h ../AssociatedData.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../DataSet_NameMap.h ../DataSet_Parameters.h ../DataSet_PdbResMap.h ../Dimension.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/../AtomType.h ../Parm/../CmapParmHolder.h ../Parm/../Constants.h ../Parm/../FileName.h ../Parm/../NameType.h ../Parm/../ParameterTypes.h ../Parm/../Parm/ParmEnum.h ../Parm/../TypeNameHolder.h ../Parm/DihedralParmHolder.h ../Parm/ImproperParmHolder.h ../Parm/ParameterSet.h ../Parm/ParmEnum.h ../Parm/ParmHolder.h ../PdbResMapType.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/StructureEnum.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h Creator.h GenerateConnectivityArrays.h StructureEnum.h
-Disulfide.o : Disulfide.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h Disulfide.h ResStatArray.h StructureRoutines.h
-FunctionalGroup.o : FunctionalGroup.cpp ../Atom.h ../AtomMap.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h FunctionalGroup.h
-FxnGroupBuilder.o : FxnGroupBuilder.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h FunctionalGroup.h FxnGroupBuilder.h StructureRoutines.h Sugar.h SugarToken.h
+AddIons.o : AddIons.cpp ../AssociatedData.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../Dimension.h ../DistRoutines.h ../FileIO.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/../AtomType.h ../Parm/../CmapParmHolder.h ../Parm/../Constants.h ../Parm/../FileName.h ../Parm/../NameType.h ../Parm/../ParameterTypes.h ../Parm/../Parm/ParmEnum.h ../Parm/../TypeNameHolder.h ../Parm/DihedralParmHolder.h ../Parm/ImproperParmHolder.h ../Parm/ParameterSet.h ../Parm/ParmEnum.h ../Parm/ParmHolder.h ../Random.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/ModXNA_Info.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h AddIons.h
+Builder.o : Builder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/../AtomType.h ../Parm/../CmapParmHolder.h ../Parm/../Constants.h ../Parm/../FileName.h ../Parm/../NameType.h ../Parm/../ParameterTypes.h ../Parm/../Parm/ParmEnum.h ../Parm/../TypeNameHolder.h ../Parm/DihedralParmHolder.h ../Parm/ImproperParmHolder.h ../Parm/ParameterSet.h ../Parm/ParmEnum.h ../Parm/ParmHolder.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/ModXNA_Info.h ../SymbolExporting.h ../Timer.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Builder.h Chirality.h GenerateConnectivityArrays.h InternalCoords.h StructureEnum.h Zmatrix.h
+Chirality.o : Chirality.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/ModXNA_Info.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../Unit.h ../Vec3.h Chirality.h StructureEnum.h
+Creator.o : Creator.cpp ../ArgList.h ../AssociatedData.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../DataSet_NameMap.h ../DataSet_Parameters.h ../DataSet_PdbResMap.h ../Dimension.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/../AtomType.h ../Parm/../CmapParmHolder.h ../Parm/../Constants.h ../Parm/../FileName.h ../Parm/../NameType.h ../Parm/../ParameterTypes.h ../Parm/../Parm/ParmEnum.h ../Parm/../TypeNameHolder.h ../Parm/DihedralParmHolder.h ../Parm/ImproperParmHolder.h ../Parm/ParameterSet.h ../Parm/ParmEnum.h ../Parm/ParmHolder.h ../PdbResMapType.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/ModXNA_Info.h ../Structure/StructureEnum.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h Creator.h GenerateConnectivityArrays.h StructureEnum.h
+Disulfide.o : Disulfide.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/ModXNA_Info.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h Disulfide.h ResStatArray.h StructureRoutines.h
+FunctionalGroup.o : FunctionalGroup.cpp ../Atom.h ../AtomMap.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/ModXNA_Info.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h FunctionalGroup.h
+FxnGroupBuilder.o : FxnGroupBuilder.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/ModXNA_Info.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h FunctionalGroup.h FxnGroupBuilder.h StructureRoutines.h Sugar.h SugarToken.h
 GenerateConnectivityArrays.o : GenerateConnectivityArrays.cpp ../Atom.h ../Constants.h ../CpptrajStdio.h ../NameType.h ../ParameterTypes.h ../Residue.h ../SymbolExporting.h GenerateConnectivityArrays.h
-HisProt.o : HisProt.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h HisProt.h StructureRoutines.h
-InternalCoords.o : InternalCoords.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h InternalCoords.h
+HisProt.o : HisProt.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/ModXNA_Info.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h HisProt.h StructureRoutines.h
+InternalCoords.o : InternalCoords.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/ModXNA_Info.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h InternalCoords.h
 LeastSquaresPlane.o : LeastSquaresPlane.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Unit.h ../Vec3.h LeastSquaresPlane.h
-MetalCenterFinder.o : MetalCenterFinder.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h MetalCenterFinder.h
-ModXNA_Info.o : ModXNA_Info.cpp ../ArgList.h ../CpptrajStdio.h ModXNA_Info.h
-PdbCleaner.o : PdbCleaner.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h PdbCleaner.h
-RingFinder.o : RingFinder.cpp ../Atom.h ../AtomMask.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h RingFinder.h
-Solvate.o : Solvate.cpp ../Action.h ../ActionState.h ../Action_AutoImage.h ../ArgList.h ../AssociatedData.h ../Atom.h ../AtomMask.h ../BaseIOtype.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataFile.h ../DataFileList.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../Dimension.h ../DispatchObject.h ../FileIO.h ../FileName.h ../FileTypes.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/../AtomType.h ../Parm/../CmapParmHolder.h ../Parm/../Constants.h ../Parm/../FileName.h ../Parm/../NameType.h ../Parm/../ParameterTypes.h ../Parm/../Parm/ParmEnum.h ../Parm/../TypeNameHolder.h ../Parm/DihedralParmHolder.h ../Parm/ImproperParmHolder.h ../Parm/ParameterSet.h ../Parm/ParmEnum.h ../Parm/ParmHolder.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h Solvate.h
+MetalCenterFinder.o : MetalCenterFinder.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/ModXNA_Info.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h MetalCenterFinder.h
+PdbCleaner.o : PdbCleaner.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/ModXNA_Info.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h PdbCleaner.h
+RingFinder.o : RingFinder.cpp ../Atom.h ../AtomMask.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/ModXNA_Info.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h RingFinder.h
+Solvate.o : Solvate.cpp ../Action.h ../ActionState.h ../Action_AutoImage.h ../ArgList.h ../AssociatedData.h ../Atom.h ../AtomMask.h ../BaseIOtype.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataFile.h ../DataFileList.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../Dimension.h ../DispatchObject.h ../FileIO.h ../FileName.h ../FileTypes.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/../AtomType.h ../Parm/../CmapParmHolder.h ../Parm/../Constants.h ../Parm/../FileName.h ../Parm/../NameType.h ../Parm/../ParameterTypes.h ../Parm/../Parm/ParmEnum.h ../Parm/../TypeNameHolder.h ../Parm/DihedralParmHolder.h ../Parm/ImproperParmHolder.h ../Parm/ParameterSet.h ../Parm/ParmEnum.h ../Parm/ParmHolder.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/ModXNA_Info.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h Solvate.h
 StructureEnum.o : StructureEnum.cpp StructureEnum.h
 StructureRoutines.o : StructureRoutines.cpp ../Atom.h ../CpptrajStdio.h ../NameType.h ../Residue.h ../SymbolExporting.h StructureRoutines.h
-Sugar.o : Sugar.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h Sugar.h SugarToken.h
-SugarBuilder.o : SugarBuilder.cpp ../ArgList.h ../Atom.h ../AtomMap.h ../AtomMask.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DistRoutines.h ../FileIO.h ../FileName.h ../Frame.h ../ImageOption.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../Unit.h ../Vec3.h Chirality.h FunctionalGroup.h FxnGroupBuilder.h LinkAtom.h ResStatArray.h StructureEnum.h StructureRoutines.h Sugar.h SugarBuilder.h SugarLinkAtoms.h SugarToken.h
-SugarLinkAtoms.o : SugarLinkAtoms.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../StringRoutines.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h LinkAtom.h SugarLinkAtoms.h
+Sugar.o : Sugar.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/ModXNA_Info.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h Sugar.h SugarToken.h
+SugarBuilder.o : SugarBuilder.cpp ../ArgList.h ../Atom.h ../AtomMap.h ../AtomMask.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DistRoutines.h ../FileIO.h ../FileName.h ../Frame.h ../ImageOption.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/ModXNA_Info.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../Unit.h ../Vec3.h Chirality.h FunctionalGroup.h FxnGroupBuilder.h LinkAtom.h ResStatArray.h StructureEnum.h StructureRoutines.h Sugar.h SugarBuilder.h SugarLinkAtoms.h SugarToken.h
+SugarLinkAtoms.o : SugarLinkAtoms.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../StringRoutines.h ../Structure/ModXNA_Info.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h LinkAtom.h SugarLinkAtoms.h
 SugarToken.o : SugarToken.cpp ../ArgList.h ../CpptrajStdio.h SugarToken.h
-Zmatrix.o : Zmatrix.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../Unit.h ../Vec3.h GenerateConnectivityArrays.h InternalCoords.h Zmatrix.h
+Zmatrix.o : Zmatrix.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/ModXNA_Info.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../Unit.h ../Vec3.h GenerateConnectivityArrays.h InternalCoords.h Zmatrix.h
diff --git a/src/Structure/structurefiles b/src/Structure/structurefiles
index 6073081a65..3f53f820b1 100644
--- a/src/Structure/structurefiles
+++ b/src/Structure/structurefiles
@@ -12,7 +12,6 @@ STRUCTURE_SOURCES= \
   InternalCoords.cpp \
   LeastSquaresPlane.cpp \
   MetalCenterFinder.cpp \
-  ModXNA_Info.cpp \
   PdbCleaner.cpp \
   RingFinder.cpp \
   Solvate.cpp \

From d1da6dea411505ca240160061be332758c4a4aa9 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 5 Mar 2026 09:26:53 -0500
Subject: [PATCH 1465/1492] Save ModXNA info in Topology

---
 src/Cluster/clusterdepend     |  16 +-
 src/Energy/energydepend       |  14 +-
 src/ModXNA_Info.cpp           |   4 +-
 src/Mol2File.cpp              |   5 +-
 src/Mol2File.h                |   6 +-
 src/Parm/parmdepend           |  10 +-
 src/Parm_Mol2.cpp             |   9 +-
 src/Structure/structuredepend |  34 +-
 src/Topology.h                |   8 +
 src/cpptrajdepend             | 753 +++++++++++++++++-----------------
 src/cpptrajfiles              |   1 +
 11 files changed, 434 insertions(+), 426 deletions(-)

diff --git a/src/Cluster/clusterdepend b/src/Cluster/clusterdepend
index 7db106bca2..77b22ca3a2 100644
--- a/src/Cluster/clusterdepend
+++ b/src/Cluster/clusterdepend
@@ -1,5 +1,5 @@
 Algorithm.o : Algorithm.cpp ../CpptrajStdio.h Algorithm.h CentroidArray.h Cframes.h Metric.h MetricArray.h Node.h
-Algorithm_DBscan.o : Algorithm_DBscan.cpp ../ArgList.h ../ArrayIterator.h ../AssociatedData.h ../Atom.h ../AtomMask.h ../BaseIOtype.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataFile.h ../DataSet.h ../DataSetList.h ../DataSet_2D.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../DataSet_MatrixDbl.h ../Dimension.h ../FileIO.h ../FileName.h ../FileTypes.h ../Frame.h ../MaskToken.h ../Matrix.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../ProgressBar.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../StringRoutines.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h Algorithm.h Algorithm_DBscan.h CentroidArray.h Cframes.h List.h Metric.h MetricArray.h Node.h
+Algorithm_DBscan.o : Algorithm_DBscan.cpp ../ArgList.h ../ArrayIterator.h ../AssociatedData.h ../Atom.h ../AtomMask.h ../BaseIOtype.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataFile.h ../DataSet.h ../DataSetList.h ../DataSet_2D.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../DataSet_MatrixDbl.h ../Dimension.h ../FileIO.h ../FileName.h ../FileTypes.h ../Frame.h ../MaskToken.h ../Matrix.h ../Matrix_3x3.h ../MetaData.h ../ModXNA_Info.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../ProgressBar.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../StringRoutines.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h Algorithm.h Algorithm_DBscan.h CentroidArray.h Cframes.h List.h Metric.h MetricArray.h Node.h
 Algorithm_DPeaks.o : Algorithm_DPeaks.cpp ../ArgList.h ../AssociatedData.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSet_1D.h ../DataSet_Mesh.h ../Dimension.h ../FileIO.h ../FileName.h ../MetaData.h ../Parallel.h ../ProgressBar.h ../Range.h ../Spline.h ../TextFormat.h Algorithm.h Algorithm_DPeaks.h CentroidArray.h Cframes.h List.h Metric.h MetricArray.h Node.h
 Algorithm_HierAgglo.o : Algorithm_HierAgglo.cpp ../ArgList.h ../ArrayIterator.h ../CpptrajFile.h ../CpptrajStdio.h ../FileIO.h ../FileName.h ../Matrix.h ../Parallel.h ../ProgressBar.h ../Timer.h Algorithm.h Algorithm_HierAgglo.h CentroidArray.h Cframes.h DynamicMatrix.h List.h Metric.h MetricArray.h Node.h
 Algorithm_Kmeans.o : Algorithm_Kmeans.cpp ../ArgList.h ../CpptrajFile.h ../CpptrajStdio.h ../FileIO.h ../FileName.h ../Parallel.h ../ProgressBar.h ../Random.h Algorithm.h Algorithm_Kmeans.h CentroidArray.h Cframes.h List.h Metric.h MetricArray.h Node.h
@@ -9,22 +9,22 @@ Centroid_Coord.o : Centroid_Coord.cpp ../Atom.h ../AtomMask.h ../Box.h ../Coordi
 Cframes.o : Cframes.cpp Cframes.h
 Cmatrix_Binary.o : Cmatrix_Binary.cpp ../CpptrajFile.h ../CpptrajStdio.h ../FileIO.h ../FileName.h ../Parallel.h Cframes.h Cmatrix_Binary.h
 Cmatrix_NC.o : Cmatrix_NC.cpp ../CpptrajStdio.h ../FileName.h ../NC_Routines.h Cframes.h Cmatrix_NC.h
-Control.o : Control.cpp ../ArgList.h ../ArrayIterator.h ../AssociatedData.h ../Atom.h ../AtomMask.h ../BaseIOtype.h ../Box.h ../BufferedLine.h ../Cluster/Cframes.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataFile.h ../DataFileList.h ../DataSet.h ../DataSetList.h ../DataSet_1D.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../DataSet_PairwiseCache.h ../DataSet_float.h ../DataSet_integer.h ../Dimension.h ../FileIO.h ../FileName.h ../FileTypes.h ../Frame.h ../MaskToken.h ../Matrix.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../OnlineVarT.h ../Parallel.h ../ParameterTypes.h ../Random.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../TrajectoryFile.h ../Unit.h ../Vec3.h Algorithm.h Algorithm_DBscan.h Algorithm_DPeaks.h Algorithm_HierAgglo.h Algorithm_Kmeans.h BestReps.h CentroidArray.h Cframes.h Control.h DBI.h DrawGraph.h DynamicMatrix.h List.h Metric.h MetricArray.h Node.h Output.h PseudoF.h Results.h Results_Coords.h Sieve.h Silhouette.h
+Control.o : Control.cpp ../ArgList.h ../ArrayIterator.h ../AssociatedData.h ../Atom.h ../AtomMask.h ../BaseIOtype.h ../Box.h ../BufferedLine.h ../Cluster/Cframes.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataFile.h ../DataFileList.h ../DataSet.h ../DataSetList.h ../DataSet_1D.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../DataSet_PairwiseCache.h ../DataSet_float.h ../DataSet_integer.h ../Dimension.h ../FileIO.h ../FileName.h ../FileTypes.h ../Frame.h ../MaskToken.h ../Matrix.h ../Matrix_3x3.h ../MetaData.h ../ModXNA_Info.h ../Molecule.h ../NameType.h ../OnlineVarT.h ../Parallel.h ../ParameterTypes.h ../Random.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../TrajectoryFile.h ../Unit.h ../Vec3.h Algorithm.h Algorithm_DBscan.h Algorithm_DPeaks.h Algorithm_HierAgglo.h Algorithm_Kmeans.h BestReps.h CentroidArray.h Cframes.h Control.h DBI.h DrawGraph.h DynamicMatrix.h List.h Metric.h MetricArray.h Node.h Output.h PseudoF.h Results.h Results_Coords.h Sieve.h Silhouette.h
 DBI.o : DBI.cpp CentroidArray.h Cframes.h DBI.h List.h Metric.h MetricArray.h Node.h
 DrawGraph.o : DrawGraph.cpp ../AssociatedData.h ../Atom.h ../Constants.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSet_1D.h ../Dimension.h ../FileIO.h ../FileName.h ../MetaData.h ../NameType.h ../PDBfile.h ../Parallel.h ../Range.h ../Residue.h ../SymbolExporting.h ../TextFormat.h ../Vec3.h Cframes.h DrawGraph.h Metric.h MetricArray.h
 DynamicMatrix.o : DynamicMatrix.cpp ../ArrayIterator.h ../CpptrajStdio.h ../Matrix.h DynamicMatrix.h
 List.o : List.cpp ../AssociatedData.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSet_1D.h ../DataSet_integer.h ../Dimension.h ../FileIO.h ../FileName.h ../MetaData.h ../Parallel.h ../ProgressBar.h ../Range.h ../TextFormat.h CentroidArray.h Cframes.h List.h Metric.h MetricArray.h Node.h
-MetricArray.o : MetricArray.cpp ../ArgList.h ../ArrayIterator.h ../AssociatedData.h ../Atom.h ../AtomMap.h ../AtomMask.h ../BaseIOtype.h ../Box.h ../Cluster/Cframes.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataFile.h ../DataFileList.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../DataSet_PairwiseCache.h ../Dimension.h ../FileIO.h ../FileName.h ../FileTypes.h ../Frame.h ../Hungarian.h ../MapAtom.h ../MaskToken.h ../Matrix.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../OnlineVarT.h ../Parallel.h ../ParameterTypes.h ../ProgressBar.h ../QuaternionRMSD.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../StringRoutines.h ../SymbolExporting.h ../SymmetricRmsdCalc.h ../TextFormat.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h CentroidArray.h Metric.h MetricArray.h Metric_DME.h Metric_QuatRMSD.h Metric_RMS.h Metric_SRMSD.h Metric_Scalar.h Metric_Torsion.h
-Metric_DME.o : Metric_DME.cpp ../AssociatedData.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSet_Coords.h ../Dimension.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../TextFormat.h ../Topology.h ../Unit.h ../Vec3.h Centroid.h Centroid_Coord.h Cframes.h Metric.h Metric_DME.h
+MetricArray.o : MetricArray.cpp ../ArgList.h ../ArrayIterator.h ../AssociatedData.h ../Atom.h ../AtomMap.h ../AtomMask.h ../BaseIOtype.h ../Box.h ../Cluster/Cframes.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataFile.h ../DataFileList.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../DataSet_PairwiseCache.h ../Dimension.h ../FileIO.h ../FileName.h ../FileTypes.h ../Frame.h ../Hungarian.h ../MapAtom.h ../MaskToken.h ../Matrix.h ../Matrix_3x3.h ../MetaData.h ../ModXNA_Info.h ../Molecule.h ../NameType.h ../OnlineVarT.h ../Parallel.h ../ParameterTypes.h ../ProgressBar.h ../QuaternionRMSD.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../StringRoutines.h ../SymbolExporting.h ../SymmetricRmsdCalc.h ../TextFormat.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h CentroidArray.h Metric.h MetricArray.h Metric_DME.h Metric_QuatRMSD.h Metric_RMS.h Metric_SRMSD.h Metric_Scalar.h Metric_Torsion.h
+Metric_DME.o : Metric_DME.cpp ../AssociatedData.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSet_Coords.h ../Dimension.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../ModXNA_Info.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../TextFormat.h ../Topology.h ../Unit.h ../Vec3.h Centroid.h Centroid_Coord.h Cframes.h Metric.h Metric_DME.h
 Metric_Matrix2D.o : Metric_Matrix2D.cpp ../AssociatedData.h ../CpptrajFile.h ../DataSet.h ../DataSet_2D.h ../Dimension.h ../FileIO.h ../FileName.h ../MetaData.h ../Parallel.h ../Range.h ../TextFormat.h Metric.h Metric_Matrix2D.h
-Metric_QuatRMSD.o : Metric_QuatRMSD.cpp ../AssociatedData.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSet_Coords.h ../Dimension.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../QuaternionRMSD.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../TextFormat.h ../Topology.h ../Unit.h ../Vec3.h Centroid.h Centroid_Coord.h Cframes.h Metric.h Metric_QuatRMSD.h
-Metric_RMS.o : Metric_RMS.cpp ../AssociatedData.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSet_Coords.h ../Dimension.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../TextFormat.h ../Topology.h ../Unit.h ../Vec3.h Centroid.h Centroid_Coord.h Cframes.h Metric.h Metric_RMS.h
-Metric_SRMSD.o : Metric_SRMSD.cpp ../ArrayIterator.h ../AssociatedData.h ../Atom.h ../AtomMap.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSet_Coords.h ../Dimension.h ../FileIO.h ../FileName.h ../Frame.h ../Hungarian.h ../MapAtom.h ../MaskToken.h ../Matrix.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../SymmetricRmsdCalc.h ../TextFormat.h ../Topology.h ../Unit.h ../Vec3.h Centroid.h Centroid_Coord.h Cframes.h Metric.h Metric_SRMSD.h
+Metric_QuatRMSD.o : Metric_QuatRMSD.cpp ../AssociatedData.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSet_Coords.h ../Dimension.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../ModXNA_Info.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../QuaternionRMSD.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../TextFormat.h ../Topology.h ../Unit.h ../Vec3.h Centroid.h Centroid_Coord.h Cframes.h Metric.h Metric_QuatRMSD.h
+Metric_RMS.o : Metric_RMS.cpp ../AssociatedData.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSet_Coords.h ../Dimension.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../ModXNA_Info.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../TextFormat.h ../Topology.h ../Unit.h ../Vec3.h Centroid.h Centroid_Coord.h Cframes.h Metric.h Metric_RMS.h
+Metric_SRMSD.o : Metric_SRMSD.cpp ../ArrayIterator.h ../AssociatedData.h ../Atom.h ../AtomMap.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSet_Coords.h ../Dimension.h ../FileIO.h ../FileName.h ../Frame.h ../Hungarian.h ../MapAtom.h ../MaskToken.h ../Matrix.h ../Matrix_3x3.h ../MetaData.h ../ModXNA_Info.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../SymmetricRmsdCalc.h ../TextFormat.h ../Topology.h ../Unit.h ../Vec3.h Centroid.h Centroid_Coord.h Cframes.h Metric.h Metric_SRMSD.h
 Metric_Scalar.o : Metric_Scalar.cpp ../AssociatedData.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSet_1D.h ../Dimension.h ../FileIO.h ../FileName.h ../MetaData.h ../Parallel.h ../Range.h ../TextFormat.h Centroid.h Centroid_Num.h Cframes.h Metric.h Metric_Scalar.h
 Metric_Torsion.o : Metric_Torsion.cpp ../AssociatedData.h ../Constants.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSet_1D.h ../Dimension.h ../FileIO.h ../FileName.h ../MetaData.h ../Parallel.h ../Range.h ../TextFormat.h Centroid.h Centroid_Num.h Cframes.h Metric.h Metric_Torsion.h
 Node.o : Node.cpp ../AssociatedData.h ../CpptrajFile.h ../DataSet.h ../DataSet_1D.h ../DataSet_float.h ../DataSet_integer.h ../Dimension.h ../FileIO.h ../FileName.h ../MetaData.h ../Parallel.h ../Range.h ../TextFormat.h CentroidArray.h Cframes.h Metric.h MetricArray.h Node.h
 Output.o : Output.cpp ../ArrayIterator.h ../CpptrajFile.h ../CpptrajStdio.h ../FileIO.h ../FileName.h ../Matrix.h ../Parallel.h ../Timer.h Algorithm.h BestReps.h CentroidArray.h Cframes.h List.h Metric.h MetricArray.h Node.h Output.h
 PseudoF.o : PseudoF.cpp ../Constants.h ../CpptrajStdio.h CentroidArray.h Cframes.h List.h Metric.h MetricArray.h Node.h PseudoF.h
-Results_Coords.o : Results_Coords.cpp ../ActionFrameCounter.h ../ArgList.h ../ArrayIterator.h ../AssociatedData.h ../Atom.h ../AtomMap.h ../AtomMask.h ../BaseIOtype.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../Dimension.h ../FileIO.h ../FileName.h ../FileTypes.h ../Frame.h ../Hungarian.h ../MapAtom.h ../MaskToken.h ../Matrix.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../OutputTrajCommon.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../StringRoutines.h ../SymbolExporting.h ../SymmetricRmsdCalc.h ../TextFormat.h ../Timer.h ../Topology.h ../TrajectoryFile.h ../Trajout_Single.h ../Unit.h ../Vec3.h CentroidArray.h Cframes.h List.h Metric.h MetricArray.h Metric_DME.h Metric_RMS.h Metric_SRMSD.h Node.h Results.h Results_Coords.h
+Results_Coords.o : Results_Coords.cpp ../ActionFrameCounter.h ../ArgList.h ../ArrayIterator.h ../AssociatedData.h ../Atom.h ../AtomMap.h ../AtomMask.h ../BaseIOtype.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../Dimension.h ../FileIO.h ../FileName.h ../FileTypes.h ../Frame.h ../Hungarian.h ../MapAtom.h ../MaskToken.h ../Matrix.h ../Matrix_3x3.h ../MetaData.h ../ModXNA_Info.h ../Molecule.h ../NameType.h ../OutputTrajCommon.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../StringRoutines.h ../SymbolExporting.h ../SymmetricRmsdCalc.h ../TextFormat.h ../Timer.h ../Topology.h ../TrajectoryFile.h ../Trajout_Single.h ../Unit.h ../Vec3.h CentroidArray.h Cframes.h List.h Metric.h MetricArray.h Metric_DME.h Metric_RMS.h Metric_SRMSD.h Node.h Results.h Results_Coords.h
 Sieve.o : Sieve.cpp ../AssociatedData.h ../Cluster/Cframes.h ../CpptrajFile.h ../DataSet.h ../DataSet_PairwiseCache.h ../Dimension.h ../FileIO.h ../FileName.h ../MetaData.h ../Parallel.h ../Random.h ../Range.h ../TextFormat.h Cframes.h Sieve.h
 Silhouette.o : Silhouette.cpp ../CpptrajFile.h ../CpptrajStdio.h ../FileIO.h ../FileName.h ../OnlineVarT.h ../Parallel.h CentroidArray.h Cframes.h List.h Metric.h MetricArray.h Node.h Silhouette.h
diff --git a/src/Energy/energydepend b/src/Energy/energydepend
index 59677fcaf9..f50f3aacd3 100644
--- a/src/Energy/energydepend
+++ b/src/Energy/energydepend
@@ -1,17 +1,17 @@
-CMAP.o : CMAP.cpp ../ArrayIterator.h ../Atom.h ../AtomMask.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../Unit.h ../Vec3.h CMAP.h
-Ecalc_Nonbond.o : Ecalc_Nonbond.cpp ../Atom.h ../AtomMask.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../Energy/../Constants.h ../Energy/../ParameterTypes.h ../Energy/../SplineFxnTable.h ../Energy/Ene_LJPME_6_12.h ../Energy/Ene_LJ_12_6_4.h ../Energy/Ene_LJ_6_12.h ../Energy/ErfcFxn.h ../Energy/EwaldParams.h ../Energy/EwaldParams_LJPME.h ../Energy/Kernel_EwaldAdjust.h ../Energy/Kernel_LJPME_Adjust.h ../EwaldOptions.h ../ExclusionArray.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../PairList.h ../PairListEngine_Ewald_Decomp_LJCLR.h ../PairListEngine_Ewald_Decomp_LJLR.h ../PairListEngine_Ewald_Decomp_LJPME.h ../PairListEngine_Ewald_LJCLR.h ../PairListEngine_Ewald_LJLR.h ../PairListEngine_Ewald_LJPME.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h ../helpme_standalone.h Ecalc_Nonbond.h Ene_Decomp_Nonbond.h Ene_LJ_6_12.h Ene_Nonbond.h EwaldCalc.h EwaldCalc_Decomp.h EwaldCalc_Decomp_LJCPME.h EwaldCalc_Decomp_LJPME.h EwaldCalc_Decomp_PME.h EwaldCalc_LJCPME.h EwaldCalc_LJPME.h EwaldCalc_PME.h EwaldCalc_Regular.h Ewald_Recip.h PME_Recip.h PME_RecipParams.h VDW_LongRange_Correction.h
-EnergyDecomposer.o : EnergyDecomposer.cpp ../ArgList.h ../AssociatedData.h ../Atom.h ../AtomMask.h ../BaseIOtype.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataFile.h ../DataFileList.h ../DataSet.h ../DataSetList.h ../DataSet_1D.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../DataSet_Mesh.h ../Dimension.h ../DistRoutines.h ../EwaldOptions.h ../ExclusionArray.h ../FileIO.h ../FileName.h ../FileTypes.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../OnlineVarT.h ../PairList.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Spline.h ../Stats_Reduce.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../TorsionRoutines.h ../Unit.h ../Vec3.h Ecalc_Nonbond.h Ene_Angle.h Ene_Bond.h Ene_LJ_6_12.h EnergyDecomposer.h Kernel_Fourier.h Kernel_Harmonic.h
+CMAP.o : CMAP.cpp ../ArrayIterator.h ../Atom.h ../AtomMask.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix.h ../Matrix_3x3.h ../ModXNA_Info.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../Unit.h ../Vec3.h CMAP.h
+Ecalc_Nonbond.o : Ecalc_Nonbond.cpp ../Atom.h ../AtomMask.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../Energy/../Constants.h ../Energy/../ParameterTypes.h ../Energy/../SplineFxnTable.h ../Energy/Ene_LJPME_6_12.h ../Energy/Ene_LJ_12_6_4.h ../Energy/Ene_LJ_6_12.h ../Energy/ErfcFxn.h ../Energy/EwaldParams.h ../Energy/EwaldParams_LJPME.h ../Energy/Kernel_EwaldAdjust.h ../Energy/Kernel_LJPME_Adjust.h ../EwaldOptions.h ../ExclusionArray.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../ModXNA_Info.h ../Molecule.h ../NameType.h ../PairList.h ../PairListEngine_Ewald_Decomp_LJCLR.h ../PairListEngine_Ewald_Decomp_LJLR.h ../PairListEngine_Ewald_Decomp_LJPME.h ../PairListEngine_Ewald_LJCLR.h ../PairListEngine_Ewald_LJLR.h ../PairListEngine_Ewald_LJPME.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h ../helpme_standalone.h Ecalc_Nonbond.h Ene_Decomp_Nonbond.h Ene_LJ_6_12.h Ene_Nonbond.h EwaldCalc.h EwaldCalc_Decomp.h EwaldCalc_Decomp_LJCPME.h EwaldCalc_Decomp_LJPME.h EwaldCalc_Decomp_PME.h EwaldCalc_LJCPME.h EwaldCalc_LJPME.h EwaldCalc_PME.h EwaldCalc_Regular.h Ewald_Recip.h PME_Recip.h PME_RecipParams.h VDW_LongRange_Correction.h
+EnergyDecomposer.o : EnergyDecomposer.cpp ../ArgList.h ../AssociatedData.h ../Atom.h ../AtomMask.h ../BaseIOtype.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataFile.h ../DataFileList.h ../DataSet.h ../DataSetList.h ../DataSet_1D.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../DataSet_Mesh.h ../Dimension.h ../DistRoutines.h ../EwaldOptions.h ../ExclusionArray.h ../FileIO.h ../FileName.h ../FileTypes.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../ModXNA_Info.h ../Molecule.h ../NameType.h ../OnlineVarT.h ../PairList.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Spline.h ../Stats_Reduce.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../TorsionRoutines.h ../Unit.h ../Vec3.h Ecalc_Nonbond.h Ene_Angle.h Ene_Bond.h Ene_LJ_6_12.h EnergyDecomposer.h Kernel_Fourier.h Kernel_Harmonic.h
 ErfcFxn.o : ErfcFxn.cpp ../CpptrajStdio.h ../SplineFxnTable.h ErfcFxn.h
 EwaldCalc_Decomp_LJCPME.o : EwaldCalc_Decomp_LJCPME.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../Energy/../Constants.h ../Energy/../ParameterTypes.h ../Energy/../SplineFxnTable.h ../Energy/Ene_LJ_12_6_4.h ../Energy/ErfcFxn.h ../Energy/EwaldParams.h ../Energy/Kernel_EwaldAdjust.h ../EwaldOptions.h ../ExclusionArray.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../PairList.h ../PairListEngine_Ewald_Decomp_LJCLR.h ../PairListTemplate.h ../Parallel.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Timer.h ../Unit.h ../Vec3.h ../helpme_standalone.h EwaldCalc.h EwaldCalc_Decomp.h EwaldCalc_Decomp_LJCPME.h PME_Recip.h PME_RecipParams.h VDW_LongRange_Correction.h
 EwaldCalc_Decomp_LJPME.o : EwaldCalc_Decomp_LJPME.cpp ../Atom.h ../AtomMask.h ../Box.h ../CoordinateInfo.h ../CpptrajStdio.h ../Energy/../Constants.h ../Energy/../ParameterTypes.h ../Energy/../SplineFxnTable.h ../Energy/Ene_LJPME_6_12.h ../Energy/ErfcFxn.h ../Energy/EwaldParams.h ../Energy/EwaldParams_LJPME.h ../Energy/Kernel_EwaldAdjust.h ../Energy/Kernel_LJPME_Adjust.h ../EwaldOptions.h ../ExclusionArray.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../PairList.h ../PairListEngine_Ewald_Decomp_LJPME.h ../PairListTemplate.h ../Parallel.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Timer.h ../Unit.h ../Vec3.h ../helpme_standalone.h EwaldCalc.h EwaldCalc_Decomp.h EwaldCalc_Decomp_LJPME.h PME_Recip.h PME_RecipParams.h
 EwaldCalc_Decomp_PME.o : EwaldCalc_Decomp_PME.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../Energy/../Constants.h ../Energy/../ParameterTypes.h ../Energy/../SplineFxnTable.h ../Energy/Ene_LJ_6_12.h ../Energy/ErfcFxn.h ../Energy/EwaldParams.h ../Energy/Kernel_EwaldAdjust.h ../EwaldOptions.h ../ExclusionArray.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../PairList.h ../PairListEngine_Ewald_Decomp_LJLR.h ../PairListTemplate.h ../Parallel.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Timer.h ../Unit.h ../Vec3.h ../helpme_standalone.h EwaldCalc.h EwaldCalc_Decomp.h EwaldCalc_Decomp_PME.h PME_Recip.h PME_RecipParams.h VDW_LongRange_Correction.h
-EwaldCalc_LJCPME.o : EwaldCalc_LJCPME.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../Energy/../Constants.h ../Energy/../ParameterTypes.h ../Energy/../SplineFxnTable.h ../Energy/Ene_LJ_12_6_4.h ../Energy/ErfcFxn.h ../Energy/EwaldParams.h ../Energy/Kernel_EwaldAdjust.h ../EwaldOptions.h ../ExclusionArray.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../PairList.h ../PairListEngine_Ewald_LJCLR.h ../PairListTemplate.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h ../helpme_standalone.h EwaldCalc.h EwaldCalc_LJCPME.h PME_Recip.h PME_RecipParams.h VDW_LongRange_Correction.h
+EwaldCalc_LJCPME.o : EwaldCalc_LJCPME.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../Energy/../Constants.h ../Energy/../ParameterTypes.h ../Energy/../SplineFxnTable.h ../Energy/Ene_LJ_12_6_4.h ../Energy/ErfcFxn.h ../Energy/EwaldParams.h ../Energy/Kernel_EwaldAdjust.h ../EwaldOptions.h ../ExclusionArray.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../ModXNA_Info.h ../Molecule.h ../NameType.h ../PairList.h ../PairListEngine_Ewald_LJCLR.h ../PairListTemplate.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h ../helpme_standalone.h EwaldCalc.h EwaldCalc_LJCPME.h PME_Recip.h PME_RecipParams.h VDW_LongRange_Correction.h
 EwaldCalc_LJPME.o : EwaldCalc_LJPME.cpp ../Atom.h ../AtomMask.h ../Box.h ../CoordinateInfo.h ../CpptrajStdio.h ../Energy/../Constants.h ../Energy/../ParameterTypes.h ../Energy/../SplineFxnTable.h ../Energy/Ene_LJPME_6_12.h ../Energy/ErfcFxn.h ../Energy/EwaldParams.h ../Energy/EwaldParams_LJPME.h ../Energy/Kernel_EwaldAdjust.h ../Energy/Kernel_LJPME_Adjust.h ../EwaldOptions.h ../ExclusionArray.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../PairList.h ../PairListEngine_Ewald_LJPME.h ../PairListTemplate.h ../Parallel.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Timer.h ../Unit.h ../Vec3.h ../helpme_standalone.h EwaldCalc.h EwaldCalc_LJPME.h PME_Recip.h PME_RecipParams.h
 EwaldCalc_PME.o : EwaldCalc_PME.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../Energy/../Constants.h ../Energy/../ParameterTypes.h ../Energy/../SplineFxnTable.h ../Energy/Ene_LJ_6_12.h ../Energy/ErfcFxn.h ../Energy/EwaldParams.h ../Energy/Kernel_EwaldAdjust.h ../EwaldOptions.h ../ExclusionArray.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../PairList.h ../PairListEngine_Ewald_LJLR.h ../PairListTemplate.h ../Parallel.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Timer.h ../Unit.h ../Vec3.h ../helpme_standalone.h EwaldCalc.h EwaldCalc_PME.h PME_Recip.h PME_RecipParams.h VDW_LongRange_Correction.h
 EwaldCalc_Regular.o : EwaldCalc_Regular.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../Energy/../Constants.h ../Energy/../ParameterTypes.h ../Energy/../SplineFxnTable.h ../Energy/Ene_LJ_6_12.h ../Energy/ErfcFxn.h ../Energy/EwaldParams.h ../Energy/Kernel_EwaldAdjust.h ../EwaldOptions.h ../ExclusionArray.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../PairList.h ../PairListEngine_Ewald_LJLR.h ../PairListTemplate.h ../Parallel.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Timer.h ../Unit.h ../Vec3.h EwaldCalc.h EwaldCalc_Regular.h Ewald_Recip.h VDW_LongRange_Correction.h
-EwaldParams.o : EwaldParams.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../EwaldOptions.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SplineFxnTable.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h ErfcFxn.h EwaldParams.h
-EwaldParams_LJPME.o : EwaldParams_LJPME.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../EwaldOptions.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SplineFxnTable.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h ErfcFxn.h EwaldParams.h EwaldParams_LJPME.h
+EwaldParams.o : EwaldParams.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../EwaldOptions.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../ModXNA_Info.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SplineFxnTable.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h ErfcFxn.h EwaldParams.h
+EwaldParams_LJPME.o : EwaldParams_LJPME.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../EwaldOptions.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../ModXNA_Info.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SplineFxnTable.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h ErfcFxn.h EwaldParams.h EwaldParams_LJPME.h
 Ewald_Recip.o : Ewald_Recip.cpp ../Box.h ../Constants.h ../CpptrajStdio.h ../EwaldOptions.h ../Matrix_3x3.h ../Parallel.h ../ParameterTypes.h ../SplineFxnTable.h ../StringRoutines.h ../Timer.h ../Vec3.h ErfcFxn.h EwaldParams.h Ewald_Recip.h
 PME_Recip.o : PME_Recip.cpp ../Box.h ../CpptrajStdio.h ../Matrix_3x3.h ../Parallel.h ../Timer.h ../Vec3.h ../helpme_standalone.h PME_Recip.h PME_RecipParams.h
 PME_RecipParams.o : PME_RecipParams.cpp ../Box.h ../CpptrajStdio.h ../EwaldOptions.h ../Matrix_3x3.h ../Parallel.h ../Vec3.h PME_RecipParams.h
-VDW_LongRange_Correction.o : VDW_LongRange_Correction.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h VDW_LongRange_Correction.h
+VDW_LongRange_Correction.o : VDW_LongRange_Correction.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../ModXNA_Info.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h VDW_LongRange_Correction.h
diff --git a/src/ModXNA_Info.cpp b/src/ModXNA_Info.cpp
index e76cbeb450..d08b065f29 100644
--- a/src/ModXNA_Info.cpp
+++ b/src/ModXNA_Info.cpp
@@ -1,6 +1,6 @@
 #include "ModXNA_Info.h"
-#include "../ArgList.h"
-#include "../CpptrajStdio.h"
+#include "ArgList.h"
+#include "CpptrajStdio.h"
 
 /** CONSTRUCTOR */
 ModXNA_Info::ModXNA_Info() {}
diff --git a/src/Mol2File.cpp b/src/Mol2File.cpp
index 9ad61e170f..fa1ebca3bd 100644
--- a/src/Mol2File.cpp
+++ b/src/Mol2File.cpp
@@ -6,7 +6,7 @@
 #include "Residue.h"
 #include "CpptrajStdio.h" // To print debug info
 #include "StringRoutines.h" // RemoveTrailingWhitespace
-#include "Structure/ModXNA_Info.h"
+#include "ModXNA_Info.h"
 
 // CONSTRUCTOR
 Mol2File::Mol2File() : 
@@ -65,9 +65,8 @@ void Mol2File::WriteHeader( Mol2File::TRIPOSTAG tag ) {
 }
 
 /** Check for ModXNA info in the title. */
-Cpptraj::Structure::ModXNA_Info* Mol2File::CheckForModxna() {
+ModXNA_Info* Mol2File::CheckForModxna() {
   // Check for modxna info
-  using namespace Cpptraj::Structure;
   size_t pos = mol2title_.find_first_of( "modXNA-fragment" );
   if (pos != std::string::npos) {
     ModXNA_Info* minfo = new ModXNA_Info();
diff --git a/src/Mol2File.h b/src/Mol2File.h
index 035ae2b376..a61fccea68 100644
--- a/src/Mol2File.h
+++ b/src/Mol2File.h
@@ -5,11 +5,7 @@
 #include <map>
 class Atom;
 class Residue;
-namespace Cpptraj {
-namespace Structure {
 class ModXNA_Info;
-}
-}
 /// Used to access mol2 files.
 class Mol2File : private CpptrajFile {
   public: 
@@ -25,7 +21,7 @@ class Mol2File : private CpptrajFile {
     /// Read in MOLECULE section of mol2file.
     bool ReadMolecule();
     /// Check for modXNA info in the title
-    Cpptraj::Structure::ModXNA_Info* CheckForModxna();
+    ModXNA_Info* CheckForModxna();
     /// Write Mol2 info
     bool WriteMolecule(bool,int);
     //// Used to only read # atoms in next MOLECULE record.
diff --git a/src/Parm/parmdepend b/src/Parm/parmdepend
index a1541e66c1..2581210beb 100644
--- a/src/Parm/parmdepend
+++ b/src/Parm/parmdepend
@@ -1,9 +1,9 @@
-AssignParams.o : AssignParams.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/ParmEnum.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/GenerateConnectivityArrays.h ../SymbolExporting.h ../Timer.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h AssignParams.h DihedralParmHolder.h GetParams.h ImproperParmHolder.h ParameterSet.h ParmArray.h ParmEnum.h ParmHolder.h
-Bond_Params.o : Bond_Params.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h Bond_Params.h
+AssignParams.o : AssignParams.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../MaskToken.h ../Matrix_3x3.h ../ModXNA_Info.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/ParmEnum.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/GenerateConnectivityArrays.h ../SymbolExporting.h ../Timer.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h AssignParams.h DihedralParmHolder.h GetParams.h ImproperParmHolder.h ParameterSet.h ParmArray.h ParmEnum.h ParmHolder.h
+Bond_Params.o : Bond_Params.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../ModXNA_Info.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h Bond_Params.h
 DihedralParmSet.o : DihedralParmSet.cpp ../AtomType.h ../CmapParmHolder.h ../Constants.h ../CpptrajStdio.h ../FileName.h ../NameType.h ../ParameterTypes.h ../Parm/ParmEnum.h ../TypeNameHolder.h DihedralParmHolder.h DihedralParmSet.h ImproperParmHolder.h ParameterSet.h ParmEnum.h ParmHolder.h
-GB_Params.o : GB_Params.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h GB_Params.h
-GetParams.o : GetParams.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/ParmEnum.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h DihedralParmHolder.h DihedralParmSet.h GetParams.h ImproperParmHolder.h ParameterSet.h ParmEnum.h ParmHolder.h
-LJ1264_Params.o : LJ1264_Params.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../BufferedLine.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../StringRoutines.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h LJ1264_Params.h ParmEnum.h
+GB_Params.o : GB_Params.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../ModXNA_Info.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h GB_Params.h
+GetParams.o : GetParams.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../ModXNA_Info.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/ParmEnum.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h DihedralParmHolder.h DihedralParmSet.h GetParams.h ImproperParmHolder.h ParameterSet.h ParmEnum.h ParmHolder.h
+LJ1264_Params.o : LJ1264_Params.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../BufferedLine.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../ModXNA_Info.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../StringRoutines.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h LJ1264_Params.h ParmEnum.h
 Merge.o : Merge.cpp ../Atom.h ../Constants.h ../CpptrajStdio.h ../NameType.h ../ParameterTypes.h ../Residue.h ../StringRoutines.h ../SymbolExporting.h ../TypeNameHolder.h Merge.h ParmEnum.h ParmHolder.h
 ParameterSet.o : ParameterSet.cpp ../AtomType.h ../CmapParmHolder.h ../Constants.h ../CpptrajFile.h ../CpptrajStdio.h ../FileIO.h ../FileName.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/ParmEnum.h ../TypeNameHolder.h ../UpdateParameters.h DihedralParmHolder.h ImproperParmHolder.h ParameterSet.h ParmEnum.h ParmHolder.h
 ParmEnum.o : ParmEnum.cpp ParmEnum.h
diff --git a/src/Parm_Mol2.cpp b/src/Parm_Mol2.cpp
index 5597a5e8b3..c32b105a16 100644
--- a/src/Parm_Mol2.cpp
+++ b/src/Parm_Mol2.cpp
@@ -2,7 +2,7 @@
 #include "Mol2File.h"
 #include "BondSearch.h"
 #include "CpptrajStdio.h"
-#include "Structure/ModXNA_Info.h"
+#include "ModXNA_Info.h"
 
 // Parm_Mol2::ID_ParmFormat() 
 bool Parm_Mol2::ID_ParmFormat(CpptrajFile& fileIn) {
@@ -17,8 +17,11 @@ int Parm_Mol2::ReadParm(FileName const& fname, Topology &parmOut) {
   mprintf("    Reading Mol2 file %s as topology file.\n",infile.Filename().base());
   // Get @<TRIPOS>MOLECULE information
   if (infile.ReadMolecule()) return 1;
-  Cpptraj::Structure::ModXNA_Info* modxna = infile.CheckForModxna();
-  if (modxna != 0) delete modxna;
+  ModXNA_Info* modxna = infile.CheckForModxna();
+  if (modxna != 0) {
+    parmOut.SetModxna( *modxna );
+    delete modxna;
+  }
   parmOut.SetParmName( infile.Mol2Title(), infile.Filename() );
 
   // Get @<TRIPOS>ATOM information
diff --git a/src/Structure/structuredepend b/src/Structure/structuredepend
index 4f7a6a8765..2bdebfb6b5 100644
--- a/src/Structure/structuredepend
+++ b/src/Structure/structuredepend
@@ -1,22 +1,22 @@
-AddIons.o : AddIons.cpp ../AssociatedData.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../Dimension.h ../DistRoutines.h ../FileIO.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/../AtomType.h ../Parm/../CmapParmHolder.h ../Parm/../Constants.h ../Parm/../FileName.h ../Parm/../NameType.h ../Parm/../ParameterTypes.h ../Parm/../Parm/ParmEnum.h ../Parm/../TypeNameHolder.h ../Parm/DihedralParmHolder.h ../Parm/ImproperParmHolder.h ../Parm/ParameterSet.h ../Parm/ParmEnum.h ../Parm/ParmHolder.h ../Random.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/ModXNA_Info.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h AddIons.h
-Builder.o : Builder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/../AtomType.h ../Parm/../CmapParmHolder.h ../Parm/../Constants.h ../Parm/../FileName.h ../Parm/../NameType.h ../Parm/../ParameterTypes.h ../Parm/../Parm/ParmEnum.h ../Parm/../TypeNameHolder.h ../Parm/DihedralParmHolder.h ../Parm/ImproperParmHolder.h ../Parm/ParameterSet.h ../Parm/ParmEnum.h ../Parm/ParmHolder.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/ModXNA_Info.h ../SymbolExporting.h ../Timer.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Builder.h Chirality.h GenerateConnectivityArrays.h InternalCoords.h StructureEnum.h Zmatrix.h
-Chirality.o : Chirality.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/ModXNA_Info.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../Unit.h ../Vec3.h Chirality.h StructureEnum.h
-Creator.o : Creator.cpp ../ArgList.h ../AssociatedData.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../DataSet_NameMap.h ../DataSet_Parameters.h ../DataSet_PdbResMap.h ../Dimension.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/../AtomType.h ../Parm/../CmapParmHolder.h ../Parm/../Constants.h ../Parm/../FileName.h ../Parm/../NameType.h ../Parm/../ParameterTypes.h ../Parm/../Parm/ParmEnum.h ../Parm/../TypeNameHolder.h ../Parm/DihedralParmHolder.h ../Parm/ImproperParmHolder.h ../Parm/ParameterSet.h ../Parm/ParmEnum.h ../Parm/ParmHolder.h ../PdbResMapType.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/ModXNA_Info.h ../Structure/StructureEnum.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h Creator.h GenerateConnectivityArrays.h StructureEnum.h
-Disulfide.o : Disulfide.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/ModXNA_Info.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h Disulfide.h ResStatArray.h StructureRoutines.h
-FunctionalGroup.o : FunctionalGroup.cpp ../Atom.h ../AtomMap.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/ModXNA_Info.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h FunctionalGroup.h
-FxnGroupBuilder.o : FxnGroupBuilder.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/ModXNA_Info.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h FunctionalGroup.h FxnGroupBuilder.h StructureRoutines.h Sugar.h SugarToken.h
+AddIons.o : AddIons.cpp ../AssociatedData.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../Dimension.h ../DistRoutines.h ../FileIO.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../ModXNA_Info.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/../AtomType.h ../Parm/../CmapParmHolder.h ../Parm/../Constants.h ../Parm/../FileName.h ../Parm/../NameType.h ../Parm/../ParameterTypes.h ../Parm/../Parm/ParmEnum.h ../Parm/../TypeNameHolder.h ../Parm/DihedralParmHolder.h ../Parm/ImproperParmHolder.h ../Parm/ParameterSet.h ../Parm/ParmEnum.h ../Parm/ParmHolder.h ../Random.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h AddIons.h
+Builder.o : Builder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../ModXNA_Info.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/../AtomType.h ../Parm/../CmapParmHolder.h ../Parm/../Constants.h ../Parm/../FileName.h ../Parm/../NameType.h ../Parm/../ParameterTypes.h ../Parm/../Parm/ParmEnum.h ../Parm/../TypeNameHolder.h ../Parm/DihedralParmHolder.h ../Parm/ImproperParmHolder.h ../Parm/ParameterSet.h ../Parm/ParmEnum.h ../Parm/ParmHolder.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Timer.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Builder.h Chirality.h GenerateConnectivityArrays.h InternalCoords.h StructureEnum.h Zmatrix.h
+Chirality.o : Chirality.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../ModXNA_Info.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../Unit.h ../Vec3.h Chirality.h StructureEnum.h
+Creator.o : Creator.cpp ../ArgList.h ../AssociatedData.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../DataSet_NameMap.h ../DataSet_Parameters.h ../DataSet_PdbResMap.h ../Dimension.h ../FileIO.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../ModXNA_Info.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/../AtomType.h ../Parm/../CmapParmHolder.h ../Parm/../Constants.h ../Parm/../FileName.h ../Parm/../NameType.h ../Parm/../ParameterTypes.h ../Parm/../Parm/ParmEnum.h ../Parm/../TypeNameHolder.h ../Parm/DihedralParmHolder.h ../Parm/ImproperParmHolder.h ../Parm/ParameterSet.h ../Parm/ParmEnum.h ../Parm/ParmHolder.h ../PdbResMapType.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/StructureEnum.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h Creator.h GenerateConnectivityArrays.h StructureEnum.h
+Disulfide.o : Disulfide.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../ModXNA_Info.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h Disulfide.h ResStatArray.h StructureRoutines.h
+FunctionalGroup.o : FunctionalGroup.cpp ../Atom.h ../AtomMap.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../ModXNA_Info.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h FunctionalGroup.h
+FxnGroupBuilder.o : FxnGroupBuilder.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../ModXNA_Info.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h FunctionalGroup.h FxnGroupBuilder.h StructureRoutines.h Sugar.h SugarToken.h
 GenerateConnectivityArrays.o : GenerateConnectivityArrays.cpp ../Atom.h ../Constants.h ../CpptrajStdio.h ../NameType.h ../ParameterTypes.h ../Residue.h ../SymbolExporting.h GenerateConnectivityArrays.h
-HisProt.o : HisProt.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/ModXNA_Info.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h HisProt.h StructureRoutines.h
-InternalCoords.o : InternalCoords.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/ModXNA_Info.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h InternalCoords.h
+HisProt.o : HisProt.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../ModXNA_Info.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h HisProt.h StructureRoutines.h
+InternalCoords.o : InternalCoords.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../ModXNA_Info.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h InternalCoords.h
 LeastSquaresPlane.o : LeastSquaresPlane.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Unit.h ../Vec3.h LeastSquaresPlane.h
-MetalCenterFinder.o : MetalCenterFinder.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/ModXNA_Info.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h MetalCenterFinder.h
-PdbCleaner.o : PdbCleaner.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/ModXNA_Info.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h PdbCleaner.h
-RingFinder.o : RingFinder.cpp ../Atom.h ../AtomMask.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/ModXNA_Info.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h RingFinder.h
-Solvate.o : Solvate.cpp ../Action.h ../ActionState.h ../Action_AutoImage.h ../ArgList.h ../AssociatedData.h ../Atom.h ../AtomMask.h ../BaseIOtype.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataFile.h ../DataFileList.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../Dimension.h ../DispatchObject.h ../FileIO.h ../FileName.h ../FileTypes.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/../AtomType.h ../Parm/../CmapParmHolder.h ../Parm/../Constants.h ../Parm/../FileName.h ../Parm/../NameType.h ../Parm/../ParameterTypes.h ../Parm/../Parm/ParmEnum.h ../Parm/../TypeNameHolder.h ../Parm/DihedralParmHolder.h ../Parm/ImproperParmHolder.h ../Parm/ParameterSet.h ../Parm/ParmEnum.h ../Parm/ParmHolder.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/ModXNA_Info.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h Solvate.h
+MetalCenterFinder.o : MetalCenterFinder.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../ModXNA_Info.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h MetalCenterFinder.h
+PdbCleaner.o : PdbCleaner.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../ModXNA_Info.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h PdbCleaner.h
+RingFinder.o : RingFinder.cpp ../Atom.h ../AtomMask.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../ModXNA_Info.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h RingFinder.h
+Solvate.o : Solvate.cpp ../Action.h ../ActionState.h ../Action_AutoImage.h ../ArgList.h ../AssociatedData.h ../Atom.h ../AtomMask.h ../BaseIOtype.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataFile.h ../DataFileList.h ../DataSet.h ../DataSetList.h ../DataSet_Coords.h ../DataSet_Coords_REF.h ../Dimension.h ../DispatchObject.h ../FileIO.h ../FileName.h ../FileTypes.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../ModXNA_Info.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/../AtomType.h ../Parm/../CmapParmHolder.h ../Parm/../Constants.h ../Parm/../FileName.h ../Parm/../NameType.h ../Parm/../ParameterTypes.h ../Parm/../Parm/ParmEnum.h ../Parm/../TypeNameHolder.h ../Parm/DihedralParmHolder.h ../Parm/ImproperParmHolder.h ../Parm/ParameterSet.h ../Parm/ParmEnum.h ../Parm/ParmHolder.h ../Range.h ../ReferenceFrame.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../Unit.h ../Vec3.h Solvate.h
 StructureEnum.o : StructureEnum.cpp StructureEnum.h
 StructureRoutines.o : StructureRoutines.cpp ../Atom.h ../CpptrajStdio.h ../NameType.h ../Residue.h ../SymbolExporting.h StructureRoutines.h
-Sugar.o : Sugar.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/ModXNA_Info.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h Sugar.h SugarToken.h
-SugarBuilder.o : SugarBuilder.cpp ../ArgList.h ../Atom.h ../AtomMap.h ../AtomMask.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DistRoutines.h ../FileIO.h ../FileName.h ../Frame.h ../ImageOption.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/ModXNA_Info.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../Unit.h ../Vec3.h Chirality.h FunctionalGroup.h FxnGroupBuilder.h LinkAtom.h ResStatArray.h StructureEnum.h StructureRoutines.h Sugar.h SugarBuilder.h SugarLinkAtoms.h SugarToken.h
-SugarLinkAtoms.o : SugarLinkAtoms.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../StringRoutines.h ../Structure/ModXNA_Info.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h LinkAtom.h SugarLinkAtoms.h
+Sugar.o : Sugar.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../ModXNA_Info.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h Sugar.h SugarToken.h
+SugarBuilder.o : SugarBuilder.cpp ../ArgList.h ../Atom.h ../AtomMap.h ../AtomMask.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DistRoutines.h ../FileIO.h ../FileName.h ../Frame.h ../ImageOption.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../ModXNA_Info.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../Unit.h ../Vec3.h Chirality.h FunctionalGroup.h FxnGroupBuilder.h LinkAtom.h ResStatArray.h StructureEnum.h StructureRoutines.h Sugar.h SugarBuilder.h SugarLinkAtoms.h SugarToken.h
+SugarLinkAtoms.o : SugarLinkAtoms.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../ModXNA_Info.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../StringRoutines.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h LinkAtom.h SugarLinkAtoms.h
 SugarToken.o : SugarToken.cpp ../ArgList.h ../CpptrajStdio.h SugarToken.h
-Zmatrix.o : Zmatrix.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/ModXNA_Info.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../Unit.h ../Vec3.h GenerateConnectivityArrays.h InternalCoords.h Zmatrix.h
+Zmatrix.o : Zmatrix.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../ModXNA_Info.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../Unit.h ../Vec3.h GenerateConnectivityArrays.h InternalCoords.h Zmatrix.h
diff --git a/src/Topology.h b/src/Topology.h
index 6387269338..2b0baae8b6 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -9,6 +9,7 @@
 #include "Frame.h"
 #include "FileName.h"
 #include "Range.h"
+#include "ModXNA_Info.h"
 class AtomMask;
 class CharMask;
 /// Hold information for all atoms
@@ -243,6 +244,11 @@ class Topology {
     void AddCharmmImproper(DihedralType const&, DihedralParmType const&);
     void AddCharmmImproper(DihedralType const&, int);
     void AddCharmmImproper(DihedralType const& i) { AddCharmmImproper(i, -1); }
+    // ----- ModXNA ------------------------------
+    /// Set modxna info
+    void SetModxna(ModXNA_Info const& m) { modxna_ = m; }
+    /// \return modxna info
+    ModXNA_Info const& Modxna() const { return modxna_; }
     // ----- Misc routines -----------------------
     /// Format: <res name>_<res num>@<atom name>
     std::string TruncResAtomName(int) const;
@@ -404,6 +410,8 @@ class Topology {
     std::vector<Residue> missingRes_; ///< List of residues missing from PDB
     std::vector<Residue> missingHet_; ///< List of residues missing heteroatoms in PDB
 
+    ModXNA_Info modxna_;
+
     Box parmBox_;
     Frame refCoords_;       ///< Internal reference coords for distance-based masks
 
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index f24db85897..c705864995 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -1,156 +1,156 @@
 ActionFrameCounter.o : ActionFrameCounter.cpp ActionFrameCounter.h ArgList.h CpptrajStdio.h
-ActionList.o : ActionList.cpp Action.h ActionList.h ActionState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-ActionTopWriter.o : ActionTopWriter.cpp ActionState.h ActionTopWriter.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_AddAtom.o : Action_AddAtom.cpp Action.h ActionState.h ActionTopWriter.h Action_AddAtom.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_Align.o : Action_Align.cpp Action.h ActionState.h Action_Align.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_Angle.o : Action_Angle.cpp Action.h ActionState.h Action_Angle.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h Unit.h Vec3.h
-Action_AreaPerMol.o : Action_AreaPerMol.cpp Action.h ActionState.h Action_AreaPerMol.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_AtomMap.o : Action_AtomMap.cpp Action.h ActionState.h Action_AtomMap.h ArgList.h AssociatedData.h Atom.h AtomMap.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h StructureMapper.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_AtomicCorr.o : Action_AtomicCorr.cpp Action.h ActionState.h Action_AtomicCorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_AtomicFluct.o : Action_AtomicFluct.cpp Action.h ActionFrameCounter.h ActionState.h Action_AtomicFluct.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_AutoImage.o : Action_AutoImage.cpp Action.h ActionState.h Action_AutoImage.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h Dist_Imaged.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h ImageRoutines.h ImageTypes.h Image_List.h Image_List_Unit.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_Average.o : Action_Average.cpp Action.h ActionFrameCounter.h ActionState.h Action_Average.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h Unit.h Vec3.h
-Action_AvgBox.o : Action_AvgBox.cpp Action.h ActionState.h Action_AvgBox.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_Bounds.o : Action_Bounds.cpp Action.h ActionState.h Action_Bounds.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_Box.o : Action_Box.cpp Action.h ActionState.h Action_Box.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BoxArgs.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_Center.o : Action_Center.cpp Action.h ActionState.h Action_Center.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_Channel.o : Action_Channel.cpp Action.h ActionState.h Action_Channel.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_CheckChirality.o : Action_CheckChirality.cpp Action.h ActionState.h Action_CheckChirality.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h Structure/Chirality.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h Unit.h Vec3.h
-Action_CheckStructure.o : Action_CheckStructure.cpp Action.h ActionState.h Action_CheckStructure.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_integer.h DataSet_string.h Dimension.h DispatchObject.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PairList.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/RingFinder.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_Closest.o : Action_Closest.cpp Action.h ActionState.h ActionTopWriter.h Action_Closest.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h ImageRoutines.h ImageTypes.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h cuda_kernels/kernel_wrappers.cuh
-Action_ClusterDihedral.o : Action_ClusterDihedral.cpp Action.h ActionState.h Action_ClusterDihedral.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_integer.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h Unit.h Vec3.h
-Action_Contacts.o : Action_Contacts.cpp Action.h ActionState.h Action_Contacts.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_ConvertToFrac.o : Action_ConvertToFrac.cpp Action.h ActionState.h Action_ConvertToFrac.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_CreateCrd.o : Action_CreateCrd.cpp Action.h ActionState.h Action_CreateCrd.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_CreateReservoir.o : Action_CreateReservoir.cpp Action.h ActionState.h Action_CreateReservoir.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h RemdReservoirNC.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_DNAionTracker.o : Action_DNAionTracker.cpp Action.h ActionState.h Action_DNAionTracker.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_DSSP.o : Action_DSSP.cpp Action.h ActionState.h Action_DSSP.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_Density.o : Action_Density.cpp Action.h ActionState.h Action_Density.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_Diffusion.o : Action_Diffusion.cpp Action.h ActionState.h Action_Diffusion.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_double.h DiffusionResults.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_Dihedral.o : Action_Dihedral.cpp Action.h ActionState.h Action_Dihedral.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h Unit.h Vec3.h
-Action_DihedralRMS.o : Action_DihedralRMS.cpp Action.h ActionState.h Action_DihedralRMS.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h Unit.h Vec3.h
-Action_Dipole.o : Action_Dipole.cpp Action.h ActionState.h Action_Dipole.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridAction.h GridBin.h GridMover.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_DistRmsd.o : Action_DistRmsd.cpp Action.h ActionState.h Action_DistRmsd.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_Distance.o : Action_Distance.cpp Action.h ActionState.h Action_Distance.h ArgList.h AssociatedData.h AssociatedData_NOE.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_EneDecomp.o : Action_EneDecomp.cpp Action.h ActionState.h Action_EneDecomp.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h Energy/Ecalc_Nonbond.h Energy/EnergyDecomposer.h EwaldOptions.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h PairList.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_Energy.o : Action_Energy.cpp Action.h ActionState.h Action_Energy.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h Energy.h Energy/CMAP.h Energy/Ecalc_Nonbond.h EnergyArray.h EwaldOptions.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MdOpts.h MetaData.h Molecule.h NameType.h PairList.h Parallel.h ParameterTypes.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_Esander.o : Action_Esander.cpp Action.h ActionState.h Action_Esander.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h Energy_Sander.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_FilterByData.o : Action_FilterByData.cpp Action.h ActionState.h Action_FilterByData.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_FixAtomOrder.o : Action_FixAtomOrder.cpp Action.h ActionState.h ActionTopWriter.h Action_FixAtomOrder.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomTopType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_FixImagedBonds.o : Action_FixImagedBonds.cpp Action.h ActionState.h Action_FixImagedBonds.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_GIST.o : Action_GIST.cpp Action.h ActionState.h Action_GIST.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridDbl.h DataSet_GridFlt.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h DistRoutines.h Energy/ErfcFxn.h Energy/EwaldParams.h Energy/PME_RecipParams.h Energy/VDW_LongRange_Correction.h EwaldOptions.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h GIST_PME.h GistEntropyUtils.h Grid.h GridBin.h GridMover.h ImageOption.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PairList.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h cuda_kernels/GistCudaSetup.cuh helpme_standalone.h
-Action_Grid.o : Action_Grid.cpp Action.h ActionState.h Action_Grid.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridAction.h GridBin.h GridMover.h MaskArray.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_GridFreeEnergy.o : Action_GridFreeEnergy.cpp Action.h ActionState.h Action_GridFreeEnergy.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridAction.h GridBin.h GridMover.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_HydrogenBond.o : Action_HydrogenBond.cpp Action.h ActionState.h Action_HydrogenBond.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_integer.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h Unit.h Vec3.h
-Action_Image.o : Action_Image.cpp Action.h ActionState.h Action_Image.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h ImageRoutines.h ImageTypes.h Image_List.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_InfraredSpectrum.o : Action_InfraredSpectrum.cpp Action.h ActionState.h Action_InfraredSpectrum.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_Jcoupling.o : Action_Jcoupling.cpp Action.h ActionState.h Action_Jcoupling.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h Unit.h Vec3.h
-Action_Keep.o : Action_Keep.cpp Action.h ActionState.h ActionTopWriter.h Action_Keep.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_string.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_LESsplit.o : Action_LESsplit.cpp Action.h ActionFrameCounter.h ActionState.h Action_LESsplit.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h Unit.h Vec3.h
-Action_LIE.o : Action_LIE.cpp Action.h ActionState.h Action_LIE.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_LipidOrder.o : Action_LipidOrder.cpp Action.h ActionState.h Action_LipidOrder.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_MakeStructure.o : Action_MakeStructure.cpp Action.h ActionState.h Action_MakeStructure.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h Unit.h Vec3.h
-Action_Mask.o : Action_Mask.cpp Action.h ActionFrameCounter.h ActionState.h Action_Mask.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h Unit.h Vec3.h
-Action_Matrix.o : Action_Matrix.cpp Action.h ActionFrameCounter.h ActionState.h Action_Matrix.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Vector.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_MinImage.o : Action_MinImage.cpp Action.h ActionState.h Action_MinImage.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_MinMaxDist.o : Action_MinMaxDist.cpp Action.h ActionState.h Action_MinMaxDist.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h InteractionData.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_Molsurf.o : Action_Molsurf.cpp Action.h ActionState.h Action_Molsurf.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h molsurf.h
-Action_MultiDihedral.o : Action_MultiDihedral.cpp Action.h ActionState.h Action_MultiDihedral.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DihedralSearch.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h Unit.h Vec3.h
-Action_MultiPucker.o : Action_MultiPucker.cpp Action.h ActionState.h Action_MultiPucker.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Pucker.h Pucker_PuckerMask.h Pucker_PuckerSearch.h Pucker_PuckerToken.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h Unit.h Vec3.h
-Action_MultiVector.o : Action_MultiVector.cpp Action.h ActionState.h Action_MultiVector.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_NAstruct.o : Action_NAstruct.cpp Action.h ActionFrameCounter.h ActionState.h Action_NAstruct.h ArgList.h AssociatedData.h Atom.h AtomMask.h AxisType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_float.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PDBfile.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h Unit.h Vec3.h
-Action_NMRrst.o : Action_NMRrst.cpp Action.h ActionState.h Action_NMRrst.h ArgList.h AssociatedData.h AssociatedData_NOE.h Atom.h AtomMap.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_float.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h ViewRst.h
-Action_NativeContacts.o : Action_NativeContacts.cpp Action.h ActionState.h Action_NativeContacts.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_integer.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_OrderParameter.o : Action_OrderParameter.cpp Action.h ActionState.h Action_OrderParameter.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_Outtraj.o : Action_Outtraj.cpp Action.h ActionFrameCounter.h ActionState.h Action_Outtraj.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h Unit.h Vec3.h
-Action_PairDist.o : Action_PairDist.cpp Action.h ActionState.h Action_PairDist.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h Stats_Reduce.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_Pairwise.o : Action_Pairwise.cpp Action.h ActionFrameCounter.h ActionState.h Action_Pairwise.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h Dimension.h DispatchObject.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PDBfile.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h Unit.h Vec3.h
-Action_Principal.o : Action_Principal.cpp Action.h ActionState.h Action_Principal.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_Projection.o : Action_Projection.cpp Action.h ActionFrameCounter.h ActionState.h Action_Projection.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Modes.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_Pucker.o : Action_Pucker.cpp Action.h ActionState.h Action_Pucker.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h Unit.h Vec3.h
-Action_Radgyr.o : Action_Radgyr.cpp Action.h ActionState.h Action_Radgyr.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_Radial.o : Action_Radial.cpp Action.h ActionState.h Action_Radial.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h Gpu.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h cuda_kernels/kernel_rdf.cuh
-Action_RandomizeIons.o : Action_RandomizeIons.cpp Action.h ActionState.h Action_RandomizeIons.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_Remap.o : Action_Remap.cpp Action.h ActionState.h ActionTopWriter.h Action_Remap.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_ReplicateCell.o : Action_ReplicateCell.cpp Action.h ActionFrameCounter.h ActionState.h ActionTopWriter.h Action_ReplicateCell.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h Unit.h Vec3.h
-Action_Rmsd.o : Action_Rmsd.cpp Action.h ActionState.h Action_Rmsd.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_Rotate.o : Action_Rotate.cpp Action.h ActionState.h Action_Rotate.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParallelSetFrameNum.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_RunningAvg.o : Action_RunningAvg.cpp Action.h ActionState.h Action_RunningAvg.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_STFC_Diffusion.o : Action_STFC_Diffusion.cpp Action.h ActionState.h Action_STFC_Diffusion.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_Scale.o : Action_Scale.cpp Action.h ActionState.h Action_Scale.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_SetVelocity.o : Action_SetVelocity.cpp Action.h ActionState.h Action_SetVelocity.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_Spam.o : Action_Spam.cpp Action.h ActionState.h Action_Spam.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_Peaks.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h DataSet_Vector_Scalar.h DataSet_double.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h HistBin.h ImageOption.h KDE.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h PairList.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_Strip.o : Action_Strip.cpp Action.h ActionState.h ActionTopWriter.h Action_Strip.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_Surf.o : Action_Surf.cpp Action.h ActionState.h Action_Surf.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_SymmetricRmsd.o : Action_SymmetricRmsd.cpp Action.h ActionState.h Action_SymmetricRmsd.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h Hungarian.h ImageOption.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_Temperature.o : Action_Temperature.cpp Action.h ActionState.h Action_Temperature.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_Test.o : Action_Test.cpp Action.h ActionState.h Action_Test.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h Dist_Imaged.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_Time.o : Action_Time.cpp Action.h ActionState.h Action_Time.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_ToroidalDiffusion.o : Action_ToroidalDiffusion.cpp Action.h ActionState.h Action_ToroidalDiffusion.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DiffusionResults.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_Translate.o : Action_Translate.cpp Action.h ActionState.h Action_Translate.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_Unstrip.o : Action_Unstrip.cpp Action.h ActionState.h Action_Unstrip.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_Unwrap.o : Action_Unwrap.cpp Action.h ActionState.h Action_Unwrap.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h ImageRoutines.h ImageTypes.h Image_List.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_Vector.o : Action_Vector.cpp Action.h ActionState.h Action_Vector.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h GridBin.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/LeastSquaresPlane.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_VelocityAutoCorr.o : Action_VelocityAutoCorr.cpp Action.h ActionState.h Action_VelocityAutoCorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_Volmap.o : Action_Volmap.cpp Action.h ActionState.h Action_Volmap.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridDbl.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_Volume.o : Action_Volume.cpp Action.h ActionState.h Action_Volume.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_Watershell.o : Action_Watershell.cpp Action.h ActionState.h Action_Watershell.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h ImageRoutines.h ImageTypes.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h cuda_kernels/kernel_wrappers.cuh
-Action_XtalSymm.o : Action_XtalSymm.cpp Action.h ActionState.h Action_XtalSymm.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SpaceGroup.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+ActionList.o : ActionList.cpp Action.h ActionList.h ActionState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+ActionTopWriter.o : ActionTopWriter.cpp ActionState.h ActionTopWriter.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_AddAtom.o : Action_AddAtom.cpp Action.h ActionState.h ActionTopWriter.h Action_AddAtom.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Align.o : Action_Align.cpp Action.h ActionState.h Action_Align.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Angle.o : Action_Angle.cpp Action.h ActionState.h Action_Angle.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h Unit.h Vec3.h
+Action_AreaPerMol.o : Action_AreaPerMol.cpp Action.h ActionState.h Action_AreaPerMol.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_AtomMap.o : Action_AtomMap.cpp Action.h ActionState.h Action_AtomMap.h ArgList.h AssociatedData.h Atom.h AtomMap.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h StructureMapper.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_AtomicCorr.o : Action_AtomicCorr.cpp Action.h ActionState.h Action_AtomicCorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_AtomicFluct.o : Action_AtomicFluct.cpp Action.h ActionFrameCounter.h ActionState.h Action_AtomicFluct.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_AutoImage.o : Action_AutoImage.cpp Action.h ActionState.h Action_AutoImage.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h Dist_Imaged.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h ImageRoutines.h ImageTypes.h Image_List.h Image_List_Unit.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Average.o : Action_Average.cpp Action.h ActionFrameCounter.h ActionState.h Action_Average.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h Unit.h Vec3.h
+Action_AvgBox.o : Action_AvgBox.cpp Action.h ActionState.h Action_AvgBox.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Bounds.o : Action_Bounds.cpp Action.h ActionState.h Action_Bounds.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Box.o : Action_Box.cpp Action.h ActionState.h Action_Box.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BoxArgs.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Center.o : Action_Center.cpp Action.h ActionState.h Action_Center.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Channel.o : Action_Channel.cpp Action.h ActionState.h Action_Channel.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_CheckChirality.o : Action_CheckChirality.cpp Action.h ActionState.h Action_CheckChirality.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h Structure/Chirality.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h Unit.h Vec3.h
+Action_CheckStructure.o : Action_CheckStructure.cpp Action.h ActionState.h Action_CheckStructure.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_integer.h DataSet_string.h Dimension.h DispatchObject.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h PairList.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/RingFinder.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Closest.o : Action_Closest.cpp Action.h ActionState.h ActionTopWriter.h Action_Closest.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h ImageRoutines.h ImageTypes.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h cuda_kernels/kernel_wrappers.cuh
+Action_ClusterDihedral.o : Action_ClusterDihedral.cpp Action.h ActionState.h Action_ClusterDihedral.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_integer.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h Unit.h Vec3.h
+Action_Contacts.o : Action_Contacts.cpp Action.h ActionState.h Action_Contacts.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_ConvertToFrac.o : Action_ConvertToFrac.cpp Action.h ActionState.h Action_ConvertToFrac.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_CreateCrd.o : Action_CreateCrd.cpp Action.h ActionState.h Action_CreateCrd.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_CreateReservoir.o : Action_CreateReservoir.cpp Action.h ActionState.h Action_CreateReservoir.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h RemdReservoirNC.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_DNAionTracker.o : Action_DNAionTracker.cpp Action.h ActionState.h Action_DNAionTracker.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_DSSP.o : Action_DSSP.cpp Action.h ActionState.h Action_DSSP.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Density.o : Action_Density.cpp Action.h ActionState.h Action_Density.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Diffusion.o : Action_Diffusion.cpp Action.h ActionState.h Action_Diffusion.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_double.h DiffusionResults.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Dihedral.o : Action_Dihedral.cpp Action.h ActionState.h Action_Dihedral.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h Unit.h Vec3.h
+Action_DihedralRMS.o : Action_DihedralRMS.cpp Action.h ActionState.h Action_DihedralRMS.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h Unit.h Vec3.h
+Action_Dipole.o : Action_Dipole.cpp Action.h ActionState.h Action_Dipole.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridAction.h GridBin.h GridMover.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_DistRmsd.o : Action_DistRmsd.cpp Action.h ActionState.h Action_DistRmsd.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Distance.o : Action_Distance.cpp Action.h ActionState.h Action_Distance.h ArgList.h AssociatedData.h AssociatedData_NOE.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_EneDecomp.o : Action_EneDecomp.cpp Action.h ActionState.h Action_EneDecomp.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h Energy/Ecalc_Nonbond.h Energy/EnergyDecomposer.h EwaldOptions.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h OnlineVarT.h PairList.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Energy.o : Action_Energy.cpp Action.h ActionState.h Action_Energy.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h Energy.h Energy/CMAP.h Energy/Ecalc_Nonbond.h EnergyArray.h EwaldOptions.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MdOpts.h MetaData.h ModXNA_Info.h Molecule.h NameType.h PairList.h Parallel.h ParameterTypes.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Esander.o : Action_Esander.cpp Action.h ActionState.h Action_Esander.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h Energy_Sander.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_FilterByData.o : Action_FilterByData.cpp Action.h ActionState.h Action_FilterByData.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_FixAtomOrder.o : Action_FixAtomOrder.cpp Action.h ActionState.h ActionTopWriter.h Action_FixAtomOrder.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomTopType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_FixImagedBonds.o : Action_FixImagedBonds.cpp Action.h ActionState.h Action_FixImagedBonds.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_GIST.o : Action_GIST.cpp Action.h ActionState.h Action_GIST.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridDbl.h DataSet_GridFlt.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h DistRoutines.h Energy/ErfcFxn.h Energy/EwaldParams.h Energy/PME_RecipParams.h Energy/VDW_LongRange_Correction.h EwaldOptions.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h GIST_PME.h GistEntropyUtils.h Grid.h GridBin.h GridMover.h ImageOption.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h PairList.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h cuda_kernels/GistCudaSetup.cuh helpme_standalone.h
+Action_Grid.o : Action_Grid.cpp Action.h ActionState.h Action_Grid.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridAction.h GridBin.h GridMover.h MaskArray.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_GridFreeEnergy.o : Action_GridFreeEnergy.cpp Action.h ActionState.h Action_GridFreeEnergy.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridAction.h GridBin.h GridMover.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_HydrogenBond.o : Action_HydrogenBond.cpp Action.h ActionState.h Action_HydrogenBond.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_integer.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h Unit.h Vec3.h
+Action_Image.o : Action_Image.cpp Action.h ActionState.h Action_Image.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h ImageRoutines.h ImageTypes.h Image_List.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_InfraredSpectrum.o : Action_InfraredSpectrum.cpp Action.h ActionState.h Action_InfraredSpectrum.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Jcoupling.o : Action_Jcoupling.cpp Action.h ActionState.h Action_Jcoupling.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h Unit.h Vec3.h
+Action_Keep.o : Action_Keep.cpp Action.h ActionState.h ActionTopWriter.h Action_Keep.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_string.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_LESsplit.o : Action_LESsplit.cpp Action.h ActionFrameCounter.h ActionState.h Action_LESsplit.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h Unit.h Vec3.h
+Action_LIE.o : Action_LIE.cpp Action.h ActionState.h Action_LIE.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_LipidOrder.o : Action_LipidOrder.cpp Action.h ActionState.h Action_LipidOrder.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_MakeStructure.o : Action_MakeStructure.cpp Action.h ActionState.h Action_MakeStructure.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h Unit.h Vec3.h
+Action_Mask.o : Action_Mask.cpp Action.h ActionFrameCounter.h ActionState.h Action_Mask.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h Unit.h Vec3.h
+Action_Matrix.o : Action_Matrix.cpp Action.h ActionFrameCounter.h ActionState.h Action_Matrix.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Vector.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_MinImage.o : Action_MinImage.cpp Action.h ActionState.h Action_MinImage.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_MinMaxDist.o : Action_MinMaxDist.cpp Action.h ActionState.h Action_MinMaxDist.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h InteractionData.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Molsurf.o : Action_Molsurf.cpp Action.h ActionState.h Action_Molsurf.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h molsurf.h
+Action_MultiDihedral.o : Action_MultiDihedral.cpp Action.h ActionState.h Action_MultiDihedral.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DihedralSearch.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h Unit.h Vec3.h
+Action_MultiPucker.o : Action_MultiPucker.cpp Action.h ActionState.h Action_MultiPucker.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Pucker.h Pucker_PuckerMask.h Pucker_PuckerSearch.h Pucker_PuckerToken.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h Unit.h Vec3.h
+Action_MultiVector.o : Action_MultiVector.cpp Action.h ActionState.h Action_MultiVector.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_NAstruct.o : Action_NAstruct.cpp Action.h ActionFrameCounter.h ActionState.h Action_NAstruct.h ArgList.h AssociatedData.h Atom.h AtomMask.h AxisType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_float.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h OutputTrajCommon.h PDBfile.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h Unit.h Vec3.h
+Action_NMRrst.o : Action_NMRrst.cpp Action.h ActionState.h Action_NMRrst.h ArgList.h AssociatedData.h AssociatedData_NOE.h Atom.h AtomMap.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_float.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h ViewRst.h
+Action_NativeContacts.o : Action_NativeContacts.cpp Action.h ActionState.h Action_NativeContacts.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_integer.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_OrderParameter.o : Action_OrderParameter.cpp Action.h ActionState.h Action_OrderParameter.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Outtraj.o : Action_Outtraj.cpp Action.h ActionFrameCounter.h ActionState.h Action_Outtraj.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h Unit.h Vec3.h
+Action_PairDist.o : Action_PairDist.cpp Action.h ActionState.h Action_PairDist.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h Stats_Reduce.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Pairwise.o : Action_Pairwise.cpp Action.h ActionFrameCounter.h ActionState.h Action_Pairwise.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h Dimension.h DispatchObject.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h OutputTrajCommon.h PDBfile.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h Unit.h Vec3.h
+Action_Principal.o : Action_Principal.cpp Action.h ActionState.h Action_Principal.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Projection.o : Action_Projection.cpp Action.h ActionFrameCounter.h ActionState.h Action_Projection.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Modes.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Pucker.o : Action_Pucker.cpp Action.h ActionState.h Action_Pucker.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h Unit.h Vec3.h
+Action_Radgyr.o : Action_Radgyr.cpp Action.h ActionState.h Action_Radgyr.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Radial.o : Action_Radial.cpp Action.h ActionState.h Action_Radial.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h Gpu.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h cuda_kernels/kernel_rdf.cuh
+Action_RandomizeIons.o : Action_RandomizeIons.cpp Action.h ActionState.h Action_RandomizeIons.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Remap.o : Action_Remap.cpp Action.h ActionState.h ActionTopWriter.h Action_Remap.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_ReplicateCell.o : Action_ReplicateCell.cpp Action.h ActionFrameCounter.h ActionState.h ActionTopWriter.h Action_ReplicateCell.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h Unit.h Vec3.h
+Action_Rmsd.o : Action_Rmsd.cpp Action.h ActionState.h Action_Rmsd.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Rotate.o : Action_Rotate.cpp Action.h ActionState.h Action_Rotate.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParallelSetFrameNum.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_RunningAvg.o : Action_RunningAvg.cpp Action.h ActionState.h Action_RunningAvg.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_STFC_Diffusion.o : Action_STFC_Diffusion.cpp Action.h ActionState.h Action_STFC_Diffusion.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Scale.o : Action_Scale.cpp Action.h ActionState.h Action_Scale.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_SetVelocity.o : Action_SetVelocity.cpp Action.h ActionState.h Action_SetVelocity.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Spam.o : Action_Spam.cpp Action.h ActionState.h Action_Spam.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_Peaks.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h DataSet_Vector_Scalar.h DataSet_double.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h HistBin.h ImageOption.h KDE.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h OnlineVarT.h PairList.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Strip.o : Action_Strip.cpp Action.h ActionState.h ActionTopWriter.h Action_Strip.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Surf.o : Action_Surf.cpp Action.h ActionState.h Action_Surf.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_SymmetricRmsd.o : Action_SymmetricRmsd.cpp Action.h ActionState.h Action_SymmetricRmsd.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h Hungarian.h ImageOption.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Temperature.o : Action_Temperature.cpp Action.h ActionState.h Action_Temperature.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Test.o : Action_Test.cpp Action.h ActionState.h Action_Test.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h Dist_Imaged.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Time.o : Action_Time.cpp Action.h ActionState.h Action_Time.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_ToroidalDiffusion.o : Action_ToroidalDiffusion.cpp Action.h ActionState.h Action_ToroidalDiffusion.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DiffusionResults.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Translate.o : Action_Translate.cpp Action.h ActionState.h Action_Translate.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Unstrip.o : Action_Unstrip.cpp Action.h ActionState.h Action_Unstrip.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Unwrap.o : Action_Unwrap.cpp Action.h ActionState.h Action_Unwrap.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h ImageRoutines.h ImageTypes.h Image_List.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Vector.o : Action_Vector.cpp Action.h ActionState.h Action_Vector.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h GridBin.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/LeastSquaresPlane.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_VelocityAutoCorr.o : Action_VelocityAutoCorr.cpp Action.h ActionState.h Action_VelocityAutoCorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Volmap.o : Action_Volmap.cpp Action.h ActionState.h Action_Volmap.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridDbl.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Volume.o : Action_Volume.cpp Action.h ActionState.h Action_Volume.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Action_Watershell.o : Action_Watershell.cpp Action.h ActionState.h Action_Watershell.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h ImageRoutines.h ImageTypes.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h cuda_kernels/kernel_wrappers.cuh
+Action_XtalSymm.o : Action_XtalSymm.cpp Action.h ActionState.h Action_XtalSymm.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SpaceGroup.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 AmberParamFile.o : AmberParamFile.cpp AmberParamFile.h ArgList.h AtomType.h BufferedLine.h CmapParmHolder.h Constants.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/DihedralParmSet.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h StringRoutines.h TypeNameHolder.h
-AnalysisList.o : AnalysisList.cpp ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Analysis_AmdBias.o : Analysis_AmdBias.cpp ActionState.h Analysis.h AnalysisState.h Analysis_AmdBias.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Analysis_AutoCorr.o : Analysis_AutoCorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_AutoCorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Analysis_Average.o : Analysis_Average.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Average.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Analysis_CalcDiffusion.o : Analysis_CalcDiffusion.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CalcDiffusion.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_double.h DiffusionResults.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Analysis_Clustering.o : Analysis_Clustering.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Clustering.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cluster/Algorithm.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Control.h Cluster/DrawGraph.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Sieve.h Cluster/Silhouette.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Analysis_ConstantPHStats.o : Analysis_ConstantPHStats.cpp ActionState.h Analysis.h AnalysisState.h Analysis_ConstantPHStats.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h DataSet_pH.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Analysis_Corr.o : Analysis_Corr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Corr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Analysis_CrankShaft.o : Analysis_CrankShaft.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CrankShaft.h Analysis_Statistics.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_float.h DataSet_integer.h DataSet_string.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Analysis_CrdFluct.o : Analysis_CrdFluct.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CrdFluct.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Analysis_CrossCorr.o : Analysis_CrossCorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CrossCorr.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Analysis_CurveFit.o : Analysis_CurveFit.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CurveFit.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h CurveFit.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Analysis_Divergence.o : Analysis_Divergence.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Divergence.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Analysis_EvalPlateau.o : Analysis_EvalPlateau.cpp ActionState.h Analysis.h AnalysisState.h Analysis_EvalPlateau.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h CurveFit.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Analysis_FFT.o : Analysis_FFT.cpp ActionState.h Analysis.h AnalysisState.h Analysis_FFT.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Analysis_HausdorffDistance.o : Analysis_HausdorffDistance.cpp ActionState.h Analysis.h AnalysisState.h Analysis_HausdorffDistance.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Analysis_Hist.o : Analysis_Hist.cpp ActionFrameCounter.h ActionState.h Analysis.h AnalysisState.h Analysis_Hist.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridBin.h HistBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h Unit.h Vec3.h
-Analysis_IRED.o : Analysis_IRED.cpp ActionState.h Analysis.h AnalysisState.h Analysis_IRED.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Analysis_Integrate.o : Analysis_Integrate.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Integrate.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Analysis_KDE.o : Analysis_KDE.cpp ActionState.h Analysis.h AnalysisState.h Analysis_KDE.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h HistBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Analysis_Lifetime.o : Analysis_Lifetime.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Lifetime.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Analysis_LowestCurve.o : Analysis_LowestCurve.cpp ActionState.h Analysis.h AnalysisState.h Analysis_LowestCurve.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h HistBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Analysis_Matrix.o : Analysis_Matrix.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Matrix.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Analysis_MeltCurve.o : Analysis_MeltCurve.cpp ActionState.h Analysis.h AnalysisState.h Analysis_MeltCurve.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Analysis_Modes.o : Analysis_Modes.cpp ActionFrameCounter.h ActionState.h Analysis.h AnalysisState.h Analysis_Modes.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Modes.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h Unit.h Vec3.h
-Analysis_MultiHist.o : Analysis_MultiHist.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Hist.h Analysis_KDE.h Analysis_MultiHist.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h HistBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Unit.h Vec3.h
-Analysis_Multicurve.o : Analysis_Multicurve.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CurveFit.h Analysis_Multicurve.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Analysis_Overlap.o : Analysis_Overlap.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Overlap.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Analysis_PhiPsi.o : Analysis_PhiPsi.cpp ActionState.h Analysis.h AnalysisState.h Analysis_PhiPsi.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Analysis_Project.o : Analysis_Project.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Project.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Modes.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Analysis_Regression.o : Analysis_Regression.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Regression.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Analysis_RemLog.o : Analysis_RemLog.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Lifetime.h Analysis_RemLog.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h DataSet_RemLog.h DataSet_integer.h DataSet_integer_mem.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Analysis_Rms2d.o : Analysis_Rms2d.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Rms2d.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Hungarian.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h QuaternionRMSD.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h Unit.h Vec3.h
-Analysis_RmsAvgCorr.o : Analysis_RmsAvgCorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_RmsAvgCorr.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Analysis_Rotdif.o : Analysis_Rotdif.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Rotdif.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h CurveFit.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_Mesh.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h PubFFT.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SimplexMin.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Analysis_RunningAvg.o : Analysis_RunningAvg.cpp ActionState.h Analysis.h AnalysisState.h Analysis_RunningAvg.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Analysis_Slope.o : Analysis_Slope.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Slope.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Analysis_Spline.o : Analysis_Spline.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Spline.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Analysis_State.o : Analysis_State.cpp ActionState.h Analysis.h AnalysisState.h Analysis_State.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Analysis_Statistics.o : Analysis_Statistics.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Statistics.h ArgList.h Array1D.h AssociatedData.h AssociatedData_NOE.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_float.h DataSet_integer.h DataSet_string.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Analysis_TI.o : Analysis_TI.cpp ActionState.h Analysis.h AnalysisState.h Analysis_TI.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Analysis_TICA.o : Analysis_TICA.cpp ActionState.h Analysis.h AnalysisState.h Analysis_TICA.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordCovarMatrix.h CoordCovarMatrix_Full.h CoordCovarMatrix_Half.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Analysis_Timecorr.o : Analysis_Timecorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Timecorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Analysis_VectorMath.o : Analysis_VectorMath.cpp ActionState.h Analysis.h AnalysisState.h Analysis_VectorMath.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Analysis_Wavelet.o : Analysis_Wavelet.cpp ActionFrameCounter.h ActionState.h Analysis.h AnalysisState.h Analysis_Wavelet.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ClusterMap.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h ParmFile.h ProgressBar.h ProgressTimer.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h Unit.h Vec3.h
+AnalysisList.o : AnalysisList.cpp ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_AmdBias.o : Analysis_AmdBias.cpp ActionState.h Analysis.h AnalysisState.h Analysis_AmdBias.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_AutoCorr.o : Analysis_AutoCorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_AutoCorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_Average.o : Analysis_Average.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Average.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_CalcDiffusion.o : Analysis_CalcDiffusion.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CalcDiffusion.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_double.h DiffusionResults.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_Clustering.o : Analysis_Clustering.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Clustering.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cluster/Algorithm.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Control.h Cluster/DrawGraph.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Sieve.h Cluster/Silhouette.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_ConstantPHStats.o : Analysis_ConstantPHStats.cpp ActionState.h Analysis.h AnalysisState.h Analysis_ConstantPHStats.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h DataSet_pH.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_Corr.o : Analysis_Corr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Corr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_CrankShaft.o : Analysis_CrankShaft.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CrankShaft.h Analysis_Statistics.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_float.h DataSet_integer.h DataSet_string.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_CrdFluct.o : Analysis_CrdFluct.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CrdFluct.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_CrossCorr.o : Analysis_CrossCorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CrossCorr.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_CurveFit.o : Analysis_CurveFit.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CurveFit.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h CurveFit.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_Divergence.o : Analysis_Divergence.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Divergence.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_EvalPlateau.o : Analysis_EvalPlateau.cpp ActionState.h Analysis.h AnalysisState.h Analysis_EvalPlateau.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h CurveFit.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_FFT.o : Analysis_FFT.cpp ActionState.h Analysis.h AnalysisState.h Analysis_FFT.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_HausdorffDistance.o : Analysis_HausdorffDistance.cpp ActionState.h Analysis.h AnalysisState.h Analysis_HausdorffDistance.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_Hist.o : Analysis_Hist.cpp ActionFrameCounter.h ActionState.h Analysis.h AnalysisState.h Analysis_Hist.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridBin.h HistBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h Unit.h Vec3.h
+Analysis_IRED.o : Analysis_IRED.cpp ActionState.h Analysis.h AnalysisState.h Analysis_IRED.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_Integrate.o : Analysis_Integrate.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Integrate.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_KDE.o : Analysis_KDE.cpp ActionState.h Analysis.h AnalysisState.h Analysis_KDE.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h HistBin.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_Lifetime.o : Analysis_Lifetime.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Lifetime.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_LowestCurve.o : Analysis_LowestCurve.cpp ActionState.h Analysis.h AnalysisState.h Analysis_LowestCurve.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h HistBin.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_Matrix.o : Analysis_Matrix.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Matrix.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_MeltCurve.o : Analysis_MeltCurve.cpp ActionState.h Analysis.h AnalysisState.h Analysis_MeltCurve.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_Modes.o : Analysis_Modes.cpp ActionFrameCounter.h ActionState.h Analysis.h AnalysisState.h Analysis_Modes.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Modes.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h Unit.h Vec3.h
+Analysis_MultiHist.o : Analysis_MultiHist.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Hist.h Analysis_KDE.h Analysis_MultiHist.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h HistBin.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Unit.h Vec3.h
+Analysis_Multicurve.o : Analysis_Multicurve.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CurveFit.h Analysis_Multicurve.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_Overlap.o : Analysis_Overlap.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Overlap.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_PhiPsi.o : Analysis_PhiPsi.cpp ActionState.h Analysis.h AnalysisState.h Analysis_PhiPsi.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_Project.o : Analysis_Project.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Project.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Modes.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_Regression.o : Analysis_Regression.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Regression.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_RemLog.o : Analysis_RemLog.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Lifetime.h Analysis_RemLog.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h DataSet_RemLog.h DataSet_integer.h DataSet_integer_mem.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_Rms2d.o : Analysis_Rms2d.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Rms2d.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Hungarian.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h QuaternionRMSD.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h Unit.h Vec3.h
+Analysis_RmsAvgCorr.o : Analysis_RmsAvgCorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_RmsAvgCorr.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_Rotdif.o : Analysis_Rotdif.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Rotdif.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h CurveFit.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_Mesh.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h PubFFT.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SimplexMin.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_RunningAvg.o : Analysis_RunningAvg.cpp ActionState.h Analysis.h AnalysisState.h Analysis_RunningAvg.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_Slope.o : Analysis_Slope.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Slope.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_Spline.o : Analysis_Spline.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Spline.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_State.o : Analysis_State.cpp ActionState.h Analysis.h AnalysisState.h Analysis_State.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_Statistics.o : Analysis_Statistics.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Statistics.h ArgList.h Array1D.h AssociatedData.h AssociatedData_NOE.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_float.h DataSet_integer.h DataSet_string.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_TI.o : Analysis_TI.cpp ActionState.h Analysis.h AnalysisState.h Analysis_TI.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_TICA.o : Analysis_TICA.cpp ActionState.h Analysis.h AnalysisState.h Analysis_TICA.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordCovarMatrix.h CoordCovarMatrix_Full.h CoordCovarMatrix_Half.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_Timecorr.o : Analysis_Timecorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Timecorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_VectorMath.o : Analysis_VectorMath.cpp ActionState.h Analysis.h AnalysisState.h Analysis_VectorMath.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Analysis_Wavelet.o : Analysis_Wavelet.cpp ActionFrameCounter.h ActionState.h Analysis.h AnalysisState.h Analysis_Wavelet.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ClusterMap.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h ParmFile.h ProgressBar.h ProgressTimer.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h Unit.h Vec3.h
 ArgList.o : ArgList.cpp ArgList.h CpptrajStdio.h StringRoutines.h
-Array1D.o : Array1D.cpp ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Array1D.o : Array1D.cpp ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 AssociatedData_Connect.o : AssociatedData_Connect.cpp ArgList.h AssociatedData.h AssociatedData_Connect.h CpptrajStdio.h
 AssociatedData_NOE.o : AssociatedData_NOE.cpp ArgList.h AssociatedData.h AssociatedData_NOE.h CpptrajStdio.h
 Atom.o : Atom.cpp Atom.h CpptrajStdio.h NameType.h SymbolExporting.h
-AtomMap.o : AtomMap.cpp Atom.h AtomMap.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
+AtomMap.o : AtomMap.cpp Atom.h AtomMap.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
 AtomMask.o : AtomMask.cpp Atom.h AtomMask.h CpptrajStdio.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h SymbolExporting.h Unit.h
-AxisType.o : AxisType.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AxisType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h Unit.h Vec3.h
-BondSearch.o : BondSearch.cpp Atom.h AtomMask.h BondSearch.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Timer.h Topology.h Unit.h Vec3.h
+AxisType.o : AxisType.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AxisType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h Unit.h Vec3.h
+BondSearch.o : BondSearch.cpp Atom.h AtomMask.h BondSearch.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h PairList.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Timer.h Topology.h Unit.h Vec3.h
 Box.o : Box.cpp Box.h Constants.h CpptrajStdio.h Matrix_3x3.h Parallel.h Vec3.h
 BoxArgs.o : BoxArgs.cpp ArgList.h Box.h BoxArgs.h CpptrajStdio.h Matrix_3x3.h Parallel.h Vec3.h
 BufferedFrame.o : BufferedFrame.cpp BufferedFrame.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Parallel.h TextFormat.h
@@ -160,7 +160,7 @@ CIFfile.o : CIFfile.cpp ArgList.h Atom.h BufferedLine.h CIFfile.h CpptrajFile.h
 CharMask.o : CharMask.cpp Atom.h CharMask.h CpptrajStdio.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h SymbolExporting.h Unit.h
 CharmmParamFile.o : CharmmParamFile.cpp ArgList.h AtomType.h BufferedLine.h CharmmParamFile.h CmapParmHolder.h Constants.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/DihedralParmSet.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h StringRoutines.h TypeNameHolder.h
 Cluster/Algorithm.o : Cluster/Algorithm.cpp Cluster/Algorithm.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h CpptrajStdio.h
-Cluster/Algorithm_DBscan.o : Cluster/Algorithm_DBscan.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cluster/Algorithm.h Cluster/Algorithm_DBscan.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Cluster/Algorithm_DBscan.o : Cluster/Algorithm_DBscan.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cluster/Algorithm.h Cluster/Algorithm_DBscan.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 Cluster/Algorithm_DPeaks.o : Cluster/Algorithm_DPeaks.cpp ArgList.h AssociatedData.h Cluster/Algorithm.h Cluster/Algorithm_DPeaks.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_Mesh.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h ProgressBar.h Range.h Spline.h TextFormat.h
 Cluster/Algorithm_HierAgglo.o : Cluster/Algorithm_HierAgglo.cpp ArgList.h ArrayIterator.h Cluster/Algorithm.h Cluster/Algorithm_HierAgglo.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/DynamicMatrix.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Matrix.h Parallel.h ProgressBar.h Timer.h
 Cluster/Algorithm_Kmeans.o : Cluster/Algorithm_Kmeans.cpp ArgList.h Cluster/Algorithm.h Cluster/Algorithm_Kmeans.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Parallel.h ProgressBar.h Random.h
@@ -170,23 +170,23 @@ Cluster/Centroid_Coord.o : Cluster/Centroid_Coord.cpp Atom.h AtomMask.h Box.h Cl
 Cluster/Cframes.o : Cluster/Cframes.cpp Cluster/Cframes.h
 Cluster/Cmatrix_Binary.o : Cluster/Cmatrix_Binary.cpp Cluster/Cframes.h Cluster/Cmatrix_Binary.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Parallel.h
 Cluster/Cmatrix_NC.o : Cluster/Cmatrix_NC.cpp Cluster/Cframes.h Cluster/Cmatrix_NC.h CpptrajStdio.h FileName.h NC_Routines.h
-Cluster/Control.o : Cluster/Control.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Cluster/Algorithm.h Cluster/Algorithm_DBscan.h Cluster/Algorithm_DPeaks.h Cluster/Algorithm_HierAgglo.h Cluster/Algorithm_Kmeans.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Control.h Cluster/DBI.h Cluster/DrawGraph.h Cluster/DynamicMatrix.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Output.h Cluster/PseudoF.h Cluster/Results.h Cluster/Results_Coords.h Cluster/Sieve.h Cluster/Silhouette.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_float.h DataSet_integer.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Unit.h Vec3.h
+Cluster/Control.o : Cluster/Control.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Cluster/Algorithm.h Cluster/Algorithm_DBscan.h Cluster/Algorithm_DPeaks.h Cluster/Algorithm_HierAgglo.h Cluster/Algorithm_Kmeans.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Control.h Cluster/DBI.h Cluster/DrawGraph.h Cluster/DynamicMatrix.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Output.h Cluster/PseudoF.h Cluster/Results.h Cluster/Results_Coords.h Cluster/Sieve.h Cluster/Silhouette.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_float.h DataSet_integer.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Unit.h Vec3.h
 Cluster/DBI.o : Cluster/DBI.cpp Cluster/CentroidArray.h Cluster/Cframes.h Cluster/DBI.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h
 Cluster/DrawGraph.o : Cluster/DrawGraph.cpp AssociatedData.h Atom.h Cluster/Cframes.h Cluster/DrawGraph.h Cluster/Metric.h Cluster/MetricArray.h Constants.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h Dimension.h FileIO.h FileName.h MetaData.h NameType.h PDBfile.h Parallel.h Range.h Residue.h SymbolExporting.h TextFormat.h Vec3.h
 Cluster/DynamicMatrix.o : Cluster/DynamicMatrix.cpp ArrayIterator.h Cluster/DynamicMatrix.h CpptrajStdio.h Matrix.h
 Cluster/List.o : Cluster/List.cpp AssociatedData.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_integer.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h ProgressBar.h Range.h TextFormat.h
-Cluster/MetricArray.o : Cluster/MetricArray.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h BaseIOtype.h Box.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Metric_DME.h Cluster/Metric_QuatRMSD.h Cluster/Metric_RMS.h Cluster/Metric_SRMSD.h Cluster/Metric_Scalar.h Cluster/Metric_Torsion.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterTypes.h ProgressBar.h QuaternionRMSD.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Cluster/Metric_DME.o : Cluster/Metric_DME.cpp AssociatedData.h Atom.h AtomMask.h Box.h Cluster/Centroid.h Cluster/Centroid_Coord.h Cluster/Cframes.h Cluster/Metric.h Cluster/Metric_DME.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h Unit.h Vec3.h
+Cluster/MetricArray.o : Cluster/MetricArray.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h BaseIOtype.h Box.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Metric_DME.h Cluster/Metric_QuatRMSD.h Cluster/Metric_RMS.h Cluster/Metric_SRMSD.h Cluster/Metric_Scalar.h Cluster/Metric_Torsion.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterTypes.h ProgressBar.h QuaternionRMSD.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Cluster/Metric_DME.o : Cluster/Metric_DME.cpp AssociatedData.h Atom.h AtomMask.h Box.h Cluster/Centroid.h Cluster/Centroid_Coord.h Cluster/Cframes.h Cluster/Metric.h Cluster/Metric_DME.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h Unit.h Vec3.h
 Cluster/Metric_Matrix2D.o : Cluster/Metric_Matrix2D.cpp AssociatedData.h Cluster/Metric.h Cluster/Metric_Matrix2D.h CpptrajFile.h DataSet.h DataSet_2D.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
-Cluster/Metric_QuatRMSD.o : Cluster/Metric_QuatRMSD.cpp AssociatedData.h Atom.h AtomMask.h Box.h Cluster/Centroid.h Cluster/Centroid_Coord.h Cluster/Cframes.h Cluster/Metric.h Cluster/Metric_QuatRMSD.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h QuaternionRMSD.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h Unit.h Vec3.h
-Cluster/Metric_RMS.o : Cluster/Metric_RMS.cpp AssociatedData.h Atom.h AtomMask.h Box.h Cluster/Centroid.h Cluster/Centroid_Coord.h Cluster/Cframes.h Cluster/Metric.h Cluster/Metric_RMS.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h Unit.h Vec3.h
-Cluster/Metric_SRMSD.o : Cluster/Metric_SRMSD.cpp ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h Box.h Cluster/Centroid.h Cluster/Centroid_Coord.h Cluster/Cframes.h Cluster/Metric.h Cluster/Metric_SRMSD.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Topology.h Unit.h Vec3.h
+Cluster/Metric_QuatRMSD.o : Cluster/Metric_QuatRMSD.cpp AssociatedData.h Atom.h AtomMask.h Box.h Cluster/Centroid.h Cluster/Centroid_Coord.h Cluster/Cframes.h Cluster/Metric.h Cluster/Metric_QuatRMSD.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h QuaternionRMSD.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h Unit.h Vec3.h
+Cluster/Metric_RMS.o : Cluster/Metric_RMS.cpp AssociatedData.h Atom.h AtomMask.h Box.h Cluster/Centroid.h Cluster/Centroid_Coord.h Cluster/Cframes.h Cluster/Metric.h Cluster/Metric_RMS.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h Unit.h Vec3.h
+Cluster/Metric_SRMSD.o : Cluster/Metric_SRMSD.cpp ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h Box.h Cluster/Centroid.h Cluster/Centroid_Coord.h Cluster/Cframes.h Cluster/Metric.h Cluster/Metric_SRMSD.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Topology.h Unit.h Vec3.h
 Cluster/Metric_Scalar.o : Cluster/Metric_Scalar.cpp AssociatedData.h Cluster/Centroid.h Cluster/Centroid_Num.h Cluster/Cframes.h Cluster/Metric.h Cluster/Metric_Scalar.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
 Cluster/Metric_Torsion.o : Cluster/Metric_Torsion.cpp AssociatedData.h Cluster/Centroid.h Cluster/Centroid_Num.h Cluster/Cframes.h Cluster/Metric.h Cluster/Metric_Torsion.h Constants.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
 Cluster/Node.o : Cluster/Node.cpp AssociatedData.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h CpptrajFile.h DataSet.h DataSet_1D.h DataSet_float.h DataSet_integer.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
 Cluster/Output.o : Cluster/Output.cpp ArrayIterator.h Cluster/Algorithm.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Output.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Matrix.h Parallel.h Timer.h
 Cluster/PseudoF.o : Cluster/PseudoF.cpp Cluster/CentroidArray.h Cluster/Cframes.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/PseudoF.h Constants.h CpptrajStdio.h
-Cluster/Results_Coords.o : Cluster/Results_Coords.cpp ActionFrameCounter.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h BaseIOtype.h Box.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Metric_DME.h Cluster/Metric_RMS.h Cluster/Metric_SRMSD.h Cluster/Node.h Cluster/Results.h Cluster/Results_Coords.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h Unit.h Vec3.h
+Cluster/Results_Coords.o : Cluster/Results_Coords.cpp ActionFrameCounter.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h BaseIOtype.h Box.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Metric_DME.h Cluster/Metric_RMS.h Cluster/Metric_SRMSD.h Cluster/Node.h Cluster/Results.h Cluster/Results_Coords.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h Unit.h Vec3.h
 Cluster/Sieve.o : Cluster/Sieve.cpp AssociatedData.h Cluster/Cframes.h Cluster/Sieve.h CpptrajFile.h DataSet.h DataSet_PairwiseCache.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Random.h Range.h TextFormat.h
 Cluster/Silhouette.o : Cluster/Silhouette.cpp Cluster/CentroidArray.h Cluster/Cframes.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Silhouette.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h OnlineVarT.h Parallel.h
 ClusterMap.o : ClusterMap.cpp AssociatedData.h ClusterMap.h Constants.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_2D.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h ProgressBar.h ProgressTimer.h Range.h TextFormat.h Timer.h
@@ -194,64 +194,64 @@ CmapParmHolder.o : CmapParmHolder.cpp CmapParmHolder.h Constants.h CpptrajStdio.
 Cmd.o : Cmd.cpp Cmd.h DispatchObject.h
 CmdInput.o : CmdInput.cpp CmdInput.h StringRoutines.h
 CmdList.o : CmdList.cpp Cmd.h CmdList.h DispatchObject.h
-Command.o : Command.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h ActionTopWriter.h Action_AddAtom.h Action_Align.h Action_Angle.h Action_AreaPerMol.h Action_AtomMap.h Action_AtomicCorr.h Action_AtomicFluct.h Action_AutoImage.h Action_Average.h Action_AvgBox.h Action_Bounds.h Action_Box.h Action_Center.h Action_Channel.h Action_CheckChirality.h Action_CheckStructure.h Action_Closest.h Action_ClusterDihedral.h Action_Contacts.h Action_ConvertToFrac.h Action_CreateCrd.h Action_CreateReservoir.h Action_DNAionTracker.h Action_DSSP.h Action_Density.h Action_Diffusion.h Action_Dihedral.h Action_DihedralRMS.h Action_Dipole.h Action_DistRmsd.h Action_Distance.h Action_EneDecomp.h Action_Energy.h Action_Esander.h Action_FilterByData.h Action_FixAtomOrder.h Action_FixImagedBonds.h Action_GIST.h Action_Grid.h Action_GridFreeEnergy.h Action_HydrogenBond.h Action_Image.h Action_InfraredSpectrum.h Action_Jcoupling.h Action_Keep.h Action_LESsplit.h Action_LIE.h Action_LipidOrder.h Action_MakeStructure.h Action_Mask.h Action_Matrix.h Action_MinImage.h Action_MinMaxDist.h Action_Molsurf.h Action_MultiDihedral.h Action_MultiPucker.h Action_MultiVector.h Action_NAstruct.h Action_NMRrst.h Action_NativeContacts.h Action_OrderParameter.h Action_Outtraj.h Action_PairDist.h Action_Pairwise.h Action_Principal.h Action_Projection.h Action_Pucker.h Action_Radgyr.h Action_Radial.h Action_RandomizeIons.h Action_Remap.h Action_ReplicateCell.h Action_Rmsd.h Action_Rotate.h Action_RunningAvg.h Action_STFC_Diffusion.h Action_Scale.h Action_SetVelocity.h Action_Spam.h Action_Strip.h Action_Surf.h Action_SymmetricRmsd.h Action_Temperature.h Action_Test.h Action_Time.h Action_ToroidalDiffusion.h Action_Translate.h Action_Unstrip.h Action_Unwrap.h Action_Vector.h Action_VelocityAutoCorr.h Action_Volmap.h Action_Volume.h Action_Watershell.h Action_XtalSymm.h Analysis.h AnalysisList.h AnalysisState.h Analysis_AmdBias.h Analysis_AutoCorr.h Analysis_Average.h Analysis_CalcDiffusion.h Analysis_Clustering.h Analysis_ConstantPHStats.h Analysis_Corr.h Analysis_CrankShaft.h Analysis_CrdFluct.h Analysis_CrossCorr.h Analysis_CurveFit.h Analysis_Divergence.h Analysis_EvalPlateau.h Analysis_FFT.h Analysis_HausdorffDistance.h Analysis_Hist.h Analysis_IRED.h Analysis_Integrate.h Analysis_KDE.h Analysis_Lifetime.h Analysis_LowestCurve.h Analysis_Matrix.h Analysis_MeltCurve.h Analysis_Modes.h Analysis_MultiHist.h Analysis_Multicurve.h Analysis_Overlap.h Analysis_PhiPsi.h Analysis_Project.h Analysis_Regression.h Analysis_RemLog.h Analysis_Rms2d.h Analysis_RmsAvgCorr.h Analysis_Rotdif.h Analysis_RunningAvg.h Analysis_Slope.h Analysis_Spline.h Analysis_State.h Analysis_Statistics.h Analysis_TI.h Analysis_TICA.h Analysis_Timecorr.h Analysis_VectorMath.h Analysis_Wavelet.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AxisType.h BaseIOtype.h Box.h BoxArgs.h BufferedLine.h CharMask.h Cluster/Algorithm.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Control.h Cluster/DrawGraph.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Sieve.h Cluster/Silhouette.h ClusterMap.h Cmd.h CmdInput.h CmdList.h Command.h CompactFrameArray.h ComplexArray.h Constants.h Constraints.h ControlBlock.h ControlBlock_For.h CoordinateInfo.h Corr.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_RemLog.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h Deprecated.h DiffusionResults.h DihedralSearch.h Dimension.h DispatchObject.h Energy.h Energy/Ecalc_Nonbond.h Energy/EnergyDecomposer.h Energy/ErfcFxn.h Energy/EwaldParams.h Energy/PME_RecipParams.h Energy/VDW_LongRange_Correction.h Energy_Sander.h EnsembleIn.h EnsembleOutList.h EwaldOptions.h ExclusionArray.h Exec.h Exec_AddMissingRes.h Exec_Analyze.h Exec_Build.h Exec_Calc.h Exec_CatCrd.h Exec_Change.h Exec_ClusterMap.h Exec_CombineCoords.h Exec_Commands.h Exec_CompareClusters.h Exec_CompareEnergy.h Exec_CompareTop.h Exec_CrdAction.h Exec_CrdOut.h Exec_CrdTransform.h Exec_CreateSet.h Exec_DataFile.h Exec_DataFilter.h Exec_DataSetCmd.h Exec_Desc.h Exec_Emin.h Exec_ExtendedComparison.h Exec_Flatten.h Exec_GenerateAmberRst.h Exec_Graft.h Exec_Help.h Exec_HmassRepartition.h Exec_LoadCrd.h Exec_LoadTraj.h Exec_Mutate.h Exec_ParallelAnalysis.h Exec_ParmBox.h Exec_ParmSolvent.h Exec_ParmStrip.h Exec_ParmWrite.h Exec_ParseTiming.h Exec_PermuteDihedrals.h Exec_Precision.h Exec_PrepareForLeap.h Exec_PrintData.h Exec_Random.h Exec_ReadData.h Exec_ReadEnsembleData.h Exec_ReadInput.h Exec_RotateDihedral.h Exec_RunAnalysis.h Exec_ScaleDihedralK.h Exec_Sequence.h Exec_SequenceAlign.h Exec_Set.h Exec_Show.h Exec_SortEnsembleData.h Exec_Source.h Exec_SplitCoords.h Exec_System.h Exec_Top.h Exec_Traj.h Exec_UpdateParameters.h Exec_ViewRst.h Exec_Zmatrix.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h GIST_PME.h Grid.h GridAction.h GridBin.h GridMover.h HistBin.h Hungarian.h ImageOption.h ImageTypes.h InputTrajCommon.h InteractionData.h MapAtom.h MaskArray.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h OnlineVarT.h OutputTrajCommon.h PDBfile.h PairList.h Parallel.h ParallelSetFrameNum.h ParameterTypes.h Parm/GB_Params.h PubFFT.h Pucker.h Pucker_PuckerMask.h Pucker_PuckerSearch.h Pucker_PuckerToken.h RPNcalc.h Random.h Range.h ReferenceAction.h ReferenceFrame.h RemdReservoirNC.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h SplineFxnTable.h Structure/LeastSquaresPlane.h Structure/RingFinder.h StructureCheck.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Unit.h Vec3.h cuda_kernels/GistCudaSetup.cuh helpme_standalone.h molsurf.h
+Command.o : Command.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h ActionTopWriter.h Action_AddAtom.h Action_Align.h Action_Angle.h Action_AreaPerMol.h Action_AtomMap.h Action_AtomicCorr.h Action_AtomicFluct.h Action_AutoImage.h Action_Average.h Action_AvgBox.h Action_Bounds.h Action_Box.h Action_Center.h Action_Channel.h Action_CheckChirality.h Action_CheckStructure.h Action_Closest.h Action_ClusterDihedral.h Action_Contacts.h Action_ConvertToFrac.h Action_CreateCrd.h Action_CreateReservoir.h Action_DNAionTracker.h Action_DSSP.h Action_Density.h Action_Diffusion.h Action_Dihedral.h Action_DihedralRMS.h Action_Dipole.h Action_DistRmsd.h Action_Distance.h Action_EneDecomp.h Action_Energy.h Action_Esander.h Action_FilterByData.h Action_FixAtomOrder.h Action_FixImagedBonds.h Action_GIST.h Action_Grid.h Action_GridFreeEnergy.h Action_HydrogenBond.h Action_Image.h Action_InfraredSpectrum.h Action_Jcoupling.h Action_Keep.h Action_LESsplit.h Action_LIE.h Action_LipidOrder.h Action_MakeStructure.h Action_Mask.h Action_Matrix.h Action_MinImage.h Action_MinMaxDist.h Action_Molsurf.h Action_MultiDihedral.h Action_MultiPucker.h Action_MultiVector.h Action_NAstruct.h Action_NMRrst.h Action_NativeContacts.h Action_OrderParameter.h Action_Outtraj.h Action_PairDist.h Action_Pairwise.h Action_Principal.h Action_Projection.h Action_Pucker.h Action_Radgyr.h Action_Radial.h Action_RandomizeIons.h Action_Remap.h Action_ReplicateCell.h Action_Rmsd.h Action_Rotate.h Action_RunningAvg.h Action_STFC_Diffusion.h Action_Scale.h Action_SetVelocity.h Action_Spam.h Action_Strip.h Action_Surf.h Action_SymmetricRmsd.h Action_Temperature.h Action_Test.h Action_Time.h Action_ToroidalDiffusion.h Action_Translate.h Action_Unstrip.h Action_Unwrap.h Action_Vector.h Action_VelocityAutoCorr.h Action_Volmap.h Action_Volume.h Action_Watershell.h Action_XtalSymm.h Analysis.h AnalysisList.h AnalysisState.h Analysis_AmdBias.h Analysis_AutoCorr.h Analysis_Average.h Analysis_CalcDiffusion.h Analysis_Clustering.h Analysis_ConstantPHStats.h Analysis_Corr.h Analysis_CrankShaft.h Analysis_CrdFluct.h Analysis_CrossCorr.h Analysis_CurveFit.h Analysis_Divergence.h Analysis_EvalPlateau.h Analysis_FFT.h Analysis_HausdorffDistance.h Analysis_Hist.h Analysis_IRED.h Analysis_Integrate.h Analysis_KDE.h Analysis_Lifetime.h Analysis_LowestCurve.h Analysis_Matrix.h Analysis_MeltCurve.h Analysis_Modes.h Analysis_MultiHist.h Analysis_Multicurve.h Analysis_Overlap.h Analysis_PhiPsi.h Analysis_Project.h Analysis_Regression.h Analysis_RemLog.h Analysis_Rms2d.h Analysis_RmsAvgCorr.h Analysis_Rotdif.h Analysis_RunningAvg.h Analysis_Slope.h Analysis_Spline.h Analysis_State.h Analysis_Statistics.h Analysis_TI.h Analysis_TICA.h Analysis_Timecorr.h Analysis_VectorMath.h Analysis_Wavelet.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AxisType.h BaseIOtype.h Box.h BoxArgs.h BufferedLine.h CharMask.h Cluster/Algorithm.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Control.h Cluster/DrawGraph.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Sieve.h Cluster/Silhouette.h ClusterMap.h Cmd.h CmdInput.h CmdList.h Command.h CompactFrameArray.h ComplexArray.h Constants.h Constraints.h ControlBlock.h ControlBlock_For.h CoordinateInfo.h Corr.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_RemLog.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h Deprecated.h DiffusionResults.h DihedralSearch.h Dimension.h DispatchObject.h Energy.h Energy/Ecalc_Nonbond.h Energy/EnergyDecomposer.h Energy/ErfcFxn.h Energy/EwaldParams.h Energy/PME_RecipParams.h Energy/VDW_LongRange_Correction.h Energy_Sander.h EnsembleIn.h EnsembleOutList.h EwaldOptions.h ExclusionArray.h Exec.h Exec_AddMissingRes.h Exec_Analyze.h Exec_Build.h Exec_Calc.h Exec_CatCrd.h Exec_Change.h Exec_ClusterMap.h Exec_CombineCoords.h Exec_Commands.h Exec_CompareClusters.h Exec_CompareEnergy.h Exec_CompareTop.h Exec_CrdAction.h Exec_CrdOut.h Exec_CrdTransform.h Exec_CreateSet.h Exec_DataFile.h Exec_DataFilter.h Exec_DataSetCmd.h Exec_Desc.h Exec_Emin.h Exec_ExtendedComparison.h Exec_Flatten.h Exec_GenerateAmberRst.h Exec_Graft.h Exec_Help.h Exec_HmassRepartition.h Exec_LoadCrd.h Exec_LoadTraj.h Exec_Mutate.h Exec_ParallelAnalysis.h Exec_ParmBox.h Exec_ParmSolvent.h Exec_ParmStrip.h Exec_ParmWrite.h Exec_ParseTiming.h Exec_PermuteDihedrals.h Exec_Precision.h Exec_PrepareForLeap.h Exec_PrintData.h Exec_Random.h Exec_ReadData.h Exec_ReadEnsembleData.h Exec_ReadInput.h Exec_RotateDihedral.h Exec_RunAnalysis.h Exec_ScaleDihedralK.h Exec_Sequence.h Exec_SequenceAlign.h Exec_Set.h Exec_Show.h Exec_SortEnsembleData.h Exec_Source.h Exec_SplitCoords.h Exec_System.h Exec_Top.h Exec_Traj.h Exec_UpdateParameters.h Exec_ViewRst.h Exec_Zmatrix.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h GIST_PME.h Grid.h GridAction.h GridBin.h GridMover.h HistBin.h Hungarian.h ImageOption.h ImageTypes.h InputTrajCommon.h InteractionData.h MapAtom.h MaskArray.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h OnlineVarT.h OutputTrajCommon.h PDBfile.h PairList.h Parallel.h ParallelSetFrameNum.h ParameterTypes.h Parm/GB_Params.h PubFFT.h Pucker.h Pucker_PuckerMask.h Pucker_PuckerSearch.h Pucker_PuckerToken.h RPNcalc.h Random.h Range.h ReferenceAction.h ReferenceFrame.h RemdReservoirNC.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h SplineFxnTable.h Structure/LeastSquaresPlane.h Structure/RingFinder.h StructureCheck.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Unit.h Vec3.h cuda_kernels/GistCudaSetup.cuh helpme_standalone.h molsurf.h
 CompactFrameArray.o : CompactFrameArray.cpp Box.h CompactFrameArray.h CoordinateInfo.h CpptrajStdio.h Matrix_3x3.h Parallel.h ReplicaDimArray.h Vec3.h
 ComplexArray.o : ComplexArray.cpp ArrayIterator.h ComplexArray.h
-Constraints.o : Constraints.cpp ArgList.h Atom.h AtomMask.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
-ControlBlock_For.o : ControlBlock_For.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h ControlBlock.h ControlBlock_For.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_dataSetBlocks.h ForLoop_inData.h ForLoop_integer.h ForLoop_list.h ForLoop_mask.h ForLoop_overSets.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Constraints.o : Constraints.cpp ArgList.h Atom.h AtomMask.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
+ControlBlock_For.o : ControlBlock_For.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h ControlBlock.h ControlBlock_For.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_dataSetBlocks.h ForLoop_inData.h ForLoop_integer.h ForLoop_list.h ForLoop_mask.h ForLoop_overSets.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 CoordCovarMatrix.o : CoordCovarMatrix.cpp ArrayIterator.h Atom.h AtomMask.h Box.h CoordCovarMatrix.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Unit.h Vec3.h
 CoordCovarMatrix_Full.o : CoordCovarMatrix_Full.cpp ArrayIterator.h Atom.h AtomMask.h CoordCovarMatrix.h CoordCovarMatrix_Full.h CpptrajStdio.h MaskToken.h Matrix.h Molecule.h NameType.h Residue.h Segment.h SymbolExporting.h Unit.h
 CoordCovarMatrix_Half.o : CoordCovarMatrix_Half.cpp ArrayIterator.h AssociatedData.h Atom.h AtomMask.h Constants.h CoordCovarMatrix.h CoordCovarMatrix_Half.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h Dimension.h FileIO.h FileName.h MaskToken.h Matrix.h MetaData.h Molecule.h NameType.h Parallel.h Range.h Residue.h Segment.h SymbolExporting.h TextFormat.h Unit.h
 CoordinateInfo.o : CoordinateInfo.cpp Box.h CoordinateInfo.h CpptrajStdio.h Matrix_3x3.h Parallel.h ReplicaDimArray.h Vec3.h
 Corr.o : Corr.cpp ArrayIterator.h ComplexArray.h Corr.h PubFFT.h
 Cph.o : Cph.cpp Cph.h NameType.h
-Cpptraj.o : Cpptraj.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cmd.h CmdInput.h CmdList.h Command.h Constants.h CoordinateInfo.h Cpptraj.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h Gpu.h HipDefinitions.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NDiff.h NameType.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReadLine.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h TopInfo.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h Version.h
+Cpptraj.o : Cpptraj.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cmd.h CmdInput.h CmdList.h Command.h Constants.h CoordinateInfo.h Cpptraj.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h Gpu.h HipDefinitions.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NDiff.h NameType.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReadLine.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h TopInfo.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h Version.h
 CpptrajFile.o : CpptrajFile.cpp CpptrajFile.h CpptrajStdio.h FileIO.h FileIO_Bzip2.h FileIO_Gzip.h FileIO_Mpi.h FileIO_MpiShared.h FileIO_Std.h FileName.h Parallel.h StringRoutines.h
-CpptrajState.o : CpptrajState.cpp Action.h ActionList.h ActionState.h Action_CreateCrd.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_Topology.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleNavigator.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+CpptrajState.o : CpptrajState.cpp Action.h ActionList.h ActionState.h Action_CreateCrd.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_Topology.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleNavigator.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 CpptrajStdio.o : CpptrajStdio.cpp Parallel.h
 CurveFit.o : CurveFit.cpp CurveFit.h
-DataFile.o : DataFile.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Cluster/Cframes.h Cluster/Cmatrix_NC.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataFile.h DataIO.h DataIO_AmberEne.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_CCP4.h DataIO_CharmmFastRep.h DataIO_CharmmOutput.h DataIO_CharmmRepLog.h DataIO_CharmmRtfPrm.h DataIO_Cmatrix_Binary.h DataIO_Cmatrix_NC.h DataIO_Coords.h DataIO_Cpout.h DataIO_Evecs.h DataIO_Gnuplot.h DataIO_Grace.h DataIO_LeapRC.h DataIO_Mdout.h DataIO_NetCDF.h DataIO_Numpy.h DataIO_OpenDx.h DataIO_Peaks.h DataIO_RemLog.h DataIO_Std.h DataIO_VecTraj.h DataIO_XVG.h DataIO_Xplor.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Unit.h Vec3.h
-DataFileList.o : DataFileList.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-DataFilter.o : DataFilter.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_integer.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-DataIO.o : DataIO.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-DataIO_AmberEne.o : DataIO_AmberEne.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberEne.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-DataIO_AmberFF.o : DataIO_AmberFF.cpp AmberParamFile.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberFF.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_AmberFrcmod.o : DataIO_AmberFrcmod.cpp AmberParamFile.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberFrcmod.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_AmberLib.o : DataIO_AmberLib.cpp ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberLib.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-DataIO_AmberPrep.o : DataIO_AmberPrep.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberPrep.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-DataIO_CCP4.o : DataIO_CCP4.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ByteRoutines.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CCP4.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-DataIO_CharmmFastRep.o : DataIO_CharmmFastRep.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmFastRep.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-DataIO_CharmmOutput.o : DataIO_CharmmOutput.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmOutput.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-DataIO_CharmmRepLog.o : DataIO_CharmmRepLog.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmRepLog.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-DataIO_CharmmRtfPrm.o : DataIO_CharmmRtfPrm.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharmmParamFile.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmRtfPrm.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h DataSet_Topology.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/GetParams.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_Cmatrix_Binary.o : DataIO_Cmatrix_Binary.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cluster/Cframes.h Cluster/Cmatrix_Binary.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Cmatrix_Binary.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-DataIO_Cmatrix_NC.o : DataIO_Cmatrix_NC.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cluster/Cframes.h Cluster/Cmatrix_NC.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Cmatrix_NC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-DataIO_Coords.o : DataIO_Coords.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Coords.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h Trajin_Single.h Unit.h Vec3.h
-DataIO_Cpout.o : DataIO_Cpout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Cpout.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h DataSet_PHREMD_Implicit.h DataSet_pH.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-DataIO_Evecs.o : DataIO_Evecs.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Evecs.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Modes.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-DataIO_Gnuplot.o : DataIO_Gnuplot.cpp ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Gnuplot.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-DataIO_Grace.o : DataIO_Grace.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Grace.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_string.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-DataIO_LeapRC.o : DataIO_LeapRC.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_Coords.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_LeapOpts.h DataSet_NameMap.h DataSet_Parameters.h DataSet_PdbResMap.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h ParmIO.h Parm_Amber.h PdbResMapType.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/Creator.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_Mdout.o : DataIO_Mdout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Mdout.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-DataIO_NetCDF.o : DataIO_NetCDF.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cluster/Cframes.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_NetCDF.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_Mesh.h DataSet_Modes.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_Vector.h DataSet_Vector_Scalar.h DataSet_string.h DataSet_unsignedInt.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h Version.h
-DataIO_Numpy.o : DataIO_Numpy.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Numpy.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h libnpy/npy.hpp
-DataIO_OpenDx.o : DataIO_OpenDx.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_OpenDx.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridDbl.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-DataIO_Peaks.o : DataIO_Peaks.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Peaks.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector_Scalar.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-DataIO_RemLog.o : DataIO_RemLog.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_RemLog.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-DataIO_Std.o : DataIO_Std.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Cluster/Cframes.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Std.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_NameMap.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_Parameters.h DataSet_StringVar.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_string.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-DataIO_VecTraj.o : DataIO_VecTraj.cpp ActionFrameCounter.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_VecTraj.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h Unit.h Vec3.h
-DataIO_XVG.o : DataIO_XVG.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_XVG.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-DataIO_Xplor.o : DataIO_Xplor.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Xplor.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+DataFile.o : DataFile.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Cluster/Cframes.h Cluster/Cmatrix_NC.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataFile.h DataIO.h DataIO_AmberEne.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_CCP4.h DataIO_CharmmFastRep.h DataIO_CharmmOutput.h DataIO_CharmmRepLog.h DataIO_CharmmRtfPrm.h DataIO_Cmatrix_Binary.h DataIO_Cmatrix_NC.h DataIO_Coords.h DataIO_Cpout.h DataIO_Evecs.h DataIO_Gnuplot.h DataIO_Grace.h DataIO_LeapRC.h DataIO_Mdout.h DataIO_NetCDF.h DataIO_Numpy.h DataIO_OpenDx.h DataIO_Peaks.h DataIO_RemLog.h DataIO_Std.h DataIO_VecTraj.h DataIO_XVG.h DataIO_Xplor.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Unit.h Vec3.h
+DataFileList.o : DataFileList.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+DataFilter.o : DataFilter.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_integer.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+DataIO.o : DataIO.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+DataIO_AmberEne.o : DataIO_AmberEne.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberEne.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+DataIO_AmberFF.o : DataIO_AmberFF.cpp AmberParamFile.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberFF.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_AmberFrcmod.o : DataIO_AmberFrcmod.cpp AmberParamFile.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberFrcmod.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_AmberLib.o : DataIO_AmberLib.cpp ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberLib.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+DataIO_AmberPrep.o : DataIO_AmberPrep.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberPrep.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+DataIO_CCP4.o : DataIO_CCP4.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ByteRoutines.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CCP4.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+DataIO_CharmmFastRep.o : DataIO_CharmmFastRep.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmFastRep.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+DataIO_CharmmOutput.o : DataIO_CharmmOutput.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmOutput.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+DataIO_CharmmRepLog.o : DataIO_CharmmRepLog.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmRepLog.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+DataIO_CharmmRtfPrm.o : DataIO_CharmmRtfPrm.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharmmParamFile.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmRtfPrm.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h DataSet_Topology.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/GetParams.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_Cmatrix_Binary.o : DataIO_Cmatrix_Binary.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cluster/Cframes.h Cluster/Cmatrix_Binary.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Cmatrix_Binary.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+DataIO_Cmatrix_NC.o : DataIO_Cmatrix_NC.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cluster/Cframes.h Cluster/Cmatrix_NC.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Cmatrix_NC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+DataIO_Coords.o : DataIO_Coords.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Coords.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h Trajin_Single.h Unit.h Vec3.h
+DataIO_Cpout.o : DataIO_Cpout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Cpout.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h DataSet_PHREMD_Implicit.h DataSet_pH.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+DataIO_Evecs.o : DataIO_Evecs.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Evecs.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Modes.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+DataIO_Gnuplot.o : DataIO_Gnuplot.cpp ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Gnuplot.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+DataIO_Grace.o : DataIO_Grace.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Grace.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_string.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+DataIO_LeapRC.o : DataIO_LeapRC.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_AmberFF.h DataIO_AmberFrcmod.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_Coords.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_LeapOpts.h DataSet_NameMap.h DataSet_Parameters.h DataSet_PdbResMap.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h ParmIO.h Parm_Amber.h PdbResMapType.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/Creator.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_Mdout.o : DataIO_Mdout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Mdout.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+DataIO_NetCDF.o : DataIO_NetCDF.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cluster/Cframes.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_NetCDF.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_Mesh.h DataSet_Modes.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_Vector.h DataSet_Vector_Scalar.h DataSet_string.h DataSet_unsignedInt.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NC_Routines.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h Version.h
+DataIO_Numpy.o : DataIO_Numpy.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Numpy.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h libnpy/npy.hpp
+DataIO_OpenDx.o : DataIO_OpenDx.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_OpenDx.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridDbl.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+DataIO_Peaks.o : DataIO_Peaks.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Peaks.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector_Scalar.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+DataIO_RemLog.o : DataIO_RemLog.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_RemLog.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+DataIO_Std.o : DataIO_Std.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Cluster/Cframes.h CmapParmHolder.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Std.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_NameMap.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_Parameters.h DataSet_StringVar.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_string.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_VecTraj.o : DataIO_VecTraj.cpp ActionFrameCounter.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_VecTraj.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h Unit.h Vec3.h
+DataIO_XVG.o : DataIO_XVG.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_XVG.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+DataIO_Xplor.o : DataIO_Xplor.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Xplor.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 DataSet.o : DataSet.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
-DataSetList.o : DataSetList.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Cluster/Cframes.h Cluster/Cmatrix_NC.h CmapParmHolder.h CompactFrameArray.h ComplexArray.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_FRM.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_GridDbl.h DataSet_GridFlt.h DataSet_LeapOpts.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_NameMap.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h DataSet_PHREMD_Implicit.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_PairwiseCache_NC.h DataSet_Parameters.h DataSet_PdbResMap.h DataSet_RemLog.h DataSet_StringVar.h DataSet_Tensor.h DataSet_Topology.h DataSet_Vector.h DataSet_Vector_Scalar.h DataSet_Zmatrix.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_disk.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h DataSet_unsignedInt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h InputTrajCommon.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h PdbResMapType.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h Structure/StructureEnum.h SymbolExporting.h SymmetricTensor.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TypeNameHolder.h Unit.h Vec3.h
+DataSetList.o : DataSetList.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Cluster/Cframes.h Cluster/Cmatrix_NC.h CmapParmHolder.h CompactFrameArray.h ComplexArray.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_FRM.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_GridDbl.h DataSet_GridFlt.h DataSet_LeapOpts.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_NameMap.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h DataSet_PHREMD_Implicit.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_PairwiseCache_NC.h DataSet_Parameters.h DataSet_PdbResMap.h DataSet_RemLog.h DataSet_StringVar.h DataSet_Tensor.h DataSet_Topology.h DataSet_Vector.h DataSet_Vector_Scalar.h DataSet_Zmatrix.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_disk.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h DataSet_unsignedInt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h InputTrajCommon.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h PdbResMapType.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h Structure/StructureEnum.h SymbolExporting.h SymmetricTensor.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TypeNameHolder.h Unit.h Vec3.h
 DataSet_1D.o : DataSet_1D.cpp ArrayIterator.h AssociatedData.h ComplexArray.h Constants.h Corr.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h PubFFT.h Range.h TextFormat.h
 DataSet_2D.o : DataSet_2D.cpp AssociatedData.h CpptrajFile.h DataSet.h DataSet_2D.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
 DataSet_3D.o : DataSet_3D.cpp AssociatedData.h Box.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_3D.h Dimension.h FileIO.h FileName.h GridBin.h Matrix_3x3.h MetaData.h Parallel.h Range.h TextFormat.h Vec3.h
-DataSet_Coords.o : DataSet_Coords.cpp AssociatedData.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h Unit.h Vec3.h
-DataSet_Coords_CRD.o : DataSet_Coords_CRD.cpp AssociatedData.h Atom.h AtomMask.h Box.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_CRD.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h Unit.h Vec3.h
-DataSet_Coords_FRM.o : DataSet_Coords_FRM.cpp AssociatedData.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_FRM.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h Unit.h Vec3.h
-DataSet_Coords_REF.o : DataSet_Coords_REF.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TrajFrameCounter.h Trajin.h Trajin_Single.h Unit.h Vec3.h
-DataSet_Coords_TRJ.o : DataSet_Coords_TRJ.cpp AssociatedData.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_TRJ.h Dimension.h FileIO.h FileName.h Frame.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h Trajin_Single.h Unit.h Vec3.h
+DataSet_Coords.o : DataSet_Coords.cpp AssociatedData.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h Unit.h Vec3.h
+DataSet_Coords_CRD.o : DataSet_Coords_CRD.cpp AssociatedData.h Atom.h AtomMask.h Box.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_CRD.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h Unit.h Vec3.h
+DataSet_Coords_FRM.o : DataSet_Coords_FRM.cpp AssociatedData.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_FRM.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h Unit.h Vec3.h
+DataSet_Coords_REF.o : DataSet_Coords_REF.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TrajFrameCounter.h Trajin.h Trajin_Single.h Unit.h Vec3.h
+DataSet_Coords_TRJ.o : DataSet_Coords_TRJ.cpp AssociatedData.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_TRJ.h Dimension.h FileIO.h FileName.h Frame.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h Trajin_Single.h Unit.h Vec3.h
 DataSet_GridDbl.o : DataSet_GridDbl.cpp ArrayIterator.h AssociatedData.h Box.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_3D.h DataSet_GridDbl.h Dimension.h FileIO.h FileName.h Grid.h GridBin.h Matrix_3x3.h MetaData.h Parallel.h Range.h StringRoutines.h TextFormat.h Vec3.h
 DataSet_GridFlt.o : DataSet_GridFlt.cpp ArrayIterator.h AssociatedData.h Box.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_3D.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Grid.h GridBin.h Matrix_3x3.h MetaData.h Parallel.h Range.h StringRoutines.h TextFormat.h Vec3.h
 DataSet_LeapOpts.o : DataSet_LeapOpts.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_LeapOpts.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Parm/GB_Params.h Range.h TextFormat.h
@@ -271,7 +271,7 @@ DataSet_PdbResMap.o : DataSet_PdbResMap.cpp AssociatedData.h CpptrajFile.h Cpptr
 DataSet_RemLog.o : DataSet_RemLog.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h ReplicaDimArray.h TextFormat.h
 DataSet_StringVar.o : DataSet_StringVar.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_StringVar.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
 DataSet_Tensor.o : DataSet_Tensor.cpp AssociatedData.h CpptrajFile.h DataSet.h DataSet_Tensor.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h SymmetricTensor.h TextFormat.h
-DataSet_Topology.o : DataSet_Topology.cpp AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Topology.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h Unit.h Vec3.h
+DataSet_Topology.o : DataSet_Topology.cpp AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Topology.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h Unit.h Vec3.h
 DataSet_Vector.o : DataSet_Vector.cpp ArrayIterator.h AssociatedData.h ComplexArray.h Constants.h Corr.h CpptrajFile.h DataSet.h DataSet_1D.h DataSet_Vector.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h PubFFT.h Range.h SymbolExporting.h TextFormat.h Vec3.h
 DataSet_Vector_Scalar.o : DataSet_Vector_Scalar.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Vector_Scalar.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h Vec3.h
 DataSet_Zmatrix.o : DataSet_Zmatrix.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Zmatrix.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h Structure/InternalCoords.h Structure/Zmatrix.h TextFormat.h Vec3.h
@@ -283,101 +283,101 @@ DataSet_pH.o : DataSet_pH.cpp AssociatedData.h Cph.h CpptrajFile.h CpptrajStdio.
 DataSet_string.o : DataSet_string.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_string.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
 DataSet_unsignedInt.o : DataSet_unsignedInt.cpp AssociatedData.h CpptrajFile.h DataSet.h DataSet_1D.h DataSet_unsignedInt.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
 Deprecated.o : Deprecated.cpp CpptrajStdio.h Deprecated.h DispatchObject.h
-DiffusionResults.o : DiffusionResults.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DiffusionResults.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-DihedralSearch.o : DihedralSearch.cpp ArgList.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DihedralSearch.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h
+DiffusionResults.o : DiffusionResults.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DiffusionResults.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+DihedralSearch.o : DihedralSearch.cpp ArgList.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DihedralSearch.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h
 DistRoutines.o : DistRoutines.cpp Box.h DistRoutines.h ImageOption.h Matrix_3x3.h Parallel.h Vec3.h
 Dist_Imaged.o : Dist_Imaged.cpp Dist_Imaged.h Matrix_3x3.h Parallel.h Vec3.h
-Energy.o : Energy.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h Energy.h Energy/Ene_Angle.h Energy/Ene_Bond.h Energy/Ene_LJ_12_6_4.h Energy/Ene_LJ_6_12.h Energy/Kernel_Harmonic.h ExclusionArray.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TorsionRoutines.h Unit.h Vec3.h
-Energy/CMAP.o : Energy/CMAP.cpp ArrayIterator.h Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy/CMAP.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TorsionRoutines.h Unit.h Vec3.h
-Energy/Ecalc_Nonbond.o : Energy/Ecalc_Nonbond.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy/Ecalc_Nonbond.h Energy/Ene_Decomp_Nonbond.h Energy/Ene_LJPME_6_12.h Energy/Ene_LJ_12_6_4.h Energy/Ene_LJ_6_12.h Energy/Ene_Nonbond.h Energy/ErfcFxn.h Energy/EwaldCalc.h Energy/EwaldCalc_Decomp.h Energy/EwaldCalc_Decomp_LJCPME.h Energy/EwaldCalc_Decomp_LJPME.h Energy/EwaldCalc_Decomp_PME.h Energy/EwaldCalc_LJCPME.h Energy/EwaldCalc_LJPME.h Energy/EwaldCalc_PME.h Energy/EwaldCalc_Regular.h Energy/EwaldParams.h Energy/EwaldParams_LJPME.h Energy/Ewald_Recip.h Energy/Kernel_EwaldAdjust.h Energy/Kernel_LJPME_Adjust.h Energy/PME_Recip.h Energy/PME_RecipParams.h Energy/VDW_LongRange_Correction.h EwaldOptions.h ExclusionArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h PairListEngine_Ewald_Decomp_LJCLR.h PairListEngine_Ewald_Decomp_LJLR.h PairListEngine_Ewald_Decomp_LJPME.h PairListEngine_Ewald_LJCLR.h PairListEngine_Ewald_LJLR.h PairListEngine_Ewald_LJPME.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h Timer.h Topology.h Unit.h Vec3.h helpme_standalone.h
-Energy/EnergyDecomposer.o : Energy/EnergyDecomposer.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DistRoutines.h Energy/Ecalc_Nonbond.h Energy/Ene_Angle.h Energy/Ene_Bond.h Energy/Ene_LJ_6_12.h Energy/EnergyDecomposer.h Energy/Kernel_Fourier.h Energy/Kernel_Harmonic.h EwaldOptions.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h PairList.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h Stats_Reduce.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h Unit.h Vec3.h
+Energy.o : Energy.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h Energy.h Energy/Ene_Angle.h Energy/Ene_Bond.h Energy/Ene_LJ_12_6_4.h Energy/Ene_LJ_6_12.h Energy/Kernel_Harmonic.h ExclusionArray.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TorsionRoutines.h Unit.h Vec3.h
+Energy/CMAP.o : Energy/CMAP.cpp ArrayIterator.h Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy/CMAP.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TorsionRoutines.h Unit.h Vec3.h
+Energy/Ecalc_Nonbond.o : Energy/Ecalc_Nonbond.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy/Ecalc_Nonbond.h Energy/Ene_Decomp_Nonbond.h Energy/Ene_LJPME_6_12.h Energy/Ene_LJ_12_6_4.h Energy/Ene_LJ_6_12.h Energy/Ene_Nonbond.h Energy/ErfcFxn.h Energy/EwaldCalc.h Energy/EwaldCalc_Decomp.h Energy/EwaldCalc_Decomp_LJCPME.h Energy/EwaldCalc_Decomp_LJPME.h Energy/EwaldCalc_Decomp_PME.h Energy/EwaldCalc_LJCPME.h Energy/EwaldCalc_LJPME.h Energy/EwaldCalc_PME.h Energy/EwaldCalc_Regular.h Energy/EwaldParams.h Energy/EwaldParams_LJPME.h Energy/Ewald_Recip.h Energy/Kernel_EwaldAdjust.h Energy/Kernel_LJPME_Adjust.h Energy/PME_Recip.h Energy/PME_RecipParams.h Energy/VDW_LongRange_Correction.h EwaldOptions.h ExclusionArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h PairList.h PairListEngine_Ewald_Decomp_LJCLR.h PairListEngine_Ewald_Decomp_LJLR.h PairListEngine_Ewald_Decomp_LJPME.h PairListEngine_Ewald_LJCLR.h PairListEngine_Ewald_LJLR.h PairListEngine_Ewald_LJPME.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h Timer.h Topology.h Unit.h Vec3.h helpme_standalone.h
+Energy/EnergyDecomposer.o : Energy/EnergyDecomposer.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DistRoutines.h Energy/Ecalc_Nonbond.h Energy/Ene_Angle.h Energy/Ene_Bond.h Energy/Ene_LJ_6_12.h Energy/EnergyDecomposer.h Energy/Kernel_Fourier.h Energy/Kernel_Harmonic.h EwaldOptions.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h OnlineVarT.h PairList.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h Stats_Reduce.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h Unit.h Vec3.h
 Energy/ErfcFxn.o : Energy/ErfcFxn.cpp CpptrajStdio.h Energy/ErfcFxn.h SplineFxnTable.h
 Energy/EwaldCalc_Decomp_LJCPME.o : Energy/EwaldCalc_Decomp_LJCPME.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy/Ene_LJ_12_6_4.h Energy/ErfcFxn.h Energy/EwaldCalc.h Energy/EwaldCalc_Decomp.h Energy/EwaldCalc_Decomp_LJCPME.h Energy/EwaldParams.h Energy/Kernel_EwaldAdjust.h Energy/PME_Recip.h Energy/PME_RecipParams.h Energy/VDW_LongRange_Correction.h EwaldOptions.h ExclusionArray.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h PairListEngine_Ewald_Decomp_LJCLR.h PairListTemplate.h Parallel.h ParameterTypes.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h Timer.h Unit.h Vec3.h helpme_standalone.h
 Energy/EwaldCalc_Decomp_LJPME.o : Energy/EwaldCalc_Decomp_LJPME.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy/Ene_LJPME_6_12.h Energy/ErfcFxn.h Energy/EwaldCalc.h Energy/EwaldCalc_Decomp.h Energy/EwaldCalc_Decomp_LJPME.h Energy/EwaldParams.h Energy/EwaldParams_LJPME.h Energy/Kernel_EwaldAdjust.h Energy/Kernel_LJPME_Adjust.h Energy/PME_Recip.h Energy/PME_RecipParams.h EwaldOptions.h ExclusionArray.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h PairListEngine_Ewald_Decomp_LJPME.h PairListTemplate.h Parallel.h ParameterTypes.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h Timer.h Unit.h Vec3.h helpme_standalone.h
 Energy/EwaldCalc_Decomp_PME.o : Energy/EwaldCalc_Decomp_PME.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy/Ene_LJ_6_12.h Energy/ErfcFxn.h Energy/EwaldCalc.h Energy/EwaldCalc_Decomp.h Energy/EwaldCalc_Decomp_PME.h Energy/EwaldParams.h Energy/Kernel_EwaldAdjust.h Energy/PME_Recip.h Energy/PME_RecipParams.h Energy/VDW_LongRange_Correction.h EwaldOptions.h ExclusionArray.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h PairListEngine_Ewald_Decomp_LJLR.h PairListTemplate.h Parallel.h ParameterTypes.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h Timer.h Unit.h Vec3.h helpme_standalone.h
-Energy/EwaldCalc_LJCPME.o : Energy/EwaldCalc_LJCPME.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy/Ene_LJ_12_6_4.h Energy/ErfcFxn.h Energy/EwaldCalc.h Energy/EwaldCalc_LJCPME.h Energy/EwaldParams.h Energy/Kernel_EwaldAdjust.h Energy/PME_Recip.h Energy/PME_RecipParams.h Energy/VDW_LongRange_Correction.h EwaldOptions.h ExclusionArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h PairListEngine_Ewald_LJCLR.h PairListTemplate.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h Timer.h Topology.h Unit.h Vec3.h helpme_standalone.h
+Energy/EwaldCalc_LJCPME.o : Energy/EwaldCalc_LJCPME.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy/Ene_LJ_12_6_4.h Energy/ErfcFxn.h Energy/EwaldCalc.h Energy/EwaldCalc_LJCPME.h Energy/EwaldParams.h Energy/Kernel_EwaldAdjust.h Energy/PME_Recip.h Energy/PME_RecipParams.h Energy/VDW_LongRange_Correction.h EwaldOptions.h ExclusionArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h PairList.h PairListEngine_Ewald_LJCLR.h PairListTemplate.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h Timer.h Topology.h Unit.h Vec3.h helpme_standalone.h
 Energy/EwaldCalc_LJPME.o : Energy/EwaldCalc_LJPME.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy/Ene_LJPME_6_12.h Energy/ErfcFxn.h Energy/EwaldCalc.h Energy/EwaldCalc_LJPME.h Energy/EwaldParams.h Energy/EwaldParams_LJPME.h Energy/Kernel_EwaldAdjust.h Energy/Kernel_LJPME_Adjust.h Energy/PME_Recip.h Energy/PME_RecipParams.h EwaldOptions.h ExclusionArray.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h PairListEngine_Ewald_LJPME.h PairListTemplate.h Parallel.h ParameterTypes.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h Timer.h Unit.h Vec3.h helpme_standalone.h
 Energy/EwaldCalc_PME.o : Energy/EwaldCalc_PME.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy/Ene_LJ_6_12.h Energy/ErfcFxn.h Energy/EwaldCalc.h Energy/EwaldCalc_PME.h Energy/EwaldParams.h Energy/Kernel_EwaldAdjust.h Energy/PME_Recip.h Energy/PME_RecipParams.h Energy/VDW_LongRange_Correction.h EwaldOptions.h ExclusionArray.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h PairListEngine_Ewald_LJLR.h PairListTemplate.h Parallel.h ParameterTypes.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h Timer.h Unit.h Vec3.h helpme_standalone.h
 Energy/EwaldCalc_Regular.o : Energy/EwaldCalc_Regular.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy/Ene_LJ_6_12.h Energy/ErfcFxn.h Energy/EwaldCalc.h Energy/EwaldCalc_Regular.h Energy/EwaldParams.h Energy/Ewald_Recip.h Energy/Kernel_EwaldAdjust.h Energy/VDW_LongRange_Correction.h EwaldOptions.h ExclusionArray.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h PairListEngine_Ewald_LJLR.h PairListTemplate.h Parallel.h ParameterTypes.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h Timer.h Unit.h Vec3.h
-Energy/EwaldParams.o : Energy/EwaldParams.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy/ErfcFxn.h Energy/EwaldParams.h EwaldOptions.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h Topology.h Unit.h Vec3.h
-Energy/EwaldParams_LJPME.o : Energy/EwaldParams_LJPME.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy/ErfcFxn.h Energy/EwaldParams.h Energy/EwaldParams_LJPME.h EwaldOptions.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h Topology.h Unit.h Vec3.h
+Energy/EwaldParams.o : Energy/EwaldParams.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy/ErfcFxn.h Energy/EwaldParams.h EwaldOptions.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h Topology.h Unit.h Vec3.h
+Energy/EwaldParams_LJPME.o : Energy/EwaldParams_LJPME.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy/ErfcFxn.h Energy/EwaldParams.h Energy/EwaldParams_LJPME.h EwaldOptions.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Energy/Ewald_Recip.o : Energy/Ewald_Recip.cpp Box.h Constants.h CpptrajStdio.h Energy/ErfcFxn.h Energy/EwaldParams.h Energy/Ewald_Recip.h EwaldOptions.h Matrix_3x3.h Parallel.h ParameterTypes.h SplineFxnTable.h StringRoutines.h Timer.h Vec3.h
 Energy/PME_Recip.o : Energy/PME_Recip.cpp Box.h CpptrajStdio.h Energy/PME_Recip.h Energy/PME_RecipParams.h Matrix_3x3.h Parallel.h Timer.h Vec3.h helpme_standalone.h
 Energy/PME_RecipParams.o : Energy/PME_RecipParams.cpp Box.h CpptrajStdio.h Energy/PME_RecipParams.h EwaldOptions.h Matrix_3x3.h Parallel.h Vec3.h
-Energy/VDW_LongRange_Correction.o : Energy/VDW_LongRange_Correction.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy/VDW_LongRange_Correction.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
+Energy/VDW_LongRange_Correction.o : Energy/VDW_LongRange_Correction.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy/VDW_LongRange_Correction.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
 EnergyArray.o : EnergyArray.cpp CpptrajFile.h CpptrajStdio.h EnergyArray.h FileIO.h FileName.h Parallel.h
-Energy_Sander.o : Energy_Sander.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy_Sander.h FileName.h FileTypes.h File_TempName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h
+Energy_Sander.o : Energy_Sander.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy_Sander.h FileName.h FileTypes.h File_TempName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h
 EnsembleIn.o : EnsembleIn.cpp Atom.h AtomMask.h Box.h CoordinateInfo.h CpptrajStdio.h EnsembleIn.h FileName.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h Timer.h TrajFrameCounter.h Unit.h Vec3.h
-EnsembleIn_Multi.o : EnsembleIn_Multi.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h EnsembleIn.h EnsembleIn_Multi.h FileIO.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryIO.h Unit.h Vec3.h
-EnsembleIn_Single.o : EnsembleIn_Single.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h EnsembleIn.h EnsembleIn_Single.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h Unit.h Vec3.h
+EnsembleIn_Multi.o : EnsembleIn_Multi.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h EnsembleIn.h EnsembleIn_Multi.h FileIO.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryIO.h Unit.h Vec3.h
+EnsembleIn_Single.o : EnsembleIn_Single.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h EnsembleIn.h EnsembleIn_Single.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h Unit.h Vec3.h
 EnsembleNavigator.o : EnsembleNavigator.cpp Atom.h AtomMask.h Box.h CoordinateInfo.h CpptrajStdio.h EnsembleIn.h EnsembleNavigator.h FileName.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h Timer.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TrajinList.h Unit.h Vec3.h
 EnsembleOut.o : EnsembleOut.cpp ActionFrameCounter.h BaseIOtype.h Box.h CoordinateInfo.h CpptrajStdio.h EnsembleOut.h FileName.h FileTypes.h FramePtrArray.h Matrix_3x3.h OutputTrajCommon.h Parallel.h Range.h ReplicaDimArray.h TrajectoryFile.h Vec3.h
-EnsembleOutList.o : EnsembleOutList.cpp ActionFrameCounter.h ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h EnsembleOut.h EnsembleOutList.h EnsembleOut_Multi.h EnsembleOut_Single.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TrajectoryFile.h Unit.h Vec3.h
-EnsembleOut_Multi.o : EnsembleOut_Multi.cpp ActionFrameCounter.h ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h EnsembleOut.h EnsembleOut_Multi.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h Unit.h Vec3.h
-EnsembleOut_Single.o : EnsembleOut_Single.cpp ActionFrameCounter.h ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h EnsembleOut.h EnsembleOut_Single.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h Unit.h Vec3.h
+EnsembleOutList.o : EnsembleOutList.cpp ActionFrameCounter.h ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h EnsembleOut.h EnsembleOutList.h EnsembleOut_Multi.h EnsembleOut_Single.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TrajectoryFile.h Unit.h Vec3.h
+EnsembleOut_Multi.o : EnsembleOut_Multi.cpp ActionFrameCounter.h ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h EnsembleOut.h EnsembleOut_Multi.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h Unit.h Vec3.h
+EnsembleOut_Single.o : EnsembleOut_Single.cpp ActionFrameCounter.h ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h EnsembleOut.h EnsembleOut_Single.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h Unit.h Vec3.h
 EwaldOptions.o : EwaldOptions.cpp ArgList.h CpptrajStdio.h EwaldOptions.h
 ExclusionArray.o : ExclusionArray.cpp Atom.h AtomMask.h CharMask.h CpptrajStdio.h ExclusionArray.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Unit.h
-Exec_AddMissingRes.o : Exec_AddMissingRes.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h CharMask.h CompactFrameArray.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_AddMissingRes.h Exec_AddMissingRes_Pres.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h ParmFile.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h Trajout_Single.h Unit.h Vec3.h
-Exec_Analyze.o : Exec_Analyze.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Analyze.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_Build.o : Exec_Build.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h ActionTopWriter.h Action_FixAtomOrder.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_Coords.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h ExclusionArray.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PairList.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/ImproperParmHolder.h Parm/LJ1264_Params.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h ParmFile.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/AddIons.h Structure/Builder.h Structure/Creator.h Structure/Disulfide.h Structure/HisProt.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/RingFinder.h Structure/Solvate.h Structure/StructureEnum.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Calc.o : Exec_Calc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Calc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_CatCrd.o : Exec_CatCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CatCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_Change.o : Exec_Change.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Change.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/GB_Params.h Parm/LJ1264_Params.h Parm/ParmEnum.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_ClusterMap.o : Exec_ClusterMap.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ClusterMap.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ClusterMap.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_CombineCoords.o : Exec_CombineCoords.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CombineCoords.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_Commands.o : Exec_Commands.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Commands.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_CompareClusters.o : Exec_CompareClusters.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CompareClusters.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_CompareEnergy.o : Exec_CompareEnergy.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h Energy/Kernel_Fourier.h Energy/Kernel_Harmonic.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CompareEnergy.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_CompareTop.o : Exec_CompareTop.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CompareTop.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_CrdAction.o : Exec_CrdAction.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CrdAction.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_CrdOut.o : Exec_CrdOut.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CrdOut.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Unit.h Vec3.h
-Exec_CrdTransform.o : Exec_CrdTransform.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CrdTransform.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_CreateSet.o : Exec_CreateSet.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CreateSet.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_DataFile.o : Exec_DataFile.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_DataFile.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_DataFilter.o : Exec_DataFilter.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_DataFilter.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_DataSetCmd.o : Exec_DataSetCmd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h ArrayIterator.h AssociatedData.h AssociatedData_Connect.h AssociatedData_NOE.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_Mesh.h DataSet_Vector.h DataSet_string.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_DataSetCmd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_Desc.o : Exec_Desc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Desc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_Emin.o : Exec_Emin.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Emin.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h Parallel.h ParameterTypes.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_ExtendedComparison.o : Exec_ExtendedComparison.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ExtendedComparison.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_Flatten.o : Exec_Flatten.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Flatten.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_GenerateAmberRst.o : Exec_GenerateAmberRst.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_GenerateAmberRst.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_Graft.o : Exec_Graft.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Graft.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_Help.o : Exec_Help.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Help.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_HmassRepartition.o : Exec_HmassRepartition.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_HmassRepartition.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_LoadCrd.o : Exec_LoadCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_LoadCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h Unit.h Vec3.h
-Exec_LoadTraj.o : Exec_LoadTraj.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_LoadTraj.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_Mutate.o : Exec_Mutate.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Mutate.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Creator.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_ParallelAnalysis.o : Exec_ParallelAnalysis.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParallelAnalysis.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_ParmBox.o : Exec_ParmBox.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BoxArgs.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmBox.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_ParmSolvent.o : Exec_ParmSolvent.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmSolvent.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_ParmStrip.o : Exec_ParmStrip.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmStrip.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_ParmWrite.o : Exec_ParmWrite.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmWrite.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_ParseTiming.o : Exec_ParseTiming.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParseTiming.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_PermuteDihedrals.o : Exec_PermuteDihedrals.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h DistRoutines.h EnsembleIn.h EnsembleOutList.h ExclusionArray.h Exec.h Exec_PermuteDihedrals.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PairList.h Parallel.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/RingFinder.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Unit.h Vec3.h
-Exec_Precision.o : Exec_Precision.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Precision.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_PrepareForLeap.o : Exec_PrepareForLeap.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMap.h AtomMask.h BaseIOtype.h Box.h CharMask.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_PrepareForLeap.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h LeapInterface.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h Remote.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/Disulfide.h Structure/HisProt.h Structure/MetalCenterFinder.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Unit.h Vec3.h
-Exec_PrintData.o : Exec_PrintData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_PrintData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_Random.o : Exec_Random.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Random.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_ReadData.o : Exec_ReadData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ReadData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_ReadEnsembleData.o : Exec_ReadEnsembleData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ReadEnsembleData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_ReadInput.o : Exec_ReadInput.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ReadInput.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_RotateDihedral.o : Exec_RotateDihedral.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_RotateDihedral.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_RunAnalysis.o : Exec_RunAnalysis.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_RunAnalysis.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_ScaleDihedralK.o : Exec_ScaleDihedralK.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ScaleDihedralK.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_Sequence.o : Exec_Sequence.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Sequence.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/Creator.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_SequenceAlign.o : Exec_SequenceAlign.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SequenceAlign.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Unit.h Vec3.h
-Exec_Set.o : Exec_Set.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_StringVar.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Set.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_Show.o : Exec_Show.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_StringVar.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Show.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_SortEnsembleData.o : Exec_SortEnsembleData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h DataSet_PHREMD_Implicit.h DataSet_pH.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SortEnsembleData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_Source.o : Exec_Source.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Source.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_SplitCoords.o : Exec_SplitCoords.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SplitCoords.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_System.o : Exec_System.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_System.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_Top.o : Exec_Top.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Top.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h TopInfo.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_Traj.o : Exec_Traj.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Traj.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_UpdateParameters.o : Exec_UpdateParameters.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h DataSet_Topology.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_UpdateParameters.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GetParams.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_ViewRst.o : Exec_ViewRst.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ViewRst.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h ViewRst.h
-Exec_Zmatrix.o : Exec_Zmatrix.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Zmatrix.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Zmatrix.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-ExtendedSimilarity.o : ExtendedSimilarity.cpp AssociatedData.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h ExtendedSimilarity.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h Unit.h Vec3.h
+Exec_AddMissingRes.o : Exec_AddMissingRes.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h CharMask.h CompactFrameArray.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_AddMissingRes.h Exec_AddMissingRes_Pres.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Minimize_SteepestDescent.h ModXNA_Info.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h ParmFile.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h Trajout_Single.h Unit.h Vec3.h
+Exec_Analyze.o : Exec_Analyze.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Analyze.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_Build.o : Exec_Build.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h ActionTopWriter.h Action_FixAtomOrder.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_Coords.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h ExclusionArray.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h OutputTrajCommon.h PairList.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/ImproperParmHolder.h Parm/LJ1264_Params.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h ParmFile.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/AddIons.h Structure/Builder.h Structure/Creator.h Structure/Disulfide.h Structure/HisProt.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/RingFinder.h Structure/Solvate.h Structure/StructureEnum.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Calc.o : Exec_Calc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Calc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_CatCrd.o : Exec_CatCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CatCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_Change.o : Exec_Change.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Change.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/GB_Params.h Parm/LJ1264_Params.h Parm/ParmEnum.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_ClusterMap.o : Exec_ClusterMap.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ClusterMap.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ClusterMap.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_CombineCoords.o : Exec_CombineCoords.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CombineCoords.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_Commands.o : Exec_Commands.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Commands.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_CompareClusters.o : Exec_CompareClusters.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CompareClusters.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_CompareEnergy.o : Exec_CompareEnergy.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h Energy/Kernel_Fourier.h Energy/Kernel_Harmonic.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CompareEnergy.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_CompareTop.o : Exec_CompareTop.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CompareTop.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_CrdAction.o : Exec_CrdAction.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CrdAction.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_CrdOut.o : Exec_CrdOut.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CrdOut.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Unit.h Vec3.h
+Exec_CrdTransform.o : Exec_CrdTransform.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CrdTransform.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_CreateSet.o : Exec_CreateSet.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CreateSet.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_DataFile.o : Exec_DataFile.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_DataFile.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_DataFilter.o : Exec_DataFilter.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_DataFilter.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_DataSetCmd.o : Exec_DataSetCmd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h ArrayIterator.h AssociatedData.h AssociatedData_Connect.h AssociatedData_NOE.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_Mesh.h DataSet_Vector.h DataSet_string.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_DataSetCmd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_Desc.o : Exec_Desc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Desc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_Emin.o : Exec_Emin.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Emin.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Minimize_SteepestDescent.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_ExtendedComparison.o : Exec_ExtendedComparison.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ExtendedComparison.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_Flatten.o : Exec_Flatten.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Flatten.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_GenerateAmberRst.o : Exec_GenerateAmberRst.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_GenerateAmberRst.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_Graft.o : Exec_Graft.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Graft.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_Help.o : Exec_Help.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Help.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_HmassRepartition.o : Exec_HmassRepartition.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_HmassRepartition.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_LoadCrd.o : Exec_LoadCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_LoadCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h Unit.h Vec3.h
+Exec_LoadTraj.o : Exec_LoadTraj.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_LoadTraj.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_Mutate.o : Exec_Mutate.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Mutate.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Creator.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_ParallelAnalysis.o : Exec_ParallelAnalysis.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParallelAnalysis.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_ParmBox.o : Exec_ParmBox.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BoxArgs.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmBox.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_ParmSolvent.o : Exec_ParmSolvent.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmSolvent.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_ParmStrip.o : Exec_ParmStrip.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmStrip.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_ParmWrite.o : Exec_ParmWrite.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmWrite.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_ParseTiming.o : Exec_ParseTiming.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParseTiming.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_PermuteDihedrals.o : Exec_PermuteDihedrals.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h DistRoutines.h EnsembleIn.h EnsembleOutList.h ExclusionArray.h Exec.h Exec_PermuteDihedrals.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h OutputTrajCommon.h PairList.h Parallel.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/RingFinder.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Unit.h Vec3.h
+Exec_Precision.o : Exec_Precision.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Precision.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_PrepareForLeap.o : Exec_PrepareForLeap.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMap.h AtomMask.h BaseIOtype.h Box.h CharMask.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_PrepareForLeap.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h LeapInterface.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h Remote.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/Disulfide.h Structure/HisProt.h Structure/MetalCenterFinder.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Unit.h Vec3.h
+Exec_PrintData.o : Exec_PrintData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_PrintData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_Random.o : Exec_Random.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Random.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_ReadData.o : Exec_ReadData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ReadData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_ReadEnsembleData.o : Exec_ReadEnsembleData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ReadEnsembleData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_ReadInput.o : Exec_ReadInput.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ReadInput.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_RotateDihedral.o : Exec_RotateDihedral.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_RotateDihedral.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_RunAnalysis.o : Exec_RunAnalysis.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_RunAnalysis.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_ScaleDihedralK.o : Exec_ScaleDihedralK.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ScaleDihedralK.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_Sequence.o : Exec_Sequence.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Sequence.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/Creator.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_SequenceAlign.o : Exec_SequenceAlign.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SequenceAlign.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Unit.h Vec3.h
+Exec_Set.o : Exec_Set.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_StringVar.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Set.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_Show.o : Exec_Show.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_StringVar.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Show.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_SortEnsembleData.o : Exec_SortEnsembleData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h DataSet_PHREMD_Implicit.h DataSet_pH.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SortEnsembleData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_Source.o : Exec_Source.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Source.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_SplitCoords.o : Exec_SplitCoords.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SplitCoords.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_System.o : Exec_System.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_System.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_Top.o : Exec_Top.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Top.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h TopInfo.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_Traj.o : Exec_Traj.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Traj.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_UpdateParameters.o : Exec_UpdateParameters.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h DataSet_Topology.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_UpdateParameters.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GetParams.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_ViewRst.o : Exec_ViewRst.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ViewRst.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h ViewRst.h
+Exec_Zmatrix.o : Exec_Zmatrix.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Zmatrix.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Zmatrix.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+ExtendedSimilarity.o : ExtendedSimilarity.cpp AssociatedData.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h ExtendedSimilarity.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h Unit.h Vec3.h
 ExternalFxn.o : ExternalFxn.cpp Random.h
 FileIO_Bzip2.o : FileIO_Bzip2.cpp CpptrajStdio.h FileIO.h FileIO_Bzip2.h
 FileIO_Gzip.o : FileIO_Gzip.cpp CpptrajStdio.h FileIO.h FileIO_Gzip.h
@@ -388,82 +388,83 @@ FileName.o : FileName.cpp CpptrajStdio.h FileName.h StringRoutines.h
 FileType.o : FileType.cpp FileType.h
 FileTypes.o : FileTypes.cpp ArgList.h BaseIOtype.h CpptrajStdio.h FileTypes.h
 File_TempName.o : File_TempName.cpp CpptrajStdio.h FileName.h File_TempName.h StringRoutines.h
-ForLoop.o : ForLoop.cpp AssociatedData.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h ForLoop.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-ForLoop_dataSetBlocks.o : ForLoop_dataSetBlocks.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_dataSetBlocks.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-ForLoop_inData.o : ForLoop_inData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_integer.h DataSet_string.h DataSet_unsignedInt.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_inData.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-ForLoop_integer.o : ForLoop_integer.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_integer.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-ForLoop_list.o : ForLoop_list.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_list.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-ForLoop_mask.o : ForLoop_mask.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_mask.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-ForLoop_overSets.o : ForLoop_overSets.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_overSets.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+ForLoop.o : ForLoop.cpp AssociatedData.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h ForLoop.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+ForLoop_dataSetBlocks.o : ForLoop_dataSetBlocks.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_dataSetBlocks.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+ForLoop_inData.o : ForLoop_inData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_integer.h DataSet_string.h DataSet_unsignedInt.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_inData.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+ForLoop_integer.o : ForLoop_integer.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_integer.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+ForLoop_list.o : ForLoop_list.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_list.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+ForLoop_mask.o : ForLoop_mask.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_mask.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+ForLoop_overSets.o : ForLoop_overSets.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_overSets.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Frame.o : Frame.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Unit.h Vec3.h
-GIST_PME.o : GIST_PME.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy/ErfcFxn.h Energy/EwaldParams.h Energy/Kernel_EwaldAdjust.h Energy/PME_RecipParams.h Energy/VDW_LongRange_Correction.h EwaldOptions.h ExclusionArray.h FileName.h Frame.h GIST_PME.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h Timer.h Topology.h Unit.h Vec3.h helpme_standalone.h
+GIST_PME.o : GIST_PME.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy/ErfcFxn.h Energy/EwaldParams.h Energy/Kernel_EwaldAdjust.h Energy/PME_RecipParams.h Energy/VDW_LongRange_Correction.h EwaldOptions.h ExclusionArray.h FileName.h Frame.h GIST_PME.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h PairList.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h Timer.h Topology.h Unit.h Vec3.h helpme_standalone.h
 GistEntropyUtils.o : GistEntropyUtils.cpp CpptrajFile.h FileIO.h FileName.h GistEntropyUtils.h Parallel.h Vec3.h
 Gpu.o : Gpu.cpp Gpu.h
-GridAction.o : GridAction.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridAction.h GridBin.h GridMover.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+GridAction.o : GridAction.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridAction.h GridBin.h GridMover.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 GridBin.o : GridBin.cpp Box.h CpptrajStdio.h GridBin.h Matrix_3x3.h Parallel.h Vec3.h
-GridMover.o : GridMover.cpp AssociatedData.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_3D.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h GridMover.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h Unit.h Vec3.h
+GridMover.o : GridMover.cpp AssociatedData.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_3D.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h GridMover.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h Unit.h Vec3.h
 GuessAtomHybridization.o : GuessAtomHybridization.cpp Atom.h AtomType.h Constants.h GuessAtomHybridization.h NameType.h ParameterTypes.h SymbolExporting.h
 HistBin.o : HistBin.cpp Constants.h CpptrajStdio.h Dimension.h HistBin.h
 Hungarian.o : Hungarian.cpp ArrayIterator.h Constants.h CpptrajStdio.h Hungarian.h Matrix.h
 ImageRoutines.o : ImageRoutines.cpp Atom.h AtomMask.h Box.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h Frame.h ImageOption.h ImageRoutines.h ImageTypes.h Image_List.h Image_List_Mask.h Image_List_Pair.h Image_List_Pair_CoM.h Image_List_Pair_First.h Image_List_Pair_Geom.h Image_List_Unit.h Image_List_Unit_CoM.h Image_List_Unit_First.h Image_List_Unit_Geom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Unit.h Vec3.h
-Image_List_Mask.o : Image_List_Mask.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h Image_List.h Image_List_Mask.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h
-Image_List_Pair.o : Image_List_Pair.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h Image_List.h Image_List_Pair.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
-Image_List_Unit.o : Image_List_Unit.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h Image_List.h Image_List_Unit.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
+Image_List_Mask.o : Image_List_Mask.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h Image_List.h Image_List_Mask.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h
+Image_List_Pair.o : Image_List_Pair.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h Image_List.h Image_List_Pair.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
+Image_List_Unit.o : Image_List_Unit.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h Image_List.h Image_List_Unit.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
 InputTrajCommon.o : InputTrajCommon.cpp CpptrajStdio.h FileName.h InputTrajCommon.h TrajFrameCounter.h
-InteractionData.o : InteractionData.cpp AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h InteractionData.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+InteractionData.o : InteractionData.cpp AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h InteractionData.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 KDE.o : KDE.cpp AssociatedData.h Constants.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_double.h Dimension.h FileIO.h FileName.h HistBin.h KDE.h MetaData.h Parallel.h Range.h TextFormat.h
-LeapInterface.o : LeapInterface.cpp ArgList.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h File_TempName.h Frame.h LeapInterface.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h
+LeapInterface.o : LeapInterface.cpp ArgList.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h File_TempName.h Frame.h LeapInterface.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h
 MapAtom.o : MapAtom.cpp Atom.h MapAtom.h NameType.h SymbolExporting.h
-MaskArray.o : MaskArray.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
+MaskArray.o : MaskArray.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskArray.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
 MaskToken.o : MaskToken.cpp ArgList.h Atom.h CpptrajStdio.h DistRoutines.h ImageOption.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Unit.h
 Matrix_3x3.o : Matrix_3x3.cpp Constants.h CpptrajStdio.h Matrix_3x3.h Parallel.h Vec3.h
 MdOpts.o : MdOpts.cpp ArgList.h Constants.h Constraints.h CpptrajStdio.h MdOpts.h ParameterTypes.h
 MetaData.o : MetaData.cpp CpptrajStdio.h FileName.h MetaData.h Range.h StringRoutines.h
-Minimize_SteepestDescent.o : Minimize_SteepestDescent.cpp ActionFrameCounter.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h EnergyArray.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h Unit.h Vec3.h
-Mol.o : Mol.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Mol.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
-Mol2File.o : Mol2File.cpp Atom.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Mol2File.h NameType.h Parallel.h Residue.h StringRoutines.h SymbolExporting.h
+Minimize_SteepestDescent.o : Minimize_SteepestDescent.cpp ActionFrameCounter.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h EnergyArray.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Minimize_SteepestDescent.h ModXNA_Info.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h Unit.h Vec3.h
+ModXNA_Info.o : ModXNA_Info.cpp ArgList.h CpptrajStdio.h ModXNA_Info.h
+Mol.o : Mol.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Mol.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
+Mol2File.o : Mol2File.cpp Atom.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h ModXNA_Info.h Mol2File.h NameType.h Parallel.h Residue.h StringRoutines.h SymbolExporting.h
 NC_Routines.o : NC_Routines.cpp CpptrajStdio.h NC_Routines.h
 NDiff.o : NDiff.cpp ArgList.h BufferedLine.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NDiff.h Parallel.h StringRoutines.h
 NameType.o : NameType.cpp CpptrajStdio.h NameType.h
 NetcdfFile.o : NetcdfFile.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h ParallelNetcdf.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Unit.h Vec3.h Version.h
 OMM_helpers.o : OMM_helpers.cpp Constants.h OMM_helpers.h ParameterTypes.h
-OutputTrajCommon.o : OutputTrajCommon.cpp ActionFrameCounter.h ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h Unit.h Vec3.h
+OutputTrajCommon.o : OutputTrajCommon.cpp ActionFrameCounter.h ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h Unit.h Vec3.h
 PDBfile.o : PDBfile.cpp Atom.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h PDBfile.h Parallel.h Residue.h StringRoutines.h SymbolExporting.h
 PairList.o : PairList.cpp Atom.h AtomMask.h Box.h CoordinateInfo.h CpptrajStdio.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Timer.h Unit.h Vec3.h
 Parallel.o : Parallel.cpp Parallel.h
 ParallelNetcdf.o : ParallelNetcdf.cpp CpptrajStdio.h Parallel.h ParallelNetcdf.h
 ParallelSetFrameNum.o : ParallelSetFrameNum.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h ParallelSetFrameNum.h Range.h TextFormat.h
-Parm/AssignParams.o : Parm/AssignParams.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h GuessAtomHybridization.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/../Structure/GenerateConnectivityArrays.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GetParams.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmArray.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Parm/Bond_Params.o : Parm/Bond_Params.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/Bond_Params.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
+Parm/AssignParams.o : Parm/AssignParams.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h GuessAtomHybridization.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/../Structure/GenerateConnectivityArrays.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GetParams.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmArray.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Parm/Bond_Params.o : Parm/Bond_Params.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/Bond_Params.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Parm/DihedralParmSet.o : Parm/DihedralParmSet.cpp AtomType.h CmapParmHolder.h Constants.h CpptrajStdio.h FileName.h NameType.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/DihedralParmSet.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h TypeNameHolder.h
-Parm/GB_Params.o : Parm/GB_Params.cpp ArgList.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/GB_Params.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
-Parm/GetParams.o : Parm/GetParams.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/DihedralParmSet.h Parm/GetParams.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Parm/LJ1264_Params.o : Parm/LJ1264_Params.cpp ArgList.h Atom.h AtomMask.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/LJ1264_Params.h Parm/ParmEnum.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h
+Parm/GB_Params.o : Parm/GB_Params.cpp ArgList.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/GB_Params.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
+Parm/GetParams.o : Parm/GetParams.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/DihedralParmSet.h Parm/GetParams.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Parm/LJ1264_Params.o : Parm/LJ1264_Params.cpp ArgList.h Atom.h AtomMask.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/LJ1264_Params.h Parm/ParmEnum.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Parm/Merge.o : Parm/Merge.cpp Atom.h Constants.h CpptrajStdio.h NameType.h ParameterTypes.h Parm/Merge.h Parm/ParmEnum.h Parm/ParmHolder.h Residue.h StringRoutines.h SymbolExporting.h TypeNameHolder.h
 Parm/ParameterSet.o : Parm/ParameterSet.cpp AtomType.h CmapParmHolder.h Constants.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h TypeNameHolder.h UpdateParameters.h
 Parm/ParmEnum.o : Parm/ParmEnum.cpp Parm/ParmEnum.h
-ParmFile.o : ParmFile.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h ParmFile.h ParmIO.h Parm_Amber.h Parm_CIF.h Parm_CharmmPsf.h Parm_Gromacs.h Parm_Mol2.h Parm_PDB.h Parm_SDF.h Parm_Tinker.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Parm_Amber.o : Parm_Amber.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h ExclusionArray.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/GetParams.h ParmIO.h Parm_Amber.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h Unit.h Vec3.h
-Parm_CIF.o : Parm_CIF.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h CIFfile.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmIO.h Parm_CIF.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h
-Parm_CharmmPsf.o : Parm_CharmmPsf.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h CharmmParamFile.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Mol.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h ParmIO.h Parm_CharmmPsf.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Parm_Gromacs.o : Parm_Gromacs.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmIO.h Parm_Gromacs.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h
-Parm_Mol2.o : Parm_Mol2.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Mol2File.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmIO.h Parm_Mol2.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
-Parm_PDB.o : Parm_PDB.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterTypes.h ParmIO.h Parm_PDB.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Timer.h Topology.h Unit.h Vec3.h
-Parm_SDF.o : Parm_SDF.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmIO.h Parm_SDF.h Range.h ReplicaDimArray.h Residue.h SDFfile.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
-Parm_Tinker.o : Parm_Tinker.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmIO.h Parm_Tinker.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TinkerFile.h Topology.h Unit.h Vec3.h
-PotentialFunction.o : PotentialFunction.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajStdio.h EnergyArray.h ExclusionArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MdOpts.h Molecule.h NameType.h Parallel.h ParameterTypes.h PotentialFunction.h PotentialTerm.h PotentialTerm_Angle.h PotentialTerm_Bond.h PotentialTerm_Dihedral.h PotentialTerm_LJ_Coulomb.h PotentialTerm_OpenMM.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
+ParmFile.o : ParmFile.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h ParmFile.h ParmIO.h Parm_Amber.h Parm_CIF.h Parm_CharmmPsf.h Parm_Gromacs.h Parm_Mol2.h Parm_PDB.h Parm_SDF.h Parm_Tinker.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Parm_Amber.o : Parm_Amber.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h ExclusionArray.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/GetParams.h ParmIO.h Parm_Amber.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h Unit.h Vec3.h
+Parm_CIF.o : Parm_CIF.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h CIFfile.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmIO.h Parm_CIF.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h
+Parm_CharmmPsf.o : Parm_CharmmPsf.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h CharmmParamFile.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Mol.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h ParmIO.h Parm_CharmmPsf.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Parm_Gromacs.o : Parm_Gromacs.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmIO.h Parm_Gromacs.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h
+Parm_Mol2.o : Parm_Mol2.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Mol2File.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmIO.h Parm_Mol2.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
+Parm_PDB.o : Parm_PDB.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterTypes.h ParmIO.h Parm_PDB.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Timer.h Topology.h Unit.h Vec3.h
+Parm_SDF.o : Parm_SDF.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmIO.h Parm_SDF.h Range.h ReplicaDimArray.h Residue.h SDFfile.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
+Parm_Tinker.o : Parm_Tinker.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmIO.h Parm_Tinker.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TinkerFile.h Topology.h Unit.h Vec3.h
+PotentialFunction.o : PotentialFunction.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajStdio.h EnergyArray.h ExclusionArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MdOpts.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h PotentialFunction.h PotentialTerm.h PotentialTerm_Angle.h PotentialTerm_Bond.h PotentialTerm_Dihedral.h PotentialTerm_LJ_Coulomb.h PotentialTerm_OpenMM.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
 PotentialTerm.o : PotentialTerm.cpp PotentialTerm.h
-PotentialTerm_Angle.o : PotentialTerm_Angle.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h EnergyArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h PotentialTerm.h PotentialTerm_Angle.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
-PotentialTerm_Bond.o : PotentialTerm_Bond.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h EnergyArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h PotentialTerm.h PotentialTerm_Bond.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
-PotentialTerm_Dihedral.o : PotentialTerm_Dihedral.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h EnergyArray.h EnergyKernel_NonBond_Simple.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h PotentialTerm.h PotentialTerm_Dihedral.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
-PotentialTerm_LJ_Coulomb.o : PotentialTerm_LJ_Coulomb.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajStdio.h EnergyArray.h EnergyKernel_NonBond_Simple.h ExclusionArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MdOpts.h Molecule.h NameType.h Parallel.h ParameterTypes.h PotentialTerm.h PotentialTerm_LJ_Coulomb.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
-PotentialTerm_OpenMM.o : PotentialTerm_OpenMM.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajStdio.h EnergyArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MdOpts.h Molecule.h NameType.h OMM_helpers.h Parallel.h ParameterTypes.h PotentialTerm.h PotentialTerm_OpenMM.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
+PotentialTerm_Angle.o : PotentialTerm_Angle.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h EnergyArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h PotentialTerm.h PotentialTerm_Angle.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
+PotentialTerm_Bond.o : PotentialTerm_Bond.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h EnergyArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h PotentialTerm.h PotentialTerm_Bond.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
+PotentialTerm_Dihedral.o : PotentialTerm_Dihedral.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h EnergyArray.h EnergyKernel_NonBond_Simple.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h PotentialTerm.h PotentialTerm_Dihedral.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
+PotentialTerm_LJ_Coulomb.o : PotentialTerm_LJ_Coulomb.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajStdio.h EnergyArray.h EnergyKernel_NonBond_Simple.h ExclusionArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MdOpts.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h PotentialTerm.h PotentialTerm_LJ_Coulomb.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
+PotentialTerm_OpenMM.o : PotentialTerm_OpenMM.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajStdio.h EnergyArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MdOpts.h ModXNA_Info.h Molecule.h NameType.h OMM_helpers.h Parallel.h ParameterTypes.h PotentialTerm.h PotentialTerm_OpenMM.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
 ProgressBar.o : ProgressBar.cpp CpptrajStdio.h ProgressBar.h
 ProgressTimer.o : ProgressTimer.cpp CpptrajStdio.h ProgressTimer.h Timer.h
 PubFFT.o : PubFFT.cpp ArrayIterator.h ComplexArray.h CpptrajStdio.h PubFFT.h
-Pucker_PuckerMask.o : Pucker_PuckerMask.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Pucker_PuckerMask.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
-Pucker_PuckerSearch.o : Pucker_PuckerSearch.cpp ArgList.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Pucker.h Pucker_PuckerMask.h Pucker_PuckerSearch.h Pucker_PuckerToken.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
-Pucker_PuckerToken.o : Pucker_PuckerToken.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Pucker_PuckerMask.h Pucker_PuckerToken.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
+Pucker_PuckerMask.o : Pucker_PuckerMask.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Pucker_PuckerMask.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
+Pucker_PuckerSearch.o : Pucker_PuckerSearch.cpp ArgList.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Pucker.h Pucker_PuckerMask.h Pucker_PuckerSearch.h Pucker_PuckerToken.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
+Pucker_PuckerToken.o : Pucker_PuckerToken.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Pucker_PuckerMask.h Pucker_PuckerToken.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
 QuaternionRMSD.o : QuaternionRMSD.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h QuaternionRMSD.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Unit.h Vec3.h qcprot.h
 RNG.o : RNG.cpp CpptrajStdio.h RNG.h
 RNG_Marsaglia.o : RNG_Marsaglia.cpp CpptrajStdio.h RNG.h RNG_Marsaglia.h
@@ -471,11 +472,11 @@ RNG_MersenneTwister.o : RNG_MersenneTwister.cpp CpptrajStdio.h RNG.h RNG_Mersenn
 RNG_PCG32.o : RNG_PCG32.cpp CpptrajStdio.h RNG.h RNG_PCG32.h pcg_random.hpp
 RNG_Stdlib.o : RNG_Stdlib.cpp RNG.h RNG_Stdlib.h
 RNG_Xoshiro128pp.o : RNG_Xoshiro128pp.cpp RNG.h RNG_Xoshiro128pp.h xoshiro128plusplus.h
-RPNcalc.o : RPNcalc.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_Mesh.h DataSet_Vector.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+RPNcalc.o : RPNcalc.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_Mesh.h DataSet_Vector.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 Random.o : Random.cpp CpptrajStdio.h RNG.h RNG_Marsaglia.h RNG_MersenneTwister.h RNG_PCG32.h RNG_Stdlib.h RNG_Xoshiro128pp.h Random.h pcg_random.hpp
 Range.o : Range.cpp ArgList.h CpptrajStdio.h Range.h StringRoutines.h
-ReadLine.o : ReadLine.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cmd.h CmdInput.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReadLine.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-ReferenceAction.o : ReferenceAction.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h Dimension.h FileIO.h FileName.h Frame.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h Unit.h Vec3.h
+ReadLine.o : ReadLine.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cmd.h CmdInput.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReadLine.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+ReferenceAction.o : ReferenceAction.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h Dimension.h FileIO.h FileName.h Frame.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h Unit.h Vec3.h
 RemdReservoirNC.o : RemdReservoirNC.cpp Atom.h AtomMask.h Box.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h RemdReservoirNC.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Unit.h Vec3.h
 Remote.o : Remote.cpp CpptrajStdio.h FileName.h Remote.h
 Residue.o : Residue.cpp CpptrajStdio.h NameType.h Residue.h
@@ -486,76 +487,76 @@ Spline.o : Spline.cpp CpptrajStdio.h Spline.h
 SplineFxnTable.o : SplineFxnTable.cpp Constants.h CpptrajStdio.h Spline.h SplineFxnTable.h StringRoutines.h
 Stats_Reduce.o : Stats_Reduce.cpp OnlineVarT.h Parallel.h Stats_Reduce.h
 StringRoutines.o : StringRoutines.cpp CpptrajStdio.h StringRoutines.h
-Structure/AddIons.o : Structure/AddIons.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DistRoutines.h FileIO.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/../Parm/../AtomType.h Structure/../Parm/../CmapParmHolder.h Structure/../Parm/../Constants.h Structure/../Parm/../FileName.h Structure/../Parm/../NameType.h Structure/../Parm/../ParameterTypes.h Structure/../Parm/../Parm/ParmEnum.h Structure/../Parm/../TypeNameHolder.h Structure/../Parm/DihedralParmHolder.h Structure/../Parm/ImproperParmHolder.h Structure/../Parm/ParameterSet.h Structure/../Parm/ParmEnum.h Structure/../Parm/ParmHolder.h Structure/AddIons.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Structure/Builder.o : Structure/Builder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h GuessAtomHybridization.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/../Parm/../AtomType.h Structure/../Parm/../CmapParmHolder.h Structure/../Parm/../Constants.h Structure/../Parm/../FileName.h Structure/../Parm/../NameType.h Structure/../Parm/../ParameterTypes.h Structure/../Parm/../Parm/ParmEnum.h Structure/../Parm/../TypeNameHolder.h Structure/../Parm/DihedralParmHolder.h Structure/../Parm/ImproperParmHolder.h Structure/../Parm/ParameterSet.h Structure/../Parm/ParmEnum.h Structure/../Parm/ParmHolder.h Structure/Builder.h Structure/Chirality.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
-Structure/Chirality.o : Structure/Chirality.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Chirality.h Structure/StructureEnum.h SymbolExporting.h Topology.h TorsionRoutines.h Unit.h Vec3.h
-Structure/Creator.o : Structure/Creator.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h DataSet_Parameters.h DataSet_PdbResMap.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h PdbResMapType.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/Creator.h Structure/GenerateConnectivityArrays.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Structure/Disulfide.o : Structure/Disulfide.cpp ArgList.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Disulfide.h Structure/ResStatArray.h Structure/StructureRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h
-Structure/FunctionalGroup.o : Structure/FunctionalGroup.cpp Atom.h AtomMap.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h SymbolExporting.h Topology.h Unit.h Vec3.h
-Structure/FxnGroupBuilder.o : Structure/FxnGroupBuilder.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h Structure/FxnGroupBuilder.h Structure/StructureRoutines.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h Unit.h Vec3.h
+Structure/AddIons.o : Structure/AddIons.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DistRoutines.h FileIO.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/../Parm/../AtomType.h Structure/../Parm/../CmapParmHolder.h Structure/../Parm/../Constants.h Structure/../Parm/../FileName.h Structure/../Parm/../NameType.h Structure/../Parm/../ParameterTypes.h Structure/../Parm/../Parm/ParmEnum.h Structure/../Parm/../TypeNameHolder.h Structure/../Parm/DihedralParmHolder.h Structure/../Parm/ImproperParmHolder.h Structure/../Parm/ParameterSet.h Structure/../Parm/ParmEnum.h Structure/../Parm/ParmHolder.h Structure/AddIons.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Structure/Builder.o : Structure/Builder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h GuessAtomHybridization.h ImageOption.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/../Parm/../AtomType.h Structure/../Parm/../CmapParmHolder.h Structure/../Parm/../Constants.h Structure/../Parm/../FileName.h Structure/../Parm/../NameType.h Structure/../Parm/../ParameterTypes.h Structure/../Parm/../Parm/ParmEnum.h Structure/../Parm/../TypeNameHolder.h Structure/../Parm/DihedralParmHolder.h Structure/../Parm/ImproperParmHolder.h Structure/../Parm/ParameterSet.h Structure/../Parm/ParmEnum.h Structure/../Parm/ParmHolder.h Structure/Builder.h Structure/Chirality.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Structure/Chirality.o : Structure/Chirality.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Chirality.h Structure/StructureEnum.h SymbolExporting.h Topology.h TorsionRoutines.h Unit.h Vec3.h
+Structure/Creator.o : Structure/Creator.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h DataSet_Parameters.h DataSet_PdbResMap.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h PdbResMapType.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/Creator.h Structure/GenerateConnectivityArrays.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Structure/Disulfide.o : Structure/Disulfide.cpp ArgList.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Disulfide.h Structure/ResStatArray.h Structure/StructureRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h
+Structure/FunctionalGroup.o : Structure/FunctionalGroup.cpp Atom.h AtomMap.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h SymbolExporting.h Topology.h Unit.h Vec3.h
+Structure/FxnGroupBuilder.o : Structure/FxnGroupBuilder.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h Structure/FxnGroupBuilder.h Structure/StructureRoutines.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Structure/GenerateConnectivityArrays.o : Structure/GenerateConnectivityArrays.cpp Atom.h Constants.h CpptrajStdio.h NameType.h ParameterTypes.h Residue.h Structure/GenerateConnectivityArrays.h SymbolExporting.h
-Structure/HisProt.o : Structure/HisProt.cpp ArgList.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/HisProt.h Structure/StructureRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h
-Structure/InternalCoords.o : Structure/InternalCoords.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/InternalCoords.h SymbolExporting.h Topology.h Unit.h Vec3.h
+Structure/HisProt.o : Structure/HisProt.cpp ArgList.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/HisProt.h Structure/StructureRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h
+Structure/InternalCoords.o : Structure/InternalCoords.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/InternalCoords.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Structure/LeastSquaresPlane.o : Structure/LeastSquaresPlane.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h Residue.h Segment.h Structure/LeastSquaresPlane.h SymbolExporting.h Unit.h Vec3.h
-Structure/MetalCenterFinder.o : Structure/MetalCenterFinder.cpp ArgList.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/MetalCenterFinder.h SymbolExporting.h Topology.h Unit.h Vec3.h
-Structure/PdbCleaner.o : Structure/PdbCleaner.cpp ArgList.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/PdbCleaner.h SymbolExporting.h Topology.h Unit.h Vec3.h
-Structure/RingFinder.o : Structure/RingFinder.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/RingFinder.h SymbolExporting.h Topology.h Unit.h Vec3.h
-Structure/Solvate.o : Structure/Solvate.cpp Action.h ActionState.h Action_AutoImage.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/../Parm/../AtomType.h Structure/../Parm/../CmapParmHolder.h Structure/../Parm/../Constants.h Structure/../Parm/../FileName.h Structure/../Parm/../NameType.h Structure/../Parm/../ParameterTypes.h Structure/../Parm/../Parm/ParmEnum.h Structure/../Parm/../TypeNameHolder.h Structure/../Parm/DihedralParmHolder.h Structure/../Parm/ImproperParmHolder.h Structure/../Parm/ParameterSet.h Structure/../Parm/ParmEnum.h Structure/../Parm/ParmHolder.h Structure/Solvate.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
+Structure/MetalCenterFinder.o : Structure/MetalCenterFinder.cpp ArgList.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/MetalCenterFinder.h SymbolExporting.h Topology.h Unit.h Vec3.h
+Structure/PdbCleaner.o : Structure/PdbCleaner.cpp ArgList.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/PdbCleaner.h SymbolExporting.h Topology.h Unit.h Vec3.h
+Structure/RingFinder.o : Structure/RingFinder.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/RingFinder.h SymbolExporting.h Topology.h Unit.h Vec3.h
+Structure/Solvate.o : Structure/Solvate.cpp Action.h ActionState.h Action_AutoImage.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Structure/../Parm/../AtomType.h Structure/../Parm/../CmapParmHolder.h Structure/../Parm/../Constants.h Structure/../Parm/../FileName.h Structure/../Parm/../NameType.h Structure/../Parm/../ParameterTypes.h Structure/../Parm/../Parm/ParmEnum.h Structure/../Parm/../TypeNameHolder.h Structure/../Parm/DihedralParmHolder.h Structure/../Parm/ImproperParmHolder.h Structure/../Parm/ParameterSet.h Structure/../Parm/ParmEnum.h Structure/../Parm/ParmHolder.h Structure/Solvate.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 Structure/StructureEnum.o : Structure/StructureEnum.cpp Structure/StructureEnum.h
 Structure/StructureRoutines.o : Structure/StructureRoutines.cpp Atom.h CpptrajStdio.h NameType.h Residue.h Structure/StructureRoutines.h SymbolExporting.h
-Structure/Sugar.o : Structure/Sugar.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h Unit.h Vec3.h
-Structure/SugarBuilder.o : Structure/SugarBuilder.cpp ArgList.h Atom.h AtomMap.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DistRoutines.h FileIO.h FileName.h Frame.h ImageOption.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Chirality.h Structure/FunctionalGroup.h Structure/FxnGroupBuilder.h Structure/LinkAtom.h Structure/ResStatArray.h Structure/StructureEnum.h Structure/StructureRoutines.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarLinkAtoms.h Structure/SugarToken.h SymbolExporting.h Topology.h TorsionRoutines.h Unit.h Vec3.h
-Structure/SugarLinkAtoms.o : Structure/SugarLinkAtoms.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/LinkAtom.h Structure/SugarLinkAtoms.h SymbolExporting.h Topology.h Unit.h Vec3.h
+Structure/Sugar.o : Structure/Sugar.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h Unit.h Vec3.h
+Structure/SugarBuilder.o : Structure/SugarBuilder.cpp ArgList.h Atom.h AtomMap.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DistRoutines.h FileIO.h FileName.h Frame.h ImageOption.h MapAtom.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Chirality.h Structure/FunctionalGroup.h Structure/FxnGroupBuilder.h Structure/LinkAtom.h Structure/ResStatArray.h Structure/StructureEnum.h Structure/StructureRoutines.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarLinkAtoms.h Structure/SugarToken.h SymbolExporting.h Topology.h TorsionRoutines.h Unit.h Vec3.h
+Structure/SugarLinkAtoms.o : Structure/SugarLinkAtoms.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/LinkAtom.h Structure/SugarLinkAtoms.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Structure/SugarToken.o : Structure/SugarToken.cpp ArgList.h CpptrajStdio.h Structure/SugarToken.h
-Structure/Zmatrix.o : Structure/Zmatrix.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h Unit.h Vec3.h
-StructureCheck.o : StructureCheck.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DistRoutines.h ExclusionArray.h FileIO.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/LeastSquaresPlane.h Structure/RingFinder.h StructureCheck.h SymbolExporting.h Timer.h Topology.h Unit.h Vec3.h
-StructureMapper.o : StructureMapper.cpp AssociatedData.h Atom.h AtomMap.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Chirality.h Structure/StructureEnum.h StructureMapper.h SymbolExporting.h TextFormat.h Topology.h TorsionRoutines.h Unit.h Vec3.h
-SymmetricRmsdCalc.o : SymmetricRmsdCalc.cpp ArrayIterator.h Atom.h AtomMap.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h Hungarian.h ImageOption.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h Topology.h Unit.h Vec3.h
+Structure/Zmatrix.o : Structure/Zmatrix.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/GenerateConnectivityArrays.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h Unit.h Vec3.h
+StructureCheck.o : StructureCheck.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DistRoutines.h ExclusionArray.h FileIO.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h PairList.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/LeastSquaresPlane.h Structure/RingFinder.h StructureCheck.h SymbolExporting.h Timer.h Topology.h Unit.h Vec3.h
+StructureMapper.o : StructureMapper.cpp AssociatedData.h Atom.h AtomMap.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Chirality.h Structure/StructureEnum.h StructureMapper.h SymbolExporting.h TextFormat.h Topology.h TorsionRoutines.h Unit.h Vec3.h
+SymmetricRmsdCalc.o : SymmetricRmsdCalc.cpp ArrayIterator.h Atom.h AtomMap.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h Hungarian.h ImageOption.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h Topology.h Unit.h Vec3.h
 TextBlockBuffer.o : TextBlockBuffer.cpp BufferedLine.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Parallel.h TextBlockBuffer.h
 TextFormat.o : TextFormat.cpp StringRoutines.h TextFormat.h
 Timer.o : Timer.cpp CpptrajStdio.h Timer.h
 TinkerFile.o : TinkerFile.cpp ArgList.h Atom.h AtomMask.h Box.h BufferedLine.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TinkerFile.h Unit.h Vec3.h
-TopInfo.o : TopInfo.cpp AssociatedData.h Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h DistRoutines.h FileIO.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Mol.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h TopInfo.h Topology.h TorsionRoutines.h Unit.h Vec3.h
-Topology.o : Topology.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/GetParams.h Parm/Merge.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h UpdateParameters.h Vec3.h
+TopInfo.o : TopInfo.cpp AssociatedData.h Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h DistRoutines.h FileIO.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Mol.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h TopInfo.h Topology.h TorsionRoutines.h Unit.h Vec3.h
+Topology.o : Topology.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/GetParams.h Parm/Merge.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h UpdateParameters.h Vec3.h
 TorsionRoutines.o : TorsionRoutines.cpp Constants.h TorsionRoutines.h Vec3.h
 TrajFrameCounter.o : TrajFrameCounter.cpp ArgList.h CpptrajStdio.h TrajFrameCounter.h
-TrajIOarray.o : TrajIOarray.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryFile.h TrajectoryIO.h Unit.h Vec3.h
-Traj_AmberCoord.o : Traj_AmberCoord.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h Traj_AmberCoord.h TrajectoryIO.h Unit.h Vec3.h
-Traj_AmberNetcdf.o : Traj_AmberNetcdf.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h ParallelNetcdf.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_AmberNetcdf.h TrajectoryIO.h Unit.h Vec3.h
-Traj_AmberRestart.o : Traj_AmberRestart.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedFrame.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextBlockBuffer.h TextFormat.h Topology.h Traj_AmberRestart.h TrajectoryIO.h Unit.h Vec3.h
-Traj_AmberRestartNC.o : Traj_AmberRestartNC.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Traj_AmberRestartNC.h TrajectoryIO.h Unit.h Vec3.h
-Traj_Binpos.o : Traj_Binpos.cpp Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_Binpos.h TrajectoryIO.h Unit.h Vec3.h
-Traj_CIF.o : Traj_CIF.cpp Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h CIFfile.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Traj_CIF.h TrajectoryIO.h Unit.h Vec3.h
-Traj_CharmmCor.o : Traj_CharmmCor.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Traj_CharmmCor.h TrajectoryIO.h Unit.h Vec3.h
-Traj_CharmmDcd.o : Traj_CharmmDcd.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h ByteRoutines.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_CharmmDcd.h TrajectoryIO.h Unit.h Vec3.h
-Traj_CharmmRestart.o : Traj_CharmmRestart.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedFrame.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h Traj_CharmmRestart.h TrajectoryIO.h Unit.h Vec3.h
-Traj_Conflib.o : Traj_Conflib.cpp Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_Conflib.h TrajectoryIO.h Unit.h Vec3.h
-Traj_DTR.o : Traj_DTR.cpp Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_DTR.h TrajectoryIO.h Unit.h Vec3.h vmdplugin/dtrplugin.hxx
-Traj_GmxDump.o : Traj_GmxDump.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_GmxDump.h TrajectoryIO.h Unit.h Vec3.h
-Traj_GmxTng.o : Traj_GmxTng.cpp Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_GmxTng.h TrajectoryIO.h Unit.h Vec3.h
-Traj_GmxTrX.o : Traj_GmxTrX.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h ByteRoutines.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_GmxTrX.h TrajectoryIO.h Unit.h Vec3.h
-Traj_GmxXtc.o : Traj_GmxXtc.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_GmxXtc.h TrajectoryIO.h Unit.h Vec3.h
-Traj_Gro.o : Traj_Gro.cpp Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Traj_Gro.h TrajectoryIO.h Unit.h Vec3.h
-Traj_H5.o : Traj_H5.cpp Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_H5.h TrajectoryIO.h Unit.h Units.h Vec3.h
-Traj_H5MD.o : Traj_H5MD.cpp Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_H5MD.h TrajectoryIO.h Unit.h Units.h Vec3.h
-Traj_Mol2File.o : Traj_Mol2File.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Mol2File.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_Mol2File.h TrajectoryIO.h Unit.h Vec3.h
-Traj_NcEnsemble.o : Traj_NcEnsemble.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FrameArray.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h ParallelNetcdf.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_NcEnsemble.h TrajectoryIO.h Unit.h Vec3.h
-Traj_PDBfile.o : Traj_PDBfile.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Tensor.h Dimension.h DistRoutines.h FileIO.h FileName.h Frame.h FramePtrArray.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricTensor.h TextFormat.h Timer.h Topology.h Traj_PDBfile.h TrajectoryIO.h Unit.h Vec3.h
-Traj_SDF.o : Traj_SDF.cpp Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SDFfile.h Segment.h SymbolExporting.h Topology.h Traj_SDF.h TrajectoryIO.h Unit.h Vec3.h
-Traj_SQM.o : Traj_SQM.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Traj_SQM.h TrajectoryIO.h Unit.h Vec3.h
-Traj_Tinker.o : Traj_Tinker.cpp Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TinkerFile.h Topology.h Traj_Tinker.h TrajectoryIO.h Unit.h Vec3.h
-Traj_XYZ.o : Traj_XYZ.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h Traj_XYZ.h TrajectoryIO.h Unit.h Vec3.h
+TrajIOarray.o : TrajIOarray.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryFile.h TrajectoryIO.h Unit.h Vec3.h
+Traj_AmberCoord.o : Traj_AmberCoord.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h Traj_AmberCoord.h TrajectoryIO.h Unit.h Vec3.h
+Traj_AmberNetcdf.o : Traj_AmberNetcdf.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h ParallelNetcdf.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_AmberNetcdf.h TrajectoryIO.h Unit.h Vec3.h
+Traj_AmberRestart.o : Traj_AmberRestart.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedFrame.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextBlockBuffer.h TextFormat.h Topology.h Traj_AmberRestart.h TrajectoryIO.h Unit.h Vec3.h
+Traj_AmberRestartNC.o : Traj_AmberRestartNC.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Traj_AmberRestartNC.h TrajectoryIO.h Unit.h Vec3.h
+Traj_Binpos.o : Traj_Binpos.cpp Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_Binpos.h TrajectoryIO.h Unit.h Vec3.h
+Traj_CIF.o : Traj_CIF.cpp Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h CIFfile.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Traj_CIF.h TrajectoryIO.h Unit.h Vec3.h
+Traj_CharmmCor.o : Traj_CharmmCor.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Traj_CharmmCor.h TrajectoryIO.h Unit.h Vec3.h
+Traj_CharmmDcd.o : Traj_CharmmDcd.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h ByteRoutines.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_CharmmDcd.h TrajectoryIO.h Unit.h Vec3.h
+Traj_CharmmRestart.o : Traj_CharmmRestart.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedFrame.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h Traj_CharmmRestart.h TrajectoryIO.h Unit.h Vec3.h
+Traj_Conflib.o : Traj_Conflib.cpp Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_Conflib.h TrajectoryIO.h Unit.h Vec3.h
+Traj_DTR.o : Traj_DTR.cpp Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_DTR.h TrajectoryIO.h Unit.h Vec3.h vmdplugin/dtrplugin.hxx
+Traj_GmxDump.o : Traj_GmxDump.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_GmxDump.h TrajectoryIO.h Unit.h Vec3.h
+Traj_GmxTng.o : Traj_GmxTng.cpp Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_GmxTng.h TrajectoryIO.h Unit.h Vec3.h
+Traj_GmxTrX.o : Traj_GmxTrX.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h ByteRoutines.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_GmxTrX.h TrajectoryIO.h Unit.h Vec3.h
+Traj_GmxXtc.o : Traj_GmxXtc.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_GmxXtc.h TrajectoryIO.h Unit.h Vec3.h
+Traj_Gro.o : Traj_Gro.cpp Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Traj_Gro.h TrajectoryIO.h Unit.h Vec3.h
+Traj_H5.o : Traj_H5.cpp Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NC_Routines.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_H5.h TrajectoryIO.h Unit.h Units.h Vec3.h
+Traj_H5MD.o : Traj_H5MD.cpp Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NC_Routines.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_H5MD.h TrajectoryIO.h Unit.h Units.h Vec3.h
+Traj_Mol2File.o : Traj_Mol2File.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Mol2File.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_Mol2File.h TrajectoryIO.h Unit.h Vec3.h
+Traj_NcEnsemble.o : Traj_NcEnsemble.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FrameArray.h FramePtrArray.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h ParallelNetcdf.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_NcEnsemble.h TrajectoryIO.h Unit.h Vec3.h
+Traj_PDBfile.o : Traj_PDBfile.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Tensor.h Dimension.h DistRoutines.h FileIO.h FileName.h Frame.h FramePtrArray.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricTensor.h TextFormat.h Timer.h Topology.h Traj_PDBfile.h TrajectoryIO.h Unit.h Vec3.h
+Traj_SDF.o : Traj_SDF.cpp Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SDFfile.h Segment.h SymbolExporting.h Topology.h Traj_SDF.h TrajectoryIO.h Unit.h Vec3.h
+Traj_SQM.o : Traj_SQM.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Traj_SQM.h TrajectoryIO.h Unit.h Vec3.h
+Traj_Tinker.o : Traj_Tinker.cpp Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TinkerFile.h Topology.h Traj_Tinker.h TrajectoryIO.h Unit.h Vec3.h
+Traj_XYZ.o : Traj_XYZ.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h Traj_XYZ.h TrajectoryIO.h Unit.h Vec3.h
 TrajectoryFile.o : TrajectoryFile.cpp Atom.h BaseIOtype.h Box.h BufferedFrame.h BufferedLine.h CIFfile.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h FileTypes.h FramePtrArray.h Matrix_3x3.h Mol2File.h NC_Routines.h NameType.h NetcdfFile.h PDBfile.h Parallel.h ReplicaDimArray.h Residue.h SDFfile.h SymbolExporting.h TextFormat.h TinkerFile.h Traj_AmberCoord.h Traj_AmberNetcdf.h Traj_AmberRestart.h Traj_AmberRestartNC.h Traj_Binpos.h Traj_CIF.h Traj_CharmmCor.h Traj_CharmmDcd.h Traj_CharmmRestart.h Traj_Conflib.h Traj_DTR.h Traj_GmxDump.h Traj_GmxTng.h Traj_GmxTrX.h Traj_GmxXtc.h Traj_Gro.h Traj_H5.h Traj_H5MD.h Traj_Mol2File.h Traj_NcEnsemble.h Traj_PDBfile.h Traj_SDF.h Traj_SQM.h Traj_Tinker.h Traj_XYZ.h TrajectoryFile.h TrajectoryIO.h Vec3.h
 TrajectoryIO.o : TrajectoryIO.cpp BaseIOtype.h Box.h CoordinateInfo.h CpptrajStdio.h FramePtrArray.h Matrix_3x3.h Parallel.h ReplicaDimArray.h TrajectoryIO.h Vec3.h
-TrajinList.o : TrajinList.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_RemLog.h Dimension.h EnsembleIn.h EnsembleIn_Multi.h EnsembleIn_Single.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryFile.h TrajectoryIO.h Trajin.h TrajinList.h Trajin_Multi.h Trajin_Single.h Unit.h Vec3.h
-Trajin_Multi.o : Trajin_Multi.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryIO.h Trajin.h Trajin_Multi.h Unit.h Vec3.h
-Trajin_Single.o : Trajin_Single.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h Trajin.h Trajin_Single.h Unit.h Vec3.h
-TrajoutList.o : TrajoutList.cpp ActionFrameCounter.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TrajoutList.h Trajout_Single.h Unit.h Vec3.h
-Trajout_Single.o : Trajout_Single.cpp ActionFrameCounter.h ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h Trajout_Single.h Unit.h Vec3.h
+TrajinList.o : TrajinList.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_RemLog.h Dimension.h EnsembleIn.h EnsembleIn_Multi.h EnsembleIn_Single.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryFile.h TrajectoryIO.h Trajin.h TrajinList.h Trajin_Multi.h Trajin_Single.h Unit.h Vec3.h
+Trajin_Multi.o : Trajin_Multi.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryIO.h Trajin.h Trajin_Multi.h Unit.h Vec3.h
+Trajin_Single.o : Trajin_Single.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h Trajin.h Trajin_Single.h Unit.h Vec3.h
+TrajoutList.o : TrajoutList.cpp ActionFrameCounter.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TrajoutList.h Trajout_Single.h Unit.h Vec3.h
+Trajout_Single.o : Trajout_Single.cpp ActionFrameCounter.h ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h Trajout_Single.h Unit.h Vec3.h
 Units.o : Units.cpp Constants.h CpptrajStdio.h Units.h
 Vec3.o : Vec3.cpp Constants.h CpptrajStdio.h Vec3.h
-ViewRst.o : ViewRst.cpp ActionFrameCounter.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h Unit.h Vec3.h ViewRst.h
-main.o : main.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h Cpptraj.h CpptrajFile.h CpptrajState.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+ViewRst.o : ViewRst.cpp ActionFrameCounter.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h Unit.h Vec3.h ViewRst.h
+main.o : main.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h Cpptraj.h CpptrajFile.h CpptrajState.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 molsurf.o : molsurf.c molsurf.h
 qcprot.o : qcprot.cpp CpptrajStdio.h qcprot.h
 vmdplugin/dtrplugin.o : vmdplugin/dtrplugin.cpp ByteRoutines.h vmdplugin/dtrplugin.hxx vmdplugin/vmddir.h
diff --git a/src/cpptrajfiles b/src/cpptrajfiles
index 16c9cae7c1..23e461b336 100644
--- a/src/cpptrajfiles
+++ b/src/cpptrajfiles
@@ -372,6 +372,7 @@ COMMON_SOURCES= \
         MdOpts.cpp \
         MetaData.cpp \
         Minimize_SteepestDescent.cpp \
+        ModXNA_Info.cpp \
         Mol.cpp \
         Mol2File.cpp \
         NameType.cpp \

From a0b1832b9240002a2d4b35dd93a35de5a3f5069b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 5 Mar 2026 11:50:40 -0500
Subject: [PATCH 1466/1492] V7.00.0 - MAJOR VERSION BUMP! Addition of system
 build/parameterization code, among other improvements. Lots of changes under
 the hood as far as topology/parameter handling goes.

---
 src/Version.h | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Version.h b/src/Version.h
index a8fc48117a..1fe64fc8a6 100644
--- a/src/Version.h
+++ b/src/Version.h
@@ -12,7 +12,7 @@
  * Whenever a number that precedes <revision> is incremented, all subsequent
  * numbers should be reset to 0.
  */
-#define CPPTRAJ_INTERNAL_VERSION "V6.31.0"
+#define CPPTRAJ_INTERNAL_VERSION "V7.00.0"
 /// PYTRAJ relies on this
 #define CPPTRAJ_VERSION_STRING CPPTRAJ_INTERNAL_VERSION
 #endif

From 5623ee0dd89b28a0df120f87c0e02bcc1e8c0b18 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 5 Mar 2026 11:51:43 -0500
Subject: [PATCH 1467/1492] Hide debug info

---
 src/DataIO_Std.cpp | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/DataIO_Std.cpp b/src/DataIO_Std.cpp
index 7650e99c2b..400be4ff96 100644
--- a/src/DataIO_Std.cpp
+++ b/src/DataIO_Std.cpp
@@ -1113,7 +1113,8 @@ const
       }
       // Skip mapping if tgt == ref
       if (tgt != ref) {
-        mprintf("DEBUG: Map ref %s to tgt %s\n", ref.c_str(), tgt.c_str());
+        if (debug_ > 0)
+          mprintf("DEBUG: Map ref %s to tgt %s\n", ref.c_str(), tgt.c_str());
         namemap->AddNameMap(ref, tgt);
       }
     } // END if not comment

From 5efe7ba46c5984e96917a29a0120a2f4312516c1 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 5 Mar 2026 11:51:51 -0500
Subject: [PATCH 1468/1492] Update year

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 490ff4b0c8..f6706dc9d2 100644
--- a/README.md
+++ b/README.md
@@ -46,7 +46,7 @@ CPPTRAJ see the following publication:
 Disclaimer and Copyright
 ========================
 
-CPPTRAJ is Copyright (c) 2010-2025 Daniel R. Roe.
+CPPTRAJ is Copyright (c) 2010-2026 Daniel R. Roe.
 The terms for using, copying, modifying, and distributing CPPTRAJ are
 specified in the file LICENSE.
 

From 88747d034624fbff54dea32becd3d01887fd8a05 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 5 Mar 2026 12:34:50 -0500
Subject: [PATCH 1469/1492] Start adding a short libsander test

---
 test/Test_Esander_short/RunTest.sh | 52 ++++++++++++++++++++++++++++++
 1 file changed, 52 insertions(+)
 create mode 100755 test/Test_Esander_short/RunTest.sh

diff --git a/test/Test_Esander_short/RunTest.sh b/test/Test_Esander_short/RunTest.sh
new file mode 100755
index 0000000000..23e1c8db92
--- /dev/null
+++ b/test/Test_Esander_short/RunTest.sh
@@ -0,0 +1,52 @@
+#!/bin/bash
+
+. ../MasterTest.sh
+
+CleanFiles ene.in Esander.dat force.crd Edpdp.dat CpptrajEsander.parm7 NoWat.dat
+TESTNAME='SANDER energy tests (short)'
+Requires sanderlib netcdf
+
+# Set to 1 if compiled with -DCPPTRAJ_ESANDER_ENERGY_ORDER
+NEWORDER=0
+if [ $NEWORDER -eq 1 ] ; then
+  SAVEPREFIX='neworder.'
+else
+  SAVEPREFIX=''
+fi
+
+INPUT="-i ene.in"
+
+TestPME() {
+  UNITNAME='Short SANDER energy test, PME'
+  CheckFor maxthreads 3
+  if [ $? -eq 0 ] ; then
+    cat > ene.in <<EOF
+parm ../tz2.truncoct.parm7
+trajin ../tz2.truncoct.nc 1 3
+esander S out Esander.dat saveforces
+trajout force.crd
+EOF
+    RunCpptraj "$UNITNAME"
+    #DoTest "$SAVEPREFIX"Esander.dat.save Esander.dat
+    #NcTest force.nc.save force.nc -a 0.000001
+  fi
+}
+
+TestGB() {
+  UNINTNAME="Short SANDER energy test, GB"
+  CheckFor maxthreads 10
+  cat > ene.in <<EOF
+parm ../DPDP.parm7
+trajin ../DPDP.nc 1 10
+esander DPDP out Edpdp.dat gbsa 1
+EOF
+  RunCpptraj "$UNITNAME"
+  #DoTest "$SAVEPREFIX"Edpdp.dat.save Edpdp.dat
+}
+
+
+TestGB
+TestPME
+
+EndTest
+exit 0

From e6d6e4b2c2eedf12a288a1a2c6628ea3297e5435 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 5 Mar 2026 12:36:40 -0500
Subject: [PATCH 1470/1492] Finish short libsander test

---
 test/Test_Esander_short/Edpdp.dat.save   |   11 +
 test/Test_Esander_short/Esander.dat.save |    4 +
 test/Test_Esander_short/RunTest.sh       |    8 +-
 test/Test_Esander_short/force.crd.save   | 5251 ++++++++++++++++++++++
 4 files changed, 5270 insertions(+), 4 deletions(-)
 create mode 100644 test/Test_Esander_short/Edpdp.dat.save
 create mode 100644 test/Test_Esander_short/Esander.dat.save
 create mode 100644 test/Test_Esander_short/force.crd.save

diff --git a/test/Test_Esander_short/Edpdp.dat.save b/test/Test_Esander_short/Edpdp.dat.save
new file mode 100644
index 0000000000..c087fdc90d
--- /dev/null
+++ b/test/Test_Esander_short/Edpdp.dat.save
@@ -0,0 +1,11 @@
+#Frame    DPDP[total]    DPDP[vdw]   DPDP[elec]     DPDP[gb]   DPDP[bond]  DPDP[angle] DPDP[dihedral]  DPDP[vdw14] DPDP[elec14]   DPDP[surf]
+       1    -362.4643    -115.9750   -1411.3160    -287.5523      65.3607     131.8731       137.8161      65.0756    1044.0345       8.2191
+       2    -354.7133    -120.2763   -1395.6827    -291.9428      57.7708     157.4151       132.2196      64.1154    1033.1675       8.5001
+       3    -370.7565    -125.1295   -1400.7943    -300.7252      65.6276     138.9934       132.4764      63.6082    1046.7778       8.4092
+       4    -376.7324    -117.7838   -1423.3411    -290.1824      54.0259     147.7710       128.0771      65.6641    1050.8066       8.2300
+       5    -375.7554    -124.8303   -1392.5554    -307.0641      49.4597     139.9179       129.8075      70.3971    1050.8492       8.2632
+       6    -386.0375    -118.8866   -1400.8651    -295.0492      49.2628     142.8182       138.1374      61.6022    1028.5830       8.3598
+       7    -356.8886    -117.6782   -1388.2306    -303.4668      61.8618     150.0429       127.6294      66.5359    1038.1030       8.3141
+       8    -363.6296    -125.5548   -1387.9611    -293.7736      53.1676     155.3169       137.1281      63.5159    1026.4366       8.0948
+       9    -371.4302    -120.7442   -1403.4900    -293.0892      62.9546     134.8385       133.8371      63.1068    1043.1964       7.9598
+      10    -376.8531    -126.2939   -1384.7891    -287.9323      53.8934     142.4284       138.3462      63.0387    1016.3050       8.1505
diff --git a/test/Test_Esander_short/Esander.dat.save b/test/Test_Esander_short/Esander.dat.save
new file mode 100644
index 0000000000..c74206b91f
--- /dev/null
+++ b/test/Test_Esander_short/Esander.dat.save
@@ -0,0 +1,4 @@
+#Frame       S[total]       S[vdw]      S[elec]      S[bond]     S[angle]  S[dihedral]     S[vdw14]    S[elec14]
+       1  -18095.5918    2502.5936  -21563.5670      35.4705      93.3672     123.6395      46.9354     665.9690
+       2  -18032.9144    2455.6270  -21457.2687      47.5936     101.2947     125.3715      38.6891     655.7783
+       3  -18096.0464    2518.4931  -21591.4285      41.2026     111.4593     137.7342      43.2846     643.2083
diff --git a/test/Test_Esander_short/RunTest.sh b/test/Test_Esander_short/RunTest.sh
index 23e1c8db92..4cfb52cbff 100755
--- a/test/Test_Esander_short/RunTest.sh
+++ b/test/Test_Esander_short/RunTest.sh
@@ -27,13 +27,13 @@ esander S out Esander.dat saveforces
 trajout force.crd
 EOF
     RunCpptraj "$UNITNAME"
-    #DoTest "$SAVEPREFIX"Esander.dat.save Esander.dat
-    #NcTest force.nc.save force.nc -a 0.000001
+    DoTest "$SAVEPREFIX"Esander.dat.save Esander.dat
+    DoTest force.crd.save force.crd
   fi
 }
 
 TestGB() {
-  UNINTNAME="Short SANDER energy test, GB"
+  UNITNAME="Short SANDER energy test, GB"
   CheckFor maxthreads 10
   cat > ene.in <<EOF
 parm ../DPDP.parm7
@@ -41,7 +41,7 @@ trajin ../DPDP.nc 1 10
 esander DPDP out Edpdp.dat gbsa 1
 EOF
   RunCpptraj "$UNITNAME"
-  #DoTest "$SAVEPREFIX"Edpdp.dat.save Edpdp.dat
+  DoTest "$SAVEPREFIX"Edpdp.dat.save Edpdp.dat
 }
 
 
diff --git a/test/Test_Esander_short/force.crd.save b/test/Test_Esander_short/force.crd.save
new file mode 100644
index 0000000000..016dc938f8
--- /dev/null
+++ b/test/Test_Esander_short/force.crd.save
@@ -0,0 +1,5251 @@
+Cpptraj Generated trajectory                                                    
+   0.078   3.174  -8.844   0.999   3.431  -8.521  -0.183   2.306  -8.398  -0.593
+   3.841  -8.489   0.098   3.075 -10.322  -0.779   2.538 -10.682   0.153   4.463
+ -10.860  -0.841   4.761 -10.526   1.011   4.880 -10.332   0.365   4.499 -12.266
+  -0.294   5.139 -12.545   1.247   2.200 -10.778   2.360   2.377 -10.231   1.044
+   1.464 -11.869   0.133   1.489 -12.305   2.104   0.639 -12.432   2.786   0.289
+ -11.657   1.487  -0.653 -12.960   0.630  -0.448 -13.602   2.254  -1.127 -13.572
+   1.092  -1.584 -11.914  -0.167  -2.074 -11.499  -1.082  -1.694 -11.928   0.034
+  -2.946 -10.443  -0.742  -3.404  -9.987   1.353  -3.275 -10.279   2.009  -4.362
+  -9.735   1.326  -5.070  -9.289   3.401  -4.481  -9.806   3.847  -5.364  -9.371
+   4.134  -3.504 -10.495   5.197  -3.695 -10.527   3.468  -2.597 -11.213   4.037
+  -1.968 -11.881   2.054  -2.408 -11.171   2.783   1.383 -13.617   2.166   2.071
+ -14.421   4.126   1.266 -13.806   4.657   0.696 -13.163   4.842   2.076 -14.754
+   4.205   2.372 -15.588   5.470   3.225 -13.924   6.031   2.847 -13.069   6.498
+   4.029 -14.751   7.339   3.404 -15.055   6.090   4.375 -15.700   6.894   4.869
+ -14.181   4.432   4.051 -13.366   3.998   3.452 -12.753   5.829   1.040 -15.377
+   6.244   0.087 -14.670   6.200   1.253 -16.612   5.905   2.125 -17.028   7.210
+   0.481 -17.378   7.429  -0.491 -16.935   6.757   0.161 -18.799   5.848  -0.441
+ -18.814   6.574   1.135 -19.254   7.757  -0.663 -19.575   8.538  -0.285 -20.599
+   8.549   0.695 -21.052   9.172  -1.368 -21.151   9.867  -1.368 -21.884   8.950
+  -2.481 -20.381   9.509  -3.777 -20.453  10.215  -4.035 -21.228   9.136  -4.737
+ -19.512   9.382  -5.788 -19.530   8.308  -4.357 -18.400   7.953  -5.095 -17.696
+   7.701  -3.100 -18.447   6.908  -2.824 -17.768   8.007  -2.073 -19.402   8.442
+   1.297 -17.375   8.539   2.184 -18.181   9.441   1.019 -16.557   9.389   0.318
+ -15.832  10.624   1.872 -16.599  10.647   2.530 -17.468  10.541   2.701 -15.339
+   9.657   3.338 -15.335  10.355   2.068 -14.472  11.678   3.650 -15.105  12.625
+   3.111 -15.086  11.634   4.387 -15.907  11.574   4.381 -13.767  11.542   3.693
+ -12.715  11.625   5.604 -13.760  11.839   1.063 -16.553  11.951   0.149 -15.675
+  12.806   1.387 -17.464  12.573   2.103 -18.137  14.069   0.715 -17.663  14.448
+   0.992 -18.646  15.148   1.280 -16.726  14.689   1.294 -15.737  15.964   0.557
+ -16.716  15.712   2.623 -17.048  15.745   3.019 -18.173  16.266   3.236 -16.029
+  16.166   2.801 -15.123  16.882   4.027 -16.151  13.953  -0.882 -17.641  14.782
+  -1.536 -17.018  12.988  -1.522 -18.311  12.253  -1.054 -18.821  12.941  -2.965
+ -18.404  12.670  -3.316 -19.400  13.889  -3.490 -18.292  11.995  -3.707 -17.487
+  11.969  -4.976 -17.529  11.364  -2.991 -16.517  11.612  -2.019 -16.399  10.557
+  -3.625 -15.474  10.321  -4.645 -15.775  11.443  -3.614 -14.182  12.524  -3.638
+ -14.319  11.278  -2.724 -13.574  11.137  -4.841 -13.296  11.618  -4.716 -12.326
+  10.072  -4.839 -13.063  11.519  -6.210 -13.881  11.129  -6.445 -14.871  12.592
+  -6.260 -14.068  11.276  -7.393 -13.023  11.807  -8.243 -13.451  11.661  -7.296
+ -12.008   9.852  -7.803 -13.078   9.264  -7.152 -12.577   9.520  -7.775 -14.032
+   9.758  -8.715 -12.656   9.238  -2.881 -15.153   9.259  -1.656 -14.960   8.146
+  -3.609 -15.005   8.194  -4.595 -15.221   6.987  -3.067 -14.351   6.746  -2.108
+ -14.809   5.776  -4.025 -14.351   6.038  -4.983 -13.902   5.011  -3.519 -13.761
+   5.274  -4.348 -15.733   5.266  -5.584 -16.346   5.681  -6.479 -15.908   4.751
+  -5.416 -17.609   4.571  -6.148 -18.281   4.225  -4.175 -17.846   3.547  -3.662
+ -18.938   3.286  -4.231 -19.818   3.038  -2.398 -18.801   2.536  -1.988 -19.665
+   3.174  -1.653 -17.614   2.601  -0.737 -17.582   4.077  -2.123 -16.683   4.235
+  -1.507 -15.810   4.605  -3.440 -16.711   7.322  -2.806 -12.833   7.801  -3.710
+ -12.105   7.186  -1.546 -12.469   6.811  -0.968 -13.208   7.428  -1.085 -11.087
+   7.440  -1.889 -10.352   8.856  -0.494 -10.899   9.554  -1.301 -11.123   9.151
+   0.723 -11.755  10.088   1.191 -11.450   9.294   0.338 -12.765   8.434   1.544
+ -11.758   9.109  -0.127  -9.568  10.022  -0.353  -9.374   6.336  -0.160 -10.616
+   5.576   0.387 -11.412   6.283   0.017  -9.292   6.958  -0.517  -8.763   5.234
+   0.792  -8.597   4.362   0.764  -9.251   4.850   0.127  -7.266   4.640  -0.921
+  -7.478   5.675   0.118  -6.554   3.638   0.807  -6.649   3.602   1.748  -5.710
+   4.360   2.171  -5.069   2.382   2.273  -5.563   2.177   3.099  -5.021   1.505
+   1.505  -6.276   0.087   1.493  -6.257  -0.526   2.206  -5.725  -0.538   0.542
+  -7.122  -1.600   0.527  -7.317   0.257  -0.295  -7.984  -0.243  -1.027  -8.600
+   1.673  -0.256  -8.026   2.269  -1.023  -8.497   2.292   0.607  -7.049   5.641
+   2.253  -8.427   6.799   2.484  -8.024   4.727   3.197  -8.589   3.823   2.843
+  -8.867   4.877   4.656  -8.500   5.707   4.821  -7.813   5.111   5.335  -9.823
+   4.236   5.372 -10.472   5.447   6.366  -9.717   6.266   4.731 -10.712   6.082
+   3.684 -10.950   6.328   5.107 -11.734   7.719   4.862 -10.069   7.917   5.919
+  -9.890   7.755   4.364  -9.100   8.826   4.451 -10.953   8.632   3.545 -11.528
+   8.862   5.271 -11.670  10.132   4.402 -10.278  10.895   4.381 -10.940  10.238
+   5.210  -9.681  10.186   3.611  -9.653   3.613   5.276  -7.856   2.530   4.759
+  -8.048   3.690   6.391  -7.216   4.562   6.844  -6.978   2.780   6.591  -6.826
+   5.073  10.420   6.330   5.056  11.200   5.776   4.902  10.749   7.212   6.303
+  -7.766 -13.643   5.393  -7.858 -13.360   6.767  -7.465 -12.862   1.908  -2.824
+  16.587   0.980  -2.708  16.789   1.994  -2.532  15.680   2.408 -11.996   7.298
+   2.852 -11.888   6.457   2.186 -11.105   7.568  -3.547  -5.919   8.169  -3.777
+  -6.462   7.415  -2.708  -5.524   7.933  11.654  11.583  11.273  10.776  11.939
+  11.410  12.235  12.201  11.715  20.387  15.555  -0.257  20.631  15.023   0.500
+  19.670  15.072  -0.667  -4.502 -16.743  -7.844  -4.860 -17.606  -8.051  -5.080
+ -16.401  -7.162   1.743  -1.669  14.012   1.272  -1.072  13.431   1.601  -2.536
+  13.630   9.043  -0.111  14.168   8.650  -0.607  14.886   8.395   0.562  13.959
+  13.962  -5.826 -10.237  13.933  -5.394 -11.091  14.844  -5.652  -9.910  10.789
+ -17.471  11.119  11.717 -17.246  11.186  10.773 -18.428  11.135  19.894  11.231
+  -4.714  19.711  11.480  -3.808  19.313  10.488  -4.879  -8.080 -10.753 -13.409
+  -8.719 -11.347 -13.802  -7.990 -10.043 -14.045   9.102   0.918   3.616   8.432
+   1.594   3.512   9.299   0.636   2.723  -5.119 -14.445 -13.062  -4.933 -13.531
+ -13.277  -6.074 -14.497 -13.044  -1.858   6.859  15.005  -1.954   7.576  15.632
+  -1.945   6.065  15.534   1.567   1.756   6.444   0.695   1.364   6.479   2.056
+   1.199   5.837  19.389   3.108   6.839  20.003   2.714   6.220  19.941   3.620
+   7.431   2.267  10.389  14.793   2.278   9.627  15.372   3.052  10.292  14.254
+  -4.593  10.163 -20.765  -4.029   9.419 -20.975  -4.350  10.834 -21.403  12.120
+   0.860   9.019  11.993   0.035   8.552  13.053   1.051   8.919   1.797   7.255
+  -2.931   1.710   6.713  -3.715   1.112   7.919  -3.022 -14.695  13.696   0.533
+ -14.652  13.361  -0.362 -15.131  13.003   1.028   8.589  10.066   7.868   8.861
+  10.092   6.951   7.633  10.085   7.835   7.305 -12.870  -1.975   7.185 -12.136
+  -1.372   7.065 -13.642  -1.463  -8.020  -6.280   2.815  -8.777  -5.723   2.636
+  -7.347  -5.971   2.208  15.568 -14.449  -6.568  16.317 -14.775  -6.069  14.876
+ -15.090  -6.408   0.550  18.152   3.669   0.531  17.666   4.493  -0.340  18.074
+   3.325   6.086  15.889  -9.916   6.088  14.932  -9.919   5.175  16.126  -9.742
+  16.952 -15.457   2.430  17.881 -15.404   2.209  16.516 -14.932   1.759   7.663
+   6.021   7.308   7.049   6.722   7.089   7.997   6.258   8.174  18.240 -11.299
+   3.429  17.920 -11.605   4.277  17.699 -10.535   3.230   9.259  13.118  11.703
+   9.200  12.762  12.590   9.549  14.022  11.827  -4.904   5.816   6.204  -4.557
+   6.625   5.828  -5.845   5.856   6.030  15.732  10.019  -1.382  16.418   9.579
+  -0.880  14.965   9.453  -1.287 -14.506  15.662  -2.512 -14.534  14.707  -2.567
+ -14.967  15.961  -3.296   7.334  -5.247   6.515   6.492  -5.449   6.922   7.580
+  -4.398   6.882  11.280   0.864  18.065  11.831   1.625  17.884  11.142   0.459
+  17.208   1.959   7.511   4.507   2.694   7.761   3.947   1.916   6.558   4.434
+  19.871   6.951   6.143  20.281   7.786   6.371  18.943   7.161   6.039 -17.094
+ -17.597  -7.408 -17.387 -17.040  -6.687 -16.140 -17.515  -7.402 -12.497  -6.927
+  -1.928 -12.419  -6.819  -0.980 -11.668  -7.327  -2.192  12.441   9.669   3.248
+  13.299   9.258   3.350  12.310  10.155   4.062  11.405   1.243  15.009  10.607
+   0.836  14.672  11.560   1.985  14.425  17.400  17.896   0.761  16.951  17.063
+   0.908  18.094  17.913   1.420  13.340   2.725  17.584  14.081   3.040  18.101
+  12.827   3.511  17.396  -7.129  18.474 -16.620  -7.183  19.330 -16.194  -6.917
+  17.867 -15.912 -14.936  14.965   9.803 -15.629  14.528  10.298 -14.181  14.961
+  10.392   9.693  -3.129  15.364  10.231  -2.705  16.032   8.848  -2.683  15.418
+  17.735   7.706   8.044  16.942   7.975   7.579  17.436   7.506   8.931 -17.867
+  -0.001 -17.249 -17.189   0.643 -17.453 -18.687   0.433 -17.486   0.230 -22.255
+   7.430   0.928 -21.922   6.866  -0.328 -22.767   6.845   7.225 -17.002 -10.720
+   6.917 -17.420  -9.916   6.440 -16.920 -11.262   2.162 -12.658 -10.264   1.850
+ -12.753  -9.364   3.024 -12.252 -10.177  -2.161  18.564   2.941  -2.562  17.695
+   2.923  -2.387  18.950   2.095  -0.602 -14.329   2.309   0.018 -14.342   1.579
+  -0.086 -14.030   3.057   1.293 -16.434 -15.245   1.497 -15.949 -14.445   1.843
+ -16.032 -15.916  17.594   3.177  -3.075  17.339   3.648  -3.869  17.576   2.254
+  -3.328  -2.226  16.799  14.328  -1.313  16.559  14.169  -2.727  16.028  14.061
+   5.388  11.297   8.939   6.035  10.950   9.553   4.607  11.444   9.473  -9.923
+  -3.972   5.616  -9.571  -4.704   5.108 -10.537  -3.542   5.021 -15.013  10.820
+   1.236 -15.658  10.258   0.806 -14.175  10.560   0.853  11.100   6.454  -0.045
+  11.359   5.660   0.422  10.222   6.264  -0.374  -5.672 -11.342 -11.671  -6.414
+ -11.517 -12.250  -6.071 -11.052 -10.851  20.144   4.431  -2.217  19.459   3.951
+  -2.683  20.025   5.341  -2.489 -15.486   6.912   2.116 -15.780   6.947   1.206
+ -15.016   6.081   2.185 -15.460   4.508 -10.778 -15.655   3.806 -10.157 -15.046
+   4.064 -11.519   7.198 -15.790 -18.640   6.275 -15.820 -18.890   7.187 -15.718
+ -17.686  -6.727  20.237  -2.282  -6.176  19.481  -2.084  -7.620  19.892  -2.271
+ -17.215  -1.138  -6.449 -16.302  -1.297  -6.689 -17.717  -1.728  -7.011   7.928
+ -14.378 -10.528   8.866 -14.404 -10.715   7.584 -15.183 -10.916   1.202   1.395
+  24.562   0.966   1.371  23.635   2.039   1.859  24.584   1.314 -13.480  -2.645
+   2.023 -12.920  -2.961   0.536 -12.924  -2.679   2.889  21.827  10.403   2.423
+  22.145   9.630   3.063  20.905  10.216 -19.371  -4.708   0.921 -18.658  -5.065
+   1.450 -20.167  -5.032   1.341  -3.732 -10.138   3.736  -3.837 -11.073   3.911
+  -2.803  -9.969   3.891 -17.845  13.225  -2.250 -17.534  12.655  -2.953 -18.024
+  14.061  -2.681  10.303  -6.900  13.429  10.826  -6.263  12.942  10.929  -7.573
+  13.694  -4.155 -19.673  -0.734  -4.204 -20.433  -1.314  -5.066 -19.492  -0.501
+  -9.056  12.616  -7.904  -8.945  12.852  -6.983  -9.908  12.181  -7.939  -3.998
+   6.676  -8.084  -4.797   7.127  -7.809  -4.042   6.674  -9.041   2.537 -20.442
+   7.582   2.348 -20.542   6.649   2.567 -19.496   7.720 -14.717  -2.732  12.265
+ -14.431  -3.635  12.403 -15.590  -2.695  12.656  -2.352 -16.623   2.841  -2.251
+ -17.092   2.013  -1.958 -15.765   2.681   4.933   6.378 -19.642   5.478   5.840
+ -19.068   5.480   7.135 -19.851  -4.104  19.744  11.857  -4.909  19.758  11.340
+  -4.395  19.885  12.758  16.935 -10.998 -14.754  16.907 -11.949 -14.651  16.650
+ -10.657 -13.906  20.026  -7.319  -2.531  19.855  -7.363  -1.590  20.546  -6.523
+  -2.642  13.402   0.189  19.620  13.617   1.108  19.778  12.600   0.216  19.098
+   4.118 -17.989   8.259   3.796 -18.046   9.159   4.726 -17.250   8.269   8.103
+ -11.151  -7.137   8.696 -11.687  -6.612   8.440 -11.226  -8.030   4.628 -20.580
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+  -6.387  15.169  -6.041 -12.389  15.285  -5.353 -11.733  15.022  -6.837 -11.877
+ -18.953   3.315   0.730 -18.937   4.167   0.294 -18.652   2.699   0.062  -6.477
+   2.236 -21.365  -5.624   2.538 -21.676  -7.090   2.504 -22.049  -8.792   2.010
+ -12.569  -9.734   1.841 -12.579  -8.393   1.141 -12.544 -13.580   3.244  15.506
+ -12.797   3.752  15.295 -13.472   3.011  16.429   4.070  -6.254   7.212   4.401
+  -7.149   7.124   4.293  -5.834   6.382   3.074   7.733   8.399   3.616   8.274
+   7.824   2.900   6.942   7.889 -19.412  -0.341  -3.916 -19.529   0.287  -4.629
+ -19.433  -1.196  -4.345   0.526  -2.774  21.602   0.724  -2.873  20.671   1.369
+  -2.897  22.040   2.433  15.585   9.398   2.558  16.518   9.224   1.794  15.303
+   8.745  -3.457  -8.505  15.895  -4.110  -7.998  16.377  -3.222  -7.948  15.152
+ -17.805  15.127  -8.845 -17.908  15.871  -8.252 -18.608  15.123  -9.367  -6.833
+   2.843  23.050  -6.555   3.685  22.688  -7.002   3.024  23.975 -12.585  10.613
+   6.221 -12.054  10.594   7.017 -12.144  10.009   5.624   0.730   7.949  10.676
+  -0.157   7.755  10.373   1.110   7.091  10.867 -11.750 -11.357 -12.350 -11.291
+ -11.762 -13.086 -12.520 -11.909 -12.215  -5.143  -4.523  11.875  -4.755  -4.723
+  11.023  -6.069  -4.741  11.772 -11.024  -9.448   6.156 -10.543  -9.479   5.329
+ -10.420  -9.819   6.799  -7.094   3.677  12.019  -6.578   4.048  11.304  -7.365
+   2.817  11.698  15.895  -9.520  -7.802  16.091  -9.243  -6.907  16.670  -9.272
+  -8.306  -3.221  -3.637  -0.819  -4.057  -3.525  -1.271  -2.675  -4.116  -1.442
+  12.313   4.518  -0.475  13.034   4.425  -1.098  12.712   4.924   0.294  11.550
+   7.056   7.495  11.397   7.206   8.428  12.093   6.269   7.465  11.421 -14.719
+ -12.010  10.705 -14.085 -11.965  12.135 -14.243 -12.434  -8.572  -3.729 -19.433
+  -9.151  -4.225 -18.855  -9.164  -3.206 -19.974  -0.472 -16.032   7.445  -1.171
+ -16.119   6.798  -0.892 -15.613   8.196 -17.129   8.324  15.361 -16.957   7.746
+  14.617 -17.635   9.047  14.990  -6.545  17.345  -9.188  -6.690  18.142  -9.697
+  -6.988  17.508  -8.355  -4.502   7.159  13.051  -3.964   7.922  13.265  -4.730
+   6.781  13.900  13.582  12.918  -7.947  13.369  13.850  -7.903  13.728  12.662
+  -7.036 -10.910  10.427   8.341 -10.731  11.358   8.206 -11.071  10.349   9.282
+  -9.667 -10.316  -4.689  -8.920 -10.865  -4.452  -9.843  -9.799  -3.903  -5.891
+  15.056 -16.320  -6.080  14.153 -16.576  -5.028  15.235 -16.692  -7.635 -14.215
+  11.522  -7.223 -15.074  11.421  -6.906 -13.620  11.699  11.805 -17.932 -12.538
+  12.140 -17.280 -13.153  10.853 -17.847 -12.594  -6.872  16.868  -5.273  -6.000
+  17.262  -5.241  -7.291  17.275  -6.032 -21.342  11.127  -6.050 -21.639  11.856
+  -5.504 -20.403  11.065  -5.876  16.820  -2.928  -7.236  17.053  -3.856  -7.228
+  15.864  -2.921  -7.194  18.459  -1.255   2.531  18.652  -1.901   1.851  19.240
+  -0.703   2.566 -13.551  -2.289 -10.160 -13.728  -2.518 -11.072 -12.633  -2.019
+ -10.154  -7.900  -3.939  11.077  -7.803  -3.532  11.938  -8.496  -4.673  11.226
+   6.509 -16.725  15.011   5.780 -16.463  15.574   6.106 -16.888  14.158  -9.644
+  -6.586  17.850  -9.414  -6.638  16.922  -8.922  -7.024  18.301  13.848   8.514
+  -7.366  13.661   7.873  -6.680  13.859   8.003  -8.175 -16.220  -3.526  -4.900
+ -15.842  -3.312  -5.753 -15.756  -2.961  -4.283  -6.730 -22.953  -6.356  -7.593
+ -23.002  -5.944  -6.401 -23.852  -6.329   4.515   8.773  13.798   3.648   8.722
+  14.201   4.620   9.697  13.573  -3.709  -4.138   9.447  -4.439  -3.658   9.057
+  -2.930  -3.655   9.172  14.271  -2.455  -2.679  14.926  -2.138  -2.057  14.470
+  -1.993  -3.493   1.437   2.489  -0.294   2.025   2.248  -1.010   0.565   2.488
+  -0.690  -6.567 -16.463   2.338  -7.338 -15.972   2.622  -5.879 -15.802   2.258
+  -9.156   5.958  -7.867  -8.626   6.301  -8.587  -9.799   5.391  -8.292 -13.201
+ -18.246  -2.288 -13.773 -17.529  -2.013 -12.699 -17.885  -3.019  13.413 -16.169
+ -10.309  13.873 -16.661 -10.990  12.670 -15.771 -10.761  -2.212  -6.449  -3.046
+  -2.495  -7.091  -3.697  -2.188  -5.619  -3.523  -8.325 -16.667 -10.861  -7.987
+ -16.553 -11.749  -7.595 -17.050 -10.374  -8.519  15.447  -9.621  -8.108  14.890
+  -8.960  -7.854  16.103  -9.829   5.269   1.471  16.928   5.726   2.023  17.562
+   4.939   0.736  17.445  -5.416  -0.921  12.133  -5.075  -1.789  12.350  -6.149
+  -0.795  12.735   6.816 -11.309 -14.350   5.901 -11.277 -14.630   7.301 -11.530
+ -15.146   7.452  -1.517  13.042   6.819  -2.224  12.914   8.267  -1.964  13.270
+   1.226  11.394  -9.858   2.094  11.620 -10.193   0.851  10.826 -10.531 -12.048
+  -7.096  -1.460 -12.068  -6.143  -1.549 -12.327  -7.258  -0.559  17.275   9.756
+ -11.525  16.362   9.684 -11.246  17.681   8.941 -11.231  -6.530  -6.198  14.742
+  -6.172  -6.729  14.030  -5.768  -5.766  15.126 -20.561 -14.135   3.894 -21.018
+ -14.831   3.421 -19.633 -14.344   3.789   3.908   3.159  10.214   2.956   3.057
+  10.245   4.043   4.079   9.987 -14.917 -12.565  -0.210 -15.596 -13.215  -0.031
+ -14.116 -12.951   0.146  14.420   0.159   3.373  14.559  -0.758   3.610  13.609
+   0.402   3.821 -10.492  -2.854 -13.241  -9.914  -2.308 -13.774 -11.216  -2.275
+ -13.003 -10.503 -17.190   9.074 -10.853 -17.945   8.601 -10.589 -17.425   9.997
+   4.246 -10.409  -4.742   5.178 -10.523  -4.554   3.892  -9.994  -3.956 -10.346
+   7.497 -18.591  -9.475   7.105 -18.657 -10.926   6.866 -19.016   5.026  -6.616
+   0.067   5.135  -7.560   0.182   5.733  -6.364  -0.526   6.396  -3.805 -23.971
+   6.580  -3.784 -23.032   5.668  -3.195 -24.086   8.816 -16.608  -4.885   9.200
+ -17.238  -4.276   7.930 -16.462  -4.554  -1.807  13.594  -6.723  -2.020  14.183
+  -7.447  -1.656  14.175  -5.978 -12.626  16.193  10.115 -12.768  15.947   9.201
+ -12.664  15.366  10.595  21.080   5.402 -11.150  21.173   4.699 -11.792  20.640
+   6.106 -11.627  16.630   8.026  13.490  16.588   7.840  14.428  15.920   8.649
+  13.337  17.436  -7.001 -16.179  16.495  -6.897 -16.038  17.816  -6.966 -15.301
+ -14.386   8.987  -4.964 -14.887   9.418  -5.656 -14.962   8.289  -4.651  -7.758
+ -22.438  -1.039  -8.263 -22.160  -1.803  -8.189 -23.242  -0.748 -16.394   6.350
+  13.506 -16.615   5.489  13.860 -15.449   6.315  13.361 -16.640  13.363  -2.458
+ -16.590  13.656  -3.368 -16.007  12.648  -2.401  -8.419   5.962 -21.901  -7.868
+   5.946 -21.119  -9.004   6.708 -21.767 -14.685  -3.022 -12.786 -15.056  -2.837
+ -13.649 -14.301  -3.894 -12.873 -16.035   2.441  11.259 -16.946   2.704  11.383
+ -15.709   2.280  12.145   3.367  -9.351  -2.247   2.618  -8.927  -1.827   4.126
+  -8.854  -1.940   8.442  -6.695 -22.576   8.823  -6.577 -21.706   7.510  -6.841
+ -22.412 -15.631  15.222   4.470 -15.379  16.028   4.019 -15.635  14.555   3.783
+  -7.414  -1.480   1.197  -8.178  -0.998   0.881  -6.759  -1.371   0.507   1.369
+ -21.183   5.528   2.127 -20.598   5.549   1.152 -21.260   4.599  -9.221  13.792
+  -3.749  -9.513  14.464  -4.364 -10.022  13.331  -3.501   6.049 -10.114  22.172
+   6.568  -9.930  22.956   6.563  -9.746  21.454  -5.221 -23.820  -2.927  -5.501
+ -22.960  -2.612  -6.022 -24.226  -3.258   6.397 -16.464  -2.909   5.591 -16.123
+  -2.522   6.122 -17.249  -3.383   2.314  -0.530 -22.254   1.545  -0.105 -22.633
+   2.727   0.151 -21.723 -13.673 -12.941   3.686 -14.549 -12.817   4.050 -13.470
+ -12.108   3.260  -0.355 -14.050   4.938   0.113 -14.465   5.661   0.127 -14.316
+   4.155  -7.578   2.729  -5.430  -8.459   2.736  -5.056  -7.138   2.000  -4.993
+  16.859  -8.848   0.615  17.254  -9.289   1.367  16.960  -9.470  -0.107  -8.312
+ -14.622   3.783  -7.877 -13.836   4.114  -8.044 -15.315   4.385 -12.342  -0.589
+ -18.111 -13.238  -0.526 -17.781 -12.131  -1.521 -18.057 -19.091 -10.839  -7.397
+ -19.445 -11.726  -7.331 -18.209 -10.958  -7.749 -15.555  10.428  16.229 -15.965
+   9.623  15.913 -14.635  10.195  16.355 -18.997  11.446  -3.964 -18.495  12.231
+  -4.182 -19.534  11.706  -3.216  -2.958   0.526 -21.734  -2.425   0.062 -21.089
+  -3.801   0.657 -21.300   6.640  13.203 -14.880   7.200  13.931 -15.149   7.171
+  12.422 -15.035   7.396  11.236  12.180   7.977  11.972  11.992   7.022  11.439
+  13.038  11.708 -13.011  13.139  10.808 -12.718  12.996  12.037 -12.443  13.835
+  14.231   9.300   0.535  14.337   9.339   1.486  14.929   8.715   0.240   5.618
+ -14.976   4.680   5.075 -15.378   5.359   6.403 -15.523   4.646 -18.730   1.102
+  -1.257 -19.052   0.851  -2.123 -19.435   0.855  -0.658 -11.171 -21.537   8.149
+ -10.476 -21.215   8.723 -10.731 -22.149   7.560   3.931   3.231 -18.328   3.027
+   3.373 -18.609   4.459   3.467 -19.091 -13.881  -8.734  -2.643 -14.397  -9.015
+  -1.888 -13.297  -8.059  -2.297   4.924 -20.006  15.511   4.754 -20.895  15.199
+   4.919 -19.469  14.719  -0.796   3.207 -21.084  -0.455   2.428 -21.522  -0.208
+   3.912 -21.356  -0.757  -5.147  11.717  -0.543  -5.748  11.003  -1.195  -4.412
+  11.287   0.218 -22.640   0.215   0.856 -22.698  -0.496  -0.325 -21.885  -0.012
+  -7.687  -4.063   2.145  -8.312  -4.313   1.464  -7.558  -3.123   2.017   1.755
+ -20.950  -4.493   2.323 -21.700  -4.318   1.969 -20.692  -5.390  -7.748 -12.194
+   4.885  -7.525 -11.834   5.743  -7.030 -11.919   4.315  -6.865   1.505  -1.661
+  -7.653   0.965  -1.607  -6.199   1.004  -1.190   1.775  -4.672  -5.821   2.325
+  -5.447  -5.702   2.190  -4.000  -5.280  -7.078  17.627  11.185  -7.813  17.074
+  10.918  -6.592  17.091  11.812 -14.271   6.752   0.505 -14.071   7.527   1.030
+ -13.513   6.180   0.624  -4.314 -14.721   2.956  -4.394 -14.270   3.797  -3.604
+ -15.349   3.088   4.509  -1.703 -23.888   3.755  -1.157 -23.665   5.230  -1.335
+ -23.376  -7.179  10.182  13.033  -7.751  10.361  13.779  -6.328  10.536  13.291
+ -18.891  -6.951  12.034 -19.597  -7.597  12.007 -18.091  -7.466  11.931  -1.840
+  17.955   6.227  -1.908  17.042   6.507  -0.932  18.050   5.940   0.339  16.148
+ -11.147   0.645  16.182 -10.241   0.796  15.397 -11.526  -4.324 -22.729  10.013
+  -4.732 -22.989   9.187  -3.551 -22.229   9.751  15.092  -0.741  15.553  14.659
+  -1.562  15.784  15.749  -0.616  16.238   1.224   1.352  14.756   0.615   0.952
+  15.376   0.855   1.153  13.895 -11.618  16.108   4.365 -12.574  16.132   4.328
+ -11.410  16.230   5.291  -7.664  -0.182   7.597  -8.443  -0.485   8.064  -7.989
+   0.085   6.737   2.540  -5.340   9.633   2.957  -5.477   8.782   2.628  -4.401
+   9.796
+  42.437  42.437  42.437

From 4c271f38bd4c336982bbee3b98dbce6c410f958b Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 5 Mar 2026 12:44:08 -0500
Subject: [PATCH 1471/1492] Combine into the existing test dir

---
 .../Edpdp.dat.save                            |  0
 .../Esander.dat.save                          |  0
 test/Test_Esander_Short/RunTest.sh            | 57 ++++++++++++++++---
 .../force.crd.save                            |  0
 test/Test_Esander_short/RunTest.sh            | 52 -----------------
 5 files changed, 50 insertions(+), 59 deletions(-)
 rename test/{Test_Esander_short => Test_Esander_Short}/Edpdp.dat.save (100%)
 rename test/{Test_Esander_short => Test_Esander_Short}/Esander.dat.save (100%)
 rename test/{Test_Esander_short => Test_Esander_Short}/force.crd.save (100%)
 delete mode 100755 test/Test_Esander_short/RunTest.sh

diff --git a/test/Test_Esander_short/Edpdp.dat.save b/test/Test_Esander_Short/Edpdp.dat.save
similarity index 100%
rename from test/Test_Esander_short/Edpdp.dat.save
rename to test/Test_Esander_Short/Edpdp.dat.save
diff --git a/test/Test_Esander_short/Esander.dat.save b/test/Test_Esander_Short/Esander.dat.save
similarity index 100%
rename from test/Test_Esander_short/Esander.dat.save
rename to test/Test_Esander_Short/Esander.dat.save
diff --git a/test/Test_Esander_Short/RunTest.sh b/test/Test_Esander_Short/RunTest.sh
index 59dde320ed..26ba713011 100755
--- a/test/Test_Esander_Short/RunTest.sh
+++ b/test/Test_Esander_Short/RunTest.sh
@@ -2,22 +2,65 @@
 
 . ../MasterTest.sh
 
-CleanFiles esander.in gb.dat pme.dat
+CleanFiles esander.in gb.dat pme.dat Esander.dat force.crd Edpdp.dat CpptrajEsander.parm7 NoWat.dat
 
+INPUT='-i esander.in'
 TESTNAME='Energy via sander API short tests (GB/PME)'
-Requires sanderlib maxthreads 1
+Requires sanderlib maxthreads 10
 
-INPUT='-i esander.in'
-cat > esander.in <<EOF
+UNITNAME='Short libsander tests'
+CheckFor maxthreads 1
+if [ $? -eq 0 ] ; then
+  cat > esander.in <<EOF
 parm ../Test_Hbond/strip.4lztSc_nowat.parm7
 trajin ../Test_Hbond/strip.4lztSc.rst7
 esander 4lztSc out gb.dat \
   saltcon 1.0 cut 9999.0 gbsa 1 igb 1 ntb 0
 esander PME out pme.dat
 EOF
-RunCpptraj "$TESTNAME"
-DoTest gb.dat.save gb.dat
-DoTest pme.dat.save pme.dat
+  RunCpptraj "$UNITNAME"
+  DoTest gb.dat.save gb.dat
+  DoTest pme.dat.save pme.dat
+fi
+
+# Set to 1 if compiled with -DCPPTRAJ_ESANDER_ENERGY_ORDER
+NEWORDER=0
+if [ $NEWORDER -eq 1 ] ; then
+  SAVEPREFIX='neworder.'
+else
+  SAVEPREFIX=''
+fi
+
+TestPME() {
+  UNITNAME='Short SANDER energy test, PME'
+  CheckFor netcdf maxthreads 3
+  if [ $? -eq 0 ] ; then
+    cat > esander.in <<EOF
+parm ../tz2.truncoct.parm7
+trajin ../tz2.truncoct.nc 1 3
+esander S out Esander.dat saveforces
+trajout force.crd
+EOF
+    RunCpptraj "$UNITNAME"
+    DoTest "$SAVEPREFIX"Esander.dat.save Esander.dat
+    DoTest force.crd.save force.crd
+  fi
+}
+
+TestGB() {
+  UNITNAME="Short SANDER energy test, GB"
+  CheckFor netcdf maxthreads 10
+  cat > esander.in <<EOF
+parm ../DPDP.parm7
+trajin ../DPDP.nc 1 10
+esander DPDP out Edpdp.dat gbsa 1
+EOF
+  RunCpptraj "$UNITNAME"
+  DoTest "$SAVEPREFIX"Edpdp.dat.save Edpdp.dat
+}
+
+TestGB
+TestPME
 
 EndTest
 exit 0
diff --git a/test/Test_Esander_short/force.crd.save b/test/Test_Esander_Short/force.crd.save
similarity index 100%
rename from test/Test_Esander_short/force.crd.save
rename to test/Test_Esander_Short/force.crd.save
diff --git a/test/Test_Esander_short/RunTest.sh b/test/Test_Esander_short/RunTest.sh
deleted file mode 100755
index 4cfb52cbff..0000000000
--- a/test/Test_Esander_short/RunTest.sh
+++ /dev/null
@@ -1,52 +0,0 @@
-#!/bin/bash
-
-. ../MasterTest.sh
-
-CleanFiles ene.in Esander.dat force.crd Edpdp.dat CpptrajEsander.parm7 NoWat.dat
-TESTNAME='SANDER energy tests (short)'
-Requires sanderlib netcdf
-
-# Set to 1 if compiled with -DCPPTRAJ_ESANDER_ENERGY_ORDER
-NEWORDER=0
-if [ $NEWORDER -eq 1 ] ; then
-  SAVEPREFIX='neworder.'
-else
-  SAVEPREFIX=''
-fi
-
-INPUT="-i ene.in"
-
-TestPME() {
-  UNITNAME='Short SANDER energy test, PME'
-  CheckFor maxthreads 3
-  if [ $? -eq 0 ] ; then
-    cat > ene.in <<EOF
-parm ../tz2.truncoct.parm7
-trajin ../tz2.truncoct.nc 1 3
-esander S out Esander.dat saveforces
-trajout force.crd
-EOF
-    RunCpptraj "$UNITNAME"
-    DoTest "$SAVEPREFIX"Esander.dat.save Esander.dat
-    DoTest force.crd.save force.crd
-  fi
-}
-
-TestGB() {
-  UNITNAME="Short SANDER energy test, GB"
-  CheckFor maxthreads 10
-  cat > ene.in <<EOF
-parm ../DPDP.parm7
-trajin ../DPDP.nc 1 10
-esander DPDP out Edpdp.dat gbsa 1
-EOF
-  RunCpptraj "$UNITNAME"
-  DoTest "$SAVEPREFIX"Edpdp.dat.save Edpdp.dat
-}
-
-
-TestGB
-TestPME
-
-EndTest
-exit 0

From ceafe37e4e3d2005d6d9dcc47baa24a97f39f621 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 5 Mar 2026 12:58:06 -0500
Subject: [PATCH 1472/1492] Add missing inits

---
 src/Energy_Sander.cpp | 26 +++++++++++++++++++++++++-
 1 file changed, 25 insertions(+), 1 deletion(-)

diff --git a/src/Energy_Sander.cpp b/src/Energy_Sander.cpp
index 6331e343cb..2b55538128 100644
--- a/src/Energy_Sander.cpp
+++ b/src/Energy_Sander.cpp
@@ -132,10 +132,34 @@ void Energy_Sander::SetDefaultInput() {
   input_.fswitch = -1.0;
   input_.restraint_wt = 0.0;
 
+  input_.ala = 0.0;
+  input_.arg = 0.0;
+  input_.asn = 0.0;
+  input_.asp = 0.0;
+  input_.cys = 0.0;
+  input_.gln = 0.0;
+  input_.glu = 0.0;
+  input_.gly = 0.0;
+  input_.his = 0.0;
+  input_.hip = 0.0;
+  input_.ile = 0.0;
+  input_.leu = 0.0;
+  input_.lys = 0.0;
+  input_.met = 0.0;
+  input_.phe = 0.0;
+  input_.pro = 0.0;
+  input_.ser = 0.0;
+  input_.thr = 0.0;
+  input_.triptophan = 0.0;
+  input_.tyr = 0.0;
+  input_.valine = 0.0;
+  input_.bb = 0.0;
+
   input_.igb = 0;
   input_.alpb = 0;
   input_.gbsa = 0;
   input_.lj1264 = -1;
+  input_.plj1264 = -1;
   input_.ipb = 0;
   input_.inp = 2;
   input_.vdwmeth = 1;
@@ -155,7 +179,7 @@ void Energy_Sander::SetDefaultInput() {
 
 const char* Energy_Sander::supportedNamelist_ = 
 "extdiel intdiel rgbmax saltcon cut dielc igb alpb gbsa lj1264 ipb inp vdwmeth ew_type ntb";
- 
+
 /** Check and set input for Sander.*/
 int Energy_Sander::SetInput(ArgList& argIn) {
   SetDefaultInput();

From 298c45d46de5c2c8bf6cc327cf7b5969bca63d40 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 5 Mar 2026 13:08:11 -0500
Subject: [PATCH 1473/1492] Add missing init of sander var

---
 src/Energy_Sander.cpp | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/Energy_Sander.cpp b/src/Energy_Sander.cpp
index 2b55538128..afbf3cb8e0 100644
--- a/src/Energy_Sander.cpp
+++ b/src/Energy_Sander.cpp
@@ -171,6 +171,7 @@ void Energy_Sander::SetDefaultInput() {
   input_.ntc = 2;
   input_.ntr = 0;
   input_.ibelly = 0;
+  input_.mask_from_ref = 0;
 
   input_.restraintmask[0] = '\0';
   input_.bellymask[0] = '\0';

From a1d938b405a4eff115f7904bd92e8b450b23cc8f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 5 Mar 2026 13:09:54 -0500
Subject: [PATCH 1474/1492] Update manual pdf

---
 doc/CpptrajManual.pdf     | Bin 964643 -> 970940 bytes
 doc/DocumentChecksums.txt |   2 +-
 2 files changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/CpptrajManual.pdf b/doc/CpptrajManual.pdf
index 563863eaed620e08c18d9e06afe77441b40598bb..39a6312985da1ac8641a6dc5a680e3c464b55f86 100644
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diff --git a/doc/DocumentChecksums.txt b/doc/DocumentChecksums.txt
index 49ab11ff36..e3cc3e7082 100644
--- a/doc/DocumentChecksums.txt
+++ b/doc/DocumentChecksums.txt
@@ -1,3 +1,3 @@
 f6f8cb1a79951d80a9d2656fd9c30f55  CpptrajDevelopmentGuide.lyx
-ad83256a537dde12e3067e100b2e6a3a  cpptraj.lyx
+b2a805e16d88a4e9884e279000505614  cpptraj.lyx
 5d9b5b5ed47a3ded57b6464df99b3585  CpptrajManual.lyx

From 4ed7c4c92ed38db4015f6809f9057fd9feebb1b4 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 5 Mar 2026 13:38:44 -0500
Subject: [PATCH 1475/1492] Expand the build section of the manual

---
 doc/CpptrajManual.pdf     | Bin 970940 -> 974821 bytes
 doc/DocumentChecksums.txt |   2 +-
 doc/cpptraj.lyx           | 189 ++++++++++++++++++++++++++++++++++++++
 3 files changed, 190 insertions(+), 1 deletion(-)

diff --git a/doc/CpptrajManual.pdf b/doc/CpptrajManual.pdf
index 39a6312985da1ac8641a6dc5a680e3c464b55f86..b8b67311ac48104dfc38a1e4a1308078d4eb6b39 100644
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diff --git a/doc/DocumentChecksums.txt b/doc/DocumentChecksums.txt
index e3cc3e7082..5cc715037f 100644
--- a/doc/DocumentChecksums.txt
+++ b/doc/DocumentChecksums.txt
@@ -1,3 +1,3 @@
 f6f8cb1a79951d80a9d2656fd9c30f55  CpptrajDevelopmentGuide.lyx
-b2a805e16d88a4e9884e279000505614  cpptraj.lyx
+769452881b024e967b9f714297ba6305  cpptraj.lyx
 5d9b5b5ed47a3ded57b6464df99b3585  CpptrajManual.lyx
diff --git a/doc/cpptraj.lyx b/doc/cpptraj.lyx
index f2b4b1c154..31f61e856a 100644
--- a/doc/cpptraj.lyx
+++ b/doc/cpptraj.lyx
@@ -7759,6 +7759,188 @@ fixatomorder
 'doassembly'
 \series default
  keyword is specified it can create macromolecular assemblies from PDBs with multiple models.
+ The build procedure is similar to that of LEaP,
+ but CPPTRAJ's build tends to be faster and more robust,
+ particularly for large systems and/or system containing CMAP terms.
+ Note that since LEaP uses an imprecise value of PI compared to CPPTRAJ/sander/pmemd,
+ the topologies produced by CPPTRAJ will have slight differences in any terms involving PI (e.g.
+ angles,
+ dihedrals,
+ etc).
+ For 1:1 direct comparison to LEaP topologies,
+ CPPTRAJ can be compiled using LEaP's value of PI by configuring with the '-leappi' configure flag,
+ which activates the CPPTRAJ_USE_LEAP_PI compiler define.
+ Note also that CPPTRAJ retains PDB information (chain ID,
+ original residue number,
+ Bfactor/Occupancy etc) which is printed to the output Topology.
+ The parameter files used are also printed to the output Topology in the FORCE_FIELD_TYPE section.
+\end_layout
+
+\begin_layout Standard
+The output from the 
+\series bold
+\emph on
+build
+\series default
+\emph default
+ command tends to be more verbose than LEaP and is grouped into several phases:
+\end_layout
+
+\begin_layout Enumerate
+Input coordinates details and general parameters.
+ This is where the input coordinates will be cleaned up if needed (similar to 
+\series bold
+\emph on
+prepareforleap
+\series default
+\emph default
+,
+ see 
+\begin_inset CommandInset ref
+LatexCommand vref
+reference "subsec:cpptraj-prepareforleap"
+plural "false"
+caps "false"
+noprefix "false"
+nolink "false"
+
+\end_inset
+
+).
+\end_layout
+
+\begin_layout Enumerate
+Getting templates and parameters.
+ If no templates/parameters were specified,
+ all available templates and parameters will be used.
+ If multiple parameter sets are available they will be combined,
+ with later parameter sets having priority over earlier parameter sets.
+\end_layout
+
+\begin_layout Enumerate
+Structure preparation.
+ This is where histidine protonation states will be determined (if hydrogens are present),
+ disulfide bonds will be searched for,
+ and sugars will be prepared (see 
+\begin_inset CommandInset ref
+LatexCommand vref
+reference "subsec:cpptraj-prepareforleap"
+plural "false"
+caps "false"
+noprefix "false"
+nolink "false"
+
+\end_inset
+
+).
+\end_layout
+
+\begin_layout Enumerate
+Match residues to templates and build missing atoms.
+ Note that unlike LEaP,
+ if an atom name is not recognized within a residue that has a template,
+ that atom will be ignored and built back in using the template unless 
+\series bold
+keepmissingatoms
+\series default
+ is specified.
+ After all atoms are built and linked,
+ CPPTRAJ will ensure that atoms within molecules are contiguous (like 
+\series bold
+\emph on
+fixatomorder
+\series default
+\emph default
+,
+ see 
+\begin_inset CommandInset ref
+LatexCommand vref
+reference "subsec:cpptraj-fixatomorder"
+plural "false"
+caps "false"
+noprefix "false"
+nolink "false"
+
+\end_inset
+
+) unless 
+\series bold
+nofixorder
+\series default
+ is specified.
+\end_layout
+
+\begin_layout Enumerate
+Solvate/add ions.
+ If 
+\series bold
+solvatebox
+\series default
+/
+\series bold
+solvateoct
+\series default
+ and optionally 
+\series bold
+addionsrand
+\series default
+ is specified,
+ solvent/ions will be added to the system.
+ Note that the neutralization argument (i.e.
+ number of ions equal to zero) can be specified for either ion1,
+ ion2,
+ or both.
+ Note that currently CPPTRAJ does not support adding ions if no solvent has been added.
+\end_layout
+
+\begin_layout Enumerate
+Parameter assignment.
+ Here parameters will be assigned based on the atom types in templates.
+ The gb keyword can be used to pick the GB radii set used.
+ The lj1264 keyword and associated keywords can be used to add Lennard-Jones C coefficients if the loaded force field supports them.
+\end_layout
+
+\begin_layout Enumerate
+Structure check.
+ Here the final structure will be checked for long bonds,
+ overlaps,
+ and ring intersections (like the 
+\series bold
+\emph on
+checkstructure
+\series default
+\emph default
+ Action,
+ see 
+\begin_inset CommandInset ref
+LatexCommand vref
+reference "subsec:cpptraj-check"
+plural "false"
+caps "false"
+noprefix "false"
+nolink "false"
+
+\end_inset
+
+).
+ CPPTRAJ will also check if there were missing residues and for problems with the overall system charge.
+ Problems can be redirected to another file with the 
+\series bold
+reportfile
+\series default
+ keyword,
+ otherwise they will be printed to the standard output.
+\end_layout
+
+\begin_layout Enumerate
+File output.
+ If parmout/crdout were specified,
+ prints details on the file writes.
+\end_layout
+
+\begin_layout Enumerate
+Timing data.
+ Will print detailed timing data for each phase.
 \end_layout
 
 \begin_layout Subsubsection*
@@ -31087,6 +31269,13 @@ nolink "false"
 
 \begin_layout Subsection
 fixatomorder
+\begin_inset CommandInset label
+LatexCommand label
+name "subsec:cpptraj-fixatomorder"
+
+\end_inset
+
+
 \end_layout
 
 \begin_layout LyX-Code

From fe3f98f4c16ca1ba8849d810f1390182f04a44a5 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Thu, 5 Mar 2026 14:58:32 -0500
Subject: [PATCH 1476/1492] Fix checkstructure in parallel

---
 src/Action_CheckStructure.cpp | 2 +-
 src/StructureCheck.cpp        | 8 ++++++++
 src/StructureCheck.h          | 4 ++++
 3 files changed, 13 insertions(+), 1 deletion(-)

diff --git a/src/Action_CheckStructure.cpp b/src/Action_CheckStructure.cpp
index 299fe0a3f1..6a41fa7701 100644
--- a/src/Action_CheckStructure.cpp
+++ b/src/Action_CheckStructure.cpp
@@ -300,7 +300,7 @@ void Action_CheckStructure::Print() {
       DataSet_integer const& A2 = static_cast<DataSet_integer const&>( *ds_a2_ );
       DataSet_string  const& N2 = static_cast<DataSet_string  const&>( *ds_n2_ );
       DataSet_double  const& DV = static_cast<DataSet_double  const&>( *ds_d_  );
-      outfile_->Printf(Fmt_[PT[idx]], FN[idx], A1[idx], N1[idx].c_str(),
+      outfile_->Printf(StructureCheck::WriteFmt( PT[idx] ), FN[idx], A1[idx], N1[idx].c_str(),
                        A2[idx], N2[idx].c_str(), DV[idx]);
     }
   }
diff --git a/src/StructureCheck.cpp b/src/StructureCheck.cpp
index 7ed1ea3ffb..812b520c0d 100644
--- a/src/StructureCheck.cpp
+++ b/src/StructureCheck.cpp
@@ -1011,6 +1011,14 @@ const char* StructureCheck::Fmt_[] = {
   "%i\t Warning: Bond involving atom %i:%s intersects ring involving atom %i:%s (%.2f)\n" ///< F_RING
 };
 
+#ifdef MPI
+/** \return Format string of given type, for writing in parallel. */
+const char* StructureCheck::WriteFmt(int idx) {
+  if (idx < 0 || idx > (int)F_RING) return 0;
+  return Fmt_[idx];
+}
+#endif
+
 /** Write formats for problems, no frame number. */
 const char* StructureCheck::NoFrameFmt_[] = {
   "Warning: Atoms %i:%s and %i:%s are close (%.2f)\n",    ///< F_ATOM
diff --git a/src/StructureCheck.h b/src/StructureCheck.h
index d3ea7ed9ad..3c29b2426c 100644
--- a/src/StructureCheck.h
+++ b/src/StructureCheck.h
@@ -54,6 +54,10 @@ class StructureCheck {
     void WriteProblemsToFile(CpptrajFile*, int, Topology const&) const;
     /// Write existing problems to the given file, no frame number
     void WriteProblemsToFile(CpptrajFile*, Topology const&) const;
+#   ifdef MPI
+    /// \return Format string of given type, for writing in parallel
+    static const char* WriteFmt(int);
+#   endif
     /// Print timing data to stdout
     void PrintTiming(int, double) const;
     /// Format of problems currently stored in problemAtoms_

From eb2349ef5f041497b988c1b5b86f14f0f78ac59d Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 5 Mar 2026 19:20:32 -0500
Subject: [PATCH 1477/1492] Add a bunch of missing variables in printf
 statements

---
 src/AmberParamFile.cpp     | 2 +-
 src/DataIO_AmberLib.cpp    | 2 +-
 src/DataIO_LeapRC.cpp      | 2 +-
 src/Exec_Build.cpp         | 2 +-
 src/Parm/LJ1264_Params.cpp | 2 +-
 src/Topology.cpp           | 2 +-
 6 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index bf2cf477d6..6e0398e529 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -1117,7 +1117,7 @@ int AmberParamFile::WriteParams(ParameterSet& prm, FileName const& fname) const
   {
     std::string asym = at->first[0].Truncated();
     if (asym.size() > 2)
-      mprintf("Warning: Atom symbol %s is larger than 2 characters, which breaks Amber FF format.\n");
+      mprintf("Warning: Atom symbol %s is larger than 2 characters, which breaks Amber FF format.\n", asym.c_str());
     outfile.Printf("%-2s", asym.c_str());
     if (at->second.Mass() < 10.0)
       outfile.Printf(" %-10.3f", at->second.Mass());
diff --git a/src/DataIO_AmberLib.cpp b/src/DataIO_AmberLib.cpp
index 7bc04c649b..f93c8e2af4 100644
--- a/src/DataIO_AmberLib.cpp
+++ b/src/DataIO_AmberLib.cpp
@@ -114,7 +114,7 @@ int DataIO_AmberLib::ReadData(FileName const& fname, DataSetList& dsl, std::stri
         dsl.RemoveSet( set );
         ds = (DataSet_Coords*)dsl.AddSet( DataSet::COORDS, meta );
       } else {
-        mprinterr("Error: Set %s already exists and 'allowoverwrite' not specified.\n");
+        mprinterr("Error: Set %s already exists and 'allowoverwrite' not specified.\n", dsname.c_str());
         return 1;
       }
       if (ds == 0) {
diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 84fc97fab0..e121dedc0d 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -799,7 +799,7 @@ const
   }
 
   if (crd.Size() > 1)
-    mprintf("Warning: '%s' has more than 1 frame. Only using first frame.\n");
+    mprintf("Warning: '%s' has more than 1 frame. Only using first frame.\n", crdName.c_str());
 
   Trajout_Single trajOut;
   ArgList tmpargs;
diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 3ad61451cc..c585fc78a3 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -923,7 +923,7 @@ int Exec_Build::createAssembly(Topology& topIn, Frame& frameIn,
 const
 {
   if (CRDIN.Size() < 2) {
-    mprintf("Warning: Only %zu frames in COORDS set '%s'; no assembly needed.\n");
+    mprintf("Warning: Only %zu frames in COORDS set '%s'; no assembly needed.\n", CRDIN.Size(), CRDIN.legend());
     frameIn = CRDIN.AllocateFrame();
     CRDIN.GetFrame(0, frameIn);
     topIn = CRDIN.Top();
diff --git a/src/Parm/LJ1264_Params.cpp b/src/Parm/LJ1264_Params.cpp
index 130bdad224..4726a0a49d 100644
--- a/src/Parm/LJ1264_Params.cpp
+++ b/src/Parm/LJ1264_Params.cpp
@@ -595,7 +595,7 @@ int LJ1264_Params::AssignLJ1264(Topology& topOut)
   mprintf("\tAssigning LJ 12-6-4 parameters.\n");
   // Must already have nonbond info
   if (!topOut.Nonbond().HasNonbond()) {
-    mprinterr("Error: Topology %s does not have LJ A/B nonbond parameters; required before setting LJ 12-6-4 nonbond parameters.\n");
+    mprinterr("Error: Topology %s does not have LJ A/B nonbond parameters; required before setting LJ 12-6-4 nonbond parameters.\n", topOut.c_str());
     return 1;
   }
   if (topOut.SetupIntegerMask( mask_ )) {
diff --git a/src/Topology.cpp b/src/Topology.cpp
index e1077dbdd3..e3142ef857 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -493,7 +493,7 @@ int Topology::addTopAtom(Atom const& atomIn, Residue const& resIn,
   AddTopAtom(atomIn, resIn);
   atoms_.back().SetMol( molnum );
   if (molnum > molecules_.size())
-    mprintf("Warning: AddTopAtom(): Molecule number %i is not consecutive.\n");
+    mprintf("Warning: AddTopAtom(): Molecule number %i is not consecutive.\n", molnum+1);
   if (molnum >= molecules_.size()) {
     molecules_.resize( molnum+1 );
     if (isSolvent)

From fc464a13c7b26e84fe88d6b7b787d6dc902d0076 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Thu, 5 Mar 2026 19:28:38 -0500
Subject: [PATCH 1478/1492] 12-6-4 tests need PME

---
 test/Test_EneDecomp/RunTest.sh | 2 +-
 test/Test_Energy/RunTest.sh    | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/Test_EneDecomp/RunTest.sh b/test/Test_EneDecomp/RunTest.sh
index 887b13e6e7..321c18259a 100755
--- a/test/Test_EneDecomp/RunTest.sh
+++ b/test/Test_EneDecomp/RunTest.sh
@@ -73,7 +73,7 @@ EOF
 fi
 
 UNITNAME='LJ 12-6-4 decomposition'
-CheckFor maxthreads 1
+CheckFor libpme maxthreads 1
 if [ $? -eq 0 ] ; then
   cat > enedecomp.in <<EOF
 parm ../1d23.tip3p.lj1264.parm7
diff --git a/test/Test_Energy/RunTest.sh b/test/Test_Energy/RunTest.sh
index 9cb4dd0e82..eaaad9b2a5 100755
--- a/test/Test_Energy/RunTest.sh
+++ b/test/Test_Energy/RunTest.sh
@@ -59,7 +59,7 @@ EOF
 fi
 
 UNITNAME='Test LJ 12-6-4 energy'
-CheckFor maxthreads 1
+CheckFor libpme maxthreads 1
 if [ $? -eq 0 ] ; then
   cat > ene.in <<EOF
 parm ../1d23.tip3p.lj1264.parm7

From 0af425c0f8dee0157518053ca88281f97bfd8c1c Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 6 Mar 2026 08:39:03 -0500
Subject: [PATCH 1479/1492] Support more default options

---
 src/DataSet_LeapOpts.cpp | 45 +++++++++++++++++++++++++++++++++++++++-
 src/DataSet_LeapOpts.h   | 12 +++++++++++
 2 files changed, 56 insertions(+), 1 deletion(-)

diff --git a/src/DataSet_LeapOpts.cpp b/src/DataSet_LeapOpts.cpp
index ec1e8c6a78..6c2a011fcd 100644
--- a/src/DataSet_LeapOpts.cpp
+++ b/src/DataSet_LeapOpts.cpp
@@ -5,7 +5,11 @@
 DataSet_LeapOpts::DataSet_LeapOpts() :
   // 0 dim indicates DataSet-specific write
   DataSet(LEAPOPTS, GENERIC, TextFormat(TextFormat::STRING, 12, 0), 0),
-  pbradii_(Cpptraj::Parm::MBONDI)
+  pbradii_(Cpptraj::Parm::MBONDI),
+  scee_(1.2), // AMBER default
+  scnb_(2.0), // AMBER default
+  dipoleDampFactor_(0),
+  ipol_(0)
 {
 
 }
@@ -21,3 +25,42 @@ int DataSet_LeapOpts::SetGbRadii(std::string const& keyword) {
   mprintf("\tSet default GB radii: %s\n", Cpptraj::Parm::GbAmberFlag(pbradii_).c_str());
   return 0;
 }
+
+/// Set double option, warn if negative
+static inline int set_dopt(const char* desc, double& opt, double newVal)
+{
+  if (newVal < 0.0) {
+    mprintf("Warning: Illegal value: %s can not be < 0.0;\n"
+            "Warning: keeping value of %g\n", desc, opt);
+    return 1;
+  } else {
+    mprintf("\tSetting %s to %g\n", newVal);
+    opt = newVal;
+  }
+  return 0;
+}
+
+/** Set default SCEE */
+int DataSet_LeapOpts::SetSCEE(double sceeIn) { return set_dopt("1-4 SCEE factor", scee_, sceeIn); }
+
+/** Set default SCNB */
+int DataSet_LeapOpts::SetSCNB(double scnbIn) { return set_dopt("1-4 SCNB factor", scnb_, scnbIn); }
+
+/** Set dipole damping factor */
+int DataSet_LeapOpts::SetDipoleDampFactor(double ddfIn) { return set_dopt("Dipole damping factor", dipoleDampFactor_, ddfIn); }
+
+/** Set IPOL */
+int DataSet_LeapOpts::SetIpol(int ipolIn) {
+  if (ipolIn < 0 || ipolIn > 4) {
+    mprintf("Warning: Only IPOL = 0 to 4 is supported, resetting IPOL to %i.\n", ipol_);
+    return 1;
+  }
+  if (ipol_ > 0) {
+    mprintf("Warning: IPOL has already been set to %i by a previous force field.\n", ipol_);
+    return 1;
+  }
+  mprintf("\tSetting IPOL to %i\n", ipolIn);
+  ipol_ = ipolIn;
+  return 0;
+}
+
diff --git a/src/DataSet_LeapOpts.h b/src/DataSet_LeapOpts.h
index 984bfece0e..2de11bed28 100644
--- a/src/DataSet_LeapOpts.h
+++ b/src/DataSet_LeapOpts.h
@@ -20,9 +20,21 @@ class DataSet_LeapOpts : public DataSet {
 #   endif
     // -------------------------------------------
     int SetGbRadii(std::string const&);
+    int SetSCEE(double);
+    int SetSCNB(double);
+    int SetDipoleDampFactor(double);
+    int SetIpol(int);
 
     Cpptraj::Parm::GB_RadiiType PbRadii() const { return pbradii_; }
+    double SCEE() const { return scee_; }
+    double SCNB() const { return scnb_; }
+    double DipoleDampFactor() const { return dipoleDampFactor_; }
+    int IPOL() const { return ipol_; }
   private:
     Cpptraj::Parm::GB_RadiiType pbradii_;
+    double scee_;
+    double scnb_;
+    double dipoleDampFactor_;
+    int ipol_;
 };
 #endif

From 129a5ad0618d047f7fe832fc85f528aa3f3c889f Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 6 Mar 2026 08:58:13 -0500
Subject: [PATCH 1480/1492] Make unhandled set or set default options in leaprc
 files an error. Read more set default options

---
 src/DataIO_LeapRC.cpp    | 26 ++++++++++++++++++++++++--
 src/DataSet_LeapOpts.cpp | 14 ++++++++++++--
 src/DataSet_LeapOpts.h   |  3 +++
 3 files changed, 39 insertions(+), 4 deletions(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index e121dedc0d..75cd7e292c 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -690,11 +690,33 @@ int DataIO_LeapRC::LeapSet(ArgList const& argIn, DataSetList& dsl) const {
         return 1;
       } else
         mprintf("Warning: Skipping unrecognized 'set default cmap' mode: %s\n", argIn[3].c_str());
+    } else if ( ToLower(argIn[2]) == "dipole_damp_factor" ) {
+      if (OPTS.SetDipoleDampFactor( convertToDouble(argIn[3]) )) {
+        mprinterr("Error: Could not set dipole_damp_factor.\n");
+        return 1;
+      }
+    } else if ( ToLower(argIn[2]) == "sceescalefactor" ) {
+      if (OPTS.SetSCEE( convertToDouble(argIn[3]) )) {
+        mprinterr("Error: Could not set sceescalefactor.\n");
+        return 1;
+      }
+    } else if ( ToLower(argIn[2]) == "scnbscalefactor" ) {
+      if (OPTS.SetSCNB( convertToDouble(argIn[3]) )) {
+        mprinterr("Error: Could not set scnbscalefactor.\n");
+        return 1;
+      }
+    } else if (ToLower(argIn[2]) == "ipol" ) {
+      if (OPTS.SetIpol( convertToInteger(argIn[3]) )) {
+        mprinterr("Error: Could not set IPOL\n");
+        return 1;
+      }
     } else {
-      mprintf("Warning: Unhandled 'set default' command: %s\n", argIn.ArgLine());
+      mprinterr("Error: Unhandled 'set default' command: %s\n", argIn.ArgLine());
+      return 1;
     }
   } else {
-    mprintf("Warning: Unhandled 'set' command: %s\n", argIn.ArgLine());
+    mprinterr("Error: Unhandled 'set' command: %s\n", argIn.ArgLine());
+    return 1;
   }
 
   return 0;
diff --git a/src/DataSet_LeapOpts.cpp b/src/DataSet_LeapOpts.cpp
index 6c2a011fcd..18b1dd6ec6 100644
--- a/src/DataSet_LeapOpts.cpp
+++ b/src/DataSet_LeapOpts.cpp
@@ -9,7 +9,8 @@ DataSet_LeapOpts::DataSet_LeapOpts() :
   scee_(1.2), // AMBER default
   scnb_(2.0), // AMBER default
   dipoleDampFactor_(0),
-  ipol_(0)
+  ipol_(0),
+  flexibleWater_(false)
 {
 
 }
@@ -34,7 +35,7 @@ static inline int set_dopt(const char* desc, double& opt, double newVal)
             "Warning: keeping value of %g\n", desc, opt);
     return 1;
   } else {
-    mprintf("\tSetting %s to %g\n", newVal);
+    mprintf("\tSetting %s to %g\n", desc, newVal);
     opt = newVal;
   }
   return 0;
@@ -64,3 +65,12 @@ int DataSet_LeapOpts::SetIpol(int ipolIn) {
   return 0;
 }
 
+/** Set flexible water */
+int DataSet_LeapOpts::SetFlexibleWater(bool fIn) {
+  if (fIn)
+    mprintf("\tSetting flexible water to ON\n");
+  else
+    mprintf("\tSetting flexible water to OFF\n");
+  flexibleWater_ = fIn;
+  return 0;
+}
diff --git a/src/DataSet_LeapOpts.h b/src/DataSet_LeapOpts.h
index 2de11bed28..249ad79450 100644
--- a/src/DataSet_LeapOpts.h
+++ b/src/DataSet_LeapOpts.h
@@ -24,17 +24,20 @@ class DataSet_LeapOpts : public DataSet {
     int SetSCNB(double);
     int SetDipoleDampFactor(double);
     int SetIpol(int);
+    int SetFlexibleWater(bool);
 
     Cpptraj::Parm::GB_RadiiType PbRadii() const { return pbradii_; }
     double SCEE() const { return scee_; }
     double SCNB() const { return scnb_; }
     double DipoleDampFactor() const { return dipoleDampFactor_; }
     int IPOL() const { return ipol_; }
+    bool FlexibleWater() const { return flexibleWater_; }
   private:
     Cpptraj::Parm::GB_RadiiType pbradii_;
     double scee_;
     double scnb_;
     double dipoleDampFactor_;
     int ipol_;
+    bool flexibleWater_;
 };
 #endif

From c0a5789ed9985f54f69453f7760f30aeefdfe108 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 6 Mar 2026 09:18:38 -0500
Subject: [PATCH 1481/1492] Read set default flexiblewater and
 deleteextrapointangles

---
 src/DataIO_LeapRC.cpp    | 21 +++++++++++++++++++--
 src/DataSet_LeapOpts.cpp | 13 ++++++++++++-
 src/DataSet_LeapOpts.h   |  3 +++
 3 files changed, 34 insertions(+), 3 deletions(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 75cd7e292c..187ea7e4e6 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -658,6 +658,14 @@ const char* DataIO_LeapRC::LEAPOPTSNAME_ = "_LEAP_OPTIONS_";
 /** Leap pdb residue map data set default name. */
 const char* DataIO_LeapRC::PDBRESMAPNAME_ = "_LEAP_PDBRESMAP_";
 
+/// \return 1 if 'on', 0 if 'off', -1 otherwise.
+static inline int on_off_opt(const char* desc, std::string const& opt) {
+  if (opt == "off") return 0;
+  else if (opt == "on") return 1;
+  mprinterr("Error: Expected 'on' or 'off' for %s, got %s\n", desc, opt.c_str());
+  return -1;
+}
+
 /** LEaP 'set' command. */
 int DataIO_LeapRC::LeapSet(ArgList const& argIn, DataSetList& dsl) const {
   if (leapopts_ == 0) {
@@ -683,13 +691,22 @@ int DataIO_LeapRC::LeapSet(ArgList const& argIn, DataSetList& dsl) const {
         return 1;
       }
     } else if ( ToLower(argIn[2]) == "cmap" ) {
-      if ( ToLower(argIn[3]) == "on" ) {
+      int iopt = on_off_opt(argIn.ArgLine(), ToLower(argIn[3]));
+      if ( iopt == 1 ) {
         mprintf("Warning: LEaP 'set default cmap on' command ignored; CMAP terms will always be added if present.\n");
-      } else if ( ToLower(argIn[3]) == "off" ) {
+      } else if ( iopt == 0 ) {
         mprinterr("Error: LEaP 'set default cmap off' is not supported; CMAP terms will always be added if present.\n");
         return 1;
       } else
         mprintf("Warning: Skipping unrecognized 'set default cmap' mode: %s\n", argIn[3].c_str());
+    } else if ( ToLower(argIn[2]) == "flexiblewater" ) {
+      int iopt = on_off_opt(argIn.ArgLine(), ToLower(argIn[3]));
+      if (iopt < 0) return 1;
+      OPTS.SetFlexibleWater( (bool)iopt );
+    } else if ( ToLower(argIn[2]) == "deleteextrapointangles" ) {
+      int iopt = on_off_opt(argIn.ArgLine(), ToLower(argIn[3]));
+      if (iopt < 0) return 1;
+      OPTS.SetDeleteExtraPointAngles( (bool)iopt );
     } else if ( ToLower(argIn[2]) == "dipole_damp_factor" ) {
       if (OPTS.SetDipoleDampFactor( convertToDouble(argIn[3]) )) {
         mprinterr("Error: Could not set dipole_damp_factor.\n");
diff --git a/src/DataSet_LeapOpts.cpp b/src/DataSet_LeapOpts.cpp
index 18b1dd6ec6..46937954c8 100644
--- a/src/DataSet_LeapOpts.cpp
+++ b/src/DataSet_LeapOpts.cpp
@@ -10,7 +10,8 @@ DataSet_LeapOpts::DataSet_LeapOpts() :
   scnb_(2.0), // AMBER default
   dipoleDampFactor_(0),
   ipol_(0),
-  flexibleWater_(false)
+  flexibleWater_(false),
+  deleteExtraPointAngles_(true)
 {
 
 }
@@ -74,3 +75,13 @@ int DataSet_LeapOpts::SetFlexibleWater(bool fIn) {
   flexibleWater_ = fIn;
   return 0;
 }
+
+/** Set whether extra point angles should be deleted */
+int DataSet_LeapOpts::SetDeleteExtraPointAngles(bool fIn) {
+  if (fIn)
+    mprintf("\tSetting delete extra point angles to ON\n");
+  else
+    mprintf("\tSetting delete extra point angles to OFF\n");
+  deleteExtraPointAngles_ = fIn;
+  return 0;
+}
diff --git a/src/DataSet_LeapOpts.h b/src/DataSet_LeapOpts.h
index 249ad79450..d6f7c4739a 100644
--- a/src/DataSet_LeapOpts.h
+++ b/src/DataSet_LeapOpts.h
@@ -25,6 +25,7 @@ class DataSet_LeapOpts : public DataSet {
     int SetDipoleDampFactor(double);
     int SetIpol(int);
     int SetFlexibleWater(bool);
+    int SetDeleteExtraPointAngles(bool);
 
     Cpptraj::Parm::GB_RadiiType PbRadii() const { return pbradii_; }
     double SCEE() const { return scee_; }
@@ -32,6 +33,7 @@ class DataSet_LeapOpts : public DataSet {
     double DipoleDampFactor() const { return dipoleDampFactor_; }
     int IPOL() const { return ipol_; }
     bool FlexibleWater() const { return flexibleWater_; }
+    bool DeleteExtraPointAngles() const { return deleteExtraPointAngles_; }
   private:
     Cpptraj::Parm::GB_RadiiType pbradii_;
     double scee_;
@@ -39,5 +41,6 @@ class DataSet_LeapOpts : public DataSet {
     double dipoleDampFactor_;
     int ipol_;
     bool flexibleWater_;
+    bool deleteExtraPointAngles_;
 };
 #endif

From 837ea4f0d3292b16acc1bceb02e63897a1cfcb2e Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 6 Mar 2026 09:23:10 -0500
Subject: [PATCH 1482/1492] Replace option vars in AssignParams with
 DataSet_LeapOpts

---
 src/Parm/AssignParams.cpp | 12 ++++++------
 src/Parm/AssignParams.h   |  6 ++++--
 src/Parm/parmdepend       |  2 +-
 src/cpptrajdepend         | 12 ++++++------
 4 files changed, 17 insertions(+), 15 deletions(-)

diff --git a/src/Parm/AssignParams.cpp b/src/Parm/AssignParams.cpp
index ef35a443af..77c466da04 100644
--- a/src/Parm/AssignParams.cpp
+++ b/src/Parm/AssignParams.cpp
@@ -21,9 +21,9 @@ using namespace Cpptraj::Parm;
 /** CONSTRUCTOR */
 AssignParams::AssignParams() :
   debug_(0),
-  verbose_(0),
-  deleteExtraPointAngles_(true),
-  flexibleWater_(false)
+  verbose_(0)//,
+//  deleteExtraPointAngles_(true),
+//  flexibleWater_(false)
 {}
 
 /** Set debug level */
@@ -143,7 +143,7 @@ const
     types.AddName( topOut[ang->A2()].Type() );
     types.AddName( topOut[ang->A3()].Type() );
     // Skip extra points
-    if (deleteExtraPointAngles_) {
+    if (OPTS_.DeleteExtraPointAngles()) {
       if ( topOut[ang->A1()].Element() == Atom::EXTRAPT ||
            topOut[ang->A3()].Element() == Atom::EXTRAPT)
       {
@@ -167,7 +167,7 @@ const
       continue;
     }
     // Skip water angles
-    if (!flexibleWater_) {
+    if (!OPTS_.FlexibleWater()) {
       if (topOut[ang->A1()].Element() == Atom::HYDROGEN &&
           topOut[ang->A2()].Element() == Atom::OXYGEN &&
           topOut[ang->A3()].Element() == Atom::HYDROGEN)
@@ -341,7 +341,7 @@ const
     types.AddName( topOut[dih->A3()].Type() );
     types.AddName( topOut[dih->A4()].Type() );
     // Skip extra points
-    if (deleteExtraPointAngles_) {
+    if (OPTS_.DeleteExtraPointAngles()) {
       if ( topOut[dih->A1()].Element() == Atom::EXTRAPT ||
            topOut[dih->A4()].Element() == Atom::EXTRAPT)
       {
diff --git a/src/Parm/AssignParams.h b/src/Parm/AssignParams.h
index 327ad7bd48..9dbaeb3c1c 100644
--- a/src/Parm/AssignParams.h
+++ b/src/Parm/AssignParams.h
@@ -5,6 +5,7 @@
 #ifdef TIMER
 # include "../Timer.h"
 #endif
+#include "../DataSet_LeapOpts.h"
 class AngleArray;
 class AngleParmArray;
 class AngleParmType;
@@ -105,8 +106,9 @@ class AssignParams {
 
     int debug_;
     int verbose_;
-    bool deleteExtraPointAngles_; ///< If true, remove angles/torsions containing extra points.
-    bool flexibleWater_;          ///< If true, allow H-O-H angle for water
+    DataSet_LeapOpts OPTS_;       ///< Hold parameter-related options
+    //bool deleteExtraPointAngles_; ///< If true, remove angles/torsions containing extra points.
+    //bool flexibleWater_;          ///< If true, allow H-O-H angle for water
 #   ifdef TIMER
     Timer t_total_;
     Timer t_bonds_;
diff --git a/src/Parm/parmdepend b/src/Parm/parmdepend
index 2581210beb..d60ff8f7c9 100644
--- a/src/Parm/parmdepend
+++ b/src/Parm/parmdepend
@@ -1,4 +1,4 @@
-AssignParams.o : AssignParams.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../MaskToken.h ../Matrix_3x3.h ../ModXNA_Info.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/ParmEnum.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/GenerateConnectivityArrays.h ../SymbolExporting.h ../Timer.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h AssignParams.h DihedralParmHolder.h GetParams.h ImproperParmHolder.h ParameterSet.h ParmArray.h ParmEnum.h ParmHolder.h
+AssignParams.o : AssignParams.cpp ../AssociatedData.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSet_LeapOpts.h ../Dimension.h ../FileIO.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../ModXNA_Info.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/GB_Params.h ../Parm/ParmEnum.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/GenerateConnectivityArrays.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h AssignParams.h DihedralParmHolder.h GetParams.h ImproperParmHolder.h ParameterSet.h ParmArray.h ParmEnum.h ParmHolder.h
 Bond_Params.o : Bond_Params.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../ModXNA_Info.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h Bond_Params.h
 DihedralParmSet.o : DihedralParmSet.cpp ../AtomType.h ../CmapParmHolder.h ../Constants.h ../CpptrajStdio.h ../FileName.h ../NameType.h ../ParameterTypes.h ../Parm/ParmEnum.h ../TypeNameHolder.h DihedralParmHolder.h DihedralParmSet.h ImproperParmHolder.h ParameterSet.h ParmEnum.h ParmHolder.h
 GB_Params.o : GB_Params.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../ModXNA_Info.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h GB_Params.h
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index c705864995..80053a95bf 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -319,7 +319,7 @@ EwaldOptions.o : EwaldOptions.cpp ArgList.h CpptrajStdio.h EwaldOptions.h
 ExclusionArray.o : ExclusionArray.cpp Atom.h AtomMask.h CharMask.h CpptrajStdio.h ExclusionArray.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Unit.h
 Exec_AddMissingRes.o : Exec_AddMissingRes.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h CharMask.h CompactFrameArray.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_AddMissingRes.h Exec_AddMissingRes_Pres.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Minimize_SteepestDescent.h ModXNA_Info.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h ParmFile.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h Trajout_Single.h Unit.h Vec3.h
 Exec_Analyze.o : Exec_Analyze.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Analyze.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_Build.o : Exec_Build.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h ActionTopWriter.h Action_FixAtomOrder.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_Coords.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h ExclusionArray.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h OutputTrajCommon.h PairList.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/ImproperParmHolder.h Parm/LJ1264_Params.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h ParmFile.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/AddIons.h Structure/Builder.h Structure/Creator.h Structure/Disulfide.h Structure/HisProt.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/RingFinder.h Structure/Solvate.h Structure/StructureEnum.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Build.o : Exec_Build.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h ActionTopWriter.h Action_FixAtomOrder.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_Coords.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_LeapOpts.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h ExclusionArray.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h OutputTrajCommon.h PairList.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/ImproperParmHolder.h Parm/LJ1264_Params.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h ParmFile.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/AddIons.h Structure/Builder.h Structure/Creator.h Structure/Disulfide.h Structure/HisProt.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/RingFinder.h Structure/Solvate.h Structure/StructureEnum.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Calc.o : Exec_Calc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Calc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_CatCrd.o : Exec_CatCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CatCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_Change.o : Exec_Change.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Change.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/GB_Params.h Parm/LJ1264_Params.h Parm/ParmEnum.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
@@ -364,7 +364,7 @@ Exec_ReadInput.o : Exec_ReadInput.cpp Action.h ActionList.h ActionState.h Analys
 Exec_RotateDihedral.o : Exec_RotateDihedral.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_RotateDihedral.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_RunAnalysis.o : Exec_RunAnalysis.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_RunAnalysis.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_ScaleDihedralK.o : Exec_ScaleDihedralK.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ScaleDihedralK.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_Sequence.o : Exec_Sequence.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Sequence.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/Creator.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Sequence.o : Exec_Sequence.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_LeapOpts.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Sequence.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/Creator.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_SequenceAlign.o : Exec_SequenceAlign.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SequenceAlign.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Unit.h Vec3.h
 Exec_Set.o : Exec_Set.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_StringVar.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Set.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_Show.o : Exec_Show.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_StringVar.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Show.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
@@ -374,7 +374,7 @@ Exec_SplitCoords.o : Exec_SplitCoords.cpp Action.h ActionList.h ActionState.h An
 Exec_System.o : Exec_System.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_System.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_Top.o : Exec_Top.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Top.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h TopInfo.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_Traj.o : Exec_Traj.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Traj.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_UpdateParameters.o : Exec_UpdateParameters.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h DataSet_Topology.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_UpdateParameters.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GetParams.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_UpdateParameters.o : Exec_UpdateParameters.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_LeapOpts.h DataSet_Parameters.h DataSet_Topology.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_UpdateParameters.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/GetParams.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_ViewRst.o : Exec_ViewRst.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ViewRst.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h ViewRst.h
 Exec_Zmatrix.o : Exec_Zmatrix.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Zmatrix.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Zmatrix.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 ExtendedSimilarity.o : ExtendedSimilarity.cpp AssociatedData.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h ExtendedSimilarity.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h Unit.h Vec3.h
@@ -434,7 +434,7 @@ PairList.o : PairList.cpp Atom.h AtomMask.h Box.h CoordinateInfo.h CpptrajStdio.
 Parallel.o : Parallel.cpp Parallel.h
 ParallelNetcdf.o : ParallelNetcdf.cpp CpptrajStdio.h Parallel.h ParallelNetcdf.h
 ParallelSetFrameNum.o : ParallelSetFrameNum.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h ParallelSetFrameNum.h Range.h TextFormat.h
-Parm/AssignParams.o : Parm/AssignParams.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h GuessAtomHybridization.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/../Structure/GenerateConnectivityArrays.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GetParams.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmArray.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Parm/AssignParams.o : Parm/AssignParams.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_LeapOpts.h Dimension.h FileIO.h FileName.h Frame.h GuessAtomHybridization.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/../Structure/GenerateConnectivityArrays.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/GetParams.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmArray.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Parm/Bond_Params.o : Parm/Bond_Params.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/Bond_Params.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Parm/DihedralParmSet.o : Parm/DihedralParmSet.cpp AtomType.h CmapParmHolder.h Constants.h CpptrajStdio.h FileName.h NameType.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/DihedralParmSet.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h TypeNameHolder.h
 Parm/GB_Params.o : Parm/GB_Params.cpp ArgList.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/GB_Params.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
@@ -446,7 +446,7 @@ Parm/ParmEnum.o : Parm/ParmEnum.cpp Parm/ParmEnum.h
 ParmFile.o : ParmFile.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h ParmFile.h ParmIO.h Parm_Amber.h Parm_CIF.h Parm_CharmmPsf.h Parm_Gromacs.h Parm_Mol2.h Parm_PDB.h Parm_SDF.h Parm_Tinker.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Parm_Amber.o : Parm_Amber.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h ExclusionArray.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/GetParams.h ParmIO.h Parm_Amber.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h Unit.h Vec3.h
 Parm_CIF.o : Parm_CIF.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h CIFfile.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmIO.h Parm_CIF.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h
-Parm_CharmmPsf.o : Parm_CharmmPsf.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h CharmmParamFile.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Mol.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h ParmIO.h Parm_CharmmPsf.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Parm_CharmmPsf.o : Parm_CharmmPsf.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h CharmmParamFile.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_LeapOpts.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Mol.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h ParmIO.h Parm_CharmmPsf.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Parm_Gromacs.o : Parm_Gromacs.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmIO.h Parm_Gromacs.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Parm_Mol2.o : Parm_Mol2.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Mol2File.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmIO.h Parm_Mol2.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Parm_PDB.o : Parm_PDB.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterTypes.h ParmIO.h Parm_PDB.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Timer.h Topology.h Unit.h Vec3.h
@@ -517,7 +517,7 @@ TextFormat.o : TextFormat.cpp StringRoutines.h TextFormat.h
 Timer.o : Timer.cpp CpptrajStdio.h Timer.h
 TinkerFile.o : TinkerFile.cpp ArgList.h Atom.h AtomMask.h Box.h BufferedLine.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TinkerFile.h Unit.h Vec3.h
 TopInfo.o : TopInfo.cpp AssociatedData.h Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h DistRoutines.h FileIO.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Mol.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h TopInfo.h Topology.h TorsionRoutines.h Unit.h Vec3.h
-Topology.o : Topology.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/GetParams.h Parm/Merge.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h UpdateParameters.h Vec3.h
+Topology.o : Topology.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_LeapOpts.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/GB_Params.h Parm/GetParams.h Parm/Merge.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h UpdateParameters.h Vec3.h
 TorsionRoutines.o : TorsionRoutines.cpp Constants.h TorsionRoutines.h Vec3.h
 TrajFrameCounter.o : TrajFrameCounter.cpp ArgList.h CpptrajStdio.h TrajFrameCounter.h
 TrajIOarray.o : TrajIOarray.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryFile.h TrajectoryIO.h Unit.h Vec3.h

From 3daac019ff21de4946a7c730cc3bc430d3cd8f85 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 6 Mar 2026 09:51:53 -0500
Subject: [PATCH 1483/1492] Revert; not all leap options pertain to parameter
 assignment

---
 src/Parm/AssignParams.cpp | 12 ++++++------
 src/Parm/AssignParams.h   |  6 ++----
 src/Parm/parmdepend       |  2 +-
 src/cpptrajdepend         | 12 ++++++------
 4 files changed, 15 insertions(+), 17 deletions(-)

diff --git a/src/Parm/AssignParams.cpp b/src/Parm/AssignParams.cpp
index 77c466da04..ef35a443af 100644
--- a/src/Parm/AssignParams.cpp
+++ b/src/Parm/AssignParams.cpp
@@ -21,9 +21,9 @@ using namespace Cpptraj::Parm;
 /** CONSTRUCTOR */
 AssignParams::AssignParams() :
   debug_(0),
-  verbose_(0)//,
-//  deleteExtraPointAngles_(true),
-//  flexibleWater_(false)
+  verbose_(0),
+  deleteExtraPointAngles_(true),
+  flexibleWater_(false)
 {}
 
 /** Set debug level */
@@ -143,7 +143,7 @@ const
     types.AddName( topOut[ang->A2()].Type() );
     types.AddName( topOut[ang->A3()].Type() );
     // Skip extra points
-    if (OPTS_.DeleteExtraPointAngles()) {
+    if (deleteExtraPointAngles_) {
       if ( topOut[ang->A1()].Element() == Atom::EXTRAPT ||
            topOut[ang->A3()].Element() == Atom::EXTRAPT)
       {
@@ -167,7 +167,7 @@ const
       continue;
     }
     // Skip water angles
-    if (!OPTS_.FlexibleWater()) {
+    if (!flexibleWater_) {
       if (topOut[ang->A1()].Element() == Atom::HYDROGEN &&
           topOut[ang->A2()].Element() == Atom::OXYGEN &&
           topOut[ang->A3()].Element() == Atom::HYDROGEN)
@@ -341,7 +341,7 @@ const
     types.AddName( topOut[dih->A3()].Type() );
     types.AddName( topOut[dih->A4()].Type() );
     // Skip extra points
-    if (OPTS_.DeleteExtraPointAngles()) {
+    if (deleteExtraPointAngles_) {
       if ( topOut[dih->A1()].Element() == Atom::EXTRAPT ||
            topOut[dih->A4()].Element() == Atom::EXTRAPT)
       {
diff --git a/src/Parm/AssignParams.h b/src/Parm/AssignParams.h
index 9dbaeb3c1c..327ad7bd48 100644
--- a/src/Parm/AssignParams.h
+++ b/src/Parm/AssignParams.h
@@ -5,7 +5,6 @@
 #ifdef TIMER
 # include "../Timer.h"
 #endif
-#include "../DataSet_LeapOpts.h"
 class AngleArray;
 class AngleParmArray;
 class AngleParmType;
@@ -106,9 +105,8 @@ class AssignParams {
 
     int debug_;
     int verbose_;
-    DataSet_LeapOpts OPTS_;       ///< Hold parameter-related options
-    //bool deleteExtraPointAngles_; ///< If true, remove angles/torsions containing extra points.
-    //bool flexibleWater_;          ///< If true, allow H-O-H angle for water
+    bool deleteExtraPointAngles_; ///< If true, remove angles/torsions containing extra points.
+    bool flexibleWater_;          ///< If true, allow H-O-H angle for water
 #   ifdef TIMER
     Timer t_total_;
     Timer t_bonds_;
diff --git a/src/Parm/parmdepend b/src/Parm/parmdepend
index d60ff8f7c9..2581210beb 100644
--- a/src/Parm/parmdepend
+++ b/src/Parm/parmdepend
@@ -1,4 +1,4 @@
-AssignParams.o : AssignParams.cpp ../AssociatedData.h ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DataSet.h ../DataSet_LeapOpts.h ../Dimension.h ../FileIO.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../MaskToken.h ../Matrix_3x3.h ../MetaData.h ../ModXNA_Info.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/GB_Params.h ../Parm/ParmEnum.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/GenerateConnectivityArrays.h ../SymbolExporting.h ../TextFormat.h ../Timer.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h AssignParams.h DihedralParmHolder.h GetParams.h ImproperParmHolder.h ParameterSet.h ParmArray.h ParmEnum.h ParmHolder.h
+AssignParams.o : AssignParams.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../CmapParmHolder.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../GuessAtomHybridization.h ../MaskToken.h ../Matrix_3x3.h ../ModXNA_Info.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Parm/ParmEnum.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../Structure/GenerateConnectivityArrays.h ../SymbolExporting.h ../Timer.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h AssignParams.h DihedralParmHolder.h GetParams.h ImproperParmHolder.h ParameterSet.h ParmArray.h ParmEnum.h ParmHolder.h
 Bond_Params.o : Bond_Params.cpp ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../ModXNA_Info.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h Bond_Params.h
 DihedralParmSet.o : DihedralParmSet.cpp ../AtomType.h ../CmapParmHolder.h ../Constants.h ../CpptrajStdio.h ../FileName.h ../NameType.h ../ParameterTypes.h ../Parm/ParmEnum.h ../TypeNameHolder.h DihedralParmHolder.h DihedralParmSet.h ImproperParmHolder.h ParameterSet.h ParmEnum.h ParmHolder.h
 GB_Params.o : GB_Params.cpp ../ArgList.h ../Atom.h ../AtomMask.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../ModXNA_Info.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../Unit.h ../Vec3.h GB_Params.h
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 80053a95bf..c705864995 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -319,7 +319,7 @@ EwaldOptions.o : EwaldOptions.cpp ArgList.h CpptrajStdio.h EwaldOptions.h
 ExclusionArray.o : ExclusionArray.cpp Atom.h AtomMask.h CharMask.h CpptrajStdio.h ExclusionArray.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Unit.h
 Exec_AddMissingRes.o : Exec_AddMissingRes.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h CharMask.h CompactFrameArray.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_AddMissingRes.h Exec_AddMissingRes_Pres.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Minimize_SteepestDescent.h ModXNA_Info.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h ParmFile.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h Trajout_Single.h Unit.h Vec3.h
 Exec_Analyze.o : Exec_Analyze.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Analyze.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_Build.o : Exec_Build.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h ActionTopWriter.h Action_FixAtomOrder.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_Coords.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_LeapOpts.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h ExclusionArray.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h OutputTrajCommon.h PairList.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/ImproperParmHolder.h Parm/LJ1264_Params.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h ParmFile.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/AddIons.h Structure/Builder.h Structure/Creator.h Structure/Disulfide.h Structure/HisProt.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/RingFinder.h Structure/Solvate.h Structure/StructureEnum.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Build.o : Exec_Build.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h ActionTopWriter.h Action_FixAtomOrder.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_Coords.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h ExclusionArray.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h OutputTrajCommon.h PairList.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/ImproperParmHolder.h Parm/LJ1264_Params.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h ParmFile.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/AddIons.h Structure/Builder.h Structure/Creator.h Structure/Disulfide.h Structure/HisProt.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/RingFinder.h Structure/Solvate.h Structure/StructureEnum.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Calc.o : Exec_Calc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Calc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_CatCrd.o : Exec_CatCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CatCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_Change.o : Exec_Change.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Change.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/GB_Params.h Parm/LJ1264_Params.h Parm/ParmEnum.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
@@ -364,7 +364,7 @@ Exec_ReadInput.o : Exec_ReadInput.cpp Action.h ActionList.h ActionState.h Analys
 Exec_RotateDihedral.o : Exec_RotateDihedral.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_RotateDihedral.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_RunAnalysis.o : Exec_RunAnalysis.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_RunAnalysis.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_ScaleDihedralK.o : Exec_ScaleDihedralK.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ScaleDihedralK.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_Sequence.o : Exec_Sequence.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_LeapOpts.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Sequence.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/Creator.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Sequence.o : Exec_Sequence.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Sequence.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h Structure/Creator.h Structure/StructureEnum.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_SequenceAlign.o : Exec_SequenceAlign.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SequenceAlign.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Unit.h Vec3.h
 Exec_Set.o : Exec_Set.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_StringVar.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Set.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_Show.o : Exec_Show.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_StringVar.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Show.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
@@ -374,7 +374,7 @@ Exec_SplitCoords.o : Exec_SplitCoords.cpp Action.h ActionList.h ActionState.h An
 Exec_System.o : Exec_System.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_System.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_Top.o : Exec_Top.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Top.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h TopInfo.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_Traj.o : Exec_Traj.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Traj.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_UpdateParameters.o : Exec_UpdateParameters.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_LeapOpts.h DataSet_Parameters.h DataSet_Topology.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_UpdateParameters.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/GetParams.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_UpdateParameters.o : Exec_UpdateParameters.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h DataSet_Topology.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_UpdateParameters.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GetParams.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_ViewRst.o : Exec_ViewRst.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ViewRst.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h ViewRst.h
 Exec_Zmatrix.o : Exec_Zmatrix.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Zmatrix.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Zmatrix.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/InternalCoords.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 ExtendedSimilarity.o : ExtendedSimilarity.cpp AssociatedData.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h ExtendedSimilarity.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h Unit.h Vec3.h
@@ -434,7 +434,7 @@ PairList.o : PairList.cpp Atom.h AtomMask.h Box.h CoordinateInfo.h CpptrajStdio.
 Parallel.o : Parallel.cpp Parallel.h
 ParallelNetcdf.o : ParallelNetcdf.cpp CpptrajStdio.h Parallel.h ParallelNetcdf.h
 ParallelSetFrameNum.o : ParallelSetFrameNum.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h ParallelSetFrameNum.h Range.h TextFormat.h
-Parm/AssignParams.o : Parm/AssignParams.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_LeapOpts.h Dimension.h FileIO.h FileName.h Frame.h GuessAtomHybridization.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/../Structure/GenerateConnectivityArrays.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/GetParams.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmArray.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Parm/AssignParams.o : Parm/AssignParams.cpp Atom.h AtomMask.h AtomType.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h GuessAtomHybridization.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/../Structure/GenerateConnectivityArrays.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GetParams.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmArray.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Parm/Bond_Params.o : Parm/Bond_Params.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/Bond_Params.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Parm/DihedralParmSet.o : Parm/DihedralParmSet.cpp AtomType.h CmapParmHolder.h Constants.h CpptrajStdio.h FileName.h NameType.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/DihedralParmSet.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h TypeNameHolder.h
 Parm/GB_Params.o : Parm/GB_Params.cpp ArgList.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/GB_Params.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
@@ -446,7 +446,7 @@ Parm/ParmEnum.o : Parm/ParmEnum.cpp Parm/ParmEnum.h
 ParmFile.o : ParmFile.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h BufferedLine.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h ParmFile.h ParmIO.h Parm_Amber.h Parm_CIF.h Parm_CharmmPsf.h Parm_Gromacs.h Parm_Mol2.h Parm_PDB.h Parm_SDF.h Parm_Tinker.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Parm_Amber.o : Parm_Amber.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h ExclusionArray.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/GetParams.h ParmIO.h Parm_Amber.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h Unit.h Vec3.h
 Parm_CIF.o : Parm_CIF.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h CIFfile.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmIO.h Parm_CIF.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h
-Parm_CharmmPsf.o : Parm_CharmmPsf.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h CharmmParamFile.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_LeapOpts.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Mol.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h ParmIO.h Parm_CharmmPsf.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Parm_CharmmPsf.o : Parm_CharmmPsf.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h CharmmParamFile.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Mol.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h ParmIO.h Parm_CharmmPsf.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Parm_Gromacs.o : Parm_Gromacs.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmIO.h Parm_Gromacs.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Parm_Mol2.o : Parm_Mol2.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Mol2File.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmIO.h Parm_Mol2.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
 Parm_PDB.o : Parm_PDB.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h BondSearch.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterTypes.h ParmIO.h Parm_PDB.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Timer.h Topology.h Unit.h Vec3.h
@@ -517,7 +517,7 @@ TextFormat.o : TextFormat.cpp StringRoutines.h TextFormat.h
 Timer.o : Timer.cpp CpptrajStdio.h Timer.h
 TinkerFile.o : TinkerFile.cpp ArgList.h Atom.h AtomMask.h Box.h BufferedLine.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TinkerFile.h Unit.h Vec3.h
 TopInfo.o : TopInfo.cpp AssociatedData.h Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h DistRoutines.h FileIO.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Mol.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h TopInfo.h Topology.h TorsionRoutines.h Unit.h Vec3.h
-Topology.o : Topology.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_LeapOpts.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/GB_Params.h Parm/GetParams.h Parm/Merge.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h UpdateParameters.h Vec3.h
+Topology.o : Topology.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/GetParams.h Parm/Merge.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h UpdateParameters.h Vec3.h
 TorsionRoutines.o : TorsionRoutines.cpp Constants.h TorsionRoutines.h Vec3.h
 TrajFrameCounter.o : TrajFrameCounter.cpp ArgList.h CpptrajStdio.h TrajFrameCounter.h
 TrajIOarray.o : TrajIOarray.cpp ArgList.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryFile.h TrajectoryIO.h Unit.h Vec3.h

From 4b182c1c198100096d4863ac10bee3f07c946cd1 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 6 Mar 2026 09:52:12 -0500
Subject: [PATCH 1484/1492] Put the defaults in variables

---
 src/AmberParamFile.cpp | 8 +++++---
 src/AmberParamFile.h   | 2 ++
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 6e0398e529..5c1f430960 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -16,7 +16,9 @@ const int AmberParamFile::MAXSYMLEN = 16;
 
 /// CONSTRUCTOR
 AmberParamFile::AmberParamFile() :
-  debug_(0)
+  debug_(0),
+  default_scee_(1.2), // AMBER DEFAULT
+  default_scnb_(2.0)  // AMBER DEFAULT
 {}
 
 /** Set debug level */
@@ -265,8 +267,8 @@ const
     return 1;
   }
   if (PN < 0.0) PN = -PN;
-  double scee = 1.2; // AMBER DEFAULT
-  double scnb = 2.0; // AMBER DEFAULT
+  double scee = default_scee_; // AMBER DEFAULT
+  double scnb = default_scnb_; // AMBER DEFAULT
   if (nscan == 6) {
     // Check for SCEE/SCNB (GLYCAM)
     if (sSCEE[0] == 'S' && sSCEE[1] == 'C' && sSCEE[2] == 'E' && sSCEE[3] == 'E')
diff --git a/src/AmberParamFile.h b/src/AmberParamFile.h
index 0ccb83a825..41da819cc0 100644
--- a/src/AmberParamFile.h
+++ b/src/AmberParamFile.h
@@ -70,5 +70,7 @@ class AmberParamFile {
     //int ReadInput(std::string&, BufferedLine&) const;
 
     int debug_;
+    double default_scee_;
+    double default_scnb_;
 };
 #endif

From 1e477164091c65d8054787be79201e4538c439a7 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 6 Mar 2026 10:23:20 -0500
Subject: [PATCH 1485/1492] Allow default scee and scnb to be overwritten by
 set default sceescalefactor etc. Trap IPOL, not yet supported

---
 src/AmberParamFile.cpp     | 10 +++++++++-
 src/AmberParamFile.h       |  3 +++
 src/DataIO_AmberFF.cpp     |  8 +++++++-
 src/DataIO_AmberFF.h       |  3 +++
 src/DataIO_AmberFrcmod.cpp |  7 ++++++-
 src/DataIO_AmberFrcmod.h   |  3 +++
 src/DataIO_LeapRC.cpp      |  4 ++--
 src/Exec_Build.cpp         | 17 +++++++++++++++++
 src/Exec_Build.h           |  3 +++
 src/cpptrajdepend          |  4 ++--
 10 files changed, 55 insertions(+), 7 deletions(-)

diff --git a/src/AmberParamFile.cpp b/src/AmberParamFile.cpp
index 5c1f430960..e838b111ef 100644
--- a/src/AmberParamFile.cpp
+++ b/src/AmberParamFile.cpp
@@ -1,7 +1,8 @@
 #include "AmberParamFile.h"
 #include "ArgList.h"
-#include "CpptrajStdio.h"
 #include "BufferedLine.h"
+#include "CpptrajStdio.h"
+#include "DataSet_LeapOpts.h"
 #include "StringRoutines.h"
 #include "Parm/DihedralParmSet.h"
 #include "Parm/ParameterSet.h"
@@ -26,6 +27,13 @@ void AmberParamFile::SetAmberParamDebug(int d) {
   debug_ = d;
 }
 
+/** Set defaults from leap options */
+void AmberParamFile::SetDefaults(DataSet_LeapOpts* leapopts) {
+  if (leapopts == 0) return;
+  default_scee_ = leapopts->SCEE();
+  default_scnb_ = leapopts->SCNB();
+}
+
 /** Read symbols delimited by - and space. */
 int AmberParamFile::read_symbols(const char* ptrIn, std::vector<std::string>& symbols, int nsymbols)
 {
diff --git a/src/AmberParamFile.h b/src/AmberParamFile.h
index 41da819cc0..7b6c583806 100644
--- a/src/AmberParamFile.h
+++ b/src/AmberParamFile.h
@@ -3,6 +3,7 @@
 #include <vector>
 #include <string>
 class CmapGridType;
+class DataSet_LeapOpts;
 //class BufferedLine;
 class FileName;
 namespace Cpptraj {
@@ -25,6 +26,8 @@ class AmberParamFile {
     int WriteParams(ParameterSet&, FileName const&) const;
     /// Set debug level
     void SetAmberParamDebug(int);
+    /// Set defaults from leap options
+    void SetDefaults(DataSet_LeapOpts*);
   private:
     static const int MAXSYMLEN;
 
diff --git a/src/DataIO_AmberFF.cpp b/src/DataIO_AmberFF.cpp
index 300bb66b5b..592cd7f84c 100644
--- a/src/DataIO_AmberFF.cpp
+++ b/src/DataIO_AmberFF.cpp
@@ -33,8 +33,13 @@ int DataIO_AmberFF::processReadArgs(ArgList& argIn)
   return 0;
 }
 
-// DataIO_AmberFF::ReadData()
 int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::string const& dsname)
+{
+  return ReadData(fname, dsl, dsname, 0);
+}
+
+// DataIO_AmberFF::ReadData()
+int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::string const& dsname, DataSet_LeapOpts* leapopts)
 {
   ClearAddedByMe();
   // Allocate data set
@@ -55,6 +60,7 @@ int DataIO_AmberFF::ReadData(FileName const& fname, DataSetList& dsl, std::strin
 
   AmberParamFile infile;
   infile.SetAmberParamDebug( debug_ );
+  infile.SetDefaults( leapopts ); 
   int err = infile.ReadParams(prm, fname, nbsetname_);
   if (err != 0) {
     mprinterr("Error: Could not read '%s'\n", fname.full());
diff --git a/src/DataIO_AmberFF.h b/src/DataIO_AmberFF.h
index 1f73866cea..7768e3c9c2 100644
--- a/src/DataIO_AmberFF.h
+++ b/src/DataIO_AmberFF.h
@@ -1,6 +1,7 @@
 #ifndef INC_DATAIO_AMBERFF_H
 #define INC_DATAIO_AMBERFF_H
 #include "DataIO.h"
+class DataSet_LeapOpts;
 /// <Enter description of DataIO_AmberFF here>
 class DataIO_AmberFF : public DataIO {
   public:
@@ -13,6 +14,8 @@ class DataIO_AmberFF : public DataIO {
     int processWriteArgs(ArgList&);
     int WriteData(FileName const&, DataSetList const&);
     bool ID_DataFormat(CpptrajFile&);
+    /// Read in data with leap options
+    int ReadData(FileName const&, DataSetList&, std::string const&, DataSet_LeapOpts*);
   private:
 
     std::string nbsetname_; ///< Nonbonded parameter set name to use
diff --git a/src/DataIO_AmberFrcmod.cpp b/src/DataIO_AmberFrcmod.cpp
index 9f44e82d11..cc826d534e 100644
--- a/src/DataIO_AmberFrcmod.cpp
+++ b/src/DataIO_AmberFrcmod.cpp
@@ -29,8 +29,12 @@ int DataIO_AmberFrcmod::processReadArgs(ArgList& argIn)
   return 0;
 }
 
+int DataIO_AmberFrcmod::ReadData(FileName const& fname, DataSetList& dsl, std::string const& dsname) {
+  return ReadData(fname, dsl, dsname, 0);
+}
+
 // DataIO_AmberFrcmod::ReadData()
-int DataIO_AmberFrcmod::ReadData(FileName const& fname, DataSetList& dsl, std::string const& dsname)
+int DataIO_AmberFrcmod::ReadData(FileName const& fname, DataSetList& dsl, std::string const& dsname, DataSet_LeapOpts* leapopts)
 {
   ClearAddedByMe();
   // Allocate data set
@@ -51,6 +55,7 @@ int DataIO_AmberFrcmod::ReadData(FileName const& fname, DataSetList& dsl, std::s
 
   AmberParamFile infile;
   infile.SetAmberParamDebug( debug_ );
+  infile.SetDefaults( leapopts );
   if (infile.ReadFrcmod(prm, fname)) {
     mprinterr("Error: Could not read Amber frcmod file '%s'\n", fname.full());
     return 1;
diff --git a/src/DataIO_AmberFrcmod.h b/src/DataIO_AmberFrcmod.h
index bf792d4e48..545b991ab4 100644
--- a/src/DataIO_AmberFrcmod.h
+++ b/src/DataIO_AmberFrcmod.h
@@ -1,6 +1,7 @@
 #ifndef INC_DATAIO_AMBERFRCMOD_H
 #define INC_DATAIO_AMBERFRCMOD_H
 #include "DataIO.h"
+class DataSet_LeapOpts;
 /// <Enter description of DataIO_AmberFrcmod here>
 class DataIO_AmberFrcmod : public DataIO {
   public:
@@ -13,5 +14,7 @@ class DataIO_AmberFrcmod : public DataIO {
     int processWriteArgs(ArgList&);
     int WriteData(FileName const&, DataSetList const&);
     bool ID_DataFormat(CpptrajFile&);
+    // Read in data with leap options
+    int ReadData(FileName const&, DataSetList&, std::string const&, DataSet_LeapOpts*);
 };
 #endif
diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 187ea7e4e6..5156e18c03 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -241,7 +241,7 @@ const
     }
     DataIO_AmberFrcmod infile;
     infile.SetDebug( debug_ );
-    if (infile.ReadData( full_path, dsl, dsname)) {
+    if (infile.ReadData( full_path, dsl, dsname, static_cast<DataSet_LeapOpts*>(leapopts_))) {
       mprinterr("Error: Could not load force field modifications from '%s'\n", filename.c_str());
       return 1;
     }
@@ -258,7 +258,7 @@ const
     } else {
       mprintf("\tLoading force field from '%s'\n", filename.c_str());
       DataIO_AmberFF infile;
-      if (infile.ReadData( full_path, dsl, dsname)) {
+      if (infile.ReadData( full_path, dsl, dsname, static_cast<DataSet_LeapOpts*>(leapopts_))) {
         mprinterr("Error: Could not load force field from '%s'\n", filename.c_str());
         return 1;
       }
diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index c585fc78a3..14d80d259e 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -3,6 +3,7 @@
 #include "AssociatedData_Connect.h"
 #include "CpptrajStdio.h"
 #include "DataIO_Coords.h"
+#include "DataSet_LeapOpts.h"
 #include "DataSet_Parameters.h" // For casting DataSet_Parameters to ParameterSet
 #include "ParmFile.h"
 #include "StringRoutines.h" // integerToString
@@ -878,6 +879,16 @@ void Exec_Build::Help() const
   mprintf("  Build complete topology and parameters from given crdset.\n");
 }
 
+/** Check if any unhandled options have been set. */
+int Exec_Build::checkUnhandledOptions(DataSet_LeapOpts const& OPTS) const {
+  if (OPTS.IPOL() > 0) {
+    mprinterr("Error: IPOL has been set to something other than zero by a previous leaprc file.\n"
+              "Error: Creating topologies for polarizable FF is not yet supported.\n");
+    return 1;
+  }
+  return 0;
+}
+
 // Exec_Build::Execute()
 Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
 {
@@ -913,6 +924,12 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
     mprinterr("Error: Must specify file to build or COORDS set with 'crdset'\n");
     return CpptrajState::ERR;
   }
+  DataSet* leapopts = State.DSL().FindSetOfType( "*", DataSet::LEAPOPTS );
+  if (leapopts != 0) {
+    // Check for unhandled leap options
+    DataSet_LeapOpts const& OPTS = static_cast<DataSet_LeapOpts const&>( *leapopts );
+    if (checkUnhandledOptions( OPTS )) return CpptrajState::ERR;
+  }
 
   return BuildAndParmStructure(inCrdPtr, outset, State.DSL(), State.Debug(), argIn, Cpptraj::Parm::UNKNOWN_GB);
 }
diff --git a/src/Exec_Build.h b/src/Exec_Build.h
index 18d98c7008..94c3d3b9b9 100644
--- a/src/Exec_Build.h
+++ b/src/Exec_Build.h
@@ -2,6 +2,7 @@
 #define INC_EXEC_BUILD_H
 #include "Exec.h"
 #include "Parm/GB_Params.h"
+class DataSet_LeapOpts;
 namespace Cpptraj {
 namespace Structure {
 class Creator;
@@ -36,6 +37,8 @@ class Exec_Build : public Exec {
     static inline bool hasBondingPair(IParray const&, Ipair const&);
     /// \return true if given array of residue connections has target residue index.
     static inline bool resIsConnected(Iarray const&, int);
+    /// Check for unhandled LEaP options
+    int checkUnhandledOptions(DataSet_LeapOpts const&) const;
     /// Create assembly from input COORDS
     int createAssembly(Topology&, Frame&, DataSet_Coords&) const;
     /// Create new topology/frame using templates
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index c705864995..c633777ac6 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -96,7 +96,7 @@ Action_Volmap.o : Action_Volmap.cpp Action.h ActionState.h Action_Volmap.h ArgLi
 Action_Volume.o : Action_Volume.cpp Action.h ActionState.h Action_Volume.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 Action_Watershell.o : Action_Watershell.cpp Action.h ActionState.h Action_Watershell.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h ImageRoutines.h ImageTypes.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h cuda_kernels/kernel_wrappers.cuh
 Action_XtalSymm.o : Action_XtalSymm.cpp Action.h ActionState.h Action_XtalSymm.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SpaceGroup.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-AmberParamFile.o : AmberParamFile.cpp AmberParamFile.h ArgList.h AtomType.h BufferedLine.h CmapParmHolder.h Constants.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/DihedralParmSet.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h StringRoutines.h TypeNameHolder.h
+AmberParamFile.o : AmberParamFile.cpp AmberParamFile.h ArgList.h AssociatedData.h AtomType.h BufferedLine.h CmapParmHolder.h Constants.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_LeapOpts.h Dimension.h FileIO.h FileName.h MetaData.h NameType.h Parallel.h ParameterTypes.h Parm/DihedralParmHolder.h Parm/DihedralParmSet.h Parm/GB_Params.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h StringRoutines.h TextFormat.h TypeNameHolder.h
 AnalysisList.o : AnalysisList.cpp ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 Analysis_AmdBias.o : Analysis_AmdBias.cpp ActionState.h Analysis.h AnalysisState.h Analysis_AmdBias.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 Analysis_AutoCorr.o : Analysis_AutoCorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_AutoCorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
@@ -319,7 +319,7 @@ EwaldOptions.o : EwaldOptions.cpp ArgList.h CpptrajStdio.h EwaldOptions.h
 ExclusionArray.o : ExclusionArray.cpp Atom.h AtomMask.h CharMask.h CpptrajStdio.h ExclusionArray.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Unit.h
 Exec_AddMissingRes.o : Exec_AddMissingRes.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h CharMask.h CompactFrameArray.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_AddMissingRes.h Exec_AddMissingRes_Pres.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Minimize_SteepestDescent.h ModXNA_Info.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h ParmFile.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h Trajout_Single.h Unit.h Vec3.h
 Exec_Analyze.o : Exec_Analyze.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Analyze.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
-Exec_Build.o : Exec_Build.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h ActionTopWriter.h Action_FixAtomOrder.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_Coords.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h ExclusionArray.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h OutputTrajCommon.h PairList.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/ImproperParmHolder.h Parm/LJ1264_Params.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h ParmFile.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/AddIons.h Structure/Builder.h Structure/Creator.h Structure/Disulfide.h Structure/HisProt.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/RingFinder.h Structure/Solvate.h Structure/StructureEnum.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Build.o : Exec_Build.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h ActionTopWriter.h Action_FixAtomOrder.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_Coords.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_LeapOpts.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h ExclusionArray.h Exec.h Exec_Build.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h OutputTrajCommon.h PairList.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GB_Params.h Parm/ImproperParmHolder.h Parm/LJ1264_Params.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h ParmFile.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/AddIons.h Structure/Builder.h Structure/Creator.h Structure/Disulfide.h Structure/HisProt.h Structure/PdbCleaner.h Structure/ResStatArray.h Structure/RingFinder.h Structure/Solvate.h Structure/StructureEnum.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Calc.o : Exec_Calc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Calc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_CatCrd.o : Exec_CatCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CatCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_Change.o : Exec_Change.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_NameMap.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Change.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/GB_Params.h Parm/LJ1264_Params.h Parm/ParmEnum.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h

From c9d74f7ea14a4cf48b0e2869975c5192a62e0c13 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 6 Mar 2026 10:29:46 -0500
Subject: [PATCH 1486/1492] Check for bad leap options when building directly
 from leaprc

---
 src/DataIO_LeapRC.cpp | 4 ++--
 src/Exec_Build.cpp    | 7 ++++++-
 src/Exec_Build.h      | 2 +-
 3 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 5156e18c03..7aace4f103 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -600,7 +600,7 @@ int DataIO_LeapRC::LoadMol2(ArgList const& argIn, DataSetList& dsl) const {
   ArgList tmparg = args.RemainingArgs();
 
   Exec_Build build;
-  Exec::RetType ret = build.BuildStructure( coordsIn.added_back(), dsl, debug_, "", "default_name", tmparg.hasKey("prepareforleap") );
+  Exec::RetType ret = build.BuildStructure( coordsIn.added_back(), dsl, debug_, "", "default_name", tmparg.hasKey("prepareforleap"), static_cast<DataSet_LeapOpts*>(leapopts_) );
   if (ret == CpptrajState::ERR) {
     mprinterr("Error: Build of '%s' failed.\n", args[2].c_str());
     return 1;
@@ -643,7 +643,7 @@ int DataIO_LeapRC::LoadPDB(ArgList const& argIn, DataSetList& dsl) const {
   ArgList tmparg = args.RemainingArgs();
 
   Exec_Build build;
-  Exec::RetType ret = build.BuildStructure( coordsIn.added_back(), dsl, debug_, "", "default_name", tmparg.hasKey("prepareforleap") );
+  Exec::RetType ret = build.BuildStructure( coordsIn.added_back(), dsl, debug_, "", "default_name", tmparg.hasKey("prepareforleap"), static_cast<DataSet_LeapOpts*>(leapopts_) );
   if (ret == CpptrajState::ERR) {
     mprinterr("Error: Build of '%s' failed.\n", args[2].c_str());
     return 1;
diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 14d80d259e..754d79ca4e 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -970,7 +970,7 @@ const
 /** Standalone execute. For DataIO_LeapRC. Operate on inCrdPtr */
 Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, int debugIn,
                                          std::string const& outset, std::string const& title,
-                                         bool enableExtraDetection)
+                                         bool enableExtraDetection, DataSet_LeapOpts* leapopts)
                                          
 {
 #ifndef CPPTRAJ_USE_LEAP_PI
@@ -994,6 +994,11 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, in
     return CpptrajState::ERR;
   }
   debug_ = debugIn;
+  if (leapopts != 0) {
+    // Check for unhandled leap options
+    DataSet_LeapOpts const& OPTS = static_cast<DataSet_LeapOpts const&>( *leapopts );
+    if (checkUnhandledOptions( OPTS )) return CpptrajState::ERR;
+  }
 
   // TODO make it so this can be const (cant bc GetFrame)
   DataSet_Coords& coords = static_cast<DataSet_Coords&>( *((DataSet_Coords*)inCrdPtr) );
diff --git a/src/Exec_Build.h b/src/Exec_Build.h
index 94c3d3b9b9..80aedb0a1d 100644
--- a/src/Exec_Build.h
+++ b/src/Exec_Build.h
@@ -18,7 +18,7 @@ class Exec_Build : public Exec {
     RetType Execute(CpptrajState&, ArgList&);
 
     /// Stand-alone execution - only build, do not parameterize/solvate
-    RetType BuildStructure(DataSet*, DataSetList&, int, std::string const&, std::string const&, bool);
+    RetType BuildStructure(DataSet*, DataSetList&, int, std::string const&, std::string const&, bool, DataSet_LeapOpts*);
     /// \return Output COORDS set
     DataSet* OutCrdPtr() const { return outCrdPtr_; }
     /// Print Timing data

From 85022e6118437436695b4d477dadcbe94a8f9f5a Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 6 Mar 2026 10:42:35 -0500
Subject: [PATCH 1487/1492] Allow existing aliases to be overwritten

---
 src/DataIO_LeapRC.cpp | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/src/DataIO_LeapRC.cpp b/src/DataIO_LeapRC.cpp
index 7aace4f103..9623c7e53c 100644
--- a/src/DataIO_LeapRC.cpp
+++ b/src/DataIO_LeapRC.cpp
@@ -937,6 +937,18 @@ const
 {
   if (debug_ > 0)
     mprintf("DEBUG: %s = %s\n", lhs.c_str(), rhs.c_str());
+  // Check if lhs already exists.
+  DataSet* existing = dsl.CheckForSet( MetaData(dsname, lhs) );
+  if (existing != 0) {
+    // Set already exists. Is it the correct type?
+    if (existing->Type() == DataSet::COORDS) {
+      mprintf("Warning: Overwriting existing unit '%s' with '%s'\n", existing->legend(), rhs.c_str());
+      // Do not overwrite yet in case we can't find a set to copy.
+    } else {
+      mprinterr("Error: '%s' exists but is not COORDS, cannot overwrite with '%s'\n", existing->legend(), rhs.c_str());
+      return 1;
+    }
+  }
   // Find the unit to make a copy of
   DataSet* ds0 = dsl.CheckForSet( MetaData(dsname, rhs) );
   if (ds0 == 0) {
@@ -954,6 +966,11 @@ const
     mprintf("Warning: Could not find unit '%s' to copy to '%s' - skipping.\n", rhs.c_str(), lhs.c_str());
     return 0;
   }
+  // Remove set if it already exists
+  if (existing != 0) {
+    dsl.RemoveSet( existing );
+    existing = 0;
+  }
   DataSet_Coords& crd0 = static_cast<DataSet_Coords&>( *ds0 );
   // Allocate copy
   DataSet* ds1 = dsl.AddSet( DataSet::COORDS, MetaData(dsname, lhs) );

From 774ee305f5b545e436d7188aba844f602f4807fc Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 6 Mar 2026 11:21:36 -0500
Subject: [PATCH 1488/1492] Allow flexible water option to be turned on

---
 src/Exec_Build.cpp        | 4 ++++
 src/Parm/AssignParams.cpp | 5 +++++
 src/Parm/AssignParams.h   | 2 ++
 3 files changed, 11 insertions(+)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 754d79ca4e..603a0d9277 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -1177,6 +1177,9 @@ Exec::RetType Exec_Build::BuildAndParmStructure(DataSet* inCrdPtr, std::string c
 
   std::string solventResName = argIn.GetStringKey("solventresname", "HOH");
   mprintf("\tResidues named '%s' will be recognized as solvent.\n", solventResName.c_str());
+  bool flexWater = argIn.hasKey("flexiblewater");
+  if (flexWater)
+    mprintf("\tFlexible water option is on.\n");
 
   enum SolvateModeType { NO_SOLVATE = 0, SOLVATEBOX, SETBOX };
   SolvateModeType add_solvent = NO_SOLVATE;
@@ -1325,6 +1328,7 @@ Exec::RetType Exec_Build::BuildAndParmStructure(DataSet* inCrdPtr, std::string c
   Cpptraj::Parm::AssignParams AP;
   AP.SetDebug( debug_ );
   AP.SetVerbose( verbose );
+  AP.SetFlexibleWater( flexWater );
   int nmissing = 0;
   if ( AP.AssignParameters( topOut, *(creator.MainParmSetPtr()), nmissing ) ) {
     mprinterr("Error: Could not assign parameters for '%s'.\n", topOut.c_str());
diff --git a/src/Parm/AssignParams.cpp b/src/Parm/AssignParams.cpp
index ef35a443af..5eb2aed2c6 100644
--- a/src/Parm/AssignParams.cpp
+++ b/src/Parm/AssignParams.cpp
@@ -36,6 +36,11 @@ void AssignParams::SetVerbose(int verboseIn) {
   verbose_ = verboseIn;
 }
 
+/** Set flexible water option */
+void AssignParams::SetFlexibleWater(bool flexIn) {
+  flexibleWater_ = flexIn;
+}
+
 /** Set parameters for atoms via given atom type parameter holder. */
 int AssignParams::AssignAtomTypeParm(AtArray& atoms, ParmHolder<AtomType> const& newAtomTypeParams)
 const
diff --git a/src/Parm/AssignParams.h b/src/Parm/AssignParams.h
index 327ad7bd48..3c2ef6718a 100644
--- a/src/Parm/AssignParams.h
+++ b/src/Parm/AssignParams.h
@@ -39,6 +39,8 @@ class AssignParams {
     void SetDebug(int);
     /// Set verbosity
     void SetVerbose(int);
+    /// Allow flexible water
+    void SetFlexibleWater(bool);
     /// Replace existing parameters with those from given set
 #   ifdef TIMER
     int AssignParameters(Topology&, ParameterSet const&, int&);

From 937e266f4357f6b6a33be67bed2b625ccf048b77 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 6 Mar 2026 11:57:55 -0500
Subject: [PATCH 1489/1492] Handle flexible water option. Try to choose a
 better default top name

---
 src/Exec_Build.cpp | 20 ++++++++++++++++----
 src/Exec_Build.h   |  2 +-
 2 files changed, 17 insertions(+), 5 deletions(-)

diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 603a0d9277..95f22f0e9f 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -924,14 +924,14 @@ Exec::RetType Exec_Build::Execute(CpptrajState& State, ArgList& argIn)
     mprinterr("Error: Must specify file to build or COORDS set with 'crdset'\n");
     return CpptrajState::ERR;
   }
-  DataSet* leapopts = State.DSL().FindSetOfType( "*", DataSet::LEAPOPTS );
+  DataSet_LeapOpts* leapopts = (DataSet_LeapOpts*)State.DSL().FindSetOfType( "*", DataSet::LEAPOPTS );
   if (leapopts != 0) {
     // Check for unhandled leap options
     DataSet_LeapOpts const& OPTS = static_cast<DataSet_LeapOpts const&>( *leapopts );
     if (checkUnhandledOptions( OPTS )) return CpptrajState::ERR;
   }
 
-  return BuildAndParmStructure(inCrdPtr, outset, State.DSL(), State.Debug(), argIn, Cpptraj::Parm::UNKNOWN_GB);
+  return BuildAndParmStructure(inCrdPtr, outset, State.DSL(), State.Debug(), argIn, Cpptraj::Parm::UNKNOWN_GB, leapopts);
 }
 
 /** Create an assembly from all the frames in the input coordinates. */
@@ -1070,8 +1070,13 @@ Exec::RetType Exec_Build::BuildStructure(DataSet* inCrdPtr, DataSetList& DSL, in
 /** Set up output COORDS (Topology) */
 int Exec_Build::setupOutputCoords(DataSet* inCrdPtr, std::string const& outset, std::string const& title, DataSetList& DSL)
 {
+  Topology const& topIn = ((DataSet_Coords*)inCrdPtr)->Top();
+  std::string default_title;
+  if (!topIn.ParmName().empty())
+    default_title = topIn.ParmName();
+  else
+    default_title.assign( topIn.c_str() );
   // Set up Output coords
-  std::string default_title( ((DataSet_Coords*)inCrdPtr)->Top().c_str() );
   if (!outset.empty()) {
     // Separate output COORDS set.
     outCrdPtr_ = DSL.AddSet( DataSet::COORDS, outset );
@@ -1106,7 +1111,8 @@ int Exec_Build::setupOutputCoords(DataSet* inCrdPtr, std::string const& outset,
 /** Run the full build, parameterize, and check. */
 Exec::RetType Exec_Build::BuildAndParmStructure(DataSet* inCrdPtr, std::string const& outset,
                                                 DataSetList& DSL, int debugIn, ArgList& argIn,
-                                                Cpptraj::Parm::GB_RadiiType gbRadIn)
+                                                Cpptraj::Parm::GB_RadiiType gbRadIn,
+                                                DataSet_LeapOpts* leapopts)
 {
   t_total_.Start();
   debug_ = debugIn;
@@ -1178,6 +1184,12 @@ Exec::RetType Exec_Build::BuildAndParmStructure(DataSet* inCrdPtr, std::string c
   std::string solventResName = argIn.GetStringKey("solventresname", "HOH");
   mprintf("\tResidues named '%s' will be recognized as solvent.\n", solventResName.c_str());
   bool flexWater = argIn.hasKey("flexiblewater");
+  if (!flexWater && leapopts->FlexibleWater()) {
+    mprintf("Warning: Flexible water option was set to ON by previous leaprc file; turning on flexible water.\n");
+    flexWater = true;
+  } else if (flexWater && !(leapopts->FlexibleWater()))
+    mprintf("Warning: 'flexwater' specified but flexible water option not set by previous leaprc file;\n"
+            "Warning: Ensure that loaded water models are designed to be flexible.\n");
   if (flexWater)
     mprintf("\tFlexible water option is on.\n");
 
diff --git a/src/Exec_Build.h b/src/Exec_Build.h
index 80aedb0a1d..55f041f192 100644
--- a/src/Exec_Build.h
+++ b/src/Exec_Build.h
@@ -53,7 +53,7 @@ class Exec_Build : public Exec {
     /// Set up output COORDS (outCrdPtr_) and Topology
     int setupOutputCoords(DataSet*, std::string const&, std::string const&, DataSetList&);
     /// Build, parameterize, solvate, and check
-    RetType BuildAndParmStructure(DataSet*, std::string const&, DataSetList&, int, ArgList&, Cpptraj::Parm::GB_RadiiType);
+    RetType BuildAndParmStructure(DataSet*, std::string const&, DataSetList&, int, ArgList&, Cpptraj::Parm::GB_RadiiType, DataSet_LeapOpts*);
     /// Do input structure clean/prep and fill in missing atoms from templates
     int StructurePrepAndFillTemplates(ArgList&, Topology&, Frame&, Topology&, Frame&, std::string const&, Cpptraj::Structure::Creator const&); // NOTE not const bc of timers
 

From bd68d8d795246766fe6099681d6e02637efb37ab Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 6 Mar 2026 12:07:49 -0500
Subject: [PATCH 1490/1492] Add help/manual for flexiblewater

---
 doc/CpptrajManual.pdf     | Bin 974821 -> 974614 bytes
 doc/DocumentChecksums.txt |   2 +-
 doc/cpptraj.lyx           |   9 ++++++++-
 src/Exec_Build.cpp        |   2 +-
 4 files changed, 10 insertions(+), 3 deletions(-)

diff --git a/doc/CpptrajManual.pdf b/doc/CpptrajManual.pdf
index b8b67311ac48104dfc38a1e4a1308078d4eb6b39..7d3c2b8d7360e154816197a6de7778f59519ab25 100644
GIT binary patch
delta 37676
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diff --git a/doc/DocumentChecksums.txt b/doc/DocumentChecksums.txt
index 5cc715037f..501a194f85 100644
--- a/doc/DocumentChecksums.txt
+++ b/doc/DocumentChecksums.txt
@@ -1,3 +1,3 @@
 f6f8cb1a79951d80a9d2656fd9c30f55  CpptrajDevelopmentGuide.lyx
-769452881b024e967b9f714297ba6305  cpptraj.lyx
+98c794bb667297a27d520466982cdf81  cpptraj.lyx
 5d9b5b5ed47a3ded57b6464df99b3585  CpptrajManual.lyx
diff --git a/doc/cpptraj.lyx b/doc/cpptraj.lyx
index 31f61e856a..e40113bd11 100644
--- a/doc/cpptraj.lyx
+++ b/doc/cpptraj.lyx
@@ -6965,7 +6965,7 @@ build [name <output COORDS>] {crdset <COORDS set>|<file>} [{frame <#>|doassembly
 \end_layout
 
 \begin_layout LyX-Code
-    [reportfile <check file>]
+    [reportfile <check file>] [flexiblewater]
 \end_layout
 
 \begin_layout LyX-Code
@@ -7293,6 +7293,13 @@ file>] File to write details on problems with the final structure;
  if not specified write to STDOUT.
 \end_layout
 
+\begin_layout Description
+[flexiblewater] Option to turn on flexible water,
+ i.e.
+ water models with angle terms.
+ Note that the loaded force field must have water angle (H-O-O) parameters.
+\end_layout
+
 \begin_layout Description
 [gb
 \begin_inset space ~
diff --git a/src/Exec_Build.cpp b/src/Exec_Build.cpp
index 95f22f0e9f..20d9ceee3d 100644
--- a/src/Exec_Build.cpp
+++ b/src/Exec_Build.cpp
@@ -846,7 +846,7 @@ void Exec_Build::Help() const
   Cpptraj::Structure::PdbCleaner::Help();
   mprintf("\t[title <title>] [verbose <#>] [keepmissingatoms] [nofixorder]\n"
           "\t[parmout <topology file>] [crdout <coord file>] [simplecheck]\n"
-          "\t[reportfile <check file>]\n");
+          "\t[reportfile <check file>] [flexiblewater]\n");
   mprintf("\t[%s]\n", Cpptraj::Parm::GB_Params::HelpText().c_str());
   mprintf("    LJ 12-6-4 options:\n");
   mprintf("\t[lj1264 %s]\n", Cpptraj::Parm::LJ1264_Params::HelpText().c_str());

From 461e38854b2f1765b8705721ab3f8d5a90b81685 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 6 Mar 2026 12:08:51 -0500
Subject: [PATCH 1491/1492] Note IPOL > 0 not yet supported in changelog

---
 doc/ChangeLog.v7.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/ChangeLog.v7.md b/doc/ChangeLog.v7.md
index a381366652..2665ef855b 100644
--- a/doc/ChangeLog.v7.md
+++ b/doc/ChangeLog.v7.md
@@ -84,4 +84,4 @@ Not Yet Ready
 =============
 - Introduce the `byatom` keyword to `checkchirality` action to check the chirality of any atoms in specified mask that are chiral centers.
 
-
+- Cannot yet build topology files for polarizable force fields (IPOL > 0).

From 32aa363f2c89372b4f5b0cfa345132a9aaf99ecf Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.roe@nih.gov>
Date: Fri, 6 Mar 2026 12:16:29 -0500
Subject: [PATCH 1492/1492] FFTW is recommended

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index f6706dc9d2..03f01cc2e3 100644
--- a/README.md
+++ b/README.md
@@ -80,7 +80,7 @@ the following libraries:
 * Parallel NetCDF (-mpi build only, for NetCDF trajectory output in parallel)
 * CUDA (-cuda build only)
 * HIP (-hip build only)
-* FFTW (mostly optional; required for PME functionality and very large FFTs)
+* FFTW (mostly optional but recommended; required for PME functionality and very large FFTs)
 
 CPPTRAJ also makes use of the following libraries that are bundled with CPPTRAJ. External ones can be used in place of these if desired.